Modified sequence Experiment N duplicates Sequence Length Missed cleavages Proteins Leading proteins Gene names Protein names Phospho (STY) All Phospho (STY) Probabilities Max Score Min PEP Intensity Reporter intensity corrected 1 Reporter intensity corrected 2 Reporter intensity corrected 3 Reporter intensity corrected 4 Reporter intensity corrected 5 Reporter intensity corrected 6 Reporter intensity corrected 7 Reporter intensity corrected 8 Reporter intensity corrected 9 Phosphoproteome Fullproteome TMT Channel Normal 1 TMT Channel Normal 2 TMT Channel Normal 3 TMT Channel Normal 4 TMT Channel Normal 5 TMT Channel Normal 6 TMT Channel Normal 7 TMT Channel Normal 8 TMT Channel Normal 9 TMT Channel Ratio 1 TMT Channel Ratio 2 TMT Channel Ratio 3 TMT Channel Ratio 4 TMT Channel Ratio 5 TMT Channel Ratio 6 TMT Channel Ratio 7 TMT Channel Ratio 8 TMT Channel Ratio 9 Curve signal Log EC50 Curve slope Curve top Curve bottom R2 Curve RMSE Log EC50 error Curve slope error Curve top error Curve bottom error EC50 pEC50 Curve effect size Regulation (ac)AAAAAAAGDS(ph)DSWDADAFSVEDPVRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AAAAAAAGDSDSWDADAFSVEDPVRK 26 1 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 AAAAAAAGDS(0.536)DS(0.464)WDADAFSVEDPVRK;AAAAAAAGDS(0.835)DS(0.165)WDADAFSVEDPVRK;AAAAAAAGDS(0.777)DS(0.223)WDADAFSVEDPVRK;AAAAAAAGDS(0.994)DS(0.006)WDADAFSVEDPVRK;AAAAAAAGDS(0.898)DS(0.102)WDADAFSVEDPVRK 125.43 1.08E-44 1368500000 1516988 1372923 893784 1088907 1244588 1079913 1530647 1751539 1205348 TRUE FALSE 1316514.192 1363904.178 1326020.932 1336159.977 1219823.134 1121457.952 1382205.09 1376986.015 1062853.133 1.2386605 1.28324802 1.247605047 1.257144507 1.147687386 1.055139151 1.300466685 1.295556247 1 20.01951083 3.257871326 22.56023724 1.182063929 1.257916363 0.189735249 0.093367878 174.4173268 203763.4551 0.028421843 0.036605226 1810.803503 -3.257871326 0.075852434 (ac)AAAAKPNNLSLVVHGPGDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAAAKPNNLSLVVHGPGDLR 20 1 Q00796;A0A6I8PIS1;H0YKB3;Q00796-2;A0A6I8PRA7 Q00796 SORD Sorbitol dehydrogenase 0 ; 60.621 4.71E-21 295930000 365150 320680 174087 241815 306030 295930 321120 397600 309170 FALSE TRUE 316894.5023 318573.432 258276.0555 296722.7917 299940.6017 307314.6186 289977.8318 312576.3341 272620.2748 1.162402549 1.16856104 0.947383887 1.088410581 1.100213849 1.127262522 1.063669355 1.146563051 1 18.05653333 (ac)AAADGDDSLYPIAVLIDELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AAADGDDSLYPIAVLIDELR 20 0 P30153;C9J9C1;M0QXG4;M0R0K6 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ;; 65.472 5.26E-21 997300000 8236 24731.9 27856 0 8846.1 0 32440 14774.4 8809 FALSE TRUE 7147.591733 24569.43452 41327.25477 0 8670.079917 0 29293.97379 11615.00953 7767.610055 0.92017901 3.163062299 5.320459508 0 1.116183724 0 3.771298197 1.49531316 1 12.92325506 3.721134482 24.96529743 1.360825057 3.137416897 0.269234016 1.468358226 1127.858769 1615810.268 0.406786073 0.604921904 5261.801763 -3.721134482 1.776591841 (ac)AAAITDMADLEELSRLS(ph)PLPPGS(ph)PGSAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAAITDMADLEELSRLSPLPPGSPGSAAR 29 1 Q6ZN18-2;Q6ZN18 Q6ZN18-2 AEBP2 Zinc finger protein AEBP2 2 AAAIT(0.025)DMADLEELS(0.149)RLS(0.826)PLPPGS(0.862)PGS(0.138)AAR;AAAIT(0.001)DMADLEELS(0.019)RLS(0.978)PLPPGS(0.884)PGS(0.118)AAR 62.374 0.00016916 32058000 18653.9 12438.5 9987 12983.4 15557.5 13010.2 16404.6 22135.4 22955.2 TRUE FALSE 16188.73985 12356.79067 14816.7466 15931.47941 15247.93619 13510.71081 14813.68442 17401.91697 20241.46241 0.799781139 0.610469265 0.731999808 0.787071561 0.753302102 0.66747701 0.731848526 0.859716389 1 14.30502591 1.454580622 2.114738456 1.021071858 0.721837111 0.731636485 0.05494669 0.221257748 1.543134504 0.112582152 0.014953699 28.48266498 -1.454580622 -0.299234747 (ac)AAAITDMADLEELSRLS(ph)PLPPGSPGSAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAAITDMADLEELSRLSPLPPGSPGSAAR 29 1 Q6ZN18-2;Q6ZN18 Q6ZN18-2 AEBP2 Zinc finger protein AEBP2 1 AAAITDMADLEELS(0.035)RLS(0.965)PLPPGSPGSAAR 95.794 1.46E-05 7573800 2300.1 933.4 705.35 0 658.46 888.86 1552.6 1390.5 1263.5 TRUE FALSE 1996.135957 927.2684339 1046.459619 0 645.3579343 923.0550194 1402.029091 1093.152396 1114.130469 1.791653682 0.832279934 0.939261288 0 0.579248079 0.828498138 1.25840656 0.9811709 1 10.12170247 2.389547724 8.238319377 1.065713478 0.780487121 0.061291166 0.440792006 0.707612629 58.7654682 0.169484487 0.131018449 245.2153905 -2.389547724 -0.285226357 (ac)AAASVT(ph)PPGSLELLQPGFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAASVTPPGSLELLQPGFSK 20 0 Q12933-4;Q12933-3;Q12933;Q12933-2;B1AMX7;B1AMX8;B1AMY1 Q12933-4 TRAF2 TNF receptor-associated factor 2 1 AAAS(0.023)VT(0.956)PPGS(0.021)LELLQPGFSK;AAAS(0.071)VT(0.815)PPGS(0.113)LELLQPGFSK 107.61 2.44E-17 60064000 277700 266190 155164 235480 295030 237820 277380 337940 226940 TRUE FALSE 241001.2414 264441.3804 230201.8294 288949.3331 289159.4802 246969.0893 250479.7303 265674.1609 200111.4117 1.204335322 1.321470765 1.150368324 1.443942305 1.444992456 1.234157948 1.25170138 1.327631236 1 17.61044392 1.235340416 24.92255315 0.999999569 1.299991572 0.491694154 0.094971127 77.12960554 596833.7571 0.161247482 0.023149828 17.19255474 -1.235340416 0.299992004 (ac)AAAVAAAGAGEPQS(ph)PDELLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AAAVAAAGAGEPQSPDELLPK 21 0 Q9NS69 Q9NS69 TOMM22 Mitochondrial import receptor subunit TOM22 homolog 1 AAAVAAAGAGEPQS(1)PDELLPK;AAAVAAAGAGEPQS(1)PDELLPK;AAAVAAAGAGEPQS(1)PDELLPK;AAAVAAAGAGEPQS(1)PDELLPK 63.682 1.05E-21 292132000 154455 159700 146918 184762 202537 227541 147051 267135 241305 TRUE FALSE 134043.3804 158650.9202 217968.0362 226715.036 198506.91 236294.6495 132790.0167 210010.2591 212778.1978 0.629967646 0.74561643 1.024390837 1.065499371 0.932928806 1.110520965 0.624077175 0.986991436 1 17.69899081 4.393720922 4.37446637 0.954580812 0.653410606 0.441241416 0.131534498 0.184852655 6.361097424 0.032978525 0.098598359 24758.30578 -4.393720922 -0.301170207 (ac)AADVSVTHRPPLS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 AADVSVTHRPPLSPK 15 1 A0A087WZ13;Q8IY67-2;Q8IY67;Q8IY67-3 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 AADVSVT(0.001)HRPPLS(0.999)PK;AADVSVTHRPPLS(1)PK;AADVSVT(0.002)HRPPLS(0.998)PK;AADVSVTHRPPLS(1)PK;AADVSVT(0.001)HRPPLS(0.999)PK;AADVSVTHRPPLS(1)PK;AADVSVTHRPPLS(1)PK 117.84 2.29E-17 20787720000 8613580 7266270 3700140 5336560 8097920 6716610 8175990 9306710 8504770 TRUE FALSE 7475273.579 7218537.394 5489540.08 6548307.512 7936787.235 6975002.333 7383083.748 7316542.491 7499345.779 0.996790093 0.962555616 0.73200253 0.873183836 1.058330616 0.930081442 0.984497044 0.975624102 1 22.83833331 3.263895737 24.99811163 0.984574358 0.884868119 0.29548824 0.075124954 299.3775153 295393.1205 0.02218435 0.028628925 1836.097489 -3.263895737 -0.099706238 (ac)AAGGDHGS(ph)PDSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAGGDHGSPDSYR 13 0 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A1B0GTG9;A0A1B0GWF8;P30566-2;A0A096LNY5;B4DEP1;A0A1W2PRX2;A0A096LP72;A0A096LNY4 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 1 AAGGDHGS(0.941)PDS(0.059)YR;AAGGDHGS(0.73)PDS(0.27)YR 70.654 1.71E-06 398250000 53792 53666 49512 46641 53135 44423 64189 62333 61499 TRUE FALSE 46683.25091 53313.46451 73456.16881 57231.55191 52077.71746 46131.98156 57963.96066 49003.57303 54228.65828 0.860859413 0.98312343 1.354563641 1.055374662 0.960335717 0.850693766 1.068880597 0.90364716 1 15.72676786 3.267283632 5.283010034 0.952764898 1.080151685 0.131885415 0.134003399 0.344682971 25.06242372 0.040254671 0.050623686 1850.476747 -3.267283632 0.127386787 (ac)AALHTTPDS(ph)PAAQLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AALHTTPDSPAAQLER 16 0 A6NFI3 A6NFI3 ZNF316 Zinc finger protein 316 1 AALHTTPDS(1)PAAQLER;AALHTT(0.006)PDS(0.994)PAAQLER;AALHT(0.004)T(0.02)PDS(0.975)PAAQLER;AALHTT(0.005)PDS(0.995)PAAQLER;AALHTT(0.006)PDS(0.994)PAAQLER 158.76 1.69E-57 4788310000 296522 369193 250193.2 251960 309447 374781 341087 234175 262022 TRUE FALSE 257335.8664 366767.7469 371187.4684 309171.369 303289.6101 389199.0676 308008.4352 184098.4986 231046.0577 1.113786009 1.587422658 1.606551837 1.338137392 1.312680308 1.684508585 1.33310405 0.796804328 1 17.81782095 1.840680064 4.799811558 0.899707961 1.448131237 0.62131903 0.172161256 0.125605858 4.314695657 0.090568921 0.044382781 69.29151615 -1.840680064 0.548423276 (ac)AAS(ph)DTERDGLAPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AASDTERDGLAPEK 14 1 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 AAS(0.995)DT(0.005)ERDGLAPEK 69.346 0.0028223 167720000 442800 360530 255050 282040 364560 300140 371950 468540 336520 TRUE FALSE 384282.8581 358161.6547 378393.0331 346081.4927 357305.9692 311686.58 335878.3462 368346.3672 296736.989 1.295028501 1.207000367 1.275179864 1.16629037 1.204116718 1.050379938 1.131905892 1.241322723 1 18.17882525 3.454701059 1.495091263 1.131964746 1.257514222 0.428438818 0.070741281 0.452856069 2.06749481 0.024396919 0.040990709 2849.056484 -3.454701059 0.125549476 (ac)AAS(ph)DTERDGLAPEKT(ph)SPDRDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AASDTERDGLAPEKTSPDRDK 21 3 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 2 AAS(0.981)DT(0.022)ERDGLAPEKT(0.516)S(0.481)PDRDK 42.659 0.0051899 528830000 430990 241210 330820 219800 209710 140900 375420 408690 236280 TRUE FALSE 374033.5795 239625.4756 490805.6585 269708.9494 205537.1813 146320.5142 339011.8262 321294.8239 208347.2476 1.79524128 1.150125468 2.355709827 1.294516499 0.986512583 0.702291563 1.627148091 1.54211216 1 17.66863052 3.507773976 24.97616396 1.220614289 1.725298541 0.32331722 0.390711285 929.7475928 757565.9411 0.109723675 0.162512119 3219.392859 -3.507773976 0.504684252 (ac)AASAAAASAAAASAASGS(ph)PGPGEGSAGGEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AASAAAASAAAASAASGSPGPGEGSAGGEKR 31 1 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 AASAAAASAAAASAASGS(1)PGPGEGSAGGEKR;AASAAAASAAAASAASGS(0.999)PGPGEGSAGGEKR;AASAAAASAAAASAASGS(0.993)PGPGEGS(0.007)AGGEKR;AASAAAASAAAASAAS(0.001)GS(0.999)PGPGEGS(0.001)AGGEKR;AASAAAASAAAASAASGS(1)PGPGEGSAGGEKR;AASAAAASAAAASAASGS(0.995)PGPGEGS(0.005)AGGEKR 210.59 2.10E-175 9303030000 8535340 6156280 4054010 4347550 5732700 5229830 6603150 7899000 3703330 TRUE FALSE 7407373.193 6115838.991 6014542.796 5334727.676 5618630.486 5431024.944 5962777.529 6209860.32 3265526.546 2.268354916 1.872849265 1.841829399 1.633650071 1.720589438 1.663139119 1.825977356 1.901641353 1 21.63888421 7.999999914 0.640133613 1.654192875 52.1604342 0.41297002 0.243009774 235.1112052 1.591692498 0.103747933 16780.8953 99999980.16 -7.999999914 50.50624133 (ac)AATDLERFS(ph)NAEPEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AATDLERFSNAEPEPR 16 1 A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599 A0A087X142 8-Sep Septin-8 1 AAT(0.015)DLERFS(0.985)NAEPEPR;AATDLERFS(1)NAEPEPR;AATDLERFS(1)NAEPEPR 147.7 2.60E-57 1191760000 85397.6 37422.5 109560 57635.9 64466.4 37134.4 56967.8 71393.3 64859.3 TRUE FALSE 74112.09079 37176.66913 162543.5825 70723.012 63183.64477 38562.9844 51443.07152 56126.39838 57191.70744 1.295853789 0.650036007 2.842083052 1.236595569 1.104769338 0.674275802 0.8994848 0.981373015 1 15.80351836 3.315774139 3.663944456 0.916821242 1.56839328 0.229087063 0.545305909 0.341852464 9.023430833 0.161854343 0.209264726 2069.065021 -3.315774139 0.651572038 (ac)ACPLDQAIGLLVAIFHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ACPLDQAIGLLVAIFHK 17 0 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ; 147.72 3.01E-20 19711700000 15481700 18054800 11748500 14749500 13810700 12620900 15852700 18969100 19199600 FALSE TRUE 13435754.12 17936196.83 17430113.9 18098599.41 13535894.09 13106434.19 14315307.59 14912705.58 16929845.16 0.793613526 1.059442462 1.029549516 1.069035141 0.799528523 0.774161492 0.845566363 0.88085304 1 24.01306544 3.234708303 24.9998679 0.857248593 0.995993853 0.303421467 0.095888393 116.5899888 756618.2549 0.028747186 0.033832538 1716.75493 -3.234708303 0.13874526 (ac)ACS(ph)PDAVVSPSSAFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ACSPDAVVSPSSAFLR 16 0 Q93100-4;Q93100-2;I3L3F2;H3BV13;H3BQ89 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 1 ACS(1)PDAVVSPSSAFLR;ACS(1)PDAVVSPSSAFLR 75.045 2.61E-09 334810000 22207 24318 21409 15097.2 24300 25749 17302.7 19895.4 19237 TRUE FALSE 19272.28868 24158.25346 31762.46401 18525.25001 23816.47754 26739.58069 15624.68682 15640.92354 16962.82377 1.136148612 1.4241882 1.872475033 1.092108852 1.404039673 1.576363762 0.92111355 0.922070744 1 14.05008873 2.228706589 24.99270312 0.94127373 1.423126552 0.511150292 0.216516431 156.9158328 397980.9015 0.086508285 0.059120918 169.3193487 -2.228706589 0.481852823 (ac)ADANKAEVPGATGGDS(ph)PHLQPAEPPGEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ADANKAEVPGATGGDSPHLQPAEPPGEPR 29 1 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WWC8;Q9P2K5-4 A0A0A0MQW0 MYEF2 Myelin expression factor 2 1 ADANKAEVPGAT(0.009)GGDS(0.991)PHLQPAEPPGEPR;ADANKAEVPGAT(0.002)GGDS(0.998)PHLQPAEPPGEPR;ADANKAEVPGAT(0.02)GGDS(0.98)PHLQPAEPPGEPR;ADANKAEVPGAT(0.004)GGDS(0.996)PHLQPAEPPGEPR 90.287 7.31E-45 5428700000 4707440 3798110 1582780 1473410 3180400 2865130 4220710 4357870 355747 TRUE FALSE 4085339.877 3773159.965 2348217.702 1807970.26 3117116.262 2975353.405 3811386.194 3425973.413 313690.9949 13.02345283 12.02826994 7.485767013 5.763538926 9.936900685 9.484981887 12.15012944 10.92149111 1 18.25898459 4.333880864 5.527967903 8.611570453 12.74159491 0.247116658 3.125612443 0.313778651 14.4477652 0.793669389 2.174982908 21571.52577 -4.333880864 4.130024455 (ac)ADEELEALRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ADEELEALRR 10 1 O14737;O14737-2;Q3HM38;X6R2P6;K7ESJ4 O14737 PDCD5 Programmed cell death protein 5 0 ; 82.279 7.50E-05 1692130000 310330 262500 274440 293460 320830 282940 325360 352830 499050 FALSE TRUE 269319.1042 260775.6202 407160.1019 360094.5783 314446.1107 293824.8849 293806.6373 277380.0502 440052.8775 0.612015324 0.592600648 0.925252675 0.818298429 0.714564378 0.667703587 0.66766212 0.630333454 1 18.74731737 6.539678669 0.020846956 1.338388995 1.96E-06 0.064669197 0.132597026 25131.27242 73.55900291 1990.904378 2795.683263 3464803.972 -6.539678669 -1.338387038 (ac)ADFDTYDDRAYSSFGGGRGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADFDTYDDRAYSSFGGGRGSR 21 2 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 123.55 2.48E-07 148090000 0 5944.1 0 4381.7 0 9271.2 4926.6 7454.7 0 FALSE TRUE 0 5905.052816 0 5376.631955 0 9627.869063 4448.81909 5860.570418 0 0 (ac)ADGDS(ph)GS(ph)ERGGGGGPCGFQPASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ADGDSGSERGGGGGPCGFQPASR 23 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 2 ADGDS(1)GS(1)ERGGGGGPCGFQPASR;ADGDS(1)GS(1)ERGGGGGPCGFQPASR 47.639 0.00036182 1074360000 83667 63153 54564 39558 67061 62481 67719 70020 43117 TRUE FALSE 72610.19396 62738.14378 80951.33291 48540.24851 65726.6173 64884.6845 61151.6218 55046.7679 38019.75738 1.909801613 1.650145822 2.129191202 1.276711159 1.728748994 1.706604381 1.608416939 1.447846375 1 15.21446171 0.835672005 0.957195922 5.81E-18 1.738565883 0.549291713 0.211571852 3.106844108 1.327632503 6.768969303 0.069520152 6.849707163 -0.835672005 1.738565883 (ac)ADGDS(ph)GSERGGGGGPCGFQPASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ADGDSGSERGGGGGPCGFQPASR 23 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 ADGDS(0.862)GS(0.138)ERGGGGGPCGFQPASR;ADGDS(0.979)GS(0.021)ERGGGGGPCGFQPASR 138.07 2.93E-07 525410000 23115.6 17518.7 11293 17684.9 19832 14361.5 8728.4 21396.5 26448.1 TRUE FALSE 20060.81489 17403.61851 16754.33257 21700.52684 19437.382 14913.9962 7881.921111 16821.02498 23321.43575 0.860187816 0.746249875 0.718409139 0.930497036 0.833455633 0.639497343 0.337968948 0.721268843 1 14.50936899 2.736801753 24.15220396 0.650395675 0.814530812 0.144634169 0.168248482 179.8168123 2469168.291 0.058369761 0.054175012 545.5087906 -2.736801753 0.164135137 (ac)ADHS(ph)FSDGVPSDSVEAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADHSFSDGVPSDSVEAAK 18 0 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;E9PKT8;E9PS34;E9PNW0;E9PJJ2;E9PP22;E9PKI2;C9J1B1 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 ADHS(0.992)FS(0.007)DGVPS(0.001)DSVEAAK 84.892 2.11E-92 0 437020 425130 263620 295270 395890 354750 491970 493360 488670 TRUE FALSE 379266.6997 422337.293 391107.5138 362315.5664 388012.5635 368397.4621 444258.8251 387858.8033 430899.9893 0.880173379 0.980128344 0.907652642 0.840834475 0.900470116 0.854948877 1.031002173 0.900113281 1 18.71699354 2.252986699 24.99492 0.96326091 0.896441329 0.372964848 0.049609714 291.2561522 504635.989 0.018365457 0.014159774 179.0551013 -2.252986699 -0.066819581 (ac)ADILSQSETLASQDLSGDFKKPALPVS(ph)PAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADILSQSETLASQDLSGDFKKPALPVSPAAR 31 2 A0A087X0M4;A0A087WWF4 A0A087X0M4 SLC4A1AP 1 ADILSQSETLASQDLS(0.018)GDFKKPALPVS(0.981)PAAR 66.479 7.55E-06 160320000 478150 327530 190890 211080 314880 230210 438000 487660 138680 TRUE FALSE 414961.266 325378.4339 283205.0425 259008.9402 308614.5041 239066.3277 395522.8274 383377.704 122285.4084 3.393383328 2.660811606 2.315934879 2.118069061 2.523723052 1.954986542 3.234423736 3.135105889 1 16.89989274 4.70013782 2.944112313 2.434584646 3.512865387 0.210841424 0.627534891 0.623043802 8.199996144 0.159208187 1.51593104 50134.63072 -4.70013782 1.078280741 (ac)ADQLTEEQIAEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ADQLTEEQIAEFK 13 0 P0DP25;P0DP24;P0DP23;M0QZ52;F8WBR5;G3V479 P0DP25 CALM3;CALM2;CALM1 0 ; 85.958 1.28E-10 114446000 194314 174367 141627 158664 161675 158837 156276 223441 249820 FALSE TRUE 168634.9126 173221.5717 210118.2909 194691.0862 158457.9838 164947.5622 141120.3776 175659.881 220286.5642 0.765525184 0.786346513 0.953840701 0.883808266 0.719326593 0.748786304 0.64062181 0.797415319 1 17.74902198 4.470450664 24.97154297 0.809265862 0.770730423 0.022679683 0.107078974 853.6864615 3195812.992 0.028249133 0.075133903 29542.73263 -4.470450664 -0.038535439 (ac)ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMR 37 3 P0DP25;P0DP24;P0DP23;M0QZ52;F8WBR5;G3V479 P0DP25 CALM3;CALM2;CALM1 0 ; 136.12 1.08E-30 1464070000 98144 106118 61408 39161.8 73703 58891 190340 147644 42765.3 FALSE TRUE 85174.02173 105420.9039 91105.1142 48054.08524 72236.4545 61156.57488 171880.8561 116071.4796 37709.63495 2.258680622 2.79559598 2.415963833 1.274318494 1.915596759 1.621775839 4.558009016 3.078032437 1 15.20264556 (ac)ADSRDPASDQMQHWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ADSRDPASDQMQHWK 15 1 P04040 P04040 CAT Catalase 0 ;; 58.21 0.0052736 512830000 773940 573560 384780 558390 637800 724090 598010 788120 439130 FALSE TRUE 671661.8681 569792.2466 570860.895 685180.984 625109.0278 751946.2108 540015.0822 619586.6712 387216.5517 1.734589767 1.471507982 1.474267803 1.769503346 1.614365463 1.94192683 1.394607436 1.600103788 1 18.5627811 0.882283238 1.724047049 1.44E-16 1.635887927 0.591766682 0.162306278 2.004531881 2.418965471 7.494512736 0.043431602 7.625761852 -0.882283238 1.635887927 (ac)ADVLDLHEAGGEDFAMDEDGDES(ph)IHKLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ADVLDLHEAGGEDFAMDEDGDESIHKLK 28 1 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 1 ADVLDLHEAGGEDFAMDEDGDES(1)IHKLK;ADVLDLHEAGGEDFAMDEDGDES(1)IHKLK 110.09 1.28E-17 85618000 64006 59695 41284.8 36262 49939 45005 73124 67847 34531 TRUE FALSE 55547.44493 59302.85961 61250.26737 44495.84133 48945.3116 46736.37147 66032.44573 53338.44704 30448.78452 1.824291045 1.9476265 2.01158333 1.46133391 1.607463561 1.534917476 2.168639792 1.751743062 1 14.89409702 1.242677268 6.691066326 0.981363143 1.794282589 0.565585864 0.217372608 0.085368691 19.43395576 0.31649741 0.055431874 17.48546829 -1.242677268 0.812919446 (ac)ADVLDLHEAGGEDFAMDEDGDESIHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ADVLDLHEAGGEDFAMDEDGDESIHK 26 0 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ;;;; 146.5 1.17E-60 549556000 336782 267938 166949 210091 267936 265754 302260 374294 343675 FALSE TRUE 292275.4054 266177.8976 247686.0948 257795.3726 262604.5978 275977.7283 272946.8717 294254.1409 303046.133 0.964458456 0.878341179 0.817321417 0.850680291 0.866549905 0.910678931 0.900677626 0.970987941 1 18.20917791 1.659922259 1.182901463 1.02189825 0.872956636 0.565038007 0.037930271 0.567220293 1.140397492 0.092897774 0.013094252 45.70063753 -1.659922259 -0.148941615 (ac)AEAPAS(ph)PAPLS(ph)PLEVELDPEFEPQSRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEAPASPAPLSPLEVELDPEFEPQSRPR 28 1 O43524 O43524 FOXO3 Forkhead box protein O3 2 AEAPAS(1)PAPLS(0.998)PLEVELDPEFEPQS(0.002)RPR 53.865 0.020532 23724000 2178.1 1997.8 2460.5 2172.6 1440.9 3299.3 0 1351.3 2329 TRUE FALSE 1890.258566 1984.67632 3650.40603 2665.922036 1412.228909 3426.226206 0 1062.335011 2053.668273 0.92043033 0.966405503 1.777505198 1.298126903 0.687661648 1.668344518 0 0.517286567 1 11.00398745 2.240079155 24.99964797 0.487089708 1.212960045 0.411384416 0.402338651 38.12999262 627750.6874 0.153947016 0.112752635 173.8117593 -2.240079155 0.725870337 (ac)AENDVDNELLDYEDDEVETAAGGDGAEAPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AENDVDNELLDYEDDEVETAAGGDGAEAPAK 31 0 Q13838-2;Q13838;Q5STU3;F6WLT2;F6S4E6;A0A0A0MT12;F6TRA5;F6R6M7;F6U6E2;F6S2B7;A0A0G2JHN7 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 95.244 3.85E-09 32058000 47528 38051 33763 36485 38652 37208 34467 50366 74918 FALSE TRUE 41247.05438 37801.04048 50090.89973 44769.47689 37882.90082 38639.41584 31124.39565 39595.62285 66061.27939 0.624375652 0.572211753 0.758249011 0.677696183 0.573450911 0.584902627 0.471144306 0.599377172 1 16.01151729 1.238075188 24.97302618 1.000000452 0.604891086 0.733944576 0.07421699 6.496267112 333850.4129 0.111333893 0.019432777 17.30115863 -1.238075188 -0.395109367 (ac)AENDVDNELLDYEDDEVETAAGGDGAEAPAKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AENDVDNELLDYEDDEVETAAGGDGAEAPAKK 32 1 Q13838-2;Q13838;Q5STU3;F6WLT2;F6S4E6;A0A0A0MT12;F6TRA5;F6R6M7;F6U6E2;F6S2B7;A0A0G2JHN7 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 53.615 8.57E-05 61586000 47815 36706 22418 29335 30187 29932 44076 52812 33789 FALSE TRUE 41496.1266 36464.87587 33259.41978 35995.96011 29586.33776 31083.50341 39801.5163 41518.56478 29794.50291 1.392744384 1.223879317 1.11629383 1.208140985 0.993013303 1.043263031 1.335867775 1.393497482 1 14.86275856 4.700272507 3.445586132 1.178225962 1.411233156 0.22535847 0.13352381 0.49293281 10.11731694 0.036772259 0.282596916 50150.18124 -4.700272507 0.233007194 (ac)AENTEGDLNSNLLHAPYHTGDPQLDTAIGQWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AENTEGDLNSNLLHAPYHTGDPQLDTAIGQWLR 33 0 Q6PCE3 Q6PCE3 PGM2L1 "Glucose 1,6-bisphosphate synthase" 0 ; 128.35 7.12E-74 158413000 10876.1 4996.9 7133.2 7102 10017.3 8245.2 11340.4 13755 8526.2 FALSE TRUE 9438.795828 4964.075035 10582.83938 8714.617647 9817.975329 8562.398179 10240.60975 10813.60029 7518.242349 1.255452457 0.660270686 1.407621474 1.159129653 1.305887051 1.13888297 1.362101576 1.43831494 1 12.87617971 4.218583603 24.99999998 1.274237589 0.957861229 0.292205647 0.193601078 228.9170947 286476.28 0.045822722 0.095581962 16541.83189 -4.218583603 -0.31637636 (ac)AEPPS(ph)PVHCVAAAAPTATVSEKEPFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AEPPSPVHCVAAAAPTATVSEKEPFGK 27 1 Q6PCB5 Q6PCB5 RSBN1L Round spermatid basic protein 1-like protein 1 AEPPS(1)PVHCVAAAAPTATVSEKEPFGK;AEPPS(1)PVHCVAAAAPTATVSEKEPFGK;AEPPS(1)PVHCVAAAAPTATVSEKEPFGK;AEPPS(1)PVHCVAAAAPTATVSEKEPFGK 106.37 2.55E-08 1559000000 2890000 2360470 1720110 2028140 2119130 1799890 2858540 3488750 2407070 TRUE FALSE 2508079.178 2344963.917 2551960.949 2488660.185 2076963.459 1869132.933 2581319.231 2742707.962 2122508.927 1.181657776 1.104807564 1.202332257 1.172508701 0.978541684 0.880624298 1.216164134 1.292200908 1 21.01733919 (ac)AESSESFTMASS(ph)PAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AESSESFTMASSPAQR 16 0 P49736;F8WDM3 P49736 MCM2 DNA replication licensing factor MCM2 1 AESSESFTMAS(0.003)S(0.997)PAQR;AESSESFTMASS(1)PAQR;AESSESFTMAS(0.016)S(0.984)PAQR;AESSESFTMAS(0.006)S(0.994)PAQR 123.18 3.25E-122 983220000 626670.1 529106.6 337562 380702.1 545667.1 609884 551997.1 582127 605125.3 TRUE FALSE 543854.0585 525630.8639 500808.1123 467146.3305 534809.3923 633346.6321 498464.5062 457643.6712 533588.0764 1.019239527 0.98508735 0.93856691 0.875481202 1.002288874 1.186957993 0.934174747 0.857672222 1 19.0253669 2.018169151 24.9999867 0.911845822 0.997725927 0.124752259 0.085376073 425.6615244 585690.0123 0.036593276 0.024666452 104.2723475 -2.018169151 0.085880105 (ac)AHS(ph)PVQSGLPGMQNLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 AHSPVQSGLPGMQNLK 16 0 B4DR80;Q9Y6E0-2 B4DR80 STK24 Serine/threonine-protein kinase 24;Serine/threonine-protein kinase 24 36 kDa subunit;Serine/threonine-protein kinase 24 12 kDa subunit 1 AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(0.995)PVQS(0.005)GLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(0.997)PVQS(0.003)GLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(0.999)PVQS(0.001)GLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(0.999)PVQS(0.001)GLPGMQNLK 128.01 1.36E-45 9506947000 6185790 5906170 4045071 5135381 5891700 5500368 6397060 7719530 7189360 TRUE FALSE 5368322.179 5867371.98 6001280.866 6301447.745 5774466.697 5711970.716 5776674.106 6068768.583 6339442.051 0.846813037 0.925534445 0.946657579 0.99400668 0.910879325 0.901021047 0.911227527 0.957303266 1 22.59592444 4.031834126 0.013498268 1.835761872 1.81E-05 0.256795254 0.039039841 6158.651491 38.0888411 2507.414228 2673.390764 10760.54147 -4.031834126 -1.835743763 (ac)AKS(ph)PENSTLEEILGQYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKSPENSTLEEILGQYQR 18 1 Q86SQ7-3;Q86SQ7-4;Q86SQ7;Q86SQ7-2 Q86SQ7-3 SDCCAG8 Serologically defined colon cancer antigen 8 1 AKS(0.994)PENS(0.005)T(0.001)LEEILGQYQR;AKS(1)PENSTLEEILGQYQR 130.69 3.26E-30 67503000 90766 66491 48478 53173 83451 88953 82003 103727 53298 TRUE FALSE 78771.04313 66054.21624 71922.12295 65246.74235 81790.48837 92375.07947 74050.36168 81545.78825 46997.17116 1.676080521 1.40549345 1.530350044 1.388312121 1.740327904 1.965545525 1.575634445 1.735121205 1 15.5202863 3.237901575 24.99999981 1.635834364 1.495468003 0.030090654 0.256214125 54.16301664 2054646.958 0.074695125 0.089857124 1729.424374 -3.237901575 -0.140366361 (ac)ALVT(ph)VSRSPPGS(ph)GASTPVGPWDQAVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALVTVSRSPPGSGASTPVGPWDQAVQR 27 1 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 2 ALVT(0.373)VS(0.375)RS(0.375)PPGS(0.657)GAS(0.171)T(0.049)PVGPWDQAVQR 40.428 7.27E-08 36129000 6000.1 7677.2 4379.8 4385.2 3888.3 7428.6 2379.7 4990.9 6315 TRUE FALSE 5207.171583 7626.767968 6497.88593 5380.926684 3810.930437 7714.383049 2148.91706 3923.634874 5568.447894 0.935120824 1.369639819 1.166911508 0.966324331 0.684379294 1.385374021 0.385909521 0.704619123 1 12.44305954 3.183030154 0.842434349 0.743386636 1.189067009 0.1923601 0.278511384 0.874506011 1.487974914 0.169585433 0.232615339 1524.158577 -3.183030154 0.445680373 (ac)ALVTVS(ph)RSPPGSGASTPVGPWDQAVQRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALVTVSRSPPGSGASTPVGPWDQAVQRR 28 2 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 ALVT(0.089)VS(0.45)RS(0.45)PPGS(0.011)GASTPVGPWDQAVQRR 60.521 0.0021516 151050000 15249 0 4583.3 7799.7 9163.3 10155 5733.4 12434 12773 TRUE FALSE 13233.80601 0 6799.79921 9570.741096 8980.968258 10545.66942 5177.37575 9775.085861 11262.99049 1.174981549 0 0.603729464 0.849751325 0.797387538 0.936311669 0.45968038 0.867894354 1 13.45930231 3.848949323 5.292413427 0.804454661 0.524013694 0.093238796 0.312888664 0.4298243 17.33138436 0.077500202 0.137391849 7062.351405 -3.848949323 -0.280440967 (ac)ALVTVSRS(ph)PPGSGASTPVGPWDQAVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ALVTVSRSPPGSGASTPVGPWDQAVQR 27 1 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 ALVT(0.022)VS(0.118)RS(0.663)PPGS(0.146)GAS(0.041)T(0.01)PVGPWDQAVQR;ALVTVS(0.005)RS(0.834)PPGS(0.127)GAS(0.026)T(0.007)PVGPWDQAVQR;ALVT(0.014)VS(0.099)RS(0.603)PPGS(0.103)GAS(0.161)T(0.021)PVGPWDQAVQR;ALVT(0.012)VS(0.078)RS(0.624)PPGS(0.185)GAS(0.077)T(0.024)PVGPWDQAVQR 108.07 3.54E-95 2958880000 18927.3 31147.1 13596.3 25921.8 32864.9 48601.8 59490.1 65799.4 11852 TRUE FALSE 16426.00935 30942.49265 20171.51616 31807.74088 32210.95279 50471.5427 53720.75926 51728.71036 10450.87006 1.571736061 2.96075757 1.930127926 3.043549551 3.08213121 4.829410604 5.140314533 4.949703714 1 13.35133543 3.143275454 2.038036788 4.218413081 2.290177941 0.262647534 1.236808294 0.382411585 3.26289854 0.422566003 0.510659842 1390.834498 -3.143275454 -1.92823514 (ac)ALVTVSRS(ph)PPGSGASTPVGPWDQAVQRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALVTVSRSPPGSGASTPVGPWDQAVQRR 28 2 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 ALVTVS(0.007)RS(0.598)PPGS(0.39)GAS(0.004)TPVGPWDQAVQRR;ALVT(0.027)VS(0.14)RS(0.788)PPGS(0.041)GAS(0.003)TPVGPWDQAVQRR 116.49 1.68E-17 1091500000 88020 91441 62619 84064 115086 128681 103291 134174 157812 TRUE FALSE 76387.93399 90840.31805 92901.75785 103152.016 112796.0138 133631.4413 93273.85472 105481.9342 139155.6451 0.548938808 0.6527965 0.667610414 0.741270797 0.810574473 0.960301978 0.670284376 0.758014051 1 17.08633991 3.938234996 1.086557341 0.824103359 0.562330308 0.528066203 0.095288004 0.592553765 1.219212669 0.034652449 0.132331546 8674.311136 -3.938234996 -0.261773051 (ac)ALVTVSRSPPGS(ph)GASTPVGPWDQAVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALVTVSRSPPGSGASTPVGPWDQAVQR 27 1 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 ALVT(0.001)VS(0.023)RS(0.367)PPGS(0.464)GAS(0.121)T(0.024)PVGPWDQAVQR;ALVT(0.004)VS(0.037)RS(0.305)PPGS(0.476)GAS(0.141)T(0.036)PVGPWDQAVQR 66.793 9.61E-82 1149010000 14984.7 0 6245.1 5059.9 7314 14519 9500.8 18055.5 12045 TRUE FALSE 13004.43393 0 9265.251249 6208.827631 7168.46571 15077.55533 8579.413878 14194.47183 10621.05382 1.224401472 0 0.872347641 0.584577363 0.674929798 1.419591274 0.807774259 1.336446653 1 13.3746393 2.830726437 7.575350306 1.139522274 0.637341574 0.314735869 0.34259582 0.301993477 21.96510746 0.100161025 0.100219443 677.2147938 -2.830726437 -0.5021807 (ac)AMFEDTVEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AMFEDTVEER 10 0 C9JAJ9 C9JAJ9 RBBP7 0 56.258 2.57E-05 70993000 33197 27170 17069 18688 28375 33262 35090 35032 22678 FALSE TRUE 28809.93234 26991.51848 25323.62549 22931.39603 27810.39301 34541.61066 31686.9772 27540.67942 19997.03267 1.44071037 1.349776185 1.266369161 1.146739939 1.390725988 1.727336812 1.584583959 1.377238307 1 14.28749832 3.009488068 24.83749695 1.444750658 1.29777487 0.074744016 0.196836626 460.3585924 1205097.915 0.062544705 0.070833678 1022.087479 -3.009488068 -0.146975787 (ac)AQHFSLAACDVVGFDLDHTLCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQHFSLAACDVVGFDLDHTLCR 22 0 Q5TFE4;Q5QPD0 Q5TFE4 NT5DC1 5-nucleotidase domain-containing protein 1 0 56.766 0.00024003 51758000 4132 4213.6 4455.1 3050.7 3457.3 6655.1 4377.3 3549.3 3097.4 FALSE TRUE 3585.945731 4185.920584 6609.601261 3743.408062 3388.506494 6911.126003 3952.79012 2790.309816 2731.228901 1.312942218 1.532614342 2.420010004 1.370594776 1.240652694 2.530408931 1.447256991 1.021631623 1 11.41533451 1.869293241 4.070883909 1.025304903 1.734273661 0.310807808 0.437026527 0.269454902 7.049653557 0.246464228 0.117010681 74.0104835 -1.869293241 0.708968758 (ac)AQS(ph)SPQLDIQVLHDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQSSPQLDIQVLHDLR 16 0 F6SS63;Q8N5C8-2;Q8N5C8;A0A0A0MQY2 F6SS63 TAB3 TGF-beta-activated kinase 1 and MAP3K7-binding protein 3 1 AQS(0.5)S(0.5)PQLDIQVLHDLR 57.802 0.048754 17811000 6220.7 5977.1 9723.2 7295.3 6128.9 6645.6 8420.5 10037 7776.2 TRUE FALSE 5398.618734 5937.836037 14425.37204 8951.809367 6006.946881 6901.260532 7603.881206 7890.665658 6856.906495 0.787325704 0.865964271 2.103772606 1.3055172 0.876043284 1.00646852 1.108937567 1.150761741 1 12.74334213 3.266855447 24.37330375 1.048670628 1.29696282 0.094228256 0.356605875 413.2417632 355964.874 0.106732817 0.137759603 1848.653202 -3.266855447 0.248292192 (ac)AS(ph)ADELTFHEFEEATNLLADTPDAATTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASADELTFHEFEEATNLLADTPDAATTSR 29 0 K7EIP7;K7ERW0;K7ENM8;Q9BWQ6 K7EIP7 YIPF2 Protein YIPF;Protein YIPF2 1 AS(0.333)ADELT(0.333)FHEFEEAT(0.333)NLLADT(0.001)PDAATTSR 51.586 0.00038999 16862000 2670.7 1402.8 1793.6 1637 1985.3 2554.6 3046.1 2284.5 1432.5 TRUE FALSE 2317.760228 1393.584914 2660.990959 2008.70587 1945.796414 2652.877115 2750.689691 1795.977453 1263.151482 1.83490283 1.103260325 2.106628538 1.590233554 1.540429982 2.100205045 2.177640394 1.421822702 1 10.30281195 (ac)AS(ph)EDNRVPSPPPTGDDGGGGGREETPTEGGALSLKPGLPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASEDNRVPSPPPTGDDGGGGGREETPTEGGALSLKPGLPIR 41 3 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 AS(0.645)EDNRVPS(0.177)PPPT(0.177)GDDGGGGGREETPTEGGALSLKPGLPIR 50.179 0.00051548 10481000000 168200 207750 105480 125890 195300 180250 193200 208310 123250 TRUE FALSE 145971.9438 206385.2766 156490.4808 154475.2486 191413.9121 187184.3341 174463.4937 163764.5276 108679.5254 1.34314116 1.899026296 1.43992606 1.421383172 1.761269304 1.722351413 1.605302315 1.50685722 1 16.72972065 1.203983787 2.681622627 0.826388011 1.607357578 0.551155102 0.168312801 0.397149775 3.032712498 0.732361197 0.041983955 15.99498314 -1.203983787 0.780969566 (ac)AS(ph)GVAVSDGVIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 ASGVAVSDGVIK 12 0 P23528;E9PP50;E9PS23 P23528 CFL1 Cofilin-1 1 AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(0.998)GVAVS(0.002)DGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(0.997)GVAVS(0.003)DGVIK;AS(0.998)GVAVS(0.002)DGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK 79.974 1.23E-11 42649595000 21688323 20512460 17240100 15107530 18807725 18697873 18696884 17831168 23243685 TRUE FALSE 18822156.16 20377712.3 25577470.02 18537925.59 18433488.07 19417192.27 16883663.07 14018111.49 20495843.04 0.918340179 0.994236356 1.247934519 0.904472461 0.899376914 0.947372218 0.823760361 0.683949007 1 24.288828 2.947214248 1.197941642 0.813644894 1.038405894 0.270808011 0.121995841 0.514595031 1.592144361 0.060449586 0.061578112 885.5523661 -2.947214248 0.224761 (ac)AS(ph)GVAVSDGVIKVFNDMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASGVAVSDGVIKVFNDMK 18 1 P23528;E9PP50;E9PS23 P23528 CFL1 Cofilin-1 1 AS(0.988)GVAVS(0.012)DGVIKVFNDMK;AS(0.852)GVAVS(0.148)DGVIKVFNDMK;AS(0.995)GVAVS(0.005)DGVIKVFNDMK 109.22 3.50E-07 261693000 84800.3 49414.8 44839.5 52987.8 50332.7 50678.4 46109.9 40032 63212.7 TRUE FALSE 73593.7255 49090.19093 66524.03218 65019.48986 49331.17774 52628.03084 41638.169 31471.46833 55739.76662 1.320309179 0.880703202 1.193475255 1.166482994 0.885026629 0.944173864 0.747010106 0.564614282 1 15.76641934 2.774007049 1.350734868 0.730922904 1.124981395 0.471492144 0.161107141 0.335521022 1.270981226 0.076852469 0.06641309 594.3018049 -2.774007049 0.39405849 (ac)AS(ph)GVAVSDGVIKVFNDMKVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ASGVAVSDGVIKVFNDMKVR 20 2 P23528;E9PP50;E9PS23 P23528 CFL1 Cofilin-1 1 AS(1)GVAVSDGVIKVFNDMKVR;AS(1)GVAVSDGVIKVFNDMKVR;AS(1)GVAVSDGVIKVFNDMKVR;AS(1)GVAVSDGVIKVFNDMKVR;AS(1)GVAVSDGVIKVFNDMKVR;AS(1)GVAVSDGVIKVFNDMKVR;AS(1)GVAVSDGVIKVFNDMKVR;AS(0.999)GVAVS(0.001)DGVIKVFNDMKVR 99.092 9.60E-22 4624028000 239144.2 128580.6 77096.79 109344.2 118209.7 146902.8 128067 19468.934 164609.8 TRUE FALSE 207540.6881 127735.9456 114381.0555 134172.4718 115857.5582 152554.2458 115647.0821 15305.65397 145149.817 1.429837752 0.880028292 0.788020667 0.924372312 0.798192934 1.051012319 0.796742872 0.105447284 1 17.14718323 8 0.228551916 0.486920626 4.778190064 0.29762614 0.274792337 110.8171847 1.724250104 1.253226471 172.0788451 100000000 -8 4.291269438 (ac)AS(ph)GVAVSDGVIKVFNDMKVRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASGVAVSDGVIKVFNDMKVRK 21 3 P23528;E9PP50;E9PS23 P23528 CFL1 Cofilin-1 1 AS(1)GVAVSDGVIKVFNDMKVRK;AS(0.983)GVAVS(0.017)DGVIKVFNDMKVRK;AS(1)GVAVSDGVIKVFNDMKVRK 95.5 7.78E-12 1550110000 132530 57217.5 59841.4 105216.1 103573 71092 67988 104540 98870 TRUE FALSE 115015.8247 56841.63448 88780.9012 129107.0236 101512.0999 73826.95524 61394.53422 82184.93453 87181.70123 1.319265661 0.651990425 1.018343298 1.480895897 1.164373928 0.846817098 0.704213537 0.942685602 1 16.41173774 2.734329829 23.9853725 0.868386422 1.114213186 0.238931433 0.224132955 336.6992378 1908820.182 0.078719272 0.071947548 542.4126744 -2.734329829 0.245826764 (ac)AS(ph)GVQVADEVCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 94.309 2.87E-11 10241230000 595355 392255 374814 477468.5 508623.5 435537 556721 726834 580234 TRUE FALSE 516677.3283 389678.2511 556075.3041 585885.0206 498502.8875 452292.3902 502730.2831 571406.2053 511639.3975 1.009846644 0.761626749 1.086850049 1.145113186 0.974324671 0.884006182 0.982587122 1.116814319 1 18.96476783 4.221016128 24.99983457 1.029944543 0.885736599 0.273585343 0.095676543 276.8285451 394465.1014 0.025039831 0.052310821 16634.74423 -4.221016128 -0.144207943 (ac)AS(ph)GVQVADEVCRIFYDMKVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASGVQVADEVCRIFYDMKVR 20 2 P60981;F6RFD5 P60981 DSTN Destrin 1 AS(1)GVQVADEVCRIFYDMKVR;AS(1)GVQVADEVCRIFYDMKVR;AS(1)GVQVADEVCRIFYDMKVR;AS(1)GVQVADEVCRIFYDMKVR 97.271 2.39E-11 1265172000 210596 258743 112965 133726 248177 278045 219213 300017 89251 TRUE FALSE 182765.205 257043.3002 167595.2518 164090.5322 243238.7633 288741.5711 197953.757 235860.6993 78699.84846 2.32230695 3.266121921 2.129549867 2.08501713 3.090714506 3.668896151 2.515300358 2.996965101 1 16.26407324 5.045538427 15.67952612 2.649579263 0.628564375 0.008033301 0.750015743 13436461.45 126626546.9 0.177277168 799174003.7 111055.0795 -5.045538427 -2.021014888 (ac)AS(ph)GVQVADEVCRIFYDMKVRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASGVQVADEVCRIFYDMKVRK 21 3 P60981;F6RFD5 P60981 DSTN Destrin 1 AS(1)GVQVADEVCRIFYDMKVRK;AS(1)GVQVADEVCRIFYDMKVRK 71.073 0.00011495 314170000 193324 155987 87827 80380 112422 91838 188237 224258 75236 TRUE FALSE 167775.7436 154962.3111 130300.431 98631.50753 110185.0221 95371.06729 169981.8047 176302.1719 66341.68579 2.528964128 2.335821125 1.964080795 1.486719946 1.660871605 1.437573769 2.562217144 2.657487065 1 16.01762805 4.308724476 3.361990139 1.903432328 2.487080726 0.194961768 0.502429814 0.478557699 10.53476448 0.141377362 0.435485826 20357.50152 -4.308724476 0.583648397 (ac)AS(ph)LSLAPVNIFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASLSLAPVNIFK 12 0 P78371;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 1 AS(0.865)LS(0.135)LAPVNIFK 46.158 0.00075027 17044000 70605 64312 42837 47501 66387 48701 70800 66727 85319 TRUE FALSE 61274.37036 63889.53024 63553.11648 58286.82806 65066.02858 50574.55898 63933.8269 52457.95032 75232.68502 0.814464755 0.849225709 0.844754065 0.774754059 0.864863836 0.672241845 0.849814504 0.697276062 1 16.19907196 3.753344421 23.14905498 0.797161187 0.837455936 0.005525982 0.091471884 1152.238337 1804205.276 0.022555342 0.038784488 5666.885283 -3.753344421 0.040294749 (ac)AS(ph)PGIEVELLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASPGIEVELLGK 12 0 Q8TCY9 Q8TCY9 URGCP Up-regulator of cell proliferation 1 AS(1)PGIEVELLGK 58.223 0.0013757 11989000 39267 38030 25427 44703 47093 45513 49696 63632 64439 TRUE FALSE 34077.76646 37780.17843 37723.58225 54853.49939 46155.94144 47263.91456 44876.48957 50024.79198 56821.09483 0.599737942 0.664897052 0.66390101 0.965372096 0.812302923 0.831802251 0.789785725 0.880391202 1 15.79413901 3.825359928 6.517256846 0.869243325 0.641616334 0.736774628 0.066664451 0.131578192 8.24596005 0.01784227 0.031203241 6688.980472 -3.825359928 -0.227626991 (ac)AS(ph)PGKDNYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASPGKDNYR 9 1 O15131;Q5TD90 O15131 KPNA5 Importin subunit alpha-6 1 AS(1)PGKDNYR;AS(1)PGKDNYR 55.676 0.012409 1438380000 1677880 1313310 1201970 1224400 1387950 1473450 1839860 1942140 1963650 TRUE FALSE 1456143.907 1304682.78 1783246.712 1502418.734 1360332.51 1530134.575 1661430.66 1526828.475 1731509.534 0.840967883 0.753494425 1.029879811 0.867693018 0.785633855 0.883699769 0.959527296 0.881790394 1 20.7235989 -1.999999997 0.49770407 4.805366335 0.856790503 0.222520983 0.07722182 190.7706673 2.159305808 783.4618624 0.051349623 0.01 1.999999997 -3.948575832 (ac)AS(ph)PPESDGFSDVRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASPPESDGFSDVRK 14 1 P35568 P35568 IRS1 Insulin receptor substrate 1 1 AS(0.999)PPES(0.001)DGFSDVRK;AS(0.996)PPES(0.004)DGFSDVRK 80.037 1.05E-05 896740000 619260 881290 643420 834160 1126010 1016110 1348850 1518220 673280 TRUE FALSE 537423.222 875500.748 954580.0641 1023568.777 1103604.604 1055200.409 1218038.735 1193560.468 593685.6054 0.905232024 1.474687511 1.607888174 1.724092294 1.858904097 1.7773724 2.051656169 2.010425142 1 19.17933961 5.020035434 1.048441863 1.794517478 6.45E-15 0.436580183 0.290149598 2.662882054 1.619312227 0.088839042 6.116702313 104721.3988 -5.020035434 -1.794517478 (ac)AS(ph)PSKGNDLFSPDEEGPAVVAGPGPGPGGAEGAAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASPSKGNDLFSPDEEGPAVVAGPGPGPGGAEGAAEER 37 1 P35548;D6RIS4 P35548 MSX2 Homeobox protein MSX-2 1 AS(0.472)PS(0.472)KGNDLFS(0.056)PDEEGPAVVAGPGPGPGGAEGAAEER 45.192 0.0041151 68902000 22633 17903 14977 18384 20325 18019 23662 26435 15800 TRUE FALSE 19641.99171 17785.39401 22219.9273 22558.36818 19920.57227 18712.20259 21367.26288 20782.08097 13932.142 1.409832867 1.276572835 1.594867989 1.619160082 1.429828397 1.343095885 1.533666746 1.491664452 1 13.76612946 1.236609386 24.99710535 0.99999941 1.465549703 0.653436351 0.105792708 33.60704441 430421.1545 0.169459762 0.026786245 17.24286334 -1.236609386 0.465550293 (ac)AS(ph)PSLERPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASPSLERPEK 10 1 Q13601-2;Q13601 Q13601-2 KRR1 KRR1 small subunit processome component homolog 1 AS(0.646)PS(0.354)LERPEK;AS(0.985)PS(0.015)LERPEK 64.485 0.0011819 919830000 585490 549700 477470 427800 572710 446710 692020 675340 698680 TRUE FALSE 508116.0131 546088.9845 708376.089 524938.5285 561314.1915 463895.2228 624908.0069 530923.7965 616082.8463 0.824752736 0.886388881 1.149806545 0.852058342 0.911101802 0.752975392 1.014324633 0.861773379 1 19.23276484 0.96500034 0.005419254 1.094118406 0.742821659 0.002123766 0.112531608 2431924.396 3232.958392 107436.2352 102188.9127 9.225721499 -0.96500034 -0.351296747 (ac)AS(ph)PSSFTYYCPPSSSPVWSEPLYSLRPEHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASPSSFTYYCPPSSSPVWSEPLYSLRPEHAR 31 1 P49356 P49356 FNTB Protein farnesyltransferase subunit beta 1 AS(0.971)PS(0.027)S(0.002)FTYYCPPSSSPVWSEPLYSLRPEHAR;AS(0.99)PS(0.009)S(0.001)FTYYCPPSSSPVWSEPLYSLRPEHAR;AS(0.916)PS(0.071)S(0.012)FTYYCPPSSSPVWSEPLYSLRPEHAR;AS(0.186)PS(0.186)S(0.186)FT(0.186)Y(0.127)Y(0.127)CPPS(0.002)SSPVWSEPLYSLRPEHAR 194.11 2.42E-92 2917610000 6479.1 3820.9 3495.2 10104.9 5595.9 12518.1 0 4888.5 4073.6 TRUE FALSE 5622.870519 3795.800256 5185.490411 12399.37199 5484.552538 12999.67941 0 3843.132317 3592.023649 1.56537681 1.056730308 1.443612548 3.45191825 1.52686983 3.619040596 0 1.069907298 1 11.81058113 3.988878571 24.44134949 1.719977489 1.295832677 0.031618064 1.088957475 1934.824056 4252170.601 0.296332967 0.557286808 9747.170688 -3.988878571 -0.424144812 (ac)AS(ph)PTDGTDLEASLLSFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASPTDGTDLEASLLSFEK 18 0 G3V5T8 G3V5T8 LIN52 1 AS(0.491)PT(0.491)DGT(0.018)DLEASLLSFEK;AS(0.851)PT(0.064)DGT(0.085)DLEASLLSFEK;AS(0.499)PT(0.499)DGT(0.001)DLEASLLSFEK;AS(0.456)PT(0.456)DGT(0.088)DLEASLLSFEK 96.866 4.73E-62 182409000 266683 239899 162306 187367 222865 190289 255947 287587 257592 TRUE FALSE 231440.1659 238323.0877 240797.7245 229911.5411 218430.4225 197609.541 231125.2993 226088.7581 227139.7672 1.01893283 1.049235414 1.06013019 1.012202944 0.961656451 0.869990946 1.017546607 0.995372853 1 17.79322079 3.43656479 4.077253325 0.971269656 1.042875072 0.411283131 0.040620098 0.23263073 8.391477731 0.01273394 0.017269656 2732.529064 -3.43656479 0.071605415 (ac)ASAVS(ph)PANLPAVLLQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASAVSPANLPAVLLQPR 17 0 P51610-2;P51610;A6NEM2;P51610-4;P51610-3 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 1 AS(0.006)AVS(0.994)PANLPAVLLQPR;AS(0.063)AVS(0.937)PANLPAVLLQPR 89.403 3.36E-21 167282000 30449 46019 26639 28891 30878 29029 41650 39205 37682 TRUE FALSE 26425.0875 45716.69816 39521.7095 35451.14312 30263.58821 30145.76441 37610.78941 30821.31584 33227.27689 0.795282972 1.375878568 1.189435705 1.066928934 0.91080555 0.907259554 1.131925121 0.927590785 1 15.02008044 3.468171684 5.615182064 0.978102614 1.143820804 0.153315214 0.154099452 0.25603559 27.70561663 0.041841 0.056834898 2938.811188 -3.468171684 0.16571819 (ac)ASEDNRVPS(ph)PPPTGDDGGGGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ASEDNRVPSPPPTGDDGGGGGR 22 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 ASEDNRVPS(0.988)PPPT(0.012)GDDGGGGGR;ASEDNRVPS(0.949)PPPT(0.051)GDDGGGGGR;ASEDNRVPS(0.926)PPPT(0.074)GDDGGGGGR;AS(0.001)EDNRVPS(0.983)PPPT(0.015)GDDGGGGGR;ASEDNRVPS(0.992)PPPT(0.008)GDDGGGGGR;AS(0.005)EDNRVPS(0.978)PPPT(0.017)GDDGGGGGR;AS(0.009)EDNRVPS(0.975)PPPT(0.017)GDDGGGGGR;AS(0.001)EDNRVPS(0.93)PPPT(0.069)GDDGGGGGR 116.13 6.85E-22 10727173000 114366.8 138251.98 78753.13 103495.4 118272.9 126084.43 118800.4 143893.6 139054.89 TRUE FALSE 99252.93761 137343.7936 116838.4071 126995.6124 115919.5007 130934.9796 107279.1555 113123.0734 122615.9793 0.809461688 1.120113336 0.952880756 1.03571829 0.945386575 1.067845972 0.87491986 0.922580189 1 16.90378748 2.226554911 24.99274342 0.928034235 0.99310541 0.081073775 0.087675617 476.3472831 991621.6125 0.032408839 0.022039479 168.4825437 -2.226554911 0.065071175 (ac)ASEDNRVPS(ph)PPPTGDDGGGGGREETPTEGGALSLKPGLPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASEDNRVPSPPPTGDDGGGGGREETPTEGGALSLKPGLPIR 41 3 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 ASEDNRVPS(0.942)PPPT(0.057)GDDGGGGGREETPTEGGALSLKPGLPIR;AS(0.001)EDNRVPS(0.959)PPPT(0.04)GDDGGGGGREETPTEGGALSLKPGLPIR;AS(0.016)EDNRVPS(0.838)PPPT(0.097)GDDGGGGGREET(0.031)PT(0.014)EGGALS(0.003)LKPGLPIR 118.95 1.26E-44 17930700000 790263 803547 480300 501796 766119 782863 839483 934990 531978 TRUE FALSE 685827.7423 798268.4468 712574.6865 615736.4513 750874.7308 812980.2462 758070.0679 735049.6646 469088.1669 1.462044432 1.701745009 1.519063444 1.312624139 1.600711303 1.733107555 1.616050289 1.5669755 1 18.83949958 1.238619673 12.23607835 0.999316857 1.568130095 0.689357838 0.118964797 0.034876694 317.9848766 0.166684025 0.02989931 17.32286308 -1.238619673 0.568813238 (ac)ASGEHS(ph)PGSGAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASGEHSPGSGAAR 13 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 1 ASGEHS(0.998)PGS(0.002)GAAR;AS(0.006)GEHS(0.989)PGS(0.004)GAAR;AS(0.006)GEHS(0.985)PGS(0.009)GAAR 94.551 1.07E-40 2089246000 16614.1 15011.2 16973 3585 14238.3 25420 12765.6 11775 13309.5 TRUE FALSE 14418.50459 14912.59044 25181.19957 4399.029043 13954.98569 26397.92385 11527.59408 9257.007883 11736.06607 1.228563686 1.27066347 2.145625239 0.374829949 1.189068432 2.249299185 0.982236638 0.788765829 1 13.51866128 2.024624733 24.99992301 0.881155891 1.399411378 0.163312388 0.520851917 379.9815807 385769.4544 0.210827241 0.142133495 105.8338836 -2.024624733 0.518255487 (ac)ASGRPEELWEAVVGAAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASGRPEELWEAVVGAAER 18 1 Q96B36;H9KV91;M0R2V8 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 0 ; 61.423 1.72E-07 60047000 5678.9 3978.8 3545.4 2633.3 5213.2 5099.2 5335 5661.4 2953.7 FALSE TRUE 4928.418977 3952.663001 5259.967299 3231.231012 5109.467519 5295.369524 4817.612521 4450.753667 2604.516951 1.892258361 1.517618459 2.019555794 1.240625833 1.961771651 2.03314842 1.849714405 1.708859551 1 11.34680011 1.237086015 4.219785553 0.921960055 1.781025317 0.505242913 0.243065296 0.185871941 6.255350281 0.488690048 0.058812215 17.26179741 -1.237086015 0.859065262 (ac)ASGVAVSDGVIKVFNDMKVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASGVAVSDGVIKVFNDMKVR 20 2 P23528;E9PP50;E9PS23 P23528 CFL1 Cofilin-1 0 80.238 6.92E-05 197140000 27642 15081 19631 11795 20013 16944 24894 22976 18688 FALSE TRUE 23989.03966 14981.93192 29124.61726 14473.23503 19614.78045 17595.84664 22479.78371 18062.7612 16478.72593 1.455758156 0.909168098 1.767407103 0.878298182 1.190309284 1.067791692 1.36417001 1.096126077 1 14.00831708 8 0.111679065 0.928934569 2.122245439 0.088856681 0.260478628 752.9670314 7.613547405 11.28263094 139.6065384 100000000 -8 1.19331087 (ac)ASHLRPPS(ph)PLLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ASHLRPPSPLLVR 13 1 Q8TDB6;Q8TDB6-2 Q8TDB6 DTX3L E3 ubiquitin-protein ligase DTX3L 1 ASHLRPPS(1)PLLVR;ASHLRPPS(1)PLLVR;ASHLRPPS(1)PLLVR;ASHLRPPS(1)PLLVR;ASHLRPPS(1)PLLVR;ASHLRPPS(1)PLLVR;ASHLRPPS(1)PLLVR;ASHLRPPS(1)PLLVR 108.77 6.39E-05 8409000000 78660.8 64113.8 47139.8 69839.2 60752.7 89655.9 60272.8 72336 63116 TRUE FALSE 68265.57598 63692.63223 69936.76495 85697.25779 59543.84013 93105.02049 54427.55313 56867.50932 55654.49838 1.226595836 1.144429185 1.256623759 1.539808286 1.069883691 1.672910963 0.977954248 1.02179538 1 15.76421068 AAQDRDQIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 AAQDRDQIYR 10 1 P62995;P62995-3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 ;;;;;; 199.68 2.50E-07 14206070000 9131830 8396460 4427870 5269700 7605330 7357190 7191360 8315780 4138750 FALSE TRUE 7925035.528 8341303.101 6569202.742 6466265.927 7453998.813 7640225.86 6493943.014 6537515.16 3649471.69 2.171556927 2.285619347 1.800042116 1.771836166 2.04248709 2.093515585 1.779420027 1.79135933 1 21.7992562 0.985020955 1.430722636 4.14E-17 2.005728359 0.774946131 0.167965122 1.16403051 1.283389668 4.043053489 0.051253022 9.660974921 -0.985020955 2.005728359 (ac)ASLEVSRS(ph)PR ddPTM_MDA-MB-175_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;ASLEVS(0.001)RS(0.999)PR;ASLEVSRS(1)PR 125.72 8.74E-12 6754500000 208747 149938 105534 101904 180899 202606 197422 179055 159350 TRUE FALSE 181160.5551 148953.0474 156570.5954 125042.8607 177299.4638 210400.3839 178276.0448 140765.4817 140511.8245 1.289290461 1.060074822 1.114287683 0.889909879 1.261811697 1.497385609 1.268761867 1.001805237 1 17.10033202 1.658492817 6.554830809 0.998424077 1.190649875 0.206499627 0.159357532 0.223999713 19.19618591 0.107061071 0.044752492 45.55046525 -1.658492817 0.192225799 (ac)ASSDIQVKELEKRASGQAFELILSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASSDIQVKELEKRASGQAFELILSPR 26 3 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 0 ; 60.521 5.02E-05 431723000 27689.1 21418.2 22315.9 23394.3 24171.8 28888.5 27353.2 76746.3 26844.1 FALSE TRUE 24029.91528 21277.50243 33107.94388 28706.33337 23690.82847 29999.85929 24700.49087 60334.70099 23670.62108 1.015178909 0.898899203 1.398693502 1.212741029 1.000853691 1.267387923 1.043508355 2.548927668 1 14.53080994 1.776019753 25 1.873953546 1.126552154 0.314878461 0.3954794 41.06050618 27417.78741 0.193181744 0.092889652 59.70624417 -1.776019753 -0.747401392 (ac)AT(ph)PPKR ddPTM_MDA-MB-175_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 47.067 0.059859 2565200000 619760 617740 410692 454465 510890 475765 618681 750240 614570 TRUE FALSE 537857.1457 613682.0253 609304.0249 557658.2243 500724.2885 494067.9874 558681.4118 589807.0144 541916.2347 0.992509748 1.132429674 1.124350934 1.029048751 0.923988352 0.911705455 1.030936842 1.08837303 1 19.04771034 5.068882874 20.24934716 1.032466763 0.000635197 0.024140459 0.073771245 76.86634267 613664.4071 0.019324216 92986.4375 117187.9276 -5.068882874 -1.031831566 (ac)ATEGDVELELETETSGPERPPEKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATEGDVELELETETSGPERPPEKPR 25 2 J3QT56 J3QT56 HYPK 0 104.53 1.29E-10 55355000 140400 118810 76989 105870 115720 109710 122510 155350 137570 FALSE TRUE 121845.7843 118029.5293 114221.1379 129909.4016 113417.3984 113930.6147 110628.9991 122129.6114 121306.6313 1.004444546 0.972984972 0.941590222 1.07091756 0.934964537 0.939195273 0.911978165 1.006784296 1 16.88829889 4.736454658 7.403946743 0.97206346 1.004803473 0.046687806 0.045648317 0.3721946 193.8303895 0.011096935 0.062390093 54507.2985 -4.736454658 0.032740014 (ac)ATNFLAHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATNFLAHEK 9 0 P29692;P29692-4;E9PK01;E9PQ49;E9PQZ1;E9PI39;E9PPR1;E9PL12;E9PMW7;E9PK06;E9PK72;E9PKK3;E9PJD0;E9PNW6;P29692-3;E9PL71;E9PN91 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 56.563 0.013858 149630000 219000 190790 144370 167770 184750 175870 223390 239690 219200 FALSE TRUE 190058.5951 189536.6879 214187.8149 205864.7427 181073.8365 182635.8327 201725.6722 188434.1588 193286.4257 0.983300273 0.980600098 1.10813687 1.065076049 0.936816105 0.944897356 1.043661868 0.974895977 1 17.5603808 3.249501371 24.99950854 0.982422197 1.03571977 0.249967517 0.046542655 337.4056746 770964.1791 0.014140801 0.018079659 1776.238876 -3.249501371 0.053297573 (ac)ATSPQKS(ph)PSVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATSPQKSPSVPK 12 1 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 1 AT(0.006)S(0.033)PQKS(0.954)PS(0.008)VPK;AT(0.049)S(0.373)PQKS(0.563)PS(0.014)VPK 69.352 0.00020822 788040000 2114610 1637190 1260690 1228050 1515020 1134740 2060910 2314600 1756480 TRUE FALSE 1835158.931 1626435.191 1870363.901 1506897.522 1484874.066 1178394.182 1861043.265 1819640.802 1548830.935 1.184867172 1.050105053 1.2075972 0.972925765 0.958706359 0.760828154 1.201579348 1.17484792 1 20.56274824 3.733786173 24.95990006 1.027736916 1.137781332 0.193564795 0.127549734 867.6782944 4536063.488 0.038614668 0.059460479 5417.340988 -3.733786173 0.110044416 (ac)AVPETRPNHTIYINNLNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVPETRPNHTIYINNLNEK 19 1 P09012;M0R221;M0R2B8;M0R268;M0QXK2;M0R0G9 P09012 SNRPA U1 small nuclear ribonucleoprotein A 0 ; 111.01 8.81E-39 750310000 454330 386080 223480 236384 286990 267440 393180 394520 358160 FALSE TRUE 394289.1394 383543.8151 331555.6755 290058.6001 281279.4605 277728.5899 355049.4641 310154.9682 315818.7328 1.248466599 1.214442891 1.049829035 0.918433804 0.890635771 0.879392389 1.12421914 0.982066407 1 18.26873722 4.167130531 2.946737648 0.970961379 1.242793749 0.71373551 0.068752375 0.144710269 2.4984888 0.019643315 0.052861286 14693.67843 -4.167130531 0.271832369 (ac)AYHSFLVEPISCHAWNK ddPTM_MDA-MB-175_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 ; 118.47 3.24E-72 2351700000 2147730 2276800 658530 1537820 2239200 2254800 2375600 2600500 2227400 FALSE TRUE 1863902.039 2261843.551 976997.3107 1887005.535 2194644.301 2341543.615 2145214.678 2044403.312 1964079.309 0.948995303 1.151604999 0.497432719 0.960758319 1.117390876 1.192183841 1.09222406 1.040896517 1 20.90542176 3.467739581 12.86103953 1.083628477 0.867015208 0.277372401 0.165368706 0.826949052 1124.863911 0.047347518 0.061892747 2935.888654 -3.467739581 -0.216613269 (ac)AYHSGYGAHGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AYHSGYGAHGSK 12 0 E9PIZ0;C9JST7;A6NGW1;O95070 E9PIZ0 YIF1A Protein YIF1A 0 ; 61.375 5.90E-05 315800000 276645 323380 88349 202163 404410 375040 299800 404670 367400 FALSE TRUE 240085.6623 321255.6955 131074.8719 248067.199 396363.0322 389468.0315 270725.4421 318134.4696 323966.3905 0.741082005 0.991632789 0.404594044 0.765718933 1.223469606 1.202186532 0.835659038 0.981998377 1 18.30548462 3.374403739 7.646619773 1.031184181 0.715203989 0.451794581 0.176888045 0.230103107 15.2105214 0.052201108 0.067448215 2368.120182 -3.374403739 -0.315980192 (ac)DDDIAALVVDNGSGMCK ddPTM_MDA-MB-175_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 ;;;;;;;;; 179.19 9.89E-161 2939957000 4524450 4076890 2769470 3296550 3582540 3471900 4178410 4806740 4277860 FALSE TRUE 3926532.469 4050108.641 4108794.955 4045082.062 3511254.463 3605466.24 3773188.441 3778856.057 3772136.264 1.040930707 1.073690969 1.089248815 1.072358414 0.930839773 0.955815482 1.000278934 1.001781429 1 21.84695036 3.259910087 24.99930716 0.981341719 1.070830511 0.768120417 0.024878191 124.658865 145969.1244 0.007838233 0.010109362 1819.324163 -3.259910087 0.089488791 (ac)DDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPR 38 3 C9JTX5;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7 C9JTX5;P60709 ACTB "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed" 0 ;; 121.75 3.76E-31 1125100000 11309.3 2390.3 8374.5 1666.1 5500.1 11053.7 3806.9 23777.4 13338.5 FALSE TRUE 9814.747351 2374.597962 12424.43621 2044.41347 5390.658771 11478.94299 3437.707424 18692.78805 11761.63773 0.834471149 0.201893479 1.056352568 0.173820476 0.458325524 0.975964679 0.292281356 1.589301463 1 13.52180134 1.740189665 14.49699834 1.289538938 0.570999313 0.442611486 0.337832383 0.050428523 128.536462 0.16512401 0.078661177 54.9780921 -1.740189665 -0.718539626 (ac)EEEIAALVIDNGSGMCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EEEIAALVIDNGSGMCK 17 0 P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65 P63261 ACTG1 "Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 ;;;;; 140.24 1.64E-57 153683000 375650 307280 217548 248968.6 268514 262975 318449 360967 308394 FALSE TRUE 326006.9007 305261.4574 322754.9405 305500.7259 263171.0967 273091.8184 287565.865 283777.0161 271936.0126 1.198836806 1.122548847 1.186878256 1.123428717 0.967768462 1.004250286 1.057476214 1.043543344 1 18.0529077 3.397854991 5.389496493 1.021418899 1.163415137 0.838454921 0.031643783 0.081346285 4.06408903 0.009379539 0.012226664 2499.510648 -3.397854991 0.141996238 (ac)GDKKS(ph)PTRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GDKKSPTRPK 10 3 Q8IY57;Q8IY57-5;G3V1X5;A0A0B4J255;F8VRE5;G3V219;G3V212;Q8IY57-4 Q8IY57 YAF2 YY1-associated factor 2 1 GDKKS(0.917)PT(0.083)RPK;GDKKS(0.85)PT(0.15)RPK;GDKKS(0.963)PT(0.037)RPK;GDKKS(0.957)PT(0.043)RPK 53.034 0.00068701 4654290000 8394600 5675260 5190570 5122310 4470550 3081190 8421400 9855900 4826650 TRUE FALSE 7285232.341 5637978.843 7700747.013 6285408.775 4381594.801 3199725.373 7604693.924 7748292.484 4256048.936 1.711736038 1.324697843 1.809365242 1.476817788 1.02949822 0.751806528 1.786796637 1.820536512 1 22.02108331 3.475720248 24.94816443 1.347980575 1.595689881 0.14593846 0.353769258 124.3291436 2213924.557 0.112693586 0.146625966 2990.33778 -3.475720248 0.247709306 (ac)GDPERPEAAGLDQDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GDPERPEAAGLDQDER 16 1 Q7LG56;Q7LG56-5 Q7LG56 RRM2B Ribonucleoside-diphosphate reductase subunit M2 B 0 110.08 2.86E-08 464890000 0 0 0 0 15205 9265.3 0 0 0 FALSE TRUE 0 0 0 0 14902.45025 9621.742086 0 0 0 0 (ac)GDREQLLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GDREQLLQR 9 1 Q04917;F8WEB6;A2IDB1 Q04917 YWHAH 14-3-3 protein eta 0 ;; 105.12 2.22E-05 1731131000 155908 200033 147440 133786 127617 170298 155784 183004 158427 FALSE TRUE 135304.3628 198718.9701 218742.4772 164164.1561 125077.6714 176849.4743 140676.0917 143870.0187 139697.9405 0.968549445 1.422490334 1.565824638 1.175136551 0.895343703 1.265941886 1.007001901 1.029864994 1 17.09195123 3.481012047 24.79743151 1.046183837 1.336170412 0.3507378 0.17330711 148.5443956 946731.0123 0.048033079 0.063505098 3026.997394 -3.481012047 0.289986575 (ac)GDS(ph)DDEYDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 73.208 5.96E-06 6555300000 17674 0 0 0 0 0 0 13478 0 TRUE FALSE 15338.33612 0 0 0 0 0 0 10595.83459 0 0 (ac)GS(ph)PEDDLIGIPFPDHSSELLSCLNEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSPEDDLIGIPFPDHSSELLSCLNEQR 27 0 O15156 O15156 ZBTB7B Zinc finger and BTB domain-containing protein 7B 1 GS(0.998)PEDDLIGIPFPDHS(0.001)S(0.001)ELLSCLNEQR;GS(0.999)PEDDLIGIPFPDHSSELLSCLNEQR 47.237 0.0014418 31315000 1480.2 2279.2 0 1011.7 1900.6 1126 1416.9 3745.8 978.7 TRUE FALSE 1284.58782 2264.227785 0 1241.421948 1862.781778 1169.317949 1279.489256 2944.78982 862.9992009 1.488515654 2.623673096 0 1.438497216 2.158497686 1.354946734 1.482607695 3.412274098 1 9.753215413 (ac)GSELETAMETLINVFHAHSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSELETAMETLINVFHAHSGK 21 0 P23297;Q5T7Y5;Q5T7Y4 P23297 S100A1 Protein S100-A1 0 ;;; 181.14 2.93E-80 1082261000 692410 715635 442649 505606 640143 590489 714027 734772 701780 FALSE TRUE 600906.2642 710933.9466 656715.537 620411.57 627405.4067 613205.4939 644780.7714 577646.7258 618816.3679 0.971057482 1.148860928 1.061244613 1.002577828 1.013879786 0.990932893 1.041958172 0.933470341 1 19.23915183 3.724294494 3.96332374 0.99293786 1.070363123 0.256337113 0.049977605 0.246816429 9.040932327 0.013272574 0.021879683 5300.227286 -3.724294494 0.077425263 (ac)GTRDDEYDYLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GTRDDEYDYLFK 12 1 H3BMH2;H3BSC1;P62491-2;Q15907-2;P62491;Q15907;B4DQU5 H3BMH2 RAB11A;RAB11B Ras-related protein Rab-11A;Ras-related protein Rab-11B 0 ;;;;; 91.867 2.45E-15 3413890000 6105120 5103680 3586670 4287320 5128880 4740520 4932450 6936870 4751160 FALSE TRUE 5298312.924 5070153.59 5321195.609 5260821.534 5026825.322 4922890.872 4454101.758 5453474.333 4189483.277 1.264669787 1.210209769 1.270131722 1.255720858 1.199867618 1.175059201 1.063162558 1.301705717 1 21.99834089 2.947865767 2.451447406 1.153866453 1.248553837 0.3080458 0.079210344 0.433614489 5.180431036 0.026753328 0.028183099 886.8818504 -2.947865767 0.094687383 (ac)MDDREDLVYQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 MDDREDLVYQAK 12 1 P62258;B4DJF2;I3L3T1;I3L0W5 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;;; 115.71 3.85E-05 5451930000 7988450 7627920 5688890 7005770 7520900 6809000 8241650 10100030 9098730 FALSE TRUE 6932756.092 7577811.691 8440056.232 8596537.155 7371248.804 7070946.636 7442376.052 7940217.183 8023088.505 0.864100663 0.944500573 1.051970974 1.071474801 0.918754517 0.881324771 0.927619837 0.989670895 1 22.93572628 3.086523819 0.003411337 1.925385339 7.15E-05 0.015900369 0.067551309 215872.4034 1016.410042 286632.28 287002.9669 1220.460755 -3.086523819 -1.925313888 (ac)MDEET(ph)RHSLECIQANQIFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MDEETRHSLECIQANQIFPR 20 1 Q13615-3;Q13615-2;Q13615;C9JLU3 Q13615-3 MTMR3 Myotubularin-related protein 3 1 MDEET(0.5)RHS(0.5)LECIQANQIFPR 70.315 3.32E-31 111940000 3715.4 3532.2 2909.2 1230.6 4227.3 4385.4 4939.6 5121 3961.5 TRUE FALSE 3224.400476 3508.996746 4316.098851 1510.026539 4143.185001 4554.109176 4460.558352 4025.914002 3493.175983 0.923056981 1.004529048 1.235580134 0.432278976 1.186079665 1.30371593 1.276934908 1.152508211 1 11.77032361 3.061726646 24.99999976 1.19367927 0.915299903 0.307978155 0.211386155 85.17027243 34494.01914 0.062400054 0.070755005 1152.727479 -3.061726646 -0.278379367 (ac)MDEETRHS(ph)LECIQANQIFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MDEETRHSLECIQANQIFPR 20 1 Q13615-3;Q13615-2;Q13615;C9JLU3 Q13615-3 MTMR3 Myotubularin-related protein 3 1 MDEET(0.109)RHS(0.891)LECIQANQIFPR 74.561 2.71E-29 94711000 3948.4 2676.5 4438.1 0 5541.3 2813.5 5491.8 6492.4 0 TRUE FALSE 3426.608936 2658.917895 6584.380005 0 5431.038971 2921.737166 4959.206081 5104.050784 0 0 (ac)MDEPS(ph)PLAQPLELNQHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MDEPSPLAQPLELNQHSR 18 0 Q13085;A0A0C4DGT1;A0A087X2F8;A0A087X126 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 1 MDEPS(1)PLAQPLELNQHSR;MDEPS(1)PLAQPLELNQHSR;MDEPS(1)PLAQPLELNQHSR;MDEPS(1)PLAQPLELNQHSR 146.78 9.89E-19 728180000 55076.8 40574.5 33584.9 47139.6 52287.8 64754 54635.1 51548.8 84595.4 TRUE FALSE 47798.26133 40307.96344 49826.66997 57843.36666 51247.37508 67245.12828 49336.59641 40525.49027 74594.62818 0.640773505 0.540360136 0.667965927 0.775436088 0.687011603 0.90147414 0.661396103 0.543276255 1 16.18678412 4.00957723 5.222581358 0.734626339 0.591707399 0.218318181 0.128792819 0.295201939 24.82655923 0.034056292 0.069072788 10222.97338 -4.00957723 -0.14291894 (ac)MDFEDDYTHSACR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MDFEDDYTHSACR 13 0 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-2;E2QRN4 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 0 ; 117.02 1.46E-11 261460000 98899 96560 77357 85959 104255 95572 106878 123702 105664 FALSE TRUE 85829.24657 95925.691 114767.1039 105477.3048 102180.5295 99248.71668 96512.98801 97249.28995 93172.52229 0.921186252 1.029549149 1.231769851 1.132064499 1.096680942 1.065214446 1.035852477 1.043755042 1 16.50761693 2.33405504 2.204005387 1.02761083 1.090130091 0.091211274 0.078280442 0.779567246 7.814533314 0.040514335 0.026345781 215.8017885 -2.33405504 0.062519261 (ac)MDFQHRPGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MDFQHRPGGK 10 1 Q15428;K7EMT0 Q15428 SF3A2 Splicing factor 3A subunit 2 0 ;;; 82.749 0.0030442 1508190000 1646370 1532323 876389 1079945 1450970 1630223 1504034 1635550 1207470 FALSE TRUE 1428798.033 1522257.069 1300213.652 1325163.018 1422098.536 1692938.734 1358173.014 1285800.36 1064724.272 1.341941825 1.429719514 1.22117405 1.244606752 1.335649588 1.590025491 1.27561008 1.207636938 1 20.02204844 1.405725124 1.949253035 0.95838808 1.352437898 0.545334036 0.103503348 0.448820818 2.325029603 0.29356064 0.029970069 25.45218809 -1.405725124 0.394049818 (ac)MDLFGDLPEPERS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MDLFGDLPEPERSPR 15 1 Q9H0C8;E9PC05;F8SNU7;F8SNU6 Q9H0C8 ILKAP;ILKAP3;ILKAP2 Integrin-linked kinase-associated serine/threonine phosphatase 2C 1 MDLFGDLPEPERS(1)PR;MDLFGDLPEPERS(1)PR;MDLFGDLPEPERS(1)PR 96.414 6.49E-06 83753000 43060.3 34296.5 27867.1 45037.7 38143.2 36766.1 30651.9 56262.7 35552.8 TRUE FALSE 37369.77225 34071.20403 41343.72277 55264.19814 37384.22495 38180.51566 27679.28346 44231.35944 31349.78849 1.192026296 1.086808099 1.318787933 1.762825231 1.19248731 1.217887504 0.88291771 1.410898178 1 14.93616809 3.023996364 24.99958336 1.155394564 1.340140635 0.169860997 0.219294831 476.9962984 496934.5854 0.067992718 0.077093554 1056.80866 -3.023996364 0.18474607 (ac)MDLFGDLPEPERS(ph)PRPAAGK ddPTM_MDA-MB-175_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 128.07 4.49E-22 2434309000 2523766 2127004 1368738 1530362 1933677 1850496 2210150 2705165 1671508 TRUE FALSE 2190243.929 2113031.571 2030664.275 1877854.082 1895200.611 1921685.779 1995809.993 2126686.516 1473904.228 1.486015093 1.433628814 1.377745064 1.274067912 1.285837013 1.303806409 1.354097474 1.442893287 1 20.49121135 4.140897562 2.033360166 1.300502916 1.475984563 0.301551492 0.113273139 0.485099373 3.888589559 0.031249542 0.101339967 13832.40073 -4.140897562 0.175481647 (ac)MDNYADLS(ph)DTELTTLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MDNYADLSDTELTTLLR 17 0 P50402;Q5HY57;F8WEQ1 P50402 EMD Emerin 1 MDNY(0.008)ADLS(0.494)DT(0.494)ELT(0.004)T(0.001)LLR 48.659 0.0027603 12213000 5457.7 3650.4 2291.9 2057.9 3114.3 2994.8 4844 5068.5 1728 TRUE FALSE 4736.451117 3626.420282 3400.270506 2525.177648 3052.331523 3110.011894 4374.229626 3984.640718 1523.717809 3.108483139 2.379981557 2.231561833 1.657247578 2.003213132 2.041068153 2.870760978 2.615077868 1 10.57338003 4.740193908 2.159995497 2.136531794 3.371011226 0.291310739 0.508072856 0.98688909 5.186876323 0.136546733 2.36184562 54978.62927 -4.740193908 1.234479431 (ac)MDRNPS(ph)PPPPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 79.492 0.0001748 2571440000 389444.6 331212 225455.5 232384.4 294439.7 338200.2 278994.6 316487.3 272766.2 TRUE FALSE 337978.5094 329036.2466 334486.5339 285150.8298 288580.926 351210.9805 251937.7466 248808.9538 240520.0906 1.405198662 1.368019802 1.390680226 1.185559298 1.199820461 1.460214736 1.047470696 1.034462249 1 17.87579788 -0.081378664 0.290914568 1.89E-09 1.430085528 0.624166667 0.103363492 17.3372654 0.767211093 10.03168061 0.26699205 0.829127531 0.081378664 1.430085526 (ac)MDSAGQDINLNS(ph)PNKGLLSDSMTDVPVDTGVAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MDSAGQDINLNSPNKGLLSDSMTDVPVDTGVAAR 34 1 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;A0A087WZ51;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 1 MDSAGQDINLNS(0.878)PNKGLLS(0.072)DS(0.043)MT(0.007)DVPVDTGVAAR;MDS(0.042)AGQDINLNS(0.946)PNKGLLS(0.005)DS(0.006)MT(0.001)DVPVDTGVAAR;MDS(0.064)AGQDINLNS(0.929)PNKGLLS(0.001)DS(0.004)MT(0.001)DVPVDTGVAAR 76.004 1.29E-27 338436000 180765 174196 99003.8 112768 175578 157733 184821 225806 97085 TRUE FALSE 156876.4472 173051.695 146882.3688 138373.698 172084.3413 163801.0906 166897.0879 177519.1441 85607.7219 1.832503468 2.021449598 1.715760746 1.616369352 2.010149756 1.913391537 1.949556467 2.073634716 1 16.38545331 1.231637946 24.99995287 0.999998462 1.897198597 0.798457074 0.140751944 112.6434345 406754.0946 0.353956793 0.036518037 17.0466069 -1.231637946 0.897200135 (ac)MEDLDQS(ph)PLVSSSDS(ph)PPRPQPAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MEDLDQSPLVSSSDSPPRPQPAFK 24 1 Q9NQC3-5;Q9NQC3;Q9NQC3-4;Q9NQC3-2 Q9NQC3-5;Q9NQC3-2 RTN4 Reticulon-4 2 MEDLDQS(0.999)PLVS(0.001)S(0.003)S(0.021)DS(0.975)PPRPQPAFK 102.6 2.53E-08 31035000 49039 47900 33762 50434 54954 48942 45891 85278 65200 TRUE FALSE 42558.3719 47585.34175 50089.41613 61885.81054 53860.52292 50824.83041 41440.49788 67041.96333 57492.13028 0.740246912 0.827684442 0.871239522 1.07642229 0.936832966 0.884031087 0.720802964 1.166106787 1 15.81107687 4.197734521 2.301368012 0.965364912 0.762370411 0.287147249 0.117916917 0.416667067 4.315148939 0.033519022 0.108923922 15766.47189 -4.197734521 -0.202994501 (ac)MEDLDQSPLVSSSDS(ph)PPRPQPAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 MEDLDQSPLVSSSDSPPRPQPAFK 24 1 Q9NQC3-5;Q9NQC3;Q9NQC3-4;Q9NQC3-2 Q9NQC3-5;Q9NQC3-2 RTN4 Reticulon-4 1 MEDLDQSPLVS(0.002)S(0.01)S(0.038)DS(0.95)PPRPQPAFK;MEDLDQSPLVSSSDS(1)PPRPQPAFK;MEDLDQSPLVSSSDS(1)PPRPQPAFK;MEDLDQSPLVSS(0.001)S(0.006)DS(0.993)PPRPQPAFK;MEDLDQSPLVSS(0.003)S(0.024)DS(0.973)PPRPQPAFK;MEDLDQSPLVS(0.003)S(0.006)S(0.032)DS(0.959)PPRPQPAFK;MEDLDQSPLVSSS(0.001)DS(0.999)PPRPQPAFK;MEDLDQSPLVSSSDS(1)PPRPQPAFK;MEDLDQSPLVSSSDS(1)PPRPQPAFK;MEDLDQSPLVSS(0.002)S(0.003)DS(0.994)PPRPQPAFK;MEDLDQSPLVSS(0.003)S(0.01)DS(0.987)PPRPQPAFK;MEDLDQSPLVSSS(0.002)DS(0.998)PPRPQPAFK 150.48 1.53E-51 5207140000 4338715 3075242 2328977 3416623 3764511 3665882 2852202 4998270 4625110 TRUE FALSE 3765342.82 3055040.533 3455278.067 4192419.472 3689604.596 3806910.853 2575595.889 3929428.857 4078334.765 0.923254965 0.749090182 0.847227672 1.027973355 0.904684095 0.933447368 0.631531259 0.963488552 1 21.95954877 4.510275016 0.012476605 1.724904289 5.69E-07 0.021489906 0.11803407 34086.51544 137.0872121 9071.305527 9893.085806 32379.86368 -4.510275016 -1.724903721 (ac)MEDMNEYSNIEEFAEGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MEDMNEYSNIEEFAEGSK 18 0 O14979-2;O14979-3;A0A087WU03 O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 107.65 1.76E-18 24963000 57471 50028 32997 42472 41629 39571 50499 59608 52209 FALSE TRUE 49876.06174 49699.36277 48954.45957 52115.91674 40800.66435 41093.32198 45601.61475 46861.29307 46036.9115 1.083392871 1.079554669 1.063374105 1.132046331 0.886259808 0.892616829 0.990544615 1.01790697 1 15.49050343 3.248123288 24.9999383 0.964259288 1.087002342 0.673065291 0.045605476 145.2737258 379790.9134 0.014967084 0.019068527 1770.611529 -3.248123288 0.122743054 (ac)MEDS(ph)MDMDMSPLRPQNYLFGCELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 MEDSMDMDMSPLRPQNYLFGCELK 24 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 MEDS(0.898)MDMDMS(0.102)PLRPQNYLFGCELK;MEDS(0.466)MDMDMS(0.533)PLRPQNY(0.001)LFGCELK;MEDS(0.499)MDMDMS(0.499)PLRPQNY(0.003)LFGCELK;MEDS(0.872)MDMDMS(0.127)PLRPQNY(0.001)LFGCELK;MEDS(0.588)MDMDMS(0.412)PLRPQNYLFGCELK;MEDS(0.781)MDMDMS(0.219)PLRPQNYLFGCELK;MEDS(0.856)MDMDMS(0.144)PLRPQNYLFGCELK;MEDS(0.834)MDMDMS(0.166)PLRPQNYLFGCELK;MEDS(0.829)MDMDMS(0.17)PLRPQNY(0.001)LFGCELK 81.12 1.90E-08 541607000 479755 403295 272424.9 311096.2 334020 316447.5 385906 471658 401409 TRUE FALSE 416354.1612 400645.7286 404170.4928 381735.347 327373.6555 328621.4401 348480.8955 370797.6071 353954.8853 1.176291608 1.131911849 1.141870079 1.078485883 0.92490221 0.928427474 0.984534781 1.047584375 1 18.43320596 3.465984359 4.042836248 0.984193756 1.145041495 0.820361891 0.037107657 0.104161357 3.917647692 0.01272384 0.017699206 2924.047064 -3.465984359 0.160847739 (ac)MEDSMDMDMS(ph)PLRPQNYLFGCELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 26 MEDSMDMDMSPLRPQNYLFGCELK 24 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 MEDS(0.173)MDMDMS(0.821)PLRPQNY(0.007)LFGCELK;MEDS(0.014)MDMDMS(0.986)PLRPQNYLFGCELK;MEDS(0.036)MDMDMS(0.964)PLRPQNYLFGCELK;MEDSMDMDMS(0.995)PLRPQNY(0.005)LFGCELK;MEDSMDMDMS(0.982)PLRPQNY(0.017)LFGCELK;MEDS(0.015)MDMDMS(0.98)PLRPQNY(0.005)LFGCELK;MEDS(0.034)MDMDMS(0.964)PLRPQNY(0.002)LFGCELK;MEDS(0.005)MDMDMS(0.995)PLRPQNYLFGCELK;MEDS(0.026)MDMDMS(0.971)PLRPQNY(0.003)LFGCELK;MEDS(0.49)MDMDMS(0.509)PLRPQNYLFGCELK;MEDS(0.272)MDMDMS(0.722)PLRPQNY(0.006)LFGCELK;MEDS(0.335)MDMDMS(0.64)PLRPQNY(0.025)LFGCELK;MEDS(0.121)MDMDMS(0.879)PLRPQNYLFGCELK;MEDS(0.012)MDMDMS(0.988)PLRPQNYLFGCELK;MEDS(0.173)MDMDMS(0.826)PLRPQNY(0.001)LFGCELK;MEDS(0.167)MDMDMS(0.715)PLRPQNY(0.118)LFGCELK;MEDS(0.15)MDMDMS(0.708)PLRPQNY(0.142)LFGCELK;MEDS(0.002)MDMDMS(0.998)PLRPQNYLFGCELK;MEDS(0.066)MDMDMS(0.933)PLRPQNY(0.001)LFGCELK;MEDS(0.003)MDMDMS(0.996)PLRPQNY(0.001)LFGCELK;MEDS(0.005)MDMDMS(0.861)PLRPQNY(0.133)LFGCELK;MEDS(0.005)MDMDMS(0.99)PLRPQNY(0.005)LFGCELK;MEDSMDMDMS(1)PLRPQNYLFGCELK;MEDS(0.008)MDMDMS(0.992)PLRPQNY(0.001)LFGCELK;MEDSMDMDMS(1)PLRPQNYLFGCELK;MEDSMDMDMS(1)PLRPQNYLFGCELK 127.8 5.40E-38 3650800000 3953334 3024780 2113276 2439493 2625643 2442799 3116311 3751135 3438083 TRUE FALSE 3430890.895 3004910.021 3135263.342 2993417.171 2573397.841 2536775.058 2814091.639 2948983.972 3031636.744 1.131695907 0.991184061 1.034181733 0.987393089 0.848847688 0.836767486 0.928241698 0.972736584 1 21.53166547 4.54445977 0.9422978 0.926248704 1.175841683 0.538521976 0.058215954 1.422206113 1.253307734 0.022385332 0.34166129 35031.58361 -4.54445977 0.249592979 (ac)MEFDLGAALEPTSQKPGVGAGHGGDPKLS(ph)PHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 MEFDLGAALEPTSQKPGVGAGHGGDPKLSPHK 32 2 Q9GZP8-2;Q9GZP8 Q9GZP8-2 IMUP Immortalization up-regulated protein 1 MEFDLGAALEPTSQKPGVGAGHGGDPKLS(1)PHK;MEFDLGAALEPT(0.056)S(0.048)QKPGVGAGHGGDPKLS(0.896)PHK;MEFDLGAALEPT(0.008)S(0.032)QKPGVGAGHGGDPKLS(0.96)PHK;MEFDLGAALEPTSQKPGVGAGHGGDPKLS(1)PHK;MEFDLGAALEPTSQKPGVGAGHGGDPKLS(1)PHK 159.1 1.22E-89 6013190000 4116064 3258596 2748204 2878455 2993025 2068296 4488992 5281840 3115544 TRUE FALSE 3572115.714 3237190.068 4077244.647 3532052.202 2933469.658 2147864.685 4053650.247 4152359.619 2747227.938 1.300261862 1.178347826 1.484130454 1.285678612 1.067792599 0.781829806 1.475542015 1.511472551 1 21.38954519 3.463168667 24.56064992 1.210782102 1.319698148 0.076920571 0.22528584 742.0005106 1306132.76 0.071919688 0.092892218 2905.150712 -3.463168667 0.108916045 (ac)MEGLDDGPDFLSEEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MEGLDDGPDFLSEEDR 16 0 G3V5X9;Q9UNH7;G3V2U1;H0YJF8;G3V4Z5 G3V5X9 SNX6 "Sorting nexin-6;Sorting nexin-6, N-terminally processed" 0 ; 117.79 4.01E-19 60481000 73121 64156 32757 43946 70783 50799 62200 76101 62315 FALSE TRUE 63457.87458 63734.55501 48598.39477 53924.61097 69374.55678 52753.2704 56167.85357 59827.39337 54948.19169 1.154867388 1.159902684 0.884440293 0.981371894 1.262544856 0.960054713 1.022196579 1.088796401 1 15.74578438 3.07597953 0.011535343 1.80E-07 2.118271121 0.046004073 0.109338032 7628.010651 120.2211855 11013.18685 11057.60166 1191.185861 -3.07597953 2.118270941 (ac)MEGPLT(ph)PPPLQGGGAAAVPEPGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MEGPLTPPPLQGGGAAAVPEPGAR 24 0 P20839-3;P20839-7;P20839-5;P20839-6;C9K0R9;C9J029;F8WDE9 P20839-3 IMPDH1 Inosine-5-monophosphate dehydrogenase 1 1 MEGPLT(1)PPPLQGGGAAAVPEPGAR 74.428 3.39E-07 91451000 7724.6 7589.8 5889.4 4425.2 6438.8 4741.7 6001.7 6463.1 2266.4 TRUE FALSE 6703.774538 7539.942104 8737.533539 5430.009295 6310.680477 4924.116267 5419.656058 5081.016361 1998.468774 3.354455484 3.772859603 4.372114117 2.717084883 3.157757859 2.463944562 2.711904298 2.542454717 1 10.96467932 1.323659211 0.382180917 1.43E-12 3.880931289 0.703814859 0.486732176 4.31837243 0.620367388 8.00084457 0.791517955 21.06974169 -1.323659211 3.880931289 (ac)MELDLSPPHLSSSPEDLCPAPGT(ph)PPGTPRPPDTPLPEEVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MELDLSPPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR 41 2 Q14451;Q14451-4;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 MELDLSPPHLSSSPEDLCPAPGT(0.969)PPGT(0.031)PRPPDTPLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.867)PPGT(0.131)PRPPDT(0.002)PLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.993)PPGT(0.007)PRPPDTPLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.997)PPGT(0.003)PRPPDTPLPEEVKR 191.5 5.13E-97 1346430000 791690 490332 120098 280337 576620 480259 508609 627510 464383 TRUE FALSE 687066.1606 487110.9768 178177.7945 343991.8005 565146.3901 498734.8745 459284.1775 493321.8698 409484.1708 1.677882101 1.189572178 0.435127429 0.84006129 1.380142214 1.217958862 1.121616439 1.20473978 1 18.64344816 3.244823128 24.9777124 1.184280241 1.003759234 0.047193696 0.319184394 471.2795136 1879662.892 0.097164062 0.122287161 1757.207824 -3.244823128 -0.180521008 (ac)MENGYTYEDYKNTAEWLLSHTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MENGYTYEDYKNTAEWLLSHTK 22 1 P00491;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 ;; 181.29 1.03E-29 969009000 782481 630887 476153 532084 582646 521727 873258 944970 443918 FALSE TRUE 679074.1533 626742.6618 706422.1834 652901.8046 571052.4845 541798.1753 788569.5736 742895.5193 391438.5198 1.734816884 1.601126691 1.804682339 1.667954919 1.458856131 1.384120744 2.014542601 1.897860026 1 18.57842621 1.228626329 24.98735703 0.99999857 1.702413304 0.5737015 0.188328863 336.113279 845353.5274 0.661548273 0.050457771 16.92880605 -1.228626329 0.702414734 (ac)MENQVLTPHVYWAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MENQVLTPHVYWAQR 15 0 H3BS72;Q9P035;Q9P035-2 H3BS72 HACD3 Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3 0 ; 104.82 4.86E-24 288350000 13730.9 12191.1 7752.7 9374.4 16767.1 5330.8 7979.1 9089.6 12936.8 FALSE TRUE 11916.32678 12111.01586 11501.93165 11503.0008 16433.46751 5535.879325 7205.28811 7145.859775 11407.42624 1.044611337 1.061678209 1.008284551 1.008378275 1.4405938 0.485287321 0.631631356 0.626421738 1 13.47768571 2.725231341 24.99596862 0.671470165 1.098276655 0.586826931 0.17757417 545.1225565 1022249.294 0.059632177 0.052883319 531.1673125 -2.725231341 0.42680649 (ac)MEQLS(ph)DEEIDHGAEEDS(ph)DKEDQDLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MEQLSDEEIDHGAEEDSDKEDQDLDK 26 1 C9K0J5;Q70E73;C9J164;Q70E73-5;Q70E73-2;Q70E73-8;Q70E73-7;Q70E73-4;Q70E73-3;Q70E73-9;Q70E73-6;C9J0R8;C9JLG4 C9K0J5 RAPH1 Ras-associated and pleckstrin homology domains-containing protein 1 2 MEQLS(1)DEEIDHGAEEDS(1)DKEDQDLDK 82.336 5.32E-05 90499000 139790 90446 125910 112950 89564 70429 132900 155690 199150 TRUE FALSE 121316.3973 89851.85427 186800.4971 138597.0238 87781.85163 73138.4492 120011.3785 122396.9051 175606.7139 0.690841453 0.511665256 1.063743481 0.789246725 0.499877537 0.416490051 0.683409967 0.696994451 1 17.42198848 1.215795495 3.402495415 1.062472943 0.664727897 0.25400776 0.178925456 0.55754271 8.81363216 0.603261164 0.048225639 16.43597587 -1.215795495 -0.397745046 (ac)MESYHKPDQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 MESYHKPDQQK 11 1 P29401;P29401-2;E9PFF2;F8W888;F8WAX4 P29401 TKT Transketolase 0 ;;;;;;;;; 118.28 3.43E-11 11430220000 11577180 11068230 4400300 7603840 10100180 7834330 11894510 12882660 12013710 FALSE TRUE 10047226.33 10995522.07 6528299.798 9330408.089 9899206.179 8135721.745 10740982.25 10127803.41 10593462.89 0.948436449 1.037953517 0.616257391 0.880770357 0.934463667 0.767994548 1.013925509 0.956042752 1 23.33667093 2.216491049 24.9997484 0.983914569 0.864866916 0.214647982 0.113120726 392.4782425 444584.3357 0.046084017 0.031097622 164.6232035 -2.216491049 -0.119047653 (ac)METMAS(ph)PGKDNYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 METMASPGKDNYR 13 1 O60684;S4R3E5 O60684 KPNA6 Importin subunit alpha-7 1 MET(0.003)MAS(0.997)PGKDNYR;METMAS(1)PGKDNYR;METMAS(1)PGKDNYR;METMAS(1)PGKDNYR 123.26 3.21E-17 524350000 1049680 868050 666479 736516 948250 865626 1026400 1137090 1015220 TRUE FALSE 910962.1284 862347.7224 988790.4736 903753.2147 929381.6802 898927.1924 926859.886 893932.1523 895201.8481 1.017605281 0.963299757 1.104544719 1.009552445 1.038181146 1.004161457 1.035364134 0.998581665 1 19.77185349 1.665740778 6.821842662 0.999127493 1.024482186 0.082009527 0.035196846 0.321554631 29.21877399 0.020347837 0.008646475 46.31703797 -1.665740778 0.025354693 (ac)MEVAEPSS(ph)PTEEEEEEEEHSAEPRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MEVAEPSSPTEEEEEEEEHSAEPRPR 26 1 M0R3H9;M0QXG9;M0R3F4;M0R2A4;M0R2K3;M0R193;M0R0I0;J3KQS6;Q9NWV8-3;Q9NWV8 M0R3H9 BABAM1 BRISC and BRCA1-A complex member 1 1 MEVAEPS(0.15)S(0.701)PT(0.15)EEEEEEEEHSAEPRPR;MEVAEPS(0.019)S(0.564)PT(0.417)EEEEEEEEHSAEPRPR;MEVAEPS(0.041)S(0.766)PT(0.193)EEEEEEEEHSAEPRPR;MEVAEPS(0.032)S(0.829)PT(0.14)EEEEEEEEHSAEPRPR 117.88 4.83E-17 8873900000 0 0 0 0 0 16947 0 0 0 TRUE FALSE 0 0 0 0 0 17598.96206 0 0 0 0 (ac)MEVKPPPGRPQPDS(ph)GR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MEVKPPPGRPQPDSGR 16 2 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 1 MEVKPPPGRPQPDS(1)GR;MEVKPPPGRPQPDS(1)GR 76.301 7.87E-05 646250000 293360 291530 167754 227010 245940 228158 275260 340170 305900 TRUE FALSE 254591.7327 289614.9202 248880.3955 278556.0901 241046.2752 236935.3859 248565.3276 267427.2927 269736.8505 0.943852248 1.073694305 0.922678511 1.032695717 0.893634944 0.878394574 0.921510454 0.991437737 1 18.04119311 3.243277352 24.99877266 0.939709387 0.993938218 0.199886824 0.055751512 212.7483037 1127563.052 0.016611039 0.020735959 1750.964543 -3.243277352 0.054228831 (ac)MEVKPPPGRPQPDSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 MEVKPPPGRPQPDSGR 16 2 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;;;;; 93.106 8.30E-06 6021070000 2529220 2142530 1545831 1849804 1979180 1843198 2267870 2673650 2851140 FALSE TRUE 2194977.169 2128455.579 2293400.042 2269830.271 1939798.19 1914107.02 2047932.316 2101910.754 2514081.477 0.873073203 0.846613604 0.912221844 0.902846742 0.771573319 0.76135441 0.814584704 0.836055145 1 21.26159998 4.744746467 19.77317174 0.849867518 0.873073382 3.52E-05 0.070431544 309.4545184 988550.2977 0.017648429 0.141585801 55557.98256 -4.744746467 0.023205865 (ac)MEVKPPPGRPQPDSGRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 MEVKPPPGRPQPDSGRR 17 3 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;;;; 58.09 0.00067348 2491760000 1417963 1198666 705315 782722 1085074 1042482 1196799 1454236 660758 FALSE TRUE 1230575.597 1190791.884 1046407.693 960450.9933 1063483.15 1082586.957 1080733.617 1143258.948 582643.942 2.112054221 2.043772875 1.795964255 1.648435561 1.825271102 1.858059235 1.854878322 1.962191428 1 19.15225499 1.235358954 24.99940573 0.999998787 1.88121843 0.821504117 0.129992417 39.93476545 311767.2719 0.23735971 0.034107129 17.19328864 -1.235358954 0.881219643 (ac)MEVS(ph)PLQPVNENMQVNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MEVSPLQPVNENMQVNK 17 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 MEVS(1)PLQPVNENMQVNK 123.84 6.12E-10 79317000 164200 151010 96292 129650 148640 106490 141880 199440 132360 TRUE FALSE 142500.554 150018.0054 142859.1333 159089.0141 145682.3548 110586.7392 128120.4994 156791.308 116712.5516 1.22095312 1.285363085 1.224025448 1.363084021 1.248214976 0.94751368 1.097743968 1.34339714 1 16.8326002 2.97436596 24.90006579 1.13148898 1.275060308 0.35511943 0.110838483 982.9051787 954762.4241 0.037484313 0.037634483 942.6836191 -2.97436596 0.143571328 (ac)MFPTGFSSPS(ph)PSAAAAAQEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MFPTGFSSPSPSAAAAAQEVR 21 0 A0A669KAX4;Q13620-1;A0A669KAU9 A0A669KAX4 CUL4B Cullin-4B 1 MFPT(0.007)GFS(0.03)S(0.141)PS(0.701)PS(0.122)AAAAAQEVR 50.155 0.03808 0 6198.3 6159.1 4033 6348.2 8479.1 7155.8 7663.5 7822 6503.4 TRUE FALSE 5379.178951 6118.640467 5983.37229 7789.655836 8310.382499 7431.088256 6920.29495 6149.326171 5734.575461 0.938025663 1.066973573 1.043385396 1.358366611 1.449171356 1.295839301 1.206766743 1.072324571 1 12.48547097 3.883174127 6.856719674 1.224034166 1.015314639 0.371503737 0.131709282 0.321545789 16.90738813 0.040159483 0.070298178 7641.420988 -3.883174127 -0.208719528 (ac)MHGHGGYDS(ph)DFS(ph)DDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MHGHGGYDSDFSDDER 16 0 Q70Z53;Q70Z53-2;Q70Z53-4;Q70Z53-5;Q70Z53-3 Q70Z53 FRA10AC1 Protein FRA10AC1 2 MHGHGGY(0.091)DS(0.91)DFS(1)DDER;MHGHGGY(0.016)DS(0.984)DFS(1)DDER;MHGHGGY(0.025)DS(0.975)DFS(1)DDER;MHGHGGY(0.031)DS(0.971)DFS(0.999)DDER 94.973 1.07E-27 1202820000 172925 162293 117956 155934 200085 159955 138088.8 209030 191835 TRUE FALSE 150072.5231 161226.8866 174999.9161 191341.198 196103.7 166108.5724 124696.9694 164330.5612 169156.4848 0.887181613 0.953122706 1.03454453 1.131149055 1.159303471 0.981981699 0.737169311 0.971470655 1 17.36799896 1.214210425 19.49825477 1.00000113 0.980963483 0.002210507 0.118475823 2032.661449 1626254.866 1.138368513 0.031708018 16.37609785 -1.214210425 -0.019037648 (ac)MKRTRDEVDAT(ph)LQIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MKRTRDEVDATLQIAK 16 3 Q9BVC3 Q9BVC3 DSCC1 Sister chromatid cohesion protein DCC1 1 MKRT(0.122)RDEVDAT(0.878)LQIAK 40.589 0.073519 0 143220 106940 67956 84732 94350 74609 124760 149160 90912 TRUE FALSE 124293.1141 106237.5041 100819.7489 103971.6956 92472.61959 77479.25651 112660.7944 117263.2948 80164.48693 1.550476014 1.325243985 1.257661001 1.296979493 1.153535975 0.966503491 1.405370367 1.462783575 1 16.29067564 4.908750019 1.520708713 1.240407953 1.778029955 0.304654066 0.156411331 2.557487731 4.025099836 0.04606397 2.320445707 81049.44007 -4.908750019 0.537622002 (ac)MLQQDS(ph)NDDTEDVSLFDAEEETTNRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MLQQDSNDDTEDVSLFDAEEETTNRPR 27 1 A0A0A6YYB9;J3KS67;C9JYS5;Q96ET8-2;Q96ET8-3;Q9NYZ1;Q96ET8;E5RIS5;I3L376;E5RGC5 A0A0A6YYB9 TVP23C-CDRT4;TVP23B;TVP23C Golgi apparatus membrane protein TVP23 homolog;Golgi apparatus membrane protein TVP23 homolog C;Golgi apparatus membrane protein TVP23 homolog B 1 MLQQDS(0.499)NDDT(0.499)EDVS(0.002)LFDAEEETTNRPR 93.043 0.00018846 26994000 2687.8 2926.8 1798.6 1723.9 3702.5 4890.7 4065 2951.1 4065.8 TRUE FALSE 2332.60042 2907.573658 2668.408976 2115.337843 3628.827494 5078.848394 3670.776926 2320.03023 3585.145756 0.650629174 0.811005704 0.744295813 0.590028408 1.01218409 1.416636516 1.02388499 0.647122987 1 11.80781606 3.225499885 24.9369118 0.99348792 0.710227062 0.405587305 0.191385602 289.9233503 553550.5818 0.066166169 0.075480273 1680.73748 -3.225499885 -0.283260858 (ac)MNGQLNGFHEAFIEEGTFLFTSESVGEGHPDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MNGQLNGFHEAFIEEGTFLFTSESVGEGHPDK 32 0 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 91.109 4.66E-15 40142000 13960 9750.1 7037.6 9431.7 8881.1 7054.2 9941.8 13813 14794 FALSE TRUE 12115.15063 9686.050951 10441.0069 11573.31164 8704.383486 7325.579639 8977.645766 10859.19744 13045.07017 0.928714868 0.742506619 0.800379512 0.887178948 0.667254631 0.561559236 0.688202183 0.832436875 1 13.67121708 1.335290643 3.054419218 1.01805552 0.750073482 0.353029362 0.10540835 0.370308142 4.807362759 0.213128921 0.029078516 21.64166366 -1.335290643 -0.267982038 (ac)MNLLPNIES(ph)PVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MNLLPNIESPVTR 13 0 P17980;E9PM69 P17980 PSMC3 26S protease regulatory subunit 6A 1 MNLLPNIES(0.834)PVT(0.166)R 42.209 0.039565 43100000 22011 14442 16815 16134 14383 13130 17104 23316 19719 TRUE FALSE 19102.19058 14347.12955 24946.79024 19797.47129 14096.80644 13635.1196 15445.25671 18330.05485 17387.84228 1.098594654 0.825124206 1.434726048 1.138581255 0.810727761 0.784175482 0.88827909 1.054188009 1 14.08579129 3.255610158 24.9652792 0.91820876 1.125066414 0.29999517 0.164090385 339.1252094 496570.8313 0.049336146 0.06352914 1801.399997 -3.255610158 0.206857654 (ac)MNTAPS(ph)RPSPTRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MNTAPSRPSPTRR 13 2 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 MNT(0.004)APS(0.403)RPS(0.297)PT(0.297)RR 40.857 0.030139 1886500000 29352 32048 20589 20467 23195 21565 27740 29740 26384 TRUE FALSE 25473.05883 31837.47458 30545.90927 25114.34517 22733.46488 22394.6195 25049.77907 23380.33244 23264.91358 1.094913108 1.368475944 1.312960358 1.079494454 0.977156644 0.962591992 1.076719197 1.00496107 1 14.50586821 3.598139099 4.047701238 1.008954672 1.268522592 0.704429347 0.075019135 0.118611812 3.307139874 0.020436796 0.030998758 3964.049773 -3.598139099 0.259567919 (ac)MNTAPSRPS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 MNTAPSRPSPTR 12 1 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 MNT(0.001)APS(0.235)RPS(0.719)PT(0.046)R;MNTAPS(0.058)RPS(0.785)PT(0.157)R;MNTAPS(0.1)RPS(0.758)PT(0.142)R;MNTAPS(0.028)RPS(0.916)PT(0.056)R;MNTAPS(0.026)RPS(0.826)PT(0.148)R;MNTAPS(0.025)RPS(0.878)PT(0.097)R;MNTAPS(0.062)RPS(0.8)PT(0.137)R;MNTAPS(0.059)RPS(0.741)PT(0.2)R;MNTAPS(0.042)RPS(0.842)PT(0.116)R 68.463 8.73E-05 15121804000 602990 445275 359612.3 388865.8 458452 492971 510606 679393 661266.1 TRUE FALSE 523303.3437 442349.9592 533522.0111 477163.7233 449329.7021 511935.9134 461087.5087 534110.094 583091.975 0.897462778 0.758628104 0.914987745 0.818333546 0.77059833 0.877967688 0.790762913 0.915996304 1 19.15336394 1.468615122 3.073606859 0.997831301 0.83195211 0.527244638 0.052404957 0.18865523 3.199355291 0.061194546 0.012612834 29.41813399 -1.468615122 -0.165879192 (ac)MNTAPSRPS(ph)PTRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MNTAPSRPSPTRR 13 2 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 MNTAPS(0.013)RPS(0.494)PT(0.494)RR 59.261 0.0025964 399330000 8835.5 14367 4306.2 0 12005 9893.6 10548 7777.4 7152.4 TRUE FALSE 7667.866289 14272.62223 6388.692723 0 11766.12399 10274.21319 9525.056584 6114.263534 6306.85142 1.215799418 2.263034481 1.012976571 0 1.865609827 1.629055849 1.510271283 0.969463703 1 12.62270423 4.211199365 24.9999331 1.148066445 1.739417868 0.165042002 0.559353965 349.0467675 318923.6974 0.145393389 0.302775303 16262.95143 -4.211199365 0.591351423 (ac)MNTAPSRPSPT(ph)RR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MNTAPSRPSPTRR 13 2 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 MNTAPS(0.022)RPS(0.395)PT(0.583)RR 69.331 0.00034866 2159100000 27624 12628 10160 11333 17079 10315 19040 23205 17157 TRUE FALSE 23973.41841 12545.04584 15073.40998 13906.33086 16739.16131 10711.82472 17193.50373 18242.79133 15128.71901 1.584629763 0.829220625 0.996344104 0.919200817 1.10644935 0.708045719 1.136481134 1.205838467 1 13.88500221 4.749465375 24.90347292 1.004815579 1.584630112 0.617910792 0.14697175 1138.241605 2599378.803 0.037322426 0.542265633 56164.94979 -4.749465375 0.579814533 (ac)MNVDHEVNLLVEEIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 16 MNVDHEVNLLVEEIHR 16 0 Q9P1F3;Q5SZC9 Q9P1F3 ABRACL Costars family protein ABRACL 0 ;;;;;;;;;;;;;;; 120.7 6.70E-27 5704528000 273251.1 205430.3 169979.4 178219.8 239044.7 189163.1 268019 271281.2 219752.9 FALSE TRUE 237140.2748 204080.8148 252182.0064 218687.3295 234288.1782 196440.3269 242026.5586 213269.8265 193773.9625 1.223798449 1.053190079 1.301423592 1.128569219 1.209079771 1.013760179 1.24901486 1.100611371 1 17.5640152 1.377635513 3.574262865 0.998887186 1.163829296 0.277944053 0.087048614 0.313548915 5.97166046 0.110474038 0.020358869 23.85808122 -1.377635513 0.16494211 (ac)MS(ph)PTPPLFSLPEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MSPTPPLFSLPEAR 14 0 A0A087WWS1;Q96FV9;Q96FV9-2;J3KRD7;J3QQZ3;J3KT14 A0A087WWS1 THOC1 THO complex subunit 1 1 MS(0.853)PT(0.147)PPLFSLPEAR 68.069 0.00048134 13621000 7529.1 6286 4946 6335.7 5970.8 9057.7 5302 10056 6740.8 TRUE FALSE 6534.110359 6244.706852 7337.902143 7774.31752 5851.992762 9406.15558 4787.812856 7905.602656 5943.910303 1.099294913 1.050605836 1.234524374 1.307946642 0.984535846 1.582486125 0.80549884 1.330033976 1 12.53719663 4.247356719 24.5450391 1.183692116 1.074950337 0.037554719 0.215018658 526.1980081 1468284.705 0.048173197 0.123201712 17674.88996 -4.247356719 -0.10874178 (ac)MVDYSVWDHIEVS(ph)DDEDETHPNIDTASLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 MVDYSVWDHIEVSDDEDETHPNIDTASLFR 30 0 Q16543;K7EKQ2;K7EQA9;K7EJ06 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 1 MVDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;MVDY(0.006)S(0.015)VWDHIEVS(0.979)DDEDETHPNIDTASLFR;MVDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;MVDYSVWDHIEVS(0.999)DDEDET(0.001)HPNIDTASLFR;MVDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;MVDY(0.001)S(0.001)VWDHIEVS(0.993)DDEDET(0.004)HPNIDTASLFR;MVDY(0.016)S(0.017)VWDHIEVS(0.966)DDEDETHPNIDTASLFR;MVDY(0.006)S(0.006)VWDHIEVS(0.982)DDEDET(0.005)HPNIDTASLFR;MVDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;MVDY(0.004)S(0.034)VWDHIEVS(0.779)DDEDET(0.165)HPNIDT(0.009)AS(0.009)LFR 186.88 3.76E-93 602837000 96797.1 98742.2 67790.9 63430.7 105979.3 97669.3 115227.8 110628.2 86771.7 TRUE FALSE 84005.11798 98093.55599 100574.806 77833.60991 103870.5193 101426.7012 104053.0257 86971.22034 76513.64848 1.097910238 1.282039975 1.31446883 1.01725132 1.357542365 1.325602728 1.359927644 1.136675901 1 16.2234295 1.448353309 3.79148893 1.011229731 1.252462857 0.34846812 0.111880074 0.245664773 6.253791775 0.122849603 0.028541966 28.07716857 -1.448353309 0.241233126 (ac)S(ph)AADEVDGLGVARPHYGSVLDNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SAADEVDGLGVARPHYGSVLDNER 24 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 1 S(1)AADEVDGLGVARPHYGSVLDNER;S(1)AADEVDGLGVARPHYGSVLDNER;S(1)AADEVDGLGVARPHYGSVLDNER 125.62 7.80E-38 1100340000 19937 18689.7 14181.9 21862 16141 22752.6 23471.4 28626 17431.2 TRUE FALSE 17302.27494 18566.92613 21040.31428 26826.10124 15819.82568 23627.90724 21195.14724 22504.55267 15370.50339 1.125680434 1.207958234 1.36887607 1.745297506 1.029232763 1.537224035 1.378949453 1.464138948 1 13.90787679 4.327097904 3.833924503 1.379239347 1.145831892 0.119360712 0.219391072 0.412791543 11.29525921 0.052530625 0.156484301 21237.23162 -4.327097904 -0.233407454 (ac)S(ph)DAAVDTSSEITTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SDAAVDTSSEITTK 14 0 B8ZZQ6;P06454-2;P06454 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 1 S(0.99)DAAVDT(0.009)S(0.001)SEITTK;S(0.947)DAAVDT(0.014)S(0.017)S(0.021)EITTK;S(0.857)DAAVDT(0.132)S(0.01)S(0.001)EITTK;S(0.995)DAAVDT(0.002)S(0.002)S(0.001)EITTK;S(0.889)DAAVDT(0.018)S(0.064)S(0.024)EIT(0.002)T(0.002)K 81.09 6.61E-56 1693930000 4048660 3332112 2313256 2729054 3203869 2616727 3438323 4041400 3548053 TRUE FALSE 3513619.323 3310223.137 3431954.339 3348727.422 3140118.275 2717394.181 3104874.965 3177178.06 3128606.216 1.123062182 1.058050425 1.096959509 1.070357594 1.003679613 0.868563825 0.992414753 1.015525074 1 21.57708865 3.213343968 3.684777001 0.974852165 1.087696416 0.633420949 0.04264358 0.160787841 4.632799648 0.013891429 0.016839563 1634.345862 -3.213343968 0.112844251 (ac)S(ph)DCYTELEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDCYTELEK 9 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 1 S(0.996)DCY(0.003)TELEK;S(0.776)DCY(0.188)T(0.036)ELEK 73.665 5.11E-05 173876000 411340 436990 314690 418430 438980 468240 398300 567230 494980 TRUE FALSE 356980.3768 434119.3839 466875.1366 513440.9268 430245.1568 486253.4958 359672.9273 445932.2787 436464.0283 0.817891862 0.994628093 1.069676093 1.176364817 0.985751698 1.114074618 0.824060871 1.021693083 1 18.73550323 4.723477664 3.881610087 1.023373538 0.801017609 0.336116129 0.091617501 0.282704198 8.581296158 0.022869659 0.174388971 52902.67887 -4.723477664 -0.222355929 (ac)S(ph)DKPDMAEIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SDKPDMAEIEK 11 1 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 1 S(1)DKPDMAEIEK;S(1)DKPDMAEIEK;S(1)DKPDMAEIEK 93.111 0.00011895 690830000 2201820 1382540 1307310 1498670 1315430 1023430 1859680 2057720 3238180 TRUE FALSE 1910843.908 1373458.004 1939529.489 1838965.929 1289255.517 1062802.014 1679328.52 1617692.591 2855366.049 0.669211539 0.481009433 0.67925774 0.644038592 0.451520223 0.372212177 0.58813073 0.566544731 1 21.44524428 1.234789439 5.389432119 1.024472643 0.551912839 0.667148335 0.098448254 0.101089498 8.678417851 0.178071347 0.025197901 17.1707569 -1.234789439 -0.472559804 (ac)S(ph)DLEDDETPQLSAHALAALQEFYAEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SDLEDDETPQLSAHALAALQEFYAEQK 27 0 Q8WVE0 Q8WVE0 N6AMT2 Protein-lysine N-methyltransferase N6AMT2 1 S(0.783)DLEDDET(0.205)PQLS(0.012)AHALAALQEFYAEQK;S(0.952)DLEDDET(0.045)PQLS(0.003)AHALAALQEFYAEQK;S(0.802)DLEDDET(0.188)PQLS(0.009)AHALAALQEFYAEQK 88.571 5.05E-35 62715000 69840 66794 28801.9 41364 62353 56653 70042 87364 52432 TRUE FALSE 60610.46705 66355.22582 42730.59518 50756.32841 61112.29729 58832.47757 63249.33762 68681.88847 46233.54869 1.3109629 1.435218098 0.924233514 1.097824628 1.321817144 1.272506205 1.368039863 1.485542218 1 15.49665248 3.207481526 24.06620536 1.319107015 1.190297794 0.055004716 0.17888261 316.2715453 244904.4909 0.055656851 0.063116759 1612.432438 -3.207481526 -0.128809221 (ac)S(ph)DNDDIEVES(ph)DADKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDNDDIEVESDADKR 15 1 Q6V3B1;G3V563;G3V2R5;P61244-2;A0A494C130 Q6V3B1 MAX Protein max 2 S(1)DNDDIEVES(1)DADKR 62.658 0.00069004 276050000 445090 393760 294460 262060 390810 415850 457340 451920 432240 TRUE FALSE 386270.2288 391173.3646 436861.8409 321564.7283 383033.6456 431848.0186 412987.2372 355280.4248 381141.0796 1.013457351 1.02632171 1.146194583 0.843689504 1.004965526 1.133039816 1.083554776 0.93214939 1 18.53996559 1.725098743 13.86388745 0.966635328 1.034914075 0.104795971 0.084774949 0.251378811 196.714398 0.046237116 0.02198105 53.10051623 -1.725098743 0.068278748 (ac)S(ph)DNDDIEVESDADKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDNDDIEVESDADKR 15 1 Q6V3B1;G3V563;G3V2R5;P61244-2;A0A494C130 Q6V3B1 MAX Protein max 1 S(1)DNDDIEVESDADKR;S(1)DNDDIEVESDADKR 84.605 2.56E-33 3121600000 2296900 1774210 1483350 1502250 1662640 1372000 2022210 2268200 2013450 TRUE FALSE 1993358.845 1762555.098 2200703.022 1843358.823 1629556.717 1424781.728 1826096.385 1783163.081 1775422.235 1.122751989 0.992752633 1.239537829 1.038265032 0.917841787 0.802503033 1.028542028 1.004360003 1 20.75973074 3.468595763 7.800060584 0.957507567 1.111333269 0.447517929 0.085169277 0.132696926 56.43579668 0.025028154 0.033387287 2941.682268 -3.468595763 0.153825701 (ac)S(ph)DNGELEDKPPAPPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SDNGELEDKPPAPPVR 16 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 S(1)DNGELEDKPPAPPVR;S(1)DNGELEDKPPAPPVR;S(1)DNGELEDKPPAPPVR 93.258 1.84E-08 1946870000 1565770 1250840 958800 1075100 1335940 1115080 1413410 1690080 1487970 TRUE FALSE 1358849.527 1242623.15 1422478.887 1319217.887 1309357.408 1157977.849 1276337.716 1328669.544 1312063.882 1.035658055 0.94707519 1.084153681 1.005452482 0.997937239 0.882562096 0.972771016 1.012656139 1 20.32340653 2.992467035 24.23430434 0.970848004 1.015727321 0.202851002 0.047485608 446.7462177 1437236.345 0.015076611 0.016388758 982.8042713 -2.992467035 0.044879317 (ac)S(ph)DQEAKPSTEDLGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDQEAKPSTEDLGDK 15 1 B8ZZN6;P63165;B8ZZJ0;B9A032 B8ZZN6 SUMO1 Small ubiquitin-related modifier 1 1 S(0.924)DQEAKPS(0.033)T(0.043)EDLGDK;S(1)DQEAKPSTEDLGDK 95.508 0.00016926 519850000 1040730 694000 851760 825680 670060 496790 1002840 1117480 1826000 TRUE FALSE 903194.8936 689441.0683 1263673.985 1013163.264 656727.117 515901.8328 905584.7312 878515.5982 1610132.36 0.560944501 0.428189064 0.784826152 0.629242222 0.40787151 0.32040958 0.56242875 0.545617006 1 20.61874786 1.233959805 5.129052391 1.030009586 0.527622 0.573788984 0.127384866 0.136748792 9.589529048 0.245894248 0.033414605 17.13798685 -1.233959805 -0.502387586 (ac)S(ph)DQEAKPSTEDLGDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SDQEAKPSTEDLGDKK 16 2 B8ZZN6;P63165;B8ZZJ0;B9A032 B8ZZN6 SUMO1 Small ubiquitin-related modifier 1 1 S(1)DQEAKPSTEDLGDKK;S(0.999)DQEAKPS(0.001)T(0.001)EDLGDKK;S(1)DQEAKPSTEDLGDKK;S(1)DQEAKPSTEDLGDKK;S(1)DQEAKPSTEDLGDKK;S(1)DQEAKPSTEDLGDKK 115.56 3.05E-15 22013010000 12644040 7070050 9293210 7242610 5787950 3523510 11402420 12652500 10860260 TRUE FALSE 10973098.08 7023606.376 13787437.44 8887155.297 5672781.119 3659061.71 10296615.06 9946861.337 9576372.435 1.145851224 0.733430787 1.439734882 0.928029414 0.59237265 0.38209267 1.075210382 1.038687813 1 23.19104783 4.778787233 20.94509982 0.910013813 1.145856672 0.066849311 0.287450795 8297.841689 4319755.934 0.07356388 14.27043367 60087.92865 -4.778787233 0.235842859 (ac)S(ph)DQEAKPSTEDLGDKKEGEYIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDQEAKPSTEDLGDKKEGEYIK 22 3 B8ZZN6;P63165;B8ZZJ0;B9A032 B8ZZN6 SUMO1 Small ubiquitin-related modifier 1 1 S(0.443)DQEAKPS(0.243)T(0.314)EDLGDKKEGEYIK 74.698 1.65E-06 641140000 852200 482010 238840 167320 287490 180040 842420 760990 20462 TRUE FALSE 739579.6108 478843.6446 354343.8229 205312.5633 281769.5115 186966.2553 760722.2381 598258.2105 18043.00567 40.98982311 26.53901757 19.63884673 11.37906661 15.61655062 10.36225664 42.16161387 33.15734759 1 14.13915207 7.999999996 0.070521531 10 52.77637666 0.063774622 13.08871894 3605.248988 24.38690383 3277.006097 16366.90518 99999999.03 -7.999999996 42.77637666 (ac)S(ph)DSEKLNLDSIIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDSEKLNLDSIIGR 14 1 P62136;P62136-2;P62136-3;E9PMD7 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit;Serine/threonine-protein phosphatase 1 S(0.983)DS(0.017)EKLNLDSIIGR 64.439 0.012903 29479000 121060 108150 86071 86446 104810 88914 123760 133960 95166 TRUE FALSE 105061.6143 107439.5555 127695.2235 106074.8855 102724.4861 92334.57912 111757.7742 105313.6965 83915.58389 1.251991697 1.280328999 1.521710481 1.264066585 1.224140753 1.100326958 1.331788079 1.254995694 1 16.35665114 3.487528319 15.04110587 1.202605995 1.352350008 0.310058735 0.113209942 3.624369025 5235.327688 0.0319283 0.044177401 3072.757726 -3.487528319 0.149744013 (ac)S(ph)DVEENNFEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDVEENNFEGR 11 0 Q13595;F8WEH2 Q13595 TRA2A Transformer-2 protein homolog alpha 1 S(1)DVEENNFEGR 63.397 1.66E-05 200270000 32724 33948 22592 17637 27942 33686 31897 37022 35747 TRUE FALSE 28399.44049 33724.99335 33517.56677 21641.75041 27386.00887 34981.92222 28803.63385 29105.13341 31521.03038 0.900968025 1.069920397 1.06333982 0.686581313 0.868817058 1.109796279 0.913790999 0.923356028 1 14.94402708 (ac)S(ph)DVEENNFEGRES(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDVEENNFEGRESR 14 1 Q13595 Q13595 TRA2A Transformer-2 protein homolog alpha 2 S(1)DVEENNFEGRES(1)R;S(1)DVEENNFEGRES(1)R 49.708 0.00026641 9286300000 25815 30483 14878 36539 54646 46948 34556 31783 29288 TRUE FALSE 22403.48234 30282.75517 22073.05056 44835.73841 53558.65151 48754.11994 31204.76444 24986.45279 25825.606 0.867491061 1.172586431 0.854696326 1.736096276 2.073858461 1.887820945 1.208287791 0.96750693 1 14.65651458 3.750634794 24.85527906 1.450566239 0.985690774 0.299367883 0.368529838 1185.822894 2441066.624 0.116077342 0.199067624 5631.638817 -3.750634794 -0.464875465 (ac)S(ph)EGESQTVLSSGSDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEGESQTVLSSGSDPK 16 0 F8W6G1;Q9UHY1;C9JHZ6;C9JDW7 F8W6G1 NRBP1 Nuclear receptor-binding protein 1 S(0.807)EGES(0.192)QT(0.001)VLSSGSDPK 88.734 5.05E-87 172660000 462810 438820 268880 328400 417180 321990 431070 546330 429140 TRUE FALSE 401648.4859 435937.3625 398911.2673 402968.2393 408878.9342 334377.1637 389264.8977 429501.581 378407.5581 1.061417716 1.15203133 1.054184196 1.064905366 1.080525284 0.883642931 1.028692185 1.135023791 1 18.52958138 3.702211178 1.604711257 1.033820234 1.102801639 0.162567957 0.067906286 0.853216889 4.282841228 0.023028496 0.048705744 5037.454984 -3.702211178 0.068981405 (ac)S(ph)ESGHSQPGLYGIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SESGHSQPGLYGIER 15 0 Q9H0W8-2;Q9H0W8;M0R2N0;M0QZC7;M0QZH1;M0QX70;M0QYR7 Q9H0W8-2 SMG9 Protein SMG9 1 S(0.498)ES(0.498)GHS(0.004)QPGLYGIER 65.395 0.001743 0 48870 52905 36326 32231 52425 37824 52837 54529 44212 TRUE FALSE 42411.70568 52557.46357 53893.3751 39549.54117 51381.84507 39279.11376 47712.87587 42868.3977 38985.30773 1.087889468 1.348135147 1.382402198 1.014472977 1.317979723 1.007536327 1.223868135 1.099603933 1 15.2506429 -1.183796467 0.295975211 8.57E-13 1.264111222 0.219448369 0.129233218 72.5014711 1.825336546 43.03156787 0.264566617 0.065494304 1.183796467 1.264111222 (ac)S(ph)GDEMIFDPTMSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 30 SGDEMIFDPTMSK 13 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(0.997)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;S(0.999)GDEMIFDPTMSK;S(0.999)GDEMIFDPT(0.001)MSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(0.999)GDEMIFDPT(0.001)MSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK 82.261 3.18E-33 13706654000 22305420 21495180 15309580 18570960 20535880 18463770 22456810 25990010 25042820 TRUE FALSE 19357702.23 21353976.75 22713344.1 22787780.31 20127256.17 19174083.18 20278952.02 20432248.62 22082286.35 0.876616756 0.967018379 1.028577555 1.031948411 0.911466134 0.868301537 0.918335706 0.925277768 1 24.39638622 3.205382269 24.99971606 0.921457121 0.979148578 0.18752347 0.05271478 299.54086 225701.6374 0.01660568 0.018830298 1604.6572 -3.205382269 0.057691458 (ac)S(ph)GDEMIFDPTMSKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SGDEMIFDPTMSKK 14 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(0.999)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK 100.72 2.85E-06 2878890000 5109350 4385050 1876060 1970120 3551250 2871280 5212760 5804380 473917 TRUE FALSE 4434136.452 4356244.318 2783328.891 2417465.857 3480587.073 2981740 4707227.338 4563158.507 417891.0721 10.61074703 10.42435364 6.660417215 5.784918651 8.328933794 7.135208666 11.2642448 10.91949269 1 18.67276741 4.257401942 22.91592385 7.811565048 10.51755956 0.161431097 2.870396215 197.1818965 239812.3175 0.727640658 1.915123662 18088.4745 -4.257401942 2.705994508 (ac)S(ph)GEDEQQEQTIAEDLVVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 SGEDEQQEQTIAEDLVVTK 19 0 Q9UQ80;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 1 S(0.977)GEDEQQEQT(0.023)IAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(0.996)GEDEQQEQT(0.004)IAEDLVVTK;S(0.999)GEDEQQEQT(0.001)IAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(0.84)GEDEQQEQT(0.16)IAEDLVVTK;S(0.907)GEDEQQEQT(0.093)IAEDLVVTK 181.67 7.14E-240 5502860400 3127417 2733129 1845006.3 2190302.9 2505262 2273062.9 2716738.1 3340397.9 3084291 TRUE FALSE 2714120.92 2715174.896 2737257.518 2687644.65 2455412.188 2360509.101 2453269.257 2626079.804 2719669.632 0.997959785 0.998347323 1.00646692 0.98822468 0.902834726 0.867939647 0.902046789 0.965587796 1 21.37499998 3.338758614 5.93452072 0.927689333 0.999911473 0.486445407 0.035901028 0.204957837 10.2792751 0.011707898 0.015130627 2181.517059 -3.338758614 0.07222214 (ac)S(ph)KGPAVGIDLGTTYSCVGVFQHGK ddPTM_MDA-MB-175_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(1)KGPAVGIDLGTTYSCVGVFQHGK 83.602 1.29E-17 57124000 82033 59995 49590 54293 55334 42508 74165 85692 77149 TRUE FALSE 71192.1312 59600.88889 73571.88987 66621.05547 54232.96166 44143.31027 66972.48972 67367.43266 68028.53311 1.046503988 0.876116038 1.081485761 0.979310481 0.797209041 0.648894049 0.984476464 0.990282012 1 16.05385236 3.447674574 24.48051082 0.89274621 0.995769168 0.184283763 0.116552564 340.2627092 282876.1913 0.036665203 0.047335318 2803.332258 -3.447674574 0.103022959 (ac)S(ph)KSESPKEPEQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKSESPKEPEQLR 13 2 F8W6I7;P09651-2;P09651;P09651-3;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 S(0.458)KS(0.458)ES(0.084)PKEPEQLR 59.116 3.77E-05 263760000 299090 239330 38263 44515 201810 119920 319780 281040 23559 TRUE FALSE 259564.4987 237757.8255 56767.11478 54622.81112 197794.3758 124533.4 288767.7848 220941.7831 20773.88186 12.49475185 11.44503599 2.732619506 2.629398371 9.521300698 5.994710129 13.90052118 10.63555596 1 14.34248321 4.448007343 24.77700266 7.300166554 12.23232691 0.224795662 3.996758186 274.0571649 233232.3703 1.05474636 2.790687596 28054.81074 -4.448007343 4.932160358 (ac)S(ph)LDIQSLDIQCEELSDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLDIQSLDIQCEELSDAR 18 0 P13489;E9PMJ3;E9PLZ3;E9PIM9;E9PMN0;E9PIK5;E9PMA9;E9PR82;E9PMI1 P13489 RNH1 Ribonuclease inhibitor 1 S(0.989)LDIQS(0.011)LDIQCEELSDAR 61.212 7.51E-08 17119000 8930.1 8848.8 5114.7 5080.5 9430.1 8385.4 6666.9 8062.9 6553.8 TRUE FALSE 7749.964659 8790.67165 7588.186028 6234.105176 9242.45946 8707.991764 6020.345064 6338.711581 5779.01723 1.341052354 1.521136086 1.313058211 1.078748328 1.599313359 1.506829175 1.041759321 1.0968494 1 12.49660846 2.227643907 24.95243488 1.056569001 1.390575841 0.565552897 0.143322511 161.8325568 369898.9621 0.05995442 0.040867359 168.905545 -2.227643907 0.33400684 (ac)S(ph)LPLNPKPFLNGLTGKPVMVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLPLNPKPFLNGLTGKPVMVK 21 2 P62306;A0A0B4J254;F8W0W6 P62306 SNRPF Small nuclear ribonucleoprotein F 1 S(1)LPLNPKPFLNGLTGKPVMVK;S(1)LPLNPKPFLNGLTGKPVMVK 66.325 0.021496 302000000 951210 620480 419550 544330 587010 406040 736050 802650 637250 TRUE FALSE 825505.1884 616404.026 622445.7833 667928.4461 575329.6495 421660.6215 664667.9843 631009.5437 561915.031 1.469092555 1.096970168 1.107722252 1.188664494 1.023873037 0.750399257 1.182862084 1.122962564 1 19.09999247 7.504811304 1.07017751 1.050175051 199.9935146 0.522310822 0.123930025 704.7990199 2.241717204 0.038690171 342352.8442 31975055.29 -7.504811304 198.9433395 (ac)S(ph)MEDPFFVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SMEDPFFVVK 10 0 O43752 O43752 STX6 Syntaxin-6 1 S(1)MEDPFFVVK 41.029 0.0060836 7970700 43736 29187 15937 23939 21919 18381 30894 44420 25768 TRUE FALSE 37956.17679 28995.26868 23644.18651 29374.71583 21482.85478 19088.12896 27897.90464 34921.12868 22721.7364 1.670478705 1.276102679 1.040597694 1.292802422 0.945475927 0.840082317 1.227806896 1.536904049 1 14.47178547 4.696881992 3.173805863 1.157300883 1.72302747 0.421504887 0.1979581 0.351486426 5.713155155 0.055108569 0.465335734 49760.18565 -4.696881992 0.565726587 (ac)S(ph)SSPVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSPVKR 7 1 P37837;F2Z393;E9PM01;E9PKI8 P37837 TALDO1 Transaldolase 1 S(0.333)S(0.333)S(0.333)PVKR;S(0.333)S(0.333)S(0.333)PVKR 45.45 0.065402 3416900000 4709000 4493100 2793100 3656000 3221300 3566100 4705000 5467900 4722600 TRUE FALSE 4086693.719 4463584.53 4143852.502 4486150.678 3157202.432 3703290.175 4248709.824 4298632.136 4164299.608 0.981364 1.07186921 0.995089905 1.077288164 0.75815929 0.889294845 1.020269967 1.032258132 1 21.98964244 (ac)S(ph)TGGDFGNPLRK ddPTM_MDA-MB-175_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(0.5)T(0.5)GGDFGNPLRK 46.891 0.077304 143840000 303840 257320 174790 200620 273000 226680 283870 363180 238360 TRUE FALSE 263686.7742 255629.648 259319.0286 246173.8373 267567.8341 235400.5263 256340.3311 285516.7833 210181.3523 1.254567883 1.21623372 1.23378704 1.171244901 1.273033174 1.119987685 1.219615005 1.358430613 1 17.68127515 6.066863946 1.042020544 1.210697151 1.818943958 0.021142065 0.094544784 147.5281107 13.85362746 0.028162739 181.8752672 1166444.14 -6.066863946 0.608246807 (ac)S(ph)YGRPPPDVEGMTSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SYGRPPPDVEGMTSLK 16 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 S(0.557)Y(0.443)GRPPPDVEGMTSLK;S(0.56)Y(0.44)GRPPPDVEGMTSLK 76.522 0.0020651 178454000 427130 376510 223820 302770 350280 280940 377200 428630 408000 TRUE FALSE 370683.6883 374036.681 332060.1006 371518.556 343310.1133 291747.9436 340619.2021 336970.8101 359766.7048 1.030344619 1.039664527 0.922987303 1.0326652 0.954257603 0.810936476 0.946778002 0.936637008 1 18.45670215 3.010787217 16.50537071 0.922778838 1.001662352 0.323922223 0.056428528 4.676523365 7150.498855 0.017193844 0.01939896 1025.14953 -3.010787217 0.078883514 GPGQPS(ph)SPQRLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPGQPSSPQRLDR 13 1 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 GPGQPS(0.664)S(0.336)PQRLDR 60.489 0.055367 110230000 152010 133950 86706 77419 135360 131140 110500 130970 67832 TRUE FALSE 131921.4934 133070.0736 128637.3116 94998.16723 132666.6008 136185.0407 99783.72701 102963.0847 59812.97823 2.205566371 2.224769232 2.150658861 1.58825342 2.218023659 2.276847679 1.668262139 1.72141712 1 15.86817093 0.995808385 1.015973144 2.31E-18 2.093219198 0.702525172 0.222468593 1.696767225 1.015506906 4.389653871 0.075390101 9.90394877 -0.995808385 2.093219198 (ac)SAARESHPHGVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAARESHPHGVKR 13 2 E9PM92;O00193;E9PQA1;E9PRZ9 E9PM92 C11orf58;SMAP Small acidic protein 0 61.038 0.0095993 23176000 12893 10301 7907.9 10168 7029.2 10965 7921.7 14255 8397.5 FALSE TRUE 11189.15738 10233.33205 11732.18689 12476.79981 6889.332672 11386.83065 7153.454753 11206.67918 7404.757116 1.511076894 1.38199429 1.584412116 1.684970839 0.930392795 1.537772336 0.966062038 1.513443183 1 12.8542367 3.257165957 24.99886401 1.230674122 1.532412037 0.377792886 0.220284129 280.6912308 377145.4226 0.058570176 0.075476133 1807.864834 -3.257165957 0.301737915 (ac)SAHLQWMVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SAHLQWMVVR 10 0 P46779;H0YKD8;P46779-2;P46779-3;H0YLP6;H0YMF4;P46779-4;P46779-5 P46779 RPL28 60S ribosomal protein L28 0 ;;; 62.2 0.0013595 590350000 443258 390025 268327 354250 414257 451156 440629 463131 407520 FALSE TRUE 384680.3322 387462.9001 398090.8347 434687.8769 406014.0962 468512.2633 397896.8674 364094.0397 359343.4498 1.070508819 1.078252297 1.107828276 1.209672465 1.129877548 1.303800761 1.107288494 1.013220193 1 18.45500386 1.796286765 3.841238845 1.005420339 1.150187267 0.422178682 0.067909793 0.207736292 5.633925579 0.044090214 0.019102375 62.55856307 -1.796286765 0.144766928 (ac)SAIQNLHSFDPFADASKGDDLLPAGTEDYIHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAIQNLHSFDPFADASKGDDLLPAGTEDYIHIR 33 1 K7EM18;P41567 K7EM18 EIF1 Eukaryotic translation initiation factor 1 0 ; 77.439 2.28E-72 846490000 450780 418230 213069 233560 348310 317580 441060 542540 118728 FALSE TRUE 391208.2809 415482.6196 316109.8811 286593.3677 341379.3125 329797.5081 398286.0691 426522.0431 104692.1111 3.736750332 3.968614399 3.019424079 2.737487713 3.26079309 3.150165802 3.804356077 4.074060964 1 16.67579321 4.23924697 24.99740117 3.149249838 3.85268253 0.136764424 0.825256932 39.44753837 1436427.289 0.207107148 0.485846642 17347.90241 -4.23924697 0.703432692 (ac)SCINLPTVLPGS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SCINLPTVLPGSPSK 15 0 P04183;K7ERV3;K7ES52;K7ERJ1;K7ENW5 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 1 SCINLPTVLPGS(0.793)PS(0.207)K;SCINLPT(0.003)VLPGS(0.839)PS(0.158)K 74.772 8.55E-09 387270000 743180 701410 432180 614290 689010 565060 744630 960370 744390 TRUE FALSE 644966.88 696802.3915 641183.6936 753773.9333 675300.049 586798.2238 672415.8972 755002.3491 656389.0622 0.982598457 1.061569169 0.976834823 1.148364555 1.028810637 0.893979284 1.02441667 1.15023603 1 19.32419167 1.960624896 23.54916272 1.086292395 1.017101923 0.09485694 0.073673896 513.8407392 307312.0194 0.033720379 0.019473615 91.33240552 -1.960624896 -0.069190473 (ac)SDEFSLADALPEHS(ph)PAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SDEFSLADALPEHSPAK 17 0 Q8NDC0 Q8NDC0 MAPK1IP1L MAPK-interacting and spindle-stabilizing protein-like 1 SDEFS(0.001)LADALPEHS(0.999)PAK;SDEFSLADALPEHS(1)PAK;SDEFSLADALPEHS(1)PAK;SDEFSLADALPEHS(1)PAK;SDEFSLADALPEHS(1)PAK;S(0.013)DEFS(0.013)LADALPEHS(0.974)PAK 183.74 1.15E-104 4467573000 3954096 3813100 2372018 2573743 3614839 3008383 4257674 5214514 3244787 TRUE FALSE 3431552.195 3788051.495 3519133.839 3158150.685 3542910.776 3124117.441 3844765.431 4099430.76 2861191.977 1.199343568 1.323941744 1.229953763 1.10378846 1.238263914 1.091893681 1.34376353 1.432770256 1 21.44818487 2.209558573 24.99892936 1.298617394 1.202613672 0.016980306 0.128228321 483.0721497 416390.7166 0.051817191 0.034942024 162.016249 -2.209558573 -0.096003722 (ac)SDKPDMAEIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDKPDMAEIEK 11 1 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 89.08 0.0001651 282480000 649630 394230 401200 448040 347170 253220 509790 617210 977510 FALSE TRUE 563779.7495 391640.2772 595221.6619 549774.3299 340261.9962 262961.5373 460350.6443 485224.4446 861949.8814 0.654074862 0.454365486 0.690552519 0.63782633 0.394758447 0.305077526 0.534080524 0.562938119 1 19.71724446 1.223760342 3.706093979 1.07167271 0.520759728 0.608340151 0.119019238 0.217523565 4.604037303 0.341386573 0.031900266 16.74018844 -1.223760342 -0.550912982 (ac)SDKPDMAEIEKFDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 SDKPDMAEIEKFDK 14 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 ;;;;;;;;; 90.707 3.25E-05 35262700000 53713390 28928590 26926060 23711120 22649040 15070320 42631230 47817830 23943110 FALSE TRUE 46615029.42 28738556.19 39947592.68 29095092.2 22198368.42 15650084.96 38496859.88 37592359.17 21112582.81 2.207926422 1.361205137 1.892122486 1.378092508 1.051428364 0.741268139 1.823408354 1.780566571 1 24.33159975 7.533019169 0.947795267 1.378788047 199.996076 0.322695594 0.377289108 650.2218329 3.103056737 0.128718091 277340.7632 34120797.14 -7.533019169 198.617288 (ac)SDQEAKPS(ph)TEDLGDKKEGEYIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDQEAKPSTEDLGDKKEGEYIK 22 3 B8ZZN6;P63165;B8ZZJ0;B9A032 B8ZZN6 SUMO1 Small ubiquitin-related modifier 1 1 S(0.3)DQEAKPS(0.35)T(0.35)EDLGDKKEGEYIK 46.362 0.03286 85555000 144600 82314 40338 31575 50608 29312 131150 117800 10514 TRUE FALSE 125490.7436 81773.27391 59845.59172 38744.58634 49600.99981 30439.65161 118431.0932 92609.38672 9271.046898 13.5357684 8.820284787 6.455106137 4.179095066 5.350096959 3.283302516 12.77429556 9.989096997 1 13.17851654 4.666605332 2.449076385 6.655023135 14.50212224 0.326668539 3.332760447 0.617196532 5.140283674 0.911228151 9.485437023 46409.33359 -4.666605332 7.847099102 (ac)SDS(ph)EKLNLDSIIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDSEKLNLDSIIGR 14 1 P62136;P62136-2;P62136-3;E9PMD7 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit;Serine/threonine-protein phosphatase 1 S(0.455)DS(0.545)EKLNLDSIIGR 40.941 0.0020587 33326000 115170 105670 66825 68972 97084 85325 113190 124090 87846 TRUE FALSE 99949.9927 104975.8468 99141.79352 84633.14677 95152.21834 88607.50796 102212.8512 97554.31917 77460.94595 1.290327551 1.355209977 1.279893917 1.092591186 1.228389573 1.143899121 1.319540447 1.25940005 1 16.2411815 3.985515833 22.29087366 1.19246327 1.321464654 0.325075557 0.090310038 197.8414238 304481.5288 0.023675255 0.043227552 9671.989877 -3.985515833 0.129001384 (ac)SDSGEQNYGERES(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SDSGEQNYGERESR 14 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 1 SDSGEQNYGERES(1)R;SDSGEQNYGERES(1)R;SDSGEQNYGERES(1)R;SDSGEQNYGERES(1)R 100.11 6.40E-12 5234530000 0 6444.6 17167 12430 21266 13272 22830.6 12480 0 TRUE FALSE 0 6402.264998 25469.01862 15252.42148 20842.84821 13782.58243 20616.49193 9811.249119 0 0 (ac)SDVEENNFEGRES(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDVEENNFEGRESR 14 1 Q13595 Q13595 TRA2A Transformer-2 protein homolog alpha 1 SDVEENNFEGRES(1)R;SDVEENNFEGRES(1)R 69.258 0.00028148 374920000 157620 158039 119180 112998 111394 115442 215560 174803 122179 TRUE FALSE 136790.1176 157000.8314 176815.8466 138655.923 109177.4773 119883.1284 194655.0244 137422.7388 107735.1378 1.269688984 1.457285289 1.641208711 1.287007431 1.013387828 1.112757925 1.806792365 1.275560987 1 16.71712934 3.51906827 23.80147178 1.269897329 1.457504369 0.137883085 0.240519067 658.6759014 373741.6792 0.069385501 0.10289957 3304.214787 -3.51906827 0.18760704 (ac)SEGES(ph)QTVLSSGSDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEGESQTVLSSGSDPK 16 0 F8W6G1;Q9UHY1;C9JHZ6;C9JDW7 F8W6G1 NRBP1 Nuclear receptor-binding protein 1 S(0.398)EGES(0.548)QT(0.053)VLSSGSDPK 74.326 8.59E-46 143590000 425220 378000 274950 319240 356950 301470 454720 520800 441010 TRUE FALSE 369026.0996 375516.8931 407916.7397 391728.3213 349847.3934 313067.746 410621.3244 409430.9729 388874.3002 0.948959855 0.965651093 1.04896811 1.007339187 0.899641332 0.805061548 1.055923017 1.052861998 1 18.56894437 (ac)SETAPAAPAAPAPAEKT(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SETAPAAPAAPAPAEKTPVK 20 1 P10412 P10412 HIST1H1E Histone H1.4 1 SETAPAAPAAPAPAEKT(1)PVK;SETAPAAPAAPAPAEKT(1)PVK;SETAPAAPAAPAPAEKT(1)PVK;SETAPAAPAAPAPAEKT(1)PVK;SETAPAAPAAPAPAEKT(1)PVK 130.36 2.18E-29 2285290000 2518390 2766660 2195139 2467670 2822770 2453600 3471490 3993470 3857760 TRUE FALSE 2185578.381 2748485.628 3256715.563 3027992.189 2766602.4 2547991.58 3134825.434 3139497.518 3401700.008 0.642495921 0.807974137 0.957378827 0.890140866 0.813299936 0.749034769 0.921546705 0.922920161 1 21.69782449 4.636898919 3.096673027 0.889406401 0.629005108 0.556927374 0.070900395 0.23943241 3.663253327 0.01904091 0.131050542 43340.99917 -4.636898919 -0.260401293 (ac)SETAPAAPAAPAPAEKT(ph)PVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SETAPAAPAAPAPAEKTPVKK 21 2 P10412 P10412 HIST1H1E Histone H1.4 1 SETAPAAPAAPAPAEKT(1)PVKK;SETAPAAPAAPAPAEKT(1)PVKK 96.793 2.54E-17 916850000 1781970 1883430 1664670 1752190 1769510 1492270 2690500 3105300 2728600 TRUE FALSE 1546478.15 1871057.624 2469709.98 2150051.52 1734300.213 1549678.593 2429575.724 2441255.76 2406028.016 0.642751514 0.77765413 1.026467673 0.893610343 0.720814638 0.644081691 1.009786963 1.014641452 1 21.19822201 2.206413281 24.44534357 1.009565515 0.797031239 0.462324693 0.113267712 152.7745073 116170.8076 0.049834761 0.033602122 160.8471169 -2.206413281 -0.212534276 (ac)SETAPLAPTIPAPAEKT(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SETAPLAPTIPAPAEKTPVK 20 1 P16402 P16402 HIST1H1D Histone H1.3 1 S(0.001)ET(0.001)APLAPT(0.004)IPAPAEKT(0.994)PVK;S(0.002)ET(0.002)APLAPT(0.002)IPAPAEKT(0.995)PVK 46.356 1.32E-05 0 267920 300450 236432 260970 312170 257840 376630 417520 378740 TRUE FALSE 232513.6932 298476.3242 350771.306 320227.2272 305958.4278 267759.2716 340104.4806 328236.5971 333965.7887 0.696220095 0.893733233 1.050321075 0.958862369 0.916137036 0.801756589 1.0183812 0.982844975 1 18.3493408 4.682007003 3.42459869 0.959386438 0.677615925 0.599803065 0.067716463 0.186682353 3.700705188 0.017500279 0.124353239 48084.71017 -4.682007003 -0.281770513 (ac)SGDHLHNDS(ph)QIEADFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGDHLHNDSQIEADFR 16 0 P11387 P11387 TOP1 DNA topoisomerase 1 1 S(0.013)GDHLHNDS(0.987)QIEADFR;S(0.001)GDHLHNDS(0.999)QIEADFR 65.887 1.15E-11 443700000 45200 36751 23118.3 28839 22328.4 30898 37024 36251 33844 TRUE FALSE 39226.70548 36509.58026 34298.38721 35387.33573 21884.10852 32086.66605 33433.41818 28499.00576 29843.00088 1.314435691 1.223388372 1.14929418 1.185783423 0.733307907 1.075182291 1.120310197 0.954964478 1 14.86510499 3.445678714 24.9998516 0.986974657 1.218318583 0.553100748 0.108078497 152.9462632 121606.5455 0.030926119 0.039925814 2790.478712 -3.445678714 0.231343926 (ac)SHTILLVQPTKRPEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SHTILLVQPTKRPEGR 16 2 P84090;G3V279 P84090 ERH Enhancer of rudimentary homolog 0 ;; 83.966 5.36E-10 1587211000 187544 122320 52775 88324 128902 128074 145277 180219 80233.3 FALSE TRUE 162759.5852 121516.4719 78297.16652 108379.3141 126337.1024 133001.0897 131188.0589 141680.5693 70748.21068 2.30054702 1.717590745 1.106701721 1.531901841 1.785728589 1.879921603 1.854295079 2.002602864 1 16.11040604 3.21699951 24.41276321 1.761775825 1.628179709 0 0.394781647 908.734674 1028919.054 0.120901787 0.137222436 1648.160531 -3.21699951 -0.133596116 (ac)SILKIHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SILKIHAR 8 1 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 63.486 0.0035652 455940000 769530 740750 524040 727230 689560 608410 736360 988250 641410 FALSE TRUE 667834.6608 735883.9645 777467.4968 892358.6865 675839.1051 631815.9264 664947.9205 776920.4281 565583.2405 1.180789339 1.301106383 1.374629659 1.577767201 1.194941888 1.117105107 1.175685333 1.373662394 1 19.10937984 3.089479056 23.83334626 1.194829823 1.359461494 0.318509821 0.133152001 19.72638136 5247.05492 0.041351132 0.046887775 1228.793927 -3.089479056 0.164631671 (ac)SKPHSEAGTAFIQTQQLHAAMADTFLEHMCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SKPHSEAGTAFIQTQQLHAAMADTFLEHMCR 31 1 P14618;B4DNK4;H3BUW1;H3BTJ2;H3BT25;H3BN34;H3BQZ3;P14618-2;H3BTN5;H3BR70;H3BQ34;H3BU13 P14618;P14618-2;H3BU13 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;; 136.89 1.29E-175 23961310000 3945080 3231386 2414352 2447868 2728515 3047352 3575417 3702176 3058144 FALSE TRUE 3423727.682 3210158.813 3581940.703 3003693.843 2674222.89 3164585.603 3228673.61 2910494.473 2696613.7 1.269639653 1.190440741 1.328310652 1.113876208 0.991696693 1.173540579 1.197306685 1.079314576 1 21.36271743 3.643942404 6.769245062 1.0959286 1.255011058 0.554182936 0.071910692 0.200783116 12.21995991 0.020222756 0.030129493 4404.964411 -3.643942404 0.159082459 (ac)SKS(ph)ES(ph)PKEPEQLRK ddPTM_MDA-MB-175_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(0.485)KS(0.627)ES(0.888)PKEPEQLRK 48.623 0.012071 206360000 471610 354640 331190 256380 376940 221130 518270 580280 328040 TRUE FALSE 409285.5436 352310.3465 491354.5918 314594.9975 369439.6315 229637.0142 468008.2552 456191.6377 289259.4849 1.414942517 1.217973359 1.698663717 1.087587491 1.277191072 0.793878943 1.617953013 1.577101743 1 18.14200474 3.713043359 24.98987079 1.27091214 1.421271402 0.108771931 0.272255512 2417.787816 2367816.558 0.078698957 0.11678456 5164.679294 -3.713043359 0.150359261 (ac)SLHQFLLEPITCHAWNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLHQFLLEPITCHAWNR 17 0 A0A1W2PNV4;E9PF58;F8WFD3;Q92747 A0A1W2PNV4;Q92747 ARPC1A Actin-related protein 2/3 complex subunit 1A 0 ; 136.48 2.78E-20 1613480000 48536 68095 46687 43124 62273 67140 47626 59037 46442 FALSE TRUE 42121.84463 67647.67946 69264.98936 52915.96331 61033.88914 69722.91925 43007.23785 46412.39698 40951.67967 1.028574285 1.651890228 1.691383355 1.292156115 1.490387931 1.702565556 1.050194722 1.133345381 1 15.32163501 2.221060873 24.98836623 1.07575658 1.48621318 0.479061676 0.203625484 202.1717187 288684.3698 0.080205765 0.054213933 166.3645818 -2.221060873 0.4104566 (ac)SLICSISNEVPEHPCVSPVSNHVYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLICSISNEVPEHPCVSPVSNHVYER 26 0 Q9UMS4;F5GY56 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 106.12 4.17E-18 466690000 6575.4 11079 8810.3 7882.6 11082 14170 6119.6 12424 10367 FALSE TRUE 5706.44423 11006.22132 13070.99055 9672.464808 10861.48988 14715.12907 5526.122134 9767.224284 9141.42507 0.624240114 1.203994042 1.429863555 1.05809157 1.188161561 1.609719377 0.604514295 1.068457512 1 13.15820337 2.224448964 24.999719 0.916026546 1.19192379 0.197113023 0.278653768 405.5027636 718369.1592 0.110692602 0.075035739 167.6675291 -2.224448964 0.275897244 (ac)SQGDSNPAAIPHAAEDIQGDDRWMSQHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQGDSNPAAIPHAAEDIQGDDRWMSQHNR 29 1 P68402;P68402-3;P68402-2;P68402-4 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 ; 68.934 0.0027906 606860000 6943.1 0 0 0 8946.9 5048.9 0 0 5318.7 FALSE TRUE 6025.551743 0 0 0 8768.874194 5243.13445 0 0 4689.929345 1.284785185 0 0 0 1.869724158 1.117955957 0 0 1 12.19535047 (ac)SQPGQKPAAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 65.495 0.0061827 1481550000 776590 737900 640960 690730 721310 675610 764480 880580 1801300 TRUE FALSE 673961.6639 733052.6863 950930.3999 847570.8036 706957.3422 701601.1539 690340.8473 692274.8197 1588352.366 0.424314956 0.461517672 0.598689825 0.533616357 0.445088481 0.441716315 0.434627015 0.435844611 1 20.59909957 1.236158579 24.99788509 1.000000689 0.472268156 0.903164154 0.054341348 20.40717371 212328.9626 0.095345923 0.014574752 17.22497415 -1.236158579 -0.527732533 (ac)SQPGQKPAAS(ph)PRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 SQPGQKPAASPRPR 14 2 P20810-6;P20810-10;P20810-7;P20810-9;P20810-5;F8W7E0;E9PSG1 P20810-6;P20810-5 CAST Calpastatin 1 SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR 114.28 8.95E-07 80958090000 12753040 12898710 9045230 9697770 12174830 11779140 12928310 15549040 11949440 TRUE FALSE 11067693.45 12813977.52 13419533.48 11899796.9 11932574.7 12232291.14 11674524.49 12223998.8 10536790.82 1.05038561 1.216117673 1.273588298 1.129356851 1.132467647 1.160912402 1.107977248 1.160125413 1 23.3289322 0.486085976 1.553939279 2.40E-11 1.160645486 0.379062979 0.060592262 10.64980298 3.863859188 33.86693327 0.017079524 3.062569665 -0.486085976 1.160645486 (ac)SQPGQKPAASPRPR ddPTM_MDA-MB-175_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 62.287 0.016647 67438000 59422 51052 25959 34965 47584 35781 54952 60885 23667 FALSE TRUE 51569.23214 50716.63605 38512.85923 42904.33766 46637.1715 37157.51822 49622.7635 47865.21656 20869.11422 2.471079107 2.430224662 1.845447719 2.055877274 2.234746094 1.780502892 2.377808803 2.293591192 1 14.34908175 1.235265494 24.9782135 0.999998344 2.181929167 0.718828127 0.233127849 51.58773738 390987.1874 0.404889379 0.05774829 17.18958904 -1.235265494 1.181930823 (ac)SQQHTLPVTLS(ph)PALSQELLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SQQHTLPVTLSPALSQELLK 20 0 P07476 P07476 IVL Involucrin 1 SQQHTLPVT(0.016)LS(0.973)PALS(0.011)QELLK;SQQHTLPVT(0.002)LS(0.987)PALS(0.011)QELLK;SQQHTLPVT(0.003)LS(0.927)PALS(0.07)QELLK 99.092 6.18E-17 212932000 134476 131664 59341 93320 111306 106020 140426 167784 133635 TRUE FALSE 116704.6559 130799.0905 88038.50608 114509.7323 109091.2284 110098.658 126807.5081 131904.6973 117836.8225 0.990392081 1.110001846 0.7471222 0.971765275 0.925782162 0.934331524 1.076128034 1.119384369 1 16.84643091 2.23545538 24.66277395 1.076921882 0.945129844 0.263713521 0.092711937 82.52253344 655405.0293 0.036303227 0.025663719 171.9710649 -2.23545538 -0.131792038 (ac)SQQHTLPVTLSPALS(ph)QELLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SQQHTLPVTLSPALSQELLK 20 0 P07476 P07476 IVL Involucrin 1 SQQHTLPVTLS(0.001)PALS(0.999)QELLK;SQQHTLPVTLS(0.001)PALS(0.999)QELLK;SQQHTLPVTLS(0.006)PALS(0.994)QELLK 162.37 1.24E-66 509364000 932950 911850 336940 724270 805290 549190 1186970 1032220 1017240 TRUE FALSE 809658.2937 905859.9973 499885.311 888726.5733 789266.3045 570317.6947 1071857.832 811487.7857 896983.046 0.902646151 1.009896454 0.557296276 0.990795286 0.879912177 0.635817697 1.194958853 0.904685757 1 19.77472119 2.235186353 24.99999981 1.013177255 0.834863298 0.267937469 0.15748956 128.7846519 954150.7101 0.059981591 0.042299239 171.864569 -2.235186353 -0.178313957 (ac)SRLS(ph)WGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRLSWGYR 8 1 Q8N1Q1 Q8N1Q1 CA13 Carbonic anhydrase 13 1 S(0.001)RLS(0.999)WGYR;S(0.06)RLS(0.94)WGYR 93.649 0.00048194 638640000 33347 29193 15500.2 33970 36455 35795 28997 37564 39448 TRUE FALSE 28940.10946 29001.22926 22996.14857 41683.4077 35729.61682 37172.05681 26184.8754 29531.23092 34784.50238 0.831982851 0.83373995 0.661103279 1.19833273 1.027170561 1.068638453 0.752774184 0.848976668 1 15.08615706 3.766275579 24.99982524 0.95979547 0.781421843 0.35511585 0.129018289 1032.686794 931514.792 0.037154177 0.064335731 5838.154432 -3.766275579 -0.178373627 (ac)SS(ph)SPVNVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSPVNVKK 9 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(0.128)S(0.503)S(0.37)PVNVKK 47.938 0.061762 1144200000 2900300 2371700 1392900 1528300 1881600 1624100 2628700 2946400 1022600 TRUE FALSE 2517018.007 2356120.147 2066511.099 1875323.874 1844159.841 1686580.178 2373769.079 2316335.289 901709.3929 2.791384925 2.612948434 2.291770625 2.079743084 2.045182024 1.870425429 2.632521184 2.568826838 1 19.78230302 4.24428191 2.088287734 2.119893373 2.783872012 0.265479119 0.446053988 0.543177257 4.488157192 0.123445055 0.468093702 17550.19353 -4.24428191 0.663978639 (ac)SSAPTT(ph)PPSVDKVDGFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSAPTTPPSVDKVDGFSR 18 1 Q16537-2;Q16537 Q16537-2 PPP2R5E Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform 1 S(0.042)S(0.085)APT(0.146)T(0.712)PPS(0.014)VDKVDGFSR;S(0.028)S(0.124)APT(0.166)T(0.672)PPS(0.009)VDKVDGFSR 72.891 0.0014525 116060000 319040 310870 198765 237847 307630 267400 354400 402550 322800 TRUE FALSE 276878.0557 308827.8745 294888.4188 291853.7966 301508.7649 277687.051 320030.3425 316467.8151 284638.9517 0.972734244 1.08498107 1.03600866 1.025347356 1.059267409 0.975576425 1.124337834 1.111821882 1 18.11877358 2.227282632 24.99997342 1.087516888 1.030334085 0.210147975 0.04690697 300.6976269 666552.1592 0.018290115 0.012454061 168.7650965 -2.227282632 -0.057182803 (ac)SSILPFT(ph)PPVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSILPFTPPVVK 12 0 Q15796-2;Q15796;B7Z5N5;K7EJX0;K7ESI8;K7EL92;K7ERC7 Q15796-2 SMAD2 Mothers against decapentaplegic homolog 2;Mothers against decapentaplegic homolog 1 S(0.009)S(0.009)ILPFT(0.982)PPVVK 44.318 0.016824 64967000 215940 155240 116300 130160 137830 130440 164630 185070 180930 TRUE FALSE 187402.9819 154220.2182 172543.069 159714.8174 135087.4527 135458.1112 148664.2079 145494.2207 159540.6615 1.174640873 0.96665149 1.08149902 1.001091608 0.84672742 0.849050705 0.931826448 0.911956985 1 17.28356464 3.44368786 5.111250613 0.907596064 1.060871214 0.574076726 0.065521382 0.136985438 9.047279 0.01844774 0.024608822 2777.716123 -3.44368786 0.15327515 (ac)SSS(ph)PVKRQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSPVKRQR 9 2 P37837;F2Z393;E9PM01;E9PKI8 P37837 TALDO1 Transaldolase 1 S(0.087)S(0.179)S(0.734)PVKRQR;S(0.228)S(0.268)S(0.504)PVKRQR 52.247 0.016479 711360000 31040 24420.5 30305.2 30294 36094 37204 39551 90542 41020 TRUE FALSE 26937.98535 24260.08013 44960.89608 37172.71571 35375.80002 38635.26195 35715.35011 71180.2979 36170.66233 0.744746809 0.670711526 1.243021089 1.027703485 0.978024668 1.068138084 0.987412113 1.967901424 1 15.1425324 2.57255739 0.228319252 1.926643495 0.439344968 0.27029561 0.301744721 6.493681537 1.465410446 5.313335945 3.538397507 373.7295085 -2.57255739 -1.487298527 (ac)SSS(ph)PVNVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SSSPVNVKK 9 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(0.113)S(0.198)S(0.689)PVNVKK;S(0.198)S(0.198)S(0.603)PVNVKK;S(0.051)S(0.2)S(0.75)PVNVKK;S(0.051)S(0.2)S(0.75)PVNVKK;S(0.319)S(0.319)S(0.361)PVNVKK;S(0.033)S(0.033)S(0.934)PVNVKK 53.683 0.011193 96759700000 68001500 52088200 32967500 36046100 43581800 34087700 62211300 69955200 24701570 TRUE FALSE 59014929.48 51746029.18 48910693.27 44230917.94 42714607.45 35399075.88 56178057.7 54995824.87 21781378.53 2.709421233 2.375700376 2.245527903 2.030675784 1.961060792 1.625199058 2.579178247 2.52490102 1 24.37659193 4.513742303 1.30258253 2.039726441 2.836541157 0.231022807 0.446731348 1.653400745 3.341905936 0.135229604 1.581261721 32639.41022 -4.513742303 0.796814717 (ac)SYGRPPPDVEGMTSLKVDNLTYRTS(ph)PDTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYGRPPPDVEGMTSLKVDNLTYRTSPDTLR 30 3 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 SYGRPPPDVEGMT(0.003)S(0.01)LKVDNLT(0.15)Y(0.004)RT(0.198)S(0.575)PDT(0.059)LR 55.9 1.62E-06 150950000 159080 104690 17303 31103 115160 105810 155540 175020 6282.1 TRUE FALSE 138057.1749 104002.2845 25670.78868 38165.41153 112868.5413 109880.5792 140455.7547 137593.335 5539.437295 24.9225991 18.77488253 4.634187068 6.889763256 20.37545247 19.83605434 25.35559972 24.83886498 1 12.43552372 7.968341912 5.51E-14 9.734769388 24.18318244 0 8.989135556 0 0.205833118 218341012.6 218341016.1 92969803.33 -7.968341912 14.44841305 (ac)T(ph)SPEIASLSWGQMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSPEIASLSWGQMK 14 0 E9PIQ4;E9PJP1;E9PLK9;K4DI89;E9PR47;Q9H7C9-3;Q9H7C9-2;Q9H7C9 E9PIQ4 AAMDC Mth938 domain-containing protein 1 T(0.498)S(0.498)PEIAS(0.003)LSWGQMK 56.404 0.00076916 0 18263 22099 21616 25045 26050 31559 31151 36161 41848 TRUE FALSE 15849.49828 21953.83021 32069.5699 30731.85004 25531.65597 32773.09515 28129.98081 28428.25156 36900.77711 0.429516653 0.594942219 0.869075733 0.832823925 0.691900224 0.888141056 0.762314049 0.770397097 1 15.17136358 4.432773998 3.32091592 0.818601266 0.448320091 0.724047296 0.084420331 0.121048345 2.625437626 0.020858217 0.078362157 27087.81645 -4.432773998 -0.370281175 (ac)T(ph)T(ph)SQKHRDFVAEPMGEKPVGSLAGIGEVLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTSQKHRDFVAEPMGEKPVGSLAGIGEVLGK 31 3 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 2 T(0.664)T(0.664)S(0.664)QKHRDFVAEPMGEKPVGS(0.008)LAGIGEVLGK 42.121 5.16E-05 755830000 615290 487550 387470 459940 464030 327110 781080 748070 781500 TRUE FALSE 533977.8676 484347.2519 574851.788 564376.4067 454796.7109 339694.1334 705330.9818 588101.052 689111.9603 0.774878247 0.702857126 0.83419215 0.818990874 0.659975065 0.492944765 1.02353612 0.853418727 1 19.39437887 2.210935777 24.99996832 0.939681649 0.721251187 0.543809049 0.105152208 186.7813819 169032.3444 0.044157277 0.029778391 162.5308391 -2.210935777 -0.218430462 (ac)TECFLPPT(ph)SSPSEHRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TECFLPPTSSPSEHRR 16 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 TECFLPPT(0.356)S(0.296)S(0.296)PS(0.052)EHRR 68.972 0.0007991 0 16598 13084 10298 10783 18701 17596 14314 19152 14383 TRUE FALSE 14404.53225 12998.05034 15278.14724 13231.44496 18328.88669 18272.92951 12925.83048 15056.49384 12682.65813 1.135766028 1.02486799 1.20464867 1.043270648 1.445192838 1.440780736 1.019173611 1.187171782 1 13.63056953 4.223897017 24.87284389 1.194523194 1.08031701 0.0796624 0.156789986 533.819123 905484.3657 0.04141135 0.08680602 16745.45747 -4.223897017 -0.114206184 (ac)TECFLPPTS(ph)SPSEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TECFLPPTSSPSEHR 15 0 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 TECFLPPT(0.043)S(0.425)S(0.425)PS(0.108)EHR 45.722 0.0076491 597660000 186110 131380 88025 120820 140270 145720 130130 176140 141490 TRUE FALSE 161515.092 130516.9561 130594.1844 148254.0276 137478.9014 151325.9427 117510.0126 138473.8317 124763.2134 1.294573036 1.046117302 1.046736301 1.188283177 1.101918568 1.212905139 0.941864268 1.109893116 1 16.92883309 -1.999999993 0.0308896 1.11E-05 1.876619663 0.221421884 0.092567313 5122.580236 15.6626835 677.2297241 332.9757276 0.01 1.999999993 1.87660858 (ac)TECFLPPTSS(ph)PSEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TECFLPPTSSPSEHR 15 0 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 TECFLPPT(0.005)S(0.18)S(0.687)PS(0.128)EHR;TECFLPPT(0.004)S(0.144)S(0.708)PS(0.144)EHR 93.424 2.74E-05 111460000 38654 34185 38452 31952.9 36987 42216 40981 51601 50498 TRUE FALSE 33545.77596 33960.43648 57047.51581 39208.29431 36251.03106 43840.07684 37006.66893 40566.52771 44528.18397 0.753360523 0.762672839 1.281155231 0.880527585 0.814114294 0.984546706 0.831084173 0.911030365 1 15.44243115 4.420659844 24.99996566 0.945153191 0.755660823 0.284628304 0.130378277 95.53516388 42300.62707 0.031854801 0.084279909 26342.67321 -4.420659844 -0.189492367 (ac)TEKAPEPHVEEDDDDELDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TEKAPEPHVEEDDDDELDSK 20 1 P52566;F5H3P3;F5H2R5;F5H6Q0 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ;;;; 136.49 1.14E-43 2350890000 2423820 2204860 1422970 1277979 1887176 1255570 2694080 3167910 363120 FALSE TRUE 2103506.046 2190376.129 2111123.052 1568163.665 1849624.89 1303872.59 2432808.536 2490477.099 320192.3673 6.569507149 6.840813066 6.593295991 4.897567291 5.776605188 4.072153879 7.59795918 7.778065169 1 18.28857939 3.857775496 7.241890023 5.587285923 6.705248324 0.094846839 1.907076799 0.805301164 44.71182606 0.511589956 0.892878799 7207.348071 -3.857775496 1.117962401 (ac)TTTTTFKGVDPNSRNSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTTTTFKGVDPNSRNSSR 18 2 Q9UK76;J3KT51;Q9UK76-2;F2Z3M5 Q9UK76 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 0 41.422 0.047804 223190000 26413 16471 9310.5 16369 13904 10580 17630 41483 20105 FALSE TRUE 22922.45513 16362.80092 13813.08894 20085.83163 13627.3376 10987.01945 15920.24531 32612.18327 17728.2098 1.292993223 0.922981006 0.779158702 1.132987022 0.768680975 0.619747824 0.89801765 1.83956438 1 14.11375924 1.765842188 25 1.465870421 0.902586413 0.36511923 0.274020259 15.93275595 14611.55997 0.139008684 0.066762183 58.32331326 -1.765842188 -0.563284008 (ac)VDYSVWDHIEVS(ph)DDEDETHPNIDTASLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 VDYSVWDHIEVSDDEDETHPNIDTASLFR 29 0 Q16543;K7EKQ2;K7EQA9;K7EJ06 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 1 VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDY(0.1)S(0.106)VWDHIEVS(0.793)DDEDET(0.001)HPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(0.979)DDEDET(0.02)HPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(0.999)DDEDET(0.001)HPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(0.998)DDEDET(0.002)HPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR 215.15 3.51E-106 3867132000 171546.6 143681.5 93739.9 96726.9 129907.7 139506.5 135350.3 154715.5 122713.4 TRUE FALSE 148876.2822 142737.6468 139072.8292 118690.221 127322.7909 144873.4053 122224.0487 121630.7943 108206.3616 1.375855171 1.319124353 1.285255572 1.096887643 1.176666408 1.338862181 1.129545868 1.124063248 1 16.72342579 5.244455394 0.043616745 9.10E-17 2.719147436 0.577281621 0.07913668 516.9502622 4.968865147 123.2709468 193.1384634 175572.0555 -5.244455394 2.719147436 (ac)VSVINTVDTSHEDMIHDAQMDYYGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 VSVINTVDTSHEDMIHDAQMDYYGTR 26 0 P55735 P55735 SEC13 Protein SEC13 homolog 0 ;;;;;;;;;; 173.47 3.68E-82 3561569000 87512 101254.8 54851.3 66697.5 84881.7 86814.7 81982.4 97365.7 83396.8 FALSE TRUE 75947.06747 100589.6506 81377.57215 81842.18678 83192.72024 90154.51769 74031.75947 76544.80276 73537.72531 1.032763349 1.367864591 1.106609863 1.112927908 1.131293086 1.225962828 1.006718105 1.04089163 1 16.16619693 2.227149905 24.98055918 1.020701403 1.165952742 0.378882366 0.088616067 219.106119 479667.6474 0.034081802 0.023205699 168.7135272 -2.227149905 0.14525134 AAAAAATAPPS(ph)PGPAQPGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAAAAATAPPSPGPAQPGPR 20 0 Q6SPF0 Q6SPF0 SAMD1 Atherin 1 AAAAAAT(0.006)APPS(0.994)PGPAQPGPR;AAAAAAT(0.001)APPS(0.999)PGPAQPGPR 109.63 0.00020414 702630000 1085051 694866 610155 659225 658668 630908 858324 974253 877521 TRUE FALSE 941658.7612 690301.3795 905227.9988 808912.1119 645561.7955 655179.439 775083.8706 765916.5776 773781.4671 1.216956985 0.892114129 1.169875524 1.045401249 0.834294724 0.846724129 1.001683167 0.989835774 1 19.56156665 7.999999999 0.752258293 0.960061007 39.53786016 0.322442969 0.102914432 538.5309579 2.308593888 0.039299998 35211.78762 99999999.87 -7.999999999 38.57779915 AAAAGLGHPAS(ph)PGGS(ph)EDGPPGS(ph)EEEDAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAAAGLGHPASPGGSEDGPPGSEEEDAAR 29 0 Q99856 Q99856 ARID3A AT-rich interactive domain-containing protein 3A 3 AAAAGLGHPAS(1)PGGS(1)EDGPPGS(1)EEEDAAR 121.12 1.37E-05 228200000 265750 249250 170760 189010 275430 273680 258700 291890 234290 TRUE FALSE 230630.4642 247612.6603 253340.1072 231927.6093 269949.4819 284208.6467 233611.3138 229471.595 206592.5031 1.116354469 1.198555885 1.226279286 1.122633231 1.306676079 1.375696806 1.130783113 1.110745025 1 17.65642838 1.613673581 2.034142457 1.009722879 1.22112772 0.435633193 0.08062984 0.33844634 2.732181563 0.112981541 0.023636003 41.08408137 -1.613673581 0.21140484 AAAAPGASPS(ph)PGGDAAWSEAGPGPRPLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAAAPGASPSPGGDAAWSEAGPGPRPLAR 29 1 P52701;P52701-3;P52701-2;F8WAX8;F8W7G9 P52701 MSH6 DNA mismatch repair protein Msh6 1 AAAAPGAS(0.006)PS(0.994)PGGDAAWSEAGPGPRPLAR;AAAAPGAS(0.135)PS(0.865)PGGDAAWSEAGPGPRPLAR 244.31 8.29E-46 1060700000 337950 350310 217610 237150 326900 360650 298010 348690 228560 TRUE FALSE 293289.0512 348008.7905 322846.9239 290998.5321 320395.3296 374524.4389 269109.0361 274125.357 201539.8972 1.455240651 1.726748874 1.601900807 1.443875561 1.589736494 1.858314131 1.335264331 1.360154296 1 17.62070594 1.35032196 1.309300469 0.828694252 1.601374495 0.646483956 0.139896007 0.684195236 1.216121938 0.692385395 0.041959036 22.40381411 -1.35032196 0.772680243 AAACPSS(ph)PHKIPLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAACPSSPHKIPLTR 15 1 O43295-2;O43295 O43295-2 SRGAP3 SLIT-ROBO Rho GTPase-activating protein 3 1 AAACPS(0.006)S(0.994)PHKIPLTR 141.07 2.92E-06 157880000 175020 175850 109390 135000 194970 164910 200680 234870 175900 TRUE FALSE 151890.6636 174694.8298 162291.3699 165653.8133 191090.4785 171254.1944 181218.0845 184644.8783 155105.3024 0.979274475 1.126298244 1.04633025 1.068008706 1.232004809 1.104115667 1.168355186 1.190448524 1 17.24288848 3.441263939 24.94069481 1.146252602 1.058028798 0.260439457 0.069889124 212.3699487 147714.1469 0.019006943 0.02453794 2762.256083 -3.441263939 -0.088223804 AAAIGIDLGTTYSCVGVFQHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AAAIGIDLGTTYSCVGVFQHGK 22 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ;;; 343.59 1.04E-81 1721566000 1750310 1512650 977056 1318605 1453070 1379560 1755550 1973510 1834830 FALSE TRUE 1519002.099 1502713.303 1449563.55 1618014.419 1424156.75 1432632.566 1585297.031 1551490.244 1617918.488 0.938861945 0.928794197 0.895943498 1.000059293 0.880240111 0.885478828 0.979837392 0.958942157 1 20.62570749 2.213777384 24.99634152 0.975301094 0.922416847 0.37592462 0.035090084 260.4683367 262706.1218 0.014149256 0.009544348 163.5977718 -2.213777384 -0.052884247 AAAPRPPVSAASGRPQDDTDSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAAPRPPVSAASGRPQDDTDSSR 23 2 Q8TF74 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 0 97.253 0.0018878 249990000 120020 95486 87343 76272 80695 92352 90576 94931 91568 FALSE TRUE 104159.0529 94858.74618 129582.3669 93590.72334 79089.32738 95904.8412 81791.95346 74630.7444 80742.93535 1.290008252 1.174824098 1.604875602 1.159119655 0.979520091 1.187779968 1.012992073 0.92430061 1 16.30104842 3.490162501 9.444369918 1.021179074 1.345801304 0.603117162 0.124214595 0.162509135 106.0814375 0.034914231 0.048802078 3091.451955 -3.490162501 0.32462223 AAAT(ph)PAKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AAATPAKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AAAT(1)PAKK;AAAT(1)PAKK;AAAT(1)PAKK 120.09 0.00091922 1473750000 3949190 3771110 2529970 3051540 2737730 2191380 4015750 4588960 4471990 TRUE FALSE 3427294.536 3746337.33 3753471.954 3744438.797 2683254.529 2275683.807 3626303.183 3607646.615 3943316.437 0.869140124 0.95004735 0.951856645 0.949565894 0.680456304 0.577098958 0.919607453 0.914876266 1 21.91097806 AAAT(ph)PESQEPQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AAATPESQEPQAK 13 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 AAAT(1)PESQEPQAK;AAAT(1)PESQEPQAK;AAAT(0.997)PES(0.003)QEPQAK 279.55 2.62E-31 1048630000 2413460 1647920 1199980 1462590 1477530 1384240 1900950 2128930 2133010 TRUE FALSE 2094515.146 1637094.705 1780294.342 1794693.414 1448130.044 1437492.609 1716596.162 1673674.887 1880847.988 1.113601503 0.870402454 0.946538132 0.95419376 0.769934654 0.764278994 0.912671398 0.889851225 1 20.84295182 AAATGNAS(ph)PGKLEHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAATGNASPGKLEHSK 16 1 H0Y6H0;Q8NB78 H0Y6H0 KDM1B Lysine-specific histone demethylase 1B 1 AAATGNAS(1)PGKLEHSK;AAATGNAS(1)PGKLEHSK 184.34 1.11E-09 601130000 1168280 822670 650570 682740 834460 560470 1082640 1298690 791330 TRUE FALSE 1013888.838 817265.8266 965187.828 837766.552 817855.8786 582031.6436 977645.7394 1020975.25 697779.8689 1.45302105 1.171237324 1.383226818 1.200617257 1.172082938 0.834119282 1.40108046 1.463176706 1 19.41241245 6.7585776 1.620503979 1.222926998 161.4404025 0.132663964 0.189884734 2581.395833 12.08032521 0.053460761 1533515.782 5735583.408 -6.7585776 160.2174755 AAAYDIS(ph)EDEED ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAAYDISEDEED 12 0 P49585 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 AAAYDIS(1)EDEED;AAAYDIS(1)EDEED 395.71 3.75E-103 1119660000 1727630 1612450 1127470 1229290 1531410 1529790 1546780 1707420 1734090 TRUE FALSE 1499319.318 1601857.71 1672718.263 1508419.083 1500937.937 1588642.011 1396773.514 1342301.52 1529087.856 0.980531833 1.047590368 1.093932083 0.98648294 0.981590385 1.038947504 0.91346845 0.877844602 1 20.54423987 2.234844993 24.99960391 0.918773719 1.022582783 0.459351022 0.045991322 74.77990894 503128.5238 0.018519584 0.013030008 171.7295348 -2.234844993 0.103809064 AAAYNLVQHGITNLCVIGGDGSLTGANIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAAYNLVQHGITNLCVIGGDGSLTGANIFR 30 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ; 180.42 3.91E-22 598610000 288260 265850 167864 194224 267880 270150 257280 287515 277660 FALSE TRUE 250165.7106 264103.6138 249043.5919 238325.5277 262549.7121 280542.8453 232329.0252 226032.1547 244835.3511 1.021771201 1.078698859 1.017188044 0.973411424 1.072352137 1.145842886 0.948919444 0.923200648 1 17.90145235 2.162703608 24.99998677 0.949900422 1.048611694 0.448850201 0.048887074 32.8385749 10821.17577 0.020499005 0.013820429 145.4466115 -2.162703608 0.098711272 AACHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AACHLK 6 0 Q15785;Q8WXU2-3;Q8WXU2-2;Q8WXU2;Q9H3U1;A0A1W2PNX8;Q9H3U1-2 Q15785;Q9H3U1;Q9H3U1-2 TOMM34;DYX1C1;UNC45A Mitochondrial import receptor subunit TOM34;Dyslexia susceptibility 1 candidate gene 1 protein;Protein unc-45 homolog A 0 74.949 0.078979 136570000 372770 365380 216490 283270 218540 323380 364760 416890 424030 FALSE TRUE 323507.5 362979.7947 321185.2881 347590.783 214191.4816 335820.6379 329385.6313 327741.3177 373901.6565 0.865220826 0.97078948 0.85901007 0.929631568 0.572855129 0.898152314 0.880941888 0.876544172 1 18.51229934 0.771468546 1.425256755 1.31682168 0.850860968 0.156893165 0.106002926 8.190838704 5.675901515 7.71347435 0.030747061 5.90838172 -0.771468546 -0.465960712 AADAEAEVASLNRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AADAEAEVASLNRR 14 1 J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753 J3KN67 TPM3 Tropomyosin alpha-3 chain 0 224.42 5.06E-12 1560300000 1252700 1144900 416960 487280 1091700 1043000 1081300 1134200 125920 FALSE TRUE 1087152.521 1137379.077 618603.2506 597924.3716 1069977.306 1083124.885 976435.6924 891660.1564 111033.881 9.791178249 10.24353167 5.571301704 5.385062343 9.636493796 9.754904311 8.794033706 8.030523187 1 16.76064044 4.258458407 24.93675147 7.234313404 10.01735766 0.19291553 2.589398197 439.4006283 550665.6747 0.652983314 1.722621691 18132.53008 -4.258458407 2.783044255 AADEEAFEDNSEEYIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AADEEAFEDNSEEYIR 16 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;; 342.43 6.76E-72 902053000 556055 474192 380144 440915 500493 422254 470040 548084 753110 FALSE TRUE 482570.9229 471077.0015 563982.9099 541031.4897 490534.1685 438498.3846 424455.5931 430880.5018 664078.1937 0.726677863 0.709369779 0.849271841 0.814710519 0.738669291 0.660311374 0.639165082 0.64884001 1 19.3409936 3.006578418 22.96913654 0.71248765 0.775756998 0.006627624 0.109823479 185.7227406 648448.1952 0.033477328 0.037835295 1015.262669 -3.006578418 0.063269347 AADEEAFEDNSEEYIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AADEEAFEDNSEEYIRR 17 1 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;;; 297.45 5.42E-46 2816610000 1088630 806159 388976 396071 779380 705520 804430 846790 222968 FALSE TRUE 944764.7873 800863.2884 577086.0946 486004.9741 763871.8628 732661.8109 726416.5024 665710.5482 196608.977 4.805298321 4.073381086 2.935197077 2.471936843 3.885233901 3.726492157 3.694727033 3.385962117 1 17.58496967 4.43496004 3.356844225 3.122877003 4.717711593 0.342753009 0.83955137 0.286515529 6.378580856 0.214636848 0.803827972 27224.50798 -4.43496004 1.59483459 AADESER ddPTM_MDA-MB-175_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 ; 182.95 0.0015117 1553970000 1855760 1833880 1156410 1424520 1117750 1810680 1742540 2043620 2305500 FALSE TRUE 1610516.614 1821833.122 1715653.744 1747979.038 1095508.962 1880338.031 1573548.739 1606607.766 2032946.416 0.792208098 0.896154029 0.843924724 0.859825436 0.538877441 0.924932411 0.774023716 0.790285348 1 20.95514076 1.236457178 24.9358925 1.000000262 0.802214717 0.258689583 0.105053768 76.64769164 908408.2309 0.156953128 0.024550285 17.23682124 -1.236457178 -0.197785545 AADIS(ph)LDNLVEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AADISLDNLVEGK 13 0 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 AADIS(1)LDNLVEGK 173.03 2.35E-05 30349000 89139 88827 58371 71836 82210 54348 95753 91311 110950 TRUE FALSE 77359.0553 88243.48959 86599.41084 88147.46174 80574.18184 56438.80273 86466.8888 71784.85323 97833.61739 0.790720586 0.901975128 0.885170283 0.900993586 0.823583794 0.576885576 0.883815718 0.73374424 1 16.57804267 3.004359298 24.14809785 0.78577169 0.871768883 0.07952379 0.110735716 174.9020558 968838.9791 0.032157944 0.036304335 1010.088201 -3.004359298 0.085997193 AADKLIQNLDANHDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AADKLIQNLDANHDGR 16 1 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;;;; 229.02 2.15E-15 5640250000 8729710 7989270 3371940 3976250 7837030 8224780 8381810 10700840 896828 FALSE TRUE 7576056.705 7936787.959 5002621.462 4879118.336 7681088.436 8541192.609 7568943.356 8412548.64 790806.0155 9.580170809 10.03632725 6.325978008 6.169804276 9.712986858 10.80061664 9.571175747 10.63794214 1 19.59296432 4.342249739 21.32913721 8.221157977 9.808748501 0.061671979 2.917236876 14.34285247 2914.387154 0.723200977 1.913413294 21991.24105 -4.342249739 1.587590523 AADLLYAMCDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AADLLYAMCDR 11 0 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 ; 133.81 0.00035823 117995000 303380 320100 140718 178168 300720 334810 231540 268460 178227 FALSE TRUE 263287.5643 317997.242 208769.6955 218623.7675 294736.2603 347690.3574 209085.2864 211051.9182 157157.2071 1.675313332 2.023434037 1.328413118 1.391115123 1.875423124 2.212372972 1.330421241 1.342935027 1 17.26184891 1.823263823 2.340048038 1.127965742 1.729272807 0.417393305 0.284069488 0.301972504 3.099975891 0.237201596 0.083543898 66.56774165 -1.823263823 0.601307065 AADPPAENSS(ph)APEAEQGGAE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AADPPAENSSAPEAEQGGAE 20 0 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 AADPPAENS(0.248)S(0.752)APEAEQGGAE;AADPPAENS(0.435)S(0.565)APEAEQGGAE 272.14 2.13E-44 496330000 654690 539850 317350 401890 538800 572650 496630 604240 592730 TRUE FALSE 568171.0577 536303.6898 470821.5215 493145.267 528078.9341 594680.2161 448466.899 475027.9782 522658.1346 1.087079718 1.026107993 0.900821187 0.943533133 1.010371597 1.137799599 0.858050166 0.908869387 1 18.99550808 AADRLPNLSS(ph)PSAEGPPGPPSGPAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AADRLPNLSSPSAEGPPGPPSGPAPR 26 1 O60784;O60784-4;O60784-2;O60784-3 O60784 TOM1 Target of Myb protein 1 1 AADRLPNLS(0.33)S(0.669)PS(0.001)AEGPPGPPSGPAPR;AADRLPNLS(0.118)S(0.878)PS(0.004)AEGPPGPPSGPAPR;AADRLPNLS(0.034)S(0.962)PS(0.003)AEGPPGPPSGPAPR;AADRLPNLS(0.033)S(0.962)PS(0.005)AEGPPGPPSGPAPR 283.95 2.93E-61 3832810000 418746 491369 376107 445528 607512 616192 636460 770110 520457 TRUE FALSE 363407.6551 488141.1647 557993.6032 546691.9419 595423.6998 639897.305 574736.2072 605427.9695 458929.1664 0.791860012 1.063652521 1.215859972 1.191233815 1.297419609 1.39432695 1.252341863 1.319218768 1 18.80791197 4.848115406 1.213996393 1.262093135 0.482903689 0.663129207 0.102621638 1.077943625 1.148931208 0.029567822 1.123493477 70488.03528 -4.848115406 -0.779189446 AAEDDEDDDVDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 AAEDDEDDDVDTK 13 0 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;;;; 340.8 1.42E-62 30548910000 12258951 8562032 7322623 7831322 7542353 5944256 10718502 12206387 11574072 FALSE TRUE 10638899.57 8505787.448 10863867.98 9609543.354 7392274.932 6172935.375 9679023.326 9596146.13 10205798.39 1.042436775 0.833426952 1.064479971 0.941576835 0.724321082 0.604845906 0.948384727 0.940264128 1 23.28288571 3.45770199 24.88545735 0.849883101 0.971709604 0.196812184 0.128645161 438.6385306 562105.8493 0.039953237 0.051586422 2868.811347 -3.45770199 0.121826503 AAEDDEDDDVDTKK ddPTM_MDA-MB-175_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 ;;;;;;;;;;; 265.72 2.65E-24 67194020000 30816930 18093691 19544834 16758356 15019405 9915880 26334160 30042750 24152870 FALSE TRUE 26744394.62 17974832.35 28996781.1 20563596.87 14720548.23 10297350.32 23780277.22 23618341.71 21297545.22 1.255750104 0.84398611 1.361508136 0.965538359 0.691185208 0.483499399 1.116573622 1.10897014 1 24.34418382 3.493270893 24.44988406 0.899463355 1.129563831 0.226246572 0.228234564 1017.216826 1540021.57 0.06840036 0.098234561 3113.657888 -3.493270893 0.230100476 AAEDDEDDDVDTKKQKT(ph)DEDD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAEDDEDDDVDTKKQKTDEDD 21 3 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 1 AAEDDEDDDVDT(0.212)KKQKT(0.788)DEDD;AAEDDEDDDVDT(0.032)KKQKT(0.968)DEDD 136.4 5.14E-06 627910000 25507.3 21987 25767.6 13614.2 23212.9 25600.1 27739 97326 29235.3 TRUE FALSE 22136.44568 21842.56595 38228.89755 16705.51219 22751.00871 26584.95241 25048.87605 76513.59229 25779.13614 0.858696178 0.847296272 1.482939434 0.648024515 0.882535729 1.031258467 0.971672438 2.9680433 1 14.6539163 1.773443187 25 2.105212208 0.963819669 0.403012333 0.513271517 27.95115394 20043.6983 0.249816331 0.120051847 59.35306988 -1.773443187 -1.14139254 RTPAPPEPGS(ph)PAPGEGPSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RTPAPPEPGSPAPGEGPSGR 20 1 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 RTPAPPEPGS(1)PAPGEGPSGR;RTPAPPEPGS(1)PAPGEGPSGR;RTPAPPEPGS(1)PAPGEGPSGR 131.26 8.98E-06 502060000 571900 535060 267453 347727 477660 507650 445630 506760 262176 TRUE FALSE 496321.966 531545.1556 396794.1654 426683.73 468155.5005 527179.624 402412.8712 398393.3176 231181.852 2.146889826 2.299251222 1.716372466 1.845662739 2.02505299 2.280367683 1.740676735 1.723289758 1 17.81866862 0.996289705 1.253310672 6.12E-14 2.029077154 0.733553479 0.194086948 1.357345408 1.197663294 4.163242713 0.0606287 9.91493121 -0.996289705 2.029077154 AAEEAEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAEEAEEAR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 133.12 0.00066493 466550000 1045720 982010 756850 669060 674030 965090 934640 1037160 1044500 FALSE TRUE 907525.4525 975559.1117 1122865.192 820980.2989 660618.1217 1002217.637 843998.7567 815371.4052 921020.3999 0.98534783 1.059215531 1.219153443 0.891381232 0.717267632 1.088160085 0.916373575 0.885291363 1 19.81287359 3.711036278 24.78874561 0.912026573 1.085036616 0.355365848 0.108753136 685.9839723 617805.2092 0.029558427 0.043853813 5140.865926 -3.711036278 0.173010043 AAEEAFVNDIDESSPGTEWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AAEEAFVNDIDESSPGTEWER 21 0 P09496-2;P09496-5 P09496-2 CLTA Clathrin light chain A 0 ;;; 275.75 2.04E-44 798914000 1083630 893650 583170 696140 861800 882300 832550 987780 947720 FALSE TRUE 940425.5499 887779.5543 865192.9626 854209.2268 844651.8661 916242.6519 751809.4291 776550.9339 835681.6212 1.125339515 1.062341844 1.035314096 1.022170651 1.010734046 1.096401582 0.899636189 0.929242566 1 19.67259388 8 0.130615152 0.849174627 1.734024683 0.486231748 0.049067479 157.5176676 1.799473337 1.367258775 25.41288993 100000000 -8 0.884850055 AAEEEDEADPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AAEEEDEADPKR 12 1 P20962 P20962 PTMS Parathymosin 0 ;;;;; 195.25 7.86E-07 14978620000 12381660 10294370 7670690 8487770 9097300 7345100 12415830 13353630 11330390 FALSE TRUE 10745392.26 10226745.61 11380261.34 10415047.91 8916281.529 7627670.75 11211744.72 10498060.14 9990924.202 1.075515342 1.023603562 1.139059922 1.042450898 0.892438112 0.763459976 1.122192951 1.050759663 1 23.25218671 3.465658145 24.57683427 0.977049513 1.076637581 0.221245837 0.098045638 331.8283628 711434.8315 0.030890126 0.03991354 2921.851534 -3.465658145 0.099588069 AAEEPSKVEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AAEEPSKVEEK 11 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 0 ;; 93.766 0.0082128 882370000 1193570 764460 649990 789800 784970 519960 1031590 1218710 967430 FALSE TRUE 1035836.7 759438.2119 964327.3381 969136.1613 769350.6328 539963.1977 931546.5606 958098.3505 853061.5275 1.214257902 0.890250219 1.130431167 1.136068302 0.901870039 0.632970988 1.092003953 1.123129246 1 19.70229027 4.759241635 23.35435458 0.998979421 1.214258423 0.171128689 0.154687917 4237.767224 4785374.035 0.039964963 1.486797997 57443.59804 -4.759241635 0.215279002 AAEEQGDDQDS(ph)EK ddPTM_MDA-MB-175_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 223.7 1.61E-11 246090000 548960 314940 344920 370770 293540 310200 396860 443600 948970 TRUE FALSE 476413.5451 312871.1384 511724.4657 454958.9954 287699.1283 322133.5947 358372.5783 348739.5921 836783.8477 0.56933884 0.373897201 0.611537217 0.543699543 0.343815346 0.384966316 0.428273776 0.416761859 1 19.67449548 1.236156683 24.99997389 1.000000712 0.45444808 0.784276994 0.089134015 29.7839357 309672.1308 0.143647136 0.021951407 17.22489895 -1.236156683 -0.545552632 AAEEQGDDQDS(ph)EKSKPAGSDGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAEEQGDDQDSEKSKPAGSDGER 23 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 AAEEQGDDQDS(0.999)EKSKPAGSDGER;AAEEQGDDQDS(0.982)EKS(0.016)KPAGS(0.001)DGER 113.65 0.00038932 199164000 190439 118785 129027 109806 119418 100887 177533 189340 153715 TRUE FALSE 165272.0036 118004.6935 191424.8888 134739.1306 117041.8154 104768.1882 160315.877 148851.1144 135542.9878 1.219332747 0.870607144 1.412281755 0.994069356 0.863503286 0.772951739 1.182767767 1.098183808 1 17.04839095 3.575518508 20.00978767 0.995306495 1.14863917 0.196598114 0.171391768 17.0487049 3458.768064 0.047917397 0.071073012 3762.863875 -3.575518508 0.153332675 AAEHAWQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAEHAWQK 8 0 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 0 81.548 0.022576 70908000 196390 199750 137520 160170 167110 175740 219510 233910 217210 FALSE TRUE 170436.5639 198437.8291 204025.132 196539.0465 163784.8379 182500.8315 198221.954 183890.1668 191531.6812 0.88986095 1.03605747 1.06522916 1.026143797 0.855131834 0.952849316 1.034930371 0.960103131 1 17.54722352 6.009907937 13.36113801 0.981916196 0.678568951 0 0.067358964 0 0 0.015191983 0 1023076.095 -6.009907937 -0.303347245 AAELEMELNEHSLVIDTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAELEMELNEHSLVIDTLK 19 0 Q9UHV9 Q9UHV9 PFDN2 Prefoldin subunit 2 0 195.78 8.66E-16 59594000 184560 145850 105480 122780 121720 117630 143650 176550 180650 FALSE TRUE 160169.9284 144891.9017 156490.4808 150659.0756 119298.0101 122155.3022 129718.8451 138796.1564 159293.7628 1.005500313 0.909589297 0.982401809 0.94579394 0.748918276 0.766855526 0.814337252 0.871321978 1 17.28133025 3.377841581 8.753146818 0.838701807 0.960808305 0.413942332 0.071488827 0.279666 22.13186385 0.021558347 0.027840736 2386.940431 -3.377841581 0.122106498 AAELWGEQAEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAELWGEQAEAR 12 0 Q08379;Q08379-2 Q08379 GOLGA2 Golgin subfamily A member 2 0 115.14 0.0022852 111290000 115450 87779 61301 63760 95910 98007 73748 98618 86096 FALSE TRUE 100192.99 87202.37397 90946.36864 78237.68251 94001.57864 101777.3927 66595.93031 77529.30815 75917.82896 1.319755733 1.148641566 1.197957975 1.030557427 1.238201618 1.340625702 0.877210679 1.021226624 1 16.21215112 2.232089499 24.99999068 0.973915314 1.201935396 0.604494317 0.093647688 110.2464295 425912.2944 0.037678491 0.02608912 170.6434014 -2.232089499 0.228020082 AAEQYTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAEQYTPK 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 0 111.17 0.0076435 341160000 304430 272020 236150 240050 282260 264400 321140 335760 410910 FALSE TRUE 264198.8042 270233.0827 350352.9299 294557.0214 276643.5782 274571.6391 289995.8922 263960.3369 362332.6879 0.729160832 0.745814804 0.966937131 0.812946309 0.763507096 0.757788762 0.800358074 0.728502687 1 18.46695544 1.22825336 24.98705296 1.000000438 0.789229136 0.480692369 0.069199656 410.6895351 995532.2946 0.238107695 0.017428843 16.91427392 -1.22825336 -0.210771302 AAESETPGKS(ph)PEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAESETPGKSPEK 13 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 AAESET(0.001)PGKS(0.999)PEK;AAES(0.001)ET(0.038)PGKS(0.961)PEK 111.33 0.00059866 592580000 506240 467430 403020 382340 429880 391220 443610 553490 808400 TRUE FALSE 439339.1014 464359.4216 597921.82 469156.1407 421326.229 406270.4866 400588.7705 435130.4708 712831.8729 0.616329205 0.651429095 0.838797819 0.658158198 0.591059751 0.569938722 0.561968096 0.610425105 1 19.44320232 1.236081663 24.99258201 1.000000479 0.636321588 0.681108852 0.077999857 43.82922009 441785.7215 0.137272503 0.02085537 17.2219238 -1.236081663 -0.363678891 AAESLTAIPEPAS(ph)PQLLETPIHASQIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAESLTAIPEPASPQLLETPIHASQIQK 28 0 Q14676;Q14676-3;Q14676-2 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AAESLTAIPEPAS(1)PQLLETPIHASQIQK 158.97 6.86E-12 65911000 77209 65233 15252 38721 73048 65304 68676 79739 76025 TRUE FALSE 67005.63503 64804.48013 22627.91821 47513.19486 71594.48772 67816.28714 62015.81209 62687.43538 67037.41111 0.999525995 0.966691271 0.337541648 0.70875641 1.067978112 1.011618528 0.925092587 0.935111221 1 16.03267881 3.247504795 24.99133731 0.977821843 0.738698446 0.290366139 0.181414781 261.720489 731281.0036 0.055015832 0.069965629 1768.091737 -3.247504795 -0.239123397 AAFDDAIAELDTLSEESYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AAFDDAIAELDTLSEESYK 19 0 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;; 390.95 1.18E-126 336754000 617713 525881 544304 644574 537330 442427 625092 758229 1300936 FALSE TRUE 536080.662 522426.4531 807531.235 790934.3784 526638.1843 459447.453 564470.6741 596087.6289 1147140.828 0.467318963 0.455416144 0.703951263 0.689483243 0.459087648 0.4005153 0.49206746 0.519628989 1 20.12961108 1.2381935 24.92726706 1.000000543 0.524637635 0.69594971 0.098991335 5.322560008 360886.0022 0.148552743 0.026090445 17.30587249 -1.2381935 -0.475362908 AAFDDAIAELDTLSEESYKDSTLIMQLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAFDDAIAELDTLSEESYKDSTLIMQLLR 29 1 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 103.92 0.00050392 1268100000 114810 103070 57220 67778 93252 75976 97318 119700 37445 FALSE TRUE 99637.56761 102392.9264 84891.78339 83168.03082 91396.46764 78898.84588 87880.11534 94103.08651 33018.29476 3.017647287 3.101096745 2.571052927 2.518846943 2.768055356 2.389549384 2.661558266 2.850028664 1 15.01097799 1.23607146 24.99992223 0.999997731 2.726546593 0.862289924 0.217844659 24.97992145 250832.3526 0.368777651 0.056004717 17.2215192 -1.23607146 1.726548862 AAFFVTLDETEEGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAFFVTLDETEEGYR 15 0 P50416;P50416-2 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 176.8 1.81E-06 30059000 32452 31075 23521 39649 39116 42453 29187 49817 60203 FALSE TRUE 28163.38598 30870.86628 34895.83427 48651.91145 38337.66813 44086.19438 26356.44923 39164.02223 53085.86992 0.530525091 0.581526992 0.657346942 0.916475731 0.722182159 0.830469472 0.496487093 0.737748525 1 15.69604028 4.068516872 3.673488324 0.762158042 0.557041306 0.32800352 0.133440424 0.292897879 7.916362335 0.035589903 0.080503342 11708.92089 -4.068516872 -0.205116736 AAFGISDSYVDGSSFDPQRR ddPTM_MDA-MB-175_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 0 107.98 0.00035086 138760000 84261 77003 43727 50287 56341 79675 64369 85057 24742 FALSE TRUE 73125.69536 76497.16222 64873.52346 61705.43194 55219.92433 82740.14881 58126.50429 66868.22246 21817.02895 3.351771478 3.506305208 2.973526946 2.828315079 2.531046939 3.792457214 2.664272227 3.064955482 1 14.41316703 1.236955089 7.310592561 0.961368365 3.076389854 0.746983499 0.382012058 0.054309401 18.75851682 0.56077788 0.09224638 17.2565943 -1.236955089 2.115021489 AAFNSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AAFNSGK 7 0 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;; 128.37 0.0087583 8743500000 11246000 10671200 7448200 8556100 6767300 8500800 12114500 12396400 12281700 FALSE TRUE 9759812.606 10601100.18 11050174.43 10498893.28 6632643.97 8827831.277 10939637.65 9745526.329 10829771.42 0.901202087 0.978884944 1.020351585 0.969447357 0.612445426 0.815144747 1.010144834 0.89988292 1 23.36849946 3.41747931 24.99999978 0.871582732 0.972514001 0.161626026 0.112666253 145.9695425 61184.77844 0.034417693 0.044433055 2615.045865 -3.41747931 0.100931269 AAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGTVK 41 2 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 159.22 5.46E-20 1427910000 746392 1334470 323655 803936 609732 398983 1585370 1940440 426260 FALSE TRUE 647754.4061 1325703.779 480175.6406 986481.9562 597599.5261 414332.1342 1431621.061 1525492.007 375868.0284 1.723355958 3.527045874 1.277511265 2.624543408 1.589918485 1.102334072 3.808839681 4.058584107 1 18.51986668 2.228559251 24.99951415 3.221095904 2.025142953 0.141878785 1.069065984 314.09116 785098.1713 0.42490263 0.290268232 169.2619154 -2.228559251 -1.195952951 AAFTTPDHAPLS(ph)PQSSVASSGSEQTEEQGSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AAFTTPDHAPLSPQSSVASSGSEQTEEQGSSR 32 0 M0QZ22;Q5PRF9;A0A087WZT0;M0R0X3 M0QZ22 SAMD4B Protein Smaug homolog 2 1 AAFTTPDHAPLS(1)PQSSVASSGSEQTEEQGSSR;AAFTTPDHAPLS(1)PQSSVASSGSEQTEEQGSSR;AAFTTPDHAPLS(0.994)PQS(0.005)S(0.001)VASSGSEQTEEQGSSR 294.1 1.22E-89 956490000 270712 253278 171268 251920 315056 319457 326844 377839 320582 TRUE FALSE 234936.7233 251614.2001 254093.7777 309122.2864 308787.002 331746.7175 295146.7192 297041.0702 282683.1612 0.831095571 0.890092636 0.898864215 1.093529183 1.092343105 1.173563774 1.044090203 1.050791526 1 18.10882642 3.802976959 4.265168889 1.076212933 0.86864707 0.806663003 0.046843078 0.099456034 3.624705998 0.013532234 0.024024743 6352.972262 -3.802976959 -0.207565863 AAGALGSASSGS(ph)MPNLAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AAGALGSASSGSMPNLAAR 19 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 AAGALGSAS(0.061)S(0.074)GS(0.865)MPNLAAR;AAGALGSASS(0.001)GS(0.999)MPNLAAR;AAGALGSASS(0.001)GS(0.999)MPNLAAR 289.68 1.74E-49 627250000 701531 626264 425778 389125 599304 680718 539547 595632 685360 TRUE FALSE 608821.9009 622150.0305 631685.6649 477481.7787 587379.0229 706905.6619 487221.815 468260.732 604337.5216 1.007420323 1.029474438 1.045253095 0.790091235 0.971938696 1.169719961 0.806208116 0.774833128 1 19.20499499 2.18439398 24.9999753 0.840275538 0.994476735 0.264116958 0.109502745 115.3173133 53222.32434 0.045189937 0.030467071 152.8952453 -2.18439398 0.154201197 AAGDGDCGTTHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 93.348 0.0056552 170739000 400620 260683 181904 195802 233393 294791 275361 318937 242678 FALSE TRUE 347677.052 258970.5562 269873.3828 240261.8367 228748.9359 306131.8005 248656.5326 250734.8045 213988.8833 1.624743522 1.210205653 1.261156088 1.122777188 1.068975792 1.430596748 1.162006777 1.171718833 1 17.70717633 5.149764599 1.616069334 1.173453682 2.421009452 0.599438022 0.114726637 2.46547304 2.53347751 0.030436461 6.696937459 141177.2112 -5.149764599 1.24755577 AAGDVDIGDAAYYFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAGDVDIGDAAYYFER 16 0 P09758 P09758 TACSTD2 Tumor-associated calcium signal transducer 2 0 141.58 3.70E-06 99754000 156280 137690 78890 151890 156830 182540 110080 201650 161520 FALSE TRUE 135627.202 136785.5053 117041.4679 186378.946 153709.3898 189562.4319 99404.45854 158528.7167 142425.2896 0.952269098 0.960401806 0.821774477 1.30860851 1.079228206 1.330960481 0.697941067 1.113065785 1 17.11984581 3.783763847 24.9991994 1.076216122 0.916373825 0.179576916 0.176806513 847.8603734 468897.8579 0.045765365 0.079267553 6078.044108 -3.783763847 -0.159842296 AAGGAPS(ph)PPPPVR ddPTM_MDA-MB-175_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 167.22 3.39E-05 5087860000 1858070 1638330 1313370 1454260 1747630 1736760 1719790 1967780 2309990 TRUE FALSE 1612521.342 1627567.702 1948520.125 1784471.96 1712855.582 1803574.281 1553005.031 1546985.56 2036905.614 0.791652461 0.799039333 0.956607961 0.876070029 0.84091063 0.885448137 0.762433478 0.759478274 1 20.9579477 2.279245297 24.99990762 0.820470153 0.860082422 0 0.080492879 513.9248514 315794.171 0.030213647 0.023403175 190.2152344 -2.279245297 0.03961227 AAGGAPS(ph)PPPPVRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AAGGAPSPPPPVRR 14 1 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 AAGGAPS(1)PPPPVRR;AAGGAPS(1)PPPPVRR;AAGGAPS(1)PPPPVRR 92.575 0.0030039 1235860000 1651120 1537270 856850 1122150 1476380 1345750 1307130 1671770 1177100 TRUE FALSE 1432920.309 1527171.572 1271225.526 1376951.308 1447002.926 1397521.873 1180364.734 1314274.995 1037944.579 1.380536435 1.471342115 1.224752797 1.326613517 1.394104229 1.346432075 1.137213641 1.266228488 1 19.98529798 0.041798427 0.534035302 5.72E-14 1.371323861 0.634163383 0.082704505 9.594487375 0.807416664 10.83903534 0.050897669 1.101028161 -0.041798427 1.371323861 AAGGGAGS(ph)S(ph)EDDAQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAGGGAGSSEDDAQSR 16 0 Q9H4A6;D6REM1 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 2 AAGGGAGS(1)S(1)EDDAQSR 129.32 0.00030272 0 206470 191190 124640 147170 190860 190790 171720 208990 211530 TRUE FALSE 179184.4664 189934.0603 184916.3209 180587.1979 187062.2594 198129.8148 155066.6208 164299.1149 186523.1644 0.9606553 1.018286715 0.991385287 0.968175714 1.002890231 1.062226321 0.831353153 0.880850995 1 17.50899528 2.239313257 24.99999331 0.89620138 0.999618027 0.455300274 0.049518376 16.50392972 548235.6834 0.019104795 0.013911455 173.5055043 -2.239313257 0.103416648 ELSNS(ph)PLRENSFGS(ph)PLEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 ELS(0.009)NS(0.991)PLRENSFGS(1)PLEFR;ELS(0.004)NS(0.996)PLRENS(0.001)FGS(0.999)PLEFR;ELS(0.021)NS(0.979)PLRENSFGS(1)PLEFR;ELS(0.107)NS(0.893)PLRENS(0.051)FGS(0.949)PLEFR;ELS(0.004)NS(0.996)PLRENS(0.001)FGS(0.999)PLEFR;ELS(0.004)NS(0.996)PLRENSFGS(1)PLEFR 248.02 4.63E-25 3208960000 2674890 2457290 1270701 1509850 2262470 2152200 2069250 2510850 1181199 TRUE FALSE 2321396.509 2441147.9 1885216.254 1852684.519 2217451.273 2234996.527 1868574.453 1973924.267 1041559 2.228771015 2.343744234 1.809994685 1.778760991 2.128973274 2.145818458 1.794016905 1.895163181 1 19.99031313 0.999916324 1.673333737 7.90E-15 2.041923145 0.738913029 0.191325753 1.08128628 1.654322442 4.397642414 0.055682178 9.99807347 -0.999916324 2.041923145 AAGIDEQENWHEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAGIDEQENWHEGK 14 0 P28838-2;P28838 P28838-2 LAP3 Cytosol aminopeptidase 0 228.25 1.73E-12 449370000 282200 262170 220360 228860 251540 195670 255820 299560 426450 FALSE TRUE 244906.555 260447.788 326926.8331 280826.1609 246534.8461 203197.5515 231010.6158 235501.4252 376035.5668 0.651285614 0.692614771 0.869404019 0.746807445 0.655615766 0.540367905 0.614331824 0.626274337 1 18.5205096 3.243400893 23.58153938 0.666866043 0.745882488 0.024279907 0.132731374 172.825133 841980.6492 0.039054737 0.048720865 1751.462702 -3.243400893 0.079016446 AAGISLIVPGKS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAGISLIVPGKSPTR 15 1 J3KPC5;P47736-3;P47736;P47736-4;F2Z357 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 AAGISLIVPGKS(0.779)PT(0.221)R;AAGISLIVPGKS(0.86)PT(0.14)R 118.24 0.00018584 2043310000 3825200 2428200 1535440 2007600 2656600 2172320 2824400 3416600 2730900 TRUE FALSE 3319690.128 2412248.994 2277983.92 2463456.264 2603738.858 2255890.556 2550490.123 2685986.678 2408056.113 1.378576733 1.001741189 0.945984567 1.023006171 1.081261705 0.936809796 1.059148958 1.11541698 1 21.19943758 4.741036808 24.92388907 1.026701128 1.378576862 0.803285437 0.055623178 102.710406 1033759.03 0.014541656 0.095196012 55085.43809 -4.741036808 0.351875734 AAGLATMISTMRPDIDNMDEYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAGLATMISTMRPDIDNMDEYVR 23 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 193.11 6.49E-18 771780000 525040 418250 323450 328190 448310 441570 366100 504160 430080 FALSE TRUE 455654.6337 415502.4882 479871.5019 402710.5556 439389.5081 458557.4836 330595.6783 396349.3074 379236.4323 1.201505433 1.095629145 1.265362346 1.061898386 1.15861629 1.209159892 0.871740292 1.045124554 1 18.53273804 2.251622945 24.99998141 0.983272991 1.161728226 0.619806356 0.071072577 144.2104226 276004.04 0.024899503 0.019166996 178.4937217 -2.251622945 0.178455235 AAGQPYEQHAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAGQPYEQHAK 11 0 O14976-2;O14976;A0A087X1U9;H0Y8H5 O14976-2 GAK Cyclin-G-associated kinase 0 ; 117.09 0.00090123 175055000 251020 236940 143649 190480 215990 213760 249560 273360 262890 FALSE TRUE 217847.071 235383.5255 213118.1369 233731.3953 211692.2216 221983.4855 225357.7096 214904.0913 231811.4437 0.939759779 1.015409428 0.919359862 1.008282385 0.913208676 0.957603654 0.972159554 0.927064203 1 17.82259226 3.240329905 24.99999978 0.952180593 0.970228821 0.0482554 0.036316946 147.5567982 2084922.974 0.009755343 0.011951076 1739.121424 -3.240329905 0.018048229 AAGVNVEPFWPGLFAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAGVNVEPFWPGLFAK 16 0 P05386 P05386 RPLP1 60S acidic ribosomal protein P1 0 ; 179.02 6.27E-09 171120000 470090 417450 275160 351540 387170 357800 402790 522610 490940 FALSE TRUE 407966.4154 414707.7435 408228.2964 431362.53 379466.0745 371564.7975 363727.4878 410853.9185 432901.6325 0.942399808 0.957972233 0.943004751 0.996444683 0.876564203 0.858312304 0.840208169 0.949069922 1 18.72367972 3.231428975 24.99998867 0.903188158 0.958602959 0.250843128 0.04726412 257.0850326 901210.0399 0.015325092 0.017742319 1703.84065 -3.231428975 0.055414801 AAHACATVGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAHACATVGNR 11 0 G3V2H2;G3V3U8;Q9Y2U9-2;Q9Y2U9 G3V2H2 KLHDC2 Kelch domain-containing protein 2 0 ; 76.143 0.03616 27294000 22137.4 19626.4 16976.3 16078 16688.6 19348 18592.9 19388.4 16525 FALSE TRUE 19211.8865 19497.47289 25186.09546 19728.75564 16356.52951 20092.33008 16789.76342 15242.34154 14571.43333 1.318462369 1.338061428 1.728456968 1.353933769 1.122506561 1.378884948 1.15223829 1.046042706 1 13.83085518 2.099637093 0.642258288 0.908265632 1.444538392 0.535939649 0.142665512 1.127877575 0.767246287 0.409099125 0.099711151 125.7873861 -2.099637093 0.53627276 AAHGVLLQALDEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAHGVLLQALDEMR 14 0 Q8WZA9 Q8WZA9 IRGQ Immunity-related GTPase family Q protein 0 ; 162.93 4.36E-06 372610000 224780 217920 130691 146455 189700 203067 190239 210155 208677 FALSE TRUE 195074.7535 216488.4692 193893.6047 179709.8462 185925.3411 210879.1189 171789.6511 165214.9887 184007.4428 1.060145995 1.176520177 1.053726968 0.976644441 1.010422939 1.146035811 0.933601644 0.897871228 1 17.4894046 2.60763539 0.303941057 0.86407707 1.153426922 0.317537422 0.071416098 3.561520072 1.191672091 0.60842133 0.383457998 405.1682351 -2.60763539 0.289349852 AAHIFFTDTCPEPLFSELGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAHIFFTDTCPEPLFSELGR 20 0 Q15833-2;Q15833;Q15833-3;M0R0M7;M0QZ54;M0R118;A0A087WUN8 Q15833-2 STXBP2 Syntaxin-binding protein 2 0 ; 199.76 1.43E-21 323490000 321930 363880 237229 269720 336660 361870 349240 405820 355320 FALSE TRUE 279386.1348 361489.6483 351953.7379 330964.0484 329961.1247 375791.3731 315370.7586 319038.5511 313314.4744 0.891711548 1.15375981 1.123324221 1.056331818 1.053130805 1.199406359 1.006563004 1.01826943 1 18.25725189 AAHLCAEAALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAHLCAEAALR 11 0 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 140.3 3.87E-05 690150000 330160 327310 232380 230890 324800 319180 327520 356220 256470 FALSE TRUE 286528.5195 325159.8791 344759.7453 283317.1034 318337.1155 331459.0611 295757.1608 280045.1251 226150.4088 1.266982098 1.437803632 1.524471024 1.252781744 1.407634491 1.465657581 1.307789636 1.238313592 1 17.78692308 1.179799593 1.317010903 0.77888937 1.394038859 0.681055649 0.084415604 0.904186661 1.22147284 0.790385801 0.024925025 15.1286297 -1.179799593 0.615149489 AAHSEGNTTAGLDMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 AAHSEGNTTAGLDMR 15 0 P78371;P78371-2 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;;;;;;; 226.24 8.91E-13 3585377000 2052101 2044828 1300391 1448914 1926128 2105295 1955805 2181489 1981452 FALSE TRUE 1780910.653 2031395.39 1929264.437 1777912.069 1887801.821 2186287.061 1766131.332 1714994.554 1747207.002 1.019290016 1.162652959 1.104199122 1.0175738 1.080468324 1.251303972 1.01083119 0.981563462 1 20.73661911 2.027597402 24.99717854 0.991484446 1.105562273 0.370104715 0.067071577 208.5331994 188884.4201 0.026989453 0.018195895 106.5607827 -2.027597402 0.114077827 AAHSRNS(ph)MDRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAHSRNSMDRPK 12 2 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 AAHSRNS(1)MDRPK 82.55 0.0076445 55665000 29719 21172 8067.5 10615 15679 15193 30846 22820 1531.3 TRUE FALSE 25791.55885 21032.91974 11968.96998 13025.29799 15367.01858 15777.48454 27854.55967 17940.12059 1350.271458 19.10101757 15.57680836 8.864121291 9.646429174 11.38068829 11.68467603 20.6288591 13.2863066 1 10.39903376 AAHTEDINACTLTTS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AAHTEDINACTLTTSPR 17 0 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 AAHTEDINACTLT(0.001)T(0.019)S(0.98)PR;AAHTEDINACTLTT(0.025)S(0.975)PR;AAHTEDINACTLTT(0.013)S(0.987)PR;AAHTEDINACTLTT(0.026)S(0.974)PR 269.08 2.43E-28 1142110000 497540 534980 481775 573713 687740 809700 713690 821240 833030 TRUE FALSE 431788.8284 531465.6812 714763.0014 703983.3053 674055.3195 840849.6829 644476.4536 645624.2169 734550.1424 0.587827574 0.723525394 0.973062233 0.958386997 0.917643712 1.144713797 0.877375711 0.87893825 1 19.48650145 4.387280676 3.054467753 0.957451409 0.60293873 0.746361769 0.076623269 0.130033945 2.313235694 0.020455344 0.074799116 24393.86836 -4.387280676 -0.354512678 AAHVLMPHESTVEHTHVDINEMES(ph)PLATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AAHVLMPHESTVEHTHVDINEMESPLATR 29 0 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 1 AAHVLMPHESTVEHTHVDINEMES(1)PLATR;AAHVLMPHESTVEHTHVDINEMES(1)PLATR;AAHVLMPHESTVEHTHVDINEMES(1)PLATR;AAHVLMPHESTVEHTHVDINEMES(1)PLATR;AAHVLMPHESTVEHTHVDINEMES(1)PLATR 201.85 1.40E-25 4776450000 1688350 1701689 765851 1107757 1731595 1676504 1552698 1943870 1595578 TRUE FALSE 1465230.27 1690510.493 1136219.105 1359290.158 1697139.647 1741000.194 1402117.587 1528188.528 1406950.587 1.041422694 1.201542193 0.8075757 0.966125016 1.206253911 1.237428102 0.996564912 1.086170717 1 20.42414023 AAHVPENS(ph)DTEQDVLTVKPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAHVPENSDTEQDVLTVKPVR 21 1 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2;H3BS99 H3BSS6 ZNF106 Zinc finger protein 106 1 AAHVPENS(0.996)DT(0.004)EQDVLTVKPVR 96.903 0.00073085 119490000 129510 106280 63068 82789 99732 97017 101950 110330 130750 TRUE FALSE 112394.9254 105581.8397 93567.89575 101587.5078 97747.52832 100749.3068 92062.90469 86736.78809 115292.884 0.974864376 0.915770654 0.811566964 0.881125568 0.847819267 0.873855379 0.79851333 0.752316926 1 16.81494394 4.448433391 3.762912658 0.842187633 0.966669323 0.269994669 0.065517912 0.253678591 7.529661416 0.016524276 0.058948898 28082.34633 -4.448433391 0.12448169 AAIDWFDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 130.96 0.00080597 2629380000 6039500 4534470 3549010 4692250 4517260 3779100 5008890 5943220 7147170 FALSE TRUE 5241364.773 4504682.768 5265323.107 5757697.079 4427375.364 3924484.422 4523128.619 4672308.653 6302239.705 0.831666998 0.714774902 0.835468556 0.91359538 0.702508246 0.622712656 0.717701774 0.74137273 1 22.5874332 1.236355597 24.99352524 1.000000314 0.756783589 0.456638949 0.082218702 58.58419531 663880.2812 0.137445234 0.021325157 17.23279007 -1.236355597 -0.243216725 AAIDWFDGKEFSGNPIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAIDWFDGKEFSGNPIK 17 1 P35637-2;P35637;H3BPE7 P35637-2 FUS RNA-binding protein FUS 0 ; 219.95 3.80E-15 1354820000 3530300 2456830 1188560 1373720 2091130 1708250 3086900 3391600 417390 FALSE TRUE 3063761.91 2440690.922 1763351.591 1685644.122 2049520.604 1773967.483 2787532.913 2666332.733 368046.6297 8.324385182 6.631472007 4.791109194 4.579974346 5.568643859 4.819953071 7.573858007 7.244551419 1 18.48952903 4.561878428 3.071601335 5.403616777 8.339721991 0.246902297 1.796021336 0.460116127 7.434055555 0.457936219 2.588921819 36465.18561 -4.561878428 2.936105215 AAIELPSLEVLS(ph)DQEEDREQCGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAIELPSLEVLSDQEEDREQCGVK 24 1 Q9BQI3-2;Q9BQI3 Q9BQI3-2 EIF2AK1 Eukaryotic translation initiation factor 2-alpha kinase 1 1 AAIELPS(0.001)LEVLS(0.999)DQEEDREQCGVK 138.78 2.51E-06 77511000 72608 53845 46502 61050 62816 51859 67144 79045 94308 TRUE FALSE 63012.66883 53491.28865 68990.52274 74912.33559 61566.0845 53854.04929 60632.38521 62141.84188 83159.01568 0.757737069 0.643241003 0.829621685 0.900832399 0.740341669 0.647603256 0.729113791 0.747265241 1 16.34358506 1.238338157 24.77879496 1.000000314 0.748858635 0.519646251 0.075696907 4.196491613 466241.3853 0.109915407 0.019468424 17.31163781 -1.238338157 -0.251141679 AAIPPPVYEEQDRPRS(ph)PTGPSNSFLANMGGTVAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 AAIPPPVYEEQDRPRSPTGPSNSFLANMGGTVAHK 35 2 H0Y6J6;Q5W012;Q96I25 H0Y6J6 RBM17 Splicing factor 45 1 AAIPPPVYEEQDRPRS(0.998)PT(0.002)GPSNSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.909)PT(0.088)GPS(0.003)NSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.939)PT(0.061)GPS(0.001)NSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.998)PT(0.002)GPSNSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.996)PT(0.004)GPSNSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.999)PT(0.001)GPSNSFLANMGGTVAHK;AAIPPPVY(0.003)EEQDRPRS(0.403)PT(0.403)GPS(0.077)NS(0.114)FLANMGGTVAHK;AAIPPPVY(0.128)EEQDRPRS(0.843)PT(0.028)GPS(0.001)NSFLANMGGTVAHK 299.35 1.35E-90 3383234000 1803207 1620125 655944 694686 1608407 1417861 1754790 1969590 246329 TRUE FALSE 1564908.626 1609482.292 973160.7124 852425.0739 1576402.847 1472407.03 1584610.736 1548408.506 217208.2662 7.204645814 7.409857461 4.480311589 3.924459638 7.257563788 6.778779904 7.295351891 7.128681301 1 17.72871948 4.270395363 24.91329625 5.725749026 7.307254839 0.122748149 1.973060884 470.4162982 368131.6212 0.493968561 1.306670671 18637.83071 -4.270395363 1.581505813 AAKLS(ph)EGS(ph)QPAEEEEDQETPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAKLSEGSQPAEEEEDQETPSR 22 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 2 AAKLS(1)EGS(1)QPAEEEEDQETPSR 101.59 0.00038663 379930000 643020 439850 426330 404860 528790 505000 745940 702760 540030 TRUE FALSE 558043.2778 436960.5964 632504.614 496789.6509 518268.1136 524427.6768 673598.8536 552480.2429 476188.2686 1.171896316 0.917621506 1.328265847 1.043263103 1.088368084 1.101303227 1.41456415 1.160213889 1 18.86117255 AAKNS(ph)EEEEEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AAKNSEEEEEEK 12 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 AAKNS(1)EEEEEEK;AAKNS(1)EEEEEEK;AAKNS(1)EEEEEEK 225.7 1.03E-11 2125580000 1837780 1306250 1540100 1578240 1016360 927350 1726930 2162190 3635400 TRUE FALSE 1594912.717 1297669.158 2284897.511 1936603.514 996136.4245 963025.7546 1559452.594 1699822.495 3205627.153 0.497535315 0.40480976 0.712777064 0.604126251 0.31074619 0.300417269 0.486473479 0.530262071 1 21.6121752 1.217101073 3.340543289 1.099997633 0.474103554 0.639283127 0.123174071 0.254915226 3.815300516 0.428052558 0.033997925 16.48546013 -1.217101073 -0.625894078 AAKNS(ph)EEEEEEKKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAKNSEEEEEEKKK 14 3 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 AAKNS(1)EEEEEEKKK;AAKNS(1)EEEEEEKKK 111.77 0.0034945 991910000 1604230 878680 1290420 785250 582504 325496 1590800 1698710 715170 TRUE FALSE 1392226.941 872907.8932 1914471.428 963553.0143 570913.31 338018.0417 1436524.461 1335454.086 630623.4173 2.207699401 1.384198349 3.035839418 1.527937257 0.905315747 0.536006169 2.277943415 2.117672844 1 19.26641922 3.516548901 24.97461846 1.463234733 2.152599073 0.251595706 0.654152677 927.3387811 587400.9827 0.191469716 0.283941008 3285.102318 -3.516548901 0.68936434 AAKPGPAEAPS(ph)PTASPSGDAS(ph)PPATAPYDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AAKPGPAEAPSPTASPSGDASPPATAPYDPR 31 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 2 AAKPGPAEAPS(0.992)PT(0.008)ASPS(0.002)GDAS(0.995)PPAT(0.003)APYDPR;AAKPGPAEAPS(0.973)PT(0.034)AS(0.252)PS(0.226)GDAS(0.514)PPAT(0.002)APYDPR;AAKPGPAEAPS(0.715)PT(0.274)AS(0.011)PS(0.001)GDAS(0.955)PPAT(0.044)APYDPR;AAKPGPAEAPS(0.829)PT(0.167)AS(0.004)PS(0.006)GDAS(0.919)PPAT(0.074)APYDPR 126.06 3.56E-06 1939460000 729910 530730 361487 401878 547610 487584 606670 667710 579140 TRUE FALSE 633450.5441 527243.5997 536303.3223 493130.5422 536713.6324 506341.672 547835.2368 524925.4126 510674.729 1.240418819 1.032445057 1.050185748 0.965645085 1.050989215 0.991515035 1.07276747 1.027905598 1 18.96204514 4.741334713 5.016261904 1.024688789 1.251350719 0.82473779 0.031382665 0.064950354 5.14799059 0.007211043 0.051222624 55123.23701 -4.741334713 0.22666193 AAKPGPAEAPS(ph)PTASPSGDASPPATAPYDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAKPGPAEAPSPTASPSGDASPPATAPYDPR 31 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 AAKPGPAEAPS(0.951)PT(0.045)AS(0.005)PSGDASPPATAPYDPR 123.4 4.54E-06 2018900000 200060 153190 81851 125360 140680 134380 160200 169990 154780 TRUE FALSE 173621.5641 152183.6848 121434.4174 153824.904 137880.7432 139549.6856 144663.8287 133638.9614 136482.0847 1.272119813 1.115045137 0.889746208 1.127070299 1.010247928 1.022476216 1.059947384 0.979168523 1 17.05835206 4.583066128 3.663403005 1.01571868 1.267936328 0.651255551 0.060694834 0.140783599 3.134593884 0.014029531 0.071925752 38288.3039 -4.583066128 0.252217648 AAKPGPAEAPSPTAS(ph)PSGDASPPATAPYDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAKPGPAEAPSPTASPSGDASPPATAPYDPR 31 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 AAKPGPAEAPS(0.036)PT(0.217)AS(0.454)PS(0.017)GDAS(0.275)PPAT(0.001)APYDPR 103.96 9.94E-05 1999800000 299730 224550 164010 174160 210990 184400 247600 303900 234550 TRUE FALSE 260119.9211 223074.9163 243325.7846 213705.6899 206791.7118 191493.9873 223587.7901 238913.35 206821.7662 1.257700898 1.078585298 1.176499887 1.033284329 0.999854685 0.925888947 1.081065084 1.155165408 1 17.6580285 5.929881884 0.82276471 1.048039365 2.422565647 0.467892098 0.071008323 15.76221164 1.822837595 0.027274867 30.893025 850906.5837 -5.929881884 1.374526283 AAKPGPAEAPSPTASPSGDAS(ph)PPATAPYDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AAKPGPAEAPSPTASPSGDASPPATAPYDPR 31 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 AAKPGPAEAPSPTAS(0.003)PS(0.035)GDAS(0.957)PPAT(0.005)APYDPR;AAKPGPAEAPSPTASPS(0.002)GDAS(0.977)PPAT(0.021)APYDPR;AAKPGPAEAPSPTAS(0.003)PS(0.137)GDAS(0.858)PPAT(0.002)APYDPR 112.74 4.98E-05 2075760000 642520 527490 348452 411982 536154 435368 579610 680740 488066 TRUE FALSE 557609.3541 524024.8835 516964.5527 505528.8099 525485.5844 452116.8887 523399.5114 535169.0485 430367.3935 1.295658924 1.217622179 1.201216822 1.174644774 1.221016258 1.050537042 1.216169067 1.243516718 1 18.71520925 7.999999999 0.466194973 1.152836816 4.68994293 0.295235537 0.074803603 154.4684249 1.860025077 0.052620284 523.4793347 99999999.67 -7.999999999 3.537106114 AALAGGTTMIIDHVVPEPGTSLLAAFDQWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AALAGGTTMIIDHVVPEPGTSLLAAFDQWR 30 0 A0A1C7CYX9;Q16555-2;Q16555 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 0 ; 232.32 6.00E-36 352800000 346320 312620 222905 241442 303240 332120 323670 383750 314640 FALSE TRUE 300552.9345 310566.3786 330702.6036 296265.0963 297206.1173 344896.8713 292280.5332 301688.0488 277443.6176 1.083293741 1.119385558 1.191963277 1.067838932 1.071230688 1.243124186 1.053477228 1.087385075 1 18.08183509 1.264472756 1.405025491 0.955710253 1.124078052 0.297617184 0.058430785 1.54862679 2.805979481 0.373253067 0.016853789 18.38538616 -1.264472756 0.168367799 AALAPAKES(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 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 120.53 0.0002665 20722690000 19997130 16515340 10367770 13522660 15505610 12654150 17109320 20275000 17034450 TRUE FALSE 17354458.6 16406849.64 15381658.25 16593186.63 15197078.7 13140963.34 15450060.78 15939349.03 15020656.73 1.155372826 1.092285773 1.024033671 1.104691155 1.01174529 0.87485944 1.028587568 1.061161927 1 23.84044456 3.18535369 6.349610754 0.999323284 1.088915157 0.425416934 0.056907908 0.234800841 20.31863188 0.018599362 0.021374464 1532.33489 -3.18535369 0.089591873 AALCAVHVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AALCAVHVIR 10 0 O43747;O43747-2;H3BNR4;H3BR36;H3BUN9 O43747 AP1G1 AP-1 complex subunit gamma-1 0 ; 122.52 0.00048646 794630000 1396250 1608850 838520 1469610 1629170 1577010 2332700 2776700 2639300 FALSE TRUE 1211732.025 1598281.358 1244031.077 1803307.412 1596752.704 1637678.595 2106475.113 2182924.313 2327284.961 0.520663368 0.686757911 0.534541793 0.774854581 0.686101071 0.703686322 0.905121267 0.93797036 1 21.15021644 1.230940718 0.326041836 1.425059298 0.52925124 0.823243006 0.067465962 3.743789395 0.403181114 1.405376458 0.153902834 17.01926177 -1.230940718 -0.895808057 AALCHFCIDMLNAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AALCHFCIDMLNAK 14 0 P54920;M0R0Y2;M0R2M1;M0R0I4 P54920 NAPA Alpha-soluble NSF attachment protein 0 65.295 0.071594 0 145590 159730 96326 99085 128270 135980 114410 142450 132030 FALSE TRUE 126349.9126 158680.7231 142909.5758 121583.7637 125717.678 141211.2386 103314.5358 111988.176 116421.5638 1.085279294 1.362983952 1.227518091 1.044340582 1.079848731 1.212930268 0.887417523 0.961919531 1 16.82899878 2.803744883 0.651465942 0.931605403 1.237955515 0.436306561 0.104990445 0.72537923 0.820560554 0.133599338 0.100761154 636.4215589 -2.803744883 0.306350112 AALEAIDELDLFGAHGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AALEAIDELDLFGAHGGR 18 0 P46019 P46019 PHKA2 "Phosphorylase b kinase regulatory subunit alpha, liver isoform" 0 106.19 0.00045625 22475000 17123 15762 12728 9272.2 16251 19014 12565 16408 15745 FALSE TRUE 14860.15217 15658.45838 18883.30337 11377.59473 15927.63689 19745.48088 11346.44823 12899.27689 13883.64404 1.070335146 1.127834907 1.360111461 0.819496286 1.147223082 1.422211693 0.817252892 0.929098791 1 13.76109866 2.205192306 24.99995933 0.914202338 1.149832391 0.317916477 0.167107058 229.0529344 171607.8301 0.067255805 0.045346834 160.3955466 -2.205192306 0.235630053 AALEEVYPDLTPEETRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AALEEVYPDLTPEETRR 17 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ;; 240.2 4.17E-20 755309000 685311 648971 382626 442191 578327 603528 606957 706816 425103 FALSE TRUE 594745.415 644707.8668 567665.2134 542597.225 566819.4242 626746.1127 548094.4036 555668.8988 374847.8076 1.586631702 1.719919001 1.514388511 1.447513401 1.512132158 1.672001543 1.462178496 1.482385351 1 18.51594544 0.844968891 1.580444509 2.58E-10 1.56556161 0.805982702 0.085502942 1.424837068 1.363818384 4.787204077 0.024771368 6.99791867 -0.844968891 1.565561609 AALHS(ph)PVSEGAPVIPPSSGLPLPTPDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AALHSPVSEGAPVIPPSSGLPLPTPDAR 28 0 M0R344;Q9NRA0-4;Q9NRA0-2;Q9NRA0;Q9NRA0-5;E9PCV4;Q9NRA0-3 M0R344 SPHK2 Sphingosine kinase 2 1 AALHS(0.96)PVS(0.04)EGAPVIPPSSGLPLPTPDAR;AALHS(0.995)PVS(0.005)EGAPVIPPSSGLPLPTPDAR 107.71 0.0005221 227120000 89995 109213 90485 101500 142701 145570 125834 153570 149710 TRUE FALSE 78101.93273 108495.5726 134243.8487 124547.1263 139861.5293 151170.1721 113630.638 120730.2506 132011.4544 0.59162997 0.821864839 1.016910611 0.943456967 1.059465105 1.145129207 0.860763474 0.914543751 1 17.01030359 4.598644106 2.332554404 0.984212259 0.553404552 0.728394546 0.079012123 0.244465437 1.965569069 0.022170654 0.188401097 39686.61933 -4.598644106 -0.430807706 AALLELWELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AALLELWELR 10 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 98.033 0.013151 70547000 126260 130770 85363 112300 131740 111860 127230 147530 208970 FALSE TRUE 109574.4211 129910.9633 126644.8323 137799.4314 129118.6317 116163.3266 114891.2542 115981.8576 184265.8047 0.594654126 0.705019379 0.687294273 0.747829646 0.700719442 0.63041174 0.623508276 0.629426918 1 17.49142884 1.23475807 24.99995869 1.000000477 0.665852134 0.837468769 0.04639789 46.18091549 303572.7935 0.088924041 0.012178263 17.16951667 -1.23475807 -0.334148343 AALLELWELRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AALLELWELRR 11 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 160.91 0.0019579 0 145640 120830 95196 88130 104170 117260 80834 111800 140120 FALSE TRUE 126393.305 120036.2598 141233.104 108141.2635 102097.2208 121771.0681 72994.73112 87892.44003 123555.1732 1.022970562 0.971519497 1.143077221 0.875246747 0.826328984 0.985560255 0.590786522 0.711361878 1 16.91479589 3.254696699 1.206792131 0.775055884 1.039745663 0.345403855 0.130403386 0.470455368 1.475728403 0.054511257 0.078578505 1797.615065 -3.254696699 0.264689779 AALLKAS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AALLKASPK 9 1 P50914 P50914 RPL14 60S ribosomal protein L14 1 AALLKAS(1)PK 63.727 0.04492 2715200000 2981500 3073100 1951400 1761500 3061900 1715800 4236200 4553300 1386700 TRUE FALSE 2587487.221 3052912.604 2895103.567 2161475.498 3000974.181 1781807.936 3825373.976 3579612.229 1222765.906 2.116093693 2.496726961 2.367667886 1.767693626 2.454250782 1.45719465 3.128459796 2.927471409 1 20.2217168 2.233001133 24.99988763 2.504224896 2.139328298 0.011297416 0.642435286 409.8920096 1843178.015 0.252913502 0.175939444 171.0019778 -2.233001133 -0.364896599 AALPSHVVTMLDNFPTNLHPMSQLSAAVTALNSESNFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AALPSHVVTMLDNFPTNLHPMSQLSAAVTALNSESNFAR 39 0 O75390;B4DJV2;A0A0C4DGI3;F8VPA1;F8VX68;F8VPF9;F8VRI6;F8VR34;F8W1S4;H0YH82;F8VRP1 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 262.77 5.19E-63 880740000 36038 31318 12324 33156 40876 40769 33869 39848 28223 FALSE TRUE 31275.48699 31112.27 18283.92762 40684.57656 40062.64757 42337.40981 30584.38959 31326.8153 24886.50909 1.256724552 1.250166099 0.734692341 1.63480448 1.609813872 1.701219309 1.228954591 1.258787047 1 14.60307625 3.722794558 24.88404867 1.400090425 1.09749145 0.266309157 0.2537207 1152.389699 1818851.38 0.074372488 0.110718634 5281.953306 -3.722794558 -0.302598975 AALS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AALSSPR 7 0 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 AALS(0.5)S(0.5)PR 77.923 0.038531 295320000 659780 632370 375000 454430 483170 631440 561140 616050 611940 TRUE FALSE 572588.4013 628215.9198 556351.2543 557615.277 473555.8623 655731.9054 506720.7292 484312.5016 539597.1503 1.061140521 1.164231352 1.031049282 1.033391812 0.877610013 1.215224923 0.939072285 0.897544587 1 19.0415232 6.530169376 0.092574302 0.732393012 1.626587304 0.167645058 0.097580343 353.0065802 4.513432888 10.22398405 44.92689597 3389763.319 -6.530169376 0.894194292 AALS(ph)SSELLELGDSLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AALSSSELLELGDSLMR 17 0 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 AALS(0.972)S(0.014)S(0.014)ELLELGDSLMR;AALS(0.979)S(0.02)SELLELGDSLMR;AALS(0.969)S(0.01)S(0.021)ELLELGDSLMR;AALS(0.976)S(0.023)SELLELGDSLMR;AALS(0.959)S(0.018)S(0.023)ELLELGDSLMR;AALS(0.986)S(0.014)SELLELGDSLMR 336.71 3.29E-72 282072000 184453.2 196075.2 187698.5 238246.5 311659 342886 305288.2 360708 350890 TRUE FALSE 160077.2423 194787.1691 278470.1224 292344.0092 305457.5957 356077.0463 275681.3974 283573.4012 309408.1839 0.517365896 0.629547566 0.90000891 0.944848987 0.987231791 1.15083267 0.890995816 0.916502588 1 18.23915183 4.281470464 2.030616866 0.977466544 0.50839861 0.856162232 0.069185801 0.136058908 1.038020783 0.020218752 0.08438286 19119.23293 -4.281470464 -0.469067934 AALSEEELEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AALSEEELEKK 11 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 165.7 3.41E-05 137800000 311420 278780 173870 251680 239460 183150 324650 456780 469550 FALSE TRUE 270265.058 276948.6758 257954.1136 308827.7907 234695.2145 190195.899 293165.493 359101.1517 414040.3339 0.652750556 0.668892987 0.623016872 0.745888179 0.566841429 0.45936563 0.708060227 0.867309589 1 18.65941179 1.660466634 2.422459048 0.983691639 0.623749285 0.747271848 0.075857169 0.13527188 1.709794351 0.08064584 0.022037598 45.75795789 -1.660466634 -0.359942354 AALSEMVEYITHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AALSEMVEYITHNR 14 0 H0YJ75;Q13362-3;Q13362;Q13362-4;Q13362-5;Q96B13;Q13362-2;G3V2U3 H0YJ75 PPP2R5C Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform 0 ; 275.85 4.41E-33 407570000 504540 536170 328910 391810 471750 520550 440810 534040 442540 FALSE TRUE 437863.7607 532647.864 487971.9761 480776.4489 462363.098 540575.8953 398060.314 419839.7019 390223.4253 1.122084765 1.364981775 1.250493805 1.232054299 1.184867612 1.385298422 1.020083081 1.075895691 1 18.57394086 2.219536982 24.99996509 1.040642997 1.256897256 0.644653235 0.07853332 142.9390519 187842.3669 0.029768511 0.0201058 165.7818502 -2.219536982 0.216254259 AALSRDEILRYS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AALSRDEILRYSR 13 2 O95396 O95396 MOCS3 Adenylyltransferase and sulfurtransferase MOCS3;Molybdopterin-synthase adenylyltransferase;Molybdopterin-synthase sulfurtransferase 1 AALSRDEILRY(0.439)S(0.561)R 65.295 0.046448 208920000 139860 132760 81667 88056 112960 156950 118740 122620 106760 TRUE FALSE 121377.1466 131887.8908 121161.4344 108050.4607 110712.317 162987.9681 107224.6131 96398.66723 94138.95442 1.289340288 1.400991668 1.287048864 1.147776299 1.176052121 1.731355198 1.139003654 1.024004014 1 16.52250421 2.010627104 24.99949759 1.034052664 1.332496718 0.429526178 0.159012485 196.9167701 463230.7009 0.065357985 0.044015859 102.4771655 -2.010627104 0.298444055 AALSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AALSSPR 7 0 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 AALS(0.069)S(0.931)PR 73.26 0.051793 307490000 663350 659370 406000 549120 456320 611840 574890 640160 561840 TRUE FALSE 575686.6168 655038.5551 602342.958 673806.0888 447240.1248 635377.8807 519137.2563 503266.7657 495419.9153 1.162017511 1.322188582 1.215823061 1.360070655 0.902749589 1.282503713 1.047873209 1.015838787 1 18.91829234 2.393357583 0.551930703 0.950350973 1.269377728 0.339359303 0.123471791 1.500463512 0.982343068 0.303170868 0.119845156 247.3760115 -2.393357583 0.319026755 AVEES(ph)S(ph)DEERQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AVEESSDEERQR 12 1 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 AVEES(1)S(1)DEERQR;AVEES(1)S(1)DEERQR;AVEES(1)S(1)DEERQR;AVEES(1)S(1)DEERQR 126.71 0.0037846 1351970000 2727230 2258630 1346670 1568260 2236010 2292450 2198530 2518880 1204950 TRUE FALSE 2366819.646 2243792.911 1997924.116 1924357.402 2191517.776 2380642.035 1985316.899 1980237.114 1062502.184 2.227590382 2.111800752 1.880395304 1.811156186 2.062600726 2.240599663 1.868529712 1.863748747 1 20.01903438 1.008499148 1.7800865 7.92E-11 2.031044291 0.831276385 0.144583753 0.751051493 1.323031767 3.198089454 0.041503676 10.1976276 -1.008499148 2.031044291 AAMIWIVGEYAER ddPTM_MDA-MB-175_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 ; 174.98 4.43E-05 334130000 396560 368820 256130 299970 335940 326200 390790 433780 387000 FALSE TRUE 344153.5912 366397.1971 379995.3247 368082.7733 329255.4513 338749.1251 352891.2459 341019.5227 341249.3009 1.008510758 1.07369362 1.113541694 1.078633047 0.964853116 0.992673463 1.03411566 0.999326656 1 18.38046656 3.253786964 24.99974371 1.000753514 1.072169499 0.569037614 0.030327767 178.9026144 293734.083 0.008970784 0.011535461 1793.853467 -3.253786964 0.071415985 AANCNLHVPGPMAVNQFS(ph)PSLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AANCNLHVPGPMAVNQFSPSLAR 23 0 Q99990;H0Y5G3 Q99990 VGLL1 Transcription cofactor vestigial-like protein 1 1 AANCNLHVPGPMAVNQFS(0.957)PS(0.043)LAR;AANCNLHVPGPMAVNQFS(0.997)PS(0.003)LAR;AANCNLHVPGPMAVNQFS(0.984)PS(0.016)LAR;AANCNLHVPGPMAVNQFS(0.991)PS(0.009)LAR 182.64 2.50E-17 1663190000 1191130 1275100 899030 1038170 1224580 1445790 1032080 1278210 1173590 TRUE FALSE 1033719.153 1266723.784 1333803.915 1273902.366 1200213.254 1501410.477 931989.0405 1004874.739 1034849.527 0.998907692 1.224065674 1.288886819 1.231002511 1.159794948 1.450849073 0.900603437 0.97103464 1 19.98098958 2.212955336 24.99994657 0.957733432 1.225648722 0.554519578 0.113392649 160.1428641 156355.7056 0.044616575 0.03009249 163.2884008 -2.212955336 0.26791529 AANWYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AANWYER 7 0 O75489 O75489 NDUFS3 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial" 0 109.86 0.016129 228840000 169990 178390 138560 188290 187010 247490 176570 208050 205470 FALSE TRUE 147525.3908 177218.1443 205568.0795 231044.1223 183288.8669 257011.1004 159446.2686 163560.1265 181179.5707 0.814249588 0.978135359 1.134609596 1.275221712 1.01164202 1.41854349 0.880045515 0.902751485 1 17.46706076 AAPAQVRPPS(ph)PGNIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAPAQVRPPSPGNIR 15 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 AAPAQVRPPS(1)PGNIR;AAPAQVRPPS(1)PGNIR 105.91 0.00077406 314190000 162399 169304 111864 133730 160303 151239 166077 181011 357180 TRUE FALSE 140937.5607 168191.8309 165961.8046 164095.4404 157113.2839 157057.2622 149970.8781 142303.2063 314954.5873 0.44748534 0.534019308 0.526938839 0.521013019 0.498844247 0.498666375 0.476166673 0.451821348 1 18.2647843 1.235591267 24.99999999 1.000000684 0.494885269 0.967131962 0.02929394 14.41623344 121352.9659 0.052640758 0.007706867 17.20248812 -1.235591267 -0.505115416 AAPAQVRPPS(ph)PGNIRPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AAPAQVRPPSPGNIRPVK 18 2 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 AAPAQVRPPS(1)PGNIRPVK;AAPAQVRPPS(1)PGNIRPVK;AAPAQVRPPS(1)PGNIRPVK 154.84 1.20E-08 9493200000 1297550 1163110 1151210 1345030 1255480 1198350 1172640 1401830 2906940 TRUE FALSE 1126075.48 1155469.454 1707939.007 1650439.619 1230498.404 1244451.3 1058917.553 1102059.564 2563284.865 0.439309534 0.450776841 0.6663087 0.643876785 0.480047466 0.485490831 0.413109588 0.429940339 1 21.28956239 1.233610853 24.97694133 1.000000775 0.500551729 0.766156357 0.086618577 82.21063075 414792.3217 0.189864433 0.023546268 17.12422213 -1.233610853 -0.499449046 AAPAQVRPPS(ph)PGNIRPVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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;AAPAQVRPPS(1)PGNIRPVKR 105.96 0.0017871 16971900000 4114100 3478400 2424430 2943500 3702900 3442900 4094900 4817100 2313570 TRUE FALSE 3570411.261 3455550.161 3596892.457 3611866.664 3629219.535 3575350.591 3697777.228 3787000.652 2040062.39 1.750148073 1.693845334 1.763128655 1.770468727 1.778974776 1.752569239 1.812580461 1.856316096 1 20.96018184 1.234896063 24.99999997 0.999998902 1.77488833 0.970869686 0.042037021 18.58463642 126767.0977 0.085760717 0.011869384 17.174973 -1.234896063 0.774889427 AAPDEDREPESAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAPDEDREPESAR 13 1 Q99856 Q99856 ARID3A AT-rich interactive domain-containing protein 3A 0 86.467 0.0069925 0 120990 136000 85491 104320 132370 153290 132940 128320 116080 FALSE TRUE 105000.865 135106.607 126834.7336 128007.4504 129736.096 159187.1655 120047.4993 100879.7666 102357.1546 1.02582829 1.319952743 1.239138915 1.250596022 1.267484393 1.555212882 1.172829586 0.985566343 1 16.64325242 1.875515181 4.169981519 0.998436963 1.280684491 0.446762184 0.127928714 0.196549408 5.355607144 0.071077357 0.034158602 75.07842969 -1.875515181 0.282247528 AAPEAS(ph)SPPAS(ph)PLQHLLPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 2 AAPEAS(0.5)S(0.5)PPAS(1)PLQHLLPGK;AAPEAS(0.5)S(0.5)PPAS(1)PLQHLLPGK;AAPEAS(0.5)S(0.5)PPAS(1)PLQHLLPGK;AAPEAS(0.503)S(0.503)PPAS(0.993)PLQHLLPGK;AAPEAS(0.503)S(0.503)PPAS(0.994)PLQHLLPGK 172.49 3.31E-12 1406980000 1065511 1250364 874988 1283616 1561655 1281105 1739555 2257820 1844580 TRUE FALSE 924701.0217 1242150.277 1298135.123 1575080.632 1530581.121 1330389.938 1570853.224 1775002.763 1626515.854 0.568516452 0.763687777 0.798107882 0.968377055 0.941018261 0.8179385 0.965777997 1.0912914 1 20.63335345 5.376101794 0.433323813 1.02371509 6.99E-21 0.794624433 0.067394498 4.957191138 0.512732912 0.071621462 2.909351652 237739.746 -5.376101794 -1.02371509 AAPEAS(ph)SPPASPLQHLLPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 AAPEAS(0.5)S(0.5)PPASPLQHLLPGK;AAPEAS(0.499)S(0.499)PPAS(0.002)PLQHLLPGK;AAPEAS(0.5)S(0.5)PPASPLQHLLPGK;AAPEAS(0.858)S(0.142)PPASPLQHLLPGK 198.6 9.91E-22 12223862000 882007 978101 534503 856882 1125254 937217 1223182 1550657 1276083 TRUE FALSE 765447.5402 971675.7901 792990.4386 1051450.155 1102863.647 973272.3445 1104557.998 1219061.068 1125225.921 0.680261204 0.863538398 0.704738865 0.934434707 0.980126414 0.864957273 0.981632201 1.083392272 1 20.10178326 6.048014279 0.176659252 1.183424614 1.68E-15 0.687889482 0.071366537 32.56617003 0.912443761 0.889445691 9.312293365 1116899.969 -6.048014279 -1.183424614 AAPEASS(ph)PPAS(ph)PLQHLLPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 2 AAPEAS(0.455)S(0.545)PPAS(1)PLQHLLPGK;AAPEAS(0.097)S(0.906)PPAS(0.997)PLQHLLPGK;AAPEAS(0.46)S(0.55)PPAS(0.99)PLQHLLPGK;AAPEAS(0.088)S(0.912)PPAS(1)PLQHLLPGK;AAPEAS(0.083)S(0.917)PPAS(1)PLQHLLPGK;AAPEAS(0.085)S(0.915)PPAS(1)PLQHLLPGK 189.51 1.14E-17 5940570000 1811585 2117096 1591374 2193817 2678330 2115518 2939450 3819970 3146510 TRUE FALSE 1572179.452 2103188.657 2360967.789 2691956.68 2625036.473 2196903.346 2654382.591 3003099.143 2774533.172 0.566646479 0.758033343 0.850942354 0.970237699 0.946118251 0.791810085 0.956695208 1.082379974 1 21.40381362 5.26834759 0.60820807 0.987792023 4.38E-19 0.766750014 0.071170155 3.468531495 0.624623619 0.040425097 2.755740527 185501.5701 -5.26834759 -0.987792023 AAPEASS(ph)PPASPLQHLLPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 AAPEAS(0.423)S(0.577)PPASPLQHLLPGK;AAPEAS(0.249)S(0.751)PPASPLQHLLPGK;AAPEAS(0.105)S(0.895)PPASPLQHLLPGK 231.89 4.39E-26 11816760000 907230 1006070 555330 974300 1242360 1044880 1372030 1675760 1354310 TRUE FALSE 787337.2569 999461.0599 823889.4455 1195529.706 1217639.467 1085077.21 1238970.742 1317411.765 1194205.015 0.659298234 0.836925861 0.689906202 1.001109266 1.019623475 0.908618869 1.037485797 1.103170518 1 20.1876191 3.728300666 20.81492001 1.018851048 0.739531717 0.804856277 0.0655444 30.02971969 60923.44711 0.018433232 0.027836441 5349.345711 -3.728300666 -0.279319331 AAPFSLEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AAPFSLEYR 9 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;;;; 195.81 7.13E-05 3131190000 1925266 2283520 1450124 1562136 2077210 2306770 2081750 2274390 2019300 FALSE TRUE 1670837.22 2268519.407 2151408.817 1916842.855 2035877.585 2395512.935 1879862.205 1788029.398 1780580.654 0.938366491 1.274033502 1.208262491 1.076526834 1.14337847 1.345354915 1.055757963 1.004183323 1 20.76391636 2.016097691 24.89158798 1.010664469 1.169211781 0.289539145 0.108649333 253.8652978 392546.0597 0.042560361 0.02868505 103.7761826 -2.016097691 0.158547313 AAPGAEFAPNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAPGAEFAPNKR 12 1 Q15233;Q15233-2 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ; 162.68 9.94E-05 1631680000 1445900 1167840 736360 952390 1165610 1062200 1220890 1488890 1257950 FALSE TRUE 1254820.652 1160168.382 1092466.159 1168644.706 1142416.641 1103063.521 1102488.276 1170502.46 1109236.584 1.131247084 1.045916082 0.984881111 1.053557665 1.029912516 0.994434855 0.993916259 1.05523247 1 20.08113567 4.68937068 3.345724731 1.019173736 1.140514643 0.680560678 0.024677823 0.159562243 2.992711948 0.006065049 0.045941514 48906.96128 -4.68937068 0.121340907 AAPGEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAPGEFR 7 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 102.98 0.044286 0 399140 358930 261570 261490 320390 345180 389470 387390 365040 FALSE TRUE 346392.6377 356572.1652 388066.1269 320865.3011 314014.8658 358459.298 351699.2593 304549.6632 321885.3871 1.076136574 1.10776127 1.205603431 0.996830903 0.975548684 1.113624018 1.092622634 0.946143178 1 18.29618756 3.718898511 24.95142283 1.019490531 1.127626517 0.429597842 0.05919809 773.1862492 981181.9347 0.017256712 0.025633085 5234.780924 -3.718898511 0.108135986 AAPGYHMAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAPGYHMAK 9 0 P11216;H0Y4Z6;P11217;P11217-2;E9PK47;P06737-2;P06737 P11216;E9PK47 PYGB;PYGM;PYGL "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, muscle form;Glycogen phosphorylase, liver form" 0 83.206 0.016326 323150000 592080 615850 395970 478440 537660 505070 609670 685310 690770 FALSE TRUE 513835.1279 611804.4408 587462.4164 587077.1145 526961.6179 524500.3697 550544.2972 538761.7896 609107.9575 0.843586299 1.004426938 0.964463539 0.963830972 0.86513665 0.861095908 0.903853398 0.884509524 1 19.21633843 3.252459611 24.9994892 0.89859681 0.949843844 0.113206898 0.055491692 421.5108238 758147.7743 0.015461142 0.019855475 1788.379204 -3.252459611 0.051247035 AAPLDSIHSLAAYYIDCIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAPLDSIHSLAAYYIDCIR 19 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 267.38 1.23E-31 26874000000 3822600 4027000 1981890 2668300 3998600 4873300 4030100 4262100 4533800 FALSE TRUE 3317433.725 4000546.372 2940338.633 3274178.297 3919035.683 5060779.004 3639261.522 3350683.083 3997819.329 0.829810817 1.000682133 0.735485621 0.818991062 0.980293345 1.265884871 0.910311653 0.838127691 1 21.93078184 3.228636923 23.41892387 0.985526282 0.84936263 0.261851881 0.126223643 159.2404069 375790.072 0.04122066 0.047369015 1692.921899 -3.228636923 -0.136163651 AAPPPPPPPPPLES(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAPPPPPPPPPLESSPR 17 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 AAPPPPPPPPPLES(0.5)S(0.5)PR 125.96 4.74E-05 262430000 111510 88764 83939 75274 97177 107010 94102 106340 155080 TRUE FALSE 96773.67097 88180.90344 124532.1812 92366.11219 95243.36782 111126.7439 84976.00252 83600.01854 136746.6191 0.707686023 0.644848875 0.910678319 0.675454449 0.696495229 0.812647104 0.621412091 0.611349802 1 17.06114564 1.226743043 24.98705208 1.00000066 0.707218206 0.501932101 0.090724744 479.0182987 1012770.028 0.36273424 0.022587277 16.85555445 -1.226743043 -0.292782454 AAPPPPPPPPPLESS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAPPPPPPPPPLESSPR 17 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 AAPPPPPPPPPLES(0.203)S(0.797)PR 128.11 3.99E-05 244980000 140350 117420 96158 122410 121220 125790 138860 138620 192070 TRUE FALSE 121802.3919 116648.6603 142660.3304 150205.0614 118807.9592 130629.2227 125393.3786 108977.1917 169363.7034 0.719176479 0.688746514 0.842331194 0.886878702 0.701495992 0.771294085 0.740379291 0.64345069 1 17.3697652 4.263986777 24.90073611 0.779869814 0.703961428 0.112172937 0.10036506 567.9743892 556226.9533 0.025012536 0.066122241 18364.82427 -4.263986777 -0.075908386 AAPQS(ph)PSVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 AAPQSPSVPK 10 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 1 AAPQS(0.995)PS(0.005)VPK;AAPQS(0.992)PS(0.008)VPK;AAPQS(0.999)PS(0.001)VPK;AAPQS(0.998)PS(0.002)VPK;AAPQS(0.994)PS(0.006)VPK;AAPQS(0.997)PS(0.003)VPK;AAPQS(0.986)PS(0.014)VPK;AAPQS(0.987)PS(0.013)VPK 240.52 2.93E-12 6879533000 7270490 6480390 4773720 5602490 6239930 5207890 7352620 8638060 8047310 TRUE FALSE 6309676.325 6437819.891 7082306.959 6874620.983 6115767.601 5408240.898 6639564.044 6790878.09 7095966.179 0.889191995 0.907250645 0.998075073 0.968806898 0.861865382 0.762157085 0.935681467 0.95700542 1 22.7585677 1.661638472 2.795015642 0.989789102 0.90190683 0.214041238 0.063311044 0.402272596 7.078299118 0.062090177 0.018858249 45.88159132 -1.661638472 -0.087882272 EGIREETVSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EGIREETVSLR 11 1 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ;;; 234.79 1.51E-15 3858070000 3152860 2760010 1544200 1912400 2671710 2682520 2545040 2980680 1405360 FALSE TRUE 2736201.563 2741879.313 2290980.285 2346639.649 2618548.198 2785718.28 2298222.413 2343284.778 1239219.942 2.208003172 2.212584885 1.848727742 1.893642581 2.113061701 2.247961146 1.854571844 1.890935337 1 20.24100083 1.011061027 1.724546965 1.22E-12 2.060881227 0.831234455 0.148162412 0.75851171 1.263309875 3.172764564 0.042410193 10.2579606 -1.011061027 2.060881227 AAQEEYVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AAQEEYVK 8 0 P04075;J3KPS3;P04075-2;H3BQN4;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;; 152.47 0.0010624 1126140000 941370 926710 707240 834140 826220 753540 944250 1084480 1801100 FALSE TRUE 816965.5694 920622.381 1049263.63 1023544.236 809779.8385 782529.1714 852676.7803 852572.3914 1588176.01 0.51440493 0.579672766 0.660672131 0.644477835 0.509880412 0.492721944 0.536890606 0.536824877 1 20.59893938 1.236716833 24.99999968 1.000000552 0.560144816 0.861015272 0.055625962 18.71973947 253749.746 0.094069797 0.014971117 17.24712983 -1.236716833 -0.439855736 AAQEEYVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 AAQEEYVKR 9 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;;;;;; 157.75 0.00010873 48085920000 24315510 21214430 11671970 13603880 18630720 16272440 23158830 24743480 9002230 FALSE TRUE 21102153.75 21075071.01 17316573.73 16692848.88 18260005.12 16898451.3 20912890.23 19452279.36 7937996.625 2.658372728 2.654960944 2.1814791 2.102904507 2.300329162 2.128805553 2.634529998 2.450527542 1 22.92034352 1.236925223 24.99953712 0.999998285 2.385368641 0.807821105 0.212903668 19.21599704 293652.0599 0.342111241 0.055281769 17.2554076 -1.236925223 1.385370356 AAQENKHDSYIPCSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAQENKHDSYIPCSER 16 1 Q14161-3;Q14161;F8VXI9;Q14161-6;Q14161-4;R4GNG3;Q14161-9;Q14161-5;F8WAK2;Q14161-11;Q14161-7;Q14161-10;Q14161-8 Q14161-3 GIT2 ARF GTPase-activating protein GIT2 0 101.67 0.00098331 62074000 71178 78265 20816 42054 97926 95462 76895 90515 58159 FALSE TRUE 61771.64696 77750.87206 30882.68723 51603.00346 95977.46419 99134.48491 69437.73474 71159.07164 51283.50927 1.20451287 1.516098901 0.60219528 1.006229959 1.871507343 1.933067497 1.353997332 1.387562447 1 15.64620737 3.268372907 24.99864735 1.503568874 1.078957285 0.278553429 0.341354693 299.9672127 251531.0331 0.103908214 0.134126241 1855.123843 -3.268372907 -0.424611589 AAQGQAGS(ph)PDKSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAQGQAGSPDKSK 13 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 AAQGQAGS(0.996)PDKS(0.004)K;AAQGQAGS(1)PDKSK 154.39 2.78E-05 347800000 958990 528560 493610 475840 342070 355640 695550 804910 575520 TRUE FALSE 832257.0417 525087.8546 732321.447 583886.7448 335263.4762 369321.7009 628095.6681 632786.2603 507482.6812 1.639971318 1.034691181 1.44304717 1.150555017 0.660640232 0.727752325 1.237669168 1.24691203 1 18.95299906 3.481054056 24.95654253 1.005984216 1.331785238 0.363359169 0.236656842 220.3085153 1398025.551 0.072565347 0.09592243 3027.290204 -3.481054056 0.325801022 AAQMHSGYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 AAQMHSGYQR 10 0 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ;;;;;;;; 138.25 6.97E-05 2149598000 1325961 1206166 833104 869282 1128468 1287784 1108588 1246316 1208538 FALSE TRUE 1150731.894 1198242.616 1235995.881 1066665.764 1106013.695 1337325.884 1001077.306 979801.0222 1065666.014 1.079824146 1.124407272 1.159834192 1.000938146 1.037861468 1.254920271 0.939391228 0.919425982 1 20.02332393 2.185677809 24.99999568 0.945392126 1.104381953 0.517013627 0.071148318 74.53639419 35235.94382 0.028648377 0.019314749 153.3478917 -2.185677809 0.158989827 AAQQQQPSAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AAQQQQPSASPR 12 0 Q86U86-8;Q86U86 Q86U86-8 PBRM1 Protein polybromo-1 1 AAQQQQPSAS(1)PR;AAQQQQPSAS(1)PR;AAQQQQPS(0.148)AS(0.852)PR 245.72 1.82E-16 702655000 878413 674461 359085 361749 460211 548560 475223 498502 478218 TRUE FALSE 762328.4964 670030.4213 532739.7071 443889.6394 451053.7015 569663.4582 429135.9466 391901.2266 421683.6128 1.807821014 1.588941094 1.263363552 1.052660397 1.069649585 1.350926241 1.017672809 0.929372674 1 18.68580143 4.302940421 1.503367266 1.057685017 1.864745232 0.849223583 0.110129364 0.217303814 0.790351881 0.03552951 0.207460247 20088.17211 -4.302940421 0.807060214 AAS(ph)ADYLRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AASADYLRPR 10 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B0QYZ7 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 AAS(1)ADYLRPR;AAS(1)ADYLRPR;AAS(1)ADYLRPR;AAS(1)ADYLRPR 151.1 1.24E-05 1942210000 2350760 2430500 1662310 1752770 2509050 2696810 2389610 2787450 2745790 TRUE FALSE 2040101.11 2414533.885 2466208.676 2150763.218 2459124.814 2800558.026 2157865.99 2191375.509 2421185.834 0.8426041 0.997252607 1.018595368 0.888309847 1.015669586 1.156688589 0.891243439 0.905083566 1 21.20728238 4.743707685 24.09351384 0.978042704 0.842604004 0.235777469 0.079396986 557.6623321 2610281.69 0.020187756 0.162492129 55425.25309 -4.743707685 -0.135438699 AAS(ph)ALLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AASALLLR 8 0 F5H672;F5H5N2;B4DNC9;B3KQ30;Q9H1K1 F5H672 ISCU "Iron-sulfur cluster assembly enzyme ISCU, mitochondrial" 1 AAS(1)ALLLR;AAS(1)ALLLR;AAS(1)ALLLR;AAS(1)ALLLR;AAS(1)ALLLR;AAS(1)ALLLR 119.68 0.0017282 660696000 1486070 1046800 778794 906472 1014090 1077910 991040 1146030 1294800 TRUE FALSE 1289682.084 1039923.502 1155421.383 1112300.322 993911.593 1119377.895 894929.0933 900960.4029 1141730.219 1.129585661 0.910831197 1.011991593 0.974223423 0.870531038 0.980422412 0.783835865 0.789118469 1 20.12279036 8 0.296908318 0.83845143 2.938771554 0.390339047 0.082448289 77.85698585 1.243696012 0.16762058 84.84817528 99999999.99 -8 2.100320124 AAS(ph)DDGSLK ddPTM_MDA-MB-175_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 170.89 0.00067138 0 734910 566760 443900 513730 460490 425170 728130 862870 717510 TRUE FALSE 637789.7815 563036.9162 658571.5248 630380.2484 451327.1499 441526.565 657516.0647 678351.9654 632686.7852 1.008065596 0.88991414 1.040912407 0.996354378 0.71335005 0.697859629 1.039244189 1.072176599 1 19.27113194 2.054544357 24.99998887 1.045586522 0.892374923 0.263195259 0.114957367 122.6265384 56204.27307 0.050822706 0.034264654 113.3820637 -2.054544357 -0.153211599 AAS(ph)EDMTS(ph)DEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AASEDMTSDEER 12 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 2 AAS(1)EDMT(0.369)S(0.631)DEER 118.16 0.0014628 151840000 168420 166750 111950 127870 183580 182950 181320 203370 173050 TRUE FALSE 146162.8703 165654.6083 166089.3945 156904.8379 179927.1172 189988.2049 163735.6143 159880.9081 152592.2261 0.957865771 1.085603195 1.088452529 1.028262329 1.179136852 1.245071323 1.073027234 1.047765749 1 17.21932194 6.398759353 12.79522372 1.082533127 0.963868449 0 0.083262322 0 0 0.019367524 0 2504720.975 -6.398759353 -0.118664678 AAS(ph)LNYLNQPSAAPLQVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AASLNYLNQPSAAPLQVSR 19 0 Q9NSK0-3;Q9NSK0;Q9NSK0-5 Q9NSK0-3 KLC4 Kinesin light chain 4 1 AAS(1)LNYLNQPSAAPLQVSR;AAS(1)LNYLNQPSAAPLQVSR;AAS(1)LNYLNQPSAAPLQVSR;AAS(1)LNYLNQPSAAPLQVSR;AAS(1)LNYLNQPSAAPLQVSR;AAS(1)LNYLNQPSAAPLQVSR 367.05 4.58E-83 4483470000 3075440 2719730 1595056 1650155 2386880 2401990 2424300 2633970 2773310 TRUE FALSE 2669012.812 2701863.915 2366430.417 2024847.914 2339385.758 2494396.11 2189191.759 2070716.013 2445452.451 1.091418813 1.104852361 0.967686129 0.828005432 0.956626966 1.020014153 0.895209293 0.84676192 1 21.22166998 4.146847029 4.105399795 0.918521015 1.099164503 0.577043216 0.06031698 0.145193163 4.484882079 0.016252114 0.03765068 14023.19679 -4.146847029 0.180643489 AAS(ph)LTEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AASLTEDR 8 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 AAS(0.996)LT(0.004)EDR;AAS(0.996)LT(0.004)EDR;AAS(0.988)LT(0.012)EDR;AAS(0.999)LT(0.001)EDR 154.04 0.00045258 902750000 3421830 1924860 1399590 1479440 960420 942860 1128860 1047750 2994920 TRUE FALSE 2969626.496 1912215.468 2076436.405 1815369.464 941309.521 979132.4343 1019383.331 823696.8161 2640863.969 1.124490519 0.724087075 0.786271625 0.687414984 0.356439988 0.370762162 0.386003726 0.311904296 1 21.33257856 4.503310997 0.808802201 0.457566915 1.288972366 0.44027002 0.211621376 1.669115017 1.080874652 0.083004473 1.175907712 31864.78533 -4.503310997 0.831405451 AVLGDDEITREPR ddPTM_MDA-MB-175_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 ; 119.69 0.00029994 205063000 557780 545260 317820 400800 520210 587650 459950 606630 268490 FALSE TRUE 484067.9598 541678.1512 471518.815 491807.7658 509858.8388 610257.2758 415344.1198 476906.8953 236749.4181 2.044642659 2.287980919 1.991636638 2.077334635 2.153580114 2.577650584 1.754361735 2.014395217 1 17.85300135 1.020241286 1.69441791 2.80E-12 2.15012655 0.732564687 0.211664209 0.925263147 1.521077854 3.938927063 0.056023153 10.47710475 -1.020241286 2.15012655 AAS(ph)PAGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AASPAGPR 8 0 Q6NV74 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 AAS(1)PAGPR;AAS(1)PAGPR;AAS(1)PAGPR 89.886 0.014253 781124000 1097616 1025840 638871 756149 590719 883837 845412 957088 1070720 TRUE FALSE 952563.2646 1019101.189 947831.1525 927844.1875 578964.8476 917838.7813 763424.0744 752422.1793 944140.7014 1.008920877 1.079395463 1.003908794 0.982739316 0.613218821 0.972141949 0.808591424 0.796938611 1 19.84864235 3.456654427 24.99752071 0.833909335 1.028559989 0.423138954 0.105926662 206.1672382 251805.1405 0.028674172 0.03702202 2861.899819 -3.456654427 0.194650654 AAS(ph)PFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AASPFR 6 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 AAS(1)PFR;AAS(1)PFR;AAS(1)PFR;AAS(1)PFR 113.7 0.027186 11732500000 2343210 2336510 1469490 1642040 1650130 2193340 2181420 2317390 2265260 TRUE FALSE 2033548.862 2321161.312 2180140.279 2014890.279 1617295.641 2277719.209 1969866.224 1821834.182 1997463.543 1.01806557 1.162054406 1.091454353 1.008724432 0.809674673 1.140305773 0.986183818 0.912073809 1 20.92973774 3.658241782 4.25184449 0.96789814 1.098049263 0.27553037 0.088374616 0.269233213 9.028373093 0.024121703 0.037198926 4552.414333 -3.658241782 0.130151123 AAS(ph)PPASASDLIEQQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 AASPPASASDLIEQQQK 17 0 Q5VSL9;Q5VSL9-2;Q5VSL9-3 Q5VSL9 STRIP1 Striatin-interacting protein 1 1 AAS(1)PPASASDLIEQQQK;AAS(1)PPASASDLIEQQQK;AAS(1)PPASASDLIEQQQK;AAS(1)PPASASDLIEQQQK;AAS(1)PPASASDLIEQQQK;AAS(1)PPASASDLIEQQQK;AAS(1)PPASASDLIEQQQK 401.1 1.27E-123 3558584000 1974030 1605210 1243570 1403558 1567350 1520290 1997400 2208280 2211810 TRUE FALSE 1713156.934 1594665.27 1844964.611 1722257.296 1536162.801 1578776.54 1803692.455 1736056.507 1950332.342 0.878392312 0.81763771 0.945974474 0.883058369 0.787641557 0.809491032 0.924812873 0.890133681 1 20.89528855 0.829278706 1.178745233 1.217620416 0.858708179 0.439540148 0.048794714 3.752156614 2.207556236 2.115426256 0.01551452 6.749610414 -0.829278706 -0.358912237 AAS(ph)PPRPLLSNASATPVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AASPPRPLLSNASATPVGR 19 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 AAS(0.999)PPRPLLS(0.001)NASATPVGR;AAS(1)PPRPLLSNASATPVGR;AAS(1)PPRPLLSNASATPVGR;AAS(1)PPRPLLSNASATPVGR;AAS(1)PPRPLLSNASATPVGR;AAS(1)PPRPLLSNASATPVGR 167.88 1.04E-11 7070140000 937548 1015627 666854 759566 1021349 982357 967996 1225186 872738 TRUE FALSE 813648.6564 1008955.279 989346.8249 932037.0695 1001026.153 1020148.909 874119.8969 963189.5083 769563.9079 1.057285364 1.311074063 1.285594107 1.211123677 1.300770661 1.325619483 1.135863946 1.251604316 1 19.55368161 0.642240479 1.716163678 1.71E-10 1.244434993 0.416943802 0.085247228 6.094979677 3.724835784 21.25213996 0.022212379 4.387735896 -0.642240479 1.244434993 AAS(ph)PQDLAGGYTSSLACHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AASPQDLAGGYTSSLACHR 19 0 H0YJ92;P51948-2;P51948 H0YJ92 MNAT1 CDK-activating kinase assembly factor MAT1 1 AAS(1)PQDLAGGYTSSLACHR;AAS(1)PQDLAGGYTSSLACHR;AAS(1)PQDLAGGYTSSLACHR 171.91 6.03E-12 1775620000 612870 596350 349829 401502 569040 679580 494330 563420 487302 TRUE FALSE 531877.6767 592432.5376 519007.4745 492669.1657 557717.2173 705723.8823 446389.9527 442937.0175 429693.7127 1.237806514 1.378732153 1.207854477 1.146558935 1.297941303 1.642388198 1.038856142 1.030820337 1 18.71294914 2.049082743 24.99996778 1.022777724 1.310257674 0.524068556 0.132609495 86.93827487 44281.01664 0.05487656 0.036997762 111.9651182 -2.049082743 0.287479951 AAS(ph)PS(ph)PQSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AASPSPQSVR 10 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 AAS(1)PS(1)PQSVR;AAS(1)PS(1)PQSVR;AAS(1)PS(1)PQSVR;AAS(1)PS(1)PQSVR 166.7 7.99E-06 4084400000 4871980 3973980 2592080 3307990 3896170 3837440 3710840 4456420 4735720 TRUE FALSE 4228135.499 3947874.664 3845618.558 4059119.689 3818643.84 3985068.8 3350963.308 3503449.263 4175868.577 1.012516419 0.945402038 0.920914652 0.972042011 0.914454986 0.95430896 0.802458997 0.838974982 1 21.99364488 2.273237101 24.99826603 0.868580717 0.950533276 0.258565616 0.056807319 207.2085529 149375.9081 0.02095039 0.016227329 187.6018433 -2.273237101 0.081952559 AAS(ph)PSPQSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AASPSPQSVR 10 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 AAS(0.972)PS(0.028)PQSVR;AAS(0.999)PS(0.001)PQSVR;AAS(0.843)PS(0.157)PQSVR;AAS(0.966)PS(0.034)PQSVR;AAS(0.999)PS(0.001)PQSVR 179.98 2.15E-06 8769480000 8960190 7983530 5498980 6187170 6999030 7000940 6677410 7949740 9979880 TRUE FALSE 7776078.189 7931085.666 8158305.121 7592061.513 6859762.996 7270270.692 6029835.806 6249749.966 8800069.956 0.883638224 0.90125257 0.927072758 0.862727405 0.779512326 0.826160557 0.685203167 0.710193214 1 23.06908356 3.361078303 3.107575375 0.78085719 0.903481547 0.222183326 0.085197799 0.32119825 6.184758777 0.026111857 0.034895732 2296.562682 -3.361078303 0.122624357 AAS(ph)QDHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AASQDHVR 8 0 Q9Y314;A0A075B6F9;M0R3B2;A0A075B797;M0R1K2 Q9Y314 NOSIP Nitric oxide synthase-interacting protein 1 AAS(1)QDHVR 89.171 0.0079829 0 52114 30066 15600 17908 17047 16462 42185 28143 25040 TRUE FALSE 45227.00286 29868.49447 23144.21218 21974.28511 16707.79805 17095.30379 38093.90519 22124.83846 22079.79973 2.048342984 1.352752056 1.048207523 0.995221215 0.756700616 0.774250854 1.725283094 1.002039816 1 14.43043947 4.706067747 2.168823409 1.053605823 2.272194849 0.591898425 0.264240582 0.446363522 2.527735507 0.070946221 1.026655701 50823.87178 -4.706067747 1.218589026 AAS(ph)SDQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AASSDQLR 8 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 AAS(0.709)S(0.291)DQLR;AAS(0.935)S(0.065)DQLR;AAS(0.933)S(0.067)DQLR 165.58 0.00033926 2136960000 2680560 2313510 1925770 2399240 1775710 2203380 2414400 2680380 6064630 TRUE FALSE 2326317.204 2298312.4 2857078.813 2944024.112 1740376.845 2288145.454 2180251.86 2107201.596 5347676.35 0.435014584 0.429777767 0.534265469 0.550523988 0.325445433 0.427876578 0.407700788 0.3940406 1 22.35048072 1.23590338 24.99978446 1.000000747 0.437013629 0.881758618 0.064666489 24.44839873 229968.3364 0.110623723 0.016572504 17.21485544 -1.23590338 -0.562987118 AAS(ph)SDQLRDNS(ph)PPPAFKPEPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AASSDQLRDNSPPPAFKPEPPK 22 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 2 AAS(0.87)S(0.131)DQLRDNS(0.999)PPPAFKPEPPK;AAS(0.928)S(0.072)DQLRDNS(1)PPPAFKPEPPK;AAS(0.739)S(0.261)DQLRDNS(1)PPPAFKPEPPK 116.72 8.27E-05 1698230000 1682960 1200100 980150 998870 1080030 791690 1682160 1817810 1078880 TRUE FALSE 1460552.572 1192216.464 1454153.818 1225678.7 1058539.516 822146.8266 1519024.382 1429085.478 951336.0355 1.535264636 1.253202254 1.528538565 1.288376194 1.112687291 0.864202339 1.596727471 1.502187896 1 19.8595955 7.999981274 0.771649569 1.275787911 50.75560339 0.11664514 0.233142801 1257.430277 4.95116866 0.09020673 108428.3958 99995688.21 -7.999981274 49.47981548 AASAPAKES(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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;AAS(0.001)APAKES(0.999)PR;AASAPAKES(1)PR;AASAPAKES(1)PR;AASAPAKES(1)PR;AASAPAKES(1)PR 168 4.89E-05 6761130000 18796170 14834810 9843780 12564630 13406760 12038870 16036440 18687810 16624350 TRUE FALSE 16312208.51 14737359.16 14604264.93 15417621.28 13139991.71 12502013.12 14481228.52 14691567.26 14659038.28 1.112774808 1.005342839 0.99626351 1.051748483 0.896374745 0.852853569 0.987870298 1.002219039 1 23.80528712 6.083250691 0.77185769 0.962604297 2.11821345 0.413122792 0.055353321 20.34328154 1.831241919 0.022180735 32.28531967 1211297.138 -6.083250691 1.155609154 AASAPAKES(ph)PRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AASAPAKESPRK 12 2 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 AASAPAKES(1)PRK;AASAPAKES(1)PRK 87.138 0.0055919 522460000 826640 585820 469760 559780 510010 403090 791370 860000 649500 TRUE FALSE 717397.4296 581971.7098 696937.5073 686886.6047 499861.7988 418597.1331 714623.0592 676095.6925 572716.8499 1.252621482 1.016159573 1.216897158 1.199347644 0.872790453 0.730897185 1.247777256 1.180506026 1 19.12746252 7.999984339 0.759632749 1.057579438 33.16559163 0.114379404 0.164894501 1194.213782 4.958477029 0.065789215 65687.42191 99996393.98 -7.999984339 32.10801219 AASDIAMTELPPTHPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AASDIAMTELPPTHPIR 17 0 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ;;; 136.01 1.17E-05 1718150000 981630 1044784 683860 755980 937661 998683 903170 1050330 1064730 FALSE TRUE 851905.1084 1037920.745 1014576.983 927636.8134 919003.3806 1037102.981 815580.7124 825725.1032 938858.8323 0.907383601 1.105513107 1.080649133 0.988047171 0.978851505 1.104642088 0.868693657 0.879498679 1 19.84054872 2.227652887 24.9997037 0.906472532 1.029469129 0.357350944 0.070030232 207.0425445 474521.9126 0.027595046 0.018809806 168.9090374 -2.227652887 0.122996597 AASDPLLS(ph)SVSPAVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AASDPLLSSVSPAVSK 16 0 P19532 P19532 TFE3 Transcription factor E3 1 AASDPLLS(0.648)S(0.176)VS(0.176)PAVSK;AASDPLLS(0.511)S(0.305)VS(0.184)PAVSK 237.59 9.61E-20 770630000 1310720 993090 781490 956930 1048130 963480 1188500 1455170 1350420 TRUE FALSE 1137505.031 986566.3264 1159421.178 1174215.582 1027274.264 1000545.699 1073239.453 1143993.22 1190774.886 0.955264546 0.828507838 0.973669492 0.986093674 0.862693928 0.840247566 0.901295002 0.960713257 1 20.18346927 1.562981338 3.154103985 0.995034221 0.905268746 0.260100231 0.053506956 0.3057376 6.616223314 0.053963456 0.014581571 36.55790822 -1.562981338 -0.089765476 AASDPLLSSVS(ph)PAVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AASDPLLSSVSPAVSK 16 0 P19532 P19532 TFE3 Transcription factor E3 1 AASDPLLS(0.125)S(0.029)VS(0.846)PAVSK;AASDPLLS(0.008)S(0.004)VS(0.988)PAVSK 335.61 1.07E-71 782130000 979570 789930 624230 731210 828760 747480 903660 1124100 1104760 TRUE FALSE 850117.3426 784740.8978 926109.7159 897242.4063 812269.2974 776236.0393 816023.1923 883719.9628 974156.5313 0.872670167 0.805559346 0.950678547 0.921045415 0.833818048 0.796828861 0.83767153 0.907164233 1 19.89379408 1.330550304 2.766746798 1.014237546 0.86052007 0.467118079 0.047590517 0.354670274 3.629623786 0.112950918 0.013310552 21.40672866 -1.330550304 -0.153717476 AASEAPEEEVSLPWVHLAYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AASEAPEEEVSLPWVHLAYQR 21 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 116.73 0.00012307 53755000 38488 43566 24312 25666 36683 47265 25499 36210 36621 FALSE TRUE 33401.71328 43279.81208 36069.36452 31493.85758 35953.08007 49083.31513 23026.1109 28466.77329 32291.7071 1.034374342 1.340276373 1.116985374 0.975292433 1.113384311 1.519997533 0.713065767 0.881550585 1 14.97887609 2.212968498 24.99999989 0.862021546 1.174857946 0.442760054 0.168253323 208.6981724 203868.0149 0.067853971 0.045765225 163.2933499 -2.212968498 0.3128364 AASGEDSTEEALAAAAAPWEGGPVPGVDRS(ph)PFAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AASGEDSTEEALAAAAAPWEGGPVPGVDRSPFAK 34 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6 Q641Q2 FAM21A WASH complex subunit FAM21A 1 AASGEDSTEEALAAAAAPWEGGPVPGVDRS(1)PFAK;AASGEDSTEEALAAAAAPWEGGPVPGVDRS(1)PFAK 265.1 3.77E-60 237250000 84436 86865 63877 92219 99700 110944 128897 153480 136992 TRUE FALSE 73277.56867 86294.3781 94768.13086 113158.7334 97716.16506 115212.0875 116396.5888 120659.4964 120796.9618 0.606617646 0.714375401 0.784524126 0.936768042 0.808928996 0.953766434 0.963572155 0.998862012 1 16.88222464 5.517147436 0.34222164 1.026964699 1.02E-19 0.899615321 0.041970005 4.384614031 0.311814297 0.071834586 2.049600418 328963.2899 -5.517147436 -1.026964699 AASIENVLQDS(ph)SPEHCGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AASIENVLQDSSPEHCGR 18 0 K7EPJ5;O60291-4;O60291;O60291-3;O60291-2 K7EPJ5 MGRN1 E3 ubiquitin-protein ligase MGRN1 1 AASIENVLQDS(0.586)S(0.414)PEHCGR 76.807 0.0094183 67010000 62577 47168 31516 38475 54841 60039 38767 46664 51082 TRUE FALSE 54307.2909 46858.1503 46757.24301 47211.3368 53749.77139 62348.73918 35007.38231 36685.26674 45043.14415 1.205672737 1.040294837 1.038054601 1.048135908 1.193295282 1.384200423 0.777196685 0.814447291 1 15.45901992 2.214538522 24.99996467 0.849970615 1.138579266 0.567756584 0.11777434 171.1785807 178145.4124 0.050006056 0.033733556 163.8847421 -2.214538522 0.288608651 AASIFGGAKPVDTAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AASIFGGAKPVDTAAR 16 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 137.91 8.64E-06 1578890000 1660260 1443060 944240 1129090 1377310 1341600 1458480 1778520 1477370 FALSE TRUE 1440852.434 1433580.444 1400877.622 1385467.142 1349904.226 1393212.22 1317036.834 1398197.338 1302717.002 1.106036409 1.100454237 1.075350687 1.063521194 1.03622216 1.069466521 1.010992282 1.07329323 1 20.31309228 4.196822523 0.621490908 1.036514699 1.133011647 0.591824407 0.022167489 1.444638987 0.702876181 0.012560623 0.092968999 15733.39779 -4.196822523 0.096496948 AASIYSSWAEEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AASIYSSWAEEQR 13 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 0 155.97 2.72E-06 0 32469 31646 23087 26905 30830 40893 34614 30132 39740 FALSE TRUE 28178.13938 31438.11534 34251.95042 33014.19147 30216.54332 42466.18017 31257.13961 23688.50629 35041.98247 0.804125149 0.897155729 0.977454699 0.942132526 0.862295486 1.211865801 0.891991189 0.6760036 1 15.09679678 1.993909153 24.99981409 0.80560064 0.952832639 0.099025585 0.13157855 422.7490061 1735168.7 0.054058821 0.035078134 98.6073195 -1.993909153 0.147231999 RFDVSGYPTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RFDVSGYPTLK 11 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 174.23 1.80E-05 2614100000 4327500 3874800 2463050 2995400 3795700 4028500 3652700 4015700 2024080 FALSE TRUE 3755609.911 3849346.184 3654189.218 3675551.352 3720172.996 4183479.002 3298461.716 3156973.805 1784795.568 2.104224135 2.156743468 2.047399312 2.059368264 2.084369248 2.343954163 1.848089369 1.768815354 1 20.76732741 1.026923461 1.288983621 1.08E-26 2.11736238 0.909506367 0.110066638 0.605922838 0.595712022 1.95474947 0.032090534 10.63955492 -1.026923461 2.11736238 AASLTEDRDR ddPTM_MDA-MB-175_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 0 ; 160.36 6.75E-06 2847400000 1288510 1483330 958400 1082820 1607920 1746510 1387310 1562070 1186100 FALSE TRUE 1118230.139 1473585.908 1421885.446 1328690.831 1575925.538 1813699.37 1252768.89 1228033.487 1045880.609 1.069175706 1.408942756 1.359510286 1.270403925 1.506792959 1.734136147 1.197812522 1.174162209 1 19.99628674 1.767715646 2.494387585 1.057624262 1.390552206 0.33441312 0.175616706 0.306964952 3.774849862 0.146776261 0.049794527 58.57545167 -1.767715646 0.332927944 AASPS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AASPSPAR 8 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 AAS(0.053)PS(0.947)PAR 103.19 0.0050559 761080000 910090 898430 513580 575480 464150 765440 714800 870170 830980 TRUE FALSE 789819.3006 892528.1542 761949.0058 706151.5297 454914.3231 794886.9721 645478.806 684090.9172 732742.4911 1.077894772 1.218065234 1.03985918 0.96371036 0.620837919 1.084810806 0.880908114 0.933603449 1 19.48294675 3.877571046 2.914231256 0.908147429 1.145128541 0.383623703 0.123432378 0.259131265 4.213361635 0.032896234 0.065478025 7543.467896 -3.877571046 0.236981112 AASPS(ph)PQSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AASPSPQSVR 10 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 AAS(0.337)PS(0.662)PQS(0.001)VR 117.86 0.00094586 1148800000 570470 488110 330820 395480 463580 448110 466530 532210 579210 TRUE FALSE 495080.9441 484903.5733 490805.6585 485279.7785 454355.665 465349.0817 421285.9924 418401.0332 510736.4536 0.969347186 0.949420332 0.960976361 0.950156926 0.889608842 0.911133479 0.824859846 0.81921122 1 18.96221951 3.127865799 1.653196544 0.870409431 0.96074889 0.284496649 0.05082944 0.398557244 2.261476539 0.018910792 0.022972148 1342.350098 -3.127865799 0.090339459 AASPYSQRPAS(ph)PTAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AASPYSQRPASPTAIR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 AASPYSQRPAS(0.979)PT(0.021)AIR;AASPYSQRPAS(0.5)PT(0.5)AIR;AASPYSQRPAS(0.986)PT(0.014)AIR 228.19 2.63E-15 2384230000 558620 459910 285385 523590 486976 503589 329080 522710 610460 TRUE FALSE 484796.9516 456888.8209 423398.1406 642479.1121 477286.1304 522962.3947 297165.8723 410932.5342 538292.1142 0.900620572 0.848774873 0.786558319 1.193551039 0.886667513 0.97152156 0.552053178 0.763400621 1 19.03802977 AASPYSQRPASPT(ph)AIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AASPYSQRPASPTAIR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 AASPYSQRPAS(0.472)PT(0.528)AIR 157.22 1.43E-07 589310000 39022 42749 45110 55125 51189 40502 38926 59401 57755 TRUE FALSE 33865.14383 42468.179 66925.34688 67641.97378 50170.43905 42060.13815 35150.96251 46698.55841 50927.26969 0.664970732 0.833898602 1.314135772 1.328207347 0.98513899 0.825886375 0.690218869 0.916965678 1 15.63615075 2.883237259 5.042104791 0.853240331 1.053170258 0.134624315 0.209866883 0.454394694 16.99479513 0.07403927 0.074489959 764.2531885 -2.883237259 0.199929927 AASSS(ph)SPGS(ph)PVASSPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AASSSSPGSPVASSPSR 17 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 2 AAS(0.097)S(0.302)S(0.59)S(0.04)PGS(0.971)PVASSPSR;AASSS(1)S(0.001)PGS(1)PVASSPSR;AAS(0.018)S(0.157)S(0.821)S(0.016)PGS(0.988)PVASSPSR;AAS(0.003)S(0.028)S(0.958)S(0.012)PGS(0.999)PVASSPSR 363.28 7.64E-89 1050370000 1023310 1080040 835260 829680 1279240 1428350 1204920 1327170 1541780 TRUE FALSE 888076.9908 1072945.146 1239194.53 1018071.525 1253785.627 1483299.549 1088067.044 1043365.024 1359512.525 0.65323193 0.789213138 0.911499164 0.74885042 0.922231759 1.091052507 0.800336168 0.767455249 1 20.37465801 5.165169702 1.08557968 0.883905285 0.294573146 0.350953981 0.104491995 5.001072182 2.590702936 0.033289074 4.218236244 146274.8635 -5.165169702 -0.589332139 AASSSS(ph)PGSPVASSPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AASSSSPGSPVASSPSR 17 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 AASSS(0.117)S(0.861)PGS(0.022)PVASSPSR;AASSSS(0.996)PGS(0.004)PVASSPSR 317.95 1.07E-42 0 277460 269890 171895 168774 256120 286340 234650 266480 291720 TRUE FALSE 240792.958 268117.0748 255023.997 207096.7162 251023.7131 297355.6851 211893.6791 209495.3257 257233.1939 0.936088202 1.042311339 0.991411696 0.805093282 0.975860499 1.155977114 0.823741586 0.814417932 1 17.9727173 AASSSSPGS(ph)PVASSPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AASSSSPGSPVASSPSR 17 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 AASSSSPGS(0.966)PVAS(0.031)S(0.003)PSR;AASSSS(0.002)PGS(0.998)PVASSPSR;AASSSSPGS(1)PVASSPSR;AASSSSPGS(0.997)PVAS(0.003)SPSR;AASSSSPGS(1)PVASSPSR;AASSSS(0.002)PGS(0.997)PVASSPSR 416.03 8.01E-141 1381207000 1117322 1349560 938123 1183797 1793021 1609942 1695319 1882251 1952059 TRUE FALSE 969665.0668 1340694.651 1391802.421 1452596.202 1757343.39 1671877.511 1530907.224 1479746.271 1721288.809 0.563336647 0.778890007 0.808581578 0.843900335 1.020946271 0.971294011 0.889395909 0.85967344 1 20.71505775 5.175006863 0.787611157 0.930943903 0.079085545 0.810980839 0.057283918 2.19568187 0.654529598 0.023124224 1.91851904 149625.9301 -5.175006863 -0.851858359 AASVAAATTS(ph)PTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AASVAAATTSPTPR 14 0 Q9Y2D9 Q9Y2D9 ZNF652 Zinc finger protein 652 1 AASVAAATT(0.048)S(0.949)PT(0.002)PR;AASVAAATT(0.052)S(0.945)PT(0.002)PR;AASVAAATT(0.002)S(0.997)PT(0.001)PR 283.88 1.80E-33 1456140000 2805030 1783350 1215290 1652840 1752740 1790490 1674400 1973210 2012540 TRUE FALSE 2434338.178 1771635.056 1803008.309 2028142.584 1717863.903 1859371.309 1512016.946 1551254.397 1774619.814 1.371751943 0.998318086 1.015996945 1.142860329 0.968017989 1.04775755 0.852023027 0.874133369 1 20.75907855 8 0.591492779 0.942012374 23.20890259 0.634719911 0.088220499 117.315933 0.951233544 0.044473257 3364.493658 100000000 -8 22.26689022 AAT(ph)PLPSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AATPLPSLR 9 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 AAT(1)PLPSLR;AAT(0.999)PLPS(0.001)LR;AAT(0.998)PLPS(0.002)LR;AAT(1)PLPSLR 115.78 0.015876 1667160000 3192120 3510020 2311730 2606120 3610140 3440510 3149810 3653520 4052140 TRUE FALSE 2770273.254 3486962.448 3429690.36 3197879.378 3538305.277 3572868.646 2844341.911 2872243.18 3573100.625 0.775313529 0.975892597 0.959863916 0.894987215 0.990261862 0.999935076 0.796043048 0.803851747 1 21.76874511 2.235099274 24.99996875 0.85061128 0.936807643 0.109078327 0.084467026 149.517143 1079886.314 0.032874501 0.023164419 171.8301125 -2.235099274 0.086196362 AATAARPPAPPPAPQPPS(ph)PTPS(ph)PPRPTLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AATAARPPAPPPAPQPPSPTPSPPRPTLAR 30 2 Q96B36;Q96B36-3;H9KV91 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 2 AATAARPPAPPPAPQPPS(0.948)PT(0.058)PS(0.868)PPRPT(0.126)LAR;AATAARPPAPPPAPQPPS(0.869)PT(0.231)PS(0.803)PPRPT(0.097)LAR;AATAARPPAPPPAPQPPS(0.999)PT(0.002)PS(0.991)PPRPT(0.008)LAR;AATAARPPAPPPAPQPPS(0.959)PT(0.043)PS(0.999)PPRPTLAR 144.55 2.26E-08 8960610000 1073920 1019130 720830 846800 1038050 1149960 1092570 1174870 1075010 TRUE FALSE 931998.751 1012435.268 1069425.799 1039078.883 1017394.836 1194199.705 986612.7296 923633.1933 947923.5425 0.983200342 1.068055832 1.128177275 1.096163178 1.073287866 1.259805936 1.040814671 0.974375202 1 19.85441117 2.00445106 24.99995853 0.992028538 1.103848999 0.326468111 0.06841046 133.4816022 749713.1415 0.028135926 0.018888886 101.0301644 -2.00445106 0.111820462 AATAARPPAPPPAPQPPS(ph)PTPSPPRPTLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AATAARPPAPPPAPQPPSPTPSPPRPTLAR 30 2 Q96B36;Q96B36-3;H9KV91 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 AATAARPPAPPPAPQPPS(0.971)PT(0.025)PS(0.004)PPRPTLAR;AATAARPPAPPPAPQPPS(0.973)PT(0.027)PSPPRPTLAR;AATAARPPAPPPAPQPPS(1)PTPSPPRPTLAR;AATAARPPAPPPAPQPPS(0.991)PT(0.009)PSPPRPTLAR 263.86 9.25E-59 1891110000 737818 614456 349786 384185 512328 447412 481590 561477 430754 TRUE FALSE 640313.4819 610419.5981 518943.6796 471420.0762 502133.6752 464624.2292 434885.4759 441409.513 379830.7528 1.685786306 1.607083138 1.366249772 1.241131932 1.321993207 1.223240155 1.144945407 1.162121576 1 18.53499719 8 0.259000877 1.022591418 5.790998586 0.919374382 0.05911628 21.6306268 0.345295866 0.178839775 44.27656969 99999999.98 -8 4.768407168 AATAARPPAPPPAPQPPSPT(ph)PSPPRPTLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AATAARPPAPPPAPQPPSPTPSPPRPTLAR 30 2 Q96B36;Q96B36-3;H9KV91 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 AATAARPPAPPPAPQPPS(0.43)PT(0.559)PS(0.011)PPRPTLAR 95.205 0.037377 467480000 118670 105860 70177 64183 97067 80924 81571 89969 63594 TRUE FALSE 102987.4588 105164.5987 104114.8319 78756.73113 95135.55661 84037.19864 73660.25698 70729.82949 56075.98977 1.836569613 1.875394427 1.856673995 1.404464397 1.696547078 1.498630679 1.313579257 1.261321107 1 15.77509556 0.863563509 0.24124504 4.18E-18 2.061882076 0.85615396 0.110526627 7.548302802 0.448895811 5.037338788 0.593472478 7.304046151 -0.863563509 2.061882076 AATEALGEKS(ph)PDSATVSGYDIMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AATEALGEKSPDSATVSGYDIMK 23 1 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;H7C3G6;J3QRL2;K7EL39;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 AATEALGEKS(0.995)PDS(0.005)ATVSGYDIMK;AATEALGEKS(0.953)PDS(0.047)ATVSGYDIMK 271.18 7.93E-52 336360000 501850 348750 316880 330920 324620 276910 496020 545830 440980 TRUE FALSE 435529.251 346459.0383 470124.2279 406060.4438 318160.6971 287562.9069 447916.0567 429108.5022 388847.8468 1.120050566 0.890988702 1.209018468 1.044265635 0.818213859 0.739525522 1.151905714 1.103538327 1 18.56884622 0.914225064 20.70912309 0.259525576 1.0123893 0.000121738 0.151268673 6854.405973 1936751.137 41219.29867 0.037292806 8.207767837 -0.914225064 0.752863724 AATFGLILDDVSLTHLTFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AATFGLILDDVSLTHLTFGK 20 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0 P35232 PHB Prohibitin 0 ;;;; 352.84 3.53E-95 659962700 1905112 1571276 865751 1753527 1742520 1918541 1497637 2258656 2111161 FALSE TRUE 1653346.622 1560954.184 1284431.079 2151692.106 1707847.261 1992348.514 1352396.394 1775659.991 1861581.952 0.88814066 0.838509518 0.689967518 1.155840657 0.917417178 1.070244859 0.726476959 0.953844653 1 20.8280977 3.760287848 24.99990079 0.955560946 0.808836285 0.289324446 0.120404903 1167.752898 1343641.909 0.031249038 0.054068249 5758.214622 -3.760287848 -0.146724661 AATFPLQVLGFEIDAVNSVQFSNHTGYAHWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AATFPLQVLGFEIDAVNSVQFSNHTGYAHWK 31 0 O00764;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;;;; 293.47 1.66E-81 1485979000 754334 770855 237923.6 552605 709821 706460 810426 937592 1009585 FALSE TRUE 654646.8507 765791.2027 352984.2488 678082.4113 695696.9508 733637.9733 731831.0113 737095.2471 890233.0114 0.735365733 0.86021434 0.396507706 0.761690931 0.781477368 0.824096572 0.822066809 0.827980133 1 19.76382347 -2 0.367968367 4.62733813 0.681776144 0.360871433 0.122186823 91.69905806 1.38876805 252.3105881 0.146797169 0.01 2 -3.945561986 AATLPHEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AATLPHEQR 9 0 Q6PD74;Q6PD74-2 Q6PD74 AAGAB Alpha- and gamma-adaptin-binding protein p34 0 ; 89.029 0.012384 209623000 546860 549580 352860 399090 481630 529600 529490 579090 589230 FALSE TRUE 474591.0654 545969.7728 523504.2762 489709.4842 472046.5053 549974.0547 478140.1413 455256.11 519571.9007 0.913427121 1.050806966 1.007568492 0.942524959 0.908529704 1.058513853 0.920257891 0.876213878 1 18.98696388 2.084067445 25 0.919927759 0.980513628 0.117944723 0.058883186 40.39061271 12006.08361 0.023479048 0.015829574 121.3577303 -2.084067445 0.060585869 AATMEIPIHGNGEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AATMEIPIHGNGEAR 15 0 A0A087X1E4;P53365;E9PRV8;E9PPY7 A0A087X1E4 ARFIP2 Arfaptin-2 0 120.3 0.00014428 301100000 370540 336600 165460 279060 329540 334890 265980 326210 315600 FALSE TRUE 321572.2002 334388.8524 245477.0094 342424.8382 322982.7987 347773.435 240185.3005 256452.5301 278290.1275 1.155528595 1.201583597 0.882090255 1.230459884 1.160597401 1.249679383 0.863075175 0.921529385 1 18.0862302 2.230917149 24.99997877 0.92409787 1.14157039 0.486391034 0.105708645 146.1215571 477924.2051 0.042319122 0.029143727 170.1833814 -2.230917149 0.217472519 AATSDLEHYDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AATSDLEHYDK 11 0 P80303-2;P80303;E9PKG6;Q2L696;E9PLR0;E9PLE9;A0A2R8Y6G7 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 ;;;;; 149.49 3.43E-05 4601020000 10223160 9720210 6446020 7935940 9882760 9627620 10069530 12483680 11424390 FALSE TRUE 8872143.504 9656357.3 9563336.833 9737916.47 9686112.411 9998000.771 9092988.53 9814142.18 10073811.63 0.880713659 0.958560439 0.949326549 0.966656597 0.961514149 0.992474461 0.902636347 0.974223317 1 23.26410632 4.745758878 4.401199393 0.962100526 0.874463518 0.492532641 0.02630692 0.186746623 8.791094979 0.006243432 0.051435919 55687.64834 -4.745758878 -0.087637009 AATTATPAATTS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AATTATPAATTSPK 14 0 Q92766;Q92766-2;Q92766-5;Q92766-3;A0A087X055 Q92766 RREB1 Ras-responsive element-binding protein 1 1 AATTATPAATT(0.013)S(0.987)PK 159.52 2.40E-07 0 208380 136800 100500 161120 182340 109510 176020 195200 165290 TRUE FALSE 180842.055 135901.3518 149102.1362 197704.7586 178711.7907 113722.9206 158949.6075 153457.999 145749.6045 1.240772184 0.93243033 1.023001995 1.356468577 1.226156265 0.780262293 1.090566304 1.052887928 1 17.15313244 AAVAGEDGR ddPTM_MDA-MB-175_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 ;; 160.52 0.00015176 1885630000 2677830 2361870 1642140 1881210 1897160 3157040 1882090 2754230 2594340 FALSE TRUE 2323947.981 2346354.72 2436284.397 2308367.483 1859410.228 3278493.372 1699565.201 2165259.348 2287640.081 1.015871334 1.02566603 1.064977143 1.009060605 0.812807156 1.433133385 0.742933828 0.946503502 1 21.12542866 AAVEWFDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAVEWFDGK 9 0 B0QYK0;Q01844-6;Q01844-3;Q01844;Q01844-5;A0A0D9SFL3;C9JGE3;Q01844-2;H7BY36 B0QYK0 EWSR1 RNA-binding protein EWS 0 112.84 0.0044133 57550000 144800 125180 83197 112650 140590 138420 122060 144080 202460 FALSE TRUE 125664.3131 124357.6843 123431.3475 138228.9042 137792.5341 143745.107 110222.64 113269.6132 178525.4094 0.703901554 0.696582547 0.691393723 0.774281402 0.771837099 0.8051801 0.617405894 0.634473342 1 17.4457699 3.757706007 22.93909126 0.745785122 0.697221586 0.066489549 0.104665736 1121.179977 1343332.213 0.028394539 0.049035023 5724.084114 -3.757706007 -0.048563535 AAVEWFDGKDFQGSK ddPTM_MDA-MB-175_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 ; 190.87 1.81E-07 2942100000 4372700 3476700 2376880 2496720 2891700 2192570 4118000 4760900 1916190 FALSE TRUE 3794836.616 3453861.329 3526347.118 3063638.436 2834160.828 2276919.587 3718636.994 3742818.584 1689660.201 2.245917027 2.044115927 2.087015552 1.813168372 1.677355498 1.347560643 2.200819426 2.215130937 1 20.68830171 3.754540843 3.220392544 1.772363808 2.1306464 0.215860421 0.36308228 0.498730401 10.71802871 0.10635118 0.187046367 5682.518295 -3.754540843 0.358282592 AAVGQES(ph)PGGLEAGNAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AAVGQESPGGLEAGNAK 17 0 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 1 AAVGQES(1)PGGLEAGNAK;AAVGQES(1)PGGLEAGNAK;AAVGQES(1)PGGLEAGNAK;AAVGQES(1)PGGLEAGNAK;AAVGQES(1)PGGLEAGNAK;AAVGQES(1)PGGLEAGNAK 366.97 1.24E-104 2224680000 4863030 3693730 2635410 3137120 3576030 2950630 4374320 4948880 4498370 TRUE FALSE 4220368.264 3669465.644 3909903.091 3849451.044 3504873.999 3064142.645 3950099.12 3890600.524 3966577.823 1.063982216 0.925096092 0.985711932 0.970471579 0.883601471 0.772490238 0.995845612 0.98084563 1 21.91946342 6.869891472 1.518510655 0.938856894 86.97680888 0.233441909 0.069487729 1689.557506 7.28214848 0.020076997 504950.0381 7411250.141 -6.869891472 86.03795199 AAVGRPLDKHEGALETLLR ddPTM_MDA-MB-175_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 ; 203.56 3.00E-16 2138400000 1522030 1459750 840460 1026080 1368260 1232200 1513760 1687340 540470 FALSE TRUE 1320889.879 1450160.806 1246909.267 1259067.147 1341034.303 1279603.531 1366955.788 1326515.472 476576.2523 2.771623371 3.042872571 2.616389846 2.641900725 2.813892418 2.684992223 2.868283473 2.783427553 1 18.86234754 1.238486206 24.99930359 0.999998054 2.779617647 0.954810475 0.1215553 0.332328424 110896.3688 0.164029062 0.029339769 17.31754025 -1.238486206 1.779619593 AAVHLEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAVHLEGK 8 0 P18206;P18206-2 P18206 VCL Vinculin 0 ; 86.011 0.016336 707380000 2403100 2303360 1679550 2223600 2066760 2100130 2234230 2788900 4053300 FALSE TRUE 2085524.246 2288229.076 2491785.998 2728502.366 2025635.52 2180923.36 2017554.718 2192515.438 3574123.492 0.583506488 0.640221045 0.697174007 0.763404614 0.566750288 0.610198099 0.56448937 0.613441434 1 21.76915805 1.236997445 24.99253781 1.000000457 0.63006874 0.784055702 0.061040867 19.54259581 312348.9233 0.097469375 0.015842297 17.25827739 -1.236997445 -0.369931717 AAVHYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAVHYDR 7 0 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 94.262 0.033338 101300000 140490 148320 92612 99382 121560 144530 126420 123880 133560 FALSE TRUE 121923.8905 147345.6762 137399.473 121948.2021 119141.1938 150090.1626 114159.8079 97389.22604 117770.689 1.035265155 1.251123497 1.166669518 1.035471586 1.011637063 1.274427143 0.96933973 0.826939427 1 16.845621 2.036798014 9.715674616 0.900169285 1.126561077 0.485154559 0.096701759 0.264759499 67.19579864 0.038761759 0.026039687 108.8423761 -2.036798014 0.226391793 AAVLQELATHLHPAEPEEGDSNVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAVLQELATHLHPAEPEEGDSNVAR 25 0 Q96KN1 Q96KN1 FAM84B Protein FAM84B 0 ; 188.96 6.42E-18 803670000 865250 738450 691750 524540 574810 532570 978100 921950 574760 FALSE TRUE 750905.0202 733599.0733 1026282.614 643644.8241 563372.4056 553058.3125 883244.0125 724798.1671 506812.5276 1.481622847 1.447476204 2.024974834 1.269986019 1.111599211 1.091248307 1.742743055 1.430110993 1 18.95109266 AAVLS(ph)DS(ph)EDEEKASAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AAVLSDSEDEEKASAK 16 1 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 2 AAVLS(1)DS(1)EDEEKASAK 156.92 6.65E-08 349530000 794390 558120 473670 510780 519180 426530 763130 776750 836360 TRUE FALSE 689409.3488 554453.673 702738.3963 626760.4058 508849.3338 442938.8851 689121.7701 610648.0572 737486.4736 0.934809483 0.751815379 0.952883099 0.849860205 0.689977853 0.600606114 0.934419538 0.828012552 1 19.49225706 0.895771825 1.447713401 1.265409713 0.807119746 0.203772255 0.112887873 4.944183392 4.615676699 4.244476923 0.033211032 7.866323911 -0.895771825 -0.458289967 AAVPSGAS(ph)TGIYEALELR ddPTM_MDA-MB-175_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(0.982)T(0.017)GIYEALELR;AAVPSGAS(0.993)T(0.007)GIYEALELR;AAVPSGAS(0.975)T(0.025)GIYEALELR;AAVPSGAS(0.973)T(0.027)GIYEALELR 238.81 7.13E-24 356802000 72434 73878 52037 49938.3 68891 70879 56170.4 71726 75332 TRUE FALSE 62861.66338 73392.69055 77202.26725 61277.55427 67520.20388 73605.76099 50723.00325 56387.95307 66426.33678 0.946336445 1.10487337 1.162223765 0.922488839 1.016467371 1.10808099 0.763597779 0.848879463 1 16.01946774 2.245283043 24.99994138 0.861785767 1.04488481 0.439083031 0.091755479 134.4174076 499884.8698 0.034742674 0.026284538 175.906968 -2.245283043 0.183099043 AAVPSGASTGIYEALELR ddPTM_MDA-MB-175_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 ;;; 256.57 3.14E-30 883000000 72609.7 76628.9 55201.7 55581.3 65577 69491.9 62238.3 74646.6 73973 FALSE TRUE 63014.14418 76125.51971 81897.42676 68201.88367 64272.146 72165.29836 56202.43925 58684.00549 65227.99621 0.966059788 1.167068194 1.255556379 1.045592194 0.985346013 1.106354672 0.861630627 0.899675123 1 15.99320369 2.737292587 1.114681832 0.917608782 1.123376184 0.362124439 0.095253965 0.481363126 1.291054315 0.058365983 0.045571147 546.125666 -2.737292587 0.205767401 AAVS(ph)PQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAVSPQKR 8 1 E9PJF5;G5E9I4;Q9HCU9 E9PJF5 BRMS1 Breast cancer metastasis-suppressor 1 1 AAVS(1)PQKR;AAVS(1)PQKR 125.74 0.00076514 457317000 1182890 1021440 617780 769950 813600 805970 1069950 1252480 1080320 TRUE FALSE 1026568.089 1014730.093 916540.4744 944778.9154 797410.9518 836976.1874 966186.4137 984646.8988 952605.8003 1.077642073 1.065215111 0.962140346 0.991783711 0.837083872 0.878617564 1.014256278 1.033635212 1 19.86151981 4.254885082 5.514435244 0.962789344 1.073748475 0.371505398 0.06039106 0.206550266 18.89023376 0.01758435 0.044627224 17983.94984 -4.254885082 0.110959131 AAVT(ph)PGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AAVTPGKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AAVT(1)PGKK;AAVT(1)PGKK;AAVT(1)PGKK;AAVT(1)PGKK;AAVT(1)PGKK 113.93 0.0016142 4120310000 16754300 14403340 10912490 11169340 7799500 8513310 16260700 17524200 16852200 TRUE FALSE 14540176.81 14308723.51 16189806.66 13705509.36 7644305.209 8840822.545 14683739.82 13776786.2 14859952.11 0.978480731 0.962905089 1.089492519 0.922311812 0.514423273 0.594942869 0.988141799 0.927108385 1 23.82492613 3.472540724 24.991662 0.813886857 1.005612075 0.262418581 0.158125419 203.7095479 1111445.015 0.050859928 0.06592379 2968.525091 -3.472540724 0.191725218 AAVVESHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AAVVESHK 8 0 P00390-5;P00390-4;P00390-2;P00390-3;P00390;A0A2R8YF59;H0YC68 P00390-5 GSR "Glutathione reductase, mitochondrial" 0 ;;; 121.62 0.0014255 1930570000 2840030 3387860 1604300 1966740 3118230 4031230 2928330 3444110 3324100 FALSE TRUE 2464712.84 3365604.925 2380144.846 2413318.377 3056183.324 4186314.027 2644341.007 2707613.879 2931128.685 0.840875002 1.148228306 0.81202332 0.823340984 1.042664329 1.428225942 0.902157937 0.923744458 1 21.48302488 3.14900676 9.972332152 1.049495465 0.916820654 0.1634072 0.170771657 0.779540929 80.19811097 0.054501373 0.061847755 1409.310735 -3.14900676 -0.132674811 AAVVT(ph)SPPPTTAPHK ddPTM_MDA-MB-175_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 109.35 0.0037043 571740000 1140420 783110 818590 661870 715540 626890 802110 979870 947670 TRUE FALSE 989710.6075 777965.6988 1214462.862 812157.6995 701302.1539 651006.864 724321.4957 770332.4259 835637.5322 1.184377878 0.93098463 1.453336902 0.971901893 0.839242048 0.779054122 0.866789089 0.92184996 1 19.67251777 3.49128518 24.69444307 0.882536894 1.171860162 0.517634772 0.135638855 447.9625321 781010.3353 0.03635548 0.051596424 3099.453889 -3.49128518 0.289323268 AAWGEETDYTPVWCMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAWGEETDYTPVWCMR 16 0 A0A1B0GVZ4;A0A494C085;P06132;A0A1B0GVN9;H0Y5R6;Q5T446;A0A494C007;A0A494C0P4 A0A1B0GVZ4 UROD Uroporphyrinogen decarboxylase 0 ; 116.03 0.0010698 66463000 56292 50587 30849.5 41092.2 94877 72789 46934 50455 64219.7 FALSE TRUE 48852.86957 50254.69067 45768.42139 50422.81206 92989.13332 75589.23993 42382.3479 39665.59089 56627.72023 0.86270239 0.887457423 0.808233515 0.890426312 1.642113314 1.334845189 0.748438181 0.700462437 1 15.78922083 2.199590116 24.98825469 0.789339426 1.068435114 0.168636103 0.264260404 288.152424 184764.1056 0.119040114 0.080258258 158.3398086 -2.199590116 0.279095688 AAYEAELGDAR ddPTM_MDA-MB-175_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 ;;;;; 173.37 2.85E-05 5206994000 3381090 2991690 2162430 2472610 2850490 3029430 2756960 3127020 4270120 FALSE TRUE 2934270.39 2972037.391 3208188.381 3034053.892 2793770.826 3145974.132 2489590.444 2458331.107 3765311.278 0.779290256 0.789320503 0.852038024 0.805790987 0.74197606 0.835515021 0.661191137 0.65288921 1 21.84433771 3.253415877 20.57122873 0.756712 0.808620058 0 0.099244567 96.56176169 133708.8106 0.028884378 0.037010141 1792.321347 -3.253415877 0.051908057 AAYEAELGDARK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AAYEAELGDARK 12 1 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;; 134.99 0.00021752 3526160000 3925130 3624430 1766820 2246310 3348070 3285810 3633430 4056520 1797750 FALSE TRUE 3406414.125 3600620.881 2621260.062 2756369.018 3281449.957 3412217.237 3281060.518 3189064.766 1585222.043 2.148856143 2.271366902 1.653560189 1.738790493 2.07002544 2.152516899 2.069779771 2.011746417 1 20.5962535 1.238541917 24.99988521 0.99999936 2.011202414 0.743513202 0.187264478 0.246256897 320160.1916 0.268935189 0.048276565 17.3197619 -1.238541917 1.011203054 ACAELHQNVNVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ACAELHQNVNVK 12 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 156.71 0.0002951 0 277900 213750 156680 198520 213840 206450 258250 286070 284340 FALSE TRUE 241174.8109 212345.8622 232450.9721 243597.0002 209585.0024 214392.2651 233204.9547 224896.1567 250725.6491 0.961907215 0.846925167 0.927112854 0.971567931 0.835913689 0.855087088 0.930120056 0.896981053 1 17.93575007 1.236886026 24.86455391 1.00000013 0.901690731 0.299005467 0.046527563 51.59822422 765878.9627 0.068104275 0.010996047 17.2538503 -1.236886026 -0.098309399 ACDLPAWVHFPDTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ACDLPAWVHFPDTER 15 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6 A0A499FIX8 ESYT2 Extended synaptotagmin-2 0 84.874 0.0081602 85036000 15500 10451 9891.3 11838 13938 11198 14126 9968.5 16532 FALSE TRUE 13451.63573 10382.34669 14674.76576 14525.99883 13660.66107 11628.79431 12756.06269 7836.81385 14577.60579 0.922760289 0.712212063 1.006665016 0.996459847 0.937099086 0.797716338 0.875045112 0.537592658 1 13.83146617 2.3246875 2.083321726 0.741775586 0.909866644 0.092379416 0.141762205 0.510276454 4.569098065 0.070943044 0.044630543 211.1968807 -2.3246875 0.168091058 ACEVALEEIKAETEKQS(ph)PPHGEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ACEVALEEIKAETEKQSPPHGEAK 24 2 Q9Y6D6;E5RJN9 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 ACEVALEEIKAET(0.001)EKQS(0.999)PPHGEAK;ACEVALEEIKAET(0.002)EKQS(0.998)PPHGEAK 172.83 2.35E-12 408210000 584840 415870 444980 307440 352690 239937 642610 732810 305000 TRUE FALSE 507551.9122 413138.1226 660173.8164 377248.9509 345672.159 249167.5316 580289.7811 576104.2842 268943.2475 1.887208238 1.536153544 2.454695638 1.402708395 1.28529778 0.926468815 2.157666298 2.142103547 1 18.03694224 ACFHCETCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ACFHCETCK 9 0 Q14847;Q14847-2;F6S2S5;K7ESD6 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;; 175.51 5.39E-05 1337130000 4218841 1935376 1531973 1517026 1510690 1618027 1800744 1974341 2651085 FALSE TRUE 3661310.473 1922662.388 2272840.267 1861489.94 1480630.225 1680273.546 1626108.124 1552143.541 2337676.751 1.566217601 0.822467172 0.972264564 0.79629912 0.633376802 0.718779252 0.695608631 0.663968421 1 21.15664402 7.310846022 1.033566499 0.741455738 199.9999955 0.794679984 0.123753886 171.6088232 0.994393219 0.036662741 80052.27294 20457192.04 -7.310846022 199.2585398 ACGNFGIPCELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ACGNFGIPCELR 12 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;; 173.64 7.57E-05 364004000 496880 462009 319799 354853 475767 483350 418461 476481 519220 FALSE TRUE 431216.0491 458974.0325 474454.8661 435427.7972 466300.1675 501944.7873 377878.7166 374589.2461 457838.4031 0.941852073 1.002480415 1.036293292 0.951051275 1.018481989 1.096336139 0.825353911 0.818169126 1 18.80447895 2.225891593 24.99997895 0.865722388 1.006717849 0.44993102 0.065226336 182.5462449 360218.4059 0.026272059 0.017846239 168.225409 -2.225891593 0.140995461 ACLDDSYASGEGLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ACLDDSYASGEGLKR 15 1 A0A0C4DGT3;A0A3B3IU98;Q6DN90-2;A0A3B3IRZ4;Q6DN90-3;A0A2R8Y7T6;Q6DN90 A0A0C4DGT3;A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 0 77.192 0.042679 114800000 55127 44739 30213 31209 41509 33511 53663 55510 44018 FALSE TRUE 47841.82728 44445.10656 44824.10786 38295.48045 40683.05211 34800.18985 48458.77052 43639.61848 38814.24219 1.232584345 1.145072119 1.15483661 0.986634758 1.048147531 0.896583004 1.248479109 1.124319735 1 15.2442985 3.920965537 6.494519059 1.064172616 1.179809916 0.283275352 0.094326841 0.361776391 24.47780441 0.026241652 0.046274721 8336.150318 -3.920965537 0.1156373 ACLISLGYDVENDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ACLISLGYDVENDR 14 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ;;;;; 241.39 4.53E-17 1332771000 1255029 1130820 1103643 1467225 1055029 1276996 953501 1242690 3814570 FALSE TRUE 1089173.738 1123391.569 1637368.446 1800380.861 1034035.987 1326122.862 861030.6198 976950.4141 3363615.88 0.32381038 0.333983311 0.486788178 0.535251624 0.307417976 0.394255144 0.255983635 0.290446486 1 21.68158153 1.234498947 24.99972715 1.000000923 0.364410967 0.839902779 0.0869886 50.24151186 309195.1651 0.173251104 0.023206288 17.1592755 -1.234498947 -0.635589956 ACLISLGYDVENDRQGEAEFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ACLISLGYDVENDRQGEAEFNR 22 1 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ;;;;; 320.62 1.17E-67 2666297000 1235907 1126401 734535 818256 1014997 1163757 867979 1145794 724516 FALSE TRUE 1072578.759 1119001.598 1089758.583 1004053.531 994800.5455 1208527.485 783802.5302 900774.8697 638864.5439 1.678882901 1.751547505 1.705774085 1.571621936 1.55713845 1.89168032 1.226868102 1.409962219 1 19.28515055 0.699635021 0.645743451 1.92E-15 1.699493047 0.683973666 0.147853795 3.480540672 0.684452856 5.124400302 0.069063139 5.007662151 -0.699635021 1.699493047 ACNQLGQFLQHR ddPTM_MDA-MB-175_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 ; 144.55 6.31E-05 2578200000 4377600 4174400 2656200 2650300 3925300 3846600 4046200 4421900 4351500 FALSE TRUE 3799089.069 4146978.092 3940747.204 3252091.122 3847194.21 3994581.191 3653800.147 3476311.096 3837070.627 0.990101418 1.080766682 1.027019721 0.847545286 1.002638362 1.041049691 0.952236876 0.905980482 1 21.87157389 3.970544713 24.97076226 0.956150444 1.040048881 0.270605165 0.057515121 796.8620261 675542.7281 0.015325556 0.026605351 9344.255683 -3.970544713 0.083898437 ACPEEPAAPS(ph)PEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ACPEEPAAPSPEPR 14 0 O94819 O94819 KBTBD11 Kelch repeat and BTB domain-containing protein 11 1 ACPEEPAAPS(1)PEPR 126.88 0.00030777 0 294150 262720 229400 225510 247290 280700 263630 292900 347460 TRUE FALSE 255277.3322 260994.175 340338.6073 276715.4922 242369.4128 291498.7106 238063.2032 230265.6144 306383.6746 0.833194956 0.851854053 1.110824876 0.903166569 0.791065037 0.951417242 0.777010079 0.751559673 1 18.2249799 3.465617415 22.05191806 0.841055315 0.937788862 0.096501521 0.105577563 100.9191119 193449.9772 0.030642292 0.039618224 2921.577523 -3.465617415 0.096733548 ACPGPPPPS(ph)PEPLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ACPGPPPPSPEPLAR 15 0 A0A087WSV0;Q9HB09-3;Q9HB09 A0A087WSV0 BCL2L12 Bcl-2-like protein 12 1 ACPGPPPPS(1)PEPLAR;ACPGPPPPS(1)PEPLAR;ACPGPPPPS(1)PEPLAR;ACPGPPPPS(1)PEPLAR;ACPGPPPPS(1)PEPLAR 241.07 7.60E-18 1375950000 546870 571958 360127 469252 550368 575165 423448 630608 500446 TRUE FALSE 474599.7439 568200.7702 534285.6218 575802.8387 539416.7536 597291.9697 382382.0781 495757.3866 441283.844 1.075497665 1.287608368 1.210752737 1.30483553 1.222380472 1.353532376 0.866521817 1.12344332 1 18.7513474 2.245144034 24.99897539 1.017647046 1.244972659 0.593157136 0.095413135 103.1977263 391870.5838 0.033736074 0.025510948 175.8506726 -2.245144034 0.227325613 ACPRPEGLNFQDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ACPRPEGLNFQDLK 14 1 Q5TEJ0;P15927;P15927-2;P15927-3 Q5TEJ0 RPA2 Replication protein A 32 kDa subunit 0 ; 117.37 0.00028007 1462220000 826420 632400 491300 491990 648050 540310 653280 790570 757700 FALSE TRUE 717206.5031 628245.7228 728894.3233 603703.8491 635155.0729 561096.0753 589925.0062 621512.7577 668125.5692 1.073460643 0.940310851 1.090954091 0.903578424 0.950652246 0.83980632 0.882955291 0.930233457 1 19.34975975 3.719926342 24.94145352 0.915089675 1.025448762 0.479629108 0.057136349 669.9778174 896746.645 0.015245153 0.02266241 5247.184581 -3.719926342 0.110359087 ACQSIYPLHDVFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ACQSIYPLHDVFVR 14 0 P61247;D6RG13;D6RAT0;H0Y9Y4;D6RB09;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ;;; 190.87 5.53E-07 13303650000 7506000 7672650 4922250 5540640 7556480 8038670 7018060 8088670 7992180 FALSE TRUE 6514063.082 7622247.857 7302666.564 6798726.995 7406120.832 8347922.837 6337449.621 6358970.867 7047353.585 0.924327551 1.081575909 1.036228206 0.964720574 1.050908081 1.184547183 0.899266589 0.902320394 1 22.74865017 ACRPPGS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 ACRPPGSPGR 10 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 ACRPPGS(1)PGR;ACRPPGS(1)PGR;ACRPPGS(1)PGR;ACRPPGS(1)PGR;ACRPPGS(1)PGR;ACRPPGS(1)PGR;ACRPPGS(1)PGR;ACRPPGS(1)PGR;ACRPPGS(1)PGR;ACRPPGS(1)PGR 125.82 0.00024164 12868535000 2347894 2770503 2223124 2774805 2697708 3279463 2533230 3175907 4771964 TRUE FALSE 2037613.859 2752303.383 3298234.202 3404866.885 2644028.889 3405626.064 2287557.745 2496764.003 4207827.852 0.484243636 0.654091251 0.78383297 0.809174473 0.628359567 0.809354894 0.543643377 0.593361727 1 22.00464425 4.673020248 3.294802161 0.716164655 0.467809437 0.261264243 0.131450137 0.415663187 7.408152001 0.032723144 0.235861923 47099.9285 -4.673020248 -0.248355217 ACRPPGS(ph)PGRAPPPTPAPSGCDPR ddPTM_MDA-MB-175_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(0.999)PGRAPPPT(0.001)PAPSGCDPR;ACRPPGS(1)PGRAPPPTPAPSGCDPR;ACRPPGS(0.991)PGRAPPPT(0.009)PAPSGCDPR 120.93 6.83E-05 11012430000 1605820 1854020 938342 1051539 1927660 2233650 1764270 2208860 387666 TRUE FALSE 1393606.818 1841840.821 1392127.33 1290307.002 1889303.337 2319579.961 1593171.367 1736512.478 341836.5671 4.076821945 5.388074296 4.072493887 3.774631288 5.526919935 6.785640227 4.660623 5.079949442 1 18.38294721 1.237375602 24.99942119 0.999995282 4.945440235 0.66415033 0.876034048 19.0168666 401010.6242 1.323581666 0.220481909 17.2733114 -1.237375602 3.945444954 ACRT(ph)PESFLGPSASSLVNLDSLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ACRTPESFLGPSASSLVNLDSLVK 24 1 Q9H201 Q9H201 EPN3 Epsin-3 1 ACRT(0.974)PES(0.026)FLGPSASSLVNLDSLVK;ACRT(0.984)PES(0.016)FLGPSASSLVNLDSLVK;ACRT(0.996)PES(0.004)FLGPSASSLVNLDSLVK;ACRT(0.941)PES(0.058)FLGPSASSLVNLDSLVK 278.8 6.23E-52 9045950000 2540633 1998339 1323748 1481252 1700434 1593064 2057053 2437590 1620205 TRUE FALSE 2204881.912 1985211.78 1963916.96 1817592.906 1666598.69 1654350.203 1857560.317 1916330.348 1428666.211 1.543314943 1.389556052 1.374650668 1.272230625 1.166541686 1.157968314 1.300205956 1.341342249 1 20.44623746 4.338094947 0.997774348 1.217005373 1.586168783 0.592398529 0.095319471 0.877932239 1.096766475 0.034009016 0.304807282 21781.85924 -4.338094947 0.36916341 ACS(ph)LAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ACSLAK 6 0 B7Z2E6;H0YB80;P63104-2;P31946-2;P31946;P63104;E7EX29;B0AZS6 B7Z2E6;P31946-2;P63104 YWHAZ;YWHAB "14-3-3 protein zeta/delta;14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 1 ACS(1)LAK;ACS(1)LAK 87.323 0.055145 208655000 940310 716970 530800 593840 536580 578270 813400 939130 932790 TRUE FALSE 816045.6511 712260.1769 787496.6554 728680.4483 525903.1078 600516.4211 734516.5932 738304.3578 822516.6288 0.992132709 0.865952313 0.957423386 0.885915765 0.639382949 0.73009639 0.893011238 0.89761633 1 19.64968532 3.473711078 24.9969564 0.832694263 0.929651415 0.186467054 0.101364348 200.7088781 1471202.836 0.031750665 0.041193358 2976.53558 -3.473711078 0.096957151 LSMPQSAAVST(ph)TPPHNRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSMPQSAAVSTTPPHNRR 18 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 LSMPQS(0.001)AAVS(0.132)T(0.511)T(0.357)PPHNRR;LSMPQSAAVS(0.118)T(0.441)T(0.441)PPHNRR;LSMPQSAAVS(0.13)T(0.435)T(0.435)PPHNRR;LSMPQSAAVS(0.058)T(0.589)T(0.353)PPHNRR 145.62 4.07E-08 764350000 461333 394259 348326 299547 407326 394464 410397 454449 211847 TRUE FALSE 400366.6752 391669.0867 516777.6187 367563.7246 399221.0095 409639.2853 370596.7621 357268.6179 186802.689 2.1432597 2.096699404 2.766435652 1.967657568 2.137126674 2.192898226 1.983894151 1.91254537 1 17.5111557 1.033482898 1.384704437 9.30E-13 2.212347854 0.745534441 0.21780258 1.067390754 1.218474179 3.831149902 0.062708441 10.80147086 -1.033482898 2.212347854 ACSPSNIPAVIITDMGTQEDGALEETQGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ACSPSNIPAVIITDMGTQEDGALEETQGSPR 31 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 ACSPSNIPAVIITDMGTQEDGALEET(0.015)QGS(0.985)PR;ACSPSNIPAVIITDMGTQEDGALEET(0.015)QGS(0.985)PR 138.33 3.17E-07 30829000 71396 57951 36711 44890 56770 62306 59231 62795 65947 TRUE FALSE 61960.83771 57570.31607 54464.56239 55082.9606 55640.38807 64702.95214 53486.78674 49366.77792 58150.82079 1.065519573 0.990017257 0.936608661 0.947243046 0.956828938 1.112674787 0.919794184 0.848943785 1 15.82751193 ACTGLSGPGSGSKS(ph)PPATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ACTGLSGPGSGSKSPPATR 19 1 I3L2J0;I3L2I4 I3L2J0 CIC 1 ACTGLSGPGSGS(0.091)KS(0.909)PPATR;ACTGLSGPGSGS(0.032)KS(0.968)PPATR;ACTGLSGPGS(0.001)GS(0.07)KS(0.928)PPAT(0.001)R 193.73 2.82E-15 1148150000 1338490 1090280 510350 524860 1036180 916240 1232510 1290070 227462 TRUE FALSE 1161605.155 1083117.879 757156.967 644037.485 1015562.045 951488.3457 1112981.37 1014198.57 200571.7015 5.791470814 5.400153017 3.774993987 3.211008733 5.063336641 4.743881308 5.549044864 5.056538696 1 17.61375855 4.358792757 5.514793931 4.25951803 5.691176573 0.185231556 1.29799831 0.367844199 15.8485957 0.325779375 0.898110617 22845.08387 -4.358792757 1.431658543 ACTLTVFPPEENPGS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ACTLTVFPPEENPGSPSR 18 0 Q9P2J3 Q9P2J3 KLHL9 Kelch-like protein 9 1 ACTLTVFPPEENPGS(0.968)PS(0.032)R 170.61 3.12E-14 0 57815 64829 49096 62574 72160 71304 65425 79767 87382 TRUE FALSE 50174.60127 64403.13403 72838.98982 76782.38308 70724.15718 74047.11102 59080.09357 62709.4478 77051.79951 0.651180136 0.83584205 0.945324967 0.996503438 0.917878072 0.961004305 0.766758128 0.813860912 1 16.23354103 4.681177966 3.009081173 0.901990897 0.62617958 0.546818036 0.074973818 0.286494908 4.043994173 0.020816414 0.175539779 47993.00745 -4.681177966 -0.275811317 ADAAEFWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADAAEFWR 8 0 Q13191;A0A2R8Y8D8;A0A2R8Y5E1;A0A2R8YFD4;Q13191-3;Q13191-2;A0A2R8YDW4;C9JU85;A0A2R8Y7I2;P22681;A0A0U1RR39;A0A1B0GW38;A0A0U1RQX8 Q13191;P22681 CBLB;CBL E3 ubiquitin-protein ligase CBL-B;E3 ubiquitin-protein ligase CBL 0 81.296 0.054036 73943000 118250 128280 85640 91040 116880 116460 119840 128990 125480 FALSE TRUE 102622.9629 127437.3202 127055.7904 111712.0235 114554.3167 120940.2916 108217.9352 101406.4923 110645.8973 0.927489996 1.151758206 1.148310001 1.009635478 1.035323671 1.093039096 0.978056465 0.916495729 1 16.75559043 2.121292411 5.081623917 0.951067747 1.065251384 0.305231245 0.068180838 0.219959582 8.875981001 0.028257899 0.018691559 132.2185563 -2.121292411 0.114183637 ADAASSLTVDVT(ph)PPTAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ADAASSLTVDVTPPTAK 17 0 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 1 ADAASSLT(0.011)VDVT(0.989)PPTAK;ADAASSLT(0.003)VDVT(0.987)PPT(0.009)AK;ADAASSLTVDVT(1)PPTAK;ADAASSLTVDVT(1)PPTAK 307.92 5.45E-57 1317210000 2353380 1965520 1377970 1645360 1925080 1604830 2395690 2642650 2479450 TRUE FALSE 2042374.87 1952608.37 2044360.901 2018964.136 1886774.674 1666568.849 2163356.353 2077539.863 2186332.246 0.934155764 0.893097732 0.935064149 0.923447998 0.862986254 0.762266966 0.989491125 0.950239776 1 21.06008123 ADADPS(ph)PTSPPTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADADPSPTSPPTAR 14 0 Q9NWZ5;Q9NWZ5-3;Q9NWZ5-2 Q9NWZ5 UCKL1 Uridine-cytidine kinase-like 1 1 ADADPS(0.472)PT(0.285)S(0.224)PPT(0.019)AR 62.528 0.080056 275080000 473060 370380 254410 282240 353250 384670 360920 412820 385530 TRUE FALSE 410543.9224 367946.9494 377443.527 346326.9058 346221.0161 399468.5038 325918.034 324541.6556 339953.0826 1.207648771 1.082346265 1.110281231 1.018749126 1.018437643 1.175069515 0.958714748 0.954666018 1 18.37497613 8 0.169789186 0.912624524 1.973674982 0.483303071 0.0617558 113.8045413 1.550007918 0.705024007 29.7606532 100000000 -8 1.061050458 ADAETLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ADAETLRK 8 1 P08758;D6RBE9;E9PHT9;D6RCN3 P08758 ANXA5 Annexin A5;Annexin 0 ;;;; 149.65 0.00080453 2849050000 4611400 4356900 2039830 2296376 2379835 2456227 2582256 3748620 4279060 FALSE TRUE 4001991.806 4328279.237 3026298.611 2817803.269 2332480.94 2550719.642 2331829.211 2947006.785 3773194.402 1.060637587 1.147112705 0.802052131 0.746795147 0.61817142 0.676010661 0.617998694 0.781037623 1 21.847355 4.15706429 4.379261578 0.732107679 1.104999023 0.645075372 0.109894773 0.122772423 4.308674363 0.029457205 0.067469917 14357.01948 -4.15706429 0.372891344 ADAHEEDELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ADAHEEDELR 10 0 F8W9X7;Q567U6 F8W9X7 CCDC93 Coiled-coil domain-containing protein 93 0 ; 107.83 0.0022318 271790000 347200 330580 230380 261700 327530 332940 304470 387940 329910 FALSE TRUE 301316.6403 328408.3982 341792.5386 321122.9848 321012.7938 345748.4172 274942.5463 304982.05 290908.4156 1.035778355 1.128906489 1.174914579 1.103862823 1.10348404 1.188512943 0.945117197 1.04837823 1 18.15020551 2.23739394 24.9999995 1.006165873 1.1235248 0.596272087 0.048221559 21.45072772 459632.4426 0.018265963 0.013094914 172.7404075 -2.23739394 0.117358927 ADAPDAGAQS(ph)DSELPSYHQNDVSLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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(0.996)DS(0.004)ELPSYHQNDVSLDR;ADAPDAGAQS(0.997)DS(0.003)ELPSYHQNDVSLDR;ADAPDAGAQS(1)DSELPSYHQNDVSLDR;ADAPDAGAQS(1)DSELPSYHQNDVSLDR;ADAPDAGAQS(0.999)DS(0.001)ELPSYHQNDVSLDR;ADAPDAGAQS(1)DSELPSYHQNDVSLDR;ADAPDAGAQS(1)DSELPSYHQNDVSLDR;ADAPDAGAQS(0.998)DS(0.002)ELPSYHQNDVSLDR;ADAPDAGAQS(0.999)DS(0.001)ELPSYHQNDVSLDR;ADAPDAGAQS(1)DSELPSYHQNDVSLDR 368.67 1.00E-126 24481230000 3449273 3943611 1529110 2470323 4417798 4224348 3870567 4404508 4420568 TRUE FALSE 2993442.834 3917705.16 2268592.711 3031247.594 4329892.463 4386861.401 3495200.008 3462638.24 3897973.487 0.767948485 1.005062034 0.581992853 0.777647053 1.110806032 1.125421047 0.896671057 0.888317545 1 21.89429285 3.261351044 24.76166148 0.987743422 0.784643174 0.429574196 0.125790281 234.9188956 255236.0779 0.037981828 0.048998477 1825.370571 -3.261351044 -0.203100247 ADATNVNNWHWTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ADATNVNNWHWTER 14 0 O95433;O95433-2;G3V3W9 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ;; 226.24 2.48E-12 3891930000 1511010 1428230 701770 991560 1328910 1392380 1294230 1500760 1412440 FALSE TRUE 1311326.2 1418847.863 1041148.319 1216708.853 1302467.291 1445945.76 1168715.774 1179834.153 1245462.952 1.052882543 1.139213222 0.835952862 0.976912923 1.045769598 1.160970511 0.938378594 0.947305699 1 20.24825068 1.530813936 0.013544246 4.53E-07 1.970175342 0.028279406 0.094749059 18659.15281 83.58944544 6362.199261 5805.21464 33.94797988 -1.530813936 1.970174889 ADDADEFGYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ADDADEFGYSR 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;; 278.44 6.81E-27 7258150000 2316530 2198100 1424870 1660330 2014540 1979500 2150800 2401630 2321840 FALSE TRUE 2010394.691 2183660.536 2113941.898 2037333.303 1974454.595 2055652.646 1942215.747 1888060.114 2047354.72 0.981947423 1.066576551 1.032523518 0.995105188 0.964393017 1.004052999 0.94864643 0.922194916 1 20.96532965 3.277668665 1.184187753 0.956196514 1.031883782 0.395913581 0.031752154 0.407342751 1.231062219 0.013208972 0.019635281 1895.259425 -3.277668665 0.075687268 ADDDRFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ADDDRFPR 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 90.657 0.011894 269870000 838780 787510 548650 623490 721100 830510 710520 832320 992330 FALSE TRUE 727933.0978 782336.795 813978.9751 765062.9339 706751.5208 862460.2571 641613.8798 654334.8451 875017.8779 0.831906543 0.894080927 0.930242679 0.874339774 0.807699521 0.985648727 0.733258024 0.747795973 1 19.73895297 2.22618227 24.99866643 0.80660678 0.885368988 0.081744785 0.086536901 424.2881319 856863.0718 0.034423822 0.023396106 168.3380413 -2.22618227 0.078762208 ADDGRPFPQVIK ddPTM_MDA-MB-175_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 ;;;;;;; 184.34 1.32E-05 49171000000 47664040 41538270 27371690 35477330 38421240 33540200 46503890 53066900 49542680 FALSE TRUE 41365116.35 41265402.37 40608730.84 43533000.01 37656732.49 34830513.2 41993949.91 41718956.4 43685800.81 0.946877832 0.944595306 0.929563613 0.996502278 0.861990207 0.797295976 0.961272293 0.95497749 1 25.3806611 1.699871998 2.512452553 0.987149315 0.915850025 0.187036619 0.055090578 0.467560208 6.297829345 0.053316588 0.016213279 50.10395376 -1.699871998 -0.07129929 ADDLGKGGNEESTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ADDLGKGGNEESTK 14 1 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;; 174.62 2.29E-06 1649540000 2407690 1602060 610600 708130 1288470 938130 2294000 2494230 133770 FALSE TRUE 2089507.666 1591535.962 905888.2023 868921.7396 1262831.968 974220.4682 2071528.233 1960858.325 117955.863 17.71431799 13.49263972 7.679891269 7.366498939 10.70597032 8.259194952 17.5618929 16.62366138 1 16.8478876 4.522617412 3.609006474 10 17.38097078 0.228135502 4.700119351 0.40300339 10.15254103 1.277451442 5.788290837 33313.28127 -4.522617412 7.380970782 ADDPYAHLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADDPYAHLSK 10 0 Q5STZ8;Q8NE71 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 68.786 0.058934 293990000 641960 577440 280160 529700 578860 530100 625160 735420 962610 FALSE TRUE 557123.3595 573646.7586 415646.3131 649976.481 567341.8185 550493.29 564532.0794 578156.156 848811.3424 0.65635711 0.675823625 0.489680442 0.765749052 0.668395661 0.648546105 0.665085457 0.681136228 1 19.69508441 1.224188228 3.820329054 1.048730783 0.653442596 0.723067614 0.067025441 0.14737002 3.453861898 0.169315814 0.01635054 16.75668973 -1.224188228 -0.395288187 ADDTDSQSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ADDTDSQSWR 10 0 O75369-8 O75369-8 FLNB Filamin-B 0 ;; 198.61 6.83E-07 1288090000 2202910 2103660 1390400 1619700 1962730 2065920 1923680 2102780 2201290 FALSE TRUE 1911789.862 2089840.919 2062802.091 1987477.641 1923675.513 2145397.279 1737121.81 1653116.861 1941056.004 0.984922567 1.076651531 1.062721573 1.023915661 0.991045858 1.105273251 0.894936471 0.851658508 1 20.88841031 2.22297404 24.99984443 0.901366564 1.040360268 0.561230796 0.051690595 150.7068474 241721.9737 0.020321934 0.013753849 167.0990727 -2.22297404 0.138993705 ADDTDSQSWRS(ph)PLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADDTDSQSWRSPLK 14 1 O75369-8 O75369-8 FLNB Filamin-B 1 ADDTDSQS(0.004)WRS(0.996)PLK 150.91 4.29E-06 546280000 613100 717330 408340 422060 850630 681330 1066900 1219600 135420 TRUE FALSE 532077.2816 712617.812 605814.5898 517895.1738 833704.1272 707541.206 963432.2022 958798.0309 119410.8019 4.455855528 5.967783491 5.073365058 4.33708815 6.981814996 5.925269698 8.068216502 8.029407859 1 16.86557382 3.23535692 24.99671264 6.405762077 5.038816075 0.040819782 2.024335195 207.9514113 1622533.078 0.598205205 0.70699436 1719.320813 -3.23535692 -1.366946002 ADEASELACPT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 ADEASELACPTPK 13 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 ADEASELACPT(1)PK;ADEASELACPT(1)PK;ADEASELACPT(1)PK;ADEASELACPT(1)PK;ADEASELACPT(1)PK;ADEASELACPT(1)PK;ADEASELACPT(1)PK;ADEASELACPT(1)PK;ADEASELACPT(1)PK;ADEASELACPT(1)PK;ADEASELACPT(1)PK;ADEASELACPT(1)PK 266.63 2.15E-23 64823260000 16821210 16719140 16751710 13933800 18096590 17240180 26416400 25977450 34513520 TRUE FALSE 14598244.48 16609310.87 24852892.99 17097682.25 17736503.26 17903420.88 23854541.59 20422374.47 30433370.98 0.479678853 0.545759813 0.816632932 0.561807046 0.582797853 0.588282543 0.783828436 0.671052 1 24.85915081 -0.667839628 0.830688511 9.999999994 0.605088779 0.587189424 0.100682706 38.25412893 1.35101798 616.4066885 0.036573134 0.214862375 0.667839628 -9.394911215 ADEDPIMGFHQMFLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ADEDPIMGFHQMFLLK 16 0 P61970;H3BRV9 P61970 NUTF2 Nuclear transport factor 2 0 ;; 184.31 1.84E-09 3669560000 3833540 3021550 1901110 2162740 2571070 2244300 3345620 3676750 3385660 FALSE TRUE 3326927.976 3001701.239 2820493.155 2653823.172 2519910.737 2330639.673 3021162.287 2890505.625 2985411.132 1.114395247 1.005456571 0.944758705 0.888930554 0.844074945 0.780676286 1.011975287 0.968210239 1 21.50949819 4.570557857 1.849589453 0.918842816 1.140515853 0.458541535 0.069554538 0.609622241 2.810884152 0.020827523 0.208696097 37201.27774 -4.570557857 0.221673037 ADEGISFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ADEGISFR 8 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;;;;; 198.92 0.00030729 15643940000 9860020 8620810 6012490 6851250 8285800 8600200 8606080 9573020 9057130 FALSE TRUE 8556993.375 8564179.331 8920150.275 8406931.027 8120928.791 8931055.259 7771463.686 7525904.17 7986406.409 1.07144477 1.072344543 1.116916648 1.052655049 1.016843919 1.118282091 0.973086428 0.942339243 1 22.92911506 2.179415365 8.518758878 0.96514358 1.072847119 0.692659739 0.032214098 0.146791725 19.14835517 0.012986725 0.008762927 151.1525104 -2.179415365 0.107703539 ADEGS(ph)PVEPSQEQDILTSMEASGHLSTNLWHAVTDDDTGQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ADEGSPVEPSQEQDILTSMEASGHLSTNLWHAVTDDDTGQK 41 0 O15040-2;O15040 O15040-2 TECPR2 Tectonin beta-propeller repeat-containing protein 2 1 ADEGS(1)PVEPSQEQDILTSMEASGHLSTNLWHAVTDDDTGQK;ADEGS(0.81)PVEPS(0.135)QEQDILT(0.024)S(0.024)MEAS(0.005)GHLS(0.001)T(0.001)NLWHAVTDDDTGQK 296.76 3.44E-96 91412000 101959 106070 19347.1 56321 116908 98023 128115 144533 72321 TRUE FALSE 88484.85982 105373.2192 28703.42227 69109.54386 114581.7595 101794.0082 115690.427 113625.7427 63771.29377 1.387534337 1.652361321 0.450099419 1.083709296 1.79676078 1.596235582 1.814145836 1.781769445 1 15.96061953 3.24646341 24.99608026 1.636930651 1.130255172 0.258963873 0.378422437 230.059216 727660.0444 0.110982451 0.140654854 1763.857148 -3.24646341 -0.506675479 ADEHVIDQGDDGDNFYVIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ADEHVIDQGDDGDNFYVIER 20 0 P13861-2;P13861;H7C1L0 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 0 ;;; 295.66 1.32E-54 2294920000 1639110 1528160 1030590 1230210 1441460 1490250 1505700 1825380 1625280 FALSE TRUE 1422497.461 1518121.416 1528986.771 1509547.983 1412777.766 1547580.882 1359677.446 1435036.692 1433141.25 0.992573105 1.059296435 1.066877931 1.053314168 0.985791014 1.079852305 0.948739314 1.001322579 1 20.45074938 2.236632103 24.99999706 0.985655153 1.039927017 0.390360076 0.033102369 51.89286659 672682.114 0.012538638 0.008934937 172.4376529 -2.236632103 0.054271864 ADEIEMIMTDLER ddPTM_MDA-MB-175_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 ; 134.75 0.00021393 16487400 32716 30632 21265.4 24119.7 27374 29698 29909 31628 34436 FALSE TRUE 28392.49771 30430.77638 31549.41857 29596.44653 26829.31096 30840.50128 27008.42978 24864.59833 30365.01531 0.935039796 1.002165685 1.039005522 0.974689004 0.883559935 1.015659006 0.88945879 0.818856769 1 14.89012248 2.698109697 1.008793315 0.889386591 0.989911839 0.148033509 0.064213049 0.755984789 1.692761348 0.046033539 0.032931338 499.0105144 -2.698109697 0.100525248 ADELLCWEDSAGHWLYE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADELLCWEDSAGHWLYE 17 0 Q13232;H3BPR2 Q13232 NME3 Nucleoside diphosphate kinase 3;Nucleoside diphosphate kinase 0 79.741 0.030008 13013000 22950 23470 13621 17419 18007 26228 19328 24221 24432 FALSE TRUE 19917.09935 23315.82402 20208.16116 21374.25018 17648.69593 27237.00813 17453.57353 19041.52764 21543.67679 0.924498615 1.082258347 0.938008927 0.992135669 0.81920538 1.264269251 0.810148319 0.883856912 1 14.39497687 ADEVAPAKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ADEVAPAKK 9 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 76.465 0.056689 450080000 386840 309964 243412 276826 240687 263174 428400 462150 308748 FALSE TRUE 335718.1139 307927.8261 361126.8574 339683.5743 235897.7996 273298.4741 386853.8339 363322.819 272248.1632 1.233132705 1.131055661 1.326462053 1.247698315 0.866480776 1.003857917 1.420960309 1.334528082 1 18.05456279 -1.368741056 9.914662553 0.080990769 1.187106749 0 0.175170385 0 0 0 0.041511192 0.042781789 1.368741056 1.10611598 ADEVVWVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ADEVVWVR 8 0 P14868;C9J7S3;H7C278;C9JLC1;C9JQM9 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ; 133.12 0.002171 565410000 476620 361910 242440 317490 379730 348880 395460 428540 417510 FALSE TRUE 413633.4594 359532.5894 359684.7949 389580.957 372174.1159 362301.6394 357108.3501 336900.0559 368152.4434 1.123538542 0.976586183 0.976999613 1.058205545 1.010923933 0.984107659 0.970001304 0.915110199 1 18.48994375 2.523286122 1.857302992 0.951011353 1.026167109 0.312531994 0.046394125 0.398376818 2.790671514 0.021169289 0.015677492 333.6461533 -2.523286122 0.075155756 ADEWLMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ADEWLMK 7 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ;;;; 121.52 0.010306 1768127000 2303940 1924610 1353647 1654404 1841120 1633837 2128130 2527910 2130720 FALSE TRUE 1999468.492 1911967.11 2008275.217 2030061.714 1804485.314 1696691.767 1921744.28 1987336.119 1878828.709 1.064210102 1.017637798 1.06889745 1.080493237 0.960430988 0.90305825 1.022841662 1.057752689 1 20.84140211 3.244704238 24.99771086 0.995697661 1.055732216 0.381441967 0.04312956 210.838128 857872.064 0.014445703 0.018174079 1756.726845 -3.244704238 0.060034555 ADFCIIHYAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 12201960000 19235900 17187080 11953570 14565880 15913080 14328910 20316420 21247530 20023220 FALSE TRUE 16693827.08 17074176.94 17734356.43 17873285.68 15596440.84 14880152.44 18346136.72 16703911.06 17656097.74 0.945499245 0.967041369 1.004432389 1.012301016 0.88334586 0.842776963 1.03908219 0.946070378 1 24.07366319 ADFDNTVAIHPTSSEELVTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ADFDNTVAIHPTSSEELVTLR 21 0 P00390-5;P00390-4;P00390-2;P00390-3;P00390 P00390-5 GSR "Glutathione reductase, mitochondrial" 0 ;;;;; 258.4 1.63E-36 3095970000 2453772 2652494 1280016 2038977 2628713 2710804 2391541 2881265 3074748 FALSE TRUE 2129499.813 2635069.592 1899036.019 2501957.892 2576406.754 2815090.384 2159609.722 2265128.902 2711254.794 0.785429616 0.97190039 0.700426984 0.922804414 0.950263605 1.038297983 0.796535142 0.835454088 1 21.37052927 ADFFEDENGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ADFFEDENGQR 11 0 O95573 O95573 ACSL3 Long-chain-fatty-acid--CoA ligase 3 0 ;;; 208.75 5.42E-08 367000000 705270 637740 478112 697760 828860 759950 586470 948970 1072250 FALSE TRUE 612066.7826 633550.6439 709328.5624 856197.0726 812367.3076 789185.7683 529594.2297 746040.1504 945489.8265 0.647354171 0.670076638 0.750223368 0.905559265 0.85920259 0.834684569 0.560126841 0.789051484 1 19.85070241 4.134231828 3.509870498 0.807539886 0.656112982 0.263696328 0.11166709 0.359438416 8.500171956 0.030850364 0.074472815 13621.71619 -4.134231828 -0.151426904 ADGAT(ph)SDDLDLHDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADGATSDDLDLHDDR 15 0 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 ADGAT(0.5)S(0.5)DDLDLHDDR 98.062 0.013679 0 71134 66899 44134 64696 67132 70374 63873 78063 87148 TRUE FALSE 61733.46167 66459.53606 65477.35002 79386.21562 65796.20454 73081.33332 57678.60629 61369.83494 76845.46272 0.803345565 0.864846586 0.852065271 1.033063148 0.856214566 0.951016895 0.750579205 0.798613643 1 16.22967246 1.22061178 24.56227092 1.000000535 0.862819705 0.223961668 0.079709541 1581.802334 2164487.35 0.626887891 0.020293209 16.61926373 -1.22061178 -0.13718083 ADGATSDDLDLHDDRLS(ph)YLSAPGSEYSMYSTDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADGATSDDLDLHDDRLSYLSAPGSEYSMYSTDSR 34 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 ADGAT(0.026)S(0.026)DDLDLHDDRLS(0.945)Y(0.002)LS(0.001)APGSEYSMYSTDSR 77.539 0.0013656 47289000 37472 49517 26324 65607 37300 35520 45031 39476 42852 TRUE FALSE 32519.98026 49191.71957 39054.37445 80504.07209 36557.80298 36886.47738 40663.90055 31034.3646 37786.08538 0.860633747 1.301847468 1.033564977 2.130521627 0.967493791 0.976192083 1.076160712 0.821317273 1 15.20556744 3.061935158 24.99999954 0.957314352 1.338320485 0.229190576 0.330785539 96.32833003 38881.67875 0.097435198 0.110481122 1153.281055 -3.061935158 0.381006133 ADGTTPFYADSTAET(ph)Y(ph)GKIVHY(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ADGTTPFYADSTAETYGKIVHYK 23 1 Q09013-5 Q09013-5 DMPK Myotonin-protein kinase 3 ADGTTPFY(0.002)ADS(0.002)T(0.002)AET(0.998)Y(0.998)GKIVHY(0.998)K;ADGT(0.001)T(0.001)PFY(0.002)ADS(0.002)T(0.002)AET(0.997)Y(0.997)GKIVHY(0.997)K;ADGT(0.002)T(0.002)PFY(0.01)ADS(0.011)T(0.011)AET(0.988)Y(0.988)GKIVHY(0.988)K 48.229 0.050703 2383160000 1183750 1737060 792570 1115810 1825740 2154490 1120070 1175150 800710 TRUE FALSE 1027314.438 1725649.138 1175859.503 1369171.715 1789411.346 2237374.624 1011445.784 923853.3175 706050.976 1.455014543 2.444085763 1.665403127 1.939196689 2.534393984 3.168857066 1.432539318 1.308479627 1 19.42941282 2.023549968 24.99012271 1.234544324 2.200222319 0.472095406 0.480667522 195.6576998 207621.9085 0.199773515 0.134679627 105.5722963 -2.023549968 0.965677994 ADGYEPPVQES(ph)V ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADGYEPPVQESV 12 0 P61247;D6RAT0;H0Y9Y4;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 1 ADGYEPPVQES(1)V 84.17 0.012994 48086000 63152 56759 50104 50174 55574 51324 63112 76270 64479 TRUE FALSE 54806.30319 56386.14639 74334.46199 61566.77356 54468.18613 53298.46749 56991.40795 59960.25403 56856.36607 0.963943125 0.991729692 1.307407897 1.082847495 0.957996261 0.937423039 1.002375141 1.05459174 1 15.79503427 3.322364312 7.109467522 0.996927842 1.096677321 0.196699499 0.095185787 0.390438287 27.79809542 0.028848498 0.037226224 2100.701335 -3.322364312 0.099749478 ADHDFVVQEDFMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ADHDFVVQEDFMK 13 0 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ;;;; 171.36 2.52E-05 1606240000 2759980 2248970 1682760 1909660 2093210 1715330 2669480 3093100 2693470 FALSE TRUE 2395241.65 2234196.368 2496548.364 2343277.49 2051559.216 1781319.855 2410594.24 2431664.636 2375051.045 1.008501125 0.940694042 1.051155667 0.986621949 0.863795842 0.750013293 1.014965234 1.023836789 1 21.17952709 2.078508713 23.30809256 1.015485465 0.933733334 0.170904994 0.082447415 34.32388428 10186.82253 0.036414047 0.024550336 119.8143159 -2.078508713 -0.081752131 ADHGEPIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ADHGEPIGR 9 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;; 156.35 7.11E-05 28186650000 7640800 5536360 4031040 5170590 5571210 5670000 5563710 6557620 6192730 FALSE TRUE 6631048.921 5499991.287 5980464.427 6344651.487 5460353.821 5888128.569 5024142.261 5155323.994 5460632.514 1.214337149 1.007207731 1.095196282 1.161889483 0.999948963 1.078286912 0.92006599 0.944089166 1 22.38063664 2.614817802 1.362978056 0.951218773 1.105851451 0.480014109 0.066790731 0.350652053 1.347459274 0.034668996 0.025230359 411.9246693 -2.614817802 0.154632678 ADHGVPLPGS(ph)PPPTVALPLPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADHGVPLPGSPPPTVALPLPSR 22 0 A0A1W2PRX0;V9GYJ6;V9GY36;Q9UK80-2;Q9UK80-3;Q9UK80 A0A1W2PRX0 USP21 Ubiquitin carboxyl-terminal hydrolase 21 1 ADHGVPLPGS(1)PPPTVALPLPSR 95.255 0.0010593 125520000 353430 343040 220170 290780 382600 420500 326720 398300 364960 TRUE FALSE 306723.33 340786.5477 326644.9484 356806.0433 374987.0085 436676.9071 295034.7447 313126.6446 321814.8446 0.953104977 1.058952231 1.015008953 1.108730841 1.165225952 1.356919715 0.916784137 0.973002488 1 18.29587135 ADHPPAEVTSHAASGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ADHPPAEVTSHAASGAK 17 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ; 204.52 5.04E-12 423460000 727410 619480 396080 574440 609670 540270 718720 825760 1002570 FALSE TRUE 631280.9255 615410.5951 587625.6128 704875.3818 597538.7598 561054.5365 649018.645 649177.6501 884047.3167 0.714080472 0.696128571 0.664699278 0.797327664 0.675912645 0.634643108 0.734144692 0.734324552 1 19.75376406 1.15410758 2.559850397 1.122260783 0.701220658 0.817561869 0.043748685 0.293896834 1.743133049 0.300235768 0.011354304 14.25960779 -1.15410758 -0.421040125 ADHQPLTEASYVNLPTIALCNTDSPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ADHQPLTEASYVNLPTIALCNTDSPLR 27 0 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;;; 292.25 1.57E-70 1563190000 1028870 951618 605676 772038 899892 979941 943298 1116040 949464 FALSE TRUE 892902.2227 945366.7587 898582.9395 947341.0278 881985.9098 1017639.964 851817.1051 877383.531 837219.4476 1.066509175 1.12917439 1.073294394 1.131532516 1.053470404 1.215499673 1.01743588 1.047973185 1 19.6752463 ADIDLTKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADIDLTKR 8 1 P62269 P62269 RPS18 40S ribosomal protein S18 0 78.516 0.048781 153530000 348750 282790 168620 188250 261710 256100 301160 350540 131060 FALSE TRUE 302661.8039 280932.3339 250165.196 230995.0397 256502.483 265952.3327 271953.5496 275579.7489 115566.2361 2.618946624 2.430920512 2.164691042 1.99881079 2.21952788 2.301297868 2.353226675 2.384604346 1 16.81836044 1.236329868 24.995985 0.999998317 2.301189807 0.861785459 0.164721699 22.55433516 252665.2772 0.279319932 0.043201464 17.23176917 -1.236329868 1.30119149 ADIEER ddPTM_MDA-MB-175_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 573040000 2187190 2068100 1255050 1369480 1595660 2147510 2109850 2175000 2038440 FALSE TRUE 1898147.3 2054514.515 1861996.378 1680441.365 1563909.488 2230126.099 1905237.072 1709893.176 1797457.945 1.056017641 1.143011173 1.035905392 0.93489885 0.870067359 1.240711142 1.059961974 0.951284107 1 20.77752659 4.05181307 7.448480626 1.008516356 1.097998701 0.120988323 0.099047247 0.48920332 58.45957903 0.026236699 0.05494364 11267.1239 -4.05181307 0.089482345 ADILEDKDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ADILEDKDGK 10 1 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;; 132.76 0.00019606 5225660000 10183140 6495220 6027730 6255230 5572560 3825700 9116930 10440960 8060310 FALSE TRUE 8837412.248 6452552.472 8942760.39 7675575.577 5461676.959 3972877.155 8232771.532 8208241.956 7107429.334 1.24340487 0.907860236 1.258227127 1.079936953 0.768446185 0.558975259 1.158333224 1.154881965 1 22.76089642 7.999998254 0.781350895 0.982516632 50.54955029 0.124432788 0.205977134 1287.757766 4.860435196 0.081056185 112760.0583 99999598.03 -7.999998254 49.56703366 ADIPVKSS(ph)PQAAVPYKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADIPVKSSPQAAVPYKK 17 2 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 ADIPVKS(0.11)S(0.89)PQAAVPYKK 85.146 0.0026655 500710000 410830 315030 191490 165930 265020 205260 373860 386030 185340 TRUE FALSE 356537.7746 312960.5472 284095.2045 203606.9426 259746.6205 213156.485 337603.1147 303480.4886 163429.3163 2.181602313 1.914959655 1.738336859 1.245840998 1.589351448 1.304273247 2.065743909 1.856952568 1 17.31830728 4.356956315 2.210100686 1.573893407 2.160762032 0.341335324 0.306673817 0.455504828 4.050862873 0.085025741 0.384712785 22748.68596 -4.356956315 0.586868625 ADITGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ADITGR 6 0 O95994;B5MC07;H7C3Z9 O95994 AGR2 Anterior gradient protein 2 homolog 0 ;;; 137.83 0.029234 5547190000 2675330 2832800 2086290 2147380 1906300 3212310 2453060 2371480 2046930 FALSE TRUE 2321778.362 2814191.15 3095226.822 2634975.45 1868368.36 3335889.644 2215162.619 1864357.457 1804944.267 1.28634352 1.559156812 1.714860053 1.45986527 1.035139086 1.848195374 1.227274802 1.032916911 1 20.78352286 2.006504458 24.89403474 1.052195463 1.481465526 0.440086665 0.220061156 135.0219841 516757.3511 0.088211919 0.05930462 101.5089787 -2.006504458 0.429270063 ADKDES(ph)T(ph)MINEIT(ph)LAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 55.656 0.053985 4850500000 3278890 3523190 2526360 2284560 2536510 2061130 5021750 3909610 2026680 TRUE FALSE 2845576.379 3500045.933 3748116.146 2803304.265 2486038.414 2140423.005 4534741.458 3073570.326 1787088.199 1.592297672 1.958518855 2.097331373 1.568643488 1.391111202 1.197715371 2.537502883 1.719876124 1 20.76917941 3.715267652 24.24871601 1.622471587 1.890296311 0.100413181 0.422611565 1481.200718 1541976.513 0.120685308 0.179142923 5191.198691 -3.715267652 0.267824724 ADKDYHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ADKDYHFK 8 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;;;; 123.88 0.0012116 21166500000 76948060 55301210 41548910 51667560 48652840 38113720 66201340 78208560 67539950 FALSE TRUE 66779178.91 54937932.71 61642101.85 63399469.19 47684743.67 39579979.47 59781144.24 61484268.06 59555454.05 1.121294094 0.92246686 1.035037056 1.06454514 0.800678031 0.66459034 1.00378958 1.032386858 1 25.8277303 7.999978205 0.840005995 0.93417365 57.65323322 0.170850618 0.123438237 1441.112899 4.179605133 0.046617497 156079.1715 99994981.57 -7.999978205 56.71905957 ADKDYHFKVDNDENEHQLSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADKDYHFKVDNDENEHQLSLR 21 2 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 147.21 3.27E-08 653410000 1407800 1020900 209140 262890 756140 598540 1188400 1333200 20146 FALSE TRUE 1221755.663 1014193.641 310280.8035 322583.1925 741094.2934 621566.2211 1073149.151 1048105.555 17764.36283 68.77565352 57.09147299 17.46647524 18.1590072 41.71803405 34.98950269 60.41022474 59.00045867 1 14.11669832 7.999999674 0.051079539 9.999999966 97.77474208 0.063193641 21.47698305 6794.8037 33.91346117 16148.83555 52033.44542 99999924.86 -7.999999674 87.77474212 ADKLAEEHSS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADKLAEEHSS 10 1 P06576 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 107.06 0.0021292 283940000 493010 527490 139390 312890 588170 550260 562260 661100 76895 FALSE TRUE 427857.4794 524024.8835 206799.4702 383936.4567 576466.5677 571428.8583 507732.1117 519728.9097 67804.5607 6.310157827 7.728460712 3.049934519 5.662398705 8.501884855 8.427587354 7.488170508 7.665102529 1 16.0490947 6.23972763 9.810288032 6.424065779 6.499547306 0 2.451841284 0 0 0.541494034 0 1736711.3 -6.23972763 0.075481527 ADKNEVAAEVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADKNEVAAEVAK 12 1 P56192;H0YIP0 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 78.486 0.014593 0 154910 90719 61356 80575 113460 71821 120020 144030 126230 FALSE TRUE 134438.251 90123.06092 91027.96682 98870.78526 111202.368 74584.00034 108380.4789 113230.3053 111307.2332 1.207812351 0.809678386 0.817808189 0.888269184 0.999057876 0.670073258 0.973705623 1.017277153 1 16.76418782 2.016988625 24.99302006 1.005558388 0.889028772 0.101256667 0.13872777 462.8034884 680856.4813 0.054136626 0.036489424 103.9892928 -2.016988625 -0.116529616 ADKVEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ADKVEQR 7 1 Q99832-3;Q99832;Q99832-4 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 72.485 0.046948 238180000 1139380 989520 653820 772780 548300 828140 1112940 1231620 1002980 FALSE TRUE 988808.0462 983019.778 970009.5389 948251.5102 537389.9027 859999.0817 1005007.25 968247.6475 884408.847 1.118044047 1.111499259 1.096788597 1.072186821 0.607626105 0.972399908 1.136360467 1.094796429 1 19.75435393 3.458875757 24.998451 0.97851339 1.104956076 0.190439901 0.140148607 498.7628261 683360.9664 0.044508338 0.057470024 2876.575368 -3.458875757 0.126442686 ADLAEEYSKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ADLAEEYSKDR 11 1 P68036-2;P68036;P68036-3 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 ;;;; 147.33 3.22E-05 4296200000 6539430 5628850 3613260 4652050 5201150 4670920 5817450 7107900 2543080 FALSE TRUE 5675227.757 5591873.714 5360644.622 5708369.055 5097657.291 4850613.315 5253274.594 5587930.899 2242439.979 2.530827049 2.493655913 2.39054096 2.545606173 2.273263649 2.163096163 2.342660068 2.491897643 1 21.09663794 1.236287167 24.9999993 0.999998189 2.400395137 0.930392285 0.120679979 15.62150572 171741.5635 0.20404889 0.031484631 17.23007498 -1.236287167 1.400396948 ADLINNLGTIAK ddPTM_MDA-MB-175_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 ; 195.25 1.14E-06 471330000 1127000 922860 956540 845270 826130 758070 947820 1247890 993560 FALSE TRUE 978064.0945 916797.6719 1419125.943 1037201.473 809691.6293 787233.4434 855900.5623 981038.4346 876102.4687 1.116380937 1.046450278 1.619817309 1.183881463 0.924197406 0.898563206 0.97694116 1.119775905 1 19.74074009 3.386105447 5.776851648 0.997723068 1.264605136 0.398548357 0.158806217 0.22222093 11.31765851 0.047534012 0.061705401 2432.794624 -3.386105447 0.266882068 ADLNQGIGEPQS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ADLNQGIGEPQSPSR 15 0 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 ADLNQGIGEPQS(0.998)PS(0.002)R;ADLNQGIGEPQS(0.908)PS(0.092)R;ADLNQGIGEPQS(0.983)PS(0.017)R 324.73 4.34E-57 1626100000 1394140 1341290 848540 1007570 1146550 1180630 1147460 1248060 1664860 TRUE FALSE 1209900.867 1332478.978 1258896.782 1236354.168 1123735.898 1226049.6 1036179.506 981172.0814 1468042.147 0.824159489 0.907657168 0.857534495 0.842178932 0.765465692 0.835159673 0.705824085 0.668354163 1 20.48546196 3.366243447 2.26290236 0.772993191 0.86813226 0.078551064 0.091156691 0.543644089 5.66934771 0.029004437 0.04053788 2324.03919 -3.366243447 0.095139069 ADLNQGIGEPQSPS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADLNQGIGEPQSPSR 15 0 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 ADLNQGIGEPQS(0.263)PS(0.737)R 232.34 7.66E-14 276790000 354850 308800 219410 281400 318300 336570 298150 316660 419890 TRUE FALSE 307955.6734 306771.4725 325517.4099 345296.1709 311966.4527 349518.0657 269235.4589 248944.7233 370251.0825 0.831748205 0.828549833 0.879180171 0.932600031 0.842580798 0.944002819 0.727169944 0.672367307 1 18.49814443 2.229960207 24.99988336 0.77025958 0.875404385 0.105234291 0.092730339 285.0691105 828637.6046 0.036950048 0.025352377 169.8088054 -2.229960207 0.105144804 ADLSIPDLHEIVTEELEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ADLSIPDLHEIVTEELEER 19 0 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;A0A0J9YW54 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 0 ;;;; 228.39 1.05E-19 346733000 365519 414370 282137 292850 407128 454872 412421 471799 468174 FALSE TRUE 317214.738 411647.9762 418579.3969 359346.0684 399026.9493 472371.2202 372424.4749 370908.4554 412827.0031 0.768396291 0.997144017 1.013934151 0.870451947 0.966571824 1.144235277 0.90213206 0.898459773 1 18.65517782 3.02865341 24.77948038 0.974702019 0.924867545 0.109732695 0.094904544 637.3931525 551213.1584 0.029601354 0.033564263 1068.202058 -3.02865341 -0.049834473 ADPSLLGFSVNAS(ph)SER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.955)S(0.045)ER;ADPSLLGFSVNAS(0.907)S(0.093)ER 148.52 9.69E-07 170151000 85918 86386 56755 64535 72737 85372 77692 85531 80238 TRUE FALSE 74563.71861 85818.52468 84201.90783 79188.65811 71289.67601 88656.31608 70157.4418 67240.86125 70752.35505 1.05386907 1.212942306 1.190093358 1.119237064 1.00759439 1.253051097 0.991591612 0.950369231 1 16.11049055 2.107703658 8.266925918 0.97157108 1.137962604 0.516612584 0.072492028 0.180778726 12.63386389 0.028737891 0.019345607 128.1455879 -2.107703658 0.166391524 ADQEEQIHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ADQEEQIHPR 10 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;; 208.84 1.06E-07 2171380000 1926080 1713160 1199250 1439710 1468420 1725660 1713490 1918370 1985650 FALSE TRUE 1671543.648 1701906.139 1779211.311 1766618.16 1439201.315 1792047.257 1547316.004 1508141.504 1750908.719 0.954672068 0.972013058 1.016164516 1.008972164 0.821973927 1.023495535 0.883721685 0.861347875 1 20.73967244 ADQELLMYSHDNIICGITSVAFSR ddPTM_MDA-MB-175_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 ;; 339.86 2.96E-87 1057050000 891941 776336 551246 846358 806624 1037869 700020 1022830 811676 FALSE TRUE 774068.737 771236.1977 817830.4094 1038536.52 790573.7605 1077796.492 632132.1681 804105.7642 715720.5879 1.081523642 1.077566037 1.142667157 1.451036252 1.10458435 1.505890022 0.883210821 1.123491175 1 19.44903695 2.206150055 24.99999534 1.022536729 1.221166731 0.30825866 0.15772485 260.2906909 200774.3117 0.062773483 0.042325424 160.7496571 -2.206150055 0.198630001 ADRDESSPYAAMLAAQDVAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ADRDESSPYAAMLAAQDVAQR 21 1 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ;;;;;;; 322.49 3.66E-67 13293611000 7217411 6582111 4797583 5940477 6726246 6200783 6407772 7318717 7788766 FALSE TRUE 6263611.85 6538872.679 7117710.186 7289353.097 6592406.864 6439331.134 5786347.258 5753666.324 6867986.956 0.912001128 0.95207995 1.036360469 1.061352205 0.959874692 0.937586395 0.842509937 0.837751493 1 22.71145587 2.588305941 2.713319165 0.880646115 0.990653888 0.304432441 0.061033329 0.293081453 4.213583252 0.024554695 0.020583525 387.5305464 -2.588305941 0.110007773 ADRDQS(ph)PFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ADRDQSPFSK 10 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 ADRDQS(0.849)PFS(0.151)K;ADRDQS(1)PFSK;ADRDQS(1)PFSK;ADRDQS(0.996)PFS(0.004)K;ADRDQS(1)PFSK 147.66 2.04E-05 5135990000 12017310 8845420 6057730 7161990 8094810 6852510 9876960 11585040 8700990 TRUE FALSE 10429192.04 8787313.854 8987268.49 8788229.294 7933739.118 7116130.494 8919093.939 9107669.351 7672368.874 1.359318381 1.145319522 1.171381178 1.145438839 1.034066433 0.92750109 1.162495454 1.187073966 1 22.87124065 7.999999351 0.806380666 1.086338796 71.75342609 0.537786291 0.080455038 478.4134988 1.613974317 0.030563871 61795.42258 99999850.46 -7.999999351 70.6670873 ADRDQSPFS(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADRDQSPFSK 10 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 ADRDQS(0.091)PFS(0.909)K 125.36 0.0010816 369320000 562900 407260 274610 326120 412200 318190 484860 549890 414870 TRUE FALSE 488511.3388 404584.6822 407412.3145 400170.5304 403998.0265 330430.9752 437838.3518 432300.3027 365824.5412 1.335370605 1.105952818 1.113682295 1.093886509 1.104349165 0.903249886 1.196853416 1.181714877 1 18.48079234 4.741609344 4.700841289 1.094821717 1.350121186 0.458679769 0.08439532 0.187280656 11.44212887 0.021155164 0.157817434 55158.10588 -4.741609344 0.255299469 ADRPSSLPLDFNDEFS(ph)DLDGVVQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ADRPSSLPLDFNDEFSDLDGVVQQR 25 1 D6REP5;B7Z4W8;E9PD09;Q96HH9-5;Q96HH9-4;Q96HH9;Q96HH9-2;Q96HH9-3 D6REP5 GRAMD3 GRAM domain-containing protein 3 1 ADRPSSLPLDFNDEFS(1)DLDGVVQQR;ADRPS(0.159)S(0.159)LPLDFNDEFS(0.682)DLDGVVQQR 129.16 6.30E-05 133617000 63564 70401 53959 56194 82521 95538 54576 86443 89885 TRUE FALSE 55163.85635 69938.5312 80053.75288 68953.70657 80878.99355 99213.40868 49283.22792 67957.83715 79258.8977 0.695995755 0.882406054 1.010028592 0.86998064 1.020440555 1.25176367 0.621800572 0.857415875 1 16.27428528 7.497732461 10.76005862 0.909455344 0.085367396 0 0.176734046 0 0 0.039479812 0 31458098.01 -7.497732461 -0.824087947 ADS(ph)LLAVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ADSLLAVVK 9 0 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 1 ADS(1)LLAVVK;ADS(1)LLAVVK 129.89 0.00039505 121834000 412130 375020 287790 320510 430120 302510 440050 512040 524310 TRUE FALSE 357665.9763 372556.4689 426966.2066 393286.6942 421561.4535 314147.7555 397374.0187 402544.2307 462326.6691 0.773621771 0.805829501 0.923516282 0.850668414 0.911825948 0.679493043 0.859509185 0.870692213 1 18.81855306 1.202118538 2.072993618 1.063107871 0.8308058 0.375015149 0.06923763 0.918295589 3.598563278 0.422890031 0.01862324 15.92643369 -1.202118538 -0.23230207 ADS(ph)PAGPESSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADSPAGPESSR 11 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 ADS(1)PAGPESSR 71.219 0.052059 55532000 82088 65725 46314 53091 59524 62652 63900 69927 83197 TRUE FALSE 71239.86282 65293.24815 68711.60531 65146.123 58339.58886 65062.26298 57702.98784 54973.65522 73361.54544 0.97107909 0.890020075 0.93661611 0.888014594 0.795233913 0.886871488 0.786556329 0.749352469 1 16.16273641 3.447021946 4.57198801 0.829876575 0.92667624 0.234184533 0.070895856 0.254615909 12.71342227 0.020363806 0.027517069 2799.122762 -3.447021946 0.096799664 ADS(ph)PHVSGSEADVASLAPVDSSFSLLSVSHALYDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADSPHVSGSEADVASLAPVDSSFSLLSVSHALYDSR 36 0 A0A499FJD3;A0A3B3ISA1;Q96S15 A0A499FJD3 WDR24 WD repeat-containing protein 24 1 ADS(0.923)PHVS(0.039)GS(0.039)EADVASLAPVDSSFSLLSVSHALYDSR 93.177 0.0009124 36160000 8401.8 6526.6 2005.9 3444.8 8746.4 9730.3 7760 6793.7 4183.5 TRUE FALSE 7291.480843 6483.726335 2975.959949 4226.99449 8572.363752 10104.63094 7007.436394 5340.920124 3688.931396 1.976583476 1.757616404 0.806726835 1.145858797 2.32380677 2.739175618 1.899584363 1.447823109 1 11.84898724 3.253976211 24.99980682 1.871964071 1.401764314 0.144601907 0.555157966 538.0975974 872639.57 0.177105265 0.227787852 1794.635321 -3.253976211 -0.470199758 ADSEQPSKRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADSEQPSKRPR 11 2 Q9Y3Z3-4;Q9Y3Z3;A0A2R8YCS7;Q9Y3Z3-3;A0A2R8YF51;A0A2R8Y5D2;A0A2R8Y586;A0A2R8Y7R5;A0A2R8Y755 Q9Y3Z3-4 SAMHD1 Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 0 93.258 0.005278 38685000 48939 51512 17492 19167 38955 39010 47468 62776 4117.7 FALSE TRUE 42471.58715 51173.61428 25951.18971 23519.1603 38179.87171 40510.73994 42864.56067 49351.84092 3630.910197 11.69722875 14.09388046 7.14729594 6.477483337 10.51523437 11.15718587 11.80545878 13.59214033 1 11.82611553 4.250278361 24.99327169 9.461529815 12.89555506 0.166223454 3.578813952 457.2704562 975312.759 0.900596388 2.340821465 17794.19562 -4.250278361 3.434025249 ADSGPTQPPLSLS(ph)PAPETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ADSGPTQPPLSLSPAPETK 19 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 1 ADSGPTQPPLSLS(1)PAPETK;ADSGPTQPPLSLS(1)PAPETK;ADSGPTQPPLSLS(1)PAPETK;ADSGPTQPPLSLS(1)PAPETK;ADSGPTQPPLSLS(1)PAPETK;ADSGPTQPPLSLS(1)PAPETK;ADSGPTQPPLSLS(1)PAPETK;ADSGPTQPPLSLS(1)PAPETK 334.45 2.27E-75 11565020000 9651500 9750110 6450310 8663900 10560070 7254260 11422350 15479120 12434190 TRUE FALSE 8376029.821 9686060.885 9569701.491 10631170.91 10349945.27 7533336.076 10314612.26 12169030.65 10964234.22 0.763941161 0.883423383 0.87281075 0.969622748 0.943973383 0.687082739 0.940750813 1.109884229 1 23.38630172 1.994304552 24.92232551 1.051548976 0.860842762 0.487008002 0.085009586 192.058715 840416.9927 0.035736371 0.02325003 98.69713635 -1.994304552 -0.190706214 ADTLDPALLRPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ADTLDPALLRPGR 13 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;; 155.86 4.28E-05 2804120000 2925000 2870910 2040840 2353270 2847600 2890660 2666650 3267120 3177080 FALSE TRUE 2538453.839 2852050.803 3027797.05 2887615.921 2790938.331 3001865.561 2408038.693 2568471.813 2801489.222 0.906108729 1.018048108 1.08078126 1.030743184 0.996233828 1.071524937 0.859556651 0.916823735 1 21.41776251 2.24196371 24.99999945 0.920914903 1.019823931 0.357953584 0.057768564 87.53664309 643073.425 0.022054626 0.01637924 174.5676278 -2.24196371 0.098909028 ADTLDPALLRPGRLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADTLDPALLRPGRLDR 16 2 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 97.417 0.0017325 79083000 106950 100910 22706 23629 82230 89131 92574 101500 1995.7 FALSE TRUE 92816.28652 100247.1156 33686.69755 28994.3256 80593.78388 92559.92725 83596.18773 79795.01487 1759.77062 52.74340047 56.96601276 19.14266392 16.47619597 45.79789149 52.59772281 47.50402513 45.34398631 1 10.78117168 1.235589709 24.88042926 0.999940617 41.87400807 0.471284676 13.66995164 78.25474609 655230.4243 24.55269356 3.596875443 17.20242641 -1.235589709 40.87406745 ADTLTLEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ADTLTLEER 9 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4;K7EL40 Q9UHD8 9-Sep Septin-9 0 ;;; 175.51 0.00012529 1029570000 1214690 1224250 825450 962710 1147530 1174950 1193270 1369740 1236610 FALSE TRUE 1054165.639 1216207.821 1224640.381 1181308.02 1124696.398 1220151.087 1077546.859 1076831.76 1090419.375 0.966752484 1.115357861 1.123091179 1.083352009 1.031434716 1.118974145 0.988194895 0.987539093 1 20.05645167 2.22060746 24.98982971 0.990845554 1.075914677 0.40052866 0.046770642 224.6350777 312677.6504 0.018448895 0.01246726 166.1909842 -2.22060746 0.085069123 ADTQTYQPYNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADTQTYQPYNK 11 0 P84090 P84090 ERH Enhancer of rudimentary homolog 0 149.23 0.0038995 0 107650 84437 57885 69626 81448 71037 82745 88804 95517 FALSE TRUE 93423.77975 83882.32779 85878.37961 85435.64747 79827.34415 73769.83936 74720.40264 69813.95567 84225.08907 1.109215565 0.995930413 1.019629431 1.014372895 0.947785809 0.875865377 0.887151364 0.82889738 1 16.36196243 3.123507725 1.847060977 0.885170687 1.037528749 0.611187626 0.051428896 0.211063644 1.4834985 0.017730378 0.02127387 1328.947194 -3.123507725 0.152358062 ADTQTYQPYNKDWIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ADTQTYQPYNKDWIK 15 1 P84090 P84090 ERH Enhancer of rudimentary homolog 0 ; 248.81 1.75E-18 3322000000 5864900 4024800 2261600 2484700 3758300 3146500 5130200 6030600 952040 FALSE TRUE 5089838.605 3998360.824 3355317.325 3048889.111 3683517.183 3267547.891 4632673.994 4741003.12 839490.9158 6.063006174 4.762839893 3.996847687 3.631830975 4.387798741 3.892296902 5.518432548 5.647474 1 19.67915519 4.671455049 2.812848165 4.236339629 6.259468438 0.193560298 1.277746539 0.664547293 7.907547617 0.321621193 2.849225635 46930.48567 -4.671455049 2.023128809 ADTSS(ph)AENILYTVGLWEAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ADTSSAENILYTVGLWEAPR 20 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 ADT(0.01)S(0.139)S(0.85)AENILYTVGLWEAPR;ADT(0.003)S(0.019)S(0.978)AENILYTVGLWEAPR;ADT(0.006)S(0.038)S(0.956)AENILYTVGLWEAPR;ADTS(0.021)S(0.979)AENILYTVGLWEAPR;ADTS(0.003)S(0.997)AENILYTVGLWEAPR;ADT(0.003)S(0.025)S(0.971)AENILYTVGLWEAPR 381.64 3.30E-113 1589820000 1112756 962546 599608 698924 921259 936785 907014 1070291 1009216 TRUE FALSE 965702.4752 956222.9719 889580.4344 857625.3766 902927.7483 972823.7251 819051.9219 841417.5987 889907.6342 1.085171582 1.074519349 0.999632322 0.963724036 1.01463086 1.093173817 0.920378577 0.945511159 1 19.76329608 8 0.3153466 0.962435005 2.203775898 0.348550112 0.047588834 88.70760612 1.402526955 0.087298502 62.13613622 100000000 -8 1.241340893 ADVFHAYLSLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ADVFHAYLSLLK 12 0 Q86VP6;Q86VP6-2;A0A0C4DGH5;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 221.55 2.69E-11 980440000 2901600 2854800 1859370 2255780 2645500 2352230 3184200 3467000 3615300 FALSE TRUE 2518146.208 2836046.631 2758567.551 2767989.326 2592859.726 2442721.81 2875396.774 2725609.03 3187903.353 0.789906697 0.889627544 0.865323458 0.868278935 0.813343266 0.766247135 0.901971125 0.854984838 1 21.60417646 0.310984829 1.352584536 2.366169981 0.840705129 0.571167195 0.042680328 10.48294726 2.276002793 39.96181483 0.012352462 2.046373151 -0.310984829 -1.525464851 ADVQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ADVQKR 6 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 82.913 0.092983 69408000 433690 275880 127810 160730 151420 209690 302860 338250 82383 FALSE TRUE 376376.7677 274067.7261 189619.3435 197226.2031 148407.0382 217756.91 273488.6838 265917.8698 72643.77559 5.181128935 3.772762689 2.610262778 2.714977319 2.042942249 2.997599013 3.764791706 3.660573361 1 16.14855157 4.595298233 2.483779463 2.819594238 5.361535531 0.506682649 0.7926735 0.352445643 3.32854973 0.210774834 1.645451207 39382.04217 -4.595298233 2.541941292 ADVVPQQADPEFPRAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ADVVPQQADPEFPRASPR 18 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 ADVVPQQADPEFPRAS(1)PR;ADVVPQQADPEFPRAS(1)PR;ADVVPQQADPEFPRAS(1)PR;ADVVPQQADPEFPRAS(1)PR;ADVVPQQADPEFPRAS(1)PR 188.51 2.27E-14 5114320000 2124940 2051450 1298869 1470570 1891040 2140590 2024380 2161980 1210209 TRUE FALSE 1844123.795 2037973.89 1927006.393 1804485.395 1853412.004 2222939.882 1828055.939 1699657.402 1067139.471 1.728100071 1.909754016 1.80576808 1.690955535 1.736803909 2.083082805 1.71304313 1.592722834 1 20.02531731 1.151482174 1.742101488 0.55758337 1.818635495 0.831643774 0.114892733 0.468038419 1.096118935 1.071343532 0.031893331 14.17366532 -1.151482174 1.261052125 ADWWTNTAHYNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ADWWTNTAHYNR 12 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 230.59 5.45E-12 969410000 670800 678000 422200 529930 660900 694950 582980 665670 690460 FALSE TRUE 582152.0804 673546.1734 626377.3322 650258.706 647749.383 721685.1762 526442.6893 523321.6507 608834.6054 0.956174428 1.106287598 1.028813616 1.068038348 1.063916829 1.185355053 0.864672745 0.859546494 1 19.21569084 2.219430596 24.99982635 0.896154971 1.067855197 0.54494848 0.068646276 162.772231 212715.276 0.026934353 0.01819127 165.7412448 -2.219430596 0.171700225 ADYDTLSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ADYDTLSLR 9 0 Q9Y446;Q9Y446-2;E9PQ15;E9PK71;E9PKC4;E9PRW6;E9PJR7 Q9Y446 PKP3 Plakophilin-3 0 ;;; 204.36 3.89E-05 764450000 1268310 1372560 862950 1029750 1342690 1320040 1228560 1414800 1408650 FALSE TRUE 1100699.62 1363543.563 1280275.506 1263570.476 1315973.096 1370822.793 1109414.44 1112256.03 1242121.002 0.886145245 1.097754213 1.03071722 1.017268426 1.059456441 1.103614536 0.893161325 0.895449017 1 20.24437429 2.22596787 24.99947104 0.920919499 1.035912029 0.34644463 0.066198434 218.0915867 432957.8354 0.025653091 0.017428148 168.2549576 -2.22596787 0.114992529 AEADKIYSFTDNAPS(ph)PSIGGSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEADKIYSFTDNAPSPSIGGSSR 23 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 AEADKIYSFTDNAPS(0.743)PS(0.227)IGGS(0.015)S(0.015)R 76.259 0.0098107 187160000 192570 149710 88496 94665 134560 118250 141570 164300 68157 TRUE FALSE 167121.3866 148726.5452 131292.9616 116160.1351 131882.5193 122799.154 127840.5632 129165.7236 60099.5571 2.780742399 2.47466957 2.184591167 1.932795194 2.194400851 2.043262212 2.127146511 2.149195931 1 15.87506674 4.405358798 0.080059685 5.40E-37 4.885557018 0.556791753 0.302987923 113.0187736 3.162356816 73.77963116 123.0338725 25430.72829 -4.405358798 4.885557018 AEADKNDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 66.435 0.056263 374330000 485820 383370 343620 394150 746180 379520 475660 616690 639260 FALSE TRUE 421617.6561 380851.6172 509795.7813 483647.7817 731332.4779 394120.38 429530.5664 484815.6426 563687.411 0.747963584 0.675643291 0.904394477 0.858007066 1.29740786 0.699182512 0.762001347 0.86007889 1 19.10453582 4.2321026 24.87994783 0.903250493 0.711803419 0.20920465 0.16084594 212.509415 818719.3123 0.041486019 0.089790969 17064.8549 -4.2321026 -0.191447074 AEAEAEAGS(ph)PRPDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEAEAEAGSPRPDPR 15 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 AEAEAEAGS(1)PRPDPR;AEAEAEAGS(1)PRPDPR 59.872 0.061859 671730000 1273720 1357460 966340 1046640 1440370 1503620 1400100 1501280 1548250 TRUE FALSE 1105394.675 1348542.756 1433665.256 1284295.609 1411709.455 1561465.234 1264318.517 1180242.955 1365217.649 0.809683845 0.987785909 1.050136773 0.940725906 1.034054501 1.143748204 0.926093007 0.864509008 1 20.38069954 7.546353579 21.24132087 0.971585411 0.153601683 0 0.095150125 0 0 0.022128585 0 35184677.82 -7.546353579 -0.817983727 AEAEAGS(ph)PRPDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEAEAGSPRPDPR 13 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 AEAEAGS(1)PRPDPR;AEAEAGS(1)PRPDPR 54.501 0.082877 4091600000 2560500 2597800 1858920 2095530 2671200 2855000 2684500 3007900 2737600 TRUE FALSE 2222123.438 2580734.881 2757899.93 2571352.115 2618048.346 2964833.697 2424157.603 2364683.993 2413964.047 0.920528804 1.069085881 1.142477633 1.065199011 1.084543222 1.228201266 1.004222746 0.979585423 1 21.20297276 2.030209232 24.98746132 0.989405196 1.088493237 0.240633657 0.07585677 257.3142063 212835.482 0.030864281 0.020808418 107.2035659 -2.030209232 0.099088041 AEAGAGS(ph)ATEFQFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEAGAGSATEFQFR 14 0 P46783;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 1 AEAGAGS(0.954)AT(0.046)EFQFR 158.91 5.24E-06 86189000 92384 80649 53225 64231 86367 81186 74748 94059 104800 TRUE FALSE 80175.22033 80119.21141 78964.78803 78815.63026 84648.46567 84309.27795 67498.95046 73945.21482 92410.66339 0.867597065 0.866990978 0.85449866 0.852884585 0.916003225 0.912332786 0.730423828 0.800180543 1 16.49577172 AEAGVPAEFSIWTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AEAGVPAEFSIWTR 14 0 Q60FE5;P21333-2;P21333;H0Y5C6 Q60FE5 FLNA Filamin-A 0 ;; 226.73 5.33E-12 305850000 512679 421574 280445 328723 411918 428830 385359 457977 420863 FALSE TRUE 444927.1712 418804.6526 416069.14 403364.5814 403721.6377 445327.3676 347986.9435 360042.1825 371109.0556 1.198912192 1.128521782 1.121150599 1.086916569 1.087878702 1.199990571 0.937694562 0.970178919 1 18.50148368 2.230341183 24.99999743 0.968159556 1.131571771 0.787332247 0.041073077 79.82261222 242783.6957 0.016558482 0.011374634 169.9578321 -2.230341183 0.163412214 AEAPAGPALGLPS(ph)PEAESGVDRGEPEPMEVEEGELEIVPVRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AEAPAGPALGLPSPEAESGVDRGEPEPMEVEEGELEIVPVRR 42 2 Q53F19 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 AEAPAGPALGLPS(0.999)PEAES(0.001)GVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(1)PEAESGVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(1)PEAESGVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(1)PEAESGVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(1)PEAESGVDRGEPEPMEVEEGELEIVPVRR 344.78 5.57E-135 776534000 162327.2 122540.6 61416.1 76752.6 110241 108888 102239.4 134008.6 57311.1 TRUE FALSE 140875.2492 121735.6227 91117.13138 94180.45092 108047.4198 113076.9918 92324.23872 105351.9037 50535.84705 2.787630117 2.408896454 1.803019771 1.863636536 2.138035199 2.237560038 1.826905932 2.084696506 1 15.62501949 8 0.065338537 1.22E-12 6.34796566 0.4786045 0.33654484 722.4642768 4.552769052 104.001405 462.4007792 100000000 -8 6.34796566 AEAPPLEREDS(ph)GTFSLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AEAPPLEREDSGTFSLGK 18 1 O75569;G5E9Q4 O75569 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 1 AEAPPLEREDS(0.984)GT(0.016)FS(0.001)LGK;AEAPPLEREDS(0.711)GT(0.289)FSLGK;AEAPPLEREDS(0.985)GT(0.014)FS(0.001)LGK;AEAPPLEREDS(0.99)GT(0.008)FS(0.002)LGK 168.84 1.19E-11 662480000 1236340 735413 398117 535620 687044 446812 1047610 1026340 322179 TRUE FALSE 1072954.537 730582.0236 590647.7128 657240.7074 673373.1686 464001.1468 946012.9434 806865.178 284091.3656 3.776793899 2.57164459 2.079076608 2.313483572 2.370269744 1.633281412 3.329960209 2.840160862 1 18.11599546 4.720454113 3.411450469 2.324638939 3.934349168 0.365044329 0.630339226 0.336731289 6.74923032 0.156745272 1.375420094 52535.65035 -4.720454113 1.609710229 AEAPSS(ph)PDVAPAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(0.026)S(0.974)PDVAPAGK;AEAPS(0.11)S(0.89)PDVAPAGK;AEAPSS(1)PDVAPAGK;AEAPS(0.038)S(0.962)PDVAPAGK;AEAPS(0.183)S(0.817)PDVAPAGK 307.43 3.45E-45 1743080000 3708460 3426600 3180830 4362910 3500600 2952180 3683150 4804830 8939700 TRUE FALSE 3218377.615 3404090.439 4719090.027 5353575.398 3430944.909 3065752.275 3325958.68 3777354.496 7882858.85 0.408275434 0.431834504 0.598652103 0.67914135 0.435241195 0.38891376 0.421922902 0.47918586 1 22.91028751 1.238390883 24.9969099 1.000000572 0.481717071 0.762161542 0.091217875 2.141637133 314467.8738 0.135735458 0.024118384 17.31373968 -1.238390883 -0.518283501 AEASS(ph)PVPYLSPETNPASSTSAVNHNVNLTNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AEASSPVPYLSPETNPASSTSAVNHNVNLTNVR 33 0 G3V1L9;Q07157 G3V1L9 TJP1 Tight junction protein ZO-1 1 AEASS(1)PVPYLSPETNPASSTSAVNHNVNLTNVR;AEAS(0.031)S(0.969)PVPYLSPETNPASSTSAVNHNVNLTNVR;AEASS(1)PVPYLSPETNPASSTSAVNHNVNLTNVR;AEAS(0.117)S(0.883)PVPYLSPETNPASSTSAVNHNVNLTNVR 328.72 3.04E-117 6643000000 1170880 1123570 653439 975650 1327140 1363400 1214360 1484530 1176550 TRUE FALSE 1016145.241 1116189.195 969444.286 1197186.244 1300732.511 1415850.88 1096591.554 1167074.812 1037459.599 0.97945524 1.075886902 0.934440519 1.153959388 1.253766905 1.36472869 1.056996875 1.124935191 1 19.98462373 3.712716269 18.23755893 1.161646172 1.004524007 0.34715816 0.104801022 31.15218368 21982.83433 0.030468435 0.045276306 5160.790965 -3.712716269 -0.157122165 AEASSGDHPTDTEMKEEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AEASSGDHPTDTEMKEEQK 19 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;;; 326.18 1.66E-63 4287800000 8668183 6275670 3399796 5444268 5989457 4421012 9693177 10838657 7921707 FALSE TRUE 7522660.654 6234444.711 5043948.717 6680472.26 5870278.524 4591091.192 8753134.186 8520894.547 6985211.823 1.07694095 0.892520495 0.722089587 0.956373612 0.840386616 0.657258693 1.253095025 1.219847696 1 22.73587243 2.224638701 24.99999227 1.174582968 0.856730901 0.533681534 0.131900234 168.7454917 303018.8283 0.05326001 0.036111082 167.7407967 -2.224638701 -0.317852066 AEASWDSAVHGCPQLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEASWDSAVHGCPQLSR 17 0 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 0 ; 191.37 2.46E-10 769660000 578810 634730 324460 482160 620220 643030 589330 677040 592820 FALSE TRUE 502318.792 630560.4168 481369.9413 591641.7974 607878.8354 667767.7802 532176.8673 532260.2647 522737.4949 0.960938897 1.206265904 0.920863619 1.131814349 1.162875901 1.277443816 1.018057577 1.018217116 1 18.99572712 2.049869518 24.99999639 1.012725656 1.112413736 0.162567914 0.104771785 186.460835 93473.42509 0.042015258 0.028326674 112.1681399 -2.049869518 0.09968808 AEDEVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEDEVQR 7 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 0 ; 147.69 0.0049651 803760000 1363020 1218170 860210 1011500 838370 1151230 1219580 1291020 1644410 FALSE TRUE 1182893.454 1210167.761 1276210.433 1241176.535 821688.0772 1195518.563 1101305.319 1014945.42 1450009.723 0.815783118 0.834592859 0.880139225 0.855978077 0.566677633 0.824490032 0.759515817 0.699957665 1 20.46763114 AEDGATPS(ph)PSNETPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AEDGATPSPSNETPK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 AEDGAT(0.002)PS(0.997)PS(0.001)NETPK;AEDGATPS(0.995)PS(0.005)NETPK;AEDGATPS(0.999)PSNETPK;AEDGAT(0.086)PS(0.91)PS(0.003)NETPK 263.04 5.15E-25 2021100000 3200720 2679650 1887660 2591830 2602690 1977350 3214870 3889890 3522450 TRUE FALSE 2777736.742 2662047.203 2800538.69 3180344.615 2550901.561 2053419.934 2903092.402 3058067.295 3106029.974 0.894304551 0.857057796 0.901645739 1.023925925 0.821273968 0.661107572 0.934663357 0.984558205 1 21.56664032 2.007655544 24.99998839 0.981706557 0.861567549 0.279293935 0.088950117 246.9021355 806281.6856 0.038776999 0.026089971 101.7783823 -2.007655544 -0.120139008 AEDGATPSPSNET(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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;AEDGATPS(0.002)PS(0.006)NET(0.992)PK;AEDGATPSPSNET(1)PK 420.34 4.64E-152 9426642000 6715692 4890669 3541394 4313379 4821561 3527082 5308870 6633871 5986024 TRUE FALSE 5828196.287 4858541.873 5254023.984 5292797.628 4725621.369 3662771.127 4794016.605 5215269.311 5278363.062 1.104167375 0.920463753 0.995388897 1.002734667 0.895281608 0.693921787 0.908239268 0.98804672 1 22.33165916 3.238557947 24.37942132 0.89914327 0.998865497 0.251061947 0.092827073 0.111608467 820450.767 0.029606913 0.035792965 1732.040119 -3.238557947 0.099722227 AEDGATPSPSNET(ph)PKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AEDGATPSPSNETPKK 16 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 AEDGATPSPSNET(1)PKK;AEDGATPSPSNET(1)PKK;AEDGATPSPSNET(1)PKK;AEDGATPSPSNET(1)PKK 302.61 2.83E-46 4076690000 3277800 2244800 1862850 1995190 2026050 1283120 2685310 3560540 2691260 TRUE FALSE 2844630.425 2230053.761 2763730.491 2448228.384 1985735.569 1332482.457 2424889.05 2799146.229 2373102.309 1.198696919 0.939720868 1.164606549 1.031657327 0.836767788 0.561493894 1.02182238 1.179530364 1 21.17834287 7.999985658 0.793633889 0.962713628 53.039285 0.149035298 0.174587404 1244.672968 4.450958553 0.069657622 116455.8225 99996697.58 -7.999985658 52.07657137 AEDGENYDIKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AEDGENYDIKK 11 1 E5RJD8;O75347;E5RIW3;E5RHG6;O75347-2;E5RIX8;A0A494C144 E5RJD8 TBCA Tubulin-specific chaperone A 0 ;;;;; 189.33 4.42E-06 4504310000 6673110 5095810 4366210 4881840 4487640 3115660 6586110 7625950 5627730 FALSE TRUE 5791241.606 5062335.289 6477723.76 5990336.386 4398344.744 3235521.456 5947390.066 5995199.938 4962426.171 1.16701819 1.020133119 1.305354183 1.207138642 0.886329508 0.652003948 1.198484342 1.208118717 1 22.24261421 3.262711275 24.99567213 1.015241796 1.173172887 0.218970433 0.170507881 478.0019447 494723.6009 0.0549924 0.070957509 1831.096679 -3.262711275 0.157931091 AEDGHAVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEDGHAVAK 9 0 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 90.906 0.011113 282540000 600330 532860 355770 465610 412480 485250 522250 688070 699680 FALSE TRUE 520994.8695 529359.6076 527821.562 571333.8669 404272.455 503917.8815 471602.2754 540931.5851 616964.6275 0.844448525 0.858006414 0.855513491 0.926039908 0.655260346 0.816769486 0.764391108 0.87676272 1 19.23482825 1.325300983 3.072156304 1.014859507 0.818280062 0.401302078 0.070714133 0.324713528 4.232309224 0.139211425 0.018452541 21.14954276 -1.325300983 -0.196579445 AEDKEWMPVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AEDKEWMPVTK 11 1 P15880;E9PQD7;E9PPT0;E9PMM9 P15880 RPS2 40S ribosomal protein S2 0 ;; 155.42 2.88E-05 4011350000 5182110 3802100 3198980 3911520 3624380 2900560 4648780 6053540 5521700 FALSE TRUE 4497281.034 3777123.755 4746017.428 4799690.4 3552261.929 3012146.42 4197942.031 4759037.58 4868930.916 0.923669099 0.775760392 0.974755549 0.985779113 0.729577394 0.618646366 0.862189689 0.977429678 1 22.2151736 1.741121703 4.143077817 0.992060759 0.83342731 0.240888623 0.111540732 0.280945381 10.70366202 0.078106772 0.031968482 55.09620712 -1.741121703 -0.158633449 AEDMYSAQSHQAAT(ph)PPKDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 AEDMYSAQSHQAATPPKDGK 20 1 A8MXZ4;J9JIE0;A0A0C4DFY5;Q9NQ84;Q9NQ84-2 A8MXZ4 GPRC5C G-protein coupled receptor family C group 5 member C 1 AEDMYSAQSHQAAT(1)PPKDGK;AEDMYSAQSHQAAT(1)PPKDGK;AEDMYSAQSHQAAT(1)PPKDGK;AEDMYSAQSHQAAT(1)PPKDGK;AEDMYSAQSHQAAT(1)PPKDGK;AEDMYSAQSHQAAT(1)PPKDGK;AEDMYSAQSHQAAT(1)PPKDGK 162.41 3.10E-11 4705300000 3155400 1892683 1999525 3036100 2280290 1876103 1990670 3977740 3674350 TRUE FALSE 2738405.895 1880249.841 2966501.978 3725492.909 2234916.69 1948277.896 1797615.13 3127131.256 3239972.529 0.845194171 0.580328945 0.915594793 1.14985324 0.689794951 0.601325437 0.554824189 0.965172151 1 21.62755015 1.593026622 9.972695904 0.988016587 0.766325814 0.207971158 0.178955766 0.162891615 43.64879615 0.121562443 0.048077972 39.1765891 -1.593026622 -0.221690773 AEDNADTLALVFEAPNQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEDNADTLALVFEAPNQEK 19 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 118.21 0.00019475 20384000 45156 36082 28443 26729 35210 38721 43592 49934 38196 FALSE TRUE 39188.52019 35844.97497 42198.12994 32798.22798 34509.38989 40210.62193 39364.45455 39256.00269 33680.51239 1.163536936 1.064264538 1.252894536 0.973804305 1.024610002 1.193883913 1.168760561 1.165540543 1 15.03962647 5.164592874 11.2577384 1.113857267 4.705715219 0.031673144 0.090935867 936764.9545 548263.3466 0.021898396 85277250.36 146080.7111 -5.164592874 3.591857952 AEDQTES(ph)SCESHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEDQTESSCESHR 13 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 AEDQTES(0.748)S(0.252)CESHR;AEDQTES(0.815)S(0.185)CES(0.001)HR 152.37 2.91E-05 349000000 352670 369440 239090 255800 282830 337310 349880 380090 472230 TRUE FALSE 306063.7659 367013.1243 354714.7237 313883.2997 277202.2363 350286.534 315948.6915 298810.7114 416403.5074 0.735017262 0.881388168 0.851853352 0.753796003 0.665705815 0.841218981 0.758756076 0.71759893 1 18.66762269 1.229336389 24.99757031 1.000000437 0.775765581 0.533227218 0.065961745 313.0403724 848273.7123 0.203560356 0.016672515 16.95650684 -1.229336389 -0.224234856 AEDQTES(ph)SCESHRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEDQTESSCESHRK 14 1 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 AEDQT(0.005)ES(0.905)S(0.09)CES(0.001)HRK;AEDQTES(0.566)S(0.073)CES(0.361)HRK 101.5 0.00083374 507360000 282550 243210 134046 169928 198981 182502 269400 283530 248530 TRUE FALSE 245210.3016 241612.3375 198871.094 208512.7496 195021.6674 189522.97 243273.6295 222899.3159 219149.0665 1.118920128 1.102502243 0.907469501 0.951465379 0.889904167 0.864813038 1.110082892 1.017112778 1 17.74155301 4.29194327 9.29778477 0.969216862 1.111705954 0.430647923 0.070342252 0.374781423 60.8594098 0.019299729 0.051058087 19585.88813 -4.29194327 0.142489092 AEDQTESSCESHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEDQTESSCESHR 13 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 0 159 4.63E-05 147560000 74402 58702 31748 45171 56658 61469 54623 53184 69515 FALSE TRUE 64569.58719 58316.3827 47101.43899 55427.76595 55530.61665 63833.75221 49325.66987 41811.01548 61297.01589 1.053388754 0.951373927 0.768413247 0.90424901 0.905926917 1.041384336 0.804699367 0.682105236 1 15.90352922 4.479827716 5.287996479 0.859713612 1.033275569 0.229193589 0.105545852 0.229121767 20.46603274 0.028211785 0.093666953 30187.5395 -4.479827716 0.173561956 AEDREQLVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AEDREQLVAK 10 1 Q13268;C9JZP6;Q13268-2;H0YJP4 Q13268;H0YJP4 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ;;; 175.15 2.63E-06 1609780000 2505660 1748130 1215850 2191410 1974540 1840280 2061410 2562820 993880 FALSE TRUE 2174530.682 1736646.419 1803839.127 2689003.134 1935250.517 1911076.762 1861494.775 2014780.887 876384.6386 2.481251481 1.981602988 2.058273328 3.06829104 2.208220491 2.180636992 2.124061392 2.298968738 1 19.74120467 1.238365227 24.88011278 0.999998636 2.291734124 0.642124861 0.304982029 2.858285033 362966.4507 0.415918194 0.073851198 17.31271687 -1.238365227 1.291735487 AEDS(ph)DS(ph)EPEPEDNVR ddPTM_MDA-MB-175_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 195.28 2.48E-08 756610000 461940 374310 277393 300440 387790 389860 346870 381580 487790 TRUE FALSE 400893.4586 371851.133 411541.1826 368659.4939 380073.7377 404858.1665 313230.6008 299982.0865 430124.0219 0.932041547 0.864520729 0.956796556 0.857100453 0.883637552 0.941259139 0.728233218 0.697431604 1 18.71439318 2.243081601 24.99964672 0.782057504 0.903096515 0.201116271 0.086099314 135.7784143 750817.7732 0.03221699 0.024094795 175.0175502 -2.243081601 0.121039011 EEHGGLIRS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 EEHGGLIRSPR 11 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 1 EEHGGLIRS(1)PR;EEHGGLIRS(1)PR;EEHGGLIRS(1)PR;EEHGGLIRS(1)PR;EEHGGLIRS(1)PR;EEHGGLIRS(1)PR;EEHGGLIRS(1)PR;EEHGGLIRS(1)PR;EEHGGLIRS(1)PR;EEHGGLIRS(1)PR;EEHGGLIRS(1)PR;EEHGGLIRS(1)PR 144.38 2.23E-05 43761214000 15472200 13026250 8135600 8338890 12222740 12387320 12505530 13923440 6249380 TRUE FALSE 13427509.57 12940679.71 12070003.37 10232362.43 11979531.39 12863868.22 11292745.63 10946020.71 5510585.416 2.436675699 2.348331208 2.190330511 1.856855788 2.173912658 2.33439231 2.049282385 1.986362588 1 22.39377416 1.043547784 1.807060915 3.88E-16 2.199760692 0.841244749 0.162537809 0.645227634 1.2764111 2.919835695 0.047081912 11.05472094 -1.043547784 2.199760692 AEEAEAQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 108.67 0.0041275 564980000 683200 508470 384850 445410 403270 433900 617440 701630 727240 FALSE TRUE 592913.389 505129.8271 570964.7472 546547.1482 395245.716 450592.4138 557560.7638 551591.8846 641266.5157 0.924597456 0.787706538 0.890370436 0.85229329 0.616351714 0.702660131 0.869468076 0.860160122 1 19.29056455 1.251975999 1.604278176 1.071533169 0.79795769 0.315337707 0.090634265 1.37250852 3.287077639 0.596863067 0.027351981 17.8638885 -1.251975999 -0.273575479 AEEAEELRLDLEDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEEAEELRLDLEDVK 15 1 A0A2R8Y7M0;P82094;P82094-2 A0A2R8Y7M0 TMF1 TATA element modulatory factor 0 ; 194.58 4.18E-08 89096000 219590 188995 154369 167646 180368 153999 227340 255230 216350 FALSE TRUE 190570.6251 187753.4794 229022.3647 205712.5866 176779.0297 159923.4412 205292.6018 200651.0507 190773.3495 0.998937355 0.984170378 1.200494542 1.078308827 0.926644262 0.838290262 1.076107341 1.051777155 1 17.54150012 3.265224029 24.93516896 0.988017546 1.069314204 0.193991928 0.086695626 426.9020963 399228.6094 0.027167087 0.035062569 1841.7218 -3.265224029 0.081296657 AEEDAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEEDAQR 7 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 96.285 0.029881 47183000 107760 89574 61131 71388 53632 95369 90481 105740 119000 FALSE TRUE 93519.24297 88985.5825 90694.15607 87597.7365 52564.82813 99037.90714 81706.16655 83128.32387 104931.9556 0.891237016 0.848031298 0.864313979 0.834805146 0.500942042 0.943829805 0.778658571 0.792211709 1 16.67909457 3.470932402 24.99358941 0.794319155 0.863158162 0.04673079 0.12995574 507.8876267 2051085.833 0.036651397 0.047444653 2957.552088 -3.470932402 0.068839007 AEEDEILNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEEDEILNR 9 0 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 158.61 0.00015512 341390000 158860 140230 144000 185030 302830 224380 110820 227510 313570 FALSE TRUE 137866.2485 139308.8199 213638.8817 227043.8895 296804.2755 233012.0438 100072.6935 178858.757 276500.1118 0.498611909 0.503829163 0.772653871 0.821134892 1.07343275 0.842719528 0.361926412 0.646866852 1 18.07692054 4.239802207 23.86422801 0.766198116 0.501220406 0.271086483 0.193120822 27.64943454 531330.5688 0.053577411 0.126540753 17370.09551 -4.239802207 -0.26497771 AEEDEILNRS(ph)PR ddPTM_MDA-MB-175_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 223.07 1.41E-11 1.58952E+11 62275763 54971599 38216753 51545568 71748137 71986497 43998105 86041460 51769710 TRUE FALSE 54045863.13 54610486.95 56698502.58 63249777.04 70320489.45 74755864.12 39731175.55 67642163.35 45649553.86 1.183929712 1.196298372 1.242038482 1.385550826 1.540441987 1.637603389 0.870351892 1.481770524 1 25.44409742 1.218295649 24.68861874 0.999998689 1.317002242 0.174932258 0.216526051 2395.029397 2917660.129 2.082402467 0.051957948 16.53086766 -1.218295649 0.317003552 AEEDTQFNYHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEEDTQFNYHR 11 0 G8JLG1;Q14683;H0Y7K8 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 149.49 3.43E-05 320840000 711410 630160 327620 468930 675560 628400 517060 603780 533780 FALSE TRUE 617395.366 626020.4375 486058.1278 575407.7236 662117.6777 652574.9546 466915.6008 474666.3456 470677.1365 1.31171735 1.330042165 1.032678433 1.222510462 1.406734312 1.386459855 0.992008246 1.008475468 1 18.84437825 2.225068335 24.99664821 1.001553558 1.275563319 0.623139064 0.103133185 165.0388215 305758.8253 0.045296811 0.030728389 167.9068195 -2.225068335 0.27400976 AEEELDAEVLEVFHPTHEWQALQPGQAVPAGSHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEEELDAEVLEVFHPTHEWQALQPGQAVPAGSHVR 35 0 D6R940;D6RG16;D6RBP7;D6RAI3;D6RIU8;D6REA1;Q9H173 D6R940 SIL1 Nucleotide exchange factor SIL1 0 ; 96.963 9.37E-05 151744000 47508 52107 30635 37096 58565 63762 46534 46545 48550 FALSE TRUE 41229.69743 51764.70569 45450.18847 45519.21378 57399.67108 66214.9654 42021.13984 36591.71396 42810.47431 0.963074997 1.209159826 1.061660475 1.063272821 1.340785684 1.546700112 0.981562118 0.854737411 1 15.3856762 2.021137556 24.98211962 0.917339723 1.198212655 0.344713754 0.164919901 243.1560217 287380.8255 0.0702522 0.047359317 104.9874908 -2.021137556 0.280872932 AEEFKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEEFKK 6 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 86.866 0.085126 1214700000 2188900 1501300 1295800 1410800 1058300 1054200 2144900 2365200 1999900 FALSE TRUE 1899631.319 1491437.861 1922453.214 1731143.703 1037241.901 1094755.756 1936887.928 1859420.386 1763474.1 1.07720965 0.845738455 1.090151091 0.981666645 0.588180966 0.620794916 1.098336476 1.054407539 1 20.74998896 AEEGKS(ph)PFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEEGKSPFR 9 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 AEEGKS(1)PFR;AEEGKS(1)PFR 93.345 0.0066998 418550000 950510 768410 635760 710620 725960 602590 896500 1046820 1220130 TRUE FALSE 824897.6952 763362.2641 943215.6625 871977.1321 711514.8163 625772.0272 809557.568 822965.6894 1075887.621 0.766713622 0.709518586 0.876686044 0.810472316 0.661328193 0.581633262 0.752455509 0.76491789 1 20.03709596 1.206836021 3.123105369 1.060264367 0.736220596 0.515610433 0.079425083 0.38567695 4.592629345 0.325200369 0.022146447 16.10037609 -1.206836021 -0.324043771 AEEKS(ph)PISINVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AEEKSPISINVK 12 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 1 AEEKS(0.998)PIS(0.002)INVK;AEEKS(0.994)PIS(0.006)INVK;AEEKS(0.988)PIS(0.012)INVK;AEEKS(0.995)PIS(0.005)INVK 230.97 2.75E-12 7188500000 7834700 5410180 4777930 4983580 5202870 3697610 7677700 8741700 7433950 TRUE FALSE 6799324.544 5374640.171 7088552.929 6115178.008 5099343.066 3839859.449 6933117.836 6872355.483 6555116.9 1.037254506 0.819915229 1.081377043 0.932886187 0.777917945 0.585780469 1.057665018 1.048395565 1 22.64419008 AEELHYPLGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEELHYPLGER 11 0 Q14257;Q14257-2;A8MXP8;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 112.43 0.001527 204600000 273910 261760 201570 237110 273290 329270 234120 250040 325880 FALSE TRUE 237712.0995 260040.4813 299049.9262 290949.4495 267852.0637 341937.23 211415.0784 196570.8918 287354.8376 0.827242379 0.904945549 1.040699118 1.012509314 0.932129996 1.189947706 0.735728273 0.684070237 1 18.13247381 2.199557885 24.99996643 0.778119408 0.982396086 0.303324433 0.124657354 166.9452175 107007.3938 0.050289389 0.033905716 158.328058 -2.199557885 0.204276678 AEELS(ph)PAALSPLLEPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEELSPAALSPLLEPIR 17 0 A0A5F9ZH52;A5YM69 A0A5F9ZH52;A5YM69 ARHGEF35 Rho guanine nucleotide exchange factor 35 1 AEELS(1)PAALSPLLEPIR;AEELS(1)PAALSPLLEPIR 285.59 2.68E-36 110812000 90257 93308 64165 85259 112966 103499 108198 137689 117741 TRUE FALSE 78329.30877 92695.0536 95195.40862 104618.3591 110718.1976 107480.6735 97704.97461 108245.2788 103821.7931 0.754459217 0.892828479 0.916911621 1.007672435 1.066425404 1.03524193 0.941083482 1.042606524 1 16.66374978 4.591352887 1.067884111 1.017303135 0.672340455 0.84053188 0.036846825 0.537353613 0.60413492 0.011998286 0.199249525 39025.8964 -4.591352887 -0.34496268 AEELSPAALS(ph)PLLEPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEELSPAALSPLLEPIR 17 0 A0A5F9ZH52;A5YM69 A0A5F9ZH52;A5YM69 ARHGEF35 Rho guanine nucleotide exchange factor 35 1 AEELSPAALS(1)PLLEPIR;AEELSPAALS(1)PLLEPIR 150.59 2.96E-07 203818000 55566 62650 52828 66710 94369 85835 84225 106500 100128 TRUE FALSE 48222.81231 62238.44802 78375.7975 81857.5251 92491.24153 89137.12799 76056.87246 83725.80378 88290.98191 0.546180496 0.70492418 0.887698787 0.927133478 1.047572918 1.009583607 0.861434212 0.948293948 1 16.42997847 4.410954216 1.559418872 0.963756334 0.504519267 0.893298869 0.049733909 0.191455131 0.691272589 0.015209739 0.112261386 25760.49569 -4.410954216 -0.459237067 LCQSFQTFSICYAETGLLGAHFVCDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LCQSFQTFSICYAETGLLGAHFVCDR 26 0 P31930 P31930 UQCRC1 "Cytochrome b-c1 complex subunit 1, mitochondrial" 0 65.775 0.036519 21258000 26234 23907 17227 20432 22779 21111 21518 28207 11188 FALSE TRUE 22767.11043 23749.95334 25558.03482 25071.39788 22325.74247 21923.15383 19431.18767 22175.15256 9865.367385 2.307781306 2.407406883 2.590682518 2.541354711 2.263042175 2.222233899 1.969636498 2.247777674 1 13.26815706 1.052012235 1.918493245 2.80E-29 2.351172328 0.842053463 0.178554422 0.613034931 1.402831757 3.103685817 0.052334667 11.27229213 -1.052012235 2.351172328 AEENLLMVLGTDMSDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEENLLMVLGTDMSDRR 17 1 A0A6I8PIQ6;A0A0A0MS45;J3KNI1;Q9H9E3;Q9H9E3-2;Q9H9E3-3 A0A6I8PIQ6 COG4 Conserved oligomeric Golgi complex subunit 4 0 ; 98.035 0.0036867 56846000 64999 61100 38222.4 43251 57212 58393 60731 64773 43221 FALSE TRUE 56409.21746 60698.63008 56706.88049 53071.8006 56073.59313 60639.4165 54841.31697 50921.79801 38111.46262 1.480111588 1.592660735 1.487921916 1.392541691 1.4713052 1.591107041 1.438971721 1.336128149 1 15.21793736 1.144501894 1.551692392 0.704245527 1.499662318 0.873826325 0.059730105 0.486895934 0.873533868 0.643314988 0.01777133 13.94767741 -1.144501894 0.795416791 AEENTDQAS(ph)PQEDYAGFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEENTDQASPQEDYAGFER 19 0 Q9NU22 Q9NU22 MDN1 Midasin 1 AEENTDQAS(1)PQEDYAGFER;AEENTDQAS(1)PQEDYAGFER 333.75 2.42E-75 246660000 366950 271040 195875 220403 269200 267410 291140 306300 290390 TRUE FALSE 318456.6278 269259.5204 290600.8052 270448.8698 263843.4467 277697.4357 262905.2876 240800.1286 256060.425 1.243677651 1.051546799 1.134891521 1.056191599 1.030395254 1.084499628 1.026731435 0.940403534 1 17.96612477 8 0.201180811 0.932637106 2.182525523 0.668497792 0.046944046 62.27786042 0.925145687 0.29781723 23.7776783 100000000 -8 1.249888417 AEEPGDRPAEEWLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEEPGDRPAEEWLGR 15 1 Q587I9 Q587I9 SFT2D3 Vesicle transport protein SFT2C 0 89.866 0.005686 89664000 113400 87356 60243 76538 99713 114710 69534 105710 107080 FALSE TRUE 98413.90268 86782.15268 89376.7163 93917.12271 97728.90639 119122.9679 62790.60338 83104.73914 94421.12439 1.042286917 0.919096794 0.946575429 0.994662194 1.035032224 1.261613529 0.665005885 0.880149857 1 16.52682204 2.226855857 24.99917022 0.847362157 1.022416753 0.337735287 0.121378034 270.3879257 577493.045 0.049794251 0.033882195 168.5993349 -2.226855857 0.175054596 AEEPPS(ph)PPVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AEEPPSPPVPK 11 0 Q96JK2-2;Q96JK2-3;Q96JK2 Q96JK2-2 DCAF5 DDB1- and CUL4-associated factor 5 1 AEEPPS(1)PPVPK;AEEPPS(1)PPVPK;AEEPPS(1)PPVPK;AEEPPS(1)PPVPK 191.23 2.01E-06 2297650000 3417290 2783660 2033070 2332440 2643700 2226430 3166160 3619040 3325090 TRUE FALSE 2965686.468 2765373.954 3016269.452 2862056.151 2591095.542 2312082.203 2859106.291 2845136.459 2932001.648 1.011488677 0.943169304 1.028740708 0.976144114 0.883729224 0.788567839 0.975138023 0.970373417 1 21.48345448 3.417642923 8.702848676 0.926674692 0.991506901 0.222979008 0.06207186 0.518336587 69.47249672 0.01945031 0.02514175 2616.031223 -3.417642923 0.06483221 AEEVEYYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEEVEYYYR 9 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 0 ; 182.69 0.0001071 635540000 481290 496000 348320 382600 426290 500640 446050 488300 537090 FALSE TRUE 417686.3071 492741.7433 516768.7171 469475.1777 417807.663 519899.9448 402792.1397 383880.845 473595.8321 0.881946755 1.040426689 1.091159766 0.991299217 0.882202998 1.097771369 0.850497645 0.81056635 1 18.85329686 2.213012385 24.99997774 0.869571321 0.998159526 0.256073952 0.087059065 260.7821316 255183.8119 0.034848241 0.023504018 163.3098519 -2.213012385 0.128588205 AEFAER ddPTM_MDA-MB-175_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 ;;;; 160.77 0.020256 17432980000 7780340 7829410 4952830 5748410 6475810 7444840 7254430 7992350 7189590 FALSE TRUE 6752148.356 7777978.09 7348035.154 7053674.349 6346954.051 7731247.812 6550896.495 6283248.149 6339644.861 1.065067288 1.226879149 1.159061007 1.112629257 1.001152934 1.21950803 1.033322314 0.991104121 1 22.59597059 2.05183132 8.854086623 1.000035303 1.129628246 0.439624265 0.066206069 0.259633903 41.12052306 0.026723095 0.017967459 112.6759736 -2.05183132 0.129592943 AEFEDQDDEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEFEDQDDEAR 11 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 0 256.24 5.45E-09 0 235070 223110 158570 170900 229910 208830 225010 246940 241830 FALSE TRUE 204004.9039 221644.3757 235254.9824 209705.457 225335.2408 216863.8252 203188.5648 194133.8027 213241.1329 0.956686457 1.039407232 1.103234536 0.983419353 1.056715643 1.016988713 0.952858213 0.910395664 1 17.70212623 2.256557661 4.164183214 0.943962956 1.030665823 0.358024664 0.044750251 0.187166634 7.364688893 0.017789576 0.012634505 180.5334414 -2.256557661 0.086702867 AEFEVHEVYAVDVLVSSGEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AEFEVHEVYAVDVLVSSGEGK 21 0 Q9UQ80;Q9UQ80-2;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;; 124.08 2.54E-05 130503000 281728 223259 172500 224544 200313 173994 279486 311749 296757 FALSE TRUE 244496.931 221792.3969 255921.577 275530.1471 196327.1632 180687.6618 252381.4907 245083.9024 261674.7255 0.934354399 0.847588152 0.978014122 1.052949025 0.750271784 0.69050483 0.964485547 0.936597533 1 17.99741506 AEFFQHLIEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AEFFQHLIEDR 11 0 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 0 ;; 200.44 4.68E-08 480050000 770980 703380 480970 553390 705290 750080 718370 779590 759620 FALSE TRUE 669093.0396 698759.4505 713568.7007 679045.6575 691256.1089 778936.063 648702.588 612880.7453 669818.589 0.998916797 1.043207015 1.06531636 1.013775474 1.032004964 1.16290601 0.968475045 0.914995128 1 19.35341089 2.02474991 24.99769094 0.948518522 1.05141939 0.442287383 0.048321266 173.6358355 175373.4609 0.01918202 0.012931966 105.8643927 -2.02474991 0.102900868 AEFTS(ph)PPSLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AEFTSPPSLFK 11 0 Q6UN15;Q6UN15-5;Q6UN15-3;A0A0B4J203;Q6UN15-4 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 AEFT(0.027)S(0.967)PPS(0.006)LFK;AEFT(0.068)S(0.887)PPS(0.045)LFK;AEFT(0.05)S(0.947)PPS(0.003)LFK;AEFT(0.038)S(0.959)PPS(0.003)LFK 128.1 0.0010406 270440000 2624090 2511190 1535120 2000360 2532350 1884870 2521140 3352990 2582090 TRUE FALSE 2277309.858 2494693.828 2277509.167 2454572.312 2481961.189 1957382.169 2276640.231 2635979.181 2276838.262 1.000207128 1.095683374 1.000294665 1.078061781 1.090091128 0.859693111 0.999913024 1.157736685 1 21.11860038 1.769848369 25 1.088717736 1.019063682 0.094932907 0.077103308 54.91248803 43905.50159 0.0410332 0.019710494 58.86381006 -1.769848369 -0.069654054 AEGDVAALNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEGDVAALNR 10 0 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3 P67936 TPM4 Tropomyosin alpha-4 chain 0 ; 152.11 4.33E-05 807390000 549020 571300 431160 524950 547120 591890 619280 757110 936300 FALSE TRUE 476465.616 567547.0927 639670.4181 644147.9209 536233.3824 614660.3913 559222.3209 595207.9183 825611.6806 0.577106195 0.687426191 0.774783634 0.780206889 0.649498299 0.74449091 0.677343034 0.720929624 1 19.65510386 1.238552021 5.193472401 1.017071079 0.703932665 0.709628799 0.060103578 0.091182707 6.762241327 0.102900009 0.014919052 17.32016484 -1.238552021 -0.313138414 AEGDVAALNRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AEGDVAALNRR 11 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;;; 211.64 1.39E-08 3061180000 4284680 4618760 1942980 2003110 4058110 4106660 4206590 4522530 375859 FALSE TRUE 3718448.682 4588419.061 2882611.627 2457946.741 3977361.551 4264645.868 3798635.549 3555422.154 331425.3772 11.21956536 13.84450129 8.697618907 7.416290092 12.00077551 12.86758999 11.46151083 10.72767023 1 18.33832455 4.233670499 24.98614764 9.600373629 12.53203346 0.135291296 3.402091402 246.7233413 1260663.572 0.868281636 1.903342658 17126.57416 -4.233670499 2.931659832 AEGEPQEES(ph)PLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEGEPQEESPLK 12 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 AEGEPQEES(1)PLK;AEGEPQEES(1)PLK 248.61 9.26E-17 908620000 1594660 1093320 1090950 1247710 1131190 1018400 1345720 1582870 2994800 TRUE FALSE 1383921.641 1086137.909 1618537.069 1531021.626 1108681.532 1057578.507 1215212.282 1244385.568 2640758.156 0.524062242 0.411297758 0.612906209 0.579765937 0.419834558 0.400482909 0.460175529 0.471222844 1 21.33252075 1.237759033 24.99961253 1.0000006 0.483144621 0.841155132 0.070333187 7.798881555 243074.8613 0.104745427 0.017905718 17.28856843 -1.237759033 -0.516855979 AEGEPQEES(ph)PLKSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEGEPQEESPLKSK 14 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 AEGEPQEES(1)PLKSK;AEGEPQEES(1)PLKSK 189.87 4.05E-07 617500000 922710 578710 461000 460670 574430 413430 865720 941690 393660 TRUE FALSE 800771.5357 574908.4159 683941.142 565272.1644 562999.9669 429334.9196 781762.6076 740316.9217 347121.9633 2.306888127 1.656214463 1.97031941 1.628454043 1.621908224 1.236841701 2.252126602 2.132728551 1 18.40508313 4.743998888 23.59763784 1.739478546 2.306888657 0.19685662 0.380539908 501.2202621 2174730.648 0.093496297 0.766859879 55462.42923 -4.743998888 0.567410111 AEGEWEDQEALDYFS(ph)DK ddPTM_MDA-MB-175_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 171.98 1.74E-09 41265000 127040 86073 83340 95458 82433 69662 99524 114880 282160 TRUE FALSE 110251.3421 85507.5808 123643.5028 117133.1979 80792.74458 72341.94222 89872.1778 90313.806 248803.3662 0.443126409 0.343675337 0.496952693 0.470786226 0.324725287 0.290759499 0.361217692 0.362992701 1 17.92464648 1.237360796 24.99977593 1.000000737 0.384247533 0.8965347 0.065463562 9.48376954 197521.2283 0.101728939 0.01694193 17.2727225 -1.237360796 -0.615753204 AEGEWEDQEALDYFS(ph)DKESGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 AEGEWEDQEALDYFSDKESGK 21 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDY(0.01)FS(0.946)DKES(0.043)GK;AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDYFS(1)DKESGK 347.54 1.74E-95 9654632000 4064488 2363823 2587040 2451470 2439459 2032025 3595320 4102541 4571681 TRUE FALSE 3527355.613 2348294.891 3838141.197 3008113.732 2390918.539 2110198.317 3246646.42 3225244.533 4031222.08 0.875009003 0.582526798 0.952103635 0.746203923 0.593100179 0.523463673 0.805375232 0.800066201 1 21.94278583 1.243443591 1.718061808 1.099680321 0.716013116 0.299398564 0.132851606 1.255755167 3.459475758 0.80893376 0.037390149 17.51634904 -1.243443591 -0.383667204 AEGFVDALHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AEGFVDALHR 10 0 Q96I24;A0A494C1K6 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ;;;; 166.66 5.48E-06 4216940000 4090527 4023882 2602560 2928538 3608720 3603781 4140869 4230368 3924330 FALSE TRUE 3549953.493 3997448.854 3861166.721 3593507.313 3536913.532 3742420.787 3739288.162 3325736.724 3460400.178 1.025879468 1.15519843 1.115815086 1.038465821 1.022111129 1.08149942 1.080594142 0.961084427 1 21.72250746 0.90456185 0.420443549 0.84441765 1.09726709 0.34666958 0.045977649 8.698387266 1.070599219 1.178960587 0.052904138 8.027158705 -0.90456185 0.25284944 AEGLEEADTGASGCHSHPEEQPT(ph)SISPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEGLEEADTGASGCHSHPEEQPTSISPSR 29 0 Q9BV36-2;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 AEGLEEADTGASGCHSHPEEQPT(0.858)S(0.133)IS(0.009)PSR;AEGLEEADTGASGCHSHPEEQPT(0.502)S(0.307)IS(0.189)PS(0.002)R 209.75 4.06E-25 1422000000 493820 426240 280835 359550 475700 477770 498920 543260 650520 TRUE FALSE 428560.4358 423440.0014 416647.7453 441191.3229 466234.5007 496150.1211 450534.8152 427088.0767 573616.2667 0.747120437 0.738193852 0.726352737 0.769140187 0.812798604 0.864951275 0.785428938 0.744553635 1 19.12972641 3.334084175 2.678809878 0.827529012 0.7379192 0.338202203 0.066779941 0.375533031 5.466078357 0.020864218 0.0278706 2158.162665 -3.334084175 -0.089609812 AEGLEEADTGASGCHSHPEEQPTS(ph)ISPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEGLEEADTGASGCHSHPEEQPTSISPSR 29 0 Q9BV36-2;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 AEGLEEADTGASGCHSHPEEQPT(0.037)S(0.75)IS(0.212)PS(0.001)R 340.95 1.92E-105 2370900000 725630 646180 374620 656620 775150 829500 708330 756460 926790 TRUE FALSE 629736.157 641935.201 555787.485 805715.6068 759726.0316 861411.4018 639636.2656 594696.9158 817225.942 0.770577786 0.785505168 0.68009036 0.985915358 0.929640131 1.054067618 0.782692072 0.727701955 1 19.64037548 3.7445079 24.9871928 0.892377173 0.749402513 0.364755587 0.101963569 687.1505283 2887017.232 0.030384787 0.050873326 5552.74718 -3.7445079 -0.14297466 AEGLEEADTGASGCHSHPEEQPTSIS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AEGLEEADTGASGCHSHPEEQPTSISPSR 29 0 Q9BV36-2;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 AEGLEEADTGASGCHSHPEEQPT(0.002)S(0.029)IS(0.76)PS(0.209)R;AEGLEEADTGASGCHSHPEEQPT(0.124)S(0.354)IS(0.394)PS(0.128)R;AEGLEEADTGASGCHSHPEEQPTS(0.003)IS(0.991)PS(0.006)R;AEGLEEADTGASGCHSHPEEQPT(0.035)S(0.022)IS(0.94)PS(0.004)R;AEGLEEADTGASGCHSHPEEQPT(0.005)S(0.069)IS(0.915)PS(0.011)R;AEGLEEADTGASGCHSHPEEQPT(0.002)S(0.065)IS(0.93)PS(0.004)R 317.44 4.66E-92 5021020000 1755015 1610771 981721 1387725 1763423 1819876 1627457 1648959 1939346 TRUE FALSE 1523085.321 1600189.739 1456484.559 1702829.171 1728334.332 1889887.807 1469626.471 1296341.95 1710078.725 0.890652166 0.935740394 0.851706145 0.99576069 1.010675302 1.105146669 0.85939112 0.758059808 1 20.70563131 2.035447474 24.9975429 0.84584132 0.963644405 0.17107452 0.090291761 230.6523812 162655.0101 0.037716781 0.025428559 108.5044309 -2.035447474 0.117803084 AEGPLDS(ph)PSEGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTK ddPTM_MDA-MB-175_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(0.892)PS(0.044)EGHS(0.049)Y(0.012)QNS(0.003)GLDHFQNSNIDQSFWETFGSAEPTK 108.38 9.23E-06 777570000 50336 65410 29346 65074 81252 67504 86685 106770 99811 TRUE FALSE 43683.97006 64980.3174 43537.82376 79850.04629 79635.24417 70100.92256 78278.30204 83938.06639 88011.45729 0.496344129 0.738316572 0.494683591 0.907268767 0.904828151 0.796497692 0.889410362 0.953717493 1 16.42540372 5.119587348 0.304202882 1.02061516 1.11E-12 0.686092531 0.09940747 8.448589385 0.663753339 0.262665838 3.403154739 131700.477 -5.119587348 -1.02061516 AEGPLDSPSEGHS(ph)YQNSGLDHFQNSNIDQSFWETFGSAEPTK ddPTM_MDA-MB-175_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(0.32)PS(0.071)EGHS(0.56)Y(0.002)QNS(0.047)GLDHFQNSNIDQSFWETFGSAEPTK 183.52 1.87E-27 1171000000 45854 56716 33595 56233 70454 58238 75908 106470 85896 TRUE FALSE 39794.27772 56343.42886 49841.65437 69001.56212 69052.10324 60478.45355 68546.45384 83702.21905 75741.47273 0.525396144 0.743891382 0.658049713 0.911014265 0.91168155 0.798485313 0.905005559 1.105104192 1 16.20879585 5.062183629 0.231541023 1.157087241 1.84E-12 0.767266452 0.080937645 10.88670346 0.642574036 0.533774754 3.9531519 115394.1066 -5.062183629 -1.157087241 AEGPLDSPSEGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTK ddPTM_MDA-MB-175_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 0 ; 251.28 1.96E-56 187238000 69188 66237 33561.4 52086 64295 63118 76897 91050 78101 FALSE TRUE 60044.6305 65801.88479 49791.8053 63912.92238 63015.65529 65546.1903 69439.54078 71579.66605 68867.98875 0.871880123 0.955478532 0.723003622 0.928049788 0.915020991 0.951765711 1.008299241 1.039375004 1 16.07154592 2.673364219 1.221798905 1.026259017 0.863904196 0.534750329 0.060374478 0.342874405 1.078196829 0.034129506 0.025471796 471.3724747 -2.673364219 -0.162354821 AEGS(ph)PNQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEGSPNQGK 9 0 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 AEGS(1)PNQGK;AEGS(1)PNQGK 131.17 0.00035725 199702000 542900 519120 425390 565230 745680 482950 611840 840300 870640 TRUE FALSE 471154.3895 515709.8665 631110.0268 693574.1105 730842.4269 501529.399 552503.851 660608.3842 767713.931 0.613710876 0.671747438 0.822064055 0.903427804 0.951972339 0.653276408 0.719674124 0.860487686 1 19.5502093 4.290897839 3.403144464 0.839665871 0.625727936 0.412944493 0.101219494 0.249312939 5.738449507 0.027622824 0.08268443 19538.79781 -4.290897839 -0.213937935 AEGS(ph)PNQGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEGSPNQGKK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 AEGS(1)PNQGKK 65.092 0.042878 387040000 212540 168500 147820 179960 133610 131430 217430 309350 206230 TRUE FALSE 184452.3005 167393.1124 219306.2464 220822.6685 130951.4224 136486.1971 196343.6721 243197.9099 181849.7243 1.014311686 0.920502426 1.205975138 1.214314013 0.720107896 0.750543877 1.079702885 1.337356494 1 17.47238721 1.998169237 24.99359485 1.197501528 0.973683803 0.172063275 0.179195572 103.9562535 1419217.199 0.078443469 0.051992197 99.57933854 -1.998169237 -0.223817725 AEGSEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEGSEIR 7 0 P07237;H7BZ94;I3L3U6;I3L0S0;I3NI03;I3L514 P07237 P4HB Protein disulfide-isomerase 0 90.986 0.038936 763500000 979260 901570 659680 813440 676470 1054100 745050 777970 1197200 FALSE TRUE 849848.3099 895647.5273 978703.4545 998143.9847 663009.5705 1094651.909 672795.1657 611607.1697 1055668.38 0.805033405 0.8484175 0.927093653 0.945509029 0.6280472 1.036927817 0.637316773 0.579355394 1 20.00972528 2.207710893 24.9999931 0.701421926 0.860098073 0.116762736 0.15210635 322.8926751 261663.474 0.05976636 0.040299159 161.3284245 -2.207710893 0.158676147 AEGTNFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEGTNFR 7 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 81.784 0.061099 221020000 234030 209450 151550 173510 215880 249180 223140 217140 236800 FALSE TRUE 203102.3425 208074.1092 224840.0869 212908.0974 211584.4104 258766.1158 201499.9171 170706.3008 208805.7738 0.972685472 0.996495956 1.076790564 1.019646601 1.013307279 1.239267053 0.965011233 0.817536305 1 17.67180208 2.003764343 24.99977805 0.894396629 1.052712396 0.339311508 0.084756308 99.97938363 663979.8381 0.034052902 0.022842121 100.8705393 -2.003764343 0.158315767 AEGTTYRDELLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEGTTYRDELLTK 13 1 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4;A0A2R8Y4J3 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 ; 81.185 0.01437 745630000 481640 338220 255940 291870 341800 291580 418260 437030 396550 FALSE TRUE 417990.0537 335998.2106 379713.4401 358143.5445 334998.8487 302797.2713 377697.2096 343574.5355 349670.3108 1.195383311 0.960900026 1.085918445 1.024232065 0.958042014 0.86595076 1.080152355 0.982567078 1 18.41563578 6.804527426 1.660929048 0.994268759 199.9999992 0.47609109 0.064525955 1386.274622 4.849607667 0.017144873 1050128.941 6375693.43 -6.804527426 199.0057304 AEGYEVAHGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AEGYEVAHGGR 11 0 H0YDU8;P53041;A8MU39 H0YDU8 PPP5C Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5 0 ;;; 100.69 0.0038436 1233900000 1122680 1155640 653419 733390 988920 1041110 983770 1031070 1161330 FALSE TRUE 974314.9935 1148048.525 969414.614 899917.4087 969242.4268 1081162.175 888364.1368 810583.7043 1024038.89 0.951443351 1.121098559 0.946658006 0.878792219 0.946489861 1.055782339 0.867510155 0.791555586 1 19.96583908 3.509346704 0.425629126 0.867563683 1.057881181 0.117507858 0.088546482 3.297008425 1.557009305 0.18062578 0.377688482 3231.072505 -3.509346704 0.190317498 AEHDQLLLNYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEHDQLLLNYAK 12 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 ; 123.64 0.0002332 285970000 1028700 871170 533620 853130 836870 718540 756810 1103150 1619440 FALSE TRUE 892754.6886 865447.2269 791680.4169 1046846.206 820217.9243 746182.6988 683414.6827 867249.9572 1427991.648 0.62518201 0.606059026 0.554401294 0.733089866 0.574385659 0.52253996 0.47858451 0.607321449 1 20.44555611 1.241552153 5.881412648 1.015675572 0.583816374 0.789814485 0.066929211 0.061307807 7.693631573 0.106407517 0.017271574 17.44022777 -1.241552153 -0.431859198 AEHDSILAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEHDSILAEK 10 0 P26639;P26639-2;D6RCA5;D6R9F8;D6RDJ6;D6RBR8 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ; 104.43 0.0026823 699970000 2602400 2095200 790190 1540480 2194000 1872810 2482400 3013800 2798100 FALSE TRUE 2258486.246 2081436.493 1172328.527 1890269.529 2150343.692 1944858.213 2241657.23 2369322.323 2467311.806 0.915363126 0.843604967 0.475144051 0.76612511 0.871533013 0.788249871 0.908542335 0.960284921 1 21.23450862 2.110222547 0.990512766 1.013162001 0.750840744 0.359643132 0.117062853 0.797212255 1.391255459 0.172246989 0.050031841 128.8909864 -2.110222547 -0.262321257 AEHLDHVMFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEHLDHVMFR 10 0 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A494C099;A0A494C163;D6RCQ8;D6RF77;D6RC77;D6RCD1 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 163.38 3.75E-06 132520000 172860 169730 112190 149540 167140 167390 134770 186740 272730 FALSE TRUE 150016.113 168615.0325 166445.4593 183495.3426 163814.241 173829.6016 121700.0261 146807.1042 240488.1701 0.623798306 0.701136494 0.692114956 0.763011929 0.681173801 0.722819761 0.506054107 0.610454577 1 17.8756064 1.233398721 24.99976028 1.000000527 0.660522234 0.691319976 0.070848094 103.6290723 501832.3294 0.155266784 0.018884576 17.11585981 -1.233398721 -0.339478293 AEHSVDIDVDIDWPIAEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEHSVDIDVDIDWPIAEQR 19 0 Q8NFW8;Q8NFW8-2 Q8NFW8 CMAS N-acylneuraminate cytidylyltransferase 0 ; 198.42 7.42E-16 126041000 109866 92105 66308 77525 93483 85408 86269 101455 101197 FALSE TRUE 95346.92974 91499.95619 98374.77059 95128.23615 91622.8712 88693.70103 77902.64566 79759.63777 89233.60594 1.068509209 1.025397945 1.10244083 1.066058411 1.026775397 0.993949534 0.873019137 0.893829594 1 16.44529952 2.587154944 2.296373684 0.915069493 1.06184341 0.705224776 0.039678505 0.152845459 1.598702831 0.016166461 0.013266731 386.5048467 -2.587154944 0.146773917 AEIELFVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEIELFVNR 9 0 Q99805 Q99805 TM9SF2 Transmembrane 9 superfamily member 2 0 ; 133.23 0.00065763 189836000 228020 220020 154814 159051 204048 225120 177738 203781 244980 FALSE TRUE 197886.5793 218574.6741 229682.5682 195165.9605 199987.844 233780.5121 160500.9961 160204.019 216018.7435 0.916062079 1.011831986 1.063252959 0.903467715 0.925789312 1.082223275 0.742995693 0.741620919 1 17.72079697 2.231291587 24.98837644 0.806616656 0.982373819 0.379375623 0.092420303 151.1620452 519636.3531 0.03683736 0.025406907 170.3301727 -2.231291587 0.175757163 AEIIDQDLYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEIIDQDLYER 11 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 152.7 7.64E-05 248985000 267758 261347 153419 211214 231942 242274 243714 293432 242702 FALSE TRUE 232373.1019 259630.1943 227612.9416 259173.3669 227326.808 251594.4376 220078.6538 230683.8503 214010.046 1.085804644 1.213168256 1.063561948 1.211033649 1.062224938 1.175619753 1.028356649 1.077911316 1 17.707319 1.601309347 0.77736476 0.972631172 1.140152969 0.340720987 0.06015328 1.761979316 1.196087028 0.242716915 0.024060051 39.93092282 -1.601309347 0.167521797 AEIIHHLADLLTDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEIIHHLADLLTDQR 15 0 P54886-2;P54886 P54886-2 ALDH18A1 Delta-1-pyrroline-5-carboxylate synthase;Glutamate 5-kinase;Gamma-glutamyl phosphate reductase 0 126.63 4.81E-05 63000000 30558 33455 37562 51506 45151 43039 37812 39642 94077 FALSE TRUE 26519.68288 33235.2319 55727.10884 63201.22452 44252.58344 44694.73818 34144.99806 31164.86679 82955.32423 0.319686327 0.40064013 0.67177254 0.761870623 0.533450792 0.538780827 0.411607071 0.375682539 1 16.34004696 4.388138558 5.405984551 0.580490254 0.33857913 0.244669428 0.180234225 0.300514794 13.75965959 0.046354769 0.129354323 24442.10232 -4.388138558 -0.241911124 AEISFEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEISFEDR 8 0 Q60FE5;P21333-2;P21333;H0Y5C6 Q60FE5 FLNA Filamin-A 0 143.89 0.0025263 0 250860 255770 196390 204270 224080 236080 244660 234780 406120 FALSE TRUE 217708.2154 254089.83 291364.8609 250652.6256 219621.2464 245162.1504 220932.9109 184574.1241 358108.9563 0.607938482 0.709532185 0.813620703 0.699933976 0.613280519 0.684602119 0.616943271 0.515413314 1 18.45003908 3.46197952 23.26091479 0.65920372 0.718030079 0 0.134448541 399.0494843 613019.1375 0.037993778 0.049075994 2897.206962 -3.46197952 0.058826359 AEITFDDHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 AEITFDDHK 9 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;;;;;;; 205.09 1.55E-05 6115220000 7335468 7123969 5429427 5994840 6812808 6257774 7759813 8346453 8727391 FALSE TRUE 6366067.318 7077171.179 8055116.058 7356060.047 6677246.45 6498514.615 7007267.53 6561628.978 7695648.778 0.827229452 0.919632819 1.046710458 0.955872631 0.867665176 0.844440125 0.91054929 0.85264143 1 22.87561153 3.244110305 24.88998413 0.888387784 0.943905675 0.07946762 0.067906465 272.990495 1224335.902 0.019957785 0.025037507 1754.326021 -3.244110305 0.055517891 AEKDEPGAWEETFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEKDEPGAWEETFK 14 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 166.92 3.40E-06 550840000 671750 440110 404720 448010 433430 367770 542240 535870 448030 FALSE TRUE 582976.5355 437218.8884 600443.9457 549737.5179 424805.591 381918.3499 489653.6483 421278.3706 395064.4038 1.475649362 1.106702817 1.519863445 1.391513669 1.07528187 0.966724276 1.239427404 1.066353654 1 18.59172834 3.235509174 24.96298863 1.076755517 1.364839608 0.579939888 0.128334681 57.20366987 467967.0013 0.036886498 0.043641935 1719.92367 -3.235509174 0.288084091 AEKDNAEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AEKDNAEIR 9 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;;; 113.93 0.0015697 2981470000 11202600 8905520 5902890 7917380 7585370 7320240 10394600 11759900 7318100 FALSE TRUE 9722148.026 8847019.053 8757547.348 9715142.139 7434435.978 7601854.37 9386533.292 9245136.901 6452962.555 1.506617766 1.371001145 1.357135932 1.50553208 1.152096563 1.178040986 1.454608362 1.432696505 1 22.62153022 7.999999995 0.343804773 1.274004657 3.717829362 0.208576503 0.149487041 164.5470867 2.530703671 0.214209829 255.81646 99999998.88 -7.999999995 2.443824705 AEKEEENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEKEEENR 8 1 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ; 87.298 0.014066 373940000 1375940 1112890 808870 946370 618120 876270 1334220 1393220 1496580 FALSE TRUE 1194106.043 1105579.352 1200042.238 1161257.773 605820.6213 909980.6739 1204827.55 1095290.745 1319656.017 0.904861591 0.837778435 0.90935988 0.879970051 0.459074648 0.689558993 0.912986061 0.829982003 1 20.33173049 1.090924742 1.394479316 1.144543864 0.788584191 0.173370905 0.137990993 3.629859211 4.692825207 2.030985172 0.043426845 12.3289117 -1.090924742 -0.355959673 AEKEEENRR ddPTM_MDA-MB-175_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 ;; 88.681 0.0070979 371805000 1160470 1009360 679890 832870 723240 795360 1158890 1311890 1101090 FALSE TRUE 1007110.949 1002729.448 1008687.078 1021985.863 708848.939 825958.0139 1046501.026 1031352.533 970920.3946 1.037274482 1.032761752 1.038897817 1.052594908 0.730079359 0.850695915 1.077844314 1.062242114 1 19.88899349 AEKPPLSASS(ph)PQQRPPEPETGESAGTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEKPPLSASSPQQRPPEPETGESAGTSR 28 2 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 AEKPPLSAS(0.127)S(0.872)PQQRPPEPETGESAGTSR;AEKPPLS(0.009)AS(0.196)S(0.783)PQQRPPEPET(0.004)GES(0.003)AGT(0.003)S(0.003)R 235.29 2.17E-45 436720000 155504 157385 115140 140418 152705 155008 164942 220178 260804 TRUE FALSE 134953.7524 156351.1276 170822.0891 172302.0531 149666.4693 160971.2581 148945.9502 173094.6481 229972.0482 0.586826762 0.679870135 0.742795007 0.749230415 0.650802871 0.699960101 0.647669799 0.752676899 1 17.811099 1.244873713 2.822417649 1.063521135 0.684731189 0.818044058 0.04726749 0.177505165 1.694367271 0.156090649 0.012458322 17.57412506 -1.244873713 -0.378789947 AELAESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AELAESR 7 0 P06753-2;A0A087WWU8;P06753-6;P06753-3;J3KN67;A0A2R2Y2Q3;A0A494C0P6 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;; 151.29 0.0043996 3910370000 6008340 6260580 3672110 4570730 5094830 5826520 5477340 6404370 6145150 FALSE TRUE 5214322.646 6219453.838 5447954.678 5608584.106 4993452.851 6050669.995 4946148.41 5034845.314 5418677.368 0.962286974 1.147780799 1.005403036 1.035046696 0.921526142 1.116632267 0.912796255 0.929164992 1 22.36950932 2.715161294 0.668578571 0.942644431 1.049986614 0.119236706 0.074554628 1.412909439 1.601305702 0.094195085 0.062015613 518.992754 -2.715161294 0.107342182 AELDDTPMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AELDDTPMR 9 0 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 119.21 0.0039497 0 512320 456140 321770 367160 441650 437770 442110 507170 438390 FALSE TRUE 444615.6139 453143.5863 477379.0483 450529.2897 432862.0291 454611.2952 399234.2402 398715.6423 386564.0336 1.150173258 1.172234215 1.234928774 1.165471307 1.119767985 1.176031021 1.032776476 1.031434918 1 18.56034789 2.221639816 6.343898033 1.022911243 1.170619181 0.848512181 0.029557939 0.059735539 8.86861247 0.012637589 0.008815636 166.5865045 -2.221639816 0.147707937 AELDELRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AELDELRR 8 1 O00291-3;O00291-4;O00291 O00291-3 HIP1 Huntingtin-interacting protein 1 0 183.65 0.00035626 85267000 122630 115190 74236 86313 118880 117750 115120 134950 87375 FALSE TRUE 106424.1348 114433.3093 110136.7779 105911.6859 116514.5206 122279.9187 103955.6801 106091.9927 77045.62704 1.381313111 1.485266766 1.429500702 1.374661872 1.512279477 1.587110436 1.349274243 1.377002132 1 16.23342545 0.84294158 1.50192611 0.213467297 1.45444449 0.796242859 0.070358801 1.439275753 1.267345066 3.627763962 0.020040543 6.965328121 -0.84294158 1.240977192 AELELELGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AELELELGR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 182.53 0.00010752 326531000 675220 635820 437488 486603 577440 645720 631670 680070 736220 FALSE TRUE 585987.9662 631643.2566 649058.6601 597093.6484 565950.0737 670561.2662 570410.7406 534642.3228 649184.9103 0.902651859 0.972978956 0.999805525 0.919758976 0.871785626 1.032927993 0.878656807 0.823559381 1 19.30826994 AELEQHLEQEQEFQVNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AELEQHLEQEQEFQVNK 17 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ;; 243.29 1.89E-20 644380000 629570 567936 378889 459616 549896 475477 592061 727550 685790 FALSE TRUE 546370.7294 564205.191 562120.9877 563978.8376 538954.1455 493768.9079 534643.0153 571969.0943 604716.6875 0.903515217 0.933007477 0.929560899 0.932633164 0.891250658 0.816529324 0.884121484 0.945846388 1 19.20589987 1.454189935 3.028889471 0.998897856 0.89937609 0.487552002 0.034055904 0.265602872 4.215322334 0.051615905 0.010057291 28.4570538 -1.454189935 -0.099521766 AELESDPPY(ph)MEMKGKLSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AELESDPPYMEMKGKLSAK 19 2 Q1MSJ5-1;Q1MSJ5;E5RI67;F2Z2M5 Q1MSJ5-1 CSPP1 Centrosome and spindle pole-associated protein 1 1 AELES(0.181)DPPY(0.809)MEMKGKLS(0.01)AK 48.883 0.050163 1718100000 1746400 893210 1187300 1204000 461890 411810 1047900 1260100 1016300 TRUE FALSE 1515608.815 887342.4447 1761482.251 1477386.602 452699.2927 427652.5972 946274.8193 990637.4211 896154.1718 1.69123669 0.990167175 1.965601798 1.648585309 0.505157825 0.477208733 1.055928599 1.105431914 1 19.77338743 3.252706913 24.99966339 0.862793122 1.560181743 0.575354514 0.317254211 194.6140602 343924.5608 0.096781177 0.124328109 1789.397857 -3.252706913 0.697388621 AELGEYIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AELGEYIR 8 0 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 93.195 0.023925 0 180630 142710 102640 133040 188780 163880 175050 222670 217170 FALSE TRUE 156759.2878 141772.5286 152277.0473 163248.7654 185023.6473 170184.5696 158073.6779 175053.7533 191496.41 0.818601706 0.740340399 0.795195311 0.852489952 0.966199039 0.88870893 0.82546549 0.914135953 1 17.54695782 3.594097131 3.069131617 0.909857169 0.779205503 0.594621312 0.050087801 0.189842472 3.396484507 0.014828507 0.023168166 3927.327608 -3.594097131 -0.130651666 AELGMGDSTS(ph)QSPPIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AELGMGDSTSQSPPIKR 17 1 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 1 AELGMGDS(0.014)T(0.014)S(0.577)QS(0.394)PPIKR 72.644 0.011997 1071000000 372130 263460 187790 219890 262510 231370 335220 364870 322800 TRUE FALSE 322952.0776 261729.3139 278605.8721 269819.3853 257286.5646 240270.9536 302710.416 286845.3899 284638.9517 1.13460254 0.919513342 0.978804448 0.947935564 0.903904975 0.844125346 1.063489077 1.007751709 1 18.11877358 2.178777511 25 1.022070436 0.951669521 0.154833382 0.075648155 135.599895 56703.41334 0.03036408 0.020471465 150.930674 -2.178777511 -0.070400915 AELGMGDSTSQS(ph)PPIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 AELGMGDSTSQSPPIKR 17 1 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 1 AELGMGDS(0.009)T(0.007)S(0.136)QS(0.848)PPIKR;AELGMGDS(0.001)T(0.001)S(0.016)QS(0.983)PPIKR;AELGMGDS(0.001)T(0.001)S(0.005)QS(0.992)PPIKR;AELGMGDS(0.007)T(0.007)S(0.08)QS(0.906)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTS(0.001)QS(0.999)PPIKR 314.08 2.00E-58 9723730000 6867030 4570120 3533900 4080310 4665600 4301540 5633470 6195460 5688720 TRUE FALSE 5959534.587 4540098.581 5242905.86 5006806.749 4572763.688 4467023.027 5087136.946 4870609.092 5016206.002 1.188056189 0.905086151 1.04519349 0.998126223 0.911598066 0.890518257 1.014140357 0.970974695 1 22.25816517 4.749077853 24.70106095 0.968781095 1.188056335 0.651903602 0.050759681 834.628988 1960185.944 0.012361485 0.170720111 56114.85603 -4.749077853 0.21927524 AELGSWS(ph)SQEHLEWEPACQTPQPSAR ddPTM_MDA-MB-175_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 AELGSWS(0.559)S(0.441)QEHLEWEPACQTPQPSAR 262.97 4.24E-53 206610000 76255 70732 55276 61539 71149 76691 82563 88879 88284 TRUE FALSE 66177.70854 70267.35683 82007.65849 75512.37051 69733.2741 79641.3524 74556.05297 69872.91751 77847.16609 0.85009785 0.902632175 1.053444365 0.970007957 0.895771517 1.023047548 0.957723405 0.897565332 1 16.2483569 4.469433914 24.97368392 0.963936086 0.863231398 0.401100082 0.049560225 156.337052 507889.9473 0.012497054 0.033203664 29473.64948 -4.469433914 -0.100704688 AELGSWSS(ph)QEHLEWEPACQTPQPSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AELGSWSSQEHLEWEPACQTPQPSAR 26 0 B7Z896;F5H3M2;Q9BVG8-5;Q9BVG8-2;Q9BVG8;Q9BVG8-6;H3BTL6 B7Z896 KIFC3 Kinesin-like protein;Kinesin-like protein KIFC3 1 AELGS(0.002)WS(0.136)S(0.862)QEHLEWEPACQTPQPSAR;AELGS(0.003)WS(0.14)S(0.857)QEHLEWEPACQTPQPSAR;AELGS(0.006)WS(0.365)S(0.628)QEHLEWEPACQTPQPSAR 241.02 2.73E-45 476330000 228594 215060 147990 186386 225112 217406 224876 240665 263535 TRUE FALSE 198384.7237 213647.2567 219558.459 228707.79 220632.7116 225769.7495 203067.5601 189200.6626 232380.1925 0.853707545 0.919386693 0.944824327 0.984196577 0.949447151 0.971553328 0.873859161 0.814185842 1 17.82612758 0.953728567 21.86886588 1.892026351 0.913210066 0.204074207 0.053425546 341.9567344 181341.2505 32594.59385 0.014405974 8.989355724 -0.953728567 -0.978816285 AELNEFLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AELNEFLTR 9 0 P23396;P23396-2;E9PPU1;E9PL09;F2Z2S8;H0YCJ7;H0YEU2;H0YF32;E9PQ96;E9PJH4;E9PK82;E9PQX2;H0YES8 P23396 RPS3 40S ribosomal protein S3 0 ;;;; 154.75 0.00017436 3528806000 3342318 3252994 2032476 2400459 3205540 3343190 2952814 3391389 3127725 FALSE TRUE 2900622.208 3231624.868 3015388.192 2945519.905 3141756.026 3471804.683 2666450.553 2666166.854 2757968.914 1.05172404 1.171740861 1.093336541 1.068003301 1.139155706 1.258826619 0.966816754 0.966713889 1 21.39517476 2.20048343 24.99989175 0.975065199 1.128209034 0.603858909 0.058239098 107.5301695 70599.10267 0.023573255 0.015893455 158.665838 -2.20048343 0.153143835 AELNSDKK ddPTM_MDA-MB-175_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 ; 108.67 0.0060394 569010000 781850 551750 526400 495060 337920 391090 718320 789120 734740 FALSE TRUE 678526.5415 548125.5179 780968.8007 607470.9395 331196.0531 406135.4854 648657.437 620372.8289 647879.8742 1.047303009 0.846029549 1.205422227 0.937628971 0.511199786 0.626868501 1.001200165 0.957542985 1 19.30536682 3.473266882 24.99521003 0.830081344 1.023778791 0.233326853 0.17717659 193.9223122 1257555.755 0.055590472 0.072091306 2973.492736 -3.473266882 0.193697447 AELPGSS(ph)SPLLAQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AELPGSSSPLLAQPR 15 0 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 AELPGS(0.041)S(0.601)S(0.359)PLLAQPR;AELPGS(0.059)S(0.47)S(0.47)PLLAQPR 194.77 3.96E-08 344130000 540130 531780 401850 468840 592270 684080 466950 584690 724020 TRUE FALSE 468750.452 528286.7022 596186.0041 575297.2878 580484.9858 710397.0003 421665.2609 459658.5936 638427.1804 0.734226966 0.827481533 0.933835561 0.901116534 0.909242281 1.112729881 0.660475108 0.71998594 1 19.28416255 2.202936439 24.99999709 0.772632284 0.901254017 0.134406161 0.127468969 306.7094169 215237.5781 0.052433131 0.035351905 159.5645601 -2.202936439 0.128621733 AELRDDPIISTHLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AELRDDPIISTHLAK 15 1 O00231;O00231-2 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 ;;; 147.64 2.21E-06 1558690000 4660160 4509240 1622110 3120120 4500030 3973110 4975040 5606400 4020320 FALSE TRUE 4044308.049 4479618.506 2406567.822 3828590.934 4410488.207 4125958.113 4492561.387 4407514.989 3545042.35 1.140834904 1.263629053 0.678854463 1.079984541 1.244128496 1.163867087 1.267280033 1.243289799 1 21.75737143 3.407540886 6.566223855 1.194773948 1.023913231 0.162882413 0.163071193 0.34746359 25.85204844 0.047169987 0.061180884 2555.882512 -3.407540886 -0.170860717 AELSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AELSYR 6 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ;;;; 153.61 0.023518 4338580000 3217570 3314380 2028220 2478890 3103030 3239530 3108030 3426970 3154720 FALSE TRUE 2792359.972 3292607.62 3009073.976 3041759.862 3041285.774 3364156.815 2806613.729 2694139.134 2781772.595 1.003805982 1.183636515 1.081710986 1.093461006 1.09329058 1.209357235 1.008929966 0.968497259 1 21.40757306 2.058442532 10.49129284 0.984000465 1.111226236 0.500212278 0.056191975 0.325635192 56.67833909 0.021312221 0.014359562 114.4043484 -2.058442532 0.127225771 AEMDMVAWGVDLASVEQHINSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEMDMVAWGVDLASVEQHINSHR 23 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 149.73 5.31E-08 93768000 109420 87751 40067 67451 91471 83145 86611 99677 90582 FALSE TRUE 94959.86977 87174.5579 59443.53522 82766.78047 89650.90606 86343.64195 78211.47855 78361.84924 79873.49915 1.188878298 1.091407774 0.744220998 1.036223295 1.12241115 1.081004875 0.979191839 0.98107445 1 16.2854293 -0.266193226 0.013425471 1.09E-06 1.941921592 0.038324792 0.116724031 52331.17848 106.7625843 8539.180467 6976.782892 0.541759797 0.266193226 1.941920499 AEMDQILHGLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEMDQILHGLDK 12 0 A0A5F9ZHC6;A0A5F9ZHM8;P04424-3;P04424-2;P04424 A0A5F9ZHC6 ASL Argininosuccinate lyase 0 ; 151.08 6.87E-05 324110000 1281700 1173560 807360 970860 1073040 908100 1294910 1520610 1329000 FALSE TRUE 1112320.098 1165850.807 1197801.996 1191308.602 1051688.603 943035.1946 1169329.828 1195439.385 1171887.134 0.949169989 0.994849054 1.022113787 1.016572814 0.897431649 0.804715034 0.997817788 1.020097713 1 20.1604022 2.022933298 24.9920278 1.01072656 0.949502396 0.162303751 0.062985806 443.2970672 483089.9652 0.028450946 0.019180521 105.4224969 -2.022933298 -0.061224164 AEMELGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEMELGLR 8 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 143.61 0.0013928 253400000 282550 265350 189386 233232 289630 321410 202790 281790 315340 FALSE TRUE 245210.3016 263606.8984 280973.7031 286190.8903 283866.9297 333774.8507 183123.457 221531.4014 278060.8644 0.881858373 0.948018697 1.010475543 1.029238296 1.020880555 1.200366155 0.658573285 0.796701117 1 18.08504118 2.231900928 24.99927477 0.80723859 1.012778454 0.398431214 0.113643908 152.73235 573323.1103 0.046061134 0.031857205 170.5693239 -2.231900928 0.205539864 AENFFILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AENFFILR 8 0 F8WCF6;P59998;P59998-3;R4GN08;P59998-4;F8WDD7;A0A0A6YYG9;P59998-2 F8WCF6 ARPC4-TTLL3;ARPC4 Actin-related protein 2/3 complex subunit 4 0 ; 135.83 0.0019006 988180000 2106850 1855490 1414300 1715620 1851810 1821040 2193880 2581170 2185460 FALSE TRUE 1828424.434 1843301.164 2098260.211 2105177.743 1814962.604 1891096.587 1981117.855 2029206.882 1927097.408 0.948797101 0.956516861 1.088818967 1.09240858 0.941811553 0.981318629 1.028032027 1.052986151 1 20.87799807 4.368824078 10.16102475 1.026615431 0.950786228 0.310803915 0.045768726 0.370920587 31.74903622 0.012034428 0.031901786 23378.90024 -4.368824078 -0.075829203 AENGERS(ph)DLEEDNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AENGERSDLEEDNER 15 1 Q8WU90 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 1 AENGERS(1)DLEEDNER;AENGERS(1)DLEEDNER 234.22 7.25E-18 1460110000 1154680 1017390 906560 1052460 1208620 986940 1125370 1171450 1712390 TRUE FALSE 1002086.112 1010706.698 1344975.448 1291437.129 1184570.827 1024908.22 1016231.791 920944.5337 1509953.205 0.663653754 0.669362928 0.890739822 0.855282882 0.784508303 0.678768201 0.673022043 0.609915944 1 20.52607241 2.756352703 23.25554367 0.713715093 0.778112717 0 0.124373496 1105.326424 1444737.358 0.040719494 0.040611812 570.627507 -2.756352703 0.064397624 AENGKLVINGNPITIFQERDPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AENGKLVINGNPITIFQERDPSK 23 2 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 236.77 2.21E-37 1139500000 1068600 620780 493560 812340 906340 646620 1553500 1947300 282080 FALSE TRUE 927381.8025 616702.0553 732247.2669 996794.2128 888305.6072 671495.8898 1402841.809 1530885.049 248732.8237 3.728425499 2.479375444 2.943910883 4.007489634 3.571324419 2.699667377 5.639954502 6.154736741 1 17.92423738 2.24779639 24.9953163 4.715907809 3.240576337 0.074398772 1.438658068 318.7271204 862591.238 0.53640703 0.409613972 176.9279274 -2.24779639 -1.475331472 AENLQLLTENELHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AENLQLLTENELHR 14 0 O94992 O94992 HEXIM1 Protein HEXIM1 0 ;;;; 251.68 3.48E-24 1981070000 1925910 1936620 1124671 1424800 1875580 1837990 1737550 2101670 1922940 FALSE TRUE 1671396.114 1923898.216 1668565.657 1748322.617 1838259.628 1908698.665 1569042.668 1652244.226 1695612.224 0.985718368 1.134633372 0.984049085 1.031086349 1.084127374 1.125669323 0.925354657 0.974423399 1 20.69337484 2.22804118 24.99999159 0.966505834 1.057715813 0.394175611 0.053155011 207.2914174 492634.8218 0.02085629 0.014227925 169.0601228 -2.22804118 0.09120998 AENSHNAGQVDTR ddPTM_MDA-MB-175_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 378180000 441630 389830 267623 302561 391700 420740 346670 419840 420550 FALSE TRUE 383267.4766 387269.1811 397046.3779 371262.0994 383905.9363 436926.1401 313049.9968 330060.4832 370833.0581 1.033531041 1.044322162 1.070687657 1.001156966 1.035252732 1.178228668 0.844180393 0.890051402 1 18.50041033 2.223584774 24.99999995 0.9041595 1.056407163 0.578638879 0.059810689 161.4436897 269504.6926 0.024020123 0.016266035 167.3342238 -2.223584774 0.152247662 AENYDIPSADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AENYDIPSADR 11 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;;; 224.58 1.42E-11 5240060000 8126560 6906180 4801180 4872470 6514670 6629510 6941590 7659120 6922850 FALSE TRUE 7052614.506 6860812.849 7123046.707 5978838.785 6385040.813 6884551.54 6268395.67 6021276.791 6104438.56 1.15532566 1.123905627 1.166863527 0.979424844 1.045966922 1.127794386 1.026858672 0.986376836 1 22.54142718 8 0.136725686 0.909123742 1.793367333 0.506437777 0.049903142 148.6848176 1.756489977 1.190252558 25.19026091 100000000 -8 0.884243591 AEPAKIEAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AEPAKIEAFR 10 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;; 129.89 0.00026554 1741710000 4309130 3624520 1235490 1320680 2838970 2508510 3567250 3937260 379975 FALSE TRUE 3739667.553 3600710.289 1832977.096 1620560.579 2782480.051 2605014.003 3221298.644 3095307.589 335054.7884 11.16136131 10.74663134 5.470678707 4.836703237 8.304552413 7.77488964 9.614244464 9.23821326 1 18.3540375 4.259122264 20.70618879 7.041105919 10.95404258 0.328197308 2.527397773 43.4802684 43779.31454 0.63808338 1.678900537 18160.26846 -4.259122264 3.912936661 AEPDESNAR ddPTM_MDA-MB-175_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 ; 169.21 0.00013642 309770000 543680 495400 321880 376030 376460 479220 499720 537690 504530 FALSE TRUE 471831.3105 492145.6848 477542.2446 461413.3588 368969.1825 497655.9035 451257.2313 422709.1778 444885.0382 1.060569068 1.106231144 1.073405945 1.037151891 0.829358488 1.118616858 1.014323235 0.950153729 1 18.76307305 3.472176879 24.99936583 0.982697885 1.07811731 0.285096452 0.071075946 171.1122888 865158.1493 0.019982435 0.025885439 2966.039149 -3.472176879 0.095419425 AEPEAGEEQAGDDRDSGGPVLQFDYEAVANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEPEAGEEQAGDDRDSGGPVLQFDYEAVANR 31 1 P56182 P56182 RRP1 Ribosomal RNA processing protein 1 homolog A 0 224.06 4.09E-35 53144000 33769 32890 18984 19305 30399 33083 28092 30731 21549 FALSE TRUE 29306.34109 32673.94342 28164.7259 23688.49531 29794.11937 34355.72442 25367.64216 24159.4148 19001.50177 1.542317099 1.719545319 1.482236838 1.246664374 1.567987612 1.808053113 1.33503354 1.271447652 1 14.21382582 1.571225846 1.720029492 0.985255174 1.547055833 0.568571278 0.15675988 0.367252321 1.830538759 0.301469838 0.04749708 37.25854115 -1.571225846 0.561800659 AEPEDHYFLLTEPPLNTPENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEPEDHYFLLTEPPLNTPENR 21 0 B4DXW1;P61158;F8WDR7 B4DXW1 ACTR3 Actin-related protein 3 0 ; 225.18 2.90E-25 1651210000 1414140 1195830 820630 993260 1194490 1151020 1137550 1443120 1321320 FALSE TRUE 1227257.816 1187974.514 1217489.413 1218794.864 1170721.986 1195300.484 1027230.576 1134520.018 1165115.055 1.053336158 1.019619916 1.044952091 1.046072539 1.004812341 1.025907681 0.881655912 0.973740759 1 20.152041 2.403564551 14.24838866 0.953445256 1.032387905 0.580118725 0.032387193 0.851236661 163.4832761 0.011831251 0.009163635 253.2588037 -2.403564551 0.078942649 AEPHFLSILQHLLLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEPHFLSILQHLLLVR 16 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 251 2.25E-21 254790000 241490 253300 102626 195685 194232 232940 241530 271240 248830 FALSE TRUE 209576.4846 251636.0556 152256.2769 240118.2701 190367.1632 241901.3525 218106.4578 213237.4368 219413.6009 0.955166333 1.146857144 0.693923605 1.094363655 0.86761788 1.102490236 0.994042561 0.971851498 1 17.74329343 2.742734095 24.98637575 1.00786534 0.956051687 0.05997478 0.125862881 1353.463251 8103118.535 0.038693205 0.03729304 553.0114139 -2.742734095 -0.051813652 AEPPKPEVVDSTESIPVS(ph)DEDSDAMVDDPNDEDFVPFRPR ddPTM_MDA-MB-175_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(0.002)T(0.002)ES(0.009)IPVS(0.493)DEDS(0.493)DAMVDDPNDEDFVPFRPR 58.044 0.0095912 39323000 10495 9467.4 7642.9 8668.6 7886.3 5527.9 10110 12793 10255 TRUE FALSE 9108.059159 9405.208026 11339.032 10636.93812 7729.378059 5740.56189 9129.533756 10057.31651 9042.665583 1.00723167 1.040092431 1.253947954 1.176305595 0.854767655 0.634830719 1.009606479 1.11220706 1 13.1425324 3.244331987 24.99358363 0.938199688 1.123340967 0.322651522 0.140817292 208.7062936 903821.2392 0.046784534 0.05874958 1755.221732 -3.244331987 0.185141279 AEPVPGGQTSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEPVPGGQTSSPR 13 0 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 AEPVPGGQT(0.01)S(0.081)S(0.909)PR 127.78 6.84E-05 0 168360 169980 101660 137260 187020 182370 159970 192200 210680 TRUE FALSE 146110.7994 168863.3902 150823.116 168426.9809 183298.6679 189385.8919 144456.134 151099.5257 185773.6504 0.786499049 0.90897385 0.811864953 0.906624704 0.98667743 1.019444316 0.77759216 0.813352838 1 17.50318636 4.743823387 23.67971282 0.893686641 0.786498959 0.153362133 0.083527867 615.4774661 2769132.912 0.021565071 0.175032592 55440.02105 -4.743823387 -0.107187681 AEPYCSVLPGFTFIQHLPLSER ddPTM_MDA-MB-175_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 ; 230.71 1.78E-26 862820000 995400 820240 567910 663150 832430 1091910 686310 924240 800280 FALSE TRUE 863855.368 814851.7894 842553.1755 813728.3431 815866.2716 1133916.484 619751.7618 726598.4684 705671.8101 1.224160234 1.154717785 1.193973124 1.153125761 1.156155397 1.606860963 0.878243615 1.029654944 1 19.42863785 AEQEEEFISNTLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AEQEEEFISNTLFK 14 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ;; 237.3 6.35E-17 98826000 191300 162934 107566 142269 138787 119403 176139 186507 165777 FALSE TRUE 166019.2203 161863.6758 159585.2774 174573.3509 136025.4102 123996.5107 159057.0669 146623.9294 146179.0319 1.135725269 1.107297495 1.091711139 1.194243447 0.930539821 0.848251005 1.08809769 1.003043511 1 17.15737686 3.234465553 24.99994328 0.979890114 1.127567195 0.58919888 0.065508697 82.62353283 504407.9275 0.02056363 0.024167789 1715.795612 -3.234465553 0.147677081 AEQGS(ph)EEEGEGEEEEEEGGESKADDPYAHLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AEQGSEEEGEGEEEEEEGGESKADDPYAHLSK 32 1 Q5STZ8;Q8NE71 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 AEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK 197.31 5.84E-27 231370000 119040 92076 40275 43104 107890 60253 142330 147630 25679 TRUE FALSE 103308.5624 91471.14669 59752.12471 52891.422 105743.2001 62570.9719 128526.8585 116060.4734 22643.25787 4.562442515 4.039663692 2.638848396 2.335857424 4.669964043 2.763337866 5.676164588 5.125608426 1 14.46679393 3.210481374 24.99858584 4.089841208 3.386351329 0.008511211 1.441635579 742.0977046 660677.6187 0.442350912 0.501677236 1623.608715 -3.210481374 -0.70348988 AEQPHQHAMYYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AEQPHQHAMYYLR 13 0 A0A3B3ISG5;P14735;P14735-2 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ;; 152.74 2.42E-05 754160000 402460 500140 326220 327666 476790 470720 494230 461940 415130 FALSE TRUE 349273.8913 496854.5474 483981.0831 402067.5734 467302.8118 488828.903 446299.6507 363157.7258 366053.8043 0.954159982 1.35732655 1.322158321 1.098383813 1.276595971 1.335401783 1.21921872 0.99208838 1 18.48169619 1.745115583 4.8895207 0.994727323 1.234832784 0.375549763 0.121162551 0.160201328 9.053833078 0.071411363 0.030569853 55.60522247 -1.745115583 0.240105461 AERPDVDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AERPDVDEK 9 1 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 119.53 0.000741 1888100000 2132480 1852440 1393900 1666030 1690700 1646340 2424800 2837290 2843420 FALSE TRUE 1850667.365 1840271.2 2067994.702 2044327.575 1657058.378 1709675.765 2189643.269 2230557.613 2507274.127 0.738119277 0.733972875 0.824798007 0.815358621 0.660900362 0.681886255 0.873316262 0.88963452 1 21.25768831 1.764400308 1.765264976 0.980030034 0.7476553 0.681034282 0.058241953 0.235464355 1.365985677 0.070843522 0.018233558 58.12999798 -1.764400308 -0.232374734 AERS(ph)PNQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AERSPNQGK 9 1 Q9P2E9;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 AERS(1)PNQGK 71.614 0.045091 0 66255 56288 33014 48838 39095 49388 59199 83122 49602 TRUE FALSE 57499.23388 55918.24042 48979.68083 59927.41434 38317.08599 51287.98832 53457.89009 65347.00716 43738.10807 1.314625539 1.27847872 1.119839952 1.370141897 0.876057234 1.172615611 1.222226851 1.494051985 1 15.4166032 -1.413918635 10.54134939 0.139522342 1.220269917 0 0.179217939 0 0 0 0.040157903 0.038555058 1.413918635 1.080747576 AES(ph)GDSLGSEDRDLLYSIDAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AESGDSLGSEDRDLLYSIDAYR 22 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 AES(0.938)GDS(0.062)LGSEDRDLLYSIDAYR;AES(0.995)GDS(0.004)LGS(0.001)EDRDLLYSIDAYR;AES(0.894)GDS(0.079)LGS(0.027)EDRDLLYSIDAYR 235.68 1.09E-30 170011000 219309 185744 118180 133032 174680 156614 199670 226957 175664 TRUE FALSE 190326.76 184523.8354 175332.2433 163238.9489 171204.2098 162639.0419 180306.0341 178424.0117 154897.202 1.22872949 1.191266421 1.131926471 1.053853438 1.105276322 1.049980502 1.16403674 1.151886602 1 17.24095156 4.24206453 2.568464999 1.097864524 1.22193057 0.510575294 0.048856209 0.253698967 3.290740421 0.013374046 0.04329601 17460.81577 -4.24206453 0.124066046 AES(ph)GPDLR ddPTM_MDA-MB-175_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 117.3 0.0022087 5199600000 10804900 8296400 4908900 5630200 7149200 7454400 7123100 7890300 7710100 TRUE FALSE 9377005.089 8241900.402 7282860.459 6908622.962 7006944.907 7741175.592 6432302.858 6203020.747 6798620.761 1.379251089 1.212290065 1.071226167 1.016180076 1.030642119 1.138639125 0.946118791 0.912393994 1 22.69681067 8 0.474523189 0.96779062 12.29082106 0.824549555 0.057478609 44.28291664 0.521354899 0.043006684 491.508867 99999999.9 -8 11.32303044 AES(ph)KPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AESKPR 6 1 E9PD25;O43897 E9PD25 TLL1 Metalloendopeptidase;Tolloid-like protein 1 1 AES(1)KPR;AES(1)KPR 71.223 0.053777 176394000 365910 340800 287460 261830 250850 366930 336540 374170 341840 TRUE FALSE 317554.0664 338561.2624 426476.6175 321282.5033 245858.5758 381046.0345 303902.4026 294156.6573 301428.0646 1.053498674 1.123190911 1.414853717 1.065867917 0.815645936 1.264135889 1.008208718 0.975876807 1 18.20145422 3.493258525 24.77051726 1.013148039 1.198211884 0.265418786 0.140274389 836.1682555 1283506.441 0.038160051 0.054796234 3113.569219 -3.493258525 0.185063846 AES(ph)PAEKVPEESVLPLVQK ddPTM_MDA-MB-175_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 249.91 2.32E-25 2282800000 3997000 2481820 2814140 3476780 2711340 1823410 3570990 4330860 7578900 TRUE FALSE 3468786.323 2465516.761 4175067.517 4266236.038 2657389.639 1893557.763 3224675.939 3404739.292 6682931.076 0.519051638 0.368927456 0.624735983 0.63837798 0.397638343 0.283342405 0.482524195 0.509467964 1 22.67204956 1.230931475 4.267162431 1.054872296 0.473250251 0.698078099 0.108109075 0.139184424 4.844218713 0.252109685 0.0288101 17.01889956 -1.230931475 -0.581622045 AES(ph)PDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 AESPDLR 7 0 Q6UN15;Q6UN15-5;A0A0B4J203;Q6UN15-4 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 AES(1)PDLR;AES(1)PDLR;AES(1)PDLR;AES(1)PDLR;AES(1)PDLR;AES(1)PDLR;AES(1)PDLR 128.12 0.0039739 8589240000 39265500 34502240 22589460 25883060 30848080 33478340 34025700 38181900 37661100 TRUE FALSE 34076464.69 34275592.51 33513798.41 31760204.37 30234263.56 34766273.4 30725892.85 30016997.82 33208847.66 1.02612608 1.032122309 1.009182816 0.956377791 0.910427964 1.046897916 0.92523213 0.903885559 1 24.98506433 3.814848225 3.252010734 0.951003443 1.02762364 0.346409396 0.042397134 0.269557852 5.553745328 0.011924119 0.022067825 6529.023406 -3.814848225 0.076620196 AES(ph)PEEVACR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AESPEEVACR 10 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 AES(1)PEEVACR;AES(1)PEEVACR;AES(1)PEEVACR;AES(1)PEEVACR;AES(1)PEEVACR;AES(1)PEEVACR 240.78 2.86E-12 4329055000 2146040 2077530 1330035 1398917 1980300 1927580 1937820 2174210 2059810 TRUE FALSE 1862435.377 2063882.569 1973244.375 1716562.486 1940895.904 2001735.25 1749890.515 1709272.111 1816301.608 1.025399839 1.136310489 1.086407877 0.945086696 1.068597801 1.10209408 0.963436087 0.941072839 1 20.79257236 2.222043536 24.63216956 0.962327185 1.060367867 0.408302607 0.052322616 194.3610867 289850.8464 0.021846891 0.014779445 166.7414355 -2.222043536 0.098040683 AES(ph)PESSAIESTQSTPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AESPESSAIESTQSTPQK 18 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 AES(0.953)PES(0.047)SAIESTQSTPQK;AES(0.717)PES(0.276)S(0.007)AIESTQSTPQK;AES(0.999)PES(0.001)SAIESTQSTPQK;AES(0.984)PES(0.014)S(0.002)AIESTQSTPQK 486.22 8.25E-240 5393350000 3081550 2367720 1726240 2044860 2646680 1843380 3062010 3226340 2707190 TRUE FALSE 2674315.36 2352166.291 2561055.438 2509176.717 2594016.246 1914296.021 2765056.741 2536412.298 2387149.082 1.120296751 0.985345368 1.072851066 1.051118565 1.08665867 0.801917248 1.158309199 1.062527815 1 21.18685724 4.762254146 22.63263911 1.033203527 1.120297101 0.086562431 0.09318315 4872.377081 4653939.844 0.021799373 1.017835205 57843.44444 -4.762254146 0.087093574 AES(ph)PGPGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AESPGPGSR 9 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 AES(1)PGPGSR 111.73 0.0022147 0 973040 829940 737030 907530 862800 1097600 1261700 1384600 1065300 TRUE FALSE 844450.2986 824488.0695 1093460.173 1113598.557 845631.968 1139825.382 1139340.528 1088514.065 939361.4476 0.898962056 0.877711206 1.164046253 1.185484629 0.900220006 1.213404473 1.21288832 1.158780859 1 19.84132086 4.242635891 24.99607412 1.125709556 0.888336528 0.483502139 0.09905176 82.21050343 504227.1702 0.024855001 0.060971465 17483.80245 -4.242635891 -0.237373029 AES(ph)PSPAPPPGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AESPSPAPPPGLR 13 0 Q9BUA3 Q9BUA3 C11orf84 Uncharacterized protein C11orf84 1 AES(0.944)PS(0.056)PAPPPGLR;AES(0.991)PS(0.009)PAPPPGLR;AES(0.989)PS(0.011)PAPPPGLR;AES(0.998)PS(0.002)PAPPPGLR 255.24 8.24E-24 1257330000 1953690 1187090 750410 888190 1123670 1110360 1062730 1226650 1365410 TRUE FALSE 1695504.916 1179291.928 1113310.786 1089867.115 1101311.165 1153076.268 959666.6082 964340.4433 1203992.785 1.408235113 0.979484215 0.924682274 0.905210669 0.914715752 0.95771028 0.797070065 0.800952012 1 20.19939532 5.064686396 1.522826572 0.883984759 2.075232351 0.861135623 0.063433063 0.964774044 1.095883106 0.01845738 2.188905086 116061.0235 -5.064686396 1.191247592 AES(ph)PTPGMAQGMEPGAGQEGAMFVHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AESPTPGMAQGMEPGAGQEGAMFVHAR 27 0 A0A0A0MSQ9;Q86VX9-5;Q86VX9 A0A0A0MSQ9 MON1A Vacuolar fusion protein MON1 homolog A 1 AES(0.996)PT(0.004)PGMAQGMEPGAGQEGAMFVHAR;AES(0.99)PT(0.01)PGMAQGMEPGAGQEGAMFVHAR;AES(0.951)PT(0.049)PGMAQGMEPGAGQEGAMFVHAR 217.08 2.28E-34 690160000 303358 237173 162803 175068 246357 253002 276199 273112 235489 TRUE FALSE 263268.4717 235614.9949 241535.0753 214819.8651 241454.9777 262735.1507 249413.2635 214709.1242 207649.7587 1.267848676 1.134675024 1.163184956 1.034529809 1.162799221 1.265280308 1.201124745 1.033996502 1 17.66379267 1.647128748 4.777585442 1.008971958 1.170890488 0.498091899 0.06630006 0.131953205 6.661865647 0.047492018 0.01800428 44.37401722 -1.647128748 0.161918529 AESEEGPDVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AESEEGPDVLR 11 0 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 81.099 0.052581 216980000 309180 328810 232250 300460 339630 357710 275680 315540 544420 FALSE TRUE 268321.0796 326650.0255 344566.8768 368684.0352 332872.0275 371471.3352 248944.596 248064.2265 480059.2878 0.558933212 0.680436841 0.717759005 0.76799688 0.693397745 0.773803038 0.518570523 0.516736647 1 18.87285307 4.73498813 5.030580118 0.688844041 0.552953446 0.090311452 0.137346764 0.477315401 38.52914305 0.034264899 0.225494673 54323.5484 -4.73498813 -0.135890595 AESGDSLGSEDRDLLYSIDAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AESGDSLGSEDRDLLYSIDAYR 22 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 0 ;; 174.71 2.11E-12 294573000 358961 359051 204602 270936 328602 336840 304587 390837 298977 FALSE TRUE 311523.3944 356692.3703 303548.2116 332456.1598 322063.4631 349798.4528 275048.1996 307259.549 263632.2797 1.181658766 1.352992019 1.151407604 1.261060141 1.221638957 1.326842271 1.043302436 1.165485309 1 18.0081675 2.231339273 24.99999764 1.088477294 1.248813548 0.571388568 0.072745394 122.3607116 423603.2395 0.027097477 0.018702533 170.3488762 -2.231339273 0.160336255 AESLQQEVEALKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AESLQQEVEALKER 14 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 ; 132.08 4.79E-05 368100000 223074 187228 109313 129285 182915 161959 209645 234202 71608 FALSE TRUE 193594.2057 185998.0869 162177.1324 158641.1352 179275.3494 168189.6675 189313.6602 184119.7249 63142.58382 3.065984855 2.945683811 2.568427242 2.512427045 2.839214656 2.663648799 2.998193117 2.915935867 1 15.94632568 1.236530594 25 0.999997697 2.810285752 0.907017346 0.182495292 16.0475484 197575.9295 0.302252452 0.047467258 17.23973531 -1.236530594 1.810288055 AESPES(ph)SAIESTQSTPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AESPESSAIESTQSTPQK 18 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 AES(0.004)PES(0.989)S(0.007)AIESTQSTPQK 472.12 9.37E-215 1310600000 965920 797820 505890 563960 933840 556350 908480 1035800 881450 TRUE FALSE 838271.2247 792579.0679 750540.0961 692015.7376 915258.411 577753.1445 820375.7494 814302.2306 777245.9852 1.078514705 1.019727452 0.965640364 0.890343277 1.177565955 0.743333714 1.055490495 1.047676342 1 19.56801173 AESSQTCHSEQGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AESSQTCHSEQGDK 14 0 P46063 P46063 RECQL ATP-dependent DNA helicase Q1 0 73.156 0.036621 39774000 40478 31645 16913 25125 25555 29664 42339 39107 43263 FALSE TRUE 35128.72974 31437.12191 25092.18337 30830.01526 25046.5055 30805.19328 38232.9703 30744.27238 38148.49743 0.920841766 0.82407235 0.657750241 0.808158049 0.656552871 0.807507382 1.002214317 0.805910441 1 15.21933861 2.43388908 9.777617814 0.910980786 0.767823314 0.375760772 0.094276314 0.440486257 95.51049753 0.034309527 0.026586503 271.5745568 -2.43388908 -0.143157473 AESSQTCHSEQGDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AESSQTCHSEQGDKK 15 1 P46063 P46063 RECQL ATP-dependent DNA helicase Q1 0 ;;; 224.33 7.45E-13 388296000 767280 580091 358340 493428 414324 369292 732580 880720 730530 FALSE TRUE 665882.004 576280.344 531634.4226 605468.369 406079.763 383498.9022 661534.5044 692384.8818 644167.5756 1.033709285 0.894612467 0.825304537 0.939923697 0.630394603 0.595340276 1.026960265 1.074852116 1 19.29707652 2.042247091 24.98072297 1.045212946 0.819599386 0.371440132 0.131230835 145.1535896 85828.75378 0.056807024 0.038299253 110.2166207 -2.042247091 -0.22561356 AET(ph)PPLPIPPPPPDIQPLER ddPTM_MDA-MB-175_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 126.63 0.00025666 312021000 197766 182487 110666 123057 194962 187670 170356 204678 170082 TRUE FALSE 171630.722 181288.2309 164184.4478 150998.9727 191082.6376 194889.7863 153834.9013 160909.2025 149975.0997 1.144394785 1.208788867 1.094744715 1.006826953 1.274095753 1.299480959 1.025736283 1.072906121 1 17.19436347 2.180085256 24.99999848 1.040921223 1.166794535 0.368891887 0.085044824 96.72515154 41351.92341 0.036735273 0.024766928 151.3858404 -2.180085256 0.125873312 AET(ph)PTESVSEPEVATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AETPTESVSEPEVATK 16 0 P18858;P18858-3;P18858-2;M0R0Q7;B4E135 P18858 LIG1 DNA ligase 1;DNA ligase 1 AET(0.894)PT(0.106)ESVSEPEVATK;AET(0.85)PT(0.15)ESVSEPEVATK;AET(0.999)PT(0.001)ESVSEPEVATK 255.21 1.49E-25 1047130000 757990 659780 515930 558740 680120 501280 736610 955490 884850 TRUE FALSE 657819.701 655445.8617 765435.4737 685610.4568 666586.9426 520564.566 665173.6756 751165.8991 780244.041 0.843094809 0.840052378 0.981020595 0.87871284 0.854331347 0.667181726 0.852520033 0.962731991 1 19.57356591 1.676188221 3.931697934 0.98974809 0.844810139 0.362920948 0.075690377 0.203142647 7.312496141 0.058264894 0.021414364 47.44475643 -1.676188221 -0.14493795 AETEKQS(ph)PPHGEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AETEKQSPPHGEAK 14 1 Q9Y6D6;E5RJN9 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 AETEKQS(1)PPHGEAK;AET(0.002)EKQS(0.998)PPHGEAK 159.8 2.93E-06 431090000 975270 732770 956890 848450 758260 535520 1031180 1243700 2127000 TRUE FALSE 846385.5985 727956.3856 1419645.205 1041103.54 743172.1095 556121.8009 931176.3223 977744.4335 1875548.483 0.451273644 0.388129868 0.756922691 0.555092843 0.396242548 0.296511557 0.496482139 0.521311202 1 20.83888113 1.225205488 3.846630571 1.071504747 0.479447443 0.643157344 0.121450055 0.192285318 4.620719392 0.331990692 0.032589219 16.79598537 -1.225205488 -0.592057304 AETEQGEQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AETEQGEQQR 10 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 240.38 6.59E-12 105034000 55884 52271 40772 47991 41341 50254 47431 58512 82205 FALSE TRUE 48498.78781 51927.62836 60489.47557 58888.09005 40518.39498 52187.3039 42831.14892 45999.66414 72486.81855 0.669070443 0.716373396 0.834489315 0.812397222 0.558976043 0.719955779 0.590881898 0.634593504 1 16.14543105 1.232235378 24.9893892 1.000000517 0.690331796 0.553577236 0.086884693 177.4102615 700833.7026 0.207001548 0.022593693 17.070073 -1.232235378 -0.309668721 AETLMTVTDPVHDIAFAPNLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AETLMTVTDPVHDIAFAPNLGR 22 0 K7ELV2;Q96EE3;Q96EE3-1 K7ELV2 SEH1L Nucleoporin SEH1 0 92.993 0.0019889 137340000 59258 39464 38297 42695 29723 49964 33504 40991 30289 FALSE TRUE 51426.90516 39204.75839 56817.5573 52389.5523 29131.57045 51886.14741 30254.78724 32225.39364 26708.26893 1.925504993 1.467888409 2.127339569 1.96154803 1.090732257 1.942699752 1.132787277 1.20656991 1 14.70499885 2.014464293 0.639215908 0.8335257 1.842322856 0.475342436 0.306271558 1.345166496 0.844704119 0.921224457 0.194466428 103.3866094 -2.014464293 1.008797156 AEVLGHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEVLGHK 7 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJ51;K7ER34 Q9UHD8 9-Sep Septin-9 0 ; 68.915 0.061157 297970000 786590 749570 512810 657880 705670 756100 819290 948540 1000100 FALSE TRUE 682640.1385 744646.0253 760806.6312 807261.7091 691628.5476 785187.6563 739835.3819 745702.1025 881869.3173 0.774083104 0.844394981 0.862720379 0.91539834 0.784275554 0.89036736 0.838939928 0.845592525 1 19.75020536 1.238329199 24.70241997 1.000000195 0.846602232 0.571162555 0.042316699 3.431253607 365332.299 0.054857346 0.009714792 17.31128073 -1.238329199 -0.153397963 AEVLGHKT(ph)PEPAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AEVLGHKTPEPAPR 14 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EJ51;K7ER34 Q9UHD8 9-Sep Septin-9 1 AEVLGHKT(1)PEPAPR;AEVLGHKT(1)PEPAPR;AEVLGHKT(1)PEPAPR;AEVLGHKT(1)PEPAPR;AEVLGHKT(1)PEPAPR 205.65 1.75E-08 3058810000 3262230 3104980 1979030 2020380 3041020 2737870 3330600 3635180 2752950 TRUE FALSE 2831118.04 3084583.182 2936095.527 2479138.159 2980509.652 2843197.631 3007598.925 2857825.046 2427499.387 1.166269312 1.270683403 1.209514426 1.021272414 1.227810671 1.171245458 1.238970004 1.177271171 1 21.2110395 1.241565964 6.100257095 0.993761096 1.187204513 0.433306926 0.066692966 0.122728738 18.13834862 0.098833799 0.016353761 17.44078241 -1.241565964 0.193443417 AEVMLGHGLFSLLAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AEVMLGHGLFSLLAER 16 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 181.74 1.81E-12 147840000 311890 360990 240231 269700 361070 395740 363400 361530 475540 FALSE TRUE 270672.9463 358618.6329 356407.5151 330939.5071 353885.4134 410964.3739 328157.5239 284219.6229 419322.2029 0.645501107 0.855234067 0.849960991 0.78922486 0.84394628 0.980068241 0.782590384 0.677807235 1 18.6776997 4.742796039 23.96506225 0.833378135 0.645500971 0.305244782 0.09361648 341.0094607 1929381.19 0.023463659 0.174852695 55309.02964 -4.742796039 -0.187877164 AEVPGATGGDS(ph)PHLQPAEPPGEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 AEVPGATGGDSPHLQPAEPPGEPR 24 0 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WWC8;Q9P2K5-4 A0A0A0MQW0 MYEF2 Myelin expression factor 2 1 AEVPGAT(0.001)GGDS(0.999)PHLQPAEPPGEPR;AEVPGAT(0.001)GGDS(0.999)PHLQPAEPPGEPR;AEVPGAT(0.001)GGDS(0.999)PHLQPAEPPGEPR;AEVPGAT(0.077)GGDS(0.923)PHLQPAEPPGEPR;AEVPGAT(0.002)GGDS(0.998)PHLQPAEPPGEPR;AEVPGATGGDS(1)PHLQPAEPPGEPR;AEVPGATGGDS(1)PHLQPAEPPGEPR;AEVPGAT(0.001)GGDS(0.999)PHLQPAEPPGEPR;AEVPGAT(0.056)GGDS(0.944)PHLQPAEPPGEPR;AEVPGATGGDS(1)PHLQPAEPPGEPR;AEVPGAT(0.034)GGDS(0.966)PHLQPAEPPGEPR 263.01 2.45E-44 39750540000 10256639 8551676 6419313 8050697 8786883 8805421 8013864 10082820 12114590 TRUE FALSE 8901198.169 8495499.477 9523714.238 9878730.801 8612041.22 9144171.244 7236680.703 7926687.408 10682416.97 0.833256949 0.795278774 0.891531782 0.924765512 0.806188454 0.856002089 0.677438516 0.742031268 1 23.34873477 AEVWDLDMLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AEVWDLDMLR 10 0 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 ;;; 140.75 9.01E-05 162360000 423629 322739 243096 312685 345144 367428 259143 397447 479050 FALSE TRUE 367645.3543 320618.9063 360658.0387 383684.9083 338276.3097 381563.1929 234011.3517 312456.052 422417.2547 0.870336972 0.759009966 0.853795707 0.90830785 0.800810824 0.903285054 0.553981517 0.739685817 1 18.68830924 AEYLCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AEYLCR 6 0 Q15008;Q15008-4;Q15008-3;Q15008-2;C9J0E9;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ;; 124.86 0.042275 1611080000 1547260 1575780 1000890 1153240 1475610 1410810 1432920 1664450 1527390 FALSE TRUE 1342785.671 1565428.597 1484923.752 1415100.768 1446248.248 1465084.774 1293955.639 1308520.32 1346823.694 0.997001817 1.162311447 1.102537591 1.050694886 1.073821506 1.087807394 0.96074612 0.971560217 1 20.36112958 2.241599463 24.99999593 0.975516041 1.082358619 0.562055994 0.042195129 51.48237084 423540.7518 0.015589672 0.011547651 174.4212774 -2.241599463 0.106842578 AFAAVPTSHPPEDAPAQPPTPGPAAS(ph)PEQLSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AFAAVPTSHPPEDAPAQPPTPGPAASPEQLSFR 33 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 AFAAVPTSHPPEDAPAQPPTPGPAAS(1)PEQLSFR;AFAAVPTSHPPEDAPAQPPT(0.199)PGPAAS(0.801)PEQLSFR;AFAAVPTSHPPEDAPAQPPTPGPAAS(1)PEQLSFR;AFAAVPTSHPPEDAPAQPPT(0.037)PGPAAS(0.963)PEQLSFR 287.55 9.54E-75 2080370000 1056520 978090 550326 912690 1100910 1031940 765050 1340240 1029880 TRUE FALSE 916898.2051 971664.8624 816465.4943 1119930.214 1079004.045 1071639.4 690855.5688 1053640.106 908128.7596 1.00965661 1.06996376 0.899063581 1.233228441 1.188161958 1.180052265 0.760746272 1.160232065 1 19.79253734 7.910809582 17.33758309 1.058763456 0.005320179 0 0.146248351 0 0 0.031819357 0 81434715.29 -7.910809582 -1.053443278 AFAHITGGGLLENIPR ddPTM_MDA-MB-175_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 ; 178.23 2.82E-09 1380490000 826890 757420 412520 579720 781670 838580 697540 781590 793690 FALSE TRUE 717614.3914 752444.4581 612016.0518 711354.2865 766116.2963 870840.7152 629892.6782 614453.0608 699860.8724 1.025367212 1.075134341 0.874482452 1.016422427 1.094669422 1.244305475 0.900025567 0.877964586 1 19.41670863 AFAIDSSHPWLHECMIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFAIDSSHPWLHECMIR 17 0 A0A0B4J1W3;Q9BXJ9 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ; 202.41 6.14E-12 722000000 736680 768430 319750 566900 818500 781810 760060 862840 745800 FALSE TRUE 639325.8715 763382.1327 474382.1695 695623.3095 802213.4514 811886.7366 686349.4982 678328.3806 657632.3736 0.972163016 1.160803761 0.721348566 1.057769261 1.219850913 1.234560172 1.043667444 1.031470481 1 19.3269218 6.290582474 9.742784381 1.051757672 0.399917517 0 0.146158455 0 0 0.033263235 0 1952461.479 -6.290582474 -0.651840155 AFAMIIDKLEEDINSSMTNSTAASRPPVTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFAMIIDKLEEDINSSMTNSTAASRPPVTLR 31 2 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ; 148.72 7.58E-09 438450000 112337 80170 47881 74940 81041 71866 90224 82949 70712 FALSE TRUE 97491.38082 79643.35799 71036.41175 91956.27239 79428.44265 74630.73152 81474.09037 65211.00186 62352.50792 1.563551878 1.277308013 1.139271124 1.474780654 1.273861234 1.196916275 1.306669019 1.045844089 1 15.92815997 0.030469752 0.420229326 1.48E-11 1.370971568 0.520045216 0.120556917 13.66567162 0.914061951 11.51747002 0.117511263 1.072678935 -0.030469752 1.370971568 AFAMIIDKLEEDISSSMTNSTAASRPPVTLR ddPTM_MDA-MB-175_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 70.451 0.022486 377000000 114510 79493 65717 71508 74868 66560 124690 130320 83828 FALSE TRUE 99377.21337 78970.80525 97497.96101 87744.98433 73378.27328 69120.60627 112597.583 102452.0822 73917.94934 1.344426006 1.068357631 1.319002514 1.187059234 0.992698985 0.935099078 1.523277959 1.38602441 1 16.17363711 2.23626913 24.99999379 1.329550545 1.141229502 0.146228564 0.180793663 102.2489092 1115503.17 0.072173814 0.05132574 172.2935939 -2.23626913 -0.188321043 AFAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFASPR 6 0 M0R1U9;M0R364;Q8TBC5-2;Q8TBC5;Q8TBC5-3;M0R3C6 M0R1U9 ZSCAN18 Zinc finger and SCAN domain-containing protein 18 1 AFAS(1)PR;AFAS(1)PR 89.369 0.052704 812220000 1510190 1359540 873600 860790 1042060 1157250 1043840 1156200 1074530 TRUE FALSE 1310614.565 1350609.092 1296075.882 1056245.526 1021325.045 1201770.156 942608.5575 908955.6276 947500.2875 1.38323395 1.42544452 1.367889698 1.114770665 1.077915287 1.268358619 0.994837226 0.959319632 1 19.85376686 3.740934345 0.368047566 0.905262377 1.620812225 0.764568546 0.08475876 1.590592297 0.473172267 0.222914189 0.602515057 5507.244333 -3.740934345 0.715549848 AFASLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AFASLR 6 0 P26373;P26373-2;J3KS98;H3BUK8 P26373 RPL13 60S ribosomal protein L13 0 122.17 0.044989 202230000 189280 308050 187610 185480 284740 302470 252150 287160 263310 FALSE TRUE 164266.1684 306026.3993 278338.8235 227596.0689 279074.2311 314106.2166 227696.5318 225753.0687 232181.7918 0.707489451 1.318046505 1.198796949 0.980249429 1.201964327 1.352846036 0.98068212 0.972311683 1 17.82489531 2.094077761 24.99822271 0.981562048 1.137950494 0.117797748 0.181661793 29.8178373 7904.668639 0.070923563 0.04781666 124.1874646 -2.094077761 0.156388447 AFCAENLEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AFCAENLEEK 10 0 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 143.89 0.011638 0 66032 54206 46146 40303 60094 55869 68572 76217 77699 FALSE TRUE 57305.7039 53849.91722 68462.35995 49454.41214 58898.24697 58018.31658 61921.89799 59918.58767 68513.51273 0.836414623 0.785975132 0.999253391 0.72181983 0.859658841 0.846815676 0.903791026 0.874551388 1 16.06410093 -1.144290365 0.828505214 9.999999919 0.842577262 0.311041512 0.070841901 147.277653 2.235077928 2436.904488 0.024323074 0.071731454 1.144290365 -9.157422657 AFDIIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFDIIER 7 0 H3BVG0;Q8N1F7;Q8N1F7-2;H3BV15;H3BRD9 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 ; 143.85 0.0055686 266070000 523580 488610 325950 341270 482060 465050 459460 497820 477790 FALSE TRUE 454387.5764 485400.2887 483580.5102 418760.5695 472467.9491 482940.7744 414901.6399 391365.067 421306.2105 1.078520955 1.152131814 1.147812442 0.993957742 1.121435994 1.146293984 0.9847983 0.928932585 1 18.68450966 2.144256874 5.613758591 0.95926814 1.1058884 0.627157936 0.049244554 0.125029543 6.020360279 0.020618842 0.013778303 139.3981063 -2.144256874 0.14662026 AFDQDGDGHITVDELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AFDQDGDGHITVDELR 16 0 Q9NZT1 Q9NZT1 CALML5 Calmodulin-like protein 5 0 ;; 248.97 1.72E-20 1574690000 1217951 926706 608004 840618 958560 977669 865200 1142350 1480890 FALSE TRUE 1056995.689 920618.4073 902036.7681 1031493.165 939486.5314 1015280.559 781293.0372 898067.3423 1305820.871 0.809449223 0.705011252 0.690781399 0.789919343 0.719460496 0.7775037 0.59831563 0.687741605 1 20.31652558 1.234945768 24.99996121 1.000000399 0.717072177 0.672404857 0.060825787 63.28319513 437592.7928 0.108041763 0.014998417 17.17693879 -1.234945768 -0.282928223 AFDQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AFDQLR 6 0 Q9H0I9 Q9H0I9 TKTL2 Transketolase-like protein 2 0 ;;; 143.97 0.026361 3162320000 3093890 3754290 2586760 2649670 3694480 3435500 3031320 3133790 3881320 FALSE TRUE 2685024.598 3729627.822 3837725.788 3251318.071 3620967.076 3567665.908 2737343.053 2463653.396 3422474.771 0.784527214 1.089745892 1.121330629 0.949990369 1.057996718 1.042422851 0.799813946 0.719845597 1 21.70660848 2.236367814 24.9996795 0.813208262 1.016232041 0.307943853 0.115826737 55.73374612 635391.6092 0.044302931 0.031507339 172.3327483 -2.236367814 0.203023778 AFDTAGNGYCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 ;;;;;;; 298.74 2.39E-35 12198370000 4654840 4965640 3436950 3516800 5092540 5426370 4852970 4712680 5407920 FALSE TRUE 4039691.1 4933020.384 5099070.516 4315343.191 4991208.417 5635125.965 4382329.716 3704910.056 4768601.858 0.847143716 1.034479399 1.069300954 0.904949358 1.046681725 1.181714501 0.918996772 0.776938433 1 22.1851349 2.010422375 24.98192106 0.865165626 1.01703883 0.209695775 0.104575877 243.6074132 583912.6893 0.041820087 0.028162446 102.4288685 -2.010422375 0.151873204 AFEDDDITHVEGSVDPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AFEDDDITHVEGSVDPIR 18 0 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 ;; 227.22 3.09E-19 1548670000 948330 729940 694840 887550 787380 737380 697830 898870 1798690 FALSE TRUE 823005.7877 725144.9761 1030866.948 1089081.793 771712.6785 765747.4857 630154.554 706653.6455 1586050.917 0.518902501 0.457201574 0.649958294 0.686662566 0.486562361 0.482801326 0.397310419 0.44554285 1 20.59700766 1.233751957 24.9980819 1.000000742 0.512571602 0.744282516 0.089212284 84.74666813 440506.8138 0.193571349 0.024323939 17.12978677 -1.233751957 -0.48742914 AFEDDDITHVEGSVDPIRDIEIIHEELQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFEDDDITHVEGSVDPIRDIEIIHEELQLK 30 1 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 242.01 7.64E-46 227300000 98348 65791 53736 82402 63752 48446 74111 96791 125344 FALSE TRUE 85351.06262 65358.81459 79722.90934 101112.6335 62483.45993 50309.74897 66923.72663 76092.99788 110525.9751 0.77222628 0.591343479 0.721304736 0.914831409 0.565328285 0.455184846 0.60550225 0.688462579 1 16.75402594 1.240896407 4.574358708 1.026910959 0.657965454 0.418635089 0.12470332 0.205153096 9.275801922 0.2447071 0.032937913 17.41391448 -1.240896407 -0.368945505 AFEDEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AFEDEKK 7 1 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 107.66 0.011908 706240000 2694400 1958900 1859700 1857400 1459800 1208700 2779100 3220900 2333300 FALSE TRUE 2338328.213 1946031.857 2759057.14 2279151.059 1430752.836 1255199.471 2509583.31 2532135.6 2057459.932 1.136512151 0.945841922 1.341001639 1.107749912 0.695397667 0.610072377 1.219748327 1.230709556 1 20.9724329 3.452672435 24.99477867 0.981245471 1.138721962 0.142974044 0.215270055 592.0308504 605249.3439 0.07025367 0.090700579 2835.779345 -3.452672435 0.157476491 AFEDWLNDDLGSYQGAQGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 328.14 2.20E-79 249439000 219220 217389 164106 205482 212522 211986 197770 244771 338349 FALSE TRUE 190249.5216 215960.9573 243468.2105 252139.8287 208293.228 220141.2386 178590.2958 192428.6265 298349.7667 0.637672768 0.723851605 0.816049609 0.845114885 0.698151134 0.737862949 0.598593717 0.644976628 1 18.18664512 AFELLHLHLDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AFELLHLHLDLR 12 0 Q9H4A4;A6NKB8;A0A087WU27 Q9H4A4 RNPEP Aminopeptidase B 0 ;; 211.26 1.96E-08 1611944000 769672 876704 541076 636675 712203 748011 830865 949038 935746 FALSE TRUE 667957.8951 870944.8737 802742.1634 781241.7897 698031.5537 776787.4672 750287.8402 746093.6091 825123.1739 0.80952507 1.055533163 0.972875552 0.946818384 0.845972548 0.941420011 0.909304046 0.904220888 1 19.65424997 4.793918172 22.65915505 0.939375882 0.809522313 0.358647816 0.056973648 26753.09872 10949493.83 0.014097722 18.31232847 62218.30452 -4.793918172 -0.129853569 AFELMHSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFELMHSGK 9 0 P11766 P11766 ADH5 Alcohol dehydrogenase class-3 0 ; 153.24 7.85E-05 1237680000 3104700 2300600 1522380 1752620 2112420 1758980 2402600 2766700 2541100 FALSE TRUE 2694406.029 2285487.207 2258608.06 2150579.158 2070386.975 1826649.099 2169596.222 2175062.735 2240694.053 1.20248725 1.01999075 1.007994847 0.959782597 0.923993605 0.815215757 0.968269728 0.97070938 1 21.09551424 5.362140981 0.95363892 0.939330066 1.779271587 0.721468186 0.050665683 3.352147284 1.047363888 0.017521856 3.855146468 230218.9037 -5.362140981 0.839941521 AFEVMDEFDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 204.52 7.66E-08 636465000 1060456 1059863 674194 829758 966924 1036251 999538 1132068 1090378 FALSE TRUE 920314.0527 1052900.69 1000236.473 1018167.236 947684.1042 1076116.247 902602.9586 889984.068 961474.755 0.957190033 1.095089273 1.040314858 1.058964087 0.985656773 1.119235051 0.938769275 0.925644759 1 19.87488945 2.208266204 24.99994444 0.948061475 1.04315344 0.402803944 0.050250294 172.7580952 142564.4033 0.018902696 0.012745978 161.5348392 -2.208266204 0.095091965 AFFSEVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AFFSEVER 8 0 Q9UQ80;Q9UQ80-2;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;;; 205.78 0.0001785 4922641000 2845659 2852017 1832789 2215981 2894449 2850924 2528541 2938906 2882238 FALSE TRUE 2469597.953 2833281.913 2719131.891 2719153.355 2836855.128 2960600.891 2283323.483 2310443.822 2541503.107 0.971707627 1.114805606 1.069891232 1.069899678 1.116211552 1.164901543 0.898414594 0.909085579 1 21.27725056 2.227475213 24.99970112 0.928701782 1.086048175 0.612083052 0.055713387 130.8947959 295190.3324 0.022174922 0.015107207 168.8399493 -2.227475213 0.157346393 AFGAGADFVMLGGMLAGHSESGGELIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFGAGADFVMLGGMLAGHSESGGELIER 28 0 A0A087WWM4;Q9P2T1;Q9P2T1-3;F8WAN9;H0YNJ6;Q9P2T1-2;H0YMB3;H0YLV5;H0YLB8;H0YNS9 A0A087WWM4 GMPR2 GMP reductase;GMP reductase 2 0 ; 148.02 9.15E-14 20868000 72680 70906 44385.9 57253 83771 76995 84929 92386 71045 FALSE TRUE 63075.15385 70440.21382 65851.0697 70253.16871 82104.121 79957.04747 76692.59865 72629.97285 62646.14103 1.006848192 1.124414252 1.051159235 1.121428512 1.310601414 1.276328376 1.22421904 1.159368664 1 15.93493802 3.470088086 24.95673105 1.197939148 1.070355572 0.331123328 0.086615309 206.5187724 732813.9175 0.026005864 0.033647141 2951.807867 -3.470088086 -0.127583576 AFGFSHLEALLDDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFGFSHLEALLDDSK 15 0 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 218.11 1.98E-12 1464940000 3579900 2202000 1826680 2037200 2028180 1693930 2460400 2989100 3155500 FALSE TRUE 3106807.145 2187534.917 2710068.558 2499777.397 1987823.186 1759096.583 2221790.787 2349904.226 2782460.385 1.11656833 0.786187264 0.973982801 0.898405386 0.714412035 0.632209031 0.798498623 0.844541845 1 21.40792972 7.808827065 1.015352181 0.815722663 199.9999586 0.365978648 0.113349501 1425.711995 2.773805006 0.036873462 659610.612 64391280.99 -7.808827065 199.1842359 AFGFSHLEALLDDSKELQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFGFSHLEALLDDSKELQR 19 1 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 145.61 7.43E-08 315390000 621630 417950 169234 170807 332010 337250 435570 525280 58204 FALSE TRUE 539480.0205 415204.4589 251076.1285 209591.34 325403.6506 350224.2257 393328.4884 412952.9597 51323.18943 10.5114282 8.089997203 4.892060124 4.083755166 6.340285049 6.823898313 7.663757706 8.046128161 1 15.64732321 4.508749059 3.405361962 5.91480464 10.33675596 0.38627046 2.040315738 0.283194137 6.368583375 0.524977168 2.375551453 32266.29194 -4.508749059 4.421951318 AFGPGLQGGSAGS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AFGPGLQGGSAGSPAR 16 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 AFGPGLQGGSAGS(1)PAR;AFGPGLQGGSAGS(1)PAR;AFGPGLQGGSAGS(1)PAR;AFGPGLQGGSAGS(1)PAR;AFGPGLQGGSAGS(1)PAR;AFGPGLQGGSAGS(1)PAR 286.91 4.73E-36 2690450000 1604731 1467424 1007333 1202467 1405523 1536790 1346500 1536550 1391528 TRUE FALSE 1392661.732 1457784.395 1494482.608 1475505.511 1377555.842 1595911.306 1215916.637 1207970.74 1227023.145 1.134992227 1.188065931 1.217974261 1.202508296 1.122681221 1.300636677 0.990948412 0.98447266 1 20.22673103 2.217596072 24.98679487 0.99024313 1.192354785 0.798073069 0.048047069 92.31103868 110020.9681 0.018288537 0.012344271 165.0426057 -2.217596072 0.202111655 AFGSGIDIKPGT(ph)PPIAGR ddPTM_MDA-MB-175_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;AFGSGIDIKPGT(1)PPIAGR;AFGSGIDIKPGT(1)PPIAGR 136.92 8.49E-06 7216460000 7740000 6925300 4517980 5223950 6473300 5633800 6962800 8480300 7259400 TRUE FALSE 6717139.389 6879807.248 6702890.24 6410127.691 6344493.995 5850535.932 6287548.728 6666853.839 6401202.002 1.049355947 1.074768027 1.047129936 1.001394377 0.991141038 0.913974583 0.982245011 1.041500305 1 22.60991141 3.749962744 2.754308378 0.989284565 1.062222803 0.521143998 0.031476153 0.258605939 3.911841782 0.010232892 0.018509901 5622.930868 -3.749962744 0.072938238 AFGSGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AFGSGYR 7 0 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;; 131.3 0.0080945 757720000 788450 805130 570310 565270 740440 826650 786620 813090 793510 FALSE TRUE 684254.3348 799841.048 846113.8236 693623.1931 725706.6926 858451.7604 710333.7135 639217.031 699702.1518 0.977922296 1.143116462 1.209248566 0.991312077 1.037165158 1.226881693 1.01519441 0.913555903 1 19.4163814 2.005708608 24.98649004 0.954734891 1.099160724 0.330321721 0.084513156 149.1196737 652692.0243 0.034064715 0.022890305 101.3231326 -2.005708608 0.144425833 AFGYYGPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AFGYYGPLR 9 0 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;; 178.02 0.00011969 5696083000 858454 5283340 2646543 2244130 4766620 4804570 3862364 3578950 4931760 FALSE TRUE 745007.1289 5248633.392 3926420.047 2753694.016 4671773.588 4989404.917 3487792.534 2813619.394 4348732.951 0.171315907 1.206933939 0.902888287 0.633217548 1.074283852 1.147323824 0.802024997 0.646997511 1 22.05216369 4.754292121 24.7211733 0.900601702 0.171315276 0.5958817 0.19444759 2056.771606 3232038.198 0.049600699 1.211400187 56792.64827 -4.754292121 -0.729286425 AFHNEAQVNPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AFHNEAQVNPER 12 0 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;;;; 199.8 1.67E-07 6298280000 3689060 3702290 2805580 3222350 3510360 3875380 3409320 3938480 4905980 FALSE TRUE 3201541.374 3677969.413 4162367.872 3954033.818 3440510.704 4024468.376 3078684.671 3096266.701 4326000.633 0.740069557 0.850200849 0.962174587 0.914016005 0.795309801 0.930297685 0.711669954 0.715734223 1 22.04460245 2.243537778 24.99962501 0.785615258 0.86808666 0.047200623 0.101734467 259.227032 1302071.119 0.03871278 0.029029316 175.2014831 -2.243537778 0.082471402 AFHNEAQVNPERK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AFHNEAQVNPERK 13 1 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;; 239.19 5.46E-17 1402800000 2039170 1720310 875830 1058580 1549280 1328590 1976000 2154130 404640 FALSE TRUE 1769688.518 1709009.17 1299384.317 1298946.768 1518452.359 1379701.717 1784367.824 1693486.063 356803.9202 4.95983485 4.789771283 3.641732178 3.640505877 4.25570537 3.866834525 5.000975951 4.746265294 1 18.44477194 4.300399092 6.698133093 3.914519539 4.897976587 0.144441686 1.087615028 0.457227085 38.3868158 0.267248202 0.713533861 19970.96692 -4.300399092 0.983457048 AFHPFIAGPYNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFHPFIAGPYNR 12 0 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7C0A4 Q00341 HDLBP Vigilin 0 ; 126.39 0.00028839 1770260000 2621000 3139500 1795010 1834460 2778600 3017100 2738800 3096500 1873800 FALSE TRUE 2274628.209 3118876.418 2663082.84 2251002.181 2723311.296 3133169.789 2473191.598 2434337.572 1652281.499 1.376659008 1.887618073 1.611760975 1.362359975 1.648212667 1.89626876 1.496834286 1.473318907 1 20.65602807 1.088265983 1.644005309 0.554531613 1.626708668 0.53445992 0.179010258 1.206271935 2.1733475 2.353037699 0.049351416 12.25366442 -1.088265983 1.072177055 AFHPTYEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AFHPTYEEK 9 0 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 ;;; 148.14 9.07E-05 2780910000 3871420 3795020 1998160 2987670 3703290 3306990 4058100 4768780 4407740 FALSE TRUE 3359802.038 3770090.264 2964476.859 3666066.137 3629601.774 3434212.045 3664546.087 3749013.508 3886661.999 0.864444101 0.970007236 0.762730811 0.943242849 0.933860926 0.883589066 0.942851755 0.964584394 1 21.89010022 0.547816456 0.46813298 1.194199265 0.881569472 0.324274936 0.055661396 11.56483063 1.274104448 2.288508798 0.044333029 3.530339372 -0.547816456 -0.312629794 AFHSLDVNPTSQQDDSSNGLDPQEAGSRVS(ph)PDLGNDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AFHSLDVNPTSQQDDSSNGLDPQEAGSRVSPDLGNDEK 38 1 Q68DA7-5;Q68DA7-3 Q68DA7-5 FMN1 Formin-1 1 AFHSLDVNPTSQQDDSSNGLDPQEAGS(0.041)RVS(0.959)PDLGNDEK 183.77 1.61E-23 43032000 22414 21471 17906 19758 23005 19893 25499 31514 21765 TRUE FALSE 19451.93311 21329.95559 26565.40149 24244.35588 22547.24551 20658.29658 23026.1109 24774.97634 19191.96649 1.013545596 1.11140021 1.384193824 1.26325543 1.174827265 1.076403327 1.199778611 1.29090348 1 14.22821492 4.472557989 24.99676226 1.206836421 1.038009182 0.239407525 0.107068507 142.6402482 781363.2381 0.026673518 0.071140511 29686.43103 -4.472557989 -0.168827239 AFIHWVSQPLMCEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFIHWVSQPLMCEVR 15 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A0U1RQX5;A0A0U1RQX9 P47897 QARS Glutamine--tRNA ligase 0 ; 153.23 2.69E-06 1084450000 636720 966350 525320 615890 891250 985850 800450 918680 984980 FALSE TRUE 552575.8388 960001.9832 779366.5091 755737.2378 873515.8687 1023776.287 722822.4822 722227.4312 868536.7865 0.636214663 1.105309525 0.897332757 0.870126919 1.005732725 1.178736817 0.832230129 0.83154501 1 19.72822743 4.757688382 24.26489758 0.951318076 0.636214239 0.443401603 0.114890041 3089.334911 3918940.951 0.029168504 0.986750479 57238.51824 -4.757688382 -0.315103837 AFITNIPFDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AFITNIPFDVK 11 0 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 156.12 0.0032003 0 124950 98804 71442 87791 102830 88279 113180 136930 105360 FALSE TRUE 108437.5409 98154.95002 105991.5902 107725.2884 100783.8842 91675.15025 102203.821 107648.5851 92904.46083 1.167194126 1.056514931 1.140866533 1.15952762 1.08481211 0.986768013 1.100095949 1.158702006 1 16.50346025 3.079231065 8.648772655 1.07534981 1.126153522 0.235886684 0.05671599 0.55969124 54.94207357 0.018009482 0.020439895 1200.137664 -3.079231065 0.050803712 AFKPEETSSNSDPPS(ph)PPVLNNSHPVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFKPEETSSNSDPPSPPVLNNSHPVPR 27 1 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 1 AFKPEETSSNSDPPS(1)PPVLNNSHPVPR;AFKPEETSSNSDPPS(1)PPVLNNSHPVPR 154.4 2.78E-08 552310000 1629360 1487160 943070 1243560 1504710 1119530 1669190 2023500 1611970 TRUE FALSE 1414035.948 1477390.748 1399141.806 1525929.305 1474769.215 1162599.044 1507312.211 1590790.272 1421404.743 0.994815836 1.0393878 0.98433737 1.0735361 1.037543474 0.817922586 1.060438428 1.119167696 1 20.43888599 2.026841559 24.99997663 1.07460826 0.993991487 0.154178077 0.073734525 334.7761556 311806.0766 0.030128188 0.020312003 106.3754865 -2.026841559 -0.080616774 AFLIEEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFLIEEQK 8 0 P49207 P49207 RPL34 60S ribosomal protein L34 0 ; 157.54 0.0008731 87631000 394910 330670 230065 284200 298960 274220 379200 423860 391120 FALSE TRUE 342721.6429 328497.807 341325.2035 348731.9537 293011.2809 284769.4208 342425.2424 333220.8375 344882.2392 0.993735264 0.952492676 0.989686231 1.011162403 0.849598059 0.825700452 0.992875838 0.966187294 1 18.39574431 AFLLDPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AFLLDPDR 8 0 Q9BTY7 Q9BTY7 HGH1 Protein HGH1 homolog 0 77.058 0.079558 179850000 425710 494280 302660 349480 474350 503950 426410 485930 442290 FALSE TRUE 369451.3449 491033.0421 449027.3883 428834.7755 464911.3631 523337.2826 385056.8238 382017.651 390002.9801 0.947303902 1.259049462 1.15134348 1.099567945 1.192071309 1.341880215 0.987317645 0.979524954 1 18.57312562 2.139356954 18.73103132 0.98684305 1.167075325 0.400450835 0.101637535 2.197124026 408.7208183 0.039771184 0.026813754 137.8341886 -2.139356954 0.180232274 AFLQAILEHEEENEEEDEVPDDETLNQMIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AFLQAILEHEEENEEEDEVPDDETLNQMIAR 31 0 F6VDE0;P51531-2;P51531;A0A0U1RQZ9 F6VDE0 SMARCA2 Probable global transcription activator SNF2L2 0 148.22 1.42E-08 14690000 15765 12871 9073 11859 15222 13360 11612 14977 14898 FALSE TRUE 13681.61531 12786.44955 13460.73315 14551.7672 14919.11198 13873.96785 10485.87003 11774.2851 13136.77541 1.041474401 0.973332431 1.024660369 1.107712262 1.135675348 1.056116696 0.7982073 0.896284266 1 13.68132357 2.26235492 24.7246682 0.893607443 1.057195299 0.571922596 0.064531328 142.9302815 148518.4551 0.025525069 0.019759994 182.9594813 -2.26235492 0.163587856 AFLS(ph)PPTLLEGPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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(0.971)PPT(0.029)LLEGPLR;AFLS(0.978)PPT(0.022)LLEGPLR;AFLS(0.994)PPT(0.006)LLEGPLR;AFLS(0.963)PPT(0.037)LLEGPLR;AFLS(0.998)PPT(0.002)LLEGPLR;AFLS(0.945)PPT(0.055)LLEGPLR 192.39 3.97E-07 1353694000 1676336 1464252 1037586 1517318 1950125 1759395 1430830 2413266 2290035 TRUE FALSE 1454803.95 1454633.232 1539366.06 1861848.243 1911321.328 1827080.064 1292068.327 1897207.846 2019309.671 0.720446186 0.720361643 0.762322928 0.922022149 0.946522148 0.904804295 0.639856455 0.939532887 1 20.94543074 3.875754267 4.339261642 0.88373171 0.724564229 0.379234024 0.095590002 0.265246281 8.095539902 0.02672398 0.048716005 7511.977303 -3.875754267 -0.159167481 AFMES(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AFMESPK 7 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 AFMES(1)PK 86.67 0.02088 133900000 200020 195330 157980 168940 223790 161500 230060 252870 218910 TRUE FALSE 173586.8502 194046.8644 234379.6564 207300.4091 219337.0168 167713.0095 207748.8166 198795.7183 193030.7092 0.899270644 1.005264215 1.214209166 1.073924506 1.136280428 0.868841078 1.076247492 1.029865762 1 17.55847086 1.324939622 3.922949727 0.998636943 1.043714425 0.012616214 0.101412567 1.36384881 31.03539191 0.146253037 0.025858412 21.13195231 -1.324939622 0.045077482 AFMGT(ph)PVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AFMGTPVQK 9 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 AFMGT(1)PVQK;AFMGT(1)PVQK;AFMGT(1)PVQK;AFMGT(1)PVQK;AFMGT(1)PVQK 170.52 0.00064438 1125020000 3511780 3443400 2377960 2687440 2936420 2658430 3521640 3814910 3927510 TRUE FALSE 3047689.375 3420780.079 3527949.41 3297664.327 2877990.987 2760701.522 3180111.895 2999121.184 3463204.242 0.880020109 0.987750026 1.018695163 0.95220036 0.831019711 0.797152385 0.918257103 0.865996047 1 21.72367604 3.372881258 6.983091976 0.879104163 0.967990227 0.266817854 0.063310347 0.272315712 16.12910355 0.018326472 0.023694206 2359.832933 -3.372881258 0.088886063 AFPLFTHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFPLFTHR 8 0 Q8NDH3-3;Q8NDH3-2;Q8NDH3;Q8NDH3-5;Q8NDH3-4;H0YEP3 Q8NDH3-3 NPEPL1 Probable aminopeptidase NPEPL1 0 ; 190.08 0.0001883 627980000 553740 767380 455930 463020 731540 771790 617640 660400 735020 FALSE TRUE 480561.856 762339.0303 676419.273 568155.7678 716983.7852 801481.2607 557741.3679 519178.5992 648126.7729 0.741462745 1.176219009 1.043652725 0.876612094 1.106240037 1.23661187 0.860543633 0.801044828 1 19.3059165 AFREEAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AFREEAIK 8 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;; 138.4 0.0006449 1544360000 1344970 1385220 704860 787120 1260610 1190410 1423030 1733440 359623 FALSE TRUE 1167228.807 1376120.399 1045732.654 965847.6264 1235526.327 1236205.843 1285024.77 1362757.346 317108.7786 3.680846717 4.339584683 3.297709569 3.045792774 3.896222403 3.89836525 4.052315345 4.297444402 1 18.27461829 1.232753575 24.99978668 0.999995443 3.828973739 0.828420421 0.402349358 81.57966674 351170.6499 0.924000523 0.106051508 17.09045305 -1.232753575 2.828978296 AFS(ph)DPFVEAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AFSDPFVEAEK 11 0 P34932;A0A087WYC1;A0A087WTS8;P34932-2 P34932 HSPA4 Heat shock 70 kDa protein 4 1 AFS(1)DPFVEAEK 154.23 3.37E-05 64248000 239210 183070 161930 175020 183980 159390 234360 246820 248520 TRUE FALSE 207597.7924 181867.4011 240239.8896 214760.966 180319.158 165521.8364 211631.8033 194039.4638 219140.2487 0.947328451 0.829913273 1.096283732 0.980016073 0.822848194 0.755323759 0.965736803 0.885457897 1 17.74149496 3.26200251 24.89701807 0.885283663 0.963344425 0.148690601 0.092154183 459.6651835 488194.8165 0.027106604 0.034973196 1828.110781 -3.26200251 0.078060762 AFS(ph)FSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AFSFSK 6 0 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C103 Q9H8V3-2 ECT2 Protein ECT2 1 AFS(0.929)FS(0.071)K 107.01 0.033184 248170000 665380 588200 319420 440580 525350 331390 641000 632710 605190 TRUE FALSE 577448.3471 584336.0755 473892.5804 540620.4228 514896.5628 344138.7877 578835.9187 497409.8903 533645.1276 1.08208305 1.094989995 0.888029434 1.013071037 0.96486698 0.644883219 1.084683226 0.932098626 1 19.02552115 4.247827748 24.83252982 0.934392507 1.088536621 0.239638464 0.115501025 257.5342931 690081.5674 0.028063033 0.072075185 17694.07029 -4.247827748 0.154144114 AFS(ph)TEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFSTEK 6 0 Q9NZ32;H0YJD9 Q9NZ32 ACTR10 Actin-related protein 10 1 AFS(0.981)T(0.019)EK;AFS(0.967)T(0.033)EK 78.149 0.074 1599150000 1929920 1459060 1012860 1284750 1243470 1061090 2508730 2065460 1903190 TRUE FALSE 1674876.182 1449475.339 1502682.484 1576472.124 1218727.38 1101910.819 2265433.751 1623777.452 1678197.046 0.998021172 0.863709862 0.895414807 0.939384399 0.726212326 0.656603956 1.349921188 0.967572584 1 20.67848069 2.249210797 24.99995234 1.087197823 0.848307354 0.431464015 0.13974599 209.3651687 491458.5692 0.052663691 0.040358461 177.5050843 -2.249210797 -0.238890469 AFS(ph)WLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AFSWLR 6 0 Q9P206-2 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 AFS(1)WLR;AFS(1)WLR;AFS(1)WLR 100.19 0.039803 187524000 278443 281055 126971 213756 235853 166463 240061 243589 244485 TRUE FALSE 241646.0521 279208.7312 188374.6003 262292.5669 231159.9867 172866.9393 216779.9212 191499.388 215582.2618 1.120899512 1.295137776 0.873794526 1.216670447 1.072258844 0.801860681 1.005555463 0.888289168 1 17.71787895 2.942660349 8.10163692 0.926727831 1.123590586 0.394230194 0.119796432 0.324567161 42.50443786 0.036098818 0.036289752 876.3152091 -2.942660349 0.196862756 AFSDPFVEAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFSDPFVEAEK 11 0 P34932;A0A087WYC1;A0A087WTS8;P34932-2 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 172.27 3.15E-05 154398000 361590 302020 223570 257420 270250 261210 353080 409670 381610 FALSE TRUE 313804.9653 300036.0107 331689.1998 315871.1454 264872.5537 271258.9177 318838.3559 322065.2586 336496.5005 0.932565316 0.891646749 0.985713668 0.938705588 0.787148019 0.80612701 0.947523542 0.957113248 1 18.36023198 2.017400213 24.71790038 0.968540848 0.890940972 0.281571089 0.059705816 302.4184426 429599.1633 0.026816646 0.018075425 104.0878919 -2.017400213 -0.077599876 AFSMDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFSMDDR 7 0 E9PP67;E9PQ25;F2Z2Y8;E7EN89;Q9H0E2-2;Q9H0E2 E9PP67 TOLLIP Toll-interacting protein 0 ; 90.986 0.038936 407330000 908610 945420 656730 736660 845960 1004810 888950 985810 1055850 FALSE TRUE 788534.8864 939209.4738 974326.8246 903929.9121 829127.0511 1043465.691 802739.7658 775002.2031 931028.6158 0.846950215 1.008786903 1.046505777 0.970893802 0.890549482 1.120766508 0.862207404 0.832415019 1 19.82846599 AFSTVPLT(ph)PVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AFSTVPLTPVPR 12 0 H0Y5D5;Q9BTG3;Q5SYW2;F5H2X7;Q9ULV3-5;Q9ULV3-2;Q9ULV3;A0A494C0L7;Q9ULV3-3;Q9ULV3-4 H0Y5D5 CIZ1 Cip1-interacting zinc finger protein 1 AFSTVPLT(1)PVPR 148.96 0.00090154 0 116700 120220 90110 95769 127490 146850 117850 128350 192950 TRUE FALSE 101277.7993 119430.2669 133687.4974 117514.8152 124953.1984 152499.4145 106420.9251 100903.3513 170139.6708 0.595262697 0.701954261 0.785751476 0.690696148 0.734415424 0.89631897 0.625491543 0.59306187 1 17.37636004 4.676951626 3.27045595 0.740204239 0.584171643 0.144052533 0.120839765 0.622220506 10.90790428 0.030115182 0.222723398 47528.22834 -4.676951626 -0.156032596 AFSYYGPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFSYYGPLR 9 0 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ; 238.95 6.12E-10 2471900000 352670 1622520 870870 797000 1426590 1435770 1255150 1219800 1515490 FALSE TRUE 306063.7659 1611861.559 1292025.645 977971.0314 1398203.65 1491005.001 1133425.746 958955.2625 1336330.499 0.229032987 1.206184818 0.966845886 0.731833205 1.046300785 1.115745695 0.848162747 0.717603365 1 20.34984543 4.752894916 24.9515331 0.932031484 0.229032492 0.677194342 0.156664178 1654.904923 2880621.657 0.040165598 0.84688655 56610.22955 -4.752894916 -0.702998992 AFTELFQVACAKPPPLGLCDYPSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AFTELFQVACAKPPPLGLCDYPSSR 25 1 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 96.887 0.0080497 265300000 133750 115820 73468 82826 95557 100960 133830 135110 87923 FALSE TRUE 116074.5986 115059.1708 108997.3705 101632.9092 93655.60265 104843.9965 120851.1872 106217.7779 77528.8431 1.497179552 1.484082132 1.405894454 1.310904499 1.208009805 1.352322469 1.558790024 1.370042086 1 16.24244552 -2 0.040730106 2.65E-09 2.224954011 0.258946518 0.137854678 3240.070911 12.9897501 564.3407952 221.5915383 0.01 2 2.224954009 AFTHTAQYDEAISDYFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AFTHTAQYDEAISDYFR 17 0 P31939-2;P31939;C9JLK0 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ;;; 300.32 2.44E-46 3395880000 900350 846130 519775 644410 766240 850020 793130 919340 853690 FALSE TRUE 781366.4663 840571.7163 771139.9285 790733.1397 750993.3231 882720.8194 716212.3747 722746.2953 752767.7407 1.037991434 1.116641523 1.024406184 1.050434413 0.997642809 1.172633698 0.951438719 0.960118581 1 19.52184528 2.162603559 24.99998967 0.967556397 1.063117656 0.446183392 0.050336917 31.82394159 10473.04312 0.01931709 0.013023582 145.4131087 -2.162603559 0.095561259 AFVAIGDYNGHVGLGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AFVAIGDYNGHVGLGVK 17 0 P15880;H0YEN5;E9PPT0;E9PMM9;I3L404;E9PM36 P15880 RPS2 40S ribosomal protein S2 0 ;;; 205.68 7.67E-12 1181865000 1800962 1705098 1313195 1485171 1560901 1497682 1847234 2166826 2043818 FALSE TRUE 1562960.309 1693897.099 1948260.494 1822401.775 1529842.124 1555298.796 1668089.531 1703467.122 1802200.164 0.86725123 0.939905085 1.081045565 1.011209416 0.8488747 0.86300003 0.925585051 0.945215274 1 20.78132782 3.263438146 24.99362728 0.918121996 0.979941746 0.15416215 0.067354061 453.7127671 455827.0248 0.020734843 0.026756808 1834.163919 -3.263438146 0.06181975 AFVDFLSDEIKEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AFVDFLSDEIKEER 14 1 Q07021 Q07021 C1QBP "Complement component 1 Q subcomponent-binding protein, mitochondrial" 0 ;;; 225.32 2.57E-12 648040000 1166720 837700 767860 1272280 952830 925050 861880 1191690 1098130 FALSE TRUE 1012534.996 832197.0935 1139199.664 1561170.62 933870.5472 960637.2721 778295.0103 936856.3672 968310.3224 1.045672005 0.859432224 1.176482 1.612262705 0.964433122 0.992075835 0.803766099 0.967516658 1 19.88510995 3.035020463 24.99994545 0.937278375 1.168384777 0.257718568 0.192434673 266.7383453 190413.9949 0.061471714 0.069702114 1083.977988 -3.035020463 0.231106402 AFVDRT(ph)PPPAAVAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFVDRTPPPAAVAQR 15 1 Q5JTD0-4;Q5JTD0-2;Q5JTD0 Q5JTD0-4 TJAP1 Tight junction-associated protein 1 1 AFVDRT(1)PPPAAVAQR;AFVDRT(1)PPPAAVAQR 78.705 0.035764 1678990000 625040 669370 456870 538390 742450 770890 718120 835370 709530 TRUE FALSE 542439.3804 664972.8644 677813.8601 660639.6783 727676.6976 800546.6371 648476.8329 656732.6264 625650.1717 0.867001089 1.062850926 1.083375168 1.055925033 1.163072801 1.279543543 1.036484704 1.049680246 1 19.25499668 4.865002438 2.054415106 1.096608834 0.74377713 0.453564695 0.078125922 1.14453536 3.960166079 0.021873105 0.843894946 73282.86467 -4.865002438 -0.352831704 AFVEDS(ph)EDEDGAGEGGSSLLQK ddPTM_MDA-MB-175_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 336.14 3.84E-81 877400000 1081750 842590 600140 728260 798600 715270 929540 1094720 1028580 TRUE FALSE 938793.9967 837054.9708 890369.7113 893622.5638 782709.4224 742786.8997 839393.3539 860622.6471 906982.4442 1.035074055 0.922900963 0.981683512 0.985269968 0.862981888 0.818965025 0.925479164 0.948885673 1 19.7907151 4.740885963 23.81700357 0.929619745 1.035074125 0.257324563 0.055657183 171.8023871 1759435.978 0.01459341 0.093452559 55066.30837 -4.740885963 0.105454381 AFVFDVIHEGCLVTPPELLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AFVFDVIHEGCLVTPPELLR 20 0 C9J3D7;Q9UKG9;Q9UKG9-3 C9J3D7 CROT Peroxisomal carnitine O-octanoyltransferase 0 96.487 0.0010769 70838000 167690 129440 100660 101880 121170 147200 139470 178760 98044 FALSE TRUE 145529.3416 128589.7001 149339.5127 125013.4111 118758.9541 152862.8793 125944.2209 140533.5651 86453.35001 1.683327964 1.487388286 1.727399952 1.446021596 1.373676718 1.768154493 1.456788208 1.625542158 1 16.39963425 1.234932671 24.99921337 0.999999198 1.566594856 0.653396394 0.130670292 62.63784697 431554.1793 0.213227019 0.029581766 17.1764208 -1.234932671 0.566595657 AFVHWYVGEGMEEGEFSEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 25 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 ;;;;;;;;;;;;;;;;;;;;;;;; 343.26 1.06E-80 13777453600 10694888.4 8938462.3 6806614.3 7524776.3 8726005.8 10269901.7 9065135 10030909.1 9902606.3 FALSE TRUE 9281531.801 8879744.953 10098315.74 9233391.768 8552375.357 10664991.46 8185999.603 7885877.25 8731931.464 1.06294144 1.016927926 1.156481333 1.057428337 0.97943684 1.221378284 0.937478682 0.90310801 1 23.05786938 2.099905309 24.99993384 0.93728213 1.077208598 0.441424223 0.071459712 9.949239665 2474.974732 0.027637313 0.018633067 125.8650953 -2.099905309 0.139926468 AFVRPSGTEDVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFVRPSGTEDVVR 13 1 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A087WT27;A0A494C1E2;A0A494C1Q4;J3KN95;H0Y8I3 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 ; 171.29 2.31E-05 2202400000 2031140 1946760 1291680 1437930 1900640 1996480 1757600 2067510 1732430 FALSE TRUE 1762719.703 1933971.605 1916340.768 1764433.984 1862820.983 2073285.877 1587148.223 1625389.076 1527624.099 1.153896239 1.26599967 1.254458325 1.155018427 1.219423668 1.357196367 1.038965164 1.063998059 1 20.54285815 2.21210246 24.99717093 1.040697126 1.232403544 0.71578963 0.059358512 116.8817065 110426.7895 0.023720904 0.015997988 162.9680464 -2.21210246 0.191706418 AFWMAIGGDRDEIEGLS(ph)SDEEH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AFWMAIGGDRDEIEGLSSDEEH 22 1 Q6PD74;Q6PD74-2 Q6PD74 AAGAB Alpha- and gamma-adaptin-binding protein p34 1 AFWMAIGGDRDEIEGLS(0.963)S(0.037)DEEH 147.45 4.72E-08 12989000 16940 15752 8763.8 12166 15550 16259 14229 18212 15003 TRUE FALSE 14701.33608 15648.52407 13002.00299 14928.47625 15240.58542 16884.49425 12849.07377 14317.50553 13229.36243 1.111265653 1.182863056 0.982814029 1.128435049 1.152027205 1.27628934 0.971254196 1.082252119 1 13.69145591 2.199896113 24.99998054 1.029314725 1.133965128 0.350311041 0.077027269 206.7193762 133660.7776 0.031525635 0.021254993 158.4514116 -2.199896113 0.104650403 AFWMAIGGDRDEIEGLSS(ph)DEEH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFWMAIGGDRDEIEGLSSDEEH 22 1 Q6PD74;Q6PD74-2 Q6PD74 AAGAB Alpha- and gamma-adaptin-binding protein p34 1 AFWMAIGGDRDEIEGLS(0.014)S(0.986)DEEH;AFWMAIGGDRDEIEGLS(0.002)S(0.998)DEEH 220.23 6.26E-26 56267000 147799 127846 76272 104191 122051 131100 122022 139747 117350 TRUE FALSE 128266.9877 127006.1712 113157.3943 127849.159 119622.4239 136143.5018 110188.3252 109863.1916 103477.0167 1.239569827 1.22738532 1.093550993 1.235531938 1.15602892 1.315688316 1.064857963 1.061715877 1 16.65895084 2.103259602 8.065687173 1.043694152 1.205049053 0.642167324 0.059595148 0.149646424 10.44383474 0.023501491 0.015815271 126.8409838 -2.103259602 0.161354901 AFYAELYHIISSNLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AFYAELYHIISSNLEK 16 0 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ; 313.31 9.92E-58 2605600000 5835500 5582900 3583800 4235400 4843300 4354500 6533000 7262100 6866300 FALSE TRUE 5064323.89 5546225.562 5316937.667 5197112.304 4746927.806 4522020.433 5899430.666 5709156.429 6054573.836 0.836445971 0.916038967 0.878168771 0.858377888 0.78402344 0.746876751 0.974375873 0.942949344 1 22.52959399 2.209521236 24.99538255 0.966378184 0.840745644 0.633948488 0.048500919 153.8455468 132420.0962 0.021625762 0.014582716 162.0023208 -2.209521236 -0.12563254 AFYAPVHADDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AFYAPVHADDLR 12 0 G3XAL9;P55011-3;P55011 G3XAL9 SLC12A2 Solute carrier family 12 member 2 0 ;;; 159.94 7.34E-05 875160000 837276 996380 590752 1026050 1315430 1331450 572076 1322750 997980 FALSE TRUE 726627.8552 989834.7142 876441.6431 1259030.335 1289255.517 1382671.743 516596.1576 1039890.206 879999.9413 0.825713527 1.12481225 0.995956479 1.430716385 1.465063185 1.571217995 0.587041127 1.181693495 1 19.7471439 2.244082993 24.99999843 0.962829865 1.238953923 0.231874339 0.264919669 229.1618684 1037429.255 0.104594423 0.078665224 175.4215697 -2.244082993 0.276124058 AFYPEEISSMVLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AFYPEEISSMVLTK 14 0 A0A0G2JIW1;P0DMV9;P0DMV8;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 0 205.46 2.84E-08 146480000 251540 228870 178120 197590 218000 205640 256470 261290 235920 FALSE TRUE 218298.3517 227366.5379 264259.4278 242455.8295 213662.2265 213551.1039 231597.5789 205415.1669 208029.8064 1.049360933 1.092951736 1.270295985 1.165486012 1.027075063 1.026540896 1.113290364 0.987431419 1 17.66643073 3.235224495 24.99501768 1.031403396 1.149823704 0.430957208 0.064767648 83.84826598 628209.5698 0.020195433 0.02385243 1718.796634 -3.235224495 0.118420308 AFYVNVLNEEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AFYVNVLNEEQR 12 0 P04040 P04040 CAT Catalase 0 89.805 0.011747 0 60604 68585 49753 50674 57963 76430 55271 75702 60952 FALSE TRUE 52595.02785 68134.46062 73813.71721 62180.3062 56809.6497 79370.31156 49910.82693 59513.71641 53746.324 0.978579072 1.267704571 1.373372386 1.156922029 1.056996004 1.476757956 0.928637034 1.107307663 1 15.71387846 2.195795438 24.99999716 1.028368521 1.217546374 0.299360475 0.148147209 183.730394 107405.2354 0.058051279 0.039138472 156.9623303 -2.195795438 0.189177853 AGAAAGDS(ph)DEESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGAAAGDSDEESR 13 0 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 AGAAAGDS(1)DEESR 165.64 3.67E-05 32649000 37168 43703 29220 50066 40665 53426 34290 46548 90163 TRUE FALSE 32256.15463 43415.91212 43350.88974 61434.25051 39855.84606 55481.33279 30964.56108 36594.07244 79504.03285 0.405717213 0.5460844 0.54526655 0.77271867 0.501305967 0.697843 0.389471577 0.460279449 1 16.27874042 1.232435037 24.98728968 1.000000759 0.540434541 0.595815857 0.119109252 148.5444244 605877.3555 0.263931114 0.0294146 17.07792245 -1.232435037 -0.459566218 AGAAAGDS(ph)DEESRADDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGAAAGDSDEESRADDK 17 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 AGAAAGDS(1)DEESRADDK;AGAAAGDS(1)DEESRADDK 242.22 1.30E-20 510000000 414580 352480 389290 494510 408610 440760 417780 510670 767060 TRUE FALSE 359792.2026 350164.5357 577551.9461 606796.0536 400479.4604 457716.3224 377263.7599 401467.1945 676379.0406 0.531938722 0.517704593 0.853888 0.897124271 0.592093244 0.67671571 0.557769737 0.59355357 1 19.36747243 4.268882377 24.80422999 0.71428234 0.524821262 0.260615021 0.14532335 295.014386 241326.6719 0.037501358 0.099191942 18573.01362 -4.268882377 -0.189461078 AGAAAGDS(ph)DEESRADDKGVMDYYLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGAAAGDSDEESRADDKGVMDYYLK 25 2 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 AGAAAGDS(1)DEESRADDKGVMDYYLK;AGAAAGDS(0.96)DEES(0.04)RADDKGVMDYYLK 232.38 2.63E-35 748400000 836510 562380 569270 609980 666800 598630 855180 1004840 370880 TRUE FALSE 725963.0841 558685.6888 844570.8761 748485.282 653531.9846 621659.6835 772244.7752 789962.7857 327034.9889 2.219833072 1.708336134 2.582509226 2.288700926 1.998354937 1.900896554 2.361352153 2.415529874 1 18.31908547 3.222404459 23.87743343 2.025507456 2.192070259 0.062153563 0.438354175 626.839343 926411.0635 0.132982657 0.151324112 1668.800645 -3.222404459 0.166562803 AGAAS(ph)MIHYMVLISAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGAASMIHYMVLISAR 16 0 C9IYN1;Q9NV64 C9IYN1 TMEM39A Transmembrane protein 39A 1 AGAAS(0.999)MIHY(0.001)MVLISAR 57.804 0.041836 148800000 491970 240780 505830 297670 115270 114560 262630 277710 190640 TRUE FALSE 426954.918 239198.3003 750451.0799 365260.5231 112976.3525 118967.1973 237160.183 218323.8776 168102.7564 2.539844838 1.422929079 4.464240183 2.172840773 0.672067222 0.707705215 1.410804844 1.298752515 1 17.35898386 3.406871283 5.54292143 1.078919953 2.770846207 0.541626254 0.76216965 0.156591295 8.776039218 0.218215879 0.284642802 2551.944841 -3.406871283 1.691926253 AGAEDDEEKGEGT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGAEDDEEKGEGTPR 15 1 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 AGAEDDEEKGEGT(1)PR 143.57 7.10E-06 132470000 553280 309510 315420 373820 284450 297270 364600 384090 927660 TRUE FALSE 480162.6462 307476.8084 467958.167 458701.5445 278790.0015 308706.1693 329241.1481 301955.3425 817993.0916 0.587000857 0.375891693 0.57208083 0.56076457 0.340821951 0.377394592 0.40249869 0.369141678 1 19.64172913 1.234004285 24.99997844 1.000000835 0.441912445 0.776725085 0.092921688 65.91136255 361601.0028 0.180357922 0.023171758 17.13974219 -1.234004285 -0.55808839 AGAES(ph)PTMSVDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AGAESPTMSVDGR 13 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 AGAES(0.912)PT(0.088)MSVDGR;AGAES(0.988)PT(0.012)MSVDGR;AGAES(0.855)PT(0.145)MSVDGR;AGAES(0.972)PT(0.028)MSVDGR;AGAES(0.507)PT(0.493)MSVDGR 343.38 2.62E-63 6615270000 3737820 3286850 2249690 3119020 3441600 3235770 3200810 3538770 4429600 TRUE FALSE 3243857.617 3265258.466 3337647.609 3827241.162 3373118.893 3360252.166 2890395.939 2782031.574 3905937.734 0.83049394 0.835972995 0.854506097 0.979852067 0.863587472 0.860293326 0.740000516 0.712257021 1 21.89723752 2.385613297 7.485481838 0.7925201 0.874392141 0.055379365 0.086471949 0.429404124 30.31913245 0.0325399 0.025128729 243.0039298 -2.385613297 0.081872041 AGAGMITQHSSNAS(ph)PINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 AGAGMITQHSSNASPINR 18 0 Q9NWH9;Q9NWH9-3;H7C3F4;H0YKH2 Q9NWH9 SLTM SAFB-like transcription modulator 1 AGAGMITQHSSNAS(1)PINR;AGAGMITQHSSNAS(1)PINR;AGAGMITQHSSNAS(1)PINR;AGAGMITQHSS(0.001)NAS(0.999)PINR;AGAGMITQHSSNAS(1)PINR;AGAGMITQHSS(0.019)NAS(0.981)PINR;AGAGMITQHSS(0.001)NAS(0.999)PINR;AGAGMITQHSSNAS(1)PINR;AGAGMITQHSSNAS(1)PINR 276.79 2.64E-39 3550690000 2228346 2295938 785378 1207685 2592635 3048422 2195801 2252586 1553951 TRUE FALSE 1933864.43 2280855.832 1165189.428 1481908.338 2541046.636 3165696.767 1982852.557 1770888.014 1370244.683 1.411327812 1.66456098 0.850351359 1.081491763 1.854447361 2.310314943 1.447079183 1.292388166 1 20.38600211 3.251321404 24.99836776 1.571229692 1.25272203 0.143518562 0.398875918 539.7610584 1057385.349 0.126588607 0.162326061 1783.698325 -3.251321404 -0.318507662 AGAHLQGGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 AGAHLQGGAK 10 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;; 157.58 2.08E-05 1.63335E+11 184435624.1 186590041.2 127688585.1 147919526.1 133261672.3 145879199.1 198337637 218288424.2 218518866 FALSE TRUE 160061989.1 185364318.9 189439211.9 181506915.3 130610025.7 151491266.3 179102883.5 171609143.4 192685814.6 0.830689013 0.962002934 0.983150796 0.941983797 0.677839342 0.786208713 0.929507363 0.890616384 1 27.52167512 7.807395812 19.53678009 0.888273009 0.049907779 0 0.099736762 0 0 0.023364897 0 64179423.59 -7.807395812 -0.83836523 AGAHLQGGAKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGAHLQGGAKR 11 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 99.815 0.0029171 1727430000 5730600 4495000 2229300 3208600 4121800 4145000 6259700 6818300 2522700 FALSE TRUE 4973286.691 4465472.049 3307396.937 3937161.67 4039784.244 4304460.832 5652635.257 5360259.605 2224469.28 2.235718306 2.007432555 1.48682518 1.769933038 1.816066547 1.935050698 2.54111635 2.409680212 1 21.08502974 2.464330806 24.89606564 2.115951074 1.848161669 0 0.450391232 649.3792832 1263978.896 0.168355853 0.130488277 291.2935079 -2.464330806 -0.267789405 AGAPGALS(ph)PSYDGGLHGLQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AGAPGALSPSYDGGLHGLQSK 21 0 K7ENH8;A0A0A0MRB7;P15923-2;X6REB3;P15923;P15923-3 K7ENH8 TCF3 Transcription factor E2-alpha 1 AGAPGALS(0.991)PS(0.009)YDGGLHGLQSK;AGAPGALS(0.95)PS(0.05)YDGGLHGLQSK;AGAPGALS(0.861)PS(0.139)YDGGLHGLQSK 372.26 1.21E-112 2094150000 2191790 1770441 1098844 1628438 1782604 1438620 1878370 2408400 2187270 TRUE FALSE 1902139.398 1758810.856 1630248.634 1998199.737 1747133.668 1493964.642 1696205.967 1893382.402 1928693.432 0.986232113 0.911918311 0.845260634 1.036038026 0.905863855 0.774599331 0.879458569 0.981691735 1 20.87919241 1.638899244 5.218565162 0.994986148 0.903728927 0.200889548 0.070832062 0.230852544 13.48293401 0.048959658 0.018890691 43.54108474 -1.638899244 -0.091257221 AGAPVGGS(ph)PGLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AGAPVGGSPGLAK 13 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 AGAPVGGS(1)PGLAK;AGAPVGGS(1)PGLAK;AGAPVGGS(1)PGLAK;AGAPVGGS(1)PGLAK 183.96 1.04E-05 393667000 1102420 876120 570980 707460 837370 692560 890460 1053520 1035650 TRUE FALSE 956732.4038 870364.71 847107.8378 868099.6058 820707.9753 719203.2313 804103.3263 828232.9465 913216.6368 1.047651089 0.953075836 0.927608854 0.950595479 0.898700201 0.787549419 0.880517605 0.906940274 1 19.80059762 5.430867859 0.804125942 0.895702436 1.377270733 0.423230462 0.053054815 6.897189743 1.5539351 0.020154066 3.843336918 269691.8729 -5.430867859 0.481568297 AGCECLNESDEHGFDNCLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AGCECLNESDEHGFDNCLR 19 0 O43396;K7ER96;K7EML9 O43396 TXNL1 Thioredoxin-like protein 1 0 ;; 241.8 2.23E-24 1221570000 619890 442770 262263 326573 424887 420089 428682 464050 532020 FALSE TRUE 537969.9659 439861.4147 389094.264 400726.391 416432.58 436250.0957 387108.4856 364816.5187 469125.2017 1.146751366 0.937620518 0.829403883 0.854199241 0.887678979 0.929922533 0.825170944 0.777652783 1 18.83961348 4.693708228 2.741306926 0.86330721 1.185835632 0.659347501 0.061562607 0.230184688 2.504053606 0.015709295 0.159594487 49397.87054 -4.693708228 0.322528423 AGDEKPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGDEKPEK 8 1 Q8WW12;Q8WW12-2;G5E9V9;A0A0B4J1Z9 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 0 ; 78.934 0.026759 492790000 712240 505000 397700 493020 309750 342950 671240 792140 713020 FALSE TRUE 618115.6794 501682.6217 590029.0502 604967.7263 303586.581 356143.5084 606143.2481 622747.0254 628727.5879 0.983121612 0.797933209 0.938449436 0.962209609 0.482858692 0.566451219 0.964079293 0.990487832 1 19.26207554 2.033757407 24.97948704 0.989380453 0.787710436 0.249664495 0.161061226 263.4690611 194958.2643 0.070824088 0.047749342 108.0830041 -2.033757407 -0.201670017 AGDKDDITEPAVCALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AGDKDDITEPAVCALR 16 1 P14923 P14923 JUP Junction plakoglobin 0 ;;; 112.3 0.00068378 1803890000 1222710 830060 707560 1152600 1001210 803700 856060 1491280 1234040 FALSE TRUE 1061125.776 824607.2812 1049738.383 1414315.446 981287.8798 834618.8591 773039.433 1172381.377 1088153.197 0.975162117 0.757804401 0.964697237 1.299739274 0.901792029 0.767004923 0.710414154 1.077404708 1 20.05345025 4.613817051 0.003446395 1.454359077 0.417083807 0 0.173539212 4363064.866 4563.187719 677977.7111 695502.1806 41097.65587 -4.613817051 -1.03727527 AGDLLEDS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 AGDLLEDSPK 10 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 AGDLLEDS(1)PK;AGDLLEDS(1)PK;AGDLLEDS(1)PK;AGDLLEDS(1)PK;AGDLLEDS(1)PK;AGDLLEDS(1)PK;AGDLLEDS(1)PK;AGDLLEDS(1)PK;AGDLLEDS(1)PK;AGDLLEDS(1)PK 202.18 2.40E-07 97290880000 66827120 51105840 49708550 53742000 57960880 44215840 67385760 76037990 118017600 TRUE FALSE 57995746.77 50770122.37 73747771.05 65944942.5 56807571.89 45916851.98 60850699.37 59777857.57 104065693.8 0.557299381 0.487866083 0.70866554 0.633685705 0.545881835 0.44122948 0.584733519 0.574424245 1 26.63291931 1.237760848 6.826232075 1.01034341 0.566700869 0.778653228 0.072611098 0.055414159 13.77444878 0.113564755 0.018595749 17.28864065 -1.237760848 -0.443642542 AGDLLEDS(ph)PKRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 AGDLLEDSPKRPK 13 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK 195.38 1.12E-07 1.0513E+11 45467990 32428310 24449260 20551360 28851110 20215850 47771270 50684240 11260004 TRUE FALSE 39459279.92 32215286.3 36273003.91 25217860.4 28277029.36 20993566.83 43138419.59 39845809.7 9928859.155 3.974200792 3.244611067 3.653290207 2.539854781 2.847963589 2.114398694 4.344750884 4.013130721 1 23.24319653 3.768797415 23.89838884 3.003858743 3.586091982 0.118686391 0.950705424 1218.902987 963383.4183 0.260455952 0.451023552 5872.153711 -3.768797415 0.582233239 AGDNSQSVYIPMS(ph)PGAHHFDSLGYPSTTLPVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGDNSQSVYIPMSPGAHHFDSLGYPSTTLPVHR 33 0 Q9UQC2;Q9UQC2-2 Q9UQC2 GAB2 GRB2-associated-binding protein 2 1 AGDNSQSVYIPMS(0.506)PGAHHFDS(0.246)LGY(0.223)PS(0.009)T(0.009)T(0.007)LPVHR 83.022 0.00023146 176920000 9982.9 10341 5235 9105.5 12959 17384 16032 18476 15254 TRUE FALSE 8663.634472 10273.06929 7766.66351 11173.04294 12701.14125 18052.77373 14477.21911 14525.05118 13450.6895 0.644103373 0.76375782 0.577417501 0.830666929 0.944274363 1.342144857 1.076317992 1.079874097 1 13.71539251 3.24206492 2.396448424 1.113276781 0.677133528 0.782874212 0.105460818 0.126576112 1.490920005 0.033292733 0.042414612 1746.083145 -3.24206492 -0.436143252 AGDPGEMPQS(ph)PTGLGQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGDPGEMPQSPTGLGQPK 18 0 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9;A0A0C4DGI9;H0YHL2 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 AGDPGEMPQS(0.992)PT(0.008)GLGQPK 177.64 9.74E-14 290060000 342280 294530 214900 273540 295830 237050 357570 417910 372470 TRUE FALSE 297046.8308 292595.213 318826.3588 335651.4378 289943.5618 246169.4669 322892.9164 328543.1987 328437.0209 0.904425542 0.890871596 0.970738189 1.021965906 0.882798051 0.749518024 0.983119733 1.000323282 1 18.32525723 2.028847778 24.99977577 0.99764601 0.906665141 0.280209279 0.069066504 284.2148701 246302.3031 0.030141189 0.020320868 106.8680236 -2.028847778 -0.090980868 AGDRNS(ph)EDDGVVMTFSSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGDRNSEDDGVVMTFSSVK 19 1 Q9NY61 Q9NY61 AATF Protein AATF 1 AGDRNS(1)EDDGVVMTFSSVK;AGDRNS(1)EDDGVVMTFSSVK 226.7 8.73E-20 499290000 1248650 745720 648280 1066890 813040 660320 795710 1211510 1806160 TRUE FALSE 1083637.739 740821.3162 961790.3764 1309143.681 796862.0947 685722.9377 718542.1667 952438.0145 1592637.822 0.680404373 0.465153663 0.603897737 0.821997106 0.500341059 0.430557989 0.451164826 0.59802549 1 20.60298679 1.243385764 5.081439276 1.025134185 0.561769672 0.568078689 0.118417509 0.125124752 8.474190099 0.203350414 0.030637097 17.51401686 -1.243385764 -0.463364513 AGDSAVLVLPPS(ph)PGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AGDSAVLVLPPSPGPR 16 0 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;Q96JY6-4;C9JS55;C9JSR2 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR 254.59 1.45E-26 2990020000 1258820 1472240 1051370 1245300 1572360 1717630 1551620 1739280 1692920 TRUE FALSE 1092463.748 1462568.759 1559816.049 1528064.398 1541073.112 1783708.338 1401144.131 1367348.507 1492784.926 0.7318293 0.979758526 1.044903403 1.023633325 1.032347718 1.194886354 0.938610852 0.91597154 1 20.50957489 4.73306037 3.702000091 1.014331545 0.703028685 0.595513079 0.074241179 0.206666123 5.35947031 0.020235798 0.175756014 54082.94972 -4.73306037 -0.311302861 AGDTETLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGDTETLK 8 0 C9JNG9;P12111 C9JNG9 COL6A3 Collagen alpha-3(VI) chain 0 75.311 0.090077 829190000 545270 517820 438550 394920 405070 386140 756950 588770 579840 FALSE TRUE 473211.188 514418.4063 650634.2469 484592.622 397009.8995 400995.0557 683541.1055 462866.1173 511291.9758 0.925520467 1.006114766 1.272529744 0.947780613 0.776483728 0.784278015 1.336889953 0.905287271 1 18.96378786 4.739625236 18.69292773 1.004303699 0.925519779 0.018006241 0.181320155 17.35150531 302783.109 0.044471002 0.260153734 54906.68647 -4.739625236 -0.07878392 RLEELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLEELER 7 1 O95819-3;O95819-6;E7EN19;O95819;H7C360;O95819-2;A0A0D9SEY1;H7C0P6;A0A0D9SG62;G5E948;E7ENQ1;G3XAA2;C9J840;E7EX83;O95819-4;O95819-5;H7C3Z6;Q9NRD5;Q9NRD5-2;F6V107 O95819-3 MAP4K4;PICK1 Mitogen-activated protein kinase kinase kinase kinase 4;PRKCA-binding protein 0 99.136 0.017237 131250000 232520 218330 132080 137600 202770 212350 191470 223060 91147 FALSE TRUE 201791.8929 216895.7759 195954.3298 168844.1831 198735.2737 220519.2419 172901.2689 175360.3549 80371.7055 2.510732995 2.698658371 2.438100928 2.100791342 2.47270196 2.743742223 2.151270373 2.181866787 1 16.29440008 1.083012723 1.697369653 1.29E-18 2.462251953 0.836418386 0.199827144 0.599687539 1.141779199 2.77413427 0.056651344 12.10633599 -1.083012723 2.462251953 AGDWQCPNPGCGNQNFAWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AGDWQCPNPGCGNQNFAWR 19 0 B0QYK0;Q01844-6;Q01844-3;Q01844;Q01844-5;A0A0D9SFL3;C9JGE3;Q01844-2 B0QYK0 EWSR1 RNA-binding protein EWS 0 ;;; 312.91 3.25E-61 1217240000 773732 633936 464476 536440 616223 684619 616496 660546 734228 FALSE TRUE 671481.3558 629771.6327 689098.1472 658246.901 603961.3679 710956.7359 556708.3128 519293.3783 647428.4023 1.037151527 0.972727842 1.064361935 1.016709954 0.932862021 1.098124107 0.859876259 0.802086187 1 19.30436113 2.21954484 24.99107684 0.868420007 1.01602154 0.46026402 0.066750704 182.8184753 240263.4486 0.026072739 0.017609146 165.7848498 -2.21954484 0.147601533 AGEAGKLEEVMQELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AGEAGKLEEVMQELR 15 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;; 176.04 7.49E-07 1661290000 2908710 2306710 1447610 1590910 2128130 1673920 2721160 3201490 1051370 FALSE TRUE 2524316.604 2291557.07 2147679.038 1952150.431 2085784.377 1738316.786 2457262.322 2516876.278 927078.2363 2.722873329 2.471805486 2.31661035 2.10570193 2.249847203 1.875048639 2.650544718 2.714847765 1 19.82233157 4.478726524 1.603130213 2.194775584 2.781647768 0.14822212 0.474145098 1.459125316 5.241346796 0.132512577 1.151628428 30111.09326 -4.478726524 0.586872184 AGEKYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGEKYK 6 1 A0A087WU64;A6NMQ1;P09884;A0A5F9ZHW2 A0A087WU64;A0A5F9ZHW2 POLA1 DNA polymerase;DNA polymerase alpha catalytic subunit 0 66.994 0.09115 483320000 743420 618870 462850 574090 425630 478440 779640 843050 810910 FALSE TRUE 645175.1634 614804.6022 686685.8081 704445.9089 417160.7957 496845.8964 704030.6328 662770.3181 715045.1436 0.902285917 0.85981229 0.960339098 0.985176831 0.583404837 0.694845495 0.984596062 0.926892972 1 19.4476748 2.185633654 24.9997034 0.962000108 0.833922949 0.229922173 0.119949809 171.310478 80915.89679 0.053139327 0.035826562 153.3323012 -2.185633654 -0.128077158 AGELTEDEVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AGELTEDEVER 11 0 P62269 P62269 RPS18 40S ribosomal protein S18 0 ;;;; 271.26 1.14E-26 5058650000 3073370 2849070 1990370 2338680 2877500 2690580 2859180 3256550 3195180 FALSE TRUE 2667216.368 2830354.272 2952919.589 2869713.038 2820243.38 2794088.354 2581897.164 2560162.125 2817449.46 0.946677626 1.004580317 1.048082541 1.018549961 1.000991648 0.99170842 0.916395201 0.908680763 1 21.4259583 2.345862992 4.988493027 0.93401807 1.006062043 0.395460038 0.034692896 0.182012553 7.257345378 0.013534502 0.010293898 221.7496751 -2.345862992 0.072043973 AGEPDGES(ph)LDEQPSSSSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGEPDGESLDEQPSSSSSK 19 0 Q9H3Q1;J3KRZ9 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 AGEPDGES(1)LDEQPSSSSSK;AGEPDGES(1)LDEQPSSSSSK 436.45 6.87E-170 1117940000 1229100 1002160 964270 1024890 915940 898980 1273950 1339560 1883860 TRUE FALSE 1066671.321 995576.745 1430594.197 1257606.939 897714.586 933564.3423 1150402.525 1053105.518 1661152.217 0.64212738 0.599329029 0.861205965 0.757069055 0.540416812 0.561998071 0.692532878 0.633960878 1 20.66375285 1.235699902 24.99162451 1.000000457 0.661739978 0.56209613 0.09401049 64.00046174 559010.366 0.162845 0.024043148 17.20679174 -1.235699902 -0.338260479 AGEPNS(ph)PDAEEANS(ph)PDVTAGCDPAGVHPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 AGEPNSPDAEEANSPDVTAGCDPAGVHPPR 30 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 2 AGEPNS(1)PDAEEANS(1)PDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANS(1)PDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANS(1)PDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANS(1)PDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANS(1)PDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANS(1)PDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANS(1)PDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANS(1)PDVTAGCDPAGVHPPR 259.23 1.61E-58 6957050000 1555016 1275073 849970 898047 1107370 1086276 1207901 1328558 1280759 TRUE FALSE 1349516.696 1266696.962 1261018.335 1101962.297 1085335.504 1128065.741 1090758.947 1044456.211 1129349.13 1.194950844 1.121616804 1.116588574 0.975749897 0.96102744 0.998863603 0.965829714 0.924830225 1 20.10706012 3.85711964 1.893525424 0.963284374 1.165449405 0.898217776 0.027697755 0.099635073 0.692436362 0.008228481 0.01902075 7196.471997 -3.85711964 0.202165031 AGEPNS(ph)PDAEEANSPDVTAGCDPAGVHPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AGEPNSPDAEEANSPDVTAGCDPAGVHPPR 30 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 AGEPNS(1)PDAEEANSPDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANSPDVTAGCDPAGVHPPR;AGEPNS(0.999)PDAEEANS(0.001)PDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANSPDVTAGCDPAGVHPPR 237.05 1.16E-45 5000730000 957324 711600 409366 473181 595246 567147 595038 764303 665475 TRUE FALSE 830811.2079 706925.4527 607336.7668 580623.9782 583401.7692 588965.5121 537331.3063 600862.7513 586803.3036 1.415825717 1.204705986 1.034992072 0.989469511 0.99420328 1.003684724 0.915692368 1.023959387 1 19.16251747 4.580958978 1.513535044 0.986158215 1.510948746 0.96153984 0.02820622 0.138758308 0.376294161 0.007852389 0.099820127 38102.98309 -4.580958978 0.524790531 AGEPNSPDAEEANS(ph)PDVTAGCDPAGVHPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGEPNSPDAEEANSPDVTAGCDPAGVHPPR 30 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 AGEPNSPDAEEANS(1)PDVTAGCDPAGVHPPR 199.93 1.49E-25 924810000 137270 107540 71076 85346 110120 103630 103290 125440 111760 TRUE FALSE 119129.4217 106833.5627 105448.5913 104725.1137 107928.8274 107616.7132 93272.9517 98615.63218 98547.86012 1.208848387 1.084077955 1.070024161 1.062682778 1.095191994 1.09202486 0.946473638 1.000687707 1 16.58853692 8 0.165600421 0.924391738 1.899307221 0.653201149 0.041673182 87.3914605 1.172766231 0.526075642 20.36962698 100000000 -8 0.974915483 AGERPELCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGERPELCR 9 1 P19174-2;P19174 P19174-2 PLCG1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1" 0 65.627 0.060216 150050000 125120 138640 82346 120450 116790 138320 95609 117840 218560 FALSE TRUE 108585.075 137729.2647 122168.801 147800.0135 114466.1075 143641.2599 86336.8539 92640.83303 192722.0858 0.563428289 0.714652211 0.633911783 0.766907502 0.593943901 0.745328483 0.447986299 0.480696505 1 17.55616239 AGETRFT(ph)DTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGETRFTDTR 10 1 P13639 P13639 EEF2 Elongation factor 2 1 AGET(0.001)RFT(0.999)DTR;AGET(0.001)RFT(0.979)DT(0.02)R 85.554 0.018118 348120000 2141870 1906780 547590 532500 1255390 975440 1589590 1662420 497400 TRUE FALSE 1858816.453 1894254.237 812406.3556 653412.2638 1230410.195 1012965.808 1435431.806 1306924.42 438597.9386 4.238087526 4.318885407 1.852280378 1.489775045 2.805325987 2.30955442 3.272773718 2.979777844 1 18.74253951 4.247219123 24.96627718 2.360418661 4.278487635 0.596712784 0.69014948 135.5137975 390736.9697 0.179452746 0.459161366 17669.29099 -4.247219123 1.918068974 AGEVFIHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AGEVFIHK 8 0 Q15233;Q15233-2;H7C367;C9JYS8;C9IZL7 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;; 111.04 0.0033105 6085440000 11673400 9088700 6759500 8070200 8866200 7584800 10065600 11910300 11127200 FALSE TRUE 10130730.61 9028995.731 10028416.81 9902662.255 8689779.966 7876592.164 9089439.661 9363375.031 9811755.092 1.032509527 0.920222289 1.022081851 1.009265128 0.885649905 0.802770971 0.926382648 0.954301748 1 23.22607979 3.243854514 24.99876221 0.914270754 0.99246719 0.330348852 0.058053574 178.1506549 841255.6636 0.018099095 0.02267267 1753.293059 -3.243854514 0.078196435 AGFAGDDAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 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 ;;;;;;;;;; 215.42 1.91E-08 69241270000 174945295 168466021 105942023 126291685 158508013 166872193 151080951 178031704 159063853 FALSE TRUE 151825831 167359356.6 157175939.7 154968142.3 155354013.7 173291874.2 136429143.6 139961009.5 140259505.5 1.082463755 1.193212225 1.120608112 1.104867308 1.107618433 1.235508949 0.972690893 0.997871831 1 27.06352331 2.218170257 24.99999424 0.991059369 1.139051936 0.711131173 0.045215677 122.3347045 149989.6907 0.017569303 0.011860327 165.2609546 -2.218170257 0.147992567 AGFDSDYDQALADIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGFDSDYDQALADIR 15 0 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;P52701-4 P52701 MSH6 DNA mismatch repair protein Msh6 0 176.91 1.80E-06 35073000 94797 76862 55763 69378 82631 79041 74081 96349 99320 FALSE TRUE 82269.33627 76357.08846 82730.17332 85131.33528 80986.80476 82081.75842 66896.63602 75745.51614 87578.50275 0.9393782 0.87187022 0.944640188 0.972057441 0.924733836 0.937236375 0.763847679 0.864887087 1 16.41828917 AGFNYES(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGFNYESPSK 10 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97;H0YC29;E7EVN4;F8W8T0 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 AGFNYES(0.856)PS(0.144)K;AGFNYES(0.996)PS(0.004)K 189.56 1.05E-06 1661080000 1656410 1525160 1277320 1602080 1644350 1155820 1625150 2035200 3165400 TRUE FALSE 1437511.222 1515141.124 1895036.224 1965856.75 1611630.652 1200285.143 1467543.203 1599988.318 2791190.018 0.515017327 0.542829802 0.678934867 0.704307746 0.577399117 0.43002631 0.525776889 0.573228017 1 21.41244891 1.238792958 9.112782941 1.002868657 0.569323481 0.749773643 0.07835299 0.044172595 53.29121718 0.119086341 0.021062583 17.32977633 -1.238792958 -0.433545176 AGFNYES(ph)PSKGGNFPSFPHDEVTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AGFNYESPSKGGNFPSFPHDEVTDR 25 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 AGFNYES(0.947)PS(0.053)KGGNFPSFPHDEVTDR;AGFNYES(0.975)PS(0.025)KGGNFPSFPHDEVTDR;AGFNYES(0.975)PS(0.025)KGGNFPSFPHDEVTDR;AGFNYES(0.928)PS(0.072)KGGNFPSFPHDEVTDR 165.49 9.22E-12 1546350000 1660490 1573490 852991 1052719 1525130 1238790 1644390 2059940 722137 TRUE FALSE 1441052.039 1563153.641 1265500.301 1291754.939 1494782.897 1286447.053 1484917.311 1619437.861 636766.7865 2.263076639 2.454829105 1.987384279 2.028615446 2.347457387 2.020279764 2.331964139 2.54321974 1 19.28040556 1.230345818 24.99181765 0.999997683 2.252556924 0.814287 0.187154324 136.1078974 414046.6987 0.532714928 0.048446843 16.99596461 -1.230345818 1.252559241 AGFQTEDFSLYACAS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGFQTEDFSLYACASPK 17 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0 P15056 BRAF Serine/threonine-protein kinase B-raf 1 AGFQTEDFSLYACAS(1)PK 141.31 1.07E-05 0 48154 43995 32641 35304 49101 44663 54100 66683 54815 TRUE FALSE 41790.32689 43705.99395 48426.29678 43320.31279 48123.98616 46381.21451 48853.39033 52423.35938 48334.83315 0.864600624 0.904233885 1.001892292 0.896254522 0.995637784 0.959581558 1.010728436 1.084587573 1 15.56077564 7.99999994 0.107026344 1.195399323 0.226560821 0.592857811 0.041639575 171.2347103 1.672179223 2.212488877 24.74613955 99999986.12 -7.99999994 -0.968838502 AGGAS(ph)PAASSTAQPPTQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 188.24 1.07E-14 8973590000 1222666 929636 582207 711436 967852 1014972 967308 1005285 982036 TRUE FALSE 1061087.59 923529.1599 863764.2526 872978.4174 948593.6388 1054018.63 873498.619 790312.6259 865940.8228 1.225358087 1.066503779 0.997486468 1.008127108 1.095448573 1.217194757 1.008727844 0.912663551 1 19.72390891 2.007222679 24.92089251 0.953274112 1.092660214 0.387278822 0.077349083 167.3482458 577410.4632 0.032773716 0.022042038 101.6769894 -2.007222679 0.139386102 AGGGGGLGAGS(ph)PALSGGQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AGGGGGLGAGSPALSGGQGR 20 0 A0A3B3ITT1;Q6IQ22 A0A3B3ITT1 RAB12 Ras-related protein Rab-12 1 AGGGGGLGAGS(1)PALSGGQGR;AGGGGGLGAGS(0.985)PALS(0.015)GGQGR;AGGGGGLGAGS(0.963)PALS(0.037)GGQGR;AGGGGGLGAGS(1)PALSGGQGR;AGGGGGLGAGS(1)PALSGGQGR;AGGGGGLGAGS(1)PALSGGQGR 350.76 4.40E-95 6544560000 3624070 3333400 2740380 2834660 3584560 4157690 3016800 3702720 3896420 TRUE FALSE 3145139.967 3311502.676 4065636.934 3478312.878 3513234.269 4317639.025 2724231.2 2910922.143 3435789.666 0.91540527 0.963825786 1.183319507 1.012376547 1.022540554 1.2566657 0.79289813 0.847235257 1 21.71221029 2.211014398 24.99947953 0.869578098 1.056566634 0.364351846 0.111122016 222.8265088 202223.8803 0.045015436 0.030356851 162.560265 -2.211014398 0.186988536 AGGIETIANEFSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AGGIETIANEFSDR 14 0 Q92598-2;Q92598;Q92598-3;R4GN69 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;; 261.72 3.73E-24 650074000 408803 375529 274787 323077 369872 393792 383105 438607 434179 FALSE TRUE 354778.6478 373062.1253 407674.9123 396436.5708 362512.2708 408941.4331 345951.5361 344814.3063 382850.8532 0.926675871 0.974432007 1.064840025 1.035485666 0.946875964 1.068148156 0.903619603 0.900649178 1 18.54642295 2.217115592 24.97482964 0.926353241 1.003227598 0.261402546 0.053247422 283.1612077 329766.3701 0.021603144 0.014580271 164.8601125 -2.217115592 0.076874357 AGGIETIANEYSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AGGIETIANEYSDR 14 0 P34932;A0A087WYC1;A0A087WTS8;P34932-2 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;; 253.76 7.19E-24 1229950000 703540 648030 429700 521510 673870 676520 749070 782720 732140 FALSE TRUE 610565.4065 643773.0483 637504.3573 639926.8163 660461.3054 702546.1622 676425.3067 615341.4191 645587.2433 0.945751969 0.997189853 0.987479793 0.991232127 1.023039585 1.088228074 1.047767461 0.953149904 1 19.30025255 3.388360575 3.636165331 1.018851055 0.979963849 0.250576707 0.036327949 0.446026327 11.52289201 0.012356702 0.016498063 2445.460066 -3.388360575 -0.038887206 AGGLDWPEATEVS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 AGGLDWPEATEVSPSR 16 0 Q9Y446;Q9Y446-2;E9PK71;E9PKC4;E9PRW6;E9PJR7 Q9Y446 PKP3 Plakophilin-3 1 AGGLDWPEATEVS(1)PSR;AGGLDWPEATEVS(0.999)PS(0.001)R;AGGLDWPEATEVS(0.997)PS(0.003)R;AGGLDWPEATEVS(0.999)PS(0.001)R;AGGLDWPEATEVS(0.996)PS(0.004)R;AGGLDWPEATEVS(0.996)PS(0.004)R;AGGLDWPEATEVS(0.981)PS(0.019)R;AGGLDWPEAT(0.004)EVS(0.976)PS(0.02)R 295.93 1.17E-45 9027220000 8167650 7590700 5156697 6028818 7256880 7782810 7133560 8180160 8151570 TRUE FALSE 7088274.358 7540836.192 7650492.917 7397753.272 7112482.286 8082219.737 6441748.449 6430896.442 7187900.681 0.986139719 1.049101334 1.064357071 1.029195255 0.989507591 1.124420063 0.896193302 0.894683542 1 22.77713904 2.218988906 24.99997206 0.921452969 1.039105666 0.534739609 0.048194036 166.2566074 212366.6816 0.018872288 0.012744644 165.5727666 -2.218988906 0.117652697 AGGPAT(ph)PLS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGGPATPLSPTR 12 0 Q03252 Q03252 LMNB2 Lamin-B2 2 AGGPAT(1)PLS(0.952)PT(0.048)R;AGGPAT(1)PLS(0.895)PT(0.105)R 139.77 0.00031359 767660000 1090120 1005670 652110 780850 983350 1118770 879530 1201660 1121990 TRUE FALSE 946057.88 999063.6876 967472.5772 958153.927 963783.2589 1161809.806 794233.316 944694.3603 989349.6204 0.956242223 1.009818639 0.97788745 0.968468484 0.974158416 1.174316725 0.802783262 0.954864025 1 19.91612091 2.214374844 24.99999955 0.921791262 1.005136931 0.227882832 0.078496004 368.4617103 380863.2995 0.031151657 0.021014246 163.8229883 -2.214374844 0.083345669 AGGPAT(ph)PLSPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AGGPATPLSPTR 12 0 Q03252 Q03252 LMNB2 Lamin-B2 1 AGGPAT(0.998)PLS(0.002)PTR;AGGPAT(0.5)PLS(0.5)PT(0.001)R;AGGPAT(0.999)PLS(0.001)PTR 137.31 0.00057207 831940000 470135 476370 279949 424539 571136 559310 439393 532050 488078 TRUE FALSE 408005.4686 473240.6941 415333.2728 520937.0686 559771.511 580827.0176 396780.7345 418275.2479 430377.9749 0.94801661 1.099593199 0.965043048 1.210417584 1.300650925 1.349574215 0.921935502 0.971878842 1 18.71524472 2.188340526 24.99984927 0.96434202 1.145255504 0.308562437 0.12768522 142.7840079 71077.56378 0.056423236 0.03804057 154.2909759 -2.188340526 0.180913483 AGGPATPLS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AGGPATPLSPTR 12 0 Q03252 Q03252 LMNB2 Lamin-B2 1 AGGPATPLS(0.972)PT(0.028)R;AGGPATPLS(1)PTR;AGGPAT(0.001)PLS(0.986)PT(0.013)R 287.28 1.07E-28 1141350000 1350710 1327280 832250 1116020 1293590 1318880 1177800 1544520 1330740 TRUE FALSE 1172210.251 1318561.01 1234728.884 1369429.398 1267850.09 1369618.167 1063577.137 1214236.417 1173421.433 0.99896782 1.123689216 1.052246745 1.167039701 1.080472926 1.167200571 0.906389731 1.034782886 1 20.16228982 2.243188088 24.99999997 0.988639162 1.099649973 0.467118005 0.059120764 99.02268504 534975.2234 0.021096789 0.015789212 175.0604693 -2.243188088 0.111010811 AGGPTT(ph)PLS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGGPTTPLSPTR 12 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 2 AGGPT(0.109)T(0.891)PLS(0.991)PT(0.009)R 92.636 0.040445 564040000 1524100 1644700 915510 1063500 1387300 1615600 1406100 1690300 1613000 TRUE FALSE 1322686.323 1633895.857 1358253.698 1304983.93 1359695.444 1677753.177 1269736.638 1328842.499 1422312.978 0.929954479 1.14875972 0.954961193 0.917508277 0.955974856 1.17959493 0.892726607 0.934282763 1 20.43980753 AGGPTTPLS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AGGPTTPLSPTR 12 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 1 AGGPTT(0.036)PLS(0.964)PTR;AGGPTT(0.001)PLS(0.973)PT(0.026)R;AGGPTT(0.001)PLS(0.976)PT(0.023)R 221.54 2.83E-11 1693140000 1312930 1448980 776390 1041160 1303220 1155180 1106840 1556720 1220850 TRUE FALSE 1139422.974 1439461.555 1151854.801 1277571.291 1277288.472 1199620.522 999498.8272 1223827.542 1076522.504 1.058429313 1.337140236 1.069977448 1.186757626 1.18649491 1.114347836 0.928451401 1.136834147 1 20.03794705 2.471992802 24.89796841 1.038926194 1.170555842 0.344597819 0.090836348 150.717328 731702.2616 0.031154651 0.024216079 296.4782251 -2.471992802 0.131629647 AGGS(ph)PAS(ph)YHGSTSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGGSPASYHGSTSPR 15 0 I3L2B2;O95208-3;O95208-2;F6PQP6 I3L2B2 EPN2 Epsin-2 2 AGGS(1)PAS(0.999)Y(0.001)HGSTSPR;AGGS(1)PAS(0.923)Y(0.061)HGS(0.006)T(0.005)S(0.005)PR 156.17 3.18E-06 143610000 492680 382330 143350 242504 370970 395470 328891 373700 395460 TRUE FALSE 427571.0897 379818.4491 212674.5395 297568.2396 363588.4228 410683.9868 296995.2014 293787.1631 348709.1693 1.226153848 1.089212681 0.609890872 0.853342171 1.042669522 1.177726378 0.851698858 0.842499105 1 18.41166477 4.467415621 24.99236873 0.909670597 1.191918692 0.339646322 0.148992009 197.5120449 508601.7451 0.038937007 0.103282824 29336.99462 -4.467415621 0.282248094 AGGSAALS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AGGSAALSPSK 11 0 Q92522 Q92522 H1FX Histone H1x 1 AGGSAALS(0.989)PS(0.011)K;AGGSAALS(0.999)PS(0.001)K;AGGSAALS(0.999)PS(0.001)K;AGGSAALS(0.987)PS(0.013)K;AGGSAALS(0.991)PS(0.009)K;AGGSAALS(0.754)PS(0.246)K 301.74 7.18E-36 9988980000 12444000 12700720 9256660 9706750 11925440 8750540 14935710 15273520 13917500 TRUE FALSE 10799493.87 12617288.13 13733211.74 11910815.95 11688147.08 9087178.936 13487247.14 12007396.61 12272189 0.879997356 1.028120422 1.119051518 0.970553496 0.952409311 0.740469278 1.09900908 0.978423377 1 23.54888927 4.754863559 22.68637068 0.985661407 0.879997057 0.095906758 0.10228202 2272.249753 3161756.951 0.025170686 0.561127135 56867.42445 -4.754863559 -0.10566435 AGGSAALS(ph)PSKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGGSAALSPSKK 12 1 Q92522 Q92522 H1FX Histone H1x 1 AGGSAALS(0.999)PS(0.001)KK 143.97 3.84E-05 770440000 1834200 1605800 1273200 1267400 1472600 874450 1967300 2295900 1833600 TRUE FALSE 1591805.823 1595251.394 1888923.779 1555182.541 1443298.141 908090.6573 1776511.549 1804939.652 1616833.897 0.984520318 0.986651379 1.168285612 0.961869085 0.892669398 0.561647464 1.098759466 1.116342041 1 20.62474004 AGHCAVAINTR ddPTM_MDA-MB-175_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 ;; 115.18 0.0011584 614140000 354230 304420 198597 239050 298753 300497 315129 330750 312132 FALSE TRUE 307417.608 302420.245 294639.1735 293329.9562 292808.3998 312057.314 284567.8381 260021.6864 275232.1105 1.116939471 1.098782567 1.070511623 1.065754848 1.063859879 1.133796901 1.033919471 0.944736012 1 18.07028927 1.984922073 5.201222394 0.973005312 1.088542266 0.785364825 0.025795422 0.073686412 5.990689803 0.012184673 0.006979594 96.58775521 -1.984922073 0.115536954 AGHSENGVEEDTEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGHSENGVEEDTEGR 15 0 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 0 ; 159.4 1.77E-06 602720000 592020 538970 369600 391440 445840 502770 464510 574820 577060 FALSE TRUE 513783.057 535429.4706 548339.7962 480322.4348 436968.6563 522111.8872 419461.8917 451899.2163 508840.6242 1.009713125 1.052253781 1.077625823 0.943954574 0.858753479 1.026081375 0.824348277 0.88809579 1 18.95685433 3.61642486 4.775293523 0.912876602 1.046368937 0.469117798 0.061767641 0.18365611 6.35677947 0.016806247 0.025316532 4134.517743 -3.61642486 0.133492335 AGHYAASIIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGHYAASIIIR 11 0 P55263-3;P55263-2;P55263;P55263-4;A0A5F9ZHJ1 P55263-3 ADK Adenosine kinase 0 121.9 0.00040201 368750000 106620 99811 62608 88517 108770 107310 105650 103840 103990 FALSE TRUE 92529.89686 99155.33497 92885.43821 108616.1377 106605.6898 111438.2851 95404.07926 81634.62408 91696.42067 1.009089517 1.081343571 1.012966892 1.184518839 1.162593796 1.215295912 1.04043406 0.890270563 1 16.4845778 1.982367632 7.850098913 0.945138697 1.112338517 0.477924052 0.071383652 0.152675673 50.98580903 0.033830302 0.02013684 96.02131113 -1.982367632 0.16719982 AGIAHLYGIAGSTNVTGDQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGIAHLYGIAGSTNVTGDQVK 21 0 P09467 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 254.8 2.12E-36 555260000 364580 292640 244140 359240 309950 279340 371460 371150 684260 FALSE TRUE 316399.8293 290717.6286 362206.9206 440810.9326 303782.6014 290086.3906 335435.8664 291782.4608 603367.5623 0.524389856 0.481825088 0.600308905 0.730584407 0.50347851 0.480778896 0.555939509 0.483589903 1 19.20267761 1.233845406 25 1.000000688 0.544967335 0.780735859 0.075759756 70.7989113 375328.8546 0.153424748 0.019414775 17.13347306 -1.233845406 -0.455033352 AGIIQDTWHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGIIQDTWHK 10 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 137.17 9.83E-05 1137880000 1148860 1097940 663330 1101730 1271140 1139130 1003190 1386350 1169170 FALSE TRUE 997035.2402 1090727.56 984118.6067 1351894.635 1245846.801 1182953.068 905900.7882 1089889.841 1030952.055 0.967101463 1.057980878 0.954572623 1.31130699 1.208443007 1.14743752 0.878703121 1.05716831 1 19.97554581 2.264552872 24.99976583 0.990823784 1.112401426 0.220365934 0.113556365 365.8328084 351862.8407 0.044488162 0.034449064 183.8877811 -2.264552872 0.121577642 AGIPVYAWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGIPVYAWK 9 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 168.38 0.00013788 736370000 1526270 1607220 1065210 1285960 1505030 1455180 1724130 1929020 1866400 FALSE TRUE 1324569.552 1596662.066 1580349.119 1577956.873 1475082.848 1511161.716 1556924.138 1516514.085 1645756.318 0.804839415 0.970169185 0.960257057 0.958803472 0.896294811 0.918217174 0.946023491 0.921469399 1 20.65031931 AGKEPAKPS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AGKEPAKPSPSR 12 2 Q15311 Q15311 RALBP1 RalA-binding protein 1 1 AGKEPAKPS(0.855)PS(0.145)R;AGKEPAKPS(0.725)PS(0.275)R;AGKEPAKPS(0.912)PS(0.088)R;AGKEPAKPS(0.625)PS(0.375)R 97.797 0.0024625 1924420000 2146660 1677180 1332870 1428660 1554600 1192920 2147640 2441450 1715410 TRUE FALSE 1862973.442 1666162.494 1977450.39 1753059.089 1523666.502 1238812.404 1939362.203 1919364.917 1512616.184 1.23162337 1.101510424 1.307304795 1.158958305 1.007305434 0.818986612 1.282124457 1.268904126 1 20.52861453 3.473872332 24.88042854 1.100575414 1.207424114 0.155447434 0.14188455 233.0893335 1784995.242 0.044860009 0.058218091 2977.640972 -3.473872332 0.1068487 AGKFPSLLTHNENMVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGKFPSLLTHNENMVAK 17 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 130.39 4.09E-05 179940000 332700 298740 138700 177550 250620 205610 354150 339550 177100 FALSE TRUE 288732.852 296777.5573 205775.7839 217865.4412 245633.1523 213519.9497 319804.5875 266939.8749 156163.4398 1.848914525 1.900429177 1.317695001 1.395111695 1.572923552 1.367285135 2.047883858 1.709362161 1 17.25269721 4.260362333 24.79160047 1.532547701 1.874672256 0.244892042 0.274015618 353.9559325 402489.6971 0.070135932 0.185205144 18212.19671 -4.260362333 0.342124555 AGKPVICATQMLESMIK ddPTM_MDA-MB-175_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 ; 209.53 3.83E-12 944770000 3194900 2260600 1888750 2141100 2040850 1802150 2866100 3256100 3237500 FALSE TRUE 2772685.87 2245749.97 2802155.817 2627269.48 2000241.078 1871479.877 2588146.063 2559808.354 2854766.438 0.971247887 0.786666797 0.981570954 0.920309782 0.700667155 0.655563219 0.906605188 0.896678733 1 21.44494129 1.432362255 1.978875636 1.010792098 0.838668142 0.172197642 0.107555193 0.962252506 5.458145824 0.274295125 0.031371567 27.06214742 -1.432362255 -0.172123956 AGKPYQLQIYPNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGKPYQLQIYPNER 14 1 Q86TI2;Q86TI2-2 Q86TI2 DPP9 Dipeptidyl peptidase 9 0 91.207 0.0053297 0 177850 148180 84857 92874 144080 133940 172970 175690 143660 FALSE TRUE 154346.6719 147206.5958 125894.129 113962.4612 141213.0899 139092.7585 156195.396 138120.0607 126676.6785 1.218430052 1.162065485 0.993822466 0.899632534 1.114752073 1.098013937 1.233024089 1.090335351 1 16.95079142 AGLAALS(ph)PLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGLAALSPLLR 11 0 P49189-3 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 1 AGLAALS(1)PLLR;AGLAALS(1)PLLR 100.93 0.0038406 131331000 281750 372060 256510 222721 342420 382090 309390 368730 286190 TRUE FALSE 244516.0236 369615.9134 380559.094 273293.2071 335606.5119 396789.2495 279385.4054 289879.959 252356.9442 0.968929246 1.464655211 1.508019108 1.082962896 1.329888159 1.57233339 1.107104091 1.148690241 1 17.94510626 2.054998221 24.99987857 1.097843669 1.326889055 0.261953044 0.186140174 117.3483587 53340.92902 0.074023479 0.049906612 113.5006167 -2.054998221 0.229045386 AGLESGAEPGDGDS(ph)DTTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AGLESGAEPGDGDSDTTK 18 0 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 AGLESGAEPGDGDS(0.999)DT(0.001)TK;AGLESGAEPGDGDS(0.982)DT(0.013)T(0.005)K;AGLESGAEPGDGDS(0.999)DT(0.001)TK;AGLESGAEPGDGDS(0.987)DT(0.013)TK;AGLESGAEPGDGDS(1)DTTK;AGLESGAEPGDGDS(0.998)DT(0.002)TK 431.72 4.94E-169 6588870000 7963200 6088030 4927720 5298100 6199090 5096250 6800970 8426400 8961400 TRUE FALSE 6910842.944 6048037.33 7310781.874 6501114.581 6075740.237 5292306.035 6141412.976 6624479.934 7901993.501 0.874569556 0.765381208 0.925181965 0.82271829 0.76888702 0.669743152 0.777197928 0.838330218 1 22.91378523 1.24887101 3.070018296 1.033969438 0.799045775 0.456845032 0.067885903 0.354177825 4.318135075 0.202282094 0.018436977 17.73662607 -1.24887101 -0.234923663 AGLESGAEPGDGDS(ph)DTTKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AGLESGAEPGDGDSDTTKK 19 1 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 AGLESGAEPGDGDS(0.996)DT(0.002)T(0.003)KK;AGLESGAEPGDGDS(1)DTTKK;AGLESGAEPGDGDS(0.996)DT(0.002)T(0.002)KK;AGLESGAEPGDGDS(0.997)DT(0.002)T(0.002)KK;AGLESGAEPGDGDS(0.998)DT(0.001)T(0.001)KK 194.62 1.66E-15 2531320000 5572410 3655120 3507200 3371310 3478720 2517640 4738840 5820220 5339760 TRUE FALSE 4836001.9 3631109.276 5203293.651 4136817.463 3409500.278 2614495.24 4279268.026 4575611.246 4708499.656 1.027079166 0.771181808 1.105085278 0.878585062 0.724116072 0.555271409 0.90883898 0.97177691 1 22.16683599 7.99994493 0.809113201 0.859381664 37.09173318 0.081043199 0.155721226 1851.070431 6.177603176 0.05874378 123035.3393 99987320.36 -7.99994493 36.23235151 AGLGS(ph)PERPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AGLGSPERPPK 11 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 AGLGS(1)PERPPK;AGLGS(1)PERPPK;AGLGS(1)PERPPK;AGLGS(1)PERPPK;AGLGS(1)PERPPK 132.97 0.00010387 4096540000 11274210 7412790 5304220 7330060 7298210 7235120 8329220 10592520 10461970 TRUE FALSE 9784294.583 7364094.894 7869358.534 8994462.156 7152989.9 7513459.748 7521453.526 8327392.029 9225167.825 1.060608844 0.798261347 0.853031477 0.97499171 0.775377753 0.814452365 0.815318883 0.902681901 1 23.13714373 4.751383035 24.40455088 0.865621335 1.060609018 0.403401247 0.074073066 1612.260341 3068493.58 0.018075143 0.317106119 56413.49872 -4.751383035 0.194987683 AGLLALEFYTPEAFNWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGLLALEFYTPEAFNWR 17 0 G3V1D3;G3V180;Q9NY33-4;Q9NY33 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 177.93 1.86E-13 0 66259 60242 28717 44983 52478 40145 63740 69685 59835 FALSE TRUE 57502.70527 59846.26634 42604.63725 55197.07767 51433.79047 41689.40413 57558.50461 54783.40504 52761.37446 1.089863671 1.134281791 0.807496728 1.046164514 0.974837957 0.790150078 1.090921251 1.038324069 1 15.68719453 AGLLVLAVLSDGAGDHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGLLVLAVLSDGAGDHIR 18 0 Q8TEX9;Q8TEX9-2;H0YN14 Q8TEX9 IPO4 Importin-4 0 ; 151.9 4.43E-08 368120000 303530 331810 266901 313760 293730 296960 334140 389940 501470 FALSE TRUE 263417.7415 329630.3183 395975.2163 385004.0035 287885.3477 308384.2434 301735.1542 306554.3655 442186.7879 0.595715993 0.745454924 0.895493097 0.870681834 0.651049185 0.697407186 0.682370352 0.69326894 1 18.75429639 1.233531664 24.99295726 1.000000415 0.731808421 0.460568066 0.09214771 160.2858616 796497.4945 0.194330481 0.023951402 17.1211 -1.233531664 -0.268191994 AGLNEMVEYITHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AGLNEMVEYITHSR 14 0 E9PFR3;Q14738;H0Y8C4;Q14738-2;Q14738-3 E9PFR3 PPP2R5D Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform 0 ;; 161.49 4.59E-06 228150000 597390 545470 381111 385023 582600 573050 464155 613400 481550 FALSE TRUE 518443.3979 541886.7717 565417.5543 472448.3569 571007.3998 595095.6043 419141.3195 482229.1835 424621.7076 1.220953589 1.276163611 1.331579484 1.112633548 1.344743779 1.401472402 0.987093481 1.13566776 1 18.6958186 2.230258973 24.99888852 1.058416637 1.278534535 0.628821249 0.086681279 124.5763261 375135.1054 0.034540573 0.023722363 169.9256631 -2.230258973 0.220117897 AGLQFPVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AGLQFPVGR 9 0 A0A0U1RR32;A0A0U1RRH7;P20671;A0A3B3IS11;Q71UI9-5;Q7L7L0;P04908;Q99878;Q96KK5;Q6FI13;P0C0S8;Q16777;Q9BTM1;Q9BTM1-2;Q96QV6;Q8IUE6;P16104;Q71UI9;P0C0S5;C9J0D1;A0A494C189;Q71UI9-2 A0A0U1RR32;Q7L7L0;Q99878;P16104;Q71UI9 HIST1H2AD;H2AFV;HIST3H2A;HIST1H2AB;HIST1H2AJ;HIST1H2AH;HIST2H2AA3;HIST1H2AG;HIST2H2AC;H2AFJ;HIST1H2AA;HIST2H2AB;H2AFX;H2AFZ Histone H2A type 1-D;Histone H2A.V;Histone H2A type 3;Histone H2A type 1-B/E;Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-A;Histone H2A type 1;Histone H2A type 2-C;Histone H2A.J;Histone H2A type 1-A;Histone H2A type 2-B;Histone H2AX;Histone H2A.Z;Histone H2A 0 ;;; 178.08 0.00011952 14470100000 6359820 6349620 3788150 4806250 6396210 6273430 5383630 6734580 5561420 FALSE TRUE 5519353.673 6307908.928 5620112.011 5897582.521 6268937.935 6514772.912 4861526.391 5294442.476 4903955.263 1.125490217 1.286290064 1.146036558 1.202617521 1.278343215 1.328473153 0.99134803 1.079626993 1 22.22551439 2.227866235 24.99963951 1.03397218 1.227956347 0.680825842 0.065788253 123.4952431 288685.1112 0.026244529 0.017893514 168.9920347 -2.227866235 0.193984167 AGLS(ph)PANCQSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGLSPANCQSDR 12 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 1 AGLS(1)PANCQSDR 155.56 7.60E-05 363660000 93360 84166 68928 85900 78209 118710 112570 109210 103120 TRUE FALSE 81022.23946 83613.108 102261.8114 105404.9079 76652.79391 123276.8505 101652.9787 85856.29137 90929.27107 0.891046838 0.919540067 1.124630277 1.159196666 0.842993604 1.355744405 1.117934605 0.944209608 1 16.47245717 4.301631169 6.921144073 1.072348844 0.901553462 0.21634358 0.136320173 0.34381271 30.02796452 0.03398607 0.090656706 20027.70423 -4.301631169 -0.170795382 AGLVGPEFHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AGLVGPEFHEK 11 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 187.42 3.60E-06 1544850000 2164960 2002710 1346740 1557360 1840740 1679480 2157170 2370860 2312020 FALSE TRUE 1878855.051 1989554.066 1998027.969 1910982.391 1804112.875 1744090.682 1947967.985 1863870.039 2038695.629 0.921596644 0.975895586 0.980052117 0.937355416 0.884934882 0.855493413 0.95549721 0.914246351 1 20.95921497 5.146648239 12.56587158 0.934841561 0.000282365 0.009040583 0.044245519 439273.932 287993.501 0.011221567 11620461.39 140167.7941 -5.146648239 -0.934559196 AGLYGLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 166.13 0.0007451 2820900000 4185960 4683240 3531850 3133550 4652840 5379490 4539820 4393650 5214450 FALSE TRUE 3632774.78 4652475.488 5239864.473 3845070.421 4560257.587 5586442.461 4099548.955 3454102.139 4598003.661 0.790076531 1.011846843 1.139595542 0.836247794 0.991790769 1.214971295 0.891593234 0.751217788 1 22.13257618 2.01565887 24.99895515 0.846908699 1.001651331 0.13103753 0.137214801 353.3332635 564084.8065 0.054930047 0.037021307 103.6713778 -2.01565887 0.154742633 AGMSSNQS(ph)IS(ph)SPVLDAVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AGMSSNQS(0.994)IS(0.778)S(0.228)PVLDAVPR;AGMSS(0.001)NQS(0.982)IS(0.776)S(0.241)PVLDAVPR 190.26 2.73E-14 248920000 391270 367540 250450 303150 378330 358330 351520 425520 539120 TRUE FALSE 339562.6781 365125.6055 371568.4577 371984.8409 370801.9732 372115.187 317429.6445 334525.8594 475385.8478 0.714288572 0.76806158 0.781614471 0.782490355 0.780002129 0.782764545 0.667730531 0.703693349 1 18.85873943 1.232605943 24.99999826 1.000000411 0.746687667 0.796119786 0.040141986 98.54024314 413667.4458 0.097935806 0.011095711 17.08464438 -1.232605943 -0.253312745 AGMSSNQS(ph)ISS(ph)PVLDAVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AGMSSNQS(0.999)IS(0.042)S(0.959)PVLDAVPR;AGMSSNQS(0.982)IS(0.115)S(0.904)PVLDAVPR;AGMSSNQS(0.992)IS(0.279)S(0.729)PVLDAVPR 221.05 4.03E-19 440890000 641690 558000 454520 546080 624660 623980 533980 642880 879140 TRUE FALSE 556889.0407 554334.4613 674327.3923 670075.8103 612230.4881 647984.9144 482194.7018 505405.1149 775209.0707 0.71837271 0.715077367 0.869865199 0.864380766 0.78976177 0.835884072 0.622018911 0.651959754 1 19.56422593 AGMSSNQSIS(ph)SPVLDAVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AGMSSNQS(0.061)IS(0.745)S(0.194)PVLDAVPR 120.24 4.61E-05 67906000 193750 148980 107840 125160 152500 142540 131050 171980 200550 TRUE FALSE 168145.4466 148001.3406 159991.7847 153579.491 149465.5484 148023.606 118340.7912 135203.4153 176841.2075 0.950827293 0.836916591 0.904720042 0.868459864 0.84519638 0.837042498 0.669192395 0.764547004 1 17.43209496 2.950941381 1.952417269 0.794868216 0.888596753 0.119933467 0.086363844 0.581551166 4.451578725 0.032340679 0.034085034 893.1849184 -2.950941381 0.093728538 AGMSSNQSISS(ph)PVLDAVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 15 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AGMSSNQS(0.014)IS(0.321)S(0.665)PVLDAVPR;AGMSSNQS(0.049)IS(0.193)S(0.757)PVLDAVPR;AGMSSNQSIS(0.043)S(0.957)PVLDAVPR;AGMSSNQS(0.001)IS(0.287)S(0.711)PVLDAVPR;AGMSSNQSIS(0.02)S(0.98)PVLDAVPR;AGMSSNQSIS(0.002)S(0.998)PVLDAVPR;AGMSSNQS(0.005)IS(0.248)S(0.747)PVLDAVPR;AGMSSNQS(0.002)IS(0.087)S(0.911)PVLDAVPR;AGMSSNQS(0.013)IS(0.363)S(0.624)PVLDAVPR;AGMSSNQS(0.005)IS(0.063)S(0.933)PVLDAVPR;AGMSSNQS(0.001)IS(0.042)S(0.957)PVLDAVPR;AGMSSNQSIS(0.055)S(0.945)PVLDAVPR;AGMSSNQSIS(0.017)S(0.983)PVLDAVPR;AGMSSNQSIS(0.007)S(0.993)PVLDAVPR;AGMSSNQSIS(0.001)S(0.999)PVLDAVPR 340.57 9.75E-76 10401731000 5444001 4417165 3112348 3916915 4542269 4479684 4084325 5232780 5858141 TRUE FALSE 4724562.475 4388148.352 4617489.903 4806310.417 4451886.734 4652020.342 3688227.79 4113790.719 5165598.245 0.914620582 0.849494704 0.893892572 0.930446037 0.861833717 0.900577266 0.713998189 0.796382243 1 22.30050401 AGMSSNQSISS(ph)PVLDAVPRT(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AGMSSNQSISSPVLDAVPRTPSR 23 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AGMS(0.002)S(0.002)NQS(0.002)IS(0.25)S(0.745)PVLDAVPRT(0.825)PS(0.175)R;AGMSSNQS(0.002)IS(0.366)S(0.632)PVLDAVPRT(0.866)PS(0.134)R;AGMSSNQSIS(0.001)S(0.999)PVLDAVPRT(0.977)PS(0.023)R;AGMSSNQSIS(0.039)S(0.961)PVLDAVPRT(0.97)PS(0.03)R;AGMSSNQS(0.001)IS(0.182)S(0.817)PVLDAVPRT(0.844)PS(0.156)R;AGMSSNQSIS(0.121)S(0.879)PVLDAVPRT(0.972)PS(0.028)R 195.49 7.59E-24 2567290000 2070010 1991161 867009 853935 1788800 1886720 1834400 2074770 308053 TRUE FALSE 1796452.934 1978080.932 1286297.452 1047833.993 1753206.38 1959303.339 1656500.17 1631096.581 271635.3253 6.613473163 7.282119622 4.735383555 3.857502673 6.454265026 7.212991673 6.098250177 6.004729244 1 18.05131158 4.242910603 24.98601654 5.27761871 6.947796841 0.161569524 1.737322598 218.0350604 1252333.515 0.438750037 1.079679505 17494.86531 -4.242910603 1.670178131 AGMSSNQSISSPVLDAVPRT(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGMSSNQSISSPVLDAVPRTPSR 23 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AGMSSNQSISSPVLDAVPRT(0.986)PS(0.014)R 303.72 6.25E-62 355730000 371700 317280 152340 176480 297630 333920 293660 366950 62565 TRUE FALSE 322578.9032 315195.7668 226012.1335 216552.4813 291707.7453 346766.1185 265180.8984 288480.5981 55168.63697 5.847142886 5.713314377 4.096750363 3.925282429 5.287564843 6.285566175 4.806732828 5.229068796 1 15.75156072 4.259139116 19.6304364 4.559790134 5.780253605 0.140530885 1.387040853 45.6345377 43520.725 0.340839865 0.895739026 18160.97312 -4.259139116 1.220463471 AGMSYYNS(ph)PGLHVQHMGTSHGITRPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGMSYYNSPGLHVQHMGTSHGITRPSPR 28 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 AGMSYYNS(1)PGLHVQHMGT(0.278)S(0.244)HGIT(0.145)RPS(0.334)PR;AGMS(0.001)Y(0.001)Y(0.003)NS(0.995)PGLHVQHMGT(0.214)S(0.199)HGIT(0.148)RPS(0.44)PR 108.15 0.00035376 298460000 113826 107676 50900 72616 103348 114465 108555 122830 77786 TRUE FALSE 98783.6057 106968.6693 75515.41025 89104.57267 101291.577 118868.5426 98027.35281 96563.76036 68590.22769 1.440199414 1.559532208 1.100964566 1.299085535 1.476763971 1.733024464 1.429173748 1.407835542 1 16.06571542 1.234221798 4.703036839 0.965572251 1.432706132 0.412011383 0.162013302 0.214290368 10.72654119 0.334199252 0.042876795 17.14832865 -1.234221798 0.467133881 AGMSYYNSPGLHVQHMGT(ph)SHGITRPSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGMSYYNSPGLHVQHMGTSHGITRPSPR 28 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 AGMSYYNS(0.001)PGLHVQHMGT(0.25)S(0.25)HGIT(0.25)RPS(0.25)PR 74.769 0.0050545 99899000 32978 36076 17316 19629 37164 40911 25240 29757 27816 TRUE FALSE 28619.87374 35839.01438 25690.07552 24086.06446 36424.50911 42484.87264 22792.22868 23393.69712 24527.62417 1.166842477 1.46116942 1.047393557 0.981997453 1.485040249 1.732123436 0.929247306 0.953769389 1 14.58211988 AGMSYYNSPGLHVQHMGTSHGITRPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGMSYYNSPGLHVQHMGTSHGITRPSPR 28 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 AGMSYYNSPGLHVQHMGT(0.211)S(0.211)HGIT(0.159)RPS(0.419)PR 116.36 0.00015127 1128900000 648140 627020 394530 494410 600740 515930 765990 843780 661910 TRUE FALSE 562486.6568 622901.0643 585326.0276 606673.3471 588786.4493 535778.161 691704.4077 663344.2133 583659.7539 0.963723562 1.067233196 1.002854872 1.03942981 1.008783706 0.917963175 1.18511582 1.136525534 1 19.15476807 2.23260907 24.99999358 1.116566306 1.005375752 0.40551381 0.060612616 134.7360064 565963.2171 0.023971972 0.016639413 170.8476736 -2.23260907 -0.111190554 AGMTHIVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 AGMTHIVR 8 0 P39023;H7C422;H7C3M2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ;;;;;;;;;;;; 163.9 0.00033324 7797485000 6766880 7041172 4535254 5089125 6522043 7284871 6301833 7078861 6853762 FALSE TRUE 5872619.663 6994918.078 6728518.004 6244688.614 6392267.104 7565124.701 5690682.206 5565101.663 6043518.064 0.971722034 1.157424865 1.113344567 1.033286994 1.057706296 1.25177498 0.941617473 0.920838095 1 22.52695719 AGNAIHAILLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGNAIHAILLYR 12 0 P50416;P50416-2;H3BMD2 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 ; 133.07 0.00016975 1251010000 703610 942080 654720 873510 1061400 1340900 653650 1291810 1168980 FALSE TRUE 610626.1558 935891.4144 971344.7819 1071853.796 1040280.217 1392485.291 590259.1236 1015566.484 1030784.516 0.592389725 0.907940893 0.942335441 1.039842741 1.00921211 1.350898533 0.572630957 0.985236457 1 19.97531134 4.83318453 2.002252082 0.98019266 0.41091299 0.305391647 0.185463351 1.328728434 4.675052889 0.04768926 1.505017533 68105.86767 -4.83318453 -0.56927967 AGNLGGGVVTIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGNLGGGVVTIER 13 0 P35268;K7ERI7;K7EMH1;K7EP65;K7EKS7;K7ELC4;K7EJT5 P35268 RPL22 60S ribosomal protein L22 0 ; 176.18 3.95E-05 274590000 324810 276350 188742 245210 298190 307580 307180 350360 284960 FALSE TRUE 281885.5355 274534.6387 280018.2625 300888.6783 292256.6024 319412.8016 277389.7309 275438.2405 251272.3534 1.121832672 1.092577973 1.1144014 1.197460342 1.163106878 1.271181637 1.103940514 1.096174079 1 17.93889242 1.395556774 1.796270085 0.978007194 1.155958911 0.474626463 0.051821171 0.603465628 2.51049234 0.17080522 0.0154434 24.86318573 -1.395556774 0.177951718 AGNNMLLVGVHGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGNNMLLVGVHGPR 14 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 158.2 5.11E-06 1275800000 893950 698840 492510 569100 668080 675380 617720 702220 642490 FALSE TRUE 775812.2425 694249.274 730689.4833 698322.8531 654786.5151 701362.3056 557813.6095 552055.7177 566535.5641 1.369397248 1.22542929 1.289750423 1.232619622 1.155773012 1.237984603 0.984604754 0.974441417 1 19.111807 2.378283383 0.867272844 0.938709882 1.286364215 0.811235371 0.059188699 0.280728739 0.426572864 0.06931351 0.028919092 238.9369868 -2.378283383 0.347654333 AGNS(ph)DS(ph)EEDDANGR ddPTM_MDA-MB-175_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 212.34 3.77E-09 103400000 332050 274000 228720 263590 270270 287490 278840 339230 540500 TRUE FALSE 288168.7512 272200.076 339329.757 323442.1382 264892.1558 298549.9263 251798.1397 266688.3044 476602.7057 0.604630959 0.571125746 0.711976145 0.678641003 0.555792388 0.626412571 0.528318737 0.559561037 1 18.86242762 1.234776981 24.99979668 1.000000567 0.602660713 0.82801016 0.056633653 47.02968829 310695.2697 0.108160097 0.014834935 17.17026433 -1.234776981 -0.397339854 AGPDLPSLPSHALEDEGWAAAAPS(ph)PGS(ph)AR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AGPDLPSLPSHALEDEGWAAAAPSPGSAR 29 0 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 2 AGPDLPSLPSHALEDEGWAAAAPS(1)PGS(1)AR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGS(1)AR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGS(1)AR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGS(1)AR 166.88 2.18E-12 611544000 361737 359784 204352 266195 375375 372303 345655 407016 369150 TRUE FALSE 313932.5389 357420.5552 303177.3107 326638.6433 367905.7719 386625.7373 312133.4313 319978.7958 325509.5075 0.964434315 1.098034149 0.931393104 1.003468826 1.130245856 1.18775559 0.958907264 0.983009062 1 18.31234016 AGPDLPSLPSHALEDEGWAAAAPS(ph)PGSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AGPDLPSLPSHALEDEGWAAAAPSPGSAR 29 0 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(0.995)PGS(0.005)AR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR 396.65 2.30E-155 10067630000 2851450 2693910 1587780 2137980 2581260 2761080 2754750 3112640 2706770 TRUE FALSE 2474623.658 2676213.528 2355635.719 2623441.036 2529897.976 2867300.534 2487594.769 2447026.159 2386778.734 1.036804804 1.121265867 0.986951863 1.099155526 1.059963347 1.201326496 1.042239372 1.025242149 1 21.1866334 2.011312313 24.99968872 1.020219054 1.084471086 0.224020561 0.055818575 317.3747504 701380.6116 0.022241519 0.014982275 102.6389766 -2.011312313 0.064252032 AGPEEPGDS(ph)PPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGPEEPGDSPPLR 13 0 A0A0A0MTG6;Q12770-4;Q12770-2;Q12770 A0A0A0MTG6 SCAP Sterol regulatory element-binding protein cleavage-activating protein 1 AGPEEPGDS(1)PPLR 116.63 0.00059765 231640000 158820 133770 89078 163540 224460 173110 148470 242870 205040 TRUE FALSE 137831.5346 132891.2561 132156.4187 200674.2566 219993.6851 179769.6537 134071.4023 190934.1405 180800.4048 0.762340852 0.735016364 0.730952007 1.1099215 1.216776508 0.994298956 0.741543706 1.056049298 1 17.46403838 3.750164738 24.44285881 1.013303506 0.741994363 0.545701967 0.119042321 469.3023693 988532.3165 0.03414241 0.058456086 5625.546745 -3.750164738 -0.271309143 AGPGSS(ph)PLFSLLPGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGPGSSPLFSLLPGYR 16 0 Q9H0W8-2;Q9H0W8 Q9H0W8-2 SMG9 Protein SMG9 1 AGPGS(0.017)S(0.983)PLFSLLPGYR;AGPGS(0.02)S(0.98)PLFSLLPGYR 214.47 1.78E-14 496900000 714860 673590 530450 604330 751170 798290 801180 870610 862090 TRUE FALSE 620389.4398 669165.1429 786977.3942 741552.3631 736223.1866 829000.7329 723481.6869 684436.8266 760174.7023 0.816114293 0.8802781 1.035258595 0.975502553 0.968492091 1.090539754 0.951730812 0.900367803 1 19.53597149 4.419453095 4.919295231 0.981067824 0.829431853 0.580650865 0.050736824 0.139534168 6.79902313 0.013818646 0.04051494 26269.5779 -4.419453095 -0.151635971 AGPIWDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 ;;;;;;; 119.89 0.0037402 6594114000 7516810 6691620 4395386 4774810 6089720 6486730 6100610 7009550 6888240 FALSE TRUE 6523444.513 6647662.308 6521009.371 5859003.589 5968546.486 6736278.701 5508973.781 5510612.281 6073920.114 1.074008942 1.09445995 1.073608024 0.964616504 0.982651463 1.109049605 0.906988185 0.907257945 1 22.5341965 3.495379234 0.367543121 0.914411985 1.140752118 0.376512688 0.058325354 2.576898811 0.99592878 0.17559389 0.340608125 3128.810311 -3.495379234 0.226340133 AGPLT(ph)PPKPPR ddPTM_MDA-MB-175_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 79.466 0.04376 453800000 2159920 1882970 1343830 1705950 1932490 1767030 2164850 2448000 2165800 TRUE FALSE 1874481.099 1870600.646 1993710.683 2093312.021 1894037.23 1835008.788 1954903.18 1924514.25 1909761.591 0.981526232 0.979494328 1.043957891 1.096111698 0.991766322 0.960857521 1.02363729 1.00772487 1 20.86496112 AGPPPEKR ddPTM_MDA-MB-175_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 79.469 0.044828 100050000 73136 67703 54871 48840 56401 82227 55648 64261 61323 FALSE TRUE 63470.8923 67258.25454 81406.79913 59929.86847 55278.73045 85390.3259 50251.26553 50519.28523 54073.4648 1.173790001 1.243831051 1.505485166 1.108304576 1.02228941 1.579153957 0.929314696 0.934271281 1 15.72263318 2.176277061 24.99999957 0.949256008 1.262660381 0.443690365 0.167393785 60.29709011 24201.892 0.066641352 0.044929604 150.0641875 -2.176277061 0.313404373 AGPSAQEPGSQT(ph)PLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGPSAQEPGSQTPLK 15 0 O60271;A0A087X2D8;O60271-4;O60271-2;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 AGPSAQEPGSQT(1)PLK 167.18 1.48E-05 37689000 55357 40569 29748 35986 40402 43522 43562 50501 51195 TRUE FALSE 48041.43219 40302.49957 44134.2323 44157.17131 39598.07925 45196.3195 39337.36394 39701.75415 45142.78542 1.064210632 0.892778308 0.977658598 0.978166741 0.877174035 1.001185883 0.871398687 0.879470635 1 15.46220782 4.748873112 24.35431844 0.930420579 1.064210739 0.374034496 0.052378716 1093.10862 2581445.238 0.012536589 0.166711336 56088.40787 -4.748873112 0.13379016 AGQATEGHCPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGQATEGHCPR 11 0 C9J8T0;P57772-2;P57772 C9J8T0 EEFSEC Selenocysteine-specific elongation factor 0 ; 153.95 3.22E-05 214460000 124775 128673 71227 90742 108813 132030 124639 133874 134177 FALSE TRUE 108285.6676 127827.7386 105672.6154 111346.358 106647.8342 137109.2795 112551.529 105246.0869 118314.7479 0.915233895 1.080404099 0.893148296 0.941102948 0.901390875 1.158851977 0.951289091 0.889543263 1 16.85227039 2.008688503 24.99638197 0.931942114 0.98319096 0.029988549 0.086874894 557.3034732 1603328.75 0.034839146 0.02344865 102.0207479 -2.008688503 0.051248846 AGQDMGLEHGFEKPLDSAMS(ph)AEEDTDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGQDMGLEHGFEKPLDSAMSAEEDTDVR 28 1 Q99549-2;Q99549;A0A0A0MT47 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 AGQDMGLEHGFEKPLDS(0.004)AMS(0.994)AEEDT(0.002)DVR 135.77 5.93E-06 45388000 44325 41776 29563 40964 38624 36347 43465 62655 51850 TRUE FALSE 38467.33894 41501.57071 43859.76568 50265.5023 37855.45797 37745.29261 39249.77099 49256.71583 45720.35207 0.84136139 0.907726403 0.959305073 1.099411969 0.827978269 0.825568722 0.85847482 1.077347693 1 15.48054889 1.731815594 10.34960556 1.036548993 0.906927914 0.313987204 0.08322598 0.11502223 51.39716714 0.048526454 0.022627706 53.92815896 -1.731815594 -0.129621079 AGQEHLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGQEHLLR 8 0 Q3KQV9;A0A087X226;Q16222;Q16222-3;Q16222-2 Q3KQV9;Q16222 UAP1L1;UAP1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1;UDP-N-acetylhexosamine pyrophosphorylase;UDP-N-acetylgalactosamine pyrophosphorylase;UDP-N-acetylglucosamine pyrophosphorylase 0 ; 99.688 0.0066361 933230000 1430460 1383870 1188100 975800 1046210 1486130 1147280 1307090 1193840 FALSE TRUE 1241421.087 1374779.267 1762669.134 1197370.304 1025392.468 1543302.383 1036016.962 1027578.975 1052705.595 1.179267112 1.305948475 1.67441794 1.137421811 0.974054353 1.466034179 0.984146913 0.976131389 1 20.00567059 2.242446803 0.629939314 0.890975466 1.348562638 0.295207995 0.197482247 1.592207835 1.171421243 0.483891775 0.149226806 174.7619184 -2.242446803 0.457587173 AGQHS(ph)PLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGQHSPLR 8 0 A0A087X0R7;Q9H4L4 A0A087X0R7 SENP3-EIF4A1;SENP3 Sentrin-specific protease 3 1 AGQHS(1)PLR 71.153 0.051902 143510000 218040 172600 153800 168080 159450 221590 176850 216130 348580 TRUE FALSE 189225.4616 171466.1792 228178.1944 206245.1329 156277.257 230114.7107 159699.1142 169912.2814 307371.2695 0.615625077 0.557847126 0.742353685 0.670996783 0.508431569 0.748653936 0.519564221 0.552791683 1 18.22962279 1.233211562 24.99948483 1.000000609 0.612050278 0.670546609 0.084896744 102.6306025 479603.7738 0.170605548 0.020411089 17.10848535 -1.233211562 -0.387950331 AGQTQPNPGILPIQPALT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGQTQPNPGILPIQPALTPR 20 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 AGQTQPNPGILPIQPALT(1)PR 83.776 0.032235 45882000 55547 57864 36445 46568 56247 58135 50063 60140 54068 TRUE FALSE 48206.32321 57483.88757 54069.9239 57141.97615 55127.79475 60371.49107 45207.89797 47279.52901 47676.14263 1.011120459 1.205715991 1.134108611 1.19854445 1.156297295 1.266283045 0.948228935 0.991681088 1 15.54097989 2.224719283 24.9998067 0.981087227 1.164130728 0.627815454 0.066058227 138.9928741 251042.839 0.02530635 0.017161374 167.7719232 -2.224719283 0.183043501 AGRPQYDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGRPQYDTK 9 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 135.43 0.00020163 808600000 877790 748270 507720 561280 602850 581140 788680 815130 769850 FALSE TRUE 761787.8275 743354.5651 753255.0902 688727.2026 590854.4645 603496.8318 712193.935 640820.7928 678839.21 1.122191848 1.095037756 1.109622248 1.01456603 0.870389417 0.889012925 1.049134942 0.94399496 1 19.37271037 3.581277817 3.759201747 0.953177245 1.106978169 0.666168253 0.050911623 0.149463913 3.800124364 0.014991976 0.022730986 3813.096681 -3.581277817 0.153800924 AGS(ph)EECVFYTDETASPLAPDLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGSEECVFYTDETASPLAPDLAK 23 0 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 AGS(0.982)EECVFY(0.018)TDETASPLAPDLAK;AGS(0.992)EECVFY(0.007)T(0.001)DETASPLAPDLAK 157.79 1.75E-09 75788000 247050 209476 199115 177339 222278 191722 291490 323350 294670 TRUE FALSE 214401.7166 208099.9384 295407.68 217606.5304 217855.1027 199097.6694 263221.3447 254204.1188 259834.4483 0.825147389 0.800894338 1.136907296 0.83748145 0.838438106 0.766248166 1.013034824 0.978331089 1 17.98723319 2.205559511 24.9999887 0.993870335 0.874048628 0.266414137 0.100945598 284.3591768 215414.3807 0.042044074 0.028348081 160.5312218 -2.205559511 -0.119821707 AGS(ph)FTGTSDPEAAPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AGSFTGTSDPEAAPAR 16 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 AGS(0.911)FT(0.035)GT(0.027)S(0.027)DPEAAPAR;AGS(0.998)FT(0.001)GT(0.001)S(0.001)DPEAAPAR;AGS(0.999)FT(0.001)GTSDPEAAPAR 156.96 1.18E-07 1753960000 686711 682049 598371 697753 931597 828862 853226 965733 876815 TRUE FALSE 595960.4014 677568.5752 887745.217 856188.4831 913060.0423 860748.8575 770480.2738 759218.5133 773158.9296 0.770812285 0.8763639 1.148205347 1.107390021 1.180947419 1.113288387 0.99653544 0.981969533 1 19.56040548 4.398497783 4.665840453 1.068541239 0.79293697 0.714928616 0.067489531 0.117965953 4.590424335 0.020034971 0.058663171 25032.12869 -4.398497783 -0.275604269 AGS(ph)ISTLDSLDFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGSISTLDSLDFAR 14 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 AGS(0.751)IS(0.248)T(0.001)LDSLDFAR;AGS(0.999)IS(0.001)TLDSLDFAR 208.68 8.08E-09 210807000 511890 281190 217314 289980 353430 295280 355550 440230 404230 TRUE FALSE 444242.4395 279342.8444 322407.7773 355824.3911 346397.4345 306639.6127 321068.8157 346090.2404 356442.3899 1.246323255 0.783697036 0.904515811 0.998266203 0.971818853 0.860278186 0.900759351 0.970957019 1 18.44330939 4.755473238 24.99959342 0.927634002 1.246323507 0.694804174 0.06713692 2109.991749 3118858.895 0.01659536 0.465587812 56947.31314 -4.755473238 0.318689504 AGS(ph)LQLSSMSAGNSSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGSLQLSSMSAGNSSLR 17 0 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2;A0A0B4J1Z0 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 AGS(0.998)LQLS(0.001)S(0.001)MSAGNSSLR;AGS(0.996)LQLS(0.004)SMSAGNSSLR 281.53 5.86E-36 278710000 163586 148190 129519 153595 201312 209231 184458 211870 266010 TRUE FALSE 141967.6956 147216.5301 192154.8216 188471.0923 197306.2851 217280.252 166569.2916 166563.2493 234562.6008 0.605244379 0.627621495 0.819204856 0.803500181 0.841166854 0.926320953 0.710127237 0.710101477 1 17.83961348 4.253952687 6.001783336 0.816165562 0.613092061 0.501234342 0.087801405 0.138401933 17.15640411 0.022865509 0.05748262 17945.38117 -4.253952687 -0.2030735 AGS(ph)PDVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGSPDVLR 8 0 Q8NDX6 Q8NDX6 ZNF740 Zinc finger protein 740 1 AGS(1)PDVLR 99.815 0.0068662 553720000 1220400 962110 572560 940440 1126600 969310 912230 1026900 928920 TRUE FALSE 1059121.048 955789.8361 849451.9311 1153981.276 1104182.864 1006599.983 823762.075 807305.4263 819104.1358 1.293023685 1.166872189 1.037049984 1.408833414 1.348037222 1.228903553 1.005686626 0.985595593 1 19.64368735 2.242640212 5.285209924 0.992851017 1.247211192 0.584603257 0.099519689 0.127462466 10.56231218 0.042334337 0.030298961 174.839764 -2.242640212 0.254360175 AGS(ph)PFSPPPSSSSLTGEAAISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(0.993)PFS(0.007)PPPSSSSLTGEAAISR;AGS(0.998)PFS(0.002)PPPSSSSLTGEAAISR;AGS(1)PFSPPPSSSSLTGEAAISR;AGS(1)PFSPPPSSSSLTGEAAISR;AGS(0.992)PFS(0.008)PPPSSSSLTGEAAISR 269.9 1.28E-38 1441556000 916011 861663 536151 564358 989591 806866 741674 831456 715830 TRUE FALSE 794957.8255 856002.679 795435.4169 692504.1096 969900.0752 837906.6571 669746.5696 653655.6048 631205.3929 1.259428127 1.356139679 1.260184761 1.09711374 1.536583949 1.327470688 1.061059644 1.035567206 1 19.26775001 2.204149254 5.862604655 1.030814544 1.3075895 0.587779904 0.10828746 0.12718197 11.73555839 0.04469263 0.030566613 160.0107845 -2.204149254 0.276774956 AGS(ph)PLCNSNLQDS(ph)EEDIEPSYSLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGSPLCNSNLQDSEEDIEPSYSLFR 25 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 2 AGS(0.991)PLCNS(0.013)NLQDS(0.996)EEDIEPSYSLFR 77.31 0.014902 33608000 16923 11891 10144 8553.2 12884 15573 13020 16857 14063 TRUE FALSE 14686.58267 11812.88724 15049.67233 10495.33479 12627.63361 16172.10339 11757.3224 13252.26173 12400.48816 1.184355203 0.952614694 1.213635474 0.846364647 1.01831746 1.304150545 0.948133836 1.068688713 1 13.59810929 AGS(ph)PLCNSNLQDSEEDIEPSYSLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AGSPLCNSNLQDSEEDIEPSYSLFR 25 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 AGS(0.999)PLCNS(0.001)NLQDSEEDIEPSYSLFR;AGS(1)PLCNSNLQDSEEDIEPSYSLFR;AGS(1)PLCNSNLQDSEEDIEPSYSLFR;AGS(1)PLCNSNLQDSEEDIEPSYSLFR 208.53 1.76E-25 419442000 312961 277804 194647 211963 305522 295347 289577 345026 304677 TRUE FALSE 271602.4109 275979.0872 288778.9403 260092.4388 299442.7099 306709.1902 261493.8671 271244.8749 268658.4321 1.010958073 1.027248931 1.074892524 0.968115673 1.114585191 1.141632473 0.973332067 1.009627253 1 18.03541359 AGS(ph)PRGS(ph)PLAEGPQAFFPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGSPRGSPLAEGPQAFFPER 20 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 2 AGS(1)PRGS(1)PLAEGPQAFFPER 135.75 3.77E-06 67511000 49312 72076 37656 45873 107000 77719 97401 120670 22121 TRUE FALSE 42795.29426 71602.52801 55866.56755 56289.16577 104870.9093 80708.90022 87955.06601 94865.65955 19505.88058 2.193968844 3.670817511 2.864088464 2.885753634 5.376374007 4.13767017 4.509156387 4.86343896 1 14.25162151 3.327117795 24.99999999 4.136197213 2.955601518 0.155714846 1.208610484 35.34367442 9969.335679 0.336289802 0.434148159 2123.820433 -3.327117795 -1.180595694 AGSALPGFANS(ph)PAGSTSVVLVPPAHGTLVPDGNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGSALPGFANSPAGSTSVVLVPPAHGTLVPDGNK 34 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 AGSALPGFANS(0.996)PAGS(0.002)T(0.002)SVVLVPPAHGTLVPDGNK;AGSALPGFANS(0.988)PAGS(0.005)T(0.005)S(0.001)VVLVPPAHGTLVPDGNK 166.84 1.40E-14 899830000 620680 609840 295090 488390 578420 538570 670080 859390 796600 TRUE FALSE 538655.5654 605833.9209 437796.511 599286.4141 566910.5737 559289.1364 605095.7447 675616.1363 702426.8555 0.766849333 0.862486843 0.623262775 0.853165578 0.807074173 0.796224023 0.861435949 0.961831301 1 19.42198848 1.752465696 1.09659789 1.038984301 0.777357471 0.613489588 0.064483427 0.505758073 0.90061574 0.133500191 0.021717343 56.55430837 -1.752465696 -0.26162683 AGSATVLSGS(ph)IAGLEGGSQLALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 223.54 1.52E-32 49703000 96173 83028 65478 63676 93548 105314 74637 92200 110064 TRUE FALSE 83463.49438 82482.5836 97143.37981 78134.60903 91686.57782 109365.4977 67398.71523 72483.7475 97052.35931 0.859984188 0.849877161 1.000937849 0.805076864 0.944712509 1.126871088 0.694457257 0.746851988 1 16.56647566 2.202980181 24.99992035 0.794857312 0.925590728 0.173347805 0.118126769 276.5338178 194299.4178 0.047989169 0.032355616 159.5806323 -2.202980181 0.130733416 AGSGKNDHAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGSGKNDHAEK 11 1 P43487;F6WQW2 P43487 RANBP1 Ran-specific GTPase-activating protein 0 71.555 0.029267 46518000 128330 119880 49584 57242 72096 87548 144060 162050 32040 FALSE TRUE 111370.8654 119092.5004 73562.98825 70239.67099 70661.43065 90916.02821 130089.0834 127396.8686 28252.2677 3.942015081 4.215325356 2.603790571 2.486160465 2.501088812 3.218008168 4.604553686 4.509261696 1 14.78607905 2.450667437 24.94283039 3.695674293 3.113475209 0 1.139372024 743.994141 701493.8553 0.434374763 0.336473917 282.2717635 -2.450667437 -0.582199084 AGSIS(ph)TLDSLDFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGSISTLDSLDFAR 14 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 AGS(0.009)IS(0.926)T(0.065)LDSLDFAR;AGS(0.112)IS(0.888)TLDSLDFAR 335.9 1.38E-68 198937000 466220 252113 192401 264100 315150 265100 282708 389890 365410 TRUE FALSE 404607.8457 250456.8531 285446.7671 324067.9415 308879.1316 275298.5685 255291.0217 306515.0576 322211.6461 1.255720737 0.777305402 0.885898355 1.005761106 0.958621873 0.854402912 0.792308487 0.951284851 1 18.29764911 2.83640945 8.586340405 0.897611802 0.962446949 0.073334127 0.130957645 1.125516434 90.15697332 0.040987377 0.041009837 686.1348048 -2.83640945 0.064835147 AGSMKDPLLDDHGDFIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AGSMKDPLLDDHGDFIR 17 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;;;; 158.92 1.97E-09 1106650000 2544760 2033200 1398620 1666400 2105640 1781010 2270280 2749330 2238590 FALSE TRUE 2208463.518 2019843.775 2074997.31 2044781.589 2063741.884 1849526.607 2050108.595 2161407.175 1973946.44 1.118806201 1.02325156 1.051192306 1.035885041 1.045490314 0.936968992 1.038583699 1.094967488 1 20.91265141 4.742452194 24.34880174 1.032620284 1.118806248 0.32602314 0.040476301 364.895945 2282942.07 0.01032572 0.07531108 55265.25701 -4.742452194 0.086185964 AGSNEDPILAPS(ph)GTPPPTIPPDETFGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGSNEDPILAPSGTPPPTIPPDETFGGR 28 0 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 AGSNEDPILAPS(0.603)GT(0.396)PPPTIPPDETFGGR 95.56 0.0014031 101740000 124100 100400 65131 82957 101760 98813 93235 119050 109240 TRUE FALSE 107699.8706 99740.46579 96628.56945 101793.6548 99735.17509 102614.4001 84193.08405 93592.08395 96325.77165 1.1180795 1.035449435 1.003143477 1.056764488 1.03539451 1.065285004 0.874045259 0.971620391 1 16.55563422 2.262969624 24.99999235 0.950255847 1.04877735 0.568094585 0.042579684 162.650841 166588.4427 0.015573296 0.012057298 183.2186268 -2.262969624 0.098521504 AGSNEDPILAPSGT(ph)PPPTIPPDETFGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGSNEDPILAPSGTPPPTIPPDETFGGR 28 0 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 AGSNEDPILAPS(0.027)GT(0.973)PPPTIPPDETFGGR;AGSNEDPILAPS(0.188)GT(0.804)PPPT(0.008)IPPDETFGGR 120.45 0.000223 211720000 292850 232076 162556 188412 240372 239373 250536 288100 266939 TRUE FALSE 254149.1305 230551.4775 241168.6253 231193.8243 235589.0675 248581.8342 226239.0573 226492.057 235381.7755 1.079731555 0.979478878 1.024584953 0.982207836 1.000880663 1.056079357 0.961157918 0.962232766 1 17.8446431 AGSPFS(ph)PPPSSSSLTGEAAISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.401)PFS(0.599)PPPSSSSLTGEAAISR 210.12 5.11E-23 129400000 143650 114810 80081 94129 124530 101450 115820 132160 123460 TRUE FALSE 124666.2885 114055.8056 118808.4395 115502.4281 122052.0966 105352.8471 104587.7942 103898.6125 108864.6994 1.145148879 1.047684016 1.091340352 1.060972278 1.12113566 0.967741129 0.960713572 0.954382945 1 16.73217669 2.728897665 24.88544221 0.967221282 1.088824456 0.80647609 0.029763798 249.26531 641942.8181 0.009467706 0.008456612 535.6704197 -2.728897665 0.121603173 AGSS(ph)PAQGAQNEPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGSSPAQGAQNEPPR 15 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 AGS(0.132)S(0.868)PAQGAQNEPPR 160.49 1.79E-06 294750000 288430 357110 184310 286390 290580 300990 307090 293590 322780 TRUE FALSE 250313.2447 354764.1209 273442.9325 351419.2267 284798.0265 312569.2801 277308.4591 230808.0632 284621.3161 0.87946064 1.246442557 0.960725417 1.23469047 1.000620861 1.098193503 0.974306713 0.810930349 1 18.11868419 2.043147917 4.505788823 0.89126157 1.076387065 0.244315003 0.120610426 0.214247044 9.699374462 0.048847316 0.03027287 110.4454723 -2.043147917 0.185125495 AGSSPCLGSSSAASS(ph)PPPPASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGSSPCLGSSSAASSPPPPASR 22 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 AGSSPCLGSSSAAS(0.036)S(0.964)PPPPASR;AGSSPCLGSSSAAS(0.002)S(0.998)PPPPASR 370.76 4.89E-113 169470000 194394 180319 114092 146634 208782 212280 200326 219490 189176 TRUE FALSE 168704.3404 179134.4726 169267.2728 179929.4909 204627.6467 220446.549 180898.4154 172553.7716 166811.8288 1.011345188 1.073871523 1.014719844 1.078637481 1.22669746 1.321528279 1.084445969 1.034421676 1 17.34786207 3.472945579 24.96353212 1.129130298 1.038919864 0.197336327 0.092342961 236.4297525 1413443.688 0.030197341 0.039157282 2971.293681 -3.472945579 -0.090210435 AGT(ph)PVSELTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AGTPVSELTK 10 0 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 AGT(0.993)PVS(0.007)ELTK;AGT(0.998)PVS(0.002)ELTK;AGT(0.999)PVS(0.001)ELTK;AGT(0.992)PVS(0.008)ELTK 130.16 0.0031734 844762000 2461830 1828210 1877720 1815010 2223280 1680550 2340300 2612500 3338270 TRUE FALSE 2136492.928 1816200.368 2785791.673 2227135.761 2179041.078 1745201.846 2113338.066 2053837.205 2943623.524 0.725803728 0.616994787 0.946381781 0.756596672 0.740258073 0.592875357 0.71793762 0.697724145 1 21.48916174 1.235275142 24.99093457 1.000000384 0.723759858 0.457332603 0.094373047 88.56039342 673520.1597 0.161721244 0.023074848 17.18997092 -1.235275142 -0.276240526 AGTEDEEEEEEGRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGTEDEEEEEEGRR 14 1 O95456;O95456-2;F8WBH7 O95456 PSMG1 Proteasome assembly chaperone 1 0 ; 243.3 2.54E-17 960490000 963600 909020 649490 732090 866980 739140 902970 979350 1042200 FALSE TRUE 836257.8185 903048.5878 963585.5364 898322.2238 849728.7942 767575.1941 815400.1084 769923.6238 918992.3033 0.909972603 0.982650872 1.048524055 0.977507886 0.924631024 0.835235716 0.887276319 0.837791156 1 19.80969325 3.095362106 3.485311751 0.881376373 0.984936532 0.357766306 0.055772116 0.225403561 5.384925198 0.017402649 0.01994865 1245.552695 -3.095362106 0.103560159 AGTEKLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AGTEKLR 7 1 A0A0G2JR78;Q9NY99-2;Q9NY99 A0A0G2JR78 SNTG2 Gamma-2-syntrophin 0 ;; 151.17 0.0017321 1954150000 2515460 2016150 1225870 1646180 1577270 1877520 2402620 2731020 2136690 FALSE TRUE 2183035.588 2002905.778 1818704.832 2019970.329 1545885.413 1949749.409 2169614.282 2147012.626 1884092.942 1.158666613 1.063061027 0.965294647 1.072118198 0.820493182 1.034847786 1.151543129 1.139547088 1 20.8454387 0.942461063 19.88493786 0.28341665 1.051432749 0.024477324 0.100485681 405.8625312 185393.2085 30917.93591 0.025220055 8.75913183 -0.942461063 0.768016099 AGTFIAPPVYSNITPYQS(ph)HLRSPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGTFIAPPVYSNITPYQSHLRSPVR 25 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 AGTFIAPPVYSNIT(0.072)PY(0.334)QS(0.405)HLRS(0.189)PVR;AGTFIAPPVYSNIT(0.011)PYQS(0.886)HLRS(0.103)PVR 128.12 6.92E-05 1722310000 1198326 1166590 631373 749074 1286451 1465640 1280769 1579992 411410 TRUE FALSE 1039964.183 1158926.593 936707.0946 919162.7006 1260853.142 1522024.119 1156560.22 1242123.006 362773.5785 2.866703213 3.194627895 2.582070884 2.533709055 3.475592537 4.195520869 3.18810489 3.423962163 1 18.46870986 5.069774174 8.989676065 3.028611695 2.180729975 0 0.838673847 54243.13359 337401.1078 0.201521662 733097.5187 117428.6786 -5.069774174 -0.84788172 AGTFQAFEQFGQQLLAHGHYASPEIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGTFQAFEQFGQQLLAHGHYASPEIK 26 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 216.81 2.24E-34 262850000 312950 307050 205970 293180 337800 241550 367020 466830 345560 FALSE TRUE 271592.8646 305032.9683 305577.7809 359751 331078.4409 250842.5848 331426.4569 367002.0374 304708.2905 0.89132089 1.001065537 1.002853518 1.180640669 1.086542281 0.823222054 1.087684409 1.204437322 1 18.21706923 4.589098515 1.599978687 1.069650614 0.860450987 0.196247437 0.105275969 1.290808977 3.989377039 0.031075006 0.385649723 38823.84241 -4.589098515 -0.209199627 AGTGYAS(ph)PDRTHVLAAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGTGYASPDRTHVLAAGK 18 1 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 AGT(0.157)GY(0.002)AS(0.835)PDRT(0.005)HVLAAGK;AGT(0.075)GYAS(0.924)PDRTHVLAAGK 120.33 2.90E-05 675950000 1577220 1118100 1001730 1144470 945330 928490 1341920 1445590 981250 TRUE FALSE 1368786.381 1110755.127 1486169.979 1404339.406 926519.7825 964209.6111 1211780.805 1136461.828 865247.7428 1.581958915 1.2837423 1.717623641 1.62304891 1.070814446 1.114374027 1.40050155 1.31345252 1 19.72275375 3.2448892 24.99991724 1.209809257 1.544320555 0.573287764 0.158149992 127.2810977 502797.634 0.047684941 0.060035645 1757.475178 -3.2448892 0.334511298 AGTQIENIDEDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AGTQIENIDEDFR 13 0 O43707;F5GXS2;O43707-3;K7EP19 O43707 ACTN4 Alpha-actinin-4 0 ;;; 228.78 1.59E-11 595430000 575780 546371 485651 659457 538777 552930 452297 510292 1710930 FALSE TRUE 499689.2142 542781.8529 720513.448 809196.791 528056.3918 574201.5749 408433.3066 401170.0269 1508665.804 0.33121266 0.359776069 0.477583204 0.536365833 0.350015484 0.380602234 0.270724839 0.265910466 1 20.52484183 1.232796204 24.99999825 1.000001013 0.369558366 0.849747765 0.083049603 78.95494787 342388.1743 0.200688864 0.023102016 17.09213066 -1.232796204 -0.630442647 AGTQIENIDEDFRDGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AGTQIENIDEDFRDGLK 17 1 O43707;F5GXS2;O43707-3;K7EP19 O43707 ACTN4 Alpha-actinin-4 0 ;;; 280.65 5.69E-36 7426600000 3818991 2947834 2285039 2982296 3025100 2679899 3141543 3840161 3827448 FALSE TRUE 3314301.663 2928469.484 3390091.503 3659471.888 2964906.429 2782996.449 2836876.643 3018972.454 3374971.458 0.982023613 0.867702 1.004480051 1.084297137 0.878498223 0.824598514 0.840563151 0.894517922 1 21.68644387 3.119613693 19.70762316 0.881774657 0.978205621 0.322047561 0.069355912 2.543567649 419.8520152 0.021845387 0.024770441 1317.084663 -3.119613693 0.096430964 AGTQIENIEEDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGTQIENIEEDFR 13 0 P12814-3;P12814;P12814-2;P12814-4;P35609-2;P35609;G3V2N5;A0A494C1A0;Q08043;A0A494C166;A0A494C033;A0A087WSZ2;G3V5M4;A0A494C0Q3;G3V380 P12814-3 ACTN1;ACTN2;ACTN3 Alpha-actinin-1;Alpha-actinin-2;Alpha-actinin-3 0 159.64 0.00010521 34169000 48002 45838 43592 44053 44767 41620 39132 53419 114030 FALSE TRUE 41658.41408 45536.88716 64673.23701 54055.90696 43876.22429 43221.14833 35336.98466 41995.76256 100549.5033 0.414307507 0.45288028 0.643197976 0.537604913 0.436364406 0.429849446 0.351438679 0.417662556 1 16.61754643 1.235865902 24.98970983 1.000000723 0.459483294 0.820091366 0.079424196 33.48114987 310427.9213 0.144215491 0.021564223 17.2133699 -1.235865902 -0.54051743 AGTQIENIEEDFRDGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AGTQIENIEEDFRDGLK 17 1 P12814-3;P12814;P12814-2;P12814-4;G3V2N5;G3V5M4;G3V380 P12814-3 ACTN1 Alpha-actinin-1 0 ;;;; 272.76 1.11E-35 1097153000 984606 834578 589076.6 722551 759930 689789 922701 1129306 802747 FALSE TRUE 854487.8224 829095.6022 873956.0141 886617.2481 744808.8798 716325.6292 833217.599 887812.7002 707847.1642 1.207164294 1.171291833 1.234667677 1.252554637 1.052217085 1.011977819 1.177115119 1.254243494 1 19.43307837 3.24987463 24.99335111 1.119995984 1.214499633 0.337489155 0.078684748 343.2243657 758199.5043 0.02519108 0.032225155 1777.766137 -3.24987463 0.09450365 AGVLAGHDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 ;;;;;;; 155.42 1.27E-05 7583510000 9619190 8794020 6569240 8984710 10132210 13592170 7217950 10586770 10667050 FALSE TRUE 8347989.67 8736251.504 9746146.437 11024825.73 9930598.844 14115069.58 6517954.32 8322871.622 9406003.501 0.887517177 0.928795264 1.036162323 1.172105212 1.055772395 1.500644729 0.692956825 0.884846749 1 23.16515044 AGVLAHLEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 AGVLAHLEEER 11 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ;;;;;; 195.51 6.36E-08 25607891900 6582372 6757680.1 4436572.4 5516356.6 6321411.4 6679563 6526172 6982800 6841817 FALSE TRUE 5712494.863 6713288.454 6582113.652 6768929.678 6195627.681 6936530.111 5893264.844 5489582.56 6032985.188 0.946876991 1.112763954 1.09102102 1.121986789 1.026958875 1.149767469 0.976840595 0.909928069 1 22.52444061 2.078753628 6.955255189 0.947006358 1.076974681 0.440131826 0.060043659 0.16457396 11.97785385 0.023171625 0.015527551 119.8819028 -2.078753628 0.129968323 AGVVGPELHEQLLSAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGVVGPELHEQLLSAEK 17 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 204.13 9.06E-12 175230000 514930 412240 261440 321760 385120 345840 419410 469190 486410 FALSE TRUE 446880.6958 409531.9683 387873.2585 394820.5258 377456.8655 359144.6886 378735.6828 368857.3697 428907.1639 1.041905413 0.954826598 0.904329167 0.920526769 0.880043276 0.837348309 0.883024847 0.859993492 1 18.71030589 4.967516608 1.053921829 0.887454926 1.185542638 0.533487543 0.043266749 2.007543203 1.331079015 0.013175699 0.749923449 92793.29754 -4.967516608 0.298087712 AGVVNGTGAPGQS(ph)PGAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGVVNGTGAPGQSPGAGR 18 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;Q13330-2 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 AGVVNGTGAPGQS(1)PGAGR;AGVVNGTGAPGQS(1)PGAGR 262.63 7.92E-31 256150000 179539 170497 106724 132906 181922 168566 177376 197153 176973 TRUE FALSE 155812.4663 169376.994 158336.0834 163084.3386 178302.1081 175050.8431 160174.1028 154993.3652 156051.4535 0.998468535 1.085391966 1.014640234 1.045067732 1.142585372 1.121750802 1.026418525 0.993219619 1 17.25166227 2.00865533 24.57182641 1.00023356 1.0691487 0.322650456 0.043486615 179.7849616 510393.5908 0.018687849 0.012577241 102.0129555 -2.00865533 0.06891514 AGWGS(ph)PCHLSGESVILLGPTVGTESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AGWGSPCHLSGESVILLGPTVGTESK 26 0 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4;A8MXE8;Q7Z5J4-4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 AGWGS(0.84)PCHLS(0.151)GES(0.009)VILLGPTVGTESK;AGWGS(0.853)PCHLS(0.145)GES(0.002)VILLGPTVGTESK 183.47 1.11E-17 198000000 351280 352860 95686 246330 388590 305930 392790 477190 442210 TRUE FALSE 304857.458 350542.0394 141960.0697 302262.9914 380857.8193 317699.3251 354697.2863 375146.632 389932.4376 0.78182123 0.898981479 0.364063248 0.775167599 0.976727716 0.8147548 0.909637804 0.962081109 1 18.57286465 3.416585994 5.818009027 0.926416399 0.682439194 0.401333647 0.141643321 0.200199658 13.45024759 0.040965298 0.053445383 2609.672412 -3.416585994 -0.243977205 AGYTDKVVIGMDVAASEFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AGYTDKVVIGMDVAASEFFR 20 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;; 191.22 1.40E-17 1920130000 5013187 4648864 2113584 2338774 3884823 3730911 4668362 5668250 1285464 FALSE TRUE 4350681.636 4618325.306 3135720.292 2869828.383 3807522.623 3874441.56 4215624.972 4456138.848 1133497.91 3.838279362 4.074401253 2.766410298 2.531833854 3.359090994 3.418128543 3.719129019 3.931316333 1 20.1123503 4.247753605 24.79841023 3.103348739 3.956340719 0.186075018 0.824709808 333.8117522 900447.5498 0.205411199 0.527225726 17691.04982 -4.247753605 0.85299198 AHAHLDTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHAHLDTGR 9 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 76.899 0.079393 13936000 14487 13454 9267.9 10173 12411 19070 9205.8 12431 12422 FALSE TRUE 12572.50624 13365.61979 13749.88744 12482.93513 12164.04538 19803.63524 8313.022933 9772.727388 10953.48531 1.147808746 1.22021616 1.25529793 1.139631339 1.110518254 1.807975697 0.758938611 0.892202537 1 13.41910238 AHAS(ph)PFSGALTPSAPPGPEMNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 AHASPFSGALTPSAPPGPEMNR 22 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 AHAS(0.817)PFS(0.183)GALTPSAPPGPEMNR;AHAS(0.993)PFS(0.007)GALTPSAPPGPEMNR;AHAS(0.993)PFS(0.007)GALTPSAPPGPEMNR;AHAS(0.999)PFS(0.001)GALTPSAPPGPEMNR;AHAS(0.998)PFS(0.002)GALTPSAPPGPEMNR;AHAS(0.999)PFS(0.001)GALTPSAPPGPEMNR;AHAS(0.955)PFS(0.045)GALTPSAPPGPEMNR 242.8 1.04E-30 3517660000 1208097 1301092 725513 816119 1119765 1098451 948580 1218652 1114165 TRUE FALSE 1048443.921 1292545.041 1076373.513 1001431.293 1097483.867 1140709.121 856586.8576 958052.7534 982449.683 1.067173148 1.31563485 1.09560167 1.019320694 1.117089136 1.161086558 0.871888782 0.975167248 1 19.90602399 2.676539049 0.647455705 0.934269207 1.173195646 0.357548729 0.095295757 0.919507025 0.970914087 0.138431577 0.085485913 474.8309831 -2.676539049 0.238926439 AHATGAGPAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AHATGAGPAGR 11 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;; 166.97 1.98E-05 159203000 92824 98442 35173.5 45595.4 76496 95026 74316 91323 103673 FALSE TRUE 80557.07321 97795.32802 52183.52225 55948.53245 74973.87926 98681.71171 67108.84576 71794.28713 91416.89604 0.881205518 1.06977301 0.570830169 0.612015228 0.820131535 1.07946907 0.734096744 0.785350304 1 16.48017321 2.994522164 24.95430895 0.875603878 0.779638866 0.09065291 0.167131934 769.7467526 3506610.227 0.054353685 0.05985901 987.4660287 -2.994522164 -0.095965013 AHDGGIYAISWSPDSTHLLSASGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AHDGGIYAISWSPDSTHLLSASGDK 25 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 ; 229.86 1.73E-34 1231250000 1738070 1504510 593990 1198950 1534600 1287500 1645890 1894500 2170360 FALSE TRUE 1508379.646 1494626.775 881245.5508 1471189.922 1504064.462 1337030.958 1486271.841 1489375.918 1913782.513 0.788166699 0.780980474 0.460473196 0.768734123 0.785911906 0.698632655 0.776614809 0.778236768 1 20.86799546 -0.62718888 0.922172338 10 0.709378123 0.44660793 0.097205758 57.7113132 1.935509425 1042.162939 0.033262218 0.235945185 0.62718888 -9.290621877 AHEAQDAGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHEAQDAGYR 10 0 P16298-3;P16298;P16298-4;G3V111;Q5F2F8;P48454-2;P48454;P16298-2;P48454-3;Q08209-3;Q08209-2;Q08209;E7ETC2;Q08209-5;E5RJH4;H0YB04;H0YC26 P16298-3;Q08209-3 PPP3CB;PPP3CC;PPP3CA Serine/threonine-protein phosphatase 2B catalytic subunit beta isoform;Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 2B catalytic subunit gamma isoform;Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform 0 141.1 3.81E-05 351000000 218610 167200 119280 139150 126850 147010 177880 187800 160240 FALSE TRUE 189720.1346 166101.6522 176964.207 170746.1343 124325.9332 152665.5698 160629.225 147640.4315 141296.6097 1.342708328 1.175552991 1.252430665 1.208423433 0.87989325 1.080461662 1.136822924 1.044897197 1 17.10836732 3.416469344 10.73179164 1.041249673 1.245724817 0.664532283 0.076593921 0.310419414 53.38180088 0.021725918 0.028054731 2608.971556 -3.416469344 0.204475144 AHEEQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 133.81 0.0032352 1084480000 1975680 1715160 1226800 1364880 1300520 1499480 1930890 2087520 1961050 FALSE TRUE 1714588.882 1703893.001 1820084.583 1674796.865 1274642.196 1557165.966 1743632.585 1641120.093 1729216.903 0.991540667 0.985355277 1.052548457 0.968529085 0.73712106 0.900503553 1.008336538 0.949053927 1 20.72168741 3.474088806 24.99990743 0.921651766 1.00789719 0.232230327 0.075771448 150.5793812 1241385.672 0.023322052 0.030266444 2979.125549 -3.474088806 0.086245424 AHFLDADPGFVHSDGTISHHDMYDYLHLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHFLDADPGFVHSDGTISHHDMYDYLHLSR 30 0 M0R1K3;Q15102 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 237.28 5.44E-46 370300000 106410 152390 16878 62290 169980 186440 128230 135240 124660 FALSE TRUE 92347.64889 151388.9401 25040.25725 76433.89654 166597.7306 193612.4674 115794.2743 106319.9784 109922.8368 0.840113407 1.377229195 0.227798499 0.695341375 1.515587983 1.761348898 1.053414174 0.96722375 1 16.74613162 3.254480736 24.99495128 1.232612724 0.787605272 0.294627784 0.363409641 362.0552626 568431.7858 0.112424517 0.144655285 1796.721383 -3.254480736 -0.445007452 AHFNAMFQPS(ph)SPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHFNAMFQPSSPTR 14 0 Q8WUA4;H0Y4Q6 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 AHFNAMFQPS(0.566)S(0.419)PT(0.015)R 79.97 0.011339 431840000 197560 167490 103970 113420 188130 193510 140090 179360 166780 TRUE FALSE 171451.9454 166389.7472 154250.2398 139173.7445 184386.5811 200954.4549 126504.0934 141005.2598 147063.4584 1.165836485 1.131414622 1.048868573 0.946351636 1.253789235 1.366447227 0.860200724 0.958805548 1 17.16607929 2.207193831 24.99999989 0.940344389 1.141752422 0.425799796 0.115882428 211.1408706 168282.337 0.050273808 0.033898303 161.1364648 -2.207193831 0.201408033 AHFNAMFQPSS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 AHFNAMFQPSSPTR 14 0 Q8WUA4;H0Y4Q6 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 AHFNAMFQPS(0.132)S(0.679)PT(0.189)R;AHFNAMFQPSS(0.997)PT(0.003)R;AHFNAMFQPS(0.172)S(0.791)PT(0.038)R;AHFNAMFQPS(0.037)S(0.677)PT(0.286)R;AHFNAMFQPS(0.021)S(0.723)PT(0.256)R;AHFNAMFQPS(0.041)S(0.957)PT(0.002)R;AHFNAMFQPS(0.252)S(0.746)PT(0.002)R;AHFNAMFQPS(0.072)S(0.927)PT(0.001)R 249.73 3.74E-18 3178470000 1624578 1462755 930048 1158271 1453835 1509884 1321472 1635119 1558200 TRUE FALSE 1409885.901 1453146.066 1379822.324 1421274.134 1424906.528 1567970.215 1193315.849 1285461.526 1373991.371 1.026124276 1.05760931 1.004243806 1.034412707 1.037056388 1.141179084 0.868503161 0.935567394 1 20.38994151 2.229111213 24.99998402 0.932115154 1.047054502 0.568439743 0.047338316 140.8026761 372513.6523 0.018898735 0.012933506 169.4771736 -2.229111213 0.114939348 AHFNLDESGVLSLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AHFNLDESGVLSLDR 15 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 230.38 3.36E-13 482310000 208723 188876 141629 170599 195972 260820 179400 196978 195834 FALSE TRUE 181139.7267 187635.2611 210121.2581 209336.1104 192072.5406 270853.9142 162001.8156 154855.7876 172682.7276 1.048974204 1.08658963 1.2168053 1.212258535 1.11228577 1.568506115 0.93814719 0.896764776 1 17.39776426 2.07099184 25 0.933903835 1.202953035 0.4260822 0.143420927 39.81320369 14019.52567 0.05737612 0.038682975 117.7583846 -2.07099184 0.2690492 AHFPLDVQWNDLDYMDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AHFPLDVQWNDLDYMDSR 18 0 P10253 P10253 GAA Lysosomal alpha-glucosidase;76 kDa lysosomal alpha-glucosidase;70 kDa lysosomal alpha-glucosidase 0 ;;;;; 288.21 2.74E-40 825361000 723128 620855 404421 480403 614524 704161 546698 687403 606010 FALSE TRUE 627564.8026 616776.5626 600000.3483 589485.8437 602296.1747 731250.5293 493679.3121 540407.2178 534368.1882 1.174405244 1.154216468 1.122821982 1.103145465 1.12711832 1.368439487 0.923856103 1.011301252 1 19.0274746 2.202198804 24.9999981 0.982971019 1.166261413 0.591356335 0.076795202 124.0337925 85276.66893 0.030877442 0.020818267 159.293775 -2.202198804 0.183290394 AHGCFPEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AHGCFPEGR 9 0 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 0 ;; 84.213 0.015645 699355000 478460 542680 303361 352487 385464 594190 397931 449900 423787 FALSE TRUE 415230.2987 539115.0993 450067.3943 432524.5608 377794.0205 617048.8738 359339.7129 353692.3861 373687.3836 1.111170237 1.442690128 1.204395476 1.157450264 1.010989498 1.651243528 0.961605151 0.946492715 1 18.51147233 2.096217644 24.51074192 0.964070018 1.25676318 0.37568533 0.178264766 12.24579839 3108.069333 0.069155455 0.04662459 124.800879 -2.096217644 0.292693162 AHGCFQDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AHGCFQDGR 9 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 0 ; 166.09 6.10E-05 151881000 178050 152982 106625 113220 141197 161358 160345 174864 190778 FALSE TRUE 154520.2414 151977.0512 158189.2066 138928.3315 138387.4559 167565.5467 144794.7666 137470.6944 168224.4422 0.918536209 0.903418369 0.940346151 0.825851046 0.822635844 0.996083236 0.860723714 0.81718621 1 17.36002781 3.781177426 24.9996604 0.880008695 0.919032052 0.047733089 0.065923198 1444.075909 847111.5676 0.017371927 0.030088554 6041.954157 -3.781177426 0.039023357 AHGGYSVFAGVGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHGGYSVFAGVGER 14 0 P06576;H0YH81;F8W079;F8W0P7;H0YI37 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 94.728 0.00405 445870000 231660 204860 135460 263300 282060 304950 220220 278140 226910 FALSE TRUE 201045.544 203514.2612 200968.9091 323086.2893 276447.5578 316681.6238 198863.0983 218661.9255 200084.9583 1.004800889 1.017139234 1.004417877 1.614745516 1.381650876 1.582735786 0.993893294 1.092845396 1 17.61025319 AHGLLAEENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AHGLLAEENR 10 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;;; 133.83 0.00018668 1814720000 1082020 1203890 737750 902071 1148865 1200159 1120535 1138703 1121496 FALSE TRUE 939028.3155 1195981.567 1094528.368 1106900.008 1126004.834 1246329.893 1011865.688 895200.2248 988914.0205 0.949555063 1.209388827 1.106798311 1.11930864 1.138627637 1.260301571 1.023208962 0.905235649 1 19.91548557 2.007613265 24.56724449 0.951360934 1.133732282 0.454946859 0.082405293 106.9483656 345109.9121 0.031662871 0.021297316 101.7684745 -2.007613265 0.182371348 AHGNSGMVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 AHGNSGMVR 9 0 C9K025;P18077 C9K025 RPL35A 60S ribosomal protein L35a 0 ;;;;;;;;;;;; 153.97 7.68E-05 1783632000 712855 1052859 536016 623812 803158 981141 988916 971908 1003859 FALSE TRUE 618649.4056 1045942.7 795235.1305 765458.049 787176.7272 1018886.129 893011.0785 764073.0376 885183.9326 0.698893623 1.18161058 0.898384055 0.864744626 0.889280406 1.151044536 1.008842395 0.863179967 1 19.75561774 AHGPGLEGGLVGKPAEFTIDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHGPGLEGGLVGKPAEFTIDTK 22 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 229.38 1.72E-26 748470000 895580 715520 581040 602420 577300 457060 751390 966410 1127700 FALSE TRUE 777226.8339 710819.702 862032.8875 739208.6684 565812.8595 474643.394 678520.3135 759750.7421 994384.5907 0.781615927 0.714833786 0.866900891 0.743383069 0.569008073 0.477323762 0.682351999 0.764041146 1 19.92344441 1.253038848 2.578939811 1.067247499 0.688822382 0.449905247 0.107141733 0.510480968 3.871255581 0.420312002 0.031344048 17.90766032 -1.253038848 -0.378425117 AHGS(ph)FSHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHGSFSHVR 9 0 Q8N3D4 Q8N3D4 EHBP1L1 EH domain-binding protein 1-like protein 1 1 AHGS(0.997)FS(0.003)HVR 89.561 0.0077448 121850000 75513 77271 60736 74378 46252 79573 65764 68041 75747 TRUE FALSE 65533.76572 76763.40171 90108.13275 91266.6617 45331.67569 82634.2248 59386.2174 53490.96165 66792.27595 0.981157848 1.149285612 1.349080136 1.36642539 0.678696377 1.237182348 0.889118039 0.800855501 1 16.02739365 3.249581428 24.99967079 0.919527727 1.216872322 0.400332904 0.176497529 219.8277053 498655.5156 0.051040868 0.065247081 1776.566334 -3.249581428 0.297344595 AHGVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 AHGVDK 6 0 P30043;M0R192;A0A2R8Y7Y9;M0QZL1 P30043 BLVRB Flavin reductase (NADPH) 0 ;;;;;; 121.68 0.019546 4443594000 11682790 10313980 7019590 8571060 5724610 8071690 11041940 13611650 15392580 FALSE TRUE 10138879.7 10246226.79 10414287.2 10517250.17 5610701.461 8382213.137 9971094.358 10700904.57 13572886.73 0.746995087 0.754904022 0.767286091 0.774872021 0.413375693 0.617570404 0.734633285 0.788402997 1 23.69422425 1.245987939 1.715743904 1.114355136 0.681543095 0.463797193 0.107356102 0.958651657 2.646566236 0.694807727 0.032455762 17.61927114 -1.245987939 -0.432812041 AHHAACKEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHHAACKEEK 10 1 Q9UNF0-2;Q9UNF0;A0A0U1RR22 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 100.72 0.0022951 10697000 30716 25026 15914 15614 14286 15693 35967 34709 6342.4 FALSE TRUE 26656.80278 24861.60256 23610.06363 19159.39735 14001.73655 16296.71986 32478.92588 27286.75046 5592.608697 4.766434453 4.445439312 4.22165485 3.42584264 2.503614558 2.913974631 5.807473334 4.87907378 1 12.44930568 4.012948664 3.022142049 3.667027899 4.606041729 0.11384428 1.299929525 0.742495463 13.86769773 0.375184819 0.843911069 10302.64331 -4.012948664 0.93901383 AHIAQLCEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AHIAQLCEK 9 0 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ;;;;; 150.27 8.56E-05 6115360000 9321930 9872270 6477980 7129800 8703820 8183930 10243500 11250220 11187940 FALSE TRUE 8090013.332 9807418.408 9610752.796 8748730.062 8530631.011 8498771.083 9250086.947 8844448.002 9865314.479 0.820046168 0.994131351 0.974196293 0.886817149 0.864709486 0.861479997 0.937637312 0.896519622 1 23.23393361 1.234420817 24.95896988 1.000000138 0.907474428 0.243370918 0.052710731 190.8185954 1150289.162 0.096273696 0.012826329 17.1561888 -1.234420817 -0.09252571 AHIVFDFHQAADGIQEQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AHIVFDFHQAADGIQEQQR 19 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ;;; 324.63 1.09E-62 1433950000 748840 692650 496798 514510 649690 732600 650760 755510 662510 FALSE TRUE 649878.8967 688099.9365 737051.1745 631337.3593 636762.4401 760783.5961 587649.3954 593950.0659 584188.8225 1.112446647 1.177872479 1.261665999 1.080707701 1.08999422 1.302290572 1.005923723 1.016709055 1 19.15607523 2.19720817 24.98982527 1.009385773 1.167507901 0.548293852 0.069815355 110.5535873 66808.24863 0.027955826 0.01884804 157.47375 -2.19720817 0.158122128 AHLDHIPDYTPPLLTTIS(ph)PEQESDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHLDHIPDYTPPLLTTISPEQESDER 26 0 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;K7EM61 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 AHLDHIPDYTPPLLTT(0.009)IS(0.991)PEQESDER 178.63 4.03E-17 183540000 73901 71453 59325 57456 58936 76413 62095 72098 76311 TRUE FALSE 64134.79561 70983.62054 88014.76843 70502.26296 57763.28891 79352.65756 56073.03646 56680.40377 67289.60051 0.953116011 1.054897339 1.307999568 1.047743818 0.858428174 1.179270748 0.8333091 0.842335269 1 16.03809594 2.558097742 1.04178117 0.882750048 1.089568757 0.188527419 0.136457004 0.786860243 1.817449887 0.107131542 0.063970556 361.4912108 -2.558097742 0.206818709 AHLILFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AHLILFK 7 0 Q9H993;F5GZY1 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 ; 95.957 0.013085 970090000 2620000 2701600 1741850 2005370 2414600 2319300 2824500 3155700 3418800 FALSE TRUE 2273760.362 2683853.012 2584214.486 2460719.909 2366554.184 2408524.972 2550580.425 2480878.113 3014633.359 0.754241094 0.890275099 0.857223476 0.816258435 0.785022224 0.798944576 0.846066543 0.82294522 1 21.52355112 1.238376052 24.99193839 1.000000195 0.823880346 0.684452171 0.038082651 2.586777189 349322.0931 0.051183119 0.009105192 17.3131484 -1.238376052 -0.176119849 AHLLAEVIENLECDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHLLAEVIENLECDPR 16 0 Q96C86;A0A3B3ITF0 Q96C86 DCPS m7GpppX diphosphatase 0 136.48 1.72E-05 104840000 99881 89198 45083 57798 82393 77605 85011 96186 77325 FALSE TRUE 86681.47278 88612.05246 66885.28959 70921.91929 80753.5405 80590.51457 76766.6463 75617.37242 68183.72659 1.271292684 1.29960706 0.98095679 1.040159036 1.184352111 1.181961131 1.125879299 1.109023754 1 16.05713983 4.259855643 24.99977526 1.097673104 1.285450068 0.584043761 0.06864857 182.7318714 214518.4772 0.017961474 0.047422109 18190.96103 -4.259855643 0.187776964 AHLLDNTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AHLLDNTER 9 0 Q96AJ9-1;Q96AJ9 Q96AJ9-1 VTI1A Vesicle transport through interaction with t-SNAREs homolog 1A 0 ;; 126.31 0.000477 791070000 687130 675900 439512 489680 682860 729940 594850 738070 690600 FALSE TRUE 596324.0295 671459.9684 652061.4733 600869.3283 669272.422 758021.2641 537161.5386 580239.4742 608958.0547 0.979253045 1.102637469 1.070782246 0.986717104 1.099045192 1.244784034 0.882099406 0.952839805 1 19.21598333 2.201613801 24.99993003 0.943997234 1.077674926 0.404361805 0.07750195 170.7902685 115563.4495 0.031578878 0.021291071 159.0793474 -2.201613801 0.133677691 AHLMEIQVNGGTVAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHLMEIQVNGGTVAEK 16 0 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 136.01 3.36E-05 0 96603 86898 60896 70584 71730 77049 86037 117420 102010 FALSE TRUE 83836.66879 86327.16132 90345.50928 86611.17601 70302.71334 80013.12489 77693.14498 92310.64676 89950.49401 0.932031221 0.95971859 1.004391474 0.962876046 0.781571175 0.889524018 0.863732277 1.026238352 1 16.45684358 1.682004945 7.871403663 1.012374798 0.914766033 0.310461821 0.061549474 0.15607916 17.64426699 0.038896518 0.017256964 48.08448231 -1.682004945 -0.097608766 AHLTVGQAAAGGS(ph)GNLLTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AHLTVGQAAAGGSGNLLTER 20 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 1 AHLTVGQAAAGGS(1)GNLLTER;AHLTVGQAAAGGS(1)GNLLTER;AHLTVGQAAAGGS(1)GNLLTER;AHLTVGQAAAGGS(1)GNLLTER 290.1 1.25E-54 2677170000 2306510 1774000 883330 1428460 1702630 1959390 1434310 1707720 1600860 TRUE FALSE 2001698.86 1762346.477 1310511.343 1752813.676 1668750.994 2034769.001 1295210.837 1342537.367 1411608.155 1.418027271 1.248467198 0.928381816 1.241714048 1.182163045 1.441454553 0.917542756 0.951069433 1 20.42890824 2.211255309 24.99999784 0.95352329 1.226425053 0.47839895 0.140601263 198.2533111 181513.9196 0.058156591 0.039219677 162.6504649 -2.211255309 0.272901763 AHMGMFTELAILYSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHMGMFTELAILYSK 15 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;A0A087WV74;A0A087WXH4;P53675;P53675-2 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 105.14 0.0013386 388440000 648010 549200 454150 487260 427860 413120 620920 732060 770680 FALSE TRUE 562373.8367 545592.269 673778.459 597899.8303 419346.4231 429012.9937 560703.274 575514.6659 679571.0884 0.827542322 0.80284797 0.991476051 0.879819405 0.617075138 0.631299655 0.825084062 0.846879268 1 19.37426495 5.147500418 15.35414297 0.82024498 2.172580756 0 0.126136979 22658087.26 2106526.07 0.032795705 1076491835 140443.1036 -5.147500418 1.352335776 AHPPELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AHPPELK 7 0 P62308;A8MWD9;C9JVQ0 P62308 SNRPG;SNRPGP15 Small nuclear ribonucleoprotein G;Putative small nuclear ribonucleoprotein G-like protein 15 0 ; 108.24 0.0072977 1403360000 1213420 1110430 883440 910900 958180 1003770 1051740 1204760 1264240 FALSE TRUE 1053063.473 1103135.512 1310674.539 1117733.767 939114.0926 1042385.681 949742.4167 947131.4495 1114782.987 0.944635399 0.9895518 1.175721691 1.002646954 0.842418752 0.935057041 0.851952736 0.849610606 1 20.08833146 3.36873326 5.666433339 0.889325817 1.040665334 0.441296657 0.074376457 0.179521824 8.303677035 0.021587058 0.027986394 2337.401184 -3.36873326 0.151339517 AHQGTGAGIS(ph)PVILNSGEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AHQGTGAGISPVILNSGEGK 20 0 Q8IZD4;Q8IZD4-2;F5GZK9 Q8IZD4 DCP1B mRNA-decapping enzyme 1B 1 AHQGT(0.011)GAGIS(0.989)PVILNSGEGK;AHQGTGAGIS(1)PVILNSGEGK 206.3 5.01E-22 831630000 1280450 1049640 632220 773350 870050 738400 979310 1057090 971690 TRUE FALSE 1111235.288 1042744.846 937963.7066 948950.9374 852737.7072 766806.7258 884336.6669 831039.5298 856817.9152 1.296932836 1.216997016 1.094705993 1.10752929 0.995237952 0.89494712 1.032117386 0.969913811 1 19.70862912 4.243178485 0.824114478 0.97448163 1.367175418 0.869648756 0.042999324 0.445835041 0.384144715 0.017653027 0.141527429 17505.65983 -4.243178485 0.392693788 AHQLVHEGYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AHQLVHEGYK 10 0 O00743;O00743-2;O00743-3 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed" 0 ;;; 196.76 1.89E-07 913530000 1355010 1332000 864460 1122000 1199390 1068060 1278580 1503770 1431780 FALSE TRUE 1175941.995 1323250.004 1282515.747 1376767.249 1175524.486 1109148.959 1154583.508 1182200.488 1262516.599 0.931426958 1.048105035 1.015840701 1.090494374 0.931096261 0.878522278 0.914509567 0.936384114 1 20.26787093 3.165921296 11.6143195 0.928524869 1.022933187 0.451252465 0.048869706 0.495559302 77.16877083 0.014577783 0.016536143 1465.282275 -3.165921296 0.094408318 AHQLVMEGYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHQLVMEGYK 10 0 P60510;H3BTA2 P60510 PPP4C Serine/threonine-protein phosphatase 4 catalytic subunit;Serine/threonine-protein phosphatase 0 88.441 0.013352 0 448870 453430 341880 426140 494780 491060 469260 560820 519240 FALSE TRUE 389550.6922 450451.3885 507214.3115 522901.6001 484934.846 509951.396 423751.2374 440893.0073 457856.0387 0.850814796 0.983827558 1.10780304 1.142065531 1.059142623 1.113781086 0.925511955 0.962951168 1 18.80453453 2.226275238 24.99980594 0.961293604 1.048415581 0.167786181 0.083455819 398.948082 811822.0145 0.035807292 0.024336103 168.3740809 -2.226275238 0.087121978 AHQLVMEGYNWCHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AHQLVMEGYNWCHDR 15 0 P67775;P62714;H0YC23 P67775 PPP2CA;PPP2CB Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform 0 ;;;;; 245.19 2.55E-18 5533653000 1777250 1604460 921873 1145417 1415923 1551440 1401908 1422323 1228393 FALSE TRUE 1542381.91 1593920.197 1367693.866 1405501.436 1387748.903 1611124.901 1265951.178 1118170.295 1083173.779 1.423946868 1.471527679 1.262672613 1.29757705 1.281187682 1.487411283 1.168742452 1.032309235 1 20.04683329 2.002554619 3.72643343 1.030830439 1.36289275 0.781586992 0.078228085 0.104438062 3.128491002 0.041915894 0.022784605 100.5899563 -2.002554619 0.332062311 AHQSYCHSNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AHQSYCHSNK 10 0 Q96S59-2;Q96S59-3;Q96S59 Q96S59-2 RANBP9 Ran-binding protein 9 0 ; 136.02 7.44E-05 51570000 51574 65312 20929 36686 61868 78925 70693 69603 68956 FALSE TRUE 44758.36523 64882.96117 31050.3344 45016.11701 60636.94784 81961.29582 63837.20374 54718.9401 60804.10023 0.736107681 1.067082005 0.510661851 0.740346734 0.997250968 1.347956725 1.049883207 0.899921878 1 15.89188099 3.169435291 5.24658287 1.056913949 0.767325905 0.419849989 0.173603001 0.220587273 11.28139988 0.055218876 0.063734972 1477.186369 -3.169435291 -0.289588044 AHQVVEDGYEFFAK ddPTM_MDA-MB-175_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 0 120.92 0.00011757 1304100000 1161900 882910 735120 830710 888010 767040 1000500 1149000 1054500 FALSE TRUE 1008351.971 877110.1061 1090626.491 1019335.402 870340.3384 796548.5251 903471.664 903295.2915 929838.2113 1.084438087 0.943293248 1.172920706 1.096250283 0.936012661 0.856652819 0.971643941 0.97145426 1 19.82662019 3.234962843 24.99917227 0.947502257 1.071922931 0.474018354 0.066493749 86.30322502 599679.116 0.020324419 0.023959644 1717.761415 -3.234962843 0.124420674 AHS(ph)IQIMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHSIQIMK 8 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 1 AHS(1)IQIMK 65.5 0.041294 258600000 360240 317120 204290 248320 330170 267360 337560 387600 330620 TRUE FALSE 312633.3713 315036.8178 303085.3273 304704.8513 323600.263 277645.5122 304823.4832 304714.7563 291534.4802 1.072371855 1.080615979 1.039620861 1.045176032 1.109989675 0.95235909 1.045582954 1.045210008 1 18.153307 2.758008165 24.99730164 1.019428464 1.067151999 0.435869518 0.032504726 938.2050038 1205940.801 0.010419476 0.01040454 572.8068 -2.758008165 0.047723535 AHS(ph)LLFENSDSFSEDSSTLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHSLLFENSDSFSEDSSTLGR 21 0 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 AHS(0.998)LLFENS(0.002)DSFSEDSSTLGR 126.99 1.32E-05 78345000 55142 50836 29243 41146 49761 44084 46635 60829 58075 TRUE FALSE 47854.84499 50502.05497 43385.01261 50488.82818 48770.85346 45779.94001 42112.34488 47821.19172 51209.43966 0.93449265 0.98618644 0.847207329 0.985928151 0.952380143 0.893974633 0.82235512 0.933835481 1 15.64412215 2.740695028 24.91204589 0.907413568 0.940994781 0.054855462 0.057460319 548.8598777 6406135.967 0.019119958 0.018250553 550.4210414 -2.740695028 0.033581214 VALSEPQPERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VALSEPQPERR 11 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1;H7C1K0 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 94.767 0.013242 422060000 261900 253230 136874 145339 216600 247817 225793 248164 109856 FALSE TRUE 227289.2514 251566.5155 203066.7242 178340.4413 212290.0838 257350.6803 203895.6296 195096.0598 96868.94883 2.34635819 2.59697786 2.09630358 1.841048587 2.1915184 2.656689099 2.104860557 2.014020614 1 16.56374667 1.087952402 1.866045462 0.126186743 2.266579215 0.73334109 0.237897252 0.745085284 1.755959389 3.237370164 0.068717915 12.24481991 -1.087952402 2.140392471 AHS(ph)SPASLQLGAVS(ph)PGTLTPTGVVSGPAATPTAQHLR ddPTM_MDA-MB-175_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(0.712)S(0.248)PAS(0.04)LQLGAVS(0.999)PGT(0.001)LTPTGVVSGPAATPTAQHLR 98.218 0.00010012 144990000 51529 21045 16255 21855 32772 30076 17456 22899 25143 TRUE FALSE 44719.31209 20906.75401 24115.97237 26817.51178 32119.90132 31233.04318 15763.11981 18002.22705 22170.62318 2.017052553 0.942993521 1.087744452 1.209596661 1.448759516 1.408758018 0.710991282 0.811985613 1 14.4363617 8 0.120617916 0.41626568 4.021116684 0.337376566 0.306810601 280.3570056 3.013965014 11.29824071 169.5475032 100000000 -8 3.604851004 AHSEVFTKPSGQQTLS(ph)PDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHSEVFTKPSGQQTLSPDR 19 1 F5H212;P15822;A0A0D9SFF3;P15822-2;P15822-3 F5H212 HIVEP1 Zinc finger protein 40 1 AHSEVFTKPSGQQT(0.04)LS(0.96)PDR 168.56 9.56E-12 116290000 162620 118780 77144 99475 120390 106570 115260 145240 129150 TRUE FALSE 141129.355 117999.7264 114451.0964 122062.3191 117994.4745 110669.8169 104082.1029 114181.5563 113882.0341 1.239259169 1.036157523 1.004996945 1.071831216 1.036111406 0.971793468 0.913946644 1.002630109 1 16.79718064 7.999999943 0.906630316 0.990476046 128.1543847 0.769049838 0.040759108 487.5735347 1.033996435 0.014350218 128331.0378 99999986.99 -7.999999943 127.1639087 AHSIQIMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AHSIQIMK 8 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 81.548 0.022576 2556700000 5324800 5065700 3432000 4022300 4676500 4452500 5261400 5968800 5656500 FALSE TRUE 4621114.189 5032423.083 5091726.679 4935624.692 4583446.799 4623790.556 4751150.238 4692418.569 4987795.014 0.926484384 1.008947455 1.020837197 0.989540404 0.918932471 0.927020967 0.952555232 0.940780156 1 22.24997074 3.26748553 22.78765504 0.946283554 0.990515323 0.255146482 0.032376738 98.50545167 77602.99909 0.009235067 0.011918735 1851.33721 -3.26748553 0.04423177 AHSLGGLDPAFTS(ph)TEDLNCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AHSLGGLDPAFTSTEDLNCK 20 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 AHSLGGLDPAFT(0.003)S(0.883)T(0.115)EDLNCK;AHSLGGLDPAFT(0.001)S(0.988)T(0.01)EDLNCK;AHSLGGLDPAFTS(0.849)T(0.151)EDLNCK 251.02 3.50E-31 587830000 847250 644010 542050 659370 606270 491080 646770 822010 1213610 TRUE FALSE 735283.7658 639779.4559 804187.193 809090.0363 594206.4131 509972.1654 584046.3449 646229.5584 1070138.408 0.687092212 0.597847391 0.751479609 0.756061113 0.555261271 0.476547857 0.545767109 0.603874745 1 20.02936597 1.237252163 24.9784207 1.000000466 0.618232915 0.640252689 0.089073011 23.42352274 446976.4843 0.144651476 0.023867346 17.26840251 -1.237252163 -0.381767551 AHSLGGLDPAFTS(ph)TEDLNCKENLEQDLGDDNSNDLLLSCPHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AHSLGGLDPAFTSTEDLNCKENLEQDLGDDNSNDLLLSCPHFR 43 1 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 AHSLGGLDPAFT(0.094)S(0.753)T(0.153)EDLNCKENLEQDLGDDNSNDLLLSCPHFR;AHSLGGLDPAFT(0.015)S(0.493)T(0.493)EDLNCKENLEQDLGDDNSNDLLLSCPHFR 277.13 2.98E-81 209181000 133561 83148 52679 59447 71419 74925 53238 99611 39599 TRUE FALSE 115910.5754 82601.79531 78154.7406 72945.34994 69997.90163 77807.41323 48074.98695 78309.96282 34917.65133 3.319541007 2.365617164 2.238258807 2.089068055 2.004656641 2.228311764 1.376810442 2.242704187 1 15.0916689 8 0.403898966 1.697149024 26.79806053 0.644230447 0.364220693 55.8246429 0.778495023 0.321940989 1110.860775 100000000 -8 25.1009115 AHSSPASLQLGAVS(ph)PGTLTPTGVVSGPAATPTAQHLR ddPTM_MDA-MB-175_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 AHSSPASLQLGAVS(0.996)PGT(0.001)LT(0.003)PTGVVSGPAATPTAQHLR 117.15 8.33E-06 365940000 28528 26368 12753 16285 30938 31165 26030 30601 16603 TRUE FALSE 24757.95252 26194.78687 18920.39346 19982.75815 30322.39433 32363.93772 23505.61461 24057.21429 14640.21225 1.691092457 1.789235458 1.292357865 1.364922708 2.07117177 2.210619433 1.605551491 1.643228518 1 13.83764885 AHT(ph)PLNTPDPSTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHTPLNTPDPSTK 13 0 Q9BYW2;H7C3H4;A0A1W2PPX9 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 AHT(1)PLNTPDPSTK 118.31 0.0016109 375460000 797630 600300 450760 496060 656230 595940 799480 886450 819030 TRUE FALSE 692221.1746 596356.5898 668749.0437 608698.0048 643172.3069 618866.1974 721946.5527 696889.5659 722205.2064 0.95848267 0.825743964 0.925982031 0.842832479 0.890567253 0.856911847 0.999641856 0.964946749 1 19.4620493 2.235679925 24.99996574 0.983829483 0.881213017 0.608495509 0.039540243 45.09900664 391381.5627 0.014005467 0.009910986 172.0600024 -2.235679925 -0.102616467 AHT(ph)PTPGIYMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 AHTPTPGIYMGR 12 0 Q13595;Q13595-3;Q13595-4;Q13595-2 Q13595 TRA2A Transformer-2 protein homolog alpha 1 AHT(0.999)PT(0.001)PGIYMGR;AHT(0.994)PT(0.006)PGIYMGR;AHT(0.999)PT(0.001)PGIYMGR;AHT(0.998)PT(0.002)PGIYMGR;AHT(1)PTPGIYMGR;AHT(1)PTPGIYMGR;AHT(0.986)PT(0.014)PGIYMGR;AHT(0.997)PT(0.003)PGIYMGR 150.78 0.0002304 25723390000 8138100 5907090 4834570 6277780 6776890 6641640 5985200 6974450 11190990 TRUE FALSE 7062629.466 5868285.937 7172584.223 7703245.899 6642043.148 6897148.189 5404756.225 5483018.143 9868003.911 0.715710039 0.594678112 0.726852592 0.780628582 0.673088824 0.698940561 0.547705116 0.555635992 1 23.23432686 AHT(ph)PTPGIYMGRPTHSGGGGGGGGGGGGGGGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 15 AHTPTPGIYMGRPTHSGGGGGGGGGGGGGGGGR 33 1 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 AHT(0.813)PT(0.187)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.918)PT(0.082)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.997)PT(0.003)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.982)PT(0.018)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.982)PT(0.018)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.975)PT(0.025)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.997)PT(0.003)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.963)PT(0.037)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.783)PT(0.217)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.741)PT(0.258)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.834)PT(0.166)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.555)PT(0.445)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.837)PT(0.163)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.887)PT(0.113)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.957)PT(0.043)PGIYMGRPTHSGGGGGGGGGGGGGGGGR 316.37 3.58E-104 29434870000 2564788 2024351 1172677 1405912 2366006 2106260 1962921 2354756 1345882 TRUE FALSE 2225844.767 2011052.905 1739787.52 1725145.808 2318927.11 2187289.185 1772557.224 1851209.754 1186773.363 1.875543247 1.694555142 1.465981268 1.453643856 1.953976371 1.843055509 1.493593704 1.559867968 1 20.17861302 0.88047097 1.415860173 9.00E-19 1.68893733 0.607102581 0.17244155 2.268416456 1.975491942 7.089594342 0.052383665 7.5940066 -0.88047097 1.68893733 AHT(ph)SPAPAPRPTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHTSPAPAPRPTPR 14 1 Q96P48-3;Q96P48 Q96P48-3 ARAP1 "Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1" 1 AHT(0.5)S(0.5)PAPAPRPTPR 72.433 0.06247 87494000 56348 49608 40293 47604 38481 51991 49334 52828 64292 TRUE FALSE 48901.46903 49282.12178 59778.82957 58413.21578 37715.30339 53991.12741 44549.59627 41531.14331 56691.473 0.862589494 0.869303957 1.054458923 1.030370401 0.665272948 0.952367694 0.785825344 0.732581835 1 15.79084413 3.261142551 24.99991027 0.8185351 0.955280783 0.23678595 0.112667845 329.2581747 364511.2938 0.032035899 0.041328435 1824.49447 -3.261142551 0.136745683 AHTDFFEAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHTDFFEAFK 10 0 P61201;P61201-2;B4DIH5;H0YKU5 P61201 COPS2 COP9 signalosome complex subunit 2 0 103.26 0.0028386 325230000 937090 884540 576490 642760 826120 692600 881730 1038200 920940 FALSE TRUE 813251.1822 878729.3985 855282.4922 788708.482 809681.8283 719244.7702 796219.9603 816189.0093 812067.5223 1.001457588 1.08208908 1.053215981 0.971235101 0.997062197 0.885695771 0.980484921 1.005075301 1 19.63124017 3.738168533 24.99999985 0.97436806 1.049237706 0.437287694 0.038590357 32.70805565 2085537.219 0.010728428 0.01711692 5472.282799 -3.738168533 0.074869646 AHTMTDDVTFWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 AHTMTDDVTFWK 12 0 A0A087WVQ6;Q00610-2;Q00610;J3KSQ2 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;;; 174.42 2.31E-05 6104510000 13266060 10946224 7367912 9095582 10338610 9455998 11726340 13313610 12964450 FALSE TRUE 11512916.56 10874317.53 10931058.89 11160872.91 10132891.89 9819776.362 10589121.35 10466598.11 11431807.49 1.007095035 0.951233437 0.9561969 0.976299935 0.886377058 0.858987205 0.926285835 0.915568086 1 23.44655019 3.253467844 24.99807082 0.914949536 0.96999332 0.336381539 0.038397386 291.316321 488508.1628 0.011295121 0.014523026 1792.535827 -3.253467844 0.055043784 AHTPT(ph)PGIYMGRPTHSGGGGGGGGGGGGGGGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHTPTPGIYMGRPTHSGGGGGGGGGGGGGGGGR 33 1 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 AHT(0.449)PT(0.551)PGIYMGRPTHSGGGGGGGGGGGGGGGGR 179.55 1.98E-19 2895000000 145380 121300 72617 87298 135280 117630 121970 151270 125470 TRUE FALSE 126167.6647 120503.1723 107734.8241 107120.3452 132588.1927 122155.3022 110141.3682 118922.0877 110637.0795 1.140374142 1.089175282 0.973767787 0.968213782 1.198406477 1.104108159 0.995519483 1.074884552 1 16.75547545 -0.12654311 1.061614012 2.23E-10 1.068586867 0.076468796 0.073223639 94.86460587 7.77856309 213.9210932 0.024182106 0.747234456 0.12654311 1.068586866 AHVDEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AHVDEFK 7 0 A0A087WYS1;E7EUC7;Q16851;Q16851-2 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 ;;; 146.94 0.0021848 1762260000 3723380 3005890 2251370 2679740 2739190 2425070 3605830 3958270 3834880 FALSE TRUE 3231325.899 2986144.111 3340140.062 3288215.924 2684685.478 2518364.012 3256137.162 3111824.764 3381524.855 0.955582478 0.883076197 0.9877615 0.972406256 0.793927472 0.744742127 0.962919778 0.920243055 1 21.68924253 1.310552963 1.754943126 1.022219157 0.895570029 0.137519768 0.078576146 1.805252729 5.991657771 0.373698655 0.023563119 20.44339233 -1.310552963 -0.126649128 AHVIVMAATNRPNSIDPALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AHVIVMAATNRPNSIDPALR 20 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 177.67 3.89E-17 2754500000 759970 548410 425350 421150 502990 546430 509390 631650 623980 FALSE TRUE 659538.039 544807.4586 631050.6827 516778.5444 492981.4831 567451.5157 459989.4362 496576.563 550213.7952 1.198694116 0.990174117 1.146919049 0.939232256 0.895981684 1.031329132 0.836019453 0.902515654 1 19.06963279 3.705633523 9.667765147 0.92709708 1.099719194 0.554261696 0.074696884 0.360674164 103.933607 0.019439776 0.029077294 5077.308158 -3.705633523 0.172622114 AHVIVMAATNRPNSIDPALRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHVIVMAATNRPNSIDPALRR 21 2 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 174.65 1.64E-12 660410000 244630 158780 104370 131770 117650 152390 160690 180420 54949 FALSE TRUE 212301.5257 157736.9637 154843.6811 161690.3925 115308.9952 158252.5419 145106.3085 141838.587 48452.99182 4.381597869 3.255463859 3.195750671 3.337056937 2.379811666 3.266104651 2.994785318 2.927344251 1 15.56429813 1.146717607 2.335592749 9.56E-11 3.225861682 0.675479659 0.487061264 0.50956223 2.345774949 3.760667451 0.12780963 14.01901845 -1.146717607 3.225861682 AHYGGDIFITSVDAATTFEELCEEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHYGGDIFITSVDAATTFEELCEEVR 26 0 Q05513;F2Z3C5 Q05513 PRKCZ Protein kinase C zeta type 0 126.52 0.00010288 29069000 15805 16061 8697.7 7937.2 13969 17173 15085 15469 14576 FALSE TRUE 13716.32921 15955.49423 12903.93681 9739.462573 13691.04423 17833.65642 13622.05902 12161.07473 12852.84189 1.067182599 1.241398157 1.00397538 0.757767244 1.065215332 1.387526322 1.05984802 0.946177883 1 13.64979977 -0.547730642 0.014268838 1.88E-06 1.997647257 0.010473742 0.166216515 67685.07254 135.3531796 10641.30128 8429.293709 0.283314863 0.547730642 1.99764538 AIAGDEHKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AIAGDEHKR 9 1 H0YDU8;P53041;A8MU39;M0R196;A0A087WY80;E7EU14 H0YDU8 PPP5C;PPP5D1 Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5;Protein PPP5D1 0 ;;;;; 171.36 3.70E-05 873753000 3008490 2616530 1783600 2157030 2128030 2253920 3022130 3356390 2464230 FALSE TRUE 2610910.424 2599341.842 2646154.926 2646816.63 2085686.366 2340629.761 2729044.298 2638652.118 2172911.537 1.201572351 1.196248351 1.217792294 1.218096818 0.959857929 1.077185942 1.255938979 1.214339412 1 21.05119801 AIAHYEQSADYYKGEESNSSANK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AIAHYEQSADYYKGEESNSSANK 23 1 P54920;M0R0Y2;M0R2M1;M0R058;M0R027;A0A087WZQ7;Q9H115-3;Q9H115-2;Q9H115 P54920 NAPA;NAPB Alpha-soluble NSF attachment protein;Beta-soluble NSF attachment protein 0 217.82 1.40E-32 500160000 259790 181790 124600 162440 186190 125750 244650 266440 174820 FALSE TRUE 225458.0933 180595.8095 184856.9768 199324.4847 182485.1833 130587.6839 220923.8807 209463.8794 154152.9788 1.462560731 1.171536295 1.199178753 1.29303038 1.18379278 0.84713046 1.43314701 1.358805267 1 17.23400324 4.743135343 23.99329255 1.204054026 1.462560907 0.204237305 0.168282998 491.6522324 2578427.189 0.041708193 0.32070539 55352.25815 -4.743135343 0.258506881 AIAQGIQELSAELPPEESESSRVDFGS(ph)SER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AIAQGIQELSAELPPEESESSRVDFGSSER 30 1 A0A0G2JRG8;A0A0G2JNY3;E9PIR1;Q6ZUM4-3;Q6ZUM4;A0A0C4DGE6;E9PNT2;Q6ZUM4-2 A0A0G2JRG8 ARHGAP27 Rho GTPase-activating protein 27 1 AIAQGIQELSAELPPEES(0.002)ES(0.007)S(0.007)RVDFGS(0.492)S(0.492)ER;AIAQGIQELSAELPPEESESSRVDFGS(0.968)S(0.032)ER;AIAQGIQELSAELPPEESESSRVDFGS(0.955)S(0.045)ER 216.87 1.02E-34 208275000 136789 125911 65621.5 57030.1 121372 132519 129594 131866 31575.5 TRUE FALSE 118711.9871 125083.8824 97356.27689 69979.65586 118956.9347 137617.0917 117025.9938 103667.4821 27842.68036 4.263669501 4.492523016 3.496656056 2.513395081 4.272467058 4.942666794 4.203115228 3.723329821 1 14.76501048 4.236555187 24.99774201 3.564157669 4.378096436 0.105850685 1.082453102 129.6271111 1615895.98 0.280803055 0.635425775 17240.71158 -4.236555187 0.813938766 AICDHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AICDHVR 7 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 0 ;;;;; 180 0.00069287 6061530000 7382810 9401830 5519660 5673290 8108450 9732310 8256460 8690030 9550630 FALSE TRUE 6407152.953 9340068.76 8188986.038 6961497.205 7947107.709 10106718.26 7455749.78 6831734.71 8421565.402 0.760803087 1.109065633 0.972382882 0.826627459 0.94366158 1.200099718 0.885316378 0.811219101 1 23.005657 2.045742923 24.99992865 0.878965059 0.973961386 0.051299905 0.131949061 285.4721035 156018.0959 0.052711772 0.035538257 111.1073842 -2.045742923 0.094996327 AIEALKEFNEDGALAVLQQFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AIEALKEFNEDGALAVLQQFK 21 1 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ; 260.34 1.24E-36 833830000 1456150 985040 588350 632280 819050 659220 1190650 1486540 314260 FALSE TRUE 1263716.088 978569.2074 872878.0279 775848.8378 802752.5074 684580.62 1075180.946 1168654.989 277108.5408 4.560364991 3.53135708 3.149949927 2.799801246 2.896888364 2.470442152 3.879999307 4.217318549 1 18.08009165 4.716396387 1.953264015 3.059835241 4.969850044 0.261524049 0.862915889 1.157922868 4.882870235 0.231222549 3.926187609 52047.08214 -4.716396387 1.910014803 AIEEGVNHMWTVSAFQQHPR ddPTM_MDA-MB-175_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 ; 264.69 8.10E-37 1241250000 597600 495470 349990 432630 493850 483740 535390 570480 579310 FALSE TRUE 518625.6459 492215.2249 519246.3346 530865.2538 484023.3512 502349.7908 483467.9602 448487.2915 510824.6318 1.015271413 0.963569872 1.016486486 1.039231902 0.947533304 0.98340949 0.94644606 0.877967239 1 18.96246857 2.559286827 1.422337519 0.928112796 1.002351879 0.294001404 0.038864848 0.43085945 1.796039451 0.021275454 0.014781494 362.4823187 -2.559286827 0.074239083 AIELNPANAVYFCNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AIELNPANAVYFCNR 15 0 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 0 160.86 1.51E-08 0 68841 69506 38878 44499 79769 75415 59407 63212 79158 FALSE TRUE 59743.48743 69049.41051 57679.53084 54603.17807 78181.75297 78316.26385 53645.71828 49694.60572 69800.03142 0.855923503 0.989246124 0.826353938 0.782280136 1.120081917 1.122009006 0.768562953 0.711956782 1 16.09094007 AIEMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AIEMER 6 0 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;; 135.5 0.031577 2813680000 3454160 2952700 1989170 2215920 2628880 2856320 2717350 3111750 2776310 FALSE TRUE 2997684.004 2933303.519 2951139.265 2719078.504 2576570.431 2966204.479 2453821.815 2446326.478 2448097.795 1.224495202 1.198197035 1.205482588 1.110690312 1.052478556 1.211636433 1.00233815 0.999276452 1 21.22322976 -1.939428468 0.096074185 1.83E-08 1.490120048 0.675944907 0.053526118 175.5958473 1.588677791 35.42635382 4.133241044 0.011496656 1.939428468 1.49012003 AIEPPPLDAVIEAEHTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AIEPPPLDAVIEAEHTLR 18 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;; 328.73 7.77E-75 2839785000 1336930 1184775 749941 878360 1161414 1225100 1107860 1330904 1178074 FALSE TRUE 1160251.313 1176992.135 1112614.976 1077805.063 1138304.134 1272230.39 1000419.908 1046300.537 1038803.434 1.116911319 1.133026804 1.071054388 1.037544763 1.095783954 1.224707532 0.963050251 1.007217056 1 19.98649126 2.204241429 24.9999887 0.992530739 1.107931784 0.578424761 0.049384485 139.687563 101755.1882 0.020625618 0.013906605 160.0447487 -2.204241429 0.115401045 AIEQADLLQEEDES(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AIEQADLLQEEDESPR 16 0 A0A2R8YGH5;H7C1E4;P61966 A0A2R8YGH5 AP1S1 AP-1 complex subunit sigma-1A 1 AIEQADLLQEEDES(1)PR;AIEQADLLQEEDES(1)PR 405.6 3.63E-105 0 301590 235000 178912 217946 256340 262940 229420 258820 305170 TRUE FALSE 261734.1174 233456.2695 265434.4416 267433.9704 251239.3355 273055.4719 207170.8837 203473.3571 269093.1503 0.97265247 0.867566749 0.986403561 0.99383418 0.933651917 1.014724721 0.769885385 0.756144692 1 18.03774614 2.237308527 24.99923286 0.821116215 0.958543512 0.338496884 0.076824985 31.98185355 638522.5077 0.029810576 0.021366195 172.7064378 -2.237308527 0.137427297 AIEVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AIEVGR 6 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 109.7 0.068236 616800000 805270 678800 453660 502380 607960 643030 582290 665040 626530 FALSE TRUE 698851.5292 674340.9181 673051.4934 616453.0574 595862.7855 667767.7802 525819.6054 522826.3713 552462.3371 1.264975877 1.220609755 1.218275796 1.115828204 1.078558203 1.208711862 0.951774574 0.946356586 1 19.07551659 2.631790703 0.36014167 0.852190887 1.309644568 0.731092688 0.06053143 1.16801141 0.501382208 0.326763273 0.202039649 428.3420428 -2.631790703 0.457453681 AIEVLSDEHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AIEVLSDEHAR 11 0 Q9HCS7 Q9HCS7 XAB2 Pre-mRNA-splicing factor SYF1 0 ; 135.99 0.0001086 210162000 284530 256680 175510 198105 260380 285880 254490 291690 279500 FALSE TRUE 246928.6396 254993.8522 260387.223 243087.7681 255198.9474 296877.9886 229809.599 229314.3634 246457.8284 1.001910311 1.034634825 1.05651837 0.986326016 1.035466997 1.20457926 0.932449987 0.930440574 1 17.91098128 AIFAGYKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AIFAGYKR 8 1 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 71.296 0.078745 653320000 491150 558470 232420 299870 493720 382830 598820 634600 200360 FALSE TRUE 426243.2831 554801.3738 344819.0894 367960.0667 483895.9379 397557.7178 540746.5286 498895.7285 176673.6691 2.412602203 3.140260667 1.951728807 2.08271028 2.738925051 2.250237514 3.060708092 2.82382616 1 17.43072752 1.233003522 24.9994238 0.999997501 2.574176911 0.604992095 0.395341616 128.0396404 575943.4838 0.836773708 0.098296804 17.10029182 -1.233003522 1.57417941 AIFQEVHVQSLPQVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AIFQEVHVQSLPQVDR 16 0 Q96T76-5;Q96T76;Q96T76-8;Q96T76-9;Q5T454;Q96T76-7;B0QZ77;F8WCH8 Q96T76-5 MMS19 MMS19 nucleotide excision repair protein homolog 0 ; 157.74 3.79E-08 301080000 316320 334105 234786 269839 323050 331270 301685 346030 401760 FALSE TRUE 274517.5105 331910.2423 348329.2949 331110.0692 316621.937 344014.1713 272427.6351 272034.1773 354264.3905 0.774894451 0.936899816 0.983246706 0.934641127 0.893744744 0.971066188 0.768995255 0.767884621 1 18.43446693 2.240725771 24.99916195 0.826237403 0.919636884 0.115917771 0.085446713 88.51838206 1022064.838 0.032572104 0.023978188 174.0707381 -2.240725771 0.093399481 AIFQEVHVQSLPQVDRHTVYNIITNFMRTREEELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AIFQEVHVQSLPQVDRHTVYNIITNFMRTREEELK 35 3 Q96T76-5;Q96T76;Q96T76-8;Q5T454;Q96T76-7;B0QZ77 Q96T76-5 MMS19 MMS19 nucleotide excision repair protein homolog 0 48.204 0.051952 38057000 51785 31288 50193 40966 12941 16232 56109 42857 38627 FALSE TRUE 44941.48104 31082.46707 74466.50269 50267.95643 12683.49942 16856.45554 50667.55782 33692.36406 34060.56006 1.319458076 0.912564767 2.18629707 1.475840571 0.372380824 0.494896605 1.487572656 0.98918996 1 15.05581454 3.354241428 14.42899613 0.911611834 1.485743685 0.326431077 0.429075016 0.883450928 107.1836793 0.128358719 0.16570809 2260.692158 -3.354241428 0.574131851 AIFTGHSAVVEDVAWHLLHESLFGSVADDQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AIFTGHSAVVEDVAWHLLHESLFGSVADDQK 31 0 Q16576;E9PC52;Q16576-2;Q5JP01;Q5JP02 Q16576 RBBP7 Histone-binding protein RBBP7 0 ; 145.52 5.57E-09 644420000 626030 460830 424230 423150 301389 298680 444090 478910 348990 FALSE TRUE 543298.5493 457802.7774 629389.047 519232.6749 295391.9486 310170.4129 401022.2202 376498.8234 307732.7998 1.765487948 1.487663251 2.04524525 1.687284148 0.959897511 1.0079212 1.303150722 1.22346017 1 18.2313187 3.293744504 7.012400679 1.125721026 1.754422871 0.783212281 0.169056103 0.10209267 10.3656335 0.049710865 0.063893777 1966.728919 -3.293744504 0.628701845 AIGAVPLIQGEYMIPCEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AIGAVPLIQGEYMIPCEK 18 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GV23;A0A1B0GU92;A0A1B0GU03;H7C469;H7C1V0 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 174.39 1.38E-11 142680000 142450 124480 92106 115800 130710 125300 136360 157570 131970 FALSE TRUE 123624.8716 123662.2827 136648.7697 142094.1599 128109.1267 130120.3721 123135.8282 123874.8817 116368.6569 1.062355404 1.062676892 1.1742747 1.221069003 1.100890309 1.118173703 1.058152869 1.064503836 1 16.82834301 1.729617648 1.080874877 0.997399631 1.128146377 0.40196333 0.049023005 0.928963557 1.568211177 0.12243668 0.018765322 53.65592023 -1.729617648 0.130746746 AIGDHFYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AIGDHFYK 8 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 ; 100.19 0.0062812 921590000 3244900 2687200 1858100 2232140 2605200 2300900 3082000 3268300 3108000 FALSE TRUE 2816078.243 2669547.606 2756683.375 2738981.503 2553361.617 2389417.112 2783108.114 2569399.479 2740575.781 1.027549854 0.974082755 1.005877449 0.999418269 0.931688018 0.871866828 1.015519488 0.937540022 1 21.3860476 3.253445571 24.08596397 0.950441963 1.000053258 0.274987509 0.040617677 213.1479133 344900.5252 0.011497165 0.014773706 1792.443894 -3.253445571 0.049611296 AIGGIILTAS(ph)HNPGGPNGDFGIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AIGGIILTASHNPGGPNGDFGIK 23 0 A0A3B3ITK7;P36871;P36871-2 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 1 AIGGIILT(0.003)AS(0.997)HNPGGPNGDFGIK;AIGGIILT(0.001)AS(0.999)HNPGGPNGDFGIK;AIGGIILT(0.003)AS(0.997)HNPGGPNGDFGIK;AIGGIILT(0.003)AS(0.997)HNPGGPNGDFGIK 259.71 6.93E-44 13420540000 16257180 12435920 8355510 10552380 10920350 9080880 12648450 14531710 15608400 TRUE FALSE 14108752.47 12354227.62 12396262.58 12948459.16 10703056.4 9430227.33 11421805.27 11424216.9 13763192.73 1.025107527 0.897628033 0.900682191 0.940803447 0.777657961 0.685177307 0.8298805 0.830055724 1 23.71431184 4.782117229 0.818255137 0.829280622 1.126491989 0.307445884 0.084689499 3.423738681 1.704968108 0.033233919 0.94275494 60550.4296 -4.782117229 0.297211367 AIGNNSATS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AIGNNSATSPR 11 0 A0A1B0GV57;Q9NYJ8;Q9NYJ8-2 A0A1B0GV57 TAB2 TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 1 AIGNNSATS(1)PR 124.12 0.00037319 238540000 375930 419890 311560 352250 456590 562210 468150 525350 506420 TRUE FALSE 326249.898 417131.7149 462231.4581 432233.7463 447504.7523 583838.5825 422748.8851 413007.9908 446551.6045 0.730598423 0.934117604 1.035113195 0.967936834 1.002134463 1.307438103 0.946696599 0.924883007 1 18.76846738 4.728650186 2.077556468 1.020846256 0.651476402 0.437963813 0.105918873 0.715519458 3.468017364 0.029156933 0.494142422 53536.52592 -4.728650186 -0.369369854 AIGPHDVLATLLNNLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AIGPHDVLATLLNNLK 16 0 O75533;H7C341 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 151.3 6.57E-07 247610000 572670 497470 315550 411400 458130 382820 547190 616430 558690 FALSE TRUE 496990.2085 494202.0868 468151.0355 504814.6579 449014.1093 397547.3331 494123.598 484611.2416 492642.3047 1.008825681 1.003166156 0.950285899 1.024708299 0.91144042 0.806969538 1.003006833 0.983697983 1 18.910181 3.239991707 24.99983085 0.944303455 0.993886437 0.179238969 0.058879349 84.30978094 1472797.074 0.018774631 0.022936774 1737.767645 -3.239991707 0.049582982 AIGSASEGAQSSLQEVYHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AIGSASEGAQSSLQEVYHK 19 0 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ; 269.16 4.84E-32 582550000 476700 388550 277090 342710 375730 383000 432690 487750 456590 FALSE TRUE 413702.8872 385997.5895 411091.6508 420527.5435 368253.7081 397734.2578 390727.7904 383448.4582 402612.4503 1.027546185 0.958732372 1.021060453 1.044497117 0.914660507 0.987883652 0.970481142 0.952400895 1 18.61903226 3.251198615 24.99978107 0.965044302 1.00966436 0.36649787 0.031142159 265.8085762 525804.7725 0.008694151 0.011147806 1783.194084 -3.251198615 0.044620058 AIGSSPLGS(ph)GEGLLGLSPGPNGHSHLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AIGSSPLGSGEGLLGLSPGPNGHSHLLK 28 0 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67;K7EQG2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 AIGS(0.089)S(0.326)PLGS(0.582)GEGLLGLS(0.003)PGPNGHSHLLK 87.457 0.0058321 264970000 203790 213120 97841 151860 166030 157750 185850 238100 177020 TRUE FALSE 176858.6352 211720.0007 145157.2349 186342.134 162726.3278 163818.7446 167826.2956 187184.1679 156092.8973 1.133034483 1.356371779 0.92994132 1.193789963 1.042496684 1.049495188 1.075169329 1.199184404 1 17.25204537 4.248102055 24.99994681 1.084525975 1.244703069 0.353428545 0.096693828 219.4168025 574891.6105 0.022447841 0.057765196 17705.24965 -4.248102055 0.160177094 AIGSTSKPQES(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AIGSTSKPQESPK 13 1 F5H8D7;P18887;M0QYS5 F5H8D7 XRCC1 DNA repair protein XRCC1 1 AIGSTSKPQES(1)PK;AIGS(0.014)T(0.014)S(0.014)KPQES(0.958)PK 114.69 0.00043789 840310000 1078510 750120 657940 672570 746760 559740 956610 1092340 1168560 TRUE FALSE 935982.1709 745192.4123 976121.9847 825287.2981 731900.937 581273.56 863838.1094 858751.5916 1030414.168 0.9083553 0.723196978 0.947310329 0.800927747 0.71029782 0.564116428 0.838340675 0.833404293 1 19.9747929 1.213769965 1.942108068 1.081183817 0.778645357 0.284791202 0.106918407 1.196335527 4.116538155 0.678029072 0.029993659 16.3594977 -1.213769965 -0.302538461 AIGTEPDSDVLSEIMHSFAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AIGTEPDSDVLSEIMHSFAK 20 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ;; 212.72 1.45E-22 1374795400 1820719 1672113 1303485 1483879 1797261 1641606 2004853 2287343 2322335 FALSE TRUE 1580106.371 1661128.78 1933854.706 1820816.407 1761499.022 1704759.645 1810422.665 1798212.5 2047791.202 0.771614982 0.811180739 0.944361273 0.889161163 0.860194643 0.832487044 0.884085576 0.878122974 1 20.96563719 -2 0.022187693 1.997589897 1.92E-15 0.371050972 0.051202332 7716.912889 17.01101938 987.4174517 592.7041052 0.01 2 -1.997589897 AIGVKPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AIGVKPPR 8 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 98.457 0.006848 2529200000 4053200 2514400 1590400 2030520 2221100 2172800 2702300 2858100 2619200 FALSE TRUE 3517559.35 2497882.741 2359522.76 2491580.601 2176904.456 2256389.022 2440231.362 2246917.557 2309561.16 1.523042304 1.081539984 1.021632508 1.078811267 0.942561944 0.976977385 1.056577935 0.972876404 1 21.13918732 4.787508407 2.496488202 1.005466611 1.677829586 0.942095288 0.03987562 0.136579025 0.956103525 0.01016535 0.205331406 61306.76598 -4.787508407 0.672362974 AIHSWLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AIHSWLTR 8 0 P28070 P28070 PSMB4 Proteasome subunit beta type-4 0 ; 159.04 0.00036148 6695500000 4020000 3912000 2635000 3068700 3796000 3575400 3422900 4197100 4002200 FALSE TRUE 3488746.815 3886301.814 3909294.814 3765495.237 3720467.027 3712947.952 3090947.685 3299582.827 3529064.475 0.988575539 1.101227207 1.107742531 1.066995308 1.05423606 1.052105445 0.875854694 0.934973801 1 21.75085436 2.327098567 6.968216321 0.934386695 1.066662947 0.647411779 0.043410683 0.124480831 8.220041358 0.016213572 0.01247992 212.3726405 -2.327098567 0.132276252 AIHYALNCCGLAGGVEQFISDICPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AIHYALNCCGLAGGVEQFISDICPK 25 0 A6NNI4;A0A2R8Y478;G8JLH6;P21926 A6NNI4 CD9 Tetraspanin;CD9 antigen 0 ; 248.98 3.35E-39 437130000 337080 321910 225769 243932 309700 313540 326480 448610 320090 FALSE TRUE 292534.0239 319795.352 334951.6436 299320.4889 303537.5759 325602.0867 294818.0199 352678.2426 282249.3248 1.036438348 1.133024329 1.186722568 1.060482568 1.075423568 1.153597398 1.04453047 1.24952732 1 18.1066106 AIIEEYLHLNDMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AIIEEYLHLNDMK 13 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 189.33 3.70E-07 0 455420 393750 265860 335560 262300 269400 353330 463050 467710 FALSE TRUE 395235.0931 391163.4303 394430.7852 411754.0267 257080.7432 279763.9923 319064.111 364030.361 412417.8566 0.958336519 0.948463855 0.956386293 0.998390395 0.623350175 0.678350823 0.773642814 0.882673616 1 18.65374727 3.27898759 24.99880552 0.79597719 0.963541674 0.414131862 0.102630217 174.4940433 107900.6232 0.032389759 0.041814462 1901.023958 -3.27898759 0.167564485 AIIESDQEQGRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AIIESDQEQGRK 12 1 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 131.13 0.00032737 170110000 139010 101390 78284 73131 97531 97938 138070 143570 87648 FALSE TRUE 120639.4763 100723.9624 116142.4042 89736.51129 95590.32392 101705.7382 124679.9927 112868.6728 77286.35329 1.560941501 1.30325676 1.502754358 1.161091285 1.236833152 1.315959855 1.613221317 1.460395891 1 16.23792607 6.652507677 1.67702419 1.343547742 129.5129306 0.138627063 0.175996429 2114.880523 12.73805242 0.048977171 1038938.948 4492702.661 -6.652507677 128.1693829 AIIVEFAQQGLNAALFYENKDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AIIVEFAQQGLNAALFYENKDPR 23 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 152.13 5.95E-08 546320000 871840 702760 496580 623370 589760 612140 802600 927790 739390 FALSE TRUE 756624.135 698143.5233 736727.749 764915.6861 578024.9298 635689.4219 724763.9755 729389.3286 651980.1565 1.160501784 1.070804865 1.129984926 1.173219274 0.886568286 0.97501345 1.111635022 1.118729338 1 19.31446853 AIIYQYMEEIYHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AIIYQYMEEIYHR 13 0 E9PNM1;P37268;A0A1W2PQ47;P37268-4;P37268-3;P37268-2;P37268-5 E9PNM1 FDFT1 Squalene synthase 0 ; 192.15 2.96E-06 661620000 995180 941120 720830 961950 958580 1355090 782240 1194770 1104660 FALSE TRUE 863664.4415 934937.7208 1069425.799 1180375.45 939506.1334 1407221.189 706378.4852 939277.7332 974068.3532 0.886656915 0.959827632 1.097896052 1.211799404 0.964517665 1.44468423 0.725183693 0.964283184 1 19.89366349 AIKVEQATKPSFESGR ddPTM_MDA-MB-175_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" 0 119.8 9.35E-05 1199600000 2298300 1703700 922070 1116100 1468500 1235100 2074200 2431800 923280 FALSE TRUE 1994573.832 1692508.283 1367986.136 1369527.564 1439279.723 1282615.096 1873044.403 1911778.494 814130.8902 2.449942455 2.078914217 1.680302458 1.682195799 1.767872636 1.575440892 2.300667406 2.348244634 1 19.63490123 4.582834498 3.149524372 1.836820223 2.457558836 0.241575556 0.380625965 0.47417054 7.848519883 0.099417536 0.579704646 38267.88832 -4.582834498 0.620738614 AILDAEPGPRPALQPS(ph)PSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AILDAEPGPRPALQPSPSIR 20 1 B5MD46;Q9BXI6;Q9BXI6-2 B5MD46 TBC1D10A TBC1 domain family member 10A 1 AILDAEPGPRPALQPS(0.596)PS(0.404)IR;AILDAEPGPRPALQPS(0.979)PS(0.021)IR;AILDAEPGPRPALQPS(0.998)PS(0.002)IR;AILDAEPGPRPALQPS(0.989)PS(0.011)IR;AILDAEPGPRPALQPS(0.97)PS(0.03)IR;AILDAEPGPRPALQPS(0.998)PS(0.002)IR 201.58 7.54E-22 5299210000 4024740 4234950 3048060 3861730 4096280 4534640 3117270 4360370 4541450 TRUE FALSE 3492860.412 4207130.335 4522112.011 4738594.819 4014772.042 4709090.535 2814957.635 3427938.808 4004564.955 0.872219692 1.050583617 1.129239271 1.183298279 1.002548863 1.175930616 0.70293719 0.856007793 1 21.93321409 2.245029682 24.99997136 0.847360247 1.073051411 0.445396291 0.11349801 130.1464077 502958.0319 0.042721978 0.032288814 175.8043764 -2.245029682 0.225691164 AILDAEPGPRPALQPS(ph)PSIRLPLDAPLPGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AILDAEPGPRPALQPSPSIRLPLDAPLPGSK 31 2 B5MD46;Q9BXI6;Q9BXI6-2 B5MD46 TBC1D10A TBC1 domain family member 10A 1 AILDAEPGPRPALQPS(0.98)PS(0.02)IRLPLDAPLPGSK;AILDAEPGPRPALQPS(0.981)PS(0.019)IRLPLDAPLPGSK 159.2 1.15E-12 854050000 1686660 1552490 686040 733310 1422920 1318410 1306040 2038340 265267 TRUE FALSE 1463763.608 1542291.591 1017811.239 899819.2434 1394606.676 1369130.086 1179380.442 1602456.853 233907.4375 6.257875438 6.593597911 4.351341923 3.846903088 5.962216042 5.853298641 5.042081837 6.850816164 1 17.83557821 4.249581575 24.98998099 4.966876922 6.425737442 0.153686972 1.590143961 444.8214737 1008610.927 0.384286841 0.995899268 17765.66934 -4.249581575 1.45886052 AILELHYSQELSLLYLLQDDVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AILELHYSQELSLLYLLQDDVDR 23 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;; 232.07 1.27E-33 146275000 119356 124221 49089.3 90550 107967 99090 129893 133910 133231 FALSE TRUE 103582.8022 123404.9841 72829.04967 111110.7615 105818.6679 102902.0564 117295.9969 105274.3886 117480.583 0.881701466 1.050428768 0.619924143 0.945779793 0.900733255 0.875906927 0.998428795 0.896100325 1 16.8420628 2.263190778 24.15649017 0.951921046 0.879104006 0.115287085 0.110074391 379.6597503 372356.8385 0.039474177 0.030559478 183.3119502 -2.263190778 -0.07281704 AILILDNDGDR ddPTM_MDA-MB-175_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 ;;;;;;; 232.72 2.88E-13 2379717000 2589720 2423120 2058678 2244210 2407720 2532040 2343180 2820870 3770680 FALSE TRUE 2247481.94 2407202.365 3054261.567 2753792.181 2359811.083 2629449.217 2115938.764 2217648.903 3324914.506 0.675951799 0.723989252 0.918598527 0.828229471 0.709735868 0.790832129 0.636388924 0.666979226 1 21.66488581 3.235035092 24.99621966 0.741233604 0.79163535 0 0.116588427 363.3272234 2576012.204 0.035359912 0.041707058 1718.047203 -3.235035092 0.050401746 AILILDNDGDRLFAK ddPTM_MDA-MB-175_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 ; 216.46 2.01E-12 2007570000 2020330 1714240 677620 834970 1491680 1381080 1914250 2197660 314660 FALSE TRUE 1753338.272 1702979.045 1005319.299 1024562.7 1461998.486 1434211.041 1728606.33 1727707.511 277461.2533 6.319218453 6.137718419 3.623278158 3.692633433 5.269198741 5.16904982 6.230081892 6.226842454 1 18.08192679 4.358282303 8.897822388 4.739654867 6.27031228 0.169446827 1.535873286 0.504058509 36.42411005 0.387225563 1.028839279 22818.24835 -4.358282303 1.530657414 AILTGHDYEVTCAAVCAELGLVLSGSQEGPCLIHSMNGDLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AILTGHDYEVTCAAVCAELGLVLSGSQEGPCLIHSMNGDLLR 42 0 A0A494C1L5;P50851-2;P50851;A0A494BZW2;H0YAC6;A0A3B3IS13;H0YA17 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ;;; 345.58 4.12E-154 185202000 27795.7 25930.3 15807.4 15959.8 21246.75 25201.1 24146 26392.2 23896.7 FALSE TRUE 24122.42782 25759.96215 23451.91151 19583.71652 20823.98124 26170.60262 21804.32464 20748.43341 21071.65935 1.144780647 1.222493289 1.112959882 0.929386537 0.988245914 1.241981098 1.034770175 0.984660632 1 14.36301631 3.991656945 9.657434028 1.031644444 1.179861934 0.371848287 0.083565727 0.187337088 190.7330498 0.022738536 0.043286469 9809.727529 -3.991656945 0.14821749 AILVDLEPGTMDSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AILVDLEPGTMDSVR 15 0 Q13509;A0A0B4J269;G3V5W4;G3V2R8;G3V3R4;G3V2N6;Q5JP53;P07437;Q13885;Q9BVA1 Q13509;Q5JP53;Q13885;Q9BVA1 TUBB3;TUBB;TUBB2A;TUBB2B Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-2A chain;Tubulin beta-2B chain 0 ; 298.84 8.08E-44 368170000 781070 593700 387670 444620 569180 637190 556540 671540 632380 FALSE TRUE 677849.6205 589799.9456 575148.5087 545577.7666 557854.4316 661703.1116 502566.8365 527936.3969 557620.7568 1.215610453 1.057708018 1.031433105 0.978402902 1.000419057 1.186654377 0.901269959 0.946766042 1 19.08892474 7.999999938 0.827029199 0.993895606 67.97536873 0.444566437 0.073459574 573.8798012 1.769852857 0.026455195 72189.13585 99999985.81 -7.999999938 66.98147312 AIPELDAYEAEGLALDDEDVEELTAS(ph)QR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AIPELDAYEAEGLALDDEDVEELTASQR 28 0 P49736;F8WDM3;C9J013;C9JZ21;H7C4N9 P49736 MCM2 DNA replication licensing factor MCM2 1 AIPELDAYEAEGLALDDEDVEELT(0.007)AS(0.993)QR;AIPELDAYEAEGLALDDEDVEELT(0.007)AS(0.993)QR;AIPELDAYEAEGLALDDEDVEELT(0.001)AS(0.999)QR;AIPELDAYEAEGLALDDEDVEELT(0.01)AS(0.99)QR;AIPELDAYEAEGLALDDEDVEELT(0.047)AS(0.953)QR 169.65 2.77E-14 120709000 151729.4 141873 97079.3 113111.5 136172.8 140553 124313.5 152503 135296.9 TRUE FALSE 131677.9754 140941.0269 144027.1742 138795.1949 133463.2277 145960.1649 112257.5959 119891.4202 119302.2546 1.103734173 1.181377732 1.207246038 1.163391214 1.118698286 1.223448503 0.940951169 1.004938428 1 16.86426178 2.236107568 24.99999833 0.985040851 1.166563693 0.829932297 0.03933154 23.39745471 238447.1744 0.014968005 0.010630303 172.2295107 -2.236107568 0.181522842 AIPGDQHPES(ph)PVHTEPMGIQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AIPGDQHPESPVHTEPMGIQGR 22 0 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AIPGDQHPES(0.999)PVHT(0.001)EPMGIQGR;AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(0.997)PVHT(0.003)EPMGIQGR 249.96 1.20E-31 1038140000 822280 587220 385328 447238 592300 561398 526325 620310 593892 TRUE FALSE 713613.6146 583362.5132 571673.9096 548790.2235 580514.3888 582995.3443 475282.0825 487661.5338 523682.7643 1.362683027 1.113961644 1.091641636 1.047944024 1.108523 1.113260516 0.907576332 0.931215551 1 18.9983336 8 0.35339047 0.954959863 5.303667732 0.732819718 0.06497392 44.97735037 0.683332989 0.09111459 129.2438452 100000000 -8 4.348707869 AIPPERHS(ph)PHHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AIPPERHSPHHLK 13 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 AIPPERHS(1)PHHLK;AIPPERHS(1)PHHLK 100.41 0.0012107 439290000 516430 420680 299550 298260 365520 362340 443780 483130 385840 TRUE FALSE 448182.467 417916.5254 444413.3819 365984.4916 358246.8671 376279.4543 400742.2839 379816.4092 340226.4348 1.317306421 1.22834819 1.306228254 1.07570857 1.052965997 1.10596772 1.177869333 1.116363605 1 18.37613571 3.737118561 24.99955843 1.09596968 1.278399685 0.7644583 0.051084631 65.67289734 1138510.78 0.014262931 0.022491468 5459.068718 -3.737118561 0.182430005 AIPVS(ph)PSAVEEDEDEDGHTVVATAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AIPVSPSAVEEDEDEDGHTVVATAR 25 0 A0A087X0K9;G5E9E7;Q07157-2;H0Y3R8;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 AIPVS(0.52)PS(0.48)AVEEDEDEDGHTVVATAR;AIPVS(0.594)PS(0.406)AVEEDEDEDGHTVVATAR 314.77 8.38E-75 2320400000 553660 546060 365150 501230 693590 711860 607300 726060 661580 TRUE FALSE 480492.4282 542472.8959 541737.7614 615041.9323 679788.916 739245.7148 548404.1395 570797.7192 583368.7661 0.823651275 0.929897052 0.928636898 1.054293559 1.165281646 1.267201396 0.940064281 0.978450943 1 19.15404862 3.913142898 2.325607275 1.063138427 0.875103038 0.424906816 0.096579908 0.354762904 3.747174699 0.030852461 0.068830039 8187.341358 -3.913142898 -0.188035389 AIQDHLLEVEQSKDQMEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AIQDHLLEVEQSKDQMEK 18 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 206.7 4.95E-16 67203000 184810 137090 110150 119220 118000 84479 180080 201200 132870 FALSE TRUE 160386.8903 136189.4468 163418.9084 146290.7232 115652.0309 87728.9618 162615.8693 158174.9457 117162.26 1.368929639 1.162400305 1.394808435 1.248616433 0.987109935 0.748781748 1.387954358 1.350050313 1 16.8381484 3.461359005 23.72540173 1.13014787 1.298686724 0.202842637 0.19160351 278.8062842 419657.4986 0.06075064 0.078462496 2893.070422 -3.461359005 0.168538854 AIQEGANSIVSSLHQAAAAACLS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AIQEGANSIVSSLHQAAAAACLSR 24 0 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 AIQEGANSIVSSLHQAAAAACLS(1)R 117.33 0.00046696 141460000 119660 106570 79258 109850 178520 135290 172260 192670 116130 TRUE FALSE 103846.6278 105869.9347 117587.4339 134793.1215 174967.8013 140494.6938 155554.2517 151469.0199 102401.2437 1.014114908 1.033873524 1.148300838 1.316323089 1.708649182 1.372001831 1.51906604 1.479171682 1 16.64387371 3.774660476 2.591724644 1.433043103 1.035583182 0.450791474 0.17758519 0.241959514 3.202945477 0.049823786 0.093674268 5951.966471 -3.774660476 -0.397459921 AIS(ph)APT(ph)SPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AISAPTSPTR 10 0 B0QY95;Q9NQG6;Q9NQG6-2 B0QY95;Q9NQG6-2 MIEF1 Mitochondrial dynamics protein MID51 2 AIS(1)APT(0.719)S(0.281)PTR 92.19 0.051123 492880000 744220 641160 401910 482930 568170 649970 501980 580670 637370 TRUE FALSE 645869.4414 636948.1777 596275.0203 592586.6376 556864.5286 674974.7665 453298.0569 456498.2393 562020.8447 1.149191258 1.133317712 1.06094823 1.054385515 0.990825401 1.200978172 0.806550257 0.812244321 1 19.10026411 2.229643537 24.99993129 0.857522434 1.091291627 0.648617372 0.077798991 110.7247165 310424.8196 0.031235118 0.021410739 169.685033 -2.229643537 0.233769193 AIS(ph)ETEENSDELSGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AISETEENSDELSGER 16 0 Q00987-8;A7UKX8;F5GWH7;J3KN53;E7EPE2;Q00987-9;Q00987;Q00987-11 Q00987-8 MDM2;mdm2 E3 ubiquitin-protein ligase Mdm2 1 AIS(0.899)ET(0.101)EENSDELSGER 265.22 4.71E-27 456670000 144470 129490 116720 141380 162830 157470 164690 172900 189840 TRUE FALSE 125377.9235 128639.3717 173166.1824 173482.4899 159590.0016 163527.9728 148718.3891 135926.6805 167397.3315 0.748984003 0.768467278 1.034462025 1.036351585 0.953360488 0.976885183 0.888415531 0.812000283 1 17.352917 4.297088785 9.437869557 0.943986926 0.757379462 0.590431784 0.068078374 0.300863474 45.38128252 0.019746661 0.052290624 19819.32163 -4.297088785 -0.186607464 AIS(ph)PTSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AISPTSSSR 9 0 O14795;O14795-2;A0A0U1RRL2;B1AM27 O14795 UNC13B Protein unc-13 homolog B 1 AIS(0.85)PT(0.134)S(0.015)S(0.001)SR 72.922 0.036586 0 315800 242360 130600 149530 240530 264460 213530 250780 178600 TRUE FALSE 274066.2299 240767.9212 193758.5968 183483.0719 235743.9236 274633.9473 192821.8935 197152.6486 157486.1115 1.740256505 1.528820027 1.230321804 1.165074623 1.496918817 1.743861378 1.224373957 1.25187324 1 17.26486508 1.579317626 1.677366294 0.998552189 1.45493677 0.373411045 0.195942698 0.588439593 2.768821469 0.385060936 0.060628774 37.95925029 -1.579317626 0.456384581 AIS(ph)SANLLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AISSANLLVR 10 0 G3V1D0;B7WPE2;H0Y3M3;Q32P44;Q32P44-2 G3V1D0 EML3 Echinoderm microtubule-associated protein-like 3 1 AIS(0.95)S(0.05)ANLLVR;AIS(0.5)S(0.5)ANLLVR;AIS(0.808)S(0.192)ANLLVR;AIS(0.892)S(0.108)ANLLVR 137.58 9.18E-05 757609000 715393 719060 475646 492733 626438 627711 696858 688957 1192850 TRUE FALSE 620852.0025 714336.4475 705669.9965 604615.5586 613973.1094 651859.4484 629276.8184 541628.907 1051832.632 0.590257408 0.679135088 0.670895706 0.57482107 0.583717495 0.619736856 0.598267062 0.5149383 1 20.00447373 1.230732475 24.99965802 1.000000716 0.602919409 0.875667355 0.04689629 105.0714558 335524.4143 0.133982003 0.012658589 17.01110303 -1.230732475 -0.397081307 AIS(ph)SDMFFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 AISSDMFFGR 10 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;Q8N6H7-3;H0YDN9;E9PMU9 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 AIS(0.98)S(0.02)DMFFGR;AIS(0.98)S(0.02)DMFFGR;AIS(0.649)S(0.351)DMFFGR;AIS(0.5)S(0.5)DMFFGR;AIS(0.5)S(0.5)DMFFGR;AIS(0.919)S(0.081)DMFFGR;AIS(0.5)S(0.5)DMFFGR;AIS(0.983)S(0.017)DMFFGR;AIS(0.918)S(0.082)DMFFGR;AIS(0.5)S(0.5)DMFFGR;AIS(0.787)S(0.213)DMFFGR 252.51 4.87E-17 4964276000 2542450 2012474 1214676 1250428 1820255 1418905 2851972 2328722 1913728 TRUE FALSE 2206458.791 1999253.926 1802097.376 1534356.789 1784035.487 1473491.194 2575388.194 1830742.922 1687489.256 1.30753946 1.18475061 1.067916356 0.909254257 1.057212945 0.873185526 1.526165684 1.084891602 1 20.68644689 4.533797513 2.911341222 1.086179471 1.3072392 0.15712177 0.176178234 0.618030396 9.19883578 0.045777082 0.25127975 34182.00336 -4.533797513 0.221059729 AIS(ph)SPTVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AISSPTVSR 9 0 O94811 O94811 TPPP Tubulin polymerization-promoting protein 1 AIS(0.976)S(0.024)PTVSR 191.48 3.76E-05 196120000 316160 270520 141610 156900 236310 229910 216040 239010 191120 TRUE FALSE 274378.655 268742.9363 210093.0697 192526.5431 231607.8933 238754.7865 195088.4741 187899.5715 168526.0113 1.628108639 1.5946674 1.246650698 1.142414406 1.374315404 1.416723653 1.157616397 1.114958872 1 17.36261176 8 0.23168127 1.029651144 4.526410274 0.646708553 0.12305585 63.44751206 0.99097013 0.560153708 81.77088076 100000000 -8 3.49675913 AIS(ph)TGSLASSTLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AISTGSLASSTLNK 14 0 Q12923-3;Q12923;Q12923-4 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 AIS(0.894)T(0.1)GS(0.005)LASSTLNK;AIS(0.5)T(0.5)GSLASSTLNK;AIS(0.949)T(0.051)GSLASSTLNK 370.22 4.38E-97 1050510000 2019580 1988780 1295840 1585940 1652900 1753630 1891250 2207910 2197700 TRUE FALSE 1752687.386 1975715.573 1922512.558 1946051.917 1620010.524 1821093.281 1707836.866 1735765.628 1937890.41 0.9044306 1.019518732 0.992064643 1.004211542 0.835966015 0.939729756 0.881286608 0.895698549 1 20.88605556 3.267338931 24.99999889 0.907947389 0.983732878 0.311142956 0.051190542 231.6661164 201249.0662 0.013986818 0.018053815 1850.712383 -3.267338931 0.075785488 AISET(ph)EENSDELSGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AISETEENSDELSGER 16 0 Q00987-8;A7UKX8;F5GWH7;J3KN53;E7EPE2;Q00987-9;Q00987;Q00987-11 Q00987-8 MDM2;mdm2 E3 ubiquitin-protein ligase Mdm2 1 AIS(0.339)ET(0.661)EENSDELSGER 354.96 2.49E-86 334510000 161070 133870 113880 142580 162680 173510 165910 171810 184000 TRUE FALSE 139784.1914 132990.5992 168952.7489 174954.9682 159442.9863 180185.042 149820.0737 135069.7685 162247.7296 0.861547904 0.81967618 1.041325813 1.078319978 0.982713204 1.11055509 0.923403206 0.832490962 1 17.30783876 4.247677864 24.96213421 0.983726617 0.840611979 0.393669212 0.078884348 239.1062072 654635.2321 0.022861555 0.058672347 17687.96476 -4.247677864 -0.143114638 AISGVHTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AISGVHTVR 9 0 P41091;Q2VIR3;Q2VIR3-2;H7BZU1 P41091 EIF2S3;EIF2S3L Eukaryotic translation initiation factor 2 subunit 3;Putative eukaryotic translation initiation factor 2 subunit 3-like protein 0 193.1 3.40E-05 386410000 451050 461790 246780 379740 466040 477650 433040 463040 447670 FALSE TRUE 391442.5997 458756.4711 366123.6334 465965.771 456766.7158 496025.5046 391043.8475 364022.4994 394746.9626 0.991629162 1.162153264 0.927489425 1.180416356 1.15711268 1.256565728 0.990619016 0.922166689 1 18.59056864 2.02181081 24.94129342 0.955784498 1.112519056 0.332088091 0.095304851 232.3010966 265641.9249 0.038457094 0.0259255 105.1503711 -2.02181081 0.156734558 AISHEHSPSDLEAHFVPLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AISHEHSPSDLEAHFVPLVK 20 0 P30153;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 63.918 0.010574 366210000 547190 519090 203110 383460 483230 472710 544900 606170 510340 FALSE TRUE 474877.4551 515680.0636 301334.6754 470530.4538 473614.6684 490895.4596 492055.6819 476545.2627 450008.1866 1.055264036 1.14593485 0.66962043 1.045604209 1.052457894 1.090858954 1.093437179 1.058970207 1 18.77959172 3.506618743 24.99503537 1.061985313 0.956134817 0.130626551 0.121886148 1389.955113 1177790.695 0.033158731 0.049088945 3210.840577 -3.506618743 -0.105850496 AISS(ph)DMFFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AISSDMFFGR 10 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;Q8N6H7-3;H0YDN9;E9PMU9 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 AIS(0.315)S(0.685)DMFFGR;AIS(0.216)S(0.784)DMFFGR 223.87 4.44E-09 321780000 568310 478488 295245 318898 424831 374760 667340 533320 464151 TRUE FALSE 493206.3936 475344.7808 438026.4695 391308.665 416377.6943 389177.2597 602621.4695 419273.6683 409279.5975 1.205059809 1.161418218 1.070237735 0.956091306 1.017342904 0.950883606 1.472395578 1.024418688 1 18.64272723 4.36194661 3.862844022 1.077507007 1.195993559 0.092220404 0.148850776 0.598339933 16.13739887 0.038496973 0.118029097 23011.58907 -4.36194661 0.118486552 AIT(ph)PPQQPYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AITPPQQPYK 10 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 AIT(1)PPQQPYK;AIT(1)PPQQPYK;AIT(1)PPQQPYK 132.69 0.0024257 1398170000 1920810 1095060 666620 922820 1083940 930460 1166410 1405850 1340600 TRUE FALSE 1666970.092 1087866.479 988999.6617 1132360.385 1062371.715 966255.3983 1053291.738 1105219.918 1182115.795 1.410158039 0.920270656 0.836635181 0.957909868 0.898703595 0.81739488 0.891022472 0.934950639 1 20.17293993 4.73775746 5.971643553 0.903931385 1.423876313 0.898881126 0.053045433 0.038119062 6.540819391 0.013114014 0.080826551 54671.05572 -4.73775746 0.519944928 AIT(ph)PPVASPVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AITPPVASPVGR 12 0 B3KNS5;Q8WVR3-2;Q8WVR3-3;Q8WVR3 B3KNS5 C7orf43 Uncharacterized protein C7orf43 1 AIT(1)PPVASPVGR 94.547 0.073202 243210000 279610 241470 244790 258070 229260 280990 237560 248600 520090 TRUE FALSE 242658.8301 239883.7677 363171.2628 316668.7379 224698.1745 291799.8671 214521.4678 195438.8246 458605.5527 0.529123184 0.523072096 0.791903327 0.690503497 0.489959559 0.63627635 0.467769015 0.426158871 1 18.8068943 1.226858438 24.99676784 1.000000964 0.566778265 0.600532778 0.11036564 417.3024007 891333.0706 0.467258092 0.029441223 16.8600337 -1.226858438 -0.433222699 AITHLNNNFMFGQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AITHLNNNFMFGQK 14 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ; 162.67 4.40E-06 1693760000 3552400 2897100 1946510 2479300 2888800 2534300 3372500 3565800 3358100 FALSE TRUE 3082941.339 2878068.759 2887848.747 3042262.959 2831318.532 2631796.161 3045435.469 2803281.419 2961109.244 1.041144073 0.971956292 0.975259104 1.027406525 0.956168212 0.888787257 1.028477918 0.946699763 1 21.49770629 3.215879737 24.9973073 0.962932641 0.999608108 0.184087605 0.041274773 427.4585846 471113.9317 0.012097277 0.013726515 1643.916432 -3.215879737 0.036675467 AITSAYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AITSAYYR 8 0 H3BMH2;H3BSC1;P62491-2;Q15907-2;P62491;Q15907;P57735 H3BMH2;P57735 RAB11A;RAB11B;RAB25 Ras-related protein Rab-11A;Ras-related protein Rab-11B;Ras-related protein Rab-25 0 ; 151.29 0.0011062 539900000 432300 524750 396520 394810 625060 597920 470520 599390 740730 FALSE TRUE 375170.4597 521302.8827 588278.3983 484457.6448 612622.5289 620922.3693 424889.0428 471215.113 653161.7432 0.574391356 0.798122193 0.900662668 0.741711605 0.937933881 0.950641056 0.650511221 0.721437099 1 19.31708077 4.727621166 4.272447226 0.826947109 0.557453066 0.352922104 0.111861396 0.248924033 10.59060215 0.028387815 0.201050932 53409.82641 -4.727621166 -0.269494043 AITSLLGGGS(ph)PK ddPTM_MDA-MB-175_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 209.39 5.84E-08 3221800000 3062500 2119300 1499560 1710520 2436000 1793330 2623100 3135200 2341900 TRUE FALSE 2657782.866 2105378.179 2224752.232 2098919.71 2387528.366 1862320.566 2368712.166 2464761.878 2065043.25 1.287034964 1.019532244 1.077339291 1.016404722 1.156163856 0.901831265 1.147052085 1.193564289 1 20.97774057 4.748085393 24.27567136 1.074746601 1.287035136 0.389298679 0.086871803 990.1669138 2523545.863 0.02129761 0.260939827 55986.76743 -4.748085393 0.212288535 AITVFSPDGHLFQVEYAQEAVK ddPTM_MDA-MB-175_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 0 279.19 1.41E-45 328890000 355030 319250 145890 263050 252130 252150 313770 417720 556760 FALSE TRUE 308111.886 317152.8257 216442.892 322779.523 247113.1063 261850.3737 283340.6337 328393.8287 490940.4671 0.627595211 0.646010763 0.440874009 0.657471821 0.503346379 0.53336482 0.577138477 0.668907639 1 18.90518856 1.170918786 2.058475639 1.193799335 0.566476722 0.805374493 0.066312843 0.367196752 1.317999626 0.467700277 0.017128633 14.82240878 -1.170918786 -0.627322613 AITVFSPDGHLFQVEYAQEAVKK ddPTM_MDA-MB-175_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 0 276.36 6.03E-52 342650000 846940 664370 288980 521170 672690 470420 835580 1021700 496420 FALSE TRUE 735014.7331 660005.7097 428731.6946 639509.6141 659304.7851 488517.3618 754545.5802 803217.4059 437733.7931 1.679136372 1.507778746 0.979434764 1.460955549 1.506177488 1.116014732 1.723754465 1.834944933 1 18.73969424 2.215844027 24.99895329 1.593778098 1.372856197 0.03118689 0.295507784 544.5444055 599250.9789 0.11956668 0.08067525 164.3781267 -2.215844027 -0.220921901 AIVAIENPADVSVISSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AIVAIENPADVSVISSR 17 0 C9J9K3;A0A0C4DG17;P08865;F8WD59 C9J9K3 RPSA 40S ribosomal protein SA 0 155.08 2.65E-07 48940000 49340 41428 26171 37184 44222 40471 39525 41147 42797 FALSE TRUE 42819.59399 41155.85674 38827.38314 45627.19552 43342.06872 42027.94556 35691.87158 32348.03426 37737.58741 1.134666971 1.090579964 1.028878256 1.209064984 1.148511913 1.113689254 0.945791028 0.85718342 1 15.20371457 2.208642603 4.457420963 0.914366001 1.121645057 0.706291599 0.05660398 0.100021404 4.550591837 0.023898627 0.016287756 161.6749006 -2.208642603 0.207279056 AIVDALPPPCESACTVPTDVDKWFHHQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AIVDALPPPCESACTVPTDVDKWFHHQK 28 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ;; 152.88 2.34E-08 3501440000 2818740 2226380 1565800 1894920 2080550 1630450 2555720 3223060 1996390 FALSE TRUE 2446236.367 2211754.763 2323026.117 2325190.548 2039151.126 1693174.467 2307866.668 2533833.701 1760379.048 1.389607749 1.256408252 1.319616999 1.320846525 1.15835912 0.9618238 1.31100553 1.439368245 1 20.74745468 3.254034891 24.12590627 1.206921146 1.316818904 0.193177681 0.141061168 381.4649046 594735.9325 0.044411067 0.057093136 1794.877822 -3.254034891 0.109897758 AIVHDNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 115.46 0.0056756 388110000 457970 445020 374150 406120 253550 353140 432180 474230 1246600 FALSE TRUE 397448.1042 442096.6343 555090.1915 498335.7532 248504.8511 366725.5243 390267.2501 372819.605 1099228.368 0.361570094 0.40218816 0.504981683 0.453350521 0.226072087 0.33362087 0.355037462 0.339164832 1 20.06805971 1.236768817 24.99998863 1.000000786 0.371546027 0.876362619 0.074130222 16.49108872 230023.3869 0.12181689 0.019451283 17.2491944 -1.236768817 -0.628454759 AIVICPTDEDLKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AIVICPTDEDLKDR 14 1 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 169.17 3.08E-06 445270000 336540 234780 165230 206430 230970 237120 206050 281370 322560 FALSE TRUE 292065.3863 233237.7147 245135.7807 253303.0866 226374.1489 246242.1598 186067.3027 221201.2151 284427.3243 1.026854178 0.820025697 0.861857352 0.890572266 0.795894521 0.865747201 0.654182235 0.777707331 1 18.11770054 7.733936789 1.093806089 0.816183824 199.9999979 0.293092803 0.089947432 1814.298623 2.980424425 0.026879529 905719.2802 54192200.89 -7.733936789 199.1838141 AIVQQWLEYR ddPTM_MDA-MB-175_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 0 169.09 1.10E-05 594520000 161370 195800 163510 95634 161730 194400 186700 189640 230470 FALSE TRUE 140044.5456 194513.7769 242583.9829 117349.1614 158511.8894 201878.6938 168593.8627 149086.9618 203224.0992 0.689113871 0.957139324 1.193677246 0.577437232 0.779985691 0.993379696 0.829595818 0.733608673 1 17.63271197 3.736702733 24.99693649 0.816408433 0.947693047 0.112022422 0.169295578 372.0978383 5006409.622 0.045576018 0.071718275 5453.844271 -3.736702733 0.131284614 AIVWGMQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AIVWGMQTR 9 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 89.55 0.02799 275680000 383030 362990 234340 268060 339690 309070 443150 485520 375640 FALSE TRUE 332411.615 360605.4948 347667.6078 328927.12 332930.8336 320960.1229 400173.3812 381695.3263 331232.2671 1.003560486 1.088678642 1.049618779 0.993040693 1.005128022 0.968988093 1.20813526 1.152349467 1 18.33748369 2.246812824 24.99987196 1.130532962 1.021068651 0.382520172 0.060536282 173.7598171 526402.2887 0.023234906 0.017682514 176.5276841 -2.246812824 -0.109464311 AIYHDLEQSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AIYHDLEQSIR 11 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 ;;; 237.53 1.39E-15 3187130000 2908620 3049800 1701630 2234300 2845560 3114620 2664440 3141710 2833360 FALSE TRUE 2524238.497 3029765.663 2524543.96 2741631.964 2788938.923 3234441.447 2406043.019 2469879.765 2498403.409 1.010340639 1.212680727 1.010462902 1.097353596 1.116288472 1.29460336 0.963032235 0.988583252 1 21.25257501 AKADS(ph)PVNGLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKADSPVNGLPK 12 1 Q96S94;Q96S94-3;A0A0A0MSF3 Q96S94 CCNL2 Cyclin-L2 1 AKADS(1)PVNGLPK 104.41 0.0012963 232540000 699910 486090 355310 477280 485280 364910 661950 731500 530610 TRUE FALSE 607415.1202 482896.8428 527139.1044 585653.7188 475623.8774 378948.3238 597754.1909 575074.4175 467881.8903 1.29822319 1.032091331 1.126649942 1.251712731 1.016546884 0.809923042 1.277574968 1.22910168 1 18.83578486 4.753804402 23.59208409 1.107023471 1.298223497 0.167069318 0.140962808 2666.033527 4125941.414 0.035731473 0.751718222 56728.9051 -4.753804402 0.191200026 AKAEASSGDHPTDTEMKEEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKAEASSGDHPTDTEMKEEQK 21 2 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 143.93 7.95E-08 208485000 171236 124746 81911 101861 111627 79442 202236 212818 107321 FALSE TRUE 148606.7287 123926.5353 121523.4336 124990.0969 109405.8411 82498.18515 182623.1838 167308.5269 94633.63364 1.570337342 1.309540071 1.284146333 1.320778798 1.156098914 0.871763896 1.929791521 1.767960506 1 16.5300654 2.231231381 24.99994157 1.623170998 1.254934547 0.195957784 0.292035106 234.781631 800828.8298 0.11822646 0.081525687 170.3065617 -2.231231381 -0.368236452 AKAEITR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKAEITR 7 1 A0A0C4DG89;Q7L014;H0Y9U3 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 64.836 0.065862 87769000 252300 227420 155560 188650 191540 238160 227600 259070 189810 FALSE TRUE 218957.9158 225926.063 230789.3363 231485.8658 187728.7287 247322.1693 205527.387 203669.8966 167370.878 1.308219915 1.349852888 1.378909754 1.383071348 1.121633171 1.477689382 1.227975795 1.216877745 1 17.352689 0.491085597 0.937329742 1.47E-05 1.333761601 0.552906537 0.093235957 5.42480624 1.341222409 10.36334194 0.030153558 3.09802984 -0.491085597 1.333746871 AKAEKPPLSASS(ph)PQQRPPEPETGESAGTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKAEKPPLSASSPQQRPPEPETGESAGTSR 30 3 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 AKAEKPPLS(0.003)AS(0.25)S(0.748)PQQRPPEPETGESAGTSR 97.609 0.00046015 167770000 130510 119100 78117 94493 112090 98599 132540 152820 115550 TRUE FALSE 113262.7728 118317.6243 115894.6425 115949.0799 109859.6283 102392.1673 119686.2912 120140.6322 101889.8106 1.111620211 1.161231172 1.137450759 1.137985037 1.078219967 1.004930392 1.174663987 1.179123128 1 16.63665026 3.271943685 19.56905365 1.101277443 1.138825077 0.120971669 0.060334063 54.29800681 31825.81709 0.0185804 0.023979332 1870.439584 -3.271943685 0.037547634 AKDDATLSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKDDATLSGK 10 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 102.66 0.0026607 233670000 300190 295360 222460 275840 241700 215120 358560 450590 514310 FALSE TRUE 260519.1309 293419.7607 330042.4001 338473.688 236890.6429 223395.8056 323786.9064 354234.835 453508.8577 0.574452134 0.646998963 0.72775293 0.746344161 0.522350642 0.49259414 0.713959388 0.781097941 1 18.7907712 1.366492238 1.693437337 1.075193431 0.628010235 0.678469728 0.082787834 0.480710715 1.636950509 0.333846847 0.025561957 23.25370922 -1.366492238 -0.447183196 AKDDDDDDDDDAEM ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKDDDDDDDDDAEM 14 1 Q8IYL3 Q8IYL3 C1orf174 UPF0688 protein C1orf174 0 81.565 0.028517 117160000 241570 179390 143160 160320 164350 140180 217970 250600 223500 FALSE TRUE 209645.9124 178211.5753 212392.6548 196723.1063 161079.7565 145572.8153 196831.3029 197011.1402 197078.0846 1.063770804 0.904268862 1.077708134 0.998198794 0.817339771 0.738655521 0.998747798 0.999660315 1 17.58840783 3.44368879 24.99282432 0.918848899 1.009785027 0.214339839 0.094830404 354.976823 265365.9217 0.029848512 0.038534428 2777.722075 -3.44368879 0.090936127 AKDPVALHELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKDPVALHELER 12 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 0 96.591 0.0032433 80962000 112110 99383 82759 93705 105800 112360 109660 128120 123660 FALSE TRUE 97294.37945 98730.14653 122781.5292 114982.1524 103694.787 116682.5619 99025.19008 100722.535 109041.0557 0.892272904 0.90544012 1.126011927 1.054484953 0.950970131 1.070079166 0.908145922 0.923712031 1 16.73451191 0.924934447 20.32795702 1.718964779 0.97858343 0.006840814 0.079862333 654.204917 470885.6547 36500.80023 0.019705361 8.4126815 -0.924934447 -0.740381349 AKDYENAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKDYENAIK 9 1 H0YDU8;P53041 H0YDU8 PPP5C Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5 0 90.685 0.010272 177430000 178020 144440 110360 117410 151970 137580 179240 211710 160570 FALSE TRUE 154494.206 143491.1641 163730.4651 144069.735 148946.0943 142872.7916 161857.3324 166437.464 141587.5975 1.091156349 1.013444445 1.156389882 1.017530755 1.051971337 1.009077025 1.143160384 1.17550878 1 17.11133537 2.223089855 24.96482325 1.122196644 1.057183893 0.10609372 0.062393554 382.4061787 617075.3089 0.024590237 0.016645474 167.1436396 -2.223089855 -0.06501275 AKEAAEQDVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AKEAAEQDVEK 11 1 P26373;P26373-2;J3KS98 P26373 RPL13 60S ribosomal protein L13 0 ;;; 166.62 1.84E-05 1626170000 3138780 2655490 1885520 1801910 2150630 1734910 3405340 3775320 1369440 FALSE TRUE 2723982.27 2638045.911 2797363.779 2211061.206 2107836.671 1801653.11 3075090.651 2967997.198 1207546.363 2.255799324 2.184633229 2.316568426 1.831036284 1.745553409 1.491994979 2.546561146 2.457874321 1 20.20364715 3.74223369 24.51077451 1.934214013 2.245563625 0.137952311 0.443796763 648.5158288 4327584.489 0.125417046 0.206639586 5523.745875 -3.74223369 0.311349612 AKEALELTDTGLLSGSEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKEALELTDTGLLSGSEER 19 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 184.62 2.24E-14 247910000 145970 143440 76219 86339 146170 124430 154930 166790 55952 FALSE TRUE 126679.6947 142497.7332 113078.7633 105943.5896 143261.503 129216.9026 139904.9124 131123.2565 49337.4183 2.567619041 2.88822841 2.291947314 2.147327388 2.903708948 2.619044674 2.835675584 2.657683782 1 15.5903946 1.237741261 24.99979811 0.999998117 2.619500135 0.812536424 0.24360927 8.617488046 262768.8473 0.354821411 0.060561904 17.28786094 -1.237741261 1.619502018 AKEAQDDLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AKEAQDDLVK 10 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;; 84.169 0.017316 964770000 2842610 2485730 1720930 1807940 2214530 2234470 3022600 3025620 1858210 FALSE TRUE 2466951.886 2469401.076 2553177.504 2218460.41 2170465.186 2320431.507 2729468.717 2378614.708 1638534.531 1.505584313 1.507079057 1.558207933 1.353929605 1.32463805 1.416162713 1.665798716 1.451672006 1 20.64397465 1.242094763 6.628603262 0.988316005 1.475517625 0.698099402 0.09782797 0.067063689 14.60774749 0.147726149 0.02556477 17.46203133 -1.242094763 0.48720162 AKEDFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKEDFLK 7 1 P22694-2;P22694-4;A0A0A0MS54;P22694-9;P22694-6;P22694-7;P22694-5;P22694;P22694-3;P22694-10;P22694-8;B1APG3;B1APF9;B1APF8;B1APG2;B1APG1;B1APF7;B1APG0;K7ENJ5;P17612-2;P17612;Q15136 P22694-2;P17612-2 PRKACB;PRKACA;KIN27 cAMP-dependent protein kinase catalytic subunit beta;cAMP-dependent protein kinase catalytic subunit alpha 0 60.91 0.086332 516000000 1092900 853690 703170 775350 850430 593020 1031200 1158300 1295700 FALSE TRUE 948470.4959 848082.0542 1043225.364 951405.068 833508.1068 615833.8631 931194.3827 910606.5589 1142523.822 0.830153803 0.74228829 0.913088501 0.832722303 0.729532366 0.539011836 0.815032794 0.797013192 1 20.12379282 1.146382163 2.39450369 1.103923984 0.768842194 0.345395952 0.09776658 1.012777432 4.957721192 0.791256299 0.027189115 14.00819449 -1.146382163 -0.33508179 AKEEDREK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 98.044 0.0043881 581345000 1500185 1267652 900111 885974 590755 719102 1575632 1910342 684284 FALSE TRUE 1301931.751 1259324.711 1335407.69 1087147.938 579000.1313 746766.3193 1422827.451 1501830.23 603388.7251 2.157699833 2.087086911 2.213179721 1.801737243 0.959580627 1.237620606 2.358061051 2.488992862 1 19.20272821 3.675083593 5.873639083 1.726171503 2.145543721 0.170567918 0.510570144 0.531052841 36.80239759 0.159901322 0.240861914 4732.423399 -3.675083593 0.419372218 AKEEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AKEEELR 7 1 O75525-2;O75525;H0YAQ1;H0YAQ3;E5RJZ9;E5RG12;Q9H6N6;Q5STV6;A0A0A0MRT5;Q9UBC1-2;Q9UBC1-3;Q9UBC1;Q07666-2;Q07666;Q5VWX1 O75525-2;Q07666-2 KHDRBS3;MYH16;NFKBIL1;KHDRBS1;KHDRBS2 "KH domain-containing, RNA-binding, signal transduction-associated protein 3;Putative uncharacterized protein MYH16;NF-kappa-B inhibitor-like protein 1;KH domain-containing, RNA-binding, signal transduction-associated protein 1;KH domain-containing, RNA-binding, signal transduction-associated protein 2" 0 ;;; 112.84 0.0057124 2230120000 6831600 5027090 3691180 4564920 4112130 3972470 5616700 6696500 7253000 FALSE TRUE 5928786.751 4994066.715 5476246.994 5601454.856 4030306.658 4125293.491 5071993.298 5264505.587 6395558.603 0.92701625 0.78086482 0.856257809 0.875835123 0.630172735 0.645024735 0.793049304 0.823150238 1 22.60863894 7.771343025 1.09953776 0.791315489 145.2388718 0.11075271 0.107491085 4600.031689 6.613653906 0.03283967 1674938.76 59066743.11 -7.771343025 144.4475563 AKEELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKEELER 7 1 P15311;E7EQR4 P15311 EZR Ezrin 0 88.177 0.017145 943430000 1119200 1077800 808540 993560 874040 868950 1093900 1343100 1229900 FALSE TRUE 971294.8843 1070719.861 1199552.648 1219162.984 856648.314 902379.0688 987813.7464 1055888.517 1084502.623 0.895613218 0.987291167 1.106085521 1.124167851 0.789899716 0.832067207 0.910844958 0.973615457 1 20.04860211 3.24553558 24.99963543 0.907582763 1.030917833 0.347027809 0.086294221 212.5848554 761941.445 0.027386807 0.034580682 1760.092856 -3.24553558 0.123335069 AKEEQQDDTVYMGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKEEQQDDTVYMGK 14 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;E7EWF7 E7EX90 DCTN1 Dynactin subunit 1 0 172.91 1.43E-07 0 207380 175210 145800 155660 155540 137240 195540 232350 221020 FALSE TRUE 179974.2076 174059.034 216309.3677 191004.9821 152445.0583 142519.7116 176576.5609 182663.7606 194891.2674 0.923459578 0.893108431 1.109897691 0.980059213 0.78220569 0.731278079 0.906026028 0.937259853 1 17.57230992 3.293361249 22.29457272 0.875188857 0.980185541 0.240559569 0.092714174 52.88436712 21513.63644 0.029062224 0.037519068 1964.994093 -3.293361249 0.104996684 AKEFTNVYIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKEFTNVYIK 10 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;H0YBN4;B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0YCC8 P11940-2;B1ANR0 PABPC1;PABPC4 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 4 0 ; 140.24 3.61E-05 1343060000 3403100 3007300 1816500 2198850 3013500 2605040 3764800 4397800 1932820 FALSE TRUE 2953371.713 2987544.848 2694965.476 2698132.5 2953537.246 2705257.574 3399690.275 3457364.694 1704324.221 1.732869647 1.752920489 1.581251643 1.583109872 1.732966773 1.587290458 1.99474386 2.02858391 1 20.70076838 AKELATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKELATK 7 1 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 68.016 0.057998 258210000 390090 355950 222480 243430 244840 243690 464460 464050 181080 FALSE TRUE 338538.6181 353611.741 330072.0722 298704.5021 239968.163 253064.912 419416.7407 364816.5187 159672.9287 2.120200468 2.214600458 2.067176164 1.870727271 1.502873186 1.584895537 2.626724168 2.284773767 1 17.28476021 3.906623611 3.748068242 1.890536229 2.163804032 0.092057046 0.439667025 0.759676909 19.53513903 0.126443669 0.240678587 8065.357294 -3.906623611 0.273267803 AKEPAGENGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKEPAGENGGR 11 1 E7EMD0;P16435;H0Y4R2 E7EMD0;P16435 POR NADPH--cytochrome P450 reductase 0 ; 118.87 0.00060464 174542000 220275 187705 131675 199817 212050 240220 172984 372490 290250 FALSE TRUE 191165.1006 186471.9535 195353.4704 245188.5039 207830.6199 249461.4188 156208.0383 292835.9122 255936.9757 0.746922558 0.728585438 0.763287407 0.958003443 0.812038274 0.974698627 0.610337908 1.144171964 1 17.96542907 -2 0.286897098 3.311611399 0.741927547 0.297488928 0.133157713 90.93424701 1.471662173 115.4881715 0.286258341 0.01 2 -2.569683851 AKESWEMNSEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKESWEMNSEEK 12 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 98.654 0.00158 0 267080 184440 308820 188790 162480 119440 235400 235820 307210 FALSE TRUE 231784.7013 183228.4015 458166.3849 231657.655 159246.9659 124034.9341 212570.9442 185391.7282 270891.9838 0.855635143 0.676389161 1.691325002 0.855166151 0.587861492 0.457875986 0.7847074 0.684375099 1 18.04735818 3.482823813 24.85191264 0.696970969 1.074410664 0.255063066 0.289754947 313.6429998 1366867.503 0.082006953 0.109413495 3039.65163 -3.482823813 0.377439695 AKEVELVS(ph)E ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AKEVELVSE 9 1 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 AKEVELVS(1)E;AKEVELVS(1)E;AKEVELVS(1)E 117.45 0.0030257 3698600000 7548800 6371300 3571000 4472600 6385600 5568100 6481800 8405100 3449070 TRUE FALSE 6551206.954 6329446.511 5297947.544 5488172.189 6258539.053 5782308.41 5853196.034 6607734.774 3041324.874 2.154063517 2.08114778 1.741986721 1.804533359 2.05783312 1.901246545 1.924554685 2.172650094 1 21.5362685 1.231482997 24.99847464 0.999998309 1.97645633 0.825377131 0.141618762 105.7252076 373392.8969 0.356088959 0.036206168 17.04052602 -1.231482997 0.976458021 AKFEELNMDLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AKFEELNMDLFR 12 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;; 172.57 3.23E-05 8656560000 11029020 9271410 6747010 9433230 9913090 10001790 9161100 10934720 8379810 FALSE TRUE 9571507.063 9210505.497 10009886.6 11575189.05 9715838.904 10386565.33 8272657.932 8596415.222 7389158.408 1.295344684 1.246489111 1.354672082 1.566509799 1.314877604 1.405649299 1.119567003 1.163382181 1 22.81697863 2.231570787 24.80636068 1.10975712 1.365144384 0.647367074 0.093567968 97.98502443 347736.9634 0.039092583 0.02700305 170.4397101 -2.231570787 0.255387264 AKFENLCK ddPTM_MDA-MB-175_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 ; 138.98 0.00062227 7997100000 7444300 6253400 4214700 5414000 5563700 4131500 7086600 8659100 7272700 FALSE TRUE 6460516.894 6212321.004 6252943.017 6643331.448 5452993.255 4290441.478 6399342.623 6807418.85 6412929.691 1.007420509 0.96871809 0.975052483 1.035927691 0.850312341 0.669029864 0.997881301 1.061514655 1 22.61255216 2.014166004 24.99657906 1.033515355 0.917346049 0.182901067 0.10339021 382.3298023 674636.3699 0.0454796 0.030647603 103.3156242 -2.014166004 -0.116169306 AKGPS(ph)ESSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKGPSESSK 9 1 Q8TEA8;A0A087WZV9 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1;D-tyrosyl-tRNA(Tyr) deacylase 1 AKGPS(0.955)ES(0.042)S(0.003)K;AKGPS(0.99)ES(0.008)S(0.001)K 62.088 0.051424 219075000 482180 238710 483650 373270 195014 294170 506020 533720 914110 TRUE FALSE 418458.6913 237141.8983 717544.7577 458026.6586 191133.6029 305486.9103 456946.2583 419588.1314 806044.9572 0.519150561 0.294204307 0.890204388 0.568239593 0.237125239 0.378994878 0.566899221 0.520551773 1 19.62050078 1.21166782 3.705011192 1.084666567 0.492794553 0.438299035 0.178962375 0.327193713 6.725075489 0.560298991 0.046399941 16.28050304 -1.21166782 -0.591872014 AKGPS(ph)PPGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKGPSPPGAK 10 1 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 AKGPS(1)PPGAK;AKGPS(1)PPGAK 55.196 0.080049 836420000 2907700 1975180 1641130 1630400 1811590 1466290 2604600 2879200 2296700 TRUE FALSE 2523440.078 1962204.913 2434785.957 2000607.239 1775542.903 1522699.125 2352006.293 2263505.486 2025186.742 1.246028341 0.96890073 1.202252566 0.987863093 0.87673046 0.751880848 1.161377489 1.117677416 1 20.94962351 7.755609936 1.071756095 1.0088149 199.9952772 0.227787041 0.13369886 2641.341247 4.59203421 0.042702119 1290109.414 56965240.66 -7.755609936 198.9864623 AKGPSESS(ph)KER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKGPSESSKER 11 2 Q8TEA8;A0A087WZV9 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1;D-tyrosyl-tRNA(Tyr) deacylase 1 AKGPS(0.006)ES(0.071)S(0.924)KER 87.138 0.010984 81716000 172670 120570 111400 94604 100750 95063 166930 170270 99693 TRUE FALSE 149851.222 119777.9677 165273.4126 116085.2841 98745.27211 98720.13512 150741.1543 133859.0855 87907.40711 1.704648413 1.362546931 1.880085172 1.320540418 1.123287279 1.12300133 1.714771932 1.522728174 1 16.42369711 3.692827508 24.49050268 1.334927155 1.620439043 0.308564132 0.240982749 498.8858676 267157.7656 0.069152664 0.102570491 4929.779658 -3.692827508 0.285511888 AKGS(ph)ETPGATPGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKGSETPGATPGSK 14 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 AKGS(0.595)ET(0.405)PGATPGSK 73.022 0.097322 21135000 107800 84714 42111 50674 72829 55064 104170 124000 29225 TRUE FALSE 93553.95687 84157.50816 62476.02045 62180.3062 71379.84539 57182.34771 94067.60943 97483.56497 25770.05379 3.630336111 3.265709448 2.424365155 2.412890043 2.769875684 2.218945609 3.650268261 3.782823495 1 14.65340793 4.43370591 5.261804955 2.755287592 3.553097949 0.155168586 0.77898921 0.359911215 23.09046734 0.200468157 0.584889389 27146.00405 -4.43370591 0.797810357 AKGSET(ph)PGATPGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKGSETPGATPGSK 14 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 AKGS(0.109)ET(0.891)PGATPGSK;AKGS(0.035)ET(0.965)PGATPGSK 129.43 0.00010988 420704000 1075440 795982 430141 528663 720646 545772 990580 1148350 281673 TRUE FALSE 933317.8792 790753.1418 638158.6263 648704.0143 706306.5545 566768.202 894513.7041 902784.289 248373.9388 3.757712599 3.183720263 2.569346162 2.611803869 2.843722485 2.281914941 3.601479722 3.634778646 1 17.92215428 4.571011479 3.0431247 2.781886165 3.770126918 0.17987288 0.739033825 0.574472993 8.974054936 0.187408551 1.094719887 37240.15495 -4.571011479 0.988240754 RRDEDMLYSPELAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RRDEDMLYSPELAQR 15 2 Q9Y2W2 Q9Y2W2 WBP11 WW domain-binding protein 11 0 ; 137.52 9.13E-06 202073000 216400 184253 105313 127921 196589 200219 184067 207138 98716 FALSE TRUE 187802.1917 183042.6299 156242.7191 156967.4182 192677.2635 207921.5545 166216.2107 162843.1506 87045.90694 2.157507439 2.102828684 1.79494619 1.803271673 2.213513194 2.38864252 1.909523567 1.870773209 1 16.40948884 1.088328093 1.953530169 0.285029953 2.055075453 0.76264027 0.183276003 0.666894819 1.738824517 2.490636762 0.053324091 12.25541699 -1.088328093 1.7700455 AKHHAISAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKHHAISAK 9 1 P27824;P27824-2;P27824-3;H0Y9Q7;D6RDP7;D6RAU8;D6RB85;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 ; 88.496 0.0076578 299370000 328570 303757 175621 259903 325720 310661 261798 492660 222173 FALSE TRUE 285148.642 301761.6003 260551.903 318917.9485 319238.8093 322612.3297 236408.8703 387308.4929 195907.961 1.455523504 1.540323316 1.32997098 1.627896829 1.629534643 1.646754568 1.206734372 1.976992108 1 17.5798165 1.203532064 24.54240098 0.999994367 1.555976865 0.416109808 0.205335128 4674.350418 3274781.927 10.11516284 0.048086696 15.97835492 -1.203532064 0.555982497 AKLAEQAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AKLAEQAER 9 1 P27348;E9PG15;P31946-2;P31946;Q4VY19;A0A0J9YWE8;Q4VY20;P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;E5RGE1;P31947-2;P31947 P27348;P31946-2;P63104;P31947-2 YWHAQ;YWHAB;YWHAZ;SFN "14-3-3 protein theta;14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed;14-3-3 protein zeta/delta;14-3-3 protein sigma" 0 ;; 118.4 0.00090745 591280000 1254140 1145610 276901 325472 1028170 886200 1349830 1386090 97079 FALSE TRUE 1088402.221 1138084.412 410811.2498 399375.3921 1007711.429 920292.6874 1218923.694 1089685.44 85602.43121 12.7146181 13.29500105 4.79906054 4.665467867 11.77199542 10.75077745 14.23935836 12.72960855 1 16.38536415 AKLDSLQDIGMDHQALLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKLDSLQDIGMDHQALLK 18 1 P80303-2;P80303;E9PKG6;Q2L696;E9PLR0;E9PLE9;A0A2R8Y6G7 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 ; 214.46 6.03E-19 787810000 1314550 1116980 800840 911960 1155820 908220 1288870 1675410 787310 FALSE TRUE 1140828.887 1109642.485 1188128.903 1119034.456 1132821.443 943159.8111 1163875.586 1317136.61 694235.1087 1.643288956 1.598366995 1.711421517 1.611895513 1.63175476 1.358559657 1.676486209 1.897248631 1 19.4050648 2.962782766 24.83572071 1.55805829 1.640522575 0.061271452 0.232841132 2527.956312 1686949.078 0.075578829 0.075598937 917.8733613 -2.962782766 0.082464285 AKLEQLFQDEVAK ddPTM_MDA-MB-175_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 0 157.35 4.34E-05 342890000 737570 567270 462800 503070 523860 438600 723190 875030 598610 FALSE TRUE 640098.2557 563543.566 686611.628 617299.7324 513436.2109 455473.2258 653055.1451 687911.644 527843.0077 1.21266787 1.067634804 1.300787579 1.169476006 0.972706285 0.862895253 1.237214732 1.303250463 1 19.00974938 3.456554446 24.98519643 1.102146631 1.190097489 0.12702291 0.13779007 703.0373378 854068.9439 0.044549387 0.057519403 2861.241043 -3.456554446 0.087950857 AKLNWLSVDFNNWKDWEDDS(ph)DEDMSNFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AKLNWLSVDFNNWKDWEDDSDEDMSNFDR 29 2 A0A087WYT3;Q15185-4;Q15185;B4DDC6 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 1 AKLNWLSVDFNNWKDWEDDS(1)DEDMSNFDR;AKLNWLSVDFNNWKDWEDDS(1)DEDMSNFDR;AKLNWLSVDFNNWKDWEDDS(1)DEDMSNFDR;AKLNWLSVDFNNWKDWEDDS(1)DEDMSNFDR 375.6 5.02E-137 5524420000 4744680 4067220 1331590 1312920 2917440 2061350 4605240 5243560 368727 TRUE FALSE 4117658.517 4040502.164 1975551.378 1611038.553 2859388.652 2140651.468 4158624.534 4122265.499 325136.5141 12.66439891 12.42709443 6.076067412 4.954960402 8.794424888 6.583854398 12.79039527 12.6785683 1 18.31068606 4.260330709 22.94717533 8.208931865 12.54576323 0.243510041 3.513235938 156.9669202 165445.9941 0.918448509 2.423121239 18210.87061 -4.260330709 4.33683136 AKLTPGCEAEAETEAICFFVQQFTDMEHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKLTPGCEAEAETEAICFFVQQFTDMEHNR 30 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 289.98 4.73E-81 822090000 711670 775750 296250 256050 595030 579310 897850 896570 112132 FALSE TRUE 617621.0064 770654.0472 439517.4909 314190.066 583190.0672 601596.4306 810776.6452 704845.4826 98875.8827 6.246427233 7.794155927 4.445143536 3.177620845 5.898203396 6.084359645 8.199943435 7.128588523 1 16.59333105 4.244162289 24.99974319 5.467255297 7.020291488 0.110670355 2.06115914 362.96854 1619847.948 0.537467334 1.340577277 17545.3602 -4.244162289 1.553036191 AKNEQEHHAGGDS(ph)QKDIMQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKNEQEHHAGGDSQKDIMQR 20 2 Q86SF2;E9PBY3 Q86SF2 GALNT7 N-acetylgalactosaminyltransferase 7 1 AKNEQEHHAGGDS(1)QKDIMQR 149.99 4.40E-08 146380000 165190 158030 107630 110040 168160 108570 152520 248340 106050 TRUE FALSE 143359.723 156991.8905 159680.228 135026.2639 164813.945 112746.7582 137728.6339 195234.4236 93512.88981 1.533047725 1.678826211 1.707574521 1.443932105 1.762473017 1.205681467 1.472830475 2.087780882 1 16.51287762 3.759588968 24.27990106 1.554789401 1.643717126 0.025198519 0.296918393 3372.894894 3894417.707 0.078939907 0.136526327 5748.955781 -3.759588968 0.088927725 AKNEQEHHAGGDSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKNEQEHHAGGDSQK 15 1 Q86SF2;E9PBY3 Q86SF2 GALNT7 N-acetylgalactosaminyltransferase 7 0 133.66 2.40E-05 6621000 20621 15331 10699 16802 14728 14126 18345 23051 15845 FALSE TRUE 17895.8826 15230.28965 15873.07219 20617.1509 14434.94161 14669.43636 16565.90472 18121.72303 13971.82215 1.280855311 1.090071824 1.136077458 1.475623629 1.033146676 1.049930081 1.185665302 1.297019303 1 13.77023256 AKNS(ph)PPQAPSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AKNSPPQAPSTR 12 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 AKNS(0.991)PPQAPS(0.007)T(0.002)R;AKNS(0.999)PPQAPSTR;AKNS(1)PPQAPSTR;AKNS(1)PPQAPSTR;AKNS(1)PPQAPSTR;AKNS(1)PPQAPSTR 138.05 4.93E-05 2710410000 869966 709346 517002 581490 765752 635744 837829 950873 919854 TRUE FALSE 754997.7889 704686.2594 767025.8965 713526.192 750515.0334 660201.4831 756576.4725 747536.2087 811109.908 0.930820572 0.868792567 0.945649768 0.879691131 0.925293879 0.813948241 0.932766898 0.92162135 1 19.62953789 1.120305618 1.611392833 1.063915033 0.896914217 0.400051861 0.038679527 1.415171705 2.617716704 0.412265586 0.010191977 13.19184736 -1.120305618 -0.167000816 AKNWEDEDFYDS(ph)DDDTFLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AKNWEDEDFYDSDDDTFLDR 20 1 A0A087X0M4;A0A087WWF4;Q9BWU0 A0A087X0M4 SLC4A1AP Kanadaptin 1 AKNWEDEDFYDS(1)DDDTFLDR;AKNWEDEDFYDS(1)DDDTFLDR;AKNWEDEDFYDS(1)DDDTFLDR 281.23 5.68E-45 697800000 1584070 1418090 821290 991870 1341450 1209330 1526360 1847250 657360 TRUE FALSE 1374731.136 1408774.473 1218468.591 1217089.243 1314757.77 1255853.708 1378333.842 1452229.963 579647.6497 2.371666886 2.430397974 2.102084933 2.099705302 2.268201674 2.166581213 2.377882224 2.505366775 1 19.14481667 1.232783386 24.99997841 0.999997928 2.292422076 0.898172333 0.136527137 62.1235059 268800.7919 0.32281775 0.037151925 17.09162618 -1.232783386 1.292424148 AKPAMPQDSVPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 19 AKPAMPQDSVPSPR 14 1 P53396 P53396 ACLY ATP-citrate synthase 1 AKPAMPQDSVPS(1)PR;AKPAMPQDS(0.001)VPS(0.999)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDS(0.001)VPS(0.999)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDS(0.009)VPS(0.991)PR;AKPAMPQDSVPS(1)PR 199.41 1.25E-08 57071350000 24161340 21763200 14462700 18429870 21669510 19446710 24288100 27513480 26513520 TRUE FALSE 20968357.7 21620236.11 21456910.09 22614653.67 21238329.15 20194837.52 21932643.8 21629936.41 23379121.87 0.896883887 0.924766817 0.917780839 0.967301244 0.908431431 0.863797949 0.938129495 0.92518173 1 24.47871741 1.026302012 1.993030012 1.074473449 0.916738198 0.486207805 0.026623984 1.451770539 3.361655012 0.524154631 0.00731268 10.62434127 -1.026302012 -0.157735252 AKPDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKPDFK 6 1 P13489;E9PMJ3;E9PLZ3;E9PIM9 P13489 RNH1 Ribonuclease inhibitor 0 ; 66.258 0.092919 2354800000 4426800 3855300 2985400 3589200 3070100 3005500 4920700 5075600 4706500 FALSE TRUE 3841787.164 3829974.28 4429149.426 4404182.717 3009011.017 3121123.53 4443491.271 3990222.438 4150102.932 0.925708887 0.922862479 1.067238451 1.061222526 0.725044912 0.752059306 1.070694232 0.961475535 1 21.98471569 AKPPADPAAAAS(ph)PCR ddPTM_MDA-MB-175_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 156.58 1.27E-06 5389450000 7015590 6260740 4514040 4595210 5678430 5888220 6844950 7353520 7945740 TRUE FALSE 6088462.006 6219612.787 6697044.843 5638622.664 5565440.353 6114743.634 6181127.803 5781026.973 7006403.669 0.86898533 0.887704032 0.955846274 0.804781302 0.794336241 0.872736417 0.882211202 0.825106181 1 22.74024268 1.229383604 24.99287874 1.000000271 0.860984415 0.46977036 0.046252248 351.2917536 956644.0245 0.142681398 0.011739736 16.95835036 -1.229383604 -0.139015856 AKPSYLIDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKPSYLIDK 9 1 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 98.353 0.0055369 291160000 535140 606930 388760 541950 579380 552380 771040 870710 759190 FALSE TRUE 464419.8931 602943.0369 576765.6363 665008.0307 567851.4715 573630.416 696264.6595 684515.4424 669439.4231 0.693744463 0.900668554 0.861565089 0.993380443 0.848249225 0.856881738 1.040071193 1.022520364 1 19.35259399 6.976720323 0.214381081 1.064874208 1.46E-19 0.577806072 0.068622687 49.57332154 1.1332817 0.412811174 16.13562425 9478078.969 -6.976720323 -1.064874208 AKPVATAPIPGTPWCVVWTGDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKPVATAPIPGTPWCVVWTGDER 23 1 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 161.16 1.65E-11 476010000 469090 453850 311180 349190 423440 350590 463130 513740 412500 FALSE TRUE 407098.568 450868.6295 461667.6888 428478.9265 415014.3724 364077.4242 418215.7239 403880.6989 363734.7199 1.119218336 1.239553457 1.26924284 1.177998423 1.140980912 1.000942182 1.149782248 1.110371589 1 18.47252712 3.141641895 2.846672444 1.079724557 1.211666948 0.524961013 0.059954943 0.216033511 3.540323335 0.019189415 0.022688148 1385.612825 -3.141641895 0.131942391 AKPVGS(ph)PLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKPVGSPLFK 10 1 Q92576-2;Q92576;E7EVH3;D6R9X2;E9PE34;A0A1B0GX99 Q92576-2 PHF3 PHD finger protein 3 1 AKPVGS(1)PLFK;AKPVGS(1)PLFK 65.219 0.042166 2402000000 2582200 1741750 1484240 1671200 1872880 1424730 2410500 2733700 2413300 TRUE FALSE 2240955.728 1730308.33 2202023.428 2050671.503 1835613.352 1479540.285 2176730.081 2149119.529 2128002.423 1.0530795 0.813113891 1.034784267 0.963660323 0.862599277 0.695271899 1.022898309 1.009923441 1 21.02106836 AKPVNSKPDSAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKPVNSKPDSAYR 13 2 O95573;C9JC11;F5H062 O95573 ACSL3 Long-chain-fatty-acid--CoA ligase 3 0 109.22 0.00064933 490580000 1498500 1310100 1066900 1653100 1778500 1445700 1314900 2599400 2287800 FALSE TRUE 1300469.428 1301493.867 1582856.409 2028461.621 1743111.33 1501317.014 1187381.2 2043538.539 2017338.89 0.644645991 0.645153808 0.784625933 1.005513566 0.864064703 0.744206649 0.58858787 1.012987232 1 20.94402203 4.117699371 3.915443312 0.863298202 0.644431299 0.331524921 0.129837557 0.27466421 7.737312817 0.036168134 0.083332202 13112.91876 -4.117699371 -0.218866902 AKPVVS(ph)DFDS(ph)DEEQDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKPVVSDFDSDEEQDER 17 1 F6VDE0;P51531-2;P51531;B1ALG1;F6T8Q0;B1ALG2;A0A0U1RR26;A0A1W2PS06;B4DNT1;B1ALF6 F6VDE0 SMARCA2 Probable global transcription activator SNF2L2 2 AKPVVS(1)DFDS(1)DEEQDER 69.071 0.020221 91727000 143540 112320 108850 129930 130790 125940 138760 156530 293110 TRUE FALSE 124570.8253 111582.1625 161490.2241 159432.5924 128187.5349 130784.9933 125303.0766 123057.2776 258458.8697 0.481975432 0.431721158 0.624819819 0.616858661 0.495968798 0.506018592 0.484808576 0.476119383 1 17.97957519 1.235789588 24.99966124 1.000000649 0.514739048 0.862624618 0.060852582 28.51738285 257227.5027 0.106931703 0.01587599 17.21034545 -1.235789588 -0.485261601 AKQEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKQEAER 7 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDG6;H0YDQ3;U3KQE6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7;A0A087WTA5;E7ERK9;Q9UI10-3;Q9UI10;Q9UI10-2;A0A087WW69;F8W8L6 E9PMS6;Q8WWI1-3;A0A087WTA5 LMO7;EIF2B4 LIM domain only protein 7;Translation initiation factor eIF-2B subunit delta 0 66.258 0.062347 31088000 78253 81582 48224 72679 54011 69299 94038 103610 95907 FALSE TRUE 67911.66778 81046.08247 71545.2877 89181.87778 52936.28677 71964.97737 84918.20923 81453.80779 84568.98372 0.8030328 0.958342869 0.845999142 1.054545932 0.625953919 0.850961833 1.004129475 0.963164085 1 16.36784102 2.241800683 24.95158514 0.984321313 0.85915232 0.247054551 0.108972083 119.7944703 922541.8251 0.040909932 0.03034187 174.5021102 -2.241800683 -0.125168992 AKQTLENER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKQTLENER 9 1 P35579 P35579 MYH9 Myosin-9 0 ; 146.71 8.59E-05 787440000 1407210 1561100 768390 826620 1326450 1368950 1703890 1893450 228770 FALSE TRUE 1221243.633 1550845.031 1139985.974 1014316.705 1300056.24 1421614.392 1538647.01 1488550.452 201725.0712 6.054000258 7.687914159 5.651186376 5.028213395 6.444693425 7.047286605 7.627445616 7.379104855 1 17.62203087 4.218524339 24.91616697 6.033675568 6.870958381 0.039863783 1.925749723 888.6960519 1105143.133 0.489857917 1.021802296 16539.57473 -4.218524339 0.837282812 AKS(ph)LDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AKSLDRR 7 2 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 AKS(1)LDRR;AKS(1)LDRR;AKS(1)LDRR 79.986 0.024524 1294160000 3253870 2680190 1605080 1935650 1860800 2151180 3008770 3301290 1771640 TRUE FALSE 2823862.835 2662583.655 2381302.057 2375168.917 1823773.721 2233937.287 2716979.948 2595334.824 1562198.737 1.807620738 1.704382158 1.524327219 1.520401252 1.167440273 1.429995578 1.739202499 1.661334606 1 20.57514657 4.290852941 1.920690039 1.455932363 1.812107034 0.286314882 0.215533448 0.599258388 3.997482417 0.062225154 0.27863295 19536.77797 -4.290852941 0.356174671 AKS(ph)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 44 AKSPQPPVEEEDEHFDDTVVCLDTYNCDLHFK 32 1 Q00839;Q5RI18;A0A1W2PRI6;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(0.999)PQPPVEEEDEHFDDT(0.001)VVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(0.998)PQPPVEEEDEHFDDT(0.002)VVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(0.952)PQPPVEEEDEHFDDT(0.048)VVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(0.999)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK 312.73 2.74E-104 2.83518E+11 5009907.4 3809652.95 3158092.9 3364071.4 3600868.7 2990538.4 4654439.3 5257360.2 5011095.9 TRUE FALSE 4347835.444 3784627.089 4685357.19 4127935.228 3529218.458 3105586.347 4203052.493 4133114.634 4418689.851 0.983964838 0.856504352 1.060349866 0.934198907 0.798702461 0.702829674 0.951198802 0.935371065 1 22.07518724 4.769486019 20.64591629 0.905586646 0.983966196 0.057165879 0.100882481 3591.07202 2396984.364 0.025901351 1.971624704 58814.71794 -4.769486019 0.078379549 AKS(ph)PT(ph)PDGSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKSPTPDGSER 11 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 2 AKS(0.928)PT(0.804)PDGS(0.268)ER;AKS(0.971)PT(0.705)PDGS(0.324)ER 125.29 0.0083086 1353540000 3255430 2557830 1710190 1874970 2456450 2488720 3139910 3539530 3313440 TRUE FALSE 2825216.677 2541027.446 2537243.604 2300710.596 2407571.451 2584462.669 2835402.011 2782629.054 2921728.898 0.966967428 0.86969994 0.86840487 0.787448349 0.824022877 0.884566214 0.970453492 0.952391256 1 21.47839089 2.306316667 3.869966782 0.97053058 0.859295171 0.544139771 0.046519217 0.17521796 5.215314806 0.019584528 0.01429887 202.4494805 -2.306316667 -0.111235409 AKS(ph)PTPDGS(ph)ER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKSPTPDGSER 11 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 2 AKS(0.798)PT(0.203)PDGS(0.999)ER;AKS(0.783)PT(0.219)PDGS(0.999)ER 123.72 0.0043531 1480820000 4452770 3325000 2139980 2458310 3302380 3266730 4082920 4461680 4356160 TRUE FALSE 3864325.163 3303157.856 3174881.486 3016506.858 3236669.099 3392403.217 3686959.047 3507584.453 3841179.727 1.006025606 0.859933169 0.826538124 0.785307398 0.842623706 0.883167011 0.959850699 0.913152912 1 21.87311804 2.360455534 3.950039854 0.948559647 0.857717684 0.330824461 0.060154503 0.273522798 7.918864619 0.024282681 0.01822342 229.3271817 -2.360455534 -0.090841963 AKS(ph)PTPDGSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AKSPTPDGSER 11 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 AKS(0.846)PT(0.154)PDGSER;AKS(0.803)PT(0.197)PDGSER;AKS(0.874)PT(0.126)PDGSER;AKS(0.778)PT(0.216)PDGS(0.006)ER 127.71 0.00042946 375534000 853080 688692 439674 519837 581392 574304 694590 849980 795251 TRUE FALSE 740343.3166 684167.9369 652301.817 637873.9361 569823.4367 596397.8465 627228.7687 668218.3916 701237.3327 1.055767116 0.975658176 0.930215473 0.909640583 0.81259712 0.850493576 0.894460034 0.952913315 1 19.41954328 4.547910924 1.608002541 0.902908522 1.079790968 0.487641446 0.050667035 0.684408359 2.268898836 0.015763997 0.169447568 35311.07378 -4.547910924 0.176882446 AKS(ph)PTPESSTIASYVTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.712)PT(0.288)PESSTIASYVTLR;AKS(0.707)PT(0.292)PESSTIASYVTLR;AKS(0.986)PT(0.014)PESSTIASYVTLR;AKS(0.838)PT(0.159)PES(0.002)STIASYVTLR 206.03 5.43E-16 4649970000 892830 746210 513914 624210 760380 629640 858760 1010050 841790 TRUE FALSE 774840.2534 741308.0974 762444.5293 765946.421 745249.9257 653862.6582 775477.5874 794058.6677 742274.5452 1.043872861 0.998697991 1.027173213 1.031890998 1.004008464 0.880890585 1.044731484 1.069764109 1 19.50159337 2.075155138 24.99997817 1.04512382 0.997791621 0.132126696 0.047723978 65.21666396 21691.66534 0.019845748 0.01338 118.8926857 -2.075155138 -0.047332198 AKSEDS(ph)DVELS(ph)D ddPTM_MDA-MB-175_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(0.023)EDS(0.977)DVELS(1)D;AKS(0.065)EDS(0.935)DVELS(1)D 103.79 0.026398 276810000 1075900 814430 556150 683100 911180 745190 994100 1091590 860550 TRUE FALSE 933717.089 809079.9557 825106.0002 838208.2955 893049.3007 773857.9415 897692.335 858161.9733 758816.7593 1.230490863 1.066238912 1.087358694 1.104625439 1.176897175 1.01982189 1.183015957 1.130921217 1 19.53339202 4.776015675 0.009020484 1.84E-07 2.269174014 0.110597794 0.068470837 44428.41882 110.6378459 13409.88659 14436.35273 59705.68352 -4.776015675 2.26917383 AKSELTLTPDPAPPMAHS(ph)PLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AKSELTLTPDPAPPMAHSPLHR 22 1 M0R344;Q9NRA0-4;Q9NRA0-2;Q9NRA0;Q9NRA0-5;E9PCV4;Q9NRA0-3 M0R344 SPHK2 Sphingosine kinase 2 1 AKSELTLTPDPAPPMAHS(1)PLHR;AKSELTLTPDPAPPMAHS(1)PLHR;AKSELTLTPDPAPPMAHS(1)PLHR 113.15 0.00016293 587210000 250022 370690 287660 319887 479230 501600 560470 622020 249516 TRUE FALSE 216980.9592 368254.913 426773.3382 392522.2325 469694.2606 520896.8766 506115.7057 489005.8636 220018.5027 0.986194145 1.673745201 1.939715673 1.784041922 2.134794369 2.36751396 2.300332469 2.222567 1 17.74726533 4.984403022 1.146432177 2.043506418 5.40E-17 0.38151265 0.388490331 2.644308659 2.020335711 0.115724367 7.395199105 96472.38657 -4.984403022 -2.043506418 AKT(ph)PEPGAQQSGFPTLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKTPEPGAQQSGFPTLSR 18 1 Q9H9D4 Q9H9D4 ZNF408 Zinc finger protein 408 1 AKT(1)PEPGAQQSGFPTLSR 165.4 4.57E-11 214650000 89153 84481 47818 72328 82904 70181 81301 101890 102860 TRUE FALSE 77371.20517 83926.03875 70942.94474 88751.17786 81254.3726 72880.90848 73416.44153 80101.61641 90700.00798 0.853045186 0.925314569 0.782171318 0.978513452 0.895858495 0.80353806 0.809442504 0.883148946 1 16.46881506 1.253275124 4.603253704 1.00889524 0.865095812 0.339672762 0.059051795 0.213005477 9.662131236 0.09660578 0.014616589 17.91740557 -1.253275124 -0.143799427 AKT(ph)PVTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AKTPVTLK 8 1 P42167;G5E972;H0YJH7;P42167-3;P42167-2 P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 AKT(0.971)PVT(0.029)LK;AKT(0.93)PVT(0.07)LK;AKT(0.964)PVT(0.036)LK;AKT(0.954)PVT(0.046)LK 102.4 0.0080387 4947890000 6583710 5475690 4316280 6225650 7014870 4178750 5277960 10522000 8732270 TRUE FALSE 5713656.043 5439719.832 6403647.445 7639278.986 6875287.811 4339509.217 4766104.252 8271952.182 7699950.988 0.742037975 0.706461618 0.831647819 0.992120469 0.892900204 0.563576213 0.618978518 1.074286342 1 22.87641783 1.676516437 8.053131363 1.035343877 0.770867796 0.447383913 0.125637308 0.117344154 13.38717072 0.079775574 0.035475163 47.48062611 -1.676516437 -0.264476081 AKT(ph)QTPPVS(ph)PAPQPT(ph)EERLPSSPVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 3 AKT(0.561)QT(0.439)PPVS(1)PAPQPT(0.601)EERLPS(0.187)S(0.212)PVYEDAASFK 140.22 3.67E-09 472970000 161430 196620 128630 131820 225440 176240 363280 433220 53075 TRUE FALSE 140096.6165 195328.3903 190835.8982 161751.7457 220954.1851 183020.0668 328049.1615 340579.2743 46800.53396 2.993483292 4.173635934 4.07764361 3.45619445 4.721189404 3.910640571 7.009517493 7.277251892 1 15.51423737 2.27790419 24.27976369 5.629849702 3.92849895 0.068440553 1.759459082 198.1787919 122299.4206 0.647655377 0.50166118 189.6287535 -2.27790419 -1.701350751 AKT(ph)QTPPVS(ph)PAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 3 AKT(0.5)QT(0.5)PPVS(1)PAPQPT(0.001)EERLPS(0.531)S(0.468)PVYEDAASFK;AKT(0.5)QT(0.5)PPVS(1)PAPQPT(0.002)EERLPS(0.529)S(0.468)PVYEDAASFK;AKT(0.5)QT(0.5)PPVS(1)PAPQPTEERLPS(0.535)S(0.465)PVYEDAASFK 164.87 3.61E-13 5205150000 1510910 1919630 1106831 1335440 2595610 1845050 3504020 4292030 528257 TRUE FALSE 1311239.415 1907019.824 1642098.174 1638672.063 2543962.439 1916030.267 3164200.68 3374212.785 465807.0593 2.814983992 4.094012287 3.525275414 3.5179202 5.461408085 4.113356012 6.792942736 7.243799161 1 18.82937298 3.241202723 24.62562846 5.312339433 3.533989847 0.124206619 1.725936343 96.12658576 895933.1082 0.50877812 0.626799947 1742.620118 -3.241202723 -1.778349586 AKT(ph)QTPPVS(ph)PAPQPTEERLPSSPVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.5)QT(0.5)PPVS(1)PAPQPTEERLPSSPVYEDAASFK 123.4 2.92E-07 59687000 42014 43171 16757 19760 46741 42770 65820 72213 11910 TRUE FALSE 36461.74345 42887.40686 24860.74125 24246.81001 45810.94555 44415.38958 59436.78653 56770.81191 10502.01337 3.471881264 4.083731886 2.367235727 2.308777295 4.362110763 4.229226151 5.659561119 5.405707451 1 13.35837832 3.186836892 12.25778174 4.410864701 3.082126935 0.116217869 1.353289648 1.504672992 353.5598405 0.414774079 0.470613088 1537.577064 -3.186836892 -1.328737765 AKT(ph)QTPPVSPAPQPTEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKTQTPPVSPAPQPTEER 18 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKT(0.569)QT(0.431)PPVSPAPQPTEER 75.184 0.027987 2123500000 1858000 1586600 1285500 1351400 1747000 1579500 1898000 1966700 1381900 TRUE FALSE 1612460.592 1576177.52 1907172.1 1658256.025 1712238.118 1640264.387 1713932.252 1546136.51 1218533.356 1.323279814 1.293503795 1.565137376 1.360862234 1.405163108 1.346097239 1.406553414 1.268850378 1 20.21671431 1.225255221 2.014229008 0.863779804 1.388251611 0.734954498 0.073216243 0.40353621 1.552482579 0.402885729 0.019545185 16.79790886 -1.225255221 0.524471807 AKT(ph)QTPPVSPAPQPTEERLPSS(ph)PVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.6)QT(0.4)PPVSPAPQPTEERLPS(0.449)S(0.551)PVYEDAASFK 240.15 1.86E-46 2470500000 1101100 1144000 707250 768750 1326600 978200 2035000 2348000 251990 TRUE FALSE 955586.8452 1136484.989 1049278.466 943306.4371 1300203.255 1015831.987 1837646.013 1845898.472 222200.0293 4.300570294 5.114693245 4.722224696 4.245302938 5.851499029 4.571700509 8.270232994 8.307372768 1 17.76149948 2.29893676 24.99994381 6.469746547 4.834164306 0.028235081 2.064604983 149.7132606 61990.59602 0.761010545 0.58947594 199.0383489 -2.29893676 -1.635582241 AKT(ph)QTPPVSPAPQPTEERLPSSPVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKT(0.554)QT(0.442)PPVS(0.003)PAPQPTEERLPSSPVYEDAASFK;AKT(0.541)QT(0.44)PPVS(0.02)PAPQPTEERLPSSPVYEDAASFK 122.41 7.82E-06 3420600000 912514 683443 293586 294273 511562 381400 660856 741590 49001 TRUE FALSE 791922.9629 678953.4179 435565.1716 361092.1823 501382.9171 396072.7048 596766.2868 583006.7496 43208.1576 18.32808911 15.71354706 10.08062356 8.357037244 11.60389484 9.166618685 13.81142636 13.49297869 1 15.3990161 4.339884579 3.278575299 10 17.89417388 0.431393905 3.562386465 0.238352013 4.881312052 0.916081213 2.974854382 21871.80268 -4.339884579 7.89417388 AKTQT(ph)PPVS(ph)PAPQPTEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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(0.001)QT(0.999)PPVS(1)PAPQPTEER;AKTQT(1)PPVS(1)PAPQPTEER;AKTQT(1)PPVS(0.998)PAPQPT(0.002)EER;AKT(0.003)QT(0.997)PPVS(1)PAPQPTEER;AKT(0.3)QT(0.7)PPVS(1)PAPQPTEER;AKT(0.236)QT(0.765)PPVS(1)PAPQPTEER 211.81 6.00E-16 33380600000 11116930 14166600 11352420 14961140 19620740 15273810 20664500 23983480 14657510 TRUE FALSE 9647799.534 14073538.67 16842488.28 18358295.5 19230325.66 15861403.35 18660459.97 18854799.44 12924715.87 0.746461248 1.08888573 1.303122518 1.420402251 1.487872218 1.227214859 1.44378106 1.458817326 1 23.62362923 4.594683038 1.804274285 1.360763319 0.644116252 0.637586222 0.143520951 0.379851183 1.587378516 0.037557655 0.420861025 39326.29549 -4.594683038 -0.716647067 AKTQT(ph)PPVS(ph)PAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 3 AKT(0.436)QT(0.566)PPVS(0.999)PAPQPT(0.009)EERLPS(0.525)S(0.46)PVY(0.006)EDAASFK 137.46 1.22E-07 271580000 120200 144850 93900 108110 194620 132650 292890 346660 49984 TRUE FALSE 104315.2655 143898.4708 139310.3541 132658.0279 190747.4428 137753.1313 264485.5729 272529.4567 44074.94846 2.366769993 3.264858516 3.160760453 3.009828315 4.327797296 3.12542921 6.000814116 6.183318784 1 15.42767126 2.991034137 1.352290555 4.67670131 2.930895437 0.089628011 1.496047562 0.719375477 2.771524788 0.654685482 0.705447121 979.5669803 -2.991034137 -1.745805873 AKTQT(ph)PPVS(ph)PAPQPTEERLPSSPVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.12)QT(0.88)PPVS(0.997)PAPQPT(0.003)EERLPSSPVYEDAASFK 132.08 1.34E-07 589680000 423550 428710 227240 271600 492940 363710 717190 820540 72981 TRUE FALSE 367576.7944 425893.7758 337134.0241 333270.9311 483131.4584 377702.1591 647637.0242 645073.9064 64353.26932 5.711858904 6.618059662 5.238801814 5.17877234 7.507488952 5.869199235 10.06377813 10.02394926 1 15.97372582 7.805277099 14.02895049 6.727877423 5.894066055 0 2.620590508 0 0 0.598141441 0 63867085.64 -7.805277099 -0.833811368 AKTQT(ph)PPVSPAPQPT(ph)EERLPSSPVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.157)QT(0.843)PPVS(0.001)PAPQPT(0.431)EERLPS(0.259)S(0.31)PVYEDAASFK 232.16 4.41E-37 493450000 453230 463860 258680 274780 505010 367700 735050 888270 94297 TRUE FALSE 393334.5072 460812.8731 383778.5132 337172.9987 494961.289 381845.6569 663764.9641 698320.373 83149.31608 4.730459921 5.541992344 4.615534214 4.055030331 5.952680219 4.592288607 7.98280726 8.39838986 1 16.34341678 2.277919678 24.99797733 6.427586425 4.937689923 0.008744807 2.060258588 357.642912 227147.1246 0.758465085 0.587495273 189.6355162 -2.277919678 -1.489896502 AKTQT(ph)PPVSPAPQPTEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 AKTQTPPVSPAPQPTEER 18 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKT(0.216)QT(0.784)PPVSPAPQPTEER;AKT(0.073)QT(0.927)PPVSPAPQPTEER;AKT(0.25)QT(0.75)PPVSPAPQPTEER;AKT(0.014)QT(0.986)PPVSPAPQPTEER;AKT(0.076)QT(0.924)PPVSPAPQPTEER;AKT(0.025)QT(0.975)PPVSPAPQPTEER;AKT(0.097)QT(0.903)PPVSPAPQPTEER;AKT(0.021)QT(0.979)PPVSPAPQPTEER 142.32 1.84E-07 38244250000 15395550 12847590 9633680 11826060 14430330 12109780 14826470 16868600 11387530 TRUE FALSE 13360989.06 12763193.34 14292559.87 14511347.67 14143194.67 12575651.07 13388601.22 13261381.16 10041309.18 1.330602298 1.271068654 1.423376138 1.44516491 1.408501065 1.252391581 1.333352154 1.320682486 1 23.25944404 1.207750847 3.308099224 0.926487761 1.35260441 0.758622863 0.061894845 0.20481861 2.910787609 0.235566119 0.01705325 16.13432672 -1.207750847 0.426116648 AKTQT(ph)PPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.141)QT(0.858)PPVSPAPQPTEERLPS(0.531)S(0.468)PVYEDAASFK;AKT(0.048)QT(0.952)PPVSPAPQPT(0.002)EERLPS(0.55)S(0.448)PVYEDAASFK;AKT(0.19)QT(0.81)PPVSPAPQPT(0.005)EERLPS(0.544)S(0.451)PVYEDAASFK 254.34 7.63E-59 13841000000 2670080 2640820 1534660 1748520 3323580 2406150 4720370 5223530 573170 TRUE FALSE 2317222.163 2623472.28 2276826.709 2145548.19 3257447.26 2498716.147 4262589.244 4106518.759 505410.4956 4.584831901 5.190775226 4.504905872 4.245159547 6.445151593 4.943934029 8.433915167 8.125115713 1 18.9470961 3.233893409 24.90911724 6.237597442 4.662335567 0.049351759 2.055336816 249.4723884 1331445.023 0.619180702 0.725246558 1713.536694 -3.233893409 -1.575261875 AKTQT(ph)PPVSPAPQPTEERLPSSPVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKT(0.02)QT(0.975)PPVS(0.004)PAPQPTEERLPSSPVYEDAASFK 210.86 9.05E-26 2552100000 374930 240740 124900 117910 172620 149200 296020 319270 27497 TRUE FALSE 325382.0505 239158.5631 185302.0578 144683.2676 169185.1997 154939.8205 267312.026 250996.5951 24246.33598 13.41984417 9.863699127 7.642476698 5.967221923 6.977763561 6.390236473 11.02484211 10.35193916 1 14.56547913 4.605463866 2.175116114 7.486418131 14.12056928 0.361096575 2.722111764 0.598146027 3.988642973 0.728749212 6.888037496 40314.74022 -4.605463866 6.634151144 AKTQTPPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKTQTPPVSPAPQPT(0.001)EERLPS(0.576)S(0.424)PVYEDAASFK;AKTQTPPVSPAPQPTEERLPS(0.575)S(0.425)PVYEDAASFK 207.52 1.99E-27 1436350000 1076560 1101110 458330 468900 1106680 859240 1765820 1797210 50253 TRUE FALSE 934289.8683 1093876.736 679979.921 575370.9117 1084659.233 892295.5188 1594571.048 1412890.627 44312.14759 21.08428319 24.68570799 15.34522604 12.98449619 24.47769499 20.13658934 35.98496428 31.88495039 1 15.43541463 -1.998811994 5.53E-11 9.784499598 34.3305703 0 9.881228008 88523141.03 0.139197442 140221504.4 140221502.7 0.010027392 1.998811994 24.5460707 AKVDEFPLCGHMVSDEYEQLSSEALEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AKVDEFPLCGHMVSDEYEQLSSEALEAAR 29 1 P27635;X1WI28;A6QRI9;B8A6G2 P27635 RPL10 60S ribosomal protein L10 0 ;; 285.17 6.51E-72 560240000 496220 455670 244270 319988 404340 367810 455770 599570 277323 FALSE TRUE 430643.2697 452676.6738 362399.789 392646.1661 396294.4251 381959.8887 411569.4956 471356.6214 244538.1909 1.761047091 1.851149189 1.481976242 1.605663985 1.62058296 1.561964155 1.683047928 1.927537861 1 17.89970027 1.225936415 24.99970214 0.999998391 1.688003848 0.724922482 0.132920947 357.0342888 706991.241 0.615885082 0.035122022 16.82427719 -1.225936415 0.688005457 AKVEEAR ddPTM_MDA-MB-175_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 ; 111.95 0.0058957 380290000 1754090 1499830 1010530 1177050 941510 1316000 1620250 1799090 1559030 FALSE TRUE 1522282.562 1489977.518 1499225.688 1444317.193 922775.793 1366627.372 1463118.404 1414368.604 1374723.249 1.107337468 1.083838161 1.090565456 1.050623966 0.671244771 0.994110903 1.064300327 1.02883879 1 20.39070978 3.462631633 24.99998135 0.961818731 1.089187671 0.277008203 0.106608274 358.5103552 618561.355 0.032704888 0.042238692 2901.560516 -3.462631633 0.12736894 AKVEFNIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKVEFNIR 8 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ; 131.44 0.00091656 3160600000 2413600 2946000 1856730 2055630 2738000 2373800 2880400 3245500 2459900 FALSE TRUE 2094636.645 2926647.532 2754650.838 2522392.21 2683519.157 2465121.622 2601059.251 2551475.082 2169093.424 0.965673779 1.349249184 1.269954907 1.162878547 1.23716163 1.136475541 1.199145792 1.176286394 1 21.04866076 1.224036947 3.565199698 0.968495674 1.196393618 0.258362633 0.099118242 0.4134721 7.713982554 0.26142857 0.023570684 16.75085374 -1.224036947 0.227897944 AKVYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKVYGR 6 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ; 85.306 0.050036 526430000 682940 657340 345970 389400 432110 548030 717560 701780 158625 FALSE TRUE 592687.7487 653021.8903 513282.2492 477819.2216 423511.8564 569113.0687 647971.1416 551709.8083 139872.5332 4.237341922 4.668692811 3.669642906 3.416104725 3.027841469 4.068797895 4.632583158 3.944375608 1 17.09375316 4.150870861 5.372354412 3.511266322 4.448246782 0.165274047 0.966472256 0.392028715 18.17637097 0.250446661 0.546454831 14153.72851 -4.150870861 0.93698046 AKWDAWNELK ddPTM_MDA-MB-175_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 ; 198.81 2.64E-07 3692400000 6426200 5336100 4925000 5214800 4548800 3264300 5135800 6857500 15511600 FALSE TRUE 5576961.388 5301046.808 7306746.473 6398900.043 4458287.78 3389879.733 4637730.906 5391076.99 13677836.32 0.407737105 0.38756472 0.534203386 0.467829845 0.325949783 0.247837425 0.339069046 0.394146915 1 23.70533669 1.238775951 8.236753076 1.006620378 0.386300279 0.860369103 0.077481083 0.034903752 23.30509015 0.121234203 0.021129089 17.32909773 -1.238775951 -0.6203201 AKWDAWNELKGTSKEDAMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKWDAWNELKGTSKEDAMK 19 3 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 83.063 0.0015635 148540000 607540 400040 319760 287160 252790 184630 500180 576620 338710 FALSE TRUE 527252.0497 397412.1109 474397.0055 352364.067 247759.9736 191732.8356 451672.6206 453314.3003 298668.0897 1.765344434 1.330614567 1.588375263 1.179784782 0.829549531 0.64195956 1.512289515 1.517786185 1 18.18818358 3.71268466 7.610304531 1.148484799 1.538525874 0.344352804 0.288120449 0.319310958 79.08775223 0.089209236 0.135698405 5160.415375 -3.71268466 0.390041075 AKWYPEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKWYPEVR 8 1 P63000;J3KSC4;J3QLK0;P60763;P63000-2 P63000 RAC1;RAC3 Ras-related C3 botulinum toxin substrate 1;Ras-related C3 botulinum toxin substrate 3 0 ; 98.033 0.0071224 1640120000 4576400 4932000 2845200 3583100 5469200 5451500 4119800 6518900 2369200 FALSE TRUE 3971617.145 4899601.367 4221148.237 4396697.619 5360373.62 5661222.733 3720262.43 5124883.965 2089115.875 1.9010995 2.345298997 2.020542894 2.104573361 2.565857492 2.709865355 1.780783189 2.453135332 1 20.99446108 1.232589984 24.98877464 0.999997966 2.241890158 0.636007828 0.293613949 125.4062841 524806.7778 0.613591664 0.069302278 17.08401657 -1.232589984 1.241892191 AKYAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AKYAYR 6 1 J3KS46 J3KS46 HEXDC 0 69.439 0.085273 188090000 406730 454830 258810 381310 287040 371870 475810 522490 452630 FALSE TRUE 352979.6 451842.1918 383971.3817 467892.2635 281328.4656 386176.0795 429666.0194 410759.5795 399120.597 0.884393345 1.132094397 0.962043514 1.172307986 0.704870828 0.967567403 1.076531812 1.029161568 1 18.60646521 2.26096001 24.17135321 1.035687509 0.974597665 0.052924393 0.128225262 555.5960645 599545.6171 0.046849248 0.036257227 182.3727766 -2.26096001 -0.061089843 AKYHGNVMLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AKYHGNVMLLR 11 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 116.23 0.00061071 2708100000 1025140 1112050 611050 681990 1063980 1027990 1116230 1218450 656450 FALSE TRUE 889665.1516 1104744.87 906555.8238 836846.2531 1042808.88 1067537.44 1007978.186 957893.9495 578845.2288 1.536965509 1.908532394 1.566145454 1.445716767 1.801533169 1.844253675 1.741360447 1.654836046 1 19.14281813 1.237671574 5.022122898 0.955398038 1.69595715 0.694607744 0.143431884 0.09872356 6.396983839 0.256364905 0.035934997 17.28508716 -1.237671574 0.740559111 AKYPDYEVTWANDGY ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AKYPDYEVTWANDGY 15 1 Q9NRX4 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 ;; 238.2 7.53E-17 363502000 1025760 878770 552240 725600 776900 676360 871300 1069850 933910 FALSE TRUE 890203.2171 872997.302 819305.1111 890358.5701 761441.21 702380.0069 786801.4601 841070.9031 823504.2237 1.080994112 1.060100576 0.994900922 1.081182761 0.924635464 0.852916095 0.955430995 1.02133162 1 19.65141652 3.238475139 25 0.955116704 1.050466906 0.508564033 0.050364083 2.353470125 688352.9687 0.016845408 0.020357237 1731.709897 -3.238475139 0.095350202 ALAAFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALAAFLK 7 0 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 109.88 0.037422 0 382610 352940 275330 302680 351200 285930 394660 449260 442120 FALSE TRUE 332047.1191 350621.5139 408480.5089 371408.1202 344211.8071 296929.9121 356385.9339 353189.2451 389853.0773 0.851723735 0.899368337 1.047780645 0.952687414 0.882926998 0.76164568 0.914154472 0.905954745 1 18.572571 3.236583014 24.99999988 0.889590492 0.942987817 0.078579205 0.07511704 131.7715408 1665799.45 0.023374248 0.027846148 1724.18163 -3.236583014 0.053397326 ALAAFLKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALAAFLKK 8 1 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ; 114.6 0.0078716 0 1013900 979280 413310 494440 841220 680930 1087430 1141760 139921 FALSE TRUE 879910.5461 972847.0452 613188.0984 606710.159 824481.3678 707125.8177 981971.206 897603.5092 123379.6988 7.131728759 7.884984765 4.969927018 4.917422923 6.682471881 5.731297975 7.958936646 7.275131307 1 16.9127455 4.248685175 24.97928417 5.823678165 7.508357302 0.145407573 1.900697765 449.1480467 1108114.049 0.471461131 1.216783242 17729.03818 -4.248685175 1.684679138 ALAAGADS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALAAGADSPK 10 0 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 ALAAGADS(1)PK;ALAAGADS(1)PK 130.77 0.0002809 652360000 1156210 1204660 858660 1168380 1425890 1246560 1233690 1491970 1758990 TRUE FALSE 1003413.919 1196746.509 1273910.848 1433678.537 1397517.579 1294515.97 1114046.934 1172923.826 1551044.206 0.646927995 0.771574727 0.821324655 0.92433119 0.901017246 0.834609333 0.718256082 0.756215601 1 20.56480837 4.648006642 2.103666824 0.839192616 0.615385792 0.393629188 0.080749457 0.668226423 3.840444417 0.022765767 0.263777145 44463.80672 -4.648006642 -0.223806824 ALADENEFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALADENEFVR 10 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 96.143 0.016149 120780000 61396 60373 42209 41556 67927 77663 64218 72357 69035 FALSE TRUE 53282.36304 59976.40579 62621.41358 50991.92494 66575.3856 80650.74586 57990.14824 56884.01863 60873.76094 0.875292773 0.985258753 1.028709457 0.837666741 1.093663092 1.324885215 0.952629628 0.934458751 1 15.89353288 3.216056879 24.99997453 1.050344334 0.942482173 0.220925295 0.11903646 476.2142721 529037.0823 0.039401105 0.044707667 1644.5871 -3.216056879 -0.107862162 ALAEEAKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 149.65 0.00080453 884180000 1318450 1104380 698700 776060 935340 985870 1191420 1299990 596320 FALSE TRUE 1144213.492 1097125.255 1036593.657 952276.2843 916728.564 1023797.057 1075876.272 1021997.255 525823.7289 2.176040047 2.086488674 1.971371013 1.811018088 1.743414216 1.94703472 2.046077825 1.943611897 1 19.00421972 1.238877555 7.581973814 0.985171029 1.961017627 0.856070405 0.124442186 0.038583367 16.43933673 0.194072168 0.033325285 17.3331524 -1.238877555 0.975846598 ALALDLGS(ph)PAALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALALDLGSPAALR 13 0 Q8TER5;Q8TER5-4;Q8TER5-3;Q8TER5-2 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 ALALDLGS(1)PAALR;ALALDLGS(1)PAALR 135.86 8.30E-05 61154000 130930 139307 88421 106595 124136 134003 131917 154299 141175 TRUE FALSE 113627.2688 138391.8831 131181.6914 130799.024 121665.9365 139158.1821 119123.7096 121303.3596 124485.4523 0.912775482 1.111711293 1.053791338 1.050717345 0.97735064 1.117867024 0.956928761 0.974438035 1 16.92561763 2.178982713 24.99995581 0.975721513 1.039374941 0.181738366 0.060137634 113.3827085 47576.11712 0.022774446 0.015354535 151.0020045 -2.178982713 0.063653428 ALALLEDEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALALLEDEER 10 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6 A0A499FIX8 ESYT2 Extended synaptotagmin-2 0 91.867 0.022931 23778000 22784 13521 14978 15977 19459 21878 16043 22642 19826 FALSE TRUE 19773.03667 13432.17966 22221.4109 19604.82204 19071.80397 22719.66082 14487.15233 17800.1845 17482.19287 1.131038699 0.768334943 1.271088305 1.121416643 1.090927444 1.29958873 0.8286805 1.018189459 1 14.09359854 2.221827094 24.99998506 0.95836872 1.104497861 0.20936778 0.149860675 427.3059647 638393.0551 0.060113553 0.04064783 166.6583561 -2.221827094 0.146129141 ALAMPGRPES(ph)PPVFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ALAMPGRPESPPVFR 15 1 Q63ZY3-3;Q63ZY3;Q63ZY3-2;K7ERU2 Q63ZY3-3 KANK2 KN motif and ankyrin repeat domain-containing protein 2 1 ALAMPGRPES(1)PPVFR;ALAMPGRPES(1)PPVFR;ALAMPGRPES(1)PPVFR;ALAMPGRPES(1)PPVFR;ALAMPGRPES(1)PPVFR;ALAMPGRPES(1)PPVFR 133.62 2.43E-05 4677690000 1909790 1960290 1167516 1510889 1814196 1860370 1973904 2055540 1922160 TRUE FALSE 1657406.413 1947412.726 1732130.643 1853959.44 1778097.049 1931939.638 1782475.094 1615978.767 1694924.435 0.977864487 1.148967285 1.021951544 1.093830145 1.049071577 1.139838212 1.051654609 0.953422309 1 20.69278952 1.861368185 5.116647809 0.976895346 1.074655544 0.357962998 0.051782308 0.20073702 7.224238445 0.024693203 0.012498153 72.67217948 -1.861368185 0.097760198 ALAPTWEQLALGLEHSETVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALAPTWEQLALGLEHSETVK 20 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 257.22 3.26E-36 167240000 320210 292250 209230 258080 258310 306100 302930 294900 250120 FALSE TRUE 277893.4372 290330.1905 310414.3278 316681.0085 253170.1364 317875.8651 273551.8952 231837.9299 220551.0985 1.259995706 1.316385148 1.407448568 1.435862304 1.147897871 1.441279899 1.240310735 1.051175584 1 17.75075342 1.787686982 2.741546396 1.009458892 1.334132861 0.673786214 0.08780343 0.138253893 1.99822647 0.063660157 0.023492711 61.33197957 -1.787686982 0.324673969 ALASEKS(ph)PTADAKPAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALASEKSPTADAKPAPK 17 2 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 ALAS(0.009)EKS(0.867)PT(0.124)ADAKPAPK 113.51 0.00021311 297900000 742770 604130 585310 553490 497370 370250 830320 1066100 754580 TRUE FALSE 644611.0626 600161.4303 868367.8737 679168.3641 487473.3101 384493.7571 749795.6942 838122.8114 665374.412 0.968794488 0.901990548 1.305081557 1.020731113 0.732630082 0.57786075 1.126877861 1.259625853 1 19.34380686 2.030513554 24.99939287 1.161826428 0.924434855 0.19890535 0.197002991 300.7039785 246361.9766 0.086560475 0.058358449 107.2787129 -2.030513554 -0.237391573 ALASNTSFFSGCS(ph)PIEEEAH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALASNTSFFSGCSPIEEEAH 20 0 O95239;Q2VIQ3 O95239 KIF4A;KIF4B Chromosome-associated kinesin KIF4A;Chromosome-associated kinesin KIF4B 1 ALASNTSFFSGCS(1)PIEEEAH;ALASNTSFFS(0.005)GCS(0.995)PIEEEAH 199.01 1.57E-21 129788000 161401 185398 96198 123744 158807 154671 152441 190981 153748 TRUE FALSE 140071.4489 184180.1083 142719.6746 151841.9665 155647.0514 160621.2935 137657.2953 150141.1994 135572.0866 1.03318797 1.358540043 1.052721679 1.120009069 1.148075945 1.184766699 1.015380811 1.107463956 1 17.04870064 -1.261373878 0.366003126 6.97E-09 1.168430246 0.182295658 0.094865218 73.68453231 1.874098268 54.42161064 0.110025596 0.054780516 1.261373878 1.168430239 ALASVPS(ph)PALPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALASVPSPALPR 12 0 O60336-4;O60336-3;O60336-6;O60336;O60336-2 O60336-4 MAPKBP1 Mitogen-activated protein kinase-binding protein 1 1 ALAS(0.003)VPS(0.997)PALPR;ALAS(0.002)VPS(0.998)PALPR 110.64 0.0015402 295060000 178375 221250 130452 163652 218170 240240 198210 208223 220370 TRUE FALSE 154802.2918 219796.5942 193539.0235 200811.6879 213828.8438 249482.1883 178987.6247 163696.1318 194318.1096 0.796643669 1.131117396 0.995990666 1.033417257 1.100406155 1.283885422 0.921106247 0.842413155 1 17.56806083 2.034262837 24.99962054 0.901492718 1.062096083 0.199298572 0.126611207 233.6355533 170469.5124 0.050294643 0.033908474 108.2088639 -2.034262837 0.160603365 ALDDKNCWEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALDDKNCWEK 10 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 161.94 0.0037013 392040000 1079940 955850 611620 658900 794950 669400 1208390 1329340 669160 FALSE TRUE 937223.1928 949570.9584 907401.4777 808513.3157 779132.0503 695152.2512 1091200.524 1045070.986 590052.6671 1.588372098 1.609298646 1.53783133 1.370239236 1.320444926 1.178118988 1.849327331 1.771148652 1 19.17048421 3.986676014 7.315127964 1.464381624 1.59324644 0.067512463 0.251607435 0.564366973 178.0678635 0.070938342 0.133793666 9697.862318 -3.986676014 0.128864816 ALDEEVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALDEEVHK 8 0 Q06210-2;Q06210;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 124.98 0.0012814 608250000 1174420 1063630 772200 952890 1063240 1069810 1147990 1406810 1623710 FALSE TRUE 1019217.421 1056642.944 1145638.503 1169258.239 1042083.604 1110966.283 1036658.106 1105974.629 1431756.854 0.71186488 0.738004461 0.800162751 0.816659781 0.727835597 0.775946195 0.724046198 0.772459812 1 20.44935508 1.239914344 5.415182407 1.012085757 0.758527852 0.836925908 0.033581015 0.059153247 5.21103956 0.05597608 0.008479514 17.37458115 -1.239914344 -0.253557904 ALDEYYDKHFTEFVPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALDEYYDKHFTEFVPLR 17 1 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 189.81 2.01E-10 1483630000 1124840 903200 459760 567930 807420 816510 903160 1104460 389060 FALSE TRUE 976189.544 897266.8197 682101.4738 696887.1868 791353.9217 847921.6681 815571.6822 868279.8239 343065.77 2.845488036 2.615436742 1.988252788 2.031351559 2.30671198 2.471600906 2.37730416 2.530942752 1 18.38812566 4.393658846 4.786060062 2.173624076 2.795816684 0.259502471 0.436305447 0.278283933 11.01413124 0.107322224 0.310347687 24754.76715 -4.393658846 0.622192609 ALDFDISETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALDFDISETR 10 0 J3KT25;A0A3B3ITH3;Q9P2X3-2;Q9P2X3;J3QRS6 J3KT25 IMPACT Protein IMPACT 0 102.62 0.0067994 25727000 71610 66762 38124 48965 65102 59626 56420 62194 69276 FALSE TRUE 62146.55706 66323.43603 56560.89392 60083.25163 63806.59757 61919.8508 50948.39708 48894.29709 61086.2702 1.017357204 1.085733927 0.925918275 0.983580295 1.04453255 1.013645957 0.83404007 0.800413856 1 15.89856053 2.244091571 24.99901877 0.860118029 1.011457733 0.474001519 0.065452494 99.66753258 450483.4119 0.02484245 0.018685808 175.4250348 -2.244091571 0.151339704 ALDIAENEMPGLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALDIAENEMPGLMR 14 0 P23526 P23526 AHCY Adenosylhomocysteinase 0 198.81 5.01E-08 100680000 62284 55264 42515 51778 68872 64050 68888 71255 69239 FALSE TRUE 54053.01159 54900.96715 63075.3962 63534.98628 67501.58195 66514.04495 62207.25236 56017.67276 61053.6443 0.885336366 0.899225063 1.033114353 1.040641996 1.10561102 1.089436113 1.018894991 0.917515627 1 15.89778979 4.252364365 8.490277249 1.024096587 0.891653752 0.554383366 0.050913303 0.150040651 65.75146868 0.015569997 0.038691879 17879.87036 -4.252364365 -0.132442835 ALDKLDGTEINGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ALDKLDGTEINGR 13 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;; 150.9 4.06E-05 4873880000 8153100 6901900 4413300 5239070 6725300 5770400 7311300 8764300 5409400 FALSE TRUE 7075647.178 6856560.964 6547586.642 6428680.918 6591479.688 5992391.022 6602251.251 6890122.649 4769906.894 1.483393143 1.437462222 1.372686467 1.347758155 1.381888543 1.256290983 1.384146776 1.444498352 1 22.18552968 1.233292088 24.99982725 0.999999397 1.386357134 0.797654093 0.061488012 78.33189851 371653.0926 0.131267852 0.015821903 17.11165787 -1.233292088 0.386357737 ALDLLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ALDLLDR 7 0 P27361;E9PBK7;E9PQW4;P27361-3;B3KR49;E9PRH7;H0YEX6 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 ;;; 138.33 0.0071227 424640000 891070 893740 605850 642050 863020 950700 876870 924340 888210 FALSE TRUE 773312.8418 887868.9631 898841.0864 787837.2656 845847.5905 987274.0442 791831.2824 726677.0842 783206.8257 0.987367342 1.133632821 1.147642049 1.005912155 1.07997985 1.260553422 1.011011723 0.927822716 1 19.57903381 2.011015591 24.99869971 0.961954222 1.103499799 0.371024652 0.077242837 199.2684755 452216.5704 0.030970866 0.020859992 102.5688748 -2.011015591 0.141545577 ALDSEVDPDPEGDLGMPAQPHS(ph)PTGEAQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALDSEVDPDPEGDLGMPAQPHSPTGEAQHR 30 0 C9JFX4;Q6IA17-2 C9JFX4 SIGIRR Single Ig IL-1-related receptor 1 ALDSEVDPDPEGDLGMPAQPHS(0.5)PT(0.5)GEAQHR 61.415 0.041363 52376000 34503 39295 29659 34357 55576 52045 41288 55903 52468 TRUE FALSE 29943.34113 39036.86856 44002.1916 42158.28196 54470.14633 54047.20483 37283.89611 43948.57849 46265.29281 0.647209589 0.843761407 0.951084256 0.911229118 1.177343599 1.16820194 0.805871829 0.949925437 1 15.4976427 4.707074586 1.327998208 0.997455142 0.50892822 0.525268964 0.109191291 1.139306153 1.854077248 0.034030351 0.742717134 50941.83517 -4.707074586 -0.488526922 ALDSNSLENDDLSAPGREPGHFNPESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALDSNSLENDDLSAPGREPGHFNPESR 27 1 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 240.44 2.19E-45 288610000 78687 67635 51303 51205 69229 94901 76326 78165 76989 FALSE TRUE 68288.31358 67190.70123 76113.3024 62831.87787 67851.47834 98551.90288 68923.91627 61450.02303 67887.44813 1.005904854 0.989736735 1.121169001 0.925530118 0.999470156 1.451695499 1.015267449 0.905175032 1 16.05085724 2.000587712 24.99997142 0.950136341 1.082641139 0.122415256 0.144650687 39.44614402 1677902.401 0.061145623 0.040810583 100.1354173 -2.000587712 0.132504798 ALDVMVSTFHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ALDVMVSTFHK 11 0 P26447 P26447 S100A4 Protein S100-A4 0 ;; 204.69 3.24E-08 18311000000 25264000 25048200 10170700 18874320 22550000 24296800 27297200 26559400 32292900 FALSE TRUE 21925298.39 24883656.72 15089284.54 23160022.83 22101299.12 25231513.62 24649921.75 20879879 28475270.15 0.769976835 0.873869031 0.529908389 0.813338125 0.776157662 0.886085136 0.865660681 0.733263596 1 24.76320619 3.137112895 2.327483722 0.84732138 0.73685796 0.216595708 0.1087914 0.52791335 5.844752373 0.035647651 0.0425088 1371.238174 -3.137112895 -0.110463421 ALDVS(ph)ASDDEIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALDVSASDDEIAR 13 0 C9JIF9;P13798;H7C393;H7C1U0;C9JLK2 C9JIF9 APEH Acylamino-acid-releasing enzyme 1 ALDVS(0.573)AS(0.427)DDEIAR;ALDVS(0.628)AS(0.372)DDEIAR 197.06 1.44E-07 712700000 598020 591560 415840 420100 551330 576590 561380 632400 579900 TRUE FALSE 518990.1418 587674.0034 616941.6149 515490.1258 540359.6117 598771.7904 506937.454 497166.1813 511344.8826 1.014951277 1.149271311 1.20650785 1.008106551 1.056741996 1.170974446 0.991380712 0.972271745 1 18.96393714 2.157477637 8.825748777 0.983962175 1.10173023 0.410448337 0.063926664 0.273806094 26.93348126 0.026246085 0.01768751 143.7069054 -2.157477637 0.117768055 ALDVSAS(ph)DDEIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALDVSASDDEIAR 13 0 C9JIF9;P13798;H7C393;H7C1U0;C9JLK2 C9JIF9 APEH Acylamino-acid-releasing enzyme 1 ALDVS(0.015)AS(0.985)DDEIAR 148.52 4.54E-05 357980000 493910 547780 347710 357600 491120 519640 434170 531340 557720 TRUE FALSE 428638.5421 544181.5971 515863.719 438798.5456 481347.6729 539630.8871 392064.2602 417717.0759 491786.977 0.871593926 1.106539259 1.048957665 0.892253285 0.978772711 1.097285842 0.797223755 0.849386209 1 18.90767401 2.23253601 24.99997529 0.871825618 1.000578682 0.267048655 0.09083874 175.7191838 729163.4717 0.035842163 0.024878517 170.818935 -2.23253601 0.128753064 ALDYYGLYDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALDYYGLYDDR 11 0 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 0 ; 163.88 5.45E-05 257290000 287170 293750 175974 198346 290920 335770 228408 277220 310310 FALSE TRUE 249219.7569 291820.3369 261075.615 243383.4908 285131.2612 348687.2892 206257.0273 217938.6603 273625.5053 0.910806018 1.066495379 0.954134793 0.889476624 1.042049281 1.274323053 0.753793134 0.796485182 1 18.06184319 ALEAASLSQHPPSLCIS(ph)DS(ph)EEEEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALEAASLSQHPPSLCISDSEEEEEER 26 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 2 ALEAASLSQHPPS(0.002)LCIS(0.998)DS(1)EEEEEER 93.568 0.0046066 226740000 98741 110700 49152 78907 104980 114140 96520 120690 114210 TRUE FALSE 85692.12667 109972.8044 72922.0716 96824.04037 102891.1034 118531.0397 87159.50526 94881.38271 100708.2239 0.850895025 1.09199428 0.72409252 0.961431317 1.021675285 1.17697478 0.865465618 0.942141357 1 16.61982197 3.489832979 24.40218366 0.992382031 0.898205308 0.156664004 0.117251015 964.0894065 1850722.189 0.032636926 0.045827703 3089.107195 -3.489832979 -0.094176723 ALEAELDAQHLS(ph)ETFDNIDNLSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALEAELDAQHLSETFDNIDNLSPK 24 0 P25054-2;P25054-3;P25054;A0A2Q2SV78;E9PFT7 P25054-2 APC Adenomatous polyposis coli protein 1 ALEAELDAQHLS(0.388)ET(0.388)FDNIDNLS(0.223)PK 120.13 0.00036575 45968000 86244 52441 150200 95447 16959 25461 47096 54325 42901 TRUE FALSE 74846.63689 52096.51162 222837.2224 117119.7002 16621.54908 26440.50115 42528.63717 42708.02151 37829.29265 1.978536516 1.377147389 5.890599764 3.096005554 0.439383026 0.69894252 1.124225017 1.12896696 1 15.20721618 3.247268974 24.83339237 0.919112488 3.163901767 0.46520878 1.174182591 160.8573592 458709.8187 0.349175345 0.44366076 1767.13193 -3.247268974 2.244789279 ALEAELDAQHLSET(ph)FDNIDNLSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALEAELDAQHLSETFDNIDNLSPK 24 0 P25054-2;P25054-3;P25054;A0A2Q2SV78;E9PFT7 P25054-2 APC Adenomatous polyposis coli protein 1 ALEAELDAQHLS(0.127)ET(0.507)FDNIDNLS(0.365)PK 101.66 0.0067839 55807000 95300 58703 146690 88398 21322 28684 46767 57885 49582 TRUE FALSE 82705.86354 58317.37613 217629.7746 108470.117 20897.73392 29787.49204 42231.54354 45506.74321 43720.47244 1.891696473 1.333868846 4.977754413 2.480991419 0.477985089 0.681316792 0.965944355 1.040856621 1 15.41602137 3.301067147 6.212807739 0.863218358 2.764217847 0.484408702 0.942205486 0.179238319 13.18322915 0.277858017 0.357199873 2000.171095 -3.301067147 1.900999489 ALEAELDAQHLSETFDNIDNLS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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;ALEAELDAQHLSETFDNIDNLS(1)PK 281.19 1.90E-52 263811000 258736 255316 69782 174946 306130 263283 287131 351224 314072 TRUE FALSE 224543.382 253638.8124 103528.8086 214670.1632 300038.6119 273411.6674 259285.0798 276117.4808 276942.766 0.810793455 0.915852817 0.373827452 0.775142699 1.083395737 0.987249717 0.936240667 0.997020016 1 18.07922833 3.370143039 5.754368988 0.993474669 0.699086169 0.503112763 0.140436565 0.174197334 8.228563192 0.040736328 0.052802607 2345.001035 -3.370143039 -0.294388501 ALEAHCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALEAHCR 7 0 H0YJ75;Q13362-3;Q13362;Q13362-4;Q13362-5 H0YJ75 PPP2R5C Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform 0 77.741 0.037226 64484000 96617 101190 61016 61712 79188 107870 86433 98737 68098 FALSE TRUE 83848.81865 100525.2762 90523.54169 75724.65281 77612.31373 112019.8287 78050.74096 77622.86092 60047.53202 1.396374103 1.674095052 1.507531428 1.26107852 1.292514632 1.86551928 1.299815968 1.292690279 1 15.87381733 1.407872455 1.6711873 0.927151957 1.485173808 0.412082771 0.183560657 0.70474707 2.513536159 0.595558978 0.052748124 25.57834584 -1.407872455 0.558021851 ALEATTEHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ALEATTEHIR 10 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;; 175.73 7.22E-06 567470000 745100 758730 517130 562930 679550 778320 716180 754580 766470 FALSE TRUE 646633.1472 753745.8527 767215.7977 690751.8603 666028.2845 808262.474 646724.9738 593218.9391 675858.7898 0.956757768 1.115241622 1.135171739 1.022035773 0.985454794 1.195904361 0.956893635 0.877726158 1 19.36636232 2.022590507 24.85815893 0.926283405 1.068433381 0.368300915 0.076154404 189.456868 208473.7683 0.029854391 0.02012637 105.3393192 -2.022590507 0.142149976 ALEEGDGSVSGSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALEEGDGSVSGSSPR 15 0 Q8N3X1-2;Q8N3X1 Q8N3X1-2 FNBP4 Formin-binding protein 4 1 ALEEGDGSVSGS(0.001)S(0.999)PR 244.18 5.36E-18 353210000 1019600 852370 522300 674840 731660 765710 753790 827090 886820 TRUE FALSE 884857.2767 846770.7253 774886.027 828072.7363 717101.3975 795167.3592 680687.5618 650223.2399 781981.1499 1.131558321 1.082853117 0.990926734 1.058942068 0.917031565 1.016862567 0.870465435 0.831507563 1 19.57677431 4.112284431 0.421882102 0.874811886 1.224275982 0.571401304 0.061319972 2.52827894 0.655546712 0.090955015 0.460843234 12950.43721 -4.112284431 0.349464096 ALEELQEALAEKEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ALEELQEALAEKEELR 16 1 Q9UJC3;Q9UJC3-2 Q9UJC3 HOOK1 Protein Hook homolog 1 0 ;;; 198.85 3.62E-11 323382000 315587 238807 164188 201629 216105 204132 278994 313422 229200 FALSE TRUE 273881.3784 237238.2611 243589.866 247411.9462 211804.9333 211985.0901 251937.2048 246399.1444 202104.2371 1.355149116 1.173841105 1.205268477 1.224179907 1.04799848 1.048889886 1.246570623 1.219168622 1 17.62474004 7.999999512 0.828672389 1.142113955 64.09123792 0.394347108 0.084138448 715.3002496 2.184323423 0.03024943 84744.12414 99999887.53 -7.999999512 62.94912396 ALEEVPIHIEDPPFPSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALEEVPIHIEDPPFPSLR 18 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 0 ; 111.06 0.00031548 109408000 105509 105413 81124 90014 121621 123622 91213 104979 100963 FALSE TRUE 91565.71832 104720.5351 120355.8377 110453.0545 119200.98 128377.8183 82367.1773 82530.0578 89027.26916 1.028513164 1.176274821 1.351898569 1.240665422 1.338926614 1.442005574 0.925190428 0.927019986 1 16.44195968 2.219981491 24.99963558 0.94473122 1.265573539 0.634054873 0.111805135 153.5251026 206578.2375 0.04734354 0.031982763 165.9516181 -2.219981491 0.32084232 ALEFAPACHR ddPTM_MDA-MB-175_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 ; 82.749 0.017079 750420000 387000 405870 422100 331640 387400 409110 364560 419170 407300 FALSE TRUE 335856.9695 403203.8132 626228.9718 406943.9308 379691.4979 424848.7264 329205.0273 329533.7575 359149.458 0.935145416 1.122663015 1.743644485 1.133076834 1.057196355 1.182930162 0.91662404 0.917539342 1 18.45422481 2.613514228 1.259725492 0.934022758 1.248149201 0.224126412 0.213223055 0.649196973 2.152739244 0.129971289 0.091327788 410.6900942 -2.613514228 0.314126443 ALEHAFQLEHIMDLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ALEHAFQLEHIMDLTR 16 0 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 194.37 1.29E-10 1287134000 673930.8 648439.3 427998.9 438816.5 669216.3 723425.8 661723.1 681067 603131.6 FALSE TRUE 584869.1373 644179.6595 634980.5996 538456.4932 655900.2049 751256.4586 597549.2956 535426.1221 531830.0693 1.099729351 1.211250918 1.193953927 1.012459664 1.233289057 1.412587407 1.123571851 1.006761658 1 19.02060582 1.844956481 4.041517856 1.005611344 1.193100562 0.365423945 0.101592315 0.246414254 6.455283615 0.061467044 0.028556333 69.97718706 -1.844956481 0.187489218 ALEHFTDLYDIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ALEHFTDLYDIK 12 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 256.63 3.56E-21 3628300000 5727590 4466990 3104900 4500060 4655160 4092920 5250020 5987700 10817800 FALSE TRUE 4970674.47 4437646.049 4606440.025 5521867.402 4562531.424 4250377.281 4740873.868 4707276.951 9538932.008 0.521093396 0.46521414 0.48290941 0.578876901 0.478306316 0.445582092 0.497002585 0.493480502 1 23.18539632 1.238490499 24.99976399 1.000000553 0.494500263 0.951737126 0.035716742 0.328152577 116158.9873 0.048782429 0.008725596 17.31771144 -1.238490499 -0.505500289 ALEHFTDLYDIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALEHFTDLYDIKR 13 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 107.09 0.00085861 3760800000 3331700 2711900 961250 1600500 2528100 2606400 2929700 3290400 898920 FALSE TRUE 2891407.404 2694085.35 1426113.715 1963917.987 2477795.756 2706669.895 2645578.145 2586773.566 792650.7017 3.647769941 3.398830462 1.799170444 2.477658801 3.125961727 3.414706994 3.337634269 3.263447015 1 19.59632573 ALEIIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALEIIPR 7 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 99.139 0.025003 91608000 138200 141040 91726 104000 135510 136090 136210 142650 141960 FALSE TRUE 119936.5198 140113.499 136085.0004 127614.7895 132813.6161 141325.4704 123000.3752 112145.4076 125177.6505 0.95813046 1.119317213 1.087134962 1.019469442 1.06100103 1.128999224 0.982606517 0.895890018 1 16.93361748 2.039135507 7.345724178 0.9400127 1.063728839 0.450747518 0.054336016 0.148018472 22.34000329 0.02135455 0.014213555 109.4297752 -2.039135507 0.123716139 ALELDSNLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ALELDSNLYR 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 286.87 2.77E-24 3925460000 4794620 4863220 3363920 3914820 4870990 4964920 4620280 5013250 5230260 FALSE TRUE 4160998.819 4831273.188 4990722.964 4803739.715 4774066.829 5155923.685 4172205.957 3941205.501 4611944.621 0.902222199 1.047556635 1.082129855 1.0415866 1.035152679 1.117950042 0.904652224 0.854564793 1 22.13694376 2.21587455 24.78324029 0.905532329 1.04028271 0.414488517 0.065360235 176.434396 192742.974 0.02610059 0.017611198 164.38968 -2.21587455 0.134750381 ALELDSNNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALELDSNNEK 10 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 189.18 2.42E-06 308940000 593880 546880 344270 424950 503180 451860 657620 644040 580100 FALSE TRUE 515397.2533 543287.5093 510760.1235 521441.3925 493167.7025 469243.3466 593844.1136 506317.0579 511521.2389 1.007577426 1.062101567 0.998512055 1.019393434 0.964119698 0.917348706 1.160937354 0.989826071 1 18.96443462 ALELENDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALELENDR 8 0 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 136.27 0.001857 1760610000 1538520 1407800 1005890 1163620 1341100 1552670 1230080 1587180 1433860 FALSE TRUE 1335200.684 1398552.069 1492341.769 1427837.706 1314414.734 1612402.22 1110787.031 1247773.908 1264350.704 1.056036651 1.106142516 1.180322646 1.129305106 1.039596632 1.275280833 0.878543451 0.986889084 1 20.26996526 2.22395852 24.99999955 0.958566009 1.127973661 0.569067453 0.072131282 167.3063655 286440.0652 0.027851936 0.018867527 167.4782908 -2.22395852 0.169407652 ALELFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALELFR 6 0 B0QYF8;P02144;Q8WVH6 B0QYF8 MB Myoglobin 0 97.596 0.095131 110190000 105840 128680 77612 101700 122170 133900 94268 127460 140980 FALSE TRUE 91852.97584 127834.6926 115145.4228 124792.5394 119739.056 139051.2196 85125.90387 100203.6709 124313.505 0.738881715 1.028325061 0.926250312 1.003853438 0.963202317 1.118552804 0.684767949 0.806056196 1 16.92362351 2.234326591 24.99997505 0.819166444 0.966310361 0.20821193 0.121429918 149.0234226 879901.6029 0.046615167 0.032688157 171.5246694 -2.234326591 0.147143917 ALENDFFNS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 153.09 7.24E-05 123008000 129210 127600 130285 162015 200804 214070 204105 228170 273910 TRUE FALSE 112134.5711 126761.7872 193291.2618 198802.982 196808.3933 222305.4114 184310.9285 179377.6211 241528.6718 0.464270226 0.524831219 0.800282883 0.823103032 0.814844845 0.920410027 0.763101652 0.742676303 1 17.88183494 4.256899607 3.578190346 0.829845824 0.475195805 0.788587756 0.074297144 0.097980036 2.614577329 0.019265095 0.053913399 18067.56423 -4.256899607 -0.354650019 ALEQSQSLPLPAPTSTS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ALEQSQSLPLPAPTSTSPSR 20 0 O15068-4;O15068-10;O15068;H7BYP9;O15068-5;O15068-3;O15068-6;O15068-8;O15068-2;O15068-9;H3BLT1;H7C2S1;H0Y4M6;H0Y7A3 O15068-4 MCF2L Guanine nucleotide exchange factor DBS 1 ALEQSQSLPLPAPTS(0.001)T(0.012)S(0.975)PS(0.012)R;ALEQSQSLPLPAPTS(0.16)T(0.16)S(0.675)PS(0.004)R;ALEQSQSLPLPAPTST(0.007)S(0.991)PS(0.002)R;ALEQSQSLPLPAPTSTS(0.994)PS(0.005)R;ALEQSQSLPLPAPTST(0.002)S(0.992)PS(0.006)R;ALEQSQSLPLPAPTST(0.197)S(0.606)PS(0.197)R 357.09 2.28E-95 2307330000 2207150 2332000 1697420 1814610 2452140 2824480 2181430 2640680 2743340 TRUE FALSE 1915469.535 2316680.938 2518297.99 2226644.935 2403347.212 2933139.573 1969875.254 2075991.132 2419025.47 0.791835207 0.957691834 1.041038228 0.920471885 0.993518771 1.212529429 0.814325967 0.858193168 1 21.20599453 4.734900184 5.714798589 0.96688889 0.786546276 0.218399923 0.107961106 0.238676314 33.50152461 0.027752401 0.168372752 54312.54886 -4.734900184 -0.180342614 ALERPYTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ALERPYTSK 9 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;;;;; 123.79 0.00049957 1776070000 2248080 2394750 1663470 2118700 2320200 2242550 2808120 3370770 3092610 FALSE TRUE 1950990.532 2379018.73 2467929.656 2599783.217 2274032.559 2328822.35 2535788.955 2649957.067 2727005.169 0.715433383 0.872392453 0.904996325 0.953347374 0.833893747 0.853985308 0.929880509 0.971746257 1 21.378886 5.476283592 1.112865114 0.925215062 1.73E-10 0.629228163 0.049620254 5.431467174 1.693671877 0.016458093 8.76071427 299421.9208 -5.476283592 -0.925215062 ALES(ph)PERPFLAILGGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ALESPERPFLAILGGAK 17 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 1 ALES(1)PERPFLAILGGAK;ALES(1)PERPFLAILGGAK;ALES(1)PERPFLAILGGAK;ALES(1)PERPFLAILGGAK 261.26 1.68E-27 1524350000 1319940 1047840 661850 630099 904120 785780 1087220 1280070 1166010 TRUE FALSE 1145506.585 1040956.67 981922.8738 773172.6084 886129.7809 816009.4651 981781.5717 1006336.992 1028165.626 1.114126514 1.012440645 0.955024024 0.751992275 0.861855093 0.793655657 0.954886593 0.978769341 1 19.97164125 4.384343745 2.263414811 0.897073162 1.106840534 0.463764758 0.078655019 0.352990476 3.262288636 0.023326636 0.109745795 24229.46057 -4.384343745 0.209767372 ALESPERPFLAILGGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALESPERPFLAILGGAK 17 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 244.08 1.56E-20 1689200000 3338900 2926600 1713800 1606100 2221100 2103400 2667900 3026300 3338900 FALSE TRUE 2897655.905 2907374.972 2542599.412 1970789.553 2176904.456 2184319.159 2409167.469 2379149.296 2944179.046 0.984198264 0.987499376 0.86360217 0.669385089 0.739392687 0.741911115 0.818281576 0.808085806 1 21.48943398 4.10982975 3.96224955 0.792458712 0.98569374 0.451817317 0.085044915 0.194804968 5.61187288 0.022786077 0.052084914 12877.44637 -4.10982975 0.193235028 ALETNTHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALETNTHVK 9 0 Q9NYL9;H0YKU1;H0YNJ8;G5EA42;Q9NZR1 Q9NYL9 TMOD3;TMOD2 Tropomodulin-3;Tropomodulin-2 0 104.52 0.0032464 332090000 243410 263480 166990 218390 250010 269020 291590 289210 350150 FALSE TRUE 211242.7518 261749.1825 247746.9225 267978.7874 245035.2901 279369.3735 263311.6467 227364.6921 308755.6659 0.684174495 0.847755074 0.802404457 0.867931562 0.793622003 0.904823472 0.852815594 0.736390348 1 18.23610609 4.74018203 23.72082803 0.840819013 0.684174391 0.346750608 0.070687778 81.79433078 1196397.647 0.016245858 0.099838247 54977.12559 -4.74018203 -0.156644622 ALFDYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALFDYDR 7 0 Q92796-2;Q5JUW8;Q92796-3;Q92796 Q92796-2 DLG3 Disks large homolog 3 0 ; 91.041 0.038841 221910000 703900 723450 454510 482520 692330 729750 613370 680230 636930 FALSE TRUE 610877.8315 718697.6093 674312.5562 592083.5409 678553.9875 757823.9547 553885.4718 534768.1081 561632.861 1.087681783 1.279657334 1.200628744 1.054218124 1.208180708 1.349322676 0.986205598 0.9521667 1 19.09926782 2.138192795 9.125549181 0.972069929 1.194431334 0.596446383 0.084179675 0.184688602 15.24197405 0.034238818 0.023070552 137.4652085 -2.138192795 0.222361405 ALFEEVPELLTEAEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALFEEVPELLTEAEKK 16 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 143.14 2.31E-06 16467000 21669 15383 14111 14547 14806 13175 19452 22453 12532 FALSE TRUE 18805.38675 15281.94806 20935.1268 17850.11869 14511.38957 13681.85078 17565.54803 17651.60068 11050.48124 1.701770841 1.382921498 1.894499104 1.615325008 1.313190734 1.23812262 1.589573129 1.597360359 1 13.43182158 3.31226739 6.607071165 1.391939352 1.650400909 0.324949348 0.21058221 0.307492303 21.98095715 0.061831922 0.07969526 2052.425442 -3.31226739 0.258461556 ALFPGDSEIDQLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALFPGDSEIDQLFR 14 0 G3V5T9;P24941;P24941-2;E7ESI2;Q00526;K7EJ83 G3V5T9 CDK2;CDK3 Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 0 ; 189.13 1.75E-06 50319000 102572 94520 61410 75455 86870 96640 86049 108310 92532 FALSE TRUE 89016.85032 93899.0919 91108.0814 92588.21101 85141.45696 100357.8033 77703.98122 85148.74937 81592.97237 1.090986732 1.150823278 1.116616772 1.134757177 1.043490076 1.22998097 0.95233669 1.043579452 1 16.31615728 2.22244259 24.99997781 1.006072118 1.124802398 0.580014321 0.051631306 167.9248007 260458.9354 0.019242729 0.013018252 166.8947172 -2.22244259 0.11873028 ALGALVDSCAPGLCPDWDSWDASKPVTNAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALGALVDSCAPGLCPDWDSWDASKPVTNAR 30 1 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 ; 112.86 8.34E-15 294630000 132108 112229 70709 75973 77430 78482 104494 115507 114056 FALSE TRUE 114649.5931 111491.7603 104904.1089 93223.83082 75889.29449 81501.25332 94360.18796 90806.72693 100572.4296 1.139970403 1.10857181 1.043070246 0.926932273 0.754573542 0.810373714 0.938231167 0.902898809 1 16.61787534 3.850962579 2.418744735 0.882234616 1.121658251 0.696323989 0.066826903 0.177734276 2.022557258 0.020582813 0.042470181 7095.166301 -3.850962579 0.239423634 ALGALVDSCAPGLCPDWESWDPQKPVDNAR ddPTM_MDA-MB-175_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 0 201.98 1.80E-25 252290000 134350 142420 92977 95772 114080 115810 115270 136670 162450 FALSE TRUE 116595.3071 141484.4336 137940.9882 117518.4964 111810.0312 120265.2856 104091.1331 107444.1841 143245.3461 0.813955289 0.987707018 0.962970121 0.820400101 0.780549137 0.839575518 0.726663281 0.750071029 1 17.12812874 3.661294745 5.886130769 0.804800223 0.927813918 0.225664579 0.086227263 0.273692565 16.22717847 0.023450169 0.035187923 4584.529216 -3.661294745 0.123013695 ALGDEDDLAKREDEFVDLGDV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALGDEDDLAKREDEFVDLGDV 21 2 Q9C0I1-3;Q9C0I1-2;Q9C0I1 Q9C0I1-3 MTMR12 Myotubularin-related protein 12 0 116.65 0.00049659 21161000 89925 68282 37077 36273 59671 51758 87165 96069 11451 FALSE TRUE 78041.18341 67833.45105 55007.56122 44509.33905 58483.66384 53749.16375 78711.75172 75525.39196 10097.27583 7.728934493 6.717995252 5.447762562 4.408054194 5.792023993 5.323135139 7.795345307 7.479779028 1 13.3016785 4.470164946 3.115213408 5.633734704 7.652649883 0.147445216 1.863708153 0.579818272 10.84738216 0.480562443 2.084697873 29523.30315 -4.470164946 2.01891518 ALGDSS(ph)PSQAMQEYIAVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALGDSSPSQAMQEYIAVVK 19 0 A0A2R8Y544;Q9BR61 A0A2R8Y544 ACBD6 Acyl-CoA-binding domain-containing protein 6 1 ALGDS(0.145)S(0.853)PS(0.003)QAMQEYIAVVK 133.78 5.91E-07 0 38939 31431 25762 26705 32504 36988 27024 39885 39321 TRUE FALSE 33793.11249 31224.52769 38220.58937 32768.77841 31857.23399 38410.95229 24403.21664 31355.90314 34672.51617 0.974636866 0.900555574 1.102330998 0.945093752 0.918803638 1.10782131 0.703820182 0.904344611 1 15.08150492 2.252667185 24.99988732 0.869772102 0.987023162 0.25326624 0.098671635 322.4897302 571521.1788 0.035760981 0.027563102 178.9234175 -2.252667185 0.11725106 ALGEYLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALGEYLER 8 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 110.12 0.0081143 293570000 452870 420360 309280 311330 463250 496930 434640 502120 470240 FALSE TRUE 393022.0821 417598.6275 458848.8425 382022.2349 454032.2313 516047.2187 392488.6797 394745.5455 414648.7629 0.947843373 1.007114129 1.106596434 0.921315265 1.094980311 1.244540596 0.946556977 0.951999815 1 18.66153026 ALGHQLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALGHQLGR 8 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 140.98 0.0006408 508130000 654500 673810 480260 483480 665880 739230 674370 700660 701850 FALSE TRUE 568006.1667 669383.6977 712515.3424 593261.5235 652630.2908 767668.6564 608969.7012 550829.3115 618878.0926 0.917799763 1.081608326 1.151301607 0.958608053 1.054537717 1.240419827 0.983989753 0.890044935 1 19.23929573 2.010575086 24.99962439 0.937123142 1.070137136 0.241513501 0.092960006 251.8413517 595353.4633 0.03735528 0.02515782 102.4648919 -2.010575086 0.133013994 ALGNICYDSHEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALGNICYDSHEGR 13 0 P52306-4;P52306;P52306-5;D6RHH8 P52306-4 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 0 ; 149.57 3.99E-05 950590000 857910 782170 520310 616910 828310 924580 792880 866620 803080 FALSE TRUE 744535.0198 777031.8738 771933.6563 756988.8444 811828.2516 960149.1909 715986.6196 681300.057 708140.7973 1.051394049 1.097284434 1.090084993 1.068980699 1.146422088 1.355873288 1.011079467 0.962096888 1 19.43367671 2.024251296 24.99998472 0.980815027 1.133326832 0.39474029 0.084616231 220.3694438 227171.7339 0.035760898 0.02410888 105.7429192 -2.024251296 0.152511805 ALGNNFYEYYVDDPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALGNNFYEYYVDDPPR 16 0 P30047;H0YNX7;P30047-2 P30047 GCHFR GTP cyclohydrolase 1 feedback regulatory protein 0 ; 157.5 1.43E-07 373370000 452570 391290 347690 537110 397750 444410 327760 508000 1027490 FALSE TRUE 392761.7278 388719.5902 515834.047 659069.0347 389835.5532 461506.7403 295973.8856 399368.1533 906021.3027 0.433501648 0.429040232 0.569339866 0.727432162 0.430271951 0.509377361 0.326674312 0.440793337 1 19.78918545 1.235809173 24.99986384 1.000000692 0.481748592 0.698802779 0.106602681 46.1823738 419534.3177 0.185844347 0.027687751 17.2111216 -1.235809173 -0.518252101 ALGQNPT(ph)QAEVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALGQNPTQAEVLR 13 0 P08590 P08590 MYL3 Myosin light chain 3 1 ALGQNPT(1)QAEVLR 73.466 0.091837 0 231180 244260 141000 180460 233340 255350 243770 246540 160990 TRUE FALSE 200628.9773 242655.44 209188.0716 221436.2012 228696.9905 265173.4797 220129.2229 193819.3396 141957.9456 1.413298681 1.709347363 1.47359185 1.559871835 1.611019303 1.867972086 1.550665037 1.365329279 1 17.11510408 1.361824395 2.018987677 0.903882779 1.607563061 0.706155108 0.124371349 0.312296483 1.608009328 0.379934386 0.034073552 23.00511426 -1.361824395 0.703680282 ALGS(ph)PTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ALGSPTK 7 0 Q9NR45;Q5TBR0;Q5TBR1 Q9NR45 NANS Sialic acid synthase 1 ALGS(0.999)PT(0.001)K;ALGS(0.999)PT(0.001)K;ALGS(1)PTK;ALGS(0.999)PT(0.001)K;ALGS(1)PTK;ALGS(1)PTK;ALGS(1)PTK;ALGS(0.997)PT(0.003)K 139.02 0.0028627 11910930000 36888400 33100900 23783070 28264200 23716310 27502060 38351800 42987700 41620800 TRUE FALSE 32013504.48 32883458.01 35284642.2 34682018.6 23244401.83 28560082.04 34632448.34 33795114.89 36700436.44 0.872292201 0.895996375 0.961422959 0.945002893 0.633354916 0.778194616 0.943652221 0.920836866 1 25.12929388 2.146624677 10.06230308 0.947824939 0.84980639 0.22254943 0.094043411 0.623868365 63.1503729 0.041957697 0.028281206 140.1601898 -2.146624677 -0.098018549 ALGYFHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALGYFHR 7 0 E5RH53;Q96DB5-3;Q96DB5-2;Q96DB5;H0YC67;H0YB03;H0YB83;H0YC27;H0YBD9 E5RH53 RMDN1 Regulator of microtubule dynamics protein 1 0 ; 80.555 0.029595 688450000 957540 1067660 662010 754750 1056610 1198330 901950 1049860 963540 FALSE TRUE 830998.6629 1060646.471 982160.2503 926127.5231 1035585.528 1244430.531 814479.0278 825355.609 849631.3989 0.978069624 1.248360727 1.155983938 1.090034484 1.218864474 1.464671071 0.958626328 0.971427857 1 19.69647756 ALHELNPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALHELNPR 8 0 Q5T6V5 Q5T6V5 C9orf64 UPF0553 protein C9orf64 0 ; 138.54 0.00070074 86459000 196659 195662 160888 133930 181863 220431 158181 180981 193929 FALSE TRUE 170670.0149 194376.6834 238693.9749 164340.8535 178244.2821 228911.1232 142840.631 142279.6215 171002.9345 0.998053135 1.136686244 1.395847244 0.96104113 1.042346335 1.338638567 0.835310992 0.832030292 1 17.38366156 2.215552072 24.99986954 0.874979466 1.143352711 0.413441789 0.143579144 216.3418854 235063.8476 0.057927482 0.039082703 164.2676603 -2.215552072 0.268373245 ALHFVFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALHFVFK 7 0 Q9HC38-2;Q9HC38;I3L3Q4;Q9HC38-3;I3L1F4;I3NI27;I3NI24;I3L2C2;I3L277 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 ; 91.584 0.016296 728620000 2261300 2845900 1998410 2369200 2483600 2457000 2455300 2918300 5520300 FALSE TRUE 1962463.476 2827205.096 2964847.76 2907163.071 2434181.219 2551522.38 2217185.384 2294244.255 4867696.423 0.403160613 0.580809658 0.609086414 0.597235903 0.500068412 0.524174508 0.455489659 0.471320324 1 22.21480777 1.235060995 24.99999151 1.000000673 0.519550805 0.844122464 0.065133979 40.14746143 286752.765 0.119817326 0.016802558 17.18149676 -1.235060995 -0.480449868 ALHLLEEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALHLLEEYR 9 0 A0A590UJD9;A0A0C4DFT3;A0A590UJ18;E7EQD7;B4E2H8;C9JCP6;A8MUT6;A0A590UJ95;F2Z2L0;C9J110;A0A590UJE6;A0A590UJ08;Q12959-4;Q12959-2;A0A590UJC5;Q12959;Q12959-3;Q12959-5;Q12959-7;Q12959-6;A0A590UKA8;A0A590UJR5;A0A590UJ68;A0A590UJS9;C9JUA9;A0A590UJ64 A0A590UJD9;A0A590UJ08;Q12959 DLG1 Disks large homolog 1 0 ; 143.73 0.00010123 547790000 148223 220756 153056 166077 221106 256030 176539 212147 224752 FALSE TRUE 128634.955 219305.8393 227074.3935 203787.3212 216706.4232 265879.6398 159418.275 166781.015 198182.0746 0.649074621 1.106587666 1.145786742 1.028283318 1.093471363 1.341592777 0.804403099 0.841554491 1 17.59646695 ALHSLLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALHSLLLR 8 0 M0R1K3;Q15102 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ; 206.5 7.09E-05 4168600000 1554890 2134510 1261300 1478760 1940160 2031520 1814250 1963180 1945900 FALSE TRUE 1349407.347 2120488.263 1871268.899 1814535.059 1901554.612 2109673.889 1638304.314 1543369.234 1715857.919 0.786433033 1.235818094 1.090573338 1.057508923 1.108223817 1.22951549 0.954801849 0.899473795 1 20.71049867 2.0410856 22.12888671 0.937930828 1.09169469 0.200112925 0.124599567 57.2745861 30847.6163 0.04759029 0.032085215 109.9222476 -2.0410856 0.153763862 ALHSVLQAVPLNELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALHSVLQAVPLNELR 15 0 Q16401-2;Q16401;F2Z3J2 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ; 136.17 2.45E-05 1510980000 1329740 1134710 707740 802240 1198960 1339760 1139440 1236520 1220950 FALSE TRUE 1154011.49 1127256.015 1050005.431 984400.8535 1175103.042 1391301.434 1028937.284 972099.8206 1076610.682 1.071893034 1.047041455 0.975287956 0.914351743 1.091483729 1.292297631 0.955719 0.902926041 1 20.03806521 2.03292114 24.9997808 0.939966558 1.060551997 0.219562875 0.099216066 276.4460296 209927.5163 0.043068423 0.029036535 107.8750823 -2.03292114 0.120585438 ALHVNNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ALHVNNDR 8 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;;; 144.09 0.000591 1305323000 1314660 1124860 811380 915412 1035930 1201480 1035190 1224850 1383170 FALSE TRUE 1140924.35 1117470.721 1203766.082 1123270.286 1015317.02 1247701.713 934797.4331 962925.3593 1219653.218 0.935449793 0.91622004 0.986974054 0.920975134 0.832463691 1.022997106 0.766445264 0.789507497 1 20.21803958 2.230446995 24.99999099 0.835404156 0.931903293 0.191383588 0.078564009 250.9837859 773332.3618 0.031016301 0.021322939 169.9992459 -2.230446995 0.096499136 ALIEHEMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALIEHEMK 8 0 O95372;Q5QPQ1;Q5QPQ3;Q5QPQ2;Q5QPQ0 O95372 LYPLA2 Acyl-protein thioesterase 2 0 86.953 0.015668 341490000 306750 234930 178980 223000 241070 257650 254150 311320 298330 FALSE TRUE 266212.2103 233386.7294 265535.3267 273635.5583 236273.1786 267561.9622 229502.5721 244746.6407 263061.7673 1.011976058 0.88719365 1.00940296 1.040195089 0.898166165 1.01710699 0.872428459 0.930377087 1 18.00504206 2.251465853 24.99998461 0.930881114 0.973958197 0.106018198 0.058135618 503.6245654 975619.1875 0.021028062 0.016183289 178.4291689 -2.251465853 0.043077083 ALIEVLQPLIAEHQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALIEVLQPLIAEHQAR 16 0 P23381;P23381-2 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ; 195.38 6.09E-11 2937400000 1239140 1227860 913950 941940 1171370 1323070 1171300 1309850 1224810 FALSE TRUE 1075384.509 1219794.107 1355939.277 1155821.874 1148062.029 1373969.359 1057707.506 1029748.771 1080014.357 0.995713161 1.129423974 1.255482641 1.070191212 1.063006266 1.272176939 0.979345783 0.953458409 1 20.04261906 2.108479988 11.8364716 0.971328087 1.130691283 0.426537992 0.083796493 0.371398335 38.04931097 0.033465528 0.022560512 128.3748614 -2.108479988 0.159363196 ALIFVSHGAGEHSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALIFVSHGAGEHSGR 15 0 A0A0C4DFN3;Q99685-2;Q99685;A0A3B3ITT3;C9JAM4 A0A0C4DFN3 MGLL Monoglyceride lipase 0 226.19 5.20E-13 441280000 154100 182980 85631 136900 147500 181340 137980 178390 165500 FALSE TRUE 133735.2946 181777.9923 127042.438 167985.2374 144565.0386 188316.2671 124598.7208 140242.6867 145934.7785 0.916404547 1.245611184 0.870542576 1.151098039 0.990614027 1.290413903 0.853797306 0.960995646 1 17.15496422 2.173705631 25 0.93948084 1.075102029 0.188302128 0.136155072 94.7805459 36534.14171 0.050474492 0.034029904 149.1782923 -2.173705631 0.135621189 ALIQTCLNSPDS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ALIQTCLNSPDSPPR 15 0 P11831 P11831 SRF Serum response factor 1 ALIQTCLNSPDS(1)PPR;ALIQTCLNSPDS(1)PPR;ALIQTCLNSPDS(1)PPR;ALIQTCLNSPDS(1)PPR 320.06 1.61E-56 979110000 617890 448703 415777 477754 460698 479234 419704 512605 1096710 TRUE FALSE 536234.271 445755.4404 616848.1479 586235.3477 451531.0111 497670.4421 379001.1707 402988.4098 967058.1932 0.55450052 0.460939625 0.637860423 0.60620483 0.466911934 0.514623055 0.391911442 0.416715781 1 19.88324318 1.23259188 24.99888222 1.000000811 0.5015151 0.798711903 0.077872374 95.14296251 398447.1257 0.185896542 0.021027285 17.08409116 -1.23259188 -0.49848571 ALIQTCLNSPDS(ph)PPRSDPTTDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ALIQTCLNSPDSPPRSDPTTDQR 23 1 P11831 P11831 SRF Serum response factor 1 ALIQTCLNS(0.001)PDS(0.995)PPRS(0.004)DPTTDQR;ALIQTCLNSPDS(1)PPRSDPTTDQR;ALIQTCLNS(0.001)PDS(0.998)PPRSDPTTDQR;ALIQTCLNSPDS(1)PPRSDPTTDQR 255.21 9.27E-44 3241660000 1341840 1017270 569950 635144 930830 953120 970280 1034540 609201 TRUE FALSE 1164512.444 1010587.486 845579.7264 779363.1528 912308.3041 989787.1432 876182.3949 813311.6718 537181.9518 2.167817516 1.881275949 1.574103008 1.450836444 1.698322703 1.842554724 1.631071915 1.514033875 1 19.03505131 8 0.05918599 3.25E-12 4.898945451 0.52775064 0.210805774 795.5841537 4.568791807 95.4410281 369.4276103 99999999.99 -8 4.898945451 ALIQYFSPYVSADMHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALIQYFSPYVSADMHR 16 0 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;Q13098-6;J3QQX0 Q13098-7 GPS1 COP9 signalosome complex subunit 1 0 162.29 8.13E-09 580300000 919490 913800 494100 660240 901640 959270 798150 853740 858360 FALSE TRUE 797977.0668 907797.1876 733048.4127 810157.5831 883699.128 996173.7376 720745.5358 671174.3448 756885.6586 1.054290113 1.199384844 0.968506147 1.070383054 1.167546403 1.316148253 0.952251542 0.88675791 1 19.52971585 2.036091271 24.97297187 0.930554452 1.12512499 0.445006796 0.096083605 143.0261426 98964.85103 0.039774202 0.026815681 108.665397 -2.036091271 0.194570538 ALIVLAHSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ALIVLAHSER 10 0 P15559-2;P15559;B4DLR8;P15559-3;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ;;;;; 208.11 1.20E-07 43436700000 8842590 11698020 7599680 8996590 10806060 12144250 11060300 11537580 12978690 FALSE TRUE 7674019.327 11621174.94 11274910.67 11039403.26 10591040.55 12611447.16 9987673.808 9070358.303 11444364.05 0.670550088 1.015449603 0.985193289 0.964614828 0.925437228 1.101978851 0.872715492 0.792561147 1 23.44813396 4.747852285 24.52210681 0.945048488 0.670549899 0.53104923 0.083975283 901.7848574 2379879.961 0.022517023 0.272252732 55956.72453 -4.747852285 -0.274498589 ALKDEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ALKDEEK 7 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;P06753-7;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;; 92.439 0.01429 7778620000 16226760 12070400 10774470 11740830 8226870 7680540 17554090 19359700 14359030 FALSE TRUE 14082352.55 11991108.75 15985039.73 14406764.9 8063171.383 7976015.344 15851697.05 15219778.81 12661521.83 1.112216426 0.947051145 1.262489608 1.137838333 0.636824822 0.629941286 1.251958277 1.202049723 1 23.59394748 0.124640575 12.01413045 0.783561599 1.028842105 0 0.229377263 0 0 0 0.055339419 1.332418256 -0.124640575 0.245280506 ALKEDDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALKEDDPK 8 1 P61201;P61201-2;H0YKU5 P61201 COPS2 COP9 signalosome complex subunit 2 0 ; 71.349 0.044663 333440000 1385790 985020 974260 894600 730210 611150 1418660 1514670 1142310 FALSE TRUE 1202654.34 978549.3388 1445415.395 1097732.603 715680.2496 634661.336 1281078.572 1190769.608 1007267.413 1.193977215 0.971489126 1.434986753 1.089812486 0.710516632 0.630082268 1.271835617 1.18217823 1 19.94201532 3.476646731 24.99845015 0.985338579 1.191470654 0.198850377 0.218701662 33.3159859 1755040.636 0.069116177 0.090083933 2996.723894 -3.476646731 0.206132074 ALKEPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ALKEPPR 7 1 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;;; 102.71 0.0077874 3252210000 6504600 5917000 4490900 5356800 5328400 5228600 6001400 6852200 8984300 FALSE TRUE 5645000.629 5878130.837 6662714.261 6573143.314 5222375.265 5429747.625 5419385.152 5386910.354 7922186.289 0.712555906 0.741983415 0.84101964 0.829713298 0.659208844 0.685384997 0.684076965 0.679977743 1 22.9174672 1.232317031 24.99975164 1.000000449 0.728286079 0.654921808 0.061762736 148.4271351 594254.2366 0.15280689 0.016827432 17.07328268 -1.232317031 -0.27171437 ALKEPPRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ALKEPPRDR 9 2 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;;;;;;; 111.61 0.0011796 8053240000 21749960 18529560 9046570 11315090 17057700 16732170 20489630 23333220 4634640 FALSE TRUE 18875647.68 18407838.1 13421521.51 13884354.12 16718285.14 17375867.41 18502548.84 18343592.48 4086738.139 4.618756337 4.504286175 3.284164792 3.397417122 4.090862829 4.251769214 4.527461317 4.488565662 1 21.96251837 4.33420573 7.71880517 3.74643407 4.583100231 0.122093661 1.022892563 0.555673678 38.90081806 0.251411097 0.670664513 21587.668 -4.33420573 0.83666616 ALLDFERHDDDELGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ALLDFERHDDDELGFR 16 1 Q96HU1;Q96HU1-2 Q96HU1 SGSM3 Small G protein signaling modulator 3 0 ;; 191.78 3.85E-10 97265000 143115 152195 63326 65869 139243 138753 143225 154864 40920 FALSE TRUE 124201.9901 151195.221 93950.66541 80825.56319 136472.3367 144090.9177 129335.0615 121747.5388 36082.48422 3.442168488 4.190266394 2.603774863 2.240022131 3.782232285 3.993375756 3.584427856 3.37414514 1 15.13901105 4.242134567 24.99866488 3.05577032 3.816217411 0.13319875 0.892154413 207.5005774 1451341.242 0.227642765 0.554819548 17463.63182 -4.242134567 0.760447091 ALLDSQFSYQHAIEESVVLIYDPIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ALLDSQFSYQHAIEESVVLIYDPIK 25 0 A0A087WZK9;B3KS98;O15372;E5RJT0;E5RGU4 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 ;;;;;; 184.29 1.91E-17 1332657000 1038667 1025520 541531.5 848748 788871 744342 1141480 1265121 1119998 FALSE TRUE 901404.5243 1018783.292 803417.9447 1041469.206 773174.0105 772977.3184 1030779.445 994584.7193 987593.1123 0.912728646 1.031582014 0.813511085 1.054552925 0.782887204 0.782688041 1.043728872 1.007079441 1 19.91355725 2.201912315 24.99986836 1.015999082 0.900744507 0.272223879 0.092772708 237.7109641 162154.4367 0.037534892 0.025306804 159.1887289 -2.201912315 -0.115254575 ALLELQLEPEELYQTFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ALLELQLEPEELYQTFQR 18 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;; 223.58 1.18E-18 721084000 1244660 1109650 843091 943050 1133212 1251058 1124162 1310697 1227271 FALSE TRUE 1080175.027 1102360.636 1250812.628 1157183.916 1110663.298 1299187.011 1015140.942 1030414.646 1082184.42 0.998143206 1.018643972 1.155822061 1.069303803 1.026316104 1.200522745 0.93804801 0.952161782 1 20.04551495 2.19062184 24.99999925 0.960004617 1.076197874 0.422638243 0.06314068 108.4197058 56539.87549 0.025276554 0.017041484 155.1035864 -2.19062184 0.116193257 ALLENMEGLFLAVDEIVDGGVILESDPQQVVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALLENMEGLFLAVDEIVDGGVILESDPQQVVHR 33 0 F8VYZ4;F8VVA7;P61923-5;P61923;P61923-4;F8W651;F8VYK5;F8VYE0;P61923-2;P61923-3 F8VYZ4 COPZ1 Coatomer subunit zeta-1 0 225.23 2.95E-36 178630000 135870 138850 81137 109000 122910 114600 130720 131290 125980 FALSE TRUE 117914.4352 137937.8852 120375.1246 133750.116 120464.3315 119008.7362 118042.7945 103214.6552 111086.7879 1.061462281 1.241712789 1.083613334 1.204014613 1.084416371 1.071313145 1.062617767 0.929135293 1 16.76132771 2.252584973 1.083382833 0.953142384 1.147872761 0.559679199 0.05910649 0.365872202 0.831030825 0.056174579 0.021736877 178.8895508 -2.252584973 0.194730377 ALLEPELRPEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ALLEPELRPEDR 12 1 P0DPD7;P0DPD8 P0DPD7 0 ;;; 113.77 0.0010307 569174000 1167250 1121580 756812 848070 1054849 1195100 996710 1147550 1134090 FALSE TRUE 1012994.955 1114212.267 1122808.815 1040637.255 1033859.569 1241076.27 900049.2176 902155.3627 1000019.172 1.012975534 1.114190906 1.122787288 1.040617305 1.033839748 1.241052477 0.900031962 0.902138067 1 19.93159623 2.204818798 24.99994174 0.925989131 1.091264882 0.544822947 0.068854083 129.8848574 96233.22865 0.027034119 0.018227516 160.2576605 -2.204818798 0.165275751 ALLFIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALLFIPR 7 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 161.52 0.003039 1541600000 1378730 1150070 777020 949900 1100420 1200940 1053620 1261890 1185690 FALSE TRUE 1196527.337 1142515.114 1152789.471 1165589.313 1078523.795 1247140.939 951440.0946 992044.6435 1045519.079 1.144433766 1.09277309 1.102600129 1.1148427 1.03156778 1.192843788 0.910016961 0.948853697 1 19.99578796 2.228512333 24.99999746 0.950312869 1.108134888 0.731699757 0.045658251 97.18681896 241797.4574 0.017324135 0.011835072 169.2436304 -2.228512333 0.157822019 ALLFVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALLFVPR 7 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 166.66 0.0025941 3875900000 1438700 1494050 1047700 1086530 1396110 1491890 1257200 1479980 1418400 FALSE TRUE 1248572.15 1484235.487 1554371.224 1333243.243 1368330.142 1549283.974 1135276.938 1163497.794 1250718.368 0.998284012 1.186706396 1.242782759 1.065981981 1.094035378 1.238715296 0.9076999 0.930263618 1 20.25432553 2.226584556 24.99998032 0.941116583 1.139501093 0.572485422 0.07807057 150.5706594 314312.98 0.031126113 0.02116506 168.4940448 -2.226584556 0.19838451 ALLLLCGEDD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ALLLLCGEDD 10 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;; 164.53 1.43E-05 63513000 109368 148982 65600 53583.2 71661 83914 60685 88123 134829 FALSE TRUE 94914.7417 148003.3274 97324.37942 65750.08453 70235.0863 87142.22588 54799.77804 69278.58222 118889.6692 0.798343055 1.24487963 0.818610903 0.553034464 0.590758531 0.732967183 0.460929687 0.582713222 1 16.85926383 4.0060236 6.905902976 0.63804467 1.02607216 0.421240872 0.17757 0.10991216 29.0326339 0.043794507 0.087279916 10139.66485 -4.0060236 0.38802749 ALLLVGDVAQAADVAIEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALLLVGDVAQAADVAIEHR 19 0 Q9H269-2;Q9H269 Q9H269-2 VPS16 Vacuolar protein sorting-associated protein 16 homolog 0 ; 104.88 0.00034446 36282700 38630 33790 25834 28348 35837 36305 32334 35484 37106 FALSE TRUE 33524.94762 33568.03127 38327.40881 34784.84667 35123.91381 37701.67684 29198.25366 27896.02274 32719.37095 1.024620787 1.02593755 1.171398095 1.063127 1.073489887 1.15227389 0.892384322 0.852584323 1 14.99785739 2.227046842 24.99952381 0.901046515 1.084840643 0.642085953 0.059582989 123.2030358 267504.8773 0.023981038 0.016321761 168.6734943 -2.227046842 0.183794127 ALLPHVLCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALLPHVLCK 9 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 73.248 0.044458 430460000 1387800 1396500 853550 907670 1155100 1173900 1212500 1409100 1139200 FALSE TRUE 1204398.714 1387326.3 1266329.635 1113770.346 1132115.77 1219060.693 1094911.937 1107774.931 1004525.074 1.198973271 1.381076825 1.260625213 1.108753157 1.12701594 1.213569202 1.089979698 1.102784748 1 19.93808214 -1.741798222 0.079394675 1.65E-06 1.667212378 0.577279914 0.068765201 304.0481731 2.432300485 59.40066886 10.71114173 0.018121819 1.741798222 1.667210731 ALLQSHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALLQSHPR 8 0 P43155-2;P43155;P43155-3;H0Y4Z7 P43155-2 CRAT Carnitine O-acetyltransferase 0 92.439 0.012585 0 207990 161810 91719 156140 147820 193300 134710 183960 169120 FALSE TRUE 180503.5945 160747.0595 136074.6152 191593.9735 144878.6712 200736.3761 121645.8449 144621.5856 149126.8263 1.210403246 1.077921817 0.912475767 1.284772018 0.97151314 1.346078242 0.815720739 0.9697892 1 17.18618028 2.215704572 24.99999027 0.932405314 1.120735378 0.325190784 0.138556921 281.6627856 308080.9748 0.052811184 0.03563154 164.3253522 -2.215704572 0.188330063 ALLQTHPEAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALLQTHPEAQR 11 0 I3L4I0;I3L1Y9;Q96CP2 I3L4I0 FLYWCH2 FLYWCH family member 2 0 96.604 0.0068882 219970000 171490 156780 115180 104450 163760 158040 155580 144020 149620 FALSE TRUE 148827.162 155750.1019 170881.4333 128166.9689 160501.4964 164119.9011 140491.8755 113222.4438 131932.094 1.128058817 1.180532326 1.295222626 0.971461644 1.216546266 1.243972532 1.064880206 0.858187271 1 17.00943603 1.974250132 5.018808597 0.927544807 1.170921022 0.547764611 0.091203621 0.129669292 8.774336574 0.043339855 0.024082223 94.24322337 -1.974250132 0.243376216 ALLT(ph)PVAIAAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ALLTPVAIAAGR 12 0 P00390-5;P00390-4;P00390-2;P00390-3;P00390 P00390-5 GSR "Glutathione reductase, mitochondrial" 1 ALLT(1)PVAIAAGR;ALLT(1)PVAIAAGR;ALLT(1)PVAIAAGR 139.78 0.00066086 159084000 378450 392500 271940 294131 340738 387820 336779 404710 367520 TRUE FALSE 328436.8736 389921.6417 403451.0936 360917.9391 333957.9804 402739.6864 304118.2244 318165.916 324072.2043 1.0134682 1.203193722 1.244941986 1.113696066 1.030504857 1.242746774 0.938427364 0.981774777 1 18.30595576 2.224504736 24.99998585 0.97368805 1.142635981 0.500901382 0.079058507 189.634513 337284.0255 0.031719454 0.021500711 167.6890624 -2.224504736 0.168947931 ALMDSLGPEWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALMDSLGPEWR 11 0 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 ; 175.51 2.27E-05 145102000 162512 148895 107978 113620 138997 153575 130207 149630 143873 FALSE TRUE 141035.6274 147916.8989 160196.522 139419.1576 136231.2316 159483.1296 117579.5452 117632.7889 126864.4978 1.111702879 1.165943991 1.262737209 1.098961175 1.073832585 1.257113947 0.926812049 0.927231739 1 16.95292887 2.225128606 24.99972614 0.945301325 1.159652287 0.703911926 0.064267486 120.729983 224701.4737 0.025931431 0.017594377 167.930123 -2.225128606 0.214350962 ALMGS(ph)PQLVAAVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ALMGSPQLVAAVVR 14 0 P14923;C9JTX4;C9J826;C9JK18;C9JKY1 P14923 JUP Junction plakoglobin 1 ALMGS(1)PQLVAAVVR;ALMGS(1)PQLVAAVVR;ALMGS(1)PQLVAAVVR;ALMGS(1)PQLVAAVVR;ALMGS(1)PQLVAAVVR;ALMGS(1)PQLVAAVVR 231.21 6.53E-13 2333463000 1655687 1425236 980465 1556363 1601097 1801716 1074699 1576587 1594444 TRUE FALSE 1436883.768 1415873.531 1454621.153 1909759.007 1569238.302 1871029.18 970474.8564 1239446.139 1405950.647 1.02200157 1.007057776 1.034617507 1.358340004 1.116140389 1.33079293 0.690262392 0.881571584 1 20.42311452 2.235678282 24.99999823 0.855380189 1.141954824 0.484162213 0.13988926 65.3884485 567136.1702 0.056567398 0.040040862 172.0593515 -2.235678282 0.286574635 ALNHSVEDIEPDLLT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ALNHSVEDIEPDLLTPR 17 0 Q8IWR0;I3L2K5 Q8IWR0 ZC3H7A Zinc finger CCCH domain-containing protein 7A 1 ALNHSVEDIEPDLLT(1)PR;ALNHSVEDIEPDLLT(1)PR;ALNHSVEDIEPDLLT(1)PR;ALNHSVEDIEPDLLT(1)PR 233.5 1.52E-19 846150000 714790 667250 441558 537212 634010 701800 670060 728360 705870 TRUE FALSE 620328.6905 662866.7908 655096.9257 659194.1954 621394.4414 728798.7001 605077.6843 572605.8821 622422.8527 0.996635467 1.064978235 1.052494976 1.059077752 0.998347729 1.170906076 0.972132822 0.919962819 1 19.24753551 2.024625727 24.99994228 0.951799415 1.056052455 0.423725127 0.051088062 174.0734629 176717.9787 0.019417459 0.013090697 105.8341259 -2.024625727 0.104253039 ALNRPPTYPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALNRPPTYPTK 11 1 P55010;H0YLZ1;H0YN40;H0YMJ8;H0YM54;H0YK11 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 102.62 0.0025937 903370000 384100 412800 284890 306500 387680 379960 424400 471180 445300 FALSE TRUE 333340.2118 410088.2896 422663.7569 376095.5096 379965.9265 394577.3071 383241.7533 370421.8237 392657.1413 0.848934546 1.044392796 1.076419381 0.957821646 0.967678635 1.004890184 0.97602135 0.943372181 1 18.58291061 2.002803871 24.77181975 0.965257901 0.988651484 0 0.061165671 343.7189946 3036675.107 0.0247039 0.016554702 100.6477037 -2.002803871 0.023393583 ALPAAHIPAPPHEGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALPAAHIPAPPHEGSPR 17 0 P17029;E9PC66 P17029 ZKSCAN1 Zinc finger protein with KRAB and SCAN domains 1 1 ALPAAHIPAPPHEGS(1)PR;ALPAAHIPAPPHEGS(1)PR 96.848 0.0037111 228108000 178937 172163 113689 139413 158472 167847 143329 154177 142411 TRUE FALSE 155290.0221 171032.0499 168669.3807 171068.8524 155318.7172 174304.1827 129428.9756 121207.4484 125575.3338 1.236628384 1.361987619 1.343172863 1.36228069 1.236856893 1.388044749 1.030687888 0.965217011 1 16.93819358 2.176959764 5.85603408 0.98755171 1.322159902 0.896059105 0.051895319 0.051836528 3.456121436 0.020098169 0.013539534 150.300271 -2.176959764 0.334608191 ALPESLGQHALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALPESLGQHALR 12 0 O94760 O94760 DDAH1 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1" 0 ; 198.55 1.82E-07 1155510000 721670 709310 373110 487000 678330 714280 644930 770100 709400 FALSE TRUE 626299.481 704650.4959 553547.244 597580.7933 664832.5601 741758.8138 582384.7879 605420.1079 625535.5402 1.001221259 1.126475557 0.884917336 0.955310698 1.062821403 1.185798034 0.931017905 0.967842863 1 19.25473233 ALPFWNEEIVPQIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALPFWNEEIVPQIK 14 0 P18669;Q8N0Y7;P15259 P18669 PGAM1;PGAM4;PGAM2 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4;Phosphoglycerate mutase 2 0 ; 172.34 6.69E-06 147859000 259100 248570 150970 189936 199861 214537 240690 299860 231420 FALSE TRUE 224859.2785 246937.1273 223979.597 233063.8718 195884.1571 222790.3772 217347.9208 235737.2725 204061.7912 1.101917596 1.210109574 1.097606738 1.142124012 0.959925697 1.091778994 1.065108365 1.15522495 1 17.63864655 3.377290088 22.56330976 1.067982314 1.140267395 0.308376491 0.060237785 8.781863097 1967.478552 0.017266867 0.022291377 2383.911276 -3.377290088 0.072285081 ALPLALVLHELGAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALPLALVLHELGAGR 15 0 C9JGI3;P19971;A0A494C0L6;P19971-2 C9JGI3 TYMP Thymidine phosphorylase 0 170.52 3.27E-11 0 79806 85264 59329 69024 86674 89030 79323 90662 84745 FALSE TRUE 69259.4349 84703.89517 88020.70284 84696.95417 84949.35697 92455.04171 71630.26767 71274.63683 74726.54264 0.926838476 1.133518187 1.177904125 1.133425302 1.136802988 1.237245006 0.958565259 0.953806162 1 16.18933315 2.213037306 24.97514808 0.966742576 1.128129679 0.454583734 0.079144314 188.3856003 184338.2164 0.03191972 0.021529201 163.3192234 -2.213037306 0.161387102 LATAT(ph)GAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LATATGAK 8 0 Q9BZH6 Q9BZH6 WDR11 WD repeat-containing protein 11 1 LAT(0.032)AT(0.968)GAK 102.06 0.056312 604660000 1192900 1095600 1270300 1965900 961660 1017800 2015100 2252200 4692800 TRUE FALSE 1035255.243 1088402.931 1884621.329 2412287.642 942524.8475 1056955.425 1819675.912 1770584.557 4138022.53 0.250181152 0.263024893 0.455440084 0.582956623 0.227771802 0.255425246 0.439745289 0.427881807 1 21.98051007 1.090835831 2.208853224 1.413062775 0.353730739 0.757637784 0.113753316 0.581203194 2.011077692 1.43574481 0.031688077 12.32638792 -1.090835831 -1.059332036 ALPPLPRPPT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALPPLPRPPTPK 12 1 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 ALPPLPRPPT(1)PK;ALPPLPRPPT(1)PK 98.943 0.0065873 1113250000 3224400 2756400 2212500 2293200 2635600 2234800 3226900 3654100 3094900 TRUE FALSE 2798287.37 2738293.027 3282472.4 2813906.109 2583156.716 2320774.202 2913955.735 2872699.151 2729024.448 1.025380103 1.003396298 1.202800658 1.031103298 0.946549496 0.850404328 1.067764614 1.05264691 1 21.37995389 3.479950235 24.93291785 0.991518963 1.077669283 0.226942694 0.078504099 185.7431634 1637039.029 0.023982397 0.031568454 3019.605688 -3.479950235 0.086150321 ALPQT(ph)PRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ALPQTPRPR 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ALPQT(1)PRPR;ALPQT(1)PRPR;ALPQT(1)PRPR;ALPQT(1)PRPR;ALPQT(1)PRPR;ALPQT(1)PRPR;ALPQT(1)PRPR 118.9 0.0014771 31278280000 4788290 4320260 2566516 2597345 3710170 4265720 3631900 3860080 2577628 TRUE FALSE 4155505.345 4291879.928 3807691.722 3187111.88 3636344.876 4429825.009 3279678.897 3034631.931 2272903.754 1.828280382 1.88828054 1.675254271 1.402220342 1.599867513 1.948971662 1.442946667 1.335134374 1 21.11610516 1.532182615 1.452415226 0.920530711 1.707309499 0.669877066 0.16563492 0.425357642 1.288543018 0.443983111 0.053066779 34.0551357 -1.532182615 0.786778788 ALPSLNTGSSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ALPSLNTGSSSPR 13 0 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 ALPSLNTGS(0.016)S(0.264)S(0.719)PR;ALPSLNTGS(0.001)S(0.151)S(0.848)PR;ALPSLNT(0.001)GS(0.009)S(0.024)S(0.965)PR;ALPSLNTGS(0.001)S(0.292)S(0.707)PR;ALPSLNTGSS(0.001)S(0.999)PR;ALPSLNTGSS(0.003)S(0.997)PR;ALPSLNTGSS(0.011)S(0.989)PR 206.28 6.62E-08 26236870000 21880040 18541080 13193940 14705800 19059040 21833670 19762820 21024100 20179660 TRUE FALSE 18988537.28 18419282.42 19574573.52 18044976.65 18679802.39 22673625.41 17846224.76 16528259.82 17794043.58 1.067128851 1.035137536 1.100063256 1.014102082 1.049778388 1.274225575 1.002932508 0.928864749 1 24.08489106 2.01229896 24.99380248 0.961315437 1.087397766 0.356823209 0.072681973 221.912002 450965.3758 0.029694262 0.020005459 102.8724209 -2.01229896 0.126082329 ALPTSKPEGSLHS(ph)SPVGPSSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALPTSKPEGSLHSSPVGPSSSK 22 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 ALPTSKPEGS(0.001)LHS(0.548)S(0.451)PVGPSSSK 98.671 0.0006791 269110000 434690 354330 189810 356580 376100 299980 488750 581360 531610 TRUE FALSE 377244.6151 352002.3829 281602.7509 437546.939 368616.3458 311520.4247 441351.1002 457040.6881 468763.6714 0.804765041 0.750916516 0.600735014 0.933406246 0.786358603 0.664557524 0.941521554 0.974991698 1 18.83850124 2.123100439 6.185677355 0.977247814 0.759316468 0.578989321 0.08698929 0.148335993 7.458196971 0.035849018 0.023998044 132.7701479 -2.123100439 -0.217931346 ALPTSKPEGSLHSS(ph)PVGPSSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALPTSKPEGSLHSSPVGPSSSK 22 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 ALPTSKPEGS(0.001)LHS(0.16)S(0.838)PVGPSSSK;ALPTSKPEGSLHS(0.264)S(0.735)PVGPSSSK 103.12 0.00035873 654800000 547930 430988 198702 405230 482740 337352 582020 694540 562600 TRUE FALSE 475519.6622 428156.8114 294794.9518 497243.6651 473134.4185 350330.1497 525575.79 546018.0259 496090.0689 0.958534936 0.863062654 0.594236753 1.002325376 0.953726849 0.70618255 1.059436225 1.100642928 1 18.92024255 2.208427045 23.57511393 1.063464034 0.847616376 0.383344841 0.123543409 108.605464 84966.43581 0.050197951 0.033850541 161.5946748 -2.208427045 -0.215847658 ALQALEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALQALEELR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 99.815 0.011822 73169000 132253 155062 102089 108642 155725 161168 141371 157490 149543 FALSE TRUE 114775.431 154043.3875 151459.5819 133310.8266 152626.3772 167368.2372 127660.8622 123811.9891 131864.1969 0.870406325 1.168197215 1.14860277 1.010970603 1.157451232 1.269247007 0.968123761 0.938935602 1 17.00869338 2.053348887 24.99861185 0.96163207 1.108217662 0.263254017 0.10623943 111.5651176 52277.38993 0.042243647 0.028480655 113.0703892 -2.053348887 0.146585592 ALQAPHS(ph)PSKTDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALQAPHSPSKTDGK 14 1 F2Z2Z8;Q5T173;Q96AQ6-3;Q96AQ6-2;Q96AQ6 F2Z2Z8 PBXIP1 Pre-B-cell leukemia transcription factor-interacting protein 1 1 ALQAPHS(0.977)PS(0.008)KT(0.014)DGK;ALQAPHS(0.841)PS(0.158)KT(0.001)DGK 157.91 3.12E-06 582290000 1003840 882660 861260 1098590 1338090 912560 1198090 2226400 1461010 TRUE FALSE 871180.0006 876861.7483 1277768.217 1348041.65 1311464.627 947666.7737 1081899.416 1750301.686 1288291.062 0.676229174 0.680639472 0.991831935 1.046379727 1.017987833 0.735599898 0.839794242 1.358622859 1 20.29702715 5.701708481 0.242772754 1.179170249 1.97E-34 0.327596235 0.169858457 36.08184179 1.610060339 0.888475266 13.83074479 503162.749 -5.701708481 -1.179170249 ALQDEWDAVMLHSFTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ALQDEWDAVMLHSFTLR 17 0 Q9UMS4;F5GY56 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 ;;;; 237.86 3.13E-20 1032512000 991512 866651 550590 656108 735000 793666 891434 868154 658579 FALSE TRUE 860481.177 860957.9125 816857.1656 805087.3494 720374.938 824198.8446 804982.8679 682506.0231 580722.5409 1.481742341 1.482563276 1.40662211 1.386354572 1.240480414 1.419264428 1.386174655 1.175270418 1 19.14748951 0.503005222 0.745548287 9.87E-15 1.419100036 0.799935572 0.067886444 3.446902056 0.665678389 5.299136105 0.029988201 3.184235811 -0.503005222 1.419100036 ALQHMTDFAIQFNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALQHMTDFAIQFNK 14 0 P63010;P63010-2;P63010-3;A0A087X253 P63010 AP2B1 AP-2 complex subunit beta 0 87.083 0.0081174 0 265400 276150 174510 246370 240330 231990 246940 321120 298090 FALSE TRUE 230326.7176 274335.9525 258903.6197 302312.074 235547.9032 240914.8054 222991.7968 252450.987 262850.1398 0.876266293 1.043697191 0.984985665 1.150130924 0.896130028 0.916548135 0.84836096 0.960436952 1 18.00388098 ALQHTES(ph)PSETNKPHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALQHTESPSETNKPHSK 17 1 Q14669-3;Q14669;Q14669-2;G5E9G6;C9JLD7;C9JLJ5;C9JSX9 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 ALQHTES(0.987)PS(0.007)ET(0.007)NKPHSK 201.67 6.81E-12 127450000 211100 157480 125900 154090 166890 111530 216940 245150 166100 TRUE FALSE 183202.6001 156445.5035 186785.6611 189078.4896 163569.2155 115820.6313 195901.1922 192726.5803 146463.8472 1.250838371 1.068150991 1.275302163 1.290956732 1.116789014 0.79077966 1.337539577 1.315864522 1 17.16018507 5.090928045 17.19863435 1.166909725 4.325911347 0.025103745 0.169979317 533.047035 102686.5005 0.041210134 1199.188526 123290.0547 -5.090928045 3.159001623 ALQLEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ALQLEEER 8 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;; 225.4 8.37E-06 5296170000 4320790 4329170 3065850 3692780 4227240 4531270 3770000 4701360 4298300 FALSE TRUE 3749786.654 4300731.397 4548505.315 4531282.14 4143126.194 4705590.889 3404385.98 3696010.75 3790159.871 0.989347886 1.13470976 1.200082706 1.195538525 1.093127028 1.241528339 0.898216987 0.975159591 1 21.85382727 2.231751108 24.99999883 0.958928086 1.144839128 0.588829296 0.072695423 106.924982 392552.9406 0.028719861 0.019846879 170.5104923 -2.231751108 0.185911042 ALQLLHCFPLDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALQLLHCFPLDIR 13 0 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ; 140.08 3.92E-05 663170000 629920 599350 374110 405540 524630 588580 534710 575560 479850 FALSE TRUE 546674.476 595412.8304 555030.8473 497624.0553 514190.8894 611223.0535 482853.9065 452480.973 423122.6796 1.291999938 1.407187227 1.311749226 1.176075118 1.215228855 1.444552804 1.141167632 1.069384826 1 18.69071649 2.040192468 6.258588609 1.057973481 1.302533173 0.670307586 0.080671122 0.11171265 11.55519954 0.035469035 0.02331421 109.6964235 -2.040192468 0.244559692 ALQLSNS(ph)PGASSAFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALQLSNSPGASSAFLK 16 0 Q12802-2;Q12802;Q12802-4;H0YMW2 Q12802-2 AKAP13 A-kinase anchor protein 13 1 ALQLS(0.009)NS(0.99)PGASSAFLK 151.63 6.56E-07 174120000 437880 519480 320330 377110 464420 403470 502240 580460 494130 TRUE FALSE 380013.0486 516067.5017 475242.6594 462738.5893 455178.9506 418991.752 453532.8421 456333.1461 435714.5143 0.872160637 1.184416596 1.090720285 1.062022435 1.044672453 0.96161991 1.040894501 1.047321425 1 18.73302365 2.99314158 21.84373999 1.018635848 1.063112029 0.045266891 0.079482393 177.8374191 566418.5332 0.023322155 0.02538153 984.3319462 -2.99314158 0.044476181 ALQS(ph)PALGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ALQSPALGLR 10 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 1 ALQS(1)PALGLR;ALQS(1)PALGLR;ALQS(1)PALGLR;ALQS(1)PALGLR;ALQS(1)PALGLR;ALQS(1)PALGLR 190.85 8.98E-07 5013670000 3478120 3728140 2587740 3050070 3575740 3490440 3122750 3729440 4604400 TRUE FALSE 3018477.63 3703649.603 3839179.719 3742635.011 3504589.77 3624719.485 2819906.186 2931928.279 4060073.077 0.743454015 0.912212547 0.945593748 0.921814691 0.863183914 0.892771981 0.694545672 0.722136824 1 21.95307426 2.276995921 24.93193814 0.783555098 0.88544997 0.099599429 0.097131891 248.6170825 161270.1851 0.036004066 0.027888118 189.2325843 -2.276995921 0.101894872 ALQS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALQSPK 6 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 ALQS(1)PK 93.166 0.048177 2295300000 6232900 4533200 3345900 3973600 3012000 3909800 5530000 6778900 5807500 TRUE FALSE 5409206.473 4503421.111 4963988.431 4875866.613 2952067.093 4060212.536 4993701.451 5329284.988 5120943.966 1.056290893 0.8794123 0.969350273 0.952142153 0.576469321 0.792864082 0.975152527 1.040684105 1 22.28797834 -0.272282526 12.63702174 4.415522352 0.915604748 0 0.142094452 0 0 0 0.034219804 0.534216718 0.272282526 -3.499917604 ALQSGQCAGAALDVFTEEPPRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ALQSGQCAGAALDVFTEEPPRDR 23 1 A0A286YFA2;A0A286YF22;O43175;A0A2C9F2M7;A0A286YFL2;A0A286YF78 A0A286YFA2 PHGDH D-3-phosphoglycerate dehydrogenase 0 ;; 205.9 1.34E-24 503380000 307152 164050 72792 125619 169104 171166 146284 162200 105736 FALSE TRUE 266561.085 162972.3447 107994.4547 154142.7139 165739.1612 177750.8668 132097.4002 127514.7922 93236.01053 2.858992823 1.747954935 1.158291245 1.653252998 1.777630341 1.906461524 1.416806655 1.367656032 1 16.50859965 4.710773129 3.459562526 1.48795626 2.989800804 0.719543115 0.270700617 0.151629023 3.169558047 0.070680435 0.573002593 51377.51911 -4.710773129 1.501844543 ALQTS(ph)PQPPEGPGLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(0.178)S(0.822)PQPPEGPGLPR;ALQT(0.003)S(0.997)PQPPEGPGLPR;ALQT(0.005)S(0.995)PQPPEGPGLPR;ALQT(0.072)S(0.928)PQPPEGPGLPR;ALQT(0.037)S(0.963)PQPPEGPGLPR 257.15 1.22E-26 1815450000 1636060 1834910 1203030 1319610 1865570 1879390 1660810 1966900 1702980 TRUE FALSE 1419850.526 1822856.355 1784819.332 1619247.619 1828448.807 1951691.349 1499744.902 1546293.741 1501655.644 0.945523383 1.213897715 1.188567658 1.078308216 1.217621905 1.299693013 0.998727576 1.029725921 1 20.51812259 2.195210724 24.99907762 1.013253001 1.160419797 0.352915437 0.094223214 149.6625605 86306.59967 0.037548882 0.025315645 156.7511458 -2.195210724 0.147166796 ALQTVIEMKDS(ph)KISSMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALQTVIEMKDSKISSMER 18 2 G8JLD3;X6RLX0;Q8IUD2-3;Q8IUD2;Q8IUD2-2;X6RM00;Q8IUD2-4;K7EPP6 G8JLD3 ERC1 ELKS/Rab6-interacting/CAST family member 1 1 ALQTVIEMKDS(0.436)KIS(0.436)S(0.127)MER 48.899 0.063854 0 51287 53362 39742 43158 55263 50210 61759 65797 79541 TRUE FALSE 44509.29301 53011.46151 58961.36413 52957.68353 54163.37442 52141.61119 55769.62169 51726.82358 70137.75359 0.634598212 0.75581921 0.840650878 0.755052462 0.772242789 0.743417183 0.79514411 0.737503284 1 16.0979036 1.235544784 24.99969297 1.000000328 0.758419927 0.687630759 0.051976688 49.02363944 406306.8471 0.084361736 0.012286333 17.20064703 -1.235544784 -0.241580401 ALRPDLADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALRPDLADK 9 1 Q8TCD5;J3KSX6;J3KRC4;Q8TCD5-2 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 0 77.662 0.029153 177590000 122050 136790 92811 93547 130650 146680 120470 142650 106860 FALSE TRUE 105920.7833 135891.4175 137694.71 114788.2761 128050.3206 152322.8745 108786.8379 112145.4076 94227.13254 1.124100675 1.44216866 1.461306381 1.218208313 1.358953808 1.616550036 1.154517123 1.190160462 1 16.52385492 1.758780626 2.000442297 1.050245609 1.366609677 0.383644329 0.145417218 0.331781426 2.566372488 0.143268099 0.040695777 57.38265329 -1.758780626 0.316364068 ALRPEAPPPPPPAFSFQEFLPS(ph)LNSSPLDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALRPEAPPPPPPAFSFQEFLPSLNSSPLDIR 31 1 Q9P107;K7EJC2;Q9P107-2 Q9P107 GMIP GEM-interacting protein 1 ALRPEAPPPPPPAFSFQEFLPS(0.564)LNS(0.218)S(0.218)PLDIR 133.13 1.78E-06 158710000 53468 54974 33556 43141 60617 54248 71702 81435 47764 TRUE FALSE 46402.06833 54612.87217 49783.79384 52936.82342 59410.8403 56334.95566 64748.35108 64020.75898 42117.39433 1.101731697 1.29668212 1.182024544 1.256887428 1.410601041 1.337569823 1.537330409 1.520055074 1 15.36212856 3.354877098 3.710264357 1.393336153 1.205209623 0.183181925 0.154534842 0.338556208 8.857001879 0.045875466 0.060272102 2264.003522 -3.354877098 -0.188126529 ALRPEAPPPPPPAFSFQEFLPSLNS(ph)SPLDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALRPEAPPPPPPAFSFQEFLPSLNSSPLDIR 31 1 Q9P107;K7EJC2;Q9P107-2 Q9P107 GMIP GEM-interacting protein 1 ALRPEAPPPPPPAFSFQEFLPS(0.032)LNS(0.484)S(0.484)PLDIR 107.54 7.92E-05 114300000 49024 54172 41405 49412 50181 44091 56587 62508 65313 TRUE FALSE 42545.35419 53816.14057 61428.59649 60631.74982 49182.49628 45787.2093 51099.20145 49141.15064 57591.77154 0.738740154 0.934441486 1.066621061 1.052784941 0.853984779 0.795030402 0.887265665 0.85326687 1 15.81357508 3.176292459 24.99988374 0.87138677 0.955633894 0.102163057 0.101381328 137.3724585 55152.09137 0.031595032 0.035825413 1500.69508 -3.176292459 0.084247124 ALRPGDLPPS(ph)PDDVK ddPTM_MDA-MB-175_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 125.28 5.54E-05 1485000000 551690 489620 369860 419570 531200 403220 598460 643560 598650 TRUE FALSE 478782.7687 486403.654 548725.5331 514839.7812 520630.1593 418732.1343 540421.4413 505939.7022 527878.279 0.906994638 0.921431461 1.03949254 0.975300181 0.986269335 0.793236151 1.023761467 0.958440084 1 19.00984578 ALRPGDLPPS(ph)PDDVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALRPGDLPPSPDDVKR 16 2 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 ALRPGDLPPS(1)PDDVKR 113.17 0.00035603 326510000 1250900 1131100 928670 1002700 1232700 1157100 1451600 1672900 1530500 TRUE FALSE 1085590.396 1123669.73 1377777.918 1230378.36 1208171.682 1201614.386 1310824.055 1315163.354 1349566.034 0.804399613 0.832615598 1.020904412 0.911684445 0.895229764 0.890370946 0.97129301 0.974508339 1 20.36406414 4.359438207 6.80076458 0.949136904 0.811933418 0.6248868 0.043160733 0.137927791 7.48223929 0.011415362 0.030714998 22879.06157 -4.359438207 -0.137203486 ALRPPMSQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALRPPMSQAR 10 1 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ; 133.81 0.00017087 2572100000 486750 828940 540240 520040 691180 813830 769330 805380 940360 FALSE TRUE 422424.7542 823494.6386 801501.871 638123.0303 677426.8703 845138.5667 694720.495 633155.7545 829191.7121 0.509441602 0.993129365 0.966606225 0.769572369 0.816972553 1.019231807 0.837828556 0.763581866 1 19.66134617 4.749327831 24.6741607 0.88246402 0.509441346 0.607001928 0.097185863 983.6055257 2253979.512 0.024181498 0.343123395 56147.16482 -4.749327831 -0.373022674 ALRPPT(ph)SPGVFGALQNFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALRPPTSPGVFGALQNFK 18 1 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 ALRPPT(0.5)S(0.5)PGVFGALQNFK 142.85 1.77E-07 507630000 254500 239060 181890 254940 256530 206360 286550 343100 363350 TRUE FALSE 220867.1802 237489.5991 269852.6124 312828.0235 251425.5549 214298.8027 258760.4251 269730.735 320395.1769 0.68935863 0.74123962 0.842249297 0.976381812 0.784735767 0.668857767 0.807628965 0.8418689 1 18.2894929 1.215726873 2.180955356 1.069726287 0.790752781 0.381921953 0.085019878 0.866641476 3.96262452 0.490341725 0.024448679 16.43337905 -1.215726873 -0.278973506 ALRPPTS(ph)PGVFGALQNFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALRPPTSPGVFGALQNFK 18 1 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 ALRPPT(0.166)S(0.834)PGVFGALQNFK 91.337 0.0015377 473290000 180150 199840 168230 188260 178390 154970 176900 219190 327320 TRUE FALSE 156342.7211 198527.2379 249586.5907 231007.3104 174840.388 160931.7962 159744.2652 172317.9242 288624.6025 0.541681893 0.68783893 0.864744684 0.800372901 0.60577091 0.557581699 0.553467251 0.597031309 1 18.13883476 1.153966362 0.011249527 0.818890878 0.546453654 0.000927362 0.153672376 480935.7575 1438.715049 18269.82243 16603.53447 14.25497177 -1.153966362 -0.272437225 ALS(ph)GRAS(ph)PVPAPSSGLHAAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALSGRASPVPAPSSGLHAAVR 21 1 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 2 ALS(1)GRAS(1)PVPAPSSGLHAAVR 123.24 3.55E-05 69096000 101160 95981 28092 57314 79631 67706 95110 109110 58534 TRUE FALSE 87791.44969 95350.49449 41677.38516 70328.01969 78046.4989 70310.69363 85886.24684 85777.67559 51614.1772 1.700917354 1.847370232 0.807479406 1.362571749 1.512113592 1.362236065 1.664004959 1.661901443 1 15.65547977 ALS(ph)HDSIFIPESGQDATRPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALSHDSIFIPESGQDATRPVR 21 1 Q6NV74;C9JFM2;C9JXD6;C9JK00 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 ALS(0.997)HDS(0.003)IFIPESGQDATRPVR;ALS(1)HDSIFIPESGQDATRPVR 161.64 1.19E-11 322470000 140658 141068 41673 89080 137569 142813 144685 151038 127798 TRUE FALSE 122069.6889 140141.315 61826.20219 109306.9755 134831.646 148307.1085 130653.471 118739.6991 112689.866 1.083235727 1.243601754 0.548640303 0.969980526 1.196484216 1.31606429 1.159407457 1.053685689 1 16.78199826 3.284216159 8.145652704 1.143221833 0.951196856 0.186010564 0.190548444 0.451723216 71.08151221 0.057134648 0.073405245 1924.049135 -3.284216159 -0.192024976 ALS(ph)IESLSPTDSSNGVNWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(1)IESLSPTDSSNGVNWR;ALS(1)IESLSPTDSSNGVNWR;ALS(0.981)IES(0.019)LSPTDSSNGVNWR 387.95 6.84E-127 1165130000 980666 821603 563322 652883 870990 926165 767370 945526 863300 TRUE FALSE 851068.5034 816205.8358 835746.4034 801130.0638 853659.0031 961795.1669 692950.5755 743332.623 761241.6575 1.118000434 1.072203324 1.09787266 1.052399138 1.121403426 1.263455773 0.910289878 0.976473917 1 19.53799499 2.212528702 24.99999969 0.963051731 1.114540214 0.606500954 0.060088717 156.3695412 150169.7815 0.024824653 0.016742988 163.1280715 -2.212528702 0.151488484 ALS(ph)LDDKGWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALSLDDKGWR 10 1 Q9NRR6-2;Q9NRR6 Q9NRR6-2 INPP5E 72 kDa inositol polyphosphate 5-phosphatase 1 ALS(1)LDDKGWR 69.352 0.034663 124400000 347330 289440 289550 333390 187770 228410 262560 296150 344750 TRUE FALSE 301429.4605 287538.6496 429577.3485 409091.295 184033.7444 237197.0805 237096.9716 232820.6271 303994.0477 0.991563693 0.945869341 1.413111052 1.345721398 0.605386012 0.780268832 0.77993952 0.765872322 1 18.21368355 3.239154408 24.99999891 0.782962944 1.17484121 0.571067991 0.166979293 12.17622548 512634.3935 0.051581569 0.062636984 1734.420541 -3.239154408 0.391878266 ALS(ph)LEENGVGSNFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ALSLEENGVGSNFK 14 0 Q8NF50-3;Q8NF50;Q8NF50-4;Q8NF50-2;E9PDJ4 Q8NF50-3 DOCK8 Dedicator of cytokinesis protein 8 1 ALS(1)LEENGVGSNFK;ALS(1)LEENGVGSNFK;ALS(1)LEENGVGSNFK;ALS(1)LEENGVGSNFK 268.08 4.36E-25 859410000 1584200 1254060 747026 1027120 1230980 746966 2275440 1884920 1624030 TRUE FALSE 1374843.956 1245821.997 1108290.272 1260343.295 1206485.906 775702.2654 2054768.179 1481844.526 1432039.024 0.960060399 0.869963721 0.773924631 0.880104015 0.842495132 0.541676765 1.434854878 1.034779431 1 20.44963938 2.240362525 25 1.142773212 0.816871005 0.515883351 0.157378616 38.72021992 537224.2177 0.0592737 0.043514272 173.9252055 -2.240362525 -0.325902207 ALS(ph)PAELR ddPTM_MDA-MB-175_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 109.42 0.0037992 129880000 555870 545980 309670 428330 513550 495210 403470 589670 509430 TRUE FALSE 482410.3711 542393.4214 459427.4478 525588.8731 503331.3597 514261.0491 364341.5415 463573.6593 449205.7657 1.073918475 1.207449821 1.022755011 1.170040354 1.120491762 1.144822904 0.811079397 1.031985105 1 18.77701692 2.274612857 24.99992345 0.959557793 1.124507911 0.544416626 0.075440574 123.8810292 85903.1487 0.026228974 0.020316186 188.1970695 -2.274612857 0.164950118 ALS(ph)PGLEESGLGLLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ALSPGLEESGLGLLAR 16 0 H9KVB4;O15417;O15417-2 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 ALS(1)PGLEESGLGLLAR;ALS(1)PGLEESGLGLLAR;ALS(1)PGLEESGLGLLAR;ALS(1)PGLEESGLGLLAR;ALS(1)PGLEESGLGLLAR;ALS(1)PGLEESGLGLLAR;ALS(1)PGLEESGLGLLAR;ALS(1)PGLEESGLGLLAR 294.97 1.26E-45 3702350000 718247 673688 438612 555984 700284 688335 603284 745288 651801 TRUE FALSE 623328.8391 669262.4992 650726.2303 682228.6649 686349.7185 714815.6929 544777.6105 585913.961 574745.8283 1.084529558 1.164449512 1.132198266 1.187009337 1.194179557 1.243707492 0.947858312 1.019431429 1 19.13256456 2.232548432 24.9999983 0.993698059 1.168002632 0.781231474 0.044526261 65.19773558 271103.1753 0.018074773 0.012543179 170.823821 -2.232548432 0.174304573 ALS(ph)PVIPLIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ALSPVIPLIPR 11 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 ALS(1)PVIPLIPR;ALS(1)PVIPLIPR;ALS(1)PVIPLIPR;ALS(1)PVIPLIPR;ALS(1)PVIPLIPR;ALS(1)PVIPLIPR;ALS(1)PVIPLIPR;ALS(1)PVIPLIPR 187.85 3.57E-06 4458814000 3246868 3039910 2015788 2224348 3006069 3009042 2898053 3294053 3016459 TRUE FALSE 2817786.167 3019940.631 2990629.819 2729420.21 2946254.108 3124801.793 2617000.266 2589645.4 2659856.653 1.059375197 1.135377212 1.124357516 1.026153123 1.107674019 1.174800826 0.983887708 0.97360337 1 21.34291707 2.214315532 24.75060411 0.983202024 1.103489787 0.654907051 0.0406296 121.1120448 123636.1663 0.016569736 0.011177451 163.8006165 -2.214315532 0.120287763 ALS(ph)SAGPIPIRPPIVPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALSSAGPIPIRPPIVPVK 18 1 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 ALS(0.5)S(0.5)AGPIPIRPPIVPVK 215.75 5.65E-19 414270000 613810 595530 343090 337400 433530 417570 769980 679290 821890 TRUE FALSE 532693.4533 591617.9242 509009.4716 414011.8268 424903.6012 433634.1881 695307.4581 534029.1197 724727.1005 0.735026264 0.816332001 0.702346402 0.571265828 0.586294622 0.598341345 0.959405903 0.736869257 1 19.46707832 2.242375185 24.99962489 0.867558469 0.668411732 0.530046661 0.100893959 89.39678208 585887.2289 0.040752455 0.030345139 174.7331014 -2.242375185 -0.199146737 GNIYYQSYEHRS(ph)PS(ph)PNIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GNIYYQSYEHRSPSPNIR 18 1 A2AJT9-3;A2AJT9-2;A2AJT9 A2AJT9-3 CXorf23 Uncharacterized protein CXorf23 2 GNIYYQS(0.011)Y(0.001)EHRS(0.992)PS(0.995)PNIR;GNIYYQS(0.001)Y(0.081)EHRS(0.923)PS(0.995)PNIR;GNIYYQS(0.143)Y(0.003)EHRS(0.867)PS(0.988)PNIR 125.62 3.89E-05 323420000 608680 576770 327377 359838 576160 600990 503140 570340 297839 TRUE FALSE 528241.3958 572981.1599 485697.6122 441544.7177 564695.5432 624110.4742 454345.5602 448377.2294 262628.8127 2.011361169 2.181714771 1.849369105 1.6812501 2.150165998 2.376397577 1.729991297 1.70726595 1 18.00266568 1.092641775 1.388708996 0.264353108 2.017354142 0.707803847 0.204559271 1.05911047 1.362277148 2.904502701 0.062635229 12.37775195 -1.092641775 1.753001035 ALS(ph)SDSILSPAPDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 ALS(0.864)S(0.136)DSILSPAPDAR;ALS(0.497)S(0.497)DS(0.006)ILSPAPDAR;ALS(0.5)S(0.5)DSILSPAPDAR;ALS(0.978)S(0.022)DSILSPAPDAR;ALS(0.882)S(0.117)DS(0.001)ILSPAPDAR;ALS(0.722)S(0.278)DSILSPAPDAR;ALS(0.863)S(0.136)DS(0.001)ILSPAPDAR;ALS(0.5)S(0.5)DSILSPAPDAR;ALS(0.931)S(0.067)DS(0.002)ILSPAPDAR;ALS(0.982)S(0.018)DSILSPAPDAR;ALS(0.494)S(0.494)DS(0.011)ILSPAPDAR;ALS(0.992)S(0.008)DSILSPAPDAR 422.25 3.90E-153 51239840000 5974700 6157889 3811238 5136008 5671025 5451749 5288863 6322559 6807390 TRUE FALSE 5185128.257 6117437.422 5654365.445 6302217.115 5558182.698 5661481.312 4775949.88 4970528.96 6002628.109 0.863809678 1.019126508 0.941981636 1.04990964 0.925958196 0.943167094 0.795643141 0.828058789 1 22.51716286 2.398711976 7.236874918 0.861749214 0.964229819 0.221013057 0.072291694 0.271835917 21.09177557 0.026271925 0.02029037 250.4447752 -2.398711976 0.102480605 ALS(ph)YAS(ph)LDKEDLLSPINQNTLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALSYASLDKEDLLSPINQNTLQR 23 1 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 2 ALS(0.995)Y(0.011)AS(0.994)LDKEDLLSPINQNTLQR 115.18 0.00034002 100950000 171830 155630 119050 129140 182320 141170 209340 224440 196620 TRUE FALSE 149122.2301 154607.6563 176622.9782 158463.2108 178692.1887 146600.9012 189038.239 176445.2526 173375.8076 0.860109794 0.89174873 1.018729087 0.913986865 1.030663915 0.845567229 1.090338045 1.017703998 1 17.40354308 7.720653969 0.270427167 1.031472503 5.94E-12 0.306786752 0.068046803 84.08642353 1.548690139 0.174812798 38.36123237 52559832.09 -7.720653969 -1.031472503 ALSAAVADSLTNS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALSAAVADSLTNSPR 15 0 Q14687;Q14687-2;Q14687-3;H7C3B5 Q14687 GSE1 Genetic suppressor element 1 1 ALSAAVADSLTNS(1)PR;ALSAAVADSLTNS(1)PR 269.87 3.13E-26 624580000 1165340 957480 718770 773450 1006140 1001910 903040 1034400 1464410 TRUE FALSE 1011337.366 951190.2508 1066369.576 949073.6439 986119.7825 1040454.126 815463.3198 813201.6097 1291289.118 0.78319979 0.736620667 0.825817829 0.734981524 0.763670791 0.805748389 0.631511029 0.629759516 1 20.30038062 ALSAIADLLTNEHER ddPTM_MDA-MB-175_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 ;;;; 283.82 6.32E-34 1222115000 1716001 1493508 941160.7 1364787 1560869 1822911 1210218 1723038 1490402 FALSE TRUE 1489227.12 1483697.048 1396309.163 1674682.748 1529810.761 1893039.566 1092851.245 1354579.732 1314208.373 1.133174274 1.128966363 1.062471668 1.274290121 1.164054949 1.440440956 0.831566186 1.030719146 1 20.32576261 2.219386711 24.99998712 0.96495312 1.192726364 0.508445927 0.113901058 208.7672179 272200.0456 0.045806654 0.030936933 165.7244976 -2.219386711 0.227773244 ALSAS(ph)HTDLAH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ALSASHTDLAH 11 0 Q07866-6;Q07866-4;Q07866-7;H0YG16;H0YJK1 Q07866-6 KLC1 Kinesin light chain 1 1 ALSAS(0.985)HT(0.015)DLAH;ALSAS(0.995)HT(0.005)DLAH;ALSAS(0.976)HT(0.024)DLAH;ALSAS(0.983)HT(0.017)DLAH;ALS(0.073)AS(0.917)HT(0.01)DLAH;ALSAS(0.994)HT(0.005)DLAH;ALS(0.005)AS(0.95)HT(0.046)DLAH 185.25 2.93E-06 15019750000 12634670 12334110 6350630 6675340 9971720 11748490 9929860 10189600 11079300 TRUE FALSE 10964966.35 12253086.42 9421815.91 8191077.973 9773302.281 12200462.01 8966863.706 8010633.336 9769517.776 1.122365157 1.254216093 0.964409516 0.838432168 1.000387379 1.248829501 0.917840973 0.819962 1 23.21985592 4.227403374 24.75214515 0.960139248 1.188290604 0.358385683 0.120882338 186.0154452 412675.1239 0.033339454 0.070462433 16881.2023 -4.227403374 0.228151355 ALSCHPDKNPDNPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALSCHPDKNPDNPR 14 1 H0YLQ7;Q9NVM6;S4R343;H0YK99 H0YLQ7 DNAJC17 DnaJ homolog subfamily C member 17 0 ; 93.478 0.0027313 378990000 195809 204014 80406 139978 288220 260760 212966 257530 194745 FALSE TRUE 169932.3445 202673.8186 119290.6105 171762.1443 282484.9859 270791.6059 192312.5901 202459.2136 171722.468 0.989575485 1.180240542 0.694670953 1.000231049 1.645008887 1.576914245 1.119903484 1.178990822 1 17.38971929 3.444487005 24.99525455 1.291451936 0.955716719 0.3596874 0.224403928 227.1451619 173974.5476 0.068940914 0.089002904 2782.832106 -3.444487005 -0.335735218 ALSDHHIYLEGTLLKPNMVTPGHACTQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ALSDHHIYLEGTLLKPNMVTPGHACTQK 28 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BU78 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;; 266.94 2.33E-54 11056400000 7466990 6771650 2127590 5264420 7603670 5528640 8360620 9847040 8320260 FALSE TRUE 6480208.353 6727166.585 3156499.64 6459787.023 7452371.843 5741330.358 7549808.359 7741327.126 7336648.341 0.883265498 0.916926405 0.430237282 0.88048203 1.015773347 0.782554934 1.029054141 1.055158536 1 22.80668971 2.668984112 0.935958675 1.043341867 0.77043207 0.282445913 0.154214335 0.745686701 1.455798893 0.125923581 0.084105989 466.6423087 -2.668984112 -0.272909797 ALSFLVNDCSLIHNNVCMAAVFVDR ddPTM_MDA-MB-175_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 ;; 290.36 8.05E-63 181895000 90692 95350 49679.9 65999 85494 89505 95068 109220 77816 FALSE TRUE 78706.82242 94723.63957 73705.26581 80985.08168 83792.83667 92948.31527 85848.31999 85864.15295 68616.68113 1.14705085 1.380475389 1.074159586 1.180253553 1.221172976 1.354602317 1.251129005 1.25135975 1 16.06627173 1.236254603 24.92181503 0.999999682 1.235781487 0.397149198 0.089953368 61.09748663 660140.2422 0.137750391 0.021207737 17.22878307 -1.236254603 0.235781805 ALSHDS(ph)IFIPESGQDATRPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALSHDSIFIPESGQDATRPVR 21 1 Q6NV74;C9JFM2;C9JXD6;C9JK00 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 ALS(0.351)HDS(0.649)IFIPESGQDATRPVR;ALS(0.092)HDS(0.908)IFIPESGQDATRPVR 270.34 7.49E-45 1387050000 319180 323150 98396 193022 316350 309010 332290 346900 344940 TRUE FALSE 276999.5543 321027.2064 145980.6347 236850.5953 310055.2539 320897.8147 300064.5669 272718.1346 304161.5862 0.910698678 1.055449541 0.47994435 0.778699895 1.019376766 1.055024136 0.986530123 0.896622542 1 18.21447843 3.241422036 24.9858427 0.982451828 0.800697923 0.280186148 0.147077746 107.1956116 936022.1373 0.044744534 0.055219926 1743.500338 -3.241422036 -0.181753905 ALSQTVPSSGTNGVSLPADCTGAVPAAS(ph)PDTAAWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALSQTVPSSGTNGVSLPADCTGAVPAASPDTAAWR 35 0 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7EN31 Q9H6Z4 RANBP3 Ran-binding protein 3 1 ALSQTVPSSGTNGVSLPADCTGAVPAAS(0.969)PDT(0.031)AAWR;ALSQTVPSSGTNGVSLPADCTGAVPAAS(0.785)PDT(0.215)AAWR 184.45 1.80E-20 910390000 756130 743320 514300 580820 737030 811670 721510 872410 836340 TRUE FALSE 656205.5047 738437.082 763017.2002 712704.0583 722364.545 842895.4701 651538.0713 685851.9106 737468.838 0.889807773 1.001312929 1.034643311 0.966419219 0.979518737 1.142957406 0.883478783 0.930007989 1 19.49222256 ALSRQLS(ph)SGVSEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALSRQLSSGVSEIR 14 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 ALS(0.055)RQLS(0.862)S(0.081)GVS(0.001)EIR 77.037 0.013125 0 78498 93877 64583 59257 89345 126390 67882 97632 70781 TRUE FALSE 68124.29041 93260.31581 95815.55482 72712.20754 87567.2093 131252.3051 61298.81409 76754.15657 62413.35081 1.091501891 1.494236643 1.535177227 1.165010476 1.403020478 2.102952387 0.982142655 1.229771444 1 15.92956705 ALSS(ph)DSILSPAPDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 ALS(0.217)S(0.781)DS(0.002)ILSPAPDAR 416.68 1.53E-133 5896200000 261420 279420 209180 260250 310220 310940 299450 373890 366140 TRUE FALSE 226872.6846 277584.4716 310340.1477 319343.7402 304047.2289 322902.063 270409.3851 293936.5331 322855.3463 0.702706916 0.859779696 0.961235895 0.989123283 0.941744445 1.000144699 0.837555853 0.910427956 1 18.30052839 4.642818679 2.516826522 0.942010332 0.676169614 0.718459608 0.049028561 0.233590323 2.152277082 0.01319925 0.120395207 43935.81421 -4.642818679 -0.265840719 ALSSDSILS(ph)PAPDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 ALSSDSILS(1)PAPDAR;ALSSDS(0.001)ILS(0.999)PAPDAR 348.06 2.98E-82 409120000 249392 352516 322688 358575 477121 649590 429828 552796 607246 TRUE FALSE 216434.2153 350200.2992 478740.9961 439994.9342 467627.2256 674580.1476 388143.3467 434584.8773 535458.0697 0.404203854 0.654020023 0.89407747 0.82171688 0.873321838 1.259818809 0.724880936 0.811613274 1 19.03041408 4.625189826 1.501166822 0.908537422 0.266019488 0.583323447 0.143257136 0.682528542 1.700941191 0.041028133 0.612325428 42188.08631 -4.625189826 -0.642517935 TLDRS(ph)GDLGDMEPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLDRSGDLGDMEPLK 15 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;H0YC95 O60716-13 CTNND1 Catenin delta-1 1 T(0.043)LDRS(0.957)GDLGDMEPLK;T(0.015)LDRS(0.985)GDLGDMEPLK 120.71 7.24E-05 366180000 507130 378740 215944 265363 368240 341030 348340 431630 148771 TRUE FALSE 440111.4856 376252.032 320375.2407 325617.725 360912.7444 354149.6448 314558.0404 339329.2834 131183.4619 3.354931173 2.868136171 2.442192302 2.482155299 2.75120613 2.699651616 2.397848295 2.586677304 1 17.00122633 1.097989761 2.407527472 2.09E-11 2.701812164 0.788222454 0.276126129 0.474488198 2.048920701 3.178979173 0.074438033 12.53111632 -1.097989761 2.701812164 ALSSGGSITS(ph)PPLSPALPK ddPTM_MDA-MB-175_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(0.002)S(0.998)PPLSPALPK;ALSSGGSIT(0.309)S(0.69)PPLS(0.001)PALPK;ALSSGGSIT(0.001)S(0.999)PPLSPALPK;ALSSGGSIT(0.003)S(0.997)PPLSPALPK 299.89 7.55E-50 3093773000 4287480 4180700 3190820 3969050 4510540 4320370 5332870 6549830 5734240 TRUE FALSE 3720878.655 4153236.706 4733911.225 4870283.466 4420789.079 4486577.43 4815689.088 5149199.825 5056344.68 0.735883111 0.821391137 0.936231908 0.963202427 0.874305325 0.887316375 0.952405224 1.018364085 1 22.26966338 6.126837474 0.456035889 0.97835249 5.57E-37 0.730494968 0.044157787 10.96217438 0.686263471 0.039882405 7.524823692 1339175.434 -6.126837474 -0.97835249 ALSSLHGDDQDS(ph)EDEVLTIPEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ALSSLHGDDQDSEDEVLTIPEVK 23 0 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 1 ALS(0.009)S(0.009)LHGDDQDS(0.983)EDEVLTIPEVK;ALSSLHGDDQDS(1)EDEVLTIPEVK;ALS(0.003)S(0.013)LHGDDQDS(0.984)EDEVLTIPEVK;ALS(0.001)S(0.004)LHGDDQDS(0.996)EDEVLTIPEVK;ALS(0.001)S(0.001)LHGDDQDS(0.997)EDEVLTIPEVK;ALSSLHGDDQDS(1)EDEVLTIPEVK;ALSSLHGDDQDS(1)EDEVLTIPEVK;ALS(0.001)SLHGDDQDS(0.999)EDEVLTIPEVK 208.58 6.39E-25 5236502000 3240680 2735610 1211573 2228196 2639300 2607110 3064620 4011570 3409190 TRUE FALSE 2812415.927 2717639.598 1797493.755 2734141.958 2586783.094 2707407.209 2767413.624 3153726.974 3006159.442 0.935551151 0.904023772 0.597936932 0.909513288 0.86049431 0.900619964 0.920581119 1.049088392 1 21.5194901 2.155782873 1.124112972 1.040170294 0.829869123 0.365887716 0.094508317 0.60472717 1.425908169 0.10669952 0.036292059 143.1472051 -2.155782873 -0.210301171 ALSSQHQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ALSSQHQAR 9 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;;;;; 202.44 1.98E-05 4036770000 2976610 3895410 1545907 2857350 3714950 5585170 3092770 3262750 3529990 FALSE TRUE 2583243.447 3869820.795 2293512.796 3506154.989 3641029.763 5800035.104 2792833.641 2565036.303 3112678.604 0.829910111 1.243244577 0.7368293 1.126410862 1.169741636 1.863358169 0.897244463 0.824060762 1 21.56972519 2.057671088 24.99999883 0.887784217 1.164387632 0.137222084 0.299552178 146.7946587 63633.46002 0.124372283 0.083851764 114.2013105 -2.057671088 0.276603415 ALSTGEK ddPTM_MDA-MB-175_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 ;; 140.98 0.0060195 1788610000 3163370 2564170 1823710 2174890 1714260 1922440 2593360 3131630 3373060 FALSE TRUE 2745322.64 2547325.798 2705662.256 2668732.016 1680149.58 1996397.511 2341856.346 2461955.295 2974300.689 0.923014492 0.856445284 0.909680136 0.897263691 0.564888945 0.671215764 0.787363683 0.827742569 1 21.50411907 3.381254322 23.05196696 0.769879768 0.894770523 0.242352251 0.110987685 13.43011177 3214.421977 0.033990236 0.043881211 2405.771204 -3.381254322 0.124890755 ALSTGEKGFGYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 64.121 0.060044 404580000 123420 75237 82490 71985 73062 56230 88257 113210 24600 FALSE TRUE 107109.7343 74742.76319 122382.4399 88330.29447 71608.20914 58393.20449 79697.84972 89000.9225 21691.81602 4.937794704 3.445666472 5.64187156 4.072056225 3.301162478 2.691946328 3.674097624 4.102972402 1 14.40486322 3.324056902 3.539309753 3.129083038 4.589460852 0.393320196 0.975389263 0.276899496 6.806053483 0.288234614 0.374628477 2108.904445 -3.324056902 1.460377813 ALSTGLDYS(ph)PPSAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALSTGLDYSPPSAPR 15 0 P54253 P54253 ATXN1 Ataxin-1 1 ALSTGLDYS(0.958)PPS(0.042)APR;ALSTGLDYS(1)PPSAPR 193.32 1.02E-07 442220000 438480 455330 281940 320130 425090 421530 393190 468670 401100 TRUE FALSE 380533.757 452338.9072 418287.127 392820.4094 416631.5407 437746.5319 355058.4943 368448.5677 353682.4149 1.075919359 1.278940903 1.18266306 1.110658582 1.177982063 1.23768249 1.00389072 1.041749751 1 18.43209496 2.229123245 24.99990057 1.020270056 1.179172 0.637025401 0.05762587 120.8407875 320108.0745 0.022405721 0.015330709 169.4818691 -2.229123245 0.158901944 ALSYAS(ph)LDKEDLLSPINQNTLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALSYASLDKEDLLSPINQNTLQR 23 1 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 ALSYAS(1)LDKEDLLSPINQNTLQR;ALS(0.006)YAS(0.994)LDKEDLLSPINQNTLQR 327.74 1.14E-86 1392700000 1046720 826600 678250 761440 1087810 847640 1122380 1278390 1160450 TRUE FALSE 908393.2999 821170.0102 1006253.969 934336.5899 1066164.709 880249.2593 1013531.76 1005016.247 1023262.923 0.88774183 0.80250148 0.983377728 0.913095324 1.041926454 0.860237618 0.990490066 0.982168145 1 19.96474546 4.231008489 24.99953639 0.96679647 0.845121648 0.474837406 0.053428225 120.7764501 399806.3984 0.012656437 0.027187283 17021.9178 -4.231008489 -0.121674822 ALT(ph)PLTSSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALTPLTSSYR 10 0 O95486;O95486-2 O95486 SEC24A Protein transport protein Sec24A 1 ALT(0.998)PLT(0.002)SSYR;ALT(0.956)PLT(0.044)S(0.001)SYR 150.33 0.00024338 415990000 494990 446540 332730 315760 435480 498600 478160 423250 502000 TRUE FALSE 429575.8174 443606.6493 493639.3409 387458.1341 426814.8 517781.4646 431788.1168 332741.2812 442654.1319 0.970454778 1.002151832 1.115180692 0.875306715 0.964217364 1.169720166 0.975452584 0.751695867 1 18.75582036 1.981529318 24.43419752 0.859750574 1.016380159 0.244905725 0.099752295 631.7763435 835752.6781 0.043744502 0.025861851 95.83614098 -1.981529318 0.156629586 ALTAHLYSLLQTQHALGDAFADLSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALTAHLYSLLQTQHALGDAFADLSQK 26 0 A0A087X1E4;P53365;P53365-2;P53365-3;E9PRV8 A0A087X1E4 ARFIP2 Arfaptin-2 0 126.45 5.98E-05 264810000 168200 154230 69541 110550 126560 116010 160580 177850 109770 FALSE TRUE 145971.9438 153216.853 103171.2602 135652.0672 124041.7036 120472.9798 145006.9763 139818.1615 96793.11565 1.50808188 1.582931306 1.065894609 1.401464001 1.281513698 1.244644094 1.498112498 1.444505227 1 16.56261682 4.282645664 24.99999905 1.306944412 1.54550733 0.321247344 0.157780287 173.688553 98493.53212 0.038707956 0.102410509 19171.0396 -4.282645664 0.238562917 ALTDFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALTDFFR 7 0 H7C2Z6;H7BXD5;P28676 H7C2Z6 GCA Grancalcin 0 104.45 0.042826 0 338880 407650 233030 244120 366440 415540 309100 358790 367890 FALSE TRUE 294096.1494 404972.1203 345724.0874 299551.1771 359148.5609 431526.0927 279123.5296 282065.5506 324398.4633 0.906589219 1.248378664 1.06573898 0.923405044 1.107121647 1.330234701 0.860434192 0.86950335 1 18.30740746 ALTDSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ALTDSFR 7 0 C9J0K6;P30626-3;P30626-2;P30626;B4DHQ6 C9J0K6 SRI Sorcin 0 ;; 118.69 0.011517 866588000 1173660 1252260 783090 777830 1125030 1231120 1071280 1213550 1212430 FALSE TRUE 1018557.857 1244033.822 1161794.943 954448.1899 1102644.104 1278481.983 967387.4305 954041.7764 1069097.907 0.952726454 1.163629462 1.086705844 0.892760321 1.031378041 1.195851171 0.904863273 0.892380174 1 20.02796255 2.164013069 24.99999107 0.922924808 1.051992568 0.27443168 0.092614424 49.1274361 16473.49592 0.037840542 0.025512094 145.8858161 -2.164013069 0.12906776 ALTGGIAHLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALTGGIAHLFK 11 0 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 ; 87.363 0.01378 311740000 1580200 1518350 1062870 1820770 1737440 1629080 1489530 1889660 1765530 FALSE TRUE 1371372.566 1508375.859 1576877.487 2234203.657 1702868.343 1691751.762 1345075.61 1485570.914 1556811.055 0.880885681 0.968888199 1.012889446 1.435115488 1.09381825 1.086677639 0.863994128 0.9542397 1 20.57016243 2.259491461 23.76303118 0.93935819 1.088433527 0.167881276 0.146391107 235.9785743 267908.1754 0.057882211 0.044774594 181.7571319 -2.259491461 0.149075336 ALTHIDHSLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ALTHIDHSLSR 11 0 P56192;P56192-2;F5H2V6 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ;;;;; 261.75 6.08E-21 1661630000 1097299 993179 623515 700472 1011504 1111906 926446 978092 1046532 FALSE TRUE 952288.1569 986654.7418 925048.9395 859524.8736 991377.0494 1154681.743 836599.4095 768934.6373 922812.1792 1.03194147 1.069182618 1.002423852 0.931419083 1.074299919 1.251264092 0.906576038 0.833251505 1 19.81567752 2.043238549 24.99991948 0.894273972 1.054865066 0.366651493 0.089796994 131.2537625 75888.53149 0.037518094 0.025294676 110.4685235 -2.043238549 0.160591094 ALTHNGT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ALTHNGTPR 9 0 Q9HB90 Q9HB90 RRAGC Ras-related GTP-binding protein C 1 ALTHNGT(1)PR;ALTHNGT(1)PR;ALTHNGT(1)PR 125.97 0.0017905 1105190000 762490 820870 717570 1004220 1187840 1662060 1309300 1351850 1529140 TRUE FALSE 661725.0146 815477.6509 1064589.252 1232243.5 1164204.308 1726000.524 1182324.288 1062767.398 1348366.811 0.490760384 0.604789175 0.789539792 0.913878545 0.863418098 1.280067493 0.876856563 0.788188636 1 20.36278159 4.208836381 1.426558151 0.947345596 0.465631252 0.631822685 0.129334397 0.389119534 1.328400085 0.041191508 0.205509463 16174.70546 -4.208836381 -0.481714344 ALTNLPHTDFTLCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALTNLPHTDFTLCK 14 0 Q9UBQ5;A0A087WVB9;K7ERF1;Q9UBQ5-2;K7ES31;K7EQM4 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 0 146.96 8.16E-06 362860000 410510 399550 263700 276680 348010 325760 420810 445870 415580 FALSE TRUE 356260.0634 396925.3297 391226.202 339504.4228 341085.2819 338292.198 379999.911 350524.1703 366450.6058 0.972191225 1.083161887 1.067609647 0.92646708 0.930781056 0.923159063 1.036974438 0.956538657 1 18.48325922 3.744825381 24.9646524 0.963437887 1.045205019 0.404639519 0.044871932 480.2270699 1913667.661 0.011978939 0.020126593 5556.807872 -3.744825381 0.081767132 ALTQPS(ph)PVSTPSSVQFFLQEDDSADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ALTQPSPVSTPSSVQFFLQEDDSADR 26 0 P04920-2;P04920-3;P04920;C9J9M9 P04920-2 SLC4A2 Anion exchange protein 2 1 ALT(0.026)QPS(0.937)PVS(0.03)T(0.006)PSSVQFFLQEDDSADR;ALT(0.031)QPS(0.869)PVS(0.081)T(0.017)PS(0.001)S(0.001)VQFFLQEDDSADR;ALT(0.024)QPS(0.72)PVS(0.197)T(0.058)PS(0.001)S(0.001)VQFFLQEDDSADR 138.08 6.64E-06 231174000 165825 162200 139061 181240 215907 251983 147600 252179 220836 TRUE FALSE 143910.8061 161134.4975 206311.3647 222393.3121 211610.8731 261676.9491 133285.7747 198252.4833 194729.0197 0.739031123 0.827480659 1.059479296 1.142065587 1.086694081 1.343800475 0.684467959 1.018094189 1 17.57110837 4.337021576 3.95323141 1.041226014 0.758441797 0.321799697 0.16149575 0.267343321 7.581866325 0.041764256 0.124107998 21728.09121 -4.337021576 -0.282784217 ALTVPELTQQMFDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALTVPELTQQMFDAK 15 0 Q13509;A0A0B4J269;Q13509-2;P68371;P04350 Q13509;P68371;P04350 TUBB3;TUBB4B;TUBB4A Tubulin beta-3 chain;Tubulin beta-4B chain;Tubulin beta-4A chain 0 ; 182.1 1.30E-06 377160000 470820 438380 305120 371490 403220 353350 492160 569920 494030 FALSE TRUE 408599.9441 435500.2529 452677.0526 455842.4824 395196.7109 366943.6031 444430.399 448047.0431 435626.3362 0.937959692 0.99971057 1.039140692 1.04640708 0.907191963 0.842335673 1.020210125 1.028512296 1 18.73273165 ALVADSHPESER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALVADSHPESER 12 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 143.42 5.94E-05 2003500000 1874480 1828630 1056220 1350860 1782050 1910660 1669990 1712780 1842530 FALSE TRUE 1626762.719 1816617.609 1567011.525 1657593.41 1746590.692 1984164.327 1508034.627 1346515.326 1624708.202 1.001264545 1.118119307 0.964487975 1.020240685 1.07501808 1.221243497 0.928187981 0.828773637 1 20.6317492 2.024490905 24.97430783 0.895053655 1.063684212 0.421670092 0.080929866 178.829091 182358.0452 0.032608171 0.021983425 105.8012758 -2.024490905 0.168630557 ALVAT(ph)PGKK ddPTM_MDA-MB-175_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 102.4 0.0021041 7103950000 23278870 21369300 14905410 17144800 16635240 12016500 22001790 24138500 20929230 TRUE FALSE 20202508.35 21228923.66 22113716.13 21037788.88 16304231.27 12478782.53 19868059.79 18976669.62 18455000.27 1.094690222 1.150307415 1.198250653 1.139950613 0.883458739 0.676173522 1.076567841 1.028267101 1 24.13750842 3.251214168 23.85530186 0.942754746 1.149868339 0.479922195 0.109828617 130.7384631 246474.061 0.034745391 0.0445096 1783.257948 -3.251214168 0.207113593 ALVEFESNPEETREPGS(ph)PPSVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ALVEFESNPEETREPGSPPSVQR 23 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 ALVEFESNPEETREPGS(1)PPSVQR;ALVEFESNPEETREPGS(1)PPSVQR;ALVEFESNPEETREPGS(1)PPSVQR;ALVEFESNPEETREPGS(1)PPSVQR;ALVEFESNPEET(0.143)REPGS(0.85)PPS(0.007)VQR;ALVEFESNPEET(0.084)REPGS(0.861)PPS(0.055)VQR;ALVEFESNPEET(0.012)REPGS(0.988)PPSVQR;ALVEFESNPEET(0.001)REPGS(0.998)PPS(0.001)VQR 307.86 2.60E-73 12790600000 9847740 7701410 5274150 6178960 7510620 8926460 6584330 7849370 7151250 TRUE FALSE 8546336.208 7650818.931 7824746.581 7581987.307 7361173.356 9269866.692 5945782.69 6170843.309 6305837.372 1.355305522 1.213291507 1.240873514 1.202375967 1.167358579 1.470045316 0.942901369 0.978592207 1 22.58825653 2.213759655 24.99998951 0.973534159 1.262347792 0.723439121 0.087515801 115.4990761 116425.067 0.034199234 0.023068333 163.5910934 -2.213759655 0.288813633 ALVHERDEAAYGELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALVHERDEAAYGELR 15 1 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ; 159.41 1.06E-06 933910000 1085030 1216020 471830 398420 975070 1072680 1098430 1182030 81334 FALSE TRUE 941640.5364 1208031.885 700008.5662 488887.3505 955668.0147 1113946.694 991904.4277 929262.0831 71718.78718 13.12962159 16.84400883 9.760462966 6.816726408 13.3252116 15.53214628 13.83046851 12.95702451 1 16.13006347 1.238044418 24.89110872 0.999986108 12.7827135 0.636677936 2.795300214 8.284883282 399082.3026 4.15617093 0.723295076 17.29993288 -1.238044418 11.78272739 ALVHQLS(ph)NESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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;ALVHQLS(1)NESR 162.94 1.58E-05 639280000 302562 263309 167777 225082 245263 212122 321350 263209 346820 TRUE FALSE 262577.6651 261579.3058 248914.5184 276190.3083 240382.7461 220282.4706 290185.5265 206923.8036 305819.3347 0.858603873 0.855339333 0.813926689 0.903115915 0.786028609 0.720302628 0.948878941 0.676621064 1 18.22232009 3.217570646 24.99171741 0.811533378 0.854444568 0.012057618 0.097517551 845.5760539 1006782.768 0.027466655 0.031175521 1650.329436 -3.217570646 0.04291119 ALVLDCHYPEDEVGQEDEAESDIFSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALVLDCHYPEDEVGQEDEAESDIFSIR 27 0 Q07021;I3L3Q7;I3L3B0 Q07021 C1QBP "Complement component 1 Q subcomponent-binding protein, mitochondrial" 0 197.36 5.98E-25 159610000 26607 26211 15885 22423 24803 30755 19146 22943 20079 FALSE TRUE 23090.81754 26038.81822 23567.03913 27514.48486 24309.46883 31938.16475 17289.22387 18036.81799 17705.28349 1.304176663 1.470680671 1.331073809 1.554026789 1.373006472 1.803877626 0.976500821 1.018725173 1 14.11189232 2.210043451 24.9999842 1.00172806 1.465423385 0.718794645 0.139820986 104.9469928 92002.53853 0.053708852 0.036217798 162.1972368 -2.210043451 0.463695325 ALVTGYFMQVAHLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ALVTGYFMQVAHLER 15 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ;; 184 4.82E-07 1359104000 1403995 1237720 876654 1083173 1247454 1194701 1255564 1383774 1409795 FALSE TRUE 1218453.503 1229589.336 1300606.807 1329123.985 1222632.106 1240661.921 1133799.597 1087864.699 1243130.641 0.9801492 0.989107094 1.046235016 1.069174824 0.983510554 0.99801411 0.912051846 0.875100864 1 20.24554649 2.310324259 3.994365847 0.916686484 1.014918859 0.457371054 0.041566173 0.171503009 5.360314967 0.017046827 0.01253072 204.3262946 -2.310324259 0.098232375 ALVVPEPEPDSDS(ph)NQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ALVVPEPEPDSDSNQER 17 0 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 1 ALVVPEPEPDSDS(1)NQER;ALVVPEPEPDSDS(1)NQER;ALVVPEPEPDS(0.022)DS(0.978)NQER;ALVVPEPEPDS(0.004)DS(0.996)NQER;ALVVPEPEPDS(0.057)DS(0.943)NQER;ALVVPEPEPDS(0.183)DS(0.817)NQER 417.75 4.56E-141 4065370000 2767390 2034300 1659550 1714150 1866900 2534220 2218440 2092490 2640160 TRUE FALSE 2401672.4 2020936.549 2462113.931 2103373.957 1829752.343 2631713.083 2003296.03 1645027.297 2328043.292 1.031627035 0.868083749 1.057589409 0.903494348 0.785961476 1.130439924 0.860506347 0.706613705 1 21.15068646 2.013896027 24.99952029 0.817713447 0.95573597 0.132973526 0.120858993 331.5398556 596451.4247 0.046888901 0.031595844 103.2514184 -2.013896027 0.138022523 ALVVPEPEPDSDS(ph)NQERK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALVVPEPEPDSDSNQERK 18 1 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 1 ALVVPEPEPDS(0.002)DS(0.998)NQERK 148.44 4.25E-08 93455000 204730 130480 125780 140800 146500 141980 163590 169430 259530 TRUE FALSE 177674.4118 129622.8683 186607.6287 172770.792 143584.9366 147442.0625 147725.067 133198.713 228848.6591 0.776383888 0.566413056 0.815419367 0.754956541 0.627423107 0.64427759 0.645514235 0.582038425 1 17.80403431 1.228855941 24.99497991 1.000000658 0.67147179 0.603008397 0.082385586 279.1394027 718888.6761 0.259118805 0.020177797 16.93775866 -1.228855941 -0.328528868 ALWEDEGVR ddPTM_MDA-MB-175_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 ; 100.02 0.011504 322150000 1106670 973190 593220 829260 1013950 1186600 691800 995560 984610 FALSE TRUE 960420.7556 966797.0508 880103.1762 1017556.157 993774.3788 1232249.27 624709.3425 782667.2415 868210.5275 1.106207222 1.113551403 1.013697886 1.172015456 1.144623737 1.419297775 0.719536705 0.901471725 1 19.72768539 2.223589887 24.99999878 0.873039444 1.152366817 0.550286976 0.122499585 182.8689728 305375.0754 0.049908063 0.033800253 167.336194 -2.223589887 0.279327373 ALWFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ALWFER 6 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 ;;; 132.01 0.035093 1816030000 1444060 1501770 1029300 1050090 1404090 1474630 1310620 1497710 1325700 FALSE TRUE 1253223.812 1491904.774 1527072.923 1288528.984 1376151.356 1531359.97 1183516.274 1177436.372 1168977.256 1.072068601 1.276247905 1.30633245 1.102270363 1.177226801 1.309999799 1.012437383 1.007236339 1 20.15681543 2.218135331 24.99258424 1.006944097 1.208841588 0.592627536 0.078473861 160.1127083 195914.044 0.031472427 0.021246496 165.2476649 -2.218135331 0.20189749 ALWFQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALWFQGR 7 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 186.07 0.0014057 3359700000 1622760 1804540 1168980 1231660 1620080 1678260 1632330 1680790 1720080 FALSE TRUE 1408308.154 1792685.858 1734302.638 1511327.228 1587843.578 1742823.748 1474026.888 1321366.138 1516734.102 0.928513543 1.181938123 1.143445404 0.996435187 1.046883284 1.149063469 0.971842649 0.871191685 1 20.53253676 2.057830217 6.44561092 0.924819569 1.077082866 0.357677998 0.080723166 0.180515849 15.19916406 0.032458299 0.021584542 114.2431626 -2.057830217 0.152263297 ALYDYAGQEADELS(ph)FR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ALYDYAGQEADELSFR 16 0 A0A0C4DGG1;Q9UKS6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 ALYDYAGQEADELS(1)FR;ALYDYAGQEADELS(1)FR;ALYDYAGQEADELS(1)FR;ALYDYAGQEADELS(1)FR 331.4 1.54E-71 323407000 359599 353491 258596 296001 349997 407598 304681 383484 433125 TRUE FALSE 312077.081 351168.8943 383653.8906 363212.5511 343032.7445 423278.5588 275133.0835 301478.9309 381921.4559 0.817123721 0.919479356 1.004536102 0.951013737 0.898176154 1.108286932 0.720391796 0.789374166 1 18.54291645 2.221317436 24.99964447 0.82191082 0.948593385 0.212727405 0.101320101 333.2884155 483207.1491 0.040586493 0.027437422 166.4628921 -2.221317436 0.126682565 ALYDYAGQEADELSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALYDYAGQEADELSFR 16 0 A0A0C4DGG1;Q9UKS6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 0 ; 234.69 2.57E-19 121128000 109304 104882 77607 91687 101553 95756 89414 115507 106874 FALSE TRUE 94859.19946 104193.0232 115138.0048 112505.9347 99532.29399 99439.79528 80742.64404 90806.72693 94239.47747 1.006576034 1.105619705 1.221759796 1.193830205 1.056163475 1.055181947 0.856781534 0.963574177 1 16.52404392 2.627132942 2.214148365 0.943393185 1.131550025 0.547735842 0.071777866 0.22735348 2.207237476 0.029891075 0.025132173 423.772667 -2.627132942 0.18815684 ALYDYEGQEHDELSFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ALYDYEGQEHDELSFK 16 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22;H0Y923 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 ;; 226.7 5.71E-15 1176390000 1001616 880459 599327 664390 828775 741068 1008624 1170918 1024759 FALSE TRUE 869249.9078 874675.2069 889163.5418 815249.9041 812283.999 769577.3655 910807.7997 920526.2978 903613.1584 0.961971281 0.967975288 0.984009068 0.902211191 0.898928918 0.851666843 1.007962081 1.018717234 1 19.78534575 2.075681871 17.78633195 1.011488767 0.929701449 0.494215005 0.038631956 3.02578762 709.5451445 0.017252725 0.011631788 119.036972 -2.075681871 -0.081787319 ALYETELADAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALYETELADAR 11 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 ; 97.565 0.014358 403890000 440630 399550 291550 331570 352440 394080 352670 506650 542010 FALSE TRUE 382399.6291 396925.3297 432544.5552 406858.0362 345427.1335 409240.5126 318468.1177 398306.8403 477934.1953 0.800109373 0.830502052 0.90502952 0.851284633 0.722750406 0.85626958 0.666343026 0.833392639 1 18.86645247 1.257709153 5.138266444 1.008651125 0.80543632 0.443690282 0.068024777 0.143153082 9.556840781 0.098018534 0.016975923 18.10127443 -1.257709153 -0.203214805 ALYHTEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ALYHTEER 8 0 A0A0C4DGB9 A0A0C4DGB9 PPA2 0 106.04 0.0042717 103270000 227230 240060 167320 222290 178920 277480 238220 276150 277860 FALSE TRUE 197200.9798 238483.0301 248236.5117 272764.342 175359.8421 288154.8352 215117.4611 217097.4715 245011.7073 0.804863498 0.973353611 1.013161838 1.113270647 0.715720257 1.176085985 0.877988499 0.886069788 1 17.90249116 4.741031086 22.93042224 0.963042124 0.804863325 0.139699488 0.127483098 147.8921945 1372415.472 0.02904548 0.188144109 55084.71235 -4.741031086 -0.158178799 AMASVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 AMASVAR 7 0 H7C2G2;Q93070 H7C2G2 ART4 NAD(P)(+)--arginine ADP-ribosyltransferase;Ecto-ADP-ribosyltransferase 4 0 ;;;;;;; 118.01 0.018132 2609277000 2930834 3549934 2568529 2321772 3045032 3206863 4063014 3389500 3175821 FALSE TRUE 2543516.861 3526614.25 3810678.216 2848965.819 2984441.821 3330233.095 3668983.528 2664681.802 2800379.059 0.908275918 1.259334603 1.360772287 1.017350065 1.065727802 1.189207969 1.310173891 0.951543254 1 21.41719069 1.6449372 9.348249429 0.97579863 1.161994285 0.235578094 0.136507881 0.147872416 24.09571425 0.077439623 0.034772397 44.15065994 -1.6449372 0.186195656 AMDNHS(ph)DS(ph)EEELAAFCPQLDDSTVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AMDNHSDSEEELAAFCPQLDDSTVAR 26 0 K7EQI9;Q86VR2-2;Q86VR2 K7EQI9 FAM134C Protein FAM134C 2 AMDNHS(1)DS(1)EEELAAFCPQLDDSTVAR;AMDNHS(1)DS(1)EEELAAFCPQLDDSTVAR 106.3 0.0016027 312390000 135529 115766 96024 104741 144912 146810 81782 142816 130977 TRUE FALSE 117618.4993 115005.5255 142461.5276 128524.0449 142028.5347 152457.8757 73850.79423 112275.9098 115493.0483 1.018403281 0.99577877 1.233507382 1.112829273 1.2297583 1.32006106 0.639439302 0.972144311 1 16.81744649 2.248224884 24.99999243 0.882069245 1.150131247 0.48778281 0.135657778 174.0421758 450221.1517 0.05170326 0.039530458 177.1025785 -2.248224884 0.268062003 AMDQLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AMDQLAK 7 0 Q15847 Q15847 ADIRF Adipogenesis regulatory factor 0 ; 112.17 0.014922 577579000 940520 955420 659100 804580 842410 779590 1019640 1140450 1027820 FALSE TRUE 816227.899 949143.7831 977842.9646 987272.1862 825647.6891 809581.3318 920755.4697 896573.6425 906312.2905 0.900603366 1.047259088 1.078924974 1.089328917 0.910996902 0.893269726 1.015936206 0.989254644 1 19.78964872 3.238306831 25 0.965934159 1.033895215 0.216796341 0.062847836 11.18193968 1101549.719 0.019395377 0.023422506 1731.038915 -3.238306831 0.067961056 AMDSDWFAENYMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AMDSDWFAENYMGR 14 0 P55084-2;P55084;B5MD38;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ; 218.54 1.24E-11 222261000 192906 181571 115352 201277 214910 239170 160659 211817 147368 FALSE TRUE 167412.9833 180378.2481 171136.613 246980.0192 210633.7115 248371.0247 145078.3149 166521.5829 129946.3229 1.288324129 1.388098132 1.316979266 1.900631073 1.620928601 1.911335535 1.11644802 1.281464371 1 16.98755629 2.206221693 24.99973291 1.162968152 1.568433211 0.460170386 0.223026785 193.4302224 149530.6995 0.095069989 0.064101687 160.7761754 -2.206221693 0.405465059 AMENGEIDQAS(ph)EEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AMENGEIDQASEEK 14 0 Q9BXW6-4;Q9BXW6;Q9BXW6-2;J3QSB8 Q9BXW6-4 OSBPL1A Oxysterol-binding protein-related protein 1 1 AMENGEIDQAS(1)EEK 99.344 0.0014288 1687900000 403220 320540 318730 400710 347710 355070 318340 384820 958920 TRUE FALSE 349933.4554 318434.3516 472868.8941 491697.33 340791.2513 368729.7727 287467.4358 302529.2377 845557.57 0.413849355 0.376596891 0.559239147 0.581506626 0.403037313 0.43607885 0.339973818 0.357786682 1 19.68954346 1.234031589 24.99979877 1.00000085 0.431478284 0.833958982 0.079433922 59.72531558 329635.9177 0.167451235 0.021535297 17.14081978 -1.234031589 -0.568522566 AMEVDERPTEQYSDIGGLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AMEVDERPTEQYSDIGGLDK 20 1 P17980;E9PM69;R4GNH3;E9PN50;E9PMD8 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ;;;; 255.6 3.34E-36 2658090000 4651000 3880590 2849310 3328440 3685820 3152990 4445310 5302060 4664030 FALSE TRUE 4036358.566 3855098.149 4227245.846 4084213.174 3612479.393 3274287.566 4014204.52 4168255.73 4112653.687 0.981448688 0.937374854 1.027863314 0.993084632 0.878381616 0.796149595 0.976061888 1.013519748 1 21.97163816 2.006576194 24.99989535 1.003845172 0.935492675 0.178888777 0.063902022 293.3442184 1115165.315 0.028679365 0.019283901 101.5257471 -2.006576194 -0.068352497 AMGIMNSFVNDIFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 ;;;;;;; 327.1 2.13E-68 36611483000 7681378 6676752 3873612 5026173 6376855 6886233 5179434 7166747 5846974 FALSE TRUE 6666264.435 6632891.976 5746903.72 6167442.4 6249968.062 7151150.839 4677133.288 5634193.926 5155751.395 1.292976314 1.286503454 1.114658811 1.196225715 1.21223224 1.387023984 0.907168118 1.092797828 1 22.29775127 2.232493659 24.99988694 1.015456376 1.239930992 0.659965023 0.083623968 94.36704824 388850.0091 0.033427302 0.023190963 170.8022781 -2.232493659 0.224474615 AMHGELQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AMHGELQK 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 107.66 0.0039594 668740000 707670 566310 411350 488960 525450 430310 700530 729260 729860 FALSE TRUE 614149.6165 562589.8723 610280.2359 599985.8413 514994.573 446864.3041 632592.7084 573313.4241 643576.7823 0.954275594 0.874161231 0.948263288 0.932267692 0.800206886 0.694344974 0.982932769 0.890823659 1 19.29575275 1.069535693 1.469704279 1.08805737 0.877229817 0.154671419 0.084567178 3.749307868 5.166577518 1.320943041 0.025307927 11.73642135 -1.069535693 -0.210827553 AMKDEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AMKDEEK 7 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;;; 121.96 0.0040016 4557180000 10248300 8381980 7483820 8068110 3969320 5325410 11429000 13269200 12005600 FALSE TRUE 8893961.189 8326918.221 11103020.38 9900097.689 3890338.298 5530281.969 10320617.34 10431684.84 10586311.64 0.840137858 0.786574069 1.048809137 0.935179128 0.367487604 0.522399317 0.974902089 0.985393704 1 23.33569669 2.048876141 24.89699228 0.988202303 0.755712685 0.252547201 0.191918584 164.0753297 83577.45209 0.086563012 0.058360754 111.9118671 -2.048876141 -0.232489618 AMKEYEEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AMKEYEEEER 10 1 Q16543;K7EKQ2;K7EQA9;K7EL68;K7EIU0 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ; 117.98 0.00080835 749830000 1889930 1540640 743020 755070 1426990 1253670 1828180 1877140 251510 FALSE TRUE 1640170.962 1530519.434 1102346.957 926520.184 1398595.691 1301899.496 1650883.385 1475728.219 221776.7743 7.395593912 6.901170959 4.970524802 4.177715123 6.306321729 5.87031487 7.443896639 6.654115263 1 17.75874876 4.352555052 5.274355346 5.482983346 7.268191216 0.16134033 1.768620816 0.405978778 16.67783643 0.444301912 1.232409924 22519.30855 -4.352555052 1.785207871 AMKPPGGESSNLFGS(ph)PEEATPSSRPNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AMKPPGGESSNLFGSPEEATPSSRPNR 27 2 A6NGP5;Q9H910;Q9H910-3;H3BMV3;H3BMM8;B4E1P3 A6NGP5 HN1L Hematological and neurological expressed 1-like protein 1 AMKPPGGESSNLFGS(1)PEEATPSSRPNR;AMKPPGGESSNLFGS(1)PEEATPSSRPNR;AMKPPGGESSNLFGS(1)PEEATPSSRPNR;AMKPPGGESSNLFGS(1)PEEATPSSRPNR 167.86 3.96E-12 723210000 349954 346665 232141 316793 361478 316586 422451 502826 454881 TRUE FALSE 303706.6922 344387.7348 344405.1641 388725.6925 354285.295 328765.2683 381481.767 395300.5729 401105.4864 0.757174116 0.85859642 0.858639873 0.969135815 0.883272124 0.819647897 0.951075914 0.985527714 1 18.61362217 -1.999999967 0.035781323 2.256573769 7.56E-09 0.579922667 0.050773732 1671.211981 5.903802762 280.0590642 123.1211089 0.010000001 1.999999967 -2.256573761 AMLDQLMGTS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AMLDQLMGTSR 11 0 Q9Y383;V9GZ75;F8WEU3 Q9Y383 LUC7L2;C7orf55-LUC7L2 Putative RNA-binding protein Luc7-like 2 1 AMLDQLMGT(0.151)S(0.849)R 110.38 0.0018906 58878000 342470 172200 126420 126140 123080 147390 196710 164740 232850 TRUE FALSE 297211.7218 171068.8069 187557.1348 154782.0149 120630.9488 153060.1887 177633.0945 129511.633 205322.7383 1.447534376 0.833170297 0.91347474 0.753847412 0.587518703 0.745461462 0.86514088 0.63077102 1 17.64753388 AMLDSGIYPPGS(ph)PGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 AMLDSGIYPPGSPGK 15 0 O95295 O95295 SNAPIN SNARE-associated protein Snapin 1 AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK 305.9 7.53E-45 2692500000 4251320 3829410 2806580 3236210 4440740 3654510 4818190 5635900 5171860 TRUE FALSE 3689497.291 3804254.354 4163851.475 3971040.943 4352377.962 3795101.364 4350922.675 4430706.644 4560448.603 0.809020693 0.83418424 0.913035501 0.870756649 0.954374962 0.832177203 0.954055852 0.971550615 1 22.12074432 -2 0.100461243 1.617381231 0.675358731 0.629068457 0.040123766 190.6243566 1.765695244 25.26554887 2.60808245 0.01 2 -0.9420225 AMLPGS(ph)PLFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 205.8 3.00E-08 1572274000 1649213 1641442 953803 1252001 1465827 1531712 1152790 1633183 1445649 TRUE FALSE 1431265.323 1630659.259 1415065.321 1536286.963 1436659.911 1590637.952 1040992.603 1283939.525 1274746.022 1.122784695 1.279203254 1.110076279 1.205171019 1.127016587 1.247807739 0.816627458 1.007212027 1 20.28177841 2.248909266 24.99999779 0.949821842 1.181711191 0.700028172 0.074215553 104.4313614 252282.7356 0.025878647 0.019820403 177.3818849 -2.248909266 0.231889348 AMMANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AMMANR 6 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 99.228 0.090816 199980000 182970 222560 158920 154330 176550 234470 228080 240550 257900 FALSE TRUE 158790.0509 221097.9887 235774.2436 189372.9853 173037.0004 243490.2126 205960.8367 189110.2545 227411.3558 0.698250315 0.972238119 1.036774275 0.832733197 0.76089868 1.070703843 0.905675251 0.831577886 1 17.79494477 2.758550419 24.95811444 0.928833071 0.874690543 0.117370147 0.113926752 2925.784349 3652961.388 0.037639285 0.037584097 573.5224446 -2.758550419 -0.054142527 AMNGESLDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AMNGESLDGR 10 0 P98179 P98179 RBM3 RNA-binding protein 3 0 ; 145.25 7.16E-05 1103710000 1755550 1903160 1200080 1441240 1850380 1898460 1552720 1808420 1813070 FALSE TRUE 1523549.62 1890658.017 1780442.702 1768495.57 1813561.058 1971494.985 1402137.453 1421703.456 1598730.93 0.952974382 1.182599261 1.113660009 1.106187124 1.134375412 1.233162471 0.877031542 0.889270001 1 20.60849572 2.225776151 24.99990941 0.913382901 1.122986267 0.590079561 0.07781808 141.6796597 277051.0279 0.030259829 0.020549738 168.1806982 -2.225776151 0.209603366 AMREENGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AMREENGLK 9 1 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 116.12 0.0012459 174020000 228730 224030 120250 137300 194180 210800 254610 259590 142410 FALSE TRUE 198502.751 222558.3322 178403.3022 168476.0635 190316.1979 218909.6124 229917.9614 204078.6986 125574.452 1.580757453 1.772321747 1.420697437 1.341642832 1.51556463 1.74326552 1.830929442 1.625160973 1 16.93818345 4.241790759 24.9921371 1.530055435 1.676539567 0.079542636 0.233810109 261.0979394 2020062.521 0.061032448 0.148117546 17449.81228 -4.241790759 0.146484133 AMRMYERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AMRMYERR 8 2 H3BUS3;A6NCI4;H7BXL8;A6NCI4-2 H3BUS3 VWA3A von Willebrand factor A domain-containing protein 3A 0 ; 60.799 0.052784 1058820000 52833 33098 18130.8 41652 44075 46706 42702 37735 56620 FALSE TRUE 45850.98519 32880.57706 26898.91552 51109.72321 43197.99373 48502.81004 38560.76661 29665.6639 49926.4481 0.918370662 0.658580338 0.538770863 1.023700366 0.865232665 0.971485293 0.772351491 0.59418735 1 15.60751665 5.05280728 11.87755496 0.790965288 1.458328778 0.039942724 0.168707539 320327.3638 2672973.376 0.042215702 4554989.404 112929.4674 -5.05280728 0.66736349 AMS(ph)LNTLNVDAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 AMSLNTLNVDAPR 13 0 Q6P597;Q6P597-3;Q6P597-2 Q6P597 KLC3 Kinesin light chain 3 1 AMS(1)LNTLNVDAPR;AMS(0.997)LNT(0.003)LNVDAPR;AMS(0.999)LNT(0.001)LNVDAPR;AMS(0.998)LNT(0.002)LNVDAPR;AMS(0.995)LNT(0.005)LNVDAPR;AMS(1)LNTLNVDAPR;AMS(0.998)LNT(0.002)LNVDAPR;AMS(0.999)LNT(0.001)LNVDAPR;AMS(0.986)LNT(0.014)LNVDAPR;AMS(0.999)LNT(0.001)LNVDAPR 240.31 8.03E-17 5795830000 5492160 5962050 3195790 3468710 5051010 4900480 4974430 5627390 5555160 TRUE FALSE 4766357.141 5922884.901 4741284.733 4256333.621 4950504.783 5089004.637 4492010.544 4424016.441 4898435.313 0.973036661 1.209138127 0.967918209 0.86891698 1.010629817 1.038904122 0.917029675 0.903148895 1 22.22388956 4.074136491 11.78793912 0.951377111 1.090849032 0.346983804 0.075802439 0.578817272 89.51499967 0.018569356 0.038688728 11861.41474 -4.074136491 0.139471921 AMS(ph)TTSISS(ph)PQPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AMSTTSISSPQPGK 14 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 2 AMS(0.999)T(0.001)TS(0.044)IS(0.025)S(0.932)PQPGK 188.59 1.19E-06 123920000 452070 326520 170580 219970 255780 167020 457830 359740 325450 TRUE FALSE 392327.8041 324375.0686 253073.0586 269917.5505 250690.4784 173445.3675 413429.7171 282812.4005 286975.6718 1.36711172 1.130322534 0.881862414 0.940558999 0.873560037 0.604390492 1.440643782 0.985492599 1 18.13056891 4.582324567 3.0331074 0.972693303 1.375167251 0.289726528 0.204621924 0.401423501 6.133186165 0.052142264 0.314885867 38222.98211 -4.582324567 0.402473948 AMS(ph)TTSISSPQPGK ddPTM_MDA-MB-175_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(0.965)T(0.017)T(0.017)SISSPQPGK;AMS(0.947)T(0.025)T(0.025)S(0.003)ISSPQPGK;AMS(0.992)T(0.008)TSISSPQPGK;AMS(0.998)T(0.002)TSISSPQPGK;AMS(0.997)T(0.002)TSISSPQPGK;AMS(0.991)T(0.008)TSISSPQPGK;AMS(0.999)T(0.001)TSISSPQPGK;AMS(0.962)T(0.036)T(0.001)SISSPQPGK;AMS(0.983)T(0.016)T(0.001)SISSPQPGK;AMS(0.969)T(0.03)T(0.001)SISSPQPGK 293.41 1.92E-43 6199100000 8390820 6226180 3711560 4332590 5699970 3668150 9568070 7107020 6528940 TRUE FALSE 7281951.877 6185279.814 5506482.83 5316370.779 5586551.749 3809266.104 8640160.044 5587239.08 5757096.151 1.264865426 1.074374937 0.956468797 0.923446585 0.970376663 0.661664493 1.500784392 0.970496051 1 22.45690988 4.680893238 3.066735044 1.006743545 1.289332359 0.143895774 0.204324256 0.649544179 9.639961757 0.050134413 0.411414902 47961.55307 -4.680893238 0.282588814 AMSRPILYSNWLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AMSRPILYSNWLSK 14 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 143.46 8.32E-06 361640000 352920 318550 287450 248480 276160 262480 352270 382660 238420 FALSE TRUE 306280.7278 316457.4241 426461.7815 304901.1818 270664.9563 272577.7754 318106.9096 300831.1369 210234.2592 1.456854506 1.505260966 2.028507547 1.450292559 1.287444574 1.296543087 1.513106907 1.430932989 1 17.68163826 3.488688429 24.43153979 1.339334308 1.662994191 0.395090909 0.199786551 447.1955826 944540.6395 0.05604187 0.077974243 3080.976807 -3.488688429 0.323659882 AMST(ph)TSISSPQPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AMSTTSISSPQPGK 14 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 1 AMS(0.022)T(0.923)T(0.055)SISSPQPGK;AMS(0.311)T(0.634)T(0.055)SISSPQPGK;AMS(0.274)T(0.677)T(0.049)SISSPQPGK;AMS(0.033)T(0.893)T(0.074)SISSPQPGK 346.5 9.74E-81 6441300000 5975640 4538450 2645400 3123840 3994980 2429540 6949600 4709630 4407240 TRUE FALSE 5185944.034 4508636.623 3924724.288 3833155.617 3915487.714 2523005.976 6275628.862 3702512.275 3886221.108 1.334443895 1.160159573 1.009907614 0.986345221 1.007530865 0.64921833 1.614840918 0.952728157 1 21.88993656 4.583656234 2.622402282 1.039935637 1.350292741 0.147586194 0.235251136 0.713875869 7.801803393 0.058262799 0.41162469 38340.36417 -4.583656234 0.310357104 AMSTTSISS(ph)PQPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 AMSTTSISSPQPGK 14 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 1 AMSTTSIS(0.199)S(0.801)PQPGK;AMSTTSIS(0.066)S(0.934)PQPGK;AMSTTS(0.001)IS(0.013)S(0.986)PQPGK;AMSTTSIS(0.057)S(0.942)PQPGK;AMSTTSIS(0.093)S(0.907)PQPGK;AMSTT(0.003)S(0.011)IS(0.123)S(0.863)PQPGK;AMSTT(0.01)S(0.001)IS(0.125)S(0.865)PQPGK;AMSTT(0.002)S(0.019)IS(0.055)S(0.923)PQPGK;AMSTT(0.032)S(0.023)IS(0.321)S(0.623)PQPGK 320.35 4.17E-56 6423790000 13557360 12012770 7010890 8706820 9919740 8713960 10717200 13455030 12369190 TRUE FALSE 11765720.53 11933857.32 10401379.85 10683836.56 9722356.582 9049191.68 9677847.594 10577776.54 10906918.45 1.078739204 1.094154814 0.953649732 0.979546753 0.891393534 0.82967446 0.887312731 0.969822649 1 23.37874022 4.12932494 1.806185121 0.920899522 1.098463804 0.613946183 0.051141027 0.274664239 1.697771919 0.015961726 0.055597454 13468.67705 -4.12932494 0.177564283 AMT(ph)PEQEETASLLSSVTQGMESAYVSPSGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AMTPEQEETASLLSSVTQGMESAYVSPSGYR 31 0 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 AMT(0.903)PEQEET(0.077)AS(0.019)LLSSVTQGMESAYVSPSGYR 76.765 0.010096 18468000 15230 9067.5 7698.8 7386.9 13623 12986 12269 13563 11820 TRUE FALSE 13217.31691 9007.934995 11421.96543 9064.208547 13351.92895 13485.57982 11079.15427 10662.658 10422.65307 1.268133634 0.864265071 1.095878886 0.869664229 1.281048968 1.293872082 1.062987917 1.02302724 1 13.34743494 AMTGVEQWPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AMTGVEQWPYR 11 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;; 125.97 0.00073803 1648190000 765041 770602 441537 549733 694087 750899 714608 824630 812621 FALSE TRUE 663938.8935 765539.8647 655065.7701 674558.2798 680276.0267 779786.5704 645305.4261 648289.2918 716553.8711 0.926572195 1.068363309 0.914189144 0.941392276 0.949371784 1.088245562 0.900567916 0.904732104 1 19.45071565 AMTLS(ph)PQEEVAAGQMASSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AMTLSPQEEVAAGQMASSSR 20 0 Q9Y6A5;A0A494BZT8 Q9Y6A5 TACC3 Transforming acidic coiled-coil-containing protein 3 1 AMTLS(1)PQEEVAAGQMASSSR 271.67 2.19E-44 95565000 23437 22371 13638 18182 22168 21074 20215 23787 20066 TRUE FALSE 20339.74107 22224.04343 20233.38242 22310.50099 21726.90017 21884.73042 18254.55241 18700.33516 17693.82034 1.149539256 1.256034197 1.143528194 1.260920512 1.227937198 1.236857275 1.031690842 1.056885105 1 14.11095796 2.234854609 24.99994293 1.035315461 1.214221373 0.81134621 0.041548512 35.94014304 242440.2079 0.015443632 0.010865287 171.733337 -2.234854609 0.178905911 AMTVEKAS(ph)PVGDGNFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AMTVEKASPVGDGNFR 16 1 Q86YS7;H0YFC4 Q86YS7 C2CD5 C2 domain-containing protein 5 1 AMTVEKAS(1)PVGDGNFR;AMTVEKAS(1)PVGDGNFR;AMTVEKAS(1)PVGDGNFR 171.83 2.90E-09 876260000 1420150 1374280 880450 1082560 1550730 1383760 1596370 1904790 812460 TRUE FALSE 1232473.579 1365252.264 1306238.565 1328371.794 1519873.507 1436994.143 1441554.283 1497465.482 716411.9044 1.720342127 1.905680595 1.823306616 1.854201174 2.121507889 2.00582114 2.012186389 2.090229758 1 19.45042978 3.465708676 24.75835103 1.905209943 1.827597946 0 0.323111242 1373.260878 2979125.897 0.091095792 0.117703363 2922.191517 -3.465708676 -0.077611997 AMVLDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AMVLDLR 7 0 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;;; 104.11 0.019134 979613000 2763180 3522860 2617770 2493860 3349770 3568270 3193680 3456890 3520270 FALSE TRUE 2398018.762 3499718.101 3883732.328 3060129.029 3283116.131 3705543.656 2883957.405 2717660.975 3104107.691 0.772530788 1.127447386 1.251159017 0.985832108 1.057668244 1.193754864 0.929077755 0.875504733 1 21.56574718 2.125370996 10.30663066 0.921017446 1.072066577 0.174465951 0.131501352 0.476858862 41.22673876 0.052627225 0.035472019 133.466108 -2.125370996 0.151049131 ANAS(ph)PQKPLDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ANASPQKPLDLK 12 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 ANAS(1)PQKPLDLK 136.81 6.25E-05 552050000 1790400 1153700 1018800 1087200 1087500 831130 1611700 1778800 1513100 TRUE FALSE 1553794.104 1146121.269 1511495.088 1334065.377 1065860.878 863104.1089 1455397.582 1398417.463 1334223.042 1.164568483 0.859017745 1.132865376 0.99988183 0.798862592 0.64689642 1.090820303 1.04811371 1 20.34756843 4.757022912 23.33416344 0.955137345 1.164568941 0.17835489 0.14580417 3199.442335 4043553.266 0.037697469 1.09899885 57150.87874 -4.757022912 0.209431596 ANCDASLIVTEELHLITFETEVYHQGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ANCDASLIVTEELHLITFETEVYHQGLK 28 0 P40763;P40763-2;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 184 6.56E-18 59196000 6077.5 6319.9 5224.7 4485.6 6010.3 7017.2 7307.2 9959.6 9739.3 FALSE TRUE 5274.342977 6278.384161 7751.382396 5504.124038 5890.706789 7287.156225 6598.548869 7829.817046 8587.931049 0.614157583 0.73107063 0.902590199 0.64091386 0.685928515 0.848534552 0.768351403 0.911723324 1 13.06809489 0.925035057 0.687638815 1.322798067 0.722331974 0.558000417 0.083783245 3.501878013 0.955287349 1.823509155 0.039144321 8.414630638 -0.925035057 -0.600466093 ANEFHDVNCEVVAVSVDSHFSHLAWINTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ANEFHDVNCEVVAVSVDSHFSHLAWINTPR 30 0 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 ; 202.3 6.69E-26 149598000 138125 155391 87195 130573 172280 174753 146373 166108 204863 FALSE TRUE 119871.4313 154370.2263 129362.7936 160221.5953 168851.9651 181475.861 132177.769 130587.0969 180644.3295 0.66357705 0.854553402 0.716118762 0.886945058 0.934720539 1.004603142 0.731701733 0.722896186 1 17.46279244 4.740756461 23.61605714 0.843806163 0.663576908 0.234118758 0.107488901 158.3623684 1702904.56 0.027437591 0.175160339 55049.89072 -4.740756461 -0.180229254 ANEHQGIGFLNDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ANEHQGIGFLNDPR 14 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 ;;; 114.63 0.00046651 2126290000 3495710 2984210 2177900 2649220 2941690 3196570 3191450 3634190 3386360 FALSE TRUE 3033743.066 2964606.528 3231139.725 3250765.892 2883156.124 3319544.116 2881943.67 2857046.75 2986028.379 1.015979315 0.992825972 1.082086074 1.08865874 0.965548802 1.111692086 0.96514276 0.956804955 1 21.50979645 2.180894712 24.999986 0.970035272 1.040886388 0.334629527 0.045577602 86.64253344 37561.36668 0.0179241 0.012084431 151.6682626 -2.180894712 0.070851117 ANFDKESER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ANFDKESER 9 1 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ; 140.17 0.00010008 1605940000 4459200 4008300 2133500 2176500 3416800 3406500 4657100 4845200 1197880 FALSE TRUE 3869905.422 3981969.213 3165267.736 2670707.591 3348812.365 3537550.259 4205455.159 3809091.685 1056267.991 3.66375338 3.76984747 2.99665214 2.528437493 3.170419243 3.349102964 3.981428193 3.606179225 1 20.01054448 4.239596926 24.98832164 3.069007388 3.716800631 0.123626851 0.802335066 63.58407212 1532995.252 0.203968806 0.480575402 17361.88701 -4.239596926 0.647793243 ANFWYQPSFHGVDLSALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ANFWYQPSFHGVDLSALR 18 0 K7EQA8;Q86X55-2;Q86X55-1;Q86X55 K7EQA8 CARM1 Histone-arginine methyltransferase CARM1 0 75.239 0.017221 267400000 114440 137120 92117 131020 145510 175630 123890 162390 154240 FALSE TRUE 99316.46405 136219.2497 136665.0893 160770.0935 142614.6357 182386.5997 111875.1669 127664.1622 136005.9229 0.730236316 1.001568511 1.004846601 1.18208156 1.04859136 1.341019537 0.822575697 0.938666195 1 17.05330996 7.444770457 9.536364296 1.010205387 0.054165301 0 0.169759897 0 0 0.03811015 0 27846489.75 -7.444770457 -0.956040086 ANGLPAGPEPASEPGS(ph)PYPEGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ANGLPAGPEPASEPGSPYPEGPR 23 0 A0A1B0GUN5;A0A5F9ZH45;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 ANGLPAGPEPASEPGS(1)PYPEGPR;ANGLPAGPEPASEPGS(1)PYPEGPR 315.43 2.67E-73 499970000 190626 195819 131833 187812 245827 234389 208383 280803 242785 TRUE FALSE 165434.2911 194532.6521 195587.8798 230457.5851 240935.5237 243406.0965 188174.0487 220755.4637 214083.2339 0.772756876 0.90867766 0.913606714 1.076485911 1.125429205 1.136969449 0.878976113 1.031166522 1 17.70781229 4.309759527 1.548736325 1.035407298 0.778179858 0.560420228 0.076781418 0.435003211 1.695483487 0.023399282 0.134829752 20406.07728 -4.309759527 -0.25722744 ANGMELDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ANGMELDGR 9 0 P62995;P62995-3;H7BXF3;Q13595;Q13595-3;Q13595-4;Q13595-2 P62995;Q13595 TRA2B;TRA2A Transformer-2 protein homolog beta;Transformer-2 protein homolog alpha 0 ; 101.65 0.0097621 175280000 806220 776320 491180 607510 705430 709520 702500 804660 966690 FALSE TRUE 699675.9843 771220.3028 728716.2909 745454.4307 691393.3232 736815.6935 634371.6581 632589.7209 852409.0095 0.820821902 0.904753814 0.854890414 0.874526691 0.811105133 0.864392194 0.74421041 0.742119938 1 19.70118632 3.134075832 2.05369699 0.813675225 0.866654478 0 0.075599418 0.851688792 7.371807994 0.02601843 0.031219857 1361.682425 -3.134075832 0.052979252 ANGMELDGRR ddPTM_MDA-MB-175_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 ;;; 136.49 0.00018654 1542870000 1105410 946400 470679 511527 962404 993180 922130 999400 555505 FALSE TRUE 959327.2677 940183.0361 698300.9387 627677.0236 943254.0433 1031388.277 832701.9745 785686.0873 489833.8317 1.958474906 1.919391792 1.4255874 1.281408067 1.92566128 2.10558808 1.699968276 1.603984936 1 18.9019329 1.18747559 2.305352623 0.721616794 1.752274504 0.476322798 0.248825736 0.720852121 3.553008663 1.611018376 0.071565913 15.39839975 -1.18747559 1.03065771 ANGQENGHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ANGQENGHVK 10 0 P49006;P29966 P49006;P29966 MARCKSL1;MARCKS MARCKS-related protein;Myristoylated alanine-rich C-kinase substrate 0 ;;;;; 146.71 2.82E-05 831556000 1149998 859509 560656 762011 521560 695896 877443 1142245 1039573 FALSE TRUE 998022.8506 853862.8288 831791.1169 935037.2442 511181.9764 722667.5694 792348.7129 897984.7957 916675.8642 1.088741277 0.931477376 0.907399387 1.020030395 0.55764747 0.788356711 0.864371741 0.979609948 1 19.80605216 5.064378321 1.121366274 0.868057957 1.342675738 0.215463417 0.131441375 5.512499256 3.555618762 0.042156112 3.662891334 115978.7227 -5.064378321 0.474617781 ANGTTVHVGIHPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ANGTTVHVGIHPSK 14 0 P61254;E5RIT6;J3QRI7;J3QQQ9;J3QQV1;J3QRC4;J3KS10;Q9UNX3 P61254;Q9UNX3 RPL26;RPL26L1 60S ribosomal protein L26;60S ribosomal protein L26-like 1 0 63.128 0.041374 527740000 650820 647030 270360 391210 668650 772740 610390 619220 333350 FALSE TRUE 564812.488 642779.6173 401107.0003 480040.2098 655345.1732 802467.8078 551194.4717 486804.6218 293941.7428 1.921511667 2.186758544 1.364579922 1.633113437 2.229507 2.730023304 1.875182703 1.656126201 1 18.16517073 1.322957963 2.130699673 0.821166757 1.996063507 0.432798251 0.362064618 0.605544714 3.27167044 1.299284 0.105921499 21.03574815 -1.322957963 1.174896751 ANHEEVLAAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ANHEEVLAAGK 11 0 P00491 P00491 PNP Purine nucleoside phosphorylase 0 103.88 0.0026748 659570000 903650 857180 629630 768160 813470 704010 1000300 1106100 1091600 FALSE TRUE 784230.3629 851549.1281 934121.174 942582.4686 797283.5385 731093.7203 903291.06 869569.1227 962552.2916 0.814740529 0.884678303 0.970462781 0.979253259 0.828301533 0.759536626 0.938433234 0.903399358 1 19.87650539 1.072678761 1.644240837 1.086306042 0.882833561 0.223317162 0.06893128 2.850516348 4.965339091 1.06873499 0.020603632 11.82166808 -1.072678761 -0.203472481 ANHGPGMAMNWPQFEEWSADLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ANHGPGMAMNWPQFEEWSADLNR 23 0 Q9UNF0-2;Q9UNF0 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 165.66 1.29E-11 350550000 246330 260680 132240 176010 249380 256620 253900 250950 253790 FALSE TRUE 213776.8664 258967.5759 196191.7063 215975.7606 244417.8259 266492.3375 229276.8171 197286.2954 223787.2353 0.955268365 1.157204411 0.876688548 0.96509419 1.092188415 1.190829035 1.024530361 0.881579752 1 17.77176822 1.881443676 7.252362874 0.936367056 1.042123268 0.145382891 0.09763765 0.447259429 24.91919724 0.048211133 0.026392282 76.11034251 -1.881443676 0.105756212 ANKLDHVVTIIK ddPTM_MDA-MB-175_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 ; 124.86 0.0001896 1009890000 3247800 2499500 1761370 2093700 2459800 2175800 3168100 3533800 2332100 FALSE TRUE 2818595.001 2483080.62 2613174.423 2569106.585 2410854.793 2259504.434 2860858.15 2778124.37 2056401.795 1.370644107 1.207488063 1.270750896 1.249321311 1.172365633 1.098766029 1.391196096 1.350963794 1 20.97169075 4.745775045 23.31236278 1.233686342 1.370644277 0.137672689 0.114232189 779.4073862 2518368.454 0.028193284 0.269724445 55689.7214 -4.745775045 0.136957935 ANKPGDVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ANKPGDVVR 9 1 P28838-2;P28838 P28838-2 LAP3 Cytosol aminopeptidase 0 ; 73.499 0.039897 339280000 832600 798950 446360 699450 756610 738080 857080 1083790 1041370 FALSE TRUE 722569.8005 793701.6448 662221.189 858270.8129 741554.9413 766474.4152 773960.5135 852029.9426 918260.4249 0.786889842 0.864353536 0.721169258 0.934670372 0.807564958 0.834702656 0.842855134 0.927873966 1 19.80854384 1.467683028 1.524501754 1.031966532 0.824900371 0.54828955 0.053981707 0.505740948 1.585304168 0.14648154 0.014829674 29.35506379 -1.467683028 -0.207066161 ANLEAFTVDKDITLTNDKPATAIGVIGNFTDAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ANLEAFTVDKDITLTNDKPATAIGVIGNFTDAER 34 2 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 246.91 1.07E-47 701350000 954640 709480 627870 662610 647530 544360 937000 1127690 858890 FALSE TRUE 828481.9053 704819.3792 931510.0321 813065.7279 634645.4199 565301.8814 846129.8842 886542.2692 757353.0027 1.093917767 0.930635221 1.229954894 1.073562427 0.83797835 0.746417958 1.117219951 1.170579989 1 19.53060637 ANLQIDQINTDLNLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ANLQIDQINTDLNLER 16 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 333.31 2.93E-71 687151000 596998 567798 394876 448449 548485 607434 526998 607502 745176 FALSE TRUE 518103.2017 564068.0976 585839.3544 550276.1996 537571.2216 630802.379 475889.8151 477592.4249 657082.1422 0.788490766 0.85844381 0.891577045 0.8374542 0.818118751 0.960005361 0.724247068 0.726838236 1 19.32571421 2.219019357 24.99931182 0.794372974 0.857630215 0.027377359 0.088281936 579.5120357 741369.4732 0.035357944 0.023877399 165.5843764 -2.219019357 0.063257241 ANNIDYTVHSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ANNIDYTVHSVR 12 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ;; 166.6 5.15E-05 689210000 957700 929980 604950 688590 941550 999240 925470 1087590 824470 FALSE TRUE 831137.5185 923870.9001 897505.8434 844944.8839 922814.9971 1037681.409 835718.0618 855017.3421 727002.0958 1.143239508 1.270795374 1.234529926 1.162231703 1.269342967 1.427343078 1.1495401 1.176086489 1 19.4716 1.200794668 1.573546097 0.890411655 1.244763456 0.458629443 0.081469798 1.128041347 2.33637783 0.646497802 0.023344503 15.87795872 -1.200794668 0.354351801 ANPFGGASHAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ANPFGGASHAK 11 0 D6RD47;P62266;D6RDJ2;D6RIX0;D6R9I7 D6RD47 RPS23 40S ribosomal protein S23 0 ;;; 147.24 3.54E-05 3571670000 5207240 4980530 3468800 3891770 4574700 4266370 5074810 5597940 5250410 FALSE TRUE 4519090.041 4947812.57 5146323.282 4775455.86 4483672.42 4430500.015 4582655.707 4400864.094 4629712.511 0.976105974 1.068708383 1.111585929 1.03148 0.968455905 0.956970871 0.989835912 0.950569627 1 22.14249118 3.334216424 4.227250202 0.970714165 1.05615617 0.514456365 0.035837986 0.16091843 5.22879201 0.010457315 0.013563374 2158.819956 -3.334216424 0.085442005 ANPHNYDAWFDYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ANPHNYDAWFDYLR 14 0 Q5JY65;Q9BZJ0-2;Q9BZJ0-3;Q9BZJ0 Q5JY65 CRNKL1 Crooked neck-like protein 1 0 ; 183.6 1.39E-06 740000000 625400 654120 398600 459390 629060 547280 485820 638910 571180 FALSE TRUE 542751.8054 649823.0426 591364.2932 563701.5208 616542.9367 568334.2157 438705.2512 502284.0685 503655.7511 1.077624557 1.290212692 1.174143831 1.119219863 1.224135603 1.128418001 0.871041878 0.997276547 1 18.94207846 2.383042725 5.824031018 0.962350929 1.179614574 0.699956095 0.066262852 0.105902386 5.36643116 0.023697061 0.018219713 241.5698477 -2.383042725 0.217263645 ANQIS(ph)PSNSSLK ddPTM_MDA-MB-175_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(0.904)PS(0.095)NS(0.001)SLK;ANQIS(0.657)PS(0.334)NS(0.006)S(0.002)LK 168.67 4.81E-05 103672000 262160 212172 199653 229030 207400 197895 236970 285190 589870 TRUE FALSE 227514.8918 210778.2282 296205.8586 281034.762 203273.1458 205508.1487 213988.6859 224204.3379 520136.2406 0.437414035 0.405236574 0.569477447 0.540309904 0.390807504 0.39510446 0.411408914 0.431049253 1 18.98853004 1.237551865 24.99670629 1.000000653 0.447095199 0.891782451 0.060474612 8.238638671 204047.9822 0.094437957 0.015905311 17.28032337 -1.237551865 -0.552905454 ANRPYDEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ANRPYDEPK 9 1 P22676;A6NER6;H3BN14;H3BMN5 P22676 CALB2 Calretinin 0 71.451 0.045185 101860000 62280 75612 54369 46803 57875 63577 78361 83353 80035 FALSE TRUE 54049.5402 75115.29979 80662.03025 57430.33649 56723.40073 66022.84833 70761.56228 65528.6096 70573.35348 0.765863283 1.064357808 1.142953059 0.813767997 0.803750962 0.935520917 1.002666854 0.928517725 1 16.10683594 -1.094383202 1.034010928 9.993070198 0.934699103 0.030756888 0.11793718 1349.469603 12.93087199 28373.92553 0.039119717 0.080466813 1.094383202 -9.058371094 ANS(ph)DIISLNFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ANSDIISLNFR 11 0 Q8TC76 Q8TC76 FAM110B Protein FAM110B 1 ANS(1)DIISLNFR 133.13 0.00017636 24331000 74338 47214 27035 31506 46026 44401 39626 47266 41705 TRUE FALSE 64514.04495 46903.84813 40109.21643 38659.91884 45110.17265 46109.1352 35783.07662 37158.53372 36774.68241 1.754305971 1.275438564 1.09067472 1.05126452 1.226663827 1.253828237 0.97303564 1.010437923 1 15.16642526 4.753764292 1.950746428 1.081424865 1.977021853 0.840731557 0.091690494 0.336549947 1.31756118 0.026936641 0.550494573 56723.66617 -4.753764292 0.895596988 ANS(ph)FQSPTPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ANSFQSPTPSK 11 0 A0A2R8YFA9;E9PRG5;A0A2R8Y7K9 A0A2R8YFA9 MICALCL 1 ANS(0.998)FQS(0.002)PTPSK 206.45 0.00089603 0 304260 302820 167510 229990 310800 178200 351740 394440 310870 TRUE FALSE 264051.2701 300830.7555 248518.3963 282212.7447 304615.6881 185055.4693 317628.3089 310092.0755 274119.3027 0.963271347 1.097444625 0.906606699 1.029525254 1.111252236 0.675090982 1.158722884 1.131230353 1 18.0644444 ANS(ph)FVGTAQYVSPELLTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ANSFVGTAQYVSPELLTEK 19 0 E9PER6;O15530-5;O15530-2;O15530;O15530-4;Q6A1A2 E9PER6;Q6A1A2 PDPK1;PDPK2P 3-phosphoinositide-dependent protein kinase 1;Putative 3-phosphoinositide-dependent protein kinase 2 1 ANS(1)FVGTAQYVSPELLTEK;ANS(1)FVGTAQYVSPELLTEK;ANS(1)FVGTAQYVSPELLTEK;ANS(0.999)FVGT(0.001)AQYVSPELLTEK 405.8 1.53E-147 1537136000 1161810 883276 754297 744228 928269 735092 1113384 1250079 1144265 TRUE FALSE 1008273.865 877473.7018 1119077.552 913216.3422 909798.263 763371.4649 1005408.191 982759.334 1008991.295 0.999288963 0.869654382 1.109105259 0.905078514 0.901690894 0.75656893 0.996448825 0.974001796 1 19.9444823 ANS(ph)LDNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ANSLDNER 8 0 F8VW41;Q86VP3-4;Q86VP3;Q86VP3-3;Q86VP3-2 F8VW41 PACS2 Phosphofurin acidic cluster sorting protein 2 1 ANS(1)LDNER;ANS(1)LDNER 113.42 0.0029919 936700000 1706190 1443260 1238010 1307860 1447230 1516620 1641650 1830470 1931550 TRUE FALSE 1480712.669 1433779.13 1836715.777 1604829.602 1418432.954 1574965.353 1482443.036 1439038.235 1703204.359 0.869368764 0.841812741 1.078388372 0.942241366 0.832802562 0.924707211 0.870384712 0.844900512 1 20.69982012 ANS(ph)LGDLYAQK ddPTM_MDA-MB-175_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 206.88 2.61E-08 1275330000 2779590 2229700 1648320 1983940 2404380 2052970 2594780 2965550 2769310 TRUE FALSE 2412260.139 2215052.954 2445453.065 2434423.9 2356537.542 2131949.084 2343138.635 2331390.21 2441925.327 0.987851722 0.907092829 1.001444655 0.996928069 0.965032598 0.87306072 0.959545572 0.95473444 1 21.21958765 2.982096465 24.83642295 0.945903892 0.971903132 0.089134324 0.040069762 1827.388622 2535022.494 0.012910842 0.013169076 959.6137569 -2.982096465 0.02599924 ANS(ph)LVTLGSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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;ANS(1)LVTLGSHR;ANS(1)LVTLGSHR 151.22 2.16E-05 827440000 1098000 1016430 648273 739820 1050480 1000080 1173050 1161150 1049750 TRUE FALSE 952896.518 1009753.004 961779.9911 907807.4384 1029577.503 1038553.725 1059287.792 912847.1086 925649.7509 1.029435288 1.090858614 1.039032302 0.980724553 1.112275461 1.121972672 1.144372146 0.986169021 1 19.82010688 1.624118444 11.50936081 0.992826726 1.072853257 0.325906297 0.048353723 0.10857186 44.06038303 0.029131797 0.013122921 42.08413875 -1.624118444 0.080026531 ANS(ph)MEGLMPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ANSMEGLMPR 10 0 O43306-2;O43306 O43306-2 ADCY6 Adenylate cyclase type 6 1 ANS(1)MEGLMPR 99.531 0.0048587 81719000 39943 48328 32336 51046 55039 60860 46492 68865 73106 TRUE FALSE 34664.43135 48010.53019 47973.79776 62636.77449 53943.83158 63201.32358 41983.213 54138.75566 64463.49196 0.537737412 0.744770857 0.74420104 0.97166276 0.836812123 0.980420416 0.651271157 0.839835913 1 15.97619472 4.725952567 1.310149807 0.861120972 0.408304605 0.506195535 0.104953549 1.17591525 1.800584526 0.030166127 0.710177908 53205.01459 -4.725952567 -0.452816368 ANS(ph)PEKPPEAGAAHKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ANSPEKPPEAGAAHKPR 17 2 Q9UFC0;F8WDB4 Q9UFC0 LRWD1 Leucine-rich repeat and WD repeat-containing protein 1 1 ANS(1)PEKPPEAGAAHKPR;ANS(1)PEKPPEAGAAHKPR;ANS(1)PEKPPEAGAAHKPR;ANS(1)PEKPPEAGAAHKPR 151.21 1.35E-07 5296500000 3443350 2339030 2188230 2100250 2490300 1650130 3247420 3839080 3057180 TRUE FALSE 2988302.573 2323664.758 3246465.347 2577143.863 2440747.902 1713611.569 2932485.708 3018122.618 2695763.663 1.108518011 0.861969018 1.204284111 0.9559977 0.905401291 0.635668324 1.087812611 1.119579828 1 21.36226259 ANS(ph)RDGEAGR ddPTM_MDA-MB-175_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 123.28 0.00028243 309830000 104003 81425 33238 49427 40991 46671 107359 88622 22709.9 TRUE FALSE 90258.74004 80890.11381 49312.00797 60650.15579 40175.3593 48466.46357 96947.3407 69670.87496 20025.16149 4.507266524 4.039423794 2.462502387 3.028697462 2.00624396 2.420278288 4.841276348 3.479166696 1 14.28952626 4.369311753 4.995371513 2.900491142 4.397370853 0.282288766 0.999090589 0.284554263 11.01433664 0.261132273 0.736613646 23405.16748 -4.369311753 1.496879711 ANSALT(ph)PPKPESGLTLQESNTPGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ANSALTPPKPESGLTLQESNTPGLR 25 1 Q9BW04;Q9BW04-2 Q9BW04 SARG Specifically androgen-regulated gene protein 1 ANS(0.001)ALT(0.999)PPKPESGLTLQESNTPGLR;ANSALT(0.998)PPKPES(0.002)GLTLQESNTPGLR 159.25 3.83E-11 886910000 1511420 992780 813470 921530 1059340 939730 1365830 1466480 1387540 TRUE FALSE 1311682.018 986258.3628 1206866.813 1130777.471 1038261.207 975882.0212 1233372.017 1152884.664 1223506.602 1.072067789 0.806091574 0.986399919 0.924210355 0.848594691 0.797610752 1.00806323 0.942279071 1 20.22259046 2.15199493 24.27912351 0.975896617 0.903115821 0.159855163 0.083126627 34.68535861 9721.01842 0.032349621 0.02181011 141.9040955 -2.15199493 -0.072780796 ANSFTVSSVAAPSWLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ANSFTVSSVAAPSWLHR 17 0 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7C0A4 Q00341 HDLBP Vigilin 0 ; 136.34 1.06E-05 1355980000 634270 689200 304790 470270 707840 668540 639860 732210 708980 FALSE TRUE 550449.6125 684672.5998 452187.4635 577051.9911 693755.3689 694259.1664 577806.4757 575632.5896 625165.1921 0.880486661 1.095186694 0.723308766 0.92303922 1.109715284 1.110521147 0.924246076 0.920768777 1 19.25387793 ANSFVGT(ph)AQYVSPELLTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ANSFVGTAQYVSPELLTEK 19 0 E9PER6;O15530-5;O15530-2;O15530;O15530-4;Q6A1A2 E9PER6;Q6A1A2 PDPK1;PDPK2P 3-phosphoinositide-dependent protein kinase 1;Putative 3-phosphoinositide-dependent protein kinase 2 1 ANS(0.003)FVGT(0.997)AQYVSPELLTEK 485.26 4.18E-239 433910000 345080 254360 212120 222670 271050 219870 335000 355760 318920 TRUE FALSE 299476.8037 252689.0924 314701.9415 273230.6268 265656.6353 228328.5412 302511.7516 279683.4925 281217.6409 1.064928938 0.898553489 1.11906899 0.97159846 0.944665614 0.811928229 1.075721105 0.994544623 1 18.10132757 5.126656078 10.02643282 0.981132475 2.625012249 0.093390984 0.08523141 146091.5886 278058.0097 0.020271101 5135287.751 133861.6204 -5.126656078 1.643879774 ANSWQLVET(ph)PEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ANSWQLVETPEK 12 0 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 ANSWQLVET(1)PEK 133.48 0.0018156 119230000 354290 360760 235230 242920 319440 245780 443560 460160 349340 TRUE FALSE 307469.6788 358390.1438 348988.0148 298078.6988 313083.769 255235.3156 400543.6195 361758.365 308041.4232 0.998143937 1.16344789 1.132925602 0.967657842 1.016369051 0.828574654 1.30029142 1.174382202 1 18.23276484 0.932027807 16.08908103 3.81E-05 1.080610832 0.026594012 0.130749911 2037389.75 10056727.43 73901572.41 0.03329225 8.551214632 -0.932027807 1.080572693 ANSWQLVET(ph)PEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ANSWQLVETPEKR 13 1 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 ANSWQLVET(1)PEKR;ANSWQLVET(1)PEKR;ANSWQLVET(1)PEKR 214.34 1.82E-11 1660120000 1350170 1115890 700450 1077440 1148550 981490 1234030 1644060 1588610 TRUE FALSE 1171741.614 1108559.645 1039189.963 1322089.22 1125696.102 1019248.555 1114353.961 1292490.563 1400806.336 0.836476523 0.791372524 0.741851273 0.943805854 0.803605804 0.727615609 0.795508938 0.922676126 1 20.41782608 1.569970855 3.077548399 0.991024908 0.804936151 0.564871389 0.058652807 0.163050117 3.379577194 0.059025546 0.015887981 37.15102967 -1.569970855 -0.186088757 ANT(ph)PELKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ANTPELKK 8 1 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C3G1 Q9H8V3-2 ECT2 Protein ECT2 1 ANT(1)PELKK;ANT(1)PELKK;ANT(1)PELKK 93.258 0.0065612 1178360000 1250350 896450 759710 749740 941830 639330 1160710 1494620 750050 TRUE FALSE 1085113.08 890561.1609 1127108.297 919979.9261 923089.4257 663925.4388 1048144.523 1175007.144 661379.9435 1.640680354 1.346519757 1.704176711 1.391000642 1.395702175 1.003848764 1.584784258 1.776599299 1 19.33511977 3.618168933 17.82564169 1.403055405 1.543138449 0.111050915 0.25137324 7.480275002 1073.159189 0.07243726 0.10744175 4151.154838 -3.618168933 0.140083044 ANTIPIIGS(ph)PSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ANTIPIIGSPSSK 13 0 E9PGM7;O94988-6;O94988-5;O94988-1;O94988 E9PGM7 FAM13A Protein FAM13A 1 ANTIPIIGS(0.729)PS(0.247)S(0.024)K;ANTIPIIGS(0.937)PS(0.056)S(0.007)K 167.28 3.38E-05 823510000 1933530 1630060 1045780 1279610 1568560 1251270 1783610 2070930 2336600 TRUE FALSE 1678009.112 1619352.029 1551522.706 1570165.008 1537348.725 1299407.167 1610635.777 1628077.735 2060369.81 0.814421325 0.785952124 0.753031178 0.762079215 0.74615184 0.630666961 0.781721693 0.790187144 1 20.97447188 1.140554767 2.220416839 1.122646502 0.750427391 0.716866991 0.048250586 0.510309641 2.041935076 0.421085656 0.013335272 13.82148692 -1.140554767 -0.372219112 ANTLS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ANTLSPVR 8 0 Q9H792;H0YN99;H3BUZ5 Q9H792 PEAK1 Pseudopodium-enriched atypical kinase 1 1 ANT(0.008)LS(0.992)PVR 93.448 0.010226 0 243150 283040 166440 230430 268010 292830 273850 268110 271620 TRUE FALSE 211017.1114 281180.6916 246930.9407 282752.6534 262677.1254 304095.3596 247292.0691 210776.7629 239509.393 0.88103898 1.173986072 1.030986458 1.18054933 1.096729953 1.269659431 1.032494242 0.880035477 1 17.86972271 1.99712086 24.99366549 0.938893626 1.111802342 0.292895891 0.105788158 116.4650877 1011029.45 0.041366824 0.027302201 99.33924612 -1.99712086 0.172908716 ANVNEILDFFHGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ANVNEILDFFHGYR 14 0 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 0 ; 164.09 4.18E-06 365490000 625640 549640 341600 406680 542670 508670 485460 574690 525470 FALSE TRUE 542960.0888 546029.3786 506798.9026 499022.9097 531871.9287 528238.8641 438380.1639 451797.0157 463349.5352 1.171815331 1.178439466 1.093772334 1.076990202 1.147884887 1.140044014 0.946111155 0.975067377 1 18.8217414 2.242838265 24.9988086 0.972854956 1.132905728 0.838703248 0.033295924 41.34011696 241595.4576 0.013680294 0.010217774 174.9195153 -2.242838265 0.160050772 ANVS(ph)SPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ANVSSPHR 8 0 Q5QPM7;Q5QPM9;H0Y555;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 ANVS(0.663)S(0.337)PHR 85.355 0.017624 386910000 665340 732270 553430 788790 603800 814550 713620 875730 1558900 TRUE FALSE 577413.6332 727459.6702 821070.5991 967896.8254 591785.5613 845886.2656 644413.2422 688461.9544 1374608.618 0.420056753 0.529212214 0.597312274 0.704125387 0.430512041 0.61536517 0.468797615 0.500842164 1 20.39058948 1.235979364 24.99940288 1.000000614 0.53530178 0.73817372 0.087347674 36.16806177 350213.8696 0.13882631 0.020935418 17.21786762 -1.235979364 -0.464698835 ANVS(ph)SPHREFPPATAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ANVSSPHREFPPATAR 16 1 Q5QPM7;Q5QPM9;H0Y555;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 ANVS(0.568)S(0.432)PHREFPPATAR 75.55 0.007703 0 34653 34899 23956 21047 33239 34589 35925 35671 30355 TRUE FALSE 30073.51825 34669.74617 35541.20173 25826.04303 32577.60893 35919.66121 32440.99903 28043.03424 26766.46648 1.123552049 1.29526795 1.327825686 0.964865611 1.217105327 1.341965001 1.212001556 1.047692801 1 14.70813908 1.674693646 3.851103741 1.011713643 1.215674264 0.343418506 0.108797489 0.199624444 6.893578799 0.080029073 0.0291406 47.28176132 -1.674693646 0.203960621 ANVSS(ph)PHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ANVSSPHR 8 0 Q5QPM7;Q5QPM9;H0Y555;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 ANVS(0.228)S(0.772)PHR;ANVS(0.037)S(0.963)PHR;ANVS(0.057)S(0.943)PHR 96.756 0.0091424 729070000 1138720 1250520 994520 1356170 1059580 1400830 1245260 1458880 2734470 TRUE FALSE 988235.2669 1242305.252 1475473.198 1664109.126 1038496.431 1454720.837 1124494.877 1146909.865 2411204.072 0.40985136 0.515221945 0.611923817 0.6901569 0.4306962 0.603317178 0.466362383 0.475658563 1 21.20132233 1.234748712 24.99883769 1.000000677 0.527309749 0.743357519 0.087632502 57.90445391 379686.8984 0.157301824 0.021524558 17.16914672 -1.234748712 -0.472690928 ANVSSPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ANVSSPHR 8 0 Q5QPM7;Q5QPM9;H0Y555;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 0 ;;; 90.657 0.013041 499720000 344352 417301 190371 270370 352080 415870 360893 396188 423286 FALSE TRUE 298845.0107 414559.7223 282435.0524 331761.6408 345074.2968 431868.788 325893.6524 311466.2793 373245.6113 0.80066584 1.110688806 0.756700263 0.888856107 0.924523387 1.157063271 0.873134586 0.834480755 1 18.50976577 4.243142171 24.99555788 0.916807925 0.955677161 0.01349179 0.128175712 709.4402476 3870362.114 0.031611092 0.078017792 17504.19612 -4.243142171 0.038869236 ANWEAQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ANWEAQQR 8 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 ;;;;; 171.53 0.00067197 2644910000 2747350 2774880 1784290 2086050 2648680 2815200 2451550 2893760 2786010 FALSE TRUE 2384280.737 2756651.631 2647178.612 2559719.536 2595976.45 2923502.566 2213799.058 2274951.943 2456651.072 0.970541061 1.122117692 1.077555801 1.041954865 1.05671354 1.190035736 0.901145093 0.926037877 1 21.22826153 2.216573021 24.99999026 0.937267975 1.076140848 0.519773927 0.060691998 173.2412378 196974.5481 0.02369537 0.015990164 164.6542787 -2.216573021 0.138872874 ANYAVDAYFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ANYAVDAYFR 10 0 O60264;A0A0A0MRP6;B7ZLQ5;P28370-2;P28370 O60264 SMARCA5;SMARCA1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5;Probable global transcription activator SNF2L1 0 112.75 0.0036748 32966000 91593 91511 62658 69634 91428 98630 75044 83721 126410 FALSE TRUE 79488.75298 90909.85822 92959.61838 85445.46399 89608.76168 102424.3599 67766.24443 65817.91567 111465.9538 0.713121364 0.815584087 0.833973202 0.766561098 0.803911496 0.918884704 0.607954645 0.590475508 1 16.76624359 2.231888613 24.9999993 0.697954738 0.808006261 0.055174443 0.122314049 300.8701378 1127348.26 0.048500718 0.033553104 170.5644874 -2.231888613 0.110051523 ANYWWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ANYWWLR 7 0 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 160.77 0.0031031 7078500000 2312600 3785600 2625700 2569900 3676900 3897200 3308900 3432500 4295600 FALSE TRUE 2006984.051 3760732.144 3895497.302 3153435.073 3603736.884 4047127.806 2988003.387 2698486.587 3787779.062 0.529857739 0.992859426 1.028438364 0.832528778 0.951411586 1.068469871 0.788853663 0.712419215 1 21.85292075 0.95779568 21.48625319 2.05541595 0.869192663 0.065182753 0.16146851 421.1950455 251659.2693 47804.38529 0.038212548 9.073935346 -0.95779568 -1.186223287 APAAHPEGQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APAAHPEGQLK 11 0 Q02818 Q02818 NUCB1 Nucleobindin-1 0 91.549 0.010658 113420000 559450 606740 461420 573330 583100 536470 651610 817750 797280 FALSE TRUE 485517.265 602754.285 684564.2554 703513.3393 571497.4508 557108.348 588416.9625 642880.5262 703026.4667 0.690610223 0.857370687 0.973738953 1.000692538 0.812910293 0.792442923 0.836976971 0.914447118 1 19.42321948 4.702726399 3.712853625 0.898700022 0.675559636 0.447497816 0.073980335 0.242228712 6.198699154 0.019712143 0.139202536 50434.34661 -4.702726399 -0.223140386 APAASEGNHTDGAEEAAGSCAQAPS(ph)HSPPNKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APAASEGNHTDGAEEAAGSCAQAPSHSPPNKPK 33 1 Q92560;F8W6N3 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 APAASEGNHTDGAEEAAGS(0.003)CAQAPS(0.498)HS(0.498)PPNKPK 110.32 4.51E-06 98172000 18845 14484 8997.5 13026 13477 12532 16648 20477 21902 TRUE FALSE 16354.5855 14388.85365 13348.72109 15983.75239 13208.83407 13014.11415 15033.47952 16098.1529 19312.77051 0.846827517 0.745043475 0.691186233 0.827626072 0.683942993 0.67386055 0.778421693 0.83354964 1 14.23726752 1.258078388 1.737904834 1.086994847 0.743643635 0.658917229 0.057486785 0.557455048 1.625138749 0.320888644 0.015985068 18.1166706 -1.258078388 -0.343351212 APAASEGNHTDGAEEAAGSCAQAPSHS(ph)PPNKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APAASEGNHTDGAEEAAGSCAQAPSHSPPNKPK 33 1 Q92560;F8W6N3 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 APAASEGNHTDGAEEAAGSCAQAPS(0.015)HS(0.984)PPNKPK 172.57 7.11E-15 210490000 134720 97192 68328 97129 112050 77812 130090 154850 140540 TRUE FALSE 116916.4107 96553.53935 101371.6493 119183.624 109820.4242 80805.47799 117473.8918 121736.5325 123925.5213 0.943440943 0.779125545 0.818004623 0.96173591 0.886180853 0.652048724 0.947939461 0.982336255 1 16.9191138 2.019751011 24.99994635 0.982475949 0.840276858 0.363001842 0.086586363 244.7886127 309841.247 0.035106921 0.023665904 104.6528383 -2.019751011 -0.142199091 APADPAPAPADPAS(ph)PQHQLAGPAPLLSTPAPEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APADPAPAPADPASPQHQLAGPAPLLSTPAPEAR 34 0 Q96AD5-2;Q96AD5 Q96AD5-2 PNPLA2 Patatin-like phospholipase domain-containing protein 2 1 APADPAPAPADPAS(1)PQHQLAGPAPLLSTPAPEAR 115.82 3.34E-06 151950000 31023 37561 34590 35410 48154 48767 36851 53095 72061 TRUE FALSE 26923.23195 37314.25932 51317.8397 43450.38171 47195.82961 50643.09805 33277.19569 41741.04744 63542.03067 0.423707453 0.587237438 0.807620392 0.683805369 0.742749785 0.797001567 0.523703686 0.656904524 1 15.95542358 4.527715656 3.375569024 0.72432426 0.432188737 0.418008868 0.123118566 0.265655052 5.644610642 0.030962179 0.148555346 33706.655 -4.527715656 -0.292135524 APAPLGTVADSLRAS(ph)DGQLQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APAPLGTVADSLRASDGQLQAK 22 1 Q9BRG2;Q9BRG2-2 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 APAPLGTVADS(0.025)LRAS(0.975)DGQLQAK;APAPLGTVADS(0.002)LRAS(0.998)DGQLQAK 180.7 3.17E-17 1514300000 396080 388180 206832 224660 348850 304730 407970 486070 157532 TRUE FALSE 343737.0245 385630.02 306856.647 275672.4867 341908.5675 316453.1603 368405.1322 382127.7131 138908.7464 2.474552779 2.776139228 2.209052021 1.984558164 2.461389771 2.278137039 2.652137764 2.750926223 1 17.08377792 4.229594946 24.81580834 2.271007475 2.625346015 0.103299952 0.489751365 409.5657766 1133636.664 0.123384974 0.263108343 16966.60488 -4.229594946 0.35433854 APAPPQSGSCDHPLLLLEPGNLAS(ph)SPSMSLASPQPCGLASHEEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APAPPQSGSCDHPLLLLEPGNLASSPSMSLASPQPCGLASHEEHR 45 0 Q9C073;D6RJ87 Q9C073 FAM117A Protein FAM117A 1 APAPPQSGSCDHPLLLLEPGNLAS(0.528)S(0.382)PS(0.074)MS(0.015)LASPQPCGLASHEEHR 97.824 9.00E-06 51076000 15671 16202 6523.7 9350.7 12363 11542 10519 14051 13029 TRUE FALSE 13600.03764 16095.568 9678.58314 11473.91935 12117.00049 11986.02821 9498.868999 11046.303 11488.72646 1.18377243 1.400988007 0.842441777 0.998711162 1.054686133 1.043286064 0.826799126 0.961490643 1 13.48793126 4.239661629 24.99999983 0.961530471 1.292380261 0.697231126 0.09076856 14.6050256 331588.0294 0.022389289 0.052811139 17364.47386 -4.239661629 0.330849791 APDEPQQAQVPHVWGWEVAGAPALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APDEPQQAQVPHVWGWEVAGAPALR 25 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 173.44 4.48E-12 149910000 48109 66808 45558 59404 62002 58625 39759 69412 87220 FALSE TRUE 41751.27376 66369.13385 67590.00118 72892.58613 60768.2815 60880.34169 35903.1783 54568.78396 76908.95096 0.542866249 0.862957211 0.878831402 0.947777667 0.790132758 0.791589807 0.466827045 0.709524487 1 16.23086389 2.45473677 24.99324636 0.699621182 0.81694934 0.036396364 0.164459199 569.9526823 636372.6074 0.061334938 0.047513089 284.9290764 -2.45473677 0.117328158 APDFVFYAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APDFVFYAPR 10 0 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 78.149 0.071813 501450000 288050 276760 147800 227500 241910 310590 233840 272240 275740 FALSE TRUE 249983.4627 274941.9453 219276.5744 279157.3521 237096.4643 322538.5983 211162.2328 214023.5946 243142.3313 1.028136324 1.130786004 0.901844501 1.148123203 0.975134453 1.326542345 0.868471696 0.880239954 1 17.89144156 APDMS(ph)PQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APDMSPQR 8 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 APDMS(1)PQR 78.683 0.025988 0 799550 930250 573280 668560 843430 917910 822050 918050 870010 TRUE FALSE 693887.4417 924139.1265 850520.1255 820366.7663 826647.3931 953222.5917 742327.7175 721732.1518 767158.4089 0.904490433 1.20462621 1.108662977 1.069357719 1.07754459 1.242536848 0.967632902 0.94078634 1 19.54916498 2.057251781 24.98265332 0.962577219 1.103834407 0.321484509 0.090008514 80.31862625 35047.70258 0.034391231 0.02318656 114.0911036 -2.057251781 0.141257188 APDWVDAEECHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 APDWVDAEECHR 12 0 O14964-2;O14964;I3L1P5 O14964-2 HGS Hepatocyte growth factor-regulated tyrosine kinase substrate 0 ;;; 218.62 3.39E-11 2763370000 2315660 2258060 1546070 1757620 2024420 2010520 2123530 2338190 2267220 FALSE TRUE 2009639.664 2243226.655 2293754.623 2156714.485 1984138.003 2087866.005 1917590.387 1838186.264 1999191.834 1.005226026 1.122066735 1.147340932 1.078793164 0.992470041 1.044355009 0.959182783 0.919464672 1 20.93098548 2.796162125 1.134548454 0.951214525 1.095490001 0.538388169 0.048035467 0.336741864 0.936730558 0.027623995 0.023330302 625.4061176 -2.796162125 0.144275476 APEATVTLPVFIGNIAVNHAPVS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APEATVTLPVFIGNIAVNHAPVSPR 25 0 Q5T370;Q8N5I2 Q5T370 ARRDC1 Arrestin domain-containing protein 1 1 APEATVTLPVFIGNIAVNHAPVS(1)PR 114.79 0.0010996 101350000 170490 135490 137030 131450 103160 95690 173880 177230 173900 TRUE FALSE 147959.3145 134599.9573 203298.1663 161297.7316 101107.3178 99371.25622 157017.1444 139330.7437 153341.7401 0.964899149 0.877777683 1.325784918 1.051884056 0.659359401 0.64803788 1.023968714 0.908628946 1 17.22639093 3.427879047 24.87459371 0.858490178 1.06340283 0.277051159 0.165619825 150.1161618 75830.20275 0.050267353 0.064894888 2678.42227 -3.427879047 0.204912651 APELPNTSSS(ph)PSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 APELPNTSSSPSLK 14 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 APELPNT(0.003)S(0.011)S(0.038)S(0.946)PS(0.003)LK;APELPNTS(0.001)S(0.4)S(0.599)PSLK;APELPNTSS(0.011)S(0.989)PSLK;APELPNTSS(0.028)S(0.971)PSLK 300.51 8.11E-44 2065360000 3985240 3528200 2368410 2819550 3189340 2831350 3668480 4157760 3886100 TRUE FALSE 3458580.437 3505023.022 3513780.998 3459771.922 3125878.374 2940273.867 3312711.374 3268655.38 3426689.685 1.009306577 1.02285977 1.025415582 1.009654284 0.912215188 0.858050812 0.96673807 0.953881349 1 21.70838412 3.309001873 6.759516404 0.938389133 1.018741959 0.530512954 0.036783134 0.184683968 14.22026828 0.011440572 0.014741513 2037.050862 -3.309001873 0.080352826 APEPHVEEDDDDELDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 APEPHVEEDDDDELDSK 17 0 P52566;F5H3P3;F5H2R5;F5H6Q0 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ;;;; 345 6.21E-74 14584400000 8751290 7661450 8714300 10421030 8005200 6161890 8825070 10884100 25102900 FALSE TRUE 7594784.854 7611121.43 12928564.63 12787284.14 7845912.182 6398941.896 7969216.07 8556619.915 22135263.76 0.343107945 0.343845979 0.584070954 0.577688356 0.354453069 0.289083607 0.360023542 0.386560558 1 24.39984323 1.237435359 24.99940147 1.000000708 0.405797471 0.78189897 0.098781231 14.2296375 315989.6744 0.156985808 0.026256737 17.27568828 -1.237435359 -0.594203237 APEPHVEEDDDDELDSKLNYKPPPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 APEPHVEEDDDDELDSKLNYKPPPQK 26 2 P52566;F5H3P3;F5H2R5;F5H6Q0 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ;;; 260.68 5.19E-53 3693070000 4407870 3518280 3087020 3065910 2985370 1949360 4747240 5820890 2405390 FALSE TRUE 3825358.811 3495168.187 4579913.197 3762071.725 2925966.978 2024353.141 4286853.395 4576137.972 2121027.534 1.803540383 1.647865542 2.159289836 1.773702446 1.379504476 0.954420962 2.021121049 2.157509932 1 21.01633192 3.465247736 23.65208664 1.594125077 1.867745442 0.135905773 0.400758117 317.9150237 633282.5239 0.125213851 0.161811235 2919.091686 -3.465247736 0.273620366 APEPQLS(ph)PGSDASEVR ddPTM_MDA-MB-175_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(0.999)PGS(0.001)DASEVR 250.46 7.84E-21 801190000 237369 254014 159669 214996 259882 268316 234793 282275 230809 TRUE FALSE 206000.0852 252345.3653 236885.4625 263814.1278 254710.8567 278638.2901 212022.811 221912.6879 203523.023 1.012170919 1.239886091 1.163924646 1.296237271 1.251508812 1.369075037 1.041763275 1.090356681 1 17.63483248 2.202976699 24.99796641 1.053594228 1.22499847 0.440543889 0.094367411 166.8206649 117191.6316 0.037983446 0.025609428 159.5793527 -2.202976699 0.171404242 APEVNLNAPDVDVHGPDWNLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APEVNLNAPDVDVHGPDWNLK 21 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 167.24 1.24E-11 103440000 151680 109870 67700 101960 101840 91865 79233 131210 136020 FALSE TRUE 131635.1037 109148.2567 100439.9464 125111.5764 99813.58325 95399.10599 71548.99586 103151.7626 119939.8706 1.097509136 0.9100248 0.837419167 1.043119154 0.832196857 0.795391104 0.596540546 0.860028964 1 16.8719518 3.093574125 6.694926789 0.801547824 0.957426927 0.289430544 0.119516291 0.293480945 17.73433346 0.037062707 0.042140052 1240.435323 -3.093574125 0.155879103 APEYLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 120.49 0.0045458 716020000 1288620 985890 691140 765040 948130 1089300 953400 1017880 1024050 FALSE TRUE 1118325.602 979413.6237 1025377.616 938754.0249 929264.068 1131206.076 860939.4147 800214.2832 902987.9756 1.238472308 1.084636396 1.135538505 1.039608555 1.02909905 1.252736588 0.953433975 0.886184872 1 19.78434725 -1.714307427 0.161339642 1.34E-09 1.259959347 0.381634496 0.091233643 125.1292174 1.8101019 36.04103887 1.257086129 0.019306012 1.714307427 1.259959346 APFAAHGYGAFLTLSILDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APFAAHGYGAFLTLSILDR 19 0 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 ; 197.88 7.67E-16 1294820000 1383150 1414570 909940 1057620 1282950 1296190 1483240 1561900 1467050 FALSE TRUE 1200363.223 1405277.597 1349990.028 1297768.786 1257421.805 1346055.268 1339395.613 1227899.84 1293617.02 0.927912361 1.086316564 1.043577818 1.003209424 0.972020146 1.040536146 1.035388057 0.94919889 1 20.30297914 1.744250331 25 0.973632756 1.018174741 0.125298809 0.044570426 1.976570952 8726.103039 0.0227343 0.010917346 55.49454957 -1.744250331 0.044541985 APFDLFENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 APFDLFENR 9 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;; 130.75 0.00082007 1378090000 665020 584270 420553 496975 572090 649500 531730 702690 957080 FALSE TRUE 577135.9221 580431.8919 623933.8375 609820.7695 560706.5283 674486.6853 480162.9064 552425.2118 843935.0927 0.683862926 0.687768404 0.739314958 0.722592027 0.664395323 0.799216304 0.568957152 0.654582582 1 19.68677252 1.234845698 24.99979329 1.000000444 0.68783329 0.726859581 0.05969085 58.0334272 390480.9615 0.106551284 0.014696283 17.17298134 -1.234845698 -0.312167153 APGFGDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APGFGDNR 8 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 79.597 0.064268 231070000 301060 285580 238370 369460 352270 344770 257600 334070 403820 FALSE TRUE 261274.1582 283704.0062 353646.5293 453351.5398 345260.5162 358033.525 232617.9916 262631.7302 356080.8596 0.733749515 0.796740399 0.993163546 1.273170202 0.969612679 1.00548377 0.653272944 0.737562054 1 18.44184536 2.256304801 24.99101407 0.778587194 0.970383993 0.177383069 0.165324386 372.4277861 524528.7398 0.065770456 0.050833554 180.4283598 -2.256304801 0.191796799 APGFGDNRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APGFGDNRK 9 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 69.825 0.086819 676530000 411240 351300 208480 345280 368890 340300 379600 410450 227870 FALSE TRUE 356893.5921 348992.2872 309301.6253 423681.1013 361549.8107 353391.5612 342786.4504 322678.4616 200931.4682 1.776195612 1.73687223 1.539338901 2.108585107 1.79936878 1.75876663 1.70598689 1.605913024 1 17.616344 0.93063767 1.499854297 3.07E-20 1.784512989 0.754892708 0.138475503 1.273333382 1.362243659 4.299186206 0.03935167 8.523886737 -0.93063767 1.784512989 APGLITPGS(ph)PPPAQQNQYVHISSS(ph)PQNTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APGLITPGSPPPAQQNQYVHISSSPQNTGR 30 0 P54253 P54253 ATXN1 Ataxin-1 2 APGLIT(0.001)PGS(0.993)PPPAQQNQY(0.006)VHIS(0.006)S(0.292)S(0.701)PQNT(0.002)GR;APGLIT(0.004)PGS(0.988)PPPAQQNQY(0.008)VHIS(0.075)S(0.228)S(0.697)PQNTGR 108.33 0.0001407 774670000 491190 533390 262102 355840 553550 521660 486410 601640 519920 TRUE FALSE 426277.997 529886.126 388855.4039 436638.9107 542535.438 541728.5978 439238.0331 472983.968 458455.6499 0.929812943 1.155806731 0.848185433 0.952412541 1.183397867 1.181637958 0.958081841 1.031689691 1 18.80642265 APGLITPGS(ph)PPPAQQNQYVHISSSPQNTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 APGLITPGSPPPAQQNQYVHISSSPQNTGR 30 0 P54253 P54253 ATXN1 Ataxin-1 1 APGLITPGS(1)PPPAQQNQYVHISSSPQNTGR;APGLIT(0.123)PGS(0.877)PPPAQQNQYVHISSSPQNTGR;APGLITPGS(1)PPPAQQNQYVHISSSPQNTGR;APGLIT(0.001)PGS(0.999)PPPAQQNQYVHISSSPQNTGR 227.37 3.73E-35 1689980000 583082 771292 253456 388090 1014470 913391 619359 788002 618982 TRUE FALSE 506026.2364 766225.3321 376028.1694 476211.7661 994284.0318 948529.7428 559293.6595 619493.9045 545806.6531 0.927116285 1.40384022 0.688940245 0.872491684 1.821678109 1.73784936 1.024710227 1.135006144 1 19.05803045 APGS(ph)PAAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 APGSPAAPR 9 0 Q5SPY9;Q9NQX5 Q5SPY9 NPDC1 Neural proliferation differentiation and control protein 1 1 APGS(1)PAAPR;APGS(1)PAAPR;APGS(1)PAAPR;APGS(1)PAAPR;APGS(1)PAAPR;APGS(1)PAAPR 152.67 8.38E-05 4827230000 1037181 1010186 689738 925065 1054879 1370883 799750 1204113 1170172 TRUE FALSE 900114.903 1003550.022 1023297.604 1135115.147 1033888.972 1423621.756 722190.3681 946622.8054 1031835.599 0.87234333 0.972587128 0.99172543 1.100093026 1.001990019 1.379698236 0.699908366 0.917416307 1 19.9767817 APGT(ph)PHSHTKPYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APGTPHSHTKPYVR 14 1 J3QQ67;Q07020;F8VYV2;H0YHA7;Q07020-2;F8VUA6 J3QQ67 RPL18 60S ribosomal protein L18 1 APGT(1)PHSHTKPYVR;APGT(1)PHSHTKPYVR 117.4 0.00044802 179534000 255320 251600 147015 184175 197869 179723 193605 240590 218987 TRUE FALSE 221578.8151 249947.223 218111.9457 225994.7487 193931.794 186637.0601 174829.2169 189141.7008 193098.6063 1.147490494 1.294402004 1.129536613 1.170359295 1.00431483 0.966537582 0.90538829 0.979508368 1 17.55897823 3.232746696 2.060975452 0.958790745 1.201224345 0.824271026 0.049416144 0.115980666 1.014708731 0.015758011 0.020284491 1709.018231 -3.232746696 0.242433601 APGTPHSHTKPYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 APGTPHSHTKPYVR 14 1 J3QQ67;Q07020;F8VYV2;H0YHA7;Q07020-2;F8VUA6 J3QQ67 RPL18 60S ribosomal protein L18 0 ;; 179.5 1.20E-06 4432680000 2785840 2613700 1576050 1852160 2382900 2231700 2429850 3066610 2503640 FALSE TRUE 2417684.186 2596530.433 2338233.052 2272721.236 2335484.952 2317554.943 2194203.521 2410839.316 2207662.531 1.095133043 1.176144631 1.059144239 1.029469497 1.057899438 1.049777722 0.993903502 1.092032537 1 21.07408822 4.112224632 6.14963335 1.041826681 1.134746952 0.580819387 0.033945417 0.131041191 6.522031124 0.00802858 0.017101416 12948.65417 -4.112224632 0.092920271 APHLAYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APHLAYLR 8 0 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 ; 132.53 0.00095842 1473740000 362680 950630 557230 572940 781090 850430 788460 773390 877600 FALSE TRUE 314750.9191 944385.2489 826708.2918 703034.7838 765547.8372 883146.5924 711995.2706 608006.567 773851.1278 0.406733166 1.220370708 1.068304047 0.908488414 0.989270171 1.141235776 0.920067497 0.785689321 1 19.56169652 4.753589854 24.80174185 0.985996895 0.406732704 0.697447699 0.123148003 1644.799077 2714250.687 0.032762546 0.743227971 56700.8872 -4.753589854 -0.579264191 APIDTS(ph)DVEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APIDTSDVEEK 11 0 D6RIY6;Q06265-3;Q06265-4;Q06265;Q06265-2 D6RIY6 EXOSC9 Exosome complex component RRP45 1 APIDT(0.495)S(0.505)DVEEK;APIDT(0.285)S(0.715)DVEEK 159.58 2.99E-05 464790000 1578660 1120340 1155530 1479040 1202770 972250 1308010 1700700 2944100 TRUE FALSE 1370036.081 1112980.413 1714348.173 1814878.638 1178837.23 1009653.087 1181159.392 1337018.54 2596051.852 0.527738335 0.428720409 0.660367462 0.699091829 0.454088476 0.38891869 0.454982974 0.515019967 1 21.30788777 1.238580391 16.25707676 1.000064081 0.514776447 0.707978403 0.097662146 0.025549595 2902.393958 0.142493072 0.025609676 17.3212963 -1.238580391 -0.485287634 APIRPDIVNFVHTNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APIRPDIVNFVHTNLR 16 1 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 203.9 1.60E-11 8029800000 5321700 5459200 3834000 4279600 4938200 5963300 4634000 5762600 5760100 FALSE TRUE 4618423.862 5423338.156 5688135.224 5251348.59 4839939.481 6192712.01 4184595.393 4530312.835 5079147.54 0.909291141 1.06776543 1.119899585 1.033903534 0.952903896 1.219242395 0.823877503 0.89194354 1 22.27615495 2.212735692 24.99971124 0.899105074 1.049249688 0.346767046 0.093825224 234.5518528 227055.1898 0.036756908 0.024791101 163.205839 -2.212735692 0.150144614 APIRPDIVNFVHTNLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APIRPDIVNFVHTNLRK 17 2 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 82.707 0.0039674 483590000 708390 593640 294900 339700 579330 553830 695320 836400 129480 FALSE TRUE 614774.4667 589740.3398 437514.6264 416834.077 567802.4664 575136.1985 627887.9734 657542.3689 114173.0219 5.384586099 5.165321281 3.832031588 3.650898172 4.973175422 5.037408916 5.499442539 5.75917461 1 16.80086227 4.417640768 10.35121386 4.484630131 5.33004515 0.071600497 1.352578484 1.225431989 205.4928028 0.334655048 0.887606799 26160.18242 -4.417640768 0.845415018 APKPDGPGGGPGGSHMGGNYGDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 APKPDGPGGGPGGSHMGGNYGDDR 24 1 P35637-2;P35637;H3BPE7 P35637-2 FUS RNA-binding protein FUS 0 ;;;;;;;;; 252.24 5.66E-44 10651270000 7681774 6177180 4686664 6267532 4835826 4509545 5939132 7664900 11063299 FALSE TRUE 6666608.103 6136601.698 6953150.386 7690670.934 4739602.524 4683030.114 5363155.893 6025820.783 9755408.396 0.683375604 0.62904611 0.712748263 0.788349459 0.485843578 0.480044497 0.549762314 0.617690264 1 23.21777084 1.238819765 10.25110954 1.00136899 0.615152326 0.607432244 0.096391402 0.052361778 134.7019713 0.14295704 0.025573135 17.33084609 -1.238819765 -0.386216664 APKPEDIDEEDDDVPDLVENFDEASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 APKPEDIDEEDDDVPDLVENFDEASK 26 1 Q96K17;Q96K17-2 Q96K17 BTF3L4 Transcription factor BTF3 homolog 4 0 ;; 175.9 8.63E-13 291562000 584490 337550 445570 465260 309824 230205 455720 570790 1060740 FALSE TRUE 507248.1656 335332.6118 661049.1423 570904.3941 303659.1086 239061.1353 411524.3445 448731.0004 935340.5256 0.542313897 0.358513934 0.706747034 0.610370639 0.324650863 0.255587274 0.439972751 0.479751479 1 19.83513217 1.238083285 5.938102993 1.020820559 0.460621015 0.612800537 0.133773573 0.099040517 12.94549052 0.225350222 0.035097889 17.30148121 -1.238083285 -0.560199543 APLATGEDDDDEVPDLVENFDEASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 APLATGEDDDDEVPDLVENFDEASK 25 0 P20290-2;P20290 P20290-2;P20290 BTF3 Transcription factor BTF3 0 ;;; 188.72 1.15E-17 234897000 329075 272263 251399 335929 262453 230023 301525 379234 784441 FALSE TRUE 285586.905 270474.4864 372976.3973 412206.8138 257230.6988 238872.1337 272283.1519 298137.7603 691705.2786 0.412873682 0.391025621 0.539212883 0.595928391 0.371879046 0.345338023 0.393640414 0.431018484 1 19.39979794 1.238309725 24.9999993 1.000000623 0.435097524 0.842733526 0.07668948 2.446058676 243248.7233 0.114189178 0.0202045 17.31050451 -1.238309725 -0.564903099 APLATGEDDDDEVPDLVENFDEASKNEAN ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 APLATGEDDDDEVPDLVENFDEASKNEAN 29 1 P20290-2;P20290 P20290-2;P20290 BTF3 Transcription factor BTF3 0 ;;;;; 235.73 2.72E-45 1248991000 1315071 1119172 807642 860052 1024103 914285 1340990 1515650 833199 FALSE TRUE 1141281.035 1111820.085 1198220.373 1055339.952 1003725.354 949458.1356 1210940.996 1191540.042 734699.1634 1.553399122 1.513299784 1.630899329 1.4364246 1.366171903 1.29230872 1.648213387 1.621806723 1 19.48679411 3.662930512 8.30733221 1.428001976 1.560407861 0.148309388 0.182197722 0.82555901 83.77452903 0.051602652 0.076690277 4601.829377 -3.662930512 0.132405885 APLDLDKYVEIAR ddPTM_MDA-MB-175_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 ; 210.91 2.39E-08 3397800000 3693500 3441400 2328500 2614800 3115900 2927800 3848900 4436800 2108060 FALSE TRUE 3205394.617 3418793.217 3454570.388 3208530.305 3053899.686 3040434.361 3475634.27 3488024.847 1858847.548 1.724398873 1.839200434 1.858447397 1.726085772 1.642899488 1.635655578 1.869779086 1.876444817 1 20.82597702 1.234051055 24.99790976 0.99999884 1.776261238 0.879829809 0.089604666 49.18662783 272622.0068 0.189120467 0.024362243 17.14158809 -1.234051055 0.776262397 APLEHELAGEPQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 APLEHELAGEPQLR 14 0 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 ;; 93.823 0.0044092 1209730000 1087150 1141840 727539 894187 1101230 1225070 1049390 1199000 1126050 FALSE TRUE 943480.373 1134339.178 1079379.294 1097225.825 1079317.678 1272199.236 947620.3193 942603.1806 992929.6518 0.950198608 1.14241646 1.087065224 1.105038834 1.087003168 1.281258177 0.954368034 0.949315169 1 19.92133198 APLKPYPVS(ph)PSDKVLIQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APLKPYPVSPSDKVLIQEK 19 2 A0A0A0MSX9;P41252;J3KR24;Q5TCC6 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 1 APLKPY(0.005)PVS(0.939)PS(0.055)DKVLIQEK 46.295 0.092441 1521800000 216610 193770 115550 159880 172020 150220 255480 239700 139870 TRUE FALSE 187984.4397 192497.1121 171430.3665 196183.1976 168597.1386 155999.0606 230703.5889 188442.0203 123334.7279 1.524180925 1.560769747 1.389960227 1.590656589 1.366988369 1.264842946 1.870548488 1.527890996 1 16.91221956 1.237859424 24.99998579 0.999999404 1.517449781 0.497848037 0.16151069 14.88933581 530471.9696 0.228593709 0.039328568 17.29256527 -1.237859424 0.517450376 APLKPYPVSPS(ph)DKVLIQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APLKPYPVSPSDKVLIQEK 19 2 A0A0A0MSX9;P41252;J3KR24;Q5TCC6 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 1 APLKPYPVS(0.397)PS(0.603)DKVLIQEK 195.27 6.72E-16 1464200000 2354900 1648700 1426700 1491300 1421000 1134000 2526000 2811000 886560 TRUE FALSE 2043693.998 1637869.581 2116656.892 1829922.458 1392724.88 1177625.714 2281028.909 2209889.525 781751.8868 2.614248885 2.095127123 2.707581431 2.340796983 1.781543356 1.506393184 2.917842537 2.826842586 1 19.57635127 3.46676517 24.85439676 2.144112201 2.449531544 0.096187885 0.589843472 692.576995 1662163.135 0.179044296 0.231396941 2929.308895 -3.46676517 0.305419343 APLS(ph)PSLNSRPSPISATPPALVPETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APLSPSLNSRPSPISATPPALVPETR 26 1 X6RKU3;Q6P3S6 X6RKU3 FBXO42 F-box only protein 42 1 APLS(0.487)PS(0.487)LNS(0.02)RPS(0.005)PISATPPALVPETR 115.44 0.00072205 283250000 111080 88847 61288 68365 102170 89492 96405 119330 58457 TRUE FALSE 96400.49656 88263.35821 90927.0818 83888.31814 100137.0169 92934.81515 87055.65794 93812.20813 51546.28005 1.870173686 1.71231286 1.763989209 1.627436899 1.942662337 1.802939321 1.688883424 1.819960781 1 15.6535807 1.236539247 24.99997505 0.999999015 1.774927616 0.880344344 0.090195363 16.45652225 203478.108 0.133345156 0.020956039 17.24007883 -1.236539247 0.774928601 APPCEYKDWLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APPCEYKDWLTK 12 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 106.32 0.0017642 1259470000 2145900 1744480 1186540 1453850 1700980 1173900 1818920 2323000 1493840 FALSE TRUE 1862313.878 1733020.396 1760354.713 1783968.863 1667133.826 1219060.693 1642521.418 1826244.528 1317239.937 1.413800042 1.315645197 1.336396402 1.354323395 1.265626542 0.925465937 1.246941709 1.386417521 1 20.32908673 2.99815579 20.96797882 1.178001394 1.345780744 0.36763941 0.128817063 12.76211434 145127.2862 0.041836014 0.046492861 995.7625528 -2.99815579 0.16777935 APPGLTPAPAS(ph)PPVLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 APPGLTPAPASPPVLPR 17 0 C9J069 C9J069 C9orf172 Uncharacterized protein C9orf172 1 APPGLT(0.024)PAPAS(0.976)PPVLPR;APPGLT(0.011)PAPAS(0.989)PPVLPR;APPGLT(0.001)PAPAS(0.999)PPVLPR 154.51 1.42E-07 1066581000 409812 425153 273932 294505 373803 423122 389570 391485 394719 TRUE FALSE 355654.3059 422360.1419 406406.4314 361376.8615 366365.0516 439399.7771 351789.5614 307768.9793 348055.7695 1.021831376 1.213484099 1.167647449 1.038272866 1.052604449 1.262440723 1.010727568 0.884251911 1 18.40895896 2.007946819 24.93311446 0.937947671 1.125584192 0.483742837 0.080741773 129.3024755 405684.2546 0.032040341 0.021555796 101.8466666 -2.007946819 0.187636521 APPHELTEEEKQQILHSEEFLSFFDHSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APPHELTEEEKQQILHSEEFLSFFDHSTR 29 1 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7;E7EQL5;E7EV09 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 0 ; 234.37 1.09E-45 485950000 70524 59332 36368 51792 64852 62663 65728 77224 48300 FALSE TRUE 61204.07471 58942.24419 53955.68644 63552.16519 63561.57208 65073.68616 59353.70868 60710.24856 42590.02902 1.437051726 1.383944682 1.266861932 1.492184125 1.492404996 1.527908941 1.393605734 1.425456849 1 15.37822809 1.238362515 9.615724956 0.997820139 1.426709904 0.773958539 0.072593129 0.038581419 63.6140585 0.106513553 0.018758347 17.31260876 -1.238362515 0.428889766 APPKPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APPKPAR 7 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2;S4R349;S4R3C2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 70.912 0.050836 200940000 622910 668010 316760 470170 501610 665640 623090 690830 570660 FALSE TRUE 540590.8652 663621.7983 469946.1955 576929.2846 491628.9424 691247.6015 562662.8277 543101.3805 503197.2249 1.074312096 1.318810529 0.933920483 1.146527159 0.977010441 1.373711077 1.118175538 1.079301224 1 18.94076444 1.452939723 2.59330974 0.999061928 1.136850086 0.09619621 0.133488016 0.802231256 8.994278302 0.20518611 0.033907544 28.37525175 -1.452939723 0.137788158 APPQTHLPSGASS(ph)GTGSASATHGGGSPPGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APPQTHLPSGASSGTGSASATHGGGSPPGTR 31 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4;A0A0G2JJM1;X6REW1;F6S6P2;F6U341;F6TC96;F6WML8;F6VEM6;F6X9W3;A0A1B0GX79;A0A0G2JJR8;F6XTU0;F6U1F2;F6UR09 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 APPQTHLPS(0.01)GAS(0.039)S(0.182)GT(0.182)GS(0.182)AS(0.182)AT(0.153)HGGGS(0.067)PPGT(0.004)R 71.735 0.0071676 173700000 31441 31243 26581 29271 31116 38302 33042 38011 39107 TRUE FALSE 27285.99219 31037.76268 39435.66051 35917.42793 30496.85248 39775.50272 29837.59193 29882.64345 34483.81501 0.791269533 0.900067544 1.14359912 1.041573501 0.884381629 1.153454243 0.865263658 0.866570112 1 15.07363177 0.942122602 20.97718093 1.709815109 0.956645131 0.012847027 0.121625407 677.4523283 472037.5359 67879.0943 0.029263771 8.752308188 -0.942122602 -0.753169977 APPQTHLPSGASSGTGSASATHGGGS(ph)PPGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 APPQTHLPSGASSGTGSASATHGGGSPPGTR 31 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4;A0A0G2JJM1;X6REW1;F6S6P2;F6U341;F6TC96;F6WML8;F6VEM6;F6X9W3;A0A1B0GX79;A0A0G2JJR8;F6XTU0;F6U1F2;F6UR09 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 APPQTHLPSGAS(0.001)S(0.001)GT(0.001)GS(0.001)ASAT(0.003)HGGGS(0.837)PPGT(0.157)R;APPQTHLPSGASSGTGSASAT(0.002)HGGGS(0.715)PPGT(0.282)R;APPQTHLPSGASSGTGSAS(0.001)AT(0.027)HGGGS(0.846)PPGT(0.127)R;APPQTHLPSGASSGTGSASATHGGGS(0.973)PPGT(0.026)R;APPQTHLPS(0.009)GAS(0.039)S(0.036)GT(0.036)GS(0.036)AS(0.036)AT(0.03)HGGGS(0.724)PPGT(0.056)R;APPQTHLPSGAS(0.092)S(0.015)GT(0.015)GS(0.019)AS(0.01)AT(0.032)HGGGS(0.815)PPGT(0.003)R;APPQTHLPSGASSGTGSASAT(0.006)HGGGS(0.981)PPGT(0.012)R 174.69 4.31E-13 27468281000 1237465 1312704 448337 908084 1421930 1509683 1236308 1420245 1331230 TRUE FALSE 1073930.865 1304080.761 665154.2728 1114278.351 1393636.375 1567761.482 1116411.04 1116536.659 1173853.506 0.914876396 1.110939955 0.566641638 0.94924822 1.18723194 1.335568258 0.951065048 0.951172061 1 20.16282094 3.470192661 24.35202337 1.070531321 0.867016997 0.256386858 0.173003337 191.552336 673246.7133 0.052235383 0.067609101 2952.518725 -3.470192661 -0.203514324 APPQTHLPSGASSGTGSASATHGGGS(ph)PPGTRGPGASVHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APPQTHLPSGASSGTGSASATHGGGSPPGTRGPGASVHDR 40 1 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4;A0A0G2JJM1;X6REW1;F6S6P2;F6U341;F6TC96;F6WML8;F6VEM6;F6X9W3;A0A1B0GX79;A0A0G2JJR8;F6XTU0;F6U1F2;F6UR09 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 APPQTHLPS(0.042)GAS(0.039)S(0.039)GT(0.039)GS(0.039)AS(0.039)AT(0.039)HGGGS(0.646)PPGT(0.038)RGPGAS(0.038)VHDR 41.844 0.046257 118160000 10330 13417 891.35 1102.9 10681 11267 8671.6 10718 706.17 TRUE FALSE 8964.864327 13328.86284 1322.409841 1353.330302 10468.469 11700.44878 7830.629567 8426.039108 622.6873871 14.39705463 21.40538434 2.123713871 2.173370346 16.81175693 18.79024535 12.57553907 13.53173243 1 9.282364247 4.2602293 24.97978884 10 17.90121948 0.222954168 6.425864315 401.1298402 462416.8124 1.68233314 4.442328956 18206.61885 -4.2602293 7.901219475 APPQTHLPSGASSGTGSASATHGGGSPPGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APPQTHLPSGASSGTGSASATHGGGSPPGTR 31 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4;A0A0G2JJM1;X6REW1;F6S6P2;F6U341;F6TC96;F6WML8;F6VEM6;F6X9W3;A0A1B0GX79;A0A0G2JJR8;F6XTU0;F6U1F2;F6UR09 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 0 122.68 4.53E-06 78983000 18018 17191 5774.2 8401.2 19604 21293 13323 17662 16656 FALSE TRUE 15636.87565 17078.07119 8566.622434 10308.82086 19213.91875 22112.15549 12030.93751 13885.11875 14686.94665 1.064678453 1.162806102 0.583281375 0.701903609 1.308230989 1.50556518 0.819158522 0.945405405 1 13.84224688 3.245302654 24.99966089 1.091644839 0.877435481 0.180472282 0.248575439 346.7667315 1285812.841 0.079219448 0.099916335 1759.149113 -3.245302654 -0.214209358 APQPTS(ph)PPASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APQPTSPPASR 11 0 E7ET89;Q86UW9 E7ET89 DTX2 Probable E3 ubiquitin-protein ligase DTX2 1 APQPT(0.287)S(0.709)PPAS(0.004)R 72.29 0.048986 116640000 262510 283120 180020 183090 278190 296280 226110 250490 250110 TRUE FALSE 227818.6384 281260.1661 267078.2741 224663.3829 272654.5633 307678.0833 204181.887 196924.6628 220542.2807 1.032993028 1.275311769 1.211007129 1.018686223 1.236291574 1.395097948 0.925817428 0.892911156 1 17.75069574 2.204559097 24.98132231 0.929280697 1.193157254 0.536966147 0.111623028 133.9825393 98437.67487 0.04521251 0.030484135 160.1618577 -2.204559097 0.263876557 APQS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APQSPR 6 0 P12270 P12270 TPR Nucleoprotein TPR 1 APQS(1)PR 72.879 0.088567 191550000 271970 246610 169510 212680 169230 270490 230320 273780 312060 TRUE FALSE 236028.4754 244990.0027 251485.603 260972.2446 165862.6541 280895.9253 207983.6018 215234.2776 275168.6223 0.857759411 0.890326814 0.913932704 0.948408443 0.602767324 1.020813794 0.755840546 0.782190483 1 18.06995644 APQT(ph)SSS(ph)PPPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 APQT(0.555)S(0.436)S(0.469)S(0.54)PPPVR 82.529 0.078016 854150000 769800 721460 421560 554250 645480 671420 596120 729110 732490 TRUE FALSE 668068.9796 716720.6818 625427.826 680100.9337 632636.2109 697249.9619 538308.3742 573195.5004 645895.8667 1.034329238 1.109653613 0.968310618 1.052957557 0.979470908 1.07950832 0.833429043 0.887442589 1 19.30094206 2.244368226 25 0.899827987 1.035594708 0.530191574 0.057725315 98.83886115 425473.054 0.021248649 0.016006042 175.53682 -2.244368226 0.135766721 APQTS(ph)S(ph)SPPPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 APQT(0.286)S(0.701)S(0.599)S(0.414)PPPVR 80.905 0.027896 725760000 819590 740420 548470 610670 728080 762390 726640 826250 992620 TRUE FALSE 711279.1049 735556.1323 813711.9265 749331.957 713592.6325 791719.6366 656170.5646 649562.8674 875273.5944 0.812636311 0.840372813 0.9296658 0.856111691 0.815279516 0.904539611 0.749674809 0.742125515 1 19.73937452 2.248670322 24.99778463 0.808796005 0.859874856 0.00489113 0.078866753 532.5022685 1316694.125 0.029403052 0.022502136 177.2843183 -2.248670322 0.051078851 APQTSSS(ph)PPPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 APQT(0.001)S(0.015)S(0.015)S(0.969)PPPVR;APQT(0.005)S(0.028)S(0.028)S(0.939)PPPVR;APQT(0.004)S(0.062)S(0.062)S(0.872)PPPVR;APQT(0.001)S(0.027)S(0.027)S(0.946)PPPVR;APQT(0.016)S(0.04)S(0.04)S(0.904)PPPVR;APQT(0.004)S(0.159)S(0.159)S(0.679)PPPVR 171.99 3.88E-05 25627600000 4035640 3467620 2360560 2763140 3443730 3598490 3075940 3657830 3753410 TRUE FALSE 3502319.949 3444840.976 3502134.712 3390553.169 3375206.511 3736926.239 2777635.812 2875631.52 3309686.146 1.058203042 1.040836147 1.058147074 1.024433442 1.019796549 1.129087797 0.839244475 0.868853237 1 21.65826298 2.233317647 24.99999997 0.893004028 1.051578428 0.668258105 0.050418915 70.46786755 336006.7379 0.019798901 0.013797391 171.1266496 -2.233317647 0.1585744 APQTSSS(ph)PPPVRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APQTSSSPPPVRR 13 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 APQTSS(0.047)S(0.953)PPPVRR;APQTS(0.003)S(0.025)S(0.971)PPPVRR 128.45 0.00010116 2072070000 702540 603810 345390 408870 541200 570000 548860 618260 331670 TRUE FALSE 609697.559 599843.5324 512421.7593 501710.1827 530431.1788 591928.2688 495631.6417 486049.9103 292460.3504 2.084718691 2.051025144 1.752106768 1.715481028 1.81368578 2.023960745 1.694696874 1.661934377 1 18.15788152 0.949426021 1.330214353 2.03E-12 1.887584757 0.808234525 0.135053619 1.203719229 1.083837136 3.753000783 0.042025144 8.900738079 -0.949426021 1.887584757 APRPSAPS(ph)PPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 APRPSAPSPPPR 12 1 Q8IV50 Q8IV50 LYSMD2 LysM and putative peptidoglycan-binding domain-containing protein 2 1 APRPS(0.002)APS(0.998)PPPR;APRPS(0.013)APS(0.987)PPPR;APRPSAPS(1)PPPR;APRPSAPS(1)PPPR 106.6 0.0011535 1702110000 414144 443273 279854 314478 383510 374930 404231 436658 331961 TRUE FALSE 359413.8211 440361.1105 415192.3305 385885.0364 375878.9013 389353.7997 365028.7398 343282.0848 292716.9488 1.227854494 1.504392255 1.418408918 1.318287301 1.284103647 1.330137532 1.24703657 1.172744135 1 18.15914676 0.180590045 0.541469072 1.04E-10 1.380064654 0.714311163 0.072848586 6.347910475 0.613372598 7.103671598 0.043591221 1.515619013 -0.180590045 1.380064654 APRPTRPDK ddPTM_MDA-MB-175_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 ;;;;; 107.45 0.0015584 9584300000 5171050 4797200 3134810 3986200 4760350 4606590 5568860 6542680 5382360 FALSE TRUE 4487682.641 4765686.877 4650814.601 4891327.635 4665628.348 4783808.498 5028792.814 5143578.797 4746063.532 0.945558906 1.004134657 0.979930962 1.030607282 0.983052232 1.007952899 1.059571323 1.083756836 1 22.17829998 2.338341642 4.032295761 1.055831684 0.991717237 0.441186578 0.029736312 0.179099335 5.398151158 0.011396258 0.00849747 217.9423561 -2.338341642 -0.064114447 APS(ph)APPGTGALPPAAPSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APSAPPGTGALPPAAPSGR 19 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 APS(1)APPGTGALPPAAPSGR;APS(1)APPGTGALPPAAPSGR 159.26 3.54E-11 236648000 112337 121085 71547 55653 104429 116931 115947 108387 133830 TRUE FALSE 97491.38082 120289.5847 106147.3685 68289.86425 102351.0672 121429.4112 104702.4778 85209.28352 118008.7699 0.826136743 1.019327503 0.89948712 0.578684655 0.867317466 1.028986332 0.887243193 0.722058908 1 16.84853455 3.988579908 24.92734332 0.837052288 0.931900947 0.049860846 0.135659919 1390.21394 3034529.285 0.035874039 0.067234786 9740.469883 -3.988579908 0.094848659 APS(ph)AS(ph)PLALHASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APSASPLALHASR 13 0 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 2 APS(1)AS(1)PLALHASR;APS(1)AS(1)PLALHASR 66.12 0.029967 344170000 374440 413730 141747 243400 429540 482210 347930 397650 405860 TRUE FALSE 324956.8053 411012.1804 210296.3233 298667.6901 420992.9944 500760.9307 314187.8022 312615.642 357879.6932 0.908005711 1.148464661 0.587617368 0.834547743 1.176353402 1.399243769 0.877914585 0.8735216 1 18.44911516 3.260468859 24.96831121 1.044051016 0.869427694 0.186163209 0.200629987 500.87222 570828.5571 0.062671567 0.080839271 1821.666445 -3.260468859 -0.174623322 APS(ph)ASPLALHASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APSASPLALHASR 13 0 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 1 APS(0.556)AS(0.444)PLALHASR 107.34 0.00040035 0 92818 91657 47291 67606 93086 109100 76112 101430 94030 TRUE FALSE 80551.86613 91054.89913 70161.08578 82956.97559 91233.77072 113297.1476 68730.66995 79739.98383 82913.88052 0.971512437 1.098186438 0.846192282 1.000519757 1.100343756 1.366443675 0.828940456 0.961720563 1 16.33932602 APS(ph)DS(ph)SLGTPSDGRPELR ddPTM_MDA-MB-175_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(0.965)DS(0.719)S(0.298)LGT(0.011)PS(0.007)DGRPELR 129.32 0.00039839 0 193800 209790 156910 160620 214860 238480 229500 227580 228090 TRUE FALSE 168188.839 208411.8757 232792.2008 197091.2259 210584.7064 247654.4799 207243.1253 178913.788 201125.46 0.83623843 1.036228211 1.157447698 0.979941703 1.047031571 1.231343261 1.03041716 0.889563102 1 17.6177362 1.90474007 7.070814945 0.941973738 1.055807029 0.133180793 0.106316522 0.452198803 29.04491136 0.051604087 0.028236387 80.3045347 -1.90474007 0.113833292 APS(ph)DSSLGTPSDGRPELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 APSDSSLGTPSDGRPELR 18 1 Q15642;M0R0F9;W4VSQ9;Q15642-4;Q15642-2;Q15642-3;M0R2H7;Q15642-5 Q15642 TRIP10 Cdc42-interacting protein 4 1 APS(0.747)DS(0.211)S(0.042)LGTPSDGRPELR;APS(0.689)DS(0.156)S(0.156)LGTPSDGRPELR;APS(0.904)DS(0.081)S(0.015)LGTPSDGRPELR;APS(0.994)DS(0.004)S(0.002)LGTPSDGRPELR;APS(0.892)DS(0.046)S(0.062)LGTPSDGRPELR 184.34 3.56E-14 5032940000 1461290 1591490 1247605 1217420 1557450 1804790 1648880 1911610 1876290 TRUE FALSE 1268176.824 1581035.397 1850950.951 1493853.818 1526459.792 1874221.439 1488971.871 1502827.078 1654477.134 0.76651215 0.955610304 1.118752815 0.902915965 0.922623686 1.132817977 0.899965216 0.908339588 1 20.65794392 4.727105944 5.095697984 0.976437682 0.758273238 0.388596327 0.084431917 0.165248056 13.79475082 0.020661552 0.12425764 53346.50163 -4.727105944 -0.218164444 APS(ph)IDGKEELDLAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APSIDGKEELDLAEK 15 1 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;B5MCW3;Q9H0E9-3;Q9H0E9;H0YAH7;H0YA84 H7C128 BRD8 Bromodomain-containing protein 8 1 APS(1)IDGKEELDLAEK 124.2 5.94E-05 142250000 416140 319820 284190 299040 325130 257620 426880 512310 471150 TRUE FALSE 361146.0446 317719.0814 421625.2346 366941.6025 318660.5491 267530.8081 385481.2433 402756.4933 415451.1837 0.869286354 0.764756712 1.014861074 0.883236387 0.767022845 0.643952451 0.927861704 0.969443605 1 18.66431944 2.014331941 24.99859681 0.972373291 0.826293267 0.339301388 0.095433784 276.0137735 481437.2226 0.041119984 0.027710124 103.3551069 -2.014331941 -0.146080024 APS(ph)LTDLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APSLTDLVK 9 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 APS(0.997)LT(0.003)DLVK;APS(1)LTDLVK 146.71 9.87E-05 455363000 1093600 1008030 641475 745570 955470 776960 1000150 1280140 1041530 TRUE FALSE 949077.9892 1001408.185 951694.4556 914863.0638 936458.0163 806850.154 903155.6069 1006392.023 918401.5099 1.033402035 1.090381684 1.03625097 0.996147169 1.019660798 0.878537486 0.983399523 1.095808328 1 19.80876549 3.934935154 3.96977106 1.001635292 1.062584612 0.205660389 0.054152113 0.415411783 12.82035247 0.016124768 0.030915255 8608.652043 -3.934935154 0.06094932 APS(ph)PAPSSVPLGSEKPSNVSQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 APSPAPSSVPLGSEKPSNVSQDR 23 1 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 APS(0.997)PAPS(0.002)S(0.001)VPLGSEKPSNVSQDR;APS(0.999)PAPS(0.001)S(0.001)VPLGSEKPSNVSQDR;APS(0.729)PAPS(0.156)S(0.114)VPLGSEKPSNVSQDR 219.19 1.29E-32 3140800000 1612350 1555790 1106718 1277650 1421170 1587240 1558840 1943440 1809820 TRUE FALSE 1399273.862 1545569.913 1641930.527 1567759.96 1392891.497 1648302.15 1407663.937 1527850.48 1595865.141 0.876812098 0.968484036 1.028865462 0.982388749 0.872812784 1.032858045 0.882069481 0.957380696 1 20.60590731 5.49378211 0.005675873 1.268154026 0.632623139 0.012106055 0.05987691 776228.6081 875.4589823 47440.1649 50631.1461 311732.5199 -5.49378211 -0.635530887 APS(ph)PARPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 71.03 0.030158 1381280000 2125920 2170430 1446940 1719570 1840920 1742600 2163350 2667800 2139980 TRUE FALSE 1844974.286 2156172.302 2146685.024 2110024.65 1804289.294 1809638.95 1953548.65 2097311.731 1886994.002 0.977731929 1.142649261 1.13762154 1.118193618 0.956171186 0.959006201 1.035270196 1.11145649 1 20.84765841 3.265613983 24.9990846 1.023813212 1.100632875 0.281603786 0.06298293 329.5987427 304568.5307 0.019444095 0.02509568 1843.37623 -3.265613983 0.076819662 APS(ph)PEPAAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 APSPEPAAPR 10 0 P20749 P20749 BCL3 B-cell lymphoma 3 protein 1 APS(1)PEPAAPR;APS(1)PEPAAPR;APS(1)PEPAAPR;APS(1)PEPAAPR 113.69 0.0015264 6147890000 4108650 4273160 3167870 3506780 4320570 4659340 4336030 4621800 4897650 TRUE FALSE 3565681.493 4245089.331 4699862.528 4303047.997 4234599.11 4838587.825 3915522.478 3633464.037 4318655.396 0.825646217 0.982965516 1.088269866 0.996386051 0.980536468 1.120392201 0.906653141 0.841341506 1 22.04215077 2.043297927 24.99979174 0.898735446 1.002408096 0.161388014 0.086267334 188.1321425 108624.844 0.034786313 0.02345291 110.4836281 -2.043297927 0.103672651 APS(ph)PGAYK ddPTM_MDA-MB-175_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 106.88 0.0043116 929530000 2036700 1873510 1330770 1594420 1789060 1497320 1990880 2371630 2502400 TRUE FALSE 1767544.935 1861202.789 1974334.823 1956457.43 1753461.206 1554922.869 1797804.764 1864475.381 2206569.123 0.801037645 0.843482658 0.894753218 0.886651322 0.794655009 0.704678976 0.814751165 0.844965771 1 21.07337351 1.22890412 3.349573791 1.030630696 0.821401434 0.531667978 0.052647491 0.307439693 4.743073778 0.170063989 0.014949241 16.9396378 -1.22890412 -0.209229263 APS(ph)PGDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APSPGDYK 8 0 P55198 P55198 MLLT6 Protein AF-17 1 APS(0.998)PGDY(0.002)K 75.197 0.040923 194560000 833830 375560 273450 325330 368190 323590 433860 518660 628100 TRUE FALSE 723637.2528 373092.9216 405691.3346 399201.1489 360863.7394 336038.7167 391784.324 407748.5952 553846.7335 1.306565895 0.673639292 0.732497476 0.720779098 0.651558847 0.606735937 0.707387622 0.736211971 1 19.07912727 4.741451552 24.83659142 0.721862913 1.306566128 0.750839846 0.104569144 122.8645544 1055493.491 0.025288419 0.171575491 55138.06898 -4.741451552 0.584703215 APS(ph)PHVVQENLHSEVVEVCTSSTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APSPHVVQENLHSEVVEVCTSSTLK 25 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 APS(0.962)PHVVQENLHS(0.038)EVVEVCTSSTLK 95.459 0.016543 193530000 70277 60742 43066 70197 62542 56558 72581 95697 117350 TRUE FALSE 60989.71639 60342.9818 63892.86165 86136.30174 61297.53656 58733.82286 65542.10579 75232.94126 103477.0167 0.589403506 0.583153474 0.617459448 0.832419647 0.592378274 0.567602592 0.633397714 0.727049771 1 16.65895084 1.216635252 2.187189567 1.122643392 0.632555878 0.705498266 0.07497112 0.417140379 1.924685842 0.415075051 0.020861313 16.4677874 -1.216635252 -0.490087514 APS(ph)PLGPTRDPVATFLETCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APSPLGPTRDPVATFLETCR 20 1 I3L2L9;E7EVV8;Q0VG06-3;Q0VG06 I3L2L9 C17orf70;FAAP100 Fanconi anemia-associated protein of 100 kDa 1 APS(0.995)PLGPT(0.005)RDPVATFLETCR;APS(0.999)PLGPT(0.001)RDPVATFLETCR 169.6 6.38E-12 293570000 58898 56966 37861 39837 59426 63491 66100 68838 65684 TRUE FALSE 51114.48007 56591.7866 56170.70624 48882.59972 58243.53886 65933.53985 59689.63217 54117.5294 57918.91235 0.882517955 0.977086487 0.969816317 0.843983385 1.005604845 1.138376692 1.030572394 0.934367156 1 15.82174689 3.031904614 24.61196172 1.018650379 0.926043875 0.40279299 0.062430252 203.4827406 156969.8655 0.020406905 0.023139077 1076.228811 -3.031904614 -0.092606505 APS(ph)PLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APSPLPK 7 0 Q9BSL1 Q9BSL1 UBAC1 Ubiquitin-associated domain-containing protein 1 1 APS(1)PLPK 66.435 0.071206 177680000 860230 778720 609170 646590 709920 662380 861670 946050 1145300 TRUE FALSE 746548.426 773604.537 903766.6496 793408.142 695793.9809 687862.1872 778105.376 743744.5697 1009903.939 0.739227165 0.766017942 0.894903579 0.785627337 0.68897046 0.681116452 0.770474642 0.736450806 1 19.94578664 1.23540893 24.97358963 1.000000336 0.758293399 0.625391217 0.058897385 64.0660606 507561.9284 0.107287001 0.015467849 17.19526723 -1.23540893 -0.241706937 APS(ph)PPLSQVFQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 APSPPLSQVFQTR 13 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 APS(0.991)PPLS(0.009)QVFQTR;APS(0.999)PPLS(0.001)QVFQTR;APS(0.768)PPLS(0.232)QVFQTR;APS(0.999)PPLS(0.001)QVFQTR;APS(0.983)PPLS(0.017)QVFQTR;APS(0.987)PPLS(0.013)QVFQTR;APS(0.999)PPLS(0.001)QVFQTR;APS(1)PPLSQVFQTR 198.89 1.28E-07 9195834000 693017 621135 434548 477312 645115 648692 629616 688726 592668 TRUE FALSE 601433.0476 617054.7233 644696.8663 585692.9849 632278.4736 673647.601 568555.9372 541447.3046 522603.4642 1.150840147 1.180732172 1.233625321 1.120721589 1.209862768 1.289022456 1.087929905 1.036057626 1 18.99535716 2.0402959 6.280651916 1.03215946 1.195530866 0.727298459 0.046334287 0.093271711 9.712571553 0.019748477 0.012986849 109.722552 -2.0402959 0.163371406 APS(ph)PPVEHPR ddPTM_MDA-MB-175_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 107.17 0.0014944 2819750000 627385 605205 452492 507589 506120 605466 603742 663978 656984 TRUE FALSE 544474.4827 601229.3685 671318.6447 622844.8405 496049.2022 628758.6688 545191.1938 521991.4718 579316.1 0.93985733 1.0378261 1.158812339 1.075138151 0.856266902 1.085346444 0.941094497 0.901047756 1 19.14399123 3.276317867 24.99988068 0.955043598 1.059395825 0.264068322 0.079409681 215.6347187 142774.8991 0.022882459 0.02954049 1889.373704 -3.276317867 0.104352227 APS(ph)PRPGPGPLR ddPTM_MDA-MB-175_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 105.46 0.0012279 6269950000 2302660 3059690 1439304 2449980 2580380 2810660 2053690 2496500 1755840 TRUE FALSE 1998357.647 3039590.695 2135356.229 3006285.405 2529035.486 2918787.909 1854523.46 1962642.903 1548266.595 1.290706428 1.963221776 1.379191565 1.941710435 1.633462541 1.885197238 1.197806286 1.26763886 1 20.56222248 2.222747507 24.25572919 1.180360936 1.690820698 0.53762373 0.22994595 120.4513183 184758.1996 0.084726379 0.057358642 167.0119347 -2.222747507 0.510459762 APS(ph)PSGLMS(ph)PSRLPGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 APSPSGLMSPSRLPGSR 17 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 2 APS(0.995)PS(0.006)GLMS(0.985)PS(0.015)RLPGSR;APS(0.999)PS(0.001)GLMS(0.987)PS(0.013)RLPGSR;APS(0.963)PS(0.115)GLMS(0.827)PS(0.091)RLPGS(0.003)R;APS(0.991)PS(0.009)GLMS(0.913)PS(0.087)RLPGSR 158.37 1.90E-09 703673000 719890 723660 561407 615914 840500 988590 870760 963370 582176 TRUE FALSE 624754.7125 718906.2298 832905.303 755766.6874 823775.6944 1026621.697 786313.8292 757360.8225 513351.8165 1.217010815 1.400416258 1.622484379 1.472219759 1.604700067 1.99984039 1.531725035 1.475325105 1 18.96958836 1.205840355 2.755078044 0.84732899 1.561072953 0.42805808 0.197651514 0.528265574 4.366514601 0.904411658 0.054001834 16.06350655 -1.205840355 0.713743963 APS(ph)PSGLMSPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 APSPSGLMSPSR 12 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 APS(0.905)PS(0.095)GLMSPSR;APS(0.974)PS(0.026)GLMSPSR;APS(0.951)PS(0.049)GLMSPSR;APS(0.844)PS(0.156)GLMSPSR;APS(0.98)PS(0.02)GLMSPSR;APS(0.944)PS(0.056)GLMSPSR;APS(0.86)PS(0.14)GLMSPSR;APS(0.982)PS(0.018)GLMSPSR;APS(0.992)PS(0.008)GLMSPSR;APS(0.992)PS(0.008)GLMSPSR;APS(0.962)PS(0.038)GLMSPSR;APS(0.985)PS(0.015)GLMSPSR 207.47 8.20E-08 8942990000 2493900 2500686 1705942 1858234 2459470 2600350 2120300 2449090 2514960 TRUE FALSE 2164324.796 2484258.829 2530941.257 2280174.431 2410531.359 2700387.147 1914673.632 1925371.162 2217644.294 0.975956695 1.120224211 1.141274669 1.028196649 1.086978361 1.217682725 0.863381759 0.868205585 1 21.08059655 2.222029323 24.99983038 0.899747186 1.094891547 0.580816366 0.073707486 156.0602441 236003.8944 0.029357348 0.019855884 166.7359785 -2.222029323 0.195144361 APS(ph)PSINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 APSPSINR 8 0 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 APS(0.903)PS(0.097)INR;APS(0.986)PS(0.014)INR;APS(0.99)PS(0.01)INR;APS(0.998)PS(0.002)INR 170.69 0.00030812 1436400000 2314200 2072190 1015840 1167490 1702000 1584970 1472440 1830520 1567940 TRUE FALSE 2008372.607 2058577.647 1507103.622 1432586.448 1668133.53 1645944.822 1329642.995 1439077.543 1382579.919 1.452626773 1.488939351 1.090066188 1.036168997 1.206536784 1.190488013 0.961711491 1.040863912 1 20.39893145 4.229934621 9.180345638 1.073160963 1.471341797 0.822165909 0.076500458 0.051979446 40.87683084 0.020981653 0.047133956 16979.88017 -4.229934621 0.398180834 APS(ph)PSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 APSPSSR 7 0 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 APS(0.949)PS(0.048)S(0.003)R;APS(0.969)PS(0.028)S(0.003)R;APS(0.902)PS(0.097)S(0.001)R;APS(0.98)PS(0.02)SR;APS(0.763)PS(0.236)S(0.001)R;APS(0.826)PS(0.165)S(0.009)R;APS(0.912)PS(0.081)S(0.007)R;APS(0.999)PS(0.001)SR 151.97 0.0019354 23021785000 1904951 1415346 963680 1125923 884656 1416632 1397819 1519084 1534979 TRUE FALSE 1653206.899 1406048.499 1429718.871 1381581.026 867053.0764 1471130.75 1262258.729 1194239.708 1353515.531 1.221417014 1.038812239 1.056300307 1.020735259 0.640593371 1.086896098 0.932577942 0.882324348 1 20.36828001 4.537632996 1.017836296 0.918919952 1.290989421 0.373076885 0.120265517 1.485594244 1.584136518 0.038546211 0.562276341 34485.21959 -4.537632996 0.37206947 APS(ph)PTAEQPPGGGDSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APSPTAEQPPGGGDSAR 17 0 Q15742;Q15742-2;Q15742-3 Q15742 NAB2 NGFI-A-binding protein 2 1 APS(0.998)PT(0.002)AEQPPGGGDSAR;APS(0.991)PT(0.009)AEQPPGGGDSAR 281.96 5.52E-36 881490000 172197 176876 108003 119300 185380 182704 173045 211332 199655 TRUE FALSE 149440.7302 175714.0899 160233.612 146388.8884 181691.3007 189732.7411 156263.1225 166140.2964 176052.0133 0.848844198 0.998080548 0.910149274 0.831509311 1.032031939 1.077708443 0.887596339 0.943700065 1 17.4256422 3.228303739 24.99999436 0.979573164 0.905284264 0.308850336 0.066507637 327.456432 798136.3789 0.020999793 0.024073839 1691.623612 -3.228303739 -0.0742889 APS(ph)PTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 APSPTK 6 0 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BUL0;H3BTY0;H3BUG0;H3BNU7;H3BNI3;H3BTR6;H3BP82;H3BTV0;P59025;Q96FF9;B5MBX0 Q15287;Q96FF9 RNPS1;RTP1;CDCA5 RNA-binding protein with serine-rich domain 1;Receptor-transporting protein 1;Sororin 1 APS(0.979)PT(0.021)K;APS(0.953)PT(0.047)K;APS(0.991)PT(0.009)K;APS(0.96)PT(0.04)K;APS(0.994)PT(0.006)K;APS(0.96)PT(0.04)K 98.458 0.041866 27904300000 45185400 32811200 22744300 26741400 19832000 25427000 38553700 45325000 45324700 TRUE FALSE 39214034.9 32595661.07 33743519.56 32813443.59 19437382 26405193.14 34814768.11 35632601.47 39966465.6 0.981173449 0.815575272 0.844295813 0.821024404 0.48634228 0.660683719 0.871099498 0.891562487 1 25.25228666 1.705780978 2.097336345 0.978033921 0.766240851 0.240354547 0.13103367 0.478424277 4.227656529 0.149888377 0.040053797 50.79032337 -1.705780978 -0.211793069 APS(ph)PTKPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APSPTKPLR 9 1 Q96FF9;B5MBX0 Q96FF9 CDCA5 Sororin 1 APS(0.972)PT(0.028)KPLR 95.618 0.0057751 0 154400 76614 62424 75964 97527 85495 88529 111190 166940 TRUE FALSE 133995.6488 76110.71759 92612.4552 93212.78724 95586.40351 88784.04797 79943.47121 87412.88378 147204.5434 0.910268431 0.517040547 0.629141282 0.633219499 0.649344112 0.603133884 0.543077471 0.593819197 1 17.16746267 1.235744937 24.9921283 1.000000507 0.624198659 0.535481221 0.10646031 56.38586316 500386.7491 0.161791529 0.023957932 17.20857613 -1.235744937 -0.375801848 APS(ph)PTKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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(0.991)PT(0.009)KR;APS(0.782)PT(0.218)KR;APS(0.999)PT(0.001)KR;APS(0.728)PT(0.272)KR;APS(0.953)PT(0.047)KR;APS(0.991)PT(0.009)KR;APS(0.766)PT(0.234)KR 120.99 0.0027451 12980310000 8600120 6542450 4688400 5575830 4089310 5142090 7502770 8413330 7268760 TRUE FALSE 7463592.352 6499472.215 6955725.922 6841907.423 4007940.732 5339909.53 6775152.52 6614204.852 6409455.473 1.164465902 1.014044367 1.085228839 1.067470934 0.625316885 0.833129983 1.057055868 1.031944894 1 22.61177036 3.434584598 24.99978193 0.924259406 1.079832024 0.313317788 0.126560894 210.8423956 123916.2768 0.040139463 0.051819871 2720.098291 -3.434584598 0.155572618 APS(ph)PTSSAGEEGTKKPEPLSPASYHQPEGVAR ddPTM_MDA-MB-175_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(0.67)PT(0.148)S(0.033)S(0.148)AGEEGTKKPEPLSPASYHQPEGVAR 225.44 2.04E-36 397470000 295550 246390 100460 199120 248620 179640 297050 379360 255890 TRUE FALSE 256492.3187 244771.4479 149042.792 244333.2394 243672.9484 186550.867 268242.1367 298236.8162 225638.9757 1.136737649 1.084792408 0.660536556 1.08285033 1.079924014 0.826767036 1.188811179 1.321743352 1 17.78365677 2.139329233 8.904983529 1.204658605 0.97854173 0.227818029 0.162381842 0.338679066 27.44616413 0.065629855 0.044217931 137.8253909 -2.139329233 -0.226116876 APS(ph)RQDVYGPQPQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 APSRQDVYGPQPQVR 15 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 APS(1)RQDVYGPQPQVR;APS(1)RQDVYGPQPQVR;APS(1)RQDVYGPQPQVR;APS(1)RQDVYGPQPQVR;APS(1)RQDVYGPQPQVR;APS(1)RQDVYGPQPQVR 270.94 1.33E-33 10532290000 2299380 2167410 1301172 1223738 2126030 2719790 1499410 1866530 962315 TRUE FALSE 1995511.107 2153172.141 1930423.131 1501606.417 2083726.163 2824422.081 1353997.449 1467387.085 848551.217 2.351668429 2.537468685 2.2749636 1.769612 2.455628041 3.32852281 1.595657895 1.729285228 1 19.69464222 1.749800178 1.96445624 1.181252274 2.403074138 0.514227291 0.442622575 0.279490289 2.083199157 0.467982465 0.128796729 56.20826477 -1.749800178 1.221821864 APS(ph)SDEECFFDLLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 APSSDEECFFDLLTK 15 0 A0A0A0MSK4;A0A0A0MRC4;Q86YR5-4;Q86YR5 A0A0A0MSK4 GPSM1 G-protein-signaling modulator 1 1 APS(0.987)S(0.013)DEECFFDLLTK;APS(0.871)S(0.129)DEECFFDLLTK;APS(0.974)S(0.026)DEECFFDLLTK;APS(0.986)S(0.014)DEECFFDLLTK 153.24 2.82E-06 137683000 224841 163898 108383.8 156192 173189 123052 229528 239827 195674 TRUE FALSE 195127.6922 162821.3432 160798.5682 191657.7808 169742.8777 127785.8901 207268.4099 188541.8624 172541.6426 1.13090202 0.943664038 0.931940636 1.110791447 0.983779192 0.740608981 1.201266006 1.092732511 1 17.39658507 APS(ph)VATVGSICDLNLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 APSVATVGSICDLNLK 16 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-5;O75369-4;A0A0C4DGA1 O75369-8 FLNB Filamin-B 1 APS(1)VATVGSICDLNLK;APS(1)VATVGSICDLNLK;APS(1)VATVGSICDLNLK 264.52 5.36E-27 195792000 242603 243143 201446 233073 206819 216390 264152 287993 728900 TRUE FALSE 210542.3989 241545.7776 298865.9594 285995.7869 202703.7065 224714.6633 238534.5797 226407.9381 642730.2724 0.327575047 0.375812044 0.464994372 0.444970152 0.315379118 0.349625143 0.371127034 0.352259646 1 19.2938539 1.237221643 24.99970718 1.000000754 0.376283982 0.945541035 0.047121587 7.616004844 142141.8173 0.074286506 0.012248021 17.26718903 -1.237221643 -0.623716773 APSAS(ph)PLALHASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APSASPLALHASR 13 0 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 1 APS(0.045)AS(0.955)PLALHASR;APS(0.19)AS(0.81)PLALHASR 148.24 2.78E-05 1209390000 710390 851480 276570 410320 857870 878620 766990 800030 600160 TRUE FALSE 616510.1616 845886.5718 410320.1771 503489.4273 840800.0654 912421.0799 692607.4279 628949.8103 529209.7685 1.164963684 1.598395612 0.775345055 0.95139859 1.588784099 1.724119875 1.308757829 1.188469767 1 19.01348017 3.247159791 24.99787081 1.354441298 1.131717874 0.148859285 0.283872272 441.321788 1282918.635 0.088349085 0.112234594 1766.687721 -3.247159791 -0.222723424 APSEEELHGDQTDFGQGS(ph)QSPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APSEEELHGDQTDFGQGSQSPQK 23 0 Q8TE77;Q8TE77-2;A0A087WWG1;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 APSEEELHGDQTDFGQGS(1)QSPQK 281.55 3.53E-52 706200000 206520 160200 172290 223390 200460 143270 164110 187130 595000 TRUE FALSE 179227.8587 159147.6357 255610.0203 274114.1138 196471.2382 148781.6896 148194.6375 147113.7057 524659.7778 0.341607774 0.303334927 0.48719195 0.522460698 0.374473605 0.283577465 0.282458545 0.280398292 1 19.00102267 1.234367372 24.99907372 1.000000941 0.357557282 0.849630802 0.084685906 52.15038197 310865.1267 0.176864495 0.023422211 17.15407766 -1.234367372 -0.64244366 APSEEELHGDQTDFGQGS(ph)QSPQKQEEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APSEEELHGDQTDFGQGSQSPQKQEEQR 28 1 Q8TE77;Q8TE77-2;A0A087WWG1;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 APSEEELHGDQTDFGQGS(0.602)QS(0.398)PQKQEEQR;APSEEELHGDQTDFGQGS(0.651)QS(0.349)PQKQEEQR 366.1 1.32E-127 1469780000 821600 574090 498530 656330 642530 578340 726210 962260 885310 TRUE FALSE 713023.4783 570318.765 739620.7755 805359.7579 629744.9101 600589.114 655782.266 756488.1873 780649.6603 0.913371919 0.730569414 0.94744264 1.031653248 0.806693376 0.769345258 0.840046822 0.969049531 1 19.57431572 1.642038658 4.586465011 0.992005968 0.86182739 0.25449983 0.087140208 0.222672494 10.4256166 0.063624052 0.023692042 43.85697345 -1.642038658 -0.130178578 APSEEELHGDQTDFGQGSQS(ph)PQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APSEEELHGDQTDFGQGSQSPQK 23 0 Q8TE77;Q8TE77-2;A0A087WWG1;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 APSEEELHGDQTDFGQGSQS(1)PQK 322.35 6.11E-74 582560000 285570 207370 185990 296740 256690 211460 230430 316660 820920 TRUE FALSE 247831.201 206007.7728 275935.3861 364119.3524 251582.3712 219595.003 208082.9341 248944.7233 723871.7728 0.342368925 0.284591527 0.381193737 0.503016371 0.347551018 0.303361743 0.287458279 0.343907212 1 19.46537463 1.238323865 24.99998203 1.000000722 0.348347116 0.91527057 0.062230289 1.612460872 169907.3005 0.092046852 0.016295054 17.31106811 -1.238323865 -0.651653607 APSEEELHGDQTDFGQGSQS(ph)PQKQEEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 APSEEELHGDQTDFGQGSQSPQKQEEQR 28 1 Q8TE77;Q8TE77-2;A0A087WWG1;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 APSEEELHGDQTDFGQGS(0.025)QS(0.975)PQKQEEQR;APSEEELHGDQTDFGQGS(0.036)QS(0.964)PQKQEEQR;APSEEELHGDQTDFGQGS(0.002)QS(0.998)PQKQEEQR;APSEEELHGDQTDFGQGS(0.117)QS(0.883)PQKQEEQR;APSEEELHGDQTDFGQGS(0.007)QS(0.993)PQKQEEQR;APSEEELHGDQTDFGQGS(0.023)QS(0.977)PQKQEEQR 311.82 6.46E-83 10561910000 3053959 2538339 2126316 2353032 2711692 2095235 2911141 3496989 3349156 TRUE FALSE 2650370.58 2521664.484 3154609.53 2887323.879 2657734.635 2175840.046 2628818.994 2749185.116 2953222.593 0.897450327 0.85386875 1.068192265 0.977685829 0.899943892 0.736768048 0.890152676 0.930910227 1 21.49385867 3.120726257 6.88177958 0.887734313 0.950625033 0.104202995 0.084352285 0.540074445 30.40920229 0.027285942 0.031046152 1320.463063 -3.120726257 0.06289072 APSEEELHGDQTDFGQGSQSPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APSEEELHGDQTDFGQGSQSPQK 23 0 Q8TE77;Q8TE77-2;A0A087WWG1;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 170.56 7.18E-12 111880000 144070 120770 96764 120600 132430 131500 120460 145880 214550 FALSE TRUE 125030.7845 119976.6539 143559.3941 147984.0733 129794.9021 136558.8901 108777.8077 114684.6972 189186.1434 0.660887643 0.634172523 0.758826156 0.782214123 0.686069813 0.721822897 0.574977669 0.606200302 1 17.5294469 1.230963137 24.99895675 1.000000577 0.675949555 0.711065757 0.064463569 172.4833125 567495.7881 0.183130139 0.017701707 17.02014035 -1.230963137 -0.324051023 APSEEELHGDQTDFGQGSQSPQKQEEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APSEEELHGDQTDFGQGSQSPQKQEEQR 28 1 Q8TE77;Q8TE77-2;A0A087WWG1;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 88.595 0.0019859 92687000 75407 60365 27286 38920 54113 46234 82762 83194 19766 FALSE TRUE 65441.77389 59968.45834 40481.60087 47757.38085 53036.25717 48012.6519 74735.75398 65403.61052 17429.286 3.754701937 3.440672116 2.322619577 2.740065248 3.042939176 2.754711346 4.287941227 3.752512325 1 14.08922585 APSGHLAPS(ph)PPAFDGELDLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 APSGHLAPSPPAFDGELDLQR 21 0 Q9P2Y4;G3V2Q8;G3V452;G3V2W3;G3V2E3;G3V4M7;G3V3F2 Q9P2Y4 ZNF219 Zinc finger protein 219 1 APSGHLAPS(1)PPAFDGELDLQR;APSGHLAPS(1)PPAFDGELDLQR;APSGHLAPS(1)PPAFDGELDLQR;APSGHLAPS(1)PPAFDGELDLQR 143.32 8.90E-08 1118930000 1132940 998820 536740 749853 1022722 956940 948305 990340 827639 TRUE FALSE 983219.1085 992258.6857 796309.2593 920118.5844 1002371.833 993754.101 856338.5271 778563.4978 729796.4603 1.347251134 1.35963757 1.091138835 1.260787952 1.37349506 1.361686655 1.173393643 1.066822793 1 19.47713463 1.844346194 2.351266253 1.019302952 1.293124386 0.627631195 0.084188052 0.200732977 2.052810479 0.069902673 0.025384344 69.87892161 -1.844346194 0.273821435 APSLPAPPYAGAPGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 APSLPAPPYAGAPGSPR 17 0 Q69YU3 Q69YU3 ANKRD34A Ankyrin repeat domain-containing protein 34A 1 APSLPAPPYAGAPGS(1)PR;APSLPAPPYAGAPGS(1)PR;APSLPAPPYAGAPGS(1)PR;APSLPAPPYAGAPGS(1)PR 180.03 9.26E-10 1310350000 332328 353845 259716 258111 338367 353625 336209 365397 323796 TRUE FALSE 288410.0128 351520.5689 385315.5263 316719.0475 331634.1587 367229.1826 303603.5029 287259.6951 285517.2057 1.010131813 1.231171228 1.349535224 1.109281827 1.161520749 1.286189327 1.063345735 1.006102922 1 18.12321816 2.066483934 6.029312093 1.012224883 1.19486028 0.434015301 0.092161288 0.176640382 11.85239589 0.038140888 0.025301941 116.5423936 -2.066483934 0.182635397 APSPHVVQENLHS(ph)EVVEVCTSSTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APSPHVVQENLHSEVVEVCTSSTLK 25 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 APS(0.366)PHVVQENLHS(0.634)EVVEVCTSSTLK 119.83 0.00066108 51296000 29174 21346 21374 26850 23539 24959 29995 35727 38561 TRUE FALSE 25318.58198 21205.77672 31710.53789 32946.70288 23070.61995 25919.18888 27086.08952 28087.05908 34002.36251 0.744612436 0.62365598 0.932598077 0.968953345 0.6785005 0.762276118 0.79659434 0.826032576 1 15.05334737 1.171071998 2.33462589 1.085261982 0.788130089 0.29474754 0.102927463 1.065865797 5.214740545 0.705184846 0.028418227 14.8276388 -1.171071998 -0.297131893 APSPS(ph)SR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APSPSSR 7 0 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 APS(0.298)PS(0.696)S(0.006)R 110.12 0.0072126 328770000 132450 113730 73032 84830 72979 116320 99927 121850 91179 TRUE FALSE 114946.3969 112982.9001 108350.5195 104091.948 71526.86068 120794.9057 90236.09492 95793.32574 80399.92249 1.429682932 1.405261307 1.347644576 1.294677219 0.889638428 1.502425648 1.122340571 1.191460424 1 16.29490649 8 0.214468343 1.056016939 3.195562603 0.32156992 0.16085075 119.7499587 1.824893701 0.818353476 85.13953391 100000000 -8 2.139545664 APSQVSISAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 APSQVSISASPR 12 0 Q8IVL1-9;Q8IVL1-13;A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-5;Q8IVL1-4;Q8IVL1-10;Q8IVL1-8;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1;Q8IVL1-6;Q8IVL1-7 Q8IVL1-9 NAV2 Neuron navigator 2 1 APSQVSISAS(1)PR;APSQVSISAS(1)PR;APSQVSISAS(1)PR;APSQVSISAS(1)PR 213.99 2.27E-09 3558030000 1393340 1438730 979790 1211080 1438430 1392010 1456820 1583630 1313020 TRUE FALSE 1209206.589 1429278.888 1453619.721 1486074.224 1409808.057 1445561.525 1315537.821 1244983.048 1157796.271 1.044403596 1.2344822 1.255505616 1.283536889 1.217665052 1.248545674 1.136242924 1.075304075 1 20.14294998 1.730747985 1.671397754 1.001218 1.220073204 0.552985442 0.065905795 0.300717868 1.530244887 0.085731793 0.01961995 53.79575229 -1.730747985 0.218855204 APSRPYQDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APSRPYQDTR 10 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 0 ; 104.82 0.0023991 302290000 604480 676520 490880 573370 624250 711780 585260 657900 892910 FALSE TRUE 524596.4364 672075.8956 728271.2099 703562.4219 611828.6463 739162.6372 528501.5753 517213.2048 787351.197 0.666280103 0.853591 0.924963616 0.893581447 0.777072098 0.938796613 0.671239946 0.656902799 1 19.58664777 2.232480258 24.99775091 0.746858788 0.846002854 0.044588647 0.121156145 306.6628771 1260747.076 0.04791561 0.033240983 170.7970078 -2.232480258 0.099144066 APTVPPPLPPT(ph)PPQPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APTVPPPLPPTPPQPAR 17 0 Q9Y3L3;A0A2R8Y5V0 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 APTVPPPLPPT(1)PPQPAR 127.83 0.00043538 290800000 167460 165440 118170 131490 170220 199140 144350 167820 180400 TRUE FALSE 145329.7367 164353.2137 175317.4073 161346.8142 166832.955 206801.0447 130350.9592 131932.999 159073.3175 0.913602224 1.033191589 1.102116999 1.014292131 1.048780258 1.300036033 0.819439497 0.829384846 1 17.27933234 2.177093466 24.99999241 0.869137315 1.065207547 0.39529115 0.107782735 64.95210212 26416.60252 0.04341766 0.029272189 150.3465497 -2.177093466 0.196070232 APTVPPPLPPT(ph)PPQPARR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APTVPPPLPPTPPQPARR 18 1 Q9Y3L3;A0A2R8Y5V0 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 APTVPPPLPPT(1)PPQPARR 61.222 0.055065 0 109300 90343 47055 78012 100280 87598 87648 90822 62498 TRUE FALSE 94855.72807 89749.53088 69810.95539 95725.81694 98284.62419 90967.95174 79147.91045 71400.42208 55109.55764 1.721221003 1.62856562 1.266766753 1.737009351 1.78344063 1.650674686 1.436192084 1.295608695 1 15.75001493 1.48906265 1.385246443 0.899262578 1.62388858 0.673771092 0.144354615 0.489285558 1.235543013 0.461513721 0.046365062 30.83632755 -1.48906265 0.724626002 APVDEDRLS(ph)PLVAADSLLEHVR ddPTM_MDA-MB-175_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 276.46 1.09E-45 953023000 274975 276441 183571 223187 269842 302144 261419 304288 298538 TRUE FALSE 238636.3571 274625.0409 272346.5496 273865.0195 264472.6721 313767.6752 236066.6256 239218.3792 263245.1777 0.906517487 1.043229142 1.034573746 1.040342018 1.004662932 1.191921835 0.896755746 0.908728438 1 18.00604758 APVDFGYVGIDSILEQMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APVDFGYVGIDSILEQMR 18 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4;K7EL40;K7EK18;K7EIE4;K7EQD7;K7ER52;K7ELJ9;K7EJZ2;K7ENQ5;K7ER14;K7EN52;K7EKN4;K7EIR4;K7EJL9;K7EQ08 Q9UHD8 9-Sep Septin-9 0 136.33 1.52E-05 133860000 99348 66907 60875 76625 97340 69303 84415 118200 93128 FALSE TRUE 86218.91008 66467.48351 90314.35361 94023.87739 95403.12444 71969.13126 76228.44629 92923.84983 82118.51393 1.049932664 0.809409235 1.099805017 1.144977824 1.161773635 0.87640567 0.928273572 1.131582214 1 16.3254199 4.215040856 24.99974472 1.051177748 0.929670739 0.17115385 0.109064247 355.7973878 378186.4336 0.028445036 0.059266825 16407.44117 -4.215040856 -0.121507009 APVHFVEPLS(ph)PTGVAGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 APVHFVEPLSPTGVAGHR 18 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 APVHFVEPLS(0.999)PT(0.001)GVAGHR;APVHFVEPLS(0.998)PT(0.002)GVAGHR;APVHFVEPLS(0.982)PT(0.018)GVAGHR;APVHFVEPLS(0.999)PT(0.001)GVAGHR 201.52 8.98E-16 2467650000 840910 1022080 850810 1095320 1345840 1209390 1200360 1364510 1778050 TRUE FALSE 729781.6129 1015365.889 1262264.562 1344029.147 1319060.417 1255916.016 1083949.272 1072720.155 1567850.955 0.465466192 0.647616335 0.805092192 0.857242931 0.841317482 0.80104299 0.691359895 0.684197788 1 20.58035699 4.552120444 2.388638904 0.796220424 0.446980859 0.616211055 0.089294605 0.284366654 2.571930788 0.024359258 0.17240061 35655.00027 -4.552120444 -0.349239565 APVILGSPDDVLEFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APVILGSPDDVLEFLK 16 0 P09467;A0A3B3IUC7 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ; 231.83 2.27E-15 127817000 237120 220180 156156 188556 203480 181913 244380 283420 262490 FALSE TRUE 205783.9912 218733.6231 231673.5639 231370.5217 199431.1461 188911.3108 220680.0652 222812.8386 231458.7312 0.889074221 0.94502213 1.000928168 0.999618897 0.861627233 0.816177078 0.953431586 0.962646073 1 17.82039546 1.639992721 2.595050097 0.992297398 0.92333678 0.167192884 0.057349202 0.521009661 7.756723986 0.062608853 0.01725368 43.65085157 -1.639992721 -0.068960618 APVIRPGGTLGLSEAADSDAHLFQDSTEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APVIRPGGTLGLSEAADSDAHLFQDSTEPR 30 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 252.28 2.98E-58 206540000 228480 217180 123440 149630 193890 199620 204150 218480 176290 FALSE TRUE 198285.7891 215753.3303 183135.9969 183605.7785 190031.9683 207299.5106 184351.5644 171759.7522 155449.197 1.275566506 1.387934672 1.178108349 1.18113044 1.222469926 1.333551504 1.185928058 1.10492531 1 17.24608364 1.608905399 1.776915586 0.992373916 1.259366534 0.645238085 0.065519494 0.280988327 1.587035135 0.109971614 0.019925479 40.63548048 -1.608905399 0.266992618 APVPEPGLDLSLS(ph)PRPDS(ph)PQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APVPEPGLDLSLSPRPDSPQPR 22 1 Q8TAP8 Q8TAP8 PPP1R35 Protein phosphatase 1 regulatory subunit 35 2 APVPEPGLDLS(0.149)LS(0.851)PRPDS(1)PQPR 91.113 0.0012945 42526000 44994 42027 31710 28981 38661 51050 41438 46717 49025 TRUE FALSE 39047.9289 41750.92187 47045.06206 35561.579 37891.72174 53013.92653 37419.34914 36726.9331 43229.32035 0.90327418 0.965801024 1.088267446 0.822626373 0.876528278 1.226341893 0.865601144 0.849583866 1 15.39972253 APVPEPGLDLSLSPRPDS(ph)PQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 APVPEPGLDLSLSPRPDSPQPR 22 1 Q8TAP8 Q8TAP8 PPP1R35 Protein phosphatase 1 regulatory subunit 35 1 APVPEPGLDLSLS(0.001)PRPDS(0.999)PQPR;APVPEPGLDLSLSPRPDS(1)PQPR;APVPEPGLDLS(0.001)LS(0.001)PRPDS(0.999)PQPR 156.58 6.48E-09 4631900000 1558800 1462920 928990 1102440 1339660 1409370 1326320 1578470 1318340 TRUE FALSE 1352800.631 1453309.982 1378252.671 1352765.852 1313003.387 1463589.376 1197693.691 1240926.474 1162487.347 1.163712133 1.250172732 1.1856066 1.163682216 1.129477573 1.259015317 1.030285356 1.067475252 1 20.14878358 2.224062471 24.99997591 1.039759331 1.190179036 0.761138421 0.042011348 112.6173628 194190.9992 0.016660791 0.011288149 167.5183823 -2.224062471 0.150419706 APVPGT(ph)PDSLSSGSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APVPGTPDSLSSGSSR 16 0 A0A087WYB4;Q9UJZ1;Q9UJZ1-2 A0A087WYB4 STOML2 "Stomatin-like protein 2, mitochondrial" 1 APVPGT(0.999)PDS(0.001)LSSGSSR 151.9 6.69E-06 103060000 76498 73899 51412 83889 90361 104140 61260 80921 85615 TRUE FALSE 66388.59548 73413.5526 76275.01516 102937.2796 88562.99289 108146.3332 55319.01463 63616.67388 75493.69223 0.879392616 0.97244618 1.010349513 1.363521595 1.173117783 1.432521446 0.7327634 0.842675355 1 16.20406849 2.213292796 24.99938531 0.849948841 1.136976653 0.35411306 0.17817931 257.4952169 254757.7274 0.076408454 0.051536645 163.4153302 -2.213292796 0.287027812 APVPSTCSSTFPEELS(ph)PPSHQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 APVPSTCSSTFPEELSPPSHQAK 23 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5;F5H763;F5H0Z7 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 APVPSTCSSTFPEELS(0.999)PPS(0.001)HQAK;APVPSTCSSTFPEELS(1)PPSHQAK;APVPSTCSSTFPEELS(1)PPSHQAK;APVPSTCSSTFPEELS(1)PPSHQAK 302.16 3.46E-62 13175060000 1043710 1081002 639088 802222 984328 815612 1065704 1345600 1176186 TRUE FALSE 905781.0791 1073900.827 948153.0944 984378.7663 964741.7986 846989.1214 962352.1901 1057853.911 1037138.631 0.873346197 1.035445788 0.914200924 0.9491294 0.930195607 0.816659505 0.927891568 1.019973492 1 19.98417732 1.762309447 6.430160875 1.009206161 0.922348517 0.309481077 0.055223352 0.192771148 21.76178754 0.031443354 0.014493866 57.85081034 -1.762309447 -0.086857644 APVPTGEVYFADSFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APVPTGEVYFADSFDR 16 0 P27824;P27824-2;H0Y9Q7;D6RDP7;D6RAU8;D6RB85;D6RAQ8;D6RHJ3;D6RD16 P27824 CANX Calnexin 0 ; 172.76 1.04E-08 314680000 79540 83678 52160 82164 85603 81826 55245 109665 96376 FALSE TRUE 69028.58747 83128.31371 77384.75046 100820.592 83899.66778 84973.89917 49887.3484 86213.99316 84982.53907 0.812267887 0.978181102 0.910595886 1.186368319 0.98725772 0.999898333 0.587030571 1.014490672 1 16.37487883 APVQPQQS(ph)PAAAPGGTDEKPSGK ddPTM_MDA-MB-175_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 215.59 1.62E-32 1002500000 1723980 1255520 1055020 1171380 1082840 854850 1536080 1867070 1727090 TRUE FALSE 1496151.675 1247272.406 1565231.201 1437359.732 1061293.603 887736.6327 1387111.198 1467811.61 1522915.388 0.982426002 0.819003089 1.027786057 0.943821137 0.696882841 0.582919209 0.910826175 0.963816915 1 20.53840436 APVS(ph)PLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APVSPLK 7 0 Q9UBS0 Q9UBS0 RPS6KB2 Ribosomal protein S6 kinase beta-2 1 APVS(1)PLK;APVS(1)PLK 73.985 0.049731 1160250000 1227150 1499970 1278730 1707700 2047690 1609960 2204250 2478100 2446500 TRUE FALSE 1064979.018 1490116.598 1897128.105 2095459.386 2006944.975 1671896.203 1990482.174 1948177.6 2157277.557 0.493668056 0.690739397 0.879408446 0.971344359 0.930313751 0.775002826 0.922682465 0.903072297 1 21.04078038 4.47956193 2.074363375 0.912425118 0.47234203 0.851277149 0.058883193 0.156935225 1.084228938 0.016085688 0.106277675 30169.0705 -4.47956193 -0.440083088 APVSSTESVIQSNTPT(ph)PPPSQPLNETAEEESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 APVSSTESVIQSNTPTPPPSQPLNETAEEESR 32 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 APVSSTESVIQSNT(0.002)PT(0.998)PPPSQPLNETAEEESR;APVSSTESVIQSNT(0.001)PT(0.998)PPPSQPLNETAEEESR 206.53 1.61E-26 194750000 74742 76821 53164 56623 75221 78865 68828 73986 66369 TRUE FALSE 64864.65533 76316.35779 78874.28822 69480.11758 73724.24927 81898.98758 62153.07115 58164.66966 58522.93243 1.108363041 1.304041931 1.347750103 1.187228915 1.259749746 1.399434105 1.062029337 0.99387825 1 15.83671444 2.092337722 6.268519162 1.005684416 1.268360343 0.68771935 0.079898099 0.109650905 6.13591585 0.032353179 0.021615635 123.6908922 -2.092337722 0.262675927 APVVGILVLDGHSVPLPEPLEVAHDLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APVVGILVLDGHSVPLPEPLEVAHDLSK 28 0 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 0 61.109 0.019769 112960000 55357 48939 32335 40411 49125 38819 47925 58331 52483 FALSE TRUE 48041.43219 48617.51649 47972.31415 49586.93519 48147.50861 40312.39205 43277.24088 45857.36958 46278.51953 1.038093541 1.050541741 1.036600018 1.071489229 1.040385671 0.871082145 0.935147479 0.990899667 1 15.49805509 2.913729478 11.4162215 0.954496467 1.049322343 0.649808664 0.035760104 0.505526858 65.38012548 0.012150958 0.01215437 819.8407065 -2.913729478 0.094825875 APWELLELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APWELLELR 9 0 P54577;A0A0C4DGZ5 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed;Tyrosine--tRNA ligase" 0 74.2 0.097164 11743000 23693 19787 16094 18247 18827 20710 18977 19326 29085 FALSE TRUE 20561.91002 19657.01789 23877.11223 22390.26024 18452.37953 21506.7271 17136.61346 15193.2853 25646.60443 0.801740054 0.766456938 0.931004816 0.873030202 0.719486261 0.838579905 0.668182547 0.592409234 1 14.64648021 3.235322416 24.99911978 0.738892524 0.843868419 0.082512423 0.116026364 161.3012552 1245255.664 0.035222549 0.041601483 1719.18422 -3.235322416 0.104975895 APWNHGEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APWNHGEER 9 0 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 100.48 0.0046337 113430000 59556 58416 48439 56081 59692 64617 66222 68880 104900 FALSE TRUE 51685.5237 58032.26145 71864.26242 68815.04819 58504.24599 67102.8578 59799.80063 54150.54802 92498.8415 0.558769417 0.627383657 0.776920675 0.743955784 0.632486256 0.725445386 0.646492428 0.585418662 1 16.49714768 1.230295714 24.9998761 1.00000062 0.663896098 0.703285299 0.068964895 188.2653905 569424.3109 0.196316102 0.017755518 16.99400394 -1.230295714 -0.336104523 APYS(ph)PTTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 APYSPTTSK 9 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 1 APY(0.001)S(0.987)PT(0.005)T(0.006)S(0.001)K;APYS(0.927)PT(0.055)T(0.016)S(0.002)K;APYS(0.799)PT(0.176)T(0.023)S(0.002)K;APYS(0.938)PT(0.062)TSK 119.34 0.00088511 2297370000 4948180 4372620 2924850 3374710 4051750 3444540 4386150 5159350 5126390 TRUE FALSE 4294265.476 4343895.971 4339317.243 4140989.485 3971128.102 3577053.683 3960781.848 4056063.153 4520354.014 0.949984329 0.960963667 0.959950754 0.916076367 0.878499359 0.79132158 0.876210544 0.897288827 1 22.10800433 3.530772332 3.139808555 0.884303347 0.95716834 0.277275902 0.049916074 0.33876529 6.621051292 0.015358255 0.023002102 3394.472794 -3.530772332 0.072864993 APYSPT(ph)TSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 APYSPTTSK 9 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 1 APYS(0.47)PT(0.527)T(0.002)SK 108.93 0.028301 1161200000 2596900 2223400 1497600 1844700 2039200 1898300 2321200 2558200 2694900 TRUE FALSE 2253713.085 2208794.339 2221844.369 2263567.329 1998623.91 1971328.829 2096090.381 2011148.838 2376311.992 0.948407908 0.929505194 0.93499691 0.952554773 0.84106124 0.829574919 0.882077096 0.846331982 1 21.18029283 3.24914129 24.99963004 0.87328281 0.940064044 0.28903583 0.047343135 251.6909818 594683.0335 0.013395798 0.017109696 1774.766777 -3.24914129 0.066781234 AQAEAQQPTFDALRDELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 ;;;;;;; 238.68 6.26E-24 8777220000 4868300 4546110 3015801 3202695 4352710 4943470 4433900 5084780 3429490 FALSE TRUE 4224941.82 4516246.304 4474252.451 3929915.85 4266099.587 5133648.49 4003901.06 3997439.367 3024059.599 1.39710931 1.493438259 1.479551677 1.299549735 1.410719414 1.697601625 1.324015261 1.3218785 1 21.52805514 1.142556888 1.536762496 0.735903257 1.451931596 0.630643658 0.107629938 0.954797835 1.67139246 1.128118637 0.030809429 13.88535181 -1.142556888 0.716028339 AQAGEGVRPSPMQLELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 AQAGEGVRPSPMQLELR 17 1 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;;;;;; 194.05 8.76E-11 5615480000 2511218 2550612 1732251 1942939 2425085 2508278 2206993 2649406 2719573 FALSE TRUE 2179354.179 2533856.862 2569973.378 2384112.996 2376830.553 2604773.078 1992959.159 2082851.145 2398068.178 0.908795754 1.056624197 1.071684867 0.994180657 0.991143861 1.086196423 0.831068598 0.868553765 1 21.19344125 2.236733146 24.99984924 0.890482149 1.019977767 0.419665765 0.065204669 41.36742645 565890.3222 0.025102903 0.017911441 172.4777769 -2.236733146 0.129495617 AQAHAENNEFITWNDIQACVDHVNLVVQEEHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQAHAENNEFITWNDIQACVDHVNLVVQEEHER 33 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 164.55 1.44E-14 129390000 17162 15325 13831 13451 8921.4 10457 12447 14469 81197 FALSE TRUE 14893.99822 15224.32907 20519.71786 16505.25514 8743.881594 10859.28756 11239.89186 11374.91695 71597.98316 0.208022594 0.212636284 0.286596311 0.230526817 0.122124691 0.1516703 0.156986152 0.15887203 1 16.12763133 1.237253088 24.99999164 1.000000978 0.18936393 0.966835689 0.047091305 6.01485763 114958.6269 0.078071145 0.012894717 17.26843928 -1.237253088 -0.810637048 AQASLNAGLDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AQASLNAGLDLR 12 0 Q96BX8;K7EPX7;K7EKK6;K7ELS3;K7ESA9 Q96BX8 MOB3A MOB kinase activator 3A 0 ;;; 101.71 0.0025168 1212800000 596889 788960 651680 587342 851090 1384040 414025 427138 395046 FALSE TRUE 518008.6063 783777.2698 966834.6277 720706.9781 834154.9741 1437284.914 373872.9192 335797.8627 348344.1119 1.487060032 2.250008664 2.775515918 2.068951228 2.394629177 4.126049114 1.073286174 0.963983174 1 18.41015365 2.049587366 24.99987871 0.991177091 2.499797159 0.530750521 0.667187539 79.75804207 40210.29674 0.269178701 0.181480196 112.0952903 -2.049587366 1.508620068 AQAVS(ph)EEEEEEEGK ddPTM_MDA-MB-175_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 256.67 2.67E-24 1361950000 885630 683910 675380 835220 663530 507390 791020 879080 1516990 TRUE FALSE 768591.7516 679417.3502 1001996.027 1024869.467 650327.0512 526909.6216 714307.0022 691095.583 1337653.17 0.574582237 0.507917422 0.749070125 0.766169803 0.486170156 0.393906009 0.534000156 0.516647811 1 20.35127267 1.234724756 24.99292349 1.000000627 0.56451863 0.589596953 0.113772483 88.58101784 577073.1038 0.22118477 0.030178895 17.16819969 -1.234724756 -0.435481997 AQCLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQCLSR 6 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 99.139 0.09105 98609000 75948 74660 56700 55771 60269 79874 81377 88810 58980 FALSE TRUE 65911.27937 74169.55354 84120.30965 68434.65796 59069.76481 82946.80447 73485.07107 69818.67262 52007.45159 1.267342993 1.426133204 1.61746648 1.315862552 1.135794257 1.594902306 1.412971965 1.342474405 1 15.66643073 1.226241439 3.191209403 0.92408279 1.399058074 0.430988477 0.141694887 0.367178362 4.858547442 0.448465045 0.036563873 16.83609778 -1.226241439 0.474975284 AQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSR 33 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;; 352.67 7.18E-132 1154470000 373438 354211 265545 261834 296423 354222 316090 385432 311682 FALSE TRUE 324087.2221 351884.1646 393963.4502 321287.4116 290524.7622 367849.1496 285435.6405 303010.3662 274835.309 1.179205188 1.280345549 1.433452825 1.169017957 1.057086745 1.338434828 1.038569758 1.102516148 1 18.06820784 1.511513101 0.436728041 0.852821748 1.289807785 0.386752937 0.108570409 5.044098899 1.02602927 1.167174103 0.13046256 32.47230374 -1.511513101 0.436986037 AQDGSHPLSLQDLIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQDGSHPLSLQDLIEK 16 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-7;H7BXG7;H0YAB3;H0Y9K1 D6REX3 SEC31A Protein transport protein Sec31A 0 ; 205.31 2.29E-11 355250000 774110 635980 377070 584950 589100 502740 679570 847800 762050 FALSE TRUE 671809.4022 631802.2055 559422.3132 717771.8379 577378.0626 522080.7331 613665.406 666504.5676 671961.3171 0.999773923 0.940235977 0.832521603 1.068174342 0.859243007 0.776950577 0.913245138 0.99187937 1 19.35801866 1.717652862 4.852402746 0.997219232 0.909340459 0.150439627 0.081861526 0.297706669 16.85575116 0.05298224 0.021729114 52.19787964 -1.717652862 -0.087878773 AQEEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQEEAER 7 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 126.57 0.0091652 1446580000 1456940 1513870 1080280 1546920 848250 1501270 1244310 1639910 2359300 FALSE TRUE 1264401.688 1503925.288 1602707.021 1898171.829 831371.4846 1559024.828 1123637.008 1289228.008 2080386.242 0.607772568 0.722906765 0.770389166 0.912413181 0.399623622 0.749392011 0.540109805 0.619706083 1 20.98841997 1.233901114 24.98595231 1.00000051 0.664418371 0.363783621 0.139104072 160.6003763 861090.2158 0.260799648 0.033244578 17.13567094 -1.233901114 -0.335582139 AQEEAERLEADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AQEEAERLEADR 12 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;; 172.57 3.23E-05 7004880000 10879640 10788040 5211600 5886310 9791310 10073720 9367870 10258360 5143160 FALSE TRUE 9441868.009 10717172.65 7731947.192 7222886.652 9596482.087 10461262.53 8459375.409 8064689.545 4535141.484 2.081934608 2.363139649 1.704896577 1.592648582 2.116027057 2.306711392 1.865294708 1.778266361 1 22.11271613 1.0883278 1.748174958 0.291315603 2.009211688 0.634353084 0.239242011 1.009580518 2.070264008 3.327751303 0.070206961 12.25540873 -1.0883278 1.717896085 AQELDALDNSHPIEVSVGHPSEVDEIFDAISYSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQELDALDNSHPIEVSVGHPSEVDEIFDAISYSK 34 0 E9PLK3;P55786;P55786-2;A6NEC2;A6NEC2-2;E9PJ74;E9PRQ5 E9PLK3 NPEPPS;NPEPPSL1 Puromycin-sensitive aminopeptidase;Puromycin-sensitive aminopeptidase-like protein 0 ; 212.22 3.06E-28 710550000 493370 488290 148274 342020 519610 509360 564090 632830 602990 FALSE TRUE 428169.9045 485082.3908 219979.8023 419680.8684 509270.7776 528955.4088 509384.6386 497504.2292 531705.2091 0.805276866 0.912314535 0.413725122 0.789311185 0.957806636 0.994828337 0.958020779 0.935676801 1 19.02026708 3.317451917 4.332877452 0.966054002 0.712774396 0.478573357 0.125646274 0.188890161 6.650798162 0.037078805 0.047805739 2077.073749 -3.317451917 -0.253279606 AQELGHSQSALASAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AQELGHSQSALASAQR 16 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;; 238.81 8.36E-20 1294970000 814340 938110 438435 598710 850190 865480 761070 934050 808890 FALSE TRUE 706722.9057 931947.4936 650463.6325 734656.2562 833272.8824 898775.5756 687261.5485 734310.6763 713263.9457 0.990829426 1.306595545 0.911953613 1.029992138 1.168253194 1.260088332 0.963544495 1.029507633 1 19.44407652 AQEPPAGGGGSIHDLPLFTET(ph)SPTSAPWDPLPGPPPVLPHSPHSHL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQEPPAGGGGSIHDLPLFTETSPTSAPWDPLPGPPPVLPHSPHSHL 46 0 F8VZ44;Q9NRG9-2;Q9NRG9 F8VZ44 AAAS Aladin 1 AQEPPAGGGGSIHDLPLFT(0.14)ET(0.682)S(0.173)PT(0.002)S(0.002)APWDPLPGPPPVLPHSPHSHL 119.65 2.23E-08 188630000 12161 9445.9 4973.7 5929.7 11060 11462 12360 12270 4256.7 TRUE FALSE 10553.89304 9383.849261 7378.997956 7276.129015 10839.92764 11902.95056 11161.3291 9646.155985 3753.477775 2.811763828 2.500041248 1.96590959 1.93850329 2.887969048 3.171179176 2.973596694 2.569924897 1 11.87401223 3.231417004 24.98047199 2.593219723 2.293900331 0.020747243 0.636749975 609.9360899 2132880.257 0.197886956 0.229045208 1703.793683 -3.231417004 -0.299319392 AQEPPAGGGGSIHDLPLFTETSPTSAPWDPLPGPPPVLPHS(ph)PHSHL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQEPPAGGGGSIHDLPLFTETSPTSAPWDPLPGPPPVLPHSPHSHL 46 0 F8VZ44;Q9NRG9-2;Q9NRG9 F8VZ44 AAAS Aladin 1 AQEPPAGGGGSIHDLPLFTETSPTSAPWDPLPGPPPVLPHS(0.828)PHS(0.172)HL 117.39 1.79E-08 242860000 37369 34940 13237 26302 42808 44620 37592 43073 39383 TRUE FALSE 32430.59197 34710.47684 19638.45748 32274.2711 41956.20455 46336.56027 33946.33363 33862.17414 34727.18661 0.93386753 0.999518828 0.565506722 0.929366132 1.208165955 1.334302165 0.977514649 0.975091202 1 15.08377792 3.464200808 15.90142506 1.084600523 0.832590639 0.384548532 0.155524954 3.54538367 4361.158549 0.047641361 0.061774957 2912.063282 -3.464200808 -0.252009884 AQFEDRN ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQFEDRN 7 1 Q9C005 Q9C005 DPY30 Protein dpy-30 homolog 0 125.25 0.083387 724400000 898320 766000 539600 565010 739970 809840 844490 842360 801130 FALSE TRUE 779604.7359 760968.0956 800552.3649 693304.1561 725246.0447 840995.0688 762591.4898 662227.8693 706421.3241 1.103597399 1.077215636 1.133250565 0.981431523 1.026648007 1.190500683 1.079513689 0.937440373 1 19.43016937 1.765247176 10.67737136 0.969172609 1.084088376 0.41048919 0.05772284 0.224108538 85.71626662 0.031606553 0.01504932 58.24346126 -1.765247176 0.114915766 AQFSVAGVHTVPGS(ph)PQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AQFSVAGVHTVPGSPQAR 18 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 AQFSVAGVHTVPGS(1)PQAR;AQFSVAGVHT(0.001)VPGS(0.999)PQAR;AQFSVAGVHT(0.001)VPGS(0.999)PQAR 129.43 1.37E-05 2002430000 1369460 1332660 718840 985180 1370180 1464140 1320320 1542930 1318110 TRUE FALSE 1188482.391 1323905.669 1066473.428 1208880.177 1342916.099 1520466.413 1192275.57 1212986.427 1162284.537 1.022539966 1.139054703 0.917566563 1.040089701 1.155410793 1.308170559 1.02580352 1.043622614 1 20.14853187 5.059407672 13.153611 1.077052713 0.693026681 0.027106263 0.105347554 3465908.493 23956549.03 0.026784942 33510709.95 114658.8739 -5.059407672 -0.384026032 AQGAGVTLPPT(ph)PSGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQGAGVTLPPTPSGSR 16 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 AQGAGVTLPPT(0.996)PS(0.003)GSR;AQGAGVTLPPT(0.999)PS(0.001)GSR 218.85 1.86E-12 0 200415 226630 136055 133573 230560 236300 192132 228170 237520 TRUE FALSE 173929.65 225141.2526 201851.6531 163902.7912 225972.3071 245390.6139 173499.0682 179377.6211 209440.6562 0.830448362 1.074964416 0.963765378 0.7825739 1.078932387 1.171647465 0.828392497 0.856460366 1 17.676182 AQGEPVAGHES(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQGEPVAGHESPK 13 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-7;H7BXG7;H0YAB3 D6REX3 SEC31A Protein transport protein Sec31A 1 AQGEPVAGHES(1)PK;AQGEPVAGHES(1)PK 179.94 1.40E-05 901850000 949780 763750 834580 938200 911150 763730 926290 1135890 2571150 TRUE FALSE 824264.1666 758732.876 1238185.68 1151232.649 893019.8976 793111.1873 836458.5384 892988.763 2267191.576 0.363561763 0.334657593 0.546131916 0.507779167 0.393888151 0.349820984 0.368940387 0.393874418 1 21.11247487 1.23773805 24.9996599 1.000000689 0.407889438 0.882182726 0.068067152 6.978185495 211951.3174 0.104704533 0.017862121 17.28773316 -1.23773805 -0.59211125 AQGEPVAGHES(ph)PKIPYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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(0.995)PKIPY(0.005)EK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK 250.71 2.86E-25 24957700000 12828226 9596721 8112061 7746744 9617690 6851588 13462843 14677626 8767862 TRUE FALSE 11132943.43 9533679.508 12035080.83 9505760.627 9426316.786 7115173.024 12157218.56 11538929.9 7731335.343 1.439976788 1.233121975 1.556662633 1.229510842 1.219235277 0.920303248 1.572460386 1.492488605 1 22.88228618 AQGGQTQS(ph)PTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AQGGQTQSPTK 11 0 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 1 AQGGQT(0.037)QS(0.956)PT(0.007)K;AQGGQT(0.043)QS(0.957)PTK;AQGGQT(0.003)QS(0.997)PTK;AQGGQT(0.031)QS(0.969)PTK 193.34 1.05E-06 348286000 1310040 820720 608332 789530 544129 757180 1027050 1172030 1276640 TRUE FALSE 1136914.895 815328.6363 902523.3899 968804.8537 533301.8975 786309.2046 927446.8491 921400.5052 1125717.074 1.009947278 0.724274914 0.80173199 0.860611317 0.473744167 0.698496295 0.823872064 0.81850096 1 20.10241285 1.104835729 1.581628264 1.161189671 0.757980089 0.218325479 0.135415947 2.417641107 4.162384838 1.693346239 0.038596748 12.73021472 -1.104835729 -0.403209582 AQGPRPHQENNHQESYPLSVS(ph)PMENNHCPASSESHPKPS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AQGPRPHQENNHQESYPLSVSPMENNHCPASSESHPKPSSPR 42 2 P41212 P41212 ETV6 Transcription factor ETV6 2 AQGPRPHQENNHQESYPLSVS(0.998)PMENNHCPAS(0.012)S(0.01)ES(0.073)HPKPS(0.486)S(0.42)PR;AQGPRPHQENNHQESYPLS(0.04)VS(0.96)PMENNHCPASSES(0.099)HPKPS(0.491)S(0.41)PR;AQGPRPHQENNHQESYPLS(0.281)VS(0.358)PMENNHCPAS(0.17)S(0.19)ES(0.13)HPKPS(0.461)S(0.41)PR;AQGPRPHQENNHQESYPLS(0.019)VS(0.59)PMENNHCPAS(0.182)S(0.199)ES(0.019)HPKPS(0.517)S(0.473)PR 234.75 9.61E-55 1549990000 587023 552765 172766 339263 593729 495825 588931 638980 524724 TRUE FALSE 509446.4232 549133.8503 256316.2155 416297.8495 581914.9545 514899.7086 531816.5623 502339.0995 462691.7265 1.101049347 1.186824442 0.553967579 0.899730481 1.257673136 1.112835348 1.149397173 1.085688528 1 18.81969178 3.262139617 24.80151222 1.118396777 0.926107595 0.218223695 0.174241016 340.3563096 358000.2908 0.051707896 0.06671387 1828.688008 -3.262139617 -0.192289183 AQGTHVLVHCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQGTHVLVHCK 11 0 Q8TE77;Q8TE77-2;Q8TE77-3;E9PIT5;Q8TE77-5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 125.97 0.00018344 523300000 199760 189180 144410 147180 173940 199420 227660 226090 205920 FALSE TRUE 173361.2099 187937.2641 214247.159 180599.4685 170478.9343 207091.8164 205581.5682 177742.4129 181576.3722 0.954756435 1.035031496 1.179928624 0.994619874 0.938882809 1.140521831 1.132204404 0.978885142 1 17.47021696 2.731210367 24.98457558 1.056272089 1.028846539 0.054779024 0.081402537 3123.489495 10617160.01 0.029482436 0.026444984 538.530577 -2.731210367 -0.02742555 AQGVRS(ph)PLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AQGVRSPLLR 10 1 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 AQGVRS(1)PLLR;AQGVRS(1)PLLR;AQGVRS(1)PLLR;AQGVRS(1)PLLR;AQGVRS(1)PLLR;AQGVRS(1)PLLR 127.78 0.00021021 2377990000 2333580 2373370 1416560 1608680 2778980 2982190 2688790 3051750 1221803 TRUE FALSE 2025191.49 2357779.176 2101613.154 1973955.381 2723683.735 3096916.779 2428031.56 2399157.011 1077362.841 1.879767348 2.188472709 1.950701355 1.83221038 2.52810254 2.874534614 2.253680438 2.226879301 1 20.03907278 3.265286942 24.9815397 2.223592535 1.978045031 0.041131177 0.481952146 753.2041257 704027.4548 0.142103632 0.183401534 1841.988619 -3.265286942 -0.245547504 AQHEDQVEQYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 176.32 8.79E-06 896540000 2752010 2331140 2067700 2523060 2257420 2065920 2773260 3026450 6881300 FALSE TRUE 2388324.906 2315826.588 3067646.636 3095959.336 2212501.759 2145397.279 2504309.672 2379267.219 6067800.553 0.393606363 0.381658324 0.505561547 0.510227604 0.364629941 0.35357083 0.412721158 0.392113617 1 22.53274223 1.237229265 24.99991824 1.000000708 0.414536485 0.922348392 0.053411377 9.203851326 172761.0993 0.084756439 0.013971496 17.26749208 -1.237229265 -0.585464223 AQHEDQVEQYKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 220.69 1.88E-11 14206100000 9951290 7415960 5963400 6600650 6673370 5026460 9358290 10665800 7920780 FALSE TRUE 8636201.813 7367244.07 8847320.186 8099428.467 6540582.993 5219831.169 8450724.476 8385001.671 6984394.412 1.236499731 1.054815011 1.266726886 1.15964649 0.936456707 0.7473563 1.209943766 1.200533815 1 22.7357036 3.397030383 9.736983493 1.04248911 1.179565765 0.234109578 0.141254774 0.659698602 74.51729704 0.044930535 0.058017921 2494.769251 -3.397030383 0.137076655 AQHEENIKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQHEENIKK 9 1 A0A3B3IRW9;Q6P4E1-5;Q6P4E1;H0YMR0;Q6P4E1-2 A0A3B3IRW9 CASC4 Protein CASC4 0 ; 93.111 0.0062453 115565000 208244 173673 133892 160340 139676 157198 174379 215846 189931 FALSE TRUE 180724.0278 172532.1306 198642.619 196747.6476 136896.7209 163245.5088 157467.7514 169689.0126 167477.5736 1.079093899 1.030180501 1.186084888 1.174770111 0.817403297 0.974730558 0.940231866 1.013204389 1 17.3536084 3.258393161 24.99994879 0.95773994 1.116189555 0.597290898 0.068509989 185.3271405 233613.0047 0.020393998 0.026293029 1812.980616 -3.258393161 0.158449615 AQHQLGEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQHQLGEFK 9 0 H3BVG0;Q8N1F7;Q8N1F7-2;H3BPA9 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 107.24 0.0034905 0 375870 418940 341630 297620 409180 353550 452740 487990 534370 FALSE TRUE 326197.8272 416187.9556 506843.4107 365199.1698 401038.1185 367151.2973 408833.3445 383637.136 471197.3874 0.69227427 0.883256076 1.075649875 0.77504498 0.851104292 0.779187888 0.867647732 0.814175007 1 18.84597201 -1.999999999 0.007742179 1.796154599 2.32E-09 0.034637868 0.108998595 409874.3797 316.1310346 40087.08189 33537.21813 0.01 1.999999999 -1.796154597 AQHTLPQDPAIVQSSLGSASAS(ph)PFQPHVPYS(ph)PFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQHTLPQDPAIVQSSLGSASASPFQPHVPYSPFR 34 0 Q9BX40;Q9BX40-2;Q5TBQ1;A0A0C4DFV2 Q9BX40 LSM14B Protein LSM14 homolog B 2 AQHTLPQDPAIVQSS(0.001)LGS(0.001)AS(0.042)AS(0.956)PFQPHVPY(0.028)S(0.972)PFR;AQHTLPQDPAIVQSSLGSAS(0.001)AS(0.999)PFQPHVPY(0.005)S(0.995)PFR 206.23 1.02E-27 186767000 82954 105308 68213 70686 91512 111151 77077 98161 110248 TRUE FALSE 71991.41872 104616.2248 101201.035 86736.33667 89691.09024 115427.0509 69602.0844 77170.03404 97214.60703 0.740541169 1.076136889 1.041006471 0.892215062 0.922609194 1.187342668 0.715963234 0.793811099 1 16.56888548 2.210834715 24.99999995 0.822652766 0.977796684 0.1870691 0.13658639 319.8805182 288428.7785 0.053807144 0.036285593 162.4930219 -2.210834715 0.155143917 AQHTLPQDPAIVQSSLGSASAS(ph)PFQPHVPYSPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQHTLPQDPAIVQSSLGSASASPFQPHVPYSPFR 34 0 Q9BX40;Q9BX40-2;Q5TBQ1;A0A0C4DFV2 Q9BX40 LSM14B Protein LSM14 homolog B 1 AQHTLPQDPAIVQSS(0.001)LGS(0.003)AS(0.055)AS(0.94)PFQPHVPY(0.001)S(0.001)PFR 188.4 6.45E-20 1055100000 119590 139120 96527 92137 140860 163360 139180 152610 185190 TRUE FALSE 103785.8785 138206.1116 143207.7801 113058.1141 138057.1616 169644.5649 125682.345 119975.5391 163297.0492 0.635564935 0.846347881 0.876977146 0.692346338 0.84543574 1.038870976 0.769654722 0.734707331 1 17.3171392 3.025805163 24.75403538 0.861403139 0.775925954 0.190739448 0.114032589 468.1424629 449069.8058 0.035631761 0.040401271 1061.219357 -3.025805163 -0.085477185 AQIHDLVLVGGSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 AQIHDLVLVGGSTR 14 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ;;;;;; 160.8 4.70E-06 13185104000 8890840 8682297 5524960 6570674 7894265 8763830 8028409 9003620 9171670 FALSE TRUE 7715892.967 8625262.419 8196849.136 8062645.958 7737184.571 9100980.211 7249815.131 7078265.929 8087405.621 0.954062814 1.066505481 1.013532586 0.996938491 0.956695501 1.125327532 0.896432734 0.875220839 1 22.94724554 2.190200728 24.99995619 0.912602224 1.016948557 0.358884511 0.059157288 107.7995347 55726.82838 0.022919405 0.015452299 154.9532637 -2.190200728 0.104346333 AQIS(ph)SPNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AQISSPNLR 9 0 H0Y507;Q5TCZ1-2;Q5TCZ1-3;Q5TCZ1 H0Y507 SH3PXD2A SH3 and PX domain-containing protein 2A 1 AQIS(0.5)S(0.5)PNLR;AQIS(0.683)S(0.317)PNLR;AQIS(0.648)S(0.352)PNLR 133.91 0.0012301 284160000 1930810 2022050 974520 1250440 1974160 2158640 1581760 1826750 1246300 TRUE FALSE 1675648.566 2008767.02 1445801.132 1534371.514 1934878.078 2241684.278 1428361.159 1436113.728 1098963.834 1.524753149 1.827873638 1.315603924 1.39619837 1.760638539 2.039816242 1.299734454 1.30678889 1 20.06771248 1.728983048 2.05649023 1.071041541 1.626066845 0.446771374 0.227174543 0.306368324 2.560007146 0.242902674 0.066833024 53.57757435 -1.728983048 0.555025304 AQIWDTAGLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AQIWDTAGLER 11 0 P57735 P57735 RAB25 Ras-related protein Rab-25 0 ;; 199.68 1.15E-07 449771000 640190 659000 462674 517464 719960 756980 631160 768900 700940 FALSE TRUE 555587.2695 654670.9856 686424.694 634962.1101 705634.2046 786101.5104 569950.2003 604476.7186 618075.6717 0.89889846 1.059208468 1.110583583 1.027320989 1.141663128 1.271853183 0.922136603 0.977997916 1 19.23742395 AQIWDTAGQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 257.72 3.60E-20 1710240000 2014940 1849760 1267517 1492570 1931050 2114820 1635126 2173960 2243390 FALSE TRUE 1748660.574 1837608.805 1880492.461 1831480.831 1892625.883 2196178.494 1476551.732 1709075.572 1978178.99 0.8839749 0.928939603 0.950617952 0.925841817 0.956751585 1.110202113 0.746419682 0.86396407 1 20.91574154 2.223814182 24.99998388 0.863689349 0.955960714 0.199968262 0.083647234 375.577776 636721.0882 0.033949042 0.022996689 167.4226386 -2.223814182 0.092271365 RVGDPPQPLPEEPMEVQGAERAS(ph)PEPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 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 196.68 2.95E-25 6967470000 2718321 2383719 1558102 1576094 2371080 2546115 2342366 2606388 1015455 TRUE FALSE 2359087.993 2368060.193 2311605.339 1933970.232 2323900.147 2644065.692 2115203.706 2049032.209 895409.0667 2.634648319 2.644668544 2.581619312 2.159873407 2.595350252 2.95291369 2.362276399 2.288375543 1 19.7721874 1.09963708 1.952000423 7.46E-13 2.5685329 0.852429812 0.202757867 0.457071834 1.223415558 2.44812592 0.056353501 12.57873826 -1.09963708 2.5685329 AQLADSFHLQQFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQLADSFHLQQFFR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 166.09 3.86E-06 782312000 702470 694074 397335 621697 739612 827413 614641 864351 962797 FALSE TRUE 609636.8097 689514.5822 589487.535 762862.8059 724895.1682 859244.1135 555033.2104 679516.265 848976.2355 0.718084658 0.812171829 0.694351043 0.898567915 0.853846242 1.012094423 0.653767664 0.800394919 1 19.69536464 3.735264384 24.99248908 0.854316373 0.748599442 0.240043831 0.104943824 503.3158371 3816215.47 0.029023564 0.045192685 5435.811444 -3.735264384 -0.105716931 AQLEPVAS(ph)PAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AQLEPVASPAK 11 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 AQLEPVAS(1)PAK;AQLEPVAS(1)PAK;AQLEPVAS(1)PAK;AQLEPVAS(1)PAK;AQLEPVAS(1)PAK;AQLEPVAS(1)PAK 219.84 1.00E-11 2336860000 8099010 6718740 5274980 6112400 6934150 5921900 7546100 9004870 9631000 TRUE FALSE 7028705.308 6674604.155 7825977.972 7500313.842 6796173.981 6149719.325 6814280.383 7079248.626 8492434.152 0.827643192 0.785947119 0.921523539 0.883175979 0.800262193 0.724140949 0.802394256 0.833594762 1 23.0177467 1.238803238 4.847661856 1.01243471 0.821010146 0.52609232 0.053127849 0.159731979 9.012233133 0.10395613 0.014372603 17.33018658 -1.238803238 -0.191424564 AQLGEDIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQLGEDIRR 9 1 Q92734-2;Q92734;Q92734-4;Q92734-3;C9JTY3;C9JUE0;C9JJP5 Q92734-2 TFG Protein TFG 0 ; 80.24 0.039561 315960000 373500 397090 257410 314130 402790 417020 365310 426260 471700 FALSE TRUE 324141.0287 394481.4896 381894.337 385458.0177 394775.267 433063.0292 329882.2924 335107.6162 415936.1634 0.779304752 0.94841835 0.918156127 0.926723982 0.949124654 1.041176669 0.793107985 0.805670787 1 18.6660026 2.208134521 24.99901298 0.850588989 0.928688209 0.09493524 0.084021294 375.0627332 308160.5337 0.033795518 0.022787812 161.4858674 -2.208134521 0.07809922 AQLGGPEAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AQLGGPEAAK 10 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 0 ;; 147.95 6.05E-05 2765320000 2167820 1808460 1378630 1602540 1629870 1569830 2273640 2365500 2351840 FALSE TRUE 1881337.094 1796580.107 2045340.079 1966421.2 1597438.776 1630222.376 2053142.743 1859656.233 2073808.154 0.907189554 0.866319338 0.986272561 0.948217508 0.770292456 0.786100861 0.990035042 0.896734941 1 20.98385101 0.859201423 1.210679465 1.152948522 0.887852112 0.172635958 0.073382276 6.912055779 4.479127486 2.909223138 0.023560762 7.231050969 -0.859201423 -0.26509641 AQLGGPEAAKS(ph)DETAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AQLGGPEAAKSDETAAK 17 1 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 AQLGGPEAAKS(0.999)DET(0.001)AAK;AQLGGPEAAKS(0.999)DET(0.001)AAK;AQLGGPEAAKS(1)DETAAK;AQLGGPEAAKS(0.998)DET(0.002)AAK;AQLGGPEAAKS(1)DETAAK;AQLGGPEAAKS(1)DETAAK 269.53 1.45E-28 8325070000 3882880 2883620 2993350 2718750 2669860 1925120 4127940 4419140 3729030 TRUE FALSE 3369747.57 2864677.31 4440944.072 3336083.741 2616735.009 1999180.612 3727613.014 3474141.301 3288188.322 1.024803704 0.871202325 1.350574735 1.014565899 0.795798401 0.607988478 1.133637325 1.056551803 1 21.6488615 3.473800956 24.98826412 0.933732551 1.081340437 0.141079362 0.183912548 227.9494493 1715512.714 0.056416886 0.073199655 2977.151643 -3.473800956 0.147607886 AQLGGPEAAKSDETAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQLGGPEAAKSDETAAK 17 1 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 0 ; 204.29 8.13E-12 1099480000 61600 40983 12208.5 17686.5 37476 26246.2 43411 80875 20028.7 FALSE TRUE 53459.40393 40713.77997 18112.57143 21702.49015 36730.30092 27255.9083 39201.0079 63580.51062 17660.9299 3.026986926 2.305302167 1.025572919 1.228841871 2.079748978 1.543288403 2.219645744 3.60006585 1 14.10827369 1.999625314 24.81797711 2.612983012 1.834650893 0.019892391 0.842338113 23.11113232 1530852.738 0.346362169 0.230571241 99.91376265 -1.999625314 -0.778332119 AQLGINEDHS(ph)EGDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQLGINEDHSEGDEK 15 0 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1;C9J8U1;C9JLY8 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 AQLGINEDHS(1)EGDEK 95.365 0.0020317 0 92059 73785 74135 95343 71321 105140 102310 93721 157900 TRUE FALSE 79893.1699 73300.30148 109986.934 116992.0854 69901.85164 109184.8038 92387.99195 73679.49349 139233.2419 0.573808157 0.526456904 0.789947375 0.840259724 0.502048582 0.784186322 0.663548379 0.529180334 1 17.08714417 8 0.049980104 1.055803376 7.97E-08 0.105380381 0.154350559 4037.791231 19.73640841 117.0068905 367.7243366 99999999.92 -8 -1.055803296 AQLGINEDHS(ph)EGDEKSEK ddPTM_MDA-MB-175_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 243.24 2.68E-24 314480000 441060 358650 310270 294940 313740 235270 489690 557520 292340 TRUE FALSE 382772.8035 356294.0045 460317.6098 361910.6349 307497.1878 244320.9891 442199.9392 438298.6866 257779.8982 1.484882282 1.382163648 1.785700177 1.403952121 1.192867209 0.947789144 1.715416688 1.700282643 1 17.97578024 3.500262154 24.20245853 1.365341213 1.544171205 0.123360918 0.270884904 1476.269633 1543987.397 0.080903799 0.119000505 3164.187086 -3.500262154 0.178829991 AQLLHALS(ph)LDEGGPEPEPSLSDSSSGGSFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AQLLHALSLDEGGPEPEPSLSDSSSGGSFGR 31 0 O15049 O15049 N4BP3 NEDD4-binding protein 3 1 AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR 202.44 5.82E-26 649100000 286125 235917 116963.7 180746 203924 159165.6 260967 259030 180255 TRUE FALSE 248312.8563 234367.2457 173527.7365 221787.1418 199866.3114 165288.8036 235658.4605 203638.4503 158945.4592 1.562251967 1.474513628 1.091743906 1.395366328 1.257452162 1.039908937 1.482637262 1.281184447 1 17.27817228 4.388421288 6.290377148 1.242179288 1.540937251 0.400056635 0.151297533 0.192520072 10.80412254 0.036650169 0.099722651 24458.01959 -4.388421288 0.298757963 AQLS(ph)PGIYDDTSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AQLSPGIYDDTSAR 14 0 O75376;O75376-2;A0A088AWL3;E7EVK1 O75376 NCOR1 Nuclear receptor corepressor 1 1 AQLS(1)PGIYDDTSAR;AQLS(1)PGIYDDTSAR;AQLS(1)PGIYDDTSAR;AQLS(1)PGIYDDTSAR;AQLS(1)PGIYDDTSAR 294.17 1.52E-43 4003720000 3010820 2583010 1772461 1989110 2556150 2803870 2437630 2954970 3044570 TRUE FALSE 2612932.509 2566042.037 2629629.068 2440767.827 2505287.616 2911736.693 2201229.018 2323072.661 2684644.403 0.973288122 0.955821946 0.979507403 0.909158704 0.933191604 1.084589337 0.819933178 0.865318572 1 21.35629958 2.212932287 24.99999925 0.885751573 0.96747061 0.24156691 0.063603696 301.2971874 293907.9955 0.025595267 0.017263396 163.2797351 -2.212932287 0.081719037 AQLSVQTS(ph)PVPTPDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQLSVQTSPVPTPDPK 16 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 AQLSVQT(0.059)S(0.93)PVPT(0.011)PDPK 148.36 9.85E-07 49832000 87458 80600 66015 65888 70977 72519 91833 104240 91005 TRUE FALSE 75900.20371 80070.53329 97940.07481 80848.87744 69564.69656 75308.85286 82927.04979 81949.0872 80246.49257 0.94583827 0.997807265 1.220490412 1.007506682 0.86688769 0.93846909 1.033404042 1.02121706 1 16.29215072 3.486551498 24.99781177 0.977088446 1.059851014 0.169474247 0.082954292 835.7871829 2215514.533 0.024608157 0.033713928 3065.854203 -3.486551498 0.082762569 AQLYLPSTS(ph)PPHEGLDGFAQELSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AQLYLPSTSPPHEGLDGFAQELSR 24 0 I3L1Z8;I3L1A6;Q8N137-4;Q8N137-5;Q8N137;Q8N137-3;Q8N137-2;I3L465 I3L1Z8 CNTROB Centrobin 1 AQLYLPS(0.004)T(0.025)S(0.971)PPHEGLDGFAQELSR;AQLYLPS(0.031)T(0.157)S(0.812)PPHEGLDGFAQELSR;AQLYLPS(0.235)T(0.16)S(0.606)PPHEGLDGFAQELSR 171.99 3.86E-12 844140000 371832 323622 213160 265982 388453 385576 334528 382125 373992 TRUE FALSE 322693.4591 321496.1058 316244.889 326377.2784 380723.5453 400409.3582 302085.526 300410.5425 329779.0918 0.978514003 0.974883229 0.958959791 0.989684569 1.154480544 1.214174483 0.916023889 0.910944781 1 18.33114041 AQNDLIWNIKDELKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQNDLIWNIKDELKK 15 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 179.14 3.84E-07 796260000 1469000 849150 769830 836600 714020 488730 1292500 1534400 810950 FALSE TRUE 1274867.928 843571.8777 1142122.363 1026562.817 699812.399 507531.7594 1167153.549 1206280.501 715080.4148 1.782831555 1.179688131 1.5971943 1.435590733 0.978648533 0.709754804 1.632199015 1.686915871 1 19.44774596 4.74959709 23.1856355 1.313960963 1.782832325 0.18881532 0.32136618 1177.5397 2473661.536 0.083891403 1.139493363 56181.98636 -4.74959709 0.468871361 AQNTWGCGNSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 270.56 2.51E-27 538340000 122650 137840 88901 83284 115090 123170 113860 124200 121000 FALSE TRUE 106441.4917 136934.52 131893.821 102194.9051 112799.9342 127908.4296 102817.8747 97640.79653 106695.5178 0.997619149 1.283413987 1.236170212 0.957818165 1.057213428 1.198817272 0.963656926 0.915134942 1 16.70314005 2.2299908 0.697967066 0.907548393 1.150680687 0.259326604 0.110320393 1.37549683 1.227800888 0.231822929 0.070805391 169.8207676 -2.2299908 0.243132294 AQPAAGQQGPEVEPPPPT(ph)PGGPQGEAGVAPTGHVTSIEPAPQGHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQPAAGQQGPEVEPPPPTPGGPQGEAGVAPTGHVTSIEPAPQGHPR 46 0 A0A494C1T9 A0A494C1T9 1 AQPAAGQQGPEVEPPPPT(0.25)PGGPQGEAGVAPT(0.25)GHVT(0.25)S(0.25)IEPAPQGHPR 50.665 0.036022 67217000 13531 14639 6383.4 10254 12749 12631 13744 10992 12839 TRUE FALSE 11742.84407 14542.83545 9470.433591 12582.32742 12495.31984 13116.92274 12411.109 8641.44634 11321.18805 1.037244856 1.284567961 0.836522947 1.111396381 1.103711006 1.15861716 1.096272665 0.763298543 1 13.46673774 1.756714878 25 0.872868163 1.091531471 0.326719434 0.12404005 7.21619996 9950.12329 0.062120004 0.029831069 57.11035739 -1.756714878 0.218663308 AQPDVHFFQGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQPDVHFFQGLR 12 0 Q8TE68;B4DKV7;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 0 ; 138.02 8.19E-05 182000000 446660 564670 315200 397280 521650 520350 483770 552690 464390 FALSE TRUE 387632.7493 560960.6456 467631.7743 487488.496 511270.1856 540368.2012 436854.0599 434501.5445 409490.3432 0.946622444 1.369899571 1.141984865 1.190476171 1.248552485 1.319611586 1.066823839 1.061078855 1 18.6434699 2.10147736 7.864888893 1.043623888 1.208961036 0.308653151 0.113338136 0.262733234 18.03760658 0.043122274 0.029008592 126.321525 -2.10147736 0.165337147 AQPFGFIDS(ph)DTDAEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQPFGFIDSDTDAEEER 17 0 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AQPFGFIDS(0.989)DT(0.011)DAEEER 79.837 0.013317 26395000 24545 20666 15280 16388 26271 17672 18587 23079 30541 TRUE FALSE 21301.31606 20530.24369 22669.45911 20109.14587 25748.2585 18351.85328 16784.4356 18143.73545 26930.47777 0.79097431 0.762342349 0.841777086 0.746705871 0.956101066 0.681452941 0.623250569 0.673724975 1 14.7169522 AQPFGFIDS(ph)DTDAEEERIPATPVVIPMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQPFGFIDSDTDAEEERIPATPVVIPMK 28 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AQPFGFIDS(0.939)DT(0.061)DAEEERIPATPVVIPMK;AQPFGFIDS(0.76)DT(0.24)DAEEERIPATPVVIPMK 121.82 7.25E-05 180999000 150057 86753 54227 78328 85291 78562 87734 113715 89852 TRUE FALSE 130226.5873 86183.11383 80451.35858 96113.56957 83593.87597 81584.33098 79225.57018 89397.93218 79229.79892 1.643656667 1.08776136 1.015417932 1.213098744 1.055081259 1.029717759 0.999946627 1.128337234 1 16.27375552 4.737989108 5.792987376 1.068280519 1.661092127 0.88550373 0.065296799 0.041229003 6.14161837 0.015437264 0.09680145 54700.22445 -4.737989108 0.592811608 AQPFGFIDSDT(ph)DAEEERIPATPVVIPMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQPFGFIDSDTDAEEERIPATPVVIPMK 28 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AQPFGFIDS(0.436)DT(0.564)DAEEERIPATPVVIPMK 83.09 0.011702 86522000 74576 48787 25666 38437 35158 37734 44321 46983 39393 TRUE FALSE 64720.59265 48466.51498 38078.16345 47164.70832 34458.42459 39185.6514 40022.75624 36936.05107 34736.00442 1.863213508 1.395281806 1.096215989 1.35780465 0.992008873 1.128098987 1.152198041 1.063336204 1 15.08414419 7.999999967 0.748064006 1.085281985 139.5283863 0.853438009 0.100173731 128.1911457 0.558391018 0.03541955 29896.31679 99999992.31 -7.999999967 138.4431043 AQPGS(ph)PESSGQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQPGSPESSGQPK 13 0 Q05GC8;Q96PN7-2;Q96PN7-3;Q96PN7-4;Q96PN7-5;Q96PN7 Q05GC8;Q96PN7 BCAR2;TRERF1 Transcriptional-regulating factor 1 1 AQPGS(0.905)PES(0.089)S(0.006)GQPK;AQPGS(0.985)PES(0.014)S(0.001)GQPK 138.81 4.70E-05 476240000 1346400 1025170 649590 814450 935710 837210 1094350 1327590 1110690 TRUE FALSE 1168469.829 1018435.591 963733.8967 999383.3206 917091.2017 869418.0104 988220.1054 1043695.21 979385.4935 1.19306426 1.03987204 0.984018962 1.02041875 0.936394512 0.887717876 1.009020566 1.065663334 1 19.9015173 4.748767451 2.23962633 0.99014806 1.248738392 0.64853221 0.047805701 0.478392704 2.72309296 0.014171333 0.247663519 56074.76349 -4.748767451 0.258590332 AQPPKPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQPPKPER 8 1 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 0 59.245 0.091056 69665000 76283 61313 47112 51392 52377 53882 63861 74102 67597 FALSE TRUE 66202.00827 60910.23087 69895.52078 63061.33908 51334.80017 55954.87541 57667.77005 58255.86396 59605.75967 1.110664618 1.021884986 1.172630316 1.057973918 0.861238922 0.938749472 0.967486538 0.977352932 1 15.86316412 3.429486441 9.008284891 0.953700017 1.09733067 0.664448946 0.050782294 0.187529858 33.13633552 0.014512825 0.018771301 2688.353908 -3.429486441 0.143630653 AQPQDSATFAHT(ph)PPPAQATPAPGFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQPQDSATFAHTPPPAQATPAPGFK 25 0 A0A0A0MQV9;Q9UPS6-2;Q9UPS6 A0A0A0MQV9 SETD1B Histone-lysine N-methyltransferase;Histone-lysine N-methyltransferase SETD1B 1 AQPQDSATFAHT(1)PPPAQATPAPGFK;AQPQDSATFAHT(1)PPPAQATPAPGFK 195.01 2.82E-18 495580000 386820 311770 203842 241623 291210 272060 335190 384010 386350 TRUE FALSE 335700.7569 309721.9623 302420.673 296487.1951 285415.4907 282526.3242 302683.3254 301892.4499 340676.1431 0.985395554 0.909138983 0.887707223 0.870290454 0.837791247 0.829310564 0.888478197 0.886156709 1 18.3780414 4.757643485 1.991283634 0.88139793 1.019418405 0.31517029 0.045825138 0.9792037 4.012115122 0.012262929 0.251253744 57232.60126 -4.757643485 0.138020475 AQPYDPNFYDETYDYGGFTMMFDDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 AQPYDPNFYDETYDYGGFTMMFDDRR 26 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;;; 243.39 5.27E-45 3765407000 1978761 1721561 1062757 1190097 1691186 1669394 1594719 1873897 1153654 FALSE TRUE 1717262.72 1710251.952 1576709.84 1460326.713 1657534.707 1733616.667 1440063.397 1473178.709 1017270.338 1.688108515 1.68121677 1.54994182 1.435534546 1.629394513 1.704184819 1.415615243 1.448168352 1 19.95627169 0.78853972 1.131587622 5.59E-13 1.601590815 0.796483008 0.094248049 1.887810503 0.970832711 4.650465102 0.030314732 6.145252322 -0.78853972 1.601590815 AQQELVPPQQQAS(ph)PPQLPK ddPTM_MDA-MB-175_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 3261840000 4326470 4095940 2642100 3272630 4104820 3689950 4393960 5264110 4682260 TRUE FALSE 3754716.028 4069033.5 3919828.397 4015730.661 4023142.113 3831904.764 3967834.435 4138421.042 4128728.557 0.909412178 0.98554154 0.949403271 0.972631309 0.974426402 0.9281077 0.961030589 1.002347571 1 21.97726614 1.76212033 4.686816454 1.001371457 0.955553701 0.432283851 0.022321102 0.163540714 7.864900587 0.012725933 0.005563238 57.82562422 -1.76212033 -0.045817756 AQQNNVEHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AQQNNVEHK 9 0 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ;;;;; 164.97 6.19E-05 3602590000 3803690 3343850 2657010 3339140 2070830 3077190 3665210 4347420 5905530 FALSE TRUE 3301022.729 3321884.029 3941948.923 4097342.773 2029624.535 3195571.491 3309758.498 3417758.065 5207384.971 0.63391179 0.637917889 0.756992031 0.786833083 0.38975888 0.613661465 0.635589363 0.656329056 1 22.31212764 1.235627228 4.96472711 1.024623976 0.637410153 0.541177876 0.104645001 0.14647993 9.053920515 0.197452285 0.026799061 17.20391263 -1.235627228 -0.387213823 AQQNNVEHKVETFSGVYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQQNNVEHKVETFSGVYK 18 1 P62081;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 150.68 3.20E-08 506610000 282090 264480 143720 145780 278920 212270 289100 389330 124710 FALSE TRUE 244811.0918 262742.6135 213223.4727 178881.5771 273370.0377 220436.1643 261063.1265 306074.8093 109966.9259 2.226224747 2.38928761 1.938978207 1.626685257 2.485929615 2.004567851 2.374014954 2.783335142 1 16.74671015 1.222169441 24.93163591 0.999996322 2.239641959 0.593525377 0.31942046 737.3366398 1121454.255 2.230594922 0.084040638 16.67897821 -1.222169441 1.239645637 AQRLS(ph)QETEALGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQRLSQETEALGR 13 1 Q02818 Q02818 NUCB1 Nucleobindin-1 1 AQRLS(0.966)QET(0.034)EALGR;AQRLS(0.969)QET(0.031)EALGR 186.13 5.97E-06 261300000 558080 569890 441820 442020 651390 680400 558890 650440 715380 TRUE FALSE 484328.314 566146.3551 655485.6298 542387.3969 638428.6134 706575.4283 504688.9338 511348.4677 630808.5914 0.76778966 0.897493095 1.039119693 0.859828804 1.012079769 1.120110661 0.800066677 0.810623816 1 19.26684278 7.793712701 20.85755965 0.918795225 0.0610487 0 0.11682519 0 0 0.02692411 0 62188875.06 -7.793712701 -0.857746525 AQRPFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQRPFER 7 1 Q5JRA6-2;Q5JRA6;A0A0A0MRH6 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 0 62.464 0.077793 131980000 239420 201390 190000 193110 132620 149050 161800 231760 156350 FALSE TRUE 207780.0404 200067.0558 281884.6355 236958.577 129981.1215 154784.0499 146108.6609 182199.9276 137866.4811 1.507110639 1.451165317 2.044620514 1.718754081 0.942804374 1.122709804 1.059783783 1.321567984 1 17.07291222 3.247647886 24.99994654 1.11784516 1.690052818 0.715770479 0.184542021 111.747322 307425.8146 0.055464062 0.070569432 1768.674383 -3.247647886 0.572207658 AQS(ph)LLSTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQSLLSTDR 9 0 O00231;O00231-2;J3QRY4 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 1 AQS(0.995)LLS(0.005)TDR;AQS(1)LLSTDR 173.76 5.79E-05 515050000 590050 456440 231920 441560 426010 283640 515470 452870 487930 TRUE FALSE 512073.3975 453441.6156 344077.2877 541822.9468 417533.2345 294551.8143 465479.7987 356027.2747 430247.4713 1.190183398 1.053908845 0.799719489 1.259328603 0.970449015 0.684610216 1.081888517 0.827494171 1 18.71480719 3.003620457 24.92557478 0.896033666 1.062051688 0.221579816 0.1559804 160.8155045 1107140.1 0.04494371 0.050726652 1008.371255 -3.003620457 0.166018022 AQS(ph)PGAVEEILDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AQSPGAVEEILDR 13 0 H7BXT7;A0A0C4DH16;B8ZZS0;Q9NYM9;E9PHY4 H7BXT7 BET1L BET1-like protein 1 AQS(1)PGAVEEILDR;AQS(1)PGAVEEILDR;AQS(1)PGAVEEILDR;AQS(1)PGAVEEILDR;AQS(1)PGAVEEILDR;AQS(1)PGAVEEILDR 278.72 2.67E-32 3462477000 1536976 1653689 1096019 1222352 1696820 1700983 1293013 2050500 1902760 TRUE FALSE 1333860.727 1642825.808 1626057.454 1499905.704 1663056.602 1766420.917 1167616.798 1612016.532 1677817.88 0.794997325 0.979144296 0.969150152 0.893962165 0.991202097 1.052808494 0.695913908 0.960781591 1 20.6781547 4.750043864 23.19489629 0.936932369 0.794997089 0.186276354 0.096422085 1141.99141 2306572.606 0.02306797 0.327042111 56239.81245 -4.750043864 -0.141935281 AQS(ph)PGS(ph)PLHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQSPGSPLHAR 11 0 Q13796 Q13796 SHROOM2 Protein Shroom2 2 AQS(1)PGS(1)PLHAR;AQS(1)PGS(1)PLHAR 113.37 0.0020481 1002510000 1160340 1313180 875000 1100550 1311520 1414650 1335430 1538200 1414780 TRUE FALSE 1006998.129 1304553.634 1298152.927 1350446.698 1285423.318 1469072.501 1205920.204 1209267.9 1247526.32 0.807195899 1.045712313 1.040581594 1.082499565 1.030377714 1.177588382 0.966649108 0.969332575 1 20.25063882 4.740111627 24.53169598 1.035705507 0.807195802 0.591698206 0.06048119 81.17310619 1283724.555 0.015697642 0.096173568 54968.21415 -4.740111627 -0.228509705 AQS(ph)PGSPLHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQSPGSPLHAR 11 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 AQS(0.985)PGS(0.015)PLHAR 183.52 5.57E-06 121090000 297890 238930 97470 148760 188120 203260 167440 200470 181440 TRUE FALSE 258523.0817 237360.4531 144606.818 182538.2317 184376.7801 211079.5437 151201.6946 157601.0506 159990.3699 1.615866517 1.483592127 0.903847013 1.140932618 1.152424238 1.319326556 0.945067473 0.985065855 1 17.28762554 4.348912522 5.468611645 1.066394683 1.581201211 0.737599367 0.121351981 0.101819965 4.389897987 0.032205979 0.088708955 22331.22371 -4.348912522 0.514806528 AQS(ph)PSYVISTGVS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQSPSYVISTGVSPSR 16 0 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 2 AQS(0.991)PS(0.008)Y(0.001)VIS(0.001)T(0.003)GVS(0.944)PS(0.051)R;AQS(0.852)PS(0.147)Y(0.001)VISTGVS(0.965)PS(0.034)R 227.6 7.13E-15 232640000 355450 322880 211590 270830 327630 349660 266490 373830 359390 TRUE FALSE 308476.3819 320758.98 313915.6317 332326.0909 321110.804 363111.6465 240645.8408 293889.3636 316903.3236 0.973408478 1.012166664 0.990572229 1.048667105 1.013276858 1.145812049 0.759366731 0.92737861 1 18.27368326 2.24371612 24.99999921 0.896530498 1.028017846 0.423413232 0.074256535 119.9098499 581468.3698 0.0277012 0.020796919 175.273444 -2.24371612 0.131487348 AQS(ph)PTPSLPASWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQSPTPSLPASWK 13 0 H0Y9Y3;Q9UMS6-5;Q9UMS6;Q9UMS6-3;Q9UMS6-4;Q9UMS6-2 H0Y9Y3 SYNPO2 Synaptopodin-2 1 AQS(0.997)PT(0.003)PSLPASWK;AQS(0.999)PT(0.001)PSLPASWK 252.68 9.63E-24 673700000 1387750 1350580 845150 1217610 1378320 1181360 1492740 1842450 1531470 TRUE FALSE 1204355.321 1341707.951 1253867.367 1494086.961 1350894.129 1226807.684 1347974.305 1448456.405 1350421.361 0.891836693 0.993547636 0.928500839 1.106385757 1.000350089 0.908462883 0.998187931 1.072595893 1 20.3649782 6.004893513 0.879230919 1.011750868 3.02E-09 0.268420537 0.057525138 24.84453967 2.619644559 0.019816648 40.03106858 1011331.451 -6.004893513 -1.011750865 AQS(ph)SPAAPASLSAPEPASQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AQSSPAAPASLSAPEPASQAR 21 0 J3KPH8;Q8WUI4-3;Q8WUI4-4;Q8WUI4;Q8WUI4-7;Q8WUI4-6;Q8WUI4-5;Q8WUI4-8;H0YI15;Q8WUI4-10 J3KPH8 HDAC7 Histone deacetylase;Histone deacetylase 7 1 AQS(0.5)S(0.5)PAAPASLSAPEPASQAR;AQS(0.5)S(0.5)PAAPASLSAPEPASQAR;AQS(0.5)S(0.5)PAAPASLSAPEPASQAR 409.77 1.12E-151 527310000 314841 268373 163909 198847 241177 248709 281902 327824 251714 TRUE FALSE 273233.9641 266610.0401 243175.9406 243998.2505 236378.0496 258276.9962 254563.1874 257721.3887 221956.6577 1.231023962 1.20118064 1.09560102 1.099305842 1.06497391 1.163637076 1.146904941 1.161133851 1 17.75991846 4.329322787 4.667155283 1.11239801 1.22338206 0.469214878 0.049118513 0.189153418 7.029753187 0.012499074 0.035224891 21346.30876 -4.329322787 0.11098405 AQS(ph)SPASATFPVSVQEPPTKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQSSPASATFPVSVQEPPTKPR 22 1 P56524-2;P56524 P56524-2 HDAC4 Histone deacetylase 4 1 AQS(0.58)S(0.297)PAS(0.065)AT(0.057)FPVSVQEPPTKPR 205.8 6.08E-23 498730000 274590 221310 141190 166200 213980 156460 263560 268840 218740 TRUE FALSE 238302.2358 219856.2 209469.9563 203938.2502 209722.2166 162479.1174 237999.9918 211350.6581 192880.8064 1.235489628 1.139855251 1.086007261 1.05732786 1.087315117 0.842380953 1.233922629 1.095757852 1 17.55735006 4.644146945 1.469440936 1.061069673 1.285314034 0.273362498 0.096270589 1.407104149 3.230372497 0.026984013 0.438584826 44070.39515 -4.644146945 0.224244361 AQS(ph)TDS(ph)LGTSGSLQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AQSTDSLGTSGSLQSK 16 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 2 AQS(0.979)T(0.021)DS(0.998)LGT(0.002)SGSLQSK;AQS(0.986)T(0.014)DS(0.992)LGT(0.008)SGSLQSK;AQS(0.991)T(0.009)DS(0.991)LGT(0.005)S(0.004)GSLQSK 266.39 5.04E-27 698197000 3142450 2361330 1672060 1757410 2122060 1783140 2371240 2723330 3146380 TRUE FALSE 2727167.271 2345818.268 2480673.809 2156456.801 2079835.158 1851738.55 2141277.51 2140967.072 2774418.541 0.982968947 0.845517082 0.894123858 0.777264414 0.749647224 0.667433022 0.771793253 0.77168136 1 21.40375401 4.594372276 1.064332957 0.782278162 1.03253659 0.299860811 0.087801213 1.769699723 1.966695816 0.028340852 0.475401116 39298.16536 -4.594372276 0.250258428 AQS(ph)TDSLGTSGSLQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AQSTDSLGTSGSLQSK 16 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 AQS(0.97)T(0.03)DSLGTSGSLQSK;AQS(0.926)T(0.074)DSLGTSGSLQSK;AQS(0.91)T(0.066)DS(0.024)LGTSGSLQSK 419.26 4.35E-141 1466250000 3684400 2872070 2002120 2567360 2734190 2130230 3135380 3758600 4047400 TRUE FALSE 3197497.205 2853203.183 2970351.929 3150318.328 2679784.968 2212181.327 2831311.33 2954852.639 3568920.983 0.895928271 0.799458211 0.832282907 0.882708904 0.750866993 0.619845981 0.793324185 0.827940056 1 21.76705653 1.22444105 2.892724672 1.046227237 0.793412406 0.410459039 0.076023002 0.477583798 4.713840449 0.292148901 0.021014486 16.76644738 -1.22444105 -0.252814831 AQS(ph)YPDNHQEFSDYDNPIFEK ddPTM_MDA-MB-175_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 243.75 2.63E-30 744290000 507340 459640 333663 373097 410190 357399 488150 540230 506920 TRUE FALSE 440293.7336 456620.5946 495023.5428 457814.3763 402028.0215 371148.3708 440809.2881 424706.0186 446992.4951 0.985013705 1.021539734 1.107453812 1.024210432 0.899406648 0.830323495 0.98616709 0.950141274 1 18.76989108 3.327791886 6.266386034 0.93438979 1.040609473 0.455521224 0.055081422 0.201539585 11.5438386 0.016810968 0.021700585 2127.119488 -3.327791886 0.106219683 AQSDGIWGEHEIDYILLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AQSDGIWGEHEIDYILLVR 19 0 Q13907;Q13907-2 Q13907 IDI1 Isopentenyl-diphosphate Delta-isomerase 1 0 ;;; 195.93 8.59E-16 801220000 1288720 1129090 755280 979210 1060420 1084940 1137570 1258090 1302530 FALSE TRUE 1118412.387 1121672.933 1120535.934 1201554.597 1039319.717 1126678.344 1027248.636 989057.244 1148546.387 0.973763358 0.976602204 0.975612258 1.046152432 0.904900079 0.980960244 0.894390203 0.861138266 1 20.13137769 2.743186986 1.509938563 0.910127378 0.98669346 0.208645329 0.048910566 0.482118416 2.238887961 0.022145551 0.019082486 553.5884055 -2.743186986 0.076566082 AQSDIEHLFQHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQSDIEHLFQHNR 13 0 A0A087X211;Q8TCG1-2;Q8TCG1 A0A087X211 KIAA1524 Protein CIP2A 0 ; 266.97 1.01E-24 149102000 85200 104648 52562 74109 100011 104978 72776 101040 82981 FALSE TRUE 73940.60413 103960.5604 77981.15901 90936.58114 98020.97677 109016.5716 65718.19472 79433.38229 73171.08071 1.01051677 1.420787549 1.065737423 1.242794014 1.339613626 1.489886039 0.898144377 1.08558438 1 16.15898595 2.22136759 24.99999575 1.009518284 1.26258818 0.410689869 0.150402168 242.5326477 352658.617 0.058956338 0.039856939 166.4821171 -2.22136759 0.253069896 AQSEGRPCEYNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQSEGRPCEYNSR 13 1 O00622 O00622 CYR61 Protein CYR61 0 ; 85.006 0.0086488 149840000 157034 139176 91770 101378 112930 132895 131484 126766 124452 FALSE TRUE 136281.559 138261.7437 136150.279 124397.4244 110682.9139 138007.5566 118732.7019 99658.07739 109739.4263 1.241865058 1.259909481 1.240668769 1.133570937 1.008597526 1.257593203 1.081951181 0.908133756 1 16.74372241 -0.964367376 0.161981201 4.40E-14 1.39623945 0.580401682 0.081062439 65.73124069 1.218109305 20.52869042 1.216439682 0.108550699 0.964367376 1.39623945 AQSELAAHQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AQSELAAHQK 10 0 P25786;P25786-2;F5GX11;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ;;; 117.25 0.00098247 1321650000 2220830 1828050 1247270 1671120 1708510 1641230 2113990 2300390 2318130 FALSE TRUE 1927341.689 1816041.419 1850453.944 2050573.337 1674513.994 1704369.18 1908975.575 1808469.5 2044083.312 0.942888031 0.888438063 0.90527325 1.00317503 0.819200462 0.833806122 0.933903018 0.884733753 1 20.96302257 1.233047182 24.94555721 1.000000163 0.900378163 0.257102072 0.052631987 251.933904 1139748.055 0.108066846 0.012727005 17.10201101 -1.233047182 -0.099622 AQSLSHGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQSLSHGLR 9 0 Q13882 Q13882 PTK6 Protein-tyrosine kinase 6 0 66.056 0.07871 0 229210 228640 130310 156070 211780 258300 203800 216650 240670 FALSE TRUE 198919.3178 227138.0488 193328.3519 191508.0789 207565.9923 268236.9681 184035.5074 170321.0835 212218.2668 0.937333627 1.070303948 0.910988271 0.902410908 0.978077879 1.263967387 0.867199182 0.802575038 1 17.69518932 AQSLVIS(ph)PPAPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AQSLVISPPAPSPR 14 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 2 AQS(0.003)LVIS(0.997)PPAPS(1)PR;AQSLVIS(1)PPAPS(1)PR;AQSLVIS(1)PPAPS(1)PR;AQSLVIS(1)PPAPS(1)PR 153.04 9.50E-06 405400000 1432390 1463750 981120 1128470 1363990 1424240 1386300 1596530 1662220 TRUE FALSE 1243096.032 1454134.53 1455592.914 1384706.361 1336849.268 1479031.434 1251856.839 1255124.484 1465714.245 0.848116225 0.992099609 0.993094608 0.944731462 0.912080422 1.009085802 0.854093384 0.856322771 1 20.48317243 2.226703643 24.99989079 0.89159185 0.951801392 0.103603977 0.06091097 381.2768974 803898.3665 0.024044421 0.016355147 168.5402536 -2.226703643 0.060209542 AQSNGSGNGS(ph)DSEMDTSSLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AQSNGSGNGSDSEMDTSSLER 21 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 AQSNGSGNGS(1)DSEMDTSSLER;AQSNGSGNGS(0.999)DS(0.001)EMDTSSLER;AQS(0.001)NGS(0.083)GNGS(0.908)DS(0.007)EMDTSSLER 266.5 5.47E-37 798530000 353782 321162 234793 259332 329183 345125 327933 403341 373578 TRUE FALSE 307028.8123 319052.2657 348339.6801 318217.2942 322632.9023 358402.1821 296130.1081 317089.666 329414.0344 0.93204533 0.968544847 1.057452457 0.96601013 0.979414562 1.087999128 0.898960206 0.962586996 1 18.3295425 2.198801679 24.99990848 0.953382559 0.997537849 0.145562454 0.051039277 306.9569257 193008.3954 0.020485723 0.013811665 158.0526126 -2.198801679 0.04415529 AQSPGS(ph)PLHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQSPGSPLHAR 11 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 AQSPGS(1)PLHAR;AQSPGS(1)PLHAR 130.72 0.00014064 781820000 362230 303390 213811 279060 303760 331030 330070 325690 470300 TRUE FALSE 314360.3877 301397.0111 317210.7148 342424.8382 297715.7703 343764.9383 298059.8622 256043.728 414701.6698 0.758039841 0.726780317 0.76491304 0.825713671 0.717903476 0.828945151 0.71873321 0.61741668 1 18.66171433 4.203576127 21.20134974 0.764824341 0.742410141 0.004212774 0.09981658 263.1559322 159477.3204 0.025354339 0.052788995 15979.97614 -4.203576127 -0.0224142 AQSPSYVISTGVS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AQSPSYVISTGVSPSR 16 0 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 AQSPSYVIS(0.001)T(0.011)GVS(0.91)PS(0.078)R;AQSPSYVISTGVS(0.947)PS(0.052)R;AQSPSYVISTGVS(0.996)PS(0.004)R;AQSPSYVISTGVS(0.99)PS(0.01)R 282.2 1.53E-35 713360000 705390 585390 383151 440547 652430 577240 639660 817370 433008 TRUE FALSE 612170.9243 581544.5345 568444.1052 540579.9297 639447.9195 599446.7963 577625.8717 642581.7863 381818.2875 1.603304358 1.523092407 1.488781768 1.415804186 1.674744087 1.56997927 1.512829245 1.682951831 1 18.54252668 1.23070737 24.9986971 0.999998989 1.558766717 0.823054115 0.081446095 120.151416 382438.0667 0.21535608 0.020304141 17.01011973 -1.23070737 0.558767728 AQSS(ph)PAAPASLSAPEPASQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQSSPAAPASLSAPEPASQAR 21 0 J3KPH8;Q8WUI4-3;Q8WUI4-4;Q8WUI4;Q8WUI4-7;Q8WUI4-6;Q8WUI4-5;Q8WUI4-8;H0YI15;Q8WUI4-10 J3KPH8 HDAC7 Histone deacetylase;Histone deacetylase 7 1 AQS(0.107)S(0.893)PAAPASLSAPEPASQAR 303.8 2.49E-55 214150000 138230 107440 76784 82440 105710 107190 118530 122780 113520 TRUE FALSE 119962.5553 106734.2196 113916.9992 101159.262 103606.5778 111313.6687 107034.9788 96524.45248 100099.7949 1.198429581 1.066278104 1.138034292 1.010584109 1.035032868 1.11202694 1.069282699 0.96428222 1 16.61107949 8 0.223094922 0.979526473 1.990275619 0.522470105 0.048090997 80.59298758 1.244819033 0.231303284 28.53306418 100000000 -8 1.010749146 AQSTDS(ph)LGTSGSLQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AQSTDSLGTSGSLQSK 16 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 AQSTDS(0.997)LGT(0.003)SGSLQSK;AQSTDS(0.999)LGT(0.001)SGSLQSK;AQSTDS(0.999)LGT(0.001)SGSLQSK 267.38 6.55E-27 91148000 752270 608380 387430 492830 515300 448930 697440 677150 746700 TRUE FALSE 652855.6135 604383.5117 574792.4439 604734.5839 505046.5382 466200.6276 629802.3761 532346.7421 658425.9766 0.991539879 0.91792173 0.872979597 0.918454929 0.767051356 0.708053212 0.956527231 0.808514185 1 19.32866173 4.656406619 1.180889023 0.850518191 1.042684404 0.195575074 0.086156012 2.180367961 2.873984463 0.025730109 0.499018413 45332.18151 -4.656406619 0.192166213 AQSYEYVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQSYEYVYR 9 0 Q86V21;Q86V21-2;Q86V21-3 Q86V21 AACS Acetoacetyl-CoA synthetase 0 ; 109.29 0.0057536 416070000 472730 492590 432260 344250 406080 459830 461790 468830 508490 FALSE TRUE 410257.5328 489354.1439 641302.3818 422417.224 397999.8025 477519.9576 417005.6769 368574.3529 448376.8915 0.914983668 1.091390197 1.430275275 0.942103021 0.887645662 1.064996807 0.930033828 0.822019065 1 18.7743524 3.526260183 24.99987148 0.929951071 1.147809773 0.323137508 0.138948911 423.1880138 215299.5412 0.038281784 0.05677989 3359.388128 -3.526260183 0.217858702 AQT(ph)PPGPSLSGS(ph)KSPCPQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQTPPGPSLSGSKSPCPQEK 20 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AQT(1)PPGPS(0.005)LS(0.017)GS(0.885)KS(0.092)PCPQEK 89.181 0.0048476 2656400000 1776800 1146600 1063900 976380 1147500 888510 1636000 1792300 1650100 TRUE FALSE 1541991.378 1139067.909 1578405.599 1198082.002 1124666.995 922691.5546 1477340.972 1409030.593 1455027.058 1.059768181 0.782849984 1.084794671 0.823408744 0.772952633 0.634140478 1.015335738 0.968387897 1 20.47261455 AQT(ph)PPGPSLSGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AQTPPGPSLSGSK 13 0 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AQT(1)PPGPSLSGSK;AQT(1)PPGPSLSGSK;AQT(1)PPGPSLSGSK;AQT(1)PPGPSLSGSK;AQT(1)PPGPSLSGSK 213.55 5.61E-08 4169660000 3561640 2393970 2092930 2586690 2625050 2006420 2885990 3361960 6569370 TRUE FALSE 3090960.25 2378243.853 3105077.948 3174037.5 2572816.641 2083608.276 2606107.134 2643031.017 5792746.562 0.533591487 0.410555481 0.53602862 0.547933086 0.44414452 0.359692635 0.449891447 0.456265605 1 22.46581612 1.238009104 24.95859001 1.000000623 0.464746796 0.889193442 0.059095779 4.14868288 187571.5808 0.085519729 0.014845923 17.29852622 -1.238009104 -0.535253827 AQT(ph)PPGPSLSGSKS(ph)PCPQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQTPPGPSLSGSKSPCPQEK 20 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AQT(0.998)PPGPS(0.026)LS(0.336)GS(0.057)KS(0.583)PCPQEK;AQT(1)PPGPSLSGS(0.008)KS(0.992)PCPQEK 141.43 4.38E-07 2701600000 4705300 2937200 2701400 2462800 2931500 2129130 4089100 4645900 4160600 TRUE FALSE 4083482.683 2917905.34 4007806.076 3022016.382 2873168.885 2211039.009 3692539.711 3652410.439 3668738.608 1.11304814 0.795342937 1.092420721 0.823720822 0.783148976 0.602670085 1.006487544 0.995549378 1 21.80685269 AQTAPNKDVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQTAPNKDVQR 11 1 P49588;P49588-2;H3BPK7 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 82.543 0.017009 329131000 377733 259823 124625 132025 266009 260442 284904 347790 80151 FALSE TRUE 327814.627 258116.2056 184894.0668 162003.2941 260715.9413 270461.3723 257274.0539 273417.815 70675.64009 4.638297249 3.65212406 2.616093276 2.292208375 3.688908102 3.826797634 3.640208332 3.868628776 1 16.10892542 1.233402725 24.99083816 0.999996109 3.50028708 0.595339615 0.654625978 125.6439257 608695.6733 1.392630721 0.169638609 17.11601762 -1.233402725 2.500290971 AQTAPTKTS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AQTAPTKTSPR 11 1 Q14669-3;Q14669;Q14669-2;Q14669-4 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 AQTAPT(0.01)KT(0.441)S(0.548)PR;AQT(0.005)APT(0.016)KT(0.087)S(0.892)PR;AQT(0.002)APT(0.013)KT(0.065)S(0.92)PR 104.24 0.0069081 415585000 1305490 1029150 595840 703890 936130 784650 1065100 1257810 627460 TRUE FALSE 1132966.189 1022389.446 883990.217 863718.9828 917502.8445 814835.9932 961806.7659 988837.1198 553282.3936 2.047717769 1.847861883 1.597719767 1.561081633 1.658290333 1.472730748 1.738365032 1.787219567 1 19.07765649 4.445068371 2.134213031 1.575217602 2.064519123 0.386570731 0.216304756 0.440500758 3.377751543 0.056285062 0.327364771 27865.5982 -4.445068371 0.489301521 AQTLPTSVVTITSESS(ph)PGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AQTLPTSVVTITSESSPGKR 20 1 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 AQTLPTSVVTITSES(0.007)S(0.993)PGKR;AQTLPTSVVTITSES(0.199)S(0.801)PGKR;AQTLPTSVVTITSES(0.04)S(0.96)PGKR;AQTLPTSVVTITSES(0.06)S(0.94)PGKR;AQTLPTSVVTITS(0.002)ES(0.41)S(0.588)PGKR;AQTLPTSVVTITSES(0.043)S(0.957)PGKR 279.69 6.89E-45 9478650000 4303090 3407720 2640720 2758210 3425310 2947110 3599750 4377090 3839200 TRUE FALSE 3734425.754 3385334.463 3917781.025 3384503.737 3357153.033 3060487.229 3250646.799 3441083.366 3385334.15 1.103118803 1.000000093 1.157280449 0.999754703 0.991675529 0.904042878 0.960214459 1.016467862 1 21.69086681 3.536623543 8.868415295 0.97695605 1.078442277 0.531209012 0.048171472 0.347457017 49.35893964 0.0131692 0.01949075 3440.515696 -3.536623543 0.101486227 AQTPPGPSLSGSKS(ph)PCPQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AQTPPGPSLSGSKSPCPQEK 20 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AQT(0.001)PPGPS(0.01)LS(0.037)GS(0.17)KS(0.783)PCPQEK;AQTPPGPSLSGS(0.007)KS(0.993)PCPQEK;AQTPPGPSLSGS(0.203)KS(0.797)PCPQEK;AQTPPGPSLSGSKS(1)PCPQEK;AQTPPGPSLS(0.001)GS(0.017)KS(0.982)PCPQEK 229.77 1.29E-25 6158820000 7742526 4992158 3882555 4458160 4705982 3293226 6392329 7440068 5231453 TRUE FALSE 6719331.572 4959364.185 5760171.584 5470453.367 4612342.165 3419918.535 5772401.917 5849067.357 4612996.586 1.456608833 1.075085163 1.248683253 1.185878477 0.999858135 0.741365937 1.251334531 1.267953975 1 22.13727279 7.238568844 1.233175583 1.101297947 199.9999975 0.320929617 0.161380097 1287.329867 4.48228419 0.050064708 721403.1672 17320835.77 -7.238568844 198.8986996 AQVADVVVSR ddPTM_MDA-MB-175_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 ;; 179.42 4.91E-06 1274190000 1683030 1645530 1177740 1197100 1616610 1915190 1741700 1737920 1866210 FALSE TRUE 1460613.321 1634720.405 1747299.003 1468919.852 1584442.624 1988868.599 1572790.202 1366279.333 1645588.78 0.887593145 0.993395449 1.061807801 0.892640901 0.962842384 1.208606076 0.955761379 0.830267774 1 20.65017243 1.997481103 24.99597704 0.900011463 1.003987957 0.112195607 0.098784095 165.7446228 1644750.05 0.040857079 0.02701228 99.42168134 -1.997481103 0.103976494 AQVARPGGDTIFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQVARPGGDTIFGK 14 1 P49773;D6REP8;D6RE99;D6RD60;D6RC06 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ; 148.57 7.04E-06 4318300000 5593400 4514000 2586100 2959200 3914500 3717900 4845200 5404600 2016270 FALSE TRUE 4854218.018 4484347.237 3836746.61 3631131.589 3836609.109 3860930.019 4375313.25 4248868.349 1777908.858 2.730296324 2.522259349 2.158010853 2.04236093 2.157933514 2.171613017 2.460932253 2.38981224 1 20.76174994 1.236710783 24.99879924 0.999998341 2.3196235 0.802763448 0.207003004 22.69329022 306591.335 0.34139066 0.054313121 17.24688958 -1.236710783 1.319625159 AQVFHICGPEDVCEAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQVFHICGPEDVCEAYR 17 0 Q9ULW8 Q9ULW8 PADI3 Protein-arginine deiminase type-3 0 ; 164.68 2.56E-09 773890000 205829 223535 151748 145849 217777 224444 223503 229306 260361 FALSE TRUE 178628.1761 222066.5839 225133.8404 178966.2446 213443.6638 233078.5059 201827.7135 180270.6964 229581.4192 0.778060249 0.967267232 0.980627444 0.779532792 0.92970792 1.015232447 0.879111708 0.785214662 1 17.80864636 2.013616822 24.83689173 0.863734782 0.91261515 0 0.093680633 690.9724155 1260318.773 0.037508609 0.025274388 103.1850603 -2.013616822 0.048880368 AQVIYTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQVIYTR 7 0 P62851 P62851 RPS25 40S ribosomal protein S25 0 113.41 0.014274 158580000 154100 175830 104640 106630 148370 142800 129020 153160 136240 FALSE TRUE 133735.2946 174674.9612 155244.254 130841.9712 145417.7273 148293.6084 116507.6603 120407.9259 120133.8624 1.11321897 1.454002707 1.292260574 1.089134809 1.210464097 1.234403069 0.96981532 1.002281318 1 16.87428334 2.394120095 0.752944104 0.94314608 1.280428691 0.496411098 0.107167195 0.68687099 0.798219605 0.159113334 0.064616679 247.8107231 -2.394120095 0.337282612 AQVLATIHGHAGAFPAAGDAGEGAPGGGS(ph)SPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AQVLATIHGHAGAFPAAGDAGEGAPGGGSSPER 33 0 Q86WR7;D3DRR9 Q86WR7 PROSER2;C10orf47 Proline and serine-rich protein 2 1 AQVLATIHGHAGAFPAAGDAGEGAPGGGS(0.549)S(0.451)PER;AQVLATIHGHAGAFPAAGDAGEGAPGGGS(0.556)S(0.444)PER;AQVLATIHGHAGAFPAAGDAGEGAPGGGS(0.556)S(0.444)PER 99.866 0.00010499 588830000 215314 186850 125898 154719 184601 225845 180621 234299 211485 TRUE FALSE 186859.7094 185622.57 186782.6939 189850.3137 180927.8013 234533.4033 163104.4032 184195.9822 186483.4842 1.002017472 0.995383429 1.001604484 1.018054304 0.970208177 1.257663134 0.874631895 0.987733487 1 17.50868834 AQVLATIHGHAGAFPAAGDAGEGAPGGGSS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQVLATIHGHAGAFPAAGDAGEGAPGGGSSPER 33 0 Q86WR7;D3DRR9 Q86WR7 PROSER2;C10orf47 Proline and serine-rich protein 2 1 AQVLATIHGHAGAFPAAGDAGEGAPGGGS(0.168)S(0.832)PER 138.84 6.84E-09 377260000 240270 195100 114600 166190 205280 209490 190970 232070 213390 TRUE FALSE 208517.7107 193818.3753 170020.9433 203925.9796 201195.3296 217549.2159 172449.7588 182443.6365 188163.2773 1.108174314 1.030054206 0.903581962 1.083771406 1.069259276 1.156172549 0.916489983 0.969602778 1 17.52162557 2.211230811 24.99875413 0.96171086 1.051805 0.306975915 0.067834004 295.570763 270358.3268 0.028667072 0.019332601 162.6412902 -2.211230811 0.09009414 AQVLVEDISDILEEHAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AQVLVEDISDILEEHAEK 18 0 Q5VV41;Q5VV41-2;B0QZD3;B0QZD4 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 0 ;;; 199.12 1.66E-15 174108000 265939 212588 187608 208767 200562 204600 240062 293704 289987 FALSE TRUE 230794.4873 211191.4954 278335.8563 256170.7382 196571.2086 212471.0944 216780.8242 230897.6852 255705.0672 0.902580813 0.825918304 1.088503483 1.001821125 0.768741937 0.830922503 0.847776802 0.902984394 1 17.96412122 AQYDELAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 AQYDELAR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;; 278.58 7.65E-19 33329599000 15915420 15445900 10474990 11648650 14242280 15812240 14736780 16165130 15759510 FALSE TRUE 13812156.92 15344434.87 15540730.2 14293654.02 13958886.49 16420547.1 13307609.34 12708342.75 13896438.68 0.99393501 1.104199084 1.11832467 1.028583967 1.0044938 1.181637071 0.957627321 0.914503567 1 23.72821187 2.072655285 13.91529461 0.946622173 1.070399997 0.450893705 0.059285377 0.86644441 164.3826563 0.023259356 0.015681081 118.2102905 -2.072655285 0.123777824 AQYEQTLAELHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQYEQTLAELHR 12 0 A0A0C4DGG1;Q9UKS6;E9PIY1 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 0 115.12 0.0009841 480850000 252680 305400 207760 225530 298530 271030 239050 305880 310120 FALSE TRUE 219287.6978 303393.8073 308233.4309 276740.0335 292589.8371 281456.6995 215866.9678 240469.9424 273457.9669 0.801906415 1.109471451 1.127169321 1.012002088 1.069962746 1.029250318 0.789397253 0.879367111 1 18.06095957 2.303141865 10.83640909 0.883369327 1.03509259 0.279477357 0.101442186 0.549057143 89.45222935 0.036811382 0.028486984 200.9749201 -2.303141865 0.151723263 AQYSLPGILHFLQHEWAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AQYSLPGILHFLQHEWAR 18 0 O43815-2;O43815 O43815-2 STRN Striatin 0 ; 84.499 0.0022019 123891000 163594 159257 102024 119173 123986 147033 141605 159937 126787 FALSE TRUE 141974.6384 158210.8303 151363.1476 146233.0511 121518.9212 152689.4547 127872.1689 125735.7172 111798.3853 1.269916717 1.415144144 1.353893862 1.308006826 1.086947015 1.365757245 1.143774738 1.124664876 1 16.77053983 -0.51811686 0.304166492 1.10E-15 1.375590307 0.594280513 0.08692971 21.9508586 0.80080081 13.53163582 0.178895468 0.303307493 0.51811686 1.375590307 ARAEEESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ARAEEESR 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 78.113 0.028698 104760000 57899 54700 24058 31292 31860 49139 52299 58036 32555 FALSE TRUE 50247.50045 54340.6721 35692.52927 38397.32687 31226.04833 51029.40913 47227.05103 45625.45304 28706.38499 1.750394572 1.892982071 1.243365519 1.337588376 1.087773621 1.777632717 1.64517584 1.589383444 1 14.80908404 4.247593417 24.98161984 1.417391982 1.821688478 0.349864283 0.245158427 234.6974119 649077.9997 0.063247022 0.162228672 17684.52573 -4.247593417 0.404296496 ARAPS(ph)PGDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ARAPSPGDYK 10 1 P55198 P55198 MLLT6 Protein AF-17 1 ARAPS(0.97)PGDY(0.03)K;ARAPS(1)PGDYK;ARAPS(0.997)PGDY(0.003)K 97.273 0.0037373 750810000 2205940 922620 628100 646360 989760 884390 1139120 1241720 914580 TRUE FALSE 1914419.44 916559.2485 931851.2609 793125.917 970065.7124 918413.0556 1028648.318 976187.8411 806459.3943 2.3738572 1.136522502 1.155484414 0.983466648 1.202869877 1.138821201 1.275511607 1.210461243 1 19.62124237 4.738880124 24.99909508 1.147796077 2.373857567 0.949361942 0.089682096 5.365795409 419658.5589 0.022110776 0.125442692 54812.56479 -4.738880124 1.226061491 ARDDLITDLLNEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ARDDLITDLLNEAK 14 1 P36543;C9J8H1;P36543-2 P36543 ATP6V1E1 V-type proton ATPase subunit E 1 0 ;;;; 275.83 4.03E-33 1213145000 2703070 2268800 1666940 2045150 2146340 1829610 2581740 3228360 2600350 FALSE TRUE 2345852.451 2253896.103 2473077.76 2509532.566 2103632.033 1899996.281 2331363.252 2538000.337 2292939.585 1.023076432 0.982972302 1.078562111 1.094460832 0.917438927 0.82862902 1.016757383 1.106876236 1 21.12876691 1.992828006 24.95081846 1.061295551 0.987259988 0.102892791 0.079584203 665.3713414 2314773.693 0.036511085 0.023507514 98.36214838 -1.992828006 -0.074035563 AREEAER ddPTM_MDA-MB-175_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 ; 98.458 0.010258 213590000 181987 158178 116803 125475 90429 178951 156396 166446 186748 FALSE TRUE 157936.9569 157138.9183 173289.3215 153966.0165 88629.63982 185835.3608 141228.74 130852.8182 164670.8642 0.959106868 0.954260604 1.052337475 0.934992461 0.538222959 1.128526055 0.857642551 0.794632486 1 17.32922579 3.46971151 24.99986337 0.855993604 0.986558836 0.12495002 0.151247216 342.3291039 1154984.645 0.041834783 0.054121744 2949.249468 -3.46971151 0.130565232 AREEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AREEEER 7 1 Q9NWB6 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 0 ; 148.99 0.0018667 309490000 310060 298920 200881 221204 167132 286230 290870 307690 297280 FALSE TRUE 269084.7854 296956.3748 298027.7235 271431.7491 163806.4002 297241.4533 262661.4722 241892.8879 262135.8971 1.026508725 1.132833687 1.136920684 1.035461957 0.624891142 1.133921209 1.002004972 0.922776661 1 17.99995541 3.46998045 24.99972671 0.9388639 1.09950052 0.248781929 0.130148904 237.604315 831840.9381 0.036556274 0.047302575 2951.07638 -3.46998045 0.16063662 AREESWGPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AREESWGPPR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 152.54 1.63E-05 1148500000 700430 662290 415830 508400 667520 765340 638540 770760 588390 FALSE TRUE 607866.4008 657939.3734 616926.7789 623839.9904 654237.658 794783.125 576614.4891 605938.9721 518831.2045 1.17160725 1.268118355 1.189070306 1.202394893 1.260983635 1.531872251 1.11137203 1.167892306 1 18.98490573 1.479523508 1.738460193 0.988056508 1.259234181 0.345678607 0.110230288 0.650832642 2.916309967 0.267401784 0.031722548 30.16640158 -1.479523508 0.271177673 AREETDKEEPASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AREETDKEEPASK 13 2 P05455 P05455 SSB Lupus La protein 0 ;;; 187.16 4.04E-06 1410272000 2684560 1702160 1497920 1692090 1365070 1058970 2353900 2670680 1950800 FALSE TRUE 2329788.594 1690978.399 2222319.122 2076304.896 1337907.778 1099709.261 2125619.14 2099575.865 1720178.646 1.35438758 0.983024875 1.291911818 1.207028643 0.777772576 0.639299449 1.235696737 1.22055687 1 20.71412697 8 0.793693203 1.040348638 67.47821403 0.167527394 0.211078001 1147.637042 4.107047024 0.082130893 136997.8882 100000000 -8 66.43786539 ARENIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 126.57 0.0035929 2134510000 2138480 1784070 1059090 1342400 1578290 1664080 2408720 2523660 1616470 FALSE TRUE 1855874.45 1772350.327 1571269.466 1647212.437 1546885.117 1728098.234 2175122.705 1983994.948 1425372.758 1.302027445 1.243429353 1.10235688 1.155636256 1.085249531 1.212383375 1.526002719 1.391913054 1 20.44290783 2.456828302 24.99864176 1.338208433 1.173257654 0.129242842 0.144192932 366.0383081 450915.1828 0.054085567 0.041898836 286.3045846 -2.456828302 -0.164950779 AREQAEAEVASLNR ddPTM_MDA-MB-175_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 ;;; 272.96 4.90E-33 1931420000 1256260 1141460 577931 702198 1173500 1142750 1191820 1364620 348777 FALSE TRUE 1090242.058 1133961.674 857420.3647 861642.7883 1150149.646 1186712.332 1076237.48 1072806.632 307544.9804 3.544984076 3.687140895 2.787951094 2.801680545 3.739777006 3.85866266 3.499447393 3.488291798 1 18.2304379 4.262561018 24.38594835 3.13919465 3.616063082 0.070582821 0.813328593 587.1511285 596569.0205 0.200395507 0.529514835 18304.63266 -4.262561018 0.476868433 ARFEELCSDLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 ARFEELCSDLFR 12 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;P17066;P48741 A0A0G2JIW1;P17066 HSPA1B;HSPA1A;HSPA6;HSPA7 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 6;Putative heat shock 70 kDa protein 7 0 ;;;;;;;; 213.73 4.71E-09 32179090000 8060566 7435033 5223007 4938039 7459301 8324259 8528148 9275489 5288956 FALSE TRUE 6995341.78 7386191.779 7748870.655 6059296.228 7310875.504 8644498.63 7701089.52 7291997.859 4663701.647 1.499954823 1.583761642 1.661527954 1.299246111 1.56761218 1.853570251 1.65128263 1.563564398 1 22.15304407 1.239087868 5.746231631 0.975076217 1.590354602 0.639842146 0.138059065 0.094383645 10.69943708 0.228867911 0.035530873 17.34154825 -1.239087868 0.615278384 ARFEELNADLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 ARFEELNADLFR 12 1 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 ;;;;;;;;; 231.52 2.96E-12 40975058000 16231000 14706440 9924097 10110399 15056327 15907020 16100650 18305450 8878816 FALSE TRUE 14086032.23 14609832.43 14723423.5 12406119.62 14756735.55 16518973.35 14539211.44 14390971.97 7829172.487 1.79917255 1.866076198 1.880584893 1.584601647 1.884839755 2.109925842 1.857055962 1.838121716 1 22.9004284 1.23816067 6.855469942 0.980050345 1.855466971 0.818930907 0.126007341 0.047861611 12.17778105 0.194728402 0.032138301 17.30456432 -1.23816067 0.875416626 ARFEEVLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ARFEEVLSK 9 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 86.014 0.013156 811990000 710390 568250 393160 422600 644260 569730 740460 771700 605010 FALSE TRUE 616510.1616 564517.1283 583293.491 518557.789 631440.4865 591647.8818 668650.3032 606677.9604 533486.407 1.155624873 1.058165908 1.093361487 0.972016873 1.1836112 1.109021475 1.253359588 1.137194786 1 19.02509199 3.199939279 24.99982244 1.144080438 1.070644834 0.153628582 0.076855739 276.1312149 178740.5422 0.022909928 0.025977969 1584.671615 -3.199939279 -0.073435604 ARGDS(ph)EALDEES ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ARGDSEALDEES 12 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WZ99 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 1 ARGDS(1)EALDEES;ARGDS(1)EALDEES;ARGDS(1)EALDEES;ARGDS(1)EALDEES;ARGDS(1)EALDEES 266.75 2.44E-21 10562960000 3732940 3053690 2528570 2698930 3294220 3743400 3764520 3856950 4028400 TRUE FALSE 3239622.521 3033630.109 3751394.91 3311763.307 3228671.467 3887411.02 3399437.43 3032171.257 3552167.141 0.912012975 0.854022344 1.05608626 0.932321925 0.908930053 1.094377282 0.957003794 0.853611651 1 21.76026804 4.281450221 24.9996301 0.961148772 0.883017586 0.202673429 0.07078378 259.1303211 151038.6182 0.018155401 0.048034026 19118.34175 -4.281450221 -0.078131186 ARGQGAT(ph)AGGLLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ARGQGATAGGLLLR 14 1 A0A5F9ZI24;A0A5F9ZHS6;A0A5F9ZHU1;A6NHY2 A0A5F9ZI24 ANKDD1B Ankyrin repeat and death domain-containing protein 1B 1 ARGQGAT(1)AGGLLLR 124.86 0.00015297 58961000 5641.8 3869.2 3704.5 717.6 3408.8 4181.9 5363.1 3457.1 2372.3 TRUE FALSE 4896.221835 3843.78297 5496.008591 880.5420478 3340.971549 4342.780399 4842.987387 2717.826068 2091.849397 2.34061871 1.837504639 2.627344301 0.420939504 1.597137707 2.076048307 2.315170201 1.299245573 1 11.03056327 ARGQGS(ph)SPVAMQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ARGQGSSPVAMQK 13 1 P18206;P18206-2 P18206 VCL Vinculin 1 ARGQGS(0.639)S(0.361)PVAMQK;ARGQGS(0.687)S(0.313)PVAMQK 106.19 0.00084407 169184000 221366 188379 128930 155295 244245 227778 253415 293900 336430 TRUE FALSE 192111.9222 187141.5259 191280.9792 190557.1033 239385.0024 236540.7671 228838.8523 231051.7721 296657.6287 0.647588006 0.630833351 0.644786989 0.642346884 0.806940322 0.79735272 0.771390418 0.778849926 1 18.17843936 -2 0.22633232 2.510973385 0.583249635 0.774017695 0.054090556 47.89232786 0.746768198 32.96517218 0.255862076 0.01 2 -1.92772375 ARGQGSS(ph)PVAMQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ARGQGSSPVAMQK 13 1 P18206;P18206-2 P18206 VCL Vinculin 1 ARGQGS(0.205)S(0.795)PVAMQK 154.6 2.80E-05 97039000 130000 106120 70165 88157 129460 131110 142730 158300 202060 TRUE FALSE 112820.1706 105422.8907 104097.0287 108174.3942 126883.9993 136153.8865 128888.0666 124448.7769 178172.697 0.633206841 0.591689369 0.584247926 0.607132272 0.712140532 0.764168073 0.723388425 0.698472768 1 17.44291675 -1.646365851 0.551476547 10 0.621478868 0.770084787 0.058290684 50.65594224 0.735164393 545.3508104 0.036520607 0.022575332 1.646365851 -9.378521132 ARHDS(ph)PDLAPNVTYSLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ARHDSPDLAPNVTYSLPR 18 1 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 ARHDS(1)PDLAPNVTYSLPR;ARHDS(1)PDLAPNVTYSLPR;ARHDS(1)PDLAPNVTYSLPR 189.51 1.96E-14 1203020000 367865 334873 236582 244158 309250 328086 307789 350051 226924 TRUE FALSE 319250.7082 332673.1972 350993.8465 299597.8056 303096.53 340707.6807 277939.6702 275195.3177 200097.3032 1.595477315 1.662557125 1.754115827 1.497260587 1.514745702 1.702710008 1.389022569 1.375307479 1 17.6103422 0.703347437 0.784707372 2.04E-12 1.629649582 0.82015354 0.091534674 2.209820198 0.582889434 3.848655777 0.035820614 5.050651901 -0.703347437 1.629649582 ARIPS(ph)GK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ARIPSGK 7 1 Q9NTM9;A0A0B4J226 Q9NTM9 CUTC Copper homeostasis protein cutC homolog 1 ARIPS(1)GK 50.108 0.096745 165250000 255740 199300 124380 156300 246180 232770 315410 320920 235350 TRUE FALSE 221943.311 197990.7852 184530.584 191790.3039 241281.4996 241724.8125 284821.5867 252293.7554 207527.1911 1.069466174 0.954047439 0.889187499 0.924169517 1.162650053 1.16478622 1.372454305 1.215714211 1 17.66294085 3.164164206 4.614537535 1.204828583 0.953673148 0.547989596 0.100452872 0.151747173 6.043243818 0.031762349 0.036873995 1459.365941 -3.164164206 -0.251155435 ARLEIEPEWAYGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ARLEIEPEWAYGK 13 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ;; 151.99 4.10E-05 1302770000 1923580 1529540 1100899 1188050 1633600 1335810 1881530 2217480 1394940 FALSE TRUE 1669374.029 1519492.351 1633297.439 1457814.911 1601094.556 1387199.475 1699059.51 1743289.158 1230031.782 1.357179589 1.235327715 1.327849786 1.18518475 1.301669257 1.12777531 1.381313503 1.417271638 1 20.23026416 4.751480425 22.6680033 1.265212637 1.357179813 0.055567607 0.123997394 2030.761175 3562755.016 0.029560826 0.472375872 56426.15082 -4.751480425 0.091967176 ARLS(ph)SAYLLGVPGSEQPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ARLSSAYLLGVPGSEQPDR 19 1 Q96P48-3;Q96P48;E7EU13;Q96P48-7;Q96P48-2;Q96P48-4;Q96P48-1 Q96P48-3 ARAP1 "Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1" 1 ARLS(0.821)S(0.179)AYLLGVPGSEQPDR 114.2 9.82E-05 198260000 68449 91399 91244 68470 114220 153320 97428 121990 123510 TRUE FALSE 59403.29122 90798.59395 135369.9036 84017.16 111947.2455 159218.3196 87979.44756 95903.38783 108908.7885 0.545440749 0.833712276 1.242965838 0.77144518 1.027899098 1.461941885 0.807826887 0.88058447 1 16.73276085 4.590054845 3.641013932 1.010647807 0.550485474 0.360698934 0.204811199 0.285191615 6.205727479 0.051303036 0.267645586 38909.4279 -4.590054845 -0.460162334 ARLS(ph)YSDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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(0.994)YS(0.006)DK;ARLS(1)YSDK;ARLS(1)YSDK;ARLS(0.997)YS(0.003)DK;ARLS(0.996)YS(0.004)DK;ARLS(0.998)YS(0.002)DK 163.83 0.00020206 38955830000 12129170 10655460 10926580 11283160 10533010 9954790 11873940 13867880 22946950 TRUE FALSE 10526269.45 10585463.58 16210710.64 13845173.93 10323423.71 10337757.21 10722407.13 10902341.78 20234187.71 0.520221993 0.523147444 0.801154505 0.684246589 0.510197091 0.510905471 0.529915373 0.538807979 1 24.2702916 1.235345677 24.99968721 1.000000581 0.577766404 0.66394306 0.094503598 61.04756794 474630.376 0.173153636 0.024843646 17.19276302 -1.235345677 -0.422234177 ARLS(ph)YSDKNLIDSMDQSAFAGFSFVNPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ARLSYSDKNLIDSMDQSAFAGFSFVNPK 28 2 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 1 ARLS(0.5)YS(0.5)DKNLIDSMDQSAFAGFSFVNPK;ARLS(0.955)YS(0.043)DKNLIDS(0.002)MDQSAFAGFSFVNPK;ARLS(0.477)Y(0.392)S(0.131)DKNLIDS(0.001)MDQSAFAGFSFVNPK 310.88 5.94E-83 7659900000 4610040 3885420 2471530 2241640 3373480 2987080 4686710 5786570 1199550 TRUE FALSE 4000811.534 3859896.42 3666770.175 2750638.623 3306354.348 3101994.9 4232193.586 4549157.037 1057740.566 3.782412875 3.649190119 3.466606363 2.600485141 3.125865128 2.932661374 4.001164107 4.300824971 1 20.01255439 3.992543571 17.51704635 3.183170253 3.676337453 0.08262774 0.888322255 23.03318322 54150.03575 0.234480546 0.452494206 9829.774856 -3.992543571 0.4931672 ARLSS(ph)AYLLGVPGSEQPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ARLSSAYLLGVPGSEQPDR 19 1 Q96P48-3;Q96P48;E7EU13;Q96P48-7;Q96P48-2;Q96P48-4;Q96P48-1 Q96P48-3 ARAP1 "Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1" 1 ARLS(0.42)S(0.578)AY(0.002)LLGVPGSEQPDR 109.26 0.00015669 150200000 129510 141910 137720 123520 181870 279210 181410 167830 195570 TRUE FALSE 112394.9254 140977.7839 204321.8526 151567.1039 178251.1428 289951.3894 163816.8861 131940.8606 172449.9374 0.651753935 0.817499768 1.184818364 0.878904952 1.033639939 1.681365582 0.949938797 0.765096599 1 17.39581808 4.43215284 4.831722398 1.04986036 0.684837449 0.253738644 0.245409067 0.27460215 14.16136075 0.066146992 0.198828881 27049.10125 -4.43215284 -0.365022911 ARLSYS(ph)DKNLIDSMDQSAFAGFSFVNPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ARLSYSDKNLIDSMDQSAFAGFSFVNPK 28 2 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 1 ARLS(0.296)YS(0.704)DKNLIDSMDQSAFAGFSFVNPK 203.52 1.80E-25 5163000000 1430000 1165900 761220 680130 1035900 906500 1559300 1706200 321660 TRUE FALSE 1241021.877 1158241.126 1129348.538 834563.9116 1015287.617 941373.6416 1408079.326 1341342.408 283633.7212 4.375438405 4.083580475 3.981714633 2.942400177 3.579573022 3.318976451 4.964428488 4.729135879 1 18.11366954 3.989015709 21.1882065 3.642142001 4.180296172 0.070134078 1.083017159 259.7829216 501140.4156 0.288077492 0.542110949 9750.24906 -3.989015709 0.538154171 ARNS(ph)GTQSDGEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ARNSGTQSDGEEK 13 1 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 1 ARNS(0.999)GT(0.001)QSDGEEK;ARNS(0.954)GT(0.046)QSDGEEK 155 2.65E-05 442550000 446890 399670 421650 555740 302850 410970 507690 586890 1190020 TRUE FALSE 387832.3542 397044.5415 625561.3503 681929.261 296823.8775 426780.2818 458454.3019 461388.1407 1049337.191 0.369597454 0.378376507 0.596149032 0.649866665 0.282867967 0.406714148 0.436898936 0.439694833 1 20.00104691 1.238090833 24.99486216 1.000000626 0.447167515 0.726943724 0.106887202 6.294959544 334563.2939 0.154314487 0.026935877 17.3017819 -1.238090833 -0.552833111 ARNS(ph)GTQSDGEEKQPGLVMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ARNSGTQSDGEEKQPGLVMER 21 2 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 1 ARNS(0.938)GT(0.058)QS(0.004)DGEEKQPGLVMER;ARNS(0.999)GT(0.001)QSDGEEKQPGLVMER;ARNS(0.964)GT(0.015)QS(0.02)DGEEKQPGLVMER;ARNS(0.978)GT(0.022)QSDGEEKQPGLVMER;ARNS(0.945)GT(0.054)QS(0.001)DGEEKQPGLVMER;ARNS(0.718)GT(0.279)QS(0.003)DGEEKQPGLVMER 264.85 3.90E-37 2430580000 1126627 1039365 785732 901405 1151666 1083901 1256151 1427521 702685 TRUE FALSE 977740.3874 1032537.343 1165714.623 1106082.782 1128750.1 1125599.373 1134329.669 1122256.743 619614.3798 1.577982079 1.666419271 1.881355019 1.785114772 1.821697715 1.816612735 1.830702621 1.811218041 1 19.2410111 1.237237815 24.9990491 0.999999055 1.781480895 0.882531192 0.088692824 10.97403356 207312.1433 0.135718407 0.022396785 17.26783203 -1.237237815 0.78148184 ARPAEVGGMQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ARPAEVGGMQLR 12 1 P33316-2;H0YNJ9;H0YNW5;P33316;H0YKC5;H0YMM5;H0YKI0 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 ; 70.68 0.042527 691900000 1083590 1128550 738630 944480 1348580 1296270 1349000 1540520 1236450 FALSE TRUE 940390.836 1121136.481 1095833.939 1158938.619 1321745.896 1346138.346 1218174.188 1211091.786 1090278.29 0.862523674 1.028303041 1.005095625 1.06297505 1.2123014 1.234674081 1.117305737 1.110809779 1 20.05626499 4.563064613 0.964269992 1.130496376 0.792957959 0.575030285 0.070485224 1.226222804 1.117699677 0.025616971 0.407826033 36564.91879 -4.563064613 -0.337538417 ARPAPSRDPS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ARPAPSRDPSPPR 13 2 Q5C9Z4 Q5C9Z4 NOM1 Nucleolar MIF4G domain-containing protein 1 1 ARPAPS(0.006)RDPS(0.994)PPR 62.055 0.062645 214350000 124240 114700 79740 98486 112270 119750 109260 117790 134840 TRUE FALSE 107821.3692 113946.5281 118302.5307 120848.7516 110036.0467 124356.86 98663.98202 92601.52514 118899.3688 0.906828777 0.958344264 0.994980309 1.016395232 0.925455263 1.045900085 0.829810814 0.778822681 1 16.85938153 2.223168208 24.99868033 0.848988512 0.974494861 0.328287423 0.068810482 223.6967146 363301.1232 0.027292499 0.018476841 167.1737973 -2.223168208 0.125506348 ARPATDS(ph)FDDYPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ARPATDSFDDYPPR 14 1 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 ARPAT(0.003)DS(0.997)FDDYPPR;ARPAT(0.002)DS(0.998)FDDYPPR;ARPAT(0.006)DS(0.994)FDDYPPR 161.32 2.80E-06 499840000 1965402 1514171 776919 1158904 1386769 1056301 1835205 1560301 1520254 TRUE FALSE 1705669.146 1504224.311 1152639.627 1422050.866 1359175.01 1096937.583 1657227.102 1226642.773 1340531.304 1.272382928 1.122110544 0.859837904 1.060811383 1.013907699 0.81828569 1.236246477 0.915042245 1 20.35437348 4.486237554 4.987702523 0.990340802 1.244710073 0.398495702 0.115262153 0.161799956 11.58326945 0.026660226 0.092715941 30636.38753 -4.486237554 0.254369271 ARPATDSFDDYPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ARPATDSFDDYPPR 14 1 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 132.44 4.60E-05 526240000 488120 495490 316090 374460 458650 514820 480320 467410 438020 FALSE TRUE 423613.7053 492235.0936 468952.1813 459486.8663 449523.7623 534625.4585 433738.6403 367458.0089 386237.7746 1.096769226 1.274435402 1.214154109 1.189647664 1.163852404 1.384187394 1.12298348 0.951377708 1 18.55912974 1.929107249 4.541349863 0.982366166 1.221297782 0.63721684 0.075515748 0.126353539 4.816615408 0.038138931 0.01950253 84.93902051 -1.929107249 0.238931616 ARPDAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ARPDAEK 7 1 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;;;; 105.14 0.0072912 1806680000 2543740 2184420 1834370 2343970 1230020 1864700 2466870 2734410 5327290 FALSE TRUE 2207578.314 2170070.401 2721477.468 2876204.214 1205545.008 1936436.216 2227633.327 2149677.701 4697503.845 0.469947101 0.461962453 0.579345448 0.612283525 0.256635236 0.412226638 0.474216392 0.457621275 1 22.16346291 1.238054462 24.98455541 1.000000609 0.465403842 0.757835128 0.094949811 6.201502245 305807.6797 0.137155426 0.023887756 17.30033299 -1.238054462 -0.534596768 ARPDAEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ARPDAEKK 8 2 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 84.213 0.0099055 400150000 655330 490520 367800 393100 279230 316960 651230 691830 287530 FALSE TRUE 568726.4801 487297.7418 545669.3102 482359.3632 273673.8693 329153.6563 588073.8148 543887.5383 253538.531 2.243156012 1.921986926 2.15221453 1.902509103 1.079417272 1.298239187 2.319465261 2.145186912 1 17.95184549 3.471866451 24.98789771 1.665875314 2.077398663 0.236550116 0.426435411 276.8952742 1316697.618 0.134085353 0.173687758 2963.919818 -3.471866451 0.411523349 ARPEDVISEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ARPEDVISEGR 11 1 P25325-2;P25325 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 0 ;;; 177.16 7.39E-06 3604380000 1888260 1790310 1155690 1367680 1676020 1783010 1689850 1818630 1751810 FALSE TRUE 1638721.657 1778549.336 1714585.55 1678232.648 1642670.481 1851603.548 1525968.607 1429730.127 1544713.017 1.06085832 1.151378486 1.109970286 1.086436528 1.063414668 1.198671551 0.987865442 0.925563591 1 20.5589074 2.087771931 7.087363819 0.957278599 1.109804044 0.69364341 0.044221135 0.105350886 7.154212306 0.017123915 0.011489353 122.3973262 -2.087771931 0.152525445 ARPEYMLPVHFYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ARPEYMLPVHFYGR 14 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 158.93 3.00E-06 4887600000 4027300 3660700 2346900 2362400 3501300 3664600 2886500 3376400 3435700 FALSE TRUE 3495082.101 3636652.621 3481868.69 2898819.027 3431630.98 3805579.533 2606567.674 2654383.135 3029535.46 1.153669316 1.200399424 1.149307785 0.956852648 1.132725141 1.256159429 0.860385267 0.876168366 1 21.53066516 2.226430607 24.9972422 0.902522819 1.135755742 0.623725141 0.083777426 145.8615498 300585.6591 0.035330403 0.024022524 168.4343276 -2.226430607 0.233232923 ARPFPDGLAEDIDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ARPFPDGLAEDIDK 14 1 P13639;M0R0I6 P13639 EEF2 Elongation factor 2 0 100.41 0.0016372 159080000 198030 177280 164730 197190 179080 144640 182560 231020 538160 FALSE TRUE 171859.8338 176115.436 244393.979 241965.0034 175516.6584 150204.3944 164855.3593 181618.1708 474539.3379 0.362161406 0.371129266 0.515013107 0.50989451 0.369867457 0.31652675 0.347400829 0.382725216 1 18.85616816 1.237742004 24.99853494 1.000000701 0.396930457 0.893781135 0.065346198 6.726955978 205297.3655 0.103294155 0.017637806 17.28789053 -1.237742004 -0.603070244 ARPFPDGLAEDIDKGEVSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ARPFPDGLAEDIDKGEVSAR 20 2 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;; 253.99 2.29E-36 10959646000 3390570 3099450 2183384 2508629 2909970 2509467 3587310 4166470 3332820 FALSE TRUE 2942497.584 3079089.509 3239275.805 3078251.556 2852067.29 2606007.819 3239413.228 3275502.814 2938817.816 1.001252125 1.047730653 1.102237705 1.04744552 0.970481149 0.886753784 1.102284466 1.114564774 1 21.4868045 ARPPS(ph)GSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ARPPSGSSK 9 1 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 ARPPS(1)GSSK 67.519 0.036742 224750000 143780 149030 100390 137110 112560 168610 187220 202170 189850 TRUE FALSE 124779.1087 148051.0121 148938.9398 168242.9211 110320.2762 175096.5358 169063.4332 158937.5188 167406.1493 0.745367534 0.884382161 0.889686194 1.004998453 0.658997753 1.045938495 1.009899779 0.949412668 1 17.352993 ARPPSEGEFIDCFQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ARPPSEGEFIDCFQK 15 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 ; 167.69 1.18E-06 773080000 702630 637950 528770 602910 682830 582170 859610 896270 966800 FALSE TRUE 609775.6653 633759.2644 784484.9406 739809.9304 669243.0189 604566.4566 776245.1545 704609.6353 852506.0054 0.715274334 0.74340739 0.920210457 0.867806122 0.785030269 0.709163868 0.910545087 0.826515744 1 19.70135047 -0.654835629 1.009248039 10 0.802788691 0.404383874 0.073775718 90.04552507 2.474848732 1803.995219 0.024595407 0.221393248 0.654835629 -9.197211309 ARPTILSSGLPEEPDQNLSS(ph)PEEVFHSGHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ARPTILSSGLPEEPDQNLSSPEEVFHSGHSR 31 1 Q5T9C2-3;Q5T9C2;Q5T9C2-2 Q5T9C2-3 FAM102A Protein FAM102A 1 ARPTILSSGLPEEPDQNLS(0.186)S(0.799)PEEVFHS(0.015)GHS(0.001)R;ARPTILSSGLPEEPDQNLS(0.252)S(0.747)PEEVFHS(0.001)GHS(0.001)R 199.36 6.89E-26 356570000 229222 201700 133172 190084 231422 265607 285177 259463 242727 TRUE FALSE 198929.7319 200375.0194 197574.4246 233245.4775 226817.155 275825.0732 257520.5784 203978.8566 214032.0906 0.929438812 0.936191479 0.92310655 1.08976872 1.059734334 1.288708961 1.203186764 0.953029315 1 17.7074676 3.728428718 7.722834371 1.096807298 0.930028269 0.418805927 0.094100291 0.163915685 74.92552412 0.028752758 0.044979197 5350.923199 -3.728428718 -0.166779029 ARQEELYSELQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ARQEELYSELQAR 13 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 260.97 4.44E-24 1140080000 605210 565620 418880 348100 496530 608330 542040 612350 356240 FALSE TRUE 525229.9651 561904.405 621451.7691 427141.4254 486650.0244 631732.8487 489473.0442 481403.7178 314125.713 1.672037478 1.788788315 1.978353708 1.35977861 1.549220596 2.011082896 1.558207507 1.5325193 1 18.26098252 1.011312624 1.485088439 0.315599436 1.713474564 0.5661519 0.193817936 1.596534931 1.993062861 3.929142351 0.055924575 10.263905 -1.011312624 1.397875128 ARQEFEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ARQEFEER 8 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 ; 134.77 0.00078667 670120000 599170 485040 292990 366020 474000 522270 469830 558620 369400 FALSE TRUE 519988.1664 481853.7403 434680.944 449130.4353 464568.3274 542362.0649 424265.9589 439163.4602 325729.9528 1.59637811 1.479304363 1.334482568 1.378842908 1.426237665 1.665066599 1.302508275 1.348244017 1 18.31331686 0.836099302 1.247778987 0.270493107 1.460393836 0.640975266 0.107964094 2.375205528 1.546368785 4.703522253 0.032771771 6.856449826 -0.836099302 1.189900729 ARQELQEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ARQELQEAK 9 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 117.02 0.0011117 273810000 551530 564990 389260 429970 529980 476620 692010 790310 536910 FALSE TRUE 478643.9131 561278.5435 577507.438 527601.2602 519434.4349 494955.8798 624898.9767 621308.3567 473437.1114 1.010997874 1.185539811 1.219818692 1.114406217 1.097156142 1.045452221 1.319919714 1.31233556 1 18.85281327 2.241260816 24.99809877 1.23646371 1.119865175 0.144803507 0.105869579 110.6338803 1024247.601 0.040898437 0.030223839 174.2853233 -2.241260816 -0.116598534 ARQS(ph)LGTGTLVS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ARQSLGTGTLVS 12 1 Q9Y5J5 Q9Y5J5 PHLDA3 Pleckstrin homology-like domain family A member 3 1 ARQS(0.994)LGT(0.006)GTLVS 80.441 0.053485 251980000 329270 289010 225900 235980 346880 448600 382800 341000 331870 TRUE FALSE 285756.1352 287111.4743 335145.9956 289562.8657 339977.7667 465857.9323 345676.1149 268079.8037 292636.7067 0.976487668 0.981119141 1.14526301 0.989496051 1.161774169 1.591932665 1.1812466 0.916083996 1 18.15875122 4.241795275 22.83103303 1.134381174 0.978803167 0.119364339 0.182310149 68.65633575 484518.4547 0.050843804 0.122939068 17449.99372 -4.241795275 -0.155578007 ARS(ph)DPTHQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ARSDPTHQHR 10 1 A0A2R8Y6L5;A0A2R8Y6I6;Q13627-2;Q13627;Q13627-5 A0A2R8Y6L5 DYRK1A Dual specificity tyrosine-phosphorylation-regulated kinase 1A 1 ARS(1)DPTHQHR 127.32 0.00021689 257920000 30175 18275 14114 20427 28504 30051 23715 28894 22165 TRUE FALSE 26187.2973 18154.95032 20939.57761 25065.26256 27936.82617 31207.08142 21415.12295 22715.24295 19544.67895 1.339868379 0.928894783 1.07136974 1.282459672 1.42938271 1.596704735 1.095700932 1.16222134 1 14.25448827 5.065303446 21.35412871 1.202881948 4.739218405 0.047801709 0.199832755 2748.1852 920314.637 0.050427159 11072.86308 116226.0414 -5.065303446 3.536336457 ARS(ph)LEQPKS(ph)ER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ARSLEQPKSER 11 2 C9J8D8;B9ZVR7;Q15772-1;Q15772 C9J8D8 SPEG Striated muscle preferentially expressed protein kinase 2 ARS(1)LEQPKS(1)ER 63.408 0.04013 261500000 165480 220980 136360 116020 168950 349820 130680 125140 90991 TRUE FALSE 143611.3987 219528.3678 202304.1521 142364.1143 165588.2255 363277.8018 118006.6737 98379.78484 80234.14764 1.789903713 2.736096466 2.521422088 1.774358156 2.063812359 4.527720584 1.47077868 1.226158534 1 16.29192876 3.747625471 23.88456608 2.002149257 2.387836333 0.024821112 0.98993125 1768.954348 4660910.786 0.283075383 0.480558359 5592.750835 -3.747625471 0.385687076 ARS(ph)LPSS(ph)PERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ARSLPSSPERR 11 2 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 2 ARS(0.996)LPS(0.043)S(0.961)PERR 84.403 0.07864 792290000 1037400 886740 462200 590910 804120 817390 1007000 1214700 181250 TRUE FALSE 900304.9616 880914.9466 685721.466 725085.147 788119.5852 848835.5222 909341.295 954945.8578 159822.8315 5.633143608 5.511821674 4.290510058 4.536805788 4.93120775 5.311103015 5.689683298 5.975027779 1 17.28611399 1.232487262 24.99949878 0.999993066 5.241138326 0.865963869 0.523604935 79.72082385 328118.5934 1.307150402 0.146476938 17.07997624 -1.232487262 4.241145261 ARS(ph)PDLGPQEQMNPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ARSPDLGPQEQMNPK 15 1 H3BUW4;H3BMU4;A0A0C4DGM2;C9K0J8;Q8IWY8-4;Q8IWY8-3;Q8IWY8-2;Q8IWY8 H3BUW4 ZSCAN29 Zinc finger and SCAN domain-containing protein 29 1 ARS(1)PDLGPQEQMNPK;ARS(1)PDLGPQEQMNPK 225.69 5.85E-13 584800000 467220 409400 282250 353610 430800 354230 433680 514020 441520 TRUE FALSE 405475.6932 406710.6244 418747.0441 433902.5551 422227.9228 367857.4573 391621.7804 404100.8231 389324.0086 1.041486485 1.044658473 1.075574675 1.114502434 1.084515503 0.94486199 1.005901952 1.037955056 1 18.57061179 2.768752412 24.94974599 1.004368586 1.073163802 0.595195565 0.030459603 548.2468319 453056.4617 0.010613338 0.010612106 587.1545245 -2.768752412 0.068795216 ARS(ph)PGREEVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ARSPGREEVAR 11 2 A0A494BZV2;A0A1W2PPU9 A0A494BZV2 1 ARS(1)PGREEVAR 73.502 0.034167 1117600000 868350 660480 503020 652000 782310 680820 745320 745200 567450 TRUE FALSE 753595.3474 656141.2634 746282.1545 800046.5652 766743.5616 707011.5859 673038.9811 585844.7792 500366.7074 1.506086109 1.311320785 1.491470442 1.598920458 1.532363265 1.412986866 1.345091452 1.170830854 1 18.93262628 1.588461274 1.233517499 0.924038105 1.482349836 0.834400811 0.07359372 0.325461914 0.682998729 0.211053739 0.02576369 38.76691786 -1.588461274 0.558311732 ARS(ph)PINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ARSPINR 7 1 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 1 ARS(1)PINR;ARS(1)PINR 73.985 0.028712 384120000 74891 90121 54712 65697 71185 95430 73795 91460 88816 TRUE FALSE 64993.9646 89528.98922 81170.9062 80614.50797 69768.55777 99101.25385 66638.37226 71901.99074 78316.27366 0.829890923 1.14317223 1.036450056 1.029345552 0.890856453 1.265397972 0.850887934 0.9180977 1 16.2570245 ARS(ph)PPQPLGELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ARSPPQPLGELK 12 1 Q96FF7;A0A044PY82 Q96FF7 LOC113230 Uncharacterized protein LOC113230 1 ARS(1)PPQPLGELK 68.919 0.031111 234060000 235440 228330 205110 244140 205290 217150 288330 286930 542280 TRUE FALSE 204326.0075 226830.0852 304301.8821 299575.7184 201205.1306 225503.901 260367.801 225572.2524 478172.2762 0.427306261 0.47436896 0.636385456 0.626501647 0.420779582 0.471595515 0.544506267 0.471738458 1 18.86717096 1.235712814 24.99909017 1.000000657 0.511673251 0.811336713 0.07437802 34.73892404 304893.0772 0.127622352 0.0188572 17.20730331 -1.235712814 -0.488327406 ARS(ph)PSPCPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ARSPSPCPFR 10 1 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 ARS(0.994)PS(0.006)PCPFR 73.927 0.026358 236020000 167160 146380 76055 78080 163650 137440 121670 116690 91362 TRUE FALSE 145069.3825 145418.4201 112835.4524 95809.25738 160393.6852 142727.4057 109870.4621 91736.75158 80561.28844 1.800733147 1.80506572 1.400616283 1.189271662 1.990952333 1.771662401 1.363812127 1.138720015 1 16.29779914 1.879022564 2.414544977 1.049082588 1.645900938 0.532133592 0.22842046 0.245491304 2.608060563 0.179369125 0.06906449 75.68722182 -1.879022564 0.59681835 ARS(ph)PSVAAMASPQLCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 15 ARSPSVAAMASPQLCR 16 1 P25325-2 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 1 ARS(0.999)PS(0.001)VAAMASPQLCR;ARS(0.989)PS(0.011)VAAMASPQLCR;ARS(0.978)PS(0.022)VAAMASPQLCR;ARS(1)PSVAAMASPQLCR;ARS(0.873)PS(0.125)VAAMAS(0.003)PQLCR;ARS(0.999)PS(0.001)VAAMASPQLCR;ARS(0.995)PS(0.005)VAAMASPQLCR;ARS(0.998)PS(0.002)VAAMASPQLCR;ARS(0.98)PS(0.02)VAAMASPQLCR;ARS(1)PSVAAMASPQLCR;ARS(0.991)PS(0.009)VAAMASPQLCR;ARS(1)PSVAAMASPQLCR;ARS(0.938)PS(0.062)VAAMASPQLCR;ARS(0.991)PS(0.009)VAAMASPQLCR;ARS(0.981)PS(0.019)VAAMASPQLCR 248.52 3.05E-20 22953850000 6521170 6323470 3894030 4303817 6154400 6380640 5695480 6673620 4856210 TRUE FALSE 5659380.862 6281930.709 5777195.933 5281064.43 6031939.481 6626107.35 5143133.226 5246518.297 4282114.386 1.321632341 1.467016091 1.349145635 1.233284297 1.408635767 1.547391488 1.201073293 1.225216756 1 22.0298919 1.402196453 1.356360571 0.919673029 1.378296441 0.605025149 0.09675066 0.660841948 1.389954319 0.399706824 0.029643236 25.24622528 -1.402196453 0.458623412 ARS(ph)PTDDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ARSPTDDK 8 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 ARS(0.997)PT(0.003)DDK;ARS(1)PTDDK;ARS(0.999)PT(0.001)DDK;ARS(0.999)PT(0.001)DDK 92.062 0.0072941 520650000 1631030 1217120 1068010 1329140 675013 952000 1318800 1541850 3507200 TRUE FALSE 1415485.253 1209124.659 1584503.208 1630941.552 661581.5619 988624.056 1190902.979 1212137.376 3092582.811 0.457703266 0.390975677 0.512355951 0.52737199 0.213925254 0.319675856 0.385083618 0.391949852 1 21.5603808 1.23822781 24.99824163 1.000000673 0.397718065 0.812929322 0.090467282 3.493652251 262022.9025 0.131307523 0.023122723 17.30723974 -1.23822781 -0.602282608 ARS(ph)PTDDKVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ARSPTDDKVK 10 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 ARS(0.997)PT(0.003)DDKVK;ARS(0.972)PT(0.028)DDKVK;ARS(0.988)PT(0.012)DDKVK;ARS(0.824)PT(0.176)DDKVK;ARS(0.982)PT(0.018)DDKVK;ARS(0.938)PT(0.062)DDKVK 144.27 1.70E-05 10935640000 14983980 9925920 8428230 8672160 7712270 6176330 12779060 15072160 10485710 TRUE FALSE 13003809.08 9860715.978 12504150.22 10641306.47 7558810.916 6413937.412 11539748.73 11849095.88 9246101.309 1.406409971 1.066472846 1.352370021 1.150896591 0.817513313 0.693691016 1.248066438 1.281523475 1 23.14041374 3.475680936 24.99290411 1.039108722 1.25379152 0.274866407 0.194500513 83.5320742 1449455.011 0.062347319 0.081111244 2990.067111 -3.475680936 0.214682798 ARS(ph)PTDDKVKIEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ARSPTDDKVKIEDK 14 3 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 ARS(0.94)PT(0.06)DDKVKIEDK 94.387 0.023128 118960000 280990 147690 51220 43921 104350 74840 248200 240590 10104 TRUE FALSE 243856.4596 146719.8147 75990.16332 53893.93434 102273.6392 77719.14323 224129.6022 189141.7008 8909.516631 27.37033553 16.46776371 8.529100564 6.049030107 11.47914566 8.723160464 25.15620224 21.22917647 1 13.12113145 8 0.126771563 10 32.77115426 0.066943438 8.258881732 1161.855893 12.97823771 272.9292524 4673.3202 100000000 -8 22.77115426 ARS(ph)PYSPAEEDALFMDLPTGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ARSPYSPAEEDALFMDLPTGPR 22 1 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 ARS(0.998)PYS(0.002)PAEEDALFMDLPTGPR;ARS(0.998)PYS(0.002)PAEEDALFMDLPTGPR;ARS(0.997)PYS(0.003)PAEEDALFMDLPTGPR;ARS(0.857)PYS(0.142)PAEEDALFMDLPTGPR;ARS(0.99)PY(0.004)S(0.006)PAEEDALFMDLPTGPR 220.66 6.05E-26 602114000 332654 356858 236912 248396 373078 355651 323827 406876 304836 TRUE FALSE 288692.9311 354513.7763 351483.4356 304798.1083 365654.4777 369333.1241 292422.3074 319868.7337 268798.6354 1.074011893 1.318882352 1.307608706 1.133927291 1.360328624 1.374014134 1.087886131 1.18999389 1 18.03616629 1.139856248 1.121866953 0.84837135 1.256308135 0.334619599 0.10682884 2.350955243 2.122018133 1.214209111 0.033437833 13.7992743 -1.139856248 0.407936785 ARS(ph)VDALDDLTPPSTAESGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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;ARS(1)VDALDDLTPPSTAESGSR;ARS(1)VDALDDLTPPSTAESGSR 176.85 4.04E-17 858203000 602113 543757 341776 584549 714105 707388 370206 851875 410783 TRUE FALSE 522542.2415 540185.0245 507060.0168 717279.7847 699895.7076 734601.6741 334303.4791 669708.1605 362220.7017 1.442607336 1.49131461 1.399864818 1.980228577 1.932235525 2.028049945 0.92292759 1.848895321 1 18.46650948 2.251914702 24.98908803 1.366597425 1.710297456 0.273924787 0.333818712 380.2929934 711630.2739 0.126464077 0.097379209 178.6136734 -2.251914702 0.343700031 ARS(ph)VS(ph)PPPKR ddPTM_MDA-MB-175_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 68.277 0.032424 5881260000 236823 221929 158750 187832 194173 212048 223193 246027 183973 TRUE FALSE 205526.2405 220471.1338 235522.031 230482.1264 190309.3372 220205.6238 201547.7772 193416.0406 162223.9215 1.266929307 1.359054397 1.451832928 1.420765349 1.173127461 1.357417708 1.24240479 1.192278172 1 17.30762705 0.246713202 0.629541433 2.28E-13 1.357756756 0.667272023 0.076990535 6.60251744 0.791588928 8.590163551 0.038384592 1.764871955 -0.246713202 1.357756756 ARSDEGQLS(ph)PATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ARSDEGQLSPATR 13 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 ARSDEGQLS(1)PATR;ARSDEGQLS(1)PATR 195.17 2.41E-07 1515710000 769980 620050 338140 362430 762970 773510 860140 849020 169896 TRUE FALSE 668225.1921 615976.8507 501665.635 444725.2709 747788.3897 803267.4302 776723.7552 667463.6801 149811.0884 4.460452154 4.111690644 3.348654898 2.968573792 4.991542332 5.361868996 5.184688018 4.455369006 1 17.19278488 5.977219276 13.77525768 4.092827865 10.26167917 0 1.302159574 0 0 0.292583498 0 948897.4427 -5.977219276 6.168851309 ART(ph)PATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 76.228 0.066815 122890000 201340 208200 236470 226390 161310 280740 275910 314990 705040 TRUE FALSE 174732.4089 206832.3205 350827.6829 277795.3097 158100.2466 291540.2495 249152.2907 247631.8398 621690.9744 0.281059909 0.332693137 0.564312009 0.446838254 0.254306807 0.468947212 0.400765494 0.398319824 1 19.24583811 1.238545658 11.01972584 1.00141778 0.397016062 0.816246615 0.090435702 0.027448914 113.4897631 0.12344037 0.022019615 17.31991107 -1.238545658 -0.604401718 ART(ph)PLTAAQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ARTPLTAAQQK 11 1 I3L2J0 I3L2J0 CIC 1 ART(1)PLTAAQQK;ART(1)PLTAAQQK;ART(1)PLTAAQQK;ART(1)PLTAAQQK 167.37 3.12E-05 2126670000 2138020 1724300 1373280 1497680 1667760 1595210 2159300 2241440 2251220 TRUE FALSE 1855475.24 1712972.96 2037402.801 1837751.135 1634574.839 1656578.761 1949891.418 1762125.499 1985083.336 0.93470899 0.862922442 1.026356307 0.925780344 0.823428825 0.834513459 0.982271818 0.887683387 1 20.92076814 1.229830756 24.78029286 1.000000192 0.909716591 0.169416762 0.062829572 583.6281533 1656525.264 0.175834651 0.015378422 16.97581979 -1.229830756 -0.090283601 ARTEKEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ARTEKEEK 8 2 K7ELG9;Q3MHD2;Q3MHD2-2 K7ELG9 LSM12 Protein LSM12 homolog 0 ; 90.15 0.0075369 98603000 236870 164548 119219 111210 88932 121424 227010 250220 104305 FALSE TRUE 205567.0293 163467.0734 176873.7072 136461.9302 87162.42719 126095.2599 204994.6051 196712.4002 91974.18172 2.235051462 1.777314789 1.923079976 1.483698226 0.947683639 1.370985395 2.228827713 2.138778476 1 16.48894132 4.778230924 1.367677288 1.624746358 2.503676118 0.192314443 0.425877768 3.055880485 4.773202008 0.134690385 3.813350899 60011.00827 -4.778230924 0.878929759 AS(ph)DGQLQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASDGQLQAK 9 0 Q9BRG2;Q9BRG2-2 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 AS(1)DGQLQAK;AS(1)DGQLQAK;AS(1)DGQLQAK 136.53 0.00019946 1238600000 1460700 1388450 1252760 1496990 1115610 1066270 1515920 1777070 3181930 TRUE FALSE 1267664.794 1379329.181 1858598.926 1836904.46 1093411.544 1107290.097 1368906.312 1397057.41 2805765.86 0.451807049 0.491605233 0.662421249 0.654689148 0.389701635 0.394648075 0.48789043 0.497923733 1 21.41996319 1.238055316 24.99999989 1.00000056 0.505120164 0.742174693 0.0919019 6.831069895 337632.2642 0.139061245 0.024223816 17.30036698 -1.238055316 -0.494880396 AS(ph)DKDITVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASDKDITVSK 10 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 AS(1)DKDITVSK;AS(1)DKDITVSK;AS(1)DKDITVSK 147.35 1.64E-05 1359550000 2784850 1163530 1482830 1715110 1411340 893000 2233350 2491890 2752290 TRUE FALSE 2416825.017 1155886.695 2199931.548 2104551.939 1383257.095 927354.2878 2016760.061 1959018.715 2426917.412 0.995841476 0.476277721 0.906471533 0.867170811 0.569964634 0.382112009 0.830996577 0.807204525 1 21.21069358 1.412584237 1.883524605 1.029255155 0.702507173 0.174324981 0.194613781 1.00612139 4.861445637 0.533836113 0.053944219 25.85736327 -1.412584237 -0.326747981 AS(ph)DLEDEESAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASDLEDEESAAR 12 0 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 AS(1)DLEDEESAAR;AS(1)DLEDEESAAR;AS(1)DLEDEESAAR;AS(1)DLEDEESAAR 264.22 1.66E-21 6205060000 4761400 3541820 3326140 4140030 3920960 3789590 3310540 4244140 8173200 TRUE FALSE 4132168.926 3518553.551 4934672.429 5080087.088 3842940.567 3935377.979 2989484.34 3336563.689 7206973.607 0.573357022 0.488215129 0.684707992 0.70488493 0.533225287 0.546051393 0.414804397 0.462963217 1 22.78096213 1.232053342 24.98872416 1.000000764 0.546823876 0.710977854 0.089926913 136.8748116 525565.6061 0.228894299 0.024597516 17.06291952 -1.232053342 -0.453176889 AS(ph)DPGLPAEEPK ddPTM_MDA-MB-175_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 231.69 2.97E-12 2552140000 2439120 1805540 2674400 2698600 2147950 1987950 2709880 3042350 9272700 TRUE FALSE 2116784.112 1793679.289 3967748.785 3311358.376 2105209.997 2064427.723 2447076.255 2391767.128 8176491.969 0.258886589 0.219370275 0.485262971 0.404985217 0.257471053 0.252483306 0.299281925 0.292517517 1 22.96305057 1.237683176 24.9978475 1.000000807 0.309938976 0.881569188 0.079618862 7.304181372 207971.2688 0.119772517 0.020380279 17.28554895 -1.237683176 -0.690061831 AS(ph)DPGLPAEEPKEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASDPGLPAEEPKEK 14 1 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 1 AS(1)DPGLPAEEPKEK 127.78 0.00026024 0 201780 131080 148920 114280 147140 135160 257180 247730 59676 TRUE FALSE 175114.2618 130218.9268 220938.2101 140229.0207 144212.2019 140359.6927 232238.7232 194754.8673 52621.17126 3.327829038 2.474648962 4.19865626 2.664878362 2.740573773 2.667361621 4.413408474 3.701074352 1 15.68335574 3.617946292 18.96827302 3.035198079 3.27840972 0.029775278 0.962626096 21.46011064 3279.051386 0.269807302 0.400188557 4149.027297 -3.617946292 0.243211641 AS(ph)ELRSFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASELRSFSR 9 1 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 AS(0.5)ELRS(0.5)FSR 54.608 0.081109 660020000 823080 892020 255550 541550 966080 840780 872800 996780 962870 TRUE FALSE 714307.8926 886160.2619 379134.8348 664517.2046 946856.8981 873125.3507 788155.9903 783626.354 849040.6055 0.841311815 1.04371953 0.446544997 0.782668344 1.115208027 1.028367012 0.928290102 0.922955096 1 19.69547403 3.305678518 10.41665444 0.985543893 0.773265807 0.336757771 0.152986828 0.555584166 82.82902676 0.04481449 0.057836053 2021.522216 -3.305678518 -0.212278085 AS(ph)GDYDNDCTNPITPLCTQPDQVIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASGDYDNDCTNPITPLCTQPDQVIK 25 0 Q8TAF3-4;Q8TAF3-3;Q8TAF3 Q8TAF3-4 WDR48 WD repeat-containing protein 48 1 AS(0.5)GDY(0.5)DNDCTNPITPLCTQPDQVIK 151.06 1.00E-07 144140000 339320 326340 291100 351700 334690 260390 395250 486790 491050 TRUE FALSE 294478.0023 324196.2511 431876.9337 431558.8604 328030.3238 270407.3718 356918.7158 382693.7467 432998.6284 0.680089919 0.748723506 0.997409473 0.99667489 0.757578205 0.624499373 0.824295257 0.883822076 1 18.72400293 1.395289627 2.381281103 1.014359278 0.808914653 0.219499277 0.119252057 0.746417827 6.08051178 0.282457527 0.034906848 24.84789637 -1.395289627 -0.205444624 AS(ph)GEMASAQYITAALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 19 ASGEMASAQYITAALR 16 0 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 1 AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR 322.93 2.79E-58 4448487000 2502340.4 1893801.3 1976375.3 2703308.5 2370200.2 2237202.1 2281850.1 2786418 4415434 TRUE FALSE 2171649.776 1881360.795 2932157.006 3317136.012 2323037.853 2323268.712 2060556.629 2190564.195 3893446.423 0.557770556 0.483212196 0.753100643 0.851979365 0.596653351 0.596712645 0.529237186 0.56262857 1 21.89261634 1.233690754 24.97426885 1.000000594 0.616041876 0.550883617 0.108846721 127.8602822 655630.262 0.230117005 0.028800466 17.12737294 -1.233690754 -0.383958718 AS(ph)GQAFELILS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASGQAFELILSPR 13 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 2 AS(1)GQAFELILS(1)PR;AS(1)GQAFELILS(1)PR 94.281 0.0076417 58303000 93001 96587 76222 91485 118233 117764 117479 143761 137750 TRUE FALSE 80710.68222 95952.51364 113083.2141 112258.0675 115880.3946 122294.4573 106085.9047 113018.8289 121465.3519 0.664474938 0.789957894 0.930991533 0.924198265 0.954020161 1.006825859 0.87338408 0.930461462 1 16.89018532 4.495411297 1.835928985 0.945339381 0.636065673 0.863235104 0.037999182 0.182437463 0.909334743 0.010440581 0.082636437 31290.41315 -4.495411297 -0.309273709 FASEAEDKIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FASEAEDKIR 10 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 80.24 0.021795 257490000 1406180 1310910 707600 919750 1341400 1425040 1267630 1421170 644770 FALSE TRUE 1220349.75 1302298.546 1049797.727 1128593.295 1314708.764 1479862.211 1144695.438 1117263.855 568546.0251 2.146439683 2.290577171 1.84646041 1.985051773 2.312405164 2.602889028 2.01337339 1.965124732 1 19.11691762 1.100228742 1.96308441 0.245864164 2.17831545 0.756269378 0.207455727 0.634674334 1.722871276 2.568164821 0.059415204 12.5958866 -1.100228742 1.932451286 AS(ph)GQSFEVILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASGQSFEVILK 11 0 A0A0J9YW36;Q9NZ72-2;Q9NZ72;A0A0J9YXY4 A0A0J9YW36 STMN3 Stathmin-3 1 AS(1)GQSFEVILK 127.36 0.0010265 0 53236 66899 51083 63246 74734 73651 76717 99764 91430 TRUE FALSE 46200.72772 66459.53606 75786.90966 77606.97095 73246.93961 76484.40163 69276.99715 78430.24496 80621.24956 0.573058939 0.824342669 0.940036406 0.96261186 0.908531436 0.948687871 0.859289549 0.972823485 1 16.29887252 4.709516346 2.045185336 0.940620288 0.481109249 0.904239108 0.038065594 0.188047806 0.905865798 0.010033888 0.157374587 51229.05512 -4.709516346 -0.459511039 AS(ph)HS(ph)SERPPPR ddPTM_MDA-MB-175_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 2 AS(1)HS(0.573)S(0.427)ERPPPR 73.219 0.025127 165300000 151790 162020 125110 125390 159090 165270 105780 152100 325530 TRUE FALSE 131730.5669 160955.68 185613.6145 153861.716 155924.4203 171628.0438 95521.47188 119574.5986 287046.2142 0.458917625 0.560730893 0.646633208 0.536017228 0.543203193 0.597910843 0.332773843 0.416569154 1 18.1309235 1.231944408 24.9998849 1.000000828 0.508961799 0.742453194 0.09038986 130.0359977 491305.5287 0.231051611 0.02457548 17.05864015 -1.231944408 -0.491039029 AS(ph)HSS(ph)ERPPPR ddPTM_MDA-MB-175_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 2 AS(1)HS(0.26)S(0.74)ERPPPR 89.992 0.0067254 192460000 230220 246280 174030 188710 213440 248500 153980 200560 467440 TRUE FALSE 199795.8437 244662.1705 258191.4901 231559.4898 209192.9616 258059.9558 139047.0433 157671.8048 412179.7757 0.484729857 0.593581211 0.626405043 0.561792459 0.507528447 0.626085924 0.337345623 0.382531638 1 18.65291419 1.229202961 24.99722959 1.000000959 0.511100299 0.714941505 0.09621648 232.7481969 621697.6583 0.32779682 0.026524219 16.9512981 -1.229202961 -0.48890066 AS(ph)HSSERPPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ASHSSERPPPR 11 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 AS(0.36)HS(0.36)S(0.28)ERPPPR;AS(0.98)HS(0.02)SERPPPR;AS(0.5)HS(0.5)SERPPPR;AS(0.732)HS(0.209)S(0.06)ERPPPR;AS(0.997)HS(0.002)SERPPPR 206.46 1.59E-08 4968494000 438832.6 416060.2 247592.9 323933.1 492836.9 482862.3 486641.9 522952.3 461676 TRUE FALSE 380839.76 413327.0732 367329.6546 397487.0614 483030.4099 501438.3251 439447.4434 411123.0203 407097.1892 0.935500834 1.015303186 0.902314396 0.976393529 1.186523569 1.231741064 1.079465678 1.009889115 1 18.63501373 3.380493299 7.881596568 1.094641086 0.954557561 0.478999327 0.074847104 0.249695909 17.87705669 0.024421582 0.031552974 2401.55921 -3.380493299 -0.140083525 AS(ph)LADALPLHIAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASLADALPLHIAPR 14 0 H3BRB6;Q8ND25;Q8ND25-2 H3BRB6 ZNRF1 E3 ubiquitin-protein ligase ZNRF1 1 AS(1)LADALPLHIAPR;AS(1)LADALPLHIAPR 130.01 4.16E-05 112872000 124265 107905 77955 81778 110682 115348 125409 141746 144962 TRUE FALSE 107843.0654 107196.165 115654.2987 100346.9448 108479.6447 119785.5122 113246.8545 111434.721 127824.7575 0.843679014 0.838618176 0.904787938 0.785035284 0.848659109 0.937107291 0.885953994 0.871777292 1 16.96380776 2.785334092 9.024127173 0.912031364 0.843831729 0.43042636 0.044584057 0.487385805 90.65237253 0.014191018 0.014157272 610.0059793 -2.785334092 -0.068199636 AS(ph)LEDAPVDDLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASLEDAPVDDLTR 13 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 AS(1)LEDAPVDDLTR;AS(1)LEDAPVDDLTR;AS(1)LEDAPVDDLTR;AS(1)LEDAPVDDLTR 195.1 4.74E-07 1802630000 1789810 1642260 1479600 2019870 2100490 1936370 1953070 2576280 4090310 TRUE FALSE 1553282.074 1631471.886 2195139.509 2478512.355 2058694.359 2010863.407 1763661.572 2025362.571 3606758.211 0.430658775 0.45233747 0.608618427 0.687185614 0.570788015 0.557526535 0.488988024 0.561546533 1 21.78227128 1.2393378 6.542002854 1.012292205 0.546741403 0.786806741 0.074517747 0.057761659 11.79508945 0.119888623 0.019827936 17.35153099 -1.2393378 -0.465550803 AS(ph)LGS(ph)LEGEAEAEASSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 AS(1)LGS(1)LEGEAEAEASSPK 105.5 0.00069591 37291000 152020 81639 85827 102950 88483 101380 107780 112750 194700 TRUE FALSE 131930.1718 81102.70803 127333.2243 126326.371 86722.36141 105280.1542 97327.51219 88639.28992 171682.7878 0.768453108 0.472398597 0.741677287 0.735812673 0.505131368 0.613224864 0.566903144 0.516296893 1 17.38938588 1.230277558 24.95880838 1.000000742 0.60789808 0.570098855 0.104911513 221.746596 668120.4197 0.274865536 0.02486623 16.99329349 -1.230277558 -0.392102662 AS(ph)LSDIGFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASLSDIGFGK 10 0 Q07002;A0A0A0MSJ6;Q07002-3;D6R9B0;D6RA44 Q07002 CDK18 Cyclin-dependent kinase 18 1 AS(1)LSDIGFGK 142.07 0.0048921 0 245240 213000 188880 206380 206010 193070 257070 284770 388270 TRUE FALSE 212830.9126 211600.789 280222.9998 253241.7333 201910.8041 200497.5278 232139.391 223874.1516 342369.1629 0.621641595 0.618048621 0.818482007 0.739674482 0.589745882 0.585617951 0.678038258 0.653896951 1 18.38519324 1.237459034 24.99722008 1.000000399 0.664528387 0.689273165 0.071073616 17.17457287 389544.8582 0.109406147 0.018318211 17.27663008 -1.237459034 -0.335472012 AS(ph)LSDLSSLDDVEGMSVR ddPTM_MDA-MB-175_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 142.94 1.14E-07 55406000 68722 59741 41011 59461 67783 70716 55506 66526 103730 TRUE FALSE 59640.21358 59348.55744 60844.05677 72962.52885 66434.25092 73436.49028 50123.03666 52299.93261 91467.15757 0.652039652 0.648851009 0.665201132 0.797691005 0.726318087 0.802872771 0.547989442 0.571789197 1 16.4809662 3.975915154 23.97259818 0.714750836 0.652090468 0.068840319 0.126668124 1598.301634 1590860.385 0.034637907 0.060490245 9460.523181 -3.975915154 -0.062660369 AS(ph)LSDLTDLEDIEGLTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASLSDLTDLEDIEGLTVR 18 0 J3KSI3;J3KSU7;K7EN88;Q8WZ73-3;Q8WZ73-2;Q8WZ73 J3KSI3 RFFL;hCG_2039718 E3 ubiquitin-protein ligase rififylin 1 AS(0.999)LS(0.001)DLTDLEDIEGLTVR;AS(1)LSDLTDLEDIEGLTVR;AS(1)LSDLTDLEDIEGLTVR;AS(0.96)LS(0.04)DLTDLEDIEGLTVR 229.02 2.21E-19 95530000 152634 114835 100305 120631 134917 135335 109531 157604 227018 TRUE FALSE 132463.0302 114080.6413 148812.8335 148022.1123 132232.4157 140541.425 98908.70048 123901.6111 200180.1907 0.661718973 0.569889763 0.743394404 0.739444357 0.660566938 0.702074589 0.494098343 0.61895041 1 17.61093969 1.235955558 24.99799179 1.000000469 0.645479875 0.680497543 0.075604917 44.50118212 426941.9722 0.129202451 0.019447468 17.21692384 -1.235955558 -0.354520594 AS(ph)LSSAPVVLVGDHA ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASLSSAPVVLVGDHA 15 0 Q9HBH9 Q9HBH9 MKNK2 MAP kinase-interacting serine/threonine-protein kinase 2 1 AS(1)LSSAPVVLVGDHA;AS(1)LSSAPVVLVGDHA 282.12 8.80E-34 45368000 75460 60529 46043 51152 66096 67092 60480 61746 82795 TRUE FALSE 65487.76981 60131.38101 68309.5488 62766.84341 64780.81891 69673.07265 54614.65891 48542.09841 73007.06942 0.89700587 0.823637786 0.935656634 0.859736515 0.887322549 0.954333234 0.748073568 0.664895863 1 16.15574855 2.226351771 24.98970777 0.772932039 0.88997415 0.144069679 0.091560498 297.9591285 609873.4861 0.036317224 0.024688016 168.403755 -2.226351771 0.117042112 AS(ph)PALVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASPALVAK 8 0 Q92783;Q92783-2;A6NMU3 Q92783 STAM Signal transducing adapter molecule 1 1 AS(1)PALVAK 62.659 0.082074 359340000 1260400 1002600 935810 862700 976840 669720 1805700 1492700 1391400 TRUE FALSE 1093834.947 996013.8546 1388370.846 1058589.221 957402.7952 695484.5618 1630583.492 1173497.721 1226910.277 0.891536217 0.811806595 1.131599329 0.862808993 0.780336438 0.566858535 1.329016084 0.956465801 1 20.22659832 2.233727171 24.99999646 1.076009767 0.850972268 0.336362754 0.16728611 158.6683699 820667.3249 0.067622544 0.047243242 171.2880917 -2.233727171 -0.225037499 AS(ph)PAPGSGHPEGPGAHLDMNSLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 ASPAPGSGHPEGPGAHLDMNSLDR 24 0 O94826 O94826 TOMM70A Mitochondrial import receptor subunit TOM70 1 AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(0.843)PAPGS(0.157)GHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(0.981)PAPGS(0.019)GHPEGPGAHLDMNSLDR 282.94 3.83E-52 18416960000 869012 979186 571877 957849 1357890 1646149 755886 1352678 1240988 TRUE FALSE 754169.8624 972753.6627 848438.63 1175343.255 1330870.646 1709477.417 682580.2921 1063418.336 1094279.812 0.689192886 0.888944173 0.775339744 1.074079264 1.216206888 1.562194055 0.623771255 0.971797455 1 20.06155026 3.737564199 24.48788173 1.061987433 0.794937446 0.251053912 0.235360212 110.0500222 2704612.012 0.067278494 0.106665083 5464.673253 -3.737564199 -0.267049986 AS(ph)PATHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASPATHR 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AS(0.998)PAT(0.002)HR;AS(0.999)PAT(0.001)HR 85.676 0.021647 94132000 87609 70785 58784 74235 49770 85984 69946 81943 159636 TRUE FALSE 76031.24868 70320.00867 87212.13902 91091.19136 48779.67437 89291.86012 63162.64769 64420.12713 140764.0139 0.540132713 0.499559559 0.619562746 0.647119877 0.346535119 0.634337269 0.448713033 0.457646279 1 17.10291903 1.233897723 24.99993164 1.000000721 0.521483527 0.718168171 0.093657876 76.02096229 407532.8782 0.174824677 0.022246879 17.13553714 -1.233897723 -0.478517194 AS(ph)PDS(ph)SSCGERSPPPPPPPPSDEALLHCVLEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASPDSSSCGERSPPPPPPPPSDEALLHCVLEGK 33 1 Q9BRK4 Q9BRK4 LZTS2 Leucine zipper putative tumor suppressor 2 2 AS(0.999)PDS(0.333)S(0.302)S(0.248)CGERS(0.117)PPPPPPPPSDEALLHCVLEGK;AS(0.777)PDS(0.331)S(0.315)S(0.3)CGERS(0.277)PPPPPPPPSDEALLHCVLEGK 99.415 9.79E-05 114484000 39409 27511 28189 30301 30461 33191 37494 45093 30793 TRUE FALSE 34201.0008 27330.27843 41821.29469 37181.30517 29854.8857 34467.87925 33857.83765 35450.21286 27152.68662 1.259580729 1.006540488 1.540226765 1.369341667 1.099518663 1.269409533 1.246942453 1.30558767 1 14.72880733 3.252048501 24.99577912 1.208408345 1.290988264 0.097456829 0.156381635 763.1347368 1414234.777 0.045603831 0.058544011 1786.687098 -3.252048501 0.082579919 AS(ph)PDSSSCGERS(ph)PPPPPPPPSDEALLHCVLEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASPDSSSCGERSPPPPPPPPSDEALLHCVLEGK 33 1 Q9BRK4 Q9BRK4 LZTS2 Leucine zipper putative tumor suppressor 2 2 AS(1)PDSSS(0.008)CGERS(0.992)PPPPPPPPSDEALLHCVLEGK 212.81 7.59E-28 44685000 53822 49418 33101 37217 44552 36972 52977 68635 50763 TRUE FALSE 46709.28633 49093.3699 49108.75432 45667.68868 43665.50236 38394.33676 47839.29869 53957.93937 44761.85597 1.04350647 1.09676797 1.097111665 1.02023671 0.975506967 0.857746756 1.068751455 1.20544464 1 15.44998224 1.999350281 24.99999905 1.123307285 1.016197969 0.155878672 0.083342928 33.98595666 1307730.717 0.036169722 0.024052845 99.85050862 -1.999350281 -0.107109317 AS(ph)PEPPGPESSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 ASPEPPGPESSSR 13 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR 279.41 2.49E-32 21663517000 6973515 5448743 3859232 4558298 5651386 5198687 5258757 6403008 6298965 TRUE FALSE 6051947.324 5412949.848 5725569.504 5593329.23 5538934.475 5398683.853 4748763.556 5033774.567 5554308.534 1.089595093 0.974549724 1.030833896 1.007025302 0.997232048 0.971981268 0.85496935 0.90628285 1 22.40517589 2.567991013 2.959952462 0.914659868 1.017868328 0.484361204 0.046145035 0.210060115 3.577090264 0.017194051 0.014357139 369.8205268 -2.567991013 0.10320846 AS(ph)PEPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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;AS(1)PEPQR 103.8 0.0087008 2729100000 3845830 2982230 2840130 3493050 2360100 3204170 3174450 3708650 8462400 TRUE FALSE 3337593.821 2962639.535 4213626.368 4286200.39 2313138.627 3327436.493 2866592.328 2915584.058 7461984.712 0.447279638 0.397031038 0.564679041 0.574404874 0.30998973 0.445918428 0.384159502 0.390725011 1 22.83112797 1.235670041 24.98945063 1.000000763 0.437403466 0.828082791 0.080288743 32.83405022 283801.3912 0.137699032 0.020294487 17.20560869 -1.235670041 -0.562597297 AS(ph)PEPQRENAS(ph)PAPGTTAEEAMSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASPEPQRENASPAPGTTAEEAMSR 24 1 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 2 AS(1)PEPQRENAS(1)PAPGTTAEEAMSR;AS(1)PEPQRENAS(1)PAPGTTAEEAMSR;AS(1)PEPQRENAS(0.999)PAPGTTAEEAMSR 115.32 0.00061904 1175570000 559040 505650 355972 364491 493430 488350 462350 567510 322318 TRUE FALSE 485161.4476 502328.3519 528121.2499 447254.2524 483611.7084 507137.1405 417511.3682 446152.4029 284213.9332 1.707029075 1.767430422 1.858182123 1.573653506 1.701576354 1.784350031 1.469003871 1.569776674 1 18.11661776 0.827922483 1.0981456 5.88E-23 1.723217195 0.816679905 0.103814167 1.570018595 0.824952512 3.939393204 0.031920324 6.728565483 -0.827922483 1.723217195 AS(ph)PEPQRENASPAPGTTAEEAMSR ddPTM_MDA-MB-175_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 157.08 9.70E-09 590440000 44438 35024 19055 13179 37306 30055 26183 36375 12812 TRUE FALSE 38565.40571 34793.92504 28270.06174 16171.49338 36563.68359 31211.2353 23643.77669 28596.48932 11297.37996 3.413659261 3.079822505 2.502355577 1.431437505 3.236474628 2.762696786 2.092854873 2.531249673 1 13.46370061 8 0.074091882 5.67E-10 8.275737064 0.346532689 0.621420163 730.6064625 5.171383062 122.8273963 664.4614034 99999999.99 -8 8.275737063 AS(ph)PGLLPVANGNSLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ASPGLLPVANGNSLNK 16 0 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 AS(1)PGLLPVANGNSLNK;AS(1)PGLLPVANGNSLNK;AS(1)PGLLPVANGNSLNK;AS(1)PGLLPVANGNSLNK;AS(1)PGLLPVANGNSLNK;AS(1)PGLLPVANGNSLNK;AS(1)PGLLPVANGNSLNK;AS(1)PGLLPVANGNSLNK 300.35 7.31E-46 3756708000 5918200 5473512 3861998 4341103 5108813 4656842 5069945 5978592 5506990 TRUE FALSE 5136094.875 5437556.139 5729673.15 5326816.786 5007157.617 4835993.725 4578262.514 4700116.626 4855959.916 1.057688895 1.119769568 1.179925957 1.096964736 1.031136522 0.995888312 0.942813078 0.967906801 1 22.21132508 3.055408542 1.989361858 0.970842705 1.12156945 0.796007627 0.032864794 0.13729194 1.107083526 0.012022151 0.013660451 1136.079025 -3.055408542 0.150726744 AS(ph)PHDVLETIFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASPHDVLETIFVR 13 0 H0YEM7;O75143-4;O75143-3;O75143-2;O75143;O75143-5;H0YCL5 H0YEM7 ATG13 Autophagy-related protein 13 1 AS(1)PHDVLETIFVR;AS(1)PHDVLETIFVR 112.96 0.00055348 32228000 51019 48388 43428 53544 53190 50887 47671 58081 111513 TRUE FALSE 44276.70988 48070.13604 64429.92606 65701.98357 52131.62306 52844.65582 43047.87376 45660.83014 98330.06018 0.450286614 0.488865114 0.655241398 0.668178006 0.530169746 0.537421168 0.43778956 0.464362882 1 16.58534491 1.233756682 24.9993231 1.000000715 0.529063973 0.779769601 0.078657939 77.27419395 402080.4711 0.170740721 0.02143784 17.12997316 -1.233756682 -0.470936742 AS(ph)PIKMDLAPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 141 3.64E-05 2523900000 6624300 5109300 4950280 5924000 4906630 3363670 6380200 8189900 9546400 TRUE FALSE 5748881.971 5075736.672 7344251.966 7269134.743 4808997.663 3493072.561 5761449.186 6438553.619 8417835.467 0.682940644 0.602974089 0.872463235 0.863539656 0.571286726 0.414960898 0.684433571 0.764870452 1 23.00501788 1.27703527 2.350729525 1.069054901 0.670784471 0.380823853 0.132633805 0.642692699 4.02268102 0.513939643 0.038522103 18.92497308 -1.27703527 -0.39827043 AS(ph)PNLIGATGANSLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASPNLIGATGANSLGK 16 0 Q02078-8;Q02078-7;Q02078-4;Q02078-6;Q02078-3;Q02078-5;Q02078-2;Q02078 Q02078-8 MEF2A Myocyte-specific enhancer factor 2A 1 AS(1)PNLIGATGANSLGK;AS(1)PNLIGATGANSLGK;AS(1)PNLIGATGANSLGK;AS(1)PNLIGATGANSLGK 169.43 5.90E-09 520414000 811950 701480 478050 545950 676310 610480 594640 755630 696500 TRUE FALSE 704648.7503 696871.9317 709236.579 669916.2918 662852.7542 633965.5606 536971.9043 594044.4048 614160.5635 1.147336368 1.134673851 1.154806448 1.090783635 1.07928251 1.032247263 0.874318438 0.967246092 1 19.22825635 2.776787237 1.576256924 0.948527378 1.136354176 0.81598303 0.037985999 0.150927783 0.759400968 0.016855413 0.015128644 598.1185021 -2.776787237 0.187826797 AS(ph)PNPVAMETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASPNPVAMETR 11 0 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 AS(1)PNPVAMETR;AS(1)PNPVAMETR 178.67 7.81E-06 637450000 389690 349420 261802 311830 246600 291400 290850 308610 292340 TRUE FALSE 338191.4792 347124.637 388410.3229 382635.7675 241693.1425 302610.3466 262643.4118 242616.1531 257779.8982 1.311938912 1.346593118 1.506751789 1.484350681 0.937594995 1.173909791 1.018866923 0.941175611 1 17.97578024 3.239079729 24.99999242 1.013489532 1.414446357 0.843268937 0.085279736 5.354033655 257837.6023 0.026576935 0.03225311 1734.122324 -3.239079729 0.400956825 AS(ph)PPAESMSVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASPPAESMSVYR 12 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 AS(1)PPAESMSVYR;AS(1)PPAESMSVYR 149.02 0.00032226 360020000 48616 41518 26167.6 32694 50521 35456 41850 55336 48247 TRUE FALSE 42191.27242 41245.26552 38822.33889 40117.6724 49515.73094 36820.01526 37791.39344 43502.82703 42543.29462 0.991725554 0.96948922 0.912537198 0.942984617 1.163890371 0.865471647 0.888304344 1.022554257 1 15.37664414 3.61059175 0.003324391 1.711971366 0.229291865 0.000825525 0.08381651 685293.3974 1576.232631 349821.1853 353171.9039 4079.357338 -3.61059175 -1.482679502 AS(ph)PPALLPGPAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ASPPALLPGPAPR 13 0 A6NEL2 A6NEL2 SOWAHB Ankyrin repeat domain-containing protein SOWAHB 1 AS(1)PPALLPGPAPR;AS(1)PPALLPGPAPR;AS(1)PPALLPGPAPR;AS(1)PPALLPGPAPR;AS(1)PPALLPGPAPR 126.83 0.00019298 886535000 288475 276561 186358 211059 302349 291941 261047 317356 286502 TRUE FALSE 250352.2978 274744.2526 276481.3521 258983.1718 296332.8464 303172.1592 235730.7021 249491.8891 252632.0599 0.990975959 1.087527263 1.094403268 1.02513977 1.172981951 1.200054179 0.933098919 0.987570181 1 17.94667821 2.218288352 24.99981998 0.974790169 1.095150003 0.455133907 0.062727005 225.8158295 278474.7661 0.026364537 0.017799373 165.305899 -2.218288352 0.120359835 AS(ph)PPGDLQNPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASPPGDLQNPK 11 0 O00273 O00273 DFFA DNA fragmentation factor subunit alpha 1 AS(1)PPGDLQNPK;AS(1)PPGDLQNPK 107.93 0.002236 186190000 463600 382040 295420 391620 401070 320810 387100 476490 815310 TRUE FALSE 402334.0854 379530.3541 438286.1001 480543.3065 393089.4917 333151.7683 349559.1016 374596.3215 718924.9806 0.559632919 0.527913711 0.609640939 0.668419264 0.546774006 0.463402688 0.486224726 0.52105064 1 19.45548171 1.236638587 24.99986098 1.000000573 0.546132488 0.855990535 0.058275454 20.19782917 262640.8961 0.10063469 0.015917771 17.24402273 -1.236638587 -0.453868085 AS(ph)PPHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASPPHSK 7 0 Q9HCM7;A0A3B3IRR3 Q9HCM7 FBRSL1 Fibrosin-1-like protein 1 AS(1)PPHSK 67.414 0.042015 194130000 415990 452830 262500 355630 282120 362610 486070 549980 486150 TRUE FALSE 361015.8675 449855.3299 389445.878 436381.227 276506.364 376559.8413 438931.0062 432371.0569 428677.9008 0.842161135 1.049401728 0.90848135 1.017969963 0.64502127 0.878421399 1.023917971 1.008615224 1 18.70953452 2.238103744 24.99868048 1.010924736 0.892965667 0.216839966 0.107961735 19.77849878 1082096.339 0.04300685 0.031008346 173.0229626 -2.238103744 -0.117959069 AS(ph)PPPQGPLPGPPGALHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ASPPPQGPLPGPPGALHR 18 0 A0A087WXV6;Q96G74-2;Q96G74-3;Q96G74-5;Q96G74 A0A087WXV6 OTUD5 OTU domain-containing protein 5 1 AS(1)PPPQGPLPGPPGALHR;AS(1)PPPQGPLPGPPGALHR;AS(1)PPPQGPLPGPPGALHR;AS(1)PPPQGPLPGPPGALHR;AS(1)PPPQGPLPGPPGALHR 149.84 3.82E-08 2926190000 955861 775862 505798 621083 795688 860037 823162 974231 819905 TRUE FALSE 829541.547 770765.3114 750403.6046 762109.3878 779855.3655 893123.1799 743331.8759 765899.2821 722976.7649 1.147397243 1.066099699 1.03793599 1.054127082 1.078672792 1.23534147 1.028154585 1.059369152 1 19.46358976 AS(ph)PRPWT(ph)PEDPWSLYGPSPGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASPRPWTPEDPWSLYGPSPGGR 22 1 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;Q14934-12;Q14934-13;Q14934-18 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 2 AS(1)PRPWT(1)PEDPWSLYGPSPGGR;AS(1)PRPWT(0.992)PEDPWS(0.008)LYGPSPGGR 111.89 0.00071149 200608000 146046 184201 137771 150709 181467 235740 115686 172389 189022 TRUE FALSE 126745.6511 182990.9715 204397.5164 184929.7819 177856.1617 244809.0703 104466.7895 135524.9539 166676.0345 0.760431165 1.09788412 1.226316171 1.109516329 1.067076993 1.468771867 0.626765509 0.813104021 1 17.34668716 2.218083653 24.99999714 0.805479334 1.122308484 0.361597903 0.193061851 251.1405683 306611.268 0.077197669 0.052114023 165.2280027 -2.218083653 0.31682915 AS(ph)PS(ph)PQPSSQPLQIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASPSPQPSSQPLQIHR 16 0 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 2 AS(1)PS(1)PQPSSQPLQIHR;AS(1)PS(1)PQPSSQPLQIHR 172.3 2.44E-09 440480000 557370 448400 381100 346870 375150 506060 515970 448050 622740 TRUE FALSE 483712.1423 445454.4309 565401.2347 425632.1351 367685.249 525528.4557 465931.3088 352237.9942 549120.3866 0.88088542 0.81121452 1.029648959 0.77511625 0.669589507 0.957036869 0.848504845 0.6414586 1 19.06676295 AS(ph)PSPQPS(ph)SQPLQIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASPSPQPSSQPLQIHR 16 0 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 2 AS(0.716)PS(0.296)PQPS(0.583)S(0.405)QPLQIHR 139.49 2.62E-06 248290000 208290 161400 127110 129730 154250 195080 180550 155690 215970 TRUE FALSE 180763.9488 160339.7528 188580.8212 159187.1793 151180.7268 202584.8538 163040.2888 122396.9051 190438.2726 0.949199687 0.841951308 0.990246438 0.835899093 0.793856848 1.063782248 0.856131945 0.642711695 1 17.53896392 1.993977914 24.99746508 0.781911216 0.908611446 0.077426495 0.116537146 416.8563719 1730357.096 0.046685057 0.030315015 98.62293307 -1.993977914 0.126700231 AS(ph)PSPQPSSQPLQIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASPSPQPSSQPLQIHR 16 0 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 AS(0.855)PS(0.145)PQPSSQPLQIHR 64.723 0.038228 353240000 113190 97920 103370 98366 69527 89134 105410 120480 233040 TRUE FALSE 98231.65471 97276.75707 153360.0778 120701.5037 68143.54873 92563.04266 95187.35442 94716.28958 205490.2767 0.478035537 0.473388613 0.746313063 0.587383042 0.331614468 0.450449745 0.463220722 0.460928328 1 17.6487106 1.235958878 24.99989385 1.000000663 0.498417886 0.683855585 0.107070791 44.87514458 431111.9013 0.184494233 0.02777036 17.21705543 -1.235958878 -0.501582778 AS(ph)PSSPGRQDS(ph)DEDDGPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASPSSPGRQDSDEDDGPQR 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 AS(0.399)PS(0.259)S(0.341)PGRQDS(1)DEDDGPQR 155.39 1.50E-08 371810000 301590 292270 242310 288170 299150 307320 281070 348280 640410 TRUE FALSE 261734.1174 290350.0591 359491.9265 353603.4029 293197.5003 319142.7993 253811.8747 273803.0323 564701.4594 0.46349113 0.51416559 0.636605273 0.626177597 0.519207973 0.565153134 0.449462048 0.484863334 1 19.10712883 1.235007469 24.9996086 1.000000658 0.532505479 0.846962908 0.062467131 41.68510646 293246.262 0.119418071 0.016684593 17.17937931 -1.235007469 -0.467495179 AS(ph)PSSPGRQDS(ph)DEDDGPQRVEEVDQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASPSSPGRQDSDEDDGPQRVEEVDQGR 27 2 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 AS(0.661)PS(0.18)S(0.191)PGRQDS(0.968)DEDDGPQRVEEVDQGR 53.408 0.04901 292740000 87995 78494 59392 52730 63165 72662 76005 97965 72651 TRUE FALSE 76366.2378 77978.36775 88114.16985 64703.15243 61908.14008 75457.35416 68634.0468 77015.94711 64062.28154 1.192062411 1.217227452 1.37544539 1.010003872 0.966374262 1.177874911 1.071364384 1.20220425 1 15.96718756 3.729620833 24.97330118 1.085011309 1.257143324 0.506854986 0.08774715 570.4533259 1593562.245 0.024708376 0.037233796 5365.631374 -3.729620833 0.172132015 AS(ph)PSVTCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASPSVTCK 8 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 AS(0.998)PS(0.002)VTCK 108.43 0.0039985 343580000 812240 689400 455910 535940 509510 544210 719860 793760 741230 TRUE FALSE 704900.426 684871.286 676389.6009 657633.3683 499371.7478 565146.1109 650048.088 624020.601 653602.6338 1.078484678 1.047840462 1.03486364 1.00616695 0.764029583 0.864663148 0.99456161 0.954740034 1 19.31805427 3.464512339 24.99646193 0.920342506 1.047703149 0.469496356 0.068054943 225.8344922 447702.4772 0.021281945 0.02749208 2914.152932 -3.464512339 0.127360643 AS(ph)PTLDFTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASPTLDFTER 10 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 AS(0.932)PT(0.068)LDFTER;AS(0.959)PT(0.041)LDFTER;AS(0.525)PT(0.475)LDFTER 147.63 2.79E-05 1380460000 1017690 914340 856456 934667 916030 851980 1163730 1227410 950960 TRUE FALSE 883199.688 908333.6403 1270640.986 1146897.428 897802.7952 884756.2219 1050871.644 964937.9232 838538.5921 1.053260633 1.083234151 1.515304123 1.367733624 1.070675582 1.055116879 1.253217984 1.150737643 1 19.67751766 3.223637434 24.98454373 1.120051604 1.261224013 0.201653314 0.145515186 436.1359442 730181.2339 0.046908367 0.053399822 1673.545152 -3.223637434 0.141172408 AS(ph)PTPLASPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASPTPLASPGK 11 0 A0A1B0GTL5 A0A1B0GTL5 1 AS(0.946)PT(0.054)PLASPGK 65.234 0.069235 312330000 219310 199610 118290 172350 174580 195430 202440 219040 257360 TRUE FALSE 190327.6278 198298.7488 175495.4397 211484.7017 171106.1996 202948.3186 182807.4 172200.0006 226935.194 0.838687136 0.873812234 0.77332844 0.93191672 0.753987059 0.894300769 0.805548918 0.758806942 1 17.79192084 1.224061825 24.98471635 1.000000451 0.827032618 0.454927232 0.058865133 696.2265963 1199686.805 0.291995865 0.013575356 16.75181335 -1.224061825 -0.172967832 AS(ph)PTSDIESVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ASPTSDIESVER 12 0 Q96JK2-2;Q96JK2-3;Q96JK2 Q96JK2-2 DCAF5 DDB1- and CUL4-associated factor 5 1 AS(0.967)PT(0.017)S(0.017)DIESVER;AS(0.963)PT(0.036)SDIESVER;AS(0.883)PT(0.104)S(0.013)DIESVER;AS(0.76)PT(0.176)S(0.064)DIESVER;AS(0.983)PT(0.017)SDIESVER;AS(0.995)PT(0.005)SDIESVER 322.62 7.12E-47 2344600000 826670 738340 602310 752720 761020 709600 752203 811060 1410460 TRUE FALSE 717423.465 733489.7959 893589.1306 923636.5806 745877.1909 736898.7712 679254.4688 637621.1307 1243717.026 0.57683818 0.589756175 0.718482671 0.742642065 0.599716154 0.592497132 0.546148726 0.512673798 1 20.24622685 1.229896423 24.99999754 1.000000739 0.60836227 0.751023913 0.070593388 193.2182698 557476.3139 0.227713973 0.019758511 16.97838678 -1.229896423 -0.39163847 AS(ph)PVAALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASPVAALK 8 0 H9KVB4;O15417;O15417-2 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 AS(1)PVAALK;AS(1)PVAALK;AS(1)PVAALK 156.83 0.00040564 1228480000 1752090 1469190 1231220 1605260 1537860 1261920 1533660 2086490 2718340 TRUE FALSE 1520546.867 1459538.794 1826642.11 1969758.818 1507259.595 1310466.879 1384925.889 1640310.351 2396980.942 0.634359181 0.608907133 0.762059505 0.821766575 0.628815844 0.546715602 0.577779266 0.684323485 1 21.19278701 1.242812213 5.014699584 1.020641656 0.656118568 0.63458518 0.081822737 0.119910365 7.711160014 0.151773458 0.022497125 17.49090225 -1.242812213 -0.364523088 AS(ph)PVGDGNFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASPVGDGNFR 10 0 Q86YS7;Q86YS7-5;H0YFC4;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 AS(1)PVGDGNFR 86.463 0.014166 0 138060 135160 112500 143460 151230 149740 150910 158990 287360 TRUE FALSE 119815.0212 134272.1251 166905.3763 176034.7856 148220.8189 155500.5947 136274.7714 124991.2258 253388.6282 0.472850822 0.529905884 0.658693239 0.694722517 0.584954502 0.613684189 0.537809342 0.49327875 1 17.95099225 1.231834555 24.9836356 1.000000728 0.574571563 0.788375545 0.069484192 115.5248753 429071.563 0.177067858 0.018635303 17.0543258 -1.231834555 -0.425429166 AS(ph)PVPAPSSGLHAAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASPVPAPSSGLHAAVR 16 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 AS(0.999)PVPAPSSGLHAAVR 157.58 5.63E-08 342410000 161160 160830 87765 160360 197690 155780 144590 239950 196110 TRUE FALSE 139862.2977 159773.4971 130208.4476 196772.1889 193756.3558 161772.9574 130567.6841 188638.5598 172926.0992 0.808798084 0.923940908 0.752971634 1.137897575 1.120457563 0.935503421 0.755049033 1.090862285 1 17.3997961 3.749866703 24.97161021 1.001458331 0.838107284 0.341723043 0.116100441 962.7618484 2126434.025 0.032081269 0.054914827 5621.68753 -3.749866703 -0.163351047 AS(ph)QEANLLTLAQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASQEANLLTLAQK 13 0 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2;H7C1L3 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 AS(1)QEANLLTLAQK;AS(1)QEANLLTLAQK 152.32 1.33E-06 122600000 333030 332390 222394 312790 373220 339770 350320 427630 486730 TRUE FALSE 289019.2417 330206.5082 329944.4823 383813.7502 365793.6522 352841.1718 316346.0203 336184.6523 429189.3339 0.673407326 0.769372587 0.768762074 0.894276069 0.852289708 0.822110765 0.73707801 0.783301508 1 18.7112547 4.584348145 1.43578044 0.831925663 0.641870582 0.364680169 0.071866133 1.118938404 2.640518459 0.020934138 0.281864605 38401.49613 -4.584348145 -0.190055082 AS(ph)SHSS(ph)QTQGGGSVTK ddPTM_MDA-MB-175_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(0.465)S(0.465)HS(0.38)S(0.682)QT(0.007)QGGGSVTK 86.832 0.0016113 0 235610 299110 165920 235440 300620 320160 351780 384890 392120 TRUE FALSE 204473.5415 297145.1267 246159.467 288900.2505 294638.2502 332476.7624 317664.4297 302584.2687 345764.0203 0.591367319 0.859387065 0.711929098 0.83554168 0.852136813 0.961571311 0.918731884 0.875117858 1 18.39942823 6.039092696 0.330453701 0.959000084 5.96E-18 0.702804279 0.064591296 13.39248216 0.675690739 0.110660751 5.986520722 1094189.886 -6.039092696 -0.959000084 AS(ph)SHSS(ph)QTQGGGSVTKKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASSHSSQTQGGGSVTKKR 18 2 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 AS(0.5)S(0.5)HS(0.17)S(0.825)QT(0.004)QGGGSVTKKR;AS(0.5)S(0.5)HS(0.074)S(0.926)QT(0.001)QGGGSVTKKR 74.698 0.0097164 188265000 6875.5 5061.4 2518.34 3768.72 3431 6291.5 4354 33818.2 8744.2 TRUE FALSE 5966.885255 5028.15133 3736.217647 4624.465477 3362.729813 6533.538076 3931.74975 26586.4411 7710.470637 0.77386784 0.652119899 0.48456415 0.599764359 0.436125105 0.84735918 0.509923445 3.448095759 1 12.91260321 1.761395676 25 2.346410741 0.612733568 0.557974926 0.593244678 6.816368442 7469.819284 0.282454225 0.135643666 57.72921823 -1.761395676 -1.733677173 AS(ph)SHSSQTQGGGSVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 AS(0.569)S(0.407)HS(0.019)S(0.006)QTQGGGSVTK;AS(0.531)S(0.369)HS(0.077)S(0.023)QTQGGGSVTK;AS(0.217)S(0.217)HS(0.217)S(0.132)QT(0.217)QGGGSVTK;AS(0.601)S(0.395)HS(0.004)SQTQGGGSVTK;AS(0.248)S(0.248)HS(0.248)S(0.248)QT(0.007)QGGGSVTK;AS(0.484)S(0.484)HS(0.016)S(0.016)QTQGGGSVTK;AS(0.596)S(0.398)HS(0.003)S(0.004)QTQGGGSVTK 237.18 6.07E-20 35007990000 4417572 5359776 2289722 3760977 6436998 6860285 7828932 8712397 9273425 TRUE FALSE 3833778.667 5324567.279 3397039.218 4614964.311 6308914.334 7124204.603 7069683.38 6849318.701 8177131.261 0.468841522 0.651153456 0.415431661 0.564374493 0.771531498 0.871235202 0.864567677 0.837618779 1 22.96316337 3.14143634 2.479326068 0.880993116 0.518909332 0.853024171 0.072664358 0.101005398 1.266272372 0.023025323 0.027428435 1384.957161 -3.14143634 -0.362083784 AS(ph)SHSSQTQGGGSVTKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSHSSQTQGGGSVTKK 17 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 AS(0.581)S(0.418)HS(0.001)SQTQGGGSVTKK 222.06 1.64E-15 293550000 356270 403050 96281 202200 501190 447980 719740 812820 201220 TRUE FALSE 309188.0168 400402.338 142842.8136 248112.6004 491217.2996 465214.0805 649939.7256 639004.7684 177432.0008 1.742571889 2.25665233 0.805056658 1.398353168 2.768481995 2.621928842 3.663035543 3.601406541 1 17.43690671 3.198666781 5.927329297 2.914286774 1.546565211 0.331848697 0.810390689 0.193108671 17.13979056 0.249503707 0.289739884 1580.035267 -3.198666781 -1.367721563 S(ph)PEIHRR ddPTM_MDA-MB-175_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 107.56 0.0045628 3584180000 1860390 1545920 916609 1080701 1353450 1439610 1394050 1681380 596690 TRUE FALSE 1614534.748 1535764.75 1359884.178 1326090.68 1326518.993 1494992.728 1258855.246 1321829.972 526149.988 3.068582695 2.918872536 2.584594145 2.520366264 2.521180316 2.841381284 2.392578684 2.512268368 1 19.0051146 1.101310479 2.195811711 3.63E-11 2.691025523 0.864897305 0.208026469 0.38923604 1.367450215 2.402394116 0.057292824 12.62729942 -1.101310479 2.691025523 AS(ph)SPAQCVTPVQTVV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSPAQCVTPVQTVV 15 0 Q13614;Q13614-2 Q13614 MTMR2 Myotubularin-related protein 2 1 AS(0.5)S(0.5)PAQCVTPVQTVV 81.431 0.014706 100440000 162190 152160 92757 119670 171140 178360 145430 178210 137270 TRUE FALSE 140756.1806 151160.4509 137614.5955 146842.9025 167734.6488 185221.6246 131326.221 140101.1783 121042.097 1.162869647 1.248825448 1.136915163 1.213155639 1.385754651 1.530224849 1.084963201 1.157458288 1 16.88514936 AS(ph)SPFRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSPFRR 7 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 AS(0.634)S(0.366)PFRR 100.02 0.0061881 1118200000 1007300 970530 595030 710960 854890 1002300 942010 1125500 762320 TRUE FALSE 874182.7528 964154.5245 882788.4983 872394.3343 837879.3616 1040859.13 850654.0152 884820.5837 672199.398 1.300481309 1.434328158 1.313283679 1.297820761 1.24647443 1.548438057 1.265478692 1.316306718 1 19.35852973 1.027691993 2.042934298 0.690801158 1.348339229 0.589792497 0.089108787 1.069427934 2.615914822 1.644047391 0.022920127 10.65839945 -1.027691993 0.657538071 AS(ph)SPPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASSPPDR 7 0 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 AS(0.662)S(0.338)PPDR;AS(0.665)S(0.335)PPDR;AS(0.754)S(0.246)PPDR 85.731 0.021604 392600000 590042 557700 406564 519928 352601 535944 522271 642293 924390 TRUE FALSE 512066.4547 554036.432 603179.7103 637985.599 345584.93 556562.1125 471621.2388 504943.6403 815109.6673 0.628217865 0.679707841 0.739998229 0.782699095 0.423973539 0.682806418 0.57859851 0.619479391 1 19.63663465 1.236472373 24.99269004 1.00000046 0.641023253 0.573506792 0.097037208 41.24339618 493486.7338 0.150342443 0.023516092 17.23742433 -1.236472373 -0.358977208 AS(ph)SPPDRIDIFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASSPPDRIDIFGR 13 1 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 AS(0.646)S(0.354)PPDRIDIFGR;AS(0.909)S(0.091)PPDRIDIFGR;AS(0.5)S(0.5)PPDRIDIFGR 176.49 9.97E-06 15107330000 2158160 2035210 940580 1104300 1873780 1883120 2005900 2198260 373695 TRUE FALSE 1872953.688 2021840.572 1395447.634 1355048.193 1836495.444 1955564.845 1811368.127 1728179.206 329517.2028 5.683932954 6.13576637 4.234824835 4.112222918 5.573291556 5.934636578 5.497036608 5.244579619 1 18.32999426 4.245810532 24.74895124 4.70596182 5.909850099 0.136197639 1.39795639 329.800182 1125803.425 0.347734825 0.879891366 17612.07524 -4.245810532 1.203888279 AS(ph)SPSEHGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 138.63 3.85E-05 471550000 274670 291950 181459 304450 357470 570890 218004 368800 401220 TRUE FALSE 238371.6636 290032.1612 269213.1793 373580.0257 350357.0464 592852.5077 196862.0056 289934.99 353788.2287 0.673769346 0.819790309 0.760944422 1.055942497 0.990301593 1.675727058 0.556440237 0.819515649 1 18.43252652 3.749429345 22.69792255 0.993469127 0.758330155 0.163349455 0.279209258 463.4899284 967927.5093 0.077201629 0.131669229 5616.029048 -3.749429345 -0.235138972 AS(ph)SPVPSFLPTSGWPFSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSPVPSFLPTSGWPFSSR 19 0 Q86UZ6;A0A494BZW5 Q86UZ6 ZBTB46 Zinc finger and BTB domain-containing protein 46 1 AS(0.5)S(0.5)PVPSFLPTSGWPFSSR 74.786 0.0062885 0 63082 59905 41647 54315 58475 48141 59703 71692 57089 TRUE FALSE 54745.55387 59511.48011 61787.6285 66648.0509 57311.4619 49993.01542 53913.01225 56361.22371 50340.00346 1.087515894 1.182190624 1.227406124 1.323958012 1.138487445 0.993107111 1.070977524 1.119611042 1 15.6194177 2.998104075 24.99784573 1.060454185 1.208453394 0.550774311 0.067343849 60.35685157 795823.5071 0.021156405 0.02362364 995.6439858 -2.998104075 0.147999209 AS(ph)SRPGSPTADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSRPGSPTADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHK 45 1 H0Y9C1;H0Y9Z5;Q96LI5-2;Q96LI5 H0Y9C1 CNOT6L CCR4-NOT transcription complex subunit 6-like 1 AS(0.339)S(0.339)RPGS(0.319)PT(0.003)ADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHK 259.88 6.63E-68 156720000 49444 42478 28427 30010 41235 42559 46661 58545 52649 TRUE FALSE 42909.85012 42198.95922 42174.39228 36824.22917 40414.50417 44196.27227 42135.8234 46025.60735 46424.8952 0.924285342 0.908972633 0.908443457 0.79320005 0.870535173 0.95199509 0.907612677 0.991399273 1 15.50261103 1.85481356 1.17736279 1.014309822 0.883550229 0.523561216 0.040778294 0.535332492 1.211333959 0.070326025 0.014854462 71.58360402 -1.85481356 -0.130759593 AS(ph)SRS(ph)PVFTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSRSPVFTPR 11 1 P52735-3 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 2 AS(0.5)S(0.5)RS(1)PVFTPR 101.53 0.0018302 620410000 298060 324660 216340 236070 332200 318390 319200 360170 318580 TRUE FALSE 258670.6158 322527.2871 320962.7476 289673.3016 325589.8699 330638.6693 288244.0331 283150.4483 280917.8353 0.920805244 1.148119651 1.142550266 1.031167356 1.15902171 1.176994223 1.026079504 1.007947566 1 18.0997887 2.028605302 21.78694577 1.008283054 1.100829703 0.224972708 0.074903388 67.21622525 51193.56709 0.029698285 0.020021447 106.8083736 -2.028605302 0.092546648 AS(ph)SSAESEDLAVHLYPGAVTIQGVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASSSAESEDLAVHLYPGAVTIQGVLR 26 0 Q86X27 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 AS(0.333)S(0.333)S(0.333)AESEDLAVHLYPGAVTIQGVLR;AS(0.402)S(0.328)S(0.269)AES(0.002)EDLAVHLYPGAVTIQGVLR;AS(0.332)S(0.332)S(0.332)AES(0.003)EDLAVHLYPGAVTIQGVLR 146.53 1.33E-07 179919000 95443 113121 74143 87047 93905 97609 100331 117641 121542 TRUE FALSE 82829.96573 112377.9007 109998.8028 106812.3518 92036.47422 101364.0814 90600.91506 92484.38763 107173.4432 0.772859052 1.048561074 1.026362497 0.996630775 0.858761942 0.945794764 0.845367214 0.862941274 1 16.70958794 3.244105143 24.99855859 0.895489716 0.972011702 0.092627301 0.086573857 255.6825846 1152787.12 0.024425011 0.030634683 1754.30517 -3.244105143 0.076521985 AS(ph)SWPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSWPHR 7 0 A0A2R8YF49;H0Y895;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 AS(0.577)S(0.423)WPHR 60.59 0.062217 160100000 83007 75144 40805 65427 57425 68679 76505 76515 138700 TRUE FALSE 72037.41464 74650.37412 60538.43448 80283.20034 56282.35485 71321.12557 69085.55688 60152.86269 122303.044 0.589007536 0.610372168 0.494987144 0.656428472 0.460187686 0.583150862 0.564871933 0.491834551 1 16.90010079 1.233644455 24.99999999 1.000000681 0.554459585 0.84537301 0.059623952 53.25576678 270787.5973 0.10906156 0.013560738 17.1255471 -1.233644455 -0.445541096 AS(ph)SWPHRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASSWPHRR 8 1 A0A2R8YF49;H0Y895;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 AS(0.5)S(0.5)WPHRR;AS(0.5)S(0.5)WPHRR;AS(0.5)S(0.5)WPHRR 96.331 0.0055228 613270000 806470 751170 464960 561010 723560 797830 793100 808940 719100 TRUE FALSE 699892.9462 746235.5148 689816.2112 688395.895 709162.5716 828523.0364 716185.2841 635954.4762 634088.8172 1.103777463 1.176862759 1.087885786 1.085645853 1.118396276 1.306635622 1.129471558 1.002942268 1 19.27432541 1.748655732 4.707341083 1.000437992 1.14693609 0.465925885 0.063624315 0.1554259 7.911330259 0.040959655 0.017504828 56.06034055 -1.748655732 0.146498098 AS(ph)TDNEELLQFPLELCSDSLPSHPFPPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASTDNEELLQFPLELCSDSLPSHPFPPAK 29 0 Q86YS7;Q86YS7-5;H0YFC4;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 AS(0.822)T(0.178)DNEELLQFPLELCSDSLPSHPFPPAK;AS(0.5)T(0.5)DNEELLQFPLELCSDSLPSHPFPPAK;AS(0.792)T(0.208)DNEELLQFPLELCSDSLPSHPFPPAK 231.53 1.41E-35 399571000 273098 289787 170857 223110 293822 265861 314675 376701 335421 TRUE FALSE 237007.4074 287883.3701 253484.0167 273770.5355 287975.5171 276088.8447 284157.8669 296146.4226 295767.9115 0.801329009 0.973342134 0.857036909 0.925626225 0.973653685 0.933464497 0.960746098 1.001279757 1 18.17410601 8 0.158597636 1.053118707 0.274006342 0.571287406 0.041563952 103.3440862 1.350321542 0.545783987 18.27887151 100000000 -8 -0.779112366 AS(ph)TFCGTPDYIAPEILQGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASTFCGTPDYIAPEILQGLK 20 0 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 1 AS(0.465)T(0.465)FCGT(0.07)PDYIAPEILQGLK 147.92 7.50E-08 101700000 170000 112990 87867 116460 110610 82742 147670 148640 241640 TRUE FALSE 147534.0693 112247.7613 130359.7751 142904.023 108409.0774 85925.13828 133348.9861 116854.4927 213073.5945 0.692408976 0.526802777 0.611806336 0.670679177 0.508787012 0.403265071 0.625835343 0.548423154 1 17.70099229 1.236797721 24.99938215 1.000000536 0.570210967 0.716782614 0.084230697 24.83148653 352026.758 0.127399705 0.020386282 17.25034243 -1.236797721 -0.429789569 AS(ph)TPQPAPAGVPALASQHPPEEEVHYHLPVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASTPQPAPAGVPALASQHPPEEEVHYHLPVAR 32 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 AS(0.658)T(0.342)PQPAPAGVPALASQHPPEEEVHYHLPVAR;AS(0.601)T(0.399)PQPAPAGVPALASQHPPEEEVHYHLPVAR 54.691 0.024423 501980000 253240 228210 77901 141909 248770 247590 218289 242470 230880 TRUE FALSE 219773.6924 226710.8735 115574.1842 174131.6074 243819.9637 257114.9475 197119.3664 190619.6774 203585.6294 1.079514762 1.113589766 0.567693233 0.855323668 1.197628558 1.262932694 0.968238117 0.936312047 1 17.6352762 3.263740042 24.87082431 1.057570276 0.894974754 0.182038815 0.175853851 429.7022809 424432.7575 0.054826013 0.070751276 1835.439367 -3.263740042 -0.162595521 AS(ph)WESLDEEWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ASWESLDEEWR 11 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 AS(0.999)WES(0.001)LDEEWR;AS(0.999)WES(0.001)LDEEWR;AS(1)WESLDEEWR;AS(0.985)WES(0.015)LDEEWR;AS(0.5)WES(0.5)LDEEWR;AS(0.886)WES(0.114)LDEEWR 265.53 6.16E-21 816992000 1202724 937296 776804 1013758 1004844 968201 983054 1135535 1157187 TRUE FALSE 1043780.976 931138.8409 1152469.013 1243947.248 984849.5703 1005448.319 887717.5744 892709.677 1020385.671 1.022927904 0.912536178 1.129444528 1.219095175 0.965173854 0.985361072 0.869982399 0.874874768 1 19.96068311 2.754128355 2.347666386 0.910192031 1.062462766 0.329142672 0.089254897 0.343344102 3.739727529 0.035399227 0.032813407 567.7123674 -2.754128355 0.152270734 ASAGHAVSIAQDDAGADDWETDPDFVNDVSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASAGHAVSIAQDDAGADDWETDPDFVNDVSEK 32 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;; 354.21 9.28E-132 4018760000 1018680 968200 377253 858930 1025740 867080 1100840 1365400 1203700 FALSE TRUE 884058.857 961839.8304 559693.8126 1053963.184 1005329.781 900437.1287 994080.7062 1073419.836 1061399.957 0.832917743 0.906199236 0.527316596 0.99299343 0.947173376 0.848348563 0.936575039 1.011324551 1 20.01753697 ASAGHAVSIAQDDAGADDWETDPDFVNDVSEKEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASAGHAVSIAQDDAGADDWETDPDFVNDVSEKEQR 35 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ; 301.78 1.10E-90 392720000 95232 93161 15070.6 26832 95050 67680 115087 133143 11733.7 FALSE TRUE 82646.84991 92549.01926 22358.79257 32924.6157 93158.69096 70283.69339 103925.8805 104671.4056 10346.55535 7.987861379 8.944911238 2.160989025 3.182181371 9.003836328 6.792955819 10.04449084 10.11654623 1 13.33686292 7.975041976 10.8792337 6.892860775 6.655039805 0 3.351394672 0 0 0.769907396 0 94415212.76 -7.975041976 -0.23782097 ASAGTPSLSAGVS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASAGTPSLSAGVSPK 15 0 Q8TEK3;Q8TEK3-1 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 ASAGTPSLSAGVS(1)PK;ASAGTPSLSAGVS(1)PK 213.02 1.27E-11 186990000 537390 428650 334640 342820 470600 402490 508400 581010 538220 TRUE FALSE 466372.5499 425834.1699 496473.0233 420662.5207 461235.9807 417974.0507 459095.4463 456765.5329 474592.2447 0.982680512 0.897263229 1.046104374 0.886366192 0.971857391 0.880701392 0.967347131 0.962437836 1 18.856329 1.326997956 1.829617103 1.011123791 0.945359459 0.099044691 0.050173964 1.664629243 6.306502526 0.182071354 0.01278166 21.23234471 -1.326997956 -0.065764332 ASALLFS(ph)SDEEDQWNIPASQTHLASDSR ddPTM_MDA-MB-175_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 1 ASALLFS(0.553)S(0.447)DEEDQWNIPASQTHLASDSR 219.85 1.74E-34 549870000 136460 106750 54324 93901 130860 121150 106630 160560 142670 TRUE FALSE 118426.4653 106048.7522 80595.2681 115222.6572 128256.142 125810.7189 96289.03901 126225.4935 125803.7151 0.941359046 0.842969956 0.640642989 0.915892326 1.019494074 1.000055672 0.765391061 1.00335267 1 16.940815 3.496502826 24.53958471 0.952581411 0.806201756 0.308918388 0.101994923 741.5737682 938926.5239 0.028267092 0.041198884 3136.915544 -3.496502826 -0.146379655 ASALLFSS(ph)DEEDQWNIPASQTHLASDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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(0.239)S(0.76)DEEDQWNIPASQTHLASDSR;ASALLFS(0.154)S(0.846)DEEDQWNIPASQTHLASDSR;ASALLFS(0.108)S(0.892)DEEDQWNIPASQTHLASDSR;ASALLFS(0.149)S(0.851)DEEDQWNIPASQTHLASDSR;ASALLFS(0.102)S(0.898)DEEDQWNIPASQTHLASDSR;ASALLFS(0.202)S(0.798)DEEDQWNIPASQTHLASDSR 349.35 5.31E-111 2769708000 856843 745630 341362.6 562632 688823 788011 700456 881297 840408 TRUE FALSE 743609.0266 740731.9074 506446.6951 690386.1949 675116.77 818326.2931 632525.8849 692838.4948 741055.9236 1.003445223 0.999562764 0.683412249 0.93162496 0.911020003 1.104270632 0.853546763 0.934934156 1 19.49922289 2.975244633 24.86870502 0.96173337 0.898734678 0.084308894 0.10686433 2058.208682 2067633.442 0.034598839 0.034772458 944.5928054 -2.975244633 -0.062998692 ASAPS(ph)PNAQVACDHCLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ASAPSPNAQVACDHCLK 17 0 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 1 ASAPS(1)PNAQVACDHCLK;ASAPS(1)PNAQVACDHCLK;ASAPS(1)PNAQVACDHCLK;ASAPS(1)PNAQVACDHCLK;ASAPS(1)PNAQVACDHCLK;ASAPS(1)PNAQVACDHCLK 331.8 3.20E-72 6556340000 4994282 4872824 3574528 4210461 4333698 3483270 5196290 5716655 6188600 TRUE FALSE 4334274.98 4840814.098 5303181.697 5166510.523 4247465.889 3617273.651 4692354.596 4494192.815 5456990.758 0.794261008 0.8870849 0.971814308 0.946769154 0.778353139 0.662869668 0.85987952 0.82356614 1 22.37967417 4.756540624 21.96873893 0.859360977 0.794260712 0.046196707 0.098480984 2904.238919 3548205.374 0.02533782 0.630569643 57087.44728 -4.756540624 -0.065100265 ASAS(ph)PSTSSTSSRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASASPSTSSTSSRPK 15 1 J3KP75;O75167-5;O75167-2;O75167;O75167-4;F6TH74;F5H858 J3KP75 PHACTR2 Phosphatase and actin regulator;Phosphatase and actin regulator 2 1 AS(0.002)AS(0.951)PS(0.044)T(0.003)SSTSSRPK 102.69 0.0009275 117890000 124610 90677 47526 62636 60549 56835 70567 87814 70564 TRUE FALSE 108142.4728 90081.33682 70509.73256 76858.46113 59344.19336 59021.47923 63723.4232 69035.65947 62222.00431 1.738010114 1.447740841 1.133196099 1.235229594 0.953749305 0.94856281 1.024130031 1.109505556 1 15.92513725 4.757842494 0.936102467 1.02596092 2.168219856 0.908030607 0.075283193 0.612313476 0.41692749 0.026190028 0.720707495 57258.83321 -4.757842494 1.142258936 ASASRPQPAPADGADPPPAEEPEARPDGEGS(ph)PGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASASRPQPAPADGADPPPAEEPEARPDGEGSPGK 34 2 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 ASASRPQPAPADGADPPPAEEPEARPDGEGS(1)PGK 94.437 0.00015431 477100000 376620 334290 244260 255290 366670 279630 404360 452800 338220 TRUE FALSE 326848.7128 332094.027 362384.953 313257.4964 359373.9844 290387.547 365145.2294 355972.2437 298236.0169 1.095939773 1.113527569 1.215094531 1.050367758 1.204998605 0.973683695 1.224349873 1.193592402 1 18.18609497 ASAVSELS(ph)PR ddPTM_MDA-MB-175_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 183.94 1.69E-06 81215830000 11790020 10032190 6140908 7233710 9351520 9249020 8795880 10287450 9155230 TRUE FALSE 10231938.98 9966287.883 9110671.649 8876234.416 9165443.048 9604835.784 7942856.911 8087558.875 8072909.139 1.267441366 1.234534876 1.128548766 1.099508772 1.135333359 1.189761413 0.98389029 1.001814679 1 22.94465722 7.580643443 0.042638064 5.80E-07 2.857524951 0.737260484 0.050447273 717.4871115 3.292331734 70.22778577 172.0609858 38075309.57 -7.580643443 2.857524371 ASCGPPS(ph)LPDPTFLPDAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASCGPPSLPDPTFLPDAER 19 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 ASCGPPS(1)LPDPTFLPDAER;ASCGPPS(0.999)LPDPT(0.001)FLPDAER 241.74 2.35E-24 69139000 134952 129973 55495 84919 109580 104565 102037 134513 132556 TRUE FALSE 117117.7513 129119.1988 82332.56762 104201.1569 107399.5724 108587.6832 92141.46745 105748.4417 116885.3807 1.001988021 1.104665083 0.704387214 0.89148152 0.918845212 0.929009963 0.788306176 0.904719145 1 16.83473497 4.268747746 24.99999959 0.87835137 1.053326684 0.433081805 0.084007388 187.7901622 155518.6854 0.020161648 0.053328327 18567.25688 -4.268747746 0.174975315 ASDADRPCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASDADRPCR 9 1 Q86U44;H0YFV6;Q86U44-2 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 0 66.692 0.057466 138670000 177670 172030 109740 125760 124780 164300 172060 172070 175350 FALSE TRUE 154190.4593 170899.9236 162810.6311 154315.7301 122297.1221 170620.7273 155373.6477 135274.1696 154620.3228 0.997219878 1.105287588 1.052970451 0.998030061 0.79095115 1.103481899 1.004872095 0.874879622 1 17.23837043 3.479270002 24.99958442 0.950432944 1.051893506 0.210791196 0.085523575 122.5658502 1426004.146 0.024268663 0.031842421 3014.8798 -3.479270002 0.101460561 ASDPQS(ph)PPQVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASDPQSPPQVSR 12 0 Q7L7X3-3;Q7L7X3;Q7L7X3-2 Q7L7X3-3 TAOK1 Serine/threonine-protein kinase TAO1 1 ASDPQS(1)PPQVSR;AS(0.002)DPQS(0.998)PPQVSR 196.97 2.10E-07 418680000 335990 330710 201364 264308 341480 371860 265559 374550 347180 TRUE FALSE 291588.0702 328537.5442 298744.3039 324323.1711 334685.2161 386165.6948 239805.1291 294455.3973 306136.7759 0.952476452 1.073172419 0.975852388 1.059406111 1.093253874 1.261415567 0.783326761 0.961842616 1 18.22381684 2.223564321 24.99999297 0.91931491 1.065837101 0.353218519 0.09823852 278.9356146 465003.743 0.039927802 0.027040354 167.3263437 -2.223564321 0.146522192 ASDVHEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ASDVHEVR 8 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;; 155.07 0.00041492 18549650000 27369260 23330780 13653850 19361200 19531810 25455880 23162910 24360850 35510410 FALSE TRUE 23752342.95 23177518.57 20256897.53 23757456.38 19143165.19 26435184.18 20916574.55 19151471.8 31312409.78 0.758560044 0.740202326 0.646928731 0.758723348 0.611360331 0.844239851 0.667996322 0.611625612 1 24.90023121 1.227807648 24.99953541 1.000000632 0.701243664 0.613296702 0.073575892 314.8804624 732015.0372 0.251937816 0.017533119 16.8969239 -1.227807648 -0.298756968 ASDVHEVRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASDVHEVRK 9 1 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;; 71.889 0.031357 591277000 2211790 1711940 767627 942540 1370520 1498370 2024170 1989390 1141400 FALSE TRUE 1919496.348 1700694.153 1138853.985 1156558.113 1343249.333 1556013.263 1827866.305 1563974.43 1006464.992 1.907166531 1.689769805 1.131538596 1.149129003 1.334621019 1.546018267 1.81612507 1.553928296 1 19.94086556 4.445660138 7.325609629 1.400953914 1.855360395 0.370728384 0.240556019 0.196166246 35.2008755 0.065597208 0.180216408 27903.5936 -4.445660138 0.454406481 ASEAGEVPFNHEILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASEAGEVPFNHEILR 15 0 Q7L5N1;E7EM64 Q7L5N1 COPS6 COP9 signalosome complex subunit 6 0 ; 158.17 1.84E-06 1884350000 1820720 1669490 1014870 1325550 1649400 1720560 1544060 1869010 1863060 FALSE TRUE 1580107.239 1658523.01 1505664.527 1626536.387 1616580.167 1786751.057 1394317.299 1469336.756 1642811.169 0.961831322 1.009563997 0.916517099 0.990093334 0.984032856 1.087618036 0.848738629 0.894403924 1 20.64773523 2.219638204 24.99972327 0.907483927 0.988599002 0.292608614 0.056135797 290.3637282 383616.8895 0.022641782 0.015293255 165.8204938 -2.219638204 0.081115075 ASEDGESVGHCPSCQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASEDGESVGHCPSCQR 16 0 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 115.56 0.0004963 943520000 719010 667840 311150 545590 637520 648090 618450 696900 617800 FALSE TRUE 623991.0068 663452.9151 461623.1807 669474.5483 624834.5993 673022.4417 558472.8142 547873.3583 544764.3878 1.145432816 1.217871303 0.847381347 1.228924951 1.146981362 1.235437662 1.025163955 1.005707 1 19.05527287 2.068430564 11.21670903 1.0069065 1.132121406 0.22854371 0.110011588 0.784053283 124.9467839 0.044237979 0.029817595 117.0659419 -2.068430564 0.125214906 ASEDTTS(ph)GSPPKK ddPTM_MDA-MB-175_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(0.009)S(0.496)GS(0.496)PPKK;ASEDT(0.001)T(0.018)S(0.49)GS(0.49)PPKK 157.38 5.11E-07 97320000 633400 432820 361910 398190 407960 278910 610290 678050 560940 TRUE FALSE 549694.5852 429976.7769 536930.8865 488605.1255 399842.3942 289639.8482 551104.1697 533054.2841 494626.3122 1.111333084 0.869296207 1.085528354 0.987826796 0.808372673 0.58557307 1.114182881 1.077690917 1 18.91597946 ASEDTTSGS(ph)PPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASEDTTSGSPPK 12 0 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 ASEDTTS(0.001)GS(0.999)PPK;ASEDTTSGS(1)PPK;ASEDTTS(0.001)GS(0.999)PPK 217.2 3.91E-11 746380000 1717780 1280790 948220 1033650 1300120 1068990 1550130 1770930 1780600 TRUE FALSE 1490771.021 1272376.406 1406782.364 1268356.031 1274250.156 1110114.737 1399798.631 1392230.401 1570099.496 0.94947551 0.810379475 0.89598294 0.807818889 0.811572871 0.707034643 0.891534985 0.886714762 1 20.58242455 1.297655349 1.694320011 1.045472726 0.832175542 0.382360269 0.064960739 0.914151631 2.721308046 0.313613138 0.018179717 19.84519401 -1.297655349 -0.213297185 ASEDTTSGS(ph)PPKK ddPTM_MDA-MB-175_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 ASEDT(0.006)T(0.005)S(0.028)GS(0.96)PPKK;ASEDTTS(0.002)GS(0.998)PPKK;ASEDTTS(0.007)GS(0.993)PPKK;ASEDTT(0.067)S(0.353)GS(0.579)PPKK;ASEDTT(0.01)S(0.043)GS(0.948)PPKK;ASEDTTS(0.003)GS(0.997)PPKK;ASEDT(0.002)T(0.002)S(0.009)GS(0.987)PPKK 263.98 3.49E-24 3516930000 4632300 3146220 2703370 2804820 2954990 2180910 4403520 5132240 4404570 TRUE FALSE 4020129.818 3125552.274 4010728.774 3441697.25 2896191.48 2264811.019 3976467.308 4034750.415 3883866.752 1.035084382 0.804752705 1.032663845 0.886152247 0.745697951 0.583133038 1.023842362 1.038848826 1 21.88906227 2.080734029 24.99999999 1.025038943 0.847444736 0.279857277 0.130752786 37.68230398 11665.69022 0.05520521 0.037219339 120.4298178 -2.080734029 -0.177594207 ASEEHLK ddPTM_MDA-MB-175_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 ;;;;;;; 121.52 0.0044301 21913710000 19663000 19401300 9961380 13153650 12585540 15202400 21160400 23725200 23122100 FALSE TRUE 17064484.73 19273851.58 14778736.69 16140387.27 12335112.38 15787246.17 19108267.66 18651750.61 20388631.68 0.836960763 0.945323447 0.724851815 0.79163661 0.60499952 0.77431612 0.937202063 0.914811298 1 24.28126162 2.232849959 8.53001271 0.942948948 0.777212742 0.459566357 0.087253922 0.120676534 77.0662665 0.03664787 0.026076619 170.9424637 -2.232849959 -0.165736206 ASEELDGLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASEELDGLFR 10 0 Q14814-4;Q14814;Q05BX2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 0 ; 226.55 6.92E-09 59399000 205610 218110 148126 173777 207100 218020 206290 245020 241910 FALSE TRUE 178438.1176 216677.221 219760.2291 213235.7239 202979.1152 226407.3705 186284.0276 192624.3797 213311.6754 0.8365136 1.015777597 1.030230664 0.999643941 0.951561206 1.061392303 0.873295037 0.903018456 1 17.70260341 0.938990533 21.34203846 1.801694371 0.960011538 0.03138836 0.071476863 97.79241715 374809.8541 38358.8752 0.01715918 8.689414875 -0.938990533 -0.841682832 ASEENLLSSSSVPSADRDS(ph)SPTTNSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASEENLLSSSSVPSADRDSSPTTNSK 26 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 ASEENLLSSSSVPSADRDS(0.805)S(0.193)PT(0.002)TNSK;ASEENLLSSSSVPS(0.005)ADRDS(0.576)S(0.406)PT(0.01)T(0.002)NSK 134.91 2.16E-05 2341060000 787960 743500 475140 579160 684460 549400 862600 897150 701330 TRUE FALSE 683829.0896 738615.8995 704919.2932 710667.1299 670840.5851 570535.7735 778945.1848 705301.4541 618419.5664 1.105768845 1.194360495 1.139872235 1.149166631 1.084766106 0.922570702 1.259573964 1.140490199 1 19.23822644 3.245596236 23.37722198 1.094268003 1.150124129 0.108704854 0.089411362 207.1656319 688337.6968 0.026737661 0.033696446 1760.338697 -3.245596236 0.055856126 ASEENLLSSSSVPSADRDSS(ph)PTTNSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASEENLLSSSSVPSADRDSSPTTNSK 26 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 ASEENLLSSSSVPSADRDS(0.018)S(0.918)PT(0.054)T(0.01)NSK;ASEENLLSSSSVPSADRDS(0.173)S(0.653)PT(0.173)T(0.001)NSK;ASEENLLSSSSVPSADRDS(0.035)S(0.956)PT(0.009)TNSK;ASEENLLSSSSVPSADRDS(0.429)S(0.57)PT(0.001)TNSK 288.84 1.09E-62 2975980000 2387200 2112720 1527560 1823780 2076540 1635310 2492760 2874870 2246650 TRUE FALSE 2071725.472 2098841.403 2266293.125 2237897.124 2035220.917 1698221.434 2251012.519 2260101.423 1981053.596 1.045769522 1.059457153 1.143983752 1.129649964 1.027342683 0.857231443 1.136270378 1.140858292 1 20.91783648 4.477781416 24.96173746 1.069340852 1.049191401 0 0.088428984 196.5111511 7429542.221 0.023353863 0.063306123 30045.63704 -4.477781416 -0.020149451 ASEENLLSSSSVPSADRDSSPT(ph)TNSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASEENLLSSSSVPSADRDSSPTTNSK 26 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 ASEENLLSSSSVPSADRDS(0.085)S(0.269)PT(0.561)T(0.085)NSK 303.57 1.24E-70 1997300000 1014800 832050 552870 740840 906320 735310 976310 1298700 882620 TRUE FALSE 880691.6088 826584.2088 820239.7812 909059.045 888286.0052 763597.8515 881627.6065 1020983.111 778277.6691 1.13159049 1.062068516 1.053916634 1.168039481 1.141348442 0.981138072 1.132793142 1.311849423 1 19.56992544 1.994625882 24.96087504 1.191436159 1.089733716 0.058415419 0.091612869 354.4667047 1646374.291 0.036999364 0.024108669 98.77018844 -1.994625882 -0.101702443 ASEKPVS(ph)PK ddPTM_MDA-MB-175_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 78.705 0.027932 0 128110 88455 77585 85446 87441 62379 118310 149980 125110 TRUE FALSE 111179.9389 87873.93328 115105.3655 104847.8203 85701.09518 64778.76049 106836.3144 117907.9441 110319.6383 1.007798254 0.796539353 1.043380555 0.950400326 0.776843511 0.58719156 0.968425169 1.068784724 1 16.75133011 2.009181433 24.99846225 1.033095432 0.858718387 0.244955018 0.129698831 267.4017234 728056.9079 0.055383931 0.037284987 102.1366086 -2.009181433 -0.174377045 ASEPLLS(ph)PPPFGESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ASEPLLSPPPFGESR 15 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 ASEPLLS(1)PPPFGESR;ASEPLLS(1)PPPFGESR;ASEPLLS(1)PPPFGESR;ASEPLLS(1)PPPFGESR;ASEPLLS(1)PPPFGESR;ASEPLLS(1)PPPFGESR 251.49 7.87E-20 1113919000 419945 416671 261792 317664 440127 449091 436514 485615 449917 TRUE FALSE 364448.2042 413933.8608 388395.4868 389794.4664 431369.3338 466367.8214 394180.9395 381770.0113 396728.3248 0.918634192 1.043368559 0.97899611 0.982522401 1.087316702 1.175534471 0.993579018 0.962295827 1 18.59779188 4.745096516 23.58698093 1.024728658 0.918634085 0.224725283 0.063560648 610.9479956 2204673.901 0.016989504 0.152100402 55602.78136 -4.745096516 -0.106094574 ASET(ph)PPPVAQPKPEAPHPGLETTLQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASETPPPVAQPKPEAPHPGLETTLQER 27 1 Q6P1N0-2;Q6P1N0 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 AS(0.073)ET(0.927)PPPVAQPKPEAPHPGLETTLQER;AS(0.003)ET(0.997)PPPVAQPKPEAPHPGLETTLQER;AS(0.002)ET(0.998)PPPVAQPKPEAPHPGLETTLQER 217.62 5.00E-34 3059950000 2025430 1824880 1285180 1585830 1792370 1652590 2306960 2694740 2301370 TRUE FALSE 1757764.294 1812892.243 1906697.347 1945916.939 1756705.344 1716166.207 2083231.374 2118490.821 2029304.66 0.866190439 0.893356369 0.939581613 0.95890823 0.86566861 0.845691749 1.026573986 1.043949124 1 20.95255404 2.22310317 24.99868144 1.027894154 0.89844118 0.744466528 0.035447775 122.5268658 198156.0225 0.015457442 0.010463621 167.1487643 -2.22310317 -0.129452974 ASEYS(ph)PASLDAFGAFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASEYSPASLDAFGAFLK 17 0 P17029;E9PC66;B3KRF7 P17029 ZKSCAN1 Zinc finger protein with KRAB and SCAN domains 1 1 AS(0.003)EYS(0.997)PASLDAFGAFLK;AS(0.013)EY(0.017)S(0.967)PAS(0.004)LDAFGAFLK 150.05 3.17E-07 23694600 117029 93436 69137 98747 94025 82495 99558 118163 128427 TRUE FALSE 101563.3211 92822.21276 102571.8844 121169.0156 92154.08646 85668.63603 89902.88048 92894.762 113244.5064 0.896849873 0.819661949 0.905755941 1.069976986 0.813762092 0.756492644 0.79388293 0.820302591 1 16.78908154 ASFNNPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASFNNPDR 8 0 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 ; 159.28 0.00083777 888200000 1350920 1240730 754510 874860 1166670 1212700 1130080 1239570 1234450 FALSE TRUE 1172392.499 1232579.563 1119393.56 1073510.334 1143455.55 1259353.354 1020485.016 974497.6018 1088514.727 1.077057085 1.132349919 1.028367859 0.986215719 1.050473201 1.156946546 0.937502259 0.895254403 1 20.0539295 2.175764289 11.96639743 0.933579199 1.067777779 0.547145354 0.054371552 0.522856701 98.02177927 0.022929396 0.015460828 149.887111 -2.175764289 0.13419858 ASFPGPSELHSEDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASFPGPSELHSEDSR 15 0 Q99988;A0A0A0MTT8 Q99988 GDF15 Growth/differentiation factor 15 0 ;;; 154.46 2.47E-06 1375170000 1307130 1203410 565216 940068 1028590 1300270 1317040 1298080 1320060 FALSE TRUE 1134389.459 1195504.72 838556.3481 1153524.807 1008123.071 1350292.228 1189313.664 1020495.694 1164004.011 0.974558033 1.027062372 0.720406752 0.990997279 0.866082129 1.160040873 1.021743613 0.876711493 1 20.1506646 ASFTNSELHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASFTNSELHR 10 0 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 0 141.08 3.81E-05 143730000 227380 204090 94559 154330 199680 203120 189110 212090 223670 FALSE TRUE 197331.1569 202749.3194 140288.0487 189372.9853 195706.7587 210934.1578 170770.1413 166736.204 197227.9874 1.000523098 1.027994668 0.711298891 0.960172984 0.992286953 1.069494044 0.865851462 0.845398294 1 17.58950476 ASGANYSFHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASGANYSFHK 10 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ; 125.74 0.00040106 1321610000 847350 1063960 356240 644630 1192010 1053190 1117960 1228510 1262900 FALSE TRUE 735370.5506 1056970.777 528518.8556 791003.0941 1168291.333 1093706.901 1009540.411 965802.6968 1113601.401 0.660353471 0.949146415 0.47460326 0.710310793 1.049110869 0.98213499 0.906554545 0.86727863 1 20.0868015 3.256410782 24.09733065 0.946269991 0.700499203 0.525587907 0.123436344 135.8662137 183414.6832 0.035199164 0.045328901 1804.72395 -3.256410782 -0.245770788 ASGDGES(ph)LDEDSEFTLASDFEIGHFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASGDGESLDEDSEFTLASDFEIGHFFR 27 0 Q99733;Q99733-2;H0YCI4 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 AS(0.008)GDGES(0.981)LDEDS(0.011)EFTLASDFEIGHFFR;AS(0.005)GDGES(0.994)LDEDSEFTLASDFEIGHFFR;ASGDGES(1)LDEDSEFTLASDFEIGHFFR 227.25 8.11E-35 122728000 66645.5 52154 41562 49885.2 65049.2 40285.2 62211.6 72207.8 69851.3 TRUE FALSE 57838.12832 51811.39694 61661.52222 61212.39711 63754.84819 41834.99771 56178.32861 56766.72389 61593.55889 0.939028843 0.841182063 1.001103416 0.993811662 1.035089534 0.679210594 0.912081224 0.921634095 1 15.91049187 ASGDGESLDEDSEFTLASDFEIGHFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ASGDGESLDEDSEFTLASDFEIGHFFR 27 0 Q99733;Q99733-2;H0YCI4 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 ;;;;; 269.57 3.69E-54 543645000 320011 321504 199906 256925 288538 295880 314602 367217 338979 FALSE TRUE 277720.7355 319392.0191 296581.2102 315263.7481 282796.6583 307262.6951 284091.9465 288690.5022 298905.2888 0.929126201 1.068539203 0.992224699 1.054727902 0.946107911 1.027960048 0.950441351 0.965826009 1 18.1893289 3.228941007 24.99990175 0.976959659 1.013901284 0.122170403 0.043741306 369.1107274 959261.786 0.012117255 0.013912236 1694.107662 -3.228941007 0.036941625 ASGDPGASGMS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 ASGDPGASGMSPR 13 0 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 ASGDPGASGMS(1)PR;ASGDPGASGMS(1)PR;ASGDPGASGMS(1)PR;ASGDPGASGMS(1)PR;ASGDPGASGMS(1)PR;ASGDPGAS(0.002)GMS(0.998)PR;ASGDPGASGMS(1)PR;ASGDPGAS(0.011)GMS(0.989)PR;ASGDPGASGMS(1)PR;ASGDPGASGMS(1)PR 265.41 2.68E-24 7247893000 6305480 5481140 3551380 4056530 5150570 5374470 5153410 5784210 5325800 TRUE FALSE 5472194.842 5445134.03 5268839.247 4977627.137 5048083.734 5581229.339 4653633.091 4547301.704 4696189.991 1.165241366 1.159479076 1.121939116 1.059928824 1.074931752 1.188459017 0.990937994 0.968295941 1 22.16305935 1.115988044 0.315055431 0.768076877 1.176188646 0.574770553 0.05066722 8.274876087 0.790246285 1.374151659 0.137104908 13.06134931 -1.115988044 0.408111769 ASGEGHHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASGEGHHLK 9 0 Q9UD71;J3KSJ8;Q9UD71-2 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 0 99.802 0.0050904 44003000 132810 151440 69246 114830 118800 130450 163540 187490 175380 FALSE TRUE 115258.822 150445.1807 102733.5972 140903.9066 116436.1124 135468.4959 147679.916 147396.7225 154646.7762 0.745303749 0.972831018 0.664311276 0.911133811 0.752916519 0.87598655 0.954949852 0.953118624 1 17.23861723 2.357661625 2.974032704 0.967840176 0.815462974 0.414629193 0.086445139 0.243282694 4.354686176 0.033047861 0.023852709 227.8566067 -2.357661625 -0.152377202 ASGGAQS(ph)PLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ASGGAQSPLR 10 0 H7BZV9;C9JU48;D3YTC9;Q6NXT1 H7BZV9 ANKRD54 Ankyrin repeat domain-containing protein 54 1 ASGGAQS(1)PLR;ASGGAQS(1)PLR;ASGGAQS(1)PLR;ASGGAQS(1)PLR;ASGGAQS(1)PLR;ASGGAQS(1)PLR 136.01 0.00013524 6119026000 6562190 6513410 4602049 4722420 5664990 6520600 6192390 6676160 6622040 TRUE FALSE 5694979.965 6470622.981 6827615.289 5794717.639 5552267.782 6771451.701 5591852.971 5248515.138 5839189.975 0.97530308 1.108137089 1.169274389 0.992383818 0.950862672 1.159656002 0.957641898 0.898843018 1 22.47733682 2.033626639 21.13891971 0.938009933 1.058534089 0.299224039 0.076900168 37.79390008 23757.89384 0.031355454 0.021139243 108.0504648 -2.033626639 0.120524156 ASGQAFELILS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 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 222.25 1.86E-11 10225302000 6058141 5820147 3981730 5504431 6926996 6485409 7053411 8442570 7203538 TRUE FALSE 5257542.317 5781914.071 5907307.946 6754296.189 6789162.332 6734906.881 6369372.287 6637192.106 6351943.944 0.827706032 0.910258989 0.930000012 1.063343167 1.068832218 1.060290667 1.002743781 1.044907223 1 22.59876675 4.080009246 1.849802536 1.040217384 0.850463662 0.851624976 0.030414205 0.130701066 0.859906745 0.008693646 0.027449986 12022.90031 -4.080009246 -0.189753722 ASGS(ph)ENEGDYNPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASGSENEGDYNPGR 14 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 AS(0.002)GS(0.998)ENEGDYNPGR;AS(0.001)GS(0.999)ENEGDYNPGR 219.53 3.61E-08 0 386450 348260 240666 312650 368700 280040 276500 362160 388320 TRUE FALSE 335379.6534 345972.2571 357052.8826 383641.9611 361363.5913 290813.32 249685.0726 284714.9023 342413.252 0.979458743 1.010393888 1.042754276 1.120406289 1.055343475 0.849305096 0.7291922 0.831494987 1 18.38537901 2.725557275 7.884555861 0.837328268 1.044481542 0.613086245 0.074231103 0.109520779 47.07487181 0.026033169 0.02378162 531.5660976 -2.725557275 0.207153274 ASGTNDKPGGPHYILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASGTNDKPGGPHYILR 16 1 P30038-2;P30038;P30038-3 P30038-2 ALDH4A1 "Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial" 0 ;; 192.4 3.25E-10 550452000 1018330 856660 586963 1042860 936700 868420 865381 1151260 1021280 FALSE TRUE 883755.1104 851032.5441 870820.2701 1279657.302 918061.5026 901828.6793 781456.4838 905072.0081 900545.4418 0.981355376 0.94501899 0.966992036 1.420980267 1.019450502 1.001424956 0.86775908 1.005026472 1 19.78043955 2.783591956 4.019689955 0.963579887 1.076358186 0.11557877 0.138346967 0.507640661 17.70215522 0.048671452 0.047267418 607.5638923 -2.783591956 0.112778299 ASGYFTRPWQWEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASGYFTRPWQWEK 13 1 O75884;O75884-2 O75884 RBBP9 Putative hydrolase RBBP9 0 ; 240.59 6.81E-17 1775320000 1167990 1787100 969170 1107600 1715890 1537630 1986930 2105790 2327400 FALSE TRUE 1013637.162 1775360.422 1437863.854 1359097.509 1681747.146 1596783.621 1794237.834 1655483.196 2052257.423 0.493913264 0.865076867 0.700625486 0.662245142 0.819462084 0.778062052 0.874275232 0.806664494 1 20.96878027 -2 0.096718884 1.967570577 0.377693429 0.514147276 0.095449766 281.813732 2.527285989 60.93773352 6.827146016 0.01 2 -1.589877148 ASGYQSSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASGYQSSQK 9 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ; 172.59 0.00013045 100047000 68215 65444 47068 57933 34432 53936 66400 77647 102256 FALSE TRUE 59200.21492 65014.09405 69830.24223 71087.5731 33746.87057 56010.95282 59960.53822 61042.7933 90167.41217 0.656558877 0.721037595 0.774450997 0.788395401 0.374269037 0.621188426 0.664991229 0.676993959 1 16.4603185 1.233681664 4.710116872 1.027273904 0.658187224 0.469814536 0.113764453 0.188625941 9.489115157 0.232845346 0.029723302 17.12701444 -1.233681664 -0.36908668 ASHDPLVPNS(ph)SPLPTNGISGSPESFASSLDGSGHAGPEGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASHDPLVPNSSPLPTNGISGSPESFASSLDGSGHAGPEGSR 41 0 O95402;B8ZZF3 O95402 MED26 Mediator of RNA polymerase II transcription subunit 26 1 AS(0.002)HDPLVPNS(0.521)S(0.463)PLPT(0.013)NGISGSPESFASSLDGSGHAGPEGSR 69.874 0.0043118 93781000 38660 42412 16757 27179 47078 48921 47104 44757 41244 TRUE FALSE 33550.98305 42133.39278 24860.74125 33350.40736 46141.23991 50803.02253 42535.86133 35186.06385 36368.18131 0.92253673 1.158523502 0.683584946 0.917021587 1.268725525 1.396908526 1.169590004 0.967495833 1 15.15038916 3.258376922 24.62485187 1.148909625 0.920507636 0.342971626 0.164712624 274.8323482 341519.5818 0.051841499 0.066827393 1812.912826 -3.258376922 -0.228401989 ASHEEVEGLVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASHEEVEGLVEK 12 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 ;;; 182.71 1.65E-05 1757220000 3674160 4043960 2633330 3637550 3958300 3526830 4072600 5180520 4257540 FALSE TRUE 3188610.447 4017394.96 3906817.196 4463511.324 3879537.574 3662509.432 3677639.879 4072706.113 3754218.471 0.849340674 1.070101538 1.040647268 1.188932226 1.033380876 0.975571736 0.979601988 1.084834605 1 21.84008118 4.742496889 24.52482433 1.048101012 0.849340572 0.502740449 0.061648983 266.8122179 1662277.906 0.015422661 0.113395776 55270.94486 -4.742496889 -0.19876044 ASHGYGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ASHGYGGK 8 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;; 137.9 0.0010572 5248700000 8857300 8361500 5040490 6499190 4293510 6455510 8686400 9825800 9722900 FALSE TRUE 7686785.363 8306572.756 7478087.823 7974930.423 4208077.551 6703857.647 7843994.265 7724629.134 8573469.838 0.896578108 0.968869421 0.872235858 0.930187027 0.490825492 0.78193051 0.914914779 0.900992163 1 23.03144778 1.626226512 1.79424127 0.989686593 0.82671193 0.142825761 0.132709312 0.901253399 5.293939155 0.214532547 0.041122154 42.28891197 -1.626226512 -0.162974663 ASHS(ph)SERPPPR ddPTM_MDA-MB-175_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 1 ASHS(0.965)S(0.035)ERPPPR;AS(0.106)HS(0.892)S(0.002)ERPPPR 190.34 1.40E-06 3567004000 244155 186058 107028 144696 198034 187701 229639 240040 175665 TRUE FALSE 211889.2981 184835.7727 158787.0988 177551.4383 194093.5108 194921.9789 207368.6451 188709.314 154898.0838 1.367927175 1.193273462 1.025106928 1.146246835 1.253040103 1.258388575 1.338742482 1.218280493 1 17.24095977 1.755885147 0.004819125 0.000132255 2.391905408 0.027795092 0.117370801 361624.622 668.9234194 168305.8421 163702.9212 57.00135068 -1.755885147 2.391773153 ASHSAVDITK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASHSAVDITK 10 0 F5H039;Q9NQX3;Q9NQX3-2;H0YJ30;G3V582 F5H039 GPHN Gephyrin;Molybdopterin adenylyltransferase;Molybdopterin molybdenumtransferase 0 90.827 0.010434 0 208020 204750 138290 181120 197680 181530 227780 269300 250370 FALSE TRUE 180529.6299 203404.9838 205167.5066 222246.0642 193746.5548 188513.5766 205689.9307 211712.2907 220771.5438 0.817721464 0.921336963 0.929320432 1.006678942 0.87758844 0.853885303 0.931686789 0.958965485 1 17.7521947 -1.999998366 0.016653544 2.03902514 0.000897154 0.243313672 0.052075526 18180.06802 30.13281244 2232.106666 1521.507008 0.010000038 1.999998366 -2.038127986 ASHSSERPPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASHSSERPPPR 11 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 0 ;;; 133.05 0.000102 956360000 50860.9 68624.2 24080.4 31702 55821.6 69516.5 52483.5 65456.7 57331.2 FALSE TRUE 44139.5032 68173.40311 35725.76198 38900.42363 54710.85937 72190.84474 47393.65825 51459.29409 50553.57085 0.873123351 1.348537838 0.706691167 0.769489138 1.082235309 1.428006836 0.93749378 1.017916108 1 15.62552538 3.051915002 24.98586494 1.089529639 0.937529526 0.133617208 0.212243486 242.3226738 116624.2727 0.065888686 0.074710736 1126.976869 -3.051915002 -0.152000113 ASHTAPQVLFSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASHTAPQVLFSHR 13 0 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;; 203.82 4.79E-08 2971320000 1864500 1885390 1441880 1711730 1823720 2075470 1637580 1924730 2575320 FALSE TRUE 1618101.601 1873004.749 2139177.991 2100404.459 1787431.54 2155314.674 1478767.744 1513141.468 2270868.603 0.712547436 0.82479662 0.942008704 0.924934387 0.787113591 0.949114656 0.65119036 0.666327178 1 21.1148128 2.239823684 24.99999977 0.745330489 0.859109059 0.085910202 0.118840615 60.37261235 1195001.852 0.045883688 0.033543297 173.7095457 -2.239823684 0.11377857 ASIANSDGPTAGSQT(ph)PPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.003)QT(0.997)PPFK;ASIANSDGPTAGS(0.005)QT(0.995)PPFK;ASIANSDGPT(0.001)AGS(0.004)QT(0.996)PPFK 229.15 9.73E-19 363508000 652660 660680 477390 531790 636900 563820 690290 821560 872420 TRUE FALSE 566409.3274 656339.9496 708257.4008 652541.0474 624226.9361 585510.5202 623345.782 645875.7874 769283.5015 0.736281652 0.853183447 0.920671507 0.848245213 0.811439391 0.761111501 0.810293969 0.839580969 1 19.55315584 1.236514643 4.247807989 1.017437829 0.823917684 0.553163896 0.050310216 0.185686379 6.396417863 0.110619378 0.013322877 17.23910214 -1.236514643 -0.193520145 ASIANSDGPTAGSQT(ph)PPFKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ASIANSDGPTAGSQT(1)PPFKR;ASIANSDGPTAGSQT(0.999)PPFKR;ASIANSDGPTAGS(0.015)QT(0.985)PPFKR;ASIANSDGPT(0.003)AGS(0.073)QT(0.924)PPFKR 204.98 5.33E-22 1716260000 1050350 1121720 658390 848260 1082560 927850 1124900 1451710 930680 TRUE FALSE 911543.5863 1114351.347 976789.6062 1040870.398 1061019.174 963544.9899 1015807.371 1141273.114 820656.0706 1.110749824 1.357878638 1.190254531 1.268339363 1.292891397 1.174115472 1.237799131 1.390683813 1 19.6464182 1.219136338 24.99944431 0.999999121 1.259198126 0.473869415 0.08348802 1197.044418 1540538.73 0.732699306 0.019536065 16.5628984 -1.219136338 0.259199005 ASIGQS(ph)PGLPSTTFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASIGQSPGLPSTTFK 15 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 ASIGQS(1)PGLPSTTFK;ASIGQS(1)PGLPSTTFK;ASIGQS(1)PGLPSTTFK;ASIGQS(0.989)PGLPS(0.007)T(0.004)TFK 264.64 4.01E-25 936013000 2608870 2047440 1410690 1674650 1934170 1770490 2318950 2728220 2505540 TRUE FALSE 2264101.219 2033990.232 2092904.402 2054904.878 1895683.801 1838601.896 2094058.586 2144811.384 2209337.916 1.024787201 0.92063338 0.947299364 0.930099856 0.85803253 0.832195873 0.947821776 0.970793725 1 21.07518266 1.744077065 2.905693017 0.990547028 0.916884652 0.213200658 0.05170112 0.362483533 6.319534954 0.041527814 0.014865237 55.47241395 -1.744077065 -0.073662376 ASIHEAWTDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 155.97 3.13E-05 5061500000 9765910 7766210 3590370 10463910 7175170 6936420 6715180 9732250 35618630 FALSE TRUE 8475320.25 7715193.255 5326684.941 12839900.7 7032398.155 7203268.566 6063942.877 7651084.074 31407836.14 0.269847315 0.245645489 0.169597323 0.408812012 0.223905847 0.229346222 0.193071017 0.243604304 1 24.90462122 1.238433132 24.99993964 1.000000828 0.246368964 0.932345737 0.063662364 0.689851842 134748.572 0.084392447 0.015038767 17.31542407 -1.238433132 -0.753631863 ASILWLIGENCER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASILWLIGENCER 13 0 O00203;O00203-3 O00203 AP3B1 AP-3 complex subunit beta-1 0 99.215 0.0068925 194910000 182110 172980 118220 146530 154440 177040 177470 209690 151490 FALSE TRUE 158043.7021 171843.683 175391.5874 179801.8761 151366.9462 183850.8434 160258.9867 164849.4253 133581.0248 1.183129882 1.286437825 1.312997768 1.3460136 1.133147065 1.376324547 1.199713709 1.23407816 1 17.02735556 0.596413877 1.403808316 2.13E-09 1.270122399 0.543788127 0.074792397 4.766988087 2.157282107 13.5708185 0.020120577 3.948333941 -0.596413877 1.270122397 ASKS(ph)SPAGNSPAPL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASKSSPAGNSPAPL 14 1 B4DSP0;A0A087WZG9;Q86TG7-2 B4DSP0 PEG10 Retrotransposon-derived protein PEG10 1 AS(0.251)KS(0.374)S(0.374)PAGNSPAPL 91.355 0.014175 125140000 508170 328910 134730 163240 332090 289090 364420 402290 58267 TRUE FALSE 441014.047 326749.3686 199885.8786 200306.137 325482.0587 300211.4794 329078.6045 316263.4141 51378.74164 8.583589884 6.359621862 3.890439358 3.898618973 6.334955827 5.843106892 6.404956486 6.155530557 1 15.64888394 4.602024321 3.311767836 5.059226633 8.634767709 0.344714008 1.654546812 0.330636299 5.933655364 0.413913927 2.408690834 39996.71477 -4.602024321 3.575541075 ASLENSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ASLENSLR 8 0 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;; 234.91 3.31E-08 29915410000 9678310 9861500 6699470 7495300 9458090 10055310 9593830 10165770 9856410 FALSE TRUE 8399296.812 9796719.157 9939356.1 9197222.423 9269892.513 10442144.28 8663421.843 7991899.196 8691196.438 0.966414333 1.127200291 1.143611949 1.058222822 1.066584167 1.201462233 0.996804284 0.919539588 1 23.05112336 2.01550913 24.14453611 0.955267402 1.095182259 0.454098456 0.063864904 118.2492778 184088.8558 0.024964344 0.016823488 103.6356391 -2.01550913 0.139914857 ASLGLADHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASLGLADHR 9 0 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 ; 91.265 0.01087 268190000 316370 328940 187000 218180 325560 378750 302240 340480 358610 FALSE TRUE 274560.9029 326779.1715 277433.8255 267721.1037 319081.9929 393320.7576 272928.8113 267671.0016 316215.5343 0.868271394 1.033406446 0.877356725 0.846641213 1.009064889 1.243837557 0.863110068 0.846482771 1 18.27054872 4.804230448 20.38993662 0.954608444 0.868263584 0.053223666 0.121370127 36116.00275 11208959.16 0.031085864 59.38556172 63713.35109 -4.804230448 -0.08634486 ASLGS(ph)LEGEAEAEASS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 AS(0.105)LGS(0.895)LEGEAEAEAS(0.211)S(0.789)PK;AS(0.004)LGS(0.996)LEGEAEAEAS(0.482)S(0.518)PK 153.17 5.15E-08 105666000 350800 246826 211891 258718 302557 271421 281646 372570 401250 TRUE FALSE 304440.8912 245204.5838 314362.1963 317463.8762 296536.7076 281862.7415 254332.0143 292898.8048 353814.6821 0.860452962 0.693031115 0.888493927 0.897260324 0.838113065 0.796639472 0.718828322 0.827831121 1 18.43263439 1.246465228 5.704613462 1.007227924 0.811643386 0.437158806 0.066064941 0.130506144 14.14593607 0.09842635 0.016624668 17.63864535 -1.246465228 -0.195584538 ASLGS(ph)LEGEAEAEASSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK 486.24 8.24E-240 1655320000 2327650 1400290 1159270 1679470 1506420 1372350 1559330 2314140 2116700 TRUE FALSE 2020045.155 1391091.403 1719896.85 2060819.333 1476445.189 1425145.193 1408106.417 1819279.17 1866466.137 1.082283313 0.745307603 0.921472303 1.104128969 0.791037758 0.763552665 0.754423768 0.974718551 1 20.8318779 ASLGSLEGEAEAEASS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ASLGSLEGEAEAEAS(0.005)S(0.995)PK;ASLGSLEGEAEAEAS(0.003)S(0.997)PK;ASLGSLEGEAEAEAS(0.026)S(0.974)PK;ASLGSLEGEAEAEAS(0.003)S(0.997)PK 327.7 8.66E-75 1105041000 1593990 1267260 938200 1391790 1652750 1253560 1298510 2109010 2027410 TRUE FALSE 1383340.183 1258935.286 1391916.658 1707817.192 1619863.509 1301785.264 1172580.7 1658014.624 1787731.899 0.773796218 0.704208101 0.778593624 0.955298271 0.906099796 0.728177007 0.65590411 0.927440308 1 20.76969897 1.550364985 6.149504691 0.982347078 0.791036494 0.419277725 0.088726453 0.133504788 9.953608268 0.067057003 0.024643619 35.51117029 -1.550364985 -0.191310584 ASLLHSMPTHS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASLLHSMPTHSSPR 14 0 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4X8;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 ASLLHSMPTHS(0.684)S(0.315)PR 152.07 1.13E-05 115110000 56448 60734 26446 37480 72723 79853 62396 80098 55952 TRUE FALSE 48988.25378 60335.03436 39235.37406 45990.40685 71275.95458 82924.99658 56344.84552 62969.66602 49337.4183 0.992922927 1.222906192 0.795245787 0.932160791 1.44466324 1.680772919 1.142030683 1.276306467 1 15.5903946 3.247032277 24.99393952 1.310795257 0.989132739 0.380914786 0.204551332 210.9411962 622336.3425 0.061689981 0.078327327 1766.169077 -3.247032277 -0.321662518 ASLPQAATFGELSGPLKPGS(ph)PYRPPVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASLPQAATFGELSGPLKPGSPYRPPVPR 28 2 Q14687;Q14687-2;Q14687-3;H0Y613 Q14687 GSE1 Genetic suppressor element 1 1 ASLPQAATFGELSGPLKPGS(1)PYRPPVPR 243.16 1.13E-45 902530000 969480 803120 540770 572470 760240 636840 768250 948850 922860 TRUE FALSE 841360.7617 797844.2518 802288.1808 702458.0632 745112.7114 661339.6469 693745.2332 745945.8115 813760.5421 1.033916881 0.980441064 0.985902043 0.863224532 0.915641239 0.812695643 0.85251766 0.916665005 1 19.6342448 3.828651473 4.953663982 0.890988797 1.001284679 0.496515117 0.050709533 0.19593608 8.007322834 0.014057126 0.024947205 6739.869267 -3.828651473 0.110295881 ASLQVLGTVGEPINPEAWLWYHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASLQVLGTVGEPINPEAWLWYHR 23 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ; 246.73 1.29E-37 869090000 868780 597010 380400 462950 557050 620920 584580 651820 582710 FALSE TRUE 753968.5218 593088.202 564362.7124 568069.8732 545965.7948 644807.1942 527887.5216 512433.3655 513822.6876 1.467371021 1.15426628 1.098360827 1.105575692 1.062556808 1.25492161 1.027372933 0.997296106 1 18.97091107 ASMSEFLES(ph)EDGEVEQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASMSEFLESEDGEVEQQR 18 0 J3QQW9;Q15022 J3QQW9 SUZ12 Polycomb protein SUZ12 1 ASMSEFLES(1)EDGEVEQQR;ASMSEFLES(1)EDGEVEQQR;ASMSEFLES(1)EDGEVEQQR 393.56 2.06E-109 112690000 809660 785460 534400 607290 707640 766960 760830 840640 848040 TRUE FALSE 702661.3796 780300.2615 792837.6275 745184.4763 693559.3485 796465.4475 687044.8237 660875.6779 747785.6773 0.939656109 1.043481154 1.060247142 0.996521462 0.92748413 1.065098559 0.918772376 0.88377686 1 19.51226531 2.210505369 24.94063226 0.923039602 1.005690893 0.273406314 0.053725029 232.679508 206846.3242 0.021570993 0.014546506 162.3698422 -2.210505369 0.082651291 ASNDMYHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ASNDMYHSR 9 0 P01034 P01034 CST3 Cystatin-C 0 ;;;;;; 107.45 0.0027708 558433000 734360 843492 489549 645574 786073 975831 685615 879151 746005 FALSE TRUE 637312.4654 837951.0455 726296.5338 792161.4437 770431.6852 1013371.85 619124.1628 691151.4002 657813.1388 0.968835111 1.273843583 1.104107673 1.204234755 1.171201425 1.540516281 0.941185462 1.050680443 1 19.3273183 ASNEDGDIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASNEDGDIKR 10 1 Q9UBT2;Q9UBT2-2;K7EPL2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 ;;; 107.03 0.0037497 2108370000 3264540 2392550 1674370 2032090 2035500 1866840 2664130 3110250 3062240 FALSE TRUE 2833122.768 2376833.182 2484100.932 2493507.093 1994997.532 1938658.543 2405763.083 2445147.241 2700225.476 1.049217109 0.880235078 0.919960557 0.923444029 0.738826276 0.717961726 0.890948961 0.905534469 1 21.36464845 ASNGDAWVEAHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASNGDAWVEAHGK 13 0 P38646;D6RJI2;A0A3B3ITI4 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;; 154.65 4.34E-05 2505670000 5453140 5253890 3587620 6791680 6206880 5902690 5520750 7191170 6474890 FALSE TRUE 4732493.733 5219376.851 5322605.032 8333834.748 6083375.232 6129770.304 4985348.515 5653394.257 5709435.88 0.828889899 0.914166821 0.932247098 1.459659925 1.065494973 1.073621008 0.873177074 0.990184385 1 22.44491678 3.982181346 24.985356 1.065486978 0.884447898 0.253205162 0.151419397 1146.875467 1608158.418 0.042466784 0.07559668 9598.013277 -3.982181346 -0.18103908 ASNLPMSVIIVGVGGADFEAMEQLDADGGPLHTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASNLPMSVIIVGVGGADFEAMEQLDADGGPLHTR 34 0 Q99829;B0QZ18;F2Z2V0;H0Y524 Q99829 CPNE1 Copine-1 0 55.999 0.045246 55556000 30262 26785 20664 24281 26726 30431 30765 33541 31979 FALSE TRUE 26262.80003 26609.04757 30657.17952 29794.37216 26194.20489 31601.70026 27781.41504 26368.51817 28198.47905 0.931355198 0.943634142 1.087192662 1.056595007 0.928922615 1.120688112 0.985209698 0.93510427 1 14.78332973 4.442856878 24.99172439 1.009791528 0.934424772 0.220493334 0.060834095 255.2876991 186201.2746 0.015599349 0.041272394 27724.06304 -4.442856878 -0.075366756 ASNTS(ph)TPTKGNTETSASASQTNHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASNTSTPTKGNTETSASASQTNHVK 25 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YD28;A0A2R8YCQ1;A0A2R8Y7Y0 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 AS(0.009)NT(0.112)S(0.436)T(0.436)PT(0.007)KGNTETSASASQTNHVK 102.72 0.0029313 256770000 49934 36778 19913 26936 40529 30790 53969 61262 25115 TRUE FALSE 43335.09538 36536.4029 29542.9934 33052.23049 39722.55219 31974.51122 48735.09469 48161.59804 22145.93331 1.956796978 1.649801902 1.334014376 1.492474037 1.793672528 1.443809605 2.20063404 2.174737789 1 14.43475418 2.259256013 24.99971502 1.888606655 1.603712349 0.028396864 0.371545123 522.469894 631134.1861 0.138059787 0.106820547 181.6586209 -2.259256013 -0.284894306 ASNTST(ph)PTKGNTETSASASQTNHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASNTSTPTKGNTETSASASQTNHVK 25 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YD28;A0A2R8YCQ1;A0A2R8Y7Y0 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 AS(0.004)NT(0.011)S(0.042)T(0.932)PT(0.011)KGNTETSASASQTNHVK;ASNT(0.001)S(0.104)T(0.736)PT(0.159)KGNTETSASASQTNHVK;ASNT(0.001)S(0.028)T(0.969)PT(0.002)KGNTETSASASQTNHVK 338.35 5.21E-88 572440000 289803 243149 117065 203914 247721 195883 341475 375306 167855 TRUE FALSE 251504.7993 241551.7382 173678.0256 250215.7903 242791.8368 203418.7458 308358.8071 295049.7325 148011.3731 1.699226174 1.631980929 1.173410002 1.690517323 1.640359329 1.374345373 2.083345358 1.993426088 1 17.17534851 2.264959362 24.99862778 1.771296561 1.534808462 0.030716775 0.328267156 510.0227046 482970.922 0.121492013 0.094079208 184.0599764 -2.264959362 -0.236488099 ASPDQNASTHT(ph)PQSSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASPDQNASTHTPQSSVK 17 0 Q14677-2;Q14677;Q14677-3;H0YD52 Q14677-2 CLINT1 Clathrin interactor 1 1 ASPDQNASTHT(0.999)PQS(0.001)SVK;ASPDQNASTHT(1)PQSSVK;ASPDQNASTHT(1)PQSSVK;ASPDQNASTHT(1)PQSSVK 272.51 4.53E-35 6095700000 4590380 4229050 1713680 3105910 4554680 4132210 5022590 5906370 5774040 TRUE FALSE 3983749.652 4201269.092 2542421.38 3811154.336 4464050.779 4291178.793 4535499.995 4643338.739 5091439.569 0.782440722 0.825163303 0.499352167 0.748541603 0.876775756 0.842822297 0.890808961 0.911989365 1 22.2796422 3.254001204 3.603341035 0.904184307 0.701922964 0.519331552 0.092144782 0.189635176 5.230905287 0.028668253 0.03578307 1794.738601 -3.254001204 -0.202261343 ASPDS(ph)RHSPATISSSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASPDSRHSPATISSSTR 17 1 O15119;O15119-2;O15119-3 O15119 TBX3 T-box transcription factor TBX3 1 AS(0.023)PDS(0.488)RHS(0.488)PAT(0.001)ISSSTR 60.278 0.047984 165070000 199000 207010 56895 86100 190740 208300 175810 186030 53814 TRUE FALSE 172701.6458 205650.1377 84409.6123 105650.321 186944.6472 216313.4358 158759.9733 146248.9322 47452.17023 3.639488879 4.333840511 1.778835655 2.2264592 3.939643778 4.558557275 3.345684139 3.082028314 1 15.53418645 4.280445048 24.99901707 2.97292108 3.986665826 0.164201393 1.039026542 306.5052246 182935.0335 0.269300348 0.712488752 19074.14361 -4.280445048 1.013744746 ASPDSRHS(ph)PATISSSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASPDSRHSPATISSSTR 17 1 O15119;O15119-2;O15119-3 O15119 TBX3 T-box transcription factor TBX3 1 ASPDS(0.068)RHS(0.931)PAT(0.001)ISSSTR;ASPDS(0.002)RHS(0.718)PAT(0.038)IS(0.061)S(0.061)S(0.061)T(0.061)R 88.071 0.0026566 197417000 211969 213351 55233 80931 211099 216680 186187 218919 42710 TRUE FALSE 183956.7596 211949.4832 81943.86354 99307.6205 206898.5429 225015.8198 168130.6134 172104.8755 37660.87246 4.884559162 5.627843154 2.175835508 2.636891129 5.493726763 5.974790416 4.464331345 4.569858961 1 15.2007788 ASPITNDGEDEFVPSDGLDKDEYTFS(ph)PGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASPITNDGEDEFVPSDGLDKDEYTFSPGK 29 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 ASPITNDGEDEFVPS(0.002)DGLDKDEY(0.003)T(0.044)FS(0.951)PGK 84.408 1.66E-06 0 121220 88235 60297 74711 88214 70643 90784 113110 87964 TRUE FALSE 105200.4699 87655.37848 89456.83088 91675.27444 86458.71399 73360.68192 81979.78165 88922.30672 77564.99613 1.356287954 1.130089381 1.15331445 1.181915542 1.114661488 0.945796243 1.05691724 1.146423144 1 16.24311811 7.999999999 0.53971594 1.062997715 12.27449427 0.631579535 0.067203442 99.22390717 0.960284231 0.038658657 1282.350189 99999999.88 -7.999999999 11.21149655 ASPNVEAPQPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASPNVEAPQPHR 12 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 118.76 0.00059107 765530000 295170 289180 206800 214770 271990 295720 256130 256480 328400 FALSE TRUE 256162.5366 287280.3575 306809.1717 263536.8111 266577.9311 307096.5398 231290.552 201633.7479 289576.9261 0.884609627 0.992069228 1.059508352 0.910075311 0.920577253 1.060500724 0.798718859 0.696304608 1 18.14358713 2.218860028 24.74928612 0.802099174 0.971102339 0.311262511 0.094501056 205.5521857 258227.1949 0.037691045 0.025452659 165.52364 -2.218860028 0.169003165 ASPRPWT(ph)PEDPWSLYGPSPGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASPRPWTPEDPWSLYGPSPGGR 22 1 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;Q14934-12;Q14934-13;Q14934-18 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 AS(0.006)PRPWT(0.994)PEDPWSLYGPSPGGR;ASPRPWT(1)PEDPWSLYGPSPGGR 171.31 9.98E-12 1637450000 626260 748490 421560 508620 719630 669140 780350 817480 592650 TRUE FALSE 543498.1543 743573.1199 625427.826 624109.9448 705310.7709 694882.2488 704671.7771 642668.2636 522587.5921 1.040013507 1.422867919 1.196790424 1.194268586 1.349650817 1.329695269 1.348428068 1.229780946 1 18.99531335 1.255037568 3.803654858 0.971319873 1.275338698 0.377018735 0.107407453 0.244157138 5.75206424 0.204192464 0.025391133 17.9902653 -1.255037568 0.304018825 ASPS(ph)PQPSSQPLQIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ASPSPQPSSQPLQIHR 16 0 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 AS(0.112)PS(0.888)PQPSSQPLQIHR;ASPS(1)PQPSSQPLQIHR;AS(0.007)PS(0.993)PQPSSQPLQIHR;ASPS(1)PQPSSQPLQIHR;AS(0.004)PS(0.996)PQPSSQPLQIHR;AS(0.003)PS(0.997)PQPSSQPLQIHR;ASPS(1)PQPSSQPLQIHR 257.46 1.19E-26 24679980000 6936236 5890568 4023319 4448724 5523454 6413779 5993688 6258478 6413193 TRUE FALSE 6019594.838 5851872.471 5969009.526 5458874.779 5413548.072 6660521.228 5412421.06 4920151.183 5655032.629 1.064466862 1.034807906 1.055521677 0.965312693 0.957297407 1.177804208 0.957098113 0.870048239 1 22.43110392 2.014565305 24.99971706 0.922091212 1.038061437 0.326394258 0.06760522 228.9780317 393013.7055 0.026964964 0.018171886 103.4106588 -2.014565305 0.115970225 ASPSS(ph)PGRQDS(ph)DEDDGPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASPSSPGRQDSDEDDGPQR 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 AS(0.034)PS(0.417)S(0.55)PGRQDS(1)DEDDGPQR 182.03 1.71E-14 316130000 232910 226030 191630 244330 258060 248310 247620 249080 518750 TRUE FALSE 202130.3534 224545.194 284302.909 299808.8609 252925.1109 257862.6464 223605.8505 195816.1803 457423.966 0.44188842 0.490890751 0.621530418 0.655428843 0.552933667 0.563727888 0.4888372 0.428084654 1 18.80317243 1.230816851 24.99994566 1.000000842 0.530933117 0.806095756 0.0723793 137.0893654 442541.744 0.208244425 0.01983189 17.01440831 -1.230816851 -0.469067725 ASPSS(ph)PGRQDS(ph)DEDDGPQRVEEVDQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASPSSPGRQDSDEDDGPQRVEEVDQGR 27 2 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 AS(0.154)PS(0.402)S(0.444)PGRQDS(0.999)DEDDGPQRVEEVDQGR;AS(0.332)PS(0.117)S(0.552)PGRQDS(1)DEDDGPQRVEEVDQGR 121.93 4.97E-05 845580000 242230 246284 135775 158679 222291 208430 245265 248660 162086 TRUE FALSE 210218.6918 244666.1442 201436.2441 194709.4922 217867.844 216448.437 221479.2381 195485.9941 142924.3777 1.470838601 1.711857334 1.409390388 1.362325275 1.524357478 1.514426303 1.549625344 1.367758231 1 17.12489248 1.25589185 2.442525471 0.882532868 1.505284636 0.748104602 0.09240027 0.269467296 1.783698827 0.352106469 0.024891643 18.02568802 -1.25589185 0.622751768 ASPSSPGRQDS(ph)DEDDGPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ASPSSPGRQDSDEDDGPQR 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 ASPSSPGRQDS(1)DEDDGPQR;ASPSSPGRQDS(1)DEDDGPQR;ASPS(0.001)S(0.001)PGRQDS(0.999)DEDDGPQR;ASPSSPGRQDS(1)DEDDGPQR;ASPSSPGRQDS(1)DEDDGPQR 193.96 2.51E-15 3286576000 1825565 1695108 1487351 1539027 1823691 2007198 1768806 2067608 1848866 TRUE FALSE 1584311.96 1683972.724 2206638.918 1888486.603 1787403.117 2084416.206 1597267.466 1625466.119 1630295.168 0.971794551 1.032925054 1.353521106 1.158370975 1.096367794 1.278551423 0.979741275 0.99703793 1 20.63670176 2.206419703 24.9206419 0.992733434 1.150717205 0.314222463 0.108838269 229.6105405 178028.2813 0.045266441 0.030521293 160.8494956 -2.206419703 0.15798377 GEDLTEEEDGGIIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GEDLTEEEDGGIIRR 15 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;; 209.39 3.86E-09 1928780000 1176060 1000210 784034 890130 1044720 1165830 1069470 1111950 538148 FALSE TRUE 1020640.691 993639.5547 1163195.465 1092247.621 1023932.116 1210680.234 965752.964 874168.1457 474528.7565 2.150851086 2.093950137 2.451264436 2.301752225 2.157787283 2.551331648 2.035183223 1.842181604 1 18.85613599 1.108117049 1.39443181 0.112287482 2.274959589 0.875292341 0.150900398 0.561579459 0.750117563 1.888105241 0.043670268 12.82676236 -1.108117049 2.162672107 ASQEPS(ph)PKPGTEVIPAAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASQEPSPKPGTEVIPAAPR 19 1 I3L4I0;I3L1Y9;Q96CP2 I3L4I0 FLYWCH2 FLYWCH family member 2 1 ASQEPS(1)PKPGTEVIPAAPR;ASQEPS(1)PKPGTEVIPAAPR;ASQEPS(1)PKPGTEVIPAAPR 179.33 2.18E-14 1345740000 1148700 971680 699170 772340 1024680 770360 1018240 1281110 1002980 TRUE FALSE 996896.3846 965296.9701 1037290.951 947711.6015 1004290.873 799996.2477 919491.2415 1007154.596 884408.847 1.127189521 1.091460102 1.172863607 1.071576347 1.13555046 0.904554777 1.039667621 1.138788468 1 19.75435393 ASQVSNSDHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASQVSNSDHK 10 0 E9PS17;Q96KG9-2;Q96KG9;E9PK59;Q96KG9-4;E9PPN3;H0YDH0 E9PS17 SCYL1 N-terminal kinase-like protein 0 113.38 0.0025466 0 83892 71919 23200 51080 48618 63005 72292 99918 95492 FALSE TRUE 72805.45964 71446.55935 34419.5976 62678.49471 47650.59692 65428.84312 65281.13297 78551.31326 84203.04454 0.864641653 0.848503278 0.408769039 0.744373259 0.565901116 0.777036549 0.775282335 0.932879728 1 16.36158478 1.768492 1.41450386 1.020874805 0.686383062 0.407408618 0.132692211 0.51253325 1.744170737 0.199475222 0.042058431 58.68025601 -1.768492 -0.334491743 ASREEILAQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASREEILAQAK 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 138.42 0.0010613 495230000 1314160 1159440 407388 464884 1071310 979410 1484460 1561400 269999 FALSE TRUE 1140490.426 1151823.562 604402.1994 570443.0175 1049993.027 1017088.536 1340497.298 1227506.761 238080.0258 4.790365855 4.837968067 2.538651436 2.396013759 4.410252492 4.272044801 5.630448389 5.155857812 1 17.86108706 ASS(ph)ASVPAVGASAEGTRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSASVPAVGASAEGTRR 18 1 V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23;A0A2R8YFI4 V9GYZ0 PANK2 "Pantothenate kinase 2, mitochondrial" 1 AS(0.132)S(0.865)AS(0.003)VPAVGASAEGTRR 128.41 1.43E-05 268560000 57635 77026 45956 49280 81712 87496 75131 79295 53999 TRUE FALSE 50018.38872 76520.01113 68180.47531 60469.7772 80086.09107 90862.02774 67844.80718 62338.38132 47615.29974 1.050468841 1.607046717 1.43190268 1.269965274 1.68194029 1.908252773 1.424853095 1.30920905 1 15.53913759 1.37998112 2.166584226 0.943856903 1.499845957 0.308833415 0.230004409 0.614301103 3.884799303 0.606873091 0.063329764 23.98728636 -1.37998112 0.555989053 ASS(ph)DIVSLAGPSAGPGSSEGGCSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSDIVSLAGPSAGPGSSEGGCSR 24 0 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 AS(0.114)S(0.886)DIVSLAGPSAGPGSSEGGCSR 356.45 3.86E-102 108200000 38598 29938 28459 30567 36766 46725 40617 40220 46764 TRUE FALSE 33497.17651 29741.33531 42221.86759 37507.70454 36034.42853 48522.54099 36677.96959 31619.26599 41235.61319 0.812336083 0.72125362 1.023917539 0.909594926 0.873866683 1.176714428 0.889473122 0.766795096 1 15.33160324 4.248206693 24.9987323 0.933302105 0.76679481 0.311973857 0.110452375 274.5716837 711563.8864 0.028990694 0.07460947 17709.51604 -4.248206693 -0.166507294 ASS(ph)ESQIFELNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASSESQIFELNK 12 0 Q9BV36;Q9BV36-4 Q9BV36 MLPH Melanophilin 1 ASS(1)ESQIFELNK;AS(0.022)S(0.978)ESQIFELNK 296.85 2.75E-36 118279000 478150 294360 230360 279270 346510 293400 385260 470150 525020 TRUE FALSE 414961.266 292426.3298 341762.8665 342682.5219 339615.1289 304687.2879 347897.5445 369612.0812 462952.7337 0.896336139 0.631654829 0.738224103 0.740210602 0.733584887 0.658139083 0.7514753 0.798379736 1 18.82050538 1.163723068 1.890849877 1.132749675 0.72854907 0.587471621 0.069324604 0.677985154 1.962400934 0.525092825 0.017435846 14.5788433 -1.163723068 -0.404200605 ASS(ph)FADMMGILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSFADMMGILK 12 0 E9PPF9;E9PLD2;Q9H019-3;Q9H019 E9PPF9 MTFR1L Mitochondrial fission regulator 1-like 1 AS(0.025)S(0.975)FADMMGILK 101.53 0.0027458 104480000 859710 553620 289330 318920 490230 419490 478100 652680 679040 TRUE FALSE 746097.1453 549983.2338 429250.9558 391335.6604 480475.3821 435628.0517 431733.9356 513109.4612 598764.6648 1.246060747 0.918529877 0.716894267 0.653571734 0.80244445 0.727544689 0.721041105 0.856946796 1 19.19162956 4.666847216 2.801140681 0.78082661 1.294604798 0.699431958 0.095709825 0.204828447 2.419971172 0.025319677 0.221233865 46435.18882 -4.666847216 0.513778187 ASS(ph)FSGISILTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASSFSGISILTR 12 0 A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5;H0YIX9;H7C0E9;Q9Y2K5-3;Q9Y2K5-2 A0A0U1RRA6 R3HDM2 R3H domain-containing protein 2 1 AS(0.004)S(0.995)FSGISILTR;ASS(0.997)FS(0.003)GISILTR 134.18 0.00015733 113899000 436050 301460 175425 242860 292810 199853 434050 383340 315850 TRUE FALSE 378424.8877 299479.6894 260261.1168 298005.0749 286983.6539 207541.4742 391955.8978 301365.7242 278510.5728 1.358745142 1.0752902 0.934474818 1.069995555 1.030422834 0.745183467 1.407328612 1.08206206 1 18.08737257 4.731477855 4.928181535 1.049762199 1.373156514 0.271406691 0.16272196 0.231710195 17.12040666 0.03946571 0.254205803 53886.23673 -4.731477855 0.323394315 ASS(ph)FSGISVLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ASSFSGISVLTR 12 0 Q15032-2;Q15032-4;Q15032;Q15032-3;H7C1X4;H7BZ47;H7C207 Q15032-2 R3HDM1 R3H domain-containing protein 1 1 AS(0.017)S(0.982)FS(0.001)GISVLTR;AS(0.001)S(0.984)FS(0.015)GISVLTR;AS(0.031)S(0.967)FS(0.002)GISVLTR;ASS(0.997)FS(0.002)GISVLTR;AS(0.057)S(0.942)FS(0.001)GISVLTR 179.59 2.15E-05 659453000 1423683 1308780 689607 999082 1189630 1015606 1582147 1453752 1232953 TRUE FALSE 1235539.684 1300182.538 1023103.252 1225938.838 1165958.69 1054677.02 1428710.627 1142878.448 1087194.701 1.136447486 1.195905882 0.941048784 1.127616642 1.072446995 0.970090288 1.31412582 1.051217824 1 20.0521789 ASS(ph)GGGGGGLMEEMNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSGGGGGGLMEEMNK 16 0 H0YJN0;Q9UI08-5;Q9UI08;Q9UI08-2;Q9UI08-4;Q9UI08-3;G3V314;H0YJL6 H0YJN0 EVL Ena/VASP-like protein 1 AS(0.241)S(0.759)GGGGGGLMEEMNK 191.93 6.47E-10 77113000 100640 97692 78721 114730 138940 120550 119510 155680 211210 TRUE FALSE 87340.16901 97050.25482 116790.7389 140781.2 136175.3658 125187.6365 107919.9386 122389.0435 186240.9944 0.46896318 0.52110039 0.627094691 0.755908765 0.731178258 0.672180885 0.57946393 0.657154156 1 17.50681114 4.157963548 2.384869453 0.7124361 0.478904602 0.438342541 0.109686115 0.306288794 3.440399852 0.030158021 0.090115328 14386.77818 -4.157963548 -0.233531498 ASS(ph)HS(ph)SQTQGGGSVTK ddPTM_MDA-MB-175_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(0.105)S(0.895)HS(0.619)S(0.378)QT(0.003)QGGGSVTK;AS(0.123)S(0.872)HS(0.798)S(0.208)QTQGGGSVTK;AS(0.011)S(0.989)HS(0.63)S(0.363)QT(0.008)QGGGSVTK;AS(0.457)S(0.53)HS(0.537)S(0.457)QT(0.019)QGGGSVTK 161.2 4.50E-09 16251970000 5119710 5828670 3762528 4990384 6373910 6259610 8192590 9376760 9919340 TRUE FALSE 4443127.352 5790381.083 5582099.126 6123526.96 6247081.661 6500421.247 7398073.883 7371612.844 8746686.925 0.507978323 0.662008499 0.63819583 0.700096735 0.714222621 0.743186683 0.845814415 0.842789151 1 23.06030522 -2 0.156572205 2.511015127 0.42292475 0.913912139 0.03935335 36.54186153 0.474148603 17.06518216 0.534171707 0.01 2 -2.088090377 ASS(ph)HS(ph)SQTQGGGSVTKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSHSSQTQGGGSVTKK 17 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 AS(0.001)S(0.999)HS(0.822)S(0.177)QT(0.001)QGGGSVTKK 217.02 1.79E-14 473820000 930410 954830 531690 648080 980570 856710 1554100 1759200 437600 TRUE FALSE 807453.9611 948557.6589 788817.0624 795236.4693 961058.5755 889668.1881 1403383.621 1383008.77 385867.4265 2.092568343 2.458247558 2.044269633 2.060905935 2.490644479 2.305631745 3.636957993 3.58415527 1 18.55774574 2.436724266 24.65249933 2.956058168 2.239980134 0.068857331 0.736875369 230.4858221 140653.7458 0.272344016 0.21095705 273.3532652 -2.436724266 -0.716078034 ASS(ph)HSS(ph)QTQGGGSVTK ddPTM_MDA-MB-175_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(0.012)S(0.988)HS(0.001)S(0.992)QT(0.006)QGGGSVTK;ASS(1)HSS(0.777)QT(0.223)QGGGSVTK;AS(0.001)S(0.999)HSS(0.998)QT(0.002)QGGGSVTK;AS(0.038)S(0.962)HS(0.002)S(0.668)QT(0.33)QGGGSVTK 343.06 3.28E-72 13160600000 10634560 11892310 8349860 10458300 12945200 12424040 17132180 19376520 20462300 TRUE FALSE 9229175.951 11814188.63 12387880.22 12833016.86 12687615.85 12902000.86 15470703.82 15233001.99 18043270.2 0.511502397 0.654769812 0.686565134 0.711235642 0.703177179 0.715058895 0.857422388 0.844248399 1 24.1049575 -2 0.186400579 2.630810089 0.494223433 0.879390503 0.045916872 36.52555939 0.524780237 21.61167603 0.368377174 0.01 2 -2.136586656 ASS(ph)HSS(ph)QTQGGGSVTKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.117)S(0.883)HSS(1)QTQGGGSVTKK;AS(0.017)S(0.983)HS(0.011)S(0.985)QT(0.003)QGGGSVTKK;AS(0.184)S(0.816)HS(0.227)S(0.767)QT(0.006)QGGGSVTKK;AS(0.091)S(0.909)HS(0.062)S(0.931)QT(0.006)QGGGSVTKK 177.09 1.07E-09 2502920000 2420890 2459640 1368980 1715300 2568120 2096870 4143630 4595240 1128920 TRUE FALSE 2100963.253 2443482.463 2031023.307 2104785.082 2517019.436 2177537.946 3741781.4 3612583.686 995460.3637 2.110544357 2.45462557 2.040285461 2.114383614 2.528497897 2.187468256 3.758845191 3.629058291 1 19.92500435 2.290495329 24.99556157 3.009652421 2.2475082 0.085059914 0.759278785 165.3495048 79579.91999 0.280577313 0.217333992 195.2069741 -2.290495329 -0.762144221 ASS(ph)HSSQT(ph)QGGGSVTK ddPTM_MDA-MB-175_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 ASS(1)HSS(0.017)QT(0.983)QGGGSVTK 374.51 9.28E-104 1232600000 988160 1158600 787540 943840 1222200 1181700 1625000 1803300 1870100 TRUE FALSE 857572.1523 1150989.08 1168396.978 1158153.298 1197880.611 1227160.764 1467407.75 1417678.328 1649018.908 0.520049921 0.697984162 0.70854068 0.702328695 0.726420179 0.744176284 0.889867146 0.859710171 1 20.65317651 -2 0.158382148 2.441326293 0.46792407 0.85970517 0.048864105 48.67172953 0.636225018 21.77527002 0.656587183 0.01 2 -1.973402223 ASS(ph)HSSQTQGGGSVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 AS(0.003)S(0.821)HS(0.088)S(0.088)QTQGGGSVTK;AS(0.046)S(0.249)HS(0.249)S(0.249)QT(0.207)QGGGSVTK;AS(0.005)S(0.331)HS(0.331)S(0.331)QT(0.001)QGGGSVTK;AS(0.019)S(0.771)HS(0.104)S(0.104)QT(0.001)QGGGSVTK;AS(0.03)S(0.966)HS(0.002)S(0.002)QTQGGGSVTK;AS(0.162)S(0.822)HS(0.016)SQTQGGGSVTK 190.83 5.11E-10 20247723000 2335650 2902292 1199474 2123565 3463496 3820159 4200217 4909675 5204932 TRUE FALSE 2026987.935 2883226.653 1779543.638 2605752.89 3394579.206 3967122.989 3792880.602 3859779.208 4589610.868 0.441647014 0.628207213 0.38773301 0.567750287 0.739622444 0.864370227 0.826405704 0.8409818 1 22.12994041 3.127591608 2.054030915 0.872850911 0.49524755 0.845759078 0.076484465 0.11628876 1.006332367 0.025368481 0.030300128 1341.502876 -3.127591608 -0.377603361 ASS(ph)HSSQTQGGGSVTKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSHSSQTQGGGSVTKK 17 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 AS(0.295)S(0.619)HS(0.071)S(0.013)QT(0.002)QGGGSVTKK 93.572 0.0018552 218550000 101560 126330 16596 53436 150200 137160 221050 225640 43883 TRUE FALSE 88138.58868 125500.1299 24621.88111 65569.46052 147211.3139 142436.634 199612.605 177388.6419 38695.20173 2.277765323 3.243299538 0.636303211 1.694511402 3.80438161 3.680989569 5.158588044 4.584254223 1 15.23986706 3.231932146 23.39671525 3.878208212 1.959659915 0.30019972 1.248857291 78.4839791 277026.8447 0.37969294 0.441269303 1705.815851 -3.231932146 -1.918548297 ASS(ph)LEDLVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ASSLEDLVLK 10 0 Q15477 Q15477 SKIV2L Helicase SKI2W 1 AS(0.016)S(0.984)LEDLVLK;AS(0.005)S(0.995)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK 298.31 2.42E-32 5801518000 12903580 10531110 8339070 8606100 10664930 9283300 12893170 14603210 13349580 TRUE FALSE 11198339.21 10461930.44 12371872.14 10560246.54 10452718.76 9640434.558 11642792.36 11480427.18 11771407.86 0.951316898 0.888757791 1.051010405 0.897109901 0.887975243 0.818970396 0.989073907 0.975280724 1 23.48878354 ASS(ph)LGEIDESSELR ddPTM_MDA-MB-175_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;AS(0.038)S(0.962)LGEIDESSELR;ASS(1)LGEIDESSELR;ASS(1)LGEIDESSELR;ASS(1)LGEIDESSELR 392.16 4.19E-114 2611100000 3486050 3230140 2194470 2617300 3412880 3276000 3228580 3820610 3330190 TRUE FALSE 3025359.66 3208920.998 3255723.032 3211597.968 3344970.365 3402029.84 2915472.809 3003602.284 2936498.732 1.030260843 1.092771116 1.108709156 1.093682736 1.139101587 1.158532712 0.992839798 1.022851551 1 21.48566558 2.223939937 24.99129461 1.008385209 1.104701777 0.650661371 0.034032088 150.7625137 257698.1584 0.014326444 0.009707287 167.4711249 -2.223939937 0.096316568 SRTS(ph)PAPWKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRTSPAPWKR 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.257)RT(0.191)S(0.551)PAPWKR;S(0.032)RT(0.058)S(0.91)PAPWKR 88.021 0.0065113 227780000 757660 654750 366720 447740 614150 691080 614540 665760 270209 TRUE FALSE 657533.3113 650448.9041 544067.0186 549406.2103 601929.6166 717666.2948 554942.0054 523392.405 238265.1998 2.759669947 2.729936661 2.283451461 2.30586007 2.526301017 3.01204832 2.329093824 2.196680024 1 17.86220873 1.10947393 1.728087664 6.90E-11 2.57044364 0.825029704 0.226308416 0.576300869 1.209124206 2.764341807 0.065520451 12.86690013 -1.10947393 2.57044364 ASS(ph)LNFLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ASSLNFLNK 9 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 AS(0.002)S(0.998)LNFLNK;ASS(1)LNFLNK;ASS(1)LNFLNK;ASS(1)LNFLNK;ASS(1)LNFLNK;ASS(1)LNFLNK;ASS(1)LNFLNK;ASS(1)LNFLNK 234.3 3.77E-10 24542380000 33625090 30508140 18013880 19446260 25284600 22490160 33874000 34154220 35567560 TRUE FALSE 29181449.16 30307730.02 26725452.62 23861830.55 24781485.93 23355371.01 30588904.69 26850605.84 31362803.58 0.930447723 0.96635908 0.852138507 0.760832191 0.790155315 0.744683777 0.975324308 0.856129006 1 24.90255119 -0.122466417 1.084756196 3.39831394 0.850758869 0.229682596 0.080229903 48.34191365 3.948108394 266.9833213 0.026918631 0.754281721 0.122466417 -2.54755507 ASS(ph)LNVLNVGGK ddPTM_MDA-MB-175_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 ASS(1)LNVLNVGGK;ASS(1)LNVLNVGGK;AS(0.004)S(0.996)LNVLNVGGK;ASS(1)LNVLNVGGK;AS(0.002)S(0.998)LNVLNVGGK;ASS(1)LNVLNVGGK;ASS(1)LNVLNVGGK;ASS(1)LNVLNVGGK 302.2 1.40E-36 17133350000 20163870 24306880 11152440 12723690 14714780 13423020 19496990 19743660 25460200 TRUE FALSE 17499163.49 24147206.5 16545797.29 15612798.28 14421984.67 13939412.27 17606174.91 15521631.95 22450324.16 0.779461506 1.075583868 0.736995919 0.695437543 0.642395387 0.620900267 0.784228093 0.691376741 1 24.42023294 4.140000241 9.887384554 0.727189605 0.927068582 0.277077761 0.125756768 0.331217696 30.1114106 0.030566791 0.063810663 13803.85032 -4.140000241 0.199878978 ASS(ph)LSESSPPK ddPTM_MDA-MB-175_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(0.971)LS(0.029)ESSPPK 228.93 3.05E-12 791520000 2537200 1355500 795590 1216500 1233700 779050 2288700 1811700 1706100 TRUE FALSE 2201902.592 1346595.631 1180339.985 1492724.918 1209151.784 809020.5576 2066742.226 1424282.054 1504406.802 1.463635095 0.895100733 0.784588307 0.99223489 0.803739908 0.53776715 1.373792131 0.946739972 1 20.5207633 4.740418746 24.47940239 0.923367417 1.463635343 0.40069863 0.210053154 132.773308 1749000.395 0.051007184 0.319352066 55007.09964 -4.740418746 0.540267926 ASS(ph)PCPEFEQFQIVPAVETPYLAR ddPTM_MDA-MB-175_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(0.395)S(0.605)PCPEFEQFQIVPAVETPYLAR;AS(0.177)S(0.823)PCPEFEQFQIVPAVETPYLAR 133.95 2.47E-05 245890000 312600 328750 181317 227440 314190 301710 310700 354560 327320 TRUE FALSE 271289.118 326590.4196 269002.5077 279083.7282 307938.2337 313316.9789 280568.3618 278740.1032 288624.6025 0.939937606 1.131540474 0.932015169 0.966943656 1.066916095 1.085551877 0.972087478 0.965753095 1 18.13883476 ASS(ph)PFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASSPFR 6 0 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 AS(0.015)S(0.985)PFR;AS(0.018)S(0.982)PFR;AS(0.291)S(0.709)PFR;AS(0.019)S(0.981)PFR 133.79 0.015013 9626950000 8897340 9057390 6269970 8254870 6848010 8600580 7776840 9718600 16854000 TRUE FALSE 7721533.976 8997891.409 9302148.464 10129264.4 6711747.999 8931449.878 7022643.254 7640353.02 14861539.32 0.519564886 0.605448145 0.625920927 0.681575723 0.451618628 0.600977442 0.47253808 0.514102399 1 23.82508022 1.235085627 24.99999239 1.000000618 0.558148117 0.789830306 0.071496315 46.06887123 331378.5712 0.127159984 0.017886368 17.1824713 -1.235085627 -0.441852501 ASS(ph)PFRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASSPFRR 7 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 AS(0.182)S(0.818)PFRR;AS(0.084)S(0.916)PFRR;AS(0.012)S(0.988)PFRR 121.53 0.0027126 1456700000 1404990 1443530 849870 1060710 1210590 1314450 1251040 1528640 1060880 TRUE FALSE 1219317.012 1434047.356 1260869.975 1301560.417 1186501.627 1365017.742 1129714.333 1201752.232 935463.975 1.303435562 1.532979778 1.347855191 1.391352796 1.268356302 1.459187931 1.207651351 1.284659018 1 19.83532257 0.403451927 0.774027099 2.27E-14 1.387643953 0.631544728 0.087967985 5.282386421 0.941044513 8.602099588 0.032116799 2.531931355 -0.403451927 1.387643953 ASS(ph)PGHPAFLEDGS(ph)PSPVLAFAAS(ph)PRPNHSYIFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSPGHPAFLEDGSPSPVLAFAASPRPNHSYIFK 34 1 Q9C073;D6RJ87;Q9C073-2 Q9C073 FAM117A Protein FAM117A 3 AS(0.479)S(0.521)PGHPAFLEDGS(0.504)PS(0.496)PVLAFAAS(0.711)PRPNHS(0.147)Y(0.141)IFK 61.739 0.0083015 37203000 28880 26483 14497 20017 22734 22146 25892 29545 22810 TRUE FALSE 25063.43483 26309.03143 21507.79769 24562.16579 22281.63788 22997.97095 23380.99783 23227.03167 20113.42779 1.246104597 1.308033206 1.069325324 1.221182488 1.107799134 1.143413803 1.162457144 1.15480225 1 14.29587135 8 0.294910361 1.095963066 2.620814577 0.390133748 0.068796485 84.69446555 1.353898547 0.136113315 66.38328207 100000000 -8 1.524851511 ASS(ph)PGHPAFLEDGSPS(ph)PVLAFAAS(ph)PRPNHSYIFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSPGHPAFLEDGSPSPVLAFAASPRPNHSYIFK 34 1 Q9C073;D6RJ87;Q9C073-2 Q9C073 FAM117A Protein FAM117A 3 AS(0.466)S(0.534)PGHPAFLEDGS(0.22)PS(0.78)PVLAFAAS(0.963)PRPNHS(0.037)Y(0.001)IFK 121.87 4.20E-08 35697000 18870 14191 10218 14255 19055 15122 15049 20108 15797 TRUE FALSE 16376.28169 14097.77839 15159.45898 17491.81562 18675.84278 15703.75313 13589.5503 15808.06068 13929.49666 1.17565495 1.012080963 1.088299122 1.255739246 1.340740677 1.127374055 0.975595216 1.134862305 1 13.76585551 2.468301198 24.22793065 1.054235327 1.172088944 0.292606159 0.09643837 211.2549825 580290.3634 0.038737544 0.030055293 293.9687719 -2.468301198 0.117853617 ASS(ph)PPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASSPPDR 7 0 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 AS(0.101)S(0.899)PPDR;AS(0.493)S(0.507)PPDR 86.332 0.021141 1236528000 607819 525556 449511 488403 372049 550065 514861 621296 931870 TRUE FALSE 527494.1791 522103.588 666896.0231 599302.3659 364645.9528 571226.3565 464929.8595 488436.6853 821705.3902 0.641950492 0.635390244 0.811599913 0.729339704 0.443767264 0.695171729 0.565810892 0.594418256 1 19.6482617 1.234384047 24.99582435 1.000000531 0.637748678 0.571189676 0.098101523 95.58475159 571974.64 0.183978327 0.024379752 17.15473633 -1.234384047 -0.362251854 ASS(ph)PPDRIDIFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ASSPPDRIDIFGR 13 1 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 AS(0.023)S(0.977)PPDRIDIFGR;AS(0.479)S(0.521)PPDRIDIFGR;AS(0.024)S(0.976)PPDRIDIFGR;AS(0.147)S(0.853)PPDRIDIFGR;AS(0.023)S(0.977)PPDRIDIFGR 199.65 7.04E-08 21845950000 3417670 3265310 1515360 1643940 3025850 3001470 3140180 3597670 658673 TRUE FALSE 2966016.25 3243859.964 2248193.165 2017221.703 2965641.505 3116938.493 2835645.827 2828336.268 580805.4283 5.106729562 5.58510614 3.870819822 3.473145402 5.106084345 5.366579479 4.882264677 4.869679465 1 19.14769541 1.237692218 25 0.999995593 4.775340165 0.771871521 0.646245331 10.87046053 312761.2057 0.984864511 0.167541071 17.28590881 -1.237692218 3.775344572 ASS(ph)PSLIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSPSLIER 9 0 A1L170;A1L170-2 A1L170 C1orf226 Uncharacterized protein C1orf226 1 AS(0.044)S(0.931)PS(0.025)LIER 100.79 0.0044588 0 179450 179190 125430 153590 185660 201590 122460 188470 205120 TRUE FALSE 155735.2278 178012.8891 186088.3675 188464.957 181965.7292 209345.2977 110583.848 148167.1572 180870.9473 0.861029536 0.984198357 1.028846094 1.041985791 1.006052835 1.1574291 0.611396411 0.819187158 1 17.46460117 2.24675296 24.99980249 0.803784722 1.013623081 0.403610157 0.116273318 169.2438012 516466.5859 0.043560056 0.033152121 176.5033531 -2.24675296 0.20983836 ASS(ph)RS(ph)PVFTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSRSPVFTPR 11 1 P52735-3 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 2 AS(0.445)S(0.558)RS(0.997)PVFTPR 96.414 0.0040004 825260000 289320 292920 188900 199080 314270 279260 275780 326980 312860 TRUE FALSE 251085.629 290995.7892 280252.6718 244284.1567 308016.6419 290003.3129 249034.898 257057.8716 275874.0472 0.910145885 1.054813935 1.015871825 0.885491619 1.116511847 1.051216364 0.902712309 0.931794325 1 18.07365022 2.235665264 24.99349005 0.940363492 1.007947438 0.1383849 0.071122612 136.5074373 1178346.305 0.027778526 0.019658681 172.0541941 -2.235665264 0.067583946 ASS(ph)SAESEDLAVHLYPGAVTIQGVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSSAESEDLAVHLYPGAVTIQGVLR 26 0 Q86X27 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 AS(0.099)S(0.45)S(0.45)AESEDLAVHLYPGAVTIQGVLR 132.85 3.36E-05 37852000 28628 24417 22694 23269 27024 24377 28614 33125 25931 TRUE FALSE 24844.73727 24256.60312 33668.89431 28552.58209 26486.27527 25314.79896 25839.01868 26041.47653 22865.46672 1.086561563 1.060840061 1.472477895 1.248720721 1.158352707 1.107119276 1.13004554 1.138899846 1 14.48088275 2.996591401 3.563479981 1.105399107 1.223474262 0.196072597 0.115880133 0.426923346 11.65461744 0.039368852 0.04252186 992.18213 -2.996591401 0.118075155 ASS(ph)VTTFTGEPNTCPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ASSVTTFTGEPNTCPR 16 0 P52943;H0YFA4;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 1 AS(0.027)S(0.973)VTTFTGEPNTCPR;AS(0.004)S(0.992)VT(0.004)TFTGEPNTCPR;AS(0.001)S(0.986)VT(0.012)TFTGEPNTCPR;AS(0.06)S(0.937)VT(0.003)TFTGEPNTCPR;ASS(0.999)VT(0.001)TFTGEPNTCPR 371.03 2.63E-104 4757490000 4754480 3848280 1717614 2206231 3165180 1832764 4046460 3022810 3065340 TRUE FALSE 4126163.422 3823000.395 2548257.875 2707189.469 3102199.111 1903271.617 3654034.932 2376405.605 2702958.997 1.526535706 1.414376022 0.942766012 1.001565126 1.147704835 0.704143725 1.351864729 0.879186701 1 21.3661082 4.307965479 4.949613126 1.00566691 1.494577613 0.573210564 0.168092355 0.128686372 5.840119465 0.03874977 0.106738087 20321.95469 -4.307965479 0.488910703 ASSDIVSLAGPSAGPGS(ph)SEGGCSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSDIVSLAGPSAGPGSSEGGCSR 24 0 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 ASSDIVSLAGPSAGPGS(0.959)S(0.041)EGGCSR 220.88 1.02E-32 110760000 61948 54023 43385 42198 66013 66996 66265 81556 66329 TRUE FALSE 53761.41484 53668.11936 64366.13111 51779.70086 64699.47045 69573.37947 59838.6305 64115.88407 58487.66118 0.91919242 0.917597289 1.100507865 0.885309821 1.106207175 1.189539436 1.023098365 1.096229235 1 15.83584468 3.220904622 24.99983579 1.085499158 0.963280514 0.409905384 0.075655517 245.7642782 347986.656 0.022333441 0.025377936 1663.047378 -3.220904622 -0.122218644 ASSEGGTAAGAGLDSLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSEGGTAAGAGLDSLHK 18 0 A0A1W2PNV4;C9JEY1;C9K057;O15143 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 235.26 8.68E-24 275880000 196880 173370 91152 152270 192900 170640 216350 249820 234210 FALSE TRUE 170861.8092 172231.1211 135233.4121 186845.2308 189061.6674 177204.6312 195368.4103 196397.9371 206521.9606 0.827329978 0.833960323 0.654813714 0.904723305 0.915455513 0.858042557 0.945993393 0.950978465 1 17.65593567 2.808381294 0.674790067 0.98533857 0.779247031 0.541647805 0.064486506 0.630638328 0.753337503 0.077531872 0.059115636 643.2522202 -2.808381294 -0.206091538 ASSGDIGS(ph)LDYQEFVVDIESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASSGDIGSLDYQEFVVDIESR 21 0 J3KN59 J3KN59 BNIP2 1 ASSGDIGS(1)LDYQEFVVDIESR;AS(0.001)S(0.001)GDIGS(0.998)LDYQEFVVDIESR 123.41 2.78E-05 45589000 23986 29035 21824 22084.4 30772 32737 31834 32789 40672 TRUE FALSE 20816.18933 28844.26717 32378.1594 27099.00056 30159.6974 33996.41357 28746.74358 25777.32751 35863.80249 0.580423376 0.804272419 0.902808881 0.755608683 0.840950912 0.947931095 0.801553142 0.71875612 1 15.13024084 4.72533828 3.969443962 0.838247737 0.559974832 0.494127402 0.084939898 0.199474613 6.540428698 0.020834731 0.156977551 53129.81215 -4.72533828 -0.278272905 ASSHS(ph)SQTQGGGSVTK ddPTM_MDA-MB-175_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(0.269)HS(0.723)S(0.008)QTQGGGSVTK;AS(0.003)S(0.026)HS(0.929)S(0.038)QT(0.005)QGGGSVTK;AS(0.008)S(0.168)HS(0.412)S(0.412)QTQGGGSVTK 351.96 3.12E-87 9351520000 1311250 1760370 501538 1134940 2123130 2293880 2545770 3001410 3032170 TRUE FALSE 1137964.99 1748806.014 744083.4543 1392645.473 2080883.867 2382127.048 2298881.617 2359581.828 2673710.317 0.425612671 0.654074603 0.278296212 0.520866253 0.778275737 0.89094433 0.859809532 0.882512146 1 21.35041173 3.163872057 2.756326925 0.896883971 0.461357602 0.822562028 0.097152728 0.105537764 1.630412383 0.03033755 0.036398224 1458.384557 -3.163872057 -0.435526369 ASSHSSQTQGGGS(ph)VTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 ASSHSSQTQGGGS(0.988)VT(0.012)K;ASSHSSQT(0.033)QGGGS(0.966)VT(0.001)K;ASSHSSQTQGGGS(0.998)VT(0.002)K;ASSHSSQTQGGGS(1)VTK 172.24 2.99E-09 383545000 1239450 1432450 313029 680250 1334650 1246840 1269610 1515750 1505040 TRUE FALSE 1075653.542 1423040.142 464410.8714 834711.1595 1308093.076 1294806.742 1146483.418 1191618.658 1327115.886 0.810519679 1.072280241 0.349939954 0.628966293 0.985666052 0.975654617 0.863890961 0.897900983 1 20.33986292 3.233060388 24.99989285 0.934279084 0.7148099 0.284387187 0.180244994 194.2482903 882905.0957 0.055883268 0.065162559 1710.253106 -3.233060388 -0.219469185 ASSHSSQTQGGGS(ph)VTKK ddPTM_MDA-MB-175_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 ASSHSSQTQGGGS(0.953)VT(0.047)KK;ASSHSSQTQGGGS(0.932)VT(0.068)KK 187.07 2.29E-10 476020000 248410 238830 70861 141218 242590 186668 306900 336240 282390 TRUE FALSE 215581.9891 237261.11 105129.6166 173283.7053 237762.9336 193849.2388 277136.8852 264337.6926 249006.1759 0.865769647 0.952832231 0.422196824 0.695901235 0.954847536 0.77849169 1.112971934 1.061570829 1 17.925822 2.497304636 1.480436004 1.065271029 0.746937341 0.389384078 0.157559533 0.410664799 1.852034571 0.091021696 0.059848182 314.2712379 -2.497304636 -0.318333688 ASSHSSQTQGGGSVTK ddPTM_MDA-MB-175_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 0 ;; 205.95 2.13E-11 299043000 500830 474490 124138 280557 479050 445400 424779 490230 481360 FALSE TRUE 434644.0466 471373.0439 184171.552 344261.7549 469517.8422 462534.8262 383583.998 385398.1295 424454.1692 1.024007014 1.110539319 0.433902092 0.811069321 1.106168525 1.08971677 0.903711227 0.907985261 1 18.69524926 3.264319396 24.93639489 0.986899642 0.834499548 0.145557302 0.185967206 478.280911 463007.8257 0.056117397 0.072420962 1837.889497 -3.264319396 -0.152400094 ASSPHGLGSPLVAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSPHGLGSPLVASPR 16 0 Q8IZW8 Q8IZW8 TNS4 Tensin-4 1 ASSPHGLGS(0.001)PLVAS(0.999)PR 105.91 0.00080327 146470000 106430 147930 45783 84222 114250 130170 82119 113200 97104 TRUE FALSE 92365.00584 146958.2381 67923.81193 103345.8924 111976.6485 135177.7241 74155.11202 88993.06092 85624.47574 1.078722001 1.716311099 0.793275653 1.206966717 1.307764486 1.578727612 0.866050406 1.039341382 1 16.38573563 2.212217818 24.97665001 0.978962797 1.275892047 0.250649431 0.253876 316.531012 300113.2158 0.100147006 0.067541686 163.0113404 -2.212217818 0.29692925 ASSPS(ph)PLTIGTPESQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASSPSPLTIGTPESQR 16 0 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 ASSPS(1)PLTIGTPESQR;ASS(0.031)PS(0.969)PLTIGTPESQR;ASSPS(1)PLTIGTPESQR 441.21 6.41E-182 1967540000 1272580 1163980 904850 1070140 1242150 1265390 1070040 1265850 2233840 TRUE FALSE 1104405.329 1156333.739 1342438.487 1313131.643 1217433.645 1314070.372 966267.6855 995157.8284 1969757.98 0.560680723 0.587043561 0.681524583 0.666646185 0.618062553 0.667122756 0.490551477 0.505218326 1 20.90958695 1.230709927 24.99155402 1.000000735 0.595143898 0.789078286 0.065455651 148.3073883 472076.1566 0.19349096 0.018223654 17.01021987 -1.230709927 -0.404856837 ASSRPGS(ph)PTADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASSRPGSPTADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHK 45 1 H0Y9C1;H0Y9Z5;Q96LI5-2;Q96LI5 H0Y9C1 CNOT6L CCR4-NOT transcription complex subunit 6-like 1 AS(0.033)S(0.033)RPGS(0.745)PT(0.185)ADPNS(0.004)IPLVLCADLNSLPDSGVVEYLSNGGVADNHK 214.05 1.88E-38 254070000 166590 147600 114810 144330 152030 120720 169340 189920 209060 TRUE FALSE 144574.7094 146630.4059 170332.5 177102.3324 149004.9004 125364.1765 152917.4329 149307.086 184345.165 0.784260924 0.795412269 0.923986805 0.960710483 0.808292968 0.68005134 0.829516917 0.809932205 1 17.49205005 1.235530988 24.97747567 1.000000241 0.82512872 0.344803828 0.076223111 109.2296123 900366.7578 0.137484576 0.019956326 17.20010062 -1.235530988 -0.174871521 ASSRS(ph)PVFTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ASSRSPVFTPR 11 1 P52735-3 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 1 AS(0.039)S(0.039)RS(0.921)PVFTPR;AS(0.058)S(0.012)RS(0.929)PVFTPR;AS(0.012)S(0.05)RS(0.937)PVFTPR;ASSRS(1)PVFTPR;AS(0.002)S(0.003)RS(0.996)PVFTPR;AS(0.002)S(0.008)RS(0.99)PVFTPR;AS(0.021)S(0.017)RS(0.962)PVFTPR;AS(0.015)S(0.011)RS(0.974)PVFTPR 137.46 4.72E-05 7337300000 1585010 1695279 1053336 1064204 1625196 1646376 1500628 1756788 1064079 TRUE FALSE 1375546.913 1684142.601 1562732.813 1305847.784 1592857.779 1709713.15 1355097.328 1381112.558 938284.7928 1.466022814 1.794916227 1.665520772 1.39173926 1.697627193 1.822168667 1.444228168 1.471954537 1 19.83966636 0.836392562 1.245444843 1.68E-17 1.631776356 0.650289315 0.14171012 2.218262759 1.440784928 6.010588152 0.042050863 6.861081252 -0.836392562 1.631776356 ASSSGPRS(ph)PLDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASSSGPRSPLDQR 13 1 O14646;O14646-2 O14646 CHD1 Chromodomain-helicase-DNA-binding protein 1 1 AS(0.142)S(0.122)S(0.122)GPRS(0.615)PLDQR;AS(0.138)S(0.138)S(0.162)GPRS(0.561)PLDQR 60.209 0.056653 691320000 1479970 1430890 899220 1036150 1427010 1435830 1404810 1550220 989490 TRUE FALSE 1284388.215 1421490.389 1334085.8 1271423.694 1398615.293 1491067.309 1268571.742 1218717.517 872513.6194 1.472055205 1.629189915 1.529014298 1.457196387 1.602972449 1.708932991 1.453927726 1.396789104 1 19.73481813 1.087427195 1.494493386 0.588958821 1.561266943 0.829297762 0.079142678 0.672773732 0.994176153 1.09553207 0.022870422 12.23002079 -1.087427195 0.972308122 ASST(ph)STPEPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASSTSTPEPTR 11 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 1 AS(0.039)S(0.039)T(0.369)S(0.276)T(0.276)PEPTR;AS(0.005)S(0.075)T(0.457)S(0.312)T(0.151)PEPTR 90.913 0.017382 0 265571 245918 134348 152843 175250 213926 202040 223976 221946 TRUE FALSE 230475.1195 244302.5485 199319.1422 187548.3392 171762.8679 222155.8716 182446.1919 176080.4754 195707.7967 1.177649145 1.248302585 1.018452742 0.958307959 0.877649592 1.13514063 0.932237729 0.899711091 1 17.57834171 4.136805728 4.281523809 0.96298566 1.212892736 0.659450215 0.071833935 0.118730874 3.844066611 0.018669128 0.042477704 13702.68668 -4.136805728 0.249907076 ASSTST(ph)PEPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ASSTSTPEPTR 11 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 1 ASS(0.002)T(0.034)S(0.132)T(0.832)PEPTR;ASS(0.002)T(0.011)S(0.132)T(0.855)PEPTR;ASSTS(0.011)T(0.989)PEPTR;ASSTS(0.121)T(0.879)PEPTR;AS(0.001)S(0.011)T(0.092)S(0.092)T(0.804)PEPTR;ASS(0.001)T(0.003)S(0.126)T(0.871)PEPTR;ASSTS(0.122)T(0.877)PEPTR 253.88 1.19E-14 11212220000 7536770 6746410 3677125 4255290 5086320 5770460 5587960 6252480 5917920 TRUE FALSE 6540766.749 6702092.388 5455394.949 5221518.633 4985112.183 5992453.33 5046040.499 4915435.809 5218310.239 1.253426195 1.284341498 1.045433234 1.000614834 0.955311577 1.148351297 0.966987448 0.94195929 1 22.31515129 4.178729188 4.264997348 0.999688096 1.271726857 0.782968063 0.05728424 0.087824783 3.176481752 0.015417833 0.036265345 15091.38809 -4.178729188 0.272038762 ASSVSTKES(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ASSVSTKESPAR 12 1 Q13428-4;Q13428;Q13428-3;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 ASSVS(0.003)T(0.002)KES(0.995)PAR;ASSVS(0.001)T(0.004)KES(0.995)PAR;ASSVSTKES(1)PAR;ASSVSTKES(1)PAR;ASSVS(0.005)T(0.177)KES(0.818)PAR;ASSVST(0.022)KES(0.978)PAR 184.01 9.01E-06 4442840000 7255750 5646050 4006460 4742900 5558700 4813910 6584410 7737800 8043460 TRUE FALSE 6296884.254 5608960.726 5943997.457 5819847.936 5448092.745 4999104.233 5945854.932 6083131.686 7092571.322 0.887814019 0.7908219 0.838059596 0.820555433 0.768140706 0.704836653 0.838321486 0.857676491 1 22.75787732 1.196723593 1.809125312 1.084614216 0.802482679 0.615085796 0.048107536 0.698456598 1.964087766 0.355350497 0.01363771 15.72981421 -1.196723593 -0.282131537 ASSVSTKES(ph)PARK ddPTM_MDA-MB-175_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(0.015)T(0.015)KES(0.971)PARK;ASSVS(0.023)T(0.023)KES(0.954)PARK;ASSVSTKES(1)PARK;ASSVST(0.001)KES(0.999)PARK 165.44 2.14E-05 2289510000 3272060 2365130 1873996 2005512 2036920 1675535 3055730 3535040 1916768 TRUE FALSE 2839648.981 2349593.305 2780266.734 2460894.152 1996389.277 1739993.916 2759385.775 2779099.206 1690169.871 1.680096794 1.390152165 1.644962901 1.456004035 1.181176704 1.02947872 1.632608546 1.644272126 1 20.68873682 3.475502771 24.92808325 1.349493667 1.553062908 0.21523927 0.22877876 107.2287458 1651524.146 0.070687748 0.091971745 2988.840715 -3.475502771 0.203569242 AST(ph)PDWVSEGPQPGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ASTPDWVSEGPQPGLR 16 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 AST(1)PDWVSEGPQPGLR;AS(0.027)T(0.973)PDWVSEGPQPGLR;AST(1)PDWVSEGPQPGLR;AS(0.002)T(0.998)PDWVSEGPQPGLR;AST(1)PDWVSEGPQPGLR;AS(0.025)T(0.975)PDWVSEGPQPGLR;AS(0.001)T(0.999)PDWVSEGPQPGLR;AS(0.001)T(0.999)PDWVSEGPQPGLR 390.71 2.07E-120 21710920000 3420630 3609980 2364300 2906680 3727910 3548670 3114430 4069790 3847600 TRUE FALSE 2968585.079 3586265.804 3507683.388 3566686.12 3653731.885 3685189.631 2812393.058 3199497.08 3392741.111 0.874981315 1.057040807 1.033878882 1.051269756 1.076926227 1.086198301 0.828944198 0.943041916 1 21.69401992 2.252977767 24.99860162 0.92400291 1.034545523 0.327774592 0.071402841 251.9069524 436793.3812 0.02627877 0.0202619 179.051419 -2.252977767 0.110542612 AST(ph)PDWVSEGPQPGLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASTPDWVSEGPQPGLRR 17 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 AS(0.106)T(0.894)PDWVSEGPQPGLRR;AS(0.076)T(0.924)PDWVSEGPQPGLRR;AS(0.029)T(0.971)PDWVSEGPQPGLRR;AS(0.001)T(0.999)PDWVSEGPQPGLRR 259.56 1.93E-27 3526590000 2813470 2814030 986800 935980 2804810 2886040 2463850 3482090 273360 TRUE FALSE 2441662.811 2795544.452 1464019.781 1148508.565 2748999.769 2997067.826 2224906.206 2737472.151 241043.6922 10.12954452 11.5976669 6.073669745 4.764731879 11.40457045 12.43371191 9.230302547 11.35674668 1 17.87893515 4.273122801 24.99381643 8.55826613 10.86360749 0.087203849 3.498775708 550.2787779 397928.317 0.876378276 2.318450441 18755.24757 -4.273122801 2.30534136 AST(ph)PVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASTPVLK 7 0 Q04724;A0A669KBK8;A0A669KAE5;F6T2C8 Q04724 TLE1 Transducin-like enhancer protein 1 1 AS(0.151)T(0.849)PVLK;AS(0.003)T(0.997)PVLK;AS(0.066)T(0.934)PVLK 133.86 0.036111 1421900000 7794500 6358300 4021300 4780700 5260800 4758500 6674500 8193700 6798400 TRUE FALSE 6764437.076 6316531.909 5966014.13 5866231.003 5156120.373 4941562.574 6027208.017 6441541.018 5994700.897 1.128402767 1.053685917 0.995214646 0.978569424 0.860113033 0.82432179 1.005422643 1.074539185 1 22.51525634 4.443376184 1.700459017 0.963765888 1.140583789 0.389957168 0.071376955 0.721168674 3.137125159 0.023544812 0.173721087 27757.23384 -4.443376184 0.176817901 ASTAS(ph)PCNNNINAATAVALQEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASTASPCNNNINAATAVALQEPR 23 0 Q71RC2-5;Q71RC2-3;Q71RC2;Q71RC2-4;Q71RC2-6 Q71RC2-5 LARP4 La-related protein 4 1 AS(0.002)T(0.014)AS(0.984)PCNNNINAATAVALQEPR;AS(0.01)T(0.084)AS(0.906)PCNNNINAATAVALQEPR;AS(0.007)T(0.041)AS(0.952)PCNNNINAATAVALQEPR 275.37 6.45E-52 875630000 453000 407390 279212 310049 378358 457460 411430 438960 414990 TRUE FALSE 393134.9022 404713.8283 414239.8571 380450.3643 370829.416 475058.7822 371529.5819 345091.82 365930.355 1.074343511 1.105985942 1.132018297 1.039679707 1.01338796 1.29822185 1.015301346 0.943053276 1 18.48120957 2.012844688 24.99728118 0.970974452 1.108146124 0.377593273 0.076836608 213.101039 414718.1928 0.030611734 0.02062539 103.00177 -2.012844688 0.137171672 ASTFCGT(ph)PDYIAPEILQGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASTFCGTPDYIAPEILQGLK 20 0 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 1 AS(0.311)T(0.311)FCGT(0.378)PDYIAPEILQGLK 117.67 0.00028286 127970000 57623 37433 32654 42801 37075 31972 55615 53144 86337 TRUE FALSE 50007.97455 37187.10016 48445.58362 52519.62122 36337.28004 33201.98353 50221.46586 41779.56917 76130.33822 0.656873143 0.488466241 0.636350563 0.689864546 0.477303541 0.436120268 0.65967743 0.548790011 1 16.21618387 1.236628498 24.99898691 1.00000054 0.572535715 0.703701671 0.086829824 28.25753567 365514.0464 0.131942884 0.020855652 17.24362214 -1.236628498 -0.427464825 ASTRS(ph)PTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASTRSPTQR 9 1 A0A2R8Y575;Q5VVD7;Q8IWE5 A0A2R8Y575 PLEKHM2 Pleckstrin homology domain-containing family M member 2 1 AS(0.142)T(0.142)RS(0.664)PT(0.051)QR;AS(0.007)T(0.007)RS(0.493)PT(0.493)QR 83.045 0.010134 174158000 37184 28939 18246.1 18135.7 20278.3 33571 27527 30946 16060.9 TRUE FALSE 32270.04019 28748.8978 27069.97499 22253.68787 19874.8015 34862.49809 24857.43578 24328.43872 14162.1987 2.278603829 2.029974188 1.9114246 1.571344136 1.403369768 2.461658591 1.75519609 1.717843341 1 13.78975764 1.121745823 1.898087627 0.467017291 1.907662782 0.465725703 0.307223169 1.133214002 3.004477746 3.257658759 0.085195211 13.23566673 -1.121745823 1.44064549 ASTSDYQVISDRQT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASTSDYQVISDRQTPK 16 1 Q8NFH5-2;Q8NFH5;Q8NFH5-3 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 ASTSDYQVIS(0.058)DRQT(0.942)PK 70.072 0.071853 237740000 202340 159670 114320 145050 175240 157700 196320 222820 185790 TRUE FALSE 175600.2563 158621.1173 169605.5344 177985.8195 171753.0669 163766.821 177280.9166 175171.677 163826.1179 1.071869728 0.968228506 1.035277748 1.086431283 1.048386357 0.99963805 1.082128533 1.069253665 1 17.32180585 4.004112891 24.99175467 1.050906697 1.01547512 0.07443254 0.038314956 235.8869631 1433307.876 0.009378984 0.019404745 10095.15267 -4.004112891 -0.035431577 GS(ph)PRYS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 GSPRYSPR 8 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 2 GS(1)PRY(0.022)S(0.978)PR;GS(1)PRY(0.008)S(0.992)PR;GS(1)PRY(0.021)S(0.979)PR;GS(1)PRY(0.165)S(0.835)PR;GS(1)PRY(0.022)S(0.978)PR;GS(1)PRY(0.24)S(0.76)PR;GS(1)PRY(0.017)S(0.983)PR;GS(1)PRY(0.021)S(0.979)PR 110.66 0.0019249 11183740000 11207450 9943360 5913130 6081450 7826080 9574330 8917700 9554520 3631750 TRUE FALSE 9726357.086 9878041.413 8772739.446 7462336.172 7670356.319 9942660.671 8052862.827 7511360.251 3202408.652 3.037200477 3.084566177 2.739419106 2.330226084 2.395183486 3.104744506 2.514626864 2.345534586 1 21.61072599 1.127753106 1.786039192 4.30E-12 2.747689201 0.800532919 0.273168909 0.583790162 1.370855946 3.029515427 0.080191348 13.42001823 -1.127753106 2.747689201 IIS(ph)PGSSTPS(ph)STRSPPPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IISPGSSTPSSTRSPPPGR 19 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 2 IIS(0.879)PGS(0.04)S(0.043)T(0.046)PS(0.359)S(0.255)T(0.229)RS(0.15)PPPGR 51.301 0.07774 100810000 136390 123410 72752 78150 117810 129520 118380 134150 53932 TRUE FALSE 118365.7159 122599.3116 107935.1105 95895.15195 115465.8115 134502.7182 106899.5258 105463.0665 47556.2204 2.488963903 2.577986866 2.269631809 2.016458649 2.427985456 2.828288646 2.247855799 2.2176503 1 15.53734644 1.128110579 2.279093744 0.270957856 2.410201617 0.806082324 0.215023795 0.416186398 1.717150064 2.041317813 0.059890878 13.43106896 -1.128110579 2.139243761 ASTVS(ph)PGGYMVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASTVSPGGYMVPK 13 0 Q5TGY3 Q5TGY3 AHDC1 AT-hook DNA-binding motif-containing protein 1 1 ASTVS(1)PGGYMVPK 184.32 3.75E-07 0 262150 213280 119530 173070 203690 174480 220480 264220 236110 TRUE FALSE 227506.2133 211878.9496 177335.1078 212368.1887 199636.9675 181192.3585 199097.8835 207718.6092 208197.3448 1.092743106 1.017683246 0.851764503 1.020033127 0.95888335 0.870291399 0.956294057 0.997700568 1 17.66759214 4.47490873 24.99977693 0.953741633 1.073978178 0.425155538 0.053970298 55.70608632 629444.888 0.013426113 0.036050421 29847.55283 -4.47490873 0.120236544 ASVALT(ph)PTAPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASVALTPTAPSR 12 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7;H7BZ26 E9PHV5 SSFA2 Sperm-specific antigen 2 1 ASVALT(0.968)PT(0.032)APSR;ASVALT(0.976)PT(0.024)APSR 170.22 0.00041845 322650000 790030 732910 503260 532950 660340 743580 663490 749970 709560 TRUE FALSE 685625.5338 728095.466 746638.2193 653964.4431 647200.5259 772186.0038 599144.8419 589594.7518 625676.6251 1.095814525 1.163692931 1.193329252 1.045211563 1.034400999 1.234161503 0.957595054 0.942331435 1 19.25505768 2.211525903 24.94391796 0.961200328 1.124384862 0.593839375 0.062721251 143.4647531 132368.4733 0.025656166 0.01730254 162.7518384 -2.211525903 0.163184535 ASVAVSSFEHAGPSLPGLS(ph)PGACSLPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASVAVSSFEHAGPSLPGLSPGACSLPAR 28 0 Q8TER5;Q8TER5-2 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 ASVAVSSFEHAGPSLPGLS(0.999)PGACSLPAR;ASVAVSSFEHAGPS(0.023)LPGLS(0.977)PGACSLPAR 181.85 8.69E-18 597390000 227652 216395 91714 192782 289140 315310 250210 341270 242768 TRUE FALSE 197567.2114 214973.487 136067.1972 236556.0996 283386.6797 327440.1797 225944.6727 268292.0663 214068.2436 0.922916954 1.004228761 0.635625326 1.105049939 1.323814663 1.529606513 1.05547964 1.253301572 1 17.70771127 3.508756684 8.101647088 1.234881353 0.868639559 0.509094663 0.169350089 0.225611581 51.80831 0.046767093 0.067839394 3226.685843 -3.508756684 -0.366241794 ASVITQVFHVPLEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASVITQVFHVPLEER 15 0 Q00341;A0A024R4E5;Q00341-2;C9JIZ1;C9JZI8;C9J5E5;C9JHZ8;C9JES8;C9JK79;C9JHS7;C9JT62 Q00341 HDLBP Vigilin 0 ;;; 159.14 1.78E-06 1744201000 1454313 1364540 945769 934326 1178886 1253750 1308886 1450838 1264129 FALSE TRUE 1262121.852 1355576.247 1403146.052 1146478.999 1155428.475 1301982.574 1181950.437 1140587.584 1114685.11 1.132267616 1.216106894 1.258782449 1.028522754 1.036551457 1.168027241 1.06034469 1.023237481 1 20.08820479 3.731647182 24.90605083 1.054301676 1.203757779 0.631099556 0.053907706 333.2635342 1200602.727 0.015397592 0.023416551 5390.725058 -3.731647182 0.149456103 ASVLDTSMSAGSGS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASVLDTSMSAGSGSPSK 17 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 ASVLDTSMSAGS(0.029)GS(0.971)PSK;ASVLDTSMSAGSGS(0.999)PS(0.001)K;ASVLDTSMSAGSGS(0.999)PS(0.001)K 383.79 1.12E-121 519180000 678200 645420 477742 574210 655800 552880 718510 872040 844400 TRUE FALSE 588574.1517 641180.1935 708779.6292 704593.1568 642750.8631 574149.6514 648829.0108 685561.0322 744575.9939 0.79048231 0.861134657 0.951923826 0.9463012 0.863244139 0.771109539 0.871407373 0.920740177 1 19.50605958 1.390425456 2.395145632 1.010734149 0.868118041 0.373304745 0.056507955 0.508089389 4.152730121 0.134191825 0.016413628 24.57114847 -1.390425456 -0.142616108 ASVSGPNS(ph)PSESRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASVSGPNSPSESRR 14 1 A6PVI4;Q9UJV3-2;Q9UJV3 A6PVI4 MID2 Probable E3 ubiquitin-protein ligase MID2 1 AS(0.002)VS(0.002)GPNS(0.968)PS(0.027)ES(0.001)RR;ASVSGPNS(0.999)PS(0.001)ESRR;ASVSGPNS(0.993)PS(0.007)ESRR 160.81 2.88E-06 422136000 313514 322770 208623 222017 330430 308791 341298 363849 249314 TRUE FALSE 272082.3306 320649.7026 309513.7806 272429.3532 323855.0895 320670.3896 308198.9725 286042.7228 219840.3829 1.237635811 1.458556878 1.407902299 1.239214331 1.473137397 1.458650978 1.401921559 1.301138212 1 17.7460969 1.227733729 2.530314111 0.897961997 1.38656363 0.671971905 0.083502439 0.314843457 2.161695629 0.34018192 0.021395163 16.8940482 -1.227733729 0.488601633 ASVSQTSPQS(ph)ASSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASVSQTSPQSASSPR 15 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 ASVSQTS(0.008)PQS(0.478)AS(0.456)S(0.058)PR 213.56 3.28E-10 220220000 331580 292680 227170 249500 333470 315850 343510 395730 333090 TRUE FALSE 287760.8629 290757.3658 337030.1718 306152.7884 326834.5994 328000.9539 310196.4531 311106.2191 293712.4797 0.979736589 0.989938753 1.147483322 1.042355397 1.112770556 1.116741632 1.056122823 1.059220294 1 18.16404504 4.363762886 9.492052045 1.075235959 0.982414764 0.45382903 0.041801987 0.234728096 18.26477025 0.010231866 0.027150395 23108.02805 -4.363762886 -0.092821195 ASVSQTSPQSAS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASVSQTSPQSASSPR 15 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 ASVSQT(0.009)S(0.116)PQS(0.116)AS(0.643)S(0.116)PR 111.37 0.00088902 127550000 171860 157700 110800 129360 182200 176280 173220 196830 203280 TRUE FALSE 149148.2656 156664.0583 164383.2506 158733.1651 178574.5765 183061.6057 156421.1511 154739.4362 179248.47 0.832075529 0.874004996 0.917069198 0.885548229 0.99624045 1.021272905 0.872649853 0.863267822 1 17.45160128 4.466374992 1.280845826 0.933680173 0.813827746 0.313232771 0.054507633 1.331133459 2.727733111 0.017936368 0.185526424 29266.78333 -4.466374992 -0.119852427 ASYDDPYKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASYDDPYKK 9 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 90.906 0.01782 239580000 1162300 807970 673070 738220 699930 548900 1086400 1212400 1004300 FALSE TRUE 1008699.11 802662.3919 998568.9033 905844.134 686002.7624 570016.5382 981041.0952 953137.6949 885572.7981 1.139035788 0.906376521 1.127596631 1.022890649 0.774642992 0.643669882 1.107804008 1.076295136 1 19.75625138 7.999991443 0.998809938 0.958308734 160.6680979 0.112598798 0.152408384 5409.683249 7.103821959 0.050411823 1977560.231 99998029.77 -7.999991443 159.7097891 ASYDTLCVLDGDKDSVNCAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASYDTLCVLDGDKDSVNCAR 20 1 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 ; 133.26 1.01E-05 449720000 283520 254200 172732 198105 250053 228217 298600 321850 293220 FALSE TRUE 246052.1137 252530.1435 256265.773 243087.7681 245077.4345 236996.6557 269641.818 253024.8821 258555.8656 0.951640037 0.976694699 0.991142755 0.940175028 0.947870333 0.916616821 1.042876429 0.978608169 1 17.98011651 2.239272583 24.99999985 1.00270103 0.955831905 0.492053704 0.025271555 18.01194219 632514.5659 0.009984983 0.007272139 173.4892554 -2.239272583 -0.046869125 ASYHFSPEELDENT(ph)SPLLGDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.684)S(0.316)PLLGDAR 143.9 3.83E-07 203290000 20220 22451 14509 23542 31860 35204 33600 27033 32863 TRUE FALSE 17547.87577 22303.5179 21525.60093 28887.57092 31226.04833 36558.32066 30341.47717 21252.20332 28977.97358 0.605559106 0.769671414 0.742826301 0.996880297 1.077578743 1.261589965 1.047053104 0.733391632 1 14.82266909 3.784371948 3.486425104 1.005601438 0.700670375 0.550846687 0.13355725 0.231730946 5.795745441 0.04316643 0.077130174 6086.560573 -3.784371948 -0.304931063 ASYHFSPEELDENTS(ph)PLLGDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASYHFSPEELDENTSPLLGDAR 22 0 O75410-3;E7ET87;E7EVI4;O75410-2;O75410;O75410-9;O75410-7;H0YAY0;E5RFM9;R4GMT7;E5RJU4 O75410-3 TACC1 Transforming acidic coiled-coil-containing protein 1 1 ASYHFSPEELDENT(0.405)S(0.595)PLLGDAR;ASYHFSPEELDENT(0.002)S(0.998)PLLGDAR;ASYHFSPEELDENT(0.291)S(0.709)PLLGDAR 310.9 2.20E-67 529670000 160506 239228 88839 192599 325652 370130 334440 335310 360510 TRUE FALSE 139294.7254 237656.4955 131801.8375 236331.5466 319172.1623 384369.1406 302006.0603 263606.5659 317890.9185 0.438184035 0.747603916 0.414613409 0.74343598 1.004030451 1.209122747 0.950030475 0.829235913 1 18.27817228 3.424495619 3.729493228 0.982957225 0.555398448 0.73177009 0.128691056 0.127650407 3.673296611 0.03950846 0.053668496 2657.63674 -3.424495619 -0.427558777 ASYNNPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ASYNNPHR 8 0 P54725-2;P54725;A0A494C0B4;K7ELU6;P54725-3 P54725-2;P54725-3 RAD23A UV excision repair protein RAD23 homolog A 0 ;;; 155.1 0.00041434 995470000 1426050 1519400 840390 1026060 1297960 1538890 1326910 1519270 1361630 FALSE TRUE 1237593.879 1509418.961 1246805.415 1259042.605 1272133.135 1598092.094 1198226.472 1194385.933 1200659.653 1.030761612 1.257158062 1.038433675 1.048625731 1.059528512 1.331011741 0.997973464 0.994774773 1 20.19539582 2.077052503 25 0.996762545 1.126220781 0.281171077 0.097971829 42.8650147 13905.77008 0.038811711 0.026166847 119.4132457 -2.077052503 0.129458236 ASYPCMSLHGGIDQYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASYPCMSLHGGIDQYDR 17 0 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ; 208.43 5.18E-12 758520000 380110 362450 149957 285000 349960 436050 326490 382780 580380 FALSE TRUE 329877.5004 360069.0421 222476.7068 349713.606 342996.4807 452825.1257 294827.0501 300925.4758 511768.1376 0.644583897 0.703578468 0.434721684 0.683343843 0.670218514 0.884824772 0.57609497 0.588011355 1 18.9651308 3.495486672 23.58223381 0.715000353 0.597524675 0.167647577 0.144321496 781.892763 1003991.468 0.039975073 0.057970454 3129.584428 -3.495486672 -0.117475678 AT(ph)NESEDEIPQLVPIGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATNESEDEIPQLVPIGK 17 0 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 AT(0.5)NES(0.5)EDEIPQLVPIGK;AT(0.5)NES(0.5)EDEIPQLVPIGK 140.97 2.36E-06 448760000 1230130 1048420 710990 800160 1056060 776040 1066910 1377740 1167460 TRUE FALSE 1067565.204 1041532.86 1054827.142 981848.5577 1035046.472 805894.761 963441.2324 1083121.023 1029444.209 1.037030657 1.011742891 1.02465693 0.953765682 1.005442027 0.782844523 0.935884844 1.052141547 1 19.97343421 3.7406196 23.89625073 0.958862647 1.02320344 0.177038718 0.070256563 208.4688382 2419417.142 0.020633188 0.033528955 5503.254535 -3.7406196 0.064340793 AT(ph)PARAS(ph)S(ph)FLIENLLAAEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATPARASSFLIENLLAAEAK 20 1 F1T0J4;Q9NP08 F1T0J4 HMX1 Homeobox protein HMX1 3 AT(1)PARAS(1)S(1)FLIENLLAAEAK;AT(1)PARAS(1)S(1)FLIENLLAAEAK 68.82 0.01725 385690000 783830 746840 1453910 844930 187892 668750 388340 419010 448390 TRUE FALSE 680244.8795 741933.9589 2157025.739 1036784.27 184153.3168 694477.2452 350678.8466 329407.9722 395381.845 1.720475758 1.876499815 5.455550795 2.6222354 0.46576068 1.756472266 0.886937149 0.833138841 1 18.5928871 3.342748533 5.693410577 1.005832044 3.075316407 0.457441577 1.048109732 0.18780018 8.834408079 0.308305406 0.398711001 2201.651286 -3.342748533 2.069484363 AT(ph)SGSSLPVGINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATSGSSLPVGINR 13 0 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 AT(0.821)S(0.179)GSSLPVGINR 207.42 6.04E-07 227590000 362090 342180 208510 251430 381680 337970 335320 370900 360640 TRUE FALSE 314238.8891 339932.197 309346.1334 308521.0244 374085.3147 350971.9246 302800.718 291585.9213 318005.55 0.988155361 1.068950517 0.972769605 0.970174968 1.176348384 1.103666035 0.952186897 0.916920857 1 18.27869242 2.176575975 10.43494607 0.947724766 1.04671163 0.292072127 0.065825835 0.560108763 90.9452274 0.028260441 0.019058215 150.1675085 -2.176575975 0.098986864 AT(ph)SNVFAMFDQSQIQEFK ddPTM_MDA-MB-175_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(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.572)S(0.428)NVFAMFDQSQIQEFK 225.6 1.46E-18 2651026000 4693630 5625300 2574450 3256939 3340041 3103903 3385200 4193232 6050780 TRUE FALSE 4073354.903 5588347.034 3819462.631 3996476.779 3273580.719 3223312.157 3056903.825 3296541.969 5335463.681 0.763449092 1.047396696 0.715863299 0.749040199 0.613551308 0.604129716 0.572940612 0.617854823 1 22.34718222 4.091482611 7.177100236 0.675234583 0.904233113 0.276716523 0.139030022 0.2468753 16.46692376 0.034711517 0.073094582 12344.75887 -4.091482611 0.22899853 AT(ph)SPSSSVSGDFDDGHHSVSTPGPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(0.448)S(0.448)PS(0.103)S(0.001)SVSGDFDDGHHSVSTPGPSR;AT(0.518)S(0.409)PS(0.073)SSVSGDFDDGHHSVSTPGPSR;AT(0.545)S(0.452)PS(0.003)SSVSGDFDDGHHSVSTPGPSR;AT(0.481)S(0.481)PS(0.038)S(0.001)SVSGDFDDGHHSVSTPGPSR;AT(0.448)S(0.448)PS(0.103)S(0.001)SVSGDFDDGHHSVSTPGPSR 201.1 9.49E-25 2489240000 307336 249491 77836.4 172066 279917 263605 214653 263706 314413 TRUE FALSE 266720.7689 247852.0772 115478.3434 211136.2152 274347.1993 273746.0549 193835.9851 207314.5241 277243.4533 0.962045328 0.893987123 0.416523247 0.761555278 0.989553391 0.9873851 0.699154417 0.747770674 1 18.08079387 3.449835811 24.84358826 0.860374716 0.740810996 0.105325769 0.172741214 516.2893343 470083.1826 0.052465931 0.067734625 2817.317619 -3.449835811 -0.119563719 ATAAFILANEHNVALFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATAAFILANEHNVALFK 17 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 151.04 2.65E-07 23230000 81972 80234 54764 54623 76375 78437 89306 100260 68339 FALSE TRUE 71139.19251 79706.93757 81248.05357 67025.98701 74855.28693 81454.52215 80645.11787 78820.17922 60260.04127 1.180536737 1.322716279 1.348290706 1.112279142 1.242204375 1.351716999 1.338285142 1.308000751 1 15.87891404 1.235068665 24.99780132 0.999999607 1.279960221 0.549147245 0.078359378 79.59409605 569698.6394 0.138821491 0.019496084 17.18180024 -1.235068665 0.279960614 ATAGDTHLGGEDFDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 ATAGDTHLGGEDFDNR 16 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931;P17066;P48741 A0A0G2JIW1;Q53FA3;P17066 HSPA1B;HSPA1A;HSPA1L;HSPA6;HSPA7 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like;Heat shock 70 kDa protein 6;Putative heat shock 70 kDa protein 7 0 ;;;;;;;;;; 228.49 4.06E-15 1.32251E+11 65700683.3 61251009.7 40339092.2 48368738.8 58908881 65627421.1 60066727.8 67800033.3 64936037 FALSE TRUE 57018171.54 60848647.78 59847212.11 59351600.21 57736709.52 68152150.46 54241465.78 53301523.8 57259372.68 0.995787569 1.062684499 1.045195036 1.036539477 1.008336397 1.190235716 0.947294098 0.930878585 1 25.77100853 ATAPAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ATAPASPR 8 0 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 ATAPAS(1)PR;ATAPAS(1)PR;ATAPAS(1)PR 138.23 0.00074907 6404020000 5826260 5763150 3703580 4633680 4421740 6249890 4595900 5927940 5634340 TRUE FALSE 5056304.979 5725291.488 5494643.676 5685827.865 4333756.025 6490327.313 4150190.325 4660296.162 4968254.744 1.017722569 1.152374784 1.105950471 1.144431628 0.872289415 1.306359607 0.835341692 0.938014736 1 22.24430772 2.206570629 24.99999964 0.92356477 1.094201763 0.338279761 0.115462815 212.8218839 166317.7163 0.043618432 0.029410304 160.9054036 -2.206570629 0.170636994 ATAPQTQHVS(ph)PMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 28 ATAPQTQHVSPMR 13 0 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;E9PPR1;E9PL12;E9PK06;P29692-3;E9PL71 P29692;P29692-3 EEF1D Elongation factor 1-delta 1 ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQT(0.001)QHVS(0.999)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR 223.61 1.63E-11 97146138900 24854863 22785506 15168091 17141199.1 21199284.3 23977030.6 20877513.6 23222033.2 22564794 TRUE FALSE 21570229.88 22635826.51 22503430.54 21033370.34 20777460.02 24899442.48 18852815.54 18256182.11 19897209.76 1.084083152 1.137638231 1.130984234 1.057101503 1.044239884 1.251403729 0.947510519 0.917524735 1 24.2460628 2.195014452 24.14233858 0.946888858 1.113014329 0.61809518 0.060053213 58.51119368 32438.4728 0.023664054 0.015954465 156.6803208 -2.195014452 0.166125471 ATAPQTQHVSPMR ddPTM_MDA-MB-175_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 ;;;;;;; 179.39 1.38E-05 2039170000 1450493 1733153 646877 894492 2126558 2199561 1554078 1836989 1712490 FALSE TRUE 1258806.675 1721767.804 959708.8809 1097600.08 2084243.656 2284179.535 1403363.755 1444163.198 1510041.383 0.833623958 1.14021233 0.635551377 0.72686755 1.380255985 1.512660223 0.9293545 0.956373258 1 20.52615666 3.255888461 24.99999795 1.131677907 0.841752084 0.339722023 0.221310783 350.6334186 505878.4929 0.070237724 0.090456643 1802.554734 -3.255888461 -0.289925823 ATAVMPDGQFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATAVMPDGQFK 11 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 118.18 0.0022465 0 237240 206800 123130 163800 182510 170380 211430 233740 258370 FALSE TRUE 205888.1329 205441.5172 182676.0798 200993.2935 178878.4081 176934.6289 190925.5511 183756.52 227825.7929 0.90370862 0.901748281 0.801823523 0.88222361 0.785154331 0.776622465 0.838033081 0.806565919 1 17.79757156 4.258847415 24.16774533 0.83531192 0.902728576 0.130041199 0.064325768 298.5898319 355702.1034 0.015371458 0.040544955 18148.77913 -4.258847415 0.067416656 ATCAPQHGAPGPGPADASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATCAPQHGAPGPGPADASK 19 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 76.027 0.013562 33879000 33390 27503 16310 21174 25109 21167 26031 30040 32216 FALSE TRUE 28977.4269 27322.33098 24197.57055 25981.88032 24609.38002 21981.30819 23506.51763 23616.17977 28407.46118 1.020063944 0.961801226 0.851803348 0.914614656 0.866299873 0.773786438 0.82747689 0.831337219 1 14.79398228 4.594562712 1.23862245 0.855068305 1.076830041 0.420568991 0.060843956 1.060598048 1.704590679 0.018196584 0.282394534 39315.40121 -4.594562712 0.221761737 ATCIS(ph)PGVVETQFAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATCISPGVVETQFAFK 16 0 A0A087WZN3;Q6UWP2-2;Q6UWP2 A0A087WZN3 DHRS11 Dehydrogenase/reductase SDR family member 11 1 ATCIS(1)PGVVETQFAFK;ATCIS(1)PGVVETQFAFK 266.28 3.73E-27 95775000 206430 207270 127907 145092 177652 147449 183101 206516 221420 TRUE FALSE 179149.7525 205908.4297 189763.253 178037.3562 174117.0728 153121.4584 165343.8932 162354.1605 195243.9798 0.917568637 1.054621146 0.971928831 0.911871169 0.891792274 0.784257003 0.846857831 0.831545027 1 17.57491854 3.525826525 2.050546755 0.859016185 0.990627552 0.379699202 0.063849334 0.297060721 2.483018672 0.019407796 0.031406154 3356.03534 -3.525826525 0.131611366 ATDCVGHDVVTLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ATDCVGHDVVTLLR 14 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;;;; 195.87 2.56E-08 5107400000 7058090 6152070 3791540 5317670 5902700 7042780 4818540 6380600 6464090 FALSE TRUE 6125345.524 6111656.647 5625141.426 6525128.249 5785247.818 7313720.304 4351238.732 5016158.344 5699912.644 1.074638491 1.072236897 0.986882041 1.144776886 1.014971313 1.28312849 0.763386916 0.880041267 1 22.44250838 2.224441215 24.99999965 0.876006783 1.088580461 0.518882304 0.097355777 180.0823953 318853.7613 0.037845559 0.025654149 167.6645376 -2.224441215 0.212573678 ATDDYHYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATDDYHYEK 9 0 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 0 79.148 0.023826 0 390180 384340 201700 258770 343200 336790 386920 440870 337210 FALSE TRUE 338616.7244 381815.2452 299242.7946 317527.6836 336370.9915 349746.5292 349396.558 346593.3814 297345.418 1.138799201 1.284079801 1.006381052 1.067874816 1.131246595 1.176229759 1.175052773 1.165625432 1 18.18178032 4.25216436 24.99782049 1.114972314 1.211439444 0.264516484 0.073010552 353.9566642 650408.0692 0.018442248 0.04820965 17871.63805 -4.25216436 0.09646713 ATDFVADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ATDFVADR 8 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;; 125.53 0.0029268 1083670000 1480510 1718340 1237350 1946200 1926400 2101690 1472560 1802040 2026970 FALSE TRUE 1284856.852 1707052.111 1835736.599 2388114.456 1888068.409 2182543.374 1329751.358 1416687.769 1787343.916 0.718863807 0.955077585 1.027075194 1.336124757 1.056354288 1.221109913 0.743981808 0.79262181 1 20.76938583 2.226802586 24.99997672 0.830279678 1.059929488 0.2396533 0.172673556 301.132004 640262.7993 0.072587656 0.049387281 168.5786556 -2.226802586 0.22964981 ATDGAPADAPVGVLGRPFPTPS(ph)PASLDVYVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATDGAPADAPVGVLGRPFPTPSPASLDVYVAR 32 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 ATDGAPADAPVGVLGRPFPT(0.012)PS(0.976)PAS(0.012)LDVYVAR 145.31 2.90E-10 191380000 75036 89284 56381 45241 74365 82111 71806 93586 37132 TRUE FALSE 65119.80248 88697.48753 83647.04018 55513.66052 72885.28199 85269.8633 64842.26517 73573.36219 32742.29726 1.988858691 2.708957372 2.55470896 1.695472375 2.226028351 2.604272468 1.980382276 2.247043376 1 14.99886793 1.235736739 6.575940581 0.964359901 2.256937248 0.612648045 0.312461045 0.085498557 17.54701198 0.48837573 0.076438916 17.20825127 -1.235736739 1.292577347 ATDIPASAS(ph)PPPVAGVPFFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ATDIPASASPPPVAGVPFFK 20 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 ATDIPASAS(1)PPPVAGVPFFK;ATDIPASAS(1)PPPVAGVPFFK;ATDIPAS(0.027)AS(0.973)PPPVAGVPFFK;ATDIPASAS(1)PPPVAGVPFFK;ATDIPAS(0.001)AS(0.999)PPPVAGVPFFK;ATDIPAS(0.002)AS(0.998)PPPVAGVPFFK 255.93 3.76E-36 3137856000 4391550 3894970 2570200 3547660 3933510 3500550 4045630 5169300 4835170 TRUE FALSE 3811195.541 3869383.686 3813157.317 4353210.426 3855240.847 3635218.424 3653285.425 4063885.423 4263561.711 0.893899467 0.907547245 0.894359593 1.021026719 0.904230103 0.852624794 0.856862331 0.953166788 1 22.02362771 1.485848557 4.649219625 0.992302201 0.906380148 0.324472124 0.045821655 0.216939498 9.707290209 0.041933201 0.012452776 30.60895879 -1.485848557 -0.085922052 ATDLRPIYISVQPPSLHVLEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATDLRPIYISVQPPSLHVLEQR 22 1 B1ANH0;B1ANG9;Q16774;Q16774-2;B1ANH2;Q16774-3;B1ANH5;B1ANH3 B1ANH0 GUK1 Guanylate kinase 0 ; 184.2 2.40E-17 1260840000 684360 610650 272630 448700 644850 639700 589380 707200 604490 FALSE TRUE 593920.0921 606638.5999 404474.7799 550584.193 632018.7466 664309.6729 532222.0183 555970.7834 533027.8808 1.114238323 1.138099191 0.758824809 1.032936949 1.185714236 1.246294419 0.998488142 1.043042594 1 19.02385147 ATDSDLSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATDSDLSSPR 10 0 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 1 ATDSDLS(0.002)S(0.998)PR;ATDSDLS(0.233)S(0.767)PR 124.06 0.00046738 544200000 980490 836200 450290 593070 718800 777190 730840 854680 759330 TRUE FALSE 850915.7623 830706.9471 668051.7501 727735.608 704497.2863 807089.0022 659963.2493 671913.3331 669562.8724 1.270852667 1.240670565 0.997743121 1.086881663 1.052174957 1.205396887 0.98566285 1.003510441 1 19.35286001 8 0.493859559 1.027050914 9.255256843 0.532804393 0.073836722 88.29420722 0.984272375 0.047633099 749.4465088 99999999.96 -8 8.228205929 ATEDGEEDEEMIESIENLEDLKGHSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATEDGEEDEEMIESIENLEDLKGHSVR 27 1 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 221.6 1.52E-34 42613000 76495 67714 41625 39448 61820 49086 71411 90515 18759 FALSE TRUE 66385.99194 67269.18228 61754.98923 48405.27132 60589.90295 50974.37018 64485.57221 71159.07164 16541.33239 4.013340061 4.066732999 3.733374541 2.926322389 3.662939691 3.08163629 3.898450904 4.301894791 1 14.01378783 1.23090194 24.99997217 0.999995145 3.71330001 0.801548943 0.423862896 131.7643734 430077.9241 1.165892616 0.11201562 17.01774217 -1.23090194 2.713304865 ATEEDHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATEEDHER 8 0 G8JLD3;X6RLX0;Q8IUD2-3;Q8IUD2;Q8IUD2-2;X6RM00;Q8IUD2-4;K7EPP6 G8JLD3 ERC1 ELKS/Rab6-interacting/CAST family member 1 0 93.551 0.010989 30645000 6701.1 7879.2 2796.2 6751.1 4838 7665 7165.3 7279.5 7632.8 FALSE TRUE 5815.532657 7827.441016 4148.451673 8284.040439 4741.733265 7959.87751 6470.410309 5722.835574 6730.459079 0.86406181 1.162987684 0.616369793 1.230828439 0.704518549 1.18266487 0.961362402 0.850289038 1 12.7164892 ATEETGQAQSGQANCQGLS(ph)PVSVASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATEETGQAQSGQANCQGLSPVSVASK 26 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 ATEETGQAQSGQANCQGLS(1)PVSVASK;ATEETGQAQSGQANCQGLS(1)PVSVASK 286.26 1.70E-61 610620000 769410 748070 488550 647630 763350 614300 837370 1010220 925850 TRUE FALSE 667730.5191 743155.8789 724814.4141 794684.2899 748160.8285 637932.5185 756161.9863 794192.3145 816397.0677 0.817899213 0.910287296 0.887820942 0.973404145 0.916417829 0.781399816 0.926218401 0.972801528 1 19.63891148 1.785638322 3.201292437 0.989792584 0.8869278 0.389576218 0.053295968 0.247095694 4.834641303 0.037195425 0.014780317 61.04334482 -1.785638322 -0.102864785 ATENDIYNFFS(ph)PLNPVR ddPTM_MDA-MB-175_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;ATENDIY(0.007)NFFS(0.993)PLNPVR;ATENDIYNFFS(1)PLNPVR;ATENDIYNFFS(1)PLNPVR;ATENDIYNFFS(1)PLNPVR 253.48 5.42E-27 514299000 499418 420192 293635 340739 382613 390263 365294 437177 497883 TRUE FALSE 433418.6459 417431.7311 435637.8682 418108.9978 374999.7499 405276.6701 329867.8441 343690.1007 439023.8389 0.9872326 0.950817915 0.992287501 0.95236058 0.85416717 0.923131352 0.751366588 0.782850657 1 18.74393975 3.174394319 1.561927777 0.838140161 0.977704438 0.34605632 0.070763394 0.377461076 1.925234193 0.026535349 0.033763785 1494.150414 -3.174394319 0.139564277 ATENDIYNFFSPLNPMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATENDIYNFFSPLNPMR 17 0 P55795 P55795 HNRNPH2 Heterogeneous nuclear ribonucleoprotein H2 0 162.37 6.63E-09 58069000 69253 53717 49437 54505 75212 75117 67875 70117 63362 FALSE TRUE 60101.04059 53364.12949 73344.89856 66881.19331 73715.42835 78006.7996 61292.49295 55123.0252 55871.41654 1.075702825 0.955123976 1.312744568 1.197055622 1.319376399 1.39618439 1.097027724 0.986605112 1 15.76982278 2.004019849 24.99291289 1.007186943 1.210253178 0.340340656 0.125089712 133.2471546 828442.6371 0.055415497 0.037183834 100.9299015 -2.004019849 0.203066235 ATENDIYNFFSPLNPVR ddPTM_MDA-MB-175_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 ; 198.48 3.29E-11 283000000 182013 146716 83652 140900 152481 141841 141686 159658 212391 FALSE TRUE 157959.5209 145752.2129 124106.387 172893.4985 149446.9264 147297.7151 127945.3135 125516.3792 187282.3779 0.843429706 0.77824841 0.662669859 0.923170137 0.797976446 0.786500666 0.683167925 0.670198555 1 17.51485563 2.459060118 24.93825107 0.753346314 0.798252478 0 0.110103429 994.2035095 1372755.514 0.040609286 0.031461141 287.7796749 -2.459060118 0.044906164 ATEVS(ph)KTPEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATEVSKTPEAR 11 1 Q5H909;Q9UNF1-2;Q9UNF1 Q5H909 MAGED2 Melanoma-associated antigen D2 1 AT(0.003)EVS(0.563)KT(0.434)PEAR 88.075 0.0080238 316600000 247500 233520 172450 179510 244230 218090 252460 294990 260380 TRUE FALSE 214792.2479 231985.9917 255847.3968 220270.4891 239370.3008 226480.0634 227976.4681 231908.6841 229598.173 0.93551375 1.01039999 1.114326797 0.959373876 1.042561871 0.986419275 0.992936769 1.010063282 1 17.80875164 2.680400073 24.98656738 0.998926344 1.015035312 0.022155165 0.047583097 1306.123762 561126.9133 0.016047797 0.014152827 479.0712109 -2.680400073 0.016108968 ATEVSKT(ph)PEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATEVSKTPEAR 11 1 Q5H909;Q9UNF1-2;Q9UNF1 Q5H909 MAGED2 Melanoma-associated antigen D2 1 ATEVS(0.092)KT(0.908)PEAR 118.52 0.0011464 285280000 482820 469490 277560 366430 500070 375460 489440 636850 461040 TRUE FALSE 419014.1137 466405.8893 411788.9444 449633.532 490119.5854 389904.1892 441974.1841 500664.5835 406536.3764 1.030692794 1.147267296 1.01292029 1.106010576 1.205598352 0.959088071 1.087170078 1.231536985 1 18.63302492 8 0.373923928 1.111717815 0.372586611 0.004707882 0.088945203 390.5942756 5.754672228 0.100898577 206.1437944 100000000 -8 -0.739131204 ATFMVGS(ph)YGPRPEEYEFLTPVEEAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ATFMVGSYGPRPEEYEFLTPVEEAPK 26 1 P52566;H0YGX7 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 1 ATFMVGS(1)YGPRPEEYEFLTPVEEAPK;AT(0.015)FMVGS(0.985)YGPRPEEYEFLTPVEEAPK;AT(0.131)FMVGS(0.869)YGPRPEEYEFLTPVEEAPK;AT(0.019)FMVGS(0.981)YGPRPEEYEFLTPVEEAPK;ATFMVGS(1)YGPRPEEYEFLTPVEEAPK;ATFMVGS(1)YGPRPEEYEFLTPVEEAPK;ATFMVGS(1)YGPRPEEYEFLTPVEEAPK 284.98 2.33E-61 806036000 803945 788231 551251 660859 753715 627850 921783 1076878 945678 TRUE FALSE 697701.6313 783053.0587 817837.8274 810917.1365 738717.5461 652003.7958 832388.6265 846596.02 833881.0242 0.836692059 0.939046502 0.980760808 0.972461434 0.88587883 0.781890674 0.998210299 1.015247974 1 19.66948203 2.03872419 24.99299076 1.008118236 0.906184921 0.406953868 0.059480545 163.7090699 105658.8518 0.025648443 0.01729214 109.326184 -2.03872419 -0.101933315 ATFMVGSYGPRPEEYEFLTPVEEAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ATFMVGSYGPRPEEYEFLTPVEEAPK 26 1 P52566;H0YGX7 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ;;;; 242.73 3.24E-45 1886164000 1348939 1370455 958902 1096520 1239423 974054 1489941 1807776 1491975 FALSE TRUE 1170673.293 1361452.391 1422630.215 1345501.625 1214760.907 1011526.488 1345446.751 1421197.171 1315595.415 0.889842941 1.034856442 1.081358447 1.022732072 0.92335447 0.768873528 1.022690362 1.080269173 1 20.32728445 2.016334898 24.99350882 1.047551692 0.959038307 0.155732775 0.088394996 436.8027125 668335.6187 0.03894936 0.026253216 103.8328795 -2.016334898 -0.088513385 ATFYGEQVDYYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATFYGEQVDYYK 12 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 202.16 3.26E-07 384520000 819280 785540 521080 662180 769850 664440 851410 988860 906150 FALSE TRUE 711010.0722 780379.736 773076.0309 812538.0898 754531.4912 690001.4367 768840.3892 777399.9843 799025.9793 0.889846001 0.976663783 0.967523023 1.016910727 0.944314091 0.863553194 0.962222017 0.972934553 1 19.60788289 1.561435177 2.603054763 0.996897495 0.947374197 0.149019036 0.043026865 0.587718117 8.253706293 0.053020823 0.012104975 36.42798735 -1.561435177 -0.049523298 ATGDGSS(ph)PELPSLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATGDGSSPELPSLER 15 0 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2;H3BS99 H3BSS6 ZNF106 Zinc finger protein 106 1 ATGDGS(0.036)S(0.964)PELPSLER;ATGDGS(0.024)S(0.976)PELPSLER 228.73 5.84E-13 140643000 283910 246040 178804 208204 235370 246190 233230 266050 270060 TRUE FALSE 246390.5742 244423.747 265274.2125 255479.9004 230686.5975 255661.0886 210611.3905 209157.2779 238133.8145 1.034672773 1.026413437 1.113971206 1.072841759 0.968726756 1.073602626 0.884424545 0.878318261 1 17.86141297 2.23864658 24.99999998 0.91051968 1.047847228 0.590799145 0.049752835 1.445401948 420524.1981 0.019504919 0.014131496 173.2393639 -2.23864658 0.137327548 ATGDWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ATGDWK 6 0 P30050 P30050 RPL12 60S ribosomal protein L12 0 ;;; 126.24 0.040887 1861120000 4219010 3498490 2549460 3123490 2564930 2899350 4034010 4657970 4189110 FALSE TRUE 3661457.139 3475508.189 3782387.383 3832726.144 2513892.911 3010889.871 3642792.331 3661899.364 3693878.188 0.991223032 0.94088327 1.023961049 1.037588667 0.680556527 0.815102642 0.98617013 0.991342751 1 21.81670486 ATGEPGTFVCTSHLPAAASAS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ATGEPGTFVCTSHLPAAASASPK 23 0 Q8IY33;Q8IY33-4;Q8IY33-2 Q8IY33 MICALL2 MICAL-like protein 2 1 ATGEPGTFVCTSHLPAAASAS(1)PK;ATGEPGTFVCTSHLPAAAS(0.002)AS(0.998)PK;ATGEPGTFVCTSHLPAAASAS(1)PK;ATGEPGTFVCTSHLPAAAS(0.04)AS(0.96)PK 237.33 2.44E-37 3647050000 3780670 3045550 2353870 2410230 3416060 2813120 3592720 4244490 3840770 TRUE FALSE 3281044.881 3025543.582 3492209.405 2957509.56 3348087.089 2921342.547 3244298.567 3336838.844 3386718.546 0.968797624 0.893355483 1.031148399 0.873267004 0.988593249 0.862587932 0.957947501 0.985271967 1 21.69145667 1.780390668 3.419536736 0.994192138 0.936628306 0.161406324 0.051945469 0.366347384 8.256854623 0.031565881 0.012814012 60.31018607 -1.780390668 -0.057563832 ATGGGYESDDAYHNAELFFLDIHNIHVMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATGGGYESDDAYHNAELFFLDIHNIHVMR 29 0 Q13496-2;Q13496 Q13496-2 MTM1 Myotubularin 0 ; 206.88 6.33E-26 71037000 40606 36694 22856.6 27212.3 35252 37229 38791 38845 42129 FALSE TRUE 35239.81422 36452.9547 33910.12821 33391.26863 34550.55417 38661.22372 35029.05479 30538.29904 37148.55761 0.94861864 0.981275103 0.912824895 0.898857742 0.930064487 1.040719377 0.942945219 0.822058809 1 15.18101858 1.969616375 24.52377077 0.893574114 0.951823654 0.060014763 0.057755009 955.3790625 771120.1217 0.026216019 0.015164059 93.2430293 -1.969616375 0.058249541 ATGHSGGGCISQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ATGHSGGGCISQGR 14 0 Q9HA64;I3L3W5;I3L139;I3L407 Q9HA64 FN3KRP Ketosamine-3-kinase 0 ;;; 206.66 1.05E-08 512320000 398087 371816 171454 241001 328011 372845 341276 381560 330404 FALSE TRUE 345478.7943 369373.5162 254369.7279 295723.9605 321484.2228 387188.5884 308179.106 299966.3633 291344.0155 1.185810506 1.267825994 0.873090623 1.015033585 1.103452296 1.328973886 1.057784233 1.029595074 1 18.15236415 2.012103684 24.99711248 1.024944858 1.123696705 0.127515318 0.125801822 518.758346 1071360.496 0.054322703 0.036596612 102.8261758 -2.012103684 0.098751848 ATGPEAAGGGGAGGGGGGYRPIIQS(ph)PGYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATGPEAAGGGGAGGGGGGYRPIIQSPGYK 29 1 Q9ULL5;Q9ULL5-2 Q9ULL5 PRR12 Proline-rich protein 12 1 ATGPEAAGGGGAGGGGGGYRPIIQS(1)PGYK;ATGPEAAGGGGAGGGGGGYRPIIQS(1)PGYK 211.15 4.57E-26 405960000 244300 230700 162247 183021 256670 178574 247720 330400 274620 TRUE FALSE 212015.136 229184.5165 240710.1919 224578.7154 251562.7692 185443.8573 223696.1525 259746.5312 242154.7364 0.87553578 0.946438298 0.994034622 0.927418223 1.038851326 0.765807269 0.9237736 1.072646916 1 17.8855697 1.754242367 17.62319531 1.03617279 0.926466088 0.285177866 0.0735203 0.785632283 892.6692418 0.038678567 0.018523988 56.78614237 -1.754242367 -0.109706703 ATHGSNS(ph)LPSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATHGSNSLPSSAR 13 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 ATHGS(0.006)NS(0.993)LPSSAR 77.468 0.016662 153210000 122240 147480 77517 89384 152760 172080 117520 145750 162980 TRUE FALSE 106085.6743 146511.1942 115004.4805 109680.0033 149720.3749 178700.029 106122.9285 114582.4967 143712.6901 0.738178892 1.019472909 0.800238868 0.763189411 1.04180344 1.243453371 0.738438119 0.797302567 1 17.13282793 4.7675856 21.93564083 0.911290445 0.738177509 0.116592759 0.157788969 4790.805535 3620334.26 0.040124903 3.01394092 58557.91429 -4.7675856 -0.173112936 ATIAGGGVIPHIHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATIAGGGVIPHIHK 14 0 Q71UI9;P0C0S5;Q71UI9-4;Q71UI9-3 Q71UI9 H2AFV;H2AFZ Histone H2A.V;Histone H2A.Z 0 ; 151.78 3.96E-06 4666600000 7834100 6830700 3953600 5360900 6783300 5556900 6474400 8249800 5672400 FALSE TRUE 6798803.836 6785828.682 5865574.184 6578174.281 6648325.601 5770677.539 5846513.685 6485644.47 5001815.334 1.359267262 1.356673173 1.172689072 1.315157366 1.329182538 1.153716632 1.168878356 1.29665812 1 22.25402036 -0.830708748 0.390925907 1.09E-30 1.313340462 0.465553726 0.084160572 36.63376073 1.273256928 31.2119047 0.094056583 0.147669652 0.830708748 1.313340462 ATIS(ph)DEEIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ATISDEEIER 10 0 C9J0A7;Q9UQN3;Q9UQN3-2 C9J0A7 CHMP2B Charged multivesicular body protein 2b 1 ATIS(1)DEEIER;AT(0.003)IS(0.997)DEEIER;ATIS(1)DEEIER;ATIS(1)DEEIER;ATIS(1)DEEIER;AT(0.003)IS(0.997)DEEIER 294.19 3.48E-32 11068950000 2876090 2733430 1774410 2015540 2738310 2548100 2587170 2958460 2568930 TRUE FALSE 2496007.419 2715473.918 2632520.611 2473199.163 2683822.988 2646127.056 2336266.652 2325816.352 2265234.022 1.101876184 1.198760875 1.162140682 1.091807354 1.184788398 1.168147322 1.031357744 1.026744402 1 21.11122867 2.211927343 7.338430935 1.02069491 1.152777624 0.770957386 0.033885562 0.080588039 15.80271085 0.013396137 0.009206204 162.9023475 -2.211927343 0.132082714 ATISPLHLAAYHGHHQALEVLVQSLLDLDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATISPLHLAAYHGHHQALEVLVQSLLDLDVR 31 0 O15084-2;O15084;O15084-4;O15084-1;B4DIW9 O15084-2 ANKRD28 Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit A 0 91.66 0.00015571 67935000 24260 33930 10347 21628 23137 23432 28732 36935 27259 FALSE TRUE 21053.97953 33707.1116 15350.84381 26538.96796 22676.61897 24333.4442 25945.57506 29036.73768 24036.47207 0.875918041 1.402331902 0.638647958 1.104112446 0.943425429 1.012355063 1.079425258 1.208028266 1 14.55293754 2.142701925 3.862944914 1.124732018 1.000514505 0.052281973 0.195742953 0.607461944 17.2030291 0.080855205 0.051908718 138.8998973 -2.142701925 -0.124217513 ATLAENPNLFDDHEEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ATLAENPNLFDDHEEGR 17 0 Q9BU68 Q9BU68 PRR15L Proline-rich protein 15-like protein 0 ;; 212.69 1.34E-12 835680000 700230 712840 461398 558510 728590 729400 602820 759650 678730 FALSE TRUE 607692.8313 708157.3071 684531.6161 685328.2318 714092.4845 757460.49 544358.6092 597204.7591 598491.3126 1.015374523 1.183237404 1.143761992 1.145093032 1.193154302 1.265616516 0.909551397 0.997850339 1 19.19097078 2.230357876 24.99984606 0.972633883 1.159270915 0.642497819 0.066285423 110.8342929 337791.0114 0.026266114 0.018044798 169.9643651 -2.230357876 0.186637032 ATLELTHNWGTEDDETQSYHNGNSDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATLELTHNWGTEDDETQSYHNGNSDPR 27 0 Q04760 Q04760 GLO1 Lactoylglutathione lyase 0 80.52 0.0068121 195380000 60136 68945 28937 63612 69267 79274 55948 73985 159990 FALSE TRUE 52188.87523 68492.09576 42931.02999 78056.07685 67888.72222 82323.72208 50522.17157 58163.8835 141076.1645 0.369934038 0.485497292 0.304311009 0.553290325 0.481220357 0.583540972 0.358119827 0.412287106 1 17.10611473 1.236576579 24.99999961 1.000000705 0.444002258 0.802122498 0.086860925 22.23411077 280087.4821 0.131539631 0.020727063 17.24156084 -1.236576579 -0.555998447 ATLENITNLRPVGEDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ATLENITNLRPVGEDFR 17 1 Q9NWV4 Q9NWV4 C1orf123 UPF0587 protein C1orf123 0 ;;; 104.44 0.00077556 1736690000 1244320 1091950 722650 808390 1024650 1054090 947200 1125590 1020790 FALSE TRUE 1079879.959 1084776.909 1072125.957 991947.305 1004261.47 1094641.524 855340.6898 884891.3379 900113.3691 1.199715498 1.205155868 1.191101026 1.102024855 1.115705537 1.216115172 0.950258844 0.983088762 1 19.77974719 2.234847076 25 0.977741148 1.168338241 0.846778317 0.038855683 36.04445271 242651.402 0.016438509 0.011569273 171.7303584 -2.234847076 0.190597093 ATLGETHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATLGETHR 8 0 P04062-4;P04062-5;P04062-2;P04062;A0A0G2JNZ5;A0A0G2JNZ0;A0A0G2JLB3;P04062-3 P04062-4 GBA Glucosylceramidase 0 ; 156.75 0.00038786 355710000 366523 301102 189064 260790 269399 349762 273780 323735 295541 FALSE TRUE 318086.0569 299124.0411 280495.9828 320006.3554 264038.487 363217.5705 247228.8577 254506.7896 260602.4797 1.220579548 1.147817325 1.076336584 1.227948237 1.01318486 1.393760992 0.948681908 0.97660924 1 17.99149129 ATLLNVPDLSDS(ph)IHS(ph)ANASER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATLLNVPDLSDSIHSANASER 21 0 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 2 ATLLNVPDLS(0.005)DS(0.995)IHS(1)ANASER;ATLLNVPDLS(0.001)DS(0.999)IHS(1)ANASER 129.83 8.38E-06 82703000 85359 70897 51343 81466 73861 73854 62513 72038 147710 TRUE FALSE 74078.59188 70431.27294 76172.64653 99964.10043 72391.31061 76695.21117 56450.49888 56633.2343 130247.8921 0.568750793 0.540747891 0.584828248 0.767491119 0.555796408 0.588840326 0.433408157 0.434811139 1 16.9909005 1.228923795 24.99827883 1.000000886 0.555126725 0.691893989 0.092376978 255.4255507 662535.7906 0.321871265 0.025291369 16.94040523 -1.228923795 -0.444874161 ATLLNVPDLSDSIHS(ph)ANASER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATLLNVPDLSDSIHSANASER 21 0 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 ATLLNVPDLSDSIHS(1)ANASER 192.18 2.93E-24 0 61058 53396 25534 53213 50063 52602 48433 57825 108700 TRUE FALSE 52989.0306 53045.23816 37882.32781 65295.82496 49066.84425 54625.63298 43735.97511 45459.57374 95849.60983 0.55283512 0.553421535 0.395226729 0.681232037 0.511914908 0.569909811 0.456297894 0.474280217 1 16.54848494 1.235108015 24.99747568 1.00000067 0.521653949 0.7933165 0.076281391 42.34711368 306551.4093 0.127628802 0.017968151 17.18335708 -1.235108015 -0.478346721 ATLLNVPDLSDSIHSANASERDDISEIQSLASDHS(ph)GR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATLLNVPDLSDSIHSANASERDDISEIQSLASDHSGR 37 1 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 ATLLNVPDLSDS(0.001)IHS(0.005)ANAS(0.005)ERDDIS(0.003)EIQS(0.028)LAS(0.074)DHS(0.884)GR 66.604 0.002689 22503000 24846 14329 7858.7 11542 18317 13890 15708 20364 15295 TRUE FALSE 21562.53815 14234.87186 11659.19361 14162.78751 17952.52754 14424.35729 14184.64058 16009.31707 13486.84252 1.598783267 1.055463637 0.864486523 1.050118846 1.331114196 1.069513288 1.051739171 1.187032253 1 13.71926501 4.740503307 24.83183269 1.084025805 1.598783458 0.650550268 0.120249445 106.2271167 1357705.214 0.030327215 0.191976578 55017.81103 -4.740503307 0.514757654 ATLLPEAGRS(ph)PEEAGFPGDPHEDKQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATLLPEAGRSPEEAGFPGDPHEDKQ 25 2 Q8IV56 Q8IV56 PRR15 Proline-rich protein 15 1 AT(0.151)LLPEAGRS(0.849)PEEAGFPGDPHEDKQ;AT(0.003)LLPEAGRS(0.997)PEEAGFPGDPHEDKQ 133.25 3.25E-05 691930000 503430 394350 345870 361200 401660 416420 547820 609260 516110 TRUE FALSE 436900.45 391759.4889 513133.8889 443215.9806 393667.7518 432439.9469 494692.5007 478974.4903 455096.0638 0.960018081 0.86082812 1.127528735 0.973895439 0.865021219 0.950216847 1.087006767 1.052468981 1 18.79581158 2.250830445 24.89445839 1.049425255 0.956354475 0.24179016 0.075270586 296.1986212 600962.0117 0.028653958 0.02202841 178.1683035 -2.250830445 -0.09307078 ATLPDADKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ATLPDADKER 10 1 P12814-3;P12814;P12814-2;P12814-4;H9KV75;H7C5W8 P12814-3 ACTN1 Alpha-actinin-1 0 ;; 115.65 0.00109 1473180000 2428540 1919960 1886120 2404300 1886780 1923790 1976780 2534460 5739200 FALSE TRUE 2107602.286 1907347.656 2798253.941 2950233.062 1849236.769 1997799.446 1785072.18 1992485.452 5060718.314 0.41646307 0.376892674 0.552936118 0.582967255 0.365409939 0.394765984 0.35273099 0.393715937 1 22.27091074 1.236466983 24.99998699 1.000000731 0.42813398 0.842145278 0.077623577 22.74023628 271471.1526 0.131292991 0.020531405 17.23721041 -1.236466983 -0.57186675 ATLPS(ph)PDKLPGFK ddPTM_MDA-MB-175_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 83.692 0.0090035 0 380410 316990 268940 288990 336130 257360 414240 490580 394240 TRUE FALSE 330137.8547 314907.6718 399000.2836 354609.5964 329441.6706 267260.8057 374067.0686 385673.2847 347633.3963 0.949672437 0.905861391 1.147761659 1.020067693 0.947669798 0.768800721 1.076038932 1.109425299 1 18.40720716 ATLSSTSGLDLMSESGEGEIS(ph)PQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ATLSSTSGLDLMSESGEGEISPQR 24 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDG6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 ATLSSTSGLDLMSES(0.001)GEGEIS(0.999)PQR;ATLSSTSGLDLMSESGEGEIS(1)PQR;ATLSSTSGLDLMSESGEGEIS(1)PQR 232.02 4.54E-34 328698000 333004 326219 233131 279143 329350 348656 320353 390210 377700 TRUE FALSE 288996.6777 324076.0459 345873.9314 342526.6846 322796.5794 362069.0219 289285.2154 306766.6281 333048.7363 0.867730894 0.973058927 1.038508463 1.028458142 0.969217247 1.087135252 0.868597247 0.9210863 1 18.34537378 0.933658446 20.80038578 1.731283618 0.969510782 0.018363116 0.07068811 204.9984707 370468.6495 34204.47433 0.017243951 8.583382096 -0.933658446 -0.761772836 ATLSSTSGLDLMSESGEGEIS(ph)PQREVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATLSSTSGLDLMSESGEGEISPQREVSR 28 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDG6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 ATLSSTSGLDLMSES(0.008)GEGEIS(0.992)PQREVSR;ATLSSTSGLDLMSES(0.001)GEGEIS(0.999)PQREVSR 220.63 1.54E-34 284018000 107775 120474 30126 28877 106267 119748 111537 115234 19771.1 TRUE FALSE 93532.26068 119682.5984 44695.03437 35433.96421 104152.4946 124354.783 100720.1589 90592.10585 17433.78308 5.365000829 6.864981502 2.563702563 2.032488533 5.974176352 7.132977534 5.77729793 5.196353851 1 14.08959804 6.417734917 11.09624213 4.776279064 5.133876343 0 2.096582489 0 0 0.478562595 0 2616585.417 -6.417734917 0.357597279 ATLVDHGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ATLVDHGIR 9 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;; 151.44 8.28E-05 1071880000 977360 871770 619200 605590 881360 1009010 861800 908960 1021290 FALSE TRUE 848199.3997 866043.2855 918647.1911 743098.4654 863822.6604 1047827.268 778222.7686 714585.9775 900554.2597 0.941863736 0.961678073 1.020090884 0.825156794 0.959212231 1.163535963 0.864159777 0.79349575 1 19.78045368 ATLYVTAIEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATLYVTAIEDR 11 0 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;H0YDE4;E9PNR9 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ; 205.18 7.14E-08 348740000 420800 406000 287120 284650 356060 437340 399270 429250 378620 FALSE TRUE 365190.2138 403332.9593 425972.1924 349284.1331 348975.1026 454164.7528 360548.8569 337458.2279 333859.9749 1.093842453 1.208090186 1.27590075 1.046199483 1.045273854 1.360345016 1.079940346 1.010777731 1 18.34888362 2.006677343 24.9977283 1.01791877 1.171029371 0.335346369 0.097717718 183.9425967 688615.8187 0.040012527 0.026902565 101.5493957 -2.006677343 0.153110601 ATMAQNENVVVQPVVAENIPVIPLSDS(ph)PPPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATMAQNENVVVQPVVAENIPVIPLSDSPPPSR 32 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 ATMAQNENVVVQPVVAENIPVIPLS(0.143)DS(0.714)PPPS(0.143)R 72.292 0.0019076 45546000 125030 86654 57803 69913 92226 87279 90898 109030 89182 TRUE FALSE 108506.9687 86084.76417 85756.72414 85787.8152 90390.88304 90636.67961 82082.72595 85714.78297 78639.00556 1.379811049 1.094682767 1.090511299 1.090906664 1.14944082 1.152566452 1.043791505 1.089977962 1 16.26295746 4.7385958 7.072623229 1.090666786 1.383907002 0.809385406 0.044352472 0.045985366 18.27503741 0.010957758 0.064564053 54776.69184 -4.7385958 0.293240215 ATNES(ph)EDEIPQLVPIGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ATNESEDEIPQLVPIGK 17 0 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 AT(0.004)NES(0.996)EDEIPQLVPIGK;AT(0.021)NES(0.979)EDEIPQLVPIGK;ATNES(1)EDEIPQLVPIGK;AT(0.004)NES(0.996)EDEIPQLVPIGK;AT(0.001)NES(0.999)EDEIPQLVPIGK;AT(0.007)NES(0.993)EDEIPQLVPIGK 315.96 2.90E-58 2545250000 3519830 3049490 1967280 2582210 2973500 2182070 2999410 3909120 3287210 TRUE FALSE 3054675.547 3029457.699 2918663.188 3168540.247 2914333.168 2266015.645 2708527.68 3073185.109 2898599.779 1.053845229 1.045145219 1.006921759 1.093127886 1.005427927 0.781762167 0.934426236 1.06023092 1 21.46692472 2.996124541 24.96257393 0.95381471 1.046733955 0.317567475 0.072438467 241.5150028 1555659.852 0.024470283 0.02713504 991.1161218 -2.996124541 0.092919245 ATPATAPGTS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATPATAPGTSPR 12 0 Q96P47;Q96P47-2;Q96P47-4;H0Y873;Q96P47-5 Q96P47 AGAP3 "Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3" 1 ATPATAPGT(0.077)S(0.923)PR 96.313 0.0058266 218580000 334640 309770 207990 230510 313480 325880 335660 347880 348330 TRUE FALSE 290416.4761 307735.1005 308574.6597 282850.8186 307242.3613 338416.8145 303107.7449 273488.5692 307150.8242 0.945517489 1.001902245 1.004635623 0.920885755 1.00029802 1.101793607 0.986836827 0.890404803 1 18.22858773 1.972274287 23.82741652 0.937748132 0.997560418 0.12694962 0.053380311 655.1816871 563059.4752 0.024744895 0.014340397 93.81543293 -1.972274287 0.059812286 ATQQQHDFTLTQTADGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ATQQQHDFTLTQTADGR 17 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 297.99 3.21E-46 2360510000 1940480 1755680 1046630 1204080 1915160 1591790 1712450 1814280 1727300 FALSE TRUE 1684040.651 1744146.822 1552783.769 1477484.767 1877052.063 1653027.191 1546376.863 1426310.341 1523100.562 1.105666096 1.145129131 1.019488672 0.970050701 1.232388793 1.085304039 1.015282183 0.936451851 1 20.53857977 2.097431295 3.476719059 0.966142351 1.092789985 0.358470853 0.070730798 0.251991474 5.96593217 0.034214301 0.020635164 125.1501272 -2.097431295 0.126647634 ATRPASTSQPDPS(ph)PDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ATRPASTSQPDPSPDR 16 1 P20749;H7C0A2 P20749 BCL3 B-cell lymphoma 3 protein 1 ATRPAS(0.036)T(0.038)S(0.318)QPDPS(0.608)PDR;ATRPAS(0.012)T(0.007)S(0.007)QPDPS(0.974)PDR;AT(0.021)RPAS(0.071)T(0.071)S(0.047)QPDPS(0.79)PDR 174.59 1.00E-08 1354040000 1412630 1484410 1254600 1431010 1668510 1764380 1615460 1844920 2070510 TRUE FALSE 1225947.366 1474658.813 1861328.756 1755942.692 1635309.915 1832256.84 1458792.938 1450398.215 1825736.667 0.671480936 0.807706193 1.019494646 0.961772157 0.895698676 1.003571256 0.799016071 0.794418079 1 20.80004726 4.531610979 4.077492327 0.910139051 0.686096978 0.507689431 0.080521219 0.211288217 6.901184993 0.021855495 0.095024176 34010.34039 -4.531610979 -0.224042073 ATS(ph)FSSAGEVPKPRPPSTR ddPTM_MDA-MB-175_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(0.171)S(0.702)FS(0.127)S(0.001)AGEVPKPRPPSTR 133.94 5.59E-06 1089800000 97036 199570 159250 89404 256940 310960 295890 340750 390560 TRUE FALSE 84212.44674 198259.0115 236263.8327 109704.5447 251827.3967 322922.8324 267194.6333 267883.2642 344388.4417 0.244527506 0.575684278 0.686038798 0.318548858 0.731230687 0.937670355 0.7758525 0.777852076 1 18.3936772 3.057031835 5.940927652 0.847760945 0.482804143 0.663180568 0.139608431 0.129338864 9.431222355 0.041807893 0.04733614 1140.333375 -3.057031835 -0.364956802 ATS(ph)LPSIPNPFPELCS(ph)PPSQSPILGGPSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 AT(0.149)S(0.848)LPS(0.003)IPNPFPELCS(0.434)PPS(0.375)QS(0.191)PILGGPSSAR 171.37 3.56E-13 96404000 147690 55264 60954 69277 81970 93453 84543 85486 122480 TRUE FALSE 128172.3923 54900.96715 90431.55828 85007.40168 80338.95737 97048.19738 76344.03287 67205.48415 108000.5539 1.186775323 0.508339681 0.837324949 0.787101534 0.74387542 0.898589811 0.706885568 0.62226981 1 16.72067919 4.761915309 24.37953164 0.756126724 1.186776006 0.484773495 0.137118521 4071.561336 4250131.716 0.031615634 1.733001917 57798.33251 -4.761915309 0.430649283 ATS(ph)LPSIPNPFPELCSPPSQS(ph)PILGGPSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 AT(0.115)S(0.841)LPS(0.044)IPNPFPELCS(0.163)PPS(0.179)QS(0.658)PILGGPSSAR 211.33 1.16E-26 99806000 89532 38808 35581 42913 47390 56208 48368 59945 80507 TRUE FALSE 77700.11935 38553.06769 52788.09061 52657.05253 46447.03172 58370.35813 43677.2788 47126.22824 70989.55417 1.09452891 0.543080854 0.743603636 0.741757758 0.654279806 0.822238691 0.615263461 0.663847362 1 16.11531913 1.23137598 24.90625998 1.000000512 0.720607135 0.232178623 0.149575895 328.4942735 1138652.609 0.328055352 0.033065493 17.0363275 -1.23137598 -0.279393377 ATS(ph)PGPTDLETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATSPGPTDLETR 12 0 Q5VT06 Q5VT06 CEP350 Centrosome-associated protein 350 1 AT(0.002)S(0.993)PGPT(0.005)DLETR 120.84 0.00020697 0 199600 182740 113760 151570 200440 195900 186870 200050 269630 TRUE FALSE 173222.3543 181539.5689 168774.7165 185986.2851 196451.6362 203436.3998 168747.3762 157270.8643 237754.6486 0.728576099 0.763558441 0.70986926 0.782261404 0.826278844 0.855656876 0.709754266 0.661483867 1 17.85911402 3.62948617 6.975837764 0.788141145 0.737155791 0.101637348 0.091049176 0.81948185 45.97767512 0.025999893 0.038687717 4260.751148 -3.62948617 -0.050985354 ATS(ph)PLVSLYPALECR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ATSPLVSLYPALECR 15 0 A0A087WXV6;Q96G74-2;Q96G74-3;Q96G74-5;Q96G74;H7BZQ3;Q96G74-4 A0A087WXV6 OTUD5 OTU domain-containing protein 5 1 AT(0.429)S(0.571)PLVSLYPALECR;AT(0.003)S(0.997)PLVSLYPALECR;AT(0.015)S(0.985)PLVSLYPALECR;AT(0.022)S(0.978)PLVSLYPALECR;AT(0.014)S(0.986)PLVSLYPALECR;AT(0.151)S(0.849)PLVSLYPALECR;AT(0.114)S(0.886)PLVSLYPALECR 289.61 7.43E-44 1709402000 1601741 1437927 952938 1075037 1396053 1500902 1382419 1593834 1351879 TRUE FALSE 1390066.869 1428481.163 1413782.004 1319140.582 1368274.277 1558642.671 1248352.218 1253005.002 1192061.405 1.16610341 1.198328507 1.185997633 1.106604556 1.147821976 1.307518778 1.047221404 1.051124546 1 20.18502712 2.091201425 11.47524384 1.035202918 1.180685465 0.653443088 0.052388433 0.275402278 32.73968648 0.021255436 0.014328443 123.3676877 -2.091201425 0.145482547 ATS(ph)PVKSTTSITDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATSPVKSTTSITDAK 15 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 AT(0.042)S(0.957)PVKS(0.001)TTSITDAK;AT(0.023)S(0.977)PVKSTTSITDAK 182.98 3.18E-07 651490000 963390 849630 337190 331890 693180 568940 1277660 1397460 30968 TRUE FALSE 836075.5706 844048.7246 500256.2118 407250.6971 679387.0742 590827.49 1153752.73 1098624.054 27306.99832 30.61762999 30.90961206 18.31970713 14.91378482 24.87959556 21.63648611 42.25117372 40.23232584 1 14.73698312 -1.963028159 6.52E-11 8.566758529 44.14977189 0 12.23405479 0 0.113411172 2312931622 2312931657 0.010888595 1.963028159 35.58301336 ATS(ph)SPMLYEVVYEAGALER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.064)S(0.468)S(0.468)PMLYEVVYEAGALER 104.44 0.00037044 129350000 36081 39078 24304 28350 42609 38010 32746 47547 36670 TRUE FALSE 31312.80443 38821.29404 36057.49569 34787.3008 41761.16426 39472.2693 29570.29796 37379.44406 32334.91437 0.968389898 1.200599872 1.115125752 1.075843294 1.291519247 1.220732142 0.91450058 1.156008754 1 14.98080517 2.262259942 24.99997008 1.046566516 1.149987196 0.220556291 0.104814945 383.6919884 404748.3644 0.038143881 0.029529501 182.9194731 -2.262259942 0.10342068 ATS(ph)SSSGSLSATGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATSSSSGSLSATGR 14 0 Q03252 Q03252 LMNB2 Lamin-B2 1 ATS(0.557)S(0.221)S(0.221)S(0.001)GSLSATGR;ATS(0.499)S(0.499)S(0.001)SGSLSATGR 274.92 4.95E-33 563630000 488840 575260 323923 402845 567130 582700 433530 665800 538330 TRUE FALSE 424238.5554 571481.0792 480573.2463 494317.1144 555845.2226 605116.8461 391486.3273 523423.8513 474689.2407 0.893718499 1.203905693 1.01239549 1.041348891 1.17096655 1.274764191 0.824721299 1.102666348 1 18.85662382 2.237684122 25 0.995932503 1.100905186 0.172693993 0.125066164 46.72244946 1332560.384 0.047228176 0.033939326 172.8558661 -2.237684122 0.104972683 ATS(ph)VDYSSFADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATSVDYSSFADR 12 0 Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 AT(0.001)S(0.999)VDYSSFADR 190.26 7.21E-06 254410000 537540 508670 333890 397660 514830 557160 570570 519160 458370 TRUE FALSE 466502.727 505328.5133 495360.3208 487954.7809 504585.8902 578594.3057 515236.2092 408141.6741 404182.0208 1.154189704 1.250249856 1.225587224 1.207264935 1.248412508 1.431519157 1.274762812 1.009796708 1 18.62464562 1.707505084 5.277181418 1.002190773 1.259375266 0.683101806 0.070969388 0.085398803 5.708299192 0.047554278 0.01961957 50.99235666 -1.707505084 0.257184493 ATSAGSS(ph)PSCSLAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATSAGSSPSCSLAGR 15 0 Q9BXB5;Q9BXB5-2 Q9BXB5 OSBPL10 Oxysterol-binding protein-related protein 10 1 ATSAGS(0.045)S(0.909)PS(0.045)CSLAGR;ATSAGS(0.002)S(0.987)PS(0.01)CSLAGR 295.98 4.82E-44 441140000 1027480 984700 669010 654810 991130 1005610 914430 1012900 942680 TRUE FALSE 891695.9147 978231.4409 992545.4737 803494.6186 971408.4521 1044296.467 825748.7193 796299.2174 831237.4443 1.072733093 1.176837554 1.194057703 0.966624668 1.168629323 1.256315478 0.993396923 0.957968415 1 19.66490112 2.104997792 8.891999966 0.975975591 1.136728383 0.471737315 0.077578311 0.22353821 17.18702127 0.03180589 0.02142314 127.3496608 -2.104997792 0.160752791 ATSCFPRPMT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ATSCFPRPMTPR 12 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 ATSCFPRPMT(1)PR;ATSCFPRPMT(1)PR;ATSCFPRPMT(1)PR 72.898 0.065724 3044940000 2689140 3056390 1810580 2068340 2580990 2937570 2431800 2670820 2929220 TRUE FALSE 2333763.336 3036312.373 2686182.544 2537988.21 2529633.349 3050580.219 2195964.41 2099685.927 2582930.949 0.903532995 1.175529828 1.039974586 0.9826001 0.979365457 1.181053725 0.850183166 0.812908269 1 21.30057764 2.210098198 24.99994416 0.870552926 1.043801858 0.36181119 0.096765735 197.7246104 173669.8522 0.037764101 0.025465913 162.2176846 -2.210098198 0.173248932 ATSGSS(ph)LPVGINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATSGSSLPVGINR 13 0 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 ATSGS(0.209)S(0.791)LPVGINR 151.3 4.69E-05 130260000 248490 230910 144860 161550 243030 237050 224960 260020 225540 TRUE FALSE 215651.4169 229393.137 214914.7805 198232.3966 238194.1785 246169.4669 203143.4138 204416.7465 198876.9181 1.084346132 1.153442738 1.080642151 0.996759194 1.197696448 1.237798077 1.021452946 1.027855562 1 17.60151632 2.061526747 24.99999645 1.018536652 1.122493854 0.37463245 0.066126811 76.09929163 30920.61626 0.02835981 0.019120178 115.2197017 -2.061526747 0.103957202 ATSILSYLS(ph)DSDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ATSILSYLSDSDLR 14 0 A0A499FJE4;Q96MK2;Q96MK2-2 A0A499FJE4 FAM65C Protein FAM65C 1 ATSILS(0.004)YLS(0.996)DSDLR;ATSILS(0.008)YLS(0.991)DS(0.001)DLR;ATSILSYLS(1)DSDLR;ATSILSYLS(1)DSDLR;ATSILS(0.001)YLS(0.991)DS(0.007)DLR 222.75 3.96E-12 121829000 218445 203555 145029 172453 206160 257925 171978 201950 197494 TRUE FALSE 189576.9398 202217.8338 215165.5095 211611.0894 202057.8193 267847.5416 155299.6 158764.5641 174146.4843 1.088606184 1.161193891 1.235543229 1.21513271 1.160275042 1.538058852 0.891775683 0.911672519 1 17.40994182 2.181838539 24.99999996 0.927950083 1.225846718 0.574544995 0.120998248 57.31709459 25261.6872 0.048001562 0.032362663 151.998233 -2.181838539 0.297896635 ATSS(ph)PMLYEVVYEAGALER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.016)S(0.116)S(0.867)PMLYEVVYEAGALER;AT(0.011)S(0.108)S(0.88)PMLYEVVYEAGALER;AT(0.112)S(0.112)S(0.777)PMLYEVVYEAGALER;AT(0.033)S(0.206)S(0.762)PMLYEVVYEAGALER 111.06 0.00023445 232996000 127757 130273 84944 104960 140106 133264 114878 163427 123225 TRUE FALSE 110873.5888 129417.2281 126023.2025 128792.7722 137318.1647 138390.7523 103737.1492 128479.4078 108657.4809 1.020395355 1.191056769 1.159820764 1.185309757 1.263770921 1.273642194 0.954717047 1.182425792 1 16.72942798 2.24705043 24.99941477 1.070404285 1.185542962 0.327604475 0.089898758 241.9183904 712362.6951 0.033340971 0.025401924 176.6242904 -2.24705043 0.115138678 ATSS(ph)SSGSLSATGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ATSSSSGSLSATGR 14 0 Q03252 Q03252 LMNB2 Lamin-B2 1 ATS(0.044)S(0.478)S(0.478)SGSLSATGR;ATS(0.004)S(0.976)S(0.019)SGSLSATGR;ATS(0.061)S(0.467)S(0.467)S(0.006)GSLSATGR;ATS(0.027)S(0.897)S(0.076)SGSLSATGR 293.75 1.57E-43 1322632000 1405720 1717190 1024000 1199870 1764640 1714500 1318170 2039330 1678360 TRUE FALSE 1219950.54 1705909.666 1519209.825 1472318.822 1729527.116 1780457.924 1190334.076 1603235.15 1479946.193 0.824320875 1.152683573 1.026530446 0.994846184 1.16864189 1.20305585 0.804309023 1.083306378 1 20.49711329 7.798831986 19.90188383 1.034265809 0.067504692 0 0.134461742 0 0 0.028400868 0 62926269.51 -7.798831986 -0.966761117 ATSSSNPSS(ph)PAPDWYKDFVTDADAEVLEHSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ATSSSNPSSPAPDWYKDFVTDADAEVLEHSGK 32 1 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 ATSSSNPS(0.371)S(0.628)PAPDWYKDFVTDADAEVLEHSGK 158.54 5.10E-14 70679000 86008 58476 60742 67903 86085 66146 127350 131700 84114 TRUE FALSE 74641.82488 58091.86731 90117.03437 83321.41398 84372.07692 68690.67942 114999.6166 103536.9799 74170.13874 1.006359515 0.783224466 1.215004258 1.123382205 1.137547783 0.926123108 1.550484043 1.395938873 1 16.17855085 3.65184931 0.525399458 1.314476579 0.848241918 0.216388365 0.197665637 2.128920352 1.229449804 0.22047153 0.616032551 4485.897131 -3.65184931 -0.466234661 ATSSSSGS(ph)LSATGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ATSSSSGSLSATGR 14 0 Q03252 Q03252 LMNB2 Lamin-B2 1 ATSSS(0.002)S(0.081)GS(0.916)LS(0.001)ATGR;ATSSS(0.018)S(0.373)GS(0.607)LS(0.002)ATGR;ATSSS(0.003)S(0.077)GS(0.92)LSATGR 184.97 1.29E-06 469820000 328851 344618 274561 274494 380791 405879 323989 417506 407243 TRUE FALSE 285392.5071 342354.1817 407339.618 336822.0581 373214.0041 421493.4278 292568.5966 328225.5909 359099.1965 0.794745602 0.953369389 1.134337314 0.937963831 1.039306152 1.173752077 0.814729188 0.914024855 1 18.4540229 2.205777492 24.99998322 0.90655752 1.007518547 0.137810626 0.113033522 373.4461614 284782.631 0.046246455 0.031181936 160.6118156 -2.205777492 0.100961028 ATSTS(ph)PNSQSSK ddPTM_MDA-MB-175_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(0.997)PNS(0.001)QSSK;ATST(0.013)S(0.956)PNS(0.032)QSSK;ATST(0.002)S(0.985)PNS(0.013)QSSK;ATST(0.003)S(0.995)PNS(0.003)QSSK;ATST(0.002)S(0.998)PNSQSSK;ATST(0.003)S(0.872)PNS(0.125)QSSK;ATST(0.002)S(0.995)PNS(0.003)QSSK;ATSTS(0.998)PNS(0.002)QSSK 297.53 2.58E-36 5365479000 14962890 12829160 8454590 10649850 7620880 10271310 14167170 16381040 16395970 TRUE FALSE 12985506.18 12744884.4 12543258 13068061.22 7469239.398 10666453.94 12793240.03 12878082.07 14457657.1 0.898175 0.881531794 0.8675858 0.903885126 0.516628617 0.737771955 0.884876432 0.890744744 1 23.78533044 1.544892219 1.780441014 1.002730965 0.803373112 0.222111808 0.11578636 0.789788658 4.1705013 0.23721829 0.035676319 35.06648366 -1.544892219 -0.199357853 ATSVALPGWS(ph)PSETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATSVALPGWSPSETR 15 0 Q16513-3;Q16513-2;Q16513;Q16513-4;Q16513-5;B1AL79 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 ATSVALPGWS(0.999)PS(0.001)ETR;ATSVALPGWS(0.977)PS(0.023)ETR 251.49 7.87E-20 177835000 368960 379300 225160 244280 331860 345330 294470 363490 358060 TRUE FALSE 320201.0012 376808.3533 334048.1291 299747.5076 325256.6353 358615.0686 265912.3447 285760.4922 315730.5547 1.014159056 1.193449122 1.058016477 0.949377572 1.030171551 1.135826303 0.842212896 0.905077092 1 18.26833436 2.237391686 24.99999987 0.910472426 1.062455227 0.458596532 0.07559206 27.54022803 588978.1649 0.030372913 0.021779012 172.7395112 -2.237391686 0.1519828 ATT(ph)PPNQGRPDS(ph)PVYANLQELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ATTPPNQGRPDSPVYANLQELK 22 1 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 2 AT(0.456)T(0.544)PPNQGRPDS(0.985)PVY(0.015)ANLQELK;AT(0.466)T(0.534)PPNQGRPDS(0.938)PVY(0.062)ANLQELK;AT(0.303)T(0.697)PPNQGRPDS(0.953)PVY(0.047)ANLQELK;AT(0.467)T(0.533)PPNQGRPDS(0.825)PVY(0.175)ANLQELK;AT(0.46)T(0.54)PPNQGRPDS(0.981)PVY(0.019)ANLQELK 122.47 5.90E-05 4798800000 1208040 958939 734529 847829 962291 784975 1186640 1374670 1227620 TRUE FALSE 1048394.453 952639.6666 1089749.681 1040341.533 943143.2918 815173.4962 1071559.835 1080707.518 1082492.162 0.968500734 0.880043015 1.006704454 0.961061492 0.871270319 0.753052562 0.98990078 0.998351356 1 20.04592515 2.041178359 24.99999855 0.997579264 0.907663751 0.274169556 0.068605135 196.5446007 119324.3768 0.029335333 0.019777854 109.9457279 -2.041178359 -0.089915513 ATTVPDFQETRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ATTVPDFQETRPR 13 1 B7ZC38;Q9NR46 B7ZC38 SH3GLB2 Endophilin-B2 0 ;;;; 214.23 2.84E-11 3206600000 2812940 2921160 2031210 2128300 2930630 3133350 2572680 3014670 2715330 FALSE TRUE 2441202.852 2901970.708 3013509.95 2611563.044 2872316.197 3253892.002 2323181.89 2370006.281 2394326.781 1.019577976 1.212019483 1.258604287 1.09072958 1.19963416 1.359000796 0.970286056 0.989842447 1 21.19118864 2.204701761 24.99998942 0.986677674 1.189985805 0.530152366 0.090185001 140.439408 103693.7349 0.036073001 0.024321862 160.2144787 -2.204701761 0.203308131 ATVMLYDDGNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATVMLYDDGNKR 12 1 P50552;K7ENR7;K7ENL7;K7EIG8 P50552 VASP Vasodilator-stimulated phosphoprotein 0 ; 133.15 0.00026994 848160000 801020 673970 471740 577380 586910 626730 757710 812330 723360 FALSE TRUE 695163.1775 669542.6467 699875.0419 708482.9537 575231.6393 650840.7086 684227.4008 638619.5511 637845.2049 1.089861885 1.049694568 1.097249045 1.110744344 0.901835798 1.020374071 1.07271701 1.001214003 1 19.28284682 ATVT(ph)PS(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ATVTPSPVK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 ATVT(1)PS(1)PVK;ATVT(1)PS(1)PVK;ATVT(1)PS(1)PVK;ATVT(1)PS(1)PVK 199.19 0.00013345 3422800000 9335000 8241300 8073700 9642700 7448200 6546400 8542700 10372000 38116500 TRUE FALSE 8101356.098 8187162.358 11978168.32 11832222.41 7299995.392 6798244.244 7714230.269 8154028.515 33610410.79 0.241037104 0.243590071 0.356382682 0.352040399 0.217194471 0.202266027 0.229519071 0.24260425 1 25.00240484 1.23772328 24.9993434 1.000000861 0.260423732 0.951476609 0.052477185 4.488085734 133913.7768 0.082577134 0.014083843 17.2871452 -1.23772328 -0.739577129 ATVT(ph)PS(ph)PVKGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ATVTPSPVKGK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 AT(0.061)VT(0.939)PS(1)PVKGK;AT(0.038)VT(0.962)PS(1)PVKGK;AT(0.005)VT(0.995)PS(1)PVKGK;AT(0.005)VT(0.995)PS(1)PVKGK;ATVT(1)PS(1)PVKGK;AT(0.222)VT(0.778)PS(1)PVKGK 176.42 0.00021732 2773870000 7306560 6140250 5032550 5208010 5350720 4019040 7249800 8711600 7824560 TRUE FALSE 6340979.584 6099914.293 7466308.013 6390568.27 5244251.141 4173655.069 6546715.512 6848692.134 6899549.431 0.919042562 0.884103282 1.082144289 0.926229797 0.760086031 0.604917047 0.94886131 0.992628896 1 22.71807072 2.013326015 24.99350549 0.988275184 0.863996301 0.179496729 0.121550979 424.8887267 796893.8736 0.054745097 0.036887364 103.1159899 -2.013326015 -0.124278883 ATVT(ph)PSPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ATVTPSPVK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 ATVT(0.81)PS(0.19)PVK;ATVT(0.996)PS(0.004)PVK 158.08 0.00074988 50001000000 3179800 2900900 2437640 2982700 2681000 2315660 3012100 3527500 6479800 TRUE FALSE 2759581.373 2881843.797 3616490.857 3659967.623 2627653.345 2404744.939 2719987.006 2773171.576 5713765.426 0.482970715 0.504368587 0.63294353 0.640552657 0.459881208 0.420868685 0.47604107 0.485349217 1 22.44601038 1.23660082 24.99970458 1.000000617 0.512800823 0.823935232 0.070767726 23.08708306 294425.5945 0.120984961 0.019103289 17.24252322 -1.23660082 -0.487199794 ATVTPS(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ATVTPSPVK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 ATVT(0.007)PS(0.993)PVK;ATVT(0.08)PS(0.92)PVK;ATVT(0.048)PS(0.952)PVK;ATVT(0.337)PS(0.663)PVK;ATVT(0.098)PS(0.902)PVK;ATVT(0.088)PS(0.912)PVK;ATVT(0.01)PS(0.99)PVK;ATVT(0.004)PS(0.996)PVK 196.11 3.16E-05 23112560000 15285570 14557800 14381700 17646660 13537120 11536710 15160070 18397180 48467800 TRUE FALSE 13265543.2 14462168.85 21336738.22 21653603.87 13267757.8 11980534.7 13689848.74 14463086.22 42737991.9 0.31039229 0.338391399 0.499245221 0.506659366 0.310444109 0.280325167 0.320320355 0.338412864 1 25.34901579 1.2371838 24.99923143 1.000000772 0.363616759 0.868513914 0.077888879 13.10084092 237785.7774 0.126839158 0.020856456 17.26568448 -1.2371838 -0.636384014 ATVTPS(ph)PVKGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ATVTPSPVKGK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 ATVT(0.001)PS(0.999)PVKGK;ATVT(0.002)PS(0.998)PVKGK;ATVT(0.009)PS(0.991)PVKGK;ATVT(0.004)PS(0.996)PVKGK;ATVT(0.009)PS(0.991)PVKGK;ATVT(0.001)PS(0.999)PVKGK;ATVT(0.003)PS(0.997)PVKGK;ATVT(0.057)PS(0.943)PVKGK 197.19 3.51E-08 79727190000 79104100 62559900 45815150 52248500 53822800 38443540 74284400 87856100 43235620 TRUE FALSE 68650292.76 62148939.9 67971509.78 64112320.49 52751831.58 39922487.86 67080310.32 69068756.71 38124354.26 1.800693916 1.630163739 1.782889471 1.681663119 1.383678035 1.047164959 1.759513351 1.811670205 1 25.18420957 3.334191275 5.780272369 1.461742895 1.726927004 0.257290008 0.262644801 0.386406114 19.18050557 0.081443829 0.105221702 2158.694949 -3.334191275 0.265184109 ATVWDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ATVWDLR 7 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-5;H0Y9T9 D6REX3 SEC31A Protein transport protein Sec31A 0 ;;; 108.09 0.017056 1552320000 4042030 4498460 2946250 3396030 4454510 4511570 4041480 4646210 4950050 FALSE TRUE 3507865.494 4468909.32 4371066.355 4167150.517 4365873.966 4685133.017 3649537.892 3652654.148 4364860.728 0.803660349 1.02383778 1.001421724 0.954704119 1.000232135 1.073375145 0.836117833 0.836831774 1 22.05750419 2.218842015 24.97151699 0.877415593 0.97963137 0.184117489 0.082736533 327.6559449 414938.3112 0.032773741 0.022129805 165.5167746 -2.218842015 0.102215777 AVAAPRPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AVAAPRPDR 9 1 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;;;; 91.087 0.010023 1313420000 2191100 2186170 1406810 1537310 1818420 2172120 1909300 2189480 2137630 FALSE TRUE 1901540.583 2171808.905 2087148.021 1886379.732 1782237 2255682.862 1724136.38 1721276.741 1884921.817 1.008816688 1.152201055 1.107286256 1.000773462 0.945523037 1.196698368 0.914699148 0.913182035 1 20.84607325 2.194892019 24.99973191 0.935328823 1.065440317 0.371103341 0.077009289 138.7955676 79457.72257 0.031121608 0.020982333 156.6361569 -2.194892019 0.130111494 AVAFNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVAFNKR 7 1 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ; 148.28 0.0033584 2334200000 2195000 2638800 1470930 1811140 2250100 2188400 2392700 2805100 1701260 FALSE TRUE 1904925.189 2621465.549 2182276.668 2222387.019 2205327.412 2272589.164 2160656.322 2205251.194 1500138.981 1.269832471 1.747481788 1.454716327 1.481454083 1.470082066 1.51491908 1.440304098 1.470031259 1 20.51666474 1.231518648 4.842476481 0.962631113 1.489439125 0.631880611 0.115310934 0.114445075 6.3754642 0.206441798 0.026200533 17.04192492 -1.231518648 0.526808012 AVAGVMITAS(ph)HNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AVAGVMITASHNR 13 0 Q6PCE3 Q6PCE3 PGM2L1 "Glucose 1,6-bisphosphate synthase" 1 AVAGVMITAS(1)HNR;AVAGVMITAS(1)HNR;AVAGVMITAS(1)HNR;AVAGVMITAS(1)HNR;AVAGVMITAS(1)HNR;AVAGVMIT(0.001)AS(0.999)HNR 204.82 4.82E-08 3405680000 3711170 3206700 2383000 2349020 2861310 3266730 3151790 2964740 4434470 TRUE FALSE 3220729.482 3185634.977 3535426.771 2882400.894 2804375.529 3392403.217 2846129.891 2330753.423 3910232.008 0.823667106 0.814692062 0.904147571 0.737143189 0.717189037 0.867570827 0.727867268 0.596065251 1 21.89882278 3.720087053 24.30797655 0.754342937 0.844221233 0.07288074 0.10826028 1157.080196 1522514.887 0.029760609 0.044245468 5249.126663 -3.720087053 0.089878296 AVAHHTDCTFIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AVAHHTDCTFIR 12 0 P62195-2;P62195;J3QSA9;J3KRP2;J3QQM1;J3QLH6;J3QRW1;J3QRR3 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ;; 127.42 0.00015613 1396200000 598500 517320 309690 514470 533800 540450 482940 584020 570630 FALSE TRUE 519406.7086 513921.6909 459457.1199 631288.2767 523178.4244 561241.4612 436104.5531 459131.8678 503170.7715 1.03226725 1.021366343 0.913123627 1.254620325 1.039763146 1.115409505 0.86671281 0.912477222 1 18.94068859 2.238718307 24.99999997 0.921009957 1.061751096 0.332674686 0.090928563 4.676713694 741640.7095 0.035202193 0.025523533 173.2679781 -2.238718307 0.140741138 AVAPS(ph)PSGAIGGLLEQFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVAPSPSGAIGGLLEQFAR 19 0 Q8NCE2;Q8NCE2-2;C9JSR1;Q8NCE2-3 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 AVAPS(0.984)PS(0.016)GAIGGLLEQFAR 60.768 0.062897 43158000 37779 53384 33678 28951 42056 47177 43088 56691 48626 TRUE FALSE 32786.40943 53033.31699 49964.79345 35524.76704 41219.16788 48991.92972 38909.33239 44568.07082 42877.48967 0.764653194 1.236856854 1.165291947 0.828517885 0.961324187 1.142602566 0.907453601 1.039428174 1 15.38793282 3.775169599 24.99941025 0.987568887 1.073726232 0.050643677 0.145222391 1672.123525 1141848.583 0.036764667 0.063675985 5958.948052 -3.775169599 0.086157344 AVCMLS(ph)NTTAIAEAWAR ddPTM_MDA-MB-175_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(0.978)NT(0.009)T(0.013)AIAEAWAR 97.836 0.0020732 20245000 20372 14670 12800 12753 19075 20877 14760 18480 15132 TRUE FALSE 17679.78858 14573.6318 18990.12281 15648.76357 18695.44482 21680.1517 13328.57747 14528.19581 13343.1122 1.32501236 1.092221334 1.423215404 1.172797121 1.401130751 1.62481971 0.998910694 1.088816132 1 13.70380759 2.18909191 24.99999956 1.040389049 1.327590035 0.504919825 0.144514979 96.94477559 48992.22129 0.059111566 0.039853082 154.5581497 -2.18909191 0.287200986 AVCMLSNTTAIAEAWAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AVCMLSNTTAIAEAWAR 17 0 P68363;P68363-2;P68366-2;P68366 P68363;P68366-2 TUBA1B;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 ;; 236.05 8.25E-20 814806000 226199 199791 137389 164399 229898 229988 211619 237144 211925 FALSE TRUE 196306.229 198478.5598 203830.7799 201728.3056 225323.4796 238835.7872 191096.222 186432.6011 186871.4679 1.05048797 1.062112702 1.090753887 1.079502975 1.205767162 1.278075192 1.022607807 0.997651504 1 17.51168679 2.028206039 24.99941043 1.002099363 1.126621674 0.409817897 0.068872495 214.6180276 190218.1668 0.030722342 0.020712489 106.7102259 -2.028206039 0.124522311 AVCST(ph)YLQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVCSTYLQSR 10 0 Q5SQL3;J3KP92;Q86Z02;Q86Z02-2;H7BXX9;Q9H2X6-2;Q9H2X6-3;Q9H2X6 Q5SQL3 HIPK1;HIPK2 Homeodomain-interacting protein kinase 1;Homeodomain-interacting protein kinase 2 1 AVCS(0.106)T(0.637)Y(0.257)LQSR;AVCS(0.177)T(0.548)Y(0.275)LQSR 137.06 0.00113 997680000 594350 640960 302340 443600 767200 781840 554240 712370 634300 TRUE FALSE 515805.1416 636749.4916 448552.6353 544326.16 751934.221 811917.8907 500489.8901 560035.2192 559313.7766 0.922210686 1.138447716 0.801969581 0.973203563 1.344387091 1.451632205 0.894828468 1.001289871 1 19.09329834 4.758641413 21.78498427 1.069810467 0.92220986 0.056189103 0.196398166 2842.230173 3083144.364 0.05095577 1.525103484 57364.2623 -4.758641413 -0.147600608 AVDFAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AVDFAER 7 0 P62917;E9PKZ0;G3V1A1;E9PKU4;E9PP36 P62917 RPL8 60S ribosomal protein L8 0 ;;;; 171.47 0.0021788 4529040000 5964930 5950570 3561940 4133790 5803570 6652680 5169390 5550140 5417510 FALSE TRUE 5176649.387 5911480.314 5284506.098 5072430.201 5688090.311 6908612.904 4668063.353 4363285.752 4777058.139 1.083647977 1.237472968 1.106226038 1.061831372 1.190709877 1.446206578 0.977183701 0.913383431 1 22.187691 2.034520482 24.9999965 0.948938111 1.183246571 0.485343286 0.108836939 141.3105284 102337.6003 0.044704534 0.030139658 108.2730777 -2.034520482 0.23430846 AVDIPHMDIEALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AVDIPHMDIEALK 13 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;;; 203.82 8.28E-08 2843500000 5453377 4849563 3569836 4154122 4613424 3759344 5577586 6362075 6827330 FALSE TRUE 4732699.412 4817705.901 5296220.63 5097378.892 4521625.888 3903968.396 5036672.568 5001594.771 6020210.825 0.786135162 0.800255347 0.87974006 0.846711027 0.751074343 0.648477023 0.836627273 0.830800601 1 22.52138258 1.120301622 1.943281126 1.121234171 0.791697111 0.518731929 0.062386026 1.039614898 2.896321137 0.69777179 0.018248278 13.19172598 -1.120301622 -0.32953706 AVDIPHMDIEALKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVDIPHMDIEALKK 14 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ; 157.86 3.36E-06 3196500000 9731500 8129800 6734100 7168100 8003900 5977200 11070100 12336300 9637200 FALSE TRUE 8445457.619 8076394.808 9990733.284 8795726.663 7844638.049 6207146.752 9996523.406 9698278.246 8497901.195 0.993828644 0.950398766 1.175670681 1.035046944 0.923126531 0.730432916 1.17635204 1.141255708 1 23.01867514 AVDLGPPKPSDQETGEQVS(ph)SPSSHPALHTTTEDSAGVQTEF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVDLGPPKPSDQETGEQVSSPSSHPALHTTTEDSAGVQTEF 41 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 AVDLGPPKPSDQET(0.006)GEQVS(0.541)S(0.444)PS(0.004)S(0.004)HPALHTTTEDSAGVQTEF 128.83 4.84E-09 335540000 98323 109430 29384 70885 104720 98581 112090 132700 122270 TRUE FALSE 85329.36643 108711.1471 43594.20068 86980.52266 102636.2769 102373.4749 101219.5291 104323.1377 107815.3799 0.791439649 1.008308344 0.404341206 0.806754312 0.951963226 0.949525707 0.938822728 0.967609053 1 16.71820347 3.312018 4.476008923 0.96052773 0.739870855 0.343167764 0.145563672 0.244343508 9.267195519 0.042435846 0.054594472 2051.247193 -3.312018 -0.220656875 AVDLGPPKPSDQETGEQVSS(ph)PSSHPALHTTTEDSAGVQTEF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVDLGPPKPSDQETGEQVSSPSSHPALHTTTEDSAGVQTEF 41 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 AVDLGPPKPSDQET(0.009)GEQVS(0.178)S(0.799)PS(0.007)S(0.007)HPALHTTTEDSAGVQTEF 163.75 7.61E-20 322830000 198030 224120 59023 169740 199700 175330 229910 274110 246310 TRUE FALSE 171859.8338 222647.741 87566.72022 208282.0613 195726.3607 182075.0586 207613.3636 215493.7096 217191.5124 0.791282458 1.025121739 0.40317745 0.958978825 0.901169473 0.838315718 0.955899986 0.992182923 1 17.7286082 2.464340188 0.827240195 1.014813929 0.785654464 0.198978203 0.162622158 1.203767265 1.742092137 0.188100435 0.088091498 291.2998013 -2.464340188 -0.229159465 AVDLGPPKPSDQETGEQVSSPSSHPALHTTTEDSAGVQTEF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVDLGPPKPSDQETGEQVSSPSSHPALHTTTEDSAGVQTEF 41 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 164.8 6.96E-20 105470000 56687 49383 12312 39659 58482 50582 63631 72272 58341 FALSE TRUE 49195.66932 49058.59982 18266.12438 48664.1821 57318.32262 52527.92227 57460.07541 56817.19522 51443.99344 0.956295692 0.953631251 0.355068166 0.945964317 1.114188825 1.021070076 1.116944303 1.104447603 1 15.65071502 3.484616205 24.25987177 1.072168744 0.754137425 0.426290215 0.1675158 215.8325127 698613.4974 0.04701321 0.063480674 3052.22261 -3.484616205 -0.318031319 AVDLMTHNYYELLYAFHIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVDLMTHNYYELLYAFHIYR 20 0 Q12769;G3V198;E9PR16 Q12769 NUP160 Nuclear pore complex protein Nup160 0 107.72 0.00012869 25412000 5348.4 5613.2 3428.2 5793.8 5406.1 3736.9 6891.6 6989.4 5951.9 FALSE TRUE 4641.595389 5576.32652 5086.088987 7109.370843 5298.529187 3880.660961 6223.253693 5494.771202 5248.273162 0.884404307 1.062506914 0.969097612 1.354611436 1.009575726 0.739416726 1.185771681 1.046967456 1 12.3576271 4.74162389 23.02399029 1.049144388 0.884404134 0.095734255 0.155806146 247.1710385 1857466.261 0.037429246 0.252544322 55159.95327 -4.74162389 -0.164740254 AVDPDGDGHVSWDEYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVDPDGDGHVSWDEYK 16 0 A0A5F9UP49;Q9BRK5;A0A5F9UJX7;Q9BRK5-6;G3V1E2;Q9BRK5-4;Q9BRK5-3;H0Y3T6;Q9BRK5-2 A0A5F9UP49 SDF4 45 kDa calcium-binding protein 0 120.66 0.00010294 250300000 117380 84638 43842 77678 105210 103460 103120 117600 108520 FALSE TRUE 101867.9356 84082.00741 65044.13784 95315.97713 103116.5268 107440.1731 93119.43827 92452.15516 95690.88923 1.064552085 0.87868352 0.679731774 0.99608205 1.077600257 1.122783726 0.973127526 0.966154207 1 16.54609395 3.504788135 24.82500298 1.022297295 0.868616601 0.323088536 0.10186721 789.9010779 708762.4164 0.028765562 0.042540124 3197.334947 -3.504788135 -0.153680694 AVDS(ph)SSEEIEVEVPVVDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVDSSSEEIEVEVPVVDRR 19 1 D6RB01;Q9Y6X4 D6RB01 FAM169A Soluble lamin-associated protein of 75 kDa 1 AVDS(0.942)S(0.049)S(0.009)EEIEVEVPVVDRR 222.62 1.46E-19 91882000 30974 32881 16891 21543 26676 37563 29365 38341 26694 TRUE FALSE 26880.70742 32665.00255 25059.5441 26434.66741 26145.19979 39008.07292 26517.18682 30142.07552 23538.26573 1.142000338 1.38774041 1.064630011 1.123050768 1.110753022 1.657219498 1.126556524 1.280556345 1 14.52272041 AVDTWSWGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AVDTWSWGER 10 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 ;;; 206.38 3.52E-07 3284800000 629040 694950 456688 555176 688580 724740 595074 758860 649895 FALSE TRUE 545910.7702 690384.8277 677543.8443 681237.1961 674878.6052 752621.2168 537363.8151 596583.6945 573065.1535 0.952615539 1.204723099 1.182315554 1.188760461 1.177664705 1.31332574 0.937701083 1.041039908 1 19.12833965 2.22185907 24.9999866 1.000639426 1.173258166 0.45340521 0.091425644 216.4621773 324012.5034 0.035946346 0.024307388 166.6706272 -2.22185907 0.17261874 AVDWIFSHIDDLDAEAAMDISEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AVDWIFSHIDDLDAEAAMDISEGR 24 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;; 240.85 1.11E-37 306587000 195838 186609 128030 155300 169520 156670 219544 242438 162522 FALSE TRUE 169957.5121 185383.1532 189945.7362 190563.2386 166146.8837 162697.1963 198252.6567 190594.5204 143308.8343 1.185952792 1.293591941 1.325429358 1.329738251 1.159362467 1.135290766 1.383394524 1.329956533 1 17.12876802 3.255041455 24.99067484 1.227964317 1.287368436 0.091649195 0.112245272 818.8673489 1241680.928 0.033754484 0.043445445 1799.042631 -3.255041455 0.059404118 AVEDIHGLFSLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVEDIHGLFSLSK 13 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 171.29 2.53E-05 728860000 2465400 2450100 1478110 1982380 2276400 2138470 2581500 2983300 2893200 FALSE TRUE 2139591.143 2434005.132 2192928.94 2432509.678 2231104.094 2220738.325 2331146.527 2345344.511 2551169.192 0.838670814 0.954074367 0.859578011 0.953488183 0.874541799 0.870478654 0.913756145 0.919321431 1 21.28272715 1.010565017 1.591669605 1.100467482 0.895886083 0.436416663 0.03751949 1.811528198 2.578578685 0.697363382 0.00960045 10.24625161 -1.010565017 -0.204581399 AVEDINEHITDAQLEAMTELHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVEDINEHITDAQLEAMTELHDR 23 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 ; 174.28 1.66E-12 127316000 102399 85496 65310 105974 90242 102295 81378 95090 201910 FALSE TRUE 88866.7127 84934.37115 96894.13445 130037.0164 88446.36076 106230.3548 73485.97409 74755.74349 178040.4298 0.499137824 0.477051034 0.544225458 0.730379142 0.496776832 0.596664224 0.412748802 0.419880718 1 17.44184536 1.231248679 24.99686036 1.000000843 0.519519778 0.729938612 0.091340401 148.8247413 508733.2709 0.241339012 0.023981187 17.03133449 -1.231248679 -0.480481066 AVEEEDKMTPEQLAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVEEEDKMTPEQLAIK 16 1 O00487 O00487 PSMD14 26S proteasome non-ATPase regulatory subunit 14 0 181.51 1.72E-12 0 151040 105930 90682 99611 106040 74142 143590 158920 110350 FALSE TRUE 131079.6813 105234.1389 134536.1185 122229.2 103930.0115 76994.29072 129664.6639 124936.1947 97304.54871 1.347107438 1.081492492 1.382629284 1.256150937 1.068089959 0.791271238 1.332565287 1.283970753 1 16.57021963 3.255777956 22.59277878 1.121386923 1.2618761 0.197335486 0.167331429 169.9575555 223015.6483 0.051113796 0.06575223 1802.096139 -3.255777956 0.140489177 AVEELHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AVEELHK 7 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ;; 94.887 0.013871 415450000 675720 606350 377855 473115 567580 542567 687920 750460 721710 FALSE TRUE 586421.8899 602366.8469 560586.9418 580542.9919 556286.2685 563439.9036 621205.6243 589979.9691 636390.266 0.921481552 0.946536864 0.880885475 0.91224367 0.874127557 0.885368513 0.976139419 0.927072585 1 19.27955224 0.984883425 0.906399973 1.080422469 0.906355575 0.476449265 0.029527804 3.011245244 1.438974714 0.583327395 0.010751476 9.657916017 -0.984883425 -0.174066894 AVEES(ph)S(ph)DEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVEESSDEER 10 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 AVEES(1)S(1)DEER;AVEES(1)S(1)DEER 110.08 0.0028272 130100000 654370 585890 483170 531500 491440 555960 543800 587180 901520 TRUE FALSE 567893.3465 582041.25 716832.6281 652185.1985 481661.3055 577348.141 491062.3597 461616.1264 794943.3326 0.714382174 0.732179548 0.901740538 0.820417219 0.605906466 0.726275845 0.617732535 0.580690607 1 19.6004925 4.742560421 17.31902636 0.730859168 0.714381946 0 0.13360058 123.353705 531989.767 0.033360177 0.224348245 55279.03099 -4.742560421 -0.016477222 GDAAVRDELMAAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GDAAVRDELMAAVR 14 1 Q15008;Q15008-4;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ;;; 200.55 1.74E-08 1811570000 1442430 1567360 919650 829120 1421230 1586550 1381000 1478780 557860 FALSE TRUE 1251809.221 1557063.909 1364395.816 1017384.368 1392950.304 1647585.605 1247070.833 1162554.405 491910.4263 2.54479099 3.165340326 2.773667203 2.06823095 2.831715347 3.349361016 2.535158366 2.363345729 1 18.90803611 1.132297017 1.84914851 1.42E-16 2.771355625 0.713574101 0.348006357 0.661886434 1.696096856 3.549618694 0.097693956 13.56116554 -1.132297017 2.771355625 AVEHINK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 AVEHINK 7 0 P06733;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8Y6I8 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;;;;; 147.69 0.0021342 39193000000 76937100 75202200 53342400 50787300 58425400 61631200 73404500 79199900 89969600 FALSE TRUE 66769667.3 74708191.8 79138963.06 62319332.7 57262848.85 64002192.14 66285742.89 62263617.72 79333496.38 0.841632732 0.941697961 0.997547904 0.785536193 0.721799132 0.806748663 0.835532857 0.784833904 1 26.2414268 3.725682388 24.84540246 0.814470168 0.928433378 0.271203406 0.080079895 838.815859 1618290.482 0.021794231 0.032553506 5317.192552 -3.725682388 0.11396321 AVEQHNGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AVEQHNGK 8 0 Q9BRA2;I3L0K2;I3L3M7 Q9BRA2 TXNDC17 Thioredoxin domain-containing protein 17 0 ;;; 111.95 0.0031354 815080000 2019510 1476800 843880 1090890 881290 1171940 1523460 1751590 1998560 FALSE TRUE 1752626.637 1467098.804 1251983.191 1338593.248 863754.0532 1217025.29 1375715.084 1377026.109 1762292.514 0.994515169 0.832494488 0.710428706 0.75957495 0.490130921 0.690592101 0.780639464 0.781383396 1 20.74902198 4.627552443 2.535170381 0.739534186 1.019123397 0.291606326 0.123700529 0.524368317 5.011254279 0.032899402 0.280732306 42418.22026 -4.627552443 0.279589212 AVEQLAEGLLSHYLPDLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVEQLAEGLLSHYLPDLQR 19 0 H3BST1;Q9UL45;H3BPR6;H3BN13;Q9UL45-2 H3BST1 BLOC1S6 Biogenesis of lysosome-related organelles complex 1 subunit 6 0 126.22 2.58E-05 73441000 76614 67983 51059 56904 60978 56967 54661 68198 56561 FALSE TRUE 66489.26578 67536.4152 75751.30318 69824.92292 59764.6571 59158.55735 49359.98463 53614.38842 49874.42301 1.333133534 1.354129253 1.518840692 1.400014651 1.198302727 1.18615021 0.989685327 1.074987643 1 15.60601253 2.853180749 1.451642708 1.032831362 1.408964916 0.856323836 0.066373636 0.1403505 0.608467465 0.029782359 0.028277725 713.1497738 -2.853180749 0.376133554 AVEVAWETLQEEFSR ddPTM_MDA-MB-175_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 ; 198.49 1.84E-08 21423300 21056.9 17685.4 11167.3 16424 20743.2 20831.6 13791.4 18796.6 19856.7 FALSE TRUE 18274.17731 17569.22344 16567.84363 20153.32023 20330.4509 21633.00513 12453.91215 14777.09337 17509.26355 1.043686233 1.003424467 0.946233038 1.151009017 1.161125415 1.235517706 0.711275612 0.843958589 1 14.09583078 2.23613133 25 0.84426975 1.085671796 0.52566732 0.106628208 52.02092538 535338.779 0.044654189 0.031704659 172.2389343 -2.23613133 0.241402046 AVEYLLTGIPGS(ph)PEPEHGSVQESQVSEQPATEAAGENPLEFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AVEYLLTGIPGSPEPEHGSVQESQVSEQPATEAAGENPLEFLR 43 0 P54725-2;P54725;A0A494C0B4 P54725-2 RAD23A UV excision repair protein RAD23 homolog A 1 AVEYLLT(0.002)GIPGS(0.991)PEPEHGS(0.008)VQESQVSEQPATEAAGENPLEFLR;AVEY(0.001)LLT(0.103)GIPGS(0.445)PEPEHGS(0.445)VQES(0.005)QVSEQPATEAAGENPLEFLR;AVEYLLTGIPGS(0.994)PEPEHGS(0.006)VQESQVSEQPATEAAGENPLEFLR 237.6 1.75E-54 654720000 138693.3 137578.4 44325.9 94527.1 147117.7 144353 115168.5 151519.8 146895 TRUE FALSE 120364.629 136674.6384 65762.0535 115990.9228 144190.3456 149906.3533 103999.4766 119118.4699 129529.2404 0.929246775 1.055164363 0.507700449 0.895480607 1.11318761 1.157316702 0.80290347 0.919626097 1 16.98291829 3.472414724 24.91503133 0.984023061 0.827890019 0.176425747 0.166122072 238.7458717 1263844.128 0.049307099 0.063900805 2967.663969 -3.472414724 -0.156133042 AVEYLLTGIPGS(ph)PEPEHGSVQESQVSEQPATEAGENPLEFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AVEYLLTGIPGSPEPEHGSVQESQVSEQPATEAGENPLEFLR 42 0 P54725-3 P54725-3 RAD23A UV excision repair protein RAD23 homolog A 1 AVEYLLTGIPGS(0.817)PEPEHGS(0.182)VQES(0.001)QVSEQPATEAGENPLEFLR;AVEYLLTGIPGS(0.998)PEPEHGS(0.002)VQESQVSEQPATEAGENPLEFLR;AVEYLLTGIPGS(0.958)PEPEHGS(0.041)VQESQVSEQPATEAGENPLEFLR;AVEYLLTGIPGS(0.937)PEPEHGS(0.054)VQES(0.009)QVSEQPATEAGENPLEFLR;AVEYLLTGIPGS(0.966)PEPEHGS(0.033)VQES(0.001)QVSEQPATEAGENPLEFLR 275.6 1.58E-80 727866000 178368 212665 69211.8 134437 219847 232422 178180 228786 226653 TRUE FALSE 154796.2169 211267.9896 102682.858 164962.9756 215472.4748 241363.4247 160900.131 179861.8943 199858.3405 0.774529682 1.057088681 0.513778198 0.825399506 1.078126008 1.207672515 0.805070885 0.899946902 1 17.60861826 3.374291681 6.986307518 0.981115265 0.786902861 0.275060616 0.165521376 0.333107311 19.88246796 0.048972164 0.063318624 2367.509233 -3.374291681 -0.194212404 AVEYLLTGIPGSPEPEHGS(ph)VQESQVSEQPATEAAGENPLEFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVEYLLTGIPGSPEPEHGSVQESQVSEQPATEAAGENPLEFLR 43 0 P54725-2;P54725;A0A494C0B4 P54725-2 RAD23A UV excision repair protein RAD23 homolog A 1 AVEYLLT(0.001)GIPGS(0.308)PEPEHGS(0.342)VQES(0.342)QVS(0.007)EQPATEAAGENPLEFLR 87.686 0.00029239 330630000 22537 26259 6652.9 16355 23403 23469 21009 30002 20321 TRUE FALSE 19558.67835 26086.5029 9870.264693 20068.65272 22937.32609 24371.86762 18971.55041 23586.30578 17918.67453 1.09152484 1.45582771 0.550836764 1.119985336 1.280079397 1.360137859 1.058758581 1.31629746 1 14.1291763 3.475540083 24.97857208 1.212950211 1.035101505 0.094305549 0.240527316 117.0617 1849250.406 0.067208407 0.087408263 2989.097515 -3.475540083 -0.177848706 AVEYLLTGIPGSPEPEHGS(ph)VQESQVSEQPATEAGENPLEFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVEYLLTGIPGSPEPEHGSVQESQVSEQPATEAGENPLEFLR 42 0 P54725-3 P54725-3 RAD23A UV excision repair protein RAD23 homolog A 1 AVEYLLT(0.001)GIPGS(0.395)PEPEHGS(0.601)VQES(0.002)QVSEQPATEAGENPLEFLR 166.74 1.27E-19 112530000 25107 25437 10367 20109 28817 33383 25100 27648 28066 TRUE FALSE 21789.04634 25269.90267 15380.51588 24675.0558 28243.59808 34667.26561 22665.80586 21735.69036 24748.06945 0.880434184 1.021085815 0.621483462 0.997049723 1.141244497 1.400806866 0.915861575 0.878278219 1 14.59502837 3.494978718 24.36456962 1.050780131 0.850719097 0.263865182 0.171171729 880.0133893 1200680.312 0.051374222 0.074415755 3125.926179 -3.494978718 -0.200061033 AVEYYFASDASAVIEHTNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVEYYFASDASAVIEHTNR 19 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 102.89 0.00038333 60703000 121797 115851 78181 87354 110773 114925 103471 115777 118918 FALSE TRUE 105701.2179 115089.9672 115989.5931 107189.0608 108568.834 119346.2391 93436.39835 91018.98953 104859.6495 1.008025664 1.097562005 1.106141339 1.022214563 1.035372849 1.138152184 0.891061517 0.86800776 1 16.6781001 2.22632087 24.99818002 0.907729786 1.067440754 0.640897489 0.052045418 125.153626 255608.7267 0.020697252 0.014067872 168.391773 -2.22632087 0.159710967 AVFHEEEQR ddPTM_MDA-MB-175_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 0 134.25 0.00025426 1048000000 862490 820810 541580 596280 818420 820190 802650 937740 828120 FALSE TRUE 748509.7612 815418.0451 803489.8995 731674.4876 802135.0432 851743.24 724809.1265 737211.5985 730220.597 1.025046081 1.116673576 1.100338586 1.001991029 1.09848318 1.166419084 0.992589266 1.009573821 1 19.47797284 2.188512447 24.99999924 1.002226338 1.083833975 0.430580504 0.04557274 104.6807976 52289.20309 0.018534145 0.012495734 154.3520662 -2.188512447 0.081607637 AVFPS(ph)IVGRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVFPSIVGRPR 11 1 C9JTX5;F8WCH0;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;P63267-2;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65;P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6;Q6S8J3;A5A3E0;P0CG38 C9JTX5;P60709;P63261;P68133;Q6S8J3 ACTB;ACTG2;ACTG1;ACTA1;ACTC1;ACTA2;POTEE;POTEF;POTEI "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I" 1 AVFPS(1)IVGRPR 93.649 0.0038901 0 649220 823760 385910 419940 619630 643100 531380 658130 572800 TRUE FALSE 563423.9321 818348.6663 572537.3668 515293.7954 607300.5753 667840.4731 479846.8494 517394.0211 505084.2365 1.115504883 1.620222147 1.133548278 1.020213576 1.202374834 1.322235827 0.950033311 1.024371746 1 18.94616449 2.082141806 0.21160329 0.6879956 1.471347005 0.253868902 0.170323602 15.03671773 1.789985548 4.596090268 2.023249692 120.8208275 -2.082141806 0.783351405 AVFPSIVGR ddPTM_MDA-MB-175_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 ;; 211.39 1.22E-05 4917945000 906801 881481 786101 858140 856766 935956 805574 919101 1694240 FALSE TRUE 786964.9503 875690.4933 1166262.073 1052993.803 839718.0328 971962.833 727449.5575 722558.4036 1493948.877 0.526768327 0.586158273 0.780657284 0.704839248 0.562079497 0.650599795 0.48693069 0.483656713 1 20.51069935 1.228588015 24.99920306 1.000000819 0.596415147 0.644119541 0.09396992 300.8180525 754034.0362 0.337119009 0.025560764 16.92731261 -1.228588015 -0.403585672 AVFPSIVGRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 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 ;;;;;;;;;;; 248.68 2.63E-16 1.54154E+11 46085303 43679198.7 24417758.9 25812935.7 40825870.1 42466260.4 35295498.8 41732365.8 22622335.1 FALSE TRUE 39995013.44 43392267.17 36226268.78 31674157.28 40013515.16 44099964.92 31872546.76 32808224.14 19947948.42 2.004968762 2.175274683 1.816039826 1.587840344 2.005896262 2.210751903 1.597785702 1.644691647 1 24.24973704 0.95839723 1.11268542 1.55E-17 1.944608239 0.686929416 0.199268465 1.798175141 1.198078822 4.80893696 0.065770977 9.086512527 -0.95839723 1.944608239 AVFQFYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVFQFYQR 8 0 Q9BVJ7 Q9BVJ7 DUSP23 Dual specificity protein phosphatase 23 0 117.62 0.0047548 229550000 118070 176030 116820 134300 177480 173370 183870 174170 168590 FALSE TRUE 102466.7503 174873.6473 173314.5427 164794.8676 173948.4952 180039.6561 166038.3157 136925.1009 148659.4823 0.689271541 1.176336986 1.165849229 1.108539228 1.170113689 1.211087603 1.116903632 0.921065369 1 17.18165196 4.745030176 24.70491854 1.101352997 0.689271321 0.691375106 0.087953029 443.426949 1693234.688 0.025162624 0.232430908 55594.28846 -4.745030176 -0.412081675 AVFVDLEPTVIDEVR ddPTM_MDA-MB-175_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 ;;;;;;; 371.12 3.22E-97 4392708000 2666880 2403035 1657424 1832632 2317990 2644630 2317208 2594234 2418166 FALSE TRUE 2314445.051 2387249.305 2458959.79 2248759.106 2271866.534 2746370.627 2092485.525 2039477.247 2132293.17 1.085425345 1.119568987 1.153199675 1.054620039 1.06545693 1.287989225 0.981331064 0.956471313 1 21.02397438 2.049805767 24.99999077 0.973258122 1.123372974 0.532714054 0.065422383 76.24982979 38273.21039 0.025813952 0.017403757 112.1516758 -2.049805767 0.150114852 AVGEPMRPLAEECCQLGLGLCDQVDDPDLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AVGEPMRPLAEECCQLGLGLCDQVDDPDLRR 31 2 Q8TEX9;Q8TEX9-2;H0YN14;H0YMR4 Q8TEX9 IPO4 Importin-4 0 ;; 195.74 7.98E-26 681600000 164790 166481 113056 112267 152541 142638 159575 169365 120356 FALSE TRUE 143012.584 165387.3753 167730.2597 137758.9382 149505.7325 148125.3762 144099.4411 133147.6127 106127.6508 1.347552527 1.558381573 1.580457671 1.298049445 1.408734966 1.395728399 1.357793563 1.2545987 1 16.69544106 0.494854869 0.739280315 2.07E-13 1.452764813 0.73282632 0.083727621 4.024225008 0.761678578 6.288741433 0.035490323 3.12503488 -0.494854869 1.452764813 AVGESVQKPLDYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVGESVQKPLDYYR 14 1 Q14376;Q14376-2;Q5QPP4;Q5QPP3;Q5QPP1 Q14376 GALE UDP-glucose 4-epimerase 0 100.11 0.0017441 406940000 287150 247710 216710 192250 245230 274000 246830 256040 352450 FALSE TRUE 249202.4 246082.7767 321511.6809 235903.3009 240350.4028 284540.9573 222892.4646 201287.8385 310783.7625 0.801851416 0.791813493 1.034518915 0.759059286 0.773368598 0.915559278 0.717194691 0.647678105 1 18.2455516 AVGHPFVIQLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVGHPFVIQLGR 12 0 O14980 O14980 XPO1 Exportin-1 0 ; 102.52 0.0023448 2270100000 3975300 3942800 2370400 2621100 3682200 3783800 3526800 3916500 3408700 FALSE TRUE 3449954.033 3916899.487 3516733.369 3216260.816 3608931.424 3929365.234 3184771.479 3078986.953 3005727.369 1.147793399 1.303145298 1.170010762 1.070044093 1.200684886 1.307292629 1.059567648 1.02437333 1 21.51928273 2.07660227 7.364644813 1.02217428 1.197056588 0.582210324 0.069322333 0.161365738 13.0792434 0.029309638 0.019671779 119.2895143 -2.07660227 0.174882308 AVGIWHCGSCMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVGIWHCGSCMK 12 0 Q6P4E4;E9PEL3;P61513;M0R0A1;C9J4Z3;M0R2L6 Q6P4E4 RPL37A 60S ribosomal protein L37a 0 ; 203.83 1.21E-07 3407200000 5435500 5698500 2833500 4570300 5507400 5352700 6412800 6890100 6432900 FALSE TRUE 4717184.903 5661066.178 4203790.077 5608056.468 5397813.515 5558621.833 5790887.643 5416705.734 5672409.89 0.831601558 0.998000195 0.741094201 0.988655012 0.951590879 0.979940085 1.02088667 0.954921425 1 22.43553036 AVGMPSPVS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AVGMPSPVSPK 11 0 Q9UHB7 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 AVGMPS(0.004)PVS(0.996)PK;AVGMPS(0.001)PVS(0.999)PK;AVGMPSPVS(1)PK;AVGMPS(0.002)PVS(0.998)PK;AVGMPS(0.002)PVS(0.998)PK 140.45 4.05E-05 752895000 2025690 1715530 1263650 1396780 1958490 1515180 1936090 2372240 2307500 TRUE FALSE 1757989.934 1704260.57 1874755.367 1713940.247 1919519.881 1573469.955 1748328.29 1864954.937 2034709.979 0.864000252 0.837593853 0.921387021 0.842351129 0.943387461 0.773314119 0.859251838 0.916570399 1 20.95639174 1.374520384 2.463514892 1.012258992 0.863587932 0.477510989 0.04609108 0.348201139 2.940257818 0.098062206 0.011725777 23.6875631 -1.374520384 -0.14867106 AVGNIVTGTDEQTQVVLNCDALSHFPALLTHPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVGNIVTGTDEQTQVVLNCDALSHFPALLTHPK 33 0 O00629;H7C4F6 O00629 KPNA4 Importin subunit alpha-3 0 197.36 4.08E-27 27573000 28941 25277 15277 23599 27862 20334 25683 29734 26259 FALSE TRUE 25116.37352 25110.95372 22665.0083 28957.51364 27307.60071 21116.26214 23192.26661 23375.61549 23154.69093 1.084720742 1.084486672 0.978851688 1.250611106 1.179355008 0.911964759 1.001622811 1.009541244 1 14.49901688 2.741225915 24.99991989 0.987229611 1.113779172 0.448407512 0.074134938 248.9169929 2334798.708 0.025474918 0.024392599 551.0942952 -2.741225915 0.126549562 AVGWNELEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AVGWNELEGR 10 0 P61457 P61457 PCBD1 Pterin-4-alpha-carbinolamine dehydratase 0 ;;; 220.39 1.36E-08 886320000 729950 934680 533330 523693 537255 735810 480940 360553 1026950 FALSE TRUE 633485.258 928540.0255 791250.1719 642605.4998 526564.6766 764117.0868 434298.5128 283451.5468 905545.1409 0.699562318 1.025393416 0.873783245 0.709633867 0.581489153 0.843819985 0.479598966 0.313017578 1 19.78842703 3.555479162 2.53011811 0.598965337 0.884380933 0.180179896 0.203258357 0.39611927 4.977673351 0.062236027 0.098007274 3593.181556 -3.555479162 0.285415597 AVHADFFNDFEDLFDDDDIQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AVHADFFNDFEDLFDDDDIQ 20 0 Q8WXC6 Q8WXC6 MYEOV2 Myeloma-overexpressed gene 2 protein 0 ;;; 115.34 4.29E-05 27434100 56932 54409 40187.3 42847.8 53259.5 54519 50672.9 61284 53517.9 FALSE TRUE 49408.29195 54051.5837 59622.0127 52577.04788 52199.74015 56616.38121 45758.64996 48178.89351 47191.07483 1.046983823 1.145377254 1.263417138 1.11413118 1.10613586 1.199726461 0.969646276 1.02093232 1 15.52622641 2.233665267 24.99979069 1.00074079 1.148017121 0.592882985 0.058198085 84.47304994 431384.6111 0.023277478 0.016252763 171.2636782 -2.233665267 0.14727633 AVHS(ph)PIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AVHSPIR 7 0 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 AVHS(1)PIR;AVHS(1)PIR;AVHS(1)PIR;AVHS(1)PIR 103.55 0.0053795 1201590000 1563500 1845470 1633960 1636040 1511220 2107740 1887630 2026230 1864190 TRUE FALSE 1356879.514 1833346.986 2424148.521 2007527.887 1481149.679 2188826.122 1704567.933 1592936.483 1643807.582 0.825449115 1.115305104 1.474715501 1.221266959 0.901048088 1.3315586 1.036963177 0.969052887 1 20.64861 2.015336823 24.90739247 0.988523514 1.153703666 0.118786802 0.186433464 442.5843612 718765.436 0.077043975 0.051923529 103.5945295 -2.015336823 0.165180152 AVIDQCNHDNILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVIDQCNHDNILR 13 0 E9PB77;E7EMF1;E7ESP4;P17301 E9PB77 ITGA2 Integrin alpha-2 0 152.99 1.45E-06 0 177990 174160 117930 190670 202770 258600 143850 224510 205980 FALSE TRUE 154468.1705 173015.9315 174961.3425 233964.5377 198735.2737 268548.5093 129899.4491 176500.2836 181629.2791 0.850458535 0.952577318 0.963288206 1.288143293 1.094180821 1.478552966 0.715190028 0.971761186 1 17.47063726 3.983514057 22.61161187 1.075763008 0.915621377 0.138701006 0.199962657 468.8070305 643011.6832 0.054838577 0.098698034 9627.511733 -3.983514057 -0.160141631 AVIFCLSADKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVIFCLSADKK 11 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ; 196.48 9.67E-08 7520000000 6103700 6321800 4289300 5647100 5617500 4626300 9487600 10094800 7744200 FALSE TRUE 5297080.58 6280271.68 6363619.827 6929360.366 5505722.74 4804276.755 8567494.012 7936105.578 6828689.498 0.775709685 0.919689156 0.93189474 1.014742341 0.806263448 0.703543009 1.254632242 1.162171099 1 22.70317731 2.230989853 24.99999384 1.148596169 0.86945985 0.606407106 0.106117488 118.1476812 390140.3021 0.044130005 0.030399821 170.211874 -2.230989853 -0.279136319 AVIFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AVIFDR 6 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 ;;; 109.7 0.068236 1447170000 2385050 2364840 1815540 1821620 2612550 3787860 1565430 2110380 2246210 FALSE TRUE 2069859.6 2349305.21 2693541.217 2235246.663 2560565.366 3933581.425 1413614.84 1659091.66 1980665.613 1.04503233 1.186119048 1.359917191 1.128533079 1.29278024 1.985989659 0.713706963 0.837643492 1 20.91755391 AVIGIGIEEEDRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVIGIGIEEEDRK 13 1 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 112.82 0.00057209 0 107330 95182 44306 60152 100290 108150 93058 90839 51795 FALSE TRUE 93146.06856 94556.74317 65732.52979 73810.43097 98294.42521 112310.6005 84033.24948 71413.78676 45671.85411 2.039463262 2.070350439 1.439234975 1.616103231 2.152188194 2.45907688 1.839935145 1.563627931 1 15.47901774 1.384205539 2.093570004 0.883706534 1.945794537 0.544516876 0.280101018 0.444352958 2.61344737 0.822082268 0.083762531 24.22175123 -1.384205539 1.062088004 AVIPGDEDASFPPLKSEDSGIGLSAS(ph)SPELSEHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVIPGDEDASFPPLKSEDSGIGLSASSPELSEHLR 35 1 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 AVIPGDEDASFPPLKSEDS(0.012)GIGLS(0.168)AS(0.483)S(0.328)PELS(0.009)EHLR 103.14 1.48E-05 178570000 72065 87921 33799 41770 76141 71930 107220 118260 23391 TRUE FALSE 62541.42766 87343.44116 50144.30945 51254.51691 74625.94307 74697.19364 96821.8209 92971.0193 20625.74263 3.032202466 4.234681036 2.43115171 2.484978012 3.618097269 3.621551718 4.694222296 4.507523486 1 14.33215844 3.030288329 23.33530313 3.72331605 3.082370763 0.014623871 1.110342625 290.1016106 223501.8731 0.338686422 0.384026609 1072.230926 -3.030288329 -0.640945287 AVIVPGNGGGDVTTHGWYGWVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVIVPGNGGGDVTTHGWYGWVK 22 0 O75884;O75884-2 O75884 RBBP9 Putative hydrolase RBBP9 0 235.68 1.80E-30 452930000 645310 544910 397990 441750 531020 463450 566120 657500 665620 FALSE TRUE 560030.6485 541330.4503 590459.2952 542056.0892 520453.7409 481279.2214 511217.7695 516898.7417 586931.1619 0.954167515 0.922306542 1.006011154 0.923542869 0.886737278 0.81999262 0.87100124 0.880680351 1 19.16283178 3.424638652 4.13946474 0.8856029 0.958250144 0.290218077 0.048649928 0.258136879 9.259930177 0.01438641 0.019327122 2658.512166 -3.424638652 0.072647244 AVIVSS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AVIVSSPK 8 0 Q14966;Q14966-3;Q14966-5 Q14966 ZNF638 Zinc finger protein 638 1 AVIVS(0.025)S(0.975)PK;AVIVS(0.235)S(0.765)PK;AVIVS(0.246)S(0.754)PK 142.83 0.00064117 1250120000 4979200 3962050 2856180 3298180 4282600 3359110 4664600 5448900 4566670 TRUE FALSE 4321186.104 3936023.033 4237438.201 4047082.179 4197384.639 3488337.135 4212227.81 4283695.138 4026803.475 1.073105785 0.977455954 1.052308171 1.005035931 1.042361433 0.866279459 1.046047525 1.063795431 1 21.94120363 AVLFCLSEDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVLFCLSEDKK 11 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 169.58 2.68E-05 18437200000 7268000 5753100 3976600 5058600 4709200 3797700 8649700 9832600 6851000 FALSE TRUE 6307515.385 5715307.507 5899697.061 6207232.446 4615496.133 3943799.976 7810853.425 7729975.007 6041082.585 1.044103486 0.946073394 0.976595996 1.027503326 0.76401805 0.652830005 1.292955909 1.279567842 1 22.52637568 2.216128874 24.99487436 1.213580821 0.90670736 0.477398682 0.141809385 198.3679184 221032.4811 0.060425073 0.040772135 164.4859753 -2.216128874 -0.306873461 AGDVIS(ph)VYSDIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AGDVISVYSDIK 12 0 U3KQU2;Q8TEA1 U3KQU2 NSUN6 Putative methyltransferase NSUN6 1 AGDVIS(0.919)VY(0.037)S(0.044)DIK 64.091 0.07268 0 32176 21966 28676 37545 58175 39875 53410 62084 129570 TRUE FALSE 27923.86008 21821.7039 42543.80952 46070.16609 57017.43132 41409.01705 48230.30642 48807.81974 114252.3822 0.244405058 0.190995614 0.372366936 0.403231558 0.499048074 0.362434605 0.4221383 0.427193016 1 16.80186472 1.134188785 2.460197904 1.305127562 0.358112094 0.840093091 0.087367511 0.349667768 1.771245535 0.799161302 0.025296614 13.62036622 -1.134188785 -0.947015468 AVLHTDS(ph)SLPFSFPDELPNSCLLAALSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVLHTDSSLPFSFPDELPNSCLLAALSDR 29 0 Q8NCE2 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 AVLHT(0.112)DS(0.436)S(0.436)LPFS(0.017)FPDELPNSCLLAALSDR;AVLHT(0.054)DS(0.456)S(0.456)LPFS(0.035)FPDELPNSCLLAALSDR 83.36 0.0014165 115229000 31072.5 31905.5 35802.1 36343 47861 61732 50820 52728 63417 TRUE FALSE 26966.1904 31695.91067 53116.11531 44595.23362 46908.65974 64106.86999 45891.48422 41452.52753 55919.9145 0.482228749 0.566808997 0.949860453 0.797483938 0.838854282 1.146405007 0.82066442 0.741283814 1 15.77107453 4.312967428 5.194295182 0.883812146 0.506698799 0.64034832 0.116718645 0.130240437 6.21149128 0.030312148 0.083153936 20557.36409 -4.312967428 -0.377113347 AVLHTDSSLPFS(ph)FPDELPNSCLLAALSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVLHTDSSLPFSFPDELPNSCLLAALSDR 29 0 Q8NCE2 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 AVLHTDS(0.001)S(0.001)LPFS(0.998)FPDELPNSCLLAALSDR;AVLHTDS(0.005)S(0.004)LPFS(0.991)FPDELPNSCLLAALSDR 180.33 7.19E-18 375970000 145019 137903 86503 131193 143240 130097 150571 165530 165141 TRUE FALSE 125854.3717 136997.1061 128336.1401 160982.3758 140389.8042 135101.9158 135968.6476 130132.6977 145618.2191 0.864276273 0.940796467 0.881319253 1.105509852 0.96409505 0.927781679 0.933733762 0.893656703 1 17.15183134 AVLLDEDDDLWVELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVLLDEDDDLWVELR 15 0 Q15833-2;Q15833;Q15833-3;M0R0M7 Q15833-2 STXBP2 Syntaxin-binding protein 2 0 ; 142.07 1.08E-05 45849000 41418 43492 34489 36014 49760 46681 47305 46504 55122 FALSE TRUE 35944.50636 43206.29819 51167.99576 44191.52914 48769.87335 48476.84828 42717.36838 36559.48149 48605.53996 0.739514598 0.888917153 1.052719419 0.909187084 1.00338096 0.997352325 0.878858015 0.752166965 1 15.56883314 0.95314503 23.08825456 2.16589111 0.903427956 0.083930059 0.100937395 100.5117666 583497.3476 67165.22628 0.025563055 8.977285359 -0.95314503 -1.262463154 S(ph)PDREASGSGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPDREASGSGGR 12 1 Q8N5F7;A0A494C050 Q8N5F7 NKAP NF-kappa-B-activating protein 1 S(0.961)PDREAS(0.037)GS(0.002)GGR 83.358 0.033789 208130000 282100 253560 141030 168040 184070 236200 227510 258540 91647 TRUE FALSE 244819.7702 251894.3477 209232.5797 206196.0503 180407.3671 245286.7668 205446.1152 203253.233 80812.59606 3.029475381 3.117018385 2.589108504 2.551533553 2.232416429 3.035254141 2.542253624 2.515118222 1 16.30229256 1.134983756 2.39729846 0.170005277 2.72285034 0.793509642 0.274340393 0.394136947 1.875758209 2.379125025 0.075012785 13.64532098 -1.134983756 2.552845063 AVLS(ph)PGSVFSPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVLSPGSVFSPGR 13 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 AVLS(0.861)PGS(0.139)VFSPGR;AVLS(1)PGSVFSPGR 230.96 3.38E-12 871830000 508770 638370 546290 692230 935480 980840 900580 1145240 990570 TRUE FALSE 441534.7554 634176.5054 810477.6712 849411.4016 916865.7782 1018573.549 813241.8902 900339.3383 873465.9431 0.505497391 0.726046059 0.927886974 0.972460814 1.049686923 1.166128522 0.93105163 1.030766392 1 19.73639193 4.530432672 1.240971004 1.03128325 0.373813379 0.898321784 0.059020888 0.298205519 0.522450136 0.017986444 0.229294118 33918.19026 -4.530432672 -0.657469871 AVLSAEQLRDEEVHAGLGELLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AVLSAEQLRDEEVHAGLGELLR 22 1 P50454;E9PR70;E9PPV6;E9PK86;E9PMI5;E9PQ34;E9PIG2;E9PRS3;E9PNX1;E9PJH8 P50454 SERPINH1 Serpin H1 0 ;;;; 200.23 1.00E-22 2880378000 2368287 2404500 1499053 1607421 2464633 3331236 2226761 2282769 572938 FALSE TRUE 2055311.872 2388704.681 2224000.045 1972410.506 2415591.625 3459390.805 2010810.061 1794616.614 505205.9223 4.068265596 4.728180284 4.402165427 3.904171386 4.781400056 6.847486642 3.980179115 3.552247776 1 18.94651203 1.278278668 1.864562386 5.00E-11 4.727445922 0.664310327 0.829509625 0.497480869 1.782823664 4.081017121 0.23671147 18.97923347 -1.278278668 4.727445922 AVLTPNHVEFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVLTPNHVEFSR 12 0 Q8IW45-2;Q8IW45;Q8IW45-4 Q8IW45-2 CARKD ATP-dependent (S)-NAD(P)H-hydrate dehydratase 0 147.33 6.55E-05 199520000 142240 143200 89383 129200 129870 143930 127620 153340 137820 FALSE TRUE 123442.6236 142259.3098 132608.9178 158536.8347 127285.8411 149467.0802 115243.432 120549.4343 121527.0766 1.015762306 1.170597646 1.091188248 1.304539195 1.047386678 1.229907642 0.948294284 0.991955354 1 16.89091826 2.227167076 24.99972657 0.981232004 1.145084408 0.453977034 0.084325918 181.7009324 398685.2447 0.03165676 0.021552282 168.7201978 -2.227167076 0.163852404 AVLVDLEPGTMDSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVLVDLEPGTMDSVR 15 0 P68371;M0QY85;M0R0X0;M0QY37;M0QX14;M0QZL7;A0A075B724;Q3ZCM7;P04350;M0R278 P68371;Q3ZCM7;P04350 TUBB4B;TUBB4A;TUBB8 Tubulin beta-4B chain;Tubulin beta-8 chain;Tubulin beta-4A chain 0 110.66 0.0032111 52183000 64097 67824 37432 45915 74508 72323 49269 55400 66389 FALSE TRUE 55626.41905 67378.45968 55534.2404 56340.70252 73025.43657 75105.31261 44490.89996 43553.14112 58540.56805 0.950220008 1.150970377 0.948645397 0.962421521 1.247433003 1.282961801 0.760001166 0.743982209 1 15.83714912 2.218704236 24.99983916 0.812658762 1.088064874 0.440734882 0.135052061 214.111689 269571.6825 0.05697195 0.038467387 165.4642734 -2.218704236 0.275406113 AVMLLHTHTITSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVMLLHTHTITSR 13 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 227.31 5.39E-12 556180000 176561 173238 96567 107957 141899 202778 158276 183196 148243 FALSE TRUE 153228.0165 172099.9882 143267.1242 132470.2869 139075.4875 210579.0009 142926.4179 144020.961 130717.8814 1.172203947 1.316575715 1.096002495 1.013406012 1.063936211 1.610942578 1.09339607 1.101769394 1 16.99609698 2.027718947 24.9999089 1.069981813 1.208894085 0.147555263 0.16748641 445.1238646 401458.4863 0.070260043 0.047368342 106.5906099 -2.027718947 0.138912272 AVNENHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVNENHK 7 0 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;Q15257-4;A6PVN9;H0Y6E5;H0Y562 Q15257 PPP2R4 Serine/threonine-protein phosphatase 2A activator 0 67.032 0.066262 82336000 74124 72347 50718 65656 44472 62140 81605 79957 168480 FALSE TRUE 64328.32559 71871.74779 75245.39444 80564.19829 43587.09421 64530.56601 73690.95966 62858.81778 148562.4863 0.433005176 0.483781267 0.50648987 0.542291666 0.293392331 0.434366492 0.496026699 0.423113663 1 17.18071034 1.236701405 24.99955705 1.000000688 0.452388524 0.867780326 0.067277759 16.71745154 224724.4101 0.103697409 0.016497768 17.24651716 -1.236701405 -0.547612164 AVNTQALS(ph)GAGILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVNTQALSGAGILR 14 0 O60749;O60749-2 O60749 SNX2 Sorting nexin-2 1 AVNTQALS(1)GAGILR;AVNTQALS(1)GAGILR 143.83 9.46E-06 199315000 186877 193122 124196 126516 184168 188457 196829 208691 199588 TRUE FALSE 162180.731 191853.3689 184257.601 155243.3915 180503.4171 195707.0627 177740.5539 164064.0537 175992.934 0.921518423 1.090119725 1.046960221 0.882100139 1.025628774 1.112016592 1.009930057 0.93221955 1 17.42515798 1.864909597 7.923485756 0.963074908 1.016566755 0.06780586 0.070684335 0.666937569 39.75567559 0.03406108 0.018827666 73.26720044 -1.864909597 0.053491847 AVPALGKS(ph)PPHHSGFQQYQQADASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVPALGKSPPHHSGFQQYQQADASK 25 1 E9PD50;B1ALB4;Q92540-2;Q92540;Q92540-5;Q92540-4 E9PD50 SMG7 Protein SMG7 1 AVPALGKS(1)PPHHSGFQQYQQADASK;AVPALGKS(1)PPHHSGFQQYQQADASK 240.64 8.45E-39 1342170000 742180 832750 263070 612260 1101080 802730 1294740 1502960 766960 TRUE FALSE 644099.0326 827279.6104 390291.5319 751282.9908 1079170.662 833611.5425 1169176.314 1181563.7 676290.8625 0.952399431 1.223260074 0.577106026 1.110887389 1.595719715 1.232622809 1.728806907 1.747123561 1 19.36728434 3.372640336 4.650003819 1.503655128 0.932904528 0.458137871 0.27095256 0.177494541 6.512614203 0.078824381 0.102894757 2358.524197 -3.372640336 -0.5707506 AVPAPSPGPTHNS(ph)PELGRPPAAGVLAPDMSDKDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVPAPSPGPTHNSPELGRPPAAGVLAPDMSDKDK 34 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 AVPAPSPGPTHNS(1)PELGRPPAAGVLAPDMSDKDK;AVPAPSPGPT(0.001)HNS(0.999)PELGRPPAAGVLAPDMSDKDK 223.1 1.16E-36 592610000 413020 287150 207943 232040 250010 184945 375080 447910 352500 TRUE FALSE 358438.3605 285263.6927 308504.9303 284728.2285 245035.2901 192059.9538 338704.7993 352127.9321 310827.8516 1.15317324 0.917754607 0.992526663 0.916031903 0.78833119 0.617898148 1.089686132 1.132871235 1 18.24575626 AVPDSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVPDSER 7 0 O00743;O00743-2;O00743-3 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed" 0 110.9 0.015585 293760000 277480 287000 225460 214060 258650 321010 284630 322580 337850 FALSE TRUE 240810.315 285114.6781 334493.2101 262665.5947 253503.371 333359.4624 257026.6264 253598.7773 297909.7579 0.808333089 0.957050484 1.12280045 0.88169517 0.85094014 1.118994775 0.862766726 0.851260392 1 18.18451585 AVPEHAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AVPEHAAR 8 0 X6RA56;X6RLR1;O75935-2;O75935 X6RA56 DCTN3 Dynactin subunit 3 0 ;; 152.63 0.00045401 137670000 819030 818900 595600 674240 709650 848530 793310 855490 858470 FALSE TRUE 710793.1103 813520.592 883634.1522 827336.4971 695529.3534 881173.4982 716374.9183 672550.1209 756982.6546 0.938982031 1.074688551 1.167310964 1.092939834 0.918818085 1.164060356 0.94635579 0.888461733 1 19.52990072 2.086586049 10.00560442 0.930634088 1.06009443 0.285193227 0.084863846 0.378987018 40.53217284 0.033992527 0.022906869 122.0635648 -2.086586049 0.129460342 AVPIGT(ph)PPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AVPIGTPPK 9 0 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 AVPIGT(1)PPK;AVPIGT(1)PPK;AVPIGT(1)PPK 112.36 0.022085 2199700000 1841010 1860020 2230920 2823980 2886330 2571220 3294450 3680300 6143000 TRUE FALSE 1597715.864 1847801.406 3309800.374 3465207.821 2828897.68 2670136.497 2974954.746 2893296.485 5416781.538 0.294956674 0.341125333 0.611027111 0.639717108 0.522246958 0.492937823 0.549210768 0.534135716 1 22.36900448 1.216223232 3.716884874 1.079539072 0.500910051 0.686181791 0.106794952 0.20084847 4.221833632 0.335054293 0.02915707 16.45217166 -1.216223232 -0.578629021 AVPKEDIYSGGGGGGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVPKEDIYSGGGGGGSR 17 1 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ; 130.39 2.78E-05 707450000 538130 419650 199217 220231 386820 366900 456860 484480 104288 FALSE TRUE 467014.7571 416893.2915 295559.0075 270237.8146 379123.0388 381014.8804 412553.7875 380877.7222 91959.19145 5.078500036 4.533459733 3.214023556 2.93867106 4.122731321 4.143303942 4.48627028 4.141812431 1 16.48870616 4.402448404 4.564204816 3.589965271 4.966646616 0.242124761 0.99998923 0.298958657 11.42952081 0.251838699 0.746221174 25260.8758 -4.402448404 1.376681345 AVPMAPAPAS(ph)PGSSNDSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 AVPMAPAPASPGSSNDSSAR 20 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 AVPMAPAPAS(1)PGSSNDSSAR;AVPMAPAPAS(0.738)PGS(0.262)SNDSSAR;AVPMAPAPAS(1)PGSSNDSSAR;AVPMAPAPAS(0.997)PGS(0.002)SNDSSAR;AVPMAPAPAS(1)PGSSNDSSAR;AVPMAPAPAS(1)PGSSNDSSAR;AVPMAPAPAS(1)PGSSNDSSAR;AVPMAPAPAS(1)PGSSNDSSAR;AVPMAPAPAS(0.996)PGS(0.003)S(0.001)NDSSAR;AVPMAPAPAS(1)PGSSNDSSAR;AVPMAPAPAS(0.984)PGS(0.012)S(0.004)NDSSAR;AVPMAPAPAS(0.99)PGS(0.01)SNDSSAR;AVPMAPAPAS(0.992)PGS(0.006)S(0.002)NDSSAR 399.62 1.01E-131 8114080000 4798791 5008418 3754450 4461355 5973307 6314528 5602770 6214471 6455868 TRUE FALSE 4164618.611 4975517.372 5570114.578 5474373.84 5854449.877 6557451.978 5059414.228 4885554.738 5692662.64 0.73157657 0.874022876 0.978472629 0.961654359 1.02842031 1.151912979 0.888760594 0.858219615 1 22.44067217 4.615553559 2.09855664 0.972915719 0.697476661 0.50928931 0.079309158 0.509576349 3.054363801 0.023538602 0.240824442 41262.31205 -4.615553559 -0.275439059 AVPMIEGYMFEEHEMIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVPMIEGYMFEEHEMIR 17 0 Q9H3U1;A0A1W2PNX8;Q9H3U1-3;Q9H3U1-2 Q9H3U1;Q9H3U1-2 UNC45A Protein unc-45 homolog A 0 ; 211.7 2.23E-12 145692000 91909 98818 70893 72307 91086 95933 93898 105519 106385 FALSE TRUE 79762.99278 98168.85805 105177.0919 88725.40949 89273.56681 99623.60459 84791.78641 82954.583 93808.28649 0.85027662 1.046483863 1.12119191 0.945816333 0.951659711 1.061991518 0.903883757 0.884299097 1 16.51742775 2.21538749 24.90556098 0.918936481 0.999882364 0.131398772 0.079143563 379.1125965 407451.9484 0.032037173 0.021614547 164.2054206 -2.21538749 0.080945883 AVPPVS(ph)PELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AVPPVSPELR 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 AVPPVS(1)PELR;AVPPVS(1)PELR;AVPPVS(1)PELR 119.34 0.00074053 2314270000 1373860 1374590 831270 1028240 1331760 1368160 1159000 1418450 1258850 TRUE FALSE 1192300.92 1365560.228 1233274.952 1261717.608 1305260.582 1420794.001 1046600.358 1115125.506 1110030.187 1.074115762 1.230200983 1.111028301 1.136651618 1.175878455 1.279959786 0.942857564 1.004590252 1 20.08216748 2.224396429 24.99997585 0.985437286 1.167148375 0.683130093 0.059539755 129.6571291 228844.7366 0.023302352 0.015794198 167.6472481 -2.224396429 0.181711089 AVPSWFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVPSWFVR 8 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 138.55 0.0016298 285930000 296370 306350 226550 216400 264700 301880 252620 334320 281170 FALSE TRUE 257203.9536 304337.5667 336110.3378 265536.9275 259432.9879 313493.5189 228120.9513 262828.2697 247930.4029 1.037403846 1.227512088 1.355664065 1.07101398 1.046394411 1.264441615 0.920100757 1.060088906 1 17.91957567 2.421340135 0.887584361 0.99258208 1.186465575 0.244177064 0.115734254 0.947827976 1.539180934 0.128674461 0.058032117 263.839694 -2.421340135 0.193883495 AVPTWASVQVVDDPGSLASVESPGT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVPTWASVQVVDDPGSLASVESPGTPK 27 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 AVPTWASVQVVDDPGSLAS(0.002)VES(0.018)PGT(0.979)PK 86.519 0.029904 81268000 99546 98553 103030 118670 133500 130750 163990 207630 187300 TRUE FALSE 86390.74388 97905.59885 152855.6526 145615.8373 130843.6112 135780.0371 148086.275 163229.9403 165157.6074 0.523080621 0.592801024 0.925513847 0.88167805 0.792234843 0.822124026 0.896636113 0.988328318 1 17.3334839 5.090646459 0.7091773 0.925752086 4.36E-19 0.750371507 0.078452269 2.429951995 0.665730776 0.035590455 2.013547066 123210.1424 -5.090646459 -0.925752086 AVPVES(ph)PVQKV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AVPVESPVQKV 11 1 Q8TB61-5;Q8TB61-4;Q8TB61-3;Q8TB61-2;Q8TB61 Q8TB61-5 SLC35B2 Adenosine 3-phospho 5-phosphosulfate transporter 1 1 AVPVES(1)PVQKV;AVPVES(1)PVQKV;AVPVES(1)PVQKV;AVPVES(1)PVQKV;AVPVES(1)PVQKV 159.5 3.03E-05 1160400000 2277480 1885900 1306854 1483021 2033200 1968790 1947400 2795060 2028090 TRUE FALSE 1976505.248 1873511.399 1938852.966 1819763.585 1992743.298 2044530.625 1758541.448 2197358.17 1788331.511 1.105223073 1.047630927 1.084168653 1.017576201 1.114303073 1.143261534 0.98334198 1.228719707 1 20.77018277 3.186724319 24.99950178 1.104947679 1.063970586 0.029382275 0.072423232 280.2739717 135168.6427 0.020668584 0.023435989 1537.178563 -3.186724319 -0.040977092 AVQALCAVYEHWVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVQALCAVYEHWVPR 15 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ; 188.31 3.05E-07 4387800000 740470 832070 503780 487660 717010 777900 713790 850720 594120 FALSE TRUE 642615.0134 826604.0774 747409.693 598390.6564 702742.9038 807826.3164 644566.7557 668800.1483 523883.8104 1.226636519 1.577838561 1.42667072 1.142220173 1.34140985 1.541995191 1.230362044 1.276619233 1 18.99888735 0.610703731 1.090272446 0.022166002 1.371240472 0.408178619 0.135385349 6.106860427 2.181450411 13.39022995 0.042729409 4.080409322 -0.610703731 1.34907447 AVQELVHPVVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVQELVHPVVDR 12 0 A5YKK6-3;A5YKK6-2;A5YKK6;A5YKK6-4;H3BNB1 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 88.075 0.01019 135930000 303520 275070 179250 219740 286700 311900 252550 288760 285360 FALSE TRUE 263409.063 273263.0471 265935.8996 269635.3255 280995.2309 323898.9948 228057.7399 227010.9211 251625.0659 1.046831571 1.085992948 1.056873641 1.071575777 1.116721937 1.287228654 0.906339514 0.902179281 1 17.94091612 2.187604793 24.9999972 0.927847407 1.10576609 0.564546719 0.072111022 74.69251699 36645.11975 0.029844204 0.020120988 154.0298146 -2.187604793 0.177918683 AVQGMLDFDYVCSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AVQGMLDFDYVCSR 14 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;; 196.15 5.87E-08 280013000 271614 266995 187888 223783 224837 263311 271849 291785 266435 FALSE TRUE 235719.5217 265241.0923 278751.2652 274596.3505 220363.1836 273440.7446 245485.1258 229389.0484 234937.3578 1.003329244 1.128986444 1.186491871 1.168806668 0.937965701 1.163887885 1.044896087 0.976383878 1 17.84191661 1.996676238 6.048958328 0.992774454 1.100170055 0.260164587 0.076803846 0.197678495 30.11171007 0.034553089 0.020921349 99.23759667 -1.996676238 0.107395601 AVQQHQHGYDS(ph)DEEVDSELGTWEHQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 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;AVQQHQHGYDS(1)DEEVDSELGTWEHQLR;AVQQHQHGYDS(1)DEEVDSELGTWEHQLR;AVQQHQHGYDS(1)DEEVDSELGTWEHQLR 400.26 4.90E-146 6779260000 1394216 1275444 902194 1066447 1288065 1284344 1200070 1424139 1436474.2 TRUE FALSE 1209966.823 1267065.524 1338498.036 1308600.091 1262435.027 1333753.545 1083687.396 1119597.958 1266655.857 0.955245118 1.000323425 1.056717994 1.033114152 0.996667737 1.052972311 0.855549983 0.883900668 1 20.27259317 2.242615319 24.99999981 0.904656548 1.016906619 0.516067617 0.046628288 73.73183566 454610.9532 0.017871038 0.013323998 174.8297428 -2.242615319 0.112250072 AVQTLAGSQPTSDKPSQRPS(ph)ESTNCSPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVQTLAGSQPTSDKPSQRPSESTNCSPTR 29 2 Q9NR48-2;Q9NR48 Q9NR48-2 ASH1L Histone-lysine N-methyltransferase ASH1L 1 AVQTLAGSQPTSDKPS(0.044)QRPS(0.23)ES(0.23)T(0.23)NCS(0.23)PT(0.036)R 84.516 0.0010959 322830000 109490 96592 95177 101970 133790 117660 131030 158800 145360 TRUE FALSE 95020.61909 95957.48079 141204.9155 125123.847 131127.8408 122186.4563 118322.7308 124841.8558 128175.7064 0.741330957 0.748640156 1.101651159 0.976190033 1.023031934 0.953273126 0.923129149 0.973989996 1 16.96776332 4.257250519 24.97696857 0.986641417 0.744985283 0.825491234 0.047344166 94.06758517 125708.6358 0.011857308 0.031250906 18082.16881 -4.257250519 -0.241656135 AVQTLAGSQPTSDKPSQRPSESTNCS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVQTLAGSQPTSDKPSQRPSESTNCSPTR 29 2 Q9NR48-2;Q9NR48 Q9NR48-2 ASH1L Histone-lysine N-methyltransferase ASH1L 1 AVQTLAGSQPTSDKPS(0.003)QRPS(0.059)ES(0.021)T(0.021)NCS(0.892)PT(0.004)R 258.96 2.46E-58 371000000 194800 217540 136650 185130 237810 193030 216240 269950 247380 TRUE FALSE 169056.6864 216110.9654 202734.3971 227166.596 233078.0463 200455.989 195269.0781 212223.2933 218135.0182 0.775009386 0.990721101 0.929398676 1.041403613 1.068503573 0.918953732 0.89517529 0.972898781 1 17.73486187 4.741422539 24.70834888 0.974513558 0.7750093 0.585778692 0.053375049 180.7427682 1560343.293 0.013728739 0.093236815 55134.3856 -4.741422539 -0.199504257 AVQVHQDTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVQVHQDTLR 10 0 Q9UKV8-2;Q9UKV8;Q5TA58;A0A6I8PTZ8;Q9UL18 Q9UKV8-2 AGO2;AGO1 Protein argonaute-2;Protein argonaute;Protein argonaute-1 0 ; 126.67 0.0003764 355710000 180915 181683 134405 144846 177048 187861 174153 187804 170662 FALSE TRUE 157006.6244 180489.5124 199403.7076 177735.4981 173525.0912 195088.1342 157263.6689 147643.5761 150486.5328 1.043326745 1.199373187 1.325060149 1.181072451 1.153093822 1.296382677 1.045034834 0.981108232 1 17.19927486 2.087432167 5.933113729 0.996015038 1.20187556 0.58717818 0.076371201 0.134415375 7.256057718 0.031659625 0.021072738 122.3016079 -2.087432167 0.205860522 AVS(ph)LDSPVSVGSSPPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVSLDSPVSVGSSPPVK 17 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 AVS(0.975)LDS(0.025)PVSVGSSPPVK;AVS(0.562)LDS(0.438)PVSVGSSPPVK 340.9 1.66E-72 267130000 1271730 441570 223980 333180 381150 279610 670650 616800 483590 TRUE FALSE 1103667.658 438669.2976 332297.4772 408833.6113 373565.8607 290366.7776 605610.4662 484902.1199 426420.5411 2.588214103 1.028724593 0.77927174 0.958756842 0.876050342 0.68093994 1.420218793 1.137145314 1 18.70191741 4.738096333 6.707321999 0.995412986 2.616062275 0.863281932 0.200500376 0.042041088 12.73113166 0.052422573 0.310923105 54713.73127 -4.738096333 1.620649288 AVS(ph)PAPQSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVSPAPQSSSR 11 0 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 AVS(1)PAPQSSSR;AVS(1)PAPQSSSR 120.59 0.00089739 0 2077240 1905980 1112440 1401860 1817310 2084990 1830310 2198650 2083570 TRUE FALSE 1802727.471 1893459.492 1650419.705 1720173.739 1781149.087 2165200.914 1652806.818 1728485.807 1837252.728 0.981208216 1.030592832 0.89830848 0.936274968 0.969463297 1.178499224 0.899607764 0.940799151 1 20.80911866 AVS(ph)PAVPFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 AVSPAVPFSR 10 0 I3L2J0 I3L2J0 CIC 1 AVS(1)PAVPFSR;AVS(1)PAVPFSR;AVS(1)PAVPFSR;AVS(1)PAVPFSR;AVS(1)PAVPFSR;AVS(1)PAVPFSR;AVS(1)PAVPFSR 161.99 7.24E-06 4700710000 3687670 3432510 2140367 2212947 3028510 3213230 3029717 3370570 2700391 TRUE FALSE 3200335.066 3409961.616 3175455.64 2715430.439 2968248.576 3336845.037 2735895.512 2649799.835 2381153.852 1.344026999 1.4320627 1.333578524 1.140384287 1.246558921 1.401356336 1.148978891 1.112821766 1 21.18322941 -0.218460613 0.376179517 6.04E-12 1.361969466 0.624726587 0.085307093 15.30035982 0.784454626 11.66214215 0.113289034 0.604699191 0.218460613 1.361969466 AVS(ph)PPHLDGPPS(ph)PR ddPTM_MDA-MB-175_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 144.75 4.63E-06 3173060000 2214730 1816470 1498480 1654930 1915020 1883240 1785720 1968390 2757060 TRUE FALSE 1922047.819 1804537.489 2223149.94 2030707.151 1876914.849 1955689.461 1612541.149 1547465.117 2431123.508 0.790600647 0.742264835 0.914453722 0.835295757 0.772035992 0.804438547 0.663290509 0.636522625 1 21.21319176 2.435326571 23.56585225 0.735008354 0.81162212 0.007494186 0.106987869 191.9819026 108246.4474 0.039723965 0.030770102 272.4749433 -2.435326571 0.076613765 AVS(ph)PPHLDGPPS(ph)PRS(ph)PVIGSEVFLPNSNHVASGAGEAEER ddPTM_MDA-MB-175_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 3 AVS(1)PPHLDGPPS(1)PRS(0.998)PVIGS(0.002)EVFLPNSNHVASGAGEAEER 114.63 2.03E-05 168260000 19449 20779 10006 9556.1 23680 21267 19913 21730 11831 TRUE FALSE 16878.76537 20642.50138 14844.93507 11725.95856 23208.81433 22085.15525 17981.84032 17083.2086 10432.35266 1.617925115 1.978700496 1.422970978 1.123999441 2.224696105 2.116987028 1.723661087 1.637522155 1 13.34877692 3.24694563 24.99995772 1.745244179 1.559461611 0.064200684 0.383400323 691.1643494 2060697.579 0.116954805 0.148451248 1765.816743 -3.24694563 -0.185782568 AVS(ph)PQCPEEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVSPQCPEEPR 11 0 A0A2R8YFA9;E9PRG5;A0A2R8Y7K9 A0A2R8YFA9 MICALCL 1 AVS(1)PQCPEEPR 118.58 0.00073597 239330000 138350 147880 85415 111180 142850 150350 142080 163950 154500 TRUE FALSE 120066.697 146908.5665 126721.9797 136425.1183 140007.5645 156134.0618 128301.1035 128890.5684 136235.186 0.881319287 1.078345256 0.93017071 1.00139415 1.027690192 1.146062676 0.94176187 0.946088688 1 17.05573984 4.765390349 23.39176898 1.003053836 0.881318888 0.266652648 0.06587281 5688.542964 4959416.984 0.016480503 1.18294185 58262.66548 -4.765390349 -0.121734947 AVS(ph)PSNPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AVSPSNPK 8 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 AVS(0.965)PS(0.035)NPK;AVS(0.997)PS(0.003)NPK;AVS(0.992)PS(0.008)NPK;AVS(0.953)PS(0.047)NPK 153.7 0.00045825 9626080000 8460000 7338880 5709490 6382600 5473460 7202800 7574500 8934500 9581100 TRUE FALSE 7341989.565 7290670.414 8470618.461 7831866.882 5364548.855 7479896.377 6839926.156 7023926.703 8448433.273 0.869035634 0.862961235 1.002625953 0.927020032 0.634975584 0.885358993 0.809608827 0.831388078 1 23.01025239 AVSDWIDEQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVSDWIDEQEK 11 0 Q12906;Q12906-5;Q12906-2;Q12906-3;K7EKJ9;K7ER69;K7EM82;K7EJ09;K7ERM6;K7ENK6;K7EQ75;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 173.71 2.76E-05 69017000 177350 121590 117910 154330 118790 114350 145270 191370 243860 FALSE TRUE 153912.7482 120791.2673 174931.6704 189372.9853 116426.3114 118749.1185 131181.7378 150447.0147 215031.1486 0.715769549 0.561738465 0.813517816 0.880676993 0.541439285 0.552241474 0.610059234 0.699652193 1 17.71418613 1.241924447 4.482049223 1.027199959 0.667484345 0.461228985 0.111943542 0.194355254 8.143917325 0.22202414 0.029630777 17.45518463 -1.241924447 -0.359715614 AVSETPAVPPVS(ph)EDEDDDDDDATPPPVIAPRPEHTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVSETPAVPPVSEDEDDDDDDATPPPVIAPRPEHTK 36 1 E9PM17;B3KNX7;Q13153;Q13153-2;H0YCM0 E9PM17 PAK1 Non-specific serine/threonine protein kinase;Serine/threonine-protein kinase PAK 1 1 AVSETPAVPPVS(1)EDEDDDDDDATPPPVIAPRPEHTK 67.947 0.0033694 412630000 89750 74264 46121 63353 72096 61750 63559 98764 95227 TRUE FALSE 77889.3101 73776.15489 68425.26987 77738.26694 70661.43065 64125.56246 57395.05796 77644.08718 83969.37254 0.927591903 0.87860791 0.814883663 0.925793115 0.841514334 0.763678 0.683523721 0.924671518 1 16.35757559 4.59003974 3.337692567 0.847358253 0.928147004 0.069964615 0.088492035 0.804832488 14.86032336 0.023266009 0.130769675 38908.07462 -4.59003974 0.080788751 AVSEVARPAS(ph)TPPIMASAIKDEDDEDRIIAELEVFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVSEVARPASTPPIMASAIKDEDDEDRIIAELEVFER 37 3 A0A087WTE6 A0A087WTE6 SRCIN1 1 AVSEVARPAS(0.966)T(0.033)PPIMASAIKDEDDEDRIIAELEVFER 239.61 5.92E-50 70989000 59829 28113 15554 23469 22446 24982 28397 28110 31302 TRUE FALSE 51922.44606 27928.32385 23075.96643 28797.99515 21999.36851 25943.07371 25643.06331 22098.89525 27601.51322 1.881144909 1.011840316 0.836039903 1.043348418 0.797034871 0.939914906 0.92904556 0.800640714 1 14.75245974 4.737553898 3.655292701 0.900894618 1.988624127 0.934998508 0.08010923 0.056739499 1.405281851 0.018394953 0.168241816 54645.43633 -4.737553898 1.087729509 AVSGGS(ph)PERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVSGGSPERR 10 1 Q96HB5-2;Q96HB5;Q96HB5-5;Q96HB5-3;Q96HB5-4 Q96HB5-2 CCDC120 Coiled-coil domain-containing protein 120 1 AVSGGS(1)PERR 104.59 0.00163 420190000 241890 216500 187420 139460 179980 229150 229060 276370 225950 TRUE FALSE 209923.6236 215077.7972 278056.9389 171126.5245 176398.7501 237965.5488 206845.7965 217270.4262 199238.4484 1.053630087 1.079499459 1.395598797 0.858903118 0.885365006 1.194375637 1.038182129 1.090504508 1 17.60413656 3.721689238 24.96397052 1.023552778 1.166568496 0.257721503 0.130566343 1253.145652 1854234.413 0.036485632 0.054270351 5268.527343 -3.721689238 0.143015718 AVSGYQSHDDSS(ph)DNSECSFPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVSGYQSHDDSSDNSECSFPFK 22 0 Q9UBW7 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 1 AVS(0.006)GYQS(0.123)HDDS(0.356)S(0.516)DNSECSFPFK 114.74 0.00014068 89335000 87597 84215 57673 63143 87395 99243 79332 92279 84181 TRUE FALSE 76020.83451 83661.78612 85563.8557 77480.58323 85656.01049 103060.9424 71638.39485 72545.85397 74229.21808 1.02413627 1.12707352 1.152697791 1.043801689 1.15393928 1.388414766 0.965096989 0.977322082 1 16.17969955 AVSLFSLNDPALSPDIPPAHS(ph)PVHSHLSLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVSLFSLNDPALSPDIPPAHSPVHSHLSLER 31 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 AVSLFSLNDPALSPDIPPAHS(0.333)PVHS(0.333)HLS(0.333)LER;AVSLFSLNDPALSPDIPPAHS(0.545)PVHS(0.183)HLS(0.272)LER 167.95 1.84E-12 418362000 141716 128083 43241 80141 138850 144661 116992 136929 125080 TRUE FALSE 122987.8715 127241.6143 64152.49223 98338.23893 136087.1567 150226.2023 105646.1338 107647.7989 110293.1849 1.115099466 1.15366706 0.581654182 0.891607573 1.233867322 1.36206242 0.957866381 0.976014964 1 16.75098412 3.265803059 24.92021217 1.091416704 0.925814651 0.156445087 0.194483256 457.0500946 418086.4654 0.060423137 0.077986274 1844.178945 -3.265803059 -0.165602053 AVSLFSLNDPALSPDIPPAHSPVHS(ph)HLSLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVSLFSLNDPALSPDIPPAHSPVHSHLSLER 31 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 AVSLFSLNDPALSPDIPPAHS(0.251)PVHS(0.375)HLS(0.375)LER 171.48 1.10E-12 153090000 47198 44278 16974 31823 55014 58207 47473 55583 40476 TRUE FALSE 40960.66472 43987.1349 25182.68317 39048.89853 53919.32903 60446.26095 42869.07577 43697.008 35690.97339 1.147647733 1.232444249 0.70557569 1.094083316 1.510727333 1.693600796 1.201118145 1.22431539 1 15.12327163 3.416862144 8.838834058 1.321221576 1.024321771 0.278818215 0.226502744 0.415041256 56.08852982 0.069220739 0.089461101 2611.332322 -3.416862144 -0.296899805 AVSPPHLDGPPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVSPPHLDGPPSPR 14 0 P29590-2;P29590-5;P29590-9;P29590-3;P29590-8;P29590;P29590-4;H3BVD2;H3BRN3;P29590-12;P29590-13;P29590-11;H3BT57;H3BUJ5 P29590-2;P29590-12 PML Protein PML 1 AVSPPHLDGPPS(1)PR;AVSPPHLDGPPS(1)PR 185.99 7.18E-07 703170000 453020 406740 247330 339170 436150 396810 372860 435040 486090 TRUE FALSE 393152.2592 404068.0982 366939.6153 416183.7324 427471.4683 412075.5375 336700.0946 342010.0815 428624.994 0.917240629 0.942707737 0.856085437 0.970974018 0.997308777 0.961389427 0.785535373 0.797923794 1 18.70935645 2.253500813 24.98759648 0.844829548 0.941099741 0.221065538 0.068359107 286.4605374 479107.1325 0.025949748 0.020017938 179.2671907 -2.253500813 0.096270193 AVSTCAHLFWSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVSTCAHLFWSGR 13 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 80.534 0.017528 474160000 332860 320680 174110 208780 303660 310770 308910 327570 275900 FALSE TRUE 288871.7076 318573.432 258310.1784 256186.69 297617.7601 322725.523 278951.9557 257521.7047 243283.4163 1.187387583 1.309474508 1.061766487 1.053038032 1.223337639 1.326541397 1.146613115 1.05852552 1 17.89227846 1.696897378 2.891371383 1.013226321 1.190306294 0.368221333 0.088434872 0.258543365 4.776802615 0.077426464 0.025606353 49.76194855 -1.696897378 0.177079973 AVSTVVVTTAPS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVSTVVVTTAPSPK 14 0 Q6P4R8-3;Q6P4R8;Q6P4R8-2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 1 AVSTVVVTTAPS(1)PK 144.29 9.33E-06 87549000 171650 128930 104820 123270 147080 145890 153670 192920 155200 TRUE FALSE 148966.0176 128083.0503 155511.3026 151260.3376 144153.3958 151502.4827 138767.1071 151665.5593 136852.4328 1.08851567 0.935920887 1.136342989 1.105280589 1.053349165 1.107049978 1.013990794 1.108241602 1 17.06226156 4.229650131 24.99999898 1.076072679 1.012218265 0.177446085 0.056055746 265.2654997 744257.1148 0.013081675 0.027871808 16968.76093 -4.229650131 -0.063854414 AVT(ph)PENHESMTSIFPSAAVGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVTPENHESMTSIFPSAAVGLK 22 0 H0YA93;Q86UW6-2;Q86UW6 H0YA93 N4BP2 NEDD4-binding protein 2 1 AVT(0.965)PENHES(0.034)MT(0.001)SIFPSAAVGLK;AVT(0.984)PENHES(0.014)MT(0.001)S(0.001)IFPSAAVGLK 136.16 1.82E-05 194983000 283930 303870 62647 168979 345610 318870 261350 340230 233480 TRUE FALSE 246407.9311 301873.858 92943.29874 207348.2646 338733.0372 331137.1352 236004.3172 267474.4622 205878.2604 1.196862314 1.4662736 0.451447854 1.007140163 1.645307458 1.608412343 1.146329471 1.299187499 1 17.65143197 3.30302923 24.99887732 1.333681663 1.020204841 0.195306846 0.311637698 106.4993336 41295.58649 0.092533522 0.11946023 2009.228038 -3.30302923 -0.313476822 AVT(ph)PLRPGELLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVTPLRPGELLFR 13 1 Q9H7B4;B0QZ88 Q9H7B4 SMYD3 Histone-lysine N-methyltransferase SMYD3 1 AVT(1)PLRPGELLFR;AVT(1)PLRPGELLFR 158.45 7.64E-05 108779000 132389 151240 102300 113304 138125 149751 136410 156189 151028 TRUE FALSE 114893.4582 150246.4945 151772.6222 139031.4049 135376.5827 155512.0179 123180.9792 122789.1978 133173.6419 0.862734221 1.128199938 1.13965962 1.043985904 1.016541868 1.167738718 0.924965162 0.922023278 1 17.02294904 2.207600824 24.98787014 0.942375417 1.063862238 0.264079525 0.086794535 238.3659115 192385.2148 0.034053395 0.022961408 161.2875421 -2.207600824 0.121486821 AVT(ph)PSSEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AVTPSSEAK 9 0 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5 Q99700 ATXN2 Ataxin-2 1 AVT(0.989)PS(0.011)S(0.001)EAK;AVT(0.935)PS(0.062)S(0.003)EAK;AVT(0.977)PS(0.017)S(0.006)EAK;AVT(0.986)PS(0.014)SEAK;AVT(0.978)PS(0.014)S(0.008)EAK;AVT(0.953)PS(0.04)S(0.007)EAK 173.64 0.00061792 2810100000 7788470 6259440 4985920 5558280 4987100 5599770 7461280 8078020 7776000 TRUE FALSE 6759203.956 6218321.326 7397127.589 6820372.427 4887866.467 5815196.775 6737686.214 6350598.286 6856730.138 0.985776576 0.906893111 1.078812705 0.994697515 0.712856765 0.848100575 0.982638383 0.926184662 1 22.70908931 AVT(ph)PVPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AVTPVPTK 8 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 1 AVT(0.999)PVPT(0.001)K;AVT(0.997)PVPT(0.003)K;AVT(1)PVPTK;AVT(1)PVPTK;AVT(1)PVPTK;AVT(1)PVPTK 148.56 0.0058054 20009670000 18624000 16669800 14163300 17696000 15778700 14340700 18125600 21713800 34964200 TRUE FALSE 16162791.21 16560294.99 21012719.25 21714147.27 15464734.74 14892396.01 16367782.1 17070472.85 30830772.11 0.524242181 0.537135266 0.681550212 0.704301118 0.501600631 0.483036752 0.530891087 0.55368295 1 24.87786768 1.23764636 24.98963914 1.000000512 0.5651189 0.780292859 0.072614901 11.39681039 311336.6468 0.113624603 0.019256731 17.28408366 -1.23764636 -0.434881612 AVT(ph)PVPTKTEEVSNLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AVTPVPTKTEEVSNLK 16 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 1 AVT(0.999)PVPT(0.001)KTEEVSNLK;AVT(0.973)PVPT(0.027)KTEEVSNLK;AVT(1)PVPTKTEEVSNLK;AVT(1)PVPTKTEEVSNLK 195.39 9.57E-11 10416610000 21215800 16847100 10403890 11719210 15117300 11474600 22346800 25859900 5837500 TRUE FALSE 18412078.28 16736430.29 15435246 14380235.75 14816495.31 11916035.29 20179610.78 20329961.63 5147397.4 3.576968484 3.251435432 2.998650542 2.793690603 2.878444028 2.314963148 3.92035221 3.949561312 1 22.29541174 4.536563402 2.271343435 2.974196453 3.610755037 0.065841401 0.83145298 1.471870851 11.96743559 0.220561439 1.569918657 34400.39287 -4.536563402 0.636558584 AVT(ph)PVSQGSNSSSADPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVTPVSQGSNSSSADPK 17 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 AVT(0.635)PVS(0.365)QGSNSSSADPK;AVT(1)PVSQGSNSSSADPK 196.71 1.76E-10 313400000 218476 201223 129283 168333 177670 163981 220458 265672 210609 TRUE FALSE 189603.8431 199901.1529 191804.6912 206555.5805 174134.7146 170289.4552 199078.0171 208860.1103 185711.0439 1.020961592 1.076409613 1.03281252 1.112241771 0.937664831 0.916959226 1.071977266 1.124650994 1 17.50270009 0.925238502 18.62775158 6.66E-05 1.040491648 0.025876587 0.067318749 207.2511389 84697.53628 5690.353256 0.017179235 8.418573377 -0.925238502 1.04042509 AVT(ph)TPGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AVTTPGKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AVT(0.5)T(0.5)PGKK;AVT(0.853)T(0.147)PGKK;AVT(0.884)T(0.116)PGKK 98.943 0.0041984 3171380000 15495800 13407700 9223500 10701100 7070900 7669200 14934700 16620800 14214100 TRUE FALSE 13447990.77 13319623.94 13684015.45 13130948.31 6930202.924 7964239.087 13486335.09 13066571.26 12533725.29 1.072944432 1.062702718 1.0917756 1.047649283 0.552924431 0.635424736 1.076003724 1.042512977 1 23.57931194 3.444861535 24.99998795 0.880767446 1.073700255 0.276573052 0.165535342 316.5029336 245276.142 0.054540651 0.070412172 2785.23302 -3.444861535 0.192932808 AVTDKFLSAIVSSVDKIPYGMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVTDKFLSAIVSSVDKIPYGMR 22 2 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 173.78 1.90E-12 377040000 711260 785870 294870 306350 641970 533590 927440 1067860 69391 FALSE TRUE 617265.1889 780707.5682 437470.1183 375911.4498 629196.053 554117.5526 837497.0115 839506.4491 61187.67503 10.08806412 12.75922917 7.149644402 6.143581196 10.28305215 9.056032155 13.68734816 13.72018873 1 15.90095346 4.255759302 24.99037265 9.408345912 11.42364559 0.05927485 3.768574262 921.9498027 1339606.107 0.964470025 2.538471512 18020.18734 -4.255759302 2.015299675 AVTELNEPLSNEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AVTELNEPLSNEDR 14 0 Q04917 Q04917 YWHAH 14-3-3 protein eta 0 ;;; 289.75 4.48E-43 1121450000 700490 665320 460247 523000 615740 696400 611460 650200 732230 FALSE TRUE 607918.4717 660949.4691 682823.9886 641755.1436 603487.9787 723190.9586 552160.7033 511159.7899 645666.6036 0.941536187 1.023669902 1.057548873 0.993941982 0.934674297 1.120068708 0.855179283 0.791677604 1 19.30042988 2.208769919 24.9966862 0.862279392 1.010188869 0.397043943 0.073921805 172.6661104 144878.9652 0.02906346 0.019597568 161.7223036 -2.208769919 0.147909476 AVTEQGAELSNEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AVTEQGAELSNEER 14 0 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;; 232.7 1.60E-13 1077420000 373088 380801 235831 256072 359166 380543 349144 366527 382126 FALSE TRUE 323783.4755 378299.4932 349879.6604 314217.0614 352019.2993 395182.7355 315284.0686 288148.0534 336951.4996 0.96092012 1.122712003 1.038368017 0.932529049 1.044718008 1.172817856 0.935695698 0.855161807 1 18.36218142 2.025522488 24.99095934 0.910693307 1.044293202 0.327784106 0.076887445 212.2751904 207853.4286 0.030964863 0.020875842 106.0528851 -2.025522488 0.133599895 AVTEQGHELSNEER ddPTM_MDA-MB-175_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 ;;;;;;;;;;; 297.72 1.07E-43 82886470000 27752199 22036323 13984672 17673659 21868081 22925120 20424409 24029714 24965746 FALSE TRUE 24084675.59 21891564.94 20747706.16 21686733.4 21432948.97 23807064.2 18443652.96 18891146.66 22014323.95 1.094045661 0.994423676 0.942463925 0.985119209 0.973591059 1.081435172 0.837802378 0.858129766 1 24.3919392 8 0.195372839 0.875236426 1.73359334 0.242994608 0.07112317 149.5325243 2.192392654 0.531241794 37.74490042 100000000 -8 0.858356914 AVTFS(ph)PDLGPVPHEGLGEYNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVTFSPDLGPVPHEGLGEYNR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 AVT(0.155)FS(0.845)PDLGPVPHEGLGEYNR;AVT(0.002)FS(0.998)PDLGPVPHEGLGEYNR 169.91 5.72E-12 477330000 255460 304110 167974 188255 281530 311570 282680 290120 286990 TRUE FALSE 221700.3137 302112.2814 249206.7882 231001.175 275928.1038 323556.2995 255265.7371 228080.0957 253062.3691 0.876069858 1.193825389 0.984764306 0.912823095 1.090356123 1.278563465 1.008706818 0.901280173 1 17.94913347 1.997322884 24.99692633 0.947010094 1.061593567 0.112668046 0.121445949 197.5615491 1844685.862 0.05043537 0.033327529 99.38546722 -1.997322884 0.114583473 AVTGYRDPYTEQTISLFQAMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVTGYRDPYTEQTISLFQAMK 21 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 175.32 9.59E-18 0 243090 183710 134700 147730 181160 188710 210420 254880 136710 FALSE TRUE 210965.0406 182503.1969 199841.3705 181274.3544 177555.2704 195969.7958 190013.5008 200375.8955 120548.2995 1.750045761 1.513942524 1.657770133 1.503748747 1.472897346 1.625653755 1.576243726 1.662204247 1 16.87925177 1.2343692 24.99986065 0.999999134 1.591225119 0.831684821 0.084146891 47.50833778 283326.7667 0.148334064 0.019667011 17.15414989 -1.2343692 0.591225984 AVTIANS(ph)PSKPSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVTIANSPSKPSEK 14 1 Q8NEF9 Q8NEF9 SRFBP1 Serum response factor-binding protein 1 1 AVTIANS(0.965)PS(0.035)KPSEK 195.78 1.56E-08 387200000 567360 454590 472220 589250 462320 314100 592960 738620 1074500 TRUE FALSE 492381.9385 451603.7684 700587.1715 723048.2186 453120.7365 326183.6302 535454.8305 580671.8609 947473.8341 0.519678666 0.476639831 0.739426406 0.763132651 0.478240897 0.344266637 0.565139438 0.612863216 1 19.85372658 1.215012318 3.131621572 1.094634975 0.557576551 0.560734139 0.122653343 0.338949565 4.145001244 0.4694547 0.034310397 16.40636305 -1.215012318 -0.537058424 AVTIANS(ph)PSKPSEKDSVVSLESQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVTIANSPSKPSEKDSVVSLESQK 24 2 Q8NEF9 Q8NEF9 SRFBP1 Serum response factor-binding protein 1 1 AVT(0.016)IANS(0.821)PS(0.163)KPSEKDSVVSLESQK 132.76 2.45E-05 260880000 211550 155760 161310 140640 157340 104330 294230 239190 128370 TRUE FALSE 183593.1315 154736.8023 239320.0555 172574.4615 154209.2418 108343.6426 265695.6199 188041.0799 113194.2448 1.621929911 1.367002382 2.114242256 1.524586889 1.362341717 0.957147978 2.347253787 1.661224739 1 16.78844108 3.553708775 24.99969332 1.522792405 1.69294593 0.052018898 0.422516686 540.9255997 176564.8261 0.1190868 0.176634225 3578.563888 -3.553708775 0.170153525 AVTIFIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVTIFIR 7 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 114.19 0.013869 95695000 138040 166470 108120 114620 166470 217800 143320 136840 124910 FALSE TRUE 119797.6643 165376.4476 160407.1936 140646.2229 163157.5727 226178.9069 129420.8485 107577.8309 110143.2821 1.087652937 1.501466494 1.456350225 1.276938731 1.481321144 2.053497069 1.175022625 0.976708056 1 16.74902198 2.011027347 24.99731065 1.013442698 1.479844858 0.421826363 0.241893932 193.9340218 439617.1147 0.099310349 0.066888853 102.5716513 -2.011027347 0.46640216 AVTIHDTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVTIHDTEK 9 0 A0AVT1;A0AVT1-4;A0AVT1-3 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 159.37 6.61E-05 344930000 546520 419680 224420 325040 436760 373830 496970 543400 516160 FALSE TRUE 474295.9973 416923.0944 332950.2626 398845.2999 428069.3305 388211.482 448773.9259 427198.1387 455140.1528 1.042087793 0.91603233 0.731533486 0.876313148 0.940522008 0.852949316 0.986012601 0.938607891 1 18.79595134 2.230952072 24.99009486 0.967782303 0.888305236 0.190602805 0.078412846 303.9960043 998457.3514 0.032435272 0.022342966 170.1970672 -2.230952072 -0.079477067 AVTLHDQGTAQWADLSSQFYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AVTLHDQGTAQWADLSSQFYLR 22 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 344.28 5.86E-82 4256060000 1502310 1198993 849234 977549 1221667 1298613 1130081 1260970 1277900 FALSE TRUE 1303775.927 1191116.736 1259926.403 1199516.441 1197358.217 1348571.482 1020485.919 991321.3784 1126828.118 1.157031766 1.057052728 1.118117646 1.06450702 1.06259171 1.196785438 0.905626956 0.879744979 1 20.10383604 2.222134584 24.99775119 0.917357568 1.103205818 0.717467552 0.053266691 115.7311108 176122.5595 0.020762049 0.014042705 166.7763959 -2.222134584 0.18584825 AVTT(ph)PGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVTTPGKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AVT(0.433)T(0.567)PGKK 53.756 0.078858 1693000000 9409500 8414100 6002300 6734000 4985400 5102800 9608800 10235000 9108500 TRUE FALSE 8166010.734 8358827.223 8905032.356 8263057.623 4886200.294 5299108.018 8676940.055 8046324.899 8031703.506 1.016722135 1.040729058 1.108735195 1.028805112 0.608364127 0.659773859 1.080336201 1.00182046 1 22.93727458 3.448462716 24.99969351 0.88513101 1.056402707 0.263265075 0.147896748 342.8958356 299117.1655 0.047966336 0.061925306 2808.424263 -3.448462716 0.171271697 AVTTNQWHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVTTNQWHR 9 0 Q9Y6Y8;Q9Y6Y8-2;A0A0C4DH82 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 ; 170.5 5.77E-05 722350000 817380 746480 560560 639500 658880 744850 784420 790820 736420 FALSE TRUE 709361.162 741576.3237 831648.691 784708.2491 645769.5771 773504.8615 708347.0691 621709.2972 649361.2665 1.092398328 1.142008866 1.280718044 1.208430945 0.994468889 1.19117801 1.090836651 0.957416663 1 19.30866181 1.910698401 3.635083667 0.97939034 1.152250572 0.46702165 0.075295962 0.208356456 4.818399104 0.04499322 0.021314292 81.41387027 -1.910698401 0.172860232 AVTTVTQSTPVPGPSVPPPEELQVS(ph)PGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 111.72 0.00019842 680910000 482865 437881 276736 327089 445158 451931 380671 483050 426555 TRUE FALSE 419053.1668 435004.5309 410566.4552 401359.5567 436300.2267 469317.078 343753.585 379753.5166 376128.1538 1.114123371 1.156532757 1.09156002 1.067081931 1.159977583 1.247758439 0.91392676 1.009638637 1 18.52086477 2.227878771 25 0.979313011 1.135738853 0.673436521 0.054082324 131.2153078 307096.2147 0.022447916 0.015306389 168.9969128 -2.227878771 0.156425842 AVVHTHLLNPEWLVNYFGSLSVEDSLECLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AVVHTHLLNPEWLVNYFGSLSVEDSLECLR 30 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 291.65 4.12E-81 4446200000 597590 536011 410291 436787 485327 515129 539377 628404 618912 FALSE TRUE 518616.9674 532489.9084 608709.0999 535966.1642 475669.9422 534946.346 487068.3016 494024.6948 545744.9284 0.950291868 0.97571206 1.115372894 0.982081805 0.871597549 0.980213133 0.892483423 0.905230024 1 19.05786729 3.468624421 24.53090954 0.926557484 1.016441434 0.3196532 0.056501041 162.5351709 469246.5611 0.015942853 0.020614998 2941.876393 -3.468624421 0.08988395 AVVIVDDR ddPTM_MDA-MB-175_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 ;;;;; 175.86 0.00061346 3987590000 7413410 6345290 4175620 4860580 5896790 6175970 5752750 6540690 6149880 FALSE TRUE 6433709.085 6303607.372 6194963.799 5964248.978 5779455.416 6413563.562 5194849.19 5142014.343 5422848.192 1.186407743 1.162416344 1.142381933 1.09983698 1.065760134 1.182692809 0.957955858 0.948212851 1 22.37061935 2.230148984 24.98460556 0.964001299 1.13585833 0.814747873 0.038426894 74.54516185 221415.1856 0.016124499 0.011068805 169.8826331 -2.230148984 0.171857031 AVVLPGGTATS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVVLPGGTATSPK 13 0 Q8N1G0;F8WCX2;Q8N1G0-2;H0Y5I5 Q8N1G0 ZNF687 Zinc finger protein 687 1 AVVLPGGT(0.049)AT(0.108)S(0.843)PK 72.497 0.041316 73110000 243520 234310 199340 195390 270750 212380 288350 296070 369260 TRUE FALSE 211338.215 232770.8022 295741.4908 239756.2858 265362.6047 220550.396 260385.8614 232757.7345 325606.5035 0.649060178 0.714883762 0.90827882 0.736337522 0.814979437 0.677352552 0.799694904 0.714843629 1 18.31276999 1.232756779 24.9799395 1.000000399 0.755310379 0.522393695 0.074481995 153.6811476 661380.0217 0.152152846 0.017476484 17.09057911 -1.232756779 -0.244690019 AVVPGPAEHPLQYNYTFWYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVVPGPAEHPLQYNYTFWYSR 21 0 B9A044;B8ZZ50;O60573-2;O60573;C9JEL3 B9A044 EIF4E2 Eukaryotic translation initiation factor 4E type 2 0 ; 220.73 4.57E-25 765330000 422350 413730 271320 296510 367950 380800 405550 411770 382240 FALSE TRUE 366535.3774 411012.1804 402531.2595 363837.1274 360628.5149 395449.6224 366219.8234 323716.1899 337052.0226 1.087474196 1.21943247 1.194270417 1.079468755 1.06994912 1.1732599 1.086537979 0.960433904 1 18.36261176 1.895350143 3.752931869 0.980834093 1.137752151 0.618521893 0.050246832 0.152881187 3.628060499 0.030308837 0.014304001 78.58689745 -1.895350143 0.156918058 AVVPSKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVVPSKR 7 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;G3V576;G3V555;G3V575;P07910-2;G3V4C1;B2R5W2;G3V2D6 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ; 115.46 0.0091004 5915800000 5502400 3971300 2580970 3399800 3930200 4464300 3786700 5530100 3058800 FALSE TRUE 4775243.899 3945212.269 3829135.725 4171776.553 3851996.709 4636044.51 3419466.417 4347531.15 2697192.149 1.770450022 1.462710868 1.4196748 1.546710921 1.428150646 1.718841022 1.267787472 1.611872982 1 21.36302687 1.232188943 24.99878501 0.999999139 1.517942982 0.556370259 0.147993245 155.6985713 610812.5358 0.300699602 0.03271325 17.06824795 -1.232188943 0.517943843 AVVS(ph)PPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AVVSPPK 7 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 AVVS(1)PPK;AVVS(1)PPK 83.998 0.022939 201072000 375090 357620 303060 381710 364680 316470 394550 440970 855220 TRUE FALSE 325520.9061 355270.7707 449620.8297 468383.0896 357423.5815 328644.8057 356286.6017 346671.9971 754116.8659 0.431658435 0.471108374 0.596221687 0.621101464 0.473963119 0.435800896 0.472455422 0.459705933 1 19.52442859 1.236029798 24.99875185 1.000000664 0.496327588 0.861388175 0.063631028 26.47419302 261449.2675 0.112209423 0.016991724 17.2198672 -1.236029798 -0.503673075 AVVS(ph)PPKFVFGSESVK ddPTM_MDA-MB-175_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 183.45 1.20E-09 1309550000 2097010 1751280 1333750 1383210 1878220 1344960 2409600 2902900 1527780 TRUE FALSE 1819884.815 1739775.726 1978755.961 1697288.972 1840847.097 1396701.482 2175917.363 2282137.425 1347167.589 1.35089712 1.291432292 1.468826876 1.259894452 1.366457382 1.036768917 1.615179419 1.694026374 1 20.3614979 2.202083459 24.99975905 1.497522666 1.304973895 0.064095274 0.212621845 323.8071554 221920.2582 0.084989316 0.057301638 159.2514735 -2.202083459 -0.192548771 AVVVS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AVVVSPK 7 0 O75909;G3V5E1;O75909-1 O75909 CCNK Cyclin-K 1 AVVVS(1)PK 96.665 0.01318 1133200000 2390500 1520700 1346700 1579400 1696200 1370400 1816200 2141500 3122500 TRUE FALSE 2074589.368 1510710.422 1997968.624 1938026.91 1662448.939 1423120.175 1640065.204 1683556.89 2753361.607 0.753475084 0.548678538 0.725647012 0.703876637 0.603788814 0.516866427 0.595659211 0.611455061 1 21.39276267 1.237039109 24.99928974 1.000000457 0.627745892 0.699146865 0.07572109 21.99913942 361335.0811 0.112916973 0.018405256 17.25993313 -1.237039109 -0.372254564 AVVVS(ph)PKEENK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AVVVSPKEENK 11 1 O75909;G3V5E1;O75909-1 O75909 CCNK Cyclin-K 1 AVVVS(1)PKEENK;AVVVS(1)PKEENK;AVVVS(1)PKEENK;AVVVS(1)PKEENK 128.96 0.00015437 1719800000 7321800 4513460 3224000 2578200 4185810 3079620 6113300 6816400 1559030 TRUE FALSE 6354205.579 4483810.784 4783137.184 3163619.715 4102520.57 3198094.974 5520433.107 5358765.905 1374723.249 4.62217074 3.261609772 3.479345523 2.301277524 2.984251974 2.326355487 4.015668688 3.898068871 1 20.39070978 5.072703751 1.399984311 2.964621825 6.713219756 0.28219692 0.876031706 4.218896481 4.038680906 0.246435701 27.82755592 118223.4832 -5.072703751 3.748597931 AVYDEQGTVDEDSPVLTQDRDWEAYWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AVYDEQGTVDEDSPVLTQDRDWEAYWR 27 1 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 ;;; 367.99 8.19E-127 1298880000 528023 514284 301402 341221 483533 499411 427598 541827 328747 FALSE TRUE 458243.4227 510905.6345 447161.0153 418700.4433 473911.6393 518623.6643 386129.6118 425961.5126 289882.9042 1.580788022 1.762455209 1.542557387 1.444377841 1.634838179 1.789079856 1.332019261 1.469426125 1 18.14511073 0.763268399 1.043008854 2.81E-12 1.610181253 0.674772104 0.129051483 2.682492825 1.171533434 6.152902298 0.041487966 5.797869003 -0.763268399 1.610181253 AWALLQLDGT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AWALLQLDGTPR 12 0 A0A499FJE4;Q96MK2 A0A499FJE4 FAM65C Protein FAM65C 1 AWALLQLDGT(1)PR 98.337 0.049359 224140000 296500 252670 218120 233810 268940 319070 246570 292720 292650 TRUE FALSE 257316.7738 251010.1941 323603.5616 286900.1341 263588.6202 331344.8294 222657.6794 230124.1059 258053.2504 0.997146028 0.972706966 1.254018545 1.111786554 1.021450494 1.284017267 0.862836174 0.891769841 1 17.97730928 2.209356424 24.99414574 0.910388307 1.103788303 0.412373186 0.105981242 197.0446631 168637.5112 0.042818583 0.028873171 161.9408535 -2.209356424 0.193399996 AWDDFFPGSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 AWDDFFPGSDR 11 0 F8WF90;C9JQU6;F8WF33;O75915 F8WF90 ARL6IP5 PRA1 family protein 3 0 ;;;;;; 260.04 2.94E-20 2238959000 1515025 1542890 1081048 1577587 1999267 2016564 1183962 2314899 1974075 FALSE TRUE 1314810.608 1532754.654 1603846.429 1935802.24 1959485.498 2094142.522 1069141.547 1819875.863 1740702.102 0.755333498 0.880538176 0.921379038 1.11208129 1.125686868 1.203044748 0.614201331 1.045483808 1 20.7312379 4.391015072 1.93826338 1.005438457 0.758028778 0.222826477 0.157644681 0.706247114 4.486141137 0.043883608 0.245222151 24604.52992 -4.391015072 -0.247409679 AWEDYYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AWEDYYK 7 0 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ; 105.12 0.018609 473100000 802370 654260 447300 524740 564430 509910 622700 715740 753040 FALSE TRUE 696334.7716 649962.123 663615.7761 643890.2371 553198.9473 529526.5677 562310.6498 562684.5709 664016.4691 1.048670935 0.978834341 0.999396562 0.969690162 0.833110281 0.797459991 0.846832384 0.847395505 1 19.3408595 3.350270431 4.437808642 0.858239801 1.0028272 0.595600905 0.055353813 0.148023507 5.048687765 0.016429069 0.021374206 2240.115602 -3.350270431 0.1445874 AWEEYYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AWEEYYK 7 0 A0A087WTP3;Q92945;M0R3J3;M0R251;M0QYG1;M0R263;M0R0C6;Q96AE4;E9PEB5;Q96AE4-2 A0A087WTP3;Q96AE4 KHSRP;FUBP1 Far upstream element-binding protein 2;Far upstream element-binding protein 1 0 ;;;;; 164.53 0.0027788 8565270000 6091400 5259020 4151090 4770740 4991840 4260660 5566770 6339980 7395710 FALSE TRUE 5286406.056 5224473.151 6158571.009 5854009.433 4892512.15 4424570.347 5026905.502 4984224.615 6521397.589 0.810624714 0.801127838 0.944363677 0.89766179 0.750224485 0.678469651 0.770832545 0.7642878 1 22.63674975 3.238028955 24.9999258 0.781844069 0.864773258 0.124091274 0.090741796 27.25228569 1281481.906 0.027404914 0.032992623 1729.931691 -3.238028955 0.082929189 AWEVDTCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AWEVDTCR 8 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;;; 176.41 0.00060597 2655540000 3491700 3754870 2258720 2536030 3512200 3442530 3356950 3747560 3711870 FALSE TRUE 3030262.998 3730204.012 3351044.547 3111874.372 3442314.092 3574966.357 3031393.506 2946173.458 3273056.957 0.92582043 1.139669752 1.023827141 0.950754727 1.051712248 1.092240802 0.926165828 0.900128991 1 21.64220728 2.217996615 24.98862416 0.93269077 1.032638144 0.282080929 0.06599495 267.0529507 324510.4986 0.026045134 0.017582708 165.1948924 -2.217996615 0.099947375 AWGPGLHGGIVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AWGPGLHGGIVGR 13 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ; 155 4.07E-05 4178500000 1966840 2211990 1410150 1425990 1753300 2209060 1809580 1839360 2027930 FALSE TRUE 1706917.111 2197459.292 2092103.257 1749782.824 1718412.76 2294043.968 1634087.21 1446027.178 1788190.426 0.954549966 1.228873201 1.169955519 0.978521526 0.960978616 1.282885723 0.913821697 0.808653909 1 20.77006895 2.030749963 24.43333625 0.881832863 1.094263889 0.351239609 0.11991986 144.115059 114510.3689 0.047855263 0.032263581 107.337126 -2.030749963 0.212431025 AWKPSSK ddPTM_MDA-MB-175_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 ; 80.067 0.028198 1123260000 2201500 1948710 1331110 1680090 1783940 1605330 2380300 2649200 2714900 FALSE TRUE 1910566.197 1935908.796 1974839.248 2061580.113 1748443.084 1667088.084 2149458.872 2082689.196 2393947.615 0.798081873 0.808667986 0.824930018 0.861163419 0.730359793 0.696376175 0.897872142 0.869981107 1 21.19096015 1.389251871 1.398472242 1.042074946 0.794402841 0.580848548 0.055157645 0.712924252 1.583974466 0.239031839 0.017267687 24.50483999 -1.389251871 -0.247672105 AWLDEDSNLSPS(ph)PLR ddPTM_MDA-MB-175_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 376.84 7.28E-98 495528000 776357 663998 476851 647847 685273 690900 623799 763250 888994 TRUE FALSE 673759.4554 659636.1534 707457.7386 794950.5631 671637.408 717479.3701 563303.069 600034.9271 783898.1421 0.859498727 0.841481971 0.902486816 1.014099308 0.856791682 0.915271171 0.718592173 0.76545012 1 19.58030668 2.282627286 24.99971189 0.810420241 0.899261378 0.118363361 0.08600575 218.4729094 123942.196 0.032327363 0.025040521 191.7022834 -2.282627286 0.088841138 AWLDEDSNLSPS(ph)PLRDLSGGLGGQEEEEEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AWLDEDSNLSPSPLRDLSGGLGGQEEEEEQR 31 1 Q9C086;B8ZZ93;B8ZZH7;F8WCL7;J3KQ70 Q9C086 INO80B;INO80B-WBP1 INO80 complex subunit B 1 AWLDEDS(0.024)NLS(0.173)PS(0.785)PLRDLS(0.019)GGLGGQEEEEEQR;AWLDEDS(0.097)NLS(0.281)PS(0.622)PLRDLSGGLGGQEEEEEQR 164.8 9.07E-13 83906000 74218 60950 30844 38408 65270 60309 62285 65757 32495 TRUE FALSE 64409.90326 60549.61544 45760.26157 47129.12343 63971.2547 62629.12626 56244.61029 51695.37727 28653.47812 2.247891268 2.113168083 1.59702293 1.644795903 2.232582531 2.185742547 1.962924363 1.804157145 1 14.80642265 1.18831936 2.409322819 0.650052996 1.988130672 0.657419226 0.224832783 0.460023938 2.543821529 1.375511302 0.063903083 15.42834565 -1.18831936 1.338077677 AWMAFMSEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AWMAFMSEAER 11 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22;B0QYG7;B0QYG8 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 91.867 0.024245 305100000 179320 181230 79546 122490 147560 188160 147680 189970 137300 FALSE TRUE 155622.4077 180039.4882 118014.7117 150303.2266 144623.8447 195398.637 133358.0163 149346.3938 121068.5504 1.285407376 1.487087172 0.974775953 1.241472093 1.194561628 1.613950413 1.101508326 1.233568861 1 16.88546462 0.976810834 1.403259112 0.712842868 1.27803661 0.185923337 0.178461362 4.268536703 4.466591962 4.123512937 0.050767452 9.480054494 -0.976810834 0.565193742 AWNAYPYCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AWNAYPYCR 9 0 F5GWE5;Q00169;I3L4H1;I3L2X8;I3L471;I3L4C0;I3L4U7;I3L459;I3L3W1;A0A0A0MSW4;P48739;P48739-3;P48739-2;B3KYB7;B3KYB6 F5GWE5;A0A0A0MSW4 PITPNA;PITPNB Phosphatidylinositol transfer protein alpha isoform;Phosphatidylinositol transfer protein beta isoform 0 ; 181.81 0.00010948 1034070000 497140 551430 300200 361390 540020 568270 513050 552070 381080 FALSE TRUE 431441.6894 547807.62 445377.7241 443449.123 529274.6585 590131.7146 463294.49 434014.1267 336029.1565 1.283941233 1.630238357 1.325413928 1.319674541 1.575085519 1.756191995 1.378733009 1.291596632 1 18.35822689 1.37050447 1.892356764 0.922755493 1.478828728 0.500283926 0.150522064 0.532989971 2.392264677 0.491623054 0.04253269 23.4695342 -1.37050447 0.556073235 AWNDIKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AWNDIKK 7 1 P36578;H3BM89;H3BTP7 P36578 RPL4 60S ribosomal protein L4 0 ; 116.73 0.0086442 1960050000 5368100 4394500 2852300 3176000 3602700 2890400 4922000 5517700 2124500 FALSE TRUE 4658691.984 4365632.24 4231681.82 3897159.342 3531013.319 3001595.558 4444665.198 4337782.794 1873344.03 2.486832055 2.330395362 2.258891988 2.08032229 1.884871792 1.60226606 2.372583533 2.315529195 1 20.83718444 3.83156955 1.552055355 1.925237908 2.430142285 0.269236308 0.384126002 0.687268865 3.174957553 0.12263455 0.308475466 6785.307745 -3.83156955 0.504904377 AWNPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AWNPFR 6 0 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ; 126.07 0.041062 3539400000 2969500 2957900 1938670 2289900 2877800 2817800 2413100 2817100 2572400 FALSE TRUE 2577073.051 2938469.36 2876217.296 2809856.794 2820537.41 2926202.589 2179077.933 2214685.088 2268293.802 1.136128419 1.295453595 1.26800915 1.238753459 1.243462116 1.290045666 0.960668292 0.976366062 1 21.11317609 2.235369362 24.99993398 0.977695977 1.248237992 0.888236435 0.044520442 22.45314421 175891.8121 0.016679778 0.011778067 171.9370067 -2.235369362 0.270542016 AWRDPDEPVLLEEPVVLALAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AWRDPDEPVLLEEPVVLALAEK 22 1 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ;;; 195.71 2.02E-22 428737000 699724 556874 345942 402412 513599 477711 629608 736193 308171 FALSE TRUE 607253.7005 553215.858 513240.7083 493785.7951 503379.3847 496088.8513 568548.7131 578763.856 271739.3754 2.234691603 2.035832522 1.888724104 1.817130087 1.852434466 1.825605327 2.092257378 2.12984907 1 18.0518641 1.233235344 24.99991963 0.999998465 1.980701894 0.828800224 0.140618881 74.46512294 349543.5124 0.313823418 0.037599303 17.10942222 -1.233235344 0.980703429 AWSS(ph)QDEVSTNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AWSSQDEVSTNVR 13 0 A1L390-3;A1L390;A0A0U1RR71 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 AWS(0.096)S(0.904)QDEVSTNVR 113.52 0.00032209 0 69928 56513 31663 37700 59120 51662 62390 62848 68374 TRUE FALSE 60686.83763 56141.76238 46975.33271 46260.36121 57943.62767 53649.47057 56339.4274 49408.44428 60290.90361 1.006567061 0.931181306 0.779144612 0.767285916 0.961067494 0.889843531 0.934459828 0.819500809 1 15.87965273 AWTVEQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AWTVEQLR 8 0 Q00688;G3V5F2 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ;;;; 193.86 0.00039181 4068440000 3611840 3491950 2065420 2220730 3512350 3565440 3262290 3579970 3045080 FALSE TRUE 3134526.193 3469011.151 3064264.02 2724980.688 3442461.107 3702604.784 2945913.618 2814421.275 2685094.111 1.167380383 1.29195142 1.141212894 1.014854815 1.282063482 1.378947862 1.097136076 1.048164853 1 21.35654122 2.012223918 24.79089517 1.041061042 1.209808316 0.395977828 0.098220436 214.4089822 434833.4362 0.042353278 0.028532309 102.8546469 -2.012223918 0.168747274 AWVESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AWVESR 6 0 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 110.54 0.066582 2672290000 2987000 2695100 1727410 2113300 2668600 2726600 2619500 2965000 2592200 FALSE TRUE 2592260.382 2677395.711 2562791.254 2593157.065 2615500.081 2831494.066 2365461.293 2330957.824 2285753.069 1.134094674 1.171340748 1.121202149 1.134486966 1.14426187 1.238757635 1.034871756 1.019776745 1 21.12423813 2.112643751 7.438018071 1.016213408 1.154469058 0.800055438 0.032891453 0.09346576 5.73315345 0.013360303 0.008982149 129.611564 -2.112643751 0.138255651 AWVWNTHADFADECPKPELLAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AWVWNTHADFADECPKPELLAIR 23 1 P43487;F6WQW2;P43487-2;C9JXG8;C9JJ34;C9JGV6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ; 277.71 4.99E-52 4934100000 2328500 2101500 1383340 1701140 1880600 1521710 2126100 2517800 2161000 FALSE TRUE 2020782.825 2087695.108 2052327.851 2087409.837 1843179.739 1580251.168 1919911.149 1979388.064 1905529.042 1.060483877 1.095598683 1.077038348 1.095448976 0.967279794 0.829297866 1.007547567 1.038760376 1 20.86176017 3.236436544 24.99640287 0.973308836 1.082739059 0.506637552 0.055576603 54.19410402 637764.2633 0.018426247 0.021933246 1723.600231 -3.236436544 0.109430223 AWWILVPAADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AWWILVPAADR 11 0 Q9Y5X5-4;Q9Y5X5 Q9Y5X5-4 NPFFR2 Neuropeptide FF receptor 2 0 51.927 0.085344 31001000 51113 48500 37155 42849 43998 48927 48109 52780 53754 FALSE TRUE 44358.28755 48181.40031 55123.28228 52578.52036 43122.52588 50809.25335 43443.39658 41493.40773 47399.26336 0.935843395 1.016501036 1.162956518 1.109268723 0.909772069 1.071941835 0.916541598 0.875401953 1 15.53257702 2.228589195 24.71870522 0.918550484 1.03715223 0.267328111 0.080037036 215.7568201 534845.9617 0.033265092 0.022734003 169.2735862 -2.228589195 0.118601747 AYADFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AYADFYR 7 0 P09669 P09669 COX6C Cytochrome c oxidase subunit 6C 0 ;; 107.43 0.0174 1011730000 1099890 1837100 1298270 1810020 2321940 2609230 1113200 2092330 2415800 FALSE TRUE 954536.7497 1825031.969 1926117.714 2221012.705 2275737.937 2709608.766 1005242.035 1644901.512 2130206.876 0.448095798 0.85673931 0.904192797 1.042627705 1.068317806 1.27199325 0.471898784 0.772179233 1 21.02256211 7.564507949 20.70904962 0.869175033 0.056865574 0 0.257130874 0 0 0.058733175 0 36686640.93 -7.564507949 -0.812309458 AYAQQLADWAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AYAQQLADWAR 11 0 A0A0C4DGG1;Q9UKS6;E9PIY1;E9PJ75;E9PNM9;E9PJ33 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 0 134.57 0.0003215 414930000 197050 235800 150200 171040 242230 242280 189000 241160 245760 FALSE TRUE 171009.3432 234251.0143 222837.2224 209877.2462 237410.0969 251600.6684 170670.8091 189589.8107 216706.5328 0.789128694 1.080959634 1.028290285 0.968486014 1.095537333 1.161020229 0.787566516 0.874868922 1 17.72538312 2.227810031 24.99857168 0.880688514 1.024706368 0.245095084 0.109734133 277.363969 644954.6383 0.043643124 0.029754795 168.9701662 -2.227810031 0.144017853 AYAQQLTEWAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AYAQQLTEWAR 11 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22;B0QYG7;B0QYG8 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 ; 194.94 6.83E-07 981770000 368630 318450 255584 306170 331560 346050 356560 385290 347440 FALSE TRUE 319914.6115 316358.081 379185.2773 375690.578 324962.6047 359362.7674 321980.8661 302898.7318 306366.039 1.04422348 1.032614718 1.237687044 1.226280103 1.06070048 1.172984997 1.050967879 0.988682469 1 18.22489686 2.031388787 4.198470883 0.99882251 1.130738316 0.391710249 0.070435916 0.214790731 8.559799645 0.034756702 0.020720229 107.4951295 -2.031388787 0.131915807 AYDATHLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AYDATHLVK 9 0 P10768;X6RA14;U3KQT1;H7BZT7 P10768 ESD S-formylglutathione hydrolase 0 ; 110.87 0.0022166 937050000 2777200 2922800 1900620 2223300 2669200 2321800 2913200 3419500 3166600 FALSE TRUE 2410185.983 2903599.934 2819766.189 2728134.246 2616088.142 2411121.148 2630678.312 2688266.536 2792248.155 0.863170409 1.039878898 1.009855153 0.977038606 0.936911047 0.863505324 0.942136288 0.962760609 1 21.41299573 3.256755254 7.986697809 0.939957629 0.980084921 0.06510981 0.055899212 0.415090357 130.920249 0.016352276 0.020530117 1806.155984 -3.256755254 0.040127292 AYDPDYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AYDPDYER 8 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83 Q9UDY2-7 TJP2 Tight junction protein ZO-2 0 ; 89.046 0.032997 1435990000 1786870 1676140 1225030 1312630 1624340 1660190 1690080 1886780 1781990 FALSE TRUE 1550730.602 1665129.326 1817458.605 1610682.704 1592018.812 1724058.584 1526176.302 1483306.78 1571325.172 0.986893502 1.05969748 1.156640673 1.02504735 1.013169546 1.097200385 0.97126701 0.94398461 1 20.58355033 2.191830293 10.22037554 0.965757731 1.057724937 0.402837662 0.048410756 0.422104162 89.3438234 0.019906241 0.013443656 155.5357733 -2.191830293 0.091967206 AYEFAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 AYEFAER 7 0 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ;;;;;; 171.47 0.0021788 14048560000 10940780 9910620 6833370 6879320 9689640 10412050 9748210 10072360 10334860 FALSE TRUE 9494928.203 9845516.485 10138010.59 8441374.75 9496835.121 10812608.3 8802830.095 7918464.197 9113084.624 1.041900585 1.080371454 1.112467513 0.926291711 1.042109836 1.186492691 0.965955048 0.868911518 1 23.11950803 2.013864101 24.98273636 0.922794573 1.061774588 0.385240147 0.071857553 202.6677171 365200.3244 0.029165261 0.019653185 103.2438285 -2.013864101 0.138980015 AYEKPPEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AYEKPPEKK 9 2 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 64.439 0.039095 528380000 860430 595780 462210 527530 502370 360270 839960 997780 602180 FALSE TRUE 746721.9954 591866.282 685736.302 647313.7493 492373.8199 374129.82 758500.8085 784412.5117 530990.9664 1.406280036 1.114644729 1.291427435 1.219067348 0.92727344 0.704587919 1.428462736 1.4772615 1 19.01832779 -1.439633659 10.58183689 0.22546459 1.188885115 0 0.24572308 0 0 0 0.058724365 0.036338445 1.439633659 0.963420526 AYELALYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AYELALYLR 9 0 C9J0J7;G5E9Q6;P35080-2 C9J0J7 PFN2 Profilin;Profilin-2 0 ; 127.56 0.001028 634500000 579620 798100 509110 556740 699730 678910 675220 733100 748060 FALSE TRUE 503021.7484 792857.2285 755317.2989 683156.3262 685806.742 705028.107 609737.2683 576332.27 659625.199 0.762587223 1.201981413 1.145070413 1.035673481 1.039691545 1.068831373 0.924369277 0.873726884 1 19.33128699 2.233218008 23.64961331 0.920065783 1.053814701 0.154623033 0.117569737 97.89800513 433344.8016 0.044892304 0.03131809 171.0873929 -2.233218008 0.133748918 AYFETEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AYFETEK 7 0 P15170-2;P15170-3;P15170;H3BR35;H3BSV8 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 89.142 0.067793 0 145020 136670 93848 96233 433400 281730 163400 139360 198070 FALSE TRUE 125855.2396 135772.2058 139233.2067 118084.1735 424776.1879 292568.3354 147553.4931 109558.9485 174654.3902 0.720595912 0.777376427 0.79719271 0.676101948 2.43209568 1.67512729 0.844831286 0.627289977 1 17.41414338 AYFETEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AYFETEKK 8 1 P15170-2;P15170-3;P15170;H3BR35;H3BSV8 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 97.431 0.013207 397430000 805320 646150 507650 481080 525620 455830 798590 880350 571080 FALSE TRUE 698894.9216 641905.3981 753151.238 590316.5668 515161.1904 473366.0751 721142.8647 692094.0034 503567.573 1.387887066 1.274715515 1.495630931 1.172268825 1.023022963 0.940024935 1.432067717 1.374381594 1 18.94182586 3.714547685 23.67341038 1.182183364 1.374941605 0.294544781 0.163782698 628.5729345 619685.1285 0.049823588 0.073956706 5182.599938 -3.714547685 0.192758241 AYFQQYGCTFTAVIPTNVFGPHDNFNIEDGHVLPGLIHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AYFQQYGCTFTAVIPTNVFGPHDNFNIEDGHVLPGLIHK 39 0 Q13630;E9PP14;A0A0J9YX13;E9PKL9 Q13630 TSTA3 GDP-L-fucose synthase 0 ; 217.1 6.62E-40 5966000000 2283600 1920950 1446940 1927050 2183180 1842490 2228380 3126240 2642830 FALSE TRUE 1981816.474 1908331.153 2146685.024 2364616.156 2139738.989 1913371.783 2012272.051 2457717.904 2330397.648 0.850419874 0.818886491 0.921166834 1.014683549 0.918186212 0.821049482 0.863488706 1.054634563 1 21.15214472 1.7383017 8.812228758 1.024969293 0.889146651 0.497032703 0.058631259 0.090377296 27.01647108 0.035868621 0.016481302 54.73961009 -1.7383017 -0.135822642 AYGDFAWSNPLHPDIFPGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AYGDFAWSNPLHPDIFPGLR 20 0 O95470;H0Y3V8;H7BXL7 O95470 SGPL1 Sphingosine-1-phosphate lyase 1 0 128.79 1.91E-05 94943000 97525 78307 58826 83611 108370 89846 66006 123170 111360 FALSE TRUE 84636.82415 77792.59616 87274.45036 102596.1555 106213.649 93302.43376 59604.74828 96831.05401 98195.14766 0.86192471 0.792224443 0.888785774 1.044818995 1.081658835 0.950173567 0.60700299 0.98610834 1 16.58336411 4.005810386 15.04448909 0.936557396 0.830420831 0.122621057 0.12931367 2.899776916 7460.924171 0.035230987 0.071891143 10134.68807 -4.005810386 -0.106136565 AYGELPEHAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AYGELPEHAK 10 0 P47813;O14602;X6RAC9;A6NJH9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 ;;; 131.28 0.0002542 3853340000 11580800 9898900 6749370 8086480 9343500 7909890 10652900 12272800 11001600 FALSE TRUE 10050367.94 9833873.474 10013387.91 9922638.878 9157582.63 8214188.587 9619783.398 9648357.227 9701003.381 1.036013239 1.013696531 1.032201259 1.022846657 0.943983037 0.846735978 0.991627672 0.994573123 1 23.20970254 3.247650518 23.5494224 0.957568486 1.025726534 0.393979557 0.043587674 114.7315594 297233.9355 0.013883708 0.017635756 1768.685103 -3.247650518 0.068158048 AYGSELYGPGRPLS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AYGSELYGPGRPLSPR 16 1 A7MCY6 A7MCY6 TBKBP1 TANK-binding kinase 1-binding protein 1 1 AYGSELYGPGRPLS(1)PR 150.13 4.66E-07 333760000 339570 335520 204200 243020 332010 376750 293270 353140 337080 TRUE FALSE 294694.9641 333315.947 302951.803 298201.4053 325403.6506 391243.8163 264828.7205 277623.7591 297230.7864 0.991468507 1.121404519 1.019247726 1.00326554 1.094784475 1.316296407 0.890986845 0.934034332 1 18.18122403 AYHEQLSVAEITNACFEPANQMVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AYHEQLSVAEITNACFEPANQMVK 24 0 P68363;P68363-2;C9JDS9;P68366-2;P68366 P68363;P68366-2 TUBA1B;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 ;;; 292.14 7.72E-62 1198564000 1643195 1259271 943588 1111815 1250628 1239794 1458527 1677900 1588913 FALSE TRUE 1426042.617 1250998.766 1399910.313 1364269.589 1225742.95 1287489.677 1317079.276 1319094.142 1401073.515 1.017821408 0.892885885 0.999169778 0.973731624 0.874859839 0.918930851 0.940050084 0.941488172 1 20.41810123 4.767578499 23.4393332 0.942307389 1.017821678 0.249714787 0.040951378 6818.998161 5507862.044 0.009860687 0.89477106 58556.95688 -4.767578499 0.075514289 AYHLQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AYHLQK 6 0 P61927;D6RG19;D6R9X9 P61927 RPL37 60S ribosomal protein L37;Ribosomal protein L37 0 ;;;;; 135.81 0.013442 4626070000 10685550 10163190 6738150 7983590 8885030 9391950 10465410 11482470 12056150 FALSE TRUE 9273427.494 10096427.34 9996741.878 9796386.131 8708235.286 9753264.394 9450476.149 9027033.147 10630885.68 0.872309963 0.949725887 0.940348921 0.921502349 0.819144853 0.91744608 0.88896414 0.849132746 1 23.34175846 5.078480405 13.3308065 0.903987304 0.520284477 0.038622959 0.051157164 3581614.366 14660031.11 0.012359992 37771379.25 119806.5067 -5.078480405 -0.383702826 AYHPHCFTCVMCHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AYHPHCFTCVMCHR 14 0 Q93052;A0A087WZF1 Q93052 LPP Lipoma-preferred partner 0 ; 162.22 1.55E-06 990760000 499900 398530 475920 320580 309710 368790 366690 468060 361440 FALSE TRUE 433836.9484 395912.0302 706076.5039 393372.5888 303547.3769 382977.5899 331128.4602 367969.0114 318710.975 1.36122375 1.242229045 2.215413209 1.234261195 0.952422103 1.201645441 1.038961587 1.154553939 1 18.28188917 3.492587321 24.88527757 1.085268371 1.59570848 0.46974966 0.260207611 574.7119018 924724.1053 0.069919926 0.100063367 3108.760899 -3.492587321 0.510440108 AYINKVEELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AYINKVEELK 10 1 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 135.66 0.00012606 746260000 1384700 1067500 839620 900860 845900 761120 1120600 1284500 1421600 FALSE TRUE 1201708.387 1060487.522 1245663.04 1105414.032 829068.245 790400.7789 1011924.384 1009819.671 1253540.067 0.958651756 0.845994117 0.993716174 0.881833824 0.661381528 0.630534914 0.807253323 0.805574307 1 20.25757668 3.462004954 24.34968393 0.777854421 0.926385867 0.312969257 0.104502849 217.6785048 350639.6676 0.031297098 0.040421097 2897.37664 -3.462004954 0.148531446 AYINKVEELKK ddPTM_MDA-MB-175_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 ; 136.7 5.27E-05 1643450000 3355210 2343700 2145920 1961380 1644740 1085660 2750670 3229910 3668690 FALSE TRUE 2911810.497 2328304.08 3183694.09 2406741.307 1612012.892 1127426.043 2483910.447 2539218.882 3234981.648 0.900101087 0.719727137 0.984145951 0.743973713 0.498306657 0.3485108 0.767828296 0.784925282 1 21.6253261 3.486125579 24.681927 0.677434546 0.854980797 0.17940939 0.182897792 711.2313682 1949570.522 0.055797578 0.076127222 3062.848947 -3.486125579 0.177546251 AYLPVNESFGFTADLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AYLPVNESFGFTADLR 16 0 P13639 P13639 EEF2 Elongation factor 2 0 ;; 176.25 7.52E-09 1131738000 249752 229590 185810 201169 208014 238242 193010 262521 203154 FALSE TRUE 216746.6404 228081.8082 275668.3375 246847.4961 203874.9284 247407.3239 174291.9199 206382.9271 179137.3656 1.209946567 1.273222968 1.538865645 1.377978823 1.138092702 1.381103954 0.972951229 1.152093124 1 17.45070677 2.242562571 24.99999642 1.061820111 1.322081477 0.55663995 0.116564482 79.67523429 497731.4186 0.045439868 0.033880054 174.80851 -2.242562571 0.260261366 AYLQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AYLQAR 6 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 154.44 0.023273 4306950000 1827600 2414210 1552930 1569790 2350090 2831250 2234170 2254880 2576820 FALSE TRUE 1586078.029 2398350.896 2303932.142 1926234.812 2303327.807 2940170.02 2017500.537 1772691.459 2272191.275 0.698038958 1.055523328 1.013969276 0.847743248 1.013703306 1.293979979 0.88790964 0.780168236 1 21.11565286 2.024851726 24.99666551 0.862278604 0.995070928 0.06980537 0.15963436 451.7469906 454379.6475 0.064610364 0.043558268 105.8892145 -2.024851726 0.132792324 AYLQQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AYLQQLR 7 0 O15145 O15145 ARPC3 Actin-related protein 2/3 complex subunit 3 0 ; 119.22 0.011238 41647000 529193 886440 615205 566075 834959 957380 764676 814829 847248 FALSE TRUE 459258.8042 880616.9173 912720.1957 694610.9807 818344.9495 994211.0281 690517.8392 640584.1594 747087.3066 0.614732442 1.178733609 1.221704863 0.929758777 1.09538061 1.330782921 0.924279978 0.857442167 1 19.51091732 2.041184779 24.99999422 0.910233874 1.074746737 0.091834492 0.194898785 282.5664198 171522.4083 0.077192864 0.052043367 109.9473531 -2.041184779 0.164512863 AYMCPFMQFIEGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AYMCPFMQFIEGGR 14 0 O94855;O94855-2;P53992;G5EA31 O94855;P53992 SEC24D;SEC24C Protein transport protein Sec24D;Protein transport protein Sec24C 0 149.49 1.74E-05 63250000 63365 72849 41910 38648 63049 58711 62878 67471 54625 FALSE TRUE 54991.1547 72370.45012 62177.81618 47423.6191 61794.44825 60969.65016 56780.10124 53042.85171 48167.29473 1.141669986 1.502481103 1.290872085 0.984560569 1.282912993 1.265789381 1.17881026 1.101221316 1 15.55576628 -0.361952892 0.425934026 5.16E-12 1.280774485 0.287622653 0.129135854 29.6042515 1.50734297 25.44948127 0.122159431 0.434557358 0.361952892 1.280774485 AYMCPFMQFIEGGRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AYMCPFMQFIEGGRR 15 1 O94855;O94855-2;P53992;G5EA31 O94855;P53992 SEC24D;SEC24C Protein transport protein Sec24D;Protein transport protein Sec24C 0 ; 136.99 3.12E-05 256520000 206139 239475 142686 89898 224270 241802 236387 233154 46185 FALSE TRUE 178897.2089 237901.873 211689.4269 110310.7149 219807.4658 251104.2794 213462.2251 183295.8315 40725.06191 4.392803852 5.841657735 5.198013629 2.708669053 5.397351298 6.165841563 5.241544521 4.500811611 1 15.31362927 3.935446405 24.99995081 4.37026444 5.217933294 0.075058396 1.499801046 615.5672303 238392.8655 0.403591206 0.699041205 8618.792093 -3.935446405 0.847668854 AYNHHIQELQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AYNHHIQELQR 11 0 Q9P253 Q9P253 VPS18 Vacuolar protein sorting-associated protein 18 homolog 0 157.38 1.77E-05 70659000 116310 110700 54772 49879 85270 84284 99827 118110 35061 FALSE TRUE 100939.3388 109972.8044 81259.9224 61204.7893 83573.29383 87526.46002 90145.7929 92853.09563 30916.12852 3.264941105 3.557133757 2.628399036 1.979704194 2.703226368 2.831093808 2.91581764 3.003386908 1 14.91607205 4.188164572 6.198319091 2.515945458 3.410556288 0.312020104 0.593267835 0.226605566 19.3520708 0.150774125 0.327744112 15422.84776 -4.188164572 0.89461083 AYPLADAHLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AYPLADAHLTK 11 0 A0A3B3IUA2;B1AHD1;P55769 A0A3B3IUA2 NHP2L1 "NHP2-like protein 1;NHP2-like protein 1, N-terminally processed" 0 ;;; 172.8 1.29E-05 1609300000 2308230 2115050 1228470 1715740 2132760 2008080 2083440 2614500 2808480 FALSE TRUE 2003191.557 2101156.097 1822562.201 2105324.99 2090322.249 2085332.137 1881388.309 2055409.521 2476464.694 0.808891628 0.84844985 0.735953234 0.850133255 0.844075126 0.842060112 0.759707301 0.829977317 1 21.23985062 1.244563575 5.057179595 1.010667957 0.813455062 0.698238995 0.038388033 0.08871419 5.883105948 0.060946746 0.009261104 17.56157955 -1.244563575 -0.197212896 AYPVSGCFDYLSEDLPDTIHIGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AYPVSGCFDYLSEDLPDTIHIGGR 24 0 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 0 ; 254.26 8.37E-44 212865000 153601 127581 87239 103604 120991 138172 119899 149946 134680 FALSE TRUE 133302.2387 126742.912 129428.0722 127128.8717 118583.5158 143487.5662 108271.2134 117881.2148 118758.2838 1.122466866 1.067234284 1.089844582 1.070484244 0.998528372 1.208232063 0.911693988 0.992614671 1 16.85766862 2.217324109 24.99999949 0.970859148 1.086202902 0.512284729 0.05709274 193.9946273 228372.1155 0.021852834 0.014749168 164.9392854 -2.217324109 0.115343754 AYQDQIS(ph)PVPGAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AYQDQISPVPGAPK 14 0 E7ER32;A0A087X287;A0A087WU73;A0A494BZX7;W0Z7M9;B0QY83;A0A499FIJ6;Q969V6 E7ER32 MKL1;mkl1 MKL/myocardin-like protein 1 1 AYQDQIS(1)PVPGAPK;AYQDQIS(1)PVPGAPK 138.91 1.33E-05 335270000 419250 465700 298960 451220 565280 439480 574140 734020 628430 TRUE FALSE 363845.0503 462640.786 443538.056 553676.3975 554032.034 456387.08 518459.9912 577055.5352 554137.7213 0.656596792 0.834884124 0.800411232 0.999167492 0.999809276 0.823598651 0.935615771 1.041357614 1 19.07988505 5.60775698 0.550131729 0.983177475 2.15E-10 0.683426899 0.067694353 6.213403539 0.719025036 0.040871417 4.798958751 405281.6866 -5.60775698 -0.983177475 AYQFAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AYQFAGR 7 0 Q15006 Q15006 EMC2 ER membrane protein complex subunit 2 0 99.279 0.047969 0 65935 60676 35591 55104 61566 69639 45575 62627 54508 FALSE TRUE 57221.52269 60277.41536 52802.92664 67616.20541 60340.95705 72318.05739 41155.14351 49234.70341 48064.12634 1.190524557 1.254104047 1.098593289 1.406791521 1.255426066 1.504616081 0.856254896 1.024354486 1 15.55267289 2.225378621 24.99999999 0.969236796 1.279321913 0.626534564 0.118091395 150.3220719 285087.3732 0.04697146 0.031881513 168.0268248 -2.225378621 0.310085117 AYRPPS(ph)GEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AYRPPSGEK 9 1 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 AYRPPS(1)GEK;AYRPPS(1)GEK 88.021 0.0079132 533910000 1047920 699870 571180 676720 647770 619400 804470 901050 1082490 TRUE FALSE 909434.7169 695272.5079 847404.5585 830379.619 634880.6443 643228.7188 726452.6232 708367.4695 954519.2654 0.952767272 0.728400707 0.887781514 0.869945374 0.665131305 0.673877146 0.761066486 0.742119615 1 19.86441479 4.750923292 23.86063245 0.783706268 0.952767474 0.191284657 0.103534748 1754.835111 3386808.826 0.025244974 0.404934148 56353.81118 -4.750923292 0.169061205 AYS(ph)FCGTVEYMAPEVVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AYSFCGTVEYMAPEVVNR 18 0 E9PGT3;Q15418-4;Q15418;Q15418-2;Q15418-3;B4DG22;B1AXG1;B7ZB17;P51812;Q9UK32-2;Q9UK32 E9PGT3;B4DG22;Q9UK32-2 RPS6KA1;RPS6KA3;RPS6KA6 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1;Ribosomal protein S6 kinase alpha-3;Ribosomal protein S6 kinase alpha-6 1 AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR 366.92 1.76E-107 2878062000 1909289 1906259 1434509 1477436 1919372 1910606 1822008 2053659 2602394 TRUE FALSE 1656971.621 1893736.659 2128242.351 1812910.425 1881180.252 1984108.249 1645309.945 1614500.004 2294741.946 0.722073183 0.825250378 0.927442998 0.790028015 0.819778562 0.864632406 0.716991271 0.703564951 1 21.12990049 2.262659011 24.99678542 0.781589631 0.827732557 0 0.095407103 789.8076129 819249.8415 0.035281305 0.027315177 183.0876335 -2.262659011 0.046142927 NAS(ph)AS(ph)FQELEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NASASFQELEDK 12 0 Q99543;Q99543-2;H7C3L7;F2Z3H0;F2Z3N9 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 2 NAS(1)AS(1)FQELEDK;NAS(1)AS(1)FQELEDK 112.74 0.0018141 240470000 542420 525850 645460 758190 813720 703820 964080 1083340 1920900 TRUE FALSE 470737.8227 522395.6567 957606.6149 930348.6277 797528.564 730896.4108 870583.67 851676.1716 1693813.39 0.277915988 0.308413937 0.56535544 0.549262766 0.470847951 0.431509407 0.513978503 0.502815822 1 20.69184351 1.140135609 2.540532363 1.246571348 0.449468041 0.772308615 0.093677006 0.398308819 2.226164461 0.779148478 0.026206356 13.80815358 -1.140135609 -0.797103307 AYS(ph)PEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 AYSPEYR 7 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR 126.41 0.0041482 28662320000 18307000 17801860 12488880 14111580 17357160 18646370 17344780 18893470 19134750 TRUE FALSE 15887683.57 17684918.41 18528544.14 17315829.92 17011786.47 19363707.92 15662685.91 14853248.47 16872661.65 0.941622839 1.048140404 1.098139969 1.026265463 1.008245576 1.147638015 0.928287796 0.880314486 1 24.00818424 2.127357415 11.20230802 0.923491542 1.04500085 0.409471695 0.060989955 0.314853146 30.01117834 0.024081632 0.016233824 134.0779666 -2.127357415 0.121509307 AYS(ph)QEEITQGFEETGDTLYAPYSTHFQLQNQPPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AYSQEEITQGFEETGDTLYAPYSTHFQLQNQPPQK 35 0 Q8NFJ5 Q8NFJ5 GPRC5A Retinoic acid-induced protein 3 1 AY(0.08)S(0.916)QEEIT(0.004)QGFEETGDTLYAPYSTHFQLQNQPPQK 236.31 4.83E-47 93146000 64476 42224 25512 55502 45967 42718 41934 71223 63468 TRUE FALSE 55955.33324 41946.62776 37849.68853 68104.57739 45052.34663 44361.3891 37867.24713 55992.51571 55964.88534 0.99982932 0.749516907 0.676311375 1.216916232 0.80501097 0.792664701 0.676625118 1.000493709 1 15.77223428 1.606374649 24.99999651 1.000278023 0.845286774 0.138420778 0.160746368 0.289311579 4664.246352 0.095041261 0.040074122 40.39937523 -1.606374649 -0.154991249 AYSEAHEISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AYSEAHEISK 10 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ; 117.52 0.00094675 7829100000 18615500 15930000 8670500 13979900 14062500 13887700 17227900 19024300 24502000 FALSE TRUE 16155414.51 15825354.78 12863582.8 17154249.96 13782683.76 14421968.81 15557140.91 14956101.49 21605401.47 0.747748869 0.732472146 0.595387353 0.79397969 0.637927686 0.667516816 0.720057941 0.692238999 1 24.3648887 1.238001064 24.99924137 1.000000345 0.697116156 0.739501765 0.056247985 6.497452824 290025.3684 0.073210057 0.012698073 17.29820596 -1.238001064 -0.302884189 RNAET(ph)PEATTQQETDTDLPEAPPPPLEPAVIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNAETPEATTQQETDTDLPEAPPPPLEPAVIAR 33 1 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 1 RNAET(0.974)PEAT(0.012)T(0.012)QQET(0.002)DTDLPEAPPPPLEPAVIAR;RNAET(0.555)PEAT(0.126)T(0.126)QQET(0.192)DT(0.001)DLPEAPPPPLEPAVIAR 147.74 1.66E-10 349190000 245686 226615 134653 142624 213644 236707 219051 232681 80338 TRUE FALSE 213217.9726 225126.3511 199771.6412 175008.9591 209392.9024 245813.2715 197807.4677 182923.9789 70840.53316 3.009830151 3.177931349 2.820018883 2.470463607 2.955834648 3.469952307 2.792292194 2.582193706 1 16.11228745 1.141213802 2.085547963 5.05E-11 2.960940506 0.848181687 0.258526486 0.381334414 1.315583995 2.383438435 0.073338147 13.84247674 -1.141213802 2.960940506 AYSNS(ph)IVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AYSNSIVR 8 0 Q9H1Z4 Q9H1Z4 WDR13 WD repeat-containing protein 13 1 AYS(0.321)NS(0.679)IVR 87.913 0.015721 275910000 318630 310860 204240 216460 323140 301820 272780 312610 294680 TRUE FALSE 276522.2382 308817.9402 303011.1471 265610.5514 316710.1462 313431.2107 246325.8376 245760.7842 259843.2661 1.064188587 1.18847775 1.166130459 1.022195246 1.218850698 1.2062318 0.947978531 0.945803938 1 17.98728215 2.229133943 24.99940628 0.959987158 1.145176263 0.647782253 0.062449583 115.9646455 307533.6345 0.025051931 0.017142604 169.4860441 -2.229133943 0.185189106 AYSPELIVHPVLDSPNAVHEVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AYSPELIVHPVLDSPNAVHEVEK 23 0 Q8IW45-2;Q8IW45 Q8IW45-2 CARKD ATP-dependent (S)-NAD(P)H-hydrate dehydratase 0 ; 175.47 8.60E-13 301170000 275080 244730 163438 230800 241180 226900 286360 317930 304680 FALSE TRUE 238727.481 243122.3525 242477.1635 283206.6676 236380.9899 235628.9898 258588.8513 249943.1436 268661.0775 0.888582311 0.904940733 0.902539235 1.05414104 0.879848291 0.877049225 0.962509544 0.930328822 1 18.0354278 0.272389734 0.011451143 1.933238863 8.66E-08 0.117490244 0.053951795 31365.84137 65.26165883 5918.112696 5125.314473 1.872361638 -0.272389734 -1.933238777 AYSPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AYSPKR 6 1 A6NM62 A6NM62 LRRC53 Leucine-rich repeat-containing protein 53 0 81.716 0.098042 297830000 611500 552540 299230 356480 444150 614130 568630 590920 394350 FALSE TRUE 530688.7257 548910.3284 443938.6289 437424.2325 435312.284 637755.9785 513484.3501 464556.3565 347730.3922 1.526149964 1.578551489 1.2766748 1.257940756 1.251867233 1.834053027 1.476673772 1.335967079 1 18.40760964 1.270546839 2.669635231 0.918354052 1.452137723 0.401599302 0.175469974 0.485626695 4.156572013 0.564340047 0.048370924 18.64433249 -1.270546839 0.533783671 AYSSFGGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AYSSFGGGR 9 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;; 221.33 9.86E-07 1379620000 1498970 1515120 983110 1114450 1390150 1556360 1450840 1534840 1455560 FALSE TRUE 1300877.317 1505167.077 1458545.284 1367502.906 1362488.735 1616234.176 1310137.76 1206626.41 1283485.355 1.013550573 1.172718544 1.136394178 1.065460467 1.061553784 1.259254085 1.020765648 0.940117007 1 20.2916354 2.011436161 24.992021 0.970179177 1.118455916 0.462871946 0.068260006 164.8102552 360166.7304 0.026646313 0.017948459 102.6682505 -2.011436161 0.148276739 AYSSFGGGRGS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AYSSFGGGRGSR 12 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 1 AYSSFGGGRGS(1)R;AYSSFGGGRGS(1)R;AYSSFGGGRGS(1)R;AYSSFGGGRGS(1)R;AYSSFGGGRGS(1)R 123.29 0.00020795 2134180000 2755900 2475210 989845 1550030 1710730 1115270 2978720 2639150 1359551 TRUE FALSE 2391700.832 2458950.183 1468537.353 1901988.002 1676689.82 1158175.159 2689844.193 2074788.31 1198826.43 1.995035122 2.051131108 1.224979127 1.5865416 1.398609322 0.966090778 2.243731141 1.730682824 1 20.19319136 4.256844161 24.95655043 1.503408929 2.023083605 0.283764892 0.371012501 344.9504984 470839.9641 0.094333657 0.248529435 18065.25769 -4.256844161 0.519674676 AYT(ph)PPPPLGPHPNLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AYTPPPPLGPHPNLGK 16 0 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 AYT(1)PPPPLGPHPNLGK;AYT(1)PPPPLGPHPNLGK 144.17 4.94E-06 679020000 1112120 932210 686370 792490 1097670 881970 1130610 1317710 1186200 TRUE FALSE 965150.5242 926086.2511 1018300.828 972436.967 1075828.515 915899.9566 1020963.616 1035927.971 1045968.787 0.922733581 0.885386125 0.973548007 0.929699795 1.028547436 0.875647503 0.976093769 0.990400463 1 19.99640837 7.999994807 0.019941422 1.711146412 3.09E-06 0.241994733 0.043320263 9479.90241 18.79774298 640.6812299 1013.636605 99998804.21 -7.999994807 -1.711143319 AYT(ph)PVVVTLWYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 AYTPVVVTLWYR 12 0 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12 P21127-2 CDK11B Cyclin-dependent kinase 11B 1 AYT(1)PVVVTLWYR;AYT(1)PVVVTLWYR;AYT(1)PVVVTLWYR 156.36 0.0007792 1757299000 762203 625124 543966 600057 796410 637638 672804 778766 1035870 TRUE FALSE 661475.9424 621017.5193 807029.7771 736309.1131 780562.9991 662168.3465 607555.5716 612232.9513 913410.6287 0.724182445 0.67988865 0.883534471 0.80610964 0.8545587 0.724940488 0.665150539 0.670271324 1 19.80090405 4.494236513 0.004341178 1.523813436 0.000161014 0.007184915 0.108514722 857309.9475 1208.707235 208954.6871 215305.2146 31205.8857 -4.494236513 -1.523652422 AYT(ph)PVVVTQWYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AYTPVVVTQWYR 12 0 Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;Q9UQ88-5;Q9UQ88-10 Q5QPR3 CDK11A Cyclin-dependent kinase 11A 1 AYT(1)PVVVTQWYR;AYT(1)PVVVTQWYR;AYT(1)PVVVTQWYR;AYT(1)PVVVTQWYR 189.99 8.07E-05 1751520000 1198950 1026730 870570 1061250 1442370 1315260 1179330 1436160 1808730 TRUE FALSE 1040505.72 1019985.343 1291580.564 1302223.033 1413669.659 1365858.903 1064958.758 1129048.36 1594904 0.65239395 0.639527735 0.80981712 0.816489916 0.886366615 0.856389415 0.667725931 0.707909918 1 20.60503816 4.238017753 24.99738805 0.805882383 0.645960792 0.378014213 0.0916557 15.97294544 735675.735 0.024445119 0.056401064 17298.87072 -4.238017753 -0.159921591 AYTDDLGAVGGACLEDEASALRLDEDSEHPPMILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AYTDDLGAVGGACLEDEASALRLDEDSEHPPMILR 35 1 Q9Y4P8-2;Q9Y4P8-6;Q9Y4P8-3;Q9Y4P8-5 Q9Y4P8-2 WIPI2 WD repeat domain phosphoinositide-interacting protein 2 0 103.07 1.48E-05 25932000 17978 15398 6065.3 7838.9 15144 15019 12187 15339 6181.5 FALSE TRUE 15602.16175 15296.84952 8998.499367 9618.842055 14842.66403 15596.79065 11005.10662 12058.87422 5450.730112 2.86239851 2.806385422 1.65087964 1.76468874 2.723059796 2.861413119 2.019015139 2.212341094 1 12.41223377 1.066097671 1.91421676 6.83E-13 2.381697145 0.4797701 0.44852661 1.3815168 3.260367035 6.973092999 0.129060501 11.64387865 -1.066097671 2.381697145 AYTDELVELHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AYTDELVELHR 11 0 Q03111 Q03111 MLLT1 Protein ENL 0 135.66 0.00011535 131310000 110990 116570 86425 99255 105880 110120 99277 109840 140440 FALSE TRUE 96322.39029 115804.244 128220.4191 121792.3648 103773.1952 114356.3877 89649.13182 86351.57078 123837.3432 0.777813766 0.935131851 1.035393814 0.983486577 0.837979825 0.923440254 0.723926479 0.697298315 1 16.9180869 2.253005213 24.73179976 0.780740294 0.921442324 0.171118066 0.106919586 268.0942623 459026.2129 0.040387343 0.031135375 179.0627348 -2.253005213 0.14070203 AYTNFDAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AYTNFDAER 9 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YKS4;H0YMM1;H0YMW4;H0YKX9;H0YMT9;H0YLV6;H0YKZ7;H0YKL9;H0YKV8;H0YNB8;H0YKN4;H0YMD9 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 ;;; 208.72 2.23E-05 2979620000 2399860 2243720 1835280 2800100 2682120 2742650 1225180 2540860 3805330 FALSE TRUE 2082712.421 2228980.856 2722827.547 3435905.502 2628751.059 2848161.52 1106362.232 1997516.862 3355468.222 0.620692041 0.664283107 0.811459792 1.023971999 0.783423023 0.848811949 0.32971918 0.595301976 1 21.67808266 AYTNFDAERDALNIETAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AYTNFDAERDALNIETAIK 19 1 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YKS4;H0YMM1;H0YMW4;H0YKX9;H0YMT9;H0YLV6;H0YKZ7;H0YKL9;H0YKV8;H0YNB8;H0YKN4;H0YMD9 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 ; 123.83 2.78E-05 135292000 204686 169259 96705 119527 162633 174926 127599 226790 87122 FALSE TRUE 177636.2265 168147.1265 143471.8615 146667.4322 159396.9215 181655.5164 115224.4686 178292.7234 76822.53641 2.312293173 2.18877343 1.86757517 1.909171957 2.074871892 2.364612325 1.499878473 2.320838802 1 16.22924198 1.229599366 24.99941664 0.999997976 2.054691451 0.621576152 0.26154147 228.5538986 637554.0895 0.711669263 0.059883055 16.96677755 -1.229599366 1.054693476 AYVFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AYVFER 6 0 A0A1W2PPX5;A0A1W2PQR6;A0A1W2PQB7;A0A1W2PS43;Q14108;A0A1W2PRS1;A0A1W2PPU6;A0A1W2PSE4;A0A1W2PS70;A0A1W2PNX7 A0A1W2PPX5 SCARB2 Lysosome membrane protein 2 0 ; 106.76 0.074087 592120000 909690 646800 449240 641900 668830 1030990 526920 852750 698050 FALSE TRUE 789472.1616 642551.1282 666493.9666 787653.2058 655521.5915 1070652.852 475819.3795 670396.0486 615527.3242 1.282594827 1.0439035 1.082801592 1.279639709 1.064975616 1.739407513 0.773027225 1.089141005 1 19.23146338 AYVHEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AYVHEFK 7 0 Q9H4A4;A6NKB8;C9JMZ3;H7C2T3 Q9H4A4 RNPEP Aminopeptidase B 0 ;;; 108.98 0.0071304 2419600000 5689600 4916800 3564130 4187660 4700620 4436370 5978800 6063200 6618600 FALSE TRUE 4937704.944 4884501.217 5287755.189 5138532.207 4607086.859 4607040.025 5398976.896 4766631.864 5836156.648 0.846054217 0.83693799 0.906033801 0.880465093 0.789404249 0.789396225 0.925091155 0.816741591 1 22.47658718 1.230862434 24.99935868 1.00000027 0.849542481 0.525729494 0.045137081 233.6297381 758633.9218 0.114234511 0.01095214 17.01619422 -1.230862434 -0.150457788 AYVWDNNKDLAEWLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AYVWDNNKDLAEWLEK 16 1 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 107.34 0.0010357 236980000 136380 101710 79804 73837 89149 75324 121640 130110 45290 FALSE TRUE 118357.0375 101041.8603 118397.4813 90602.81938 87375.10932 78221.76302 109843.3715 102286.989 39935.86779 2.963677616 2.530103035 2.964690336 2.268707916 2.187885581 1.958684444 2.750494169 2.561281241 1 15.28539744 3.659174356 5.756908733 2.197701518 2.789024662 0.313177774 0.47850097 0.319982334 17.9113286 0.132429365 0.198862792 4562.200381 -3.659174356 0.591323144 AYWQVHLDQVEVASGLTLCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AYWQVHLDQVEVASGLTLCK 20 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GU92;A0A1B0GU03;C9JH19;H7C469 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ;;; 295.17 1.38E-54 8530866000 8343250 7810077 7384030 9719100 6947508 7466477 8572120 10340030 14158430 FALSE TRUE 7240668.373 7758772.09 10954971.61 11925970.2 6809266.183 7753717.202 7740797.122 8128895.051 12484636.53 0.579966293 0.621465596 0.877476215 0.955251694 0.545411648 0.621060708 0.620025829 0.651111871 1 23.57365048 1.234706003 24.90476604 1.000000475 0.685708801 0.365443393 0.130856438 132.6624584 857003.4482 0.249094589 0.033935084 17.16745837 -1.234706003 -0.314291674 AYYEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AYYEFR 6 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;; 116.87 0.053984 3786410000 5901740 5110660 3333260 3712550 4879710 5298750 4527430 5333770 5028540 FALSE TRUE 5121810.106 5077087.738 4945235.685 4555541.22 4782613.318 5502596.341 4088360.535 4193184.793 4434071.73 1.155103124 1.145017051 1.11528094 1.02739457 1.078605311 1.240980452 0.922033017 0.945673649 1 22.08020068 2.217796969 24.98852988 0.952359992 1.120611029 0.660339779 0.057725796 145.836076 175508.7099 0.024006458 0.016204955 165.1189692 -2.217796969 0.168251037 CAAPRPPSS(ph)SPEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 CAAPRPPSSSPEQR 14 1 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 CAAPRPPS(0.072)S(0.464)S(0.464)PEQR;CAAPRPPS(0.068)S(0.466)S(0.466)PEQR;CAAPRPPS(0.043)S(0.478)S(0.478)PEQR;CAAPRPPS(0.06)S(0.47)S(0.47)PEQR;CAAPRPPS(0.137)S(0.775)S(0.088)PEQR 139.04 7.19E-06 1770720000 1814780 1955260 984209 1373362 2101920 2125780 1780480 2099000 1874690 TRUE FALSE 1574952.225 1942415.768 1460175.764 1685204.833 2060095.904 2207560.132 1607809.324 1650145.184 1653066.284 0.952745961 1.175038041 0.8833135 1.019441779 1.246227042 1.335433524 0.972622417 0.998232921 1 20.65671314 4.790062391 21.27393548 1.072808086 0.95274189 0.075608171 0.137094058 21728.79695 8973870.919 0.035399681 22.17031135 61668.35889 -4.790062391 -0.120066196 CAAPRPPSSS(ph)PEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.028)S(0.152)S(0.82)PEQR;CAAPRPPS(0.034)S(0.185)S(0.781)PEQR 143.88 5.45E-06 2369400000 865070 924770 413780 559050 1086780 1051210 851000 1053750 885600 TRUE FALSE 750748.8077 918695.125 613885.392 685990.847 1065155.204 1091650.729 768470.151 828413.7628 780905.3769 0.961382557 1.176448712 0.786120073 0.878455787 1.364000346 1.397929584 0.984075886 1.06083757 1 19.57478822 3.270718544 24.99939714 1.147333685 0.954984985 0.281671014 0.166347713 310.8672661 241664.4819 0.051735607 0.066785067 1865.170525 -3.270718544 -0.1923487 CAAPRPPSSSPEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 CAAPRPPSSSPEQR 14 1 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 ;;; 162.93 3.98E-06 446142000 486510 491582 237784 331052 609340 621940 521340 610400 543370 FALSE TRUE 422216.4708 488352.7655 352777.1377 406222.4164 597215.3262 645866.4342 470780.527 479870.7101 479133.4176 0.881208564 1.019241713 0.736281638 0.847827351 1.24644891 1.347988703 0.982566671 1.001538804 1 18.87006791 3.258385603 24.99573738 1.103065758 0.872085709 0.457337778 0.131978816 260.669345 328654.9993 0.041854285 0.053959785 1812.949068 -3.258385603 -0.230980048 CAFISQASATMHLPATIGDYTDFYSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CAFISQASATMHLPATIGDYTDFYSSR 27 0 P16930;H0YLC7;P16930-2 P16930 FAH Fumarylacetoacetase 0 96.44 0.0045045 252700000 90152 95759 30315 69712 106860 93494 83782 117610 87864 FALSE TRUE 78238.18478 95129.95282 44975.4354 85541.17508 104733.6951 97090.77468 75656.83454 92460.01674 77476.81801 1.009827027 1.22785054 0.58050184 1.104087355 1.351806873 1.253159037 0.976509316 1.193389444 1 16.24147708 3.495653817 24.90807435 1.158267513 0.947248167 0.213567478 0.189425083 1122.259312 1508332.676 0.051501824 0.074839477 3130.789128 -3.495653817 -0.211019347 CAGFVVGDLYALLTHSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CAGFVVGDLYALLTHSSR 18 0 Q13608-2;Q13608;Q13608-3 Q13608-2 PEX6 Peroxisome assembly factor 2 0 65.949 0.033051 0 106430 84642 60345 76627 86187 96360 106990 103990 119690 FALSE TRUE 92365.00584 84085.98113 89528.04384 94026.33152 84472.04732 100067.0316 96614.12627 81752.54775 105540.3846 0.87516268 0.79671854 0.848282335 0.890903818 0.800376535 0.948139728 0.915423292 0.774609152 1 16.68743562 2.751728646 24.9830289 0.8890109 0.842790916 0.184720095 0.064044046 1825.733728 3463869.418 0.020793416 0.020684343 564.5841031 -2.751728646 -0.046219983 CAGGHDDATLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CAGGHDDATLAR 12 0 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 0 79.86 0.021897 352640000 174400 142170 114220 161230 118270 152850 147870 167050 225500 FALSE TRUE 151352.5981 141236.0759 169457.174 197839.7357 115916.6584 158730.2384 133529.5902 131327.6575 198841.6469 0.761171518 0.710294237 0.852221739 0.994961261 0.582959658 0.798274611 0.671537338 0.660463537 1 17.60126043 3.228836429 24.99999234 0.729822293 0.822747324 0.092884847 0.130988485 474.2386308 1219221.337 0.039059797 0.044839992 1693.699772 -3.228836429 0.092925031 CAHIEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CAHIEAK 7 0 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;A8MXH2;E9PKT8;E9PS34;E9PNW0;E9PJJ2;C9J1B1 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 ; 79.116 0.033497 691910000 1299290 1144250 737160 1030610 1103320 1176410 1539580 1722760 1523630 FALSE TRUE 1127585.535 1136733.346 1093653.042 1264625.752 1081366.091 1221667.254 1390271.769 1354361.181 1343508.197 0.839284447 0.846093346 0.814027815 0.94128622 0.804882391 0.909311351 1.034807061 1.008078092 1 20.35757369 2.395572074 4.04426928 1.013281464 0.852190499 0.799173893 0.037675983 0.087792387 2.767865707 0.013906533 0.010593482 248.6406167 -2.395572074 -0.161090965 CAIKVEQSAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CAIKVEQSAER 11 1 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1;K7EJ01;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7;H7C034 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 ; 108.56 0.001866 525870000 528210 510950 181529 217060 551300 503050 654680 731430 110392 FALSE TRUE 458405.7102 507593.5358 269317.0316 266346.7906 540330.2086 522402.659 591189.2344 575019.3865 97341.58352 4.709248541 5.214560083 2.766721291 2.736207702 5.550867256 5.366695714 6.073347207 5.907232713 1 16.57076862 3.217408701 24.97159213 5.046961362 3.875820339 0.061176359 1.617378942 551.7341337 651366.0844 0.494750845 0.561541773 1649.714155 -3.217408701 -1.171141023 CALGWDHQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 CALGWDHQEK 10 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;; 211.78 5.26E-08 5497560000 10500550 9531810 5248060 7174070 10129830 9083270 10986260 13053680 11378960 FALSE TRUE 9112875.712 9469194.912 7786039.37 8803052.242 9928266.202 9432709.275 9920814.196 10262252.12 10033752.31 0.908222112 0.94373417 0.775984809 0.877343985 0.989486873 0.94009788 0.988744179 1.022773116 1 23.25835789 3.241639622 7.367428739 0.990360065 0.873655515 0.589832853 0.046333876 0.09288272 30.56629285 0.014318519 0.017459295 1744.374068 -3.241639622 -0.116704549 CALSS(ph)PSLAFTPPIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CALSSPSLAFTPPIK 15 0 Q8NFH5-2;Q8NFH5;Q8NFH5-3 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 CALS(0.075)S(0.832)PS(0.093)LAFTPPIK;CALS(0.008)S(0.966)PS(0.026)LAFTPPIK 272.72 2.08E-33 1238020000 4092600 3936100 2177980 2745900 4285300 3925600 4724000 5490000 4816200 TRUE FALSE 3551752.541 3910243.5 3231258.413 3369398.563 4200030.914 4076620.372 4265867.207 4316006.223 4246834.323 0.836329433 0.920743124 0.760862837 0.793390631 0.988979224 0.959919804 1.004481664 1.016287874 1 22.0179564 3.2293216 24.98042659 0.99581842 0.829684574 0.790539773 0.042474201 87.42136439 236369.1487 0.013389676 0.015389225 1695.59294 -3.2293216 -0.166133846 CAPSAGS(ph)PAAAVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 CAPSAGSPAAAVGR 14 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 CAPSAGS(1)PAAAVGR;CAPSAGS(1)PAAAVGR;CAPS(0.07)AGS(0.93)PAAAVGR;CAPS(0.002)AGS(0.998)PAAAVGR 274.44 5.12E-33 1447090000 1102870 817390 450289 642135 1000550 1021220 891370 978070 1136410 TRUE FALSE 957122.9352 812020.5113 668050.2665 787941.5662 980641.0125 1060506.994 804925.0746 768917.3418 1002064.904 0.95515064 0.810347222 0.666673649 0.786317895 0.978620255 1.058321661 0.803266406 0.767332873 1 19.93454453 3.266344291 24.90604647 0.900208868 0.795177725 0.200533337 0.110841928 408.4587915 366150.8928 0.034841766 0.044970327 1846.478653 -3.266344291 -0.105031143 CAPSAGS(ph)PAAAVGRES(ph)PGAAATSSSGPQAQQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CAPSAGSPAAAVGRESPGAAATSSSGPQAQQHR 33 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 2 CAPS(0.298)AGS(0.702)PAAAVGRES(1)PGAAATSSSGPQAQQHR;CAPS(0.103)AGS(0.849)PAAAVGRES(0.926)PGAAAT(0.042)S(0.033)S(0.033)S(0.014)GPQAQQHR 120.48 3.10E-07 352210000 126664 93733 57565 72177 94340 93806 102517 115274 90769 TRUE FALSE 109925.0315 93117.26175 85403.62654 88565.89101 92462.81857 97414.77752 92574.91712 90623.55216 80038.39222 1.373403793 1.163407449 1.06703326 1.106542605 1.155230834 1.217100629 1.156631393 1.132251032 1 16.28840457 4.721277726 3.771623283 1.12613832 1.394722493 0.651856269 0.057743986 0.156509637 4.313292215 0.014659653 0.113892943 52635.37557 -4.721277726 0.268584173 CAPSAGSPAAAVGRES(ph)PGAAATSSSGPQAQQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CAPSAGSPAAAVGRESPGAAATSSSGPQAQQHR 33 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR;CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR 304.14 2.22E-90 1206420000 500170 383450 189601 254425 527060 502560 423590 511220 258070 TRUE FALSE 434071.2672 380931.0917 281292.6778 312196.0849 516572.5372 521893.8084 382510.307 401899.5813 227561.2586 1.907491943 1.673971633 1.236118483 1.371921068 2.270037265 2.293421172 1.68091137 1.766116007 1 17.79589544 CAS(ph)CLKEFRSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CASCLKEFRSK 11 2 J3QQI2;J3KTI4;H7BYU6;Q96K83 J3QQI2 ZNF521 Zinc finger protein 521 1 CAS(1)CLKEFRSK 59.871 0.076582 9779400000 15521000 12733000 4884800 8371300 11393000 9990200 11397000 13652000 7310500 TRUE FALSE 13469860.52 12649356.08 7247105.619 10272131.61 11166301.59 10374529.46 10291720.69 10732626.04 6446261.018 2.089561761 1.962277985 1.12423397 1.593502277 1.732213691 1.609387121 1.596541106 1.664938173 1 22.62003118 4.400041923 8.696081906 1.516646389 2.057958548 0.477642363 0.238374523 0.213289205 21.32968659 0.057838994 0.153928633 25121.28919 -4.400041923 0.541312159 CATITPDEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 CATITPDEKR 10 1 O75874;C9J4N6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;;; 155.11 2.13E-05 1839850000 1225290 975440 457863 698248 1136400 1054790 1423910 1614060 860852 FALSE TRUE 1063364.822 969032.2704 679287.0783 856795.8805 1113787.863 1095368.454 1285819.427 1268905.83 759083.0572 1.400854375 1.276582663 0.894878461 1.128724811 1.467280626 1.443015285 1.693911378 1.671629761 1 19.53389823 3.203583939 6.172291042 1.501638954 1.162127725 0.259850824 0.227143786 0.213893474 22.56109392 0.070308982 0.081738127 1598.026362 -3.203583939 -0.339511229 CAVSDVEMQEHYDEFFEEVFTEMEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 CAVSDVEMQEHYDEFFEEVFTEMEEK 26 0 P0DN76;Q01081 P0DN76 U2AF1 Splicing factor U2AF 35 kDa subunit 0 ;;;; 210.2 1.54E-25 233922000 209984 156008 105050.7 133725.5 133890 121288.1 192713 212851 193628 FALSE TRUE 182234.0824 154983.1732 155853.5699 164089.9186 131225.851 125954.1317 174023.7229 167334.4701 170737.5184 1.067334726 0.90772769 0.912825554 0.961065384 0.768582396 0.737706234 1.019247114 0.980068538 1 17.38142059 CCHLFSTYVASHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CCHLFSTYVASHK 13 0 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 ; 192.68 1.45E-06 904310000 780470 798440 364950 521260 887590 778550 854310 985720 861330 FALSE TRUE 677328.912 793194.9951 541441.0407 639620.05 869928.6955 808501.3223 771459.1477 774931.4489 759504.5486 0.891803628 1.044358452 0.71288716 0.842154337 1.145389711 1.064511495 1.015739997 1.020311794 1 19.53469908 3.253766336 24.99987055 1.043838005 0.873632558 0.495270341 0.088388296 218.0833061 358550.8358 0.026046641 0.03349364 1793.768265 -3.253766336 -0.170205447 CCLTYCFNKPEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CCLTYCFNKPEDK 13 1 P62979;A0A2R8Y422 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ; 218.31 2.22E-11 3319500000 4646300 3676500 2486900 2916900 3715500 2986000 4966800 6318900 4454800 FALSE TRUE 4032279.683 3652348.829 3689573.158 3579226.727 3641568.819 3100873.352 4485120.5 4967652.409 3928158.619 1.026506329 0.929786494 0.939262773 0.911171639 0.927042203 0.789396166 1.141787014 1.264626226 1 21.90542176 2.143425163 7.726202706 1.165771839 0.922040123 0.575177032 0.085940143 0.142619691 10.12528007 0.034197162 0.023019203 139.1314025 -2.143425163 -0.243731716 CCSFDGDADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CCSFDGDADR 10 0 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A087WT27;A0A494C1E2;A0A494C1Q4;J3KN95 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 225.72 7.84E-09 570560000 453110 476560 214040 297760 498940 537890 473910 477820 533920 FALSE TRUE 393230.3655 473429.446 317550.4599 365370.959 489012.0702 558582.9764 427950.2811 375641.9114 470800.5858 0.83523763 1.005583808 0.674490367 0.776063093 1.038681949 1.186453444 0.908984173 0.797879023 1 18.84475659 3.24410183 24.99882312 0.967031153 0.825299913 0.285355657 0.126542781 230.93659 1041849.16 0.040913245 0.051319034 1754.291785 -3.24410183 -0.141731241 CDDSPRT(ph)PSNTPSAEADWSPGLELHPDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CDDSPRTPSNTPSAEADWSPGLELHPDYK 29 1 Q9Y3Z3-4;Q9Y3Z3;A0A2R8YCS7;Q9Y3Z3-3;A0A2R8YF51;A0A2R8Y5D2;A0A2R8Y586;A0A2R8Y7R5;A0A2R8Y755 Q9Y3Z3-4 SAMHD1 Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 1 CDDS(0.037)PRT(0.956)PS(0.007)NTPSAEADWSPGLELHPDYK 209.27 1.80E-25 99632000 147290 147180 87275 86099 145510 149360 179560 198800 96796 TRUE FALSE 127825.2533 146213.1649 129481.4819 105649.0939 142614.6357 155105.9758 162146.2988 156288.1671 85352.88715 1.497609016 1.713042989 1.517013498 1.237791684 1.670882385 1.817231743 1.899716626 1.831082372 1 16.38115233 3.032105981 24.84908433 1.697749543 1.5021938 0.052437747 0.273720309 433.4588531 335481.468 0.083281655 0.09443186 1076.727936 -3.032105981 -0.195555743 CDDSPRTPS(ph)NTPSAEADWSPGLELHPDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CDDSPRTPSNTPSAEADWSPGLELHPDYK 29 1 Q9Y3Z3-4;Q9Y3Z3;A0A2R8YCS7;Q9Y3Z3-3;A0A2R8YF51;A0A2R8Y5D2;A0A2R8Y586;A0A2R8Y7R5;A0A2R8Y755 Q9Y3Z3-4 SAMHD1 Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 1 CDDS(0.246)PRT(0.246)PS(0.251)NT(0.251)PS(0.006)AEADWSPGLELHPDYK 52.685 0.045362 123660000 69665 69097 42145 39178 81053 74720 82539 79776 52110 TRUE FALSE 60458.59374 68643.09726 62526.46297 48073.9637 79440.20388 77594.52675 74534.38048 62716.52322 45949.61516 1.315758435 1.493877522 1.360761407 1.046232129 1.728854607 1.688687195 1.62208933 1.364897682 1 15.48776516 3.231315636 24.99964112 1.487382525 1.321751954 0.124816186 0.230125271 414.3082448 1429616.079 0.073029797 0.084482055 1703.396051 -3.231315636 -0.165630571 CDENILWLDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 CDENILWLDYK 11 0 P14618;P14618-3;B4DNK4;H3BUW1;H3BTJ2;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;; 164.04 5.41E-05 4104953000 5143567 3616580 2596141 3252848 3914617 3468385 5068998 5250620 5062131 FALSE TRUE 4463831.589 3592822.448 3851643.471 3991456.855 3836723.781 3601816.015 4577407.354 4127815.773 4463691.64 1.000031353 0.804899338 0.862882964 0.89420533 0.859540508 0.806914166 1.02547571 0.924753793 1 22.08980594 2.235542476 24.99993175 0.972942568 0.868497687 0.437820819 0.059371752 72.84875111 603410.4854 0.022044688 0.015585746 172.0055561 -2.235542476 -0.104444881 CDFTEDQTAGDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 CDFTEDQTAGDGK 13 0 F8VPF3 F8VPF3 MYL6 0 ;;; 77.185 0.026638 15265455000 11160520 10971900 8177710 12204920 10884040 11183290 11149140 12929570 25067790 FALSE TRUE 9685629.005 10899824.87 12132477.91 14976233.63 10667468.9 11613518.4 10067898.12 10164682.07 22104304.42 0.438178412 0.493108702 0.548873997 0.677525668 0.482596905 0.525396239 0.455472288 0.4598508 1 24.397824 1.234933734 24.99725787 1.000000693 0.510734206 0.837137615 0.067904152 43.02550098 296495.2826 0.126651244 0.017583719 17.17646284 -1.234933734 -0.489266486 CDILVQEELLAS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 208.07 8.97E-09 730582000 1274836 1029314 784707 1016902 1352585 1052936 1331358 1656350 2040770 TRUE FALSE 1106363.193 1022552.369 1164193.93 1247805.141 1325671.205 1093443.129 1202243.106 1302152.442 1799512.495 0.614812731 0.568238549 0.646949623 0.69341288 0.736683523 0.607632974 0.66809378 0.723614004 1 20.77917469 1.103868353 1.895288267 1.226380131 0.647567391 0.848259534 0.046590361 0.498170286 1.261878276 0.584300874 0.013713575 12.70189018 -1.103868353 -0.578812741 CDLEDER ddPTM_MDA-MB-175_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 1053870000 2805600 2645800 1541040 2135870 2985300 3384800 2457800 3402800 3140600 FALSE TRUE 2434832.852 2628419.566 2286292.098 2620851.928 2925898.371 3515015.446 2219442.934 2675137.701 2769321.846 0.87921628 0.949120294 0.825578328 0.946387626 1.056539663 1.269269389 0.801439146 0.965990177 1 21.4011013 3.471647469 8.03043112 1.007845369 0.89012516 0.213823701 0.116856604 0.223395606 119.3089004 0.034686107 0.046459871 2962.425715 -3.471647469 -0.117720209 CDLVNYSYGEATHWPNSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CDLVNYSYGEATHWPNSGR 19 0 A0A494C0U1;Q5VZU9;P29144;A0A494C0X4 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 155.49 2.53E-08 116520000 53341 44688 21264 31333 56404 55555 52825 60452 47708 FALSE TRUE 46291.8517 44394.44159 31547.34152 38447.63654 55281.67075 57692.2368 47702.03963 47524.81024 42068.01459 1.100404955 1.055301564 0.749912774 0.913939888 1.314102205 1.371403841 1.133926573 1.129713648 1 15.36043611 3.252851994 24.99996223 1.187200836 0.947420789 0.423833039 0.135971669 247.8187509 433507.8343 0.042215482 0.054238695 1789.995725 -3.252851994 -0.239780047 CDMDDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CDMDDKR 7 1 P61026 P61026 RAB10 Ras-related protein Rab-10 0 75.38 0.069955 141670000 267470 240000 137270 170210 228920 268250 226830 277090 247330 FALSE TRUE 232123.1618 238423.4242 203654.2311 208858.782 224364.9399 278569.7511 204832.0615 217836.4598 218090.9292 1.064341203 1.093229439 0.933804225 0.957668358 1.028767866 1.277310121 0.939204864 0.998833196 1 17.73457024 CDNFTSSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 CDNFTSSWR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8;E9PKG0 Q15149-3;Q15149-4;Q15149-5;Q15149-8;E9PKG0 PLEC Plectin 0 ;;;;; 173.37 0.00012908 1790994000 1284175 1186318 713246 824339 1396527 1660290 1265959 1335040 1191617 FALSE TRUE 1114468.02 1178524.999 1058174.151 1011517.769 1368738.845 1724162.431 1143186.491 1049552.085 1050745.396 1.060645162 1.12160853 1.007069986 0.962666858 1.302636062 1.640894586 1.087976684 0.99886432 1 20.0029817 2.004148996 24.99972398 1.012571802 1.183725638 0.139018908 0.18931767 249.7401946 1504796.602 0.085192496 0.057159385 100.9599196 -2.004148996 0.171153836 CDPAPFYLFDEIDQALDAQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 CDPAPFYLFDEIDQALDAQHR 21 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ;;;; 237 7.59E-30 326059000 266971 226965 120990.5 188492 278874 259681 249834 293369 281169 FALSE TRUE 231690.1059 225474.052 179501.9105 231291.9895 273324.953 269671.0961 225605.1371 230634.3224 247929.5211 0.934499873 0.909428014 0.72400378 0.932894108 1.102430044 1.087692562 0.909956733 0.930241471 1 17.91957054 3.480684501 24.99212768 0.995659912 0.855843402 0.419898668 0.080244869 158.2638763 1110045.752 0.024697939 0.032590251 3024.715283 -3.480684501 -0.13981651 CDPDAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CDPDAAR 7 0 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 110.61 0.015737 1798480000 1232300 1279400 594760 756390 900820 1366450 1171760 1317950 1242390 FALSE TRUE 1069448.433 1270995.537 882387.9254 928139.9102 882895.4444 1419018.216 1058122.896 1036116.649 1095516.07 0.976205153 1.160179729 0.805454114 0.847217066 0.805917384 1.295296578 0.965867069 0.945779508 1 20.06317922 CDRVDQLTAQLADLAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CDRVDQLTAQLADLAAR 17 1 P18206;P18206-2 P18206 VCL Vinculin 0 ;; 142.26 5.41E-07 587277000 226784 273050 149544 189586 283317 271272 241698 341847 374916 FALSE TRUE 196813.9198 271256.3166 221863.9786 232634.3989 277679.546 281708.0094 218258.1652 268745.6793 330593.8576 0.595334472 0.82051227 0.671107383 0.703686392 0.839941637 0.852127173 0.660200304 0.812917945 1 18.33470039 1.294381245 3.198644533 1.026686887 0.742570729 0.498135831 0.083687766 0.256442194 3.625378203 0.16927378 0.02086263 19.69614554 -1.294381245 -0.284116157 CDVDIRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 CDVDIRK 7 1 P60709;A0A2R8Y793;Q562R1;P63261 P60709;P63261 ACTB;ACTBL2;ACTG1 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Beta-actin-like protein 2;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 ;;;; 91.041 0.02677 76452920000 125976300 101315900 35144460 47359200 101311900 87638400 116576500 129989700 13712490 FALSE TRUE 109328212.8 100650349.2 52140438.41 58112830.2 99295991.4 91009905.96 105270929 102192414.2 12091415.05 9.041804643 8.324116635 4.312186636 4.806123183 8.212106769 7.526820108 8.706253859 8.451650513 1 23.52747976 4.456088193 24.65911451 6.547175617 8.862384564 0.151973856 2.376975921 359.911596 421959.3872 0.599390941 1.586186995 28581.70898 -4.456088193 2.315208948 CEAFGWHAIIVDGHSVEELCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 CEAFGWHAIIVDGHSVEELCK 21 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ;;; 293.25 5.05E-55 1889880000 1731100 1735820 1023162 1049183 1667920 1340494 1676410 1631170 2080590 FALSE TRUE 1502330.749 1724417.284 1517966.565 1287416.036 1634731.655 1392063.672 1513832.016 1282356.989 1834625.02 0.818876191 0.939929013 0.827398814 0.701732518 0.891044021 0.758772859 0.825145193 0.698974981 1 20.80705379 4.011644774 24.1920312 0.79965816 0.880467989 0.068051727 0.093014409 306.0597777 635823.6813 0.022058385 0.045852137 10271.75787 -4.011644774 0.080809829 CEAKNYSGRFTCWWLTT(ph)ISTDLT(ph)FSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CEAKNYSGRFTCWWLTTISTDLTFSVK 27 2 P29460 P29460 IL12B Interleukin-12 subunit beta 2 CEAKNY(0.018)S(0.011)GRFT(0.012)CWWLT(0.391)T(0.41)IS(0.097)T(0.1)DLT(0.503)FS(0.458)VK 40.112 0.0957 981920000 545060 377180 312480 375710 437640 301190 603090 687640 312580 TRUE FALSE 473028.94 374702.2797 463596.3732 461020.6979 428931.8202 312776.9742 544602.4246 540593.5372 275627.1485 1.716191393 1.359453457 1.681969195 1.672624415 1.55620309 1.134782898 1.975866411 1.961321808 1 18.07235847 2.206299844 24.9999162 1.725233131 1.528813732 0.013149763 0.317710662 539.1200125 417777.9704 0.128060892 0.086346186 160.8051096 -2.206299844 -0.196419399 CEDCGKPLSIEADDNGCFPLDGHVLCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CEDCGKPLSIEADDNGCFPLDGHVLCR 27 1 Q15942;Q15942-2;H0Y2Y8 Q15942 ZYX Zyxin 0 ; 189.08 4.63E-18 286500000 233640 234512 115136 145588 237373 203100 276590 308200 257840 FALSE TRUE 202763.882 232971.4752 170816.1547 178645.9806 232649.7417 210913.3884 249766.3444 242293.8284 227358.4489 0.891824707 1.024688004 0.751307706 0.785745951 1.02327291 0.927669015 1.098557566 1.065690893 1 17.79460909 2.773052702 1.672457062 1.051788787 0.873975287 0.411321154 0.088300142 0.357788446 2.01161875 0.038394436 0.034721532 592.9972807 -2.773052702 -0.1778135 CEELSGLHGQLQEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CEELSGLHGQLQEAR 15 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 126.16 8.60E-05 378250000 299020 256190 165130 222050 288310 232460 294450 342150 333020 FALSE TRUE 259503.7494 254507.071 244987.4203 272469.8463 282573.1951 241402.8866 265894.2843 268983.8851 293650.755 0.883715587 0.86669987 0.834281595 0.92787041 0.962276413 0.822074803 0.905477952 0.915999297 1 18.16374182 1.130553984 1.684947584 1.068622196 0.885123496 0.436102849 0.04087715 1.337886407 2.783458584 0.440977238 0.011621145 13.50684711 -1.130553984 -0.183498701 CEGINISGNFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CEGINISGNFYR 12 0 P40429;M0QYS1 P40429 RPL13A 60S ribosomal protein L13a 0 ;; 232.88 2.45E-14 472240000 597390 534710 302873 399878 615940 593070 538240 651800 672540 FALSE TRUE 518443.3979 531197.4548 449343.3958 490676.4117 603683.9991 615885.7867 486041.5676 512417.6423 593033.0874 0.874223393 0.895729878 0.757703753 0.827401408 1.017960063 1.038535285 0.819585919 0.864062484 1 19.17775307 3.276320379 24.99635624 0.932425154 0.837043393 0.328315418 0.075837773 245.9178723 162792.0958 0.023884674 0.030834298 1889.384633 -3.276320379 -0.095381761 CETS(ph)PPS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.162)S(0.838)PPS(0.516)S(0.484)PR;CET(0.154)S(0.846)PPS(0.575)S(0.425)PR 90.614 0.015659 368500000 658250 723760 358210 482650 733480 806380 718830 834790 759150 TRUE FALSE 571260.5947 719005.5729 531441.5541 592243.0593 718885.183 837401.9604 649117.9772 656276.6548 669404.1518 0.853386692 1.074097869 0.793902387 0.884731679 1.073918023 1.250966189 0.969695177 0.980389281 1 19.35251797 3.23939035 24.99995794 1.049069417 0.906168279 0.345027043 0.104803633 29.11636805 877264.6407 0.032203751 0.039170476 1735.363065 -3.23939035 -0.142901138 CETS(ph)PPSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.019)S(0.981)PPS(0.032)S(0.968)PR;CET(0.112)S(0.888)PPS(0.075)S(0.925)PR 144.28 4.75E-05 540910000 899920 974480 474500 624810 1025830 1066270 991260 1022950 879500 TRUE FALSE 780993.2919 968078.5767 703969.7871 766682.6601 1005417.99 1107290.097 895127.7578 804200.1031 775526.5119 1.007049121 1.248285599 0.907731427 0.988596326 1.296432778 1.427791416 1.154219416 1.036973064 1 19.56481658 4.855453479 17.08750951 1.128887297 1.00664725 0.057892288 0.158452404 45025.99559 6531964.827 0.041363176 1628.992587 71689.15793 -4.855453479 -0.122240047 CEYLMELMTPAACPEPPPEAPTEDDHDEL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CEYLMELMTPAACPEPPPEAPTEDDHDEL 29 0 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 106.12 0.00048353 13174000 20843 21841 14722 13841 23564 28591 23212 25087 19048 FALSE TRUE 18088.54474 21697.52503 21841.60844 16983.8106 23095.1225 29690.91427 20960.90381 19722.34028 16796.16714 1.076944793 1.29181407 1.300392421 1.011171802 1.375023379 1.767719625 1.247957563 1.174216719 1 14.03584443 1.469862692 2.509495531 0.999762702 1.304905795 0.185512727 0.200268642 0.601779016 6.497284468 0.335053236 0.056376999 29.50276309 -1.469862692 0.305143093 CEYSAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CEYSAHK 7 0 Q9GZN8-2;Q9GZN8 Q9GZN8-2 C20orf27 UPF0687 protein C20orf27 0 ; 91.041 0.016695 236510000 411030 302440 168647 227190 299490 335600 348960 434710 417400 FALSE TRUE 356711.3441 300453.2517 250205.2533 278776.9619 293530.7349 348510.7492 315117.9129 341750.6494 368055.4475 0.969178276 0.816326056 0.679803152 0.757431968 0.797517703 0.946897408 0.856169675 0.928530339 1 18.4895636 2.745663521 23.02240188 0.925023292 0.79524068 0.391670567 0.079100845 202.3218796 655778.3521 0.02665757 0.026059928 556.7542242 -2.745663521 -0.129782612 CFSEENHEPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CFSEENHEPLR 11 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;; 197.43 5.71E-08 1353280000 1510960 1346070 635380 1002210 1466670 1479080 1341810 1550650 1531910 FALSE TRUE 1311282.808 1337227.578 942651.8932 1229777.098 1437486.136 1535981.165 1211681.473 1219055.565 1350809.345 0.970738626 0.989945459 0.697842295 0.9104002 1.064166562 1.137082128 0.897004064 0.902463082 1 20.36539263 3.45918406 23.32666255 0.987066442 0.881147272 0.206839944 0.104003068 197.1018893 256321.5223 0.032138307 0.041499267 2878.618155 -3.45918406 -0.10591917 CFSIDNPGYEPEVVAVHPGGDTVAIGGVDGNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CFSIDNPGYEPEVVAVHPGGDTVAIGGVDGNVR 33 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 ; 140.24 4.91E-10 473560000 131760 105569 68227 81200 125182 145663 111636 136873 145142 FALSE TRUE 114347.5822 104875.5103 101221.8054 99637.70106 122691.1231 151266.7499 100809.5579 107603.7741 127983.4781 0.893455811 0.819445696 0.790897442 0.778520029 0.958648139 1.181924043 0.787676342 0.840763009 1 16.96559805 3.232772425 24.97505528 0.938619046 0.818378573 0.269542494 0.107345379 226.2593663 976269.1003 0.034616077 0.04031408 1709.119482 -3.232772425 -0.120240473 CGDLEEELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CGDLEEELK 9 0 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;K7EPB9;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 151.44 0.00019274 65592000 165420 151400 125430 145620 156650 129110 182840 219720 314730 FALSE TRUE 143559.3279 150405.4434 186088.3675 178685.2467 153532.9715 134076.9452 165108.2049 172734.5879 277522.9779 0.517288078 0.541956722 0.670533189 0.643857485 0.55322616 0.483120159 0.59493526 0.622415445 1 18.0822477 1.202959056 3.046301315 1.103743803 0.574565891 0.851335802 0.05568832 0.1761104 1.929601579 0.239758524 0.015438036 15.95728699 -1.202959056 -0.529177911 CGDLEEELKNVTNNLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CGDLEEELKNVTNNLK 16 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;K7EPB9;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 153.23 4.30E-07 355290000 399690 308940 188240 195030 323690 228870 439620 446720 113310 FALSE TRUE 346869.9538 306910.5528 279273.4936 239314.5423 317249.2023 237674.777 396985.7201 351192.4044 99914.62088 3.471663614 3.071728142 2.795121386 2.395190416 3.175202983 2.37877875 3.973249526 3.514925056 1 16.60840819 1.231717166 24.99969832 0.999996407 3.105495755 0.640907747 0.493253597 164.6271281 601341.7358 1.224095358 0.127351547 17.04971666 -1.231717166 2.105499348 CGEDDETIPSEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 CGEDDETIPSEYR 13 0 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;D6RAA8;P20810-5;E9PCH5;P20810-2;P20810-3;F8W7E0;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ;;; 240.8 1.70E-16 1163880000 1246080 1347710 709535 887640 1416600 1260200 1260840 1513710 1277840 FALSE TRUE 1081407.371 1338856.804 1052668.499 1089192.229 1388412.432 1308680.709 1138563.931 1190014.896 1126775.211 0.959736565 1.188219967 0.934231148 0.966645537 1.232200015 1.161439031 1.010462353 1.056124491 1 20.1037683 5.041717105 14.1560579 1.066073326 0.545526821 0.108255391 0.098001126 926737.85 9921267.996 0.024050889 12117563.94 110082.2013 -5.041717105 -0.520546505 CGESGHLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 182.76 4.59E-05 1080820000 1364400 1313160 437260 796310 1621650 1562860 1357240 1561350 1401180 FALSE TRUE 1184091.083 1304533.765 648720.3985 977124.3563 1589382.338 1622984.236 1225615.074 1227467.453 1235534.097 0.958363744 1.055846026 0.525052607 0.790851794 1.286392939 1.313589192 0.991971874 0.993471128 1 20.23670339 3.259526786 24.99732057 1.102075032 0.826517122 0.393676097 0.174857532 281.8185445 336001.4786 0.054416439 0.070176801 1817.719166 -3.259526786 -0.27555791 CGETGHVAINCSK ddPTM_MDA-MB-175_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 ;;; 176.25 1.69E-05 852000000 1411440 1036650 661350 1085550 1450090 1058780 1358590 1552200 2326710 FALSE TRUE 1224914.628 1029840.178 981181.0721 1332040.719 1421236.046 1099511.952 1226834.151 1220274.109 2051648.994 0.59703908 0.501957294 0.478240223 0.649253709 0.692728654 0.535916209 0.59797468 0.594777232 1 20.9683525 1.235626915 5.395984832 1.022626384 0.579348106 0.810509515 0.063709664 0.070743301 6.115136834 0.117012096 0.016754288 17.2039002 -1.235626915 -0.443278278 CGFCHVGEEENEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CGFCHVGEEENEAR 14 0 A0A0D9SGE8;Q8IWS0-3;Q5JRC6;Q8IWS0-2;Q8IWS0-4;Q8IWS0-5;Q8IWS0 A0A0D9SGE8;Q8IWS0-5 PHF6 PHD finger protein 6 0 93.348 0.0044719 0 69604 70830 35684 42843 75292 82748 58720 66629 61726 FALSE TRUE 60405.65505 70364.71307 52940.90176 52571.15796 73793.83651 85931.36911 53025.34344 52380.90686 54428.8226 1.109810063 1.292784038 0.972662998 0.965869836 1.355786015 1.578784273 0.974214413 0.962374425 1 15.73208321 2.089068524 24.51844883 0.974987652 1.206968071 0.272562511 0.179819439 24.14126077 6637.783402 0.0781915 0.052716692 122.7632914 -2.089068524 0.231980419 CGFSELYSWQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CGFSELYSWQR 11 0 Q9NSE4 Q9NSE4 IARS2 "Isoleucine--tRNA ligase, mitochondrial" 0 ; 183.67 1.22E-05 339060000 169146 167181 99802 166509 234590 240090 187351 211512 191976 FALSE TRUE 146792.9275 166082.777 148066.581 204317.4134 229922.118 249326.4177 169181.7289 166281.8048 169280.816 0.867156309 0.981108084 0.874680218 1.206973231 1.358229027 1.472856899 0.999414658 0.982283809 1 17.36905896 3.739473647 24.99999983 1.160216266 0.914994182 0.372477371 0.160073087 109.8252162 3007126.527 0.050115401 0.080758968 5488.752487 -3.739473647 -0.245222084 CGGVEQASSS(ph)PR ddPTM_MDA-MB-175_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;CGGVEQASSS(1)PR 176.83 2.52E-05 646770000 1367650 1138840 509590 691120 1328810 1294080 1259110 1352500 1136610 TRUE FALSE 1186911.587 1131358.885 756029.4285 848049.3591 1302369.281 1343864.095 1137001.706 1063278.4 1002241.261 1.184257358 1.128828885 0.754338759 0.84615291 1.299456859 1.340858881 1.134459088 1.060900645 1 19.93479841 3.240865143 24.99999898 1.160091271 0.973135828 0.262820392 0.156714268 96.32188058 1044912.61 0.050646413 0.062254592 1741.266093 -3.240865143 -0.186955443 CGHTNNLRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CGHTNNLRPK 10 1 M0R2S1;P62987 M0R2S1 UBA52 Ubiquitin-60S ribosomal protein L40;Ubiquitin;60S ribosomal protein L40 0 ; 145.25 1.85E-05 1640660000 2389000 2359200 1357520 1815200 2535200 2167600 2806300 2749600 2409000 FALSE TRUE 2073287.597 2343702.26 2014021.213 2227368.904 2484754.48 2250988.975 2534145.458 2161619.437 2124210.764 0.976027253 1.103328492 0.948126827 1.048563043 1.16973067 1.059682501 1.192982119 1.017610622 1 21.01849549 3.474303127 24.99701489 1.087795169 1.0152055 0.205380941 0.070712289 142.6327588 1265146.54 0.019944107 0.025905061 2980.596085 -3.474303127 -0.072589668 CGLGQENS(ph)DNEHLVENEVSLLLEESDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CGLGQENSDNEHLVENEVSLLLEESDLR 28 0 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 CGLGQENS(1)DNEHLVENEVSLLLEESDLR;CGLGQENS(1)DNEHLVENEVSLLLEESDLR;CGLGQENS(1)DNEHLVENEVSLLLEESDLR 114.7 0.00025714 90970000 44952 38189.9 22543.7 30185.8 43400 44964.2 42200 41205.1 50092 TRUE FALSE 39011.47931 37939.02803 33445.90872 37039.94725 42536.42491 46694.00187 38107.4505 32393.71002 44170.18082 0.883208504 0.85892852 0.75720561 0.838573593 0.963012243 1.057138572 0.862741555 0.733384139 1 15.43078512 5.062175985 10.38087436 0.873487005 0.926126291 0 0.10134909 580601.3011 4067423.469 0.026470016 570752.3935 115392.0754 -5.062175985 0.052639287 CGSGPVHISGQHLVAVEEDAES(ph)EDEEEEDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 39 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;CGS(0.002)GPVHIS(0.002)GQHLVAVEEDAES(0.996)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGS(0.003)GPVHIS(0.003)GQHLVAVEEDAES(0.994)EDEEEEDVK;CGS(0.001)GPVHIS(0.001)GQHLVAVEEDAES(0.997)EDEEEEDVK;CGS(0.004)GPVHIS(0.003)GQHLVAVEEDAES(0.993)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHIS(0.002)GQHLVAVEEDAES(0.998)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGS(0.016)GPVHIS(0.014)GQHLVAVEEDAES(0.971)EDEEEEDVK;CGS(0.001)GPVHIS(0.001)GQHLVAVEEDAES(0.998)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGS(0.002)GPVHIS(0.001)GQHLVAVEEDAES(0.997)EDEEEEDVK;CGS(0.005)GPVHIS(0.004)GQHLVAVEEDAES(0.991)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGS(0.006)GPVHIS(0.006)GQHLVAVEEDAES(0.988)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK 323.87 3.88E-93 52911189000 4411403 4087106 1744054 2797972.4 5395102.8 4476510.7 4903237 5754605.7 5620904 TRUE FALSE 3828424.916 4060257.532 2587484.348 3433294.798 5287750.81 4648724.963 4427721.83 4524028.053 4956407.132 0.772419378 0.819193707 0.522048387 0.692698301 1.066851586 0.937922338 0.893332955 0.912763607 1 22.24086327 3.255258892 24.99514325 0.949622104 0.697165714 0.675160962 0.089557305 151.6499435 226998.8617 0.026567516 0.034203234 1799.943578 -3.255258892 -0.252456389 CGSGPVHISGQHLVAVEEDAES(ph)EDEEEEDVKLLSISGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 CGSGPVHISGQHLVAVEEDAESEDEEEEDVKLLSISGK 38 1 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 1 CGSGPVHISGQHLVAVEEDAES(0.981)EDEEEEDVKLLS(0.016)IS(0.003)GK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK 355.3 1.34E-145 2761640000 1385175 1400537 127000 311576 1763860 1245789 1961570 2103510 108370.9 TRUE FALSE 1202120.614 1391336.78 188417.6248 382324.0929 1728762.637 1293715.309 1771337.243 1653690.756 95559.41566 12.57982383 14.55991302 1.971732701 4.000904467 18.0909712 13.53833424 18.53650141 17.30536698 1 16.54411041 CGYAGSNFPEHIFPALVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CGYAGSNFPEHIFPALVGR 19 0 P61160;P61160-2;A0A1B0GWD0;A0A1B0GWH0 P61160 ACTR2 Actin-related protein 2 0 ; 84.035 0.0032611 505690000 496010 448630 254700 403900 493380 468180 446030 569930 566570 FALSE TRUE 430461.0218 445682.92 377873.7719 495611.6682 483562.7033 486191.1876 402774.0793 448054.9047 499590.74 0.861627303 0.892096038 0.756366645 0.992035337 0.967917666 0.973178941 0.806208056 0.896843894 1 18.93038721 3.729127302 24.99379917 0.929211252 0.842236597 0.344255612 0.065661006 900.8753888 2386890.13 0.01892943 0.028504155 5359.537351 -3.729127302 -0.086974655 CGYAGSNFPEHIFPALVGRPIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CGYAGSNFPEHIFPALVGRPIIR 23 1 P61160;P61160-2;A0A1B0GWD0;A0A1B0GWH0 P61160 ACTR2 Actin-related protein 2 0 201.38 1.36E-24 579890000 444140 417090 159290 256250 446330 515170 426790 461660 244170 FALSE TRUE 385445.7737 414350.1083 236323.1768 314435.479 437448.9062 534988.9233 385399.9715 362937.6016 215304.5008 1.790235561 1.924484193 1.097623022 1.46042223 2.031768517 2.484801392 1.790022829 1.685694448 1 17.71601895 3.255075874 24.98359161 1.818046711 1.560028724 0.067907201 0.419961024 711.3943093 1076161.145 0.128238189 0.165070226 1799.185216 -3.255075874 -0.258017986 CHDCS(ph)QPCPWPMIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CHDCSQPCPWPMIEK 15 0 O75509 O75509 TNFRSF21 Tumor necrosis factor receptor superfamily member 21 1 CHDCS(1)QPCPWPMIEK 73.464 0.02428 65947000 176960 144020 98265 130890 135390 131060 138130 168180 156390 TRUE FALSE 153574.2876 143073.9231 145786.2827 160610.575 132696.0039 136101.963 124734.1739 132216.0158 137901.7524 1.113650008 1.037506201 1.057174983 1.164673924 0.962250309 0.986948756 0.904514785 0.958769657 1 17.07328126 3.210447817 23.23830301 0.958904604 1.086692542 0.708380119 0.041557397 52.7301666 43586.8752 0.012462027 0.014135021 1623.483269 -3.210447817 0.127787937 CHEFLIFEDR ddPTM_MDA-MB-175_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 ; 150.94 2.07E-05 264730000 280970 277220 144857 179516 240820 237310 219500 232020 236490 FALSE TRUE 243839.1026 275398.9236 214910.3297 220277.8515 236028.1532 246439.4693 198212.9238 182404.3286 208532.4216 1.169310272 1.320652786 1.030584731 1.056324239 1.131853509 1.181780115 0.950513701 0.874704888 1 17.66991218 1.793056393 0.233103476 0.651100336 1.311865393 0.466371265 0.093438921 10.51964063 1.096562962 2.525868942 0.784808339 62.09496587 -1.793056393 0.660765057 CHEHIEILTVNGELLFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 CHEHIEILTVNGELLFFR 18 0 Q9ULC4-2;Q9ULC4;Q9ULC4-3 Q9ULC4-2 MCTS1 Malignant T-cell-amplified sequence 1 0 ;;; 129.32 1.24E-05 397492000 770575.8 692001.5 386944.5 395592.3 532493.3 451078.2 915612.3 957825.7 220317.4 FALSE TRUE 668742.2556 687455.6966 574072.1545 485417.578 521897.7251 468431.4702 826816.3601 753002.1279 194271.728 3.442303534 3.538629649 2.954995873 2.498652702 2.686431683 2.411217912 4.255978823 3.876025275 1 17.56771644 6.211164823 8.966457554 3.059930754 3.240659822 0 0.919032814 0 0 0.206217318 0 1626165.799 -6.211164823 0.180729068 CHELS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CHELSPR 7 0 Q9UGI8-2;Q9UGI8 Q9UGI8-2 TES Testin 1 CHELS(1)PR;CHELS(1)PR 90.906 0.017617 648260000 1322990 1630310 742520 914260 1362340 1529220 1307740 1428330 1308270 TRUE FALSE 1148153.519 1619600.386 1101605.156 1121856.707 1335232.099 1588050.083 1180915.576 1122892.745 1153607.811 0.995271971 1.403943672 0.95492172 0.972476691 1.157440238 1.376594426 1.023671619 0.973374776 1 20.13772141 2.021660886 24.9969155 0.988906717 1.14462478 0.169009174 0.15257538 388.6866278 448547.016 0.062224492 0.041948024 105.1140781 -2.021660886 0.155718063 CHQPLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 CHQPLAR 7 0 Q15942;Q15942-2;H0Y2Y8;C9JJK5 Q15942 ZYX Zyxin 0 ;;; 153.61 0.0017343 595524000 534730 538653 262887 374407 515662 618943 496378 516460 457591 FALSE TRUE 464064.0757 535114.553 390020.0325 459421.8318 505401.3351 642754.1377 448239.338 406019.0481 403495.1133 1.150110771 1.326198349 0.966604104 1.13860569 1.252558751 1.59296635 1.110891615 1.006255181 1 18.62219168 2.005593864 24.99623205 1.020074027 1.236206523 0.276199909 0.158416221 196.0475712 876036.342 0.067720354 0.045503504 101.2963656 -2.005593864 0.216132496 CHTPPLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CHTPPLYR 8 0 Q02543;M0R117 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 111.01 0.0033162 1665570000 384510 411620 211190 257820 430040 454010 362640 399740 345090 FALSE TRUE 333696.0293 408916.0411 313322.1904 316361.9715 421483.0454 471476.0585 327471.2286 314258.7118 304293.8533 1.096624285 1.34381959 1.029669798 1.039659422 1.385118499 1.549410392 1.076167741 1.032747485 1 18.21510567 2.021776672 24.99964114 1.029436075 1.239864654 0.268367442 0.16103248 321.315823 368869.3034 0.06943862 0.046811652 105.1421061 -2.021776672 0.21042858 CIALAQLLVEQNFPAIAIHR ddPTM_MDA-MB-175_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 ; 171.71 7.43E-12 678750000 1073810 980750 538830 697540 956710 1105770 1003820 1093750 1157120 FALSE TRUE 931903.2878 974307.3887 799409.9903 855927.1182 937673.3428 1148309.687 906469.6909 859860.0741 1020326.592 0.913338234 0.954897575 0.783484422 0.838875636 0.91899334 1.125433461 0.888411317 0.84273024 1 19.96059958 3.008908563 23.43926222 0.947421891 0.87300236 0.190463695 0.085898564 200.4465281 527383.6967 0.028088527 0.03179057 1020.724557 -3.008908563 -0.074419531 CIDHYTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 CIDHYTK 7 0 A0A087WW66;Q99460-2;Q99460;C9J9M4;H7BZR6 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;; 114.78 0.0058274 701540000 2405000 2187500 1125180 1597680 2208610 2260320 2556900 2832840 2574520 FALSE TRUE 2087173.157 2173130.168 1669320.812 1960457.663 2164662.982 2347275.973 2308932.232 2227059.211 2270163.179 0.91939345 0.957257253 0.735330758 0.863575659 0.953527483 1.033967952 1.01707765 0.981012833 1 21.11436457 3.090966044 3.63373374 1.004022952 0.865890131 0.56272335 0.057769523 0.180291582 4.652092232 0.018928891 0.021641235 1233.008425 -3.090966044 -0.138132821 CIESLIAVFQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CIESLIAVFQK 11 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ; 181.25 1.47E-05 482930000 1579250 1691690 927660 1171190 1508150 1461870 2113690 1946140 2030170 FALSE TRUE 1370548.111 1680577.177 1376279.479 1437126.59 1478140.766 1518109.085 1908704.669 1529973.106 1790165.615 0.765598501 0.938783073 0.768800086 0.802789741 0.825700568 0.848027172 1.066216809 0.854654504 1 20.77166163 2.450776958 24.67501957 0.953328855 0.824455815 0.493002539 0.070523398 169.5443889 158800.1011 0.02463547 0.019083103 282.3429567 -2.450776958 -0.12887304 CIIPNHEK ddPTM_MDA-MB-175_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 ;;;;; 138.78 0.00069046 4346170000 6632300 5998080 3974800 5103270 5891580 5757250 7106970 7703490 8326930 FALSE TRUE 5755824.751 5958678.218 5897026.575 6262045.452 5774349.085 5978735.133 6417737.143 6056158.612 7342529.821 0.783902128 0.811529318 0.803132805 0.852845764 0.78642501 0.814260926 0.874049857 0.82480545 1 22.80784579 -0.345626484 1.256879329 10 0.81386936 0.802930518 0.028074612 30.63745644 1.207816953 766.2590196 0.008026458 0.451204597 0.345626484 -9.186130639 CIIPNHEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CIIPNHEKK 9 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 94.692 0.0055504 356650000 646540 574560 298310 319350 467060 404220 731430 804650 144470 FALSE TRUE 561098.1009 570785.6775 442573.7138 391863.2985 457766.4198 419770.605 660496.0312 632581.8593 127390.9212 4.404537589 4.480583642 3.474138578 3.076069274 3.593399086 3.295137527 5.184796727 4.965674582 1 16.95890294 4.248722478 23.9165662 3.711558393 4.442561365 0.083357412 1.142427345 381.1046624 896920.6023 0.291875302 0.751707472 17730.56104 -4.248722478 0.731002972 CIIVEEGKEILVGDVGVTITDPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 CIIVEEGKEILVGDVGVTITDPFK 24 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;;;; 225.39 5.54E-33 626237000 1130979 855677 607818 631796 723054 587829 1292978 1449213 320166 FALSE TRUE 981517.2596 850056.0014 901760.8178 775254.9382 708666.64 610443.162 1167585.193 1139310.078 282316.3402 3.476657635 3.011005317 3.194150282 2.746050539 2.510186408 2.16226649 4.135733666 4.035579651 1 18.10695311 5.464668764 15.25587423 3.020308295 3.182465599 0 0.922968338 1888647.349 55713.02166 0.21335816 343379.67 291520.2745 -5.464668764 0.162157304 CILQDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 117.93 0.019001 603850000 2108590 1860060 1261390 1627070 1904260 2088480 1976320 2122520 3310860 FALSE TRUE 1829934.489 1847841.143 1871402.423 1996521.112 1866368.952 2168825.177 1784656.791 1668635.615 2919453.903 0.626807119 0.632940682 0.641011122 0.683868004 0.639287008 0.742887283 0.611298157 0.571557446 1 21.4772671 1.231560979 24.99996805 1.000000615 0.642601494 0.861470734 0.044899475 92.18314467 329212.5185 0.114545608 0.011748231 17.0435861 -1.231560979 -0.357399121 CKDDEFTHLYTLIVRPDNTYEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CKDDEFTHLYTLIVRPDNTYEVK 23 2 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;; 305 1.58E-62 3057030000 3456000 2465290 2100660 2486650 2444750 2362180 3290280 3686320 2758370 FALSE TRUE 2999280.844 2449095.348 3116546.202 3051281.889 2396104.258 2453054.593 2971189.152 2898029.155 2432278.641 1.233115644 1.006913972 1.281327784 1.254495203 0.985127369 1.008541765 1.221566108 1.191487318 1 21.21387708 3.261573117 24.99779874 1.101988756 1.186842785 0.200438962 0.107040615 534.0409981 580109.2312 0.032478301 0.041900997 1826.304196 -3.261573117 0.08485403 CKDGVVFGVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CKDGVVFGVEK 11 1 P25788-2;P25788 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 153.81 2.95E-05 444950000 2052600 1590200 1059200 1360800 1789300 1362700 2282800 2398500 2134500 FALSE TRUE 1781343.709 1579753.871 1571432.663 1669790.439 1753696.431 1415123.951 2061414.407 1885599.44 1882161.842 0.946434929 0.839329454 0.834908363 0.887166237 0.931745821 0.751860929 1.095237594 1.00182641 1 20.84395926 2.227890144 24.99998896 1.028614739 0.866703951 0.63603505 0.0595637 129.0695338 302396.0976 0.022871789 0.015597202 169.0013384 -2.227890144 -0.161910789 CKDISSALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CKDISSALR 9 1 P13489;E9PMJ3;E9PLZ3;E9PIM9;E9PMN0;E9PIK5;E9PMA9 P13489 RNH1 Ribonuclease inhibitor 0 118.03 0.00096216 240680000 746380 753960 405320 393720 867510 857220 827180 947530 349070 FALSE TRUE 647743.9919 749007.1871 601334.1077 483120.1436 850248.2483 890197.8081 746960.2109 744908.0832 307803.3423 2.104408572 2.433395237 1.953630858 1.569574067 2.762309993 2.892099227 2.426744965 2.420077955 1 18.23164937 3.231468579 24.9999305 2.354305295 2.040718015 0.057283245 0.546424727 493.1745601 1738472.634 0.167259898 0.193680702 1703.996033 -3.231468579 -0.313587279 CKELGITALHIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CKELGITALHIK 12 1 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ; 86.772 0.0065631 519120000 1014540 905500 363590 398580 997940 788540 1183120 1271360 186251 FALSE TRUE 880465.9685 899551.7109 539423.3401 489083.6809 978082.9464 818875.6441 1068381.205 999489.5577 164232.619 5.361090714 5.477302357 3.284507935 2.977993556 5.955473113 4.986071885 6.505292379 6.08581635 1 17.32538117 6.994353888 10.0468363 4.793210267 4.606850179 0 1.723698057 0 0 0.384781369 0 9870834.91 -6.994353888 -0.186360088 CKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIK 36 3 P63279;H3BQQ9;B0QYN7 P63279 UBE2I SUMO-conjugating enzyme UBC9 0 121.93 1.56E-08 242590000 826620 481220 323270 399160 422570 331520 730690 834720 516930 FALSE TRUE 717380.0726 478058.8341 479604.4533 489795.3788 414161.6837 344273.7889 659827.7963 656221.6238 455819.1243 1.573826183 1.048790647 1.052181507 1.074538896 0.908609713 0.755285969 1.447564968 1.439653557 1 18.79810193 0.964044927 18.73075589 0.235866566 1.162095591 0.038259979 0.256122306 17934042.22 240141805.9 575865975.4 0.066809528 9.205447955 -0.964044927 0.926229025 CLAFHDISPQAPTHFLVIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CLAFHDISPQAPTHFLVIPK 20 0 P49773;D6REP8;D6RE99;D6RD60 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ; 215.57 6.86E-25 3684800000 3855640 3412410 1664260 2348800 3535430 2836630 3774900 4244780 4159420 FALSE TRUE 3346107.405 3389993.654 2469101.703 2882130.939 3465081.86 2945756.992 3408810.779 3337066.83 3667698.106 0.91231811 0.924283721 0.673202001 0.78581466 0.944756564 0.80316234 0.929414221 0.909853192 1 21.80644346 1.202077183 0.758841074 1.097697459 0.834296772 0.281781453 0.081050513 3.917035439 1.708283621 0.909403766 0.035874937 15.92491719 -1.202077183 -0.263400687 CLATHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 160.17 0.0031553 700036000 402497 369840 215652 270598 339162 478129 404412 379602 414835 FALSE TRUE 349306.0017 367410.4967 319942.0285 332041.4117 332413.3398 496522.932 365192.1865 298427.0664 365793.6789 0.954926293 1.004420027 0.874651605 0.907728676 0.908745446 1.357385217 0.998355651 0.8158344 1 18.48067062 CLDWNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CLDWNR 6 0 Q9Y2J8 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ;; 99.919 0.088987 2055640000 3384420 3800420 1798110 2298600 3895290 4251870 3571330 3873790 3594590 FALSE TRUE 2937160.322 3775454.791 2667682.01 2820532.262 3817781.35 4415442.19 3224982.966 3045410.154 3169641.665 0.926653746 1.191129847 0.841635204 0.8898584 1.204483583 1.39304144 1.017459797 0.960805818 1 21.59588832 5.030848112 12.80075888 1.055011892 0.608024707 0.061943688 0.163724161 721594.5869 9809918.945 0.042331331 6554934.23 107361.3865 -5.030848112 -0.446987185 CLELFSELAEDKENYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CLELFSELAEDKENYK 16 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 188.44 1.08E-09 913180000 1039130 628560 651390 786110 619700 489640 936340 1122190 1837130 FALSE TRUE 901806.3377 624430.948 966404.3828 964608.2904 607369.1824 508476.7676 845533.8909 882218.4014 1619946.584 0.556688934 0.385463912 0.596565586 0.59545685 0.374931611 0.313884898 0.521951711 0.544597217 1 20.62751481 1.161762301 2.491101279 1.21055531 0.474047736 0.74149599 0.095969929 0.381454716 2.15231602 0.662397554 0.026156208 14.51317061 -1.161762301 -0.736507575 CLELFSELAEDKENYKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CLELFSELAEDKENYKK 17 2 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 286.34 1.13E-36 3691800000 3330090 1854010 1520010 1788160 1671980 1142400 2865610 3323680 2337500 FALSE TRUE 2890010.169 1841830.886 2255091.92 2194189.058 1638710.869 1186348.867 2587703.583 2612936.897 2061163.413 1.402125688 0.893587997 1.094086915 1.064539107 0.795041703 0.575572446 1.255457751 1.267700019 1 20.97502746 0.941413715 21.85924594 0.147379278 1.044694089 0.003144807 0.242665355 1225.75568 1535630.905 229232.4658 0.060015571 8.738033693 -0.941413715 0.897314811 CLELFTELAEDKENYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CLELFTELAEDKENYK 16 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 149 8.00E-07 2732100000 1996880 1888790 1133750 1193570 1848910 2052790 1626490 1966690 1961790 FALSE TRUE 1732987.249 1876382.414 1682035.292 1464588.311 1812120.308 2131762.16 1468753.25 1546128.648 1729869.421 1.001802348 1.084695984 0.972348127 0.846646743 1.047547454 1.232325477 0.849054404 0.893783444 1 20.72223171 CLELFTELAEDKENYKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CLELFTELAEDKENYKK 17 2 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 194.4 4.31E-11 2167400000 1666600 1054500 967510 1036900 1005300 578180 1758400 1893000 1404800 FALSE TRUE 1446354.587 1047572.92 1435401.072 1272343.993 985296.4968 600422.9587 1587870.639 1488196.681 1238726.144 1.167614484 0.845685646 1.15877192 1.027139048 0.795411077 0.484710008 1.281857694 1.201392808 1 20.24042584 0.299949742 7.657163835 1.410307486 1.003492619 0 0.237020153 16384368.47 120188722.2 195085634.7 0.061036529 1.995031432 -0.299949742 -0.406814867 CLFTLLGHLDYIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CLFTLLGHLDYIR 13 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1;A0A3B3ITX2 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 199.4 1.18E-07 489100000 634850 821060 368593 476560 740040 669430 920370 876810 669430 FALSE TRUE 550952.964 815666.4028 546845.8077 584770.2318 725314.6519 695183.4053 831112.6591 689311.0048 590290.748 0.93335863 1.381804485 0.926400777 0.990647801 1.228741352 1.177696597 1.407971685 1.167748279 1 19.1710662 3.221986137 24.90016001 1.207774954 1.071774302 0.152235777 0.159578683 445.8049873 669739.5227 0.047558676 0.054074223 1667.193993 -3.221986137 -0.136000652 CLGHPEEFYNLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CLGHPEEFYNLVR 13 0 E9PNM1;P37268;P37268-5;E9PJG4;E9PQ90;E9PNJ2;E9PSH1 E9PNM1 FDFT1 Squalene synthase 0 110.38 0.0010631 367900000 281370 255660 157290 240050 345220 433190 278750 373930 331510 FALSE TRUE 244186.2416 253980.5526 233355.9701 294557.0214 338350.7974 449855.0996 251716.8679 293967.9794 292319.2655 0.835340911 0.868846438 0.798291449 1.007655178 1.157470059 1.538917043 0.86110256 1.005640114 1 18.15718539 3.561746853 3.904298506 1.100937797 0.839309011 0.3434192 0.174838747 0.303514029 8.549362193 0.053057882 0.079565416 3645.413964 -3.561746853 -0.261628785 CLIKS(ph)PDR ddPTM_MDA-MB-175_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 51.854 0.088536 172130000 213850 191950 164760 179860 187860 198760 163660 182810 258830 TRUE FALSE 185589.1807 190689.0678 244438.4871 220699.962 184121.9535 206406.4258 147788.2784 143717.5041 228231.4123 0.813162302 0.835507549 1.071011587 0.967000816 0.806733621 0.904373433 0.647536975 0.629700805 1 17.80013784 2.255547388 24.70007296 0.727477838 0.903346486 0.201405755 0.126689955 258.2773111 375554.5466 0.048068172 0.037131767 180.1139655 -2.255547388 0.175868648 CLKDEDPYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 CLKDEDPYVR 10 1 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;K7ERB2;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 ;;; 113.22 0.001383 3714550000 11500000 9547400 6353690 8327900 10309800 10065000 11923800 13211100 13126400 FALSE TRUE 9980245.863 9484682.501 9426355.736 10218876.98 10104655.15 10452207.06 10767431.71 10386009.07 11574611.95 0.862253172 0.819438487 0.814399289 0.882869942 0.873001635 0.903028725 0.930262869 0.897309484 1 23.46446049 -2 0.228137551 1.740300619 0.809071031 0.759403978 0.02619335 45.26009015 0.707479115 15.2110526 0.114014888 0.01 2 -0.931229589 CLS(ph)PGGHPTYRPAYLLENEEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 110.75 0.00061992 279422000 113512 140976 54274.8 88156 150543 174080 147174 164279 82933 TRUE FALSE 98511.1016 140049.9194 80522.27482 108173.1672 147547.4888 180776.9702 132901.0881 129149.2143 73128.75522 1.347091186 1.915114225 1.101102768 1.479215212 2.017639824 2.472036748 1.81735745 1.766052408 1 16.15815118 3.259706326 22.66625609 1.84162303 1.467412679 0.155429609 0.407194832 156.8736275 168150.7929 0.12030137 0.155060986 1818.470776 -3.259706326 -0.374210352 CLSSLKDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CLSSLKDER 9 1 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ; 68.893 0.051785 2020850000 5997800 4938400 2820900 3860900 5396300 4811300 6491200 6947400 5181000 FALSE TRUE 5205175.534 4905959.325 4185096.675 4737576.355 5288924.188 4996393.824 5861684.423 5461752.575 4568508.082 1.139360036 1.073864648 0.916075139 1.037007327 1.157691766 1.093659841 1.283063161 1.195522143 1 22.12329168 3.238447949 7.434962929 1.160058062 1.034623239 0.240059568 0.090048632 0.161617558 56.35113903 0.027402617 0.033195683 1731.601481 -3.238447949 -0.125434823 CLTTDEYDGHSTYPSHQYQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 CLTTDEYDGHSTYPSHQYQ 19 0 P30043;M0R192;A0A2R8YEP4 P30043 BLVRB Flavin reductase (NADPH) 0 ;;;;; 235.45 3.67E-24 6879850000 3228300 3204160 1129400 1670880 3083220 3174480 2886120 3355190 2842660 FALSE TRUE 2801671.976 3183111.662 1675581.618 2050278.842 3021869.954 3296604.3 2606224.527 2637708.729 2506603.973 1.117716243 1.269890137 0.668466832 0.817950847 1.205563378 1.315167587 1.039743236 1.052303737 1 21.25730265 3.223042008 24.99887915 1.117193766 0.968602033 0.15055387 0.181577372 528.4537191 851282.42 0.05904198 0.067177047 1671.252262 -3.223042008 -0.148591733 CLVAGLLS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CLVAGLLSPR 10 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 CLVAGLLS(1)PR;CLVAGLLS(1)PR;CLVAGLLS(1)PR 140.14 4.18E-05 413590000 371165 423832 214008 294904 440618 426800 416678 420200 343243 TRUE FALSE 322114.6048 421047.8197 317502.9846 361866.4605 431850.5639 443219.2722 376268.6317 330343.5 302665.2036 1.064260447 1.391133882 1.049023743 1.195599812 1.426825941 1.464387934 1.243184308 1.091448558 1 18.2073633 1.641090099 3.080165517 1.016983081 1.271393388 0.303691854 0.139355687 0.259178496 5.66792084 0.123270747 0.038294227 43.76128834 -1.641090099 0.254410307 CLWEESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 81.32 0.064023 278850000 254890 227020 149990 165340 260530 262520 246430 275480 247540 FALSE TRUE 221205.6407 225528.6907 222525.6657 202882.9741 255345.9627 272619.3143 222531.2565 216570.7458 218276.1032 1.013421247 1.033226667 1.019468748 0.929478633 1.169830132 1.248965463 1.019494362 0.992187155 1 17.73579467 3.247589275 24.99998179 1.077505317 1.002820118 0.21182351 0.082507312 416.9457227 1154498.117 0.027108833 0.034487505 1768.435706 -3.247589275 -0.074685199 CMIDQAHQEERPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CMIDQAHQEERPIR 14 1 Q9UBQ5;A0A087WVB9;K7ERF1;Q9UBQ5-2;K7ES31;K7EQM4 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 0 ; 207.72 5.43E-09 717790000 466390 390900 210179 281110 411410 464760 394440 435330 387980 FALSE TRUE 404755.3798 388332.1522 311822.2674 344940.322 403223.7459 482639.6179 356187.2695 342238.0672 342113.4464 1.18310281 1.135097601 0.911458672 1.008262977 1.178625834 1.410758984 1.041137884 1.000364268 1 18.38411528 2.016683816 24.9968806 1.006370882 1.13196925 0.177439018 0.127597372 450.999941 675717.4907 0.056801533 0.038285379 103.9163337 -2.016683816 0.125598367 CMPTFQFFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CMPTFQFFK 9 0 P10599;P10599-2 P10599 TXN Thioredoxin 0 ; 145.92 0.0002234 354610000 349070 413450 212967 319650 390070 376960 444060 477800 630130 FALSE TRUE 302939.5151 410734.0197 315958.5535 392231.418 382308.3702 391461.8951 400995.1295 375626.1882 555636.7492 0.545211445 0.739213201 0.56864229 0.705913384 0.688054508 0.704528445 0.72168576 0.676028338 1 19.0837825 1.23711196 7.110453016 1.006764599 0.673010189 0.728613666 0.063500847 0.055274933 16.67056682 0.088049265 0.014426581 17.26282868 -1.23711196 -0.33375441 CNAEEHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 CNAEEHVR 8 0 P11279-2;P11279 P11279-2 LAMP1 Lysosome-associated membrane glycoprotein 1 0 ;;; 144.5 0.00058444 2145800000 2232919 1939465 1089916 1806033 2454497 3146789 1853952 2662299 2482458 FALSE TRUE 1937833.097 1926724.527 1617003.023 2216120.396 2405657.312 3267848.009 1674156.02 2092987.077 2188984.643 0.885265734 0.880190975 0.738700031 1.012396502 1.098983183 1.49286018 0.764809395 0.956145162 1 21.0618304 3.600370256 5.985767065 1.048952916 0.840460396 0.241442804 0.184222402 0.385172273 17.21850598 0.05365198 0.079969729 3984.467195 -3.600370256 -0.20849252 ERLDQPMTEIVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERLDQPMTEIVSR 13 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 209.39 3.49E-08 230400000 93487 65400 44093 54244 75629 72070 75126 80038 28386 FALSE TRUE 81132.45608 64970.38309 65416.52228 66560.92927 74124.13087 74842.57954 67840.29208 62922.49656 25030.23942 3.241377549 2.595675655 2.613499663 2.659220639 2.961383214 2.990086443 2.710333327 2.513859157 1 14.61138447 1.147973162 2.273776019 0.154187632 2.812967382 0.88873001 0.201250969 0.26589021 1.149094323 1.582957391 0.053465336 14.05960637 -1.147973162 2.65877975 CNEIINWLDKNQTAEKEEFEHQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CNEIINWLDKNQTAEKEEFEHQQK 24 2 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 293.4 4.26E-62 1740440000 1000630 617540 473500 427740 578210 357960 833310 982650 515850 FALSE TRUE 868394.2102 613483.3391 702486.1838 524864.9046 566704.7522 371730.9528 752495.7245 772517.9445 454866.8007 1.90911759 1.34870986 1.544377789 1.153887036 1.245869673 0.817230346 1.654321053 1.698338818 1 18.79508461 5.875965573 1.30228569 1.325746966 10.00315447 0.313404449 0.278202416 33.91968236 4.611550953 0.083829681 751.8094962 751563.3151 -5.875965573 8.677407507 CNEWGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CNEWGK 6 0 P52743 P52743 ZNF137P Putative zinc finger protein 137 0 69.39 0.09363 529850000 909230 815800 1039100 832590 396930 948880 481530 429720 468180 FALSE TRUE 789072.9518 810440.9561 1541612.236 1021642.285 389031.8696 985384.0276 434831.2947 337827.7221 412832.2938 1.911364406 1.963123933 3.734233632 2.474715036 0.942348444 2.386886982 1.053287985 0.818317092 1 18.6551963 2.532195296 0.89910398 0.785449882 2.501338527 0.434999839 0.685074535 0.598564791 1.042856572 0.68392252 0.367574865 340.561301 -2.532195296 1.715888645 CNNVLYIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CNNVLYIR 8 0 P62306 P62306 SNRPF Small nuclear ribonucleoprotein F 0 95.541 0.02228 86156000 92186 107210 55054 66114 131370 114640 102530 116000 86174 FALSE TRUE 80003.38653 106505.7305 81678.29854 81126.19419 128755.994 119050.275 92586.65638 91194.30271 75986.60789 1.052861665 1.401638176 1.074903865 1.067638054 1.6944564 1.566727063 1.218460186 1.200136514 1 16.21345756 1.369438574 1.979654952 0.957255059 1.308965187 0.163568721 0.213296602 1.138484332 5.681614808 0.681907008 0.061647431 23.41200314 -1.369438574 0.351710128 CNREPS(ph)KGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CNREPSKGR 9 2 Q02040 Q02040 AKAP17A A-kinase anchor protein 17A 1 CNREPS(1)KGR;CNREPS(1)KGR 100.04 0.0025731 151407000 181261 164549 91119 99810 134468 171866 182989 193446 153869 TRUE FALSE 157306.8996 163468.0668 135184.4532 122473.386 131792.3499 178477.7962 165242.7549 152079.0783 135678.7821 1.159406778 1.204816731 0.996356623 0.90267162 0.971355637 1.315443679 1.217896803 1.12087591 1 17.0498356 2.767543362 24.996976 1.161980329 1.044870405 0.19935092 0.116086554 1295.228281 1117103.535 0.040706964 0.040700998 585.5221953 -2.767543362 -0.117109924 CNVWILDGDLYHK ddPTM_MDA-MB-175_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 0 128.22 0.0001678 703720000 506660 402210 214130 356850 540210 425290 551450 567990 554400 FALSE TRUE 439703.5973 399567.856 317683.9842 437878.2466 529460.8779 441651.1815 497970.4639 446529.7586 488859.4636 0.899447858 0.817347082 0.649847263 0.895713961 1.083053346 0.903431793 1.018637259 0.913411301 1 18.89906026 3.482363981 24.97717013 0.974967481 0.788569565 0.561265246 0.078520179 161.5783325 769786.0229 0.021509052 0.028618272 3036.434945 -3.482363981 -0.186397915 CPEALFQPSFLGMESCGIHETTFNSIMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 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 ;;;;;;;;;;; 389.87 6.95E-146 10561932000 10099805 8505831 4821623 7337493 8232995 8053740 9138786 10782294 9143177 FALSE TRUE 8765090.18 8449955.636 7153376.01 9003582.932 8069174.507 8363572.589 8252507.94 8476584.336 8062281.031 1.087172494 1.048084978 0.887264533 1.116753794 1.000855028 1.037370511 1.023594676 1.051387852 1 22.94275664 CPFPAGAALACCS(ph)EDEEDDEEHEGGGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 CPFPAGAALACCSEDEEDDEEHEGGGSR 28 0 Q147X3 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 CPFPAGAALACCS(1)EDEEDDEEHEGGGSR;CPFPAGAALACCS(1)EDEEDDEEHEGGGSR;CPFPAGAALACCS(1)EDEEDDEEHEGGGSR;CPFPAGAALACCS(1)EDEEDDEEHEGGGSR 248.69 4.78E-46 2327300000 757500 854490 425805 540990 782670 819720 756200 855590 913630 TRUE FALSE 657394.4557 848876.7989 631725.7222 663830.048 767096.3983 851255.1588 682863.8404 672628.7367 805621.7022 0.816008871 1.053691573 0.784146853 0.823997226 0.952179411 1.056643778 0.847623442 0.83491884 1 19.61974302 4.232298459 24.99567302 0.896074359 0.934850211 0.019157892 0.100988325 672.3609319 2683798.159 0.025757448 0.055829925 17072.55259 -4.232298459 0.038775852 CPGESSHICDFIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CPGESSHICDFIR 13 0 A0A2C9F2P4;A0A286YFF7;P50897;Q5T0S4;A0A286YFE3;A0A286YFL8;P50897-2;A0A286YFL6 A0A2C9F2P4 PPT1 Palmitoyl-protein thioesterase 1 0 ; 160.69 4.34E-05 1012790000 744230 712740 306910 531150 720140 932850 653170 728360 707900 FALSE TRUE 645878.1199 708057.964 455332.7026 651755.7256 705810.6229 968737.3431 589825.6739 572605.8821 624212.8684 1.034708114 1.134321319 0.729451002 1.044124142 1.130721039 1.551934271 0.944911109 0.9173247 1 19.25167857 CPHPLTFDVNNPLHLDYVMAAANLFAQTYGLTGSQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CPHPLTFDVNNPLHLDYVMAAANLFAQTYGLTGSQDR 37 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 363.08 1.71E-146 1858247000 1251658 981611 574555 828200 1191130 1188569 1204923 1317586 1180356 FALSE TRUE 1086248.224 975162.7327 852411.7198 1016255.468 1167428.843 1234294.019 1088069.753 1035830.487 1040815.658 1.043650924 0.936921658 0.818984335 0.976402939 1.12164804 1.185891093 1.045401022 0.995210323 1 19.98928314 3.437985743 7.231247433 1.063448387 0.927658385 0.406801869 0.076561969 0.214521143 31.22709259 0.024016153 0.031271726 2741.48417 -3.437985743 -0.135790002 CPHVTEHIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CPHVTEHIPR 10 0 P48449-2;P48449;A0A0G2JQD0;P48449-3 P48449-2 LSS Lanosterol synthase 0 ;; 93.649 0.0049974 136249000 241598 213653 117604 178821 238311 327330 198069 245310 214856 FALSE TRUE 209670.2122 212249.4994 174477.6878 219425.0412 233569.0773 339922.5969 178860.2989 192852.3655 189455.9684 1.106696262 1.12031044 0.920940571 1.158184896 1.232840956 1.794203686 0.944073181 1.017927105 1 17.53150306 CPLLKPWALTFSYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CPLLKPWALTFSYGR 15 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ; 171.08 1.01E-06 4347400000 1264000 1238460 520320 710970 1330180 1247850 1436110 1544620 1157800 FALSE TRUE 1096959.197 1230324.475 771948.4924 872406.605 1303712.02 1295855.597 1296836.273 1214315.033 1020926.203 1.074474525 1.205106178 0.756125653 0.854524649 1.276989479 1.269294091 1.270254666 1.189424887 1 19.96144715 3.230962497 24.99943593 1.208306398 0.973708911 0.390026505 0.141918748 186.0846261 612257.2164 0.044980323 0.051974348 1702.011528 -3.230962497 -0.234597487 CPNLTHLNLSGNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CPNLTHLNLSGNK 13 0 P39687;H0YN26 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 206.49 6.15E-08 1257900000 1481100 1233100 591280 947310 1341000 1253900 1491900 1712300 1433300 FALSE TRUE 1285368.882 1224999.685 877224.9857 1162411.214 1314316.724 1302138.344 1347215.768 1346137.97 1263856.907 1.017020895 0.969255046 0.694085684 0.919733245 1.039925261 1.030289376 1.065955932 1.065103148 1 20.2694017 3.279397303 4.680598104 1.045450827 0.887351661 0.404983834 0.08449088 0.193427983 9.429434487 0.025698863 0.032550342 1902.818227 -3.279397303 -0.158099166 CPPGVVPACHNSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 ;;;;;;; 186.76 7.53E-06 4419340000 7303960 7640760 2568680 4807000 9500620 9888060 8844260 9359750 9470800 FALSE TRUE 6338723.18 7590567.344 3810902.24 5898502.82 9311576.25 10268460.07 7986545.026 7358240.3 8351172.813 0.759021915 0.908922317 0.456331383 0.706308318 1.115002223 1.229582993 0.956338134 0.881102627 1 22.99354739 3.249551941 24.90512575 1.02064623 0.704071718 0.566298216 0.142577636 171.6370451 388908.3066 0.044508037 0.056895533 1776.445716 -3.249551941 -0.316574512 CPQIVIAFYEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CPQIVIAFYEER 12 0 Q13185;P45973 Q13185;P45973 CBX3;CBX5 Chromobox protein homolog 3;Chromobox protein homolog 5 0 ;; 143 0.00014385 423250000 435070 374310 221445 317571 394130 392690 383880 429900 378690 FALSE TRUE 377574.3972 371851.133 328536.5427 389680.3493 386287.5841 407797.0384 346651.3767 337969.2305 333921.6996 1.130727346 1.113587806 0.983872995 1.166981211 1.156820849 1.221235514 1.038121743 1.012121198 1 18.34915032 2.021471849 24.60955108 1.012384901 1.125012425 0.44294849 0.059878594 186.1109067 213306.4202 0.025713597 0.01733442 105.0683348 -2.021471849 0.112627524 CPQVVISFYEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CPQVVISFYEER 12 0 P83916;J3KS05 P83916 CBX1 Chromobox protein homolog 1 0 ; 162.68 0.00014203 242900000 134759 140293 68910 95713 138639 137330 140690 159595 133456 FALSE TRUE 116950.2567 139371.406 102235.1065 117446.0995 135880.3551 142613.174 127045.9055 125466.8512 117678.9837 0.993807501 1.184335568 0.868762656 0.998021021 1.154669686 1.21188312 1.079597235 1.066178915 1 16.84449717 3.254418426 24.90954453 1.10168566 1.013419869 0.19189857 0.09297494 426.9408965 670637.6035 0.027462014 0.03533136 1796.463618 -3.254418426 -0.088265792 CPS(ph)DEDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CPSDEDFR 8 0 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 CPS(1)DEDFR 85.533 0.017491 174000000 434970 391410 294110 357980 392770 408000 441240 498370 646870 TRUE FALSE 377487.6124 388838.8019 436342.5797 439264.8304 384954.6454 423696.024 398448.6127 391797.4538 570397.7655 0.661797144 0.681697625 0.764979469 0.770102649 0.674888067 0.742808001 0.698545185 0.686884622 1 19.1216088 1.235631147 24.99988783 1.00000039 0.711179013 0.854182928 0.037626047 30.37133218 259138.5111 0.064229697 0.009421996 17.20406787 -1.235631147 -0.288821377 CPS(ph)QSSSRPAAMISQPPTPPTGQPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CPSQSSSRPAAMISQPPTPPTGQPVR 26 1 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 CPS(0.952)QS(0.029)S(0.007)S(0.012)RPAAMISQPPTPPTGQPVR;CPS(0.962)QS(0.006)S(0.026)S(0.006)RPAAMISQPPTPPTGQPVR 196.06 4.27E-25 848480000 63380 75452 67338 96269 124044 131629 92773 117935 164529 TRUE FALSE 55004.17242 74956.35084 99902.88203 118128.3478 121575.7671 136692.8528 83775.88874 92715.51802 145078.5691 0.379133684 0.516660395 0.688612265 0.814237062 0.837999491 0.942198794 0.577451854 0.639071081 1 17.1464749 4.316093319 1.985338681 0.7780517 0.379146701 0.576287285 0.125617057 0.312874256 2.222341698 0.036645449 0.167854673 20705.8622 -4.316093319 -0.398905 CPS(ph)QSSSRPAAMISQPPTPPTGQPVREDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CPSQSSSRPAAMISQPPTPPTGQPVREDAK 30 2 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 CPS(0.498)QS(0.176)S(0.163)S(0.163)RPAAMISQPPTPPTGQPVREDAK 146.12 1.95E-08 390110000 44480 40171 31971 33696 58106 60064 71794 80425 27652 TRUE FALSE 38601.8553 39907.11406 47432.28254 41347.19181 56949.80428 62374.70095 64831.42893 63226.73962 24383.01206 1.583145479 1.63667696 1.945300376 1.69573766 2.335634504 2.558121236 2.658876958 2.593065182 1 14.57358873 3.237509529 24.87297329 2.323309733 1.726039837 0.207603401 0.479491437 36.02564745 852518.432 0.141719451 0.169978697 1727.863892 -3.237509529 -0.597269896 CPSQSSS(ph)RPAAMISQPPTPPTGQPVREDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CPSQSSSRPAAMISQPPTPPTGQPVREDAK 30 2 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 CPS(0.21)QS(0.218)S(0.244)S(0.328)RPAAMISQPPTPPTGQPVREDAK 114.62 7.30E-05 400170000 52918 58053 35323 44699 86388 90449 93795 111510 24307 TRUE FALSE 45924.75222 57671.64602 52405.32095 54848.59113 84669.04782 93928.63156 84698.77534 87664.45427 21433.45415 2.142666875 2.69073037 2.44502452 2.559017821 3.95032211 4.382337578 3.951709078 4.0900759 1 14.38757675 3.273818405 9.350750946 3.63269089 2.472428992 0.211685319 0.946883165 0.459381335 114.7855272 0.270657145 0.34713821 1878.531168 -3.273818405 -1.160261898 CPSSSGKPNHADILLINLQYVSEVEIINDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CPSSSGKPNHADILLINLQYVSEVEIINDR 30 1 K7ELG9;Q3MHD2 K7ELG9 LSM12 Protein LSM12 homolog 0 96.982 0.00040929 22224000 58940 49778 19931 42728 50049 45281 61571 68225 79829 FALSE TRUE 51150.92967 49451.00504 29569.69827 52430.04546 49053.12282 47022.98937 55599.8539 53635.61468 70391.70656 0.726661309 0.702511808 0.42007361 0.744832709 0.696859406 0.668018886 0.789863701 0.761959289 1 16.10311784 -1.406417122 0.596032239 10 0.644931194 0.558249357 0.093758547 59.73088001 1.047469478 691.050153 0.047141755 0.0392268 1.406417122 -9.355068806 CPSSSGKPNHADILLINLQYVSEVEIINDRTET(ph)PPPLASLNVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CPSSSGKPNHADILLINLQYVSEVEIINDRTETPPPLASLNVSK 44 2 K7ELG9;Q3MHD2 K7ELG9 LSM12 Protein LSM12 homolog 1 CPSSSGKPNHADILLINLQYVSEVEIINDRT(0.036)ET(0.964)PPPLASLNVSK 128 2.97E-09 28264000 14236 9361.1 4013.6 9342.9 10725 8955 14433 13558 7819.3 TRUE FALSE 12354.67653 9299.606318 5954.590385 11464.34824 10511.59348 9299.504645 13033.28988 10658.72721 6894.911262 1.79185432 1.348763743 0.863621033 1.662726003 1.524543694 1.348748996 1.890276667 1.54588316 1 12.75131627 CPT(ph)PEIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CPTPEIQK 8 0 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 CPT(1)PEIQK 108.47 0.042529 353820000 1023000 943360 737920 831120 1017500 896090 1172500 1237000 1703400 TRUE FALSE 887807.958 937163.006 1094780.58 1019838.499 997253.7407 930563.1621 1058791.13 972477.1763 1502025.993 0.591073632 0.623932615 0.728869264 0.678975267 0.66393907 0.619538654 0.704908661 0.64744364 1 20.51847835 1.237277467 24.9998067 1.00000041 0.659994535 0.874418331 0.040799781 10.80838095 210496.5344 0.059873919 0.009921243 17.26940868 -1.237277467 -0.340005875 CPT(ph)PEIQKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CPTPEIQKK 9 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 CPT(1)PEIQKK;CPT(1)PEIQKK 120.96 0.0003676 1369500000 2696000 2200440 1506590 1505990 2157830 1676020 2966500 3240100 1433190 TRUE FALSE 2339716.769 2185985.165 2235181.963 1847948.047 2114893.405 1740497.574 2678809.287 2547229.829 1263759.911 1.851393409 1.729747198 1.76867611 1.462261962 1.673493032 1.377237527 2.119713771 2.015596323 1 20.26929098 4.601142411 1.801123647 1.677141753 1.873931835 0.035210175 0.318374462 3.315050904 13.66142573 0.088044222 1.011785289 39915.5769 -4.601142411 0.196790082 CPTQFPLILWHPYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CPTQFPLILWHPYAR 15 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 125.28 9.14E-05 523630000 350560 303780 165320 202060 325330 322750 328140 361690 284040 FALSE TRUE 304232.6078 301784.4492 245269.305 247940.8113 318856.5695 335166.4013 296317.0333 284345.4082 250461.1148 1.214689985 1.20491538 0.979270995 0.989937346 1.273078137 1.338197355 1.18308598 1.135287641 1 17.93422711 1.248568674 3.162209427 0.973312571 1.166264368 0.183867551 0.111148874 0.696932295 9.261386952 0.333049708 0.031469862 17.72428293 -1.248568674 0.192951797 CPVTVCGDVHGQFHDLMELFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CPVTVCGDVHGQFHDLMELFR 21 0 P67775;P62714;P67775-2;E7ESG8 P67775 PPP2CA;PPP2CB Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform;Serine/threonine-protein phosphatase 0 ; 183.09 2.57E-17 769420000 159108 195195 100606 129665 213361 214184 175000 187830 166505 FALSE TRUE 138081.4747 193912.7512 149259.3981 159107.4201 209115.5335 222423.7971 158028.5269 147664.0162 146820.9686 0.940475165 1.320742896 1.016608183 1.08368322 1.424289293 1.514932092 1.076334862 1.005742011 1 17.1636985 2.014983474 24.97469772 1.014608233 1.2224493 0.212611705 0.175554743 349.1799579 582016.5288 0.074350754 0.050108298 103.5102777 -2.014983474 0.207841067 CQEHSKES(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CQEHSKESPAR 11 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 CQEHS(0.006)KES(0.994)PAR 84.759 0.0095213 228780000 152180 140070 82166 100470 123040 119900 141000 170600 169090 TRUE FALSE 132069.0274 139149.8709 121901.7524 123283.2491 120591.7447 124512.6306 127325.8417 134118.5176 149100.3728 0.885772617 0.933263065 0.817581808 0.826847356 0.808795729 0.835092684 0.853960586 0.899518325 1 17.18592434 1.250901058 1.934554715 1.04783651 0.849945842 0.629182133 0.036167546 0.569019218 2.100608841 0.204252984 0.01081984 17.81972748 -1.250901058 -0.197890668 CQEVINWLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CQEVINWLDR 10 0 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 114.89 0.0030129 307970000 210250 194090 150410 182330 210570 223270 240540 250260 276510 FALSE TRUE 182464.9298 192815.01 223148.7791 223730.8132 206380.069 231859.3414 217212.4678 196743.8465 243821.3028 0.748355159 0.790804609 0.915214448 0.917601582 0.846439858 0.950939638 0.890867473 0.806918199 1 17.89546465 4.349315423 4.336234397 0.894637162 0.758013676 0.523848855 0.053275267 0.169464337 5.439026186 0.013369719 0.038844812 22351.95029 -4.349315423 -0.136623487 CQEVISWLDANTLAEKDEFEHK ddPTM_MDA-MB-175_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 ;;; 342.99 8.62E-82 6888420000 9406890 6825800 5132070 5040510 6303410 4972770 9421930 10800930 9371050 FALSE TRUE 8163745.652 6780960.87 7613956.218 6185034.835 6177984.473 5164075.68 8508192.679 8491235.172 8263215.145 0.987962374 0.820620152 0.921427808 0.748502215 0.747648992 0.624947504 1.029646757 1.027594589 1 22.9782718 2.197819606 24.9982993 1.02129486 0.808705669 0.505687759 0.09812894 124.3317224 76287.91122 0.041263502 0.027820198 157.6956109 -2.197819606 -0.21258919 CQEVISWLDANTLAEKDEFEHKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CQEVISWLDANTLAEKDEFEHKR 23 2 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 123.99 3.58E-05 295850000 400070 295700 202920 258670 256870 265200 389400 456530 329880 FALSE TRUE 347199.7359 293757.5272 301052.7907 317404.977 251758.7896 275402.4156 351636.0479 358904.6122 290881.9622 1.193610402 1.009885677 1.034965484 1.091181367 0.865501551 0.946784096 1.208861647 1.233849667 1 18.15007431 2.230993946 24.99975255 1.168099095 1.019423625 0.228542953 0.104898522 214.4399271 708487.2412 0.042721487 0.029424164 170.2134779 -2.230993946 -0.14867547 CQHAAEIITDLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CQHAAEIITDLLR 13 0 Q96AE4;E9PEB5;Q96AE4-2 Q96AE4 FUBP1 Far upstream element-binding protein 1 0 ; 157.38 4.76E-05 856360000 418330 299800 138169 190022 330140 304680 285160 336890 303270 FALSE TRUE 363046.6306 297830.5941 204987.9905 233169.3994 323570.8599 316401.2368 257505.2271 264848.6952 267417.7661 1.357601015 1.113727777 0.766545894 0.871929352 1.20998266 1.183172088 0.962932384 0.990393043 1 18.02873579 4.641683001 3.832134598 1.002078329 1.363294871 0.429789114 0.130231341 0.233859412 5.567773389 0.034409259 0.188773792 43821.0723 -4.641683001 0.361216542 CQHGEEECK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CQHGEEECK 9 0 P13284 P13284 IFI30 Gamma-interferon-inducible lysosomal thiol reductase 0 128.81 0.00040688 149710000 373430 258120 180480 202740 169460 216100 255970 295880 329550 FALSE TRUE 324080.2793 256424.3927 267760.7317 248775.2157 166088.0775 224413.5068 231146.0688 232608.3645 290590.9744 1.11524551 0.882423803 0.921435128 0.856100972 0.571552774 0.772265922 0.795434439 0.800466584 1 18.14863037 5.071241284 0.999837154 0.79441385 1.470958502 0.439594403 0.108075863 3.303790502 1.707021699 0.03516225 2.800230023 117826.0405 -5.071241284 0.676544652 CQHLQAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 CQHLQAEK 8 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 107.57 0.0039768 4870800000 12770600 12685300 7400200 9402500 12866000 12689500 15147500 16328900 15623100 FALSE TRUE 11082932.85 12601969.43 10978961.47 11537481.33 12609991.77 13177673.28 13678497.78 12837091.81 13776154.92 0.804501178 0.91476682 0.796953979 0.837496486 0.915349156 0.956556699 0.992911147 0.931834165 1 23.71566994 3.033357316 2.600975375 0.966325179 0.84051061 0.743471907 0.036469146 0.141351199 1.939376168 0.011725795 0.013036296 1079.834791 -3.033357316 -0.125814569 CQSLTEDLEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CQSLTEDLEFR 11 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 136.5 0.00022776 128790000 185770 174470 85579 131140 198240 194960 190460 214200 251120 FALSE TRUE 161220.0238 173323.8951 126965.2906 160917.3413 194295.4118 202460.2374 171989.2185 168394.9969 221432.8797 0.728076264 0.782737845 0.573380479 0.726709338 0.877446078 0.914318766 0.776710391 0.760478738 1 17.75650993 3.326478712 5.429750788 0.848093857 0.695835611 0.471724255 0.084958184 0.20833106 9.928994334 0.02541225 0.032805185 2120.697441 -3.326478712 -0.152258246 CQSLTEDLEFRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CQSLTEDLEFRK 12 1 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ; 104.7 0.0033835 763440000 475730 348330 218575 253919 428980 364140 434690 559620 164553 FALSE TRUE 412861.0752 346041.7973 324278.6011 311575.1899 420444.1373 378148.7014 392533.8307 439949.618 145099.7318 2.845360705 2.384854837 2.234866992 2.147317476 2.89762174 2.606129569 2.705269168 3.032049836 1 17.14668533 3.266941936 24.99331911 2.548369112 2.389780446 0 0.584207897 1308.655861 1152427.009 0.16408705 0.211796443 1849.021393 -3.266941936 -0.158588665 CQYVTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CQYVTEK 7 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;P09972 H3BPS8;P04075;P09972 ALDOA;ALDOC Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase C 0 ; 143.61 0.0056069 1328780000 1041640 921830 542850 729480 898530 878900 1111420 1064150 1083170 FALSE TRUE 903984.6348 915774.438 805374.0757 895119.5834 880651.0109 912711.8517 1003634.659 836589.8037 955118.8766 0.946462956 0.958806763 0.843218677 0.937181335 0.922032883 0.955600265 1.050795544 0.875901235 1 19.86532078 2.711841002 5.023019438 0.963708239 0.919950135 0.171425734 0.052746722 0.406137527 28.8459253 0.018078291 0.016404391 515.0400508 -2.711841002 -0.043758104 CRDDSFFGETSHNYHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CRDDSFFGETSHNYHK 16 1 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 262.36 4.52E-27 1812840000 1456460 1100880 621870 945150 1255470 1241200 1320660 1511360 1395440 FALSE TRUE 1263985.121 1093648.247 922608.412 1159760.753 1230488.603 1288949.767 1192582.596 1188167.425 1230472.673 1.027235426 0.888803361 0.749800002 0.942532718 1.000012947 1.04752409 0.969206893 0.965618702 1 20.23078119 3.481790426 21.0896913 0.991137174 0.881554394 0.334685019 0.069204747 29.16323323 131725.7731 0.019980254 0.026654047 3032.427496 -3.481790426 -0.109582779 CRDDSFFGETSHNYHKFDSEYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CRDDSFFGETSHNYHKFDSEYER 23 2 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;; 329.12 5.60E-87 2592410000 2342380 1833240 559706 739900 1965280 1722540 1971880 2434840 238513 FALSE TRUE 2032828.548 1821197.326 830381.6937 907905.6037 1926174.773 1788807.228 1780647.381 1914168.414 210316.2649 9.665579358 8.659327071 3.948252382 4.316858728 9.158467959 8.50532045 8.466522465 9.101380796 1 17.6822009 4.461288886 24.96215616 6.784395421 9.41401819 0.150388009 2.676040484 419.2518353 661014.976 0.679592049 1.799190409 28926.03359 -4.461288886 2.629622768 CRHENLLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CRHENLLLR 9 1 Q6ZMV8 Q6ZMV8 ZNF730 Putative zinc finger protein 730 0 68.735 0.052194 1834900000 77593 38521 27284 20628 43717 68343 52057 47361 42342 FALSE TRUE 67338.88845 38267.95301 40478.63366 25311.90268 42847.11723 70972.19943 47008.52015 37233.21871 37336.377 1.803573187 1.024950895 1.084160728 0.677942123 1.14759708 1.900886083 1.259054143 0.997237057 1 15.18829432 2.98056111 24.88704951 1.272316003 1.106658171 0.029171163 0.368445814 2874.077998 3679602.94 0.122579914 0.124435487 956.2272378 -2.98056111 -0.165657832 CRS(ph)PGMLEPLGSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 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 166.21 2.33E-06 11738050000 3583140 2970410 1806876 2144893 3155060 3104910 3544120 3576940 2719530 TRUE FALSE 3109618.97 2950897.181 2680687.277 2631923.738 3092280.479 3224357.897 3200411.788 2812039.217 2398030.261 1.296738836 1.230550435 1.117870496 1.097535665 1.289508531 1.344585992 1.334600251 1.172645426 1 21.19341843 1.305121205 3.469528481 0.98263426 1.239606382 0.464639898 0.082540728 0.26927252 4.68698221 0.163898416 0.023518824 20.18929738 -1.305121205 0.256972122 CS(ph)LEFLEDAVGCAPAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CSLEFLEDAVGCAPAQR 17 0 Q9BTV7 Q9BTV7 CABLES2 CDK5 and ABL1 enzyme substrate 2 1 CS(1)LEFLEDAVGCAPAQR 126.88 4.42E-05 29015000 14509 20232 8177.8 13433 18278 14971 19902 22708 19626 TRUE FALSE 12591.59889 20099.09466 12132.61143 16483.16796 17914.30356 15546.94406 17971.9071 17852.07091 17305.83664 0.727592612 1.161405547 0.701070494 0.952462935 1.035159636 0.898364198 1.038488198 1.031563587 1 14.07897107 3.483421171 24.87366169 1.001516146 0.882095415 0.18756201 0.128538614 465.212537 1836778.121 0.033698421 0.045132032 3043.835454 -3.483421171 -0.119420731 CS(ph)PTVAFVEFPSSPQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CSPTVAFVEFPSSPQLK 17 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 CS(0.996)PT(0.004)VAFVEFPSSPQLK 127.75 4.11E-05 87339000 114000 98449 60239 67192 101060 90830 124100 133240 98966 TRUE FALSE 98934.61116 97802.28204 89370.78189 82448.97057 99049.10372 94324.28887 112064.8011 104747.6629 87266.35222 1.133708567 1.120733015 1.024115018 0.944796803 1.135020557 1.080878099 1.284169651 1.200321318 1 16.41313787 2.440932228 24.97655795 1.175815029 1.069033219 0.17268144 0.089389682 251.7872081 173774.2984 0.033995194 0.026332659 276.0147098 -2.440932228 -0.10678181 CSATPSAQVKPIVSAS(ph)PPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CSATPSAQVKPIVSASPPSR 20 1 Q96EV2;H0Y3K4 Q96EV2 RBM33 RNA-binding protein 33 1 CSATPSAQVKPIVS(0.007)AS(0.992)PPSR;CSATPSAQVKPIVSAS(1)PPSR 249.34 1.29E-30 1155300000 1777830 1341300 691370 1033760 1761110 1601720 1726070 2061470 1733250 TRUE FALSE 1542885.261 1332488.912 1025718.844 1268491.008 1726067.357 1663339.205 1558675.997 1620640.683 1528347.16 1.009512303 0.871849634 0.671129487 0.829975703 1.129368642 1.088325512 1.019844207 1.0603878 1 20.54354085 3.249186159 24.9964747 1.058141989 0.835027115 0.592954907 0.087892287 147.5940004 347211.3937 0.026254762 0.03353691 1774.950145 -3.249186159 -0.223114874 CSCSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CSCSFR 6 0 Q9H3K6;A0A087WZT3;H3BV85;Q9H3K6-2;H3BTW0;A0A0B4J295;H3BVE0 Q9H3K6 BOLA2;BOLA2B BolA-like protein 2 0 ; 113.25 0.061181 412320000 474510 473610 249940 318050 534390 618330 525860 550400 513970 FALSE TRUE 411802.3012 470498.8247 370811.82 390268.1136 523756.6845 642117.5552 474862.1781 432701.2432 453209.0521 0.908636532 1.038149663 0.818191557 0.861121621 1.155662452 1.416824206 1.047777347 0.954749781 1 18.78981715 3.238942332 24.99999983 1.105020312 0.90961708 0.3694813 0.134950861 13.61523976 891675.3361 0.044707439 0.054221325 1733.57379 -3.238942332 -0.195403232 CSDAAGYPHATHDLEGPPLDAYS(ph)IQGQHTISPLDLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAK 37 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 CSDAAGYPHATHDLEGPPLDAY(0.104)S(0.426)IQGQHT(0.296)IS(0.174)PLDLAK 90.699 0.00098532 421810000 160990 149030 41814 93899 165070 133600 169160 236880 175500 TRUE FALSE 139714.7636 148051.0121 62035.39026 115220.2031 161785.43 138739.6785 152754.8892 186225.0554 154752.5899 0.902826658 0.956694891 0.400868188 0.744544587 1.045445702 0.896525729 0.987091003 1.203372787 1 17.23960403 3.239796323 23.48377947 1.039145055 0.74088317 0.410499342 0.163304986 15.0858829 286684.5079 0.05057087 0.061665651 1736.98602 -3.239796323 -0.298261885 CSDAAGYPHATHDLEGPPLDAYSIQGQHT(ph)ISPLDLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAK 37 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 CSDAAGYPHATHDLEGPPLDAYSIQGQHT(0.8)IS(0.2)PLDLAK 249.04 3.30E-50 110860000 68595 68809 33085 50044 81048 57758 96470 109720 95478 TRUE FALSE 59529.99695 68356.98915 49085.01666 61407.25507 79435.30337 59979.98763 87114.35425 86257.23184 84190.69961 0.707085191 0.811930409 0.583021841 0.729382881 0.943516371 0.712430089 1.034726575 1.024545849 1 16.36137325 2.427695714 0.913408779 1.054891714 0.711377162 0.6083779 0.098124443 0.424453872 0.731124612 0.102179358 0.04716348 267.7291836 -2.427695714 -0.343514553 CSDAAGYPHATHDLEGPPLDAYSIQGQHTIS(ph)PLDLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAK 37 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 CSDAAGYPHATHDLEGPPLDAYSIQGQHT(0.007)IS(0.993)PLDLAK;CSDAAGYPHATHDLEGPPLDAYSIQGQHT(0.047)IS(0.953)PLDLAK;CSDAAGYPHATHDLEGPPLDAYSIQGQHT(0.109)IS(0.891)PLDLAK 270.28 1.43E-64 735535000 339587 331460 110006 219180 357717 354709 400774 494861 391115 TRUE FALSE 294709.7175 329282.6174 163205.2695 268948.169 350599.1316 368354.8848 361906.9992 389038.8262 344877.8303 0.854533669 0.954780472 0.473226329 0.779836062 1.016589357 1.068073539 1.049377395 1.12804823 1 18.39572587 3.208094861 4.189200332 1.06700262 0.755480139 0.571697333 0.12382866 0.149749336 5.797456005 0.038533515 0.046145722 1614.711214 -3.208094861 -0.311522481 CSDIVFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CSDIVFAR 8 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 90.37 0.030813 107290000 93558 92009 45795 71370 107810 114070 77236 88845 94487 FALSE TRUE 81194.07325 91404.58682 67941.61518 87575.64932 105664.7919 118458.3467 69745.66461 69846.18814 83316.8545 0.974521587 1.097071983 0.815460636 1.051115646 1.26822829 1.421781312 0.837113511 0.838320032 1 16.34632075 CSDVSELSS(ph)SPPGPYHQEPYVCKPEER ddPTM_MDA-MB-175_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(0.499)S(0.499)PPGPYHQEPYVCKPEER;CSDVSELS(0.008)S(0.599)S(0.385)PPGPY(0.008)HQEPYVCKPEER;CSDVS(0.001)ELS(0.101)S(0.487)S(0.41)PPGPY(0.001)HQEPYVCKPEER;CSDVSELS(0.41)S(0.502)S(0.088)PPGPYHQEPYVCKPEER 187.98 5.47E-18 6146930000 959760 852180 458803 596450 943250 824870 1028740 1199170 966540 TRUE FALSE 832925.2843 846581.9735 680681.6654 731883.0887 924481.1704 856603.2827 928972.9531 942736.8275 852276.7423 0.977294396 0.993318169 0.798662725 0.858738779 1.084719463 1.00507645 1.089989797 1.106139333 1 19.70096244 3.232976975 24.99853635 1.063159248 0.905430215 0.575290797 0.063999022 98.85979751 442604.7662 0.020225393 0.023572138 1709.924656 -3.232976975 -0.157729033 CSDVSELSSS(ph)PPGPYHQEPYVCKPEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 CSDVSELSSSPPGPYHQEPYVCKPEER 27 1 Q9Y478;F5H610;F5H2X8 Q9Y478 PRKAB1 5-AMP-activated protein kinase subunit beta-1 1 CSDVSELS(0.014)S(0.115)S(0.871)PPGPYHQEPYVCKPEER;CSDVSELS(0.003)S(0.195)S(0.802)PPGPYHQEPYVCKPEER;CSDVSELS(0.001)S(0.21)S(0.789)PPGPYHQEPYVCKPEER;CSDVSELS(0.021)S(0.244)S(0.735)PPGPYHQEPYVCKPEER;CSDVSELS(0.007)S(0.192)S(0.801)PPGPYHQEPYVCKPEER 187.29 5.96E-18 4678400000 1897585 1708971 1047951 1262199 1984428 1736131 2257745 2519632 2137245 TRUE FALSE 1646814.334 1697744.657 1554743.609 1548800.574 1944941.765 1802921.083 2038789.237 1980828.305 1884582.331 0.873835177 0.900859904 0.824980466 0.821826964 1.032028017 0.956668782 1.081825508 1.051070188 1 20.84581339 3.232194515 24.99878782 1.028593027 0.856453415 0.821028132 0.039164876 61.22484048 240420.8876 0.012329821 0.014318041 1706.846692 -3.232194515 -0.172139613 CSGPGLS(ph)PGMVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 CSGPGLSPGMVR 12 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 CSGPGLS(1)PGMVR;CSGPGLS(1)PGMVR;CSGPGLS(1)PGMVR;CSGPGLS(1)PGMVR;CSGPGLS(1)PGMVR;CSGPGLS(1)PGMVR;CSGPGLS(1)PGMVR;CSGPGLS(1)PGMVR;CSGPGLS(1)PGMVR 301.74 1.52E-36 9743760000 6376710 6570100 3114940 4086070 7728640 7934640 6689970 7394110 6266100 TRUE FALSE 5534011.617 6526940.58 4621335.403 5013874.645 7574855.185 8239890.735 6041177.739 5812937.118 5525328.796 1.001571458 1.181276413 0.836391023 0.907434622 1.370932928 1.491294191 1.093360769 1.052052707 1 22.39762889 3.258048754 24.9996719 1.189219499 0.985549128 0.294808061 0.168322629 381.5010107 489392.185 0.053826786 0.069386609 1811.543445 -3.258048754 -0.203670371 CSGQHWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CSGQHWER 8 0 Q9HCN8 Q9HCN8 SDF2L1 Stromal cell-derived factor 2-like protein 1 0 74.162 0.041692 166290000 202080 235590 120950 169470 264280 354040 217380 251430 180240 FALSE TRUE 175374.616 234042.3938 179441.8246 207950.7537 259021.3451 367660.1479 196298.5211 197663.6511 158932.2325 1.10345531 1.472592375 1.129046146 1.308424039 1.629759684 2.313313933 1.23510831 1.243697694 1 17.27805222 3.427382304 9.65328341 1.47663593 1.252129908 0.095575874 0.357323003 1.100728747 204.2474092 0.111084756 0.143565469 2675.360459 -3.427382304 -0.224506023 CSKQSPSGAHGT(ph)HFGDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CSKQSPSGAHGTHFGDDR 18 1 A0A0A0MRP9;Q96C92-3;Q96C92 A0A0A0MRP9 SDCCAG3 Serologically defined colon cancer antigen 3 1 CS(0.012)KQS(0.012)PS(0.012)GAHGT(0.964)HFGDDR;CS(0.006)KQS(0.006)PS(0.006)GAHGT(0.982)HFGDDR;CS(0.018)KQS(0.016)PS(0.016)GAHGT(0.951)HFGDDR 66.809 0.045727 1627160000 453020 498071 357115 329748 400217 640630 275371 331983 515822 TRUE FALSE 393152.2592 494799.1388 529817.0085 404622.3233 392253.4647 665275.4506 248665.5628 260991.0189 454842.1108 0.864370844 1.087848128 1.164837195 0.889588527 0.862394786 1.462651401 0.546707433 0.573805751 1 18.7950063 2.202119452 24.99999268 0.67245048 1.045443563 0.365971635 0.214354846 167.1304282 114656.5545 0.0848879 0.057233326 159.264672 -2.202119452 0.372993083 CSLHSAS(ph)PASVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CSLHSASPASVR 12 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 CSLHSAS(1)PASVR;CSLHSAS(1)PASVR;CSLHS(0.004)AS(0.996)PASVR 193.45 1.80E-06 863950000 1496870 1400990 578186 986770 1677830 1653220 1337370 1736630 1441520 TRUE FALSE 1299054.837 1391786.804 857798.6835 1210831.21 1644444.466 1716820.443 1207672.063 1365265.189 1271105.148 1.021988495 1.094942308 0.674844788 0.95258147 1.29371238 1.35065179 0.950096115 1.074077303 1 20.27765195 3.439343082 20.87508186 1.123314604 0.924808035 0.273988364 0.159591278 41.37155059 22859.72985 0.048370181 0.062446498 2750.065782 -3.439343082 -0.198506569 LEDFRDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEDFRDYR 8 1 O43707;O43707-2;K7EJH8;F6THM6;P12814-3;P12814;P12814-2;P12814-4;H9KV75;P35609-2;P35609;A0A494C1A0;Q08043;A0A087WSZ2 O43707;P12814-3 ACTN4;ACTN2;ACTN1;ACTN3 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2;Alpha-actinin-3 0 ;;; 105.78 0.003941 4400210000 8729900 8437400 4898580 5782820 7450580 8229670 6919140 8634660 2620950 FALSE TRUE 7576221.596 8381974.164 7267549.673 7095897.666 7302328.035 8546270.73 6248122.868 6788205.154 2311104.277 3.2781825 3.626826469 3.144622138 3.070349416 3.159670513 3.69791654 2.703522697 2.937212839 1 21.14015092 1.15178592 1.989754715 9.12E-23 3.264481135 0.859166932 0.282066024 0.352390161 1.116624833 2.317569901 0.074114229 14.18358187 -1.15178592 3.264481135 CSS(ph)PTVGPPPLPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CSSPTVGPPPLPQK 14 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 CS(0.003)S(0.993)PT(0.003)VGPPPLPQK;CS(0.001)S(0.999)PTVGPPPLPQK;CS(0.002)S(0.995)PT(0.003)VGPPPLPQK 209.19 7.33E-09 642371000 2013440 1793270 865733 1284590 2275800 1720750 2225070 2576090 2034620 TRUE FALSE 1747358.803 1781489.891 1284404.375 1576275.793 2230516.033 1786948.366 2009283.054 2025213.201 1794089.541 0.973952951 0.992977134 0.715908735 0.878593714 1.243257921 0.99601961 1.119945804 1.128825041 1 20.77482047 3.265729818 24.82370016 1.0981073 0.88522723 0.512397501 0.100405414 160.9439344 147048.5706 0.028511603 0.036798476 1843.867961 -3.265729818 -0.212880071 CSSVAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CSSVAAK 7 0 F5H3V4;F5GZH5;Q9ULI2-2;Q9ULI2 F5H3V4 RIMKLB Beta-citrylglutamate synthase B 0 77.748 0.086555 372550000 249070 274110 156880 179240 180470 209190 432820 336730 299670 FALSE TRUE 216154.7684 272309.3534 232747.6927 219939.1815 176879.0001 217237.6747 390845.183 264722.9099 264243.354 0.818014021 1.03052489 0.880808123 0.832335717 0.669379182 0.822112161 1.479110741 1.001814827 1 18.01150766 CSVCSEPIMPEPGRDETVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CSVCSEPIMPEPGRDETVR 19 1 Q15942;Q15942-2;H0Y2Y8 Q15942 ZYX Zyxin 0 ;; 204.23 4.27E-16 1074610000 537600 534070 271185 361736 599940 650330 553030 675520 548040 FALSE TRUE 466554.7979 530561.659 402330.9731 443873.6876 588002.3678 675348.6159 499397.2357 531065.3049 483251.3355 0.965449578 1.097900037 0.832550152 0.91851518 1.216763048 1.397510087 1.033410979 1.098942239 1 18.88241419 3.244661193 24.99298321 1.146743065 0.955263906 0.375821546 0.125302964 174.0795178 713168.6643 0.038616502 0.048568153 1756.552735 -3.244661193 -0.191479159 CSWQDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CSWQDLK 7 0 Q08170;A0A0D9SEM4;Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q08170;Q13247 SRSF4;SRSF6 Serine/arginine-rich splicing factor 4;Serine/arginine-rich splicing factor 6 0 79.906 0.072942 304330000 349560 286970 278260 217940 284030 223100 332910 371960 322400 FALSE TRUE 303364.7603 285084.8752 412827.4667 267426.608 278378.3587 231682.8014 300624.4394 292419.2486 284286.2393 1.067110252 1.002809267 1.452154236 0.940694874 0.979218549 0.814963123 1.05747095 1.028608523 1 18.11698474 CT(ph)CPDQFPMIK ddPTM_MDA-MB-175_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 83.204 0.062116 448250000 187520 198510 183040 218090 138130 219690 135410 156520 299320 TRUE FALSE 162738.7569 197205.9747 271558.7562 267610.6678 135381.4832 228141.6165 122277.959 123049.416 263934.7306 0.616587126 0.747177055 1.028886027 1.013927448 0.512935463 0.864386494 0.463288627 0.466211536 1 18.00982168 3.232663829 24.99996176 0.632265738 0.856842577 0.165609722 0.206424444 226.5057055 960289.6726 0.063140045 0.073482785 1708.692167 -3.232663829 0.224576839 CTEYLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CTEYLDR 7 0 O75351;K7EKZ3;K7EL71 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 0 99.139 0.025003 178770000 236980 218040 123720 158320 224620 270790 211200 211170 214110 FALSE TRUE 205662.4926 216607.6809 183551.4058 194268.9758 220150.5015 281207.4665 190717.8565 166012.9388 188798.1597 1.089324668 1.147297628 0.972209719 1.028977062 1.166062751 1.489460845 1.010167985 0.879314391 1 17.52648518 2.010260539 24.99927847 0.93514803 1.145590574 0.294668147 0.138571059 251.235417 612119.7621 0.059690655 0.040195247 102.3907063 -2.010260539 0.210442544 CTHWAEGGK ddPTM_MDA-MB-175_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 ;;;; 111.65 0.0020901 2631890000 4270790 4016490 2265030 2936470 4173960 3895680 4670680 5286270 4633340 FALSE TRUE 3706394.281 3990105.413 3360406.084 3603240.395 4090906.362 4045549.33 4217718.172 4155842.298 4085591.824 0.907186631 0.9766285 0.822501667 0.881938419 1.0013008 0.990199096 1.032339586 1.017194688 1 21.96211365 3.209925607 7.523943535 1.010586584 0.897386137 0.672783829 0.038502589 0.113499568 22.75217582 0.011885851 0.013750314 1621.532311 -3.209925607 -0.113200447 CTKEEHLCTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 CTKEEHLCTQR 11 1 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;; 171.32 8.82E-06 4207740000 5655450 5651540 1796220 2281570 5597750 5009580 6298320 7065240 665510 FALSE TRUE 4908067.953 5614414.662 2664878 2799635.34 5486365.727 5202301.784 5687509.896 5554393.408 586834.166 8.363637017 9.567293432 4.541109149 4.770743598 9.349090501 8.865028804 9.691852019 9.465013679 1 19.16259334 CTLAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CTLAEK 6 0 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 122.78 0.044374 537840000 560540 468630 261510 325370 385350 449840 533410 621160 516260 FALSE TRUE 486463.2188 465551.5387 387977.1107 399250.2315 377682.2889 467145.6359 481679.9803 488329.7679 455228.3309 1.068613673 1.022676989 0.852269256 0.877032918 0.829654622 1.026178742 1.058106334 1.072713921 1 18.79623082 2.531776101 11.54696906 1.049124035 0.927878824 0.348300689 0.074381545 1.226995696 257.7402913 0.027547801 0.024259629 340.2327389 -2.531776101 -0.121245212 CTLPEHES(ph)PSQDISDACEAESTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CTLPEHESPSQDISDACEAESTER 24 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 CTLPEHES(1)PSQDISDACEAESTER;CTLPEHES(0.998)PS(0.002)QDISDACEAESTER;CTLPEHES(0.999)PS(0.001)QDISDACEAESTER 402.71 1.18E-157 860940000 314909 363890 172305 217274 337111 370560 322040 369090 302804 TRUE FALSE 273292.9778 361499.5826 255632.2743 266609.3825 330403.1506 384815.683 290808.6104 290162.9758 267006.8561 1.023542922 1.353896255 0.957399664 0.998511373 1.237433209 1.441220232 1.089142858 1.086724813 1 18.02651726 1.646974279 2.581294928 1.019704416 1.16635379 0.099954381 0.154065342 0.612221093 9.004012773 0.155039169 0.043205264 44.35823717 -1.646974279 0.146649374 CTVFHGAQVEDAFR ddPTM_MDA-MB-175_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 ;;;;;;; 233.19 3.51E-17 96131270000 35762290 36506520 20524540 25648770 43995060 51612940 39857110 43435370 46015940 FALSE TRUE 31036212.77 36266706.27 30450276.19 31472715.25 43119644.38 53598523.2 35991773.61 34147054.14 40575987.99 0.764891117 0.893797245 0.750450641 0.775648772 1.062688711 1.320941913 0.887021497 0.841558168 1 25.27412289 3.244358632 24.99239853 1.004600028 0.799900766 0.416654297 0.132056694 174.4238358 751850.9079 0.043130057 0.054166169 1755.329421 -3.244358632 -0.204699262 CVFSYNS(ph)NCQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CVFSYNSNCQEK 12 0 Q6NT55 Q6NT55 CYP4F22 Cytochrome P450 4F22 1 CVFS(0.067)Y(0.058)NS(0.875)NCQEK 63.537 0.045076 1045100000 638950 499240 404650 575210 726150 391570 666380 646540 650290 TRUE FALSE 554511.1386 495960.4596 600340.0935 705820.222 711701.0357 406633.9513 601754.5702 508282.4524 573413.457 0.967035447 0.864926439 1.046958501 1.230909762 1.241165562 0.70914616 1.049425267 0.886415284 1 19.12921624 0.901437431 20.15729943 1.370228574 0.996212718 0 0.160914537 35610.4281 4872203.911 202529.0287 0.039044283 7.969616635 -0.901437431 -0.374015855 CVGAELEYDS(ph)EHSDWHGFD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CVGAELEYDSEHSDWHGFD 19 0 Q9GZN8-2;Q9GZN8;H7BYU9 Q9GZN8-2 C20orf27 UPF0687 protein C20orf27 1 CVGAELEYDS(1)EHSDWHGFD;CVGAELEYDS(1)EHSDWHGFD;CVGAELEYDS(0.972)EHS(0.028)DWHGFD 263.92 1.73E-31 227278000 321634 343690 158447 221391 326546 361841 307430 365250 323179 TRUE FALSE 279129.252 341432.2778 235072.4992 271661.2103 320048.3735 375761.2574 277615.4859 287144.1299 284973.1468 0.979493174 1.198120881 0.82489351 0.95328705 1.123082568 1.318584792 0.974181213 1.007618202 1 18.12046645 CVGAELEYDSEHSDWHGFD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CVGAELEYDSEHSDWHGFD 19 0 Q9GZN8-2;Q9GZN8;H7BYU9 Q9GZN8-2 C20orf27 UPF0687 protein C20orf27 0 216.99 3.70E-19 81456000 127960 138730 45839 79902 137930 124010 117780 145620 123370 FALSE TRUE 111049.7618 137818.6735 68006.89372 98044.97033 135185.4629 128780.7449 106357.7137 114480.2962 108785.3391 1.020815513 1.266886463 0.6251476 0.901270071 1.242680897 1.183806071 0.977684259 1.05235041 1 16.73112461 3.28069049 24.99993603 1.082539364 0.952456603 0.13494525 0.172533236 336.0501568 199410.4845 0.051242438 0.066153106 1908.492642 -3.28069049 -0.130082761 CVMDDDNEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CVMDDDNEVR 10 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 138.08 0.0001726 114830000 79930 76787 51054 61486 75028 90518 73440 86551 103880 FALSE TRUE 69367.04798 76282.58114 75743.88517 75447.33605 73535.08959 94000.28603 66317.8001 68042.74219 91599.42474 0.757286939 0.8327845 0.826903503 0.823666047 0.802789862 1.026210441 0.723997998 0.742829361 1 16.48305092 4.744749728 4.382351923 0.8366173 0.751197118 0.068619827 0.097483113 0.726396192 33.73510667 0.023771046 0.194297785 55558.39967 -4.744749728 -0.085420182 CVPASGELS(ph)PELQEWAPYSPGHSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CVPASGELSPELQEWAPYSPGHSSR 25 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1 Q8TDM6-4 DLG5 Disks large homolog 5 1 CVPAS(0.002)GELS(0.998)PELQEWAPYSPGHSSR;CVPASGELS(1)PELQEWAPYSPGHSSR 268.88 4.49E-46 181335000 70488 96914 23450.1 67136 184387 171568 131632 141491 138749 TRUE FALSE 61172.83221 96277.36555 34790.6468 82380.25491 180718.0594 178168.332 118866.3489 111234.2507 122346.2513 0.499997602 0.786925341 0.284362181 0.673336976 1.477103365 1.456263107 0.971556935 0.909175799 1 16.90061037 3.401735551 7.314891768 1.129778815 0.538455971 0.646170195 0.22262605 0.162104969 13.22477607 0.070489239 0.091199438 2521.944653 -3.401735551 -0.591322844 CVSSPHFQVAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CVSSPHFQVAER 12 0 Q16537-2;Q16537;Q16537-3;H0YN84;E9PFR3;Q14738;H0Y8C4;Q14738-2;Q14738-3;H7C5Q9;H0YJ75;Q13362-3;Q13362;Q13362-4;Q13362-5;Q96B13;Q13362-2;Q15173-2;Q15173 Q16537-2;E9PFR3;H0YJ75;Q15173-2 PPP2R5E;PPP2R5C;PPP2R5D;PPP2R5B Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform;Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform;Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform;Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform 0 129.77 0.0002283 577710000 254160 236610 118080 153760 294800 278950 247490 261410 255890 FALSE TRUE 220572.112 235055.6933 175183.883 188673.5581 288934.0568 289681.387 223488.4579 205509.5058 225638.9757 0.977544377 1.04173356 0.776390171 0.836174502 1.280514839 1.283826901 0.990469209 0.910789039 1 17.78365677 3.2799938 24.9999299 1.072166063 0.908117946 0.301601402 0.137975802 241.7939355 145891.8442 0.045415386 0.058630416 1905.433517 -3.2799938 -0.164048117 CYEMASHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 CYEMASHLR 9 0 P07737;K7EJ44;CON__P02584 P07737 PFN1 Profilin-1 0 ;;;;;;;;;; 242.08 1.98E-10 31240940000 14578870 14280520 6209640 8851990 15572670 16112470 12941580 15047620 15676120 FALSE TRUE 12652235.39 14186710.32 9212642.674 10861969.62 15262804.33 16732327.15 11686507.56 11829803.56 13822906.95 0.915309308 1.026318876 0.666476502 0.785794888 1.10416748 1.210478173 0.845445 0.85581156 1 23.72055771 3.254662021 24.99998693 0.983294086 0.848178153 0.22647334 0.139405153 472.6226327 733817.5759 0.044358389 0.057084774 1797.471531 -3.254662021 -0.135115933 CYPDRVDYVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CYPDRVDYVDK 11 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 141.38 3.48E-05 795900000 1412860 1106540 706650 860630 1246100 1028030 1428170 1536400 1149230 FALSE TRUE 1226146.971 1099271.066 1048388.304 1056049.195 1221305.048 1067578.979 1289666.293 1207852.816 1013369.339 1.209970466 1.084768429 1.034556961 1.042116783 1.205192422 1.053494455 1.272651781 1.191917665 1 19.95072865 3.240413467 24.99961152 1.155601761 1.08811167 0.068270775 0.089418485 112.3193308 1515464.694 0.026229699 0.032136902 1739.456079 -3.240413467 -0.06749009 CYQSEFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CYQSEFGR 8 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;; 176.09 0.00061035 784210000 1080880 889650 434080 870890 1018610 1082780 773150 1247650 1574730 FALSE TRUE 938038.9694 883805.8306 644002.5399 1068638.885 998341.6539 1124435.247 698170.032 980849.7567 1388567.213 0.675544518 0.636487613 0.463789245 0.769598241 0.718972509 0.809780928 0.502798874 0.706375426 1 20.40516558 1.256682073 4.473490565 1.023486537 0.655128815 0.506193974 0.106463906 0.156509815 6.347309706 0.176331288 0.026614409 18.05851663 -1.256682073 -0.368357722 CYYFDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CYYFDYK 7 0 K7EJR3;R4GMR5;P48556;K7EJC1;K7ERW6 K7EJR3 PSMD8 26S proteasome non-ATPase regulatory subunit 8 0 ; 105.39 0.018466 164610000 566930 462700 319450 375400 487540 440880 626200 615210 768330 FALSE TRUE 492008.7641 459660.4932 473937.0885 460640.3076 477838.9079 457840.9389 565471.2204 483652.1291 677498.9027 0.726213374 0.678466772 0.699539271 0.679912994 0.705298423 0.675781078 0.83464522 0.713878838 1 19.36985908 -0.310620377 1.14263703 10 0.70203765 0.777276164 0.047577841 22.54472587 1.130521424 505.4252275 0.01375509 0.489079684 0.310620377 -9.29796235 CYYSNTDAVIYVVDSCDRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CYYSNTDAVIYVVDSCDRDR 20 1 B4DZG7;F8VYN9;P40616-2;P40616 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ; 231.77 7.00E-26 456980000 260230 231410 114109 134807 261970 225590 249550 283390 165924 FALSE TRUE 225839.9462 229889.8525 169292.4941 165416.9897 256757.3095 234268.5933 225348.6794 222789.2538 146308.6537 1.543585703 1.571266269 1.157091462 1.13060291 1.75490173 1.601194374 1.540227961 1.522734631 1 17.15865558 3.246829502 24.99985488 1.498777459 1.352571292 0.071249213 0.235456153 521.5675314 1576879.341 0.070234514 0.089093074 1765.344636 -3.246829502 -0.146206167 CYYYHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 CYYYHAR 7 0 O43242;O43242-2;H0YGV8 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 132.8 0.0033333 653970000 426620 527430 244750 284570 577670 548170 524250 479150 468350 FALSE TRUE 370241.0861 523965.2776 363111.9186 349185.9679 566175.4972 569258.4546 473408.3157 376687.5012 412982.1965 0.896506167 1.268735752 0.879243516 0.845523054 1.370944079 1.378409189 1.146316523 0.912115593 1 18.65572006 4.806647109 20.64445317 1.089929525 0.896486988 0.09551851 0.194698941 36531.05567 11072041.41 0.050717766 131.4336394 64068.87653 -4.806647109 -0.193442537 DAAAVGNHVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DAAAVGNHVAK 11 0 Q13564-2;Q13564;Q13564-4;Q13564-3 Q13564-2 NAE1 NEDD8-activating enzyme E1 regulatory subunit 0 115.18 0.0011584 145650000 351600 282700 198690 263210 326440 316580 425470 428570 386890 FALSE TRUE 305135.1692 280842.9251 294777.1486 322975.8534 319944.4827 328759.0375 384207.9849 336923.6406 341152.3049 0.894425055 0.823218607 0.864063189 0.94672042 0.937834738 0.963672333 1.126206622 0.987604761 1 18.38005644 3.171622548 1.076931204 1.029223542 0.854324506 0.677845774 0.047052818 0.282608452 0.728116688 0.022184547 0.029454247 1484.644755 -3.171622548 -0.174899036 DAADKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DAADKPR 7 1 Q13185 Q13185 CBX3 Chromobox protein homolog 3 0 ; 110.63 0.0061649 516260000 1990260 1471870 945810 1307960 854950 1130940 1739810 2029800 2109800 FALSE TRUE 1727242.098 1462201.189 1403206.88 1604952.309 837938.1677 1174447.994 1571083.494 1595743.066 1860381.847 0.928434182 0.785968317 0.754257456 0.862700478 0.450411924 0.631294051 0.844495175 0.857750288 1 20.82716734 -0.590705089 10.93338005 5.558266276 0.784488046 0 0.155721483 0 0 0 0.03631805 0.256622606 0.590705089 -4.77377823 DAAEAIKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DAAEAIKK 8 1 O75874;C9J4N6;C9JLU6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 104.17 0.0074277 553710000 1020900 697910 558940 641130 526850 486720 980840 1097400 751950 FALSE TRUE 885985.4784 693325.3833 829245.2535 786708.3656 516366.7158 505444.4333 885718.2878 862729.55 663055.3276 1.336216514 1.045652383 1.250642622 1.186489774 0.77876867 0.762296014 1.335813545 1.301142626 1 19.33876973 6.93033273 1.51749324 1.09682521 199.6184809 0.127534296 0.19964972 3386.225604 11.67512634 0.060460363 2336268.325 8517903.781 -6.93033273 198.5216557 DADADAGGGADGGDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DADADAGGGADGGDGR 16 0 Q14657 Q14657 LAGE3 EKC/KEOPS complex subunit LAGE3 0 133.07 8.30E-05 99994000 223270 182340 132210 148360 175280 191190 217130 265270 186330 FALSE TRUE 193764.3038 181142.1965 196147.1982 182047.4055 171792.2709 198545.203 196072.766 208544.0748 164302.2797 1.179315979 1.102493507 1.193819091 1.108002919 1.045586655 1.208414171 1.193366071 1.269270732 1 17.32599297 DADAGDEDEESEEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DADAGDEDEESEEPR 15 0 Q9NZT2-2;Q9NZT2;A0A087X028 Q9NZT2-2 OGFR Opioid growth factor receptor 0 ; 391.38 3.61E-114 1507560000 770600 695710 489610 536790 646690 582190 703680 814570 743030 FALSE TRUE 668763.2575 691139.8352 726387.0336 658676.3738 633822.1342 604587.226 635437.2219 640380.5445 655189.8399 1.020716771 1.054869586 1.108666511 1.00532141 0.967387001 0.922766486 0.969852069 0.97739694 1 19.32155346 3.494702498 4.574767873 0.967601132 1.06103304 0.697209918 0.028204042 0.111420407 5.903180435 0.008340332 0.011855144 3123.938662 -3.494702498 0.093431908 DADDAVYELDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DADDAVYELDGK 12 0 Q13243;Q13243-3;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ;;; 255.19 9.15E-21 500210000 2133760 1528980 1366470 1565940 1435680 1129430 1754110 2063490 2466510 FALSE TRUE 1851778.21 1518936.03 2027299.463 1921510.611 1407112.777 1172879.903 1583996.682 1622228.722 2174921.998 0.851422815 0.698386439 0.932125136 0.883484839 0.646971606 0.539274468 0.728300456 0.745879035 1 21.05253223 4.781032222 20.97925089 0.765070963 0.851425007 0.030390155 0.136715171 12923.05743 6382338.885 0.034564449 8.45578459 60399.34404 -4.781032222 0.086354044 DADDAVYELNGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DADDAVYELNGK 12 0 Q08170;A0A0D9SEM4;Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q08170;Q13247 SRSF4;SRSF6 Serine/arginine-rich splicing factor 4;Serine/arginine-rich splicing factor 6 0 ;;; 280.49 1.16E-27 849800000 2452500 1844690 1744620 2140660 1802360 1446640 2148080 2634160 4276650 FALSE TRUE 2128395.911 1832572.11 2588324.067 2626729.571 1766496.562 1502293.177 1939759.532 2070865.383 3771069.309 0.564401165 0.485955563 0.68636343 0.696547678 0.468433863 0.398373261 0.514379178 0.549145405 1 21.84654224 1.238718914 8.474798571 1.004320051 0.54413462 0.709733103 0.091358344 0.052171458 40.89844463 0.138240625 0.024177493 17.32682202 -1.238718914 -0.460185431 DADLWSSHDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DADLWSSHDK 10 0 P34896-2;P34896;P34896-3;J3KRZ5;J3KRK5 P34896-2 SHMT1 "Serine hydroxymethyltransferase, cytosolic" 0 ; 155.15 1.32E-05 1240580000 1852820 1643500 978510 1438490 1870450 1713670 1946360 2190300 2108420 FALSE TRUE 1607965.143 1632703.74 1451720.709 1765121.14 1833231.704 1779595.994 1757602.307 1721921.39 1859164.99 0.864885662 0.878191957 0.78084555 0.949416082 0.986051112 0.957201757 0.945371883 0.926179978 1 20.82622338 3.646602104 7.777952346 0.957519313 0.845246395 0.751516284 0.032320686 0.14333395 10.77860049 0.008811206 0.013097215 4432.024005 -3.646602104 -0.112272918 DADPILISLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DADPILISLR 10 0 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;;;; 199.46 6.47E-07 1100227000 1937770 1825100 1172613 1321749 1770570 1656130 1824270 2133020 1894100 FALSE TRUE 1681688.785 1813110.798 1739692.569 1621872.312 1735339.121 1719842.393 1647352.576 1676890.272 1670181.656 1.006889747 1.085577004 1.041618774 0.971075396 1.039012203 1.029733734 0.986331379 1.004016699 1 20.67157359 3.975140214 24.0144394 1.006211037 1.050574499 0.326151287 0.026741297 443.9698254 428874.818 0.006719096 0.011722613 9443.657207 -3.975140214 0.044363462 DAEDAIYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DAEDAIYGR 9 0 Q13242;H0YIB4;S4R3G0 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 ;;;; 187.78 9.34E-05 3983430000 4921020 4316900 3157690 3455550 4192500 4043080 4415500 4847090 4572830 FALSE TRUE 4270694.739 4288542 4684759.446 4240185.442 4109077.452 4198619.904 3987285.49 3810577.524 4032235.247 1.059138289 1.063564434 1.161826917 1.05157194 1.019056975 1.041263628 0.988852397 0.945028574 1 21.94314838 2.725281461 0.997303354 0.966617981 1.090254518 0.611276399 0.035680183 0.34713472 0.765463435 0.025591717 0.018922786 531.2286157 -2.725281461 0.123636537 DAEDALHNLDR ddPTM_MDA-MB-175_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 ;;; 167.44 1.92E-05 2613910000 3835880 3224710 2647280 3407140 3298180 2987800 3094990 3801140 6016800 FALSE TRUE 3328958.739 3203526.668 3927513.463 4180783.212 3232552.671 3102742.599 2794838.346 2988295.792 5305500.758 0.627454201 0.60381231 0.740271963 0.788009163 0.609283236 0.584816164 0.526781255 0.563244815 1 22.3390575 1.232463631 24.99995312 1.000000609 0.627882845 0.686333848 0.078493916 135.9047551 557205.3816 0.195045335 0.021778584 17.07904689 -1.232463631 -0.372117764 DAEDALHNLDRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 156.52 3.84E-05 1705690000 2969380 2368640 1666460 1838370 2179280 1871690 2714410 3132420 2197930 FALSE TRUE 2576968.91 2353080.248 2472365.63 2255800.006 2135916.592 1943695.125 2451166.936 2462576.36 1938093.219 1.329641363 1.214121294 1.275669099 1.163927506 1.102071134 1.002890421 1.264731186 1.270618118 1 20.88620653 3.696326094 4.996448357 1.148758115 1.267687675 0.316676476 0.094732036 0.305501313 18.72121177 0.028140368 0.043577157 4969.653319 -3.696326094 0.11892956 DAEDAMDAMDGAVLDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DAEDAMDAMDGAVLDGR 17 0 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ;;;;; 336.93 7.11E-72 1560435000 1567587 1242395 865893 991415 1199030 1121871 1350502 1504670 1390492 FALSE TRUE 1360426.406 1234233.625 1284641.751 1216530.929 1175171.649 1165030.103 1219530.524 1182908.03 1226109.62 1.109547127 1.00662584 1.04773809 0.992187737 0.958455614 0.950184294 0.99463417 0.964765312 1 20.22565654 7.999994406 0.576069387 0.972718245 8.031039865 0.741208134 0.023859389 79.03992911 0.676725816 0.011742963 696.1792028 99998712.04 -7.999994406 7.05832162 DAEDAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DAEDAVR 7 0 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 106.42 0.01793 121740000 741770 574470 520310 604270 494930 563380 600140 662070 1273000 FALSE TRUE 643743.2151 570696.2687 771933.6563 741478.7392 485081.8613 585053.5932 541938.5152 520491.4827 1122507.39 0.573486839 0.508412037 0.687686926 0.660555775 0.432141352 0.521202442 0.482792826 0.463686464 1 20.09829351 1.23291288 24.99990325 1.000000737 0.538112848 0.758264167 0.081386388 96.99325539 429298.3948 0.183530594 0.021371881 17.09672318 -1.23291288 -0.461887889 DAEDAVYGR ddPTM_MDA-MB-175_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 3136560000 4449140 3255990 2827630 3496700 3360060 3057980 3455980 3992460 6293530 FALSE TRUE 3861174.876 3234601.187 4195081.326 4290679.179 3293201.38 3175622.469 3120819.592 3138703.498 5549516.053 0.695767854 0.582861849 0.755936425 0.773162765 0.593421363 0.572234126 0.562358873 0.565581479 1 22.40393054 1.232024839 24.9371896 1.000000636 0.633546908 0.67560402 0.078858941 142.4362333 543410.6784 0.196720937 0.021095625 17.06179968 -1.232024839 -0.366453728 DAEDDGEEEDD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DAEDDGEEEDD 11 0 Q9BTT0;Q5TB19;Q9BTT0-3;Q9BTT0-2;Q5TB25;H0YCE2 Q9BTT0 ANP32E Acidic leucine-rich nuclear phosphoprotein 32 family member E 0 ;; 306.39 3.58E-36 649239700 1998749 1883365 1463690 1496717 1500241 1669615 1998741 2231491 2261503 FALSE TRUE 1734609.255 1870993.051 2171535.38 1836569.471 1470389.139 1733846.169 1804903.405 1754304.015 1994150.692 0.869848634 0.938240555 1.088952499 0.920978278 0.737351067 0.869465972 0.905098804 0.879724899 1 20.927343 4.767982758 20.98903934 0.912285756 0.869848096 0.024010072 0.090186031 6478.597149 4620995.457 0.023226258 1.595849517 58611.48949 -4.767982758 -0.04243766 DAEDVDLNHYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 188.06 3.32E-06 1068610000 1357310 1018460 813720 1064220 1058030 1028370 1019200 1250470 1680280 FALSE TRUE 1177938.045 1011769.669 1207237.714 1305867.417 1036977.273 1067932.059 920358.1409 983066.7217 1481639.213 0.795023535 0.682871822 0.814798706 0.881366668 0.699885144 0.7207774 0.621175609 0.663499395 1 20.49876276 DAEFYEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DAEFYEHR 8 0 O95340;O95340-2 O95340 PAPSS2 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 2;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 118.26 0.00192 182000000 153240 149780 99991 126090 136120 138950 151390 159210 170280 FALSE TRUE 132988.9457 148796.0853 148346.982 154720.6617 133411.4783 144295.4964 136708.2211 125164.1805 150149.6924 0.885709079 0.990984949 0.987993913 1.030442748 0.888523154 0.961010936 0.910479528 0.833595983 1 17.19604199 3.219361959 24.9762045 0.909577443 0.976026514 0.180880598 0.056297102 341.3493543 444072.0968 0.017085719 0.019403863 1657.150527 -3.219361959 0.066449071 DAEGILEDLQSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DAEGILEDLQSYR 13 0 E5RI16;Q9NUQ9;E5RGI7;E5RJE1;E5RIR8;E5RJL8;E5RK61;E5RFS4;E5RHU5 E5RI16 FAM49B Protein FAM49B 0 ;;;; 257.13 1.60E-23 305891000 570572 486459 346693 374462 477985 477603 495539 590472 566941 FALSE TRUE 495169.4646 483263.4188 514354.8944 459489.3204 468474.0337 495976.6965 447481.7041 464204.1579 499917.8808 0.990501607 0.966685604 1.02887877 0.919129597 0.937101975 0.992116336 0.89511042 0.928560821 1 18.9313316 3.729054148 24.99825641 0.942055977 0.992488356 0.312863169 0.034630924 764.4284844 2010146.965 0.009364209 0.014095886 5358.634655 -3.729054148 0.050432379 DAEGLQELALAPCHEWLSDEDLVPVLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DAEGLQELALAPCHEWLSDEDLVPVLAR 28 0 X6RJB2;X6RGT4;X6RHD7;A0A0C4DFV0;Q9H469 X6RJB2 FBXL15 F-box/LRR-repeat protein 15 0 135.3 1.11E-05 25195000 20082 19802 11870 12932 20473 19536 24106 24420 22270 FALSE TRUE 17428.11282 19671.91936 17610.3717 15868.40825 20065.62735 20287.56256 21768.20383 19197.97304 19637.26597 0.887502 1.001764675 0.896783276 0.80807625 1.021813698 1.033115434 1.108514997 0.977629629 1 14.26130646 3.124679827 10.07792208 1.02881195 0.905893288 0.561834527 0.056773065 0.251256458 21.16044787 0.017639471 0.020014156 1332.538689 -3.124679827 -0.122918662 DAELAWIDGVLDMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DAELAWIDGVLDMR 14 0 Q9P2I0;H0YJF4 Q9P2I0 CPSF2 Cleavage and polyadenylation specificity factor subunit 2 0 ; 140.39 2.32E-05 36328000 98620 84421 65236 75870 95100 99420 112738 117995 99609 FALSE TRUE 85587.11713 83866.43289 96784.3478 93097.4431 93207.69606 103244.7517 101804.6861 92762.68749 87833.33749 0.974426335 0.954836003 1.101909031 1.059932888 1.06118814 1.175462013 1.15906658 1.056121629 1 16.422481 4.239181507 24.99982077 1.089876001 0.964631129 0.501370876 0.050974535 13.30289818 535521.8226 0.01370365 0.032122708 17345.28767 -4.239181507 -0.125244873 DAELLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DAELLR 6 0 A0A087WYM3 A0A087WYM3 SIRT2 0 112.66 0.062352 119050000 316370 258200 129790 294770 293070 324740 200240 365030 445110 FALSE TRUE 274560.9029 256503.8672 192556.8781 361702.0338 287238.4804 337232.9579 180820.7556 286971.1752 392489.6029 0.699536754 0.653530349 0.490603768 0.921558256 0.73183717 0.85921501 0.460702027 0.73115612 1 18.58229491 3.747227868 24.97859632 0.759308388 0.618454314 0.204481469 0.152425668 1236.133954 3562469.651 0.040895933 0.069420747 5587.63293 -3.747227868 -0.140854074 DAELQDQEFGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DAELQDQEFGKR 12 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ; 121.04 0.00061462 424170000 560360 404590 270530 319870 372750 305340 413170 541590 395410 FALSE TRUE 486307.0062 401932.2217 401359.2129 392501.3724 365333.0043 317086.6274 373100.837 425775.1932 348665.0803 1.394768314 1.152774523 1.151131087 1.125726075 1.047804971 0.909430411 1.070083751 1.221158118 1 18.41148236 DAELQDQEFGKRDS(ph)LGTYSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DAELQDQEFGKRDSLGTYSSR 21 2 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DAELQDQEFGKRDS(1)LGTYSSR;DAELQDQEFGKRDS(1)LGTYSSR;DAELQDQEFGKRDS(0.998)LGT(0.002)YSSR;DAELQDQEFGKRDS(1)LGTYSSR 224.91 1.56E-25 3132170000 2205320 2078660 1148150 1217630 2018570 1838900 2747670 3026880 593068 TRUE FALSE 1913881.374 2065005.146 1703399.18 1494111.502 1978404.406 1909643.673 2481201.386 2379605.267 522956.1767 3.659735672 3.948715471 3.257250333 2.857049153 3.783117008 3.651632313 4.744568469 4.550295748 1 18.99633053 4.278449411 24.98073893 3.582717729 3.804225169 0.002928435 1.03686084 1434.957455 898634.0487 0.259868845 0.687528544 18986.69661 -4.278449411 0.22150744 DAEPPS(ph)PTPAGPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DAEPPSPTPAGPPR 14 0 O43306-2;O43306 O43306-2 ADCY6 Adenylate cyclase type 6 1 DAEPPS(1)PTPAGPPR;DAEPPS(0.998)PT(0.002)PAGPPR 190.87 5.80E-07 772210000 425450 460600 302950 526130 610750 656100 376910 748200 621250 TRUE FALSE 369225.7045 457574.2883 449457.6333 645595.8579 598597.2699 681340.5916 340357.3262 588203.2525 547806.5327 0.674007487 0.835284468 0.820467823 1.178510696 1.09271656 1.243761348 0.62130936 1.073742676 1 19.06330695 3.906033591 6.187335901 1.024036314 0.771579717 0.345364151 0.16860566 0.279416673 15.10878097 0.044919358 0.079266022 8054.407361 -3.906033591 -0.252456598 DAEQSGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DAEQSGSPR 9 0 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5 P08651-3 NFIC Nuclear factor 1 C-type 1 DAEQSGS(1)PR;DAEQSGS(1)PR 132.17 0.00032784 184070000 347280 319040 210890 280670 225970 286540 314240 348110 400030 TRUE FALSE 301386.0681 316944.2052 312877.1094 344400.4133 221473.6391 297563.3792 283765.0532 273669.3855 352738.9091 0.854416851 0.898523517 0.886993471 0.976360714 0.62786847 0.843579689 0.804462014 0.77584122 1 18.4282412 DAESIHQYLLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DAESIHQYLLQR 12 0 E9PLK3;P55786;P55786-2;H0YDG0 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ;;; 253.79 4.30E-21 3194040000 3900830 3789250 1700730 2762840 4129250 4349280 3928760 4266620 4168330 FALSE TRUE 3385325.432 3764358.167 2523208.717 3390185.049 4047086.004 4516599.616 3547749.46 3354236.516 3675554.776 0.921037949 1.024160541 0.686483775 0.922360094 1.101081673 1.228821196 0.965228292 0.912579657 1 21.80953059 3.42378897 7.782055485 1.028053042 0.877592693 0.298633258 0.117200265 0.345232235 43.54130541 0.036515315 0.04729304 2653.315966 -3.42378897 -0.150460349 DAEVERDEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DAEVERDEER 10 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;A1L2Z2 Q7Z406 MYH14 Myosin-14 0 ; 186.87 1.18E-06 746160000 876580 807170 535350 617840 704340 738540 820740 850420 649300 FALSE TRUE 760737.732 801867.6471 794247.0506 758130.0151 690325.012 766952.1117 741144.7611 668564.301 572540.4937 1.328705551 1.400543116 1.387232972 1.324150909 1.205722599 1.339559595 1.294484441 1.167715312 1 19.12701821 0.332935679 0.703053372 7.73E-17 1.347228543 0.823615053 0.050487026 4.046724345 0.597497161 5.82715131 0.023421239 2.152462924 -0.332935679 1.347228543 DAEVIVDWRPLDDALDSSSILYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DAEVIVDWRPLDDALDSSSILYAR 24 1 Q8TC07-2;Q8TC07-3;Q8TC07;F8WCB5;F8WDJ1;F8WF35 Q8TC07-2 TBC1D15 TBC1 domain family member 15 0 ; 199.46 1.50E-24 172861000 51748 45986 28251.5 29744 43483 40954 43388 50914 46360 FALSE TRUE 44909.37069 45683.91494 41914.0199 36497.82981 42617.77337 42529.52688 39180.23844 40026.43731 40879.37361 1.098582652 1.11752972 1.025309739 0.892817736 1.042525108 1.040366403 0.958435391 0.979135289 1 15.31908547 4.115846272 4.456613618 0.985999842 1.107258524 0.579340752 0.042476507 0.14248568 4.827340728 0.010974438 0.024488167 13057.08621 -4.115846272 0.121258682 DAFADAVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DAFADAVQR 9 0 A0A087WTP3;Q92945;M0R0I5 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 94.309 0.020493 371460000 818090 726230 512770 626860 810880 757100 765310 828920 861550 FALSE TRUE 709977.3337 721459.3473 760747.2871 769198.144 794745.0745 786226.1269 691090.354 651661.9087 759698.5405 0.934551399 0.949665307 1.001380477 1.012504438 1.046132159 1.03491857 0.909690248 0.857790129 1 19.53506752 2.222309999 24.73680707 0.908480081 0.997597242 0.328336204 0.048538804 212.8908431 324061.1062 0.020711326 0.014012204 166.8437715 -2.222309999 0.089117161 DAFDRNPELQNLLLDDFFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DAFDRNPELQNLLLDDFFK 19 1 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;; 234.47 3.55E-24 1052221000 1847208 1403664 1235816 1441109 1401668 1109092 1890417 2073376 2255710 FALSE TRUE 1603094.783 1394443.239 1833460.751 1768334.824 1373777.549 1151759.487 1707084.65 1630000.677 1989042.534 0.805963048 0.701062554 0.921780565 0.889038215 0.690672787 0.579052216 0.858244417 0.819490106 1 20.9236427 1.100075255 1.692957081 1.149249818 0.774021078 0.31896305 0.101688288 1.917596965 3.77121672 1.329833922 0.029823647 12.59143578 -1.100075255 -0.375228741 DAFPEAIIVKPSDIFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DAFPEAIIVKPSDIFGR 17 1 Q16795;A0A3B3ISG8 Q16795 NDUFA9 "NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial" 0 ; 106.38 0.00068944 490390000 387050 338462 205595 304844 338810 304980 363275 481150 435300 FALSE TRUE 335900.3618 336238.6208 305021.4297 374063.4894 332068.3439 316712.7779 328044.6464 378259.8168 383839.3299 0.875106681 0.875987932 0.794659134 0.974531426 0.86512329 0.825118098 0.854640525 0.985463936 1 18.55014302 1.686878473 4.879547594 0.996109836 0.866528862 0.566497179 0.045911863 0.10697713 5.898697392 0.029787915 0.011813022 48.62711152 -1.686878473 -0.129580974 DAGGPRPES(ph)PVPAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DAGGPRPESPVPAGR 15 1 Q9BVG9;E9PS47;E9PLE4 Q9BVG9 PTDSS2 Phosphatidylserine synthase 2 1 DAGGPRPES(1)PVPAGR;DAGGPRPES(1)PVPAGR;DAGGPRPES(1)PVPAGR 121.77 6.84E-05 2636110000 2218050 2242730 1552010 2398530 3328300 3137860 1786850 3588390 2984100 TRUE FALSE 1924929.073 2227997.359 2302567.227 2943152.896 3262073.342 3258575.505 1613561.562 2821040.723 2631323.097 0.731544171 0.846721317 0.875060622 1.118506845 1.239708398 1.238379091 0.613213012 1.072099708 1 21.32735698 3.97198722 3.294379061 1.037858071 0.793684101 0.279929927 0.175852761 0.354590304 7.892413248 0.049839946 0.10428788 9375.344167 -3.97198722 -0.24417397 DAGHPLYPFNDPY ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DAGHPLYPFNDPY 13 0 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ;;; 110.08 0.0025288 1790420000 2985330 2799550 1774330 1972090 2547340 2689900 2530570 2980230 2736380 FALSE TRUE 2590811.077 2781159.572 2632401.923 2419883.176 2496652.918 2793382.194 2285155.711 2342931.007 2412888.274 1.073738517 1.152626751 1.090975472 1.002898975 1.034715509 1.157692308 0.94706238 0.971006835 1 21.20232968 2.122511654 0.367715641 0.90817925 1.123892036 0.343585915 0.05799745 4.160964848 1.078381632 0.455507827 0.142032107 132.5902696 -2.122511654 0.215712786 DAGLLVEQPPLAGVAAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DAGLLVEQPPLAGVAASPR 19 0 Q13469-3;Q13469-4;Q13469-2;Q13469 Q13469-3 NFATC2 "Nuclear factor of activated T-cells, cytoplasmic 2" 1 DAGLLVEQPPLAGVAAS(1)PR 63.337 0.029462 0 12569 15128 9867.2 13643 16109 18113 15231 16023 19115 TRUE FALSE 10907.9748 15028.62317 14639.01092 16740.85167 15788.46242 18809.81883 13753.89996 12596.60614 16855.24648 0.647156054 0.891628799 0.868513608 0.993213104 0.93670908 1.115962253 0.816001118 0.74734037 1 14.0409101 4.812274892 2.618183338 0.91301389 0.559989823 0.41223951 0.102620514 0.808743529 6.007541873 0.028535072 0.676048847 64904.51239 -4.812274892 -0.353024068 DAGRPGERGS(ph)GGLFSPSTAHVPDGALGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DAGRPGERGSGGLFSPSTAHVPDGALGQR 29 2 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DAGRPGERGS(0.944)GGLFS(0.054)PS(0.001)T(0.001)AHVPDGALGQR;DAGRPGERGS(0.998)GGLFS(0.001)PSTAHVPDGALGQR;DAGRPGERGS(0.785)GGLFS(0.208)PS(0.003)T(0.003)AHVPDGALGQR;DAGRPGERGS(0.763)GGLFS(0.231)PS(0.004)T(0.001)AHVPDGALGQR 103.3 0.00029844 4033290000 891944 1006153 345850 456256 1049883 1122880 1112774 1302460 221129 TRUE FALSE 774071.3405 999543.5147 513104.2168 559855.8982 1028992.382 1166077.92 1004857.349 1023939.065 194987.3815 3.969853508 5.126195895 2.631473959 2.871241687 5.277225502 5.980273754 5.153448089 5.251309376 1 17.57302124 3.229317362 24.99937285 4.741274441 3.682426007 0.069593358 1.497372866 470.9418168 1273709.614 0.455078941 0.523016285 1695.576396 -3.229317362 -1.058848434 DAGTIAGLNVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DAGTIAGLNVLR 12 0 P11142;E9PKE3;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;; 204.64 2.58E-07 1907700000 1194973 1163377 761904 793244 1102646 1029855 1250872 1437120 936011 FALSE TRUE 1037054.29 1155734.7 1130363.323 973362.1742 1080705.502 1069474.188 1129562.626 1129803.072 825356.8459 1.25649202 1.400284865 1.369544977 1.179322834 1.309379703 1.295771876 1.368574855 1.368866179 1 19.65465848 1.233471711 24.99759648 0.999999502 1.322036813 0.701950681 0.065193759 92.12245338 452469.442 0.132586953 0.016241337 17.11873665 -1.233471711 0.32203731 DAGTIAGLNVMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DAGTIAGLNVMR 12 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 138.25 0.000588 0 43315 42136 30521 41542 47305 53344 40174 42083 43014 FALSE TRUE 37590.813 41859.20584 45281.05769 50974.74603 46363.72305 55396.1782 36277.93166 33083.87794 37928.93392 0.991085409 1.103621998 1.193839452 1.343954094 1.222384029 1.46052558 0.956471166 0.872259632 1 15.2110112 2.087624084 10.28582778 0.92324593 1.218470819 0.507108171 0.128390868 0.278446802 30.39574305 0.054238435 0.036553829 122.3556655 -2.087624084 0.295224889 DAHNALLDIQSSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 173.19 2.74E-06 1240670000 814610 774910 516680 598120 828830 772450 729520 774740 713960 FALSE TRUE 706957.2245 769819.5652 766548.1762 733932.2877 812337.9046 802166.6513 658771.2627 609067.88 629556.4621 1.12294491 1.222796701 1.217600362 1.165792636 1.290333677 1.274177456 1.04640537 0.967455529 1 19.26397625 2.10625958 4.776351558 0.988320534 1.216566096 0.811299177 0.048527733 0.082324743 3.121064472 0.021196104 0.013873017 127.7201969 -2.10625958 0.228245562 DAIAQAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DAIAQAVR 8 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;;; 113.14 0.0067622 2355870000 1524110 1761630 1016540 1002640 1559950 1443430 1458040 1468680 1530010 FALSE TRUE 1322695.002 1750057.737 1508142.144 1230304.736 1528910.047 1498959.686 1316639.505 1154614.211 1349133.961 0.980403014 1.297171213 1.117859448 0.911921849 1.133252954 1.111053261 0.975914582 0.855818803 1 20.36360218 2.106178594 4.161160383 0.917010899 1.09587155 0.307097418 0.105827675 0.23536444 7.403826274 0.046502091 0.029718388 127.6963825 -2.106178594 0.178860651 DAIHFYNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DAIHFYNK 8 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;; 109.86 0.0035366 1962150000 5122450 3614170 2541420 3198930 3461520 3245850 3644130 4518720 8160700 FALSE TRUE 4445505.254 3590428.279 3770459.213 3925295.949 3392642.524 3370719.95 3290722.833 3552426.893 7195951.343 0.617778671 0.498951161 0.523969526 0.545486727 0.471465462 0.468418947 0.457301985 0.493670221 1 22.778754 1.237752 24.99938749 1.000000575 0.505183665 0.915917476 0.04667561 5.269639287 162814.8405 0.06717931 0.0114855 17.28828844 -1.237752 -0.49481691 DAIKPNLMQTLEGTPVFVHAGPFANIAHGNSSIIADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DAIKPNLMQTLEGTPVFVHAGPFANIAHGNSSIIADR 37 1 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 171.57 2.90E-18 415140000 225340 263540 114020 200670 228910 258700 305350 364830 176660 FALSE TRUE 195560.7481 261808.7884 169160.4534 246235.1905 224355.1389 268652.3564 275737.204 286813.9436 155775.4561 1.255401544 1.680680609 1.085924944 1.580705952 1.440247036 1.72461287 1.770094025 1.841201117 1 17.24910842 3.152318677 1.972634994 1.635098168 1.383040083 0.074338754 0.279988908 0.66169692 5.299599337 0.093886883 0.114505639 1420.099181 -3.152318677 -0.252058085 DAILDALENLTAEELKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DAILDALENLTAEELKK 17 1 H3BP42;Q9ULZ3-3;Q9ULZ3-2;Q9ULZ3 H3BP42 PYCARD Apoptosis-associated speck-like protein containing a CARD 0 ; 193.9 1.68E-10 255390000 349870 301190 244472 238141 243058 176692 368030 377510 296944 FALSE TRUE 303633.793 299211.4631 362699.4769 292214.5538 238221.6213 183489.4556 332338.5072 296782.4243 261839.6186 1.159617458 1.142727998 1.385197087 1.116005879 0.909799757 0.700770405 1.269244544 1.133451179 1 17.99832388 3.479985979 24.64223423 1.022903094 1.225546559 0.294974537 0.158704907 141.1240455 1213951.721 0.048824228 0.064265789 3019.854228 -3.479985979 0.202643465 DAKPPTGPSPAT(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DAKPPTGPSPATPAR 15 1 P41231 P41231 P2RY2 P2Y purinoceptor 2 1 DAKPPT(0.001)GPS(0.061)PAT(0.938)PAR 75.358 0.051842 230840000 98775 96465 63172 107090 102620 100040 75032 103490 118090 TRUE FALSE 85721.63349 95831.31506 93722.1905 131406.4213 100578.0628 103888.6035 67755.40819 81359.46886 104129.5347 0.823221132 0.920308684 0.900053868 1.261951488 0.965893711 0.997686236 0.650683866 0.781329419 1 16.6680198 2.2699684 24.98384022 0.797892048 0.984343418 0.237843128 0.140452628 252.1699658 200591.9334 0.053410345 0.041367445 186.1951655 -2.2699684 0.18645137 DALDGPAAEAEPEHSFDGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DALDGPAAEAEPEHSFDGLR 20 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 203.17 1.09E-21 2284700000 769270 704010 635350 642700 685580 688330 735450 770570 1058930 FALSE TRUE 667609.0204 699385.312 942607.3851 788634.8581 671938.2993 714810.5005 664126.1722 605789.6021 933744.5017 0.714980403 0.749011438 1.009491765 0.844593844 0.719616874 0.765531148 0.711250423 0.648774478 1 19.83266832 3.247555573 24.80694387 0.749493087 0.836623988 0.044931648 0.119224426 414.5866959 1143370.651 0.034736578 0.044169627 1768.298478 -3.247555573 0.087130901 DALDGPAAEAEPEHSFDGLRR ddPTM_MDA-MB-175_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 866690000 737410 677235 380744 437616 608424 627301 678021 759850 366938 FALSE TRUE 639959.4001 672786.1987 564873.0719 536983.4013 596317.5528 651433.6754 612266.6278 597361.9907 323559.0077 1.977875395 2.079330764 1.745811609 1.659615058 1.842994751 2.013338093 1.892287383 1.846222718 1 18.30366932 1.237121657 5.520644018 0.956601655 1.882000402 0.836911435 0.122496437 0.062937381 5.99938923 0.22158292 0.032784136 17.2632141 -1.237121657 0.925398747 DALEPGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DALEPGQR 8 0 H3BQB1;P07741-2;P07741;H3BQZ9 H3BQB1 APRT Adenine phosphoribosyltransferase 0 81.548 0.052267 0 369240 310980 193370 235890 289070 297820 318550 392730 342450 FALSE TRUE 320443.9985 308937.1519 286884.3788 289452.4299 283318.0726 309277.3281 287657.07 308747.7457 301965.9511 1.061192486 1.023086049 0.950055388 0.958559827 0.938245095 1.024212587 0.952614257 1.022458806 1 18.20402636 4.456786241 4.905123038 0.980216455 1.053826286 0.463660685 0.02999873 0.15352366 9.793718138 0.007735265 0.024397541 28627.68572 -4.456786241 0.073609831 DALGDSLQVPVS(ph)PSSTTSSR ddPTM_MDA-MB-175_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 DALGDS(0.001)LQVPVS(0.769)PS(0.151)S(0.016)T(0.016)T(0.016)S(0.016)S(0.016)R;DALGDSLQVPVS(0.711)PS(0.208)S(0.061)T(0.018)T(0.002)SSR;DALGDSLQVPVS(1)PSSTTSSR 332.9 7.14E-80 459226000 330759 388568 263109 362622 447265 424620 473165 574035 528769 TRUE FALSE 287048.3601 386015.4712 390349.3924 444960.8674 438365.3016 440955.4062 427277.5311 451282.0824 466258.5312 0.615642055 0.827900071 0.837195175 0.9543222 0.940176473 0.945731556 0.916396168 0.967879518 1 18.8307706 5.370574676 0.75165801 0.958569441 1.75E-13 0.9317777 0.028946549 1.471515998 0.325023552 0.010840577 1.477405516 234733.2848 -5.370574676 -0.958569441 DALQPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DALQPGR 7 0 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ; 111.65 0.015195 420790000 510220 500210 328660 384780 489400 550640 539720 554730 589300 FALSE TRUE 442793.1343 496924.0876 487601.0753 472150.18 479661.8975 571823.4771 487378.0375 436105.3064 519633.6253 0.852125638 0.95629702 0.93835551 0.9086213 0.923077095 1.100435863 0.937926288 0.839255362 1 18.98713526 2.967943212 24.99415212 0.953410722 0.918284246 0.110283233 0.069423281 2374.604494 1851439.869 0.024180507 0.02419979 928.8449233 -2.967943212 -0.035126476 DALSDLALHFLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DALSDLALHFLNK 13 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ; 241.15 7.08E-17 3157300000 5302200 4649300 3087100 3860500 4379000 3745800 5470800 6336700 5884800 FALSE TRUE 4601500.836 4618758.442 4580031.886 4737085.529 4291866.467 3889903.35 4940242.658 4981646.017 5189105.648 0.886761833 0.890087571 0.882624521 0.912890554 0.827091749 0.74962886 0.952041256 0.960020157 1 22.30705448 2.027445315 24.99860285 0.97081733 0.860900786 0.571802906 0.046173848 160.5583861 146244.1573 0.019952098 0.013451384 106.5234725 -2.027445315 -0.109916544 DALSEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DALSEER 7 0 H7BZ55 H7BZ55 Putative ciliary rootlet coiled-coil protein-like 3 protein 0 100.82 0.022129 86517000 139210 130110 86350 113880 109720 154900 132450 149910 147040 FALSE TRUE 120813.0458 129255.2988 128109.1488 139738.1945 107536.7867 160859.1032 119605.0194 117852.9131 129657.0987 0.931788903 0.996901058 0.988061202 1.077751978 0.829393745 1.240650183 0.922471817 0.908958432 1 16.98434167 DALYDVITVGAPAAHFQGFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DALYDVITVGAPAAHFQGFK 20 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 ; 246.45 4.88E-30 497850000 741310 573020 459960 562270 647670 533730 724160 920140 846680 FALSE TRUE 643344.0053 569255.7939 682398.1945 689941.9973 634782.6341 554262.9385 653931.0747 723375.2215 746586.4549 0.861714006 0.762478063 0.914024344 0.924128736 0.850246653 0.742396188 0.875894641 0.968910187 1 19.50994981 1.73584343 3.301709403 0.991697814 0.8439804 0.510326652 0.056824115 0.176098439 4.086644764 0.042701662 0.016039815 54.43063859 -1.73584343 -0.147717414 DANDPVDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DANDPVDDR 9 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 85.377 0.034562 75687000 340780 271860 234700 202450 240850 249990 265200 325730 290690 FALSE TRUE 295745.0596 270074.1338 348201.705 248419.3668 236057.5562 259607.2771 239480.9448 256075.1743 256324.9594 1.15378955 1.053639624 1.358438546 0.969157929 0.920930825 1.012805299 0.934286483 0.999025514 1 17.96761444 3.689245223 24.89058582 0.972556072 1.175124327 0.623258628 0.078904227 218.1521262 110106.1625 0.020345298 0.030176999 4889.283529 -3.689245223 0.202568255 DANQVHSTTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DANQVHSTTR 10 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 0 ;;;;; 189.57 9.96E-07 1047543000 873233 952036 329195 625680 870456 1039823 965209 1117781 987722 FALSE TRUE 757833.0466 945782.0128 488394.8031 767750.2069 853135.6286 1079825.664 871603.1797 878752.2317 870954.6304 0.870117708 1.085914214 0.56075803 0.881504248 0.979540838 1.2398185 1.000744642 1.008952936 1 19.73223804 3.167951163 3.808870776 1.052914139 0.844252579 0.328500223 0.142930426 0.274350453 7.862879986 0.044248598 0.052114582 1472.14695 -3.167951163 -0.208661561 DANSSFFDNSSS(ph)PHLLDQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DANSSFFDNSSSPHLLDQLK 20 0 P49454 P49454 CENPF Centromere protein F 1 DANSSFFDNS(0.004)S(0.02)S(0.977)PHLLDQLK 160 1.59E-11 222860000 283730 303320 184870 247990 259240 199230 283330 413930 320890 TRUE FALSE 246234.3616 301327.4709 274273.7504 304299.9198 254081.6312 206894.507 255852.7002 325414.2907 282954.7498 0.870225228 1.064931659 0.969320185 1.075436691 0.89795853 0.731192911 0.904217725 1.150057707 1 18.11021183 1.748968957 25 1.078428893 0.933795591 0.250326957 0.103843276 3.766909281 9070.462889 0.058491705 0.028088166 56.10078738 -1.748968957 -0.144633302 DAPAPRPLPASEGHLQPPAQTSGPT(ph)GSPPCIQTSPDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DAPAPRPLPASEGHLQPPAQTSGPTGSPPCIQTSPDPR 38 1 B4DF95;Q15735 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 DAPAPRPLPASEGHLQPPAQT(0.001)S(0.005)GPT(0.459)GS(0.425)PPCIQT(0.091)S(0.019)PDPR 85.239 0.0010516 225240000 39959 42548 17440 22769 41478 45537 44068 45602 18139 TRUE FALSE 34678.31691 42268.49939 25874.04233 27939.04945 40652.66895 47288.83786 39794.29214 35850.36718 15994.62808 2.168122743 2.642668474 1.61767077 1.746777062 2.541645153 2.95654501 2.487978585 2.241400487 1 13.96529983 3.228783069 24.97360379 2.298736019 2.056146849 0.025747439 0.563919848 813.847736 2078708.69 0.176817278 0.202941306 1693.491687 -3.228783069 -0.24258917 DAPIS(ph)PASIASSSSTPSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DAPISPASIASSSSTPSSK 19 0 Q04727-4;Q04727;Q04727-3;H7C4E4;H0Y5S0 Q04727-4 TLE4 Transducin-like enhancer protein 4 1 DAPIS(0.998)PAS(0.002)IASSSSTPSSK 141.07 1.77E-07 78879000 76182 79574 52730 67505 74523 62763 91326 101400 91662 TRUE FALSE 66114.35568 79051.27315 78230.40437 82833.042 73040.1381 65177.53322 82469.21858 79716.3991 80825.82278 0.817985557 0.978044769 0.967888747 1.024833885 0.903673301 0.806394924 1.020332559 0.986273896 1 16.30252867 DAPQDFHPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DAPQDFHPDR 10 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;;; 124.12 0.00044388 2792780000 2027120 3010740 1197120 1024610 1804500 2373360 1917550 2134160 2445090 FALSE TRUE 1759230.956 2990962.251 1776051.236 1257263.361 1768593.98 2464664.695 1731586.296 1677786.492 2156034.246 0.815956871 1.387251736 0.823758361 0.583137009 0.820299577 1.143147285 0.803134876 0.778181745 1 21.03994866 4.134193787 21.86637144 0.84111396 1.102909234 0.217067507 0.197866766 5.501234401 1130.747689 0.048946377 0.101890365 13620.52308 -4.134193787 0.261795273 DAPTS(ph)PASVASSSSTPSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DAPTSPASVASSSSTPSSK 19 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 DAPTS(1)PASVASSSSTPSSK;DAPTS(1)PASVASSSSTPSSK;DAPTS(0.885)PAS(0.115)VASSSSTPSSK;DAPT(0.016)S(0.982)PAS(0.001)VASSSSTPSSK 333.98 2.37E-75 2390970000 2159510 1148260 904590 1093540 1158530 979140 1569970 1690240 1579470 TRUE FALSE 1874125.282 1140717.004 1342052.75 1341844.971 1135477.52 1016808.149 1417714.551 1328795.329 1392746.856 1.345632391 0.819041163 0.963601349 0.963452163 0.815279184 0.730073915 1.017926944 0.954082448 1 20.40950163 4.746112673 24.94812064 0.911714831 1.345632604 0.688149654 0.092568859 557.0413759 1840134.566 0.023367008 0.239605596 55733.03238 -4.746112673 0.433917772 DAQHYGGWEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DAQHYGGWEHR 11 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;; 159.5 1.65E-05 4624591000 1275620 948790 671662 822897 1015810 1230720 845970 846330 800090 FALSE TRUE 1107043.585 942557.336 996479.9898 1009748.341 995597.3684 1278066.595 763927.9596 665348.9156 705504.2717 1.569152207 1.336005144 1.412436508 1.431243412 1.411185458 1.811564644 1.082811246 0.94308276 1 19.42829529 2.073410295 8.030841416 0.980916495 1.476909696 0.75821276 0.130343555 0.111340628 10.66413738 0.052275485 0.035146029 118.4159751 -2.073410295 0.495993202 DAQIGWIQTVEDLHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DAQIGWIQTVEDLHER 16 0 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 ;;;;; 235.24 1.07E-19 883539000 1156225 1149130 823189 935201 1211794 1313377 1189512 1357209 1604800 FALSE TRUE 1003426.937 1141581.289 1221285.954 1147552.681 1187681.67 1363903.463 1074153.309 1066980.417 1415082.372 0.709094365 0.806724267 0.863049373 0.810944086 0.839302145 0.963833265 0.759074758 0.754005871 1 20.4324546 4.690198744 2.72088591 0.84313348 0.690751831 0.24861764 0.078693064 0.622661919 6.663340163 0.020047708 0.202251118 49000.30056 -4.690198744 -0.15238165 DAQRLS(ph)PIPEEVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DAQRLSPIPEEVPK 14 1 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 DAQRLS(1)PIPEEVPK;DAQRLS(1)PIPEEVPK;DAQRLS(1)PIPEEVPK;DAQRLS(1)PIPEEVPK;DAQRLS(1)PIPEEVPK 165.45 3.40E-06 4534480000 6578660 5107470 4624910 5472090 5304620 4113780 6275430 7566330 8984850 TRUE FALSE 5709273.413 5073918.693 6861531.945 6714611.67 5199068.44 4272039.779 5666839.764 5948329.211 7922671.269 0.720624802 0.640430294 0.866062937 0.847518652 0.656226702 0.539217094 0.715268824 0.750798438 1 22.91755551 1.217667984 3.106430706 1.060938502 0.712673985 0.47390984 0.094495232 0.39854068 4.783511929 0.354813679 0.026266548 16.50699363 -1.217667984 -0.348264518 DAS(ph)PESPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DASPESPSK 9 0 H0Y7Z6;A2A2S1;O95467 H0Y7Z6 GNAS Neuroendocrine secretory protein 55;LHAL tetrapeptide;GPIPIRRH peptide 1 DAS(1)PESPSK;DAS(1)PESPSK;DAS(1)PESPSK;DAS(0.999)PES(0.001)PSK 169.82 6.10E-05 800150000 1567820 1411640 1149610 1250060 1100400 1396510 1580510 2050280 2001050 TRUE FALSE 1360628.615 1402366.844 1705565.241 1533905.229 1078504.193 1450234.643 1427232.383 1611843.577 1764488.149 0.771118024 0.794772606 0.966606232 0.869320222 0.611227791 0.821901039 0.808864817 0.913490736 1 20.75081831 1.508105 2.203288988 1.007609799 0.806386062 0.357935653 0.087903867 0.444348414 3.807765278 0.152885485 0.025330168 32.21847647 -1.508105 -0.201223736 DAS(ph)PSKEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DASPSKEER 9 1 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 DAS(0.968)PS(0.032)KEER;DAS(0.999)PS(0.001)KEER;DAS(0.717)PS(0.283)KEER;DAS(0.633)PS(0.367)KEER;DAS(0.754)PS(0.246)KEER 185.18 4.69E-05 6483430000 9030880 6714580 4891980 5304080 4888120 4892960 7988080 8668640 8199420 TRUE FALSE 7837426.327 6670471.482 7257757.891 6508452.432 4790855.975 5081195.337 7213397.231 6814918.795 7230093.908 1.084000627 0.92259818 1.003826227 0.900189197 0.662627075 0.702784141 0.997690669 0.942576802 1 22.78558296 4.56873204 1.19894173 0.875121711 1.116176333 0.230637915 0.11703888 2.071769962 3.175587346 0.039598531 0.579261791 37045.20824 -4.56873204 0.241054622 DAS(ph)SPVPPPHVPPPVPPLRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DASSPVPPPHVPPPVPPLRPR 21 1 O94875-12;O94875-10;O94875-3;H7BXR3;O94875-9;O94875-5;O94875-4;O94875-11;O94875-2;O94875-8;H7BZK1;H7BZX1;H7C1R7;O94875-7;O94875;O94875-6 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 DAS(0.5)S(0.5)PVPPPHVPPPVPPLRPR;DAS(0.519)S(0.481)PVPPPHVPPPVPPLRPR 57.981 0.04602 520000000 217849 228913 196823 156584 196229 246157 200933 214980 182170 TRUE FALSE 189059.7027 227409.2554 292007.2611 192138.7904 192324.4268 255626.8191 181446.5486 169008.2 160634.0701 1.176958926 1.415697524 1.817841389 1.196127262 1.197282909 1.591361153 1.129564534 1.052131717 1 17.29341839 2.079596542 6.462682133 1.047423146 1.399875989 0.404360561 0.196213092 0.207310295 13.46500696 0.082253846 0.054955625 120.1148053 -2.079596542 0.352452842 DASDDLDDLNFFNQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DASDDLDDLNFFNQK 15 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;;;; 316.34 5.64E-56 517106000 1262448 1087762 940096 1182171 1120008 897124 1290132 1548849 1845536 FALSE TRUE 1095612.298 1080616.42 1394729.57 1450600.994 1097722.032 931636.9408 1165015.197 1217639.695 1627358.837 0.673245675 0.664030818 0.857051032 0.89138361 0.674542091 0.572484027 0.715893244 0.74823061 1 20.63410097 1.232408709 4.038536895 1.031948593 0.723921658 0.467649181 0.092725517 0.251403253 7.218186383 0.231265756 0.02550528 17.07688715 -1.232408709 -0.308026935 DASIVGFFDDSFSEAHSEFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 DASIVGFFDDSFSEAHSEFLK 21 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;;;;; 374.44 1.48E-112 2305378000 2776462 2389292 2100477 3119449 2505361 2423062 2890217 2772167 5596302 FALSE TRUE 2409545.512 2373596.584 3116274.703 3827767.573 2455509.218 2516278.763 2609924.2 2179360.66 4934713.553 0.488284778 0.480999871 0.631500627 0.775681817 0.49759914 0.509913845 0.528890719 0.441638737 1 22.23453491 1.230604738 24.99995966 1.000000827 0.544219311 0.69129158 0.095699993 185.5874198 583128.2182 0.268815102 0.025101073 17.00610035 -1.230604738 -0.455781516 DASSGKENRS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DASSGKENRSPSR 13 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 DASSGKENRS(0.876)PS(0.124)R 80.603 0.0090475 34512000 58709 47909 22827 25255 34937 42701 55997 63478 6276.6 TRUE FALSE 50950.4569 47594.28262 33866.21355 30989.53375 34241.82205 44343.7351 50566.41956 49903.72369 5534.587498 9.205827339 8.599427263 6.119013126 5.599249042 6.186878799 8.012112034 9.136438727 9.016701552 1 12.43426008 4.356765293 5.428473712 6.835156993 9.050558688 0.149860877 2.309728481 0.429488127 18.18250129 0.58688841 1.621439812 22738.68223 -4.356765293 2.215401695 DASSS(ph)PASTASSASSTSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DASSSPASTASSASSTSLK 19 0 Q04724;A0A669KBK8 Q04724 TLE1 Transducin-like enhancer protein 1 1 DASSS(1)PASTASSASSTSLK 350.46 1.01E-90 303370000 279050 250280 156350 193680 253500 192740 275340 335590 304870 TRUE FALSE 242172.8355 248635.8942 231961.383 237658.0042 248455.846 200154.8325 248637.5692 263826.6901 268828.6159 0.900844706 0.924886264 0.862859715 0.884050247 0.924216513 0.74454437 0.924892495 0.981393626 1 18.03632719 1.848898953 3.69676639 0.989673498 0.875762505 0.461228254 0.051321649 0.202453334 4.584544706 0.030531985 0.013783358 70.61532355 -1.848898953 -0.113910994 DASVPLIDVTNLPT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DASVPLIDVTNLPTPR 16 0 Q96A65;Q96A65-2 Q96A65 EXOC4 Exocyst complex component 4 1 DASVPLIDVTNLPT(1)PR;DASVPLIDVTNLPT(1)PR 186.98 1.58E-08 151166000 96923 112110 64430 69470 85923 109173 91743 106782 110734 TRUE FALSE 84114.37998 111373.542 95588.56351 85244.22528 84213.30041 113372.956 82845.77798 83947.50028 97643.15267 0.861446785 1.140618046 0.978958185 0.873017953 0.862459866 1.161094791 0.848454558 0.859737708 1 16.57523126 3.99410894 24.96304092 0.9273789 1.015721326 0.054134405 0.114149387 609.6387051 2583354.696 0.028709639 0.056847939 9865.269197 -3.99410894 0.088342425 DATNRS(ph)PTQIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DATNRSPTQIVK 12 1 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 DATNRS(1)PTQIVK;DATNRS(0.999)PT(0.001)QIVK 178.85 1.30E-05 1455920000 1492490 1201960 763100 916910 1148600 1003700 1357700 1590720 1128890 TRUE FALSE 1295253.665 1194064.246 1132137.712 1125108.43 1125745.107 1042312.988 1226030.463 1250556.907 995433.9102 1.301195038 1.19954146 1.137330867 1.130269341 1.130908939 1.047094114 1.231654307 1.256293255 1 19.92496601 4.651851025 2.379252647 1.14638478 1.322201465 0.328559979 0.075543563 0.619848697 4.884057493 0.020398052 0.207000587 44859.14843 -4.651851025 0.175816686 DATSLLAAGEGGLLDEVEPLRPDELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DATSLLAAGEGGLLDEVEPLRPDELER 27 1 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 0 ;;; 303.76 3.68E-71 351094000 204388 192036 140445 165776 196504 214222 212208 223525 237623 FALSE TRUE 177377.6079 190774.5029 208364.6718 203417.9745 192593.9549 222463.259 191628.1008 175725.9182 209531.4796 0.846543957 0.910481342 0.994431348 0.970822976 0.919164773 1.061717597 0.914555184 0.838661181 1 17.67680748 4.601699749 3.591460934 0.947352387 0.84667714 0.249354212 0.060083481 0.418149996 8.752326179 0.016124534 0.086951157 39966.8342 -4.601699749 -0.100675247 DATYYSYQNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DATYYSYQNR 10 0 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 0 98.044 0.013134 69369000 125300 115870 51946 76115 138040 143690 121850 118890 121480 FALSE TRUE 108741.2875 115108.8423 77067.25935 93398.07409 135293.2741 149217.8473 110033.0058 93466.2987 107118.7728 1.015146876 1.07459075 0.719456145 0.871911353 1.263021136 1.39301304 1.027205623 0.872548259 1 16.70885181 3.27223331 24.99982754 1.089128029 0.916954365 0.23411595 0.168916628 358.9340295 266483.2885 0.055703059 0.07190831 1871.68737 -3.27223331 -0.172173664 DAVDFDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DAVDFDVR 8 0 Q9Y6D6;E5RIF2;E5RHL7;E5RHZ1 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 0 83.265 0.042536 161810000 623350 612060 420580 448810 599860 609980 644430 654750 687030 FALSE TRUE 540972.7181 608039.3376 623973.8948 550719.1701 587923.9596 633446.3253 581933.2778 514736.8078 605810.0961 0.892974088 1.003679769 1.029982661 0.909062384 0.970475671 1.045618634 0.960586959 0.849666935 1 19.2085061 1.981607426 24.35978333 0.911404845 0.97811607 0.097446718 0.059289176 840.07974 1112629.013 0.025764564 0.015246186 95.85337874 -1.981607426 0.066711225 DAVDFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DAVDFLR 7 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 ;;;; 130.77 0.0082156 1087198000 2359659 2412287 1528715 1867229 2325944 2245398 2452065 2617112 2520373 FALSE TRUE 2047824.085 2396440.528 2268006.687 2291211.883 2279662.265 2331779.914 2214264.114 2057462.965 2222417.375 0.921439918 1.078303542 1.020513389 1.03095481 1.025757938 1.049208821 0.996331355 0.925777034 1 21.08369835 1.984106636 8.356149844 0.958499541 1.024192166 0.229834618 0.043419359 0.218825129 92.54939828 0.01791463 0.010758035 96.40657101 -1.984106636 0.065692626 DAVDWVHYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 DAVDWVHYK 9 0 P49902-2;P49902;Q5JUV4;Q5JUV3 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;;;;;;;; 135.83 0.00027316 11180950000 16170420 17304480 11609670 14209610 17169610 12906940 18390770 22455970 18800930 FALSE TRUE 14033458.03 17190805.73 17224145.24 17436119.13 16827968.35 13403478.33 16607235.96 17653935.57 16578305.47 0.846495322 1.03694589 1.038956923 1.051743145 1.015059614 0.808495075 1.001745081 1.064881788 1 23.98279322 4.493952507 0.009362035 1.95054031 5.51E-05 0.029407523 0.085755841 52595.8572 160.4368134 16180.77265 17256.07517 31185.48535 -4.493952507 -1.950485234 DAVFIPAGWDNDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DAVFIPAGWDNDKK 14 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 87.566 0.011051 313410000 267830 206830 185370 185750 201840 152690 271530 307350 265810 FALSE TRUE 232435.5869 205471.3201 275015.552 227927.3765 197823.7789 158564.0831 245197.0624 241625.5943 234386.2446 0.991677593 0.876635574 1.173343395 0.972443485 0.84400763 0.676507631 1.046123943 1.03088641 1 17.83852838 DAVLLVFANK ddPTM_MDA-MB-175_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 ; 146.81 6.51E-05 502130000 2450400 2119000 1531720 2217900 1982260 1587570 2290800 2937300 3201200 FALSE TRUE 2126573.431 2105080.149 2272464.915 2721508.093 1942816.904 1648644.845 2068638.569 2309181.253 2822757.783 0.753367308 0.745753023 0.805051333 0.964130933 0.688269081 0.584054663 0.732843102 0.81805859 1 21.42867391 1.273803865 2.750372382 1.041096137 0.755023916 0.401131267 0.094682909 0.467178512 4.346235519 0.294808155 0.026748879 18.78468274 -1.273803865 -0.28607222 DAVSGMGVIVHIIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DAVSGMGVIVHIIEK 15 0 P49720 P49720 PSMB3 Proteasome subunit beta type-3 0 ; 154.6 2.45E-06 689180000 1443790 1018490 1054820 1455710 1055990 922620 1449930 1698110 2553900 FALSE TRUE 1252989.493 1011799.472 1564934.48 1786251.205 1034977.865 958113.7884 1309316.012 1334982.391 2251980.851 0.556394382 0.449293106 0.694914648 0.793191116 0.459585553 0.42545379 0.58140637 0.592803616 1 21.10276313 1.231800659 4.485911768 1.039777904 0.567210905 0.59359428 0.11222795 0.1623397 6.785146755 0.247684429 0.029793327 17.05299479 -1.231800659 -0.472566999 DAVTYTEHAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DAVTYTEHAK 10 0 P62805 P62805 HIST1H4A Histone H4 0 ; 119.34 0.00070596 2632800000 4548700 3814400 2778200 6343300 3344100 5360200 4273500 5475100 6229600 FALSE TRUE 3947577.77 3789342.955 4121746.813 7783643.216 3277558.953 5566410.363 3859056.628 4304292.472 5493143.785 0.718637255 0.68983138 0.750343878 1.416974236 0.596663601 1.013337823 0.702522413 0.783575424 1 22.38920062 3.978299801 24.99281301 0.897279296 0.708197455 0.151799173 0.220045164 1478.77894 1703163.247 0.056274352 0.098673094 9512.612382 -3.978299801 -0.189081841 DAWAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DAWAIR 6 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ;;; 126.04 0.041095 1659460000 1697540 1706390 1054520 1361330 1674110 1765670 1743740 1765060 1949900 FALSE TRUE 1473205.788 1695180.612 1564489.399 1670440.783 1640798.486 1833596.467 1574632.363 1387615.655 1719385.043 0.856821335 0.985922623 0.909912184 0.971533857 0.9542938 1.06642574 0.915811365 0.807041832 1 20.71346123 2.00424359 24.99920605 0.8812447 0.95994284 0.082609001 0.070652372 180.8450801 1065362.113 0.027754899 0.018625565 100.9819121 -2.00424359 0.07869814 DAWWAEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DAWWAEIR 8 0 Q86YS7;Q86YS7-5;H0YGU7;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 0 ; 126.67 0.0028134 342680000 171358 195672 118158 137424 200890 185810 188486 206978 200321 FALSE TRUE 148712.6061 194386.6177 175299.604 168628.2196 196892.682 192958.2309 170206.6567 162717.3654 176639.2796 0.841899981 1.100472206 0.992415755 0.954647347 1.114659675 1.092385744 0.963583282 0.921184494 1 17.43044667 2.026804852 24.8805979 0.951188927 1.02115028 0.084557278 0.082173418 394.2257599 365923.3993 0.032455574 0.021880997 106.3664959 -2.026804852 0.069961352 DAYELEVLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DAYELEVLLR 10 0 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;J3QRL2;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 0 82.287 0.042959 12189000 20519 24763 16200 17636 21948 28609 19802 27178 23782 FALSE TRUE 17807.36216 24600.33022 24034.37419 21640.52335 21511.27774 29709.60674 17881.60509 21366.1962 20970.51905 0.849161726 1.173091146 1.146102971 1.031949819 1.025786614 1.416732064 0.852702074 1.018868257 1 14.35607495 DAYELQEVIGSGATAVVQAALCKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DAYELQEVIGSGATAVVQAALCKPR 25 1 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 0 190.87 7.16E-18 78319000 129280 123620 83102 80830 120910 96163 128030 155450 125720 FALSE TRUE 112195.3204 122807.9321 123290.4052 99183.68691 118504.1276 99862.45284 115613.6703 122208.2272 110857.5248 1.012067702 1.107799694 1.112151885 0.894695124 1.068976849 0.900817991 1.042903226 1.102390004 1 16.75834718 DAYSGGAVNLYHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DAYSGGAVNLYHVR 14 0 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;;;; 246.25 1.02E-17 5027720000 5229360 5055280 3157570 3852560 5056470 4719130 4687860 5529450 5538780 FALSE TRUE 4538286.826 5022071.533 4684581.413 4727342.631 4955856.14 4900677.985 4233232.059 4347020.148 4883991.738 0.929216729 1.028271914 0.959170626 0.967926009 1.014714276 1.003416518 0.866756597 0.890054771 1 22.21962933 2.251167221 24.99670273 0.910745773 0.985374145 0.318905707 0.044096861 219.9752454 436172.589 0.016116037 0.01239765 178.3065188 -2.251167221 0.074628372 DCDHADEQK ddPTM_MDA-MB-175_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 ;;; 209.6 8.15E-06 3076620000 6921730 5099060 5014540 6577000 3017040 3939280 6177440 7616510 13326760 FALSE TRUE 6007005.843 5065563.939 7439588.317 8070408.373 2957006.807 4090826.651 5578352.82 5987778.608 11751285.61 0.51117861 0.43106466 0.633087184 0.686768124 0.251632622 0.348117371 0.474701492 0.509542428 1 23.48631526 1.234071876 4.587066075 1.044379333 0.47682553 0.633579509 0.124325276 0.141225388 6.432708928 0.262490312 0.03296658 17.14240991 -1.234071876 -0.567553803 DCDLQEDACYNCGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DCDLQEDACYNCGR 14 0 P62633-2;P62633;P62633-7;P62633-3 P62633-2 CNBP Cellular nucleic acid-binding protein 0 ; 381.24 3.20E-83 641200000 759470 609330 557560 773980 721050 571840 647580 779120 1530810 FALSE TRUE 659104.1152 605327.2711 827197.8809 949723.9885 706702.5157 593839.0548 584777.7913 612511.2511 1349839.386 0.488283363 0.448443924 0.612812079 0.703582959 0.523545633 0.439933122 0.433220276 0.453766024 1 20.36435632 1.234431125 24.99994791 1.000000712 0.511548712 0.760496243 0.085895196 67.43045357 408167.7501 0.176048953 0.023466646 17.15659599 -1.234431125 -0.488452 DCDPGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DCDPGSPR 8 0 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 1 DCDPGS(1)PR;DCDPGS(1)PR;DCDPGS(1)PR;DCDPGS(1)PR;DCDPGS(1)PR;DCDPGS(1)PR 143.4 0.00063157 5143520000 12298590 12343560 7734840 9291750 8434670 11313240 12415240 14402820 13589590 TRUE FALSE 10673300.17 12262474.34 11475434.5 11401583.85 8266836.569 11748467.66 11211211.94 11322889.03 11983044.15 0.890700229 1.023318798 0.95763934 0.951476412 0.689877836 0.980424299 0.935589638 0.94490923 1 23.51449112 1.16229635 1.312598714 1.047029896 0.916972962 0.082192889 0.088516251 4.990776469 6.490574051 0.928505794 0.027236066 14.53102835 -1.16229635 -0.130056934 DCEQAENWMAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DCEQAENWMAAR 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 202.96 3.04E-07 1016510000 753190 685510 462700 544430 663260 667110 708500 852500 745710 FALSE TRUE 653654.0332 681006.8397 686463.2676 668051.1526 650062.4236 692774.1534 639789.779 670199.5092 657553.0133 0.99407047 1.035668343 1.043966424 1.015965464 0.988608387 1.053563955 0.972985852 1.019232664 1 19.32674769 2.613009873 0.882281321 1.003026634 1.023303712 0.070316505 0.024653137 1.683880543 2.915890732 0.021833093 0.013145416 410.2134285 -2.613009873 0.020277078 DCEVTNDGHTIQVILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DCEVTNDGHTIQVILK 16 0 P35219 P35219 CA8 Carbonic anhydrase-related protein 0 ; 159.31 9.18E-09 431160000 713570 722810 465280 554120 653400 501430 832340 938570 875990 FALSE TRUE 619269.9165 718061.8135 690290.9643 679941.4152 640398.6184 520720.3366 751619.7949 737864.1095 772431.4601 0.801715037 0.929612335 0.893659826 0.880261163 0.829068534 0.674131445 0.973056943 0.95524865 1 19.5590474 2.098380046 22.5740112 0.97175581 0.841875312 0.480341769 0.068994603 6.155823325 1401.945529 0.029080114 0.019605815 125.4238265 -2.098380046 -0.129880499 DCFGCLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DCFGCLR 7 0 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 0 ;;;;; 153.67 0.0040255 6360290000 4451830 4041360 2273150 2536320 3703620 3527040 3463170 3979270 4021660 FALSE TRUE 3863509.386 4014812.04 3372452.943 3112230.221 3629925.208 3662727.511 3127312.306 3128334.077 3546223.936 1.089471352 1.132137201 0.950998302 0.877618074 1.023602929 1.032852853 0.881871073 0.882159202 1 21.75785221 4.232312232 24.40839681 0.943199462 1.110804298 0.567327751 0.058202485 71.64159417 279863.1769 0.015862295 0.03442391 17073.09401 -4.232312232 0.167604836 DCGATWVVLGHSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DCGATWVVLGHSER 14 0 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3;U3KPS5 P60174 TPI1 Triosephosphate isomerase 0 ;;; 198.23 2.23E-08 5931230000 5625530 5991400 2941090 2805820 4435800 4756930 4747240 5054940 5279010 FALSE TRUE 4882101.957 5952042.099 4363410.961 3442924.315 4347536.258 4939932.175 4286853.395 3973980.419 4654931.452 1.048802116 1.278653007 0.937373838 0.739629434 0.93396354 1.061225547 0.920927288 0.853714058 1 22.15032849 4.157266243 7.59201354 0.912791259 1.162483467 0.503120102 0.100197056 0.164900039 13.0524152 0.02546996 0.053667214 14363.69725 -4.157266243 0.249692208 DCHEEVYAGSHQYPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DCHEEVYAGSHQYPGR 16 0 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 ;;;; 277.94 1.37E-35 2681530000 682373 640993 428275 461231 593780 647733 500685 637124 560567 FALSE TRUE 592195.6791 636782.2748 635390.2225 565960.548 581964.9397 672651.7076 452128.6458 500879.9907 494297.4079 1.198055401 1.288257362 1.285441138 1.144979802 1.177357863 1.360823862 0.914689494 1.013317049 1 18.91501982 2.231012511 24.99999997 0.981221384 1.23912648 0.782031297 0.066285828 76.45424072 253220.5873 0.026464259 0.018233616 170.2207545 -2.231012511 0.257905095 DCHYLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DCHYLK 6 0 F8WC14;Q9BSY4;Q9BSY4-2 F8WC14 CHCHD5 Coiled-coil-helix-coiled-coil-helix domain-containing protein 5 0 72.021 0.086696 134430000 276860 249100 199810 217200 229490 235160 210960 272000 219380 FALSE TRUE 240272.2495 247463.6457 296438.7843 266518.5797 224923.598 244206.7574 190501.1317 213834.9167 193445.1463 1.242069156 1.279244532 1.532417794 1.377747567 1.162725466 1.262408295 0.98478114 1.10540337 1 17.56156501 2.647895111 1.285140917 1.038116839 1.357464284 0.633582669 0.100544319 0.287453592 0.990556812 0.057283193 0.042308344 444.5238946 -2.647895111 0.319347446 DCLASIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DCLASIAR 8 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 96.253 0.020937 0 101790 89667 59999 62940 104650 101990 75985 95065 90300 FALSE TRUE 88338.1936 89077.97157 89014.71708 77231.48898 102567.6697 105913.6213 68615.9864 74736.08955 79624.83687 1.109430136 1.11872093 1.117926524 0.969942194 1.288136639 1.330158095 0.861740998 0.938602734 1 16.28093089 2.219201024 24.99976056 0.93153401 1.149894125 0.503487032 0.103938321 211.6602363 273322.6096 0.04453 0.030071446 165.6536555 -2.219201024 0.218360115 DCLFRPLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DCLFRPLNK 9 1 A0A590UJ56;A0A590UJR3;A0A590UJ21;A0A0C4DGX4;Q13616;A0A590UJC4;A0A590UK34;A0A590UJM8 A0A590UJ56 CUL1 Cullin-1 0 ; 71.614 0.044764 485800000 716520 700390 476010 528910 660120 603740 760450 873970 729780 FALSE TRUE 621830.0666 695789.092 706210.0282 649007.0994 646984.9035 626966.2685 686701.676 687078.3167 643506.2398 0.96631552 1.081246846 1.09744084 1.008548262 1.005405796 0.974297108 1.067125124 1.067710419 1 19.29559461 DCLIEDS(ph)DDEAGQS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DCLIEDSDDEAGQS 14 0 H3BSW6;Q2VPK5-3;Q2VPK5;H3BPG4 H3BSW6 CTU2 Cytoplasmic tRNA 2-thiolation protein 2 1 DCLIEDS(1)DDEAGQS;DCLIEDS(1)DDEAGQS 197.06 2.52E-08 364000000 560500 506970 339510 379300 519400 487630 521950 585990 553400 TRUE FALSE 486428.5049 503639.6807 503698.1716 465425.8622 509064.9562 506389.4416 471331.3693 460680.5987 487977.6824 0.996825311 1.032095727 1.03221559 0.95378514 1.043213603 1.03773074 0.965887143 0.944060795 1 18.89645564 2.220901123 24.07450489 0.964411569 1.015859467 0.350846552 0.029166438 154.0533808 210012.6586 0.011764666 0.007953836 166.3033979 -2.220901123 0.051447898 DCQLNAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DCQLNAHK 8 0 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;;; 152.89 0.00044991 5164980000 5137720 3907760 2980460 3613450 3637030 3383420 4565760 5346050 6209140 FALSE TRUE 4458757.285 3882089.667 4421820.425 4433939.051 3564660.219 3513582.357 4122973.298 4202838.811 5475102.543 0.81436964 0.709044194 0.807623308 0.809836714 0.651067298 0.641738183 0.75304038 0.767627415 1 22.38445455 1.203928824 3.063844676 1.062773993 0.738517604 0.633907538 0.061310401 0.303931403 3.395019059 0.254186265 0.016589127 15.992959 -1.203928824 -0.324256389 DCQLNAHKDHQYQFLEDAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DCQLNAHKDHQYQFLEDAVR 20 1 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 198.05 1.03E-21 1491640000 2525980 1824270 693060 773340 1679940 1475590 2007480 2282140 257200 FALSE TRUE 2192165.343 1812286.25 1028226.134 948938.6668 1646512.481 1532356.902 1812794.899 1794122.121 226794.109 9.665883089 7.990887674 4.533742691 4.184141603 7.259943779 6.756599229 7.99313045 7.910796839 1 17.79102364 4.451853075 5.405262687 6.033053609 9.314465622 0.281192082 2.12289137 0.220351657 18.34257324 0.538090964 1.611524667 28304.34277 -4.451853075 3.281412013 DCS(ph)PSSPLKLDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DCSPSSPLKLDAR 13 1 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 DCS(0.413)PS(0.345)S(0.242)PLKLDAR 69.729 0.028413 263900000 562940 509830 314460 347160 579270 465400 708630 693130 228870 TRUE FALSE 488546.0527 506480.8932 466533.9078 425987.984 567743.6603 483304.2392 639907.1717 544909.5434 201813.2493 2.420782849 2.509651348 2.311710997 2.110802861 2.813213019 2.394809264 3.170788706 2.700068233 1 17.62266137 3.254672625 24.98613827 2.506890148 2.348586348 0 0.571960382 1485.18697 2303181.633 0.16450343 0.211684511 1797.515423 -3.254672625 -0.1583038 DCSCTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DCSCTSR 7 0 B1AH88 B1AH88 TSPO Putative peripheral benzodiazepine receptor-related protein 0 92.692 0.036019 123000000 12493 15477 12462 12395 15509 16632 18023 15333 14409 FALSE TRUE 10842.0184 15375.33057 18488.66488 15209.4742 15200.40124 17271.8438 16275.13223 12054.15727 12705.58443 0.853327012 1.210123835 1.455160522 1.197070019 1.196355927 1.359389951 1.28094322 0.948729067 1 13.63317512 1.720908852 7.10573458 0.977483304 1.233586349 0.301593332 0.15524589 0.140253114 18.70159883 0.090451632 0.039984106 52.5906879 -1.720908852 0.256103045 DCSPSS(ph)PLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DCSPSSPLK 9 0 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 DCS(0.002)PS(0.138)S(0.86)PLK;DCS(0.009)PS(0.203)S(0.788)PLK 162 6.72E-05 407210000 1166030 1016010 1129020 1164140 1213340 1042630 1418040 1570270 2774600 TRUE FALSE 1011936.181 1009335.763 1675017.848 1428475.78 1189196.908 1082740.651 1280518.699 1234479.98 2446589.949 0.413610863 0.412547989 0.684633667 0.583863994 0.486063024 0.442550927 0.523389177 0.504571672 1 21.22234089 1.238208593 24.99999987 1.000000549 0.509540431 0.782859245 0.081681572 4.067227468 288433.2116 0.117595497 0.020685785 17.30647395 -1.238208593 -0.490460118 DCTSALALVPFSIKPLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DCTSALALVPFSIKPLLR 18 1 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 ; 100.35 0.00079023 177692000 395590 380380 189496 256808 318580 321241 351380 473680 206620 FALSE TRUE 343311.7792 377881.2587 281136.8994 315120.1815 312240.8813 333599.3491 317303.2217 372387.2182 182193.619 1.884323837 2.074064179 1.543066662 1.729589561 1.713786043 1.831015548 1.741571541 2.043909223 1 17.47511291 1.22885138 24.99973672 0.999998359 1.82042884 0.729919963 0.156787881 216.8109472 558213.6329 0.501509943 0.039085091 16.9375808 -1.22885138 0.820430482 DCVGPEVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DCVGPEVEK 9 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;; 111.06 0.0050843 1064190000 2790250 2261790 1256680 1366800 1767900 1587530 2212170 2557690 2639320 FALSE TRUE 2421511.393 2246932.153 1864414.651 1677152.83 1732722.249 1648603.306 1997634.094 2010747.897 2327302.596 1.040479823 0.965466268 0.801105389 0.720642358 0.744519536 0.708375142 0.858347383 0.863982149 1 21.15022737 4.353596444 3.650327854 0.810950259 1.026042805 0.472271186 0.08470983 0.208352604 5.129375995 0.023472659 0.073281701 22573.37226 -4.353596444 0.215092546 DDAT(ph)PVRDEPMDAESITFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DDATPVRDEPMDAESITFK 19 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 DDAT(1)PVRDEPMDAESITFK 188.23 2.69E-14 206590000 514960 334030 366980 400330 367590 298490 428430 505870 966020 TRUE FALSE 446906.7313 331835.7349 544452.7555 491231.0452 360275.6782 309973.1034 386880.9245 397693.6372 851818.2161 0.524650357 0.38956168 0.639165429 0.576685302 0.422949018 0.363895838 0.454182497 0.466876183 1 19.70018606 1.237837606 24.99939667 1.000000603 0.477741974 0.793874454 0.083306537 8.189718247 282975.3219 0.123222812 0.021156732 17.29169658 -1.237837606 -0.522258628 DDAVANLTQLIGGAQELHAYSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DDAVANLTQLIGGAQELHAYSVR 23 0 O75843 O75843 AP1G2 AP-1 complex subunit gamma-like 2 0 217.7 2.35E-32 302950000 313090 263060 183830 206620 282090 277950 274900 373180 318840 FALSE TRUE 271714.3632 261331.9415 272730.8029 253536.229 276476.9609 288642.9164 248240.2403 293378.3611 281147.0984 0.966449111 0.929520322 0.970064441 0.901792088 0.983388989 1.026661552 0.882955014 1.043504851 1 18.10096563 0.842049775 0.54963716 1.105611151 0.947098789 0.165211215 0.046687485 10.20882459 1.787249129 1.14410789 0.028601989 6.951039791 -0.842049775 -0.158512362 DDAYWPEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DDAYWPEAK 9 0 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 105.4 0.0072229 134210000 375300 289190 226790 261400 284310 239880 354100 419470 370710 FALSE TRUE 325703.1541 287290.2918 336466.4026 320754.8652 278652.7872 249108.3388 319759.4365 329769.6048 326885.0861 0.996384258 0.878872436 1.029310962 0.981246557 0.852448763 0.762067006 0.978201362 1.008824259 1 18.31842403 2.017010195 24.99359622 1.001583622 0.915964049 0.196640581 0.076540441 385.1833135 565959.4275 0.033089867 0.022303732 103.9944578 -2.017010195 -0.085619573 DDDDIDLFGS(ph)DDEEESEEAKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DDDDIDLFGSDDEEESEEAKR 21 1 P24534;C9JZW3 P24534 EEF1B2 Elongation factor 1-beta 1 DDDDIDLFGS(1)DDEEESEEAKR;DDDDIDLFGS(1)DDEEESEEAKR;DDDDIDLFGS(1)DDEEESEEAKR;DDDDIDLFGS(1)DDEEESEEAKR;DDDDIDLFGS(1)DDEEESEEAKR 321.7 2.95E-67 1353040000 1458580 902319 1197965 1257426 913521 766037 1155977 1404010 3181960 TRUE FALSE 1265824.957 896391.6071 1777304.881 1542943.792 895343.7194 795506.9391 1043870.528 1103773.388 2805792.314 0.451147061 0.319478959 0.633441354 0.549913757 0.319105486 0.283523102 0.372041267 0.39339098 1 21.41997679 1.237391999 24.99203989 1.000000704 0.413116745 0.742885853 0.108104707 15.88487921 339563.3925 0.167374438 0.02791659 17.27396354 -1.237391999 -0.586883959 DDDHNGHIDFITAASNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DDDHNGHIDFITAASNLR 18 0 A0AVT1;A0AVT1-2;H0Y9U5 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 67.645 0.017237 43777000 76874 66133 41007 54711 65588 74621 57657 72740 96287 FALSE TRUE 66714.90613 65698.56797 60838.12236 67133.96876 64282.92712 77491.71816 52065.43301 57185.11706 84904.06055 0.785768145 0.773797714 0.716551387 0.790703864 0.757124297 0.912697433 0.613226655 0.673526292 1 16.37354593 3.331779984 0.003344782 1.532188351 4.82E-05 0 0.110658961 568989.158 1952.144887 445981.5304 448217.5961 2146.742646 -3.331779984 -1.532140136 DDDKNNDGYIDYAEFAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DDDKNNDGYIDYAEFAK 17 1 Q8NI22-2;Q8NI22-3;Q8NI22 Q8NI22-2 MCFD2 Multiple coagulation factor deficiency protein 2 0 ; 176.42 1.01E-09 650140000 1027640 661940 788290 825390 666640 481590 861230 1077770 1055460 FALSE TRUE 891834.7703 657591.6726 1169509.681 1012807.415 653375.1683 500117.0789 777708.0472 847297.2727 930684.7212 0.958256593 0.706567603 1.256612099 1.088239005 0.702037063 0.53736466 0.835629972 0.910402044 1 19.827933 3.240371041 24.99976544 0.801155796 0.999443259 0.241704947 0.180605643 80.66891134 1113928.102 0.056981768 0.069825416 1739.286158 -3.240371041 0.198287463 DDDSNFHMDFIVAASNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DDDSNFHMDFIVAASNLR 18 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 169.43 1.83E-11 190305000 278470 221950 203737 246500 233630 214490 246390 293870 700590 FALSE TRUE 241669.4839 220491.9958 302264.8947 302471.5925 228981.2201 222741.5691 222495.1357 231028.1874 617767.0483 0.391198405 0.356917703 0.489286205 0.489620794 0.370659492 0.360559162 0.360160252 0.373972985 1 19.23670339 1.237155492 24.99897541 1.000000732 0.398292723 0.934185266 0.050128538 9.057179381 161079.1916 0.081317017 0.013345445 17.26455911 -1.237155492 -0.601708008 DDDVPLDWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DDDVPLDWR 9 0 O95340;O95340-2 O95340 PAPSS2 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 2;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ; 143.73 0.00023552 259650000 867100 853510 553660 612050 783260 696280 836710 1034180 861860 FALSE TRUE 752510.538 847903.2366 821411.8279 751025.3071 767674.6584 723066.3422 755565.993 813028.655 759971.8926 0.990182065 1.115703416 1.08084501 0.988227742 1.010135593 0.951438269 0.994202549 1.069814111 1 19.53558654 3.741759169 24.97222951 1.007036156 1.067589491 0.302090031 0.042285193 362.6302078 2831179.017 0.011758008 0.019312926 5517.713786 -3.741759169 0.060553335 DDDVPLMWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DDDVPLMWR 9 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ;;; 180.93 0.00011185 289229000 644730 461157 321299 376401 447313 413955 465978 536809 501379 FALSE TRUE 559527.297 458127.6293 476680.2711 461868.6 438412.3465 429880.1167 420787.5253 422016.5728 442106.5458 1.265593786 1.03623806 1.078202247 1.044699755 0.991644097 0.972345062 0.951778546 0.954558526 1 18.75403457 8 0.544282834 0.967417233 12.79336712 0.864348434 0.033737857 47.21755462 0.450209938 0.018214974 650.3756902 100000000 -8 11.82594989 DDEAAAVALSSLIHALDDLDMVAIVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DDEAAAVALSSLIHALDDLDMVAIVR 26 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 116.74 0.00070563 1147190000 359297 280762 223901 181587 244896 201641 311221 437893 222564 FALSE TRUE 311814.9911 278917.6559 332180.2725 222819.1037 240023.0487 209398.2597 281038.8353 344252.9896 196252.7375 1.588844034 1.421216639 1.692614721 1.135368131 1.223030322 1.066982619 1.432025046 1.754130893 1 17.58235325 3.745192352 24.95426964 1.319082865 1.552924272 0.266339296 0.223238518 965.497108 3633016.245 0.065589139 0.110269117 5561.50526 -3.745192352 0.233841406 DDEEMNTWIQAISSAISSDKHEVSASTQS(ph)TPASSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DDEEMNTWIQAISSAISSDKHEVSASTQSTPASSR 35 1 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 DDEEMNTWIQAISSAISSDKHEVS(0.079)AS(0.079)T(0.079)QS(0.363)T(0.363)PAS(0.018)S(0.018)R;DDEEMNTWIQAISSAISSDKHEVS(0.002)AS(0.002)T(0.002)QS(0.573)T(0.417)PAS(0.002)S(0.002)R 169.7 4.33E-15 41554000 45783 41550 17191.3 28192 40769 34993 39500 50502 46014 TRUE FALSE 39732.66055 41277.05531 25505.07018 34593.42449 39957.77666 36339.20335 35669.29608 39702.54031 40574.27734 0.979257381 1.017320776 0.628601958 0.852594963 0.984805628 0.895621703 0.879111063 0.978515032 1 15.30827778 3.252754703 24.57405092 0.943736809 0.862803401 0.112677262 0.10798403 457.6338079 792290.3265 0.032301027 0.041483364 1789.594773 -3.252754703 -0.080933408 DDEENYLDLFSHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DDEENYLDLFSHK 13 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ; 216.88 2.67E-11 307090000 622010 448640 423150 505100 490270 423210 613520 718590 869310 FALSE TRUE 539809.8025 445692.8543 627786.7554 619790.675 480514.5862 439491.1626 554020.9248 564925.1206 766541.1621 0.704215024 0.581433687 0.818986359 0.808554981 0.626860774 0.5733432 0.722754305 0.736979498 1 19.54800374 1.145966319 2.291623512 1.145143337 0.689592803 0.575484278 0.08270234 0.668034129 2.928061655 0.686951571 0.022978846 13.99478786 -1.145966319 -0.455550535 DDEFSVSSVLASDVIHATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DDEFSVSSVLASDVIHATR 19 0 Q9Y5S2;H0YLY0 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 0 144.17 1.38E-07 12937000 34272 34219 22283 25636 32645 27860 32725 35118 54813 FALSE TRUE 29742.86837 33994.21314 33059.13333 31457.04562 31995.42837 28931.79223 29551.33454 27608.28899 48333.06958 0.615373048 0.703332386 0.683985801 0.650838978 0.661977992 0.598592071 0.611410258 0.571209096 1 15.560723 1.232270415 24.99998562 1.000000602 0.636337967 0.890778952 0.039935692 73.62800056 292600.9676 0.100871152 0.011044793 17.0714502 -1.232270415 -0.363662635 DDEKEAEEGEDDRDS(ph)ANGEDDS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.998)ANGEDDS(0.002);DDEKEAEEGEDDRDS(0.993)ANGEDDS(0.007);DDEKEAEEGEDDRDS(1)ANGEDDS 253.39 3.96E-37 5480796000 4572809 2360042 3218990 3247172 2831235 2947914 3035224 4289228 6869406 TRUE FALSE 3968500.705 2344538.729 4775704.331 3984492.033 2774898.963 3061322.159 2740868.444 3372009.971 6057312.648 0.655158638 0.387059223 0.788419652 0.657798642 0.45810727 0.505392793 0.452489182 0.556684155 1 22.53024645 1.238960716 9.984551128 1.001835311 0.552809579 0.580119457 0.118212798 0.051468011 111.8648939 0.159879235 0.028638664 17.33647174 -1.238960716 -0.449025732 DDFNSGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DDFNSGFR 8 0 Q15056 Q15056 EIF4H Eukaryotic translation initiation factor 4H 0 175.12 0.00062339 322310000 317550 263730 117290 160620 223450 215580 299340 285210 172500 FALSE TRUE 275584.9629 261997.5403 174011.8363 197091.2259 219003.7822 223873.5021 270310.0529 224220.061 152107.2465 1.81178063 1.722452719 1.144007536 1.295738569 1.439798479 1.471813521 1.777101743 1.474091907 1 17.21472936 4.392962076 8.068270003 1.406333085 1.789551705 0.376542398 0.209298122 0.256246679 21.01304823 0.054419943 0.145207068 24715.08318 -4.392962076 0.38321862 DDFTEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DDFTEER 7 0 P21912 P21912 SDHB "Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial" 0 ; 117.16 0.012315 325130000 518610 467770 347000 623320 580150 552340 483770 646670 560430 FALSE TRUE 450074.3745 464697.1881 514810.3606 764854.3328 568606.15 573588.8772 436854.0599 508384.6529 494176.6038 0.910756137 0.940346395 1.041753812 1.547734812 1.150613254 1.160696141 0.88400393 1.028750954 1 18.91466718 2.255131171 24.87778789 0.97934532 1.133461386 0.143941872 0.176357354 470.1943177 705913.5465 0.070717231 0.054617128 179.9414315 -2.255131171 0.154116066 DDFTEFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DDFTEFGK 8 0 O75822;O75822-3;H0YGJ7;H0YLP3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 0 ; 100.15 0.014677 71218000 493600 418500 317390 352480 375190 312850 389800 500320 561450 FALSE TRUE 428369.5094 415750.8459 470880.8656 432515.9713 367724.453 324885.5419 351997.256 393330.4615 495076.0206 0.865260064 0.839771729 0.951128405 0.873635469 0.742763612 0.656233646 0.710996375 0.794484978 1 18.91729055 3.286554947 7.416581565 0.771182973 0.885018336 0.224714725 0.09276729 0.327788945 41.74215891 0.028030633 0.035983689 1934.43859 -3.286554947 0.113835363 DDGEMAAAGTFLHPFPSESYS(ph)PGMTMSV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DDGEMAAAGTFLHPFPSESYSPGMTMSV 28 0 V9GYB2;Q9BWG4-2;Q9BWG4 V9GYB2 SSBP4 Single-stranded DNA-binding protein 4 1 DDGEMAAAGTFLHPFPS(0.011)ES(0.011)Y(0.089)S(0.887)PGMT(0.001)MSV 67.614 0.0085786 11996000 27682 30104 12177 21208 24972 24233 25028 30549 26281 TRUE FALSE 24023.75356 29906.24484 18065.83793 26023.60054 24475.10606 25165.25919 22600.78841 24016.33408 23174.09012 1.036664371 1.290503519 0.779570539 1.122961049 1.056140972 1.085922211 0.975261091 1.036344209 1 14.50022508 4.273061524 24.99998505 1.017405806 1.163583615 0.254321168 0.109826984 247.5291332 179360.3232 0.024881405 0.06582264 18752.60148 -4.273061524 0.14617781 DDGLFSGDPNWFPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DDGLFSGDPNWFPK 14 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 105.86 0.0022684 14621000 58928 50301 31505 33665 36331 32244 37693 60940 76500 FALSE TRUE 51140.5155 49970.56942 46740.92338 41309.15279 35608.08418 33484.44754 34037.53866 47908.45524 67456.25715 0.758128566 0.740784792 0.692907157 0.6123843 0.527869255 0.49638757 0.504586826 0.710215142 1 16.04166465 1.28201592 3.353163995 1.039961863 0.617696031 0.625129302 0.092365322 0.211601969 3.387443706 0.216996088 0.026867958 19.14326099 -1.28201592 -0.422265832 DDGLFSGDPNWFPKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DDGLFSGDPNWFPKK 15 1 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ; 167.55 2.09E-06 1719260000 4330200 3307400 1926170 1847410 2484500 2010290 2991000 4329700 2668100 FALSE TRUE 3757953.099 3285673.472 2857672.255 2266892.676 2435063.311 2087627.157 2700933.28 3403827.349 2352680.258 1.597307193 1.396566091 1.214645401 0.963536235 1.035016681 0.887339939 1.148023949 1.446787058 1 21.16587383 4.367541589 2.152504814 1.112035553 1.590780481 0.565387746 0.152221946 0.327573707 2.721925629 0.047440841 0.225443904 23309.96324 -4.367541589 0.478744929 DDGLSAAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DDGLSAAAR 9 0 F8WBN3;B9A031;C9JQZ0;B8ZZY7;F8WBV6;P84101-4;P84101;P84101-3;P84101-2 F8WBN3 SERF2 Small EDRK-rich factor 2 0 107 0.0072599 0 448190 450830 277150 312890 382860 433570 390170 459400 446550 FALSE TRUE 388960.5559 447868.468 411180.667 383936.4567 375241.8351 450249.7185 352331.3735 361160.8851 393759.3677 0.987812831 1.137416668 1.044243517 0.975053518 0.952972464 1.143464144 0.894788549 0.917212172 1 18.58695472 2.588615104 0.570872798 0.925050487 1.060620796 0.151882417 0.076447191 1.78776006 1.455713927 0.154657555 0.082807888 387.8065183 -2.588615104 0.135570308 DDGSWEVIEGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DDGSWEVIEGYR 12 0 P00367;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 ;;;;;;; 328.77 9.89E-58 4942181000 2796331 2998207 2040854 3357903 3552468 3248551 2690202 3619336 3123553 FALSE TRUE 2426788.773 2978511.581 3027817.821 4120366.198 3481780.837 3373524.859 2429306.624 2845369.162 2754290.123 0.881094099 1.081408075 1.09930969 1.495981184 1.264130023 1.22482553 0.882008255 1.033068063 1 21.3932491 2.248945372 24.98597062 0.98074193 1.185503421 0.262807742 0.159133885 289.1791276 695772.7048 0.063602236 0.048716746 177.3966326 -2.248945372 0.20476149 DDGVFVQEVTQNS(ph)PAAR ddPTM_MDA-MB-175_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;DDGVFVQEVT(0.001)QNS(0.999)PAAR;DDGVFVQEVTQNS(1)PAAR;DDGVFVQEVTQNS(1)PAAR 324.74 4.72E-59 495190000 434873 403642 270115 342371 429102 454808 374256 517460 490479 TRUE FALSE 377403.4312 400990.4491 400743.5175 420111.5684 420563.7097 472304.7581 337960.7107 406805.2059 432495.1314 0.872618913 0.927155984 0.926585037 0.971367162 0.972412587 1.092046416 0.781420844 0.94060066 1 18.72232437 4.760699807 1.470511893 0.951372252 0.839880093 0.107465154 0.076310722 3.312666441 6.329039391 0.021491692 0.549363467 57636.79291 -4.760699807 -0.111492159 DDGYSTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DDGYSTK 7 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ; 108.46 0.016861 694100000 1331730 1028350 687650 757570 704200 879770 1095160 1305750 1306570 FALSE TRUE 1155738.506 1021594.701 1020199.84 929587.8472 690187.7977 913615.3212 988951.5518 1026525.524 1152108.783 1.003150504 0.886717223 0.885506521 0.806857704 0.599064783 0.792993973 0.858383832 0.890997047 1 20.13584551 4.656992369 1.554099792 0.826862643 1.047073396 0.22929872 0.10043348 1.546744461 4.010189097 0.0304478 0.496043959 45393.36406 -4.656992369 0.220210753 DDHNWWQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DDHNWWQGK 9 0 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8YEK3;O14936-6;O14936-2;A0A2U3TZN6;A0A2R8Y3B3;Q5JS79;A0A2R8Y6F8;O14936-3;A0A2U3TZM4;A0A2R8YFN5;O14936-4;Q5JS72;O14936-5 A0A2U3TZM1;A0A2R8Y6F8 CASK Peripheral plasma membrane protein CASK 0 ;; 98.943 0.0056723 1268680000 3680100 3272040 2260910 3369090 3306820 3061590 3132300 4092890 3800460 FALSE TRUE 3193765.461 3250545.754 3354293.638 4134093.378 3241020.752 3179371.348 2828530.028 3217657.324 3351173.948 0.953028852 0.969972256 1.000930925 1.233625422 0.967129967 0.948733607 0.844041542 0.960158253 1 21.67623514 3.014626744 24.9997728 0.935617831 1.040270669 0.243476424 0.084847716 343.3365302 586820.5067 0.026537772 0.030079656 1034.252892 -3.014626744 0.104652838 DDIIENAPTTHTEEYSGEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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" 0 237.09 4.98E-27 0 134630 87602 92025 107370 87027 78558 129930 149860 184250 FALSE TRUE 116838.3044 87026.53669 136528.5978 131749.9995 85295.33297 81580.17709 117329.4086 117813.6052 162468.1749 0.719145792 0.535652824 0.840340564 0.810928046 0.524997176 0.5021302 0.722168564 0.725148819 1 17.30979762 1.103710687 1.909561302 1.215253462 0.660920117 0.448233207 0.116019855 1.240444831 3.19347762 1.402333196 0.032942686 12.69727972 -1.103710687 -0.554333346 DDILNGSHPVSFDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DDILNGSHPVSFDK 14 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;; 192.32 3.88E-07 1641420000 2970270 2620250 1711210 2223100 2435780 2150070 3153890 3593300 3308960 FALSE TRUE 2577741.294 2603037.405 2538756.88 2727888.833 2387312.744 2232784.584 2848026.233 2824900.758 2917778.518 0.883460234 0.892129882 0.870099243 0.934919774 0.818195325 0.765234431 0.976094044 0.968168331 1 21.47643895 2.137415396 12.15901266 0.978840659 0.863998497 0.60921899 0.045525168 0.34460347 39.14748795 0.019472115 0.013127457 137.2193621 -2.137415396 -0.114842162 DDIPVFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DDIPVFLR 8 0 A0A1W2PQD2;Q9UBB4-2;Q9UBB4;B1AHE4 A0A1W2PQD2 ATXN10 Ataxin-10 0 ;;;;; 143.85 0.0013837 359330000 491165 461167 370405 439191 468918 403504 438650 547142 881187 FALSE TRUE 426256.3008 458137.5636 549534.0969 538916.0292 459587.4492 419027.06 396109.7905 430139.9412 777014.0767 0.548582469 0.589612952 0.707238277 0.693573058 0.591478923 0.539278596 0.509784575 0.553580629 1 19.56758121 1.235362381 24.99994299 1.000000562 0.591113048 0.802391945 0.063686906 44.66504553 349077.2061 0.123146827 0.017708272 17.19342431 -1.235362381 -0.408887515 DDIVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DDIVDR 6 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;;; 110.61 0.066431 3554580000 4089570 3161300 2127560 2435040 2712250 2852390 3287170 3453010 3277990 FALSE TRUE 3549122.963 3140533.212 3156455.132 2987953.049 2658281.531 2962123.289 2968380.759 2714610.683 2890469.756 1.227870645 1.086513085 1.092021505 1.033725761 0.919671111 1.02478958 1.026954443 0.939158999 1 21.46287255 6.057026128 0.55209579 0.976091083 2.15952652 0.787563385 0.039721511 7.036868139 0.540862345 0.021980887 7.343349027 1140318.388 -6.057026128 1.183435438 DDIYVFEININR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DDIYVFEININR 12 0 Q9Y4E8;Q9Y4E8-2;Q9Y4E8-3 Q9Y4E8;Q9Y4E8-2 USP15 Ubiquitin carboxyl-terminal hydrolase 15 0 89.805 0.021442 18071000 48818 41685 43635 42494 53475 29248 51524 53866 91068 FALSE TRUE 42366.57761 41411.16849 64737.03195 52142.91218 52410.95212 30373.18949 46527.21041 42347.17509 80302.04479 0.527590272 0.515692578 0.806169159 0.6493348 0.652672697 0.378236813 0.579402561 0.527348652 1 16.2931491 1.23414678 24.99405109 1.000000625 0.580361721 0.584690678 0.111359232 101.6375232 575463.3467 0.215950859 0.028043071 17.14536679 -1.23414678 -0.419638905 DDKEEEEDGTGS(ph)PQLNNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DDKEEEEDGTGSPQLNNR 18 1 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 DDKEEEEDGT(0.09)GS(0.91)PQLNNR;DDKEEEEDGT(0.03)GS(0.97)PQLNNR;DDKEEEEDGT(0.058)GS(0.942)PQLNNR;DDKEEEEDGT(0.011)GS(0.989)PQLNNR;DDKEEEEDGT(0.259)GS(0.741)PQLNNR 282.87 1.25E-39 5719880000 4700720 3316890 3991080 3520340 3186770 2518790 4870790 4678190 6846500 TRUE FALSE 4079507.942 3295101.131 5921179.637 4319687.002 3123359.512 2615689.481 4398421.535 3677795.474 6037114.57 0.675738036 0.545807288 0.980796301 0.715521786 0.517359655 0.433268153 0.728563536 0.609197561 1 22.52542775 1.234423734 24.97430228 1.000000518 0.650567232 0.354211806 0.148187791 147.1349643 888127.6191 0.277746324 0.037048117 17.15630402 -1.234423734 -0.349433285 DDKHGS(ph)YEDAVHSGALND ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DDKHGSYEDAVHSGALND 18 1 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 1 DDKHGS(1)YEDAVHSGALND 99.838 0.00058093 91934000 182950 141330 92981 102520 135530 132880 155330 177970 104000 TRUE FALSE 158772.694 140401.5939 137946.9226 125798.7329 132833.2182 137991.9796 140266.1205 139912.5005 91705.23848 1.731337234 1.531009529 1.504242559 1.371772595 1.448480156 1.504733883 1.529532258 1.525676208 1 16.48471653 1.237630896 24.99654317 0.999999399 1.511981427 0.766201118 0.089924646 11.44110885 307436.4343 0.131691737 0.022318041 17.28346825 -1.237630896 0.511982028 DDKLTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DDKLTPK 7 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 101.54 0.0081925 1744370000 2648880 1892320 1915800 2423840 1444710 1301610 2543980 3075220 3233620 FALSE TRUE 2298823.797 1879889.225 2842287.288 2974209.918 1415963.098 1351683.779 2297265.211 2417608.134 2851345.127 0.806224324 0.659299082 0.99682331 1.043090115 0.496594777 0.47405127 0.805677709 0.847883377 1 21.44321124 1.41713674 2.246797789 1.015778774 0.751317913 0.157428692 0.183006229 0.914499572 6.81290891 0.429228141 0.05352106 26.12983936 -1.41713674 -0.264460861 DDLALFCLQELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DDLALFCLQELR 12 0 Q15006;E5RGJ2;H0YAS9 Q15006 EMC2 ER membrane protein complex subunit 2 0 ; 124.42 0.00075206 23383000 36747 35213 29991 37462 33474 35816 34780 39633 60069 FALSE TRUE 31890.79084 34981.68348 44494.74791 45968.31967 32807.93289 37193.8647 31407.04095 31157.79137 52967.71125 0.602079835 0.660434115 0.840035313 0.867855503 0.619394951 0.702198827 0.592946914 0.588241225 1 15.69282555 DDLLGFALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DDLLGFALR 9 0 Q9Y617;Q9Y617-2 Q9Y617 PSAT1 Phosphoserine aminotransferase 0 ; 131.03 0.00080154 279950000 326020 289590 183271 216487 242050 232590 235860 293960 367150 FALSE TRUE 282935.631 287687.6642 271901.4686 265643.6821 237233.6786 241537.8878 212986.3335 231098.9416 323745.9453 0.873943396 0.888621675 0.839860615 0.820531303 0.732777297 0.746072318 0.657881084 0.713828065 1 18.3045026 3.598086382 1.951351912 0.753748512 0.876278758 0.182451363 0.090308722 0.491075755 3.679900804 0.028116967 0.0492122 3963.568627 -3.598086382 0.122530245 DDNGKPYVLPSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DDNGKPYVLPSVR 13 1 P00505;P00505-2 P00505 GOT2 "Aspartate aminotransferase, mitochondrial" 0 ; 105.46 0.0013234 397690000 427760 449850 368210 492840 537300 411480 447610 535540 547200 FALSE TRUE 371230.4322 446894.9057 546277.5876 604746.8546 526608.7812 427309.9019 404200.8511 421018.9386 482510.6394 0.769372532 0.926186636 1.132156564 1.25333372 1.091393097 0.885596849 0.837703499 0.872558871 1 18.88020123 2.728400179 23.34729786 0.889095604 1.046055808 0.200446701 0.132741119 449.6002827 1033115.896 0.049213454 0.043959997 535.0571588 -2.728400179 0.156960204 DDNMFQIGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DDNMFQIGK 9 0 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 ;; 131.44 0.00077488 392077000 853820 589917 394338 505250 570329 457674 665710 788130 686780 FALSE TRUE 740985.5237 586041.7964 585041.1758 619974.7348 558980.5687 475281.0149 601149.5467 619594.5327 605589.6508 1.223576927 0.967720957 0.966068649 1.023753847 0.923035207 0.784823542 0.992668131 1.023126026 1 19.20798103 4.738789481 6.170157375 0.96171668 1.229983845 0.590149129 0.069000615 0.099542735 19.85995663 0.018153789 0.112008798 54801.12592 -4.738789481 0.268267164 DDPDGKQEAKPQQAAGMLS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 118.63 4.06E-05 213790000 339630 187840 213440 158240 157120 111240 316620 352660 115720 TRUE FALSE 294747.035 186606.0667 316660.2979 194170.8105 153993.6194 115519.4748 285914.2411 277246.4034 102039.7134 2.888552163 1.828759219 3.103304461 1.902894511 1.509153782 1.132103089 2.801989848 2.71704412 1 16.63877123 3.685422472 24.98145167 1.951100084 2.529061947 0.21079079 0.669417937 657.1752023 308952.6578 0.194162619 0.28798996 4846.435883 -3.685422472 0.577961863 DDPSKPVHLTAFLGYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DDPSKPVHLTAFLGYK 16 1 P39023;H7C422;H7C3M2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ; 170.45 3.17E-09 2714800000 5935500 5013000 2155790 4911600 5364100 4135900 6107900 7766900 11580900 FALSE TRUE 5151108.636 4980069.273 3198337.255 6026853.849 5257364.905 4295010.749 5515556.798 6106008.877 10211819.2 0.50442615 0.487676992 0.313199558 0.590184152 0.514831374 0.420592126 0.540115007 0.597935467 1 23.28373656 0.814166735 1.376138924 1.958110043 0.473357413 0.831954137 0.073138618 1.391945834 1.00696113 3.890365386 0.020910983 6.518786164 -0.814166735 -1.484752631 DDREDLVYQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DDREDLVYQAK 11 1 P62258;B4DJF2;I3L3T1;I3L0W5 P62258 YWHAE 14-3-3 protein epsilon 0 ;;; 212.9 3.97E-09 4233000000 4719510 3563160 3019680 3145800 4004930 3415190 5387140 6910300 6577500 FALSE TRUE 4095814.796 3539753.367 4480007.348 3860101.971 3925239.729 3546574.569 4864695.992 5432586.121 5799915.443 0.70618526 0.610311202 0.772426321 0.665544525 0.676775337 0.611487289 0.838752916 0.936666435 1 22.46760044 1.943442718 2.433518155 0.97245743 0.675365467 0.852573773 0.050925571 0.09866275 1.074074109 0.033584651 0.014051527 87.78952875 -1.943442718 -0.297091963 DDRGPPQRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DDRGPPQRPK 10 2 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;; 113.69 0.00081843 1721700000 2722630 2412660 1344480 1612880 2178860 1908530 2759050 2962500 1221240 FALSE TRUE 2362827.547 2396811.078 1994675.025 1979109.055 2135504.949 1981952.384 2491477.756 2328992.429 1076866.398 2.19416963 2.225727426 1.852295724 1.837840848 1.98307325 1.840481221 2.313636826 2.162749653 1 20.03840784 1.234912278 24.99998364 0.999998512 2.052622599 0.786685258 0.172033774 52.05244647 356630.9016 0.327351345 0.045326956 17.17561426 -1.234912278 1.052624087 DDRLEDALLS(ph)LGS(ph)VIDISGLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DDRLEDALLSLGSVIDISGLQR 22 1 F5H5P8;F5H130;O00408-6;O00408-2 F5H5P8 PDE2A 2 DDRLEDALLS(0.92)LGS(0.54)VIDIS(0.54)GLQR 57.482 0.039198 896080000 663580 547520 388630 402720 530020 450950 654830 834710 178850 TRUE FALSE 575886.2217 543923.3051 576572.7679 494163.7312 519473.639 468298.3383 591324.6874 656213.7622 157706.5567 3.651631445 3.448958092 3.655984759 3.133438085 3.293925438 2.969428462 3.749525065 4.16097958 1 17.26688312 3.7385214 24.2275663 3.217165853 3.571868085 0.061408801 0.829513647 9.298049893 5746281.389 0.221750853 0.354485125 5476.730877 -3.7385214 0.354702232 DDRNEEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DDRNEEKR 8 2 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 150.08 0.0002784 1456440000 794838 567452 556458 835126 354587 484404 570199 908737 840792 FALSE TRUE 689798.1444 563724.3704 825562.95 1024754.122 347531.4124 503039.3353 514901.1887 714410.6643 741394.5276 0.930406307 0.7603568 1.11352717 1.38219812 0.468753679 0.678504247 0.694503627 0.963603908 1 19.49988194 3.232652416 24.99978659 0.777268363 1.030953502 0.303975272 0.213343714 218.9248014 926350.5679 0.068801569 0.080065912 1708.647266 -3.232652416 0.253685139 DDS(ph)HS(ph)AEDS(ph)EDEKEDHK ddPTM_MDA-MB-175_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 213.05 4.59E-12 475000000 405070 224370 347080 214570 277400 198010 310840 362240 778370 TRUE FALSE 351538.9732 222896.0987 514929.0489 263291.398 271880.2827 205627.5728 280694.7846 284777.795 686351.9853 0.512184682 0.324754796 0.750240489 0.383609873 0.396123692 0.299594927 0.408966231 0.414915089 1 19.38858911 1.237441249 24.9939077 1.000000677 0.433166064 0.666770448 0.12522029 16.77732362 374441.5246 0.177938654 0.029788167 17.27592259 -1.237441249 -0.566834613 DDS(ph)HS(ph)AEDS(ph)EDEKEDHKNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DDSHSAEDSEDEKEDHKNVR 20 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 DDS(1)HS(1)AEDS(1)EDEKEDHKNVR;DDS(1)HS(1)AEDS(1)EDEKEDHKNVR;DDS(1)HS(1)AEDS(1)EDEKEDHKNVR 117.08 6.31E-05 789915000 1097270 781100 646500 451740 862630 521500 941800 1140630 649220 TRUE FALSE 952262.9894 775968.9027 959149.5624 554314.4714 845465.3507 541562.4425 850464.381 896715.1509 572469.9512 1.663428775 1.355475342 1.675458354 0.968285707 1.476872889 0.946010251 1.485605278 1.56639689 1 19.12684044 3.770964255 24.94778425 1.287366383 1.543856262 0.273135089 0.240621771 1059.38577 815624.9876 0.062780954 0.108728419 5901.525056 -3.770964255 0.256489879 DDS(ph)HSAEDS(ph)EDEKEDHKNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DDSHSAEDSEDEKEDHKNVR 20 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 DDS(0.501)HS(0.501)AEDS(0.998)EDEKEDHKNVR 86.856 0.0013118 92820000 80321 52956 45762 27387 45343 31464 66622 73430 29438 TRUE FALSE 69706.37634 52608.12855 67892.65626 33605.63693 44440.76301 32674.44044 60161.00869 57727.56593 25957.87318 2.685365472 2.026673302 2.615493797 1.294622125 1.71203406 1.258748751 2.317640135 2.22389429 1 14.66388456 3.750153148 24.97804954 1.726158194 2.400927121 0.410302833 0.446816206 903.3684973 1946453.409 0.122347014 0.209630068 5625.39662 -3.750153148 0.674768927 DDS(ph)PVSHR ddPTM_MDA-MB-175_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 103.91 0.0030158 118870000 108381 94118 75023 84515 84286 95963 88983 111238 184604 TRUE FALSE 94058.17625 93499.73266 111304.3737 103705.4225 82608.8735 99654.75871 80353.44236 87450.61936 162780.3254 0.577822756 0.574392098 0.683770434 0.637088187 0.507486843 0.612203953 0.493631169 0.537230892 1 17.31256681 1.235374506 24.99995741 1.000000583 0.576003533 0.842271144 0.057391934 36.04382688 282770.544 0.103615588 0.014885864 17.19390435 -1.235374506 -0.42399705 DDSFFGETSHNYHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DDSFFGETSHNYHK 14 0 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 162.32 2.58E-06 527730000 382250 286380 250920 401600 323130 308270 328560 412780 1311900 FALSE TRUE 331734.694 284498.7509 372265.7513 492789.4181 316700.3452 320129.3464 296696.3018 324510.2093 1156808.677 0.286767121 0.245934143 0.321804079 0.425990424 0.273770721 0.276734911 0.256478282 0.280521936 1 20.14171885 1.237825364 24.99999899 1.000000813 0.295429315 0.950741997 0.050359427 3.788671526 128732.8901 0.075597595 0.012970678 17.29120917 -1.237825364 -0.704571498 DDSHS(ph)AEDS(ph)EDEKEDHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DDSHSAEDSEDEKEDHK 17 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 DDS(0.01)HS(0.99)AEDS(1)EDEKEDHK;DDSHS(1)AEDS(1)EDEKEDHK;DDS(0.002)HS(0.998)AEDS(1)EDEKEDHK;DDS(0.001)HS(0.999)AEDS(1)EDEKEDHK;DDS(0.066)HS(0.934)AEDS(1)EDEKEDHK;DDS(0.03)HS(0.97)AEDS(1)EDEKEDHK;DDS(0.004)HS(0.996)AEDS(1)EDEKEDHK;DDS(0.357)HS(0.643)AEDS(1)EDEKEDHK 209.24 5.91E-12 23024828000 9237450 5649128 8327260 6549541 5184051 3710180 8075350 8781240 15744710 TRUE FALSE 8016697.578 5612018.506 12354350.79 8036714.388 5080898.528 3852913.025 7292203.8 6903440.162 13883388.32 0.577430912 0.404225422 0.88986568 0.578872693 0.365969633 0.277519647 0.525246693 0.497244621 1 23.72685637 1.23746843 24.85568597 1.000000618 0.512478594 0.466182464 0.163242301 24.55753978 558589.454 0.246349017 0.041293877 17.27700384 -1.23746843 -0.487522024 DDSHS(ph)AEDS(ph)EDEKEDHKNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 DDSHSAEDSEDEKEDHKNVR 20 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 DDS(0.02)HS(0.98)AEDS(1)EDEKEDHKNVR;DDSHS(1)AEDS(1)EDEKEDHKNVR;DDS(0.13)HS(0.87)AEDS(1)EDEKEDHKNVR;DDSHS(1)AEDS(1)EDEKEDHKNVR;DDS(0.027)HS(0.973)AEDS(1)EDEKEDHKNVR;DDSHS(1)AEDS(1)EDEKEDHKNVR;DDS(0.004)HS(0.996)AEDS(1)EDEKEDHKNVR;DDS(0.013)HS(0.987)AEDS(1)EDEKEDHKNVR;DDS(0.002)HS(0.998)AEDS(1)EDEKEDHKNVR;DDS(0.001)HS(0.999)AEDS(1)EDEKEDHKNVR;DDS(0.46)HS(0.54)AEDS(1)EDEKEDHKNVR;DDS(0.004)HS(0.996)AEDS(1)EDEKEDHKNVR 229.87 3.64E-25 16784040000 10769624 7089577 6781256 4621241 6271227 4088917 9843490 10732340 4351785 TRUE FALSE 9346390.902 7043005.102 10060694.08 5670564.4 6146441.852 4246220.283 8888869.855 8437312.61 3837321.935 2.435654621 1.835395941 2.621800895 1.477740074 1.601752982 1.10655826 2.316425363 2.198750262 1 21.87166838 3.728896306 24.84304323 1.699312739 2.251395043 0.31950659 0.456250651 910.0415058 2339349.675 0.130292193 0.196073453 5356.687438 -3.728896306 0.552082305 DDSHSAEDS(ph)EDEKEDHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DDSHSAEDSEDEKEDHK 17 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 DDSHSAEDS(1)EDEKEDHK;DDSHSAEDS(1)EDEKEDHK;DDSHSAEDS(1)EDEKEDHK;DDSHSAEDS(1)EDEKEDHK 297.37 1.71E-46 545823000 986749 541174 826982 600259 511672 440899 789059 924298 1588822 TRUE FALSE 856347.6195 537618.9924 1226913.261 736556.9803 501490.7283 457860.6698 712536.1796 726644.0656 1400993.273 0.611243206 0.383741309 0.875745291 0.525739127 0.357953702 0.326811469 0.508593577 0.518663494 1 20.4180186 1.23824886 7.084876982 1.010063675 0.509806128 0.492274557 0.155240329 0.09716014 29.08629277 0.233230481 0.038929633 17.30807864 -1.23824886 -0.500257547 DDSHSAEDS(ph)EDEKEDHKNVR ddPTM_MDA-MB-175_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 310.88 1.36E-66 5246060000 5277490 2972070 2929030 2072427 2516660 2155333 4628050 4715310 2392380 TRUE FALSE 4580056.325 2952546.276 4345518.705 2543003.225 2466583.39 2238250.055 4179222.423 3706977.651 2109555.562 2.171100116 1.399605836 2.059921428 1.205468712 1.16924315 1.061005501 1.98109142 1.757231579 1 21.00850766 3.737307179 24.99501171 1.421545244 1.829148795 0.295052387 0.364920985 184.8059983 3685264.034 0.104058961 0.164554817 5461.440156 -3.737307179 0.407603551 DDTHKVDVINFAQNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DDTHKVDVINFAQNK 15 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 ; 178.07 4.37E-07 1094600000 2845920 2218920 1651250 1762520 2062730 1469650 2896750 3513940 2022880 FALSE TRUE 2469824.461 2204343.768 2449800.023 2162727.104 2021685.709 1526188.386 2615823.631 2762511.277 1783737.431 1.384634542 1.235800589 1.373408429 1.212469429 1.133398713 0.855612693 1.466484689 1.548720809 1 20.76647183 7.300908042 1.08777908 1.248853543 43.19612402 0.04503192 0.206667585 2522.939045 12.39904315 0.067151841 261635.5795 19994384.59 -7.300908042 41.94727048 DDTIPPEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DDTIPPEYR 9 0 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;A0A0C4DGD1;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ;; 118.06 0.0040738 110550000 911910 917670 791420 791180 797920 988210 748310 838630 975580 FALSE TRUE 791398.783 911641.7653 1174153.359 970829.5114 782042.9531 1026227.078 675739.0114 659295.5007 860248.0438 0.919965804 1.05974291 1.364900935 1.128546026 0.909090069 1.192943228 0.785516475 0.766401627 1 19.71439318 2.232210439 24.99851803 0.830376338 1.09944759 0.391426754 0.143355512 143.2172151 563791.3517 0.058690725 0.040654457 170.6909276 -2.232210439 0.269071252 DDTIYEDEDVKEAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DDTIYEDEDVKEAIR 15 1 B7Z2R2;P14927;P14927-2;E5RHG9 B7Z2R2 UQCRB Cytochrome b-c1 complex subunit 7 0 ; 185.26 3.92E-07 266430000 197411 182764 181306 245880 234270 188385 194975 301380 203374 FALSE TRUE 171322.6362 181563.4113 268986.188 301710.812 229608.4853 195632.2929 176066.3545 236932.2323 179331.3574 0.955341211 1.012446534 1.499939508 1.682420835 1.280358821 1.090898411 0.981793464 1.321198009 1 17.45226825 2.785498725 6.722240287 1.122406671 1.305673298 0.137846111 0.227087684 0.541061699 62.6992243 0.08021439 0.079634257 610.2372651 -2.785498725 0.183266627 DDWEEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DDWEEKR 7 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 130.27 0.0057394 3463680000 3369790 2470910 1859770 1930860 2085510 1811080 2862660 3278790 2518460 FALSE TRUE 2924463.714 2454678.43 2759160.993 2369291.274 2044012.431 1880753.42 2585039.674 2577646.274 2220730.528 1.316892652 1.105347271 1.242456461 1.066897242 0.92042344 0.846907536 1.164049236 1.160719971 1 21.08260291 3.656159891 5.137076929 1.035302383 1.20961787 0.416831637 0.108567483 0.269516301 12.24886423 0.03334609 0.050409669 4530.64351 -3.656159891 0.174315487 DDYPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DDYPSR 6 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ; 148.07 0.025152 2567100000 1580890 1277950 793830 1008020 943990 1106800 1295100 1496590 1507180 FALSE TRUE 1371971.381 1269555.062 1177728.843 1236906.348 925206.4459 1149379.312 1169501.401 1176555.875 1329002.897 1.032331369 0.955268845 0.886174775 0.930702521 0.696165861 0.864843346 0.879984087 0.885292182 1 20.34191282 4.532178508 1.564452359 0.870398551 1.059034824 0.320013866 0.075274576 0.870932529 2.747185344 0.021346742 0.224107328 34054.81367 -4.532178508 0.188636273 DDYVHEFCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DDYVHEFCR 9 0 Q13564-2;Q13564;Q13564-4;Q13564-3 Q13564-2 NAE1 NEDD8-activating enzyme E1 regulatory subunit 0 ; 137.95 0.0001502 675070000 982770 903100 616400 661720 942820 775020 854850 942300 1024300 FALSE TRUE 852894.4545 897167.4766 914493.1017 811973.6398 924059.7266 804835.5209 771946.7786 740796.478 903208.4209 0.944294179 0.993311683 1.012493994 0.898988119 1.023085819 0.89108505 0.854671813 0.820183316 1 19.78469941 2.602476091 6.121194613 0.874964742 0.973119047 0.325440828 0.057607716 0.2340587 10.70853109 0.019399206 0.017019893 400.3834256 -2.602476091 0.098154305 DEAAYGELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DEAAYGELR 9 0 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;;;; 137.06 0.00040751 6019130000 5560020 5175930 3835860 4329500 5102690 4884450 5368130 5887340 6821690 FALSE TRUE 4825249.27 5141928.975 5690894.726 5312579.147 5001156.452 5072357.952 4847529.579 4628378.156 6015237.579 0.802171021 0.854817271 0.946079793 0.883186919 0.831414618 0.843251473 0.805874999 0.769442286 1 22.52019029 3.236217543 24.76701421 0.836280987 0.875690151 0.000577855 0.069217663 165.0857453 1745018.295 0.02063179 0.024543197 1722.731295 -3.236217543 0.039409163 DEADVLEVDQGFDDHNLPCDVIWLDIEHADGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DEADVLEVDQGFDDHNLPCDVIWLDIEHADGK 32 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 129.03 5.79E-08 42479000 11887 6035.3 8496.2 9041.2 8794.9 8441.5 8881.9 9628.8 24692 FALSE TRUE 10316.10283 5995.653717 12604.99074 11094.14265 8619.898697 8766.249967 8020.534705 7569.756051 21772.93989 0.473803854 0.275371803 0.578929203 0.50953811 0.395899623 0.402621328 0.368371692 0.347668073 1 14.4102486 1.234516485 24.99981609 1.000000848 0.415407192 0.819712254 0.085612289 49.55381145 306286.1517 0.158113959 0.02117208 17.15996844 -1.234516485 -0.584593656 DEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR 33 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 172.52 5.84E-15 231267000 187561 119215 111677 119712 111487 121701 145042 136832 102069 FALSE TRUE 162774.3386 118431.8688 165684.3707 146894.4393 109268.6268 126382.9162 130975.8492 107571.5416 90002.5191 1.808553141 1.315872822 1.840885926 1.632114754 1.214061872 1.404215321 1.455246481 1.195205898 1 16.45767776 0.260137776 0.304506477 5.33E-13 1.702008862 0.557668005 0.179279071 16.51547854 0.91784701 11.57686123 0.418138563 1.820278235 -0.260137776 1.702008862 DEALQNIS(ph)ADDLPDSASQAAHPQDSAFSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.998)ADDLPDS(0.002)ASQAAHPQDSAFSYR;DEALQNIS(0.936)ADDLPDS(0.064)ASQAAHPQDSAFSYR 309.8 2.12E-92 1059610000 311156 285772 160700 207304 253151 252254 275898 334000 339146 TRUE FALSE 270035.9462 283894.7449 238415.0575 254375.5416 248113.7904 261958.3746 249141.4544 262576.6992 299052.5462 0.902971567 0.94931392 0.797234668 0.850604835 0.829666202 0.875961024 0.833102602 0.878028636 1 18.19003948 1.244694442 4.231214652 1.01259344 0.861872345 0.511992476 0.04178383 0.181684831 6.17472638 0.082810587 0.010712106 17.5668722 -1.244694442 -0.150721094 DEALQNISADDLPDSASQAAHPQDSAFSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DEALQNISADDLPDSASQAAHPQDSAFSYR 30 0 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 0 ; 274.96 2.53E-71 494150000 177238 161548 98988 122785 170497 175177 184316 203414 219487 FALSE TRUE 153815.5492 160486.7806 146858.9279 150665.2109 167104.4433 181916.1725 166441.0627 159915.4991 193539.4969 0.794750176 0.829219788 0.758805981 0.77847268 0.863412616 0.939943399 0.859984992 0.826268031 1 17.56226849 3.125494827 4.569558229 0.890719397 0.791101405 0.539802539 0.049721752 0.19180146 6.805771635 0.015588126 0.017915589 1335.041688 -3.125494827 -0.099617993 DEAQNEGPATESEAPLKEDGLLPKPLS(ph)SGGEEEEKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DEAQNEGPATESEAPLKEDGLLPKPLSSGGEEEEKPR 37 3 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 1 DEAQNEGPATESEAPLKEDGLLPKPLS(0.5)S(0.5)GGEEEEKPR 81.208 0.001064 95673000 67900 42967 49367 38309 36528 30455 58207 87184 70567 TRUE FALSE 58926.84296 42684.74695 73241.04632 47007.64397 35801.16427 31626.62356 52562.0941 68540.38007 62224.64965 0.947001603 0.6859781 1.177042325 0.755450521 0.575353408 0.508265193 0.844714987 1.101498851 1 15.92519858 1.858155685 4.991853115 1.048599582 0.772051036 0.262605525 0.18767091 0.299504998 10.46529842 0.105262258 0.052815973 72.13660265 -1.858155685 -0.276548546 DEASS(ph)VTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DEASSVTR 8 0 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 DEAS(0.275)S(0.723)VT(0.002)R 74.941 0.030701 0 499300 391040 374760 377920 300920 416790 379650 461550 726400 TRUE FALSE 433316.2399 388471.2325 555995.1895 463732.5121 294932.2807 432824.181 342831.6014 362851.1243 640525.8195 0.676500817 0.606488014 0.868029317 0.723987227 0.460453383 0.675732606 0.535234632 0.566489458 1 19.2888972 1.23193807 24.99699767 1.000000617 0.635188215 0.509083951 0.111313901 201.1154803 759045.1402 0.265660868 0.02828709 17.05839121 -1.23193807 -0.364812402 DEATAAVIDLNDRPIGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DEATAAVIDLNDRPIGSR 18 1 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 ; 243.29 4.03E-24 451170000 346590 293050 190657 237770 289220 281590 295260 342260 336490 FALSE TRUE 300787.2534 291124.9353 282859.3629 291759.3126 283465.0878 292422.9495 266625.7306 269070.3625 296710.5355 1.013739714 0.981174918 0.953317557 0.983312952 0.955359025 0.9855496 0.898605539 0.906844652 1 18.17869663 2.253936193 24.99854734 0.927730411 0.976842086 0.286034532 0.031658239 257.0939706 417998.5783 0.011740252 0.009060162 179.4469964 -2.253936193 0.049111675 DEDDADYKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DEDDADYKPK 10 1 P11387 P11387 TOP1 DNA topoisomerase 1 0 ;; 126.71 0.00034241 945010000 2155880 1482180 1738520 2122710 1437830 878070 1955650 2422420 2148540 FALSE TRUE 1870974.996 1472443.462 2579274.087 2604703.749 1409219.996 911849.9211 1765991.364 1904404.334 1894542.049 0.987560554 0.777202841 1.361423511 1.374846101 0.743831469 0.481303607 0.932146829 1.00520563 1 20.85341773 3.215751486 24.99957404 0.844000006 1.117266263 0.292668865 0.22561093 356.8091272 391073.6972 0.075155272 0.085275033 1643.431042 -3.215751486 0.273266257 DEDGES(ph)GGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DEDGESGGQR 10 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 DEDGES(1)GGQR 137.55 0.0043623 0 102880 86380 98367 149680 56814 88940 91497 122500 375620 TRUE FALSE 89284.14734 85812.56409 145937.6102 183667.1317 55683.51255 92361.57935 82623.63502 96304.3283 331214.6315 0.269565831 0.25908446 0.440613416 0.554526021 0.168119121 0.278857184 0.249456477 0.290761093 1 18.33740688 1.23738882 24.99761567 1.000000821 0.313889879 0.797742431 0.108574553 13.492891 287713.3399 0.165261121 0.027562949 17.27383713 -1.23738882 -0.686110942 DEDGES(ph)GGQRS(ph)EAEEGEVR ddPTM_MDA-MB-175_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 212.82 3.65E-17 1187030000 1299840 923960 975530 1346130 1051880 924120 843900 1228400 2044500 TRUE FALSE 1128062.851 917890.4459 1447299.571 1651789.391 1030949.646 959671.4944 762058.7079 965716.2194 1802801.539 0.625727694 0.509146695 0.802805822 0.916234735 0.571859755 0.532322318 0.422708042 0.53567528 1 20.78180916 DEDGESGGQRS(ph)EAEEGEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DEDGESGGQRSEAEEGEVR 19 1 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 DEDGESGGQRS(1)EAEEGEVR 143.36 8.84E-08 296060000 134010 101120 97805 139060 112660 104290 85257 126330 154190 TRUE FALSE 116300.239 100455.7361 145103.8251 170635.6984 110418.2864 108302.1038 76988.78926 99315.3126 135961.8339 0.855388867 0.738852465 1.067239394 1.255026455 0.812127075 0.79656254 0.566252948 0.730464644 1 17.0528422 3.017932196 24.98073299 0.753559442 0.976422966 0.253776206 0.168376507 328.6774419 457866.2408 0.053864558 0.061066061 1042.154711 -3.017932196 0.222863525 DEDGSTLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DEDGSTLFR 9 0 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ;; 125.49 0.0011633 345340000 554890 452983 338781 402584 476450 458731 480670 522600 491010 FALSE TRUE 481559.8806 450007.3248 502616.6248 493996.8503 466969.5772 476378.6784 434054.6974 410846.0569 432963.3572 1.112241654 1.039365843 1.160875664 1.140966879 1.078542952 1.100274817 1.00252063 0.948916462 1 18.72388541 2.178972525 3.333091751 0.971421138 1.106487844 0.734450987 0.034731665 0.115586986 2.612864545 0.01592756 0.010166057 150.9984622 -2.178972525 0.135066706 DEDLFR ddPTM_MDA-MB-175_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 ; 132.94 0.034151 1476760000 3572500 3663600 1798570 3001800 2920500 2606400 3081500 3402200 3263500 FALSE TRUE 3100385.073 3639533.57 2668364.468 3683404.57 2862387.764 2706669.895 2782656.604 2674666.006 2877692.748 1.07738572 1.264740154 0.927258294 1.279985354 0.994681509 0.940569453 0.966974882 0.929448082 1 21.45648113 3.022802485 24.49370921 0.956683916 1.132173473 0.429722185 0.098543763 160.8537617 172782.5109 0.026970027 0.030579095 1053.907476 -3.022802485 0.175489557 DEDMLYS(ph)PELAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DEDMLYSPELAQR 13 0 Q9Y2W2 Q9Y2W2 WBP11 WW domain-binding protein 11 1 DEDMLYS(1)PELAQR;DEDMLYS(1)PELAQR 216.27 2.91E-11 648340000 1057650 836960 769930 876850 839200 798270 873930 1063640 1782450 TRUE FALSE 917878.8728 831461.9547 1142270.723 1075952.194 822501.5619 828979.9634 789176.4031 836188.8633 1571730.792 0.583992423 0.529010413 0.726759779 0.684565194 0.523309441 0.527431267 0.5021066 0.532017867 1 20.5839227 1.23511976 24.99650572 1.000000597 0.574057538 0.763873879 0.074050691 52.20780753 379208.3365 0.14045582 0.019805175 17.1838218 -1.23511976 -0.425943058 DEDYKQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 119.21 0.0044074 3472210000 7141480 5628130 2626870 2540540 3549150 3881080 6418340 7196470 1006590 FALSE TRUE 6197715.324 5591158.443 3897233.118 3117408.437 3478528.859 4030387.659 5795890.375 5657560.893 887592.0769 6.982616773 6.2992433 4.390793045 3.5122085 3.919062539 4.540810766 6.529903235 6.3740552 1 19.75953726 4.336147141 4.17922781 4.589143229 6.822828099 0.271132164 1.547685404 0.322693601 9.994380981 0.409826529 1.194270105 21684.38656 -4.336147141 2.23368487 DEEFSVSSVLASDVIHASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DEEFSVSSVLASDVIHASR 19 0 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;H0Y6V3;H0Y6R0;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 0 180.1 3.44E-14 35523000 26792 24892 12595 20253 27882 22163 31935 31908 33876 FALSE TRUE 23251.36932 24728.48281 18685.98413 24851.7532 27327.20275 23015.62495 28837.94862 25084.72251 29871.21787 0.778387055 0.827836445 0.625551466 0.831963173 0.9148339 0.770495031 0.965409202 0.839762296 1 14.86646844 1.885630758 0.378677694 1.041190831 0.738061713 0.409470409 0.081709122 4.842921445 1.060323954 0.72009017 0.159114532 76.84767944 -1.885630758 -0.303129118 DEELEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DEELEER 7 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ; 128.57 0.0087129 153050000 337350 244083 211193 262544 256510 245519 297342 308540 511680 FALSE TRUE 292768.3428 242479.6027 313326.6412 322158.6279 251405.9529 254964.2748 268505.8186 242561.1221 451189.7733 0.648880715 0.537422648 0.694445353 0.714020235 0.557206674 0.565093204 0.595106171 0.537603324 1 18.78337484 1.232717171 24.99999995 1.000000639 0.603643346 0.797722553 0.062304226 87.68889123 375120.3582 0.138567478 0.015850099 17.0890205 -1.232717171 -0.396357294 DEEPSGWEEPS(ph)PQSISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DEEPSGWEEPSPQSISR 17 0 Q9UPQ9-1;Q9UPQ9;H0Y720 Q9UPQ9-1 TNRC6B Trinucleotide repeat-containing gene 6B protein 1 DEEPSGWEEPS(1)PQSISR;DEEPSGWEEPS(1)PQSISR;DEEPSGWEEPS(1)PQSISR 344.29 3.39E-73 398199000 375357 311724 257280 308590 306197 307023 294309 359618 549422 TRUE FALSE 325752.6214 309676.2645 381701.4685 378660.076 300104.2788 318834.3735 265766.9585 282716.4893 484469.9571 0.672389725 0.639206333 0.787874383 0.78159661 0.619448687 0.65810969 0.54857263 0.583558351 1 18.88604768 3.224528735 24.95970118 0.658446639 0.719305866 0.003267607 0.13040921 832.6049382 1481021.122 0.039581957 0.045102028 1676.983288 -3.224528735 0.060859227 DEESGGGSNPFQHLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DEESGGGSNPFQHLEK 16 0 Q9Y678;D6RG17 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ; 234.77 1.10E-19 460220000 455470 415420 269220 346550 392100 327600 475830 526960 636430 FALSE TRUE 395278.4855 412691.0787 399415.6925 425239.4742 384297.9771 340202.984 429684.0798 414273.7048 561191.9704 0.704355205 0.735383078 0.711727383 0.757743333 0.684788802 0.606214989 0.765663271 0.738203194 1 19.09813484 1.011973989 1.969582643 1.280695359 0.707053581 0.80415762 0.044596632 0.728874787 1.584606647 0.961095274 0.012157273 10.2795473 -1.011973989 -0.573641778 DEESHEFVIEAGALMLADNGVCCIDEFDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DEESHEFVIEAGALMLADNGVCCIDEFDK 29 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 214.19 3.01E-34 19927000 23295 21105 21221 24228 18476 14933 21239 25316 40065 FALSE TRUE 20216.50673 20966.35987 31483.54658 29729.3377 18108.36375 15507.48217 19179.24505 19902.37041 35328.56134 0.57224257 0.593467695 0.891164129 0.841510001 0.512570087 0.438950288 0.542882142 0.563350718 1 15.10854738 3.229311542 24.9955454 0.59174551 0.72712751 0.085824574 0.176800725 444.5261178 1201325.468 0.054926263 0.063133255 1695.553672 -3.229311542 0.135382 DEEVHAGLGELLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DEEVHAGLGELLR 13 0 P50454;E9PR70;E9PPV6;E9PK86;E9PMI5;E9PQ34;E9PIG2;E9PRS3;E9PNX1;E9PJH8 P50454 SERPINH1 Serpin H1 0 ;;;;; 190.37 4.47E-06 3613580000 3430960 3083090 3271010 4144890 3717880 4391430 3250930 3516850 5849650 FALSE TRUE 2977549.943 3062836.979 4852881.377 5086050.625 3643901.462 4560371.154 2935655.309 2764798.996 5158111.041 0.577255883 0.593790431 0.940825302 0.986029689 0.706441066 0.884116514 0.569133794 0.53600998 1 22.2984114 4.376124458 11.53820795 0.772743137 0.58143452 0.219303282 0.163200017 0.696263459 73.16530109 0.044320803 0.11735794 23775.21529 -4.376124458 -0.191308617 DEEVLKK ddPTM_MDA-MB-175_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 86.011 0.032694 272380000 139380 110590 100120 98395 92865 86010 120960 152120 118780 FALSE TRUE 120960.5799 109863.527 148538.3669 120737.0886 91017.16819 89318.86036 109229.3178 119590.3218 104737.9637 1.154887641 1.048937015 1.418190326 1.152753828 0.868998833 0.852784007 1.042881816 1.141804915 1 16.67642494 3.430152814 9.751257569 1.000305509 1.20708488 0.430564723 0.121629813 0.41957813 83.61566734 0.037862839 0.048940635 2692.482035 -3.430152814 0.206779371 DEFEFLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DEFEFLEK 8 0 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 ; 163.99 0.001108 51358000 263480 230370 163660 186684 202558 161653 253290 336150 277440 FALSE TRUE 228660.4504 228856.6843 242806.5234 229073.4555 198527.4921 167871.8955 228725.9748 264266.9384 244641.3593 0.934676177 0.935478306 0.992499895 0.936364383 0.811504206 0.686195891 0.934944016 1.080221837 1 17.9003088 1.988725967 24.85812641 1.034363644 0.882797646 0.355717336 0.086531594 569.6539761 1256029.422 0.04155602 0.02585954 97.43746275 -1.988725967 -0.151565998 DEFEGLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DEFEGLFK 8 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;;; 148.38 0.0012147 1138295000 2587789 1891952 1458168 1539230 1851519 1449751 2221577 2636239 2160224 FALSE TRUE 2245806.127 1879523.643 2163342.922 1888735.697 1814677.394 1505523.859 2006128.804 2072499.805 1904844.78 1.178996919 0.986706981 1.13570562 0.9915431 0.952664182 0.790365638 1.0531718 1.088015059 1 20.86124201 7.999984102 0.825355317 0.994307165 52.42944173 0.276806125 0.091406279 953.4683252 2.957155672 0.034235813 91902.6382 99996339.51 -7.999984102 51.43513457 DEFSHQVQEWNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DEFSHQVQEWNR 12 0 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 198.55 1.82E-07 207300000 226580 218280 131690 159910 198290 205220 186200 214080 238620 FALSE TRUE 196636.8789 216846.1043 195375.7245 196220.0096 194344.4169 213114.9462 168142.3527 168300.658 210410.6154 0.934538776 1.030585381 0.928544998 0.932557557 0.923643593 1.012852635 0.79911535 0.799867714 1 17.68284797 2.237597493 24.99999793 0.849681345 0.959250016 0.301369 0.065937482 26.54880135 689091.6641 0.025541554 0.0183418 172.8213898 -2.237597493 0.109568671 DEHLDFIQSHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DEHLDFIQSHLR 12 0 O43237;O43237-2;B4E2E0 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 ;; 186.13 7.03E-06 298107000 92012 68806 59806 81265 83722 76066 66726 91296 161446 FALSE TRUE 79852.38107 68354.00886 88728.38164 99717.46031 82056.096 78992.30824 60254.92279 71773.06087 142360.0378 0.560918516 0.480148853 0.623267477 0.700459636 0.576398386 0.554876983 0.423257283 0.50416579 1 17.1191847 1.235017388 24.99442496 1.000000635 0.549898881 0.773859014 0.075934652 53.09893614 374508.102 0.147174461 0.020570551 17.17977167 -1.235017388 -0.450101754 DEHLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DEHLLK 6 0 O00505;O00629 O00505;O00629 KPNA3;KPNA4 Importin subunit alpha-4;Importin subunit alpha-3 0 ;;; 121.68 0.019546 1595400000 4772260 4179140 3065710 3718390 3578910 3389700 4610680 5347900 5198700 FALSE TRUE 4141593.75 4151686.954 4548297.61 4562707.282 3507696.693 3520103.952 4163536.963 4204293.202 4584115.608 0.903466252 0.90566803 0.992186498 0.995329889 0.765185042 0.767891618 0.908253046 0.917143799 1 22.128212 5.07028159 7.536420231 0.90411599 0.901359468 0 0.083877072 256414.053 1572820.486 0.021914515 8927.290204 117565.9589 -5.07028159 -0.002756523 DEILEWESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DEILEWESR 9 0 Q13596-2;Q13596;H0YK42;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 0 ;;; 145.16 0.00022763 1292200000 1300300 1112870 868160 1072350 1078160 1066440 1243740 1383450 1512470 FALSE TRUE 1128462.06 1105559.484 1288005.08 1315843.457 1056706.725 1107466.637 1123122.286 1087609.984 1333667.52 0.84613447 0.828961842 0.965761752 0.986635303 0.792331454 0.830391848 0.842130643 0.81550309 1 20.34696762 3.222328211 24.99963627 0.848670853 0.905514587 0.103682798 0.072378841 525.6019916 809481.1666 0.022329201 0.025394685 1668.507685 -3.222328211 0.056843735 DEILPTT(ph)PISEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DEILPTTPISEQK 13 0 P23396;P23396-2;E9PPU1;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 1 DEILPT(0.021)T(0.979)PISEQK;DEILPT(0.013)T(0.987)PISEQK;DEILPT(0.022)T(0.978)PISEQK;DEILPT(0.002)T(0.998)PISEQK;DEILPT(0.001)T(0.999)PISEQK;DEILPTT(1)PISEQK;DEILPT(0.002)T(0.998)PISEQK;DEILPT(0.026)T(0.974)PISEQK 355.89 4.07E-75 52878300000 51266990 41762970 36135650 39437280 39554550 31055380 54273520 60335200 54834220 TRUE FALSE 44491927.38 41488626.3 53610971.21 48392117.19 38767491.84 32250100.56 49010082.38 47432987.01 48351780.98 0.920171429 0.858057872 1.108769318 1.000834224 0.801780018 0.666988887 1.013614833 0.980997722 1 25.52706569 DEILSLIHVFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DEILSLIHVFR 11 0 A0A1W2PPX5;A0A1W2PQR6;A0A1W2PQB7;A0A1W2PS43;Q14108;A0A1W2PRS1;A0A1W2PPU6;A0A1W2PRF6;A0A1W2PSE4 A0A1W2PPX5 SCARB2 Lysosome membrane protein 2 0 60.518 0.093137 3775800000 2028400 2446700 599920 563680 2378100 3342100 1669500 1676900 13561 FALSE TRUE 1760341.801 2430627.467 890043.3186 691672.1593 2330780.463 3470672.75 1507592.147 1318307.985 11957.83403 147.2124296 203.2665331 74.43181737 57.84259571 194.9166092 290.2425925 126.0756876 110.2463859 1 13.54566847 1.38989659 2.361769386 9.51E-18 157.4251254 0.353760854 66.05135043 0.544277749 4.301486961 157.7410262 18.93323756 24.54124493 -1.38989659 157.4251254 DEKDEHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DEKDEHGR 8 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 81.972 0.012906 225380000 1297880 829970 770400 921540 506680 632860 1026420 1294750 1851580 FALSE TRUE 1126361.87 824517.8724 1142968.017 1130789.742 496598.0593 657206.5337 926877.9464 1017877.788 1632688.322 0.689881746 0.50500629 0.700052791 0.692593759 0.304159742 0.402530308 0.567700481 0.623436681 1 20.63881798 1.187951435 2.493369446 1.155168798 0.546733456 0.5435687 0.127984644 0.533257412 3.222561972 0.742826492 0.035495127 15.4152806 -1.187951435 -0.608435342 DEKPVEAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DEKPVEAIR 9 1 Q13217;X6R9L0 Q13217 DNAJC3 DnaJ homolog subfamily C member 3 0 83.862 0.014485 310830000 418840 429400 358970 392000 438810 505320 437800 456850 459170 FALSE TRUE 363489.2328 426579.2431 532569.0927 481009.5913 430078.5395 524759.9874 395342.2234 359156.1827 404887.4457 0.897753775 1.053574883 1.315350966 1.188008165 1.062217523 1.296063864 0.976424998 0.887051912 1 18.62716138 2.053029496 11.07114499 0.934333149 1.138923258 0.326571655 0.122976523 0.592827606 121.4552191 0.050765497 0.034207419 112.9872651 -2.053029496 0.204590109 DELEVIHLIEEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DELEVIHLIEEHR 13 0 P10155-3;P10155-5;P10155-4;P10155 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 ;;;; 283.83 7.42E-33 451115000 641104 544078 405010 519243 566642 512301 606177 656607 770508 FALSE TRUE 556380.482 540503.9158 600874.1907 637145.0593 555366.9328 532009.551 547390.0478 516196.7028 679419.422 0.818905766 0.795537923 0.884393603 0.937778696 0.817413979 0.783035536 0.805673241 0.759761476 1 19.37394293 DELHIVEAEAMNYEGS(ph)PIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 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;DELHIVEAEAMNYEGS(1)PIK 289.43 1.08E-49 4635314000 3414185 2190484 2640708 2828057 2236669 2214033 2470099 3042972 8724210 TRUE FALSE 2962991.802 2176094.566 3917763.221 3470210.566 2192163.663 2299208.282 2230549.179 2392256.118 7692843.832 0.385162089 0.282872578 0.509273723 0.451095933 0.284961415 0.298876246 0.289951184 0.310971621 1 22.87508559 1.236528775 24.99998751 1.000000828 0.34899867 0.875068319 0.0769835 18.79918617 231246.5953 0.127284277 0.019979388 17.2396631 -1.236528775 -0.651002158 DELHIVEAEAMNYEGS(ph)PIKVTLATLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 DELHIVEAEAMNYEGSPIKVTLATLK 26 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 DELHIVEAEAMNY(0.015)EGS(0.985)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.011)EGS(0.809)PIKVT(0.179)LATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.081)EGS(0.902)PIKVT(0.017)LATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.023)EGS(0.953)PIKVT(0.024)LATLK;DELHIVEAEAMNY(0.134)EGS(0.694)PIKVT(0.171)LAT(0.001)LK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.085)EGS(0.881)PIKVT(0.034)LATLK 341.99 7.76E-96 11674768000 5053420.9 3289440.8 3050996.6 3533948.4 3377284.5 2754010.4 4391336.2 5532834.4 5504946.9 TRUE FALSE 4385598.524 3267832.247 4526468.761 4336385.397 3310083.146 2859958.962 3965465.091 4349680.82 4854158.349 0.903472489 0.673202646 0.932493016 0.893334145 0.681906709 0.589177105 0.816921247 0.896073121 1 22.21078974 1.56089608 2.517428792 0.992265862 0.777937386 0.298503332 0.110653827 0.36661666 4.753380087 0.141101556 0.031192093 36.38279671 -1.56089608 -0.214328476 DELHIVEAEAMNYEGSPIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DELHIVEAEAMNYEGSPIK 19 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;;;;; 274.81 2.03E-39 5530831000 3382970 2438307 2179220 2822317 2403332 1879885 2688647 3638763 5365236 FALSE TRUE 2935901.943 2422289.601 3233098.081 3463167.211 2355510.395 1952205.392 2427902.428 2860641.849 4730963.912 0.620571621 0.512007626 0.683390984 0.732021481 0.497892277 0.412644321 0.513194028 0.604663638 1 22.17370273 1.239467106 4.500261543 1.036114295 0.566996496 0.677138611 0.093208176 0.129052649 5.491848916 0.193746043 0.025337257 17.35669795 -1.239467106 -0.469117798 DELKEALDDVTLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DELKEALDDVTLPR 14 1 A0A3B3ISG5;P14735;P14735-2 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 128.06 6.92E-05 63759000 64774 49737 46430 54921 54086 47106 72096 77266 62181 FALSE TRUE 56213.95178 49410.27437 68883.7033 67391.65246 53009.79442 48918.1983 65104.14102 60743.26718 54830.03302 1.025240159 0.901153467 1.256313365 1.229101074 0.966802161 0.892178896 1.187381029 1.107846628 1 15.74267872 4.277028808 24.99999064 1.091344665 0.963196822 0.167625767 0.118746884 308.9862903 200801.5666 0.030690274 0.081195172 18924.69147 -4.277028808 -0.128147842 DELTES(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DELTESPK 8 0 Q8NC51;Q8NC51-2 Q8NC51 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 DELT(0.001)ES(0.999)PK;DELTES(1)PK;DELTES(1)PK;DELTES(1)PK 181.53 0.00024476 1426490000 3220610 2303540 2694600 3043460 2997000 2333760 3316810 3845140 7288000 TRUE FALSE 2794998.229 2288407.894 3997717.573 3734524.109 2937365.564 2423541.257 2995146.277 3022886.734 6426420.943 0.434922993 0.356093682 0.622075275 0.581120369 0.457076433 0.377121461 0.466067552 0.470384178 1 22.61558405 1.238475592 24.43652661 1.00000072 0.471648414 0.809837492 0.080618743 0.67638022 192831.9752 0.115367494 0.02061447 17.31711702 -1.238475592 -0.528352306 DENGELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DENGELR 7 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 154.01 0.0039719 268510000 581800 504260 310220 389260 360330 459670 493170 543510 579510 FALSE TRUE 504913.6559 500947.4829 460243.4296 477647.4325 353160.138 477353.8023 445342.4493 427284.6161 511000.988 0.988087436 0.98032586 0.900670332 0.93472898 0.691114394 0.934154363 0.871509957 0.8361718 1 18.96296655 4.094698306 1.840153364 0.867509846 0.992013796 0.221840895 0.080502393 0.516570431 3.352263505 0.022154983 0.071865291 12436.50376 -4.094698306 0.12450395 DENQSINHQMAQEDAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DENQSINHQMAQEDAQR 17 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;; 210.98 2.89E-12 1485900000 458784 363062 186471 391665 403653 398616 249910 499772 735797 FALSE TRUE 398154.532 360677.0218 276648.9993 480598.5245 395621.095 413951.0155 225673.7667 392899.647 648811.9169 0.613667107 0.555903818 0.426393215 0.740736278 0.609762374 0.638013891 0.347826174 0.605567865 1 19.30744079 1.248671067 5.32507976 1.020248792 0.560800158 0.60985898 0.109208675 0.098515437 7.940774488 0.162876438 0.02683372 17.72846226 -1.248671067 -0.459448633 DENWDKEIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DENWDKEIEK 10 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 ; 114.72 0.001202 709410000 2123300 1729070 1402990 1658430 1641170 1174470 2648900 2917500 2186000 FALSE TRUE 1842700.525 1717711.625 2081480.657 2035001.879 1608513.928 1219652.621 2392010.086 2293615.329 1927573.57 0.955968972 0.891126363 1.079844987 1.055732404 0.834476023 0.632739855 1.2409436 1.189897685 1 20.87835449 2.195214848 24.99999969 1.157311797 0.918673616 0.393849103 0.136854394 143.9147701 83002.92329 0.058499533 0.039440603 156.7526342 -2.195214848 -0.238638181 DEPDWESLIFLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DEPDWESLIFLAR 13 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;;;;; 254.24 1.95E-23 524188000 310748 235613.4 189315 238645.3 244620 225461.1 263608.3 327349.1 311084.9 FALSE TRUE 269681.8645 234065.6401 280868.3672 292833.3628 239752.5406 234134.7344 238043.6076 257348.0424 274308.7975 0.983132393 0.853292502 1.023913085 1.067531794 0.874024248 0.853544387 0.867794288 0.938169117 1 18.06544137 3.193821166 24.99999209 0.905062728 0.97577331 0.232898263 0.067419423 220.0250597 122947.1069 0.02154995 0.024435463 1562.504101 -3.193821166 0.070710582 DEPIHILNVAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DEPIHILNVAIK 12 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 96.64 0.0053703 242800000 397600 327460 249680 252860 340060 307070 385850 466950 428900 FALSE TRUE 345056.1526 325308.8937 370426.0831 310275.7277 333293.4713 318883.1816 348430.3264 367096.3763 378195.9306 0.912374049 0.860159688 0.979455497 0.820410011 0.881271966 0.843169256 0.92129581 0.970651312 1 18.52877431 1.771729104 2.457346898 0.993650741 0.883312086 0.488171893 0.043016475 0.218115644 2.589405131 0.034225466 0.011569044 59.11927558 -1.771729104 -0.110338655 DEPSVAAMVYPFTGDHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 DEPSVAAMVYPFTGDHK 17 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;;;;; 225.7 2.31E-15 2290500000 2202720 1813580 1329811 1618790 1761310 1406742 2259130 2612010 2190900 FALSE TRUE 1911624.971 1801666.474 1972912.048 1986361.011 1726263.377 1460860.275 2040039.92 2053451.988 1931894.298 0.989508056 0.932590606 1.021231881 1.028193423 0.893559952 0.75618023 1.055979058 1.062921502 1 20.88158473 DEQLESLFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DEQLESLFQR 10 0 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ;;; 183.72 3.81E-06 214364000 224428 190516 161062 199926 193813 193718 207941 235446 485007 FALSE TRUE 194769.2712 189264.4879 238952.1219 245322.254 189956.5005 201170.4568 187774.9138 185097.7051 427670.025 0.455419505 0.442547938 0.558730114 0.573625084 0.444166038 0.470387086 0.43906494 0.432804953 1 18.70613857 1.235654969 24.99980584 1.000000707 0.476484293 0.916353242 0.049649762 23.32000243 200604.515 0.090123264 0.013252847 17.20501159 -1.235654969 -0.523516414 DESANQEEPEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DESANQEEPEAR 12 0 P50552;K7EM16 P50552 VASP Vasodilator-stimulated phosphoprotein 0 ; 234.9 1.15E-15 607540000 376620 369460 261190 300970 346640 356930 394120 399850 422700 FALSE TRUE 326848.7128 367032.9929 387502.3576 369309.8385 339742.5422 370661.3281 355898.3031 314345.1891 372728.8875 0.876907381 0.984718398 1.039635968 0.990826981 0.911500432 0.994452913 0.954844969 0.843361488 1 18.50776711 1.97888567 24.17964552 0.907075551 0.96958775 0.074985883 0.058559839 834.1904747 955292.9999 0.0259548 0.015197974 95.25453684 -1.97888567 0.0625122 DESETEKEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DESETEKEK 9 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 79.986 0.023158 159260000 328980 192090 177730 183870 125410 138360 285690 342450 277530 FALSE TRUE 285504.4595 190828.1481 263680.8225 225620.4938 122914.5864 143682.7987 257983.8278 269219.7324 244720.7196 1.166654217 0.779779287 1.077476492 0.921950925 0.502264731 0.587129684 1.054196916 1.100110088 1 17.90077673 2.05549318 24.99912971 1.063191905 0.83452306 0.20068318 0.199146299 133.2031146 60005.89455 0.085565719 0.057688387 113.6300453 -2.05549318 -0.228668845 DETEFYLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DETEFYLGK 9 0 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ;;;; 217.81 1.29E-06 1855320000 2986960 2575300 1837790 2183810 2417490 1651730 3067800 3222360 3330060 FALSE TRUE 2592225.668 2558382.685 2726551.391 2679677.438 2369386.679 1715273.122 2770285.228 2533283.39 2936384.1 0.882795159 0.871269765 0.928540442 0.912577288 0.806906249 0.58414467 0.943434215 0.862722077 1 21.48560926 1.06439727 1.698773632 1.117490645 0.843066155 0.180435733 0.101569067 3.052654418 5.583276458 1.600035226 0.029421804 11.5983783 -1.06439727 -0.27442449 DETEFYLGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DETEFYLGKR 10 1 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ; 123.75 0.00072767 864830000 1741120 1524610 502970 584840 1291030 1065050 2045510 1933340 127216 FALSE TRUE 1511026.581 1514594.737 746207.9743 717636.8607 1265341.029 1106023.163 1847136.755 1519910.286 112176.6694 13.47006101 13.50186937 6.652078175 6.397380708 11.27989479 9.859654138 16.4663184 13.54925489 1 16.77541313 4.305384994 24.63033346 10 13.48603237 0.128503774 4.232890672 120.9472738 44575.2104 1.096895163 2.902111047 20201.56402 -4.305384994 3.486032369 DETNYGIPQR ddPTM_MDA-MB-175_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 ;;;; 220.39 1.36E-08 2041170000 2006780 1749580 1215830 1607800 1719130 1676950 1838590 2006700 2110060 FALSE TRUE 1741578.938 1738086.894 1803809.455 1972875.564 1684922.676 1741463.352 1660283.825 1577582.821 1860611.111 0.936025228 0.934148401 0.969471506 1.060337409 0.905574876 0.935963105 0.892332533 0.847884231 1 20.82734512 3.101512686 20.99660536 0.906925962 0.973100111 0.232400611 0.051341444 5.260922259 1074.067354 0.015850098 0.017972356 1263.318006 -3.101512686 0.066174148 DETSGLHLLPLPESAPALPTEEQVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DETSGLHLLPLPESAPALPTEEQVQR 26 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 63.573 0.043626 54520000 18764 17740 9105.2 17218 13660 19274 17022 19379 22968 FALSE TRUE 16284.28986 17623.46477 13508.50518 21127.61006 13388.19273 20015.48325 15371.20906 15234.95166 20252.74921 0.804053301 0.870176419 0.666996122 1.043197141 0.661055573 0.988284753 0.758969012 0.752241165 1 14.30583014 3.55171348 0.009264226 1.648963678 7.26E-07 0.018901019 0.135036032 38448.11139 270.8963173 23822.59124 24390.02333 3562.160471 -3.55171348 -1.648962952 DETVSDCSPHIANIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DETVSDCSPHIANIGR 16 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;; 220.6 1.13E-14 1333230000 1049360 965210 591910 942560 913410 882170 927760 1159680 1813460 FALSE TRUE 910684.4173 958869.472 878159.6558 1156582.654 895234.9281 916107.6507 837785.978 911691.4566 1599074.825 0.569507069 0.599640153 0.549167332 0.723282386 0.559845552 0.572898551 0.523919184 0.570136833 1 20.60880602 1.23750164 24.99992642 1.000000494 0.582847138 0.857688151 0.053310896 9.385604453 221464.3366 0.077165944 0.012961258 17.27832506 -1.23750164 -0.417153356 DEVFHIHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DEVFHIHK 8 0 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 117.04 0.001247 62828000 216760 187640 141230 183370 190230 156240 218580 246890 296050 FALSE TRUE 188114.6168 186407.3805 209529.3004 225006.9611 186444.7952 162250.6539 197382.1452 194094.4948 261051.3063 0.720604005 0.714064155 0.802636476 0.861926203 0.714207478 0.621527838 0.756104798 0.743510912 1 17.99397385 1.238425621 9.716270414 1.001242028 0.742653979 0.630034671 0.062172837 0.054338913 96.00022669 0.091670623 0.016181557 17.31512459 -1.238425621 -0.25858805 DEVLDNLLAFVCDIRPEIHENYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DEVLDNLLAFVCDIRPEIHENYR 23 1 O75348 O75348 ATP6V1G1 V-type proton ATPase subunit G 1 0 ; 106.43 0.00086747 551380000 294810 227180 215244 232201 216712 240400 268360 319950 393880 FALSE TRUE 255850.1115 225687.6396 319336.7183 284925.786 212399.8552 249648.3436 242334.4885 251531.1824 347315.9551 0.736649462 0.649804987 0.919441545 0.820364806 0.611546496 0.718793191 0.697734973 0.724214303 1 18.40588916 1.237278934 24.98574677 1.000000322 0.734016367 0.487985953 0.085362026 29.35411226 572010.3588 0.128301449 0.021249681 17.26946702 -1.237278934 -0.265983955 DEVLYVFPSDFCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DEVLYVFPSDFCR 13 0 A0A1W2PPX5;A0A1W2PQR6;A0A1W2PQB7;A0A1W2PS43;Q14108;A0A1W2PRS1;A0A1W2PRF6;Q14108-2 A0A1W2PPX5 SCARB2 Lysosome membrane protein 2 0 ;;; 209.85 8.05E-08 226695000 728010 497011 407945 593730 513276 623061 409713 738810 731950 FALSE TRUE 631801.634 493746.102 605228.5665 728545.4711 503062.8118 647030.5598 369979.0963 580821.2309 645419.7048 0.978900441 0.765000043 0.937728678 1.12879335 0.779435161 1.002495826 0.573237993 0.899912455 1 19.2998781 DEVQEVVFVPAGTHT(ph)PGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DEVQEVVFVPAGTHTPGSR 19 0 J3KS57;J3KT79;J3QR84;J3QRJ1;J3QL71;Q96FV2-2;Q96FV2 J3KS57 SCRN2 Secernin-2 1 DEVQEVVFVPAGT(0.035)HT(0.965)PGSR;DEVQEVVFVPAGTHT(1)PGSR 199.83 2.49E-15 766980000 737910 685780 482040 609400 702590 600690 746170 847810 793300 TRUE FALSE 640393.3239 681275.066 715156.1563 747773.5841 688609.8336 623798.933 673806.5482 666512.4292 699516.9777 0.915479315 0.973922132 1.022357111 1.068985611 0.984407606 0.891756673 0.963245453 0.952818088 1 19.41599955 2.986419031 24.96472241 0.95147435 0.999494058 0.164554235 0.046098325 1081.398789 1987844.571 0.015073289 0.015728913 969.2125539 -2.986419031 0.048019709 DEVQEVVFVPAGTHTPGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DEVQEVVFVPAGTHTPGSR 19 0 J3KS57;J3KT79;J3QR84;J3QRJ1;J3QL71;Q96FV2-2;Q96FV2 J3KS57 SCRN2 Secernin-2 0 82.36 0.0045682 140240000 81814 61751 57583 64179 70068 66772 80024 82533 88945 FALSE TRUE 71002.07261 61345.35362 85430.3314 78751.82286 68673.78389 69340.76205 72263.2848 64883.96022 78430.02343 0.905291998 0.782166713 1.089255462 1.004103013 0.875605806 0.884109924 0.92137273 0.827284723 1 16.25911841 3.195791988 24.99994143 0.892975 0.943848485 0.052265704 0.087786161 412.6127957 241186.7777 0.027144789 0.030779553 1569.610834 -3.195791988 0.050873485 DEVQEVVYFSAADHEPESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DEVQEVVYFSAADHEPESK 19 0 Q12765;Q12765-2;C9K052;B8ZZP4;C9J7U9 Q12765 SCRN1 Secernin-1 0 ;;; 261.78 3.58E-31 601568000 1759450 1265720 907410 1065980 1139940 985520 1661350 1867940 1571270 FALSE TRUE 1526934.225 1257405.402 1346236.511 1308027.051 1117257.424 1023433.592 1500232.533 1468495.567 1385516.251 1.102068795 0.907535658 0.971649745 0.944071967 0.806383486 0.738665888 1.082796779 1.05989054 1 20.4019922 DEVVS(ph)PLPSALQGPSGSLSAPPAASVISAPPSSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DEVVSPLPSALQGPSGSLSAPPAASVISAPPSSSSR 36 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 DEVVS(0.977)PLPS(0.023)ALQGPSGSLSAPPAASVISAPPSSSSR;DEVVS(0.979)PLPS(0.021)ALQGPSGSLSAPPAASVISAPPSSSSR 206.41 1.51E-30 377080000 127646 99052 70699 72504 93118 87386 100949 127042 113187 TRUE FALSE 110777.2577 98401.32089 104889.2729 88967.14135 91265.13398 90747.79597 91158.98152 99875.05694 99806.1618 1.109924034 0.985924307 1.050929832 0.891399286 0.914423843 0.909240415 0.913360256 1.000690289 1 16.60684127 4.750519537 1.091634722 0.944934072 1.179920605 0.530922131 0.047973134 1.551999058 1.500761145 0.015785002 0.425610055 56301.44448 -4.750519537 0.234986533 DEWLRPEDLPIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DEWLRPEDLPIK 12 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 132.47 0.00016448 202820000 280200 172050 116950 148410 156140 142930 195710 212040 227210 FALSE TRUE 243170.8601 170919.7922 173507.4112 182108.7588 153033.1195 148428.6096 176730.0743 166696.8961 200349.4926 1.213733346 0.853108186 0.866023711 0.908955428 0.763830831 0.740848443 0.882108919 0.832030538 1 17.61215933 4.738626551 8.10638699 0.850563877 1.216496606 0.707924499 0.072171432 0.050171148 42.7695891 0.01749243 0.100429353 54780.57048 -4.738626551 0.365932729 DEYLADLYHFVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DEYLADLYHFVTK 13 0 Q9Y3L3;Q6ZT62-2;Q6ZT62;Q9Y3L3-2 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 0 ; 138.87 4.41E-05 544540000 543690 503120 446200 559120 481710 447750 630940 763920 1047870 FALSE TRUE 471839.989 499814.9716 661983.8124 686076.7416 472124.9134 464975.2322 569751.5359 600561.6528 923992.0023 0.510653759 0.540929976 0.716438899 0.742513723 0.510962121 0.503224304 0.616619553 0.649964124 1 19.81752084 1.184592954 2.669940492 1.131895499 0.594586296 0.698588631 0.083541024 0.365814189 2.634099628 0.473587053 0.023428182 15.29653112 -1.184592954 -0.537309203 DFADWYLEQLNSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DFADWYLEQLNSDR 14 0 F2Z2E2;Q86VI3 F2Z2E2 IQGAP3 Ras GTPase-activating-like protein IQGAP3 0 103.34 0.0026088 21480000 22723 27389 17159 14783 25904 29072 18190 20231 25441 FALSE TRUE 19720.09798 27209.07986 25457.14979 18139.70609 25388.56108 30190.41865 16425.9366 15904.75809 22433.39396 0.879051026 1.212882897 1.134788157 0.808602841 1.131730719 1.345780255 0.732209162 0.708976899 1 14.45336028 2.208359612 24.99982618 0.788508573 1.083023437 0.357361365 0.17064967 204.7346496 169474.0959 0.069224127 0.046677281 161.5695859 -2.208359612 0.294514864 DFALDSEESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DFALDSEESR 10 0 A5YKK6-3;A5YKK6-2;A5YKK6;A5YKK6-4;H3BNB1;H3BTH2 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 107.79 0.0073002 0 145210 126310 90335 96244 118080 119170 133460 143720 139380 FALSE TRUE 126020.1306 125480.2613 134021.3082 118097.6712 115730.439 123754.547 120517.0697 112986.5964 122902.6552 1.025365403 1.020972746 1.09046715 0.960904148 0.941643115 1.006931436 0.980589635 0.919317783 1 16.90715656 3.716209127 24.40042661 0.964412983 1.043138863 0.57012741 0.031530401 398.0319202 434518.8953 0.008734457 0.01296759 5202.46452 -3.716209127 0.07872588 DFAVSTVPVSGPSHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DFAVSTVPVSGPSHLR 16 0 O95865;A0A140T971;Q5SSV3;Q5SRR8;H0Y7N1 O95865 DDAH2 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 2" 0 69.485 0.046081 670890000 442880 359780 218350 260190 417900 452560 373420 362170 439790 FALSE TRUE 384352.2859 357416.5815 323944.7903 319270.1163 409584.6076 469970.276 337205.7859 284722.7639 387798.5272 0.99111332 0.921655335 0.835343013 0.823288625 1.056178863 1.211892885 0.869538593 0.734202798 1 18.5649478 2.017852631 24.99960254 0.834242204 0.968179717 0.119879716 0.127345974 412.3292581 577395.5285 0.055236255 0.037232674 104.1963801 -2.017852631 0.133937513 DFAYGETDPLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DFAYGETDPLIR 12 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ;;; 166.97 0.00011743 475001000 1377260 1230560 856730 946070 1240330 1266800 1238220 1393130 1384770 FALSE TRUE 1195251.601 1222476.37 1271047.494 1160889.653 1215649.86 1315534.616 1118137.615 1095219.991 1221064.068 0.978860678 1.001156616 1.040934318 0.950719691 0.995565991 1.077367396 0.915707574 0.896939005 1 20.21970747 2.203372626 24.99999845 0.92817835 1.005554185 0.364454681 0.042865607 169.4447122 120384.1702 0.017201498 0.011597789 159.7249006 -2.203372626 0.077375835 DFCHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFCHSK 6 0 Q8N573-2;Q8N573-3;Q8N573-5;Q8N573-8;Q8N573;H0YC07 Q8N573-2 OXR1 Oxidation resistance protein 1 0 ; 99.171 0.039102 149360000 465630 405710 273570 303410 269910 327840 424550 500410 442620 FALSE TRUE 404095.8157 403044.8643 405869.367 372303.8778 264539.3191 340452.2169 383377.2063 393401.2157 390293.9678 1.035362698 1.032669981 1.039906841 0.953906308 0.677795049 0.872296897 0.982278072 1.007961301 1 18.57420164 3.644755665 4.906788207 0.916050081 1.035281216 0.273550443 0.093777513 0.354571517 13.97120994 0.029562935 0.044714028 4413.220882 -3.644755665 0.119231135 DFDFESANAQFNKEEIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DFDFESANAQFNKEEIDR 18 1 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;;; 348.64 2.34E-90 2323850000 2277400 1984930 1349600 1450320 1763110 1479040 2338880 2665510 1434500 FALSE TRUE 1976435.82 1971890.864 2002271.074 1779637.323 1728027.56 1535939.626 2112055.778 2095511.43 1264915.044 1.562504793 1.558911702 1.582929291 1.40692241 1.366121439 1.214263071 1.669721447 1.656642032 1 20.27060906 3.738808928 24.15832787 1.423649287 1.567194913 0.144822245 0.194960355 35.05302275 3410063.419 0.054939204 0.087940037 5480.35798 -3.738808928 0.143545625 DFDGEDSDS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFDGEDSDSPR 11 0 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 1 DFDGEDS(0.002)DS(0.998)PR;DFDGEDSDS(1)PR 248.91 2.78E-16 1288870000 1029270 1054040 848170 849500 1016620 1088130 1108310 1162040 1306660 TRUE FALSE 893249.3617 1047115.942 1258347.849 1042391.959 996391.251 1129991.065 1000826.267 913546.789 1152188.143 0.775263456 0.908806385 1.092137474 0.904706375 0.864781726 0.980734849 0.868630937 0.792879873 1 20.13594489 2.088754226 15.77398846 0.866379935 0.924983132 0.01116963 0.094879127 3.770994436 660.5817559 0.038871869 0.026207368 122.67448 -2.088754226 0.058603197 DFDPAVTEYIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DFDPAVTEYIQR 12 0 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;;;;;;; 296.25 6.44E-36 14013600000 7491680 6946540 4522660 5402060 6768470 6817180 7325420 7976780 7361150 FALSE TRUE 6501635.507 6900907.721 6709833.503 6628680.288 6633790.689 7079441.326 6615001.896 6271007.672 6490923.233 1.001650347 1.063162739 1.033725598 1.02122303 1.022010344 1.090667856 1.019115719 0.966119525 1 22.62999226 1.990581146 24.84408324 0.984233087 1.039467709 0.443660489 0.02551766 326.9571134 862413.3092 0.010521836 0.006666955 97.85457744 -1.990581146 0.055234622 DFDS(ph)S(ph)EDEKHSK ddPTM_MDA-MB-175_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 128.9 0.00013875 346070000 1656930 892350 888210 759140 881210 772840 1306910 1439060 1510370 TRUE FALSE 1437962.502 886488.0941 1317751.327 931514.3397 863675.6451 802571.6549 1180166.069 1131328.218 1331815.779 1.079700755 0.665623661 0.989439641 0.699431824 0.648494828 0.602614616 0.886133118 0.849462993 1 20.34496311 1.350960764 1.667093329 1.042388729 0.779977388 0.147945169 0.15342851 1.48019543 4.709464872 0.601394511 0.042749589 22.43679211 -1.350960764 -0.262411341 DFDWNLK ddPTM_MDA-MB-175_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 ;; 131.04 0.0081542 1046360000 2058360 1729580 1169070 1427940 1522490 1298410 1795780 2216250 2351210 FALSE TRUE 1786342.511 1718218.275 1734436.162 1752175.602 1492195.428 1348360.673 1621625.532 1742322.184 2073252.632 0.861613526 0.828754899 0.836577335 0.845133668 0.71973642 0.650360044 0.782164945 0.840381031 1 20.98346449 1.256490958 2.557226379 1.045447866 0.787481037 0.51879355 0.063647663 0.445588307 3.325790736 0.247866613 0.018634231 18.05057157 -1.256490958 -0.257966829 DFEEYPEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DFEEYPEHR 9 0 O14980 O14980 XPO1 Exportin-1 0 79.986 0.025392 338930000 349450 379530 337930 467720 434010 528590 345720 459930 507730 FALSE TRUE 303269.2971 377036.8424 501354.0783 573922.9747 425374.0501 548925.1993 312192.1276 361577.5487 447706.7378 0.677383813 0.84215137 1.119826967 1.281917215 0.950117598 1.22608206 0.697313892 0.807621414 1 18.7721945 2.224191152 24.99892142 0.823543073 1.02211141 0.168045214 0.189262243 408.7699766 711141.9873 0.080042531 0.054246527 167.5680253 -2.224191152 0.198568337 DFEPYDFTLDD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFEPYDFTLDD 11 0 Q69YN2;Q69YN2-2;Q69YN2-3 Q69YN2 CWF19L1 CWF19-like protein 1 0 ; 146.81 8.28E-05 46344000 293860 255870 186542 200066 251040 222530 244050 314120 281450 FALSE TRUE 255025.6565 254189.1731 276754.3351 245494.0431 246044.7952 231090.8731 220382.0686 246947.8825 248177.3016 1.027594606 1.024224099 1.115147652 0.989188139 0.991407327 0.931152332 0.888002517 0.995046206 1 17.92101165 3.406478057 2.666935696 0.957143459 1.052395502 0.505688228 0.041886157 0.229454239 3.305509821 0.013192498 0.018476987 2549.635264 -3.406478057 0.095252043 DFEQDILEDMYHAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DFEQDILEDMYHAIK 15 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 0 ;;; 202.03 6.11E-09 289375000 641708 535989 541973 570632 569214 461195 673628 800464 1005088 FALSE TRUE 556904.6619 532468.053 804072.9556 700202.7172 557887.755 478937.4701 608299.6602 629291.0028 886267.6416 0.628370749 0.600798255 0.90725749 0.790057861 0.62948 0.540398236 0.68636113 0.710046236 1 19.75738291 1.231224509 4.1664333 1.034363907 0.686188553 0.480925509 0.102634528 0.231562124 7.405343527 0.246658518 0.027679989 17.03038668 -1.231224509 -0.348175355 DFESHITSYK ddPTM_MDA-MB-175_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 ;;; 208.6 1.11E-07 2247760000 6439900 6142500 3164430 4736800 6107100 5376520 6973200 8319300 7257000 FALSE TRUE 5588850.898 6102149.513 4694758.932 5812362.837 5985580.658 5583358.203 6296940.137 6540282.436 6399085.727 0.87338272 0.953597088 0.73366089 0.90831145 0.935380602 0.872524364 0.984037471 1.022065138 1 22.60943436 2.164477272 3.912167156 1.010357635 0.879603547 0.493174551 0.058882605 0.181821003 5.452549856 0.025535485 0.016643882 146.0418319 -2.164477272 -0.130754088 DFFHGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DFFHGLR 7 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 ;;; 132.09 0.0034023 1545760000 2600860 2383350 1452280 1771040 2376640 2433560 2257510 2700850 2479930 FALSE TRUE 2257149.761 2367693.617 2154607.466 2173181.701 2329349.514 2527180.628 2038577.028 2123294.246 2186755.501 1.03219119 1.082742728 0.985298752 0.993792722 1.065208028 1.155675899 0.932238207 0.970979264 1 21.06036049 2.190245027 24.99999963 0.966934943 1.048717708 0.388247245 0.049994611 126.6723294 65543.24306 0.021071009 0.014206104 154.96907 -2.190245027 0.081782765 DFFLANASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFFLANASR 9 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 162.49 0.00034118 383330000 679660 558160 307650 389390 563550 541360 494260 514710 516460 FALSE TRUE 589841.209 554493.4102 456430.569 477806.951 552336.4576 562186.4695 446326.7413 404643.272 455404.6872 1.295202324 1.217583889 1.002252682 1.049191992 1.212847547 1.234476687 0.9800662 0.888535589 1 18.79678961 2.123986182 5.671667762 0.936270766 1.159246416 0.549189876 0.090619303 0.161279856 7.385625024 0.040388056 0.02693334 133.0412089 -2.123986182 0.22297565 DFFQSYGNVVELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DFFQSYGNVVELR 13 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ;; 334.9 3.35E-62 327672000 192705 170761 128654 172397 174732 156439 171027 205372 254010 FALSE TRUE 167238.546 169639.2597 190871.5047 211542.3738 171255.1751 162457.3096 154440.8279 161454.796 223981.2272 0.746663228 0.757381598 0.85217635 0.94446475 0.76459611 0.725316633 0.689525769 0.720840751 1 17.77301829 3.062583723 24.99998211 0.762959456 0.826292317 0.032701245 0.100275111 179.542454 71718.77391 0.031014643 0.035167297 1155.004623 -3.062583723 0.063332861 DFHHHHFPDMEIFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFHHHHFPDMEIFLR 15 0 O75976-2;O75976 O75976-2 CPD Carboxypeptidase D 0 ; 164.65 8.50E-07 228354000 409860 351100 287200 269230 331970 432120 283820 423020 353000 FALSE TRUE 355695.9625 348793.601 426090.8806 330362.7864 325364.4465 448743.936 256295.1801 332560.4649 311268.7421 1.142729463 1.120554536 1.368884256 1.061342633 1.045284677 1.441660775 0.823388749 1.068403023 1 18.24780118 2.22099399 24.99999917 0.979839844 1.188065314 0.382850772 0.138560533 270.9092452 385542.4594 0.05416155 0.036608657 166.338963 -2.22099399 0.208225469 DFIDNLDRPPGSSYFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFIDNLDRPPGSSYFR 16 1 Q3YEC7;G3V154;F2Z2T0;Q3YEC7-4;Q3YEC7-6;Q3YEC7-3 Q3YEC7 RABL6 Rab-like protein 6 0 ; 225.13 6.53E-15 971960000 800460 818050 550200 638670 736970 769260 750250 796770 917380 FALSE TRUE 694677.1829 812676.1757 816278.5603 783689.785 722305.7389 798853.93 677490.8705 626386.936 808928.3815 0.858762282 1.004633036 1.009086316 0.968799962 0.892916796 0.987545929 0.837516505 0.774341648 1 19.62565245 2.232157264 24.93116398 0.849182213 0.956394051 0.203783874 0.073236571 172.1440574 670226.8778 0.028831417 0.019969326 170.6700296 -2.232157264 0.107211839 DFIEDYVDILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFIEDYVDILR 11 0 Q9NRL2;Q9NRL2-2;A0A087WWN7 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 0 ; 158.79 6.84E-05 42722000 165074 129498 87737 108003 118822 118342 123303 148428 129473 FALSE TRUE 143259.0527 128647.3191 130166.9067 132526.7319 116457.6747 122894.6933 111345.094 116687.8273 114166.8494 1.25482181 1.126836028 1.140146262 1.160816231 1.02006559 1.076448145 0.975283934 1.022081522 1 16.80078427 8 0.196876977 0.935196343 2.36340275 0.800984895 0.038455127 43.75756375 0.643816539 0.2534532 18.56118615 100000000 -8 1.428206407 DFIHTASISFLTPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFIHTASISFLTPLR 15 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39 B7ZC38 SH3GLB2 Endophilin-B2 0 ; 238.43 9.07E-18 831090000 693200 774940 381540 574670 716830 722120 771770 903150 891370 FALSE TRUE 601591.8637 769849.3681 566054.0202 705157.6068 702566.4855 749900.4237 696923.8642 710018.4008 785993.2541 0.76539062 0.979460529 0.72017669 0.897154782 0.893858162 0.954079974 0.886679193 0.903339052 1 19.5841574 3.495265107 24.49606276 0.92033313 0.832656289 0.297660521 0.073284669 790.7775362 1067628.601 0.018792439 0.027253183 3127.988204 -3.495265107 -0.087676841 DFIIFEAAPQETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DFIIFEAAPQETR 13 0 P60510;H3BTA2 P60510 PPP4C Serine/threonine-protein phosphatase 4 catalytic subunit;Serine/threonine-protein phosphatase 0 ;;;; 152.85 9.54E-05 138600000 361410 303656 211127 253502 307406 299314 289058 354890 333156 FALSE TRUE 313648.7528 301661.2637 313228.7234 311063.5036 301289.222 310828.8033 261025.1997 278999.5353 293770.6772 1.067665282 1.02685968 1.066235495 1.058865053 1.025593245 1.058066129 0.88853388 0.949718801 1 18.16433087 2.255413522 24.9985794 0.944443498 1.049427665 0.729270038 0.029993414 113.4452749 168277.5991 0.010962924 0.008468619 180.058456 -2.255413522 0.104984166 DFILEHYSEDGYLYEDEIADLMDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DFILEHYSEDGYLYEDEIADLMDLR 25 0 Q8IUC4 Q8IUC4 RHPN2 Rhophilin-2 0 80.061 0.023948 12924000 8315.2 7752.4 4228.2 6537.9 9103.1 7191.7 6512.1 10883 12260 FALSE TRUE 7216.325252 7701.473974 6272.971662 8022.430121 8921.96612 7468.369353 5880.557544 8555.755142 10810.63677 0.667520832 0.712397812 0.58025922 0.742086733 0.825295153 0.690835287 0.54396033 0.791420092 1 13.40016388 1.341643852 3.446006476 1.012919035 0.685249273 0.623374201 0.078871024 0.176961009 3.02468709 0.128796719 0.020753249 21.96058232 -1.341643852 -0.327669762 DFIS(ph)RFEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DFISRFEEK 9 1 F6XZQ7 F6XZQ7 GSTM2 1 DFIS(1)RFEEK 64.297 0.083127 0 360230 371700 222820 251070 377750 460450 297600 315590 318740 TRUE FALSE 312624.6928 369258.2782 330576.4973 308079.2809 370233.5141 478163.8095 268738.7978 248103.5344 281058.9203 1.112310161 1.313810918 1.176182193 1.096137709 1.317280781 1.701293839 0.956165339 0.882745633 1 18.10051308 2.042985657 24.99996993 0.928933392 1.279663499 0.470099377 0.169945827 113.8752728 66228.09868 0.070472109 0.047512251 110.4042156 -2.042985657 0.350730108 DFKPGDLIFAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFKPGDLIFAK 11 1 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 0 ; 111.39 0.00095254 420510000 1360510 1283050 892110 1147390 1107920 772160 1511370 1666950 1381140 FALSE TRUE 1180715.156 1274621.56 1323537.38 1407922.436 1085874.56 801865.4949 1364797.57 1310485.715 1217863.203 0.969497357 1.046604871 1.086770154 1.156059591 0.891622768 0.658420004 1.12064932 1.076053297 1 20.21592066 4.860494401 15.77952728 1.008516023 0.969255553 0.005240216 0.142510239 56414.81392 7202399.847 0.036707112 1070.827147 72526.11287 -4.860494401 -0.03926047 DFLDEYIFLAVGR ddPTM_MDA-MB-175_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 ; 159.83 2.38E-06 149420000 546220 426080 362420 478090 354230 379140 595630 572200 522400 FALSE TRUE 474035.6431 423281.0524 537687.5242 586647.6416 347181.516 393725.7611 537865.8943 449839.4829 460642.4671 1.029074992 0.918892813 1.167255654 1.273542245 0.753689772 0.854731791 1.167642874 0.976548006 1 18.8132879 3.246382926 24.99944179 0.965270167 1.089460322 0.212780421 0.138223292 358.1489101 1144608.073 0.042440494 0.053760586 1763.530302 -3.246382926 0.124190155 DFLDGVYAFEYYPST(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFLDGVYAFEYYPSTPGR 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 1 DFLDGVYAFEYYPS(0.189)T(0.811)PGR;DFLDGVYAFEYYPS(0.168)T(0.832)PGR 212.72 1.80E-15 212879000 569980 672750 445590 467660 514610 558530 533910 547460 1185320 TRUE FALSE 494655.6989 668330.661 661078.8144 573849.3507 504370.2678 580017.0105 482131.4904 430389.9393 1045192.82 0.47326741 0.639432886 0.6324946 0.549036828 0.482561933 0.554937806 0.461284733 0.411780421 1 19.99533769 1.230168752 24.99825775 1.000000885 0.524451611 0.808152427 0.072638613 152.9939754 455712.8431 0.223522967 0.019942706 16.98903661 -1.230168752 -0.475549274 DFLEEANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DFLEEANR 8 0 O43159;E9PPP6 O43159 RRP8 Ribosomal RNA-processing protein 8 0 84.368 0.040715 115690000 251390 265890 187580 194800 261140 308290 257940 269990 279930 FALSE TRUE 218168.1746 264143.3511 278294.3154 239032.3173 255943.8249 320150.1158 232925.0185 212254.7396 246836.9943 0.883855255 1.070112492 1.12744168 0.968381251 1.036894108 1.297010267 0.943639016 0.859898413 1 17.91319911 2.024982575 24.99919663 0.914489767 1.066440176 0.229770531 0.111063159 272.1324415 272312.3297 0.044565425 0.03004483 105.9211227 -2.024982575 0.15195041 DFLFPHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFLFPHLR 8 0 Q9H2M9;F8WDJ2;Q9H2M9-2 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 ; 148.04 0.00052758 1188390000 1383350 1460440 932410 1046270 1508230 1563680 1515660 1617500 1452110 FALSE TRUE 1200536.793 1450846.273 1383326.595 1283841.595 1478219.174 1623835.781 1368671.526 1271610.212 1280443.21 0.93759472 1.133081313 1.080349823 1.002654069 1.154458989 1.268182586 1.068904513 0.993101609 1 20.28821184 1.824874313 4.611863905 0.997715054 1.100397674 0.172305784 0.087562339 0.359201121 12.26846932 0.050375346 0.024029927 66.81505239 -1.824874313 0.10268262 DFLLALER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFLLALER 8 0 Q9NWM3;J3QLQ8;V9GY27;B1AQP5;O75618;O75618-2 Q9NWM3 CUEDC1;DEDD CUE domain-containing protein 1;Death effector domain-containing protein 0 ; 83.005 0.043746 42568000 79211 75112 61314 67151 81255 79593 74378 77835 125493 FALSE TRUE 68743.06565 74618.58433 90965.65548 82398.66089 79638.18447 82654.99421 67164.83301 61190.59096 110657.3605 0.62122452 0.674321021 0.822047942 0.74462883 0.719682668 0.74694529 0.606962182 0.552973527 1 16.75573989 1.22303927 24.93612532 1.00000089 0.684808985 0.61387125 0.078233107 678.9859682 1090774.448 0.525493849 0.021803351 16.71241724 -1.22303927 -0.315191905 DFLLKPELLR ddPTM_MDA-MB-175_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 ; 160.18 6.80E-06 13424400000 15988700 13134200 7981100 10767500 13625000 12033300 13371000 17007400 15852900 FALSE TRUE 13875752.78 13047920.58 11840786.66 13212425.45 13353889.16 12496228.84 12074282.48 13370499.86 13978788.22 0.992629158 0.933408559 0.84705387 0.945176738 0.955296621 0.89394221 0.863757451 0.956484901 1 23.73673597 1.47318295 5.117104889 0.992331845 0.917498634 0.277068372 0.04292545 0.212030852 11.70461013 0.036586939 0.011061335 29.7291813 -1.47318295 -0.074833211 DFLLPFLEEPMDTEADLQFRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DFLLPFLEEPMDTEADLQFRPR 22 1 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;;;;; 240.21 1.17E-30 863248000 704441 639405 362551 472803 582255 584429 698634 737136 658254 FALSE TRUE 611347.337 635204.7065 537881.8763 580160.1475 570669.2647 606912.3618 630880.5822 579505.2028 580435.962 1.053255444 1.094357945 0.926685994 0.999524815 0.983173514 1.045614679 1.086908158 0.998396448 1 19.14677738 4.313986934 25 1.009832819 1.073807335 0.306648179 0.042194944 51.13098893 16944.79805 0.010846413 0.028696907 20605.6792 -4.313986934 0.063974516 DFLRPFEHIMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFLRPFEHIMK 11 1 Q9Y6D6;E5RIF2;E5RHL7;Q9Y6D5 Q9Y6D6;Q9Y6D5 ARFGEF1;ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 1;Brefeldin A-inhibited guanine nucleotide-exchange protein 2 0 ; 81.676 0.012631 882890000 1229110 1127230 729870 772790 1101910 1030910 1218990 1322070 1230930 FALSE TRUE 1066679.999 1119825.152 1082837.573 948263.7809 1079984.147 1070569.775 1100772.537 1039355.619 1085410.858 0.982743071 1.031706237 0.997629207 0.873645011 0.995000316 0.98632676 1.014152871 0.957568843 1 20.04980981 3.985361707 24.94539446 0.971070545 1.009085437 0.133784753 0.039969485 1198.980016 2043216.447 0.010404253 0.018913565 9668.558011 -3.985361707 0.038014892 DFLSCRPTEIPENDILLCESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DFLSCRPTEIPENDILLCESR 21 1 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9 Q86U86-8 PBRM1 Protein polybromo-1 0 181.69 4.50E-17 222450000 83400 72735 43316 53646 80928 68830 72727 85430 66757 FALSE TRUE 72378.47869 72257.199 64263.76248 65827.14423 79317.69113 71477.93464 65673.94673 67161.45932 58865.06351 1.229565966 1.227505666 1.091713126 1.118271863 1.347449343 1.214267519 1.115669343 1.140939214 1 15.84512403 0.91481588 1.094340563 0.765309222 1.198492195 0.425364604 0.072172859 3.466574381 2.090067299 2.078672195 0.024244323 8.218941329 -0.91481588 0.433182973 DFLSNEASLGAIGTS(ph)LPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFLSNEASLGAIGTSLPSR 19 0 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 DFLSNEASLGAIGT(0.167)S(0.831)LPS(0.002)R;DFLSNEASLGAIGT(0.083)S(0.916)LPS(0.001)R 203.06 5.49E-16 274600000 200697 266220 346560 416290 531860 558180 467750 564720 927220 TRUE FALSE 174174.3829 264471.1833 514157.5752 510815.0071 521277.0266 579653.5458 422387.677 443959.0227 817605.1079 0.213029959 0.323470561 0.628858076 0.624769833 0.637565766 0.708965172 0.516615751 0.542999326 1 19.64104468 4.30456092 3.074841642 0.649012267 0.228190088 0.613565652 0.132119207 0.169629509 3.134894193 0.033826476 0.108342594 20163.26787 -4.30456092 -0.420822179 DFLYSYFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFLYSYFK 8 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ; 111.04 0.0077015 486940000 1047110 1042780 798190 1267260 1020890 876810 1067810 1203700 1714990 FALSE TRUE 908731.7605 1035929.91 1184197.354 1555010.752 1000576.286 910541.4481 964253.9506 946298.1222 1512245.836 0.600915366 0.685027451 0.783071988 1.028279077 0.661649226 0.602112055 0.637630422 0.625756805 1 20.52826126 3.292412448 0.005144911 1.449703659 5.11E-05 0.008310166 0.156918931 234481.8796 1312.064489 184206.4676 185469.2083 1960.705866 -3.292412448 -1.449652534 DFMHVLEHECQHHHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DFMHVLEHECQHHHSK 16 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;; 226.25 1.88E-15 1721520000 1111240 1047940 319259 731190 1079260 924930 1017600 1277220 1371410 FALSE TRUE 964386.8185 1041056.013 473653.7203 897217.865 1057784.838 960512.6556 918913.3086 1004096.442 1209283.472 0.797486148 0.860886663 0.391681298 0.741941725 0.87472033 0.794282464 0.759882467 0.830323465 1 20.20572104 3.462687861 12.43610272 0.836591234 0.678747697 0.245760081 0.135626329 1.050565662 898.8553144 0.039216313 0.05103063 2901.936207 -3.462687861 -0.157843538 DFMIQGGDFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DFMIQGGDFTR 11 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ;;; 186.87 8.93E-06 1753880000 1095140 1005560 692157 962680 813030 1033630 716870 885610 1701530 FALSE TRUE 950414.4743 998954.4101 1026886.44 1181271.208 796852.2937 1073394.415 647348.0577 696229.1933 1500377.062 0.633450416 0.665802241 0.684418915 0.787316227 0.531101357 0.715416439 0.431456915 0.464036149 1 20.51689368 3.22659309 24.99790275 0.597436251 0.690227486 0.017999164 0.162959494 654.6228828 1367380.779 0.049040285 0.056029517 1684.973558 -3.22659309 0.092791235 DFNGDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DFNGDFR 7 0 A0A2R8YFH5;Q15437 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;; 109.36 0.016393 3277430000 7215700 6727200 4337160 5379000 6769200 6626700 7016000 7748300 7834600 FALSE TRUE 6262126.963 6683008.58 6434625.083 6600384.163 6634506.164 6881633.437 6335589.4 6091386.342 6908402.513 0.906450797 0.967373943 0.931420118 0.955413954 0.960353157 0.996125142 0.917084577 0.881735876 1 22.71992071 4.763177524 22.60897343 0.945368724 0.906450623 0.11670703 0.035612352 4941.611912 4538267.002 0.009240835 0.471867156 57966.55951 -4.763177524 -0.038918101 DFNHINVELSLLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DFNHINVELSLLGK 14 0 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ;; 176.75 2.18E-06 4261020000 2886890 2310410 1586680 2218240 2272670 1903660 2862000 3334060 3012260 FALSE TRUE 2505380.172 2295232.765 2354003.755 2721925.296 2227448.313 1976895.032 2584443.681 2621097.215 2656154.054 0.943236017 0.864118842 0.88624519 1.024761832 0.838599068 0.744269719 0.973002178 0.986801654 1 21.34090739 2.029998903 24.9989342 0.98869142 0.884778678 0.320815759 0.071062025 240.348019 200287.8529 0.029910601 0.020165473 107.1516599 -2.029998903 -0.103912742 DFNTNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DFNTNK 6 0 Q15717;Q15717-2;A0A494C015;A0A0A0MRX1;A0A494C147;B1APY9;A0A0R4J2E6;A0A494C1D9;Q12926;A0A494C0F8;P26378-4;P26378-5;Q12926-2;P26378-1;P26378-3;P26378;P26378-2 Q15717 ELAVL1;ELAVL2;ELAVL4 ELAV-like protein 1;ELAV-like protein;ELAV-like protein 2;ELAV-like protein 4 0 110.34 0.066976 141520000 227100 181590 109120 139830 146810 147100 199050 227950 214250 FALSE TRUE 197088.1596 180397.1233 161890.797 171580.5387 143888.7682 152759.0322 179746.1616 179204.6664 188921.6091 1.043227191 0.954878186 0.856920486 0.908210233 0.761632134 0.808584221 0.951432515 0.948566272 1 17.5274282 2.028586463 24.76985494 0.964426363 0.885083928 0.18428472 0.077329104 333.0607814 288592.0516 0.033873919 0.022837316 106.8037405 -2.028586463 -0.079342434 DFPAMVQELHQGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFPAMVQELHQGGR 14 0 P10253 P10253 GAA Lysosomal alpha-glucosidase;76 kDa lysosomal alpha-glucosidase;70 kDa lysosomal alpha-glucosidase 0 ; 102.26 0.0011842 582800000 333830 319100 214754 271677 277426 293898 290190 346870 321440 FALSE TRUE 289713.5197 317003.8111 318609.7527 333365.4152 271905.7654 305204.4462 262047.4185 272694.5498 283439.7294 1.022134477 1.118416997 1.124082899 1.176142159 0.959307173 1.076787813 0.924526068 0.962090073 1 18.11268247 3.226962769 24.99994932 0.981846756 1.111773539 0.574970518 0.053646501 152.4167478 328543.8527 0.016178067 0.018495694 1686.408449 -3.226962769 0.129926782 DFPQMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DFPQMGR 7 0 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ;; 132.53 0.0078173 662690000 749030 784000 548868 743200 823760 887550 746930 853890 1406960 FALSE TRUE 650043.7877 778849.8524 814302.4007 911954.9191 807368.7877 921694.6228 674492.8436 671292.2685 1240630.792 0.52396232 0.627785363 0.656361591 0.735073581 0.650772811 0.742924187 0.543669275 0.541089479 1 20.24264241 -1.999999994 0.030331056 1.581922573 1.25E-10 0.146646094 0.1286985 9551.349119 28.68340847 1058.01191 526.888131 0.01 1.999999994 -1.581922573 DFPYEEDSRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFPYEEDSRPR 11 1 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 0 ; 207.88 1.96E-08 497540000 514180 476160 274960 375560 436670 431170 452260 515960 477350 FALSE TRUE 446229.8102 473032.0736 407931.5757 460836.6381 427981.1213 447757.3889 408399.8948 405625.9692 420918.2268 1.060134206 1.123809908 0.969146855 1.0948365 1.016779731 1.063763364 0.970259468 0.963669291 1 18.68318046 2.236256292 24.99550888 0.974674088 1.054090218 0.422837896 0.042217216 52.57749338 570306.5333 0.01567594 0.011148863 172.288501 -2.236256292 0.07941613 DFQDYMEPEEGCQGS(ph)PQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DFQDYMEPEEGCQGSPQR 18 0 O43237;O43237-2;B4E2E0;H3BUM4 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 DFQDYMEPEEGCQGS(1)PQR;DFQDYMEPEEGCQGS(1)PQR;DFQDYMEPEEGCQGS(1)PQR;DFQDYMEPEEGCQGS(1)PQR 415.96 1.02E-147 3159540000 1746280 1727330 1190630 1348710 1725100 1580210 1688510 1913040 2444440 TRUE FALSE 1515504.673 1715983.055 1766422.65 1654955.219 1690773.885 1641001.701 1524758.56 1503951.283 2155461.088 0.703099992 0.796109503 0.819510341 0.767796379 0.784414015 0.761322814 0.70739322 0.697739937 1 21.03956509 1.230350996 24.99999881 1.000000452 0.754656604 0.779213576 0.041039795 161.3190956 491210.5731 0.123418507 0.011215971 16.99616724 -1.230350996 -0.245343847 DFQDYMEPEEGCQGS(ph)PQRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 DFQDYMEPEEGCQGSPQRR 19 1 O43237;O43237-2;B4E2E0;H3BUM4 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 DFQDYMEPEEGCQGS(1)PQRR;DFQDYMEPEEGCQGS(1)PQRR;DFQDYMEPEEGCQGS(1)PQRR;DFQDYMEPEEGCQGS(1)PQRR;DFQDYMEPEEGCQGS(1)PQRR;DFQDYMEPEEGCQGS(1)PQRR;DFQDYMEPEEGCQGS(1)PQRR;DFQDYMEPEEGCQGS(1)PQRR;DFQDYMEPEEGCQGS(1)PQRR 238.72 1.79E-24 8900750000 4469720 4357280 2640150 2941860 4219890 4010140 4249340 4956280 3086750 TRUE FALSE 3879035.177 4328656.741 3916935.371 3609854.277 4135922.445 4164412.681 3837239.661 3896418.092 2721837.931 1.425152884 1.590343308 1.43907737 1.326256143 1.519532959 1.530000237 1.409797261 1.431539346 1 21.37614974 1.204391287 3.398832891 0.904751521 1.464263587 0.796059138 0.073056633 0.169979391 2.603492686 0.26243093 0.018838015 16.00999834 -1.204391287 0.559512066 DFQEYVEPGEDFPAS(ph)PQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DFQEYVEPGEDFPASPQR 18 0 Q9Y6G9;E9PHI6;C9JGM7 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 DFQEYVEPGEDFPAS(1)PQR;DFQEYVEPGEDFPAS(1)PQR;DFQEYVEPGEDFPAS(1)PQR;DFQEYVEPGEDFPAS(1)PQR 377.42 5.81E-108 1968930000 1844690 1918230 1539960 1982210 2040880 1991960 2018560 2343950 4348790 TRUE FALSE 1600909.543 1905629.021 2284689.807 2432301.077 2000270.481 2068591.99 1822800.362 1842714.533 3834681 0.417481804 0.496945905 0.595796575 0.63429033 0.521626305 0.539443044 0.475346023 0.480539198 1 21.87067514 1.235533559 24.99993287 1.00000065 0.522073028 0.858197814 0.061290751 32.56231984 268877.658 0.110503909 0.016102487 17.20020246 -1.235533559 -0.477927622 DFQEYVEPGEDFPAS(ph)PQRR ddPTM_MDA-MB-175_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 263.87 1.66E-31 8774190000 2741289 2793267 1756766 2091614 2928060 2797550 3055230 3378420 1968414 TRUE FALSE 2379020.713 2774917.845 2606343.914 2566546.927 2869797.335 2905173.559 2758934.265 2655971.174 1735710.339 1.370632334 1.598721735 1.501600731 1.478672373 1.65338494 1.67376635 1.589513067 1.530192633 1 20.72709478 1.237891806 5.350142381 0.970211029 1.557761531 0.793969903 0.088014825 0.069130096 5.787601466 0.150292453 0.022039233 17.29385471 -1.237891806 0.587550502 ELREELGEAAAAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELREELGEAAAAFR 14 1 Q96DE0-3;Q96DE0;Q96DE0-2;Q96DE0-4 Q96DE0-3 NUDT16 U8 snoRNA-decapping enzyme 0 208.39 7.40E-09 78157000 57052 58804 34647 39334 56718 50286 55808 60987 22052 FALSE TRUE 49512.43365 58417.71265 51402.40509 48265.38588 55589.42277 52220.53496 50395.74875 47945.40465 19445.03768 2.546276045 3.00424785 2.643471611 2.482144117 2.858797379 2.685545578 2.591702293 2.465688441 1 14.24711441 1.152416119 2.441689745 0.269126418 2.696359809 0.921728174 0.153082944 0.189658419 0.991360356 1.081369971 0.03930343 14.20417842 -1.152416119 2.427233392 DFQQLLQGISEDVPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFQQLLQGISEDVPHR 16 0 G5E9X1;B3KQH5;Q9UL03-3;Q9UL03 G5E9X1 INTS6 Integrator complex subunit 6 0 ; 78.234 0.0075557 21734000 33863 26899 13570.6 21075 23069 25000 29331 29660 26887 FALSE TRUE 29387.91875 26722.2987 20133.38755 25860.40086 22609.97203 25961.76618 26486.48413 23317.43981 23708.44949 1.239554648 1.127121312 0.849207265 1.090767276 0.953667259 1.095042769 1.117174877 0.983507581 1 14.53311369 4.472510178 24.89700535 1.017281263 1.211446377 0.475117994 0.078846383 83.82654279 452615.2106 0.018825437 0.050224674 29683.16305 -4.472510178 0.194165114 DFS(ph)PLQTQTFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DFSPLQTQTFNR 12 0 Q6P4F7-3;Q6P4F7 Q6P4F7-3 ARHGAP11A Rho GTPase-activating protein 11A 1 DFS(0.958)PLQT(0.042)QT(0.001)FNR 70.638 0.049031 62603000 148850 160660 103290 111070 204230 228510 131830 128150 246510 TRUE FALSE 129179.0954 159604.6139 153241.3895 136290.1411 200166.2226 237300.9276 119045.1469 100746.1198 217367.8686 0.594287905 0.73426038 0.704986392 0.627002243 0.920863897 1.091701957 0.547666717 0.463482116 1 17.72977917 DFSAFINLVEFCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFSAFINLVEFCR 13 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 173.11 5.17E-05 279680000 270660 294947 167362 203171 262899 211588 295934 321805 231431 FALSE TRUE 234891.5952 293009.4737 248298.823 249304.0808 257667.8243 219727.9273 267234.3662 252989.505 204071.4908 1.151026017 1.435817774 1.216724698 1.221650706 1.262635085 1.076720351 1.309513471 1.239710182 1 17.63871512 1.239291013 9.032724284 0.998328033 1.243203404 0.390374179 0.093842035 0.079849189 92.58547989 0.122124699 0.021805183 17.3496618 -1.239291013 0.244875371 DFSALESQLQDTQELLQEENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DFSALESQLQDTQELLQEENR 21 0 P35579 P35579 MYH9 Myosin-9 0 ;; 345.2 3.28E-95 163397000 148755 153681 97439 114253 152545 167348 154415 179239 171572 FALSE TRUE 129096.6499 152671.4594 144560.8263 140195.8899 149509.6529 173785.9858 139439.8571 140910.1347 151288.9536 0.853311803 1.009138181 0.955527967 0.926676314 0.988239058 1.148702411 0.921679037 0.931397378 1 17.20694713 3.207456965 11.86340192 0.991508064 0.942764232 0.14962029 0.071578352 2.021236993 765.2396399 0.02258469 0.025725036 1612.34125 -3.207456965 -0.048743833 DFSAPTLEDHFNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFSAPTLEDHFNK 13 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 0 ; 202.32 9.48E-08 728740000 555430 481460 311280 361780 441890 453080 493710 559680 532810 FALSE TRUE 482028.5182 478297.2576 461816.0492 443927.6785 433097.2535 470510.2808 445830.0802 439996.7874 469821.8088 1.025981573 1.018039709 0.982960009 0.94488521 0.921833013 1.00146539 0.948934408 0.93651844 1 18.84175416 4.107630824 2.781527355 0.956377355 1.024068169 0.508693592 0.025305599 0.202169628 3.115772691 0.006698618 0.017269465 12812.4099 -4.107630824 0.067690814 DFSASYFSGEQEVT(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DFSASYFSGEQEVTPSR 17 0 P49454 P49454 CENPF Centromere protein F 1 DFSASYFSGEQEVT(1)PSR;DFSASYFSGEQEVT(0.996)PS(0.004)R;DFSASYFSGEQEVT(0.997)PS(0.003)R 322.43 1.18E-57 226049000 168456 190351 104567 120609 158310 174691 159314 180274 177224 TRUE FALSE 146194.1128 189100.5717 155135.951 147995.1168 155159.9407 181411.4758 143863.7528 141723.808 156272.7806 0.935505929 1.210067236 0.992725351 0.947030675 0.992878863 1.160864196 0.920593799 0.906900149 1 17.25370699 DFSESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DFSESR 6 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;; 130.05 0.037058 7106820000 9016100 7703920 5045630 6284480 6446420 7189220 6961780 8377530 9604440 FALSE TRUE 7824599.541 7653312.442 7485713.545 7711467.236 6318148.854 7465793.945 6286627.647 6586060.404 8469014.045 0.923909147 0.903683995 0.883894336 0.910550767 0.746031217 0.881542279 0.742309272 0.777665543 1 23.01376259 3.275182343 24.96801893 0.819090707 0.90383531 0.195862733 0.074850389 248.6710578 169537.7376 0.020981591 0.027086333 1884.440127 -3.275182343 0.084744603 DFSETYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFSETYER 8 0 O94992;Q96MH2 O94992;Q96MH2 HEXIM1;HEXIM2 Protein HEXIM1;Protein HEXIM2 0 ; 137.9 0.0016941 1493980000 1163860 1150180 712710 841400 1164830 1027750 1124530 1310020 1174250 FALSE TRUE 1010052.952 1142624.392 1057378.94 1032452.73 1141652.162 1067288.208 1015473.254 1029882.418 1035431.503 0.97548988 1.103524848 1.021196416 0.997123158 1.102585887 1.030766598 0.980724704 0.994640799 1 19.98180069 2.342619285 5.542212109 0.992164493 1.042470069 0.230400132 0.040232219 0.276818311 12.61648199 0.014456939 0.011051739 220.0996162 -2.342619285 0.050305576 DFSGGWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFSGGWR 7 0 Q9UG63;Q9UG63-2;C9JHK9;C9JZV3 Q9UG63 ABCF2 ATP-binding cassette sub-family F member 2 0 ; 148.07 0.0049053 906100000 783510 759510 457870 574260 764290 829820 694500 845500 789380 FALSE TRUE 679967.1683 754520.7288 679297.4635 704654.51 749082.1243 861743.7124 627147.4969 664696.4047 696060.3957 0.976879553 1.083987443 0.975917417 1.012346794 1.076174035 1.238030087 0.900995806 0.954940705 1 19.40885297 DFSHDDTLDVPTQVELLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DFSHDDTLDVPTQVELLIK 19 0 P42345;B1AKP8 P42345 MTOR Serine/threonine-protein kinase mTOR 0 110.33 0.00023792 38769000 51036 39379 32575 31088 35941 40931 54416 53547 56994 FALSE TRUE 44291.46329 39120.31676 48328.37896 38147.00555 35225.84442 42505.64206 49138.7447 42096.39075 50256.23425 0.881312815 0.778417192 0.96163948 0.759050218 0.700924869 0.845778493 0.977764161 0.837635199 1 15.61701495 -1.598645866 0.674531667 10 0.824983045 0.263934829 0.08440381 202.9195643 2.237540951 2728.345933 0.037610708 0.025197307 1.598645866 -9.175016955 DFSMADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DFSMADK 7 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 86.833 0.046031 181680000 459250 407180 305930 404570 454590 347330 501410 561510 624590 FALSE TRUE 398558.9489 404505.2078 453878.7713 496433.802 445544.5484 360692.0099 452783.3354 441435.4562 550751.6817 0.723663608 0.734460232 0.824107826 0.901375009 0.808975375 0.654908595 0.822118843 0.801514495 1 19.07104247 1.14006618 2.559088337 1.096581595 0.78266374 0.507244818 0.067021374 0.70647434 4.021745438 0.547219295 0.01844736 13.80594632 -1.14006618 -0.313917856 DFSNSPLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DFSNSPLHR 9 0 O95758-1;O95758-6;O95758;O95758-5;O95758-4;O95758-2;O95758-7 O95758-1 PTBP3 Polypyrimidine tract-binding protein 3 0 ;;; 166.19 6.09E-05 1857020000 1181140 1192130 381917 756617 1177020 1280390 1108910 1303580 1231530 FALSE TRUE 1025049.356 1184298.82 566613.3386 928418.454 1153599.605 1329647.432 1001368.079 1024819.561 1085939.926 0.943928233 1.090574893 0.521772268 0.85494458 1.062305176 1.224420799 0.922121063 0.943716624 1 20.05051287 3.249730005 22.78242408 1.021229235 0.846143168 0.229278548 0.161196258 121.029607 246861.8844 0.048378799 0.06173252 1777.174221 -3.249730005 -0.175086067 DFSSVFQFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFSSVFQFLR 10 0 P31937 P31937 HIBADH "3-hydroxyisobutyrate dehydrogenase, mitochondrial" 0 ; 217.64 1.66E-08 237030000 284600 270690 210792 316030 352980 322950 272270 352500 350260 FALSE TRUE 246989.3889 268911.8196 312731.7163 387789.4417 345956.3886 335374.0955 245865.2973 277120.6182 308852.6618 0.799699726 0.870679948 1.012559563 1.255580701 1.120134068 1.085870828 0.796060153 0.897258313 1 18.23655924 2.24974781 24.99895625 0.893427592 1.031478584 0.163049093 0.134093026 389.5739582 870544.1703 0.055370395 0.042486787 177.7247083 -2.24974781 0.138050992 DFSVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFSVDR 6 0 A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7;B4DSP0;A0A087WZG9;Q86TG7-2 A0A087WXK2;B4DSP0 PEG10 Retrotransposon-derived protein PEG10 0 ; 126.16 0.040975 808110000 1104640 867780 503080 677890 867150 837390 879730 950000 927780 FALSE TRUE 958659.0252 862079.496 746371.1707 831815.2854 849895.4116 869604.9352 794413.92 746849.8929 818098.9053 1.171813113 1.053759503 0.912323884 1.016766164 1.038866335 1.062958194 0.971048751 0.912909048 1 19.64191574 4.605158294 3.384613963 0.985538052 1.174209072 0.588142227 0.048820633 0.199197056 3.720851762 0.013459508 0.077227787 40286.38454 -4.605158294 0.188671019 DFSWSPGGNIIAFWVPEDKDIPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DFSWSPGGNIIAFWVPEDKDIPAR 24 1 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 161.16 1.79E-11 193630000 257750 239570 152270 140180 187540 190520 278610 315260 92800 FALSE TRUE 223687.6844 237996.2489 225908.2813 172010.0115 183808.3209 197849.4277 251590.4451 247844.1024 81829.28972 2.733589467 2.908448182 2.760726411 2.102059203 2.246241188 2.417831419 3.074576914 3.028794497 1 16.32032971 3.965991334 20.82756561 2.435354062 2.824411205 0.115447065 0.575758985 212.817436 130334.8638 0.15582594 0.270388973 9246.797231 -3.965991334 0.389057142 DFSYNYFGFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DFSYNYFGFK 10 0 P23921 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ;; 152.97 3.97E-05 690310000 687697 705978 457415 664947 745954 519412 661322 894818 876585 FALSE TRUE 596816.099 701340.384 678622.424 815933.3794 731110.9748 539394.1157 597187.0942 703468.1342 772956.1199 0.772121578 0.907348252 0.877957243 1.055601163 0.945863492 0.697832777 0.772601547 0.910100995 1 19.56002699 4.000575922 0.003180366 1.756089513 8.33E-05 0.009059941 0.108818254 1345039.274 1996.606773 547139.7139 555274.0219 10013.26989 -4.000575922 -1.756006214 DFT(ph)PVCTTELGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFTPVCTTELGR 12 0 P30041 P30041 PRDX6 Peroxiredoxin-6 1 DFT(1)PVCTTELGR;DFT(1)PVCTTELGR 183 0.00018967 103440000 322140 308050 231860 201372 413510 338700 334050 361300 361730 TRUE FALSE 279568.3828 306026.3993 343988.2715 247096.5904 405281.96 351730.0082 301653.8824 284038.8066 318966.6915 0.876481433 0.959430585 1.078445746 0.77467835 1.270609035 1.102717047 0.945722204 0.890496764 1 18.28304625 4.632987548 3.693674465 1.00024667 0.874419757 0.090343409 0.1316205 0.671450748 14.76002139 0.032997817 0.184359817 42952.41114 -4.632987548 -0.125826913 DFTEVLS(ph)PNMYNSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DFTEVLSPNMYNSK 14 0 B7ZLP8;A2RTX5-2;A2RTX5 B7ZLP8 TARSL2 "Probable threonine--tRNA ligase 2, cytoplasmic" 1 DFTEVLS(1)PNMYNSK 168.41 3.67E-06 60651000 58411 50709 36239 46467 51924 41310 66820 75966 60916 TRUE FALSE 50691.83836 50375.88924 53764.30161 57018.04255 50890.81399 42899.22243 60339.80668 59721.26207 53714.57988 0.943725865 0.937843866 1.000925666 1.061500298 0.947430178 0.798651363 1.123341313 1.111825918 1 15.71302612 2.18462542 24.99998774 1.087228329 0.955358773 0.409930021 0.072970877 92.40189936 42829.20359 0.03068979 0.02069107 152.9767465 -2.18462542 -0.131869556 DFTNEAPPAPLPDAS(ph)ASPLSPHRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DFTNEAPPAPLPDASASPLSPHRR 24 1 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 DFTNEAPPAPLPDAS(0.333)AS(0.333)PLS(0.333)PHRR 40.937 0.09621 627410000 245640 232370 175660 226720 263290 252070 238630 298020 235980 TRUE FALSE 213178.0516 230843.5462 260609.7635 278200.2412 258051.0441 261767.296 215487.6993 234290.7422 208082.7132 1.024487082 1.109383584 1.252433513 1.336969501 1.240136867 1.257996361 1.035586743 1.125950054 1 17.66679759 2.23454171 24.98508108 1.068106558 1.20923383 0.370974026 0.091079187 123.3859033 767063.757 0.039031869 0.027413299 171.6096519 -2.23454171 0.141127272 DFTNEAPPAPLPDASASPLS(ph)PHRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DFTNEAPPAPLPDASASPLSPHRR 24 1 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 DFTNEAPPAPLPDAS(0.073)AS(0.036)PLS(0.891)PHRR;DFTNEAPPAPLPDASASPLS(1)PHRR;DFTNEAPPAPLPDASAS(0.003)PLS(0.997)PHRR 283.77 1.21E-52 1856170000 636450 531260 405510 520800 595760 632440 616500 706670 640890 TRUE FALSE 552341.5199 527770.1181 601615.9923 639055.5999 583905.5416 656770.376 556711.9249 555554.1198 565124.7143 0.97737987 0.933900261 1.06457208 1.130822248 1.033233067 1.162168915 0.985113393 0.983064633 1 19.10820976 7.167330421 9.021671545 1.029744212 0.150537705 0 0.071462439 0 0 0.016897953 0 14700442.94 -7.167330421 -0.879206508 DFTPAELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DFTPAELR 8 0 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 0 ;;;;; 120.46 0.0034852 1143830000 2704750 2584250 1725430 2364340 3235520 3200130 2123390 3464060 3321310 FALSE TRUE 2347310.435 2567273.892 2559853.719 2901199.534 3171139.482 3323241.072 1917463.965 2723297.726 2928668.515 0.801494065 0.876601049 0.874067415 0.990620659 1.08279222 1.134727626 0.654722088 0.929875714 1 21.48181348 3.948130961 3.435900368 0.953932443 0.84269642 0.151404766 0.127361419 0.559650679 13.22593057 0.036741028 0.074061214 8874.235727 -3.948130961 -0.111236023 DFTPVCTTELGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DFTPVCTTELGR 12 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;;; 186.95 2.59E-05 4703310000 1714040 1646170 911256 1055670 1497420 1476980 1613380 1702600 1697330 FALSE TRUE 1487525.271 1635356.201 1351942.45 1295376.008 1467624.272 1533800.376 1456914.656 1338512.24 1496673.581 0.993887572 1.092660565 0.903298132 0.865503357 0.980590752 1.024806207 0.973435139 0.894324759 1 20.51332818 4.236225984 24.9999999 0.946169284 1.04327407 0.339194239 0.054691691 64.31862476 688778.2844 0.014380099 0.032424182 17227.64779 -4.236225984 0.097104787 DFTSEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 102.98 0.019726 864240000 2645150 2674170 1548620 1997850 2561230 2685050 2538800 2769750 2640550 FALSE TRUE 2295586.726 2656603.201 2297537.812 2451492.378 2510266.534 2788345.611 2292587.567 2177460.517 2328387.187 0.985912798 1.140962816 0.986750754 1.052871443 1.078113875 1.197543788 0.984624713 0.935179737 1 21.15089955 2.023827606 24.99963803 0.962042501 1.073638934 0.349757117 0.06475942 216.5430021 227193.3948 0.025518026 0.01720326 105.6398088 -2.023827606 0.111596433 DFTVSALHGDMDQK ddPTM_MDA-MB-175_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 ;;; 256.57 2.56E-24 1796840000 3733530 2611130 1522700 2338740 2577670 2336680 3516050 3985540 3896600 FALSE TRUE 3240134.551 2593977.315 2259082.813 2869786.662 2526379.41 2426573.592 3175064.012 3133263.287 3435948.387 0.943010251 0.754952352 0.657484502 0.835224031 0.735278626 0.706231095 0.924072091 0.911906389 1 21.71227693 2.17915485 7.666895066 0.938793526 0.767389062 0.51182283 0.079643624 0.193294386 21.34823642 0.032125819 0.021680694 151.0618677 -2.17915485 -0.171404464 DFTVSAMHGDMDQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 DFTVSAMHGDMDQK 14 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QL52 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;;;;;;;; 277.54 3.84E-33 10896960000 13661490 10450280 5031734 8763148 10724520 9001160 12768670 15013430 13621540 FALSE TRUE 11856089.48 10381631.42 7465097.393 10752954.69 10511123.03 9347440.45 11530366.35 11802924.83 12011217.06 0.987084775 0.864328017 0.621510489 0.895242725 0.875108907 0.77822592 0.959966529 0.982658524 1 23.51787901 2.134909087 5.898586121 0.984193307 0.833085759 0.347104599 0.093403415 0.232286386 11.40097258 0.039194852 0.026216162 136.4297512 -2.134909087 -0.151107548 DFVAEPMGEKPVGSLAGIGEVLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFVAEPMGEKPVGSLAGIGEVLGK 24 1 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 0 ; 172.61 4.76E-12 257620000 1079510 763520 579230 681290 661170 457840 886450 1113400 960930 FALSE TRUE 936850.0184 758504.3868 859347.5654 835987.3074 648014.0106 475453.4011 800482.2154 875308.0745 847329.9501 1.105649598 0.895170042 1.014182923 0.986613665 0.764771752 0.561119551 0.944711343 1.033019161 1 19.69256434 7.99999401 0.862313137 0.892168175 79.26910293 0.173325139 0.142474337 1595.800383 4.162243925 0.053201195 245579.7234 99998620.8 -7.99999401 78.37693475 DFVDDDDDDDLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFVDDDDDDDLER 13 0 G3V4K3;Q9H9C1;Q9H9C1-2 G3V4K3 VIPAS39 Spermatogenesis-defective protein 39 homolog 0 ; 346.01 1.89E-75 1793980000 1315260 1203280 799310 937590 1216290 1200450 1217280 1446300 1320390 FALSE TRUE 1141445.059 1195375.574 1185858.99 1150484.14 1192088.209 1246632.088 1099228.373 1137020 1164294.998 0.980374441 1.02669476 1.018521072 0.988138007 1.023871279 1.070718409 0.944115 0.976573808 1 20.15102521 2.216994221 24.99989473 0.972963217 1.017371801 0.36854937 0.027438854 254.8053592 295369.64 0.011097102 0.00748918 164.8140459 -2.216994221 0.044408584 DFVDHIDLVDPVDGVVLVDPEYLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DFVDHIDLVDPVDGVVLVDPEYLK 24 0 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 ;;;; 252.11 9.49E-44 1811424400 2365099 1862470.3 1712362.2 1934718 1782175.7 1598684.8 2600040 2728271 2871632 FALSE TRUE 2052545.175 1850235.61 2540466.287 2374025.292 1746713.89 1660187.239 2347888.521 2144851.478 2532150.936 0.810593533 0.730697204 1.003283908 0.937552836 0.689814286 0.65564308 0.927230872 0.847047246 1 21.27193197 0.98559707 1.41886336 1.182864206 0.817802718 0.203270242 0.110767368 4.234251156 4.602599357 2.65403254 0.033915392 9.673799225 -0.98559707 -0.365061488 DFVEHSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DFVEHSAR 8 0 Q16822;H0YM31;Q16822-2 Q16822 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 0 164.96 0.00032708 275240000 192810 183030 128180 208560 206630 225310 166550 220450 209670 FALSE TRUE 167329.67 181827.6639 190168.2767 255916.7356 202518.4673 233977.8215 150398.0066 173308.483 184883.0515 0.905056838 0.983473944 1.028586857 1.38420874 1.095386871 1.265545001 0.813476441 0.937395189 1 17.49625345 2.229587332 24.99930252 0.916903437 1.112655969 0.290923573 0.142317877 254.4826032 708973.9127 0.05986148 0.041027416 169.6630741 -2.229587332 0.195752532 DFVNYLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFVNYLVR 8 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 183.74 0.00051576 4241500000 6425300 6806400 3739800 4496000 6582700 6391000 6500500 6999400 6774100 FALSE TRUE 5576180.325 6761688.31 5548379.789 5516885.517 6451717.149 6636865.906 5870082.511 5502632.779 5973273.615 0.933521664 1.131990387 0.92886751 0.923594979 1.080097375 1.11109357 0.982724531 0.921208894 1 22.51009038 2.004691293 24.96329707 0.954073557 1.020244365 0.090699711 0.07653911 259.5360454 1381036.534 0.031474307 0.021129766 101.0860654 -2.004691293 0.066170808 DFVTEALQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFVTEALQSR 10 0 Q15126 Q15126 PMVK Phosphomevalonate kinase 0 ; 127.76 0.00080827 85117000 176285 154077 112539 134110 171200 167333 153185 184451 212663 FALSE TRUE 152988.4906 153064.858 166963.2368 164561.7252 167793.4549 173770.4088 138329.1423 145007.589 187522.2224 0.815841923 0.816249168 0.890365071 0.877558527 0.894792376 0.926665686 0.737667997 0.773282159 1 17.51670205 4.277814207 21.65825392 0.858561377 0.816044894 0.068372609 0.07394891 143.5418554 79190.79214 0.019474054 0.051517603 18958.94675 -4.277814207 -0.042516483 DFWEQEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DFWEQEVR 8 0 Q16822;Q16822-3;H0YML5 Q16822 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 0 133.05 0.0021774 117070000 169420 184980 125300 161200 189750 218690 170910 204420 200400 FALSE TRUE 147030.7177 183764.8542 185895.4991 197802.9238 185974.3462 227103.1458 154335.1745 160706.3738 176708.9403 0.832050249 1.039929581 1.05198695 1.119371343 1.052433148 1.28518198 0.873386339 0.909441104 1 17.43101551 DFYDKIEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DFYDKIEAK 9 1 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 90.685 0.010272 212690000 487740 373750 318360 292560 335530 282230 490300 576370 345040 FALSE TRUE 423283.9232 371294.8116 472319.9609 358990.2195 328853.6095 293087.5707 442750.7815 453117.7608 304249.7643 1.391238295 1.220361871 1.552408634 1.179919466 1.080867261 0.9633124 1.455221445 1.489295355 1 18.21489662 3.681116311 24.99537396 1.227337388 1.371240967 0.173401852 0.189042261 659.7649175 287078.8147 0.057123319 0.084727611 4798.619464 -3.681116311 0.143903579 DFYELEPEKFQNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFYELEPEKFQNK 13 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 172.99 2.05E-05 270840000 681120 456280 392520 426380 436960 334260 654140 727250 279660 FALSE TRUE 591108.2663 453282.6666 582343.9849 523196.0958 428265.3509 347119.1985 590701.6035 571733.247 246598.9134 2.397043272 1.838137324 2.36150264 2.121648018 1.736687908 1.407626634 2.395394186 2.318474316 1 17.91180692 3.354796786 6.452997141 1.869514561 2.174795299 0.163087277 0.429894144 0.540296795 28.42952251 0.128164365 0.165701309 2263.58489 -3.354796786 0.305280738 DFYFGK ddPTM_MDA-MB-175_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 ; 106.29 0.075031 4227800000 8076300 7805900 4593300 5848100 7168500 6364400 8086300 8998500 8348300 FALSE TRUE 7008996.492 7754622.529 6814635.244 7176000.488 7025860.875 6609242.586 7302091.871 7074240.801 7361373.484 0.952131624 1.053420608 0.925728773 0.974818151 0.954422553 0.897827369 0.991946936 0.960994686 1 22.81154354 7.355146905 10.12662472 0.967513796 0.00486372 0 0.042345592 0 0 0.009052174 0 22654104.79 -7.355146905 -0.962650076 TVPLFPHPPVPSLSTSESKPPPQPS(ph)PPT(ph)SPVR ddPTM_MDA-MB-175_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 2 TVPLFPHPPVPSLSTSESKPPPQPS(1)PPT(0.598)S(0.402)PVR;TVPLFPHPPVPSLSTSESKPPPQPS(1)PPT(0.588)S(0.412)PVR 127.2 1.80E-06 1453020000 727300 844190 779820 1098000 1304360 1051570 1222530 1636560 2535750 TRUE FALSE 631185.4623 838644.4603 1156943.56 1347317.682 1278405.788 1092024.578 1103969.229 1286594.38 2235976.524 0.282286265 0.375068545 0.517422052 0.602563429 0.571743833 0.488388213 0.493730241 0.575406032 1 21.09247361 1.155622797 2.261941068 1.233170005 0.482270512 0.760260304 0.091814888 0.451026889 1.961921789 0.749186156 0.026587602 14.30944523 -1.155622797 -0.750899493 DFYLATS(ph)PPDSFLDDHHLTRPHPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 DFYLATSPPDSFLDDHHLTRPHPER 25 1 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 1 DFYLAT(0.195)S(0.794)PPDS(0.011)FLDDHHLTRPHPER;DFYLAT(0.032)S(0.968)PPDSFLDDHHLTRPHPER;DFYLAT(0.007)S(0.993)PPDSFLDDHHLTRPHPER;DFYLAT(0.002)S(0.834)PPDS(0.164)FLDDHHLTRPHPER;DFYLAT(0.028)S(0.972)PPDSFLDDHHLTRPHPER;DFYLAT(0.002)S(0.998)PPDSFLDDHHLTRPHPER;DFYLAT(0.01)S(0.99)PPDSFLDDHHLTRPHPER;DFYLAT(0.002)S(0.998)PPDSFLDDHHLTRPHPER;DFYLAT(0.004)S(0.996)PPDSFLDDHHLTRPHPER 158.83 1.22E-11 7640820000 813446 889861 589608 793923 1080453 1109806 1132448 1229971 1055058 TRUE FALSE 705947.0501 884015.4445 874744.4009 974195.3515 1058954.099 1152500.955 1022623.367 966951.2733 930330.2452 0.758813393 0.950216817 0.940251492 1.047150038 1.138256124 1.238808435 1.099204688 1.039363472 1 19.8273834 4.480230999 1.001764941 1.098769262 0.691425536 0.705280597 0.069847085 0.818211574 0.894151344 0.02602015 0.328745379 30215.58444 -4.480230999 -0.407343726 DGADFAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DGADFAK 7 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78;P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;K7EKH5 H3BPS8;P04075;P09972 ALDOA;ALDOC Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase C 0 ;;;;; 130.77 0.0082156 7739170000 9000400 7454640 5295680 5992400 5820890 5536880 8807860 9534810 8747490 FALSE TRUE 7810974.336 7405669.979 7856688.561 7353066.008 5705065.677 5749887.356 7953675.093 7495865.081 7713371.697 1.012653693 0.960108014 1.018580313 0.953288172 0.739633185 0.745444091 1.031154131 0.971801357 1 22.8789302 3.472851231 24.99572189 0.903577207 0.992166902 0.180945125 0.096756645 258.1850602 1511343.197 0.031245225 0.040502417 2970.648251 -3.472851231 0.088589695 DGAGFLINLIDSPGHVDFSSEVTAALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 DGAGFLINLIDSPGHVDFSSEVTAALR 27 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;;;;;;; 309.96 5.58E-82 8493480000 1933862 1928431.1 882756.2 1468462.2 2011989.6 1849471.3 1994894.9 2191818.1 2106810.3 FALSE TRUE 1678297.237 1915763.109 1309660.051 1801898.987 1971954.943 1920621.658 1801430.3 1723114.856 1857745.586 0.903405315 1.031230069 0.704972769 0.96993851 1.061477394 1.033845362 0.969686222 0.92753005 1 20.82512151 3.500786871 24.94519353 0.991646965 0.885413818 0.286511846 0.085287139 1047.099386 1103712.726 0.023428899 0.034508475 3168.012384 -3.500786871 -0.106233147 DGAHVVISSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DGAHVVISSR 10 0 Q13268;C9JZP6;Q13268-2 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ;;;; 136.49 0.00011634 3772120000 1863688 1364167 915616 1872292 1570210 1781136 1238018 1615661 1576609 FALSE TRUE 1617396.909 1355205.697 1358410.96 2297424.515 1538965.893 1849657.454 1117955.205 1270164.468 1390224.08 1.163407347 0.974810979 0.977116552 1.652556985 1.106991251 1.330474332 0.804154683 0.9136401 1 20.40688601 2.234441264 24.99946719 0.90329681 1.196706736 0.33089754 0.197651858 124.8387719 757607.5227 0.079857259 0.056041138 171.5699653 -2.234441264 0.293409926 DGAPWCGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DGAPWCGR 8 0 Q9NZU5;B4DEY6;Q9NZU5-2 Q9NZU5 LMCD1 LIM and cysteine-rich domains protein 1 0 ;;; 120.52 0.0034564 704450000 957790 932470 614640 716190 924200 1103970 893030 996660 971820 FALSE TRUE 831215.6248 926344.5432 911881.9598 878811.8858 905810.2282 1146440.44 806424.0881 783532.015 856932.5467 0.969989561 1.081000537 1.064123382 1.02553216 1.057037957 1.337842103 0.941059003 0.91434503 1 19.70882212 DGASS(ph)SPESASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DGASSSPESASR 12 0 Q14135-4;G5E9M7;Q14135;Q14135-2;A0A0A6YYI5;A0A075B6E4;Q14135-6;G5E9M9;Q14135-5 Q14135-4 VGLL4 Transcription cofactor vestigial-like protein 4 1 DGAS(0.001)S(0.882)S(0.116)PESASR;DGAS(0.001)S(0.5)S(0.5)PESASR;DGAS(0.001)S(0.569)S(0.43)PESASR 168.98 4.73E-05 163101000 510833 478211 327722 338766 401863 488344 422674 475053 452611 TRUE FALSE 443325.1248 475069.6005 486209.4554 415687.998 393866.7125 507130.9097 381683.1405 373466.6128 399103.8432 1.110801443 1.190340831 1.218253003 1.041553483 0.986877774 1.270674082 0.956350451 0.935763008 1 18.60640465 2.200537189 24.663311 0.957826605 1.131478492 0.488063505 0.083040156 119.6109344 77582.87361 0.034228539 0.023077497 158.6854797 -2.200537189 0.173651887 DGASSS(ph)PESASR ddPTM_MDA-MB-175_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(0.076)S(0.23)S(0.694)PESASR 108.01 0.0018382 177460000 228710 211310 118340 136750 177940 220900 166530 195730 192050 TRUE FALSE 198485.394 209921.8907 175569.6198 167801.1776 174399.3421 229398.1659 150379.9462 153874.6627 169346.0678 1.172069695 1.239602982 1.036750496 0.990877319 1.029839927 1.354611707 0.888003768 0.908640305 1 17.36961496 -1.999999979 0.116836785 0.001794292 1.349580876 0.215851132 0.129747432 333.30483 3.495330409 72.9886751 5.282974256 0.01 1.999999979 1.347786584 DGATILTHAYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGATILTHAYSR 12 0 F5H0D0;Q14232-2;Q14232 F5H0D0 EIF2B1 Translation initiation factor eIF-2B subunit alpha 0 124.86 0.00031556 359170000 241670 198930 115770 145710 206340 194110 200750 235150 189460 FALSE TRUE 209732.6972 197623.2157 171756.7592 178795.6825 202234.2377 201577.5373 181281.2959 184865.0024 167062.2546 1.255416417 1.182931573 1.028100331 1.070233865 1.210532194 1.206601322 1.085112231 1.106563555 1 17.35002629 1.018504379 1.212991934 0.864877354 1.149291558 0.321388514 0.069595737 3.375909932 2.914693322 1.388463602 0.022757662 10.43528654 -1.018504379 0.284414204 DGAWGAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 DGAWGAFR 8 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;;;;;; 217.5 1.72E-05 72960810000 13650690 16328110 11443610 11328400 17354260 18380740 17291360 17750320 20461970 FALSE TRUE 11846716.73 16220849.57 16977778.07 13900686.36 17008944.18 19087858.96 15614446.57 13954552.2 18042979.22 0.656583183 0.899011708 0.940963123 0.770420793 0.942690449 1.0579106 0.865402902 0.773406212 1 24.10493424 4.738900289 24.9999971 0.896656945 0.656583153 0.428613171 0.089983529 29.98920762 2206342.649 0.022655624 0.129181753 54815.10986 -4.738900289 -0.240073792 DGDDVIIIGVFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGDDVIIIGVFK 12 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 194.54 3.24E-06 85814000 405340 328910 376570 468800 305610 304620 353800 386930 732480 FALSE TRUE 351773.292 326749.3686 558680.5116 575248.2052 299528.9589 316338.9285 319488.5305 304188.0306 645887.0488 0.544635928 0.50589243 0.864981753 0.890632822 0.463748204 0.489774379 0.494650777 0.470961651 1 19.30092237 3.20929214 24.99708336 0.558328024 0.69923632 0.073711483 0.196014238 493.8166094 421748.267 0.060607397 0.068732728 1619.168848 -3.20929214 0.140908296 DGDKPEETQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DGDKPEETQGK 11 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 124.12 0.00032447 730950000 1712530 979830 1198510 1124730 701440 759620 1387610 1365760 1144070 FALSE TRUE 1486214.822 973393.4322 1778113.445 1380117.137 687482.7163 788843.0729 1253039.796 1073702.852 1008819.348 1.473221964 0.964883786 1.762568738 1.368051812 0.681472573 0.781946812 1.242085412 1.064316277 1 19.94423642 3.338374021 9.696528364 0.981089215 1.390710373 0.443453143 0.242990521 0.31817491 28.30555797 0.070979145 0.091630625 2179.586055 -3.338374021 0.409621158 DGDKS(ph)PMSSLQISNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGDKSPMSSLQISNEK 16 1 Q9UER7-3;Q9UER7;Q9UER7-2;Q9UER7-5;Q9UER7-4 Q9UER7-3 DAXX Death domain-associated protein 6 1 DGDKS(0.994)PMS(0.006)SLQISNEK;DGDKS(0.798)PMS(0.199)S(0.003)LQISNEK 267.24 1.64E-27 624490000 1015620 553150 552250 576400 571630 439600 817970 933980 934020 TRUE FALSE 881403.2437 549516.3212 819319.9472 707280.4297 560255.6814 456511.6965 738643.3953 734255.6452 823601.2196 1.070182053 0.667211641 0.994801765 0.858765641 0.680251156 0.5542873 0.896845922 0.891518404 1 19.65158644 1.610871725 2.274734585 0.983398737 0.802846448 0.125862848 0.154407273 0.612330171 6.549410886 0.185276497 0.042664961 40.81988014 -1.610871725 -0.18055229 DGDLFMSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 DGDLFMSYR 9 0 P49902-2;P49902;Q5JUV4;Q5JUV3 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;;;;;;;;;;; 236.82 7.15E-10 9609360000 6608850 7645540 5122697 6338435 7764110 6644670 7071740 8674620 9949370 FALSE TRUE 5735473.728 7595315.944 7600050.404 7777673.544 7609619.401 6900294.755 6385923.743 6819620.019 8773166.813 0.653751815 0.865743933 0.866283586 0.886529768 0.867374297 0.786522689 0.727892662 0.777327066 1 23.06466627 4.744213993 24.58139444 0.836715282 0.653751715 0.394593392 0.074303377 580.5062723 2523999.171 0.018908115 0.16074881 55489.90651 -4.744213993 -0.182963567 DGDSVMVLPTIPEEEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGDSVMVLPTIPEEEAK 17 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ; 164.68 6.34E-09 33586000 244008 203783 179476 204526 182276 158293 266510 299440 315080 FALSE TRUE 211761.7246 202444.3361 266271.1939 250966.7543 178649.0642 164382.6341 240663.9012 235407.0862 277831.6013 0.762194522 0.728658421 0.958390596 0.903305287 0.643012038 0.591662839 0.866222201 0.847301333 1 18.08385118 1.32266512 1.723521983 1.050883895 0.77551456 0.28973282 0.110893341 1.1709088 3.815181437 0.517373922 0.033763212 21.02156865 -1.32266512 -0.275369335 DGDSYDPYDFS(ph)DTEEEMPQVHT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DGDSYDPYDFSDTEEEMPQVHTPK 24 0 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 2 DGDSYDPYDFS(1)DTEEEMPQVHT(1)PK;DGDSYDPYDFS(0.998)DT(0.003)EEEMPQVHT(0.999)PK;DGDSYDPYDFS(0.999)DT(0.001)EEEMPQVHT(1)PK;DGDSYDPYDFS(1)DTEEEMPQVHT(1)PK;DGDSYDPYDFS(1)DTEEEMPQVHT(1)PK;DGDSYDPYDFS(1)DTEEEMPQVHT(1)PK 273.86 1.02E-51 4631980000 3610780 2536190 2339360 2438340 2423380 2156430 3003770 3781620 3221740 TRUE FALSE 3133606.274 2519529.601 3470682.321 2992002.365 2375159.479 2239389.257 2712464.848 2972949.992 2840869.567 1.103044754 0.886886758 1.221697173 1.053199485 0.836067768 0.788275985 0.95480091 1.046492956 1 21.43790116 3.37146024 9.397723078 0.9358464 1.066249251 0.292176071 0.108601608 0.435887573 35.52998538 0.033358918 0.043071956 2352.124145 -3.37146024 0.130402851 DGDSYDPYDFS(ph)DTEEEMPQVHTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 DGDSYDPYDFSDTEEEMPQVHTPK 24 0 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 1 DGDSYDPYDFS(0.997)DT(0.003)EEEMPQVHTPK;DGDSYDPYDFS(0.999)DT(0.001)EEEMPQVHTPK;DGDSYDPYDFS(0.997)DT(0.003)EEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(0.999)DT(0.001)EEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(0.998)DT(0.002)EEEMPQVHTPK 318.57 6.03E-74 6811710000 5771530 4993060 3567647 4221138 4643390 3428829 5234480 6973500 5541160 TRUE FALSE 5008807.687 4960260.26 5292973.022 5179611.899 4550995.624 3560738.27 4726840.935 5482271.293 4886090.377 1.025115645 1.015179802 1.083273663 1.06007288 0.931418634 0.728749981 0.967407594 1.122015941 1 22.22024912 3.245464952 24.94266913 0.961683882 1.046384259 0.188165405 0.097385676 360.2631112 1301482.811 0.032885903 0.041507149 1759.806639 -3.245464952 0.084700377 DGDSYDPYDFSDTEEEMPQVHT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGDSYDPYDFSDTEEEMPQVHTPK 24 0 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 1 DGDSYDPYDFSDTEEEMPQVHT(1)PK 125.74 0.00035589 66273000 86298 59025 51551 63194 58271 50275 75234 84980 68201 TRUE FALSE 74893.50065 58637.26089 76481.23603 77543.16356 57111.52111 52209.11178 67937.81826 66807.68832 60138.35547 1.24535332 0.975039314 1.271754697 1.289412771 0.94966882 0.868149975 1.129691986 1.110899821 1 15.8759978 3.232342529 24.99965989 1.025758467 1.185105311 0.389176539 0.113279677 189.9173276 763556.7875 0.035991886 0.041821137 1707.428513 -3.232342529 0.159346844 DGDSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGDSYR 6 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 108.98 0.069669 105850000 350460 301250 200450 235970 183700 282200 313450 365050 357740 FALSE TRUE 304145.823 299271.0689 297388.2905 289550.5951 180044.7294 293056.4166 283051.6672 286986.8983 315448.3847 0.964169854 0.948716441 0.942747863 0.917901657 0.570758128 0.929015429 0.897299466 0.909774506 1 18.26704444 3.466302884 24.99771212 0.861754734 0.94802245 0.123243793 0.111640867 493.3051178 1139862.108 0.033149902 0.042838655 2926.192442 -3.466302884 0.086267715 DGDVTVTNDGATILSMMDVDHQIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DGDVTVTNDGATILSMMDVDHQIAK 25 0 P48643;B7ZAR1;E9PCA1 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;; 197.28 8.19E-25 199874000 134933 100138 102357 128132 117736 100349 135142 145784 274247 FALSE TRUE 117101.2622 99480.18688 151857.1876 157226.329 115393.2839 104209.491 122035.9496 114609.2261 241825.8321 0.48423802 0.411371217 0.627960984 0.650163498 0.477175176 0.430927871 0.504643977 0.473932934 1 17.88360884 1.236172804 24.9976988 1.000000643 0.507709513 0.80395766 0.076422499 29.51676719 308937.5841 0.129460187 0.019782922 17.22553835 -1.236172804 -0.49229113 DGEEAGAYDGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 DGEEAGAYDGPR 12 0 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;;; 234.28 1.19E-15 7568930000 4480690 3963975 3157144 3335768 3988084 4192700 4032812 3727788 3157118 FALSE TRUE 3888555.464 3937935.387 4683949.398 4093205.108 3908728.931 4353995.882 3641710.513 2930629.546 2783887.107 1.396807886 1.414545647 1.682521316 1.470320078 1.404054396 1.563998724 1.308138719 1.052711347 1 21.40866928 1.858236286 2.38796716 1.005725808 1.4897133 0.825620171 0.086981316 0.110224401 1.153462545 0.066838119 0.024929888 72.14999184 -1.858236286 0.483987492 DGELPVEDDIDLSDVELDDLGKDEL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DGELPVEDDIDLSDVELDDLGKDEL 25 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;;;; 239.1 1.46E-38 458180000 1120563 797608 781182 754926 620070 675560 752632 891602 1018753 FALSE TRUE 972477.7604 792368.4605 1158964.228 926343.4866 607731.8201 701549.2303 679641.8645 700939.8508 898317.1809 1.082555005 0.882058673 1.290150353 1.031198675 0.676522539 0.780959382 0.756572265 0.780281025 1 19.7768654 3.346772068 6.407667226 0.793282934 1.079286232 0.539843975 0.125587784 0.159393902 8.461065129 0.035462209 0.045832306 2222.143331 -3.346772068 0.286003299 DGFIDKEDLHDMLASLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DGFIDKEDLHDMLASLGK 18 1 J3QRS3;P19105;O14950;J3KTJ1;P24844 J3QRS3;P24844 MYL12A;MYL12B;MYL9 Myosin regulatory light chain 12A;Myosin regulatory light chain 12B;Myosin regulatory light polypeptide 9 0 ;; 265.07 4.70E-31 7466680000 11820300 9173000 8034600 9366500 8395050 6314060 12257500 14704600 14997100 FALSE TRUE 10258217.41 9112741.959 11920159.43 11493306.98 8228004.93 6556965.974 11068769.54 11560135.72 13224159.92 0.775717888 0.689097985 0.901392565 0.869114337 0.622194905 0.495832326 0.837011168 0.874167871 1 23.65667274 1.644967599 2.303133602 0.979645879 0.733133875 0.351800762 0.119087784 0.346783283 3.881479318 0.140505695 0.035574481 44.15375043 -1.644967599 -0.246512004 DGFNPADVEAGLYGSHLYVWDWQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DGFNPADVEAGLYGSHLYVWDWQR 24 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ;; 250.95 8.90E-39 562079000 636949 573959 363975 514739 689540 554823 700191 779354 613718 FALSE TRUE 552774.5758 570188.6255 539994.5274 631618.3572 675819.5031 576167.3998 632286.5846 612695.212 541164.9572 1.021453013 1.053631833 0.997837203 1.167145708 1.248823476 1.064679803 1.168380502 1.132178283 1 19.0457089 3.739443399 24.99598528 1.135005962 1.027239795 0.358273816 0.066563392 86.93506751 2461541.28 0.017827195 0.028724603 5488.370217 -3.739443399 -0.107766167 DGFQHPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGFQHPAR 8 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6;F5H3E1 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ; 111.95 0.0031354 360380000 842380 730600 462930 560580 695010 704670 695840 761150 748900 FALSE TRUE 731057.3487 725800.6405 686804.4964 687868.2569 681180.6608 731779.1109 628357.5439 598383.9958 660365.8951 1.107048916 1.09908862 1.040036291 1.041647156 1.031520049 1.10814189 0.95152937 0.906140066 1 19.33290609 2.199645208 9.614108884 0.942552292 1.067913621 0.705357804 0.035927647 0.187779658 44.17238137 0.014860821 0.010063434 158.359896 -2.199645208 0.125361329 DGFYEAELCPDR ddPTM_MDA-MB-175_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 ;;; 219.5 3.48E-07 569610000 818770 739490 461260 566790 716640 682520 718000 842920 789530 FALSE TRUE 710567.47 734632.2415 684326.8788 695488.3323 702380.2661 708776.986 648368.4705 662668.1176 696192.6628 1.020647743 1.055213996 0.982956178 0.998988311 1.008887774 1.01807592 0.931306095 0.95184588 1 19.40912708 2.25318142 24.99140754 0.95789364 1.013652557 0.504998928 0.024703315 179.5797013 306956.0216 0.009438645 0.007277681 179.135401 -2.25318142 0.055758918 DGGFCEVCKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGGFCEVCKK 10 1 P07602;C9JIZ6;P07602-2;P07602-3;Q5BJH1 P07602 PSAP Prosaposin;Saposin-A;Saposin-B-Val;Saposin-B;Saposin-C;Saposin-D 0 149.31 3.78E-05 230610000 890900 568210 409210 466030 523690 466550 812580 961260 359160 FALSE TRUE 773165.3077 564477.3911 607105.3247 571849.2343 513269.5936 484498.4804 733776.1167 755702.0295 316700.514 2.441313713 1.782369672 1.916969812 1.805646689 1.62067812 1.529831683 2.316940088 2.386172413 1 18.27275968 4.743179027 23.74844245 1.855931021 2.44131419 0.196197703 0.394356504 453.7328766 2332979.006 0.098529597 0.756093322 55357.82606 -4.743179027 0.585383168 DGGGLAPPPGSCS(ph)PSLSPSSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGGGLAPPPGSCSPSLSPSSNR 22 0 A8MUP8;P10276-3;P10276-2;P10276 A8MUP8 RARA Retinoic acid receptor alpha 1 DGGGLAPPPGS(0.025)CS(0.867)PS(0.108)LSPSSNR 154.55 2.69E-08 88447000 44672 42839 29794 35297 41431 43640 48534 46147 52963 TRUE FALSE 38768.48202 42557.58779 44202.47805 43311.72333 40606.60416 45318.85904 43827.18015 36278.82317 46701.77448 0.830128672 0.911262757 0.946483909 0.927410657 0.869487393 0.970388375 0.938447856 0.776818945 1 15.51118975 4.739696204 23.04273406 0.908887164 0.830128606 0.155178966 0.061204954 71.17573558 1443657.039 0.015221131 0.09069059 54915.65954 -4.739696204 -0.078758558 DGGLQNMELHGMIMLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGGLQNMELHGMIMLR 16 0 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 104.21 0.0013793 285430000 197940 157070 125840 150980 157660 186430 187040 233030 184890 FALSE TRUE 171781.7275 156038.1968 186696.6449 185262.3166 154522.8745 193602.0827 168900.8896 183198.3479 163032.5148 1.053665446 0.957098631 1.145149758 1.136351953 0.947804029 1.187505958 1.035995119 1.123692094 1 17.3148002 4.244066041 24.99998675 1.084442199 1.005382054 0.151743186 0.075537269 226.241006 1027323.038 0.017412292 0.043414107 17541.47227 -4.244066041 -0.079060146 DGGNPFAEPSELDNPFQDPAVIQHRPS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DGGNPFAEPSELDNPFQDPAVIQHRPSR 28 1 O14828 O14828 SCAMP3 Secretory carrier-associated membrane protein 3 1 DGGNPFAEPSELDNPFQDPAVIQHRPS(1)R;DGGNPFAEPSELDNPFQDPAVIQHRPS(1)R;DGGNPFAEPSELDNPFQDPAVIQHRPS(1)R;DGGNPFAEPS(0.008)ELDNPFQDPAVIQHRPS(0.992)R 129.59 1.61E-05 673600000 312562 254433 200818 209221 274899 325244 245534 290535 304059 TRUE FALSE 271256.1398 252761.6129 297934.2565 256727.8258 269429.0477 337756.3471 221722.1505 228406.3512 268113.4914 1.011721336 0.942741119 1.111224411 0.957534156 1.004906714 1.259751404 0.826971255 0.851901745 1 18.03248429 DGGQTES(ph)NEEGKENR ddPTM_MDA-MB-175_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;DGGQT(0.016)ES(0.984)NEEGKENR;DGGQTES(1)NEEGKENR 188.26 3.27E-11 563500000 573780 469028 351475 358675 419323 341851 547189 654546 572592 TRUE FALSE 497953.5192 465946.9242 521449.4856 440117.6408 410979.2927 355002.2292 494122.695 514576.4316 504900.8261 0.986240255 0.922848409 1.03277606 0.871691267 0.813980234 0.703112791 0.978652974 1.019163378 1 18.94564051 2.019964925 24.99931045 1.00733791 0.888125363 0.259354332 0.089409771 328.8078882 411718.9107 0.039584583 0.026684516 104.7043982 -2.019964925 -0.119212546 DGGQTESNEEGKENR ddPTM_MDA-MB-175_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 ;;; 293.52 5.07E-44 2139684400 2197223.7 1566914.7 1210374.6 1277885.9 1439218.3 1180891.9 1951632.6 2380966.3 1606851.2 FALSE TRUE 1906855.021 1556621.534 1795715.805 1568049.425 1410580.672 1226321.576 1762363.571 1871815.185 1416891.082 1.34580212 1.098617639 1.267363334 1.106683107 0.995546298 0.865501655 1.243824309 1.321072036 1 20.43429743 7.531545273 1.170695076 1.121394895 199.980464 0.208881489 0.139300935 2882.933469 5.661639383 0.044549007 1537479.312 34005195.23 -7.531545273 198.8590691 DGGS(ph)GNSTIIVSR ddPTM_MDA-MB-175_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(0.999)GNS(0.001)TIIVSR 172.43 2.45E-05 651910000 552400 461630 287544 370220 483540 411060 457350 525500 466080 TRUE FALSE 479398.9404 458597.5221 426601.2402 454284.1095 473918.5 426873.7442 412996.2674 413125.9144 410980.5534 1.166475972 1.115861854 1.038008336 1.105366436 1.153140936 1.038671394 1.004904646 1.005220104 1 18.6487106 2.541069518 4.570883121 1.005453596 1.110608577 0.703157416 0.033933688 0.12970916 5.368739713 0.012717801 0.010863423 347.5917963 -2.541069518 0.105154981 DGGSEGSGGNNDGEKEPSLTDAIPSHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGGSEGSGGNNDGEKEPSLTDAIPSHPR 28 1 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 168.17 3.09E-12 157680000 146800 112910 90200 123210 104370 83048 160830 159170 179090 FALSE TRUE 127400.0081 112168.2868 133821.0217 151186.7136 102293.2412 86242.9103 145232.7314 125132.7342 157918.1842 0.806746916 0.710293671 0.847407297 0.957373683 0.647761002 0.546123999 0.919670727 0.792389646 1 17.26881778 0.749316216 1.346615433 1.492455934 0.769030911 0.248426866 0.121587097 6.703203406 4.093965664 9.31920613 0.036653431 5.614566315 -0.749316216 -0.723425023 DGGT(ph)SYSPQENSHNHSALHSSNSHSSNPSNNPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGGTSYSPQENSHNHSALHSSNSHSSNPSNNPSK 34 0 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5;Q9BTA9-3;A0A494C0B7;A0A494C0C1;A0A494C0S5;C9JVK6;C9JD58;J3QTA0 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 DGGT(0.396)S(0.32)YS(0.26)PQENS(0.009)HNHS(0.009)ALHS(0.002)S(0.002)NS(0.002)HSSNPSNNPSK;DGGT(0.402)S(0.316)YS(0.281)PQENSHNHSALHSSNSHSSNPSNNPSK 108.45 1.05E-05 410490000 119082 163807 15189 61573 311930 274857 209338 233593 212711 TRUE FALSE 103345.012 162730.941 22534.4512 75554.09073 305723.2033 285430.9266 189036.433 183640.9548 187564.5479 0.550983718 0.867599676 0.12014238 0.402816479 1.629962627 1.521774396 1.007847352 0.979081371 1 17.51702764 3.257462955 24.99858078 1.194862332 0.48659753 0.633185867 0.280140557 179.6988362 237652.5333 0.088014802 0.113434176 1809.101589 -3.257462955 -0.708264802 DGGTSYS(ph)PQENSHNHSALHSSNSHSSNPSNNPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGGTSYSPQENSHNHSALHSSNSHSSNPSNNPSK 34 0 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5;Q9BTA9-3;A0A494C0B7;A0A494C0C1;A0A494C0S5;C9JVK6;C9JD58;J3QTA0 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 DGGTSY(0.001)S(0.999)PQENSHNHSALHSSNSHSSNPSNNPSK 88.056 0.00026155 50295000 16736 16407 5741.3 7912.9 10204 13358 11181 11713 9373.8 TRUE FALSE 14524.2952 16299.22134 8517.811883 9709.644886 10000.96036 13871.8909 10096.66834 9208.266101 8265.640043 1.757189416 1.971924891 1.030508447 1.174699701 1.209943853 1.678259739 1.221522869 1.114041508 1 13.01291082 4.242591362 24.99998811 1.213114973 1.864557355 0.672884341 0.191355074 60.03294577 372329.5001 0.050329341 0.123335223 17482.00992 -4.242591362 0.651442382 DGHADAAQDTEQFVATVLQAASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DGHADAAQDTEQFVATVLQAASR 23 0 Q6PJG6;Q6PJG6-3 Q6PJG6 BRAT1 BRCA1-associated ATM activator 1 0 ;;; 208.39 1.02E-24 125770000 121868 125131 85544 96510 119520 119492 118382 135064 136319 FALSE TRUE 105762.835 124309.0062 126913.3645 118424.0706 117141.7858 124088.9346 106901.3319 106181.6147 120203.5231 0.879864685 1.034154432 1.055820672 0.985196336 0.974528723 1.032323607 0.889336095 0.883348607 1 16.87511966 2.234199404 24.99985852 0.914257799 0.997062071 0.23982248 0.057138985 130.1741222 746188.8344 0.022306602 0.01562726 171.4744442 -2.234199404 0.082804272 DGHGEAIMFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DGHGEAIMFK 10 0 Q9Y2J8 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ;;; 125.75 0.00040089 2076670000 4392230 4413790 3074950 3671820 4187570 3599540 4498550 5295700 5384800 FALSE TRUE 3811785.677 4384795.523 4562006.105 4505562.851 4104245.55 3738016.633 4062281.313 4163255.766 4748215.078 0.802782859 0.923461859 0.960783374 0.948896117 0.864376504 0.787246696 0.855538607 0.876804378 1 22.17895386 3.210191818 24.85795686 0.870723189 0.913715585 0.048445001 0.066535506 529.9581958 464370.0749 0.020691519 0.02346627 1622.526572 -3.210191818 0.042992396 DGHNLISLLEVLSGDSLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGHNLISLLEVLSGDSLPR 19 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;E9PIA2;Q15149-4;Q15149-5;Q15149-8;E9PKG0 Q15149-3;Q15149-4;Q15149-5;Q15149-8;E9PKG0 PLEC Plectin 0 ; 169.28 1.44E-11 504200000 597210 608400 392520 564510 586910 605790 577360 583180 642240 FALSE TRUE 518287.1854 604403.3803 582343.9849 692690.6235 575231.6393 629095.1333 521367.7161 458471.4953 566315.1188 0.91519221 1.067256303 1.028303793 1.223154036 1.015744804 1.110857034 0.920631816 0.809569584 1 19.11124552 2.136258834 5.469237696 0.884344606 1.063965587 0.377106913 0.089794462 0.179956519 8.119474841 0.0363474 0.02422943 136.8544216 -2.136258834 0.17962098 DGHPNVLHDCQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DGHPNVLHDCQR 12 0 O75146;O75146-2 O75146 HIP1R Huntingtin-interacting protein 1-related protein 0 ;; 83.877 0.0072587 326952000 210778 185007 126201 128802 188743 238225 182310 183454 217128 FALSE TRUE 182923.1533 183791.6768 187232.2257 158048.4627 184987.3836 247389.6699 164629.6043 144223.7897 191459.3752 0.95541497 0.959951304 0.977921429 0.825493463 0.966196528 1.292126174 0.85986703 0.753286642 1 17.54667878 2.036074581 24.99999069 0.84328655 0.992202793 0.159593102 0.130673006 257.3472812 178342.8354 0.054134825 0.036497563 108.6612212 -2.036074581 0.148916243 DGHQSSHGDIFSHFFGDFGFMFGGTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGHQSSHGDIFSHFFGDFGFMFGGTPR 27 0 Q9UBS4 Q9UBS4 DNAJB11 DnaJ homolog subfamily B member 11 0 ; 98.7 0.001279 31335000 43860 54835 15119.8 50012 77450 98754 59719 56147 77525 FALSE TRUE 38063.78987 54474.78527 22431.78585 61367.98899 75908.89653 102553.1303 53927.46057 44140.40099 68360.08282 0.556813104 0.796880036 0.328141584 0.897716715 1.110427217 1.500190258 0.788873541 0.645704323 1 16.06086652 3.561143876 7.456792216 0.974578451 0.58593745 0.403451239 0.247192606 0.351602633 27.51637238 0.075605213 0.112169375 3640.356165 -3.561143876 -0.388641001 DGHRYS(ph)RS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGHRYSRSPAR 11 2 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 2 DGHRY(0.211)S(0.88)RS(0.909)PAR;DGHRY(0.018)S(0.985)RS(0.997)PAR 64.52 0.036446 1106400000 184840 202721 97978 135623 172187 205433 159640 216640 131531 TRUE FALSE 160412.9257 201389.3124 145360.4885 166418.275 168760.8156 213336.1404 144158.1374 170313.2219 115981.555 1.383089972 1.736390863 1.253306946 1.434868458 1.455065985 1.839397139 1.242940202 1.468450926 1 16.82353586 0.792281663 1.53748562 2.15E-18 1.492969629 0.383705291 0.188077744 3.980476186 3.219010977 12.90618106 0.050432287 6.198429459 -0.792281663 1.492969629 DGIDDESYEAIFKPVMSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGIDDESYEAIFKPVMSK 18 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 0 150.45 5.00E-08 93813000 116900 104670 81784 99439 88504 73001 124690 151270 142860 FALSE TRUE 101451.3688 103982.4159 121335.016 122018.1448 86742.94356 75809.39571 112597.583 118922.0877 125971.2535 0.805353332 0.825445591 0.963196067 0.968618961 0.68859316 0.601799169 0.893835536 0.944041472 1 16.94273502 1.818793025 3.323351 0.974084529 0.815095971 0.26168277 0.111008858 0.361949825 7.12427335 0.07946838 0.033379408 65.88598227 -1.818793025 -0.158988558 DGIDDESYGQIFKPIISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGIDDESYGQIFKPIISK 18 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 0 203.63 1.06E-15 488900000 1863600 1156000 1015300 1205200 1074700 829160 1511100 1915800 1671500 FALSE TRUE 1617320.538 1148406.16 1506302.476 1478859.08 1053315.573 861058.3217 1364553.755 1506121.079 1473897.174 1.097308935 0.779163011 1.021986135 1.003366521 0.714646579 0.584205151 0.9258134 1.021863062 1 20.49120445 4.760085857 23.31477104 0.88814731 1.097309477 0.172281082 0.148083643 4587.632987 4968831.328 0.039220826 1.602564042 57555.37085 -4.760085857 0.209162167 DGIEPGHIPGTVNIPFTDFLSQEGLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGIEPGHIPGTVNIPFTDFLSQEGLEK 27 0 P25325-2;P25325 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 0 141.23 2.13E-07 160420000 258440 249230 192370 206140 215700 193560 274260 339800 306550 FALSE TRUE 224286.4992 247592.7917 285400.7754 252947.2377 211407.992 201006.3784 247662.3074 267136.4143 270310.0082 0.82973805 0.915958656 1.05582763 0.935767193 0.782094579 0.743614266 0.916215826 0.988259429 1 18.0442554 1.794209867 3.928723513 0.994881919 0.881966237 0.231725641 0.086008447 0.355621676 10.14984703 0.059311605 0.025837572 62.26010765 -1.794209867 -0.112915682 DGIPVS(ph)SEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGIPVSSEAER 11 0 A6PVJ2;A0A0C4DH46;H0Y621;H0Y5K5;Q9Y282-2;Q9Y282;Q9Y282-3 A6PVJ2 ERGIC3 Endoplasmic reticulum-Golgi intermediate compartment protein 3 1 DGIPVS(0.948)S(0.052)EAER 75.102 0.020675 0 237380 195440 197090 196560 215470 230720 184020 254860 491310 TRUE FALSE 206009.6316 194156.1418 292403.3832 241191.9522 211182.5686 239595.9477 166173.7687 200360.1723 433227.8915 0.47552255 0.448161685 0.67494127 0.556732281 0.487463002 0.553048297 0.383571261 0.462482163 1 18.7247666 1.235676072 24.99985544 1.000000669 0.503599798 0.798666663 0.078063916 36.93438299 320043.3733 0.13617498 0.020073378 17.2058476 -1.235676072 -0.496400871 DGISCEASNPHGNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGISCEASNPHGNKR 15 1 P50895;A0A087WXM8 P50895 BCAM Basal cell adhesion molecule 0 115.83 0.00032256 55720000 95411 87182 50954 80812 90899 104480 67046 115330 72634 FALSE TRUE 82802.19461 86609.2957 75595.52483 99161.59973 89090.28774 108499.4132 60543.88924 90667.577 64047.29126 1.292828986 1.352271017 1.180307915 1.548255949 1.391007894 1.694051553 0.945299763 1.415634841 1 15.96684994 0.504444163 1.01694912 1.96E-10 1.373199861 0.215555508 0.2023761 12.03991148 3.310150214 26.02834439 0.063117129 3.194803586 -0.504444163 1.373199861 DGIVLGADTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DGIVLGADTR 10 0 Q99436;Q5TBG5;Q99436-2 Q99436 PSMB7 Proteasome subunit beta type-7;Proteasome subunit beta type 0 ;;; 157.99 1.90E-05 1477050000 2517700 2441350 1494100 1758600 2344800 2430410 2393650 2643370 2572140 FALSE TRUE 2184979.566 2425312.611 2216651.757 2157917.009 2298143.068 2523909.445 2161514.191 2078105.896 2268064.539 0.963367456 1.069331392 0.97733187 0.951435451 1.01326176 1.112803186 0.953021466 0.916246368 1 21.11303026 2.039936925 24.99999973 0.946888318 1.014157461 0.211092817 0.052074224 197.6650177 123734.9301 0.021199978 0.014293007 109.6318961 -2.039936925 0.067269143 DGKDQGVNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGKDQGVNVR 10 1 Q9H201;I6L9I8;Q9H201-2;D6RFG3;D6REL6;Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9H201;Q9Y6I3 EPN3;EPN1 Epsin-3;Epsin-1 0 ; 94.584 0.0073001 258390000 873370 654670 531530 465760 622220 530520 776770 902690 200061 FALSE TRUE 757951.9417 650369.4297 788579.6859 571517.9267 609839.0394 550929.4477 701438.965 709656.7682 176410.0165 4.296535745 3.686692188 4.470152555 3.239713584 3.456941116 3.123005477 3.976185587 4.022769128 1 17.42857295 3.723849713 23.88486882 3.294041278 4.104683356 0.222224373 0.86041486 783.8592064 1272686.949 0.232800179 0.347179644 5294.801868 -3.723849713 0.810642078 DGKLPLLLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGKLPLLLSR 10 1 P49902-2;P49902;Q5JUV4 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ; 129.34 0.00027873 4078400000 4715400 5718000 2852700 3410300 5656900 4260000 5650200 7345300 3081700 FALSE TRUE 4092247.943 5680438.082 4232275.262 4184660.738 5544338.758 4423884.957 5102244.474 5774564.756 2717384.937 1.505950772 2.090406112 1.557480946 1.53995876 2.040321444 1.627993479 1.877630366 2.12504481 1 21.37378752 DGKS(ph)PTVPCLQEEAGEPLGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGKSPTVPCLQEEAGEPLGGK 21 1 A1L390-3;A1L390;A1L390-2;G3V311 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 DGKS(0.974)PT(0.026)VPCLQEEAGEPLGGK 174.4 1.85E-12 307300000 263620 289740 306530 373890 401280 258150 608980 764280 570690 TRUE FALSE 228781.9491 287836.6789 454768.9333 458787.4391 393295.3131 268081.1975 549921.2133 600844.6696 503223.6783 0.454632719 0.571985563 0.903711317 0.911696843 0.781551684 0.53272771 1.092796776 1.193991252 1 18.94084028 1.854842345 0.127539116 2.001950135 1.91E-11 0.493945178 0.174358584 34.88756508 1.923397469 20.25832016 10.56109057 71.58834877 -1.854842345 -2.001950135 DGLAFNALIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DGLAFNALIHR 11 0 O43707 O43707 ACTN4 Alpha-actinin-4 0 ;;;;; 208.46 1.95E-08 8133750000 6133500 6130760 3700030 5295080 5906750 6435540 5113520 5876350 8216690 FALSE TRUE 5322942.435 6090486.634 5489376.884 6497408.844 5789217.231 6683119.388 4617611.617 4619738.282 7245322.269 0.734672971 0.840609487 0.757644268 0.896772925 0.799028258 0.92240471 0.637323151 0.637616673 1 22.78861843 1.213544589 24.73565494 1.000001184 0.775221472 0.349569924 0.094976139 2747.586784 2716627.208 1.754270655 0.025369044 16.35101018 -1.213544589 -0.224779712 DGLAPEKT(ph)SPDRDK ddPTM_MDA-MB-175_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(0.5)S(0.5)PDRDK;DGLAPEKT(0.917)S(0.083)PDRDK 219.68 7.91E-12 1796360000 1175600 645670 855300 809270 718640 506730 1144740 1334050 1382100 TRUE FALSE 1020241.481 641428.5513 1268925.941 993027.1224 704340.47 526224.231 1033723.291 1048773.789 1218709.712 0.837148889 0.526317748 1.041204421 0.81481842 0.57793949 0.431788001 0.848211252 0.860560787 1 20.2169231 1.698533728 2.354884116 0.966027299 0.711317836 0.216420238 0.176531912 0.439408824 5.109909757 0.174990319 0.050615515 49.94979707 -1.698533728 -0.254709463 DGLEMEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGLEMEK 7 0 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;P13693-2;H0YCX0 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 ; 98.523 0.026056 300390000 534210 484040 382390 442760 512330 458870 569870 644510 680050 FALSE TRUE 463612.795 480860.3094 567315.083 543295.4252 502135.6354 476523.0258 514604.0951 506686.5521 599655.2637 0.773132203 0.801894586 0.946068712 0.906012934 0.837373848 0.794661624 0.85816656 0.844963069 1 19.19377382 -1.999757986 0.018243925 1.784550478 0.10836196 0.18474081 0.063847764 20618.12343 37.41719975 2118.965514 1392.489023 0.010005574 1.999757986 -1.676188518 DGLGFCALIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGLGFCALIHR 11 0 P12814-3;P12814;P12814-2;P12814-4;H9KV75;G3V2N5;G3V2W4;G3V2X9 P12814-3 ACTN1 Alpha-actinin-1 0 ; 125.74 0.000322 1401930000 2010780 1876740 1186960 1580290 1676560 2091100 1662770 1926710 2525300 FALSE TRUE 1745050.328 1864411.571 1760977.826 1939118.998 1643199.736 2171545.97 1501514.821 1514698.06 2226761.911 0.783671716 0.837274772 0.790824478 0.870824576 0.737932389 0.975203482 0.674304161 0.680224524 1 21.08651588 2.188189259 24.99995921 0.75844196 0.828368661 0.021716759 0.108819957 278.4489607 138195.5732 0.042776725 0.028840114 154.237245 -2.188189259 0.069926701 DGLILTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DGLILTSR 8 0 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ;;; 161.02 0.00081417 1722110000 1693620 1667340 905110 1129380 1557040 1479950 1400390 1800800 1553860 FALSE TRUE 1469803.826 1656387.134 1342824.223 1385822.99 1526057.95 1536884.634 1264580.393 1415712.934 1370164.441 1.072720749 1.2088966 0.980046032 1.011428226 1.113777226 1.121678967 0.922940602 1.033243085 1 20.38591762 7.999999964 0.089350552 0.856775626 1.591820304 0.181200058 0.074037706 606.8965918 5.081243061 7.466324276 56.68595211 99999991.64 -7.999999964 0.735044678 DGLIPLEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGLIPLEIR 9 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 98.392 0.014063 58258000 99381 103000 56973 73658 94868 89407 88065 97102 113640 FALSE TRUE 86247.54905 102323.3862 84525.33336 90383.17469 92980.31241 92846.54514 79524.46985 76337.49295 100205.6087 0.860705805 1.021134322 0.843518986 0.901977204 0.927895291 0.926560363 0.793612962 0.761808585 1 16.61260374 2.249599387 24.82818396 0.830632714 0.91545009 0.103161985 0.077883478 296.2079646 666225.3032 0.028331743 0.021730694 177.6639799 -2.249599387 0.084817376 DGLLENQTPEFFQDVCKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DGLLENQTPEFFQDVCKPK 19 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 282.86 8.05E-40 10236378000 7186706 5681358 5307279 4638908 5310237 4368422 7764892 8753987 8456970 FALSE TRUE 6236964.593 5644036.785 7873896.876 5692242.963 5204573.673 4536478.021 7011853.969 6882015.004 7457196.641 0.83636853 0.756857712 1.055878939 0.763322095 0.697926302 0.608335577 0.940280149 0.922868919 1 22.83020195 2.050133092 24.99502765 0.948621088 0.790777642 0.320154993 0.115215277 136.7722001 68190.33429 0.049386863 0.033296608 112.2362357 -2.050133092 -0.157843445 DGLLPENTFIVGYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DGLLPENTFIVGYAR 15 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;; 227.48 1.69E-12 1379763000 676180 643530 437210 480772 651199 674509 693937 739533 634894 FALSE TRUE 586821.0998 639302.6091 648646.2184 589938.6307 638241.4139 700457.7977 626639.0965 581389.623 559837.5546 1.048198884 1.141943058 1.158632916 1.053767519 1.140047517 1.25118044 1.119323081 1.038497004 1 19.09464874 1.671527432 3.372999362 1.009067477 1.134573706 0.410709735 0.056258116 0.190650832 5.02066797 0.04471177 0.015345938 46.93830815 -1.671527432 0.125506228 DGLNDDDFEPYLS(ph)PQAR ddPTM_MDA-MB-175_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 354.7 8.39E-88 1015240000 1119170 1158530 908590 1025330 1272420 1277340 1340300 1591260 1563620 TRUE FALSE 971268.8489 1150919.54 1347987.163 1258146.848 1247101.331 1326480.096 1210317.912 1250981.432 1378770.625 0.704445563 0.834743299 0.977673254 0.912513528 0.904502394 0.962074527 0.877823976 0.907316569 1 20.39495104 4.570242007 2.983934175 0.928001303 0.70058282 0.789469742 0.038409912 0.129224512 1.934931216 0.00948182 0.056309555 37174.23221 -4.570242007 -0.227418483 DGLNQTTIPVS(ph)PPSTTKPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DGLNQTTIPVSPPSTTKPSR 20 1 Q71RC2-5;Q71RC2-3;Q71RC2;Q71RC2-4;X6RLN4;Q71RC2-2;Q71RC2-6 Q71RC2-5 LARP4 La-related protein 4 1 DGLNQTTIPVS(0.984)PPS(0.004)T(0.006)T(0.006)KPSR;DGLNQTTIPVS(0.909)PPS(0.024)T(0.033)T(0.033)KPS(0.001)R;DGLNQTTIPVS(0.998)PPST(0.001)T(0.001)KPSR;DGLNQTTIPVS(0.489)PPS(0.129)T(0.174)T(0.174)KPS(0.034)R;DGLNQTT(0.005)IPVS(0.964)PPS(0.003)T(0.004)T(0.02)KPS(0.003)R 179.79 3.45E-17 8857200000 2048700 1576870 1214060 1378330 1821500 1584290 2071900 2316320 2248090 TRUE FALSE 1777959.104 1566511.437 1801183.477 1691300.893 1785255.714 1645238.661 1870967.457 1820992.994 1982323.361 0.8969067 0.790240113 0.908622434 0.853191223 0.900587537 0.829954736 0.94382556 0.918615514 1 20.91876089 -2 0.491837818 5.130962704 0.856616198 0.533996952 0.040142474 77.8516247 0.896195855 340.9243158 0.024593549 0.01 2 -4.274346506 DGLPRT(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DGLPRTPSR 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DGLPRT(0.957)PS(0.043)R;DGLPRT(0.942)PS(0.058)R;DGLPRT(0.982)PS(0.018)R 97.779 0.010444 943160000 536952 458868 281102 319124 440983 430391 445830 521254 289502 TRUE FALSE 465992.4327 455853.6659 417043.8674 391585.9817 432208.3011 446948.4203 402593.4752 409787.8885 255277.4034 1.825435493 1.785718829 1.633688928 1.53396257 1.693092672 1.750834247 1.577082303 1.60526503 1 17.96170631 0.909032616 1.743038661 1.37E-14 1.688218281 0.848755384 0.090072343 0.999653103 1.317120822 3.806115241 0.026068603 8.110219641 -0.909032616 1.688218281 GDRSEDFGVNEDLADSDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GDRSEDFGVNEDLADSDAR 19 1 P04083 P04083 ANXA1 Annexin A1 0 ;;; 248.52 6.37E-25 1574710000 1173840 1202980 689276 758252 1271390 1289070 925810 1332060 331621 FALSE TRUE 1018714.07 1195077.545 1022612.179 930424.7058 1246091.826 1338661.357 836025.0887 1047209.335 292417.1432 3.483769997 4.086892896 3.497100642 3.181840489 4.261350114 4.577916816 2.859015308 3.581217311 1 18.15766837 1.157386865 2.563083752 7.68E-16 3.735425134 0.728001978 0.514246189 0.382586002 2.297501628 3.456996701 0.134300165 14.36768723 -1.157386865 3.735425134 DGMEYPFIGEGEPHVDGEPGDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DGMEYPFIGEGEPHVDGEPGDLR 23 0 Q9UBS4;H7C2Y5 Q9UBS4 DNAJB11 DnaJ homolog subfamily B member 11 0 ;;; 222.51 1.61E-32 737841000 689630 628670 509208 591732 680630 840960 626320 676944 551253 FALSE TRUE 598493.6482 624540.2254 755462.692 726093.7947 667086.7946 873312.2754 565579.5828 532184.7936 486084.4983 1.23125434 1.284838804 1.554179766 1.493760441 1.372367967 1.796626468 1.163541698 1.094840085 1 18.8908476 2.02095327 24.92900982 1.07669322 1.452683369 0.559926317 0.156400496 161.9808483 192714.7969 0.064101563 0.043212897 104.9429505 -2.02095327 0.375990148 DGMVSFHDNPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGMVSFHDNPEK 12 0 Q9UNS2-2;Q9UNS2;H7C3P9;K7ELN6 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 0 ; 145.31 6.38E-05 558780000 698340 578770 220190 539190 625490 559580 656630 832510 984080 FALSE TRUE 606052.5996 574968.0218 326674.6205 661621.3305 613043.9728 581107.4047 592950.1237 654484.2151 867743.1835 0.698423924 0.6626016 0.376464635 0.762462147 0.706480886 0.669676715 0.683324439 0.75423723 1 19.7269086 -0.72500854 0.811865438 10 0.633751523 0.545688877 0.101512059 42.63703618 1.399382969 671.1219088 0.038030969 0.188361205 0.72500854 -9.366248477 DGNASGTTLLEALDCILPPTRPTDKPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGNASGTTLLEALDCILPPTRPTDKPLR 28 2 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ; 266.17 2.49E-54 19123500000 3955800 3306700 2842000 3282100 3121800 2748520 4013700 4561200 6603000 FALSE TRUE 3433031.007 3284978.07 4216400.706 4027350.969 3059682.288 2854257.343 3624451.992 3585822.875 5822400.862 0.589624639 0.56419648 0.724168742 0.691699363 0.525501827 0.490219999 0.62250128 0.615866712 1 22.47318274 1.235865006 5.532041461 1.019796565 0.602489147 0.763900619 0.069404564 0.079927875 7.666630327 0.127127442 0.018518362 17.21333441 -1.235865006 -0.417307418 DGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYK 36 3 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ; 196.77 6.41E-30 456230000 1026630 824940 442720 461990 679490 547160 1076330 1241230 219985 FALSE TRUE 890958.2444 819520.9148 656820.8728 566891.8906 665969.4784 568209.5993 971947.6823 975802.6238 193978.6239 4.593074363 4.224800126 3.386047697 2.92244516 3.433210655 2.929238221 5.010591697 5.030464719 1 17.56553815 1.225284179 24.96875834 0.999992751 3.954591962 0.584509232 0.779249746 550.5247751 1035298.707 4.071557406 0.216254769 16.79902898 -1.225284179 2.954599212 DGNDLHMTYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DGNDLHMTYK 10 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ;; 133.07 0.00020691 1018040000 3644810 2912000 1214410 2250500 2857960 2477870 3255800 3957790 3705390 FALSE TRUE 3163139.124 2892870.88 1801702.738 2761510.422 2801092.188 2573195.262 2940053.017 3111447.408 3267343.015 0.968107453 0.885389403 0.551427484 0.845185341 0.8572997 0.787549777 0.899829924 0.952286734 1 21.63968649 1.85358954 1.536265161 1.000400762 0.808136142 0.278011089 0.107001531 0.589205674 2.487242746 0.128285582 0.034162537 71.3821361 -1.85358954 -0.19226462 DGNGYISAAELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DGNGYISAAELR 12 0 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2 P0DP25 CALM2;CALM1 0 ;;;;; 240.33 7.75E-16 2084000000 1142454 1035989 957495 1737890 1368100 1307420 1072408 1460123 5257260 FALSE TRUE 991475.8093 1029183.52 1420542.785 2132504.486 1340877.487 1357717.293 968406.0372 1147887.059 4635752.712 0.213875906 0.222010013 0.306431959 0.460012563 0.289246983 0.292879577 0.208899417 0.247616111 1 22.14437218 1.236967949 24.99977278 1.000000887 0.280570961 0.907066149 0.072414969 12.40281355 194620.2301 0.117618463 0.019064102 17.25710528 -1.236967949 -0.719429926 DGNLELLTRPDTPPWAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGNLELLTRPDTPPWAR 17 1 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 ; 91.475 0.0032344 262097000 146124 123672 114655 133701 145759 156090 169205 167033 268680 FALSE TRUE 126813.3432 122859.5905 170102.5415 164059.8555 142858.6811 162094.8833 152795.5251 131314.2928 236916.9565 0.535264951 0.518576603 0.71798382 0.692478318 0.60299053 0.68418439 0.644932838 0.554262957 1 17.85402193 1.232395455 24.99989708 1.000000623 0.620844698 0.755897748 0.068063805 107.8720593 437380.6501 0.15645341 0.017344466 17.076366 -1.232395455 -0.379155925 DGNLHEGDIILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGNLHEGDIILK 12 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83 Q9UDY2-7 TJP2 Tight junction protein ZO-2 0 106.58 0.0019069 538570000 886890 799500 527500 646020 749000 687660 889860 1042400 942380 FALSE TRUE 769685.2394 794248.0319 782600.7644 792708.7148 734096.3654 714114.7252 803561.5142 819490.872 830972.91 0.926245886 0.955804963 0.941788541 0.953952536 0.883417927 0.859371848 0.967012889 0.986182416 1 19.66444192 2.013820604 24.95060622 0.987452275 0.921795566 0.514987003 0.030071869 196.1925323 354188.9321 0.01348974 0.009089919 103.2334886 -2.013820604 -0.065656708 DGNVLLHEMQIQHPTASLIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGNVLLHEMQIQHPTASLIAK 21 0 P40227 P40227 CCT6A T-complex protein 1 subunit zeta 0 ; 252.01 1.45E-36 4022100000 2174960 2017340 796780 1461520 1994410 1827140 2277600 2760390 2339370 FALSE TRUE 1887533.525 2004087.961 1182105.473 1793380.454 1954725.143 1897431.258 2056718.703 2170102.08 2062812.344 0.915029198 0.971531883 0.573055264 0.869386137 0.94760202 0.919827373 0.997045955 1.052011389 1 20.97618115 2.725175455 1.288932607 1.025316791 0.828750498 0.343640596 0.106664351 0.49470719 1.718514262 0.057896458 0.046796277 531.0989652 -2.725175455 -0.196566292 DGPEETDWWWAALHGQEGYVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DGPEETDWWWAALHGQEGYVPR 22 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 0 ;; 193.63 6.49E-18 246504000 415836 354739 268291.5 299524 355963 288564 370877 427978 384948 FALSE TRUE 360882.219 352408.6962 398038.1668 367535.5021 348880.0327 299665.2438 334909.4056 336458.2352 339439.886 1.063169751 1.038206501 1.172632278 1.082770521 1.027810953 0.882822721 0.98665307 0.991215968 1 18.37279657 3.06616552 3.940319478 0.969723019 1.090809384 0.605303318 0.046909946 0.15620652 4.881154011 0.0150776 0.017046021 1164.56979 -3.06616552 0.121086365 DGPLNMILDDGGDLTNLIHTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DGPLNMILDDGGDLTNLIHTK 21 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;;; 215.32 6.61E-25 2628811000 3116067 2763291 1973171 2502709 2680187 2309625 3175998 3876988 3280143 FALSE TRUE 2704270.851 2745138.759 2927403.095 3070987.33 2626856.522 2398477.768 2867990.203 3047924.287 2892368.231 0.934967692 0.949097259 1.012112864 1.061755311 0.90820266 0.829243574 0.991571603 1.053781553 1 21.4638198 2.001467463 24.99997204 1.02831561 0.951588394 0.216065433 0.061809096 73.38222143 1250137.539 0.027539074 0.018408074 100.3384672 -2.001467463 -0.076727216 DGPPHQVLVVPLHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGPPHQVLVVPLHSR 15 0 Q2NL82;I3L1Q5 Q2NL82 TSR1 Pre-rRNA-processing protein TSR1 homolog 0 95.662 0.0023125 85533000 196000 225900 110300 141490 230940 253200 179430 168620 183020 FALSE TRUE 170098.1034 224416.048 163641.4489 173617.467 226344.7458 262940.7678 162028.9062 132561.9252 161383.5841 1.053998796 1.390575437 1.013990672 1.075806241 1.402526453 1.62929067 1.003998685 0.82140898 1 17.30013431 2.015980798 24.99580309 0.902374653 1.25894809 0.390636114 0.19053421 223.2103594 349125.3158 0.080043535 0.053948215 103.7482543 -2.015980798 0.356573437 DGPVRPQNAEEEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGPVRPQNAEEEKR 14 2 Q92504 Q92504 SLC39A7 Zinc transporter SLC39A7 0 58.071 0.062861 110180000 81915 77976 57500 57556 74011 85116 70804 91094 78246 FALSE TRUE 71089.7252 77463.77052 85307.19233 70624.96949 72538.3259 88390.4676 63937.43898 71614.25699 68995.84702 1.030347887 1.122730916 1.236410538 1.023611892 1.051343364 1.281098376 0.926685326 1.037950255 1 16.07422191 2.2069734 24.99995703 0.996010447 1.121396861 0.35080174 0.086970472 231.8006932 183458.9156 0.034537945 0.023287817 161.0546987 -2.2069734 0.125386414 DGQAMLWDLNEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DGQAMLWDLNEGK 13 0 P63244;J3KPE3;H0YAF8;D6R9L0;H0Y8W2;D6RAC2;D6R9Z1;D6RFX4;D6REE5;H0YAM7;H0Y8R5 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 ;;; 281.54 4.30E-32 694010000 1854200 1521020 1090920 1347790 1484390 1179460 1830600 2245810 1827180 FALSE TRUE 1609162.772 1511028.319 1618492.561 1653826.319 1454853.543 1224834.589 1653068.694 1765561.008 1611172.862 0.998752406 0.937843701 1.004543087 1.026473545 0.902977935 0.760213021 1.026003313 1.095823453 1 20.61967986 2.018031204 24.99991969 1.056603479 0.939602735 0.282026567 0.077121672 281.4208899 390183.2455 0.032985188 0.022234246 104.2392322 -2.018031204 -0.117000744 DGQDAIAQS(ph)PEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DGQDAIAQSPEK 12 0 Q9NWH9;H7BXE3;H0YL55 Q9NWH9 SLTM SAFB-like transcription modulator 1 DGQDAIAQS(1)PEK;DGQDAIAQS(1)PEK;DGQDAIAQS(1)PEK;DGQDAIAQS(1)PEK 330.54 3.98E-58 3654500000 6132220 4098840 4315040 5086820 4609520 3309080 5236290 6433010 12626100 TRUE FALSE 5321831.59 4071914.45 6401807.777 6241860.228 4517799.57 3436382.449 4728475.402 5057360.873 11133456.84 0.478003523 0.365736762 0.575006296 0.560639909 0.405785879 0.308653682 0.424708648 0.454248931 1 23.40839827 1.238551554 7.392734924 1.009570872 0.444723219 0.823925625 0.080407622 0.043610926 16.2362663 0.12346136 0.020950492 17.32014621 -1.238551554 -0.564847654 DGQDAIAQS(ph)PEKESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 207.67 1.98E-09 5332310000 4531530 2846410 2786170 2346900 2820030 1777760 4245280 4561800 2572860 TRUE FALSE 3932676.829 2827711.745 4133571.131 2879799.515 2763916.92 1846151.578 3833573.399 3586294.57 2268699.422 1.733449919 1.24640211 1.822000346 1.269361418 1.218282552 0.813748864 1.689766993 1.580771139 1 21.11343405 3.694564386 24.94200591 1.301433385 1.565196241 0.221194311 0.29085333 846.5743338 479933.2987 0.082995746 0.123103457 4949.534843 -3.694564386 0.263762856 DGQPCMDHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGQPCMDHDR 10 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRU9 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 107.97 0.0016793 349610000 432230 385720 249140 270710 362420 389750 416280 418950 363230 FALSE TRUE 375109.7104 383186.1799 369624.9373 332178.843 355208.5511 404743.9347 375909.2297 329360.8028 320289.3632 1.171158813 1.196374978 1.154034382 1.037121057 1.109023876 1.263682099 1.173655053 1.028322638 1 18.28901636 1.664152304 4.640533909 1.00772265 1.156673937 0.515690985 0.05804448 0.133162184 6.502840887 0.042831862 0.016371454 46.14793834 -1.664152304 0.148951287 NKEPGAEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NKEPGAEEK 9 1 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 108.35 0.0023948 241520000 481410 424620 303870 371410 346970 340489 479390 704210 1272010 FALSE TRUE 417790.4488 421830.6433 450822.5484 455744.3171 340065.9758 353587.8322 432898.8316 553620.1717 1121634.427 0.372483617 0.376085677 0.401933587 0.40632162 0.303187891 0.315243384 0.385953588 0.493583434 1 20.09717111 1.157601543 2.15062304 1.293859597 0.3645196 0.970872265 0.034318202 0.147602964 0.570306369 0.291590449 0.010144862 14.37479112 -1.157601543 -0.929339996 DGQSS(ph)PQPSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DGQSSPQPSPR 11 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 DGQS(0.032)S(0.968)PQPSPR;DGQS(0.045)S(0.955)PQPSPR;DGQS(0.215)S(0.782)PQPS(0.003)PR;DGQS(0.215)S(0.785)PQPSPR;DGQS(0.207)S(0.792)PQPS(0.001)PR;DGQS(0.191)S(0.809)PQPSPR 189.23 2.94E-06 1397766000 2254680 1975351 1235040 1369595 1655410 1764089 1849307 1970506 1894467 TRUE FALSE 1956718.325 1962374.789 1832309.475 1680582.478 1622470.58 1831954.645 1669961.492 1549128.626 1670505.269 1.171333225 1.174719305 1.09685944 1.006032431 0.971245413 1.096647032 0.999674483 0.927341359 1 20.6718531 3.939257281 2.149136857 0.993741966 1.176512361 0.748988492 0.041870092 0.166128152 1.500276005 0.013152539 0.031335285 8694.753644 -3.939257281 0.182770395 DGQWFTDWDAVPHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DGQWFTDWDAVPHSR 15 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ;; 172.2 1.04E-06 1522400000 1537560 1175040 669530 829510 1101490 1175820 1084500 1255150 890280 FALSE TRUE 1334367.55 1167321.085 993316.9474 1017862.924 1079572.504 1221054.556 979325.3569 986745.9401 785032.1126 1.699761741 1.4869724 1.265320146 1.296587627 1.375195341 1.555419882 1.247497193 1.256949779 1 19.58239214 0.471190712 0.721983146 4.53E-17 1.439051431 0.533691224 0.131842343 6.870247756 1.228634757 10.42629198 0.058354993 2.959311704 -0.471190712 1.439051431 DGQYLLTGGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGQYLLTGGDR 11 0 A0A494C1L5;P50851-2;P50851;A0A494BZW2;H0YAC6;A0A3B3IS13 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 130.56 0.00051546 1470120000 750210 730450 433300 548260 714570 769030 667100 790630 737960 FALSE TRUE 651067.8477 725651.6259 642845.3293 672750.8126 700351.455 798615.0817 602404.7447 621559.9272 650719.2095 1.000535774 1.115153226 0.987899727 1.033857312 1.076272907 1.227280631 0.925752208 0.955189148 1 19.31167562 DGRHPQGEQMYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DGRHPQGEQMYR 12 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;;; 130.1 0.00013369 716918000 293963 275011 121658.3 141128.1 256031 292303 295192.9 293600 98190.8 FALSE TRUE 255115.0447 273204.4346 180492.6608 173173.3921 250936.484 303548.0856 266565.138 230815.9248 86582.79548 2.946486578 3.155412494 2.084625009 2.0000901 2.898225711 3.505870697 3.078731017 2.665840523 1 16.40179276 4.270198617 24.85225197 2.549536612 3.050950168 0.102168162 0.688852196 521.9561039 409997.734 0.177594523 0.469775448 18629.38926 -4.270198617 0.501413556 DGSAFEDGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DGSAFEDGLR 10 0 A0A3B3IRQ9;P55265-3;P55265-2;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ;; 128.57 0.00075847 1217440000 2390600 2298650 1912300 1960110 1997880 1993550 2166060 2455680 2630530 FALSE TRUE 2074676.153 2283550.017 2837094.676 2405182.934 1958126.097 2070243.158 1955995.835 1930551.942 2319551.74 0.89442978 0.984479017 1.223121962 1.03691713 0.844182979 0.892518637 0.843264585 0.83229527 1 21.1454146 3.246499516 24.24079519 0.873746903 1.044603263 0.394531859 0.093040412 116.7747245 356559.1446 0.02753899 0.034873862 1764.003799 -3.246499516 0.17085636 DGSDEPGTAACPNGSFHCTNTGYKPLYIPSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGSDEPGTAACPNGSFHCTNTGYKPLYIPSNR 32 1 K7ELL7;P14314-2;P14314;K7EPW7;K7EKX1;K7EJ70 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 259.47 1.65E-59 352360000 147200 111660 47394 122150 141330 172150 116540 142740 210960 FALSE TRUE 127747.147 110926.4981 70313.89692 149886.0244 138517.8095 178772.7219 105237.9687 112216.1618 186020.5491 0.686736748 0.596313142 0.377989944 0.805749823 0.744637139 0.961037491 0.565733029 0.603246052 1 17.50510247 3.711328704 24.97617317 0.754316672 0.557943204 0.3144663 0.154438847 987.7015481 905885.9382 0.043668335 0.064788593 5144.328621 -3.711328704 -0.196373468 DGSDVIYPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DGSDVIYPAR 10 0 P25685;P25685-2;M0R080 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ;; 161.79 1.62E-05 595790000 1073410 1022010 671220 779790 995310 950270 1058740 1159570 1067000 FALSE TRUE 931556.1488 1015296.349 995824.2371 956853.2378 975505.2783 986827.5018 956063.5578 911604.9793 940860.4755 0.990110833 1.079114678 1.05841861 1.016998017 1.036822466 1.048856369 1.0161587 0.968905595 1 19.84362127 1.97199374 4.335583631 0.983933868 1.03984984 0.445495059 0.024665903 0.167203239 7.209943944 0.012126642 0.006511252 93.75484938 -1.97199374 0.055915972 DGSTEDTASSLCGEEDT(ph)EDEELEAAASHLNK ddPTM_MDA-MB-175_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 DGSTEDTASSLCGEEDT(1)EDEELEAAASHLNK 108.11 0.00046154 115770000 46165 48634 35362 41426 58568 48425 72822 87050 38330 TRUE FALSE 40064.17828 48314.52005 52463.18148 50832.40646 57402.61139 50287.94109 65759.73365 68435.03492 33798.67107 1.185377325 1.429479874 1.552226162 1.503976484 1.698368888 1.487867407 1.945630747 2.024784785 1 15.0446789 5.449144839 0.566097055 1.706992963 0.293035563 0.16593733 0.282024022 12.65349898 1.74758728 0.157703157 13.95216572 281283.877 -5.449144839 -1.4139574 DGSYAWEIKDFLVGQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGSYAWEIKDFLVGQDR 17 1 Q14696 Q14696 MESDC2 LDLR chaperone MESD 0 126 4.11E-05 169220000 248170 156470 183990 167470 176830 142900 223460 296770 221870 FALSE TRUE 215373.7057 155442.1383 272968.1794 205496.6231 173311.429 148397.4555 201788.8836 233308.045 195640.7814 1.100863042 0.794528304 1.395251938 1.050377236 0.885865553 0.758520051 1.031425464 1.19253278 1 17.57784761 1.985955408 23.7336077 1.110606889 0.994674485 0.045063425 0.183015977 968.0850607 1635938.502 0.082339338 0.050060192 96.81784417 -1.985955408 -0.115932404 DGTAPPPQSPGSPGTGQDEEWS(ph)DEESPRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DGTAPPPQSPGSPGTGQDEEWSDEESPRK 29 1 A0A0C4DGG1;Q9UKS6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 DGTAPPPQSPGSPGT(0.001)GQDEEWS(0.975)DEES(0.024)PRK;DGTAPPPQSPGSPGTGQDEEWS(0.997)DEES(0.003)PRK;DGTAPPPQSPGSPGTGQDEEWS(0.999)DEES(0.001)PRK;DGTAPPPQSPGSPGTGQDEEWS(0.999)DEES(0.001)PRK;DGTAPPPQSPGSPGTGQDEEWS(0.985)DEES(0.015)PRK;DGTAPPPQSPGSPGTGQDEEWS(0.999)DEES(0.001)PRK 317.88 1.63E-92 7142940000 1701979 1395615 926716 1129853 1384547 1132906 1543502 1922946 1425240 TRUE FALSE 1477058.163 1386447.113 1374878.957 1386403.392 1356997.224 1176489.627 1393813.414 1511738.962 1256749.751 1.175300144 1.103200627 1.093995807 1.103165838 1.079767251 0.93613675 1.109062017 1.202895772 1 20.26126597 5.298739914 1.215860086 1.083047127 1.389664431 0.164457096 0.069895405 11.59408459 5.648120214 0.021873289 6.237605933 198948.1543 -5.298739914 0.306617304 DGTGQIQVNIQEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGTGQIQVNIQEVR 14 0 A0A0C4DGQ5 A0A0C4DGQ5 CAPNS1 0 62.162 0.08961 0 152490 148460 94846 106290 139960 193370 115110 124880 172160 FALSE TRUE 132338.0601 147484.7565 140713.8428 130424.769 137175.0698 200809.069 103946.6499 98175.38382 151807.4409 0.871749496 0.971525214 0.926923226 0.859146088 0.903612293 1.322788052 0.684726976 0.646709958 1 17.21188298 DGTGVVEFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DGTGVVEFVR 10 0 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;; 189.38 2.37E-06 1348320000 2170250 1793900 1119990 1335640 1822610 1681810 1795320 2080200 1813340 FALSE TRUE 1883445.964 1782115.753 1661620.91 1638917.476 1786343.627 1746510.319 1621210.143 1635365.418 1598969.011 1.177912737 1.11454052 1.039182685 1.024983889 1.117184645 1.092272775 1.01390967 1.022762422 1 20.60871055 8 0.562840856 1.034901743 8.07835908 0.593174052 0.036530927 115.8653889 1.038247298 0.020608653 990.2164185 100000000 -8 7.043457337 DGTSFGEYGGWYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGTSFGEYGGWYK 13 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;H0YG16;G5E9S8;H0YJU9;H0YJT3;H0YJL0 Q07866-6 KLC1 Kinesin light chain 1 0 96.604 0.00968 126680000 349930 55538 43571 41081 72653 52939 62105 69382 62630 FALSE TRUE 303685.8639 55173.16722 64642.08134 50409.06893 71207.34744 54975.59759 56082.06666 54545.19923 55225.95275 5.498970118 0.99904419 1.170501877 0.91277862 1.289381964 0.995466712 1.015502022 0.987673304 1 15.75305878 4.738926921 24.99999988 1.045987784 5.498971455 0.994150749 0.107336544 1.882994376 128466.2171 0.024545177 0.139531404 54818.47134 -4.738926921 4.452983671 DGTSLWDLLSSCHFTEEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGTSLWDLLSSCHFTEEQR 19 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 317.83 8.88E-62 122517000 129164 150203 56516 109928 170856 167199 155401 171687 231650 FALSE TRUE 112094.6501 149216.3066 83847.32663 134888.8325 167456.2999 173631.2537 140330.2349 134973.0711 204264.6009 0.548771787 0.730504972 0.410483883 0.660363235 0.819800881 0.850031053 0.687002223 0.660775634 1 17.64007968 3.439172716 5.597321626 0.777456312 0.572754345 0.450457467 0.120360214 0.188597255 15.15204992 0.034685581 0.045796705 2748.987188 -3.439172716 -0.204701968 DGVADVSIEDSVISLSGDHCIIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DGVADVSIEDSVISLSGDHCIIGR 24 0 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;; 292.97 7.31E-62 796630000 389346 375937 222001 359660 369115 338194 350432 433020 1108520 FALSE TRUE 337892.9396 373467.4451 329361.4261 441326.3001 361770.3337 351204.542 316447.1586 340422.0428 977472.0284 0.345680418 0.382074816 0.336952277 0.451497626 0.370108119 0.359298816 0.323740372 0.34826781 1 19.89869589 1.237678557 24.99999627 1.000000742 0.364400109 0.970318271 0.03491939 3.403953196 96421.48357 0.051124898 0.008692784 17.2853651 -1.237678557 -0.635600634 DGVFCLLSDDHGASWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGVFCLLSDDHGASWR 16 0 Q99519;E9PIF4 Q99519 NEU1 Sialidase-1 0 159.34 9.16E-09 82699000 72828 65493 31600 54277 61257 74577 62258 66746 59452 FALSE TRUE 63203.59528 65062.77217 46881.8657 66601.42242 60038.10555 77446.02545 56220.22874 52472.88732 52423.65229 1.205631285 1.241095752 0.89428843 1.270446059 1.145248431 1.477310757 1.07242106 1.000939176 1 15.67793025 2.01282448 24.99528404 1.011379624 1.200119692 0.275956017 0.141528252 291.5362208 568210.3784 0.057478178 0.038726189 102.9969775 -2.01282448 0.188740068 DGVGMVEYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGVGMVEYLR 10 0 Q13242;H0YIB4 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 ; 150.27 5.09E-05 967640000 960240 820320 567510 589480 836500 837270 829380 907890 900100 FALSE TRUE 833341.8511 814931.2639 841959.7342 723330.4436 819855.2866 869480.3187 748946.8553 713744.7887 793691.2034 1.049957272 1.026761114 1.060815252 0.911349956 1.032965066 1.095489423 0.943624992 0.899272646 1 19.59821829 2.111671805 9.596455091 0.936212743 1.025558321 0.339497989 0.052984314 0.2978312 23.96036406 0.021657904 0.014594234 129.3218191 -2.111671805 0.089345578 DGVIEASINHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGVIEASINHEK 12 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 140.01 5.93E-05 1493260000 5641600 4672300 6843400 6490500 1950840 2320900 5635600 5170200 5657900 FALSE TRUE 4896048.266 4641607.354 10152891.13 7964267.226 1912022.101 2410186.525 5089060.379 4064592.965 4989029.508 0.98136286 0.930362778 2.035043311 1.596356008 0.383245298 0.483097268 1.020050166 0.814706138 1 22.25032777 3.248434654 24.9999594 0.757661705 1.399627267 0.438279757 0.362707978 210.3565552 532596.3455 0.111632051 0.142341291 1771.881419 -3.248434654 0.641965563 DGVLEEQIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGVLEEQIER 10 0 Q09161;X6R941 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 96.015 0.01281 0 98549 103510 72299 65044 97994 99372 87650 106490 96066 FALSE TRUE 85525.49996 102830.036 107263.0382 79813.23434 96044.11112 103194.9051 79149.71649 83717.94221 84709.18692 1.009636653 1.213918345 1.266250358 0.942202815 1.133809857 1.21822566 0.934369923 0.988298262 1 16.37023082 2.228315475 24.99468767 0.975494576 1.132196024 0.363662849 0.097540164 223.8639056 546147.6172 0.039296467 0.026827266 169.1669329 -2.228315475 0.156701447 DGVPEGAQLQGPVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGVPEGAQLQGPVHR 15 0 P16989;P16989-3;P16989-2 P16989;P16989-2 YBX3 Y-box-binding protein 3 0 ; 154.65 2.44E-06 271930000 639770 551070 418500 517700 565910 552500 533070 602940 1033450 FALSE TRUE 555222.7735 547449.9849 620887.9998 635251.6975 554649.4982 573755.0325 481372.9534 474005.9731 911276.7183 0.609280104 0.600750545 0.681338596 0.697100765 0.608651014 0.629616692 0.528240153 0.520155913 1 19.79752968 1.23078436 24.99950135 1.000000708 0.606732904 0.829023956 0.055736202 131.663433 423243.0263 0.167152454 0.015880597 17.01313547 -1.23078436 -0.393267804 DGVSEGQFQQVLHHELLAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGVSEGQFQQVLHHELLAIR 20 0 Q9UKV8-2;Q9UKV8 Q9UKV8-2 AGO2 Protein argonaute-2 0 ; 195.56 1.06E-21 104891000 174514 136379 78559 107490 137313 125780 131888 160484 158054 FALSE TRUE 151451.5327 135483.1174 116550.3952 131897.2474 134580.7399 130618.838 119097.5221 126165.7455 139369.0362 1.086694268 0.972117775 0.836271803 0.946388459 0.965643041 0.937215622 0.854547935 0.905263816 1 17.08855055 4.638898239 3.54389011 0.918283285 1.091449736 0.531769114 0.048871503 0.18904766 3.856451529 0.012116664 0.071680377 43540.98393 -4.638898239 0.173166451 DGVVEITGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 DGVVEITGK 9 0 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;; 186.76 9.61E-05 7376212000 9640400 8229270 6773140 7970800 7580920 6893710 10760800 11202420 13834790 FALSE TRUE 8366396.714 8175211.384 10048653.16 9780691.966 7430074.524 7158915.485 9717219.272 8806869.66 12199256.89 0.685811996 0.670140113 0.823710268 0.801744898 0.6090596 0.586832096 0.796541901 0.721918535 1 23.54028993 0.825716401 1.786290106 1.604928711 0.707318569 0.559680511 0.079819424 2.789886914 3.049059363 6.281534918 0.022938557 6.694473104 -0.825716401 -0.897610141 DGVVEITGKHEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DGVVEITGKHEER 13 1 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;; 209.21 2.39E-08 4510370000 14608050 13084250 2698314 2437190 9905100 8960730 17345660 16581580 521576 FALSE TRUE 12677559.18 12998298.7 4003227.676 2990591.24 9708007.889 9305455.081 15663480.56 13035738.16 459915.8795 27.56495208 28.26233944 8.704260615 6.502474416 21.10822505 20.23295019 34.05727278 28.34374445 1 18.81101048 5.095757333 1.42E-20 9.3534749 31.42897939 0 10.90087428 0 0.161993277 5.160177288 5.160177419 124668.672 -5.095757333 22.07550449 DGVVRPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 DGVVRPLK 8 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;; 109.11 0.0033574 41458880000 45153960 39160810 30208880 34908580 40656870 37155600 47257880 50909280 60020290 FALSE TRUE 39186749.78 38903560.06 44817995.41 42835106.63 39847877.83 38584999.97 42674818.07 40022726.65 52924759.69 0.740423764 0.735072966 0.846824731 0.809358548 0.752915612 0.729053853 0.806329936 0.756219336 1 25.65743948 1.235937341 24.99740441 1.000000301 0.773301423 0.7802931 0.038012081 34.11650755 325031.9716 0.062910161 0.009462512 17.21620165 -1.235937341 -0.226698878 DGVYFLYEALHGPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGVYFLYEALHGPPK 15 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ; 126.48 8.40E-05 958760000 1637440 1556250 1297220 1661890 1569950 1276260 2001330 2299800 3198100 FALSE TRUE 1421048.155 1546026.891 1924559.931 2039247.525 1538711.067 1325358.548 1807241.325 1808005.667 2820024.261 0.50391345 0.54823177 0.682462189 0.723131199 0.545637528 0.469981257 0.640860204 0.641131246 1 21.42727614 1.123377974 2.298686682 1.21662401 0.589230194 0.72958905 0.078110331 0.532600416 2.214895507 0.775354283 0.022034097 13.28550216 -1.123377974 -0.627393816 DGVYFLYEALHGPPKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGVYFLYEALHGPPKK 16 1 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 163.23 5.06E-09 738900000 709880 641260 435220 474130 517940 441710 824930 923750 471310 FALSE TRUE 616067.5594 637047.5208 645693.8477 581788.4631 507634.0073 458702.8695 744928.4156 726213.2511 415592.2687 1.482384553 1.532866631 1.553671462 1.399902036 1.221471248 1.103732923 1.792450129 1.747417615 1 18.66480929 3.736549241 23.98702543 1.424056053 1.523963453 0.049163001 0.251002878 495.0715266 5904133.018 0.074617229 0.11723336 5451.91707 -3.736549241 0.0999074 DGWENVPPFDHPLIWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGWENVPPFDHPLIWK 16 0 Q96GA7;F8VYZ3;H0YID3 Q96GA7 SDSL Serine dehydratase-like 0 ; 102.58 0.001506 375420000 447800 491650 265880 377380 403760 322050 420880 556770 461620 FALSE TRUE 388622.0954 488420.3188 394460.4573 463069.8969 395725.9659 334439.4719 380063.1224 437709.0683 407047.8095 0.954733293 1.199908972 0.969076477 1.137630239 0.97218547 0.82162209 0.933706345 1.07532594 1 18.63483873 3.142020357 9.203230068 0.965450561 1.067925812 0.233169775 0.094185433 0.455384673 39.29023657 0.028909925 0.032818358 1386.820834 -3.142020357 0.102475251 DGWGGYGSDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DGWGGYGSDKR 11 1 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 ;; 144.1 5.91E-05 2278090000 2603230 2224570 1360290 1646120 2040250 1760550 2576830 2744190 2312020 FALSE TRUE 2259206.56 2209956.653 2018130.794 2019896.705 1999653.017 1828279.498 2326929.423 2157366.324 2038695.629 1.108162752 1.084005195 0.989912748 0.990778945 0.980849219 0.896788844 1.141381474 1.058209128 1 20.95921497 4.351487717 5.205660873 1.014437873 1.101996564 0.25679734 0.061893299 0.311601689 12.6199326 0.016682713 0.046372871 22464.03243 -4.351487717 0.087558691 DGWLYGEHDVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGWLYGEHDVSK 12 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 0 83.204 0.012931 226360000 424390 387230 280770 309780 365290 318100 407660 458260 474620 FALSE TRUE 368305.7862 384686.2606 416551.3111 380120.2837 358021.4437 330337.5128 368125.1959 360264.6652 418510.9643 0.88003856 0.919178453 0.995317558 0.908268399 0.855464908 0.789316269 0.879607053 0.860824915 1 18.67490589 3.441369715 6.415400388 0.871459615 0.933758223 0.151983912 0.058313332 0.29920248 35.2101393 0.016966675 0.022244472 2762.928938 -3.441369715 0.062298608 DGWPAMCIHGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DGWPAMCIHGDK 12 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;; 133.71 0.00015835 3191730000 3723930 3034410 2095160 2586370 2777040 2527660 3420710 3818880 3539340 FALSE TRUE 3231803.215 3014476.761 3108386.384 3173644.839 2721782.337 2624900.716 3088970.071 3002242.231 3120923.257 1.035527935 0.965892626 0.99598296 1.016892944 0.872108063 0.841065447 0.989761624 0.961972462 1 21.57354145 3.271817777 24.99763514 0.936268015 1.000340385 0.318576955 0.051079331 277.7949114 208801.7678 0.015882529 0.020502903 1869.897397 -3.271817777 0.06407237 DGWPAMGIHGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DGWPAMGIHGDK 12 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;;; 123.64 0.00033718 2175570000 2792190 2339230 1576680 1855610 2176340 1853970 2499370 2989930 2609990 FALSE TRUE 2423195.017 2323863.444 2339167.722 2276954.612 2133035.092 1925293.426 2256981.482 2350556.737 2301439.956 1.052903862 1.009743243 1.016393113 0.989360859 0.926826306 0.836560355 0.980682323 1.021341761 1 21.13410537 3.598931984 3.033291838 0.957973195 1.025583333 0.298388526 0.050799273 0.421024286 7.369354885 0.016901434 0.026533723 3971.293494 -3.598931984 0.067610137 DGWPVSLSNSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGWPVSLSNSVR 12 0 Q96RW7-2;Q96RW7 Q96RW7-2 HMCN1 Hemicentin-1 0 49.934 0.096225 663530000 150490 119090 111310 107900 43635 51296 114060 129890 113840 FALSE TRUE 130602.3652 118307.6899 165139.8883 132400.3441 42766.74887 53269.39031 102998.4788 102114.0343 100381.9649 1.301054082 1.178575156 1.645115121 1.318965457 0.426040165 0.530666942 1.026065577 1.017254787 1 16.61514057 3.370130785 8.989968936 0.831329767 1.375978569 0.595605087 0.229209689 0.214392711 16.50535203 0.072542207 0.093670595 2344.93487 -3.370130785 0.544648802 DGWQVEEADDWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DGWQVEEADDWLR 13 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ;; 144.28 9.59E-05 249850000 664152 659381 589751 621706 752501 860210 736730 855820 880488 FALSE TRUE 576382.6305 655049.4828 874956.5562 762873.8495 737527.7023 893302.8353 665282.038 672809.553 776397.7117 0.74238064 0.843703521 1.12694376 0.98258127 0.949935441 1.150573761 0.856883048 0.866578485 1 19.56643634 4.467171433 24.48412091 0.976866559 0.767711306 0.440182647 0.094980467 134.972052 332134.5626 0.024949956 0.066191289 29320.50411 -4.467171433 -0.209155253 DGWSLWYSEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DGWSLWYSEYR 11 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;; 258.52 3.37E-20 530630000 566680 545850 469080 451440 339949 345703 342523 439210 1853890 FALSE TRUE 491791.8022 542264.2754 695928.657 553946.3518 333184.68 359002.4181 309305.1722 345288.3594 1634725.236 0.30084065 0.331715853 0.425715981 0.338862054 0.203816931 0.21961025 0.189209272 0.211221037 1 20.64061674 1.235523546 24.99998814 1.000000987 0.274479427 0.902214169 0.074732904 28.23517291 232379.0198 0.145055269 0.02111341 17.19980589 -1.235523546 -0.725521561 DGWVYYANHTEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DGWVYYANHTEEK 13 0 F5H3R5;Q9NZC7-3;Q9NZC7-7;Q9NZC7-5;Q9NZC7-6;Q9NZC7-2;Q9NZC7 F5H3R5 WWOX WW domain-containing oxidoreductase 0 98.582 0.0032533 139180000 314260 261590 217400 323030 316880 282660 275960 292330 388850 FALSE TRUE 272729.7448 259871.5981 322535.3672 396378.8987 310574.708 293534.1131 249197.4417 229817.5044 342880.596 0.795407346 0.757906983 0.940663808 1.156026043 0.905780938 0.856082603 0.726776156 0.670255206 1 18.38734674 2.462626612 3.869689244 0.769841505 0.916067144 0.113208408 0.134526282 0.385021776 12.92267839 0.054589371 0.043261455 290.1526969 -2.462626612 0.146225639 DGYAQILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DGYAQILR 8 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ;; 113.91 0.010765 185470000 602870 621560 383401 554100 686740 737600 537390 627540 652520 FALSE TRUE 523199.202 617476.9314 568815.006 679916.8739 673075.2176 765975.9493 485274.0005 493345.4545 575379.829 0.90931099 1.073164022 0.988590453 1.181683541 1.169792863 1.331252697 0.843397659 0.857425703 1 19.13415512 2.199233426 24.99996048 0.88897755 1.10793742 0.401171672 0.119925391 154.9098516 98473.80664 0.050530729 0.03406842 158.2098163 -2.199233426 0.218959869 DGYDYDGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DGYDYDGYR 9 0 J3KTL2;Q07955;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;; 190.52 8.60E-05 22318100000 16015900 13197300 8616400 9375800 12859500 12331600 13031100 15121300 13490600 FALSE TRUE 13899358.24 13110606.07 12783319.86 11504718.69 12603621.11 12806004.63 11767345.93 11887727.67 11895756.64 1.168429942 1.102124604 1.07461175 0.967127947 1.059505628 1.076518714 0.989205335 0.999325056 1 23.5039437 7.999999996 0.496139932 1.006692952 6.263829978 0.684934913 0.034375142 67.24619047 0.744671236 0.0224556 366.8245682 99999999.19 -7.999999996 5.257137026 DGYGGSRDS(ph)YSSSR ddPTM_MDA-MB-175_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(1)YSSSR;DGYGGS(0.001)RDS(0.999)YSSSR 193.3 1.66E-07 1045510000 700390 687290 563320 578920 764710 860580 821690 840150 788770 TRUE FALSE 607831.6869 682775.1467 835743.4362 710372.6342 749493.7671 893687.0695 742002.6303 660490.4606 695522.5092 0.873920943 0.98167225 1.20160516 1.021351034 1.077598147 1.284914662 1.06682763 0.949632042 1 19.40773768 7.408669166 10.57954169 1.053168452 0.135010547 0 0.119407585 0 0 0.027750842 0 25625312.22 -7.408669166 -0.918157906 DGYNYTLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DGYNYTLSK 9 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;;; 213.45 4.35E-06 5571436000 2629040 2450100 1881024 2079431 2497870 2162420 2779590 3050990 3423890 FALSE TRUE 2281605.703 2434005.132 2790693.498 2551597.591 2448167.274 2245609.697 2510025.79 2398559.531 3019121.625 0.75571838 0.806196449 0.924339541 0.845145677 0.810887264 0.743795705 0.831376175 0.79445608 1 21.52569745 1.234517164 24.9732947 1.000000271 0.815776832 0.580026368 0.049721786 92.29510259 569954.6389 0.093894774 0.012582013 17.15999527 -1.234517164 -0.184223439 DGYSYGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGYSYGSR 8 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ; 113.41 0.0066389 1156650000 1181090 1339680 852040 990660 1265330 1287690 1248910 1324470 1208160 FALSE TRUE 1025005.964 1330879.554 1264089.394 1215604.494 1240152.409 1337228.268 1127790.9 1041242.398 1065332.701 0.962146344 1.2492619 1.18656772 1.14105621 1.164098696 1.255221271 1.058627881 0.977387061 1 20.02287262 2.03224212 6.382971855 0.995600318 1.164367368 0.446552668 0.080132792 0.138691547 17.23167762 0.031921454 0.020881903 107.7065513 -2.03224212 0.168767049 DGYWFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGYWFLK 7 0 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49;A0A087X246 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 0 ; 97.068 0.028543 496480000 779960 747680 454210 567000 696360 571220 780260 890710 818390 FALSE TRUE 676886.3098 742768.4408 673867.4752 695746.0161 682503.7984 593195.203 704590.5053 700238.598 721640.8665 0.937982231 1.029277131 0.933798939 0.964116707 0.945766558 0.822008884 0.976372789 0.970342217 1 19.46092152 2.039138188 24.99997434 0.980144951 0.940424722 0.140105874 0.050604227 346.0306065 221029.6547 0.021355661 0.014397972 109.4304508 -2.039138188 -0.039720229 DHAGVMGESNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DHAGVMGESNR 11 0 P52306-4;P52306;P52306-5;P52306-6;P52306-2;P52306-3 P52306-4 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 0 ; 72.089 0.047249 185040000 283320 265253 162205 173722 208548 316470 225663 247660 246250 FALSE TRUE 245878.5442 263510.5356 240647.8805 213168.2353 204398.3028 328644.8057 203778.237 194699.8363 217138.6055 1.132357572 1.213559122 1.108268518 0.981715042 0.941326404 1.51352545 0.938470782 0.896661539 1 17.72825672 2.065137692 25 0.933900837 1.140380196 0.274973985 0.155005734 72.82180554 27948.36763 0.062668663 0.042251199 116.1816907 -2.065137692 0.206479359 DHAISLSEPR ddPTM_MDA-MB-175_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 ; 156.48 0.0051152 0 386510 330660 199524 260230 349980 362160 332250 326380 348480 FALSE TRUE 335431.7242 328487.8727 296014.4738 319319.1989 343016.0827 376092.5295 300028.4461 256586.1769 307283.0914 1.091604887 1.069007316 0.963328221 1.039169443 1.116286878 1.223928488 0.976391004 0.835015606 1 18.22920886 2.006491762 24.9999322 0.905717218 1.079086976 0.466128509 0.07564732 128.1631774 493557.3087 0.032060043 0.021553712 101.5060113 -2.006491762 0.173369758 DHALLEEQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DHALLEEQSK 10 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;; 192.38 6.89E-07 984170000 2359380 1728740 1623860 2317400 1486320 1431050 1584880 2275570 5904100 FALSE TRUE 2047581.955 1717383.793 2409164.127 2843601.089 1456745.14 1486103.42 1431178.582 1788957.064 5206124.024 0.393302569 0.329877618 0.462755808 0.546203102 0.27981376 0.285452942 0.274902898 0.343625518 1 22.31177825 1.237567086 24.9963677 1.000000753 0.361865541 0.843419405 0.086047338 9.999696001 251453.4276 0.134239634 0.022652926 17.280929 -1.237567086 -0.638135212 LYSEVSLTIDHSLIPEERLS(ph)PTPSMQDGLDLPSETDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYSEVSLTIDHSLIPEERLSPTPSMQDGLDLPSETDLR 38 1 Q9UK58;Q9UK58-6;Q9UK58-5;Q9UK58-4 Q9UK58 CCNL1 Cyclin-L1 1 LYSEVSLTIDHSLIPEERLS(0.951)PT(0.041)PS(0.009)MQDGLDLPSETDLR;LYSEVSLTIDHSLIPEERLS(0.92)PT(0.045)PS(0.034)MQDGLDLPSETDLR 149.97 1.37E-13 152027000 40897 34356 18923.2 25771.9 37965 33398 36262 37574 14209.6 TRUE FALSE 35492.35783 34130.31317 28074.52281 31623.80379 37209.57078 34682.84267 32745.31682 29539.0925 12529.75728 2.832645282 2.72394049 2.240627827 2.523895962 2.969696057 2.768037872 2.613403923 2.357515142 1 13.61307085 1.16679633 2.293496132 0.30360287 2.663024002 0.876786813 0.195077071 0.275045373 1.273268379 1.433036053 0.055368442 14.68237559 -1.16679633 2.359421132 DHASIQMNVAEVDKVTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DHASIQMNVAEVDKVTGR 18 1 Q8WVC2;P63220;Q9BYK1 Q8WVC2 RPS21 40S ribosomal protein S21 0 ;;; 229.96 9.60E-20 1532138000 1054771 1085066 268644 606766 1261256 1056946 1174061 1507006 736547 FALSE TRUE 915380.3399 1077938.13 398561.137 744541.4941 1236159.473 1097607.397 1060200.745 1184744.494 649473.2527 1.409419612 1.659711351 0.613668285 1.146377454 1.903326223 1.689996304 1.632400935 1.824162103 1 19.30891059 3.256465647 24.85674867 1.642432995 1.197207683 0.240797282 0.352486334 308.6549908 428489.0956 0.101472611 0.130712804 1804.951957 -3.256465647 -0.445225312 DHDRFWVLAAHPNLNLFAAGHDGGMIVFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DHDRFWVLAAHPNLNLFAAGHDGGMIVFK 29 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 37.673 0.067056 82513000 246520 178880 80701 87564 123540 110980 176910 183500 22691 FALSE TRUE 213941.7574 177704.9255 119728.2735 107446.7445 121081.7957 115249.4724 159753.2954 144259.953 20008.49583 10.69254577 8.881473501 5.983871779 5.370056073 6.051519151 5.76002681 7.98427312 7.209934931 1 14.28832509 4.387161207 2.707978192 5.879866701 10.56175495 0.479055317 1.839783313 0.26117162 3.606978309 0.477451688 1.920833233 24387.15886 -4.387161207 4.681888247 DHDTFLAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DHDTFLAVR 9 0 Q12907;D6RBV2;D6RDX1;D6RIU4 Q12907 LMAN2 Vesicular integral-membrane protein VIP36 0 ; 186.16 4.20E-05 457860000 161598 206030 75839 163455 237200 207876 138440 194444 302940 FALSE TRUE 140242.4149 204676.5754 112514.9941 200569.956 232480.1841 215873.1242 125014.1101 152863.6638 267126.7783 0.525003205 0.766215116 0.421204474 0.750841819 0.87029906 0.808129854 0.467995425 0.572251366 1 18.02716508 DHEDYDPQTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DHEDYDPQTVR 11 0 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 89.805 0.0080326 0 167530 142930 218480 118070 111900 106570 141100 159560 154380 FALSE TRUE 145390.486 141991.0834 324137.6588 144879.5981 109673.4089 110669.8169 127416.1437 125439.3357 136129.3723 1.068031708 1.043059856 2.381100077 1.064278749 0.805655731 0.812975297 0.935993031 0.921471491 1 17.05461886 3.49417751 24.79886886 0.900857405 1.497084471 0.362591511 0.365145868 707.3521202 1028450.006 0.099920169 0.144259902 3120.164637 -3.49417751 0.596227066 DHENIVIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DHENIVIAK 9 0 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ;;;;; 107.79 0.0027168 4520330000 11995600 9855010 9926630 13193940 9614180 9930410 10037610 10120410 18432040 FALSE TRUE 10410351.07 9790271.79 14727181.47 16189825.73 9422876.628 10312439.3 9064164.127 7956239.079 16253025.23 0.640517745 0.602366123 0.9061194 0.996111524 0.579761398 0.634493527 0.557690891 0.489523579 1 23.95420494 DHENYVACSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DHENYVACSR 10 0 Q96HU1;Q96HU1-2 Q96HU1 SGSM3 Small G protein signaling modulator 3 0 70.942 0.052472 127760000 168370 148920 97024 111400 125590 137640 165680 179130 175510 FALSE TRUE 146119.4779 147941.7347 143945.1309 136695.0726 123091.0047 142935.0999 149612.3791 140824.4435 154761.4077 0.944159659 0.955934279 0.930109987 0.883263306 0.795359816 0.923583611 0.966729247 0.90994548 1 17.23968623 -0.928973235 1.043509451 9.999999999 0.908445683 0.235417061 0.048304186 286.2955788 3.928895007 6044.879636 0.016680982 0.117767855 0.928973235 -9.091554316 DHFEEAMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 DHFEEAMR 8 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;;;;;; 201.39 0.00011215 10753030000 12597680 8730813 5583864 6511136 8473370 8271600 8251941 9071289 8709730 FALSE TRUE 10932864.67 8673459.715 8284239.307 7989588.945 8304766.515 8589813.804 7451669.032 7131464.44 7680075.642 1.423536067 1.129345611 1.078666369 1.040300814 1.081339156 1.118454323 0.970259849 0.928566953 1 22.87268909 8 0.689197179 1.002597107 48.61943206 0.845475752 0.053161214 115.9714953 0.646696674 0.024648171 8490.998886 100000000 -8 47.61683495 DHGGALGPEEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DHGGALGPEEFK 12 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 118.87 0.00057936 214220000 377190 366790 241690 390350 330920 314060 307800 421080 1284200 FALSE TRUE 327343.3858 364380.5323 358572.0924 478984.9336 324335.3394 326142.0914 277949.6034 331035.3188 1132383.339 0.28907471 0.321781962 0.316652568 0.422988327 0.286418325 0.288013856 0.245455398 0.292335031 1 20.110931 1.237814516 24.9999751 1.0000008 0.307209371 0.9575673 0.04579025 3.569673865 119529.1464 0.069015394 0.011834175 17.29077725 -1.237814516 -0.69279143 DHGSWS(ph)LSPPPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DHGSWSLSPPPER 13 0 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 DHGS(0.001)WS(0.971)LS(0.028)PPPER 120.66 0.00016468 120960000 93494 88991 51650 79512 135130 121210 106760 125840 122560 TRUE FALSE 81138.53102 88406.41226 76628.11276 97566.41486 132441.1774 125873.0271 96406.43163 98930.09529 108071.0964 0.75078845 0.818039376 0.709052793 0.902798418 1.225500451 1.164724254 0.892064898 0.915416782 1 16.7216212 3.478549986 24.99447291 1.023308263 0.771961012 0.601850654 0.103718512 44.17381261 772793.8305 0.033751738 0.044205515 3009.885579 -3.478549986 -0.251347252 DHIIDDALVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DHIIDDALVR 10 0 A0A1B0GVL3;Q05086-2;Q05086-3;Q05086;A0A0D9SG77 A0A1B0GVL3 UBE3A Ubiquitin-protein ligase E3A 0 ;;; 182.28 1.79E-06 653570000 708430 642960 391365 494134 645580 619650 603220 672390 652720 FALSE TRUE 614809.1806 638736.3534 580630.423 606334.6771 632734.2211 643488.3365 544719.8172 528604.631 575556.1852 1.06820011 1.109772373 1.008816234 1.053476086 1.099343969 1.118028705 0.946423358 0.91842403 1 19.13459724 2.226475835 24.99855177 0.946984445 1.074741866 0.70600209 0.03677867 115.0811588 238054.7061 0.015270833 0.010382852 168.4518694 -2.226475835 0.127757421 DHIKDEWEGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DHIKDEWEGLR 11 1 O60306;H0YH15 O60306 AQR Intron-binding protein aquarius 0 162.22 1.52E-05 195400000 203090 149710 130910 146060 139550 140530 164110 192510 144360 FALSE TRUE 176251.1419 148726.5452 194218.5139 179225.1554 136773.228 145936.28 148194.6375 151343.2346 127293.9253 1.384599788 1.168371113 1.525748487 1.407963145 1.074467833 1.146451252 1.164192534 1.188927392 1 16.95780405 3.240758138 24.99834231 1.129358767 1.368154828 0.61418739 0.100777617 42.00954533 477883.953 0.029566235 0.036321289 1740.837119 -3.240758138 0.238796061 DHINDIIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DHINDIIK 8 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;;;; 146.03 0.00055986 5414120000 13169700 12531900 9406700 11685500 12462600 9950100 11994100 15339400 15036100 FALSE TRUE 11429290.78 12449577.12 13955811.58 14338871.38 12214618.64 10332886.79 10830914.03 12059188.68 13258549.39 0.862031769 0.938984859 1.052589629 1.08148116 0.921263578 0.779337655 0.81690038 0.909540579 1 23.6604196 3.00557145 24.92649963 0.87317439 0.987473857 0.275393542 0.082018744 190.8847699 854002.2912 0.026434957 0.029884836 1012.911378 -3.00557145 0.114299468 DHINLPGFSGQNPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DHINLPGFSGQNPLR 15 0 P00491;G3V5M2 P00491 PNP Purine nucleoside phosphorylase 0 ;;; 191.89 1.57E-07 3709640000 1205710 1487490 973870 1063405 1301242 1240860 1208260 1425090 1887440 FALSE TRUE 1046372.369 1477718.58 1444836.789 1304867.358 1275349.83 1288596.687 1091083.131 1120345.594 1664308.993 0.628712801 0.887887157 0.868130134 0.784029506 0.7662939 0.774253274 0.655577261 0.67315961 1 20.66649188 3.207032553 2.602576976 0.750266033 0.806071496 0 0.115503763 1.042406136 14.45573374 0.036950933 0.045695022 1610.766366 -3.207032553 0.055805463 DHLDDPLDDTATVFQQLEQLCTVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DHLDDPLDDTATVFQQLEQLCTVSR 25 0 H0YBM6;Q8IVM9;Q9H2T7-2;Q9H2T7 H0YBM6 RANBP17 Ran-binding protein 17 0 ; 80.293 0.023588 24143000 13331.4 14197.7 10789.3 9582.8 13963.9 12629.1 11977.4 12799 14636.5 FALSE TRUE 11569.62171 14104.43437 16007.04157 11758.7212 13686.04571 13114.94965 10815.83359 10062.03345 12906.18964 0.896439773 1.092842641 1.240260837 0.911091618 1.060424966 1.016175185 0.838034609 0.779628514 1 13.65577551 2.291578307 4.967259891 0.851313879 1.045717977 0.325150676 0.109756221 0.195434465 10.12107781 0.042257816 0.031552837 195.694359 -2.291578307 0.194404098 DHLVTAYNHLFETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DHLVTAYNHLFETK 14 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ; 226.24 1.43E-12 1698200000 1581750 1315430 1089200 1494830 1156240 995370 1341340 1522800 2853200 FALSE TRUE 1372717.73 1306788.854 1615940.763 1834253.999 1133233.086 1033662.528 1211257.053 1197161.07 2515897.946 0.545617413 0.519412505 0.642291857 0.729065343 0.450428877 0.410852328 0.48144125 0.475838486 1 21.26264197 1.234549016 24.94596718 1.000000701 0.529775443 0.712942138 0.093344514 70.080267 435727.8622 0.185775273 0.024988926 17.16125388 -1.234549016 -0.470225258 DHLYGTLDPNTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DHLYGTLDPNTR 12 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 186.76 1.13E-05 3361380000 2653040 2523030 1651690 1814560 2456150 2577650 2312030 2601800 2712960 FALSE TRUE 2302434.042 2506456.05 2450452.809 2226583.582 2407277.42 2676813.863 2087809.686 2045425.317 2392236.959 0.962460693 1.047745726 1.024335319 0.930753775 1.006287195 1.118958493 0.87274368 0.855026217 1 21.18992887 2.207780869 24.99264425 0.896437186 1.012761234 0.385068057 0.06230263 185.8023286 150867.1376 0.025243185 0.017020934 161.354421 -2.207780869 0.116324048 DHMVTMHDVLDAQWLYDNHKDESYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DHMVTMHDVLDAQWLYDNHKDESYLR 26 1 O60832;O60832-2;H7C2Q2 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 38.746 0.071337 14023000 14738 13730 13892 14228 9763.6 8105.1 10573 14009 10328 FALSE TRUE 12790.33596 13639.80673 20610.21767 17458.68486 9569.323462 8416.908442 9547.632087 11013.28437 9107.035606 1.404445586 1.497721906 2.263109376 1.91705464 1.050761617 0.924220439 1.048379791 1.209316055 1 13.15276581 3.232728129 24.99993262 1.060905585 1.786273306 0.691758781 0.239955705 84.6615374 362886.2516 0.076933868 0.089565044 1708.945168 -3.232728129 0.725367721 DHNEEEGEETGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DHNEEEGEETGLR 13 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 142.45 4.03E-05 120580000 83786 70883 57997 83373 73654 80754 69187 82187 157530 FALSE TRUE 72713.46781 70417.36491 86044.54319 102304.1139 72188.4295 83860.65863 62477.25539 64611.94963 138906.9829 0.523468773 0.506938985 0.619440012 0.736493672 0.519688989 0.603718092 0.449777643 0.46514544 1 17.0837596 1.231832221 24.99969279 1.000000761 0.551021218 0.737540902 0.083776939 131.9568682 490247.0293 0.211718484 0.022273385 17.05423414 -1.231832221 -0.448979543 DHNS(ph)EDEDEDKYADDIDMPGQNFDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DHNSEDEDEDKYADDIDMPGQNFDSK 26 1 O95391 O95391 SLU7 Pre-mRNA-splicing factor SLU7 1 DHNS(1)EDEDEDKYADDIDMPGQNFDSK 214.92 2.61E-34 64308000 156500 80247 118850 117360 84000 64921 125420 135660 219180 TRUE FALSE 135818.1285 79719.85217 176326.2575 144008.3817 82328.56434 67418.55288 113256.7877 106650.1647 193268.7901 0.702742168 0.412481768 0.912336945 0.745119694 0.425979613 0.348833109 0.586006606 0.551823006 1 17.56024916 1.236089052 24.94652307 1.000000564 0.58148324 0.370789582 0.169546442 75.38614241 760732.8326 0.279009958 0.042444743 17.2222168 -1.236089052 -0.418517324 DHNVGSPPKS(ph)PTHASPQHTQTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DHNVGSPPKSPTHASPQHTQTEK 23 1 A0A0C4DGH6;A0JNW5;F8W665;A0JNW5-2 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 DHNVGS(0.018)PPKS(0.924)PT(0.054)HAS(0.001)PQHT(0.002)QTEK;DHNVGSPPKS(0.976)PT(0.024)HASPQHTQTEK;DHNVGSPPKS(0.997)PT(0.002)HASPQHTQTEK;DHNVGSPPKS(1)PTHASPQHTQTEK 327.55 9.58E-87 645700000 347082 405620 117259.9 411346 565956 432432 636410 682440 1009515 TRUE FALSE 301214.2343 402955.4555 173967.1799 504748.3963 554694.5829 449067.9389 574691.0562 536505.5168 890171.2867 0.338377837 0.452671819 0.195431129 0.567023902 0.623132414 0.504473628 0.645596038 0.602699194 1 19.76372344 -2 0.303470693 5.273183499 0.336284997 0.696616407 0.116417343 46.7956118 0.754197148 123.4421814 0.226010684 0.01 2 -4.936898503 DHPDVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DHPDVAK 7 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;G5E9S8 Q07866-6 KLC1 Kinesin light chain 1 0 ;;; 132.09 0.0034023 774910000 3818650 3264030 2364720 2791110 2550790 2800320 3893250 4484900 4074160 FALSE TRUE 3314005.727 3242588.372 3508306.502 3424874.185 2500034.27 2908050.122 3515683.214 3525839.037 3592517.446 0.922474498 0.902595024 0.97655935 0.953335436 0.695900384 0.809474182 0.978612705 0.981439642 1 21.77656373 2.144538787 8.593241249 0.986277777 0.877814023 0.301604418 0.078924119 0.370365055 30.24332709 0.035401023 0.023848617 139.4886228 -2.144538787 -0.108463754 DHPESYHSFMWNNFFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DHPESYHSFMWNNFFK 16 0 D6RAY7;D6R9P4;D6RFF8;P46926;D6R917;D6RB13 D6RAY7 GNPDA1 Glucosamine-6-phosphate isomerase;Glucosamine-6-phosphate isomerase 1 0 112.96 0.00040365 390460000 961340 904590 372940 675970 926820 852910 1042400 1162200 1023000 FALSE TRUE 834296.4833 898647.6887 553295.0314 829459.3201 908378.0953 885721.9996 941308.2084 913672.5743 902062.1054 0.924876988 0.996214876 0.613366894 0.919514649 1.007001724 0.981885831 1.043507096 1.01287103 1 19.78286724 3.3995962 4.758351106 1.009552645 0.84635531 0.371323286 0.097537503 0.218124275 9.080119989 0.028340985 0.03720415 2509.552008 -3.3995962 -0.163197336 DHQLDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DHQLDTR 7 0 O95671;O95671-2;O95671-3 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 0 ; 95.741 0.025148 0 1330300 1231070 800670 926120 954790 1094640 1206730 1353010 1257550 FALSE TRUE 1154497.484 1222983.02 1187876.69 1136409.701 935791.547 1136751.509 1089701.51 1063679.341 1108883.872 1.041134707 1.102895489 1.071236331 1.024823004 0.843904011 1.02513125 0.982701199 0.959234206 1 20.08067686 3.471989339 24.99963652 0.963586705 1.070396217 0.513095834 0.049142716 107.0489738 521475.4358 0.01365343 0.017687768 2964.758607 -3.471989339 0.106809512 DHQPCIIFMDEIDAIGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DHQPCIIFMDEIDAIGGR 18 0 A0A087X2I1;P62333;H0YJX2 A0A087X2I1;H0YJX2 PSMC6 26S protease regulatory subunit 10B 0 ;;; 211.43 3.03E-16 900360000 279782 267013 182710 208943 245562 243655 258058 287886 282478 FALSE TRUE 242808.0998 265258.974 271069.1671 256386.7016 240675.7966 253028.5655 233031.5749 226323.8192 249083.7726 0.974804971 1.0649388 1.088265061 1.029319168 0.966244385 1.015837213 0.935555024 0.908625306 1 17.92627151 2.854279027 1.202274286 0.942545555 1.045059187 0.41659637 0.042117349 0.38911007 1.203355334 0.021963571 0.020153393 714.9555254 -2.854279027 0.102513632 DHQYQFLEDAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DHQYQFLEDAVR 12 0 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;;;; 237.41 4.19E-16 8275560000 6860950 5694750 4025290 4716620 5553610 5659140 5175320 5995130 7409600 FALSE TRUE 5954258.074 5657340.812 5971933.708 5787600.66 5443104.026 5876850.778 4673418.263 4713118.104 6533645.529 0.911322484 0.865878136 0.914027809 0.885814915 0.833088358 0.899474995 0.715284942 0.721361158 1 22.63945676 2.263394797 24.99060053 0.789248602 0.883074083 0.131384279 0.081187286 325.2287782 327276.2609 0.029984106 0.023215388 183.3980853 -2.263394797 0.093825481 DHRDNLEFFLAGIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 DHRDNLEFFLAGIGR 15 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;; 142.1 2.79E-06 3438648000 4343115 4576560 1925122 2023624 4244673 4602692 4663005 5049070 573550.6 FALSE TRUE 3769161.349 4546496.276 2856117.438 2483118.758 4160212.312 4779760.54 4210787.493 3969365.672 505746.1015 7.452675044 8.98968131 5.647334562 4.90981295 8.225891015 9.450909312 8.325892144 7.848534395 1 18.94805377 4.248838807 24.97139703 6.818639602 8.221177842 0.069538649 2.410510223 698.4097399 1696788.156 0.60775587 1.569617353 17735.31092 -4.248838807 1.402538241 DHRPPCAQEAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DHRPPCAQEAPR 12 1 Q13501;Q13501-2;E7EMC7;C9JRJ8;E9PFW8;E3W990 Q13501 SQSTM1 Sequestosome-1 0 ; 131.06 0.00012343 95903000 88068 86588 53572 68611 78316 89981 85712 97095 92191 FALSE TRUE 76429.59066 86019.19773 79479.59839 84190.1762 76757.66482 93442.6273 77399.66343 76331.98984 81292.285 0.940182585 1.058147126 0.977701616 1.035647801 0.944218321 1.149464888 0.952115732 0.938981969 1 16.31083082 DHS(ph)PPSQGSPGNSAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DHSPPSQGSPGNSAAR 16 0 A0A2R8Y701;Q18PE1-2;Q18PE1;Q18PE1-3;A0A1W2PRA3 A0A2R8Y701 DOK7 Protein Dok-7 1 DHS(1)PPSQGSPGNSAAR;DHS(1)PPSQGSPGNSAAR;DHS(1)PPSQGSPGNSAAR 162.99 5.08E-09 1271952000 435661 453180 242038 276900 498200 462125 412872 492231 432436 TRUE FALSE 378087.295 450203.0307 359088.3864 339774.3772 488286.7947 479903.2478 372831.737 386971.2312 381313.9087 0.991538169 1.180662495 0.941713319 0.891062113 1.280537593 1.258551647 0.97775541 1.014836392 1 18.54061963 DHS(ph)PTPSVFNS(ph)DEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DHSPTPSVFNSDEER 15 0 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 2 DHS(0.912)PT(0.088)PSVFNS(1)DEER 137.23 9.50E-06 334620000 271870 233970 157820 177960 247870 199600 260470 314810 334360 TRUE FALSE 235941.6907 232433.0357 234142.2799 218368.5379 242937.8719 207278.7412 235209.6595 247490.3314 294832.3417 0.800257154 0.788356645 0.794153988 0.74065327 0.823986509 0.703039361 0.797774281 0.83942735 1 18.16953526 1.188189128 1.858414303 1.098832375 0.776439094 0.809484363 0.033926689 0.394057984 1.157131701 0.235342936 0.008809444 15.42371985 -1.188189128 -0.32239328 DHS(ph)PTPSVFNSDEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 DHSPTPSVFNSDEER 15 0 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 DHS(0.99)PT(0.01)PSVFNSDEER;DHS(0.994)PT(0.006)PSVFNSDEER;DHS(0.999)PT(0.001)PSVFNSDEER;DHS(0.997)PT(0.003)PSVFNSDEER;DHS(0.962)PT(0.038)PSVFNSDEER;DHS(0.997)PT(0.003)PSVFNSDEER;DHS(0.992)PT(0.008)PSVFNSDEER 247.28 1.92E-18 11474930000 3124920 2729360 1540509 1900450 3183200 2814300 2600480 2814910 2946400 TRUE FALSE 2711953.904 2711430.654 2285504.305 2331976.219 3119860.548 2922567.942 2348285.85 2212963.402 2598079.949 1.043830043 1.043628644 0.879689752 0.897576774 1.200833157 1.124895307 0.903854345 0.851768785 1 21.3090144 2.198798002 23.71547774 0.904017816 1.026958588 0.215013504 0.100419587 138.9814725 82890.59219 0.044094207 0.029729027 158.0512744 -2.198798002 0.122940771 DHSGGIGDICK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DHSGGIGDICK 11 0 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 62.408 0.081166 206010000 71092 59693 58936 55313 69547 57257 72009 67725 73937 FALSE TRUE 61697.01208 59300.87275 87437.64673 67872.66206 68163.15077 59459.71384 65025.57826 53242.53579 65196.25209 0.946327589 0.909574874 1.341145295 1.041051592 1.045507197 0.912011227 0.997382153 0.816650253 1 15.99250141 2.798572104 2.962702065 0.917683732 1.067667937 0.195041621 0.124228749 0.404317609 7.030858119 0.044422163 0.042949204 628.8862567 -2.798572104 0.149984206 DHSVAESLNYVASWNMSMLQTQDLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DHSVAESLNYVASWNMSMLQTQDLVK 26 0 Q13011 Q13011 ECH1 "Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial" 0 152.35 1.02E-07 164550000 86737 65301 48567 76300 79196 68033 72073 101830 78341 FALSE TRUE 75274.48569 64872.03343 72054.16365 93625.08117 77620.15454 70650.27353 65083.37155 80054.44694 69079.61623 1.089677242 0.93909082 1.043059698 1.355321385 1.123633262 1.022736914 0.942150161 1.158872202 1 16.07597245 -1.056964845 0.626260464 1.48E-05 1.089652663 0.028956727 0.120102237 356.8067719 9.254116723 491.1546964 0.061337929 0.087707181 1.056964845 1.08963786 DHTLEDEDVIQIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DHTLEDEDVIQIVK 14 0 Q9Y295 Q9Y295 DRG1 Developmentally-regulated GTP-binding protein 1 0 ; 130.07 6.42E-05 292980000 542030 444370 312283 400050 429280 371530 490710 568600 559090 FALSE TRUE 470399.3622 441450.9042 463304.1033 490887.4669 420738.1679 385822.9995 443121.0197 447009.3149 492995.0171 0.954166565 0.89544699 0.939774414 0.995725007 0.853432901 0.782610343 0.898834683 0.906721771 1 18.91121354 3.224986895 24.99988924 0.886123299 0.942182893 0.194495301 0.058250224 430.0582328 792073.1711 0.018636056 0.021247758 1678.753361 -3.224986895 0.056059594 DHTPSQELALTQSVGGDSSADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DHTPSQELALTQSVGGDSSADR 22 0 Q86U44;H0YFV6;Q86U44-2 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 0 92.01 0.00077751 0 170240 166390 56865 105540 165470 163080 139540 164080 142370 FALSE TRUE 147742.3527 165296.9731 84365.1042 129504.4701 162177.4707 169353.7931 126007.4323 128992.7689 125539.1808 1.176862488 1.316696286 0.672022102 1.03158607 1.291847451 1.349011457 1.003729923 1.027510042 1 16.93777817 DHTYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DHTYAK 6 0 Q06210-2;Q06210;A0A6I8PRN4 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 103.71 0.034451 1322590000 2253290 1934600 1235460 1602720 1065860 1654240 2095410 2451390 3059000 FALSE TRUE 1955512.017 1921891.485 1832932.588 1966642.072 1044651.471 1717879.683 1892197.461 1927179.325 2697368.505 0.724970286 0.712506089 0.679526207 0.72909655 0.387285411 0.636872448 0.701497573 0.714466459 1 21.3631212 0.951203578 1.60306654 1.426299278 0.64649285 0.544382807 0.099104341 1.907811657 2.405862877 2.962425648 0.028833632 8.937243234 -0.951203578 -0.779806428 DHVFEDSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DHVFEDSYR 9 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 77.049 0.033703 327390000 253020 229760 116490 177600 226300 229150 210720 230280 241470 FALSE TRUE 219582.7659 228250.6914 172824.9536 217926.7944 221797.0727 237965.5488 190284.4068 181036.414 212923.6917 1.031274464 1.071983534 0.811675546 1.023497163 1.041673996 1.117609538 0.893674186 0.850240819 1 17.69997696 2.186830638 24.99927885 0.900348335 1.010999016 0.224189865 0.08743811 141.722232 68488.22677 0.036274317 0.02445617 153.7554923 -2.186830638 0.110650681 DHVFLCEGEEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DHVFLCEGEEPK 12 0 A6NGP5;Q9H910;Q9H910-3;H3BMV3;H3BTV5;Q9H910-2;H3BU16;H3BMT0 A6NGP5;Q9H910-2 HN1L Hematological and neurological expressed 1-like protein 0 106.26 0.0019414 161660000 408440 361340 206630 328110 300450 238490 388460 433020 405260 FALSE TRUE 354463.6191 358966.3337 306556.9591 402612.3903 294471.6328 247664.8646 350787.209 340422.0428 357350.6245 0.991921085 1.004521356 0.857860427 1.126659261 0.824041187 0.693058435 0.981633122 0.95262753 1 18.44698078 4.273177483 24.42013144 0.921622018 0.998221435 0.075048248 0.114820788 430.4405192 303641.6261 0.029168688 0.077163713 18757.60917 -4.273177483 0.076599418 DHYEATAMHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 DHYEATAMHR 10 0 O75832;B1AJY5;B1AJY7;O75832-2;B1AJY6 O75832 PSMD10 26S proteasome non-ATPase regulatory subunit 10 0 ;;;;;;;;; 218.49 3.91E-09 1872605000 2302414 2135941 1299656 1655695 1950068 1995219 1947626 2128018 2266964 FALSE TRUE 1998144.156 2121909.863 1928173.989 2031645.855 1911265.462 2071976.366 1758745.53 1672957.911 1998966.098 0.999588816 1.061503677 0.964585638 1.01634833 0.956127002 1.036524015 0.879827593 0.836911598 1 20.93082257 2.23195817 24.99233966 0.890200838 1.004663506 0.453079617 0.050961233 116.9410812 442653.6453 0.019803436 0.013695196 170.5918073 -2.23195817 0.114462668 DHYSNGFCTVYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DHYSNGFCTVYAK 13 0 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 ; 118.67 0.00040956 1066240000 814860 796370 256070 523600 940820 830760 775170 943810 896960 FALSE TRUE 707174.1864 791138.593 379906.3085 642491.3827 922099.5227 862719.8748 699994.1327 741983.5762 790922.4106 0.894113224 1.000273329 0.48033322 0.812331746 1.165853326 1.090776874 0.885035148 0.938124355 1 19.59317665 3.388781554 9.734200756 0.999817745 0.784932722 0.341280653 0.15052094 0.402321934 40.7311227 0.044963158 0.058056792 2447.831694 -3.388781554 -0.214885022 DIAAHIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DIAAHIK 7 0 P63167;F8VXL2;F8VRV5 P63167 DYNLL1 "Dynein light chain 1, cytoplasmic" 0 ;;; 102.72 0.0085375 2814270000 4746700 4355100 3252710 3862670 4180200 3951510 5062600 5845200 5101100 FALSE TRUE 4119411.568 4326491.061 4825731.436 4739748.261 4097022.198 4103527.147 4571629.831 4595249.467 4498053.769 0.915820882 0.961858458 1.072848766 1.053733126 0.910843313 0.912289483 1.01635731 1.02160839 1 22.10086948 DIAANEENRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DIAANEENRK 10 1 O75368 O75368 SH3BGRL SH3 domain-binding glutamic acid-rich-like protein 0 ;;;;; 159.94 1.21E-05 5990240000 3523090 3066690 2543470 2959320 2654570 2559720 3583890 4126900 6727450 FALSE TRUE 3057504.73 3046544.711 3773500.599 3631278.836 2601749.251 2658194.085 3236324.899 3244394.551 5932138.525 0.515413576 0.51356601 0.636111342 0.612136554 0.438585384 0.448100474 0.545557877 0.546918204 1 22.50012086 1.236632276 5.704185171 1.021012383 0.531504458 0.852063029 0.061312025 0.057261325 6.264670263 0.109736525 0.016418084 17.24377216 -1.236632276 -0.489507925 DIAAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DIAAYR 6 0 P26583;P09429;P23497 P26583;P09429;P23497 HMGB2;HMGB1;SP100 High mobility group protein B2;High mobility group protein B1;Nuclear autoantigen Sp-100 0 ;; 138.38 0.028678 2644150000 2140700 1904370 1157730 1321690 1686350 1700590 1592230 1870920 1864530 FALSE TRUE 1857801.071 1891860.068 1717612.1 1621799.915 1652794.934 1766012.798 1437815.78 1470838.318 1644107.387 1.129975502 1.150691301 1.044707976 0.986431864 1.005284051 1.074146866 0.874526683 0.894612073 1 20.6488731 4.343551948 0.386422806 0.906966275 1.286417825 0.599108682 0.056356519 3.616136298 0.673157706 0.101096823 0.66168 22057.27959 -4.343551948 0.37945155 DIAWTEDSKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DIAWTEDSKR 10 1 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ;;; 176.95 3.82E-06 2599340000 1634380 1295960 1062180 1347820 1238480 1076340 1529450 1788670 2668730 FALSE TRUE 1418392.542 1287446.753 1575853.801 1653863.131 1213836.671 1117747.496 1381124.174 1406176.84 2353235.78 0.602741363 0.54709637 0.66965402 0.702803835 0.515816002 0.474983215 0.58690429 0.59755034 1 21.16621445 1.237684457 6.171614373 1.014160332 0.585847102 0.79250551 0.066407966 0.061875037 9.598995741 0.111473718 0.017568449 17.28559994 -1.237684457 -0.42831323 DICNDVLSLLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DICNDVLSLLEK 12 0 P63104;E7EX29;B0AZS6;E7ESK7 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;; 194.96 1.99E-06 1099027000 1764642 1381978 1009046 1167372 1233210 1042325 1649526 1819964 1830732 FALSE TRUE 1531440.089 1372899.696 1497024.021 1432441.655 1208671.534 1082423.917 1489555.222 1430778.862 1614304.949 0.948668398 0.850458705 0.927348963 0.887342665 0.748725657 0.670520101 0.922722329 0.886312628 1 20.6224817 1.29236711 1.734010125 1.039842352 0.844166152 0.235105322 0.084788627 1.366199844 4.248779119 0.438073758 0.025310454 19.60501188 -1.29236711 -0.1956762 DIDAFWLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DIDAFWLQR 9 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;;; 187.8 9.33E-05 624758000 1155661 1045916 635076 666549 890343 920209 803424 1007847 1240710 FALSE TRUE 1002937.471 1039045.309 942200.8778 817899.138 872626.9162 955610.0357 725508.0641 792326.7621 1094034.677 0.916732798 0.949737088 0.861216648 0.747598915 0.797622721 0.87347326 0.663149057 0.724224541 1 20.06122704 4.003438589 3.904598074 0.787595502 0.931286839 0.255951751 0.090941538 0.261538398 9.055022687 0.024275017 0.050637752 10079.4907 -4.003438589 0.143691337 DIDEVSSLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DIDEVSSLLR 10 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;;;;; 260.4 6.02E-17 2522502000 2704675 2553866 1674632 1969971 2516133 2401659 2639166 2831548 2627401 FALSE TRUE 2347245.346 2537089.486 2484489.637 2417283.025 2466066.876 2494052.376 2383220.088 2226043.495 2316792.647 1.013144335 1.09508699 1.072383254 1.043374783 1.064431415 1.07651083 1.028672156 0.960829834 1 21.1436975 1.959788325 4.213532107 0.980246832 1.061966145 0.66313495 0.02348739 0.111382766 4.21840714 0.011622782 0.006072286 91.15664338 -1.959788325 0.081719313 DIDFLKEEEHDCFLEEIMTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIDFLKEEEHDCFLEEIMTK 20 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 235.84 8.97E-30 507350000 1207410 998230 935880 885190 837880 606570 1411110 1639060 1164020 FALSE TRUE 1047847.709 991672.5614 1388474.698 1086185.919 821207.8273 629905.1404 1274260.769 1288559.774 1026410.882 1.02088523 0.966155542 1.352747446 1.058236948 0.800077086 0.613696865 1.241472389 1.255403462 1 19.96917694 0.937318389 20.6811722 0.000639287 1.050519257 0.000425911 0.218929865 474.2518231 672728.3805 74463.38387 0.056065997 8.656022749 -0.937318389 1.04987997 DIDHETVVEEQIIGENS(ph)PPDYSEYMTGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 DIDHETVVEEQIIGENSPPDYSEYMTGK 28 0 P25490;A0A494C032;H0YJV7;H0YJU4 P25490 YY1 Transcriptional repressor protein YY1 1 DIDHETVVEEQIIGENS(1)PPDYSEYMTGK;DIDHETVVEEQIIGENS(1)PPDYSEYMTGK;DIDHETVVEEQIIGENS(1)PPDYSEYMTGK;DIDHETVVEEQIIGENS(1)PPDYSEYMTGK;DIDHETVVEEQIIGENS(1)PPDYSEYMTGK;DIDHETVVEEQIIGENS(1)PPDYSEYMTGK;DIDHETVVEEQIIGENS(1)PPDYSEYMTGK 321.61 1.19E-82 2799330000 1244495 1010950 693221 878852 962088 823065 1143281 1322744 1271385 TRUE FALSE 1080031.833 1004309.003 1028464.994 1078408.779 942944.3311 854728.8431 1032405.785 1039885.489 1121083.314 0.96338231 0.895837973 0.917384981 0.961934556 0.841101031 0.762413313 0.920900144 0.927571998 1 20.09646207 1.34967547 2.093303961 1.01566399 0.891480515 0.245650862 0.058520194 0.859047572 4.701225071 0.189504123 0.016880536 22.37048863 -1.34967547 -0.124183475 DIDIEDLEELDPDFIMAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 DIDIEDLEELDPDFIMAK 18 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;;;; 243.7 9.76E-24 172426000 846219 711372 550779 645487 689399 611343 844627 1048354 924500 FALSE TRUE 734389.0151 706698.9505 817137.5666 792054.689 675681.3087 634861.7608 762715.2035 824171.6554 815206.6632 0.90086238 0.866895454 1.002368606 0.971599871 0.828846646 0.778774008 0.935609629 1.010997202 1 19.63680632 1.887251464 4.431902128 1.002716996 0.893689376 0.346142417 0.063660713 0.276021458 8.400164416 0.038065432 0.018775181 77.1349965 -1.887251464 -0.10902762 DIDIHEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 DIDIHEVR 8 0 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;;;;;; 190.26 0.00018737 21869220000 46245540 38033030 26848230 31674380 38553150 36925650 39394170 42944650 41389630 FALSE TRUE 40134074.72 37783188.52 39832123.83 38866532.09 37786017.74 38346203.65 35573729.46 33761270.79 36496595.09 1.099666273 1.035252424 1.091392875 1.064935838 1.035329944 1.050678935 0.974713651 0.925052617 1 25.12125854 2.2281978 3.173677077 0.954725332 1.06349421 0.737978837 0.027135358 0.108674425 2.283315789 0.011627051 0.007668634 169.1211019 -2.2281978 0.108768878 DIDISS(ph)PEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DIDISSPEFK 10 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 DIDISS(1)PEFK;DIDISS(1)PEFK;DIDIS(0.003)S(0.997)PEFK;DIDISS(1)PEFK;DIDIS(0.003)S(0.997)PEFK;DIDIS(0.039)S(0.961)PEFK 299.29 2.17E-32 3357900000 13426780 10079770 6953410 9889500 11027620 8436300 10271370 16167780 12821580 TRUE FALSE 11652397 10013555.33 10316102.33 12135062.13 10808191.94 8760849.92 9275254.118 12710426.06 11305827.42 1.030654066 0.885698583 0.912458854 1.073345778 0.955984161 0.774896838 0.82039587 1.124236696 1 23.43056324 1.717455431 11.98203879 1.06042785 0.921671779 0.283961781 0.092493932 0.138922868 55.89310721 0.052430974 0.02471784 52.17415579 -1.717455431 -0.138756071 DIDLICSNALEYNPDRDPGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DIDLICSNALEYNPDRDPGDR 21 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 134.29 7.74E-06 104980000 140550 133020 73756 113690 117300 101620 120930 146930 113760 FALSE TRUE 121975.9614 132146.1829 109424.6483 139505.0521 114965.9595 105529.3872 109202.2272 115510.1629 100311.4224 1.215972802 1.317359277 1.090849334 1.390719509 1.146090413 1.052017653 1.088632028 1.151515552 1 16.61412637 3.010038373 24.98702762 1.088130027 1.249357608 0.502476028 0.084285108 175.4774757 436786.2936 0.023684116 0.026826076 1023.383412 -3.010038373 0.161227581 DIDPQNDLTFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DIDPQNDLTFLR 12 0 Q9NP97;B1AKR6;Q8TF09;H3BQI1 Q9NP97 DYNLRB1;DYNLRB2 Dynein light chain roadblock-type 1;Dynein light chain roadblock-type 2 0 ;;;;; 161.94 0.00014891 760295000 1293749 996548 612520 816064 1021091 975496 990344 1152666 1092846 FALSE TRUE 1122776.792 990001.6106 908736.7208 1001363.804 1000773.287 1013023.962 894300.5913 906177.346 963650.9909 1.165128042 1.027344568 0.943014358 1.039135344 1.038522553 1.051235325 0.928033697 0.940358444 1 19.87815121 4.700088103 3.319516206 0.98877954 1.181827852 0.603308151 0.04387825 0.210594541 3.885588478 0.012138753 0.098003845 50128.89173 -4.700088103 0.193048312 DIDTHTHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIDTHTHR 8 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ; 170.24 0.00029635 120318000 453110 440160 273970 316520 358010 461510 427820 458030 417920 FALSE TRUE 393230.3655 437268.56 406462.8084 388390.7037 350886.3014 479264.5883 386330.0822 360083.8489 368513.9737 1.067070433 1.186572535 1.102978007 1.05393752 0.952165526 1.300533012 1.048345815 0.977124002 1 18.4913598 2.002340317 24.99812091 0.994670046 1.109762638 0.242025065 0.089722608 97.92087623 1045935.857 0.036276667 0.024286791 100.5403324 -2.002340317 0.115092593 DIEAYLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIEAYLER 8 0 P18440 P18440 NAT1 Arylamine N-acetyltransferase 1 0 ; 104.06 0.010826 148144000 258940 225320 160033 153207 247010 287040 227510 274480 244020 FALSE TRUE 224720.4229 223839.8581 237425.4941 187994.991 242094.9843 298082.6145 205446.1152 215784.588 215172.2336 1.044374635 1.040282263 1.103420688 0.873695401 1.125121863 1.385321003 0.95479845 1.00284588 1 17.7151324 DIEDVFYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DIEDVFYK 8 0 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;; 157.54 0.0008731 737310000 1525400 1118850 941880 1097460 1041830 838680 1292390 1485250 2151280 FALSE TRUE 1323814.525 1111500.201 1397376.318 1346655.067 1021099.621 870944.5623 1167054.217 1167640.846 1896958.129 0.697861753 0.585938184 0.73664057 0.709902367 0.538282636 0.45912693 0.615224026 0.615533273 1 20.8552564 1.238405902 24.97382172 1.000000415 0.617236095 0.675967095 0.08270673 2.313957389 372285.4272 0.12016624 0.021366321 17.31433843 -1.238405902 -0.382764319 DIEEHLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DIEEHLQR 8 0 Q9UNE7;Q9UNE7-2;H3BTA3 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 108.98 0.0037068 324350000 151810 143350 102620 104010 147980 196880 126090 152660 142650 FALSE TRUE 131747.9239 142408.3244 152247.3752 127627.0602 145035.4875 204454.101 113861.8112 120014.847 125786.0795 1.047396694 1.132146935 1.210367442 1.014635806 1.153032896 1.625411189 0.905202004 0.954118671 1 16.94061275 DIEEIIDELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIEEIIDELK 10 0 E7EPT4;P19404 E7EPT4 NDUFV2 "NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial" 0 ; 166.33 1.30E-05 23406000 60196 55251 50482 70404 62962 50395 62891 79571 78599 FALSE TRUE 52240.94608 54888.05254 74895.26405 86390.30426 61709.17938 52333.72826 56791.8405 62555.36087 69307.11576 0.753760209 0.791954072 1.080628781 1.246485347 0.890372925 0.75509892 0.819422939 0.902582082 1 16.08071586 3.020990988 24.99974085 0.86457617 0.976745352 0.090034095 0.149528804 589.1554975 701664.7655 0.049064793 0.055629041 1049.520649 -3.020990988 0.112169182 DIELQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DIELQIR 7 0 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;F8VZ52;B4DDQ3;F8VUJ9;F8W1W3;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 0 81.119 0.065295 44372000 108330 106150 58017 73537 91668 88712 108010 101850 100080 FALSE TRUE 94013.91603 105452.6937 86074.21526 90234.69979 89843.98615 92124.80804 97535.20682 80070.1701 88248.65641 1.065329715 1.194949566 0.975360065 1.022505083 1.018077666 1.043923067 1.105231635 0.907324523 1 16.42928669 8 0.12483584 0.893685858 1.610555735 0.217809073 0.067873402 281.5945629 3.10880607 2.135841448 35.0877208 99999999.94 -8 0.716869877 DIELVMSQANVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 132.79 0.0002669 290533000 283600 276308 195988 205183 277677 264356 283611 320916 298758 FALSE TRUE 246121.5414 274492.9146 290768.4523 251772.9362 272151.771 274525.9464 256106.4489 252290.6108 263439.1696 0.934263275 1.041959383 1.103740392 0.955715646 1.033072536 1.04208477 0.972165412 0.957680709 1 18.00711034 2.222799469 24.76325386 0.972485212 1.021227087 0.141667983 0.047893893 361.0611655 567279.347 0.019109785 0.012934286 167.0319183 -2.222799469 0.048741875 DIEREDIEFICK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DIEREDIEFICK 12 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;;; 220.53 2.68E-11 3768850000 5663260 5289220 3326330 3996630 4764570 3765390 5912090 6650770 3881930 FALSE TRUE 4914845.842 5254474.766 4934954.314 4904125.926 4669764.379 3910246.99 5338736.422 5228554.592 3423012.658 1.435824618 1.535043919 1.441699113 1.432692898 1.364226442 1.142340792 1.559660146 1.527471591 1 21.7068352 3.443961025 2.569351509 1.354567963 1.476539513 0.137828398 0.166347142 0.736840393 9.829433407 0.052386022 0.075771741 2779.463822 -3.443961025 0.12197155 DIFQEIFDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DIFQEIFDK 9 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 132.78 0.0027385 0 179380 195110 160360 249320 182380 171280 201420 245890 379020 FALSE TRUE 155674.4785 193828.3096 237910.6324 305931.9166 178750.9948 177869.2524 181886.3194 193308.337 334212.6874 0.46579464 0.579954971 0.711853982 0.915380918 0.534842038 0.532203771 0.544223263 0.578399158 1 18.35040698 1.235658202 24.9857877 1.000000529 0.610816469 0.489690617 0.125781767 76.03152723 654402.4425 0.22060019 0.032437798 17.20513964 -1.235658202 -0.38918406 DIFQEIYDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIFQEIYDK 9 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 148.96 0.00020652 164919000 320290 248210 203256 242330 219860 195045 271010 312830 519350 FALSE TRUE 277962.865 246579.4922 301551.2815 297354.7303 215485.2161 202548.5074 244727.4919 245933.7389 457953.0346 0.60696806 0.538438385 0.658476435 0.649312719 0.47053999 0.442291004 0.534394301 0.537028298 1 18.80484012 1.237362496 24.99867503 1.000000536 0.55245435 0.803128878 0.069282422 14.03597455 292733.178 0.109651078 0.018251767 17.27279012 -1.237362496 -0.447546186 DIGKPIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DIGKPIEK 8 1 O60869 O60869 EDF1 Endothelial differentiation-related factor 1 0 59.426 0.090012 361160000 821760 632190 500390 560110 583370 527420 754230 900530 1002200 FALSE TRUE 713162.3339 628037.1023 742380.2777 687291.5362 571762.0783 547710.1887 681084.8907 707958.6674 883721.0577 0.806999367 0.710673461 0.840061772 0.777724521 0.646993837 0.619777229 0.770701212 0.801111008 1 19.75323154 1.179627861 1.94014708 1.117209595 0.735320294 0.596646358 0.067348414 0.720725631 2.29470252 0.530409139 0.01955541 15.12264862 -1.179627861 -0.381889301 DIGPNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DIGPNKR 7 1 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 ;;; 91.626 0.026081 3428160000 9018450 10444620 7267050 6549910 6284270 9864430 10424450 8696650 8932690 FALSE TRUE 7826638.983 10376008.6 10781419.69 8037167.175 6159225.322 10243921.01 9413488.443 6836939.075 7876677.564 0.993647248 1.317307776 1.368777584 1.020375293 0.781957275 1.30053832 1.195109025 0.867997835 1 22.90915579 -1.264146319 0.234885633 1.02E-16 1.225855407 0.100104624 0.187345748 134.3731566 2.903737938 57.70783971 0.81901576 0.054431923 1.264146319 1.225855407 DIHELFVPENK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIHELFVPENK 11 0 O95340;O95340-2 O95340 PAPSS2 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 2;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ; 121.02 0.00042029 381930000 1056370 955240 763670 886680 1019830 752850 1046960 1296000 1349700 FALSE TRUE 916768.028 948964.9655 1132983.366 1088014.246 999537.3783 781812.6267 945425.9803 1018860.485 1190140.004 0.770302675 0.797355742 0.951974863 0.914190131 0.839848568 0.656908115 0.794382155 0.856084564 1 20.18269987 1.255871839 3.231204137 1.025951405 0.820917076 0.338109965 0.079589134 0.430748876 6.142822021 0.219213444 0.022313615 18.02485744 -1.255871839 -0.205034328 DIHFGQCYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIHFGQCYK 9 0 A0A6E1XD66;H7C835;Q9UF56-3;Q9UF56-2;Q9UF56 A0A6E1XD66 FBXL17 F-box/LRR-repeat protein 17 0 ; 51.346 0.08981 352270000 174919 252520 168073 68933 203133 455690 114343 98110 49847 FALSE TRUE 151803.011 250861.1795 249353.665 84585.29122 199091.0507 473220.6892 103254.0335 77129.93999 43954.14445 3.453667746 5.70733847 5.673041032 1.924398536 4.529517142 10.76623593 2.349130776 1.754781966 1 15.42371158 3.797335711 24.99957092 3.757427675 5.020947881 0.040695824 2.789455288 1107.920216 471241.544 0.794102546 1.375425652 6270.984268 -3.797335711 1.263520206 DIHFMPCSGLTGANLK ddPTM_MDA-MB-175_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 0 167.71 1.30E-09 0 296220 264080 164170 228110 275610 252190 321240 366880 361390 FALSE TRUE 257073.7765 262345.2411 243563.1611 279905.8619 270125.9002 261891.9125 290086.1942 288425.5671 318666.8859 0.806716317 0.823258558 0.764319017 0.878365071 0.847674836 0.82183598 0.910311699 0.905100529 1 18.28168958 -2 0.383304741 3.597937707 0.80335415 0.786545042 0.030576898 35.07328259 0.518521265 72.26617572 0.032229999 0.01 2 -2.794583557 DIHYSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DIHYSVK 7 0 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ;;; 139.31 0.0027006 1459310000 3890210 4622400 1044440 2646100 5419300 5016200 5091700 5629800 5919000 FALSE TRUE 3376108.892 4592035.15 1549534.677 3246937.448 5311466.533 5209176.46 4597907.718 4425911.081 5219262.563 0.646855538 0.879824514 0.296887665 0.622106554 1.017666091 0.998067523 0.880949686 0.847995484 1 22.31541455 3.249559492 24.52342237 0.933675845 0.608123786 0.559812883 0.148363521 135.0965484 301213.1426 0.043379049 0.055428968 1776.476602 -3.249559492 -0.325552059 DIIFELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 102.72 0.019862 115052000 179079 191122 119420 146171 178746 191292 191705 206930 208027 FALSE TRUE 155413.2564 189866.507 177171.9114 179361.3596 175189.3043 198651.127 173113.4786 162679.6298 183434.285 0.847242141 1.035065538 0.965860397 0.97779627 0.955052128 1.082955277 0.943735674 0.886855092 1 17.48490379 4.757850514 23.90188918 0.973636449 0.847241931 0.379585507 0.052985729 2982.056031 3694921.63 0.01367283 0.461856263 57259.89064 -4.757850514 -0.126394518 DIIHDPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 DIIHDPGR 8 0 P62917;E9PKZ0;G3V1A1;E9PKU4 P62917 RPL8 60S ribosomal protein L8 0 ;;;;;;;; 144.09 0.000591 19276160000 18033880 17525210 11002880 12316780 16952160 17541150 17599600 19351050 17701450 FALSE TRUE 15650657.07 17410085.74 16323909.57 15113493.15 16614845.18 18215969.39 15892793.5 15212978.55 15608804.75 1.002681328 1.115401597 1.045814195 0.968267167 1.064453394 1.167031665 1.018194138 0.974640839 1 23.89585673 2.006623297 24.99327435 0.988781563 1.061254589 0.242393688 0.054541144 218.7223322 825353.3391 0.022764363 0.015306748 101.5367591 -2.006623297 0.072473027 DIIHFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIIHFFR 7 0 F8W7U8;P49959-2;P49959;P49959-3 F8W7U8 MRE11A Double-strand break repair protein MRE11A 0 ; 138.37 0.0027925 581520000 952090 850810 510620 639330 800290 820080 791210 939740 889840 FALSE TRUE 826268.8942 845220.9731 757557.5399 784499.648 784365.7947 851629.0083 714478.576 738783.9141 784644.1289 1.053049228 1.077202953 0.965479141 0.999815864 0.999645273 1.085369758 0.910576591 0.941552848 1 19.58167895 8 0.162445002 0.920823414 1.481106429 0.244038391 0.048968657 180.3696906 2.392301483 0.65081701 23.60761405 99999999.91 -8 0.560283014 DIIIFVGT(ph)PVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DIIIFVGTPVQK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 DIIIFVGT(1)PVQK 121.76 0.0041421 52671000 206820 170580 156110 213750 132560 129440 176860 210750 528120 TRUE FALSE 179488.213 169459.4487 231605.3182 262285.2045 129922.3153 134419.6406 159708.1444 165682.7526 465686.2552 0.385427336 0.363891884 0.497341967 0.563222989 0.278991089 0.288648503 0.34295224 0.355781925 1 18.82899878 1.237003019 24.99988964 1.000000758 0.383405326 0.832012842 0.086910899 16.94674329 271908.8148 0.140822678 0.022874873 17.25849888 -1.237003019 -0.616595432 DIILPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIILPFR 7 0 A0A087WY71;Q96CW1-2;Q96CW1;E9PFW3;C9JJ47 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 ; 139.92 0.0061873 78606000 175665 171875 115122 143683 168661 193872 165170 198190 171075 FALSE TRUE 152450.4252 170745.9418 170795.3843 176308.4212 165304.9761 201330.3813 149151.8388 155808.6108 150850.7084 1.010604636 1.131886907 1.132214665 1.168760976 1.095818361 1.334633317 0.988738074 1.032866285 1 17.20276195 DIILREDLEELQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIILREDLEELQAR 14 1 Q9UHQ9;H7C0R7 Q9UHQ9 CYB5R1 NADH-cytochrome b5 reductase 1 0 ; 127.66 7.14E-05 126408000 145366 125905 83650 110130 153690 195260 111029 161388 82524 FALSE TRUE 126155.5148 125077.9218 124103.4198 135136.6997 150631.8697 202771.7786 100261.4247 126876.4321 72768.10673 1.733664932 1.718856342 1.705464459 1.857086927 2.070025956 2.786547399 1.377820987 1.743571983 1 16.15101865 1.061610993 1.408274383 0.290451898 1.924176568 0.378064793 0.361015338 2.194800235 2.734911525 5.797256785 0.10787567 11.52420548 -1.061610993 1.63372467 DIINMLFYHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIINMLFYHDR 11 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ; 147.26 3.54E-05 517730000 751210 784350 626450 658180 751960 797360 853030 915980 1017600 FALSE TRUE 651935.6952 779197.5532 929403.3153 807629.8287 736997.4672 828034.9552 770303.2819 720104.8052 897300.4873 0.726552258 0.868379728 1.035777121 0.900066188 0.821349679 0.92280676 0.858467473 0.802523586 1 19.77523167 4.713378578 4.642177937 0.894792664 0.719388224 0.366252419 0.072410346 0.200106068 10.88294079 0.018208753 0.106574285 51686.67299 -4.713378578 -0.17540444 DIIRQPS(ph)EEEIIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DIIRQPSEEEIIK 13 1 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 1 DIIRQPS(1)EEEIIK;DIIRQPS(1)EEEIIK;DIIRQPS(1)EEEIIK;DIIRQPS(1)EEEIIK;DIIRQPS(1)EEEIIK 244.1 3.08E-17 2513770000 2404783 2096425 616436 795520 1622948 948997 3030186 2460519 579534.7 TRUE FALSE 2086984.834 2082653.446 914546.5115 976154.9748 1590654.51 985505.5287 2736319.028 1934356.16 511022.768 4.083937085 4.075461167 1.789639462 1.910198598 3.112688142 1.928496322 5.35459318 3.785264143 1 18.96302804 DIISDTSGDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIISDTSGDFR 11 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;A6NMY6;H0YL33;H0YNP5;H0YN28;H0YKS4;H0YNA0;H0YN52 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 ; 140.16 9.01E-05 220849000 323510 277110 235880 441830 276330 307650 146923 319350 1122380 FALSE TRUE 280757.3338 275289.6462 349952.357 542154.2544 270831.5736 319485.4946 132674.4301 251059.4877 989693.515 0.283681089 0.278156462 0.353596696 0.547800148 0.273651963 0.322812557 0.134056077 0.253673975 1 19.9166223 1.236091137 24.99993452 1.000000913 0.303121837 0.817311139 0.103118586 29.62483443 299843.5089 0.177854545 0.027042025 17.22229949 -1.236091137 -0.696879076 DIISDTSGDFRK ddPTM_MDA-MB-175_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 ; 147.24 0.0001049 1357300000 776490 573890 556540 906930 680850 532040 382280 838570 1242280 FALSE TRUE 673874.8791 570120.0788 825684.6055 1112862.318 667302.4171 552507.9231 345206.5444 659248.3313 1095419.074 0.615175411 0.520458419 0.753761392 1.015923809 0.609175459 0.504380411 0.315136511 0.601822944 1 20.06305148 3.021483335 24.99826958 0.575268628 0.725954737 0.067627393 0.20900606 589.1522905 685540.0419 0.066258628 0.075124307 1050.711135 -3.021483335 0.150686109 DIISIAEDEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DIISIAEDEDLR 12 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;; 270.72 2.49E-27 4008860000 3326940 2716000 1903380 2324160 2650860 2631140 2944080 3268950 3219070 FALSE TRUE 2887276.45 2698158.417 2823860.934 2851896.051 2598113.072 2732361.658 2658563.575 2569910.481 2838515.212 1.017178431 0.950552742 0.994837344 1.004714028 0.915307081 0.962602436 0.936603603 0.905371397 1 21.43670504 3.244649007 24.99994211 0.939529493 0.989088412 0.368338567 0.030736092 150.1916288 616707.6396 0.008643244 0.010870368 1756.503448 -3.244649007 0.049558919 DIISIAEDEDLRVHFEESSKLEDLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIISIAEDEDLRVHFEESSKLEDLLR 26 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 79.445 0.011645 47967000 40883 38261 13359.7 13077.5 29847 26599 39927 46421 6689.4 FALSE TRUE 35480.20797 38009.66097 19820.49561 16046.94625 29253.10309 27622.28074 36054.88569 36494.2304 5898.586753 6.015035373 6.443858939 3.360210918 2.720473043 4.959340995 4.682864201 6.112461713 6.18694476 1 12.52615362 4.256570612 24.97887709 4.430914947 6.229448521 0.217951178 1.570176829 433.2994104 600952.128 0.405868407 1.069040928 18053.88253 -4.256570612 1.798533574 DIKDTTVGTLSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DIKDTTVGTLSQR 13 1 P51665 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 101.75 0.0016398 738260000 505050 436550 227820 335070 410180 337620 475500 554040 151270 FALSE TRUE 438306.3629 433682.2743 337994.514 411152.7647 402018.2205 350608.4599 429386.0832 435562.8575 133387.0329 3.285974305 3.251307603 2.533938319 3.082404306 3.013922806 2.628504827 3.219099142 3.265406299 1 17.0252589 1.234584907 24.9999971 0.999997063 3.03370347 0.856701892 0.261568962 42.94624593 270015.4525 0.48321211 0.065141425 17.16267218 -1.234584907 2.033706408 DIKEES(ph)DEEEEDDEESGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DIKEESDEEEEDDEESGR 18 1 Q96EV2;A8MTF7;Q96EV2-2;H7BXM6;H7C0H2 Q96EV2 RBM33 RNA-binding protein 33 1 DIKEES(1)DEEEEDDEESGR;DIKEES(1)DEEEEDDEESGR;DIKEES(1)DEEEEDDEESGR;DIKEES(1)DEEEEDDEESGR 237.32 4.59E-24 2855990000 1768090 1197090 1029620 1098510 1294000 1103470 1501070 1755710 1748330 TRUE FALSE 1534432.427 1189226.237 1527547.676 1347943.485 1268251.932 1145921.205 1355496.462 1380265.079 1541644.419 0.995321883 0.771401124 0.990856035 0.874354338 0.822661773 0.743310968 0.879253637 0.895319999 1 20.55603861 1.224475523 2.265897898 1.041310445 0.863488807 0.205474013 0.080669533 1.043334188 5.348584031 0.382888463 0.020867241 16.76777828 -1.224475523 -0.177821638 DIKPDNFLMGIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIKPDNFLMGIGR 13 1 P48729-2;A0A5F9W493;U3KPX3;A0A590UJ43;P48729;E7ETM0;P48729-3;D6REM4;A0A590UK94 P48729-2 CSNK1A1 Casein kinase I isoform alpha 0 ; 111.12 0.00091659 1068840000 1704330 1519250 933190 1252480 1494500 1169000 1754550 1928810 1766020 FALSE TRUE 1479098.472 1509269.947 1384483.805 1536874.727 1464762.374 1213972.186 1584394.011 1516348.992 1557243.127 0.94981859 0.969193519 0.88906079 0.986920218 0.940612515 0.779564966 1.017435225 0.973739402 1 20.57056277 DILEIGAQWSILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DILEIGAQWSILR 13 0 K7EJR3;R4GMR5;P48556 K7EJR3 PSMD8 26S proteasome non-ATPase regulatory subunit 8 0 ; 178.81 3.32E-05 176010000 265190 271930 206219 217420 239120 271710 314840 327920 270740 FALSE TRUE 230144.4696 270143.6739 305947.1982 266788.5341 234361.9798 282162.8595 284306.8653 257796.8599 238733.4256 0.964022817 1.131570383 1.2815432 1.117516466 0.981689008 1.181916017 1.190896769 1.079852388 1 17.86504105 1.363175032 3.66365719 0.998605206 1.125190214 0.143231079 0.093601728 0.481233677 9.460041348 0.133247558 0.024251167 23.07677056 -1.363175032 0.126585007 DILETHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DILETHLR 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;;; 195.27 0.000161 2671940000 3793150 3390520 2220970 2926110 3595190 2853840 3625960 3807280 4453220 FALSE TRUE 3291875.617 3368247.451 3295038.521 3590527.998 3523652.753 2963629.071 3274314.957 2993122.8 3926765.405 0.838317362 0.857766407 0.839122835 0.914372932 0.897342314 0.754725268 0.83384532 0.762236215 1 21.90490998 2.814678436 24.99999999 0.825542333 0.869557066 0.035640698 0.070197229 323.7114494 106317.4098 0.021857997 0.021857994 652.6471352 -2.814678436 0.044014734 DILIQYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DILIQYDR 8 0 P62249;M0R210 P62249 RPS16 40S ribosomal protein S16 0 ;;;;;;; 177.97 0.0005864 9464920000 5964330 5992730 3877310 4843180 5788310 6054680 5195930 6116260 7270370 FALSE TRUE 5176128.679 5953363.362 5752390.085 5942898.042 5673133.956 6287607.457 4692029.508 4808345.396 6410875.141 0.807398142 0.928635051 0.897286245 0.927002618 0.884923482 0.980772097 0.73188596 0.750029487 1 22.61208988 2.238504067 25 0.807230263 0.905268191 0.144869241 0.083589139 2.186048526 965318.6466 0.031891933 0.023072789 173.1825247 -2.238504067 0.098037927 DILKPEIMEEIVMETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DILKPEIMEEIVMETR 16 1 A3KFL2;Q13868-3;Q13868-2;Q13868 A3KFL2 EXOSC2 Exosome complex component RRP4 0 ; 179.78 2.35E-09 81180000 155848 128078 86578 119793 121042 106041 124277 163808 157014 FALSE TRUE 135252.2919 127236.6472 128447.4104 146993.8316 118633.501 110120.4659 112224.6357 128778.934 138451.9838 0.97688952 0.918994757 0.927739761 1.06169538 0.856856636 0.795369361 0.810567192 0.930134263 1 17.0790262 3.190361174 24.99977614 0.875766822 0.964478799 0.307741914 0.068706901 159.0266924 82482.26877 0.022134461 0.025098174 1550.105202 -3.190361174 0.088711977 DILQDVHDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DILQDVHDK 9 0 Q92621 Q92621 NUP205 Nuclear pore complex protein Nup205 0 ;; 116.77 0.0020579 0 703990 577110 417290 467340 591210 506790 693300 832200 726810 FALSE TRUE 610955.9378 573318.9264 619092.8398 573456.6898 579446.0777 526286.5392 626063.8727 654240.5062 640887.3498 0.953296922 0.894570515 0.965993228 0.894785472 0.904130933 0.821184159 0.976870386 1.020835419 1 19.28971127 2.014157866 24.96653986 1.007990051 0.906642415 0.5743105 0.03876388 148.6776202 262183.047 0.015627196 0.01053089 103.3136883 -2.014157866 -0.101347635 DILQDYTHEFHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DILQDYTHEFHK 12 0 B4DQA8;E9PCW1;K7EJC8;G5E9T8;O95249;O95249-2 B4DQA8 GOSR1 Golgi SNAP receptor complex member 1 0 121.45 0.00021747 178410000 273740 270990 159230 183370 255760 256280 213560 288380 380110 FALSE TRUE 237564.5654 269209.8488 236234.1606 225006.9611 250670.8764 266139.2574 192848.9841 226712.1812 335173.8288 0.708780176 0.803194718 0.704810878 0.671314231 0.747883202 0.794033527 0.575370054 0.6764018 1 18.35454998 1.234834047 24.99389964 1.000000417 0.707633118 0.662397474 0.064990932 69.79111005 468014.5627 0.119960467 0.016518254 17.17252065 -1.234834047 -0.2923673 DILVDLGHLEGADAGEEDLEQQFHYHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DILVDLGHLEGADAGEEDLEQQFHYHLR 28 0 Q9NPA3 Q9NPA3 MID1IP1 Mid1-interacting protein 1 0 ;; 203.79 1.17E-25 187463000 109398 96682 81797 97157 85728 94347 92917 115794 191287 FALSE TRUE 94940.77712 96046.88958 121354.3028 119217.9818 84022.18052 97976.59014 83905.92364 91032.35421 168673.2688 0.562867951 0.569425673 0.719463752 0.706798313 0.498135722 0.580866138 0.497446479 0.53969639 1 17.36387183 1.234941992 24.98687784 1.000000594 0.582953271 0.750907529 0.075233042 56.64776645 391096.1201 0.143281225 0.019901964 17.17678945 -1.234941992 -0.417047323 DILYIGDHIFGDILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DILYIGDHIFGDILK 15 0 P49902-2;P49902;Q5JUV6 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;; 229.32 4.78E-13 1767892000 1383617 1387844 1132094 1442236 1308624 1045546 1515895 1958095 2911340 FALSE TRUE 1200768.508 1378727.161 1679578.445 1769717.727 1282584.943 1085768.831 1368883.736 1539371.622 2567164.702 0.467741126 0.537062215 0.654254261 0.689366649 0.499611475 0.422944749 0.533227858 0.599638824 1 21.29174443 1.227714637 3.521432554 1.071754048 0.547792631 0.764361311 0.078983053 0.167042319 3.013715262 0.23956826 0.022023239 16.89330553 -1.227714637 -0.523961417 DIMLATGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DIMLATGK 8 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 107.66 0.0092114 319440000 573640 512260 401610 437370 551720 492470 645740 663480 729130 FALSE TRUE 497832.0206 508894.9303 595829.9393 536681.5433 540741.8514 511415.6396 583116.2342 521599.9652 642933.082 0.774313898 0.791520836 0.926737099 0.83473935 0.841054639 0.795441476 0.90696256 0.811281889 1 19.29430906 1.23280142 24.99955145 1.00000026 0.837906725 0.529492918 0.048748071 152.2665593 660890.0651 0.099690412 0.011491737 17.09233596 -1.23280142 -0.162093535 DIMLATGKLS(ph)PDAIPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DIMLATGKLSPDAIPGK 17 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 DIMLATGKLS(1)PDAIPGK 193.64 7.21E-11 901030000 2068600 1714400 1603000 1564500 1774700 1466200 2747300 2775800 2535500 TRUE FALSE 1795229.269 1703137.994 2378216.162 1919743.637 1739386.942 1522605.663 2480867.269 2182216.771 2235756.078 0.802962938 0.761772722 1.063718974 0.858655224 0.777986006 0.681024946 1.109632349 0.976053154 1 21.09233137 2.226698837 24.99970989 1.021000458 0.831840684 0.462871153 0.103383167 220.3135345 464325.5681 0.043555504 0.029624696 168.5383886 -2.226698837 -0.189159774 DINAVAASLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DINAVAASLR 10 0 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;C9IZ80;C9JFN4 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 145.46 0.012057 0 99511 96978 73540 81312 119930 98815 101600 112100 119870 FALSE TRUE 86360.36922 96340.94513 109104.19 99775.13238 117543.6276 102616.477 91746.84764 88128.28736 105699.1052 0.817039738 0.911464151 1.032214888 0.943954372 1.112058872 0.970835816 0.86800023 0.83376569 1 16.68960364 2.245979926 24.23121083 0.885309339 0.971018011 0.09663132 0.086754014 203.0552634 663173.6946 0.033522635 0.025414222 176.1894607 -2.245979926 0.085708673 DINAVLIDMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DINAVLIDMER 11 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ;;;; 174.84 2.45E-05 244133000 370878 359410 208130 253624 335088 337559 358305 392942 370949 FALSE TRUE 321865.5326 357049.012 308782.3642 311213.2056 328420.4044 350545.1132 323556.6362 308914.4112 327095.8318 0.984009887 1.091573103 0.94401192 0.951443508 1.004049494 1.071689331 0.989179943 0.944415615 1 18.31935385 2.00452144 0.007693436 7.14E-06 1.975700905 0.011972089 0.049648268 36988.93397 134.3471314 17555.63548 16946.35151 101.0465382 -2.00452144 1.975693768 DINAYNCEEPTEKLPFPIIDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DINAYNCEEPTEKLPFPIIDDR 22 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;;; 307.21 6.33E-57 11819710000 5800810 5440290 2559450 2891110 4666950 4005920 6455810 6884300 1280868 FALSE TRUE 5034218.261 5404552.377 3797208.581 3547580.713 4574086.826 4160030.335 5829726.54 5412146.019 1129445.244 4.457248624 4.785138903 3.362012103 3.14099398 4.049852659 3.683251008 5.161584034 4.791862241 1 20.1071829 4.250128144 24.91864959 3.791599895 4.62119408 0.106911497 1.125977896 568.5514066 1224742.942 0.282588069 0.733916756 17788.04192 -4.250128144 0.829594185 DINLDVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DINLDVNR 8 0 P26640;A0A140T936;H0Y426 P26640 VARS Valine--tRNA ligase 0 ; 96.668 0.020421 717400000 1156340 1163260 728870 894380 1239800 1294780 1129190 1385710 1400810 FALSE TRUE 1003526.739 1155618.468 1081353.97 1097462.649 1215130.406 1344591.024 1019681.328 1089386.7 1235207.838 0.812435534 0.93556601 0.875442931 0.888484201 0.983745705 1.088554479 0.825513971 0.881946072 1 20.23632238 3.362847978 7.851621615 0.943436906 0.880879578 0.199032628 0.075485434 0.522865394 33.87925594 0.02313571 0.029883505 2305.939865 -3.362847978 -0.062557328 DINTFVGT(ph)PVEK ddPTM_MDA-MB-175_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 236.78 4.89E-15 745140000 2063850 1869040 1705460 1941920 1679090 1423600 2053040 2356980 3671260 TRUE FALSE 1791106.993 1856762.153 2530226.16 2382862.616 1645679.394 1478366.813 1853936.497 1852958.169 3237247.825 0.553280777 0.573561943 0.781597918 0.736076675 0.508357556 0.456673969 0.572689086 0.572386876 1 21.62633638 1.236624934 24.99888158 1.000000512 0.594929867 0.633657651 0.09693694 37.02632493 478055.7719 0.163235814 0.025827986 17.24348063 -1.236624934 -0.405070645 DINVSVGSQQPDTKDS(ph)PVCPHFTTNGNENSSIEK ddPTM_MDA-MB-175_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(0.001)KDS(0.999)PVCPHFTTNGNENSSIEK;DINVSVGSQQPDT(0.003)KDS(0.997)PVCPHFTTNGNENSSIEK;DINVSVGSQQPDT(0.027)KDS(0.973)PVCPHFTTNGNENSSIEK 327.46 1.98E-117 1727930000 1091480 918140 509014 652850 858970 564570 1176350 1341380 1184860 TRUE FALSE 947238.1525 912108.6779 755174.8729 801089.5707 841878.1775 586289.3732 1062267.758 1054536.326 1044787.201 0.906632616 0.873009047 0.722802569 0.766749028 0.805789138 0.561156734 1.016731213 1.009331206 1 19.9947777 2.18904016 24.99998637 1.009157421 0.776216488 0.592410423 0.092247498 76.14496421 38440.54474 0.037738345 0.025443235 154.5397339 -2.18904016 -0.232940933 DINWDSSQWQPLIQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DINWDSSQWQPLIQDR 16 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 ;;; 268.93 2.83E-27 674442000 448552 420673 292392 327886 394412 438599 394181 485780 450519 FALSE TRUE 389274.7167 417909.5714 433793.7492 402337.5277 386563.9729 455472.1873 355953.3873 381899.7273 397259.1571 0.97990118 1.051982224 1.091966646 1.012783521 0.973077564 1.146536661 0.896023115 0.961336499 1 18.59972095 2.216583524 24.99996611 0.951952661 1.040843389 0.363196589 0.056299799 253.0556006 287860.4316 0.022129766 0.014933137 164.6582607 -2.216583524 0.088890728 DIPGLTDTTVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIPGLTDTTVPR 12 0 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ; 149.96 0.00015753 139691000 132025 138493 83345 100279 121605 137897 131845 146943 146073 FALSE TRUE 114577.5617 137583.2304 123650.9208 123048.8796 119185.2984 143201.9868 119058.6922 115520.383 128804.4163 0.889546842 1.068156157 0.95998976 0.955315688 0.925319968 1.111778547 0.924337034 0.896866631 1 16.97482253 DIPNENEAQFQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DIPNENEAQFQIR 13 0 Q10567-4;Q10567-3;Q10567-2;Q10567 Q10567-4 AP1B1 AP-1 complex subunit beta-1 0 85.672 0.021351 26757000 62182 58983 43314 54776 56243 51594 65291 72217 65330 FALSE TRUE 53964.49115 58595.53679 64260.79528 67213.728 55123.87434 53578.85457 58959.08887 56773.95654 57606.76182 0.936773556 1.017164217 1.115507854 1.16676803 0.956899374 0.930079263 1.023475144 0.985543272 1 15.81395054 DIPRTPS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIPRTPSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DIPRT(0.003)PS(0.997)R;DIPRT(0.005)PS(0.995)R 97.284 0.021942 962400000 1582890 1376010 899960 1018130 1319320 1370450 1252360 1514940 1189920 TRUE FALSE 1373707.076 1366970.9 1335183.666 1249311.978 1293068.113 1423172.098 1130906.32 1190981.87 1049249.013 1.309228847 1.30280885 1.272513626 1.190672531 1.232374867 1.35637211 1.077824526 1.135080286 1 20.00092568 2.223347098 24.99999976 1.084610541 1.272285558 0.75523024 0.055149129 124.6700542 204865.6468 0.022824224 0.015452937 167.2426722 -2.223347098 0.187675018 DIPSFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DIPSFER 7 0 K7EJR3;R4GMR5;P48556 K7EJR3 PSMD8 26S proteasome non-ATPase regulatory subunit 8 0 ;;; 200.12 0.0008406 1596730000 1286900 1194200 837310 1023940 1206480 1221730 1260130 1316840 1366900 FALSE TRUE 1116832.904 1186355.222 1242235.917 1256441.227 1182473.408 1268730.744 1137922.787 1035244.014 1205306.639 0.926596493 0.984276684 1.030638907 1.042424547 0.981056082 1.052620721 0.944094017 0.858905095 1 20.2009688 2.035706829 8.621929713 0.914016824 1.003810937 0.293050762 0.049313879 0.243529075 53.5913931 0.019829876 0.013275472 108.5692479 -2.035706829 0.089794113 DIPVVHQLLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIPVVHQLLTR 11 0 P30419;P30419-2 P30419 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 0 ; 210.15 1.37E-08 826610000 1292830 1235800 820030 966780 1218700 1350310 1135930 1366310 1247950 FALSE TRUE 1121979.24 1227681.948 1216599.251 1186302.175 1194450.254 1402257.299 1025767.683 1074135.239 1100418.773 1.019592966 1.115649768 1.105578423 1.078046108 1.085450634 1.274294236 0.9321612 0.976114972 1 20.06962123 2.186825292 24.99999979 0.969266149 1.110026913 0.512557605 0.066003958 80.10159227 38706.71998 0.026081239 0.01758399 153.7535994 -2.186825292 0.140760765 DIQLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 167.98 0.015103 1672890000 1195480 1014030 812140 2289690 898920 3294310 1055900 1613270 1588770 FALSE TRUE 1037494.289 1007368.77 1204893.62 2809599.11 881033.2507 3421044.237 953498.9805 1268284.765 1400947.421 0.740566187 0.719062511 0.860056275 2.005499328 0.628883881 2.441950488 0.680610112 0.905305043 1 20.41797138 3.979223444 24.85553356 1.238742859 0.744750366 0.150021043 0.56646276 1361.69951 1629042.973 0.145122743 0.255156066 9532.865023 -3.979223444 -0.493992493 DIQMPDGIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DIQMPDGIRR 10 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 110.39 0.0030349 166730000 236970 230720 105120 128740 228780 237450 242720 224920 165000 FALSE TRUE 205653.8141 229204.3851 155956.3836 157972.3847 224227.7256 246584.8552 219181.0518 176822.6083 145493.888 1.413487652 1.575354046 1.071910207 1.085766467 1.541148764 1.694812467 1.506462263 1.215326711 1 17.15059902 1.460754533 3.303398817 1.011455817 1.407982039 0.317419096 0.199026253 0.333596422 6.498091825 0.264431138 0.056918612 28.89046504 -1.460754533 0.396526222 DIQNTQCLLNVEHLSAGCPHVTLQFADSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DIQNTQCLLNVEHLSAGCPHVTLQFADSK 29 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 197.28 2.44E-25 579120000 242230 246620 111110 200000 380030 319230 451840 559420 216380 FALSE TRUE 210218.6918 244999.937 164843.1676 245413.0568 372468.1465 331510.9847 408020.6263 439792.3864 190799.8029 1.101776252 1.284068082 0.863958794 1.286233283 1.952141149 1.73748075 2.138475093 2.304993924 1 17.54170016 3.321485635 4.128617781 1.907105791 1.099773025 0.476508252 0.359244197 0.173014885 5.561283614 0.106152726 0.137156551 2096.455437 -3.321485635 -0.807332766 DIREEAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DIREEAEK 8 1 P25788-2;P25788;G3V4X5;H0YJ03 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;;; 140.45 0.00059228 2060660000 5038190 4058960 2366540 2468520 3188110 3003690 4460100 4986010 1693880 FALSE TRUE 4372380.426 4032296.425 3511006.66 3029035.195 3124672.848 3119243.898 4027560.188 3919790.563 1493631.436 2.927348957 2.699659586 2.350651288 2.027966955 2.091997244 2.088362512 2.696488632 2.624335876 1 20.51039277 4.274790175 2.352226994 2.181692316 2.902387315 0.285799091 0.459973357 0.457102854 4.858460178 0.124486315 0.453499104 18827.39245 -4.274790175 0.720694998 DIRPGAAFEPTYIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DIRPGAAFEPTYIYR 15 1 Q14694;Q14694-3;Q14694-2;J3KT19 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 0 122.12 0.00010112 353200000 120670 88267 55921 83414 90174 91236 109600 102540 79203 FALSE TRUE 104723.1538 87687.16827 82964.58264 102354.4236 88379.71382 94745.90796 98971.00887 80612.61897 69839.71157 1.499478612 1.255548832 1.187928483 1.465561946 1.265465046 1.356619405 1.417116518 1.154251888 1 16.09175998 1.514062163 3.375009402 1.015188647 1.340796217 0.596491098 0.097038431 0.147312115 3.395388351 0.096698141 0.024564672 32.66345821 -1.514062163 0.325607571 DIRPVCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DIRPVCR 7 1 O00148;O00148-2;O00148-3;K7EQN7 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ;;; 127.12 0.003544 3065290000 390235 314341 254304 237516 315650 468197 267885 251419 260987 FALSE TRUE 338664.456 312276.0733 377286.265 291447.638 309369.1826 486208.8416 241905.5539 197655.0034 230133.4142 1.471600538 1.356934952 1.639424098 1.266429037 1.344303623 2.112725974 1.051153544 0.858871382 1 17.81211095 2.023319986 24.98458097 0.930052062 1.514384562 0.560892108 0.235852368 151.2434663 162038.6515 0.093351582 0.062933896 105.516405 -2.023319986 0.5843325 DIS(ph)ENKR ddPTM_MDA-MB-175_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 123.86 0.0025741 1636730000 3583900 2723040 2187590 2274870 2028220 2341480 3423100 3717710 3738940 TRUE FALSE 3110278.535 2705152.171 3245515.841 2791414.003 1987862.39 2431558.251 3091128.289 2922706.648 3296926.773 0.943387205 0.820507205 0.984406408 0.84667152 0.602944053 0.737522674 0.937578691 0.886494256 1 21.65269041 1.601740361 1.683430302 0.989474781 0.826400556 0.184186964 0.109188526 0.878790951 4.2722354 0.203962881 0.034359083 39.97057182 -1.601740361 -0.163074225 DIS(ph)S(ph)MKLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DISSMKLKR 9 2 H3BSD9 H3BSD9 MYO7B 2 DIS(1)S(1)MKLKR 53.237 0.079437 2024600000 1163700 1189600 614380 923150 1358200 1406600 1151300 1329000 1359900 TRUE FALSE 1009914.097 1181785.439 911496.223 1132765.317 1331174.477 1460712.812 1039647.103 1044803.692 1199134.171 0.84220275 0.985532285 0.760128637 0.944652687 1.110113038 1.218139594 0.866998146 0.871298406 1 20.19356166 3.482760647 24.98216168 0.997786189 0.871158711 0.255129497 0.115724748 438.7334278 1943565.372 0.036456254 0.048606757 3039.209562 -3.482760647 -0.126627479 DISEMFLQIYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DISEMFLQIYK 11 0 P15941-2;A0A087WWM1;A0A087X2A4;A0A0C4DGW3;P15941-7;P15941-11;P15941-4;P15941-3;P15941;P15941-8;A0A087WVJ0;A0A0A0MSH4;P15941-17;P15941-13;Q7Z536;A0A087WZZ6;A0A087X061 P15941-2 MUC1 Mucin-1;Mucin-1 subunit alpha;Mucin-1 subunit beta 0 ; 201.1 1.04E-07 360310000 843370 817000 579750 647560 652600 768740 673250 814630 928370 FALSE TRUE 731916.5177 811633.0732 860119.0391 794598.3953 639614.5368 798313.9252 607958.3186 640427.714 818619.1562 0.894086722 0.991466016 1.050694981 0.970656977 0.781333459 0.975195754 0.742663196 0.782326811 1 19.6428329 3.318956046 7.481680165 0.844683673 0.984406081 0.30321215 0.089546669 0.258420547 20.50448461 0.025667804 0.033118156 2084.279925 -3.318956046 0.139722409 DISENKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DISENKR 7 1 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;; 188.81 0.00090467 44144620000 25406480 21057050 13839030 18201130 14921840 16793140 24323650 27265830 24202440 FALSE TRUE 22048949.3 20918724.85 20531631.2 22333974.75 14624924.58 17439182.96 21964746.17 21435244.44 21341255.11 1.033160851 0.980201246 0.962062966 1.04651646 0.685288869 0.817158263 1.029215294 1.004404114 1 24.34714169 2.179285414 24.99998991 1.010539967 0.920327199 0.140223365 0.10560219 164.1582511 69233.78806 0.04615519 0.031117833 151.1072892 -2.179285414 -0.090212767 DISGPS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DISGPSPSK 9 0 Q96GX9;S4R3D6;Q96GX9-3 Q96GX9 APIP Methylthioribulose-1-phosphate dehydratase 1 DISGPS(1)PSK;DISGPS(1)PSK;DISGPS(0.999)PS(0.001)K;DISGPS(0.999)PS(0.001)K 206.36 1.41E-05 1345200000 3551910 2507070 1933320 2114170 2451120 2173520 2879710 3333360 3421940 TRUE FALSE 3082516.094 2490600.892 2868280.019 2594224.612 2402347.508 2257136.721 2600436.167 2620546.904 3017402.151 1.021579471 0.825412314 0.950579298 0.859754345 0.796164179 0.74803974 0.861812923 0.86847784 1 21.52487556 DISGPS(ph)PSKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DISGPSPSKK 10 1 Q96GX9;S4R3D6;Q96GX9-3 Q96GX9 APIP Methylthioribulose-1-phosphate dehydratase 1 DIS(0.003)GPS(0.993)PS(0.004)KK;DISGPS(0.997)PS(0.003)KK;DISGPS(0.737)PS(0.263)KK;DISGPS(0.964)PS(0.036)KK;DIS(0.001)GPS(0.811)PS(0.188)KK 159.52 4.69E-06 2514810000 7333850 4439370 4236690 4276750 4405320 3173290 6238830 6965580 6467970 TRUE FALSE 6364663.141 4410207.486 6285567.455 5247851.454 4317662.751 3295368.52 5633789.227 5476044.923 5703333.955 1.115954842 0.773268324 1.102086517 0.920137501 0.757041896 0.577796872 0.987806303 0.960148041 1 22.44337408 4.760066092 23.0211653 0.889812468 1.115955529 0.19031278 0.149530884 3389.293759 3627995.86 0.037983218 1.486335586 57552.75153 -4.760066092 0.226143062 DISLDSELHDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DISLDSELHDLR 12 0 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 ;;; 229.29 8.53E-12 713820000 1082120 943650 478074 715450 940160 911020 924520 1067770 981580 FALSE TRUE 939115.1003 937451.101 709272.1855 877903.8575 921452.6554 946067.5289 834860.1927 839435.6949 865538.7306 1.085006444 1.083083943 0.819457478 1.014286047 1.064600142 1.093038931 0.964555557 0.969841863 1 19.72323885 DISMEIDS(ph)PENMMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 330.28 2.21E-68 1132520000 3225890 3274630 2159310 2590320 3122220 3148060 3066890 3703630 3368840 TRUE FALSE 2799580.463 3253118.74 3203559.538 3178491.747 3060093.931 3269167.905 2769463.48 2911637.546 2970579.573 0.942435775 1.095112472 1.078429128 1.069990441 1.030133634 1.100515177 0.932297355 0.980158072 1 21.502313 2.236072042 24.99995905 0.971159178 1.055614344 0.398682504 0.047358043 60.57225836 608488.9422 0.017759123 0.012605797 172.2154227 -2.236072042 0.084455166 DISMEIDSPENMMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DISMEIDSPENMMR 14 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 90.614 0.01322 41760000 28504 31304 13984 18083 25919 31123 21169 29147 17908 FALSE TRUE 24737.12418 31098.36196 20746.70917 22189.02153 25403.26261 32320.32195 19116.03364 22914.14087 15790.93664 1.566539385 1.969380453 1.313836516 1.405174502 1.608724244 2.046764083 1.210569966 1.451094472 1 13.94680913 1.129895668 1.125650025 0.613678114 1.620743741 0.358847361 0.255276444 2.390957854 2.139859237 3.071444015 0.081413018 13.48638855 -1.129895668 1.007065626 DISPVLKDPASFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DISPVLKDPASFR 13 1 H3BQB1;P07741-2;P07741;H3BQZ9;H3BQF1;H3BSW3 H3BQB1 APRT Adenine phosphoribosyltransferase 0 ; 145.43 3.81E-05 4432900000 10372900 8266000 5378400 6468000 7678500 7214100 9247100 11001800 8289400 FALSE TRUE 9002094.983 8211700.102 7979412.23 7936658.257 7525712.873 7491631.095 8350317.665 8649150.686 7309436.575 1.231571666 1.123438177 1.091659001 1.085809854 1.029588641 1.024925932 1.14240237 1.183285551 1 22.80132877 4.759791747 2.135788476 1.08857467 1.275479845 0.425302353 0.055040097 0.840642951 4.120314501 0.01578502 0.307413412 57516.40685 -4.759791747 0.186905175 DISQNKR ddPTM_MDA-MB-175_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 ;;;;;; 133.6 0.0052206 28918570000 16708430 15239450 9130330 11826870 9136090 13399650 17705500 18968600 15158200 FALSE TRUE 14500368.64 15139341.05 13545788.13 14512341.6 8954299.683 13915143.21 15988423.34 14912312.5 13366214.86 1.084852278 1.132657316 1.013434863 1.08574804 0.669920376 1.041068346 1.196181828 1.115672062 1 23.67208764 0.935393082 19.67662606 0.151770256 1.045437897 0.008401768 0.141617205 181.2250223 269255.926 27011.78018 0.035059903 8.617733948 -0.935393082 0.893667641 DITDPLSLNTCTDEGHVVLAS(ph)PLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DITDPLSLNTCTDEGHVVLASPLK 24 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 DITDPLSLNTCTDEGHVVLAS(1)PLK;DITDPLSLNTCTDEGHVVLAS(1)PLK;DITDPLSLNTCTDEGHVVLAS(1)PLK 277.81 2.72E-52 1920460000 1493050 1078780 757830 921190 1120090 885360 1322920 1553910 1386510 TRUE FALSE 1295739.66 1071693.423 1124319.123 1130360.269 1097802.4 919420.3721 1194623.422 1221618.439 1222598.367 1.059824464 0.876570305 0.919614448 0.924555683 0.897925623 0.752021593 0.97711845 0.999198487 1 20.22151911 2.023954746 24.99908459 0.996127067 0.901639265 0.239258651 0.073728444 295.4403755 308319.1391 0.029571592 0.019936194 105.6707392 -2.023954746 -0.094487801 DITDTLVAVTISEGAHHLDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DITDTLVAVTISEGAHHLDLR 21 0 P42785;P42785-2 P42785 PRCP Lysosomal Pro-X carboxypeptidase 0 ; 184.78 2.22E-17 110296000 115476 103971 42039 89008 109098 116310 99076 114715 111219 FALSE TRUE 100215.554 103288.0077 62369.20101 109218.6268 106927.1632 120784.521 89467.62477 90184.08996 98070.81652 1.021869273 1.053198202 0.635960862 1.113671025 1.090305629 1.231605132 0.91227572 0.91958131 1 16.58153627 DITEEIMSGAR ddPTM_MDA-MB-175_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 ; 130.53 0.00093375 112880000 119873 104109 74503 95208 121063 116835 113811 131798 122157 FALSE TRUE 104031.4793 103425.1011 110532.9 116826.4316 118654.0832 121329.7181 102773.6267 103614.0234 107715.7386 0.965796463 0.960167033 1.026153665 1.084580889 1.101548248 1.126388025 0.954118944 0.961920929 1 16.71686954 7.941114898 19.61524994 1.018804061 0.005500801 0 0.063964462 0 0 0.016128553 0 87320235.39 -7.941114898 -1.013303261 DITLFHAMDTLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DITLFHAMDTLYR 13 0 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2;E9PCS8 Q9BTC8 MTA3 Metastasis-associated protein MTA3 0 106.13 0.00092988 0 306930 279770 152980 195900 295660 313250 295790 305290 223900 FALSE TRUE 266368.4228 277932.1724 226961.6397 240382.0891 289776.9444 325300.9302 267104.3313 240006.1093 197430.7971 1.349173618 1.407744772 1.149575664 1.217551125 1.467739323 1.647670652 1.352901043 1.215646762 1 17.59098753 1.414562584 2.391747055 0.977191772 1.370864652 0.446182052 0.13383497 0.414347271 3.551384314 0.297965243 0.039595224 25.97542031 -1.414562584 0.39367288 DITSDTSGDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DITSDTSGDFR 11 0 P04083;Q5T3N1 P04083 ANXA1 Annexin A1;Annexin 0 142.92 0.0034116 0 145640 133040 108440 142750 170540 172780 115760 168510 160790 FALSE TRUE 126393.305 132166.0515 160881.9467 175163.5693 167146.5877 179426.9584 104533.613 132475.4478 141781.5894 0.891464862 0.932180631 1.134716767 1.235446507 1.178901918 1.265516625 0.737286227 0.934362835 1 17.11331068 2.238463046 25 0.893291467 1.108905797 0.364905231 0.134176029 3.03226739 776485.5046 0.056404767 0.040794277 173.1661678 -2.238463046 0.215614331 DITSSIHFEAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DITSSIHFEAYR 12 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4 Q9UHD8 9-Sep Septin-9 0 ;;; 237.49 4.17E-16 3066180000 2660260 3807270 1356750 2554610 4125750 4057610 3531730 4097120 4184300 FALSE TRUE 2308699.901 3782259.793 2012878.838 3134673.245 4043655.647 4213708.882 3189223.368 3220982.772 3689636.821 0.625725515 1.025103547 0.545549314 0.849588563 1.095949505 1.142038929 0.864373249 0.872980981 1 21.81504738 3.472527529 23.98602617 0.976937205 0.750781382 0.39377667 0.14849009 87.70715549 457955.4108 0.042496407 0.055108356 2968.434901 -3.472527529 -0.226155823 DIVAAIQHNYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIVAAIQHNYK 11 0 Q5TFE4;Q5TFE4-2;Q5QPD0 Q5TFE4 NT5DC1 5-nucleotidase domain-containing protein 1 0 ; 149.96 3.41E-05 1802080000 1748620 1534240 1603070 1397100 1425790 1110170 1700340 1867360 1781090 FALSE TRUE 1517535.437 1524161.476 2378320.014 1714332.908 1397419.569 1152878.958 1535441.289 1468039.596 1570531.569 0.966255927 0.970474906 1.514340788 1.091562209 0.889774899 0.734069267 0.977657068 0.934740584 1 20.58282151 3.323292016 5.045800872 0.907580348 1.157242465 0.323825067 0.164887652 0.247776247 10.81789194 0.049440094 0.063796502 2105.19348 -3.323292016 0.249662118 DIVEAHYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DIVEAHYR 8 0 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ;;;;; 174.16 0.00027356 6987070000 7419280 7120480 5549770 6362840 6770140 7711990 8117470 7654310 8387170 FALSE TRUE 6438803.35 7073705.098 8233657.335 7807620.072 6635427.46 8008675.246 7330239.009 6017495.372 7395648.317 0.870620542 0.95646856 1.113311096 1.055704617 0.897207003 1.082890222 0.991155703 0.813653532 1 22.81824519 1.896296299 9.896034558 0.895567677 1.001003292 0.144843741 0.087993257 0.635173296 56.8006144 0.040741174 0.023039896 78.75829375 -1.896296299 0.105435615 DIVENYFMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 DIVENYFMR 9 0 Q13263;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;;;;;;;; 252.81 1.62E-14 7456740000 2559760 2097023 1334388 1502674 2006319 1950390 1982404 2278370 2158220 FALSE TRUE 2221481.23 2083247.518 1979702.5 1843879.099 1966397.177 2025422.765 1790150.765 1791158.306 1903077.69 1.167309796 1.09467287 1.040263627 0.968893234 1.03327215 1.064288009 0.940660896 0.941190323 1 20.85990303 8 0.40563565 0.966329692 4.454391897 0.70944314 0.038025908 49.33623118 0.685593037 0.038589121 137.2144578 99999999.99 -8 3.488062206 DIVHSGLAYTMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DIVHSGLAYTMER 13 0 P00367;P00367-2;P00367-3 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ;;;;; 224.43 1.41E-11 3077140000 1841090 2059850 1406570 2186650 2404660 2532710 1838730 2393750 1974370 FALSE TRUE 1597785.292 2046318.71 2086791.957 2683162.303 2356811.971 2630144.993 1660410.248 1881865.191 1740962.228 0.917759884 1.175395237 1.198642867 1.541195013 1.353741013 1.510742135 0.953731345 1.080933957 1 20.73145347 2.215995142 24.99964659 1.023599633 1.289154729 0.339990144 0.177823367 289.1436271 320331.4915 0.076204506 0.051417752 164.4353328 -2.215995142 0.265555096 DIVNGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DIVNGLR 7 0 P47756-2;B1AK88;B1AK87;P47756 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;; 108.98 0.016588 891960000 791970 750170 496890 639220 760570 865420 696040 796310 986660 FALSE TRUE 687309.1579 745242.0839 737187.666 784364.6709 745436.145 898713.2674 628538.1479 626025.3034 870018.1788 0.789994019 0.856582198 0.84732444 0.901549749 0.856805252 1.032982171 0.722442546 0.719554279 1 19.73068602 DIVNMLMHHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 140.31 2.24E-05 2007685000 2466747 2140281 1713987 1919620 2136232 2189481 1891018 2169726 3588381 FALSE TRUE 2140760.134 2126221.353 2542876.846 2355499.061 2093725.163 2273711.751 1707627.365 1705746.98 3164166.686 0.676563641 0.67196882 0.803648195 0.744429512 0.661698757 0.718581534 0.539676804 0.539082529 1 21.59339417 3.228108733 23.34042159 0.662646068 0.726103388 0 0.132941308 331.7392642 740814.0841 0.040434746 0.04641153 1690.864217 -3.228108733 0.063457319 DIVPGDIVEIAVGDKVPADIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIVPGDIVEIAVGDKVPADIR 21 1 P16615-5;P16615-2;P16615-3;P16615 P16615-5 ATP2A2 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 0 ; 171.79 5.88E-12 71024000 142975 119476 91796 148431 153202 127508 120074 235114 204221 FALSE TRUE 124080.4915 118691.1543 136188.8526 182134.5272 150153.5799 132413.3153 108429.242 184836.7008 180078.226 0.689036616 0.65910886 0.756276068 1.011418933 0.833824184 0.735309972 0.602123001 1.026424487 1 17.45826422 1.644553597 8.050525361 1.01480155 0.764363312 0.480617069 0.11089384 0.10349692 12.96760667 0.070704455 0.030696966 44.11167987 -1.644553597 -0.250438238 DIVQFVPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DIVQFVPYR 9 0 Q99829;B0QZ18;F2Z2V0;H0Y524 Q99829 CPNE1 Copine-1 0 84.568 0.035837 96745000 70438 84589 57019 65116 80074 83775 81271 100940 102310 FALSE TRUE 61129.43983 84033.32929 84593.57912 79901.58304 78480.68406 86997.87846 73389.35093 79354.76652 90215.02835 0.677597081 0.931478167 0.937688328 0.885679299 0.869929163 0.964339091 0.81349363 0.879618041 1 16.46108016 4.742891138 24.60273529 0.903862458 0.677596967 0.656184289 0.052750022 223.9824617 1272440.075 0.012604879 0.095339864 55321.14215 -4.742891138 -0.226265491 DIWAELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIWAELR 7 0 A0A1B0GV75;A0A1B0GTB8;A0A1B0GWC0;A0A1B0GVF3;P23786 A0A1B0GV75 CPT2 "Carnitine O-palmitoyltransferase 2, mitochondrial" 0 ; 93.262 0.035045 88547000 246101 231767 167112 271326 282711 285856 232158 297997 271555 FALSE TRUE 213578.1293 230244.5073 247927.9222 332934.7153 277085.6042 296853.0653 209643.3529 234272.6606 239452.0773 0.891945193 0.961547337 1.035396832 1.390402285 1.157165172 1.239718063 0.875512776 0.978369715 1 17.86937743 2.228840206 24.99888663 0.953777351 1.116956201 0.222361741 0.142111275 331.5021705 852547.0708 0.062064061 0.04243012 169.3714503 -2.228840206 0.16317885 DIWDFLR ddPTM_MDA-MB-175_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 212507000 562660 525550 451670 535340 590380 538130 682270 664520 819150 FALSE TRUE 488303.0554 522097.6274 670099.1227 656897.1292 578632.5931 558832.2093 616103.5604 522417.5693 722311.0202 0.676028804 0.722815536 0.927715491 0.909438055 0.801085096 0.773672551 0.852961596 0.723258478 1 19.46226066 4.400327606 6.840908684 0.840332213 0.687374417 0.390940067 0.080230743 0.207726216 14.74678632 0.020059425 0.054191246 25137.81967 -4.400327606 -0.152957796 DIWDIQMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DIWDIQMR 8 0 P32456 P32456 GBP2 Interferon-induced guanylate-binding protein 2 0 ;;; 141.39 0.0014757 509782000 1019130 1079830 690030 770650 997210 951880 1077150 1149380 1083380 FALSE TRUE 884449.3884 1072736.526 1023730.816 945637.8611 977367.472 988499.4395 972688.1588 903594.0315 955304.0506 0.92583025 1.122926805 1.071628258 0.989881557 1.023095706 1.034748506 1.018197461 0.945870617 1 19.86560046 1.902565635 5.675144507 0.971317559 1.03192093 0.154163436 0.052121289 0.354681658 16.51455777 0.025414064 0.013400575 79.90346901 -1.902565635 0.060603371 DIWPTRDEIQAVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DIWPTRDEIQAVER 14 1 P21399 P21399 ACO1 Cytoplasmic aconitate hydratase 0 ;;; 271.08 5.48E-33 945950000 585196 618909 315213 361537 575518 581309 628100 691430 253686 FALSE TRUE 507860.8659 614843.346 467651.0611 443629.5016 564066.3178 603672.3334 567186.9587 543573.0752 223695.5301 2.270321922 2.748572338 2.090569539 1.983184471 2.521580639 2.698633867 2.535531034 2.429968426 1 17.7711769 1.238228316 24.97971212 0.9999984 2.416433741 0.768990648 0.242811608 3.90735297 293275.042 0.349228497 0.061495894 17.30725992 -1.238228316 1.416435341 DIYDKYGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DIYDKYGK 8 1 E9PH18;A0A0J9YX62;O75190-3;O75190;C9JDX6;F8WCZ4;C9J2P2;C9J2C4;O75190-2;O75190-4;C9JDR7 E9PH18 DNAJB6 DnaJ homolog subfamily B member 6 0 76.465 0.032587 174340000 406080 413500 220870 314730 402660 382940 542630 727200 291820 FALSE TRUE 352415.4991 410783.6913 327683.4708 386194.2568 394647.8538 397671.9496 490005.8261 571693.9391 257321.372 1.369553941 1.596383884 1.273440555 1.500824645 1.533676937 1.545429151 1.904256231 2.22171184 1 17.97321176 2.363941363 4.586551861 1.82203133 1.462444314 0.081317853 0.318388021 0.331208681 11.82307976 0.120713021 0.091690669 231.1752643 -2.363941363 -0.359587016 DIYLS(ph)PDRTGSSFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DIYLSPDRTGSSFGK 15 1 Q15696 Q15696 ZRSR2 U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 1 DIYLS(1)PDRTGSSFGK;DIY(0.001)LS(0.999)PDRTGSSFGK 122.49 6.58E-05 500310000 913910 761880 379170 478490 747410 584740 881650 990030 306870 TRUE FALSE 793134.4779 756875.1601 562537.8802 587138.4678 732538.0033 607235.3262 796147.7187 778319.7889 270592.1782 2.931106447 2.797106573 2.078914047 2.169827937 2.707166217 2.244097853 2.942242174 2.876357307 1 18.04576061 4.39012902 7.139259289 2.385841709 2.897951497 0.142959307 0.551419538 0.435092845 29.31517672 0.135783338 0.364913568 24554.38265 -4.39012902 0.512109788 DKADFCIIHYAGK ddPTM_MDA-MB-175_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 ; 125.54 0.00011954 8536600000 19088100 15790900 12355400 15433900 14606200 11649100 20668600 24335000 22149000 FALSE TRUE 16565559.22 15687168.54 18330512.77 18938402.89 14315565.2 12097248.41 18664162.35 19131149.63 19530570.45 0.848186143 0.803210975 0.938554909 0.969679966 0.732982441 0.61940067 0.955638362 0.979548942 1 24.21923075 2.027984827 24.99851113 0.982097873 0.823146324 0.375424136 0.097629948 236.280744 211065.7724 0.042966541 0.028967434 106.6558858 -2.027984827 -0.158951549 DKADKDEQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKADKDEQIR 10 2 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494C1B7;A0A494BZX5;A0A494C122;A0A494C0Y7;H7C0P8 Q92878-2 RAD50 DNA repair protein RAD50 0 48.741 0.097951 77615000 116070 81089 72654 72812 67753 57071 93134 124030 106200 FALSE TRUE 100731.0554 80556.32102 107789.7174 89345.07746 66404.84786 59266.5583 84101.87901 97507.1497 93645.15698 1.075667538 0.860229441 1.151044228 0.954081133 0.709111394 0.632884393 0.898091068 1.04124071 1 16.51491676 3.472125661 24.99324211 0.867740811 1.018848215 0.24253 0.139324087 243.6465149 1218969.179 0.044815085 0.058060934 2965.689373 -3.472125661 0.151107404 DKALQDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKALQDYR 8 1 A0A087X2I1;P62333;H0YJC0;H0YJS8;H0YJT1;H0YJD2;H0YJY8;H0YJE9 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ; 65.224 0.05912 1293030000 1977190 1841310 979500 1168690 1754980 1561060 2056320 2250420 719280 FALSE TRUE 1715899.332 1829214.313 1453189.476 1434058.927 1720059.332 1621114.988 1856898.403 1769185.196 634247.5378 2.705409528 2.884070027 2.291202393 2.261039801 2.711968481 2.555965757 2.927718741 2.78942383 1 19.27468649 4.245265132 24.90453481 2.44664531 2.794739844 0.084891925 0.537342291 441.4879709 1639901.679 0.132247655 0.333250836 17589.97133 -4.245265132 0.348094535 DKANMQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 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 ;;;;;;;;;;; 162.97 0.00020346 3476009000 7150452 6360193 3688374 4593804 4094585 5180596 6310176 7232827 7083874 FALSE TRUE 6205501.651 6318412.473 5472084.003 5636897.41 4013110.769 5379896.88 5698216.103 5686143.232 6246426.486 0.99344828 1.011524347 0.876034324 0.902419555 0.64246506 0.861275946 0.912236159 0.910303394 1 22.57459964 4.230990867 13.05972015 0.870149292 1.002504324 0.264643347 0.090310001 0.666281994 1150.39868 0.024182764 0.053556484 17021.22714 -4.230990867 0.132355032 DKAPVQPQQS(ph)PAAAPGGTDEKPSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DKAPVQPQQSPAAAPGGTDEKPSGK 25 2 Q13200;C9JPC0;F8WBS8 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 1 DKAPVQPQQS(1)PAAAPGGTDEKPSGK;DKAPVQPQQS(1)PAAAPGGTDEKPSGK;DKAPVQPQQS(1)PAAAPGGTDEKPSGK;DKAPVQPQQS(1)PAAAPGGTDEKPSGK 205.03 2.31E-25 3331540000 7227050 4650800 4339140 4684230 4058350 2725650 7160860 8069330 6764850 TRUE FALSE 6271977.031 4620248.589 6437562.618 5747856.015 3977596.775 2830507.519 6466400.899 6343766.575 5965117.14 1.051442392 0.774544486 1.079201375 0.963578062 0.6668095 0.474509964 1.084035862 1.063477284 1 22.50811904 DKAS(ph)PEPEKDFSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.991)PEPEKDFS(0.009)EK;DKAS(1)PEPEKDFSEK;DKAS(0.595)PEPEKDFS(0.405)EK 144.5 6.96E-06 2233550000 2721440 1591960 1925690 1555290 1457140 1118980 2650560 2875440 2633420 TRUE FALSE 2361794.809 1581502.31 2856960.125 1908442.366 1428145.765 1162027.885 2393509.099 2260549.533 2322100.088 1.01709432 0.681065523 1.230334618 0.821860511 0.615023346 0.500421102 1.030751909 0.973493582 1 21.14699873 DKAVESLR ddPTM_MDA-MB-175_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 ;;; 116.3 0.0020949 3987710000 3513100 3112810 1907310 2296350 2941800 2805860 3557830 3892540 2453320 FALSE TRUE 3048834.934 3092361.746 2829691.496 2817771.365 2883263.936 2913803.25 3212792.194 3060150.613 2163291.304 1.409350154 1.429470797 1.308049216 1.302539034 1.332813537 1.346930598 1.485140807 1.414580924 1 21.04479652 1.235377499 25 0.999999478 1.379875358 0.809131973 0.057786831 42.34636443 332527.8258 0.109014402 0.015696391 17.19402283 -1.235377499 0.37987588 DKDALWQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKDALWQK 8 1 Q9BQS8;Q9BQS8-4 Q9BQS8 FYCO1 FYVE and coiled-coil domain-containing protein 1 0 79.148 0.026455 0 284070 259560 179840 201650 233550 194720 319420 328300 277510 FALSE TRUE 246529.4298 257854.9333 266811.2255 247437.7145 228902.8119 202211.0044 288442.6976 258095.5998 244703.0839 1.007463518 1.053746153 1.090346804 1.011175301 0.935430842 0.826352497 1.178745657 1.054729657 1 17.90067276 2.201278472 24.99999902 1.077218373 0.993828579 0.207120485 0.082749694 307.3027231 206063.4625 0.035783532 0.024125875 158.9565658 -2.201278472 -0.083389794 DKDAVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DKDAVDK 7 1 P25815 P25815 S100P Protein S100-P 0 ;;;;; 128.12 0.0034551 10965240000 14096000 11247190 11350080 11416610 4984380 5805700 15664900 16468600 29850700 FALSE TRUE 12233177.89 11173306.47 16839016.65 14008925.79 4885200.59 6029049.036 14145720.41 12946918.05 26321784.25 0.464754888 0.424488947 0.6397369 0.53221794 0.185595343 0.229051685 0.537414952 0.491870837 1 24.64975395 1.033815944 1.986720416 1.498303249 0.424605724 0.625899631 0.136953813 1.113987618 2.615227054 2.708139443 0.039927959 10.80975732 -1.033815944 -1.073697525 DKDAVDKLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKDAVDKLLK 10 2 P25815 P25815 S100P Protein S100-P 0 ; 100.93 0.0020682 1998810000 2991400 2186100 1636690 1347350 1882450 1257820 3317400 3694800 700580 FALSE TRUE 2596078.911 2171739.365 2428198.758 1653286.41 1844992.928 1306209.149 2995679.059 2904695.773 617758.2305 4.202418977 3.515516683 3.93066193 2.676267719 2.986593843 2.114434231 4.849274216 4.701994453 1 19.2366828 4.689642404 1.40037998 3.326906117 4.445476453 0.06641549 1.152227152 4.415312973 8.395030817 0.342103985 6.79566845 48937.5704 -4.689642404 1.118570336 DKDAYSSFGSR ddPTM_MDA-MB-175_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 ;;; 195.77 5.72E-08 6112400000 5737200 4763130 2987080 3652920 4636890 4136700 5414800 5922000 4832000 FALSE TRUE 4979014.484 4731840.685 4431641.879 4482371.317 4544624.961 4295841.526 4889673.529 4655626.385 4260766.465 1.168572492 1.110560911 1.040104384 1.052010561 1.066621463 1.008232101 1.147604209 1.092673448 1 22.02268155 4.541289387 3.194121448 1.064471568 1.167270622 0.420076584 0.042086642 0.28834976 5.258102915 0.01088578 0.056411731 34776.78155 -4.541289387 0.102799054 DKDDDEVFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 115.92 0.0010569 1178310000 3088760 2090300 3016340 2712320 1922360 1579120 3135610 3515950 6170890 FALSE TRUE 2680572.54 2076568.682 4475052.113 3328193.711 1884108.797 1639869.768 2831519.025 2764091.454 5441374.414 0.492627843 0.381625767 0.822412092 0.611645782 0.346256047 0.301370507 0.52036835 0.507976706 1 22.37553967 1.237513962 6.545369278 1.014041307 0.497727884 0.536052309 0.146790193 0.103539195 21.04141 0.237260564 0.038159941 17.27881528 -1.237513962 -0.516313423 DKDDDEVFEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 84.297 0.0090365 283000000 584750 411970 467530 420060 377280 249430 660700 758120 553760 FALSE TRUE 507473.8059 409263.7419 693629.0718 515441.0432 369772.8661 259025.7335 596625.4157 596001.9377 488295.1236 1.039276825 0.838148329 1.420511978 1.055593264 0.757273313 0.53046963 1.221854135 1.220577288 1 18.89739385 0.926009248 21.03815176 0.218546948 1.021686279 0 0.254959702 2084.635321 2183256.456 369582.2267 0.063908348 8.433527159 -0.926009248 0.803139331 DKDDDGGEDDDANCNLICGDEYGPETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DKDDDGGEDDDANCNLICGDEYGPETR 27 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;; 313.19 4.09E-82 3970060000 2196990 1760316 1597057 1371330 1487171 1090406 2031545 2361840 2236983 FALSE TRUE 1906652.205 1748752.368 2369399.107 1682711.436 1457579.207 1132354.624 1834526.079 1856778.896 1972529.418 0.966602671 0.886553251 1.201198363 0.853072923 0.738939148 0.574062224 0.930037373 0.941318735 1 20.91161539 3.519714515 24.81804763 0.839431733 1.008657363 0.262775465 0.14088699 686.9159512 400247.2051 0.04158116 0.061668565 3309.135225 -3.519714515 0.16922563 DKDDQEWESPS(ph)PPKPTVFISGVIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKDDQEWESPSPPKPTVFISGVIAR 25 2 P51397 P51397 DAP Death-associated protein 1 1 DKDDQEWES(0.043)PS(0.95)PPKPT(0.006)VFISGVIAR;DKDDQEWES(0.002)PS(0.998)PPKPTVFISGVIAR 155.17 3.33E-08 817340000 993690 677940 751710 622680 628760 488230 1081840 1066890 1050430 TRUE FALSE 862371.3488 673486.5675 1115239.47 764069.0111 616248.9061 507012.524 976923.3233 838743.876 926249.3621 0.931035836 0.727111505 1.204038044 0.824906383 0.665316416 0.547382319 1.054708768 0.905527076 1 19.82104112 DKDFAIDIIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DKDFAIDIIK 10 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;; 117.23 0.00089818 5998930000 36249390 28309660 21951310 25391650 26073260 20679730 37106660 44010500 34778760 FALSE TRUE 31458941.27 28123691.98 32567036.94 31157212.22 25554453.14 21475292.59 33508061.82 34599197.07 30667254.61 1.025815374 0.91705933 1.061948236 1.015976572 0.833281409 0.700267855 1.092633242 1.128213057 1 24.87019568 DKDGKPLLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKDGKPLLPK 10 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 ; 69.721 0.03157 1644950000 1474420 1265800 1281150 1437670 1218960 812520 1615400 2011970 2576800 FALSE TRUE 1279571.661 1257484.876 1900718.425 1764114.947 1194705.081 843778.1702 1458738.757 1581725.873 2272173.64 0.563148713 0.55342816 0.836519882 0.776399707 0.525798319 0.371352856 0.642001444 0.69612896 1 21.11564166 1.205834984 2.285971834 1.130342812 0.611626809 0.472984457 0.128943454 0.690400564 3.473947585 0.757494362 0.037394328 16.0633079 -1.205834984 -0.518716003 DKDLEIDELQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKDLEIDELQKR 12 2 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 50.843 0.089965 156220000 382930 268400 192650 203710 207780 223330 308140 368550 296830 FALSE TRUE 332324.8303 266636.8627 285816.1844 249965.469 203645.5845 231921.6496 278256.6302 289738.4506 261739.0955 1.269679753 1.018712402 1.09198889 0.9550177 0.778048018 0.88607951 1.063106868 1.106974294 1 17.99776991 5.39185944 1.224672259 0.982796162 2.131394114 0.46394732 0.097018883 7.01383514 2.865774174 0.032426901 15.07910409 246524.1328 -5.39185944 1.148597952 DKDNFWMTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DKDNFWMTR 9 1 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ;;; 145.91 8.76E-05 7786990000 7439370 6265140 4051780 5490110 6233470 5187580 6546520 7713910 6832070 FALSE TRUE 6456238.406 6223983.883 6011234.36 6736723.387 6109436.143 5387149.559 5911639.498 6064350.376 6024390.468 1.071683258 1.03313089 0.997816193 1.118241492 1.014116893 0.894223173 0.981284253 1.006633021 1 22.52238385 2.99910286 24.99980896 0.974626128 1.051620065 0.466701315 0.042498226 32.4562322 904464.8775 0.013126722 0.014703458 997.9363912 -2.99910286 0.076993938 DKDPILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKDPILR 7 1 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ; 91.065 0.01521 1050660000 2090340 1928410 1935040 1767620 1915220 1877060 2370600 2527600 2742000 FALSE TRUE 1814096.273 1915742.148 2870831.816 2168985.137 1877110.869 1949271.713 2140699.577 1987092.41 2417843.884 0.75029504 0.792334923 1.187352019 0.897074105 0.77635735 0.806202471 0.885375434 0.821844795 1 21.20528966 3.466736643 24.91552584 0.851438593 0.922225581 0.031043371 0.128454582 644.4095351 1546108.028 0.037580021 0.048567038 2929.116487 -3.466736643 0.070786988 DKDTDKFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKDTDKFK 8 2 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 89.047 0.0079769 2425900000 1223200 782220 730880 766150 495850 403030 1148600 1272500 798110 FALSE TRUE 1061551.021 777081.5453 1084336.013 940116.0674 485983.5551 418534.8249 1037208.949 1000385.778 703758.345 1.508402747 1.104188037 1.540778906 1.335850685 0.69055459 0.594713836 1.473814067 1.421490466 1 19.4247206 4.745825515 23.12968796 1.169078659 1.508403189 0.109748451 0.318717572 849.8737685 2705590.074 0.083941334 0.798864595 55696.19348 -4.745825515 0.33932453 DKEDPQEMPHS(ph)PLGSMPEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKEDPQEMPHSPLGSMPEIR 20 1 Q9HB58;Q9HB58-6;G5E9C0;Q9HB58-2;Q9HB58-5;Q9HB58-3;Q9HB58-7 Q9HB58 SP110 Sp110 nuclear body protein 1 DKEDPQEMPHS(0.995)PLGS(0.005)MPEIR;DKEDPQEMPHS(1)PLGSMPEIR 145.52 8.70E-08 513850000 648990 433820 352380 366540 389360 345060 468380 543000 536400 TRUE FALSE 563224.3272 430970.2079 522792.1466 449768.5092 381612.4978 358334.6815 422956.5797 426883.6756 472987.4031 1.190780819 0.911166355 1.105298245 0.950910122 0.806813237 0.757598784 0.894223772 0.902526522 1 18.85144224 3.50385351 5.069282975 0.871947545 1.051286234 0.480861102 0.09267072 0.175304946 12.1969398 0.025993673 0.037244201 3190.46151 -3.50385351 0.179338689 DKEDQWIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKEDQWIR 8 1 Q9BV57;Q9BV57-2;A0A0G2JQN5 Q9BV57 ADI1 "1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase" 0 83.998 0.016201 251930000 411250 294640 246420 259080 253910 234770 263550 376940 570750 FALSE TRUE 356902.2705 292704.4904 365589.5362 317908.0738 248857.6878 243801.7538 237990.9616 296334.3144 503276.5852 0.709157312 0.581597672 0.726418727 0.631676663 0.494474997 0.484428962 0.47288304 0.588810056 1 18.94099195 1.239560951 8.14008512 1.004691894 0.580271293 0.688693382 0.087373617 0.055165687 34.86666834 0.130914233 0.023109155 17.36044893 -1.239560951 -0.424420601 DKEEIVICDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DKEEIVICDR 10 1 Q9NRR5;Q9NRR5-2 Q9NRR5 UBQLN4 Ubiquilin-4 0 ;;; 127.17 0.00033113 1479850000 2092280 1689340 1273810 1401090 1587520 1402540 1813110 2260570 2201720 FALSE TRUE 1815779.897 1678242.614 1889828.777 1719228.899 1555931.458 1456496.621 1637274.871 1777164.697 1941435.17 0.935277121 0.864434023 0.973418431 0.885545356 0.801433642 0.75021646 0.84333224 0.915387093 1 20.8886921 4.74711045 22.33478334 0.877043179 0.935277252 0.053187847 0.073821369 906.3571046 2367424.865 0.019307976 0.201353445 55861.22437 -4.74711045 0.058234073 DKEGYTSFWNDCISSGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKEGYTSFWNDCISSGLR 18 1 Q9H4A5 Q9H4A5 GOLPH3L Golgi phosphoprotein 3-like 0 134.32 9.85E-06 479130000 206750 205150 173970 183700 232410 184580 257500 296960 261540 FALSE TRUE 179427.4637 203802.3561 258102.4739 225411.8927 227785.4957 191680.912 232527.6896 233457.4149 230621.0391 0.778018625 0.88371103 1.119162739 0.977412527 0.98770475 0.831151021 1.008267461 1.01229886 1 17.81516461 4.472297085 24.99024348 0.988342763 0.804441683 0.505165116 0.069720031 89.62767272 464293.5428 0.017561379 0.046835643 29668.60218 -4.472297085 -0.18390108 DKEIS(ph)PSVTKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKEISPSVTKK 11 2 Q8N488 Q8N488 RYBP RING1 and YY1-binding protein 1 DKEIS(0.947)PS(0.042)VT(0.011)KK;DKEIS(0.955)PS(0.02)VT(0.026)KK 70.281 0.027235 271770000 384430 286160 248730 260820 257600 163865 432760 502490 226000 TRUE FALSE 333626.6015 284280.1961 369016.66 320043.1674 252474.264 170168.9926 390791.0018 395036.4239 199282.5375 1.674138666 1.426518348 1.85172602 1.605976979 1.266916144 0.853908199 1.960989692 1.982293225 1 17.60445577 3.458199622 24.60187605 1.491651847 1.645114315 0.063339496 0.372866765 899.0462627 1168933.404 0.117385855 0.151570181 2872.100432 -3.458199622 0.153462469 DKELTGALIASLINCYIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKELTGALIASLINCYIR 18 1 O75694;O75694-2 O75694 NUP155 Nuclear pore complex protein Nup155 0 68.567 0.025791 102540000 179330 144860 87083 130940 140150 119890 196950 202340 160100 FALSE TRUE 155631.0861 143908.4051 129196.6301 160671.9283 137361.2892 124502.2459 177849.8193 159071.1656 141173.1604 1.102412709 1.019375105 0.915164254 1.138119511 0.972998613 0.881911587 1.259799092 1.12678051 1 17.10710631 2.239013426 24.99999778 1.133882448 1.006163777 0.263566255 0.097468045 15.78939014 871835.4776 0.037488579 0.027227457 173.3857599 -2.239013426 -0.127718671 DKENALMPNWLHLPVGYHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKENALMPNWLHLPVGYHGR 20 1 P16930;P16930-2 P16930 FAH Fumarylacetoacetase 0 192.18 7.70E-18 273120000 561790 525380 413580 492970 555700 455100 647240 761670 617630 FALSE TRUE 487548.0281 521928.7442 613588.6713 604906.3731 544642.6572 472607.9915 584470.7644 598792.7978 544614.485 0.895216785 0.958345322 1.126647726 1.110705627 1.000051729 0.867784469 1.073182555 1.099480117 1 19.05487583 4.450036133 8.833702339 1.041961833 0.910699763 0.299987533 0.07474234 0.268157166 80.33149376 0.019953943 0.053960759 28186.1743 -4.450036133 -0.13126207 DKEPEVVFIGDS(ph)LVQLMHQCEIWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKEPEVVFIGDSLVQLMHQCEIWR 24 1 M0R1K3;Q15102;M0R389;M0QZT2;M0QXS6;M0R323 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 1 DKEPEVVFIGDS(1)LVQLMHQCEIWR 78.913 0.011771 19725000 29369 33993 25104 25042 26597 24806 34535 37119 43365 TRUE FALSE 25487.81224 33769.69774 37244.37837 30728.16884 26067.77174 25760.30287 31185.80102 29181.39071 38238.4391 0.666549494 0.883134839 0.974003627 0.803593702 0.681716418 0.673675586 0.815561559 0.763142832 1 15.22273601 1.234736528 24.96027058 1.000000312 0.786509834 0.33189389 0.096767712 146.1927324 954073.5807 0.182272072 0.024946393 17.16866504 -1.234736528 -0.213490478 DKEPEVVFIGDSLVQLMHQCEIWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKEPEVVFIGDSLVQLMHQCEIWR 24 1 M0R1K3;Q15102;M0R389;M0QZT2;M0QXS6;M0R323 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ; 248.07 2.89E-38 3331500000 942130 708740 608560 660950 624990 547890 922180 1056140 906670 FALSE TRUE 817625.1334 704084.2403 902861.6515 811028.7995 612553.9218 568967.6828 832747.1255 830292.6799 799484.5055 1.022690406 0.880672778 1.129304752 1.014439672 0.766186108 0.71166818 1.041605084 1.038535049 1 19.60871055 DKEVANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKEVANR 7 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 0 ; 68.735 0.056221 180147000 403040 373820 243690 286810 221540 356130 433680 464580 487870 FALSE TRUE 349777.2428 371364.3518 361539.2991 351934.5941 217131.7874 369830.5515 391621.7804 365233.1824 430194.5644 0.813067555 0.863247429 0.840408803 0.818082382 0.504729268 0.859682065 0.910336422 0.848995344 1 18.71462977 1.424170935 1.083487424 1.038081818 0.784415951 0.270221768 0.108066914 1.910277695 2.381022849 0.537472886 0.038097512 26.55650599 -1.424170935 -0.253665867 DKEVS(ph)DDEAEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DKEVSDDEAEEK 12 1 P07900;P07900-2;G3V2J8 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 DKEVS(1)DDEAEEK;DKEVS(1)DDEAEEK;DKEVS(1)DDEAEEK;DKEVS(1)DDEAEEK 202.33 4.67E-07 2766540000 5179530 2836680 3817670 3721010 2743750 2245650 4397620 5128450 10141290 TRUE FALSE 4495041.987 2818045.662 5663907.981 4565922.193 2689154.743 2332041.609 3971139.489 4031770.877 8942398.249 0.502666272 0.315133098 0.633376844 0.51059258 0.300719636 0.260784808 0.444079919 0.450860134 1 23.09223037 1.233717161 4.839055298 1.042991476 0.422450053 0.723311605 0.11142122 0.104376148 5.82305505 0.221274592 0.028826628 17.12841439 -1.233717161 -0.620541424 DKEVS(ph)DDEAEEKEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKEVSDDEAEEKEDK 15 2 P07900;P07900-2;G3V2J8 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 DKEVS(1)DDEAEEKEDK 62.362 0.064355 96624000 144620 79917 124950 97081 77886 68450 129700 147920 252750 TRUE FALSE 125508.1006 79392.01996 185376.2379 119124.7248 76336.22098 71083.31579 117121.714 116288.4591 222870.1829 0.563144423 0.3562254 0.831767783 0.534502746 0.342514283 0.318944934 0.525515403 0.521776658 1 17.76584409 1.230767393 4.519060419 1.046165579 0.49482065 0.534811404 0.14689436 0.176142625 7.551772239 0.315657249 0.037750577 17.01247079 -1.230767393 -0.551344929 DKEVS(ph)DDEAEEKEDKEEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKEVSDDEAEEKEDKEEEK 19 3 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 DKEVS(1)DDEAEEKEDKEEEK 150.18 5.58E-08 894230000 2078100 753380 1893000 901930 564510 574490 1378700 1480300 2844800 TRUE FALSE 1803473.82 748430.9972 2808461.132 1106726.992 553277.3554 596591.002 1244993.886 1163749.365 2508490.985 0.718947698 0.298359054 1.119581911 0.441192334 0.220561827 0.237828641 0.496311884 0.463924077 1 21.25838832 -0.921629263 20.72921385 5.795008134 0.533664557 0 0.307467919 0 0 0 0.067571992 0.119776257 0.921629263 -5.261343576 DKFEEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DKFEEDR 7 1 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;; 126.41 0.0065522 598360000 2748290 2037440 1651200 1690670 1960200 1848590 2502040 2864610 2844540 FALSE TRUE 2385096.513 2024055.922 2449725.843 2074562.464 1921195.855 1919706.453 2259392.546 2252035.444 2508261.722 0.950896189 0.806955632 0.976662771 0.827091705 0.765947125 0.765353327 0.90078022 0.897847073 1 21.25825646 1.273631501 1.655013417 1.046943576 0.850131207 0.294261777 0.070685127 1.255086229 3.371326042 0.396371526 0.020371424 18.77722893 -1.273631501 -0.196812369 DKFNECGHVLYADIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKFNECGHVLYADIK 15 1 A0A087X0X3;P52272-2;P52272 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 165.02 8.70E-07 3544000000 5917300 4185200 3194390 3492120 3657630 2781090 5191000 6461300 5176300 FALSE TRUE 5135313.812 4157707.146 4739207.689 4285059.22 3584850.319 2888080.332 4687577.619 5079601.277 4564363.711 1.125088652 0.910906187 1.03830632 0.938807573 0.785399794 0.632745442 1.026994761 1.112882671 1 22.12198233 2.020292342 24.99912562 1.066134846 0.901121749 0.198694048 0.134359934 345.6081258 425769.8809 0.057749125 0.038930039 104.7833653 -2.020292342 -0.165013097 DKFPEVIINFPDPAQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKFPEVIINFPDPAQK 16 1 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7BZC3 Q00341 HDLBP Vigilin 0 116.3 0.00040016 441470000 624560 457000 379410 416510 408870 305420 612430 754270 600070 FALSE TRUE 542022.8136 453997.9369 562893.9451 511084.9615 400734.2869 317169.705 553036.6329 592975.2302 529130.4082 1.02436527 0.858007648 1.063809481 0.965896032 0.757345034 0.599416893 1.045180213 1.1206599 1 19.0132638 2.030958664 24.99998388 1.073140413 0.879007311 0.276366686 0.134928601 244.8396347 197713.8523 0.058276832 0.039289811 107.3887195 -2.030958664 -0.194133103 DKFQETSDEFEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKFQETSDEFEAAR 14 1 G8JLG1;Q14683;V9GY57 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 ; 178.14 1.84E-06 783470000 679080 553510 364760 441660 523370 495650 624340 783960 636310 FALSE TRUE 589337.8574 549873.9564 541159.156 541945.6534 512955.961 514717.9762 563791.6029 616316.2548 561086.1567 1.050351805 0.980016972 0.964484954 0.965886695 0.914219599 0.917359964 1.004821802 1.098434255 1 19.09786279 1.996364486 22.82140289 1.054862138 0.963489564 0.383605706 0.043828953 41.54906659 260818.2388 0.018636515 0.01221812 99.16638597 -1.996364486 -0.091372574 DKFSFDLGK ddPTM_MDA-MB-175_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 ; 150.04 7.86E-05 12014500000 24189000 17453800 18403700 24182000 17912800 13512800 25492000 30003000 42210000 FALSE TRUE 20992362.36 17339144.84 27303790.88 29672892.7 17556370.33 14032646.16 23019789.76 23587091.93 37219981.89 0.564007861 0.465855811 0.733578833 0.797230176 0.471692071 0.377019156 0.618479338 0.633721209 1 25.14957402 1.166496727 2.495285123 1.164929879 0.57525734 0.531399636 0.124163383 0.614881546 3.52823559 0.851209351 0.034867388 14.67225028 -1.166496727 -0.589672539 DKFSFDLGKGEVIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKFSFDLGKGEVIK 14 2 Q02790;F5H1U3 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ; 138.91 7.14E-06 1397430000 3488400 2594400 1729940 1758230 2475000 1729480 4500300 5156800 468270 FALSE TRUE 3027399.102 2577357.216 2566544.77 2157462.994 2425752.342 1796014.215 4063861.599 4054058.45 412911.6541 7.33183254 6.241909596 6.215723739 5.224999036 5.874749038 4.349633141 9.841963913 9.818222398 1 18.65547361 4.749006348 21.03784661 6.458600371 7.331836662 0.003563304 2.559228814 1270.785198 2558863.12 0.641369761 7.477869612 56105.61765 -4.749006348 0.873236291 DKGATKES(ph)SEKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKGATKESSEKDR 13 3 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BUL0;H3BTY0;H3BUG0;H3BNU7;H3BNI3;H3BTR6;H3BP82 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 1 DKGAT(0.007)KES(0.818)S(0.176)EKDR 82.59 0.065962 134410000 359760 209520 234870 174520 149280 130120 338240 384880 290990 TRUE FALSE 312216.8045 208143.6493 348453.9176 214147.4334 146309.6201 135125.8006 305437.5369 302576.4071 256589.4937 1.216794967 0.811193188 1.358020987 0.834591589 0.570208928 0.5266225 1.190374292 1.179223681 1 17.96910257 DKGETIQGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DKGETIQGLR 10 1 F5H0D0;Q14232-2;Q14232;H0YGG4 F5H0D0;H0YGG4 EIF2B1 Translation initiation factor eIF-2B subunit alpha 0 ;; 80.245 0.022423 1130220000 1219820 987080 587837 771700 856720 803510 1089750 1278470 1106010 FALSE TRUE 1058617.696 980595.8065 872116.9394 946926.2797 839672.9481 834421.5496 984066.2127 1005079.14 975258.7578 1.085473663 1.005472444 0.894241587 0.970948758 0.860974527 0.855589907 1.00903089 1.030576892 1 19.89542552 2.034625886 24.93811983 1.018172048 0.942264995 0.177728319 0.068506062 279.6409938 201400.8465 0.029506748 0.019893384 108.299359 -2.034625886 -0.075907053 DKGEYTLVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKGEYTLVVK 10 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 111.91 0.0015423 465070000 1160400 754360 521990 663620 712040 569610 941070 1048800 1027500 FALSE TRUE 1007050.2 749404.5595 774426.11 814305.0638 697871.7971 591523.2653 849805.1762 824522.2818 906030.1205 1.111497485 0.827129852 0.854746539 0.898761581 0.770252314 0.652873731 0.937943626 0.910038489 1 19.78919949 4.742684096 24.53945966 0.856683879 1.111497615 0.414551119 0.095245936 352.3290661 2096660.679 0.024440723 0.181822571 55294.77511 -4.742684096 0.254813736 DKGFGFIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKGFGFIR 8 1 Q15233;Q15233-2;H7C367;C9JYS8;C9IZL7 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ; 118.18 0.0017663 3856900000 8612400 7852400 4694300 6134300 7753000 6415000 8258600 9388900 7012800 FALSE TRUE 7474249.519 7800817.067 6964479.181 7527186.572 7598730.468 6661789.201 7457682.243 7381156.8 6183754.773 1.208691126 1.261501685 1.126254102 1.217251791 1.228821444 1.077304881 1.206011965 1.193636726 1 22.56005168 1.237830785 24.97674065 0.999999779 1.18965714 0.564428079 0.05243571 13.21009735 451762.7243 0.072103798 0.012360179 17.29142501 -1.237830785 0.189657361 DKGLQTSQDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DKGLQTSQDAR 11 1 P27797 P27797 CALR Calreticulin 0 ;;;;; 146.79 3.25E-05 3188240000 8468400 7638330 5465030 6827720 7937740 8971900 8039800 8337500 6147440 FALSE TRUE 7349279.484 7588153.307 8107936.787 8378058.181 7779794.504 9317054.799 7260101.433 6554590.507 5420696.646 1.355781362 1.399848359 1.495737046 1.545568536 1.43520197 1.71879288 1.339329962 1.209178623 1 22.37004684 1.620740827 2.026116819 1.008741455 1.48730677 0.70829762 0.104068416 0.184848147 1.484388234 0.13879477 0.029475478 41.75810935 -1.620740827 0.478565315 DKHIEEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKHIEEVR 8 1 P16949 P16949 STMN1 Stathmin 0 ; 93.058 0.0068125 635790000 2534400 1910590 1422050 1777050 1908840 1679860 1928580 2195040 2827060 FALSE TRUE 2199472.619 1898039.208 2109758.136 2180556.363 1870857.819 1744485.301 1741546.608 1725647.778 2492848.187 0.882313103 0.761393822 0.846324356 0.874724893 0.750490073 0.699796045 0.698617195 0.692239418 1 21.2493636 3.220854938 24.26327135 0.75008739 0.835856182 0.111426595 0.094460171 313.385189 429450.9107 0.028247403 0.032106316 1662.857135 -3.220854938 0.085768792 DKHIEEVRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DKHIEEVRK 9 2 P16949 P16949 STMN1 Stathmin 0 ;; 94.616 0.0051658 1187290000 4518650 2641600 1775440 2103860 2474590 1898960 3293280 3783760 1667120 FALSE TRUE 3921498.954 2624247.156 2634048.722 2581573.568 2425350.5 1972014.22 2973898.212 2974632.369 1470034.973 2.667622898 1.785159676 1.79182725 1.756130715 1.649859048 1.341474357 2.023011879 2.023511293 1 20.48741905 4.764183461 3.208899175 1.701922302 2.839203615 0.510807686 0.306167077 0.344773156 5.318862732 0.076032957 1.010348256 58100.98039 -4.764183461 1.137281313 DKHKEEDKNSER ddPTM_MDA-MB-175_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 0 186.13 7.29E-06 110130000 374150 196450 202500 164290 134850 115270 314010 381340 127200 FALSE TRUE 324705.1295 195159.507 300429.6773 201594.5555 132166.7488 119704.5115 283557.3585 299793.4086 112162.5609 2.894951104 1.739970142 2.678520131 1.797342659 1.178349957 1.067241248 2.528092763 2.672847394 1 16.77523167 3.716234045 23.13766656 1.810477824 2.368029384 0.213794195 0.635626997 642.095982 665421.9583 0.189753964 0.281800893 5202.763026 -3.716234045 0.55755156 DKHLEFSSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKHLEFSSLR 10 1 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 0 89.403 0.0069314 39609000 30985 35271 15800 30298 30890 37557 31697 37185 32730 FALSE TRUE 26890.25374 35039.30248 23440.93285 37177.62398 30275.34944 39001.84209 28623.02982 29233.27712 28860.69669 0.931725732 1.214083737 0.812209529 1.288174862 1.049016584 1.351382557 0.991765034 1.012909613 1 14.81681851 4.79135664 21.12441443 1.083729059 0.931719838 0.088554876 0.158408745 17232.95387 6893700.181 0.036437748 24.68635841 61852.41199 -4.79135664 -0.152009221 DKIIVNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DKIIVNDR 8 1 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;;;;; 132.78 0.00086424 3897280000 6594550 5835420 3359130 4296450 5576160 4961740 6291840 7355810 4567490 FALSE TRUE 5723063.509 5797086.742 4983616.504 5272024.64 5465205.326 5152621.348 5681658.325 5782827.274 4027526.536 1.420987164 1.439366492 1.237388869 1.308998114 1.356963207 1.27935131 1.410706615 1.43582599 1 21.94146266 1.231285215 24.99752375 0.999999366 1.361269697 0.731918643 0.068698956 146.6759651 503919.1146 0.179179742 0.017853013 17.03276737 -1.231285215 0.361270331 DKKS(ph)PLIESTANMDNNQSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKKSPLIESTANMDNNQSQK 20 2 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 DKKS(0.999)PLIESTANMDNNQSQK;DKKS(0.995)PLIES(0.003)T(0.003)ANMDNNQSQK 138.44 1.59E-06 455960000 739820 387860 328050 342340 410460 263753 600900 621720 360810 TRUE FALSE 642050.9125 385312.1221 486696.0773 420073.5293 402292.6491 273899.7486 542624.8105 488770.0162 318155.4528 2.018041517 1.211081308 1.529743001 1.320340499 1.264453101 0.860899118 1.705533586 1.536261635 1 18.27937232 4.745026823 24.18778276 1.333103962 2.018042011 0.438405276 0.25217826 485.6940383 1816730.645 0.061982002 0.563254442 55593.85919 -4.745026823 0.684938049 DKLCGPYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKLCGPYEK 9 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 89.805 0.010815 464830000 712640 651410 498860 462700 604190 571230 820990 900250 675320 FALSE TRUE 618462.8184 647130.8448 740110.3646 567763.1069 592167.8011 593205.5877 741370.5162 707738.5433 595484.4389 1.038587708 1.086730068 1.242871041 0.953447428 0.994430353 0.996173114 1.24498722 1.188508879 1 19.18370428 2.248324976 24.99823026 1.157854518 1.055190826 0.158718703 0.098584862 338.3450718 866215.6798 0.038301755 0.029291989 177.1434 -2.248324976 -0.102663693 DKLEEILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKLEEILR 8 1 O15042-2;O15042;E7ET15;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 ; 121.73 0.0012956 557100000 842840 751990 494790 599270 767520 644820 920920 1140860 945340 FALSE TRUE 731456.5585 747050.1282 734072.099 735343.4128 752247.8536 669626.6427 831609.3201 896895.9672 833582.9821 0.877484995 0.896191674 0.880622703 0.882147823 0.902427077 0.803311316 0.997632315 1.075952828 1 19.6689663 2.077118253 5.978858125 1.041608303 0.877237903 0.829842171 0.032506229 0.066821103 3.968746453 0.01273217 0.008463163 119.4313258 -2.077118253 -0.164370399 DKLESEMEDAYHEHQANLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DKLESEMEDAYHEHQANLLR 20 1 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;; 316.6 1.17E-66 7751400000 5065510 3513290 2470560 3129790 3483720 2771740 4105010 4950550 4262530 FALSE TRUE 4396090.019 3490210.967 3665331.08 3840456.655 3414400.788 2878370.631 3706906.762 3891913.408 3758618.559 1.169602595 0.928588765 0.975180381 1.021773451 0.908419073 0.765805464 0.986241808 1.035463787 1 21.84177108 4.74321391 24.45137227 0.956363083 1.169602714 0.440120157 0.076788814 385.8015834 2027149.684 0.020331847 0.158100267 55362.27266 -4.74321391 0.21323963 DKLFDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKLFDQR 7 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 78.496 0.032082 2682600000 16358400 13560100 9157600 11457000 13851200 12330100 16737900 18370100 14900800 FALSE TRUE 14196595.99 13471022.81 13586245.99 14058486.96 13575588.22 12804446.93 15114661.03 14441797.07 13139244.4 1.080472785 1.025250951 1.034020342 1.0699616 1.033209202 0.974519275 1.150344767 1.099134519 1 23.64737898 2.237591636 24.9999834 1.089287197 1.03703385 0.185364064 0.045751758 38.90190813 1003625.075 0.017786454 0.01278113 172.8190589 -2.237591636 -0.052253347 DKLNNLVLFDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKLNNLVLFDK 11 1 P62851 P62851 RPS25 40S ribosomal protein S25 0 ; 166.38 1.87E-05 5830700000 14350100 11575500 8620100 9814700 11223800 8721300 15157400 16706600 14615000 FALSE TRUE 12453697.93 11499459.78 12788809.19 12043277.64 11000468.34 9056814.054 13687437.68 13134023.6 12887231.35 0.96635946 0.892314219 0.992362816 0.934512411 0.853594387 0.702774227 1.062092959 1.019150137 1 23.61943902 DKLPLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKLPLEK 7 1 Q92831 Q92831 KAT2B Histone acetyltransferase KAT2B 0 ; 109.21 0.0064555 1186330000 1987540 1659020 1664400 1459370 1328820 1084960 2750500 2128400 2585900 FALSE TRUE 1724881.553 1648121.788 2469309.407 1790742.264 1302379.082 1126699.113 2483756.933 1673258.223 2280197.848 0.756461355 0.722797712 1.082936469 0.785345125 0.571169332 0.4941234 1.089272554 0.733821508 1 21.12072758 -0.564529501 1.040495744 9.999997292 0.771222156 0.112051495 0.188974997 185.6001453 5.914156749 3827.600363 0.061766345 0.272565258 0.564529501 -9.228775136 DKLSELQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DKLSELQLR 9 1 Q9BVK6 Q9BVK6 TMED9 Transmembrane emp24 domain-containing protein 9 0 ;;; 162.36 5.82E-05 3941280000 5917460 6476980 4585210 4922020 6729320 6478310 6162370 8146180 7604060 FALSE TRUE 5135452.668 6434432.292 6802632.893 6039639.869 6595419.698 6727534.778 5564744.306 6404182.801 6705116.689 0.765900566 0.959630173 1.014543551 0.900750897 0.983639809 1.00334343 0.82992505 0.955118769 1 22.67683101 4.739941145 24.50315894 0.952369292 0.765900488 0.53831438 0.055204532 73.5820111 1305834.51 0.013231253 0.080644506 54946.64065 -4.739941145 -0.186468804 DKLSGEYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DKLSGEYEK 9 1 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;; 145.28 8.90E-05 3868200000 4490890 3927090 2760100 3371610 3837130 3032820 5529900 6952860 5308700 FALSE TRUE 3897407.508 3901292.687 4094893.592 4137185.582 3760778.62 3149494.548 4993611.149 5466044.996 4681111.534 0.832581638 0.833411607 0.874769499 0.883804103 0.803394363 0.672809123 1.066757567 1.167681 1 22.15841971 2.129087651 7.24134942 1.101432937 0.823162004 0.753013867 0.070312428 0.100490081 6.060631342 0.029151999 0.019598916 134.6132008 -2.129087651 -0.278270933 DKLTELQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKLTELQLR 9 1 Q7Z7H5-3;Q7Z7H5;Q7Z7H5-2 Q7Z7H5-3 TMED4 Transmembrane emp24 domain-containing protein 4 0 ; 164.64 5.66E-05 1577460000 1800090 1637190 1802120 1366230 1635040 1508700 1490790 1979960 1939130 FALSE TRUE 1562203.546 1626435.191 2673631.26 1676453.403 1602505.903 1566740.665 1346213.415 1556560.962 1709888.26 0.913629026 0.951193846 1.563629227 0.980446174 0.937199196 0.916282486 0.787310754 0.910329054 1 20.70547062 3.491445609 24.88817744 0.906549098 1.148385449 0.259042594 0.179635993 830.7007949 1443318.45 0.050251495 0.071381841 3100.599047 -3.491445609 0.241836351 DKLYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKLYER 6 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 0 ; 76.899 0.067343 584610000 1081980 813730 491200 583360 797360 744680 881880 985330 744340 FALSE TRUE 938993.6016 808384.5541 728745.963 715820.8041 781494.096 773328.3215 796355.4133 774624.8473 656344.9732 1.430640349 1.231645837 1.110309354 1.090616723 1.190675831 1.178234546 1.213318371 1.180209919 1 19.32409477 4.668434325 2.752747911 1.147540824 1.461962845 0.686341118 0.06246469 0.219639696 2.477380016 0.016018544 0.144217682 46605.19452 -4.668434325 0.314422021 DKMCSMVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKMCSMVK 8 1 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;D6RB09;D6RAS7;D6RED7 P61247 RPS3A 40S ribosomal protein S3a 0 ; 111.06 0.0030158 1043060000 640440 774170 504600 456540 672000 517170 908240 925770 358500 FALSE TRUE 555804.2313 769084.4263 748626.2478 560204.3848 658628.5147 537065.8646 820159.0246 727801.2899 316118.5384 1.758214606 2.432898843 2.368182048 1.77213392 2.083485891 1.698938212 2.594466711 2.302304995 1 18.27010612 3.748656954 24.8042335 1.990994823 2.211078511 0.056602584 0.455080749 2349.738395 5772715.353 0.120679734 0.20586414 5606.049839 -3.748656954 0.220083688 DKMMNGGHYTYSENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKMMNGGHYTYSENR 15 1 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 163.8 9.12E-07 73279000 106200 105540 46563 59758 114340 104970 113760 134480 27539 FALSE TRUE 92165.40092 104846.7008 69081.02254 73326.96724 112064.8577 109008.2638 102727.5727 105722.4985 24283.37079 3.795412165 4.317633729 2.844787206 3.019637095 4.614880638 4.489008744 4.230367093 4.353699469 1 14.56768108 DKNEQAFEEVFQNANFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 261.15 2.57E-27 598380000 1234090 1040740 725150 984790 995940 754320 1087490 1366730 1265220 FALSE TRUE 1071001.88 1033903.31 1075834.965 1208401.621 976122.7425 783339.1785 982025.3872 1074465.425 1115647.133 0.95998264 0.92672968 0.964314732 1.083139628 0.874938602 0.702138835 0.880229383 0.963087157 1 20.08944936 DKNESLTMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKNESLTMR 9 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 180.36 4.44E-05 875690000 1505940 1312350 909330 1210180 1338330 1136820 1486580 1679280 1692470 FALSE TRUE 1306926.213 1303729.086 1349085.03 1484969.865 1311699.851 1180554.201 1342411.7 1320179.04 1492388.125 0.875728098 0.873585808 0.903977328 0.995029269 0.878926755 0.791050385 0.899505751 0.884608379 1 20.50919135 1.237399696 24.80837524 1.000000143 0.888311746 0.340219103 0.049098669 33.70567057 719920.5381 0.074675946 0.012479482 17.27426971 -1.237399696 -0.111688397 DKNNMQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 DKNNMQHR 8 1 P31942;P31942-3;P31942-2;P31942-4 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;;;;;;;;; 161.02 0.00021028 1383361000 3405751 2447931 1516697 1908395 1392446 2077585 2437970 2969688 3400401 FALSE TRUE 2955672.376 2431850.38 2250176.742 2341725.253 1364739.049 2157511.039 2201536.045 2334643.331 2998409.468 0.985746746 0.811046792 0.750456789 0.780989147 0.455154329 0.719551837 0.734234623 0.778627254 1 21.51576598 4.76657377 1.791071413 0.736625111 1.080275559 0.251187965 0.130230444 1.39508504 4.283829275 0.035667093 0.831149162 58421.64342 -4.76657377 0.343650448 DKNSIYSGLEAFGDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKNSIYSGLEAFGDVK 16 1 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 163.35 7.08E-09 271390000 658040 530920 475740 531500 453680 377150 626160 795960 663090 FALSE TRUE 571078.3467 527432.3516 705809.4553 652185.1985 444652.6556 391659.2045 565435.0996 625750.1482 584700.2556 0.976702749 0.902055962 1.207130403 1.115418015 0.760479667 0.669846132 0.967051227 1.070206729 1 19.1573377 5.124243463 17.18002444 0.965714477 2.47513574 0.000283781 0.158640238 57923308.01 40860788.08 0.042109856 3450938960 133120.0473 -5.124243463 1.509421264 DKNSVNFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKNSVNFK 8 1 P12956;B1AHC9 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 153.05 0.00040799 2268300000 5328100 3982700 2739600 3503800 3470900 2862600 4771800 5409600 4663000 FALSE TRUE 4623978.085 3956537.381 4064479.723 4299391.342 3401835.881 2972726.074 4309031.57 4252799.138 4111745.452 1.124577905 0.96225251 0.988504705 1.045636553 0.827345934 0.722983976 1.047981112 1.034305063 1 21.97131952 7.530622273 1.136279582 0.951815954 129.5192566 0.21225508 0.103521768 2414.107647 5.588122154 0.034322693 806971.3596 33933001.25 -7.530622273 128.5674407 DKNTVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKNTVVR 7 1 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 59.8 0.092434 272560000 607560 593760 406640 457920 493780 670890 607170 700900 758020 FALSE TRUE 527269.4066 589859.5515 603292.4641 561897.7349 483954.7441 696699.5724 548286.7469 551017.9894 668407.7391 0.788843958 0.882484623 0.902581506 0.84065115 0.724041204 1.042327208 0.820287849 0.824374042 1 19.35036891 2.760004029 24.99776456 0.897020927 0.835640278 0.208188608 0.084478159 1896.833097 2211240.185 0.027403382 0.027376058 575.4452764 -2.760004029 -0.06138065 DKPAQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DKPAQIR 7 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;; 116.73 0.0049167 2717570000 5251800 4685050 2825020 3666010 4062910 4035020 5401700 5836900 5363200 FALSE TRUE 4557761.324 4654273.598 4191209.121 4498433.602 3982066.04 4190249.83 4877843.965 4588724.358 4729168.606 0.963755303 0.984163177 0.886246499 0.951210239 0.84202243 0.886043654 1.031437949 0.97030255 1 22.17315515 2.240164661 24.99975908 0.995558072 0.918362101 0.43371289 0.043865847 43.35337366 675698.7038 0.017672899 0.012955292 173.8459833 -2.240164661 -0.07719597 DKPEEQWWNAEDSEGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKPEEQWWNAEDSEGKR 17 2 P46108-2;P46108 P46108-2 CRK Adapter molecule crk 0 ; 241.74 1.26E-20 1068260000 756680 511010 554340 554280 491650 321764 696730 789860 773670 FALSE TRUE 656682.8208 507653.1417 822420.6782 680137.7456 481867.1269 334142.4693 629161.2318 620954.5857 682207.614 0.962585007 0.744132917 1.205528436 0.996965926 0.706335017 0.489795866 0.922243052 0.910213508 1 19.37985133 5.085703302 18.70045689 0.87323188 4.542587574 0.02118275 0.193538767 1249.285937 277526.166 0.047907891 3484.159124 121815.7102 -5.085703302 3.669355694 DKPHNIFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKPHNIFK 8 1 P25685;P25685-2;M0R080 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 107.69 0.0023757 2873800000 4270500 3911900 3149300 3601900 3588900 2887200 4674000 5530000 5503200 FALSE TRUE 3706142.605 3886202.471 4672312.014 4419766.447 3517487.912 2998272.452 4220716.199 4347452.535 4852617.965 0.763740857 0.800846574 0.962843572 0.910800413 0.724863968 0.617866989 0.869781266 0.895898372 1 22.21033185 1.539630051 2.182516392 0.996746736 0.805450507 0.307710044 0.09593256 0.495495312 4.383603447 0.160099848 0.028985862 34.64416122 -1.539630051 -0.191296229 DKPLELWDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKPLELWDVR 10 1 Q9BZH6 Q9BZH6 WDR11 WD repeat-containing protein 11 0 94.767 0.007186 339380000 373500 358260 246350 298370 346140 287460 422800 469200 461860 FALSE TRUE 324141.0287 355906.5665 365485.684 366119.4688 339252.4912 298518.7722 381796.9211 368865.2313 407259.437 0.795907962 0.873906248 0.89742717 0.898983389 0.833013211 0.732994119 0.93747839 0.905725437 1 18.6355886 1.529613488 1.60453614 1.004205755 0.848395264 0.430006779 0.056124091 0.587755972 2.309284722 0.129920948 0.016859042 33.8542727 -1.529613488 -0.155810491 DKPLKDVIIADCGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKPLKDVIIADCGK 14 2 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 121.48 6.43E-05 1434900000 3190700 2112100 1912300 2142500 1637700 1611900 2437700 3012200 2236700 FALSE TRUE 2769040.911 2098225.476 2837094.676 2628987.371 1605112.974 1673910.836 2201292.229 2368064.471 1972279.874 1.403979702 1.063857875 1.438484828 1.332968716 0.81383631 0.848718713 1.116115546 1.200673648 1 20.91143286 3.264828373 24.99946085 1.023130396 1.301444153 0.516054529 0.149688991 221.3041431 210617.333 0.046531233 0.060052195 1840.044697 -3.264828373 0.278313758 DKPSGDTAAVFEEGGDVDDLLDMI ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 DKPSGDTAAVFEEGGDVDDLLDMI 24 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;;; 196.32 2.09E-24 168302000 627551 493583 372953 429654 474404 408127 563643 690789 608465 FALSE TRUE 544618.5453 490340.6208 553314.3183 527213.5076 464964.2886 423827.9098 508980.9886 543069.1481 536532.9609 1.015070061 0.913905867 1.031277403 0.982630232 0.866608992 0.789938253 0.948648127 1.012182266 1 19.03330728 4.757468938 22.63143597 0.945608008 1.015070289 0.087259096 0.072716113 3415.977331 4088345.361 0.019463182 0.562032771 57209.60357 -4.757468938 0.069462281 DKPSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DKPSLR 6 1 P13489 P13489 RNH1 Ribonuclease inhibitor 0 ;;;;; 114.78 0.022791 5014720000 10117460 8958040 5625250 6905780 7343390 8060100 10245280 11538310 9674610 FALSE TRUE 8780412.027 8899194.045 8345639.715 8473842.897 7197270.906 8370177.263 9251694.323 9070932.198 8530888.627 1.029249403 1.04317316 0.978284922 0.993313038 0.843671887 0.98116124 1.084493624 1.063304492 1 23.0242646 0.904154331 21.21226719 0.445825757 1.00513414 0 0.066009771 16179.72086 2695093.426 767560.1477 0.017283968 8.019629981 -0.904154331 0.559308383 RLAEDEAFQR ddPTM_MDA-MB-175_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 ; 194.17 7.91E-07 372850000 450260 439470 231683 274121 389660 476920 410560 435670 182538 FALSE TRUE 390757.0002 436583.0926 343725.6737 336364.3627 381906.5284 495267.421 370743.9544 342505.3609 160958.5656 2.427686894 2.71239428 2.135491656 2.089757457 2.372700868 3.076987044 2.303350263 2.127910122 1 17.29632983 1.167097545 2.048379459 0.341499901 2.450172239 0.719397532 0.282703626 0.521730212 1.834518736 2.233604116 0.079693275 14.69256244 -1.167097545 2.108672338 DKPTYDEIFYTLS(ph)PVNGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DKPTYDEIFYTLSPVNGK 18 1 A0A024R571;Q9H4M9 A0A024R571 EHD1 EH domain-containing protein 1 1 DKPTYDEIFYT(0.001)LS(0.999)PVNGK;DKPTYDEIFYTLS(1)PVNGK;DKPTYDEIFYTLS(1)PVNGK 189.45 1.98E-14 1060210000 1913430 1477960 1307290 1397040 1374820 1154440 1820380 2318270 2265360 TRUE FALSE 1660565.377 1468251.183 1939499.817 1714259.284 1347463.772 1198852.054 1643839.828 1822526.001 1997551.722 0.831300316 0.735025365 0.970938472 0.858180174 0.674557638 0.600160707 0.822927291 0.912379881 1 20.92980143 1.62582189 2.712626557 0.986469114 0.780285669 0.350318447 0.101224178 0.290475431 4.777429052 0.107691763 0.029750928 42.24953074 -1.62582189 -0.206183445 DKPVYDELFYTLS(ph)PINGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKPVYDELFYTLSPINGK 18 1 Q9H223 Q9H223 EHD4 EH domain-containing protein 4 1 DKPVYDELFYT(0.001)LS(0.999)PINGK 203.79 6.93E-16 212330000 698090 579360 452020 498950 501460 417250 770350 911960 804940 TRUE FALSE 605835.6378 575554.146 670618.3839 612244.2235 491481.9271 433301.8775 695641.5756 716944.4509 709780.9102 0.853553018 0.810889864 0.944824486 0.862581981 0.692441738 0.610472712 0.980079297 1.010092608 1 19.43701425 2.036277579 24.83632895 1.002562922 0.801065746 0.517548824 0.091585051 132.563379 90754.87539 0.040695052 0.027436513 108.7120234 -2.036277579 -0.201497175 DKPYLYCFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKPYLYCFR 9 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9;Q5T321;A0A0D9SF28;F5GXV7;Q8NFP9 A0A494C1L5;Q5T321 LRBA;NBEA Lipopolysaccharide-responsive and beige-like anchor protein;Neurobeachin 0 ; 93.096 0.0087833 807880000 941440 843700 833210 674270 527450 578360 665760 750270 1162870 FALSE TRUE 817026.3187 838157.6791 1236153.143 827373.3091 516954.7769 600609.8834 601194.6977 589830.5991 1025396.833 0.796790367 0.817398349 1.205536337 0.806881085 0.50415094 0.585734092 0.586304422 0.575221787 1 19.96775092 3.46956959 14.45941504 0.634916573 0.940748958 0.373929792 0.171523536 1.057763858 2020.588924 0.048546069 0.063411594 2948.28586 -3.46956959 0.305832385 DKQDEEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DKQDEEQR 8 1 P27797;K7EL50 P27797 CALR Calreticulin 0 ;;;;; 133.13 0.00085038 5187970000 9782850 7908600 6315450 7372630 4496110 7439090 8851750 9211130 8569200 FALSE TRUE 8490021.586 7856647.886 9369622.744 9046698.325 4406646.207 7725276.606 7993308.647 7241401.531 7556158.938 1.123589598 1.03976742 1.239998102 1.197261519 0.583186013 1.022381433 1.05785343 0.958344258 1 22.84922162 DKQPYEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DKQPYEQK 8 1 P26583 P26583 HMGB2 High mobility group protein B2 0 ;; 152.97 0.00040905 1700543000 4695330 2822463 2120435 2383981 2187810 1783854 3612273 4121858 3541006 FALSE TRUE 4074830.244 2803922.055 3145884.458 2925300.323 2144276.861 1852480.018 3261955.32 3240430.743 3122392.305 1.305034681 0.898004409 1.007523768 0.936877893 0.686741656 0.593288683 1.044697463 1.037803846 1 21.57422038 DKQS(ph)PSQANGCSDHRPIDILEMLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKQSPSQANGCSDHRPIDILEMLSR 25 2 Q9NPI6-2;Q9NPI6;A0A087WVE6;A0A087WT55 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 DKQS(0.954)PS(0.046)QANGCSDHRPIDILEMLSR;DKQS(0.995)PS(0.005)QANGCSDHRPIDILEMLSR 303.68 8.92E-64 252130000 183468 161148 68918 130308 187509 169909 201824 225134 201216 TRUE FALSE 159222.239 160089.4082 102246.9753 159896.423 183777.9378 176445.5092 182251.1395 176990.8461 177428.4737 0.897388314 0.902275744 0.576271515 0.901188066 1.035786049 0.994459939 1.027180901 0.997533498 1 17.43687803 3.477924726 10.22113705 1.006067257 0.79229791 0.559039064 0.089057697 0.067476568 170.2812827 0.025073226 0.033751924 3005.555323 -3.477924726 -0.213769347 DKQVYR ddPTM_MDA-MB-175_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 72.234 0.078556 93596000 154270 128150 75634 117870 113860 137130 124460 188800 115020 FALSE TRUE 133882.8286 127308.1742 112210.8554 144634.185 111594.4088 142405.4798 112389.8884 148426.5892 101422.4666 1.320051001 1.255226563 1.106370798 1.42605667 1.10029279 1.404082198 1.108136018 1.463448821 1 16.63001774 1.207952701 24.86780124 0.999998162 1.271887511 0.287393881 0.135068588 4815.561679 3912227.682 3.941367595 0.029618976 16.14182746 -1.207952701 0.27188935 DKRPLS(ph)GPDVGTPQPAGLASGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DKRPLSGPDVGTPQPAGLASGAK 23 2 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 DKRPLS(0.805)GPDVGT(0.195)PQPAGLASGAK;DKRPLS(1)GPDVGTPQPAGLASGAK;DKRPLS(0.975)GPDVGT(0.025)PQPAGLASGAK;DKRPLS(1)GPDVGTPQPAGLASGAK;DKRPLS(0.999)GPDVGT(0.001)PQPAGLASGAK 228.47 5.39E-33 9795330000 6384580 6031610 4824110 5534440 6795280 4702360 9052540 10526400 8033280 TRUE FALSE 5540841.577 5991987.957 7157065.732 6791119.191 6660067.223 4883262.832 8174626.064 8275411.277 7083594.79 0.782207585 0.845896488 1.010371985 0.958710851 0.94021008 0.689376366 1.154022259 1.168250235 1 22.75605026 2.209803636 24.99999919 1.122038011 0.883432184 0.543835526 0.101307712 158.4803138 137774.3974 0.041957551 0.02829334 162.107697 -2.209803636 -0.238605827 DKS(ph)DSDTEGLLFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKSDSDTEGLLFSR 14 1 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 DKS(0.729)DS(0.266)DT(0.005)EGLLFSR 92.563 0.0029729 112400000 80358 73018 65525 77712 76063 79499 79363 94860 123830 TRUE FALSE 69738.4867 72538.33995 97213.10917 95357.69735 74549.49511 82557.37797 71666.38848 74574.9272 109190.9585 0.638683712 0.664325517 0.890303653 0.873311295 0.682744214 0.756082547 0.656339952 0.682977128 1 16.73649387 0.62702631 0.01630024 1.572530404 4.92E-06 0.070523371 0.117616332 26643.78362 90.46491484 4767.579813 3989.794304 4.236686313 -0.62702631 -1.572525484 DKS(ph)HSHTPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKSHSHTPSR 10 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DKS(0.5)HS(0.5)HTPSR 66.498 0.039733 50973000 48286 39521 23049 33020 28043 31479 45880 45809 51384 TRUE FALSE 41904.88276 39261.38395 34195.57349 40517.69568 27484.99917 32690.0175 41430.56466 36013.10184 45309.44206 0.924859827 0.866516606 0.754711865 0.894243977 0.606606436 0.721483559 0.914391411 0.794825542 1 15.46752411 -0.135754683 1.462541914 9.999999999 0.802062605 0.258086383 0.099069386 91.4735798 5.113363957 2658.281755 0.028533883 0.731552194 0.135754683 -9.197937395 DKS(ph)PAPEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKSPAPEEK 9 1 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 DKS(1)PAPEEK 96.756 0.0043318 472080000 1208400 670540 767310 672250 492510 570340 1161100 1175400 1173500 TRUE FALSE 1048706.878 666135.1786 1138383.682 824894.6372 482710.0146 592281.3489 1048496.701 924049.857 1034770.167 1.013468412 0.64375182 1.100131912 0.797176671 0.466490077 0.572379614 1.013265297 0.893000095 1 19.98087894 2.209115879 24.9993102 0.954827485 0.763079213 0.201226588 0.190120049 372.2178704 316019.5434 0.080486932 0.054273192 161.8511833 -2.209115879 -0.191748272 DKS(ph)PGRPLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKSPGRPLER 10 2 O14578-4;H7BYJ3;O14578;O14578-3 O14578-4 CIT Citron Rho-interacting kinase 1 DKS(1)PGRPLER 59.185 0.083672 446910000 786320 725440 576190 574230 777580 688750 886760 995560 829950 TRUE FALSE 682405.8197 720674.5369 854837.4112 704617.6981 762107.6793 715246.6582 800762.1517 782667.2415 731834.2565 0.93245952 0.984751029 1.168075153 0.962810489 1.041366501 0.977334214 1.094185117 1.069459696 1 19.48115742 4.469291182 24.99509149 1.046298596 0.945532343 0.286239662 0.05937098 179.3002629 572362.5637 0.014076426 0.037391865 29463.96449 -4.469291182 -0.100766253 DKS(ph)PSSLLEDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKSPSSLLEDAK 12 1 P42684-2;P42684-6;P42684-3;P42684;P42684-4;P42684-7;P42684-10;P42684-5 P42684-2 ABL2 Abelson tyrosine-protein kinase 2 1 DKS(0.761)PS(0.237)S(0.002)LLEDAK;DKS(0.75)PS(0.244)S(0.006)LLEDAK 132.25 0.00011157 842000000 993450 775430 863910 698460 768410 523200 1156690 1318110 1105390 TRUE FALSE 862163.0654 770336.1493 1281699.766 857056.0183 753120.1444 543327.8426 1044514.382 1036242.434 974712.0535 0.884531039 0.790321764 1.314952207 0.879291495 0.772659107 0.55742395 1.071613281 1.063126726 1 19.89461656 DKS(ph)PVREPIDNLTPEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 DKSPVREPIDNLTPEER 17 2 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23;H0Y4X3;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 1 DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER 268.75 2.50E-28 33591194000 7559675 5586438 4410353 4847656 5951601 4665715 7020164 8130249 7443923 TRUE FALSE 6560644.795 5549740.321 6543214.463 5948390.387 5833175.784 4845208.075 6339349.576 6391658.521 6563910.903 0.999502414 0.845492939 0.996846935 0.906226558 0.888673821 0.738158721 0.965788486 0.97375766 1 22.64612423 2.027510867 24.99942513 0.980435209 0.894412155 0.226402816 0.07374502 306.7144507 278713.5179 0.029836761 0.020115443 106.5395521 -2.027510867 -0.086023054 DKSHS(ph)HTPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKSHSHTPSR 10 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DKS(0.124)HS(0.876)HTPSR 103.88 0.0016642 63306000 69768 58671 41792 59585 47082 50148 70362 82391 83265 TRUE FALSE 60547.98203 58285.58634 62002.75099 73114.68495 46145.16031 52077.22601 63538.30407 64772.32582 73421.50656 0.824662757 0.793848956 0.844476692 0.995821094 0.628496506 0.709291166 0.865390906 0.882198267 1 16.1639151 1.403463957 1.764793409 1.027463248 0.804566794 0.299394019 0.095223516 0.871817662 3.527211916 0.30484804 0.027919411 25.32001493 -1.403463957 -0.222896454 DKTEDDADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DKTEDDADR 9 1 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 0 ;; 93.821 0.0083356 432873000 914340 751428 763911 875586 449042 600893 1007100 1070520 2239690 FALSE TRUE 793507.6524 746491.82 1133340.915 1074401.184 440106.9427 624009.7425 909431.597 841597.6288 1974916.4 0.401793034 0.377986542 0.573867793 0.544023628 0.222848391 0.315967675 0.460491187 0.42614342 1 20.91336015 1.237183118 6.549522826 1.016395781 0.41555738 0.767090751 0.10125121 0.061920775 12.59789356 0.165002896 0.026405337 17.26565738 -1.237183118 -0.600838402 DKTEDDADREAQLLEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKTEDDADREAQLLEMR 17 2 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 0 ; 160.13 1.76E-09 510080000 626810 530540 586560 406390 518530 408590 649350 828160 348080 FALSE TRUE 543975.4704 527054.8478 870222.3779 498667.0608 508212.2675 424308.7217 586376.1369 651064.4287 306930.3789 1.772308992 1.717180455 2.835243552 1.624691119 1.65579005 1.382426605 1.91045324 2.121212084 1 18.22755192 DKTKLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKTKLR 6 2 H3BLX4;Q96JM2-2;Q96JM2;Q96JM2-3 H3BLX4 ZNF462 Zinc finger protein 462 0 67.055 0.056122 293330000 614610 466350 316760 384340 318960 388360 565810 629140 431780 FALSE TRUE 533387.7313 463286.5161 469946.1955 471610.2713 312613.32 403300.4605 510937.8333 494603.307 380735.4603 1.400940514 1.216819983 1.234311601 1.238682289 0.8210775 1.059266873 1.341975956 1.299073395 1 18.53842942 4.950477286 1.158280105 1.149541685 1.608586788 0.231089798 0.152657314 4.497518553 3.699940907 0.049898021 2.800126618 89223.09536 -4.950477286 0.459045103 DKTTNQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKTTNQSR 8 1 K7EQ55;K7EK33;Q96EP5;Q96EP5-2;K7EQ02 K7EQ55 DAZAP1 DAZ-associated protein 1 0 71.614 0.044039 18246000 29701 26731 21483 17937 26671 22694 28614 30399 22943 FALSE TRUE 25775.9376 26555.4023 31872.25066 22009.87 26140.29928 23567.05286 25839.01868 23898.41042 20230.70468 1.27409984 1.312628637 1.57543947 1.087943814 1.292110171 1.164915075 1.277217927 1.181294018 1 14.30425895 -0.651423924 0.345212449 1.50E-13 1.350117945 0.37068313 0.122000084 36.28159877 1.335066499 26.24527904 0.179379926 0.223139305 0.651423924 1.350117945 DKTYSYLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKTYSYLNK 9 1 G3V2V8;J3KMY5;H0YIZ1;G3V3E8;E7EMS2;G3V3D1;P61916-2;P61916 G3V2V8 NPC2 Epididymal secretory protein E1 0 ; 111.86 0.0018761 932520000 1862840 1586470 1340750 1746120 1633220 1492890 1789800 2041600 2795300 FALSE TRUE 1616660.974 1576048.374 1989141.185 2142603.234 1600722.117 1550322.444 1616225.471 1605019.728 2464842.818 0.65588806 0.639411309 0.807005286 0.869265666 0.64942158 0.628974161 0.655711374 0.651165144 1 21.23306422 1.2335949 24.99980462 1.000000468 0.694528758 0.590741037 0.079884827 123.1488654 619917.4017 0.171203531 0.021220168 17.12359312 -1.2335949 -0.30547171 DKVAGHSLGYGFVNYVTAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKVAGHSLGYGFVNYVTAK 19 1 Q15717;Q15717-2;M0QZR9 Q15717 ELAVL1 ELAV-like protein 1 0 78.088 0.0063898 294460000 1064300 882700 537670 601900 802820 714050 1000400 1270800 610570 FALSE TRUE 923650.0584 876901.4856 797689.0104 738570.5945 786845.4527 741519.9656 903381.362 999049.3094 538389.1102 1.715580871 1.628750413 1.48162174 1.371815627 1.461480996 1.377293767 1.677933942 1.855626889 1 19.0382897 4.410560041 3.537039209 1.501821109 1.702407795 0.120876076 0.221868623 0.578852175 14.05743153 0.058539686 0.201047143 25737.12557 -4.410560041 0.200586685 DKVNCSFYFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKVNCSFYFK 10 1 P0DN76;Q01081;Q8WU68-3;Q8WU68;A0A1B0GW87;M0QYK5;M0R2N4;Q01081-3;Q8WU68-2;Q01081-2 P0DN76;Q01081-2 U2AF1;U2AF1L4 Splicing factor U2AF 35 kDa subunit;Splicing factor U2AF 26 kDa subunit 0 ; 138.63 5.45E-05 1695090000 2812300 2383100 1625910 1992300 2338700 1840740 2964700 3302800 3050500 FALSE TRUE 2440647.43 2367445.259 2412205.514 2444682.165 2292164.446 1911554.459 2677183.85 2596521.922 2689873.365 0.907346592 0.880132608 0.896772891 0.908846564 0.852145858 0.710648495 0.995282486 0.965295228 1 21.35910682 DKVTLVVGASQDIIPQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKVTLVVGASQDIIPQLK 18 1 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 139.52 1.22E-07 321360000 294560 219610 194330 236370 244730 184880 306200 395480 423840 FALSE TRUE 255633.1497 218167.3674 288308.638 290041.4212 239860.3518 191992.4532 276504.7711 310909.6796 373734.118 0.683997359 0.583750203 0.77142713 0.776063536 0.6417941 0.513714012 0.739843535 0.831900714 1 18.51165275 1.500935455 1.956223065 1.017086762 0.667114863 0.650855076 0.080054609 0.292875059 1.840848266 0.16520214 0.023671604 31.69096436 -1.500935455 -0.349971899 DKVVALAEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DKVVALAEGR 10 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;F8W1U7;E5RHT6;E5RHC5;Q8N6T3-3;F8VWB3 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 0 ;; 112.43 0.0014791 773390000 1457360 1370360 833680 1037790 1300300 1235730 1447000 1632220 1405360 FALSE TRUE 1264766.184 1361358.015 1236850.436 1273436.081 1274426.574 1283269.333 1306670.163 1283182.455 1239219.942 1.020614776 1.098560448 0.998087906 1.02761103 1.028410318 1.035546064 1.05442958 1.035475957 1 20.24100083 4.228820949 24.99960264 1.0285923 1.059587622 0.237730626 0.024833014 261.1669627 670364.1413 0.00600529 0.012769024 16936.39401 -4.228820949 0.030995323 DKVVEDDEDDFPTTR ddPTM_MDA-MB-175_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 ; 98.796 0.0025443 439570000 376900 290690 225080 251670 307970 238040 362520 395390 340340 FALSE TRUE 327091.7101 288780.4382 333929.4408 308815.52 301841.9995 247197.5528 327362.8662 310838.9254 300105.3929 1.0899228 0.962263408 1.112707231 1.029023561 1.005786656 0.823702468 1.090826336 1.035765877 1 18.19510972 3.319600575 4.209423029 0.995836273 1.048816513 0.122397214 0.077249892 0.573777816 19.13495444 0.023291764 0.030064 2087.375469 -3.319600575 0.05298024 DKVVGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKVVGK 6 1 P47756-2;B1AK88;B1AK87;P47756;B1AK85 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ; 94.887 0.040102 2419200000 2066400 1678330 1227640 1541770 906720 1207720 2254290 2712020 2388540 FALSE TRUE 1793320.004 1667304.94 1821330.81 1891852.443 888678.046 1254181.77 2035669.303 2132075.628 2106169.522 0.851460429 0.791629032 0.864759836 0.898243196 0.421940417 0.595479973 0.966526807 1.012300105 1 21.00619013 2.123043264 7.118565844 1.001271913 0.739033607 0.424750704 0.140666141 0.227242324 13.25526379 0.062885055 0.042256987 132.7526699 -2.123043264 -0.262238306 DKWLAPDGLIFPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DKWLAPDGLIFPDR 14 1 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;H0YDE4;E9PNR9 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ;;; 123.97 9.10E-05 2479702000 1896900 1496895 930583 1131352 1424951 1355962 1729550 1911450 1328495 FALSE TRUE 1646219.859 1487061.798 1380616.051 1388242.763 1396597.263 1408126.736 1561818.507 1502701.292 1171441.835 1.405293725 1.269428626 1.178561334 1.185071868 1.192203677 1.202045799 1.333244606 1.282779262 1 20.15985389 4.663160751 2.8545257 1.211222792 1.423983582 0.36358994 0.086352178 0.413010314 5.134716867 0.022103824 0.18551281 46042.69656 -4.663160751 0.21276079 DKWLCPLSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKWLCPLSGK 10 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 65.348 0.063146 255860000 436970 332620 228060 246590 317360 305250 396750 467880 362340 FALSE TRUE 379223.3074 330434.9973 338350.5788 302582.0284 311045.1569 316993.165 358273.2461 367827.503 319504.578 1.186910403 1.034210525 1.058985073 0.947035033 0.973523318 0.992139665 1.121339946 1.151243295 1 18.28547708 0.938018404 19.98559079 3.50E-05 1.057711021 0.05303629 0.077229564 207.2681035 142268.543 10765.65062 0.019887037 8.669986153 -0.938018404 1.057676067 DKWSPALQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKWSPALQIR 10 1 P61088;F8VQQ8;Q5JXB2 P61088 UBE2N;UBE2NL Ubiquitin-conjugating enzyme E2 N;Putative ubiquitin-conjugating enzyme E2 N-like 0 ; 155.97 1.07E-05 3746300000 5085400 5704600 3440300 4127300 5669400 5072300 6252400 6827500 6252000 FALSE TRUE 4413351.505 5667126.107 5104040.587 5064466.547 5556590.032 5267434.663 5646043.21 5367492.257 5512895.682 0.80055052 1.0279763 0.925836599 0.91865815 1.007925844 0.95547512 1.024152013 0.973624855 1 22.39437887 4.748824125 24.84804902 0.977472891 0.800550413 0.689114176 0.037695536 788.9973549 1910128.897 0.00895306 0.121877279 56082.08161 -4.748824125 -0.176922477 DKYEPAAVSEQGDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKYEPAAVSEQGDKK 15 2 P05023-4;P05023;P05023-2 P05023-4 ATP1A1 Sodium/potassium-transporting ATPase subunit alpha-1 0 78.285 0.013143 47357000 60910 45324 44715 66619 44597 32335 44724 94961 77295 FALSE TRUE 52860.58917 45026.26366 66339.32356 81745.86216 43709.60695 33578.94837 40386.67336 74654.32914 68157.27315 0.775567841 0.66062302 0.973327137 1.199371078 0.641305101 0.4926686 0.592551191 1.095324471 1 16.05658 1.675901521 8.434148694 1.045395639 0.768715723 0.254629814 0.20217328 0.177187921 21.32592464 0.126984463 0.056975646 47.41344602 -1.675901521 -0.276679916 DKYGPPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKYGPPVR 8 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ; 82.287 0.018845 1036920000 3149760 3060060 1719210 2486190 2923080 2870320 3199560 3431240 2772730 FALSE TRUE 2733511.236 3039958.264 2550625.706 3050717.439 2864916.427 2980743.068 2889267.164 2697496.028 2444941.018 1.118027476 1.243366708 1.043225864 1.247767294 1.171773227 1.219147229 1.181732869 1.103296974 1 21.22136823 1.380266118 2.257299705 0.98008816 1.176885389 0.467259852 0.060379866 0.384330649 2.678792925 0.13711907 0.01504247 24.00303278 -1.380266118 0.196797229 DKYVGVSSDSVGGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DKYVGVSSDSVGGFR 15 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 161.08 1.53E-06 860260000 1055200 871250 620460 685660 973320 829950 1084820 1196000 1112420 FALSE TRUE 915752.6465 865526.7014 920516.5313 841349.5827 953952.8363 861878.7135 979614.3234 940244.7073 980910.9749 0.933573657 0.88237029 0.93843025 0.857722672 0.972517242 0.87865131 0.998678115 0.958542346 1 19.90376268 2.231362179 24.99960546 0.980613034 0.910947123 0.50651868 0.034864792 131.0874071 455251.0967 0.012629368 0.008714965 170.3578614 -2.231362179 -0.069665911 DLADELALVDVIEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 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 ;;;;;;;; 300.55 6.54E-44 1124769300 1627858 1066719 1225424 1296665 1116736 832727 1508532 1641620 2094625 FALSE TRUE 1412732.441 1059711.653 1818043.145 1591092.607 1094515.138 864762.5465 1362234.799 1290572.338 1847000.819 0.764879163 0.573747257 0.984321786 0.861446617 0.5925905 0.468198248 0.737538817 0.698739451 1 20.81675308 1.237347698 24.54010984 1.000000427 0.708722085 0.278976929 0.146408912 35.14233527 710620.9599 0.222877728 0.037082122 17.2722016 -1.237347698 -0.291278342 DLADVDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLADVDLR 8 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 0 ; 92.439 0.025765 78157000 658580 615630 429460 508520 612380 675270 611820 707940 709300 FALSE TRUE 571546.9844 611585.886 637148.2925 623987.2382 600194.8361 701248.0739 552485.7906 556552.5402 625447.362 0.913821081 0.977837502 1.018708098 0.997665473 0.959624858 1.12119439 0.883344985 0.88984713 1 19.25452895 DLAEDAPWK ddPTM_MDA-MB-175_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 ; 135.79 0.00049067 295257000 809390 756370 561230 699470 665720 619480 827420 922730 1489350 FALSE TRUE 702427.0608 751401.3557 832642.7052 858295.3542 652473.4745 643311.7965 747176.9358 725411.3702 1313280.74 0.534864359 0.572155924 0.634017297 0.653550553 0.49682711 0.489850934 0.568939232 0.552365803 1 20.32474392 1.237663706 24.99854446 1.000000511 0.563627256 0.876208853 0.051641126 7.840357852 218400.6106 0.079525305 0.013520917 17.28477402 -1.237663706 -0.436373255 DLAEDAPWKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLAEDAPWKK 10 1 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98;O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;O75369-5;O75369-4;Q14315-2;Q14315 Q60FE5;O75369-8;Q14315-2 FLNA;FLNB;FLNC Filamin-A;Filamin-B;Filamin-C 0 ;;; 136.96 0.00016658 4247520000 12153700 9858800 7796170 9429850 9840920 8199700 14109300 17036200 11534400 FALSE TRUE 10547557.75 9794036.894 11566423.89 11571041.57 9645104.945 8515147.765 12740982.26 13393141.21 10170816.37 1.03704141 0.962954844 1.137216863 1.137670876 0.948311777 0.837213794 1.252700058 1.316820668 1 23.27793215 2.206989628 24.9999795 1.218913801 1.016699123 0.325728702 0.119258534 207.8605547 164596.1995 0.049958019 0.033685051 161.0607169 -2.206989628 -0.202214677 DLAEITTLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLAEITTLDR 10 0 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 112.01 0.0039033 84660000 64482 70157 34724 45202 69087 69288 49572 73813 56328 FALSE TRUE 55960.54032 69696.13405 51516.64254 55465.80497 67712.30387 71953.5542 44764.51507 58028.66436 49668.96801 1.126670083 1.403212848 1.037199777 1.11670943 1.363271809 1.448662154 0.901257201 1.168308235 1 15.60005715 2.228471848 24.99974374 1.048341339 1.24579875 0.342529652 0.146236015 267.080372 661813.1975 0.059508526 0.040646859 169.2278544 -2.228471848 0.197457411 DLAFTLEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLAFTLEER 9 0 P48163 P48163 ME1 NADP-dependent malic enzyme 0 105.94 0.0070194 106170000 182270 176830 131320 179210 213870 250000 176370 192700 201740 FALSE TRUE 158182.5577 175668.3921 194826.7912 219902.3696 209614.4054 259617.6618 159265.6645 151492.6046 177890.527 0.889212935 0.987508413 1.095206105 1.236166834 1.178333714 1.45942376 0.89530155 0.8516058 1 17.44063016 2.10300629 20.95472146 0.901190529 1.141249111 0.321274141 0.153903656 4.156864961 831.3560605 0.066011331 0.044504843 126.7670226 -2.10300629 0.240058582 DLAGAPPGEVVGCFT(ph)PQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLAGAPPGEVVGCFTPQSR 19 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 1 DLAGAPPGEVVGCFT(0.994)PQS(0.006)R 253.52 7.88E-30 253080000 57755 56493 41777 43548 61503 60777 47598 56914 70054 TRUE FALSE 50122.53042 56121.89376 61980.49694 53436.23899 60279.21063 63115.13052 42981.95329 44743.38401 61772.29593 0.811407924 0.908528539 1.003370459 0.865051852 0.975829208 1.02173846 0.695812785 0.724327683 1 15.91467233 2.238484202 25 0.784928923 0.932298151 0.241484114 0.101388758 2.427066908 793364.884 0.039421848 0.02851011 173.1746035 -2.238484202 0.147369228 DLAHCHAYLVEMSQLLQSMDVLHR ddPTM_MDA-MB-175_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 0 126.45 3.19E-05 102890000 53745 55171 44020 45640 67124 66993 56135 73849 57025 FALSE TRUE 46642.46208 54808.57807 65308.21924 56003.25956 65788.36373 69570.26406 50691.03634 58056.96604 50283.56946 0.927588526 1.089989805 1.298798393 1.113748689 1.308347129 1.383558582 1.00810338 1.154591185 1 15.61779945 4.612109351 3.536466957 1.179551556 0.925310075 0.293254105 0.124796798 0.330057597 6.670292809 0.031434733 0.175495333 40936.37207 -4.612109351 -0.254241481 DLAILQCHGELDPMVPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 DLAILQCHGELDPMVPVR 18 0 O95372;Q5QPQ1;Q5QPQ0 O95372 LYPLA2 Acyl-protein thioesterase 2 0 ;;;;;; 184.15 5.97E-14 1294800000 1066574 919997 608569 711200 891392 932459 893104 1043372 999405 FALSE TRUE 925623.5435 913953.4791 902875.0039 872688.83 873655.0432 968331.3011 806490.9115 820255.0173 881256.4794 1.050345235 1.037102706 1.024531479 0.990277916 0.99137432 1.098807582 0.915160263 0.930778992 1 19.74920243 2.219536551 24.99999979 0.94352877 1.028209295 0.523471072 0.037295652 185.765774 244117.6669 0.015129146 0.010218941 165.7816854 -2.219536551 0.084680525 DLAMMIHDQGDLIDSIEANVESSEVHVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DLAMMIHDQGDLIDSIEANVESSEVHVER 29 0 Q86Y82 Q86Y82 STX12 Syntaxin-12 0 ;; 213.44 1.06E-26 63296000 47213 47836 30671.4 35675.1 43708.8 51402 37342.8 45411.9 45353 FALSE TRUE 40973.68243 47521.76217 45504.19163 43775.67671 42839.08039 53379.4682 33721.301 35700.91858 39991.42001 1.024561829 1.188298944 1.137848859 1.094626715 1.071206784 1.334773014 0.843213394 0.892714452 1 15.28740289 2.215747648 24.99976985 0.905097965 1.138451412 0.589625637 0.090326681 151.3371602 165842.7192 0.035135774 0.023706567 164.3416517 -2.215747648 0.233353447 DLANDIMTLMSHTKPYIR ddPTM_MDA-MB-175_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 165424000 688480 653150 401630 478350 609520 534520 719420 761830 570580 FALSE TRUE 597495.6236 648859.4146 595859.6114 586966.6786 597391.7445 555083.3303 649650.7591 598918.5831 503126.6824 1.18756497 1.289654151 1.18431328 1.166637945 1.187358503 1.103267526 1.291227005 1.190393203 1 18.94056218 1.243026612 6.407037256 0.99447052 1.202195433 0.565304591 0.055187269 0.085607194 15.82792317 0.077532858 0.013389982 17.49953915 -1.243026612 0.207724914 DLAQHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLAQHLR 7 0 Q96IQ9-2;Q96IQ9 Q96IQ9-2 ZNF414 Zinc finger protein 414 0 129.68 0.01008 0 117080 105090 68221 91512 119420 116790 106230 120640 120550 FALSE TRUE 101607.5814 104399.6569 101212.9038 112291.1983 117043.7756 121282.9869 95927.83095 94842.07482 106298.7163 0.955868376 0.982134691 0.952155466 1.056373982 1.101083622 1.140963796 0.902436401 0.892222203 1 16.69776465 2.195169192 24.9999882 0.922145646 1.029886074 0.333825556 0.066042955 159.5319416 91913.21921 0.029322172 0.019769157 156.7361562 -2.195169192 0.107740428 DLATVAFCDAQSTQEIHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLATVAFCDAQSTQEIHEK 19 0 P56545;P56545-3;P56545-2 P56545 CTBP2 C-terminal-binding protein 2 0 ; 316.14 1.06E-61 366470000 578870 539510 371660 443480 482500 444990 584690 688970 600690 FALSE TRUE 502370.8628 535965.9233 551396.0191 544178.9122 472899.194 462109.0532 527986.8538 541639.1271 529677.1125 0.948447367 1.011872914 1.04100405 1.027378566 0.892806547 0.872435381 0.996808889 1.022583597 1 19.01475365 2.011380953 24.99644493 1.01194234 0.967672541 0.116222202 0.053951099 513.0603256 1126850.646 0.02469647 0.016635575 102.6551998 -2.011380953 -0.044269799 DLAVPAALT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLAVPAALTPR 11 0 Q8TEM1 Q8TEM1 NUP210 Nuclear pore membrane glycoprotein 210 1 DLAVPAALT(1)PR;DLAVPAALT(1)PR;DLAVPAALT(1)PR;DLAVPAALT(1)PR 141.54 0.00042568 693640000 877020 892510 605950 959360 1204720 1034860 651650 1409790 1155390 TRUE FALSE 761119.5849 886647.043 898989.4468 1177197.351 1180748.429 1074671.734 588453.0833 1108317.379 1018801.11 0.747073768 0.870284724 0.882399359 1.155473172 1.158958718 1.054839578 0.577593681 1.087864322 1 19.95844101 4.247799148 2.270111994 0.995100646 0.777234024 0.198586462 0.165915713 0.571778921 5.675581891 0.046565935 0.166200441 17692.90508 -4.247799148 -0.217866622 DLCNTHLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLCNTHLMR 9 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 182.64 4.61E-05 1110180000 575430 507160 300730 356330 557310 431850 555820 517920 537880 FALSE TRUE 499385.4675 503828.4326 446164.0339 437240.1727 546220.6214 448463.5489 501916.6619 407166.8385 474292.4392 1.052906237 1.062273802 0.940693962 0.921878859 1.151653656 0.945542269 1.058243017 0.858472126 1 18.85541734 1.747645868 25 0.924027997 1.016216303 0.189292965 0.076915744 3.198527099 8827.09655 0.039152108 0.018801177 55.93013504 -1.747645868 0.092188305 DLDADREVTFLEASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLDADREVTFLEASR 15 1 A0A087WYT5;P20338 A0A087WYT5 RAB4A Ras-related protein Rab-4A 0 ; 173.03 9.06E-07 240370000 396030 389810 232470 249280 349180 381500 373910 465140 205258 FALSE TRUE 343693.6321 387249.3124 344893.2696 305882.834 342232.0012 396176.5519 337648.2658 365673.4307 180992.6331 1.898937135 2.139586048 1.905565236 1.690029195 1.890861497 2.18890982 1.865535961 2.020377429 1 17.46557145 1.236034527 24.99269346 0.999998743 1.951350945 0.816077338 0.141730273 28.5801346 282706.3392 0.230034277 0.034816991 17.22005472 -1.236034527 0.951352202 DLDANGDAQVDFSEFIVFVAAITSACHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 DLDANGDAQVDFSEFIVFVAAITSACHK 28 0 P25815 P25815 S100P Protein S100-P 0 ;;;;;;;; 337.48 3.70E-96 24905450000 17124775 18280673 9744928 16489254 12295518 10585066 22126455 23591507 34816043 FALSE TRUE 14861692.6 18160586.06 14457607.78 20233391.14 12050861.25 10992280.34 19980634.8 18546646.82 30700130.06 0.484092171 0.591547528 0.470929854 0.659065323 0.392534534 0.358053217 0.650832253 0.604122744 1 24.87174143 0.751779961 1.324336672 2.050490192 0.506817294 0.709814985 0.097341132 2.379535762 1.428180024 6.911564359 0.028458754 5.646508178 -0.751779961 -1.543672897 DLDAPDDVDFF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLDAPDDVDFF 11 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 95.099 0.018637 29820000 136550 118080 81108 103570 112040 106390 115310 136960 122990 FALSE TRUE 118504.5715 117304.3247 120332.1001 127087.1515 109810.6232 110482.8921 104127.2539 107672.1698 108450.2623 1.092708943 1.081641687 1.109560249 1.171847341 1.012543639 1.018742507 0.960138332 0.992825352 1 16.72667402 3.109188229 6.474422756 0.992660829 1.110915346 0.819559746 0.027394882 0.089227028 4.783075794 0.008646741 0.009841556 1285.843841 -3.109188229 0.118254517 DLDDFQSWLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLDDFQSWLSR 11 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;; 195.51 1.48E-07 1159690000 1517460 1467910 896410 932680 1187420 1265530 1343630 1573080 1593120 FALSE TRUE 1316923.816 1458267.203 1329916.874 1144459.249 1163792.665 1314215.758 1213324.969 1236689.084 1404783.168 0.937457001 1.038072804 0.946706157 0.814687473 0.828450035 0.93552926 0.863709786 0.880341615 1 20.42191603 3.992966299 24.20065108 0.884228693 0.988921073 0.354547347 0.057234956 211.8423972 728895.0262 0.014470648 0.028345959 9839.347494 -3.992966299 0.10469238 DLDEEGS(ph)EK ddPTM_MDA-MB-175_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 193.3 3.54E-05 1608790000 3313320 1969120 2536870 3084590 2133640 1833970 2842790 3369190 7347700 TRUE FALSE 2875456.367 1956184.721 3763708.817 3784993.305 2091184.738 1904524.013 2567096.663 2648714.938 6479063.277 0.443807422 0.301924003 0.580903235 0.584188353 0.322760351 0.293950519 0.396214168 0.408811401 1 22.62735382 1.238176125 24.99192621 1.000000659 0.415279436 0.764287883 0.101822602 4.67277265 303330.3814 0.148139805 0.025990241 17.30518017 -1.238176125 -0.584721222 DLDEEGS(ph)EKELHENVLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DLDEEGSEKELHENVLDK 18 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 DLDEEGS(1)EKELHENVLDK;DLDEEGS(1)EKELHENVLDK;DLDEEGS(1)EKELHENVLDK;DLDEEGS(1)EKELHENVLDK;DLDEEGS(1)EKELHENVLDK 224.83 2.65E-19 1747050000 2490960 1348070 2186400 1981390 1424900 1136609 2059510 2452010 4349550 TRUE FALSE 2161773.325 1339214.439 3243750.353 2431294.883 1396547.278 1180335.084 1859779.037 1927666.743 3835351.154 0.563644172 0.349176486 0.845750551 0.633917153 0.36412501 0.307751503 0.484904501 0.50260502 1 21.87092724 1.238437765 24.14224738 1.000000668 0.504300216 0.49635867 0.156216912 1.716853672 335193.0875 0.221075557 0.039417863 17.31560877 -1.238437765 -0.495700452 DLDEEIFDDDDFYHQLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLDEEIFDDDDFYHQLLR 18 0 Q9NY61;A0A087WTH8;A0A087WWS8 Q9NY61 AATF Protein AATF 0 ;;; 233.48 9.63E-24 277612000 378273 298550 216182 275508 297785 257092 283397 362706 351981 FALSE TRUE 328283.2646 296588.8054 320728.3383 338066.3023 291859.6611 266982.4956 255913.2026 285144.1445 310370.2072 1.057715132 0.955596892 1.033373471 1.089235676 0.940359784 0.860206584 0.824541778 0.918722667 1 18.24363055 3.050030514 6.212581189 0.896775024 1.02776172 0.564452907 0.055423883 0.14923756 13.04059316 0.017526556 0.019816718 1122.097292 -3.050030514 0.130986696 DLDELSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLDELSR 7 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 204.1 0.00063089 1315070000 3053700 2732300 2104100 2795800 2501500 2576200 2747300 3058600 5334500 FALSE TRUE 2650145.808 2714351.341 3121649.798 3430629.121 2451725.044 2675308.081 2480867.269 2404542.192 4703861.487 0.563397926 0.577047464 0.66363557 0.729321884 0.521215399 0.568747207 0.527410783 0.511184736 1 22.16541415 1.232679414 24.99577617 1.000000678 0.581366982 0.79209972 0.067176926 94.89060291 403254.2354 0.157952819 0.018007009 17.0875349 -1.232679414 -0.418633696 DLDELSRYPEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLDELSRYPEDK 12 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 237.41 3.82E-16 3036070000 7070240 4851320 3191390 3581620 4607680 3765960 6113160 7034340 2717150 FALSE TRUE 6135889.87 4819451.359 4734756.879 4394881.563 4515996.183 3910838.918 5520306.684 5530101.132 2395931.622 2.560962013 2.011514567 1.976165277 1.834310095 1.884860211 1.632283193 2.304033484 2.308121434 1 21.1921553 4.879299802 1.924042638 1.904899196 2.950156862 0.258432733 0.368970371 1.968151235 5.625354027 0.096673164 4.134052523 75735.55327 -4.879299802 1.045257666 DLDEMDDDDDDDDVGDHDDDHPGMEVVLHEDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLDEMDDDDDDDDVGDHDDDHPGMEVVLHEDKK 33 1 Q15029;Q15029-3;K7EIV5;K7EIT3 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 129.03 2.32E-08 324140000 128810 88082 84354 88131 69455 51017 111640 128860 116270 FALSE TRUE 111787.4321 87503.38354 125147.8765 108142.4905 68072.98139 52979.657 100813.17 101304.2918 102524.6931 1.090346421 0.853485935 1.220660826 1.05479458 0.663966693 0.516750213 0.983306236 0.988096514 1 16.6456119 3.285067925 24.85814903 0.84591545 1.052286914 0.287995012 0.174360825 184.3018184 98507.89022 0.054998131 0.071002039 1927.826406 -3.285067925 0.206371463 DLDEVLQTHSVFVNVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLDEVLQTHSVFVNVSK 17 0 Q9Y3A5;A0A087X020;F8WE72 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 173.87 1.42E-09 834450000 1695200 1598400 922190 994510 1471900 1433300 1516400 1711000 1195600 FALSE TRUE 1471175.025 1587900.005 1368164.169 1220328.696 1442612.07 1488439.978 1369339.761 1345115.965 1054257.53 1.39546077 1.506178481 1.297751384 1.157524287 1.368367812 1.41183718 1.298866475 1.27588936 1 20.0077959 0.921652637 1.524806193 0.534890105 1.35032197 0.595713946 0.089839513 2.014099689 2.173728904 3.183536303 0.027270504 8.349349432 -0.921652637 0.815431866 DLDFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLDFEK 6 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-4 Q04637-9;A0A0A0MSA7 EIF4G1;EIF4G3 Eukaryotic translation initiation factor 4 gamma 1;Eukaryotic translation initiation factor 4 gamma 3 0 107.66 0.072303 103340000 357020 301050 197910 232070 281200 247570 383750 390880 283230 FALSE TRUE 309838.9024 299072.3827 293619.938 284765.0405 275604.6702 257094.1781 346533.9841 307293.3538 249746.8721 1.240611744 1.197502016 1.175670132 1.140214643 1.103536024 1.029419011 1.387540838 1.230419229 1 17.93010708 4.55605807 2.06262449 1.165118614 1.247179892 0.061057337 0.107440397 1.888774278 11.75104025 0.02978918 0.251635749 35979.74405 -4.55605807 0.082061277 DLDGFRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLDGFRK 7 1 A0A087WYS1;E7EUC7;Q16851;Q16851-2;C9JVG3;C9JQU9;C9JNZ1;C9JWG0;C9JTZ5;C9JUW1;F2Z3H1 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 71.342 0.087507 367780000 1182700 1047800 599480 717780 946860 867490 1108900 1335100 547600 FALSE TRUE 1026403.198 1040916.933 889390.5331 880762.9196 928019.3385 900862.9016 1001359.049 1049599.255 482863.3518 2.125659764 2.155717407 1.841909372 1.824041763 1.921908828 1.86566841 2.073793848 2.173698316 1 18.88125545 1.232368534 24.99999608 0.999998358 1.99773993 0.85037532 0.131535228 85.04057256 343309.9584 0.323257203 0.035802165 17.07530753 -1.232368534 0.997741572 DLDIFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DLDIFDR 7 0 Q14165;F5H1S8;H0YG07 Q14165 MLEC Malectin 0 ;;;;; 147.34 0.005021 914415000 2080750 1973800 1425730 2059080 2638780 2465220 1614140 3079040 2841840 FALSE TRUE 1805773.616 1960833.978 2115217.797 2526625.585 2586273.441 2560058.609 1457600.951 2420611.257 2505880.913 0.720614298 0.782492882 0.844101484 1.008278395 1.032081544 1.02162022 0.581672075 0.965972184 1 21.25688642 4.154502968 2.71060698 0.923657625 0.740879626 0.248028612 0.131346658 0.424897591 6.204262143 0.036535391 0.100955136 14272.59584 -4.154502968 -0.182777999 DLDIIDNYDYSHTVK ddPTM_MDA-MB-175_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 ;;;;;; 333.62 5.86E-69 3703416000 5654025 4788058 3560315 4039945 4085305 3536434 4895855 5751314 7781023 FALSE TRUE 4906831.271 4756604.932 5282095.243 4957276.259 4004015.423 3672482.904 4421055.736 4521440.258 6861159.325 0.715160666 0.693265483 0.769854625 0.72251292 0.583577094 0.535256905 0.644359871 0.65899071 1 22.71002094 1.238106603 24.99711889 1.000000381 0.663388345 0.705315123 0.067964638 6.845169651 376461.0258 0.105561614 0.018422936 17.30241018 -1.238106603 -0.336612036 DLDKADSMIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 99.5 0.0042435 471330000 327540 271290 160590 169580 275760 248450 330600 359070 84952 FALSE TRUE 284254.7591 269507.8781 238251.8611 208085.7309 270272.9155 258008.0323 298538.4629 282285.6748 74909.07134 3.794664038 3.597800284 3.180547521 2.77784422 3.608013164 3.444282884 3.985344599 3.768377711 1 16.19285282 1.235158106 24.99877005 0.999996487 3.522178059 0.844471448 0.339817854 40.09212579 294514.8302 0.645076736 0.091128293 17.18533912 -1.235158106 2.522181572 DLDLDAFAEELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLDLDAFAEELER 13 0 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ; 103.91 0.0036604 46971000 74110 63413 46688.6 61738.7 57507.5 59154.7 60459.4 75885 109962 FALSE TRUE 64316.17573 62996.43583 69267.36312 75757.41545 56363.21326 61430.41959 54596.05669 59657.58329 96962.41763 0.663310356 0.649699516 0.714373309 0.781306998 0.581289273 0.633548761 0.563064103 0.615265014 1 16.56513805 1.235326726 24.97947163 1.000000491 0.647915096 0.754541827 0.062682111 48.55839155 375013.6839 0.115318889 0.016526014 17.1920128 -1.235326726 -0.352085395 DLDLEPLS(ph)DLEEGLEETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLDLEPLSDLEEGLEETR 18 0 P29375;P29375-2 P29375 KDM5A Lysine-specific demethylase 5A 1 DLDLEPLS(1)DLEEGLEETR 150.59 5.65E-08 66753000 71529 62299 52136 53938 60815 67500 59867 72247 78081 TRUE FALSE 62076.26142 61889.75377 77349.14398 66185.44729 59604.90048 70096.76868 54061.10755 56797.54128 68850.35313 0.901611373 0.898902489 1.123438595 0.961294231 0.8657167 1.018103256 0.785197244 0.824941902 1 16.07117643 2.243741413 24.99991594 0.857114235 0.961661449 0.182436308 0.089895764 189.2702197 913328.2182 0.034478236 0.025890245 175.283652 -2.243741413 0.104547215 DLDLKKPIYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLDLKKPIYQR 11 2 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 57.225 0.064121 382800000 808410 641090 422550 523880 636410 516130 753330 926240 593340 FALSE TRUE 701576.5703 636878.6376 626896.5933 642834.961 623746.6861 535985.8551 680272.1725 728170.784 523196.0211 1.340944009 1.217284941 1.198205965 1.228669438 1.192185454 1.024445587 1.300224285 1.391774315 1 18.99699204 4.737497373 4.92303904 1.209901745 1.347613449 0.125063291 0.115706743 0.428052223 31.61630063 0.02933116 0.201673177 54638.32454 -4.737497373 0.137711704 DLDLLASVPS(ph)PSSSGSR ddPTM_MDA-MB-175_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(0.003)VPS(0.899)PS(0.011)S(0.066)S(0.011)GS(0.011)R;DLDLLASVPS(0.997)PS(0.003)SSGSR;DLDLLASVPS(0.963)PS(0.032)S(0.003)S(0.001)GS(0.001)R;DLDLLASVPS(0.999)PS(0.001)SSGSR;DLDLLASVPS(1)PSSSGSR;DLDLLASVPS(0.994)PS(0.005)SSGSR;DLDLLASVPS(0.998)PS(0.001)SSGSR 407.59 2.50E-140 3308168000 3292640 2898151 1865857 2136646 2893938 2953635 2983430 3408110 3214130 TRUE FALSE 2857509.282 2879112.855 2768191.686 2621804.131 2836354.296 3067263.25 2694097.418 2679312.198 2834159.213 1.008238799 1.015861368 0.976724128 0.925072988 1.000774509 1.082248039 0.95058083 0.945364038 1 21.43448938 2.120478218 0.00599079 8.36E-05 1.961678679 0.010767795 0.044060749 65052.77393 204.8054908 33938.14316 33122.52382 131.970912 -2.120478218 1.961595119 DLDQCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLDQCR 6 0 P60903 P60903 S100A10 Protein S100-A10 0 ; 153.26 0.023621 2442800000 3626300 3359700 2282400 3331800 3075600 4019200 2559000 4299600 4181600 FALSE TRUE 3147075.267 3337629.909 3386176.274 4088336.113 3014401.577 4173821.225 2310828.574 3380164 3687256.012 0.853500613 0.905179868 0.918345855 1.108774682 0.817518927 1.13195862 0.626706843 0.9167153 1 21.81411616 1.248332035 8.771980845 1.000576284 0.907214739 0.038202364 0.141795356 0.366254579 266.2419943 0.159119079 0.032919616 17.71462794 -1.248332035 -0.093361545 DLDSLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLDSLHR 7 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;;; 150.17 0.0019672 3985910000 7276200 6456100 3405970 5379000 6806800 8219700 6237900 6504300 5582800 FALSE TRUE 6314631.734 6413689.454 5053108.484 6600384.163 6671357.997 8535917.178 5632949.418 5113406.062 4922807.744 1.282729707 1.302851906 1.026468785 1.340776343 1.355193691 1.733952984 1.144255415 1.0387174 1 22.23104997 2.010949634 24.99940384 1.042932787 1.334559144 0.388035033 0.170115053 227.6953808 519855.44 0.072998199 0.049167267 102.5532986 -2.010949634 0.291626358 DLDWEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLDWEVR 7 0 Q6PJG6;Q6PJG6-3 Q6PJG6 BRAT1 BRCA1-associated ATM activator 1 0 ; 112.17 0.014922 99597000 164291 164120 116721 131723 174715 181283 171852 196503 189572 FALSE TRUE 142579.5281 163041.8849 173167.666 161632.7204 171238.5133 188257.0743 155185.8195 154482.3626 167161.0141 0.852947255 0.975358314 1.03593333 0.966928331 1.024392645 1.126202035 0.928361319 0.92415306 1 17.35087889 4.723061124 4.004458357 0.994825394 0.842236435 0.385698919 0.0578153 0.262536479 8.847768722 0.015472713 0.1134297 52851.96317 -4.723061124 -0.152588959 DLEADIIGDTSGHFQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLEADIIGDTSGHFQK 16 0 P08133;P08133-2;E5RJF5;E5RK63 P08133 ANXA6 Annexin A6;Annexin 0 217.48 1.42E-14 217350000 205410 164660 94951 183860 207890 205310 108030 227610 296490 FALSE TRUE 178264.5481 163578.3376 140869.6212 225608.2231 203753.3957 213208.4086 97553.26723 178937.3728 261439.29 0.681858293 0.625683835 0.538823454 0.862946894 0.77935262 0.815517853 0.373139275 0.684431834 1 17.99611644 3.760371376 24.54231552 0.725492708 0.616478079 0.120859178 0.163802674 1789.493659 2013599.871 0.045137111 0.078088036 5759.322206 -3.760371376 -0.109014629 DLEAEHVEVEDTTLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DLEAEHVEVEDTTLNR 16 0 Q9H3K6;A0A087WZT3;H3BV85;Q9H3K6-2;H3BTW0;A0A0B4J295;H3BVE0 Q9H3K6 BOLA2;BOLA2B BolA-like protein 2 0 ;;;;;;; 337.49 1.77E-58 7388200000 5932880 6404230 4046735 4902120 6296160 5760590 6321040 7219120 6496980 FALSE TRUE 5148834.876 6362160.191 6003749.582 6015221.27 6170878.734 5982203.625 5708026.514 5675367.367 5728914.426 0.898745293 1.110535037 1.047973339 1.049975759 1.077146258 1.044212425 0.996353949 0.990653193 1 22.44983036 2.233680168 7.494484563 0.99449635 1.044216427 0.112036464 0.054506115 0.23201524 81.35700727 0.020155438 0.01437011 171.2695543 -2.233680168 0.049720076 DLEAHIDSANK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DLEAHIDSANK 11 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;; 220.1 9.40E-12 25133450000 36445800 34250400 22172300 29004900 33268100 27971100 41711900 46787500 41404200 FALSE TRUE 31629395.19 34025406.87 32894898.44 35590905.86 32606129.9 29047166.32 37666686.36 36782357.23 36509442.64 0.866334649 0.931961827 0.900997004 0.974841117 0.893087583 0.79560695 1.031697107 1.007475178 1 25.12176631 2.204745419 24.99999113 1.012671205 0.899516961 0.595106249 0.0462095 133.2563632 98517.17394 0.019025248 0.0128276 160.2305851 -2.204745419 -0.113154244 DLEALMFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLEALMFDR 9 0 A0A3B3ITK7;P36871;P36871-2;P36871-3 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 0 ;;; 148.52 0.00020894 214293000 406723 308079 196132 235847 303308 293481 308887 339167 328011 FALSE TRUE 352973.525 306055.2088 290982.0912 289399.666 297272.7642 304771.404 278931.1863 266638.7765 289233.9133 1.220373922 1.058158102 1.006044167 1.000573075 1.027793597 1.053719464 0.964379257 0.921879366 1 18.1418772 7.999999995 0.781111982 0.982633335 53.04706497 0.800729012 0.035182817 221.8928876 0.83881084 0.014751781 20401.71393 99999998.87 -7.999999995 52.06443164 DLEDSLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 6147581000 7227160 6295590 4925700 5760470 5971970 6003330 6270440 7121440 9486840 FALSE TRUE 6272072.495 6254233.855 7307784.995 7068472.757 5853139.481 6234281.99 5662333.694 5598575.475 8365316.583 0.749771085 0.747638633 0.873581403 0.84497373 0.699691329 0.745253563 0.676882176 0.669260442 1 22.99598871 3.238894804 24.99979591 0.740349526 0.804936753 0.032555717 0.100453778 23.82680176 1782363.53 0.029604297 0.035885988 1733.384083 -3.238894804 0.064587227 DLEEAEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLEEAEGR 8 0 P54886-2;P54886 P54886-2 ALDH18A1 Delta-1-pyrroline-5-carboxylate synthase;Glutamate 5-kinase;Gamma-glutamyl phosphate reductase 0 ; 142.79 0.0014234 389830000 649350 710850 470020 729770 761720 749200 716250 770970 780490 FALSE TRUE 563536.7523 706180.3795 697323.2441 895475.4323 746563.2623 778022.2088 646788.1852 606104.0652 688221.3613 0.818830661 1.026094828 1.013225226 1.30114449 1.084772 1.130482505 0.93979673 0.880681855 1 19.39251315 2.166774327 7.586228922 0.926381563 1.070240994 0.178954224 0.121648149 0.365496175 33.00236776 0.051371501 0.03461536 146.8163177 -2.166774327 0.143859431 DLEEALEMGVDWSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DLEEALEMGVDWSLR 15 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;;;; 169.23 2.81E-06 98384000 163427 146069 96257 112125 130869 130937 150812 164721 154271 FALSE TRUE 141829.7079 145109.4631 142807.2072 137584.695 128264.9629 135974.2311 136186.2755 129496.696 136033.2581 1.042610534 1.066720485 1.049796271 1.011404835 0.942894147 0.999566084 1.001124852 0.951948794 1 17.05359989 3.579832444 3.31994723 0.978224523 1.054537537 0.725140754 0.020650524 0.122233378 2.52847711 0.005802481 0.008898298 3800.427429 -3.579832444 0.076313014 DLEEDHACIPIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLEEDHACIPIK 12 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;; 142.08 6.11E-05 3316090000 4415390 4112140 3004980 3683250 3866290 3073680 4166000 5128110 7612310 FALSE TRUE 3831885.024 4085127.082 4458198.379 4519588.207 3789358.393 3191926.459 3761981.961 4031503.583 6712391.384 0.570867341 0.608594888 0.664174379 0.673320125 0.5645318 0.475527465 0.560453309 0.600606156 1 22.67839541 1.238739128 6.615834968 1.010810292 0.589272458 0.843556063 0.055545192 0.048818866 10.49534017 0.092631676 0.015244648 17.3276285 -1.238739128 -0.421537834 DLEEDHACIPIKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DLEEDHACIPIKK 13 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;; 188.91 3.71E-06 17260510000 30253800 25069500 20167100 22048600 22547900 16929700 33211700 38488600 28713500 FALSE TRUE 26255683.68 24904816.8 29919977.01 27055071.62 22099240.9 17580996.51 29990834.45 30258112.41 25319022.74 1.036994356 0.983640524 1.181719268 1.068566978 0.872831512 0.694378953 1.184517853 1.195074262 1 24.59371839 DLEELEVILRD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLEELEVILRD 11 1 Q96TC7;H0YMB1;Q96TC7-2 Q96TC7 RMDN3 Regulator of microtubule dynamics protein 3 0 131.82 0.0040062 14671000 49205 39612 30313 45034 48749 58001 37179 56291 52143 FALSE TRUE 42702.43458 39351.78616 44972.46819 55259.658 47778.99028 60232.336 33573.3863 44253.60771 45978.71394 0.928743562 0.855869658 0.978114965 1.201853059 1.03915456 1.310004801 0.730194114 0.962480329 1 15.48867849 7.375329698 9.605435778 0.997381508 0.058103873 0 0.162961805 0 0 0.036940567 0 23731746.35 -7.375329698 -0.939277635 DLEEWNQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLEEWNQR 8 0 P09497-2;P09497 P09497-2 CLTB Clathrin light chain B 0 ;;; 221.56 1.27E-05 6825100000 5743200 5109130 3351240 4050180 4938750 4834670 5089120 5832640 5211240 FALSE TRUE 4984221.569 5075567.789 4971910.873 4969835.272 4840478.538 5020662.883 4595577.926 4585375.326 4595173.144 1.084664584 1.104543317 1.081985535 1.081533844 1.053383275 1.092594931 1.000088088 0.997867802 1 22.13168779 2.23395056 24.98695523 0.999048414 1.082616478 0.906754489 0.012667028 31.53809272 170937.0113 0.005254023 0.003675301 171.3762202 -2.23395056 0.083568064 DLEFTIYDDDDVSPFLEGLEERPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DLEFTIYDDDDVSPFLEGLEERPQR 25 1 P25786;P25786-2;F5GX11 P25786 PSMA1 Proteasome subunit alpha type-1 0 ;;;;;;; 340.76 2.10E-88 3006519000 269588.9 257127.2 197857.8 202817.6 242437.8 230397.8 240289.4 319880 296759 FALSE TRUE 233962.0438 255438.1145 293542.4939 248870.436 237613.7621 239261.3525 216986.171 251476.1513 261676.4891 0.894088898 0.976159973 1.121776339 0.951061507 0.908043986 0.914340273 0.829215386 0.961019281 1 17.99742478 3.486502195 24.19346817 0.92080334 1.002089451 0.194437028 0.069236926 445.8361688 1149812.89 0.019938586 0.027318325 3065.506175 -3.486502195 0.081286111 DLEFTIYDDDDVSPFLEGLEERPQRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLEFTIYDDDDVSPFLEGLEERPQRK 26 2 P25786;P25786-2;F5GX11 P25786 PSMA1 Proteasome subunit alpha type-1 0 ; 248.03 8.05E-46 109514000 250960 211824 75486 66895 162127 137581 262210 269490 19144.1 FALSE TRUE 217795.0001 210432.5142 111991.2821 82084.53218 158900.9899 142873.8301 236780.9146 211861.6607 16880.90631 12.90185469 12.46571187 6.634198428 4.862566659 9.413060354 8.463635038 14.02655226 12.5503724 1 14.04310474 4.317527114 8.460095129 8.78896705 12.74420678 0.192075342 3.69497235 0.524255677 49.8564405 0.966081978 2.567517797 20774.33419 -4.317527114 3.955239733 DLEGENIEIVFAKPPDQK ddPTM_MDA-MB-175_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 ; 225.6 3.62E-19 489780000 2221600 1307990 1294490 1394930 1195960 846010 1837320 2236900 2169100 FALSE TRUE 1928009.931 1299397.728 1920509.694 1711670.177 1172162.736 878556.5521 1659136.989 1758556.343 1912671.469 1.008019392 0.679362739 1.004098051 0.894910707 0.612840603 0.459334792 0.867444836 0.919424152 1 20.86715766 1.76885546 3.199053812 0.96819879 0.774715926 0.157014593 0.170863492 0.427215982 8.650741273 0.125211151 0.048649643 58.72938592 -1.76885546 -0.193482864 DLEGSDIDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLEGSDIDTR 10 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;;; 203.29 4.84E-07 3212700000 5003600 3809330 2359670 2973470 3895120 3691820 3996380 4528200 4298450 FALSE TRUE 4342361.582 3784306.26 3500814.305 3648641.81 3817614.733 3833846.704 3608811.683 3559879.668 3790292.138 1.145653534 0.998420735 0.923626511 0.962628124 1.007208572 1.011491084 0.952119666 0.939209839 1 21.85387762 4.716664688 3.68393302 0.969081451 1.161004442 0.778316802 0.029034138 0.116688069 2.971140625 0.007637932 0.059214513 52079.24606 -4.716664688 0.191922991 DLEGYR ddPTM_MDA-MB-175_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 ; 150.07 0.024564 634690000 1169210 1119480 771040 920920 1039950 1084090 1136230 1192160 1174740 FALSE TRUE 1014695.936 1112126.062 1143917.523 1130028.961 1019257.03 1125795.644 1026038.589 937225.8614 1035863.575 0.979565225 1.073622134 1.104312913 1.0909052 0.983968404 1.086818448 0.990515174 0.904777312 1 19.98240258 2.036017483 5.384354626 0.94577218 1.054473949 0.444061486 0.047692671 0.140034997 10.45527191 0.02022342 0.012950863 108.646936 -2.036017483 0.108701769 DLEHLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DLEHLSK 7 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;; 111.01 0.0066756 1498440000 3342720 3231660 1271860 3467530 3959660 4111480 3548410 3712180 7524800 FALSE TRUE 2900971.083 3210431.013 1886935.75 4254885.684 3880870.513 4269651.296 3204285.744 2918359.195 6635226.716 0.43720753 0.483846468 0.284381504 0.641257016 0.584888909 0.643482352 0.48292031 0.439828105 1 22.66171433 1.234316292 24.97272352 1.000000745 0.500481717 0.684875708 0.106645005 77.2619366 454531.1534 0.204052798 0.026947629 17.1520602 -1.234316292 -0.499519028 DLEHSLQMEAYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLEHSLQMEAYER 13 0 Q9Y5S2 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 0 206.2 6.38E-08 73593000 44283 46738 31504 36106 53282 57010 46411 56716 50144 FALSE TRUE 38430.88935 46430.975 46739.43977 44304.41915 52221.79244 59203.21159 41910.06836 44587.72476 44216.03344 0.869161848 1.050093629 1.057069939 1.001998951 1.18106009 1.338953474 0.947847762 1.008406257 1 15.43228199 5.378643761 1.365500742 1.076520481 0.180360731 0.249747989 0.111967517 10.53890979 4.999841852 0.03364866 20.04440513 239135.3397 -5.378643761 -0.896159751 DLEIERPILGQNDNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DLEIERPILGQNDNK 15 1 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 0 ;; 210.9 1.50E-09 1071540000 513286 508218 384881 446816 464345 415278 563500 742290 601050 FALSE TRUE 445453.9546 504879.4825 571010.7389 548272.402 455105.443 431254.0134 508851.8567 583557.06 529994.5537 0.840487796 0.952612586 1.077389824 1.03448686 0.858698339 0.813695179 0.960107709 1.101062371 1 19.01561801 1.886039026 6.326921708 1.052801868 0.93490401 0.249835685 0.085073949 0.345953053 16.80952771 0.045870769 0.024581994 76.91995588 -1.886039026 -0.117897857 DLEKPFLLPVEAVYSVPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLEKPFLLPVEAVYSVPGR 19 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ; 207.22 2.99E-16 954990000 1930900 1806630 1280750 2333300 2132400 1997390 1919200 2514000 2095060 FALSE TRUE 1675726.673 1794762.129 1900124.984 2863111.427 2089969.412 2074230.886 1733076.279 1976400.664 1847384.394 0.90708067 0.97151526 1.028548791 1.549818997 1.131312692 1.122793336 0.938124348 1.069837263 1 20.81705265 3.994726516 24.96331775 1.128842813 0.95448139 0.202223075 0.162020672 422.7730719 2001338.393 0.04444321 0.088387522 9879.307788 -3.994726516 -0.174361423 DLELALS(ph)PIHNSSALPTTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLELALSPIHNSSALPTTGR 20 0 A0A087WUU7;Q96GX5-2;Q96GX5-3;Q96GX5 A0A087WUU7 MASTL Serine/threonine-protein kinase greatwall 1 DLELALS(1)PIHNSSALPTTGR;DLELALS(1)PIHNSSALPTTGR;DLELALS(1)PIHNSSALPTTGR;DLELALS(1)PIHNSSALPTTGR 223.68 4.06E-25 673963000 259833 326850 81982.6 174691 397136 368134 287368 350236 297380 TRUE FALSE 225495.4107 324702.9008 121629.6596 214357.2615 389233.7706 382296.3532 259499.0956 275340.7569 262224.0752 0.859934049 1.238265024 0.463838644 0.817458357 1.484355585 1.457899519 0.989608202 1.050020891 1 18.00044062 3.282207861 24.99453848 1.175651267 0.845756044 0.328387128 0.248805381 184.8500013 105852.8354 0.0754506 0.097405711 1915.172342 -3.282207861 -0.329895223 DLELPLS(ph)PSLLGGPGPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLELPLSPSLLGGPGPER 18 0 P19419 P19419 ELK1 ETS domain-containing protein Elk-1 1 DLELPLS(0.5)PS(0.5)LLGGPGPER;DLELPLS(0.977)PS(0.023)LLGGPGPER;DLELPLS(1)PSLLGGPGPER;DLELPLS(1)PSLLGGPGPER 289.1 4.19E-49 316001000 409993 462409 333028 427743 566094 564669 512177 660671 684717 TRUE FALSE 355811.3863 459371.4048 494081.4547 524868.5858 554829.8369 586392.1818 462506.1534 519391.648 603770.5363 0.589315584 0.760837731 0.818326541 0.869317985 0.918941557 0.971216955 0.766029684 0.860246761 1 19.20364083 4.898288724 1.02341542 0.890921105 0.356770869 0.707693722 0.063809879 1.457126363 1.002902026 0.020918758 0.918616725 79120.44544 -4.898288724 -0.534150236 DLENGSHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DLENGSHIR 9 0 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 0 ;; 143.5 0.00010179 969500000 1242620 1111580 759540 897770 1159110 1027370 1159210 1251590 1123120 FALSE TRUE 1078404.619 1104277.958 1126856.085 1101622.4 1136045.979 1066893.589 1046789.993 983947.2184 990346.0331 1.088916987 1.115042542 1.137840762 1.112361097 1.14712024 1.077293747 1.056994179 0.993538809 1 19.91757317 2.094696368 1.602028753 0.99266092 1.120051427 0.88018361 0.018099971 0.118844089 0.582822644 0.014271996 0.005674134 124.3644826 -2.094696368 0.127390507 DLEPHSFGGLLEGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLEPHSFGGLLEGIR 15 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 0 ; 210.34 1.93E-09 273540000 489430 489350 286380 330400 469040 473700 457350 560720 370070 FALSE TRUE 424750.5854 486135.4276 424874.3259 405422.3698 459707.0217 491923.5455 412996.2674 440814.3915 326320.7462 1.301635248 1.48974723 1.302014447 1.242404519 1.408758184 1.507484741 1.265614498 1.350862293 1 18.31593119 0.960240459 2.040514184 0.553401122 1.366088533 0.608667843 0.089645007 1.40821593 2.828828558 2.881853377 0.023862088 9.125159398 -0.960240459 0.812687412 DLESAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DLESAEER 8 0 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;; 117.39 0.004859 2234570000 2886670 2871470 1728420 1941870 2502630 2671410 2790990 2917990 2883680 FALSE TRUE 2505189.246 2852607.124 2564289.693 2382801.263 2452832.559 2774180.871 2520320.219 2294000.546 2542774.635 0.985218749 1.121848191 1.008461252 0.937087082 0.964628373 1.091005405 0.991169325 0.902164319 1 21.27797217 2.743378039 0.08412551 0.765584897 1.219881733 0.085455266 0.062366941 65.00304805 6.271014192 17.53792318 15.89825382 553.8319917 -2.743378039 0.454296836 DLESAEERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DLESAEERR 9 1 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;; 119.62 0.0012799 523608000 618110 543760 289382 288330 581974 649980 651800 831070 385431 FALSE TRUE 536425.1974 540188.0048 429328.1031 353799.7333 570393.856 674985.1512 588588.5363 653352.1479 339865.7863 1.578344214 1.589415665 1.26322837 1.040998381 1.678291488 1.986034424 1.731826386 1.922382818 1 18.37460561 3.03402916 24.87224268 1.721597503 1.374243039 0.17548215 0.305937906 259.2690186 189500.5621 0.092242056 0.104592213 1081.506565 -3.03402916 -0.347354464 DLESLFHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLESLFHR 8 0 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 152.47 0.00045665 383160000 544960 562210 268250 530340 597820 611470 479170 667840 1220400 FALSE TRUE 472942.1552 558516.8055 397976.5972 650761.8027 585924.5516 634993.6466 432700.1672 525027.6131 1076125.702 0.439485977 0.519007031 0.369823522 0.604726568 0.544475938 0.59007386 0.402090728 0.487886882 1 20.03741518 1.238080197 24.99035849 1.000000573 0.494868245 0.814948732 0.075672068 4.744415969 246533.1451 0.104106591 0.018164069 17.30135819 -1.238080197 -0.505132329 DLESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLESLR 6 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;;; 160.69 0.020314 1808650000 2875090 2532980 1696960 2095290 2526900 3044960 2357910 2362730 2099880 FALSE TRUE 2495139.572 2516340.688 2517615.532 2571057.619 2476619.634 3162101.582 2129240.251 1857478.576 1851634.579 1.347533472 1.358983418 1.359671914 1.388534028 1.337531532 1.707735218 1.149924653 1.003156129 1 20.82036798 2.01253767 24.97551244 1.024224533 1.408431292 0.728529296 0.107789577 105.5775604 210313.7172 0.043152415 0.02907326 102.9289802 -2.01253767 0.384206759 DLETMRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLETMRR 7 1 O00629 O00629 KPNA4 Importin subunit alpha-3 0 67.035 0.069529 339520000 387170 321510 240090 266430 271130 318720 361610 373690 340530 FALSE TRUE 336004.5035 319397.9796 356198.3271 326927.0036 265735.0435 330981.3646 326541.1179 293779.3016 300272.9313 1.118996981 1.063692216 1.186248542 1.088766151 0.88497835 1.102268404 1.087481034 0.978374242 1 18.1959149 3.462245541 24.97625802 1.014203452 1.120460039 0.388982702 0.065711905 244.0974185 409837.0159 0.018658206 0.024096421 2898.982145 -3.462245541 0.106256587 DLEWVIFDEVHYINDVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLEWVIFDEVHYINDVER 18 0 Q15477 Q15477 SKIV2L Helicase SKI2W 0 ; 155.79 1.62E-08 57186000 89305 74905 64899 70434 71534 68631 83017 90686 108864 FALSE TRUE 77503.11798 74412.94412 96284.37347 86427.11622 70110.61335 71271.27898 74966.02412 71293.50462 95994.22194 0.80737274 0.775181491 1.003022594 0.90033665 0.730362848 0.742453843 0.780943088 0.742685374 1 16.55065995 3.251809962 24.99883021 0.787995863 0.873996045 0.115035565 0.096602766 448.3660574 845970.9603 0.028022226 0.035958768 1785.706019 -3.251809962 0.086000182 DLFAFQES(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLFAFQESPPR 11 0 E7EX48;P51957-3;P51957-2;P51957 E7EX48 NEK4 Serine/threonine-protein kinase Nek4 1 DLFAFQES(1)PPR;DLFAFQES(1)PPR;DLFAFQES(1)PPR;DLFAFQES(1)PPR 174.37 1.16E-05 417003000 692951 635216 451674 497481 648605 725085 684467 727168 746477 TRUE FALSE 601375.7696 631043.2243 670105.0572 610441.6646 635699.0295 752979.4891 618087.4957 571668.782 658229.3394 0.913626503 0.958698111 1.018041915 0.927399658 0.965771337 1.143947017 0.939015414 0.868494836 1 19.32823081 2.015480373 24.99998059 0.918524404 0.988971949 0.099030579 0.070652846 406.6094171 656650.192 0.028889142 0.019470168 103.6287769 -2.015480373 0.070447545 DLFDFSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLFDFSTR 8 0 U3KQC1;A0A0A0MQU0;Q9BV38;K7EIR0 U3KQC1 WDR18 WD repeat-containing protein 18 0 ; 147.29 0.0012555 281860000 629770 545710 339100 416350 553020 569690 528730 616350 553530 FALSE TRUE 546544.2989 542125.1951 503089.8942 510888.631 542015.984 591606.3429 477453.846 484548.3489 488092.314 1.119756004 1.110702176 1.030726934 1.046704929 1.110478425 1.212078793 0.978203984 0.99273915 1 18.89679451 2.183522895 24.99995682 0.990314576 1.09954404 0.553605002 0.04840896 72.27849158 32830.59563 0.020763905 0.013999033 152.5888835 -2.183522895 0.109229465 DLFDYS(ph)PPLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 138.55 3.56E-05 3708748000 1633040 1273990 1012280 1202850 1199400 1063180 1361030 1609480 2880090 TRUE FALSE 1417229.626 1265621.076 1501821.994 1475975.477 1175534.287 1104081.223 1229037.52 1265305.227 2539609.041 0.558050315 0.498352721 0.591359524 0.581182163 0.462880021 0.434744563 0.483947529 0.498228352 1 21.27617499 1.237616343 24.9987391 1.000000574 0.511500546 0.902316041 0.050291926 7.281179871 192657.4655 0.078633804 0.013311666 17.28288911 -1.237616343 -0.488500028 DLFEDELVPLFEK ddPTM_MDA-MB-175_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 ;;; 241.54 1.59E-16 224790000 1581360 1055852 791083 906488 940225 828652 1117955 1456902 1629310 FALSE TRUE 1372379.269 1048916.039 1173653.385 1112319.955 921516.362 860530.7786 1009535.896 1145354.845 1436694.828 0.955233667 0.73008966 0.816912097 0.774221452 0.641414129 0.598965599 0.702679425 0.797215124 1 20.45432222 1.261010117 3.024344316 1.04090748 0.739780852 0.400412066 0.097005124 0.379738209 4.49920718 0.27084984 0.026052457 18.23938193 -1.261010117 -0.301126629 DLFFELDAMDHLESFIAECDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLFFELDAMDHLESFIAECDRR 22 1 Q9NQ29-3;Q9NQ29;Q9NQ29-2;A8MYV2 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 0 204.78 7.31E-23 46436000 33097 29668 16398 21282 29688 24450 27741 33437 29758 FALSE TRUE 28723.14759 29473.10895 24328.12765 26114.40338 29097.26688 25390.60732 25050.68209 26286.75776 26240.04314 1.094630349 1.123211147 0.927137487 0.995211907 1.108887921 0.967628261 0.954673815 1.00178028 1 14.67948247 4.256587569 24.99932924 0.995505301 1.108920832 0.502601152 0.047658772 205.331426 284743.6108 0.012001508 0.031611251 18054.58744 -4.256587569 0.113415531 DLFPYEESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DLFPYEESK 9 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;;;;; 206.78 2.97E-05 1515433000 5144050 4189300 3372480 3925680 3908260 3328360 4920670 5854650 6065690 FALSE TRUE 4464250.759 4161780.212 5003422.608 4817065.644 3830493.272 3456404.163 4443464.181 4602678.658 5348611.038 0.834656087 0.778104854 0.935462043 0.90061992 0.716165981 0.646224625 0.830769736 0.86053718 1 22.35073286 1.266460896 2.147575293 1.049086351 0.804716175 0.354294825 0.082675488 0.811549688 3.979312598 0.380362187 0.024269398 18.46974483 -1.266460896 -0.244370177 DLFPYEESKEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLFPYEESKEK 11 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ; 142.83 3.42E-05 660880000 895780 750330 304520 319990 608180 428250 1026830 1116830 172767 FALSE TRUE 777400.4034 745401.0328 451786.8906 392648.6202 596078.4079 444725.0546 927248.1846 878004.5957 152342.6821 5.102971753 4.89292313 2.965596275 2.577403882 3.912747234 2.919241335 6.086594853 5.763352619 1 17.21696067 2.266103268 24.99945501 4.666796533 3.702787705 0.007519804 1.581440044 601.9230958 546341.623 0.597880525 0.463008112 184.5454184 -2.266103268 -0.964008828 DLFQVAFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLFQVAFNR 9 0 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 131.41 0.0017637 355610000 1672920 1439630 1423980 1341320 722500 891700 1156940 1476820 1322770 FALSE TRUE 1451839.383 1430172.976 2112621.491 1645887.207 708123.6635 926004.276 1044740.137 1161013.536 1166393.638 1.244725054 1.2261495 1.811242297 1.411090693 0.607105218 0.793903744 0.895701162 0.995387405 1 20.15362332 3.263136952 20.51045366 0.87511173 1.436933282 0.68106606 0.191792242 18.70736756 15611.50573 0.057923144 0.07468312 1832.892321 -3.263136952 0.561821552 DLFSLDSEDPSPAS(ph)PPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLFSLDSEDPSPASPPLR 18 0 Q9BTK6;H3BTX0 Q9BTK6 PAGR1 PAXIP1-associated glutamate-rich protein 1 1 DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPSPAS(1)PPLR 369.65 1.46E-107 2653030000 923200 775180 479044 620470 745350 775800 808180 908310 825250 TRUE FALSE 801196.7809 770087.7915 710711.2807 761357.1968 730518.9933 805645.528 729802.828 714074.975 727689.8851 1.101014041 1.058263702 0.976667802 1.046266016 1.003887794 1.107127561 1.002903631 0.98129023 1 19.47296423 6.723998784 0.013520826 9.07E-08 2.183936331 0.226416433 0.041026142 17792.6607 32.13715608 2310.617783 2913.29303 5296619.611 -6.723998784 2.18393624 DLFVMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLFVMR 6 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 105.42 0.076756 121810000 235230 266570 155250 196040 271660 274620 221650 265490 296060 FALSE TRUE 204143.7595 264818.8841 230329.4193 240553.8783 266254.4975 285184.8091 200154.4171 208717.0295 261060.1241 0.781979861 1.014398063 0.882284953 0.921450103 1.01989723 1.092410456 0.766698544 0.799497933 1 17.99402258 2.215602234 24.99999243 0.840056996 0.953422463 0.158340485 0.103030883 368.2652297 401010.7348 0.041610312 0.028073975 164.2866348 -2.215602234 0.113365468 DLGEELEALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLGEELEALK 10 0 P35579;P35749;P35749-2;P35749-4;P35749-3 P35579;P35749 MYH9;MYH11 Myosin-9;Myosin-11 0 123.86 0.0010487 24372000 49199 53329 44394 57768 59180 62873 40712 60015 119060 FALSE TRUE 42697.2275 52978.67829 65863.08689 70885.10733 58002.43378 65291.76499 36763.75651 47181.25929 104984.8624 0.406698895 0.504631592 0.627357939 0.675193601 0.552483781 0.621915993 0.350181499 0.449410117 1 16.6798218 1.233133842 24.99857473 1.000000752 0.523268444 0.682602062 0.102116895 113.3391191 522042.1239 0.228830724 0.027193133 17.10542394 -1.233133842 -0.476732307 DLGEELEALKTELEDTLDSTAAQQELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLGEELEALKTELEDTLDSTAAQQELR 27 1 P35579 P35579 MYH9 Myosin-9 0 ; 302.8 4.57E-71 8563400000 2665890 2347010 1809250 1822630 1855440 2034720 2754740 3159200 2569740 FALSE TRUE 2313585.882 2331592.337 2684209.352 2236485.999 1818520.374 2112996.995 2487585.739 2483629.665 2265948.265 1.021023259 1.028969802 1.184585453 0.986997821 0.80254276 0.932500105 1.097812239 1.096066359 1 21.11168349 -1.789947516 19.89552793 0.068846768 1.021500498 0 0.103038578 0 0 0 0.025103041 0.016220061 1.789947516 0.95265373 DLGEELEALRGELEDTLDSTNAQQELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLGEELEALRGELEDTLDSTNAQQELR 27 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 ;;; 192.18 3.61E-18 309244000 161399 153624 88395 98703 149955 138936 151534 186692 90000 FALSE TRUE 140069.7132 152614.8338 131143.1177 121115.0247 146971.1889 144280.9578 136838.256 146769.3686 79360.30253 1.764984618 1.923062652 1.652502744 1.526141167 1.851948445 1.818049494 1.724265806 1.849405357 1 16.2761299 1.234684823 25 0.999998904 1.764477905 0.819983057 0.112468773 47.72399477 307788.8463 0.206433755 0.028071204 17.16662117 -1.234684823 0.764479001 DLGGACPPQDHDMQGLAERIS(ph)VL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLGGACPPQDHDMQGLAERISVL 23 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 DLGGACPPQDHDMQGLAERIS(1)VL;DLGGACPPQDHDMQGLAERIS(1)VL 147.55 7.02E-08 92140000 178225 169942 64619 100664 122687 56322 213250 163930 137481 TRUE FALSE 154672.1147 168825.6398 95868.96454 123521.2998 120245.7687 58488.74379 192569.0478 128874.8452 121228.1528 1.275876198 1.392627339 0.790814364 1.018915961 0.991896403 0.482468325 1.588484551 1.06307687 1 16.88736525 4.257926334 24.99781395 1.012166732 1.334251982 0.211602496 0.273197406 404.991565 522765.5023 0.06747933 0.177957051 18110.32876 -4.257926334 0.32208525 DLGGFDEDAEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLGGFDEDAEPR 12 0 A0A5F9UP49;Q9BRK5;A0A5F9UJX7;Q9BRK5-6;G3V1E2;Q9BRK5-4;Q9BRK5-3;H0Y3T6 A0A5F9UP49 SDF4 45 kDa calcium-binding protein 0 106.62 0.004426 213380000 225480 194230 158740 171020 215150 236010 229120 256950 278220 FALSE TRUE 195682.2467 192954.0903 235507.195 209852.7049 210868.9359 245089.4574 206899.9777 202003.2421 245329.1485 0.797631459 0.786511067 0.95996418 0.855392464 0.859534781 0.999022981 0.843356686 0.823396825 1 17.90435913 4.261458693 24.98200684 0.894981467 0.792071138 0.344357208 0.063902146 284.8613398 310780.7733 0.015766054 0.041652266 18258.23083 -4.261458693 -0.102910329 DLGHPVEEEDELES(ph)GDQEDEDDESEDPGKDLDHI ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLGHPVEEEDELESGDQEDEDDESEDPGKDLDHI 34 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 1 DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;DLGHPVEEEDELES(0.984)GDQEDEDDES(0.016)EDPGKDLDHI 384.69 1.30E-166 3192610000 509234 310776 240316 280945 288419 274755 344034 402548 442947 TRUE FALSE 441937.4367 308734.492 356533.6214 344737.8562 282680.0262 285325.0026 310669.6356 316466.2428 390582.3103 1.131483493 0.790446684 0.91282583 0.88262537 0.723739961 0.730511841 0.795401193 0.81024213 1 18.57526708 DLGKMAHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLGKMAHIR 9 1 A0A1W2PS94;A0A2R8Y358;Q9BXT5 A0A1W2PS94 TEX15 Testis-expressed sequence 15 protein 0 66.692 0.07009 0 122460 82262 101890 106490 126340 125040 114910 126890 107590 FALSE TRUE 106276.6007 81721.61551 151164.3448 130670.1821 123826.0812 129850.3697 103766.0459 99755.56096 94870.83277 1.120224179 0.861398737 1.593370063 1.37734832 1.305207065 1.368706966 1.093761305 1.051488198 1 16.53367699 2.096836897 5.58439544 1.041704809 1.272850902 0.241308666 0.18816155 0.313739363 14.84367385 0.082800122 0.054957636 124.9789574 -2.096836897 0.231146093 DLGLSESGEDVNAAILDESGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLGLSESGEDVNAAILDESGKK 22 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 287.93 2.52E-46 358880000 312370 221210 214730 230970 203020 171200 291380 291610 241560 FALSE TRUE 271089.5131 219756.8569 318574.1462 283415.2687 198980.2992 177786.1748 263122.0124 229251.4708 213003.052 1.272702483 1.03170755 1.495631838 1.330569051 0.934166423 0.834664917 1.235296912 1.076282563 1 17.70051458 3.245082078 24.99595818 1.030977452 1.2799409 0.435236375 0.150343178 166.4406977 637942.8768 0.045359169 0.05716112 1758.255877 -3.245082078 0.248963448 DLGMMIHEQGDVIDSIEANVENAEVHVQQANQQLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLGMMIHEQGDVIDSIEANVENAEVHVQQANQQLSR 36 0 O15400-2;O15400 O15400-2 STX7 Syntaxin-7 0 ; 291.82 3.74E-92 110430000 58447 47143 35117 38980 52484 56817 38921 58444 55672 FALSE TRUE 50723.08086 46833.31453 52099.69866 47831.00477 51439.67108 59002.78676 35146.44741 45946.20541 49090.51958 1.033256142 0.954019532 1.061298579 0.974343013 1.047853466 1.201918156 0.715951832 0.935948648 1 15.58315682 2.240590036 24.99999994 0.887795773 1.038890035 0.384500751 0.09603278 57.83247147 712441.4247 0.036610517 0.026920197 174.0163423 -2.240590036 0.151094262 DLGTESQIFISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLGTESQIFISR 12 0 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ; 140.09 0.00013814 358226000 379267 461975 228316 247704 412119 481195 347808 373800 363993 FALSE TRUE 329145.905 458940.2558 338730.3813 303948.9791 403918.6382 499706.883 314077.6337 293865.7789 320962.1622 1.025497531 1.429888971 1.055359233 0.946993181 1.258461856 1.556902781 0.978550342 0.91557764 1 18.2920437 2.036582342 24.9991268 0.950349397 1.210227894 0.28892179 0.183132424 203.0337306 138745.5429 0.07570388 0.051039401 108.7883381 -2.036582342 0.259878497 DLGVLDVIFHPTQPWVFSSGADGTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLGVLDVIFHPTQPWVFSSGADGTVR 26 0 Q14137;Q14137-2 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 179.58 3.09E-23 0 129270 113650 56799 70683 100440 108550 106250 110790 93640 FALSE TRUE 112186.642 112903.4257 84267.18638 86732.65547 98441.44051 112725.9887 95945.89135 87098.42067 82569.98588 1.358685493 1.367366416 1.020554691 1.050413834 1.192218207 1.365217488 1.161994765 1.054843594 1 16.33332984 7.999991161 0.033879273 2.31E-07 2.90634858 0.269938602 0.124743017 3903.684581 13.07288975 379.1131853 825.5769039 99997964.66 -7.999991161 2.906348349 DLGYIYFYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DLGYIYFYQR 10 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;; 184.49 3.61E-06 2148361000 2168369 2181073 1428595 1704630 2026970 1860453 1846411 2186465 2446100 FALSE TRUE 1881813.543 2166745.388 2119468.32 2091692.295 1986637.263 1932025.831 1667346.345 1718906.475 2156924.845 0.872452069 1.00455303 0.982634293 0.969756689 0.921050758 0.895731641 0.77302014 0.796924603 1 21.04054448 2.711672372 2.375270018 0.841469535 0.96016918 0.262056727 0.069609701 0.323429491 3.608415806 0.026536938 0.02389018 514.8401071 -2.711672372 0.118699644 DLHEEMNYITAIIEEQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLHEEMNYITAIIEEQPK 18 0 P49354;P49354-2;E9PQP6;H0YCW1;E9PN85 P49354 FNTA Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha 0 ; 103.13 0.00054444 49215000 69909 61942 43411 54188 58847 47240 62805 83084 73653 FALSE TRUE 60670.34852 61535.09892 64404.7048 66492.21361 57676.05983 49057.35337 56714.18077 65317.13316 64945.82625 0.934168553 0.947483502 0.991668111 1.023810419 0.888064148 0.755358061 0.873253665 1.005717179 1 15.98694919 3.220940644 24.93393737 0.907335526 0.973610254 0.183532334 0.073014589 496.4992947 702591.9371 0.025277206 0.028725169 1663.185324 -3.220940644 0.066274728 DLHPDLEGQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLHPDLEGQLK 11 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 94.82 0.0082192 103900000 365180 285980 177740 234410 308780 296010 280040 340490 317010 FALSE TRUE 316920.5378 284101.3785 263695.6585 287636.3732 302635.8821 307397.6962 252881.7639 267678.8632 279533.4389 1.133748216 1.016341299 0.94334209 1.028987352 1.082646439 1.099681303 0.904656577 0.957591565 1 18.09266135 2.235994685 24.99999959 0.952754304 1.044798058 0.39527384 0.056054385 74.82152871 728972.3945 0.023247168 0.01648371 172.1847504 -2.235994685 0.092043753 DLHQGIEAAS(ph)DEEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLHQGIEAASDEEDLR 16 0 A0A0C4DGG1;Q9UKS6;E9PIY1 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 DLHQGIEAAS(1)DEEDLR 202.17 2.00E-11 155570000 126440 117810 100720 113710 129650 117620 112470 137290 152430 TRUE FALSE 109730.6336 117036.0984 149428.5289 139529.5934 127070.2187 122144.9175 101562.6767 107931.6019 134409.899 0.816388037 0.87074017 1.111737528 1.038090159 0.945393305 0.908749418 0.755619024 0.80300337 1 17.03627987 2.496747243 4.279231713 0.837160536 0.962968665 0.16926485 0.101516864 0.315130472 13.70129447 0.03959052 0.032522661 313.8681465 -2.496747243 0.125808129 DLHQGIEAASDEEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLHQGIEAASDEEDLR 16 0 A0A0C4DGG1;Q9UKS6;E9PIY1 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 0 ;;; 270.42 3.98E-35 2135580000 2071230 2004490 1324030 1750530 2030130 2099590 1756930 2272810 2194840 FALSE TRUE 1797511.708 1991322.373 1964335.337 2148014.592 1989734.385 2180362.586 1586543.199 1786787.269 1935368.516 0.928769737 1.028911216 1.014967083 1.109873688 1.028090707 1.126587814 0.819762844 0.923228447 1 20.88417687 2.24032254 24.99999993 0.912243874 1.040611059 0.427120499 0.068332231 42.35026577 600924.3662 0.026089294 0.019142572 173.9091932 -2.24032254 0.128367185 DLIDFDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DLIDFDDR 8 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;;; 208.35 0.00013031 3110660000 7372340 6084620 4083040 4584610 5887110 5564760 5601960 6872630 7298100 FALSE TRUE 6398066.59 6044649.731 6057611.801 5625615.772 5769968.029 5778839.918 5058682.781 5402971.557 6435326.932 0.994210031 0.939291786 0.941305992 0.874177152 0.896608376 0.897986999 0.786080153 0.839579965 1 22.61758201 4.246015569 0.866663321 0.868053893 1.010909899 0.299749547 0.055017402 1.44490044 1.396775601 0.021820365 0.172525258 17620.39211 -4.246015569 0.142856006 DLIDYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLIDYVR 7 0 D6RIC3;A0A0C4DGU5;A0A087X2G6;Q9Y3C1;Q9Y3C1-3;Q9Y3C1-2 D6RIC3 NOP16 Nucleolar protein 16 0 ; 105.12 0.018609 246010000 661220 587020 354780 457870 573820 583350 588780 626520 613660 FALSE TRUE 573838.1017 583163.827 526352.7947 561836.3816 562402.1047 605791.852 531680.2062 492543.5736 541113.8139 1.060475794 1.077710108 0.972721045 1.038296135 1.039341614 1.119527605 0.982566315 0.910240251 1 19.04557255 2.011343107 24.50976714 0.948017078 1.048099176 0.490302046 0.042316241 124.2383573 268448.4335 0.017089565 0.011509865 102.6462546 -2.011343107 0.100082098 DLIFCLENER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLIFCLENER 10 0 O00268;A0A0G2JRY5 O00268 TAF4 Transcription initiation factor TFIID subunit 4 0 98.048 0.013127 13770000 24780 28671 20428 22339 29725 25040 33323 36396 36014 FALSE TRUE 21505.26022 28482.65831 30307.04913 27411.41138 29133.53066 26003.305 30091.34059 28612.99863 31756.46595 0.677193119 0.896908943 0.954358372 0.863175752 0.917404686 0.818834975 0.947565785 0.901013314 1 14.95476275 4.735880203 5.05638138 0.910947329 0.666465112 0.690938022 0.04952407 0.08881887 7.324695191 0.011463442 0.075916281 54435.24768 -4.735880203 -0.244482217 DLIHDQDEDEEEEEGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DLIHDQDEDEEEEEGQR 17 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;R4GNE6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ;;;; 341.37 1.41E-72 13714900000 4352470 4455350 2817010 3275320 3963790 4132130 4295240 4833620 4497240 FALSE TRUE 3777280.062 4426082.512 4179325.458 4019031.466 3884918.334 4291095.715 3878688.286 3799987.978 3965581.41 0.95251608 1.116124486 1.053899801 1.013478492 0.979659206 1.082084888 0.978088175 0.958242332 1 21.91910097 2.117489869 9.772066286 0.973792291 1.034341069 0.221430037 0.047611526 0.388914804 31.42007282 0.018764243 0.012645447 131.0659467 -2.117489869 0.060548779 DLIHDVSFDFHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DLIHDVSFDFHGR 13 0 K7ELV2;Q96EE3;Q96EE3-1;K7EP88;K7ENI5 K7ELV2 SEH1L Nucleoporin SEH1 0 ;;;; 248.77 1.11E-17 793671000 749545 702016 417521 546002 642093 714854 641680 731134 723260 FALSE TRUE 650490.7291 697404.4107 619435.5521 669980.0992 629316.6055 742354.896 579449.9724 574786.6838 637757.0267 1.019966385 1.093526816 0.971272015 1.050525625 0.986765459 1.164008964 0.908574815 0.9012628 1 19.28264736 2.191872414 24.99999545 0.928079571 1.043649754 0.429664467 0.059934035 103.7772054 55568.4935 0.022991089 0.015500635 155.5508591 -2.191872414 0.115570183 DLILQCLDDKDESIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DLILQCLDDKDESIR 15 1 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4;A0A2R8Y4J3 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 ;; 229.16 4.56E-13 810340000 826680 724950 525170 561430 644270 564700 816410 950160 800270 FALSE TRUE 717432.1435 720187.7557 779143.9686 688911.2624 631450.2875 586424.3744 737234.6839 746975.6782 705662.9923 1.016678147 1.020583145 1.104130409 0.976261006 0.894832653 0.831026114 1.044740467 1.058544498 1 19.42861983 3.614284871 10.07700737 0.972907104 1.044399913 0.219528491 0.070204855 0.770239202 59.38655523 0.022259429 0.033024863 4114.194993 -3.614284871 0.071492809 DLIQSDIAALHHFYSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLIQSDIAALHHFYSK 16 0 Q9NRG4-2;Q9NRG4 Q9NRG4-2 SMYD2 N-lysine methyltransferase SMYD2 0 68.82 0.027719 325120000 100400 94130 61272 71994 88465 95974 99512 118810 80062 FALSE TRUE 87131.88562 93511.65383 90903.34414 88341.33806 86704.71958 99666.18188 89861.34156 93403.40608 70597.16157 1.234212307 1.324580929 1.287634547 1.25134405 1.228161553 1.411759052 1.27287471 1.323047613 1 16.10732256 1.235076438 24.99999969 0.999999589 1.293694008 0.745194862 0.053594424 48.60300756 348684.9557 0.089085039 0.012547092 17.18210776 -1.235076438 0.293694419 DLISHDEMFSDIYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 DLISHDEMFSDIYK 14 0 Q5W0H4;A0A0B4J2C3;P13693 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 ;;;;;;;;; 300.07 8.21E-44 16251400000 20226840 16763640 12852770 14927730 16074910 13890610 21089500 23286410 21712400 FALSE TRUE 17553811.85 16653518.55 19068412.56 18317299.25 15755050.74 14424990.76 19044243.54 18306792.44 19145584.81 0.916859528 0.869835981 0.995969188 0.956737516 0.822907783 0.753436936 0.994706807 0.956188731 1 24.19050839 DLISLDS(ph)SPAKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLISLDSSPAKER 13 1 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLIS(0.001)LDS(0.541)S(0.458)PAKER 75.239 0.019337 169570000 235300 239800 148850 148550 222020 182250 251040 317740 150740 TRUE FALSE 204204.5088 238224.738 220834.3579 182280.5479 217602.2364 189261.2754 226694.1794 249793.7737 132919.6889 1.53629993 1.792245678 1.661411937 1.37135852 1.637095589 1.423876906 1.705497367 1.879283466 1 17.0201953 3.968855341 24.53209199 1.55390512 1.67991194 0.063012225 0.241765885 1712.776535 1349126.618 0.063716838 0.110536531 9307.977858 -3.968855341 0.12600682 DLISLDSS(ph)PAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLISLDSSPAK 11 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLISLDSS(1)PAK;DLISLDS(0.009)S(0.991)PAK 272.59 4.77E-27 300240000 1458280 1340410 1242700 1511870 1446540 1103520 1597990 1896070 3598100 TRUE FALSE 1265564.603 1331604.758 1843673.877 1855163.191 1417756.684 1145973.128 1443017.176 1490610.186 3172736.717 0.39888737 0.419702256 0.581098919 0.584720182 0.446856077 0.361193894 0.454817813 0.469818431 1 21.59729638 1.238576518 9.239748777 1.003332711 0.466396786 0.848522788 0.071085609 0.031744721 41.33966156 0.106661394 0.018805132 17.32114183 -1.238576518 -0.536935926 DLISLDSS(ph)PAKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DLISLDSSPAKER 13 1 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLISLDS(0.479)S(0.52)PAKER;DLISLDS(0.068)S(0.932)PAKER;DLISLDS(0.435)S(0.565)PAKER 168.05 1.87E-05 1146850000 1677910 1546590 1093460 1129140 1454790 1227220 1754710 2094860 1038670 TRUE FALSE 1456169.942 1536430.348 1622260.913 1385528.495 1425842.525 1274431.948 1584538.494 1646890.491 915879.6159 1.58991413 1.677546177 1.771259984 1.512784509 1.556801244 1.391484127 1.73007289 1.798151703 1 19.80479846 3.720725539 24.00006735 1.54194405 1.679370716 0.111012969 0.219822363 1317.428861 1772819.607 0.060846581 0.09051451 5256.849444 -3.720725539 0.137426666 DLKDEIVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLKDEIVR 8 1 P15924;P15924-3 P15924 DSP Desmoplakin 0 65.719 0.057951 363140000 841620 678820 480760 509470 706150 721810 640570 808900 732500 FALSE TRUE 730397.7846 674360.7867 713257.144 625152.9503 692098.9966 749578.4978 578447.62 635923.0299 645904.6845 1.130813574 1.044056194 1.104276159 0.967871832 1.071518775 1.160509462 0.89556189 0.984546242 1 19.30096176 2.23233275 24.99994079 0.962455923 1.073857317 0.485483743 0.057904906 132.8900812 533442.0599 0.022861985 0.015846799 170.7390064 -2.23233275 0.111401394 DLKDYFSK ddPTM_MDA-MB-175_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 ; 100.58 0.005472 3879300000 10916000 7606100 4160800 4675000 6234800 5384300 9277300 10417600 2781390 FALSE TRUE 9473422.942 7556135.028 6172976.797 5736530.203 6110739.678 5591437.505 8377588.874 8189877.31 2452577.243 3.862639992 3.080895842 2.516934712 2.338980442 2.491558501 2.279821164 3.415830795 3.339294342 1 21.22586714 4.612214904 2.466728265 2.59855429 3.976538452 0.30226177 0.664271836 0.565864773 5.14531633 0.173883985 1.451260633 40946.32267 -4.612214904 1.377984163 DLKDYFTK ddPTM_MDA-MB-175_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 ; 112.75 0.002719 4113300000 10382000 7143700 4889100 5756000 6678000 5197800 9752300 11033600 3947300 FALSE TRUE 9009992.395 7096772.564 7253485.113 7062987.775 6545120.865 5397762.729 8806523.447 8674150.504 3480654.691 2.588591284 2.03891888 2.083942751 2.029212433 1.880428094 1.550789495 2.530134193 2.492103146 1 21.73092726 4.746599693 4.204690782 2.00915404 2.638928616 0.16027757 0.44169221 0.491527085 19.52862677 0.108940625 0.941360439 55795.56676 -4.746599693 0.629774576 DLKEEFTEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLKEEFTEALR 11 1 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 139.78 3.55E-05 189680000 321060 292700 208020 265620 303480 237020 338330 411570 340820 FALSE TRUE 278631.1075 290777.2344 308619.1678 325933.0807 297441.3417 246138.3128 305518.8087 323558.9583 300528.6479 0.927136596 0.967552466 1.026920961 1.084532483 0.989727082 0.819017803 1.016604609 1.076632663 1 18.197143 2.007725701 24.99054462 1.044638689 0.972875744 0.149549847 0.070301715 324.9314771 1051060.964 0.030467719 0.02049844 101.7948253 -2.007725701 -0.071762945 DLKNPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLKNPDR 7 1 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 58.981 0.096935 817960000 2676100 2434500 1546600 1899300 2069900 2118800 2860900 3208200 2173300 FALSE TRUE 2322446.605 2418507.609 2294540.933 2330565.094 2028713.04 2200311.607 2583450.358 2522151.396 1916374.95 1.211895723 1.262022137 1.197334026 1.216132101 1.058620099 1.148163415 1.348092323 1.316105388 1 20.86994843 4.212382217 23.52020352 1.199594966 1.236958938 0.025763782 0.105155087 576.2093352 517700.5842 0.028690319 0.059764564 16307.30585 -4.212382217 0.037363972 DLKPANILLDEHGHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLKPANILLDEHGHVR 16 1 P25098;E9PRV7 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 0 77.562 0.015212 113700000 93702 85388 56623 88349 94691 67660 94961 106730 99962 FALSE TRUE 81319.04329 84827.08061 84006.07219 108409.9908 92806.83436 70262.92398 85751.69684 83906.62007 88144.60624 0.922564032 0.962362693 0.953048357 1.229910659 1.052892949 0.797132428 0.972852458 0.951920074 1 16.42758467 DLKPENILLDEEGHIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLKPENILLDEEGHIK 16 1 E9PGT3;Q15418-4;Q15418;Q15418-2;Q15418-3;B7Z3B5;F2Z2J1;Q15349;Q15349-3;Q15349-2;E9PMM7;D6R910;A0A2R8Y7S9;B4DG22;B1AXG1;B7ZB17;P51812 E9PGT3;B4DG22 RPS6KA1;RPS6KA2;RPS6KA3 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1;Ribosomal protein S6 kinase alpha-2;Ribosomal protein S6 kinase alpha-3 0 ; 147.56 6.10E-07 359288000 340170 280770 203231 221482 250752 203448 295400 412720 352320 FALSE TRUE 295215.6726 278925.6034 301514.1914 271772.8732 245762.5258 211274.7762 266752.1535 324463.0398 310669.131 0.950257503 0.897822074 0.970531544 0.874798447 0.791074817 0.680063628 0.85863746 1.044400642 1 18.24501937 1.755080605 7.164923591 1.020242561 0.85687997 0.401871405 0.081856899 0.14749597 23.84686824 0.051362737 0.023551238 56.89585201 -1.755080605 -0.163362591 DLKPENLLLASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLKPENLLLASK 12 1 Q13555-8;Q13555-9;Q13555-10;Q13555-3;Q13555-7;Q13555-4;Q13555-2;A0A2Q3DQE3;Q13555;Q8WU40;Q5SWX3;Q13555-6;Q13555-11;Q13555-5;E9PBE8;E9PF82;E9PBG7;E7EQE4;A0A5F9ZH90;H7BXS4;A0A5F9ZHY2;A0A5K1VW76;A0A5F9ZHM9;A0A5F9ZH21;A0A5F9ZHR5;D6RFJ0;A0A5F9ZH50;Q9UQM7;Q9UQM7-2;Q13557;D6R938;Q13557-8;Q13557-6;Q13557-11;Q13557-12;Q13557-10;Q13557-3;Q13557-4;Q13557-9;Q13557-5 Q13555-8;E9PF82;Q13557 CAMK2G;CAMK2B;CAMK2D;CAMK2A Calcium/calmodulin-dependent protein kinase type II subunit gamma;Calcium/calmodulin-dependent protein kinase type II subunit alpha;Calcium/calmodulin-dependent protein kinase type II subunit delta 0 123.88 0.00030361 367770000 811950 468090 422950 491150 468800 359150 700470 788380 773910 FALSE TRUE 704648.7503 465015.086 627490.0347 602673.1143 459471.7972 372966.7329 632538.5272 619791.0722 682419.2414 1.032574563 0.681421416 0.919508121 0.88314203 0.67329842 0.546536074 0.926906055 0.908226255 1 19.3802988 2.043402326 24.99999389 0.938561904 0.785010525 0.217610994 0.138957468 207.2380662 119369.4681 0.056959911 0.038402335 110.5101901 -2.043402326 -0.153551379 DLKPSNLLLNTTCDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLKPSNLLLNTTCDLK 16 1 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 133.86 2.87E-05 293660000 487530 417870 274910 350610 353900 285200 479740 596340 526580 FALSE TRUE 423101.6753 415124.9845 407857.3955 430221.3592 346858.0824 296171.8285 433214.8886 468817.3317 464328.3123 0.911212313 0.894033324 0.878381492 0.92654561 0.747010409 0.637850031 0.93299262 1.00966777 1 18.82478573 2.008154564 24.99976694 0.995266202 0.833413038 0.416072583 0.085870382 186.673927 572291.473 0.038148504 0.02567171 101.8953965 -2.008154564 -0.161853165 DLLDDLKSELTGKFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLLDDLKSELTGKFEK 16 2 P08758;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 ; 177.67 1.64E-09 1443870000 3540200 1906700 1837910 1622700 1489140 937890 2541200 3567900 1352640 FALSE TRUE 3072353.6 1894174.762 2726729.423 1991158.836 1459509.027 973971.2352 2294754.815 2804932.35 1192732.44 2.57589506 1.58809696 2.286119948 1.669409475 1.223668426 0.816588199 1.923947683 2.351686142 1 20.18583902 7.79224225 0.839049051 1.61213936 200 0.272965832 0.499962829 725.7898726 3.140519427 0.184970952 273162.5907 61978669.65 -7.79224225 198.3878606 DLLDTVLPHLYNETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLLDTVLPHLYNETK 15 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 226.93 7.99E-13 1006010000 1905350 1512380 1136980 1327120 1457960 1299730 1902570 2136580 1904900 FALSE TRUE 1653553.17 1502445.076 1686827.331 1628462.88 1428949.448 1349731.454 1718059.054 1679688.994 1679704.892 0.984430764 0.894469667 1.004240292 0.969493443 0.850714584 0.803552732 1.022833869 0.999990535 1 20.67977636 DLLEEEEAWEASHKNDLQDTEIS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLLEEEEAWEASHKNDLQDTEISPR 25 1 Q9NS91 Q9NS91 RAD18 E3 ubiquitin-protein ligase RAD18 1 DLLEEEEAWEASHKNDLQDT(0.047)EIS(0.953)PR 210.32 1.13E-25 75788000 122530 101760 84353 98552 100740 91236 123630 144860 105050 TRUE FALSE 106337.35 101091.5319 125146.3929 120929.7379 98735.47109 94745.90796 111640.3816 113882.8163 92631.10867 1.147965857 1.091334578 1.351019055 1.305498116 1.065899702 1.022830335 1.205214784 1.229423008 1 16.49920916 3.229996324 24.99964765 1.123715682 1.223557609 0.243091114 0.101543638 347.2638021 1013681.275 0.033107472 0.038122898 1698.229278 -3.229996324 0.099841927 DLLFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLLFGR 6 0 O43633;M0R1L7;M0QXX8 O43633 CHMP2A Charged multivesicular body protein 2a 0 ;;; 130.01 0.037103 1456800000 1051640 1107890 742259 773640 1126160 1175560 1069280 1185580 1128520 FALSE TRUE 912663.1095 1100612.198 1101217.935 949306.7863 1103751.619 1220784.554 965581.3902 932052.9432 995107.6512 0.917150128 1.106023249 1.106631965 0.95397396 1.109178105 1.226786421 0.970328576 0.93663529 1 19.92449308 2.040964608 24.99954754 0.96069805 1.072173127 0.230125082 0.086752979 190.9999074 116561.083 0.035092461 0.023659307 109.8916283 -2.040964608 0.111475077 DLLHNEDRHDDYFQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLLHNEDRHDDYFQER 16 1 Q8N684-2;Q8N684;Q8N684-3 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 0 121.82 6.24E-05 165440000 242370 228790 97659 149070 214080 287310 164860 185980 162740 FALSE TRUE 210340.1904 227287.0634 144887.219 182918.6219 209820.2268 298363.0016 148871.9026 146209.6243 143501.0626 1.465774445 1.583870247 1.009659555 1.27468479 1.462151033 2.079169284 1.037427179 1.018874855 1 17.13070189 2.051804731 24.99991519 1.015987013 1.461370862 0.399234065 0.265802707 103.6475665 50017.69216 0.112301472 0.075713621 112.6690756 -2.051804731 0.445383849 DLLHPS(ph)PEEEKRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLLHPSPEEEKRK 13 2 P42677 P42677 RPS27 40S ribosomal protein S27 1 DLLHPS(1)PEEEKRK;DLLHPS(1)PEEEKRK 115.31 0.00035175 611760000 1329640 874130 766020 680770 804780 656780 1356190 1375010 523900 TRUE FALSE 1153924.705 868387.7825 1136469.834 835349.2334 788766.4525 682046.7516 1224666.903 1080974.812 461965.1388 2.497861003 1.879769077 2.460077046 1.808251669 1.70741553 1.476403075 2.650994198 2.339948886 1 18.81742446 3.725433423 24.31017573 1.914967586 2.239289062 0.14758296 0.477397625 1394.172576 2581861.033 0.136017025 0.203209744 5314.145281 -3.725433423 0.324321476 DLLHPSLEEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DLLHPSLEEEK 11 0 H0YMV8;Q71UM5;C9JLI6 H0YMV8 RPS27L 40S ribosomal protein S27;40S ribosomal protein S27-like 0 ;;;;; 217.83 1.11E-11 2358380000 4592380 4647410 1773676 3700430 4917040 3789210 5425100 6717170 6436770 FALSE TRUE 3985485.347 4616880.858 2631431.646 4540669.189 4819200.524 3934983.361 4898974.637 5280755.469 5675822.383 0.702186411 0.813429411 0.463621211 0.800001988 0.849075288 0.693288672 0.863130364 0.930394771 1 22.43639801 1.322261112 0.540685565 1.217731734 0.68617336 0.500224981 0.104560859 3.334598181 0.844404993 1.135172107 0.074487444 21.00202213 -1.322261112 -0.531558373 DLLHPSPEEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DLLHPSPEEEK 11 0 P42677 P42677 RPS27 40S ribosomal protein S27 0 ;;;;;;; 190.53 2.23E-06 6275090000 12085830 10316620 5851310 9308190 10721220 8597850 12785850 14518850 14937060 FALSE TRUE 10488656.94 10248849.44 8681023.087 11421756.81 10507888.7 8928614.853 11545880.23 11414106.91 13171217.78 0.796331601 0.778124666 0.659090392 0.867175457 0.797791736 0.677888332 0.876599296 0.866594654 1 23.6508854 1.308876362 1.123568436 1.090870455 0.766335939 0.56035751 0.065746675 1.091275572 1.270889469 0.419235755 0.020937879 20.36462242 -1.308876362 -0.324534515 DLLHPSPEEEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLLHPSPEEEKR 12 1 P42677 P42677 RPS27 40S ribosomal protein S27 0 82.505 0.0095893 548890000 896680 883060 554700 650570 826540 684690 968850 1061600 1005000 FALSE TRUE 778181.4661 877259.1207 822954.7754 798291.8618 810093.4711 711030.4674 874891.0761 834585.1014 886190.0449 0.878120298 0.989922112 0.92864367 0.900813394 0.914130638 0.802345356 0.987249948 0.941767633 1 19.75725659 DLLHPSPEEEKRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLLHPSPEEEKRK 13 2 P42677 P42677 RPS27 40S ribosomal protein S27 0 ; 167.14 1.95E-05 384990000 652990 496200 132632 163583 420670 334320 710290 776210 36860.3 FALSE TRUE 566695.717 492940.4295 196773.2788 200727.0204 412299.49 347181.5067 641406.1851 610223.532 32502.71733 17.43533352 15.16612979 6.054056246 6.175699661 12.68507756 10.68161481 19.73392497 18.77453894 1 14.98827272 7.99999444 2.40E-20 9.788197476 15.23507693 0 6.150120199 0 0.368893714 6.054475523 6.054475523 99998719.8 -7.99999444 5.446879457 DLLIAYYDVDYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DLLIAYYDVDYEK 13 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 250.94 1.05E-17 960383000 2014970 1689930 1356030 1595070 1503720 1472310 1859820 1987360 1613710 FALSE TRUE 1748686.609 1678828.739 2011810.644 1957255.023 1473798.914 1528950.718 1679454.943 1562378.53 1422939.042 1.228925876 1.179831805 1.413841763 1.375501666 1.035742832 1.07450191 1.180271883 1.097993999 1 20.44044243 3.234543173 24.99917626 1.087771316 1.299141215 0.654712591 0.079860868 69.82480833 434495.6534 0.025348326 0.029800372 1716.102299 -3.234543173 0.211369898 DLLIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLLIFR 6 0 H3BPB8;P34949-2;P34949;F5GX71 H3BPB8 MPI Mannose-6-phosphate isomerase 0 122.5 0.044655 133280000 227120 209440 119090 150270 199560 188210 234230 235810 249390 FALSE TRUE 197105.5166 208064.1748 176682.3223 184391.1002 195589.1464 195450.5605 211514.4107 185383.8666 219907.3983 0.896311439 0.946144497 0.803439646 0.838494301 0.889415945 0.888785743 0.961833991 0.843008776 1 17.74653662 2.581530605 3.014568585 0.91748891 0.872476938 0.17633354 0.054488221 0.581101246 10.16760588 0.020731318 0.017475131 381.5316805 -2.581530605 -0.045011972 DLLLDPAWEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLLLDPAWEK 10 0 O43707;O43707-2;F5GXS2;O43707-3;K7EP19;D6RH00;P12814-3;P12814;P12814-2;P12814-4;P35609-2;P35609;A0A494C1A0;Q08043;A0A494C166;A0A494C033;A0A494C0Q3 O43707;P12814-3 ACTN4;ACTN3;ACTN1;ACTN2 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2;Alpha-actinin-3 0 ; 114.5 0.0031355 92093000 315190 260010 262090 378110 304090 256152 307140 366180 1049750 FALSE TRUE 273536.8429 258301.9772 388837.6006 463965.6545 298039.2039 266006.3332 277353.6101 287875.2566 925649.7509 0.295507931 0.279049367 0.420069903 0.501232409 0.321978376 0.287372554 0.29963127 0.310998038 1 19.82010688 1.237044633 24.99999671 1.000000809 0.339786406 0.898799693 0.069654228 12.43321628 204964.974 0.113498276 0.018497865 17.26015268 -1.237044633 -0.660214403 DLLPYGFAIHHAGMTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLLPYGFAIHHAGMTR 16 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 88.992 0.003436 592300000 740930 736200 537080 504580 692940 687940 621640 768850 599120 FALSE TRUE 643014.2232 731363.8537 796813.6844 619152.601 679151.8497 714405.497 561353.4485 604437.4107 528292.7161 1.217155194 1.384391326 1.508280656 1.171987768 1.285559746 1.352291022 1.06258033 1.144133531 1 19.01097799 1.906946324 0.761892489 0.965241357 1.345460756 0.534283207 0.104441561 0.983105617 0.825417058 0.286039453 0.051188785 80.71352668 -1.906946324 0.380219399 DLLQFFKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLLQFFKPR 9 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 193.82 3.02E-05 969850000 1039430 884460 529250 694730 891980 819640 968300 1125040 913250 FALSE TRUE 902066.6919 878649.924 785197.0702 852479.0648 874231.3431 851172.0812 874394.415 884458.9511 805286.6254 1.120180894 1.091102095 0.975052913 1.058603282 1.085615128 1.056980278 1.08581763 1.098315709 1 19.61914285 DLLSDLQDIS(ph)DSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLLSDLQDISDSER 14 0 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;Q9UQ88-9;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;J3KS35;E7ESP2 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 DLLSDLQDIS(0.996)DS(0.004)ER;DLLSDLQDIS(0.773)DS(0.227)ER 309.35 1.17E-55 2693800000 1833400 1429640 1091920 1453740 1562940 1415040 1527860 1964350 2946500 TRUE FALSE 1591111.545 1420248.601 1619976.164 1783833.886 1531840.552 1469477.504 1379688.372 1544289.039 2598168.127 0.612397454 0.546634602 0.623507058 0.686573693 0.589584845 0.565582146 0.531023515 0.5943761 1 21.30906336 1.238771647 10.49766305 1.001269356 0.592072866 0.897079035 0.043246389 0.021223313 63.99998428 0.062819707 0.011242021 17.328926 -1.238771647 -0.409196489 DLLVEGLAEILHQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLLVEGLAEILHQK 14 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 0 ; 173.68 2.66E-06 164041000 547080 514790 384160 408470 487890 450730 623980 683430 618760 FALSE TRUE 474781.9919 511408.3106 569941.0609 501219.3566 478181.9435 468069.8748 563466.5156 537283.813 545610.8977 0.870184217 0.937313226 1.044592517 0.91863883 0.876415676 0.857882195 1.032725919 0.984738053 1 19.05751293 2.222673398 24.99937598 1.002550006 0.922365455 0.37781264 0.053128256 297.3952689 467963.4413 0.023188333 0.015689127 166.9834379 -2.222673398 -0.080184551 MCINTEWGAFGDDGSLEDIRTEFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MCINTEWGAFGDDGSLEDIRTEFDR 25 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;; 194.75 1.10E-18 718760000 152295 146689 69014.9 83658.9 132677 149825.1 111879 153144 33421 FALSE TRUE 132168.8299 145725.3903 102390.7365 102654.9319 130036.9873 155588.9685 101028.9918 120395.3474 29470.00745 4.484859059 4.944871172 3.474404838 3.48336973 4.41251966 5.279570044 3.428197022 4.085351779 1 14.8469598 1.168832765 3.019581776 8.68E-11 4.218163217 0.71750649 0.628701634 0.31283844 3.030868859 3.525962871 0.165546608 14.75138389 -1.168832765 4.218163216 DLLYFDGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DLLYFDGLR 9 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ;;;;; 152.63 0.00018614 657956000 1135371 1229474 866129 1069879 1179283 1231436 1156902 1334152 1735710 FALSE TRUE 985328.8457 1221397.504 1284991.881 1312811.379 1155817.576 1278810.14 1044705.822 1048853.977 1530516.341 0.643788517 0.798029705 0.839580635 0.857757179 0.755181467 0.835541644 0.682583906 0.685294204 1 20.54558702 4.739756559 22.72330428 0.79334621 0.643788357 0.225371211 0.092011259 49.15436908 933504.7616 0.022622962 0.134765015 54923.29185 -4.739756559 -0.149557853 S(ph)VDEVNYWDKQDHPISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVDEVNYWDKQDHPISR 17 1 F5H5P2;P12694;P12694-2 F5H5P2 BCKDHA "2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial" 1 S(1)VDEVNYWDKQDHPISR 199.6 1.68E-17 0 350600 269460 169880 256910 301970 273500 268900 331040 82269 TRUE FALSE 304267.3217 267689.8995 252034.5362 315245.3421 295961.3878 284021.722 242822.1194 260249.6722 72543.25254 4.194288387 3.690073027 3.47426573 4.345619077 4.079792089 3.915205233 3.347273673 3.587510389 1 16.14655381 1.169373633 2.581784219 1.15E-14 3.863892805 0.89033936 0.312629744 0.210851518 1.33332283 1.952855464 0.083735446 14.76976662 -1.169373633 3.863892805 DLMHGLITLMLDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLMHGLITLMLDSR 14 0 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 ; 142.97 9.25E-06 184508000 263020 275780 194800 235000 279810 268670 304400 317690 336460 FALSE TRUE 228261.2406 273968.383 289005.9316 288360.3418 274242.3284 279005.9088 274879.3349 249754.4658 296684.0821 0.769374747 0.923434723 0.974120113 0.971944095 0.92435808 0.94041415 0.926505166 0.841819568 1 18.178568 4.73570091 5.412286716 0.932088801 0.763382051 0.605856652 0.042533729 0.112318145 12.37230986 0.011145448 0.070440425 54412.77942 -4.73570091 -0.16870675 DLMLMSHLQDNIQHADPPVQILYNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLMLMSHLQDNIQHADPPVQILYNR 25 0 Q99613-2;Q99613;B5ME19 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 209.76 1.24E-25 663450000 197760 191150 114830 143160 182700 196430 164290 216110 169590 FALSE TRUE 171625.5149 189894.3231 170362.1721 175666.6661 179064.6274 203986.7892 148357.1811 169896.5583 149541.2634 1.147679985 1.269845652 1.139231863 1.174703637 1.197426205 1.364083629 0.992081902 1.136118249 1 17.1901841 2.216811674 24.99989887 1.060078086 1.211823711 0.53254569 0.07567024 199.0217807 228769.1868 0.029671974 0.020023806 164.7447842 -2.216811674 0.151745625 DLMPHDLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLMPHDLAR 9 0 P55084-2;P55084;B5MD38;C9JEY0;C9JE81;C9K0M0 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ; 142.55 0.00010406 533520000 682960 660170 425290 759000 797230 815230 577750 774010 727900 FALSE TRUE 592705.1056 655833.2998 630961.6665 931342.5506 781366.6828 846592.4256 521719.8939 608493.9849 641848.4912 0.923434601 1.021788333 0.983038326 1.451031767 1.217369353 1.318991066 0.812839636 0.948033676 1 19.29187326 2.230269655 24.99999184 0.921593666 1.155463103 0.311877174 0.162632952 236.1509183 712066.2887 0.069674287 0.047854018 169.9298427 -2.230269655 0.233869437 DLMSWINGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLMSWINGIR 10 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 136.57 0.00026585 338020000 283050 286620 197261 223276 261370 289070 231710 337140 292180 FALSE TRUE 245644.2253 284737.1743 292657.0794 273974.2284 256169.2484 300190.71 209238.7999 265045.2346 257638.8133 0.953444173 1.105179653 1.135919995 1.063404325 0.994296027 1.165161049 0.812140055 1.028747304 1 17.97499043 2.255841621 24.99996171 0.958383277 1.070500684 0.323384864 0.083048072 288.0219144 416672.8771 0.02968678 0.022939224 180.2360332 -2.255841621 0.112117407 DLMVGDEASELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLMVGDEASELR 12 0 P61160 P61160 ACTR2 Actin-related protein 2 0 ;;; 217.78 8.34E-11 1567270000 1682490 1520150 980020 1163500 1392060 1526930 1523470 1755920 1515330 FALSE TRUE 1460144.684 1510164.035 1453960.95 1427690.458 1364360.73 1585671.985 1375724.114 1380430.173 1336189.414 1.092767738 1.130202065 1.088139851 1.068479097 1.021083325 1.18671198 1.029587647 1.033109646 1 20.3496931 2.039040035 24.99952848 1.022648199 1.095264878 0.418340762 0.042795307 151.0263222 96710.00455 0.016996099 0.011458757 109.4057215 -2.039040035 0.072616679 DLNAVAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLNAVAFR 8 0 A0A3B3ISG5;P14735 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 111.74 0.0073876 112860000 242660 299050 140050 138200 253780 283890 284480 241150 159220 FALSE TRUE 210591.8662 297085.5209 207778.6484 169580.4223 248730.2745 294811.432 256891.1734 189581.9491 140397.193 1.499972056 2.116036044 1.479934492 1.207861914 1.771618572 2.099838506 1.829745794 1.35032578 1 17.09915457 1.493639035 3.133796072 1.022525885 1.717124078 0.423987179 0.276978394 0.248698149 4.664963783 0.33924783 0.076460399 31.1629839 -1.493639035 0.694598193 DLNES(ph)PVK ddPTM_MDA-MB-175_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 105.13 0.0046641 1357410000 3442130 2008460 1787610 2040440 2006580 1854290 2484580 2896730 3572180 TRUE FALSE 2987243.799 1995266.294 2652104.175 2503753.088 1966652.984 1925625.736 2243625.814 2277286.832 3149880.95 0.948367207 0.633441811 0.841969655 0.794872291 0.624357877 0.611332862 0.712289083 0.722975525 1 21.58686587 1.237775996 24.5694476 1.000000388 0.728990303 0.381843015 0.10512788 16.14330683 505093.8885 0.144588347 0.024770052 17.28924371 -1.237775996 -0.271010085 DLNFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLNFER 6 0 Q9UN36;Q9UN36-5;G3V578;H0YJT9;A0A0A0MS87;Q9UN36-2;Q9UN36-3;Q9UN36-6;Q9UN36-4;G3V5H8;G3V4S9;G3V5L7;A0A0U1RR50;G3V2I9 Q9UN36 NDRG2 Protein NDRG2 0 ;;; 149.4 0.024761 882820000 1188850 1331260 816320 943820 1309970 1252890 1229910 1456750 1256040 FALSE TRUE 1031740.46 1322514.865 1211095.082 1158128.756 1283904.16 1301089.489 1110633.518 1145235.349 1107552.382 0.931550035 1.194087871 1.093487858 1.045664995 1.15922658 1.174743073 1.002781932 1.034023643 1 20.0789435 2.21152336 24.98714513 1.016405516 1.104034047 0.232005508 0.074676884 307.3171761 284012.6095 0.028958167 0.01952937 162.7508854 -2.21152336 0.087628531 DLNHVCVISETGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLNHVCVISETGK 13 0 P00492 P00492 HPRT1 Hypoxanthine-guanine phosphoribosyltransferase 0 ; 154.65 4.63E-05 787390000 1284200 1147090 779340 986820 1211640 962500 1310960 1493750 1482470 FALSE TRUE 1114489.716 1139554.69 1156231.431 1210892.564 1187530.735 999527.9978 1183823.301 1174323.187 1307214.085 0.852568626 0.871742971 0.884500438 0.926315419 0.908443956 0.764624562 0.905607822 0.898340371 1 20.318064 1.121228003 1.87337054 1.074477406 0.873248276 0.447868987 0.043998319 1.179620778 3.033502802 0.468844735 0.012165623 13.21989492 -1.121228003 -0.20122913 DLNQYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DLNQYR 6 0 P02786;G3V0E5;H7C3V5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ;; 111.81 0.064042 985690000 1045480 1000680 597770 743690 934450 923270 1027270 1030260 918540 FALSE TRUE 907317.1691 994106.4672 886853.5714 912556.1811 915856.2732 958788.7943 927645.5135 809946.9165 809951.2476 1.120212077 1.227365808 1.094946855 1.126680382 1.130754815 1.183761118 1.145310309 0.999994653 1 19.62747555 1.730362052 4.9066134 0.998623898 1.148558828 0.736783068 0.036492529 0.075815501 4.408180793 0.022331221 0.009342951 53.74796822 -1.730362052 0.14993493 DLNYCFSGMSDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 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 ;;;;;;;;;;;;; 246.5 3.46E-17 27145920000 9182220 8663750 2524189 5291893 9165660 8805740 7974520 9193790 8174980 FALSE TRUE 7968766.362 8606837.256 3744895.243 6493498.187 8983281.298 9144502.516 7201152.278 7227769.555 7208543.177 1.105461418 1.193977347 0.519507916 0.900805895 1.246199277 1.268564576 0.998974703 1.002667165 1 22.78127629 3.276305508 24.92931615 1.091145728 0.919481456 0.157684885 0.197319472 334.0732234 220642.5866 0.060050972 0.077523606 1889.31994 -3.276305508 -0.171664272 DLPDEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 162.31 0.0029707 514790000 1205900 1090300 728240 878410 1148300 1089900 1147200 1379400 1180400 FALSE TRUE 1046537.26 1083137.748 1080419.3 1077866.416 1125451.077 1131829.158 1035944.721 1084426.045 1040854.457 1.005459748 1.040623634 1.038011888 1.035559207 1.081276128 1.087403864 0.995282975 1.041861364 1 19.98933692 4.738564836 15.5917784 1.04062149 1.005458978 0.122421466 0.029023076 0.109677869 16162.48654 0.007174336 0.039957966 54772.78655 -4.738564836 -0.035162511 DLPDGHAAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLPDGHAASPR 11 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 DLPDGHAAS(1)PR;DLPDGHAAS(1)PR;DLPDGHAAS(1)PR;DLPDGHAAS(1)PR 153.14 2.10E-05 4883730000 3857080 3889430 2873340 3502280 4384090 4695590 4674990 5003340 4939040 TRUE FALSE 3347357.105 3863880.078 4262896.835 4297526.203 4296855.186 4876232.386 4221610.189 3933414.677 4355152.318 0.768597023 0.887197461 0.978816933 0.986768289 0.986614215 1.119646807 0.969336979 0.903163515 1 22.05429175 4.589339919 1.815587915 0.988778892 0.732270359 0.660650993 0.052801805 0.436844007 1.869679095 0.015868753 0.173290928 38845.42873 -4.589339919 -0.256508533 DLPEHAVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 DLPEHAVLK 9 0 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;;;;;;; 132.01 0.00031705 13995175000 25695320 20220270 13826716 16776390 19541328 16317181 22417180 25805960 24191710 FALSE TRUE 22299618.36 20087441.71 20513362.11 20585725.76 19152493.8 16944913.51 20243165.33 20287556.28 21331793.6 1.04537006 0.941666795 0.961633254 0.965025546 0.897837948 0.794350153 0.948966867 0.951047842 1 24.34650194 7.999999063 0.91377999 0.925380022 65.82017029 0.299010613 0.054944631 1383.889771 2.837359979 0.018823022 187416.571 99999784.13 -7.999999063 64.89479027 DLPHWNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLPHWNK 7 0 Q7LG56;A0A0C4DGZ6;H0YAV1;Q7LG56-2;Q7LG56-6 Q7LG56 RRM2B Ribonucleoside-diphosphate reductase subunit M2 B 0 ; 96.964 0.012345 440640000 875070 785440 545870 670360 760400 682290 822330 927430 932030 FALSE TRUE 759427.2824 780280.3929 809854.5578 822575.4838 745269.5277 708538.1378 742580.5632 729106.3118 821846.4752 0.924050057 0.949423544 0.985408568 1.000887037 0.906823294 0.862129557 0.903551436 0.887156341 1 19.64850939 3.212120583 23.6022071 0.905716411 0.965295674 0.290701919 0.040502397 134.9075546 120427.0472 0.012305166 0.01395837 1629.748472 -3.212120583 0.059579263 DLPLLLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLPLLLFR 8 0 A0A286YFA2;A0A286YF22;O43175;A0A2C9F2M7 A0A286YFA2 PHGDH D-3-phosphoglycerate dehydrogenase 0 ; 132.29 0.0022538 219900000 687530 413020 252490 298342 396350 399050 366880 443780 399540 FALSE TRUE 596671.1685 410306.8444 374595.0085 366085.111 388463.4104 414401.7117 331300.0341 348881.1005 352306.8364 1.693612235 1.164629244 1.063263524 1.039108735 1.10262808 1.176252258 0.94037356 0.990276272 1 18.42647294 4.806321625 2.139047805 1.039421537 1.948752201 0.90867854 0.064250753 0.253454457 1.123520166 0.018292111 0.470333328 64020.87789 -4.806321625 0.909330664 DLPS(ph)PDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLPSPDSR 8 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 DLPS(0.995)PDS(0.005)R;DLPS(1)PDSR 157.66 0.00039157 766200000 1350310 1347060 842320 967100 1256470 1282620 1276390 1502790 1386150 TRUE FALSE 1171863.112 1338211.074 1249668.769 1186694.836 1231468.705 1331963.221 1152605.894 1181430.053 1222280.926 0.958751043 1.094847384 1.022407159 0.970885507 1.007516913 1.08973575 0.942995894 0.966578164 1 20.22114448 2.206522252 24.9998504 0.968055459 1.024004102 0.242050274 0.045146654 266.6725204 208085.4096 0.017958859 0.01210895 160.8874811 -2.206522252 0.055948643 DLPTIPGVT(ph)SPSSDEPPMEASQSHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLPTIPGVTSPSSDEPPMEASQSHLR 26 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVT(0.608)S(0.364)PS(0.012)S(0.016)DEPPMEASQSHLR;DLPTIPGVT(0.522)S(0.465)PS(0.011)S(0.002)DEPPMEASQSHLR 137.64 5.08E-05 224700000 105331 76112 55130 96223 89338 96057 82923 99841 233520 TRUE FALSE 91411.24148 75612.01526 81791.0524 118071.9028 87560.34859 99752.37495 74881.14022 78490.77911 205913.5316 0.44393023 0.367202751 0.397210673 0.573405263 0.425228725 0.484438172 0.363653324 0.381183201 1 17.65167911 1.235756969 24.99996858 1.000000768 0.427296769 0.890440832 0.062881938 24.49938443 218417.2023 0.107151842 0.015883307 17.20905288 -1.235756969 -0.572703999 DLPTIPGVTS(ph)PSSDEPPMEASQSHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLPTIPGVTSPSSDEPPMEASQSHLR 26 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVT(0.094)S(0.678)PS(0.163)S(0.064)DEPPMEASQSHLR 100.45 7.64E-09 0 43318 33484 24796 43566 39102 32289 36015 37601 79268 TRUE FALSE 37593.41655 33264.0414 36787.42854 53458.32616 38323.9467 33531.17872 32522.27084 29560.31876 69897.02734 0.537839991 0.475900659 0.526308914 0.764815446 0.548291511 0.479722529 0.465288326 0.422912388 1 16.09294348 1.231002401 24.99954217 1.000000845 0.524705602 0.721105961 0.092304962 162.0098756 535818.1184 0.253446016 0.024611322 17.0216792 -1.231002401 -0.475295243 DLPTIPGVTSPSSDEPPMEAS(ph)QSHLRNSPEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDK 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPSSDEPPMEAS(0.359)QS(0.359)HLRNS(0.282)PEDK 122.89 9.63E-08 372250000 291450 194770 97233 139790 159320 126210 198720 240020 179890 TRUE FALSE 252934.1441 193490.543 144255.204 171531.4561 156149.8437 131065.3804 179448.165 188693.5908 158623.6091 1.594555473 1.219809233 0.909418244 1.081374059 0.984404809 0.826266538 1.131282827 1.189568135 1 17.27524799 4.63989572 2.918694555 1.033579683 1.634376518 0.748013796 0.106190516 0.175984443 2.344427246 0.029201028 0.218406762 43641.10314 -4.63989572 0.600796836 DLPTIPGVTSPSSDEPPMEAS(ph)QSHLRNSPEDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 33 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPS(0.001)S(0.003)DEPPMEAS(0.332)QS(0.332)HLRNS(0.332)PEDKR;DLPTIPGVTSPS(0.072)S(0.072)DEPPMEAS(0.285)QS(0.285)HLRNS(0.285)PEDKR;DLPTIPGVTSPSSDEPPMEAS(0.433)QS(0.433)HLRNS(0.134)PEDKR 230.67 4.47E-37 697220000 1356520 1002540 420910 600400 772020 587320 878090 1037250 513730 TRUE FALSE 1177252.445 995954.2487 624463.4839 736729.9965 756658.3124 609914.5804 792932.967 815442.1594 452997.4246 2.598806044 2.198587 1.378514424 1.626344779 1.670336897 1.346397457 1.750413852 1.800103301 1 18.78914332 4.405701282 3.804079101 1.554118624 2.532652877 0.713234175 0.23902972 0.113133754 3.146382435 0.059630293 0.194063917 25450.79086 -4.405701282 0.978534253 DLPTIPGVTSPSSDEPPMEASQS(ph)HLRNSPEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDK 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPSSDEPPMEAS(0.086)QS(0.512)HLRNS(0.402)PEDK 99.34 2.14E-05 174460000 240690 173090 81376 112560 143990 123690 165320 193520 146950 TRUE FALSE 208882.2067 171952.9604 120729.7058 138118.4684 141124.8807 128448.4343 149287.2918 152137.254 129577.7384 1.612022321 1.327025479 0.931716414 1.065912016 1.089113627 0.991284737 1.152106015 1.174100242 1 16.98345836 4.512106251 3.453318849 1.072754264 1.591385336 0.848788412 0.076848144 0.093555375 2.165153354 0.020474665 0.092659682 32516.68402 -4.512106251 0.518631073 DLPTIPGVTSPSSDEPPMEASQS(ph)HLRNSPEDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 33 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPSSDEPPMEAS(0.278)QS(0.361)HLRNS(0.361)PEDKR;DLPTIPGVTSPSSDEPPMEAS(0.126)QS(0.437)HLRNS(0.437)PEDKR 222.61 2.07E-36 581450000 998720 745220 453620 486640 689710 558640 781700 956410 662480 TRUE FALSE 866736.6216 740324.6008 672992.1493 597139.0498 675986.1204 580131.2423 705890.8543 751889.1643 584162.3691 1.483725531 1.267326757 1.15206351 1.022214168 1.157188748 0.993099304 1.208381251 1.287123588 1 19.1560099 4.623362667 2.063450969 1.130145802 1.536247145 0.614079401 0.093853136 0.40840762 2.316694978 0.026386828 0.283575762 42010.96589 -4.623362667 0.406101343 DLPTIPGVTSPSSDEPPMEASQSHLRNS(ph)PEDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 33 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPSSDEPPMEAS(0.184)QS(0.184)HLRNS(0.632)PEDKR 134.22 3.42E-08 182430000 70911 47108 28275 27170 46276 30361 53285 60595 38521 TRUE FALSE 61539.93168 46798.54445 41948.88457 33339.36377 45355.19814 31529.00732 48117.4289 47637.2308 33967.09126 1.811751592 1.377761319 1.234986071 0.981519539 1.335268828 0.928222175 1.41658962 1.402452463 1 15.05185006 4.7138964 2.180158805 1.206347948 1.951965398 0.565245831 0.173363556 0.479340117 2.714263302 0.045583871 0.681484152 51748.33725 -4.7138964 0.745617451 DLPVSEQQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLPVSEQQER 10 0 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2;H0YD73;E9PL38 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ; 200.56 6.00E-07 717540000 362080 313990 218786 260431 327030 322060 299650 332840 307300 FALSE TRUE 314230.2106 311927.379 324591.6414 319565.839 320522.7428 334449.8566 270589.9891 261664.7562 270971.3441 1.159643695 1.151145263 1.1978818 1.179334442 1.182865826 1.234262825 0.998592637 0.965654715 1 18.04778077 2.203337581 9.001778903 0.983272642 1.182991801 0.936189743 0.024124452 0.063216359 14.91910252 0.009869478 0.006702481 159.7120121 -2.203337581 0.199719158 DLPWRPAEDGHSHACR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLPWRPAEDGHSHACR 16 1 P55268 P55268 LAMB2 Laminin subunit beta-2 0 81.346 0.0084097 59444000 67799 80469 33938 55249 83243 93779 70018 68318 67018 FALSE TRUE 58839.19037 79940.39384 50350.53032 67794.12988 81586.62716 97386.73881 63227.66514 53708.72735 59095.20839 0.995667703 1.352739013 0.852023907 1.147201808 1.380596319 1.647963371 1.069928796 0.908850799 1 15.85075354 2.006849572 24.99884898 0.960357183 1.232459555 0.222490755 0.216371614 242.3911332 884649.5401 0.092239898 0.062029372 101.5896752 -2.006849572 0.272102373 DLQEQDADAGS(ph)ER ddPTM_MDA-MB-175_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 270.51 4.80E-32 3534500000 2793400 2523950 1824350 2021240 2498500 2639320 2682060 2811050 2687060 TRUE FALSE 2424245.112 2507370.006 2706611.762 2480193.435 2448784.738 2740856.348 2421954.234 2209928.833 2369398.828 1.023147764 1.058230458 1.142320039 1.046760641 1.033504663 1.156772898 1.022180903 0.93269601 1 21.17608963 1.999590098 24.99978942 0.96630993 1.076749131 0.499870041 0.045890819 10.43220696 636265.0175 0.018382903 0.012239115 99.90566114 -1.999590098 0.110439201 DLQGLTVEHAIDSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLQGLTVEHAIDSFR 15 0 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 205.68 4.28E-09 218360000 214420 204240 117530 143280 202140 184710 168450 215020 189490 FALSE TRUE 186083.8537 202898.334 174367.9011 175813.9139 198117.8095 191815.9132 152113.7449 169039.6463 167088.7081 1.113683 1.214315057 1.043564841 1.052219003 1.185704359 1.147988487 0.910377168 1.011676063 1 17.35025471 2.250019138 24.99989323 0.979211533 1.125828542 0.602968697 0.058179354 148.7469838 324532.1418 0.022180798 0.017028597 177.8357773 -2.250019138 0.146617009 DLQHPNEFIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DLQHPNEFIR 10 0 P53618;E9PP73;E9PP63;E9PKQ1 P53618 COPB1 Coatomer subunit beta 0 ;;;; 142.07 3.64E-05 4623857000 5661610 5572220 3580389 4178920 5458980 5314760 5342170 5980760 6120600 FALSE TRUE 4913413.894 5535615.72 5311877.096 5127807.657 5350356.978 5519222.256 4824087.176 4701821.016 5397029.641 0.910392238 1.025678213 0.984222332 0.950116638 0.991352158 1.022640716 0.893841149 0.871186806 1 22.36373418 2.226275351 24.99964156 0.909997608 0.982026194 0.250048744 0.046743064 246.8387753 502295.1948 0.018373622 0.012485724 168.3741248 -2.226275351 0.072028586 DLQIYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLQIYSR 7 0 O00159-3;F5H6E2;O00159-2;O00159;I3L3F5;I3L501;I3L3Y6 O00159-3 MYO1C Unconventional myosin-Ic 0 102.95 0.019743 220750000 317700 268570 177080 191540 271340 307880 266240 251890 275200 FALSE TRUE 275715.1401 266805.746 262716.4803 235032.0845 265940.8649 319724.3428 240420.0858 198025.2837 242666.1695 1.136191092 1.09947648 1.082625076 0.968540794 1.095912403 1.317548068 0.990744141 0.816039929 1 17.88861347 2.004357247 24.9990052 0.897433556 1.110655373 0.459780838 0.09540908 96.79798052 555360.0344 0.039488662 0.026507147 101.008343 -2.004357247 0.213221817 DLQQSIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLQQSIAR 8 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 83.623 0.041945 116720000 234500 212420 171900 201460 214340 209570 202700 268750 213260 FALSE TRUE 203510.2309 211024.599 255031.415 247204.5721 210075.0533 217632.2935 183042.1852 211279.9039 188048.6457 1.082221199 1.122180903 1.356199158 1.314577785 1.117131434 1.157319122 0.97337678 1.123538556 1 17.52074639 2.672636979 1.987716075 1.051424302 1.216471356 0.380143857 0.094372272 0.371724765 2.918491937 0.040608941 0.0347932 470.5838067 -2.672636979 0.165047054 DLQS(ph)PDFTTGFHSDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLQSPDFTTGFHSDK 15 0 E9PDR5;Q9P2D0-2;Q9P2D0;E7EPI0 E9PDR5 IBTK Inhibitor of Bruton tyrosine kinase 1 DLQS(0.988)PDFT(0.009)T(0.003)GFHSDK;DLQS(0.996)PDFT(0.004)TGFHSDK 147.9 2.34E-06 371600000 315428 236854 233691 287032 253402 212389 255151 308667 690560 TRUE FALSE 273743.3906 235298.0905 346704.7492 352207.0026 248359.796 220559.7423 230406.4953 242660.9641 608922.7835 0.449553536 0.386416959 0.569373915 0.57840996 0.407867471 0.36221299 0.378383765 0.398508597 1 19.21589977 1.236018415 24.98742869 1.000000743 0.439431269 0.843481857 0.075625971 28.4532438 279608.7568 0.134374482 0.02033435 17.21941587 -1.236018415 -0.560569474 DLQS(ph)PDFTTGFHSDKIEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLQSPDFTTGFHSDKIEAK 19 1 E9PDR5;Q9P2D0-2;Q9P2D0;E7EPI0 E9PDR5 IBTK Inhibitor of Bruton tyrosine kinase 1 DLQS(1)PDFTTGFHSDKIEAK;DLQS(1)PDFTTGFHSDKIEAK 289.23 1.02E-49 624820000 722260 435690 418040 383680 428700 362770 646340 679300 470410 TRUE FALSE 626811.511 432827.9237 620205.5423 470800.4082 420169.7087 376725.9966 583658.0463 534036.9813 414798.6657 1.511122293 1.043465082 1.49519657 1.135009457 1.012948554 0.9082141 1.407087569 1.287460702 1 18.66205173 4.754380906 23.97254907 1.179649938 1.511122735 0.250695667 0.187735241 2749.84402 4166726.409 0.046372531 1.09010541 56804.25995 -4.754380906 0.331472797 DLQSS(ph)PPSLPLGFLGEGDAVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DLQSSPPSLPLGFLGEGDAVTK 22 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLQS(0.163)S(0.674)PPS(0.163)LPLGFLGEGDAVTK;DLQS(0.108)S(0.891)PPS(0.001)LPLGFLGEGDAVTK;DLQS(0.184)S(0.815)PPS(0.001)LPLGFLGEGDAVTK 258.09 2.34E-37 394830000 235454 197148 145262 174138 198660 160101 232371 277039 236571 TRUE FALSE 204338.1573 195852.9218 215511.1891 213678.6944 194707.0547 166260.1891 209835.6962 217796.3658 208603.8459 0.979551247 0.938874933 1.033112252 1.024327685 0.933381903 0.797014017 1.005905214 1.044066876 1 17.67040623 2.017870708 24.99997183 1.025122652 0.952141767 0.186891205 0.065064837 387.8723271 542606.0633 0.028313795 0.01908544 104.2007171 -2.017870708 -0.072980885 DLQSSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DLQSSDR 7 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;; 203.07 0.00068531 13242500000 11056700 10703900 7507590 8500240 7547090 12274790 12132770 11861030 12918640 FALSE TRUE 9595529.081 10633585.38 11138285.64 10430349.41 7396917.675 12747009.11 10956135.83 9324641.037 11391413.1 0.842347565 0.933473774 0.977779099 0.915632619 0.649341536 1.119001568 0.961789002 0.818567544 1 23.44144339 2.700724514 24.99950991 0.949198451 0.876811204 0.170572117 0.113763582 1541.048848 1018218.309 0.040277022 0.035521589 502.0240398 -2.700724514 -0.072387247 DLQYITVS(ph)KEELSSGDSLSPDPWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLQYITVSKEELSSGDSLSPDPWK 24 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 DLQYIT(0.417)VS(0.583)KEELSSGDSLSPDPWK 121.09 7.85E-05 92381000 153100 131750 137930 123780 157990 93635 140500 187140 285480 TRUE FALSE 132867.4471 130884.5256 204633.4093 151886.1409 154846.3081 97237.19904 126874.3316 147121.5673 251730.8796 0.527815448 0.5199383 0.812905471 0.60336714 0.615126393 0.386274418 0.504007819 0.584439889 1 17.94152268 1.239628287 6.422996501 1.01242356 0.568800637 0.612457216 0.107764083 0.087127355 16.32599342 0.169316704 0.027919223 17.36314079 -1.239628287 -0.443622923 DLQYITVS(ph)KEELSSGDSLSPDPWKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLQYITVSKEELSSGDSLSPDPWKR 25 2 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 DLQYIT(0.007)VS(0.993)KEELSSGDSLSPDPWKR 173.03 2.63E-12 185580000 130840 98350 82653 68297 109540 70698 134930 163760 59687 TRUE FALSE 113549.1625 97703.93237 122624.2673 83804.8777 107360.3683 73417.79781 121844.5094 128741.1984 52630.87086 2.157463113 1.856399691 2.329892424 1.592314099 2.039874442 1.394956926 2.315076824 2.446115679 1 15.68362165 3.749026657 24.96580535 1.891156231 2.088766496 0.07692974 0.441756708 2820.467891 6727956.521 0.118542833 0.202503199 5610.824136 -3.749026657 0.197610265 DLRDDRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLRDDRDR 8 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 81.594 0.079928 0 45107 40229 13130 25470 29921 42744 43033 48315 8378.9 FALSE TRUE 39145.99566 39964.73305 19479.71192 31253.35278 29325.63064 44388.38934 38859.66628 37983.21324 7388.355987 5.298336427 5.409150983 2.636542142 4.230082151 3.969168607 6.00788449 5.259582287 5.140956026 1 12.85103766 DLREEVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLREEVEK 8 1 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 0 ; 125.97 0.0011302 375880000 669408 571592 376307 424725 535666 467678 678947 731468 401458 FALSE TRUE 580944.0367 567837.1745 558290.3239 521165.3028 525007.2946 485669.8753 613102.8244 575049.2605 353998.0926 1.641093692 1.604068458 1.577099808 1.472226302 1.483079445 1.371956193 1.731938215 1.624441692 1 18.43338206 1.234850226 24.99977703 0.999999198 1.564397254 0.755137848 0.100793796 57.09246261 384617.8432 0.189719511 0.026186463 17.17316037 -1.234850226 0.564398056 DLRPVDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLRPVDNR 8 1 P42285 P42285 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 ; 78.934 0.026759 485090000 476300 461850 262990 371160 421960 461730 438260 523890 456510 FALSE TRUE 413355.7482 458816.0769 390172.8436 455437.5508 413563.8216 479493.0519 395757.6127 411860.2004 402541.9079 1.026863887 1.139797045 0.969272605 1.131404065 1.027380786 1.191163063 0.983146363 1.023148627 1 18.61877946 DLS(ph)ENNDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLSENNDQR 9 0 Q8NBJ4-2;Q8NBJ4 Q8NBJ4-2 GOLM1 Golgi membrane protein 1 1 DLS(1)ENNDQR 124.89 0.00054217 192880000 277050 279850 208020 183290 252930 297890 224380 290340 393500 TRUE FALSE 240437.1405 278011.6469 308619.1678 224908.7959 247897.1878 309350.0211 202619.6621 228253.0504 346980.8783 0.692940607 0.801230455 0.889441428 0.648187869 0.714440488 0.891547749 0.583950514 0.657826021 1 18.40449663 1.228551106 24.97205296 1.000000551 0.732694006 0.406050192 0.100712014 443.9666613 1107543.357 0.334059195 0.025294886 16.92587409 -1.228551106 -0.267306544 DLS(ph)PEPAPDEGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLSPEPAPDEGPR 13 0 Q8TBE0-3;Q8TBE0-2;Q8TBE0 Q8TBE0-3 BAHD1 Bromo adjacent homology domain-containing 1 protein 1 DLS(1)PEPAPDEGPR 153.75 4.81E-05 394810000 318220 308510 237330 330650 407800 376650 361560 483990 628930 TRUE FALSE 276166.4207 306483.3775 352103.5818 405729.1362 399685.5778 391139.9692 326495.9668 380492.5049 554578.6119 0.497975246 0.5526419 0.634902923 0.731598961 0.720701393 0.7052922 0.588728018 0.686093002 1 19.08103245 -2 0.060825656 2.011318351 6.53E-20 0.50127402 0.096230917 815.1182433 4.802530918 157.9860589 39.32834264 0.01 2 -2.011318351 DLS(ph)PEPAPDEGPRR ddPTM_MDA-MB-175_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 107.98 0.00052211 1284330000 1465820 1540120 1011050 1145430 1645870 1579960 1728650 1857220 1180760 TRUE FALSE 1272108.173 1530002.85 1499997.162 1405517.388 1613120.407 1640742.084 1561005.789 1460067.956 1041171.898 1.221804176 1.469500717 1.440681567 1.349937884 1.549331489 1.575860899 1.499277681 1.402331314 1 19.98977685 1.238248733 4.041056878 0.951044437 1.450098236 0.654856939 0.100410768 0.148597198 4.297421297 0.219505512 0.02558136 17.3080736 -1.238248733 0.499053799 DLSELGSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLSELGSVR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 195.45 7.27E-05 620990000 665240 673380 478709 531530 640806 677450 629076 647580 657500 FALSE TRUE 577326.8485 668956.5224 710214.2736 652222.0104 628055.2143 703511.9399 568068.3063 509100.0565 579771.099 0.995784111 1.153828681 1.224990819 1.124964683 1.083281342 1.213430509 0.979814805 0.878105268 1 19.14512389 2.095993702 5.684018769 0.930010691 1.134599819 0.59507439 0.070387851 0.122825475 5.962140793 0.028669192 0.019051484 124.7365424 -2.095993702 0.204589127 DLSENNDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLSENNDQR 9 0 Q8NBJ4-2;Q8NBJ4 Q8NBJ4-2 GOLM1 Golgi membrane protein 1 0 ; 107.79 0.0068922 231940000 555450 585570 383240 414180 513740 685970 497730 600410 607590 FALSE TRUE 482045.8752 581723.3521 568576.1459 508225.8993 503517.5791 712359.7098 449460.2212 472016.9939 535761.4024 0.899739834 1.085788094 1.061248801 0.948604915 0.939816823 1.329621183 0.838918629 0.881020902 1 19.03123112 DLSHIGDAVVISCAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DLSHIGDAVVISCAK 15 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ;; 153.09 2.72E-06 3244330000 5411000 4671200 2685950 3641910 4353800 3741990 4875000 6007400 4941100 FALSE TRUE 4695922.64 4640514.58 3984884.404 4468861.329 4267167.898 3885946.777 4402223.25 4722764.26 4356968.787 1.077795796 1.065078684 0.914600172 1.025681281 0.979389137 0.891892269 1.010386685 1.083956413 1 22.05489335 1.989669605 24.62835906 1.047734042 0.989597516 0.096665186 0.061141101 790.7791047 1885268.874 0.026926586 0.016888176 97.64940572 -1.989669605 -0.058136525 DLSHILGIPQSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLSHILGIPQSWR 13 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4;Q63HN8-5 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 94.09 0.0053148 221000000 183160 177580 113640 133260 192970 197510 176330 199920 206460 FALSE TRUE 158954.9419 176413.4653 168596.6841 163518.7198 189130.2745 205108.3375 159229.5437 157168.6638 182052.534 0.873126775 0.969025047 0.926088093 0.898195242 1.038877462 1.126643684 0.874635141 0.863314892 1 17.4739953 4.745275033 22.94225319 0.954699472 0.873126657 0.102652146 0.08005615 717.6347749 2451843.392 0.021153203 0.190909792 55625.64153 -4.745275033 -0.081572815 DLSIEEQSECAQDFYHNVAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLSIEEQSECAQDFYHNVAER 21 0 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 0 213.48 3.84E-23 104170000 68615 64346 48017 49263 64462 62805 71276 77711 66828 FALSE TRUE 59547.3539 63923.30689 71238.18181 60448.91709 63179.33232 65221.14899 64363.66449 61093.1074 58927.66997 1.010516009 1.084775742 1.208908851 1.025815498 1.072150525 1.106800066 1.092248591 1.036747379 1 15.8466576 1.550616457 2.784942105 1.002211184 1.088659637 0.232108055 0.052947306 0.367892612 5.935938372 0.059691403 0.014081385 35.53173851 -1.550616457 0.086448453 DLSLDDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLSLDDFK 8 0 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 ; 127.02 0.0027782 254460000 832640 817740 643580 1023340 913030 797840 889740 1175170 1128380 FALSE TRUE 722604.5144 812368.2121 954817.4406 1255704.988 894862.4893 828533.4211 803453.1517 923869.0407 994984.2019 0.726247224 0.816463428 0.959630755 1.262035101 0.899373566 0.832710127 0.807503426 0.928526341 1 19.92431409 4.398733845 3.628237476 0.949453268 0.741928124 0.289517972 0.123670458 0.316758223 7.953267809 0.034031785 0.112769072 25045.73866 -4.398733845 -0.207525144 DLSLEVDRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLSLEVDRDR 10 1 E7EMW7;O95071-2;O95071;E5RFK7 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 0 ; 113.69 0.0015155 289540000 312520 291296 160945 197057 255455 284540 249233 270148 238243 FALSE TRUE 271219.6902 289382.4574 238778.5403 241801.8037 250371.9453 295486.4379 225062.422 212378.9525 210078.1839 1.291041674 1.377498853 1.1366175 1.151008635 1.191803645 1.406554609 1.071326959 1.010951963 1 17.68056682 2.06448737 7.940585461 1.016529906 1.250721168 0.614321513 0.087406453 0.16647283 17.93254329 0.037376167 0.025108019 116.0078477 -2.06448737 0.234191262 DLSSHQLNEFLAQTLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLSSHQLNEFLAQTLQR 17 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ; 211.99 1.98E-12 2148200000 2506160 2216330 1292270 1586450 2187930 2171380 2430110 2647300 2287170 FALSE TRUE 2174964.606 2201770.782 1917216.094 1946677.72 2144394.474 2254914.394 2194438.306 2081195.496 2016783.368 1.078432439 1.091723988 0.950630655 0.96523888 1.063274573 1.118074667 1.08808826 1.03193805 1 20.9436247 3.10659765 22.60842175 1.061723571 1.020555437 0.117671334 0.052635594 11.78137697 2455.466857 0.017355466 0.019679252 1278.196577 -3.10659765 -0.041168134 DLSSS(ph)PPGPYGQEMYAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 DLSSSPPGPYGQEMYAFR 18 0 O43741;O43741-2 O43741 PRKAB2 5-AMP-activated protein kinase subunit beta-2 1 DLS(0.001)S(0.025)S(0.975)PPGPYGQEMYAFR;DLS(0.003)S(0.03)S(0.967)PPGPYGQEMYAFR;DLSS(0.024)S(0.976)PPGPYGQEMYAFR;DLSS(0.037)S(0.963)PPGPYGQEMYAFR;DLSS(0.017)S(0.983)PPGPYGQEMYAFR;DLSS(0.003)S(0.997)PPGPYGQEMYAFR;DLS(0.02)S(0.161)S(0.819)PPGPYGQEMYAFR;DLSS(0.003)S(0.997)PPGPYGQEMYAFR;DLS(0.003)S(0.024)S(0.973)PPGPYGQEMYAFR;DLS(0.033)S(0.175)S(0.792)PPGPYGQEMYAFR 345.56 3.23E-90 5123900000 4943520 4813280 3262790 3810540 5026700 4917700 5002430 6051970 5414660 TRUE FALSE 4290221.307 4781661.247 4840686.157 4675781.347 4926678.505 5106887.101 4517295.109 4757803.312 4774545.063 0.898561277 1.001490442 1.013852858 0.979314529 1.031863442 1.069607059 0.946120531 0.99649354 1 22.18693184 4.738192976 6.440150082 1.003931788 0.896392946 0.521532041 0.031991114 0.100857887 24.86833872 0.007895008 0.047524443 54725.90796 -4.738192976 -0.107538843 DLSTIEPLKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLSTIEPLKK 10 1 P39687;H0YN26;O95626 P39687 ANP32A;ANP32D Acidic leucine-rich nuclear phosphoprotein 32 family member A;Acidic leucine-rich nuclear phosphoprotein 32 family member D 0 91.855 0.014094 0 339400 308270 202980 265710 232900 191080 349130 402390 435170 FALSE TRUE 294547.4301 306244.9541 301141.8069 326043.5166 228265.7457 198430.9712 315271.4263 316342.0299 383724.6983 0.767600916 0.798085073 0.784786093 0.849680821 0.594868526 0.517118059 0.821608376 0.824398407 1 18.5497121 1.364676771 1.807040493 1.045853796 0.727700284 0.413066879 0.102281801 0.74644615 2.962895297 0.384339885 0.031026589 23.15670542 -1.364676771 -0.318153512 DLSYCLSGMYDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 DLSYCLSGMYDHR 13 0 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ;;;;;;;;; 233.37 1.24E-16 19002470000 15316290 15369380 8039290 10638800 14744810 15024040 14392120 16509490 14921590 FALSE TRUE 13292203.47 15268417.53 11927117.53 13054502.14 14451417.13 15602024.54 12996374.42 12979064.04 13157576.63 1.010231887 1.160427787 0.906482848 0.99216615 1.098334255 1.185782533 0.987748336 0.986432715 1 23.64939046 DLTAHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLTAHFR 7 0 A0A5F9ZHZ6;A0A0A0MRL7;P55210-4;P55210;P55210-3;Q5SVL2 A0A5F9ZHZ6 CASP7 Caspase-7;Caspase-7 subunit p20;Caspase-7 subunit p11 0 ;;; 134.06 0.0036649 562760000 649274 696029 513008 644364 717402 729265 664370 783992 1163310 FALSE TRUE 563470.7958 691456.7397 761100.3847 790676.6947 703127.1038 757320.2964 599939.4997 616341.4118 1025784.817 0.549307015 0.674075818 0.741968854 0.770801714 0.685452828 0.738283784 0.584859017 0.60084864 1 19.96829669 -1.999965057 0.023911747 1.60598603 1.86E-05 0.128082344 0.118395401 17506.96256 41.56295653 1835.42599 1058.958647 0.010000805 1.999965057 -1.60596745 DLTDYLMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 DLTDYLMK 8 0 P60709;A0A2R8Y793;P63267-2;A0A2R8YEA7;Q562R1;P63261;I3L3I0;I3L1U9;I3L4N8;P68133;P68032;P63267;P62736 P60709;P63261;P68133 ACTB;ACTG2;ACTBL2;ACTG1;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Beta-actin-like protein 2;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 ;;;;;;;;;;;; 204.65 0.00019968 35523121000 26482570 21900630 15213370 19826120 21821530 18063800 25065750 28690250 26416540 FALSE TRUE 22982831.28 21756763.32 22570606.62 24327943.57 21387324.25 18758726.07 22634877.42 22555063.31 23293606.74 0.986658337 0.934022952 0.968961435 1.044404323 0.918162846 0.80531651 0.971720596 0.968294157 1 24.47343071 4.760685089 21.38679288 0.951494063 0.986658594 0.030868986 0.062151871 3571.200135 3451718.918 0.015802562 0.560315091 57634.83968 -4.760685089 0.035164531 DLTEYLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DLTEYLSR 8 0 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 ;;;;;;; 245.65 1.18E-08 6647946000 3951650 3774800 2239427 2676390 3730820 3630500 3554410 3967170 3717270 FALSE TRUE 3429429.44 3750003.09 3322421.388 3284105.256 3656583.981 3770167.684 3209703.865 3118821.568 3277818.575 1.046253586 1.1440545 1.013607468 1.001917946 1.115554109 1.150206333 0.9792195 0.951493042 1 21.64430457 2.127349647 8.677050077 0.970381218 1.076694214 0.470288104 0.05077101 0.222235246 16.15218975 0.021429688 0.014434536 134.0755683 -2.127349647 0.106312996 DLTPEHLPLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLTPEHLPLLR 11 0 Q96C86;A0A3B3ITF0 Q96C86 DCPS m7GpppX diphosphatase 0 113.22 0.0014204 90055000 125920 106680 64094 79426 105510 111450 101540 121930 112380 FALSE TRUE 109279.353 105979.2121 95090.07278 97460.88725 103410.5574 115737.5536 91692.66643 95856.21836 99094.56442 1.102778478 1.069475533 0.95958919 0.983513958 1.043554286 1.167950576 0.925304702 0.967320649 1 16.5965183 1.124385436 0.018500298 2.02E-08 1.963576668 0.119404581 0.069024755 6837.449852 33.1282513 1902.961926 1622.008918 13.31635719 -1.124385436 1.963576648 DLTQMADELRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLTQMADELRR 11 1 P41227-2;P41227;C9JN83 P41227-2 NAA10 N-alpha-acetyltransferase 10 0 ;;; 206.36 4.27E-08 2567180000 1503780 1579670 868552 960800 1562760 1960210 1314000 1518310 1037020 FALSE TRUE 1305051.663 1569293.044 1288586.652 1178964.325 1531664.133 2035620.547 1186568.482 1193631.222 914424.677 1.427183338 1.716153428 1.409177469 1.28929627 1.675003062 2.226121624 1.297612053 1.305335751 1 19.80250481 1.698439185 2.292963074 1.07401125 1.604870922 0.343162482 0.268629708 0.332856001 3.639250171 0.273433883 0.077457921 49.93892454 -1.698439185 0.530859672 DLTTAGAVTQCYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLTTAGAVTQCYR 13 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 250.7 1.42E-17 282820000 96835 94492 46240 66125 100620 89896 80357 87761 95484 FALSE TRUE 84038.0094 93871.27583 68601.81866 81139.69191 98617.85886 93354.35729 72563.99051 68993.99311 84195.9903 0.998123653 1.114913852 0.814787241 0.963700191 1.171289256 1.108774384 0.861846155 0.819445117 1 16.36146391 2.221684265 24.99214427 0.876950751 1.026338923 0.254745753 0.107394256 316.4940813 468691.6649 0.045663783 0.030877145 166.6035553 -2.221684265 0.149388172 DLTTGYDDSQPDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLTTGYDDSQPDKK 14 1 Q96G03 Q96G03 PGM2 Phosphoglucomutase-2 0 ; 176.89 3.46E-06 394390000 431680 301770 278640 265790 270508 199888 394880 492740 417740 FALSE TRUE 374632.3943 299787.653 413391.236 326141.6818 265125.42 207577.8207 356584.5984 387371.3855 368355.2531 1.017040998 0.813854697 1.122262361 0.885399839 0.719754687 0.563526158 0.968045373 1.051624437 1 18.49073829 2.012858639 24.99424383 1.023600338 0.851598315 0.192846494 0.150889241 363.6574618 706863.7773 0.065476183 0.044116367 103.0050789 -2.012858639 -0.172002023 DLTVLCHLEQLLLVTHLDLSHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DLTVLCHLEQLLLVTHLDLSHNR 23 0 Q92696;H0YKZ8;H0YMG5;H0YLG7 Q92696 RABGGTA Geranylgeranyl transferase type-2 subunit alpha 0 ;; 284.97 1.03E-52 467839200 239793.8 221759 151418.3 206659.8 173001.6 177178.8 228767.7 252777.5 299895 FALSE TRUE 208104.4418 220302.2505 224644.6963 253585.0662 169559.2066 183994.9831 206581.8437 198722.9987 264441.7547 0.786957574 0.833084211 0.849505391 0.958944878 0.641196799 0.695786425 0.781199791 0.751481168 1 18.01259047 5.083521952 11.24672514 0.804400072 0.635346748 0 0.108919744 1263624.963 5423907.281 0.026657061 4803348.075 121205.3952 -5.083521952 -0.169053324 DLVDDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLVDDFR 7 0 Q6NUQ1 Q6NUQ1 RINT1 RAD50-interacting protein 1 0 ; 102.71 0.019865 141126000 801930 753360 491650 568540 704540 703230 734840 888300 762110 FALSE TRUE 695952.9187 748411.1286 729413.5845 697635.6966 690521.0324 730283.7132 663575.3299 698343.9578 672014.224 1.035622304 1.113683464 1.085413907 1.038126384 1.027539311 1.086708714 0.987442388 1.039180322 1 19.35813224 2.696681013 0.551724549 1.004464947 1.082196038 0.338106289 0.031965509 1.22362719 1.020871586 0.060012592 0.038052237 497.3716337 -2.696681013 0.077731092 DLVDEDLSHFQSGS(ph)PPAPNGFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLVDEDLSHFQSGSPPAPNGFK 22 0 Q70EK8 Q70EK8 USP53 Inactive ubiquitin carboxyl-terminal hydrolase 53 1 DLVDEDLSHFQS(0.002)GS(0.998)PPAPNGFK 139.67 8.71E-08 78452000 40118 39396 52307 60560 71150 61326 88357 99327 141140 TRUE FALSE 34816.30465 39137.20508 77602.84016 74311.0736 69734.2542 63685.2509 79788.15174 78086.69401 124454.59 0.27975107 0.31446976 0.623543416 0.597093877 0.560318862 0.511714762 0.641102524 0.62743121 1 16.92525991 -2 0.111257892 2.533159609 4.61E-12 0.666378238 0.113874002 174.3856864 1.758179267 68.39535216 5.583507016 0.01 2 -2.533159609 DLVDSPASLASSLGS(ph)PLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DLVDSPASLASSLGSPLPR 19 0 K7EMK7;Q04725;Q04725-2;Q04725-3 K7EMK7 TLE2 Transducin-like enhancer protein 2 1 DLVDSPASLAS(0.001)S(0.005)LGS(0.995)PLPR;DLVDSPASLASS(0.008)LGS(0.992)PLPR;DLVDSPASLASSLGS(1)PLPR 358.17 4.30E-91 211872000 158022 144231 89324 118191 148715 147295 165967 174023 147454 TRUE FALSE 137138.9923 143283.5371 132521.3852 145028.073 145755.8625 152961.534 149871.5459 136809.5357 130022.1561 1.054735565 1.10199324 1.019221563 1.11541046 1.121007887 1.176426684 1.152661595 1.052201715 1 16.98839796 4.74638393 22.82979051 1.094010396 1.054735515 0.042804588 0.055439909 1145.965714 3343841.824 0.014310392 0.139705085 55767.8537 -4.74638393 -0.039274881 DLVEAVAHILGIR ddPTM_MDA-MB-175_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 ;; 207.34 1.27E-07 5277500000 3572645 3455048 2120885 2580026 3333132 3614346 3572843 3632891 3943599 FALSE TRUE 3100510.911 3432351.562 3146552.08 3165860.337 3266809.194 3753392.229 3226349.236 2856025.531 3477391.219 0.891619814 0.98704786 0.90485996 0.910412472 0.939442527 1.079370135 0.92780738 0.821312688 1 21.72957395 1.99378442 24.96024707 0.890893079 0.95363327 0.044570881 0.06828532 524.7074898 2107095.528 0.028420837 0.018417825 98.5790026 -1.99378442 0.062740192 DLVHSNKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLVHSNKK 8 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 126.41 0.00079214 518710000 685900 460560 367190 441750 415200 375690 577280 692400 550970 FALSE TRUE 595256.5772 457534.551 544764.3122 542056.0892 406938.3323 390143.0374 521295.4745 544335.6483 485834.9543 1.225223858 0.941748936 1.121295015 1.115720646 0.837606123 0.803036163 1.07298882 1.120412691 1 18.89010677 4.750450112 24.09670243 1.010206191 1.225224076 0.272547351 0.114047715 1766.459828 3580011.677 0.030181441 0.462721141 56292.44498 -4.750450112 0.215017885 DLVHTEGQLQNEEIVAHDGSATYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DLVHTEGQLQNEEIVAHDGSATYLR 25 0 Q9Y547 Q9Y547 HSPB11 Intraflagellar transport protein 25 homolog 0 ;; 413.17 3.93E-159 715832000 142429 128540 73164 130114 137070 131023 134976 147866 170789 FALSE TRUE 123606.6468 127695.6123 108546.3551 159658.3724 134342.5752 136063.5396 121886.0483 116246.0066 150598.519 0.820769338 0.847920771 0.720766418 1.060158981 0.892057745 0.903485243 0.809344269 0.771893425 1 17.20034806 DLVILLYETALLSSGFSLEDPQTHANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 DLVILLYETALLSSGFSLEDPQTHANR 27 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;; 304.96 2.82E-71 45979210000 30021480 28055460 21717400 27735140 18161920 19682210 30596760 35508070 33825070 FALSE TRUE 26054065.35 27871161.84 32220007.28 34032827.44 17800533.33 20439397.35 27629490.92 27914945.55 29826308.76 0.873526307 0.934448914 1.080254601 1.141033834 0.596806446 0.685280821 0.926346305 0.935916871 1 24.83008211 4.773263198 19.45242576 0.910404683 0.873525134 0.0054382 0.163494432 7872.202814 4411191.003 0.042513901 3.808606809 59328.47677 -4.773263198 -0.036879549 DLVLPTQALPAS(ph)PALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLVLPTQALPASPALK 16 0 Q15554;J3KSZ6;U3KQ35;H3BR06 Q15554 TERF2 Telomeric repeat-binding factor 2 1 DLVLPTQALPAS(1)PALK;DLVLPTQALPAS(1)PALK;DLVLPTQALPAS(1)PALK;DLVLPTQALPAS(1)PALK 258.38 1.10E-26 825830000 2242950 1547370 1055780 1338790 1562590 1228950 1810000 2176070 1788600 TRUE FALSE 1946538.475 1537205.225 1566358.739 1642782.732 1531497.516 1276228.502 1634466.479 1710734.365 1577153.746 1.234209715 0.974670497 0.993155388 1.041612294 0.971051504 0.809197268 1.036339344 1.084697272 1 20.58889187 4.741413834 24.78455095 0.994169976 1.234209813 0.529303498 0.072563258 216.4206875 1879832.897 0.019146092 0.129580072 55133.28048 -4.741413834 0.240039837 DLVMGS(ph)SPQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLVMGSSPQLK 11 0 Q53LP3 Q53LP3 SOWAHC Ankyrin repeat domain-containing protein SOWAHC 1 DLVMGS(0.657)S(0.343)PQLK;DLVMGS(0.54)S(0.46)PQLK 152.4 3.46E-05 416150000 1180960 949480 834790 1115110 972040 831420 1092340 1306960 2150000 TRUE FALSE 1024893.144 943242.8034 1238497.236 1368312.769 952698.3058 863405.2654 986405.0349 1027476.775 1895829.449 0.540604085 0.497535685 0.653274606 0.721748873 0.502523213 0.455423491 0.520302623 0.541966882 1 20.85439775 1.237632177 24.98163454 1.000000528 0.553876489 0.762564873 0.078181251 11.98123955 322201.2109 0.121248326 0.02055628 17.28351922 -1.237632177 -0.446124039 DLVMGS(ph)SPQLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLVMGSSPQLKR 12 1 Q53LP3 Q53LP3 SOWAHC Ankyrin repeat domain-containing protein SOWAHC 1 DLVMGS(0.5)S(0.5)PQLKR 71.279 0.027571 502640000 246780 219430 128420 155890 221220 212990 219070 290550 153730 TRUE FALSE 214167.3977 217988.5499 190524.3415 191287.2071 216818.1548 221183.8631 197824.6251 228418.1436 135556.2145 1.579915746 1.608104436 1.405500605 1.411128275 1.599470416 1.631676304 1.459354894 1.685043687 1 17.04853173 1.229622546 24.99898956 0.999998952 1.547283158 0.769191275 0.094257161 172.6767131 482924.9012 0.279279683 0.023584432 16.96768318 -1.229622546 0.547284206 DLVMGSS(ph)PQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLVMGSSPQLK 11 0 Q53LP3 Q53LP3 SOWAHC Ankyrin repeat domain-containing protein SOWAHC 1 DLVMGS(0.278)S(0.722)PQLK;DLVMGS(0.379)S(0.621)PQLK 177.36 8.41E-06 512640000 1778180 1521460 1275030 1610250 1580610 1332630 1741790 2085340 3341900 TRUE FALSE 1543189.008 1511465.429 1891638.773 1975881.874 1549158.953 1383897.138 1572871.474 1639406.269 2946824.389 0.523678647 0.512913302 0.6419245 0.670512258 0.525704538 0.469623213 0.533751343 0.556329816 1 21.49072966 1.238612222 10.84946852 1.001146915 0.554897472 0.845566474 0.05985996 0.026973722 100.7733832 0.088876702 0.015870113 17.32256591 -1.238612222 -0.446249442 DLVQPDKPAS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 176.4 3.80E-05 4284090000 4007750 2589610 2508030 2235810 2798800 1824580 3895670 4382090 3632070 TRUE FALSE 3478115.683 2572598.681 3720921.697 2743484.833 2743109.356 1894772.773 3517868.523 3445014.155 3202690.822 1.085997955 0.80326164 1.161811084 0.856618695 0.856501457 0.59161901 1.09841028 1.075662418 1 21.6108531 DLVSSLTSGLLTIGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLVSSLTSGLLTIGDR 16 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 190.85 4.98E-12 252970000 135422 108131 82815 102978 130079 136623 146922 162315 119886 FALSE TRUE 117525.6396 107420.6803 122864.611 126360.7288 127490.6824 141878.9752 132673.5271 127605.2004 105713.2137 1.111740297 1.016151876 1.162244593 1.195316313 1.206005172 1.342112025 1.255032578 1.207088461 1 16.68979619 4.054460321 4.161408534 1.209507413 1.064713221 0.285718198 0.087313612 0.251014663 9.044398666 0.023263311 0.050829953 11336.01263 -4.054460321 -0.144794192 DLVVLLFETALLSSGFSLEDPQTHSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DLVVLLFETALLSSGFSLEDPQTHSNR 27 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;; 254.33 7.90E-53 20039491000 14142690 11107510 8491775 11683090 7246096 6610919 11893380 13303420 12283750 FALSE TRUE 12273697.68 11034544.04 12598425.79 14335914.15 7101912.866 6865245.332 10739961.84 10458587.16 10831579.07 1.133140201 1.018738262 1.163119958 1.323529474 0.655667361 0.633817589 0.991541655 0.965564401 1 23.36874024 3.242753915 24.99999985 0.863740708 1.14981726 0.529022509 0.145005694 102.6499435 611983.8661 0.046748171 0.058195737 1748.855452 -3.242753915 0.286076552 DLYANTVLSGGTTMYPGIADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 ;;;;;;; 370.22 5.22E-112 3359046000 1750190 1586289 966097 1259963 1523703 1561378 1409871 1717335 1580775 FALSE TRUE 1518897.957 1575868.563 1433304.741 1546056.856 1493384.291 1621445.222 1273141.927 1350096.275 1393897.58 1.089676873 1.130548317 1.028271202 1.109161016 1.071373042 1.163245596 0.913368346 0.968576382 1 20.41069313 2.233384057 24.99996706 0.960329934 1.09619008 0.71792689 0.040775264 64.01439417 309150.6891 0.015548338 0.010839354 171.1528191 -2.233384057 0.135860146 DLYDAGVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLYDAGVKR 9 1 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;H0YL33;H0YNP5;H0YN28 P07355-2 ANXA2 Annexin A2;Annexin 0 ;;; 99.688 0.0082864 2759810000 4108220 3157790 2161910 3502070 3519710 3085070 2210190 4403100 2872450 FALSE TRUE 3565308.318 3137046.27 3207416.907 4297268.519 3449674.657 3203754.639 1995846.114 3461531.33 2532872.233 1.407614751 1.238533167 1.266316107 1.696599008 1.361961575 1.264870212 0.787977415 1.366642693 1 21.27234287 2.471378066 24.99357505 1.094807365 1.387067722 0.408309904 0.185751651 169.2484148 736536.4997 0.068568941 0.053275836 296.0588627 -2.471378066 0.292260356 DLYDDKDGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLYDDKDGLR 10 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ;;; 146.71 1.71E-05 1449110000 5145200 3766760 3148290 3441500 3484290 2789430 4486520 5172700 5098100 FALSE TRUE 4465248.784 3742015.906 4670813.574 4222945.175 3414959.446 2896741.177 4051417.981 4066558.359 4495408.426 0.993291012 0.832408438 1.039018735 0.939390768 0.759654991 0.644377752 0.901234682 0.904602646 1 22.10002077 4.753866003 22.77058736 0.876808283 0.9932913 0.092649899 0.113770905 2265.391127 3370134.386 0.029424455 0.598893128 56736.95221 -4.753866003 0.116483016 DLYEDELVPLFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DLYEDELVPLFEK 13 0 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;; 227.2 2.21E-11 288399000 1446213 1126520 828727 955072 1013269 806519 1325305 1540456 1340070 FALSE TRUE 1255092.288 1119119.816 1229502.149 1171935.695 993106.9293 837546.3078 1196777.125 1211041.472 1181648.451 1.062153711 0.947083555 1.040497407 0.991780333 0.840441951 0.708794826 1.012803024 1.02487459 1 20.17236946 3.455134965 24.44669552 0.92650685 1.010713809 0.184103799 0.097132277 398.5986324 443202.4017 0.031368047 0.040499755 2851.904409 -3.455134965 0.084206959 DLYLASVFHATAFELDTDGNPFDQDIYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 DLYLASVFHATAFELDTDGNPFDQDIYGR 29 0 P50454;E9PKH2 P50454 SERPINH1 Serpin H1 0 ;;;;;; 298.38 6.48E-81 2174143000 822560 874324 370924.4 760220 853842 1133153 897935.5 909496 839196 FALSE TRUE 713856.6119 868580.5081 550304.6805 932839.5702 836852.2147 1176746.129 810853.8534 715007.3581 739987.2049 0.964687777 1.173777739 0.743667832 1.260615811 1.130900925 1.590224968 1.095767397 0.966242867 1 19.4971408 4.754761433 22.35861503 1.114633133 0.964687269 0.047661608 0.217151475 2783.068405 3840604.399 0.05426192 1.158486775 56854.05336 -4.754761433 -0.149945864 DLYPFTVNT(ph)SNQGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLYPFTVNTSNQGSR 15 0 H7C0I3;A0A2R8YD85;Q96BY6-3;Q96BY6 H7C0I3 DOCK10 Dedicator of cytokinesis protein 10 1 DLYPFT(0.003)VNT(0.657)S(0.329)NQGS(0.011)R 109.35 0.011254 71009000 146770 146740 97406 135320 147110 142890 144460 160390 236310 TRUE FALSE 127373.9726 145776.0553 144511.8674 166046.4742 144182.7988 148387.0708 130450.2914 126091.8467 208373.701 0.611276625 0.699589509 0.693522583 0.796868671 0.69194336 0.712119956 0.626040094 0.605123612 1 17.66881368 1.230320584 24.99979832 1.000000591 0.679695088 0.761165526 0.056410116 166.7070879 505739.5793 0.165762002 0.015042802 16.99497709 -1.230320584 -0.320305503 DLYQEWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLYQEWK 7 0 Q9NQT8;H0Y307;A0A1B0GUA8;Q9H1H9-3;Q9H1H9-4;Q9H1H9-2;Q9H1H9 Q9NQT8;A0A1B0GUA8 KIF13B;KIF13A Kinesin-like protein KIF13B;Kinesin-like protein KIF13A 0 119.27 0.01121 183720000 214880 198750 143770 184290 199720 172860 224660 252640 271470 FALSE TRUE 186483.0636 197444.3982 213297.6529 226135.8612 195745.9627 179510.0361 202872.5078 198614.902 239377.1259 0.7790346 0.82482567 0.891052778 0.944684503 0.817730441 0.749904718 0.847501644 0.82971546 1 17.86892577 1.236912234 24.98323221 1.000000203 0.837417904 0.478593529 0.053910588 41.31988059 626051.905 0.086202305 0.013906377 17.25489155 -1.236912234 -0.162582299 DLYVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DLYVLR 6 0 Q5QPM7;Q5QPM9;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 0 ; 116 0.055721 231290000 283750 312220 232830 257870 301950 384800 272060 293340 364780 FALSE TRUE 246251.7186 310169.0063 345427.3668 316423.3248 295941.7858 399603.505 245675.6631 230611.5238 321656.124 0.765574476 0.964287583 1.073902659 0.983731697 0.920056432 1.242331407 0.763783571 0.716950515 1 18.29515963 DMAEAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DMAEAHK 7 0 F5H169;F5H5V4;F5GX23;J3KN29;O00233-2;O00233 F5H169 PSMD9 26S proteasome non-ATPase regulatory subunit 9 0 ; 78.496 0.026683 195576000 300950 264700 165358 205823 186453 215078 284700 346970 304680 FALSE TRUE 261178.695 262961.1683 245325.6819 252558.258 182742.9501 223352.1898 257089.8378 272773.1656 268661.0775 0.972149362 0.978784016 0.913141882 0.9400627 0.680198828 0.831352989 0.956929974 1.015305857 1 18.0354278 2.030603215 5.46447201 1.002950416 0.884650654 0.26538307 0.085149714 0.250507082 20.61554326 0.040473862 0.025812511 107.3008631 -2.030603215 -0.118299761 DMDDAYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DMDDAYDR 8 0 P07686;Q5URX0;H0Y9B6;H0YA83;H0Y9M3 P07686 HEXB Beta-hexosaminidase subunit beta;Beta-hexosaminidase subunit beta chain B;Beta-hexosaminidase subunit beta chain A 0 ;;;;;;; 121.05 0.0033731 2913057000 3846440 3697170 2400400 2859510 3568300 3703330 3545740 4157340 3672400 FALSE TRUE 3338123.208 3672883.047 3561241.469 3508805.45 3497297.811 3845799.501 3201874.681 3268325.193 3238253.056 1.03084075 1.134217426 1.099741561 1.083548873 1.079995217 1.187615494 0.988766049 1.009286531 1 21.6267843 2.206624212 24.99999918 1.000979672 1.102062813 0.59570369 0.040111029 127.1862239 99561.27399 0.015416786 0.010394934 160.9252572 -2.206624212 0.10108314 DMDEPS(ph)PVPNVEEVTLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DMDEPSPVPNVEEVTLPK 18 0 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK 245.74 3.26E-24 1167633000 2456484 1476384 1278270 1467452 1413574 1218227 1865766 2224495 2312736 TRUE FALSE 2131853.415 1466685.536 1896445.648 1800659.405 1385446.643 1265092.981 1684824.3 1748804.055 2039326.985 1.045371062 0.719200769 0.929937014 0.882967478 0.67936464 0.620348277 0.826166825 0.8575398 1 20.95966168 4.754432385 23.74960448 0.813821615 1.045371413 0.284082729 0.115206934 2148.180288 3214305.244 0.029243508 0.668840505 56810.99367 -4.754432385 0.231549798 DMEDLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DMEDLLR 7 0 M0QZR4;Q92888;Q92888-3;M0QYC1;Q92888-2;Q92888-4;M0R2C7 M0QZR4 ARHGEF1 Rho guanine nucleotide exchange factor 1 0 86.953 0.045825 28478000 124470 100370 72485 77056 100220 104630 101770 118960 114950 FALSE TRUE 108020.9741 99710.66286 107538.9884 94552.74253 98225.81808 108655.1838 91900.36106 93521.32975 101360.742 1.065708203 0.983720728 1.060953051 0.932833962 0.969071617 1.071965158 0.906666223 0.922658299 1 16.62913946 8 0.234516636 0.935407744 1.614335522 0.222448002 0.053239211 129.7232745 2.032617752 0.213890688 33.00050696 100000000 -8 0.678927778 DMEESIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DMEESIR 7 0 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 158.36 0.003312 624160000 982150 779920 723030 872610 844220 1031590 822290 828100 1051470 FALSE TRUE 852356.389 774796.6542 1072689.726 1070749.438 827421.6737 1071275.935 742544.4424 651017.2593 927166.4144 0.919313271 0.835660829 1.1569549 1.154862192 0.892419808 1.155430048 0.800875043 0.70215794 1 19.82246878 2.212736443 24.90143164 0.805410773 1.017446396 0.285871077 0.135088315 239.234866 230684.6875 0.055366829 0.037343237 163.2061211 -2.212736443 0.212035622 DMES(ph)PTKLDVTLAK ddPTM_MDA-MB-175_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(0.992)PT(0.008)KLDVTLAK;DMES(0.976)PT(0.024)KLDVTLAK;DMES(0.592)PT(0.408)KLDVTLAK;DMES(0.995)PT(0.005)KLDVTLAK;DMES(0.708)PT(0.292)KLDVTLAK;DMES(0.961)PT(0.039)KLDVTLAK;DMES(0.991)PT(0.009)KLDVTLAK;DMES(0.971)PT(0.029)KLDVTLAK;DMES(0.88)PT(0.12)KLDVTLAK;DMES(0.935)PT(0.065)KLDVTLAK;DMES(0.984)PT(0.016)KLDVTLAK;DMES(0.985)PT(0.015)KLDVTLAK;DMES(0.992)PT(0.008)KLDVTLAK 239.33 6.16E-17 15294850000 15464610 10593270 10145010 10378180 11067810 7058840 15983130 18377270 14853180 TRUE FALSE 13420922.61 10523682.11 15051170.77 12734704.39 10847582.23 7330398.142 14433088.51 14447433.82 13097253.98 1.024712709 0.803502942 1.149185225 0.972318656 0.828233327 0.559689699 1.101993481 1.103088773 1 23.64276103 DMESPT(ph)KLDVTLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.201)PT(0.799)KLDVTLAK;DMES(0.475)PT(0.525)KLDVTLAK 237.4 1.73E-16 4640840000 5340590 3610980 3326640 3489260 3513330 2297390 5282930 5739620 4509900 TRUE FALSE 4634817.5 3587259.235 4935414.231 4281549.813 3443421.607 2385772.08 4770592.262 4512246.929 3976744.76 1.165480256 0.90205921 1.241068897 1.076646874 0.865889519 0.599930904 1.199622442 1.134658421 1 21.92315654 4.777122987 21.89973109 1.014976422 1.165481954 0.067134574 0.185832443 13394.60333 7606077.671 0.047500366 9.065999439 59858.1082 -4.777122987 0.150505532 DMFCAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DMFCAGR 7 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;;;; 148.28 0.0048727 2807810000 2664190 2837610 2051740 2382980 2538170 2974650 2569420 3036260 3249770 FALSE TRUE 2312110.541 2818969.553 3043968.327 2924072.031 2487665.383 3089086.71 2320238.044 2386979.427 2865585.893 0.806854384 0.983732353 1.0622499 1.020409836 0.868117542 1.077994807 0.809690629 0.832981288 1 21.45039871 2.221570512 24.99440569 0.867942872 0.972390304 0.157281328 0.095447071 378.5906729 556946.2347 0.038147059 0.025793066 166.5599233 -2.221570512 0.104447432 DMFEEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DMFEEALR 8 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ; 138.83 0.0016017 394880000 812890 783940 475250 615110 738020 700320 737810 873790 768600 FALSE TRUE 705464.5269 778790.2465 705082.4896 754780.1269 723334.8459 727261.7636 666257.2998 686936.8083 677736.9836 1.040911953 1.149103952 1.040348257 1.113677053 1.067279584 1.073073746 0.983061742 1.013574329 1 19.37036597 2.307469718 5.720122571 1.00139913 1.083716036 0.579643314 0.032835231 0.127350376 7.5665875 0.011342525 0.008628992 202.9876978 -2.307469718 0.082316906 DMFQETMEAMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DMFQETMEAMR 11 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 202.03 9.63E-08 387430000 358920 336280 311520 375860 354810 360910 380460 419760 917990 FALSE TRUE 311487.8126 334070.9545 462172.114 461204.7577 347749.9752 374794.4412 343563.0478 329997.5906 809466.268 0.384806415 0.41270522 0.570959078 0.569764023 0.429604035 0.46301428 0.424431581 0.40767306 1 19.62661144 1.235265254 24.99993081 1.000000749 0.458846125 0.875474101 0.064255153 33.46784397 253857.6877 0.11890088 0.016958553 17.18957954 -1.235265254 -0.541154624 DMGEDLECLCQIMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DMGEDLECLCQIMR 14 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 110.08 0.0035928 0 44990 42021 23235 32040 36058 35446 40149 48951 52102 FALSE TRUE 39044.45751 41744.96128 34471.52372 39315.1717 35340.51635 36809.63056 36255.35616 38483.20959 45942.56091 0.849853746 0.908633747 0.750317854 0.855746195 0.769232617 0.801209811 0.789145303 0.83763745 1 15.48754366 1.241412625 4.13505379 1.018232026 0.817372031 0.60802697 0.045628146 0.153199617 4.805123726 0.092088388 0.011303898 17.43462558 -1.241412625 -0.200859995 DMGSCEIYPQTIQHNPNGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DMGSCEIYPQTIQHNPNGR 19 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ;;;; 326.49 3.77E-75 4816590000 2982160 2646860 1641010 1846580 2756600 2668480 2619140 2987050 2788960 FALSE TRUE 2588060 2629472.602 2434607.925 2265874.212 2701749.053 2771138.152 2365136.206 2348292.603 2459252.326 1.052376762 1.069216271 0.989978905 0.921367112 1.098605875 1.126821401 0.961729783 0.954880708 1 21.22978834 DMGYGNWISKPQEEK ddPTM_MDA-MB-175_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 0 171.56 9.82E-07 618500000 332240 268580 215640 203710 245320 206620 382370 375050 246220 FALSE TRUE 288333.6422 266815.6803 319924.2253 249965.469 240438.612 214568.8051 345287.8163 294848.4761 217112.1521 1.328040091 1.228930199 1.473543614 1.151319567 1.107439679 0.988285561 1.590366145 1.358046859 1 17.72808095 3.712854052 24.73441988 1.22761522 1.332047283 0.105498324 0.185179083 2107.756141 2028046.379 0.054429733 0.08076542 5162.428527 -3.712854052 0.104432064 DMGYTYLNIDDCWIGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DMGYTYLNIDDCWIGGR 17 0 P17050 P17050 NAGA Alpha-N-acetylgalactosaminidase 0 224.05 6.61E-15 51893000 52373 47824 41390 43138 56554 58301 53216 57980 44432 FALSE TRUE 45451.77535 47509.841 61406.34244 52933.14222 55428.68605 60543.8772 48055.12051 45581.4282 39179.29958 1.16009668 1.212626094 1.567315983 1.351048712 1.41474418 1.545302694 1.226543635 1.163405898 1 15.25780399 1.669517665 1.942247248 1.016236943 1.3750503 0.46745949 0.130605462 0.315010446 2.314870555 0.167259481 0.038541966 46.72159548 -1.669517665 0.358813357 DMHSAYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 DMHSAYK 7 0 P08621;P08621-2 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;;;;;; 150.17 0.0019672 2775825000 10995100 9850300 5339310 7210620 8567090 9812280 9246580 9816620 9450290 FALSE TRUE 9542069.677 9785592.731 7921418.175 8847901.478 8396621.67 10189764.76 8349848.095 7717412.206 8333087.482 1.145082144 1.174305772 0.950598226 1.061779502 1.007624328 1.222807847 1.002011333 0.926116787 1 22.9904197 -2 0.216215827 0.147297939 1.137768472 0.204134973 0.087276981 145.8594906 2.238861588 48.52518346 0.458429606 0.01 2 0.990470533 DMILQFISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DMILQFISR 9 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 ; 91.867 0.024341 59985000 186014 182393 134404 149727 157385 169435 177888 193534 189991 FALSE TRUE 161431.7786 181194.8484 199402.224 183724.8038 154253.3464 175953.2741 160636.4491 152148.2602 167530.4804 0.963596464 1.081563474 1.190244447 1.096664937 0.92074795 1.050276186 0.958849093 0.908182558 1 17.35406408 3.248954117 24.96083265 0.963658679 1.090572597 0.423079428 0.066617527 189.8775063 456003.7525 0.019807613 0.025288599 1774.002049 -3.248954117 0.126913918 DMLGS(ph)LR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DMLGSLR 7 0 Q9H3Q1;J3KRZ9 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 DMLGS(1)LR;DMLGS(1)LR 76.17 0.043517 85077000 244390 284950 117538 143836 191390 162975 230450 203521 251400 TRUE FALSE 212093.2423 283078.1447 174379.7699 176496.1622 187581.7134 169244.7537 208100.9945 159999.618 221679.7784 0.956755027 1.276968728 0.786629124 0.796176194 0.846183241 0.763465008 0.938745951 0.721760095 1 17.75811765 4.223351713 24.98374744 0.827757907 1.116861901 0.522341119 0.11138112 137.3409514 225611.5646 0.025429485 0.053254043 16724.44493 -4.223351713 0.289103994 DMLLANKVPAAAR ddPTM_MDA-MB-175_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 ; 173.06 2.04E-05 3964100000 5148500 4422000 2576800 3049600 4497100 4049100 5294800 6275900 2039100 FALSE TRUE 4468112.68 4392951.591 3822949.099 3742058.29 4407616.508 4204871.497 4781311.111 4933847.624 1798039.921 2.48499081 2.44318913 2.126175873 2.081187546 2.451345188 2.338586284 2.659179618 2.744014505 1 20.77799362 1.230580898 24.99996033 0.999997413 2.422852577 0.825798583 0.204378601 137.1976678 429796.6098 0.619164992 0.057633917 17.00516688 -1.230580898 1.422855164 DMLLELEEQLAESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DMLLELEEQLAESR 14 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ;;;; 189.33 1.70E-06 153388000 174358 153720 110610.6 142776 150120 157917 161812 178952 213850 FALSE TRUE 151316.1485 152710.2032 164102.2561 175195.473 147132.9057 163992.1692 146119.4971 140684.5074 188568.8966 0.802444895 0.809837709 0.870250922 0.929079377 0.780260734 0.86966712 0.774886526 0.746064223 1 17.52473221 4.43929419 19.39053955 0.839907377 0.80429299 0.041377241 0.075999307 57.46944999 29458.12411 0.01906245 0.05043766 27497.56202 -4.43929419 -0.035614388 DMLQAASHYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DMLQAASHYR 10 0 Q8WUM0 Q8WUM0 NUP133 Nuclear pore complex protein Nup133 0 ; 120.96 0.0010759 139170000 214300 218300 156397 151670 217560 219680 184732 215470 193308 FALSE TRUE 185979.712 216865.9729 232031.1123 186108.9916 213230.9816 228131.2318 166816.7191 169393.4173 170455.3485 1.091075837 1.272274381 1.36124278 1.091834274 1.250949199 1.338363588 0.978653475 0.993770033 1 17.37903434 2.225172055 24.99206603 0.99091844 1.236069125 0.629634645 0.08802314 142.3508601 265720.3123 0.035108028 0.023820151 167.9469245 -2.225172055 0.245150685 DMNQVLDAYENKKPFYLYTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DMNQVLDAYENKKPFYLYTGR 21 2 P23381;P23381-2;G3V277;G3V5U1;G3V3Y5;G3V3H8;G3V456;G3V423 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ; 183.09 2.50E-17 1763030000 1741970 1526090 741580 826350 1495500 1132640 1875610 2219100 573088 FALSE TRUE 1511764.251 1516065.014 1100210.568 1013985.397 1465742.476 1176213.394 1693713.631 1744562.734 505338.1895 2.991589162 3.000099826 2.177176772 2.006548127 2.900517923 2.327576696 3.351643842 3.452267749 1 18.94688969 DMPGGFLFEGLS(ph)DDEDDFHPNTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 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 284.13 1.20E-51 2068499000 1135441 989808 631213 763705 985499 983204 900318 1092048 1007069 TRUE FALSE 985389.595 983305.8861 936469.7181 937115.8928 965889.498 1021028.494 813005.2989 858522.0335 888014.4501 1.10965491 1.107308429 1.054565855 1.055293518 1.087695699 1.149788153 0.91553161 0.96678836 1 19.76022363 2.234724218 24.99999608 0.960141376 1.090808329 0.774691507 0.033851845 45.49780188 296482.917 0.013819362 0.009718017 171.6817841 -2.234724218 0.130666953 DMPHPLAGSSSEEAVGGDST(ph)PSPDLLMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DMPHPLAGSSSEEAVGGDSTPSPDLLMAR 29 0 Q5VWJ9 Q5VWJ9 SNX30 Sorting nexin-30 1 DMPHPLAGSSSEEAVGGDS(0.095)T(0.485)PS(0.419)PDLLMAR 106.3 0.0017585 113040000 23605 26943 13415 19977 25863 28869 23617 29249 27369 TRUE FALSE 20485.53944 26766.00966 19902.53887 24513.08318 25348.3769 29979.60911 21326.62698 22994.32897 24133.468 0.848843583 1.109082609 0.824686235 1.015729823 1.050341248 1.242242065 0.883695082 0.95279837 1 14.55874763 3.535371396 24.99965884 1.01832237 0.941444616 0.1258545 0.117487028 716.7835773 307625.2889 0.032628328 0.048395433 3430.610372 -3.535371396 -0.076877753 DMPHPLAGSSSEEAVGGDSTPS(ph)PDLLMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DMPHPLAGSSSEEAVGGDSTPSPDLLMAR 29 0 Q5VWJ9 Q5VWJ9 SNX30 Sorting nexin-30 1 DMPHPLAGSSSEEAVGGDS(0.012)T(0.064)PS(0.923)PDLLMAR 101.59 0.00041336 72005000 16084 20952 14946 12606 24098 16682 19019 20192 19209 TRUE FALSE 13958.45865 20814.36493 22173.93559 15468.38497 23618.49695 17323.76733 17174.54031 15874.09793 16938.1339 0.824084798 1.228846404 1.309113254 0.913228403 1.394397818 1.022767173 1.013957051 0.937181039 1 14.04798732 2.496103182 24.5936738 0.981433491 1.143868254 0.147964141 0.168690787 1034.000037 1339689.281 0.055254384 0.047927606 313.4030239 -2.496103182 0.162434763 DMQGLS(ph)LDAASQPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DMQGLSLDAASQPSK 15 0 E9PLZ8;Q96EY5;M0QZK6;E9PQA6;Q96EY5-3;E9PLL0 E9PLZ8 MVB12A Multivesicular body subunit 12A 1 DMQGLS(1)LDAASQPSK;DMQGLS(1)LDAASQPSK 267.6 1.92E-25 361670000 814610 688040 323900 297320 510780 351310 816100 643460 546300 TRUE FALSE 706957.2245 683520.2199 480539.1234 364831.0503 500616.4773 364825.123 736954.7476 505861.0864 481717.0363 1.467577792 1.418924739 0.997554762 0.757355507 1.039233491 0.757343203 1.529849875 1.050120814 1 18.87782642 4.254903286 8.341429215 1.03088725 1.445502731 0.409795933 0.211410885 0.177030132 66.39988131 0.054162466 0.135749335 17984.70367 -4.254903286 0.414615481 DMQPLS(ph)PISVHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DMQPLSPISVHER 13 0 P28749;P28749-2 P28749 RBL1 Retinoblastoma-like protein 1 1 DMQPLS(1)PISVHER 87.676 0.027662 90227000 78967 94825 29303 62232 103420 87323 76141 103490 85969 TRUE FALSE 68531.31087 94202.08833 43474.02881 76362.72676 101362.1443 90682.37232 68756.85754 81359.46886 75805.84276 0.904037319 1.242675827 0.573491795 1.007346188 1.337128388 1.196245158 0.90701264 1.073261188 1 16.21002143 3.477646992 24.99939925 1.096606079 0.91534405 0.175805757 0.193717783 35.53669893 1689878.634 0.055479347 0.07248749 3003.633862 -3.477646992 -0.181262029 DMS(ph)PLSETEMALGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 DMSPLSETEMALGK 14 0 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 DMS(1)PLSETEMALGK;DMS(0.996)PLS(0.004)ETEMALGK;DMS(1)PLSETEMALGK;DMS(0.999)PLS(0.001)ETEMALGK;DMS(1)PLSETEMALGK;DMS(0.994)PLS(0.004)ET(0.002)EMALGK;DMS(1)PLSETEMALGK;DMS(1)PLSETEMALGK;DMS(1)PLSETEMALGK;DMS(1)PLSETEMALGK 281.54 9.79E-33 584412000 2058920 1645036 1389873 1681337 1743837 1454291 2052997 2390720 2694330 TRUE FALSE 1786828.505 1634229.65 2062020.232 2063110.263 1709138.055 1510238.516 1853897.667 1879483.133 2375809.377 0.752092539 0.687862278 0.867923265 0.86838207 0.719391914 0.63567327 0.780322565 0.791091723 1 21.17998766 1.180091678 2.630517101 1.081840659 0.758950353 0.523070257 0.071723606 0.547570105 3.743648535 0.423934148 0.020017805 15.1388079 -1.180091678 -0.322890306 DMSGHYQNALYLGDVSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DMSGHYQNALYLGDVSER 18 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;;;;; 174.82 4.88E-12 1271830000 1099787 1056149 546342 771624 1079820 1136135 927174 1166067 1175350 FALSE TRUE 954447.3614 1049211.088 810554.8186 946833.0227 1058333.695 1179842.849 837256.8082 916712.6464 1036401.462 0.920924368 1.012359714 0.782085754 0.913577467 1.021161908 1.138403304 0.807849891 0.884515007 1 19.98315153 6.189894229 14.66211802 0.937032858 0.947290783 0 0.106213285 0 0 0.024231854 0 1548439.456 -6.189894229 0.010257925 DMSPLSETEMALGKDVT(ph)PPPETEVVLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DMSPLSETEMALGKDVTPPPETEVVLIK 28 1 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 DMSPLSETEMALGKDVT(0.977)PPPET(0.023)EVVLIK;DMSPLSETEMALGKDVT(1)PPPETEVVLIK;DMSPLSETEMALGKDVT(0.966)PPPET(0.034)EVVLIK 179.54 2.55E-17 372030000 2022790 1371730 872910 966750 1303240 999970 1874900 2141740 654521 TRUE FALSE 1755473.176 1362719.015 1295052.196 1186265.363 1277308.074 1038439.493 1693072.487 1683745.568 577144.273 3.041653982 2.361141016 2.243896814 2.055405241 2.213152124 1.799271935 2.93353424 2.917373778 1 19.13857248 4.741450842 3.297403906 2.260020431 3.151526858 0.183940791 0.550772904 0.648604339 11.45504835 0.138797038 1.479115049 55137.97882 -4.741450842 0.891506427 DMVTELFDPLVQGEVQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DMVTELFDPLVQGEVQHR 18 0 Q9BXV9 Q9BXV9 C14orf142 Uncharacterized protein C14orf142 0 ;;; 193.69 1.11E-14 472360000 379461 342954 222568 285294 321544 350389 331029 385848 359135 FALSE TRUE 329314.2674 340701.1126 330202.6292 350074.3631 315145.9035 363868.6916 298925.8585 303337.4079 316678.4694 1.039901033 1.075858151 1.042706281 1.105456786 0.995160498 1.1490162 0.943941213 0.957871902 1 18.27265926 2.21325163 24.99999891 0.964340765 1.06561269 0.550471027 0.042853191 150.7821316 148940.0907 0.015792679 0.010651926 163.3998412 -2.21325163 0.101271925 DNAMLEYLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DNAMLEYLK 9 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 140.45 0.00025377 285280000 406730 417210 322200 448630 454310 351680 460770 550540 571040 FALSE TRUE 352979.6 414469.32 478016.9977 550498.2984 445270.1198 365209.3572 416084.5963 432811.3053 503532.3017 0.701006864 0.823123598 0.949327374 1.093273056 0.88429306 0.725294794 0.826331488 0.859550229 1 18.9417248 4.594136167 3.286227801 0.89633581 0.699086046 0.302024181 0.099182465 0.392006402 6.98304033 0.027058795 0.155758558 39276.80629 -4.594136167 -0.197249764 DNDFIYHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DNDFIYHDR 9 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;; 135.66 0.00021452 2824790000 4525440 4690020 2650690 3492040 4931480 4706460 4182550 5206450 5034880 FALSE TRUE 3927391.638 4659210.95 3932572.55 4284961.054 4833353.196 4887520.562 3776926.945 4093091.184 4439662.222 0.884614964 1.049451674 0.885781925 0.965154744 1.088675884 1.10087667 0.850723942 0.921937521 1 22.08201849 2.221152345 24.9999694 0.920682556 0.9960333 0.147074973 0.081061209 464.9179915 667662.5121 0.033656521 0.022749221 166.3996258 -2.221152345 0.075350745 DNDTLKDLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DNDTLKDLLK 10 1 Q9H8Y8;Q9H8Y8-3 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 0 72.958 0.042342 316860000 381900 309720 257340 224930 254930 209200 413230 455060 159530 FALSE TRUE 331430.9474 307685.4289 381790.4848 276003.7943 249857.3918 217248.0594 373155.0182 357748.9603 140670.5451 2.356079214 2.187276865 2.714075533 1.962058184 1.776188409 1.544374902 2.652687653 2.543168934 1 17.10196075 3.707050846 24.1588107 2.00387291 2.39595729 0.177921378 0.486555447 961.7692613 737396.0619 0.140083916 0.207805498 5093.905056 -3.707050846 0.39208438 DNEEKDSAFR ddPTM_MDA-MB-175_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 ; 123.67 0.00041576 750070000 1201080 903390 638100 699510 833780 688670 1080850 1191550 726360 FALSE TRUE 1042354.235 897455.5716 946687.2943 858344.4368 817189.4093 715163.5805 976029.3334 936746.3052 640490.5483 1.627431096 1.401200336 1.478065987 1.340135993 1.275880513 1.116587251 1.523877809 1.462545088 1 19.28881776 6.630192265 0.622635349 1.309599751 4.786327427 0.318087045 0.15591136 45.91626532 1.982816535 0.073038065 187.1639467 4267684.099 -6.630192265 3.476727677 DNEGSWFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DNEGSWFR 8 0 Q9BPW8;H7C2U6;F8WCR5 Q9BPW8 NIPSNAP1 Protein NipSnap homolog 1 0 ; 129.42 0.0037508 104730000 149079 159717 124382 186418 170452 168494 138952 174102 292160 FALSE TRUE 129377.8324 158667.8085 184533.5512 228747.0561 167060.3387 174976.0732 125476.4564 136871.6422 257621.1776 0.502201852 0.615895828 0.716298066 0.887920233 0.648472848 0.679199105 0.487058003 0.531290337 1 17.97489167 4.599221618 3.105963704 0.682547083 0.497852341 0.148190396 0.15156295 0.662501519 10.44876706 0.039680698 0.244655484 39739.42858 -4.599221618 -0.184694743 DNFDEMDTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DNFDEMDTSR 10 0 P23258 P23258 TUBG1 Tubulin gamma-1 chain 0 115.29 0.0055391 0 150150 129220 99654 112460 146740 135190 127980 130890 200610 FALSE TRUE 130307.2971 128371.1453 147847.0077 137995.7618 143820.1611 140390.8468 115568.5193 102900.1921 176894.1143 0.736640094 0.725694836 0.835793821 0.780103749 0.813029657 0.793643402 0.65332032 0.581705007 1 17.43252652 2.260871055 24.94224235 0.707166538 0.782242688 0 0.112357972 569.4254765 636595.1087 0.041447967 0.03208022 182.3354254 -2.260871055 0.07507615 DNFFEVFTPVFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DNFFEVFTPVFER 13 0 Q99543;Q99543-2;H7C3L7;C9IZ83 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 0 ; 113.65 0.00072895 0 304760 266730 199282 218450 275413 216334 323910 350920 227611 FALSE TRUE 264485.1938 264977.8331 295655.4418 268052.4113 269932.8201 224656.509 292497.2581 275878.4889 200703.0869 1.317793353 1.32024792 1.473098627 1.335566958 1.344936066 1.119347552 1.457363026 1.374560268 1 17.61470328 2.976453928 24.72716984 1.274474523 1.363373173 0.145189736 0.133173308 1715.738915 1801803.608 0.043093051 0.043356251 947.2266925 -2.976453928 0.08889865 DNFGFIETANHDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DNFGFIETANHDK 13 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;;; 188.39 3.57E-07 852570000 1091210 832125 778236 1063436 887938 799495 1121147 1306010 1983690 FALSE TRUE 947003.8337 826658.7161 1154593.533 1304905.397 870269.771 830252.09 1012418.337 1026729.925 1749180.428 0.541398599 0.472597739 0.660076865 0.746009603 0.497530019 0.474652058 0.578795829 0.586977712 1 20.73824768 1.235897766 5.303426527 1.024265205 0.569287161 0.720882781 0.084208793 0.093106756 7.500044716 0.155758307 0.022151656 17.21463292 -1.235897766 -0.454978045 DNFHGLAIFLDTYPNDETTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DNFHGLAIFLDTYPNDETTER 21 0 Q12907;D6RBV2;D6RIU4 Q12907 LMAN2 Vesicular integral-membrane protein VIP36 0 ;;;; 244.95 3.46E-30 857608000 977284 1003944 584711 756482 1040942 1035024 783154 1129500 1165738 FALSE TRUE 848133.4433 997349.0258 867479.1953 928252.8002 1020229.291 1074842.043 707203.8456 887965.2148 1027925.782 0.825092101 0.970253926 0.843912285 0.903034846 0.992512601 1.045641682 0.687991155 0.863841758 1 19.97130467 2.258235101 24.99988355 0.846591399 0.929593398 0.126280769 0.098337472 480.339651 610354.5677 0.036719113 0.028401975 181.2320908 -2.258235101 0.083001999 DNFWEMGDTGPCGPCSEIHYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DNFWEMGDTGPCGPCSEIHYDR 22 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;;;; 255.94 4.27E-37 3177840000 1599909 1231864 588429 796189 1076157 1115031 1122446 1390452 1202751 FALSE TRUE 1388476.972 1223771.804 872995.2326 976975.8814 1054743.581 1157926.964 1013591.36 1093114.66 1060563.147 1.309188402 1.153888675 0.823143096 0.921185961 0.994512759 1.091803885 0.955710523 1.030692669 1 20.01639909 4.455959041 6.220400873 0.980779446 1.274274794 0.712784307 0.071325237 0.076405489 10.59935066 0.018614192 0.053949893 28573.21049 -4.455959041 0.293495349 DNGLLAKPTHGDIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DNGLLAKPTHGDIIR 15 1 P04181;P04181-2 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 ; 101.05 0.0011528 402180000 121127 138754 96962 172137 164139 153672 148516 187121 155751 FALSE TRUE 105119.7601 137842.5158 143853.1475 211223.3368 160872.955 159583.8613 134112.9412 147106.6303 137338.2942 0.765407497 1.003671384 1.047436539 1.53797845 1.171362699 1.161976433 0.976515268 1.071126092 1 17.06737442 4.59755506 2.124012769 1.139494131 0.726539962 0.374129295 0.155526038 0.585379764 3.712875044 0.043601594 0.411598908 39587.22507 -4.59755506 -0.412954169 DNHLLGTFDLTGIPPAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DNHLLGTFDLTGIPPAPR 18 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 149.36 6.27E-08 324770000 257920 178000 125050 157420 196430 202120 128700 163200 148630 FALSE TRUE 223835.2185 176830.7063 185524.5983 193164.617 192521.4273 209895.6872 116218.6938 128300.95 131059.1307 1.707894881 1.349243699 1.415579344 1.473873785 1.468966155 1.601534254 0.886765334 0.978954685 1 16.99985834 2.235815145 24.99999554 0.957327368 1.489042721 0.865037266 0.101867187 23.0772762 210134.6598 0.038819496 0.027504202 172.1135826 -2.235815145 0.531715353 DNIACVILTFKEPFGTEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DNIACVILTFKEPFGTEGR 19 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 252.4 6.86E-31 3606200000 4112000 3845900 1828430 2117710 3248700 3127100 4584900 4643100 968780 FALSE TRUE 3568588.782 3820636.03 2712664.864 2598568.423 3184057.226 3247401.561 4140257.104 3650209.198 854251.932 4.177443033 4.472493285 3.175485781 3.041922793 3.727304682 3.801456501 4.846646462 4.272989104 1 19.70430208 4.25076404 24.98624307 3.575733644 4.324968469 0.106670318 1.016442242 603.1292995 1234870.703 0.255364144 0.664916618 17814.10632 -4.25076404 0.749234825 DNIPALVEEYLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DNIPALVEEYLER 13 0 Q9H1I8;B1AH59 Q9H1I8 ASCC2 Activating signal cointegrator 1 complex subunit 2 0 ; 112.44 0.0020957 25066000 35435 34164 22184 27280 30844 31436 32055 31016 38898 FALSE TRUE 30752.17497 33939.57443 32912.2566 33474.34095 30230.26475 32645.36326 28946.31103 24383.46977 34299.52275 0.896577343 0.989505734 0.95955436 0.975941887 0.88136109 0.951773105 0.843927516 0.710898223 1 15.06590088 2.179982155 5.073841424 0.819212983 0.944252946 0.202364087 0.077594038 0.215548771 11.2086535 0.031341934 0.021066702 151.3499058 -2.179982155 0.125039963 DNIQGITKPAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DNIQGITKPAIR 12 1 P62805 P62805 HIST1H4A Histone H4 0 ;; 172.57 3.23E-05 4444440000 3186760 2972890 2705910 6640990 2491170 5969040 4085720 5392600 4590160 FALSE TRUE 2765621.592 2953360.89 4014497.127 8148928.281 2441600.591 6198672.831 3689487.503 4239434.455 4047516.514 0.683288526 0.729672351 0.991842062 2.013315635 0.603234251 1.531475612 0.911543533 1.047416222 1 21.94860554 4.134441067 4.563319829 1.166626284 0.707968123 0.208480252 0.377586862 0.312847255 11.02848767 0.092471803 0.20693744 13628.2806 -4.134441067 -0.45865816 DNKPLVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DNKPLVER 8 1 Q9UHB9;Q9UHB9-4;Q9UHB9-2;Q9UHB9-3 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;; 118.03 0.0017916 1120990000 2171790 1860480 1401080 1697150 1893650 1838040 2305910 2720940 2633080 FALSE TRUE 1884782.449 1848258.384 2078646.974 2082513.847 1855970.07 1908750.588 2082283.203 2139088.155 2321800.282 0.811776303 0.796045379 0.895273806 0.896939269 0.799366804 0.822099387 0.89683993 0.921305838 1 21.14681245 1.457372628 1.262068407 1.0342969 0.839195074 0.674553066 0.036946657 0.608268773 1.157635654 0.146003483 0.012412115 28.66636513 -1.457372628 -0.195101826 DNLEDETEDDDLFETEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DNLEDETEDDDLFETEFR 18 0 Q8IZH2-2;Q8IZH2;Q8IZH2-3 Q8IZH2-2 XRN1 5-3 exoribonuclease 1 0 97.551 0.0032249 115910000 23453 19570 14417 18876 20772 22158 20997 25943 23536 FALSE TRUE 20353.62663 19441.44338 21389.10942 23162.0843 20358.67784 23010.4326 18960.71417 20395.29134 20753.60089 0.980727476 0.936774465 1.030621603 1.11605135 0.980970866 1.108744103 0.913610812 0.982735066 1 14.34107406 2.216911501 24.99930022 0.966890099 1.023913138 0.187907945 0.058896304 434.949609 502254.1127 0.024339407 0.016426018 164.7826567 -2.216911501 0.057023039 DNLEFFLAGIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 DNLEFFLAGIGR 12 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;; 201.33 3.48E-07 12430830000 6260214 6887395 4792375 5040316 7102102 7450576 7317757 7596826 8162343 FALSE TRUE 5432910.859 6842151.249 7109983.58 6184796.784 6960784.065 7737204.48 6608082.052 5972303.878 7197400.109 0.754843524 0.950642058 0.98785443 0.859309847 0.967124789 1.074999911 0.918120704 0.829786282 1 22.77904443 4.740457087 24.34901275 0.94076406 0.754843434 0.427466135 0.069921945 129.5032474 1662520.725 0.0180559 0.113315296 55011.95601 -4.740457087 -0.185920626 DNLEWLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DNLEWLAR 8 0 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;;;; 185.05 0.00049972 2956638000 3138600 2917500 1927950 2249080 2861200 2813340 2882700 3227450 3145380 FALSE TRUE 2723826.058 2898334.75 2860313.069 2759767.989 2804267.718 2921571.01 2603136.198 2537284.934 2773536.76 0.982076783 1.044995975 1.03128724 0.995035663 1.011080062 1.05337382 0.938561996 0.914819292 1 21.40329542 2.224709578 24.99738854 0.943039396 1.019815798 0.532583448 0.029939408 155.295207 280263.6775 0.011844001 0.008032241 167.7681741 -2.224709578 0.076776401 MEITIRNS(ph)PYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 MEITIRNSPYR 11 1 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;Q9UQ88-9;A0A087X1I0;A0A087WYI9 P21127-2 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 MEITIRNS(1)PYR;MEITIRNS(1)PYR;MEITIRNS(1)PYR;MEITIRNS(0.982)PY(0.018)R;MEIT(0.044)IRNS(0.956)PYR;MEITIRNS(1)PYR 179.27 4.35E-06 2796030000 3811960 3540770 1906970 2161630 3321550 3671660 3379860 3795430 1731960 TRUE FALSE 3308199.828 3517510.449 2829187.07 2652461.13 3255457.654 3812911.136 3052081.697 2983806.831 1527209.662 2.166172668 2.303226948 1.852520411 1.736802219 2.131637675 2.496652052 1.998469348 1.95376372 1 20.5424667 1.169997282 2.57112714 0.594181454 2.096699572 0.719309939 0.213552062 0.386192317 2.419460703 1.385812008 0.059533274 14.79099133 -1.169997282 1.502518118 DNLHQIDAVEGPAAFLDILAPPYDPDDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DNLHQIDAVEGPAAFLDILAPPYDPDDGR 29 0 Q96SZ5 Q96SZ5 ADO 2-aminoethanethiol dioxygenase 0 ;;; 149.07 4.37E-08 158413000 127054 101557 89642 120275 117412 107696 117623 141340 214025 FALSE TRUE 110263.492 100889.8654 132993.171 147585.277 115075.7309 111839.1348 106215.9396 111115.5409 188723.2083 0.584260372 0.534591724 0.704699609 0.782019755 0.609759297 0.592609334 0.562813342 0.58877518 1 17.52591232 1.23573113 24.99750782 1.000000511 0.619676494 0.731627222 0.072339705 44.95142087 397053.0559 0.129725532 0.01918086 17.20802902 -1.23573113 -0.380324017 DNLLFGDEIITNGFHSCES(ph)DEEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DNLLFGDEIITNGFHSCESDEEDR 24 0 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 DNLLFGDEIITNGFHS(0.28)CES(0.719)DEEDR;DNLLFGDEIITNGFHS(0.094)CES(0.906)DEEDR 83.633 0.008592 38764000 31953 29314 18016.3 26088 32060 27978 31078 32865 39687 TRUE FALSE 27730.33009 29121.4344 26729.04294 32011.67913 31422.06872 29054.33176 28064.06034 25837.07551 34995.24807 0.792402729 0.832153964 0.763790641 0.914743598 0.897895299 0.830236485 0.801939174 0.738302396 1 15.09487141 3.767101552 24.98523181 0.84692283 0.799719607 0.135995566 0.072362706 2045.527625 1790683.423 0.019978923 0.03459647 5849.268422 -3.767101552 -0.047203223 DNLSSWLEHLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DNLSSWLEHLPR 12 0 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 ; 208.27 6.88E-08 695410000 672500 703300 388080 574750 681440 714590 629820 767760 840180 FALSE TRUE 583627.4211 698679.976 575756.786 705255.772 667880.6772 742080.7397 568740.1533 603580.4987 740854.8775 0.787775634 0.943072655 0.777151914 0.951948612 0.901500007 1.001654659 0.767680919 0.814708139 1 19.49883144 4.76655807 22.03788322 0.884178043 0.787774941 0.124181255 0.085263774 4268.236042 3359416.847 0.020531919 1.400141936 58419.53158 -4.76655807 -0.096403102 DNLSYIEHIFEISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DNLSYIEHIFEISR 14 0 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 ;;;;; 252.17 3.39E-24 2116321000 1814930 1835205 1237404 1669725 1791500 1766807 1801650 2058501 2991970 FALSE TRUE 1575082.402 1823149.418 1835816.713 2048861.581 1755852.655 1834777.209 1626926.26 1618306.58 2638262.715 0.597014995 0.691041649 0.695843027 0.77659498 0.665533665 0.695449016 0.616665752 0.613398571 1 21.3311568 1.232604542 24.99996669 1.000000536 0.669505737 0.798984825 0.052184927 93.08011093 390653.693 0.120846695 0.013658666 17.08458925 -1.232604542 -0.3304948 DNLTLWTSDQQDDDGGEGNN ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DNLTLWTSDQQDDDGGEGNN 20 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;;;;;; 489.45 3.14E-249 7110080000 10713470 8839910 6081010 7259350 8597170 9095730 9148950 10460070 10325860 FALSE TRUE 9297657.795 8781840.049 9021806.776 8907696.37 8426103.137 9445648.619 8261686.237 8223265.431 9105148.594 1.021142895 0.964491678 0.990846737 0.978314223 0.925421815 1.037396427 0.90736424 0.903144561 1 23.11825113 8 0.205706046 0.925177186 1.339775836 0.138305589 0.042619447 172.0168488 2.579398189 0.256618365 22.42866046 100000000 -8 0.41459865 DNLTLWTSDQQDEEAGEGN ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DNLTLWTSDQQDEEAGEGN 19 0 Q04917 Q04917 YWHAH 14-3-3 protein eta 0 ; 345.69 3.04E-90 192114000 512130 446810 284540 382730 462190 467740 468400 519790 497570 FALSE TRUE 444450.7229 443874.8757 422144.4957 469634.6962 452993.3233 485734.2605 422974.6401 408636.9535 438747.8414 1.012998084 1.011685606 0.96215743 1.070397736 1.032468494 1.10709208 0.964049507 0.931370858 1 18.7430325 2.038702441 24.99945973 0.956861308 1.030760435 0.369814327 0.041226994 149.9102844 96832.45127 0.016988465 0.011453603 109.3207093 -2.038702441 0.073899127 DNLTLWTSENQGDEGDAGEGEN ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 DNLTLWTSENQGDEGDAGEGEN 22 0 P31946-2;P31946 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 ;;;;;;;;;;;; 332.29 1.98E-80 10544527000 13041269 10327330 6925443 8261220 9943567 10183361 10564256 11712187 11000359 FALSE TRUE 11317832.26 10259489.09 10274610.4 10137056.27 9745709.471 10575121.49 9539736.079 9207626.954 9699909.091 1.166797766 1.0576892 1.059248113 1.045067141 1.004721733 1.090228928 0.983487164 0.949248789 1 23.2095398 8 0.223981997 0.951624834 1.977962148 0.647887778 0.036247237 59.93103662 0.926840481 0.172551846 21.66027424 100000000 -8 1.026337313 DNNLLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 95.531 0.03117 364980000 738440 658280 476030 597560 612430 612460 651790 747280 1114940 FALSE TRUE 640853.283 653955.7153 706239.7002 733245.1311 600243.8412 636021.7325 588579.5061 587479.9873 983133.0633 0.651847961 0.665175183 0.718356168 0.745824913 0.610541811 0.646933519 0.598677359 0.597558977 1 19.90702717 1.232998951 24.99997466 1.000000551 0.652685422 0.835459407 0.048200163 78.33663064 352089.3283 0.11271218 0.013253497 17.10011183 -1.232998951 -0.347315129 DNNLLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 ;;;;;;; 177.71 0.0016898 10128540000 7544350 6783870 4269880 4990880 6635070 6651870 6961660 8038320 7545030 FALSE TRUE 6547345.033 6739306.311 6334808.25 6124135.585 6503045.088 6907771.743 6286519.285 6319387.822 6653065.149 0.984109562 1.012962621 0.952163869 0.920498364 0.977450986 1.038284097 0.944905716 0.949846076 1 22.66558773 4.239078015 24.99894857 0.96705909 0.998536092 0.118717273 0.033097796 28.12156998 1358383.508 0.008688074 0.020315446 17341.15478 -4.239078015 0.031477002 DNNQFASASLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DNNQFASASLDR 12 0 P35606;P35606-2;D6R997 P35606 COPB2 Coatomer subunit beta 0 140.63 0.0001392 166520000 128250 102610 75196 93642 112280 97908 105940 119000 135050 FALSE TRUE 111301.4376 101935.9482 111561.0371 114904.8473 110045.8477 101674.5841 95665.95511 93552.77606 119084.5428 0.934642187 0.855996469 0.936822147 0.964901444 0.924098502 0.853801691 0.803344857 0.785599657 1 16.86162664 2.703997784 5.085577907 0.842767381 0.922799048 0.171718493 0.063391449 0.27594168 19.01630752 0.022033862 0.019843302 505.8220811 -2.703997784 0.080031666 DNPGVVTCLDEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DNPGVVTCLDEAR 13 0 P22314;P22314-2;Q5JRR9;Q5JRS0 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 128.61 0.00012216 0 76383 62537 34182 43585 72183 60538 56465 65681 64163 FALSE TRUE 66288.79302 62126.19033 50712.52953 53481.64041 70746.69952 62866.93603 50989.03299 51635.62928 56577.72323 1.171641226 1.098068052 0.896333868 0.945277352 1.250433836 1.111160585 0.901221012 0.912649473 1 15.7879465 2.236576777 24.99962152 0.931153787 1.073129909 0.289046045 0.103704026 71.22271717 897494.0838 0.043698001 0.031138382 172.4156869 -2.236576777 0.141976122 DNPHFENGETSIVISDVLPGGPADGLLQENDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DNPHFENGETSIVISDVLPGGPADGLLQENDR 32 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IU26;B1AN86;U3KQJ2 Q9UDY2-7 TJP2 Tight junction protein ZO-2 0 123.73 1.51E-07 53747000 19286 17155 14289 20341 16609 18861 16301 19885 27814 FALSE TRUE 16737.30624 17042.30768 21199.20819 24959.73494 16278.51339 19586.59487 14720.13153 15632.7475 24525.86061 0.682435023 0.694870934 0.86436144 1.017690484 0.66372853 0.798609891 0.600188175 0.63739853 1 14.58201614 DNPS(ph)PGPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DNPSPGPSR 9 0 Q9NQS1 Q9NQS1 AVEN Cell death regulator Aven 1 DNPS(0.981)PGPS(0.019)R 72.187 0.049785 345300000 216840 235060 134440 185680 220430 285330 227320 265790 252310 TRUE FALSE 188184.0446 233515.8754 199455.6337 227841.4819 216043.8743 296306.8297 205274.5414 208952.8769 222482.1992 0.845838657 1.049593523 0.896501537 1.024088591 0.971061393 1.331822639 0.922656024 0.939189192 1 17.76333039 3.712116573 21.25044503 1.025054013 0.942539507 0.124351375 0.124025114 297.0227818 238686.8061 0.034802622 0.051662934 5153.669607 -3.712116573 -0.082514506 DNPSIFVHSPHALMLQDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DNPSIFVHSPHALMLQDVK 19 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 124.37 1.70E-05 313040000 816880 719010 335270 581500 737630 525170 843030 945020 570740 FALSE TRUE 708927.2383 714286.776 497407.6934 713538.4627 722952.6061 545373.6297 761273.0804 742934.8272 503267.7674 1.408648207 1.419297683 0.988355952 1.417810774 1.436516807 1.08366493 1.512660118 1.476221756 1 18.94096668 DNQESS(ph)DAELSSSEYIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DNQESSDAELSSSEYIK 17 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 DNQES(0.001)S(0.999)DAELSSSEYIK;DNQES(0.006)S(0.994)DAELSSSEYIK 359.69 3.83E-88 647150000 1126520 944170 660810 838420 981500 752320 1038330 1352580 1201820 TRUE FALSE 977647.5278 937967.6851 980379.9263 1028796.075 961970.0703 781262.2372 937632.9164 1063341.293 1059742.209 0.922533348 0.885090428 0.925111709 0.970798433 0.907739696 0.737219138 0.884774532 1.003396188 1 20.01528193 1.721943616 5.769024043 1.001607465 0.889368405 0.370256747 0.060191191 0.158343869 13.34872791 0.039359723 0.016780561 52.71614164 -1.721943616 -0.11223906 DNQHQGSYSEGAQMNGIQPEEIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DNQHQGSYSEGAQMNGIQPEEIGR 24 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ; 229.69 2.59E-33 220550000 159001 126938 69021 102406 130353 144241 118247 151884 137350 FALSE TRUE 137988.615 126104.1359 102399.7865 125658.8475 127759.2303 149790.0446 106779.4241 119404.7886 121112.6395 1.139341159 1.041213671 0.845492154 1.037537024 1.054879415 1.236782926 0.881653844 0.985898657 1 16.88598991 DNQVVQLHPSTVLDHKPEWVLYNEFVLTTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DNQVVQLHPSTVLDHKPEWVLYNEFVLTTK 30 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 99.976 0.00032739 169600000 218450 177810 60975 173280 193040 143480 250440 300160 283780 FALSE TRUE 189581.279 176641.9544 90462.71395 212625.8724 189198.8817 148999.7684 226152.3673 235973.1198 250231.8517 0.757622492 0.705913149 0.361515584 0.849715458 0.75609432 0.595446852 0.903771306 0.943017918 1 17.93290591 2.138600425 5.216908785 0.95427661 0.671030313 0.506075815 0.130119155 0.171907382 7.376798138 0.054775124 0.03642474 137.5942941 -2.138600425 -0.283246297 DNS(ph)PPPAFKPEPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DNSPPPAFKPEPPK 14 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 DNS(1)PPPAFKPEPPK;DNS(1)PPPAFKPEPPK;DNS(1)PPPAFKPEPPK 120.31 8.28E-05 6558250000 6701900 4355990 6148110 5604020 5037440 3491620 7046700 8415600 11963500 TRUE FALSE 5816226.935 4327375.215 9121356.56 6876498.393 4937204.8 3625944.881 6363312.119 6615989.43 10549188.66 0.551343532 0.410209292 0.864650056 0.651850926 0.46801749 0.343717891 0.603203936 0.627156234 1 23.33062871 1.15781541 2.308351433 1.193623323 0.555470575 0.487443325 0.141859442 0.753489327 3.466351672 1.077256971 0.039324628 14.38187171 -1.15781541 -0.638152748 DNSTMGYMAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DNSTMGYMAAK 11 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 174.4 0.0017337 0 195450 165870 95362 143160 156610 125060 186080 227250 167210 FALSE TRUE 169620.7873 164780.389 141479.3822 175666.6661 153493.7674 129871.1391 168033.9902 178654.356 147442.6243 1.150418938 1.117589909 0.959555507 1.191423897 1.041040663 0.880824929 1.139656806 1.211687304 1 17.16979413 DNTFFRES(ph)PVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 177.04 1.44E-05 12544600000 6616600 5239160 3503820 3912290 5270130 5364750 5669400 6277200 4497740 TRUE FALSE 5742199.546 5204743.613 5198279.072 4800635.24 5165264.724 5571135.404 5119582.461 4934869.629 3966022.301 1.447848527 1.312333421 1.31070344 1.210440808 1.302379143 1.404716106 1.290860735 1.244286909 1 21.91926136 1.12586513 1.821753113 0.809096804 1.322904113 0.720455556 0.063750779 0.68497525 1.673191826 0.676646411 0.017850676 13.36180501 -1.12586513 0.513807309 DNTIEHLLPLFLAQLKDECPEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DNTIEHLLPLFLAQLKDECPEVR 23 1 P30153;B3KQV6 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ; 128.12 2.62E-05 674290000 638800 537140 374602 370129 522020 425840 682800 786360 215217 FALSE TRUE 554380.9615 533611.492 555760.7802 454172.4465 511632.8233 442222.3404 616582.1611 618203.0335 189774.2914 2.921264821 2.811821812 2.928535662 2.393224304 2.696007027 2.330254204 3.24902892 3.257569973 1 17.53392504 3.768208022 23.72424476 2.617582554 2.879668946 0.057466616 0.630048308 1611.899763 1289854.545 0.16671502 0.288688546 5864.189855 -3.768208022 0.262086392 DNTINLIHTFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DNTINLIHTFR 11 0 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;;;; 180.28 6.73E-06 6605820000 6832280 5883910 3783470 5196530 6390980 6218290 6246960 6957690 6962010 FALSE TRUE 5929376.887 5845258.208 5613168.747 6376481.56 6263812.002 6457511.64 5641130.781 5469842.138 6138969.109 0.965858727 0.952156316 0.914350382 1.038689306 1.020336133 1.051888603 0.918905223 0.891003366 1 22.54956498 2.189419982 24.99996392 0.926390422 0.988880685 0.202391224 0.048990313 161.2374078 82027.17541 0.021130122 0.014245954 154.6749492 -2.189419982 0.062490263 DNTRPGANS(ph)PEMWSEAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DNTRPGANSPEMWSEAIK 18 1 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 1 DNTRPGANS(1)PEMWSEAIK;DNTRPGANS(1)PEMWSEAIK;DNTRPGANS(1)PEMWSEAIK;DNTRPGANS(1)PEMWSEAIK 291.24 2.14E-49 1451550000 1310240 1083520 762060 1003900 1124540 893900 1272510 1532310 1411460 TRUE FALSE 1137088.464 1076402.286 1130594.765 1231850.839 1102163.854 928288.9114 1149102.176 1204637.431 1244598.807 0.913618475 0.864858844 0.908400971 0.989757368 0.885557537 0.74585393 0.923271154 0.967892163 1 20.24724934 1.751874677 3.309081309 0.988546613 0.88666938 0.306049426 0.060565968 0.277467044 6.254645124 0.044800988 0.017247566 56.47739768 -1.751874677 -0.101877233 DNTVHDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DNTVHDLR 8 0 Q08378;Q08378-4;Q08378-2 Q08378 GOLGA3 Golgin subfamily A member 3 0 ;; 115.71 0.0024106 1076550000 824800 795360 438257 548100 732170 786780 737880 887670 847570 FALSE TRUE 715800.5902 790135.2278 650199.5511 672554.4822 717601.2495 817047.9357 666320.5112 697848.6784 747371.2402 0.95775774 1.057219204 0.869982033 0.899893448 0.960167064 1.09322903 0.891552251 0.933737667 1 19.51146552 2.183583859 0.003083073 0.34274827 1.573109923 0 0.071549694 1135847.768 1986.037421 398570.4388 393995.4729 152.6103047 -2.183583859 1.230361652 DNVKNEDKDQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DNVKNEDKDQK 11 2 Q8IX12-2;Q8IX12 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 49.423 0.091929 39529000 85654 54976 46630 43845 47039 45776 81014 96749 35157 FALSE TRUE 74334.60688 54614.85904 69180.42397 53800.67738 46103.01593 47537.03234 73157.27475 76059.97925 31000.77951 2.39783025 1.761725347 2.231570466 1.735462083 1.487156667 1.533414098 2.359852749 2.453486024 1 14.92001687 6.340822494 1.869238804 1.882547692 167.5363673 0.124806555 0.444788201 1240.732283 16.64915982 0.12135813 873645.4974 2191908.872 -6.340822494 165.6538197 DNVYYYDEEGGGEEDQDFDLSQLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DNVYYYDEEGGGEEDQDFDLSQLHR 25 0 A0A087WXI5;P12830-2;P12830 A0A087WXI5 CDH1 Cadherin-1;E-Cad/CTF1;E-Cad/CTF2;E-Cad/CTF3 0 117.82 0.00091761 49667000 34744 29779 22493 43593 39217 37598 19624 44903 60973 FALSE TRUE 30152.49237 29583.37979 33370.69003 53491.45693 38436.65843 39044.41939 17720.8675 35300.84289 53764.8414 0.560821749 0.55023653 0.620678666 0.994915181 0.714903223 0.726207283 0.329599549 0.656578574 1 15.71437543 3.992001093 23.73212478 0.709967738 0.563011127 0.136169232 0.186577415 475.1103732 1409647.452 0.050959951 0.098810428 9817.504127 -3.992001093 -0.146956611 DNWEELYNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DNWEELYNR 9 0 E9PLK3;P55786;P55786-2;H0YDG0 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ; 209.86 1.80E-05 1016460000 766680 676290 660980 715640 671870 723080 801470 833450 1620980 FALSE TRUE 665361.2955 671847.4065 980632.1388 878136.9999 658501.1015 750897.3555 723743.5628 655223.2034 1429349.591 0.465499343 0.470037149 0.686068786 0.614361249 0.460699822 0.525341988 0.506344681 0.458406542 1 20.44692738 1.233749669 24.98274454 1.00000073 0.523872315 0.803503756 0.074077686 67.92665237 352692.694 0.152801607 0.019177401 17.12969651 -1.233749669 -0.476128415 DNWGHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DNWGHFR 7 0 G3V2F4;E7EPD8;Q9NUW8;H0YJ44;Q9NUW8-2 G3V2F4 TDP1 Tyrosyl-DNA phosphodiesterase 1 0 ; 90.308 0.017234 257050000 250400 268490 145401 181144 257580 250010 237480 273690 248440 FALSE TRUE 217309.0056 266726.2715 215717.4099 222275.5138 252454.6619 259628.0465 214449.2262 215163.5234 219069.7062 0.991962829 1.217540645 0.984697582 1.014633733 1.152394214 1.185138972 0.978908631 0.982169224 1 17.74103047 2.197803558 24.95062729 0.985675735 1.091289614 0.279278008 0.078773857 188.8473067 115607.0858 0.031770851 0.021420164 157.689784 -2.197803558 0.10561388 DNWVFCGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DNWVFCGGK 9 0 Q92520 Q92520 FAM3C Protein FAM3C 0 76.064 0.056208 0 24530 20385 15111 16793 20169 19358 18094 22999 23404 FALSE TRUE 21288.29835 20251.08959 22418.73014 20606.10731 19767.67636 20102.71479 16339.24666 18080.84283 20637.20578 1.031549454 0.981290287 1.086325851 0.998493087 0.957865932 0.974100612 0.791737352 0.876128436 1 14.33296003 2.819360583 1.636520525 0.88654001 1.025475017 0.447751117 0.060573152 0.313553483 1.69434871 0.025617776 0.024026766 659.7214173 -2.819360583 0.138935007 DNYLFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DNYLFLK 7 0 Q9Y2J8;Q9Y2J8-2 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ; 101.99 0.020244 475750000 504080 533420 374350 436720 499610 428060 598310 657120 681000 FALSE TRUE 437464.5508 529915.9289 555386.9121 535883.9508 489668.7385 444527.7452 540285.9883 516600.0017 600492.9558 0.728509047 0.882468185 0.924884975 0.892406723 0.815444601 0.740271374 0.899737429 0.860293192 1 19.1957878 0.832260195 1.573396659 1.290330358 0.842227508 0.367069784 0.065256301 4.02635268 3.71128568 3.893777086 0.018741699 6.796106796 -0.832260195 -0.44810285 DNYSPGWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DNYSPGWK 8 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;;; 120.15 0.0036205 808410000 1200140 1049230 697750 808310 1019030 898300 1150450 1324050 1299300 FALSE TRUE 1041538.458 1042337.539 1035184.234 991849.1397 998753.2967 932858.1823 1038879.536 1040912.211 1145698.234 0.909086204 0.909783666 0.903540045 0.865715867 0.871742023 0.814226778 0.906765416 0.908539596 1 20.12779567 1.129939305 1.785114214 1.068928061 0.881038016 0.617436187 0.028884743 0.893294739 2.105532232 0.316270261 0.008471779 13.48774371 -1.129939305 -0.187890045 DPAQPMS(ph)PGEATQSGARPADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DPAQPMSPGEATQSGARPADR 21 1 Q9BQG0;Q9BQG0-2 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 DPAQPMS(1)PGEATQSGARPADR;DPAQPMS(0.975)PGEAT(0.012)QS(0.012)GARPADR 173.21 2.78E-12 897140000 348580 302880 158643 182555 299420 331340 312320 325440 152973 TRUE FALSE 302514.2698 300890.3613 235363.2854 224006.9029 293462.1278 344086.8642 282031.2545 255847.1886 134888.7062 2.242695318 2.230656441 1.744870212 1.660679454 2.17558709 2.55089454 2.090844092 1.896728019 1 17.04141004 1.214195216 2.686515765 0.709372731 2.091371582 0.65105818 0.251171278 0.360165109 2.827304951 1.162497981 0.071699234 16.37552439 -1.214195216 1.381998851 DPDAQPGGELMLGGTDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DPDAQPGGELMLGGTDSK 18 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;A0A1B0GU92;A0A1B0GU03;C9JH19;H7C469;F8WD96 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ; 197.49 4.28E-15 351600000 223447 201423 167212 221779 194197 177743 246027 270501 293430 FALSE TRUE 193917.9128 200099.8391 248076.2825 272137.3116 190332.8596 184580.8882 222167.3394 212656.4662 258741.0397 0.749467162 0.773359492 0.95878212 1.051774825 0.735611405 0.713380794 0.858647471 0.8218892 1 17.98114938 1.235622756 24.91455917 1.000000233 0.835701588 0.200335906 0.104805161 146.3133982 1240570.784 0.183516572 0.026936004 17.20373547 -1.235622756 -0.164298645 DPDASKPEDWDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DPDASKPEDWDER 13 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 78.401 0.021276 155660000 486310 389510 405570 453370 369700 360950 416640 452050 665240 FALSE TRUE 422042.9013 386951.2832 601705.0086 556314.5878 362343.6933 374835.9801 376234.3169 355382.6254 586596.085 0.719477869 0.659655414 1.025756946 0.948377601 0.617705611 0.639001844 0.64138566 0.605838727 1 19.16200792 3.228169595 24.99756727 0.681373631 0.838944 0.161807138 0.15201159 346.4074627 833346.8636 0.046892974 0.05373842 1691.101191 -3.228169595 0.157570368 DPDQTDGLGLSYLSSHIANVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DPDQTDGLGLSYLSSHIANVER 22 0 P06396-2;A0A0A0MS51;A0A0A0MT01;P06396-4;P06396-3;P06396 P06396-2 GSN Gelsolin 0 ;;;;; 322.36 9.00E-68 1567860000 1339648 968369 515299 862460 989761 942959 965511 1193730 1692267 FALSE TRUE 1162610.123 962007.7203 764499.32 1058294.725 970066.6925 979235.2429 871875.8918 938460.1291 1492209.123 0.779120101 0.644686931 0.512327199 0.709213413 0.65008763 0.65623191 0.584285325 0.628906575 1 20.5090183 1.237467934 24.99609716 1.000000428 0.640215985 0.716684469 0.069952872 14.34136636 327916.9 0.098706493 0.016564734 17.27698411 -1.237467934 -0.359784443 DPEEIEKEEQAAAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DPEEIEKEEQAAAEK 15 1 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;;;; 208.2 2.75E-09 1053120000 1252040 845220 1160160 1269270 800377 586232 1253730 1447580 2849640 FALSE TRUE 1086579.742 839667.6942 1721217.257 1557477.153 784451.0636 608784.7244 1132143.458 1138026.282 2512758.806 0.432425006 0.334161676 0.684991036 0.619827558 0.312187171 0.242277422 0.450557951 0.452899132 1 21.26084077 1.23783519 6.592541089 1.015151736 0.440700355 0.635681889 0.132988981 0.084061517 17.69999692 0.216005564 0.03500634 17.29160038 -1.23783519 -0.574451381 DPEQRPCFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DPEQRPCFK 9 1 Q13882 Q13882 PTK6 Protein-tyrosine kinase 6 0 84.213 0.014268 115200000 158960 146900 109870 119330 143890 127860 156630 187200 160440 FALSE TRUE 137953.0332 145935.0042 163003.4995 146425.7003 141026.8705 132778.8569 141440.0467 147168.7368 141472.966 0.975119397 1.031539865 1.152188324 1.035008345 0.996846779 0.938545792 0.999767311 1.040260489 1 17.11016687 3.367804615 4.881807718 0.998541395 1.057042606 0.225788498 0.049274326 0.330609969 12.80410343 0.015184515 0.019763951 2332.408498 -3.367804615 0.058501211 DPETLVGYSMVGCQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 265.26 7.93E-25 522921000 485107 440378 314961 368872 411302 448448 490030 500609 539659 FALSE TRUE 420998.8808 437485.1279 467277.1931 452630.0255 403117.8949 465700.0847 442506.966 393557.6611 475861.1278 0.884709543 0.919354623 0.981961261 0.95118092 0.847133484 0.978647041 0.929907782 0.827043097 1 18.86018108 DPGMS(ph)QSHNDLVFLEQPEGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DPGMSQSHNDLVFLEQPEGSR 21 0 Q9Y426-2;Q9Y426-3;Q9Y426;H7BZB0 Q9Y426-2 C2CD2 C2 domain-containing protein 2 1 DPGMS(0.557)QS(0.443)HNDLVFLEQPEGSR 136.24 3.39E-06 166010000 86825 82608 51377 89535 93429 96585 64093 98793 110520 TRUE FALSE 75350.85626 82065.34261 76223.08905 109865.2902 91569.94569 100300.6874 57877.27072 77666.88576 97454.4515 0.773190502 0.842089215 0.78214066 1.127350147 0.939617886 1.029205807 0.593890477 0.796955753 1 16.57244047 2.264950817 24.99997423 0.788489063 0.916908154 0.131478426 0.143179983 422.0541125 399819.2003 0.054516865 0.042215883 184.0563548 -2.264950817 0.12841909 DPGMSQS(ph)HNDLVFLEQPEGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DPGMSQSHNDLVFLEQPEGSR 21 0 Q9Y426-2;Q9Y426-3;Q9Y426;H7BZB0 Q9Y426-2 C2CD2 C2 domain-containing protein 2 1 DPGMS(0.039)QS(0.961)HNDLVFLEQPEGSR 256.7 1.20E-36 152800000 97869 90786 58177 85133 107840 132040 51236 96046 116040 TRUE FALSE 84935.36368 90189.62079 86311.59179 104463.7488 105694.195 137119.6642 46267.14061 75507.31033 102321.8834 0.830080144 0.881430421 0.843530132 1.020932623 1.032957873 1.340081512 0.452172488 0.73793902 1 16.6427552 2.226292964 24.99999892 0.720105826 0.982995013 0.288717198 0.192942867 294.5396018 600231.2186 0.079980651 0.054361979 168.3809532 -2.226292964 0.262889187 DPGT(ph)PNDDSDIKECNSADHIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DPGTPNDDSDIKECNSADHIK 21 1 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 DPGT(1)PNDDSDIKECNSADHIK;DPGT(1)PNDDSDIKECNSADHIK 120 6.69E-05 333802000 159033 127953 104598 112127 106384 94759 162885 196464 202285 TRUE FALSE 138016.3861 127112.4683 155181.9427 137587.1491 104267.1665 98404.44005 147088.4378 154451.7025 178371.0977 0.773759807 0.712629288 0.869994885 0.77135338 0.584551914 0.551683772 0.824620354 0.865900947 1 17.44452234 1.628454285 2.046545163 0.987541033 0.71667634 0.485451032 0.095754184 0.315788413 2.614034462 0.13424956 0.029363984 42.5063961 -1.628454285 -0.270864693 DPGTPDQFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DPGTPDQFLR 10 0 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 102.55 0.0068228 112780000 62518 54252 40691 50168 60557 69179 62764 69040 66007 FALSE TRUE 54256.0879 53895.61504 60369.3037 61559.41117 59352.03418 71840.36089 56677.15694 54276.33327 58203.72766 0.932175482 0.925982187 1.037206827 1.0576541 1.019729089 1.234291407 0.973771943 0.932523319 1 15.82882393 4.23960764 24.97143768 1.031041823 0.929078797 0.239969264 0.078988819 43.10951308 1028028.79 0.021741144 0.051247623 17362.31537 -4.23960764 -0.101963026 DPGVLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DPGVLDR 7 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;;; 120.65 0.010504 40725300000 10010740 11245850 7079250 8580980 10459090 11024980 10401610 10995900 14394000 FALSE TRUE 8687795.345 11171975.27 10502798.98 10529422.66 10250974.57 11449118.11 9392863.463 8644512.355 12692357.72 0.684490269 0.880212764 0.827489991 0.829587607 0.807649359 0.902048175 0.740040871 0.681080107 1 23.59745675 4.757059973 23.54594686 0.818245726 0.684490008 0.205395794 0.087657267 3297.495962 4196895.084 0.021707664 0.649931684 57155.75587 -4.757059973 -0.133755718 DPHLACVAYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DPHLACVAYER 11 0 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ;;;;; 124.86 0.0003404 8973340000 1994601 1681242 1063261 1372889 1784035 2375773 1714284 1817727 1746185 FALSE TRUE 1731009.424 1670197.811 1577457.576 1684624.431 1748536.194 2467170.525 1548033.002 1429020.227 1539752.999 1.124212407 1.084718011 1.024487419 1.094087449 1.135595252 1.602315779 1.005377488 0.928084068 1 20.55426751 2.02314462 24.99999421 0.961252447 1.172617902 0.262627555 0.158742143 304.6603981 329081.9605 0.067355628 0.045408337 105.4738065 -2.02314462 0.211365455 DPILFPSFIHSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DPILFPSFIHSQK 13 0 P04040 P04040 CAT Catalase 0 186.13 8.07E-06 153960000 302370 209920 226060 399510 237410 281700 263410 393330 526530 FALSE TRUE 262411.0384 208541.0217 335383.3721 490224.8516 232686.0055 292537.1813 237864.5387 309219.4404 464284.2232 0.565194821 0.44916672 0.722366506 1.055872302 0.501171467 0.630082106 0.512325267 0.666013241 1 18.82464873 -1.999997625 0.039070509 1.709440228 2.57E-07 0.09464721 0.194142796 6517.453579 25.09115024 856.9396388 349.4697901 0.010000055 1.999997625 -1.709439971 DPILVSLRPGSELLRPHPLPAERPIFNSMAPAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DPILVSLRPGSELLRPHPLPAERPIFNSMAPASPR 35 3 Q92828 Q92828 CORO2A Coronin-2A 1 DPILVSLRPGSELLRPHPLPAERPIFNS(0.051)MAPAS(0.949)PR 116.27 4.39E-06 1353800000 147130 219270 149540 215290 356390 311270 260830 281110 545650 TRUE FALSE 127686.3977 217829.6009 221858.0442 264174.885 349298.5363 323244.7583 235534.7467 220996.8141 481143.8786 0.265380905 0.45273277 0.461105407 0.549055899 0.725975227 0.671825565 0.489530798 0.459315444 1 18.87610885 4.761864953 0.753136366 0.632928318 0.047791352 0.423184552 0.151225874 3.26701899 1.402906464 0.063250221 1.638511716 57791.63123 -4.761864953 -0.585136966 DPLEEMVPLSHLEEEQPPAPES(ph)PESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DPLEEMVPLSHLEEEQPPAPESPESR 26 0 O60307 O60307 MAST3 Microtubule-associated serine/threonine-protein kinase 3 1 DPLEEMVPLSHLEEEQPPAPES(0.975)PES(0.025)R;DPLEEMVPLSHLEEEQPPAPES(0.969)PES(0.031)R 127.23 6.26E-05 55210000 22835.5 28059 21524 26274 26883 26138 26117 32021 35761 TRUE FALSE 19817.73082 27874.67858 31933.07839 32239.91327 26348.0809 27143.54577 23584.17736 25173.55834 31533.37532 0.628468428 0.883973831 1.012675556 1.022406036 0.835561707 0.860787832 0.747911605 0.798314741 1 14.94459198 3.08005256 24.9999827 0.835245376 0.899824379 0.012274939 0.124022672 102.5722431 32025.70543 0.038589913 0.043756848 1202.409945 -3.08005256 0.064579003 DPLELFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DPLELFR 7 0 Q16401-2;Q16401;Q4VXH0 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ;;;;; 124.34 0.0096679 655565000 837524 765389 583539 646176 768158 804529 727753 822865 1005431 FALSE TRUE 726843.0814 760361.1093 865740.4122 792900.137 752873.1587 835479.7512 657175.6261 646901.7233 886570.0926 0.819837131 0.857643536 0.97650532 0.894345685 0.849197559 0.942373038 0.741256254 0.729667884 1 19.75787517 2.241571026 24.9992703 0.800630856 0.890790857 0.098228097 0.085759787 127.2589317 1056808.484 0.032792185 0.024281113 174.4098569 -2.241571026 0.09016 DPLGGLADMFGQMPGSGIGTGPGVIQDRFS(ph)PTMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DPLGGLADMFGQMPGSGIGTGPGVIQDRFSPTMGR 35 1 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 DPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.999)PT(0.001)MGR;DPLGGLADMFGQMPGSGIGT(0.001)GPGVIQDRFS(0.998)PT(0.001)MGR 338.13 3.67E-118 3303700000 1214890 1282050 720900 727670 1149790 1162700 1150390 1259180 830330 TRUE FALSE 1054339.208 1273628.129 1069529.651 892898.5952 1126911.429 1207429.821 1038825.355 989914.1559 732169.3333 1.44002099 1.739526734 1.460768162 1.219524712 1.539140438 1.649112803 1.418832103 1.352028979 1 19.48181782 1.132135326 1.575398507 0.692271636 1.503183683 0.566323436 0.137418146 1.124619673 2.032088225 1.547496952 0.040397535 13.55611756 -1.132135326 0.810912047 DPLLDDHGDFIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DPLLDDHGDFIR 12 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 125.28 0.00030799 56665000 12510 10366 8630.7 12337 10337 12938 10268 14541 26550 FALSE TRUE 10856.7718 10297.90506 12804.53539 15138.30441 10131.31392 13435.73323 9272.21094 11431.52031 23411.28925 0.463740877 0.4398692 0.546938498 0.646624124 0.432753353 0.573899758 0.396057254 0.488290935 1 14.51491676 1.23789913 24.99434352 1.000000578 0.497847757 0.818575511 0.074194144 6.567820091 247974.9091 0.103999275 0.017940291 17.29414637 -1.23789913 -0.502152821 DPNDVRPIQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DPNDVRPIQAR 11 1 Q9H307;G3V5F0;G3V579 Q9H307 PNN Pinin 0 ;;; 130.1 0.0002109 1966280000 2163020 1934830 1301980 1657490 1858950 1919780 1806450 2042930 2688580 FALSE TRUE 1877171.427 1922119.974 1931621.883 2033848.438 1821960.532 1993635.179 1631260.757 1606065.318 2370739.135 0.791808512 0.810768231 0.814776225 0.857896344 0.768520039 0.840934015 0.688081085 0.677453413 1 21.17690549 2.285431572 24.99972378 0.761188725 0.81391231 0 0.091050436 344.9500582 183985.5607 0.033469273 0.025925117 192.9441308 -2.285431572 0.052723585 DPNNYRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DPNNYRPR 8 1 P61221 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 ; 114.99 0.002326 141453000 86634 77855 52221 71042 70770 84583 77025 86496 117033 FALSE TRUE 75185.0974 77343.56538 77475.25027 87173.17191 69361.81546 87836.96274 69555.12736 67999.50351 103197.4921 0.728555471 0.749471366 0.750747414 0.844721806 0.672126949 0.851154044 0.674000172 0.658925931 1 16.65504838 1.22748962 24.98966606 1.000000564 0.739272508 0.602760191 0.066006884 348.1562298 785812.5339 0.240777309 0.016230908 16.88455502 -1.22748962 -0.260728056 DPNTKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DPNTKR 6 1 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;A0A2R8Y4L2;F8W646;F8VYN5 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ; 103.02 0.056192 497820000 1400970 1198260 813520 1050660 814370 994210 1301390 1591170 1186320 FALSE TRUE 1215828.265 1190388.551 1206940.993 1289228.411 798165.6303 1032457.902 1175181.398 1250910.678 1046074.601 1.162276824 1.137957608 1.153780994 1.232444044 0.763010238 0.986983052 1.123420258 1.195814024 1 19.99655431 DPPHNNFFFFDGMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DPPHNNFFFFDGMK 14 0 Q9UBE0;M0QZS6 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 ; 187.37 9.56E-07 1201430000 1319670 1021940 768380 920020 1037390 928030 1198320 1288560 1317570 FALSE TRUE 1145272.266 1015226.809 1139971.138 1128924.603 1016747.969 963731.9146 1082107.111 1013011.472 1161808.376 0.985766922 0.873833267 0.981204097 0.971696044 0.875142571 0.829510214 0.931398958 0.871926466 1 20.1479407 3.238000464 24.99998892 0.896517971 0.949467027 0.180187652 0.053765361 25.34759954 1131297.172 0.015445895 0.018599304 1729.818208 -3.238000464 0.052949055 DPPQECSTFSPTDSGEEPGQLS(ph)PGVQFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DPPQECSTFSPTDSGEEPGQLSPGVQFQR 29 0 Q07002;A0A0A0MSJ6;Q07002-3 Q07002 CDK18 Cyclin-dependent kinase 18 1 DPPQECSTFSPTDSGEEPGQLS(1)PGVQFQR;DPPQECSTFSPTDSGEEPGQLS(1)PGVQFQR 304.28 1.54E-81 285070000 132350 117500 103956 95237 126407 138783 127875 145581 164117 TRUE FALSE 114859.6122 116728.1348 154229.4693 116862.0165 123891.748 144122.0718 115473.7022 114449.6361 144715.2752 0.793693769 0.806605485 1.065744228 0.807530624 0.856106916 0.995900893 0.797937205 0.790860784 1 17.14285769 4.440093685 24.99995258 0.888272922 0.796919841 0.155661185 0.094737549 293.3069856 198032.0511 0.023486599 0.06214 27548.22903 -4.440093685 -0.091353082 DPPSWSVLAGHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DPPSWSVLAGHSR 13 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 175.74 1.77E-05 188090000 98689 106130 49017 60613 92892 95158 95808 111950 63118 FALSE TRUE 85646.9986 105432.825 72721.78515 74376.10806 91043.63094 98818.78984 86516.55491 88010.3637 55656.26194 1.538856467 1.894356922 1.306623597 1.336347528 1.635820081 1.775519706 1.554480159 1.581320064 1 15.7642564 1.238407138 24.38974541 0.999999235 1.578823225 0.517688697 0.17530384 2.289813909 362217.1167 0.243735472 0.04334692 17.31438769 -1.238407138 0.578823989 DPQALSEHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DPQALSEHLK 10 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 127.87 0.0003447 587770000 594660 477720 259280 447060 522180 458900 462580 594280 958400 FALSE TRUE 516074.1743 474581.8259 384668.6752 548571.8059 511789.6396 476554.1799 417719.0628 467197.8467 845099.0438 0.610667091 0.561569474 0.45517585 0.649121319 0.60559723 0.563903348 0.49428415 0.552832062 1 19.68876091 1.238080862 24.99893635 1.000000499 0.558921632 0.85910686 0.055779622 4.098554555 213341.7171 0.078335937 0.013674761 17.30138467 -1.238080862 -0.441078868 DPQALSEHLKNPVIAQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DPQALSEHLKNPVIAQK 17 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 237.59 1.92E-20 629680000 1194700 724290 267020 469890 722200 526130 921070 1124400 301680 FALSE TRUE 1036817.368 719532.0913 396151.7651 576585.7063 707829.633 546370.5616 831744.7732 883955.8101 266015.7341 3.89757911 2.704847868 1.489204263 2.167487229 2.660856266 2.053903178 3.126675105 3.322945589 1 18.02115205 2.245149879 24.96961646 2.684963622 2.452001453 0 0.869539361 975.5320139 3696729.467 0.3320206 0.251126288 175.8530395 -2.245149879 -0.23296217 DPS(ph)KIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DPSKIK 6 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 DPS(1)KIK;DPS(1)KIK 62.582 0.070956 2205450000 5404400 4172800 3717000 3620300 2543600 2578200 6307700 5955300 3253600 TRUE FALSE 4690194.847 4145388.602 5514553.633 4442344.448 2492987.336 2677385.022 5695980.225 4681805.439 2868963.115 1.634804861 1.444908295 1.922141698 1.548414626 0.868950641 0.933223926 1.985379385 1.631880666 1 21.45209799 3.467002876 24.99694434 1.348484727 1.660085849 0.192077687 0.353615912 445.4561964 1100472.764 0.111094049 0.143579499 2930.912653 -3.467002876 0.311601122 DPS(ph)PESNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DPSPESNK 8 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 DPS(1)PESNK;DPS(0.999)PES(0.001)NK 97.456 0.008621 1306580000 2223640 1677990 1524240 1681100 1062800 1320760 1930700 2263520 3666400 TRUE FALSE 1929780.34 1666967.173 2261367.562 2062819.449 1041652.359 1371570.492 1743461.011 1779483.863 3232962.369 0.596907764 0.515616015 0.699472281 0.638058602 0.32219749 0.424245734 0.539276618 0.550418984 1 21.62442528 1.236487445 5.478595095 1.0237567 0.532417792 0.658467133 0.10512918 0.102883328 9.487905737 0.191068938 0.027912738 17.23802257 -1.236487445 -0.491338908 DPS(ph)PESNKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DPSPESNKK 9 1 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 DPS(1)PESNKK;DPS(1)PESNKK 67.385 0.037393 452500000 750580 499110 599900 596410 366430 350130 704440 828940 1245420 TRUE FALSE 651388.9513 495831.3135 890013.6465 731834.0061 359138.7599 363599.7277 636123.5172 651677.6318 1098187.866 0.593148924 0.451499537 0.810438427 0.666401468 0.327028527 0.331090644 0.579248357 0.593411794 1 20.06669345 1.174656923 2.624505101 1.16393803 0.534468033 0.494945686 0.145613415 0.593660153 3.977217949 0.90041619 0.040702086 14.95054152 -1.174656923 -0.629469997 DPS(ph)PESNKKGESPSLESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DPSPESNKKGESPSLESR 18 2 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 DPS(0.969)PES(0.028)NKKGES(0.002)PS(0.001)LESR 49.125 0.083001 121430000 207300 125790 80804 66485 133600 89031 197820 217680 34794 TRUE FALSE 179904.7798 124963.6772 119881.0847 81581.43541 130941.6214 92456.08018 178635.4468 171130.826 30680.69296 5.863778241 4.073039595 3.907378651 2.659048005 4.267883439 3.013493871 5.822405872 5.577801852 1 14.90504345 1.225895364 24.99959818 0.99999207 4.392988819 0.485576574 1.09917312 594.6043735 1173601.069 5.051265638 0.286985202 16.82268696 -1.225895364 3.392996749 DPSAS(ph)PGDAGEQAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DPSASPGDAGEQAIR 15 0 P18206;P18206-2 P18206 VCL Vinculin 1 DPSAS(1)PGDAGEQAIR;DPSAS(1)PGDAGEQAIR;DPSAS(1)PGDAGEQAIR;DPSAS(1)PGDAGEQAIR 335.58 5.10E-69 2027950000 1153080 1007810 985150 1357440 1035990 1027790 892970 1152730 5565670 TRUE FALSE 1000697.556 1001189.63 1461571.835 1665667.499 1015375.826 1067329.746 806369.9068 906227.6601 4907702.833 0.203903454 0.204003719 0.297811804 0.339398606 0.206894317 0.217480516 0.164306995 0.184654143 1 22.22661646 1.236684486 24.99999967 1.000000973 0.22638719 0.955124882 0.052635598 10.37968038 138273.3389 0.090250622 0.014323245 17.2458453 -1.236684486 -0.773613783 DPSQQELPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 85.733 0.034002 1294600000 1818600 2105700 1493500 1180300 1398900 1629200 2121400 2202600 2689300 FALSE TRUE 1578267.402 2091867.518 2215761.595 1448305.155 1371064.627 1691876.378 1915666.955 1731591.131 2371374.018 0.665549757 0.882133102 0.934378794 0.610745139 0.578173083 0.713458259 0.80782995 0.730205829 1 21.17729179 1.236748088 24.94310801 1.000000331 0.743542605 0.348505 0.111508203 58.74845146 808224.9884 0.180117682 0.02875186 17.24837113 -1.236748088 -0.256457726 DPSVDITQDLVDESEEERFDDMSS(ph)PGLELPSCELSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DPSVDITQDLVDESEEERFDDMSSPGLELPSCELSR 36 1 Q6IN85-2;Q6IN85;G3V5Z3;G3V231;H0YIY8;Q6IN85-5 Q6IN85-2 SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3A 1 DPSVDITQDLVDESEEERFDDMS(0.173)S(0.827)PGLELPSCELSR;DPSVDITQDLVDESEEERFDDMS(0.039)S(0.961)PGLELPSCELSR 137.69 1.47E-09 47858000 60845 47333 37412.5 41270 42430 49856 40575 50751 49654 TRUE FALSE 52804.17909 47022.06641 55505.31014 50640.98427 41585.72601 51773.99258 36640.04275 39898.29359 43783.96069 1.206016502 1.073956437 1.267708752 1.1566104 0.949793608 1.182487645 0.836837101 0.911253641 1 15.41811485 2.75265798 1.000751531 0.91533527 1.176806515 0.48239168 0.100736212 0.433160557 0.965075172 0.066409639 0.051026069 565.7935341 -2.75265798 0.261471244 DPTEEIEILLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DPTEEIEILLR 11 0 B4DG22;B1AXG1;B7ZB17;P51812;A0A2R8Y603 B4DG22 RPS6KA3 Ribosomal protein S6 kinase alpha-3 0 ; 115.78 0.0025057 20475600 34038 32147 25943 29068 30787 30518 30837 33278 34393 FALSE TRUE 29539.79206 31935.82424 38489.12157 35668.33368 30174.39893 31692.04721 27846.43249 26161.75867 30327.09872 0.974039499 1.05304581 1.269132993 1.176120868 0.994964906 1.045007552 0.918202982 0.862652867 1 14.88831987 2.603304337 1.55078813 0.912767248 1.116044252 0.418070941 0.089900178 0.35427846 1.738386101 0.046985437 0.035481352 401.1477281 -2.603304337 0.203277004 DPTSLLGVLQAEADS(ph)TSEGLEDAVHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DPTSLLGVLQAEADSTSEGLEDAVHSR 27 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 DPTSLLGVLQAEADS(0.453)T(0.453)S(0.093)EGLEDAVHSR;DPTSLLGVLQAEADS(0.74)T(0.203)S(0.057)EGLEDAVHSR 97.346 0.0026884 63446000 53340 49821 37556 48979 57105 55984 51039 59574 89151 TRUE FALSE 46290.98385 49493.72257 55718.20722 60100.43055 55968.72222 58137.74071 46089.24564 46834.56371 78611.67034 0.588856383 0.629597646 0.708777806 0.764523006 0.711964546 0.739556105 0.58629012 0.59577113 1 16.26245588 -2 0.026923122 1.629104982 2.40E-11 0.150886381 0.113681516 11780.22754 31.45020786 1294.860532 697.2039138 0.01 2 -1.629104982 DPTSLLGVLQAEADST(ph)SEGLEDAVHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DPTSLLGVLQAEADSTSEGLEDAVHSR 27 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 DPTSLLGVLQAEADS(0.383)T(0.507)S(0.11)EGLEDAVHSR;DPTSLLGVLQAEADS(0.383)T(0.513)S(0.104)EGLEDAVHSR;DPTSLLGVLQAEADS(0.326)T(0.588)S(0.087)EGLEDAVHSR 156.44 7.42E-08 141718000 47196 52328 36997 44863 56739 53725 54272 62657 88603 TRUE FALSE 40958.92902 51984.25392 54888.87295 55049.82984 55610.00491 55791.83551 49008.70979 49258.28815 78128.45428 0.524251112 0.665369031 0.702546511 0.704606668 0.711776592 0.714103921 0.62728375 0.630478212 1 16.25356045 1.235160463 24.99999448 1.000000469 0.663321645 0.774452022 0.05763102 47.41171505 348542.853 0.101761094 0.014389103 17.18543238 -1.235160463 -0.336678824 DPTSLLGVLQAEADSTS(ph)EGLEDAVHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DPTSLLGVLQAEADSTSEGLEDAVHSR 27 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 DPTSLLGVLQAEADS(0.108)T(0.36)S(0.532)EGLEDAVHSR;DPTSLLGVLQAEADS(0.014)T(0.174)S(0.812)EGLEDAVHSR;DPTSLLGVLQAEADS(0.311)T(0.311)S(0.377)EGLEDAVHS(0.001)R 138.82 1.87E-06 142081000 61517 61598 49857 54835 67308 68523 60627 65687 107709 TRUE FALSE 53387.37259 61193.35868 73968.01196 67286.12485 65968.70249 71159.12415 54747.40287 51640.34623 94975.76472 0.562115743 0.644304985 0.778809333 0.708455731 0.694584589 0.749234548 0.576435505 0.5437213 1 16.5352718 -1.182198832 0.017613115 1.488347772 1.20E-06 0.069063542 0.12878408 42298.961 88.61148981 4432.824816 3158.196737 0.065735681 1.182198832 -1.488346575 DPTSLLGVLQAEADSTSEGLEDAVHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DPTSLLGVLQAEADSTSEGLEDAVHSR 27 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 ;;;;; 263.18 3.52E-53 309852000 247951.5 223650.6 164521 216677.5 230044.5 244609.5 222968.9 276621 399574 FALSE TRUE 215184.081 222181.4245 244083.9059 265877.4381 225467.0645 254019.7857 201345.4104 217467.7518 352336.8169 0.610734021 0.630593835 0.692757311 0.754611569 0.639919116 0.720957259 0.571457199 0.61721552 1 18.42659571 1.234822637 24.9998194 1.000000492 0.65426829 0.797550327 0.054660381 50.50255992 337713.2891 0.10201669 0.014046591 17.17206948 -1.234822637 -0.345732203 DPTVHDDVLELEMDELNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 DPTVHDDVLELEMDELNR 18 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;;;;;; 379.24 3.59E-108 2479769000 2572373 2196797 1585598 2085392 2430270 2028646 2418380 2668465 3614742 FALSE TRUE 2232427.39 2182366.096 2352398.496 2558912.127 2381912.382 2106689.324 2183845.88 2097834.526 3187411.319 0.700388863 0.684682922 0.738027904 0.802818297 0.74728742 0.660940529 0.685147181 0.658162476 1 21.60395377 1.23245917 24.99997712 1.000000477 0.708784005 0.812904528 0.043769303 95.88547572 392840.4195 0.107651879 0.012015051 17.07887146 -1.23245917 -0.291216472 DPTVHDDVLELEMDELNRHECMAPLTALVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DPTVHDDVLELEMDELNRHECMAPLTALVK 30 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 52.824 0.045433 56288000 61630 51316 20517 25967 50672 36049 65391 69223 11216 FALSE TRUE 53485.43935 50978.90182 30439.08983 31863.20423 49663.72634 37435.82836 59049.39088 54420.20014 9890.057257 5.408000981 5.154560837 3.077746572 3.221741129 5.021581276 3.785198344 5.970581297 5.502516187 1 13.27176316 4.448536426 24.66983505 4.190369072 5.34464236 0.116524155 1.418316714 382.8702466 330431.7721 0.357391263 0.945607717 28089.00955 -4.448536426 1.154273288 DPVQEAWAEDVDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DPVQEAWAEDVDLR 14 0 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;; 264.22 2.65E-24 11466290000 1457844 1023478 1032977 1327460 1074001 1122829 1185912 1254647 2591660 FALSE TRUE 1265186.222 1016754.706 1532528.132 1628880.082 1052630.481 1166024.958 1070902.437 986350.5027 2285276.907 0.55362491 0.44491532 0.670609381 0.712771427 0.460613975 0.510233554 0.468609486 0.431610935 1 21.12393756 1.231324934 24.98858621 1.000000828 0.528388783 0.709801508 0.094098623 153.6049189 530430.9601 0.247335527 0.024751014 17.03432519 -1.231324934 -0.471612045 DPWDAVLLEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DPWDAVLLEER 11 0 O00443;A0A0C4DGF9;O00443-2 O00443 PIK3C2A Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha 0 ; 97.813 0.013927 40634000 42672 40632 30060 32385 32828 37564 35865 48046 48597 FALSE TRUE 37032.78708 40365.08572 44597.11654 39738.50922 32174.78703 39009.11139 32386.81782 37771.73679 42851.91802 0.864203723 0.941966838 1.040726264 0.927344937 0.750836567 0.910323579 0.755784556 0.881447985 1 15.38707216 3.459990196 24.92115795 0.855499072 0.954227398 0.205378752 0.082457701 322.7741728 469549.3053 0.023316492 0.030108167 2883.966397 -3.459990196 0.098728326 DQADFSVLHYAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQADFSVLHYAGK 13 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 136.51 7.14E-05 174530000 309100 273600 180610 218130 287590 233290 306180 353520 312340 FALSE TRUE 268251.6518 271802.7036 267953.6001 267659.7504 281867.5217 242264.8173 276486.7107 277922.4991 275415.521 0.973988869 0.986882303 0.97290668 0.971839748 1.023426424 0.879633858 1.003889359 1.00910253 1 18.07125034 2.052138413 24.99999995 1.005592221 0.969358871 0.186896548 0.035535151 155.4296 74526.50479 0.013883819 0.009360465 112.7556761 -2.052138413 -0.03623335 DQDGYYWITGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DQDGYYWITGR 11 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ;; 145.23 8.45E-05 579549000 923980 697490 470449 543620 673990 651260 746110 850110 803660 FALSE TRUE 801873.7019 692908.1423 697959.71 667057.2297 660578.9176 676314.3936 673752.367 668320.5921 708652.2303 1.13154756 0.977783054 0.98491147 0.941304072 0.932162335 0.954367128 0.950751777 0.943086839 1 19.43471828 5.293091226 1.370451055 0.952875529 1.586030569 0.872999954 0.020593834 1.606106556 0.929139253 0.005569607 2.046547961 196377.2734 -5.293091226 0.63315504 DQDLTQEIAMEHFVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DQDLTQEIAMEHFVK 15 0 Q9ULX6;Q9ULX6-2 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 0 ; 147.7 3.66E-06 247740000 151720 119307 75385 82863 118973 93780 103555 132977 134741 FALSE TRUE 131669.8176 118523.2645 111841.4381 101678.3106 116605.6701 97387.77728 93512.25204 104540.9034 118812.0725 1.10821918 0.997569203 0.941330589 0.85579107 0.981429476 0.819679139 0.787060187 0.87988452 1 16.85832191 4.856797906 0.90730625 0.876478433 1.279132099 0.548895832 0.065126642 1.980991163 1.121255014 0.022707798 0.830659321 71911.42691 -4.856797906 0.402653666 DQDNMQAELNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQDNMQAELNR 11 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 103.91 0.0062138 327960000 201460 211990 113120 123840 210210 228830 180540 192730 177800 FALSE TRUE 174836.5506 210597.4237 167825.2104 151959.7648 206027.2323 237633.2382 163031.2586 151516.1893 156780.6866 1.115166379 1.343261267 1.070445691 0.969250538 1.314111048 1.515704794 1.039868253 0.966421264 1 17.25838832 2.021290022 24.99799594 0.987511773 1.218185892 0.320237358 0.152159545 275.351395 323306.5601 0.065068876 0.043865365 105.0243548 -2.021290022 0.230674119 DQDS(ph)SDDERALEDWVSSETSALPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQDSSDDERALEDWVSSETSALPR 24 1 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2;V9GYQ9 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 DQDS(0.5)S(0.5)DDERALEDWVSSETSALPR 65.207 0.0078581 0 26041 21527 11809 18648 20288 21128 23781 22304 16929 TRUE FALSE 22599.61587 21385.58772 17519.8719 22882.31342 19884.30849 21940.80783 21474.72228 17534.46317 14927.67291 1.513940988 1.432613633 1.173650576 1.532878806 1.332043422 1.46980765 1.438584729 1.17462804 1 13.86570166 1.537163265 2.832168326 1.009602686 1.408756545 0.652945926 0.102655251 0.151822815 2.485653223 0.114666738 0.02651138 34.44794069 -1.537163265 0.399153859 DQDS(ph)SDDERALEDWVSSETSALPRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DQDSSDDERALEDWVSSETSALPRPR 26 2 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 DQDS(0.59)S(0.41)DDERALEDWVSSETSALPRPR;DQDS(0.5)S(0.5)DDERALEDWVSSETSALPRPR;DQDS(0.366)S(0.366)DDERALEDWVS(0.067)S(0.067)ET(0.067)S(0.067)ALPRPR 161.32 9.01E-12 181469000 338083 306108 146670 148261 286835 268520 310356 355163 73059 TRUE FALSE 293404.475 304097.1564 217600.1026 181925.9261 281127.5447 278850.1382 280257.7229 279214.1563 64422.04825 4.554410841 4.720389442 3.377727168 2.823969914 4.363840522 4.32848917 4.350338595 4.334139692 1 15.97526691 4.246028612 24.76392672 3.66473827 4.637400663 0.156404184 1.040903845 313.1105759 1038248.105 0.258554589 0.655496874 17620.92133 -4.246028612 0.972662393 DQDSS(ph)DDERALEDWVSSETSALPRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQDSSDDERALEDWVSSETSALPRPR 26 2 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 DQDS(0.249)S(0.751)DDERALEDWVSSETSALPRPR 218.16 1.85E-34 46933000 105830 92742 46992 44711 91678 93046 97822 106710 19325 TRUE FALSE 91844.29736 92132.7717 69717.48838 54863.31591 89853.78716 96625.53983 88335.2375 83890.89692 17040.42052 5.389790544 5.406719371 4.091300935 3.21959871 5.272979448 5.670372967 5.183864883 4.92305321 1 14.05667332 4.248215864 24.07474244 4.368924733 5.398256021 0.111712997 1.342886251 326.7349754 814664.7256 0.336243374 0.863901873 17709.89003 -4.248215864 1.029331289 DQDWPALAVDLAHHLQVSEDVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DQDWPALAVDLAHHLQVSEDVVR 23 0 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 ; 146.15 7.60E-08 117049000 50813 57197 25513 34310 53698 55817 54188 59800 33888 FALSE TRUE 44097.93331 56821.26914 37851.17214 42100.6099 52629.51486 57964.31611 48932.8561 47012.23536 29881.79925 1.475745585 1.901534398 1.266696554 1.408904783 1.761256557 1.939786679 1.63754718 1.573273248 1 14.8669794 1.229358777 3.858289303 0.91722883 1.631017253 0.467901713 0.208671041 0.255428749 6.244658315 0.529682398 0.054272616 16.95738096 -1.229358777 0.713788423 DQECDKFNQCGTCNEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DQECDKFNQCGTCNEFK 17 1 Q9UBR2 Q9UBR2 CTSZ Cathepsin Z 0 ;; 256.67 3.82E-27 1712930000 1370240 1070130 1030170 1039120 963380 781870 1394440 1616620 1230830 FALSE TRUE 1189159.312 1063100.246 1528363.658 1275068.078 944210.6228 811949.0448 1259207.423 1270918.394 1085322.68 1.095673512 0.979524583 1.408211296 1.174828557 0.869981472 0.748117643 1.160214789 1.171005101 1 20.04969261 3.286852569 24.86947216 1.013195307 1.168746785 0.216021626 0.16193077 214.2171523 110316.2961 0.051170402 0.066060539 1935.764715 -3.286852569 0.155551478 DQEDDEQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQEDDEQQR 9 0 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 149.27 0.00020479 26598000 50825 48122 36917 33121 33682 45964 47480 55020 55868 FALSE TRUE 44108.34748 47805.88341 54770.18468 40641.62927 33011.7941 47732.26482 42875.39691 43254.40117 49263.34869 0.895358287 0.970414815 1.111783631 0.824987143 0.67010861 0.968920427 0.870330541 0.878023974 1 15.58822708 3.711638176 24.90906879 0.865695699 0.990308548 0.247549894 0.101623203 980.0613661 906768.3989 0.028302599 0.041991963 5147.995709 -3.711638176 0.12461285 DQEVEHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DQEVEHVR 8 0 Q9P2M7;Q9P2M7-2 Q9P2M7 CGN Cingulin 0 ; 148.62 0.00051832 569316000 570690 547730 371990 435940 506570 597070 548330 600140 611610 FALSE TRUE 495271.8706 544131.9256 551885.6082 534926.8399 496490.2481 620039.6693 495153.041 471804.7313 539306.1625 0.918350104 1.008948095 1.02332524 0.99187971 0.920609262 1.14969884 0.918129766 0.874836529 1 19.04074499 DQFLDTLQAHGHDVNSFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQFLDTLQAHGHDVNSFVR 19 0 Q15021;E7EN77 Q15021 NCAPD2 Condensin complex subunit 1 0 163.11 1.52E-11 74421000 35590 32107 18433 22439 33440 31989 37071 38421 31660 FALSE TRUE 30886.69133 31896.087 27347.26045 27534.11791 32774.60942 33219.63753 33475.86013 30204.96814 27917.19087 1.106368168 1.142524947 0.979584966 0.986278241 1.173993816 1.189934821 1.199112772 1.081948692 1 14.76886616 3.226350553 24.9999797 1.131422296 1.054741337 0.200104864 0.074717613 398.1299049 815164.0665 0.024413273 0.027882966 1684.032827 -3.226350553 -0.076680959 DQGELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DQGELER 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 161.12 0.0030731 7229400000 5300490 5173330 3346800 3833090 4154110 4716310 5204760 5757850 5533800 FALSE TRUE 4600016.817 5139346.055 4965323.674 4703451.67 4071451.338 4897749.498 4700003.176 4526578.585 4879600.468 0.942703577 1.053230913 1.017567669 0.963900979 0.834382111 1.003719368 0.963194263 0.927653527 1 22.2183316 3.619312311 5.13473706 0.943955064 1.008830376 0.19533419 0.053638007 0.324506843 12.30116436 0.014484327 0.021742503 4162.098087 -3.619312311 0.064875313 DQGGELLSLR ddPTM_MDA-MB-175_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 ;;; 152.04 4.36E-05 333933000 1022110 1004660 605250 776660 967420 963460 980790 1137470 1137160 FALSE TRUE 887035.5738 998060.3223 897950.9244 953012.5235 948170.2347 1000524.93 885673.1368 894230.8923 1002726.24 0.884623877 0.995346768 0.89550955 0.950421446 0.945592323 0.997804674 0.883265144 0.891799632 1 19.93549635 5.124437012 9.778244584 0.938329953 5.02E-05 0.139299534 0.044498616 74809.50748 155444.7517 0.010717728 1450548.46 133179.3871 -5.124437012 -0.938279717 DQGGFGDRNEYGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DQGGFGDRNEYGSR 14 1 A0A087WTP3;Q92945;M0R0I5 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;;;;; 275.42 4.15E-33 8906730000 3767580 3564080 1999660 2395730 3384010 3513820 3481880 3855290 1979180 FALSE TRUE 3269684.757 3540667.324 2966702.264 2939717.113 3316674.822 3648998.929 3144207.814 3030866.235 1745203.595 1.873526256 2.028799009 1.699917576 1.68445511 1.900451518 2.090872916 1.801628086 1.73668347 1 20.73496392 1.154698801 2.353593487 0.619463524 1.869998029 0.820074575 0.126739339 0.341702498 1.637233477 0.974483147 0.035234534 14.27903313 -1.154698801 1.250534506 DQGSCGSCWAFGAVEAISDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DQGSCGSCWAFGAVEAISDR 20 0 P07858;E9PKQ7;E9PNL5;E9PHZ5;E9PLY3;E9PSG5;E9PQM1 P07858 CTSB Cathepsin B;Cathepsin B light chain;Cathepsin B heavy chain 0 ; 263.2 4.13E-36 306010000 170614 137448 92752 144211 152071 170767 144136 172072 177728 FALSE TRUE 148066.9276 136545.095 137607.1774 176956.3117 149045.0846 177336.517 130157.7129 135275.7419 156717.1983 0.94480331 0.871283411 0.878060474 1.129144176 0.951044852 1.131570235 0.830526032 0.863183769 1 17.25780399 7.874862043 19.07834452 0.948991682 0.004757381 0 0.105872237 0 0 0.024273403 0 74965603.78 -7.874862043 -0.944234301 DQGTYEDYVEGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DQGTYEDYVEGLR 13 0 F8VPF3;H0YI43;P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;G3V1Y7;P60660-2;G8JLA2;F8VZU9;F8W180 F8VPF3;P60660;P60660-2 MYL6 Myosin light polypeptide 6 0 ;;;;; 237.49 2.22E-16 7525550000 3796770 3844630 2960120 3721870 3839860 3731250 3829620 4406330 8956890 FALSE TRUE 3295017.225 3819374.372 4391643.933 4566977.469 3763454.299 3874793.602 3458224.042 3464070.62 7898016.668 0.417195527 0.483586517 0.556043893 0.578243585 0.476506249 0.490603371 0.437859805 0.438600064 1 22.91305898 1.235385601 24.99999952 1.000000706 0.485487181 0.911788611 0.050357618 26.9250841 211970.7537 0.094103984 0.013551677 17.19434359 -1.235385601 -0.514513525 DQHDTFFLRDPAEALQLPMDYVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DQHDTFFLRDPAEALQLPMDYVQR 24 1 K7ER00;Q9Y285;Q9Y285-2;K7EPH2;K7ERS0 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ; 108.4 0.0014028 222285000 233270 220070 98532 153159 197066 210740 180232 218290 137541 FALSE TRUE 202442.7785 218624.3457 146182.4048 187936.0918 193144.7722 218847.3042 162753.1284 171610.3822 121281.0597 1.669203576 1.802625622 1.205319323 1.54959144 1.592538626 1.804463984 1.341950085 1.414980894 1 16.88799474 0.842476125 1.095323153 0.156152568 1.583252949 0.505758711 0.180213519 3.242358949 1.738455279 6.665783797 0.057634135 6.957867032 -0.842476125 1.427100381 DQHFVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQHFVK 6 0 P02786;G3V0E5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 70.912 0.089617 436930000 1171300 943720 635480 832860 825410 852110 860530 1066400 971780 FALSE TRUE 1016509.737 937520.6412 942800.2536 1021973.592 808985.9559 884891.2231 777075.933 838358.6587 856897.2755 1.186267907 1.094087551 1.100248864 1.192644231 0.944087441 1.032668966 0.906848411 0.978365415 1 19.70876274 3.232457213 24.9985591 0.971238274 1.136720154 0.779943919 0.045049589 64.61693547 264660.3376 0.012936802 0.015037167 1707.879451 -3.232457213 0.16548188 DQHHLGS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DQHHLGSPSR 10 0 Q9H8M2;Q9H8M2-3;Q9H8M2-1;Q9H8M2-6;Q9H8M2-2 Q9H8M2 BRD9 Bromodomain-containing protein 9 1 DQHHLGS(0.982)PS(0.018)R;DQHHLGS(0.965)PS(0.035)R 107.46 0.0014688 1716310000 1193830 1074610 609410 696990 921920 1017340 907910 941910 997510 TRUE FALSE 1036062.341 1067550.816 904122.7144 855252.2323 903575.5957 1056477.728 819861.0279 740489.8765 879585.5042 1.17789838 1.213697601 1.027896333 0.972335524 1.027274314 1.201108617 0.932099295 0.841862301 1 19.7464643 7.999999998 0.130158198 0.756088566 2.242976542 0.404234865 0.093618584 187.8332181 2.140195743 2.756153777 50.73152705 99999999.65 -7.999999998 1.486887975 DQHLNNSS(ph)SSPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DQHLNNSSSSPQR 13 0 A0A4W8VX11;A0A5H1ZRS1;E7EV93;E9PGW9 A0A4W8VX11 PCM1 1 DQHLNNS(0.07)S(0.51)S(0.174)S(0.246)PQR;DQHLNNS(0.031)S(0.432)S(0.269)S(0.269)PQR;DQHLNNS(0.02)S(0.473)S(0.306)S(0.2)PQR 244.56 5.01E-17 294793000 364962 387105 194979 262431 340845 341735 303582 363858 324260 TRUE FALSE 316731.347 384562.0818 289271.4966 322019.9696 334062.8514 354881.7666 274140.6644 286049.7982 285926.3522 1.107737516 1.344969006 1.011699322 1.126233966 1.16835279 1.24116495 0.958780687 1.000431741 1 18.12528407 2.229408961 24.99977381 0.988175546 1.165987627 0.490090688 0.086682046 161.350243 440759.7222 0.03407866 0.023337715 169.5934057 -2.229408961 0.177812081 DQHLNNSSS(ph)SPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQHLNNSSSSPQR 13 0 A0A4W8VX11;A0A5H1ZRS1;E7EV93;E9PGW9 A0A4W8VX11 PCM1 1 DQHLNNS(0.001)S(0.012)S(0.643)S(0.344)PQR 157.7 5.01E-05 23604000 54983 56001 26934 33190 50122 51784 42605 48524 45714 TRUE FALSE 47716.85724 55633.12574 39959.37249 40726.29678 49124.67026 53776.16399 38473.17366 38147.52021 40309.743 1.183754936 1.380140919 0.991308044 1.010333824 1.218679818 1.334073601 0.954438575 0.946359797 1 15.29884096 2.209940398 24.79924132 0.962125949 1.179788005 0.422024423 0.120855841 196.9543172 170658.1557 0.051816431 0.034942077 162.1587537 -2.209940398 0.217662055 DQHLNNSSSS(ph)PQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQHLNNSSSSPQR 13 0 A0A4W8VX11;A0A5H1ZRS1;E7EV93;E9PGW9 A0A4W8VX11 PCM1 1 DQHLNNSS(0.076)S(0.23)S(0.694)PQR 295.49 1.19E-40 243130000 279690 262540 133050 175770 248540 253340 236190 247740 237520 TRUE FALSE 242728.2579 260815.3575 197393.425 215681.265 243594.5403 263086.1537 213284.3302 194762.7289 209440.6562 1.158935721 1.245294788 0.942479023 1.029796549 1.163071892 1.256136982 1.018352091 0.929918443 1 17.676182 2.012291516 24.52892612 0.964207936 1.126761539 0.371189673 0.093666579 186.8785726 372932.832 0.040315435 0.027158595 102.8706576 -2.012291516 0.162553603 DQITAGNAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQITAGNAAR 10 0 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 97.472 0.014042 33863000 31692 31237 22374 26804 25108 27735 34995 34577 37470 FALSE TRUE 27503.8219 31031.80209 33194.14124 32890.25787 24608.39992 28801.9834 31601.19029 27182.97763 33040.33929 0.832431582 0.939209547 1.004654975 0.995457631 0.744798645 0.871721781 0.956442669 0.822720899 1 15.01194088 4.754023657 22.49469653 0.909784926 0.83243135 0.085159815 0.084176452 2079.561596 3025009.933 0.020812987 0.419967116 56757.55218 -4.754023657 -0.077353576 DQKEEGNDYDT(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQKEEGNDYDTR 12 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 DQKEEGNDYDT(1)R 93.754 0.0024434 0 228310 153590 152010 162440 142400 139190 187410 217810 319650 TRUE FALSE 198138.255 152581.0572 225522.5444 199324.4847 139566.5186 144544.7294 169235.007 171233.0265 281861.3411 0.702963571 0.541333751 0.800118752 0.707172129 0.495160202 0.512822116 0.600419363 0.607508024 1 18.10462609 1.237616771 24.89398301 1.000000473 0.617843469 0.612387917 0.094747709 15.80402814 416592.4793 0.140884615 0.023844754 17.28290614 -1.237616771 -0.382157004 DQKLPHLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DQKLPHLER 9 1 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ; 94.297 0.0052981 200792000 506450 446790 219899 264070 417890 378270 507740 558990 127860 FALSE TRUE 439521.3493 443855.0071 326242.8919 324031.1296 409574.8066 392822.2917 458499.4529 439454.3386 112744.5365 3.89838269 3.936820541 2.89364702 2.874029552 3.632768553 3.484180289 4.066711056 3.897788331 1 16.782698 1.234384117 24.99998989 0.999996209 3.588161932 0.793348957 0.414704291 61.32398934 367027.3701 0.84036388 0.111479072 17.15473908 -1.234384117 2.588165723 DQLESVLEVLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DQLESVLEVLHR 12 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3;A0A1B0GUN0;E9PL74 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 0 ; 145.71 6.17E-05 71677000 135110 135564 107509 132030 129906 149867 139429 161084 227090 FALSE TRUE 117254.8712 134673.4712 159500.712 162009.4295 127321.1248 155632.4805 125907.197 126637.4402 200243.6789 0.585560912 0.672547927 0.796533068 0.809061391 0.635830931 0.777215447 0.628769895 0.632416668 1 17.61139718 -1.903103586 0.023022725 1.643364353 2.37E-07 0.123896656 0.116110466 18199.43942 42.44189389 1961.79576 1167.116442 0.012499609 1.903103586 -1.643364115 DQLIYNLLK ddPTM_MDA-MB-175_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 ; 142.92 0.00024002 791090000 2176000 1816860 1486730 1621410 1820580 1626260 2249500 2389800 3179900 FALSE TRUE 1888436.087 1804924.927 2205717.601 1989575.922 1784354.02 1688823.275 2031343.836 1878759.867 2803975.845 0.673485148 0.643702024 0.786639302 0.7095553 0.636365689 0.602295943 0.724451261 0.670034255 1 21.41904249 1.237302641 24.99930464 1.000000383 0.681558523 0.79311163 0.051231105 14.55044427 289036.7484 0.077160961 0.012767783 17.27040972 -1.237302641 -0.31844186 DQLIYNLLKEEQTPQNK ddPTM_MDA-MB-175_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 841590000 1381460 1033970 469260 481260 916580 640940 1370790 1441290 89465 FALSE TRUE 1198896.561 1027177.783 696195.7056 590537.4386 898341.8513 665597.3765 1237850.997 1133081.35 78888.54962 15.19734571 13.02061944 8.825053939 7.485718035 11.38748089 8.437186129 15.69113645 14.36306479 1 16.26752829 4.428000074 4.144684961 10 14.81565656 0.183365944 4.011878119 0.37236336 13.19164329 1.042340418 3.350979125 26791.6878 -4.428000074 4.815656558 DQMEGS(ph)PNSSESFEHIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQMEGSPNSSESFEHIAR 18 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 DQMEGS(0.995)PNS(0.005)SESFEHIAR 130.65 5.24E-06 0 54367 52602 34352 41421 52572 46157 53437 63708 71266 TRUE FALSE 47182.2632 52256.454 50964.7421 50826.27113 51525.92006 47932.68966 48254.68796 50084.53998 62841.01467 0.750819563 0.831566044 0.811010808 0.808807296 0.819940931 0.76276123 0.767885245 0.797003999 1 15.93941885 1.238919949 8.738416878 1.001675843 0.794597569 0.860636857 0.026086134 0.02943808 27.71103958 0.036398443 0.006420507 17.33484445 -1.238919949 -0.207078274 DQPAFTPSGILT(ph)PHALGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DQPAFTPSGILTPHALGSR 19 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 1 DQPAFTPSGILT(1)PHALGSR;DQPAFTPSGILT(1)PHALGSR 127.94 8.25E-05 356684000 269315 252039 126376 166265 192210 198946 190802 240815 200998 TRUE FALSE 233724.3404 250383.3392 187491.8563 204018.0095 188385.3971 206599.5814 172298.0514 189318.5863 177236.2454 1.318716382 1.412709565 1.057864072 1.151107715 1.062905596 1.165673426 0.972137787 1.068170824 1 17.43531414 4.234377849 24.99996939 1.069353498 1.365713021 0.798099576 0.062195441 38.23259377 228517.8108 0.015391233 0.03397536 17154.49148 -4.234377849 0.296359523 DQPGHQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQPGHQEK 8 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 68.657 0.069203 0 110160 94933 72764 78122 60268 88087 120890 119400 115370 FALSE TRUE 95602.07689 94309.37887 107952.9138 95860.79412 59068.78471 91475.76389 109166.1064 93867.23917 101731.09 0.939752802 0.927045791 1.061159511 0.94229595 0.580636506 0.899191819 1.073084997 0.92269963 1 16.63440112 2.437520687 22.59757074 0.985923451 0.888150084 0.135245152 0.126225939 134.9474055 77003.70372 0.049880318 0.038637297 273.8550079 -2.437520687 -0.097773367 DQPGRQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DQPGRQEK 8 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 62.582 0.0718 85326000 220120 157959 147060 102005 81628 125907 142103 162088 40460 FALSE TRUE 191030.5843 156921.3569 218178.7079 125166.7943 80003.7625 130750.7238 128321.8729 127426.7426 35676.86489 5.354466679 4.39840657 6.115411445 3.508346226 2.242454956 3.664860244 3.596781088 3.571691149 1 15.12270122 3.582498102 5.538248732 2.99948174 5.184233482 0.609599616 0.896693509 0.164038063 7.145620519 0.24404725 0.363798204 3823.825827 -3.582498102 2.184751742 DQQNLPYGVTPAS(ph)PSGHSQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQQNLPYGVTPASPSGHSQGR 21 0 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 DQQNLPYGVTPAS(0.986)PS(0.014)GHSQGR 182.89 2.90E-17 784750000 233920 199060 106870 158030 222980 209890 221080 263330 242980 TRUE FALSE 203006.8793 197752.3618 158552.6895 193913.1268 218543.1343 217964.6041 199639.6956 207018.9287 214255.1812 0.947500444 0.922975868 0.740017994 0.905056885 1.020013299 1.017313107 0.931784681 0.966226009 1 17.70897057 3.416118303 6.346126777 0.980967345 0.867000606 0.457285524 0.059284942 0.187941272 14.71220014 0.017582698 0.022858581 2606.863571 -3.416118303 -0.113966739 DQRPS(ph)SPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQRPSSPIR 9 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 DQRPS(0.5)S(0.5)PIR 95.162 0.021655 976640000 999720 845910 606510 604690 778500 836010 837800 924920 857790 TRUE FALSE 867604.469 840353.1615 899820.2647 741994.1066 763009.3731 868171.8457 756550.285 727133.0557 756383.0434 1.147043785 1.111015337 1.189635691 0.980976653 1.008760548 1.147793903 1.000221107 0.961329134 1 19.5287575 7.999999996 0.093682675 0.780878409 1.862561845 0.432666598 0.061738595 313.3522566 2.733993898 5.367209981 44.83161249 99999999.03 -7.999999996 1.081683437 DQRPSS(ph)PIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQRPSSPIR 9 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 DQRPS(0.124)S(0.876)PIR 103.65 0.0089134 938880000 827150 648730 448820 532190 667870 622670 639700 755510 652390 TRUE FALSE 717840.0318 644468.4499 665870.8532 653031.8735 654580.6937 646624.5178 577661.9925 593950.0659 575265.1974 1.247841926 1.120298 1.157502411 1.135184045 1.137876403 1.124045954 1.004166418 1.032480443 1 19.13386767 -1.999999998 0.134378388 0.178625601 1.312182205 0.787308136 0.035115255 78.49822884 0.916284005 16.73304294 0.833131388 0.01 1.999999998 1.133556604 DQS(ph)PFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 DQSPFSK 7 0 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 DQS(0.998)PFS(0.002)K;DQS(0.982)PFS(0.018)K;DQS(0.967)PFS(0.033)K;DQS(0.994)PFS(0.006)K;DQS(0.989)PFS(0.011)K;DQS(1)PFSK;DQS(1)PFSK;DQS(1)PFSK;DQS(0.972)PFS(0.028)K 172.88 0.0009273 14511540000 34158250 23659490 18392690 20074100 22826680 18419680 28193330 33422620 32680460 TRUE FALSE 29644150.72 23504069.25 27287456.4 24632231.22 22372473.73 19128297.01 25459145.2 26275452.81 28817013.25 1.028703095 0.815631691 0.946921743 0.854780855 0.776363377 0.663784857 0.883476194 0.911803475 1 24.78041748 4.747330642 23.887652 0.856401887 1.028703263 0.252880736 0.092968896 967.0142259 2633827.671 0.024045836 0.268286009 55889.55373 -4.747330642 0.172301376 DQS(ph)PPPS(ph)PPPSYHPPPPPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQSPPPSPPPSYHPPPPPTK 20 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 2 DQS(0.986)PPPS(0.979)PPPS(0.018)Y(0.017)HPPPPPTK 83.755 0.0015248 347510000 288870 251580 83242 233590 308880 243470 287640 368590 320720 TRUE FALSE 250695.0976 249927.3544 123498.1096 286630.1797 302733.8923 252836.4484 259744.7171 289769.8969 282804.847 0.886459692 0.883744947 0.436690216 1.013526404 1.07046925 0.894031524 0.918459213 1.024628467 1 18.10944732 DQS(ph)TPIIEVEGPLLSDTHVTFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQSTPIIEVEGPLLSDTHVTFK 22 0 P49116;P49116-2 P49116 NR2C2 Nuclear receptor subfamily 2 group C member 2 1 DQS(0.5)T(0.5)PIIEVEGPLLSDTHVTFK 217.67 8.00E-26 108940000 173000 144120 47673 100820 155600 125610 172020 188060 172400 TRUE FALSE 150137.6117 143173.2662 70727.82226 123712.7219 152503.8644 130442.298 155337.5269 147844.8325 152019.0684 0.987623548 0.941811233 0.465256254 0.813797396 1.003189047 0.858065369 1.021829225 0.972541366 1 17.21389277 3.296467445 6.320192566 0.969337711 0.785941891 0.252871176 0.143549299 0.283783991 22.8194057 0.042692648 0.054828764 1979.098662 -3.296467445 -0.18339582 DQSCKPCAEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQSCKPCAEGR 11 1 Q6UXG2-2;Q6UXG2-4;Q6UXG2;Q6UXG2-3;E9PB18;E9PS21;E9PLY8;E9PLQ2 Q6UXG2-2 KIAA1324 UPF0577 protein KIAA1324 0 92.906 0.0087974 132140000 237180 178360 134270 197180 207520 204230 158880 305610 267380 FALSE TRUE 205836.0621 177188.3414 199203.4211 241952.7327 203390.758 212086.8603 143471.8421 240257.6798 235770.641 0.873035172 0.751528437 0.844903421 1.026220787 0.862663634 0.899547371 0.608522933 1.019031372 1 17.84702455 1.603628495 25 1.009550922 0.843271701 0.309464985 0.106253879 0.481253483 2815.151575 0.0649957 0.026457156 40.14472574 -1.603628495 -0.166279221 DQSSWQNSDASQEVGGHQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQSSWQNSDASQEVGGHQER 20 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 254.24 4.01E-36 189060000 143070 115310 70195 98308 119340 119300 106060 123600 120700 FALSE TRUE 124162.937 114552.521 104141.5368 120630.3339 116965.3675 123889.5482 95774.31752 97169.10186 106430.9835 1.166605183 1.076308019 0.978488908 1.133413692 1.098978546 1.164036488 0.899872522 0.912977581 1 16.69955867 2.230989662 24.99923455 0.930910848 1.097303715 0.635488005 0.058858392 107.9136947 356326.5152 0.024048146 0.016564292 170.211799 -2.230989662 0.166392867 DQST(ph)PIIEVEGPLLSDTHVTFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DQSTPIIEVEGPLLSDTHVTFK 22 0 P49116;P49116-2 P49116 NR2C2 Nuclear receptor subfamily 2 group C member 2 1 DQS(0.186)T(0.814)PIIEVEGPLLSDTHVTFK;DQS(0.119)T(0.881)PIIEVEGPLLSDTHVTFK 204.05 4.47E-22 209211000 252588 187993 67914.3 160923 190482 144609 212238 245532 218247 TRUE FALSE 219207.8558 186758.0616 100757.8826 197463.0267 186691.7809 150172.2018 191655.1914 193026.8925 192446.0883 1.139061115 0.970443532 0.523564202 1.026069319 0.97009912 0.780333875 0.995890294 1.00301801 1 17.55409482 2.051679023 24.93525222 1.001044136 0.895629581 0.073713146 0.163008864 255.0949589 123082.5929 0.066775262 0.045019863 112.6364677 -2.051679023 -0.105414555 DQTDFEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQTDFEHR 8 0 A0A2R8Y891;P08237;P08237-3;P08237-2;F8VZI0 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 73.885 0.040063 0 66565 69903 39057 52940 58344 69289 64181 67105 83615 FALSE TRUE 57768.2666 69443.80259 57945.09584 64960.83614 57183.06855 71954.59267 57956.7365 52755.11796 73730.12995 0.783509627 0.941864644 0.785907957 0.881062276 0.775572599 0.97591843 0.786065839 0.715516411 1 16.16996668 DQVANSAFVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DQVANSAFVER 11 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;; 284.45 2.94E-27 13877480000 3216380 2922810 1757074 2192200 3023080 2833860 2906810 3186730 2770910 FALSE TRUE 2791327.234 2903609.869 2606800.863 2689972.516 2962926.623 2942880.428 2624908.014 2505272.589 2443336.176 1.142424551 1.188379191 1.06690225 1.10094245 1.212656143 1.204451707 1.07431308 1.025349116 1 21.22042095 1.981687155 3.49967682 1.018470584 1.15065361 0.621370928 0.045431194 0.167236687 4.171102834 0.026523846 0.013611193 95.87097742 -1.981687155 0.132183026 DQVLHEHIQR ddPTM_MDA-MB-175_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 ; 143.97 1.91E-05 1302050000 956610 957430 608300 632210 979380 996330 893750 988650 957300 FALSE TRUE 830191.5648 951140.5793 902475.9146 775762.9432 959892.2541 1034659.46 807074.2626 777234.8912 844129.0846 0.983488876 1.126771482 1.069120744 0.91900985 1.137139179 1.225712369 0.956102896 0.920753597 1 19.68710411 2.05119206 24.99995328 0.949828714 1.075732831 0.296889842 0.085210084 117.9763834 57613.9175 0.035306377 0.023803548 112.5102424 -2.05119206 0.125904117 DQVTAQEIFQDNHEDGPTAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DQVTAQEIFQDNHEDGPTAK 20 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;; 288.98 4.86E-47 880130000 1563690 1274283 1010322 1181519 1193222 938152 1373546 1716770 2776980 FALSE TRUE 1357044.405 1265912.151 1498917.099 1449800.947 1169479.217 974243.3145 1240339.72 1349652.095 2448688.588 0.554192318 0.516975559 0.612130553 0.592072407 0.477594098 0.397863297 0.506532242 0.551173433 1 21.22357788 1.236233232 4.840414257 1.034406747 0.522624925 0.863262818 0.059381487 0.069834409 3.912316049 0.121797589 0.016343092 17.22793529 -1.236233232 -0.511781822 DQWEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DQWEDR 6 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;; 224.39 1.02E-05 16750070000 16728990 15354420 10482470 13854920 14807970 15113300 15077580 18211610 16609290 FALSE TRUE 14518211.59 15253555.8 15551827.55 17000891.35 14513320.37 15694718.43 13615358.61 14317198.92 14645758.66 0.991291194 1.041499875 1.061865617 1.160806466 0.990957226 1.071622085 0.929645157 0.97756622 1 23.80397959 2.248082972 24.95535061 0.969197686 1.054966216 0.385297908 0.049937079 191.5230101 501927.1179 0.018673624 0.014271488 177.0447169 -2.248082972 0.085768531 DQWLQDAFHIS(ph)L ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DQWLQDAFHISL 12 0 Q8N5H3-1;Q8N5H3;Q8N5H3-2 Q8N5H3-1 FAM89B Protein FAM89B 1 DQWLQDAFHIS(1)L 92.039 0.0083493 11089000 29796 26436 19674 28914 33997 33945 34062 43486 38358 TRUE FALSE 25858.38311 26262.34018 29188.41221 35479.36562 33320.52621 35250.88612 30758.67248 34186.85731 33823.36094 0.764512526 0.776455664 0.862966051 1.048960382 0.985133508 1.042205302 0.909391368 1.010746903 1 15.0457324 3.97333379 3.293357488 0.995808101 0.772907266 0.860405825 0.038783901 0.079624978 1.773399565 0.010214094 0.021406472 9404.45841 -3.97333379 -0.222900835 DQYSVIFESGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DQYSVIFESGDR 12 0 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;;; 287.94 1.47E-28 1995540000 2082670 1912310 1231870 1556710 1867400 1911830 1875390 2256490 2082940 FALSE TRUE 1807439.883 1899747.91 1827606.452 1910184.798 1830242.394 1985379.337 1693514.966 1773957.174 1836697.206 0.984070688 1.034328306 0.995050489 1.040010728 0.996485641 1.080950812 0.922043634 0.965840841 1 20.80868238 2.225989778 24.99893087 0.961606457 1.020843878 0.415837112 0.033049049 206.5802911 410811.2502 0.012559371 0.008535105 168.2634457 -2.225989778 0.059237421 DRAEAEAR ddPTM_MDA-MB-175_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 ;;; 186.78 0.00018757 3100990000 3069990 3035370 1819610 2168870 2021390 2920290 2972010 3359400 3050150 FALSE TRUE 2664283.043 3015430.455 2699579.482 2661345.083 1981168.294 3032635.446 2683784.928 2641018.453 2689564.742 0.990600078 1.121159275 1.003723554 0.989507723 0.736612978 1.127556217 0.997851023 0.981950132 1 21.35894129 4.011015412 22.65576734 0.973441776 1.057520231 0.10516541 0.099999463 155.032785 318843.0908 0.024949016 0.051818763 10256.88324 -4.011015412 0.084078455 DRCPLPCIPTLIGT(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DRCPLPCIPTLIGTPVK 17 1 Q9H0H5 Q9H0H5 RACGAP1 Rac GTPase-activating protein 1 1 DRCPLPCIPT(0.007)LIGT(0.993)PVK 90.832 0.0059902 217570000 273450 221810 121320 196120 218310 167700 189020 265250 258600 TRUE FALSE 237312.8897 220352.9155 179990.7578 240652.0435 213966.0581 174151.5275 170688.8695 208528.3517 228028.6026 1.04071545 0.966338929 0.789334126 1.055359024 0.93832991 0.76372668 0.748541488 0.914483312 1 17.79885527 2.972569617 24.06647409 0.85507395 0.956537783 0.206011819 0.099516143 781.0602642 685275.4531 0.032887781 0.032982902 938.7925124 -2.972569617 0.101463833 DRDAS(ph)PSKEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DRDASPSKEER 11 2 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 DRDAS(0.995)PS(0.005)KEER;DRDAS(0.985)PS(0.015)KEER;DRDAS(0.988)PS(0.012)KEER;DRDAS(0.883)PS(0.117)KEER;DRDAS(0.992)PS(0.008)KEER 142.45 2.97E-05 2810677000 3277793 2406146 1961817 1865335 2110361 2058858 2815271 3059815 2612547 TRUE FALSE 2844624.35 2390339.868 2910558.263 2288887.822 2068368.945 2138063.6 2542246.452 2405497.374 2303694.67 1.234809624 1.037611407 1.263430567 0.993572565 0.897848561 0.928101987 1.103551823 1.044191058 1 21.13551808 3.71588101 24.39739373 0.999731394 1.164516617 0.531208788 0.081058446 495.0920025 532590.9691 0.022836472 0.033903153 5198.53545 -3.71588101 0.164785224 DRDASPS(ph)KEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DRDASPSKEER 11 2 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 DRDAS(0.291)PS(0.709)KEER 123.42 0.00029171 213400000 546770 430570 301200 330450 363080 356470 508350 559450 438370 TRUE FALSE 474512.9592 427741.5573 446861.3275 405483.7231 355855.4184 370183.6316 459050.2952 439815.9711 386546.398 1.227570511 1.106572353 1.15603542 1.048991079 0.920602081 0.957669334 1.18756842 1.137809002 1 18.56028207 4.521962137 1.265785478 1.057101413 1.248042995 0.313745662 0.083232375 1.524882573 2.837608222 0.028073116 0.343954946 33263.05523 -4.521962137 0.190941582 DRDGYSYGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DRDGYSYGSR 10 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ; 147.39 2.46E-05 476320000 361580 302810 162490 200313 287810 316810 327380 351410 327718 FALSE TRUE 313796.2869 300820.8212 241070.7075 245797.1282 282083.1441 328997.8857 295630.738 276263.7062 288975.5514 1.085892164 1.04099056 0.83422527 0.850581051 0.976148822 1.138497302 1.023030276 0.956010655 1 18.14058791 2.992752907 24.94728059 1.021768494 0.946063303 0.143257188 0.087313654 719.9704124 2478426.542 0.029350813 0.031977414 983.4514103 -2.992752907 -0.07570519 DRDNDSDDVESNLLLPAGIALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DRDNDSDDVESNLLLPAGIALR 22 1 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-2;Q9NZM1-5;Q9NZM1-8;Q9NZM1-7 Q9NZM1-6 MYOF Myoferlin 0 ;;;; 219.65 9.86E-26 1529724000 1280909 1179793 842677 960274 1236635 1339267 1171141 1620286 1487242 FALSE TRUE 1111633.63 1172042.862 1250198.416 1178318.889 1212028.383 1390789.468 1057563.926 1273800.448 1311421.945 0.847655199 0.893719117 0.953315156 0.898504782 0.924209319 1.060520204 0.806425369 0.971312439 1 20.32270051 6.40359135 0.658994408 0.947048334 3.72E-11 0.197151573 0.065813892 43.3115475 2.463585553 0.027043255 49.50667528 2532744.321 -6.40359135 -0.947048334 DRDNQDREENDKDPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DRDNQDREENDKDPER 16 3 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 182.15 9.59E-10 1079340000 1185340 930230 988760 979490 961860 689210 1133050 1298210 1759360 FALSE TRUE 1028694.316 924119.2579 1466927.643 1201898.175 942720.8678 715724.3547 1023166.985 1020597.894 1551370.465 0.663087469 0.59567929 0.945568886 0.774733181 0.607669728 0.461349736 0.6595246 0.657868586 1 20.56511181 1.237221719 24.98002512 1.000000403 0.670547951 0.407517253 0.124789559 37.62199753 701643.7635 0.195858297 0.032308521 17.26719203 -1.237221719 -0.329452451 DRDPEAQFEMPYVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DRDPEAQFEMPYVVR 15 1 O14744-2;O14744;O14744-4;O14744-3;O14744-5;H0YJD3;H7BZ44 O14744-2 PRMT5 "Protein arginine N-methyltransferase 5;Protein arginine N-methyltransferase 5, N-terminally processed" 0 120.63 0.00010946 63107000 21797 30491 17335 18038 27768 21592 19993 30209 35147 FALSE TRUE 18916.47122 30290.70261 25718.26398 22133.80359 27215.47113 22422.65821 18054.08194 23749.04044 30991.9617 0.610367017 0.977372872 0.829836595 0.714178851 0.878146127 0.723499159 0.582540793 0.766296779 1 14.91960646 3.777740641 23.79383649 0.766049288 0.823010272 0 0.139270596 1310.814154 796044.3503 0.036269782 0.062819067 5994.329896 -3.777740641 0.056960984 DRDS(ph)QRDLVEAVAHILGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DRDSQRDLVEAVAHILGIR 19 2 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 DRDS(1)QRDLVEAVAHILGIR;DRDS(1)QRDLVEAVAHILGIR;DRDS(1)QRDLVEAVAHILGIR;DRDS(1)QRDLVEAVAHILGIR 267.18 6.87E-32 1674408000 559494.8 659318.8 219667 190150 492240.7 550900 743978.9 668118.6 137487.3 TRUE FALSE 485556.1446 654987.6914 325898.6959 233326.4638 482446.0731 572093.4795 671827.9408 525246.6367 121233.708 4.005124916 5.402686283 2.688185499 1.924600572 3.979471395 4.718930806 5.541593603 4.33251317 1 16.88743136 3.018289062 24.98750713 4.145622142 3.503546252 0.006865402 1.461486408 978.9041539 1337422.716 0.460886264 0.52251826 1043.011417 -3.018289062 -0.64207589 DRDVTFSPATIENELIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DRDVTFSPATIENELIK 17 1 P55145;H7C2D6 P55145 MANF Mesencephalic astrocyte-derived neurotrophic factor 0 ;;; 214.24 5.47E-15 473862000 573600 492206 392071 434381 501057 491682 547113 647290 510683 FALSE TRUE 497797.3067 488972.6664 581677.847 533013.8451 491086.946 510597.3247 494054.0655 508872.0707 450310.6375 1.105453137 1.085856353 1.291725752 1.183658126 1.090551511 1.133877999 1.097140561 1.130046746 1 18.78056103 3.235458311 24.99902233 1.0979778 1.16983302 0.24825379 0.065165232 127.1596464 1024676.291 0.019814677 0.023430117 1719.722252 -3.235458311 0.07185522 DRDWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DRDWER 6 1 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6;X6RC15 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 0 ;; 111.82 0.025104 1549870000 1237050 1083890 833268 997120 960960 1147400 996830 1403960 1284120 FALSE TRUE 1073570.708 1076769.855 1236239.192 1223531.336 941838.7761 1191541.22 900157.58 1103734.08 1132312.796 0.948122031 0.950947352 1.091782408 1.080559488 0.831783213 1.052307476 0.79497254 0.974760758 1 20.11084112 3.255088086 24.99990715 0.932156977 1.01835452 0.197392283 0.087232666 408.7774708 618324.6341 0.024422103 0.031438267 1799.235808 -3.255088086 0.086197543 DRDYSDHPSGGSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DRDYSDHPSGGSYR 14 1 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;;;;; 187.08 5.94E-07 8013810000 7874430 7995050 1580798 4321830 9859340 8649430 7366120 8752890 6887860 FALSE TRUE 6833804.124 7942529.99 2345277.2 5303167.557 9663158.423 8982179.169 6651754.816 6881152.589 6073585.037 1.125168098 1.307716932 0.386143799 0.873152763 1.591013934 1.478892469 1.095194152 1.1329639 1 22.53411691 3.298115826 24.99999757 1.242418331 0.912170621 0.249853679 0.288658407 117.4196019 49288.99681 0.087655958 0.11316331 1986.624679 -3.298115826 -0.330247709 DREDRS(ph)KDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DREDRSKDR 9 3 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 1 DREDRS(1)KDR 92.925 0.053857 196800000 222050 150830 136040 126530 82250 125800 204570 236600 92121 TRUE FALSE 192705.5299 149839.1878 201829.399 155260.5704 80613.38592 130639.6074 184730.8329 186004.9312 81230.56032 2.372327965 1.844615957 2.484648613 1.911356634 0.992402189 1.608256879 2.274154359 2.289839323 1 16.30973498 3.485297175 24.94146007 1.733718396 2.19544996 0.243201663 0.464636142 709.5218359 2164467.518 0.141052904 0.191261434 3057.012218 -3.485297175 0.461731564 DREDYVPYTGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DREDYVPYTGEK 12 1 Q9NYL9 Q9NYL9 TMOD3 Tropomodulin-3 0 ;;;;; 199.31 1.58E-07 2768330000 3717670 3152800 2328757 2628670 2953730 2456890 3592740 4141170 3698780 FALSE TRUE 3226370.49 3132089.049 3454951.674 3225549.7 2894956.552 2551408.148 3244316.628 3255613.022 3261514.442 0.989224652 0.960317394 1.059309022 0.988972993 0.88761114 0.782277127 0.994727046 0.998190589 1 21.63711059 3.448241798 19.4927514 0.93794706 1.002929337 0.189087491 0.06884194 36.99797424 24970.79643 0.021987225 0.028388705 2806.996025 -3.448241798 0.064982277 DREEALHQFR ddPTM_MDA-MB-175_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 ;;; 211.68 3.27E-08 5211610000 4346530 4016750 2672750 2888630 3874950 4044390 4083060 4524420 4300550 FALSE TRUE 3772125.048 3990363.705 3965300.84 3544537.591 3797846.076 4199980.3 3687085.47 3556907.992 3792143.878 0.994720973 1.052271178 1.045662023 0.934705461 1.001503687 1.107547718 0.972295775 0.937967574 1 21.85458227 2.026822823 24.99998892 0.961726445 1.021800799 0.217167951 0.046679252 287.4086018 267875.6092 0.019258055 0.012983465 106.3708973 -2.026822823 0.060074353 DREEDEEDAYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DREEDEEDAYER 12 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 247.73 1.04E-16 1479730000 938030 807890 552910 616290 724130 708170 758440 903010 931900 FALSE TRUE 814066.9588 802582.9174 820299.1254 756228.0639 709721.2297 735413.7581 684886.6055 709908.3387 821731.8436 0.99067228 0.976696867 0.998256465 0.920285699 0.863689579 0.894955896 0.833467281 0.863917279 1 19.64830815 3.571543377 3.52749192 0.883869296 0.987139759 0.501105493 0.043882043 0.189870539 4.401137823 0.012549203 0.019044004 3728.579239 -3.571543377 0.103270463 LSGS(ph)RQDLIPSYSLGSNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSGSRQDLIPSYSLGSNK 18 1 Q9NQT8;H0YBA8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 LS(0.097)GS(0.903)RQDLIPSYSLGSNK;LS(0.043)GS(0.957)RQDLIPSYSLGSNK;LS(0.261)GS(0.739)RQDLIPSYSLGSNK;LS(0.262)GS(0.738)RQDLIPSYSLGSNK 309.64 2.45E-61 12505800000 10202800 10017400 5723870 6326610 8337390 7512710 9039520 10109600 4523210 TRUE FALSE 8854474.129 9951595.04 8491952.677 7763163.497 8171492.251 7801728.815 8162868.742 7947740.713 3988481.267 2.220011462 2.495083811 2.129119359 1.946395878 2.04877288 1.956065052 2.046610776 1.992673447 1 21.92740807 1.170573173 2.700087692 0.606321914 2.118379201 0.831469355 0.157013974 0.272705991 1.950728019 1.018414646 0.045468687 14.81061774 -1.170573173 1.512057287 DREEILLQELEPVISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DREEILLQELEPVISR 16 1 Q5JU69 Q5JU69 TOR2A Torsin-2A 0 ;;; 176.81 2.78E-09 125701000 112949 113461 78710 105294 117727 125222 109284 111829 96647 FALSE TRUE 98022.50347 112715.6672 116774.4193 129202.612 115384.463 130039.3714 98685.6545 87915.2386 85221.50176 1.150208591 1.322620054 1.370245969 1.516079972 1.353936045 1.525898613 1.15799009 1.031608653 1 16.37892985 2.040729655 5.038037021 1.037238509 1.376030968 0.674084076 0.104668312 0.107957221 6.508863543 0.046956561 0.029833467 109.8321931 -2.040729655 0.33879246 DREGFFTNGLTLGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DREGFFTNGLTLGAK 15 1 C9J0J7;G5E9Q6;P35080-2;C9J712;C9JQ45;C9J2N0;P35080 C9J0J7 PFN2 Profilin;Profilin-2 0 ; 176.04 5.37E-09 596400000 1175110 1007140 665210 792970 968210 802150 1189270 1372110 967340 FALSE TRUE 1019816.236 1000524.031 986907.781 973025.9583 948944.5153 833009.2296 1073934.778 1078694.954 852982.1672 1.195589164 1.172971804 1.157008691 1.140734233 1.112502174 0.976584578 1.25903544 1.264616068 1 19.70215605 4.334679708 1.882102007 1.142066722 1.194981343 0.04897181 0.092622494 1.948170195 12.03876838 0.027361029 0.137594035 21611.24106 -4.334679708 0.05291462 DREGPTDHLESACPLNLPLQNNHTAADMYLS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DREGPTDHLESACPLNLPLQNNHTAADMYLSPVR 34 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 DREGPTDHLESACPLNLPLQNNHTAADMYLS(1)PVR 109.01 7.50E-06 60700000 17707 17850 9522.7 15185 19747 17288 23132 23606 26119 TRUE FALSE 15366.97509 17732.74217 14127.90957 18632.98634 19354.07333 17953.08055 20888.6622 18558.0406 23031.24157 0.667223043 0.769942954 0.613423706 0.80903091 0.840339991 0.779509888 0.906970739 0.80577682 1 14.49130457 -1.999999998 0.114878146 1.879449285 0.495513504 0.621598674 0.067054687 160.551111 1.661105989 35.49866967 2.680096612 0.01 1.999999998 -1.38393578 DRELALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DRELALR 7 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;Q5JVM0 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ; 163.9 0.0011107 440100000 538340 493500 294670 365660 497780 511620 493980 561640 437250 FALSE TRUE 467197.005 490258.166 437173.3976 448688.6918 487875.1519 531302.3525 446073.8956 441537.6567 385558.8031 1.211739951 1.271552256 1.133869579 1.163736084 1.26537158 1.378006022 1.156954249 1.145188887 1 18.55659138 1.352873672 1.712419047 0.953199985 1.230516765 0.526875517 0.069226302 0.643644108 2.192471317 0.280924832 0.020591031 22.5358359 -1.352873672 0.27731678 DRELDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DRELDLR 7 1 P09661;H0YKK0 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 0 ;;; 132.76 0.0030441 2777380000 6473000 5643200 3536350 4289110 5386200 5405500 5395200 6371400 5392100 FALSE TRUE 5617576.65 5606129.448 5246540.688 5263017.98 5279025.158 5613453.083 4871974.334 5008925.692 4754652.081 1.181490581 1.179083002 1.103454175 1.106919684 1.110286319 1.180623311 1.024675255 1.05347891 1 22.18090835 -2 0.244199942 0.028065456 1.184328168 0.65127962 0.037976054 53.39269998 0.849801374 24.43409479 0.134607147 0.01 2 1.156262711 DRELWVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DRELWVQR 8 1 Q9Y3C8 Q9Y3C8 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1 0 ;;;; 140.83 0.00058659 2458360000 2912240 2746780 1667340 2039610 2764550 2466780 2681300 3085720 2668450 FALSE TRUE 2527380.105 2728736.221 2473671.201 2502734.624 2709540.864 2561678.623 2421267.939 2425862.791 2352988.881 1.074114768 1.159689382 1.051288946 1.063640651 1.15153152 1.088691342 1.029018011 1.030970784 1 21.16606307 2.247695923 4.01890151 1.021208393 1.100544774 0.525867527 0.03519389 0.167350879 6.074768375 0.014385551 0.010082087 176.8870027 -2.247695923 0.07933638 DRENYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DRENYDR 7 1 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ; 157.91 0.001317 164800000 310040 270290 165850 195418 206053 255190 244120 297360 270270 FALSE TRUE 269067.4285 268514.4472 246055.6147 239790.6437 201952.9484 265007.3244 220445.28 233771.8781 238318.9885 1.129022199 1.126701858 1.032463323 1.006175149 0.847406032 1.111985772 0.925000905 0.980920067 1 17.86253438 4.07275128 2.190118048 0.975556894 1.134123339 0.462512511 0.065925055 0.263473152 2.493226606 0.017230269 0.048113177 11823.64223 -4.07275128 0.158566444 DREPEREER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DREPEREER 9 2 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 0 ; 136.96 0.00010019 279770000 97559 75869 55609 61027 64935 82227 85635 93866 63642 FALSE TRUE 84666.33097 75370.61154 82501.6984 74884.11309 63642.92054 85390.3259 77330.13088 73793.48637 56118.31526 1.508711204 1.343066184 1.470138546 1.334397028 1.134084661 1.521612427 1.377983828 1.314962611 1 15.77618408 1.209747824 2.715275894 0.897416772 1.378838137 0.54252803 0.110025443 0.409647128 3.280026089 0.466307863 0.028206254 16.20868657 -1.209747824 0.481421365 DREPHGYS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DREPHGYSPER 11 1 Q9HCM7;A0A3B3IRR3 Q9HCM7 FBRSL1 Fibrosin-1-like protein 1 DREPHGYS(1)PER;DREPHGY(0.014)S(0.986)PER 101.71 0.0018671 1198830000 816470 676340 438750 516880 621930 655340 653010 682700 683640 TRUE FALSE 708571.4208 671897.078 650930.9675 634245.504 609554.8098 680551.3539 589681.1907 536709.9178 602820.858 1.175426184 1.114588304 1.079808303 1.052129328 1.011170735 1.128944602 0.978203031 0.890330702 1 19.20136981 7.999998262 0.044505085 0.195425826 2.45457213 0.602680447 0.052166657 910.9221933 3.981011218 60.4159589 167.6573698 99999599.75 -7.999998262 2.259146304 DRFGIDDQDYLVSLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DRFGIDDQDYLVSLTR 16 1 Q8TBX8;Q8TBX8-3;F8VNT5;F8VU68 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 ;; 196.66 4.13E-11 1123010000 775200 734200 427542 512922 664421 693950 710620 809300 608374 FALSE TRUE 672755.3559 729376.9919 634302.7412 629388.7796 651200.322 720646.7055 641704.1818 636237.493 536452.7188 1.254081361 1.359629593 1.182401951 1.173241849 1.213900684 1.343355491 1.196198955 1.186008516 1 19.0330915 1.013043958 1.488349471 0.762348743 1.249246797 0.60864399 0.062234609 1.49269541 1.878015822 1.280563125 0.018373861 10.30490419 -1.013043958 0.486898054 DRFPEAQWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DRFPEAQWR 9 1 B4DYU2;Q96MW5;H3BQV3;H3BSH5;A0A087X1T3 B4DYU2 COG8 Conserved oligomeric Golgi complex subunit 8 0 ; 164.33 5.69E-05 801560000 475890 445840 303270 314540 405130 500690 416530 424790 410210 FALSE TRUE 412999.9307 442911.2477 449932.3864 385961.1144 397068.7056 519951.8683 376134.9847 333951.9642 361715.4411 1.141781312 1.224474262 1.243884931 1.067029688 1.097737781 1.437461079 1.03986433 0.923244977 1 18.46449566 2.012697083 24.97682647 0.963764339 1.197814993 0.506297123 0.10191405 165.0467781 324667.4145 0.040925733 0.027573212 102.9667686 -2.012697083 0.234050654 DRFTQNLSAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DRFTQNLSAFR 11 1 E7ESC6;Q9UIA9 E7ESC6 XPO7 Exportin-7 0 ; 158.11 2.76E-05 584180000 300170 359970 264800 270810 402440 389430 378780 384370 351230 FALSE TRUE 260501.774 357605.3334 392858.1657 332301.5496 394432.2314 404411.6241 342045.9739 302175.4667 309707.9895 0.841120613 1.154653239 1.268479274 1.07295117 1.273561693 1.305783634 1.104414434 0.975678629 1 18.24054908 1.868664341 4.262776578 0.990369907 1.162840701 0.201634673 0.131868608 0.33364163 9.343595587 0.074081608 0.035680349 73.90338676 -1.868664341 0.172470795 DRGDAYYDTDYRHS(ph)YEYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DRGDAYYDTDYRHSYEYQR 19 2 B1AVT0;P49760-3;P49760;P49760-2 B1AVT0 CLK2 Dual specificity protein kinase CLK2 1 DRGDAYYDT(0.001)DYRHS(0.999)YEYQR;DRGDAYYDTDYRHS(1)YEYQR;DRGDAYYDT(0.003)DYRHS(0.997)YEYQR;DRGDAYYDT(0.056)DYRHS(0.942)Y(0.002)EYQR 234.39 2.04E-24 1709110000 832160 800840 527248 593186 734670 741380 797620 832500 787550 TRUE FALSE 722187.9476 795579.2293 782226.8963 727877.9476 720051.5044 769901.3683 720266.9352 654476.3535 694446.7362 1.039947213 1.14563031 1.126403013 1.048140786 1.036870744 1.108654312 1.037180964 0.942442839 1 19.40550452 1.964950225 4.362622484 0.970843964 1.084805364 0.591704079 0.038571491 0.137923392 5.866705641 0.020336253 0.010799726 92.2465697 -1.964950225 0.1139614 DRGEEDADGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DRGEEDADGSK 11 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 121.86 0.00036728 148840000 360560 278310 276790 307140 181050 184170 329530 405920 684110 FALSE TRUE 312911.0825 276481.7633 410646.5698 376880.8313 177447.4592 191255.1391 297572.2313 319117.1669 603235.2951 0.518721442 0.458331542 0.68074029 0.624765882 0.29415961 0.317048987 0.4932938 0.529009442 1 19.20236132 1.225358251 3.767064665 1.073734214 0.483899948 0.651805175 0.117657081 0.198882068 4.456946334 0.337158061 0.032493751 16.8018944 -1.225358251 -0.589834265 DRGEWDSLTPEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DRGEWDSLTPEAR 13 1 B7Z7P0;Q14139;Q14139-2 B7Z7P0 UBE4A Ubiquitin conjugation factor E4 A 0 108.06 0.0011362 76151000 71272 62138 43315 54398 65394 58549 65542 72020 65077 FALSE TRUE 61853.22462 61729.81139 64262.27888 66749.89732 64092.78734 60801.41792 59185.74693 56619.08346 57383.6712 1.077888942 1.075738274 1.119870471 1.163221103 1.116916816 1.059559569 1.031403981 0.986675866 1 15.80835265 2.313240765 1.857067705 0.994837077 1.111731581 0.782774143 0.02548775 0.164847753 1.168539952 0.015761291 0.009265603 205.7030662 -2.313240765 0.116894504 DRGFGAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DRGFGAPR 8 1 P17844;P17844-2;J3QRQ7;J3KRX8;J3QR02;X6RLV5;J3QKN9 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;; 120.12 0.0014256 756460000 1563710 1607730 821340 1129020 1303330 1688720 1428040 1750840 1372030 FALSE TRUE 1357061.762 1597168.716 1218542.771 1385381.247 1277396.283 1753686.151 1289548.901 1376436.491 1209830.176 1.121696076 1.32015943 1.007201502 1.145103895 1.055847596 1.449530839 1.065892491 1.137710497 1 20.20637312 1.17497025 1.645862792 0.919458865 1.171605177 0.137786219 0.130672154 2.516555142 5.462986473 1.081687679 0.035313796 14.96133164 -1.17497025 0.252146312 DRGYIYWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DRGYIYWR 8 1 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 ;; 103.55 0.0043337 1188780000 511664 540429 324199 330682 553203 573064 570618 623150 394934 FALSE TRUE 444046.306 536878.8863 480982.7208 405768.4023 542195.3426 595110.1429 515279.5542 489894.2219 348245.3524 1.275096144 1.541668489 1.381160488 1.165179663 1.556934899 1.708881795 1.479645171 1.406750208 1 18.40974457 1.23573034 4.120967399 0.952014482 1.448673869 0.458247038 0.150602441 0.227396225 7.030319576 0.340460636 0.039529573 17.20799775 -1.23573034 0.496659387 DRIELLQDAEPLDFNAETFTDDPLESESGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DRIELLQDAEPLDFNAETFTDDPLESESGR 30 1 Q68DH5 Q68DH5 LMBRD2 LMBR1 domain-containing protein 2 0 ; 138.52 7.98E-07 75864000 68608 65891 39667.2 54205.8 68112 68149 62466 73027 70080 FALSE TRUE 59541.27897 65458.15768 58850.3906 66514.05537 66756.70446 70770.73613 56408.05693 57410.74435 61795.22224 0.963525606 1.059275383 0.952345318 1.076362427 1.080289091 1.145246082 0.912822301 0.929048271 1 15.91520768 2.209571811 24.99999555 0.94205359 1.045427521 0.377685239 0.059704325 214.1708381 184699.823 0.024676034 0.016639678 162.0211877 -2.209571811 0.103373932 DRIPQILTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DRIPQILTK 9 1 Q9H993 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 99.752 0.0046735 826860000 1054000 928310 583270 643670 942360 865890 1003700 1160700 1175800 FALSE TRUE 914711.2295 922211.8705 865341.3229 789825.1114 923608.8797 899201.3486 906361.3285 912493.3376 1036798.263 0.882246105 0.889480532 0.834628445 0.761792471 0.890827958 0.867286704 0.87419256 0.880106931 1 19.98370378 -0.618542464 1.104219724 9.999999896 0.852608894 0.584207725 0.037639837 74.55824395 1.873038147 1646.632492 0.012239227 0.240689717 0.618542464 -9.147391002 DRKPGSHASS(ph)SAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DRKPGSHASSSAR 13 2 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 DRKPGSHAS(0.081)S(0.553)S(0.365)AR 76.82 0.014417 19959000 20089 21485 7809.2 11994 21685 20156 21824 24022 20974 TRUE FALSE 17434.18775 21343.86362 11585.75524 14717.42102 21253.51093 20931.41436 19707.51184 18885.08224 18494.47761 0.942669921 1.154066855 0.626444038 0.795773816 1.149181468 1.131765644 1.065588996 1.021120068 1 14.17480693 3.237529106 24.99999052 1.069295894 0.881241053 0.331822838 0.136566795 35.86089521 869141.9352 0.042362934 0.050819623 1727.94178 -3.237529106 -0.188054842 DRLDYEDKFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DRLDYEDKFR 10 2 F5GZP6;Q86W92-3;Q86W92-4;Q86W92;A0A0A0MTP2;Q86W92-2 F5GZP6;Q86W92-2 PPFIBP1 Liprin-beta-1 0 ; 112.13 0.0009349 233290000 163577 152422 97295 131468 179133 164000 151310 209042 160146 FALSE TRUE 141959.885 151420.7298 144347.1874 161319.8188 175568.6038 170309.1861 136635.9795 164339.9951 141213.7223 1.005283925 1.072280564 1.022189523 1.142380614 1.243282883 1.206038502 0.967582875 1.163767886 1 17.10752076 3.739877376 24.87096933 1.124136404 1.037154257 0.188076532 0.085114118 190.0413747 3589456.18 0.023200037 0.037527951 5493.857321 -3.739877376 -0.086982147 DRLEFWCTDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DRLEFWCTDVK 11 1 Q9UNM6;J3KNQ3;Q9UNM6-2;H0YD73 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ; 131.26 0.00018885 322460000 429870 345700 228290 275590 360810 290730 418510 482860 431950 FALSE TRUE 373061.5903 343429.0739 338691.8076 338166.9216 353630.5869 301914.5712 377922.9646 379604.1466 380885.3631 0.979458983 0.901659941 0.889222429 0.887844361 0.928443624 0.792665197 0.992222336 0.996636215 1 18.53899732 2.052018019 24.99958614 0.996983672 0.897080732 0.513734701 0.045764691 72.83349992 35003.01388 0.017850296 0.012034665 112.7244225 -2.052018019 -0.09990294 DRLEIYEDVLFFLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DRLEIYEDVLFFLSK 15 1 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 71.692 0.028125 0 19706 16376 13181 13610 12559 11578 17242 21722 15016 FALSE TRUE 17101.80217 16268.42498 19555.37569 16700.35852 12309.10047 12023.41315 15569.87349 17076.91934 13240.82559 1.291596363 1.228656391 1.476900029 1.261277736 0.9296324 0.908056154 1.175898995 1.289717112 1 13.69270546 3.444882305 12.30195937 1.090708111 1.329855805 0.491116971 0.128116502 0.950324308 360.6200601 0.041295188 0.053375544 2785.366227 -3.444882305 0.239147694 DRLGS(ph)YSGPTSVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DRLGSYSGPTSVSR 14 1 V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23;A0A2R8YFI4 V9GYZ0 PANK2 "Pantothenate kinase 2, mitochondrial" 1 DRLGS(0.989)YS(0.011)GPTSVSR 156 1.50E-05 210220000 189940 195510 118730 133420 232770 236800 246960 250680 131310 TRUE FALSE 164838.9478 194225.6819 176148.2251 163715.0502 228138.3324 245909.8492 223009.8572 197074.0328 115786.6814 1.423643426 1.677444069 1.521316813 1.413936804 1.970333113 2.123818096 1.926040668 1.702044056 1 16.82110979 3.251758038 24.99821411 1.771734877 1.521984589 0.124714045 0.304258523 501.9997695 950869.6227 0.091340383 0.117200966 1785.492532 -3.251758038 -0.249750288 DRLPQEPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DRLPQEPGR 9 1 Q8NBJ4-2;Q8NBJ4 Q8NBJ4-2 GOLM1 Golgi membrane protein 1 0 ; 159.83 6.00E-05 427020000 375440 415630 284410 321190 414500 481560 362300 453720 491010 FALSE TRUE 325824.6528 412899.6992 421951.6273 394121.0986 406252.261 500085.9248 327164.2018 356695.5089 432963.3572 0.752545562 0.953659686 0.974566601 0.910287423 0.938306335 1.155030597 0.75563947 0.823846875 1 18.72388541 DRLQYFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DRLQYFR 7 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;; 172.15 0.00083115 2197670000 1692120 1889540 1231110 1398430 1948650 1831910 1712360 2122670 1656240 FALSE TRUE 1468502.055 1877127.487 1826478.914 1715964.905 1909875.677 1902384.763 1546295.591 1668753.539 1460441.194 1.00551947 1.285315352 1.250635028 1.174963369 1.307738843 1.30260963 1.058786617 1.142636585 1 20.47797284 2.225587965 24.99752514 1.082521162 1.227227169 0.37060045 0.093665825 251.1489746 483945.2319 0.036827527 0.025005682 168.1078389 -2.225587965 0.144706007 DRLSASSLTMESFAFLWAGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 ;;;;;; 236.19 7.31E-30 1318660400 979754 818224 421157.2 510911.2 714149.8 686030.8 884797.3 983826 288529.9 FALSE TRUE 850277.0265 812849.0327 624830.2306 626921.3967 699939.6162 712422.8488 798989.794 773442.466 254420.2239 3.34201823 3.194907308 2.455898438 2.464117778 2.751116265 2.800181675 3.140433499 3.040019595 1 17.95685383 4.317314957 5.658245009 2.617871373 3.297106356 0.2026563 0.594043659 0.350589231 18.56192632 0.14668243 0.398936868 20764.18822 -4.317314957 0.679234983 DRNEPCHIIQILEIMSAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DRNEPCHIIQILEIMSAVR 19 1 E5RG17;Q6P1N9;Q6P1N9-2;A0A0D9SGD3 E5RG17 TATDN1 Putative deoxyribonuclease TATDN1 0 166.91 1.14E-11 33181000 37945 35351 27964 35435 31380 28400 32359 39234 54008 FALSE TRUE 32930.47211 35118.77695 41487.48393 43481.05834 30755.59939 29492.56638 29220.82916 30844.11442 47623.23577 0.691479098 0.737429458 0.871160543 0.913021924 0.645810788 0.619289427 0.613583447 0.64766944 1 15.53937803 3.215121299 24.99926029 0.686894865 0.803418865 0.11959181 0.126795262 431.533343 460251.4466 0.039087443 0.044345999 1641.048057 -3.215121299 0.116524001 DRNVATPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DRNVATPR 8 1 P11216;P11217;P11217-2 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form" 0 ;;; 109.66 0.0032602 322029000 469560 418792 235647 263743 385634 452310 367564 395135 276120 FALSE TRUE 407506.4563 416040.9278 349606.6774 323629.8792 377960.6379 469710.6584 331917.6999 310638.4552 243477.4082 1.673693093 1.708745509 1.435889597 1.329198802 1.552343771 1.929175532 1.363238184 1.275840981 1 17.89342839 1.615067136 1.935868969 1.012870383 1.584739127 0.566879114 0.170904962 0.28989757 2.060734707 0.254540911 0.05097956 41.21612285 -1.615067136 0.571868744 DRNVIPDT(ph)PPSTPLVPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DRNVIPDTPPSTPLVPSR 18 1 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 DRNVIPDT(0.952)PPS(0.018)T(0.03)PLVPSR;DRNVIPDT(0.997)PPS(0.001)T(0.002)PLVPSR 103.29 0.00087299 341510000 240580 251660 142546 203006 287260 293670 263080 344590 172987 TRUE FALSE 208786.7434 250006.8289 211481.7224 249101.6151 281544.088 304967.6749 237566.5421 270902.1101 152536.6739 1.368764233 1.638994889 1.386431977 1.633060487 1.845746867 1.999307229 1.55743885 1.775980183 1 17.21879662 1.232389669 24.98724279 0.999998906 1.660026392 0.52905078 0.192766473 172.818129 699700.7883 0.438470558 0.048605039 17.0761385 -1.232389669 0.660027486 DRPASGSPFQLFLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DRPASGSPFQLFLSK 15 1 A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2;A0A087WWG9 A0A087WVR3 UHRF1 E3 ubiquitin-protein ligase UHRF1 0 79.013 0.019339 413680000 292380 270450 184160 264300 306360 262170 315170 384680 342550 FALSE TRUE 253741.2422 268673.3961 273220.392 324313.3546 300264.0354 272255.8495 284604.8619 302419.1756 302054.1292 0.840052221 0.889487579 0.904541158 1.073692836 0.994073599 0.901347882 0.942231323 1.001208546 1 18.20444758 3.970344281 12.99204708 0.981840696 0.872809168 0.561333585 0.045571102 1.585002869 694.7590368 0.01272499 0.022372138 9339.944177 -3.970344281 -0.109031527 DRPFFAGLVK ddPTM_MDA-MB-175_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 13579300000 5527000 6882400 4128600 4837400 6486300 5949000 7768800 9353500 9156300 FALSE TRUE 4796592.946 6837189.061 6125204.769 5935805.605 6357235.32 6177861.88 7015382.972 7353326.814 8073852.645 0.594089731 0.846831044 0.758647084 0.735188746 0.787385601 0.765169015 0.868901537 0.910758115 1 22.94482583 -2 0.347935534 4.16942026 0.714408779 0.690376221 0.061065163 42.43744829 0.659938774 94.68279332 0.078247624 0.01 2 -3.455011481 DRPFFPGLVK ddPTM_MDA-MB-175_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 ; 141.88 3.35E-05 34808000000 18088300 17911200 10833900 13702200 17097800 14845700 19647900 21339700 21996700 FALSE TRUE 15697885.33 17793540.15 16073210.28 16813493.94 16757587.23 15416823.69 17742449.68 16776371.22 19396275.18 0.809324738 0.917368927 0.8286751 0.866841379 0.863959037 0.794834242 0.914734892 0.86492747 1 24.20927629 -0.432075796 1.252517556 10 0.854435329 0.561050459 0.039599447 65.33826439 2.044881703 1638.413983 0.010765793 0.369763641 0.432075796 -9.145564671 DRPGGSMVVSDVVPGGPAEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DRPGGSMVVSDVVPGGPAEGR 21 1 O95049;O95049-4;O95049-3;K7ESC0 O95049 TJP3 Tight junction protein ZO-3 0 ; 112.54 0.00020268 493210000 299380 236924 202095 247581 290741 262267 289925 325550 311590 FALSE TRUE 259816.1745 235367.6306 299828.818 303798.0501 284955.8229 272356.5812 261808.1181 255933.6659 274754.1852 0.945631362 0.856648027 1.09126206 1.105708544 1.037130054 0.99127364 0.952881274 0.931500518 1 18.06778193 4.251814437 24.99855613 1.007909069 0.901139692 0.395619731 0.058243729 289.342852 545730.9947 0.01682667 0.043967138 17857.24417 -4.251814437 -0.106769377 DRPGS(ph)PES(ph)PLLDAPFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DRPGSPESPLLDAPFSR 17 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 2 DRPGS(1)PES(1)PLLDAPFSR;DRPGS(1)PES(1)PLLDAPFSR 129.9 1.83E-05 228990000 281170 262600 165883 216110 292510 268550 288550 343800 320080 TRUE FALSE 244012.6721 260874.9633 246104.5736 265181.0785 286689.6233 278881.2923 260566.4654 270281.0455 282240.507 0.864555817 0.924300222 0.871967586 0.939557122 1.015763564 0.988098042 0.92320719 0.9576267 1 18.10656553 3.526510046 5.145081407 0.971704667 0.891901208 0.657310308 0.029427668 0.141311156 8.465025887 0.008535945 0.012494173 3361.321444 -3.526510046 -0.079803458 DRPGS(ph)PESPLLDAPFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DRPGSPESPLLDAPFSR 17 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 DRPGS(1)PESPLLDAPFSR;DRPGS(0.999)PES(0.001)PLLDAPFSR;DRPGS(1)PESPLLDAPFSR;DRPGS(0.939)PES(0.061)PLLDAPFSR;DRPGS(0.999)PES(0.001)PLLDAPFSR;DRPGS(1)PESPLLDAPFSR 198.22 8.72E-12 3263550000 1948920 1391639 912002 1096066 1308325 1362501 1366112 1457900 1410150 TRUE FALSE 1691365.284 1382497.232 1353049.218 1344944.538 1282291.892 1414917.295 1233626.669 1146139.43 1243443.673 1.3602267 1.111829399 1.088146771 1.08162884 1.031242444 1.137902203 0.992104986 0.921746159 1 20.24590973 8 0.478077723 0.991187712 10.24768044 0.76806674 0.056644267 55.05521042 0.641856897 0.041601474 504.361494 100000000 -8 9.256492732 DRPHEGTRPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DRPHEGTRPVR 11 2 P31146;H3BRY3;H3BTU6;H3BRJ0 P31146 CORO1A Coronin-1A;Coronin 0 61.11 0.050275 19696000 36494 37621 16174 22653 33325 46281 21714 32454 16126 FALSE TRUE 31671.22544 37373.86517 23995.8005 27796.70988 32661.8977 48061.46002 19608.17962 25513.96466 14219.60265 2.227293281 2.628334004 1.687515544 1.954816218 2.296962756 3.379943955 1.378954117 1.794281126 1 13.79559353 DRPMEESLLLFEAMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DRPMEESLLLFEAMR 15 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A1B0GTT3;A0A0U1RQQ5 P47897 QARS Glutamine--tRNA ligase 0 ;;; 198.61 7.15E-09 604723000 232072 227251 159823 215682 233060 240948 254246 282593 283212 FALSE TRUE 201403.0972 225758.1732 237113.9374 264655.8946 228422.562 250217.4255 229589.2621 222162.6861 249731 0.806480161 0.904005403 0.949477387 1.059763884 0.914674438 1.001947798 0.919346265 0.889607963 1 17.93001539 4.63492698 2.34988865 0.956276304 0.788628355 0.499193212 0.049804699 0.413279091 3.227110331 0.013353691 0.128630903 43144.65293 -4.63492698 -0.167647948 DRPPCS(ph)PSR ddPTM_MDA-MB-175_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(0.5)PS(0.5)R 81.923 0.052374 617210000 581450 502890 329460 375080 495110 525880 525800 554430 538950 TRUE FALSE 504609.9093 499586.4825 488787.958 460247.6467 485258.2797 546110.9439 474807.9969 435869.4591 475235.945 1.061809223 1.051238838 1.028516389 0.968461354 1.021089176 1.149136444 0.999099504 0.917164334 1 18.85828443 2.00007804 25 0.954305297 1.044095666 0.362659876 0.04871502 2.664220032 853246.7812 0.020509773 0.013667631 100.0179709 -2.00007804 0.089790369 DRPPCSPSR ddPTM_MDA-MB-175_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 0 81.017 0.020161 0 38270 38421 28120 29646 34579 39584 34316 37879 40005 FALSE TRUE 33212.52254 38168.60992 41718.92606 36377.57741 33890.94555 41106.82209 30988.0396 29778.87062 35275.65447 0.941514 1.082009972 1.182654913 1.031237491 0.960746046 1.16530289 0.878453995 0.844176276 1 15.10638523 2.217959737 24.98858573 0.893129793 1.061229293 0.414163654 0.08522426 209.1892344 253741.7342 0.034345534 0.023184675 165.1808652 -2.217959737 0.1680995 DRPQEADGIDSVIVVDNVPQVGPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DRPQEADGIDSVIVVDNVPQVGPDR 25 1 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;;;; 271.04 5.79E-53 3522830000 2003240 1663580 1208733 1512482 1845490 1822500 1841430 2149890 2234540 FALSE TRUE 1738506.758 1652651.833 1793280.322 1855914.155 1808768.36 1892612.754 1662848.402 1690152.754 1970375.227 0.882322684 0.838749803 0.910121228 0.941908998 0.917981679 0.960534181 0.843924741 0.857782178 1 20.91003896 4.220025373 23.10235275 0.911697406 0.860536284 0.201254488 0.04665045 160.0171349 199447.1668 0.012455616 0.02603006 16596.83868 -4.220025373 -0.051161121 DRPSAAHIVEALETDV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DRPSAAHIVEALETDV 16 1 Q96KB5;Q96KB5-2 Q96KB5 PBK Lymphokine-activated killer T-cell-originated protein kinase 0 ;; 97.836 0.0026796 129108000 152441 152097 86636 129899 149000 158584 140309 166409 235145 FALSE TRUE 132295.5356 151097.8648 128533.4594 159394.5533 146035.1915 164684.8291 126701.8548 130823.7303 207346.426 0.638041071 0.728721819 0.619897154 0.768735475 0.704305323 0.794249664 0.611063606 0.63094278 1 17.66168365 1.232340008 24.98870063 1.00000052 0.686462172 0.70732105 0.063275565 117.8116865 473212.443 0.141027895 0.015572566 17.07418599 -1.232340008 -0.313538348 DRPVGGS(ph)PGGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DRPVGGSPGGPR 12 1 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 DRPVGGS(1)PGGPR;DRPVGGS(1)PGGPR;DRPVGGS(1)PGGPR 117.33 0.0019617 4041600000 1123550 1079080 781540 1048540 1297730 1356330 1399870 1499650 1475490 TRUE FALSE 975070.0208 1071991.452 1159495.358 1286627.033 1271907.712 1408508.893 1264110.823 1178961.518 1301059.253 0.749443208 0.823937457 0.891193353 0.988907331 0.977593994 1.082586277 0.97160127 0.906155131 1 20.31125524 4.20075645 1.593203037 0.982757626 0.749874063 0.787084548 0.043915716 0.237405868 1.066364352 0.014292672 0.063298458 15876.56152 -4.20075645 -0.232883563 DRPWSNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DRPWSNSR 8 1 Q9NRR8 Q9NRR8 CDC42SE1 CDC42 small effector protein 1 0 ;; 79.148 0.026254 382080000 894790 670720 530280 661720 479120 715470 635920 864490 1497020 FALSE TRUE 776541.2344 666313.9962 786725.1817 811973.6398 469586.4494 742994.5939 574248.5763 679625.541 1320044.001 0.588269205 0.504766504 0.595984059 0.615111041 0.355735452 0.56285593 0.435022299 0.514850672 1 20.33215459 1.238331185 24.99834574 1.000000534 0.518032716 0.784505557 0.078782507 2.409058633 261908.9073 0.105130854 0.018599427 17.3113599 -1.238331185 -0.481967818 DRPYDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DRPYDYK 7 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 ; 88.819 0.016715 552810000 1043210 1120040 626840 776460 1080080 1337090 985580 1031550 951470 FALSE TRUE 905347.1553 1112682.383 929981.9207 952767.1104 1058588.521 1388528.718 889998.6033 810961.06 838988.3005 1.079093898 1.326219189 1.108456364 1.135614299 1.26174408 1.655003671 1.060799778 0.966594003 1 19.67829117 2.01817706 24.99929694 0.990746488 1.260259672 0.36026299 0.160639834 246.4106922 338892.4997 0.066521848 0.04484033 104.2742465 -2.01817706 0.269513184 DRQS(ph)PLHGNHITISHTQATGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DRQSPLHGNHITISHTQATGSR 22 1 Q86VQ1;H7C2L5 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 DRQS(1)PLHGNHITISHTQATGSR 192.62 5.04E-18 204650000 47729 48396 23728 31608 40372 44677 53226 47775 50632 TRUE FALSE 41421.49172 48078.08349 35202.94017 38785.0795 39568.67619 46395.7531 48064.15071 37558.68804 44646.34264 0.927768979 1.076864994 0.788484299 0.868717955 0.886269151 1.039183735 1.076552924 0.841248931 1 15.44625438 2.765094003 24.83663075 0.974306799 0.909910187 0.144351302 0.093226497 1771.988334 1658670.432 0.031422754 0.03141373 582.2292272 -2.765094003 -0.064396612 DRRPVHLDQAAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DRRPVHLDQAAFR 13 2 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 150.69 2.50E-05 150510000 60366 59340 28779 36226 49772 55202 61629 59454 41336 FALSE TRUE 52388.48015 58950.19163 42696.62066 44451.66698 48781.63458 57325.65666 55652.22907 46740.22477 36449.30517 1.437297087 1.617320038 1.171397382 1.219547719 1.338341962 1.572750328 1.526839231 1.282335138 1 15.15360369 1.317074761 3.157341341 0.96647991 1.406264072 0.453723172 0.14282444 0.302394787 4.181985104 0.296761838 0.039510776 20.75270732 -1.317074761 0.439784162 DRS(ph)PAAET(ph)PPLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DRSPAAETPPLQR 13 1 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 2 DRS(1)PAAET(1)PPLQR;DRS(1)PAAET(1)PPLQR;DRS(1)PAAET(1)PPLQR;DRS(1)PAAET(1)PPLQR;DRS(1)PAAET(1)PPLQR;DRS(1)PAAET(1)PPLQR 120.59 0.002992 6823000000 3745660 3681760 2496540 2954530 3563190 3699960 3578120 3871980 3764840 TRUE FALSE 3250661.541 3657574.276 3703875.094 3625401.194 3492289.49 3842299.855 3231114.473 3043987.209 3319764.904 0.97918426 1.101757016 1.115704034 1.092065643 1.051968917 1.157401191 0.973296172 0.916928547 1 21.66264965 2.105494884 6.937723484 0.950491632 1.084030679 0.560299354 0.049910265 0.136615297 7.972563762 0.019593924 0.013150656 127.4955082 -2.105494884 0.133539046 DRS(ph)PAAETPPLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DRSPAAETPPLQR 13 1 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 DRS(1)PAAETPPLQR 108.71 0.00072341 1050700000 322930 249330 250070 253490 231900 228800 282170 315080 239190 TRUE FALSE 280253.9823 247692.1348 371004.6884 311048.7789 227285.6437 237602.0841 254805.1968 247702.594 210913.2307 1.328764352 1.174379312 1.759039427 1.474771297 1.077626297 1.126539493 1.208104375 1.174428902 1 17.68629007 3.240624479 24.99996132 1.131743257 1.438877321 0.509407904 0.154143284 48.48699557 587326.7896 0.0466387 0.05723375 1740.301437 -3.240624479 0.307134064 DRS(ph)PHRS(ph)SPSDTRPK ddPTM_MDA-MB-175_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(0.996)PHRS(0.54)S(0.459)PS(0.005)DT(0.001)RPK;DRS(1)PHRS(0.716)S(0.28)PS(0.004)DTRPK;DRS(1)PHRS(0.539)S(0.461)PS(0.001)DTRPK;DRS(0.938)PHRS(0.573)S(0.487)PS(0.001)DTRPK 107.45 0.0011353 1101478000 800353 772714 264297 473735 933619 731773 894790 1025038 792722 TRUE FALSE 694584.3232 767637.9909 392111.9132 581303.7723 915041.8085 759924.7808 808013.4035 805841.6006 699007.3082 0.993672477 1.098183069 0.560955384 0.831613297 1.309059001 1.087148549 1.155944143 1.152837161 1 19.41494801 3.257101783 24.99724263 1.140906222 0.865172133 0.428310328 0.154872294 237.5585989 320275.1238 0.045271987 0.058339436 1807.597713 -3.257101783 -0.275734089 DRS(ph)PHRSS(ph)PSDTRPK ddPTM_MDA-MB-175_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(0.998)PHRS(0.44)S(0.542)PS(0.018)DT(0.003)RPK;DRS(0.991)PHRS(0.178)S(0.829)PS(0.001)DTRPK 121.26 0.00016673 596540000 455760 482610 152340 356370 570720 463960 550390 637990 541070 TRUE FALSE 395530.1613 479439.7031 226012.1335 437289.2553 559363.7886 481808.8414 497013.2625 501560.8033 477105.321 0.829020646 1.004892803 0.473715391 0.916546591 1.172411549 1.009858453 1.041726513 1.051258037 1 18.86394825 3.477868174 24.99831698 1.050696172 0.776503441 0.481350133 0.1357013 22.62122085 757120.3933 0.037309179 0.048768426 3005.163974 -3.477868174 -0.27419273 DRS(ph)PLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 68.335 0.049402 24860250000 3327951 2987986 2047808 1886552 2392518 3145369 2886968 3023710 2577346 TRUE FALSE 2888153.843 2968357.723 3038134.798 2314922.466 2344911.573 3266373.381 2606990.288 2377113.147 2272655.092 1.270828052 1.30611888 1.336821768 1.018598235 1.031793861 1.437249934 1.147112158 1.045963004 1 21.11594732 -0.203955205 0.480791599 1.16E-30 1.247933248 0.275043387 0.131390254 26.42344598 1.653829419 25.09394159 0.102034325 0.62523718 0.203955205 1.247933248 DRS(ph)PSRLDTFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DRSPSRLDTFLK 12 2 Q66GS9 Q66GS9 CEP135 Centrosomal protein of 135 kDa 1 DRS(0.845)PS(0.154)RLDTFLK 60.549 0.071791 178480000 196080 189850 131120 138650 149050 140520 180500 228780 145420 TRUE FALSE 170167.5312 188602.8628 194530.0706 170132.6016 146084.1966 145925.8953 162995.1378 179857.1774 128228.6133 1.327063647 1.470832898 1.517056651 1.326791247 1.139248042 1.138013518 1.271129225 1.402629045 1 16.9683587 3.483255662 5.673206979 1.22058586 1.439720448 0.488804891 0.114276688 0.159129462 18.42707543 0.034053141 0.0472851 3042.675672 -3.483255662 0.219134588 DRS(ph)SPPPGYIPDELHQVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DRSSPPPGYIPDELHQVAR 19 1 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 1 DRS(0.629)S(0.371)PPPGYIPDELHQVAR;DRS(0.5)S(0.5)PPPGYIPDELHQVAR;DRS(0.5)S(0.5)PPPGYIPDELHQVAR;DRS(0.647)S(0.353)PPPGYIPDELHQVAR;DRS(0.5)S(0.5)PPPGYIPDELHQVAR 221.85 1.56E-19 2421260000 839319 816280 506363 584314 798014 805452 783479 913300 785708 TRUE FALSE 728400.8676 810917.8029 751241.8405 716991.4244 782135.0827 836438.2596 707497.3272 717997.9023 692822.4953 1.051352796 1.17045536 1.084320797 1.034884735 1.128911212 1.207290851 1.021181229 1.036337456 1 19.40212625 2.115157489 21.94615943 1.022790519 1.111625692 0.42297265 0.051516479 3.379217489 628.7059384 0.021069291 0.014204924 130.3639434 -2.115157489 0.088835173 DRS(ph)SSAPNVHINTIEPVNIDDLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DRSSSAPNVHINTIEPVNIDDLIR 24 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 DRS(0.333)S(0.333)S(0.333)APNVHINTIEPVNIDDLIR;DRS(0.333)S(0.333)S(0.333)APNVHINTIEPVNIDDLIR;DRS(0.333)S(0.333)S(0.333)APNVHINTIEPVNIDDLIR;DRS(0.333)S(0.333)S(0.333)APNVHINTIEPVNIDDLIR;DRS(0.382)S(0.382)S(0.235)APNVHINTIEPVNIDDLIR;DRS(0.333)S(0.333)S(0.333)APNVHINTIEPVNIDDLIR 255.9 4.54E-44 1309027000 737454 645268 340103 396845 586823 597510 649375 723952 274613.2 TRUE FALSE 639997.5854 641029.192 504577.9484 486954.7226 575146.3704 620496.5963 586398.7124 569140.4986 242148.7403 2.64299366 2.647253878 2.083752109 2.010973594 2.37517804 2.562460558 2.42164676 2.350375632 1 17.88553397 1.238394924 6.831913533 0.967514152 2.381113608 0.81067902 0.210662281 0.051557458 12.91829587 0.337979845 0.055931966 17.31390075 -1.238394924 1.413599456 DRSPAAET(ph)PPLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DRSPAAETPPLQR 13 1 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 DRSPAAET(1)PPLQR;DRSPAAET(1)PPLQR;DRSPAAET(1)PPLQR;DRSPAAET(1)PPLQR;DRSPAAET(1)PPLQR 127.88 0.00027773 9505410000 3066170 3272240 1880050 2398530 3166260 3070780 2972330 3594170 3133590 TRUE FALSE 2660967.866 3250744.44 2789248.468 2943152.896 3103257.621 3188914.894 2684073.894 2825584.715 2763140.56 0.963022983 1.176467273 1.009448636 1.06514773 1.123090756 1.154090726 0.971385218 1.022598979 1 21.39787752 2.220328626 24.9999242 1.002011881 1.083998139 0.274982026 0.06403609 313.5815025 429983.614 0.024642927 0.016650356 166.0843173 -2.220328626 0.081986258 DRT(ph)PPHLLYSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DRTPPHLLYSDR 12 1 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 DRT(1)PPHLLYSDR;DRT(1)PPHLLYSDR;DRT(1)PPHLLYSDR;DRT(1)PPHLLYSDR 112.3 0.0018893 993580000 402653 371512 311824 349480 407702 384702 356506 399307 684280 TRUE FALSE 349441.3859 369071.5132 462623.1294 428834.7755 399589.5279 399501.7349 321932.103 313918.3055 603385.1979 0.579134833 0.611668159 0.766712758 0.710714775 0.662246156 0.662100655 0.533543256 0.52026186 1 19.20271978 1.228047512 24.99930533 1.000000774 0.62916555 0.701447336 0.075690506 296.7591342 705620.8013 0.297656457 0.021299145 16.90625876 -1.228047512 -0.370835224 DRT(ph)PPHLLYSDRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DRTPPHLLYSDRDR 14 2 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 DRT(1)PPHLLYSDRDR;DRT(1)PPHLLYSDRDR;DRT(1)PPHLLYSDRDR 130.36 0.00298 2624730000 2143050 1988510 1371880 1477300 2060240 2099930 2039530 2149900 2136180 TRUE FALSE 1859840.513 1975447.347 2035325.757 1812743.544 2019245.255 2180715.666 1841736.695 1690160.616 1883643.234 0.987363466 1.048737527 1.080526142 0.962360341 1.071989227 1.157711623 0.977752401 0.897282768 1 20.84509431 2.011612976 24.97776345 0.940168365 1.051047605 0.371581795 0.057764064 194.1479906 417581.6262 0.023397943 0.015761503 102.7100583 -2.011612976 0.11087924 DRT(ph)PPLLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DRTPPLLYR 9 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 DRT(1)PPLLYR;DRT(1)PPLLYR;DRT(1)PPLLYR;DRT(1)PPLLYR 85.274 0.02413 2172440000 1158740 1024740 716290 781430 1046300 1072350 907130 942870 1446870 TRUE FALSE 1005609.573 1018008.415 1062690.24 958865.6249 1025480.677 1113603.998 819156.6722 741244.5879 1275822.677 0.788204812 0.797923124 0.832945094 0.751566532 0.803779942 0.872851705 0.64206154 0.580993426 1 20.2829964 2.236677569 24.99997875 0.703556608 0.805819467 0.039228883 0.113152493 94.41389549 1253434.094 0.04392964 0.03131766 172.4557064 -2.236677569 0.102262859 DRTDIQCLIPCAIDQDPYFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DRTDIQCLIPCAIDQDPYFR 20 1 P23381;P23381-2;H0YJP3 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ;;; 143.14 1.56E-07 1562920000 1299210 1245810 738290 805920 1158900 1198050 1200780 1425220 1012500 FALSE TRUE 1127516.107 1237626.192 1095329.513 988916.4537 1135840.157 1244139.759 1084328.54 1120447.794 892803.4034 1.262894051 1.386224769 1.226842896 1.107653096 1.272217549 1.393520403 1.214521065 1.254977064 1 19.767983 1.206768171 3.682304073 0.953055668 1.266483948 0.507850656 0.081841062 0.303329434 6.024813548 0.275583098 0.021564085 16.09786093 -1.206768171 0.31342828 DRVDCGYPHVTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DRVDCGYPHVTPK 13 1 X6R3S7;Q07654 X6R3S7 TFF3 Trefoil factor 3 0 ;;;;; 159.02 2.78E-05 4910070000 2864789 2933790 1566670 2024340 2764120 2004232 2655650 3111460 2484662 FALSE TRUE 2486199.875 2914517.74 2324316.852 2483997.337 2709119.42 2081336.102 2398105.472 2446098.492 2190928.089 1.134770186 1.330266272 1.06088231 1.133764887 1.236516814 0.949979195 1.094561471 1.116466809 1 21.0631107 3.437932351 0.674486992 1.056497882 1.221995885 0.264889551 0.092872278 1.274567509 1.351397292 0.067460189 0.138310695 2741.147159 -3.437932351 0.165498004 DRVEISPEQLSAASTEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DRVEISPEQLSAASTEAER 19 1 X6RJS7;P46736-2;P46736-3;P46736;A0A0A0MS96;P46736-5 X6RJS7 BRCC3 Lys-63-specific deubiquitinase BRCC36 0 119.38 5.55E-05 110690000 86480 81036 58420 83724 68095 79565 88774 88038 87179 FALSE TRUE 75051.44889 80503.66918 86672.1074 102734.8138 66740.04273 82625.91704 80164.71114 69211.75881 76872.79793 0.976306976 1.047232198 1.127474344 1.336426104 0.868188026 1.074839465 1.042822862 0.900341352 1 16.23018556 3.201317826 24.99999972 0.977425198 1.116931582 0.306237854 0.108050021 220.6030863 148083.6788 0.033260873 0.037715209 1589.709706 -3.201317826 0.139506384 DRVGQNLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DRVGQNLPR 9 1 A2A2Q9;Q9Y312 A2A2Q9 AAR2 Protein AAR2 homolog 0 107.57 0.0025093 41076000 53648 48401 29388 32435 38954 43803 44943 54975 35589 FALSE TRUE 46558.28087 48083.05064 43600.1351 39799.86249 38178.89161 45488.12975 40584.43478 43219.02407 31381.70896 1.483612028 1.532199878 1.389348654 1.268250322 1.216596956 1.449510918 1.293251264 1.377204285 1 14.9376363 7.999999997 0.036098168 1.91E-14 3.385101004 0.435010456 0.115161847 2403.431769 8.565352793 264.6477294 606.2936546 99999999.31 -7.999999997 3.385101004 DRVHHEPQLSDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DRVHHEPQLSDK 12 1 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-9;O43852-13;O43852-14;O43852-11;O43852-12;O43852-2;O43852-4;O43852-8;O43852-7 O43852;O43852-2 CALU Calumenin 0 ; 77.593 0.016826 111308000 376760 277601 224965 264129 297830 307262 330780 344850 308640 FALSE TRUE 326970.2114 275777.4208 333758.8265 324103.5264 291903.7657 319082.568 298701.0065 271106.5111 272152.9308 1.201420872 1.013317843 1.226364991 1.190887511 1.07257256 1.172438478 1.097548373 0.996155031 1 18.05405805 1.850332717 3.059560862 0.995846718 1.14241328 0.47876186 0.062876461 0.20718589 3.412385411 0.03966058 0.016617973 70.84883561 -1.850332717 0.146566561 DRVTSAVEALLSADSASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DRVTSAVEALLSADSASR 18 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;;; 220.34 6.23E-19 1508672000 1422396 1278853 766837 875366 1240239 1245423 1189402 1488370 1126575 FALSE TRUE 1234422.765 1270452.13 1137681.938 1074131.229 1215560.67 1293335.229 1074053.977 1170093.658 993392.5869 1.242633357 1.278902367 1.145249072 1.081275664 1.223645804 1.301937669 1.081197898 1.177876374 1 19.92200446 0.307085014 1.039342562 9.39E-11 1.200616147 0.404272535 0.074010416 12.11677354 2.380504626 25.74874433 0.024410446 2.028079679 -0.307085014 1.200616147 DRWSEVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DRWSEVTR 8 1 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 0 ;; 134.25 0.00080692 579940000 250878 251600 193052 198747 259327 257364 243877 282728 224666 FALSE TRUE 217723.8367 249947.223 286412.5929 243875.544 254166.9001 267264.9596 220225.8461 222268.8174 198106.2414 1.099025629 1.261682728 1.445752496 1.231034127 1.282982799 1.349099138 1.111655264 1.121967767 1 17.59591481 2.148371104 5.946927996 1.084214835 1.282841035 0.512174677 0.092303182 0.172894835 9.181819454 0.038388999 0.025722519 140.7249502 -2.148371104 0.198626199 DRYDSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DRYDSDR 7 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 116.37 0.0049892 192145000 238660 213680 156613 194257 155852 231590 213928 230470 313810 FALSE TRUE 207120.4763 212276.322 232351.5706 238366.0209 152750.8501 240499.4172 193181.2955 181185.784 276711.7393 0.748506286 0.767138838 0.839688158 0.861423594 0.552021575 0.869133409 0.698131911 0.654781703 1 18.07802432 1.225343637 24.94602766 1.000000629 0.746601643 0.394670184 0.097712879 681.7015178 1286578.902 0.437519813 0.023485361 16.80132902 -1.225343637 -0.253398986 DRYDSDRYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DRYDSDRYR 9 2 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;; 163.65 3.54E-05 2305390000 1021480 1156460 521816 603527 1085560 1053083 1112060 1315020 285549 FALSE TRUE 886488.8299 1148863.138 774167.963 740567.0297 1063959.48 1093595.784 1004212.592 1033813.206 251791.7225 3.520722687 4.562751812 3.074636272 2.941188941 4.22555384 4.343255503 3.988266899 4.105826817 1 17.94187133 1.235589695 24.99967423 0.99999612 3.861723096 0.741001057 0.528568176 43.90341567 369369.7872 0.908420825 0.132864751 17.20242586 -1.235589695 2.861726975 DRYDSFIELQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DRYDSFIELQEK 12 1 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 ; 207.73 6.85E-08 1001650000 1036190 742810 545010 707450 732010 635320 858730 995390 949510 FALSE TRUE 899254.8661 737930.4322 808578.6589 868087.3352 717444.4332 659761.1715 775450.4968 782533.5946 837260.0095 1.074044927 0.881363524 0.965743795 1.036819298 0.856895618 0.788000339 0.926176442 0.934636297 1 19.67531619 3.233167215 24.99996233 0.901549095 0.980072997 0.260307987 0.07324303 216.4423066 1003270.712 0.022687235 0.026469657 1710.673844 -3.233167215 0.078523902 DRYLPDTLLLEECGLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DRYLPDTLLLEECGLLR 17 1 P21964-2;P21964;E7EMS6 P21964-2 COMT Catechol O-methyltransferase 0 ;;; 214.34 5.44E-15 921700000 628170 630860 313306 368089 578340 600120 640130 671220 226535 FALSE TRUE 545155.7429 626715.8391 464821.8295 451669.2333 566832.1655 623207.0047 578050.2911 527684.8264 199754.2904 2.729131584 3.137433684 2.32696794 2.261124066 2.837647014 3.119867932 2.893806636 2.64166955 1 17.60786696 4.237183346 24.99992735 2.514527578 2.933282643 0.098508051 0.587594172 93.61356416 1699397.534 0.149977146 0.342141266 17265.66642 -4.237183346 0.418755065 DS(ph)HSPDLQLPTPEVIPSSGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSHSPDLQLPTPEVIPSSGSK 21 0 H3BQK9;H3BPE1;H0Y4F5;H0Y6T5 H3BQK9 MACF1 1 DS(0.612)HS(0.388)PDLQLPTPEVIPSSGSK 168.26 7.11E-12 203410000 381400 298810 235450 304520 263320 281270 338930 358180 421300 TRUE FALSE 330997.0237 296847.0974 349314.4075 373665.9203 258080.4472 292090.6389 306060.6208 281585.9944 371494.3939 0.890987937 0.799062118 0.940295233 1.005845381 0.694708861 0.786258538 0.823863363 0.757981813 1 18.50298091 3.241449129 24.99999772 0.8052723 0.903423502 0.210798793 0.091883045 120.4593366 1042564.941 0.026717938 0.032972695 1743.609106 -3.241449129 0.098151203 DS(ph)LGAYASQDANEQGQDLGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSLGAYASQDANEQGQDLGKR 21 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DS(1)LGAYASQDANEQGQDLGKR;DS(1)LGAYASQDANEQGQDLGKR 259.82 8.79E-37 843730000 572800 478080 422540 477200 612290 490390 736350 851150 400560 TRUE FALSE 497103.0287 474939.461 626881.7573 585555.5535 600106.6269 509255.6206 664938.8903 669138.1962 353206.2531 1.407401552 1.344651905 1.774831991 1.657828955 1.699026055 1.441808054 1.88257961 1.894468714 1 18.43015136 4.249540621 24.94897038 1.657511944 1.376026575 0.12309731 0.258867285 368.8996717 838203.8166 0.062795618 0.162702451 17763.99411 -4.249540621 -0.281485369 DS(ph)LGTYSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DSLGTYSSR 9 0 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DS(1)LGTYSSR;DS(1)LGTYSSR;DS(0.999)LGT(0.001)YSSR;DS(1)LGTYSSR 258.72 4.84E-15 4250070000 2230940 1908790 1863620 2406030 2437140 2132740 2479520 2613650 3722330 TRUE FALSE 1936115.627 1896251.033 2764872.865 2952355.885 2388645.682 2214787.888 2239056.532 2054741.287 3282280.388 0.589869054 0.577723658 0.842363399 0.899483145 0.727739681 0.674771082 0.682164918 0.626010287 1 21.64626706 4.255091624 24.96632925 0.758852301 0.583796199 0.326159802 0.113794516 319.4004799 482373.3231 0.029476721 0.077501494 17992.50467 -4.255091624 -0.175056102 DS(ph)PGIPPSANAHQLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSPGIPPSANAHQLFR 16 0 B4DG22;B1AXG1;B7ZB17;P51812 B4DG22 RPS6KA3 Ribosomal protein S6 kinase alpha-3 1 DS(1)PGIPPSANAHQLFR;DS(1)PGIPPSANAHQLFR 118.46 0.00017445 802310000 526880 653990 382920 622320 789980 658220 682910 898600 1266080 TRUE FALSE 457251.4731 649693.8966 568101.3928 763627.2676 774260.9436 683542.1493 616681.4933 706441.3829 1116405.465 0.409574736 0.581951555 0.508866546 0.684005311 0.693530234 0.612270515 0.552381292 0.63278209 1 20.09042966 1.234065812 3.735315798 1.055498327 0.585371693 0.72159963 0.08169672 0.154869024 3.417248604 0.205390565 0.021239993 17.14217056 -1.234065812 -0.470126634 DS(ph)PTLSNSGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSPTLSNSGIR 11 0 Q9HD20;Q9HD20-2;Q9HD20-3 Q9HD20 ATP13A1 Manganese-transporting ATPase 13A1 1 DS(0.888)PT(0.111)LS(0.001)NSGIR;DS(0.996)PT(0.004)LSNSGIR 94.402 0.0089481 279590000 362220 315110 221412 309370 482090 380730 312000 475670 501610 TRUE FALSE 314351.7093 313040.0217 328487.5838 379617.1869 472497.3522 395376.9295 281742.288 373951.6722 442310.2372 0.710704123 0.707738586 0.742663308 0.858260006 1.068248737 0.893890523 0.636978899 0.84545109 1 18.75469911 3.774463681 4.069891111 0.873106651 0.71451187 0.324221984 0.111253744 0.309064177 11.50418316 0.032984551 0.05745231 5949.270024 -3.774463681 -0.158594781 DS(ph)QDGSSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSQDGSSYR 9 0 Q14847;Q14847-2;C9J9W2;Q14847-3;J3KSN1 Q14847 LASP1 LIM and SH3 domain protein 1 1 DS(0.999)QDGS(0.001)SYR 90.697 0.011806 700870000 211900 111540 100590 105740 90520 120510 142300 144020 189570 TRUE FALSE 183896.8781 110807.2864 149235.6605 129749.8831 88718.8291 125146.0977 128499.7679 113222.4438 167159.2506 1.100129831 0.662884561 0.892775362 0.776205222 0.530744358 0.748663907 0.768726633 0.677332803 1 17.35086367 4.747417118 24.53954878 0.748962792 1.100130066 0.417717901 0.126927013 874.7544393 2423696.377 0.029712231 0.345663954 55900.68351 -4.747417118 0.351167274 DS(ph)REHEEPTTSEMAEETYSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSREHEEPTTSEMAEETYSPK 21 1 P24593;C9JXX4 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 1 DS(0.98)REHEEPT(0.008)T(0.008)S(0.003)EMAEETYSPK 68.411 0.012646 0 51540 37908 29034 22416 38138 34821 43364 51328 41191 TRUE FALSE 44728.85841 37658.97985 43074.93951 27505.89541 37379.12842 36160.5864 39158.56595 40351.90663 36321.4469 1.231472373 1.036824881 1.185936772 0.75729074 1.029120027 0.995571198 1.078111399 1.110966387 1 15.14853405 5.124559617 1.342089947 1.021905422 1.529789726 0.266861313 0.109652021 4.912487277 3.929806052 0.030989323 4.359812633 133216.9902 -5.124559617 0.507884304 DS(ph)RPLSPILHIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DSRPLSPILHIVK 13 1 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 1 DS(0.589)RPLS(0.411)PILHIVK;DS(0.5)RPLS(0.5)PILHIVK;DS(0.605)RPLS(0.395)PILHIVK 127.88 0.00010404 846776000 1410913 1028659 801246 1049308 1072694 1032323 1291659 1518347 1934966 TRUE FALSE 1224457.272 1021901.671 1188731.246 1287569.419 1051349.488 1072037.134 1166394.109 1193660.31 1706216.524 0.717644716 0.598928481 0.696705974 0.754634245 0.616187614 0.628312479 0.683614355 0.69959486 1 20.70236931 1.217423985 3.50823612 1.05770245 0.669717228 0.824601937 0.047328697 0.133735412 2.337751732 0.143721097 0.01200813 16.49772216 -1.217423985 -0.387985223 DS(ph)SQEYTDSTGIDLHEFLVNTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DSSQEYTDSTGIDLHEFLVNTLK 23 0 A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5;H0YIX9;Q15032-2;Q15032-4;Q15032;Q15032-3;H7C2F9 A0A0U1RRA6;Q15032-2 R3HDM2;R3HDM1 R3H domain-containing protein 2;R3H domain-containing protein 1 1 DS(0.486)S(0.486)QEYT(0.028)DSTGIDLHEFLVNTLK;DS(0.277)S(0.277)QEY(0.21)T(0.23)DS(0.003)T(0.003)GIDLHEFLVNTLK;DS(0.5)S(0.5)QEYT(0.001)DSTGIDLHEFLVNTLK;DS(0.406)S(0.406)QEYT(0.049)DS(0.07)T(0.07)GIDLHEFLVNTLK 166.22 7.87E-12 768342000 416697 292348 198250 258664 280620 189309 450526 427132 355387 TRUE FALSE 361629.4357 290427.5467 294124.3631 317397.6146 275036.211 196591.8397 406834.0579 335793.1457 313373.5537 1.153988368 0.926777462 0.938574298 1.012841099 0.877662482 0.627340238 1.298239922 1.071542706 1 18.25752391 2.21345655 24.99998534 1.119776896 0.925790957 0.286578035 0.14896972 303.1567986 301897.5673 0.060595962 0.040872019 163.4769587 -2.21345655 -0.193985939 DSAATTDEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSAATTDEER 10 0 Q16531;F5GY55;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 ; 162.88 4.33E-05 115250000 216520 189776 122176 157066 173078 217960 198254 201905 207030 FALSE TRUE 187906.3334 188529.349 181260.7223 192730.2359 169634.0864 226345.0622 179027.3576 158729.187 182555.1492 1.029312699 1.032725452 0.992909392 1.055737056 0.929221044 1.239872242 0.980675474 0.869486222 1 17.47797284 2.002500526 24.99992142 0.925318718 1.044603089 0.238773383 0.083870732 91.06981197 910497.3488 0.032769183 0.021945013 100.5774282 -2.002500526 0.119284371 DSAIPVES(ph)DTDDEGAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSAIPVESDTDDEGAPR 17 0 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 1 DSAIPVES(0.997)DT(0.003)DDEGAPR 290.5 5.95E-46 479460000 264860 228230 137910 169120 209960 179760 219680 254320 222900 TRUE FALSE 229858.0799 226730.7421 204603.7373 207521.2808 205782.2068 186675.4835 198375.4674 199935.6471 196549.0159 1.169469503 1.153558267 1.040980726 1.055824573 1.046976531 0.949765546 1.0092926 1.017230466 1 17.58452962 4.351173468 0.853646335 1.001870281 1.228137193 0.829528803 0.027660764 0.552502004 0.46855484 0.010665297 0.106106855 22447.78365 -4.351173468 0.226266912 DSAIPVESDT(ph)DDEGAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSAIPVESDTDDEGAPR 17 0 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 1 DSAIPVES(0.106)DT(0.894)DDEGAPR 390.77 7.19E-121 396100000 250330 248090 157200 191940 238610 222190 247740 304770 269610 TRUE FALSE 217248.2562 246460.2805 233222.4458 235522.9106 233862.1278 230737.7931 223714.2129 239597.3072 237737.0129 0.913817556 1.03669293 0.981010247 0.990686758 0.98370096 0.970558981 0.941015495 1.007825009 1 17.85900701 1.60921049 25 1.003915526 0.977282653 0.125653758 0.03194334 0.277655383 5000.327939 0.017388028 0.007617613 40.66403687 -1.60921049 -0.026632873 DSALAEAPEGLS(ph)PAPPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DSALAEAPEGLSPAPPAR 18 0 C9JPC9;Q9H9J4-2;Q9H9J4 C9JPC9 USP42 Ubiquitin carboxyl-terminal hydrolase 42 1 DSALAEAPEGLS(1)PAPPAR;DSALAEAPEGLS(1)PAPPAR;DSALAEAPEGLS(1)PAPPAR;DSALAEAPEGLS(1)PAPPAR 343.63 7.62E-76 1318490000 1384540 1193240 722790 885380 1159440 1194340 1124390 1332750 1202480 TRUE FALSE 1201569.531 1185401.528 1072333.662 1086419.061 1136369.412 1240287.033 1015346.831 1047751.784 1060324.184 1.133209587 1.117961417 1.011326232 1.024610282 1.071718847 1.169724365 0.957581508 0.988142871 1 20.01607399 -1.999999999 0.176381306 0.440361356 1.138342566 0.291122158 0.058393012 158.8141476 2.214836524 28.63977839 0.597544514 0.01 1.999999999 0.69798121 QLSESESSLEMDDERYFNEMSAQGLRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 80.664 0.0031831 278880000 35684 36917 23234 19032 29755 32786 25818 30931 11890 FALSE TRUE 30968.26899 36674.4898 34470.04011 23353.50649 29162.93371 34047.29864 23314.17433 24316.64636 10484.37775 2.953753646 3.498013014 3.287752593 2.227457561 2.781560759 3.247431508 2.223706061 2.319321847 1 13.35595362 1.17087806 0.993396336 6.52E-19 3.000682041 0.709844599 0.392303953 1.288236637 0.944438517 4.350520625 0.138913887 14.82101886 -1.17087806 3.000682041 DSAYPEELSR ddPTM_MDA-MB-175_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 91.584 0.02338 135950000 82240 91027 58982 68029 78852 81646 70462 94432 86300 FALSE TRUE 71371.77563 90429.03764 87505.89248 83476.02421 77282.99947 84786.97445 63628.60609 74238.45167 76097.71231 0.937896468 1.188327939 1.14991489 1.096958393 1.015575858 1.114185589 0.836143481 0.975567457 1 16.21556546 2.259485659 24.99691205 0.941010238 1.089061598 0.423643146 0.08039667 211.6955604 252889.5133 0.029200995 0.022594748 181.7547037 -2.259485659 0.148051361 DSAYQSITHYRPVS(ph)ASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSAYQSITHYRPVSASR 17 1 P50402;Q5HY57 P50402 EMD Emerin 1 DSAYQSITHYRPVS(0.975)AS(0.025)R;DSAYQSITHYRPVS(0.98)AS(0.02)R 177.38 6.23E-10 594170000 387920 420060 191466 321383 518430 478750 360891 541690 489518 TRUE FALSE 336655.3891 417300.5982 284059.598 394357.9222 508114.2573 497167.8223 325891.8464 425853.8089 431647.7397 0.779930851 0.966761921 0.658081977 0.913610534 1.177150279 1.151790631 0.75499491 0.986577178 1 18.71949491 3.479336926 24.99859784 1.002410266 0.812731545 0.340044475 0.134592864 109.9282615 1240289.415 0.039501418 0.051862876 3015.344427 -3.479336926 -0.189678721 DSDAGSST(ph)PTTSTR ddPTM_MDA-MB-175_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(0.099)S(0.222)T(0.68)PTTSTR;DSDAGS(0.068)S(0.143)T(0.789)PTTSTR 167.56 4.06E-05 336150000 1163580 812130 493750 556300 703350 691580 783780 847900 849410 TRUE FALSE 1009809.955 806795.0646 732529.1515 682616.4175 689354.7111 718185.5301 707769.1362 666583.1834 748993.7175 1.348222196 1.077172005 0.978017752 0.911378028 0.92037449 0.958867229 0.944960044 0.889971662 1 19.51459409 4.801280088 1.490320659 0.93308046 1.557479007 0.947742342 0.030348741 0.259501465 0.47720907 0.008254991 0.249827764 63281.98415 -4.801280088 0.624398547 DSDGVHRVS(ph)AR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSDGVHRVSAR 11 1 A0A5F9ZHH3;Q8NEP4 A0A5F9ZHH3 C17orf47 Uncharacterized protein C17orf47 1 DSDGVHRVS(1)AR;DS(0.002)DGVHRVS(0.998)AR 91.069 0.028981 76479000 13500.3 10398.1 10191.6 12823.9 9914.3 12288.7 12474.2 18082 14572.4 TRUE FALSE 11716.20115 10329.7942 15120.29185 15735.7625 9717.024827 12761.45424 11264.454 14215.30501 12849.66747 0.911790221 0.803895838 1.176706859 1.224604647 0.756208271 0.993134979 0.876633892 1.106278045 1 13.64944341 4.266873359 24.99751607 1.016260592 0.857842955 0.191053133 0.137838925 372.078607 328504.6125 0.034656436 0.091655693 18487.29449 -4.266873359 -0.158417637 DSDKTDTDWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DSDKTDTDWR 10 1 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;; 102.4 0.0026923 2833640000 10039400 8010900 6307900 7370500 7781800 6446400 9929600 11553200 10429800 FALSE TRUE 8712667.853 7958275.87 9358421.539 9044084.676 7626957.405 6694397.179 8966628.92 9082638.087 9196800.926 0.947358535 0.865330884 1.017573569 0.983394634 0.82930548 0.727904978 0.974972601 0.987586679 1 23.13270068 2.029440917 24.99997518 0.989418855 0.896295268 0.226830609 0.080842243 322.0656726 273483.1882 0.03543431 0.023889427 107.0140788 -2.029440917 -0.093123586 DSDLSHVQNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSDLSHVQNK 10 0 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ; 127.76 0.00034743 357990000 1437900 1004190 564710 789580 940230 810440 1151750 1317350 1106030 FALSE TRUE 1247877.872 997593.4098 837805.6448 968866.207 921521.2625 841618.1512 1040053.462 1035644.954 975276.3934 1.279512024 1.022882761 0.859044319 0.993427313 0.944882157 0.862953473 1.066419191 1.061898925 1 19.89545161 4.717705012 4.085511847 0.977381882 1.299742583 0.653006753 0.070168524 0.142127696 5.076938193 0.018833443 0.129814571 52204.14803 -4.717705012 0.322360701 DSDPVMAGIGEEIAHFQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSDPVMAGIGEEIAHFQK 18 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 0 ; 192.24 1.84E-14 110239000 219694 181964 124012 143889 169249 146069 200384 243523 206136 FALSE TRUE 190660.8813 180768.6665 183984.618 176561.1967 165881.276 151688.3689 180950.7905 191447.5015 181766.8369 1.048931062 0.994508512 1.012201242 0.971360891 0.912604735 0.834521696 0.995510477 1.053258696 1 17.47172948 DSEGTWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSEGTWR 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 132.09 0.0079152 1589360000 1807720 1733170 1100580 1318010 1457640 1686320 1635960 1790310 1728190 FALSE TRUE 1568825.222 1721784.692 1632824.169 1617284.315 1428635.816 1751193.822 1477304.851 1407466.139 1523885.347 1.029490325 1.129864983 1.071487545 1.061290023 0.937495605 1.149163764 0.969433071 0.923603696 1 20.53932293 2.064598012 11.70712124 0.953398385 1.060711735 0.377633383 0.059571706 0.579293019 103.0108602 0.023446613 0.015804575 116.0374061 -2.064598012 0.10731335 DSEGYIYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSEGYIYAR 9 0 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-3;Q03154-4;C9JMV9;A0A1B0GV31;C9JYZ0;A0A1B0GVA5;F8WC59 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 151.04 0.00019499 267880000 441650 371180 281180 354830 395410 379460 345220 433750 580950 FALSE TRUE 383284.8335 368741.6941 417159.5885 435399.5747 387542.1146 394058.0717 311740.6175 340995.9379 512270.7528 0.748207528 0.719817971 0.81433419 0.849940334 0.756518135 0.769237888 0.608546586 0.665655683 1 18.966547 2.451072025 24.99459762 0.726343149 0.778815233 0 0.107332358 788.8455324 756902.8064 0.040213862 0.031150524 282.5348504 -2.451072025 0.052472084 DSEHIDDETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSEHIDDETR 10 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 97.734 0.0058569 143750000 232640 209080 103930 160800 197170 201890 192590 226010 278970 FALSE TRUE 201896.0346 207706.5397 154190.8956 197312.0977 193246.7028 209656.8389 173912.6514 177679.5203 245990.4844 0.820747335 0.844368189 0.626816505 0.802112725 0.78558609 0.852296541 0.706989345 0.722302412 1 17.90824298 1.231833541 24.9684736 1.000000403 0.766836719 0.521614183 0.069111415 188.5902095 699912.5378 0.160060139 0.016860358 17.05428595 -1.231833541 -0.233163684 DSEHIDDETRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DSEHIDDETRR 11 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 171.92 9.06E-06 797960000 510414 493641 240498 361716 483174 544681 478133 537058 483914 FALSE TRUE 442961.4967 490398.2398 356803.6372 443849.1463 473559.7827 565635.2305 431763.7353 422212.3261 426706.2382 1.038094729 1.149264285 0.836180972 1.040174965 1.109802811 1.325584629 1.011852409 0.98946837 1 18.70288368 3.472870782 23.81542395 1.080778962 1.008020043 0.083418197 0.120539999 205.4537229 1151145.049 0.036866993 0.047841068 2970.781984 -3.472870782 -0.072758918 DSELASQNKPLWQCYLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSELASQNKPLWQCYLGR 18 1 Q9NTI5-2;Q9NTI5;Q9NTI5-3 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 0 147.56 6.90E-08 355000000 153840 123390 77339 91897 122550 102610 150130 147840 139370 FALSE TRUE 133509.6542 122579.443 114740.3991 112763.6184 120111.4948 106557.4731 135570.4157 116225.5665 122893.8374 1.086382011 0.99744174 0.93365462 0.917569349 0.977359787 0.867069296 1.103150643 0.945739583 1 16.90705305 4.673996937 3.210711627 0.964819317 1.095807753 0.283810041 0.061259883 0.369739709 6.176487799 0.014638588 0.109630449 47205.97116 -4.673996937 0.130988435 DSENLAS(ph)PSEYPENGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 DSENLASPSEYPENGER 17 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 DSENLAS(0.995)PS(0.005)EYPENGER;DSENLAS(1)PSEYPENGER;DSENLAS(0.999)PS(0.001)EYPENGER;DSENLAS(0.994)PS(0.006)EYPENGER;DSENLAS(0.963)PS(0.037)EYPENGER;DSENLAS(1)PSEYPENGER;DSENLAS(0.993)PS(0.007)EYPENGER 505.22 1.53E-258 8056673000 3106218 3028309 2198604 2662028 3245526 3195815 3470396 3927582 3709636 TRUE FALSE 2695723.421 3008415.839 3261856.248 3266482.144 3180946.382 3318760.071 3133837.53 3087699.154 3271087.058 0.82410629 0.919699105 0.99717806 0.998592237 0.972443205 1.014574058 0.958041616 0.943936709 1 21.64133873 4.605828621 2.594764423 0.979729237 0.812783324 0.845067194 0.021932575 0.14945196 1.551176542 0.006139439 0.04720052 40348.61397 -4.605828621 -0.166945914 DSES(ph)PSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSESPSQK 8 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 DSES(1)PSQK 226.39 3.28E-06 269490000 287380 247000 222720 209100 302020 237940 329710 411780 388910 TRUE FALSE 249402.0049 245377.4407 330428.137 256579.3509 296010.3929 247093.7058 297734.7749 323724.0515 342933.5028 0.727260541 0.715524843 0.963534138 0.748189806 0.863171403 0.720529501 0.868199731 0.943984909 1 18.38756933 1.772904148 2.283368547 0.989071495 0.795644213 0.485001406 0.077106983 0.243551281 2.482520879 0.065672837 0.021156213 59.27944758 -1.772904148 -0.193427282 DSES(ph)PSQKK ddPTM_MDA-MB-175_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(0.054)ES(0.804)PS(0.141)QKK 55.261 0.079411 163190000 584960 392290 332030 358680 264040 220270 593860 660270 456090 TRUE FALSE 507656.0539 389713.0212 492600.8186 440123.7761 258786.1206 228743.9294 536267.5486 519076.3987 402171.5598 1.262287304 0.969021831 1.224852446 1.094368225 0.643471957 0.568772017 1.333429815 1.290684003 1 18.61745154 0.935454569 19.45117855 9.15E-05 1.055529464 0.00268427 0.262395283 386.4736044 373347.2882 38174.42185 0.067408341 8.618954114 -0.935454569 1.055437927 DSEWIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSEWIR 6 0 E9PLZ6;E9PRJ3;K4DIB7;K4DIA7;E9PMR4;P48509 E9PLZ6 CD151 Tetraspanin;CD151 antigen 0 133.95 0.061791 0 560600 406750 306430 522090 456990 609690 415230 638490 506000 FALSE TRUE 486515.2896 404078.0325 454620.5729 640638.5141 447896.7931 633145.1688 374961.0585 501953.8822 446181.2564 1.090398314 0.905636502 1.018914547 1.435825698 1.003844932 1.419031301 0.840378329 1.12499993 1 18.76727038 3.976871776 24.96320541 1.13165093 0.989081832 0.101129041 0.185857838 1587.912453 1713902.051 0.046725027 0.081655419 9481.384864 -3.976871776 -0.142569098 DSFDDRGPSLNPVLDYDHGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DSFDDRGPSLNPVLDYDHGSR 21 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;; 208.39 1.89E-22 7008770000 8769160 8368250 2294455 4849900 8856830 8532600 8307790 9838630 6338190 FALSE TRUE 7610293.288 8313278.415 3404061.112 5951143.921 8680596.411 8860854.643 7502101.804 7734715.539 5588896.399 1.361680866 1.487463324 0.609075723 1.064815573 1.553186138 1.585439058 1.342322575 1.383943267 1 22.414132 3.255023779 24.99572948 1.382672727 1.118974621 0.160640649 0.274039256 446.120262 677332.6841 0.081700095 0.105161989 1798.969413 -3.255023779 -0.263698106 DSFIENSSSNCTSGSSKPNS(ph)PSIS(ph)PSILSNTEHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSFIENSSSNCTSGSSKPNSPSISPSILSNTEHK 34 1 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 2 DSFIENSSSNCTSGSSKPNS(0.999)PS(0.007)IS(0.971)PS(0.023)ILSNTEHK 147.41 2.51E-10 156400000 192400 133920 96927 150500 149770 97821 230580 235260 182030 TRUE FALSE 166973.8525 133040.2707 143801.2214 184673.3252 146789.87 101584.2372 208218.3871 184951.4798 160510.6208 1.040266692 0.828856496 0.895898481 1.150536484 0.914518113 0.632881716 1.297224982 1.152269419 1 17.29230924 2.214471997 24.99804118 1.156480716 0.9172127 0.359939305 0.150188025 252.8724189 262417.155 0.061342283 0.041380391 163.8596404 -2.214471997 -0.239268016 DSFLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSFLKR 6 1 P46778;M0R181;Q9H553-2;Q9H553 P46778;Q9H553 RPL21;ALG2 "60S ribosomal protein L21;Alpha-1,3/1,6-mannosyltransferase ALG2" 0 ; 105.27 0.053107 2426700000 3556930 3167540 1694530 2175590 3041660 2695840 3507600 3723890 1828570 FALSE TRUE 3086872.688 3146732.221 2514010.376 2669590.961 2981136.917 2799550.709 3167433.492 2927565.103 1612398.538 1.914460114 1.951584641 1.559174309 1.655664464 1.848883416 1.736264728 1.964423446 1.815658495 1 20.62077695 1.23810056 24.99823921 0.99999909 1.805001155 0.795476997 0.128400277 5.103857061 277025.8249 0.185660063 0.032427154 17.30216942 -1.23810056 0.805002065 DSFTYEDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSFTYEDYR 9 0 Q86TU7;Q6NXR6;Q86TU7-3;Q86TU7-2 Q86TU7 SETD3 Histone-lysine N-methyltransferase setd3 0 ; 117.04 0.0028307 735940000 900010 818220 641310 811210 830000 871370 806020 963310 1364970 FALSE TRUE 781071.3982 812845.0589 951449.6611 995407.6291 813484.6239 904892.1678 727852.3045 757313.653 1203604.802 0.648943405 0.675342154 0.790500054 0.827021982 0.675873528 0.751818343 0.604726986 0.629204579 1 20.19893034 1.230290078 24.99922025 1.000000556 0.699429576 0.63981815 0.070633908 224.8968546 679737.6988 0.209683119 0.018943223 16.99378336 -1.230290078 -0.300570979 DSFWAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSFWAK 6 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ; 116.35 0.055015 1632190000 1322060 1106540 907370 946250 1112790 954910 1158350 1346800 1138760 FALSE TRUE 1147346.421 1099271.066 1346177.167 1161110.525 1090647.656 991646.0056 1046013.395 1058797.301 1004137.09 1.142619302 1.09474202 1.340630856 1.156326697 1.086154139 0.987560379 1.041703773 1.054435008 1 19.93752482 3.157193689 3.02454098 1.028916028 1.190769651 0.580857201 0.06518107 0.186138444 3.434471463 0.020838626 0.024767544 1436.129783 -3.157193689 0.161853623 DSGACFSASEPDAVHVVLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DSGACFSASEPDAVHVVLDR 20 0 H0YER3;Q8NB37-3;Q8NB37 H0YER3 PDDC1 Parkinson disease 7 domain-containing protein 1 0 ;; 195.48 1.85E-21 399909000 316750 301178 178174 204915 291575 272859 273118 322329 307472 FALSE TRUE 274890.685 299199.5419 264339.5424 251444.0827 285773.228 283356.0623 246631.0584 253401.4517 271123.0104 1.01389655 1.103556431 0.974980109 0.927416977 1.054035316 1.045119932 0.909664798 0.934636464 1 18.04858804 4.922217532 0.238631447 0.929358299 1.160936448 0.159530544 0.056389671 32.13729467 2.126592001 0.356890062 2.414163003 83602.16645 -4.922217532 0.231578148 DSGPPTKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSGPPTKK 8 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 82.287 0.033132 537500000 728010 496760 368020 468110 311000 396620 684010 742910 590800 FALSE TRUE 631801.634 493496.7509 545995.703 574401.5301 304811.7085 411878.228 617674.8155 584044.4778 520956.297 1.212772813 0.947290116 1.048064312 1.102590627 0.585100344 0.79061954 1.185655724 1.121100716 1 18.99080282 0.882196156 19.11158855 0.817266358 1.001014051 0 0.190328073 693072.0832 9826150.503 5085929.773 0.047530554 7.624232931 -0.882196156 0.183747693 DSGREDEPGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSGREDEPGSPR 12 1 Q2TAM9 Q2TAM9 TUSC1 Tumor suppressor candidate gene 1 protein 1 DSGREDEPGS(1)PR;DSGREDEPGS(1)PR 139.34 3.56E-05 315150000 741430 739610 467760 533170 690960 653950 707520 795760 712240 TRUE FALSE 643448.147 734751.4532 693970.3006 654234.3975 677211.2478 679107.8797 638904.8193 625592.9166 628039.7986 1.024534032 1.169912249 1.104978223 1.041708502 1.078293524 1.081313447 1.017299892 0.996103938 1 19.26049646 2.170169399 0.953630261 0.982197648 1.094596857 0.465074704 0.039247859 0.594521233 0.986621147 0.052936385 0.016595117 147.9685434 -2.170169399 0.112399209 GNVVPS(ph)PLPTRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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(0.999)PLPT(0.001)RR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR 140.49 3.66E-05 36768280000 9083610 9020980 5860070 5775460 8928110 9756430 8537020 9332280 2858140 TRUE FALSE 7883187.924 8961720.588 8694019.453 7086866.465 8750458.079 10131766.18 7709101.114 7336644.546 2520253.945 3.127933968 3.555879996 3.449660091 2.81196523 3.472054114 4.020137016 3.058858862 2.911073529 1 21.26513768 1.171229417 2.074124699 6.92E-15 3.377047753 0.83763913 0.324008739 0.346155025 1.26608373 2.386218038 0.088036071 14.83301434 -1.171229417 3.377047753 DSGRGDSVSDSGSDALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSGRGDSVSDSGSDALR 17 1 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 0 ; 135.38 1.26E-05 449390000 397110 449120 223800 224840 360910 370210 327670 415300 177063 FALSE TRUE 344630.9074 446169.7011 332030.4286 275893.3585 353728.5971 384452.2183 295892.6138 326491.3269 156130.8139 2.207321533 2.85766589 2.126616908 1.767065396 2.265591195 2.462372473 1.895158339 2.091139595 1 17.25239577 1.038794572 1.735062232 2.16E-17 2.247132511 0.622144411 0.297081725 1.192390276 2.146568378 5.334517099 0.08422308 10.9343903 -1.038794572 2.247132511 DSGS(ph)ISLQETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSGSISLQETR 11 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 DSGS(0.855)IS(0.145)LQETR;DSGS(0.867)IS(0.133)LQETR 195.16 2.07E-07 605040000 490930 448320 374880 469180 513620 562880 568480 582610 831810 TRUE FALSE 426052.3566 445374.9564 556173.2219 575714.49 503399.9669 584534.3578 513348.8971 458023.3854 733474.3694 0.580868773 0.607212706 0.758272198 0.784914257 0.686322505 0.796939037 0.69988662 0.624457247 1 19.48438703 4.272600695 5.714766032 0.747716572 0.590116439 0.327142118 0.099475633 0.219450763 18.87207125 0.024346684 0.063808361 18732.71369 -4.272600695 -0.157600133 DSGSDGHSVSSRDS(ph)AAPS(ph)PIPGADNLSADPVVSPPTSIPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSGSDGHSVSSRDSAAPSPIPGADNLSADPVVSPPTSIPFK 41 1 Q5T1M5;Q5T1M5-2;Q5T1M5-3 Q5T1M5 FKBP15 FK506-binding protein 15 2 DS(0.012)GS(0.013)DGHS(0.087)VS(0.096)S(0.101)RDS(0.713)AAPS(0.962)PIPGADNLS(0.017)ADPVVSPPTSIPFK 85.595 0.0004386 35667000 14969 11964 7379.4 9706.6 13532 13523 14289 16907 17099 TRUE FALSE 12990.80872 11885.4077 10948.10252 11910.63189 13262.73967 14043.23856 12903.25498 13291.56962 15077.5757 0.861597977 0.788283736 0.726118226 0.789956696 0.879633433 0.931398976 0.855791092 0.881545541 1 13.88011686 3.178303995 3.951413904 0.905658602 0.785799698 0.588303353 0.04945554 0.163949327 5.150882198 0.015509622 0.018313935 1507.662022 -3.178303995 -0.119858904 DSGSDLSHRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSGSDLSHRPK 11 1 O95251-4;O95251;E7EUP3;D6RFZ5 O95251-4 KAT7 Histone acetyltransferase KAT7;Histone acetyltransferase 0 ; 136.96 5.31E-05 144364000 286210 216021 113677 184765 208029 197608 234570 287220 258640 FALSE TRUE 248386.6233 214601.9438 168651.5774 226718.7172 203889.6299 205210.1076 211821.4375 225800.2381 228063.8738 1.089109902 0.940972984 0.739492733 0.994101843 0.894002309 0.899792256 0.928781196 0.990074554 1 17.79907841 1.730707603 3.560626299 0.998158216 0.919595056 0.093756597 0.087076636 0.450408361 12.44845366 0.060270907 0.023142845 53.7907504 -1.730707603 -0.078563161 EFTGS(ph)PPSSATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EFTGSPPSSATK 12 0 Q92609;Q92609-2;C9J3F6 Q92609 TBC1D5 TBC1 domain family member 5 1 EFTGS(0.958)PPS(0.039)S(0.003)ATK;EFTGS(0.999)PPS(0.001)SATK;EFTGS(0.676)PPS(0.318)S(0.006)ATK;EFTGS(0.926)PPS(0.073)S(0.001)ATK 194.83 1.07E-06 1478010000 2871260 2332980 2218920 2889960 3070030 2538870 3408410 4263880 6767960 TRUE FALSE 2491815.716 2317654.501 3291997.134 3546169.588 3008942.409 2636541.972 3077862.923 3352082.444 5967859.479 0.417539274 0.388356078 0.551621087 0.594211308 0.50419123 0.441790223 0.515739845 0.561689238 1 22.50878214 1.172603685 2.552319467 1.187490564 0.489794599 0.870858209 0.061452346 0.242374332 1.499425209 0.400548095 0.017458169 14.88002582 -1.172603685 -0.697695966 DSGSDTASAIIPSTTPSVDS(ph)DDESVVKDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSGSDTASAIIPSTTPSVDSDDESVVKDK 29 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 DSGSDTASAIIPSTT(0.001)PS(0.016)VDS(0.978)DDES(0.006)VVKDK;DSGSDTASAIIPSTTPS(0.002)VDS(0.993)DDES(0.005)VVKDK 248.06 4.03E-46 550680000 699620 465860 496840 569820 489230 374580 690620 865040 717430 TRUE FALSE 607163.4444 462799.735 737113.4858 699206.3402 479495.2802 388990.335 623643.7787 680057.9277 632616.2427 0.959765816 0.731564737 1.165182675 1.105261441 0.757956005 0.614891476 0.985816893 1.074992834 1 19.27097107 2.010153581 24.99927681 1.039118662 0.890189167 0.127318133 0.165989219 428.2264923 1054338.38 0.072268356 0.048666417 102.3654928 -2.010153581 -0.148929495 DSGSSSVFAES(ph)PGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSGSSSVFAESPGGK 15 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 DSGSSSVFAES(1)PGGK 266.45 2.73E-25 340410000 416560 293080 190450 232940 298900 294640 325380 344770 302120 TRUE FALSE 361510.5406 291154.7382 282552.257 285832.5873 292952.4748 305974.9915 293824.6977 271043.6185 266403.7178 1.357002611 1.092907939 1.060616794 1.072930174 1.099656106 1.148538744 1.10293017 1.017416802 1 18.02325469 4.738657899 4.36425966 1.07247494 1.377587133 0.818019051 0.042006935 0.09325064 4.30527656 0.011495409 0.088350908 54784.52486 -4.738657899 0.305112193 DSGYIDCWDSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DSGYIDCWDSER 12 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3;D6RJ93;D6R8Y0;Q9UPQ0-7;Q6NVB9 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 0 ;;; 203.02 3.02E-07 750730000 878020 901930 555374 691425 847100 896550 804820 872160 1004140 FALSE TRUE 761987.4324 896005.1624 823954.724 848423.614 830244.3673 931040.8586 726768.6803 685655.3712 885431.7131 0.860582946 1.011941575 0.930568345 0.958203328 0.937671822 1.05151063 0.820807149 0.774374083 1 19.75602152 2.214104032 24.99963889 0.844323494 0.958628256 0.236889169 0.076004519 254.5464503 260196.6062 0.029675944 0.020017632 163.7208654 -2.214104032 0.114304762 DSHGVAQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DSHGVAQVR 9 0 P62277;J3KMX5;E9PS50 P62277 RPS13 40S ribosomal protein S13 0 ;;;;; 192.6 3.45E-05 9510780000 2608140 2656970 1744490 2037020 2343670 2468810 2445060 2790760 2661310 FALSE TRUE 2263467.691 2639516.189 2588131.199 2499556.525 2297035.552 2563786.718 2207938.458 2193977.692 2346692.964 0.964535082 1.124781226 1.102884459 1.065139992 0.978839408 1.092510506 0.940872322 0.934923199 1 21.16219766 2.230664904 24.99585072 0.952927537 1.057168961 0.419949859 0.053099228 155.0343022 490794.894 0.021065453 0.014495727 170.084565 -2.230664904 0.104241424 DSHS(ph)PDLQLPTPEVIPSSGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSHSPDLQLPTPEVIPSSGSK 21 0 H3BQK9;H3BPE1;H0Y4F5;H0Y6T5 H3BQK9 MACF1 1 DS(0.208)HS(0.792)PDLQLPTPEVIPSSGSK;DS(0.173)HS(0.827)PDLQLPTPEVIPSSGSK 170.27 7.08E-18 237840000 646110 468970 392374 497110 484920 476540 553260 613490 749380 TRUE FALSE 560724.9265 465889.3052 582127.3788 609986.4234 475271.0407 494872.8022 499604.9304 482299.9377 660789.1501 0.848568604 0.705049871 0.880957835 0.923118098 0.719247646 0.748911816 0.756073144 0.729884771 1 19.33383047 1.229301558 24.99571464 1.000000419 0.785676796 0.450485021 0.07316519 362.7577244 979226.7678 0.225356105 0.018403231 16.95514695 -1.229301558 -0.214323622 DSIANATVLLDYHLNYLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSIANATVLLDYHLNYLK 18 0 Q06787;Q06787-2;R9WNI0;G3V0J0;Q06787-9;Q06787-7;Q06787-6;Q06787-5;Q06787-8;Q06787-3;Q06787-4;A8MQB8;Q06787-10;Q06787-11;A0A087WXI3 Q06787 FMR1 Fragile X mental retardation protein 1 0 ; 144.68 9.65E-08 228700000 411060 356870 258520 304020 377540 344190 395090 474940 369560 FALSE TRUE 356737.3795 354525.6975 383541.1367 373052.3877 370027.6926 357431.212 356774.2326 373377.777 325871.0378 1.0947195 1.087932514 1.176972152 1.144785343 1.135503465 1.096848663 1.094832591 1.145783864 1 18.31394161 1.232039887 24.9998584 0.999999794 1.122971911 0.636641047 0.029000928 151.520222 580859.8441 0.068134149 0.007330117 17.06239089 -1.232039887 0.122972117 DSIKLDDDSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSIKLDDDSER 11 1 Q86VP6;Q86VP6-2;F5H6I6 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 193.28 9.31E-07 1204630000 2548200 1872390 1248850 1209370 1833700 1513150 2423000 2554400 934870 FALSE TRUE 2211448.914 1860090.147 1852798.037 1483975.943 1797212.958 1571361.86 2188017.833 2008161.438 824350.7336 2.68265536 2.256430511 2.247584628 1.800175438 2.180155708 1.906181187 2.65423168 2.436052224 1 19.65289876 4.807145405 1.568254554 2.090113845 2.970244082 0.173500815 0.443518019 2.598810639 5.336316557 0.120940447 3.686708937 64142.42942 -4.807145405 0.880130237 DSIPVTELSASGPFESHDLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSIPVTELSASGPFESHDLLR 21 0 Q9Y244 Q9Y244 POMP Proteasome maturation protein 0 ; 200.39 7.50E-22 253110000 157593 167493 108853 155782 157857 149609 161653 199983 317450 FALSE TRUE 136766.6858 166392.7275 161494.6749 191154.6841 154715.9545 155364.555 145975.9169 157218.1917 279921.4226 0.488589564 0.594426557 0.576928601 0.682886941 0.55271209 0.555029171 0.521488908 0.56165116 1 18.09466238 1.238019697 24.99813512 1.000000491 0.568369737 0.879330319 0.050439588 4.299357776 198504.8329 0.07143099 0.0123962 17.29894816 -1.238019697 -0.431630755 DSIVAELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DSIVAELDR 9 0 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 0 ;;; 169.44 0.00013602 1640270000 2760230 2514040 1633870 1964320 2781830 2803450 2631690 2947930 2526050 FALSE TRUE 2395458.612 2497525.106 2424014.997 2410348.879 2726477.026 2911300.536 2376469.109 2317538.11 2227423.247 1.075439352 1.121262028 1.088259719 1.082124326 1.224049821 1.307026197 1.066914028 1.040457001 1 21.08694429 2.015083004 24.97175593 1.032288402 1.149338357 0.370530229 0.071534136 264.8905338 438556.9476 0.031747723 0.021395407 103.5340025 -2.015083004 0.117049955 DSIVAELDREMSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSIVAELDREMSR 13 1 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 0 95.264 0.0043555 22400000 27005 29907 5753.3 8445.2 22756 23764 31827 31643 4724.3 FALSE TRUE 23436.22083 29710.53895 8535.615124 10362.81174 22303.20012 24678.21646 28740.42244 24876.3907 4165.798636 5.62586502 7.132015141 2.048974487 2.487593051 5.35388339 5.924006082 6.899138665 5.97157781 1 12.02437739 DSIVQLCTARPERPMAFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSIVQLCTARPERPMAFLR 19 2 P10644;P10644-2;K7EPB2;K7EIE5;K7EID3;K7EJ40;K7EK41;K7EMU2;K7EMZ6;K7EQK3;X6RAV4 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 0 ; 119.8 2.96E-05 1139360000 299330 249170 155444 157160 253910 233210 239500 299070 156852 FALSE TRUE 259772.7821 247533.1859 230617.2383 192845.58 248857.6878 242181.7396 216273.3269 235116.2079 138309.1352 1.87820408 1.789709591 1.667404238 1.394308335 1.799285979 1.751017669 1.563695171 1.6999326 1 17.07753692 1.237815735 24.99865193 0.999999208 1.685245056 0.720451482 0.135576949 10.13457576 339889.5092 0.194348178 0.033325121 17.2908258 -1.237815735 0.685245848 DSKPSS(ph)TPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSKPSSTPR 9 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 DS(0.018)KPS(0.088)S(0.544)T(0.35)PR;DS(0.004)KPS(0.052)S(0.472)T(0.472)PR 130.16 0.00097044 3553670000 8347910 7412040 4763960 5977830 4254640 5536270 7543900 8865840 9925660 TRUE FALSE 7244712.543 7363349.821 7067826.99 7335187.667 4169980.988 5749253.889 6812293.739 6969949.11 8752259.782 0.827753371 0.841308417 0.807543099 0.838090716 0.476446208 0.656887939 0.778346839 0.796359944 1 23.06122413 -1.987186932 15.11034483 9.350772968 0.773525169 0 0.136037933 0 0 0 0.031547192 0.010299427 1.987186932 -8.577247799 DSKPSST(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSKPSSTPR 9 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 DS(0.036)KPS(0.085)S(0.085)T(0.793)PR 77.062 0.054424 2664900000 8024200 7133100 4365400 5745300 3912700 5339500 7246900 8145800 9150400 TRUE FALSE 6963781.639 7086242.196 6476522.041 7049858.176 3834844.925 5544914.02 6544096.753 6403884.061 8068650.136 0.863066501 0.87824383 0.802677267 0.873734523 0.475277136 0.687217059 0.811052238 0.793674772 1 22.9438959 DSKPSSTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 DSKPSSTPR 9 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 0 ;;;;;; 133.81 0.00024314 33248600000 10691230 7999350 5473690 6995510 6408140 6081400 8778810 10531960 10421950 FALSE TRUE 9278356.867 7946801.743 8120784.792 8583947.465 6280630.551 6315355.393 7927442.357 8279782.314 9189878.944 1.009627757 0.864734105 0.883666133 0.934065347 0.683429084 0.687207681 0.862627506 0.900967506 1 23.13161443 6.688356907 1.026143767 0.842820182 9.983681593 0.203660456 0.098633001 172.1113435 4.25941747 0.032756952 3509.336153 4879293.095 -6.688356907 9.140861411 DSLDPSFTHAMQLLTAEIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DSLDPSFTHAMQLLTAEIEK 20 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ;;; 221.85 7.56E-25 1029852000 1739285 1281025 867517 1220466 1240955 1043610 1598251 1769650 1947738 FALSE TRUE 1509434.08 1272609.862 1287051.123 1497591.459 1216262.423 1083758.352 1443252.864 1391224.119 1717478.633 0.878866294 0.74097566 0.749384067 0.871970941 0.708167427 0.63101708 0.840332355 0.810038677 1 20.71186072 0.994101606 1.599662604 1.236462435 0.76735819 0.463908918 0.075641683 1.885892033 2.612427635 1.695613077 0.021218154 9.865102588 -0.994101606 -0.469104245 DSLGDFIEHYAQLGPS(ph)SPEQLAAGAEEGGGPRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPRR 33 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 DSLGDFIEHY(0.002)AQLGPS(0.499)S(0.499)PEQLAAGAEEGGGPRR 46.449 0.056566 45471000 13081 11136 6509 4788 12372 9006.2 8434.2 14825 4062.8 TRUE FALSE 11352.31271 11062.84688 9656.774171 5875.18858 12125.82141 9352.674342 7616.252582 11654.78912 3582.500412 3.168823838 3.088023897 2.695540282 1.63996871 3.384736918 2.610655482 2.125960002 3.253255485 1 11.80675116 1.227736829 24.99622912 0.999996309 2.730895063 0.510957371 0.536601187 397.0056799 916775.0569 1.836974667 0.127306336 16.89416881 -1.227736829 1.730898753 DSLGDFIEHYAQLGPSS(ph)PEQLAAGAEEGGGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR 32 0 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 DSLGDFIEHYAQLGPS(0.213)S(0.787)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.159)S(0.841)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.115)S(0.885)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.122)S(0.878)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.181)S(0.819)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.18)S(0.82)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.222)S(0.778)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.25)S(0.75)PEQLAAGAEEGGGPR 400.28 1.80E-167 9168354000 1735225 1582449 1181352 1504653 1638019 1640847 1775516 2008890 2012867 TRUE FALSE 1505910.62 1572053.788 1752657.779 1846307.461 1605425.627 1703971.446 1603326.732 1579304.507 1774908.156 0.84844425 0.885709935 0.987463927 1.040227042 0.904511944 0.960033588 0.903329407 0.889795058 1 20.75931294 4.41944287 5.602229291 0.947687751 0.85677756 0.37612539 0.047517104 0.204828945 12.94573852 0.012762475 0.035954526 26268.95946 -4.41944287 -0.090910191 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR 32 0 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 0 ;; 229.48 1.79E-36 361288000 193705 150140 97797 118693 142263 135279 146839 167457 177670 FALSE TRUE 168106.3935 149153.7205 145091.9563 145644.0598 139432.2446 140483.2707 132598.5764 131647.6237 156666.055 1.073023722 0.952048741 0.926122486 0.929646564 0.889996526 0.896705229 0.846377196 0.840307262 1 17.2573331 8 0.649968324 0.884868992 17.51121527 0.588563189 0.0446327 150.1300826 0.978770508 0.019079026 3590.064946 100000000 -8 16.62634628 FQQAVDAVEEFLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FQQAVDAVEEFLRR 14 1 K7EMM8;Q49A26-4;Q49A26-2;Q49A26-3;Q49A26;K7EQB2;Q49A26-5 K7EMM8 GLYR1 Putative oxidoreductase GLYR1 0 95.981 0.0056964 62568000 38098 31946 17891 22962 32728 38713 29764 35033 10059 FALSE TRUE 33063.25277 31736.14462 26543.14744 28175.87305 32076.77683 40202.31416 26877.49186 27541.46558 8869.836479 3.727605672 3.57798531 2.992518239 3.176594418 3.616388747 4.532475233 3.030212781 3.105070273 1 13.11469179 1.173691091 2.12128734 5.83E-18 3.530698146 0.763087932 0.438103329 0.435902673 1.692734145 3.186819699 0.121341495 14.91732979 -1.173691091 3.530698146 DSLHEKFPDAGEDELLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSLHEKFPDAGEDELLK 17 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 121.26 3.65E-05 1444980000 1429600 1209830 576630 988380 1137540 838180 1599280 1969450 937360 FALSE TRUE 1240674.738 1201882.547 855490.1967 1212806.785 1114905.18 870425.327 1444182.072 1548298.444 826546.3686 1.501034648 1.454101781 1.035017791 1.467318509 1.348871911 1.05308711 1.747248704 1.873214259 1 19.65673623 2.222644284 24.97776581 1.618170745 1.312891101 0.112926346 0.276694025 372.0255966 583821.4386 0.110976817 0.075093645 166.972244 -2.222644284 -0.305279644 DSLHQPQYVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSLHQPQYVEK 11 0 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 121.68 0.0010223 0 444550 401180 171500 293250 455310 385620 444490 502880 489790 FALSE TRUE 385801.5912 398544.6222 254437.9736 359836.8945 446250.2218 400455.0509 401383.4282 395343.0254 431887.5842 0.893291693 0.922797128 0.589130095 0.833172584 1.0332555 0.927220568 0.929370148 0.915384095 1 18.72029632 3.400165758 7.480339149 0.950542359 0.797135025 0.389973705 0.094199242 0.247991745 20.4831167 0.027430532 0.035477095 2512.845333 -3.400165758 -0.153407334 DSLIIIDELGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSLIIIDELGR 11 0 A0A2R8YFH0;E9PHA6;A0A2R8Y6P0;A0A2R8YG02;P43246;P43246-2;A0A2R8Y713 A0A2R8YFH0 MSH2 DNA mismatch repair protein Msh2 0 129.7 0.00055713 12071000 39518 37705 24152 27842 33463 34060 34704 38882 41941 FALSE TRUE 34295.59617 37457.31337 35831.98798 34163.95164 32797.15177 35370.31024 31338.41142 30567.38688 36982.78276 0.927339524 1.012831122 0.968882959 0.923779908 0.886822173 0.956399373 0.847378404 0.826530201 1 15.17456616 3.567773932 2.425598399 0.891929349 0.975050034 0.224187625 0.053631471 0.368228407 4.248844832 0.016390723 0.026287372 3696.357196 -3.567773932 0.083120685 DSLITPHVS(ph)R ddPTM_MDA-MB-175_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 118.76 0.00050411 404850000 411930 397490 250490 291270 360090 372210 339200 392900 487560 TRUE FALSE 357492.4068 394878.862 371627.8018 357407.3053 352924.9135 386529.1596 306304.4362 308881.3926 429921.2122 0.831530049 0.918491228 0.864409085 0.831332103 0.820906025 0.899069756 0.712466442 0.718460462 1 18.71371277 3.148403219 1.078467529 0.800541344 0.874669882 0.00263417 0.086324664 1.240095076 3.207681181 0.04193439 0.054080113 1407.35357 -3.148403219 0.074128538 DSLLDGHFVLATLSDTDS(ph)HSQDLGSPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSLLDGHFVLATLSDTDSHSQDLGSPER 28 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 1 DSLLDGHFVLAT(0.002)LS(0.2)DT(0.182)DS(0.359)HS(0.219)QDLGS(0.037)PER 120.43 0.00010292 1053500000 86651 67844 39303 62075 70198 65684 72164 80770 78554 TRUE FALSE 75199.8508 67398.3283 58310.06226 76170.07751 68801.19714 68210.90598 65165.54639 63497.96405 69267.43561 1.085645082 0.973016075 0.841810611 1.099652049 0.993269009 0.984747095 0.940781852 0.916707303 1 16.07988964 2.041977637 0.013337742 3.13E-07 1.92441578 0.054147002 0.07302264 10008.39525 65.27356601 4847.831148 4570.803654 110.148259 -2.041977637 1.924415467 DSLLDGHFVLATLSDTDSHS(ph)QDLGS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSLLDGHFVLATLSDTDSHSQDLGSPER 28 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 2 DSLLDGHFVLAT(0.004)LS(0.004)DT(0.005)DS(0.048)HS(0.939)QDLGS(1)PER;DSLLDGHFVLAT(0.004)LS(0.001)DT(0.008)DS(0.482)HS(0.579)QDLGS(0.926)PER 125.73 1.76E-05 54824000 102141 82816 61778 77930 92670 95614 95471 113850 102576 TRUE FALSE 88642.80806 82271.97624 91654.04744 95625.19759 90826.04831 99292.33245 86212.23711 89504.06348 90449.58213 0.980024517 0.909589346 1.013316427 1.057220999 1.004162166 1.097764413 0.953152409 0.989546456 1 16.46482622 4.218000937 24.51442714 1.014579701 0.944806955 0.333041026 0.042086153 195.7724954 233430.8465 0.010865431 0.02266276 16519.65362 -4.218000937 -0.069772746 DSLLDGHFVLATLSDTDSHSQDLGS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 DSLLDGHFVLATLSDTDSHSQDLGSPER 28 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 1 DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER 338.18 2.16E-96 2266530000 1350073 1073852 609733 819479 1110218 1071199 1126262 1298994 1240532 TRUE FALSE 1171657.432 1066797.796 904601.9182 1005554.232 1088126.834 1112408.719 1017037.285 1021214.242 1093877.72 1.071104577 0.975244103 0.826968044 0.919256525 0.994742661 1.016940649 0.92975409 0.933572577 1 20.06102004 3.243796139 24.96821404 0.968526657 0.941423713 0.03069492 0.065234021 556.836707 2655541.847 0.020147096 0.02522088 1753.05741 -3.243796139 -0.027102944 DSLLQDGEFSMDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 20 DSLLQDGEFSMDLR 14 0 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 ;;;;;;;;;;;;;;;;;;; 340.83 1.43E-68 14413522000 6732309 5732020.7 3661628.3 4267726.3 5486702.6 5446648.3 5827385.6 6515236.1 6039428 FALSE TRUE 5842617.308 5694366.679 5432403.993 5236778.785 5377527.953 5656184.385 5262246.641 5122003.562 5325453.702 1.097111652 1.06927353 1.020082851 0.983348852 1.009778369 1.062103757 0.988131141 0.961796656 1 22.34447301 8 0.437060676 0.98850182 3.41387438 0.607745457 0.026721286 67.0784767 0.869455962 0.023517075 143.2725188 99999999.99 -8 2.42537256 DSLLTHIQNLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSLLTHIQNLK 11 0 E9PFH4;C9J7E5;Q9Y5L0-5;Q9Y5L0-3;Q9Y5L0;Q9Y5L0-1 E9PFH4 TNPO3 Transportin-3 0 131.82 0.0001954 275320000 577580 432560 327450 516740 517350 418980 537440 655340 818820 FALSE TRUE 501251.3396 429718.4849 485805.9153 634073.7149 507055.7472 435098.4317 485319.1515 515200.6409 722020.0324 0.694234671 0.595161444 0.67284271 0.878194076 0.702273794 0.602612687 0.672168541 0.713554497 1 19.46167934 1.235558092 4.373804601 1.029081329 0.689004133 0.617300256 0.076612053 0.154450885 5.908931107 0.165517275 0.020282453 17.2011741 -1.235558092 -0.340077196 DSLRDESQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSLRDESQR 9 1 Q96MW1;Q86WV7 Q96MW1 CCDC43 Coiled-coil domain-containing protein 43 0 ; 120.27 0.00063093 705160000 1067230 1107610 1740550 958044 341183 929370 782030 649890 760250 FALSE TRUE 926192.8515 1100334.037 2582285.802 1175582.533 334394.1258 965123.4653 706188.851 510916.0809 670374.1111 1.381605936 1.641373106 3.85200705 1.753621617 0.498817183 1.439678904 1.053425004 0.762135757 1 19.35460691 3.465505197 12.0163767 0.974218924 2.322573544 0.451642431 0.681763066 0.441763799 450.9739436 0.195403832 0.255213847 2920.822715 -3.465505197 1.34835462 DSLS(ph)PVLHPSDLILTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DSLSPVLHPSDLILTR 16 0 Q9HCN4-3;Q9HCN4-2;Q9HCN4-4;Q9HCN4;Q9HCN4-5 Q9HCN4-3 GPN1 GPN-loop GTPase 1 1 DS(0.007)LS(0.993)PVLHPSDLILTR;DS(0.032)LS(0.968)PVLHPSDLILTR;DS(0.034)LS(0.966)PVLHPSDLILTR;DS(0.02)LS(0.98)PVLHPSDLILTR;DS(0.006)LS(0.994)PVLHPSDLILTR;DS(0.025)LS(0.975)PVLHPSDLILTR 175.59 2.23E-09 1338511000 1367650 1421360 420870 992704 1690280 1661620 1528400 1787610 1696640 TRUE FALSE 1186911.587 1412022.993 624404.1397 1218112.616 1656646.735 1725543.597 1380176.003 1405343.513 1496065.152 0.793355547 0.943824532 0.41736427 0.814210941 1.107335956 1.153388002 0.922537365 0.939359834 1 20.51274157 3.407652142 6.083612625 1.010705625 0.720990258 0.489922396 0.145363092 0.18160692 11.95685709 0.042971681 0.055858146 2556.537353 -3.407652142 -0.289715367 DSLSVNEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSLSVNEFK 9 0 Q99584 Q99584 S100A13 Protein S100-A13 0 ; 155.84 0.0001683 390660000 545410 529360 335200 420980 528340 377670 572180 643080 605620 FALSE TRUE 473332.6866 525882.5993 497303.8412 516569.9433 517827.0677 392199.2093 516690.0717 505562.3465 534024.2935 0.886350476 0.984754075 0.931238236 0.967315438 0.969669496 0.734422037 0.967540387 0.946702898 1 19.02654585 1.501483491 2.218961064 0.997178704 0.919783775 0.111235156 0.072122405 0.910772265 7.841876882 0.12111797 0.019791272 31.73098045 -1.501483491 -0.077394929 DSLYVDGDCTMDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSLYVDGDCTMDIR 14 0 C9J0J7;G5E9Q6;P35080-2;C9J712;C9JQ45;C9J2N0;P35080 C9J0J7 PFN2 Profilin;Profilin-2 0 ; 134.13 4.16E-05 65996000 132305 119705 79862 81394 112657 115360 117925 128693 134822 FALSE TRUE 114820.559 118918.65 118483.5303 99875.75173 110415.3461 119797.9738 106488.6517 101173.0034 118883.4967 0.965824207 1.000295695 0.996635644 0.840114519 0.928769334 1.007692212 0.895739565 0.851026477 1 16.85918893 3.795617251 24.99769579 0.915735838 0.988856322 0.248383172 0.054522061 381.4357338 167113.4384 0.014772959 0.025587505 6246.219636 -3.795617251 0.073120483 DSNNLCLHFNPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DSNNLCLHFNPR 12 0 P09382 P09382 LGALS1 Galectin-1 0 ;;;;;;; 222.99 2.35E-11 33389430000 12423510 13960250 7860150 10911480 14088120 15445200 13583740 15999920 15407400 FALSE TRUE 10781711.68 13868544.2 11661344.83 13389098.31 13807793.97 16039386.84 12266390.99 12578461.62 13585954.72 0.793592493 1.020800119 0.858338267 0.985510299 1.016328573 1.180585919 0.902872947 0.92584304 1 23.69561262 3.628657559 6.479600805 0.996590644 0.904263844 0.239954355 0.091906247 0.433380573 22.2086971 0.026067335 0.038843829 4252.629614 -3.628657559 -0.0923268 DSNPDEIEIDFETLKPTTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSNPDEIEIDFETLKPTTLR 20 1 Q15059 Q15059 BRD3 Bromodomain-containing protein 3 0 ; 92.492 0.0015001 103393000 83622 58789 51900 55059 66084 40752 65296 79318 80051 FALSE TRUE 72571.14083 58402.81119 76999.0136 67560.98747 64769.05769 42319.75581 58963.60397 62356.46295 70587.46197 1.028102425 0.827382223 1.09083131 0.957124475 0.917571703 0.599536442 0.835326874 0.883392903 1 16.10712433 2.990535015 24.65828482 0.829630526 0.968951973 0.257525666 0.11710732 563.8322315 1468907.694 0.036833652 0.039538595 978.4418387 -2.990535015 0.139321447 DSNYHLLMSVQESLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DSNYHLLMSVQESLER 16 0 P00367;P00367-2;P00367-3 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ;; 245.18 4.20E-20 887710000 863940 882620 512720 1146970 1171330 1193850 887630 1203590 1126240 FALSE TRUE 749768.1401 876822.0111 760673.1069 1407407.069 1148022.825 1239778.182 801547.7792 946211.6448 993097.1902 0.754979621 0.882916617 0.765960386 1.417189659 1.15600249 1.24839562 0.807119169 0.952788563 1 19.92157539 DSPAFPDS(ph)PWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSPAFPDSPWR 11 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 DSPAFPDS(1)PWR;DSPAFPDS(1)PWR 135.04 0.00013455 110566000 197897 156770 128637 156013 176045 181551 168122 205080 203177 TRUE FALSE 171744.41 155740.1675 190846.2835 191438.1362 172542.0489 188535.3844 151817.5543 161225.2379 179157.6465 0.958621713 0.869291211 1.065242188 1.068545719 0.963073875 1.052343498 0.847396454 0.899907099 1 17.45087009 0.927441272 20.03287595 2.075995902 0.962135981 0.016948413 0.078713469 555.9613744 227171.2625 13244.3124 0.01980359 8.461381406 -0.927441272 -1.113859921 DSPCQLEALKLESCGVTSDNCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSPCQLEALKLESCGVTSDNCR 22 1 P13489 P13489 RNH1 Ribonuclease inhibitor 0 ; 208.17 6.57E-23 482840000 434640 398690 237368 210478 368960 321750 478420 534020 69702 FALSE TRUE 377201.2228 396070.9791 352159.9587 258270.2469 361618.4179 334127.9307 432022.902 419823.9787 61461.90896 6.137154363 6.444169825 5.729726992 4.20211886 5.88361839 5.43634157 7.029116233 6.830636826 1 15.90740496 1.23262069 24.99932568 0.99999195 5.986383051 0.79634257 0.788454281 95.53859019 402051.5 1.875285782 0.212547134 17.0852245 -1.23262069 4.986391101 DSPLFDFIESCLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSPLFDFIESCLR 13 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ; 96.89 0.0093753 288860000 116302 137657 100092 91104 110827 112495 164042 158489 115210 FALSE TRUE 100932.396 136752.7221 148496.826 111790.5556 108621.7595 116822.7554 148133.2321 124597.3607 101590.005 0.993526833 1.346123785 1.461726731 1.100408998 1.069216991 1.149943396 1.458147699 1.22647263 1 16.63239894 DSPSKSS(ph)AEAQTPEDTPNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSPSKSSAEAQTPEDTPNK 19 1 A0A5F9UY30;A0A5H1ZRP2;O43493-4;O43493;O43493-5;O43493-3;O43493-7 A0A5F9UY30 TGOLN2 Trans-Golgi network integral membrane protein 2 1 DSPS(0.013)KS(0.482)S(0.505)AEAQTPEDTPNK 216.87 2.26E-19 429500000 757680 551040 590960 552380 591890 389600 730330 906590 888030 TRUE FALSE 657550.6683 547420.182 876750.2326 677806.3216 580112.547 404588.1641 659502.709 712722.7836 783048.105 0.839732149 0.699088828 1.119663309 0.865599849 0.740838964 0.516683664 0.842225024 0.910190292 1 19.57874141 1.598474685 2.844276258 0.985383261 0.800263462 0.162890932 0.150508224 0.458270355 8.250189831 0.158361068 0.042699521 39.6711404 -1.598474685 -0.185119799 DSPSVWAAVPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DSPSVWAAVPGK 12 0 P07737;CON__P02584;I3L3D5 P07737 PFN1 Profilin-1 0 ;;; 193.82 5.38E-06 779173000 1733660 1372470 1041330 1238020 1293310 1153750 1529100 1826730 2073210 FALSE TRUE 1504552.438 1363454.154 1544920.671 1519131.363 1267575.661 1198135.509 1380808.117 1436098.005 1828117.476 0.823006431 0.745824146 0.84508829 0.83098126 0.693377575 0.655393061 0.755316951 0.785561116 1 20.80192735 1.23129367 3.872817345 1.030305758 0.762762242 0.605207365 0.059411243 0.199655416 4.957155897 0.155146554 0.016247957 17.03309898 -1.23129367 -0.267543515 DSQDAGGFGPEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DSQDAGGFGPEDR 13 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 210.31 7.19E-08 1657820000 1105070 1021280 687770 825116 1045440 1085890 1045790 1134810 1124770 FALSE TRUE 959032.1996 1014571.144 1020377.872 1012471.199 1024637.789 1127664.891 944369.4468 892139.7126 991800.9719 0.966960335 1.022958409 1.02881314 1.020841104 1.033108273 1.13698708 0.952176368 0.89951486 1 19.91969111 2.029997956 24.99336479 0.937559557 1.034328763 0.401728163 0.048035354 166.4076329 138645.0253 0.01931515 0.013022083 107.1514262 -2.029997956 0.096769206 DSQDAS(ph)AEQSDHDDEVASLASASGGFGTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSQDASAEQSDHDDEVASLASASGGFGTK 29 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 DS(0.028)QDAS(0.68)AEQS(0.293)DHDDEVASLASASGGFGTK 178.81 7.91E-18 159520000 96531 78041 54701 64887 79120 65642 90547 97160 95628 TRUE FALSE 83774.18377 77528.34353 81154.58656 79620.58509 77545.6668 68167.29022 81765.76588 76383.0901 84322.96678 0.993491892 0.91942144 0.962425655 0.944233678 0.919626879 0.808407161 0.969673732 0.90583969 1 16.36363801 4.742368522 23.55826067 0.926333996 0.993491951 0.136356196 0.05093301 342.1938242 2116831.904 0.0120421 0.08637076 55254.61055 -4.742368522 0.067157956 DSQDASAEQS(ph)DHDDEVASLASASGGFGTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DSQDASAEQSDHDDEVASLASASGGFGTK 29 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 DSQDAS(0.004)AEQS(0.996)DHDDEVASLASASGGFGTK;DSQDAS(0.007)AEQS(0.993)DHDDEVASLASASGGFGTK;DSQDASAEQS(1)DHDDEVASLASASGGFGTK;DSQDAS(0.003)AEQS(0.997)DHDDEVASLASASGGFGTK 348.45 4.51E-120 4374710000 1417465 1073115 716568 1000178 1112825 957417 1243237 1511039 1500092 TRUE FALSE 1230143.409 1066065.637 1063102.682 1227283.702 1090681.96 994249.4515 1122668.067 1187915.069 1322752.833 0.929987356 0.805944702 0.80370471 0.927825419 0.82455462 0.751651727 0.84873609 0.898062767 1 20.33511208 1.342010116 2.152435794 1.025657339 0.838346454 0.46409331 0.054278712 0.483746798 2.784432299 0.164236226 0.014662202 21.97911068 -1.342010116 -0.187310885 RRDELSEEINNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RRDELSEEINNLR 13 2 A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7;A0A087WYS2;B4DSP0;A0A087WZG9;Q86TG7-2 A0A087WXK2;B4DSP0 PEG10 Retrotransposon-derived protein PEG10 0 ;; 194.7 4.49E-07 720010000 556960 465270 330597 256134 420270 435210 388410 420920 165871 FALSE TRUE 483356.3248 462213.6107 490474.815 314293.1395 411907.4492 451952.8103 350742.058 330909.5336 146261.9193 3.304731177 3.160177391 3.353400647 2.14883779 2.816231669 3.09002379 2.398040854 2.262444901 1 17.15819467 1.174877103 1.105844938 2.67E-22 2.96606534 0.745546892 0.359892961 1.045493786 0.965887635 3.818563846 0.119949538 14.95812309 -1.174877103 2.96606534 DSQQTLINIPSLNDSDS(ph)EIEDISEIESNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.004)LNDS(0.418)DS(0.578)EIEDISEIESNR 123.36 1.64E-05 72759000 139530 118810 82839 109700 118740 115610 121760 148520 149880 TRUE FALSE 121090.757 118029.5293 122900.2175 134609.0617 116377.3063 120057.5915 109951.7339 116760.1538 132161.3571 0.916234212 0.893071408 0.92992551 1.018520576 0.880569849 0.908416757 0.831950703 0.883466668 1 17.01194088 DSRPSQAAGDNQGDEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DSRPSQAAGDNQGDEAK 17 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;;; 167.38 9.41E-10 1310084000 1019244 962089 704314 761965 866385 753585 1111881 1334072 1179093 FALSE TRUE 884548.323 955768.974 1044922.606 934980.7992 849145.6336 782575.9026 1004050.952 1048791.085 1039701.969 0.850771038 0.919272063 1.005021283 0.899277704 0.816720232 0.752692527 0.96571035 1.00874204 1 19.98773861 2.01634566 24.98690338 0.999664707 0.878748262 0.424142415 0.065499171 241.9298135 369826.2388 0.029485358 0.019873103 103.8354524 -2.01634566 -0.120916445 DSS(ph)TSPGDYVLSVSENSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DSSTSPGDYVLSVSENSR 18 0 P46108-2;P46108;I3L297 P46108-2 CRK Adapter molecule crk 1 DS(0.036)S(0.963)T(0.001)SPGDYVLSVSENSR;DSS(0.985)T(0.015)SPGDYVLSVSENSR;DSS(0.999)TSPGDYVLSVSENSR 420.63 1.28E-168 654290000 831130 725940 599630 698340 718410 680980 721330 818380 1686090 TRUE FALSE 721294.0647 721171.2523 889613.0736 856908.7705 704115.0465 707177.7413 651375.5276 643375.8056 1486762.361 0.485144152 0.485061548 0.598355929 0.576358935 0.473589502 0.475649478 0.438116773 0.43273614 1 20.50374264 1.234327546 24.99996453 1.000000742 0.494072863 0.898797359 0.053186465 42.497927 250953.3257 0.11249639 0.014844168 17.15250464 -1.234327546 -0.505927879 DSS(ph)VEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSSVEVR 7 0 O15371-2;O15371;O15371-3;B0QYA5;B0QYA6 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 1 DS(0.01)S(0.99)VEVR;DS(0.024)S(0.976)VEVR 141.2 0.0026991 335550000 659450 591920 458670 488740 463460 617810 625960 677380 687140 TRUE FALSE 572302.0117 588031.6385 680484.3462 599715.8869 454238.0527 641577.5505 565254.4955 532527.5584 605907.092 0.944537569 0.970498029 1.123083646 0.989781923 0.74968268 1.058871168 0.932906221 0.878893093 1 19.20873707 3.460611101 24.99990765 0.920726703 1.016476838 0.171569962 0.091394699 377.2957258 571304.591 0.025501544 0.032931461 2888.092517 -3.460611101 0.095750135 DSSEATGWEEPS(ph)PPSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DSSEATGWEEPSPPSIR 17 0 A0A1B0GU24;Q9HCJ0-2;Q9HCJ0 A0A1B0GU24 TNRC6C Trinucleotide repeat-containing gene 6C protein 1 DSSEATGWEEPS(1)PPSIR;DSSEATGWEEPS(1)PPSIR;DSSEATGWEEPS(1)PPSIR 312.28 3.91E-58 287860000 380197 368050 259465 314947 363400 352641 328829 423190 470920 TRUE FALSE 329953.0032 365632.2553 384943.1419 386460.53 356169.051 366207.3275 296939.2142 332694.1118 415248.3741 0.794591921 0.880514598 0.927019023 0.930673193 0.857725336 0.881899486 0.715088204 0.801193051 1 18.66361499 DSSFFDKFFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSSFFDKFFK 10 1 O75363;G3XAF7;O75363-2;H0Y542 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 ; 134.75 0.00014812 466410000 1140830 1060590 409905 617620 1080060 866980 1436270 1755640 276910 FALSE TRUE 990066.425 1053622.914 608136.429 757860.0607 1058568.919 900333.2816 1296980.756 1380210.048 244174.0153 4.054757522 4.315049303 2.490586185 3.103770317 4.335305368 3.687260828 5.311706715 5.652567276 1 17.89755015 2.429281684 24.99415931 4.405648593 3.641516272 0 1.361933227 357.5359074 186795.1004 0.506904022 0.392646256 268.7086727 -2.429281684 -0.76413232 DSSFTEVPRS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DSSFTEVPRSPK 12 1 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 DSSFTEVPRS(1)PK;DSSFTEVPRS(1)PK;DSSFTEVPRS(0.999)PK;DSSFTEVPRS(1)PK;DSSFTEVPRS(1)PK 137.79 5.21E-05 3038360000 5669280 4080160 2899970 3256560 4592890 3586900 4982220 5593900 4105320 TRUE FALSE 4920070.284 4053357.16 4302405.192 3996011.721 4501500.475 3724890.364 4499045.071 4397688.017 3619993.746 1.359137785 1.119713857 1.188511775 1.103872548 1.243510567 1.028977016 1.242832277 1.214833043 1 21.78755577 4.744362484 24.30424694 1.152904879 1.359137919 0.390579598 0.084091954 462.7523404 1938401.699 0.019182532 0.164772676 55508.88249 -4.744362484 0.20623304 DSSGNLHGYVAEGGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSSGNLHGYVAEGGAK 16 0 Q8IZ83;F5H4B6;Q8IZ83-3;M0QY06 Q8IZ83 ALDH16A1 Aldehyde dehydrogenase family 16 member A1 0 129.62 5.44E-05 240150000 453580 361230 200720 321250 378040 375450 460520 501720 530390 FALSE TRUE 393638.2538 358857.0563 297788.8634 394194.7225 370517.7436 389893.8044 415858.8413 394431.0824 467687.8984 0.841668675 0.767300282 0.636725612 0.842858504 0.792232908 0.833662376 0.889180248 0.843363884 1 18.83518657 -2 0.38884886 4.085519343 0.757053265 0.545004143 0.061801429 64.67612934 0.947128049 161.8423477 0.065603908 0.01 2 -3.328466077 DSSGQHVDVSPTSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DSSGQHVDVSPTSQR 15 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ;; 123.28 0.00010374 844710000 1074530 1187580 503830 1243190 1645920 1745480 1157960 1520540 1558380 FALSE TRUE 932528.138 1179778.709 747483.8732 1525475.29 1613169.412 1812629.745 1045661.217 1195384.354 1374150.092 0.678621749 0.858551563 0.543960865 1.110122759 1.173939748 1.319091529 0.760951241 0.869908143 1 20.39010816 3.72971236 24.95008284 1.021302869 0.710195406 0.473959677 0.1705099 645.2776554 1819537.507 0.051536109 0.077748316 5366.762299 -3.72971236 -0.311107463 DSSGWSSSK ddPTM_MDA-MB-175_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 ; 145.72 0.00022448 168128000 173503 161194 101933 121310 128520 135556 172510 196723 171987 FALSE TRUE 150574.1389 160135.106 151228.1397 148855.2896 125962.7034 140770.927 155780.0068 154655.3174 151654.8928 0.992873597 1.055917835 0.997186025 0.981539645 0.830587798 0.928232017 1.027200665 1.019784555 1 17.21043252 2.219264704 24.92804122 1.017001465 0.96473827 0.148257669 0.057898697 507.466171 655581.3422 0.026427337 0.017848237 165.6779468 -2.219264704 -0.052263195 DSSSEKDGRS(ph)PNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSSSEKDGRSPNKR 14 3 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 DSSSEKDGRS(1)PNKR;DSSSEKDGRS(1)PNKR 89.468 0.033914 225137000 363530 236191 179440 168197 184883 156584 356440 370760 97749 TRUE FALSE 315488.5894 234639.4458 266217.7842 206388.6996 181204.19 162607.8878 321872.5037 291475.8593 86193.22458 3.660248134 2.722249306 3.088616135 2.394488669 2.102302019 1.886550696 3.734313286 3.381656281 1 16.39528685 5.696449203 1.08945106 2.595893464 9.708707237 0.172390757 0.778944046 25.37397454 5.087070841 0.243097822 340.0883023 497106.227 -5.696449203 7.112813773 DSSVPGS(ph)PSSIVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSSVPGSPSSIVAK 14 0 Q08495;Q08495-2;E5RGQ0;E5RJ61;A0A087WT94 Q08495 DMTN Dematin 1 DSSVPGS(0.972)PS(0.023)S(0.005)IVAK;DSSVPGS(0.976)PS(0.02)S(0.004)IVAK 167.37 3.84E-06 269740000 509690 683340 573060 834820 877790 688780 1046030 1250200 1365380 TRUE FALSE 442333.1751 678851.0945 850193.7328 1024378.64 860323.6964 715277.8123 944586.1716 982854.4591 1203966.332 0.367396632 0.56384558 0.706160721 0.850836617 0.714574547 0.594101175 0.784561949 0.81634713 1 20.19936362 4.918816354 0.950808711 0.792432057 8.93E-10 0.654023079 0.102444018 1.838313607 1.059661859 0.03574495 1.622740587 82949.99301 -4.918816354 -0.792432056 DSTEEKS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DSTEEKSPR 9 1 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 DSTEEKS(1)PR;DSTEEKS(1)PR;DSTEEKS(1)PR;DS(0.001)T(0.001)EEKS(0.997)PR 123.2 0.00034184 986790000 2797240 2394420 1765350 1938660 1477430 1940098 2895540 3319290 3140540 TRUE FALSE 2427577.647 2378690.897 2619079.165 2378862.384 1448032.034 2014734.825 2614730.976 2609485.664 2769268.939 0.876613179 0.858959873 0.945765551 0.859021798 0.522893249 0.727533103 0.944195394 0.942301279 1 21.40107374 2.161788106 7.490201995 0.958981236 0.798341828 0.312225064 0.114597084 0.325965837 27.06250508 0.051930963 0.034976064 145.1403301 -2.161788106 -0.160639408 DSTLIMQLLR ddPTM_MDA-MB-175_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 ; 195.32 8.53E-07 9427500000 1884890 1849690 1326440 1652490 1770110 1834050 1758240 2001610 3310600 FALSE TRUE 1635797.011 1837539.265 1967910.821 2027713.111 1734888.274 1904607.09 1587726.155 1573581.278 2919224.639 0.560353249 0.629461412 0.674121064 0.69460674 0.594297626 0.652435946 0.543886255 0.539040832 1 21.4771538 1.232120437 24.99996708 1.000000651 0.610435081 0.84028983 0.05329309 93.09787645 361359.5989 0.134073212 0.01449728 17.06555581 -1.232120437 -0.38956557 DSVFLSCSEDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DSVFLSCSEDNR 12 0 Q9BQA1;Q9BQA1-2;H0Y711 Q9BQA1 WDR77 Methylosome protein 50 0 130.01 0.00052145 157710000 93617 72413 53883 78107 81686 82081 80229 94685 129240 FALSE TRUE 81245.27625 71937.31424 79940.99903 95842.38814 80060.60842 85238.70918 72448.40393 74437.34959 113961.3944 0.712919289 0.63124284 0.701474385 0.841007506 0.702523945 0.747961269 0.635727601 0.653180403 1 16.79818565 1.232939886 24.99994328 1.000000476 0.701115108 0.701058843 0.060883602 109.6592125 487691.4375 0.134814351 0.015726079 17.09778635 -1.232939886 -0.298885368 DSYCSYMGHFDLLNYFAIAENESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSYCSYMGHFDLLNYFAIAENESK 24 0 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 ; 175.97 9.75E-13 147554000 243992 214410 106976 147282 172991 121423 238760 261429 232304 FALSE TRUE 211747.839 213001.5266 158709.9514 180724.6292 169548.8176 126094.2214 215605.0919 205524.4428 204841.2858 1.033716608 1.039836895 0.774794743 0.882266622 0.827708227 0.615570347 1.052547054 1.003335055 1 17.64414699 DSYDSYATHNE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 DSYDSYATHNE 11 0 Q14011 Q14011 CIRBP Cold-inducible RNA-binding protein 0 ;;;;;; 224.51 1.43E-11 5458700000 7302360 6246634 3371016 4510809 6013452 5672397 5741648 6621274 6058134 FALSE TRUE 6337334.624 6205599.45 5001250.613 5535057.127 5893796.07 5890617.783 5184823.861 5205366.082 5341948.3 1.186333949 1.161673439 0.936222204 1.036149513 1.103304588 1.102709621 0.970586679 0.974432134 1 22.34893458 4.334743919 7.315730318 1.018220538 1.178759914 0.593874253 0.053857947 0.163127674 10.63666058 0.014756687 0.03946227 21614.43656 -4.334743919 0.160539377 DSYESYGNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 ;;;;;; 262.83 4.54E-17 6466235000 2390924 1961282 1227021 1504134 1887426 1878190 1959767 2116934 2019108 FALSE TRUE 2074957.336 1948398.209 1820412.46 1845670.614 1849869.915 1950445.185 1769709.098 1664244.138 1780411.352 1.165437039 1.094352834 1.02246734 1.036654036 1.039012649 1.095502555 0.993988887 0.934752599 1 20.76377917 8 0.191033351 0.93316422 1.887288848 0.615670014 0.039657124 79.75709668 1.157018057 0.333981207 21.74102108 100000000 -8 0.954124628 DSYGGPPRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSYGGPPRR 9 1 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ; 104.01 0.0064927 252780000 623260 600650 382550 407490 454260 605470 520680 620120 355620 FALSE TRUE 540894.6119 596704.2906 567552.4596 500016.8326 445221.1147 628762.8227 470184.5337 487512.1638 313579.0087 1.724906951 1.902883401 1.809918533 1.594548164 1.419805224 2.005117706 1.499413292 1.554670913 1 18.25846946 0.872947756 1.238810983 1.45E-20 1.726741958 0.626159722 0.172795639 2.222831063 1.533425436 6.191636673 0.051884932 7.463589681 -0.872947756 1.726741958 DSYLILETLPTEYDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DSYLILETLPTEYDSR 16 0 P17980;E9PM69;E9PKD5;E9PLG2;R4GNH3;E9PN50;E9PMD8 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ;;;; 194.06 6.38E-10 513754000 755125 701932 414304 536141 664081 685178 664954 820926 747838 FALSE TRUE 655333.318 697320.9625 614662.8002 657880.0085 650867.0874 711537.241 600466.8634 645377.3634 659429.4436 0.993788379 1.057461066 0.932113066 0.99765034 0.987015508 1.079019519 0.91058546 0.978690548 1 19.33085878 2.396558214 0.007008212 6.35E-06 1.973714355 0.016098994 0.049447691 30362.11665 151.8047668 21583.19284 21167.10987 249.2058394 -2.396558214 1.973708005 DSYSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSYSSSR 7 0 P38159;P38159-2;H3BUY5;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ; 166.05 0.002647 324360000 386590 384000 234530 297800 269010 380500 416980 422600 421960 FALSE TRUE 335501.152 381477.4787 347949.4925 365420.0416 263657.2273 395138.0812 376541.3438 332230.2787 372076.3695 0.901699703 1.025266612 0.935156116 0.982110318 0.708610514 1.061981124 1.012000155 0.892908838 1 18.50523924 1.191147031 21.89316285 1.000003694 0.941552786 0.035545309 0.097966127 11298.42726 5215175.19 10.94188455 0.022952669 15.52912663 -1.191147031 -0.058450908 DSYVGDEAQS(ph)KR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSYVGDEAQSKR 12 1 C9JTX5;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;P63261;I3L3I0;I3L1U9;K7EM38;I3L3R2;J3KT65;P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 C9JTX5;P60709;P63261;P68133 ACTB;ACTG1;ACTA1;ACTC1;ACTG2;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, gamma-enteric smooth muscle;Actin, aortic smooth muscle" 1 DSYVGDEAQS(1)KR;DSYVGDEAQS(1)KR 73.833 0.011102 438200000 437710 527460 351810 313850 447090 362340 482840 536410 555270 TRUE FALSE 379865.5145 523995.0805 521946.4927 385114.4394 438193.7837 376279.4543 436014.2511 421702.8958 489626.6132 0.775826935 1.070193218 1.066009238 0.786547195 0.894954996 0.768502864 0.890503578 0.861274458 1 18.90132245 3.736446924 24.96597733 0.864906195 0.980628136 0.186366976 0.101385292 270.7634797 3198143.318 0.026440141 0.04149396 5450.632782 -3.736446924 0.115721941 DSYVGDEAQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 DSYVGDEAQSK 11 0 C9JTX5;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;P63261;I3L3I0;I3L1U9;K7EM38;I3L3R2;J3KT65;P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 C9JTX5;P60709;P63261;P68133 ACTB;ACTG1;ACTA1;ACTC1;ACTG2;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, gamma-enteric smooth muscle;Actin, aortic smooth muscle" 0 ;;;;;;;;; 319.75 1.31E-45 22181210000 18286580 15116520 12017370 14435350 13203690 11093269 17042100 20063170 22716440 FALSE TRUE 15869962.12 15017218.58 17829010.33 17713116.85 12940962.4 11520034.24 15389359.77 15772817.23 20030928.34 0.792272922 0.749701578 0.890074091 0.884288364 0.646049059 0.575112348 0.768279907 0.787423177 1 24.25572595 1.210442286 3.047167203 1.055911524 0.757181608 0.387710179 0.094756959 0.514122379 5.737456198 0.391394316 0.02680992 16.23462592 -1.210442286 -0.298729916 DSYVGDEAQSKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 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 ;;;;;;;;;;; 206.64 1.41E-07 30150425000 36760366 28668365 13069309 15940723 25242549 21071537 32359398 36735239 4189603.5 FALSE TRUE 31902390.49 28480040.62 19389670.55 19560307.8 24740271.66 21882172.66 29221188.56 28879694.01 3694313.347 8.635539949 7.709156736 5.248518121 5.294707286 6.696852524 5.923204289 7.909775327 7.817337432 1 21.81687481 4.403398119 4.912368557 6.04109981 8.436645888 0.211285844 1.937049806 0.316677691 13.76952213 0.481901503 1.391765051 25316.17676 -4.403398119 2.395546077 DSYYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DSYYDR 6 0 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 0 ; 122.54 0.04461 1862520000 2947600 2285500 1403190 1648520 2157500 2253700 2341600 2689600 2506700 FALSE TRUE 2558067.192 2270486.4 2081777.377 2022841.662 2114569.971 2340401.297 2114511.992 2114449.97 2210360.782 1.157307537 1.027201721 0.941826961 0.915163569 0.956662817 1.058832258 0.956636586 0.956608527 1 21.07585044 4.656651259 2.799237135 0.968678817 1.175228623 0.702772337 0.038580891 0.199124005 2.367488273 0.010163544 0.08530893 45357.72454 -4.656651259 0.206549806 DT(ph)PGHGSGWAETPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DTPGHGSGWAETPR 14 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 DT(1)PGHGSGWAETPR;DT(1)PGHGSGWAETPR 200.33 7.14E-08 619390000 545290 483240 255180 416300 513050 515720 522510 546680 711380 TRUE FALSE 473228.5449 480065.5646 378585.9015 510827.2777 502841.3088 535560.0821 471837.0606 429776.7363 627281.4668 0.754411807 0.765311252 0.603534333 0.814350981 0.801619903 0.85377954 0.75219353 0.685141773 1 19.25875341 DTAAWTVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DTAAWTVGR 9 0 Q14974;Q14974-2;J3KTM9;J3QKQ5 Q14974 KPNB1 Importin subunit beta-1 0 ;;; 176.6 0.00012337 2460320000 1136660 1059620 761930 775070 1014690 1084440 1013010 1128300 1118440 FALSE TRUE 986447.5011 1052659.286 1130401.897 951061.4897 994499.6542 1126159.109 914768.4461 887021.8254 986219.2973 1.000231392 1.067368373 1.146197301 0.964350923 1.00839606 1.141895227 0.927550747 0.899416416 1 19.91154896 2.208932863 24.99212472 0.932768049 1.053255937 0.415984365 0.062433959 184.4751205 155610.4083 0.02524865 0.017025402 161.782992 -2.208932863 0.120487888 DTATYWPLNWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DTATYWPLNWR 11 0 E9PCJ7;Q8N806 E9PCJ7 UBR7 Putative E3 ubiquitin-protein ligase UBR7 0 138.66 0.0030819 0 110040 117800 85458 81745 119970 102090 123330 130690 116300 FALSE TRUE 95497.93519 117026.164 126785.7746 100306.4516 117582.8317 106017.4684 111369.4756 102742.9605 102551.1465 0.931222502 1.141149251 1.236317476 0.97811146 1.146577447 1.033800908 1.085989571 1.001870423 1 16.6459841 1.703562546 1.126565563 0.977209377 1.090571845 0.108945894 0.087184132 1.632983675 3.000574828 0.193709902 0.028984702 50.53154141 -1.703562546 0.113362468 DTCVQS(ph)PISSFPCTDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DTCVQSPISSFPCTDLK 17 0 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 DTCVQS(1)PISSFPCTDLK;DTCVQS(0.999)PISSFPCTDLK 300.18 2.61E-46 375520000 543190 423470 362590 496500 538680 417950 668250 821860 717640 TRUE FALSE 471406.0652 420688.1977 537939.7368 609237.9135 527961.3219 434028.8069 603443.2179 646111.6347 632801.4167 0.744951027 0.66480287 0.850092498 0.962763195 0.834323862 0.685884695 0.953605984 1.021033799 1 19.2713933 -2 0.195001471 2.391411221 0.676087905 0.465071635 0.093539386 98.05824172 1.440691164 49.34723933 0.70824183 0.01 2 -1.715323316 DTCYS(ph)PKPSVYLSTPSSASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DTCYSPKPSVYLSTPSSASK 20 1 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 DT(0.011)CYS(0.98)PKPS(0.009)VYLSTPSSASK 133.76 6.17E-06 225040000 540640 542030 464290 506950 637990 490530 850120 1008700 823520 TRUE FALSE 469193.0542 538469.3692 688822.197 622060.7457 625295.2472 509401.0065 767675.4932 792997.3547 726164.4038 0.646125109 0.741525427 0.948576098 0.856638996 0.861093223 0.701495424 1.057164864 1.092035565 1 19.46993669 -1.999999996 0.081561944 2.541039862 0.230043872 0.517638043 0.104065888 356.3000359 2.75102808 97.23650872 15.21936145 0.01 1.999999996 -2.31099599 DTDFEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DTDFEHR 7 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ;;;;; 176.29 0.00075732 4998630000 6022440 5561000 3648190 4248250 5291480 5577850 5583870 6418950 6239880 FALSE TRUE 5226559.295 5524469.425 5412466.886 5212880.093 5186189.901 5792433.499 5042347.147 5046307.495 5502208.495 0.94990208 1.004045817 0.983689893 0.947415951 0.942565136 1.052747002 0.916422406 0.91714218 1 22.39157938 DTDIVDEAIYYFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DTDIVDEAIYYFK 13 0 O15145;C9JZD1;F8VR50 O15145 ARPC3 Actin-related protein 2/3 complex subunit 3 0 ;;; 207.29 1.28E-07 265904000 477148 384619 313217 420827 385272 308201 475416 542157 592337 FALSE TRUE 414091.6829 382092.4125 464689.7888 516382.2023 377605.841 320057.6919 429310.2295 426220.9446 522311.5947 0.792805841 0.731541127 0.889679252 0.988647787 0.72295129 0.612771562 0.821942752 0.816028112 1 18.9945512 1.182688891 2.8084093 1.063867062 0.794262478 0.291384795 0.099855672 0.810913423 6.67924372 0.546526471 0.027734542 15.22961382 -1.182688891 -0.269604584 DTDPDSKPFSLQETYEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DTDPDSKPFSLQETYEAK 18 1 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;H0Y961;B1AMS2;Q14141-2;Q14141-4;Q14141 D6RGI3;B1AMS2 SEPT11;SEPT6 Septin-11;Septin-6 0 ; 224.4 4.22E-19 863970000 1874030 1118180 1213890 1432200 1099860 705950 1509210 1900530 2339100 FALSE TRUE 1626372.187 1110834.602 1800931.264 1757402.9 1077974.938 733108.3533 1362847.046 1494116.449 2062574.263 0.788515699 0.538567082 0.873147356 0.852043454 0.522635697 0.355433677 0.660750534 0.724394014 1 20.97601463 1.231001453 2.596975569 1.086191706 0.652126229 0.315617119 0.158239473 0.684965397 5.074938285 0.666110223 0.044064149 17.02164201 -1.231001453 -0.434065477 DTDSEEEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DTDSEEEIR 9 0 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ;;; 217.81 1.29E-06 11049600000 5584860 4336870 5172270 8628120 4635900 4524480 2776080 5650230 20319550 FALSE TRUE 4846806.601 4308380.815 7673597.072 10587266.52 4543654.66 4698539.673 2506856.189 4441972.285 17917395.95 0.270508427 0.240457979 0.428276358 0.590893149 0.253589008 0.262233401 0.13991186 0.247913943 1 24.09485764 1.235872163 24.99983737 1.000000929 0.301829375 0.758073758 0.123519389 39.76483192 369697.1821 0.220605326 0.032984891 17.21361807 -1.235872163 -0.698171554 DTDSEEEIREAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DTDSEEEIREAFR 13 1 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ;;;;; 309.17 1.40E-50 24508710000 14796010 12741890 8990740 11132100 13238110 12232780 8366030 14698540 6279850 FALSE TRUE 12840679.79 12658187.69 13338691.94 13659813.45 12974697.51 12703382.96 7554693.698 11555371.61 5537453.287 2.318878214 2.285922252 2.408813446 2.466804276 2.343080264 2.294083996 1.364290281 2.086766426 1 22.40079119 0.940359582 0.602564358 7.87E-13 2.400737063 0.683217648 0.27498907 3.054767498 0.675782558 5.561779487 0.148669566 8.716850179 -0.940359582 2.400737063 DTDSEEEIREAFRVFDKDGNGYISAAELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DTDSEEEIREAFRVFDKDGNGYISAAELR 29 3 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2 P0DP25 CALM2;CALM1 0 ;; 220.41 8.80E-35 1121930000 634614 548601 350088 291602 480243 401437 646057 719233 182958 FALSE TRUE 550748.152 544997.2039 519391.7278 357814.691 470687.1039 416880.5412 583402.4916 565430.62 161328.9137 3.413821735 3.378174386 3.219458409 2.217920414 2.917561974 2.584041085 3.616230211 3.504831262 1 17.2996455 3.979799152 22.08490111 2.794121417 3.371703394 0.150481376 0.729766915 372.3760461 407112.5647 0.194072007 0.343175503 9545.510322 -3.979799152 0.577581977 DTDYKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DTDYKR 6 1 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ; 97.596 0.065567 736610000 2098620 2125640 1322020 1503090 1180170 1555410 2257520 2699630 2126490 FALSE TRUE 1821282.05 2111676.531 1961353.294 1844389.558 1156686.926 1615247.629 2038586.058 2122335.133 1875098.775 0.971299259 1.126168157 1.045999987 0.983622614 0.616867197 0.861420023 1.087188625 1.131852445 1 20.83853516 2.219591785 24.38435742 1.085862495 0.935854087 0.183909455 0.136899005 321.9626805 413877.4729 0.061967733 0.041862111 165.8027712 -2.219591785 -0.150008408 DTEEPLPVKESDQTLAALLS(ph)PK ddPTM_MDA-MB-175_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 128.06 1.04E-05 143451000 271832 206340 81023 92747 218719 140247 329426 353623 32433.4 TRUE FALSE 235908.7125 204984.539 120205.9938 113806.6239 214366.9198 145642.3928 297478.3172 278003.4733 28599.1604 8.248798537 7.167501986 4.203130166 3.979369405 7.495566891 5.092540858 10.40164512 9.720686533 1 14.80368517 4.479270082 24.94144456 6.450703793 7.978475258 0.048945574 2.792477938 282.0303698 3273452.045 0.729096302 2.000366239 30148.80355 -4.479270082 1.527771465 DTEEQNPETVNWEDRPS(ph)TPTILGYEVMEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DTEEQNPETVNWEDRPSTPTILGYEVMEER 30 1 A0A0C4DGW2;P57768-2;P57768;E5RGS8;E5RH07;E5RGQ6 A0A0C4DGW2 SNX16 Sorting nexin-16 1 DTEEQNPETVNWEDRPS(0.468)T(0.468)PT(0.064)ILGYEVMEER 131.56 4.83E-06 371470000 56282 64583 42633 55515 77262 67080 58805 82984 64042 TRUE FALSE 48844.1911 64158.75002 63250.4614 68120.52924 75724.63736 69660.61101 53102.10015 65238.51738 56471.02772 0.864942486 1.13613569 1.120051537 1.206291651 1.340946684 1.23356372 0.940342372 1.155256421 1 15.78522327 7.384119104 10.2572253 1.120228766 0.002612765 0 0.142373993 0 0 0.032034766 0 24216930.97 -7.384119104 -1.117616001 DTEEQNPETVNWEDRPST(ph)PTILGYEVMEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DTEEQNPETVNWEDRPSTPTILGYEVMEER 30 1 A0A0C4DGW2;P57768-2;P57768;E5RGS8;E5RH07;E5RGQ6 A0A0C4DGW2 SNX16 Sorting nexin-16 1 DTEEQNPETVNWEDRPS(0.013)T(0.752)PT(0.234)ILGYEVMEER;DTEEQNPETVNWEDRPS(0.103)T(0.874)PT(0.023)ILGYEVMEER 233.75 3.56E-45 463530000 193810 188219 149001 160853 178026 174488 204332 222251 217401 TRUE FALSE 168197.5174 186982.577 221058.382 197377.1321 174483.6309 181200.6663 184515.9141 174724.3532 191700.1014 0.877399209 0.975391122 1.153146922 1.029614125 0.910190603 0.945229892 0.962523821 0.911446326 1 17.54849157 3.248095672 24.95820693 0.942790167 1.016799454 0.157455612 0.071192568 335.2847611 877610.0796 0.021252917 0.027070114 1770.498944 -3.248095672 0.074009287 DTFEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DTFEER 6 0 Q9P2M7;Q9P2M7-2;A6PVU7 Q9P2M7 CGN Cingulin 0 ; 119.22 0.049314 497190000 798910 816050 562160 712290 738890 832790 806030 918510 1031140 FALSE TRUE 693332.0193 810689.3138 834022.4563 874026.3312 724187.5346 864827.9702 727861.3347 722093.7844 909239.8039 0.762540329 0.891612213 0.917274467 0.961271523 0.796475838 0.951154983 0.800516356 0.79417309 1 19.79430132 4.742274735 23.89671378 0.879681861 0.762540244 0.218765047 0.073257114 339.8758181 2186590.347 0.017813709 0.127473772 55242.67944 -4.742274735 -0.117141616 DTFEHDPSESIDEFNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DTFEHDPSESIDEFNK 16 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 107.07 0.0011562 160100000 94021 69675 60495 83161 71466 61243 73754 94775 181370 FALSE TRUE 81595.88663 69217.30034 89750.58434 102043.9761 70043.96642 63599.05784 66601.34843 74508.10379 159928.6452 0.510201825 0.432801142 0.561191425 0.638059404 0.437970111 0.39767146 0.416444148 0.465883417 1 17.28706884 1.237591697 24.99998513 1.000000611 0.480370397 0.833664542 0.07263605 10.12407775 261082.3785 0.113255565 0.019140978 17.28190833 -1.237591697 -0.519630214 DTFNHLTTWLEDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DTFNHLTTWLEDAR 14 0 P61019;P61019-2;E9PKL7;H7C125 P61019 RAB2A Ras-related protein Rab-2A 0 ;;;; 210.9 4.58E-09 2039832000 2487089 2286059 1177141 1861689 2781928 2686105 2032339 3023442 2942120 FALSE TRUE 2158413.887 2271041.728 1746410.325 2284413.942 2726573.076 2789441.197 1835243.077 2376902.457 2594305.925 0.83198125 0.875394727 0.673170542 0.880549175 1.050983637 1.075216755 0.707411974 0.916199756 1 21.30691718 3.483940988 24.85362352 0.936718334 0.797562825 0.287005197 0.111535362 424.4318991 1546788.675 0.032990108 0.04431661 3047.480867 -3.483940988 -0.13915551 DTFYIFNHVDIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DTFYIFNHVDIK 12 0 Q99805 Q99805 TM9SF2 Transmembrane 9 superfamily member 2 0 ; 147.18 6.26E-05 939900000 2394900 2230500 2076250 1833570 2085350 1786010 2309500 2859300 3439500 FALSE TRUE 2078407.897 2215847.699 3080331.445 2249910.093 2043855.615 1854718.96 2085525.045 2247860.946 3032886.228 0.685290427 0.730606931 1.015643586 0.741837947 0.673897885 0.61153595 0.687637085 0.741162304 1 21.53225995 1.239243678 8.219860058 1.00283684 0.7366607 0.376775826 0.106736966 0.105847964 70.3950472 0.158570434 0.027875509 17.34777091 -1.239243678 -0.26617614 DTGIFLDLMHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DTGIFLDLMHLK 12 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;; 206.36 9.10E-08 4750700000 5407980 4213740 2856040 3546290 4185020 3486950 5139700 5753340 5039150 FALSE TRUE 4693301.741 4186059.664 4237230.497 4351529.346 4101746.29 3621095.223 4641252.685 4523033.014 4443427.428 1.056234589 0.942078999 0.953595072 0.979318199 0.923104148 0.814932905 1.044520871 1.017915356 1 22.08324149 DTGKTPVEPEVAIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DTGKTPVEPEVAIHR 15 1 P60866;P60866-2;E5RJX2;E5RIP1 P60866 RPS20 40S ribosomal protein S20 0 ;; 184 2.90E-07 2249590000 8837200 7596100 3574200 4442500 7414000 6126600 9174300 10327900 1851780 FALSE TRUE 7669341.629 7546200.719 5302695.075 5451237.524 7266475.905 6362294.266 8284577.798 8119358.957 1632864.678 4.696862963 4.62144893 3.247479811 3.33845027 4.450139686 3.896400205 5.073646279 4.972462854 1 20.6389738 4.382801579 11.64906043 3.916666693 4.677912368 0.084125527 1.156037099 1.211093437 139.1808675 0.286364354 0.758238976 24143.57507 -4.382801579 0.761245675 DTGNIGQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DTGNIGQER 9 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 103.01 0.008125 174660000 138060 144790 81372 91007 128250 134570 140400 154130 146620 FALSE TRUE 119815.0212 143838.865 120723.7714 111671.5303 125698.0759 139746.995 126784.0296 121170.4989 129286.7506 0.926738592 1.112556888 0.933767542 0.863750769 0.972242518 1.080907319 0.980642092 0.937222866 1 16.98021491 DTGQLYAALHHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DTGQLYAALHHR 12 0 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7EIJ4 Q9H6Z4 RANBP3 Ran-binding protein 3 0 134.75 8.09E-05 337410000 198800 187420 113790 146650 183970 203230 178040 205540 212520 FALSE TRUE 172528.0763 186188.8257 168819.2246 179949.1239 180309.3569 211048.3896 160773.7082 161586.8705 187396.1277 0.920659773 0.993557487 0.900868266 0.960260631 0.962182939 1.126215318 0.857935061 0.86227433 1 17.51573162 DTHDQLSEPSEVR ddPTM_MDA-MB-175_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 ;;;;;;; 213.99 1.49E-09 7739590000 6099391 5349537 3356902 4307324 5719685 6038303 5318642 5721310 5467414 FALSE TRUE 5293341.025 5314395.539 4980311.035 5285367.748 5605874.459 6270600.424 4802840.917 4497852.38 4821062.545 1.097961492 1.102328686 1.033031824 1.09630765 1.162788163 1.300667719 0.996220412 0.932958728 1 22.20091972 2.023701624 24.99962364 0.962560291 1.127941753 0.521840968 0.070624179 174.1596719 183696.602 0.030403629 0.020497033 105.6091686 -2.023701624 0.165381461 DTHEDHDT(ph)STENTDESNHDPQFEPIVSLPEQEIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK 34 0 P43487;P43487-2;C9JJ34 P43487 RANBP1 Ran-specific GTPase-activating protein 1 DT(0.011)HEDHDT(0.327)S(0.327)T(0.327)ENT(0.007)DESNHDPQFEPIVSLPEQEIK;DT(0.017)HEDHDT(0.349)S(0.281)T(0.349)ENT(0.003)DESNHDPQFEPIVSLPEQEIK 290.17 2.16E-89 938500000 561850 574740 190444 452990 525870 433580 630590 793330 637320 TRUE FALSE 487600.099 570964.4951 282543.3554 555848.303 515406.2158 450260.1032 569435.4789 623682.5532 561976.7556 0.867651721 1.01599308 0.502766978 0.989094829 0.917130843 0.801207699 1.013272298 1.109801334 1 19.10015093 2.123718315 4.968085967 1.062112543 0.850745726 0.290894201 0.14191457 0.245286245 9.646765542 0.058204911 0.038440383 132.9591759 -2.123718315 -0.211366817 DTHEDHDTS(ph)TENTDESNHDPQFEPIVSLPEQEIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK 34 0 P43487;P43487-2;C9JJ34 P43487 RANBP1 Ran-specific GTPase-activating protein 1 DT(0.001)HEDHDT(0.041)S(0.239)T(0.239)ENT(0.239)DES(0.239)NHDPQFEPIVSLPEQEIK 66.479 0.0088528 124640000 45348 50415 19588 40978 55464 39721 51021 67681 61375 TRUE FALSE 39355.1469 50083.82055 29060.82232 50282.68121 54360.37491 41249.09257 46072.99127 53207.94484 54119.31742 0.727192226 0.925433338 0.536976882 0.929107823 1.004454186 0.762187968 0.851322475 0.98315994 1 15.72385602 -2 0.201211194 2.129252085 0.715286176 0.260223412 0.127015918 145.5291043 2.169197173 62.87298266 0.797710212 0.01 2 -1.413965908 DTHEDHDTST(ph)ENT(ph)DESNHDPQFEPIVSLPEQEIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK 34 0 P43487;P43487-2;C9JJ34 P43487 RANBP1 Ran-specific GTPase-activating protein 2 DT(0.007)HEDHDT(0.319)S(0.414)T(0.453)ENT(0.785)DES(0.023)NHDPQFEPIVSLPEQEIK 171.1 1.27E-14 75462000 60189 50102 21464 33699 47859 36974 60542 69329 60391 TRUE FALSE 52234.87115 49772.87666 31844.06219 41350.87301 46906.69953 38396.41371 54670.64616 54503.53287 53251.64478 0.980906249 0.934673039 0.597992087 0.776518231 0.880849779 0.721037141 1.02664709 1.023508909 1 15.70053847 2.223760213 24.98734243 1.018547067 0.812089219 0.437773003 0.107538936 222.0827766 374936.7145 0.045145639 0.030580197 167.4018346 -2.223760213 -0.206457849 DTHEDHDTST(ph)ENTDESNHDPQFEPIVSLPEQEIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK 34 0 P43487;P43487-2;C9JJ34 P43487 RANBP1 Ran-specific GTPase-activating protein 1 DT(0.002)HEDHDT(0.292)S(0.292)T(0.363)ENT(0.05)DESNHDPQFEPIVSLPEQEIK 297.11 1.31E-89 402400000 824930 814670 282370 568980 756940 554180 874130 1121000 886030 TRUE FALSE 715913.4104 809318.3791 418925.0765 698175.6053 741878.3749 575499.6632 789357.0071 881282.8736 781284.5428 0.91632865 1.035881724 0.53620039 0.893625263 0.949562335 0.736607 1.010332298 1.127992204 1 19.57548855 2.069520721 6.345268967 1.072147514 0.847030044 0.326847221 0.137606733 0.217071497 15.30467091 0.056363672 0.037556307 117.3601676 -2.069520721 -0.22511747 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK 34 0 P43487;P43487-2;C9JJ34 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;;; 188.54 1.32E-20 2670420000 1821462 1599207 636121 1222630 1504470 1260799 1811120 2200839 1914306 FALSE TRUE 1580751.182 1588701.704 943751.2433 1500246.828 1474533.99 1309302.753 1635477.861 1730206.707 1687998.925 0.936464566 0.941174594 0.559094694 0.888772383 0.87353965 0.775653784 0.968885606 1.025004626 1 20.68688255 2.117822044 5.071108321 1.009278733 0.827093982 0.353330767 0.108547119 0.224265959 9.027956339 0.046020297 0.030413303 131.1662324 -2.117822044 -0.18218475 DTHPGS(ph)PGSPGPALRPLPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DTHPGSPGSPGPALRPLPAR 20 1 Q8N0Y2-2;Q8N0Y2 Q8N0Y2-2 ZNF444 Zinc finger protein 444 1 DTHPGS(0.938)PGS(0.061)PGPALRPLPAR;DTHPGS(0.603)PGS(0.397)PGPALRPLPAR 136.64 3.04E-06 588270000 660190 547590 374641 521520 607820 640910 466330 591390 785820 TRUE FALSE 572944.2188 543992.8452 555818.6407 639939.0869 595725.5712 665566.2224 421105.3884 464925.8507 692921.2548 0.826853289 0.785071668 0.802138247 0.923537967 0.85973055 0.960522163 0.607724738 0.670964915 1 19.40233188 2.245226349 24.99877739 0.734778634 0.856547259 0.136378661 0.11294877 249.0001509 933838.9499 0.043095932 0.032603814 175.8840062 -2.245226349 0.121768625 DTHPGSPGS(ph)PGPALRPLPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DTHPGSPGSPGPALRPLPAR 20 1 Q8N0Y2-2;Q8N0Y2 Q8N0Y2-2 ZNF444 Zinc finger protein 444 1 DTHPGS(0.05)PGS(0.95)PGPALRPLPAR 157.3 5.15E-09 362330000 200140 162020 116970 151670 165570 179440 154570 173170 249340 TRUE FALSE 173690.9919 160955.68 173537.0832 186108.9916 162275.4809 186343.1729 139579.8252 136138.9431 219863.3092 0.78999535 0.732071579 0.78929533 0.846475896 0.738074404 0.847541018 0.634848196 0.619198099 1 17.74624734 2.251499079 24.99746486 0.718963161 0.788012618 0 0.109848639 603.3752547 1165737.143 0.040542524 0.031203961 178.4428204 -2.251499079 0.069049457 DTIEEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DTIEEHR 7 0 P23381;P23381-2 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ;;;;; 170.87 0.0009588 4045300000 6895030 6339610 4346710 5329920 5612650 6365160 6874260 7443520 6990390 FALSE TRUE 5983834.316 6297964.684 6448793.495 6540159.799 5500969.246 6610031.824 6207595.323 5851781.174 6163994.058 0.97077224 1.021734386 1.046203717 1.061026298 0.892435845 1.07236181 1.007073541 0.949348932 1 22.55543404 DTIIDVVGAPLT(ph)PNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DTIIDVVGAPLTPNSR 16 0 Q9NPF5 Q9NPF5 DMAP1 DNA methyltransferase 1-associated protein 1 1 DTIIDVVGAPLT(0.984)PNS(0.016)R;DTIIDVVGAPLT(1)PNSR;DTIIDVVGAPLT(1)PNSR;DTIIDVVGAPLT(1)PNSR;DTIIDVVGAPLT(0.998)PNS(0.002)R 317.75 7.34E-57 1187531000 3087490 2513100 1649755 1872150 2479070 2361850 2517990 2848540 2751380 TRUE FALSE 2679470.374 2496591.281 2447582.036 2297250.272 2429741.357 2452711.898 2273795.717 2239401.888 2426114.991 1.104428431 1.029049031 1.008848321 0.946884332 1.001494722 1.010962756 0.937216796 0.923040292 1 21.2102165 8 0.514034896 0.957454495 6.140677104 0.673318181 0.029805663 73.15422131 0.76781965 0.018793779 411.4082041 99999999.99 -8 5.183222608 DTILDWEDSLPDRDLALADEASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DTILDWEDSLPDRDLALADEASR 23 1 M0QZ09;Q8N6T7;M0R1N9;M0QXA0;M0R1F6 M0QZ09;M0R1F6 SIRT6 NAD-dependent protein deacetylase sirtuin-6 0 ; 199.75 2.33E-24 36666000 65320 68015 37861 35363 61278 59924 63070 79809 36785 FALSE TRUE 56687.7965 67568.20499 56170.70624 43392.70964 60058.68769 62229.31506 56953.48111 62742.46642 32436.31921 1.747664282 2.083103343 1.731722576 1.337781558 1.851587639 1.918507296 1.755855242 1.934327567 1 14.98532249 1.232572102 24.99940994 0.999998699 1.798113301 0.624528766 0.193727164 137.8193553 575276.8131 0.429929496 0.048501821 17.08331317 -1.232572102 0.798114602 DTLGLFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DTLGLFLR 8 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 157.52 0.001431 0 201600 174830 133800 149060 190620 191390 174610 204750 192200 FALSE TRUE 174958.0492 173681.5302 198506.1275 182906.3512 186827.0349 198752.8971 157676.3491 160965.8059 169478.335 1.03233283 1.024800782 1.171277306 1.079231462 1.102365296 1.17273336 0.930362864 0.949772169 1 17.37074133 2.225634429 24.99999218 0.956668048 1.096631729 0.613930943 0.05121881 148.9164322 288010.705 0.021123523 0.01434467 168.1258252 -2.225634429 0.139963681 DTLRT(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DTLRTPPR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DTLRT(1)PPR;DT(0.006)LRT(0.994)PPR;DT(0.003)LRT(0.997)PPR;DT(0.109)LRT(0.891)PPR 101.39 0.0087725 3059176000 852701 683916 536790 655728 717603 694368 639515 750490 1234820 TRUE FALSE 740014.4024 679423.3108 796383.4395 804621.0646 703324.1043 721080.7863 577494.9337 590003.5538 1088840.986 0.679634962 0.623987634 0.731404723 0.738970221 0.645938308 0.662246182 0.530375823 0.541863836 1 20.05436185 3.123699234 20.58568928 0.647675764 0.691415536 0 0.132434242 12.87893198 2251.557229 0.040203106 0.045586156 1329.533346 -3.123699234 0.043739772 DTLRT(ph)PPRER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DTLRTPPRER 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DT(0.004)LRT(0.996)PPRER;DT(0.001)LRT(0.999)PPRER;DT(0.009)LRT(0.991)PPRER;DTLRT(1)PPRER 119.88 0.030199 3553060000 1835600 1535300 894180 1055010 1395590 1494070 1414500 1701460 984830 TRUE FALSE 1593020.809 1525214.513 1326608.439 1294566.145 1367820.489 1551547.84 1277322.008 1337616.02 868404.5193 1.834422523 1.756341059 1.527638801 1.490740912 1.575096005 1.786664861 1.470883648 1.540314439 1 19.72800771 0.860958231 1.467889184 1.05E-13 1.639107435 0.718029698 0.124263517 1.809571735 1.601081097 5.791984922 0.036686834 7.260361262 -0.860958231 1.639107435 DTLWHLFNTLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DTLWHLFNTLQR 12 0 Q7Z434;Q7Z434-5;Q7Z434-2 Q7Z434 MAVS Mitochondrial antiviral-signaling protein 0 ; 136.99 0.00010019 341440000 466290 438950 278970 358020 503150 599570 373380 548940 518290 FALSE TRUE 404668.5951 436066.5085 413880.8251 439313.913 493138.2994 622635.8459 337169.6651 431553.4529 457018.3466 0.88545372 0.954155368 0.905610963 0.961261 1.079033923 1.362386982 0.737759584 0.944280369 1 18.80189256 3.47310554 23.75692293 1.010927503 0.921390607 0.094479569 0.15273732 193.0308502 1141951.547 0.046228544 0.059991449 2972.388277 -3.47310554 -0.089536897 DTLYEAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DTLYEAVR 8 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;;;; 152.47 0.0010622 5069100000 3349130 3808280 2237080 2690670 3735970 3259750 3822050 3840730 3593210 FALSE TRUE 2906533.985 3783263.158 3318939.371 3301627.748 3661631.506 3385154.692 3451388.179 3019419.778 3168424.807 0.917343526 1.194051741 1.04750454 1.042040745 1.155663059 1.068403039 1.089307271 0.95297189 1 21.59533435 1.750240205 9.681616281 0.977928301 1.078882738 0.227376847 0.073744339 0.137832053 60.26341723 0.037017566 0.017267715 56.26524382 -1.750240205 0.100954437 DTMS(ph)DQALEALSASLGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DTMSDQALEALSASLGTR 18 0 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;P20810-5;E9PCH5;P20810-2;P20810-3;F8W7E0;A0A0C4DGB5;E7EVY3;H0Y9H6 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 1 DT(0.041)MS(0.959)DQALEALSASLGTR 76.301 0.016218 13943000 14370 13793 8778.9 10155 13470 10674 14304 14184 13992 TRUE FALSE 12470.96809 13702.39287 13024.4054 12460.84796 13201.97335 11084.63569 12916.80028 11150.86198 12337.8817 1.01078681 1.110595255 1.055643564 1.009966562 1.070035657 0.898422919 1.04692204 0.903790639 1 13.5908071 2.757443554 24.91590267 0.96107915 1.052627168 0.430470335 0.050918902 689.7860603 910166.7719 0.015182437 0.015156337 572.0625976 -2.757443554 0.091548018 DTNGENIAESLVAEGLATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DTNGENIAESLVAEGLATR 19 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 165.75 4.94E-11 28277000 29878 29045 17339 24426 31977 28889 17788 30918 26172 FALSE TRUE 25929.5466 28854.20148 25724.1984 29972.29663 31340.72026 30000.37852 16062.9225 24306.4263 23077.97598 1.123562423 1.250291686 1.114664407 1.298740265 1.358035917 1.299957091 0.696028218 1.053230419 1 14.49422908 2.262398494 24.99919796 0.935738731 1.243522237 0.624712331 0.118219643 147.9134892 155119.0169 0.04384576 0.033944107 182.9778391 -2.262398494 0.307783506 DTPDEPWAFPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DTPDEPWAFPAR 12 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;; 208.03 1.67E-07 1782840000 1013000 1003690 678109 790563 993554 984910 1022160 1128510 1057860 FALSE TRUE 879129.4834 997096.6943 1006044.781 970072.4121 973784.2193 1022800.125 923031.0805 887186.9186 932800.9959 0.942461991 1.068927562 1.078520268 1.03995645 1.043935656 1.096482668 0.98952626 0.951099884 1 19.8312098 2.063204085 8.105403959 0.971520597 1.047247821 0.34415258 0.042357895 0.237434162 26.92961984 0.01674208 0.01125047 115.6655654 -2.063204085 0.075727224 DTPGHGSGWAET(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DTPGHGSGWAETPR 14 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 DTPGHGSGWAET(1)PR 122.97 0.00038862 566170000 418270 398520 154670 271390 515160 464040 390770 452590 479370 TRUE FALSE 362994.5597 395902.0959 229468.9293 333013.2474 504909.3239 481891.9191 352873.1855 355807.1506 422699.4247 0.85875338 0.936604293 0.542865488 0.787825173 1.194487843 1.140034481 0.834808767 0.841749787 1 18.68927262 3.432188212 24.98065994 0.977826495 0.77349661 0.344982065 0.148989084 170.6551801 94875.65982 0.046744121 0.060346432 2705.130441 -3.432188212 -0.204329884 DTPGHGSGWAETPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DTPGHGSGWAETPR 14 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;; 192.65 3.49E-07 1623820000 1064180 1118980 495969 835320 1225670 1208340 1023260 1273720 1224980 FALSE TRUE 923545.9167 1111629.347 735821.2673 1024992.173 1201281.565 1254825.622 924024.4027 1001344.89 1080164.26 0.855005068 1.029129909 0.681212381 0.948922503 1.112128599 1.16169889 0.855448043 0.9270302 1 20.04281929 3.486336878 24.86101369 0.999655221 0.862942236 0.263083591 0.118173937 650.1123851 1753810.4 0.034751918 0.047483247 3064.339491 -3.486336878 -0.136712985 DTPRPDHPPHDGHS(ph)PASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DTPRPDHPPHDGHSPASR 18 1 Q9C0J8 Q9C0J8 WDR33 pre-mRNA 3 end processing protein WDR33 1 DTPRPDHPPHDGHS(0.935)PAS(0.065)R;DTPRPDHPPHDGHS(0.988)PAS(0.012)R;DTPRPDHPPHDGHS(0.999)PAS(0.001)R;DTPRPDHPPHDGHS(0.986)PAS(0.014)R;DTPRPDHPPHDGHS(0.999)PAS(0.001)R;DTPRPDHPPHDGHS(0.929)PAS(0.071)R;DTPRPDHPPHDGHS(0.999)PAS(0.001)R;DTPRPDHPPHDGHS(0.972)PAS(0.028)R 170.18 8.22E-12 3579837700 472929.8 370728.9 242898.6 305133.8 416872.2 418285.3 405616 430640 427743.9 TRUE FALSE 410430.9287 368293.5574 360365.1754 374419.093 408577.2588 434377.0062 366279.4228 338550.9872 377176.5034 1.088166747 0.976448835 0.955428485 0.992689337 1.083252151 1.15165447 0.971108803 0.897592995 1 18.52488028 2.012519959 24.98846319 0.939342442 1.03639593 0.288805646 0.062930524 267.0737539 533047.7987 0.027365455 0.018437083 102.9247828 -2.012519959 0.097053488 DTQS(ph)PSTCSEGLLGWSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DTQSPSTCSEGLLGWSQK 18 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DTQS(0.81)PS(0.176)T(0.015)CSEGLLGWSQK;DTQS(0.995)PS(0.005)TCSEGLLGWSQK;DTQS(0.855)PS(0.144)TCSEGLLGWSQK;DT(0.003)QS(0.935)PS(0.031)T(0.031)CSEGLLGWSQK 380.71 2.11E-108 1019790000 1031040 784380 670850 882370 850590 723280 1056690 1329390 1582050 TRUE FALSE 894785.4517 779227.3561 995275.3039 1082725.595 833664.9232 751105.0496 954212.3664 1045110.294 1395021.851 0.641413216 0.558577169 0.713447824 0.776135222 0.597599903 0.538418125 0.684012487 0.749171271 1 20.41185629 1.193110915 1.774548046 1.159883713 0.641915732 0.721334701 0.070051942 0.601370515 1.605691432 0.555181053 0.020655399 15.5995085 -1.193110915 -0.517967981 DTRPSSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DTRPSSEK 8 1 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A087WT27;A0A494C1E2;A0A494C1Q4;J3KN95;A0A494C099;A0A494C163;D6RCQ8;D6RIS6 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 ;;; 107.57 0.0036269 934700000 2474480 2034300 1319840 1741180 1253250 1890480 2346520 2662810 2620290 FALSE TRUE 2147471.198 2020936.549 1958119.039 2136541.531 1228312.777 1963207.989 2118954.852 2093388.804 2310522.301 0.929431063 0.874666541 0.847478961 0.924700675 0.531616932 0.849681472 0.917089115 0.906024063 1 21.13978758 2.256790214 4.348958398 0.934613622 0.819290126 0.187732141 0.113252272 0.362639939 15.99440953 0.046963583 0.033546088 180.630138 -2.256790214 -0.115323496 DTS(ph)GLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DTSGLER 7 0 Q9H307 Q9H307 PNN Pinin 1 DT(0.001)S(0.999)GLER;DT(0.021)S(0.979)GLER 131.5 0.003629 662640000 1774890 1411790 994730 1090240 1172100 1492350 1488860 1702280 1664240 TRUE FALSE 1540333.79 1402515.859 1475784.755 1337795.655 1148777.503 1549761.67 1344470.586 1338260.669 1467495.443 1.049634462 0.955720759 1.005648612 0.911618269 0.782815039 1.056058932 0.916166788 0.911935145 1 20.48492459 4.827251155 1.149322917 0.930718107 1.113163338 0.184377289 0.072904011 3.281680799 3.198872826 0.021560099 0.75610929 67181.72557 -4.827251155 0.182445231 DTS(ph)PSSGSAVSSSK ddPTM_MDA-MB-175_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(0.956)PS(0.001)S(0.043)GSAVSSSK;DTS(0.939)PS(0.019)S(0.042)GSAVSSSK;DTS(0.988)PS(0.012)SGSAVSSSK;DTS(0.87)PS(0.13)SGSAVSSSK;DTS(1)PSSGSAVSSSK;DTS(0.996)PS(0.004)SGSAVSSSK;DT(0.002)S(0.874)PS(0.097)S(0.025)GS(0.002)AVSSSK;DT(0.015)S(0.983)PS(0.002)SGSAVSSSK 408.62 1.46E-132 10258570000 16808260 12725200 9615480 12146060 12931020 10817070 16563580 19505590 17318940 TRUE FALSE 14587005.85 12641607.32 14265558.29 14904008.56 12673718 11233209.68 14957246.56 15334471.37 15271514.64 0.955177413 0.827790014 0.93412858 0.975935191 0.829892666 0.73556618 0.979421289 1.004122494 1 23.86433982 2.028516607 24.99549795 0.999180685 0.877425133 0.39158409 0.06979093 207.8239288 182161.8639 0.029313668 0.019762939 106.7865627 -2.028516607 -0.121755552 DTS(ph)SDKDLDDALDKLSDSLGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DTSSDKDLDDALDKLSDSLGQR 22 2 E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 E7EVY3 CAST 1 DT(0.012)S(0.551)S(0.437)DKDLDDALDKLSDSLGQR 170.27 3.83E-12 46405000 75746 55904 62849 53022 56104 40393 85195 106870 68149 TRUE FALSE 65735.97418 55536.76294 93242.98662 65061.45549 54987.64017 41946.94485 76932.80201 84016.68216 60092.50286 1.093913068 0.924187882 1.551657564 1.082688395 0.915049924 0.69803957 1.280239603 1.398122531 1 15.87489739 0.961286948 22.88715422 0.000295806 1.129970145 0.01996823 0.247418591 2199.996551 868603.8543 193309.3183 0.061940364 9.147174155 -0.961286948 1.129674339 DTSEDIEELVEPVAAHGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DTSEDIEELVEPVAAHGPK 19 0 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;; 274.23 2.12E-39 936990000 1101209 964468 685028 745236 853660 707627 1062069 1260340 1066638 FALSE TRUE 955681.4405 958132.3462 1016309.832 914453.224 836673.8362 734849.8686 959069.7118 990826.099 940541.2708 1.016097294 1.01870314 1.080558465 0.97226273 0.889566319 0.781305288 1.019699764 1.053463713 1 19.84313172 3.577562254 6.825908996 0.956420792 1.035870996 0.218192468 0.076850474 0.498710334 29.21068469 0.024486338 0.036381198 3780.613266 -3.577562254 0.079450203 DTSFEQHVLWHTGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 DTSFEQHVLWHTGGK 15 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;;;;; 242.19 3.75E-18 51953087000 29671492 27038083 16676919 21040045 28391065 27764366 34991352 37677637 34544960 FALSE TRUE 25750329.15 26860468.05 24741932.81 25817508.79 27826138.35 28832479.13 31597896.07 29620567.54 30461094.18 0.845351418 0.881795903 0.812247015 0.847556842 0.913497663 0.946534585 1.037319798 0.972406551 1 24.86046443 2.838814412 1.759076419 0.997556248 0.846403318 0.874875769 0.025694344 0.112067845 0.694648842 0.010075537 0.009691279 689.9449051 -2.838814412 -0.15115293 DTSFLGSDDIGNIDVREPELEDLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DTSFLGSDDIGNIDVREPELEDLTR 25 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 0 86.551 0.015121 45337000 58084 52133 21542 30602 48029 46177 57626 58683 34631 FALSE TRUE 50408.05223 51790.53489 31959.78325 37550.65182 47073.31687 47953.45907 52037.43939 46134.09712 30536.96263 1.650722531 1.695994966 1.04659339 1.229678677 1.541519287 1.570341479 1.704080397 1.510762471 1 14.89826895 -1.999846384 0.014710049 1.89E-05 2.681216287 0.039778626 0.253973161 98192.84528 143.8320891 15519.16146 11062.1273 0.010003538 1.999846384 2.68119741 DTSGPTPGTPS(ph)PAMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DTSGPTPGTPSPAMAR 16 0 Q9H6K5-2;Q9H6K5 Q9H6K5-2 PRR36 Proline-rich protein 36 1 DTSGPTPGT(0.001)PS(0.999)PAMAR 353.06 2.83E-87 237820000 275720 273620 160340 210830 270560 241820 231630 288160 248550 TRUE FALSE 239282.9034 271822.5722 237880.9603 258702.1738 265176.3853 251122.9719 209166.5583 226539.2265 219166.7021 1.091784934 1.240254882 1.085388236 1.180389956 1.209930079 1.145808051 0.954371974 1.033638889 1 17.7416691 2.302304314 6.821683913 1.002400925 1.163584728 0.696557035 0.050625989 0.107170233 9.139070133 0.01770422 0.013576433 200.5877072 -2.302304314 0.161183803 DTSLDFRPVVS(ph)PANGVEGVRVDQDDDQDSSSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DTSLDFRPVVSPANGVEGVRVDQDDDQDSSSLK 33 2 Q8ND24 Q8ND24 RNF214 RING finger protein 214 1 DT(0.003)S(0.003)LDFRPVVS(0.994)PANGVEGVRVDQDDDQDSSSLK;DT(0.039)S(0.039)LDFRPVVS(0.921)PANGVEGVRVDQDDDQDSSSLK 108.14 4.71E-06 139962000 149238 127401 76941 90033 131708 109307 158898 188584 55901 TRUE FALSE 129515.8202 126564.0944 114149.925 110476.3687 129087.2685 113512.111 143488.0964 148256.7792 49292.44746 2.627498265 2.567616358 2.315769065 2.241243322 2.618804201 2.30282968 2.910955 3.007697666 1 15.58907899 1.229047927 24.99968016 0.999996864 2.584421321 0.797687954 0.249075443 193.228043 507773.1679 0.872472001 0.069416676 16.94524793 -1.229047927 1.584424458 DTSLYRPALEELRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DTSLYRPALEELRR 14 2 Q13200;C9JPC0;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;;; 227.92 1.04E-12 3726270000 1623000 1559690 908580 1040990 1587160 1578030 1585950 1821160 939120 FALSE TRUE 1408516.438 1549444.294 1347972.327 1277362.69 1555578.621 1638737.835 1432144.813 1431719.106 828098.3034 1.700904871 1.871087391 1.627792644 1.542525428 1.878495119 1.97891703 1.729438168 1.728924091 1 19.65944251 1.234655359 5.086719422 0.950950644 1.761665731 0.780424263 0.126329909 0.084195673 5.720164036 0.242579784 0.033078016 17.16545657 -1.234655359 0.810715088 DTSPDKGELVS(ph)DEEEDT ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DTSPDKGELVSDEEEDT 17 1 Q9UPU7 Q9UPU7 TBC1D2B TBC1 domain family member 2B 1 DTSPDKGELVS(0.997)DEEEDT(0.003);DTSPDKGELVS(0.942)DEEEDT(0.058) 143.67 1.42E-06 352750000 990510 823220 577650 671460 822390 679010 942200 1133030 975310 TRUE FALSE 859611.5939 817812.2136 857003.4721 823925.2556 806026.048 705131.9541 850825.589 890740.3517 860009.9629 0.999536786 0.950933418 0.996504121 0.958041524 0.937228733 0.819911378 0.989320619 1.035732596 1 19.71399385 2.008196596 24.99997231 1.018051046 0.94326699 0.286538783 0.049630958 223.9665285 683104.8958 0.021087047 0.014190824 101.9052587 -2.008196596 -0.074784056 DTSPDKGELVSDEEEDT(ph) ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DTSPDKGELVSDEEEDT 17 1 Q9UPU7 Q9UPU7 TBC1D2B TBC1 domain family member 2B 1 DTSPDKGELVS(0.272)DEEEDT(0.728) 148.57 2.27E-06 190310000 506430 421950 321310 349490 423100 333780 500500 584590 528970 TRUE FALSE 439503.9924 419178.1827 476696.5907 428847.0461 414681.1378 346620.7326 451961.587 459579.9778 466435.7692 0.942260481 0.898683614 1.021998359 0.919412863 0.889042319 0.743126397 0.968968542 0.985301746 1 18.8313189 2.022139869 24.99997711 0.987261376 0.903533516 0.248586486 0.068244596 338.7962881 382561.675 0.029281855 0.019740293 105.2300724 -2.022139869 -0.08372786 DTSQSDKDLDDALDKLSDSLGQR ddPTM_MDA-MB-175_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 ; 187.79 1.31E-17 1301780000 2208180 1694240 1577920 1424170 1521390 1021140 2338460 2853300 1463620 FALSE TRUE 1916363.418 1683110.426 2341007.39 1747549.566 1491117.316 1060423.917 2111676.509 2243143.999 1290592.511 1.48487102 1.30413776 1.813901266 1.354067648 1.15537422 0.821656648 1.636207007 1.738073002 1 20.29960213 3.509296468 24.53426464 1.326569202 1.523403089 0.126791731 0.296283272 1502.538451 1145712.429 0.089096699 0.131998457 3230.698779 -3.509296468 0.196833888 DTSSDKDLDDALDKLSDSLGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DTSSDKDLDDALDKLSDSLGQR 22 2 E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 E7EVY3 CAST 0 ;;; 153.77 1.77E-08 719884000 724980 568059 496373 468575 511486 341874 771349 913210 509224 FALSE TRUE 629172.0561 564327.383 736420.6431 574972.1155 501308.4293 355026.114 696543.6927 717927.1481 449024.1188 1.401198799 1.256786349 1.640046964 1.28049272 1.116439871 0.790661568 1.551238928 1.598860992 1 18.77643341 3.510415682 24.23704614 1.258327625 1.422618569 0.121603286 0.254421147 1308.765113 952726.3479 0.076792354 0.113797449 3239.035305 -3.510415682 0.164290943 DTSSS(ph)PTTGSTVQSVDLIFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DTSSSPTTGSTVQSVDLIFTR 21 0 P57060 P57060 RWDD2B RWD domain-containing protein 2B 1 DT(0.005)S(0.037)S(0.282)S(0.674)PT(0.002)TGSTVQSVDLIFTR;DTSS(0.001)S(0.997)PT(0.002)TGSTVQSVDLIFTR;DTSS(0.002)S(0.955)PT(0.043)TGSTVQSVDLIFTR 268.07 3.22E-37 184531000 301075 267553 197093 234476 275942 267953 297900 331688 313502 TRUE FALSE 261287.1759 265795.4267 292407.834 287717.3595 270451.2941 278261.3253 269009.7039 260759.1024 276440.1507 0.945185333 0.961493568 1.05776181 1.040794395 0.978335793 1.006587953 0.973120956 0.94327507 1 18.07660765 0.924702759 22.06109405 1.56276881 0.987720803 0.009129137 0.037789342 1139.008315 1059910.986 70856.21552 0.009752726 8.408194688 -0.924702759 -0.575048007 DTSVLQWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DTSVLQWR 8 0 O95834;O95834-2;O95834-3 O95834 EML2 Echinoderm microtubule-associated protein-like 2 0 ;; 155.82 0.00093732 1235890000 1327570 1411320 791270 992780 1477560 1376470 1385910 1493870 1387290 FALSE TRUE 1152128.261 1402048.946 1173930.819 1218205.873 1448159.447 1429423.692 1251504.662 1174417.526 1223286.157 0.94183054 1.146133256 0.959653481 0.995847019 1.183827217 1.168511295 1.023067787 0.96005135 1 20.22233049 2.001862155 24.99903653 0.981488397 1.069352021 0.152695542 0.083886961 101.7171869 1365516.768 0.035114732 0.023488916 100.4296976 -2.001862155 0.087863624 DTTALSFFHMLNGAALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DTTALSFFHMLNGAALR 17 0 P42704 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ; 159.18 3.25E-09 236590000 161145 182837 97550 177511 194614 215020 164636 205511 182147 FALSE TRUE 139849.28 181635.9317 144725.5063 217817.5856 190741.5622 223291.9585 148669.6261 161564.0719 160613.7892 0.870717768 1.130886287 0.901077716 1.356157443 1.187578994 1.390241521 0.925634261 1.00591657 1 17.29323623 4.742211984 23.89138824 1.107211781 0.870717595 0.17328823 0.165434071 386.4338079 2528280.001 0.041598928 0.29698327 55234.69803 -4.742211984 -0.236494186 DTTINEIEDTFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DTTINEIEDTFR 12 0 Q16864;Q16864-2 Q16864 ATP6V1F V-type proton ATPase subunit F 0 ;; 251.81 1.12E-20 192730000 227131 202315 143305.1 164915.7 208021 191723 181560 235126 219547 FALSE TRUE 197115.0629 200985.9794 212607.9257 202362.3303 203881.7891 199098.7079 163952.3391 184846.1347 193592.4038 1.018196267 1.038191456 1.098224525 1.045300985 1.053149737 1.028442769 0.846894485 0.954821217 1 17.56266282 2.413004821 9.590481909 0.934722616 1.051137985 0.620210468 0.042017378 0.224119362 31.62827665 0.015555111 0.012039935 258.8241644 -2.413004821 0.116415369 DTTLIRHS(ph)PQPSPSSSFNEGLLTGGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DTTLIRHSPQPSPSSSFNEGLLTGGHR 27 1 Q9Y2J4;Q9Y2J4-2;Q9Y2J4-4;Q9Y2J4-3 Q9Y2J4 AMOTL2 Angiomotin-like protein 2 1 DT(0.063)T(0.063)LIRHS(0.875)PQPSPSSSFNEGLLTGGHR;DT(0.105)T(0.084)LIRHS(0.811)PQPS(0.001)PSSSFNEGLLTGGHR 241.4 2.01E-45 570480000 264485 199336 98837 140765 202707 224753 203568 216425 129830 TRUE FALSE 229532.6371 198026.5487 146634.9038 172727.8447 198673.5273 233399.3933 183826.0067 170144.198 114481.6453 2.004973256 1.729766795 1.280859507 1.508781991 1.735418169 2.038749467 1.60572471 1.486213773 1 16.80475679 1.238512754 1.943085872 0.770594943 1.692170847 0.507624263 0.218769738 0.751727063 2.731351907 1.272571248 0.06376306 17.31859888 -1.238512754 0.921575904 DTTS(ph)PMELAALEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DTTSPMELAALEK 13 0 Q6VY07-2;Q6VY07 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 DTT(0.001)S(0.999)PMELAALEK;DTTS(1)PMELAALEK 293.8 1.35E-40 91498000 398450 360860 269260 338690 365190 291870 433900 547640 473110 TRUE FALSE 345793.823 358489.4869 399475.0366 415594.7411 357923.4335 303098.4278 391820.4448 430531.4477 417179.4748 0.828885034 0.859317173 0.957561579 0.996201314 0.857960315 0.726542043 0.939213141 1.032005345 1 18.67030865 1.998499035 24.99989701 1.008484931 0.875674915 0.407014599 0.072163804 58.3096511 971203.2371 0.032300432 0.021413808 99.65498668 -1.998499035 -0.132810017 DTTVISHS(ph)PNTSYDTALEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DTTVISHSPNTSYDTALEAR 20 0 Q4VCS5;E7ERM3;Q4VCS5-2;A6NP16 Q4VCS5 AMOT Angiomotin 1 DTTVISHS(1)PNTSYDTALEAR 197.38 1.07E-21 108950000 114220 85091 54615 70615 82535 99958 96442 101870 103020 TRUE FALSE 99125.5376 84532.03162 81026.99668 86649.21503 80892.71498 103803.4489 87089.06968 80085.89325 90841.09296 1.091197104 0.930548377 0.891964132 0.953854827 0.890485928 1.142692647 0.95869685 0.881604246 1 16.47105744 2.550294618 0.005702876 1.40E-07 1.921804167 0.001139038 0.086597231 86779.18665 429.7598358 72836.56422 71980.73714 355.0541701 -2.550294618 1.921804026 DTVTISGPQAPVFEFVEQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DTVTISGPQAPVFEFVEQLR 20 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 206.63 1.74E-21 311265000 77183.1 64569.6 52726 64068.8 81267.7 76774.6 76037 87189.3 121844.2 FALSE TRUE 66983.15778 64145.43805 78224.46996 78616.60027 79650.63177 79728.16854 68662.94344 68544.5467 107439.9175 0.623447591 0.597035437 0.728076415 0.731726179 0.741350456 0.742072131 0.639082243 0.637980262 1 16.71317058 1.233900705 24.99990097 1.000000481 0.680567694 0.776870889 0.053879194 74.30871736 398608.1728 0.114191065 0.014535925 17.13565482 -1.233900705 -0.319432787 DTVTISGPQAPVFEFVEQLRK ddPTM_MDA-MB-175_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 ; 269.9 9.02E-38 7474400000 2822900 2654000 1673260 1656710 2417880 2443200 3248400 3656600 1125170 FALSE TRUE 2449846.613 2636565.699 2482454.133 2032891.327 2369768.919 2537191.485 2933370.668 2874664.546 992153.6844 2.469220899 2.657416629 2.502086291 2.048968178 2.388509921 2.557256527 2.95656884 2.897398448 1 19.92020409 1.231318468 24.99993803 0.999997252 2.573983322 0.787110308 0.254819388 134.4336998 464025.1468 0.717286036 0.0718057 17.03407158 -1.231318468 1.57398607 DTYGVRPLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DTYGVRPLFK 10 1 P08243-2;P08243;P08243-3;F8WEJ5;C9J057;C9JT45 P08243-2 ASNS Asparagine synthetase [glutamine-hydrolyzing] 0 ; 112.13 0.0015155 378300000 1430650 1092670 551300 741310 1090850 929310 1122650 1446780 1102520 FALSE TRUE 1241585.978 1085492.179 817910.524 909635.7657 1069144.219 965061.157 1013775.576 1137397.356 972181.3416 1.277113564 1.116553191 0.841314772 0.935664702 1.099737439 0.992676074 1.04278444 1.169943618 1 19.89086592 0.94163042 21.45241812 6.56E-05 1.055951343 0.022511606 0.121203059 605.2987919 493340.0644 36403.51142 0.029820462 8.742394894 -0.94163042 1.055885786 DTYHPMSEYPTYHTHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 DTYHPMSEYPTYHTHGR 17 0 P15941-2;A0A087WWM1;A0A087X2A4;A0A0C4DGW3;P15941-7;P15941-11;P15941-4;P15941-3;P15941;P15941-8;A0A087WVJ0;A0A0A0MSH4;A0A0A0MRB3;B1AVQ7;A0A087X0L2;P15941-15;P15941-17;P15941-6;A6ZIE3;A6ZIE4;P15941-12;P15941-16;P15941-9;P15941-10 P15941-2 MUC1 Mucin-1;Mucin-1 subunit alpha;Mucin-1 subunit beta 0 ;;;;;;;;; 129.38 1.18E-05 5670490000 1752848 1610993 913054 1698791 2117659 2315640 1065382 2286006 1842967 FALSE TRUE 1521204.696 1600410.281 1354609.968 2084527.461 2075521.729 2404724.169 962061.4176 1797161.407 1625093.541 0.936072083 0.984811176 0.833558152 1.282712292 1.277170622 1.479745079 0.592003718 1.105881823 1 20.63209133 3.755229909 24.97362081 1.109256944 0.924813544 0.145004024 0.23264103 1908.433012 2859170.979 0.063871349 0.110253654 5691.541526 -3.755229909 -0.1844434 DVAEAKPELSLLGDGDH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVAEAKPELSLLGDGDH 17 1 H7C5G1;Q2TAA2-2;Q2TAA2 H7C5G1 IAH1 Isoamyl acetate-hydrolyzing esterase 1 homolog 0 75.376 0.020209 221380000 112480 88383 56595 52538 74964 82255 90912 99355 104210 FALSE TRUE 97615.48301 87802.40625 83964.5313 64467.55589 73472.36306 85419.40308 82095.36823 78108.70643 91890.41252 1.062303241 0.955512157 0.913746375 0.701569991 0.799565059 0.929579058 0.893405155 0.850020196 1 16.48762672 4.46375072 2.176581742 0.861788411 1.063593042 0.391794704 0.079057845 0.414098347 3.274898011 0.021643045 0.129793689 29090.46876 -4.46375072 0.201804631 DVAIKEPLVDVVDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVAIKEPLVDVVDPK 15 1 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ; 173.34 8.90E-07 372270000 1004200 711310 594020 643130 648720 457540 1028880 1207870 833520 FALSE TRUE 871492.4257 706637.3578 881290.0589 789162.4961 635811.7412 475141.8599 929099.376 949576.4002 734982.2151 1.185732672 0.961434635 1.199063108 1.073716452 0.86507092 0.646467153 1.264111371 1.291971942 1 19.48734981 0.93911075 19.1041299 0.000229999 1.068663308 0.008007541 0.197202381 59.61462685 183792.8262 23140.57051 0.050531911 8.69182052 -0.93911075 1.068433309 DVCLYPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DVCLYPR 7 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;; 114.19 0.013869 1160490000 1689530 1317660 846070 979640 1336490 1397650 1330410 1463560 1424030 FALSE TRUE 1466254.33 1309004.205 1255232.282 1202082.235 1309896.464 1451418.5 1201387.043 1150589.083 1255682.796 1.167694847 1.042464076 0.99964122 0.957313614 1.043174652 1.155879897 0.956759977 0.916305525 1 20.26004063 DVCTELLPLIKPQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVCTELLPLIKPQGR 15 1 P16152 P16152 CBR1 Carbonyl reductase [NADPH] 1 0 93.494 0.0044098 414000000 178240 192820 118810 151670 172260 161190 187580 230860 194380 FALSE TRUE 154685.1324 191553.3527 176266.9134 186108.9916 168832.363 167391.0836 169388.5205 181492.3856 171400.6178 0.902477099 1.117576793 1.028391354 1.08581284 0.98501607 0.976607236 0.988260851 1.058878246 1 17.38701278 3.203306447 24.99985863 1.006624078 1.039196073 0.059609275 0.059259311 518.7868617 367887.0502 0.017176314 0.019476887 1597.005628 -3.203306447 0.032571995 DVDAVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVDAVDK 7 0 P23297;Q5T7Y6 P23297 S100A1 Protein S100-A1;Protein S100 0 ;;; 102.72 0.019862 2221120000 4163140 3866660 3184720 3393650 2451030 2935470 4006910 4139670 5782100 FALSE TRUE 3612970.501 3841259.656 4724861.244 4164230.101 2402259.298 3048399.43 3618320.485 3254433.785 5098546.725 0.708627516 0.753402854 0.926707452 0.816748443 0.471165496 0.597895752 0.709676831 0.638306161 1 22.28165465 5.071756947 12.78831998 0.725780856 0.56684385 0 0.154092489 4652659.503 23832727.29 0.03859381 18868221.88 117966.0253 -5.071756947 -0.158937006 DVDDDGEEKELMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVDDDGEEKELMER 14 1 Q5STZ8;Q8NE71;Q8NE71-2;A0A0G2JIC2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 153.09 5.92E-06 262230000 339610 239400 249420 215350 226100 164270 328480 354650 265710 FALSE TRUE 294729.678 237827.3656 370040.3463 264248.5089 221601.0524 170589.5732 296624.0602 278810.8574 234298.0665 1.257926207 1.015063288 1.579357234 1.127830515 0.945808285 0.72808784 1.266011558 1.189983603 1 17.83798552 3.487717006 24.80696377 1.048426201 1.27327427 0.262245141 0.195354191 732.4713108 1714874.039 0.057086495 0.078855795 3074.093025 -3.487717006 0.224848069 DVDDFFEHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVDDFFEHER 10 0 G3V5X9;Q9UNH7;A0A0A0MRI2;Q9UNH7-2 G3V5X9;Q9UNH7-2 SNX6 "Sorting nexin-6;Sorting nexin-6, N-terminally processed" 0 ;;; 192.5 6.76E-07 1145170000 1643945 1479993 1079019 1330721 1487867 1378429 1433504 1738951 1770440 FALSE TRUE 1426693.503 1470270.829 1600836.198 1632881.542 1458261.358 1431458.056 1294483.003 1367089.861 1561140.6 0.913878931 0.941792705 1.025427305 1.045954184 0.934099951 0.9169309 0.829190531 0.875699384 1 20.57416905 2.89343913 3.212386534 0.893440933 0.982388363 0.270019902 0.05676761 0.306720838 5.996872214 0.020035899 0.020403052 782.4185346 -2.89343913 0.08894743 DVDDGSGS(ph)PHS(ph)PHQLSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DVDDGSGSPHSPHQLSSK 18 0 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 2 DVDDGS(0.045)GS(0.955)PHS(1)PHQLSSK;DVDDGS(0.001)GS(0.999)PHS(0.997)PHQLS(0.002)SK;DVDDGS(0.444)GS(0.556)PHS(1)PHQLSSK 185.62 2.75E-14 1019120000 1750040 1381020 929340 1158290 1373940 1143280 1688830 1857280 1736350 TRUE FALSE 1518767.78 1371947.989 1378771.932 1421297.448 1346601.282 1187262.721 1525047.527 1460115.125 1531080.681 0.991958032 0.896065116 0.900522062 0.928296899 0.879510335 0.775440992 0.996059545 0.953650022 1 20.54611888 DVDEIEAWISEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DVDEIEAWISEK 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;;; 267.57 1.66E-21 414601000 749422 634421 484024 578632 578140 508375 722254 893910 770347 FALSE TRUE 650383.9839 630253.4467 718099.6254 710019.2394 566636.1451 527932.5152 652209.9182 702754.3029 679277.4552 0.957464404 0.927829184 1.057152155 1.045256594 0.834174814 0.777197169 0.960152458 1.0345615 1 19.37364145 1.905833418 5.987424009 1.015226099 0.933790824 0.142492717 0.083922333 0.497501614 25.63433638 0.04652583 0.024806069 80.50695812 -1.905833418 -0.081435275 DVDELPSLQPSVGS(ph)PSRPSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVDELPSLQPSVGSPSRPSSSR 22 1 O43815-2;O43815 O43815-2 STRN Striatin 1 DVDELPSLQPS(0.051)VGS(0.915)PS(0.034)RPSSSR 156.08 8.72E-09 390150000 441130 437410 331650 409970 486880 457550 502470 530990 525160 TRUE FALSE 382833.5528 434536.6249 492037.0493 503059.9545 477192.0406 475152.2446 453740.5367 417441.9207 463076.1831 0.826718296 0.938369626 1.062540177 1.08634383 1.030482797 1.026077915 0.979839934 0.901454093 1 18.82089003 4.598734988 3.327325045 1.004479933 0.824727116 0.578808954 0.050493144 0.240820461 4.375755949 0.015292175 0.087916546 39694.92516 -4.598734988 -0.179752817 DVDELPSLQPSVGSPS(ph)RPSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVDELPSLQPSVGSPSRPSSSR 22 1 O43815-2;O43815 O43815-2 STRN Striatin 1 DVDELPS(0.006)LQPS(0.26)VGS(0.324)PS(0.404)RPS(0.002)S(0.002)S(0.002)R 64.289 0.015413 340810000 350790 357690 257910 316960 284410 307670 323030 422280 365930 TRUE FALSE 304432.2127 355340.3108 382636.1387 388930.6124 278750.7974 319506.264 291702.6003 331978.7082 322670.1723 0.943478012 1.101249329 1.185842918 1.205350373 0.863887714 0.990194606 0.904027163 1.028848455 1 18.2997007 3.240564994 24.99999871 0.963961518 1.113918145 0.447941457 0.083365048 51.75298988 645495.2853 0.025003928 0.030674479 1740.063086 -3.240564994 0.149956627 DVDFELIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DVDFELIK 8 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;; 140.09 0.0015242 244194000 861130 754940 597650 753860 714820 601880 875510 1046720 1143500 FALSE TRUE 747329.4887 749980.7494 886675.539 925035.435 700596.4805 625034.7131 790603.175 822887.0736 1008316.733 0.741165414 0.743794807 0.879362119 0.917405618 0.694817866 0.619879342 0.784082173 0.81609979 1 19.94351746 1.207736728 2.421507669 1.071893349 0.769935174 0.425044158 0.0841029 0.690781051 4.047102769 0.457961645 0.024248297 16.13380219 -1.207736728 -0.301958175 DVDFMYVELIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVDFMYVELIQR 12 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 172.8 8.09E-05 303642000 295191 282708 170688 206352 230251 203050 327710 305500 294442 FALSE TRUE 256180.7614 280850.8725 253233.2877 253207.3755 225669.4556 210861.4649 295928.7346 240171.2024 259633.4022 0.986701862 1.081720881 0.975349418 0.975249615 0.869184988 0.81215076 1.139794542 0.925039692 1 17.98611647 4.063595241 6.564443775 0.954442868 1.034093354 0.122459691 0.088049153 0.433589681 34.7012969 0.022521122 0.047491921 11576.97888 -4.063595241 0.079650487 DVDIIDHHDNTYTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DVDIIDHHDNTYTVK 15 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;; 144.12 2.48E-06 2285360000 5709450 4409980 2960180 3540540 3941800 3382520 5223990 5558380 5464820 FALSE TRUE 4954931.717 4381010.551 4391732.949 4344473.721 3863365.892 3512647.733 4717368.254 4369763.692 4818775.205 1.028255419 0.909154373 0.911379503 0.901572191 0.801731919 0.728950321 0.978955866 0.906820407 1 22.20023507 5.104425652 1.465682488 0.886418459 1.231344046 0.235076871 0.077880381 4.932169834 4.793447985 0.02260329 3.213534307 127182.0005 -5.104425652 0.344925586 DVDKFGNEITQLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVDKFGNEITQLAR 14 1 Q8TAT6;Q8TAT6-2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 ; 145.55 7.80E-06 594350000 502020 406730 285770 378850 412510 390310 400270 554910 542190 FALSE TRUE 435676.785 404058.1638 423969.3278 464873.6829 404301.8581 405325.4783 361451.877 436246.8148 478092.9159 0.91128057 0.845145683 0.886792742 0.972350076 0.845655404 0.847796453 0.756028515 0.912472869 1 18.8669315 1.345952355 4.193004604 1.000112796 0.866851632 0.369102034 0.055182966 0.236466777 5.999240075 0.072795941 0.014376216 22.17953083 -1.345952355 -0.133261164 DVDLEFLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVDLEFLAK 9 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 157.68 0.00015813 592288000 2424710 1413420 994250 1219120 1306810 1099370 1648360 1962900 1741970 FALSE TRUE 2104278.43 1404135.151 1475072.626 1495939.829 1280807.038 1141663.475 1488502.301 1543149.11 1536036.291 1.369940569 0.914128891 0.960311051 0.973896149 0.833839047 0.743252931 0.969054123 1.004630632 1 20.55078087 4.739597242 24.95221235 0.9273061 1.369940713 0.748788932 0.081001814 48.25871527 1161459.718 0.021762119 0.129402445 54903.14744 -4.739597242 0.442634613 DVDREDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVDREDR 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 153.71 0.0015757 1461952000 2233566 2148450 1304988 1610833 1439055 2208056 2086830 2431073 2102842 FALSE TRUE 1938394.594 2134336.69 1936084.562 1976597.253 1410420.621 2293001.343 1884449.548 1911206.958 1854246.414 1.045381336 1.151053427 1.04413553 1.065984131 0.760643575 1.236621695 1.01628863 1.030718972 1 20.82240155 3.916810937 2.981967748 1.018094153 1.097331193 0.068757794 0.116865382 0.719302475 12.38016197 0.030819937 0.062971329 8256.784263 -3.916810937 0.079237039 DVDVSEDS(ph)PPPLPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DVDVSEDSPPPLPER 15 0 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 DVDVSEDS(1)PPPLPER;DVDVS(0.016)EDS(0.984)PPPLPER;DVDVSEDS(1)PPPLPER;DVDVS(0.012)EDS(0.988)PPPLPER;DVDVS(0.003)EDS(0.997)PPPLPER;DVDVS(0.025)EDS(0.975)PPPLPER 260.29 7.10E-25 6866150000 3526250 3301050 2756700 3383990 3444430 3424260 3486540 4018690 5460340 TRUE FALSE 3060247.128 3279365.185 4089849.341 4152376.651 3375892.582 3555993.498 3148415.887 3159324.417 4814824.826 0.635588467 0.681097507 0.849428482 0.862414896 0.701145463 0.73855096 0.653900402 0.656166015 1 22.19905188 4.461163159 23.24425856 0.761290765 0.646965661 0.174371814 0.106366424 171.3854881 249637.0125 0.027124095 0.071832964 28917.66075 -4.461163159 -0.114325105 DVDVSEDS(ph)PPPLPERTPESFVLASEHNTPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVDVSEDSPPPLPERTPESFVLASEHNTPVR 31 1 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 DVDVS(0.038)EDS(0.961)PPPLPERT(0.001)PESFVLASEHNTPVR 144.82 1.15E-08 125250000 111210 101720 20355 38763 106920 95884 137530 154150 22947 TRUE FALSE 96513.31673 101051.7946 30198.74608 47564.73161 104792.5012 99572.71953 124192.3618 121186.2221 20234.2318 4.769803849 4.994100869 1.492458245 2.350706074 5.178971073 4.921003204 6.137735447 5.989168419 1 14.30451046 3.219201983 24.97499727 4.939058439 3.379125997 0.099202674 1.740782651 457.1373049 589761.2065 0.538426563 0.611412686 1656.540212 -3.219201983 -1.559932443 DVDWGEVDYLIVDTPPGTSDEHLSVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVDWGEVDYLIVDTPPGTSDEHLSVVR 27 0 I3L3A0;I3L531;P53384-2;P53384 I3L3A0 NUBP1 Cytosolic Fe-S cluster assembly factor NUBP1 0 118.05 0.00042971 67741000 26300 30724 6041.6 19680 33296 35087 33219 34370 34654 FALSE TRUE 22824.38836 30522.17202 8963.337968 24148.64479 32633.47474 36436.81959 29997.42649 27020.24297 30557.2436 0.746938718 0.998852266 0.293329401 0.790275625 1.067945629 1.192411857 0.981679725 0.88425001 1 14.89922679 3.375228784 5.219717261 1.011046692 0.686186838 0.42678577 0.185728349 0.212913416 9.100389161 0.054968745 0.071471891 2372.62326 -3.375228784 -0.324859854 DVDYVCISDNYWLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVDYVCISDNYWLGK 15 0 Q96KP4;Q96KP4-2;J3QKT2;J3QRH4;J3QRA8;J3KRJ8 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 155.02 5.53E-06 33682000 114210 83444 62574 75282 88099 75568 106910 108770 105060 FALSE TRUE 99116.85913 82895.85087 92834.9957 92375.92871 86346.00226 78475.14986 96541.88466 85510.38195 92639.92648 1.069915132 0.894817753 1.002105671 0.997150281 0.93206035 0.847098577 1.042119616 0.923040261 1 16.49934649 4.759967515 23.69337999 0.955136643 1.069915371 0.279097582 0.058140903 3548.303299 3927171.14 0.013406615 0.55934322 57539.68962 -4.759967515 0.114778728 DVEDEETWIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DVEDEETWIR 10 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;;;; 260.23 6.12E-17 2961260000 2777930 2575970 1842160 2095550 2549120 2488840 2515030 3017060 2639720 FALSE TRUE 2410819.512 2559048.283 2733034.738 2571376.656 2498397.499 2584587.285 2271122.778 2371885.198 2327655.309 1.035728745 1.099410327 1.174157843 1.104706804 1.073353726 1.110382313 0.975712671 1.019001907 1 21.150446 2.244708204 24.9780907 1.001625398 1.102038557 0.64088174 0.035716023 90.4939886 367685.5881 0.013903908 0.010492107 175.6742887 -2.244708204 0.100413158 DVEDEILWVGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DVEDEILWVGER 12 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;;;; 250.76 5.76E-17 1152101000 1245166 1129894 813292 869023 1118064 1060373 1105321 1351671 1215579 FALSE TRUE 1080614.158 1122471.652 1206602.731 1066347.954 1095816.714 1101166.235 998127.1395 1062626.675 1071874.635 1.008153493 1.04720423 1.125693893 0.994843911 1.022336641 1.02732745 0.931197648 0.991372163 1 20.03170475 2.94300689 1.259013187 0.978776118 1.053528734 0.34441749 0.039790889 0.472660115 1.595904702 0.01862258 0.018988173 877.0147352 -2.94300689 0.074752616 DVEDEILWVTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVEDEILWVTER 12 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 ;;; 182.46 3.92E-05 181945000 252798 231417 194900 220372 261403 257106 235482 307237 294375 FALSE TRUE 219390.1038 229896.8065 289154.2919 270410.8308 256201.5917 266997.0342 212644.9919 241536.7585 259574.3229 0.845191856 0.885668521 1.113955682 1.041747226 0.987006684 1.028595707 0.819206575 0.930510984 1 17.98578815 1.209409792 22.1693764 1.000000956 0.957412508 0.02182547 0.091363877 4547.353479 3457511.335 1.844959767 0.023564243 16.19607547 -1.209409792 -0.042588447 DVEDMELS(ph)DVEDDGSK ddPTM_MDA-MB-175_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 401.65 1.06E-139 1719390000 3154429 2018618 2289945 2491831 2054858 1684216 2682919 3194078 4425469 TRUE FALSE 2737563.215 2005357.565 3397370.061 3057639.314 2013970.346 1749008.879 2422729.928 2511049.276 3902295.096 0.701526447 0.513891829 0.870608188 0.783548973 0.516098936 0.448200056 0.620847442 0.64348011 1 21.89589145 1.238419566 6.661640297 1.009436711 0.634429052 0.444939215 0.127330078 0.118281618 26.24486704 0.200794089 0.032961951 17.3148832 -1.238419566 -0.37500766 DVEDMFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVEDMFSR 8 0 Q15717;Q15717-2;M0QZR9;M0R055 Q15717 ELAVL1 ELAV-like protein 1 0 ;;; 245.65 1.18E-08 1909480000 3086350 2703850 1739170 2087610 2681310 2576510 2784170 3157850 2796030 FALSE TRUE 2678481.028 2686088.231 2580238.429 2561633.758 2627957.177 2675630.007 2514161.622 2482568.352 2465486.519 1.086390458 1.089475935 1.046543313 1.038997268 1.065898011 1.085234085 1.019742596 1.006928382 1 21.23344093 2.115328366 5.076526421 1.006616515 1.06706272 0.744790798 0.016642545 0.113029821 4.561316406 0.007704191 0.005089295 130.4152463 -2.115328366 0.060446205 DVEEEKFPTQLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DVEEEKFPTQLSR 13 1 Q2TAY7;Q2TAY7-2 Q2TAY7 SMU1 "WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed" 0 ;; 95.195 0.0043845 1154770000 1112630 790880 686830 767890 838630 595292 989780 1091100 1234920 FALSE TRUE 965593.1265 785684.6572 1018983.285 942251.161 821942.9038 618193.2684 893791.2879 857776.7559 1088929.164 0.886736399 0.721520447 0.935766364 0.865300693 0.754817605 0.567707514 0.820798374 0.787725027 1 20.05447868 5.060794429 9.734715542 0.802725214 1.214940215 0.042566619 0.117948876 31107.47531 224801.5922 0.028923352 218520.9476 115025.5793 -5.060794429 0.412215 DVEPEDPMFLMDPFAIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVEPEDPMFLMDPFAIHR 18 0 Q15773;F5H7L5;F5H800;F5H0Y3 Q15773 MLF2 Myeloid leukemia factor 2 0 ;;; 208.26 6.52E-16 273554000 371558 349049 228782 278665 306234 317323 334188 395187 362222 FALSE TRUE 322455.6689 346756.0741 339421.7404 341940.1474 300140.5425 329530.6211 301778.4992 310679.3354 319400.5278 1.009565235 1.085646528 1.062683718 1.070568511 0.939699582 1.031715957 0.944827804 0.972695122 1 18.28500717 3.250257036 24.99423 0.977375542 1.059551605 0.60078201 0.032104444 138.8398335 296686.8769 0.008665301 0.011090506 1779.332191 -3.250257036 0.082176063 DVES(ph)PSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DVESPSWR 8 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 1 DVES(0.925)PS(0.075)WR;DVES(1)PSWR;DVES(0.993)PS(0.007)WR;DVES(1)PSWR;DVES(1)PSWR;DVES(1)PSWR 222.07 5.45E-06 3764140000 3050610 2810350 2035940 2469680 2831740 3056420 2796150 3370330 3265440 TRUE FALSE 2647464.159 2791888.626 3020527.394 3030458.591 2775393.914 3174002.455 2524979.803 2649611.157 2879403.403 0.919448854 0.969606628 1.049011538 1.052460585 0.963878111 1.102312532 0.876910752 0.920194494 1 21.45733849 2.218625175 24.99451737 0.927521465 1.009323293 0.2716686 0.059321511 302.5775501 379360.7287 0.023994922 0.01620243 165.434154 -2.218625175 0.081801828 DVESCHDMAALNILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVESCHDMAALNILK 15 0 O95793-2;O95793-3;O95793;Q5JW30;A0A087X1A5 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 117.08 0.00039807 141350000 156010 151270 54650 118170 164770 132230 169690 170150 170290 FALSE TRUE 135392.8832 150276.2974 81078.92279 145002.3046 161491.3994 137316.9737 153233.4899 133764.7466 150158.5102 0.901666399 1.000784419 0.539955562 0.965661583 1.07547284 0.914480128 1.020478225 0.890823613 1 17.19612672 3.527915671 24.99953406 0.973507674 0.819468378 0.274332609 0.125337461 490.9845883 241646.9927 0.033414806 0.049561469 3372.218222 -3.527915671 -0.154039296 DVESPSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVESPSWR 8 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 155.88 0.0011524 257760000 464470 426010 295050 371610 449740 465970 396780 479130 487820 FALSE TRUE 403089.1127 423211.5123 437737.1669 455989.7302 440791.0539 483896.1674 358300.3367 376671.7781 430150.4753 0.937088614 0.983868522 1.017637297 1.060070269 1.024736875 1.124946258 0.832965107 0.875674443 1 18.71448191 2.227658678 24.9999917 0.894298946 1.024152574 0.450285386 0.063225037 184.8434646 423873.6407 0.026024258 0.017734426 168.9112899 -2.227658678 0.129853628 DVESYIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVESYIHR 8 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;; 201.39 0.00011215 1622160000 2165550 2143910 1414500 1954370 2228380 1950770 1847400 2141660 3284520 FALSE TRUE 1879367.081 2129826.514 2098556.931 2398139.579 2184039.598 2025817.384 1668239.432 1683682.675 2896227.787 0.648901681 0.73537949 0.724582832 0.828021743 0.754098005 0.69946756 0.576004222 0.581336414 1 21.46574364 2.58283587 5.487090264 0.678505947 0.741717243 0 0.124692722 0.789498975 33.99036075 0.043712663 0.038183321 382.6800919 -2.58283587 0.063211296 DVFFYQADDEHYIPR ddPTM_MDA-MB-175_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 ;;;; 284.38 5.65E-34 1750580000 1785412.8 1832788 1098155.1 1345900.2 1633980.5 1774914.7 1723557.7 2067078.8 1974336.9 FALSE TRUE 1549465.975 1820748.295 1629226.579 1651507.411 1601467.485 1843196.817 1556407.34 1625050.085 1740933.041 0.890020431 1.045846252 0.935835291 0.948633504 0.919890339 1.058740787 0.894007583 0.933436293 1 20.73142928 DVFHMVVEVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVFHMVVEVPR 11 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;; 151.79 3.33E-05 1397060000 1222921 1125416 975909 1204209 1110924 1112920 1093945 1271380 3039700 FALSE TRUE 1061308.891 1118023.068 1447861.857 1477643.059 1088818.786 1155734.753 987854.3823 999505.2809 2680350.129 0.39595905 0.417118292 0.54017639 0.551287327 0.406222595 0.431187978 0.368554232 0.372901014 1 21.35399004 1.234751448 24.99999999 1.000000808 0.434637358 0.888523767 0.062845795 38.68141963 253832.9235 0.125641245 0.01719071 17.16925487 -1.234751448 -0.56536345 DVFHTTVNFINQNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVFHTTVNFINQNLR 15 0 P55957;P55957-2;P55957-4 P55957 BID BH3-interacting domain death agonist;BH3-interacting domain death agonist p15;BH3-interacting domain death agonist p13;BH3-interacting domain death agonist p11 0 ; 282.24 8.24E-34 2445100000 572350 586690 227087 473540 704940 663660 594260 689860 700180 FALSE TRUE 496712.4973 582835.9948 336907.0328 581064.4946 690913.0732 689191.4296 536628.7567 542338.8075 617405.518 0.804515805 0.944008399 0.545681927 0.941139134 1.119058792 1.116270279 0.869167413 0.878415874 1 19.23585885 3.50124688 24.71203408 0.982954381 0.776120624 0.413122185 0.125856378 733.1541026 750972.5688 0.036120018 0.053229917 3171.369751 -3.50124688 -0.206833757 DVFISAAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DVFISAAER 9 0 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ;; 168.25 0.00013811 931352000 1248480 1201380 728476 918956 1205880 1372730 1101960 1177850 1154070 FALSE TRUE 1083490.205 1193488.056 1080769.43 1127619.005 1181885.347 1425539.811 995092.0888 925975.9435 1017637.159 1.064711715 1.17280314 1.062038095 1.108075698 1.161401524 1.400833095 0.977845669 0.909927409 1 19.95679183 2.030736501 24.9999793 0.947136689 1.158024535 0.486552802 0.096482833 153.7903444 125086.9978 0.039542556 0.02665929 107.3337991 -2.030736501 0.210887846 DVFLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DVFLYR 6 0 O14579;M0QXB4;O14579-3;O14579-2;M0R061 O14579 COPE Coatomer subunit epsilon 0 ;;;;; 155.88 0.022848 5953300000 3545950 3301580 2201100 2736430 3630180 3460850 3563640 4053830 3683210 FALSE TRUE 3077343.723 3279891.704 3265559.322 3357778.255 3557946.52 3593991.139 3218038.741 3186950.001 3247785.11 0.947520732 1.009885689 1.005472718 1.033867125 1.095499363 1.106597579 0.990841029 0.98126874 1 21.63102475 4.90837226 1.399386973 1.030104499 0.887667693 0.290081779 0.041372061 3.008132316 3.953290169 0.01352753 0.672098632 80978.97214 -4.90837226 -0.142436806 DVFRDPALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DVFRDPALK 9 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;;;;; 143.96 9.18E-05 7688650000 11375500 9890920 6594010 7984520 9230070 7406240 11249600 13000950 11806280 FALSE TRUE 9872198.853 9825945.895 9782895.292 9797527.302 9046409.665 7691162.845 10158615.52 10220798.02 10410555.03 0.948287467 0.943844576 0.939709292 0.941114789 0.868965165 0.738785091 0.975799609 0.981772633 1 23.31154365 2.034725672 24.99995516 0.986345373 0.897930735 0.315634179 0.062028569 225.4997305 162342.4981 0.027080672 0.018257726 108.3242454 -2.034725672 -0.088414638 DVFRDPALKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVFRDPALKR 10 2 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;;; 114.86 0.00073073 5012920000 6982690 5873610 3480250 4819050 5577720 4865740 6971160 7899260 4542400 FALSE TRUE 6059909.825 5835025.869 5163310.541 5913288.957 5466734.285 5052928.166 6295097.976 6210064.721 4005402.647 1.512933994 1.456788838 1.289086515 1.476328219 1.364840134 1.261528144 1.571651724 1.550422085 1 21.93351585 1.229322981 24.99035611 0.999999144 1.436950673 0.635708663 0.103588186 257.170985 695666.7256 0.327426755 0.026858927 16.95598333 -1.229322981 0.436951529 DVFSPIGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVFSPIGER 9 0 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ; 126.62 0.0010896 241140000 327380 259510 207246 316770 326140 326100 284060 348610 422220 FALSE TRUE 284115.9035 257805.2617 307470.8588 388697.47 319650.4521 338645.278 256511.9049 274062.4644 372305.6326 0.76312545 0.69245598 0.825856049 1.044027906 0.858570014 0.909589457 0.688982069 0.736122262 1 18.50612792 4.126840258 5.942314453 0.854223212 0.729286169 0.219970889 0.107647152 0.358919896 17.15933042 0.029945382 0.064105803 13391.84018 -4.126840258 -0.124937043 DVGAQILLHSHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVGAQILLHSHK 12 0 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 90.412 0.0051322 696250000 797620 594960 469230 579080 641520 529490 672200 831780 1217100 FALSE TRUE 692212.4961 591051.6686 696151.1975 710568.9647 628755.0071 549859.8229 607010.1475 653910.3199 1073215.825 0.644989088 0.55072955 0.648659088 0.662093261 0.585860731 0.512347852 0.565599326 0.609299924 1 20.0335088 1.238640033 6.054466108 1.014551765 0.594559316 0.880199729 0.046697042 0.043948252 6.269265602 0.076352256 0.012095867 17.32367523 -1.238640033 -0.419992449 DVGRPNFEEGGPTSVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVGRPNFEEGGPTSVGR 17 1 Q6Y7W6;Q6Y7W6-4;Q6Y7W6-5;E7ESB6 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 0 92.236 0.0030631 239200000 36011 24904 25606 27714 38505 30986 30267 33092 36604 FALSE TRUE 31252.05511 24740.40398 37989.14725 34006.88728 37738.82583 32178.05147 27331.711 26015.53332 32276.71682 0.968253843 0.766509311 1.176983008 1.053604289 1.169227528 0.996943142 0.846793407 0.806015478 1 14.97820622 2.307239155 5.373681551 0.866532936 1.027406024 0.214402125 0.123347957 0.280339799 14.99031332 0.048939461 0.037065204 202.8799622 -2.307239155 0.160873088 DVGRPQPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DVGRPQPGR 9 1 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ;;;;;;; 144.77 9.01E-05 3137436000 2577860 2314247 1217389 1153903 1751203 2096279 1597410 2090389 2894232 FALSE TRUE 2237189.27 2299044.559 1806122.392 1415914.312 1716357.486 2176924.21 1442493.424 1643375.58 2552079.19 0.876614361 0.900851575 0.70770625 0.554808142 0.672533005 0.853000259 0.565222831 0.643935966 1 21.28324167 4.226665907 8.963824636 0.697341663 0.888986682 0.22473228 0.132272954 0.192189582 115.372421 0.033153315 0.073677972 16852.56098 -4.226665907 0.191645019 DVGSLDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVGSLDEK 8 0 Q99584 Q99584 S100A13 Protein S100-A13 0 140.5 0.0015088 369910000 628350 612860 427860 497060 537030 481870 631290 767960 700020 FALSE TRUE 545311.9555 608834.0823 634774.5271 609925.0701 526344.1537 500407.8507 570067.593 603737.7303 617264.4331 0.883433301 0.9863424 1.028367249 0.988109856 0.85270449 0.810686351 0.923538701 0.978086049 1 19.23552914 4.772706287 21.76163989 0.944184256 0.883432615 0.076486701 0.068047983 8701.510326 5545059.516 0.018438349 2.296186105 59252.44646 -4.772706287 -0.060751641 DVHAAS(ph)SPGMGGAAASWAGWAVTGVSSLTSK ddPTM_MDA-MB-175_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(0.471)S(0.471)PGMGGAAAS(0.059)WAGWAVTGVSSLTSK 76.164 0.0018864 37207000 21177 23862 20024 25768 25561 25358 34048 38699 54015 TRUE FALSE 18378.40579 23705.24895 29707.67338 31619.01824 25052.38611 26333.53867 30746.0302 30423.52001 47629.40823 0.385862568 0.497701942 0.623725435 0.663854946 0.525985668 0.552884019 0.645526185 0.638754944 1 15.539565 -0.243203961 1.05030376 10 0.549612761 0.762268129 0.077983415 18.45652045 1.18471468 373.1926671 0.025901061 0.571210312 0.243203961 -9.450387239 DVHEDSLTVVFENNWQPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVHEDSLTVVFENNWQPER 19 0 B4DXZ6;P51114;C9JAJ4;P51114-2 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 ; 235.45 2.07E-26 288620000 279500 244420 157714 208870 247100 228450 236120 288100 257120 FALSE TRUE 242563.3668 242814.3889 233985.0179 256297.1259 242183.1934 237238.6193 213221.1187 226492.057 226723.5665 1.069863934 1.070971107 1.032027775 1.130438842 1.06818712 1.046378297 0.940445327 0.998978891 1 17.79057483 2.414384674 5.512851803 0.982463807 1.073383763 0.693336675 0.028669279 0.109877657 6.549069102 0.010698014 0.008258844 259.6478159 -2.414384674 0.090919955 DVHNIYGLYVHMATADGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVHNIYGLYVHMATADGLR 19 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 161.47 1.71E-11 312890000 842954 809340 668736 553540 647623 826716 640232 740446 569109 FALSE TRUE 731555.4931 804023.3922 992138.9664 679229.7173 634736.5694 858520.2995 578142.3992 582107.3851 501829.5824 1.457776741 1.602184129 1.977043605 1.353506731 1.264844863 1.710780571 1.152069187 1.159970248 1 18.93683799 1.558843056 0.528438546 0.675743479 1.640098594 0.503183909 0.206517963 2.753038487 0.810788601 1.628236024 0.166384188 36.2112116 -1.558843056 0.964355114 DVHTLLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVHTLLDR 8 0 E9PI41;Q9NPD3 E9PI41 EXOSC4 Exosome complex component RRP41 0 ; 128.36 0.0011368 389140000 169030 162588 89086 98889 137159 152972 122869 163534 144536 FALSE TRUE 146692.2572 161519.9487 132168.2876 121343.2589 134429.8042 158856.9318 110953.1833 128563.5267 127449.1187 1.150986831 1.267328879 1.037027866 0.952091784 1.054772333 1.246434133 0.870568462 1.008743944 1 16.95956187 4.187782202 7.892542696 1.020572596 1.208760431 0.37941536 0.098279356 0.218018909 29.53151943 0.025182049 0.053289208 15409.27486 -4.187782202 0.188187835 DVIATDKEDVAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVIATDKEDVAFK 13 1 A0A5K1VW95;P40925;P40925-3;C9JF79;C9JRL4;C9JLV6 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic;Malate dehydrogenase" 0 ; 189.86 4.47E-06 2004770000 2883300 1821260 1737810 1851510 1714450 1293230 2514600 3220600 3527300 FALSE TRUE 2502264.6 1809296.023 2578220.729 2271923.644 1680335.799 1342981.395 2270734.479 2531899.753 3110306.612 0.804507372 0.58170986 0.828928157 0.730450058 0.540247638 0.431784246 0.730067727 0.814035421 1 21.56862538 1.481181259 2.088022063 1.014398607 0.654571258 0.455593861 0.120720888 0.402722882 2.871722643 0.242971119 0.034855965 30.28177015 -1.481181259 -0.359827349 DVIEEYFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVIEEYFK 8 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 ;;; 139.19 0.0015663 3409940000 7512700 6210200 4642100 5500500 6078600 5018900 7170600 8439600 7500600 FALSE TRUE 6519877.66 6169404.787 6887035.087 6749472.595 5957647.753 5211980.331 6475196.316 6634857.217 6613887.613 0.985785977 0.932795528 1.04129908 1.020500043 0.900778498 0.788035817 0.979030291 1.003170541 1 22.6570671 5.044892788 11.63086727 0.960071686 1.071199416 0.01335075 0.072966278 466086.5411 4604778.66 0.019131905 1025930.385 110890.1032 -5.044892788 0.111127731 DVIKEIEDFDSLEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVIKEIEDFDSLEALR 16 1 P46060;B0QYT5;B0QYT4 P46060 RANGAP1 Ran GTPase-activating protein 1 0 ; 166.6 6.04E-09 144772000 428720 355660 197842 194624 342140 275490 439410 506900 52128 FALSE TRUE 372063.5658 353323.646 293519.0529 238816.3538 335332.0834 286088.2786 396796.0858 398503.3797 45965.48722 8.094411443 7.686715999 6.38563998 5.195557978 7.295301402 6.223980117 8.632478622 8.669621574 1 15.48826341 4.328289339 4.612564347 6.555998177 7.986826202 0.078774514 2.165810067 0.638415519 23.39954519 0.542044424 1.530765959 21295.57343 -4.328289339 1.430828025 DVIRPGMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DVIRPGMR 8 1 P25685;P25685-2 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ;;;;; 104.44 0.0041774 2651070000 2218930 2151660 1275946 1559204 1996000 2099610 2126530 2349810 1907880 FALSE TRUE 1925692.778 2137525.604 1892997.753 1913245.099 1956283.505 2180383.355 1920299.448 1847321.418 1682332.6 1.144656401 1.27057254 1.12522206 1.137257341 1.16283992 1.296047735 1.141450536 1.098071462 1 20.68203153 1.489212209 1.949672596 0.98959978 1.187036828 0.531918474 0.056799551 0.362253721 2.210681082 0.115438663 0.015851159 30.84694857 -1.489212209 0.197437048 DVITLR ddPTM_MDA-MB-175_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 ;;; 116.35 0.055015 1169730000 1667410 1367950 841340 1027610 1276940 1325160 1337740 1507470 1533300 FALSE TRUE 1447057.544 1358963.846 1248214.838 1260944.557 1251531.392 1376139.763 1208006.181 1185109.272 1352035.021 1.070281111 1.005124738 0.923211913 0.932627141 0.925664922 1.017828489 0.893472552 0.876537407 1 20.36670109 4.480573772 2.630176424 0.932513909 1.070614127 0.501532662 0.043275337 0.256633908 3.167536409 0.011587561 0.060058208 30239.4419 -4.480573772 0.138100218 DVKPHNVMIDHEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVKPHNVMIDHEHR 14 1 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YFU2;A0A2R8YDP2;P68400-2;A0A2R8Y4H0;A0A2R8Y4D6;V9GYW6 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 ; 217.48 3.70E-12 908900000 1552270 1234370 898330 1002370 1005770 960110 1308590 1550780 2098800 FALSE TRUE 1347133.587 1226261.342 1332765.393 1229973.429 985757.1448 997046.053 1181683.143 1219157.765 1850682.255 0.727911873 0.662599611 0.720148145 0.664605405 0.532645268 0.538745131 0.63851217 0.658761255 1 20.81962579 1.234832446 4.789256868 1.027259968 0.638476743 0.7536631 0.064207837 0.102221012 5.488695048 0.134506351 0.01761923 17.17245732 -1.234832446 -0.388783225 DVKPKPIADAK ddPTM_MDA-MB-175_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 72.937 0.025271 418710000 636340 511810 413040 437940 382960 321310 651180 746910 656690 FALSE TRUE 552246.0567 508447.8864 612787.5255 537380.9705 375339.8452 333671.0036 588028.6638 587189.109 579056.8563 0.953699193 0.878062112 1.058251049 0.92802799 0.648191695 0.57623185 1.015493828 1.014043962 1 19.14334548 DVKPSNILVNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVKPSNILVNSR 12 1 P36507;G5E9C7;Q02750;Q02750-2 P36507;Q02750 MAP2K2;MAP2K1 Dual specificity mitogen-activated protein kinase kinase 2;Dual specificity mitogen-activated protein kinase kinase 1 0 ; 129.77 0.00020821 1569530000 1419030 1212290 902910 1067300 1209140 1168550 1405520 1717840 1451880 FALSE TRUE 1231501.59 1204326.387 1339560.296 1309646.778 1185080.48 1213504.875 1269212.887 1350493.284 1280240.4 0.961929955 0.940703314 1.046334966 1.022969418 0.925670272 0.947872661 0.991386373 1.054874759 1 20.28798331 1.942199992 7.033911864 1.029375912 0.97547681 0.239897672 0.038625652 0.363846261 37.5844237 0.019629719 0.010850604 87.53867968 -1.942199992 -0.053899102 DVLDGHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVLDGHLR 8 0 P15924 P15924 DSP Desmoplakin 0 ; 171.73 0.00028767 703030000 1000180 918290 535170 649960 898280 859950 792070 973110 912160 FALSE TRUE 868003.6789 912257.6925 793980.002 797543.352 880405.9855 893032.833 715255.1733 765017.9993 804325.4839 1.079169685 1.134189716 0.987137692 0.991567926 1.094589197 1.110287876 0.889260862 0.951129878 1 19.6174199 2.241302448 24.99999973 0.945302276 1.063559584 0.526642992 0.053300233 58.25360071 531163.258 0.021523685 0.015906208 174.3020313 -2.241302448 0.118257308 DVLDVYIEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVLDVYIEHR 10 0 P33993;P33993-2 P33993 MCM7 DNA replication licensing factor MCM7 0 ;;; 164.64 6.10E-06 714930000 1142950 1052180 816900 1080060 1042000 1014780 986470 1177170 1784900 FALSE TRUE 991906.2616 1045268.16 1211955.572 1325304.131 1021266.239 1053819.243 890802.2912 925441.3562 1573891.155 0.63022545 0.66412989 0.77003773 0.842055771 0.648879838 0.669562974 0.565987227 0.587995779 1 20.58590434 DVLEVLDDSR ddPTM_MDA-MB-175_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 ; 152.97 3.97E-05 57949000 125080 131255 91615 117576 122726 115438 123460 151636 190973 FALSE TRUE 108550.3611 130392.7773 135920.3204 144273.4278 120283.9927 119878.9746 111486.8682 119209.8214 168396.3895 0.644612164 0.774320504 0.807145099 0.856748938 0.714290806 0.711885658 0.662050229 0.70791198 1 17.36150168 1.234829277 24.9914395 1.000000378 0.736132192 0.629454147 0.063922667 78.55913807 526086.9187 0.121760141 0.016793757 17.17233204 -1.234829277 -0.263868185 DVLFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVLFLK 6 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 103.71 0.080148 922220000 1819100 1656200 849020 877060 1226100 1123800 1344300 1665400 1468500 FALSE TRUE 1578701.326 1645320.313 1259608.912 1076209.878 1201703.009 1167033.313 1213929.993 1309267.17 1294895.603 1.219172667 1.270620048 0.972749393 0.8311171 0.928030805 0.901256681 0.937473253 1.01109863 1 20.30440436 4.204298827 5.957453279 0.939223594 1.246065372 0.857336896 0.051747357 0.059387375 5.77653143 0.014590583 0.03251429 16006.59022 -4.204298827 0.306841778 DVLLPWYNAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVLLPWYNAYR 11 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 175.91 2.16E-05 1458170000 1937070 1739250 1296030 1370690 1898510 1715790 1775210 1920230 2133940 FALSE TRUE 1681081.292 1727824.752 1922794.443 1681926.114 1860733.365 1781797.552 1603050.407 1509603.758 1881668.044 0.893399501 0.918241003 1.021856352 0.893848476 0.988874404 0.946924489 0.851930505 0.802268903 1 20.84358071 2.244487929 24.72627337 0.866186307 0.946011509 0.1413047 0.063285488 163.7069228 682920.916 0.023400244 0.017627421 175.585209 -2.244487929 0.079825203 DVLLQVDDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DVLLQVDDER 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 225.67 7.88E-09 1011640000 1128980 1132240 923540 1158420 1101070 1013090 1061950 1193720 2563140 FALSE TRUE 979782.4325 1124802.241 1370167.033 1421456.966 1079160.861 1052064.228 958962.2525 938452.2675 2260128.509 0.433507399 0.497671808 0.606234127 0.628927497 0.477477655 0.465488676 0.424295454 0.415220756 1 21.10797337 1.233173911 24.99927133 1.000000797 0.493173244 0.830185521 0.07197671 77.61161468 360149.5263 0.167622786 0.019982937 17.10700218 -1.233173911 -0.506827553 DVLLQVDDERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DVLLQVDDERR 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;; 251.03 9.08E-17 11713210000 6325425 6210286 4317930 4905153 5690595 5906451 6106568 6696160 6129847 FALSE TRUE 5489504.06 6169490.222 6406095.391 6018942.959 5577363.293 6133675.992 5514353.975 5264238.294 5405183.471 1.015599949 1.141402555 1.185176308 1.113550167 1.031854575 1.13477665 1.020197373 0.973924072 1 22.36591216 2.100575658 4.564411552 0.988107045 1.106079638 0.503758757 0.050066511 0.165565715 5.98257837 0.022006008 0.014276561 126.0595226 -2.100575658 0.117972593 DVLSVAFSSDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVLSVAFSSDNR 12 0 P63244;J3KPE3;D6RHH4;H0YAF8;D6R9L0;H0Y8W2;D6R9Z1;D6RFX4;E9PD14;D6RFZ9;D6RAU2;H0YAM7 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 ;;; 255.7 8.84E-21 3038330000 972950 850160 589898 682660 850360 827980 924630 988900 875230 FALSE TRUE 844372.1924 844575.243 875174.6459 837668.3868 833439.4997 859832.9264 834959.5249 777431.4306 771761.3065 1.094084642 1.094347742 1.133996533 1.08539827 1.079918743 1.114117693 1.081888296 1.007346992 1 19.55779519 1.769210052 3.164775972 0.999993927 1.099972089 0.871370589 0.015170226 0.071072822 1.407166379 0.010730932 0.004151265 58.7773568 -1.769210052 0.099978162 DVMEDAVEDRLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVMEDAVEDRLDR 13 1 Q15833-2;Q15833;Q15833-3;R4GMY7;M0R1A1 Q15833-2 STXBP2 Syntaxin-binding protein 2 0 ; 143.25 3.71E-05 337070000 171498 185293 111780 124519 176641 177927 172144 202710 102901 FALSE TRUE 148834.1048 184075.7981 165837.1819 152792.9421 173126.1897 184771.9668 155449.5014 159362.044 90736.16101 1.64029537 2.028692817 1.827685677 1.683925575 1.908017573 2.036365268 1.71320342 1.756323413 1 16.46939 1.067569665 2.14526744 0.385042361 1.846844239 0.787188991 0.134783828 0.547055585 1.660820128 1.867920626 0.034624265 11.68341127 -1.067569665 1.461801878 DVMQNHLLQMLCLVAMEKPASTNSDDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVMQNHLLQMLCLVAMEKPASTNSDDVR 28 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;; 210.21 7.71E-26 4392520000 1550124 1299005 1034008 1432129 1318497 1301309 1679757 1851803 2471025 FALSE TRUE 1345271.186 1290471.751 1534057.727 1757315.778 1292261.489 1351371.199 1516854.425 1455809.339 2178903.24 0.617407493 0.592257484 0.704050414 0.806513913 0.593078878 0.620207072 0.696155018 0.66813859 1 21.0551707 1.237417644 6.993112951 1.0073737 0.66374837 0.731553319 0.064301449 0.061493339 17.14356336 0.099597927 0.016331758 17.2749836 -1.237417644 -0.343625331 DVMQNHLLQMLCLVAMEKPASTNSDDVRDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVMQNHLLQMLCLVAMEKPASTNSDDVRDEK 31 2 E7EUI8;E7EM57;P11413;P11413-3;P11413-2 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 248.51 1.13E-46 919600000 1357700 1103700 797750 804340 947230 731220 1749800 1699700 452540 FALSE TRUE 1178276.505 1096449.722 1183544.568 986977.6906 928381.9762 759350.5066 1580104.665 1336232.382 399041.2367 2.952768778 2.747710314 2.96597058 2.473372674 2.326531423 1.902937433 3.959752827 3.348607259 1 18.60617832 3.753179188 23.28863104 2.648925863 2.874705896 0.029067316 0.792225049 2138.470792 3406740.175 0.219227816 0.377063161 5664.729652 -3.753179188 0.225780033 DVNFEFPEFQL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVNFEFPEFQL 11 0 P62081 P62081 RPS7 40S ribosomal protein S7 0 ;;; 158.05 7.05E-05 144163000 648790 608060 390323 468234 602610 613760 593640 696270 639270 FALSE TRUE 563050.7577 604065.6138 579084.5084 574553.6862 590619.24 637371.7444 536068.8842 547378.0789 563696.2289 0.998854931 1.071615496 1.027298887 1.019261185 1.04776156 1.130700742 0.950988949 0.971051518 1 19.10455839 2.198948523 24.99993777 0.972437002 1.047837263 0.479021048 0.036955146 130.495625 82357.38753 0.014792204 0.009973063 158.1060626 -2.198948523 0.075400261 DVNQQEFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVNQQEFVR 9 0 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ;;; 241.96 4.66E-10 3736980000 1996490 1924910 1228520 1407060 1824950 1606560 1760930 2045510 1897960 FALSE TRUE 1732648.788 1912265.139 1822636.381 1726554.479 1788637.065 1668365.403 1590155.28 1608093.605 1673585.331 1.035291572 1.142615858 1.089060921 1.031650103 1.068745664 0.996880991 0.950148911 0.960867411 1 20.67451068 2.812627269 1.348390854 0.965085044 1.086437967 0.675126628 0.033371513 0.228392836 0.863957713 0.015775815 0.014187361 649.5719589 -2.812627269 0.121352923 DVNSSS(ph)PVMLAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DVNSSSPVMLAFK 13 0 C4P0D6;C4P0D8;Q99598;C4P0D4;Q5VVQ1;Q9NRI2 C4P0D6 DISC1;TSNAX;TRAX Translin-associated protein X 1 DVNS(0.014)S(0.164)S(0.822)PVMLAFK;DVNS(0.002)S(0.02)S(0.978)PVMLAFK;DVNSS(0.001)S(0.999)PVMLAFK;DVNSS(0.001)S(0.999)PVMLAFK;DVNSS(0.006)S(0.994)PVMLAFK 183.31 2.68E-05 735550000 2348070 2252020 1509450 1989370 2120480 1840340 2357970 2839880 2893780 TRUE FALSE 2037766.6 2237226.332 2239425.069 2441086.864 2078286.597 1911139.071 2129294.432 2232593.762 2551680.625 0.798597826 0.876765811 0.877627493 0.956658463 0.814477555 0.748972678 0.834467453 0.874950313 1 21.28301634 1.241232068 3.022426894 1.028330938 0.846453794 0.441383868 0.054797804 0.403346987 4.650853985 0.178515155 0.015180507 17.42737869 -1.241232068 -0.181877143 DVPLTIKDPAVGFLETISPGYSIHTYLWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVPLTIKDPAVGFLETISPGYSIHTYLWR 29 1 P04062-4;P04062-5;P04062-2;P04062 P04062-4 GBA Glucosylceramidase 0 ; 202.98 1.68E-25 771540000 968340 826720 303270 619610 724970 743720 800830 940050 644460 FALSE TRUE 840371.4155 821289.2219 449932.3864 760301.9206 710544.5154 772331.3897 723165.6299 739027.623 568272.673 1.478817222 1.445237931 0.791754395 1.337917441 1.250358409 1.359085922 1.272568019 1.300480664 1 19.11622382 DVPLVHLDEITLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVPLVHLDEITLFK 14 0 Q96ME1-4 Q96ME1-4 FBXL18 F-box/LRR-repeat protein 18 0 189.5 7.11E-07 145030000 157220 140310 84679 118080 138160 102180 130360 160730 137170 FALSE TRUE 136442.9787 139388.2944 125630.0476 144891.8687 135410.8863 106110.9307 117717.7073 126359.1403 120953.9189 1.128057527 1.152408253 1.038660416 1.197909668 1.119524589 0.877283942 0.97324426 1.04468827 1 16.88409799 2.856970675 8.794663903 0.984983701 1.128560575 0.641604944 0.056768515 0.222402078 15.31306647 0.018575968 0.018588047 719.4004 -2.856970675 0.143576874 DVPNETLQVEEDDRPELPWWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DVPNETLQVEEDDRPELPWWK 21 1 O95373 O95373 IPO7 Importin-7 0 ;;;;; 266.53 4.71E-37 1889488000 1381920 1147509 831636 1005907 1086035 1054928 1388802 1504991 1515182 FALSE TRUE 1199295.771 1139970.938 1233817.951 1234313.559 1064425.028 1095511.763 1254116.196 1183160.387 1336058.91 0.897636894 0.853234037 0.923475711 0.923846658 0.796690191 0.819957679 0.938668337 0.885560043 1 20.34955219 -0.461005952 1.191668376 7.870384994 0.874810512 0.405606022 0.045743723 90.50645703 2.898313972 1642.731615 0.014250031 0.345934637 0.461005952 -6.995574481 DVPPDILLDS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DVPPDILLDSPER 13 0 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 DVPPDILLDS(1)PER;DVPPDILLDS(1)PER;DVPPDILLDS(1)PER 180.27 1.37E-05 86796000 240022 201563 128551 161396 171526 197454 198026 212664 219065 TRUE FALSE 208302.4846 200238.9194 190718.6936 198043.4286 168112.9682 205050.1831 178821.469 167187.4586 193167.3853 1.07835225 1.036608323 0.987323472 1.025242581 0.870296857 1.06151555 0.925733238 0.865505625 1 17.559492 7.999999049 0.278773452 0.912619748 2.209343364 0.329011682 0.061059706 84.40418762 1.353126397 0.144340168 52.022387 99999781.06 -7.999999049 1.296723616 DVPPDILLDS(ph)PERK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 192.55 2.21E-07 381630000 472880 358209 318354 320991 404604 365726 465700 508440 460839 TRUE FALSE 410387.7099 355855.9015 472311.0592 393876.9126 396553.172 379795.7159 420536.4857 399714.0627 406359.1384 1.00991382 0.875717728 1.162299588 0.969282773 0.975868719 0.934630675 1.034888713 0.983647284 1 18.63239581 LHHYDERS(ph)DGESDSPEKEAEFAPYPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHHYDERSDGESDSPEKEAEFAPYPR 26 2 Q02410-2;Q02410 Q02410-2 APBA1 Amyloid beta A4 precursor protein-binding family A member 1 1 LHHY(0.003)DERS(0.982)DGES(0.015)DSPEKEAEFAPYPR 99.494 0.0025197 121920000 41107 32286 21955 32948 34491 32282 38096 40214 18651 TRUE FALSE 35674.6058 32073.91114 32572.51144 40429.34698 33804.69658 33523.90943 34401.45578 31614.54905 16446.10003 2.169183316 1.950244197 1.980561433 2.458293876 2.055484068 2.038410892 2.091769825 1.922312828 1 14.00545789 1.17775643 2.475631101 0.594054895 2.104205288 0.857629741 0.140514415 0.242192637 1.400977082 0.842888885 0.037259705 15.05762336 -1.17775643 1.510150392 DVPYPPPLS(ph)PAIEAIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVPYPPPLSPAIEAIQK 17 0 G3V3Y1;Q8N8N7;G3V2R9 G3V3Y1 PTGR2 Prostaglandin reductase 2 1 DVPYPPPLS(1)PAIEAIQK 85.469 0.0052751 47114000 75218 60961 47255 63776 75994 55494 87718 109650 87496 TRUE FALSE 65277.75072 60560.54318 70107.67606 78257.31556 74481.86808 57628.89009 79211.12186 86202.2008 77152.32256 0.84608925 0.784947765 0.908691712 1.014322226 0.965387245 0.746949517 1.026684865 1.117298844 1 16.23542197 -1.999999983 0.124326439 1.995105616 0.676841003 0.338174623 0.093762791 224.368084 2.470194263 51.20301689 3.156471966 0.01 1.999999983 -1.318264613 DVQEIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DVQEIFR 7 0 O00148;O00148-2;O00148-3;K7EQN7;Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;F6S4E6;A0A0A0MT12;F6TRA5;A0A140T9K1;A0A140T973;A0A140T9L4 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ;;;;; 172.97 0.0020487 4200350000 6310520 5595190 3436100 4234160 5673300 5806720 4984530 6144800 6024300 FALSE TRUE 5476568.793 5558434.828 5097809.453 5195590.743 5560412.43 6030108.276 4501131.048 4830782.339 5312114.117 1.030958423 1.04636962 0.959657368 0.978064595 1.046741901 1.135161659 0.847333274 0.90938979 1 22.34085471 2.225766051 24.99999887 0.91394254 1.02825884 0.452249377 0.058872937 212.1531882 414534.1489 0.02466534 0.016751575 168.1767869 -2.225766051 0.1143163 DVQFAVEQVLQEEHFDASHVALMGGSHGGFISCHLIGQYPETYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVQFAVEQVLQEEHFDASHVALMGGSHGGFISCHLIGQYPETYR 44 0 C9JIF9;P13798 C9JIF9 APEH Acylamino-acid-releasing enzyme 0 ; 229.94 1.16E-45 1176160000 397070 444162 158671 237932 397124 433346 386264 433937 325193 FALSE TRUE 344596.1935 441244.2706 235404.8263 291958.0972 389222.0094 450017.101 348804.1767 341142.9495 286749.054 1.201734369 1.538781957 0.820943689 1.01816586 1.357361093 1.569376062 1.216409163 1.18969163 1 18.1294292 1.243967995 2.398955996 0.938258833 1.247285467 0.108867599 0.220646848 1.447846453 8.93819327 0.939783501 0.060931519 17.53751254 -1.243967995 0.309026634 DVQFEHGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVQFEHGYR 9 0 A0A0C4DFM1;Q92544 A0A0C4DFM1 TM9SF4 Transmembrane 9 superfamily member 4 0 ; 138.65 0.00013057 802900000 1106980 1022530 704890 776620 1065090 1236490 888310 1191690 1127320 FALSE TRUE 960689.7883 1015812.933 1045777.162 952963.4409 1043896.793 1284058.57 802161.8329 936856.3672 994049.5138 0.96644058 1.021893697 1.052037295 0.958667981 1.05014567 1.291745082 0.806963659 0.942464489 1 19.92295819 DVQIGDIVTVGECRPLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVQIGDIVTVGECRPLSK 18 1 P62280;M0R1H5 P62280 RPS11 40S ribosomal protein S11 0 ;;; 218.88 6.96E-19 3857820000 2417500 2218200 1455980 1905070 2117150 1707770 2512620 2811360 2466390 FALSE TRUE 2098021.25 2203628.498 2160096.798 2337645.261 2075022.857 1773469.017 2268946.499 2210172.542 2174816.184 0.964689 1.013248161 0.993231894 1.074870271 0.954114133 0.815456971 1.043281964 1.016257171 1 21.05246204 DVQIILESCHNQNILGTILHPNGNITELLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVQIILESCHNQNILGTILHPNGNITELLLK 31 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 345.56 1.40E-120 686800000 807910 721760 218230 554180 707100 587410 859700 919040 874920 FALSE TRUE 701142.6465 717018.711 323766.7579 680015.0391 693030.0934 610008.0428 776326.4263 722510.448 771487.9543 0.908818657 0.929397157 0.419665344 0.881433126 0.898303194 0.790690301 1.006271611 0.936515527 1 19.55728411 2.467456133 1.108673727 0.985497268 0.779395589 0.217859526 0.148738012 0.821796377 2.096064645 0.118077436 0.064000886 293.3973136 -2.467456133 -0.206101679 DVRPYIVGAVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVRPYIVGAVVR 12 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 147.33 5.97E-05 490080000 152800 165340 108230 100660 152250 166000 139160 171990 148530 FALSE TRUE 132607.0929 164253.8707 160570.39 123516.3915 149220.5229 172386.1274 125664.2846 135211.2769 130970.9526 1.01249239 1.254124425 1.226000016 0.943082333 1.139340593 1.316216489 0.9594821 1.032376067 1 16.99888735 2.19205047 24.9999605 1.003021168 1.147106172 0.295452363 0.109974258 162.6887847 87446.65958 0.044667554 0.030114966 155.6146465 -2.19205047 0.144085004 DVS(ph)PDPSLSTPGSAGSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVSPDPSLSTPGSAGSAR 18 0 P23771;P23771-2 P23771 GATA3 Trans-acting T-cell-specific transcription factor GATA-3 1 DVS(1)PDPSLSTPGSAGSAR 185.63 3.29E-15 0 135680 142250 97206 155680 150120 125640 125340 168470 230830 TRUE FALSE 117749.5442 141315.5504 144215.1467 191029.5234 147132.9057 130473.4521 113184.5461 132444.0015 203541.5404 0.578503749 0.694283585 0.708529308 0.938528435 0.722864264 0.641016334 0.556075904 0.650697648 1 17.63496374 -1.569860849 0.014995664 1.543458059 5.00E-07 0.049243552 0.139750998 80182.46533 130.9888181 7889.112106 5755.062525 0.026923973 1.569860849 -1.543457559 DVSGFSDPYCLLGIEQGVGVPGGS(ph)PGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVSGFSDPYCLLGIEQGVGVPGGSPGSR 28 0 Q70J99;Q70J99-3;K7EQ37;Q70J99-2;K7EN81;K7EIH3 Q70J99 UNC13D Protein unc-13 homolog D 1 DVSGFSDPYCLLGIEQGVGVPGGS(0.826)PGS(0.174)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.833)PGS(0.167)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.819)PGS(0.181)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.801)PGS(0.199)R 109.26 0.0004633 216534000 178876 127037 97160 128317 138003 140796 136272 149141 155060 TRUE FALSE 155237.0834 126202.4856 144146.901 157453.3361 135257.0103 146212.5132 123056.3624 117248.3578 136728.9834 1.135363399 0.92301195 1.054252707 1.151572491 0.989234374 1.069360055 0.900002028 0.857523802 1 17.06095957 2.235056945 24.978375 0.905532303 1.049384391 0.420088888 0.073865566 77.30284181 551097.4585 0.028361959 0.019987799 171.8133656 -2.235056945 0.143852088 DVSLGDWEFGKRDS(ph)LGAYASQDANEQGQDLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVSLGDWEFGKRDSLGAYASQDANEQGQDLGK 32 2 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DVS(0.007)LGDWEFGKRDS(0.991)LGAY(0.001)AS(0.001)QDANEQGQDLGK 116.84 7.87E-07 121930000 35883 30590 17342 19368 30315 24756 45568 50017 11113 TRUE FALSE 31140.97063 30389.05228 25728.64921 23765.80042 29711.79081 25708.37934 41148.82237 39321.25378 9799.2338 3.177898524 3.101166162 2.625577645 2.425271292 3.032052446 2.62350913 4.199187734 4.012686562 1 13.25845323 DVT(ph)PPPETEVVLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DVTPPPETEVVLIK 14 0 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 DVT(1)PPPETEVVLIK;DVT(1)PPPETEVVLIK;DVT(1)PPPETEVVLIK;DVT(1)PPPETEVVLIK;DVT(1)PPPETEVVLIK;DVT(1)PPPETEVVLIK;DVT(0.994)PPPET(0.006)EVVLIK;DVT(1)PPPETEVVLIK 168.5 3.89E-05 4731098000 1319080 911216 852081 1054540 978997 805017 1086668 1296100 2058680 TRUE FALSE 1144760.236 905230.1621 1264150.222 1293989.425 959516.8751 835986.5249 981283.1046 1018939.101 1815305.196 0.630615854 0.498665549 0.696384401 0.712821969 0.528570555 0.460521199 0.540560952 0.561304569 1 20.79178069 1.23733902 24.98480044 1.000000512 0.576190511 0.727025722 0.081120681 17.18574702 351343.1861 0.125601035 0.020899878 17.27185645 -1.23733902 -0.423810002 DVTGPDEESFLYFAYGSNLLTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DVTGPDEESFLYFAYGSNLLTER 23 0 O75223;O75223-3;B8ZZK2;O75223-2;O75223-4;A0A0B4J1Y4 O75223 GGCT Gamma-glutamylcyclotransferase 0 ;; 155.87 4.82E-14 23660000 61083 53832 35668.7 44746 54575 48969 55929 62658 57251 FALSE TRUE 53010.72679 53478.37405 52918.20262 54906.2632 53489.06427 50852.86912 50505.01419 49259.07431 50482.852 1.05007393 1.059337417 1.048241146 1.087622054 1.059549177 1.00732956 1.000439004 0.975758547 1 15.6235058 2.631224797 2.778647339 0.989686109 1.06216954 0.870562432 0.012567727 0.089660021 1.347692907 0.004907085 0.004230855 427.7842561 -2.631224797 0.072483431 DVTGS(ph)PPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVTGSPPAK 9 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 DVT(0.018)GS(0.982)PPAK 123.67 0.00057817 272680000 567310 502970 329020 443530 470980 375590 584140 702700 568250 TRUE FALSE 492338.5461 499665.957 488135.1725 544240.2654 461608.4195 390039.1903 527490.1927 552433.0734 501072.1324 0.982570202 0.997193667 0.974181442 1.086151534 0.921241453 0.778409265 1.052723068 1.102502091 1 18.93465878 2.036243969 24.99993192 1.064285232 0.959547622 0.233677665 0.080319881 229.5523757 158336.9986 0.034139759 0.023016961 108.7036104 -2.036243969 -0.10473761 DVTNFTVGGFAPMS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 DVTNFTVGGFAPMSPR 16 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 1 DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR 267.69 2.42E-27 9219320000 4421410 3939670 2669079 3181866 4304900 4674010 3773752 4834410 4364160 TRUE FALSE 3837109.466 3913790.048 3959854.532 3904357.307 4219240.912 4853822.189 3407774.112 3800609.043 3848233.976 0.997109191 1.017035365 1.029005657 1.014584178 1.096409662 1.261311609 0.885542338 0.987624211 1 21.87576509 DVTNNVHYENYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DVTNNVHYENYR 12 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4 E7EPK1 7-Sep Septin-7 0 ;;;;; 252.42 4.65E-21 12257480000 7825220 7762000 5082200 6160640 7946080 7764030 7791090 8666780 8552090 FALSE TRUE 6791097.35 7711010.911 7539968.919 7559507.471 7787968.554 8062717.258 7035511.291 6813456.542 7541071.663 0.900548046 1.022535159 0.999853768 1.00244472 1.032740292 1.069173934 0.932959081 0.903513035 1 22.84633813 2.194966155 24.99813441 0.936223065 1.006339211 0.239217438 0.048653687 161.9630675 92872.51747 0.019525257 0.01316402 156.6628976 -2.194966155 0.070116146 DVTQIFNNILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVTQIFNNILR 11 0 Q9H9S4;B7ZBJ5;Q5TAW7;B7ZBJ6 Q9H9S4 CAB39L Calcium-binding protein 39-like 0 91.549 0.024796 76206000 150790 102890 99128 79097 61884 67184 156950 136390 87672 FALSE TRUE 130862.7194 102214.1088 147066.6324 97057.18277 60652.62947 69768.61195 141729.0132 107224.0599 77307.51604 1.692755455 1.322175567 1.902358786 1.255468908 0.784563165 0.902481615 1.833314798 1.386981052 1 16.23832106 3.601361397 8.843690796 1.222284421 1.606442169 0.297522711 0.319667215 0.499068839 33.66866611 0.094211184 0.139822008 3993.570877 -3.601361397 0.384157748 DVVENGETADQTLSLMEQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVVENGETADQTLSLMEQLR 20 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RQT0;C9J165;A0A0U1RR66;A0A0U1RQJ6 P47897 QARS Glutamine--tRNA ligase 0 74.678 0.031206 16235000 12171 13601 9517.3 7921.1 10517 11925 9940.8 10544 15781 FALSE TRUE 10562.57151 13511.65414 14119.89811 9719.706821 10307.73228 12383.76247 8976.742746 8289.247653 13915.38816 0.759056908 0.970986507 1.014696676 0.698486216 0.740743424 0.889932952 0.645094671 0.595689287 1 13.76439353 3.728279153 24.81371035 0.741557548 0.92052068 0.218792133 0.132804235 805.7781852 1944698.787 0.036750857 0.055198761 5349.080742 -3.728279153 0.178963132 DVVEPLLRPQWYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVVEPLLRPQWYVR 14 1 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 87.083 0.0064603 309650000 254950 208800 165610 191620 217590 234280 207400 225940 226290 FALSE TRUE 221257.7115 207428.3791 245699.5499 235130.2497 213260.3847 243292.9032 187286.3799 177624.4893 199538.254 1.10884859 1.039541917 1.231340583 1.178371791 1.068769424 1.219279503 0.938598871 0.890177626 1 17.60630583 2.222868802 24.83906066 0.931755972 1.138930859 0.668685403 0.06556559 121.4391066 192228.0869 0.026352017 0.017836152 167.0585862 -2.222868802 0.207174887 DVVICPDASLEDAKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVVICPDASLEDAKK 15 1 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ;;; 204.72 7.63E-09 2467490000 2188630 1556050 1386530 1507680 1324500 946970 2194000 2505430 1876720 FALSE TRUE 1899397 1545828.205 2057060.546 1850021.787 1298145.041 983400.5487 1981226.218 1969663.292 1654856.3 1.147771562 0.934116277 1.243044817 1.117935006 0.78444578 0.594251325 1.197219492 1.190232223 1 20.65827451 DVVNVYEPQLQHHVAQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVVNVYEPQLQHHVAQK 17 0 Q16222;Q16222-3;Q16222-2 Q16222 UAP1 UDP-N-acetylhexosamine pyrophosphorylase;UDP-N-acetylgalactosamine pyrophosphorylase;UDP-N-acetylglucosamine pyrophosphorylase 0 173.37 8.59E-10 334350000 530580 480790 323100 377710 448120 384910 527270 635090 561210 FALSE TRUE 460462.5087 477631.6588 479352.2407 463474.8284 439203.2887 399717.7368 476135.4366 499280.9458 494864.3931 0.930482199 0.965176855 0.968653731 0.936569361 0.887522511 0.80773186 0.962153356 1.008924774 1 18.91667371 2.003290445 24.9998502 0.999231645 0.917342386 0.397500638 0.045291109 104.8187095 796377.8012 0.020527106 0.013762186 100.7605305 -2.003290445 -0.08188926 DVWLEWSDAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVWLEWSDAEK 11 0 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 0 ; 178.08 1.79E-05 50758000 203499 178442 130000 140172 171529 139709 187851 237090 198174 FALSE TRUE 176606.0915 177269.8028 192868.4348 172000.195 168115.9085 145083.6956 169633.2389 186390.1485 174746.0955 1.010643992 1.014442138 1.103706691 0.984286341 0.962058168 0.830254291 0.970741226 1.066634124 1 17.41490069 3.506111658 23.08589648 0.972198143 1.040734513 0.236575573 0.062810403 494.4688871 393757.3613 0.019499895 0.02884145 3207.093767 -3.506111658 0.06853637 DVYDYFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DVYDYFR 7 0 P49354;E9PQP6;H0YCW1 P49354 FNTA Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha 0 ;;;; 119.89 0.01089 1000198000 2010600 2306200 1438140 1589680 2016680 1906640 2359790 2491310 2175670 FALSE TRUE 1744894.116 2291050.42 2133629.314 1950641.141 1976552.014 1979989.675 2130937.929 1958562.744 1918464.771 0.909526274 1.194210316 1.112154545 1.016771937 1.030277982 1.032069864 1.11075166 1.020901073 1 20.87152084 3.733410071 24.63855953 1.038043566 1.084188372 0.041634959 0.075255049 927.9601423 4439078.501 0.019509073 0.029997942 5412.651575 -3.733410071 0.046144807 DVYEDELVPVFEAVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVYEDELVPVFEAVGR 16 0 B7Z8Z7;A0AV96;A0AV96-2;D6R9D6;D6RBS9;D6REZ6;D6R9M7;D6RBP6;D6RFL5;D6RA49 B7Z8Z7 RBM47 RNA-binding protein 47 0 ; 147.71 2.33E-06 90079000 192269 165979 117018 141830 163178 157219 162899 195740 189095 FALSE TRUE 166860.1645 164888.673 173608.2962 174034.6692 159931.0771 163267.3167 147101.0801 153882.5243 166740.4045 1.000718242 0.988894524 1.041189127 1.043746234 0.959162103 0.979170688 0.882216164 0.922886835 1 17.34724421 2.882480249 2.034439182 0.933594782 1.016855028 0.458001563 0.036377535 0.269730527 2.216827755 0.013803845 0.013872417 762.9221936 -2.882480249 0.083260246 DVYHHTFFEMLGSWSFGDYFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DVYHHTFFEMLGSWSFGDYFK 21 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;; 149.57 4.60E-08 81777600 146112 96102 53537.8 114213.6 70937.3 61200.8 121223 136618 193465 FALSE TRUE 126802.929 95470.69963 79428.85915 140147.5435 69525.78652 63555.23438 109466.8121 107403.3039 170593.7881 0.74330332 0.559637609 0.465602294 0.821527824 0.407551689 0.37255304 0.641681115 0.629585081 1 17.38020559 1.082259009 2.006711478 1.300441299 0.564135624 0.474461795 0.139697345 1.132319736 3.084880182 1.81071008 0.03734448 12.08534378 -1.082259009 -0.736305675 DVYIVQDLMETDLYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVYIVQDLMETDLYK 15 0 P28482;P28482-2;P27361;E9PBK7;E9PQW4;P27361-3;P27361-2;E9PJF0;B3KR49;H0YDH9 P28482;P27361 MAPK1;MAPK3 Mitogen-activated protein kinase 1;Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 ; 224.46 2.71E-12 13242000 73241 67468 54786 64369 62142 50649 74412 93084 94805 FALSE TRUE 63562.01628 67024.79827 81280.69285 78984.96527 60905.49578 52597.4998 67195.53569 73178.71098 83597.2609 0.760336111 0.801758306 0.972288948 0.944827192 0.728558509 0.629177311 0.803800686 0.875372114 1 16.35116805 1.347585632 2.557503531 1.019639186 0.808593492 0.285513628 0.09805446 0.611371021 5.348654017 0.253809552 0.028802601 22.26309972 -1.347585632 -0.211045693 DVYKEHFQDDVFNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVYKEHFQDDVFNEK 15 1 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ; 189.37 1.57E-07 542990000 634180 475210 261900 278370 462730 366020 659580 733330 101919 FALSE TRUE 550371.5062 472088.3142 388555.716 341578.1631 453522.5783 380101.0262 595614.0331 576513.0863 89870.25193 6.124067691 5.252998674 4.323518714 3.800792318 5.046414899 4.229442091 6.627488188 6.41494904 1 16.45555603 4.60798133 3.333105321 4.764099876 6.146914635 0.086060924 1.559249122 0.809905923 14.65045547 0.392795436 2.303010495 40549.11036 -4.60798133 1.382814759 DVYLS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 DVYLSPR 7 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 1 DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR 139.38 0.0028279 1.16859E+11 104850014 95974729 64200321 73698122 91710923 90821592 89660410 103677287 103138057 TRUE FALSE 90993818.99 95344264.69 95247810.97 90432407.01 89886055.06 94315557.41 80965157.24 81506705.99 90945193.4 1.000534669 1.048370575 1.047310005 0.994361589 0.988354103 1.037059287 0.890263182 0.896217853 1 26.43849406 2.242967542 24.99987174 0.920426606 1.019380324 0.580105143 0.036062601 70.2011997 398244.5842 0.013938266 0.0104139 174.9715914 -2.242967542 0.098953719 DVYLS(ph)PRDDGYSTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(0.999)PRDDGYS(0.001)TK;DVYLS(1)PRDDGYSTK;DVYLS(1)PRDDGYSTK 181.51 4.29E-06 3738940000 2966890 2824730 555945 493171 2105180 1802330 3129370 3164420 187947.7 TRUE FALSE 2574807.969 2806174.163 824801.8615 605153.0132 2063291.037 1871666.801 2825884.179 2487733.409 165728.737 15.53627944 16.932333 4.976818604 3.651466994 12.44980849 11.29355618 17.05126238 15.01087532 1 17.33846426 4.268285047 24.98917111 10 16.23431577 0.235346592 5.055412856 355.6276465 298968.4932 1.351358658 3.57429112 18547.48579 -4.268285047 6.234315772 DVYLSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DVYLSPR 7 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ; 143.85 0.0055686 1289760000 1020690 1082920 598420 729440 976620 993180 947710 1007620 1076280 FALSE TRUE 885803.2304 1075806.227 887817.9136 895070.5008 957187.1727 1031388.277 855801.2301 792148.3043 949043.4045 0.933364297 1.133569047 0.935487154 0.943129151 1.008581028 1.086766182 0.901751412 0.834680796 1 19.85611454 2.13480025 9.313766508 0.894565901 1.006425024 0.24778437 0.075804791 0.328486148 26.96943791 0.030160357 0.02032358 136.3955652 -2.13480025 0.111859123 DVYLSPRDDGYS(ph)TK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVYLSPRDDGYSTK 14 1 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 1 DVYLS(0.024)PRDDGYS(0.884)T(0.091)K 224.97 7.76E-12 255070000 586780 550380 99777 98704 371970 333110 596460 556510 16512 TRUE FALSE 509235.5363 546764.5175 148029.4909 121116.2518 364568.5247 345924.9573 538615.401 437504.6673 14559.97017 34.97503981 37.55258501 10.16688147 8.318440929 25.03909833 23.7586309 36.99289179 30.04845904 1 13.82971978 7.999999998 0.069788255 9.999999999 54.99510479 0.064187191 12.36134047 3309.17245 22.16919771 3193.205452 15688.50665 99999999.58 -7.999999998 44.99510479 DVYTGDALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVYTGDALR 9 0 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 76.827 0.079869 319550000 877390 732110 338840 455180 744800 699320 694680 726360 504520 FALSE TRUE 761440.6885 727300.7212 502704.1574 558535.576 729979.9372 726223.2929 627310.0405 571033.5665 444876.2204 1.711578758 1.634838384 1.129986577 1.255485347 1.640860769 1.632416523 1.410077707 1.283578534 1 18.76304446 1.362984179 1.80161358 0.906972452 1.485003696 0.430362789 0.183261535 0.741165683 2.910786083 0.692633692 0.055381309 23.06663156 -1.362984179 0.578031243 DVYVPEASRPHQWQTDEEGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DVYVPEASRPHQWQTDEEGVR 21 1 P49757-3;P49757;P49757-8;P49757-7;P49757-6;P49757-5;P49757-4;P49757-2;G3V4S6;G3V433;G3V3R1;G3V3M5 P49757-3 NUMB Protein numb homolog 0 204.55 3.15E-22 366430000 419530 338370 243100 287970 341980 362820 342400 362220 421320 FALSE TRUE 364088.0475 336147.2252 360663.9731 353357.9898 335175.2671 376777.9202 309194.1007 284762.0718 371512.0296 0.980016846 0.904808454 0.970800255 0.951134719 0.902192232 1.014174213 0.832258651 0.766494889 1 18.5030494 2.219684313 24.99968106 0.844052221 0.949923449 0.254968903 0.066881873 257.9065717 341567.6571 0.026281087 0.017751474 165.8380999 -2.219684313 0.105871229 DVYVQLYLQHLTAR ddPTM_MDA-MB-175_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 ; 143.64 9.07E-06 517446000 216996 213644 125822.7 198652.8 216565 214530 198812 286144 222412 FALSE TRUE 188319.4288 212240.5585 186670.9786 243759.9545 212255.7802 222783.1079 179531.2428 224954.3324 196118.7067 0.960231851 1.082204559 0.951826481 1.242920466 1.082282174 1.135960519 0.915421307 1.14703149 1 17.58136763 5.629156373 1.16372757 1.077089173 0.347972161 0.109762814 0.096373842 24.13317767 5.767786911 0.026632686 35.03828457 425751.6825 -5.629156373 -0.729117012 DWDAWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DWDAWK 6 0 P04181;P04181-2 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 ;;; 117.7 0.05234 1567100000 2500090 2629540 1958710 3280100 3017360 2550950 2750820 3623840 3277500 FALSE TRUE 2169696.772 2612266.379 2905948.707 4024896.838 2957320.439 2649086.697 2484045.9 2848910.017 2890037.684 0.750750339 0.903886615 1.005505473 1.392679708 1.023280927 0.916627043 0.859520246 0.985769159 1 21.46265687 4.52831335 2.720540601 1.021802681 0.74977395 0.291439394 0.14032305 0.463499853 5.913754267 0.03919587 0.225528122 33753.07542 -4.52831335 -0.272028732 DWDDDQND ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DWDDDQND 8 0 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 158.07 0.00085402 645070000 1722510 1536920 1173570 1263980 1393850 1437550 1646580 1767450 1596280 FALSE TRUE 1494875.939 1526823.871 1741112.377 1550985.978 1366115.112 1492853.479 1486894.925 1389494.572 1407569.597 1.062026306 1.084723537 1.236963615 1.101889371 0.970548892 1.06058946 1.056356239 0.987158699 1 20.42477483 3.387870946 6.260859091 1.017384447 1.130824895 0.50592401 0.052684878 0.172768491 9.879648179 0.015516524 0.020107893 2442.704577 -3.387870946 0.113440448 DWEDDS(ph)DEDMSNFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 34 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 463.62 1.14E-198 2.75646E+11 20717218 16595452 13727856 16498054 17936462 16202190 18037846 21037460 25491136 TRUE FALSE 17979385.15 16486435.38 20366693.08 20244189.32 17579561.5 16825498.73 16288538.47 16538762.89 22477602.94 0.799880005 0.733460566 0.906088302 0.900638265 0.782092359 0.748545064 0.724656384 0.735788551 1 24.42198486 DWEDDSDEDMSNFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DWEDDSDEDMSNFDR 15 0 A0A087WYT3;Q15185-4;Q15185;B4DDC6;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ;; 329.15 1.89E-68 675480000 597660 444900 352412 431440 451580 420052 460920 553310 569970 FALSE TRUE 518677.7167 441977.4226 522839.6219 529405.0461 442594.4415 436211.6722 416220.0493 434988.9624 502588.7959 1.032012096 0.879401662 1.040293031 1.053356244 0.880629344 0.86792956 0.828152264 0.865496736 1 18.93901898 3.218951958 24.82114344 0.880026132 0.995348831 0.424917659 0.064648802 209.5910706 265304.9208 0.019630108 0.022289885 1655.586813 -3.218951958 0.1153227 DWEMHVHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DWEMHVHFK 9 0 Q12907;D6RBV2;D6RDX1;D6RIU4;D6RBH1 Q12907 LMAN2 Vesicular integral-membrane protein VIP36 0 107.21 0.0016257 299790000 184490 180280 132710 160210 148110 141120 158090 188640 250890 FALSE TRUE 160109.1791 179095.7288 196888.9999 196588.1292 145162.9008 146548.9777 142758.4561 148300.804 221230.07 0.723722499 0.809545144 0.889973953 0.888613963 0.656162613 0.662427932 0.645294087 0.670346504 1 17.75518797 5.051290716 14.13073087 0.762981262 0.5154184 0.006244344 0.122115365 27435079.43 228283565.2 0.031358594 180329702.9 112535.8036 -5.051290716 -0.247562862 DWEQFEYK ddPTM_MDA-MB-175_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 ;; 147.51 0.0020987 177910000 897290 857220 606680 697080 805640 659110 880670 1080520 946820 FALSE TRUE 778710.8531 851588.8654 900072.4772 855362.6682 789609.3402 684466.3882 795262.7589 849459.2066 834888.0182 0.932712934 1.020003697 1.078075691 1.024523828 0.945766765 0.819830173 0.952538235 1.017452866 1 19.67122318 3.237814143 24.99065042 0.949951683 1.01885914 0.217955924 0.062341554 33.77651896 1130787.657 0.020354264 0.024472267 1729.076241 -3.237814143 0.068907456 DWEQFHQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DWEQFHQPR 9 0 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 ;;;; 160.82 6.50E-05 3027780000 2378710 2483200 1406680 1656690 2479050 2542550 2192090 2622050 1985450 FALSE TRUE 2064357.447 2466887.696 2086955.153 2032866.785 2429721.755 2640363.544 1979501.449 2061345.012 1750732.363 1.179139365 1.40906043 1.192046938 1.161152229 1.387831634 1.508148018 1.130670508 1.177418694 1 20.73952712 1.570471239 1.694520106 1.003069932 1.297474942 0.371121765 0.120558903 0.537783254 2.573873359 0.229262773 0.035519677 37.19385886 -1.570471239 0.294405009 DWGEHNQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DWGEHNQR 8 0 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 113.18 0.0028991 108600000 103520 111450 63432 78181 87415 93154 84505 115500 103200 FALSE TRUE 89839.56971 110717.8776 94107.92737 95933.19097 85675.61252 96737.69466 76309.71811 90801.22382 90999.81357 0.987250041 1.216682466 1.034155167 1.05421305 0.941492176 1.063053768 0.838570049 0.997817691 1 16.47357597 3.508515399 1.693733893 0.965091038 1.098929847 0.286259344 0.080989576 0.410782662 2.366288115 0.024634939 0.041719401 3224.893662 -3.508515399 0.133838809 DWHRPCLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DWHRPCLK 8 1 P50238 P50238 CRIP1 Cysteine-rich protein 1 0 ;;;; 147.36 0.00032355 17094510000 11178550 8666840 5298527 6483620 7579050 6312420 7951550 9212740 8405010 FALSE TRUE 9701276.295 8609906.957 7860912.38 7955825.017 7428241.733 6555262.882 7180409.905 7242667.245 7411379.293 1.308970424 1.161714523 1.060654444 1.073460783 1.002275209 0.884486224 0.968835843 0.97723608 1 22.82131063 5.180342225 0.631006254 0.960400314 1.753267578 0.893863619 0.038278471 1.78955508 0.370339689 0.01956283 1.157896061 151475.4409 -5.180342225 0.792867263 DWHRPCLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DWHRPCLR 8 1 P52943;H0YFA4;H0YHD8;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 72.23 0.042584 268220000 164150 164380 108180 117900 133930 126240 152490 183240 173660 FALSE TRUE 142457.1616 163300.177 160496.2098 144670.997 131265.055 131096.5345 137701.5433 144055.552 153130.1126 0.930301422 1.066414529 1.048103519 0.94475864 0.857212555 0.856112049 0.89924536 0.940739542 1 17.22439849 3.56661484 4.871802168 0.91000722 1.018922412 0.43879662 0.053657678 0.206191947 8.189774586 0.015612387 0.023268811 3686.505106 -3.56661484 0.108915192 DWILPSDYDHAEAEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DWILPSDYDHAEAEAR 16 0 O43852;O43852-3;O43852-15;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;;; 275.83 2.82E-35 2597190000 2299120 1866230 1657050 2291550 2002580 2420990 1724240 1943960 3615010 FALSE TRUE 1995285.467 1853970.612 2458404.922 2811881.452 1962732.576 2514127.052 1557023.47 1528259.282 3187647.636 0.625942919 0.581610901 0.771228568 0.88211803 0.615730721 0.788709211 0.488455328 0.479431686 1 21.60406073 2.256158216 24.99690208 0.612205585 0.711214036 0.001132407 0.168433376 693.48905 985080.4259 0.063028173 0.048711291 180.3674712 -2.256158216 0.099008451 DWLFAPHYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DWLFAPHYR 9 0 Q15008;Q15008-4;Q15008-3;Q15008-2 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 114.84 0.0015728 561560000 639190 629270 397030 495260 667830 731470 652420 652960 861630 FALSE TRUE 554719.422 625136.2839 589035.036 607716.3526 654541.4896 759610.1242 589148.4088 513329.5853 759769.083 0.730115813 0.822797739 0.77528166 0.799869811 0.861500559 0.99979078 0.77543088 0.67563895 1 19.53520148 3.414417156 5.376091456 0.839243507 0.781672842 0.120790561 0.098521324 0.643348906 36.54183754 0.030873632 0.040415779 2596.672364 -3.414417156 -0.057570664 DWNDMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DWNDMER 7 0 P61163;R4GMT0;A0A1B0GVS3;P42025 P61163;P42025 ACTR1A;ACTR1B Alpha-centractin;Beta-centractin 0 ; 105.81 0.018247 5122600000 9556000 7784400 5938500 7170400 7912600 7958800 8530000 10188600 10352100 FALSE TRUE 8293150.388 7733263.764 8810378.463 8798548.913 7755154.741 8264980.186 7702761.913 8009847.178 9128286.531 0.908511182 0.847175835 0.965173303 0.963877381 0.849573982 0.905425148 0.84383437 0.877475433 1 23.12191265 3.232922338 24.9981502 0.889689614 0.919040158 0.048856533 0.053428177 429.1759158 1902810.451 0.016173352 0.018860762 1709.709551 -3.232922338 0.029350544 DWPELQDDIPHILAQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DWPELQDDIPHILAQAR 17 0 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 0 ; 208.26 5.34E-12 183518000 120048 96178 71777 78080 103242 99988 100019 120749 108854 FALSE TRUE 104183.3526 95546.20039 106488.5973 95809.25738 101187.6862 103834.6031 90319.17277 94927.76602 95985.40413 1.085408282 0.995424265 1.109424899 0.998164859 1.054198679 1.081774922 0.940967781 0.988981261 1 16.55052742 2.241573675 24.99985521 0.977732013 1.051381838 0.471266136 0.038580068 65.51175705 543567.5311 0.013726076 0.010158363 174.4109209 -2.241573675 0.073649825 DWQSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DWQSGR 6 0 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 154.92 0.023133 1202500000 395280 324130 181550 254900 248940 279950 292860 350120 317120 FALSE TRUE 343042.7465 322000.7687 269348.1872 312778.9409 243986.581 290719.8577 264458.4823 275249.5626 279630.4349 1.226771852 1.151522612 0.963229154 1.118543985 0.872532281 1.039657424 0.945742842 0.98433335 1 18.09316187 4.57771688 1.21835218 0.981296646 1.312029538 0.613998254 0.065700031 0.682992457 1.077004687 0.0178767 0.266055744 37819.59555 -4.57771688 0.330732892 DWQSYYYHHPQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DWQSYYYHHPQDR 13 0 Q1KMD3 Q1KMD3 HNRNPUL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;;; 179.39 7.97E-06 5382710000 2089890 1788910 974087 1394150 1787000 1890810 1643960 1847180 1939210 FALSE TRUE 1813705.741 1777158.532 1445158.731 1710713.066 1751442.196 1963550.684 1484529.012 1452174.932 1709958.803 1.060672186 1.039299034 0.845142426 1.0004411 1.024259879 1.148302919 0.868166537 0.849245566 1 20.70553014 2.179076776 24.99999963 0.892452401 1.011979295 0.281773848 0.084224102 93.9959664 39503.81995 0.035311588 0.023807074 151.0347133 -2.179076776 0.119526894 DWQSYYYHHPQDRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DWQSYYYHHPQDRDR 15 1 Q1KMD3 Q1KMD3 HNRNPUL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 87.647 0.0045743 352140000 223952 183000 60643 87766 172183 189788 171421 211522 80144 FALSE TRUE 194356.1758 181797.861 89970.15764 107694.6117 168756.8952 197089.2672 154796.6178 166289.6664 70669.46762 2.750214234 2.572509276 1.273112147 1.523919952 2.387974621 2.788888523 2.190431356 2.35306239 1 16.10879942 DWSNDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DWSNDVR 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 80.229 0.070907 722740000 1591600 1317500 877900 1103800 1470400 1186800 1546800 1638200 1417300 FALSE TRUE 1381266.027 1308845.256 1302455.376 1354434.661 1441141.917 1232456.964 1396791.574 1287883.678 1249748.409 1.105235276 1.047286995 1.042174063 1.083765861 1.153145631 0.986164059 1.117658214 1.030514358 1 20.25320626 1.528081485 5.475051141 1.006597332 1.073961726 0.248337613 0.045636829 0.186962627 11.75613173 0.031486221 0.011012413 33.73505985 -1.528081485 0.067364393 DWTISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DWTISR 6 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 127.66 0.039465 313030000 384280 367070 227170 284530 376420 397370 359860 445850 422650 FALSE TRUE 333496.4244 364658.693 337030.1718 349136.8853 368929.9785 412657.081 324960.8326 350508.4471 372684.7985 0.894848477 0.978464092 0.904330344 0.936815472 0.989924944 1.107254932 0.871945499 0.940495691 1 18.50759645 3.332273383 6.274165625 0.974646704 0.929645622 0.150124593 0.061847888 0.528139763 29.36522043 0.018623662 0.024049559 2149.182931 -3.332273383 -0.045001082 DWVLNEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DWVLNEFK 8 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 130.96 0.0023855 1074100000 1043300 987340 563000 689890 867560 690120 1010400 1200900 959110 FALSE TRUE 905425.2616 980854.0985 835268.6831 846540.0688 850297.2534 716669.363 912411.5635 944096.8804 845725.1084 1.070590494 1.159778856 0.987636142 1.000963623 1.005406183 0.847402254 1.078851218 1.116316485 1 19.68982929 4.2320311 24.99997504 1.013305988 1.115184682 0.278849318 0.072617274 208.6290481 798802.6585 0.020318126 0.043935285 17062.04568 -4.2320311 0.101878693 DWVLNEFR ddPTM_MDA-MB-175_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 ;;;;; 200.16 0.00028405 4807967000 1952870 2068090 1433391 1640390 2025970 2050130 1980990 2206170 2442720 FALSE TRUE 1694793.282 2054504.581 2126583.682 2012865.621 1985657.161 2128999.828 1788873.895 1734397.714 2153944.424 0.78683241 0.953833607 0.987297378 0.934502116 0.921870192 0.988419109 0.830510701 0.805219343 1 21.0385496 0.924202312 11.52336036 1.731867031 0.902052767 0.15715617 0.071974928 70687.27819 387804.2726 1323143.033 0.018901024 8.398511331 -0.924202312 -0.829814264 DWYDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DWYDVK 6 0 P61247;E9PFI5;D6RG13;H0Y8L7;H0Y9Y4;D6RI02 P61247 RPS3A 40S ribosomal protein S3a 0 101.52 0.084748 939460000 1719900 1480800 1103300 1316400 1430200 1149700 1770100 1983500 1821900 FALSE TRUE 1492610.857 1471072.527 1636859.57 1615308.74 1401741.818 1193929.703 1598435.974 1559343.961 1606517.058 0.929097422 0.915690574 1.01888714 1.005472511 0.872534662 0.743178977 0.994969812 0.970636417 1 20.61550487 DWYPHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 16 DWYPHSR 7 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;;;;;;;;;; 157.58 0.0014664 3.29278E+11 21241332.7 21689347 15894940 18624678 19912322 22331346.1 20734759.2 22153305 29659364 FALSE TRUE 18434236.77 21546868.25 23581786.15 22853695.8 19516105.75 23190447.43 18723905.44 17415993.12 26153067.78 0.704859442 0.823875365 0.901683365 0.873843788 0.746226252 0.886719969 0.715935339 0.665925438 1 24.64047685 2.2309034 24.99922914 0.764030314 0.825329697 0 0.105590519 514.8142163 1680744.652 0.042043459 0.02895508 170.1779938 -2.2309034 0.061299383 DYAAYNVLDDPELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DYAAYNVLDDPELR 14 0 Q86SX6 Q86SX6 GLRX5 "Glutaredoxin-related protein 5, mitochondrial" 0 ;; 214.81 1.57E-11 218651000 415334 459441 321729 528235 550268 577377 420870 559327 532965 FALSE TRUE 360446.5596 456422.9018 477318.2205 648178.8303 539318.7434 599589.0668 380054.0922 439719.2737 469958.4849 0.766975321 0.971198343 1.015660395 1.379225721 1.147588055 1.275834113 0.80869716 0.935655569 1 18.84217379 2.224557677 24.99899217 0.914712166 1.09923268 0.192499666 0.171479326 402.5995035 718742.2814 0.073689738 0.049962358 167.7095049 -2.224557677 0.184520515 DYAESVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYAESVGR 8 0 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 0 78.178 0.060466 0 484130 389260 345040 399000 377250 324780 438250 505210 864560 FALSE TRUE 420150.9939 386702.9254 511902.4981 489599.0483 369743.4631 337274.4968 395748.5825 397174.773 762352.7017 0.551124162 0.507249367 0.671477253 0.642221176 0.485003152 0.442412673 0.519114816 0.520985591 1 19.54009909 1.237006771 24.99928075 1.000000564 0.541477438 0.815010456 0.068505528 18.03421982 290048.5622 0.111702238 0.018143004 17.25864798 -1.237006771 -0.458523126 DYAFIHFDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DYAFIHFDER 10 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;;;;; 165.11 5.95E-06 5845230000 7253805 5876895 4005311 5133586 5544554 5777475 5399148 6386582 9134910 FALSE TRUE 6295196.29 5838289.29 5942292.797 6299245.163 5434228.223 5999738.202 4875539.458 5020861.14 8054991.346 0.781527381 0.724803918 0.737715603 0.782030035 0.6746411 0.744847256 0.605281775 0.623322971 1 22.94145161 3.241653608 24.99417353 0.707767834 0.752910734 0 0.109642838 332.5680693 2687431.799 0.031894835 0.039423261 1744.430247 -3.241653608 0.0451429 DYAFVHFEDR ddPTM_MDA-MB-175_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 ;;;;; 174.4 3.12E-06 3999660000 4321600 3908800 2568580 3083640 3664890 3609660 3716160 4167290 4533660 FALSE TRUE 3750489.61 3883122.835 3810753.879 3783827.592 3591965.859 3748525.956 3355767.375 3276147.463 3997695.88 0.938162813 0.97134023 0.953237563 0.946502112 0.898509033 0.937671616 0.839425378 0.819508928 1 21.93073729 2.941805984 1.319379373 0.875993621 0.955980292 0.176936194 0.051027304 0.548350709 2.012731561 0.023303215 0.023847028 874.5929736 -2.941805984 0.079986671 DYAFVHFTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DYAFVHFTSR 10 0 B7Z8Z7;A0AV96;A0AV96-2;D6R9D6 B7Z8Z7 RBM47 RNA-binding protein 47 0 ;;; 105.46 0.0025462 874153000 760680 725803 369602 549523 790619 766375 666565 740048 868860 FALSE TRUE 660154.2107 721035.1523 548342.7634 674300.5961 774887.2287 795857.9422 601921.6289 581794.4943 766144.3606 0.86165773 0.94112179 0.715717287 0.880122116 1.011411515 1.038783267 0.785650407 0.759379726 1 19.54725673 5.618808084 18.61848552 0.879048996 0.865549292 0 0.111326315 0 0 0.026141383 0 415726.8588 -5.618808084 -0.013499704 DYAFVHMEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DYAFVHMEK 9 0 Q96PK6;Q96PK6-2 Q96PK6 RBM14 RNA-binding protein 14 0 ;;; 139.43 0.0001115 1859480000 3799120 2972040 2322680 2861730 2888010 2649430 3400470 4053050 4795030 FALSE TRUE 3297056.666 2952516.474 3445935.817 3511529.535 2830544.251 2751355.287 3070692.943 3186336.798 4228167.016 0.779783924 0.698297031 0.814995199 0.83050871 0.66944949 0.650720578 0.726246842 0.753597667 1 22.01160093 1.236695785 4.875269438 1.018437115 0.737772344 0.664928164 0.057994536 0.117989831 6.799413873 0.113448251 0.015386067 17.246294 -1.236695785 -0.280664771 DYAFVHMER ddPTM_MDA-MB-175_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 ;;; 143.61 0.00010153 1415690000 2074710 1878500 1208400 1506820 1709500 1786350 1649720 1975180 2379980 FALSE TRUE 1800531.817 1866160.01 1792786.282 1848966.511 1675484.295 1855072.04 1489730.408 1552803.128 2098621.476 0.857959302 0.889231351 0.854268529 0.881038593 0.798373749 0.883947897 0.709861414 0.739915771 1 21.00101054 3.09411724 1.575704439 0.805077718 0.872023636 0.021220957 0.081127881 0.890391682 4.597802068 0.031124902 0.036859375 1241.987542 -3.09411724 0.066945917 DYALHWLVLGTHTSDEQNHLVVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYALHWLVLGTHTSDEQNHLVVAR 24 0 Q16576;E9PC52;Q16576-2;C9J7L0 Q16576 RBBP7 Histone-binding protein RBBP7 0 202.43 4.55E-25 55138000 44474 46515 10956 29684 49772 45190 40634 50200 54698 FALSE TRUE 38596.64822 46209.4399 16254.35825 36424.20589 48781.63458 46928.48854 36693.32093 39465.12066 48231.66475 0.800234626 0.958072672 0.337005955 0.755192799 1.011402671 0.972980899 0.760772433 0.818240898 1 15.55769299 3.46109709 22.03117169 0.891660613 0.694684404 0.252581616 0.17115907 89.09431289 122491.1312 0.050077963 0.064689629 2891.326186 -3.46109709 -0.196976208 DYAPPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DYAPPPR 7 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;;; 123.99 0.009748 846860000 1094910 955780 769750 763930 913720 948910 926980 1075660 1019670 FALSE TRUE 950214.8694 949501.4182 1142003.675 937391.9824 895538.7597 985415.1817 837081.6223 845638.4798 899125.7742 1.056820855 1.056027361 1.270126725 1.04255935 0.996010553 1.095970341 0.930995025 0.940511888 1 19.77816342 2.764918596 1.038113703 0.953772365 1.114732312 0.375061258 0.075392854 0.525424346 1.248931365 0.049116867 0.038815396 581.9941187 -2.764918596 0.160959947 DYAVSTVPVADGLHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYAVSTVPVADGLHLK 16 0 O94760;B4DYP1;O94760-2 O94760 DDAH1 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1" 0 174.62 3.81E-09 502990000 269730 260650 188340 198120 224620 226240 291780 312420 369560 FALSE TRUE 234084.4971 258937.773 279421.854 243106.1741 220150.5015 234943.5992 263483.2205 245611.4143 325871.0378 0.71833477 0.794601983 0.857461454 0.746019578 0.675575537 0.720971096 0.808550592 0.753707405 1 18.31394161 1.237445225 24.99850169 1.000000284 0.761365108 0.684496173 0.05131919 17.59840148 394238.481 0.078769549 0.013186443 17.27608073 -1.237445225 -0.238635176 DYDDMS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 19 DYDDMSPR 8 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR 184.9 0.00022614 91090240000 60076090 51821890 34213460 39635970 48077040 47004800 53186520 57934490 53880910 TRUE FALSE 52136882.49 51481468.59 50759203.69 48635922.79 47120400.97 48813105.07 48028499.48 45545650.16 47511170.2 1.097360521 1.083565578 1.068363576 1.023673435 0.991775213 1.027402711 1.010888582 0.958630359 1 25.50176341 3.994275402 0.578005351 0.982240901 1.132990517 0.828922766 0.017836944 0.752444092 0.378908356 0.014178543 0.071788402 9869.051206 -3.994275402 0.150749616 DYDDMSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 DYDDMSPR 8 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;;;;;; 214.69 2.03E-05 21892620000 24589940 20370250 13547330 15416310 19451870 18291860 20708570 23334070 21438360 FALSE TRUE 21340317.13 20236436.49 20098864.1 18916818.81 19064815.84 18995559.69 18700256.07 18344260.72 18903941.5 1.128881885 1.07048768 1.063210236 1.000681197 1.008510095 1.004846512 0.98922524 0.970393434 1 24.17218373 5.259722001 0.496270922 0.980710124 1.322430636 0.932356429 0.012401498 1.788116105 0.241781128 0.008912002 0.395695309 181853.6412 -5.259722001 0.341720512 DYDEEEQGYDS(ph)EK ddPTM_MDA-MB-175_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 292.76 1.45E-40 598120000 741150 460420 458970 458980 459960 433130 532850 602780 1129910 TRUE FALSE 643205.1497 457395.4707 680929.4272 563198.4241 450807.6959 449792.7914 481174.289 473880.1878 996333.327 0.645572252 0.459078762 0.683435361 0.565271088 0.452466743 0.451448104 0.482945091 0.475624146 1 19.92626896 1.235195348 24.99155698 1.000000668 0.521783686 0.766063544 0.082103625 46.22125609 343196.9601 0.14287278 0.020279406 17.18681284 -1.235195348 -0.478216981 DYDEEEQGYDS(ph)EKEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DYDEEEQGYDSEKEK 15 1 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 DYDEEEQGYDS(1)EKEK;DYDEEEQGYDS(1)EKEK 223.51 7.62E-13 2624160000 1775350 984540 1059360 964550 983320 985230 1408330 1640590 2367680 TRUE FALSE 1540732.999 978072.4919 1571670.039 1183565.82 963753.8558 1023132.436 1271750.373 1289762.596 2087775.568 0.737978269 0.468475878 0.752796452 0.566902802 0.461617556 0.490058631 0.609141324 0.617768794 1 20.9935352 1.20482556 3.222395554 1.093500763 0.578429221 0.624762821 0.100467557 0.264946787 3.449780644 0.363426621 0.025028073 16.02601555 -1.20482556 -0.515071542 DYDEEEQGYDS(ph)EKEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 185.61 8.52E-10 2112970000 1806150 839210 1099810 845670 886650 818850 1422720 1628080 1704530 TRUE FALSE 1567462.701 833697.1743 1631681.795 1037692.299 869007.3997 850351.6894 1284744.833 1279927.762 1503022.405 1.042873809 0.55468047 1.085600447 0.690403746 0.578173284 0.565761153 0.85477424 0.851569316 1 20.51943508 1.481778588 1.857915136 1.011595516 0.751215238 0.138000018 0.18631091 0.980181894 5.224321085 0.40184734 0.051255157 30.32344841 -1.481778588 -0.260380278 DYDEEEQGYDS(ph)EKEKKEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYDEEEQGYDSEKEKKEEK 19 3 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 DYDEEEQGYDS(1)EKEKKEEK 195.34 8.20E-16 226750000 749590 369940 404210 205060 258660 184300 650780 584390 273180 TRUE FALSE 650529.7823 367509.8398 599687.308 251622.0071 253513.1721 191390.1403 587667.4558 459422.7462 240884.9716 2.70058268 1.525665289 2.489517316 1.044573289 1.052424194 0.794529185 2.439618594 1.907228762 1 17.87798486 3.743064741 24.90264719 1.457898969 2.16729611 0.327951695 0.57257324 553.5593761 3060538.54 0.162262223 0.269153894 5534.326047 -3.743064741 0.709397141 DYDHLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DYDHLFK 7 0 F5H157;Q15286-2;Q15286;F5H7F8 F5H157 RAB35 Ras-related protein Rab-35 0 ; 91.626 0.019815 248780000 1279930 1113110 772890 1169030 1288530 1163650 1257390 1757160 1566690 FALSE TRUE 1110784.008 1105797.907 1146662.189 1434476.129 1262890.774 1208416.368 1135448.511 1381405.008 1381477.693 0.804054972 0.80044572 0.830025845 1.038363584 0.914159367 0.874727384 0.821908683 0.999947386 1 20.39778084 3.932039844 9.303824922 0.936207226 0.805422878 0.487163511 0.063180973 0.399319238 52.64594689 0.017630814 0.030663953 8551.451641 -3.932039844 -0.130784348 DYDPVAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYDPVAAR 8 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 82.241 0.048351 313380000 966160 998220 741390 1033000 1080300 1031500 941360 1027700 1852400 FALSE TRUE 838479.5081 991662.6271 1099928.684 1267558.438 1058804.144 1071182.472 850067.0521 807934.3526 1633411.382 0.513330271 0.607111373 0.673393547 0.776019105 0.64821646 0.655794666 0.520424347 0.494630049 1 20.63945676 -1.999988344 0.019740945 1.440265444 2.23E-08 0.064912232 0.144239749 42036.18076 82.50242259 3774.126288 2396.253156 0.010000268 1.999988344 -1.440265422 DYDRDKDDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYDRDKDDK 9 2 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 131.28 0.00018979 255880000 347290 229690 302500 263230 159670 187060 349000 344170 240870 FALSE TRUE 301394.7466 228181.1513 448790.0118 323000.3947 156492.8794 194256.3192 315154.0337 270571.9238 212394.623 1.419031905 1.074326403 2.113000816 1.520755988 0.736802454 0.914600928 1.483813617 1.273911364 1 17.69638772 3.404852075 17.0187781 1.127673507 1.543926061 0.322568614 0.320185784 4.014816704 943.3529581 0.09588016 0.123780293 2540.107371 -3.404852075 0.416252554 DYDRDKDDKISWEEYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYDRDKDDKISWEEYK 16 3 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 212.69 1.69E-12 130400000 713930 398170 351850 234190 345360 248290 614000 590240 73296 FALSE TRUE 619582.3416 395554.3951 522005.8369 287366.4189 338488.0117 257841.877 554454.3745 464021.7693 64631.03038 9.586453102 6.120193237 8.076706093 4.446260831 5.237236815 3.989444009 8.578764275 7.179550852 1 15.97993937 7.183051013 0.774495223 5.552280161 199.9970921 0.275269499 2.147380383 165.4135996 2.630814907 0.782766948 53853.11069 15242317.82 -7.183051013 194.444812 DYDS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYDSPER 7 0 P52756;C9JR02;C9J9P7;C9JFQ5;P52756-4;P52756-2;P52756-5;F8W910;P52756-3 P52756 RBM5 RNA-binding protein 5 1 DYDS(1)PER 131.62 0.0036176 110270000 281010 221150 222470 255700 237940 227310 217840 259430 643550 TRUE FALSE 243873.8165 219697.2511 330057.2361 313760.5931 233205.4595 236054.7628 196713.9103 203952.9134 567470.2521 0.429756125 0.387152014 0.581629142 0.552911086 0.410956272 0.415977334 0.346650612 0.359407233 1 19.11418524 1.234014408 24.99996471 1.000000847 0.433157235 0.844283646 0.076174872 58.23078418 320175.1377 0.162013863 0.020845628 17.14014169 -1.234014408 -0.566843612 DYDS(ph)PERER ddPTM_MDA-MB-175_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(0.002)DS(0.998)PERER;DYDS(1)PERER;DYDS(1)PERER 118.76 0.00056779 606910000 857430 782230 561190 624200 778280 764660 798960 904410 716380 TRUE FALSE 744118.453 777091.4796 832583.3611 765934.1503 762793.7507 794076.965 721476.9822 711008.9596 631690.3725 1.177979728 1.230177811 1.318024458 1.212515156 1.207543733 1.257066752 1.142137056 1.12556561 1 19.26885806 0.951803046 0.810792598 0.749623409 1.239276713 0.772715194 0.040774977 1.711007201 0.641455183 0.847151649 0.015903087 8.949588072 -0.951803046 0.489653304 DYDSTCVFCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DYDSTCVFCR 10 0 Q9NQE9 Q9NQE9 HINT3 Histidine triad nucleotide-binding protein 3 0 ; 203.02 4.95E-07 433750000 377000 352140 283230 277320 294290 293550 328500 368670 330380 FALSE TRUE 327178.4948 349826.7692 420200.9753 340289.7446 288434.2048 304843.0585 296642.1206 289832.7895 291322.8528 1.123078714 1.200821583 1.442389333 1.168084623 0.990084376 1.046409698 1.018259013 0.994885182 1 18.15225935 3.381401515 4.420248513 1.011283883 1.257919566 0.664709648 0.080619757 0.125534294 4.376850856 0.023827875 0.031255441 2406.586717 -3.381401515 0.246635684 DYDVYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DYDVYAR 7 0 P49585;C9JEJ2;C9J050;H7C1T3;H7BZN1;Q9Y5K3-2;Q9Y5K3-4;Q9Y5K3-3;Q9Y5K3 P49585 PCYT1A;PCYT1B Choline-phosphate cytidylyltransferase A;Choline-phosphate cytidylyltransferase B 0 ;;; 118.01 0.01187 1663000000 3220320 3077980 1816280 2337770 2945140 3222010 2890170 3249130 2953550 FALSE TRUE 2794746.553 3057760.547 2694639.083 2868596.409 2886537.476 3345962.81 2609881.758 2554328.834 2604384.684 1.073092838 1.174081758 1.034654788 1.101448809 1.108337602 1.284742162 1.0021107 0.980780163 1 21.31251113 2.040091465 24.99938689 0.989745317 1.126435496 0.479040076 0.066447728 121.1981745 75573.70278 0.026545244 0.017896771 109.6709146 -2.040091465 0.136690178 DYDWINAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DYDWINAER 9 0 O95347-2;O95347;A0A0C4DGE5 O95347-2 SMC2 Structural maintenance of chromosomes protein 2 0 ;;; 215.14 1.51E-06 455884000 801260 739080 495140 681910 748730 762850 728480 845130 918860 FALSE TRUE 695371.4609 734224.9348 734591.3601 836748.0878 733831.7379 792197.3331 657832.1217 664405.5263 810233.4176 0.858235967 0.9061894 0.906641647 1.032724731 0.905704112 0.977739644 0.811904456 0.820017432 1 19.62797806 1.196297719 23.73433648 1.000002163 0.901073592 0.175769021 0.066369859 10704.71279 6010826.761 7.164185524 0.017622752 15.71439694 -1.196297719 -0.098928571 DYEEIGPSICR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DYEEIGPSICR 11 0 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ;;; 223.08 1.68E-11 1156610000 837810 780950 529138 567060 710730 684140 713040 862670 832630 FALSE TRUE 727091.2858 775819.888 785030.9067 695819.64 696587.8635 710459.3085 643889.4905 678194.7338 734197.4299 0.990321208 1.056691098 1.069236795 0.947728243 0.948774587 0.967667932 0.876997745 0.923722566 1 19.48580854 3.682628721 6.791100646 0.938611921 1.040410925 0.58819778 0.037128976 0.155909559 15.79593715 0.01043539 0.015636753 4815.359558 -3.682628721 0.101799004 DYEEVGADS(ph)ADGEDEGEEY ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYEEVGADSADGEDEGEEY 19 0 Q9BQE3;F5H5D3 Q9BQE3 TUBA1C Tubulin alpha-1C chain 1 DYEEVGADS(1)ADGEDEGEEY 186.17 2.22E-14 64901000 141200 98284 85577 95004 107870 100670 113800 124510 125710 TRUE FALSE 122540.0622 97638.36593 126962.3234 116576.1102 105723.598 104542.84 102763.6935 97884.50544 110848.707 1.105471282 0.880825483 1.145365849 1.051668652 0.953764829 0.943112851 0.927062627 0.883045983 1 16.75823242 3.146992537 4.274691877 0.930613918 1.041129859 0.332491823 0.073158364 0.244831503 8.165740567 0.021760833 0.025230068 1402.789599 -3.146992537 0.110515941 DYEEVGADSADGEDEGEEY ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 DYEEVGADSADGEDEGEEY 19 0 Q9BQE3;F5H5D3 Q9BQE3 TUBA1C Tubulin alpha-1C chain 0 ;;;;;; 462.91 2.92E-214 5329500000 6259180 5051348 4294897 4643615 5056002 5085367 5423450 6004010 6382030 FALSE TRUE 5432013.504 5018165.362 6371923.555 5698018.759 4955397.452 5281004.359 4897484.654 4720099.185 5627553.684 0.965253076 0.891713459 1.132272371 1.01252144 0.880559783 0.938419188 0.870268847 0.838747962 1 22.42407648 3.240283884 24.98585982 0.896233978 1.002090506 0.292033661 0.072547078 54.31430549 787500.8777 0.021662867 0.026521574 1738.937143 -3.240283884 0.105856527 DYEEVGVDSVEGEGEEEGEEY ddPTM_MDA-MB-175_Pertuzumab_2h_R1 39 DYEEVGVDSVEGEGEEEGEEY 21 0 P68363;P68363-2 P68363 TUBA1B Tubulin alpha-1B chain 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 382.04 2.31E-113 7004207000 16870139 14114032 11656560 12739387 14100442 14660930 15026925 17507346 18003907 FALSE TRUE 14640707.39 14021315.99 17293711.4 15632059.53 13819870.79 15224945.46 13569616.13 13763536.3 15875505.62 0.922219911 0.883204373 1.089332952 0.984665301 0.870515316 0.959021138 0.854751744 0.866966799 1 23.92029921 3.248992181 24.99432357 0.903116536 0.972200365 0.155057973 0.067916846 358.5707224 859141.1313 0.019939241 0.025462003 1774.157539 -3.248992181 0.069083828 DYEHQFHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DYEHQFHLR 9 0 Q15276-2;Q15276;A0A087WZZ3 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 ;;; 183.43 2.61E-05 818040000 671226 665482 462234 523153 675621 673600 637910 711260 730430 FALSE TRUE 582521.7834 661110.4049 685771.9085 641942.8845 662177.4639 699513.8279 576045.5864 559162.584 644079.3975 0.904425426 1.026442404 1.064731943 0.996682842 1.028099123 1.086067697 0.894370459 0.868157849 1 19.29687902 2.220956023 24.99933938 0.908763691 1.019786577 0.374829878 0.058260648 218.6237492 310453.5891 0.023350751 0.01578337 166.3244221 -2.220956023 0.111022886 DYEIESQNPLAS(ph)PTNTLLGSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DYEIESQNPLASPTNTLLGSAK 22 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 DYEIESQNPLAS(0.984)PT(0.013)NT(0.003)LLGSAK;DYEIESQNPLAS(0.996)PT(0.004)NTLLGSAK;DYEIESQNPLAS(0.997)PT(0.003)NTLLGSAK;DYEIESQNPLAS(0.981)PT(0.019)NTLLGSAK 323.61 4.03E-68 1502850000 1159602 944123 764959 931244 1086410 882514 1291690 1532390 1353150 TRUE FALSE 1006357.658 937920.9938 1134895.731 1142697.183 1064792.567 916464.8846 1166422.103 1204700.324 1193182.149 0.843423327 0.786066901 0.951150445 0.957688803 0.892397333 0.768084643 0.977572539 1.009653325 1 20.18638287 2.05338207 11.91871943 1.001952369 0.871991378 0.504737018 0.060631607 0.631368349 139.3986383 0.026146256 0.017622599 113.0790289 -2.05338207 -0.129960991 DYEMNANHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DYEMNANHK 9 0 Q9NWH9;H7BXE3;H0YL55 Q9NWH9 SLTM SAFB-like transcription modulator 0 ; 88.681 0.01262 204132000 160681 132514 98930 115432 121190 112834 146388 167954 174954 FALSE TRUE 139446.5987 131643.5068 146772.8789 141642.5999 118778.5561 117174.797 132191.3143 132038.3441 154271.1374 0.903905948 0.853325573 0.951395584 0.918140634 0.769933755 0.759538038 0.856876513 0.855884946 1 17.23510865 DYENDEDVNKQLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYENDEDVNKQLDK 14 1 A6NKE1;A0A087WWM0;O43617 A6NKE1 TRAPPC3 Trafficking protein particle complex subunit 3 0 130.06 5.86E-05 104670000 220410 128650 106490 113230 107750 85456 210990 213090 67706 FALSE TRUE 191282.2601 127804.8897 157988.9202 138940.6021 105605.9858 88743.54762 190528.2223 167522.3618 59701.87381 3.203957394 2.140718231 2.646297513 2.327240223 1.768888966 1.48644493 3.191327342 2.80598164 1 15.86548859 6.585359858 1.459173774 2.238286545 199.9991581 0.189040322 0.647003219 601.957938 7.95476844 0.182477323 392556.4191 3849105.885 -6.585359858 197.7608716 DYEYNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DYEYNR 6 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 153.61 0.023518 2484300000 2358610 1799590 1131380 1395990 1639900 1748930 1782560 1926450 2018290 FALSE TRUE 2046913.713 1787768.375 1678519.152 1712970.866 1607269.198 1816212.469 1609687.606 1514493.659 1779690.055 1.150151795 1.004539172 0.943152515 0.962510781 0.90311748 1.020521783 0.904476373 0.850987314 1 20.76319458 7.999999964 0.804811628 0.925893789 59.92194922 0.639443686 0.049352447 327.6869427 1.113733078 0.017793754 35261.65781 99999991.72 -7.999999964 58.99605543 DYFEEYGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 DYFEEYGK 8 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;;; 145.63 0.0015663 31466640000 21316960 13889750 12789293 14892040 13238496 10490736 16240640 19637150 26267500 FALSE TRUE 18499869.73 13798507.32 18974237.87 18273505.29 12975075.83 10894321.4 14665625.23 15437898.29 23162186.07 0.798710004 0.59573424 0.819190288 0.788936987 0.560183559 0.470349447 0.633171031 0.666513007 1 24.46526809 1.238819127 8.042193164 1.004058003 0.66166442 0.468598417 0.111481547 0.088245649 51.6220656 0.165222352 0.028695409 17.33082061 -1.238819127 -0.342393584 DYFEEYGKIDTIEIITDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 DYFEEYGKIDTIEIITDR 18 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;;;; 253.26 1.53E-30 4222736300 5105978 3472418 1781041.6 1979921.3 2797088 2418160.4 4062453 4821166 701853.7 FALSE TRUE 4431210.07 3449607.458 2642359.275 2429492.692 2741431.421 2511188.595 3668476.933 3790197.169 618881.3551 7.160031618 5.573939866 4.269573244 3.925619462 4.42965586 4.057625221 5.927593234 6.124271054 1 19.23930333 4.588334403 2.564071701 4.496241178 7.326205099 0.30602515 1.396961588 0.507206724 5.221439888 0.360937772 2.654707416 38755.5945 -4.588334403 2.829963921 DYFEQYGK ddPTM_MDA-MB-175_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 ;;;;;;; 164.77 0.00076339 28698970000 9880450 8183420 5612590 6768420 7891380 6342610 9168270 10419640 9310640 FALSE TRUE 8574723.499 8129662.575 8326857.297 8305293.21 7734356.977 6586614.311 8279132.587 8191481.072 8209946.746 1.044431074 0.990221109 1.014240111 1.01161353 0.942071516 0.802272477 1.008427075 0.997750817 1 22.96894143 3.246360851 23.71886455 0.953042788 1.013284225 0.22794936 0.059281815 169.7255222 516093.2233 0.018568764 0.023490809 1763.440664 -3.246360851 0.060241437 DYFFALAHTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DYFFALAHTVR 11 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 214.26 1.37E-11 3330000000 3914100 4209200 2394100 2654700 3644200 3728500 3895600 4084600 2853000 FALSE TRUE 3396841.768 4181549.488 3551894.768 3257490.21 3571687.55 3871937.808 3517805.312 3211140.076 2515721.59 1.350245505 1.662167032 1.411879113 1.294853223 1.419746749 1.539096307 1.398328545 1.276429033 1 21.26254084 1.261782426 1.652460507 0.84076389 1.44745822 0.664677059 0.100413378 0.602050524 1.57372225 0.589612238 0.028755222 18.27184598 -1.261782426 0.606694331 DYFGAHTYELLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DYFGAHTYELLAK 13 0 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;; 213.73 3.54E-09 3964680000 4723550 4034380 3558520 4677230 4015370 3632760 4952170 5502280 8761170 FALSE TRUE 4099320.9 4007877.892 5279432.175 5739266.558 3935471.993 3772514.628 4471909.316 4325660.241 7725434.463 0.530626584 0.518789967 0.683383206 0.742905345 0.509417562 0.488323944 0.578855382 0.559924527 1 22.88118464 1.237093649 24.99593211 1.000000517 0.577739647 0.73619113 0.07966366 20.90935028 356151.4325 0.126375585 0.020653477 17.26210083 -1.237093649 -0.422260869 DYFGAHTYELLAKPGQFIHTNWTGHGGTVSSSSYNA ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYFGAHTYELLAKPGQFIHTNWTGHGGTVSSSSYNA 36 1 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 214.92 4.49E-39 465180000 234460 241490 41575 109440 214720 210620 247790 307600 72360 FALSE TRUE 203475.517 239903.6363 61680.80906 134290.0247 210447.4921 218722.6877 223759.3639 241822.1337 63805.68323 3.188987354 3.759910154 0.966697729 2.104671839 3.298256228 3.427949935 3.506887672 3.789977969 1 15.96139731 3.225399363 24.85566887 3.161622175 2.484814906 0.041807895 1.046006428 566.9101269 1070634.736 0.320635416 0.365737264 1680.348503 -3.225399363 -0.676807269 DYGHS(ph)SSRDDYPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DYGHSSSRDDYPSR 14 1 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 1 DYGHS(0.459)S(0.459)S(0.082)RDDYPSR;DYGHS(0.333)S(0.333)S(0.333)RDDYPSR 139.03 7.23E-06 388800000 231479 246538 95863 137053 251405 289129 248118 272093 228947 TRUE FALSE 200888.4637 244918.4756 142222.6674 168172.9784 246402.5324 300251.9797 224055.5545 213908.0294 201881.1465 0.995082835 1.213181518 0.70448712 0.833029638 1.220532658 1.487271025 1.109838925 1.059574077 1 17.62314666 3.229731751 24.99886507 1.171630756 0.939643706 0.302503863 0.180251031 269.0059652 761686.6908 0.058493692 0.067310403 1697.195031 -3.229731751 -0.23198705 DYGHSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 ;;;;;; 188.98 0.00019411 483091000 456056 511699 199577 282194 384221.1 591123 462905 489607 607709 FALSE TRUE 395787.0441 508337.6156 296093.1047 346270.4608 376575.8518 613863.8843 418012.5443 384908.3532 535866.3343 0.738592852 0.948627639 0.552550302 0.646188123 0.702742135 1.145554115 0.780068681 0.718291724 1 19.03151366 DYGHSSSRDDYPSR ddPTM_MDA-MB-175_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 ;;; 154.69 3.63E-06 2328220000 405320 416766 97320.7 129971 500652 510657 433092 466594 93032.3 FALSE TRUE 351755.935 414028.2367 144385.316 159482.902 490690.0047 530302.3052 391090.8045 366816.5041 82034.12748 4.28792194 5.047024323 1.760064018 1.944104325 5.981535 6.464410868 4.76741591 4.471511009 1 16.3239366 DYGNSPLHR ddPTM_MDA-MB-175_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 ;;;;;;; 170.85 5.74E-05 17554130000 6267350 6412360 2064718 4007930 6769400 6854230 5875690 6803260 6423710 FALSE TRUE 5439103.818 6370236.785 3063222.531 4917991.764 6634702.184 7117916.663 5305866.488 5348435.792 5664306.322 0.960241821 1.124627876 0.54079394 0.86824255 1.171317688 1.256626365 0.936719553 0.944234914 1 22.43346786 3.270095959 23.47195355 1.047449384 0.867652525 0.226109631 0.171823599 175.5479941 130659.386 0.052267022 0.067466441 1862.498619 -3.270095959 -0.179796859 DYGRPLDEQESQFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYGRPLDEQESQFR 14 1 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 144.38 8.09E-06 187570000 77732 66885 54861 61377 62106 58846 57905 71878 124270 FALSE TRUE 67459.51925 66445.62803 81391.9631 75313.58594 60870.21211 61109.8437 52289.38201 56507.44906 109578.9422 0.615624845 0.606372235 0.742770112 0.687299808 0.555491876 0.557678715 0.477184585 0.515677994 1 16.74161106 1.232080168 24.98389508 1.00000069 0.591037715 0.729275255 0.077564872 133.9460467 516348.8298 0.203096125 0.021886837 17.06397351 -1.232080168 -0.408962975 DYGVLLEGSGLALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYGVLLEGSGLALR 14 0 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 150.06 1.70E-05 42518000 43770 43789 26736 47464 48350 56455 40063 54662 43746 FALSE TRUE 37985.6836 43501.34718 39665.61903 58241.42664 47387.9296 58626.86038 36177.69643 42972.95668 38574.39772 0.984738216 1.127725895 1.028288745 1.509846688 1.228481387 1.519838646 0.937868083 1.114027936 1 15.23535601 DYGVYLEDSGHTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DYGVYLEDSGHTLR 14 0 Q13162;H7C3T4 Q13162 PRDX4 Peroxiredoxin-4 0 ;; 192.14 4.07E-07 1590440000 2090900 2154070 1100100 1655120 2137840 2744350 1801040 1647550 1776680 FALSE TRUE 1814582.267 2139919.772 1632112.04 2030940.293 2095301.167 2849926.92 1626375.418 1295234.254 1566642.914 1.158261561 1.365926947 1.041789437 1.296364522 1.337446554 1.819129869 1.038127708 0.826757803 1 20.57924495 2.014461309 24.9784915 0.910435821 1.331480943 0.449385759 0.202541252 193.1176487 333563.7804 0.083581862 0.056326046 103.3858991 -2.014461309 0.421045122 DYHFVTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DYHFVTSR 8 0 A0A590UJD9;A0A0C4DFT3;A0A590UJ18;A0A590UJ08;Q12959-4;Q12959-2;A0A590UJC5;Q12959;Q12959-3;Q12959-5;Q12959-7;Q12959-6;A0A590UKA8;A0A590UJR5;A0A590UJ68;A0A590UJS9;A0A590UK48;A0A590UJ81;C9JUA9;Q12959-8;A0A590UJX2;A0A590UK81;A0A590UJ29;Q12959-9;A0A590UJR4 A0A590UJD9;A0A590UJ08;Q12959 DLG1 Disks large homolog 1 0 ; 91.867 0.012183 379060000 199205 204500 121352 161659 196743 226594 158950 201414 180818 FALSE TRUE 172879.5545 203156.626 180038.2331 198366.1468 192828.1992 235311.2178 143535.0535 158343.1835 159441.902 1.084279304 1.274173373 1.129177655 1.244128076 1.20939475 1.475843018 0.900234202 0.993108973 1 17.2826713 2.210633604 24.9999863 0.967743148 1.2321757 0.594757505 0.105684513 143.6936277 128632.0617 0.04136921 0.027897843 162.4177926 -2.210633604 0.264432552 DYIHVVDLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYIHVVDLAK 10 0 Q14376;Q14376-2;Q5QPP4;Q5QPP3;Q5QPP9 Q14376 GALE UDP-glucose 4-epimerase 0 119.16 0.00072987 209720000 634830 481370 360310 487590 457000 394140 549480 632740 698070 FALSE TRUE 550935.607 478207.8488 534557.1212 598304.7618 447906.5941 409302.8208 496191.5142 497433.475 615544.9598 0.895037151 0.776885329 0.868429044 0.971991976 0.727658617 0.664943826 0.806101173 0.808118834 1 19.23150471 4.768003281 22.30362171 0.822964343 0.895037562 0.039428019 0.101269496 9425.289694 7139395.639 0.025187963 2.074592293 58614.25925 -4.768003281 0.072073219 DYIPVDQEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DYIPVDQEELR 11 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 188.99 6.77E-06 844910000 776410 761810 484220 507950 778750 777230 758140 844200 799810 FALSE TRUE 673805.4513 756805.6199 718390.4116 623287.811 763254.3986 807130.541 684615.6995 663674.3996 705257.3729 0.955403626 1.073091398 1.018621625 0.883773548 1.082235263 1.144448214 0.970731715 0.941038584 1 19.42779032 2.034853335 24.99999785 0.96318061 1.026900948 0.11572469 0.071898545 346.7180057 248696.5427 0.030104572 0.020296402 108.3560925 -2.034853335 0.063720339 DYIVVGSDSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYIVVGSDSGR 11 0 Q15393;Q15393-2;J3QL37;J3QRB2 Q15393 SF3B3 Splicing factor 3B subunit 3 0 201.33 1.02E-07 262080000 363650 274320 206740 247790 313840 274740 275800 346410 349630 FALSE TRUE 315592.7311 272517.9739 306720.1555 304054.5067 307595.198 285309.4256 249052.9584 272332.9173 308297.1397 1.023664155 0.883945839 0.994884856 0.986238494 0.997723165 0.925436499 0.807834152 0.883345585 1 18.23396198 2.480639095 24.93299548 0.887077921 0.972379925 0.281330061 0.058534294 168.7418 1195988.863 0.021211231 0.016788523 302.4399063 -2.480639095 0.085302005 DYIYAVTPLLEDALMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYIYAVTPLLEDALMDR 17 0 O75533;H7C341 O75533 SF3B1 Splicing factor 3B subunit 1 0 136.27 2.53E-05 70194000 95028 65013 67540 75083 85892 65608 68594 85398 114300 FALSE TRUE 82469.80903 64585.92532 100202.5699 92131.74272 84182.91724 68131.98221 61941.76444 67136.30227 100787.5842 0.818253654 0.640812317 0.994195572 0.914117978 0.835250868 0.675995786 0.61457733 0.666116792 1 16.6209584 2.756113721 19.34318806 0.71607681 0.842056818 0.111706395 0.135182302 81.23849202 89521.21529 0.044425292 0.04419401 570.313591 -2.756113721 0.125980008 DYLEHITSIGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DYLEHITSIGPR 12 0 E7ER77;Q7Z2K6 E7ER77 ERMP1 Endoplasmic reticulum metallopeptidase 1 0 ; 147.26 6.54E-05 428900000 338090 395770 193584 354210 525100 512080 288540 508740 527770 FALSE TRUE 293410.5499 393170.1608 287201.8699 434638.7943 514651.5373 531780.049 260557.4352 399949.91 465377.6318 0.630478411 0.844841122 0.617137246 0.933948614 1.105879402 1.142685021 0.559883882 0.859409397 1 18.82804234 3.723808664 23.95848691 0.918430547 0.712221148 0.298214447 0.169204555 680.8783814 1105807.064 0.049444526 0.073729722 5294.301428 -3.723808664 -0.206209399 DYLGDFIEHYAQLGPSQPPDLAQAQDEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DYLGDFIEHYAQLGPSQPPDLAQAQDEPR 29 0 Q00577 Q00577 PURA Transcriptional activator protein Pur-alpha 0 ;;; 265.23 2.11E-58 477631000 307723 251634 166238 227862 257074 265260 256426 308815 291615 FALSE TRUE 267056.6259 249980.9997 246631.2528 279601.5498 251958.7304 275464.7238 231557.846 242777.3155 257140.6069 1.038562633 0.972156839 0.959129932 1.087348875 0.979848082 1.071261078 0.900510615 0.944142267 1 17.97219793 2.232644771 24.99999963 0.945380809 1.014700275 0.324018189 0.047325326 165.0625389 697535.366 0.018393252 0.012775634 170.861719 -2.232644771 0.069319466 DYLHLPPEIVPATLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DYLHLPPEIVPATLR 15 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;;; 88.507 0.0067586 4587300000 1726610 1437780 953985 1400670 1634840 1538320 1243700 1783070 2119020 FALSE TRUE 1498434.114 1428335.129 1415335.337 1718713.531 1602309.883 1597500.166 1123086.165 1401774.356 1868511.87 0.801939842 0.764423899 0.757466602 0.919830138 0.857532622 0.854958532 0.601059155 0.750208965 1 20.8334583 5.000121058 0.003708495 1.036089388 0.562666379 0 0.108103589 5953480.023 5407.381038 339266.8319 351116.8969 100027.8786 -5.000121058 -0.473423009 DYLHYHIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DYLHYHIK 8 0 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;;;; 131.06 0.00059051 3041426000 3354580 3235310 2271911 2857180 3271280 2866720 3647960 3888820 3874090 FALSE TRUE 2911263.754 3214057.036 3370614.759 3505946.388 3206187.928 2977004.573 3294181.401 3057226.106 3416099.494 0.852218666 0.940855804 0.986685184 1.026301018 0.938552268 0.871463076 0.964310731 0.894946447 1 21.70391856 4.730217623 4.809614811 0.949666775 0.847410018 0.318548703 0.046231135 0.225797532 15.09591397 0.011788152 0.076490892 53730.09681 -4.730217623 -0.102256757 DYLHYIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 DYLHYIR 7 0 P62280;M0QZC5;M0R1H5 P62280 RPS11 40S ribosomal protein S11 0 ;;;;;;; 157.99 0.0014387 11345980000 6582090 7377340 4794000 5565550 7406090 7055090 6831550 7319100 8024120 FALSE TRUE 5712250.13 7328877.768 7112394.435 6829293.192 7258723.299 7326503.878 6169027.332 5753967.422 7075517.675 0.807326106 1.035807994 1.005211882 0.965200499 1.025892893 1.035472486 0.871883531 0.813222111 1 22.75440427 2.222641519 24.94090998 0.877026119 0.984402218 0.182348311 0.080519067 295.9250122 463630.6468 0.031628211 0.02140225 166.971181 -2.222641519 0.1073761 DYLIDGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DYLIDGSR 8 0 P18206;P18206-2;P18206-3 P18206 VCL Vinculin 0 ;;;;; 139.88 0.001532 3395270000 5565630 5509190 3687770 4246280 5448760 5851730 5560300 6206210 5817560 FALSE TRUE 4830117.894 5472999.768 5471187.907 5210462.774 5340340.336 6076849.84 5021062.962 4879060.288 5129814.684 0.941577463 1.066900094 1.066546892 1.015721443 1.041039621 1.184613912 0.978800068 0.951118235 1 22.29047528 2.037200627 24.99972826 0.969934605 1.054284199 0.25906419 0.060478339 195.7461378 131545.3993 0.024142207 0.016276627 108.9433253 -2.037200627 0.084349595 DYLLCDYNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DYLLCDYNR 9 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;;; 175.44 0.00012542 5075670000 3349110 3894140 2430070 2638850 3770270 3735290 3484110 4044360 3824610 FALSE TRUE 2906516.628 3868559.138 3605259.98 3238041.225 3695249.003 3878989.023 3146221.548 3179505.087 3372468.963 0.861836435 1.147099997 1.069026882 0.960139666 1.095710307 1.150192653 0.932913418 0.942782609 1 21.68537374 2.200093633 24.99998999 0.954208356 1.051090833 0.186508238 0.087000518 242.7912659 157790.3253 0.034085756 0.022981066 158.5234928 -2.200093633 0.096882476 DYLLS(ph)ES(ph)EDEGDNDGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYLLSESEDEGDNDGER 17 0 Q9BVJ6-3;Q9BVJ6 Q9BVJ6-3 UTP14A U3 small nucleolar RNA-associated protein 14 homolog A 2 DYLLS(1)ES(1)EDEGDNDGER 202.5 1.54E-11 153150000 139280 132940 88729 87994 115950 118300 115700 130500 126060 TRUE FALSE 120873.7951 132066.7084 131638.6412 107974.3826 113642.8219 122851.0776 104479.4318 102593.5906 111157.3304 1.087411821 1.188106155 1.184255152 0.971365381 1.022360122 1.105199964 0.939923903 0.922958389 1 16.76224357 3.279899981 0.645976479 0.94705657 1.170742298 0.506502959 0.06588241 0.685866369 0.742641871 0.06091923 0.096966194 1905.021936 -3.279899981 0.223685728 DYMLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DYMLFR 6 0 Q9NXG2 Q9NXG2 THUMPD1 THUMP domain-containing protein 1 0 ; 110.54 0.066582 152903000 312670 273380 162999 195403 263070 243330 248740 264450 293770 FALSE TRUE 271349.8673 271584.1488 241825.8616 239772.2377 257835.4217 252691.0626 224617.2331 207899.4255 259040.8453 1.047517688 1.048422107 0.933543362 0.925615562 0.995346589 0.97548733 0.867111258 0.802573915 1 17.98282007 7.999996485 0.223798138 0.851924761 2.012425947 0.353212328 0.062088472 93.21976529 1.441284083 0.304244779 38.05366031 99999190.68 -7.999996485 1.160501185 DYNDADMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DYNDADMAR 9 0 Q14696;H0YLI4;Q14696-2 Q14696 MESDC2 LDLR chaperone MESD 0 ; 143.03 0.0002394 1039830000 1474940 1433490 1103050 1191370 1337260 1717520 1408650 1290880 1174730 FALSE TRUE 1280022.942 1424073.31 1636488.669 1461888.767 1310651.142 1783594.106 1272039.34 1014835.358 1035854.758 1.235716622 1.374780875 1.579843755 1.4112874 1.265284667 1.721857329 1.228009362 0.979708159 1 19.9823903 1.958897581 4.616155987 1.00997165 1.431166304 0.623172444 0.141221921 0.128498292 6.158024617 0.070609215 0.03756712 90.96987135 -1.958897581 0.421194654 LSIVPVRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSIVPVRR 8 1 P15880;H0YEN5;E9PPT0;E9PMM9;I3L404;E9PM36 P15880 RPS2 40S ribosomal protein S2 0 ; 161.02 0.00056114 3043800000 3536500 3923900 2097900 2323800 3972900 3986500 3694100 3791800 1492870 FALSE TRUE 3069142.565 3898123.643 3112451.457 2851454.307 3893847.063 4139863.235 3335846.751 2980953.078 1316384.609 2.331493807 2.961234593 2.364393685 2.166125528 2.957985862 3.144873622 2.53409735 2.264500099 1 20.32814963 1.177832911 2.056684113 0.289447314 2.652109925 0.731414081 0.310780861 0.477470895 1.73775832 2.274122996 0.086673368 15.06027532 -1.177832911 2.36266261 DYNVTANSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DYNVTANSK 9 0 P00338;P00338-3;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;; 194.06 7.64E-05 1275510000 1277920 1060850 700830 829540 915730 813290 1172640 1205680 1127240 FALSE TRUE 1109039.634 1053881.206 1039753.732 1017899.736 897508.7646 844577.7926 1058917.553 947854.7146 993978.9714 1.115757643 1.060265093 1.046052041 1.024065664 0.902945425 0.849693823 1.065331947 0.953596346 1 19.9228558 3.618875681 2.424911114 0.958075917 1.077573204 0.459268039 0.05909757 0.287258587 3.293931471 0.018037868 0.030101785 4157.915713 -3.618875681 0.119497287 DYPFHEEF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DYPFHEEF 8 0 P15121 P15121 AKR1B1 Aldose reductase 0 ; 97.602 0.01888 198646000 521890 584780 389940 378470 478810 496960 320220 380160 674590 FALSE TRUE 452920.9142 580938.5417 578516.2883 464407.3981 469282.6178 516078.3728 289165.1137 298865.7424 594840.7387 0.761415426 0.976628707 0.972556603 0.780725609 0.788921449 0.867590834 0.486121906 0.502429849 1 19.18214393 2.259774673 24.91873538 0.62206592 0.861925001 0.24158902 0.15743824 253.8564283 298187.474 0.058943132 0.045610997 181.8756979 -2.259774673 0.239859081 DYPSSR ddPTM_MDA-MB-175_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 1228160000 712750 576080 362215 445010 422030 581140 572460 628400 631600 FALSE TRUE 618558.2816 572295.6925 537383.3855 546056.3221 413632.4287 603496.8318 516942.9173 494021.5502 556932.9675 1.110651223 1.027584514 0.964897783 0.980470459 0.742696972 1.083607664 0.928195936 0.887039516 1 19.08714417 4.48971658 1.440330131 0.93023131 1.138235266 0.303230794 0.086807675 0.904157459 2.433506532 0.023895811 0.238367986 30882.79366 -4.48971658 0.208003955 DYPVVSIEDPFDQDDWGAWQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DYPVVSIEDPFDQDDWGAWQK 21 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;; 312.74 1.39E-66 1884142000 2926610 2675400 1980937 1963059 2309830 2135691 2676531 2992226 3731629 FALSE TRUE 2539851.073 2657825.121 2938924.759 2408801.549 2263868.902 2217852.415 2416961.436 2352361.755 3290480.071 0.771878577 0.807731718 0.893159872 0.732051706 0.688005657 0.674020923 0.734531553 0.714899256 1 21.64986665 3.704994191 24.71516466 0.74506663 0.822604259 0.089446287 0.095601781 1126.21012 829235.238 0.026084404 0.038692176 5069.839267 -3.704994191 0.07753763 DYQASEDKVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYQASEDKVR 10 1 Q96ME1-4;Q96ME1-2;Q96ME1;Q96ME1-3 Q96ME1-4 FBXL18 F-box/LRR-repeat protein 18 0 67.252 0.057941 119660000 150270 127150 99123 91674 132660 123800 143790 120680 118840 FALSE TRUE 130411.4388 126314.7433 147059.2143 112489.9828 130020.3255 128562.6661 129845.2679 94873.52113 104790.8706 1.244492369 1.205398357 1.403359029 1.073471212 1.240760047 1.226849872 1.239089505 0.905360559 1 16.67715351 1.754322147 7.892753791 0.956238625 1.23289209 0.669951831 0.081811742 0.069437403 15.21137406 0.043340564 0.020000544 56.79657498 -1.754322147 0.276653464 DYQDDTLELYNREDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYQDDTLELYNREDR 15 1 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 103.39 0.0013466 130980000 71479 72035 29446 38160 63149 64495 71060 66794 22588 FALSE TRUE 62032.86905 71561.79734 43686.18409 46824.81124 61892.45845 66976.16438 64168.61214 52510.62289 19917.67237 3.114463773 3.59287953 2.19333782 2.350917836 3.107414225 3.36265017 3.221692321 2.636383505 1 14.28176144 4.248818392 24.99751658 2.637916664 3.353671759 0.18521658 0.6801711 396.4168362 966021.6736 0.173790294 0.448966721 17734.47727 -4.248818392 0.715755095 DYQDNKADVILK ddPTM_MDA-MB-175_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 ; 113.53 0.0010544 1221490000 1219650 1079540 642860 537940 872680 846670 1231950 1257090 356780 FALSE TRUE 1058470.162 1072448.431 953749.2462 660087.4989 855315.3754 879241.9428 1112475.679 988271.0862 314601.8748 3.364475062 3.408906674 3.031607001 2.098167721 2.718723071 2.794776551 3.536138108 3.141338832 1 18.26316774 4.002710574 6.530967632 2.679404675 3.352816502 0.197456426 0.676970362 0.264632185 56.38340042 0.179021332 0.354295337 10062.60844 -4.002710574 0.673411827 DYQGPLKEHEVTIFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYQGPLKEHEVTIFVR 16 1 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 86.213 0.0041372 502020000 334130 296720 172660 186400 287740 291870 344270 357540 182960 FALSE TRUE 289973.8739 294770.8268 256158.9535 228724.9689 282014.537 303098.4278 310882.7484 281082.8534 161330.6772 1.797388314 1.827121982 1.587788249 1.417740091 1.748052768 1.878740194 1.926990909 1.742277775 1 17.29966127 1.238541664 21.8716968 0.999996187 1.741926711 0.717337609 0.146133195 0.065603947 63579.82216 0.218444169 0.039198521 17.3197518 -1.238541664 0.741930524 DYRPTWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DYRPTWK 7 1 O00754;O00754-2 O00754 MAN2B1 Lysosomal alpha-mannosidase;Lysosomal alpha-mannosidase A peptide;Lysosomal alpha-mannosidase B peptide;Lysosomal alpha-mannosidase C peptide;Lysosomal alpha-mannosidase D peptide;Lysosomal alpha-mannosidase E peptide 0 ; 77.923 0.033501 645300000 918450 781210 704410 819430 779720 779600 869560 1058520 1058130 FALSE TRUE 797074.5054 776078.1801 1045065.032 1005494.106 764205.0975 809591.7165 785230.205 832163.7354 933039.0768 0.854277731 0.831774573 1.120065663 1.077654871 0.819049402 0.867693258 0.841583407 0.891885191 1 19.83157798 3.220128474 24.9998669 0.881020772 0.971654254 0.162171447 0.09800973 467.9412866 634676.0534 0.031567776 0.035859531 1660.077923 -3.220128474 0.090633482 DYS(ph)YER ddPTM_MDA-MB-175_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(0.999)Y(0.001)ER 133.33 0.015222 2691730000 3545960 2704800 2012190 2143630 2763460 2769980 2775640 2978740 3202680 TRUE FALSE 3077352.402 2687031.991 2985291.814 2630373.955 2708472.553 2876542.923 2506458.86 2341759.632 2824062.819 1.089689783 0.951477415 1.057091151 0.931414817 0.959069513 1.018583193 0.887536511 0.829216551 1 21.42934075 6.007691609 0.214146386 0.858036315 1.370854437 0.32223485 0.063615251 45.72158194 1.564869527 0.434344982 6.797762931 1017868.347 -6.007691609 0.512818122 DYSAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYSAYR 6 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;X6R960;Q5TBN9 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 0 113.07 0.061539 87634000 226120 207650 148980 135010 198060 207610 203150 223510 241220 FALSE TRUE 196237.6691 206285.9335 221027.2263 165666.084 194118.9935 215596.891 183448.5443 175714.1259 212703.2464 0.92258897 0.969829737 1.03913424 0.778860158 0.912628259 1.01360414 0.862462362 0.826099878 1 17.69848253 3.765220276 24.95794897 0.894422471 0.976448842 0.190197206 0.075719205 1225.798414 1147550.223 0.020218185 0.035007935 5823.985383 -3.765220276 0.082026371 DYSDHPSGGSYR ddPTM_MDA-MB-175_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 ;;;;; 151.55 6.48E-05 3762910000 5618150 5499290 1770199 3452830 6413250 6245500 5082180 5865270 7398180 FALSE TRUE 4875697.243 5463164.802 2626273.157 4236847.825 6285638.872 6485768.426 4589310.966 4611027.654 6523575.588 0.747396451 0.837449452 0.402581854 0.649467116 0.963526641 0.994204534 0.70349625 0.706825205 1 22.6372315 3.262304422 24.73640782 0.846033482 0.653622438 0.324128398 0.150844069 294.4051295 306710.3285 0.046196948 0.059604144 1829.382087 -3.262304422 -0.192411044 DYSDHPSGGSYRDS(ph)YESYGNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYSDHPSGGSYRDSYESYGNSR 22 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 DYSDHPSGGS(0.013)YRDS(0.987)YES(0.001)YGNSR 129.72 8.88E-06 155870000 125250 141810 68150 98747 136560 181510 111510 150900 173420 TRUE FALSE 108697.8952 140878.4408 101107.5679 121169.0156 133842.7232 188492.8072 100695.7774 118631.2093 152918.4852 0.710822469 0.921264951 0.661186042 0.79237651 0.875255356 1.232635851 0.658493166 0.775780699 1 17.22240329 3.251490516 5.242958568 0.889829468 0.772931031 0.14659273 0.161510149 0.442542915 34.66756663 0.049611697 0.061395228 1784.393021 -3.251490516 -0.116898437 DYSEADGLS(ph)ER ddPTM_MDA-MB-175_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 207.12 2.52E-08 911380000 1164130 1111380 924030 1302100 1207530 1263760 910010 1220860 2087900 TRUE FALSE 1010287.271 1104079.272 1370893.999 1597761.706 1183502.515 1312377.665 821757.3703 959788.5897 1841070.841 0.548749808 0.599694073 0.744617735 0.867843687 0.642833773 0.712833877 0.446347502 0.521320836 1 20.81211371 4.433382706 6.789185306 0.678625732 0.560747334 0.092375905 0.15802656 0.495685791 57.47195012 0.041315527 0.113319321 27125.80942 -4.433382706 -0.117878398 DYSEADGLSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYSEADGLSER 11 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;Q4VXN0;Q4VXN1;Q4VXN5;Q4VXN6;Q4VXN7;Q4VXN2 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 0 160.53 0.0026572 0 275480 255460 173340 231720 225330 265150 224060 296810 387720 FALSE TRUE 239074.62 253781.8664 257167.8038 284335.5676 220846.3739 275350.4921 202330.6957 233339.4913 341884.1833 0.699285406 0.742303619 0.752207374 0.831672191 0.645968385 0.80539114 0.591810635 0.682510343 1 18.38314815 1.234311424 24.99760021 1.000000416 0.716952224 0.609065862 0.070761909 88.39218214 519933.1303 0.130340594 0.017204681 17.15186793 -1.234311424 -0.283048192 DYSNFDQEFLNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 327.06 5.90E-62 432676000 564270 493610 439830 448890 494750 484780 587260 713890 644220 FALSE TRUE 489700.2898 490367.4434 652533.2591 550817.3354 484905.443 503429.8003 530307.6156 561230.179 568061.0455 0.862055749 0.863230189 1.148702704 0.969644618 0.853615024 0.886224824 0.933539837 0.987975119 1 19.11568645 1.68526705 4.2156626 0.996717741 0.93344464 0.085244738 0.085828535 0.491776605 20.38903671 0.062643049 0.023817606 48.4470179 -1.68526705 -0.063273101 DYSPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYSPSR 6 0 Q9HCM7;A0A3B3IRR3 Q9HCM7 FBRSL1 Fibrosin-1-like protein 0 121.68 0.045473 522580000 262800 211840 144490 165140 161630 182140 215680 246260 208390 FALSE TRUE 228070.3141 210448.4091 214365.8473 202637.561 158413.8792 189147.0437 194763.3868 193599.2154 183754.3716 1.24116946 1.145270217 1.166589102 1.102763212 0.862095839 1.029347177 1.059911583 1.053576107 1 17.48741905 3.472350759 24.99880573 1.01058208 1.172809092 0.661837652 0.059874291 87.65228426 459321.0169 0.017899412 0.023194417 2967.226911 -3.472350759 0.162227012 DYSSGFGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DYSSGFGGK 9 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;; 149.65 0.00020266 1368180000 1816000 1627150 1026910 1220550 1485550 1295110 1734110 1953620 1769700 FALSE TRUE 1576010.999 1616461.145 1523527.111 1497694.532 1455990.461 1344933.72 1565936.279 1535853.566 1560488.082 1.009947475 1.035868946 0.97631448 0.959760315 0.933035297 0.861867345 1.003491342 0.984213583 1 20.57356591 4.09613623 4.08953194 0.958359932 1.022594672 0.303905736 0.04052148 0.288886894 8.892946592 0.011424856 0.025720901 12477.74857 -4.09613623 0.06423474 DYTKVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYTKVDR 7 1 P31153;P31153-2;Q00266 P31153 MAT2A;MAT1A S-adenosylmethionine synthase isoform type-2;S-adenosylmethionine synthase isoform type-1 0 74.127 0.042886 192490000 387350 386050 188040 199440 328790 302580 392310 437680 140020 FALSE TRUE 336160.7161 383514.0121 278976.773 244725.9002 322247.7223 314220.4484 354263.8366 344085.538 123466.9951 2.722676743 3.106206738 2.259525088 1.98211595 2.609990807 2.544975263 2.869299899 2.786862495 1 16.91376591 4.233748232 24.99894773 2.377374849 2.914441785 0.172995172 0.540853039 211.4200453 1098288.913 0.13725589 0.301141057 17129.63984 -4.233748232 0.537066936 DYTQINVGNLELSANHNILQIVDVCMESEKDHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DYTQINVGNLELSANHNILQIVDVCMESEKDHK 33 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 246.22 2.18E-47 338490000 256340 167090 88163 140150 156470 109380 249070 261180 154500 FALSE TRUE 222464.0195 165992.3748 130798.9217 171973.1996 153356.5531 113587.9194 224915.2297 205328.6895 136235.186 1.63294099 1.218425134 0.960096474 1.262325869 1.125675074 0.833763455 1.65093348 1.507163425 1 17.05573984 1.188402449 22.59634659 0.999985066 1.272231272 0.093962163 0.267264769 13624.06311 6135942.41 50.7551543 0.068518799 15.43129766 -1.188402449 0.272246206 DYTYEELLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DYTYEELLNR 10 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;;;;; 261.49 5.36E-17 6395670000 4364280 4656430 3219410 3445670 4330760 4433640 4458930 4945140 4496490 FALSE TRUE 3787529.34 4625841.605 4776327.444 4228062.037 4244586.349 4604205 4026503.655 3887660.294 3964920.075 0.955259947 1.166692271 1.204646589 1.066367533 1.070535161 1.161235262 1.015532111 0.980514164 1 21.91886035 2.1016934 6.090766786 0.991597505 1.107977976 0.34700558 0.068592656 0.21414809 10.98465137 0.027999946 0.018698334 126.3843793 -2.1016934 0.11638047 DYVAVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DYVAVAR 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 102.98 0.019726 479130000 655060 570030 327530 451560 608800 549590 657080 636620 611000 FALSE TRUE 568492.1613 566285.4354 485924.6035 554093.5997 596686.0711 570733.0829 593356.4827 500483.7672 538768.2761 1.055170073 1.051074201 0.901917624 1.028445111 1.107500381 1.059329415 1.10132038 0.928940677 1 19.03930538 1.713835778 12.11993132 0.965343764 1.040849236 0.23912787 0.058445532 0.168896274 61.55900724 0.033293034 0.015706046 51.74111438 -1.713835778 0.075505472 DYVDLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DYVDLFR 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;;; 143 0.005702 2236450000 4462840 3408660 2866660 4183840 4042510 3291810 4177990 4623050 6491220 FALSE TRUE 3873064.387 3386268.288 4252986.364 5133844.818 3962071.96 3418448.061 3772809.173 3634446.734 5723835.366 0.676655448 0.591608261 0.743030869 0.896923914 0.692205786 0.597230326 0.659140058 0.634967028 1 22.44855075 1.232920458 24.98729718 1.000000505 0.685545145 0.562383282 0.086915047 150.8234961 668113.7927 0.195742891 0.022818386 17.09702151 -1.232920458 -0.31445536 DYYINIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DYYINIR 7 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 153.15 0.0041078 2032530000 3235800 2680690 1809850 2127580 2616540 2680730 2708600 3005500 3220100 FALSE TRUE 2808180.832 2663080.371 2685099.514 2610679.557 2564475.973 2783859.418 2445920.389 2362797.214 2839423.446 0.988996846 0.93789476 0.945649553 0.919440022 0.903167851 0.980431229 0.861414451 0.832139784 1 21.43716659 7.999999507 0.322775268 0.89180597 1.811076038 0.136471544 0.050274881 127.5342852 2.004548107 0.083790073 68.33232748 99999886.6 -7.999999507 0.919270068 DYYSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DYYSSR 6 0 C9J384;Q9BQ75-2;Q9BQ75;H7C515;Q14011;K7EMY9;K7EPM4;K7EQR7;D6W5Y5;Q14011-2;K7EJV1;Q14011-3 C9J384;Q14011 CMSS1;CIRBP Protein CMSS1;Cold-inducible RNA-binding protein 0 ;;; 153.61 0.023518 6285100000 3905710 3461750 3020020 2378410 2647510 3013910 2719780 3086340 3013820 FALSE TRUE 3389560.528 3439009.536 4480511.773 2918464.342 2594829.731 3129857.068 2456016.154 2426350.209 2657529.633 1.275455403 1.294062536 1.685968697 1.098186943 0.976406697 1.177731766 0.924172632 0.913009653 1 21.34165435 3.539848776 7.403098256 0.994878428 1.405939132 0.684687402 0.130621726 0.159163952 16.57274 0.036272417 0.053645214 3466.16136 -3.539848776 0.411060703 EAAAAALKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAAAAALKK 9 1 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ; 127.3 0.0007204 3050200000 2292100 2265900 1579590 1788660 1835710 1624550 3089600 2941600 2086400 FALSE TRUE 1989193.178 2251015.154 2343485.007 2194802.591 1799182.963 1687047.49 2789971.068 2312561.732 1839748.169 1.081231231 1.223545261 1.273807496 1.192990773 0.977950674 0.916999141 1.516496179 1.256999067 1 20.81107687 1.225249805 24.28196825 0.999999331 1.18954986 0.100769191 0.166833657 1177.457345 2147763.181 0.77654476 0.042754551 16.79769941 -1.225249805 0.189550529 EAAAALVEEETRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAAAALVEEETRR 13 1 O75934 O75934 BCAS2 Pre-mRNA-splicing factor SPF27 0 ; 201.48 1.63E-07 589450000 648090 527120 302800 374980 510120 498410 467050 545070 469290 FALSE TRUE 562443.2644 523657.314 449235.0928 460124.9402 499969.61 517584.1552 421755.5629 428511.0222 413811.0708 1.359178872 1.265450228 1.085604336 1.111920325 1.208207429 1.250774065 1.019198356 1.03552334 1 18.65861272 7.99999679 0.041964051 4.43E-06 3.001168314 0.578851776 0.077669552 1248.867337 5.155235885 113.5111751 297.2900666 99999260.78 -7.99999679 3.001163885 EAAATEIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAAATEIRR 9 1 P56545;P56545-3;P56545-2 P56545 CTBP2 C-terminal-binding protein 2 0 112.11 0.0032328 247530000 203430 196170 88805 127140 185940 223780 213830 189990 86697 FALSE TRUE 176546.2101 194881.3464 131751.395 156009.0802 182240.1578 232388.9614 193092.7995 149362.117 76447.77943 2.309370022 2.549208725 1.7234169 2.040727427 2.383851554 3.039839262 2.525813058 1.953779667 1 16.22218698 1.2998026 2.696775435 0.806864515 2.359346048 0.616430714 0.340723684 0.295691567 2.717124351 0.971862598 0.097280732 19.94355613 -1.2998026 1.552481533 EAADAIDAEGASAPLMELLHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EAADAIDAEGASAPLMELLHSR 22 0 P14923 P14923 JUP Junction plakoglobin 0 ;; 92.932 0.0019982 78612000 68632 58254 56524 87742 68763 80448 54076 73879 110420 FALSE TRUE 59562.10731 57871.32564 83859.19546 107665.1622 67394.75083 83542.88662 48831.71784 58080.55078 97366.27339 0.611732433 0.594367265 0.861275599 1.105774704 0.692177573 0.85802695 0.501526002 0.596516111 1 16.5711345 4.255203434 24.49576496 0.776623187 0.603049657 0.165761057 0.178708145 419.3142809 617154.6512 0.047889419 0.125882793 17997.13746 -4.255203434 -0.17357353 EAADGYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAADGYQR 8 0 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 122.18 0.0032608 1572430000 4309500 3165700 1959040 2355900 2804500 3280700 3015800 3244800 3221100 FALSE TRUE 3739988.656 3144904.308 2906438.297 2890843.103 2748695.937 3406910.652 2723328.18 2550924.771 2840305.227 1.316755896 1.107241672 1.02328379 1.017793114 0.967746674 1.199487512 0.958815325 0.898116423 1 21.43761454 7.999999869 0.780370807 0.991221107 72.99867246 0.614073329 0.077206736 321.5310677 1.216865597 0.029721599 40845.74124 99999969.89 -7.999999869 72.00745136 EAAEIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAAEIYR 7 0 A0A0B4J1W3;Q9BXJ9 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ; 120.49 0.015195 190880000 444310 448800 311460 321690 416700 474060 354160 395750 513690 FALSE TRUE 385593.3078 445851.8032 462083.0978 394734.6312 408408.4853 492297.395 319813.6177 311121.9422 452962.1534 0.851270476 0.984302551 1.020136217 0.871451684 0.901639314 1.086840018 0.706049314 0.686860789 1 18.78903099 2.224095991 24.99995049 0.770742231 0.951111405 0.30029164 0.108949621 245.4908434 424290.9476 0.043560337 0.029516786 167.5313125 -2.224095991 0.180369174 EAAELEEAS(ph)AESEDEMIHPEGVASLLPPDFQSSLERPELELSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAAELEEASAESEDEMIHPEGVASLLPPDFQSSLERPELELSR 43 1 S4R3H4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 EAAELEEAS(0.533)AES(0.467)EDEMIHPEGVASLLPPDFQSSLERPELELSR;EAAELEEAS(0.589)AES(0.411)EDEMIHPEGVASLLPPDFQSSLERPELELSR 185.22 4.25E-28 63446000 29716.3 22652.1 17783.7 21664.8 21325.7 23246 19760.3 20705.7 27896.5 TRUE FALSE 25789.21566 22503.29686 26383.9568 26584.12397 20901.36029 24140.28866 17843.94915 16277.94719 24598.60755 1.048401444 0.914819947 1.072579281 1.080716618 0.849696888 0.981368096 0.725404847 0.661742627 1 14.58628903 2.564843279 1.623602671 0.769630912 1.011313999 0.36308759 0.11440951 0.344841897 1.852851466 0.056064312 0.041347331 367.149786 -2.564843279 0.241683086 EAAEMGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 EAAEMGK 7 0 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;A0A2R8YDN5;P68104;A0A087WVQ9;Q5VTE0;A0A087WV01;A6PW80;Q5JR01 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;;;;; 114.6 0.013652 4333190000 7315330 5778770 4066570 5006320 3642140 4857280 7075140 7570580 7977450 FALSE TRUE 6348590.606 5740808.879 6033176.854 6143081.473 3569668.54 5044142.705 6388994.012 5951670.381 7034364.949 0.902510838 0.816109048 0.857671858 0.873295815 0.507461379 0.717071511 0.908254556 0.846084959 1 22.74598875 1.308878723 1.377672056 1.060669677 0.784702267 0.236593339 0.116485082 1.819435695 3.406044176 0.694038579 0.036963942 20.36473311 -1.308878723 -0.27596741 EAAENSLVAYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EAAENSLVAYK 11 0 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ;; 160.36 6.42E-05 533660000 679080 598490 384650 498940 582060 516640 652160 711770 713040 FALSE TRUE 589337.8574 594558.4798 570668.0266 612231.9528 570478.1448 536515.4751 588913.6236 559563.5245 628745.2235 0.937323793 0.945627032 0.907629999 0.973736149 0.907327998 0.853311413 0.936649062 0.889968629 1 19.26211601 4.253591842 24.92266353 0.920362159 0.941475423 0.02388655 0.041153197 858.5627279 1423520.122 0.009943839 0.026075428 17930.47696 -4.253591842 0.021113264 EAAEVLQNNRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EAAEVLQNNRR 11 1 P61081;M0QX69 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ;;; 142.08 6.06E-05 1396920000 2055320 2078880 1102900 1406020 2001710 2493310 1627700 1848270 1981510 FALSE TRUE 1783704.254 2065223.7 1636266.129 1725278.331 1961879.887 2589229.249 1469845.905 1453031.844 1747258.145 1.02085903 1.181979724 0.936476464 0.987420397 1.122833448 1.481881344 0.841229963 0.831606851 1 20.73666134 EAAFDDAVEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAAFDDAVEER 11 0 Q09028-3;Q09028;E9PNS2;E9PIC4;E9PNS6 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 113.63 0.0031779 71220000 141230 132260 105250 139350 113000 127380 112250 142730 287510 FALSE TRUE 122566.0977 131391.1754 156149.252 170991.5473 110751.5211 132280.391 101364.0123 112208.3002 253520.8953 0.483455604 0.518265665 0.615922612 0.674467275 0.436853621 0.52177313 0.39982508 0.44259981 1 17.95174513 1.233775496 24.99911157 1.000000744 0.509700237 0.775896752 0.082476241 76.09937323 397520.8264 0.175515678 0.022067093 17.13071524 -1.233775496 -0.490300507 EAAFS(ph)PGQQDWSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAAFSPGQQDWSR 13 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 EAAFS(1)PGQQDWSR;EAAFS(1)PGQQDWSR 138.05 5.62E-05 188980000 539730 481190 270729 373180 545280 499210 486720 623060 401480 TRUE FALSE 468403.313 478029.0312 401654.4499 457916.2227 534429.9948 518414.9317 439517.9693 489823.4677 354017.4918 1.323107823 1.350297774 1.13456103 1.293484738 1.509614658 1.464376602 1.241514839 1.383613745 1 18.43346112 1.233735727 24.91182749 0.999999462 1.337241926 0.501827759 0.105700887 130.3492683 672932.8005 0.214587871 0.026926828 17.12914665 -1.233735727 0.337242463 EAAGPAPS(ph)PMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAAGPAPSPMR 11 0 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 EAAGPAPS(1)PMR 111.79 0.0016915 163790000 198540 188910 140070 162040 189130 191010 168960 196470 207390 TRUE FALSE 172302.436 187669.0378 207808.3205 198833.6586 185366.683 198358.2783 152574.2852 154456.4194 182872.5905 0.942199351 1.026228355 1.136355754 1.087279718 1.013638417 1.084680202 0.83432014 0.844612192 1 17.48047933 2.241211798 24.99939534 0.880457283 1.051574905 0.536326079 0.067747259 47.92153007 451884.5837 0.026485181 0.019568923 174.2656532 -2.241211798 0.171117621 EAAHLLNDALAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EAAHLLNDALAIR 13 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 0 ;; 207.12 5.59E-07 400490000 412570 382615 251910 311201 363939 409163 392091 423524 429267 FALSE TRUE 358047.8292 380101.5769 373734.5186 381863.9435 356697.3259 424903.7654 354066.0752 332956.6885 378519.5443 0.945916359 1.004179527 0.987358577 1.008835473 0.942348503 1.122541152 0.935397077 0.879628789 1 18.53000827 2.030676262 24.99970214 0.92410519 1.001424971 0.206049573 0.056997956 233.6969543 190451.0739 0.021980844 0.014819307 107.3189121 -2.030676262 0.077319781 EAAIWELEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAAIWELEER 10 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 104.22 0.0089693 0 42302 45453 28722 37248 37555 46308 35540 45133 43682 FALSE TRUE 36711.68352 45154.41625 42612.05527 45705.7277 36807.72898 48089.49873 32093.33627 35481.65918 38517.96372 0.953105512 1.172294999 1.106290446 1.186608099 0.955599035 1.248495353 0.833204385 0.921171727 1 15.23324382 2.226611957 24.99999902 0.915221653 1.103998782 0.430494399 0.100617067 191.3985939 400457.0244 0.037724363 0.025656689 168.504676 -2.226611957 0.188777128 EAALHIFWNFPGIFGNQQQHYLDVIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAALHIFWNFPGIFGNQQQHYLDVIK 26 0 H0Y8C6;O00410-2;O00410;O00410-3;H0Y3V4 H0Y8C6 IPO5 Importin-5 0 115.88 0.00063853 99748000 113970 86372 49945 86471 70521 70856 120600 139230 148690 FALSE TRUE 98908.57574 85804.61664 74098.56906 106105.5622 69117.77007 73581.87617 108904.2306 109456.748 131112.0376 0.754382111 0.654437367 0.565154584 0.809273993 0.527165708 0.561213734 0.830619618 0.834833704 1 17.00044062 1.740292438 1.62984196 0.977799659 0.647480058 0.587688077 0.096504294 0.296283128 1.419034922 0.124938355 0.028471022 54.99110398 -1.740292438 -0.330319601 EAALPPVS(ph)PLK ddPTM_MDA-MB-175_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 179.67 7.34E-06 12248978000 14589590 13234360 10581860 13863080 13972440 12323300 14914630 20567220 27119900 TRUE FALSE 12661538.72 13147422.62 15699282.89 17010904.2 13694415.78 12797385.33 13468211.48 16169080.06 23913816.32 0.529465416 0.549783541 0.656494249 0.711342095 0.572657061 0.535146091 0.563197915 0.676139678 1 24.51134105 1.233798448 2.734346428 1.093086974 0.592220736 0.837910359 0.056607226 0.194850154 1.670474367 0.22518522 0.01612624 17.1316206 -1.233798448 -0.500866238 EAALSTALSEKR ddPTM_MDA-MB-175_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 ;; 238.2 6.35E-16 2191610000 4285350 3536920 2514170 2503950 3325200 2731220 4967210 5728220 1590510 FALSE TRUE 3719030.14 3513685.74 3730031.021 3072510.118 3259035.026 2836291.801 4485490.739 4503284.73 1402481.72 2.651749458 2.50533443 2.659593326 2.190766607 2.323762927 2.022337804 3.198252552 3.210940055 1 20.41955054 EAALVQQEEEKAEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAALVQQEEEKAEQR 15 1 A0A499FI31;Q15020-4;Q15020 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 ; 118.55 0.0002577 313160000 192390 190039 128054 115334 148394 165194 169765 162316 138100 FALSE TRUE 166965.174 188790.6213 189981.3427 141522.3475 145441.2497 171549.1201 153301.2164 127605.9865 121773.9753 1.371107198 1.550336357 1.560114484 1.162172353 1.194354125 1.408750266 1.258899662 1.047892098 1 16.89384632 -0.082478247 0.240742399 3.75E-13 1.559882128 0.596769125 0.121637463 25.45495268 0.943593607 13.03993586 0.583860537 0.827030932 0.082478247 1.559882128 EAAMLWLEY(ph)NTESRSQY(ph)LSS(ph)VLSQIRIDALS(ph)EVTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAAMLWLEYNTESRSQYLSSVLSQIRIDALSEVTQR 36 2 A0A087WXP9;Q8IY47 A0A087WXP9 KBTBD2 Kelch repeat and BTB domain-containing protein 2 4 EAAMLWLEY(0.714)NT(0.167)ES(0.186)RS(0.447)QY(0.486)LS(0.496)S(0.503)VLS(0.073)QIRIDALS(0.502)EVT(0.426)QR 48.025 0.039503 48672000 0 0 0 0 0 0 2009.7 1804.6 0 TRUE FALSE 0 0 0 0 0 0 1814.799603 1418.700333 0 0 EAARS(ph)PDKPGGS(ph)PSASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAARSPDKPGGSPSASR 17 2 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 2 EAARS(1)PDKPGGS(0.681)PS(0.155)AS(0.164)R 75.326 0.011941 146870000 137830 105660 80259 92595 116960 97522 113060 148720 120200 TRUE FALSE 119615.4163 104965.9125 119072.5209 113620.11 114632.7248 101273.7344 102095.4586 116917.3853 105990.0929 1.128552801 0.990337017 1.123430667 1.071988021 1.081541884 0.955501893 0.963254732 1.1030973 1 16.69356989 2.799209428 24.99037897 1.016761482 1.076294878 0.30112528 0.054505905 375.6481865 154784.9127 0.017745567 0.017745566 629.8098195 -2.799209428 0.059533396 EAARSPDKPGGSPSAS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAARSPDKPGGSPSASR 17 2 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 EAARSPDKPGGSPS(0.003)AS(0.996)R;EAARSPDKPGGS(0.176)PS(0.11)AS(0.713)R 121.46 4.74E-05 290270000 379040 252180 182792 229210 312150 230270 298240 377750 281130 TRUE FALSE 328948.9036 250523.413 271190.8226 281255.6338 305938.8257 239128.6359 269316.7307 296971.1022 247895.1317 1.326967986 1.010602392 1.093973975 1.134575059 1.234146164 0.964636273 1.086413956 1.197970691 1 17.91937041 2.760128478 24.98892694 1.085725618 1.14666377 0.158743833 0.103391802 2301.485117 2666540.674 0.033041069 0.03301886 575.6101957 -2.760128478 0.060938152 EAASGT(ph)TPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAASGTTPQK 10 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 EAASGT(0.584)T(0.415)PQK 126.76 0.0041798 103940000 395710 336690 201400 249410 186650 233280 331570 412660 362880 TRUE FALSE 343415.9209 334478.2612 298797.7136 306042.3525 182936.0302 242254.4326 299414.3924 324415.8703 319980.7398 1.073239349 1.045307481 0.933799059 0.956439918 0.571709504 0.75709067 0.935726296 1.013860617 1 18.28762554 4.121976827 2.040931345 0.874824919 1.072218263 0.262135144 0.129324825 0.555591417 4.503542915 0.041021621 0.128802149 13242.70874 -4.121976827 0.197393344 EAASGTT(ph)PQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EAASGTTPQK 10 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 EAAS(0.01)GT(0.158)T(0.832)PQK;EAASGT(0.155)T(0.845)PQK;EAAS(0.001)GT(0.129)T(0.87)PQK;EAAS(0.001)GT(0.105)T(0.894)PQK 176.32 2.83E-05 2773890000 5485850 4563630 2938900 3838310 2686970 3416660 4853690 6007730 5091120 TRUE FALSE 4760881.023 4533651.214 4360161.87 4709856.95 2633504.554 3548101.121 4382979.891 4723023.692 4489253.593 1.060506145 1.009889756 0.971244279 1.04914032 0.586624146 0.790354353 0.976327089 1.052073266 1 22.09804416 EAASS(ph)PAGEPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EAASSPAGEPLR 12 0 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 EAAS(0.021)S(0.979)PAGEPLR;EAAS(0.034)S(0.966)PAGEPLR;EAAS(0.009)S(0.991)PAGEPLR;EAAS(0.018)S(0.982)PAGEPLR 212.68 1.83E-08 1752490000 3310940 2745780 1709980 2108790 2606280 2552900 2307910 2879310 3037290 TRUE FALSE 2873390.89 2727742.79 2536932.048 2587623 2554420.127 2651111.715 2084089.243 2263591.963 2678225.036 1.072871342 1.018489019 0.947243795 0.966170865 0.953773523 0.989876384 0.778160616 0.845183632 1 21.35284576 5.154319795 0.35981389 0.866508418 1.287473283 0.397464782 0.065775995 11.07619402 1.049151825 0.113478441 2.154784359 142665.7733 -5.154319795 0.420964865 EAASSSSGTQPAPPAPAS(ph)PWDSKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EAASSSSGTQPAPPAPASPWDSKK 24 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 EAASSSSGTQPAPPAPAS(0.972)PWDS(0.028)KK;EAASSSSGTQPAPPAPAS(0.999)PWDS(0.001)KK;EAASSSSGTQPAPPAPAS(0.961)PWDS(0.039)KK 201.51 8.65E-25 1905380000 2538270 1621260 1371250 1497900 1514340 1158140 2285570 2513020 2087500 TRUE FALSE 2202831.188 1610609.836 2034391.087 1838021.089 1484207.597 1202694.395 2063915.773 1975630.229 1840718.128 1.196723797 0.874989936 1.105215978 0.99853479 0.806319867 0.653383251 1.121255743 1.073293189 1 20.81183729 4.753114052 23.78457381 0.963360901 1.196724121 0.21521811 0.144635882 2412.966492 3943358.923 0.037734438 0.757270842 56638.80109 -4.753114052 0.23336322 EAATLEVERPLPMEVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAATLEVERPLPMEVEK 17 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 240.21 2.37E-20 323130000 494490 341120 321300 393260 331510 316280 394790 491620 1019700 FALSE TRUE 429141.8936 338879.1603 476681.7547 482555.6936 324913.5996 328447.4963 356503.3266 386490.8888 899152.2276 0.477273904 0.376887417 0.530145775 0.536678528 0.361355496 0.36528575 0.396488287 0.429839216 1 19.77820586 1.238413618 24.99918322 1.000000625 0.432240817 0.886628455 0.063575255 1.138871514 193019.5932 0.091088903 0.016219577 17.31464606 -1.238413618 -0.567759808 EAATQEDPEQLPELEAHGVS(ph)ESEGEERPVAEEEILLR ddPTM_MDA-MB-175_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(1)ESEGEERPVAEEEILLR;EAATQEDPEQLPELEAHGVS(0.966)ES(0.034)EGEERPVAEEEILLR 348.83 3.36E-145 350370000 230805 204483 145783 180234 201013 209602 194066 240470 199236 TRUE FALSE 200303.5345 203139.7377 216284.1464 221158.8844 197013.2346 217665.5246 175245.5092 189047.3618 175682.5471 1.140144754 1.156288665 1.231107757 1.25885518 1.121416088 1.238970679 0.997512343 1.076073662 1 17.42261135 2.236109309 24.99993036 1.034141511 1.191273508 0.720632946 0.048777147 34.22785434 349067.7937 0.018931109 0.013442616 172.2302014 -2.236109309 0.157131996 EAAVGVPPPAQPAPGEPTPPAPPS(ph)PDWTSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EAAVGVPPPAQPAPGEPTPPAPPSPDWTSSSR 32 0 Q8IV56 Q8IV56 PRR15 Proline-rich protein 15 1 EAAVGVPPPAQPAPGEPT(0.001)PPAPPS(0.705)PDWT(0.161)S(0.037)S(0.048)S(0.048)R;EAAVGVPPPAQPAPGEPTPPAPPS(0.84)PDWT(0.052)S(0.072)S(0.018)S(0.018)R;EAAVGVPPPAQPAPGEPTPPAPPS(0.921)PDWT(0.047)S(0.011)S(0.011)S(0.011)R;EAAVGVPPPAQPAPGEPTPPAPPS(0.928)PDWT(0.043)S(0.01)S(0.01)S(0.01)R 155.98 5.00E-11 2315590000 1515920 1485910 960680 1088000 1328730 1362940 1444000 1532240 1730990 TRUE FALSE 1315587.331 1476148.959 1425268.061 1335047.029 1302290.873 1415373.184 1303961.102 1204582.4 1526354.334 0.861914761 0.967107654 0.933772735 0.874663896 0.853203508 0.927290048 0.854297769 0.789189229 1 20.54165848 3.729988939 20.70233082 0.872118579 0.925549314 0.05943931 0.060369918 116.6106529 281642.2017 0.016368834 0.024871102 5370.181186 -3.729988939 0.053430735 EAAVSASDILQESAIHS(ph)PGTVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAAVSASDILQESAIHSPGTVEK 23 0 F5H3K2;F5H8B7;E7ENF1;G5EA44;F5H7W8;Q96C57 F5H3K2 C12orf43 Uncharacterized protein C12orf43 1 EAAVSASDILQESAIHS(1)PGTVEK;EAAVSASDILQESAIHS(1)PGTVEK 249.96 2.81E-38 1315870000 708400 560400 377280 501940 575850 480580 719960 804150 693400 TRUE FALSE 614783.1451 556718.6955 559733.8699 615913.1487 564391.7116 499068.2236 650138.39 632188.7804 611427.0419 1.005488968 0.910523509 0.915454881 1.007337109 0.923072865 0.816235118 1.063313111 1.033956199 1 19.22182083 2.196524044 24.99997039 1.034029666 0.931396269 0.435830192 0.055069177 133.3481774 79303.82604 0.022281317 0.015022209 157.2258836 -2.196524044 -0.102633397 EACANENAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EACANENAHK 10 0 B4DXZ6;P51114;P51114-3;C9JZE0;C9JY20;C9J5B4;C9IZ22;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 93.561 0.0087018 190370000 104110 88911 67231 76314 75582 81635 77594 105130 137300 FALSE TRUE 90351.59972 88326.93779 99744.13647 93642.26009 74078.06607 84775.55127 70068.94582 82648.76762 121068.5504 0.746284641 0.729561372 0.82386496 0.773464783 0.611868779 0.700227689 0.578754314 0.682660917 1 16.88546462 1.236274505 24.99782875 1.000000386 0.702224136 0.623640421 0.071768127 44.61058654 487686.8125 0.12329229 0.019004588 17.22957264 -1.236274505 -0.29777625 EACAVPEPQES(ph)GSEEHLPLSQFTTVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EACAVPEPQESGSEEHLPLSQFTTVDR 27 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 EACAVPEPQES(0.752)GS(0.248)EEHLPLSQFTTVDR;EACAVPEPQES(0.57)GS(0.43)EEHLPLSQFTTVDR;EACAVPEPQES(0.5)GS(0.5)EEHLPLSQFTTVDR 187.74 6.00E-18 262957000 255111 264199 172087 176769 271653 276014 260217 279658 282060 TRUE FALSE 221397.435 262463.4594 255308.8488 216907.1032 266247.6368 286632.4372 234981.1954 219855.313 248715.1881 0.890164516 1.055277168 1.026510889 0.872110404 1.070492071 1.152452487 0.944780241 0.883964163 1 17.92413508 2.024375049 24.99439227 0.927897195 1.013443579 0.117502746 0.086152662 385.4487988 395241.0309 0.035286649 0.023789258 105.7730553 -2.024375049 0.085546384 EACPELDYFVVFSSVSCGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EACPELDYFVVFSSVSCGR 19 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;; 271.04 5.99E-39 709211000 489207 478988 347190 346664 479425 521109 548710 574837 537537 FALSE TRUE 424557.0555 475841.4963 515092.2453 425379.3596 469885.3805 541156.4004 495496.1887 451912.5809 473989.9882 0.895708909 1.003906218 1.086715454 0.897443765 0.991340307 1.141704285 1.045372689 0.953422208 1 18.85449706 2.983591505 24.7822329 1.028119812 0.976920544 0.150525843 0.070918253 1607.343615 2427623.115 0.023603624 0.024227538 962.9228783 -2.983591505 -0.051199268 EADAALFSELHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EADAALFSELHR 12 0 Q96CW5-2;Q96CW5;A0A087WU06;A0A3B3ITE3;Q96CW5-3 Q96CW5-2 TUBGCP3 Gamma-tubulin complex component 3 0 ; 176.29 2.54E-05 201971000 172533 169540 99154 120785 178769 190266 177984 198883 212733 FALSE TRUE 149732.3269 168426.2806 147105.2061 148211.0803 175211.8467 197585.6561 160723.1391 156353.4182 187583.9471 0.798215035 0.897871503 0.784209994 0.790105351 0.934044994 1.053318577 0.856806468 0.833511719 1 17.51717685 3.231794582 24.98029483 0.922767655 0.820949079 0.404767245 0.070069852 196.7363676 726352.254 0.022617435 0.026225202 1705.275615 -3.231794582 -0.101818577 EADDIVNWLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EADDIVNWLK 10 0 P07237;I3L312;I3L3P5 P07237 P4HB Protein disulfide-isomerase 0 ;;; 185.81 3.28E-06 1394350000 4125610 3361300 2621440 3388100 3458680 3622420 3904390 3714230 3268740 FALSE TRUE 3580400.186 3339219.399 3889177.152 4157419.889 3389859.035 3761776.841 3525742.859 2919970.819 2882313.281 1.242196748 1.15852063 1.349324925 1.442390012 1.176089725 1.305124209 1.223233741 1.01306504 1 21.45879572 1.785230222 3.027988179 0.996458538 1.279152482 0.653078329 0.08102562 0.144636063 2.543010569 0.059304754 0.022955573 60.98601026 -1.785230222 0.282693944 EADGSDSLEGFVLCHSIAGGTGSGLGSYLLER ddPTM_MDA-MB-175_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 ; 409.75 3.52E-186 325720000 212893 209645 122506 158166 213140 227414 230680 249320 162502 FALSE TRUE 184758.6506 208267.8282 181750.3114 194080.0077 208898.931 236162.7637 208308.6891 196004.8582 143291.1987 1.289392875 1.453458622 1.26839829 1.354444722 1.45786296 1.648131678 1.453743782 1.36787786 1 17.12859047 1.235049959 3.604685767 0.940207396 1.420819719 0.60382656 0.105504867 0.215398779 4.233374806 0.284665156 0.028551062 17.18106019 -1.235049959 0.480612324 EADIDGDGQVNYEEFVQMMTAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EADIDGDGQVNYEEFVQMMTAK 22 0 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;M0QZ52 P0DP25 CALM2;CALM3 0 181.29 5.02E-17 33184000 40502 36182 40047 51044 34904 38880 27695 46626 89619 FALSE TRUE 35149.55808 35944.31806 59413.86315 62634.32036 34209.47869 40375.73876 25009.14316 36655.39274 79024.34391 0.444794051 0.454851205 0.751842536 0.792595259 0.432897978 0.510927858 0.316473911 0.463849378 1 16.27000953 1.234532352 24.99557981 1.000000699 0.519321743 0.517355586 0.145380404 109.2152203 677590.1268 0.287679815 0.038631489 17.16059538 -1.234532352 -0.480678955 EADKSHPEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EADKSHPEQR 10 1 O14745 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;; 147.62 1.60E-05 2476960000 6685400 5293020 3441360 4325940 3869120 4499770 6225350 7509800 3907150 FALSE TRUE 5801907.451 5258249.803 5105613.207 5308210.795 3792132.082 4672879.064 5621616.515 5903887.711 3445251.178 1.684030322 1.526231189 1.481927715 1.540732597 1.100683778 1.35632464 1.631700049 1.713630562 1 21.71617774 4.749141651 1.277292269 1.430011421 1.79738518 0.144893216 0.219180475 3.573275824 4.974826346 0.067064342 1.737284044 56123.09994 -4.749141651 0.367373759 EADLLQESLEHIEMYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EADLLQESLEHIEMYEK 17 0 Q6N069;Q6N069-5;Q6N069-4;Q6N069-3;Q6N069-2 Q6N069 NAA16 "N-alpha-acetyltransferase 16, NatA auxiliary subunit" 0 85.362 0.0050551 11977000 25880 21195 16105 16883 20943 20683 18105 29572 27634 FALSE TRUE 22459.89243 21055.76865 23893.43187 20716.54319 20526.27527 21478.68839 16349.17989 23248.25793 24367.14 0.921728706 0.864105047 0.980559551 0.850183616 0.842375235 0.881461197 0.670951941 0.954082339 1 14.57264931 3.66928743 24.99923523 0.863026347 0.916330695 0.077326512 0.089292792 475.864692 171728.4788 0.024983629 0.037056716 4669.683326 -3.66928743 0.053304348 EADPEDGKPVMDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EADPEDGKPVMDK 13 1 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ;; 128.76 0.00014731 1015260000 2604050 2265590 2111710 2220580 1991980 1394520 3042940 3604540 3238170 FALSE TRUE 2259918.195 2250707.19 3132940.019 2724796.628 1952343.495 1448168.087 2747836.147 2833737.172 2855357.232 0.79146601 0.788240142 1.097214732 0.954275212 0.683747544 0.5071758 0.962344087 0.992428247 1 21.44523982 2.02943318 24.99664048 0.990187648 0.810806488 0.237692326 0.153453983 322.8212573 274160.2687 0.068497479 0.046180296 107.0121723 -2.02943318 -0.179381161 EADVDQDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EADVDQDGR 9 0 Q9NZT1 Q9NZT1 CALML5 Calmodulin-like protein 5 0 ; 132.84 0.0027421 0 383990 305920 203031 246370 251570 284630 294220 342820 363200 FALSE TRUE 333244.7486 303910.3914 301217.4707 302312.074 246564.2492 295579.9003 265686.5897 269510.6108 320262.9098 1.040534943 0.94894033 0.940531862 0.943949689 0.76988075 0.922928916 0.829589008 0.841529264 1 18.2888972 4.47740035 0.933452337 0.871219614 1.077570012 0.371516515 0.064426827 1.468037325 1.358250067 0.021948296 0.28361784 30019.28539 -4.47740035 0.206350399 EAEAAIYHLQLFEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 EAEAAIYHLQLFEELR 16 0 P14618;P14618-3;B4DNK4 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;;;;; 266.71 3.18E-27 10895432300 6281752.4 5002036.5 4321217.3 5571810.9 4805182.3 5276361.7 5605706.6 6039713.6 11679253 FALSE TRUE 5451602.904 4969177.793 6410972.44 6836975.725 4709568.573 5479346.749 5062066.037 4748167.848 10298545.02 0.529356613 0.482512606 0.622512445 0.663877831 0.457304266 0.53205057 0.491532156 0.461052298 1 23.29593719 1.233567653 24.99999457 1.000000724 0.528366574 0.829743419 0.066901066 65.7135319 328992.0043 0.140506282 0.017358511 17.12251887 -1.233567653 -0.47163415 EAEAAIYHLQLFEELRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 26 EAEAAIYHLQLFEELRR 17 1 P14618;P14618-3;B4DNK4 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;;;;;;;;;;;;;;;;; 278.22 5.23E-36 33646276400 19398238.3 15872206.3 10554300.7 11798531.7 13725589.4 15051591 16409224.6 17712419.7 10069482.5 FALSE TRUE 16834711.96 15767940.73 15658395.82 14477568.65 13452477.02 15630635.45 14817860.52 13924756.59 8879079.75 1.895997382 1.775853036 1.763515619 1.630525804 1.515075594 1.760389127 1.668850933 1.568265741 1 23.08197873 1.056244863 1.817541557 0.428858394 1.713394748 0.83259209 0.100347611 0.636647726 1.314402336 1.671172882 0.029144904 11.38268881 -1.056244863 1.284536354 EAEALLQSMGLTPESPIVPPPMS(ph)PSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 EAEALLQSMGLTPESPIVPPPMSPSSK 27 0 Q13409-2;Q13409-3;Q13409-6;E7EQL5;E7EV09;E7EQU2;E7ETL8;E9PGG1 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 1 EAEALLQSMGLTPESPIVPPPMS(0.8)PS(0.17)S(0.029)K;EAEALLQSMGLTPESPIVPPPMS(0.671)PS(0.146)S(0.183)K;EAEALLQSMGLTPESPIVPPPMS(0.725)PS(0.137)S(0.137)K;EAEALLQSMGLTPESPIVPPPMS(0.711)PS(0.237)S(0.052)K;EAEALLQSMGLTPESPIVPPPMS(0.629)PS(0.194)S(0.176)K;EAEALLQSMGLTPESPIVPPPMS(0.771)PS(0.186)S(0.043)K;EAEALLQSMGLTPESPIVPPPMS(0.931)PS(0.056)S(0.014)K;EAEALLQSMGLTPESPIVPPPMS(0.881)PS(0.098)S(0.021)K;EAEALLQSMGLTPESPIVPPPMS(0.944)PS(0.044)S(0.012)K 166.24 5.79E-12 2910508000 2675341 2659871 2015340 2540086 3085619 2522360 3741528 4586595 3966954 TRUE FALSE 2321787.908 2642398.132 2989965.165 3116851.349 3024221.219 2619396.821 3378675.19 3605787.352 3497985.217 0.663750063 0.755405746 0.85476781 0.891041887 0.864560892 0.748830158 0.965891786 1.030818351 1 21.73809276 -2 0.057615556 2.544181076 1.45E-14 0.683883865 0.065643043 513.7340799 2.87564903 121.9246074 32.6317038 0.01 2 -2.544181076 EAEAMALLAEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EAEAMALLAEAER 13 0 P54920;M0R0Y2;M0R2M1;M0QZM9;M0QZN5;M0R031 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;;; 161.94 2.20E-06 84643000 339902 295299 205356 218663 280602 284852 293977 334283 303427 FALSE TRUE 294983.0895 293359.1614 304666.8485 268313.7762 275018.5692 295810.4408 265467.1558 262799.1818 267556.2057 1.102508868 1.096439384 1.138702231 1.002831444 1.027890826 1.10560112 0.992192108 0.982220469 1 18.02948247 2.793715726 0.245075736 0.915616154 1.169359696 0.510872394 0.039715302 3.16014967 1.005610056 0.517538394 0.420532627 621.8930819 -2.793715726 0.253743543 EAEAYTGLS(ph)PPVPSFNCEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAEAYTGLSPPVPSFNCEVR 20 0 O43164-2;O43164 O43164-2 PJA2 E3 ubiquitin-protein ligase Praja-2 1 EAEAYTGLS(1)PPVPSFNCEVR;EAEAYTGLS(1)PPVPSFNCEVR 155.94 2.53E-08 97866000 166016 186189 124061 165002 194780 183816 147365 199608 264930 TRUE FALSE 144076.565 184965.9122 184057.3146 202468.226 190904.2591 190887.5205 133073.565 156923.3826 233610.2772 0.616738984 0.791771297 0.787881924 0.866692289 0.817191184 0.817119532 0.569639172 0.671731503 1 17.83374422 4.742598344 23.41060399 0.774648539 0.61673883 0.176270201 0.11350872 344.3428641 1996284.996 0.028937389 0.210977467 55283.85811 -4.742598344 -0.157909709 EAEDGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EAEDGFR 7 0 F6U236;Q9BY11;Q9UNF0-2;Q9UNF0;A0A0U1RR22;B0QYG7;B0QYG8 F6U236;Q9UNF0-2 PACSIN1;PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 1;Protein kinase C and casein kinase substrate in neurons protein 2 0 ;; 148.33 0.0048655 814150000 1648200 1540330 1054760 1298850 1400230 1506360 1488860 1753750 1877560 FALSE TRUE 1430386.194 1530211.471 1564845.464 1593773.744 1372368.163 1564310.644 1344470.586 1378724.21 1655596.996 0.863970035 0.924265673 0.945185011 0.962658031 0.828926463 0.944861973 0.812076 0.832765591 1 20.65892011 3.244820508 24.99999824 0.875039002 0.925549059 0.086719687 0.061395371 309.9541501 1237849.489 0.017651522 0.022221174 1757.197223 -3.244820508 0.050510057 EAEDNIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAEDNIR 7 0 O60925 O60925 PFDN1 Prefoldin subunit 1 0 85.272 0.048698 1514700000 418470 366130 255680 288050 341640 363000 404040 474110 409190 FALSE TRUE 363168.1292 363724.8679 379327.7032 353456.1551 334842.0324 376964.8449 364856.263 372725.266 360816.0244 1.006518848 1.008061847 1.051305035 0.979602155 0.928013197 1.044756384 1.011197503 1.03300641 1 18.46090389 EAEDS(ph)DS(ph)DDNIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAEDSDSDDNIK 12 0 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 2 EAEDS(1)DS(1)DDNIK 168.1 0.00022064 0 405160 382130 234500 155930 305570 296040 571350 441330 168100 TRUE FALSE 351617.0795 379619.7629 347904.9844 191336.2897 299489.7548 307428.8504 515940.5649 346955.0139 148227.4095 2.372146155 2.561063194 2.347102911 1.290829344 2.020474863 2.074035102 3.48073657 2.34069404 1 17.17745272 EAEDS(ph)DS(ph)DDNIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EAEDSDSDDNIKR 13 1 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 2 EAEDS(1)DS(1)DDNIKR;EAEDS(1)DS(1)DDNIKR;EAEDS(1)DS(1)DDNIKR 184.44 6.35E-06 485100000 2899030 1897590 1456270 1856300 2102470 1584890 2046660 2842680 3061650 TRUE FALSE 2515915.84 1885124.606 2160527.043 2277801.287 2060634.96 1645861.744 1848175.228 2234795.004 2699705.225 0.931922425 0.698270533 0.800282573 0.84372222 0.763281465 0.609644982 0.684584084 0.827792228 1 21.36437046 1.307909223 3.240650566 1.020593795 0.758169066 0.416010953 0.088666153 0.290475525 4.264111973 0.174434078 0.023177133 20.31932248 -1.307909223 -0.262424728 EAEDSLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EAEDSLRR 8 1 O43776;K7EIU7;O43776-2;K7EJ19;K7EPK2;K7EMQ6 O43776;REV__H7BZ55 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;;; 171.53 0.00046314 3321940000 5369980 3821120 2250805 2684350 3249850 3823270 3746770 4317160 2772290 FALSE TRUE 4660323.537 3796018.811 3339301.826 3293872.695 3185184.343 3970353.671 3383408.822 3393968.93 2444553.034 1.906411304 1.552847804 1.366017337 1.347433518 1.302972076 1.624163442 1.384060307 1.388380159 1 21.22113927 4.691797407 1.903314793 1.357187701 2.045407349 0.587887153 0.150636307 0.522767764 2.152383197 0.039545911 0.615986921 49181.00586 -4.691797407 0.688219648 EAEDTQVFGDLPRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAEDTQVFGDLPRPR 15 1 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 0 106.6 0.0011157 230630000 140130 138430 62290 93673 129660 114950 121920 163680 80751 FALSE TRUE 121611.4655 137520.6442 92413.65235 114942.8864 127080.0197 119372.2009 110096.2172 128678.3058 71204.70877 1.707913248 1.931341994 1.297858722 1.614259623 1.784713706 1.676464983 1.546192928 1.80716006 1 16.11968503 1.231326916 24.98764381 0.999998824 1.669762018 0.607213277 0.169534878 176.2185197 608664.5681 0.402981371 0.040426563 17.03440294 -1.231326916 0.669763193 EAEEAEREER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAEEAEREER 10 1 A0A0A0MRX2;Q96HY6-2;Q96HY6 A0A0A0MRX2 DDRGK1 DDRGK domain-containing protein 1 0 ; 104.82 0.0023991 126966000 116236 116002 70208 103248 127540 138549 80848 167878 91059 FALSE TRUE 100875.1181 115239.9752 104160.8236 126692.0364 125002.2035 143879.0697 73007.3734 131978.5961 80294.10875 1.256320291 1.435223294 1.297241171 1.577849713 1.556804172 1.7919007 0.90924944 1.643689658 1 16.29300652 1.220112733 24.78291336 0.999998447 1.434164452 0.238480773 0.243464688 1636.214849 2197961.115 1.850404031 0.055799981 16.60017754 -1.220112733 0.434166006 EAEEES(ph)DHN ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EAEEESDHN 9 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 EAEEES(1)DHN;EAEEES(1)DHN;EAEEES(1)DHN;EAEEES(1)DHN;EAEEES(1)DHN 183.85 4.69E-05 2444758000 4582540 4040480 2926680 3327190 3236280 4148620 4377850 5029770 5419870 TRUE FALSE 3976945.728 4013937.821 4342032.237 4082679.342 3171884.36 4308220.096 3953286.781 3954192.827 4779139.143 0.83214688 0.839887206 0.908538569 0.854270868 0.663693662 0.901463625 0.827196418 0.827386002 1 22.18831934 1.237674564 24.96112261 1.000000201 0.831671154 0.388252159 0.066343291 23.07656538 649711.6568 0.093144422 0.015843475 17.28520615 -1.237674564 -0.168329047 EAEEGEDDRDS(ph)ANGEDDS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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(0.999)ANGEDDS(0.001);EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(0.999)ANGEDDS(0.001);EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(1)ANGEDDS 248.46 4.39E-24 53189928000 3783648 2645260 2743144 3672912 3117848 3530606 2617269 3675412 6955980 TRUE FALSE 3283629.33 2627883.113 4069737.614 4506902.807 3055808.925 3666430.697 2363446.655 2889453.746 6133651.969 0.535346535 0.428436945 0.663509706 0.734782937 0.498203834 0.597756559 0.385324545 0.471082116 1 22.54831488 1.233671204 24.99982973 1.000000708 0.535957159 0.654581809 0.105148464 102.2613517 522805.2614 0.219098266 0.027329907 17.12660195 -1.233671204 -0.464043549 EAEEGEDDRDSANGEDDS ddPTM_MDA-MB-175_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 ; 159.18 3.56E-10 379260000 524680 363730 367860 513820 443640 456430 342500 545490 900420 FALSE TRUE 455342.2086 361340.6337 545758.3264 630490.6842 434812.432 473989.1574 309284.4027 428841.2085 793973.3734 0.573498084 0.455104221 0.687376107 0.794095502 0.547641075 0.596983694 0.389540019 0.540120391 1 19.5987311 1.236170356 24.97354283 1.00000057 0.569648995 0.591342831 0.111511817 48.78243915 509564.6449 0.189362985 0.02893648 17.22544126 -1.236170356 -0.430351574 EAEEGPTGASESQDS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAEEGPTGASESQDSPR 17 0 H0Y507;Q5TCZ1-2;Q5TCZ1-3;Q5TCZ1 H0Y507 SH3PXD2A SH3 and PX domain-containing protein 2A 1 EAEEGPTGASESQDS(1)PR;EAEEGPTGASESQDS(1)PR 351.47 1.13E-87 791480000 368580 371810 268000 303360 394040 395840 369490 461020 436920 TRUE FALSE 319871.2191 369367.5556 397605.6964 372242.5246 386199.3749 411068.2209 333656.9167 362434.4607 385267.8153 0.830256789 0.958729333 1.032024168 0.966191594 1.002417953 1.066967456 0.866038904 0.940733812 1 18.55550215 4.724789499 4.367573029 0.97642025 0.821366486 0.432455746 0.053883074 0.199147619 9.127835755 0.013814884 0.093440878 53062.71891 -4.724789499 -0.155053763 EAEEVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAEEVYR 7 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ; 146.87 0.0050945 1095690000 1002660 808150 508330 639790 735720 714190 746290 859250 791910 FALSE TRUE 870155.9406 802841.2094 754160.0883 785064.0981 721080.6114 741665.3514 673914.9107 675506.0742 698291.3019 1.246121695 1.149722483 1.080007851 1.124264467 1.03263582 1.062114549 0.965091372 0.967370025 1 19.41346948 8 0.223844141 0.925903485 2.635636396 0.873177158 0.031026813 29.63000517 0.458143148 0.142382386 17.82472417 100000000 -8 1.709732911 EAEGSSAEYKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EAEGSSAEYKK 11 1 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 ;;; 103.44 0.0043838 722770000 1302580 887770 619440 719270 681840 609505 1054030 1275490 929950 FALSE TRUE 1130440.753 881938.1804 919003.2559 882591.2469 668272.718 632953.0518 951810.3328 1002736.389 820012.3704 1.378565487 1.075518141 1.120718771 1.076314552 0.814954435 0.771882321 1.160726798 1.222830808 1 19.64528615 5.575033196 1.19611376 1.029255863 3.083183559 0.386105562 0.140222129 12.58105314 3.433255086 0.046788725 51.92097763 375866.1332 -5.575033196 2.053927696 EAEILEVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAEILEVLR 9 0 P36551 P36551 CPOX "Oxygen-dependent coproporphyrinogen-III oxidase, mitochondrial" 0 ; 117.89 0.0025086 53934000 91979 83913 56020 70975 78459 89099 64848 89336 98412 FALSE TRUE 79823.7421 83361.76998 83111.45938 87090.95853 76897.8194 92526.69618 58559.05094 70232.19161 86777.84547 0.919863148 0.960634244 0.957749745 1.003608214 0.886145755 1.066247908 0.674815682 0.809333203 1 16.40503915 2.248347629 24.99970318 0.817765608 0.963222029 0.337142446 0.090564898 206.2831463 526925.273 0.033060417 0.025284007 177.1526401 -2.248347629 0.145456421 EAEKLESEHPDQAQAILSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAEKLESEHPDQAQAILSR 19 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 164.59 1.41E-11 273780000 348030 311150 156180 254960 303750 265330 378530 381040 267830 FALSE TRUE 302036.9537 309106.0352 231709.1704 312852.5648 297705.9693 275537.4168 341820.2189 299557.5613 236167.4425 1.278910211 1.308842709 0.98112241 1.324706579 1.260571593 1.166703648 1.44736385 1.268411759 1 17.84945057 EAELDKYLECR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAELDKYLECR 11 1 P35813;P35813-3;P35813-2 P35813 PPM1A Protein phosphatase 1A 0 ; 94.122 0.0079707 240550000 455860 425350 246740 231410 398790 318490 527390 566560 101472 FALSE TRUE 395616.946 422555.8478 366064.2893 283955.1774 390854.8592 330742.5164 476243.799 445405.553 89476.09576 4.421481991 4.72255572 4.091196494 3.173531154 4.368260102 3.696434378 5.322581355 4.977927895 1 16.44921469 4.148329447 5.973126119 3.978566073 4.567508555 0.053517591 1.183496184 0.756016934 39.79385938 0.303394699 0.651572443 14071.14528 -4.148329447 0.588942482 EAELGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAELGAR 7 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YBN4;Q4VXU2;Q4VXU2-2 P11940-2 PABPC1;PABPC3;PABPC1L Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3;Polyadenylate-binding protein 1-like 0 134.66 0.0073342 631250000 982400 914800 634870 641330 764060 1012600 852920 1042200 1024400 FALSE TRUE 852573.3509 908790.6186 941895.2555 786953.7786 748856.7009 1051555.377 770203.9497 819333.6404 903296.599 0.943846519 1.006082188 1.042730878 0.871201972 0.82902637 1.164130783 0.852658972 0.907048295 1 19.78484025 3.748711841 24.9379205 0.933831896 0.998406089 0.078145221 0.096970366 1810.52672 4447806.035 0.025390146 0.043315547 5606.758387 -3.748711841 0.064574194 EAEMEEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EAEMEEHR 8 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C044 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;;;; 162.97 0.00033863 1567110000 1543136 1385164 1166836 1440903 1259757 1407744 1367341 1562887 2835800 FALSE TRUE 1339206.668 1376064.766 1731121.792 1768082.049 1234690.3 1461900.823 1234736.48 1228675.777 2500554.955 0.535563782 0.550303749 0.69229504 0.707075862 0.493766513 0.584630552 0.493784981 0.491361238 1 21.25381688 1.232403701 24.99991236 1.000000711 0.567254248 0.75617638 0.07698254 111.4385258 452446.8824 0.18460506 0.020506235 17.07669026 -1.232403701 -0.432746463 EAENPEGEEKEAATLEVERPLPMEVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EAENPEGEEKEAATLEVERPLPMEVEK 27 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;;;;; 211.33 5.69E-26 1314600000 1275622 923337 802966 767572 797743 643369 1361783 1567994 656022 FALSE TRUE 1107045.321 917271.5385 1191283.043 941860.9542 781869.4751 668119.8217 1229717.494 1232690.685 578467.8265 1.913754352 1.58569154 2.059376492 1.628199376 1.351621368 1.154981818 2.125818305 2.130958074 1 19.1418772 EAEQEAAR ddPTM_MDA-MB-175_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 ; 167.23 0.00073018 119939000 230520 226000 166919 166663 132552 252330 198910 221800 279320 FALSE TRUE 200056.1979 224515.3911 247641.5867 204506.3814 129914.4745 262037.2984 179619.7388 174369.796 246299.1078 0.812248975 0.911555844 1.005450604 0.830317183 0.527466282 1.063898691 0.729274825 0.707959512 1 17.91005188 3.489064696 24.98741251 0.789604156 0.911257507 0.081108302 0.155349342 1244.618198 2603919.654 0.042044725 0.058720642 3083.647277 -3.489064696 0.121653351 EAEQEAARR ddPTM_MDA-MB-175_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 ; 112.3 0.0031839 355460000 355600 293390 149423 137597 247160 311630 275270 297850 54543 FALSE TRUE 308606.559 291462.7018 221684.4626 168840.5019 242241.9996 323618.6078 248574.3578 234157.0954 48094.98868 6.416605296 6.060147009 4.609304809 3.510563294 5.036740963 6.72873862 5.168404539 4.868638123 1 15.55359896 1.21531238 3.335390691 0.165505448 5.314155588 0.684783388 0.921640508 0.235067084 3.487920542 3.251567966 0.253857639 16.41770242 -1.21531238 5.14865014 EAEQMGNELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAEQMGNELER 11 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 162 0.0024758 0 142200 128390 76791 97360 139820 161920 117660 138160 135160 FALSE TRUE 123407.9097 127546.5976 113927.3845 119467.0761 137037.8556 168149.1672 106249.3513 108615.5592 119181.5388 1.035461624 1.070187539 0.955914696 1.002395818 1.149824519 1.410865885 0.891491689 0.911345501 1 16.86280125 EAESAKHS(ph)PEKGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAESAKHSPEKGK 13 2 J3KN75;Q0IIM8 J3KN75 TBC1D8B TBC1 domain family member 8B 1 EAES(0.008)AKHS(0.992)PEKGK 66.673 0.028817 43554000 155050 123000 86669 75576 101980 72830 204020 218290 41396 TRUE FALSE 134559.7497 122192.0049 128582.4183 92736.68591 99950.79752 75631.81723 184234.1718 171610.3822 36502.21204 3.686345077 3.347523289 3.522592498 2.540577152 2.738212068 2.071979012 5.047205676 4.701369387 1 15.15569627 2.248597761 24.99992689 3.876896129 2.994118057 0.035665114 1.170508091 460.9798884 1148182.565 0.442105025 0.338364414 177.2547005 -2.248597761 -0.882778072 EAESSPFVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAESSPFVER 10 0 P14625 P14625 HSP90B1 Endoplasmin 0 98.055 0.011856 0 527600 422790 209300 412650 444760 363640 395900 473880 456580 FALSE TRUE 457876.3232 420012.6647 310518.1801 506348.4895 435910.1462 377629.4661 357505.6789 372544.4497 402603.6325 1.137288107 1.04324112 0.771275157 1.257684851 1.082727802 0.937968353 0.887984236 0.925338024 1 18.61900066 2.725421823 20.63049672 0.931199447 1.052713978 0.190387669 0.122947805 132.9337295 208728.8946 0.042177873 0.037557441 531.400334 -2.725421823 0.121514531 EAETEPHEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAETEPHEGK 10 0 P41223;P41223-2 P41223 BUD31 Protein BUD31 homolog 0 ; 73.327 0.045323 145070000 681170 542600 451780 572550 456410 469510 569820 704910 1204690 FALSE TRUE 591151.6586 539035.6249 670262.3191 702556.2284 447328.334 487572.3535 514558.9441 554170.4821 1062272.921 0.556496967 0.507436097 0.630969976 0.661370741 0.421104902 0.458989723 0.484394297 0.521683714 1 20.01872304 1.238048139 24.99876939 1.000000535 0.528635211 0.804212376 0.072828303 5.690215893 277296.2798 0.10880405 0.018946935 17.30008108 -1.238048139 -0.471365324 EAFEETHLTSLDPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAFEETHLTSLDPVK 15 0 J3QQZ9;Q9NVS9-3;Q9NVS9;Q9NVS9-4;A0A286YFL3 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 ; 211.13 1.54E-09 668270000 1323320 1249630 554600 934760 1159890 1019340 1449230 1696060 1692470 FALSE TRUE 1148439.909 1241421.098 822806.415 1147011.545 1136810.458 1058554.669 1308683.898 1333370.768 1492388.125 0.769531659 0.831835283 0.551335408 0.768574559 0.761739148 0.709302528 0.876905864 0.89344772 1 20.50919135 1.760472994 1.141919971 1.014718748 0.727048928 0.591025887 0.076547289 0.512091117 1.015237269 0.152009981 0.02598631 57.6066995 -1.760472994 -0.28766982 EAFGFIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EAFGFIER 8 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0;E9PNG3 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;;; 117.04 0.0050165 738070000 986590 964730 695640 829420 1039340 1079430 1007520 1060630 1023740 FALSE TRUE 856209.6318 958392.6251 1032053.831 1017752.488 1018659.167 1120956.371 909810.8655 833822.5283 902714.6234 0.948483175 1.061678409 1.143278068 1.127435472 1.128439865 1.241761617 1.007861003 0.923683417 1 19.78391045 2.013062024 24.97539085 0.959205011 1.110986867 0.415292002 0.074896009 196.305814 375347.2757 0.031319235 0.021102192 103.0533287 -2.013062024 0.151781855 EAFLEQFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EAFLEQFR 8 0 P23258 P23258 TUBG1 Tubulin gamma-1 chain 0 ;; 101.72 0.012083 523660000 452510 508710 337109 413480 517180 535330 464940 533860 576580 FALSE TRUE 392709.657 505368.2505 500136.04 507366.9536 506889.1298 555924.4915 419850.1904 419698.1935 508417.3692 0.772415894 0.994002725 0.983711553 0.99793395 0.996994124 1.093441187 0.825798283 0.825499322 1 18.95565379 2.209648347 24.99988005 0.869211676 0.976733772 0.16437303 0.092780738 311.6554767 269480.2399 0.037294589 0.025148547 162.0497432 -2.209648347 0.107522096 EAFNMIDQNR ddPTM_MDA-MB-175_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 ;;;;; 237.44 8.31E-12 5562220000 3227490 3080180 1992590 2286190 2902770 3108850 2993330 3347830 3200490 FALSE TRUE 2800969.019 3059946.095 2956213.189 2805304.382 2845010.556 3228449.471 2703037.317 2631922.607 2822131.718 0.992501165 1.084267639 1.047510706 0.994037367 1.008106935 1.143975474 0.957799843 0.93260091 1 21.42835389 2.073523167 24.99999677 0.956592982 1.043621111 0.390682816 0.047762271 36.31668743 12347.69788 0.018908734 0.012748264 118.446755 -2.073523167 0.087028129 EAFQLFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 EAFQLFDR 8 0 P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;G3V1Y7;P60660-2;G8JLA2 P60660;P60660-2 MYL6 Myosin light polypeptide 6 0 ;;;;;;;;; 219.51 1.49E-05 33988935000 7420180 7945980 4949020 5674790 7512300 7814930 7488620 8538390 7727410 FALSE TRUE 6439584.413 7893782.334 7342382.625 6963337.803 7362819.928 8115575.414 6762374.785 6712521.744 6813884.393 0.945068047 1.158484923 1.077561961 1.021933658 1.080561322 1.19103509 0.992440493 0.985124102 1 22.70004604 2.06777268 24.99999991 0.990678663 1.08108166 0.271213847 0.066841115 61.76634926 22783.50362 0.026031185 0.017550219 116.8887407 -2.06777268 0.090402998 EAFSLFDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAFSLFDK 8 0 P0DP25;P0DP24;P0DP23;E7EMB3;M0QZ52;F8WBR5;G3V479;P27482 P0DP25 CALM2;CALM3;CALM1;CALML3 Calmodulin-like protein 3 0 ; 109.71 0.0082939 664780000 504480 418200 546110 541960 371880 360370 370590 558490 1424820 FALSE TRUE 437811.6898 415452.8167 810210.6226 665020.3013 364480.3156 374233.6671 334650.2388 439061.2597 1256379.403 0.348470923 0.330674648 0.644877352 0.529314871 0.290103702 0.297866764 0.266360813 0.349465503 1 20.26084077 1.236796132 24.99498405 1.000000775 0.38087436 0.731526606 0.117630136 26.44881661 374551.4197 0.195827806 0.031350451 17.25027934 -1.236796132 -0.619126415 EAFSLFDKDGDGTITTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAFSLFDKDGDGTITTK 17 1 P0DP25;P0DP24;P0DP23;E7EMB3;M0QZ52;F8WBR5;G3V479 P0DP25 CALM2;CALM3;CALM1 0 ; 305.33 7.22E-47 17406060000 9196800 6643200 6310300 7175000 5918400 4529300 7951800 11178000 9016000 FALSE TRUE 7981419.578 6599560.382 9361982.187 8804193.413 5800635.419 4703545.102 7180635.66 8787671.687 7950138.751 1.003934627 0.830118893 1.17758727 1.107426384 0.729626941 0.591630568 0.903208848 1.105348216 1 22.92254861 5.091236463 18.23942361 0.938039657 4.044730492 0.014528822 0.180801104 1362.56489 278066.0234 0.046561185 3622.137036 123377.6414 -5.091236463 3.106690835 EAFVHVVTLEDMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAFVHVVTLEDMR 13 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 ; 157.52 4.77E-05 333540000 410780 378970 220100 265060 321620 335330 307220 401080 366810 FALSE TRUE 356494.3822 376480.5211 326541.0962 325245.9242 315220.3912 348230.3621 277425.8517 315312.1632 323446.1397 1.102175412 1.163966655 1.009568692 1.005564403 0.974568414 1.076625501 0.857718852 0.974852145 1 18.30316597 4.132785137 4.491037655 0.978822187 1.132589232 0.553301978 0.055390396 0.144745643 4.982497148 0.014249097 0.031978328 13576.41601 -4.132785137 0.153767045 EAFVVEEWVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAFVVEEWVK 10 0 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 0 ; 179 5.01E-06 68303000 187050 163693 107055 128424 161564 141800 168690 198271 173914 FALSE TRUE 162330.8686 162617.6899 158827.1561 157584.632 158349.1925 147255.1378 152330.4698 155872.2896 153354.085 1.058536318 1.060406639 1.035689111 1.02758679 1.032572379 0.960229639 0.993325152 1.016420851 1 17.22650707 3.485451965 1.200319304 0.997598528 1.057936009 0.673130788 0.017334825 0.308852506 0.918904376 0.006932914 0.013156392 3058.101988 -3.485451965 0.060337482 EAGDVCYADVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EAGDVCYADVYR 12 0 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;;;; 262.32 4.84E-21 8341340000 4796900 3830400 2392650 2887100 3579810 3427270 3685000 4095120 4091260 FALSE TRUE 4162977.511 3805237.85 3549743.543 3542660.182 3508578.785 3559119.295 3327629.267 3219410.456 3607595.904 1.153947843 1.054784946 0.983963736 0.982000278 0.972553157 0.986562628 0.922395234 0.892397747 1 21.78260632 8 0.500425417 0.936539638 7.998643813 0.809377735 0.031051601 48.13673491 0.526378111 0.020346921 356.599596 100000000 -8 7.062104175 EAGELPT(ph)SPLHLLS(ph)PGTPR ddPTM_MDA-MB-175_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(0.574)S(0.426)PLHLLS(0.815)PGT(0.185)PR 82.885 0.0067812 22393000 39172 34337 21509 31945 32558 30419 27812 35197 48858 TRUE FALSE 33995.32095 34111.43799 31910.82434 39198.6005 31910.1595 31589.23861 25114.79652 27670.39545 43082.0629 0.789082942 0.791778195 0.740698616 0.90985895 0.740683183 0.733234123 0.582952506 0.642271832 1 15.39479971 3.014541761 24.8196082 0.712744482 0.804829702 0.057647191 0.115619179 472.7971203 806955.4758 0.035133751 0.039821443 1034.050528 -3.014541761 0.09208522 EAGELPTS(ph)PLHLLSPGTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EAGELPTSPLHLLSPGTPR 19 0 Q969R5;H7C228;Q969R5-2;Q969R5-3 Q969R5 L3MBTL2 Lethal(3)malignant brain tumor-like protein 2 1 EAGELPT(0.025)S(0.975)PLHLLSPGTPR;EAGELPT(0.023)S(0.977)PLHLLSPGTPR;EAGELPT(0.082)S(0.918)PLHLLSPGTPR;EAGELPT(0.041)S(0.959)PLHLLSPGTPR 172.24 5.62E-12 695500000 489150 391675 249074 380463 441595 409707 382212 478890 649610 TRUE FALSE 424507.5882 389102.0611 369527.0195 466852.9392 432808.1235 425468.6934 345145.1391 376483.1002 572813.8458 0.741091702 0.679281871 0.645108393 0.815016855 0.75558251 0.742769569 0.60254329 0.657252095 1 19.12770684 1.233391568 24.9988482 1.000000464 0.701355965 0.69146138 0.061926035 101.5974211 491295.099 0.133707183 0.01626677 17.11557793 -1.233391568 -0.298644498 EAGEQGDIEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EAGEQGDIEPR 11 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ;;; 203.02 8.85E-08 1579380000 1732110 1529300 937040 1147290 1413930 1428400 1412170 1613300 1488810 FALSE TRUE 1503207.275 1519253.928 1390195.678 1407799.73 1385795.559 1483351.472 1275217.971 1268308.35 1312804.578 1.145035065 1.157258249 1.058950968 1.072360467 1.055599274 1.129910344 0.971369229 0.966105977 1 20.32422074 -2 0.061723782 0.098693228 1.534705762 0.63284618 0.041388986 451.258712 2.695686336 63.01292137 15.37196244 0.01 2 1.436012534 EAGLAHLCEFIEDCEHTVLATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAGLAHLCEFIEDCEHTVLATK 22 0 Q9UBF2;Q9UBF2-2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 ; 290.94 1.27E-55 95566000 155058 125567 99054 112408 123980 111163 150563 185050 152175 FALSE TRUE 134566.6924 124742.1421 146956.8457 137931.9544 121513.0406 115439.5125 135961.4234 145478.4976 134185.0449 1.002844189 0.929627756 1.095180509 1.027923451 0.905563215 0.860300883 1.013238275 1.084163274 1 17.03386436 2.003387119 24.95283276 1.048275558 0.97067309 0.165216058 0.067937208 158.6433481 1168718.232 0.029598003 0.019839221 100.7829623 -2.003387119 -0.077602468 EAGLSQS(ph)HDDLSNATATPSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAGLSQSHDDLSNATATPSVR 21 0 O14523;O14523-2 O14523 C2CD2L C2 domain-containing protein 2-like 1 EAGLS(0.026)QS(0.974)HDDLSNATATPSVR 247.13 1.50E-30 376840000 153750 100690 123160 122790 116680 124260 106580 160110 154790 TRUE FALSE 133431.5479 100028.5608 182720.5879 150671.3462 114358.2963 129040.3626 96243.888 125871.7225 136490.9025 0.977585652 0.732858813 1.338701588 1.103892959 0.837845557 0.945413652 0.705130424 0.922198624 1 17.05844527 3.232714153 24.99386221 0.87701852 1.037905535 0.181067669 0.164805694 249.808275 1067938.08 0.050321426 0.058577544 1708.890176 -3.232714153 0.160887016 EAGRPGVLQAPPGS(ph)PRPLDRPEGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAGRPGVLQAPPGSPRPLDRPEGLR 25 3 H9KVB4;O15417;O15417-2 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 EAGRPGVLQAPPGS(1)PRPLDRPEGLR;EAGRPGVLQAPPGS(1)PRPLDRPEGLR 106.94 0.020742 666620000 181919 180474 115332 132333 175244 164538 177447 191784 178411 TRUE FALSE 157877.9432 179288.4544 171106.941 162381.2302 171756.9873 170867.8833 160238.2173 150772.4841 157319.4548 1.003550028 1.13964579 1.087640058 1.03217514 1.091772073 1.08612049 1.018553093 0.958384227 1 17.26333757 2.054958888 3.768207805 0.978363096 1.075868185 0.526609051 0.037507158 0.152691033 4.458192745 0.016998169 0.010084199 113.4903377 -2.054958888 0.097505089 EAGS(ph)PAQEFK ddPTM_MDA-MB-175_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 184.96 1.57E-06 3501220000 4500780 3375990 2730240 3041190 3192790 2753960 4026520 4518400 4419050 TRUE FALSE 3905990.519 3353812.899 4050593.196 3731738.671 3129259.726 2859906.623 3636028.71 3552175.322 3896634.943 1.002400937 0.860694663 1.039510566 0.957682391 0.803067203 0.733942662 0.933120183 0.911600746 1 21.89379735 4.757132369 22.18916373 0.904116886 1.002401347 0.104422121 0.089658167 2111.267076 2522303.04 0.022938265 0.617156081 57165.2844 -4.757132369 0.098284461 EAGSQKDENLALYVENQFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EAGSQKDENLALYVENQFR 19 1 P02786;G3V0E5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ;;; 210.98 1.37E-16 658700000 1039400 805273 517074 655400 745585 704813 824290 1035980 560060 FALSE TRUE 902040.6565 799983.1086 767132.7159 804218.5872 730749.3172 731927.6122 744350.4827 814443.739 493850.3448 1.826546576 1.619889744 1.553370822 1.628466185 1.479697898 1.482083833 1.507238965 1.649171146 1 18.91371439 1.234769394 24.9928892 0.99999916 1.585547494 0.768284107 0.102321078 54.36270662 358322.0418 0.184447875 0.025288482 17.16996437 -1.234769394 0.585548334 EAGVFVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EAGVFVPR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;; 143 0.0014154 473889000 839360 839760 563070 650330 804930 864140 823530 869550 813800 FALSE TRUE 728436.4493 834243.5613 835372.5354 797997.3662 788913.4678 897384.025 743664.1874 683603.4993 717593.4911 1.015110168 1.162557314 1.164130592 1.11204655 1.099387714 1.250546495 1.036330731 0.952633361 1 19.45280728 2.009565269 24.89693354 0.979397945 1.134847351 0.555154856 0.059876433 122.7383331 319467.7947 0.023327673 0.015704649 102.2269183 -2.009565269 0.155449406 EAHEREMAEQFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAHEREMAEQFR 12 1 Q9UNN5;B3KT28;B1ANM7;Q9UNN5-2 Q9UNN5 FAF1 FAS-associated factor 1 0 68.536 0.047794 1168000000 1290600 1115900 558660 1149200 1297700 1185700 1058400 1316500 1538300 FALSE TRUE 1120043.94 1108569.579 828829.8446 1410143.424 1271878.309 1231314.646 955756.5309 1034976.72 1356443.926 0.825720782 0.817261634 0.61103141 1.039588439 0.937656385 0.90775197 0.704604527 0.763007375 1 20.37139798 7.917637514 12.93076046 0.836043962 0.823078063 0 0.132279049 0 0 0.029850643 0 82725140.66 -7.917637514 -0.012965899 EAHFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAHFVR 6 0 P46778 P46778 RPL21 60S ribosomal protein L21 0 122.5 0.044655 157680000 219420 242740 150210 169730 211920 298220 228840 234020 249230 FALSE TRUE 190423.0911 241145.425 222852.0584 208269.7907 207703.2066 309692.7164 206647.132 183976.6441 219766.3133 0.86647989 1.097281113 1.014041029 0.947687512 0.945109391 1.409191025 0.940303948 0.837146701 1 17.74561074 2.017994367 24.99991665 0.901476058 1.049707624 0.125287883 0.149640379 406.7810736 565146.5401 0.060411801 0.040721579 104.2303911 -2.017994367 0.148231567 EAHLPPGAMAAVGLSWEECK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EAHLPPGAMAAVGLSWEECK 20 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;; 234.38 1.63E-29 4567795000 4667360 4273580 3255685 3248139 3933120 3816690 5135740 5631470 5632670 FALSE TRUE 4050556.55 4245506.572 4830145.156 3985678.605 3854858.607 3963520.534 4637676.725 4427223.965 4966782.169 0.815529333 0.854780102 0.972489832 0.802466963 0.776127979 0.798005711 0.9337387 0.891366646 1 22.24388004 1.242451659 1.175905405 1.065821156 0.84376184 0.403138342 0.059651121 1.788311036 2.092204155 0.499915501 0.019943979 17.47638725 -1.242451659 -0.222059317 EAHQLFLEPEVLDPESVELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EAHQLFLEPEVLDPESVELK 20 0 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 ;; 172 7.00E-12 282827000 578759 385471 270631 347378 339106 307828 435999 506271 425686 FALSE TRUE 502274.5318 382938.8156 401509.0568 426255.4842 332358.454 319670.3424 393715.8841 398008.8865 375361.886 1.338107438 1.020185666 1.069658566 1.135585418 0.88543474 0.851632396 1.048896808 1.060333777 1 18.51792264 7.544274973 1.092326663 1.000704112 199.9870982 0.595033202 0.084972887 742.0405162 1.980694231 0.027290797 368575.4821 35016680.45 -7.544274973 198.9863941 EAHS(ph)PGPLVKPFETASVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAHSPGPLVKPFETASVK 18 1 P35548;D6RIS4 P35548 MSX2 Homeobox protein MSX-2 1 EAHS(1)PGPLVKPFETASVK 149.85 3.57E-08 193120000 361520 249400 214570 240150 244520 206100 352890 352720 333540 TRUE FALSE 313744.216 247761.675 318336.7697 294679.728 239654.5304 214028.8004 318666.7821 277293.5729 294109.2812 1.066760677 0.842413657 1.082375804 1.001939574 0.814848581 0.72771862 1.083497878 0.942824965 1 18.16599279 5.432331484 5.24440727 0.940988636 24.37554985 0.110913671 0.114822309 7254.79599 740.2726732 0.028372273 2024831.37 270602.3002 -5.432331484 23.43456122 EAIDSYIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAIDSYIK 8 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 96.711 0.02035 288200000 557120 524000 340680 361780 473970 382060 539250 581170 571880 FALSE TRUE 483495.1804 520557.8095 505433.9875 443927.6785 464538.9243 396758.0954 486953.618 456891.3182 504272.9979 0.95879649 1.032293642 1.002302304 0.880332043 0.921205233 0.786792267 0.965654755 0.906039626 1 18.94384545 3.749518504 23.74861908 0.908402103 1.001247116 0.337337449 0.057909393 403.0727752 873559.3211 0.014991541 0.025599273 5617.182115 -3.749518504 0.092845013 EAIEGTYIDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EAIEGTYIDKK 11 1 P62280;M0QZC5 P62280 RPS11 40S ribosomal protein S11 0 ;;; 176.8 1.32E-05 7254900000 5590160 5217960 4000970 4425000 5091380 3664390 8607600 8229300 7051490 FALSE TRUE 4851406.192 5183682.877 5935852.474 5429763.882 4990071.499 3805361.454 7772836.277 6469528.235 6217870.885 0.780235917 0.833674898 0.954643894 0.873251308 0.802537008 0.612003936 1.250080039 1.040473235 1 22.56798923 2.232215476 24.99999972 1.091490222 0.819688543 0.616432655 0.106658989 105.6126023 416111.2152 0.043631475 0.030228068 170.6929075 -2.232215476 -0.271801679 EAIESAIGGNAYQHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAIESAIGGNAYQHSK 16 0 P63172 P63172 DYNLT1 Dynein light chain Tctex-type 1 0 142.35 1.52E-06 282750000 139520 146300 90951 108420 136600 130760 178060 164320 139820 FALSE TRUE 121082.0785 145338.9457 134935.2078 133038.4181 133881.9273 135790.4218 160791.7686 129181.4467 123290.6389 0.982086553 1.178831961 1.094448119 1.079063417 1.085905049 1.101384688 1.304168508 1.047779847 1 16.91170374 2.465319721 24.99887787 1.123780815 1.090031892 0.023833666 0.090266302 1041.691094 2206569.638 0.033568921 0.026027723 291.9575569 -2.465319721 -0.033748924 EAIHSQLLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAIHSQLLEK 10 0 O60925;E5RGS4 O60925 PFDN1 Prefoldin subunit 1 0 ; 146.71 2.82E-05 983320000 2436400 2169500 1370560 1671390 1984470 1750830 2196900 2612500 2377400 FALSE TRUE 2114423.567 2155248.412 2033367.4 2050904.645 1944982.93 1818185.563 1983844.976 2053837.205 2096346.48 1.008623139 1.028097422 0.969957695 0.978323318 0.927796501 0.867311573 0.946334489 0.979722209 1 20.99944575 3.963195911 1.77428781 0.94692922 1.019469502 0.369933286 0.036234076 0.445281169 2.700652444 0.011816672 0.032409772 9187.469506 -3.963195911 0.072540282 EAILAIHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EAILAIHK 8 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;; 98.392 0.0075549 2589840000 3278860 2766210 2446510 3485120 2347260 2337960 2253560 2985280 8138360 FALSE TRUE 2845550.343 2748038.584 3629650.419 4276469.763 2300554.118 2427902.834 2035010.098 2346901.103 7176252.352 0.396523172 0.382935054 0.505786341 0.595919646 0.320578765 0.338324618 0.283575604 0.327037148 1 22.77479919 1.234898943 24.99998463 1.000000863 0.390984497 0.805936776 0.09346977 50.40872578 344111.577 0.183056433 0.025326521 17.1750869 -1.234898943 -0.609016366 EAILEYILHQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAILEYILHQK 11 0 Q9Y314;A0A075B6F9;M0R3B2;A0A075B797;M0R1K2;M0QX85 Q9Y314 NOSIP Nitric oxide synthase-interacting protein 0 ; 138.71 5.18E-05 153801000 704110 577330 401400 490770 540140 514220 665620 757520 671730 FALSE TRUE 611060.0795 573537.4812 595518.3826 602206.8294 529392.2708 534002.3761 601068.2748 595530.243 592318.8446 1.03164045 0.968291802 1.005401716 1.016693686 0.89376233 0.901545478 1.014771487 1.005421739 1 19.17601446 EALAEAALES(ph)PRPALVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 EALAEAALESPRPALVR 17 1 O14745;O14745-2;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR 277.22 5.33E-36 38763760000 9575830 9867763 5700355 8110650 9886434 8689963 9469102 12003420 10455277 TRUE FALSE 8310359.803 9802941.015 8457065.745 9952297.046 9689713.306 9024271.5 8550789.945 9436582.044 9219266.064 0.901412297 1.063310349 0.917325271 1.079510774 1.051028709 0.978849231 0.927491395 1.023571939 1 23.13622047 4.76332192 23.86029888 1.003129495 0.901412066 0.269374971 0.053594026 5731.421112 5522701.663 0.012608271 0.763535962 57985.83567 -4.76332192 -0.10171743 EALAEAALESPRPALVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EALAEAALESPRPALVR 17 1 O14745;O14745-2;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;;; 266.44 1.08E-27 2712490000 1695850 1587852 959453 1181555 1514469 1681252 1493797 1806620 1396461 FALSE TRUE 1471739.126 1577421.296 1423447.68 1449845.122 1484334.03 1745930.852 1348928.797 1420288.372 1231372.971 1.195201746 1.281026409 1.155984184 1.17742159 1.205430088 1.417873295 1.095467278 1.153418505 1 20.23183638 1.376986242 1.46483644 0.955783159 1.227805361 0.417590489 0.083630261 0.895264585 2.183349156 0.342038214 0.024363611 23.82244001 -1.376986242 0.272022203 EALEALVPVTIEVEVPFDLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EALEALVPVTIEVEVPFDLHR 21 0 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 0 ;;; 183.22 4.39E-17 1407329000 2246010 2189833 1310670 1561412 1960114 2131265 2094442 2427358 2217838 FALSE TRUE 1949194.088 2175447.843 1944514.396 1915954.459 1921111.566 2213256.144 1891323.337 1908286.381 1955647.718 0.996700004 1.112392494 0.994307092 0.979703267 0.9823403 1.131725373 0.967108401 0.975782276 1 20.89921508 EALEAYRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EALEAYRR 8 1 Q9NRF9 Q9NRF9 POLE3 DNA polymerase epsilon subunit 3 0 ; 130.75 0.0016589 442840000 519180 530110 261900 320490 474210 538350 435960 498500 256750 FALSE TRUE 450569.0476 526627.6725 388555.716 393262.1529 464774.1488 559060.6729 393680.6663 391899.6543 226397.3075 1.990169638 2.326121624 1.716255906 1.737044302 2.052913764 2.469378629 1.738892881 1.731026127 1 17.78849727 1.094473242 1.460378635 0.27332911 2.022682229 0.632013209 0.243438378 1.169940278 1.672722172 3.342395016 0.072300515 12.43006049 -1.094473242 1.749353118 EALEHLCTYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EALEHLCTYEK 11 0 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ; 164.04 2.32E-05 601120000 1477600 1362200 939950 1112600 1290590 1202710 1508990 1738510 1596210 FALSE TRUE 1282331.416 1353251.619 1394512.964 1365232.835 1264909.784 1248979.032 1362648.382 1366743.166 1407507.872 0.911065182 0.961452256 0.990767435 0.969964618 0.898687538 0.887369127 0.968128427 0.971037671 1 20.42471156 1.692732005 2.303174015 0.993360457 0.940112285 0.270330163 0.033115739 0.433605894 4.805393988 0.036049409 0.010131017 49.28695694 -1.692732005 -0.053248172 EALEVDWSSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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" 0 152.07 7.71E-05 56227000 151490 136970 95909 106010 126460 128710 131680 148900 150340 FALSE TRUE 131470.2127 136070.2351 142290.9132 130081.1908 123943.6934 133661.557 118909.6939 117058.8937 132566.9765 0.991726719 1.026426329 1.073351124 0.981248832 0.934951499 1.008256811 0.896978245 0.883016999 1 17.01636191 3.199995824 1.273867217 0.92747185 1.030255411 0.390352454 0.045431822 0.402322284 1.399172023 0.019052147 0.025586885 1584.877951 -3.199995824 0.10278356 EALGLGPPAAQLT(ph)PPPAPVGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EALGLGPPAAQLTPPPAPVGLR 22 0 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 EALGLGPPAAQLT(1)PPPAPVGLR;EALGLGPPAAQLT(1)PPPAPVGLR;EALGLGPPAAQLT(1)PPPAPVGLR;EALGLGPPAAQLT(1)PPPAPVGLR;EALGLGPPAAQLT(1)PPPAPVGLR 220.17 1.16E-24 1604228000 786150 748044 517959 615190 782700 790557 758816 943220 927220 TRUE FALSE 682258.2856 743130.0497 768445.7049 754878.2921 767125.8013 820970.2393 685226.1411 741519.7431 817605.1079 0.834459422 0.908910723 0.939873904 0.923279814 0.938259551 1.00411584 0.838089359 0.906941182 1 19.64104468 4.71598307 2.819117296 0.930012281 0.819650828 0.312354851 0.046674877 0.526046083 6.023550203 0.011839189 0.130340349 51997.57263 -4.71598307 -0.110361453 EALLDESRPLFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EALLDESRPLFER 13 1 A0A5F9ZGM7;Q9BU89 A0A5F9ZGM7 DOHH Deoxyhypusine hydroxylase 0 ;; 126.48 0.00017146 370734000 522080 525890 322798 391443 503191 568330 472490 575580 492286 FALSE TRUE 453085.8052 522435.394 478904.1925 480326.116 493178.4836 590194.0229 426667.9925 452496.6962 434088.5099 1.043763645 1.203522743 1.103240887 1.10651654 1.136124252 1.359616782 0.98290552 1.042406527 1 18.72762971 EALLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EALLGR 6 0 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;; 114.67 0.058367 1530050000 1048030 976580 633270 826310 944210 1008520 870870 1020520 1031840 FALSE TRUE 909530.1801 970164.7817 939521.4902 1013936.315 925422.0683 1047318.417 786413.1614 802289.7397 909857.0507 0.999640745 1.066282644 1.032603407 1.114390787 1.017107102 1.151080179 0.864326062 0.881775592 1 19.79528037 2.227840212 24.99997795 0.906242226 1.062440847 0.604049202 0.056377601 126.9734878 296099.4801 0.021682935 0.014784189 168.9819089 -2.227840212 0.15619862 EALLSSAVDHGSDEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EALLSSAVDHGSDEVK 16 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 209.89 1.71E-12 1377400000 1077470 879100 351810 699790 923170 742250 1089900 1201650 1065400 FALSE TRUE 935079.6095 873325.1342 521946.4927 858688.0151 904800.7232 770804.8378 984201.6658 944686.4988 939449.6257 0.995348323 0.929613585 0.555587525 0.914033059 0.963117871 0.820485545 1.047636445 1.005574405 1 19.84145628 2.236954071 24.99918717 1.016448918 0.858950437 0.265179371 0.121267713 58.4262571 909128.4395 0.048828579 0.034886485 172.5655386 -2.236954071 -0.157498481 EALNIIGDISTSTVSTPVPPPVDDT(ph)WLQSASSHSPTPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EALNIIGDISTSTVSTPVPPPVDDTWLQSASSHSPTPQR 39 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4;K7ENE7 P50570-2 DNM2 Dynamin-2 1 EALNIIGDISTSTVSTPVPPPVDDT(0.193)WLQS(0.193)AS(0.193)S(0.193)HS(0.193)PT(0.037)PQR;EALNIIGDISTSTVSTPVPPPVDDT(0.348)WLQS(0.181)AS(0.181)S(0.131)HS(0.131)PT(0.027)PQR 167.74 6.04E-18 413140000 285520 236004 80973 162948 249930 276700 204601 258750 264800 TRUE FALSE 247787.8086 234453.6742 120131.8136 199947.8339 244956.882 287344.828 184758.8265 203418.3261 233495.6457 1.061209548 1.004102982 0.514492736 0.856323609 1.049085439 1.230621784 0.791273113 0.871186807 1 17.83303612 3.341374916 8.401507305 0.970878073 0.843484091 0.104591813 0.18199845 0.663938617 48.899275 0.055626874 0.071819329 2194.698748 -3.341374916 -0.127393981 EALNSCNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EALNSCNKR 9 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;;;; 176.6 8.50E-05 8770890000 6650890 5172520 3049400 3672270 3811480 3524260 4679760 5428600 3415790 FALSE TRUE 5771958.035 5138541.376 4524100.04 4506115.031 3735639.005 3659840.563 4225917.595 4267736.135 3011979.197 1.916333964 1.706034816 1.502035619 1.49606446 1.24026056 1.2150949 1.40303678 1.416920854 1 21.52228038 4.661950926 0.6961392 1.27305121 2.286980753 0.770775763 0.122602948 1.425118613 0.575642415 0.057400119 1.129148321 45914.61282 -4.661950926 1.013929543 EALPESGELLDVWTELQDIHDAHGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EALPESGELLDVWTELQDIHDAHGLR 26 0 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9 Q6ULP2-7 AFTPH Aftiphilin 0 ;;; 193.54 1.59E-18 165262000 57044 58105.9 36015.3 43099.3 54056.4 55000.9 55198.5 64186.2 53192 FALSE TRUE 49505.49087 57724.19852 53432.41954 52885.6548 52980.7834 57116.82021 49845.35797 50460.48063 46903.70236 1.055470856 1.230695992 1.139194069 1.127536892 1.129565061 1.217746518 1.062716917 1.075831504 1 15.51741419 1.731173446 1.609627018 1.010337943 1.149873371 0.440084013 0.053456125 0.38129055 1.767744437 0.06798814 0.015022096 53.8484796 -1.731173446 0.139535428 EALPWGLEPQDVQSSDEMRS(ph)PEGYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EALPWGLEPQDVQSSDEMRSPEGYLR 26 1 Q9H5H4 Q9H5H4 ZNF768 Zinc finger protein 768 1 EALPWGLEPQDVQS(0.001)SDEMRS(0.999)PEGYLR;EALPWGLEPQDVQS(0.007)S(0.007)DEMRS(0.985)PEGYLR 292.91 1.65E-70 251800000 112701 84124 58348 72431 87007 90675 96236 93129 81513 TRUE FALSE 97807.2773 83571.3839 86565.28796 88877.56559 85275.73093 94163.32592 86903.04753 73214.08808 71876.626 1.360766118 1.162705994 1.204359369 1.236529461 1.186418112 1.31006881 1.209058527 1.018607747 1 16.13323507 1.742026323 3.823405863 1.00288093 1.236899954 0.73392345 0.05766952 0.091971108 2.907300652 0.03652362 0.014618268 55.21109021 -1.742026323 0.234019023 EALQDVEDENQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EALQDVEDENQ 11 0 P62258;P62258-2;I3L0W5 P62258 YWHAE 14-3-3 protein epsilon 0 ; 257.72 3.60E-20 1127430000 1831060 1748300 1572920 1911030 1786060 1750510 1642540 2027390 4036300 FALSE TRUE 1589080.782 1736815.302 2333589.373 2344958.57 1750520.9 1817853.252 1483246.724 1593848.426 3559133.212 0.446479715 0.487988282 0.655662273 0.658856646 0.491839107 0.510757295 0.416743807 0.447819267 1 21.7630945 1.233793627 25 1.000000737 0.514074592 0.775563446 0.08207517 77.53372946 406568.0788 0.177857848 0.022392259 17.13143042 -1.233793627 -0.485926144 EALRDEEWDCLFLHDVDLLPENDHNLYVCDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EALRDEEWDCLFLHDVDLLPENDHNLYVCDPR 32 1 O60512 O60512 B4GALT3 "Beta-1,4-galactosyltransferase 3;N-acetyllactosamine synthase;Beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase;Beta-N-acetylglucosaminyl-glycolipid beta-1,4-galactosyltransferase" 0 ; 87.25 0.00011043 72910000 30456.3 33695.8 22845.2 23442.7 33990.7 40943.6 27205.2 34337.4 35521.7 FALSE TRUE 26431.42279 33474.45007 33893.21513 28765.72333 33314.35157 42518.72679 24566.84389 26994.61422 31322.36509 0.843851437 1.068707614 1.082077137 0.918376478 1.063596298 1.35745582 0.784322762 0.861831926 1 14.93490553 EALTYDGALLGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EALTYDGALLGDR 13 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;;; 217.14 6.12E-11 1543806000 1781050 1684800 1272630 1587670 1691010 1681750 1545870 1919860 2520920 FALSE TRUE 1545679.73 1673732.438 1888078.125 1948174.74 1657362.209 1746448.011 1395951.765 1509312.879 2222899.709 0.695343889 0.752950046 0.849376207 0.876411442 0.745585688 0.785662081 0.627986841 0.678983794 1 21.08401143 EAMEDGEIDGNKVTLDWAKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAMEDGEIDGNKVTLDWAKPK 21 2 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 186.06 1.90E-17 2573800000 3218800 1745140 1636350 1585330 1453380 920580 2633700 2992300 1374950 FALSE TRUE 2793427.425 1733676.06 2427694.333 1945303.407 1424460.581 955995.3083 2378284.179 2352419.931 1212404.977 2.304038235 1.42994799 2.002379055 1.604499687 1.174904927 0.788511534 1.961625219 1.940292209 1 20.20944025 7.526129947 0.958834454 1.498297978 199.999996 0.268842291 0.415799347 775.8412055 3.60569017 0.139655205 334807.1084 33583808.67 -7.526129947 198.501698 EAMQQADDWLGVPQVITPEEIIHPDVDEHSVMTYLSQFPK ddPTM_MDA-MB-175_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 ; 179.43 3.68E-24 270000000 233868 206823 149305 170063 182001 182132 226786 282342 251776 FALSE TRUE 202961.7513 205464.3661 221509.3974 208678.4034 178379.5362 189138.7359 204792.3286 221965.3605 222011.3281 0.914195474 0.925467938 0.997739166 0.939944845 0.803470425 0.851932816 0.922440897 0.999792949 1 17.76027377 1.771638196 4.132378994 1.000899023 0.90618641 0.361819456 0.051127988 0.236958758 8.164119762 0.035654136 0.015299595 59.10690184 -1.771638196 -0.094712613 EANELQQWINEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EANELQQWINEK 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 183.08 3.74E-05 95262000 244840 192222 128749 179403 183079 182675 216700 251840 220360 FALSE TRUE 212483.7737 190959.281 191012.447 220139.1932 179436.0861 189702.6255 195684.4674 197985.9758 194309.2918 1.093533776 0.98275939 0.983033005 1.13293189 0.923456024 0.976292094 1.00707725 1.018921812 1 17.56799537 3.216494122 24.99988243 0.990572742 1.038754867 0.25714999 0.051622584 423.5082129 479805.5839 0.015588358 0.017689824 1646.243686 -3.216494122 0.048182125 EANHDGDFGITLAELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EANHDGDFGITLAELR 16 0 P20020-6;P20020;P20020-4;P20020-1;F8W1V5;P20020-5;P20020-2 P20020-6 ATP2B1 Plasma membrane calcium-transporting ATPase 1 0 151.95 2.22E-08 0 47563 46569 28497 59646 56997 68345 27197 68002 54581 FALSE TRUE 41277.42904 46263.08517 42278.24452 73189.53593 55862.87121 70974.27638 24559.43913 53460.30149 48128.49636 0.857650502 0.961241025 0.878445157 1.520711044 1.160702607 1.47468302 0.510288934 1.110782707 1 15.55460373 EANHNVSAPYGR ddPTM_MDA-MB-175_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 77.279 0.028852 122820000 85086 66691 46970 42547 75209 61371 61528 70890 70635 FALSE TRUE 73841.66952 66252.90243 69684.84911 52207.94664 73712.48804 63731.98208 55561.02403 55730.72517 62284.61077 1.185552396 1.063712233 1.118813271 0.838215829 1.183478345 1.023238025 0.892050594 0.894775202 1 15.92658813 8 0.222604705 0.891760406 2.385565221 0.326164404 0.099138422 108.4614384 1.674090908 0.463146534 56.58418795 100000000 -8 1.493804815 EANNFLWPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EANNFLWPFK 10 0 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 138.66 0.00013688 632410000 1807360 1574030 1002030 1379760 1724000 1522930 1703160 2012550 2334590 FALSE TRUE 1568512.797 1563690.093 1486615.06 1693055.596 1689695.773 1581518.103 1537987.805 1582181.844 2058597.43 0.761932748 0.759590035 0.722149478 0.822431609 0.820799515 0.768250305 0.747104695 0.768572729 1 20.9732303 1.238157442 24.98790752 1.000000258 0.771225936 0.848340653 0.030381914 3.765740236 233099.4473 0.04459248 0.007823209 17.30443573 -1.238157442 -0.228774322 EANYIAEELDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EANYIAEELDKR 12 1 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 0 ; 176.89 3.84E-05 652590000 756910 667460 537210 585680 661990 579450 818740 978960 806120 FALSE TRUE 656882.4257 663075.4113 797006.5529 718667.5956 648817.6942 601741.8165 739338.7208 769617.0223 710821.4119 0.924117387 0.932829822 1.121247249 1.011038193 0.912771736 0.846544303 1.04011881 1.082715024 1 19.43912761 2.033236589 24.99983104 1.051511281 0.962924812 0.212905259 0.074146593 280.744965 211169.1188 0.032375797 0.021827645 107.9534656 -2.033236589 -0.088586469 EAPADMGAHQGVAVLGIALIAMGEEIGAEMALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAPADMGAHQGVAVLGIALIAMGEEIGAEMALR 33 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 223.34 3.68E-36 244900000 139720 127220 88966 115060 100630 117020 113120 144910 109970 FALSE TRUE 121255.648 126384.2834 131990.2552 141186.1316 98627.65988 121521.8351 102149.6398 113922.1242 96969.47188 1.250451773 1.303340948 1.361152666 1.455985362 1.017100103 1.253196834 1.053420606 1.174824633 1 16.56524301 3.235726843 24.99999867 1.11330079 1.341234707 0.643240857 0.089613605 47.4526027 418634.5996 0.025497876 0.030215313 1720.785916 -3.235726843 0.227933917 EAPGS(ph)PPLS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 122.66 0.00056448 587590000 977670 975370 581790 736750 940240 902940 872550 1066810 906200 TRUE FALSE 848468.4324 968962.7302 863145.59 904040.348 921531.0635 937676.6861 787930.2353 838680.9834 799070.0683 1.061819815 1.212612972 1.080187613 1.131365551 1.153254389 1.173459904 0.986059003 1.049571266 1 19.60796249 2.237446548 24.99966442 1.01865403 1.137069152 0.620436395 0.045448289 18.359082 411956.7311 0.016508936 0.011836525 172.7613338 -2.237446548 0.118415123 EAPGS(ph)PPLSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAPGSPPLSPR 11 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;E9PNR0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 EAPGS(0.51)PPLS(0.49)PR;EAPGS(0.794)PPLS(0.206)PR 118.37 0.00076573 961360000 1114220 898520 577570 625150 748250 905300 844730 868140 839500 TRUE FALSE 966973.0039 892617.563 856884.7839 767099.8623 733361.2889 940127.4768 762808.2146 682495.0169 740255.2664 1.306269672 1.205823995 1.157553107 1.036263972 0.990687027 1.270004442 1.030466448 0.921972525 1 19.49766332 8 0.24553686 0.950339619 3.118983618 0.523612369 0.088646868 72.79022762 1.152382417 0.329515643 62.96901586 100000000 -8 2.168643999 EAPIDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAPIDKK 7 1 J3QRS3;P19105;O14950;P24844-2;P24844 J3QRS3;P24844 MYL12A;MYL12B;MYL9 Myosin regulatory light chain 12A;Myosin regulatory light chain 12B;Myosin regulatory light polypeptide 9 0 ; 75.738 0.068396 2782400000 2037300 1628830 1278910 1440120 1043250 1073980 2377200 2538100 1935710 FALSE TRUE 1768065.643 1618130.108 1897395.154 1767121.257 1022491.366 1115296.706 2146659.51 1995347.067 1706872.569 1.035850992 0.948008737 1.11162086 1.035297707 0.599043763 0.653415332 1.257656575 1.169007636 1 20.70292392 2.215926254 24.99952566 1.152611679 0.901985492 0.307057543 0.173176817 309.5897216 341937.4923 0.077125589 0.052038799 164.4092521 -2.215926254 -0.250626187 EAPPMEKPEVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAPPMEKPEVVK 12 1 K7EM56;A0A0B4J2B4;S4R417;K7ELC2;P62841;K7EQJ5;S4R456;K7EJ78 K7EM56 RPS15 40S ribosomal protein S15 0 98.105 0.0016342 0 241600 194920 152760 169350 173290 125370 242240 292140 244460 FALSE TRUE 209671.9479 193639.5577 226635.247 207803.5059 169841.868 130193.065 218747.6021 229668.1344 215560.2173 0.972683877 0.898308418 1.051377892 0.964016034 0.787909152 0.603975384 1.014786517 1.065447685 1 17.71773142 2.0302038 24.99954486 1.038214714 0.88146607 0.246974203 0.121218285 283.1193605 234335.4116 0.053413881 0.036011199 107.2022252 -2.0302038 -0.156748644 EAPS(ph)PLMIHS(ph)PQMSQFQS(ph)LTHQSPPQQNVQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPK 32 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 3 EAPS(0.995)PLMIHS(0.775)PQMS(0.269)QFQS(0.361)LT(0.325)HQS(0.276)PPQQNVQPK 46.449 0.046175 133980000 31124 27737 13558 21821 28963 26322 33297 35218 35530 TRUE FALSE 27010.88454 27554.79382 20114.69415 26775.79156 28386.69297 27334.62437 30067.86206 27686.90477 31329.68388 0.862149923 0.879510752 0.642033103 0.854646082 0.906063817 0.872483249 0.9597244 0.88372755 1 14.93524259 3.382343737 4.058138183 0.919162959 0.795719128 0.397702321 0.072572499 0.22883169 7.03055188 0.021095094 0.027836349 2411.813584 -3.382343737 -0.123443831 EAPS(ph)PTLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAPSPTLRR 9 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 EAPS(1)PTLRR 107.03 0.0017398 343340000 244730 232100 184110 209610 236400 223840 285070 347880 215030 TRUE FALSE 212388.3104 230575.3198 273146.2118 257205.1542 231696.1025 232451.2696 257423.9553 273488.5692 189609.3984 1.120135986 1.216054277 1.440573169 1.356500028 1.221965285 1.225948037 1.357653985 1.442378762 1 17.53267095 4.472866981 24.99488191 1.307950892 1.144115513 0.148751665 0.12910534 165.1811764 970485.2155 0.031581241 0.084299404 29707.55986 -4.472866981 -0.163835379 EAPSPLMIHS(ph)PQMSQFQS(ph)LTHQSPPQQNVQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPK 32 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 2 EAPSPLMIHS(1)PQMS(0.021)QFQS(0.569)LT(0.408)HQS(0.003)PPQQNVQPK;EAPSPLMIHS(1)PQMS(0.021)QFQS(0.398)LT(0.373)HQS(0.208)PPQQNVQPK 219.27 3.39E-36 190408000 184434 163421 74207 116769 168383 133468 179803 211362 145947 TRUE FALSE 160060.5796 162347.4767 110093.7534 143283.1862 165032.5077 138602.6003 162365.7327 166163.8811 128693.3119 1.24373658 1.261506711 0.855473775 1.113369328 1.282370508 1.076999249 1.261648568 1.291161744 1 16.97357755 3.421772351 23.84314824 1.196802898 1.109374924 0.041342802 0.141097914 153.5511006 66145.13967 0.04101175 0.052945952 2641.024019 -3.421772351 -0.087427973 EAPSPLMIHSPQMSQFQS(ph)LTHQSPPQQNVQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPK 32 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 1 EAPSPLMIHSPQMS(0.001)QFQS(0.399)LT(0.399)HQS(0.201)PPQQNVQPK 90.843 0.00021868 697840000 86698 75201 49304 60190 63873 44118 59087 81980 69165 TRUE FALSE 75240.63964 74706.99968 73147.57931 73857.05945 62602.05227 45815.24801 53356.75183 64449.21497 60988.39249 1.233687864 1.224938003 1.199368869 1.211001904 1.026458474 0.751212585 0.874867326 1.056745593 1 15.89624707 3.13882302 3.84562811 0.933458293 1.21767736 0.751578318 0.08033227 0.127219647 3.556010509 0.027906674 0.032444047 1376.648353 -3.13882302 0.284219067 EAPSPLMIHSPQMSQFQSLTHQS(ph)PPQQNVQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPK 32 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 1 EAPSPLMIHSPQMS(0.003)QFQS(0.01)LT(0.051)HQS(0.937)PPQQNVQPK 122.48 1.86E-07 114080000 135960 117690 57011 91267 136240 113690 146680 167440 125410 TRUE FALSE 117992.5415 116916.8866 84581.71029 111990.5673 133529.0905 118063.7279 132454.9962 131634.259 110584.1727 1.066993031 1.057266007 0.764862713 1.012717865 1.207488263 1.06763676 1.19777535 1.190353518 1 16.75478539 3.400258832 6.196498229 1.140414302 0.959216869 0.373253684 0.102447254 0.202857073 12.73677257 0.029537912 0.038334268 2513.38392 -3.400258832 -0.181197433 EAQLFHPGDLQDLSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EAQLFHPGDLQDLSNR 16 0 E9PMS6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 0 ;; 136.34 1.80E-05 633860000 472580 475200 294924 362060 473360 509860 459240 521920 503780 FALSE TRUE 410127.3556 472078.3799 437550.2329 444271.2567 463941.0621 529474.6441 414702.9755 410311.4696 444223.7023 0.923245098 1.062704168 0.984977232 1.000107051 1.044386105 1.191909935 0.933545359 0.92365956 1 18.76092685 EAQLYAAQAHLK ddPTM_MDA-MB-175_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 ; 109.84 0.0005088 232850000 397250 299930 215335 252000 313260 276920 308400 377870 314200 FALSE TRUE 344752.406 297959.7401 319471.7263 309220.4516 307026.7389 287573.2916 278491.4155 297065.4411 277055.6339 1.244343604 1.075450933 1.153095939 1.116095158 1.108177208 1.037962259 1.005182286 1.072223065 1 18.07981618 7.999999999 0.199333569 0.98333698 2.026394104 0.680273759 0.041010726 64.84356197 0.95937994 0.265331016 20.41379116 99999999.76 -7.999999999 1.043057124 EAQSFISAAIEPESGKS(ph)NER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAQSFISAAIEPESGKSNER 20 1 Q8WXA9-2;Q8WXA9 Q8WXA9-2 SREK1 Splicing regulatory glutamine/lysine-rich protein 1 1 EAQSFISAAIEPES(0.241)GKS(0.759)NER 93.229 0.001605 0 81870 73920 47910 52350 73765 70572 67592 80703 78808 TRUE FALSE 71050.67207 73434.41465 71079.43625 64236.86762 72297.22082 73286.95051 61036.93824 63445.29148 69491.40802 1.022438228 1.056740923 1.022852152 0.924385754 1.040376399 1.054618874 0.878337912 0.912994761 1 16.08454699 2.2423682 24.99999997 0.924637821 1.018572376 0.443388658 0.047251927 86.21658866 566089.6032 0.018563619 0.013816985 174.7302909 -2.2423682 0.093934554 EAQTSFLHLGYLPNQLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAQTSFLHLGYLPNQLFR 18 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ; 170.61 1.53E-11 2108040000 1996250 1910950 944650 1376900 1794800 1844410 1729570 2061950 1690340 FALSE TRUE 1732440.505 1898396.844 1401485.9 1689546.19 1759086.991 1915365.646 1561836.568 1621018.039 1490509.931 1.162313963 1.273655951 0.940272769 1.133535681 1.180191393 1.285040513 1.047853849 1.087559368 1 20.50737456 EARS(ph)PQPNK ddPTM_MDA-MB-175_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 107.09 0.0017137 6535300000 12358600 10759200 3678250 3888860 5890400 7767100 11261400 12132800 906798 TRUE FALSE 10725379.7 10688522.11 5457064.003 4771885.101 5773192.564 8065905.363 10169271.16 9538295.138 799597.3735 13.4134754 13.36738021 6.824764793 5.967859899 7.220124473 10.08745855 12.7179897 11.92887252 1 19.60891421 4.25211064 24.25776224 8.550565121 13.39043369 0.303542344 3.326215122 232.3170487 415891.5481 0.869778018 2.271326297 17869.42753 -4.25211064 4.839868574 EAS(ph)HVLEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EASHVLEVK 9 0 Q9Y5S2 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 1 EAS(1)HVLEVK;EAS(1)HVLEVK;EAS(1)HVLEVK;EAS(1)HVLEVK;EAS(1)HVLEVK 110.35 0.0024143 313831000 789120 799128 1414870 801985 298976 806711 400934 414620 460607 TRUE FALSE 684835.7926 793878.4755 2099105.864 984087.9518 293026.9625 837745.6942 362051.4824 325956.7396 406154.5652 1.686145747 1.954621574 5.168243926 2.422939531 0.721466623 2.062627792 0.891413057 0.802543582 1 18.63166933 3.368071861 5.252586931 1.099990338 2.981882801 0.431553838 0.9873227 0.195544615 8.276054363 0.291767239 0.378916107 2333.844202 -3.368071861 1.881892463 EAS(ph)PAPLAQGEPGREDLPTR ddPTM_MDA-MB-175_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 248.24 1.93E-30 5159860000 2507330 2297900 1752020 2224720 2515420 2343350 2299590 2678790 3217460 TRUE FALSE 2175979.988 2282804.944 2599302.732 2729876.679 2465368.063 2433500.191 2076576.116 2105951.605 2837095.544 0.766974518 0.804627447 0.916184419 0.962208229 0.868976044 0.857743475 0.731937322 0.742291393 1 21.43598331 1.218457214 24.89089301 1.000000629 0.830434733 0.339731227 0.073871267 1973.730775 2443624.404 0.834634286 0.020745162 16.53701859 -1.218457214 -0.169565896 EAS(ph)PLPAESASAGATLRPLLLSGHGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EASPLPAESASAGATLRPLLLSGHGAR 27 1 P35548;D6RIS4 P35548 MSX2 Homeobox protein MSX-2 1 EAS(1)PLPAESASAGATLRPLLLSGHGAR 80.847 0.0069334 80357000 125880 86112 48643 71935 99160 97818 97186 97884 106820 TRUE FALSE 109244.6391 85546.3246 72166.9175 88268.94121 97186.91 101581.1218 87760.91668 76952.26833 94191.86129 1.15980975 0.908213549 0.766169354 0.937118558 1.03179732 1.078449033 0.93172505 0.816973646 1 16.52331479 1.998466774 24.98945239 0.889094254 0.970756062 0.059193277 0.113267306 146.7346513 2391592.101 0.048749137 0.032349493 99.64758418 -1.998466774 0.081661808 EASDGEVRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EASDGEVRR 9 1 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 ; 90.696 0.018048 414730000 969980 850170 504180 632490 762700 849550 806090 930260 627320 FALSE TRUE 841794.6854 844585.1773 748003.1344 776106.5215 747523.7622 882232.7382 727915.5159 731331.1383 553158.9442 1.521795307 1.526839955 1.352239066 1.403044332 1.351372458 1.594899165 1.315924697 1.322099454 1 19.07733456 0.68332205 1.112982268 1.33E-08 1.447141312 0.725959682 0.08579051 2.732536618 1.140002793 6.332434762 0.026669841 4.823053171 -0.68332205 1.447141298 EASEVKPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EASEVKPPR 9 1 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 ;; 104.39 0.0029797 301405000 684920 563150 359223 437810 510530 470500 624780 694730 649370 FALSE TRUE 594406.0866 559450.6306 532944.4443 537221.452 500371.4518 488600.4395 564188.9318 546167.3959 572602.2184 1.038078561 0.977031895 0.930741145 0.938210567 0.873855245 0.853298195 0.985306926 0.95383388 1 19.12717373 4.599254365 2.161311339 0.933103404 1.050457485 0.369014968 0.044234409 0.577126031 3.818770934 0.012521971 0.116566041 39742.42515 -4.599254365 0.117354082 EASIDILHSIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EASIDILHSIVK 12 0 O00231;O00231-2;J3QRY4 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 ; 115.14 0.00098226 600450000 2324700 2312200 1588690 1977450 2234700 2090100 2405200 2823800 3003000 FALSE TRUE 2017485.005 2297011.006 2356985.798 2426460.246 2190233.842 2170507.499 2171944.074 2219952.345 2647988.761 0.761893341 0.867454968 0.890104155 0.91634084 0.827131094 0.819681538 0.820224053 0.838354142 1 21.33646557 1.237125153 24.95959296 1.000000193 0.844754125 0.576456672 0.042353555 28.07407773 487965.2772 0.064889456 0.010642016 17.26335307 -1.237125153 -0.155246068 EASRPPEEPSAPS(ph)PTLPAQFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EASRPPEEPSAPSPTLPAQFK 21 1 A0A0C4DFX9;Q9H3P2;H0Y3X6;Q9H3P2-7 A0A0C4DFX9 NELFA Negative elongation factor A 1 EASRPPEEPSAPS(0.99)PT(0.009)LPAQFK;EASRPPEEPSAPS(0.81)PT(0.19)LPAQFK;EASRPPEEPSAPS(0.762)PT(0.238)LPAQFK;EASRPPEEPS(0.002)APS(0.923)PT(0.075)LPAQFK;EASRPPEEPSAPS(0.982)PT(0.018)LPAQFK 240.8 3.40E-30 3255590000 3962360 2807930 2178460 2387040 2599810 2483540 3298050 3501360 3629420 TRUE FALSE 3438724.087 2789484.523 3231970.543 2929053.916 2548078.867 2579083.391 2978205.619 2752621.412 3200354.102 1.074482378 0.871617463 1.009879044 0.915228072 0.796186542 0.805874384 0.93058628 0.860099015 1 21.60980011 8 0.858336555 0.885024981 66.18598554 0.3489033 0.07253813 834.3287107 2.222121307 0.024326072 106449.2134 100000000 -8 65.30096056 EATAQKPTGSVGSTVT(ph)TPPPLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EATAQKPTGSVGSTVTTPPPLVR 23 1 Q86YP4-2;Q86YP4;Q86YP4-3 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 1 EATAQKPTGSVGS(0.001)T(0.024)VT(0.488)T(0.488)PPPLVR;EATAQKPTGSVGST(0.004)VT(0.769)T(0.227)PPPLVR 153.81 7.55E-08 1286290000 1443010 1458510 924140 1275530 1417970 1289920 1514100 1819510 1589820 TRUE FALSE 1252312.572 1448928.952 1371057.195 1565158.582 1389755.171 1339544.057 1367262.815 1430421.946 1401873.291 0.893313669 1.033566273 0.978017917 1.116476498 0.991355767 0.955538611 0.975311267 1.020364647 1 20.41892453 4.746415586 24.64050542 1.008348758 0.8933136 0.402145674 0.044260247 835.5356796 2620943.625 0.010779548 0.110343456 55771.91878 -4.746415586 -0.115035158 EATDAIGHLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EATDAIGHLDR 11 0 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;;;;; 200.76 4.57E-08 10951670000 13730100 11376900 7522900 9189600 11135800 11205100 10622700 12724200 12202100 FALSE TRUE 11915632.5 11302164.39 11160999.6 11276239.13 10914219.37 11636167.45 9592512.189 10003228.85 10759581.64 1.107443848 1.050427867 1.037307953 1.048018363 1.014372095 1.08147025 0.891532079 0.929704257 1 23.35911865 2.243405756 24.99999747 0.936144636 1.053056708 0.697218918 0.03598054 62.58281384 322917.49 0.013552892 0.010155904 175.1482311 -2.243405756 0.116912072 EATGHFQESEPFSHIDPEESEETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EATGHFQESEPFSHIDPEESEETR 24 0 Q15021;E7EN77 Q15021 NCAPD2 Condensin complex subunit 1 0 130.83 3.50E-05 17923000 20764 20831 11010 13954 19336 15930 16028 21824 25228 FALSE TRUE 18019.98479 20694.15979 16334.47283 17122.46897 18951.25143 16542.83741 14473.60703 17157.10743 22245.57458 0.810048072 0.930259622 0.734279655 0.769702258 0.851911078 0.743646218 0.650628599 0.771259352 1 14.44123074 4.232893504 24.99941259 0.779772584 0.870153848 0.107098615 0.094959806 252.3816342 1113352.84 0.024161098 0.052588288 17095.96043 -4.232893504 0.090381264 EATNPPVIQEEKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EATNPPVIQEEKPK 14 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 184 1.23E-06 555130000 409720 306680 296785 310501 310450 248941 399940 418300 347910 FALSE TRUE 355574.4639 304665.3989 440311.2187 381004.9978 304272.6524 258517.9214 361153.8804 328849.8002 306780.4761 1.159051803 0.993105568 1.4352648 1.241946693 0.991825348 0.842680488 1.177238802 1.07193849 1 18.22684715 3.238851741 24.99999985 1.026971703 1.208319801 0.33127652 0.134125784 10.26124649 881133.8021 0.041037208 0.049708054 1733.212215 -3.238851741 0.181348098 EATNTTSEPSAPSQDLLDLS(ph)PSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EATNTTSEPSAPSQDLLDLSPSPR 24 0 J3KQU4;I3L4I4;O75674;O75674-2;O75674-3;I3NI44 J3KQU4 TOM1L1 TOM1-like protein 1 1 EATNTTSEPSAPSQDLLDLS(0.975)PS(0.024)PR 122.11 7.89E-05 86665000 130820 129970 82400 99779 126630 148970 130080 147070 140580 TRUE FALSE 113531.8055 129116.2185 122248.9156 122435.347 124110.3107 154700.9723 117464.8616 115620.225 123960.7925 0.915868665 1.041589166 0.986190174 0.987694129 1.001206173 1.247983085 0.947596891 0.932716084 1 16.91952436 4.750227938 22.74258887 1.012849568 0.915868453 0.117039573 0.087201698 1245.209759 2427063.69 0.022085829 0.308360979 56263.65456 -4.750227938 -0.096981116 EATNTTSEPSAPSQDLLDLSPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EATNTTSEPSAPSQDLLDLSPSPR 24 0 J3KQU4;I3L4I4;O75674;O75674-2;O75674-3;I3NI44 J3KQU4 TOM1L1 TOM1-like protein 1 1 EATNTTSEPSAPSQDLLDLS(0.003)PS(0.997)PR;EATNTTSEPSAPSQDLLDLSPS(1)PR;EATNTTSEPSAPSQDLLDLSPS(1)PR;EATNTTSEPSAPSQDLLDLSPS(1)PR 213.19 7.09E-26 1923450000 2466020 2295750 1479300 1702460 2183870 2415430 1908470 2368740 2182230 TRUE FALSE 2140129.209 2280669.067 2194694.428 2089029.563 2140415.26 2508353.155 1723386.873 1862203.385 1924249.255 1.112189184 1.185225386 1.140545811 1.085633557 1.11233784 1.30354898 0.895615196 0.967755804 1 20.87586426 2.220881237 24.99999867 0.95477581 1.15191752 0.68517432 0.064535145 135.9075572 192182.2731 0.025726145 0.017386203 166.2957834 -2.220881237 0.19714171 EATSDPS(ph)RTPEEEPLNLEGLVAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EATSDPSRTPEEEPLNLEGLVAHR 24 1 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7 E9PGF5 TNS1 Tensin-1 1 EAT(0.013)S(0.087)DPS(0.573)RT(0.327)PEEEPLNLEGLVAHR 160.41 1.24E-11 147320000 88093 61776 56897 53766 74552 80288 69804 86672 83854 TRUE FALSE 76451.28685 61370.18939 84412.57951 65974.39206 73068.56106 83376.73131 63034.41882 68137.86728 73940.87565 1.033951602 0.829990027 1.141622665 0.892258734 0.988202539 1.127613523 0.852497597 0.921518263 1 16.17408451 EATSDPSRT(ph)PEEEPLNLEGLVAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EATSDPSRTPEEEPLNLEGLVAHR 24 1 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7 E9PGF5 TNS1 Tensin-1 1 EAT(0.01)S(0.054)DPS(0.223)RT(0.713)PEEEPLNLEGLVAHR 188.55 2.39E-17 106890000 63635 46062 41337 56175 58471 64739 63171 62977 67452 TRUE FALSE 55225.47352 45759.41569 61327.71146 68930.39233 57307.5415 67229.55122 57044.68614 49509.85864 59477.9014 0.92850407 0.769351551 1.031100796 1.158924419 0.96350981 1.130328233 0.959090432 0.832407625 1 15.86006612 4.227009553 24.99130118 0.999946481 0.848927799 0.314607201 0.09830502 266.0967395 575717.0496 0.027717786 0.058487163 16865.90123 -4.227009553 -0.151018682 EATTDFTVDSRPLTQVGGDHIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EATTDFTVDSRPLTQVGGDHIK 22 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ;;;; 295.87 9.32E-56 3378760000 2426090 2452860 1560830 1696086 2031690 1962890 2306980 2787290 2696800 FALSE TRUE 2105476.06 2436747.001 2315652.609 2081208.249 1991263.344 2038403.648 2083249.435 2191249.724 2377987.376 0.885402539 1.024709814 0.973786754 0.87519735 0.837373387 0.857197001 0.876055716 0.921472396 1 21.18130963 5.089905633 16.14071646 0.916729615 0.000267989 0.027203673 0.062443334 22454863.32 43701009.44 0.016434666 730677506.8 123000.1477 -5.089905633 -0.916461626 EAVELPLTHFELYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EAVELPLTHFELYK 14 0 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;; 188.4 8.38E-07 724844000 1599680 1313330 970820 1153790 1409320 1121000 1517690 1847190 1622240 FALSE TRUE 1388278.235 1304702.649 1440311.799 1415775.654 1381277.289 1164125.595 1370504.657 1452182.793 1430460.635 0.970511317 0.912085671 1.006886707 0.989734089 0.965617127 0.813811696 0.958086244 1.015185429 1 20.44804837 1.812800507 5.380629719 1.007063579 0.943231801 0.194499096 0.053124579 0.34307749 16.50973211 0.029898114 0.014746483 64.98311219 -1.812800507 -0.063831778 EAVFFQSHSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAVFFQSHSAR 11 0 P36954 P36954 POLR2I DNA-directed RNA polymerase II subunit RPB9 0 140.63 3.85E-05 260930000 201690 199870 100870 97484 169330 177580 193740 205610 134350 FALSE TRUE 175036.1555 198557.0408 149651.0694 119619.2321 165960.6643 184411.6175 174951.1246 161641.9016 118467.2961 1.477506125 1.676049403 1.263226851 1.009723663 1.400898559 1.556645789 1.476788366 1.364443243 1 16.85412932 6.479756106 0.027036353 7.79E-08 3.073111141 0.123567871 0.204472061 7881.394964 30.40960652 1390.105762 2142.448905 3018256.233 -6.479756106 3.073111063 EAVILPIKFPHLFTGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAVILPIKFPHLFTGK 16 1 O75351;I3L4J1;Q9UN37 O75351;I3L4J1 VPS4B;VPS4A Vacuolar protein sorting-associated protein 4B;Vacuolar protein sorting-associated protein 4A 0 168.32 3.61E-09 178580000 540000 432720 289200 350960 441630 337050 484890 616760 295430 FALSE TRUE 468637.6318 429877.4338 429058.0873 430650.8321 432842.427 350016.5316 437865.4424 484870.6736 260504.602 1.798961048 1.65017213 1.647026901 1.653140977 1.66155386 1.343609783 1.680835729 1.861274887 1 17.99094933 1.22770758 24.99999977 0.999998596 1.661199856 0.708063555 0.133601769 282.4127161 650494.9063 0.497492833 0.034398661 16.89303104 -1.22770758 0.66120126 EAVIT(ph)PVASATQSVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAVITPVASATQSVSR 16 0 P28749;P28749-2;H0YE05 P28749 RBL1 Retinoblastoma-like protein 1 1 EAVIT(1)PVASATQSVSR;EAVIT(0.963)PVAS(0.036)ATQSVSR 197.51 3.29E-10 340950000 543260 625260 346950 404760 552770 551940 480890 622780 592720 TRUE FALSE 471466.8146 621152.6259 514736.1805 496666.9444 541770.9585 573173.489 434253.3618 489603.3435 522649.3168 0.902071043 1.18846922 0.984859568 0.950287178 1.036585988 1.096669355 0.830869472 0.936772187 1 18.99548374 2.246164338 24.99999585 0.921690844 1.028955857 0.238341813 0.087514557 229.7566157 755410.2857 0.031808565 0.024155191 176.2642908 -2.246164338 0.107265013 EAVLDVIPTDIHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 EAVLDVIPTDIHQR 14 0 P09467;A0A3B3IUC7 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;;;;;;; 185.95 1.12E-06 22958710000 11156790 11116580 7178970 8148070 10734200 11278830 11252700 11755790 11678010 FALSE TRUE 9682391.934 11043554.45 10650743.9 9998213.829 10520610.42 11712733.89 10161414.89 9241905.792 10297448.96 0.940270932 1.072455372 1.034308977 0.970940848 1.021671529 1.137440344 0.986789536 0.897494693 1 23.29578364 1.999812031 25 0.9416405 1.031452942 0.249935332 0.058069802 7.356837412 978521.797 0.023299923 0.015515995 99.95672799 -1.999812031 0.089812442 EAVTEILGIEPDREK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EAVTEILGIEPDREK 15 1 E9PGT1;Q15631;H7C1D4 E9PGT1 TSN Translin 0 ;;;;; 249.6 1.25E-18 1848491000 1478759 1173381 824615 881447 1074885 878096 1362944 1562245 1186419 FALSE TRUE 1283337.251 1165672.983 1223401.572 1081593.013 1053496.891 911876.9213 1230765.901 1228171.064 1046161.897 1.226709991 1.114237658 1.169418974 1.033867718 1.007011337 0.871640349 1.176458351 1.173978012 1 19.9966747 3.744735548 24.04291373 1.056964647 1.164533767 0.290902641 0.091292685 499.4755429 1944761.356 0.027058013 0.045341685 5555.658578 -3.744735548 0.10756912 EAVTHIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EAVTHIGR 8 0 D6RBW1;P06730;P06730-3;P06730-2 D6RBW1 EIF4E Eukaryotic translation initiation factor 4E 0 ;;;; 156.51 0.00039182 2359140000 3625980 3358610 2132900 2438520 2986120 3500220 3157760 3578140 3237690 FALSE TRUE 3146797.556 3336547.07 3164377.574 2992223.236 2926702.054 3634875.728 2851520.921 2812982.606 2854933.977 1.102231289 1.168695002 1.108389056 1.048088418 1.025138262 1.273190819 0.998804506 0.98530566 1 21.44502595 2.048865757 24.99999337 0.991737621 1.116646153 0.438706038 0.067226629 99.04683642 50672.44522 0.0269473 0.018167861 111.9091911 -2.048865757 0.124908532 EAVVDLHADDSRIS(ph)EDETER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EAVVDLHADDSRISEDETER 20 1 Q9UKV3-5;G3V3T3 Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 EAVVDLHADDS(0.005)RIS(0.995)EDETER;EAVVDLHADDSRIS(1)EDETER;EAVVDLHADDS(0.021)RIS(0.979)EDETER 228.71 1.73E-25 1356020000 1083540 1006040 729971 864139 1025000 1001180 954140 1091140 1153490 TRUE FALSE 940347.4437 999431.257 1082987.417 1060354.967 1004604.505 1039696.042 861607.6497 857808.2023 1017125.726 0.924514462 0.982603459 1.064752753 1.042501374 0.987689604 1.022190291 0.847100439 0.843364965 1 19.95606659 2.244585544 24.99830406 0.883613232 1.006831969 0.435265931 0.056854223 115.6403878 479811.0841 0.02192998 0.016536082 175.624679 -2.244585544 0.123218737 EAWPHIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EAWPHIK 7 0 P52209-2;P52209;K7EM49;K7EPF6;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;; 84.244 0.021688 1027090000 1490820 1326740 881640 998230 1245760 1254060 1386670 1583630 1302530 FALSE TRUE 1293804.36 1318024.558 1308004.053 1224893.378 1220971.813 1302304.5 1252190.957 1244983.048 1148546.387 1.126471141 1.147558838 1.138834328 1.06647271 1.063058338 1.133871922 1.090239777 1.083964098 1 20.13137769 0.030100528 0.986557669 9.60E-16 1.112398138 0.592346145 0.028701204 14.37043148 1.64976562 29.27631422 0.010241262 1.071767363 -0.030100528 1.112398138 EAYFWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAYFWLR 7 0 Q8TCJ2 Q8TCJ2 STT3B Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B 0 ; 114.19 0.013869 530750000 483540 581200 413230 504220 724910 677870 419990 749320 753520 FALSE TRUE 419638.9639 577382.0589 613069.4102 618710.8575 710485.7093 703948.0975 379259.4344 589083.7492 664439.724 0.631568145 0.868975827 0.922686269 0.931176802 1.06930047 1.059461185 0.570795846 0.886587192 1 19.3417788 4.737633539 3.234903096 0.908752535 0.592387889 0.294969689 0.13834621 0.481980036 8.065954305 0.036184605 0.383379094 54655.45816 -4.737633539 -0.316364646 EAYPEEAYIADLDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EAYPEEAYIADLDAK 15 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ;; 194.7 9.52E-08 153637000 204543 165514 132045 155660 160115 131283 200118 245328 206034 FALSE TRUE 177512.1243 164426.7276 195902.4037 191004.9821 156929.0248 136333.542 180710.5872 192866.5163 181676.8952 0.977075946 0.905050295 1.078301142 1.051344376 0.86378086 0.750417612 0.994681172 1.061590777 1 17.47101543 2.006644619 24.99813321 1.03307714 0.938395269 0.152671463 0.092945187 306.4243004 1152812.442 0.04125578 0.02774399 101.5417442 -2.006644619 -0.094681871 EAYPGDVFYLHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 EAYPGDVFYLHSR 13 0 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;;;;;; 191.06 3.88E-06 7402170000 5792010 5924930 4052950 6674250 7238170 7528350 5076590 7293160 5474240 FALSE TRUE 5026581.203 5886008.745 6012970.176 8189740.472 7094144.578 7817970.496 4584263.083 5733574.489 4827081.583 1.041329241 1.219372128 1.245674031 1.696623587 1.469654999 1.619606042 0.949696624 1.18779316 1 22.20271978 2.225762783 24.99979332 1.071400032 1.38673206 0.384992237 0.19938973 267.5045505 522549.5643 0.085941345 0.058360214 168.1755214 -2.225762783 0.315332028 EAYSGCSGPVDSECPPPPS(ph)SPVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EAYSGCSGPVDSECPPPPSSPVHK 24 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 EAYSGCSGPVDSECPPPPS(0.575)S(0.425)PVHK 77.63 0.013698 299140000 40892 35648 25513 36796 48918 34359 54596 61406 57265 TRUE FALSE 35488.01859 35413.82594 37851.17214 45151.09419 47944.62751 35680.81296 49301.28832 48274.80476 50495.19694 0.702799885 0.701330584 0.749599456 0.894166117 0.949488871 0.706617958 0.976355996 0.956027656 1 15.62385855 5.979150953 0.132803098 1.199264224 8.05E-13 0.600779318 0.077654528 66.68546495 1.4563808 2.631018761 15.33961848 953127.3969 -5.979150953 -1.199264224 EAYSGCSGPVDSECPPPPSS(ph)PVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EAYSGCSGPVDSECPPPPSSPVHK 24 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 EAYSGCSGPVDSECPPPPS(0.249)S(0.751)PVHK;EAYSGCSGPVDSECPPPPS(0.287)S(0.713)PVHK 172.32 3.60E-12 814210000 177374 202758 129088 161840 237200 180720 205769 301320 264460 TRUE FALSE 153933.5765 201426.0693 191515.3886 198588.2456 232480.1841 187672.4153 185813.5541 236885.0629 233195.8401 0.660104299 0.863763561 0.821264172 0.851594289 0.996931094 0.804784576 0.796813331 1.015820277 1 17.83118253 6.715893855 0.283220604 0.969420954 1.36E-86 0.461123662 0.081396584 41.41436876 1.285994823 0.215992709 16.84487877 5198689.204 -6.715893855 -0.969420954 EAYVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EAYVHK 6 0 P61326;Q96A72;F5H6N1;F5H6P7;F5H3U9 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ;; 76.592 0.07465 1834300000 4477600 3909000 2480690 2933060 2994780 3496260 4102500 4754800 4251000 FALSE TRUE 3885873.815 3883321.522 3680359.981 3599056.102 2935189.737 3630763.385 3704640.181 3738023.022 3748451.623 1.036661055 1.035980163 0.981834729 0.960144738 0.783040581 0.968603506 0.988312123 0.997217891 1 21.83786335 4.095236089 2.809010148 0.951462729 1.038113304 0.247169724 0.061972219 0.422316356 6.650747891 0.018129048 0.0458855 12451.91332 -4.095236089 0.086650575 ECADLWPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ECADLWPR 8 0 J3KTJ3;P62829 J3KTJ3 RPL23 60S ribosomal protein L23 0 ;; 126.04 0.0028764 1436630000 1361220 1371920 938200 1056130 1395970 1309180 1287550 1429640 1419510 FALSE TRUE 1181331.328 1362907.767 1391916.658 1295940.458 1368192.928 1359545.002 1162683.599 1123922.611 1251697.145 0.943783672 1.088847868 1.112023514 1.03534666 1.093070264 1.086161303 0.928885716 0.89791897 1 20.25545411 2.233606385 24.99896723 0.932471164 1.063954012 0.518793875 0.053017242 84.28561495 425297.4729 0.02058806 0.01437126 171.2404598 -2.233606385 0.131482848 ECFGACLFTCYDLLRPDVVLETAWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ECFGACLFTCYDLLRPDVVLETAWR 25 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5;J3KRF5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 221.39 1.04E-33 2883120000 478736 404434 286593 318050 360793 379936 445821 476148 433570 FALSE TRUE 415469.8246 401777.2464 425190.3334 390268.1136 353613.9252 394552.3838 402585.348 374327.4556 382313.8485 1.086724497 1.050909477 1.112149965 1.02080559 0.924930987 1.03201175 1.053023189 0.979110375 1 18.54439793 3.565763593 6.068619436 0.998925946 1.079060187 0.535306561 0.036313529 0.189825884 10.52445464 0.010106039 0.015014079 3679.286384 -3.565763593 0.080134241 ECHGLVDALVTSINHALDAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ECHGLVDALVTSINHALDAGK 21 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ; 261.93 6.63E-37 433300000 760050 786520 345570 674700 762340 719680 883190 1066200 1017310 FALSE TRUE 659607.4668 781353.2983 512688.8079 827900.9471 747170.9255 747366.5553 797538.3697 838201.4272 897044.7707 0.735311646 0.871030437 0.571530903 0.922920432 0.832924899 0.833142982 0.889073094 0.934403114 1 19.77482047 -1.999998809 0.228532912 2.363178915 0.711293576 0.447439921 0.088575804 80.70293144 1.262171293 48.22465981 0.358721336 0.010000027 1.999998809 -1.651885339 ECHLNADTVSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ECHLNADTVSSK 12 0 P63010;P63010-2;P63010-3;A0A087X253 P63010 AP2B1 AP-2 complex subunit beta 0 ;;; 238.13 3.98E-16 2825310000 5394060 4557260 3109140 3921150 4356640 4241610 4961210 5880400 5461280 FALSE TRUE 4681221.304 4527323.059 4612730.503 4811507.039 4269951.388 4404787.481 4480072.618 4622922.221 4815653.7 0.972084289 0.940126376 0.957861755 0.99913892 0.886681571 0.914681112 0.930314532 0.959978127 1 22.19930022 1.312835541 2.950948203 1.005941495 0.942485483 0.257622503 0.030519782 0.496547664 5.803585141 0.068633339 0.008214132 20.55112218 -1.312835541 -0.063456012 ECINAAPDS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ECINAAPDSPSK 12 0 J3KNN7;Q7Z569 J3KNN7 BRAP BRCA1-associated protein 1 ECINAAPDS(0.906)PS(0.094)K;ECINAAPDS(0.94)PS(0.06)K;ECINAAPDS(0.999)PS(0.001)K;ECINAAPDS(1)PSK;ECINAAPDS(1)PSK;ECINAAPDS(0.973)PS(0.027)K 299.46 2.09E-36 3999100000 8238610 6926860 5535140 6519680 7751110 6258840 8385280 9714580 10917560 TRUE FALSE 7149856.815 6881357.001 8211952.218 8000072.991 7596878.076 6499621.625 7572076.836 7637192.666 9626898.494 0.742695773 0.714805189 0.853021586 0.831012501 0.789130381 0.675152192 0.786554137 0.793318084 1 23.19863965 1.209964829 3.299130298 1.046912826 0.771647003 0.656174466 0.051794887 0.256138859 3.629377234 0.189411094 0.013955209 16.21678762 -1.209964829 -0.275265822 ECINAAPDS(ph)PSKQLPDQISFFSGNPSVEIVHGIMHLYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ECINAAPDSPSKQLPDQISFFSGNPSVEIVHGIMHLYK 38 1 J3KNN7;Q7Z569 J3KNN7 BRAP BRCA1-associated protein 1 ECINAAPDS(0.5)PS(0.5)KQLPDQISFFSGNPSVEIVHGIMHLYK;ECINAAPDS(0.833)PS(0.167)KQLPDQISFFSGNPSVEIVHGIMHLYK 110.41 6.14E-06 309843000 332894 281717 111419 111235 277237 202736 361380 433564 43835.9 TRUE FALSE 288901.2145 279866.3825 165301.6011 136492.6069 271720.5261 210535.3851 326333.4232 340849.7126 38653.66984 7.474095361 7.240357349 4.276478838 3.531168125 7.029617815 5.446711424 8.442495229 8.818042737 1 15.23831777 4.442108053 24.95957435 5.928890238 7.415666229 0.077431537 2.33062742 480.8428298 342773.9408 0.600674301 1.589248025 27676.30149 -4.442108053 1.486775991 ECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDK ddPTM_MDA-MB-175_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 ;;; 378.28 4.55E-162 2094683000 514454 453400 175090 376753 417031 409307 548686 620140 750657 FALSE TRUE 446467.6004 450421.5855 259764.1096 462300.527 408732.899 425053.3051 495474.5162 487527.8869 661915.1846 0.674508775 0.680482328 0.392443195 0.698428647 0.617500412 0.642156752 0.748546835 0.736541325 1 19.33628684 -1.103051419 0.655828632 9.999999535 0.60539964 0.641826385 0.088799472 39.6365005 0.924568067 502.2536376 0.039333514 0.078876672 1.103051419 -9.394599894 ECLAETER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ECLAETER 8 0 O14519-2;O14519;O75956 O14519-2 CDK2AP1;CDK2AP2 Cyclin-dependent kinase 2-associated protein 1;Cyclin-dependent kinase 2-associated protein 2 0 97.635 0.018825 102780000 187750 146650 77568 132600 163840 168550 149800 169580 169190 FALSE TRUE 162938.3618 145686.6465 115080.1442 162708.8567 160579.9045 175034.2276 135272.4191 133316.6367 149188.5509 1.092163982 0.976526989 0.771373832 1.090625625 1.076355414 1.17324169 0.906721181 0.893611714 1 17.1867773 ECLIDPDLTQYAIIMLDEAHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ECLIDPDLTQYAIIMLDEAHER 22 0 Q14562;F5H658 Q14562 DHX8 ATP-dependent RNA helicase DHX8 0 ; 147.93 7.44E-08 60509000 165026 152432 94621 116713 137452 148224 145334 167625 153278 FALSE TRUE 143217.396 151430.6642 140380.0321 143214.4705 134716.9741 153926.2732 131239.531 131779.6982 135157.6495 1.059632189 1.120400249 1.038639194 1.059610544 0.996739546 1.13886468 0.971010754 0.975007325 1 17.04428364 2.205704759 24.99997496 0.980089747 1.06622952 0.511546061 0.039989503 147.260073 112048.9284 0.015592352 0.01051318 160.5849197 -2.205704759 0.086139773 ECLPLIIFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ECLPLIIFLR 10 0 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ; 114.89 0.0030127 194060000 613680 600720 385120 467320 603140 589480 633340 682750 617450 FALSE TRUE 532580.6331 596773.8308 571365.3201 573432.1485 591138.694 612157.677 571918.7843 536749.2257 544455.7644 0.978188988 1.09609241 1.049424687 1.053220823 1.085742374 1.124347866 1.050441233 0.985845427 1 19.05445531 1.819407141 4.589019957 0.993247805 1.067112645 0.366697954 0.038104445 0.205213478 7.112205867 0.020983414 0.009936123 65.9792146 -1.819407141 0.07386484 ECLQALEFLHANQVIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ECLQALEFLHANQVIHR 17 0 Q13177;H7C1X3 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 0 149.86 1.79E-07 376820000 205240 172250 120360 178150 224410 179420 147080 192510 213410 FALSE TRUE 178117.014 171118.4784 178566.4986 218601.6804 219944.6801 186322.4035 132816.2042 151343.2346 188180.9129 0.946520087 0.909329622 0.948908664 1.16165703 1.168793777 0.990123815 0.705789988 0.80424328 1 17.52176078 2.386014083 7.365801573 0.825464703 1.029038888 0.383847621 0.110552082 0.23397406 16.2501315 0.044605755 0.034440298 243.2282881 -2.386014083 0.203574185 ECPGIEPVCVDLGDWEATER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ECPGIEPVCVDLGDWEATER 20 0 Q7Z4W1;J3KS22;J3QS36 Q7Z4W1 DCXR L-xylulose reductase 0 ;; 228.25 7.38E-25 173640000 247298 175098 97451 135695 160192 162282 154720 190370 161672 FALSE TRUE 214616.9427 173947.7697 144578.6296 166506.6237 157004.4926 168525.0936 139715.2782 149660.857 142559.3203 1.505457112 1.220178164 1.014164694 1.167981324 1.101327449 1.182140131 0.980050114 1.049814608 1 17.12120284 4.653573874 2.486207978 1.072485013 1.560239275 0.805911847 0.067778848 0.179888959 1.584983949 0.017679876 0.170949738 45037.45842 -4.653573874 0.487754262 ECPHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ECPHSK 6 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 0 76.592 0.07465 66959000 138860 149470 103060 114150 95317 121470 157850 179120 203290 FALSE TRUE 120509.2992 148488.1217 152900.1607 140069.5022 93420.37818 126143.0295 142541.7313 140816.5819 179257.2878 0.672270013 0.828351938 0.852964823 0.781388048 0.521152469 0.703698193 0.79517956 0.785555687 1 17.45167225 0.904132357 1.50276331 1.369971213 0.73496541 0.438722554 0.093457602 2.945348124 2.98162684 3.620889842 0.028490795 8.019224227 -0.904132357 -0.635005803 ECPPHAEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ECPPHAEQR 9 0 J3QT73;A0A087X1P5;J3KQ34;Q9H9Q2-2;Q9H9Q2 J3QT73 COPS7B COP9 signalosome complex subunit 7b 0 ; 130.94 0.0003471 596400000 386590 359030 265602 282454 391630 418510 333843 371170 346834 FALSE TRUE 335501.152 356671.5083 394048.0156 346589.4977 383837.3292 434610.3505 301466.9572 291798.1839 305831.6796 1.097012423 1.166234671 1.288447345 1.133268791 1.255060724 1.42107695 0.985728351 0.954113662 1 18.22237833 2.130343775 10.131496 0.972871308 1.223781493 0.626055339 0.089926085 0.199528125 17.39960953 0.036982332 0.024926367 135.0031107 -2.130343775 0.250910186 ECPSDECGAGVFMASHFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 ECPSDECGAGVFMASHFDR 19 0 P62979;A0A2R8Y422 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ;;;;;;;;;;;; 362.49 9.97E-92 29935350000 8270508 8143539 5092410 5914110 7491639 8126810 7804683 9105910 8170499 FALSE TRUE 7177539.413 8090043.556 7555116.509 7256999.067 7342570.041 8439453.639 7047786.044 7158682.009 7204591.916 0.996245103 1.122901012 1.048652942 1.007274132 1.019151414 1.17139926 0.978235287 0.993627688 1 22.78048528 ECREPELGLEELLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ECREPELGLEELLR 14 1 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 0 ;;; 168.93 3.11E-06 240073000 229616 237799 121357 127868 209118 222925 213780 246960 82938 FALSE TRUE 199271.6638 236236.8827 180045.6511 156902.3837 204956.9609 231501.069 193047.6485 194149.5258 73133.16412 2.724778371 3.230229206 2.46188789 2.145434094 2.802517345 3.165473172 2.639673134 2.654739859 1 16.15823816 4.21995302 24.17716283 2.475676995 2.977503684 0.133489316 0.582734476 320.3620282 416253.4256 0.148317847 0.309740107 16594.07389 -4.21995302 0.501826689 ECS(ph)PTSSLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ECSPTSSLER 10 0 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 ECS(0.891)PT(0.1)S(0.009)SLER;ECS(0.873)PT(0.126)S(0.001)SLER;ECS(0.891)PT(0.095)S(0.014)SLER 228.13 2.34E-09 1550240000 2047570 1937860 1376760 1523530 2049550 1771580 1829230 2109900 2387430 TRUE FALSE 1776978.437 1925130.07 2042565.741 1869470.772 2008767.965 1839733.829 1651831.556 1658714.304 2105190.745 0.844093791 0.914468237 0.9702521 0.888029161 0.954197604 0.873903628 0.784646978 0.787916396 1 21.00551953 2.480033585 24.55460248 0.838453936 0.915698675 0.111271147 0.068230802 144.3454467 1217040.966 0.024763712 0.019562327 302.0185267 -2.480033585 0.077244739 ECSEAMEVETSVISIDS(ph)PQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ECSEAMEVETSVISIDSPQK 20 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 ECSEAMEVETSVIS(0.001)IDS(0.999)PQK 107.57 0.00014478 31618000 108250 93803 68801 81089 92242 72196 106230 141330 127050 TRUE FALSE 93944.48823 93186.80192 102073.3937 99501.49682 90406.56467 74973.42684 95927.83095 111107.6793 112030.2937 0.838563259 0.831800032 0.911123146 0.888165991 0.806983198 0.669224585 0.856266888 0.991764599 1 16.77352937 1.761445435 4.221871479 0.997920156 0.826066442 0.546263117 0.063714015 0.153251693 5.751398009 0.043495132 0.018485135 57.73583288 -1.761445435 -0.171853713 ECSEAMEVETSVISIDS(ph)PQKLAILDQELEHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ECSEAMEVETSVISIDSPQKLAILDQELEHK 31 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 ECSEAMEVETSVIS(0.038)IDS(0.961)PQKLAILDQELEHK 132.17 2.04E-06 35007000 52796 42425 17982 13351 33977 30446 54953 65368 5506.7 TRUE FALSE 45818.87483 42146.30738 26678.15535 16382.54861 33300.92417 31617.27732 49623.66652 51389.56189 4855.704199 9.436092676 8.679751824 5.494188742 3.373876977 6.858103955 6.511368078 10.21966423 10.58333864 1 12.24546482 4.398236048 6.589579483 6.813547664 9.253168862 0.12247883 2.854325137 0.486291988 31.90082225 0.758368799 2.056105262 25017.04718 -4.398236048 2.439621198 ECSEFGHSDTCWMPGQS(ph)SPSRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ECSEFGHSDTCWMPGQSSPSRR 22 1 Q08174-2 Q08174-2 PCDH1 Protocadherin-1 1 ECSEFGHSDTCWMPGQS(0.442)S(0.442)PS(0.116)RR;ECSEFGHSDTCWMPGQS(0.692)S(0.241)PS(0.068)RR;ECSEFGHSDTCWMPGQS(0.612)S(0.386)PS(0.002)RR 160.04 8.91E-12 577090000 340792 396388 172249 389204 471360 534180 273497 560570 322634 TRUE FALSE 295755.4737 393784.1011 255549.1925 477578.7168 461980.8582 554730.2503 246973.303 440696.4679 284492.5761 1.039589426 1.384163013 0.898263132 1.678703618 1.623876674 1.949893589 0.868118622 1.549061399 1 18.11803148 3.737863245 24.99998674 1.448231804 1.135020982 0.182505578 0.335074765 115.709021 4148069.525 0.089055006 0.141479789 5468.437404 -3.737863245 -0.313210823 ECYQSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ECYQSHR 7 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 163.72 0.0012243 771480000 1524520 1549880 920060 1090840 1145700 1571520 1384670 1692930 1631440 FALSE TRUE 1323050.819 1539698.736 1365004.093 1338531.894 1122902.812 1631977.391 1250384.917 1330910.094 1438573.022 0.919696671 1.070295851 0.948859789 0.930458082 0.780567128 1.134441816 0.869184183 0.925159915 1 20.45620702 4.023466259 24.74222353 0.935785992 0.998641692 0.05032699 0.096392835 556.0059468 586229.1776 0.023188945 0.048267632 10555.19496 -4.023466259 0.0628557 EDAANNYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 EDAANNYAR 9 0 P68363;P68363-2;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;F8VWV9;F8VX09;P68366-2;P68366;C9JEV8;C9JQ00;C9JJQ8;C9JDL2;Q9BQE3;F5H5D3;A0A1W2PQM2;A6NHL2-2;A6NHL2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA1A;TUBA1C;TUBA4A;TUBAL3 Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain;Tubulin alpha chain-like 3 0 ;;;;;;; 216.57 1.39E-06 25326243000 6475425 5324150 3788251 4413061 5033070 5587179 5492837 6010607 6321375 FALSE TRUE 5619681.18 5289175.308 5620261.855 5415113.949 4932921.754 5802121.392 4960142.513 4725285.468 5574069.249 1.008182878 0.948889415 1.008287053 0.971483078 0.884976762 1.040913044 0.889860225 0.847726366 1 22.4102995 2.200263903 24.99796245 0.898083723 0.972810651 0.211107294 0.056200945 204.2565147 133325.8981 0.022031416 0.014853934 158.5856562 -2.200263903 0.074726929 EDAEGVAAEEEQEGDS(ph)GEQETGATDARPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDAEGVAAEEEQEGDSGEQETGATDARPR 29 1 Q96KC8 Q96KC8 DNAJC1 DnaJ homolog subfamily C member 1 1 EDAEGVAAEEEQEGDS(1)GEQETGATDARPR 230.63 2.20E-35 168670000 57508 54099 36345 57005 70463 56636 37024 94329 60136 TRUE FALSE 49908.17209 53743.62011 53921.56357 69948.85652 69060.92416 58814.82357 33433.41818 74157.47742 53026.79059 0.94118787 1.013518252 1.01687398 1.319122952 1.302377975 1.109152994 0.630500504 1.398490774 1 15.69443381 3.975552591 24.06583974 1.133401592 0.986813707 0.084537034 0.212761225 1165.357422 1147173.825 0.05658805 0.098741734 9452.628521 -3.975552591 -0.146587885 EDAEHHPDEDVDESES ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EDAEHHPDEDVDESES 16 0 Q5JY65;Q9BZJ0-2;Q9BZJ0-3;Q9BZJ0 Q5JY65 CRNKL1 Crooked neck-like protein 1 0 ; 166.38 6.70E-09 1200340000 766360 737990 523500 648290 763320 675670 740910 822730 985030 FALSE TRUE 665083.5843 733142.0951 776666.351 795494.153 748131.4254 701663.4621 669056.6622 646795.592 868580.8755 0.765712904 0.84406889 0.894178508 0.915855018 0.861326155 0.807827437 0.770287121 0.744657878 1 19.72830066 2.741227513 22.4458847 0.811587042 0.860973719 0 0.07829702 155.8102986 1311380.34 0.025980208 0.024817715 551.096322 -2.741227513 0.049386677 EDAIEHFMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDAIEHFMK 9 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 70.552 0.053844 0 608170 490190 322030 446760 508840 477570 531210 610650 890360 FALSE TRUE 527798.7936 486969.9096 477764.7851 548203.6863 498715.0795 495942.4269 479693.336 480067.2496 785102.6551 0.672267238 0.620262722 0.608537982 0.698257333 0.635222765 0.631691185 0.610994413 0.611470674 1 19.58252178 1.23640091 24.99992502 1.000000469 0.634180687 0.940328222 0.028806457 12.7626814 147699.307 0.04575832 0.0071215 17.23458815 -1.23640091 -0.365819782 EDALDDSVSSSSVHAS(ph)PLAS(ph)SPVRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EDALDDSVSSSSVHASPLASSPVRK 25 1 P49792;J3KNE0;A6NKT7;Q7Z3J3;O14715;Q99666;J3KQ37 P49792 RANBP2;RGPD3;RGPD4;RGPD8;RGPD5 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6 2 EDALDDSVSSSSVHAS(1)PLAS(0.931)S(0.069)PVRK;EDALDDSVSS(0.001)S(0.002)S(0.007)VHAS(0.989)PLAS(0.533)S(0.468)PVRK;EDALDDSVSSSSVHAS(1)PLAS(0.887)S(0.113)PVRK 257.26 6.50E-45 637080000 253042 233804 112173 259666 290797 235554 287841 393731 554935 TRUE FALSE 219601.8586 232268.1261 166420.238 318627.134 285010.7086 244615.9148 259926.2241 309534.6897 489331.2165 0.448779582 0.474664436 0.340097325 0.651148186 0.582449472 0.499898446 0.53118668 0.632566816 1 18.9004518 -0.177845539 1.058820382 10 0.495850577 0.789418382 0.080725025 14.65694985 1.077503494 296.7064622 0.026676844 0.663979179 0.177845539 -9.504149423 EDALDDSVSSSSVHASPLAS(ph)SPVRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.499)S(0.499)PVRK;EDALDDSVSSSSVHAS(0.001)PLAS(0.499)S(0.499)PVRK 273.93 2.51E-53 2015810000 424905 513350 122523 471207 849637 678129 684711 873622 1437770 TRUE FALSE 368752.7277 509977.77 181775.5326 578201.7513 832730.886 704217.0614 618307.8326 686804.7338 1267798.469 0.290860682 0.402254603 0.143378886 0.456067558 0.656832223 0.555464515 0.487701987 0.541730213 1 20.273894 -2 0.354025224 6.96596648 0.317045384 0.64101676 0.135725071 58.74798334 0.906835604 258.3398719 0.191804912 0.01 2 -6.648921096 EDALDDSVSSSSVHASPLASS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDALDDSVSSSSVHASPLASSPVR 24 0 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(0.247)S(0.753)PVR 199.43 1.06E-24 206580000 37625 51232 23798 40897 78256 57303 52022 59244 212970 TRUE FALSE 32652.76092 50895.45362 35306.7924 50183.28892 76698.85871 59507.48349 46976.91445 46575.13164 187792.9292 0.173876413 0.271019009 0.188009168 0.267226722 0.408422506 0.31687819 0.250152733 0.248013234 1 17.51878322 1.237621456 24.99999812 1.000000859 0.267799909 0.926427172 0.065051462 6.041004173 160720.6779 0.098223292 0.016633128 17.28309255 -1.237621456 -0.73220095 EDALDDSVSSSSVHASPLASS(ph)PVRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EDALDDSVSSSSVHASPLASSPVRK 25 1 P49792;J3KNE0;A6NKT7;Q7Z3J3;O14715;Q99666;J3KQ37 P49792 RANBP2;RGPD3;RGPD4;RGPD8;RGPD5 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6 1 EDALDDSVSSSSVHASPLAS(0.425)S(0.574)PVRK;EDALDDSVSSSSVHASPLAS(0.159)S(0.841)PVRK 267.93 7.12E-46 1708670000 343540 395170 88235 372960 603020 505340 550140 655460 1179460 TRUE FALSE 298140.3186 392574.1023 130905.7411 457646.2683 591021.0818 524780.7568 496787.5075 515294.9798 1040025.582 0.286666332 0.377465813 0.125867809 0.440033665 0.568275523 0.50458447 0.477668546 0.495463754 1 19.98818759 -0.384897562 0.858330405 10 0.369582645 0.710186048 0.120874482 20.38028223 1.145758611 333.5039271 0.046740764 0.412194733 0.384897562 -9.630417355 EDAMAMVDHCLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EDAMAMVDHCLK 12 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;; 165.7 5.39E-05 993190000 1408250 1133010 981330 1044370 1091060 966790 1179920 1559860 2233730 FALSE TRUE 1222146.194 1125567.183 1455904.47 1281510.171 1069350.041 1003983.037 1065491.54 1226296.078 1969660.984 0.620485558 0.571452241 0.739165005 0.650624743 0.542910709 0.509723777 0.540951742 0.62259246 1 20.90951591 1.239890538 5.16923142 1.023136365 0.59661809 0.790123776 0.064964136 0.07851689 5.714219619 0.119986148 0.01761403 17.37362881 -1.239890538 -0.426518275 EDAMAMVDHCLKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDAMAMVDHCLKK 13 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 160.69 2.82E-05 301470000 824280 663150 366820 458460 500740 454590 779480 800550 332910 FALSE TRUE 715349.3095 658793.724 544215.3789 562560.3501 490776.2537 472078.3715 703886.1496 629358.6124 293553.7591 2.436859647 2.244201287 1.853886595 1.91637931 1.671844555 1.608149638 2.397810036 2.143929665 1 18.16326521 4.360296147 2.80099351 1.851273818 2.4204201 0.272815405 0.366264971 0.41013257 6.127074444 0.097145 0.36127714 22924.30338 -4.360296147 0.569146282 EDDDVIVNKPHVS(ph)DEEEEEPPFYHHPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 272.7 9.29E-62 9547960000 8056490 4944122 5771381 6220896 5037278 3936495 6393010 8160990 11004040 TRUE FALSE 6991804.434 4911643.737 8562440.156 7633445.517 4937046.023 4087934.51 5773016.874 6415825.797 9703154.927 0.720570215 0.506190386 0.882438776 0.786697273 0.508808327 0.42129952 0.594962867 0.661210281 1 23.21002248 1.237894043 4.41074254 1.033049717 0.629597331 0.4098587 0.137963717 0.227339948 8.981252563 0.289802126 0.036637371 17.2939438 -1.237894043 -0.403452386 EDDRVAIHEAMEQQTISIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EDDRVAIHEAMEQQTISIAK 20 1 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ; 140.95 1.18E-07 421650000 594820 452240 249050 281340 424020 325490 546140 669810 132036 FALSE TRUE 516213.0299 449269.2057 369491.413 345222.547 415582.8316 338011.8109 493175.4269 526576.344 116426.8545 4.433796929 3.858810818 3.173592679 2.965145357 3.569475731 2.903211741 4.235925028 4.522808301 1 16.82906434 4.523215864 3.147403456 3.366449067 4.41396101 0.142025581 0.952359701 0.613858039 11.14651109 0.240721329 1.201604187 33359.2182 -4.523215864 1.047511942 EDDSIRPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EDDSIRPFK 9 1 P07099;B1AQP8;B1AQP9 P07099 EPHX1 Epoxide hydrolase 1 0 ; 108.43 0.0023823 597650000 945750 836090 798250 1232830 1100580 1086540 709730 1588270 2188700 FALSE TRUE 820766.7413 830597.6697 1184286.37 1512762.894 1078680.611 1128339.897 640900.4938 1248630.82 1929954.379 0.425277794 0.43037166 0.613634386 0.783833499 0.558915083 0.584645891 0.332080644 0.646974267 1 20.88013531 1.281943479 3.799692436 1.034850826 0.541485019 0.583472251 0.123419301 0.176737735 4.016182498 0.226046503 0.032869387 19.14006812 -1.281943479 -0.493365807 EDEEESLNEVGYDDIGGCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EDEEESLNEVGYDDIGGCR 19 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 425.34 8.95E-169 524520000 357948 216933 166208 219034 198346 197903 188624 232391 404526 FALSE TRUE 310644.2649 215507.9528 246586.7447 268769.0174 194399.3027 205516.4565 170331.2735 182695.9931 356703.3971 0.870875544 0.604165687 0.691293514 0.753480397 0.544988649 0.57615503 0.477515143 0.512179011 1 18.44436543 3.242824394 24.99311803 0.595269436 0.718207482 0.087502049 0.158377913 235.0713933 1377916.824 0.04552964 0.056693303 1749.139284 -3.242824394 0.122938046 EDEEESLNEVGYDDIGGCRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDEEESLNEVGYDDIGGCRK 20 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 139.11 9.55E-07 200300000 103660 74174 41467 41630 47320 41065 69939 81201 33190 FALSE TRUE 89961.06836 73686.74611 61520.5799 51082.72777 46378.42458 42644.79712 63156.32654 63836.79806 29266.31601 3.073877434 2.517800535 2.102095114 1.745444413 1.584703198 1.457128977 2.157986899 2.181237913 1 14.83695353 4.415553552 1.465373914 1.753164836 3.21092962 0.653090046 0.341069733 0.455191791 1.394525192 0.10309888 0.819783972 26034.75841 -4.415553552 1.457764784 EDEGPPGYPEPLAPGHGS(ph)PFPSLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EDEGPPGYPEPLAPGHGSPFPSLSK 25 0 B1AKB5;B0QYS6;B0QYS7;P19484-2;P19484 B1AKB5 TFEB Transcription factor EB 1 EDEGPPGYPEPLAPGHGS(0.941)PFPS(0.042)LS(0.016)K;EDEGPPGYPEPLAPGHGS(0.979)PFPS(0.018)LS(0.004)K 130.87 5.57E-05 148190000 59285 77430 86324 112976 107932 97144 126050 140064 220570 TRUE FALSE 51450.33704 76921.35723 128070.5751 138628.9275 105784.3644 100881.1925 113825.6904 110112.4036 194494.4659 0.264533681 0.395493809 0.658479276 0.712765409 0.543893955 0.518684129 0.58523871 0.566146718 1 17.56936958 -2 0.086191343 2.095500423 1.40E-14 0.450038283 0.143919155 477.5358035 3.873117852 123.4619253 17.44013001 0.01 2 -2.095500423 EDEIPVLKDELIHELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDEIPVLKDELIHELK 16 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 95.347 0.0022732 12132000 53509 34746 41074 45003 36166 23143 49528 61559 84137 FALSE TRUE 46437.65008 34517.75124 60937.52378 55221.61898 35446.36736 24033.32619 44724.78218 48395.0869 74190.41971 0.625925157 0.465258875 0.821366479 0.744322774 0.477775534 0.3239411 0.602837703 0.652309113 1 16.17894528 1.199114298 2.537821641 1.131859277 0.578975172 0.465218798 0.140372964 0.593082321 3.856580232 0.750319886 0.039363363 15.81664248 -1.199114298 -0.552884104 EDEIS(ph)PPPPNPVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EDEISPPPPNPVVK 14 0 P10644;P10644-2;K7EPB2;K7EIE5;K7EID3;K7EJ40;K7EK41;K7EMU2;K7EMZ6 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 1 EDEIS(1)PPPPNPVVK;EDEIS(1)PPPPNPVVK;EDEIS(1)PPPPNPVVK;EDEIS(1)PPPPNPVVK;EDEIS(1)PPPPNPVVK;EDEIS(1)PPPPNPVVK 227.34 2.17E-12 3699520000 4765940 3399610 3575950 4252750 3433940 2767820 4162810 5062240 11575100 TRUE FALSE 4136108.954 3377277.738 5305291.381 5218401.887 3365611.312 2874299.826 3759101.327 3979719.37 10206704.86 0.405234501 0.330888155 0.519784931 0.511271949 0.329745139 0.281608988 0.368297249 0.389912261 1 23.28301385 1.238482725 24.99706134 1.000000667 0.391276301 0.865383932 0.075349471 0.680368146 216934.8735 0.109791686 0.019641898 17.31740148 -1.238482725 -0.608724366 EDEKDDKPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDEKDDKPIR 10 2 P35998;C9JLS9 P35998 PSMC2 26S protease regulatory subunit 7 0 67.385 0.035508 116540000 250480 156330 187660 182970 119290 84773 207900 214710 262050 FALSE TRUE 217378.4334 155303.0579 278413.0037 224516.135 116916.3624 88034.27217 187737.89 168795.9374 231070.7475 0.940744061 0.672101768 1.204882083 0.971633742 0.505976475 0.380984063 0.812469307 0.730494618 1 17.81797511 3.262292713 24.94864225 0.685784876 0.94607647 0.28290637 0.206757459 320.910012 337358.0743 0.06183063 0.079777916 1829.332765 -3.262292713 0.260291594 EDENDAS(ph)DDEDDDEKRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDENDASDDEDDDEKRR 17 2 Q9Y5B6-2;Q9Y5B6;Q9Y5B6-3;Q9Y5B6-4 Q9Y5B6-2 PAXBP1 PAX3- and PAX7-binding protein 1 1 EDENDAS(1)DDEDDDEKRR 170.8 9.41E-10 361640000 212820 135870 171080 138900 144830 124090 199370 205010 276300 TRUE FALSE 184695.2978 134977.461 253814.8602 170439.368 141948.1664 128863.8226 180035.1281 161170.2069 243636.1288 0.758078446 0.554012501 1.041778416 0.699565244 0.582623633 0.528919185 0.738950865 0.661520144 1 17.89436856 1.234863123 24.91908111 1.000000454 0.693873451 0.305116802 0.144306305 134.2540853 904655.5187 0.253014121 0.034959416 17.17367038 -1.234863123 -0.306127003 EDEVEEWQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EDEVEEWQHR 10 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;; 175.86 2.67E-06 1752710000 2206090 2010400 1638650 2052660 2114930 1987880 2099760 2621190 3046470 FALSE TRUE 1914549.617 1997193.55 2431106.621 2518747.826 2072847.031 2064355.03 1896125.598 2060668.917 2686319.787 0.712703538 0.743468279 0.90499524 0.937620248 0.771630779 0.768469577 0.705845078 0.767097397 1 21.35719963 0.544666382 0.009709015 1.657070598 1.43E-06 0.047806345 0.098194858 104397.2655 204.0003411 18388.43902 16474.99971 3.504825352 -0.544666382 -1.657069172 EDFATFDYILCMDESNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EDFATFDYILCMDESNLR 18 0 P24666;P24666-3;P24666-2 P24666;P24666-2 ACP1 Low molecular weight phosphotyrosine protein phosphatase 0 ;; 198.14 4.11E-15 115646000 101730 95441 67041 80195 90091 82032 94154 106694 114170 FALSE TRUE 88286.12275 94814.04179 99462.25184 98404.50045 88298.36536 85187.82412 85022.95957 83878.31839 100672.9527 0.876959704 0.941802533 0.987973922 0.977467114 0.877081312 0.846183825 0.8445462 0.833176302 1 16.61931661 3.173871033 7.457294593 0.869515685 0.948618315 0.25040165 0.054890109 0.276030145 26.89872266 0.016706486 0.019043237 1492.351178 -3.173871033 0.079102629 EDFLQLFNLRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EDFLQLFNLRPK 12 1 O75362 O75362 ZNF217 Zinc finger protein 217 0 ; 77.597 0.015319 0 129545 159076 78622 95564 124119 97131 135724 162502 104764 FALSE TRUE 112425.3 158031.0193 116643.8622 117263.2668 121649.2747 100867.6924 122561.5074 127752.2119 92378.91927 1.217001681 1.710682703 1.262667534 1.269372577 1.316851027 1.091890804 1.326725928 1.382915203 1 16.49527605 4.051456957 24.99974355 1.251977363 1.46955138 0.249275872 0.162716254 132.0546656 64155.39116 0.038693942 0.080547849 11257.88887 -4.051456957 0.217574017 EDFPLIETEDEAYLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDFPLIETEDEAYLRR 16 1 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 0 124.16 0.00013464 28577000 18780 19463 14567 14916 17768 18227 17319 22244 14928 FALSE TRUE 16298.17542 19335.14627 21611.64992 18302.90578 17414.45156 18928.20448 15639.40605 17487.2937 13163.22885 1.238159391 1.468875646 1.641819813 1.390457158 1.322962 1.437960603 1.188113208 1.328495759 1 13.68422579 0.263293525 0.606097092 7.96E-16 1.437167693 0.512763801 0.120700176 9.087645873 1.066094694 11.89352411 0.062476987 1.833553241 -0.263293525 1.437167693 EDGKVFDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EDGKVFDEK 9 1 Q9Y5Z4-2;Q9Y5Z4 Q9Y5Z4-2 HEBP2 Heme-binding protein 2 0 ; 100.72 0.0040746 609850000 2102770 1665640 1223560 1251100 1335500 1025090 2364830 2656120 632060 FALSE TRUE 1824883.617 1654698.301 1815277.709 1535181.377 1308926.163 1064525.876 2135489.151 2088129.408 557338.5868 3.274281846 2.968928296 3.257046527 2.754486076 2.34852959 1.910016462 3.831583172 3.746608358 1 19.08819452 3.727127604 21.62795802 2.756087908 3.146969761 0.07442703 0.8275555 456.8114957 864158.3111 0.238913075 0.359202648 5334.916223 -3.727127604 0.390881853 EDGLAQQQTQLNLR ddPTM_MDA-MB-175_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 2971050000 1248940 1284072 894002 968238 1265860 1362150 1397980 1442920 1448115 FALSE TRUE 1083889.415 1275636.846 1326344.357 1188091.236 1240671.863 1414552.792 1262404.115 1134362.787 1276920.494 0.848830776 0.998994732 1.038705513 0.930434778 0.97161246 1.107784547 0.988631728 0.888358196 1 20.28423727 4.742252272 23.90753349 0.985185822 0.848830678 0.363408127 0.058570308 249.9464815 1618547.674 0.01529542 0.109069888 55239.8222 -4.742252272 -0.136355145 EDGNEEDKENQGDETQGQQPPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EDGNEEDKENQGDETQGQQPPQR 23 1 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;;; 309.21 3.63E-73 1524456000 1435974 1003709 969054 1055621 1051701 894640 1266672 1630990 1764140 FALSE TRUE 1246206.398 997115.5695 1437691.756 1295315.882 1030774.208 929057.3797 1143830.344 1282215.481 1555585.379 0.801117325 0.640990577 0.924212695 0.832687103 0.662627858 0.597239722 0.73530541 0.824265578 1 20.56902615 1.307458712 2.403403457 1.042943823 0.740898134 0.421190586 0.095857891 0.505918039 3.543912354 0.302053371 0.026807286 20.29825535 -1.307458712 -0.302045689 EDGNEEDKENQGDETQGQQPPQRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EDGNEEDKENQGDETQGQQPPQRR 24 2 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;;; 258.55 3.45E-44 923503500 926120 603775.4 333405.2 298649.1 506493.3 409827.4 760499 838411 58722.87 FALSE TRUE 803730.8955 599809.1596 494641.0699 366461.9427 496415.0743 425593.7253 686745.924 659123.3322 51780.71921 15.52181792 11.58363902 9.552611039 7.077189123 9.58687098 8.219154384 13.26257987 12.72912664 1 15.66012738 4.636709181 2.181659128 9.315582656 16.41739929 0.285978867 3.379250076 0.742641608 4.773319348 0.887320539 9.413541484 43322.06817 -4.636709181 7.10181663 EDGSGDRGDGPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EDGSGDRGDGPFR 13 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;; 174.89 1.75E-05 5471360000 5363500 4416080 2871090 3646040 4317990 4147590 4246020 5266140 4191360 FALSE TRUE 4654699.886 4387070.48 4259558.727 4473929.108 4232070.447 4307150.471 3834241.634 4140016.942 3695862.196 1.259435455 1.187022201 1.152520982 1.210523789 1.145083399 1.165398016 1.03744172 1.12017622 1 21.81747953 -2 0.181697718 0.178124791 1.276051435 0.729784331 0.039798024 60.05751956 0.851345357 17.68051118 0.331285552 0.01 2 1.097926644 EDGTFYEFGEDIPEAPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDGTFYEFGEDIPEAPER 18 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 269.7 1.39E-31 49729000 69790 46071 31678 39834 39796 43138 51042 55761 59202 FALSE TRUE 60567.07467 45768.35657 46997.58676 48878.91852 39004.13746 44797.54677 46091.9547 43836.94408 52203.207 1.160217507 0.876734576 0.900281601 0.936320225 0.747159795 0.85813783 0.882933393 0.83973661 1 15.67185082 4.738725744 7.787386184 0.874507627 1.162857277 0.646402353 0.06497779 0.058650993 39.50437049 0.015329819 0.088739615 54793.08391 -4.738725744 0.288349649 EDGWIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EDGWIR 6 0 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;; 120.76 0.046406 2069610000 2192500 1884510 1225480 1590020 1801230 1856400 1888570 2125970 2042290 FALSE TRUE 1902755.57 1872130.53 1818126.227 1951058.343 1765389.047 1927816.909 1705416.772 1671347.86 1800852.803 1.056585839 1.039579985 1.009591802 1.083408005 0.980307243 1.070502212 0.947005091 0.92808688 1 20.78024883 2.226830205 24.99993 0.951582944 1.037855104 0.555722852 0.034193119 142.1613236 302972.6218 0.01289543 0.008773181 168.5893766 -2.226830205 0.086272161 EDHLVYADEESSNITDGRIT(ph)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EDHLVYADEESSNITDGRITPEPAVSNTEEPSTTSTASNYPDVLTRPSLHR 51 2 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 EDHLVYADEES(0.002)S(0.008)NIT(0.167)DGRIT(0.672)PEPAVS(0.121)NT(0.03)EEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEES(0.005)S(0.019)NIT(0.062)DGRIT(0.873)PEPAVS(0.032)NT(0.009)EEPSTTSTASNYPDVLTRPSLHR 118.46 4.44E-09 1456180000 33863 28484 17615.3 21357.1 31611 31581 31202 41292 27948 TRUE FALSE 29387.91875 28296.88673 26134.118 26206.55598 30982.00295 32795.94151 28176.03484 32462.02713 24644.01928 1.192496988 1.148225312 1.060464923 1.063404296 1.257181412 1.330787041 1.143321409 1.317237532 1 14.58894995 3.232778829 24.99907653 1.224222264 1.114461768 0.168597925 0.100369753 209.3077413 904996.4339 0.029044909 0.033824168 1709.144687 -3.232778829 -0.109760496 EDIHDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EDIHDK 6 0 P54851 P54851 EMP2 Epithelial membrane protein 2 0 ; 83.843 0.056526 1006450000 3873600 2498300 3271600 4572000 1830160 2844800 1894910 4898000 6967200 FALSE TRUE 3361693.946 2481888.503 4853756.703 5610142.479 1793743.397 2954241.297 1711141.92 3850600.816 6143545.553 0.547191181 0.403983088 0.790057901 0.913176671 0.291972019 0.480869112 0.278526773 0.626771753 1 22.55064007 1.272606337 4.199887848 1.030353735 0.532924569 0.353387975 0.198430225 0.239507109 7.491721799 0.333969788 0.052105746 18.73295703 -1.272606337 -0.497429166 EDINAIEMEEDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDINAIEMEEDKR 13 1 P49756;P49756-2;P49756-3;H0YE46 P49756 RBM25 RNA-binding protein 25 0 202.4 1.51E-07 171320000 170670 133620 110340 109480 128430 121920 154250 175620 173190 FALSE TRUE 148115.5271 132742.2414 163700.7931 134339.1073 125874.4943 126610.3413 139290.8587 138065.0297 152715.6755 0.969877693 0.869211631 1.071931827 0.879668095 0.824240824 0.829059236 0.912092739 0.904065868 1 17.22048863 4.770568631 21.86601826 0.909500457 0.969878273 0.056157715 0.07517648 7789.488715 5320826.468 0.018580902 1.862750783 58961.51458 -4.770568631 0.060377816 EDIQGALHNYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EDIQGALHNYR 11 0 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 0 ;;; 154.15 3.21E-05 2141620000 1754160 1783700 1132150 1301310 1676760 1739770 1703940 1904560 1753100 FALSE TRUE 1522343.312 1771982.757 1679661.527 1596792.325 1643395.757 1806700.078 1538692.161 1497284.665 1545850.515 0.984793353 1.146283382 1.086561417 1.032953904 1.063101342 1.168741777 0.99536931 0.968583088 1 20.55996939 2.033048509 24.40563847 0.982026078 1.080846604 0.413022013 0.052045707 122.2312389 90264.63381 0.020242569 0.013647431 107.9067244 -2.033048509 0.098820527 EDIQSVMTEIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EDIQSVMTEIRR 12 1 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ; 191.06 9.37E-06 176020000 332346 324421 108268 139856 295780 275438 307959 320486 68997 FALSE TRUE 288425.634 322289.8571 160626.7669 171612.4424 289894.5567 286034.2781 278093.1836 251952.5629 60840.25326 4.740704034 5.297312878 2.640139683 2.820705588 4.764847961 4.701398544 4.570874851 4.141214893 1 15.89273854 4.261818748 24.99625012 3.693351424 5.019009408 0.209253466 1.174483861 418.0772455 449312.9786 0.297426416 0.785851728 18273.37421 -4.261818748 1.325657984 EDITQSAQHALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EDITQSAQHALR 12 0 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ; 234.63 5.01E-16 4937900000 3442900 3182000 1346520 2209010 3282100 3259600 2865040 3257800 2970410 FALSE TRUE 2987912.042 3161097.232 1997701.576 2710599.483 3216792.631 3384998.921 2587188.862 2561144.822 2619251.514 1.140750335 1.206870442 0.762699407 1.034875601 1.228134303 1.292353523 0.98775885 0.977815536 1 21.32072317 2.070964637 24.999993 0.985935434 1.104572879 0.138840054 0.143101185 98.21942035 34599.50675 0.062342499 0.0420313 117.7510088 -2.070964637 0.118637444 EDKHECPFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDKHECPFAR 10 1 F8W9E7;Q96BJ8-2;Q96BJ8;Q96BJ8-3 F8W9E7 ELMO3 Engulfment and cell motility protein 3 0 67.385 0.037933 59643000 90105 62108 54900 57840 81359 69063 93437 103810 73908 FALSE TRUE 78197.39595 61700.00846 81449.82363 70973.45603 79740.11508 71719.8983 84375.49412 81611.03935 65170.68044 1.199886136 0.946744887 1.249792439 1.089039666 1.223558118 1.100493317 1.294684873 1.252266185 1 15.99193544 4.217388519 24.99940373 1.182688834 1.073315293 0.123514317 0.107754403 372.9770214 440401.3679 0.026085574 0.054384584 16496.37495 -4.217388519 -0.109373541 EDKLECSEELGDLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EDKLECSEELGDLVK 15 1 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ;;; 212.95 5.62E-10 1880400000 2692500 1801370 2209670 2009580 1613860 1120580 2491140 2878310 4888330 FALSE TRUE 2336679.303 1789536.682 3278273.803 2465885.854 1581747.343 1163689.438 2249549.626 2262805.806 4310437.196 0.542097981 0.415163613 0.760543224 0.572073259 0.36695752 0.269970164 0.52188433 0.524959697 1 22.03940277 1.226978149 4.123273221 1.059470682 0.491989017 0.596178621 0.13037634 0.189242701 5.793129321 0.327959666 0.034894142 16.86468171 -1.226978149 -0.567481665 EDKNGHDGDTHQEDDGEKS(ph)D ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EDKNGHDGDTHQEDDGEKSD 20 2 K7EQH5;Q08117;Q08117-2 K7EQH5 AES Amino-terminal enhancer of split 1 EDKNGHDGDTHQEDDGEKS(1)D;EDKNGHDGDTHQEDDGEKS(1)D;EDKNGHDGDTHQEDDGEKS(1)D;EDKNGHDGDTHQEDDGEKS(1)D 280.36 5.45E-45 2482280000 1662000 1132700 1059212 768628 1009687 754692 1696020 1800930 674026 TRUE FALSE 1442362.489 1125259.219 1571450.466 943156.7351 989596.2041 783725.4896 1531540.241 1415815.134 594343.4141 2.426816643 1.893281211 2.644010901 1.58688851 1.665024261 1.318640824 2.576860793 2.38214995 1 19.18093724 3.7300703 24.96641508 1.849709347 2.278560756 0.207542783 0.497040067 1279.038972 3761111.601 0.143170039 0.216116782 5371.187341 -3.7300703 0.428851409 EDKPAETK ddPTM_MDA-MB-175_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 77.677 0.029725 110080000 279820 218860 237590 242240 142990 150330 272830 316710 531060 FALSE TRUE 242841.078 217422.2942 352489.3187 297244.2944 140144.7788 156113.2924 246370.9886 248984.0311 468278.6918 0.518582379 0.464301063 0.752734055 0.634759385 0.299276438 0.333376887 0.526120434 0.531700535 1 18.83700787 1.232168613 4.604949727 1.042541469 0.504879031 0.586437101 0.130117418 0.161542033 7.446087304 0.285931739 0.035257622 17.06744895 -1.232168613 -0.537662438 EDKS(ph)PSEESAPTTSPESVSGSVPSSGSSGR ddPTM_MDA-MB-175_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(0.78)PS(0.213)EES(0.006)APTTSPESVSGSVPSSGSSGR;EDKS(0.963)PS(0.037)EESAPTTSPESVSGSVPSSGSSGR;EDKS(0.93)PS(0.07)EESAPTTSPESVSGSVPSSGSSGR 228.73 2.64E-35 2682620000 374767 255549 282775 280250 311286 229498 374995 394839 429008 TRUE FALSE 325240.5914 253870.2818 419525.9358 343885.0459 305092.0176 238326.9366 338628.0426 310405.7525 378291.163 0.859762594 0.671097574 1.109002739 0.909048584 0.806500515 0.630009262 0.895151872 0.820547195 1 18.52913755 1.234812942 24.39397623 1.00000032 0.837580251 0.131583986 0.131082127 178.7093225 1162995.258 0.229372198 0.031823866 17.17168615 -1.234812942 -0.162420069 EDKSPSEESAPTTS(ph)PESVSGSVPSSGSSGR ddPTM_MDA-MB-175_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(0.005)T(0.029)S(0.966)PESVSGSVPSSGSSGR 242.67 6.68E-46 320360000 146100 133480 114970 131790 150960 118130 172260 193980 132560 TRUE FALSE 126792.5148 132603.1611 170569.8766 161714.9338 147956.1913 122674.5375 155554.2517 152498.8866 116888.9078 1.084726662 1.134437506 1.459247757 1.383492556 1.265784702 1.049496824 1.330787109 1.304648058 1 16.83477851 2.968926451 24.65062884 1.201548803 1.276792315 0.074707215 0.146402321 1954.225311 1550285.561 0.049474591 0.049537609 930.9502023 -2.968926451 0.075243512 GRYPDHSVDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GRYPDHSVDRR 11 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 ;;;;; 203.61 2.03E-08 334096000 320422 322664 183557 163830.1 280198 327680 286561 306080 87470.8 FALSE TRUE 278077.4209 320544.3989 272325.7792 201030.2282 274622.608 340286.0616 258770.3583 240627.1739 77130.10167 3.60530344 4.155892343 3.530732791 2.606378364 3.560511422 4.411845107 3.354985313 3.119756991 1 16.23500639 1.180898667 2.234659177 2.11E-18 3.609937225 0.745500919 0.47490496 0.415263695 1.863761801 3.200934365 0.132806426 15.16696439 -1.180898667 3.609937225 EDLAAFVEELDKVESQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDLAAFVEELDKVESQER 18 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 0 101.67 0.00056766 68558000 26098 14835 15480 19911 15317 11583 14936 18901 27382 FALSE TRUE 22649.08318 14737.54791 22966.17978 24432.09687 15012.22167 12028.60551 13487.50902 14859.16824 24144.93115 0.938047122 0.610378543 0.951180172 1.011893416 0.621754586 0.498183467 0.558606232 0.615415639 1 14.55943273 3.215343953 24.94280372 0.637825502 0.864004045 0.287494153 0.16897919 287.2250293 308578.9837 0.051674606 0.058629349 1641.889605 -3.215343953 0.226178542 EDLAAFVEELDKVESQEREDVLAGMSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDLAAFVEELDKVESQEREDVLAGMSGK 28 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 0 178.5 9.45E-18 39704000 59837 39818 28501 24051 32386 22102 46355 53744 15688 FALSE TRUE 51929.38884 39556.43294 42284.17893 29512.14715 31741.58196 22952.27824 41859.49923 42251.26384 13833.38251 3.753918378 2.85949101 3.056676767 2.133400643 2.294564033 1.659194938 3.025977139 3.054297371 1 13.75586634 4.673123241 1.022371646 2.325780723 4.295255923 0.379916341 0.627564813 2.109433021 1.938624952 0.208355996 4.454798502 47111.0996 -4.673123241 1.9694752 EDLAYMNHIMVS(ph)VSPPEEHAMPIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDLAYMNHIMVSVSPPEEHAMPIGR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 1 EDLAYMNHIMVS(0.859)VS(0.141)PPEEHAMPIGR 86.551 0.027711 214400000 56914 58254 40143 56771 59116 56487 58566 69042 68401 TRUE FALSE 49392.6707 57871.32564 59556.28907 69661.72324 57939.70726 58660.09144 52886.27833 54277.90559 60314.7117 0.818915805 0.959489385 0.987425578 1.154970674 0.960623132 0.972566888 0.876838782 0.899911548 1 15.88022232 0.941520865 20.43244344 1.694942037 0.955656972 0.026322014 0.087609296 487.8225821 253871.7644 39704.3568 0.021857385 8.740189834 -0.941520865 -0.739285065 EDLAYMNHIMVSVS(ph)PPEEHAMPIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EDLAYMNHIMVSVSPPEEHAMPIGR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 1 EDLAYMNHIMVS(0.327)VS(0.673)PPEEHAMPIGR;EDLAYMNHIMVS(0.435)VS(0.565)PPEEHAMPIGR;EDLAYMNHIMVS(0.042)VS(0.958)PPEEHAMPIGR 167.98 1.98E-11 278438000 184536 169174 136073 155599 188078 177300 165615 197009 217558 TRUE FALSE 160149.1 168062.6849 201878.3579 190930.1311 184335.6158 184120.8457 149553.6828 154880.1585 191838.5411 0.834811916 0.876063193 1.052334723 0.995264716 0.960889375 0.959769839 0.779581006 0.807346415 1 17.54953307 2.261194227 24.85687147 0.847411559 0.95099791 0.180064413 0.082332206 303.1846565 332965.1645 0.03177473 0.0245936 182.4711576 -2.261194227 0.103586351 EDLDVLGLTFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EDLDVLGLTFR 11 0 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 ;; 141.25 8.89E-05 253456000 176911 160906 160909 169289 158855 174185 166232 196810 360825 FALSE TRUE 153531.7631 159848.9979 238725.1306 207728.6549 155694.0963 180886.0097 150110.8462 154723.7131 318168.6796 0.482548324 0.50240331 0.750309964 0.652888446 0.489344509 0.568522363 0.471796427 0.486294607 1 18.2794323 1.233572337 24.99992629 1.00000069 0.550404019 0.714615573 0.089268424 92.82031079 465136.0775 0.189359541 0.023422753 17.12270354 -1.233572337 -0.449596671 EDLHILFSNHGEIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDLHILFSNHGEIK 14 0 P05455 P05455 SSB Lupus La protein 0 172.1 1.68E-06 389840000 620630 529600 238620 378650 562620 502360 610780 687330 623040 FALSE TRUE 538612.173 526121.0227 354017.4301 464628.2698 551424.9627 521686.1143 551546.6496 540349.8283 549384.921 0.980391257 0.957654647 0.644388691 0.845724468 1.00371332 0.94958215 1.003934816 0.983554167 1 19.06745779 3.242003252 24.91417762 0.986836165 0.849037153 0.341694354 0.090118906 99.30515665 718661.2886 0.027321771 0.033847355 1745.835227 -3.242003252 -0.137799012 EDLMGLAIGTHGANIQQAR ddPTM_MDA-MB-175_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 89.557 0.0023775 294820000 411510 356970 320670 298790 350160 338170 407110 442110 499430 FALSE TRUE 357127.9109 354625.0406 475747.0846 366634.8362 343192.5011 351179.6187 367628.5349 347568.217 440387.9544 0.810939326 0.805255995 1.080290866 0.83252694 0.779295841 0.797432389 0.834783357 0.789231889 1 18.74841548 EDLQELNDR ddPTM_MDA-MB-175_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 ;;; 161.63 0.00014979 3798530000 3078740 2935350 2491560 2991320 2753760 2549170 2562730 3103520 7533020 FALSE TRUE 2671876.708 2916067.493 3696486.75 3670544.925 2698965.564 2647238.219 2314196.839 2439856.4 6642474.957 0.402241141 0.439003159 0.556492388 0.552586942 0.406319268 0.398531908 0.348393762 0.367311343 1 22.66328945 1.23455375 24.99999198 1.000000821 0.432472827 0.866435893 0.06985399 46.61691209 290815.1077 0.145387644 0.019551475 17.16144092 -1.23455375 -0.567527995 EDLRLPEGDLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 EDLRLPEGDLGK 12 1 P63241;P63241-2;I3L397;I3L504 P63241 EIF5A Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A 0 ;;;;;;;; 182.33 1.55E-05 25524990000 39794580 29893490 22405780 26902880 27529220 22525510 34375240 41509670 34439490 FALSE TRUE 34535625.43 29697117.7 33241290.15 33011590.09 26981442.38 23392080.95 31041534.52 32633150.1 30368092.73 1.13723393 0.977905263 1.094612377 1.087048515 0.888479979 0.770284824 1.022175966 1.074586751 1 24.85605297 3.259037022 24.99294407 0.962829899 1.068779882 0.307722556 0.09063965 396.4018642 483834.3993 0.029346966 0.03784203 1815.670436 -3.259037022 0.105949984 EDLRPSAPQQEGEASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EDLRPSAPQQEGEASK 16 1 O76070 O76070 SNCG Gamma-synuclein 0 ;;; 197.49 3.94E-11 2138020000 1647750 1514850 1349330 1520750 1425840 1227860 1767700 2064000 2666750 FALSE TRUE 1429995.663 1504898.851 2001870.501 1866059.531 1397468.574 1275096.569 1596268.726 1622629.662 2351489.853 0.608123255 0.639976757 0.851320068 0.793564781 0.59429071 0.542250509 0.678832921 0.690043234 1 21.16514368 1.23606211 5.242326348 1.01883604 0.675800729 0.55657345 0.091311252 0.13947078 10.71952041 0.174188133 0.024646916 17.22114843 -1.23606211 -0.343035311 EDLRVECSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDLRVECSK 9 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 112.11 0.0018388 126760000 634530 522900 332800 398470 491450 447960 622640 736280 394880 FALSE TRUE 550675.2528 519465.0355 493743.1931 488948.7037 481671.1065 465193.3111 562256.4686 578832.2517 348197.7362 1.581501531 1.491867928 1.417996563 1.404227118 1.383326358 1.336003261 1.614761988 1.662366499 1 18.4095473 4.597343052 2.658403968 1.434412229 1.59030212 0.079230134 0.178541358 1.137175902 12.63503218 0.046189893 0.335764534 39567.90464 -4.597343052 0.155889891 EDLSKS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.077)KS(0.923)PK 51.286 0.090962 227080000 666370 540870 282860 255100 443760 315120 739850 860300 77290 TRUE FALSE 578307.5161 537316.9894 419652.0421 313024.354 434930.0442 327242.8703 668099.4609 676331.5399 68152.86425 8.48544698 7.883997177 6.157511452 4.5929743 6.381684013 4.801601135 9.802954993 9.923743445 1 16.05648667 4.367994755 4.676704263 6.549283236 8.345671524 0.083842401 2.579414434 0.628862933 22.35281532 0.67726726 1.943095679 23334.29881 -4.367994755 1.796388288 EDLTEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 132.29 0.007872 3671520000 7144250 6339090 4718350 5678250 6426570 6322070 6599580 7404790 7508280 FALSE TRUE 6200119.261 6297448.1 7000159.842 6967583.449 6298693.83 6565284.124 5959553.747 5821333.283 6620659.692 0.936480585 0.951181362 1.057320595 1.05240018 0.95136952 0.991635944 0.900145004 0.879267861 1 22.65854355 2.246028368 24.85960983 0.91554006 0.992428932 0.25062916 0.050565387 183.8228646 611934.6397 0.019838501 0.015056373 176.209114 -2.246028368 0.076888872 EDLVGPEVGAS(ph)PQSGRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EDLVGPEVGASPQSGRK 17 1 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 EDLVGPEVGAS(0.999)PQS(0.001)GRK;EDLVGPEVGAS(0.964)PQS(0.036)GRK;EDLVGPEVGAS(0.981)PQS(0.019)GRK;EDLVGPEVGAS(0.998)PQS(0.002)GRK 200.29 7.67E-12 1201060000 1085310 952030 598200 702950 843760 654910 1092750 1285960 674580 TRUE FALSE 941883.5337 945776.0522 887491.5209 862565.5414 826970.8268 680104.8115 986775.2732 1010967.461 594831.9209 1.583444836 1.589988733 1.492003858 1.450099618 1.390259665 1.143356279 1.658914457 1.699585086 1 19.18212254 4.046652525 2.25271269 1.428721606 1.591426182 0.115410032 0.209138034 0.872990165 8.767564775 0.060833858 0.161436724 11134.03354 -4.046652525 0.162704575 EDLYEAADKWVAAVGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDLYEAADKWVAAVGK 16 1 Q9H7Z7;A6NHH0 Q9H7Z7 PTGES2 Prostaglandin E synthase 2;Prostaglandin E synthase 2 truncated form 0 123.36 0.00078986 0 316810 273330 248780 304400 273440 223070 324460 386110 415260 FALSE TRUE 274942.7558 271534.4772 369090.8401 373518.6725 267999.079 231651.6472 292993.9191 303543.3812 366168.4359 0.750864162 0.741556209 1.007981038 1.020073376 0.731901094 0.632636854 0.800161594 0.828972002 1 18.48214791 1.237700802 4.612496571 1.014814961 0.815044154 0.192764837 0.119810135 0.381022856 17.77059144 0.249069413 0.032680889 17.28625051 -1.237700802 -0.199770807 EDLYLKPIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EDLYLKPIQR 10 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;; 138.25 6.36E-05 14041090000 22307410 20296810 14207320 17366070 20187460 16811770 21901080 25505750 24642300 FALSE TRUE 19359429.25 20163478.92 21078027.47 21309301.62 19785769.04 17458529.67 19777116.63 20051543.85 21729115.37 0.890944197 0.927947529 0.970036153 0.980679667 0.910564867 0.803462515 0.910166673 0.922796143 1 24.37312611 1.234771839 4.0155056 1.009763183 0.914559485 0.241630585 0.047802862 0.41596807 11.73804954 0.117357968 0.013162764 17.17006105 -1.234771839 -0.095203698 EDMAALEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 ;;;;;; 149.65 0.0011673 3766970000 6909350 5387790 4075330 4855840 5109270 4354670 6215750 7174930 7589750 FALSE TRUE 5996261.891 5352397.253 6046173.219 5958432.689 5007605.523 4522196.973 5612947.522 5640627.055 6692498.401 0.895967624 0.799760707 0.903425426 0.890315146 0.748241572 0.675711327 0.838692396 0.842828301 1 22.67411346 1.18454027 2.663208906 1.058884485 0.818960863 0.383479284 0.070322175 0.687535449 4.916114601 0.396788241 0.019579838 15.29467558 -1.18454027 -0.239923622 EDMAALEKDYEEVGVDSVEGEGEEEGEEY ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDMAALEKDYEEVGVDSVEGEGEEEGEEY 29 1 P68363;P68363-2 P68363 TUBA1B Tubulin alpha-1B chain 0 213.05 2.56E-26 50602000 471000 443030 144620 120290 327960 299560 464290 505930 29889 FALSE TRUE 408756.1566 440119.7068 214558.7157 147603.683 321434.2376 311084.267 419263.2273 397740.8067 26355.55647 15.50929714 16.69931376 8.140929066 5.600476817 12.19607099 11.80336554 15.90796338 15.09134543 1 14.68581953 4.245864358 24.98758727 10 16.10430822 0.252761394 4.389643517 248.7993011 851171.853 1.172852457 2.970922776 17614.25821 -4.245864358 6.10430822 EDNS(ph)EGEEILEEVGGDLEEEDDHHMEFCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 EDNSEGEEILEEVGGDLEEEDDHHMEFCR 29 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR 238.85 1.54E-45 909279000 335922.9 258253.1 234549.8 336994.6 267823.2 249890 202513.2 268974.8 600881 TRUE FALSE 291529.8376 256556.6184 347978.8678 413514.3746 262494.0423 259503.43 182873.501 211456.6322 529845.5327 0.550216657 0.484210213 0.656755311 0.780443259 0.495416166 0.489771856 0.345144933 0.399091092 1 19.0152123 1.229656263 24.99416749 1.000000921 0.519565602 0.596406015 0.122689887 281.3759613 789751.0217 0.401704026 0.033984361 16.96900054 -1.229656263 -0.480435319 EDPDGEHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDPDGEHAR 9 0 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 87.258 0.014287 0 114780 93713 82599 104800 79711 109350 100380 103140 144360 FALSE TRUE 99611.53218 93097.39313 122544.1527 128596.4418 78124.90705 113556.7653 90645.16305 81084.31364 127293.9253 0.782531704 0.731357706 0.962686573 1.010232354 0.613736334 0.892083146 0.712093392 0.636984942 1 16.95780405 3.238584334 24.9999999 0.755868971 0.86817635 0.11183991 0.137263804 1.338023787 1407367.979 0.040668663 0.049166654 1732.145355 -3.238584334 0.112307379 EDQDKVAVLSQNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EDQDKVAVLSQNR 13 1 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 ;;; 160.78 3.95E-05 2079830000 2864970 2256320 1287390 1497250 2167700 1783850 2826100 3204700 808350 FALSE TRUE 2486356.956 2241498.085 1909976.11 1837223.497 2124567.011 1852475.864 2552025.257 2519399.844 712787.7839 3.488214882 3.144692061 2.679585921 2.577518215 2.980644533 2.598916404 3.580343708 3.534572142 1 19.44311309 1.23074068 24.99999725 0.999996257 3.075224847 0.748787835 0.377357774 161.8455851 517370.3266 1.079387013 0.10211826 17.01142441 -1.23074068 2.07522859 EDQEAAELLS(ph)EPEEESER ddPTM_MDA-MB-175_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 228.15 2.71E-19 362230000 293731 313980 281198 292798 361490 335680 312927 384480 559490 TRUE FALSE 254913.7041 311917.4447 417186.2934 359282.261 354297.0562 348593.8268 282579.3877 302261.944 493347.7296 0.51670189 0.632246641 0.845623215 0.728253602 0.718148752 0.706588489 0.572779342 0.612675251 1 18.91224534 7.999991648 0.036592864 1.148256403 5.26E-08 0.120492472 0.130494358 7892.75479 28.50546858 293.0363507 678.9620505 99998076.95 -7.999991648 -1.14825635 EDQIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EDQIYR 6 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;; 178.24 0.0081811 25332270000 13744410 13090480 9734180 10439520 11648270 14433390 14220900 14497070 16030410 FALSE TRUE 11928051.39 13004487.77 14441662.01 12809972.57 11416492.22 14988651.85 12841759.31 11396984.4 14135313.19 0.843847691 0.919999974 1.021672588 0.906239034 0.807657536 1.060369279 0.90848778 0.806277459 1 23.75280051 1.994394467 24.9742197 0.879725764 0.929324345 0 0.087108148 749.4141271 3338855.953 0.035804909 0.023292449 98.71757249 -1.994394467 0.049598581 EDQKMS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EDQKMSPK 8 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 EDQKMS(1)PK;EDQKMS(1)PK;EDQKMS(1)PK 62.466 0.048122 1834190000 4793200 3809800 3610000 3433650 2917060 2427440 5489300 6360300 4789600 TRUE FALSE 4159766.476 3784773.173 5355808.075 4213312.713 2859016.213 2520825.188 4956948.531 5000199.341 4223378.944 0.984938015 0.896148137 1.268133441 0.997616545 0.676949961 0.596874025 1.17369258 1.183933388 1 22.00996627 EDQTEYLEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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 ;;;;;;;;; 297.13 6.05E-32 75010670000 13293030 11181940 9282530 11538410 11263500 10351100 11713880 13383020 18281430 FALSE TRUE 11536322.41 11108485.1 13771592.56 14158382.34 11039378.39 10749313.52 10577869.72 10521165.32 16120220.17 0.71564298 0.689102567 0.854305488 0.878299564 0.684815609 0.666821756 0.65618643 0.652668835 1 23.94236811 3.167037819 24.99997772 0.713212488 0.782549389 0.034440919 0.115301122 125.7875218 43964.88363 0.035309713 0.040037465 1469.054199 -3.167037819 0.069336901 EDQTEYLEERR ddPTM_MDA-MB-175_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 ; 219.42 1.59E-11 1402880000 1282550 1086270 557790 330520 813820 767250 1173500 1195740 178657 FALSE TRUE 1113057.768 1079134.221 827539.1097 405569.6177 797626.5742 796766.604 1059694.151 940040.3063 157536.373 7.065401766 6.850063896 5.253003443 2.574450649 5.063126433 5.057667565 6.726663376 5.967131834 1 17.26532544 4.191841753 4.191824862 4.709247581 7.002495681 0.275683199 1.642593327 0.294779498 10.78377258 0.435085726 1.044742425 15553.98776 -4.191841753 2.293248099 EDRMS(ph)S(ph)DTMVGSCDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDRMSSDTMVGSCDR 15 1 Q0VG73 Q0VG73 Putative uncharacterized protein LOC152225 2 EDRMS(0.997)S(0.997)DT(0.004)MVGS(0.003)CDR 45.347 0.083674 282570000 354170 292520 219760 266890 322390 294670 293970 372530 369520 TRUE FALSE 307365.5371 290598.4169 326036.6711 327491.4537 315975.0697 306006.1456 265460.8346 292867.3585 325835.7666 0.943314297 0.891855489 1.000616582 1.005081355 0.969737218 0.939142283 0.814707475 0.898818941 1 18.31378545 2.466157533 24.99567351 0.896345002 0.961912396 0.187595101 0.053843214 323.7439574 738082.8156 0.020630784 0.015994569 292.521326 -2.466157533 0.065567394 EDS(ph)CHRLSPVKGEFHQEFQPEPSLLGDSTNSGEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EDSCHRLSPVKGEFHQEFQPEPSLLGDSTNSGEER 35 2 Q9Y2L9-2;Q9Y2L9;Q9Y2L9-3 Q9Y2L9-2 LRCH1 Leucine-rich repeat and calponin homology domain-containing protein 1 1 EDS(0.499)CHRLS(0.499)PVKGEFHQEFQPEPS(0.002)LLGDSTNSGEER;EDS(0.5)CHRLS(0.5)PVKGEFHQEFQPEPSLLGDSTNSGEER 221.72 6.14E-37 161499000 80383 85133 36779 70014 100166 97252 98068 123331 111817 TRUE FALSE 69760.18289 84573.75572 54565.44742 85911.7488 98172.89257 100993.3474 88557.38045 96957.62541 98598.12164 0.707520404 0.857762342 0.553412646 0.87133251 0.99568725 1.024292813 0.898164985 0.98336179 1 16.58927254 3.498825883 6.249219737 0.973646698 0.718884429 0.7128147 0.079185821 0.090757665 13.23983004 0.021092034 0.029993403 3153.739978 -3.498825883 -0.25476227 EDS(ph)GTFSLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EDSGTFSLGK 10 0 O75569;G5E9Q4 O75569 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 1 EDS(0.85)GT(0.15)FSLGK;EDS(0.851)GT(0.149)FSLGK;EDS(0.946)GT(0.054)FSLGK;EDS(0.999)GT(0.001)FSLGK;EDS(0.655)GT(0.343)FS(0.002)LGK 257.13 3.61E-17 2588370000 7567140 3941310 3139500 4429250 4177750 2310560 6688540 6236990 7233880 TRUE FALSE 6567123.276 3915419.275 4657772.701 5434978.909 4094620.949 2399448.738 6039886.42 4903258.225 6378698.947 1.029539618 0.613827257 0.730207326 0.852051328 0.641921022 0.376165854 0.946883756 0.768692529 1 22.60483076 1.188453199 1.404758788 1.1260607 0.719964702 0.162782098 0.181895469 2.627948181 4.144094252 1.590359803 0.052425889 15.43310104 -1.188453199 -0.406095999 EDS(ph)LPEESSAPDFANLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDSLPEESSAPDFANLK 17 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 EDS(1)LPEESSAPDFANLK 150.39 3.03E-07 48790000 111250 57298 44796 47348 58740 43675 94555 79105 66705 TRUE FALSE 96548.03063 56921.60567 66459.49543 58099.08707 57571.18892 45355.20551 85385.07065 62189.01135 58819.21089 1.641437027 0.967738343 1.129894373 0.987756996 0.978782069 0.771095104 1.451652774 1.057290814 1 15.84399981 4.743786832 24.50909939 1.053777062 1.641437354 0.545630245 0.17136638 340.5441857 1596964.489 0.041170678 0.337283798 55435.35485 -4.743786832 0.587660292 EDSARPGAHAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EDSARPGAHAK 11 1 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ;;; 84.309 0.0096482 2846300000 4902840 3757650 2117050 2806730 2974800 3017930 4093690 4542560 3286870 FALSE TRUE 4254917.272 3732965.75 3140862.461 3444040.945 2915607.3 3134031.72 3696684.574 3571168.894 2898299.973 1.468073461 1.287984606 1.083691298 1.188296925 1.005971544 1.081334489 1.275466518 1.232159862 1 21.46677549 4.54417659 2.805993677 1.138377218 1.473632749 0.60388596 0.091023006 0.234251589 3.154223227 0.024616326 0.144014441 35008.74882 -4.54417659 0.33525553 EDSGLFS(ph)PIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EDSGLFSPIR 10 0 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 EDSGLFS(1)PIR;EDSGLFS(1)PIR;EDSGLFS(1)PIR;EDSGLFS(1)PIR 187.93 1.23E-06 1445820000 1227150 1355510 983790 1229200 1671900 1728490 1682550 1874420 1770020 TRUE FALSE 1064979.018 1346605.566 1459554.135 1508308.647 1638632.461 1794986.129 1519376.56 1473589.87 1560770.252 0.682341951 0.862782696 0.935149893 0.966387362 1.049887041 1.150064288 0.973478677 0.944142719 1 20.57382676 4.778160663 1.071768679 1.012707465 0.49893379 0.783979881 0.056458547 0.991218513 0.886282133 0.020041197 0.59257985 60001.30042 -4.778160663 -0.513773675 EDSGT(ph)FSLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDSGTFSLGK 10 0 O75569;G5E9Q4 O75569 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 1 EDS(0.285)GT(0.712)FS(0.004)LGK 130.1 0.0031929 408580000 412100 244110 175630 241030 232110 135450 334380 336260 429790 TRUE FALSE 357639.9409 242506.4253 260565.2554 295759.5454 227491.4651 140660.8491 301951.8791 264353.4158 378980.7158 0.943689021 0.639891201 0.687542254 0.780407902 0.600271876 0.37115569 0.796747345 0.697537908 1 18.53176491 0.968021332 1.91572323 1.376218117 0.675325018 0.296676892 0.148404005 2.602488071 4.753132497 4.275557896 0.040079386 9.290120169 -0.968021332 -0.700893099 EDSHPFDLGLYNEAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EDSHPFDLGLYNEAVK 16 0 P35244;B5MC59 P35244 RPA3 Replication protein A 14 kDa subunit 0 ; 205.42 2.27E-11 1126030000 1023610 847040 607250 769230 769700 654680 941150 1170680 1067330 FALSE TRUE 888337.345 841475.7385 900918.1311 943895.4284 754384.4759 679865.9632 849877.4179 920339.1922 941151.4633 0.943883508 0.894091728 0.957250949 1.00291554 0.801554803 0.72237678 0.90301875 0.977886374 1 19.84406739 1.717621588 4.040047937 0.992591997 0.886176107 0.218221459 0.079066395 0.297966377 11.15904633 0.05865138 0.023004064 52.19412096 -1.717621588 -0.10641589 EDSLDEEFFHHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EDSLDEEFFHHK 12 0 Q5JRA6-2;Q5JRA6;A0A0A0MRH6 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 0 ; 208.72 3.68E-08 204656000 509020 529220 423840 565030 663180 508050 446970 855870 761170 FALSE TRUE 441751.7173 525743.519 628810.4417 693328.6974 649984.0155 527595.0123 403622.9182 672848.8609 671185.3497 0.658166507 0.783306011 0.936865565 1.032991405 0.968412102 0.786064554 0.601358356 1.002478468 1 19.3563517 4.503402589 3.221561767 0.898811536 0.665658063 0.286587388 0.127900763 0.374018665 7.391599902 0.034872815 0.161735991 31871.50626 -4.503402589 -0.233153473 EDSQRPGAHLTVK ddPTM_MDA-MB-175_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 ;;;;;; 98.942 0.0018555 24915530000 32856510 29271690 11281580 22645790 29213590 24482280 32139860 37031020 34030140 FALSE TRUE 28514438.96 29079402.34 16737389.82 27787862.74 28632296.71 25424129.15 29022941.32 29112224.55 30007135.62 0.950255277 0.969082911 0.557780324 0.926041829 0.954182934 0.847269445 0.967201325 0.970176725 1 24.83880227 2.214253466 0.89697605 1.005544493 0.849998642 0.159961494 0.118344699 1.434038794 2.137630363 0.170153561 0.055446214 163.7772089 -2.214253466 -0.155545851 EDSQRPGAHLTVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDSQRPGAHLTVKK 14 2 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8W646;F8VYN5 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 57.159 0.071483 497000000 445660 352590 238810 148820 322710 302670 478890 559440 49544 FALSE TRUE 386764.9018 350273.8131 354299.3148 182611.8556 316288.7024 314313.9108 432447.3215 439808.1096 43686.96476 8.853096203 8.01781069 8.109954919 4.180007848 7.239887323 7.1946841 9.898772411 10.06726176 1 15.41491525 3.974818081 24.73189794 7.133949647 8.342562588 0.064037623 2.645345915 2491.89283 2447369.748 0.719283742 1.2532641 9436.655063 -3.974818081 1.20861294 EDSVKPGAHLTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EDSVKPGAHLTVK 13 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 123.38 0.00013461 6795690000 14046590 11486370 5168670 10048850 11404730 8588100 14918520 18292920 16620160 FALSE TRUE 12190297.54 11410915.28 7668256.1 12330594.98 11177798.19 8918489.764 13471724.23 14381121.41 14655343.62 0.831798821 0.778618064 0.523239598 0.841371946 0.762711437 0.608548663 0.919236326 0.981288586 1 23.80492346 2.088704862 5.897295982 0.978157173 0.725409366 0.588057875 0.096786109 0.137880892 7.31856064 0.039858506 0.026524585 122.660537 -2.088704862 -0.252747807 EDSYANYFIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EDSYANYFIR 10 0 Q9Y3L3;Q6ZT62-2;Q6ZT62;Q9Y3L3-2 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 0 ;; 111.61 0.004027 391420000 344709 337586 233437 257377 337228 365164 312904 371060 356086 FALSE TRUE 299154.8323 335368.3753 346327.914 315818.3816 330517.8226 379212.0954 282558.6182 291711.7066 313989.9187 0.952752985 1.068086443 1.102990553 1.005823317 1.052638326 1.207720607 0.899897103 0.929048002 1 18.26035871 2.195730745 24.99999739 0.938283559 1.063617571 0.405985586 0.069486549 132.4146489 77290.10832 0.027772475 0.018724356 156.938951 -2.195730745 0.125334011 EDTEEHHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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 ;;;;;;;;; 196.79 2.91E-05 12081973000 12540780 9858520 7706185 9100448 9727084 9892520 10032182 11579852 15199241 FALSE TRUE 10883484.15 9793758.733 11432921.84 11166843.81 9533534.059 10273091.65 9059262.534 9103590.764 13402404.04 0.812054622 0.730746417 0.85305008 0.833197072 0.711330149 0.766511113 0.6759431 0.679250583 1 23.67598847 3.244443163 24.99962336 0.748882852 0.805067218 0.02430565 0.096387932 416.1327225 1768468.721 0.027775335 0.034900115 1755.671113 -3.244443163 0.056184365 EDTEEYNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EDTEEYNLR 9 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;;; 270.4 1.09E-20 6464740000 3854710 3386240 2764650 3246900 3089520 2836010 3156700 3917670 6971190 FALSE TRUE 3345300.307 3363995.566 4101643.987 3984158.271 3028044.597 2945113.14 2850563.72 3079906.758 6147063.86 0.544211087 0.547252419 0.667252542 0.648140049 0.492600153 0.479108922 0.463727689 0.501037052 1 22.55146604 1.235529232 24.9998513 1.000000625 0.540984073 0.818372516 0.067667258 39.53030401 325947.7304 0.128712402 0.018752748 17.2000311 -1.235529232 -0.459016552 EDTHHLVNYIPQGSIDSLFEGTWYLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EDTHHLVNYIPQGSIDSLFEGTWYLVR 27 0 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 ;;; 184.06 8.30E-18 2446850000 756753 660855 431935 567983 617103 637594 669332 797674 686500 FALSE TRUE 656746.1737 656513.8 640820.2107 696952.2212 604823.8576 662122.6538 604420.2857 627097.6226 605342.7521 1.084916225 1.084532354 1.058607225 1.151334874 0.999142809 1.093797938 0.998476125 1.035938104 1 19.20739272 2.503739432 0.953002825 1.010290692 1.087516059 0.361531104 0.039732978 0.645740891 1.242484542 0.033773833 0.017853116 318.962357 -2.503739432 0.077225367 EDTLLLIGHLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EDTLLLIGHLER 12 0 Q92621 Q92621 NUP205 Nuclear pore complex protein Nup205 0 ; 146.5 6.48E-05 160706000 249260 222854 172070 189736 239471 222957 230939 245688 289580 FALSE TRUE 216319.6595 221390.0574 255283.6275 232818.4587 234705.9956 231534.3001 208542.5713 193149.5331 255346.1823 0.847162301 0.867019258 0.99975502 0.911775757 0.919167827 0.906746668 0.816705264 0.756422248 1 17.96209496 2.251008543 21.52494578 0.834899288 0.911481855 0.069585147 0.072828243 67.69077291 117050.7851 0.027227401 0.020870843 178.2413828 -2.251008543 0.076582567 EDVETGLDPLSLLATECTGGKT(ph)PDSEDKLFSPVIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDVETGLDPLSLLATECTGGKTPDSEDKLFSPVIAR 36 2 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 EDVETGLDPLSLLATECT(0.018)GGKT(0.982)PDSEDKLFSPVIAR 266.86 6.30E-61 71496000 111200 76482 73431 71898 74579 45869 110340 120860 93754 TRUE FALSE 96504.63826 75979.58471 108942.4772 88223.53979 73095.02381 47633.61011 99639.24378 95015.02953 82670.50892 1.167340561 0.919065162 1.317791297 1.067170638 0.884172902 0.576186245 1.205257414 1.149321938 1 16.33508515 4.781671536 20.88462252 1.027606563 1.167344198 0.049860734 0.202496596 11573.59264 5605648.42 0.051520079 13.00022045 60488.32186 -4.781671536 0.139737634 EDVEVAES(ph)PLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EDVEVAESPLR 11 0 Q99567;J3KMX1 Q99567 NUP88 Nuclear pore complex protein Nup88 1 EDVEVAES(1)PLR;EDVEVAES(1)PLR;EDVEVAES(1)PLR 264.98 6.87E-21 1461440000 1249180 1172090 793120 953830 1142000 1081370 1119170 1319760 1295920 TRUE FALSE 1084097.698 1164390.464 1176675.485 1170411.68 1119276.434 1122971.004 1010633.066 1037539.594 1142717.814 0.948701145 1.018965881 1.029716585 1.024235087 0.979486292 0.982719434 0.884411754 0.907957837 1 20.12403775 2.402088215 5.801017236 0.924305732 1.002136925 0.416315698 0.037295963 0.175018811 10.13952298 0.01424721 0.010977748 252.3993398 -2.402088215 0.077831193 EDVFVHQTAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EDVFVHQTAIK 11 0 P67809;H0Y449;A0A0D9SEI8;P16989;P16989-3;P16989-2;Q9Y2T7 P67809;P16989;P16989-2;Q9Y2T7 YBX1;YBX3;YBX2 Nuclease-sensitive element-binding protein 1;Y-box-binding protein 3;Y-box-binding protein 2 0 ; 186.02 4.21E-06 1206460000 1979540 1707310 873450 2026560 1794380 1535040 1852940 2213300 5931700 FALSE TRUE 1717938.773 1696094.568 1295853.342 2486721.422 1758675.349 1594093.982 1673242.164 1740003.019 5230461.183 0.328448814 0.32427247 0.247751259 0.475430624 0.336237148 0.30477121 0.319903371 0.332667227 1 22.31850673 1.238511042 24.9952549 1.00000071 0.333617612 0.932369585 0.056397371 0.269936214 134706.822 0.074788951 0.013388362 17.31853062 -1.238511042 -0.666383098 EDVRPEEIADQELAEALQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EDVRPEEIADQELAEALQK 19 1 Q5TDH0;Q5TDH0-3 Q5TDH0 DDI2 Protein DDI1 homolog 2 0 ; 121.74 3.15E-05 74573000 103180 73257 53800 60782 74643 60553 85463 105453 93589 FALSE TRUE 89544.50158 72775.76994 79817.85995 74583.48209 73157.75034 62882.51309 77174.81141 82902.69659 82525.01504 1.085058894 0.881863153 0.967195946 0.903768173 0.886491815 0.761981238 0.935168705 1.00457657 1 16.33254388 1.810795455 4.588712713 1.00159936 0.909135978 0.162332116 0.079960218 0.348969179 12.58305958 0.04568723 0.021419817 64.68378943 -1.810795455 -0.092463381 EDVSLHGYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDVSLHGYK 9 0 Q12792;Q12792-3;Q12792-4;F8VS81;F8W1Q9 Q12792 TWF1 Twinfilin-1 0 141.48 0.00010661 552980000 869330 783350 405310 898810 759580 757710 848200 1054600 2311000 FALSE TRUE 754445.8379 778204.1223 601319.2717 1102898.548 744465.8441 786859.594 765941.6946 829081.9969 2037796.213 0.370226342 0.381885155 0.295083124 0.541221218 0.365328898 0.386132622 0.37586766 0.406852261 1 20.95857835 1.23810638 6.312236274 1.019188849 0.389596097 0.908889662 0.060690425 0.032936245 5.670075279 0.089130642 0.014268547 17.30240128 -1.23810638 -0.629592752 EDVSNFDDEFTSEAPILT(ph)PPREPR ddPTM_MDA-MB-175_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(0.999)PPREPR;EDVSNFDDEFTSEAPILT(1)PPREPR 147.55 2.85E-07 117878000 85728 73410 58090 60780 60389 76461 77370 82546 113870 TRUE FALSE 74398.82759 72927.76488 86182.5183 74581.02796 59187.37705 79402.50415 69866.66931 64894.18027 100408.4183 0.740962051 0.726311261 0.858319648 0.742776644 0.589466282 0.790795289 0.695824817 0.646302186 1 16.61552071 1.228900335 24.9659844 1.000000565 0.721660443 0.584721542 0.073118709 292.6777383 756339.4664 0.234034984 0.018328919 16.93949015 -1.228900335 -0.278340122 EDVSNFDPDFIKEEPVLT(ph)PIDEGHLPMINQDEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EDVSNFDPDFIKEEPVLTPIDEGHLPMINQDEFR 34 1 P24723-2;P24723 P24723-2 PRKCH Protein kinase C eta type 1 EDVSNFDPDFIKEEPVLT(1)PIDEGHLPMINQDEFR;EDVS(0.004)NFDPDFIKEEPVLT(0.996)PIDEGHLPMINQDEFR 166.52 3.28E-14 186878000 154005 115323 97741 108755 124179 135253 131980 182049 149920 TRUE FALSE 133652.8491 114565.4356 145008.8745 133449.485 121708.0809 140456.2704 119180.5999 143119.2381 132196.6284 1.011015566 0.866629028 1.096918101 1.00947722 0.920659493 1.062479975 0.90154039 1.082623966 1 17.01232586 EDYAGLKEEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDYAGLKEEFR 11 1 Q5TA02;P78417-3;P78417 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 108.56 0.001866 229900000 254470 269140 294960 347860 291680 246340 293540 325980 938900 FALSE TRUE 220841.1448 267372.0016 437603.6426 426846.9297 285876.1387 255816.8592 265072.536 256271.7138 827904.3116 0.266747185 0.322950367 0.528567899 0.515575198 0.345300942 0.308993268 0.320172914 0.309542673 1 19.65910451 1.235442078 24.98200129 1.000000876 0.366234737 0.83774148 0.087861315 36.80962541 294822.1649 0.162640138 0.023531637 17.19657976 -1.235442078 -0.633766139 EDYLHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EDYLHLK 7 0 Q9BYZ6-2;Q9BYZ6;Q9BYZ6-3 Q9BYZ6-2 RHOBTB2 Rho-related BTB domain-containing protein 2 0 75.311 0.043815 201900000 891240 661960 520660 486640 701290 665700 853680 921740 496150 FALSE TRUE 773460.3759 657611.5412 772452.9175 597139.0498 687335.7011 691309.9098 770890.245 724633.074 437495.7122 1.767926757 1.503126826 1.765623973 1.364902634 1.571068428 1.580152423 1.762052115 1.656320402 1 18.73890935 1.236496744 24.99962739 0.999999209 1.619561084 0.699675871 0.127938427 30.2684054 366546.0021 0.191974752 0.030108691 17.23839168 -1.236496744 0.619561875 EEADEYIDIGALNGIFVLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EEADEYIDIGALNGIFVLGR 20 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;; 265.95 2.53E-36 135198000 118303 111263 80270.2 85259.5 105807 101579 112916 138334 135029 FALSE TRUE 102668.9588 110532.106 119089.1372 104618.9726 103701.6477 105486.8099 101965.4237 108752.3506 119066.0254 0.862285933 0.928326159 1.000194109 0.878663516 0.870959178 0.885952222 0.856377151 0.913378524 1 16.86140228 1.25448783 4.566314354 1.006671527 0.89939455 0.368567162 0.041724925 0.216776428 9.517678729 0.07265218 0.01101062 17.96750731 -1.25448783 -0.107276977 EEAEKLSADCGMKY(ph)IETSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEAEKLSADCGMKYIETSAK 20 2 Q14964 Q14964 RAB39A Ras-related protein Rab-39A 1 EEAEKLS(0.007)ADCGMKY(0.916)IET(0.038)S(0.038)AK 45.257 0.087145 489530000 88381 80458 44611 52157 94811 70593 95936 107610 100260 TRUE FALSE 76701.22692 79929.4661 66185.02881 64000.04402 92924.44659 73308.75839 86632.14149 84598.43892 88407.37702 0.867588537 0.904104033 0.748636947 0.723921987 1.051093808 0.829215399 0.979919826 0.95691606 1 16.43187914 3.239677762 24.99986894 0.957141025 0.813249685 0.502266067 0.075210395 26.88953146 601735.1155 0.02223913 0.027101639 1736.511894 -3.239677762 -0.14389134 EEAEKPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEAEKPER 8 1 K7ELL7;P14314-2;P14314 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 91.867 0.011111 445970000 826360 607780 636050 789890 552990 678610 701330 640290 1251900 FALSE TRUE 717154.4323 603787.4532 943645.9075 969246.5972 541986.5809 704716.5658 633315.1245 503368.9662 1103901.808 0.649654188 0.546957572 0.854827758 0.878018851 0.490973542 0.638387002 0.573706031 0.455990707 1 20.07418042 3.228212186 24.9993631 0.605804762 0.727868623 0.065622241 0.173404592 498.5227389 1204310.238 0.052246314 0.059877315 1691.267043 -3.228212186 0.122063861 EEAIEHNYGGHDDDLSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EEAIEHNYGGHDDDLSVR 18 0 Q93009;A0A669KBL1;Q93009-3;H3BND8;F5H2X1 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ;; 188.26 2.24E-14 1334480000 884770 694362 466120 656431 685432 675275 667424 772790 937530 FALSE TRUE 767845.4028 689800.6903 691537.1911 805483.6915 671793.2442 701253.2662 602697.3232 607534.8724 826696.2714 0.928811982 0.834406437 0.836506968 0.97434054 0.812624016 0.848259863 0.729043234 0.734894898 1 19.65699785 3.0450709 24.99960496 0.807126507 0.88625485 0.117800272 0.084944327 235.4680627 130606.1701 0.0257529 0.029201032 1109.355905 -3.0450709 0.079128344 EEAPAS(ph)PLRPLYPQIS(ph)PLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EEAPASPLRPLYPQISPLK 19 1 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 2 EEAPAS(1)PLRPLYPQIS(1)PLK;EEAPAS(1)PLRPLYPQIS(1)PLK;EEAPAS(1)PLRPLYPQIS(1)PLK;EEAPAS(1)PLRPLYPQIS(1)PLK;EEAPAS(1)PLRPLY(0.05)PQIS(0.951)PLK 157.43 3.45E-09 628077000 1972890 1577294 1422463 1750673 1699403 1491782 1926790 2401090 3228030 TRUE FALSE 1712167.588 1566932.652 2110370.865 2148190.062 1665588.205 1549171.819 1739930.202 1887635.589 2846415.971 0.601516997 0.550493205 0.741413373 0.754699975 0.585152775 0.544253487 0.611270531 0.663162239 1 21.44071508 1.233540475 4.040723004 1.042373871 0.629188739 0.730992328 0.070566351 0.139805543 4.026791229 0.172282807 0.019218024 17.12144735 -1.233540475 -0.413185132 EEAPAS(ph)PLRPLYPQISPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EEAPASPLRPLYPQISPLK 19 1 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 1 EEAPAS(1)PLRPLYPQISPLK;EEAPAS(1)PLRPLYPQISPLK;EEAPAS(1)PLRPLYPQISPLK;EEAPAS(1)PLRPLYPQISPLK;EEAPAS(1)PLRPLYPQISPLK 200.98 3.76E-16 2279310000 2742670 2087990 1988410 2569910 2341610 1996310 2637410 3356800 5603970 TRUE FALSE 2380219.21 2074273.856 2950011.727 3153447.344 2295016.542 2073109.337 2381634.384 2638974.443 4941475.051 0.481681924 0.419768153 0.596990109 0.638159115 0.464439569 0.419532491 0.481968311 0.53404589 1 22.23651033 1.236243178 4.754707302 1.037559755 0.50247438 0.834722581 0.069430477 0.078433298 4.101823172 0.140980879 0.018662109 17.22832986 -1.236243178 -0.535085376 EEAQAEIEQYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEAQAEIEQYR 11 0 O75348 O75348 ATP6V1G1 V-type proton ATPase subunit G 1 0 170.89 3.53E-05 365990000 256600 225970 149620 187920 200100 192680 200580 244710 236960 FALSE TRUE 222689.6599 224485.5882 221976.7324 230590.1082 196118.4015 200092.5243 181127.7825 192380.6708 208946.8587 1.065771753 1.074366897 1.062359749 1.103582555 0.938604211 0.957623989 0.866860519 0.920715784 1 17.67277654 3.229503637 24.54880033 0.930555847 1.075354965 0.799550521 0.034692876 63.78381433 172884.6259 0.010629918 0.012228664 1696.303808 -3.229503637 0.144799118 EEAS(ph)DDDMEGDEAVVR ddPTM_MDA-MB-175_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 395.79 1.08E-121 6492330000 4458230 2814780 2375340 3997940 3195140 2839740 2609030 3502840 6851680 TRUE FALSE 3869063.61 2796289.525 3524062.369 4905733.382 3131562.965 2948986.635 2356006.672 2753784.925 6041682.196 0.640395089 0.462832939 0.583291583 0.811981369 0.518326331 0.488106878 0.389958723 0.455797713 1 22.52651887 1.232395365 24.98154125 1.000000768 0.537038917 0.596441366 0.117803493 156.0454048 632231.0859 0.278680417 0.030925305 17.07636247 -1.232395365 -0.462961851 EEASLLSHS(ph)PGTSNQSQPCS(ph)PKPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEASLLSHSPGTSNQSQPCSPKPIR 25 1 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 2 EEASLLS(0.002)HS(0.997)PGT(0.033)S(0.026)NQS(0.058)QPCS(0.884)PKPIR;EEASLLSHS(0.995)PGT(0.01)S(0.174)NQS(0.266)QPCS(0.555)PKPIR 103.85 0.0060514 230090000 270130 223190 145937 197529 224790 214707 275120 304360 273450 TRUE FALSE 234431.6361 221723.8502 216512.6213 242380.9785 220317.1188 222966.9172 248438.9047 239274.9825 241123.0525 0.972248956 0.919546463 0.897934142 1.005216946 0.913712383 0.924701786 1.030340742 0.992335573 1 17.87941006 2.24465273 24.99986911 1.005336523 0.938022356 0.504945965 0.032017579 114.9213788 471598.9257 0.011791361 0.008901015 175.6518509 -2.24465273 -0.067314167 EEASLLSHS(ph)PGTSNQSQPCSPKPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EEASLLSHSPGTSNQSQPCSPKPIR 25 1 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 1 EEASLLSHS(1)PGTSNQSQPCSPKPIR;EEASLLSHS(0.985)PGT(0.015)SNQSQPCSPKPIR;EEASLLS(0.001)HS(0.907)PGT(0.08)S(0.01)NQS(0.001)QPCS(0.001)PKPIR;EEASLLSHS(0.998)PGT(0.002)SNQSQPCSPKPIR 242.94 6.68E-39 5855060000 2138940 1739140 838282 1433310 2018560 1764530 2188870 2451930 2014170 TRUE FALSE 1856273.66 1727715.475 1243677.979 1758764.942 1978394.605 1832412.611 1976593.724 1927603.85 1776057.117 1.04516552 0.972781482 0.700246612 0.990263728 1.113925102 1.031730676 1.112911125 1.085327624 1 20.76024655 3.478934519 24.30472018 1.070467709 0.901489399 0.394163701 0.092256351 46.22312053 619575.6445 0.026313197 0.034536348 3012.551772 -3.478934519 -0.16897831 EEASLLSHSPGTSNQSQPCS(ph)PKPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEASLLSHSPGTSNQSQPCSPKPIR 25 1 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 1 EEASLLSHS(0.144)PGT(0.025)S(0.118)NQS(0.106)QPCS(0.607)PKPIR 166.78 8.16E-12 887150000 774250 638970 271010 471790 707950 640760 747530 828140 695280 TRUE FALSE 671930.9008 634772.564 402071.3425 578917.1304 693863.1801 665410.4518 675034.6557 651048.7056 613084.7905 1.095983641 1.035374835 0.65581686 0.944269275 1.131757289 1.085348164 1.101046162 1.061922781 1 19.22572709 3.331174864 6.544264345 1.076206062 0.917836811 0.266324001 0.117492438 0.285643004 16.87120969 0.034973767 0.045155719 2143.753586 -3.331174864 -0.15836925 EEASNFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EEASNFR 7 0 P25788-2;P25788;G3V4X5 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;;; 217.21 8.29E-05 2846050000 2698270 2482420 1481250 1835920 2205200 2410170 2280250 2655780 2601800 FALSE TRUE 2341686.783 2466112.82 2197587.454 2252793.696 2161320.834 2502890.799 2059111.706 2087862.114 2294218.168 1.020690541 1.074925155 0.957880765 0.98194397 0.942072931 1.09095588 0.897522186 0.910053866 1 21.12957116 6.689338052 0.225767194 0.923423925 1.332141039 0.159708832 0.058500797 80.98701473 2.165536598 0.301521789 10.52855733 4890328.707 -6.689338052 0.408717114 EEAT(ph)SPGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEATSPGAK 9 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 EEAT(0.5)S(0.5)PGAK 103.31 0.038485 318220000 829520 688380 492280 619600 453570 597490 813770 973670 993630 TRUE FALSE 719896.8303 683857.9865 730348.2546 760289.65 444544.8444 620475.8269 734850.7107 765458.2476 876164.1933 0.821646029 0.780513506 0.833574643 0.867747913 0.507376183 0.708173002 0.83871347 0.873647033 1 19.74084173 1.530828047 1.698119223 1.012892062 0.755688383 0.378671448 0.100889525 0.594638484 2.717832345 0.224852464 0.03090236 33.94908292 -1.530828047 -0.257203679 EEATS(ph)PGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EEATSPGAK 9 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 EEAT(0.131)S(0.869)PGAK;EEAT(0.004)S(0.996)PGAK;EEAT(0.036)S(0.964)PGAK 160.91 6.81E-05 1718460000 6006360 5207690 3658940 4394290 3068240 3856830 6001390 7267700 6700670 TRUE FALSE 5212604.308 5173480.341 5428415.622 5392080.707 3007188.027 4005204.746 5419376.122 5713558.912 5908524.426 0.882217612 0.875595998 0.918743028 0.912593453 0.508957535 0.677868865 0.91721312 0.967002673 1 22.49436645 -0.391030843 10.42270279 4.840210358 0.851879502 0 0.147940106 0 0 0 0.03616007 0.406414466 0.391030843 -3.988330855 EEATYGVWAERDS(ph)DDERPSFGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 EEATYGVWAERDSDDERPSFGGK 23 2 Q9UBB9;F6XM96;F6UKU9;F6SQZ1 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 EEATYGVWAERDS(1)DDERPSFGGK;EEATYGVWAERDS(1)DDERPSFGGK;EEATYGVWAERDS(1)DDERPSFGGK;EEATYGVWAERDS(1)DDERPSFGGK;EEATYGVWAERDS(1)DDERPSFGGK;EEATYGVWAERDS(1)DDERPSFGGK;EEATYGVWAERDS(1)DDERPSFGGK 249.24 4.93E-38 7324690000 2802150 2341881 1685472 2001475 2200973 1944479 2693450 3207080 2948980 TRUE FALSE 2431838.778 2326497.03 2500571.897 2455940.489 2157177.943 2019284.365 2432239.634 2521270.9 2600354.944 0.935194937 0.89468441 0.961627143 0.944463561 0.829570574 0.776541822 0.935349091 0.969587212 1 21.31027713 1.807531271 3.262971456 0.986779865 0.891753989 0.321641322 0.055545985 0.300834991 5.842973874 0.040207442 0.016546101 64.19944454 -1.807531271 -0.095025877 EEAYHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEAYHSR 7 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 111.29 0.0066128 41798000 150240 138570 88145 105940 108660 152380 120810 169090 122760 FALSE TRUE 130385.4033 137659.7245 130772.2168 129995.2962 106497.8786 158242.1572 109093.8648 132931.4194 108247.4526 1.20451244 1.271713294 1.208085859 1.200908594 0.983837273 1.461855714 1.007819234 1.228032772 1 16.72397355 0.512190821 1.488222589 3.67E-23 1.199246739 0.165236371 0.133516886 15.92039646 6.077003353 48.65944182 0.034853757 3.252301659 -0.512190821 1.199246739 EEDAFHFVSYVPVNGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEDAFHFVSYVPVNGR 16 0 Q5LJB0;Q5LJA5;Q5LJA9;Q9Y5K5-2;Q9Y5K5-4;Q9Y5K5-3;Q9Y5K5;H0Y4E0;H0Y6Y4 Q5LJB0 UCHL5 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L5 0 ; 103.39 0.001443 804070000 716930 700100 540680 713070 714740 748720 711450 842450 1419700 FALSE TRUE 622185.884 695500.997 802154.6565 874983.4421 700518.0724 777523.7429 642453.6885 662298.6235 1251864.683 0.497007298 0.555572025 0.640767862 0.698944106 0.559579707 0.621092482 0.51319739 0.529049691 1 20.2556472 1.234544259 24.99958724 1.000000612 0.577654938 0.822166983 0.061839232 51.98052724 323504.1562 0.120338761 0.016166061 17.1610659 -1.234544259 -0.422345673 DFQQLLAELEQEVERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFQQLLAELEQEVERR 16 1 Q6N063 Q6N063 OGFOD2 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 2 0 ; 125.89 0.0001196 57309000 61155 66551 35696 37212 57071 63347 58610 66565 20544.6 FALSE TRUE 53073.2118 66113.8221 52958.705 45661.55335 55935.39876 65784.00008 52926.01122 52330.59276 18115.84079 2.929657663 3.649503374 2.923336852 2.52053183 3.087651266 3.631297097 2.921532146 2.888664863 1 14.14496415 1.1909859 2.960960429 0.420211125 3.101496539 0.789117491 0.337262584 0.228856031 2.238733262 1.573066931 0.089265942 15.52336609 -1.1909859 2.681285414 EEDEENDNDNES(ph)DHDEADS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EEDEENDNDNESDHDEADS 19 0 H0YBP8;Q9NRG0 H0YBP8 CHRAC1 Chromatin accessibility complex protein 1 1 EEDEENDNDNES(1)DHDEADS;EEDEENDNDNES(1)DHDEADS;EEDEENDNDNES(1)DHDEADS 290.92 1.62E-49 356282000 834621 690412 501622 588243 703761 654430 708971 838615 862324 TRUE FALSE 724323.7202 685876.6381 744208.077 721812.5639 689757.533 679606.3456 640215.1015 659283.7084 760381.0391 0.952579934 0.902017019 0.978730451 0.949277437 0.907120901 0.893770768 0.841966157 0.867043856 1 19.53636303 3.097689568 3.536755313 0.890630772 0.944865296 0.175790596 0.044703194 0.350886945 8.584785144 0.014267671 0.016367337 1252.245753 -3.097689568 0.054234524 EEDEEPES(ph)PPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EEDEEPESPPEK 12 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 EEDEEPES(1)PPEK;EEDEEPES(1)PPEK;EEDEEPES(1)PPEK;EEDEEPES(1)PPEK 255.85 3.95E-21 2466970000 2736600 1918700 2219350 2522320 2023340 1664610 2478680 2982340 8259700 TRUE FALSE 2374951.376 1906095.933 3292635.083 3095051.307 1983079.493 1728648.624 2238297.995 2344589.8 7283247.675 0.326084116 0.261709613 0.45208336 0.424954834 0.272279563 0.237345852 0.307321417 0.321915429 1 22.79615048 1.23839644 24.99537124 1.000000745 0.325103425 0.908095712 0.067438915 1.152465043 174921.7906 0.098319206 0.017487576 17.31396121 -1.23839644 -0.674897319 EEDEEPES(ph)PPEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 EEDEEPESPPEKK 13 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK 253.15 9.47E-24 34065170000 26511910 16618440 22953180 21720900 16277040 12559970 24776900 29043300 54153520 TRUE FALSE 23008293.92 16509272.37 34053414.62 26652962.33 15953158.75 13043160.17 22374040.05 22832616.31 47751552.56 0.481833421 0.345732683 0.713137328 0.558159073 0.334086703 0.273146306 0.468551049 0.478154428 1 25.5090443 1.235182115 5.109661109 1.034499072 0.453827939 0.65606177 0.123760763 0.113918297 7.886384963 0.235872956 0.032470495 17.18628917 -1.235182115 -0.580671133 EEDEPEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEDEPEER 8 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 178.99 0.00057395 811930000 1441150 1171850 814150 945240 956480 986530 1133910 1305460 1426500 FALSE TRUE 1250698.376 1164152.04 1207875.663 1159871.189 937447.9193 1024482.447 1023943.583 1026297.538 1257860.795 0.994305873 0.92550149 0.960261794 0.922098211 0.745271594 0.81446409 0.814035692 0.815907088 1 20.26254084 3.430684995 9.631567561 0.832196996 0.954042647 0.425707258 0.065911937 0.338958209 67.2624698 0.018683275 0.024153059 2695.783399 -3.430684995 0.121845652 EEDEPEERS(ph)GDETPGSEVPGDK ddPTM_MDA-MB-175_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(0.999)GDET(0.001)PGSEVPGDK;EEDEPEERS(1)GDETPGSEVPGDK;EEDEPEERS(1)GDETPGSEVPGDK 347.28 3.83E-96 6685050000 9717850 5969520 5060270 4675310 5772090 4966700 7244780 8420450 5762790 TRUE FALSE 8433611.501 5930305.83 7507433.498 5736910.593 5657236.702 5157772.163 6542182.351 6619802.296 5081519.531 1.659663305 1.167033954 1.47739932 1.128975409 1.113296263 1.015005872 1.28744607 1.302721018 1 22.27682854 7.999999425 0.861103613 1.17413929 174.5137513 0.521016622 0.142318605 651.994302 1.710359507 0.047959237 221570.1108 99999867.55 -7.999999425 173.339612 THQPERPRS(ph)PAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 THQPERPRSPAAR 13 2 Q9P2Y4;G3V2Q8 Q9P2Y4 ZNF219 Zinc finger protein 219 1 THQPERPRS(1)PAAR;THQPERPRS(1)PAAR;THQPERPRS(1)PAAR 136.99 3.44E-05 309519000 172082 155469 76928 94746 141162 142200 138881 134438 60667 TRUE FALSE 149340.9277 154447.7139 114130.6381 116259.5274 138353.1524 147670.526 125412.342 105689.4799 53495.01637 2.79167926 2.8871421 2.133481693 2.173277724 2.586281148 2.76045389 2.344374308 1.975688336 1 15.70711687 1.192661356 1.525195205 0.23331711 2.535416847 0.796158477 0.248256484 0.614201739 1.168411231 2.243608204 0.077096431 15.58336904 -1.192661356 2.302099737 EEDFKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEDFKR 6 1 P50416;P50416-2 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 ; 112.75 0.042861 809070000 1122030 1141660 927290 1348390 1309620 1423860 1067750 2191490 2012280 FALSE TRUE 973750.8926 1134160.36 1375730.546 1654562.558 1283561.124 1478636.816 964199.7693 1722856.918 1774390.551 0.548780477 0.639183048 0.775325672 0.932468085 0.723381402 0.833320948 0.543397714 0.970956995 1 20.75889216 -2 0.057711176 2.269371861 4.16E-13 0.342341645 0.133292919 1116.039163 6.256889537 236.4894197 63.15691257 0.01 2 -2.269371861 EEDGADAS(ph)EEDLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEDGADASEEDLTR 14 0 E5RHA3;Q86X53 E5RHA3 ERICH1 Glutamate-rich protein 1 1 EEDGADAS(1)EEDLTR;EEDGADAS(1)EEDLTR 257.48 2.51E-24 479910000 1146610 830060 673180 784480 892080 892480 844080 1006750 1103260 TRUE FALSE 995082.5834 824607.2812 998732.0997 962608.174 874329.3533 926814.2831 762221.2515 791464.347 972833.8596 1.022870014 0.847634232 1.026621442 0.989488765 0.89874478 0.952695338 0.783506088 0.813565789 1 19.89183392 2.267980329 24.0920314 0.851406961 0.953484311 0.226781352 0.077304155 171.5101315 140450.1945 0.02806383 0.021733933 185.3447671 -2.267980329 0.102077349 EEDNTYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEDNTYR 7 0 O43747;O43747-2;H3BNR4;H3BR36;H3BUN9;H3BN71;B4DGE1;H3BRM7;H3BN75;H3BS13;H3BV30 O43747 AP1G1 AP-1 complex subunit gamma-1 0 105.57 0.018373 251650000 554940 474000 355930 427110 415910 489140 498880 559580 679930 FALSE TRUE 481603.273 470886.2628 528058.9385 524091.8535 407634.2047 507957.5323 450498.6944 439918.1717 599549.45 0.803275314 0.785400208 0.880759608 0.874142831 0.67990089 0.847232088 0.751395393 0.733747936 1 19.19351922 1.228423008 24.990089 1.000000426 0.792584795 0.514263682 0.062747079 363.4277212 895818.2266 0.208615596 0.01556445 16.92088243 -1.228423008 -0.207415631 EEDRPPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEDRPPLR 8 1 P53618 P53618 COPB1 Coatomer subunit beta 0 ; 143.45 0.00054832 1252030000 1713930 1571370 1137630 1258860 1483140 1585420 1563460 1709670 1779410 FALSE TRUE 1487429.808 1561047.567 1687791.673 1544703.403 1453628.416 1646412.133 1411835.89 1344070.375 1569050.177 0.947981033 0.994899711 1.07567731 0.984483114 0.926438451 1.04930496 0.899802894 0.856614017 1 20.58146006 2.218344468 24.99287869 0.905057222 0.996266014 0.292104741 0.055633528 253.9406294 313940.2147 0.022516536 0.015202133 165.3272601 -2.218344468 0.091208792 EEEADMSS(ph)PTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EEEADMSSPTQR 12 0 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 EEEADMSS(1)PTQR;EEEADMS(0.02)S(0.978)PT(0.002)QR;EEEADMS(0.047)S(0.953)PTQR;EEEADMS(0.023)S(0.977)PTQR;EEEADMS(0.027)S(0.888)PT(0.085)QR 301.62 1.55E-36 1091780000 1557740 1787220 1723330 2527340 2230780 2148030 2161460 2721890 6729740 TRUE FALSE 1351880.712 1775479.634 2556738.152 3101211.175 2186391.842 2230666.104 1951841.942 2139835.005 5934157.804 0.227813408 0.299196566 0.430851055 0.522603422 0.36844181 0.375902728 0.32891642 0.360596242 1 22.50061186 1.238156485 24.99026985 1.000000713 0.367944632 0.869538183 0.077373843 3.490590657 215576.9257 0.113938747 0.019962772 17.30439759 -1.238156485 -0.632056081 EEEDDVDLELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEEDDVDLELR 11 0 Q9HCS7 Q9HCS7 XAB2 Pre-mRNA-splicing factor SYF1 0 145.25 0.0035914 0 192370 143700 105000 163840 166440 152700 168140 223660 256430 FALSE TRUE 166947.8171 142756.0252 155778.3512 201042.3761 163128.1696 158574.4678 151833.8087 175832.0495 226115.1375 0.738331007 0.631342186 0.688933757 0.889115069 0.721438518 0.701299654 0.671488916 0.777621753 1 17.78669805 1.255479199 3.196174747 1.041513682 0.721580504 0.628538448 0.067188333 0.226631653 3.129194344 0.178898799 0.017908988 18.00856879 -1.255479199 -0.319933177 EEEEGISQES(ph)S(ph)EEEQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEEEGISQESSEEEQ 15 0 P17096;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 2 EEEEGISQES(1)S(1)EEEQ 166.77 1.97E-06 281540000 294470 236160 188850 250040 241900 239240 231880 268410 342300 TRUE FALSE 255555.0434 234608.6494 280178.4917 306815.4036 237086.6633 248443.7176 209392.3133 211012.6103 301833.6839 0.84667503 0.777277891 0.928254554 1.01650485 0.785487757 0.823114618 0.693734081 0.699102259 1 18.20339429 3.051760302 24.99989958 0.78026674 0.888354096 0.148024576 0.103432184 168.2253447 81250.53026 0.032157498 0.036463169 1126.575498 -3.051760302 0.108087356 EEEEQQEGGFAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEEEQQEGGFASPR 14 0 A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2;A0A087WWG9 A0A087WVR3 UHRF1 E3 ubiquitin-protein ligase UHRF1 1 EEEEQQEGGFAS(1)PR 342.28 7.13E-55 0 174030 166800 133600 115790 151140 132070 141920 202730 194040 TRUE FALSE 151031.4946 165704.2798 198209.4069 142081.8892 148132.6097 137150.8184 128156.6202 159377.7671 171100.8123 0.88270472 0.968459925 1.158436388 0.830398684 0.865762165 0.801579002 0.749012343 0.931484574 1 17.38448708 3.682523117 24.99998729 0.860595012 0.999727408 0.325704799 0.094980552 339.6820698 151541.9561 0.026849224 0.039823855 4814.188788 -3.682523117 0.139132396 EEEERER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEEERER 7 1 Q9H3P7;E9PEW5;A0A0A0MQX1;Q9HD67-3;Q9HD67 Q9H3P7;E9PEW5 ACBD3;MYO10 Golgi resident protein GCP60;Unconventional myosin-X 0 123.72 0.0038452 260650000 94300 97841 45694 60065 51813 82841 94854 89076 65532 FALSE TRUE 81838.01607 97198.27603 67791.77124 73703.67629 50782.02267 86027.94688 85655.07368 70027.79059 57784.88161 1.416253072 1.682071042 1.173174875 1.275483729 0.878811572 1.48876219 1.482309408 1.211870452 1 15.81840447 4.230076379 24.99999813 1.229551203 1.549162075 0.330391363 0.196559152 197.8258677 582927.4862 0.050660093 0.108214119 16985.42346 -4.230076379 0.319610872 EEEGTGVVHQAPYFGAEDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEEGTGVVHQAPYFGAEDYR 20 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 128.55 1.95E-05 681560000 727540 592010 506300 721580 625880 633340 664490 770380 1353930 FALSE TRUE 631393.7456 588121.0473 751148.3735 885425.7677 613426.2125 657704.9996 600047.8621 605640.2321 1193869.938 0.528863091 0.492617352 0.629171026 0.741643407 0.513813266 0.550901718 0.502607397 0.507291634 1 20.18721424 1.234590761 24.99836894 1.00000064 0.557616297 0.770769691 0.075689458 59.74148296 376141.1383 0.146530545 0.019765993 17.1629035 -1.234590761 -0.442384342 EEEHDCFLEEIMTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEEHDCFLEEIMTK 14 0 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 164.68 4.08E-06 68188000 95187 84155 84555 105329 79884 65547 93980 118883 290704 FALSE TRUE 82607.79678 83602.18026 125446.0808 129245.5593 78294.46469 68068.6355 84865.83406 93460.7956 256337.3043 0.322262095 0.326141295 0.48937895 0.504201133 0.305435313 0.265543229 0.331070947 0.364600837 1 17.96768392 1.238570736 15.71300308 1.000113309 0.364371254 0.872177501 0.076567601 0.016424664 1302.946266 0.112990295 0.020297385 17.32091124 -1.238570736 -0.635742055 EEEIEVDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEEIEVDSR 9 0 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 87.476 0.031256 74605000 164880 161650 91599 137790 173550 158260 151540 188140 222010 FALSE TRUE 143090.6902 160588.1105 135896.5828 169077.3255 170096.6945 164348.3646 136843.6741 147907.7251 195764.2307 0.730933786 0.820313854 0.69418495 0.863678338 0.868885465 0.839521929 0.699022869 0.755540093 1 17.57875766 EEEMGEEEEVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 220.82 1.02E-10 955030000 718940 585930 429988 515470 592730 581059 601000 697600 646500 FALSE TRUE 623930.2574 582080.9872 637931.635 632515.342 580935.8327 603412.7157 542715.1125 548423.6687 570071.5065 1.094477185 1.021066622 1.119037924 1.109536847 1.019057831 1.058486012 0.952012346 0.962026101 1 19.12078337 2.493593279 1.652572801 0.967627521 1.078622782 0.614015487 0.0361938 0.233812374 1.308318332 0.018347347 0.012620489 311.5970081 -2.493593279 0.110995262 EEEPVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EEEPVKK 7 1 Q14103-3;Q14103;H0Y8G5;H0YA96;Q14103-2;Q14103-4;Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q14103-3;Q14103-2;Q99729-3 HNRNPD;HNRNPAB Heterogeneous nuclear ribonucleoprotein D0;Heterogeneous nuclear ribonucleoprotein A/B 0 ;;;; 114.93 0.0092902 5628420000 9461220 6335750 6418280 7539660 4459770 4043140 7960860 10420190 15775600 FALSE TRUE 8210895.805 6294130.041 9522181.676 9251655.039 4371029.302 4198682.212 7188817.023 8191913.459 13910626.54 0.590260675 0.452469199 0.684525722 0.665078242 0.314222317 0.301832718 0.516785998 0.588896081 1 23.72968407 1.200403913 2.555107955 1.154125224 0.501029525 0.596163648 0.127409448 0.451531011 2.998871124 0.676892972 0.036064974 15.86367898 -1.200403913 -0.653095699 EEEWDPEYT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEEWDPEYTPK 11 0 Q9NYF8;Q9NYF8-2;H0YF14;Q9NYF8-4;Q9Y2W1;A0A3B3ITZ9 Q9NYF8;Q9NYF8-4;Q9Y2W1 BCLAF1;THRAP3 Bcl-2-associated transcription factor 1;Thyroid hormone receptor-associated protein 3 1 EEEWDPEYT(1)PK 124.07 0.0026992 0 420290 314280 280300 328880 289910 272300 356320 421110 552440 TRUE FALSE 364747.6116 312215.474 415854.0175 403557.2306 284141.3582 282775.5572 321764.1412 331058.9036 487131.1725 0.748766723 0.640926903 0.85367975 0.828436473 0.583295371 0.580491607 0.660528743 0.679609358 1 18.89395078 1.236864728 24.99802652 1.00000038 0.694507548 0.518250036 0.091792034 39.05442222 575498.7002 0.148065388 0.023844316 17.25300421 -1.236864728 -0.305492832 EEFTAFLHPEEFEHMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EEFTAFLHPEEFEHMK 16 0 Q15293;Q15293-2;E9PP27 Q15293 RCN1 Reticulocalbin-1 0 ;;;; 231.23 8.86E-16 1065302000 1257650 1039906 846447 958385 1021687 1014280 1128259 1237833 980001 FALSE TRUE 1091448.366 1033074.789 1255791.6 1176000.962 1001357.428 1053300.008 1018840.616 973132.0458 864146.3982 1.263036412 1.195485847 1.453216264 1.360881634 1.158782157 1.2188907 1.179013901 1.126119426 1 19.72091622 0.811727042 0.509800239 0.650762402 1.309801044 0.597835754 0.078886481 5.21733469 0.794402427 2.265668667 0.060848069 6.482268892 -0.811727042 0.659038642 EEFTAFLHPEEYDYMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EEFTAFLHPEEYDYMK 16 0 O43852;O43852-3;O43852-15;O43852-6;H0Y875;O43852-10;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;;;; 204.82 2.42E-11 1720050000 4503050 3252040 3004570 3723900 3502080 3486770 3630900 3924070 3997600 FALSE TRUE 3907960.533 3230677.135 4457590.102 4569468.411 3432395.46 3620908.298 3278775.877 3084938.168 3525008.282 1.108638681 0.916501998 1.264561597 1.29630005 0.973726921 1.027205614 0.930147 0.875157708 1 21.74919522 3.076220111 10.75574554 0.948956028 1.138485654 0.418292116 0.108268954 0.462454959 62.46185274 0.034885781 0.039570741 1191.845912 -3.076220111 0.189529626 EEGAQTLEEDRAQT(ph)PHEDGGPQPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEGAQTLEEDRAQTPHEDGGPQPHR 25 1 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 1 EEGAQT(0.006)LEEDRAQT(0.994)PHEDGGPQPHR;EEGAQTLEEDRAQT(1)PHEDGGPQPHR 121.96 9.83E-05 463340000 92695 72610 68154 56877 76157 76386 74328 90678 59559 TRUE FALSE 80445.12089 72133.02013 101113.5024 69791.79216 74641.6247 79324.61885 67119.682 71287.21536 52518.00287 1.531762757 1.373491302 1.925311262 1.32891177 1.421257866 1.510427178 1.278031881 1.357386257 1 15.68052443 0.343515461 0.542415705 1.21E-13 1.547419363 0.47714902 0.168138063 9.453008532 1.058041145 11.4296053 0.100513829 2.205542653 -0.343515461 1.547419363 EEGCTHVIVTTACGSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEGCTHVIVTTACGSLR 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 89.311 0.0040804 161620000 62177 57870 54478 68062 63808 62371 61582 61643 132530 FALSE TRUE 53960.15191 57489.84816 80823.74302 83516.51736 62538.34564 64770.45273 55609.78712 48461.12416 116862.4544 0.461740704 0.491944555 0.691614287 0.714656541 0.535144893 0.554245186 0.475856745 0.414685148 1 16.83445197 1.228644515 24.9999495 1.000000925 0.541971328 0.694296699 0.095407348 269.053212 678274.6308 0.343500166 0.026200614 16.92951493 -1.228644515 -0.458029597 EEGDLGPVYGFQWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EEGDLGPVYGFQWR 14 0 P04818;P04818-2 P04818 TYMS Thymidylate synthase 0 ;; 207.34 2.23E-08 340242000 178346 168860 123007 144620 160120 165440 161341 193779 164312 FALSE TRUE 154777.1242 167750.7475 182493.5966 177458.1814 156933.9253 171804.5839 145694.1747 152340.8688 144887.2225 1.068259309 1.157802217 1.259556181 1.224802148 1.083145377 1.185781471 1.005569519 1.051444469 1 17.14457085 2.238651078 25 1.02520314 1.166515739 0.573395638 0.058514161 1.790965685 495170.8984 0.02354667 0.01706775 173.2411581 -2.238651078 0.141312599 EEGFPIRPHYFWPLLVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEGFPIRPHYFWPLLVGR 18 1 P42704;B8ZZ38;A0A0C4DG06 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ; 137.14 2.88E-06 496520000 587150 593800 456400 713430 683460 707680 462040 743540 721660 FALSE TRUE 509556.6399 589899.2887 677116.5666 875425.1856 669860.4832 734904.9075 417231.4319 584539.7572 636346.1769 0.800753832 0.92701003 1.064069513 1.375705893 1.052666783 1.154882255 0.655667382 0.918587678 1 19.27945229 2.261907668 24.99835639 0.862255492 1.070214422 0.243232524 0.169568587 331.9164499 355391.525 0.066066698 0.051143809 182.7711599 -2.261907668 0.20795893 EEGGFEYKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEGGFEYKR 9 1 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 93.111 0.01137 0 239440 206760 167270 186280 209030 184110 263990 296590 207250 FALSE TRUE 207797.3973 205401.7799 248162.3315 228577.7211 204870.712 191192.8308 238388.2904 233166.5366 182749.1411 1.137063606 1.123954831 1.357939797 1.250773162 1.121048836 1.046203718 1.30445642 1.275883078 1 17.4795051 3.254261011 24.97088081 1.171768597 1.22079205 0.064348507 0.111746563 985.3047988 1567081.356 0.034197221 0.04400214 1795.812586 -3.254261011 0.049023452 EEGLGFPSFLDPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EEGLGFPSFLDPDR 14 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 0 ;;;; 188.96 1.80E-06 190227000 228355 201735 175716 221295 220864 219339 181112 230945 403016 FALSE TRUE 198177.3082 200409.7895 260692.8453 271543.412 216469.2385 227777.1133 163547.7861 181559.209 355371.9076 0.557661717 0.563943816 0.733577528 0.764110517 0.609134357 0.64095419 0.460215854 0.51089916 1 18.43897011 1.230370321 24.99295667 1.000000734 0.602808883 0.643035607 0.09246183 225.6530066 688532.0419 0.280341093 0.025548855 16.99692353 -1.230370321 -0.39719185 EEGLREWGSGS(ph)PPCVPGPQEGLRPMSDSVGGAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEGLREWGSGSPPCVPGPQEGLRPMSDSVGGAFR 34 2 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 EEGLREWGS(0.049)GS(0.951)PPCVPGPQEGLRPMSDSVGGAFR 54.389 0.027515 75584000 44178 26912 15665 18062 24623 33913 33860 31727 15623 TRUE FALSE 38339.76537 26735.2133 23240.6464 22163.25316 24133.05047 35217.65505 30576.26241 24942.42795 13776.06674 2.783070531 1.940700042 1.687030619 1.60882301 1.751809928 2.556437605 2.219520491 1.810562363 1 13.74987642 4.732111337 4.15348113 1.843688205 2.854705218 0.362870898 0.40150515 0.259742757 10.02051689 0.102557731 0.777498941 53964.89504 -4.732111337 1.011017012 EEGS(ph)DIEDEDMEELLNDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEGSDIEDEDMEELLNDTR 19 0 F5H5U2;Q8NHQ9;Q8NHQ9-2 F5H5U2 DDX55 ATP-dependent RNA helicase DDX55 1 EEGS(1)DIEDEDMEELLNDTR;EEGS(1)DIEDEDMEELLNDTR 183.74 2.77E-14 136390000 158416 158226 107211 119615 150531 146034 156706 185035 187244 TRUE FALSE 137480.9242 157186.603 159058.5982 146775.414 147535.7276 151652.0225 141508.6762 145466.7052 165108.2276 0.832671552 0.952021624 0.963359613 0.888964869 0.89356981 0.918500699 0.85706617 0.8810385 1 17.33305249 EEGS(ph)LSDTEADAVSGQLPDPTTNPSAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEGSLSDTEADAVSGQLPDPTTNPSAGK 28 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 EEGS(0.541)LS(0.44)DT(0.018)EADAVSGQLPDPTTNPSAGK;EEGS(0.333)LS(0.333)DT(0.333)EADAVSGQLPDPTTNPSAGK 170.29 2.49E-12 384950000 208373 153229 166745 228603 154046 143725 183070 223221 469010 TRUE FALSE 180835.9801 152222.4286 247383.4397 280510.8051 150980.786 149254.1938 165315.8996 175486.9263 413564.1721 0.437262201 0.368074507 0.598174253 0.678276369 0.365072209 0.360897302 0.399734577 0.424328165 1 18.65775168 1.23672508 24.9998129 1.000000686 0.453188957 0.72771701 0.104963416 27.4313812 373504.8182 0.172342877 0.02742272 17.24745738 -1.23672508 -0.546811729 EEGSLSDT(ph)EADAVSGQLPDPTTNPSAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEGSLSDTEADAVSGQLPDPTTNPSAGK 28 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 EEGS(0.153)LS(0.353)DT(0.494)EADAVSGQLPDPTTNPSAGK 181.18 5.21E-17 360860000 302000 183780 234100 300930 227050 183320 255400 308940 678230 TRUE FALSE 262089.9348 182572.7371 347311.543 369260.7559 222532.1492 190372.439 230631.3473 242875.5852 598050.422 0.438240532 0.30527984 0.580739567 0.617440842 0.372095966 0.31832172 0.385638633 0.406112221 1 19.1899076 1.237314813 24.99830311 1.000000689 0.426659723 0.760034614 0.101008528 16.34504383 327843.628 0.157281699 0.026123548 17.27089378 -1.237314813 -0.573340966 EEGVIDSSDKEIVAEAERLDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEGVIDSSDKEIVAEAERLDVK 22 2 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 181.69 2.74E-17 29420000 211820 169330 114460 115610 140390 91897 215000 262210 40716 FALSE TRUE 183827.4503 168217.6601 169813.2388 141861.0175 137596.5137 95432.33706 194149.3331 206138.432 35902.60086 5.120170848 4.685389249 4.72983112 3.951274116 3.832494314 2.658089797 5.407667646 5.741601641 1 15.13180074 3.817402146 3.983575866 4.029487728 4.861347008 0.107097185 1.3349309 0.714473339 21.48445801 0.374251399 0.674184552 6567.531215 -3.817402146 0.83185928 EEGWWVVIGDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEGWWVVIGDAK 12 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 125.75 0.00069738 38403000 124034 99458 65169 79884 88760 92505 104990 129409 116278 FALSE TRUE 107642.5926 98804.65385 96684.94638 98022.88315 86993.84966 96063.72721 94808.08596 101735.8924 102531.7473 1.049846467 0.963649372 0.942975702 0.956024702 0.848457692 0.936916904 0.924670538 0.992237966 1 16.64571116 4.762052617 2.453683881 0.94328144 1.077817262 0.397919499 0.041044653 0.669659613 4.752638678 0.01126153 0.194236184 57816.60911 -4.762052617 0.134535822 EEHDKEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEHDKEER 8 1 Q9Y6I3 Q9Y6I3 EPN1 Epsin-1 0 82.749 0.011696 268340000 163400 149270 128350 104400 73558 113870 147430 186680 178920 FALSE TRUE 141806.276 148289.4355 190420.4893 128105.6157 72094.33971 118250.6526 133132.2613 146759.9347 157768.2814 0.89882627 0.939919192 1.20696307 0.811985873 0.45696346 0.749521079 0.843846812 0.930224589 1 17.26744766 3.525291679 23.66961622 0.797794108 1.007999784 0.285046504 0.161651867 315.5388196 155045.6637 0.048356199 0.071720915 3351.904825 -3.525291679 0.210205676 EEHETDEKR ddPTM_MDA-MB-175_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 ; 123.63 0.00035864 518930000 359229 253099 218655 226374 205164 226983 293247 351087 258966 FALSE TRUE 311755.9775 251436.376 324397.2894 277775.6766 201081.6378 235715.1829 264807.9511 276009.7772 228351.3345 1.365247014 1.101094402 1.420606059 1.216439909 0.880580086 1.032247889 1.159651428 1.208706653 1 17.8008957 3.464559173 24.98311779 1.078821329 1.283248592 0.456041577 0.120118527 232.4615793 462311.4341 0.035438278 0.045780006 2914.467204 -3.464559173 0.204427262 EEHGGLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EEHGGLIR 8 0 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ;;; 164.53 0.00032954 1445930000 2479460 2055370 1695120 2075590 1816290 2081590 1904950 2175650 3657710 FALSE TRUE 2151793.079 2041868.139 2514885.702 2546884.433 1780149.383 2161670.114 1720208.242 1710404.178 3225299.691 0.667160663 0.633078577 0.779737061 0.789658226 0.551933015 0.670223025 0.533348342 0.530308605 1 21.62100179 3.241458043 24.99601344 0.632672806 0.715837071 0.027041767 0.142186552 220.2086561 1899718.877 0.0413632 0.051065629 1743.644896 -3.241458043 0.083164264 RSQAGVSSGAPPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSQAGVSSGAPPGR 14 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 132.44 8.08E-05 65359000 42785 43489 23960 27582 43614 47144 43204 46512 17197.1 FALSE TRUE 37130.85385 43203.3179 35547.13614 33844.91466 42746.16673 48957.66019 39014.08273 36565.77076 15164.07843 2.448606028 2.849056611 2.344167257 2.231913718 2.818909631 3.228528553 2.572796159 2.411341443 1 13.8883702 1.19370872 2.709482662 0.503012731 2.647983086 0.765276707 0.283281157 0.281716445 2.160502987 1.454561634 0.078112205 15.62099594 -1.19370872 2.144970355 EEHLCTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 EEHLCTQR 8 0 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;;;;;; 166.52 0.00031801 19600038000 5140384 5327158 3779336 4230433 4599460 4934890 4706222 5284455 6684472 FALSE TRUE 4461069.23 5292163.548 5607035.531 5191017.471 4507939.745 5124738.412 4249813.315 4154415.422 5894241.335 0.756852151 0.897853218 0.951273491 0.880693066 0.764804067 0.869448351 0.721011081 0.704826149 1 22.4908747 3.251522698 23.40564721 0.794664969 0.879224526 0.069490709 0.095834264 207.8870636 375377.1151 0.02769186 0.035475154 1784.525251 -3.251522698 0.084559556 EEHSKT(ph)PEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EEHSKTPEER 10 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 EEHS(0.003)KT(0.997)PEER;EEHS(0.004)KT(0.996)PEER;EEHS(0.047)KT(0.953)PEER;EEHS(0.16)KT(0.84)PEER;EEHS(0.127)KT(0.873)PEER 139.86 5.91E-05 1304265000 1941580 1323391 1028984 1061490 1135013 1247515 1466496 1817645 1691295 TRUE FALSE 1684995.284 1314697.557 1526604.104 1302517.528 1112428.462 1295507.709 1324275.444 1428955.762 1491352.032 1.129844093 0.881547434 1.02363766 0.873380329 0.745919433 0.868680018 0.887969718 0.958161273 1 20.50818941 7.277057473 1.293045073 0.899521152 199.9831145 0.434155941 0.07903921 1301.043713 3.32586033 0.023408774 767001.7154 18925940.63 -7.277057473 199.0835933 EEIDIRLS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEIDIRLSR 9 1 A0A1W2PQS0;X6R6F3;A0A1W2PQP6;X6R6S3;Q9BWL3-5;Q9BWL3-3;Q9BWL3-4;Q9BWL3-2;Q9BWL3 A0A1W2PQS0 C1orf43 Uncharacterized protein C1orf43 1 EEIDIRLS(1)R 57.59 0.069276 384780000 261270 279310 191510 192480 285570 420540 167310 195690 125240 TRUE FALSE 226742.5075 277475.1942 284124.8766 236185.5259 279887.7157 436718.4459 151084.302 153843.2164 110434.2699 2.053189719 2.512582322 2.57279626 2.138697762 2.53442809 3.954555469 1.368092551 1.393074962 1 16.75282841 2.044208482 24.99157596 1.271402875 2.599163941 0.606880893 0.521541426 86.21861849 48740.03267 0.211479386 0.142579286 110.7155144 -2.044208482 1.327761066 EEIDSILNKVEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEIDSILNKVEER 13 1 P52788;H7C2R7 P52788 SMS Spermine synthase 0 ; 144.8 3.78E-05 172211000 231320 149745 112513 127107 138347 110291 170615 206813 104950 FALSE TRUE 200750.4759 148761.3152 166924.6631 155968.5871 135594.1654 114533.9661 154068.7836 162587.6494 92542.93056 2.169268627 1.607484379 1.803753805 1.685364686 1.465202847 1.237630637 1.664835797 1.756888921 1 16.49783517 7.999999991 0.512365145 1.472953465 23.3719398 0.46414079 0.232924152 127.0559249 1.340382338 0.141131794 3006.642783 99999997.96 -7.999999991 21.89898634 EEIFRES(ph)PIPIEIPPAAVPSYVPESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEIFRESPIPIEIPPAAVPSYVPESR 26 1 Q5TC82-2;Q5TC82 Q5TC82-2 RC3H1 Roquin-1 1 EEIFRES(1)PIPIEIPPAAVPSYVPESR;EEIFRES(1)PIPIEIPPAAVPSYVPESR 103.78 0.0021447 85285000 39177 36546 24574.9 27687 42735 32577 39857 42071 38138 TRUE FALSE 33999.66019 36305.92692 36459.40384 33973.75652 41884.65711 33830.25827 35991.67427 33074.44405 33629.36909 1.011010944 1.079589891 1.084153668 1.010240675 1.245478528 1.005973623 1.070245302 0.983498797 1 15.03743409 1.898600543 1.864682714 0.988105901 1.079429462 0.183077742 0.068996194 0.563859232 3.604243256 0.059026103 0.01973701 79.17727364 -1.898600543 0.091323561 EEILQPPEPHPVPPILTPS(ph)PPSAFPTVTTVWQDNDRYHPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEILQPPEPHPVPPILTPSPPSAFPTVTTVWQDNDRYHPK 40 1 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 EEILQPPEPHPVPPILT(0.002)PS(0.996)PPS(0.001)AFPTVTTVWQDNDRYHPK;EEILQPPEPHPVPPILT(0.002)PS(0.998)PPSAFPTVTTVWQDNDRYHPK 142.41 1.83E-13 603690000 240120 172356 233040 249640 220422 211784 258340 307000 348720 TRUE FALSE 208387.5336 171223.7821 345738.9235 306324.5775 216036.0334 219931.4675 233286.2266 241350.4391 307494.7189 0.677694675 0.556834871 1.124373533 0.996194597 0.702568273 0.715236568 0.758667425 0.784892957 1 18.23020211 4.296334646 24.99999882 0.848576216 0.617263682 0.347682369 0.141156271 102.1512991 44200.87855 0.037037723 0.097992539 19784.93585 -4.296334646 -0.231312533 EEIQPGDIVIIDQFIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 159.02 7.60E-09 63197000 115228 100775.8 81013.6 93081.2 104281.4 102858 102901 125138 136105 FALSE TRUE 100000.3278 100113.7971 120192.0479 114216.7091 102206.4042 106815.0138 92921.67686 98378.21253 120014.822 0.833233148 0.834178608 1.001476701 0.95168836 0.851614846 0.890015184 0.774251674 0.819717189 1 16.87285307 3.200723351 24.86117363 0.855374073 0.906956167 0.046345555 0.075755319 395.4250467 259814.638 0.023796099 0.026982777 1587.535155 -3.200723351 0.051582094 EEIVDKYDLFVGSQATDFGEALVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EEIVDKYDLFVGSQATDFGEALVR 24 1 O43852;O43852-3;O43852-15;O43852-6;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4;O43852-8 O43852;O43852-2 CALU Calumenin 0 ;;; 205.38 8.94E-25 1988562000 1751110 1335017 1190138 1464621 1385330 1365414 1454407 1559660 1726300 FALSE TRUE 1519696.377 1326247.185 1765692.718 1797185.583 1357764.643 1417942.36 1313358.833 1226138.846 1522218.781 0.998342943 0.871259245 1.159946744 1.180635534 0.891964191 0.931497087 0.862792425 0.805494494 1 20.53774429 3.129162716 10.77215492 0.885095016 1.047166828 0.376117889 0.097785723 0.379174825 34.99644819 0.03123826 0.035436967 1346.364699 -3.129162716 0.162071812 EEIVELMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EEIVELMR 8 0 P42574;A8MVM1;C9JXR7 P42574 CASP3 Caspase-3;Caspase-3 subunit p17;Caspase-3 subunit p12 0 ;;; 153.78 0.0010134 407943000 652580 617273 383046 453224 576234 571071 574769 675510 642330 FALSE TRUE 566339.8996 613218.093 568288.3268 556135.4363 564768.0708 593040.4709 519027.9908 531057.4433 566394.4791 0.999903637 1.082669616 1.00334369 0.981887107 0.997128488 1.047044936 0.91637191 0.937610557 1 19.11144768 2.76704883 0.703313507 0.947349858 1.033150336 0.260528705 0.040691371 0.91713041 1.150235482 0.047577375 0.034197839 584.8558394 -2.76704883 0.085800479 EEIVYLPCIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEIVYLPCIYR 11 0 Q13228;Q13228-4;Q13228-3;H0Y532;F2Z2W8;F8WCR4;C9JVL0 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 181.41 1.45E-05 526710000 540570 546320 331320 374760 499430 504320 496860 592710 533010 FALSE TRUE 469132.3049 542731.1879 491547.4602 459854.9858 489492.3201 523721.5167 448674.5937 465963.579 469998.165 0.998157737 1.154751717 1.045849743 0.978418683 1.041477088 1.11430545 0.954630522 0.991415741 1 18.8422956 2.222881509 24.97474274 0.98283278 1.055426304 0.310334676 0.051631394 295.3456875 470442.9907 0.021046522 0.014244642 167.0634742 -2.222881509 0.072593524 EEKDKDDQEWESPS(ph)PPKPTVFISGVIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEKDKDDQEWESPSPPKPTVFISGVIAR 28 3 P51397 P51397 DAP Death-associated protein 1 1 EEKDKDDQEWES(0.033)PS(0.965)PPKPT(0.002)VFISGVIAR;EEKDKDDQEWES(0.003)PS(0.996)PPKPT(0.001)VFISGVIAR 155.28 1.49E-08 1110470000 844820 439130 522410 388370 430760 293210 713680 862070 419280 TRUE FALSE 733174.8965 436245.3261 775049.2234 476555.3444 422188.7188 304489.9784 644467.4234 677723.0391 369713.196 1.983090959 1.17995606 2.09635261 1.28898657 1.141935758 0.823584286 1.743155047 1.833104813 1 18.49604701 7.697208124 0.966398736 1.409389586 199.9961014 0.157339545 0.401665878 1708.013649 5.307532324 0.131862295 746713.2912 49797566.91 -7.697208124 198.5867118 EELAQFHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EELAQFHR 8 0 E7EMD0;P16435;H0Y4R2 E7EMD0;P16435 POR NADPH--cytochrome P450 reductase 0 ; 108.98 0.0037068 425970000 605380 544090 477440 712730 691390 946840 455500 765680 949230 FALSE TRUE 525377.4992 540515.837 708331.5809 874566.2399 677632.6917 983265.5475 411325.6801 601945.2905 837013.1108 0.627681326 0.645767468 0.846261034 1.04486564 0.809584322 1.174731357 0.491420833 0.719158736 1 19.6748907 4.243813387 6.392414747 0.851193068 0.634247861 0.207655139 0.186487268 0.244834449 42.35174738 0.048803727 0.118606529 17531.27033 -4.243813387 -0.216945207 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR 36 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 241.09 5.72E-50 253630000 444330 363390 388200 502600 327670 303680 433590 524760 1095280 FALSE TRUE 385610.6647 361002.8672 575934.8185 616723.0118 321150.0081 315362.7661 391540.5085 412544.1577 965797.2461 0.399266685 0.373787427 0.59633098 0.638563647 0.332523218 0.326531026 0.405406528 0.427154001 1 19.88136082 1.237891379 24.99801455 1.000000646 0.437977079 0.746257394 0.103090288 8.944493558 333849.747 0.156486128 0.026964253 17.29383772 -1.237891379 -0.562023567 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 15 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR 37 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;;;; 314.22 5.13E-110 18250253000 1418249 1252455 854294 1019410 1146260 1033153 1414640 1679262 715820.2 FALSE TRUE 1230823.801 1244227.541 1267433.436 1250882.621 1123451.669 1072899.064 1277448.431 1320164.889 631196.7514 1.949984373 1.97121981 2.007984726 1.981763402 1.779875556 1.699785466 2.023851402 2.091526749 1 19.26773025 1.232981651 24.99998935 0.999998504 1.941614729 0.866215106 0.115874004 68.96614674 309012.1053 0.268620007 0.031496183 17.09943066 -1.232981651 0.941616225 EELDWTTNELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EELDWTTNELR 11 0 F6RTM7;K7EK75;K7ELY2;X6R2W0;K7EIY4;Q5U8S2;O60499-2;O60499 F6RTM7 STX10 Syntaxin-10 0 118.4 0.0019505 0 76961 69817 42317 57449 74911 63976 67827 90812 71831 FALSE TRUE 66790.40886 69358.36753 62781.64274 70493.6735 73420.41766 66437.19812 61249.14798 71392.5605 63339.22101 1.054487374 1.095030321 0.991196951 1.112954539 1.159161993 1.048910881 0.967001914 1.127146172 1 15.9508115 1.194186748 23.6360466 0.99999822 1.069254592 0.120950638 0.058868397 14479.73449 7711583.352 7.544068025 0.014215841 15.63819947 -1.194186748 0.069256372 EELEALRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EELEALRR 8 1 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 ;; 184.49 0.00034911 428394000 546210 460200 319445 369570 457950 517130 455600 521070 389980 FALSE TRUE 474026.9646 457176.9159 473929.6705 453486.517 448837.691 537024.3257 411415.9821 409643.2355 343877.0087 1.378478214 1.329477995 1.378195281 1.318746254 1.305227391 1.561675576 1.196404446 1.19124927 1 18.39153314 1.577961784 1.60884896 0.989737779 1.367001288 0.666074573 0.084921859 0.303250098 1.274750196 0.159827538 0.024074886 37.84092846 -1.577961784 0.377263509 EELEEVIKDI ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EELEEVIKDI 10 1 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ;;; 176.83 1.95E-05 270430000 1176060 932850 660740 798950 887487 684788 1034077 1249840 954576 FALSE TRUE 1020640.691 926722.0469 980276.074 980363.8087 869827.745 711132.2375 933792.3717 982571.4423 841727.1127 1.212555323 1.100976828 1.164600806 1.164705038 1.033384492 0.844848914 1.109376611 1.16732778 1 19.68299306 3.239563364 24.98911863 1.044602325 1.156720846 0.349946067 0.086682439 39.06772388 973577.0564 0.02819951 0.034345044 1736.054537 -3.239563364 0.112118521 EELEFEVPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EELEFEVPFR 10 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ;;; 158.76 1.84E-05 408309000 825680 551250 418408 525280 568870 537750 538220 664140 934900 FALSE TRUE 716564.296 547628.8025 620751.5083 644552.8524 557550.6 558437.5905 486023.5072 522118.8293 824377.187 0.869218978 0.66429398 0.752994525 0.781866435 0.676329487 0.677405439 0.58956448 0.633349439 1 19.65294506 3.235505377 24.99265249 0.693753611 0.758743592 0.025002171 0.120441326 247.4199868 2023958.976 0.03550631 0.041996244 1719.908634 -3.235505377 0.064989981 EELEQASQAHGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EELEQASQAHGAR 13 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;;; 240.11 7.79E-17 3371360000 3475610 3162490 1812455 2584373 3359700 3199340 3330040 3947940 3623940 FALSE TRUE 3016299.332 3141715.395 2688964.3 3171194.389 3292848.543 3322420.68 3007093.233 3103703.754 3195521.942 0.943914449 0.983161891 0.841478904 0.992386986 1.030457185 1.039711428 0.941033511 0.971266607 1 21.60762016 3.553601695 24.99984749 0.993168969 0.926890943 0.375531985 0.044161987 145.0973604 47428.20128 0.012379303 0.01836147 3577.681661 -3.553601695 -0.066278026 EELFQGDAFHQSDTHIFIIMGASGDLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EELFQGDAFHQSDTHIFIIMGASGDLAK 28 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;; 200.12 2.63E-25 1389765000 1190525 1312449 239496 973596 1438660 1308597 1867670 1930340 1952920 FALSE TRUE 1033194.105 1303827.436 355317.0667 1194665.852 1410033.481 1358939.573 1686543.651 1517551.813 1722048.022 0.599979845 0.757137675 0.206334006 0.693747118 0.818811939 0.789141508 0.979382473 0.881248254 1 20.71569394 3.264921608 2.513542523 0.904695424 0.535807964 0.568065088 0.148556125 0.205459107 2.658201314 0.046517836 0.059868335 1840.439763 -3.264921608 -0.36888746 EELGFRPEYSASQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EELGFRPEYSASQLK 15 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 99.991 0.0021242 220820000 90620 73971 57813 78888 89423 77207 119090 124940 213840 FALSE TRUE 78644.3374 73485.07963 85771.56017 96800.72613 87643.65725 80177.20325 107540.6701 98222.55328 188560.0788 0.417078408 0.38971706 0.454876561 0.513368083 0.464804946 0.425207731 0.570325759 0.520908529 1 17.52466474 0.034361775 1.259120118 10 0.451914899 0.91606922 0.05074906 6.942620289 0.751308068 166.9696234 0.015204112 1.082335179 -0.034361775 -9.548085101 EELGLIEQAYDNPHEALSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EELGLIEQAYDNPHEALSR 19 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;;; 268.3 8.44E-32 815186000 1439136 1249678 780117 1031775 1235362 1179588 1135484 1485439 1395467 FALSE TRUE 1248950.531 1241468.783 1157384.191 1266055.283 1210780.713 1224967.514 1025364.936 1167789.43 1230496.481 1.014997239 1.008916971 0.940583097 1.028897931 0.983977388 0.995506718 0.833293676 0.949039227 1 20.2308091 EELHRWS(ph)DMSGDS(ph)S(ph)ATQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EELHRWSDMSGDSSATQK 18 1 Q8NF91;Q8NF91-4;A0A0C4DG40;E7ENN3;Q8NF91-7;Q8NF91-10 Q8NF91 SYNE1 Nesprin-1 3 EELHRWS(0.954)DMS(0.208)GDS(0.638)S(0.632)AT(0.567)QK 53.342 0.054019 2852100000 285060 262770 168970 231220 290330 266840 262350 282130 403580 TRUE FALSE 247388.5987 261043.8466 250684.4572 283722.035 284553.001 277105.5075 236907.3374 221798.695 355869.2322 0.695167147 0.733538679 0.704428578 0.797264864 0.799599896 0.778672283 0.665714583 0.623258981 1 18.44098768 3.777193253 23.82736216 0.75535517 0.713294169 0.061016442 0.10022789 1375.751396 848512.0302 0.027250973 0.047198745 5986.779368 -3.777193253 -0.042061001 EELMS(ph)SDLEETAGSTSIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EELMSSDLEETAGSTSIPK 19 0 O00567 O00567 NOP56 Nucleolar protein 56 1 EELMS(0.5)S(0.5)DLEETAGSTSIPK;EELMS(0.5)S(0.5)DLEETAGSTSIPK 131.51 9.96E-06 225198000 500220 361870 340110 445210 387850 333300 438860 548470 707740 TRUE FALSE 434114.6596 359492.8521 504588.3336 546301.7351 380132.5438 346122.2667 396299.4247 431183.9587 624071.7835 0.695616548 0.576044073 0.808542137 0.875382848 0.609116698 0.554619318 0.635022181 0.690920452 1 19.25135246 1.239513964 6.293456371 1.009957593 0.678877954 0.506270774 0.099172021 0.112617792 19.1893577 0.160108799 0.026132216 17.35857074 -1.239513964 -0.331079639 EELMSS(ph)DLEETAGSTSIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EELMSSDLEETAGSTSIPK 19 0 O00567 O00567 NOP56 Nucleolar protein 56 1 EELMS(0.205)S(0.795)DLEETAGSTSIPK;EELMS(0.083)S(0.917)DLEETAGSTSIPK;EELMS(0.07)S(0.93)DLEETAGSTSIPK;EELMS(0.005)S(0.995)DLEETAGSTSIPK;EELMS(0.247)S(0.753)DLEETAGSTSIPK;EELMS(0.137)S(0.863)DLEETAGSTSIPK 439.59 6.67E-191 2192144000 2844001 2192468 2048842 2457458 2148163 1706045 2527242 3104698 4272798 TRUE FALSE 2468159.062 2178065.533 3039668.844 3015461.399 2105418.759 1771677.655 2282150.46 2440782.493 3767672.688 0.655088503 0.578093087 0.80677625 0.800351211 0.558811482 0.470231308 0.605718874 0.647822328 1 21.84524221 1.238946314 6.956926162 1.007848164 0.638907682 0.549847079 0.102292484 0.09322719 25.60905839 0.162744605 0.027330611 17.33589686 -1.238946314 -0.368940482 EELMSS(ph)DLEETAGSTSIPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EELMSSDLEETAGSTSIPKR 20 1 O00567 O00567 NOP56 Nucleolar protein 56 1 EELMS(0.166)S(0.834)DLEETAGSTSIPKR;EELMS(0.187)S(0.813)DLEETAGSTSIPKR;EELMS(0.246)S(0.754)DLEETAGSTSIPKR 186.55 1.98E-17 320428000 338093 270460 151010 167502 246303 216202 307189 317273 167089 TRUE FALSE 293413.1534 268683.3305 224038.9411 205535.8892 241402.0522 224519.4308 277397.8581 249426.638 147335.9288 1.99145691 1.82361039 1.52059951 1.395015397 1.638446604 1.523860695 1.882757725 1.692911159 1 17.16874976 4.397465342 3.473112945 1.556389533 1.965891266 0.332021728 0.229054413 0.288504489 6.653054199 0.058873108 0.200188594 24972.69092 -4.397465342 0.409501734 EELRHT(ph)PELPLAPRPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EELRHTPELPLAPRPLK 17 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 EELRHT(1)PELPLAPRPLK 144.88 2.36E-05 256670000 578180 436320 277050 300240 349880 323490 424100 472830 286860 TRUE FALSE 501772.0481 433453.7852 411032.3067 368414.0809 342918.0725 335934.8696 382970.8473 371718.9841 252947.7376 1.983698502 1.71361005 1.624969294 1.456483005 1.355687447 1.328080151 1.514031519 1.469548562 1 17.94847981 7.999999999 0.394173003 1.308441488 12.19477683 0.733004363 0.133225138 47.66921251 0.677560732 0.13660756 398.0925369 99999999.86 -7.999999999 10.88633535 GAGATS(ph)GSPPAGRN ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GAGATSGSPPAGRN 14 1 B4DEE8;P16455 B4DEE8 MGMT Methylated-DNA--protein-cysteine methyltransferase 1 GAGAT(0.138)S(0.571)GS(0.29)PPAGRN;GAGAT(0.02)S(0.66)GS(0.32)PPAGRN;GAGAT(0.019)S(0.581)GS(0.4)PPAGRN;GAGAT(0.042)S(0.479)GS(0.479)PPAGRN 120.84 0.00012506 1831500000 2189570 2239310 1307350 1299040 1950530 2358330 2139520 2338320 918124 TRUE FALSE 1900212.777 2224599.825 1939588.833 1594006.887 1911718.269 2449056.481 1932029.68 1838288.465 809584.4267 2.347145911 2.747829321 2.39578328 1.968919898 2.361357514 3.025078547 2.386446201 2.2706569 1 19.62682201 1.194094471 2.784266887 0.573268727 2.465133801 0.733072363 0.274743682 0.290070561 2.401773099 1.344793671 0.074241811 15.63487707 -1.194094471 1.891865075 EELSHS(ph)PEPCTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EELSHSPEPCTK 12 0 P41229-4;P41229-3;P41229-2;P41229-5;P41229 P41229-4 KDM5C Lysine-specific demethylase 5C 1 EELS(0.001)HS(0.999)PEPCTK;EELSHS(1)PEPCTK 136.39 7.13E-05 812370000 1145090 1016480 736140 824200 1041840 788450 1126400 1298710 1306050 TRUE FALSE 993763.4552 1009802.676 1092139.766 1011347.207 1021109.422 818782.1817 1017161.901 1020990.973 1151650.257 0.862903863 0.876831026 0.9483259 0.878172172 0.88664889 0.710964268 0.883221182 0.886546039 1 20.13527122 1.189054763 2.444489799 1.046881472 0.863894463 0.337690876 0.059448148 0.833279724 4.793257681 0.343909607 0.016266931 15.45449303 -1.189054763 -0.182987009 EELSNVLAAMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EELSNVLAAMR 11 0 Q9Y3U8 Q9Y3U8 RPL36 60S ribosomal protein L36 0 ; 183.13 1.28E-05 78264000 119170 120743 76539 92297 111411 110669 118868 134750 158933 FALSE TRUE 103421.3826 119949.8313 113553.5164 113254.4445 109194.1391 114926.508 107340.1997 105934.7611 140144.1218 0.73796447 0.855903407 0.810262428 0.808128397 0.779156041 0.820059426 0.765927235 0.755898712 1 17.09655171 1.232388726 24.98779128 1.000000344 0.792379651 0.785481495 0.034214569 94.47598069 382461.4609 0.075441403 0.00836505 17.07610143 -1.232388726 -0.207620693 EELSSGDSLS(ph)PDPWKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EELSSGDSLSPDPWKR 16 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 EELSSGDSLS(1)PDPWKR;EELSSGDS(0.005)LS(0.995)PDPWKR;EELSSGDSLS(1)PDPWKR 184.8 1.08E-09 555214000 771560 609900 447894 555100 597610 451523 673620 857160 640640 TRUE FALSE 669596.3911 605893.5267 664497.0365 681143.9392 585718.7302 468893.382 608292.4361 673863.0044 564904.269 1.185327192 1.072559653 1.176300256 1.205768794 1.036845997 0.830040429 1.07680623 1.19288 1 19.10764688 3.223279035 24.45585344 1.041858351 1.154909109 0.317941886 0.095116281 291.5022703 466503.9053 0.032124836 0.036569407 1672.164639 -3.223279035 0.113050758 EELTLEGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EELTLEGIR 9 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3KTB5;J3KTN0 P60842;J3KTN0 EIF4A1 Eukaryotic initiation factor 4A-I 0 163.99 0.00014564 62842000 143210 119890 87444 109480 131660 114710 125850 138990 143350 FALSE TRUE 124284.4357 119102.4347 129732.2109 134339.1073 129040.2236 119122.9679 113645.0864 109268.0701 126403.3263 0.983237066 0.942241302 1.026335419 1.062781425 1.02086098 0.942403744 0.899067214 0.864439832 1 16.9476749 2.566482419 3.722830732 0.909307759 1.007313999 0.430445173 0.045792928 0.210225711 5.414498589 0.01765421 0.015019673 368.5381225 -2.566482419 0.09800624 EELYQNLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EELYQNLTR 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 149.27 0.0036898 175840000 352210 348760 217620 256040 300350 338040 347520 352810 332430 FALSE TRUE 305664.5561 346468.9726 322861.7599 314177.7953 294373.6226 351044.6175 313817.5639 277364.3271 293130.5041 1.042759289 1.181961508 1.101426687 1.071801777 1.004240836 1.197571091 1.070572866 0.946214478 1 18.16118358 1.854120978 5.060097223 0.973585814 1.100580066 0.434489622 0.058824299 0.188331745 6.740600417 0.03044735 0.015299491 71.46953846 -1.854120978 0.126994252 EEMAAEAGEAVASPMDDGFVSLDS(ph)PSYVLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEMAAEAGEAVASPMDDGFVSLDSPSYVLYR 31 0 P49354;P49354-2;E9PN85 P49354 FNTA Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha 1 EEMAAEAGEAVASPMDDGFVS(0.069)LDS(0.653)PS(0.145)Y(0.128)VLY(0.006)R 89.181 0.00037631 14526000 28137 24096 17807 23658 23314 22327 19547 26375 37348 TRUE FALSE 24418.62416 23937.71179 26418.52476 29029.91049 22850.09701 23185.93414 17651.33495 20734.9115 32932.76199 0.741469063 0.726866207 0.802195843 0.881490307 0.693840894 0.704038554 0.535981007 0.629613499 1 15.00723589 3.048526886 24.6587709 0.688043451 0.78502883 0.06437741 0.12427105 219.6128792 111593.8146 0.038195614 0.043309745 1118.219048 -3.048526886 0.096985379 EENEGVYNGSWGGR ddPTM_MDA-MB-175_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 ; 337.27 2.60E-68 975420000 549410 476560 358060 461610 493880 502810 465480 555670 589260 FALSE TRUE 476804.0765 473429.446 531219.0136 566425.6058 484052.7543 522153.4261 420337.8212 436844.2947 519598.3541 0.917639698 0.911145007 1.022364697 1.090122017 0.931590238 1.004917398 0.808966807 0.840734562 1 18.98703734 2.251329457 24.99613789 0.87128532 0.981298154 0.278829255 0.072200444 258.8882471 506796.7401 0.027796535 0.021388084 178.3731396 -2.251329457 0.110012833 EENHYLTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EENHYLTPR 9 0 Q5SXH7-4;Q5SXH7-3;Q5SXH7-2;Q5SXH7-1;Q5SXH7 Q5SXH7-4 PLEKHS1 Pleckstrin homology domain-containing family S member 1 0 ; 112.71 0.0019183 417810000 476410 491000 346830 429600 511810 530560 461770 534420 680780 FALSE TRUE 413451.2114 487774.5887 514558.1481 527147.246 501625.9823 550970.9865 416987.6165 420138.4419 600298.9639 0.688742171 0.812552774 0.857169809 0.878141189 0.835626933 0.917827649 0.694633244 0.699882004 1 19.19532165 4.732195275 4.55578555 0.824650089 0.680665551 0.195444307 0.091865091 0.358364039 19.46212164 0.023678198 0.164162941 53975.32616 -4.732195275 -0.143984539 EENKGGEDKLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EENKGGEDKLK 11 2 P62258;P62258-2;B4DJF2;I3L3T1;K7EIT4 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;; 91.937 0.0058318 8515110000 10834330 6677360 7982460 7104000 4803820 3400390 10743880 12479640 6212540 FALSE TRUE 9402545.84 6633495.982 11842804.36 8717071.778 4708233.381 3531205.204 9701940.171 9810966.103 5478100.599 1.716387947 1.210911677 2.161844994 1.591258069 0.859464571 0.644603935 1.771040892 1.790943033 1 22.38524433 3.456989742 24.81031432 1.292154593 1.685954181 0.213535004 0.424667513 437.1349166 538728.2509 0.133775795 0.172724279 2864.110321 -3.456989742 0.393799588 EENKVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EENKVR 6 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 79.454 0.061202 238450000 303740 320140 217170 243510 217280 323200 287360 338050 229970 FALSE TRUE 263599.9894 318036.9793 322194.1384 298802.6673 212956.5531 335633.7131 259491.8714 265760.6382 202783.2086 1.299910339 1.568359538 1.588860047 1.473507937 1.050168575 1.655135627 1.27965167 1.310565308 1 17.62957867 0.595669589 0.941570313 2.53E-16 1.439910178 0.365124648 0.174944365 6.878622266 2.009332264 13.61099454 0.058666005 3.941573134 -0.595669589 1.439910178 EENPES(ph)DGEPVVEDGTSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EENPESDGEPVVEDGTSVK 19 0 Q13439-5;Q13439-3;Q13439-4;Q13439;H0Y6I0;E7EVX2;A0A087WTW2 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 EENPES(1)DGEPVVEDGTSVK;EENPES(1)DGEPVVEDGTSVK;EENPES(1)DGEPVVEDGTSVK 287.37 5.30E-40 121570000 590340 463500 417060 538100 479440 413050 531780 669440 985850 TRUE FALSE 512325.0733 460455.238 618751.611 660283.8293 469900.082 428940.3008 480208.0574 526285.4656 869303.9361 0.589350919 0.529682679 0.711778223 0.75955463 0.540547515 0.493429608 0.552405249 0.605410195 1 19.72950115 1.239035311 7.390775399 1.006887096 0.596950237 0.70538393 0.081712618 0.06152208 22.96954248 0.12684342 0.021704265 17.33944973 -1.239035311 -0.409936859 EENSGLLQELEELRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EENSGLLQELEELRK 15 1 A0A3B3ISJ8;J3KP58;P30622-2;P30622-1;P30622;F5H0N7;A0A3B3ITA2 A0A3B3ISJ8;J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 0 ;;; 220.59 2.65E-12 171268000 187359 159611 115943 145089 155375 136606 180092 212690 180853 FALSE TRUE 162599.0334 158562.5048 172013.4226 178033.675 152283.3415 141861.3212 162626.7056 167207.8987 159472.7644 1.019603781 0.994292069 1.078638245 1.11638922 0.95491755 0.889564571 1.019777303 1.048504422 1 17.28295053 3.218027609 24.99999231 0.988939161 1.049978632 0.297813952 0.052609161 392.2519608 477585.8969 0.017999994 0.020434444 1652.06682 -3.218027609 0.061039471 EENVGLHQTLDQTLNELNCI ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EENVGLHQTLDQTLNELNCI 20 0 P67936;A0A2R8YE05;K7ENT6;A0A5F9UN72;K7EPB9;P67936-2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;;; 222.45 1.66E-24 265633000 470260 543563 240917 331772 473457 497775 495974 564161 496555 FALSE TRUE 408113.9495 539992.2989 357425.267 407105.9034 464036.132 516924.7264 447874.5178 443519.5605 437852.8336 0.932080184 1.233273505 0.816313701 0.929777935 1.059799313 1.180590113 1.022888248 1.012942081 1 18.74008652 3.207755646 24.71103934 1.053796887 0.984565912 0.100380333 0.114286128 490.8126523 393716.9838 0.034838114 0.039507425 1613.4505 -3.207755646 -0.069230974 EEPCLLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEPCLLKR 8 1 Q60FE5;P21333-2;P21333;H0Y5F3;H7C2E7 Q60FE5 FLNA Filamin-A 0 85.161 0.027161 226970000 362950 380130 177540 259590 383940 386530 465270 536170 231050 FALSE TRUE 314985.2379 377632.901 263398.9378 318533.8771 376300.3452 401400.0592 420148.187 421514.218 203735.5322 1.546049599 1.853544627 1.292847325 1.56346747 1.847004011 1.97020154 2.062223425 2.068928347 1 17.63633809 3.235392128 8.913230926 1.854290568 1.565025142 0.085285445 0.331708583 0.21775773 191.3615035 0.097599594 0.117157544 1719.460201 -3.235392128 -0.289265426 EEPDSENIPQELLSNLGHPES(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EEPDSENIPQELLSNLGHPESPPR 24 0 D6RF40;D6RAG5;D6R9R7;A0A0A0MTL5;Q13309-2;Q13309 D6RF40 SKP2 S-phase kinase-associated protein 2 1 EEPDSENIPQELLS(0.002)NLGHPES(0.998)PPR;EEPDSENIPQELLSNLGHPES(1)PPR;EEPDSENIPQELLSNLGHPES(1)PPR;EEPDSENIPQELLSNLGHPES(1)PPR 197.12 1.23E-24 372734000 495413 452250 355357 489494 483813 510251 492832 602080 838783 TRUE FALSE 429942.9168 449279.14 527208.8338 600641.0941 474186.0679 529880.6861 445037.2285 473329.8774 739623.0293 0.581300067 0.607443417 0.712807488 0.812090849 0.641118582 0.71641994 0.601708182 0.639960978 1 19.49643062 1.235920483 24.99957397 1.000000444 0.665341627 0.704341008 0.068388341 42.91531037 406284.1808 0.115945089 0.01742484 17.21553338 -1.235920483 -0.334658817 EEPFFPPPEEFVFIHAVPVEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EEPFFPPPEEFVFIHAVPVEER 22 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;;; 206.34 9.40E-23 929782000 829203 635696 520896 575574 608401 628131 611465 805724 856634 FALSE TRUE 719621.7226 631520.0711 772803.0479 706266.8738 596295.0104 652295.606 552165.2184 633426.1928 755363.7044 0.952682421 0.836047678 1.023087346 0.935002396 0.789414433 0.863551693 0.730992521 0.838571127 1 19.52681194 3.257061922 24.38127276 0.836202889 0.935685389 0.240053146 0.080758616 251.0244555 330800.8024 0.023024365 0.029661991 1807.431812 -3.257061922 0.0994825 EEPGPRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EEPGPRPR 8 1 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ;;;;; 130.22 0.00096415 1875578000 5030501 4885938 3179088 3391091 4362606 4852342 4779062 5343205 4266335 FALSE TRUE 4365707.547 4853841.952 4716505.59 4161090.041 4275798.676 5039014.737 4315589.303 4200602.192 3761973.737 1.16048326 1.290238128 1.253731663 1.106092262 1.136583872 1.339460371 1.147160933 1.1165953 1 21.84305835 1.447577946 1.730586788 0.975569963 1.210985616 0.468636881 0.071958885 0.549017884 2.298560113 0.197243798 0.020838206 28.02708597 -1.447577946 0.235415653 EEPGS(ph)PLSPAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEPGSPLSPAPR 12 0 B2RBV5 B2RBV5 LOC93622 1 EEPGS(1)PLSPAPR 85.845 0.012005 297530000 216890 194530 122840 126570 195450 189670 178620 208650 152610 TRUE FALSE 188227.437 193252.1196 182245.8349 155309.653 191560.9274 196966.7276 161297.4599 164031.8212 134568.6197 1.398746881 1.436086066 1.35429668 1.154129792 1.423518558 1.463689887 1.198626101 1.218945558 1 17.0379825 1.157733871 1.048647484 0.772369686 1.363420271 0.599367005 0.094613261 1.549121947 1.248450349 1.085231569 0.03255278 14.37917176 -1.157733871 0.591050585 EEPLDPEEAEGPLSLVT(ph)TANHSPDFDHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EEPLDPEEAEGPLSLVTTANHSPDFDHDR 29 0 A0A3B3IUB6;Q9H334-8;C9J0F0;Q9H334-3;Q9H334-7;Q9H334-6;Q9H334;Q9H334-4;A0A3B3IRS5;A0A3B3IST0;H0Y882;A0A0B4J2F3;A0A3B3IRW5;A0A3B3IT66 A0A3B3IUB6 FOXP1 Forkhead box protein P1 1 EEPLDPEEAEGPLS(0.003)LVT(0.442)T(0.37)ANHS(0.185)PDFDHDR;EEPLDPEEAEGPLS(0.073)LVT(0.309)T(0.309)ANHS(0.309)PDFDHDR;EEPLDPEEAEGPLS(0.058)LVT(0.314)T(0.314)ANHS(0.314)PDFDHDR 163.15 1.06E-11 149058000 179646 143810 157656 209998 180779 162752 175291 201905 455697 TRUE FALSE 155905.3259 142865.3026 233898.9689 257681.2555 177181.8516 169013.1748 158291.3058 158729.187 401825.0198 0.387993077 0.355541083 0.582091601 0.641277279 0.440942806 0.420613865 0.393930935 0.395020666 1 18.61620787 1.234908059 24.99978933 1.000000775 0.452378979 0.783123849 0.090601121 53.41595842 365547.3232 0.174851343 0.024209535 17.17544741 -1.234908059 -0.547621796 EEPLDPEEAEGPLSLVTTANHS(ph)PDFDHDRDYEDEPVNEDME ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.027)T(0.147)ANHS(0.826)PDFDHDRDYEDEPVNEDME;EEPLDPEEAEGPLSLVT(0.14)T(0.14)ANHS(0.721)PDFDHDRDYEDEPVNEDME;EEPLDPEEAEGPLSLVTT(0.021)ANHS(0.979)PDFDHDRDYEDEPVNEDME;EEPLDPEEAEGPLSLVT(0.013)T(0.209)ANHS(0.778)PDFDHDRDYEDEPVNEDME 294.8 1.47E-96 852050000 541110 527060 352167 436184 524160 511600 530830 656620 488200 TRUE FALSE 469600.9425 523597.7082 522476.1391 535226.2439 513730.2415 531281.583 479350.1883 516206.9228 430485.5522 1.090863422 1.216295659 1.2136903 1.243308262 1.193373945 1.23414498 1.113510514 1.199127172 1 18.71560529 0.56450333 1.64027493 1.32E-16 1.194643137 0.566434516 0.050632199 5.7572249 2.700152626 19.23771921 0.013468494 3.668625077 -0.56450333 1.194643137 EEPLS(ph)EEEPCTSTAIASPEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EEPLSEEEPCTSTAIASPEKK 21 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 1 EEPLS(1)EEEPCTSTAIASPEKK;EEPLS(1)EEEPCTSTAIASPEKK;EEPLS(1)EEEPCTSTAIASPEKK;EEPLS(1)EEEPCTSTAIASPEKK 178.39 3.75E-17 1512530000 1733610 1063920 1089200 1184900 981800 771370 1452220 1742070 1671340 TRUE FALSE 1504509.046 1056931.039 1615940.763 1453949.655 962264.1009 801045.103 1311383.928 1369541.887 1473756.089 1.02086706 0.717168226 1.096477752 0.986560575 0.652933079 0.543539809 0.889824264 0.929286669 1 20.49106634 4.789346169 20.86012534 0.855776144 1.020873659 0.088407456 0.17005046 13988.92471 5744641.753 0.043813871 23.03273522 61566.7416 -4.789346169 0.165097515 EEPVLT(ph)PIDEGHLPMINQDEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEPVLTPIDEGHLPMINQDEFR 22 0 P24723-2;P24723 P24723-2 PRKCH Protein kinase C eta type 1 EEPVLT(1)PIDEGHLPMINQDEFR 175 7.30E-12 52451000 58820 52882 49618 64227 45449 62954 48570 65377 137130 TRUE FALSE 51046.78797 52534.61466 73613.43076 78810.722 44544.65382 65375.88112 43859.68888 51396.63731 120918.6476 0.422158112 0.434462473 0.608784767 0.651766486 0.368385313 0.540660042 0.362720637 0.425051374 1 16.88367722 1.235181229 24.99701496 1.000000731 0.475865127 0.742630259 0.096805414 51.34824114 379755.5986 0.172973841 0.024484047 17.18625411 -1.235181229 -0.524135604 EEPVSS(ph)GPEEAVGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EEPVSSGPEEAVGK 14 0 O00567 O00567 NOP56 Nucleolar protein 56 1 EEPVS(0.014)S(0.986)GPEEAVGK;EEPVS(0.005)S(0.995)GPEEAVGK;EEPVS(0.016)S(0.984)GPEEAVGK;EEPVS(0.004)S(0.996)GPEEAVGK 280.97 2.83E-33 1050310000 2992490 2081650 1569030 2023940 2067590 1746380 2302810 2727740 2897750 TRUE FALSE 2597024.864 2067975.504 2327818.156 2483506.511 2026449.004 1813564.369 2079483.841 2144434.028 2555181.296 1.016375968 0.809326331 0.911018784 0.971949237 0.793074451 0.709759566 0.813830253 0.839249266 1 21.28499423 3.229917874 24.99200069 0.824818433 0.917596866 0.222036476 0.088028456 304.446777 880359.6515 0.026870613 0.030943474 1697.922543 -3.229917874 0.092778433 EEQKLEAHSDWVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEQKLEAHSDWVR 13 1 P55735;P55735-4;P55735-3;P55735-2;A8MXL6 P55735 SEC13 Protein SEC13 homolog 0 ; 131.53 7.77E-05 1311270000 646612 534610 398613 517413 501995 409692 538251 659420 796260 FALSE TRUE 561160.5859 531098.1117 591383.5801 634899.5298 492006.2816 425453.1163 486051.5009 518408.1646 702127.0499 0.799229407 0.756413119 0.842274315 0.904251631 0.700736828 0.605948904 0.692255769 0.738339542 1 19.42137258 3.216841835 24.99772783 0.735101223 0.821799538 0.111075166 0.106396116 504.3234555 580460.9344 0.033261298 0.037746469 1647.562259 -3.216841835 0.086698315 EEQNGEDEDGGWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEQNGEDEDGGWR 13 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;C9IYH5;C9JH78;Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 0 ; 253.76 2.01E-23 338850000 499100 417810 365100 450670 429890 440790 432300 521850 744850 FALSE TRUE 433142.6704 415065.3786 541663.5812 553001.5116 421336.0301 457747.4765 390375.6125 410256.4385 656794.6815 0.659479564 0.631956059 0.824707624 0.841970142 0.641503413 0.696941509 0.594364759 0.624634228 1 19.32508292 1.231410857 24.96398821 1.000000553 0.687882781 0.582711035 0.082581696 200.452336 699833.0131 0.21809729 0.022053979 17.03769571 -1.231410857 -0.312117772 EEQRS(ph)PFNDRFPLK ddPTM_MDA-MB-175_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 215.57 3.37E-12 1216090000 2463570 1755700 1321040 1491180 1654960 1550080 1996670 2237480 1901560 TRUE FALSE 2138002.983 1744166.691 1959899.363 1829775.21 1622029.534 1609712.581 1803033.251 1759012.314 1676759.743 1.275080101 1.040200719 1.168861174 1.091256644 0.96735954 0.960013852 1.075308051 1.049054476 1 20.67724455 8 0.609191533 1.023417303 16.27799984 0.603412149 0.059805913 139.3797969 1.059828074 0.028386607 2835.770351 99999999.99 -8 15.25458254 EEQT(ph)DTS(ph)DGESVTHHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEQTDTSDGESVTHHIR 17 0 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 2 EEQT(1)DT(0.012)S(0.988)DGESVTHHIR;EEQT(1)DT(0.005)S(0.995)DGESVTHHIR 143.47 9.72E-07 446530000 353550 278050 220670 262780 346390 341830 288920 332880 494380 TRUE FALSE 306827.4717 276223.4712 327386.7501 322448.2153 339497.5167 354980.4213 260900.5829 261696.2025 435934.9596 0.703837728 0.633634594 0.750999072 0.739670467 0.778780204 0.814296751 0.598485111 0.600310199 1 18.73375338 4.228038506 24.45076053 0.734959862 0.668736156 0.069186859 0.114484557 484.6868984 1126302.385 0.029964403 0.063487714 16905.90818 -4.228038506 -0.066223707 EEQTDTS(ph)DGESVTHHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEQTDTSDGESVTHHIR 17 0 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 1 EEQTDT(0.004)S(0.982)DGES(0.006)VT(0.008)HHIR;EEQTDT(0.004)S(0.995)DGES(0.001)VT(0.001)HHIR 115.76 0.00049993 1877270000 486600 390920 235419 326370 378600 339490 394570 449950 489850 TRUE FALSE 422294.5771 388352.0208 349268.4158 400477.2968 371066.6007 352550.4 356304.6621 353731.694 431940.491 0.977668419 0.899086862 0.80860309 0.927158498 0.859068803 0.816201322 0.824892941 0.818936176 1 18.72047304 4.627361031 3.372843411 0.858707814 0.981196849 0.255674777 0.059553455 0.336124828 6.182228983 0.014398435 0.087366458 42399.52892 -4.627361031 0.122489035 EEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK 40 0 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ;; 406.56 4.56E-200 1974260000 1034620 930120 477690 920730 914870 710810 1114740 1212910 1380700 FALSE TRUE 897892.3456 924009.9805 708702.4818 1129795.819 896665.8769 738155.3207 1006632.686 953538.6354 1217475.219 0.737503591 0.758955884 0.582108343 0.9279826 0.736496204 0.606300078 0.826819857 0.783209893 1 20.21546098 0.595527759 1.241980735 1.846020898 0.733553669 0.413784153 0.097373113 6.25820317 2.506508201 13.38845621 0.0281955 3.940286117 -0.595527759 -1.112467229 EERLS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EERLSPR 7 1 A0A0G2JHC2;Q6NYC8-2;Q6NYC8 A0A0G2JHC2 PPP1R18 Phostensin 1 EERLS(1)PR;EERLS(1)PR;EERLS(1)PR;EERLS(1)PR 103.87 0.0050134 1629910000 1952110 1858110 1184150 1462120 1690880 1819880 1745190 2012920 1573310 TRUE FALSE 1694133.717 1845903.953 1756808.901 1794116.693 1657234.796 1889891.961 1575941.742 1582472.723 1387315.084 1.221160021 1.330558555 1.266337345 1.293229428 1.194562659 1.362265849 1.135965262 1.140672902 1 20.40386406 1.449904508 1.076418386 0.927919098 1.277562903 0.701943557 0.058187943 0.620066566 0.784999971 0.23748542 0.018087028 28.17763296 -1.449904508 0.349643805 EERS(ph)PQTLAPVGEDAMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EERSPQTLAPVGEDAMK 17 1 Q92797 Q92797 SYMPK Symplekin 1 EERS(0.683)PQT(0.317)LAPVGEDAMK;EERS(0.995)PQT(0.005)LAPVGEDAMK;EERS(0.995)PQT(0.005)LAPVGEDAMK 192.09 1.25E-10 657730000 1370910 1063110 878050 1016145 1076349 878973 1213860 1488190 1231674 TRUE FALSE 1189740.77 1056126.36 1302677.917 1246876.253 1054931.761 912787.6601 1096140.044 1169952.15 1086066.903 1.095458085 0.972432138 1.199445369 1.148065787 0.971332206 0.840452515 1.009274881 1.077237642 1 20.05068155 3.228887509 24.99811105 0.987117518 1.101291548 0.365389109 0.080965792 262.7704677 679073.778 0.026697426 0.030647042 1693.898991 -3.228887509 0.11417403 EES(ph)DGEYDEFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EESDGEYDEFGR 12 0 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 EES(1)DGEYDEFGR;EES(1)DGEYDEFGR;EES(1)DGEYDEFGR;EES(1)DGEYDEFGR 320.42 1.12E-46 7248370000 3087490 2201980 1981800 2444490 2360030 2302160 2284610 2705720 4651050 TRUE FALSE 2679470.374 2187515.048 2940205.109 2999548.816 2313070.02 2390725.585 2063048.874 2127122.834 4101208.167 0.653336837 0.533383081 0.716911941 0.731381752 0.563997224 0.582932026 0.50303442 0.518657612 1 21.96761754 1.231825536 24.99856717 1.000000687 0.596001517 0.716889064 0.078863905 138.8171043 515199.01 0.200612148 0.021055093 17.05397162 -1.231825536 -0.403999169 EES(ph)DGEYDEFGRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EESDGEYDEFGRK 13 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 EES(1)DGEYDEFGRK 137.39 3.75E-05 187280000 203590 121220 124000 135420 141590 132970 169520 184460 249500 TRUE FALSE 176685.0657 120423.6978 183966.8148 166169.1808 138772.636 138085.4419 153079.9765 145014.6645 220004.3942 0.803097894 0.547369512 0.836196092 0.755299372 0.63077211 0.627648563 0.695804177 0.6591444 1 17.74717281 1.23502599 24.97372077 1.000000441 0.690490766 0.55253801 0.086358787 73.94976337 522404.7455 0.142677405 0.019965012 17.18011197 -1.23502599 -0.309509676 EES(ph)EEEEDEDDEEEEEEEKEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EESEEEEDEDDEEEEEEEKEK 21 1 H0Y993;A0A494C028;P35659;B4DFG0;H0Y8X0;A0A494C198;D6R9L5 H0Y993 DEK Protein DEK 1 EES(1)EEEEDEDDEEEEEEEKEK;EES(1)EEEEDEDDEEEEEEEKEK;EES(1)EEEEDEDDEEEEEEEKEK 246.17 1.71E-30 1274390000 773644 468829 602164 405775 477532 301916 675639 780935 756493 TRUE FALSE 671404.9852 465749.2314 893372.5245 497912.4156 468030.0475 313530.9039 610115.6338 613938.1275 667061.2593 1.006511735 0.698210584 1.33926609 0.746426822 0.701629784 0.470018157 0.91463209 0.920362439 1 19.34745973 EES(ph)EES(ph)DEDMGFGLFD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EESEESDEDMGFGLFD 16 0 F8VWS0;P05388;P05388-2;Q8NHW5;F8W1K8 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 2 EES(1)EES(1)DEDMGFGLFD;EES(1)EES(1)DEDMGFGLFD;EES(1)EES(1)DEDMGFGLFD;EES(1)EES(1)DEDMGFGLFD 224.16 1.80E-14 514467000 673402 615519 392051 544487 706562 661811 698741 801777 913731 TRUE FALSE 584410.2195 611475.6152 581648.1749 668121.0953 692502.7986 687271.2974 630977.2054 630323.228 805710.7621 0.725335005 0.758926955 0.72190692 0.829231936 0.859493048 0.853000022 0.783131162 0.782319484 1 19.6199025 -1.999999055 0.032381046 1.972872453 1.24E-06 0.457129169 0.060025292 3028.844372 9.700905634 427.8179035 203.2882207 0.010000022 1.999999055 -1.972871215 EES(ph)EES(ph)EAEPVQR ddPTM_MDA-MB-175_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 326.36 1.19E-52 1913090000 1695350 1378530 946310 1024520 1424060 1327080 1490420 1464590 1500160 TRUE FALSE 1471305.202 1369474.346 1403948.681 1257152.925 1395723.992 1378133.626 1345879.298 1151398.826 1322812.794 1.112255044 1.035274494 1.06133588 0.950363446 1.055118304 1.041820606 1.017437467 0.870417062 1 20.33517747 -1.99999277 0.048985055 0.153917991 1.499604594 0.363517353 0.052953 1158.328461 5.552546888 133.0638532 43.30103835 0.010000166 1.99999277 1.345686604 EES(ph)EESEAEPVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EESEESEAEPVQR 13 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 EES(0.986)EES(0.014)EAEPVQR;EES(0.994)EES(0.006)EAEPVQR 374.2 2.17E-91 448740000 594370 426120 263520 348690 425640 416050 415890 550650 464660 TRUE FALSE 515822.4986 423320.7897 390959.1534 427865.3939 417170.5968 432055.7127 375557.0518 432897.7827 409728.4241 1.25893755 1.033174085 0.954190948 1.044265832 1.018163672 1.054492896 0.916599947 1.056548087 1 18.64430845 4.731573646 4.343143737 1.008606075 1.275793657 0.763124303 0.043859301 0.08851477 4.01522775 0.010035153 0.072364438 53898.12361 -4.731573646 0.267187581 EES(ph)LPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EESLPR 6 0 I3L461;Q6ZMQ8-2;Q6ZMQ8-3 I3L461 AATK 1 EES(1)LPR 89.401 0.052667 11477000000 2722500 2145600 1815800 1940500 1762500 2009300 2177400 2453600 3317100 TRUE FALSE 2362714.727 2131505.412 2693926.953 2381120.184 1727429.698 2086599.071 1966236.083 1928916.734 2924956.217 0.80777781 0.728730707 0.921014454 0.814070368 0.590583096 0.713377882 0.672227527 0.659468584 1 21.4799836 3.426934507 24.99934959 0.712818729 0.819699323 0.125477397 0.115754048 188.8948737 94092.71758 0.032530966 0.041997305 2672.60334 -3.426934507 0.106880594 EES(ph)PLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 129.77 0.016835 6706350000 8270270 6950140 5439120 6679080 5500290 6620190 6708280 7824480 10739700 TRUE FALSE 7177332.865 6904484.073 8069496.625 8195667.197 5390844.99 6874872.993 6057712.038 6151275.842 9470064.901 0.757896904 0.729085191 0.852105736 0.865428831 0.569251114 0.725958382 0.639669538 0.649549492 1 23.17494288 4.77336198 18.71732891 0.740289614 0.757897666 0 0.126295692 7554.114423 4060747.285 0.030669064 2.468183601 59341.97284 -4.77336198 0.017608052 EES(ph)WESGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EESWESGR 8 0 Q9NQ29-3;Q9NQ29;B8ZZ08 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 1 EES(0.999)WES(0.001)GR;EES(0.998)WES(0.002)GR 143.39 0.00063163 575390000 968250 828190 613290 785770 822240 842850 862560 1000020 1245880 TRUE FALSE 840293.3093 822749.5654 909879.0953 964191.0882 805879.0327 875274.9849 778909.064 786173.5052 1098593.486 0.764881023 0.748911746 0.828221819 0.877659572 0.733555262 0.796723261 0.709005719 0.715618211 1 20.06722621 1.230150116 24.99515285 1.000000429 0.770179292 0.65684919 0.051818446 217.6507513 646784.6692 0.153783026 0.013735467 16.98830761 -1.230150116 -0.229821137 EES(ph)YSPSKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EESYSPSKDR 10 1 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 EES(0.568)Y(0.001)S(0.377)PS(0.053)KDR 62.89 0.04975 788630000 1925300 1611300 1280200 1496700 1628100 1493200 1928800 2260600 2089000 TRUE FALSE 1670866.727 1600715.264 1899309.002 1836548.611 1595703.995 1550644.37 1741745.273 1777188.282 1842040.8 0.90707368 0.868990125 1.031089541 0.997018422 0.866269626 0.841807831 0.945551951 0.964793115 1 20.81287359 1.628023113 2.543131917 0.994225507 0.921690652 0.170396299 0.05827615 0.515089801 7.292766605 0.065197385 0.017216849 42.46421631 -1.628023113 -0.072534855 EESEES(ph)DEDMGFGLFD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EESEESDEDMGFGLFD 16 0 F8VWS0;P05388;P05388-2;Q8NHW5;F8W1K8 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 1 EESEES(1)DEDMGFGLFD;EESEES(1)DEDMGFGLFD 249.32 5.82E-20 166432000 216155 186839 141655 162951 187841 202282 204441 231062 232544 TRUE FALSE 187589.5691 185611.6423 210159.8318 199951.5151 184103.3316 210063.9194 184614.3433 181651.1894 205052.9132 0.914834938 0.905189004 1.02490537 0.975121553 0.897833289 1.024437625 0.900325386 0.885874707 1 17.64563671 1.179324541 22.78229038 1.000004856 0.940386034 0.115161097 0.051308989 24095.63451 9264032.523 24.92373234 0.012824076 15.11209035 -1.179324541 -0.059618822 EESEKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EESEKPR 7 1 P83916;J3KS05;K7ELA4 P83916 CBX1 Chromobox protein homolog 1 0 122.79 0.0039277 351440000 717410 677710 511160 721570 411050 618000 939960 1107200 1673600 FALSE TRUE 622602.4508 673258.0784 758358.6857 885413.497 402870.9092 641774.8599 848802.8239 870433.8962 1475748.915 0.421889147 0.456214517 0.513880565 0.599975706 0.27299421 0.434880794 0.575167507 0.589825198 1 20.49301585 0.552270106 1.160744098 2.800582221 0.457158872 0.788130445 0.087187185 3.131657311 1.072963045 13.29418539 0.027279151 3.566728942 -0.552270106 -2.343423349 EESELQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EESELQR 7 0 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 84.916 0.049308 62132000 150770 145020 105990 130020 119020 142170 139410 166230 169320 FALSE TRUE 130845.3625 144067.3541 157247.1185 159543.0282 116651.7349 147639.3719 125890.0397 130683.0081 149303.1825 0.876373566 0.964931569 1.053206743 1.068584243 0.781307759 0.988856161 0.8431839 0.875286152 1 17.18788539 3.253145624 24.99988343 0.89538744 0.993387592 0.243636958 0.081348753 332.1643795 569353.4074 0.023046192 0.029619598 1791.206364 -3.253145624 0.098000152 EESGKPGAHVTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 EESGKPGAHVTVK 13 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;; 161.63 2.51E-05 11500930000 25403740 17475450 8769719 15375020 16439479 11854461 21703606 24933540 24008190 FALSE TRUE 22046571.39 17360652.62 13010784.44 18866153.28 16112365.53 12310509.79 19598793.63 19601696.5 21169969.13 1.04140782 0.820060365 0.614586841 0.891175286 0.761095372 0.58150816 0.925782816 0.925919938 1 24.33551583 2.032564742 24.99973001 0.948123637 0.780154533 0.265599321 0.130210009 246.2770495 189064.2727 0.052892965 0.035660145 107.7865923 -2.032564742 -0.167969104 EESGKPGAHVTVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EESGKPGAHVTVKK 14 2 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 68.972 0.029008 447990000 1000900 699080 362070 399600 420550 460850 903460 1046300 428160 FALSE TRUE 868628.529 694487.6974 537168.2631 490335.2875 412181.8778 478579.1977 815842.5883 822556.8873 377543.4126 2.300738141 1.839490968 1.422798664 1.298752067 1.091746973 1.267613688 2.160923913 2.17870809 1 18.52628302 4.599538282 2.9390013 1.558795705 2.32872131 0.28902161 0.402032087 0.500613128 6.99849793 0.115928629 0.758600055 39768.41502 -4.599538282 0.769925605 EESHSNDQSPQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EESHSNDQSPQIR 13 0 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 ; 180.48 1.29E-05 969350000 1213830 1045970 649460 809670 977030 1151040 1014200 1209110 1285860 FALSE TRUE 1053419.29 1039098.954 963541.0283 993517.9485 957589.0145 1195321.254 915843.0401 950551.2358 1133847.096 0.929066445 0.91643658 0.84979803 0.876236269 0.844548633 1.054217326 0.80773064 0.838341642 1 20.11279467 1.887122664 0.003701693 0.698424054 1.08863597 0 0.077434627 2999704.865 4568.145673 243162.1458 238396.9424 77.11212362 -1.887122664 0.390211916 EESLADDLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EESLADDLFR 10 0 O60934;A0A0C4DG07;A0A087X1V5 O60934 NBN Nibrin 0 ; 119.75 0.0015155 54176000 151793 120596 73311 102886 116259 115050 117209 149231 123174 FALSE TRUE 131733.1705 119803.7969 108764.4448 126247.8388 113945.6734 119476.0479 105842.0892 117319.112 108612.51 1.212872904 1.103038654 1.00139887 1.162369222 1.049102662 1.100021056 0.974492618 1.080162054 1 16.72883076 EESQDTLTHS(ph)SPSFNLDTLLVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EESQDTLTHSSPSFNLDTLLVPK 23 0 A0A0U1RR27;Q7Z401;Q7Z401-2 A0A0U1RR27 DENND4A C-myc promoter-binding protein 1 EES(0.014)QDT(0.062)LT(0.062)HS(0.441)S(0.385)PS(0.031)FNLDT(0.005)LLVPK 53.844 0.06967 46650000 22016 28518 23372 28951 33306 35095 43175 44654 58834 TRUE FALSE 19106.52982 28330.66338 34674.77737 35524.76704 32643.27576 36445.12736 38987.89515 35105.0896 51878.71154 0.368292297 0.546094198 0.668381622 0.684765793 0.629222947 0.702506409 0.751520113 0.676676204 1 15.66285503 5.167032115 0.250967614 0.878008249 4.53E-44 0.681921146 0.089155921 14.1853376 0.86566008 0.437405388 4.155568111 146903.4905 -5.167032115 -0.878008249 EESQDTLTHSS(ph)PSFNLDTLLVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EESQDTLTHSSPSFNLDTLLVPK 23 0 A0A0U1RR27;Q7Z401;Q7Z401-2 A0A0U1RR27 DENND4A C-myc promoter-binding protein 1 EESQDT(0.002)LT(0.002)HS(0.094)S(0.898)PS(0.003)FNLDTLLVPK 138.71 1.67E-06 47700000 16556 22091 18859 21114 23416 24190 35320 33109 43786 TRUE FALSE 14368.08265 21945.88277 27979.27548 25908.25641 22950.06741 25120.60495 31894.67184 26028.898 38609.66896 0.372136904 0.568403805 0.724670173 0.671030265 0.594412437 0.650629897 0.826079909 0.674154913 1 15.23667456 -2 0.078657645 2.308989647 6.01E-13 0.608540318 0.102406222 364.3860573 2.72305582 96.63480235 16.13373464 0.01 2 -2.308989647 EESSIHCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EESSIHCK 8 0 A0A669KBJ7;Q9H2P0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 65.038 0.065307 63549000 87560 85338 38739 63950 67688 81661 78873 110700 91764 FALSE TRUE 75988.72415 84777.40906 57473.30997 78470.82491 66341.14123 84802.55151 71223.9086 87027.66647 80915.76446 0.939109019 1.047724255 0.710285695 0.969784138 0.819879064 1.048034979 0.880222897 1.075534132 1 16.30413318 1.739423263 11.26813456 1.036093152 0.916963252 0.195822711 0.10215913 0.120744622 92.56320826 0.052382642 0.02462124 54.88115755 -1.739423263 -0.1191299 EESTSSGNVSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EESTSSGNVSNR 12 0 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 0 145.41 0.0006854 0 156850 106650 87635 110830 100800 108500 110070 124720 161230 FALSE TRUE 136121.8751 105949.4091 130015.5791 135995.6454 98794.27721 112674.0652 99395.42834 98049.59857 142169.5731 0.957461376 0.74523266 0.914510583 0.956573495 0.694904508 0.792532908 0.699132917 0.689666547 1 17.11725321 3.236492989 24.99997426 0.759705466 0.884362683 0.223673059 0.106675348 78.18589467 945359.1901 0.030980883 0.036903653 1723.824264 -3.236492989 0.124657217 EESYS(ph)PSKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EESYSPSKDR 10 1 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 EES(0.023)YS(0.918)PS(0.06)KDR;EES(0.062)YS(0.913)PS(0.025)KDR;EESYS(0.972)PS(0.028)KDR 168.02 1.33E-05 1210420000 2372590 2112940 1726730 1855040 2009030 1734310 2425750 2840850 2580970 TRUE FALSE 2059046.22 2099059.958 2561782.404 2276255.185 1969054.234 1801030.028 2190501.138 2233356.335 2275850.667 0.904736963 0.922318845 1.125637302 1.000177743 0.865194831 0.791365644 0.962497747 0.981328155 1 21.11797447 4.459187576 24.99944453 0.9593455 0.909132149 0.049981705 0.087284398 780.7854 1088411.058 0.023647143 0.062593012 28786.41461 -4.459187576 -0.050213351 EETEELKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EETEELKR 8 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;; 146.58 0.00088346 2700000000 1382120 1140760 874020 1265670 1094830 1077070 1398460 1741630 2593410 FALSE TRUE 1199469.34 1133266.272 1296698.995 1553059.718 1073045.025 1118505.58 1262837.564 1369195.978 2286820.024 0.524514097 0.49556426 0.567031503 0.679135088 0.469230203 0.489109579 0.55222429 0.598733597 1 21.1249114 1.203539104 2.955797268 1.116283313 0.54067071 0.859013774 0.058111295 0.171016866 1.718034713 0.24808009 0.015601301 15.97861396 -1.203539104 -0.575612603 EETKEDAEEKQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EETKEDAEEKQ 11 2 P43487;F6WQW2;P43487-2 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;;;;; 171.32 5.83E-05 4621630000 7927420 5551850 6303830 6176390 4343560 3195680 8334240 9484960 8996860 FALSE TRUE 6879791.361 5515379.532 9352383.273 7578833.75 4257131.654 3318619.877 7525986.688 7456675.116 7933261.46 0.867208448 0.695222206 1.178882521 0.955323833 0.536618095 0.41831722 0.948662379 0.939925547 1 22.91948267 2.0481523 24.99999351 0.959263699 0.778655991 0.15071775 0.20993526 243.0181203 126170.467 0.093076473 0.062752128 111.7254982 -2.0481523 -0.180607708 EETPGQRPAVTETHQLAELNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EETPGQRPAVTETHQLAELNEK 22 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1;I3L1C0 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ;;; 246.22 3.65E-31 820390000 1683910 1203830 878230 1023800 1061340 979890 1338580 1626890 1339000 FALSE TRUE 1461377.027 1195921.961 1302944.966 1256269.438 1040221.41 1017587.002 1208764.718 1278992.234 1180704.945 1.237715682 1.012888077 1.103531387 1.063999471 0.881017239 0.861846989 1.02376527 1.083244581 1 20.17121705 7.999999993 0.85379146 0.994221417 85.83546756 0.480676988 0.077558174 732.2969375 1.99339048 0.029436294 120705.8075 99999998.39 -7.999999993 84.84124614 EETVNDPEEAGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EETVNDPEEAGHR 13 0 O00567 O00567 NOP56 Nucleolar protein 56 0 ; 189.3 5.38E-06 285490000 412630 373930 255860 350280 352430 337310 323100 365030 574780 FALSE TRUE 358099.9 371473.6292 379594.7518 429816.4277 345417.3325 350286.534 291765.8117 286971.1752 506830.1632 0.706548122 0.732935125 0.748958486 0.84804824 0.681524814 0.69113198 0.575667813 0.566207767 1 18.95114286 3.042887573 24.92383152 0.675038793 0.757558648 0.022303462 0.124297261 344.7343797 200337.8497 0.037606417 0.042641641 1103.792841 -3.042887573 0.082519854 EEVEGRPPIGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEVEGRPPIGVK 12 1 Q9Y6Q5;K7ERH5;K7EL08;Q9Y6Q5-2 Q9Y6Q5;Q9Y6Q5-2 AP1M2 AP-1 complex subunit mu-2 0 88.187 0.0092361 477410000 327570 283030 228540 271520 278070 257690 335280 373900 563050 FALSE TRUE 284280.7945 281170.7573 339062.7084 333172.7659 272536.951 267603.501 302764.5972 293944.3947 496486.8704 0.572584718 0.56632063 0.682923817 0.671060577 0.548930832 0.538994114 0.609813905 0.592048677 1 18.92139604 1.237982785 24.99592957 1.000000458 0.598720464 0.876425239 0.047457525 4.892534753 211456.2241 0.070787602 0.012276698 17.29747791 -1.237982785 -0.401279994 EEVFWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EEVFWR 6 0 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 ;;;; 166.66 0.016052 1900084000 2176200 2192830 1669140 1961650 2140730 2127740 1965190 2372660 3622070 FALSE TRUE 1888609.656 2178425.155 2476341.687 2407072.614 2098133.661 2209595.535 1774606.176 1865285.123 3193873.011 0.591322714 0.682063798 0.775341311 0.7536532 0.656924572 0.691823228 0.555628283 0.584019814 1 21.60687552 1.230573139 24.99731349 1.000000619 0.660675279 0.693960384 0.07067584 194.5337366 608755.7344 0.209665823 0.019487386 17.00486307 -1.230573139 -0.33932534 EEVGEEAIVELVENGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEVGEEAIVELVENGKK 17 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 230.93 1.01E-15 163400000 258120 178080 224760 256170 180830 133360 275360 325090 580540 FALSE TRUE 224008.788 176910.1808 333454.6878 314337.3138 177231.8368 138490.4455 248655.6296 255572.0334 511909.2226 0.437594749 0.34558897 0.651394179 0.614048937 0.346217315 0.270537118 0.485741648 0.499252645 1 18.96552847 1.214645813 3.469888799 1.099950573 0.451439624 0.682047051 0.117026619 0.221141491 3.709450945 0.395822829 0.031897888 16.39252343 -1.214645813 -0.648510949 EEVITLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEVITLIR 8 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 105.57 0.01015 66860000 43500 48210 29686 37428 43566 48714 48075 44507 52989 FALSE TRUE 37751.36479 47893.30534 44042.24889 45926.59945 42699.12184 50588.0591 43412.6939 34989.5244 46724.70079 0.807953056 1.025010423 0.942590282 0.98291907 0.913844736 1.082683426 0.929116574 0.748844269 1 15.5118978 1.98596624 24.66608728 0.851231819 0.96421531 0.109581437 0.093165612 759.555683 1335012.659 0.038220504 0.02323231 96.82025898 -1.98596624 0.112983491 EEVNDRPVRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EEVNDRPVRR 10 2 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 ;; 166.66 3.08E-06 202715000 219610 184057 127376 130856 183760 193837 182182 236958 58371 FALSE TRUE 190587.9821 182847.9174 188975.4596 160568.8548 180103.5355 201294.0348 164514.0177 186286.3757 51470.44688 3.702862393 3.552483581 3.6715333 3.119632033 3.499164014 3.910866274 3.196281122 3.619288097 1 15.65145669 1.237259623 25 0.999996956 3.524792812 0.921715333 0.232073481 8.050037524 154628.577 0.326904265 0.054037001 17.26869915 -1.237259623 2.524795856 EEVQSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEVQSLR 7 0 Q14980;Q14980-2;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 101.69 0.020643 204420000 521060 492700 362480 420050 421570 495050 466630 582260 486290 FALSE TRUE 452200.6008 489463.4213 537776.5404 515428.7726 413181.5818 514094.8938 421376.2944 457748.2302 428801.3502 1.054568976 1.141468937 1.254139102 1.202022271 0.963573416 1.198911556 0.98268416 1.067506504 1 18.70994992 3.254619371 24.99937587 1.048986536 1.168014723 0.351190585 0.081007652 274.5211693 427356.8633 0.022718987 0.029233566 1797.29502 -3.254619371 0.119028188 EEVSEILDEMSHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EEVSEILDEMSHK 13 0 Q5TBH8;O15228;Q5TBH6;O15228-2 Q5TBH8 GNPAT Dihydroxyacetone phosphate acyltransferase 0 120.84 0.00025362 18250000 54141 31070 29670 41555 36322 39139 35828 56842 51259 FALSE TRUE 46986.12967 30865.89912 44018.51124 50990.69788 35599.26326 40644.70266 32353.40607 44686.78064 45199.21941 1.039534096 0.682885668 0.973877687 1.128132267 0.787607922 0.899234615 0.715795682 0.988662663 1 15.46401024 1.593602735 24.99999996 0.994381593 0.88776617 0.091136857 0.137437026 2.161940612 3774.450052 0.086992145 0.033223006 39.22859328 -1.593602735 -0.106615423 EEVVGGDDS(ph)DGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEVVGGDDSDGLR 13 0 P25490 P25490 YY1 Transcriptional repressor protein YY1 1 EEVVGGDDS(1)DGLR;EEVVGGDDS(1)DGLR 220.85 2.11E-11 533910000 951840 853480 793490 1016000 858550 817340 806200 936280 2188180 TRUE FALSE 826051.9323 847873.4337 1177224.418 1246698.329 841466.5347 848783.5987 728014.8481 736063.8081 1929495.853 0.428118014 0.439427445 0.610120212 0.646126462 0.436106941 0.439899157 0.377308325 0.38147986 1 20.87979251 1.232836028 24.99992228 1.000000852 0.468300668 0.776661262 0.089345595 98.80007792 431425.8224 0.212770885 0.024610056 17.09369806 -1.232836028 -0.531700184 EEWYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EEWYAR 6 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 ;;; 162.47 0.019043 2824100000 2410440 2015680 1320710 1545380 1967540 1950980 1891590 2215970 2030080 FALSE TRUE 2091894.247 2002438.865 1959409.774 1896282.149 1928389.803 2026035.463 1708143.893 1742102.06 1790086.255 1.168599692 1.118627027 1.094589586 1.059324456 1.077260829 1.131808848 0.95422435 0.973194479 1 20.77159767 -1.999999364 0.083125783 0.199884639 1.396823197 0.650850141 0.041338178 254.3818766 1.997789438 36.49449229 5.517285268 0.010000015 1.999999364 1.196938557 EEYLLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EEYLLLR 7 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;;;; 166.34 0.0026222 3291230000 4888470 4801160 3293530 4281280 4808290 4519680 4562590 5325460 5815040 FALSE TRUE 4242446.304 4769620.864 4886292.124 5253410.059 4712614.436 4693555.014 4120110.724 4186651.822 5127592.596 0.827375854 0.930187174 0.952940787 1.024537336 0.919069592 0.915352561 0.803517566 0.81649463 1 22.28985021 2.426295476 8.796783733 0.858476379 0.935257703 0.108267343 0.07072894 0.489046746 78.05208243 0.026703761 0.020679257 266.8673702 -2.426295476 0.076781324 EFADFEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 EFADFEYR 8 0 Q8ND56-2;Q8ND56;Q8ND56-3;A0A0G2JQ95;A0A096LP11;A0A140TA66 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;;;;;; 164.53 0.00076672 3309570000 6050840 5737050 3982060 4666840 5822600 5897660 5612770 6327860 6940490 FALSE TRUE 5251206.163 5699362.941 5907797.535 5726517.35 5706741.652 6124546.796 5068444.429 4974696.382 6119993.179 0.858041179 0.931269492 0.965327471 0.935706492 0.932475165 1.000744056 0.828178117 0.812859792 1 22.54509861 2.225335134 24.99998625 0.864112692 0.937975925 0.144925966 0.061047727 329.8001324 623412.5347 0.024526009 0.01664512 168.0100008 -2.225335134 0.073863233 EFAEILHFTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EFAEILHFTLR 11 0 Q9H0Q0 Q9H0Q0 FAM49A Protein FAM49A 0 153.95 3.22E-05 77075000 158440 152150 81294 114960 166050 194640 161940 174230 141880 FALSE TRUE 137501.7526 151150.5166 120608.0503 141063.4251 162745.9299 202127.9267 146235.0837 136972.2704 125107.108 1.099072265 1.208168896 0.964038353 1.127541251 1.300852785 1.615639031 1.168879099 1.094840034 1 16.93280423 3.399162653 6.937286452 1.231695247 1.093109632 0.14025523 0.169487499 0.507360992 37.1568374 0.053679228 0.069492629 2507.048025 -3.399162653 -0.138585616 EFAFPPPVS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EFAFPPPVSPR 11 0 Q13191 Q13191 CBLB E3 ubiquitin-protein ligase CBL-B 1 EFAFPPPVS(1)PR 103.85 0.0028096 49249000 34817 45318 27362 36750 46809 47843 46397 63590 46580 TRUE FALSE 30215.84523 45020.30307 40594.35472 45094.64919 45877.59248 49683.55117 41897.42608 49991.77336 41073.36546 0.735655452 1.096094819 0.98833768 1.0979049 1.116966968 1.209629418 1.020063138 1.217133605 1 15.32591554 5.234446444 1.347092042 1.111774223 1.12E-18 0.652341676 0.080610457 2.55628126 1.640555129 0.021150884 5.383112016 171572.0118 -5.234446444 -1.111774223 EFAGEDTSDLFLEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFAGEDTSDLFLEER 15 0 O14980 O14980 XPO1 Exportin-1 0 ; 189.3 6.14E-07 206600000 333240 255820 203955 233010 283350 278030 284060 326670 393320 FALSE TRUE 289201.4897 254139.5016 302588.3202 285918.4818 277711.8894 288725.994 256511.9049 256814.1626 346822.1577 0.833861053 0.732766047 0.872459598 0.824395084 0.800732834 0.832490046 0.73960645 0.740477957 1 18.40383655 1.229265632 24.95117636 1.000000413 0.794166794 0.648931199 0.046857135 239.6873324 643360.6864 0.145787835 0.011879768 16.95374443 -1.229265632 -0.205833618 EFALHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EFALHK 6 0 A0A087WW66;Q99460-2;Q99460;C9J9M4;F8WCE3 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;; 74.743 0.079523 1509080000 2862800 2685720 1879450 2299120 2629740 2473010 3003330 3308050 3487950 FALSE TRUE 2484473.727 2668077.328 2788358.306 2821170.336 2577413.319 2568148.295 2712067.519 2600649.251 3075608.524 0.807799077 0.867495752 0.906603777 0.917272245 0.838017354 0.835004935 0.881798674 0.84557226 1 21.55244045 1.233766592 24.99830116 1.000000206 0.864191955 0.626764443 0.033335062 103.6908337 540627.342 0.066268951 0.008332454 17.13036403 -1.233766592 -0.135808251 EFCENLSADCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EFCENLSADCR 11 0 P30153;B3KQV6;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ;; 221.59 1.93E-11 1133770000 708550 739690 496860 520780 652720 704090 600670 686400 928070 FALSE TRUE 614913.3223 734830.9277 737143.1579 639031.0586 639732.149 731176.7979 542417.1159 539618.7016 818354.6219 0.751402028 0.897937041 0.900762503 0.780873037 0.781729744 0.893471826 0.662814263 0.659394701 1 19.64236662 2.248359654 24.99887747 0.745543389 0.835446849 0.044525485 0.107227338 405.2311243 1033808.765 0.040003954 0.030599697 177.1575454 -2.248359654 0.089903461 EFDEDS(ph)DEKEEEEDTYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EFDEDSDEKEEEEDTYEK 18 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 EFDEDS(1)DEKEEEEDTYEK;EFDEDS(1)DEKEEEEDTYEK;EFDEDS(1)DEKEEEEDTYEK 266.09 2.51E-31 1443780000 2037970 999390 1594750 1429360 1105730 942130 1503030 1853870 3523350 TRUE FALSE 1768647.101 992824.9413 2365976.434 1753918.034 1083728.136 978374.3507 1357266.382 1457434.327 3106823.577 0.569278254 0.319562703 0.761541934 0.564537377 0.348821911 0.314911461 0.436866255 0.469107528 1 21.56700889 1.238537074 23.37301863 1.000000695 0.46944428 0.597347206 0.135927528 0.185431412 174101.1671 0.187523978 0.033642277 17.31956875 -1.238537074 -0.530556415 EFDEDSEDRLVNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFDEDSEDRLVNEK 14 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4 Q9UHD8 9-Sep Septin-9 0 ; 173.44 2.46E-06 417260000 709480 630920 532170 719670 604560 504870 758360 915180 946230 FALSE TRUE 615720.4204 626775.445 789529.192 883082.073 592530.4388 524292.6756 684814.3639 719475.8789 834367.7673 0.737948474 0.751198056 0.946260418 1.058384693 0.710154996 0.6283712 0.820758412 0.862300663 1 19.6703239 1.272835442 2.410535928 1.039144307 0.810759353 0.200380072 0.121141886 0.983136934 6.500512321 0.459448437 0.034837145 18.74284191 -1.272835442 -0.228384955 EFDRHS(ph)GSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFDRHSGSDR 10 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 EFDRHS(0.894)GS(0.106)DR;EFDRHS(0.964)GS(0.036)DR 116.96 0.00061825 3375400000 1881690 1766420 1199730 1416290 1734270 2127000 2045290 2160470 2155830 TRUE FALSE 1633019.899 1754816.271 1779923.441 1737880.291 1699761.42 2208827.066 1846938.091 1698470.303 1900970.233 0.859045486 0.923116122 0.936323678 0.914206998 0.894154674 1.161947214 0.971576545 0.893475486 1 20.85830451 EFDSDS(ph)LR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFDSDSLR 8 0 Q12955;D6RFK6;B1AQT1;A0A087WZ26;Q12955-4;Q12955-5;Q12955-6;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 EFDSDS(1)LR;EFDSDS(1)LR 145.91 0.00058927 522090000 831790 627060 521850 653870 664750 774240 715110 764210 1041030 TRUE FALSE 721866.844 622940.8016 774218.4055 802341.1773 651522.7756 804025.5138 645758.7423 600789.6386 917960.6193 0.786381059 0.678613863 0.84341135 0.874047492 0.709750246 0.87588236 0.703471073 0.65448302 1 19.80807274 4.148843863 0.004365963 1.548775525 2.29E-06 0.002129863 0.108448716 629295.5968 1143.320877 200454.1278 205136.9584 14087.82222 -4.148843863 -1.548773236 EFEDRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EFEDRDR 7 1 Q13951-2;A0A494C0A9;Q13951;J3KS23 Q13951-2 CBFB Core-binding factor subunit beta 0 ;; 129.77 0.0033087 1702230000 1402690 1282930 800020 1008850 1157600 1287950 1294230 1422270 1290410 FALSE TRUE 1217320.963 1274502.348 1186912.348 1237924.812 1134566.025 1337498.27 1168715.774 1118128.629 1137859.2 1.069834442 1.120087923 1.043110033 1.087941998 0.997105815 1.175451471 1.027118095 0.982659919 1 20.11789062 2.008577251 24.96607075 0.994530652 1.080475437 0.408185793 0.046279431 164.6408013 479223.4179 0.017643584 0.011875297 101.9946169 -2.008577251 0.085944785 EFEFLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFEFLMR 7 0 P85037 P85037 FOXK1 Forkhead box protein K1 0 ; 117.93 0.01231 64308000 148089 129237 79460 94810 126737 117662 126004 138192 128043 FALSE TRUE 128518.6634 128388.0336 117887.1218 116338.0596 124215.1817 122188.5333 113784.1515 108640.7162 112905.9024 1.138281177 1.137124197 1.044118326 1.030398386 1.100165527 1.082215639 1.007778593 0.962223532 1 16.78476138 -1.999997411 0.045616922 0.068472411 1.637930657 0.644608044 0.03501056 859.2141398 3.845199324 111.1423072 39.04487905 0.01000006 1.999997411 1.569458246 EFENLYIENLELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EFENLYIENLELR 13 0 A0A3B3IT47;Q9Y2I8;Q9Y2I8-2;E7EQ49;A0A087WTQ2;Q9Y2I8-3;C9JGR9 A0A3B3IT47 WDR37 WD repeat-containing protein 37 0 ;; 139.89 9.09E-05 94989000 181791 201289 155639 162660 213304 227908 202602 226982 275200 FALSE TRUE 157766.8588 199966.7193 230906.541 199594.4391 209059.6677 236675.7682 182953.6892 178443.6657 242666.1695 0.650139486 0.824040367 0.951539893 0.822506242 0.861511385 0.97531423 0.753931583 0.735346283 1 17.88861347 4.715220862 4.152662565 0.856308368 0.637379455 0.370540482 0.088410488 0.240294695 9.006647705 0.022491597 0.149636161 51906.39433 -4.715220862 -0.218928913 EFEPLLNWMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFEPLLNWMK 10 0 P14625 P14625 HSP90B1 Endoplasmin 0 ; 180.8 4.55E-06 359380000 683460 687960 608030 719630 736020 736920 736520 720050 744670 FALSE TRUE 593139.0293 683440.7455 902075.3417 883032.9904 721374.642 765269.7893 665092.4038 566072.9109 656635.9609 0.903299643 1.040821378 1.373783033 1.344783172 1.098591434 1.165439962 1.012878434 0.862080277 1 19.32473424 2.106367964 3.30897067 0.923446315 1.166276003 0.313833504 0.139288832 0.27911075 6.022678825 0.071435791 0.042686018 127.7520754 -2.106367964 0.242829688 EFESVLVDAFSHVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EFESVLVDAFSHVAR 15 0 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ;;;;; 223.06 1.32E-12 1221797000 1219198 1287221 796930 986540 1293181 1227879 1250007 1520455 1378668 FALSE TRUE 1058077.895 1278765.16 1182328.014 1210548.985 1267449.228 1275116.3 1128781.514 1195317.53 1215683.44 0.870356427 1.051889924 0.972562408 0.995776487 1.042581635 1.048888434 0.928515991 0.983247358 1 20.21333617 4.753790219 24.61577393 0.999409001 0.870356312 0.542579667 0.038133744 1958.744048 3165873.93 0.009507313 0.216838786 56727.05256 -4.753790219 -0.129052689 EFETAETLLNSEVHMLLEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 EFETAETLLNSEVHMLLEHR 20 0 O15514;E9PHV4 O15514 POLR2D DNA-directed RNA polymerase II subunit RPB4 0 ;;;;;; 278.74 7.17E-45 172191100 114906.8 100054 58547.8 78058.7 94955.8 94087.5 93967.4 112269.9 88666.7 FALSE TRUE 99721.57524 99396.73869 86861.71191 95783.12089 93066.36536 97707.10701 84854.45601 88261.85557 78184.62374 1.275462751 1.271308013 1.110982029 1.225088979 1.190341028 1.249697221 1.085308747 1.128890201 1 16.25459729 -0.449551677 0.464580719 1.86E-17 1.231828771 0.625371709 0.05490685 15.71112794 0.785916835 14.7862552 0.041906843 0.355179853 0.449551677 1.231828771 EFEVYGPIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFEVYGPIKR 10 1 P08621;P08621-2;M0QYR1;P08621-3 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ; 120.09 0.00097144 1339140000 883360 720300 404530 537780 661280 573980 722490 834420 568660 FALSE TRUE 766621.7379 715568.3019 600162.0611 659891.1685 648121.8218 596061.382 652423.031 655985.7765 501433.6626 1.528859738 1.427044802 1.196892243 1.316008911 1.292537518 1.188714333 1.301115341 1.308220459 1 18.93569933 7.999999994 0.587942084 1.225922257 19.88137681 0.531435307 0.096729306 137.56602 1.129648431 0.045875785 3281.726988 99999998.7 -7.999999994 18.65545456 EFFNGKEPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFFNGKEPSR 10 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 152.85 1.58E-05 2318800000 4723300 3801000 2416800 3243500 4126200 3977900 3956500 4349600 2630800 FALSE TRUE 4099103.938 3776030.981 3585572.564 3979986.249 4044096.693 4130932.387 3572799.239 3419471.889 2319789.821 1.767015227 1.627747025 1.545645442 1.715666744 1.74330306 1.780735629 1.5401392 1.474043837 1 21.14556267 0.944539224 1.261559099 0.199703236 1.685520007 0.882505162 0.078576644 0.924083551 0.750802649 2.157083227 0.024723288 8.801145978 -0.944539224 1.485816772 EFFSQYGDVMDVFIPKPFR ddPTM_MDA-MB-175_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 ; 154.75 2.99E-08 455630000 854400 600060 548840 697230 644500 636010 714090 818550 1257360 FALSE TRUE 741488.8752 596118.1663 814260.8598 855546.728 631675.7109 660477.7163 644837.6617 643509.4525 1108716.333 0.668781412 0.53766518 0.734417664 0.771655204 0.569736092 0.595713887 0.581607434 0.580409464 1 20.08045887 1.234169157 24.99047692 1.000000556 0.627255375 0.705929722 0.075031489 77.44639947 440666.1266 0.146920599 0.019124643 17.14625023 -1.234169157 -0.37274518 EFGDTGEGWETVEMHPAYTEEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EFGDTGEGWETVEMHPAYTEEELR 24 0 Q02818 Q02818 NUCB1 Nucleobindin-1 0 81.696 0.01564 59811000 6634.6 8932 6751.3 5961.7 6927.3 8770.9 7903.2 10931 8379.6 FALSE TRUE 5757.8208 8873.325104 10016.25126 7315.395104 6789.460283 9108.322199 7136.74888 8593.490715 7388.973234 0.779245048 1.200887434 1.355567404 0.990042171 0.918863835 1.232691189 0.965864763 1.163015543 1 12.85115819 EFGGGHIKDEVFGTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EFGGGHIKDEVFGTVK 16 1 Q12792;Q12792-3;Q12792-4;F8VS81;F8W1Q9 Q12792 TWF1 Twinfilin-1 0 156 1.23E-07 454030000 1073800 952870 789640 752470 887690 613040 1061300 1240800 1229400 FALSE TRUE 931894.6093 946610.5342 1171512.545 923329.8143 870026.7057 636624.0455 958375.2894 975464.5759 1084061.733 0.859632419 0.873207222 1.080669587 0.851731766 0.802561957 0.587258111 0.884059699 0.899823826 1 20.04801548 4.75439695 18.54901926 0.869868966 0.859632138 0.000634059 0.127892702 2529.83453 2961188.657 0.032803274 0.52339235 56806.35846 -4.75439695 -0.010236828 EFGIADPDEIMWFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFGIADPDEIMWFK 14 0 Q15067-2;Q15067;Q15067-3;I3L0T4;I3L4S5;K7ELT1 Q15067-2;K7ELT1 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ; 94.616 0.0095251 30289000 115565 83703 73094 100704 92565 103623 85228 130329 105088 FALSE TRUE 100292.7924 83153.14948 108442.5029 123570.3824 90723.1376 107609.4439 76962.60168 102459.1576 92664.61636 1.082320268 0.897356 1.17026873 1.33352284 0.979048327 1.161278685 0.830550049 1.105698827 1 16.49973094 EFGSVDDENKPIWMHAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EFGSVDDENKPIWMHAEER 19 1 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;H0YG16;G5E9S8 Q07866-6 KLC1 Kinesin light chain 1 0 ;; 176.67 1.12E-13 719550000 573720 503380 395074 474910 503010 414590 530690 652770 694430 FALSE TRUE 497901.4484 500073.2636 586133.1078 582745.574 493001.0851 430539.5456 479223.7655 513180.2154 612335.2765 0.813119001 0.816665776 0.957209441 0.951677286 0.805116256 0.703110799 0.782616622 0.838070637 1 19.22396227 4.431368803 24.99935235 0.853876111 0.814002173 0.040133269 0.089462126 513.7229336 280699.569 0.02402566 0.063565986 27000.31327 -4.431368803 -0.039873938 EFGSVNGDNKPIWMHAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFGSVNGDNKPIWMHAEER 19 1 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 0 ; 190.63 6.86E-15 235590000 303430 260420 199414 205122 284290 241430 292970 343910 367910 FALSE TRUE 263330.9567 258709.2839 295851.2774 251698.0852 278633.1852 250717.9683 264557.8145 270367.5228 324416.0989 0.811707426 0.7974613 0.911950049 0.775849553 0.85887595 0.77282838 0.815489168 0.833397367 1 18.30748589 1.235443711 4.606591863 1.014745711 0.821448298 0.656947925 0.040475734 0.116663545 5.407043917 0.073960974 0.009462438 17.19664442 -1.235443711 -0.193297414 EFGVTTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EFGVTTGR 8 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ;;; 180.93 0.00055023 721620000 694010 720790 491300 590760 736650 792030 739550 777460 932320 FALSE TRUE 602294.8201 716055.083 728894.3233 724901.0872 721992.1062 822499.9066 667828.5548 611206.2292 822102.1917 0.732627678 0.871004956 0.886622528 0.88176518 0.878226714 1.000483778 0.812342506 0.743467461 1 19.64895821 4.738303159 6.922801825 0.873453555 0.730456944 0.268864806 0.076773121 0.172235795 61.33588207 0.019639189 0.115801394 54739.79408 -4.738303159 -0.142996611 EFHAPLIIDENGVHELVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EFHAPLIIDENGVHELVK 18 0 Q16222;Q16222-3;Q16222-2 Q16222 UAP1 UDP-N-acetylhexosamine pyrophosphorylase;UDP-N-acetylgalactosamine pyrophosphorylase;UDP-N-acetylglucosamine pyrophosphorylase 0 96.447 0.0009201 81772000 131900 118980 88221 115090 117130 121900 142180 167730 234300 FALSE TRUE 114469.0808 118198.4125 130884.9707 141222.9435 114799.3422 126589.5719 128391.4055 131862.2448 206601.3209 0.554057836 0.572108697 0.633514685 0.683552956 0.55565638 0.612723923 0.62144523 0.638244926 1 17.65648995 1.224360713 3.844516375 1.054431547 0.607462729 0.909441326 0.038896818 0.079779298 1.910512434 0.10406829 0.010125918 16.76334615 -1.224360713 -0.446968818 EFHGNIIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFHGNIIK 8 0 Q92804-2;Q92804;A0A075B7D9 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ; 97.635 0.0080918 553870000 2467710 2183520 1350280 1764380 2084340 1908740 2254630 2533000 2756540 FALSE TRUE 2141595.871 2169176.313 2003279.924 2165009.446 2042865.712 1982170.463 2035976.33 1991337.662 2430664.981 0.881074063 0.892420934 0.824169493 0.890706643 0.840455483 0.815484848 0.837621122 0.819256326 1 21.21291963 1.231767547 24.99906514 1.000000258 0.848503757 0.726884834 0.028851453 130.6604561 480796.921 0.070320993 0.007349422 17.05169466 -1.231767547 -0.151496501 EFHLNESGDPSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 EFHLNESGDPSSK 13 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;;;;;;;;;; 209.21 3.97E-08 42509948000 42470470 31022941 18057908 24944326 28442466 25474361 33805378 39638610 35212650 FALSE TRUE 36857889.78 30819149.26 26790772.71 30608316.47 27876516.57 26454376.15 30526937.64 31162201.72 31049850.63 1.187055301 0.992569968 0.862830969 0.98577983 0.897798734 0.851996889 0.983158921 1.00361841 1 24.88808299 4.704403652 3.635104761 0.944687016 1.20605037 0.658591319 0.055282044 0.160038126 3.857044576 0.014595564 0.1068883 50629.50157 -4.704403652 0.261363354 EFHTTGLAWSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EFHTTGLAWSK 11 0 Q01518-2;Q01518;Q5T0R1;Q5T0R9;Q5T0S3 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 0 190.26 2.35E-06 1705700000 4546600 3851900 1495800 3535400 4615600 4082700 3785400 5025600 8877100 FALSE TRUE 3945755.29 3826596.615 2219173.883 4338166.605 4523758.59 4239764.111 3418292.491 3950914.549 7827659.351 0.504078565 0.488855792 0.283504146 0.554209938 0.577919706 0.541638812 0.436694079 0.504737671 1 22.90014954 1.238909063 5.933848592 1.019706999 0.483911764 0.796643251 0.081607452 0.060617595 7.908916589 0.131863911 0.02076602 17.33440994 -1.238909063 -0.535795235 EFITGDVEPTDAES(ph)EWHSENEEEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EFITGDVEPTDAESEWHSENEEEEK 25 0 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;A8MXH2;E9PKT8;E9PS34 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 EFITGDVEPT(0.002)DAES(0.499)EWHS(0.499)ENEEEEK 59.573 0.051014 61436000 45943 29163 162510 63825 14374 18190 24915 27314 53300 TRUE FALSE 39871.51615 28971.42633 241100.3796 78317.44175 14087.98552 18889.78107 22498.74713 21473.11366 46998.93472 0.848349359 0.616427298 5.129911582 1.666366317 0.299751167 0.401919345 0.478707598 0.456885114 1 15.52034044 3.367512839 5.22098681 0.517326082 2.243678757 0.289066257 1.214888594 0.26192764 10.99620944 0.358263917 0.465316695 2330.842021 -3.367512839 1.726352675 EFITGDVEPTDAESEWHS(ph)ENEEEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 EFITGDVEPTDAESEWHSENEEEEK 25 0 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;A8MXH2;E9PKT8;E9PS34 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 EFITGDVEPTDAESEWHS(1)ENEEEEK;EFITGDVEPTDAESEWHS(1)ENEEEEK;EFITGDVEPTDAESEWHS(1)ENEEEEK;EFITGDVEPTDAESEWHS(1)ENEEEEK;EFITGDVEPTDAESEWHS(1)ENEEEEK;EFITGDVEPTDAESEWHS(1)ENEEEEK;EFITGDVEPTDAESEWHS(1)ENEEEEK;EFITGDVEPTDAESEWHS(1)ENEEEEK;EFITGDVEPTDAESEWHS(1)ENEEEEK 387.22 1.84E-138 17731460000 6415227 5449186 4549691 6274102 5755901 4777881 6791685 7747578 13842830 TRUE FALSE 5567438.498 5413389.938 6749936.785 7698732.753 5641369.831 4961689.174 6133028.434 6090818.736 12206346.41 0.456110151 0.443489785 0.552985845 0.630715572 0.462166945 0.406484382 0.502445878 0.498987865 1 23.5411281 1.238444827 8.687316206 1.004283331 0.495280124 0.866891276 0.06229148 0.031156602 27.97898157 0.09297226 0.0162271 17.31589033 -1.238444827 -0.509003207 EFITGDVEPTDAESEWHS(ph)ENEEEEKLAGDMK ddPTM_MDA-MB-175_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;EFITGDVEPTDAES(0.006)EWHS(0.994)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPT(0.05)DAES(0.179)EWHS(0.772)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK 342.26 1.39E-106 16356590000 3658149 3081999 2132886 2205389 2609491 2048819 4006560 4680955 1958009 TRUE FALSE 3174715.341 3061753.146 3164356.804 2706156.28 2557567.234 2127638.393 3618004.428 3679969.2 1726535.407 1.838778011 1.773350916 1.832778402 1.567391129 1.481329155 1.232316687 2.09552866 2.131418323 1 20.71944849 3.755778738 22.41118522 1.654559852 1.810807353 0.066967392 0.344619073 907.3988926 1181060.582 0.098098897 0.169122513 5698.738614 -3.755778738 0.156247501 EFLEDYDDDRDDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFLEDYDDDRDDPK 14 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 136.17 2.61E-05 493830000 789580 544770 578090 591120 536890 451250 619440 843520 950330 FALSE TRUE 685235.0025 541191.37 857656.2576 725342.8307 526206.9394 468609.8795 559366.8041 663139.8123 837983.07 0.817719387 0.645826138 1.023476832 0.865581724 0.627944595 0.559211631 0.667515639 0.791352279 1 19.67656157 5.087370574 19.68088604 0.766533555 3.503245087 0.006906526 0.15546241 3014.845923 696264.706 0.038202076 9264.363015 122284.2639 -5.087370574 2.736711533 EFLEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFLEFR 6 0 O75323;C9K068;H7C333;C9J7B1 O75323 GBAS Protein NipSnap homolog 2 0 ; 110.36 0.066925 309385000 1064060 865530 588110 949900 1040200 1136550 746570 1010310 1016660 FALSE TRUE 923441.775 859844.2764 872521.9631 1165589.313 1019502.055 1180273.814 674167.7563 794263.0687 896471.613 1.030084792 0.959142782 0.973284542 1.300196567 1.137238525 1.316576896 0.75202354 0.885987975 1 19.77389837 2.226689059 24.99997722 0.875418038 1.11451978 0.421595497 0.132453988 226.2606924 476472.0105 0.056571144 0.03847985 168.5345939 -2.226689059 0.239101742 EFLEKEELPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EFLEKEELPR 10 1 Q13596-2;Q13596;H0YK42;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 0 113.22 0.001383 155160000 376480 304170 191210 222790 288090 324820 344340 384780 179600 FALSE TRUE 326727.2141 302171.8872 283679.7956 273377.8746 282357.5726 337316.0356 310945.9598 302497.7914 158367.8926 2.063089991 1.908037559 1.791270888 1.726220322 1.782921828 2.129952164 1.963440661 1.910095452 1 17.27292035 1.238381604 24.99999965 0.999999001 1.905431108 0.841129546 0.12419397 1.724381029 240142.7349 0.180724376 0.032109978 17.31336975 -1.238381604 0.905432107 EFLHAQEEVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EFLHAQEEVKR 11 1 P43686 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;;; 174.05 7.44E-06 2368945000 2424139 2082412 1458713 1730890 2012628 1757459 2400848 2859856 2072377 FALSE TRUE 2103782.889 2068732.498 2164151.486 2123915.029 1972580.64 1825069.585 2168014.13 2248298.05 1827382.952 1.151254523 1.132073874 1.184290071 1.162271448 1.079456629 0.998734055 1.186403829 1.230337652 1 20.80134757 3.277959844 24.66798243 1.116948967 1.157573887 0.110577679 0.073154695 460.3069067 288196.296 0.023016975 0.029714264 1896.530557 -3.277959844 0.04062492 EFLHNQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EFLHNQGK 8 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ;; 133.55 0.0009147 619300000 1839480 1747220 1226960 1311050 1579750 1524370 1877890 1991190 2542280 FALSE TRUE 1596388.057 1735742.397 1820321.96 1608743.941 1548316.066 1583013.5 1695772.517 1565389.514 2241734.555 0.712121805 0.774285427 0.812014945 0.717633556 0.6906777 0.706155641 0.756455537 0.698293877 1 21.09618403 1.233878813 24.99997554 1.000000401 0.733931456 0.830522929 0.037839613 60.38935426 322428.0962 0.076998065 0.009777665 17.13479106 -1.233878813 -0.266068945 EFLLIFHK ddPTM_MDA-MB-175_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 605340000 903750 784580 577240 774800 658220 580790 589370 917330 1575170 FALSE TRUE 784317.1477 779426.0423 856395.1948 950730.1821 645122.7098 603133.3671 532212.9881 721166.1182 1388955.197 0.564681387 0.56115996 0.616575104 0.684493052 0.464466177 0.434235293 0.383175058 0.519214817 1 20.40556863 1.238140655 24.98770173 1.000000536 0.524953624 0.741768366 0.087406564 5.745763141 341458.8686 0.135916761 0.023782313 17.30376685 -1.238140655 -0.475046912 EFLLIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EFLLIFR 7 0 Q96C19;H0Y4Y4 Q96C19 EFHD2 EF-hand domain-containing protein D2 0 100.07 0.023419 30549000 73966 73624 40731 54616 61244 58759 54574 76228 73076 FALSE TRUE 64191.20569 73140.3591 60428.64784 67017.39755 60025.36422 61019.49675 49281.42188 59927.23541 64437.03853 0.996184914 1.135067048 0.937793685 1.040044656 0.931535117 0.946963084 0.764799609 0.930012253 1 15.97560257 3.169645523 1.531799107 0.898504725 1.03759805 0.341085047 0.07664637 0.405405323 1.992124336 0.028236051 0.035860155 1477.901613 -3.169645523 0.139093325 EFLLSLDDSVDETEAVKR ddPTM_MDA-MB-175_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 ;;; 276.18 6.90E-39 312586000 600709 470868 315082 399911 457605 371103 540418 647814 526898 FALSE TRUE 521323.7836 467774.8371 467456.7091 490716.9048 448499.5558 385379.5725 488008.3455 509284.0174 464608.7187 1.1220706 1.006814591 1.006129869 1.056193922 0.965327463 0.829471245 1.050364158 1.096156824 1 18.8256567 4.738561747 9.196692074 1.006359909 1.122526639 0.219020386 0.071100126 0.14786624 277.1624573 0.018885248 0.106746608 54772.39691 -4.738561747 0.116166729 EFLSELQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFLSELQR 8 0 A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599;Q92599-3 A0A087X142 8-Sep Septin-8 0 ; 166.68 0.00073762 350800000 485070 536440 350050 425020 532330 543790 464220 564550 671680 FALSE TRUE 420966.7705 532916.0903 519335.3508 521527.287 521737.6745 564709.9532 419200.0159 443825.3758 592274.7556 0.710762643 0.899778499 0.876848702 0.88054958 0.880904799 0.953459434 0.707779644 0.749357239 1 19.17590707 1.219146005 24.61923535 1.000000685 0.832986506 0.28352843 0.083710145 1668.716221 2115924.601 0.786535451 0.021613611 16.56326709 -1.219146005 -0.167014179 EFNAEVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EFNAEVHR 8 0 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;;; 239.66 1.02E-08 15958300000 13549780 13701980 9478080 10675050 13183440 14150000 12794160 13495220 17784220 FALSE TRUE 11759142.24 13611970.79 14061711.19 13098983.26 12921115.34 14694359.66 11553384.33 10609372.22 15681789.77 0.749859704 0.868011304 0.896690454 0.835298997 0.823956674 0.937033328 0.736738886 0.676540904 1 23.90258689 2.214704208 24.99968183 0.774963428 0.852568631 0.022234796 0.095902208 487.8674973 511243.7369 0.038285421 0.025827154 163.947277 -2.214704208 0.077605203 EFNAEVHRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EFNAEVHRK 9 1 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;; 144.65 6.43E-05 2506250000 4369700 3842840 1670160 1974620 3305890 3074440 4226650 4631690 609760 FALSE TRUE 3792233.074 3817596.131 2477854.962 2422987.651 3240109.257 3192715.696 3816750.134 3641239.137 537674.8674 7.053022753 7.10019449 4.608463427 4.506417908 6.026149729 5.93800434 7.098621053 6.772195164 1 19.03637451 4.257371344 24.15257695 5.424948168 7.076611296 0.166872954 1.710508417 335.4483885 430697.3306 0.424767051 1.119040273 18087.20014 -4.257371344 1.651663128 EFNKYDTDGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EFNKYDTDGSK 11 1 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ;;;; 152.47 3.00E-05 5402990000 7707540 6087330 4798080 5805170 5780240 4272420 8617430 9825880 7451120 FALSE TRUE 6688969.061 6047341.928 7118447.537 7123322.575 5665224.533 4436782.762 7781712.965 7724692.027 6570257.082 1.018068087 0.920411767 1.083435161 1.084177147 0.862253099 0.675282977 1.184384853 1.175706206 1 22.64751839 EFNSYGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFNSYGSR 8 0 P21399 P21399 ACO1 Cytoplasmic aconitate hydratase 0 ; 147.36 0.0012528 408660000 374840 378350 246150 286210 404750 423620 350800 400400 400710 FALSE TRUE 325303.9443 375864.5939 365188.9633 351198.3549 396696.2669 439916.9355 316779.47 314777.5759 353338.5203 0.920658025 1.063752103 1.033538497 0.993943017 1.122708802 1.245029654 0.896532509 0.890866854 1 18.43069151 EFQQNNWHAVGCGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EFQQNNWHAVGCGFR 15 0 Q9NZL9;Q9NZL9-2;Q9NZL9-3;Q9NZL9-4;E5RJR3;Q9NZL9-5 Q9NZL9 MAT2B Methionine adenosyltransferase 2 subunit beta 0 76.151 0.029712 216250000 321150 267720 166800 211370 240850 172560 313390 349020 323870 FALSE TRUE 278709.2138 265961.3297 247465.0379 259364.7891 236057.5562 179198.4949 282997.486 274384.7891 285582.4576 0.975932542 0.931294352 0.866527447 0.908195802 0.826582831 0.627484252 0.990948423 0.960790069 1 18.12354784 EFRPEDQPWLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EFRPEDQPWLLR 12 1 P35269;M0QXD6;M0R0R9;M0R0Z3 P35269 GTF2F1 General transcription factor IIF subunit 1 0 ;;; 227.56 1.15E-11 1017020000 794702 753939 444383 582955 731693 722503 709568 849162 745635 FALSE TRUE 689680.1172 748986.3251 659288.1052 715323.8427 717133.7408 750298.1579 640754.2046 667575.3145 657486.8797 1.048964076 1.139165432 1.002739561 1.087966718 1.09071947 1.141160654 0.974550557 1.015343933 1 19.32660258 2.224757406 24.94477613 0.99960987 1.08421541 0.509011058 0.040927183 185.3563719 334968.1778 0.015982721 0.010836754 167.7866511 -2.224757406 0.08460554 EFS(ph)AHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EFSAHK 6 0 Q5SVQ8-2;Q5SVQ8 Q5SVQ8-2 ZBTB41 Zinc finger and BTB domain-containing protein 41 1 EFS(1)AHK 63.653 0.071609 307420000 410960 515410 571520 453320 177000 361050 481210 327010 525370 TRUE FALSE 356650.5948 512024.2378 847908.9836 556253.2346 173478.0463 374939.8271 434542.3283 257081.4563 463261.3571 0.76986908 1.105259979 1.830303717 1.200733077 0.374471222 0.809348376 0.938006854 0.55493827 1 18.82146682 3.368787257 8.220513977 0.73278687 1.270016525 0.379586679 0.31109848 0.246273061 17.08806412 0.090055082 0.11631037 2337.691819 -3.368787257 0.537229655 EFS(ph)GGSYSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EFSGGSYSAK 10 0 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 1 EFS(1)GGSYSAK;EFS(0.834)GGS(0.165)YS(0.001)AK;EFS(0.998)GGS(0.002)YSAK 204.34 1.98E-07 1470240000 1780230 1572460 1158470 1464330 1803830 1313680 2315260 2191380 1991900 TRUE FALSE 1544968.095 1562130.407 1718709.967 1796828.507 1767937.312 1364218.12 2090726.442 1722770.44 1756419.851 0.879612067 0.889383256 0.978530256 1.023006263 1.006557351 0.776703884 1.190334099 0.980842046 1 20.74420631 6.999645324 0.38641844 1.017495478 7.16E-12 0.157682713 0.099514513 70.87621111 2.140653939 0.105186672 47.35106168 9991836.627 -6.999645324 -1.017495478 EFS(ph)IPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFSIPR 6 0 Q8NFJ5 Q8NFJ5 GPRC5A Retinoic acid-induced protein 3 1 EFS(1)IPR;EFS(1)IPR 92.439 0.049043 306960000 517010 404940 337600 498320 540760 599590 351940 572470 715030 TRUE FALSE 448685.8186 402279.9225 500864.4892 611471.1723 529999.934 622656.6153 317808.913 450051.7455 630499.968 0.711634959 0.638033216 0.794392569 0.969819514 0.840602634 0.987560106 0.504058571 0.713801377 1 19.26613677 4.168205811 6.458229606 0.814056399 0.675464499 0.152943338 0.148584344 0.420155411 29.80952832 0.040294993 0.086211882 14730.10391 -4.168205811 -0.1385919 EFSDFIQAVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EFSDFIQAVER 11 0 A3KN83-3;A3KN83-2;A3KN83;A3KN83-4 A3KN83-3 SBNO1 Protein strawberry notch homolog 1 0 ;; 138.99 0.00010706 47021800 99482 87243.6 58819.6 64820 82818 85153.7 82068.4 90251 88757 FALSE TRUE 86335.20164 86670.49105 87264.9553 79538.37171 81170.08383 88429.61794 74109.4192 70951.52598 78264.24857 1.103124392 1.107408461 1.115004065 1.016279759 1.037128514 1.129885223 0.946912806 0.90656369 1 16.25606581 2.224549049 24.74614968 0.941691187 1.081923268 0.695908753 0.041460073 110.3033125 194807.4575 0.017330458 0.01175087 167.7061732 -2.224549049 0.140232082 EFSDIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EFSDIFR 7 0 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 ;;;;; 158.38 0.0033101 1644503000 2730320 2862030 2344290 2907670 2945040 2973800 2770110 3237580 5589970 FALSE TRUE 2369501.294 2843229.136 3477996.485 3567900.914 2886439.466 3088204.01 2501465.159 2545248.712 4929130.115 0.480713886 0.576821685 0.705600462 0.723839873 0.585588004 0.626521098 0.507486128 0.516368741 1 22.23290163 1.232113185 24.99946532 1.000000683 0.591342901 0.723555489 0.079570818 130.8567133 507339.1257 0.197477275 0.021347288 17.06527083 -1.232113185 -0.408657782 EFSFEAWNAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFSFEAWNAK 10 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 ; 138.66 0.00013688 467930000 622120 533590 537950 444580 482510 392260 519590 630570 503980 FALSE TRUE 539905.2657 530084.8122 798104.4193 545528.684 472908.995 407350.496 469200.2418 495727.5126 444400.0585 1.214908179 1.192809951 1.795914298 1.227562133 1.064151514 0.916630158 1.055805986 1.115498306 1 18.76149948 3.402835724 4.31340069 1.039298799 1.398756004 0.496273892 0.170207714 0.180994082 6.486745054 0.050209592 0.06646116 2528.341444 -3.402835724 0.359457205 EFSGGWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EFSGGWR 7 0 Q9NUQ8-2;Q9NUQ8 Q9NUQ8-2 ABCF3 ATP-binding cassette sub-family F member 3 0 106.43 0.017923 196580000 266930 225390 152040 185970 239700 254120 217360 234350 236130 FALSE TRUE 231654.5242 223909.3982 225567.0525 228197.3309 234930.439 263896.1608 196280.4607 184236.0762 208214.9804 1.112573763 1.075376026 1.08333729 1.095969802 1.128307092 1.267421587 0.942681743 0.884835836 1 17.66771434 2.12102714 9.367882941 0.928260203 1.121287468 0.673657802 0.060304065 0.154003799 11.91935533 0.024953391 0.016813984 132.1378208 -2.12102714 0.193027265 EFSHIAFLTIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFSHIAFLTIK 11 0 X6R5C5;X6R8A1;P10619-2;P10619 X6R5C5 CTSA Carboxypeptidase;Lysosomal protective protein;Lysosomal protective protein 32 kDa chain;Lysosomal protective protein 20 kDa chain 0 ; 150.04 3.41E-05 562850000 1397750 1402800 1095090 1310930 1260610 1218890 1674310 1721800 1642450 FALSE TRUE 1213033.796 1393584.914 1624679.187 1608596.693 1235526.327 1265781.487 1511935.674 1353606.469 1448281.432 0.837567733 0.962233502 1.121797981 1.110693445 0.853098231 0.873988618 1.043951569 0.934629444 1 20.46591055 3.235398223 24.99903392 0.944674677 1.012922093 0.107780504 0.0949457 204.2070328 1614279.763 0.029731071 0.035150541 1719.484334 -3.235398223 0.068247416 EFSIDVGYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EFSIDVGYER 10 0 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ;;; 244.55 4.14E-12 1107920000 2276500 2115830 1335390 1636300 1944190 2058620 1971030 2192200 2127400 FALSE TRUE 1975654.757 2101930.973 1981189.071 2007846.924 1905504.423 2137816.444 1779879.814 1723415.09 1875901.196 1.053176341 1.120491302 1.056126557 1.070337249 1.015780803 1.139621025 0.948813199 0.918713146 1 20.83915241 2.218037438 24.81299415 0.947813957 1.074060707 0.668515642 0.039712021 114.5603585 138504.9836 0.015315651 0.010339645 165.2104212 -2.218037438 0.12624675 EFSIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EFSIPR 6 0 Q8NFJ5 Q8NFJ5 GPRC5A Retinoic acid-induced protein 3 0 129.96 0.037149 173500000 141380 118630 82357 142120 136830 168340 84646 150210 150870 FALSE TRUE 122696.2748 117850.7117 122185.1207 174390.5182 134107.3507 174816.1487 76437.04395 118088.7604 133034.3205 0.922290386 0.88586698 0.918448113 1.310868636 1.008065815 1.31406804 0.57456635 0.887656358 1 17.02143896 2.23711551 24.99999923 0.824424408 1.05463968 0.277803843 0.181637169 53.25822811 921318.3137 0.072040084 0.051544984 172.6296976 -2.23711551 0.230215271 EFSITDVVPYPISLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFSITDVVPYPISLR 15 0 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 189.33 6.11E-07 173689000 477290 481910 333120 351000 449600 462450 478080 584420 514650 FALSE TRUE 414214.9172 478744.3015 494217.9462 430699.9147 440653.8396 480240.7507 431715.8752 459446.331 453808.6633 0.912752335 1.054947471 1.089044759 0.949078212 0.971012401 1.058245004 0.951316954 1.012423006 1 18.79172463 3.702955645 24.99161386 0.992229891 1.022518271 0.05632717 0.054096871 1725.857135 1211403.256 0.014483146 0.021482432 5046.097588 -3.702955645 0.03028838 ELSNS(ph)PLRENSFGSPLEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ELS(0.011)NS(0.989)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR;ELS(0.003)NS(0.997)PLRENSFGSPLEFR;ELS(0.001)NS(0.999)PLRENSFGSPLEFR;ELS(0.001)NS(0.999)PLRENSFGSPLEFR;ELS(0.005)NS(0.995)PLRENSFGSPLEFR 284.59 3.84E-40 24247126000 2446569 2166295 1129909 1343301 2015267 1899032 1836231 2335115 914274 TRUE FALSE 2123248.708 2152064.466 1676336.772 1648318.023 1975167.13 1972088.99 1658153.6 1835768.829 806189.5693 2.633684172 2.669427325 2.079333243 2.044578702 2.45000333 2.446185196 2.056778782 2.277093253 1 19.62075959 1.197952701 3.509806078 0.726333018 2.330984214 0.772667331 0.226690721 0.193462696 3.211867667 0.881758391 0.060725339 15.77439461 -1.197952701 1.604651196 EFTGS(ph)PPSSATKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EFTGSPPSSATKK 13 1 Q92609;Q92609-2;C9J3F6 Q92609 TBC1D5 TBC1 domain family member 5 1 EFT(0.03)GS(0.931)PPS(0.035)S(0.003)AT(0.001)KK;EFT(0.012)GS(0.823)PPS(0.16)S(0.005)ATKK;EFT(0.102)GS(0.898)PPSSATKK;EFT(0.04)GS(0.918)PPS(0.04)S(0.002)ATKK 110.12 0.00066358 1879030000 4093130 2815820 2286910 2702260 3408000 2549660 4886320 5899400 2352770 TRUE FALSE 3552212.5 2797322.693 3392867.325 3315849.434 3340187.468 2647747.07 4412445.438 4637859.219 2074628.211 1.712216426 1.348348913 1.635409809 1.598286101 1.610017376 1.276251357 2.126860811 2.235513426 1 20.98442139 2.236137317 24.99997379 1.894944695 1.533347833 0.080042244 0.353321942 106.4561159 1098229.121 0.136920038 0.097248422 172.241309 -2.236137317 -0.361596862 EFTKLEEVLTNKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EFTKLEEVLTNKK 13 2 Q5TA02;P78417-3;P78417 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 99.566 0.0015758 170130000 740960 565220 326980 332430 478510 349250 887460 950140 83560 FALSE TRUE 643040.2586 561507.0326 485108.6217 407913.3124 468988.5872 362685.8735 801394.2658 746959.955 73681.63199 8.727280345 7.620719268 6.583847406 5.536160117 6.365067854 4.92233768 10.87644565 10.13766844 1 16.1690174 4.597204461 3.113681629 6.959026339 8.767684987 0.048416093 2.741966119 1.210730595 19.23523042 0.714467526 4.370751527 39555.27985 -4.597204461 1.808658648 EFTLEFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFTLEFSR 8 0 P16615-5;P16615-2;P16615-3;P16615;H7C5W9;P16615-4;O14983-3;O14983-2;O14983;Q93084-4;Q93084-2;Q93084-3;Q93084-7;Q93084;Q93084-6;Q93084-5 P16615-5;Q93084-4 ATP2A2;ATP2A1;ATP2A3 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2;Sarcoplasmic/endoplasmic reticulum calcium ATPase 1;Sarcoplasmic/endoplasmic reticulum calcium ATPase 3 0 ; 198.92 0.00030729 334830000 295850 299070 209770 311460 400080 414750 237840 428490 417830 FALSE TRUE 256752.6729 297105.3895 311215.4736 382181.7534 392119.1907 430705.7009 214774.3134 336860.748 368434.6134 0.696874462 0.806399233 0.844696623 1.037312292 1.064284344 1.169015302 0.582937394 0.914302663 1 18.49104908 4.25392096 2.101704537 0.944322266 0.717337328 0.243701157 0.153939001 0.572621535 4.78189128 0.044338395 0.170257669 17944.0702 -4.25392096 -0.226984938 EFTMAEIEHFVDPSEKDHPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EFTMAEIEHFVDPSEKDHPK 20 1 P41250 P41250 GARS Glycine--tRNA ligase 0 258.95 1.83E-36 191230000 471590 273420 277160 338910 269110 200640 400280 459050 525320 FALSE TRUE 409268.1866 271623.886 411195.503 415864.6954 263755.2375 208358.7506 361460.9072 360885.7298 463217.268 0.883533959 0.586385493 0.887694677 0.897774595 0.569398543 0.449807822 0.780326927 0.779085226 1 18.82132951 1.193699266 2.026140965 1.112421082 0.714904477 0.249615317 0.150485675 1.308749526 4.764171114 1.022315123 0.042126927 15.62065593 -1.193699266 -0.397516605 EFVAVTGAEEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EFVAVTGAEEDR 12 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;R4GNE6;G3V4V8;R4GMY2 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 73.781 0.089041 376480000 94173 98628 84266 103620 83239 89339 96645 98699 218140 FALSE TRUE 81727.79945 97980.10617 125017.3195 127148.5047 81582.70675 92775.92914 87272.38278 77592.98693 192351.7377 0.424887243 0.509379886 0.649941201 0.661020827 0.424132933 0.482324362 0.453712474 0.403391141 1 17.55338734 1.231657183 24.99998044 1.000000854 0.501213269 0.755311 0.08924034 132.1945225 478683.4823 0.231528716 0.023951673 17.04736197 -1.231657183 -0.498787586 EFVEAVLELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EFVEAVLELR 10 0 O75367-2;O75367-3;O75367;B4DJC3 O75367-2 H2AFY Core histone macro-H2A.1;Histone H2A 0 ;;;; 213.53 4.77E-08 411230700 621174 474963 387944 506149 551732 869224 318203.2 540908 569763 FALSE TRUE 539084.282 471842.9368 575555.016 621077.8665 540753.6126 902663.6097 287343.9026 425239.0336 502406.2672 1.073004692 0.939166104 1.145596808 1.236206447 1.076327363 1.796680632 0.571935347 0.846404715 1 18.93849494 EFVISDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFVISDR 7 0 Q14019;H3BT58 Q14019 COTL1 Coactosin-like protein 0 ; 123.69 0.0098156 267560000 564460 470950 364810 440470 498620 524700 503370 543050 752070 FALSE TRUE 489865.1808 467856.2984 541233.3362 540485.4457 488698.4375 544885.5485 454553.2549 426922.9835 663161.1414 0.738681974 0.705494139 0.816141511 0.815013745 0.736922608 0.821648789 0.685434092 0.643769601 1 19.33899995 4.263120806 24.91177131 0.770283995 0.722088042 0.051077991 0.096827769 879.4117635 891983.7119 0.024135936 0.063794142 18328.24183 -4.263120806 -0.048195953 EFVISDRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EFVISDRK 8 1 Q14019;H3BT58 Q14019 COTL1 Coactosin-like protein 0 110.41 0.0055024 132520000 286470 235870 111310 140960 248900 237420 255760 265230 122810 FALSE TRUE 248612.2637 234320.5544 165139.8883 172967.1224 243947.377 246553.701 230956.4346 208512.6285 108291.5417 2.29576807 2.163793688 1.524956481 1.597235756 2.252690959 2.27675862 2.13272829 1.925474744 1 16.72456104 1.238468896 4.282264742 0.902875172 2.021256618 0.58896993 0.269400877 0.172190602 6.111899418 0.594456564 0.073523329 17.31685003 -1.238468896 1.118381445 EFVTHPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EFVTHPK 7 0 P28838-2;P28838 P28838-2 LAP3 Cytosol aminopeptidase 0 ;; 81.958 0.043885 333530000 2519770 2296060 1460460 1855570 2069680 1900510 2334580 2689620 2512300 FALSE TRUE 2186776.01 2280977.031 2166743.341 2276905.529 2028497.417 1973623.849 2108172.791 2114465.694 2215298.756 0.98712465 1.029647592 0.978081776 1.027809691 0.915676683 0.890906404 0.951642656 0.954483312 1 21.07906984 3.240791686 24.99990082 0.94213529 1.00540861 0.493523916 0.031773587 52.89660088 592720.455 0.009663084 0.011873931 1740.971596 -3.240791686 0.063273319 EFWEIVHSFTDEQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFWEIVHSFTDEQKR 15 1 A0A1B0GVL3;Q05086-2;Q05086-3;Q05086;A0A0D9SG63;S4R306 A0A1B0GVL3 UBE3A Ubiquitin-protein ligase E3A 0 ; 168.5 8.12E-07 165020000 371912 287573 203599 232895 264688 255639 364308 406516 253363 FALSE TRUE 322762.8869 285683.914 302060.1574 285777.3693 259421.2267 265473.5978 328977.4662 319585.7169 223410.7148 1.444706389 1.278738642 1.352039707 1.279156954 1.16118525 1.188276032 1.472523225 1.430485182 1 17.76933885 6.901659537 1.379556275 1.286098426 67.86697832 0.127147678 0.136500257 1580.897996 9.314377066 0.039307703 330966.7984 7973693.488 -6.901659537 66.5808799 EFWGDIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFWGDIAK 8 0 Q9NR19;Q9NR19-2;F8WCJ4;C9IYL0;B4DEH9;C9JY31 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ; 103.74 0.010969 125330000 369480 292050 198942 234171 246870 244027 359750 353070 300276 FALSE TRUE 320652.2819 290131.5043 295151.0166 287343.1046 241957.77 253414.8766 324861.5004 277568.7281 264777.7134 1.211024439 1.095755004 1.114712462 1.085223907 0.913814712 0.957085373 1.226921618 1.048308502 1 18.01442217 4.864211527 1.048870547 1.045975944 1.316926632 0.284950643 0.084496048 3.433925261 2.606845001 0.028045225 1.104980344 73149.52777 -4.864211527 0.270950689 EFWPQEVWSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFWPQEVWSR 10 0 E9PNM1;P37268;A0A1W2PQ47;P37268-4;P37268-3;P37268-2;P37268-5 E9PNM1 FDFT1 Squalene synthase 0 ; 172.88 8.33E-06 677350000 467530 436470 332090 411440 514230 658890 367870 532160 466500 FALSE TRUE 405744.7259 433602.7998 492689.8348 504863.7405 503997.8291 684237.9247 332194.024 418361.7253 411350.9014 0.986371306 1.054094687 1.197736125 1.227331066 1.225226023 1.663392306 0.807568484 1.017043414 1 18.65001008 EFYHEVHRPSHFLNFALLQEGEVYSADREDLYA ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EFYHEVHRPSHFLNFALLQEGEVYSADREDLYA 33 2 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 129.46 2.39E-08 136030000 90255 78766 42604 51702 71800 68746 67475 88900 60114 FALSE TRUE 78327.57307 78248.58096 63207.4369 63441.72932 70371.32047 71390.7031 60931.28489 69889.42682 53007.3914 1.47767266 1.476182451 1.192426853 1.196846848 1.327575619 1.346806572 1.149486577 1.318484554 1 15.69390592 7.999999987 0.477753614 1.208670301 9.661913478 0.431631709 0.111157459 105.8296264 1.234930869 0.073362327 884.6047809 99999996.93 -7.999999987 8.453243177 EGALCEENMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 EGALCEENMR 10 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;; 206.23 3.59E-07 9630470000 2525838 2475093 1586304 1830586 2384778 2524982 2304583 2563371 2482029 FALSE TRUE 2192042.109 2458833.951 2353445.92 2246248.53 2337325.584 2622119.691 2081084.895 2015214.06 2188606.359 1.001569834 1.123470167 1.075317135 1.026337386 1.067951564 1.198077343 0.950872178 0.920775018 1 21.06158107 2.141587269 13.70409064 0.949110091 1.080499369 0.521711795 0.056186472 0.507072527 69.06908528 0.022228669 0.014986418 138.5438555 -2.141587269 0.131389277 EGALTAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGALTAFR 8 0 Q15008;Q15008-4;Q15008-3;Q15008-2;C9J0E9 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 133.6 0.0021228 250800000 392580 453390 315530 361040 413930 439150 411950 468990 554860 FALSE TRUE 340699.5583 450411.6512 468121.3634 443019.6502 405693.6028 456044.3847 371999.1524 368700.1382 489265.0829 0.696349628 0.920588178 0.956784736 0.905479802 0.829189773 0.932100819 0.760322299 0.753579503 1 18.9002568 1.214167602 24.80129725 1.000000757 0.84619314 0.242145145 0.086508477 3429.166753 3486357.488 1.439834111 0.022083416 16.3744832 -1.214167602 -0.153807618 EGAPIEPDPPVSHWKPEAVQYYEDGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGAPIEPDPPVSHWKPEAVQYYEDGAR 27 1 Q96HS1;Q96HS1-2;F5GXG4 Q96HS1 PGAM5 "Serine/threonine-protein phosphatase PGAM5, mitochondrial" 0 ; 62.677 0.022217 172783000 287440 213086 166945 229252 239120 258840 210834 297820 259080 FALSE TRUE 249454.0757 211686.224 247680.1604 281307.1705 234361.9798 268797.7423 190387.3511 234133.5106 228451.8575 1.091932797 0.926611962 1.084167855 1.231363026 1.025870318 1.176605632 0.833380622 1.024870242 1 17.80153065 2.249751876 24.99997733 0.962801519 1.085348526 0.314875035 0.094524471 281.5185369 628880.4009 0.035372982 0.027144165 177.7263724 -2.249751876 0.122547007 EGARPPS(ph)SPPMPVIDNVFSLAPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGARPPSSPPMPVIDNVFSLAPYR 24 1 Q6ZRI6;H3BMJ2;Q6ZRI6-2 Q6ZRI6 C15orf39 Uncharacterized protein C15orf39 1 EGARPPS(0.5)S(0.5)PPMPVIDNVFSLAPYR;EGARPPS(0.5)S(0.5)PPMPVIDNVFSLAPYR 79.365 0.011425 104606000 113563 103261 66021 83572 101432 81028 111370 102614 114890 TRUE FALSE 98555.36182 102582.6717 97948.97643 102548.2999 99413.70165 84145.19959 100569.3545 80670.79464 101307.8351 0.972830598 1.012583791 0.966845026 1.01224451 0.981303189 0.830589258 0.992710529 0.796293738 1 16.62838623 2.874611421 7.655688925 0.896339784 0.991586085 0.300425079 0.063428749 0.286833275 16.61049825 0.018732618 0.018757313 749.2235511 -2.874611421 0.095246301 EGAS(ph)PVTEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGASPVTEVR 10 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 EGAS(0.996)PVT(0.004)EVR 69.342 0.060068 265360000 405860 276840 216640 235550 353470 373120 311330 387590 303120 TRUE FALSE 352224.5727 275021.4198 321407.8286 289035.2277 346436.6386 387474.1678 281137.2645 304706.8947 267285.4989 1.31778407 1.028942539 1.202488837 1.081372648 1.296129569 1.449664009 1.051823857 1.140005335 1 18.02802204 EGASGRPGS(ph)PK ddPTM_MDA-MB-175_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 EGASGRPGS(1)PK;EGAS(0.074)GRPGS(0.926)PK 84.859 0.022119 417100000 891610 700270 518260 531390 593690 553890 863070 989690 815990 TRUE FALSE 773781.4794 695669.8803 768892.2695 652050.2213 581876.7305 575198.5067 779369.6042 778052.4953 719524.5918 1.075406579 0.966846565 1.068611522 0.906223677 0.808696099 0.79941466 1.083172991 1.081342464 1 19.45668447 2.178446347 24.99999718 1.061541213 0.937542174 0.258995894 0.093305601 103.4616302 43025.9098 0.04136325 0.027887106 150.8156281 -2.178446347 -0.123999039 EGATVYATGTHAQVEDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 216.17 9.11E-19 1189780000 477768 470582 305045 483012 580749 574283 436272 500001 500567 FALSE TRUE 414629.7483 467490.7159 452565.7823 592687.257 569193.2311 596376.0386 393962.4086 393079.6772 441390.5395 0.939371625 1.059131708 1.025318265 1.342772905 1.289545607 1.351130088 0.892548375 0.890548487 1 18.75169618 2.213513453 24.99747495 0.918494517 1.169935438 0.40164638 0.138025585 236.5041998 236033.1769 0.061313073 0.041356107 163.4983796 -2.213513453 0.251440922 EGCEAIVDTGTSLMVGPVDEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EGCEAIVDTGTSLMVGPVDEVR 22 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;A0A1B0GU92;A0A1B0GU03;C9JH19;H7C469;H7C1V0 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ;;; 253.79 1.14E-36 324483000 534420 525122 366452 462046 519008 596519 501927 612485 584832 FALSE TRUE 463795.043 521672.439 543669.4129 566960.6062 508680.7562 619467.4719 453250.1968 481509.8491 515693.8272 0.899361246 1.011593336 1.05424844 1.099413211 0.986400708 1.201231117 0.878913365 0.933712648 1 18.97615525 EGDELEDNGKNFYES(ph)DDDQKEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EGDELEDNGKNFYESDDDQKEK 22 2 O00203;O00203-3 O00203 AP3B1 AP-3 complex subunit beta-1 1 EGDELEDNGKNFYES(1)DDDQKEK;EGDELEDNGKNFYES(1)DDDQKEK;EGDELEDNGKNFYES(1)DDDQKEK 207.86 3.95E-23 983260000 1913010 1110280 1387830 814700 945560 624910 1753160 1971800 657340 TRUE FALSE 1660200.882 1102986.498 2058989.23 999690.0869 926745.206 648950.6921 1583138.813 1550145.915 579630.014 2.864242433 1.90291474 3.552247434 1.724703798 1.598856483 1.119594701 2.731291987 2.67437137 1 19.14477278 3.691393793 24.99853962 1.918657062 2.686115468 0.293644771 0.687113114 631.2304954 334553.5632 0.196325604 0.29119882 4913.53205 -3.691393793 0.767458405 EGDIIPPLTGAT(ph)PPLIGHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EGDIIPPLTGATPPLIGHLK 20 0 Q12888;Q12888-2;A6NNK5;Q12888-3;H7C3N7 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 EGDIIPPLT(0.003)GAT(0.997)PPLIGHLK;EGDIIPPLTGAT(1)PPLIGHLK;EGDIIPPLTGAT(1)PPLIGHLK 193.87 2.12E-17 153436000 840420 708550 443700 493600 561950 516230 775440 935850 694560 TRUE FALSE 729356.3676 703895.4884 658274.8041 605679.4242 550768.2944 536089.7021 700237.9482 735725.7603 612449.908 1.1908833 1.149311118 1.074822276 0.988945245 0.899287088 0.875320079 1.143339135 1.201283159 1 19.22423233 4.225935055 2.744357377 1.034034106 1.181805722 0.280532278 0.098263467 0.462792874 6.928934427 0.031223304 0.094643344 16824.22451 -4.225935055 0.147771616 EGDIVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EGDIVKR 7 1 P25705;P25705-2;P25705-3;K7EK77;K7ERX7;K7EJP1;K7EQH4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;; 107.43 0.011993 1431110000 3080020 2756520 1803120 3062770 2807310 2908470 2984890 3769880 1552920 FALSE TRUE 2672987.553 2738412.239 2675114.863 3758218.74 2751450.023 3020360.723 2695415.827 2963720.499 1369335.567 1.952032517 1.999810934 1.953586052 2.744556434 2.009332183 2.205712607 1.968411464 2.164349318 1 20.3850446 1.237449836 24.99485932 0.999998654 2.128297374 0.690107707 0.23685122 15.8242971 355913.6709 0.336687207 0.056390901 17.27626415 -1.237449836 1.12829872 EGDKHTLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 EGDKHTLSK 9 1 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;;;;;;;; 121.83 0.00036223 85721948200 86094073 69288173 37879495 40279600 48478537 45774194 87540772 97931594 6696527.6 FALSE TRUE 74716523.12 68833014.43 56198145.48 49425698.82 47513908.96 47535156.86 79051081.41 76989684.73 5904871.736 12.65336936 11.65698723 9.517250839 8.370325559 8.046560719 8.050159087 13.38743413 13.03833312 1 22.49347429 4.318380029 3.219617619 9.317730258 12.47504282 0.134968476 3.395626689 0.583673377 11.70692353 0.896757171 2.857527156 20815.17318 -4.318380029 3.157312559 EGDKHTLSKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EGDKHTLSKK 10 2 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;; 97.734 0.0032942 4840870000 8694000 6546190 3056960 3406880 5158870 3991270 12480400 11201200 393740 FALSE TRUE 7545065.872 6503187.647 4535316.081 4180464.175 5056218.58 4144816.74 11270052.73 8805910.548 347192.5058 21.73164958 18.73078347 13.06282827 12.04076731 14.56315588 11.93809391 32.46052994 25.36319305 1 18.40537628 -1.997002038 5.20E-13 9.660284048 25.62346392 0 8.617984801 0 0.176565036 440531352.9 440531352.6 0.010069269 1.997002038 15.96317987 EGDLIAAQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 154.35 3.40E-05 409520000 1054100 1042200 633590 859770 1013200 1053500 899290 1036800 1477300 FALSE TRUE 914798.0143 1035353.72 939996.2432 1054993.919 993039.3023 1094028.827 812076.9942 815088.3884 1302655.277 0.702256407 0.794802537 0.72160015 0.809879588 0.762319333 0.839845235 0.623401301 0.625713036 1 20.31302392 2.258166226 24.99800742 0.718610428 0.771850485 0 0.111020715 829.6426763 1057827.92 0.040750724 0.031520785 181.2033515 -2.258166226 0.053240057 EGDLLFTVAKDPIVNVWYSVNGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGDLLFTVAKDPIVNVWYSVNGER 24 1 Q13347;Q5TFK1 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ; 139.36 2.86E-07 1057690000 505190 432890 249040 309440 421610 350220 533210 621050 186207 FALSE TRUE 438427.8615 430046.3171 369476.577 379703.0815 413220.7859 363693.19 481499.3763 488243.2905 164193.8206 2.670184907 2.619138257 2.250246542 2.312529669 2.516664661 2.215023615 2.932506075 2.973578962 1 17.32504031 1.2294264 24.99904992 0.99999696 2.570073389 0.781911051 0.259087181 189.287931 518015.4796 0.866935726 0.07166592 16.96002157 -1.2294264 1.570076429 EGDNVNYDWIHWDPEHSYEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGDNVNYDWIHWDPEHSYEFK 21 0 Q04446;E9PGM4 Q04446 GBE1 "1,4-alpha-glucan-branching enzyme" 0 191.65 7.91E-18 93029000 140230 128220 99096 92317 120360 100100 135510 155060 153660 FALSE TRUE 121698.2502 127377.7144 147019.1571 113278.9858 117965.0715 103950.9118 122368.2611 121901.6257 135494.4899 0.898178593 0.940095162 1.085056353 0.836041273 0.870626338 0.767196599 0.903123523 0.89967958 1 17.04787466 5.114212614 11.60031435 0.909015763 0.66953549 0.001157307 0.086453541 10037387.8 19711213.92 0.021977937 60119392.84 130080.6246 -5.114212614 -0.239480273 EGDQIVGATIYFDNLQSGEVTQLLNTMGHHTVGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGDQIVGATIYFDNLQSGEVTQLLNTMGHHTVGLK 35 0 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2;E9PQE3 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 190.25 7.67E-21 117520000 77294 55419 24071 48471 49746 42005 55063 67896 62580 FALSE TRUE 67079.40206 55054.94894 35711.81611 59477.08138 48756.15193 43620.95953 49722.99874 53376.96877 55181.86369 1.215605954 0.997700064 0.647165821 1.077837489 0.883553919 0.790494496 0.901075016 0.967291882 1 15.75190656 4.646679048 3.972298381 0.900526192 1.220054177 0.421628252 0.117650654 0.206299373 5.308152016 0.027987666 0.149822141 44328.09299 -4.646679048 0.319527985 EGDVLTLLESER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EGDVLTLLESER 12 0 P62857 P62857 RPS28 40S ribosomal protein S28 0 ;;;;; 280.25 1.19E-27 3503160000 2383220 2163960 1386380 1663350 2190730 2124720 2280070 2632550 2344280 FALSE TRUE 2068271.439 2149744.804 2056838.005 2041039.04 2147138.759 2206459.353 2058949.162 2069599.669 2067141.889 1.000546431 1.039959964 0.995015396 0.987372493 1.038699264 1.067396179 0.996036689 1.001188975 1 20.97920599 4.228022977 24.99852166 1.01241509 1.020253205 0.016409005 0.025752638 1236.64776 2933710.883 0.006993047 0.014749604 16905.30368 -4.228022977 0.007838115 EGEEDGRDQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGEEDGRDQSR 11 1 E7ESY4;Q13330-3;Q13330;Q13330-2 E7ESY4 MTA1 Metastasis-associated protein MTA1 0 77.062 0.030683 110360000 132500 107330 76379 85748 86888 101680 110290 129970 95704 FALSE TRUE 114989.7893 106624.9422 113316.1399 105218.394 85159.09879 105591.6954 99594.09278 102176.9269 84389.98215 1.362599995 1.263478667 1.342767672 1.246811426 1.009113838 1.251234954 1.180164876 1.210770809 1 16.36478413 3.470246819 24.96488544 1.148099438 1.313299747 0.525991219 0.083416146 141.4086809 513530.6793 0.023199953 0.030020459 2952.886943 -3.470246819 0.165200309 EGEEPTVYS(ph)DEEEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EGEEPTVYSDEEEPK 15 0 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 1 EGEEPTVYS(1)DEEEPK;EGEEPTVYS(1)DEEEPK;EGEEPTVYS(1)DEEEPK 296.13 4.76E-44 287820000 309158 214364 277069 411501 291836 241907 253687 389078 889340 TRUE FALSE 268301.987 212955.8288 411060.4951 504938.5914 286029.0346 251213.3188 229084.4738 305876.6975 784203.2383 0.34213323 0.271556936 0.524175973 0.643887409 0.3647384 0.320342108 0.292123856 0.390047736 1 19.58086807 1.238357471 24.99999966 1.000000669 0.393592934 0.741825867 0.112421308 2.69305115 330600.105 0.166667152 0.02956971 17.31240771 -1.238357471 -0.606407735 EGEEPTVYS(ph)DEEEPKDESAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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;EGEEPTVYS(1)DEEEPKDESAR 324.23 2.48E-67 24314970000 9754070 7393130 8308550 9801500 9492200 8028510 7281290 14378580 16231040 TRUE FALSE 8465044.936 7344564.042 12326592.57 12027080.38 9303323.791 8337371.975 6575151.617 11303832.56 14312224.94 0.591455554 0.513167175 0.861263194 0.840336176 0.650026382 0.582535001 0.459408069 0.789802606 1 23.77074463 1.395408892 3.801640945 0.993731511 0.650160632 0.449903055 0.127176563 0.237141491 5.266511531 0.172911098 0.035049461 24.85472095 -1.395408892 -0.343570879 EGENNKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGENNKPR 8 1 P45973;F8VNY3 P45973 CBX5 Chromobox protein homolog 5 0 ; 128.38 0.0010359 306880000 800970 573790 351980 473970 338470 463020 638100 724080 849300 FALSE TRUE 695119.7851 570020.7357 522198.7053 581592.1327 331735.1092 480832.679 576217.1602 569241.1268 748896.7215 0.928191785 0.761147324 0.697290681 0.776598583 0.442965097 0.642054726 0.769421395 0.760106314 1 19.51440725 1.002906572 1.667439188 1.291571449 0.705725654 0.341156069 0.122257379 2.356757081 3.606342169 2.733585356 0.035293288 10.06715074 -1.002906572 -0.585845795 EGEQHVDDVSSALKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGEQHVDDVSSALKR 15 1 Q96P48-3;Q96P48;E7EU13;Q96P48-7;Q96P48-2;Q96P48-4;Q96P48-1;A0A0A0MSJ2;Q96P48-5 Q96P48-3 ARAP1 "Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1" 0 59.513 0.068218 83869000 203610 179500 112900 138590 148100 123070 181880 199530 156440 FALSE TRUE 176702.4226 178320.8527 167498.8176 170058.9777 145153.0998 127804.5825 164241.3056 156862.0622 137945.8414 1.280955053 1.292687412 1.214236079 1.232795248 1.052247014 0.926483765 1.190621652 1.13712788 1 17.07374244 3.295996912 5.207895143 1.073675539 1.258095942 0.628118067 0.073926617 0.150832753 8.326329312 0.023290801 0.029813507 1976.955582 -3.295996912 0.184420403 EGERPSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EGERPSLR 8 1 Q7L2H7;J3KNJ2;E9PN86;E7ESM3 Q7L2H7 EIF3M Eukaryotic translation initiation factor 3 subunit M 0 ;; 155.07 0.00037841 2903790000 2039860 1801760 1290310 1446870 1950030 1801740 1772810 2139880 1975660 FALSE TRUE 1770287.333 1789924.12 1914308.232 1775403.948 1911228.218 1871054.104 1600883.159 1682283.315 1742099.725 1.016180249 1.027452157 1.098851118 1.019117288 1.097083129 1.074022386 0.918938873 0.965664187 1 20.73239578 2.247476218 24.99998102 0.960619921 1.056391949 0.617403685 0.034843833 116.1450184 325679.5687 0.012999682 0.009916518 176.7975399 -2.247476218 0.095772028 EGES(ph)LEDLMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EGESLEDLMK 10 0 P13796 P13796 LCP1 Plastin-2 1 EGES(1)LEDLMK;EGES(1)LEDLMK;EGES(1)LEDLMK 167.71 5.41E-06 491660000 1499300 1013904 1026286 973110 920419 764751 1311715 1510780 1883940 TRUE FALSE 1301163.706 1007243.598 1522601.342 1194069.499 902104.4627 794171.4658 1184505.081 1187711.454 1661222.759 0.78325661 0.60632663 0.916554588 0.718789513 0.543036422 0.478064402 0.713032057 0.714962185 1 20.66381411 1.175063466 2.650897395 1.112652644 0.675723395 0.398868409 0.122283642 0.691902068 4.766976083 0.733159697 0.033494688 14.96454326 -1.175063466 -0.436929249 EGESLEDLMKLS(ph)PEELLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EGESLEDLMKLSPEELLLR 19 1 P13796 P13796 LCP1 Plastin-2 1 EGES(0.004)LEDLMKLS(0.996)PEELLLR;EGESLEDLMKLS(1)PEELLLR;EGESLEDLMKLS(1)PEELLLR 110.94 0.00013682 95213000 193685 144594 127471 121551 129628 108569 175975 197355 229049 TRUE FALSE 168089.0365 143644.1525 189116.402 149151.0123 127048.6564 112745.7197 158908.9716 155152.1691 201971.0882 0.83224306 0.71121146 0.93635383 0.738477045 0.629043778 0.558227025 0.786790689 0.768189994 1 17.62378926 1.126524984 2.318364603 1.135028718 0.737336342 0.377093595 0.103172068 1.067360463 4.570614283 0.987941315 0.028831422 13.38212197 -1.126524984 -0.397692377 EGETQGVAFEHESPADFQNS(ph)QSPVQDQDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGETQGVAFEHESPADFQNSQSPVQDQDK 29 0 P78332;E9PGM9;P78332-3;F8WCA5 P78332 RBM6 RNA-binding protein 6 1 EGETQGVAFEHESPADFQNS(0.634)QS(0.366)PVQDQDK 155.28 8.64E-09 245580000 57160 48177 18642 42495 51286 36817 57719 72019 68130 TRUE FALSE 49606.16118 47860.52211 27657.33355 52144.13925 50265.50894 38233.37381 52121.42026 56618.2973 60075.74901 0.825726886 0.796669586 0.460374344 0.867973186 0.83670216 0.636419428 0.867595013 0.942448463 1 15.87449511 1.924841463 2.741859552 0.971718792 0.737935916 0.39445432 0.119847286 0.280730545 3.834762916 0.077981505 0.033768368 84.10880509 -1.924841463 -0.233782876 EGFES(ph)DTDSEFTFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGFESDTDSEFTFK 14 0 E9PMS6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 EGFES(0.907)DT(0.093)DSEFTFK;EGFES(0.981)DT(0.019)DSEFTFK 300.61 8.00E-44 373360000 969060 788860 616150 731610 742880 630370 919840 1104190 1256650 TRUE FALSE 840996.2657 783677.9267 914122.2009 897733.2325 728098.1414 654620.7418 830634.0584 868067.5613 1108090.269 0.758960068 0.707232929 0.824952828 0.810162545 0.657074755 0.590764814 0.749608657 0.783390655 1 20.07964398 1.187259767 2.24034465 1.103711427 0.727065609 0.607183898 0.068278564 0.570855497 2.617038688 0.456964143 0.019769165 15.3907494 -1.187259767 -0.376645818 EGFHFEETLTGFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGFHFEETLTGFK 13 0 Q96G03-2;H0Y921;Q96G03 Q96G03-2;Q96G03 PGM2 Phosphoglucomutase-2 0 ; 171.57 2.49E-05 172407000 754900 679020 474800 604520 612310 585470 757740 885460 848720 FALSE TRUE 655138.0523 674559.4729 704414.8681 741785.5055 600126.229 607993.4097 684254.4914 696111.2697 748385.2885 0.875402099 0.901353198 0.941246279 0.991181303 0.801894744 0.81240695 0.91430778 0.930150927 1 19.51342167 1.353404564 2.000234197 1.017369406 0.890879843 0.286167107 0.05527407 0.870594424 4.308106209 0.190292392 0.01633423 22.56340113 -1.353404564 -0.126489563 EGFTFEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGFTFEYR 8 0 O75175;H7C5J4;A0A0G2JPP0 O75175 CNOT3 CCR4-NOT transcription complex subunit 3 0 85.212 0.039324 95724000 365660 289870 199230 258750 280520 279280 244980 312970 392460 FALSE TRUE 317337.1045 287965.8249 295578.2944 317503.1422 274938.2008 290024.0823 221221.8773 246043.801 346063.8259 0.916990106 0.832117671 0.85411497 0.917469896 0.794472523 0.838065295 0.639251666 0.710978099 1 18.40067862 2.898810665 2.153280249 0.766140594 0.873393226 0.111644124 0.097575766 0.536343627 4.928855766 0.035947687 0.036618378 792.1559074 -2.898810665 0.107252632 EGGDGEEQDVGDAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGGDGEEQDVGDAGR 15 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 271.6 4.93E-33 407070000 610240 516210 366520 413590 442580 498540 560960 545650 656290 FALSE TRUE 529595.2378 512818.9825 543770.2979 507501.9308 433773.5239 517719.1564 506558.1855 428966.9938 578704.1438 0.915139875 0.886150528 0.93963436 0.876962669 0.749560079 0.894618022 0.875331879 0.741254401 1 19.14246645 3.475189764 24.99811713 0.839525807 0.910460163 0.112770967 0.074000215 107.8274121 1395524.018 0.02041338 0.026531812 2986.687364 -3.475189764 0.070934356 EGGFLLLHTLLR ddPTM_MDA-MB-175_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 ;; 227.2 1.35E-11 22845969000 5512120 5538637 4882685 5103841 5851110 6663110 6728840 6898790 8984830 FALSE TRUE 4783679.376 5502253.329 7243967.798 6262746.106 5734684.359 6919444.153 6076278.132 5423537.445 7922653.633 0.603797616 0.694496261 0.914336046 0.790485915 0.723833784 0.873374563 0.766949865 0.684560716 1 22.9175523 4.452742929 7.910708498 0.804181457 0.625685799 0.379965417 0.093152147 0.172085633 45.28882616 0.022693008 0.062354902 28362.39685 -4.452742929 -0.178495658 EGGVIVDYHGCDFFPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGGVIVDYHGCDFFPER 17 0 A0A087WVD7;D6RDH4;Q9Y3D8-2;Q9Y3D8 A0A087WVD7 TAF9;AK6 Adenylate kinase isoenzyme 6 0 ; 191.37 2.46E-10 305720000 346830 335710 235710 272360 326400 326680 330800 357720 370760 FALSE TRUE 300995.5367 333504.6989 349700.1444 334203.5008 319905.2786 339247.591 298719.0669 281224.3618 326929.1752 0.920675056 1.020112992 1.069651077 1.022250463 0.978515541 1.037679157 0.913711867 0.860199649 1 18.3186186 2.227686866 24.58880892 0.91075742 1.010781041 0.356131274 0.051744062 156.3600013 353572.8859 0.020746633 0.014148617 168.9222531 -2.227686866 0.100023621 EGHALGGGMEADGPASLQELPPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGHALGGGMEADGPASLQELPPSPR 25 0 Q6ZVX7 Q6ZVX7 NCCRP1 F-box only protein 50 1 EGHALGGGMEADGPASLQELPPS(1)PR 121.83 0.00011509 125820000 68369 62003 48990 62798 61053 73810 59209 69535 100400 TRUE FALSE 59333.86343 61595.69821 72681.72786 77057.24571 59838.16475 76649.51846 53466.92029 54665.48137 88530.82638 0.670205688 0.695754244 0.820976499 0.870400163 0.675902024 0.86579468 0.603935629 0.617473976 1 16.43389227 4.44730383 17.17247486 0.758063555 0.676592087 0.077799545 0.123391401 18.01216556 10372.98951 0.031190699 0.082567036 28009.40157 -4.44730383 -0.081471468 EGHDAFELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGHDAFELK 9 0 H3BRF9;Q96K21-2;Q96K21;Q96K21-4;Q96K21-3 H3BRF9;Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 0 95.775 0.0078171 108610000 414830 388960 285130 320580 364680 350930 375860 470150 504590 FALSE TRUE 360009.1645 386404.8961 423019.8217 393372.5888 357423.5815 364430.5042 339409.1551 369612.0812 444937.945 0.80912219 0.868446714 0.950738921 0.884106634 0.803311081 0.819059171 0.762823578 0.830704788 1 18.76324461 4.747754262 22.07186847 0.857368305 0.80912206 0.049981799 0.069872077 963.5633245 2313021.214 0.01772056 0.194577451 55944.09623 -4.747754262 -0.048246246 EGHGSS(ph)SFDRELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGHGSSSFDRELER 14 1 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 EGHGS(0.003)S(0.589)S(0.408)FDRELER 148.97 4.61E-06 464610000 179190 172310 75123 101260 185240 168280 185800 185750 97940 TRUE FALSE 155509.5875 171178.0843 111452.7341 124252.6307 181554.0864 174753.8405 167781.1446 146028.808 86361.64477 1.800678853 1.982107737 1.290535102 1.438747849 2.10225369 2.023512185 1.942773844 1.690898875 1 16.3981031 1.24493681 3.995561173 0.917648186 1.792868599 0.487001724 0.255027026 0.223529361 6.224963798 0.567545967 0.069220104 17.57667855 -1.24493681 0.875220413 EGHILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EGHILK 6 0 P98174 P98174 FGD1 "FYVE, RhoGEF and PH domain-containing protein 1" 0 ;;;;; 106.84 0.03178 1848200000 9599860 7934310 5110920 6451720 6927670 6858000 8546250 9832640 9112150 FALSE TRUE 8331214.178 7882188.995 7582578.007 7916681.634 6789822.921 7121831.698 7717435.99 7730006.454 8034922.008 1.03687555 0.980991351 0.943702752 0.985284192 0.845039058 0.886359779 0.960486733 0.962051212 1 22.93785259 4.713476995 1.386034596 0.937902906 1.075722638 0.326619956 0.04521807 1.579301674 2.822680089 0.013777029 0.301077158 51698.38719 -4.713476995 0.137819732 EGHLS(ph)PDIVAEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGHLSPDIVAEQK 13 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 1 EGHLS(1)PDIVAEQK;EGHLS(1)PDIVAEQK 118.47 0.00027377 1049630000 3606900 3310100 2640500 3261000 3205500 2961700 3936800 4196200 4408400 TRUE FALSE 3130239.026 3288355.735 3917454.632 4001459.891 3141716.821 3075638.515 3555009.742 3298875.285 3887243.974 0.805259214 0.845935001 1.007771742 1.029382235 0.808211896 0.791213141 0.914532189 0.848641173 1 21.89031623 4.007435442 0.003728433 1.776511945 7.01E-05 0.015073359 0.089438223 665190.1573 1162.958007 274665.7522 279440.0802 10172.68139 -4.007435442 -1.776441827 EGHLSPDIVAEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 EGHLSPDIVAEQK 13 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ;;;;;;;;; 208.08 4.87E-08 28214840800 37292947 39035057 9926679.9 28597600 41537137 38163918 47532420 52471656 50598650 FALSE TRUE 32364589.57 38778633.14 14727255.5 35091122.17 40710629.24 39632108.62 42922733.22 41251000.7 44616935.24 0.725388003 0.869146053 0.330082186 0.786497817 0.912447908 0.888275011 0.962027826 0.924559262 1 25.41108808 3.400966316 4.235514582 0.933889701 0.649570971 0.495162029 0.135885717 0.179782983 6.203759435 0.039112075 0.05180966 2517.481661 -3.400966316 -0.28431873 EGHSLEMENENLVENGADS(ph)DEDDNSFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 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(0.979)DEDDNS(0.021)FLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(0.999)DEDDNS(0.001)FLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK 319.2 3.42E-83 9589030000 2557647 1900117 1823882 2124978 2036850 1804761 2333581 2791617 3635990 TRUE FALSE 2219647.469 1887635.006 2705917.436 2607486.733 1996320.67 1874191.324 2107270.674 2194651.429 3206147.404 0.692309863 0.588754904 0.843977863 0.813277247 0.622654051 0.584561808 0.657259448 0.684513577 1 21.61240933 1.238480269 24.93291345 1.000000059 0.685244112 0.571343157 0.085496652 1.471075685 453530.8692 0.123012125 0.021981758 17.31730354 -1.238480269 -0.314755947 EGHVEVVSELLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGHVEVVSELLQR 13 0 Q12955;D6RHY3;A0A087X0B4;Q12955-4;Q12955-5 Q12955;Q12955-4 ANK3 Ankyrin-3 0 98.942 0.0030881 133840000 218640 208710 130220 166870 196630 264280 168160 225920 225350 FALSE TRUE 189746.17 207338.9703 193194.8276 204760.3839 192717.4477 274447.0226 151851.8691 177608.7661 198709.3797 0.954892871 1.043428199 0.972248154 1.030451528 0.969845751 1.3811478 0.764190746 0.893811688 1 17.60030045 EGIDPTPYYWYTDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGIDPTPYYWYTDQR 15 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 196.15 2.11E-08 1466060000 392830 319510 164235 234930 302880 304360 289940 331330 347040 FALSE TRUE 340916.5202 317411.1178 243659.5953 288274.4472 296853.2806 316068.9261 261821.6634 260477.6579 306013.3265 1.114057757 1.037246062 0.796238511 0.942032331 0.970066513 1.032860006 0.855589089 0.851197106 1 18.22323496 4.447297129 10.54046943 0.917721259 1.094980665 0.458764036 0.072085213 0.338275721 117.61301 0.018512501 0.049399112 28008.96938 -4.447297129 0.177259406 EGILPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EGILPER 7 0 A6NMQ3;Q5T5H1;O43768-2;O43768;O43768-9;O43768-3;O43768-4;A0A1W2PRU0;O43768-6;O43768-5;O43768-7;O43768-8 A6NMQ3 ENSA Alpha-endosulfine 0 ;;; 104.75 0.018802 661930000 776380 777030 585920 788660 809230 806150 744490 889480 1135650 FALSE TRUE 673779.4159 771925.6388 869272.8718 967737.3069 793127.9062 837163.1121 672289.4744 699271.6239 1001394.751 0.67284097 0.770850494 0.868062141 0.966389435 0.792023231 0.835997105 0.671353104 0.698297673 1 19.93357937 4.640304903 3.425464037 0.815958036 0.667813239 0.185735372 0.102864099 0.522918424 9.961834494 0.027351025 0.168699917 43682.24019 -4.640304903 -0.148144796 EGILPERAEEAK ddPTM_MDA-MB-175_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 ;; 133.71 0.00014442 580040000 918958 891117 424139 389398 764564 661740 991006 1074160 92327 FALSE TRUE 797515.372 885263.1938 629254.0391 477816.7675 749350.6722 687197.566 894898.3907 844459.2431 81412.20724 9.796017072 10.8738385 7.729234477 5.869104692 9.204401866 8.440964682 10.99218927 10.37263663 1 16.31295751 4.235920349 24.99304211 8.098569207 10.33492812 0.121208501 2.807964448 154.9596387 1466925.664 0.713306113 1.602148442 17215.52808 -4.235920349 2.236358916 EGIPALDNFLDKL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGIPALDNFLDKL 13 1 P13639 P13639 EEF2 Elongation factor 2 0 155.02 0.00095297 214680000 249200 228900 163020 186840 210610 193420 263180 314730 253910 FALSE TRUE 216267.5886 227396.3408 241857.0173 229264.8777 206419.2731 200860.9926 237656.8441 247427.4387 223893.0491 0.965941504 1.015647166 1.080234595 1.023992833 0.921954808 0.897129203 1.061474865 1.105114428 1 17.77245021 2.044807554 24.9992727 1.067034501 0.988130503 0.247228571 0.057371067 170.8399252 95315.28132 0.025353854 0.017093556 110.8683422 -2.044807554 -0.078903998 DLLYFDGLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DLLYFDGLRK 10 1 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 92.611 0.014991 378580000 356640 357330 168810 218140 339460 367250 343550 354340 124260 FALSE TRUE 309509.1204 354982.6757 250447.0806 267672.0211 332705.4101 381378.3451 310232.5739 278567.1485 109570.1244 2.82475832 3.239776151 2.285724162 2.442928879 3.036461007 3.480678218 2.831360973 2.542364081 1 16.74149496 1.197990807 2.52711938 0.403631943 2.87722592 0.742685055 0.344757874 0.328985843 2.109781788 1.859133018 0.096392646 15.77577877 -1.197990807 2.473593977 EGIVALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGIVALR 7 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 99.919 0.02367 139200000 317350 317020 212390 245250 318310 343170 292940 354520 414330 FALSE TRUE 275411.3934 314937.4747 315102.5144 300937.7609 311976.2538 356371.972 264530.7239 278708.6569 365348.3794 0.753832257 0.86201963 0.862471362 0.823700823 0.853914432 0.975430554 0.724050629 0.762857241 1 18.47891328 4.744670814 23.21971225 0.846939695 0.753832143 0.120655031 0.083776336 627.4707133 2384291.684 0.020560172 0.176447434 55548.30528 -4.744670814 -0.093107552 EGIVALRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGIVALRR 8 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ; 127.02 0.0019148 729780000 1073360 1147110 472980 494660 1031430 1130770 1071960 1100670 205969 FALSE TRUE 931512.7565 1139574.559 701714.71 606980.1134 1010906.561 1174271.454 968001.4842 865300.2859 181619.5795 5.128922549 6.274513807 3.863651221 3.342041179 5.566065971 6.465555405 5.329830005 4.76435574 1 17.47056021 4.240701565 24.99077145 4.509778417 5.701718129 0.116531309 1.506796795 136.2902597 1590778.381 0.388328418 0.929294801 17406.10362 -4.240701565 1.191939712 EGKPSWGLPIDAVQWDICNLPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGKPSWGLPIDAVQWDICNLPLR 23 1 Q9BV44 Q9BV44 THUMPD3 THUMP domain-containing protein 3 0 134.34 1.78E-05 72081000 161240 126810 82620 101540 128250 129540 140370 165400 111320 FALSE TRUE 139931.7255 125976.9768 122575.3083 124596.2089 125698.0759 134523.4876 126756.939 130030.4971 98159.87642 1.42554912 1.28338565 1.248731282 1.26931913 1.280544358 1.370452903 1.291331485 1.324680734 1 16.58284581 1.236686154 24.99998069 0.999999612 1.308076129 0.777871239 0.052322085 22.77585977 303679.2532 0.078893447 0.012526738 17.24591155 -1.236686154 0.308076517 EGLDWDLIYVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGLDWDLIYVGR 12 0 Q8NBJ5;M0QX72 Q8NBJ5 COLGALT1 Procollagen galactosyltransferase 1 0 ; 131.28 0.00046866 47453000 145267 142120 107880 130470 137425 172951 125175 139925 126863 FALSE TRUE 126069.5979 141186.4044 160051.1288 160095.2076 134690.5114 179604.5369 113035.5478 110003.1276 111865.4007 1.126975786 1.262109674 1.430747379 1.431141413 1.204040843 1.605541444 1.010460313 0.983352556 1 16.77140436 2.135850651 9.922799039 0.992880794 1.341137755 0.603118721 0.132148991 0.201527421 17.9249614 0.052351033 0.035283895 136.725856 -2.135850651 0.348256962 EGLELLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EGLELLK 7 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;; 114.6 0.013652 1142690000 3056110 2940210 2019305 2046310 2605680 2370280 2908140 3370290 3958480 FALSE TRUE 2652237.32 2920895.567 2995847.652 2510955.961 2553832.066 2461466.205 2626109.03 2649579.711 3490513.004 0.759841696 0.836809822 0.858282908 0.719365881 0.731649492 0.705187519 0.75235618 0.759080315 1 21.73500766 1.237655664 24.99230227 1.000000276 0.765192855 0.701293924 0.048133424 13.90664582 383845.3086 0.075580296 0.012824789 17.28445396 -1.237655664 -0.234807421 EGLELPEDEEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EGLELPEDEEEK 12 0 P08238;Q58FF7;Q58FF6;P07900;P07900-2;Q58FG0 P08238;P07900 HSP90AB1;HSP90AB3P;HSP90AB4P;HSP90AA1;HSP90AA5P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Putative heat shock protein HSP 90-beta 4;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5 0 ;;; 235.06 1.14E-15 1416224000 2712830 1963950 2205380 2557200 1974150 1640510 2452230 3035640 6448620 FALSE TRUE 2354322.642 1951048.683 3271909.145 3137851.344 1934868.277 1703621.481 2214413.112 2386492.009 5686271.49 0.414036271 0.34311564 0.575405017 0.551829323 0.340270119 0.299602558 0.389431478 0.419693645 1 22.43905155 1.238633156 9.556753893 1.003059103 0.41617345 0.813892128 0.087663907 0.034077982 54.8573736 0.129816507 0.022991986 17.32340088 -1.238633156 -0.586885654 EGLELPEDEEEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 194.85 1.07E-06 3250980000 4090740 2454830 3157990 2812890 2211300 1539470 3669510 4253070 5366500 FALSE TRUE 3550138.344 2438704.06 4685204.527 3451599.667 2167299.456 1598694.407 3313641.485 3343584.078 4732078.484 0.75022812 0.515355793 0.990094425 0.729404569 0.458001587 0.337841904 0.700250745 0.706578323 1 22.17404257 1.172115148 2.137067965 1.155241285 0.63506756 0.283775602 0.178416003 1.224448542 4.823253911 1.328138334 0.050369262 14.86329673 -1.172115148 -0.520173725 EGLELPEDEEEKKK ddPTM_MDA-MB-175_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 ;;; 175.45 1.34E-06 4935880000 4204220 2250390 3166630 2542090 1949260 1173720 3673050 4425430 3334140 FALSE TRUE 3648621.675 2235607.04 4698022.86 3119310.388 1910473.54 1218873.768 3316838.176 3479086.233 2939981.767 1.241035477 0.760415274 1.597976869 1.060996508 0.649824962 0.414585485 1.128183247 1.183370003 1 21.48737578 3.473065081 24.92880959 0.904727159 1.184805966 0.197767001 0.297367109 222.0285218 1364553.208 0.091594775 0.118771957 2972.111382 -3.473065081 0.280078807 EGLELPEDEEEKKKQEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGLELPEDEEEKKKQEEK 18 3 P07900;P07900-2;Q58FG0 P07900 HSP90AA1;HSP90AA5P Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5 0 194.49 3.07E-15 670800000 1687800 884360 1541600 792640 474560 305510 1669900 1665800 626690 FALSE TRUE 1464752.954 878550.5809 2287122.916 972621.0267 465117.1845 317263.1674 1507953.355 1309581.633 552603.4221 2.650640396 1.589839197 4.138814247 1.760070582 0.841683504 0.574124507 2.728816534 2.36983989 1 19.07588497 3.511500517 24.70286503 1.624413126 2.718884034 0.300053452 0.892974604 797.2812515 572876.1028 0.25630162 0.379907088 3247.136286 -3.511500517 1.094470908 EGLEQALPSGKPS(ph)SPVELDLFGDPSPSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGLEQALPSGKPSSPVELDLFGDPSPSSK 29 1 Q9H201 Q9H201 EPN3 Epsin-3 1 EGLEQALPS(0.079)GKPS(0.533)S(0.388)PVELDLFGDPSPSSK;EGLEQALPS(0.123)GKPS(0.438)S(0.438)PVELDLFGDPSPSSK 152.18 1.73E-08 2244780000 1112530 825080 719870 832750 832550 582200 1146530 1377750 1202570 TRUE FALSE 965506.3417 819659.9952 1068001.54 1021838.615 815983.8839 604597.6107 1035339.697 1083128.884 1060403.545 0.910508407 0.772969875 1.007165192 0.963631837 0.769503165 0.570158044 0.976363859 1.021430841 1 20.01618197 2.02586449 24.99990188 1.008241809 0.835066716 0.302165145 0.120375064 273.4457679 264303.9992 0.0518654 0.034966625 106.1364335 -2.02586449 -0.173175093 EGLEQALPSGKPSS(ph)PVELDLFGDPSPSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EGLEQALPSGKPSSPVELDLFGDPSPSSK 29 1 Q9H201 Q9H201 EPN3 Epsin-3 1 EGLEQALPS(0.017)GKPS(0.181)S(0.802)PVELDLFGDPSPSSK;EGLEQALPS(0.01)GKPS(0.035)S(0.955)PVELDLFGDPSPSSK;EGLEQALPS(0.008)GKPS(0.174)S(0.817)PVELDLFGDPSPSSK 318.46 1.50E-92 1162680000 2100910 1525320 1220860 1379700 1528720 1100850 2081190 2535410 2096320 TRUE FALSE 1823269.42 1515300.072 1811271.98 1692981.972 1498301.463 1143200.412 1879356.514 1993232.302 1848495.438 0.986353216 0.819747802 0.979862835 0.915870247 0.810551886 0.618449139 1.016695241 1.078299822 1 20.81792005 2.02977716 24.997954 1.045569454 0.856403386 0.387534689 0.104818133 193.5530813 162487.2206 0.043645536 0.029425435 107.0969641 -2.02977716 -0.189166067 EGLEQALPSGKPSSPVELDLFGDPS(ph)PSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGLEQALPSGKPSSPVELDLFGDPSPSSK 29 1 Q9H201 Q9H201 EPN3 Epsin-3 1 EGLEQALPSGKPSSPVELDLFGDPS(0.927)PS(0.056)S(0.016)K 72.348 0.0042603 46640000 127650 93212 82638 82022 96753 85542 121280 151960 143950 TRUE FALSE 110780.7291 92599.68423 122602.0132 100646.3487 94827.80459 88832.85609 109518.2843 119464.5366 126932.395 0.872753792 0.729519712 0.965884345 0.792913021 0.747073311 0.699843851 0.862807987 0.941166647 1 16.95370079 1.736853476 2.606209783 0.98629651 0.802188196 0.452504765 0.076290794 0.226914362 3.18020734 0.063833354 0.021219472 54.55737616 -1.736853476 -0.184108315 EGLGQGQS(ph)LEQLEALVQTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EGLGQGQSLEQLEALVQTK 19 0 Q9NSC5-2;Q9NSC5;M0QYF9;Q9NSC5-5 Q9NSC5-2 HOMER3 Homer protein homolog 3 1 EGLGQGQS(1)LEQLEALVQTK;EGLGQGQS(1)LEQLEALVQTK;EGLGQGQS(1)LEQLEALVQTK 197.85 8.06E-16 89391000 259888 101407 79877 91861 101859 89483 106805 125847 128157 TRUE FALSE 225543.1423 100740.8507 118505.7844 112719.4441 99832.20518 92925.46891 96447.06754 98935.59839 113006.4255 1.995843523 0.891461263 1.048664126 0.997460486 0.883420609 0.822302524 0.853465342 0.875486487 1 16.78604528 4.739376638 24.99870626 0.916798248 1.995843859 0.955989684 0.072434448 13.89610182 425634.2329 0.019222058 0.112423397 54875.26598 -4.739376638 1.079045612 EGLHNAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGLHNAK 7 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 79.116 0.048147 0 788470 610840 480990 690170 362220 566570 640540 792410 992150 FALSE TRUE 684271.6918 606827.3518 713598.3728 846883.6471 355012.5307 588366.3145 578420.5294 622959.288 874859.1573 0.782150688 0.693628622 0.815672291 0.968022841 0.405793924 0.672526897 0.661158456 0.712068089 1 19.73869125 1.238730223 11.30395875 1.000577811 0.710854384 0.288253037 0.141226084 0.084637615 430.7891998 0.192044889 0.034462932 17.32727321 -1.238730223 -0.289723427 EGLHYTEVCGYDIASPNAGPLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGLHYTEVCGYDIASPNAGPLFR 23 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ; 203.64 1.87E-24 388860000 130906 119204 72121 85203 121065 129494 119582 133443 131819 FALSE TRUE 113606.4404 118420.9411 106998.9568 104549.6434 118656.0434 134475.718 107984.956 104907.2529 116235.508 0.977381545 1.018801768 0.92053589 0.899463901 1.020824406 1.156924595 0.929018661 0.902540495 1 16.82669133 EGLLFEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EGLLFEGR 8 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;; 142.79 0.0014234 1900640000 2261720 2071600 1305910 1737130 2037080 2373120 1656320 2213970 2072520 FALSE TRUE 1962827.972 2057991.523 1937452.444 2131571.917 1996546.093 2464415.462 1495690.341 1740529.745 1827509.047 1.074045557 1.126118378 1.060160248 1.166381048 1.092495874 1.348510677 0.818431156 0.952405542 1 20.80144712 2.220230475 24.99999106 0.925228309 1.138558736 0.564545426 0.091392887 175.0440794 238736.2271 0.035884934 0.024244465 166.0467866 -2.220230475 0.213330427 EGLLLWCQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EGLLLWCQR 9 0 O43707;P12814-3;P12814;P12814-2;P12814-4;H9KV75;P35609-2;P35609;G3V2N5;A0A494C1A0;G3V2W4;Q08043;A0A494C166;A0A494C033;A0A087WSZ2;G3V2X9 O43707;P12814-3 ACTN4;ACTN1;ACTN2;ACTN3 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2;Alpha-actinin-3 0 ;;; 170.66 0.00013385 4793910000 2811070 2819980 1842269 2169960 2500740 2805200 2120790 2604620 3806670 FALSE TRUE 2439579.977 2801455.366 2733196.45 2662682.584 2450980.167 2913117.859 1915116.112 2047642.282 3356649.809 0.726790138 0.83459864 0.814263211 0.793255995 0.730186438 0.867864694 0.570543912 0.610025591 1 21.6785906 2.258949875 24.99895943 0.696003593 0.794235506 0.045622259 0.120945301 488.5410125 598991.5526 0.04451288 0.03443807 181.5306133 -2.258949875 0.098231912 EGLQNMEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EGLQNMEAR 9 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;; 126.49 0.0010985 952030000 1278400 934130 567370 687400 946480 969380 920200 991190 1023020 FALSE TRUE 1109456.201 927993.6385 841752.0297 843484.6763 927646.8998 1006672.676 830959.1456 779231.7319 902079.741 1.22988706 1.028726837 0.933123749 0.935044473 1.02834246 1.11594644 0.921159303 0.863816907 1 19.78289544 4.702067469 2.848741405 0.964998276 1.265914788 0.580683869 0.068606116 0.29153292 3.494392076 0.019360816 0.194778097 50357.88351 -4.702067469 0.300916512 EGLRGS(ph)PPGPQELDVWLLGTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGLRGSPPGPQELDVWLLGTVR 22 1 Q8NC06-2 Q8NC06-2 1 EGLRGS(1)PPGPQELDVWLLGTVR 153.77 1.90E-08 15559000 35022 28543 20338 28642 36789 48281 25464 49880 26793 TRUE FALSE 30393.75397 28355.49915 30173.52483 35145.60387 36056.97088 50138.40131 22994.5052 39213.55017 23625.56206 1.286477498 1.200204214 1.277155851 1.487609216 1.52618468 2.122209883 0.973289234 1.659793323 1 14.52806103 3.780137764 4.572849641 1.482431882 1.243903434 0.081599748 0.32296345 0.497948583 24.35120234 0.083612223 0.1453297 6027.507558 -3.780137764 -0.238528449 EGLSES(ph)VR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGLSESVR 8 0 Q6PHR2-3;Q6PHR2;Q6PHR2-4 Q6PHR2-3 ULK3 Serine/threonine-protein kinase ULK3 1 EGLS(0.015)ES(0.985)VR 67.704 0.066927 0 117750 133600 87271 107180 108940 119920 105950 110890 169990 TRUE FALSE 102189.0392 132722.3728 129475.5475 131516.8571 106772.3071 124533.4 95674.98531 87177.03645 149893.9759 0.681742135 0.885441673 0.863780861 0.877399218 0.712318868 0.830809906 0.638284392 0.581591328 1 17.19358288 2.861183127 1.70850969 0.714618012 0.829326598 0.013892404 0.129050076 0.775747526 4.556438485 0.052027854 0.050803359 726.4121963 -2.861183127 0.114708586 EGMNIVEAMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 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 ;;;;;;;;;; 325.1 2.63E-46 9444720000 7794800 6565310 4667128 5530358 6110650 6332507 5779055 6834177 11309460 FALSE TRUE 6764697.43 6522182.046 6924166.711 6786110.31 5989060.02 6576122.642 5218603.136 5372741.432 9972468.523 0.678337306 0.654018815 0.694328259 0.680484505 0.600559431 0.659427766 0.523301039 0.538757422 1 23.24951923 1.230538791 24.99998616 1.000000685 0.624048438 0.796896343 0.058876384 150.3310321 468467.8895 0.178610611 0.016546005 17.00351822 -1.230538791 -0.375952247 EGMNPSYDEYADS(ph)DEDQHDAYLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 21 EGMNPSYDEYADSDEDQHDAYLER 24 0 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 1 EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;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 370.69 6.24E-119 86115160000 18540283 15004358 10328595 12804488 14392863 14593266 14918582 15951541 15820265 TRUE FALSE 16090137.63 14905793.38 15323538.09 15711942.7 14106473.19 15154678.39 13471780.21 12540428.09 13950011.29 1.15341395 1.06851479 1.098460622 1.126303225 1.011215897 1.086355994 0.96571823 0.898954691 1 23.73376295 2.197158171 3.916138455 0.939373603 1.089081084 0.677486799 0.044097168 0.114182741 3.697190965 0.018461404 0.012312262 157.4556216 -2.197158171 0.149707481 EGNASGVSLLEALDTILPPTRPTDKPLRLPLQDVYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGNASGVSLLEALDTILPPTRPTDKPLRLPLQDVYK 36 3 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 262.77 1.26E-62 1074600000 1682900 1155600 655490 700830 993050 792020 1464400 1650300 319190 FALSE TRUE 1460500.501 1148008.788 972487.1565 859964.163 973290.2479 822489.5219 1322382.713 1297396.188 281455.7218 5.189095079 4.078825543 3.455204784 3.055415457 3.458058133 2.922269679 4.698368556 4.609592512 1 18.10254845 4.648374177 2.316539142 3.486699859 5.425867611 0.247695032 1.023687131 0.763359152 5.638573798 0.267026945 2.761392728 44501.45158 -4.648374177 1.939167751 EGNDKDFTLNDFGFMIFHSPYCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGNDKDFTLNDFGFMIFHSPYCK 23 1 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 217.84 1.40E-32 496250000 1069900 751240 537930 697500 665740 534150 1013200 1202500 797450 FALSE TRUE 928510.0042 746305.055 798074.7473 855878.0356 652493.0765 554699.0961 914940.0199 945354.7329 703176.3695 1.320451091 1.061334094 1.134956722 1.217159838 0.92792236 0.788847749 1.301152968 1.344406288 1 19.42352706 0.973003015 19.01218033 0.54633616 1.139166669 0.056001206 0.176614136 1547.318854 33785.54793 31683.93245 0.044880989 9.397298336 -0.973003015 0.592830509 EGNDLYHEMIESGVINLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGNDLYHEMIESGVINLK 18 0 P06576;H0YH81;F8W079;F8W0P7;H0YI37 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ; 225.6 3.97E-19 904923000 1374638 1346474 982504 1864021 1540315 1319710 1415455 1974199 2020434 FALSE TRUE 1192976.105 1337628.924 1457646.221 2287275.458 1509665.745 1370480.098 1278184.392 1552031.907 1781580.594 0.669616693 0.750810223 0.818175852 1.28384619 0.847374376 0.769249565 0.717444047 0.871154475 1 20.76472632 4.200152683 3.686414377 0.898546614 0.70161384 0.221121862 0.155105217 0.368578938 10.33330062 0.042567997 0.108235602 15854.50483 -4.200152683 -0.196932775 EGNNPAENGDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGNNPAENGDAK 12 0 P05204 P05204 HMGN2 Non-histone chromosomal protein HMG-17 0 160.56 0.00015758 126840000 232850 213060 160280 182410 168030 160580 250650 265930 224040 FALSE TRUE 202078.2825 211660.3948 237791.9441 223828.9785 164686.5317 166757.6165 226342.0016 209062.939 197554.2464 1.022900222 1.071403924 1.203679234 1.133000087 0.833626888 0.844110514 1.145720761 1.05825586 1 17.59188933 5.11096544 16.12856838 1.039480419 0.001314073 0.000559312 0.120401918 43157583.39 47322969.03 0.031456779 1625004552 129111.6526 -5.11096544 -1.038166346 EGNTTEDDFPSS(ph)PGNGNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EGNTTEDDFPSSPGNGNK 18 0 Q15007 Q15007 WTAP Pre-mRNA-splicing regulator WTAP 1 EGNTTEDDFPSS(1)PGNGNK;EGNTTEDDFPSS(1)PGNGNK;EGNTTEDDFPSS(1)PGNGNK;EGNTTEDDFPS(0.002)S(0.998)PGNGNK 415.1 1.24E-147 1943630000 4658430 3572600 2552500 2942520 3532280 2776190 4171740 5040050 4196690 TRUE FALSE 4042806.673 3549131.355 3786897.538 3610664.14 3461994.539 2882991.826 3767165.297 3962274.529 3700562.089 1.092484486 0.959078991 1.023330361 0.975706947 0.935532077 0.779068627 1.017998133 1.070722348 1 21.81931299 2.016277375 24.99996226 1.041597097 0.95776333 0.141291222 0.080122929 399.4441074 613492.8196 0.033637759 0.02267226 103.8191277 -2.016277375 -0.083833767 EGPDLDRPGS(ph)DR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EGPDLDRPGSDR 12 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WZ99 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 1 EGPDLDRPGS(1)DR;EGPDLDRPGS(1)DR;EGPDLDRPGS(1)DR;EGPDLDRPGS(1)DR 127.66 0.00016092 1630310000 1983190 1712270 1421610 1768750 1774140 1723240 1751930 2116370 3393650 TRUE FALSE 1721106.417 1701021.986 2109105.351 2170371.721 1738838.085 1789534.158 1582028.098 1663800.745 2992456.563 0.575148337 0.568436651 0.70480734 0.725280944 0.581073793 0.598015082 0.528672034 0.555998294 1 21.51289888 1.234362798 25 1.00000058 0.603653635 0.796392445 0.062816319 61.67341921 367244.4991 0.128925927 0.017047302 17.15389699 -1.234362798 -0.396346945 TFDQLTPDESKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TFDQLTPDESKER 13 1 Q15293 Q15293 RCN1 Reticulocalbin-1 0 122.97 0.00020876 388420000 511680 423670 248190 272850 439880 430240 441400 441680 111100 FALSE TRUE 444060.1916 420886.8839 368215.5141 334804.7628 431127.2486 446791.6112 398593.0959 347230.1692 97965.88457 4.532804389 4.296259721 3.758609599 3.417564841 4.400789627 4.560685724 4.068692869 3.544398856 1 16.57999182 1.200016032 2.456811215 1.16E-13 4.131886925 0.886559998 0.351560063 0.211516005 1.264791621 1.954168667 0.099910311 15.84951701 -1.200016032 4.131886925 EGPDLDRPGSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EGPDLDRPGSDR 12 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WZ99 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 0 ;;; 93.011 0.0067604 3477990000 5385760 4950890 3221710 3911340 5088000 4653790 5139720 5753940 5643920 FALSE TRUE 4674018.17 4918367.278 4779739.732 4799469.528 4986758.755 4832824.313 4641270.745 4523504.708 4976702.207 0.939179797 0.988278397 0.960423094 0.964387526 1.002020725 0.971089712 0.932599652 0.908936183 1 22.24675863 2.246539846 23.74329947 0.938603983 0.972329443 0.111257854 0.028140351 132.0654176 392980.6794 0.010349832 0.007859921 176.4167617 -2.246539846 0.033725461 EGPET(ph)PPRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGPETPPRPR 10 1 A0A5E8;Q99501 A0A5E8 GAS2L1 GAS2-like protein 1 1 EGPET(1)PPRPR 89.805 0.018208 163110000 221100 211740 124550 136080 182930 191730 205460 235020 196600 TRUE FALSE 191881.0748 210349.066 184782.7966 166979.0439 179290.0509 199105.9772 185534.5208 184762.8019 173358.172 1.10684759 1.213378427 1.065901852 0.963202611 1.034217475 1.148523747 1.070238101 1.065786515 1 17.40339632 4.131936877 7.10660931 1.051264314 1.159265105 0.419567507 0.054194295 0.205123828 12.10143346 0.014181097 0.029935879 13549.92454 -4.131936877 0.108000791 EGPLGWSSDGSLGSVLLDSPSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EGPLGWSSDGSLGSVLLDSPSSPR 24 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 EGPLGWSSDGSLGSVLLDS(0.001)PS(0.118)S(0.882)PR;EGPLGWSSDGSLGSVLLDSPS(0.134)S(0.865)PR;EGPLGWSSDGSLGSVLLDSPS(0.026)S(0.973)PR;EGPLGWSSDGSLGSVLLDSPS(0.006)S(0.994)PR 220.05 6.69E-33 286617000 131884 162333 128214 166735 217156 219876 209440 271216 247919 TRUE FALSE 114455.1952 161266.6238 190218.7193 204594.7301 212835.0205 228334.772 189128.541 213218.569 218610.2983 0.523558113 0.737689968 0.870126983 0.935887887 0.973581859 1.044483146 0.865140126 0.975336344 1 17.73800184 4.691899723 1.090169866 0.968399146 0.32287741 0.914249691 0.044735256 0.425360687 0.442978867 0.01397664 0.312114674 49192.59388 -4.691899723 -0.645521736 EGPLSVFGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGPLSVFGDR 10 0 P17987;E7ERF2;F5GZ03;F5GZI8;F5GYL4 P17987 TCP1 T-complex protein 1 subunit alpha 0 79.16 0.050573 0 104480 108950 75474 76651 126200 142860 100630 118410 109510 FALSE TRUE 90672.70328 108234.3003 111973.4788 94055.78109 123688.8669 148355.9166 90870.91809 93088.94297 96563.85255 0.938992189 1.120857313 1.159579655 0.974026808 1.280902363 1.536350433 0.94104487 0.964014385 1 16.55919562 EGPPAPPPVKPPPS(ph)PVNIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 169.88 8.05E-12 7060810000 7088190 6762780 4779090 6320790 7362910 6615880 7121460 9283440 8871360 TRUE FALSE 6151467.732 6718354.853 7090273.909 7756021.977 7216402.496 6870397.185 6430821.905 7298248.6 7822597.927 0.786371457 0.858839342 0.906383528 0.991489279 0.922507147 0.878275638 0.822082634 0.932969925 1 22.89921638 4.530681212 2.272754826 0.918718175 0.779990301 0.435912102 0.050787165 0.427464254 3.505191606 0.014166806 0.098917844 33937.6067 -4.530681212 -0.138727874 EGPSCPS(ph)PGPFCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGPSCPSPGPFCR 13 0 Q4AC94 Q4AC94 C2CD3 C2 domain-containing protein 3 1 EGPSCPS(1)PGPFCR;EGPS(0.001)CPS(0.999)PGPFCR 186.51 8.13E-06 282010000 381540 352150 230080 241010 360410 371850 375420 434660 353270 TRUE FALSE 331118.5223 349836.7035 341347.4576 295735.0041 353238.5461 386155.3101 339011.8262 341711.3415 311506.823 1.062957527 1.12304668 1.095794481 0.949369267 1.133967284 1.239636764 1.088296631 1.096962622 1 18.24890424 3.971621775 24.76124389 1.089166063 1.097106905 0.000414465 0.077490434 10891.53432 9503363.615 0.021497994 0.03734321 9367.458441 -3.971621775 0.007940842 EGPVAS(ph)PPFMDLEQAVLPAVIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGPVASPPFMDLEQAVLPAVIPK 23 0 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 EGPVAS(1)PPFMDLEQAVLPAVIPK 74.274 0.062307 17503000 46960 36048 23058 33540 40855 32750 46405 60436 47662 TRUE FALSE 40754.11702 35811.19831 34208.92592 41155.76963 40042.06543 34009.91369 41904.65024 47512.23171 42027.45266 0.969702288 0.852090623 0.8139662 0.979259199 0.952759753 0.809230908 0.997078043 1.130504675 1 15.35904439 2.016967592 7.516643815 1.07166306 0.896992736 0.531633234 0.06698801 0.103458895 29.57439708 0.027681344 0.018061909 103.9842567 -2.016967592 -0.174670325 EGPYSISVLYGDEEVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EGPYSISVLYGDEEVPR 17 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;; 215.51 1.30E-14 132074000 181259 164954 108332 121041 152609 160247 156488 176117 150112 FALSE TRUE 157305.1639 163870.4063 160721.7175 148525.209 149572.3795 166411.8058 141311.8178 138455.7501 132365.9304 1.188411274 1.23801046 1.214222701 1.122080347 1.129991525 1.25721026 1.067584517 1.046007456 1 17.01417231 2.098581437 5.810813364 1.035069006 1.188449718 0.737306946 0.043656061 0.109490314 5.391162004 0.019065457 0.012693434 125.4820013 -2.098581437 0.153380712 EGQHYPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EGQHYPER 8 0 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 ;; 85.355 0.016802 1564782000 730510 616580 427912 471659 582561 638849 589086 629487 666444 FALSE TRUE 633971.2526 612529.6454 634851.6745 578756.3848 570969.1759 663425.9344 531956.5304 494876.1037 587657.7495 1.078810333 1.042323778 1.080308521 0.984852808 0.971601542 1.128932504 0.905214865 0.842116188 1 19.16461665 2.178375991 11.17746302 0.89973516 1.042672638 0.5150008 0.05958947 0.411634884 74.6989094 0.023860248 0.016090516 150.7911977 -2.178375991 0.142937479 EGQLLHVYPVLFNVGINEQQTLAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGQLLHVYPVLFNVGINEQQTLAER 25 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 163.94 1.74E-11 191430000 126240 135660 78669 72156 139240 119140 131230 144280 153830 FALSE TRUE 109557.0641 134768.8405 116713.5915 88540.12264 136469.3964 123723.3929 118503.3348 113426.8448 135644.3926 0.807678534 0.993545239 0.860438012 0.652737064 1.006082107 0.912115794 0.873632389 0.836207399 1 17.04946988 EGQPSPADEKGNDS(ph)DGEGESDDPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGQPSPADEKGNDSDGEGESDDPEK 25 1 O75351;K7EKZ3 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 1 EGQPSPADEKGNDS(1)DGEGESDDPEK;EGQPSPADEKGNDS(1)DGEGESDDPEK 225.05 4.70E-34 998390000 1634760 916210 1121380 1014050 854580 714830 1352060 1506460 1781800 TRUE FALSE 1418722.324 910191.3562 1663683.119 1244305.551 837575.53 742329.9727 1220937.429 1184315.252 1571157.634 0.902978984 0.579312563 1.058890008 0.791967352 0.533094523 0.472473262 0.777094165 0.753785124 1 20.5833965 3.465424279 24.78863756 0.702590012 0.837809575 0.110863735 0.182041284 472.6235573 1001596.181 0.053491217 0.069112817 2920.278556 -3.465424279 0.135219563 EGQPSPADEKGNDS(ph)DGEGESDDPEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGQPSPADEKGNDSDGEGESDDPEKK 26 2 O75351;K7EKZ3 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 1 EGQPSPADEKGNDS(1)DGEGESDDPEKK 176.94 1.38E-17 144960000 117840 58692 79999 62996 58282 46060 101380 112690 93505 TRUE FALSE 102267.1454 58306.44839 118686.784 77300.20463 57122.30223 47831.958 91548.1832 88592.12045 82450.94542 1.24033927 0.70716531 1.439483603 0.937529633 0.692803484 0.580126253 1.110335154 1.074482773 1 16.33124842 5.312182743 6.443964051 0.95772576 30.2845284 0.123247102 0.246489625 15055.70602 3468.933946 0.061681382 6415836.087 205202.545 -5.312182743 29.32680264 EGRGESENAGTNQET(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGRGESENAGTNQETR 16 1 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 EGRGES(0.022)ENAGT(0.022)NQET(0.956)R 103.77 0.0090027 86263000 155670 123250 63467 74960 124080 129940 127330 131740 48473 TRUE FALSE 135097.8151 122440.3626 94159.85348 91980.81369 121611.0508 134938.8759 114981.5562 103568.4262 42742.57716 3.160731618 2.864599441 2.202952179 2.151971636 2.845196964 3.157013097 2.690094136 2.423073972 1 15.38338628 4.421142697 4.640800701 2.417882668 3.101897992 0.188983162 0.571284225 0.3398139 14.86284992 0.146943496 0.441863492 26371.97751 -4.421142697 0.684015324 EGRPPEPTPAKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGRPPEPTPAKR 12 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 107.17 0.0010368 147750000 141420 125040 81983 92738 95761 84765 119160 138660 129560 FALSE TRUE 122730.9887 124218.604 121630.253 113795.5803 93855.54345 88025.9644 107603.8815 109008.6381 114243.5644 1.074292362 1.087313799 1.064657372 0.996078693 0.821538998 0.770511362 0.94188134 0.954177495 1 16.80175337 3.495141482 3.989551879 0.9014596 1.073349791 0.607734159 0.06536031 0.169274916 6.067853324 0.021314369 0.03050917 3127.097933 -3.495141482 0.171890192 EGRPSGEAFVELESEDEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 252.77 6.71E-31 301428000 801540 505148 395279 454497 517059 412713 654810 738000 524775 FALSE TRUE 695614.4582 501829.6495 586437.2465 557697.4904 506770.5375 428590.3362 591306.627 580184.4431 462736.6973 1.503261924 1.084482066 1.267323836 1.205215609 1.095159603 0.926207795 1.277846841 1.253811177 1 18.81983199 4.745438702 24.73746274 1.152354556 1.503262112 0.484094219 0.117514161 667.5941945 2400972.791 0.029241489 0.279467165 55646.60873 -4.745438702 0.350907557 EGS(ph)GGPQESSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGSGGPQESSR 11 0 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 EGS(0.927)GGPQES(0.072)SR;EGS(0.95)GGPQES(0.05)SR 100.69 0.0040278 144394000 187706 170188 135779 143303 162106 198322 194600 213658 208098 TRUE FALSE 162900.1765 169070.0238 201442.1786 175842.1364 158880.4078 205951.5757 175727.722 167968.8994 183496.8915 0.88775442 0.921378136 1.097796136 0.958284007 0.865847952 1.122370924 0.957660484 0.915377356 1 17.4853961 4.462002728 24.9191968 0.981420731 0.896160249 0.173508585 0.076481436 349.5015693 576068.28 0.018862549 0.049946556 28973.61785 -4.462002728 -0.085260482 EGS(ph)PANWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EGSPANWK 8 0 O96019-2;O96019 O96019-2 ACTL6A Actin-like protein 6A 1 EGS(1)PANWK;EGS(1)PANWK;EGS(1)PANWK;EGS(1)PANWK 149.33 0.00053173 1763670000 5898900 4585640 3717280 3969500 5101740 3800620 5259340 6288480 6215780 TRUE FALSE 5119345.419 4555516.629 5514969.042 4870835.645 5000225.355 3946832.311 4749290.016 4943737.489 5480957.569 0.93402391 0.83115342 1.006205389 0.888683334 0.91229047 0.720099045 0.86650735 0.901984266 1 22.38599654 5.095417998 18.22834399 0.889057228 3.401649356 0.026811856 0.08106735 16457926.97 10544782.86 0.0197556 1698855273 124571.3005 -5.095417998 2.512592128 EGS(ph)PAPLEPEPGAAQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EGSPAPLEPEPGAAQPK 17 0 Q01167;Q01167-2 Q01167 FOXK2 Forkhead box protein K2 1 EGS(1)PAPLEPEPGAAQPK;EGS(1)PAPLEPEPGAAQPK;EGS(1)PAPLEPEPGAAQPK;EGS(1)PAPLEPEPGAAQPK 239.7 2.85E-20 1269930000 1759010 1145920 1277790 1234010 1450010 1063150 1636350 1797680 2094990 TRUE FALSE 1526552.372 1138392.376 1895733.518 1514210.831 1421157.638 1104050.068 1477657.029 1413260.122 1847322.669 0.826359356 0.616239055 1.026205952 0.819678585 0.769306663 0.597648742 0.799891136 0.765031548 1 20.81700445 1.236824103 24.91762318 1.00000029 0.776173305 0.260063702 0.117903674 62.12001398 891091.7783 0.175885496 0.028171069 17.25139039 -1.236824103 -0.223826985 EGS(ph)PIPHDPEFGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EGSPIPHDPEFGSK 14 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 EGS(0.997)PIPHDPEFGS(0.003)K;EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK 186.68 1.29E-07 5793090000 23143820 15657910 14642920 14952740 19164380 14809400 21729940 24506890 23950560 TRUE FALSE 20085305.55 15555052.16 21724285.09 18347988.16 18783046.33 15379127.2 19622573.76 19266282.29 21119152.08 0.951046968 0.736537722 1.028653281 0.868784319 0.889384491 0.728207607 0.929136439 0.9122659 1 24.33204858 1.35168194 1.758684088 1.023491408 0.870637607 0.160851297 0.090131734 1.316407994 4.769526667 0.322258751 0.024082829 22.47408091 -1.35168194 -0.152853801 EGSALSHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGSALSHVR 9 0 K7ELG9;Q3MHD2;Q3MHD2-2 K7ELG9 LSM12 Protein LSM12 homolog 0 140.45 0.00010908 138310000 197030 231130 108650 161900 230090 238530 198950 221960 258880 FALSE TRUE 170991.9863 229611.6918 161193.5034 198661.8695 225511.6592 247706.4034 179655.8596 174495.5813 228275.5013 0.749059734 1.005853412 0.706135799 0.870272405 0.987892515 1.085120401 0.787013318 0.764407833 1 17.80041651 3.479541734 24.99993225 0.904914868 0.830450703 0.120039342 0.12242381 289.6727756 2991899.166 0.036999422 0.048614902 3016.766759 -3.479541734 -0.074464165 EGSGGGGGMDDIFSHIFGGGLFGFMGNQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGSGGGGGMDDIFSHIFGGGLFGFMGNQSR 30 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 124.79 1.13E-05 93005000 16753 16061 8911.2 11755 19340 19445 16773 18003 19475 FALSE TRUE 14539.0486 15955.49423 13220.68613 14424.15241 18955.17184 20193.06173 15146.35704 14153.19855 17172.68769 0.846637921 0.929120387 0.769867034 0.839947286 1.103797622 1.17588243 0.882002708 0.8241691 1 14.06782823 3.298450898 24.99899641 0.975843976 0.846835533 0.322125338 0.106209949 118.7512174 49567.05772 0.035117359 0.045336299 1988.158012 -3.298450898 -0.129008443 EGSGIGAIDSNLDWSHNFTNMLGYTDHQFTELTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGSGIGAIDSNLDWSHNFTNMLGYTDHQFTELTR 34 0 O75390;B4DJV2;A0A0C4DGI3 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ; 347.66 4.25E-132 617510000 208568 185557 140810 204132 238540 240870 162807 227860 248570 FALSE TRUE 181005.2104 184338.0638 208906.187 250483.2906 233793.5207 250136.4248 147018.0022 179133.9122 219184.3378 0.825812703 0.841018413 0.953107275 1.142797397 1.066652495 1.141214866 0.670750491 0.817275149 1 17.74178519 2.239431389 24.99999993 0.820220022 0.996153852 0.258217394 0.132129554 32.40207445 930318.4065 0.055076598 0.040139756 173.552706 -2.239431389 0.17593383 EGSGSSGTGEQKEDQKEEKQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGSGSSGTGEQKEDQKEEKQ 20 3 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 136.14 7.23E-06 142180000 420680 288300 315640 386400 278190 184020 441870 585640 116520 FALSE TRUE 365086.0721 286406.1383 468284.5598 474138.0258 272654.5633 191099.3685 399017.5154 460405.4435 102745.1383 3.553317247 2.787539566 4.557729614 4.614700349 2.653697953 1.859935872 3.883565898 4.481043589 1 16.6487106 3.22047911 24.99951278 3.026131188 3.848938129 0.181444883 1.093344925 573.2498955 792573.8143 0.350841025 0.398596405 1661.418759 -3.22047911 0.822806941 EGSLS(ph)PASVGSDTLSDLGISSLQDGLALHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EGSLSPASVGSDTLSDLGISSLQDGLALHIR 31 0 Q13085;Q13085-4;A0A0C4DGT1;A0A087WYK6 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 1 EGS(0.026)LS(0.971)PAS(0.003)VGSDTLSDLGISSLQDGLALHIR;EGS(0.034)LS(0.965)PASVGSDTLSDLGISSLQDGLALHIR;EGS(0.038)LS(0.962)PASVGSDTLSDLGISSLQDGLALHIR;EGS(0.026)LS(0.974)PASVGSDTLSDLGISSLQDGLALHIR 195.67 9.17E-26 946987000 119779 81868 63503.8 73522.3 82257 101367 102762 100779 99315 TRUE FALSE 103949.9017 81330.20372 94214.45009 90216.66193 80620.24663 105266.6541 92796.15706 79228.19511 87574.09384 1.186993746 0.92870163 1.075825578 1.030175226 0.9205947 1.202029612 1.059630228 0.904699 1 16.41821653 1.75226076 24.99983064 0.950115521 1.052660789 0.178118721 0.093574461 6.82710009 12480.61009 0.04721881 0.022675398 56.52762775 -1.75226076 0.102545268 EGSQGELT(ph)PANSQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGSQGELTPANSQSR 15 0 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;J3QQX0 Q13098-7 GPS1 COP9 signalosome complex subunit 1 1 EGSQGELT(1)PANSQSR 161.86 1.62E-08 0 174520 180590 100420 121260 160560 164000 163980 167660 170510 TRUE FALSE 151456.7398 179403.6924 148983.4479 148793.9363 157365.1701 170309.1861 148077.2448 131807.2137 150352.502 1.007344326 1.193220531 0.990894371 0.989633922 1.046641512 1.132732637 0.984867181 0.876654608 1 17.19798935 2.010371881 12.59788018 0.929880144 1.059155731 0.354455558 0.069498708 0.549106396 661.9168106 0.028164444 0.018732294 102.4169601 -2.010371881 0.129275587 EGSRPMMGDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGSRPMMGDHR 11 1 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 72.29 0.028058 54514000 40683 40248 22597 30942 38945 43022 37575 47523 34461 FALSE TRUE 35306.63847 39983.60824 33524.98478 37967.85402 38170.07069 44677.08418 33930.98228 37360.57627 30387.05984 1.161897158 1.315810363 1.103265171 1.249474422 1.256129119 1.470266765 1.11662604 1.229489673 1 14.89116947 0.623832346 1.442201024 0.139834928 1.247205012 0.33292158 0.105268327 7.184209717 3.565733515 18.11661698 0.029226099 4.205642437 -0.623832346 1.107370084 EGSS(ph)PEGSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGSSPEGSTR 10 0 Q9Y2I9;F8VZ81;Q9Y2I9-2 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 EGS(0.325)S(0.675)PEGSTR;EGS(0.014)S(0.986)PEGSTR 111.5 0.0018311 65174000 292300 279140 196390 251660 201525 239430 277090 315870 404230 TRUE FALSE 253671.8144 277306.311 291364.8609 308803.2494 197515.0468 248641.027 250217.8544 248323.6586 356442.3899 0.711676898 0.777983536 0.817424833 0.866348274 0.554128949 0.697563012 0.701986805 0.696672634 1 18.44330939 1.2346004 24.99845838 1.000000394 0.727587259 0.511894184 0.083478997 103.5423194 653506.6486 0.156658169 0.021171084 17.16328443 -1.2346004 -0.272413135 EGSS(ph)PEGSTRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGSSPEGSTRR 11 1 Q9Y2I9;F8VZ81;Q9Y2I9-2 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 EGS(0.236)S(0.764)PEGSTRR 64.224 0.035256 0 308360 278700 132050 171150 191000 273980 293020 339880 54495 TRUE FALSE 267609.4447 276869.2013 195909.8217 210012.2234 187199.4737 284520.1879 264602.9655 267199.3069 48052.66318 5.569086644 5.761786819 4.07698156 4.370459605 3.895714853 5.921007683 5.506520305 5.560551471 1 15.55232877 4.25071194 24.92415499 4.547930277 5.665437433 0.124702596 1.378996761 519.9682392 1066510.502 0.339519804 0.883741069 17811.96939 -4.25071194 1.117507156 EGSVIDHIHLISVGDMIEAINGQSLLGCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGSVIDHIHLISVGDMIEAINGQSLLGCR 29 0 O14908;O14908-2;K7ESN1;K7EIT0 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 ; 181.37 6.01E-18 713380000 633750 563500 347490 560710 686460 642690 776880 854670 705280 FALSE TRUE 549998.3318 559798.3314 515537.3263 688027.7754 672800.789 667414.7002 701538.2972 671905.4715 621902.6019 0.884380175 0.900138269 0.828967952 1.106327218 1.081842699 1.073182036 1.128051716 1.080403056 1 19.24632913 3.735144667 24.99034023 1.08156376 0.874059741 0.87435502 0.03699634 91.22591421 667389.4351 0.009948525 0.015464331 5434.313222 -3.735144667 -0.207504019 EGTETFADHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EGTETFADHR 10 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;; 180.36 2.01E-06 2320095000 2165000 2185290 1382811 1766549 2049502 2155910 2110890 2320350 2306700 FALSE TRUE 1878889.765 2170934.686 2051543.025 2167670.95 2008720.92 2238849.253 1906176.213 1824161.209 2034004.554 0.923739212 1.067320465 1.008622631 1.065715879 0.987569529 1.100710049 0.937154349 0.896832412 1 20.95589148 2.141537906 10.93697215 0.933952079 1.026795012 0.322119815 0.054623457 0.367396706 38.69887529 0.020573671 0.013868982 138.5281091 -2.141537906 0.092842933 EGTGQQERES(ph)PRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGTGQQERESPRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR 48 2 Q6PKG0;A0A0B4J210 Q6PKG0 LARP1 La-related protein 1 1 EGT(0.16)GQQERES(0.84)PRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR 108.02 4.91E-08 246510000 81553 59396 79111 90629 52101 60672 82541 80683 88205 TRUE FALSE 70775.56442 59005.82377 117369.3442 111207.6996 51064.29203 63006.0911 74536.18652 63429.56833 77777.50538 0.909974729 0.758648963 1.509039711 1.429818288 0.656543197 0.810081151 0.958325754 0.815525877 1 16.24706534 3.228188406 24.99982367 0.850390651 1.149295301 0.293944942 0.233913232 292.2354158 704364.6739 0.074966029 0.085918484 1691.174438 -3.228188406 0.29890465 EGTGTEMPMIGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGTGTEMPMIGDR 13 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 202.68 2.14E-07 216540000 166620 161410 134580 155390 151010 149520 160390 167820 208710 FALSE TRUE 144600.7448 160349.6871 199663.3381 190673.6745 148005.1964 155272.1312 144835.4025 131932.999 184036.5416 0.785717573 0.871292656 1.084911379 1.036064212 0.804216354 0.843702722 0.786992633 0.716884798 1 17.48963272 3.215769264 24.69384846 0.813589606 0.949297255 0.207937448 0.107788608 281.7288802 305244.9513 0.033860721 0.038421569 1643.498317 -3.215769264 0.135707649 EGTINVHDVETQFNQYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EGTINVHDVETQFNQYK 17 0 P15941-2;A0A087WWM1;A0A087X2A4;A0A0C4DGW3;P15941-7;P15941-11;P15941-4;P15941-3;P15941;P15941-8;A0A087WVJ0;A0A0A0MSH4;A0A0A0MRB3;B1AVQ7;A0A087X0L2;P15941-15;P15941-17;P15941-6;P15941-13 P15941-2 MUC1 Mucin-1;Mucin-1 subunit alpha;Mucin-1 subunit beta 0 ;;;; 302.62 1.68E-46 5129880000 5184280 4584370 3266130 4228960 4049290 4653920 3525190 5223260 5721340 FALSE TRUE 4499164.263 4554254.972 4845641.393 5189210.004 3968717.051 4832959.314 3183317.616 4106306.496 5044969.703 0.891811949 0.902731877 0.960489691 1.028590915 0.786668164 0.957975885 0.630988451 0.813940764 1 22.26641417 3.224324179 24.99882011 0.825401505 0.943863933 0.201799982 0.105063484 351.4684672 617168.228 0.031806362 0.036232745 1676.193603 -3.224324179 0.118462428 EGTPGS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EGTPGSPGR 9 0 Q99856 Q99856 ARID3A AT-rich interactive domain-containing protein 3A 1 EGT(0.007)PGS(0.993)PGR;EGT(0.009)PGS(0.991)PGR;EGT(0.4)PGS(0.6)PGR;EGT(0.023)PGS(0.977)PGR;EGT(0.012)PGS(0.988)PGR 104.94 0.0033337 1814400000 2329140 2354680 1476380 1756020 1957020 2244300 2361300 2687160 2402370 TRUE FALSE 2021338.248 2339211.952 2190362.306 2154751.18 1918079.131 2330639.673 2132301.489 2112531.746 2118364.555 0.95419754 1.104253725 1.033987422 1.017176753 0.905452806 1.100207076 1.006579101 0.99724655 1 21.01451946 3.65327592 4.798330008 1.003174596 1.038072021 0.04160456 0.058258274 0.630789215 25.22235826 0.015504529 0.023551441 4500.657042 -3.65327592 0.034897425 EGTTPKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGTTPKPK 8 1 P61927 P61927 RPL37 60S ribosomal protein L37 0 67.993 0.052586 840050000 1457100 1250600 878460 1073500 729070 906250 1549500 1941500 1690800 FALSE TRUE 1264540.543 1242384.726 1303286.194 1317254.582 714562.9334 941114.0239 1399229.728 1526325.334 1490915.55 0.848163763 0.833303218 0.874151587 0.883520587 0.47927794 0.631232281 0.938503679 1.023750362 1 20.50776711 2.066917738 6.442875522 1.004351395 0.760488703 0.440864301 0.123545772 0.200835132 14.97940549 0.056419604 0.037607908 116.6588627 -2.066917738 -0.243862692 EGVFVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EGVFVNR 7 0 P49902-2 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;;; 114.72 0.01359 963080000 817380 906910 520943 635820 876840 833100 830150 957470 866570 FALSE TRUE 709361.162 900952.4485 772872.7772 780192.6489 859392.5995 865149.8961 749642.1808 752722.4915 764125.0818 0.92833121 1.179064096 1.011447989 1.021027404 1.124675292 1.132209787 0.981046426 0.985077587 1 19.54344929 2.209189613 24.9579381 0.987632368 1.069385564 0.210050528 0.070575169 291.166378 247415.8218 0.027285049 0.018398968 161.8786646 -2.209189613 0.081753196 EGVHGGLINK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EGVHGGLINK 10 0 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 ;;;;; 153.24 1.66E-05 11554600000 13357480 10955330 8588410 11202820 10284710 9036060 11587610 13750510 26791400 FALSE TRUE 11592255.17 10883363.72 12741793.8 13746591.51 10080064.39 9383683.075 10463845.37 10810070.44 23624151.21 0.490695097 0.460688031 0.539354565 0.581887213 0.426684722 0.397207205 0.442930003 0.457585559 1 24.49375916 1.23751923 24.99999295 1.000000623 0.473365353 0.905020587 0.053486321 8.018313739 192396.1852 0.084591921 0.014236647 17.27902488 -1.23751923 -0.52663527 EGVHGGLINKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EGVHGGLINKK 11 1 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 ;;; 178.46 4.89E-06 18850100000 49140830 37790400 24829730 31493480 33885300 25666040 46892490 54004440 29627140 FALSE TRUE 42646744.81 37542152.37 36837470.48 38644555.98 33211048.83 26653429.17 42344863.54 42456010.77 26124653.26 1.632432951 1.437039259 1.410065432 1.479237087 1.271253191 1.020240495 1.620877533 1.625132029 1 24.63890855 5.617363531 0.99045706 1.369893948 2.703920539 0.150043567 0.2130983 22.34606888 4.837949715 0.070105346 48.0223768 414346.3629 -5.617363531 1.334026591 EGVIEAGAFQGSPAPPLPSVMS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGVIEAGAFQGSPAPPLPSVMSPSR 25 0 P53367 P53367 ARFIP1 Arfaptin-1 1 EGVIEAGAFQGSPAPPLPSVMS(0.779)PS(0.221)R 121.82 0.00011513 74190000 18813 20005 11381 13459 18437 23846 18923 23242 20324 TRUE FALSE 16326.81438 19873.58584 16884.88967 16515.07166 18070.13977 24763.37105 17087.85037 18271.87917 17921.31987 0.911027452 1.10893539 0.942167753 0.921532107 1.00830407 1.381782772 0.953492851 1.01956102 1 14.12938927 2.985652514 24.93182944 1.07965213 0.976995437 0.162010302 0.126140824 1401.913776 2436130.192 0.040424365 0.04198227 967.5034316 -2.985652514 -0.102656693 EGVKFDESEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGVKFDESEK 10 1 P14625 P14625 HSP90B1 Endoplasmin 0 ; 142.08 3.32E-05 1586840000 4735600 3586100 3278500 3556900 3653000 3572000 5661600 5750400 2094440 FALSE TRUE 4109778.462 3562542.673 4863993.566 4364548.509 3580312.447 3709417.151 5112538.903 4520721.71 1846837.689 2.225305713 1.928996085 2.633687624 2.363255057 1.938617816 2.008523636 2.768266499 2.447817551 1 20.81662565 3.280157959 24.96235527 2.138506113 2.286886894 0.040444209 0.483425261 818.7587246 491327.9205 0.142070714 0.183410291 1906.153886 -3.280157959 0.14838078 EGVMYVGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGVMYVGAK 9 0 O76070;F8W754 O76070 SNCG Gamma-synuclein 0 103.83 0.0078128 79811000 136830 166890 103830 118700 130390 141450 145930 154340 171850 FALSE TRUE 118747.5688 165793.6886 154042.5353 145652.6492 127795.4941 146891.673 131777.7311 121335.5921 151534.0888 0.783636011 1.094101597 1.016553678 0.96118735 0.843344855 0.969363885 0.869624334 0.80071483 1 17.20928285 3.37043597 6.340871013 0.886525138 0.97939355 0.097461535 0.095541153 0.367818896 19.38274131 0.026742654 0.034608916 2346.583268 -3.37043597 0.092868411 EGVVGAVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EGVVGAVEK 9 0 O76070;F8W754 O76070 SNCG Gamma-synuclein 0 ;;;; 135.79 0.00049067 1056621000 2161770 2192150 1431530 1736440 2070220 1846630 2414780 2708890 2497070 FALSE TRUE 1876086.617 2177749.622 2123822.696 2130725.242 2029026.672 1917671.051 2180595.007 2129614.954 2201869.229 0.852042706 0.989045849 0.964554419 0.967689277 0.921501897 0.870928675 0.990338108 0.967185029 1 21.07029736 EGVVGPELHHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGVVGPELHHK 11 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 58.676 0.06061 52052000 111200 94965 62216 79118 95526 96739 106170 105280 115680 FALSE TRUE 96504.63826 94341.16866 92303.8657 97082.95114 93625.21949 100460.6119 95873.64974 82766.69129 102004.4422 0.946082702 0.924873139 0.904900451 0.951752189 0.917854335 0.984865068 0.939896809 0.811402813 1 16.63827246 EGYAWAEDKEHCEEYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGYAWAEDKEHCEEYGR 17 1 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ; 237.59 1.92E-20 1750520000 1583190 1334660 933840 1036380 1266710 1058200 1360420 1657660 1520500 FALSE TRUE 1373967.43 1325892.531 1385448.148 1271705.919 1241504.949 1098909.639 1228486.678 1303182.309 1340748.222 1.024776619 0.98891985 1.033339537 0.948504647 0.925979187 0.819624163 0.916269481 0.971981381 1 20.35460691 3.593874074 4.133102276 0.92694976 1.012653629 0.423317965 0.047390063 0.256980198 7.407546489 0.014711739 0.0222503 3925.311024 -3.593874074 0.085703868 EGYGGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EGYGGFR 7 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 109.63 0.037671 0 647110 547320 717890 467580 461910 462760 504190 500090 495320 FALSE TRUE 561592.7739 543724.6189 1065064.005 573751.1855 452718.8947 480562.6766 455293.7314 393149.6452 436763.8339 1.285804204 1.244893869 2.438535251 1.313641701 1.036530179 1.100280379 1.042425439 0.900142399 1 18.73649387 3.48205281 14.92415125 1.02281856 1.658727916 0.450775296 0.323277173 1.048750901 3168.580241 0.091999366 0.124168753 3034.260125 -3.48205281 0.635909356 EGYGLSWNPNLSGHLLSASDDHTICLWDISAVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EGYGLSWNPNLSGHLLSASDDHTICLWDISAVPK 34 0 Q09028-3;Q09028;Q09028-2;Q09028-4 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 153.99 4.17E-11 165930000 131960 113170 34867 89848 121470 93851 133790 150450 128250 FALSE TRUE 114521.1517 112426.5788 51728.79782 110249.3616 119052.9847 97461.5087 120815.0664 118277.4383 113088.4311 1.012669028 0.99414748 0.457419007 0.974895138 1.052742385 0.86181679 1.068323835 1.04588451 1 16.78709182 3.50383365 24.89373117 1.008770699 0.818264025 0.222094297 0.158978447 1012.73542 943782.7293 0.043429594 0.064182243 3190.315616 -3.50383365 -0.190506674 EHAALEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHAALEPR 8 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ; 87.308 0.015416 719820000 415310 491060 381280 529770 528380 668680 505450 617720 545830 FALSE TRUE 360425.7312 487834.1945 565668.2833 650062.3755 517866.2718 694404.5523 456431.5368 485625.3851 481302.5992 0.748854737 1.013570663 1.175286159 1.350631342 1.075968159 1.442760861 0.948325518 1.008981431 1 18.87658469 4.652195067 2.753288015 1.135514846 0.712321196 0.393610221 0.154997372 0.400437269 4.584078894 0.04114324 0.346847237 44894.69928 -4.652195067 -0.42319365 EHALLAYTLGVK ddPTM_MDA-MB-175_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 ;; 186.46 1.17E-05 23181580000 22166970 19446130 11670070 15258750 17378860 15957510 21411370 23200410 17616100 FALSE TRUE 19237548.75 19318387.09 17313754.89 18723482.4 17033054.69 16571405.74 19334898.63 18239182.87 15533544.73 1.23845195 1.243656064 1.114604245 1.205358 1.096533662 1.066814177 1.244719024 1.174180343 1 23.88888375 4.246002339 24.58507968 1.138495127 1.241054078 0.302234282 0.06967523 182.2532162 602088.2915 0.01739132 0.044054039 17619.85537 -4.246002339 0.102558951 EHALTSGTIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EHALTSGTIK 10 0 E5RHG8;Q15369-2;Q15369;R4GMY8 E5RHG8 TCEB1 Transcription elongation factor B polypeptide 1 0 ;; 137.98 7.69E-05 690220000 1537290 1531980 960940 1218360 1461720 1366660 1538020 1764420 1756650 FALSE TRUE 1334133.232 1521916.323 1425653.798 1495007.259 1432634.632 1419236.295 1388863.057 1387112.514 1548980.838 0.861297441 0.982527534 0.920381817 0.965155425 0.924888544 0.916238768 0.896630238 0.895500112 1 20.56288787 3.013150847 24.45779134 0.919440565 0.936314995 0 0.04274264 745.8155071 1387047.255 0.012307838 0.013946719 1030.744075 -3.013150847 0.01687443 EHAMLAK ddPTM_MDA-MB-175_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 ;;; 92.925 0.011615 1658100000 2967000 2644180 1786490 2270380 2341570 2373200 2903740 3155990 3169390 FALSE TRUE 2574903.433 2626810.207 2650442.539 2785904.48 2294977.338 2464498.54 2622135.742 2481106.098 2794708.325 0.921349613 0.939922848 0.948378947 0.996849816 0.821186711 0.881844634 0.938250235 0.887787136 1 21.41426629 5.150665283 12.93573614 0.922912691 0.78280149 0 0.05359398 6186360.449 3141563.22 0.012971158 25379493.38 141470.3028 -5.150665283 -0.140111202 EHAPSIIFMDEIDSIGSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EHAPSIIFMDEIDSIGSSR 19 0 P62195-2;P62195;J3QSA9;J3QQM1 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ;;; 336.88 1.67E-75 1588390000 612630 549158 306824 414760 496372 544524 517542 578465 587889 FALSE TRUE 531669.3933 545550.5449 455205.1127 508937.5972 486495.1683 565472.1906 467350.8565 454764.7614 518389.4321 1.025617731 1.05239519 0.878114183 0.981766922 0.938474317 1.090825074 0.90154395 0.877264723 1 18.98367678 4.264400072 24.9988983 0.948589684 1.039006559 0.238750158 0.063859964 320.8624697 310419.1017 0.016239155 0.042933528 18382.30941 -4.264400072 0.090416875 EHASGSGAQSEAAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EHASGSGAQSEAAGR 15 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;; 258.96 7.67E-25 1035870000 483829.4 730751 187207.6 360635.6 895415 890206 592123.1 746250 846635 FALSE TRUE 419890.1189 725950.6486 277741.8215 442523.425 877597.9933 924452.8009 534699.0929 586670.2448 746546.7748 0.562443149 0.972411473 0.372035391 0.592760481 1.175543212 1.238305264 0.716229861 0.785845261 1 19.50987313 3.261580962 24.99971056 0.951251732 0.631671173 0.407239448 0.212785434 284.4056176 308857.7152 0.065090587 0.083976309 1826.337186 -3.261580962 -0.319580559 EHCPAGQPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EHCPAGQPVK 10 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 102.52 0.0029357 48428000 106310 93666 67798 80434 86179 86865 99796 115950 116480 FALSE TRUE 92260.86414 93050.70188 100585.3396 98697.76906 84464.20651 90206.75276 90117.79928 91154.99482 102709.8671 0.898266805 0.905956794 0.979315254 0.96093756 0.822357276 0.878267642 0.877401576 0.887499881 1 16.64821526 4.672060829 5.96152521 0.90977957 0.898373922 0.003235841 0.053522791 2.111649573 139.7052719 0.013509438 0.057518656 46995.99289 -4.672060829 -0.011405648 EHDPVGQMVNNPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHDPVGQMVNNPK 13 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ; 174.9 1.92E-05 363220000 1075840 756910 502820 630360 714610 618960 876040 1005650 882960 FALSE TRUE 933665.0182 751937.8084 745985.4338 773492.8724 700390.6591 642771.7917 791081.7756 790599.5735 778577.4747 1.199193463 0.965784181 0.958138988 0.993469369 0.899577347 0.825572037 1.016060445 1.015441108 1 19.57048108 4.738587792 6.472304736 0.960988053 1.204035713 0.625088021 0.058397094 0.088207544 22.23761106 0.015580928 0.094194933 54775.68181 -4.738587792 0.243047659 EHDQLIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EHDQLIEK 8 0 O14980 O14980 XPO1 Exportin-1 0 ;;; 136.21 0.00080079 1360660000 5037990 4058020 2900280 3493570 3824030 3212990 4845520 5325910 5256850 FALSE TRUE 4372206.857 4031362.599 4302865.109 4286838.464 3747939.285 3336595.804 4375602.216 4187005.593 4635391.182 0.943222845 0.869691994 0.928263644 0.924806191 0.808548651 0.719808895 0.943955331 0.903269094 1 22.14425966 1.263376962 1.668639107 1.039199666 0.87160424 0.238919752 0.069181323 1.523936068 4.08716605 0.414735376 0.020509386 18.33905539 -1.263376962 -0.167595426 EHDYRDEHFDFIQSHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EHDYRDEHFDFIQSHIR 17 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 ;;;;; 218.83 1.52E-15 5103320000 1359443 1378752 822039 967816 1415115 1428453 1283156 1473321 705802 FALSE TRUE 1179789.163 1369694.887 1219579.81 1187573.415 1386956.98 1483406.511 1158715.729 1158262.77 622362.8916 1.895661163 2.200797807 1.959595963 1.90816874 2.228534186 2.383507325 1.861800799 1.861072993 1 19.24739652 1.01872318 1.624553439 4.49E-17 2.081629939 0.79918296 0.16663216 0.829411321 1.250971199 3.289989032 0.047059215 10.44054526 -1.01872318 2.081629939 EHDYRDEHLDFIQSHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EHDYRDEHLDFIQSHLR 17 1 O43237;O43237-2;B4E2E0 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 ;;; 194.37 2.62E-11 4342990000 1330940 1148380 798940 815520 1310690 1208300 1102570 1326090 814730 FALSE TRUE 1155052.907 1140836.216 1185310.056 1000696.28 1284609.833 1254784.083 995642.9311 1042515.973 718413.5475 1.607782747 1.58799374 1.649899366 1.392925125 1.788120279 1.746604149 1.385891085 1.451136294 1 19.45445503 0.797771825 1.113532679 7.77E-16 1.614237687 0.702574273 0.123453078 2.285067631 1.165572145 5.544667373 0.038646579 6.277284691 -0.797771825 1.614237687 EHEEAVSVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHEEAVSVDR 10 0 B4DUC8;Q13126-4;Q13126;Q13126-3;Q13126-2 B4DUC8 MTAP S-methyl-5-thioadenosine phosphorylase 0 ; 157.78 8.57E-06 840730000 1170870 1124220 852970 1049580 901190 1162670 1160280 1414490 1550620 FALSE TRUE 1016136.563 1116834.925 1265469.145 1287903.181 883258.0821 1207398.667 1047756.224 1112012.321 1367307.47 0.743166102 0.816813299 0.925519075 0.94192653 0.645983512 0.883048395 0.766291597 0.813286218 1 20.38290627 1.237561318 24.77781936 1.000000234 0.818461292 0.301123803 0.087588466 29.11010528 721374.3027 0.123656015 0.020844828 17.2806995 -1.237561318 -0.181538942 EHEVFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EHEVFQR 7 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ;;; 187.63 0.00058141 1860360000 2130580 1707110 1145310 1357450 1549200 1630060 1580980 1921480 2010410 FALSE TRUE 1849018.455 1695895.882 1699185.747 1665679.77 1518373.951 1692769.463 1427656.803 1510586.455 1772741.62 1.04302761 0.956651473 0.958507279 0.939606625 0.856511707 0.954887866 0.805338345 0.852118796 1 20.75755085 4.852081848 0.621227174 0.881839429 1.152548753 0.384651492 0.056636456 3.98669902 1.087696713 0.029127742 0.797941837 71134.75625 -4.852081848 0.270709324 EHEVTIFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EHEVTIFVR 9 0 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 ;;;; 185.81 4.24E-05 4721890000 2089970 1809180 1326108 1857040 1877190 1872460 1812110 2110400 2819770 FALSE TRUE 1813775.169 1797295.377 1967418.264 2278709.315 1839837.592 1944494.748 1636371.851 1659107.383 2486420.003 0.729472562 0.722844642 0.791265459 0.916461946 0.739954468 0.782045972 0.658123667 0.66726755 1 21.24563858 5.041966078 0.002839262 1.524398599 1.86E-06 0.000379483 0.106501181 3934899.771 2710.634027 718067.3792 737373.9304 110145.3274 -5.041966078 -1.524396736 EHEWFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHEWFK 6 0 Q13131-2;Q13131;A0A087WXX9;P54646 Q13131-2;A0A087WXX9 PRKAA1;PRKAA2 5-AMP-activated protein kinase catalytic subunit alpha-1;5-AMP-activated protein kinase catalytic subunit alpha-2 0 ; 110.54 0.02862 532590000 1335830 1195470 827270 1014910 1067220 987570 1250190 1430260 1299050 FALSE TRUE 1159296.681 1187616.879 1227340.539 1245360.827 1045984.41 1025562.457 1128946.766 1124410.029 1145477.789 1.012063867 1.036787348 1.07146603 1.087197709 0.913142463 0.895314136 0.985568448 0.981607885 1 20.12751805 3.242099354 24.99988982 0.957729264 1.052199878 0.62501085 0.037208346 67.8751967 479510.1157 0.012011324 0.014894015 1746.22159 -3.242099354 0.094470614 EHFAQFGHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHFAQFGHVR 10 0 Q9GZT3-2;Q9GZT3;H0YJW7;A0A087WUN7;H0YJ40;G3V4X6;G3V2S9;H0YJ07;H0YJU7 Q9GZT3-2 SLIRP "SRA stem-loop-interacting RNA-binding protein, mitochondrial" 0 ; 129.89 0.00016837 355770000 207144 251094 156826 261589 302327 305662 207732 255529 229481 FALSE TRUE 179769.3956 249444.547 232667.5782 320986.7806 296311.2842 317421.0149 187586.1826 200886.1119 202352.0176 0.888399324 1.232725771 1.149815954 1.586279121 1.464335704 1.568657524 0.927028971 0.992755665 1 17.62650771 2.216164839 24.99968434 0.975396304 1.322899887 0.380398985 0.205452335 256.8974329 286764.1902 0.088369372 0.059628408 164.4995972 -2.216164839 0.347503583 EHFGTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EHFGTVK 7 0 E9PGT1;Q15631;H7C1D4;Q15631-2 E9PGT1 TSN Translin 0 ;;; 140.98 0.0025874 1678030000 2619420 2301560 1467720 1895160 2039420 1896060 2502990 2760090 3015310 FALSE TRUE 2273257.01 2286440.901 2177514.301 2325485.044 1998839.532 1969002.655 2260250.415 2169866.233 2658843.487 0.854979626 0.859938132 0.81897047 0.874622766 0.751770287 0.740548537 0.850087802 0.816094006 1 21.34236742 1.237767883 24.97957363 1.000000211 0.82019242 0.617162613 0.044333704 13.79069816 434271.4371 0.065811288 0.011231582 17.28892074 -1.237767883 -0.179807791 EHFPEILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EHFPEILK 8 0 O15479 O15479 MAGEB2 Melanoma-associated antigen B2 0 98.299 0.0076207 5346200000 2420700 2425300 1880900 1850300 1999700 1852100 3678200 3025900 2373500 FALSE TRUE 2100798.362 2409368.045 2790509.531 2270438.895 1959909.882 1923351.485 3321488.73 2378834.833 2092907.534 1.003770271 1.15120616 1.333317161 1.084825229 0.936453164 0.918985409 1.58702125 1.136617263 1 20.99707714 EHFQDDVFNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHFQDDVFNEK 11 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ; 144.28 3.68E-05 1107920000 1785850 1641300 1081710 1363220 1605250 1590580 1590650 1756230 2176290 FALSE TRUE 1549845.398 1630518.192 1604828.574 1672759.937 1573308.666 1651770.642 1436389.008 1380673.881 1919011.475 0.807626957 0.849665681 0.836278779 0.871677923 0.819853704 0.860740367 0.748504647 0.719471405 1 20.87193191 2.268619669 24.99940892 0.798071482 0.841591197 0 0.076304499 590.2848517 490924.1612 0.027978553 0.021668999 185.6178205 -2.268619669 0.043519715 EHFQSYDLDHMEK ddPTM_MDA-MB-175_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 ;; 189.86 2.84E-06 950340000 899810 810420 491705 637900 803180 668960 868640 1034190 939270 FALSE TRUE 780897.8287 805096.2977 729495.1827 782744.9447 787198.2894 694695.3241 784399.4265 813036.5166 828230.5706 0.942850767 0.972067835 0.880787559 0.945080962 0.950457901 0.838770445 0.947078572 0.981654802 1 19.65967293 1.767554438 3.35613258 0.993291003 0.922753475 0.348091295 0.038355685 0.240802399 5.391387887 0.026072893 0.010323142 58.55371274 -1.767554438 -0.070537528 EHGAFDAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHGAFDAVK 9 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ; 102.07 0.0036447 1639710000 4580800 4270700 2555000 3612000 4183500 3621600 4744700 5477000 4950900 FALSE TRUE 3975435.674 4242645.49 3790606.546 4432159.806 4100256.535 3760925.295 4284559.724 4305786.172 4365610.242 0.910625423 0.971833319 0.868287899 1.015244046 0.93921727 0.861489021 0.981434321 0.986296516 1 22.0577519 2.031595121 24.96732455 0.989678312 0.930733179 0.294670732 0.044869873 236.3780074 186791.303 0.017608356 0.011871424 107.5462127 -2.031595121 -0.058945133 EHGAVAVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EHGAVAVER 9 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ;; 104.22 0.0032953 3333060000 1409540 1384380 838780 953610 1282270 1509220 1365010 1492990 1208130 FALSE TRUE 1223265.718 1375285.917 1244416.814 1170141.726 1256755.336 1567280.67 1232631.54 1173725.707 1065306.248 1.148276113 1.29097705 1.168130588 1.09840877 1.179712724 1.471201989 1.157067785 1.101773044 1 20.0228368 1.614273674 2.528954377 1.014935069 1.222479669 0.333791088 0.10323052 0.310874397 4.314917831 0.113431901 0.028870769 41.14088916 -1.614273674 0.2075446 EHGHS(ph)YSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHGHSYSNR 9 0 O00418 O00418 EEF2K Eukaryotic elongation factor 2 kinase 1 EHGHS(0.987)YS(0.013)NR;EHGHS(0.99)YS(0.01)NR 73.881 0.017174 14591000 54500 51972 38550 36995 48167 72397 40720 51473 38579 TRUE FALSE 47297.68691 51630.59251 57192.90894 45395.28018 47208.57094 75182.15944 36770.98067 40465.89951 34018.23457 1.390362772 1.517732862 1.681242712 1.334439625 1.387743119 2.210054707 1.080919722 1.189535554 1 15.05402065 EHGLIFMETSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHGLIFMETSAK 12 0 P61019;P61019-2;A0A3B3ITL1;Q8WUD1;H7C125;Q8WUD1-2 P61019 RAB2A;RAB2B Ras-related protein Rab-2A;Ras-related protein Rab-2B 0 ; 168.02 4.77E-05 854700000 885220 781680 512560 680080 798270 714630 791110 1112490 918430 FALSE TRUE 768235.9341 776545.0926 760435.7304 834502.5584 782385.9888 742122.2785 714388.274 874592.6709 809854.2517 0.948610114 0.958870181 0.9389785 1.030435485 0.966082461 0.916365231 0.882119557 1.079938358 1 19.62730277 1.712776208 11.84333929 1.038898668 0.951374552 0.447013904 0.042058353 0.101625694 34.23724808 0.023391374 0.011016523 51.61503284 -1.712776208 -0.087524116 EHGVLGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHGVLGGK 8 0 O95865;A0A140T971;Q5SSV3;Q5SRR8 O95865 DDAH2 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 2" 0 ; 71.223 0.049298 564330000 1505130 1139430 729560 915630 1001230 1158370 1272740 1407360 1374070 FALSE TRUE 1306223.257 1131945.009 1082377.656 1123537.786 981307.4819 1202933.243 1149309.871 1106407.016 1211629.01 1.078071956 0.934233994 0.893324316 0.927295217 0.809907549 0.992823078 0.948565824 0.913156591 1 20.2085166 4.735208022 4.932363336 0.924034454 1.085626477 0.444640314 0.052923288 0.152000482 11.31772144 0.012542948 0.083957512 54351.06044 -4.735208022 0.161592023 EHHFGSSGMTLHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHHFGSSGMTLHER 14 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ; 137.8 6.66E-06 504430000 142281 177192 34450 87355 160022 173074 108334 127149 113070 FALSE TRUE 123478.2054 176028.0141 51110.13523 107190.2879 156837.8753 179732.2688 97827.78535 99959.17582 99702.99341 1.238460362 1.765523863 0.512623879 1.075095985 1.573050817 1.802676757 0.981192059 1.002569456 1 16.6053492 EHIEELLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EHIEELLR 8 0 P61201;P61201-2;B4DIH5;H0YMC2 P61201 COPS2 COP9 signalosome complex subunit 2 0 ;;; 157.91 0.00036932 1571660000 2488970 2371210 1500960 1713780 2259340 2357520 2170400 2466800 2337280 FALSE TRUE 2160046.308 2355633.365 2226829.276 2102919.942 2214383.554 2448215.32 1959914.942 1939294.017 2060969.421 1.048072954 1.142973467 1.080476621 1.020354752 1.07443785 1.187895024 0.950967502 0.940962053 1 20.97489167 2.209342205 24.99982353 0.958639683 1.09003977 0.605405696 0.048775871 134.5922314 115158.7044 0.019826736 0.013369616 161.9355518 -2.209342205 0.131400087 EHIKNPDWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EHIKNPDWR 9 1 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;; 140.07 6.61E-05 2146660000 3995880 3808250 2274850 2793280 3765660 3489970 4148530 4454710 2748510 FALSE TRUE 3467814.334 3783233.355 3374975.069 3427536.917 3690730.733 3624231.404 3746206.199 3502104.933 2423584.279 1.43086187 1.561007549 1.392555274 1.414242924 1.522839856 1.495401433 1.545729699 1.445010584 1 21.20871082 1.239855295 4.860033213 0.967275041 1.480737576 0.880948752 0.055133847 0.055655182 3.171278199 0.097195255 0.013619757 17.37221897 -1.239855295 0.513462536 EHIYDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EHIYDLR 7 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ;;; 143.02 0.00245 2568940000 3567850 3254510 1833360 1908370 2937990 3258400 2607560 3301730 3517530 FALSE TRUE 3096349.583 3233130.91 2719979.028 2341694.576 2879529.747 3383752.756 2354679.233 2595680.734 3101691.611 0.998277705 1.04237665 0.876934064 0.754973373 0.928373968 1.090937843 0.759159687 0.836859707 1 21.56462382 4.234679978 24.9686985 0.883817484 1.020327198 0.209925788 0.102060795 132.0335956 849549.8962 0.026572879 0.05885092 17166.42963 -4.234679978 0.136509714 EHKLDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EHKLDGK 7 1 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 ;; 95.741 0.0079571 739830000 2726320 1997020 1052740 1098260 1157360 1230510 2571650 2854900 355985 FALSE TRUE 2366029.904 1983901.444 1561848.585 1347636.719 1134330.8 1277848.516 2322251.779 2244401.852 313900.8588 7.537506948 6.320152966 4.975611061 4.2931922 3.613659435 4.070866581 7.398042132 7.150034123 1 18.25994945 4.46211138 2.554126231 4.939474455 7.527273102 0.218241121 1.80805693 0.59033856 6.888445269 0.497096779 2.520430794 28980.86742 -4.46211138 2.587798647 EHLASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EHLASK 6 0 Q96TA1;Q96TA1-2;Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q96TA1;Q9P0K7-3 FAM129B;RAI14 Niban-like protein 1;Ankycorbin 0 ;;;; 119.06 0.021335 1173484000 6945300 6241270 3808400 5209530 3311410 5005450 6847280 7614880 7617870 FALSE TRUE 6027461.008 6200270.686 5650154.978 6392433.409 3245519.42 5198012.9 6183231.84 5986497.171 6717294.087 0.897304916 0.923031001 0.841135568 0.951638164 0.483158751 0.773825417 0.920494437 0.891206652 1 22.67944876 1.709360875 1.794433129 0.977128721 0.814468441 0.157082893 0.132485392 0.778000247 4.708744978 0.173843984 0.040672303 51.21071917 -1.709360875 -0.16266028 EHLDENSPLGDLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EHLDENSPLGDLLR 14 0 P19174-2;P19174;A0A0D9SEK2 P19174-2 PLCG1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1" 0 71.344 0.04168 69196000 61170 53800 33135 36124 46747 51732 47871 59980 56838 FALSE TRUE 53086.22951 53446.58426 49159.19683 44326.50632 45816.82616 53722.16352 43228.47779 47153.74376 50118.67639 1.059210525 1.066400554 0.980855848 0.884430905 0.914166723 1.071899088 0.862522335 0.940841761 1 15.61306069 4.12895103 3.944419718 0.943204997 1.06327198 0.398498022 0.058503962 0.206203034 5.877016547 0.014960984 0.03464747 13457.08606 -4.12895103 0.120066983 EHLELFWSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EHLELFWSR 9 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 230.06 1.04E-07 8165140000 8018810 7346500 5281660 5905440 7397660 7785100 6974060 7965770 9122310 FALSE TRUE 6959103.941 7298240.358 7835888.442 7246360.411 7250461.039 8084597.835 6297716.735 6262352.075 8043880.904 0.865142588 0.907303383 0.974142772 0.900853767 0.901363549 1.005061852 0.782920186 0.778523719 1 22.93946029 2.227319547 24.99979528 0.835175103 0.92478488 0.16485857 0.072243328 302.0924578 671838.5251 0.028902625 0.019683634 168.7794419 -2.227319547 0.089609777 EHLIQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EHLIQLR 7 0 B5MD46;Q9BXI6;Q9BXI6-2;H0Y2U5;H7C1Q1 B5MD46 TBC1D10A TBC1 domain family member 10A 0 81.635 0.026668 83623000 62723 53748 35217 49174 49367 65757 56433 61475 54673 FALSE TRUE 54433.99663 53394.92585 52248.05899 60339.70828 48384.69328 68286.71434 50960.13635 48329.04965 48209.62022 1.129110671 1.107557488 1.083768317 1.251611359 1.003631496 1.416454102 1.057053263 1.002477294 1 15.55703344 2.013964715 24.99816484 1.009920413 1.162353173 0.290185945 0.109627603 269.0463355 481616.6597 0.04212269 0.0283837 103.2677501 -2.013964715 0.15243276 EHLLLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHLLLAR 7 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ; 100.67 0.009623 269650000 345265 356478 274065 474430 435920 467190 326139 402650 407370 FALSE TRUE 299637.3555 354136.2725 406603.7507 582156.5827 427246.0449 485163.1016 294510.09 316546.4309 359211.1827 0.834153751 0.985872071 1.131935113 1.620652727 1.189400735 1.350634738 0.819880071 0.881226549 1 18.45447274 2.228622101 24.93512867 0.893027144 1.193900372 0.28809536 0.210863217 257.72546 646611.2685 0.090841495 0.062068833 169.2864124 -2.228622101 0.300873229 EHLLTNHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EHLLTNHLK 9 0 P10155-3;P10155-5;P10155-4;P10155 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 137.95 8.69E-05 431400000 426600 377260 234240 318500 322950 332720 410340 405040 384170 FALSE TRUE 370223.7291 374781.7542 347519.2475 390820.293 316523.9268 345519.9537 370545.29 318425.348 338753.8602 1.092898923 1.106354195 1.025875387 1.153699895 0.934377328 1.01997348 1.09384817 0.939990316 1 18.36987786 3.239056034 24.99999391 0.998764474 1.090622478 0.449868502 0.053245766 12.99406261 655686.9818 0.01542749 0.018715318 1734.027712 -3.239056034 0.091858005 EHLLVSIPLLINHLQAESIVVHTYAAHALER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EHLLVSIPLLINHLQAESIVVHTYAAHALER 31 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;; 254.65 6.71E-59 3106390000 1349766 1022746 531984 663645 744847 691970 917374 1000074 690972 FALSE TRUE 1171391.003 1016027.514 789253.2418 814335.7404 730026.002 718590.5337 828407.2107 786215.9577 609286.0773 1.922563221 1.667570542 1.295373834 1.336540864 1.19816623 1.179397594 1.359635878 1.290388845 1 19.21676025 4.454062366 1.580122541 1.234276518 2.014208695 0.852609465 0.099870881 0.22343082 0.795968389 0.027938815 0.229339741 28448.69609 -4.454062366 0.779932177 EHLMLEEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EHLMLEEELR 10 0 P15924 P15924 DSP Desmoplakin 0 79.659 0.026342 48295000 37191 41380 27501 29393 41946 40797 39666 33402 38195 FALSE TRUE 32276.11512 41108.17206 40800.57559 36067.12989 41111.35667 42366.48699 35819.19743 26259.24223 33679.63061 0.958327468 1.220564813 1.211431801 1.070888523 1.220659369 1.257926118 1.063527027 0.779677264 1 15.03958869 1.950767055 5.834221182 0.884340923 1.161356262 0.535754218 0.101516391 0.137629557 11.0766913 0.047557682 0.025943303 89.28264658 -1.950767055 0.277015339 EHMDAINHDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EHMDAINHDTK 11 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 149.23 1.99E-05 296350000 241370 182770 112840 183660 192980 166230 208100 222750 208910 FALSE TRUE 209472.3429 181569.3718 167409.8014 225362.8101 189140.0756 172624.9757 187918.494 175116.6459 184212.8978 1.137120937 0.985649615 0.908784365 1.223382362 1.026747192 0.937094947 1.020115835 0.950620983 1 17.49101455 2.991410575 24.96550535 0.977447972 1.056835946 0.184580616 0.085535793 750.2281727 2180575.577 0.026257103 0.028345052 980.4164174 -2.991410575 0.079387974 EHMGDILYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EHMGDILYK 9 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 86.898 0.014711 0 1306100 1069400 774010 908200 991100 992200 1184500 1356800 1195000 FALSE TRUE 1133495.576 1062375.041 1148323.825 1114420.691 971379.0491 1030370.576 1069627.372 1066658.879 1053728.461 1.075699877 1.0082057 1.089772049 1.057597599 0.921849494 0.977833108 1.015088243 1.012271109 1 20.00707171 3.356021589 21.82102436 0.99051666 1.056578074 0.538916212 0.033085315 2.846796061 522.0832249 0.009780282 0.012626275 2269.97769 -3.356021589 0.066061414 EHMQPTHPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 EHMQPTHPIR 10 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;;;;;;;;;;; 124.42 0.00030517 6046100000 3710249 2974975 2094923 2600203 2470521 3053766 2903917 3240290 4040144 FALSE TRUE 3219930.194 2955432.193 3108034.77 3190618.833 2421362.466 3171246.354 2622295.576 2547379.199 3562522.779 0.903834275 0.829589697 0.872425234 0.895606577 0.679676346 0.890168723 0.736078262 0.715049238 1 21.76446781 EHNGQVTGIDWAPESNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHNGQVTGIDWAPESNR 17 0 A0A1W2PNV4;C9JEY1;C9K057;O15143;F8VXW2;C9JBJ7;C9JTT6 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 ; 138.75 2.61E-06 3142000000 1890850 1812330 1123990 1608460 1889820 2017210 1881660 2062650 1936820 FALSE TRUE 1640969.382 1800424.685 1667555.324 1973685.427 1852216.279 2094813.374 1699176.903 1621568.349 1707851.346 0.960838533 1.054204565 0.976405427 1.15565411 1.084530152 1.226578284 0.994920844 0.949478626 1 20.70375098 2.02191454 24.99998598 0.97145128 1.077788618 0.25240303 0.077500363 293.4286174 334740.4292 0.032092229 0.021634662 105.1754889 -2.02191454 0.106337338 EHNS(ph)MWASLSSPDAEAVEPDFSSIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EHNSMWASLSSPDAEAVEPDFSSIER 26 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 EHNS(0.25)MWAS(0.25)LS(0.25)S(0.25)PDAEAVEPDFSSIER 67.832 0.05673 24148000 19704 22320 31692 17707 12112 15321 16441 17546 15689 TRUE FALSE 17100.06648 22173.37845 47018.3572 21727.64498 11870.9949 15910.40878 14846.55435 13793.92444 13834.26429 1.236066199 1.602786963 3.398688662 1.570567435 0.858086462 1.150072635 1.07317267 0.997084063 1 13.7559583 3.477470793 17.18961044 1.041644416 2.107053679 0.438911211 0.550897164 0.220035423 10564.5077 0.157867986 0.208559525 3002.415495 -3.477470793 1.065409263 EHNSMWASLS(ph)SPDAEAVEPDFSSIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EHNSMWASLSSPDAEAVEPDFSSIER 26 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 EHNSMWAS(0.046)LS(0.616)S(0.337)PDAEAVEPDFSSIER 138.92 1.20E-05 105900000 29967 42453 13579 27991 53929 58884 45284 36203 42845 TRUE FALSE 26006.78502 42174.12345 20145.84982 34346.78437 52855.91841 61149.30558 40892.36465 28461.27018 37779.91291 0.688375992 1.116310764 0.533242357 0.909128204 1.39904818 1.618566611 1.082383772 0.753343986 1 15.20533176 3.46458555 24.64494046 1.136077629 0.797705704 0.308837495 0.269410334 293.2328127 576487.1435 0.087043808 0.112450761 2914.644222 -3.46458555 -0.338371925 EHNSMWASLSS(ph)PDAEAVEPDFSSIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 EHNSMWASLSSPDAEAVEPDFSSIER 26 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 EHNSMWAS(0.002)LS(0.2)S(0.797)PDAEAVEPDFSSIER;EHNSMWASLS(0.249)S(0.751)PDAEAVEPDFSSIER;EHNSMWAS(0.003)LS(0.319)S(0.678)PDAEAVEPDFSSIER;EHNSMWAS(0.003)LS(0.184)S(0.814)PDAEAVEPDFSSIER;EHNSMWASLS(0.239)S(0.761)PDAEAVEPDFSSIER;EHNSMWAS(0.001)LS(0.052)S(0.948)PDAEAVEPDFSSIER;EHNSMWASLS(0.046)S(0.954)PDAEAVEPDFSSIER;EHNSMWAS(0.006)LS(0.111)S(0.883)PDAEAVEPDFSSIER;EHNS(0.001)MWAS(0.01)LS(0.187)S(0.802)PDAEAVEPDFSSIER 227.77 7.93E-35 3350892000 742223 935297 321346 526259 1276355 1359020 887216 1090121 1052662 TRUE FALSE 644136.35 929152.9724 476750.0004 645754.1493 1250958.033 1411302.379 801173.9289 857007.1075 928217.4976 0.693949803 1.001007819 0.513618847 0.695692713 1.347699258 1.520443627 0.863131681 0.923282646 1 19.82410337 3.260437033 24.9980601 1.104350987 0.730530851 0.441069605 0.225332772 269.1593032 307564.9067 0.071088485 0.091697501 1821.532957 -3.260437033 -0.373820136 EHPDAWTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EHPDAWTR 8 0 O14980;C9JKM9;C9J673;C9IYM2;F8WF71;C9IZS4;C9JQ02;C9JV99;H7BZC5 O14980 XPO1 Exportin-1 0 ;;;;; 97.431 0.0082369 3387860000 4485510 3921690 2762980 3181260 3792810 3884460 4061460 4344000 4297180 FALSE TRUE 3892738.489 3895928.16 4099166.37 3903613.706 3717340.502 4033897.69 3667580.234 3415069.405 3789172.276 1.027332147 1.028173933 1.081810504 1.030202224 0.981042885 1.064585455 0.967910659 0.901270556 1 21.8534513 2.085954465 5.459857226 0.941011864 1.034202387 0.526179539 0.035323723 0.134425781 6.55264388 0.014503463 0.009586048 121.8861798 -2.085954465 0.093190524 EHPDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHPDYK 6 0 P48431;O95416;Q9Y651;O00570 P48431 SOX2;SOX14;SOX21;SOX1 Transcription factor SOX-2;Transcription factor SOX-14;Transcription factor SOX-21;Transcription factor SOX-1 0 ; 77.748 0.071601 246280000 892140 996760 596260 751290 743770 803220 962130 1272640 1027680 FALSE TRUE 774241.4386 990212.2179 884613.3304 921881.8772 728970.4322 834120.3932 868822.7807 1000495.84 906188.8411 0.85439304 1.092721708 0.976190933 1.017317622 0.804435454 0.920470828 0.958765702 1.104069918 1 19.7894522 1.759530671 25 1.055963931 0.949385424 0.217240312 0.083188438 14.28058571 17043.27241 0.044102836 0.021179428 57.48184124 -1.759530671 -0.106578507 EHPFLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHPFLVK 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 105.12 0.0079989 1449010000 2367870 1995920 1208110 1521600 1969000 1469530 2181490 2450430 2286120 FALSE TRUE 2054949.98 1982808.67 1792356.037 1867102.536 1929820.752 1526063.77 1969929.436 1926424.614 2015857.498 1.019392483 0.983605573 0.889128343 0.926207601 0.957320026 0.757029587 0.977216613 0.955635314 1 20.94296223 4.417978007 5.320673133 0.924570921 1.011586305 0.201260256 0.066605514 0.286459439 16.11442857 0.016791458 0.047907387 26180.50425 -4.417978007 0.087015384 EHPHS(ph)RS(ph)PS(ph)PEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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;EHPHS(1)RS(1)PS(1)PEPR;EHPHS(1)RS(1)PS(1)PEPR 111.22 0.0016769 1179900000 970800 921010 557120 631610 879900 859880 698550 814580 833420 TRUE FALSE 842506.3203 914959.8247 826545.0955 775026.7041 862391.7115 892960.14 630804.7285 640388.4061 734894.037 1.146432381 1.24502279 1.124713297 1.054610141 1.173491236 1.215086931 0.858361474 0.871402371 1 19.48717672 2.236445204 24.99999999 0.899748147 1.157995821 0.777977755 0.062866758 24.38193177 288138.4821 0.025595981 0.018217511 172.3634601 -2.236445204 0.258247674 EHPNYVDCYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EHPNYVDCYLR 11 0 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 0 75.479 0.037977 144160000 127930 103150 86496 85526 114730 98983 96987 125070 137160 FALSE TRUE 111023.7264 102472.4009 128325.7549 104945.9855 112447.0975 102790.9401 87581.21567 98324.7538 120945.1011 0.917967949 0.847263758 1.061024827 0.867715886 0.929736686 0.849897509 0.72414025 0.812970124 1 16.88399281 2.672169325 4.645420236 0.828310671 0.924996926 0.153604321 0.087324359 0.34639481 14.82648265 0.030380913 0.026908978 470.0773495 -2.672169325 0.096686256 EHPSLLPHSACFPDPSTASTSQSAAHSNDS(ph)PPPPSAAAPSSASPHASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EHPSLLPHSACFPDPSTASTSQSAAHSNDSPPPPSAAAPSSASPHASR 48 0 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 EHPSLLPHSACFPDPS(0.007)T(0.007)AS(0.007)T(0.007)S(0.007)QS(0.007)AAHS(0.074)NDS(0.885)PPPPSAAAPSSASPHASR 97.308 3.06E-06 144300000 14545 12255 2731.3 6568.5 23494 20337 15980 17372 6049.6 TRUE FALSE 12622.8414 12174.4961 4052.165816 8059.978318 23026.51537 21119.37755 14430.26206 13657.13299 5334.42318 2.366299218 2.282251649 0.759625864 1.51093718 4.316589552 3.959074269 2.705121355 2.560189271 1 12.38111656 EHPVIESHPDNALEDLR ddPTM_MDA-MB-175_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 0 198.07 8.40E-12 169840000 125460 97566 92348 116150 134570 130700 106940 130690 244410 FALSE TRUE 108880.1431 96925.08252 137007.8017 142523.6327 131892.3203 135728.1136 96568.97526 102742.9605 215516.1282 0.505206473 0.449734706 0.635719483 0.661313072 0.611983527 0.6297817 0.44808236 0.476729799 1 17.71743631 1.232761954 24.99998383 1.000000723 0.550981368 0.755234714 0.080091732 105.2205404 453593.804 0.189640709 0.021776082 17.09078277 -1.232761954 -0.449019355 EHPWEVMPDLYFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EHPWEVMPDLYFYR 14 0 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;;; 182.57 1.51E-06 1639789000 1241190 1066418 1065571 1387540 1197630 1156290 1059321 1352110 3482540 FALSE TRUE 1077163.597 1059412.63 1580884.7 1702602.164 1173799.506 1200773.225 956588.2125 1062971.799 3070838.089 0.350771863 0.344991367 0.514805618 0.55444218 0.382240767 0.391024597 0.311507212 0.346150389 1 21.55020102 1.235509727 25 1.000000819 0.398806004 0.856713446 0.077179827 33.87565642 277538.4496 0.143570221 0.020876391 17.19925864 -1.235509727 -0.601194815 EHPWEVMPDLYFYRDPEEIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EHPWEVMPDLYFYRDPEEIEK 21 1 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;;; 184.7 2.32E-17 304408000 470082 359642 330851 466121 355283 308715 426390 519578 950270 FALSE TRUE 407959.4727 357279.488 490851.6502 571960.8973 348213.5634 320591.4658 385038.7634 408470.2881 837930.1632 0.486865721 0.426383371 0.585790644 0.682587789 0.415563944 0.382599267 0.459511759 0.487475336 1 19.67647048 1.238359188 24.99999959 1.000000561 0.490429315 0.771288789 0.087133366 2.430475537 300901.9109 0.127468887 0.022612818 17.31247613 -1.238359188 -0.509571245 EHPWEVMPDLYFYRDPEEIEKEEQAAAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EHPWEVMPDLYFYRDPEEIEKEEQAAAEK 29 2 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;; 234.52 1.93E-45 2852050000 3628200 2561510 2476640 2350640 2246110 1679940 3592900 4346000 2534900 FALSE TRUE 3148724.177 2544683.272 3674351.388 2884388.739 2201416.805 1744568.379 3244461.111 3416641.721 2235227.01 1.408682055 1.138445116 1.64383813 1.290423177 0.984873928 0.780488233 1.451513022 1.528543502 1 21.09198993 3.477359616 24.99999933 1.195030436 1.387133535 0.159920657 0.249281114 21.22019279 2225790.021 0.078829271 0.102938899 3001.646994 -3.477359616 0.192103099 EHPYLFSQCQAIHCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EHPYLFSQCQAIHCR 15 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ;;; 242.26 3.72E-18 1833440000 93349 86938 52190.2 73138 85095 85754 90509 80506 82387 FALSE TRUE 81012.69313 86366.89855 77429.55529 89745.10074 83401.77599 89053.01187 81731.45111 63290.4184 72647.30272 1.115150737 1.188852102 1.065828357 1.235353515 1.148036787 1.225826817 1.125044538 0.871201215 1 16.14862161 1.838877606 5.476312294 0.934423691 1.163001933 0.717407892 0.058259784 0.097063488 4.077908135 0.028207373 0.014345344 69.00453062 -1.838877606 0.228578242 EHQEALHQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EHQEALHQQR 10 0 F8W785;O00461 F8W785 GOLIM4 Golgi integral membrane protein 4 0 113.63 0.00084589 18372000 52492 30770 24822 23268 26399 35885 36278 51667 21980 FALSE TRUE 45555.0492 30567.86984 36826.00222 28551.35503 25873.71155 37265.51917 32759.76514 40618.41412 19381.54944 2.350433816 1.577163371 1.900054603 1.473120357 1.334966104 1.922731683 1.690255222 2.095725847 1 14.24239629 4.743388311 24.1984224 1.668363173 2.350434259 0.33347017 0.317245527 404.2887422 2026354.338 0.074732093 0.589539102 55384.50909 -4.743388311 0.682071086 EHQEDPEMLIDLMYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHQEDPEMLIDLMYR 15 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GWE0;K7ESB7;Q96HP0 Q96N67-2;K7ESB7;Q96HP0 DOCK7;DOCK6 Dedicator of cytokinesis protein 7;Dedicator of cytokinesis protein 6 0 ; 151.48 3.00E-06 45019000 84615 83293 65661 71332 82457 93702 76679 91417 129285 FALSE TRUE 73432.91336 82745.8428 97414.87922 87529.02084 80816.26702 97306.77657 69242.68238 71868.18596 114001.0746 0.644142291 0.725833884 0.85450843 0.767791191 0.708907941 0.85356017 0.607386225 0.630416741 1 16.7986879 4.487288668 0.007050007 1.468749331 7.92E-08 0.019811517 0.120072539 223404.3984 514.5580334 52315.36473 54904.73758 30710.6259 -4.487288668 -1.468749252 EHQISPGDFPSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHQISPGDFPSLR 13 0 A0A024R571;Q9H4M9;C9JC03;C9J2Z4 A0A024R571 EHD1 EH domain-containing protein 1 0 ; 91.845 0.0063451 1686280000 1706500 1496170 962540 1240770 1514260 1668260 1573840 1676040 1320660 FALSE TRUE 1480981.701 1486341.561 1428027.564 1522505.792 1484129.189 1732439.042 1421209.239 1317631.889 1164533.079 1.271738629 1.276341211 1.226266208 1.307395916 1.274441418 1.487668382 1.220411223 1.131467978 1 20.15132019 1.610091835 2.225965649 1.009730633 1.301941673 0.662007848 0.072303721 0.186557576 1.889088558 0.090417593 0.020375393 40.74664303 -1.610091835 0.29221104 EHQMAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 85.849 0.041148 429091000 1389151 1179315 759063 908675 577222 928414 1181852 1360984 1465322 FALSE TRUE 1205571.176 1171568.002 1126148.406 1115003.547 565736.4115 964130.6873 1067236.175 1069948.163 1292093.302 0.933037245 0.9067209 0.871568952 0.862943523 0.43784486 0.746177297 0.825974543 0.828073453 1 20.30127882 3.45956993 24.99996115 0.766832839 0.89793472 0.174426654 0.138355162 455.0454773 648160.8962 0.042021884 0.054261011 2881.176939 -3.45956993 0.131101881 EHQTSAYS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EHQTSAYSPPR 11 0 H3BRF9;Q96K21-2;Q96K21;Q96K21-4;Q96K21-3 H3BRF9;Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 EHQTS(0.008)AY(0.001)S(0.992)PPR;EHQTSAY(0.003)S(0.997)PPR;EHQTS(0.001)AYS(0.999)PPR;EHQTSAY(0.002)S(0.998)PPR;EHQT(0.001)S(0.001)AYS(0.998)PPR;EHQTS(0.001)AY(0.429)S(0.57)PPR 132.84 0.0001122 4143160000 1989908 1744797 1158736 1354845 1656325 1717781 1801735 2056669 1796944 TRUE FALSE 1726936.616 1733335.314 1719104.605 1662483.265 1623367.373 1783865.147 1627003.017 1616866.339 1584511.327 1.089885939 1.093924217 1.084943083 1.049208823 1.024522416 1.12581407 1.026816905 1.020419552 1 20.59560654 -2 0.31706161 0.167921417 1.090559935 0.473114127 0.029209659 67.12352478 1.073949356 35.16689076 0.050360768 0.01 2 0.922638518 EHS(ph)PSESEKEVVGADPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EHSPSESEKEVVGADPR 17 1 Q12986;Q12986-2;Q12986-3 Q12986 NFX1 Transcriptional repressor NF-X1 1 EHS(0.767)PS(0.229)ES(0.004)EKEVVGADPR 63.936 0.029985 93679000 206380 176420 108260 144660 176350 130670 206160 223990 145150 TRUE FALSE 179106.3601 175261.0854 160614.8981 177507.264 172840.98 135696.9595 186166.6349 176091.4816 127990.5324 1.399371944 1.369328513 1.254896711 1.386878082 1.350420042 1.060210915 1.454534421 1.375816464 1 16.96567757 1.233938175 24.99358555 0.999999499 1.331926006 0.479399548 0.108541587 126.596409 684422.0013 0.204269365 0.026120365 17.13713332 -1.233938175 0.331926506 EHS(ph)PSKEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EHSPSKEK 8 1 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 EHS(0.97)PS(0.03)KEK 69.65 0.03232 148800000 176290 93794 75297 84926 70161 75666 144330 135040 132900 TRUE FALSE 152992.8298 93177.86104 111710.8811 104209.7463 68764.93337 78576.91998 130332.8988 106162.7469 117188.7134 1.305525297 0.795109515 0.953256315 0.889247294 0.586788022 0.670516108 1.112162554 0.905912727 1 16.8384741 4.744541005 24.3720263 0.86786909 1.305525574 0.452297347 0.1526004 480.0889281 1956437.785 0.039176415 0.341597628 55531.7046 -4.744541005 0.437656483 EHS(ph)PYGPS(ph)PLGWPSSETR ddPTM_MDA-MB-175_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 2 EHS(0.835)PY(0.165)GPS(1)PLGWPSSETR 81.51 0.00998 130370000 97973 95909 64859 84107 145350 134490 66300 127450 115140 TRUE FALSE 85025.61982 95278.96746 96225.02934 103204.7798 142457.8194 139663.9173 59870.2362 100195.8093 101528.2804 0.8374575 0.938447565 0.947765775 1.016512635 1.403134367 1.375615905 0.589690242 0.986875863 1 16.63152212 3.978885046 2.401747348 1.050524265 0.885750353 0.098623034 0.22474409 0.896170641 10.22099817 0.068380248 0.16173824 9525.439996 -3.978885046 -0.164773911 EHS(ph)PYGPSPLGWPS(ph)SETR ddPTM_MDA-MB-175_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 2 EHS(0.999)PY(0.001)GPS(0.176)PLGWPS(0.814)S(0.01)ET(0.001)R 267.26 3.30E-27 0 115840 135500 81614 92559 173470 158590 85241 145430 118370 TRUE FALSE 100531.4505 134609.8916 121082.8034 113575.9356 170018.2864 164691.0599 76974.34094 114330.9262 104376.4334 0.963162346 1.289657896 1.160058831 1.088137733 1.628895343 1.577856749 0.737468587 1.095371076 1 16.67143649 2.23168508 24.99999816 0.967140137 1.285911663 0.347381321 0.219159175 200.1821886 727870.1631 0.091481713 0.063209587 170.4845706 -2.23168508 0.318771526 EHSAFGDRPEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EHSAFGDRPEKR 12 2 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 ;;; 196.38 1.24E-07 704390000 826390 681130 354821 444436 674020 556010 766120 881840 261075 FALSE TRUE 717180.4677 676655.6122 526413.6224 545351.9866 660608.3207 577400.0645 691821.8003 693265.3785 230211.0109 3.115317833 2.939284309 2.286657012 2.368922253 2.869577428 2.508134004 3.005163817 3.011434491 1 17.81259731 1.233556164 24.99899348 0.999997288 2.759717106 0.790061971 0.285612894 75.73672401 378287.1083 0.603667294 0.074425812 17.12206588 -1.233556164 1.759719818 EHSLQVS(ph)PSLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EHSLQVSPSLEK 12 0 O95235-2;O95235 O95235-2 KIF20A Kinesin-like protein KIF20A 1 EHS(0.002)LQVS(0.966)PS(0.032)LEK;EHSLQVS(1)PSLEK;EHSLQVS(0.985)PS(0.015)LEK 220.34 1.92E-11 967660000 2045020 2013040 1147400 1489660 1956700 1696550 2184360 2752140 2524330 TRUE FALSE 1774765.426 1999816.208 1702286.478 1827910.071 1917765.498 1761817.376 1972521.103 2163616.278 2225906.583 0.797322511 0.898427734 0.76476097 0.821198017 0.86156603 0.791505533 0.886165268 0.97201576 1 21.08596162 1.826332142 2.334193583 0.995898333 0.824941333 0.759310687 0.037717704 0.128758398 1.312619107 0.028624241 0.010106951 67.03971225 -1.826332142 -0.170957 EHSNPNYDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EHSNPNYDK 9 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 152.04 8.14E-05 1201510000 2803800 2467310 1731100 1981120 2040840 2060140 2627230 3068670 3451930 FALSE TRUE 2433270.726 2451102.078 2568265.75 2430963.576 2000231.277 2139394.919 2372441.639 2412458.801 3043846.768 0.799406446 0.805264609 0.843756584 0.798648474 0.657139281 0.702858942 0.779422165 0.79256907 1 21.5374643 1.210828738 3.248747929 1.048339134 0.768733374 0.642927332 0.053528616 0.281825881 3.816848162 0.209324714 0.015317608 16.24907853 -1.210828738 -0.279605759 EHSNPS(ph)PSQDTDGTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHSNPSPSQDTDGTK 15 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 EHS(0.024)NPS(0.947)PS(0.029)QDTDGTK;EHS(0.001)NPS(0.984)PS(0.015)QDTDGTK 128.67 4.55E-05 556000000 1415340 1111250 766110 1032870 1274510 972370 1197360 1626790 1592130 TRUE FALSE 1228299.233 1103950.126 1136603.358 1267398.92 1249149.745 1009777.703 1081240.211 1278913.618 1403910.205 0.87491296 0.786339555 0.809598331 0.902763521 0.889764701 0.71926089 0.770163368 0.910965398 1 20.42101923 1.482236768 3.576392629 0.991533144 0.822127243 0.519628963 0.05674729 0.183523987 4.485743152 0.063618844 0.015560849 30.35545646 -1.482236768 -0.1694059 EHSPYGPS(ph)PLGWPSSETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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;EHSPYGPS(1)PLGWPSSETR 188.26 2.49E-14 1698070000 879455 926050 573202 905981 1215360 1190820 808000 1358400 1144800 TRUE FALSE 763232.7935 919966.7166 850404.4044 1111697.833 1191176.714 1236631.616 729640.2844 1067916.731 1009463.048 0.756077991 0.911342637 0.842432426 1.101276401 1.18001022 1.225039013 0.722800389 1.057905718 1 19.94515667 3.749885384 23.28785314 1.041462887 0.844090119 0.340168531 0.138355554 382.4355325 786420.8525 0.038058151 0.065042921 5621.929358 -3.749885384 -0.197372768 EHTALLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EHTALLK 7 0 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ;;; 121.52 0.0044301 2978020000 7104000 6367200 4193770 5106100 5688500 4988900 7249700 7601100 7233600 FALSE TRUE 6165188.401 6325373.444 6221891.199 6265518.047 5575309.979 5180826.211 6546625.21 5975663.917 6378452.049 0.966564984 0.99167845 0.975454727 0.98229445 0.874085113 0.812238796 1.026365827 0.936851743 1 22.60477492 EHTEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHTEPK 6 0 P20810-6;P20810-10;P20810;P20810-8;B7Z574;E7ES10;E9PDE4;H0YA91;E7EQK6;P20810-5;E9PCH5;P20810-2;F8W7E0;A0A0C4DGB5;H0Y944;E7EN75;E7EVY3 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ; 89.903 0.049638 227470000 952530 932760 599390 743960 532090 691020 1024790 1213340 1213250 FALSE TRUE 826650.7471 926632.6381 889257.0088 912887.4887 521502.45 717603.9865 925406.0235 953876.6832 1069820.967 0.77270008 0.866156737 0.831220397 0.853308653 0.48746703 0.670770165 0.865010176 0.891622722 1 20.02893795 1.743852983 2.051906703 0.975381979 0.75225154 0.351578944 0.112534276 0.396609609 3.272937548 0.124076571 0.03503837 55.44379934 -1.743852983 -0.223130439 EHTLAWK ddPTM_MDA-MB-175_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 0 116.54 0.0054322 189840000 455150 504790 315970 382820 501960 468590 570420 533260 577540 FALSE TRUE 395000.7743 501474.0013 468774.1489 469745.132 491971.9781 486616.9605 515100.7562 419226.4988 509263.8791 0.775630848 0.984703651 0.920493615 0.922400255 0.966045302 0.95553009 1.0114614 0.82320093 1 18.95805387 4.748329255 24.54805114 0.940349044 0.775630733 0.50023546 0.053658776 949.1875997 2385193.86 0.012906815 0.1642364 56018.21361 -4.748329255 -0.164718312 EHVEEISELFYDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EHVEEISELFYDAK 14 0 Q9Y265;H7C4G5 Q9Y265 RUVBL1 RuvB-like 1 0 ;;; 184.21 1.32E-06 806885000 1476320 1148960 884350 1103630 1116850 982680 1396190 1586910 1565770 FALSE TRUE 1281220.571 1141412.406 1312024.618 1354226.059 1094626.87 1020484.335 1260787.709 1247561.646 1380666.454 0.927972551 0.826711189 0.950283549 0.980849542 0.792824992 0.739124451 0.913173276 0.903593798 1 20.3969334 1.213699128 1.917752681 1.046774492 0.872933096 0.219134604 0.07351882 1.50158003 5.014845775 0.484644319 0.021201284 16.35682957 -1.213699128 -0.173841395 EHVIEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EHVIEALR 8 0 P27635;X1WI28;A0A087WV22;H7C123;H7C2C5;F8W7C6 P27635;F8W7C6 RPL10 60S ribosomal protein L10 0 ;; 122.52 0.0013871 3186680000 2651830 2455890 1817450 2412390 2569270 2568990 2086540 2706980 4053500 FALSE TRUE 2301383.947 2439757.097 2696374.899 2960160.021 2518146.554 2667820.708 1884187.672 2128113.393 3574299.848 0.643869861 0.682583219 0.754378484 0.828178985 0.704514635 0.746389733 0.527148743 0.595393079 1 21.76922924 0.643994544 0.005742095 0.976064137 0.445379006 0 0.130283688 1897357.95 2301.157239 109669.1669 103092.1509 4.405493285 -0.643994544 -0.530685131 EHVMNEVDTNKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EHVMNEVDTNKDR 13 1 P80303-2;P80303;E9PKG6;H0YD18 P80303-2 NUCB2 Nucleobindin-2;Nesfatin-1 0 ;;;; 185.87 4.98E-06 1493203000 1904037 1656025 1383172 1491817 1712943 1612985 1864306 2252229 1862601 FALSE TRUE 1652413.686 1645146.463 2052078.606 1830556.851 1678858.786 1675037.577 1683505.891 1770607.355 1642406.432 1.006093044 1.001668303 1.249434102 1.114557771 1.022194478 1.019867887 1.025023927 1.078056759 1 20.64737975 3.235940827 24.99892776 1.034398737 1.097597294 0.165956594 0.070280984 136.410514 1301680.322 0.021924295 0.026003652 1721.633985 -3.235940827 0.063198557 EHVVAASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHVVAASK 8 0 Q99613-2;Q99613;B5ME19 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 ; 117.89 0.001992 530330000 1801670 1770910 1097390 1236940 1437630 1488330 1905080 2072300 1919810 FALSE TRUE 1563574.745 1759276.776 1628091.475 1517806.132 1409023.976 1545587.018 1720325.635 1629154.772 1692852.249 0.923633321 1.039238231 0.96174458 0.896596932 0.832337244 0.913007629 1.016229051 0.96237269 1 20.69102463 2.24645111 24.97339404 0.987487624 0.92861776 0.247409856 0.053241026 297.2241582 940715.8233 0.022351775 0.016987917 176.3807195 -2.24645111 -0.058869864 EHVYDLFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHVYDLFEK 9 0 A0A499FI31;Q15020-4;Q15020;Q15020-2;A0A494C0L2;F8W667;F8VVK9;F8VZM2 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 ; 147.95 9.12E-05 644200000 719670 605440 469430 589390 592700 538610 608700 788370 898190 FALSE TRUE 624563.7861 601462.8248 696447.9181 723220.0078 580906.4296 559330.6752 549668.3677 619783.2106 792007.0014 0.788583668 0.759416045 0.879345658 0.913148503 0.73346123 0.706219357 0.694019582 0.782547641 1 19.59515366 1.239100903 10.64545717 1.000623756 0.780478712 0.494731566 0.069191831 0.062295969 211.9171458 0.103137082 0.018624593 17.34206873 -1.239100903 -0.220145044 EHWDAVYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHWDAVYER 9 0 G3V238;A0A494BZY7;Q5JPI9 G3V238 METTL10 Protein-lysine N-methyltransferase METTL10 0 ; 130.66 0.00035508 438760000 297250 335170 215690 250450 345940 339080 313670 341370 322590 FALSE TRUE 257967.6594 332968.2462 319998.4054 307318.5004 339056.4708 352124.627 283250.3317 268370.682 284453.7777 0.906887795 1.170553082 1.124957482 1.080381153 1.191956295 1.237897524 0.995769274 0.943459722 1 18.11783472 2.072507289 9.206054065 0.968260427 1.122852624 0.356092954 0.08842088 0.301301326 35.29238908 0.035391399 0.023834096 118.1700145 -2.072507289 0.154592197 EHWSHDPFEAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHWSHDPFEAFK 12 0 A0A1B0GW23;Q03154;Q03154-2;Q03154-3;Q03154-4;C9JMV9;A0A1B0GV31;C9JYZ0;A0A1B0GVA5;F8WC59 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 ; 98.353 0.0025481 106477000 202280 209440 67640 172260 260870 240820 210506 268650 329630 FALSE TRUE 175548.1855 208064.1748 100350.9302 211374.2658 255679.1974 250084.5012 190091.1605 211201.2881 290661.5169 0.60396088 0.715829798 0.345250143 0.727217927 0.879645851 0.860397702 0.653994937 0.72662281 1 18.14898055 3.491083958 24.35717672 0.801217966 0.565285003 0.471416749 0.128660374 447.1801049 780080.3439 0.035849554 0.050791966 3098.018151 -3.491083958 -0.235932964 EHYLDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EHYLDSK 7 0 Q96JB2 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 0 84.568 0.02145 252560000 373470 345430 227930 245350 326830 307910 361990 410500 409880 FALSE TRUE 324114.9932 343160.8476 338157.7104 301060.4674 320326.7224 319755.4969 326884.2655 322717.7695 361424.4533 0.896771069 0.949467709 0.935624879 0.832983116 0.886289568 0.884709084 0.904433174 0.892905188 1 18.46333459 1.236838693 24.99504848 1.000000127 0.897957284 0.516502803 0.031045367 39.38606711 571542.1658 0.049409767 0.007907761 17.25196994 -1.236838693 -0.102042843 EHYPNGVCTVYGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHYPNGVCTVYGK 13 0 P47755;F8W9N7;A0A0D9SET8 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 ; 150.12 4.41E-05 1014810000 2161500 1789270 1203570 1712180 1953350 1727690 2095900 2431200 2376500 FALSE TRUE 1875852.298 1777516.168 1785620.478 2100956.638 1914482.157 1794155.352 1892639.941 1911306.8 2095552.877 0.895158657 0.848232553 0.852099938 1.00257868 0.913592865 0.856172789 0.903169737 0.912077581 1 20.99889949 EHYPVSSPSS(ph)PS(ph)PPAQPGGVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHYPVSSPSSPSPPAQPGGVSR 22 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 2 EHYPVSS(0.002)PS(0.251)S(0.748)PS(0.999)PPAQPGGVSR;EHYPVSSPS(0.264)S(0.739)PS(0.997)PPAQPGGVSR 219.58 5.74E-26 882220000 154473 164293 107832 143622 158761 160628 167761 167660 198233 TRUE FALSE 134059.0017 163213.7485 159979.9159 176233.5702 155601.9667 166807.4631 151491.564 131807.2137 174798.1206 0.766936173 0.933727136 0.91522675 1.008212043 0.890181005 0.954286365 0.866665863 0.754053953 1 17.41533015 0.957516391 22.11639879 1.984118068 0.886900989 0.173870653 0.077968874 401.8265027 212002.6284 40547.0842 0.019555459 9.06810188 -0.957516391 -1.097217079 EHYPVSSPSSPS(ph)PPAQPGGVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EHYPVSSPSSPSPPAQPGGVSR 22 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 EHYPVSSPS(0.009)S(0.03)PS(0.961)PPAQPGGVSR;EHYPVSSPSS(0.092)PS(0.907)PPAQPGGVSR 221.11 6.19E-26 390040000 106238 87061 49196 62615 89183 81417 79213 82441 85979 TRUE FALSE 92198.37913 86489.09056 72987.35015 76832.69276 87408.43278 84549.16467 71530.93545 64811.63371 75814.66057 1.216102248 1.140796383 0.962707603 1.013427907 1.152922563 1.115208642 0.943497404 0.854869404 1 16.21018923 4.083763321 0.047338611 3.68E-12 2.202954351 0.405576199 0.085727578 282.52235 5.891955606 121.3481316 153.5114153 12127.27765 -4.083763321 2.202954351 EHYVDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 ;;;;;; 139.28 0.0027038 25903360000 27415540 26173200 17227000 19288840 22752490 19947870 28819490 32041940 31859140 FALSE TRUE 23792506.93 26001266.53 25558034.82 23668665.93 22299759.96 20715277.47 26024580.3 25190020.48 28092788.76 0.846925776 0.925549498 0.909772078 0.842517492 0.793789472 0.73738772 0.926379382 0.896672121 1 24.74369651 1.322999168 1.558175 1.036697329 0.850669961 0.394720232 0.057914606 1.078014753 2.766983225 0.300676632 0.018162418 21.03774409 -1.322999168 -0.186027368 EHYVVEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EHYVVEVK 8 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 93.551 0.010989 287020000 327000 275680 209820 250190 284180 268690 359610 382540 370490 FALSE TRUE 283786.1215 273869.0399 311289.6538 306999.4634 278525.374 279026.6782 324735.0775 300736.7979 326691.0943 0.868668067 0.838311924 0.952856259 0.939724005 0.852564942 0.854099432 0.994012641 0.920554013 1 18.3175676 -1.999999595 0.420393462 2.982143401 0.881570664 0.360437116 0.047053052 104.7490437 1.442632607 183.7046031 0.043479241 0.010000009 1.999999595 -2.100572737 EIAATCSGTEWGQSSGAAS(ph)PGLFQAGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EIAATCSGTEWGQSSGAASPGLFQAGHR 28 0 P49757-3;P49757;G3V3Z8 P49757-3 NUMB Protein numb homolog 1 EIAATCSGTEWGQSSGAAS(1)PGLFQAGHR;EIAATCSGTEWGQSSGAAS(1)PGLFQAGHR;EIAATCSGTEWGQSSGAAS(1)PGLFQAGHR 337.67 2.32E-96 2735820000 671260 665500 456230 597790 656730 719780 626500 731950 831470 TRUE FALSE 582551.2902 661128.2867 676864.354 733527.3561 643662.3579 747470.4024 565742.1264 575428.1885 733174.5638 0.794560148 0.901733802 0.923196722 1.000481185 0.877911468 1.019498547 0.771633598 0.784844724 1 19.48379721 1.192676675 23.80121885 1.000002982 0.88372251 0.156340409 0.084508238 15786.93508 8187918.319 13.57058326 0.021982316 15.58391876 -1.192676675 -0.116280472 EIADYLAAGKDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIADYLAAGKDER 13 1 P53990-2;P53990;P53990-4;P53990-5;H3BQF7;H3BMU1;H3BUI0;P53990-3;F5GXM3;H3BPP6;H3BRE2 P53990-2 IST1 IST1 homolog 0 ; 202.13 8.79E-08 1319890000 1758660 1498190 1056720 1250930 1460010 1283970 1787060 2024640 1278780 FALSE TRUE 1526248.625 1488348.291 1567753.327 1534972.776 1430958.657 1333365.157 1613751.196 1591686.492 1127604.085 1.353532366 1.319920982 1.390340233 1.361269257 1.269025783 1.182476345 1.431132804 1.411565028 1 20.10482918 3.245177869 24.69189605 1.287034399 1.356103568 0.114463704 0.121304163 413.0426742 1541234.77 0.036101174 0.045505908 1758.643734 -3.245177869 0.069069169 EIAEAYDVLSDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIAEAYDVLSDPR 13 0 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 151.15 0.00010374 78828000 98323 105000 59161 76159 74081 97405 72621 94838 199730 FALSE TRUE 85329.36643 104310.2481 87771.45748 93452.06497 72606.93304 101152.2334 65578.2266 74557.63173 176118.1469 0.484500705 0.592274277 0.498366915 0.530621441 0.412262645 0.574343048 0.372353603 0.423338725 1 17.42618404 1.234510425 24.99979025 1.00000075 0.483299698 0.843428848 0.069588339 46.45651826 286712.3904 0.130592668 0.017507916 17.15972899 -1.234510425 -0.516701051 EIAIVHS(ph)DAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIAIVHSDAEK 11 0 Q9H307 Q9H307 PNN Pinin 1 EIAIVHS(1)DAEK 169.04 1.12E-05 211150000 125830 76198 108820 148310 88115 75454 90542 116020 665920 TRUE FALSE 109201.2467 75697.45032 161445.716 181986.0523 86361.68389 78356.76421 81761.25078 91210.02587 587195.6962 0.185970789 0.128913496 0.27494363 0.309924023 0.14707479 0.133442334 0.139240208 0.155331564 1 19.16348187 1.237377071 24.99998748 1.000000976 0.183146155 0.945748591 0.061392731 6.74859769 142488.2363 0.097271816 0.016223356 17.2733698 -1.237377071 -0.816854822 EIAIVHS(ph)DAEKEQEEEEQKQEMEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIAIVHSDAEKEQEEEEQKQEMEVK 25 2 Q9H307 Q9H307 PNN Pinin 1 EIAIVHS(1)DAEKEQEEEEQKQEMEVK 116.28 0.00068787 110560000 119200 51208 90562 72795 47278 37773 75750 92476 188950 TRUE FALSE 103447.418 50871.61128 134358.0861 89324.21735 46337.2603 39226.15175 68403.77666 72700.72705 166612.5463 0.620886124 0.305328815 0.806410376 0.536119394 0.278113872 0.235433361 0.410555977 0.436346054 1 17.34613752 1.237859741 24.97547222 1.000000643 0.447479365 0.502776679 0.170652567 14.86157662 529197.5692 0.246994543 0.042460115 17.29257791 -1.237859741 -0.552521278 EIAVHIGDRDNAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIAVHIGDRDNAVR 14 1 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 ; 98.676 0.001492 295310000 273670 287540 182449 136083 226410 300630 220900 219830 151383 FALSE TRUE 237503.8161 285651.1308 270681.9467 166982.725 221904.884 312195.4306 199477.152 172821.0652 133486.6742 1.779232403 2.139922449 2.027782535 1.250931796 1.662374805 2.338776005 1.494360042 1.294669047 1 17.0263362 1.771524299 2.355065594 1.078515459 1.848676842 0.489876876 0.301534008 0.24594787 2.67652292 0.266680208 0.087596141 59.0914027 -1.771524299 0.770161383 EIDCLS(ph)PEAQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIDCLSPEAQK 11 0 Q32MZ4-2;Q32MZ4;C9JTC6;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 EIDCLS(1)PEAQK;EIDCLS(1)PEAQK 192.4 1.48E-06 365130000 932890 950530 683690 723960 814700 734260 1038660 1137980 1117430 TRUE FALSE 809606.2229 944285.9058 1014324.771 888346.183 798489.0639 762507.4573 937930.9131 894631.8328 985328.6984 0.82166106 0.95834609 1.029427817 0.901573439 0.810378369 0.773861006 0.951896473 0.90795268 1 19.91024555 1.027375887 1.631589021 1.093765152 0.893181012 0.162650579 0.076351727 4.037714257 6.26228867 1.5384025 0.023080377 10.65064444 -1.027375887 -0.200584139 EIDDEANSYFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIDDEANSYFQR 12 0 A5YKK6-3;A5YKK6-2;A5YKK6;A5YKK6-4;H3BR89;H3BMH0 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 151.07 0.00015972 96994000 143730 128430 74580 97468 139760 104680 132660 145560 158340 FALSE TRUE 124735.7163 127586.3349 110647.1375 119599.5991 136979.0494 108707.1073 119794.6536 114433.1267 139621.2256 0.893386488 0.913803287 0.792480778 0.85660041 0.981076114 0.778585827 0.857997436 0.819596922 1 17.09115875 EIDDTYIEDAADVDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIDDTYIEDAADVDAR 16 0 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 0 231.06 3.92E-15 67912000 57611 43222 33637 39351 51790 49458 50391 52004 52171 FALSE TRUE 49997.56038 42938.07184 49903.96571 48286.24599 50759.48033 51360.68126 45504.08858 40883.3493 46003.40381 1.086823066 0.933367279 1.08478855 1.049623332 1.103385318 1.116453936 0.989146124 0.888702703 1 15.48945299 2.016728956 7.62769067 0.936977109 1.058553667 0.436613368 0.05667522 0.128485155 38.78449611 0.023794304 0.015540335 103.9271351 -2.016728956 0.121576558 EIDKNDHLYILLSTLEPTDAGILGTTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIDKNDHLYILLSTLEPTDAGILGTTK 27 1 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 0 56.298 0.044714 75301000 138300 116000 81754 121090 112850 72091 144010 195140 133170 FALSE TRUE 120023.3046 115237.9884 121290.5079 148585.3352 110604.5058 74864.38742 130043.9324 153410.8296 117426.7943 1.022111736 0.981360251 1.032903168 1.265344389 0.941901773 0.637540928 1.107446841 1.306438028 1 16.84140211 2.008189439 24.99214165 1.184658011 0.983749352 0.162207835 0.167905294 280.0940149 854774.1774 0.071113993 0.047855823 101.9035794 -2.008189439 -0.200908659 EIDLLLGQTDDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIDLLLGQTDDTR 13 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 93.011 0.013517 25040000 45126 34884 28439 35595 36021 37761 35825 44951 44186 FALSE TRUE 39162.48477 34654.84471 42192.19552 43677.38879 35304.25257 39213.6901 32350.69701 35338.57846 38962.38142 1.005135809 0.8894437 1.082895706 1.121014353 0.906111261 1.006450034 0.830305947 0.906992262 1 15.24979424 3.190211751 24.99999293 0.923448301 1.019129838 0.268029644 0.077069413 159.2729575 82355.37119 0.024044165 0.027263578 1549.571968 -3.190211751 0.095681537 EIDNFYPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EIDNFYPER 9 0 Q8TE77;Q8TE77-2;Q8TE77-3;A0A087WWG1;Q8TE77-5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ;;; 178.55 0.00011826 1511890000 1798850 1764450 1158970 1299480 1691300 1744060 1723780 1903710 1850270 FALSE TRUE 1561127.415 1752859.212 1719451.769 1594546.795 1657646.439 1811155.117 1556608.081 1496616.431 1631533.188 0.956846864 1.074363197 1.053887093 0.977330285 1.016005344 1.110093947 0.954076872 0.917306765 1 20.6377969 2.043530956 24.77389166 0.947630224 1.031305806 0.340628594 0.048218398 115.5068796 65735.55314 0.019053983 0.012846184 110.542926 -2.043530956 0.083675582 EIDVDAVASDGVVAAIAISEHVENAGVHSGDATLVTPPQDITAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIDVDAVASDGVVAAIAISEHVENAGVHSGDATLVTPPQDITAK 44 0 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 210.21 1.65E-36 35243000 32122 24925 8139.5 20743 23987 21316 25001 36446 26850 FALSE TRUE 27876.99631 24761.26603 12075.78942 25453.01519 23509.70563 22136.04031 22576.40687 28652.30652 23675.82359 1.177445685 1.045846027 0.51004728 1.07506356 0.992983646 0.934963898 0.953563739 1.210192601 1 14.53112699 1.762765112 25 1.115330483 0.947255517 0.103438726 0.180977414 27.27888645 28200.71711 0.095555248 0.045890188 57.91153979 -1.762765112 -0.168074966 EIEAWIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EIEAWIYR 8 0 A0A0A0MRB5;Q8WXG6-6;Q8WXG6-8;Q8WXG6-5;Q8WXG6-4;Q8WXG6-7;Q8WXG6-3;Q8WXG6-2;Q8WXG6;C9J6B0 A0A0A0MRB5 MADD MAP kinase-activating death domain protein 0 ;; 103.92 0.010888 174867000 230922 252485 164734 184043 218878 247429 220789 278159 247638 FALSE TRUE 200405.0726 250826.4094 244399.9134 225832.7761 214522.756 256947.7537 199376.9168 218676.8625 218362.5178 0.917763152 1.148669708 1.119239309 1.034210351 0.982415656 1.176702652 0.913054671 1.001439554 1 17.73636571 2.216673969 24.99980176 0.975300774 1.064615403 0.227037923 0.079601236 352.5352754 402676.9199 0.030999727 0.020920021 164.6925558 -2.216673969 0.089314629 EIEDFDSLEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EIEDFDSLEALR 12 0 P46060;B0QYT5;B0QYT4 P46060 RANGAP1 Ran GTPase-activating protein 1 0 ;;; 236.35 1.05E-15 551620000 1315980 1103740 866320 1126220 1101670 1108130 1082550 1279700 1605570 FALSE TRUE 1142069.909 1096489.459 1285275.25 1381945.464 1079748.922 1150760.478 977564.4676 1006046.114 1415761.344 0.806682506 0.774487497 0.90783327 0.976114703 0.762663091 0.812820948 0.690486763 0.710604311 1 20.43314666 EIEELKELLPEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIEELKELLPEIR 13 1 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 79.875 0.01762 25704000 133840 90139 51951 55870 70881 57653 95251 118770 34747 FALSE TRUE 116152.7049 89546.87097 77074.67737 68556.13742 69470.60678 59870.94822 86013.57268 93371.95977 30639.24924 3.790977513 2.92261962 2.515553718 2.237526673 2.26737301 1.95406055 2.80730027 3.047462391 1 14.90309333 4.693320396 1.540846793 2.332900825 4.266819902 0.45476258 0.545422786 1.007258175 2.412850884 0.152641837 2.880910567 49353.77716 -4.693320396 1.933919077 EIEENSR ddPTM_MDA-MB-175_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 ; 155.82 0.0036884 501990000 692720 704550 511380 523160 520260 767540 674890 709300 663520 FALSE TRUE 601175.2969 699921.7647 758685.0785 641951.474 509907.8439 797067.7605 609439.2717 557621.7148 585079.4215 1.027510582 1.196285049 1.296721523 1.097203987 0.87151902 1.362324039 1.041635117 0.953070121 1 19.15827295 2.008684569 24.9915505 0.980433789 1.142515889 0.211022974 0.135333507 275.3746574 792441.514 0.054721542 0.036831368 102.0198238 -2.008684569 0.1620821 EIEHVMYHDWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIEHVMYHDWR 11 0 P82930;C9JJ19 P82930 MRPS34 "28S ribosomal protein S34, mitochondrial" 0 171.05 8.67E-06 155010000 43223 56739 27984 55963 70570 70904 44209 57390 58671 FALSE TRUE 37510.97104 56366.27777 41517.156 68670.25449 69165.79507 73631.72276 39921.61798 45117.59511 51734.98122 0.725060107 1.089519633 0.802496783 1.327346659 1.336925102 1.423248275 0.77165618 0.872090683 1 15.65885249 3.768519851 24.94521264 1.095486947 0.894074925 0.205951338 0.225713702 1534.948862 1278052.626 0.067282039 0.116516656 5868.40192 -3.768519851 -0.201412022 EIEIDIEPTDKVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EIEIDIEPTDKVER 14 1 Q15843;F8VSA6;E9PS38;S4R3E9;E9PL57 Q15843 NEDD8;NEDD8-MDP1 NEDD8 0 ;;; 236.4 2.65E-17 6350810000 11187840 8692690 6393890 7142950 8425600 7046980 10165160 11698830 9128120 FALSE TRUE 9709338.598 8635587.147 9485996.59 8764865.971 8257947.044 7318081.881 9179344.348 9197126.245 8049004.052 1.206278259 1.072876481 1.178530478 1.08893795 1.025958863 0.90919098 1.140432318 1.142641522 1 22.94037885 3.523012663 5.514664255 1.056474155 1.143796315 0.295734076 0.0748697 0.335423678 24.67083735 0.022466057 0.032815494 3334.361348 -3.523012663 0.08732216 EIELTHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIELTHR 7 0 O43395;O43395-3 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 0 ; 152.39 0.0045174 110540000 320520 280590 189704 225823 278480 252326 259709 298850 270990 FALSE TRUE 278162.4699 278746.7858 281445.4889 277099.5636 272938.7928 262033.1445 234522.4612 234943.2532 238953.8709 1.164084385 1.166529694 1.177823518 1.15963622 1.142223776 1.09658464 0.981454957 0.983215933 1 17.86637261 2.442536841 2.066004805 0.983380685 1.165028889 0.977942213 0.011875511 0.040921627 0.357713548 0.005666649 0.00401635 277.0364038 -2.442536841 0.181648204 EIENGNSFDSS(ph)GDELDVHQLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIENGNSFDSSGDELDVHQLLR 22 0 Q6ZN28 Q6ZN28 MACC1 Metastasis-associated in colon cancer protein 1 1 EIENGNSFDS(0.03)S(0.97)GDELDVHQLLR;EIENGNSFDS(0.004)S(0.996)GDELDVHQLLR 215.53 9.13E-26 143055000 92761 77336 54194 76143 69039 76894 65016 91867 102173 TRUE FALSE 80502.39882 76827.97472 80402.39967 93432.43192 67665.25897 79852.16194 58710.75833 72221.95696 90094.22434 0.893535622 0.852751387 0.892425683 1.037052404 0.751049909 0.886318324 0.651659513 0.801626935 1 16.459147 3.211436501 24.9983403 0.806991959 0.91231963 0.19371489 0.100380696 345.6099591 318522.7059 0.030237402 0.03429468 1627.183384 -3.211436501 0.105327671 EIENMILNDPDFQHEDLNFLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 EIENMILNDPDFQHEDLNFLTR 22 0 Q15067-2;Q15067;I3L0T4;K7ELT1 Q15067-2;K7ELT1 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ;;;;;;;;;;; 274.97 2.02E-45 2287411000 1594040 1253634 982292 1339247 1357577 1839498 1101912 1600424 1327609 FALSE TRUE 1383383.575 1245398.796 1457331.697 1643343.5 1330563.874 1910264.678 995048.7438 1258185.782 1170660.576 1.181711935 1.063842775 1.244879794 1.40377453 1.136592365 1.631783556 0.849989112 1.074765656 1 20.15889141 2.198146098 24.9999786 0.990514454 1.265312523 0.424989721 0.164983074 154.1108369 95330.22251 0.065357233 0.044064412 157.8142074 -2.198146098 0.274798069 EIENYPHFFLDFENAQPTEGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIENYPHFFLDFENAQPTEGER 22 0 Q9H0Q0;C9JPE5;C9IYV6 Q9H0Q0 FAM49A Protein FAM49A 0 172.02 5.36E-12 39938000 50567 57921 35629 34655 50026 55639 50680 62414 54072 FALSE TRUE 43884.44283 57540.51314 52859.30357 42523.94742 49030.58047 57779.46833 45765.0614 49067.25181 47679.66976 0.920401568 1.206814423 1.108634012 0.891867491 1.028333055 1.211826102 0.959844345 1.029102174 1 15.54108662 EIEQEAAVELSQLRDPQHDLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EIEQEAAVELSQLRDPQHDLDR 22 1 P47985 P47985 UQCRFS1 "Cytochrome b-c1 complex subunit Rieske, mitochondrial;Cytochrome b-c1 complex subunit 11" 0 ;;; 229.2 1.81E-26 396070000 131401 129708 84863 132384 142135 187814 97786 161931 68827 FALSE TRUE 114036.0249 128855.9396 125903.0306 162443.8106 139306.7916 195039.3261 88302.72877 127303.3158 60690.35047 1.878981157 2.123170135 2.074514806 2.676600305 2.295369701 3.213679351 1.454971476 2.097587422 1 15.88917953 1.041672915 1.251853476 1.03E-11 2.313327215 0.419284356 0.460477731 2.257038822 2.154806766 7.672799825 0.136446519 11.00710008 -1.041672915 2.313327215 EIESEIDS(ph)EEELINK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIESEIDSEEELINK 15 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 1 EIESEIDS(1)EEELINK 115.82 0.00052204 22202000 81547 54233 48843 49213 63507 69962 64975 82540 79407 TRUE FALSE 70770.35734 53876.73985 72463.63817 60387.56382 62243.33495 72653.48341 58673.7345 64889.46333 70019.59492 1.010722176 0.769452321 1.034905133 0.862438063 0.88894166 1.037616449 0.837961639 0.926732915 1 16.0954711 EIEVGGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EIEVGGGR 8 0 P62081;B5MCP9 P62081 RPS7 40S ribosomal protein S7 0 ;;; 237.45 2.81E-08 2334090000 1968670 1869030 1338270 1583750 1700040 2014590 1763060 2133080 2593090 FALSE TRUE 1708505.272 1856752.219 1985461.848 1943364.644 1666212.53 2092092.581 1592078.713 1676937.442 2286537.854 0.747201831 0.81203651 0.868326691 0.849915797 0.728705421 0.914960833 0.696283558 0.73339588 1 21.12473337 0.575480599 0.006080138 1.320604212 0.312789446 0.011206106 0.094368548 564317.9723 700.6444715 60061.55597 56132.39278 3.762535439 -0.575480599 -1.007814767 EIEVGGGRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EIEVGGGRK 9 1 P62081;B5MCP9 P62081 RPS7 40S ribosomal protein S7 0 ;;; 96.034 0.012253 5372910000 3700940 3175990 1835080 2163590 2673770 2629580 3745100 4032680 1445880 FALSE TRUE 3211851.402 3155126.713 2722530.826 2654866.178 2620567.208 2730741.644 3381900.778 3170322.764 1274949.714 2.519198497 2.47470679 2.135402516 2.082330111 2.055427897 2.141842627 2.652575817 2.486625732 1 20.28200891 1.234153958 24.99991853 0.999998046 2.32008886 0.796714453 0.209308184 66.35851048 376416.8917 0.442320196 0.057496044 17.14565015 -1.234153958 1.320090814 EIFAPLDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIFAPLDER 9 0 F8VZZ2;Q8NFX7-2;Q8NFX7 F8VZZ2 STXBP6 Syntaxin-binding protein 6 0 87.639 0.030999 76572000 67108 66476 38638 50817 78449 75304 63119 74029 65308 FALSE TRUE 58239.50777 66039.31478 57323.46604 62355.77654 76888.01838 78200.99361 56997.7291 58198.47444 57587.36264 1.011324449 1.146767481 0.995417456 1.08280313 1.335154361 1.357954072 0.98976106 1.010611908 1 15.81346463 EIFDLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIFDLIR 7 0 Q9Y3D0;J3KS95;H3BNV7 Q9Y3D0 FAM96B Mitotic spindle-associated MMXD complex subunit MIP18 0 ; 81.297 0.064172 54458000 153425 182241 117166 130350 192643 195732 174047 198283 194896 FALSE TRUE 133149.4975 181043.8469 173827.8695 159947.9598 188809.7812 203261.9367 157167.9487 155881.7235 171855.6169 0.77477536 1.053464822 1.011476218 0.930711272 1.098653536 1.182748288 0.914534838 0.907050501 1 17.39083748 5.84910335 14.63248916 0.987131334 0.711746358 0 0.113442632 0 0 0.025562441 0 706485.6583 -5.84910335 -0.275384975 EIFDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EIFDSR 6 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 ;;; 138.48 0.028581 23325900000 21364400 23222200 14648600 13489900 19251100 21824000 19059900 20876000 22765500 FALSE TRUE 18541040.41 23069651.84 21732711.96 16552987.98 18868040.77 22663583.4 17211473.83 16411829.86 20074188.52 0.923625898 1.149219646 1.0826197 0.824590641 0.939915492 1.12899126 0.857393255 0.817558819 1 24.25883833 3.091207105 0.534819433 0.881325361 1.056308564 0.088237973 0.115242512 1.992024655 1.770638862 0.179744665 0.209522928 1233.693012 -3.091207105 0.174983202 EIFDSRGNPTVEVDLFTSKGLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIFDSRGNPTVEVDLFTSKGLFR 23 2 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 125.04 3.12E-05 328720000 197870 143630 139530 228180 130620 160150 152560 243790 137250 FALSE TRUE 171720.9782 142686.4851 207007.1747 279991.7565 128020.9176 166311.0741 137764.7547 191657.4057 121024.4614 1.418894794 1.178988805 1.710457311 2.313513759 1.057810265 1.37419388 1.138321569 1.583625356 1 16.88493915 EIFTSLEYGPVPESHACALAWLDTQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIFTSLEYGPVPESHACALAWLDTQDR 27 0 Q8IZ83;Q8IZ83-3;Q8IZ83-2 Q8IZ83 ALDH16A1 Aldehyde dehydrogenase family 16 member A1 0 147.26 2.34E-13 0 62377 56430 39766 44003 58305 51089 68368 67270 52028 FALSE TRUE 54133.72141 56059.30761 58996.97061 53994.55369 57144.84457 53054.42689 61737.68188 52884.834 45877.30911 1.179967231 1.22193975 1.285972777 1.176933755 1.24560149 1.156441559 1.345712795 1.152744898 1 15.48549315 1.338581867 3.569767232 0.991628108 1.228924371 0.629643685 0.055965732 0.148401934 2.734788475 0.079449428 0.013196831 21.80629421 -1.338581867 0.237296263 EIFVDFAPFLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIFVDFAPFLSR 12 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6;Q5T321;A0A0D9SF28;F5GXV7;Q8NFP9 A0A494C1L5;Q5T321 LRBA;NBEA Lipopolysaccharide-responsive and beige-like anchor protein;Neurobeachin 0 ; 189.58 1.80E-05 860390000 537570 536330 368210 341710 519780 565810 529890 561430 531140 FALSE TRUE 466528.7625 532806.8129 546277.5876 419300.4782 509437.3949 587577.0768 478501.3494 441372.5636 468349.2343 0.996113004 1.137627168 1.166389411 0.895273116 1.087729749 1.25457038 1.021676378 0.942400523 1 18.83722518 2.005562807 24.98802471 0.971571718 1.090682277 0.210841642 0.096373483 207.7496429 933202.7479 0.039789145 0.026735003 101.289122 -2.005562807 0.119110559 EIGDLWGHLHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIGDLWGHLHDR 12 0 O75146;O75146-2 O75146 HIP1R Huntingtin-interacting protein 1-related protein 0 ; 131.13 0.00011807 401660000 367880 337670 259900 284800 348650 400570 363210 390960 408670 FALSE TRUE 319263.7259 335451.8235 385588.5093 349468.1929 341712.5471 415980.1871 327985.9501 307356.2465 360357.4982 0.885963876 0.930886204 1.070016612 0.969781938 0.94825985 1.154354188 0.910168241 0.852920358 1 18.45906934 2.050637966 24.99999979 0.905628621 0.994218977 0.136492632 0.082672246 161.9143149 79936.43412 0.033381955 0.022506103 112.3667877 -2.050637966 0.088590356 EIGDVENWAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIGDVENWAR 10 0 G8JLQ3;P78537-2;P78537 G8JLQ3 BLOC1S1 Biogenesis of lysosome-related organelles complex 1 subunit 1 0 ; 131.12 0.00060176 230109000 303730 258140 170189 222281 279310 268840 252873 292700 288340 FALSE TRUE 263591.3109 256444.2613 252492.9696 272753.2984 273752.2775 279182.4488 228349.4154 230108.3828 254252.7737 1.036729343 1.008619326 0.993078526 1.072764299 1.076693377 1.09805075 0.898119663 0.905037847 1 17.95590399 2.231599719 24.99999754 0.926760566 1.045861929 0.624527538 0.041245477 104.1873778 374183.6759 0.017637737 0.012180425 170.4510648 -2.231599719 0.119101363 EIGDYIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIGDYIR 7 0 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ; 124.59 0.0096111 546860000 1859450 1605980 1057040 1238880 1707240 1689910 1597770 1861270 1629210 FALSE TRUE 1613718.971 1595430.212 1568228.08 1520186.639 1673269.264 1754921.931 1442818.511 1463251.895 1436606.65 1.123285188 1.110554661 1.091619672 1.058178757 1.16473724 1.221574417 1.004323982 1.018547349 1 20.45423367 2.200239924 24.99919411 1.00976186 1.124315495 0.631631878 0.043370224 113.9743487 74352.46356 0.01886005 0.01271569 158.5769003 -2.200239924 0.114553635 EIGTHKPLPGITVGDIGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIGTHKPLPGITVGDIGPK 19 1 Q15067-2;Q15067;Q15067-3 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ; 114.34 9.58E-05 469340000 1572690 1000310 880600 1234680 1180150 1104700 1232370 1863180 1434440 FALSE TRUE 1364855.032 993738.8977 1306461.105 1515032.965 1156667.324 1147198.524 1112854.947 1464753.456 1264862.137 1.079054382 0.785649968 1.032888144 1.197785055 0.914461181 0.906975148 0.879823116 1.158034076 1 20.27054872 1.734224107 25 1.081398888 0.97029453 0.123023554 0.119908643 0.972724464 5541.559703 0.064107967 0.030785454 54.22806493 -1.734224107 -0.111104358 EIHQDWANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EIHQDWANR 9 0 Q8WUW1;Q8WUW1-2 Q8WUW1 BRK1 Protein BRICK1 0 ;;;;; 183.67 4.49E-05 3767180000 1641430 1647230 998695 1229990 1565100 1636580 1416640 1653990 1558830 FALSE TRUE 1424510.867 1636409.238 1481667.242 1509278.029 1533957.572 1699540.292 1279254.471 1300297.11 1374546.893 1.036349414 1.19050812 1.077931389 1.098018581 1.115973256 1.236436749 0.930673575 0.945982357 1 20.3905247 2.218862274 24.99986479 0.95502164 1.124912914 0.647805729 0.058015235 137.2977437 174248.0824 0.022527258 0.01521195 165.5244961 -2.218862274 0.169891273 EIHQFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EIHQFNR 7 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;; 160.03 0.0013616 1662156000 1530870 1300110 809010 918590 1009720 1427550 1060620 1220310 1243180 FALSE TRUE 1328561.651 1291569.492 1200249.942 1127169.899 989628.5475 1482468.772 957761.2356 959356.203 1096212.677 1.21195611 1.178210688 1.094906096 1.028240161 0.902770574 1.352355071 0.873700201 0.875155181 1 20.06409629 7.999999995 0.109013619 0.692330698 2.275139234 0.261999926 0.134892444 332.5500804 3.296998144 6.841646565 79.89985449 99999998.87 -7.999999995 1.582808536 EIIDAS(ph)DKEGMS(ph)PAKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIIDASDKEGMSPAKR 16 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 EIIDAS(1)DKEGMS(1)PAKR;EIIDAS(1)DKEGMS(1)PAKR 87.511 0.0034564 1382450000 1148040 687030 584120 610600 782670 588340 890770 1063230 996970 TRUE FALSE 996323.6052 682516.8547 866602.3858 749246.0624 767096.3983 610973.8205 804383.2625 835866.5386 879109.3424 1.133332974 0.776373111 0.98577315 0.852278581 0.872583604 0.694991841 0.914997969 0.950810665 1 19.74568309 4.755206225 24.22629885 0.884330551 1.133333274 0.42109275 0.092915376 2262.291689 3292494.657 0.022861878 0.584349478 56912.31156 -4.755206225 0.249002722 EIIDASDKEGMS(ph)PAKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EIIDASDKEGMSPAKR 16 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 EIIDAS(0.003)DKEGMS(0.997)PAKR;EIIDASDKEGMS(1)PAKR;EIIDASDKEGMS(1)PAKR;EIIDASDKEGMS(1)PAKR 89.668 0.0029805 1833540000 1643840 948340 867780 960810 989470 765360 1313770 1550560 1214340 TRUE FALSE 1426602.379 942110.2921 1287441.311 1178976.596 969781.4829 794803.8945 1186360.788 1218984.81 1070782.109 1.332299417 0.8798338 1.202337339 1.101042487 0.905675837 0.742264825 1.10793856 1.138406031 1 20.03023351 4.756167529 24.30607286 1.02161688 1.332299795 0.346796953 0.138286776 3302.605489 4559087.09 0.035363172 1.019155033 57038.42559 -4.756167529 0.310682914 EIIDLVLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 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 ;;;;;;;; 219.51 1.14E-06 12023158000 5022734 4274326 3471316 4016143 4609111 4960107 4953795 5443034 6778750 FALSE TRUE 4358966.976 4246247.671 5150056.028 4928069.651 4517398.709 5150925.526 4473376.723 4279083.537 5977373.897 0.729244489 0.710386826 0.861591749 0.824453972 0.75574973 0.861737213 0.74838496 0.715880186 1 22.51108036 -0.6367513 0.018928486 1.71859164 6.88E-07 0.149474288 0.083019826 16356.61784 42.31812268 2249.230778 1638.525578 0.230806853 0.6367513 -1.718590952 EIIDTNGAGDAFVGGFLSQLVSDKPLTECIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIIDTNGAGDAFVGGFLSQLVSDKPLTECIR 31 1 P55263-3;P55263-2;P55263;P55263-4;A0A5F9ZHJ1 P55263-3 ADK Adenosine kinase 0 173.68 3.51E-13 106320000 137410 102560 69172 102680 104080 81426 111740 133020 132880 FALSE TRUE 119250.9203 101886.2766 102623.8106 125995.0634 102009.0116 84558.51091 100903.472 104574.7082 117171.0778 1.017750477 0.869551416 0.875845921 1.075308564 0.870598902 0.721667092 0.861163641 0.892495914 1 16.83825698 3.04178752 24.99996794 0.8634014 0.950417181 0.197859961 0.089337727 257.4362354 154013.232 0.027640125 0.031340924 1101.000509 -3.04178752 0.087015781 EIIELLFHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIIELLFHK 9 0 P52735-3;P52735-2;P52735 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 0 ; 88.417 0.012799 124115000 265291 248454 180797 227785 267554 216905 256681 314710 336080 FALSE TRUE 230232.1222 246821.8893 268231.0339 279507.0657 262230.1989 225249.4757 231788.1161 247411.7156 296349.0053 0.776895208 0.832875714 0.905118725 0.943168564 0.884869509 0.760081767 0.782145754 0.834866023 1 18.17693769 3.670340173 0.006448362 1.698586393 1.13E-07 0.040915018 0.075468102 82935.17155 352.3575393 45945.29209 46867.38417 4681.016511 -3.670340173 -1.69858628 EIIHELEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIIHELEK 8 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 0 97.431 0.0082369 233480000 433290 382490 294690 402440 378140 343860 423080 509260 480790 FALSE TRUE 376029.6287 379977.398 437203.0697 493820.1529 370615.7538 357088.5167 382049.7667 400358.7121 423951.5539 0.886963676 0.896275517 1.031257146 1.164803262 0.874193644 0.842286137 0.901163737 0.944350147 1 18.69353989 EIIKQEESVDPDYWEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIIKQEESVDPDYWEK 16 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y5M9;A0A2R8YE38 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 157.12 8.87E-08 209580000 970170 669270 517610 537310 617480 501280 962060 1071400 282980 FALSE TRUE 841959.5764 664873.5213 767927.9273 659314.4478 605193.3561 520564.566 868759.5693 842289.4476 249526.4268 3.374230086 2.664541507 3.077541474 2.642263011 2.425367781 2.086210157 3.481633511 3.375552075 1 17.92883309 3.729033539 21.40202473 2.633582703 3.00134802 0.093503107 0.710213727 322.0407179 723450.1999 0.198910164 0.300836965 5358.380369 -3.729033539 0.367765317 EIILDDDECPLQIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIILDDDECPLQIFR 15 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;H0Y7R8;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 0 ; 186.17 9.14E-07 64983000 66874 63840 40270 47753 63189 63193 57295 74267 69340 FALSE TRUE 58036.43146 63420.63084 59744.7067 58596.04851 61931.66253 65624.0756 51738.53972 58385.58 61142.70419 0.949196347 1.037255903 0.977135498 0.958348985 1.012903556 1.073293641 0.846193187 0.954906734 1 15.89989274 2.246844483 24.99999893 0.934471927 1.000456608 0.273795728 0.051922548 239.3777081 722423.0658 0.01928587 0.014682724 176.5405531 -2.246844483 0.065984681 EIIQDVTLHDLDVANAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIIQDVTLHDLDVANAR 17 0 Q9Y265;H7C4G5;Q9Y265-2;E7ETR0;H7C4I3 Q9Y265 RUVBL1 RuvB-like 1 0 ; 187.31 4.74E-10 386240000 208458 218470 194891 226860 210410 237440 188111 231990 579460 FALSE TRUE 180909.7471 217034.8562 289140.9395 278372.0303 206223.2527 246574.4704 169868.0242 182380.7438 510956.8989 0.35406068 0.424761573 0.565881271 0.544805307 0.403602052 0.482573914 0.332450789 0.356939586 1 18.96284207 1.233882787 24.99993745 1.000000855 0.432841708 0.836877203 0.078651765 61.07274407 326353.405 0.165947292 0.021093182 17.13494786 -1.233882787 -0.567159147 EIIQDVTLHDLDVANARPQGGQDILSMMGQLMKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIIQDVTLHDLDVANARPQGGQDILSMMGQLMKPK 35 2 Q9Y265;H7C4G5;Q9Y265-2;E7ETR0;H7C4I3 Q9Y265 RUVBL1 RuvB-like 1 0 161.55 9.30E-15 198800000 214150 164430 136180 143510 142590 114620 199420 240980 160370 FALSE TRUE 185849.5349 163349.8485 202037.1035 176096.1389 139752.738 119029.5056 180080.2791 189448.3023 141411.2413 1.314248664 1.155140475 1.428720246 1.245276806 0.988271772 0.841725909 1.273450947 1.339697612 1 17.10953728 3.459771367 23.61304825 1.121096897 1.29362215 0.275262925 0.156065255 214.556047 292006.789 0.049901609 0.064442541 2882.513614 -3.459771367 0.172525254 EIISHDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 111.95 0.0031354 113230000 299310 316010 182100 222630 281370 416350 215360 278490 327990 FALSE TRUE 259755.4251 313934.1095 270164.1691 273181.5442 275771.2875 432367.2539 194474.4203 218937.0807 289215.3958 0.898138304 1.08546818 0.934127896 0.944560864 0.95351524 1.494966244 0.672420705 0.757003548 1 18.14178483 EIKDILIQYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIKDILIQYDR 11 1 P62249;M0R210 P62249 RPS16 40S ribosomal protein S16 0 62.891 0.071231 111560000 174010 176420 77291 101080 162640 139640 198710 215910 51539 FALSE TRUE 151014.1376 175261.0854 114669.1861 124031.7589 159403.7822 145012.0412 179439.1348 169739.3267 45446.11813 3.322927102 3.85645887 2.523189897 2.729204693 3.507533509 3.190856494 3.948393002 3.734957653 1 15.47186945 1.233131042 24.99994551 0.999996273 3.367901091 0.722776285 0.45761777 100.7901039 464027.3969 1.008797464 0.119935175 17.10531364 -1.233131042 2.367904818 EILDESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EILDESLR 8 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;; 164.53 0.00076672 1161940000 2332720 2238310 1573570 1701640 2280180 2192830 2162470 2455380 2244180 FALSE TRUE 2024445.142 2223606.394 2334553.715 2088023.37 2234808.879 2277189.589 1952753.992 1930316.095 1978875.597 1.023027999 1.123671643 1.179737483 1.05515646 1.129332679 1.15074924 0.986799774 0.975461064 1 20.91624949 2.22720113 24.98525353 0.984902873 1.11240567 0.626061117 0.044726033 130.0652405 286076.7055 0.017752009 0.01208745 168.733428 -2.22720113 0.127502796 EILDHQDGNVEDDGLTGLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EILDHQDGNVEDDGLTGLLR 20 0 Q70CQ2-3;Q70CQ2-2;Q70CQ2;A0A0C4DG73 Q70CQ2-3 USP34 Ubiquitin carboxyl-terminal hydrolase 34;Ubiquitin carboxyl-terminal hydrolase 0 183.06 4.51E-17 41741000 42020 35953 24433 31081 38941 42075 38372 40200 42662 FALSE TRUE 36466.95053 35716.82238 36248.88052 38138.41609 38166.15029 43693.65248 34650.68935 31603.54284 37618.54696 0.969387536 0.949447155 0.963590661 1.01381949 1.014556738 1.161492296 0.921106532 0.840105357 1 15.1991565 2.025169648 24.99998367 0.900223803 1.010037286 0.266411048 0.069939436 245.2093524 243555.4184 0.029118738 0.019631061 105.9667582 -2.025169648 0.109813483 EILDKFTEEVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EILDKFTEEVVK 12 1 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ; 184.21 1.33E-05 832830000 1434170 1122130 811350 969940 1000820 804570 1472260 1744860 942320 FALSE TRUE 1244640.801 1114758.654 1203721.574 1190179.702 980905.6401 835522.3285 1329480.452 1371735.268 830920.0031 1.497906894 1.341595641 1.448661206 1.432363762 1.180505508 1.005538831 1.600010166 1.650863215 1 19.66435006 7.821408102 1.032757918 1.35612646 111.3312849 0.04177473 0.221633083 7030.868883 12.27984456 0.072675922 1828144.431 66283907.47 -7.821408102 109.9751585 EILEVLDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EILEVLDGR 9 0 Q6P1N0-2;Q6P1N0;K7EMP1 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 0 ;;; 116.37 0.0030814 106879000 307220 309489 210852 268626 295284 318803 309929 345383 351082 FALSE TRUE 266620.0986 307455.9464 312820.7325 329621.639 289408.4261 331067.5577 279872.1333 271525.5332 309577.4859 0.861238658 0.993146984 1.010476364 1.064746805 0.93484972 1.069417425 0.904045501 0.877084238 1 18.23994103 0.94129625 22.16554151 1.725886946 0.963718622 0.023450308 0.072136599 863.9884508 664821.3222 97240.21318 0.017772624 8.735670609 -0.94129625 -0.762168325 EILFYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EILFYDR 7 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ;;; 138.9 0.0063773 611888000 785931 645768 428368 507755 645684 690438 636464 701255 669700 FALSE TRUE 682068.2271 641525.9075 635528.1976 623048.5333 632836.1517 716999.5966 574739.8192 551297.0754 590528.8289 1.155012581 1.086358322 1.076201815 1.055068784 1.071643111 1.214165273 0.973262932 0.93356505 1 19.17164797 2.105511908 9.40154782 0.959521085 1.102814335 0.644349517 0.049076751 0.166973199 13.60346605 0.019803077 0.01334278 127.500506 -2.105511908 0.14329325 EILFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EILFYR 6 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 ; 105.42 0.076756 202150000 525680 657130 362980 435010 662350 795400 573080 567750 535700 FALSE TRUE 456210.0561 652813.2698 538518.3421 533785.6692 649170.5309 825999.5527 517502.7898 446341.0807 472370.1563 0.965789329 1.38199516 1.140034642 1.13001565 1.374283541 1.748627727 1.095545057 0.944896867 1 18.84955829 2.010148699 24.99222007 0.98402493 1.295530827 0.299238449 0.205768174 241.4310885 594546.6634 0.085674513 0.057691735 102.364342 -2.010148699 0.311505897 EILGTAQSVGCNVDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EILGTAQSVGCNVDGR 16 0 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ; 277.31 5.83E-35 275410000 256850 205190 129169 173281 213880 183587 206839 253410 246280 FALSE TRUE 222906.6217 203842.0934 191635.5604 212627.0995 209624.2064 190649.7107 186779.7856 199220.2435 217165.059 1.026438704 0.93865051 0.882441961 0.979103639 0.96527594 0.877902327 0.860082126 0.917367851 1 17.72843247 2.755775293 24.73708747 0.909349981 0.954218245 0.155433246 0.050606905 1407.764888 2022921.686 0.016701603 0.016662525 569.8693413 -2.755775293 0.044868263 EILHNTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EILHNTEK 8 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ;;; 124.23 0.0013137 1365070000 2633980 2214410 1133050 1894230 2070560 2030630 2518390 2900190 2855830 FALSE TRUE 2285892.869 2199863.395 1680996.77 2324343.873 2029359.907 2108749.65 2274156.925 2280006.938 2518217.031 0.907742598 0.873579746 0.667534509 0.923011736 0.805871727 0.837397899 0.90308218 0.905405257 1 21.2639712 0.901866368 0.786527407 1.189800476 0.83024722 0.351857094 0.070827442 4.584688044 1.537013625 1.645572406 0.027704424 7.977491826 -0.901866368 -0.359553256 EILKEQENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EILKEQENR 9 1 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ; 118.4 0.00090745 559940000 1830950 1468310 721600 791270 1470170 1220730 1830420 1927970 175192 FALSE TRUE 1588985.318 1458664.575 1070568.174 970939.9473 1440916.493 1267692.273 1652906.15 1515688.619 154481.0013 10.28595947 9.442355774 6.930096027 6.285173833 9.327467332 8.206137079 10.69973742 9.811488829 1 17.2370699 4.412042932 5.696391292 7.903741867 10.09401876 0.108631341 2.684551941 0.452478677 27.24743757 0.667124439 1.862041274 25825.15473 -4.412042932 2.190276894 EILNLIHLEELSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EILNLIHLEELSLR 14 0 Q96CX6 Q96CX6 LRRC58 Leucine-rich repeat-containing protein 58 0 ; 128.9 7.11E-05 162007000 172559 195530 111379 160457 183964 180941 186195 193251 179514 FALSE TRUE 149754.8909 194245.5506 165242.2569 196891.2143 180303.4763 187901.9174 168137.8376 151925.7775 158292.0594 0.946066982 1.227133889 1.04390743 1.243847702 1.139055724 1.187058391 1.062200076 0.95978142 1 17.27222936 1.979212094 4.208198584 0.982776561 1.136902306 0.337689521 0.087050269 0.20607936 8.366478682 0.040812419 0.022048601 95.32615905 -1.979212094 0.154125745 EILRPWHAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EILRPWHAAR 10 1 E7ESY4;Q13330-3;Q13330;H0Y4T7;F8W9Y9 E7ESY4 MTA1 Metastasis-associated protein MTA1 0 79.201 0.016652 154740000 170280 182750 90800 127970 214820 237040 132930 177320 131430 FALSE TRUE 147777.0666 181549.5032 134711.1837 157027.5444 210545.5023 246159.0822 120038.4691 139401.4979 115892.4951 1.275121969 1.566533735 1.162380563 1.354941441 1.816731118 2.124029532 1.035774309 1.202851813 1 16.82242762 EILSEVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EILSEVER 8 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;; 174.52 0.00063155 2445000000 2426990 2325230 1585790 1933820 2170520 2357400 2336740 2661880 2239570 FALSE TRUE 2106257.122 2309955.411 2352683.348 2372923.388 2127330.899 2448090.703 2110123.314 2092657.677 1974810.586 1.066561592 1.169709858 1.191346332 1.201595436 1.077232882 1.239658487 1.068519345 1.059675136 1 20.91328285 2.063806822 8.425849949 1.042995869 1.158076759 0.502195911 0.054605153 0.212201098 25.22868872 0.021379034 0.014377375 115.8262037 -2.063806822 0.11508089 EILSPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EILSPLR 7 0 A0A140T9S5;Q9Y334-2;Q9Y334 A0A140T9S5 VWA7 von Willebrand factor A domain-containing protein 7 0 ;;; 114.54 0.013684 895920000 1339810 1396100 929460 964850 1306110 1370050 1291410 1333900 1321460 FALSE TRUE 1162750.714 1386928.927 1378949.965 1183933.939 1280120.966 1422756.71 1166169.257 1048655.865 1165238.504 0.997864995 1.190253259 1.183405766 1.016044299 1.098591371 1.221000426 1.000798766 0.899949548 1 20.15219385 2.041305864 7.857040519 0.944938406 1.118390929 0.48381678 0.074820492 0.165900061 27.16110024 0.030038447 0.020081501 109.9780116 -2.041305864 0.173452523 EILTLLQGVHQGAGFQDIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EILTLLQGVHQGAGFQDIPK 20 0 E9PGT1;Q15631;H7C1D4;Q15631-2 E9PGT1 TSN Translin 0 217.36 1.06E-24 141720000 156650 112920 86343 132050 114690 84597 140770 151780 168370 FALSE TRUE 135948.3056 112178.2211 128098.7636 162033.9708 112407.8934 87851.50133 127118.1471 119323.0282 148465.4904 0.9156896 0.755584485 0.862818445 1.091391476 0.757131459 0.591730112 0.856213432 0.803708847 1 17.1797681 EILWRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EILWRPK 7 1 P08243-2;P08243;P08243-3 P08243-2 ASNS Asparagine synthetase [glutamine-hydrolyzing] 0 ; 80.098 0.028121 862340000 1778150 1421990 848560 1065450 1243790 1027770 1459050 1656150 1319760 FALSE TRUE 1543162.972 1412648.854 1258926.454 1307376.707 1219041.012 1067308.977 1317551.556 1301995.211 1163739.476 1.326038176 1.213887543 1.081794061 1.123427308 1.047520547 0.917137382 1.132170544 1.118802994 1 20.15033669 4.596051924 1.251098174 1.058475393 1.411029356 0.674292756 0.063697727 0.724594206 1.191473308 0.019953714 0.3091479 39450.44661 -4.596051924 0.352553962 EINYILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EINYILR 7 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 86.953 0.045825 43718000 150380 148040 88738 112760 160910 159410 138660 164750 161740 FALSE TRUE 130506.902 147067.5155 131651.9936 138363.8814 157708.2058 165542.6059 125212.7745 129519.4946 142619.2815 0.915071936 1.03118957 0.923100946 0.97016252 1.105798628 1.160730893 0.877951237 0.908148557 1 17.12180951 EIPFNEDPNPNTHS(ph)SGPST(ph)PLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIPFNEDPNPNTHSSGPSTPLK 22 0 Q86YS7;H0YFE9;Q86YS7-3 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 2 EIPFNEDPNPNT(0.022)HS(0.532)S(0.444)GPS(0.067)T(0.935)PLK 116.24 0.00030145 157540000 111900 142550 133710 241070 229030 204020 249100 331190 564650 TRUE FALSE 97112.13148 141613.5797 198372.6032 295808.628 224472.7511 211868.7814 224942.3203 260367.5958 497897.7203 0.195044338 0.284423033 0.398420389 0.594115249 0.45084109 0.425526715 0.451784194 0.522933898 1 18.92548988 -0.016061057 1.152462803 10 0.39567511 0.765639978 0.104077919 13.35259719 1.341589919 292.2321698 0.034740402 0.96369353 0.016061057 -9.60432489 EIPFNEDPNPNTHSS(ph)GPST(ph)PLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIPFNEDPNPNTHSSGPSTPLK 22 0 Q86YS7;H0YFE9;Q86YS7-3 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 2 EIPFNEDPNPNTHS(0.021)S(0.948)GPS(0.044)T(0.987)PLK 151.12 9.04E-08 179490000 122880 182900 138260 259590 267100 246310 287680 349210 640360 TRUE FALSE 106641.0967 181698.5179 205122.9985 318533.8771 261785.2326 255785.7051 259780.8379 274534.1591 564657.3703 0.188859833 0.321785436 0.36326985 0.564118869 0.463617844 0.452992768 0.46006809 0.486196008 1 19.10701619 0.099999083 1.303388143 10 0.399564041 0.776872972 0.099867476 11.7795817 1.483527606 291.9330044 0.031459662 1.258922754 -0.099999083 -9.600435959 EIPFNEDPNPNTHSSGPST(ph)PLKNQTYSFS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIPFNEDPNPNTHSSGPSTPLKNQTYSFSPSK 32 1 Q86YS7;H0YFE9;Q86YS7-3 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 2 EIPFNEDPNPNT(0.007)HS(0.038)S(0.096)GPS(0.409)T(0.441)PLKNQT(0.023)Y(0.017)S(0.276)FS(0.596)PS(0.098)K 80.125 0.015065 79430000 22283 34278 9583 30452 69040 44540 68269 88208 26276 TRUE FALSE 19338.24509 34052.82556 14217.37085 37366.59203 67666.23907 46253.48262 61648.28289 69345.40564 23169.68121 0.834635786 1.469714894 0.613619614 1.612736562 2.920464829 1.99629344 2.660730733 2.992937408 1 14.49995057 3.452140918 5.486831415 2.404703237 1.031117286 0.509353376 0.598949426 0.130101767 11.38810443 0.16673559 0.22273422 2832.31086 -3.452140918 -1.373585952 EIPSATQS(ph)PISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EIPSATQSPISK 12 0 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 EIPSAT(0.022)QS(0.978)PISK;EIPSAT(0.011)QS(0.989)PISK;EIPS(0.002)AT(0.201)QS(0.796)PIS(0.001)K 161.04 6.97E-05 1032420000 1979310 1676440 1043559 1501080 1900820 1426205 1831070 2269770 1940580 TRUE FALSE 1717739.169 1665427.355 1548227.623 1841923.157 1862997.401 1481072.029 1653493.113 1784397.349 1711166.843 1.003840844 0.973270001 0.904778882 1.076413539 1.088729254 0.865533385 0.966295671 1.042795655 1 20.706549 3.401133219 0.004903667 1.979537965 8.84E-06 0.002578304 0.069731118 101529.0077 466.8081788 93794.42139 94641.14089 2518.449341 -3.401133219 -1.979529121 EIPSHVLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EIPSHVLSK 9 0 E5RHG8;Q15369-2;Q15369 E5RHG8 TCEB1 Transcription elongation factor B polypeptide 1 0 ;;; 126.07 0.0004839 1655140000 3438160 2994100 2551880 3000950 3014840 2722630 3424590 3716900 3783970 FALSE TRUE 2983798.445 2974431.56 3785977.704 3682361.564 2954850.582 2827371.338 3092473.789 2922069.86 3336633.377 0.89425421 0.891446924 1.134669973 1.103615875 0.88557844 0.847372491 0.926824568 0.87575395 1 21.66996174 3.203538495 24.96513656 0.90167907 1.007005688 0.246751742 0.085555895 253.2236824 180506.9329 0.027379381 0.031046666 1597.859153 -3.203538495 0.105326618 EIPYTFEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EIPYTFEDR 9 0 P34897-3;P34897-2;P34897;H0YIZ0;G3V2Y4 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial;Serine hydroxymethyltransferase" 0 ;;; 197.3 6.57E-05 732100000 656969 707267 482806 767686 775753 824462 595759 779438 772291 FALSE TRUE 570148.8821 702620.9165 716292.5965 942000.8396 760317.033 856179.5866 537982.3839 612761.2493 680991.6378 0.837233309 1.031761445 1.05183758 1.383278131 1.116485124 1.257254185 0.789998517 0.899807303 1 19.37727756 2.233064698 24.99996653 0.892827915 1.118950529 0.315507313 0.150030482 160.5978837 730522.2184 0.061994841 0.04313945 171.0270079 -2.233064698 0.226122614 EIQGHQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EIQGHQPR 8 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;;;; 177.97 0.00025206 1036720000 2141600 2168110 1387470 1452210 1867370 2311690 1890890 2127920 1954230 FALSE TRUE 1858582.134 2153867.543 2058455.133 1781956.476 1830212.99 2400622.21 1707511.779 1672880.867 1723203.156 1.078562402 1.249920844 1.194551627 1.034095411 1.062099373 1.393116187 0.990894064 0.97079724 1 20.71666137 2.052795723 24.99999928 0.982570037 1.165071701 0.407301552 0.103148804 89.76000011 42502.9763 0.041399944 0.027911831 112.9264624 -2.052795723 0.182501663 EIQNASHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIQNASHR 8 0 Q9HD20;Q9HD20-2 Q9HD20 ATP13A1 Manganese-transporting ATPase 13A1 0 76.221 0.036361 31305000 73503 64173 48215 69266 68780 99860 52401 82723 78177 FALSE TRUE 63789.39232 63751.44334 71531.93527 84993.90396 67411.41257 103701.6788 47319.15909 65033.3302 68935.00412 0.925355603 0.924805099 1.037672169 1.232957117 0.977898144 1.504339923 0.686431512 0.943400686 1 16.07294913 EIQNGNLHES(ph)DSESVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EIQNGNLHESDSESVPR 17 0 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 1 EIQNGNLHES(1)DSESVPR;EIQNGNLHES(1)DSESVPR;EIQNGNLHES(1)DSESVPR;EIQNGNLHES(1)DSESVPR;EIQNGNLHES(1)DSESVPR;EIQNGNLHES(1)DSESVPR 283.19 2.80E-36 4214610000 1706580 1785940 1265630 1935080 2585340 2317490 1485990 2833390 2794930 TRUE FALSE 1481051.129 1774208.043 1877692.901 2374469.49 2533896.792 2406645.34 1341878.919 2227491.598 2464516.559 0.600949961 0.719901043 0.761890966 0.963462583 1.02815166 0.976518227 0.544479571 0.903824967 1 21.23287324 4.186760666 2.095797096 0.887130858 0.629885741 0.35130564 0.137824666 0.428503583 3.63357865 0.040120182 0.137099142 15373.07218 -4.186760666 -0.257245117 EIQSTLEGDRGS(ph)GNWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 195.53 2.92E-11 5046050000 724862 1051640 683850 874010 1227090 1250020 924090 1052870 1021370 TRUE FALSE 629069.6501 1044731.708 1014562.147 1072467.329 1202673.31 1298109.078 834471.894 827721.9439 900624.8021 0.698481375 1.160007703 1.126509224 1.19080368 1.335376626 1.441342805 0.926547761 0.91905302 1 19.78056668 EIQTAVR ddPTM_MDA-MB-175_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 ;;;;; 191.63 0.001217 16721640000 5871440 5084280 3432550 4056230 4450420 4986800 4417240 5417230 4789230 FALSE TRUE 5095514.328 5050881.03 5092542.661 4977259.017 4361865.349 5178645.423 3988856.745 4258797.521 4223052.685 1.206595017 1.196026052 1.20589134 1.178592688 1.032870218 1.226280089 0.944543448 1.008464217 1 22.00985482 2.508848247 0.670040811 0.956557864 1.211571923 0.598915334 0.066715959 0.609648508 0.615039267 0.101970052 0.04852211 322.7366208 -2.508848247 0.255014059 EIQVQHPAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIQVQHPAAK 10 0 P49368;B4DUR8;Q5SZX6;E9PRC8;Q5SZX9 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 101.93 0.0030146 1433100000 2264100 1913370 1389210 1629330 1808790 1680350 2167100 2496600 2248000 FALSE TRUE 1964893.449 1900800.946 2061036.603 1999294.279 1772798.618 1744994.152 1956934.976 1962721.519 1982244.001 0.991247015 0.958913709 1.039749194 1.008601503 0.894339252 0.88031249 0.987232134 0.990151322 1 20.91870313 EIRPALELLEPIEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIRPALELLEPIEQK 15 1 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ; 188.39 2.74E-07 584010000 1029490 831140 767090 967310 807930 661560 974620 1236010 1768910 FALSE TRUE 893440.2881 825680.1866 1138057.29 1186952.52 791853.7737 687010.6413 880101.5024 971698.8801 1559791.475 0.572794699 0.529352929 0.729621432 0.760968719 0.507666433 0.440450312 0.564243052 0.622967169 1 20.57292174 1.235449101 4.270565523 1.040744842 0.588350213 0.644943468 0.095725312 0.156472444 5.490104448 0.219147725 0.026248913 17.19685784 -1.235449101 -0.452394629 EIRPVCR ddPTM_MDA-MB-175_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 ;;;;; 186.67 0.00054303 5026720000 2172010 1995930 1242664 1366540 1790690 2160740 1826290 2064410 2068830 FALSE TRUE 1884973.375 1982818.604 1843620.467 1676833.793 1755058.772 2243865.066 1649176.677 1622951.987 1824255.274 1.033283774 1.086919486 1.010615396 0.91918813 0.96206863 1.230017036 0.904027359 0.889651799 1 20.79887619 EIS(ph)DDEAEEEK ddPTM_MDA-MB-175_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 281.26 2.25E-27 1238950000 1765310 1003880 1235310 1359420 985650 933160 1233040 1520490 3806700 TRUE FALSE 1532019.811 997285.4462 1832710.048 1668097.088 966037.4934 969059.269 1113459.971 1195345.046 3356676.263 0.456409761 0.297105043 0.545989516 0.496949053 0.287795849 0.288696077 0.331715031 0.356109721 1 21.67860197 1.237274629 24.99959571 1.000000748 0.379080678 0.8212555 0.090507704 13.75567436 267302.3104 0.139101699 0.02299836 17.26929583 -1.237274629 -0.62092007 EIS(ph)DDEAEEEKGEK ddPTM_MDA-MB-175_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 228.39 1.01E-12 2973930000 3393490 1690800 2173030 2113870 1598120 1582760 2286490 2655600 6221020 TRUE FALSE 2945031.698 1679693.023 3223914.576 2593856.492 1566320.539 1643649.801 2064746.552 2087720.606 5485578.103 0.536868064 0.306201642 0.587707351 0.472850162 0.28553427 0.2996311 0.376395434 0.380583517 1 22.38721224 1.237389389 24.9955683 1.000000718 0.400772078 0.773025804 0.101169168 13.8395499 295224.1708 0.148298608 0.024738348 17.27385974 -1.237389389 -0.59922864 EIS(ph)SS(ph)PTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EISSSPTSK 9 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 EIS(0.992)S(0.009)S(0.998)PT(0.001)SK;EIS(0.942)S(0.058)S(0.997)PT(0.002)SK;EIS(1)S(0.001)S(1)PTSK;EIS(0.995)S(0.005)S(0.998)PT(0.001)SK 180.81 7.05E-05 6337520000 14835600 10328600 7274400 8607500 7910700 8596000 12295700 14222600 13665100 TRUE FALSE 12875037.87 10260750.75 10792324.17 10561964.43 7753292.547 8926693.682 11103264.91 11181207.67 12049627.45 1.068500908 0.851540912 0.895656253 0.876538671 0.643446661 0.740827359 0.921461262 0.927929741 1 23.52248521 1.787530443 2.418179487 0.974936212 0.841942162 0.159589848 0.110321669 0.517578024 5.847201309 0.095218469 0.032598703 61.30987679 -1.787530443 -0.13299405 EIS(ph)TPTHWSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EISTPTHWSK 10 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 1 EIS(0.7)T(0.3)PTHWSK;EIS(0.964)T(0.031)PT(0.004)HWSK 156.14 7.39E-06 499610000 1693780 1181580 433010 888030 1330940 1196150 1244500 1479010 1583650 TRUE FALSE 1469942.682 1173818.123 642415.0843 1089670.784 1304456.898 1242166.665 1123808.582 1162735.221 1396432.701 1.052641263 0.840583382 0.460040132 0.780324597 0.93413517 0.889528485 0.804771029 0.832646801 1 20.41331462 3.346149519 7.354997436 0.877750983 0.762620445 0.102827106 0.151821298 0.535575402 33.12685926 0.045233291 0.058421163 2218.960234 -3.346149519 -0.115130538 EISDHVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EISDHVLR 8 0 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 0 ; 186.3 0.00020822 586760000 455530 408670 191572 400800 468280 476280 359980 516290 795410 FALSE TRUE 395330.5563 405985.4199 284216.86 491807.7658 458962.1442 494602.7998 325069.195 405885.4013 701377.5359 0.563648729 0.578840067 0.405226637 0.70120262 0.654372461 0.705187683 0.463472493 0.578697464 1 19.4198317 1.238450775 24.52159267 1.000000521 0.58000087 0.659913986 0.094450499 1.28885768 286023.248 0.12988423 0.023171119 17.31612749 -1.238450775 -0.419999651 EISEVFPDQFIHLGGDEVEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 299.51 4.96E-55 743493000 1259180 1022690 773009 959320 998180 966580 1150380 1415020 1162530 FALSE TRUE 1092776.173 1015971.882 1146838.738 1177148.268 978318.1709 1003764.958 1038816.325 1112428.985 1025097.028 1.066022184 0.991098261 1.118761158 1.148328633 0.954366411 0.979190195 1.013383413 1.085193845 1 19.96732904 3.232930773 24.99980039 1.015432588 1.077320721 0.327430576 0.05214617 214.3583845 951874.4919 0.017144345 0.019978437 1709.742758 -3.232930773 0.061888134 EISLWFKPEELVDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EISLWFKPEELVDYK 15 1 Q32Q12;P22392-2;P22392 Q32Q12 NME1-NME2;NME2 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B 0 ;; 192.24 1.30E-07 11249372000 9072410 7092120 6346530 5494540 5377560 4348656 8702200 9427370 9102390 FALSE TRUE 7873468.032 7045531.397 9415733.136 6742159.286 5270557.077 4515951.61 7858261.983 7411400.289 8026315.824 0.980956669 0.877803908 1.17310773 0.840006727 0.656659567 0.562643149 0.979062145 0.923387573 1 22.93630649 3.521860889 24.55504374 0.827346735 0.998877064 0.24547115 0.151506813 606.5461844 332896.7946 0.045191637 0.067025606 3325.530144 -3.521860889 0.171530329 EISSS(ph)PTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EISSSPTSK 9 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 EISSS(0.997)PT(0.002)SK;EISS(0.041)S(0.957)PT(0.002)SK;EISS(0.001)S(0.999)PTSK;EISS(0.001)S(0.999)PTSK 214.64 7.01E-07 2433290000 10902900 7629000 5244700 6409290 5873460 6324260 8580700 9753100 8745800 TRUE FALSE 9462054.141 7578884.597 7781054.462 7864617.254 5756589.637 6567558.375 7748545.035 7667475.464 7711881.487 1.226944962 0.982754288 1.008969663 1.019805253 0.746457223 0.851615573 1.004754164 0.994241869 1 22.87865145 EIST(ph)PTHWSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EISTPTHWSK 10 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 1 EIS(0.252)T(0.748)PTHWSK;EIS(0.141)T(0.858)PTHWSK 156.02 4.30E-05 797330000 2301350 1626920 543190 1244160 1832990 1607370 1720350 2000210 2090970 TRUE FALSE 1997220.767 1616232.655 805878.5009 1526665.544 1796517.085 1669206.564 1553510.722 1572480.657 1843777.909 1.083221985 0.876587493 0.437080029 0.828009456 0.974367399 0.90531867 0.842569333 0.852857955 1 20.81423346 3.470478299 24.59974686 0.901319774 0.777695482 0.093100139 0.163311174 319.1927602 1182005.293 0.048137623 0.062307496 2954.461255 -3.470478299 -0.123624292 EITALAPS(ph)TMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EITALAPSTMK 11 0 P60709;P63267-2;A0A2R8YFE2;P63261;P68133;P68032;P63267;P62736;A6NL76 P60709;P63261;P68133 ACTB;ACTG2;ACTG1;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 1 EITALAPS(0.992)T(0.008)MK;EITALAPS(0.993)T(0.007)MK 203.7 3.75E-08 425500000 997670 1373570 769370 767420 1121210 829400 1079420 1276420 1611730 TRUE FALSE 865825.3817 1364546.928 1141439.905 941674.4403 1098900.115 861307.5547 974738.0145 1003467.516 1421193.115 0.609224301 0.960141809 0.80315609 0.662594288 0.77322364 0.606045403 0.685858948 0.706074006 1 20.43867117 1.23568312 24.99139136 1.000000367 0.728500492 0.407440118 0.103879345 84.41807463 733041.0614 0.171361479 0.02526408 17.20612684 -1.23568312 -0.271499875 EITALAPSTMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EITALAPSTMK 11 0 P60709;P63267-2;A0A2R8YFE2;P63261;P68133;P68032;P63267;P62736;A6NL76 P60709;P63261;P68133 ACTB;ACTG2;ACTG1;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 ;; 120.09 0.0016868 1628180000 2566340 2263320 1362800 1799220 2048660 1977800 2295470 2856680 2587110 FALSE TRUE 2227191.667 2248452.102 2021854.638 2207760.4 2007895.674 2053887.246 2072855.673 2245801.213 2281264.803 0.976296861 0.985616444 0.886286693 0.967779101 0.880167735 0.900328293 0.908643166 0.984454417 1 21.12140249 1.626992646 5.061358173 0.99599203 0.92842642 0.333182349 0.037193555 0.166596963 9.157628413 0.026079009 0.009857778 42.36357928 -1.626992646 -0.067565611 EIVHLQAGQCGNQIGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EIVHLQAGQCGNQIGAK 17 0 P68371;M0R2D3;M0QY85;M0R0X0;M0QY37;M0QX14;M0QZL7;M0R2T4;P04350;M0QYM7;M0R042;M0R278 P68371;P04350 TUBB4B;TUBB4A Tubulin beta-4B chain;Tubulin beta-4A chain 0 ;;;;; 254.23 4.94E-27 10055680000 6954920 5496500 3660070 4514190 5145600 4663530 5853130 7178260 6293060 FALSE TRUE 6035809.7 5460393.13 5430092.094 5539205.835 5043212.627 4842939.017 5285494.353 5643244.96 5549101.616 1.087709348 0.984013901 0.978553371 0.998216688 0.908834074 0.872742896 0.952495506 1.016965511 1 22.40382279 5.735202489 1.095432979 0.959543733 1.910127785 0.460242368 0.043115551 13.83737692 2.574703992 0.014721948 25.37676984 543503.6804 -5.735202489 0.950584052 EIVLADVIDNDSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EIVLADVIDNDSWR 14 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;;; 332.53 4.16E-68 1620640000 2067080 1922770 1283136 1608800 1833661 1925160 1872790 2129610 2098859 FALSE TRUE 1793910.141 1910139.197 1903664.861 1974102.629 1797174.734 1999222.151 1691167.114 1674209.474 1850734.28 0.969296435 1.032098026 1.028599774 1.066659136 0.97106038 1.080231869 0.913781699 0.904619043 1 20.81966634 2.22347539 24.99995314 0.9311367 1.024647921 0.462786113 0.042956825 181.441229 300690.7562 0.016555717 0.011211276 167.2920837 -2.22347539 0.093511221 EIVQQLIDEYHAATRPDYISWGTQEQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIVQQLIDEYHAATRPDYISWGTQEQ 26 1 P23258 P23258 TUBG1 Tubulin gamma-1 chain 0 ; 155.45 4.24E-08 724180000 487350 504990 280149 365307 486230 417290 487340 601040 478780 FALSE TRUE 422945.4627 501672.6874 415629.9934 448255.5377 476554.9743 433343.4163 440077.8418 472512.2733 422179.1738 1.00181508 1.188293309 0.984487202 1.061766107 1.128797922 1.026444323 1.042395905 1.119222128 1 18.68749589 1.209714745 24.12042692 0.999999371 1.071621301 0.108280021 0.062007914 4837.284578 4044508.07 1.392339281 0.013903441 16.20745202 -1.209714745 0.07162193 EIVVIHQDPEALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIVVIHQDPEALK 13 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 153.39 4.12E-05 962920000 1644720 1316840 1035730 1263670 1311050 1163040 1516620 1890830 2001600 FALSE TRUE 1427366.085 1308189.591 1536612.492 1550605.587 1284962.67 1207782.901 1369538.426 1486490.719 1764973.128 0.80871831 0.741195189 0.870615234 0.878543454 0.72803526 0.68430668 0.775954265 0.842217196 1 20.75121479 1.26469867 2.476060366 1.046013928 0.783927764 0.563979624 0.059773357 0.413216314 2.880337249 0.227036572 0.017101032 18.39495247 -1.26469867 -0.262086164 EIVWLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIVWLER 7 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 ; 96.253 0.029935 303990000 350770 334810 202769 237430 333720 353370 306670 355570 309150 FALSE TRUE 304414.8558 332610.6111 300828.7666 291342.1104 327079.6249 366964.3726 276929.1906 279534.1225 272602.6392 1.116698124 1.220129827 1.103543119 1.068742809 1.199840273 1.34615121 1.015871275 1.025427059 1 18.05644 2.098391662 24.99811414 1.016194568 1.171653339 0.50108511 0.076151807 11.08259207 2802.574178 0.031947331 0.021538888 125.4271813 -2.098391662 0.155458772 EIYDDLQALHTDDPLTWDYVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIYDDLQALHTDDPLTWDYVAR 22 0 Q9NYH9 Q9NYH9 UTP6 U3 small nucleolar RNA-associated protein 6 homolog 0 ; 140.97 7.93E-09 16613000 43017 33327 22821.8 34803 39559 30673 38669 42130 41758 FALSE TRUE 37332.19446 33108.07274 33858.49881 42705.55308 38771.8533 31853.01016 34918.88633 33120.82736 36821.41681 1.013871754 0.899152602 0.919532754 1.159802006 1.052970164 0.865067477 0.948330873 0.899498993 1 15.16825752 0.939323271 21.5086215 1.687298103 0.965954365 0.009975071 0.087538717 513.654246 609230.225 75985.11008 0.021748146 8.696074885 -0.939323271 -0.721343737 EIYDDSFIRPVTFWIVGDFDSPSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIYDDSFIRPVTFWIVGDFDSPSGR 25 1 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 145.25 2.60E-07 174190000 145090 132310 102320 103090 129690 188550 132940 125260 84859 FALSE TRUE 125915.9889 131440.8469 151802.2942 126498.1601 127109.4227 195803.6405 120047.4993 98474.12377 74827.06569 1.682759944 1.756594966 2.028708367 1.690540167 1.698709171 2.616748882 1.604332579 1.31602279 1 16.19127258 1.713231621 2.643767451 1.076116623 1.898538857 0.538320216 0.286281063 0.18499716 2.754184667 0.242762973 0.078255994 51.66918616 -1.713231621 0.822422234 EIYEELGRPGEEDLD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EIYEELGRPGEEDLD 15 1 A6NHN7;A6NHB5;Q14202-2;Q14202 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 0 122.7 0.0012136 0 193250 127160 93196 101320 138950 117070 134740 163350 135830 FALSE TRUE 167711.5229 126324.6776 138265.8973 124326.2546 136185.1669 121573.7587 121672.9355 128418.8737 119772.3321 1.400252628 1.05470667 1.154405987 1.038021489 1.137033607 1.015040423 1.015868468 1.072191477 1 16.86993515 7.177704767 1.269050092 1.054712088 200 0.79599414 0.053320927 360.5808179 1.320876289 0.014220634 208002.7676 15055832.23 -7.177704767 198.9452879 EIYENMAPGENKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EIYENMAPGENKR 13 1 Q13200;C9JPC0;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;; 102.28 0.0027293 1040380000 661290 590640 527580 611670 548540 469140 553540 657280 1119550 FALSE TRUE 573898.851 586760.0469 782719.4526 750559.0223 537625.1272 487188.1194 499857.776 516725.787 987198.0744 0.581341137 0.594369116 0.792869712 0.760292227 0.544597018 0.493505946 0.506339902 0.523426656 1 19.91298005 1.232073876 24.93315278 1.000000699 0.597515899 0.606728442 0.101298006 169.8865387 652930.0371 0.260066249 0.028065526 17.0637263 -1.232073876 -0.4024848 EIYHFTLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EIYHFTLEK 9 0 D6RFN0;Q9BT78;D6RAX7;Q9BT78-2 D6RFN0 COPS4 COP9 signalosome complex subunit 4 0 ; 105.4 0.0031047 456010000 559160 541750 271880 371650 522850 513800 451490 616780 640360 FALSE TRUE 485265.5893 538191.2086 403362.0774 456038.8128 512446.3079 533566.2185 407704.5693 484886.3968 564657.3703 0.859398309 0.953128812 0.714348379 0.807638113 0.907534967 0.944938022 0.722038869 0.858726765 1 19.10701619 3.245461534 24.81657755 0.873726456 0.833644152 0.067102041 0.091433575 594.0073312 2136111.765 0.027340727 0.034507903 1759.792792 -3.245461534 -0.040082304 EKAEGDVAALNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EKAEGDVAALNR 12 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;;;;; 197.38 1.78E-07 12006690000 11305030 10728480 7734110 9146060 10089320 9161120 12161810 13998070 10686630 FALSE TRUE 9811041.642 10658003.91 11474351.47 11222812.71 9888562.271 9513554.214 10982359.54 11004691.66 9423268.776 1.041150568 1.131030448 1.217661486 1.190968121 1.04937708 1.009581117 1.165451161 1.167821053 1 23.16779616 3.239616049 24.99999961 1.092700089 1.149365981 0.158669138 0.072077599 66.02802547 1563986.412 0.022841466 0.027818375 1736.265155 -3.239616049 0.056665893 EKAEGDVAALNRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EKAEGDVAALNRR 13 2 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;; 144.8 2.33E-05 1675540000 4150440 3879400 1786970 2004140 3595500 3485240 4263190 4626040 1533250 FALSE TRUE 3601948.838 3853915.966 2651154.669 2459210.618 3523956.584 3619319.438 3849746.49 3636797.346 1351990.932 2.664181211 2.85054868 1.960926369 1.818954965 2.606494246 2.677029374 2.847464728 2.689956908 1 20.36665404 1.234600429 24.99998964 0.99999781 2.517711162 0.649077529 0.34994841 82.30449198 519500.003 0.69372862 0.093661711 17.16328559 -1.234600429 1.517713352 EKAPSIIFIDELDAIGTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKAPSIIFIDELDAIGTK 18 1 P17980;E9PM69;E9PKD5;R4GNH3;E9PN50;E9PMD8 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ; 149.36 1.36E-07 0 601050 546850 404000 461360 475300 348160 625620 671800 540550 FALSE TRUE 521619.7196 543257.7063 599375.7513 566118.8394 465842.4599 361553.9405 564947.4687 528140.798 476646.7948 1.094352727 1.139748997 1.25748407 1.187711416 0.977332618 0.758536393 1.185253892 1.108033881 1 18.86256107 3.24509711 24.92149924 1.019698611 1.173937509 0.328112797 0.115601156 207.6717502 791779.3496 0.036300091 0.045748165 1758.316738 -3.24509711 0.154238898 EKASATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKASATR 7 1 Q9H993;F5GZY1 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 113.71 0.0055352 45896000 100220 80125 51305 55362 58739 77527 108240 110670 53426 FALSE TRUE 86975.67307 79598.6536 76116.2696 67932.78826 57570.20882 80509.51386 97742.90146 87004.08173 47110.03914 1.846223749 1.689632508 1.615712298 1.442002373 1.222036956 1.708967246 2.074778609 1.846826777 1 15.52374691 4.617797916 2.398998893 1.601754094 1.869885153 0.075251735 0.303200257 1.483197767 12.48743332 0.083381855 0.734220457 41476.10027 -4.617797916 0.268131059 EKDDANFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKDDANFK 8 1 Q5VTR2;H3BP71;O75150-4;O75150;O75150-3 Q5VTR2;H3BP71 RNF20;RNF40 E3 ubiquitin-protein ligase BRE1A;E3 ubiquitin-protein ligase BRE1B 0 70.056 0.047714 294670000 605850 436570 393850 454850 359530 321460 616370 701210 672170 FALSE TRUE 525785.3875 433702.1429 584317.1773 558130.6444 352376.0564 333826.7742 556594.5323 551261.6983 592706.8283 0.887091834 0.731731308 0.985845193 0.941663935 0.594519988 0.563224107 0.939072246 0.930074823 1 19.17695915 2.042373579 24.99959918 0.952403003 0.786178482 0.263475673 0.135972291 207.6173015 122489.3545 0.05966008 0.040222783 110.2487257 -2.042373579 -0.16622452 EKDECT(ph)PTR ddPTM_MDA-MB-175_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(0.92)PT(0.08)R 93.162 0.032463 0 608230 548490 395210 422380 404690 417180 625750 650890 902160 TRUE FALSE 527850.8644 544886.9331 586334.8779 518287.8347 396637.4608 433229.1846 565064.8613 511702.2387 795507.6725 0.663539627 0.684954969 0.737057477 0.651518335 0.49859665 0.544594602 0.710319813 0.643239853 1 19.60151632 1.237394524 7.790063251 1.005085412 0.641808567 0.711917526 0.071621074 0.060531201 29.11791739 0.114073378 0.019167731 17.27406398 -1.237394524 -0.363276846 EKDECT(ph)PTRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EKDECTPTRK 10 2 O15042-2;O15042;E7ET15;O15042-3;H7C4V2 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 EKDECT(0.979)PT(0.021)RK;EKDECT(0.999)PT(0.001)RK;EKDECT(0.987)PT(0.013)RK;EKDECT(0.987)PT(0.013)RK 115.12 0.002035 3714100000 3619520 2776290 2331040 2152450 2002930 1783760 3663030 4207910 3318980 TRUE FALSE 3141191.261 2758052.368 3458338.741 2641196.671 1963075.612 1852382.401 3307789.914 3308081.192 2926613.965 1.073319303 0.942403884 1.181685997 0.90247525 0.670766843 0.632943881 1.130244697 1.130344224 1 21.48080103 EKDFIILSCVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKDFIILSCVR 11 1 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 ; 145.29 3.31E-05 926120000 1003720 912520 627120 774330 905490 847490 1088220 1083290 1110790 FALSE TRUE 871075.8589 906525.596 930397.3296 950153.4614 887472.5206 880093.4887 982684.5919 851636.8637 979473.6716 0.88933055 0.925523189 0.94989519 0.970065341 0.906070828 0.898537157 1.00327821 0.869484182 1 19.90164719 4.080276941 0.004907906 1.852509973 5.10E-06 0.059334948 0.044529712 137111.5542 295.4343866 55076.17408 56439.44365 12030.31339 -4.080276941 -1.852504874 EKDHSSSRPS(ph)SPRPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKDHSSSRPSSPRPQK 16 3 E9PKU9;B7Z503;Q9BSF8;Q9BSF8-2 E9PKU9 BTBD10 BTB/POZ domain-containing protein 10 1 EKDHS(0.017)S(0.017)S(0.017)RPS(0.474)S(0.474)PRPQK 60.034 0.06908 93629000 124540 134950 36854 98891 173180 141790 183920 226870 168150 TRUE FALSE 108081.7235 134063.5046 54676.71767 121345.713 169734.0568 147244.7531 166083.4667 178355.616 148271.4986 0.728944703 0.904175825 0.368760808 0.818402149 1.144751746 0.993075233 1.120130762 1.202898856 1 17.17788178 3.36887801 4.45454822 1.102155451 0.67706714 0.650227368 0.143962014 0.12713678 4.380107452 0.041535137 0.054277436 2338.18037 -3.36887801 -0.425088312 EKDIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EKDIQR 6 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;;; 107.43 0.028522 3972448000 5570170 5280420 3104005 4241509 3270458 4358921 5531250 6665240 6697710 FALSE TRUE 4834057.921 5245732.573 4605112.2 5204608.446 3205382.284 4526611.511 4994830.226 5239930.295 5905914.354 0.818511348 0.888216838 0.779745849 0.881253627 0.542741071 0.766453971 0.845733603 0.887234386 1 22.493729 1.498124163 1.642157324 1.019803772 0.781439637 0.355004972 0.095496613 0.692684897 2.761321584 0.240105764 0.028751212 31.48648372 -1.498124163 -0.238364135 EKDLEDLFYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKDLEDLFYK 10 1 Q13242;H0YIB4;S4R3G0 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 ; 116.01 0.001046 2475600000 6485800 5133300 4549400 4387000 4389600 3617500 6190300 7012200 6416800 FALSE TRUE 5628685.097 5099579.014 6749505.057 5383135.401 4302255.548 3756667.566 5589965.659 5512695.599 5658213.214 0.994781371 0.90127021 1.192868632 0.951384332 0.760355855 0.663931779 0.98793832 0.974282055 1 22.43191511 3.478955357 24.9804849 0.884218568 1.026023655 0.236347425 0.124953124 116.3622963 1584872.595 0.038699058 0.050730063 3012.696317 -3.478955357 0.141805087 EKDNIDITLQWLIQHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKDNIDITLQWLIQHSK 17 1 Q96BM9;Q9NVJ2 Q96BM9;Q9NVJ2 ARL8A;ARL8B ADP-ribosylation factor-like protein 8A;ADP-ribosylation factor-like protein 8B 0 178.88 5.69E-10 380220000 564220 410350 357070 502930 430510 379740 529590 699470 605710 FALSE TRUE 489656.8974 407654.3838 529750.2463 617127.9433 421943.6933 394348.8435 478230.4433 549893.7838 534103.6538 0.916782527 0.763249569 0.991849134 1.155446024 0.790003383 0.738337663 0.895388826 1.029563793 1 19.02676023 1.756312198 6.833558652 1.013442217 0.891818614 0.149361208 0.120680278 0.291687481 40.64917117 0.072823356 0.033332066 57.05742898 -1.756312198 -0.121623603 EKDPFEVDLSHVYLAYTEESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKDPFEVDLSHVYLAYTEESLR 22 1 J3KPF9;A0A087X011;E9PES4;Q9Y496;H7C2F6 J3KPF9 KIF3A Kinesin-like protein;Kinesin-like protein KIF3A 0 ; 155.76 1.01E-08 63237000 75307 59827 43819 54810 56360 51706 80304 90221 74032 FALSE TRUE 65354.98915 59433.9925 65010.01497 67255.44822 55238.54627 53695.16328 72516.13044 70927.94125 65280.0213 1.001148404 0.910446892 0.995863875 1.030260819 0.846178435 0.822535934 1.110847224 1.086518353 1 15.99435391 2.21688515 24.99982723 1.071984717 0.936456926 0.43191895 0.070884439 227.2002653 262043.965 0.030250053 0.020414585 164.772659 -2.21688515 -0.13552779 EKDQADFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKDQADFR 8 1 Q96I24;Q96I24-2 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ; 77.677 0.029725 1703530000 7197600 5969300 4008700 4996400 5424700 5004100 6661000 7820200 7217700 FALSE TRUE 6246418.924 5930087.275 5947320.728 6130908.985 5316759.083 5196610.965 6015017.245 6147911.087 6364431.728 0.981457448 0.931754401 0.934462177 0.963308155 0.835386302 0.816508242 0.945098872 0.96597958 1 22.60160027 1.734090563 2.825331958 0.989393886 0.910445901 0.244187709 0.051866365 0.356314997 5.951818305 0.044220527 0.015352472 54.21139245 -1.734090563 -0.078947985 EKDRES(ph)EKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKDRESEKDR 10 3 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 EKDRES(1)EKDR 91.812 0.054675 165050000 362440 225630 232840 211680 171690 165920 319410 358510 366020 TRUE FALSE 314542.6357 224147.8217 345442.2028 259745.1793 168273.7049 172303.0498 288433.6674 281845.4264 322749.5326 0.974571933 0.694494644 1.070310467 0.804788708 0.521375519 0.533859951 0.893676484 0.873263624 1 18.30005548 3.492677443 24.70708597 0.765919315 0.898977086 0.130648925 0.174220313 1495.323814 2374942.242 0.05193776 0.074358482 3109.406076 -3.492677443 0.133057772 EKDRQS(ph)PLHGNHITISHTQATGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKDRQSPLHGNHITISHTQATGSR 24 2 Q86VQ1;H7C2L5 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 EKDRQS(1)PLHGNHITISHTQATGSR;EKDRQS(1)PLHGNHITISHTQATGSR 114.68 0.00074946 435430000 144310 128149 62870 95220 126204 113444 141509 159923 110949 TRUE FALSE 125239.0679 127307.1808 93274.14229 116841.1563 123692.7873 117808.2641 127785.479 125724.711 97832.73561 1.280134579 1.301273853 0.953404213 1.194295096 1.26432923 1.204180414 1.306162791 1.285098594 1 16.57802966 3.470592508 24.73899914 1.227914033 1.171117603 0.005155681 0.124477383 548.2713637 2077519.519 0.035993832 0.046594834 2955.238308 -3.470592508 -0.05679643 EKDTAGVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKDTAGVTR 9 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8;H0YIS4;A0A3B3ISH4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 0 67.726 0.054798 40886000 192880 157670 107550 94473 146840 147070 138120 167720 111620 FALSE TRUE 167390.4193 156634.2554 159561.5397 115924.5386 143918.1713 152727.8781 124725.1437 131854.3832 98424.41076 1.700700243 1.591416745 1.621158191 1.177802719 1.462220299 1.551727634 1.26721758 1.339651233 1 16.58672855 -0.02123701 0.116980345 1.93E-21 2.064193276 0.579694436 0.142056987 99.47216065 1.889401471 35.86818312 7.347322122 0.952276332 0.02123701 2.064193276 EKDVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EKDVER 6 1 Q13243;Q13243-3;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ;; 80.18 0.059458 682506000 2152130 1923680 1109430 1505530 1046490 1662650 2066370 2494820 2519990 FALSE TRUE 1867720.568 1911043.219 1645954.059 1847383.597 1025666.896 1726613.221 1865973.755 1961322.158 2222079.653 0.840528181 0.860024625 0.740726849 0.831375957 0.461579717 0.777025801 0.839742065 0.882651599 1 21.0834791 1.606560232 1.550085558 1.007686485 0.750363586 0.341798843 0.11250888 0.639636055 2.506450519 0.221820235 0.034947728 40.41664241 -1.606560232 -0.257322899 EKDVQFEHGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKDVQFEHGYR 11 1 A0A0C4DFM1;Q92544 A0A0C4DFM1 TM9SF4 Transmembrane 9 superfamily member 4 0 69.352 0.032888 229270000 556580 498710 327460 319300 459740 583500 464700 535510 457710 FALSE TRUE 483026.5428 495433.9412 485820.7513 391801.9452 450592.0735 605947.6226 419633.4655 420995.3538 403600.0452 1.196795066 1.227536882 1.203718278 0.970767843 1.116432168 1.501356677 1.039726012 1.043100363 1 18.62256681 2.047625946 24.99999985 1.029660215 1.196223293 0.286492966 0.130128387 156.8634133 82340.62069 0.054351096 0.036643487 111.5901718 -2.047625946 0.166563078 EKEAAYQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKEAAYQER 9 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 88.187 0.0123 0 863300 655590 449220 563330 657030 618780 798910 898490 679110 FALSE TRUE 749212.7177 651283.3861 666464.2946 691242.6865 643956.3885 642584.867 721431.8312 706354.9056 598826.3894 1.251135105 1.087599674 1.112950776 1.154329032 1.075364078 1.073073729 1.204742884 1.179565427 1 19.19177827 4.747413657 24.5866608 1.119831947 1.251135191 0.347764523 0.059233712 1201.107738 3335624.498 0.014656912 0.172777751 55900.23797 -4.747413657 0.131303244 EKEDDEEEEDEDASGGDQDQEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKEDDEEEEDEDASGGDQDQEER 23 1 O60216;E5RI01;E5RFZ5 O60216 RAD21 Double-strand-break repair protein rad21 homolog 0 266.94 3.12E-44 175630000 249020 178750 177750 180610 193320 154640 214140 270680 307140 FALSE TRUE 216111.3761 177575.7795 263710.4945 221620.261 189473.3102 160589.1009 193372.7358 212797.1884 270830.2591 0.797958754 0.655671859 0.97371134 0.818299483 0.699601702 0.592951103 0.713999744 0.785721615 1 18.04702941 1.243417419 3.658996428 1.031856182 0.74995349 0.366008288 0.102441883 0.324808088 6.748169665 0.250865931 0.027358813 17.5152935 -1.243417419 -0.281902692 EKEDFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EKEDFEK 7 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;; 84.476 0.019624 827170000 2353610 1651140 1813760 1906790 1382230 1134370 2126840 2529110 3518670 FALSE TRUE 2042574.475 1640293.553 2690900.403 2339755.813 1354726.327 1178009.948 1920579.384 1988279.508 3102696.841 0.658322285 0.528667039 0.867277901 0.754103908 0.436628648 0.379672913 0.619003236 0.640823003 1 21.56509131 1.222083879 3.629496044 1.062297041 0.605239651 0.430978457 0.141090725 0.33314244 6.562524298 0.428696118 0.038644799 16.67569255 -1.222083879 -0.457057391 EKEEEEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EKEEEEQR 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 103.7 0.0043067 1684370000 3279110 2674140 2039090 2270230 1700900 2030060 3157160 3607920 3348540 FALSE TRUE 2845767.305 2656573.398 3025200.744 2785720.42 1667055.418 2108157.722 2850979.109 2836394.385 2952679.416 0.963791494 0.899716164 1.024561193 0.943455089 0.564590727 0.713981244 0.965556604 0.960617116 1 21.4935933 2.046969189 24.99814557 0.973173513 0.851756069 0.164704163 0.131421962 240.5278628 128013.7002 0.0593585 0.040019476 111.4215483 -2.046969189 -0.121417444 EKEEEEQRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKEEEEQRR 9 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 57.492 0.064698 102140000 95248 96504 65407 64539 65092 73106 99530 92785 91218 FALSE TRUE 82660.73547 95870.05887 97038.04397 79193.56637 63796.79655 75918.43513 89877.59592 72943.6498 80434.31196 1.027680022 1.191905003 1.206425984 0.984574424 0.793154004 0.943856338 1.117403677 0.906872304 1 16.29552344 3.645369762 5.857189434 0.953153722 1.146179094 0.46997717 0.09258475 0.196463341 9.964315537 0.025974839 0.038884947 4419.465647 -3.645369762 0.193025371 EKEEEERQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKEEEERQR 9 2 A0A0A0MRP0;Q8IWC1-2;Q8IWC1-4;Q8IWC1;Q8IWC1-3 A0A0A0MRP0 MAP7D3 MAP7 domain-containing protein 3 0 81.95 0.011154 160120000 276380 241210 206130 212530 159450 184990 270870 338530 284800 FALSE TRUE 239855.6827 239625.4756 305815.1575 260788.1848 156277.257 192106.685 244601.0691 266137.9939 251131.2684 0.955100829 0.954184149 1.21775022 1.03845366 0.622293106 0.764965216 0.973996869 1.059756499 1 17.93808214 3.43288893 24.99979358 0.899960613 1.049293188 0.226620396 0.142455714 237.7089522 134350.5825 0.046073841 0.059481105 2709.498593 -3.43288893 0.149332575 EKEEFAVPENSSVQQFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKEEFAVPENSSVQQFK 17 1 Q9UMX0;Q9UMX0-2;Q9UMX0-4;Q9UHD9 Q9UMX0;Q9UHD9 UBQLN1;UBQLN2 Ubiquilin-1;Ubiquilin-2 0 141.13 5.80E-07 163360000 238390 167000 160040 172510 143340 112220 162530 246610 396560 FALSE TRUE 206886.1575 165902.966 237435.8793 211681.0322 140487.8144 116537.176 146767.8656 193874.3706 349679.1286 0.591645713 0.474443432 0.679010727 0.605357926 0.401762081 0.333268893 0.419721549 0.554435066 1 18.41567216 1.241850095 4.19033649 1.048195542 0.499647606 0.693981278 0.10336978 0.137944804 4.533724565 0.228467848 0.028538568 17.45219652 -1.241850095 -0.548547936 EKEELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EKEELDR 7 1 Q16543;K7EKQ2;K7EQA9 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;;; 112.84 0.0057124 6302660000 12151900 9778000 7318090 8409860 8191500 8000730 11679300 13782800 12457100 FALSE TRUE 10545995.63 9713767.674 10857142.8 10319447.25 8028505.176 8308523.26 10546643.28 10835455.48 10984435.83 0.960085323 0.884321036 0.98841151 0.939460834 0.730898273 0.756390532 0.960144285 0.986437141 1 23.38895744 2.020008452 24.99078599 0.986562114 0.876597022 0.278821939 0.081201131 325.9407783 407102.1801 0.036377654 0.024522768 104.7148927 -2.020008452 -0.109965092 EKEELEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EKEELEQR 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;; 114.86 0.0023487 2837010000 4521880 3856800 2786640 3218400 3439040 3096720 4603060 5274780 4603560 FALSE TRUE 3924302.101 3831464.427 4134268.425 3949186.91 3370609.832 3215852.822 4156655.95 4146809.345 4059332.381 0.96673584 0.943865657 1.018460189 0.972866112 0.830336005 0.792212246 1.023975265 1.021549594 1 21.95281104 EKEELMLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 EKEELMLR 8 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;;;;; 149.72 0.00045662 9052880000 12766310 11291990 7691050 10587550 10856900 9386700 11933160 14635530 13195760 FALSE TRUE 11079209.79 11217812.17 11410467.51 12991615.05 10640868.93 9747812.423 10775883.98 11505835.8 11635772.29 0.95216798 0.964079727 0.980636886 1.116523659 0.914496148 0.837745204 0.926099593 0.988833016 1 23.47206363 EKEES(ph)PQPR ddPTM_MDA-MB-175_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 141.13 6.51E-05 1172260000 1833040 1474940 1063060 1082640 1217520 1184420 1569340 1908600 1783240 TRUE FALSE 1590799.12 1465251.022 1577159.372 1328469.959 1193293.734 1229985.404 1417145.648 1500460.743 1572427.399 1.011683669 0.931840175 1.003009343 0.844852971 0.758886379 0.782220791 0.90124711 0.954232128 1 20.58456198 3.740061045 24.99012621 0.875119844 0.977143976 0.321880464 0.074167545 199.4024585 3321095.731 0.022883735 0.037088486 5496.18123 -3.740061045 0.102024132 EKEEVAEEAQS(ph)GGD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 EKEEVAEEAQSGGD 14 1 O76070 O76070 SNCG Gamma-synuclein 1 EKEEVAEEAQS(1)GGD;EKEEVAEEAQS(1)GGD;EKEEVAEEAQS(1)GGD;EKEEVAEEAQS(1)GGD;EKEEVAEEAQS(1)GGD;EKEEVAEEAQS(1)GGD;EKEEVAEEAQS(1)GGD;EKEEVAEEAQS(1)GGD 202.84 4.18E-08 14462440000 14736790 16630870 11618490 13874610 15971290 11350900 18642850 22587850 20874750 TRUE FALSE 12789285.86 16521620.72 17237230.63 17025052.26 15653492.58 11787576.47 16834869.28 17757614.06 18406960.84 0.694807034 0.897574611 0.936451747 0.924924675 0.850411576 0.640386893 0.914592552 0.96472276 1 24.13374811 2.007381208 24.98882478 0.967786439 0.833250488 0.325005494 0.09480788 223.9454608 758156.5743 0.0403902 0.027170601 101.7141111 -2.007381208 -0.13453595 EKEEVAEEAQSGGD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 EKEEVAEEAQSGGD 14 1 O76070 O76070 SNCG Gamma-synuclein 0 ;;;;;;; 179.67 1.50E-05 13508640000 16990530 16031300 12124820 14252170 15245600 12199530 19235010 21991840 21032200 FALSE TRUE 14745188.41 15925989.33 17988423.51 17488343.03 14942242.39 12668853.81 17369601.69 17289056.16 18545797.28 0.795068996 0.858738457 0.969946087 0.942981462 0.805694259 0.683111846 0.936578861 0.9322358 1 24.14458895 2.028951566 24.99997172 0.953216757 0.848486419 0.306951611 0.080587482 291.0343091 251309.8802 0.035621834 0.024015843 106.8935661 -2.028951566 -0.104730338 EKEEYISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKEEYISR 8 1 Q08379;Q08379-2;A0A087WYC0 Q08379 GOLGA2 Golgin subfamily A member 2 0 81.525 0.020643 151460000 311570 232860 213790 221310 211990 181300 273610 274360 284430 FALSE TRUE 270395.2351 231330.3273 317179.5591 271561.818 207771.8138 188274.7283 247075.3443 215690.2491 250805.0094 1.078109387 0.922351303 1.264646028 1.082760742 0.828419712 0.75068169 0.985129224 0.85999179 1 17.93620664 3.248951138 24.83285394 0.882551116 1.08790005 0.466205848 0.107451795 172.008817 411090.4601 0.030830804 0.039358509 1773.989879 -3.248951138 0.205348934 EKEHASGSGAQSEAAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EKEHASGSGAQSEAAGR 17 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;; 219.95 2.50E-15 346258000 434068 581353 125219.7 298058 703248 610389 579054 693523 468003 FALSE TRUE 376704.814 577534.0539 185776.3658 365736.6244 689254.7407 633871.0598 522897.4322 545218.5035 412676.2185 0.912833832 1.3994847 0.450174634 0.886255636 1.670207077 1.536000941 1.267088843 1.321177424 1 18.65465078 3.265351639 24.99871124 1.356150059 0.913992989 0.381585052 0.282562984 243.4402244 227152.5073 0.082178523 0.106062674 1842.263037 -3.265351639 -0.44215707 EKEIAETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EKEIAETR 8 1 P12270 P12270 TPR Nucleoprotein TPR 0 ;;; 90.15 0.012221 732360000 2129340 1800400 1160010 1499580 1618380 1592470 1962450 2271380 1976300 FALSE TRUE 1847942.324 1788573.054 1720994.716 1840082.559 1586177.404 1653733.351 1772131.901 1785663.063 1742664.065 1.060412251 1.026344141 0.987565389 1.05590205 0.910202624 0.948968527 1.016909648 1.024674289 1 20.73286306 4.758686063 1.203063485 0.992250609 1.095677037 0.244393191 0.040022752 2.629728343 3.140155818 0.012640083 0.344791215 57370.16025 -4.758686063 0.103426428 EKEIS(ph)DDEAEEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EKEISDDEAEEEK 13 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 1 EKEIS(1)DDEAEEEK;EKEIS(1)DDEAEEEK;EKEIS(1)DDEAEEEK 203.53 2.24E-07 1763800000 2653480 1459480 1711240 1679430 1402470 1434050 1943290 2268220 4622900 TRUE FALSE 2302815.895 1449892.58 2538801.388 2060770.25 1374563.591 1489218.831 1754830.035 1783178.804 4076386.028 0.56491605 0.355680882 0.62280691 0.505538542 0.337201526 0.365328215 0.430486716 0.437441104 1 21.95885925 1.237874481 24.99734879 1.000000635 0.448332705 0.779015909 0.091631385 7.709584753 280668.0478 0.12920821 0.022240402 17.29316483 -1.237874481 -0.55166793 EKEIS(ph)DDEAEEEKGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EKEISDDEAEEEKGEK 16 2 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 1 EKEIS(1)DDEAEEEKGEK;EKEIS(1)DDEAEEEKGEK;EKEIS(1)DDEAEEEKGEK;EKEIS(1)DDEAEEEKGEK;EKEIS(1)DDEAEEEKGEK;EKEIS(1)DDEAEEEKGEK 199.94 1.92E-11 5287710000 6480950 3223390 4623020 3609920 3016850 3302670 4736050 5376490 10717280 TRUE FALSE 5624476.037 3202215.339 6858727.935 4429607.51 2956820.587 3429725.852 4276748.6 4226769.453 9450295.368 0.595164047 0.338848175 0.725768631 0.468726885 0.312881288 0.362922609 0.452551845 0.447263211 1 23.17192799 1.237840986 24.9979272 1.000000625 0.458476537 0.65480531 0.12248988 10.92085185 379091.5871 0.17122845 0.029415096 17.29183114 -1.237840986 -0.541524088 EKELAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKELAK 6 1 Q9NX55 Q9NX55 HYPK Huntingtin-interacting protein K 0 83.843 0.051552 364960000 919640 794910 500810 770480 517880 609190 1107800 1286200 1078500 FALSE TRUE 798107.2439 789688.1839 743003.3911 945429.26 507575.2012 632625.9335 1000365.727 1011156.139 951000.9586 0.839228643 0.830375802 0.781285638 0.994141227 0.533727329 0.665221131 1.051908221 1.063254595 1 19.85908727 2.224470305 24.95193877 1.044131695 0.775975883 0.521998587 0.119214725 184.5206768 326757.2383 0.050062725 0.033937625 167.6757685 -2.224470305 -0.268155812 EKELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKELER 6 1 O15042-2;O15042;E7ET15;O15042-3;H7C4V2;E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;O14776;O14776-2;G3V220 O15042-2;E7EPN9;O14776 U2SURP;PRRC2C;TCERG1 U2 snRNP-associated SURP motif-containing protein;Protein PRRC2C;Transcription elongation regulator 1 0 83.843 0.051552 576770000 812040 755190 504690 653420 560430 576930 770430 938460 849860 FALSE TRUE 704726.8566 750229.1072 748759.7721 801788.9979 549278.5395 599124.8704 695713.8172 737777.6321 749390.519 0.940400017 1.001119027 0.99915832 1.06992146 0.732967025 0.799482853 0.928372857 0.984503558 1 19.5153582 EKELETGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EKELETGPK 9 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;; 113.93 0.0015697 3011580000 5025930 4141040 3255686 3413670 3744820 3191780 5193740 5898700 4925414 FALSE TRUE 4361740.616 4113837.236 4830146.639 4188795.948 3670305.409 3314569.842 4690051.894 4637308.909 4343137.168 1.004283413 0.947204078 1.112133108 0.964463195 0.845081623 0.76317411 1.07987653 1.067732547 1 22.05030609 EKELGNDAYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKELGNDAYK 10 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 107.85 0.0020335 1046370000 1897300 1306810 958120 1113170 1146200 915990 1668290 1795440 1555600 FALSE TRUE 1646566.998 1298225.479 1421470.037 1365932.262 1123392.863 951228.728 1506499.493 1411499.128 1371698.74 1.200385296 0.946436299 1.036284422 0.995796105 0.818979292 0.693467669 1.098272856 1.0290154 1 20.38753223 EKELS(ph)PPPGLPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EKELSPPPGLPSK 13 1 A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;Q7Z4S6-3;H0YHT2;H0YI78;H0YIM6 A0A1B0GV47 KIF21A Kinesin-like protein KIF21A 1 EKELS(1)PPPGLPSK;EKELS(1)PPPGLPSK;EKELS(1)PPPGLPSK;EKELS(1)PPPGLPSK 106.94 0.00080787 1572110000 2651720 2210690 1949160 2202290 2515110 1734350 3302710 4045600 2987240 TRUE FALSE 2301288.483 2196167.832 2891780.296 2702353.604 2465064.232 1801071.567 2982413.693 3180479.923 2634091.89 0.873655354 0.833747615 1.097828176 1.025914705 0.935830766 0.683754266 1.13223601 1.207429374 1 21.32887424 2.082184642 24.99999997 1.133952995 0.919227369 0.383305002 0.120981861 26.78312671 8144.616471 0.050657491 0.034153271 120.8327452 -2.082184642 -0.214725626 EKEPIAASTNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EKEPIAASTNR 11 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;;; 168.31 1.66E-05 1384820000 1867408 1652053 1103593 1344215 1572233 1553195 1754243 1951985 1953858 FALSE TRUE 1620625.301 1641200.555 1637294.266 1649439.561 1540948.639 1612947.417 1584116.784 1534568.198 1722875.133 0.94065163 0.952594024 0.950326715 0.957376149 0.894405294 0.936195192 0.919461169 0.890701925 1 20.71638671 3.27708229 24.99973176 0.923221564 0.950411896 0.106007471 0.03002559 293.8976448 190731.2349 0.008317632 0.010737805 1892.702212 -3.27708229 0.027190331 EKEPIVGSTDYGKDEDSAEALLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EKEPIVGSTDYGKDEDSAEALLK 23 2 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 250.99 9.16E-39 615550000 1229090 810850 937250 897120 685950 503740 1265670 1444530 1197400 FALSE TRUE 1066662.642 805523.473 1390507.235 1100824.808 672300.937 523119.2038 1142925.518 1135628.501 1055844.736 1.010245736 0.762918491 1.316961848 1.042601028 0.636742235 0.49545088 1.082474988 1.075563918 1 20.00996627 EKEPS(ph)RER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKEPSRER 8 2 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477 Q8NI27 THOC2 THO complex subunit 2 1 EKEPS(1)RER;EKEPS(1)RER 89.266 0.011047 2757400000 3055200 1950420 1529910 1641790 1781280 1700720 2426400 2611400 2672000 TRUE FALSE 2651447.579 1937607.563 2269779.593 2014583.513 1745836.013 1766147.799 2191088.101 2052972.432 2356119.204 1.12534526 0.822372467 0.96335516 0.855043119 0.740979493 0.749600358 0.929956387 0.871336403 1 21.1679811 4.744364359 24.7308268 0.865005745 1.125345392 0.486615874 0.083514796 507.952164 2164405.617 0.020892241 0.180536005 55509.1221 -4.744364359 0.260339648 EKEQEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 EKEQEDR 7 1 Q14247;Q14247-3;Q14247-2;H0YCD9 Q14247 CTTN Src substrate cortactin 0 ;;;;;;;;; 147.19 0.0019777 3852586300 10758030 9185719 6828252 8084849 5655466 7025246 11468595 12614257 14324315 FALSE TRUE 9336329.078 9125377.407 10130417.51 9920637.535 5542933.291 7295511.76 10356372.42 9916796.305 12630910.8 0.73916515 0.722463926 0.80203381 0.78542535 0.438838765 0.577591899 0.819922853 0.785121237 1 23.59045534 1.234890494 1.41335655 1.128561214 0.687261284 0.426226622 0.112721985 1.388773865 2.417313858 0.894620037 0.035897152 17.17475276 -1.234890494 -0.441299931 EKEQEDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EKEQEDRR 8 2 Q14247;Q14247-3;Q14247-2;H0YCD9 Q14247 CTTN Src substrate cortactin 0 ;;;;; 189.38 0.00010799 4302370000 7863010 6856000 4486730 5163280 3998490 5121490 7741420 8790190 5481500 FALSE TRUE 6823893.306 6810962.485 6656527.635 6335681.64 3918927.872 5318517.034 6990658.28 6910476.274 4833483.315 1.411796186 1.409120926 1.37716988 1.31079001 0.810787504 1.10034869 1.446298213 1.429709347 1 22.20463183 3.470986688 24.99981932 1.196685396 1.390945211 0.250896472 0.186917893 295.8220479 1205537.829 0.060559951 0.078396368 2957.921796 -3.470986688 0.194259816 EKEQFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 EKEQFR 6 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;; 139.92 0.010803 45135300000 33505400 25055350 17359890 21260360 19674540 19287930 25750670 29228000 32109200 FALSE TRUE 29077576.5 24890759.76 25755190.87 26087849.68 19283055.15 20029949.15 23253373.99 22977819.65 28313286.95 1.026994024 0.879119397 0.909650332 0.921399544 0.68106028 0.707439909 0.821288395 0.811556062 1 24.75497591 4.571391309 0.941247101 0.811588174 1.077686419 0.304945291 0.093495408 2.128631584 1.816878242 0.033544531 0.549440226 37272.73905 -4.571391309 0.266098246 EKEQFRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKEQFRK 7 2 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 94.262 0.0080597 783880000 1421500 981980 484800 618370 894620 742110 1200900 1389000 239440 FALSE TRUE 1233645.173 975529.3087 719250.9016 758780.3597 876818.8123 770659.4519 1084436.903 1091973.159 211133.676 5.842957869 4.620434444 3.406613835 3.593838625 4.15290838 3.650101995 5.136257387 5.171951628 1 17.68779718 4.614905824 3.150401956 3.942733025 5.907519333 0.241939494 1.163502476 0.457114968 7.334034534 0.290498464 1.839140595 41200.81663 -4.614905824 1.964786308 EKEQMMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EKEQMMR 7 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 121.62 0.0040315 1902820000 2795530 2514510 1534926 2474870 2236650 2214860 2545850 3092480 2738570 FALSE TRUE 2426093.628 2497992.018 2277221.348 3036827.06 2192145.041 2300067.097 2298953.859 2431177.218 2414819.374 1.004668777 1.034442594 0.94301933 1.257579383 0.90778841 0.952479975 0.952018972 1.006773941 1 21.20348385 EKETLAVNYEKEEEFLTNELSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EKETLAVNYEKEEEFLTNELSR 22 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ;;; 189.33 1.22E-17 699644000 693062 616750 441707 461853 558555 422841 802229 1010203 552943 FALSE TRUE 601472.1007 612698.5286 655317.9826 566723.7826 547440.8483 439107.9669 724428.9551 794178.9499 487574.7085 1.233599878 1.256624919 1.344036045 1.162332198 1.122783522 0.900596276 1.48578042 1.628835409 1 18.89526377 2.189262852 24.99981368 1.429902604 1.179348199 0.169770133 0.195715818 152.4639477 77316.09383 0.080605786 0.054344505 154.618997 -2.189262852 -0.250554405 EKEVDGLLTSEPMGS(ph)PVSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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(0.992)PVS(0.006)S(0.002)K;EKEVDGLLTSEPMGS(0.928)PVS(0.055)S(0.018)K;EKEVDGLLTSEPMGS(0.997)PVS(0.002)SK;EKEVDGLLTSEPMGS(0.987)PVS(0.011)S(0.002)K;EKEVDGLLTSEPMGS(0.997)PVS(0.002)S(0.001)K 191.59 8.52E-18 5288282000 6355270 4667380 3977750 4686450 4637120 3368830 6726080 7738200 6548310 TRUE FALSE 5515404.967 4636719.673 5901403.205 5750580.1 4544850.384 3498431.07 6073785.797 6083446.149 5774176.252 0.955184727 0.803009723 1.022033784 0.995913503 0.787099352 0.605875352 1.051887842 1.053560869 1 22.46118371 EKEWQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKEWQR 6 1 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-4;C9JMV9;A0A1B0GV31 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 ; 85.359 0.049981 595650000 1178060 1034960 745610 896890 966040 894500 1162100 1273270 1216270 FALSE TRUE 1022376.386 1028161.28 1106189.49 1100542.583 946817.694 928911.9938 1049399.721 1000991.119 1072483.946 0.953278965 0.958672886 1.031427551 1.02616229 0.882826915 0.866131374 0.978475925 0.933339024 1 20.03252462 3.248163678 24.99976301 0.932475623 0.992766104 0.299259121 0.045794801 274.6138674 714901.9496 0.013930582 0.017752556 1770.776206 -3.248163678 0.06029048 EKEYEIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKEYEIER 8 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 76.465 0.032587 196530000 271640 258460 151970 140380 205140 195400 307430 257970 131180 FALSE TRUE 235742.0858 256762.1592 225463.2003 172255.4246 201058.1153 202917.1644 277615.4859 202805.123 115672.0498 2.038021165 2.219742449 1.949158856 1.489170675 1.738173704 1.754245427 2.400022186 1.753276814 1 16.81968078 1.268511697 4.198757298 0.935874522 1.929841692 0.570310802 0.254589583 0.156985728 4.969123999 0.442485518 0.067420965 18.55716791 -1.268511697 0.99396717 EKFENSIESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKFENSIESLR 11 1 P83111;P83111-2 P83111 LACTB "Serine beta-lactamase-like protein LACTB, mitochondrial" 0 130.1 0.00021088 636360000 407000 391010 247640 354330 363010 399580 386860 497310 444690 FALSE TRUE 353213.9188 388441.4296 367399.5323 434786.0421 355786.8112 414952.1012 349342.3767 390964.1266 392119.2548 0.900781878 0.990620646 0.936958662 1.108810743 0.907343383 1.058229342 0.890908499 0.997054141 1 18.58093296 5.129943691 1.897073345 0.985724397 0.749935762 0.141172167 0.065358123 6.887741073 9.554555719 0.015583842 4.147458699 134878.7992 -5.129943691 -0.235788635 EKFEPTVFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EKFEPTVFR 9 1 E7ETZ4;Q9Y6E2;Q75MG1;E9PFE3;C9JF98;F8WDX8;E7EMS9;Q9Y6E2-2 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 ;; 106.62 0.0026507 1277810000 1448160 1362460 1030850 1097760 1311260 1343910 1534830 1603770 1505180 FALSE TRUE 1256781.987 1353509.911 1529372.508 1347023.186 1285168.491 1395611.087 1385982.423 1260816.266 1327239.335 0.946914361 1.019793397 1.152295948 1.014906016 0.968301992 1.05151426 1.044259604 0.949953963 1 20.33999712 1.745579518 24.99992425 0.974610619 1.030798804 0.135402708 0.055718143 2.774826352 9921.400617 0.030207909 0.014506125 55.66465448 -1.745579518 0.056188185 EKFEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKFEVK 6 1 P33316-2;H0YNW5;P33316;A0A0C4DGL3;H0YKC5;H0YMP1 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 67.757 0.089314 180170000 93077 73715 49791 70319 77491 61826 94933 116190 99874 FALSE TRUE 80776.63862 73230.76131 73870.09414 86286.00371 75949.08071 64204.48623 85726.41227 91343.67269 88067.0095 0.917217913 0.831534552 0.83879417 0.979776697 0.862401041 0.72904129 0.973422542 1.037206477 1 16.42631406 2.016615784 24.82097111 1.016476967 0.862136104 0.536996075 0.063918454 155.7902986 232721.5335 0.026199544 0.017658493 103.9000565 -2.016615784 -0.154340863 EKFPEFCSS(ph)PSPPVEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKFPEFCSSPSPPVEVK 17 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 EKFPEFCS(0.155)S(0.608)PS(0.237)PPVEVK 173.65 8.78E-10 731090000 736850 556140 461620 477920 468950 320770 675830 744020 710260 TRUE FALSE 639473.4056 552486.6797 684860.976 586439.0405 459618.8125 333110.2295 610288.1106 584917.113 626293.8719 1.021043689 0.88215246 1.093513775 0.936364009 0.733870844 0.531875282 0.974443688 0.933933955 1 19.25648024 3.467507896 24.05648442 0.841862775 0.991846677 0.220534662 0.142219772 228.1526095 570925.3973 0.044260213 0.057224788 2934.322851 -3.467507896 0.149983902 EKFPEFCSSPS(ph)PPVEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKFPEFCSSPSPPVEVK 17 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 EKFPEFCS(0.007)S(0.024)PS(0.969)PPVEVK;EKFPEFCS(0.017)S(0.215)PS(0.768)PPVEVK 130.19 1.88E-05 1130900000 1264690 960710 787130 804910 867720 779890 1180100 1408960 1289350 TRUE FALSE 1097558.012 954399.0328 1167788.701 987677.1178 850454.0697 809892.873 1065654.084 1107664.869 1136924.512 0.96537457 0.839456818 1.027147087 0.868727086 0.748030376 0.712354131 0.937312964 0.974264216 1 20.11670504 2.01206311 24.9728443 0.976442302 0.85901244 0.257145126 0.090948304 314.4930117 651055.4578 0.039800359 0.026812048 102.8165696 -2.01206311 -0.117429862 EKFS(ph)FEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKFSFEPK 8 1 P23443-5;P23443;P23443-3;P23443-2;P23443-4;K7ERJ3 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 1 EKFS(1)FEPK;EKFS(1)FEPK 90.614 0.0079164 604980000 1622380 764380 1007550 1092790 1260810 1239710 1995390 2019810 2370900 TRUE FALSE 1407978.372 759358.7374 1494804.55 1340924.672 1235722.348 1287402.446 1801877.385 1587889.35 2090614.903 0.673475718 0.363222675 0.715007124 0.641402044 0.591080809 0.615800856 0.861888711 0.759532206 1 20.99549591 -2 0.346638241 5.609528944 0.541883585 0.600552492 0.10655135 50.3460518 0.784104038 163.9108042 0.138593804 0.01 2 -5.067645359 EKGTWVQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKGTWVQLK 9 1 P46778 P46778 RPL21 60S ribosomal protein L21 0 ; 113.93 0.0015697 2579500000 4747500 4730600 3104000 3737800 4764900 3743300 5463000 6520400 5056000 FALSE TRUE 4120105.846 4699524.377 4605104.782 4586524.619 4670087.812 3887307.173 4933199.101 5126063.202 4458285.44 0.924145818 1.054110249 1.032931795 1.028764237 1.047507585 0.871928733 1.106523835 1.149783537 1 22.08805756 EKHPDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EKHPDGK 7 1 P53396;P53396-2;K7EIE7 P53396 ACLY ATP-citrate synthase 0 ;;;;; 93.429 0.0089778 1948506000 6842960 5341180 4292340 5233720 2804470 3925210 7492900 8490300 8596850 FALSE TRUE 5938645.498 5306093.437 6368129.981 6422116.118 2748666.534 4076215.369 6766239.711 6674715.417 7580540.187 0.783406638 0.699962444 0.840062822 0.847184496 0.362595075 0.537720963 0.892580152 0.880506567 1 22.85386923 2.127708803 7.666941683 0.917809592 0.680494228 0.384651789 0.14680206 0.272420994 17.38090577 0.065118368 0.043813329 134.1864932 -2.127708803 -0.237315364 EKHPNS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKHPNSSPR 9 1 P29374 P29374 ARID4A AT-rich interactive domain-containing protein 4A 1 EKHPNS(0.759)S(0.241)PR;EKHPNS(0.842)S(0.158)PR 123.84 0.00033098 134087000 417700 319870 190453 260973 232877 266680 328600 404620 364630 TRUE FALSE 362499.8867 317768.7529 282556.7078 320230.9084 228243.2033 276939.3522 296732.4226 318095.1618 321523.8568 1.127443202 0.988320917 0.878804797 0.995978686 0.709879527 0.861333759 0.922893951 0.98933611 1 18.29456626 4.641621833 2.470245451 0.910564754 1.152978719 0.400394072 0.085527752 0.463617503 4.078865278 0.023193295 0.215570367 43814.90087 -4.641621833 0.242413965 EKHPNSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKHPNSSPR 9 1 P29374 P29374 ARID4A AT-rich interactive domain-containing protein 4A 1 EKHPNS(0.327)S(0.673)PR;EKHPNS(0.412)S(0.588)PR 84.821 0.0092252 116733000 384010 307934 198823 236584 214780 275062 342130 399720 361570 TRUE FALSE 333262.1055 305911.1613 294974.4678 290304.0132 210506.2982 285643.8131 308950.2853 314242.9886 318825.6065 1.045280237 0.959493701 0.925190643 0.910541711 0.660255305 0.895924942 0.969025947 0.985626569 1 18.28240798 2.18741211 4.612998957 0.986822646 0.892829778 0.149035402 0.096242258 0.403009071 18.03514737 0.043403785 0.029166095 153.9614915 -2.18741211 -0.093992867 EKHQTLEVSLSRDS(ph)PLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKHQTLEVSLSRDSPLK 17 2 Q8NCF5;H3BSZ7;Q8NCF5-3;Q8NCF5-2 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 EKHQTLEVS(0.002)LS(0.008)RDS(0.99)PLK 88.755 0.0022008 69741000 131850 119410 60127 95009 134750 98073 163510 181440 104990 TRUE FALSE 114425.6884 118625.5878 89204.61831 116582.2456 132068.7386 101845.9318 147652.8254 142640.468 92578.20181 1.235989533 1.281355498 0.963559635 1.259283971 1.426564095 1.100107042 1.594898394 1.540756519 1 16.49838492 3.474801644 15.16256094 1.3644236 1.162242929 0.12619358 0.19715831 0.935958476 6074.27725 0.056994728 0.075071115 2984.019411 -3.474801644 -0.20218067 EKIDLENTLEQEQEALVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EKIDLENTLEQEQEALVNR 19 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ;;; 287.31 2.24E-40 1073709000 734549 692058 502253 551081 666633 618484 770286 877938 698744 FALSE TRUE 637476.4885 687511.8254 745144.2307 676212.3638 653368.3075 642277.4797 695583.7823 690197.7908 616139.2803 1.034630495 1.11583833 1.20937628 1.097499194 1.060423071 1.04242255 1.128939194 1.120197677 1 19.23289699 3.484720013 24.78388381 1.079554325 1.125187423 0.131413736 0.055317405 685.0767358 2234429.442 0.016106225 0.021676299 3052.952259 -3.484720013 0.045633098 EKIETELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 EKIETELR 8 1 P63104;E7EX29;B0AZS6;E7ESK7;E9PD24;E7EVZ2 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;;;;; 138.66 0.00063462 37734650000 51454700 40524700 28335000 33282800 38651600 32799800 45557400 53382400 46821600 FALSE TRUE 44654831.03 40258490.58 42037900.77 40840168.44 37882508.78 34061629.53 41139250.36 41966989.18 41286403.79 1.08158684 0.975102864 1.018202045 0.989191712 0.917554093 0.82500839 0.99643579 1.016484492 1 25.29916342 7.999987566 0.877823644 0.962293162 51.04477473 0.29204401 0.057349086 1242.435619 3.019285702 0.021162041 124493.9887 99997137.12 -7.999987566 50.08248157 EKINIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EKINIR 6 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;;;;; 125.86 0.016181 4376630000 8586320 9351760 5207660 5480120 7917100 6665780 7502270 7920750 8170490 FALSE TRUE 7451616.057 9290327.673 7726101.795 6724465.004 7759565.2 6922216.87 6774701.01 6226959.252 7204583.98 1.034288181 1.289502308 1.072386944 0.933359237 1.077031682 0.960807298 0.94033202 0.86430518 1 22.7804837 3.624834709 0.923941278 0.930500033 1.172410462 0.43842677 0.086827687 0.554207585 0.945118151 0.037510201 0.09674422 4215.36038 -3.624834709 0.241910429 EKIYVLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKIYVLLR 8 1 P84090 P84090 ERH Enhancer of rudimentary homolog 0 64.654 0.060467 480570000 894380 826330 507840 627800 938810 867310 849590 949380 575300 FALSE TRUE 776185.4169 820901.7838 753433.1226 770351.5853 920129.5178 900675.9769 767196.8926 746362.4751 507288.6894 1.530066475 1.618214246 1.485215694 1.518566452 1.813818319 1.775470252 1.51234772 1.47127758 1 18.95244747 1.071739713 1.666543412 0.532416915 1.6164675 0.752388999 0.109418018 0.847675013 1.515029355 1.714889828 0.032881648 11.79613444 -1.071739713 1.084050584 EKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK 43 2 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 147.75 3.67E-14 61566000 51793 44172 21505 21219 32510 20554 59883 65995 6668.4 FALSE TRUE 44948.42382 43881.83122 31904.88993 26037.09826 31863.1146 21344.72568 54075.55588 51882.48282 5880.069349 7.64419961 7.46280845 5.425937695 4.428025712 5.418833132 3.630012575 9.196414646 8.823447437 1 12.52161745 4.249919464 22.2728339 5.824933139 7.553509961 0.104709208 2.374577131 164.1658474 321875.5 0.621180294 1.603106291 17779.49676 -4.249919464 1.728576823 EKKEEWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKKEEWDR 8 2 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 0 67.726 0.032819 376600000 1232500 743880 567860 667990 690840 510200 1022500 1194200 548210 FALSE TRUE 1069622.002 738993.4033 842478.9954 819667.3391 677093.6356 529827.7241 923338.1074 938829.6233 483401.2383 2.21270017 1.528737092 1.742815137 1.695625237 1.400686597 1.096041305 1.910086351 1.942133261 1 18.88286164 EKLCYVALDFEQEMATAASSSSLEK ddPTM_MDA-MB-175_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 ;;; 310.14 1.66E-74 2519950000 2620580 2118697 1387067 1607812 1760263 1414508 2494977 3054041 1393965 FALSE TRUE 2274263.713 2104779.14 2057857.241 1972890.288 1725237.21 1468925.038 2253014.515 2400958.099 1229172.046 1.850240348 1.712355197 1.674181615 1.605056262 1.403576673 1.195052428 1.83295294 1.953313295 1 20.22925543 4.239240207 1.476714429 1.55121853 1.840851756 0.145472253 0.278875206 1.375383966 5.01465148 0.087621102 0.451301233 17347.63226 -4.239240207 0.289633226 EKLDQLKQEFEFWYPVDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKLDQLKQEFEFWYPVDLR 19 2 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRP1 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 66.536 0.015208 110660000 236650 173740 89047 110330 163970 140990 218940 257340 77441 FALSE TRUE 205376.1029 172598.6905 132110.427 135382.1128 160707.3178 146413.9765 197707.2325 202309.8436 68286.0132 3.007586668 2.527584822 1.934663057 1.982574563 2.353444143 2.144128346 2.895281526 2.962683486 1 16.05930249 -0.856654919 16.03429005 2.382987009 2.364329605 0 0.607428262 0 0 0 0.134302645 0.13910575 0.856654919 -0.018657405 EKLDSVIEFSIPDSLLIR ddPTM_MDA-MB-175_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 ; 140.95 1.13E-07 465820000 1692330 1595270 1089320 1287750 1484180 1406460 1473220 1935220 1247980 FALSE TRUE 1468684.303 1584790.566 1616118.796 1580153.32 1454647.722 1460567.426 1330347.351 1521388.263 1100445.226 1.334627356 1.4401358 1.468604486 1.435921827 1.321871991 1.327251363 1.208917372 1.382520662 1 20.06965591 EKLEAEMEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EKLEAEMEAAR 11 1 Q8WXF1;Q8WXF1-2 Q8WXF1 PSPC1 Paraspeckle component 1 0 ;;;;; 170.66 1.41E-05 2095430000 3983330 3308370 2369540 2794140 3176170 2722050 3713510 4210380 3825580 FALSE TRUE 3456922.848 3286637.1 3515457.47 3428592.193 3112970.431 2826769.025 3353374.372 3310023.002 3373324.291 1.024782248 0.974302147 1.042134455 1.016383809 0.922819795 0.837977254 0.994085977 0.981234746 1 21.68573959 3.252244128 24.845492 0.949527321 1.013517492 0.320619016 0.048519094 307.2271485 557836.6563 0.015137024 0.019431985 1787.492087 -3.252244128 0.063990171 EKLEAYQHLFYLLQTNPTYLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKLEAYQHLFYLLQTNPTYLAK 22 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 231.76 5.55E-27 4251600000 2709270 2445900 1574370 2068970 2020730 1627860 2810640 3468530 2391270 FALSE TRUE 2351233.105 2429832.722 2335740.598 2538761.261 1980521.426 1690484.828 2538064.565 2726811.852 2108576.785 1.115080618 1.152356765 1.107733242 1.20401651 0.939269293 0.80171841 1.203686099 1.293200168 1 21.00783813 EKLEDFFK ddPTM_MDA-MB-175_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 58.699 0.094209 377700000 568470 490050 343300 400000 455940 461100 475760 620640 509040 FALSE TRUE 493345.2492 486830.8293 509321.0283 490826.1136 446867.686 478838.8154 429620.8684 487920.9658 448861.8711 1.099102599 1.084589404 1.134694348 1.093490326 0.995557241 1.066784341 0.9571338 1.087018072 1 18.77591203 3.340548924 6.378309396 1.027165991 1.105369985 0.528019023 0.038246121 0.169803903 9.190064813 0.01034295 0.013363133 2190.528581 -3.340548924 0.078203994 EKLEMEMEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EKLEMEMEAAR 11 1 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;;; 148.68 3.17E-05 4469000000 8325140 6893180 4718410 5505440 6459870 5728430 7560000 8684050 7588290 FALSE TRUE 7224951.656 6847898.247 7000248.858 6755534.297 6331331.226 5948806.409 6826832.364 6827033.487 6691211.001 1.079767423 1.023416874 1.046185639 1.009613102 0.946216047 0.889047798 1.020268583 1.02029864 1 22.67383591 3.562506891 3.634941124 0.979698838 1.046865036 0.409440769 0.040525051 0.296991847 7.361910687 0.012983266 0.019565693 3651.799217 -3.562506891 0.067166198 EKLILPHVDIQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKLILPHVDIQLK 13 1 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 121.76 0.00014595 113920000 253280 224850 160260 274950 247800 218130 250120 317180 204880 FALSE TRUE 219808.4063 223372.9455 237762.272 337381.5998 242869.2648 226521.6022 225863.4009 249353.5253 180659.3198 1.216701173 1.236431897 1.316080855 1.867501772 1.344349492 1.253860595 1.250217266 1.380241692 1 17.46291216 2.869412503 5.084817575 1.249997984 1.413420115 0.153247076 0.201900065 0.514333661 19.13386828 0.068415555 0.06870164 740.3081032 -2.869412503 0.163422131 EKLQEEGGGS(ph)DEEETGSPSEDGMQSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EKLQEEGGGSDEEETGSPSEDGMQSAR 27 1 Q13610;Q13610-2 Q13610 PWP1 Periodic tryptophan protein 1 homolog 1 EKLQEEGGGS(1)DEEETGSPSEDGMQSAR;EKLQEEGGGS(1)DEEETGSPSEDGMQSAR;EKLQEEGGGS(1)DEEETGSPSEDGMQSAR 253.21 5.12E-53 1158540000 486230 395930 279915 328174 410570 339820 462420 581170 384750 TRUE FALSE 421973.4736 393329.1098 415282.8303 402690.9225 402400.4603 352893.0953 417574.5796 456891.3182 339265.2933 1.243786152 1.159355577 1.224065174 1.186949949 1.186093798 1.040168571 1.23082021 1.346708099 1 18.37205432 3.513036322 19.61572233 1.183526536 1.204332703 0.019975513 0.09836095 397.3097039 216989.8 0.028357289 0.042000925 3258.63953 -3.513036322 0.020806167 EKLQGQDSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKLQGQDSER 10 1 A0A0C4DGG1;Q9UKS6;E9PIY1;E9PJ75;E9PNM9 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 0 106.26 0.0022257 187920000 324290 311470 211190 275170 328810 299320 397600 509550 383010 FALSE TRUE 281434.2549 309423.9331 313322.1904 337651.5542 322267.3243 310835.0341 359040.8132 400586.6978 337730.9941 0.833308934 0.916184592 0.927727084 0.999764783 0.954213057 0.920362772 1.063097019 1.186111742 1 18.36551506 2.601751832 0.365083081 1.181777977 0.83522037 0.542980538 0.064796278 1.727618447 0.731529735 0.362400171 0.214575977 399.7162751 -2.601751832 -0.346557606 EKLQSFDS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EKLQSFDSPER 11 1 P78332;E9PGM9;P78332-2 P78332 RBM6 RNA-binding protein 6 1 EKLQSFDS(1)PER;EKLQSFDS(1)PER;EKLQSFDS(1)PER 149.37 2.08E-05 1370190000 3160100 2593380 1743290 1985070 2577650 2279430 2866390 3253200 2508840 TRUE FALSE 2742484.778 2576343.916 2586350.875 2435810.483 2526359.808 2367121.147 2588407.939 2557528.496 2212247.793 1.239682456 1.16458198 1.169105415 1.101056803 1.141987718 1.070007236 1.170035268 1.156076866 1 21.07708156 8 0.532161496 1.110376426 6.22845724 0.437703353 0.048928451 137.5437703 1.363983877 0.027150855 797.4781722 100000000 -8 5.118080815 EKMLRAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 EKMLRAAR 8 2 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 0 ;;;;;; 95.531 0.015416 43188050000 37376460 41524100 22994590 22908250 32134700 28060660 60365400 45112900 11785540 FALSE TRUE 32437066.11 41251325.45 34114850.64 28109918.29 31495282.34 29140171.75 54511172.8 35465857.4 10392266.89 3.121269542 3.969425141 3.282715023 2.704888029 3.030646026 2.804024576 5.245359207 3.412716185 1 23.30900705 4.019341342 23.89423409 3.18519241 3.565528278 0.026449436 1.04517327 758.7890113 937383.19 0.272231955 0.566532523 10455.41659 -4.019341342 0.380335868 EKNPDMVAGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKNPDMVAGEK 11 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 77.527 0.029525 393800000 1187200 952160 764040 876080 962620 737950 1220400 1370200 1273700 FALSE TRUE 1030308.512 945905.1983 1133532.3 1075007.354 943465.7453 766339.414 1102045.796 1077193.393 1123124.637 0.917359016 0.842208573 1.009266703 0.957157664 0.84003655 0.682328024 0.981231966 0.959104054 1 20.09908661 EKNPGNQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKNPGNQGR 9 1 Q5JRA6-2;Q5JRA6;A0A0A0MRH6 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 0 130.75 0.00032148 20769000 38759 39362 22487 34265 38945 53869 32303 62041 34106 FALSE TRUE 33636.89995 39103.42843 33361.78841 42045.39196 38170.07069 55941.37529 29170.26003 48774.01495 30074.02753 1.118470079 1.300239164 1.109322267 1.398063226 1.269203822 1.8601225 0.969948571 1.621798574 1 14.87623047 3.727084686 23.40857575 1.374839836 1.18843337 0.085527533 0.265890956 697.2011998 1422150.486 0.066925304 0.100396079 5334.389044 -3.727084686 -0.186406466 EKPEEESLAAPTWLVHLQQVER ddPTM_MDA-MB-175_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 0 219.64 6.50E-26 212370000 254490 214460 160580 164960 198300 142160 247250 301690 228070 FALSE TRUE 220858.5017 213051.1981 238237.0251 202416.6893 194354.218 147628.9872 223271.7331 237175.9413 201107.8244 1.098209393 1.059387912 1.184623352 1.006508274 0.966417983 0.734078784 1.110209082 1.179347158 1 17.61760969 3.704584656 23.63661004 1.012660895 1.108605015 0.166868076 0.118111858 752.9305384 523802.8638 0.036713727 0.054460363 5065.060715 -3.704584656 0.09594412 EKPELSEPSHLNGPS(ph)SDPEAAFLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKPELSEPSHLNGPSSDPEAAFLSR 25 1 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 EKPELSEPSHLNGPS(0.649)S(0.351)DPEAAFLSR 244.18 5.74E-39 910880000 661020 505110 343960 544460 565820 532580 576670 790060 975770 TRUE FALSE 573664.5322 501791.8992 510300.2065 668087.9646 554561.289 553068.6972 520744.6322 621111.8173 860415.5822 0.666729594 0.583197131 0.593085733 0.776471252 0.64452725 0.642792516 0.605224548 0.721874208 1 19.71467413 1.245045383 2.825397398 1.071150792 0.645674108 0.809768621 0.05388154 0.180002052 1.72374084 0.177872316 0.014230847 17.58107324 -1.245045383 -0.425476684 EKPELSEPSHLNGPSS(ph)DPEAAFLSR ddPTM_MDA-MB-175_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(0.319)S(0.681)DPEAAFLSR;EKPELSEPSHLNGPS(0.05)S(0.95)DPEAAFLSR;EKPELSEPSHLNGPS(0.159)S(0.841)DPEAAFLSR 283.42 1.20E-53 3493770000 1535320 1294270 866550 1357420 1282180 1096880 1356240 1761460 2384810 TRUE FALSE 1332423.572 1285767.855 1285616.478 1665642.958 1256667.127 1139077.683 1224712.054 1384785.487 2102880.479 0.633618309 0.611431733 0.611359748 0.792076856 0.597593225 0.541674953 0.582397367 0.658518399 1 21.00393542 1.238889264 4.420066087 1.03288127 0.625341662 0.765416872 0.064882635 0.103169461 4.108622457 0.132838296 0.016993173 17.33361969 -1.238889264 -0.407539609 EKPEVTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKPEVTDR 8 1 O95104-2;O95104-3;O95104 O95104-2 SCAF4 "Splicing factor, arginine/serine-rich 15" 0 ; 102.06 0.0045943 666040000 1346890 1189850 799450 1038520 1170530 1050380 1354650 1689510 1564070 FALSE TRUE 1168895.074 1182033.797 1186066.694 1274331.839 1147238.743 1090788.798 1223276.252 1328221.434 1379167.426 0.847536747 0.857063308 0.859987461 0.923986323 0.83183428 0.790903829 0.886967186 0.963060328 1 20.39536618 1.72196299 2.788283397 0.992509743 0.854095084 0.720442369 0.033127781 0.127511777 2.108019761 0.028239848 0.009542854 52.7184934 -1.72196299 -0.13841466 EKPGVESMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKPGVESMR 9 1 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 ; 111.86 0.0018761 194100000 386120 323766 199623 261402 300905 277783 338130 373152 359846 FALSE TRUE 335093.2637 321639.1598 296161.3505 320757.3194 294917.5792 288469.4918 305338.2046 293356.3487 317305.4158 1.056059074 1.013657958 0.93336368 1.010878804 0.929443888 0.909122496 0.962284882 0.924523611 1 18.27551262 4.914282234 0.976668736 0.946677941 1.152456502 0.512033798 0.033496458 2.017343953 1.234946117 0.010425936 0.472993498 82088.48378 -4.914282234 0.205778561 EKPPITVVGDVGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKPPITVVGDVGGR 14 1 O60256;O60256-2;O60256-3;O60256-4;E7EPA1;I3L0S1;I3L4G9;C9J168;B4DP31;Q14558;Q14558-2 O60256;C9J168 PRPSAP2;PRPSAP1 Phosphoribosyl pyrophosphate synthase-associated protein 2;Phosphoribosyl pyrophosphate synthase-associated protein 1 0 ; 159.13 4.53E-06 333370000 891560 720520 495670 641240 729480 707550 809950 955290 955800 FALSE TRUE 773738.0871 715786.8567 735377.6699 786843.3427 714964.7752 734769.9063 731401.1737 751008.6676 842806.4129 0.918049596 0.849289761 0.872534497 0.933599141 0.848314351 0.871813379 0.867816337 0.891080865 1 19.68484177 1.237127563 4.126152662 1.012689474 0.879266819 0.657408671 0.026971781 0.137112461 4.262019892 0.055072729 0.006487145 17.26344887 -1.237127563 -0.133422655 EKPQGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EKPQGQR 7 1 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 ;;; 107.32 0.0068442 499137000 402352 434352 255267 344122 268871 385764 509548 582913 621293 FALSE TRUE 349180.1638 431498.7131 378714.975 422260.1597 263520.9931 400604.5907 460132.1134 458261.5912 547844.4493 0.637370999 0.787629981 0.691281942 0.77076652 0.481014261 0.731237838 0.839895547 0.836481216 1 19.0634068 1.618634311 1.182832467 1.021422726 0.684648689 0.569033035 0.089871726 0.623260071 1.207389421 0.234229376 0.029862648 41.55605485 -1.618634311 -0.336774037 EKPTTALLDK ddPTM_MDA-MB-175_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 73.624 0.040523 1128500000 491130 418190 321920 403070 364440 289730 422620 521640 431530 FALSE TRUE 426225.9261 415442.8824 477601.5888 494593.204 357188.357 300876.1006 381634.3774 410091.3454 380515.015 1.12012906 1.091791036 1.255145185 1.299799442 0.938697142 0.790707564 1.002941704 1.077727105 1 18.53759386 3.225486697 24.99656722 0.970982887 1.189109318 0.600738471 0.092880729 185.0250168 353756.1119 0.031623119 0.036072912 1680.686442 -3.225486697 0.218126431 EKPVCGTTYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKPVCGTTYK 10 1 Q14444-2;Q14444;G3V153 Q14444-2 CAPRIN1 Caprin-1 0 68.44 0.054692 86308000 88255 80941 49505 57388 82972 63189 95541 94780 93206 FALSE TRUE 76591.87814 80409.29324 73445.78358 70418.82252 81321.01953 65619.92172 86275.44853 74512.03458 82187.29286 0.931918737 0.97836649 0.893639163 0.856809125 0.989459766 0.798419311 1.049741943 0.906612592 1 16.32662773 2.214726953 24.99984691 0.971705422 0.912005 0.228342337 0.065160182 414.636836 434921.7917 0.024974257 0.016847522 163.9558637 -2.214726953 -0.059700422 EKPYFPIPEEYTFIQNVPLEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 241.71 1.02E-30 8816400000 4045200 3280400 2282620 2844200 3319900 2859800 3589100 4188700 3828800 FALSE TRUE 3510616.571 3258850.836 3386502.667 3490019.081 3253840.485 2969818.357 3241029.634 3292979.101 3376163.626 1.039824179 0.965252635 1.003062364 1.033723323 0.963768598 0.879642898 0.959974099 0.975361228 1 21.6869534 3.104381333 7.106249622 0.953854246 1.006432882 0.362410127 0.036076777 0.274500418 16.60959886 0.011391089 0.012949913 1271.690224 -3.104381333 0.052578636 EKQDETQTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKQDETQTK 9 1 P35221-2;P35221;P35221-3;E5RGY7 P35221-2 CTNNA1 Catenin alpha-1 0 99.283 0.0049633 82847000 536990 355810 333780 459740 243920 313700 430610 646960 645220 FALSE TRUE 466025.4109 353472.6607 495197.1244 564130.9937 239066.4692 325768.242 388849.5085 508612.6386 568942.8266 0.819107631 0.621279756 0.870381172 0.991542502 0.420194188 0.5725852 0.683459726 0.893960895 1 19.11792416 1.588718058 3.454785733 0.982566059 0.708339885 0.283659676 0.159695492 0.261103163 7.01881096 0.144924966 0.04405794 38.78984624 -1.588718058 -0.274226174 EKQELQDDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKQELQDDKR 10 2 P12270 P12270 TPR Nucleoprotein TPR 0 80.979 0.01259 83856000 121240 95470 82833 87502 89081 78008 129800 152440 151200 FALSE TRUE 105217.8268 94842.85128 122891.3159 107370.6665 87308.46238 81009.01824 117212.016 119841.8923 133325.3082 0.7891812 0.7113642 0.921740347 0.80532847 0.654852882 0.607604207 0.879143034 0.898868293 1 17.02459114 1.842515651 2.506280108 0.959069221 0.75387269 0.455340856 0.090864824 0.272966414 3.152019623 0.07212098 0.02712803 69.58500305 -1.842515651 -0.205196531 EKQLAAENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EKQLAAENR 9 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 138.25 0.00012947 7258830000 12605470 12211750 5937980 7576570 11009940 10393210 13384530 14491100 3601010 FALSE TRUE 10939625.2 12131530.21 8809606.989 9296946.019 10790863.73 10793043.51 12086500.34 11392291.03 3175302.7 3.445222782 3.820590147 2.774414858 2.927892833 3.398373243 3.399059722 3.806408863 3.587781107 1 21.5984627 1.235880311 24.99244878 0.999996792 3.402839056 0.836848993 0.332316859 30.37166216 283142.2005 0.584069199 0.087394217 17.21394103 -1.235880311 2.402842265 EKQPMVPESLADYITAAYVEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKQPMVPESLADYITAAYVEMR 22 1 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 0 140.11 1.20E-07 93986000 114590 103750 49621 79114 96281 93376 102470 126830 94888 FALSE TRUE 99446.64117 103068.4594 73617.88157 97078.04288 94365.19647 96968.23514 92532.47517 99708.39149 83670.44874 1.188551546 1.231838253 0.879855226 1.160242886 1.127819892 1.158930502 1.105915847 1.191679894 1 16.35243055 4.305205593 0.004038792 0.052914603 2.20162521 0.015238754 0.103378171 595419.6016 883.4496171 232148.1263 237882.8178 20193.22076 -4.305205593 2.148710607 EKQPPIDNIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKQPPIDNIIR 11 1 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 0 77.912 0.028564 82604000 106670 106140 67372 88051 102790 111460 115350 144160 105990 FALSE TRUE 92573.28923 105442.7594 99953.32455 108044.3253 100744.6801 115747.9383 104163.3748 113332.5059 93459.98294 0.990512584 1.12821291 1.069477239 1.156049059 1.077944559 1.23847592 1.114523794 1.212631356 1 16.51206115 6.045476553 0.81811002 1.141900547 5.91E-17 0.249127624 0.069896605 22.71448186 2.201802765 0.022743325 38.03697312 1110392.584 -6.045476553 -1.141900547 EKQPPPPAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKQPPPPAHR 10 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 0 96.171 0.0041591 71827000 156060 152620 83223 112540 134310 135200 166310 191580 156380 FALSE TRUE 135436.2756 151617.4292 123469.9212 138093.9271 131637.4938 140401.2315 150181.2818 150612.1079 137892.9345 0.982184301 1.099530079 0.895404261 1.001457598 0.954635524 1.018190177 1.089115133 1.092239485 1 17.07318901 2.423621869 5.073646784 1.067585147 0.988352537 0.263495063 0.055798476 0.240704923 13.23782985 0.020589656 0.015938572 265.2295258 -2.423621869 -0.07923261 EKQPVAGSEGAQYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKQPVAGSEGAQYR 14 1 Q9UGI8-2;Q9UGI8;F8W7T0 Q9UGI8-2 TES Testin 0 ; 106.38 0.00086207 658260000 461310 385020 258160 294420 382760 353380 412390 505430 274160 FALSE TRUE 400346.7147 382490.7783 383007.0395 361272.5609 375143.8249 366974.7573 372396.4813 397347.7278 241749.1171 1.656042096 1.582180662 1.584316187 1.494411087 1.551789844 1.517998335 1.540425403 1.643636728 1 17.8831511 1.234001314 24.99993618 0.999999148 1.569349715 0.927081124 0.050354913 35.61386674 195256.0704 0.099462925 0.012761897 17.13962493 -1.234001314 0.569350567 EKQS(ph)S(ph)EEEEKETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKQSSEEEEKETR 13 2 Q92504;A2AAT0 Q92504 SLC39A7 Zinc transporter SLC39A7 2 EKQS(1)S(0.979)EEEEKET(0.021)R 114.9 0.0011239 1183900000 2646100 1780000 1839400 1847800 2645800 2023200 2359500 4138200 3359100 TRUE FALSE 2296411.181 1768307.063 2728939.992 2267371.232 2593153.756 2101033.813 2130676.053 3253278.134 2961991.025 0.775293092 0.596999467 0.921319467 0.765488893 0.875476575 0.709331593 0.719339132 1.098341658 1 21.49813584 1.736657316 8.35062027 1.044466861 0.767640075 0.622082098 0.091540062 0.064638147 15.89895405 0.050149136 0.022883533 54.53273963 -1.736657316 -0.276826786 EKRPPQTLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKRPPQTLSR 10 2 Q8TD06;B5MC62 Q8TD06 AGR3 Anterior gradient protein 3 homolog 0 133.91 0.00010382 262170000 150130 151720 116250 121620 161080 160990 151610 164220 156330 FALSE TRUE 130289.9401 150723.3413 172468.8888 149235.6798 157874.8231 167183.3895 136906.8855 129102.831 137848.8455 0.945165262 1.093395747 1.251144964 1.08260377 1.145274903 1.212802246 0.993166719 0.936553589 1 17.07272766 2.101895786 6.820890475 0.96421325 1.125225954 0.408653931 0.082533833 0.195436198 11.39103483 0.03408968 0.022865144 126.4432896 -2.101895786 0.161012704 EKS(ph)PVREPVDNLSPEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EKSPVREPVDNLSPEER 17 2 Q86U06-3;Q86U06-5;Q86U06-2;Q86U06 Q86U06-3 RBM23 Probable RNA-binding protein 23 1 EKS(1)PVREPVDNLSPEER;EKS(1)PVREPVDNLSPEER;EKS(1)PVREPVDNLSPEER;EKS(1)PVREPVDNLSPEER 248.97 3.12E-21 1738220000 1303670 800842 643901 711614 804330 803990 891750 1031570 1023440 TRUE FALSE 1131386.706 795581.2162 955293.6773 873196.835 788325.4066 834920.0156 805268.2223 810976.7832 902450.0891 1.253683412 0.881579187 1.058555691 0.967584629 0.873539065 0.925170295 0.892313306 0.898638931 1 19.78348762 EKSTFREES(ph)PLR ddPTM_MDA-MB-175_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 EKSTFREES(1)PLR;EKSTFREES(1)PLR;EKSTFREES(1)PLR;EKSTFREES(1)PLR;EKSTFREES(1)PLR;EKS(0.09)T(0.021)FREES(0.889)PLR 186.85 5.86E-06 7768160000 7948840 6410900 2572270 2691650 5691770 5135640 7368570 7385240 848084 TRUE FALSE 6898380.654 6368786.376 3816228.376 3302830.272 5578514.913 5333211.394 6653967.216 5805963.898 747824.4757 9.224598657 8.516418736 5.103107079 4.41658488 7.459658107 7.131635253 8.897766029 7.763805662 1 19.51234016 4.370141217 6.117061644 6.330140521 9.045027515 0.218606752 2.216453842 0.331904388 16.31201133 0.5629978 1.532481494 23449.91199 -4.370141217 2.714886995 EKT(ph)PELPEPSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 EKTPELPEPSVK 12 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 EKT(1)PELPEPSVK;EKT(1)PELPEPSVK;EKT(1)PELPEPSVK;EKT(1)PELPEPSVK;EKT(1)PELPEPSVK;EKT(1)PELPEPSVK;EKT(0.994)PELPEPS(0.006)VK 138.08 0.0001305 23467110000 20721530 13447000 12304200 11095870 14331940 9638050 19519730 21385450 19516140 TRUE FALSE 17983127.31 13358665.77 18254552.28 13615356.87 14046762.43 10008832.02 17626709.59 16812337.94 17208964.16 1.04498604 0.776262048 1.060758341 0.791178176 0.816246829 0.581605722 1.024274873 0.976952348 1 24.03665693 EKT(ph)PS(ph)PKEEDEEPES(ph)PPEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKTPSPKEEDEEPESPPEKK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 EKT(1)PS(1)PKEEDEEPES(1)PPEKK 91.655 0.0029871 525900000 775710 423460 593820 308110 411600 246540 786950 738920 638810 TRUE FALSE 673197.9581 420678.2634 880993.3382 378071.0847 403409.9653 256024.5533 710631.7101 580907.7083 563290.6095 1.1951166 0.746822788 1.564012116 0.671183006 0.716166679 0.454515927 1.261572087 1.031275328 1 19.1035199 IFCCHGGLSPDLQSMEQIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 127.62 1.38E-05 458720000 208220 212610 102750 119700 196960 212150 184340 219010 61052 FALSE TRUE 180703.1994 211213.3509 152440.2437 146879.7145 193040.8813 220311.5478 166462.7352 172176.4158 53834.50211 3.356642903 3.923382638 2.831645835 2.728356514 3.585820873 4.092385722 3.092119898 3.198254077 1 15.71624346 1.202217653 3.327380328 0.488061007 3.373587652 0.746841594 0.43066156 0.211059434 3.0096952 1.661946056 0.114822788 15.93006886 -1.202217653 2.885526645 LPSS(ph)PVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 LPSSPVYEDAASFK 14 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 LPSS(1)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPS(0.001)S(0.999)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPS(0.003)S(0.997)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPS(0.001)S(0.999)PVYEDAASFK;LPS(0.129)S(0.871)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPS(0.011)S(0.989)PVYEDAASFK;LPSS(1)PVYEDAASFK 395.34 2.74E-114 1.611E+11 11859793 13495790 13244200.8 19595545 16512699 14270862 19653271 24055219 40749176 TRUE FALSE 10292491.31 13407135.27 19649140.61 24045012.99 16184128.6 14819871.3 17747299.8 18911197.61 35931854.83 0.286444754 0.373126724 0.546844595 0.66918374 0.450411722 0.412443815 0.493915493 0.526307303 1 25.09876007 1.203294504 3.085099312 1.127007288 0.468716008 0.730296347 0.101817451 0.250813964 2.855182644 0.428144798 0.027970558 15.96961714 -1.203294504 -0.65829128 ASPSSPGRQDS(ph)DEDDGPQRVEEVDQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ASPSSPGRQDSDEDDGPQRVEEVDQGR 27 2 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 ASPS(0.001)S(0.007)PGRQDS(0.992)DEDDGPQRVEEVDQGR;ASPSSPGRQDS(1)DEDDGPQRVEEVDQGR;ASPSSPGRQDS(0.999)DEDDGPQRVEEVDQGR;ASPSSPGRQDS(1)DEDDGPQRVEEVDQGR;AS(0.001)PSS(0.001)PGRQDS(0.998)DEDDGPQRVEEVDQGR 145.29 1.27E-07 2646030000 1337260 1391940 781930 770949 1328750 1394340 1341460 1427880 493130 TRUE FALSE 1160537.703 1382796.254 1160073.963 946004.7537 1302310.475 1447981.162 1211365.416 1122538.974 434832.7332 2.668929026 3.180064767 2.667862548 2.175560121 2.994968813 3.329972772 2.785819289 2.581542023 1 18.73010102 1.203482855 2.872783547 0.518359627 2.832324082 0.767064891 0.314008033 0.243159204 2.250058617 1.391619549 0.085105082 15.97654454 -1.203482855 2.313964456 EKTPSPKEEDEEPES(ph)PPEK ddPTM_MDA-MB-175_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 192.18 4.19E-15 2071480000 3394730 2257730 2276510 1800180 2021630 1248340 3519910 3897750 2073300 TRUE FALSE 2946107.829 2242898.823 3377437.85 2208938.383 1981403.518 1296364.448 3178549.67 3064246.495 1828196.836 1.61148284 1.226836618 1.847414777 1.208260697 1.083802072 0.709094569 1.738625518 1.676103161 1 20.80198998 EKTPSPKEEDEEPES(ph)PPEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EKTPSPKEEDEEPESPPEKK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 EKTPSPKEEDEEPES(1)PPEKK;EKTPSPKEEDEEPES(1)PPEKK;EKTPSPKEEDEEPES(1)PPEKK;EKTPSPKEEDEEPES(1)PPEKK;EKTPSPKEEDEEPES(1)PPEKK;EKTPSPKEEDEEPES(1)PPEKK 172.66 1.86E-11 18640990000 9543580 5618810 6737860 4492320 4242260 2617280 9975730 10527860 4068860 TRUE FALSE 8282371.723 5581899.667 9996311.633 5512369.917 4157847.326 2717968.455 9008285.24 8276559.067 3587844.006 2.308453687 1.555781037 2.786161164 1.53640178 1.158870709 0.757549228 2.510779517 2.306833589 1 21.77468573 EKVAS(ph)DTEEADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKVASDTEEADR 12 1 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 EKVAS(0.995)DT(0.005)EEADR 85.362 0.0090517 0 403670 309280 283720 294060 312900 253330 355250 378430 415370 TRUE FALSE 350323.9867 307248.3193 420927.941 360830.8174 306673.9022 263075.769 320797.9097 297505.6894 366265.4318 0.956475704 0.838867916 1.149242884 0.985162088 0.837299607 0.718265351 0.875861825 0.812267999 1 18.48253002 3.238879608 24.9999996 0.839690607 0.98409692 0.300154357 0.10090589 10.17289382 797231.7705 0.029608347 0.035873122 1733.323431 -3.238879608 0.144406313 EKVESELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EKVESELR 8 1 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;;;;; 142.92 0.00055605 10430640000 19884800 13565900 9263240 11913600 13188300 11419700 16572500 18151900 16700700 FALSE TRUE 17256973.3 13476784.71 13742973.85 14618764.97 12925878.63 11859023.25 14965301.5 14270257.44 14726362.27 1.171842236 0.915146895 0.933222584 0.992693559 0.87773738 0.805292103 1.016225272 0.969028004 1 23.81189776 4.742381801 24.59490149 0.940121589 1.17184235 0.574933191 0.062997974 237.2879796 1527216.112 0.015959498 0.115582566 55256.30005 -4.742381801 0.231720761 EKVEVFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKVEVFR 7 1 Q9BW83-2;Q9BW83 Q9BW83-2 IFT27 Intraflagellar transport protein 27 homolog 0 ; 96.711 0.011429 416050000 619200 603260 362890 468220 564340 493450 630980 654360 599240 FALSE TRUE 537371.1511 599297.1453 538384.8178 574536.5073 553110.7381 512433.3408 569787.6567 514430.2062 528398.5299 1.016980784 1.134176406 1.018899159 1.087316627 1.046768125 0.969785705 1.078329376 0.973564795 1 19.01126693 2.969023929 9.925631842 1.007354341 1.066218719 0.288397987 0.043933842 0.640150896 201.5250902 0.012892954 0.013103687 931.1591807 -2.969023929 0.058864378 EKVFDVIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKVFDVIIR 9 1 B3KWE1;P12081-4;P12081;B4DDD8;E7ETE2 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 ; 126.67 0.00042587 1159180000 1902350 1799010 1128800 1469990 1686470 1549210 1884100 2169330 1700910 FALSE TRUE 1650949.628 1787192.185 1674691.456 1803773.697 1652912.547 1608809.111 1701380.272 1705435.661 1499830.357 1.100757575 1.19159622 1.116587251 1.202651812 1.102066336 1.07266072 1.134381808 1.137085706 1 20.5163679 3.081059219 12.72026205 1.097301369 1.153048773 0.292582889 0.048353675 0.997028086 152.764979 0.014117243 0.016009759 1205.200266 -3.081059219 0.055747404 EKVGEVTYVELFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKVGEVTYVELFK 13 1 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WUT0 A0A0A0MQW0 MYEF2 Myelin expression factor 2 0 95.508 0.0017184 0 188910 144660 103410 110810 140970 131980 208990 236000 163670 FALSE TRUE 163945.0649 143709.7189 153419.4219 135971.1041 138164.9728 137057.356 188722.182 185533.2366 144321.1191 1.13597418 0.995763613 1.063042075 0.942142806 0.957344107 0.949669438 1.307654647 1.285558467 1 17.1389229 2.243834313 24.99998644 1.220613577 1.004095498 0.43953221 0.10021451 102.6381791 486559.3745 0.038133224 0.028646772 175.3211511 -2.243834313 -0.216518079 EKVLATVTKPVGGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EKVLATVTKPVGGDK 15 2 Q02878;F8VZ45;U3KQR5;F8VZA3;F8VWR1;F8VU16 Q02878 RPL6 60S ribosomal protein L6 0 ; 186.94 2.03E-07 1230720000 2427850 1800300 1394770 1634850 1542900 1182780 2431910 2802400 1334660 FALSE TRUE 2107003.471 1788473.711 2069285.437 2006067.68 1512199.309 1228282.312 2196063.743 2203128.568 1176878.015 1.790332935 1.519676371 1.758283705 1.704567214 1.284924426 1.043678526 1.866007958 1.872010981 1 20.16653336 3.292339774 24.99916924 1.486128177 1.685467745 0.153920364 0.299987048 260.4105911 121049.3034 0.093218006 0.120343834 1960.377792 -3.292339774 0.199339568 EKVMYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKVMYEK 7 1 E5RJD8;O75347;E5RHG6;O75347-2;E5RIX8;A0A494C144 E5RJD8 TBCA Tubulin-specific chaperone A 0 68.735 0.056221 211930000 268070 242210 161400 178970 224140 187790 268350 315390 194910 FALSE TRUE 232643.8703 240618.9066 239453.5799 219607.8739 219680.0525 195014.4028 242325.4583 247946.3029 171867.9618 1.353619766 1.400021877 1.393241517 1.277770863 1.278190828 1.134675717 1.409951312 1.442655747 1 17.39094111 3.736734021 23.71620192 1.281840258 1.384067138 0.160433523 0.126781107 176.1979824 2287751.726 0.035338215 0.055681917 5454.237198 -3.736734021 0.10222688 EKVS(ph)SIDLEIDSLSSLLDDMTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 EKVSSIDLEIDSLSSLLDDMTK 22 1 Q15942;H7C3R3;C9IZ41 Q15942 ZYX Zyxin 1 EKVS(0.496)S(0.496)IDLEIDS(0.007)LS(0.001)SLLDDMTK;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)IDLEIDS(0.001)LSSLLDDMTK;EKVS(0.5)S(0.5)IDLEIDSLSSLLDDMTK;EKVS(0.5)S(0.5)IDLEIDSLSSLLDDMTK;EKVS(0.499)S(0.499)IDLEIDS(0.001)LSSLLDDMTK;EKVS(0.5)S(0.5)IDLEIDSLSSLLDDMTK;EKVS(0.5)S(0.5)IDLEIDSLSSLLDDMTK;EKVS(0.5)S(0.5)IDLEIDSLSSLLDDMTK 267.24 1.38E-37 5495575000 2046074.1 1792874.5 1776290 2031596.4 2085996.4 1450725.9 3326190 3965620 2749640.1 TRUE FALSE 1775680.224 1781096.989 2635309.785 2492901.414 2044489.153 1506536.264 3003616.606 3117603.023 2424580.78 0.732365875 0.734599979 1.086913584 1.028178329 0.843234084 0.621359485 1.238818946 1.285831782 1 21.20930389 2.216049913 24.99964155 1.200661933 0.856039975 0.502620712 0.155345972 194.6879729 216212.3766 0.066513269 0.044879746 164.4560722 -2.216049913 -0.344621958 EKYDTDFYILDKYPLAVRPFYTMPDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKYDTDFYILDKYPLAVRPFYTMPDPR 27 3 P14868;P14868-2 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 56.95 0.030925 473670000 1531800 1092800 655610 816440 917780 847980 1262800 1678300 777890 FALSE TRUE 1329368.749 1085621.325 972665.1889 1001825.181 899517.9736 880602.3393 1140333.85 1319408.606 685928.7304 1.938056667 1.582702804 1.418026605 1.460538298 1.311386932 1.283810257 1.662466959 1.923535999 1 19.38769916 4.707910524 3.035735776 1.483741224 1.994849529 0.281824899 0.243720208 0.52033909 7.423429161 0.064856657 0.617354014 51039.98336 -4.707910524 0.511108305 EKYDYVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKYDYVGR 8 1 U3KQM0;O15173;O15173-2;U3KPU8 U3KQM0 PGRMC2 Membrane-associated progesterone receptor component 2 0 70.552 0.054664 0 334230 339910 178260 286980 387130 405870 276150 463290 445100 FALSE TRUE 290060.6587 337677.1088 264467.1322 352143.1952 379426.8704 421484.0815 249369.0155 364219.0388 392480.7851 0.739044228 0.860365964 0.673834599 0.897224039 0.96673999 1.073897367 0.635366176 0.927992026 1 18.5822625 3.617959517 7.766241673 0.909972456 0.768409108 0.274943627 0.121210944 0.412790415 24.52370103 0.033448084 0.049689473 4149.153644 -3.617959517 -0.141563348 EKYEITEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EKYEITEQR 9 1 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ;;;;; 140.3 9.98E-05 15112380000 21751380 18515520 14694360 17686580 18739550 17155390 21351130 24648100 26664410 FALSE TRUE 18876880.02 18393890.33 21800601.65 21702588.31 18366669.62 17815368.95 19280500.7 19377295.63 23512173.83 0.802855583 0.782313472 0.927204852 0.923036231 0.781155743 0.757708287 0.820022038 0.824138838 1 24.48690459 1.237799572 24.97681673 1.000000197 0.827905147 0.47922065 0.056574309 18.13800748 594869.5292 0.086302058 0.014769777 17.2901823 -1.237799572 -0.17209505 EKYIDQEELNK ddPTM_MDA-MB-175_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 ;;;;; 202.44 3.65E-08 10014710000 19388100 13308600 10745950 12625570 12722110 9220770 18315070 22004400 14861420 FALSE TRUE 16825913.46 13221174.93 15942727.36 15492398.64 12468964.9 9575498.989 16538877.33 17298930.3 13104519.86 1.283977868 1.008901896 1.216582335 1.182217953 0.951501088 0.730702009 1.26207427 1.320073569 1 23.64356116 -1.304462427 11.0503101 0.073703556 1.115313711 0 0.184398672 0 0 0 0.04340863 0.049606384 1.304462427 1.041610156 ELAAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELAAFR 6 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 114.67 0.058367 602580000 507700 596380 329000 396260 552720 563420 470470 557130 552480 FALSE TRUE 440606.1587 592462.3405 488105.5004 486236.8895 541721.9534 585095.132 424843.8918 437992.0851 487166.4438 0.90442633 1.21613947 1.001927589 0.998091916 1.11198536 1.2010169 0.872071337 0.899060456 1 18.89405524 2.21833622 24.99999917 0.916423481 1.074041258 0.336318397 0.098175615 251.6022573 311011.0746 0.038407042 0.025928853 165.3241203 -2.21833622 0.157617777 ELAEAMAAQHTAESECEQLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELAEAMAAQHTAESECEQLVK 21 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 309.83 1.68E-66 298500000 158163 169609 115331 142924 154243 126746 164639 233400 203760 FALSE TRUE 137261.3588 168494.8273 171105.4574 175377.0787 151173.8661 131622.0006 148672.3351 183489.2263 179671.7249 0.76395637 0.937792674 0.952322673 0.976097261 0.841389296 0.732569361 0.82746651 1.02124709 1 17.45500386 1.701335384 6.917654701 1.009616116 0.866875231 0.38064063 0.078545206 0.143311492 15.26301588 0.05054565 0.022009535 50.27306738 -1.701335384 -0.142740885 ELAEDGYSGVEVR ddPTM_MDA-MB-175_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 ;;; 211.84 4.34E-08 570370000 571110 602210 366893 475111 579250 534640 557780 631970 604100 FALSE TRUE 495636.3665 598254.0429 544323.682 582992.2142 567724.0583 555207.9468 503686.5815 496828.1335 532683.9862 0.930451035 1.123093726 1.021851034 1.094442914 1.065780224 1.042283908 0.945563588 0.932688322 1 19.02292038 2.26980773 6.094237951 0.953084691 1.05231743 0.367507832 0.053208686 0.151800164 16.32389854 0.018899502 0.014149897 186.126294 -2.26980773 0.099232739 ELAEEEPHLVEQFQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELAEEEPHLVEQFQK 15 0 Q5QNY5;P40855;E9PS71;P40855-5;B7Z8B3 Q5QNY5 PEX19 Peroxisomal biogenesis factor 19 0 ; 151.72 2.96E-06 224670000 759390 693120 424870 560590 669120 611110 717550 866390 814830 FALSE TRUE 659034.6875 688566.8491 630338.5531 687880.5276 655805.8211 634619.7971 647962.1114 681119.2408 718501.7257 0.917234662 0.958337085 0.87729581 0.957381873 0.912740774 0.883254381 0.901824016 0.947971614 1 19.4546321 1.367864502 2.764556401 1.005738218 0.916129173 0.510427373 0.026563517 0.28291468 3.069031612 0.050614719 0.006823443 23.32730146 -1.367864502 -0.089609045 ELAGHTGYLSCCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELAGHTGYLSCCR 13 0 P62873-2;P62873;B3KVK2;F6X3N5;F6UT28 P62873-2 GNB1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 0 ; 165.58 3.51E-05 978780000 990910 976920 849930 875690 885800 1326300 673270 1006420 688810 FALSE TRUE 859958.7329 970502.5482 1260958.991 1074528.799 868174.313 1377323.619 607976.379 791204.915 607379.6665 1.415850382 1.597851561 2.076063886 1.769122112 1.42937665 2.267648549 1.000982437 1.302652951 1 19.21223909 2.213568706 24.99971437 1.139002243 1.751825347 0.559907001 0.274310698 171.0599656 171112.0714 0.107829172 0.072731916 163.5191821 -2.213568706 0.612823104 ELAILLGMLDPAEKDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELAILLGMLDPAEKDEK 17 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 118.19 0.00016485 2363400000 784340 574010 509080 508220 470230 311910 880230 914020 718510 FALSE TRUE 680687.4817 570239.2905 755272.7908 623619.1187 460873.343 323909.3795 794865.4301 718563.9359 633568.5663 1.074370665 0.900043532 1.192093218 0.984296179 0.727424572 0.511245975 1.254584701 1.134153388 1 19.27314123 -1.026682898 12.53327188 1.237966315 0.982416686 0 0.222021044 0 0 0 0.05277262 0.09404097 1.026682898 -0.255549629 ELALGQDR ddPTM_MDA-MB-175_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 ;;; 140.35 0.0015143 2019290000 1675480 1873790 1104530 1357870 1738640 1862320 1775490 1843750 1932080 FALSE TRUE 1454061.073 1861480.95 1638684.402 1666195.137 1704044.466 1933964.655 1603303.253 1449478.411 1703671.703 0.853486661 1.092628906 0.961854563 0.978002472 1.000218799 1.135174489 0.941086977 0.850796787 1 20.70021593 2.012619909 24.99184201 0.909101248 1.007210999 0.141322386 0.082947959 309.6777914 613268.3394 0.031985586 0.021549581 102.9484729 -2.012619909 0.09810975 ELAPEPWVERAT(ph)PT ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELAPEPWVERATPT 14 1 Q9BTY7 Q9BTY7 HGH1 Protein HGH1 homolog 1 ELAPEPWVERAT(0.839)PT(0.161);ELAPEPWVERAT(0.888)PT(0.112) 100.11 0.012187 82504000 203448 214206 91199 116096 225260 221438 231170 233216 53824 TRUE FALSE 176561.8313 212798.8667 135303.1414 142457.3712 220777.7667 229956.8631 208751.169 183344.5733 47460.98804 3.720146559 4.48365859 2.850828587 3.001567753 4.651773506 4.845176484 4.398373856 3.863058501 1 15.53445451 4.313704716 24.99998562 3.663641881 4.101894987 0.032265105 1.127313654 198.7460644 66112.08265 0.285268677 0.754749846 20592.29331 -4.313704716 0.438253106 ELAPLFEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELAPLFEELR 10 0 Q9UHA4;Q9UHA4-2 Q9UHA4 LAMTOR3 Ragulator complex protein LAMTOR3 0 83.948 0.035491 23938000 21527 25905 22077 31627 30804 30170 19622 29707 36377 FALSE TRUE 18682.15241 25734.82835 32753.51104 38808.39374 30191.06067 31330.65942 17719.06146 23354.38923 32076.5525 0.58242395 0.802294085 1.021104467 1.209867979 0.941219 0.97674647 0.552399185 0.728082896 1 14.96923147 1.187995306 22.01869282 1.000010421 0.853574096 0.051333093 0.200130858 14204.70491 6183179.36 36.08174781 0.053529523 15.4168379 -1.187995306 -0.146436325 ELAPYDENWFYTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ELAPYDENWFYTR 13 0 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ;;;;; 274.53 8.33E-32 7656670000 914800 892677 679265 921974 919742 821897 731535 877779 1265019 FALSE TRUE 793906.8622 886812.946 1007759.826 1131322.288 901440.9336 853515.9094 660590.8483 690072.7917 1115469.895 0.711724149 0.795012891 0.903439735 1.014211404 0.808126636 0.765162658 0.592208585 0.618638652 1 20.08922015 2.700567983 3.185952723 0.705275438 0.858484102 0.109691474 0.134084876 0.412056504 8.519516129 0.049723304 0.044972471 501.8431292 -2.700567983 0.153208664 ELASS(ph)LAYEERPRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELASSLAYEERPRR 14 2 Q9Y250-5;Q9Y250-4;Q9Y250-3;Q9Y250-2;Q9Y250 Q9Y250-5 LZTS1 Leucine zipper putative tumor suppressor 1 1 ELAS(0.004)S(0.996)LAYEERPRR 52.254 0.075045 93990000 54435 35748 21940 21972 27532 27567 50983 50963 6991.9 TRUE FALSE 47241.27683 35513.16903 32550.25738 26961.07842 26984.16707 28627.52033 46038.67651 40064.95904 6165.325547 7.662414007 5.760144985 5.279568311 4.37301781 4.376762729 4.643310415 7.467355317 6.498433657 1 12.58996136 4.747616087 2.012435937 5.059675906 8.46042762 0.216030008 1.682930053 1.372183227 5.895972358 0.450103924 8.669222002 55926.29984 -4.747616087 3.400751715 ELAVEGMHR ddPTM_MDA-MB-175_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" 0 113.62 0.0017705 270540000 210380 192200 133080 143260 187510 206500 174860 213900 234020 FALSE TRUE 182577.75 190937.4255 197437.9331 175789.3726 183778.9179 214444.1886 157902.1041 168159.1496 206354.4222 0.884777501 0.925288751 0.956790414 0.851880811 0.890598398 1.039203262 0.765198547 0.814904511 1 17.65476483 2.220089578 24.99998121 0.84668087 0.921371677 0.127030579 0.077046255 432.138952 584882.3626 0.031044544 0.020971794 165.9929251 -2.220089578 0.074690808 ELAVQIYEEAR ddPTM_MDA-MB-175_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 ; 131.37 0.0004764 200821000 161089 147705 113214 135191 146619 157071 148884 173965 170836 FALSE TRUE 139800.6805 146734.7161 167964.6691 165888.1828 143701.5688 163113.623 134445.2526 136763.9385 150639.9627 0.928045108 0.974075627 1.115007373 1.101222941 0.953940549 1.082804457 0.892493932 0.907886168 1 17.20074502 2.231190908 24.99994751 0.926425217 1.027706123 0.290805651 0.067675912 200.9764345 681756.0455 0.027853597 0.019208326 170.2906912 -2.231190908 0.101280906 ELCQQIHAECK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELCQQIHAECK 11 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 75.78 0.022238 0 128160 119510 98323 101570 116020 97018 127720 134440 149990 FALSE TRUE 111223.3313 118724.9309 145872.3317 124633.0209 113711.429 100750.3452 115333.7341 105691.0522 132258.3531 0.84095506 0.897674349 1.102934736 0.942345175 0.859767465 0.761769241 0.872033648 0.799125724 1 17.01299932 3.235405007 5.094305288 0.846540128 0.954660966 0.183926224 0.089373421 0.259188047 18.9056011 0.026847553 0.032624266 1719.511194 -3.235405007 0.108120838 ELCQQIHAECKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELCQQIHAECKR 12 1 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 72.496 0.027093 85943000 100420 83735 60820 59749 86605 87292 80111 95988 60859 FALSE TRUE 87149.24257 83184.93927 90232.75543 73315.92366 84881.72994 90650.17973 72341.84755 75461.71318 53664.31835 1.623969991 1.550097753 1.681429266 1.366195005 1.581716354 1.689207699 1.348043724 1.40618041 1 15.71167553 0.72517959 0.976939474 1.74E-17 1.57137848 0.729056371 0.107790964 2.516715538 0.941224895 5.337182002 0.034942927 5.311040215 -0.72517959 1.57137848 ELCSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELCSER 6 0 Q13243;Q13243-3;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ; 109.11 0.069422 570020000 658250 594650 369220 359990 444890 597380 434670 495010 501330 FALSE TRUE 571260.5947 590743.705 547776.027 441731.2316 436037.5594 620361.5952 392515.7703 389155.9637 442063.3385 1.292259604 1.336332723 1.23913471 0.999248735 0.986368969 1.403331924 0.887917491 0.880317207 1 18.75389357 8 0.1059085 0.550579297 2.950753794 0.405547206 0.147357816 259.4318457 2.511555235 8.425150797 91.96806413 100000000 -8 2.400174498 ELDAFFLHMLMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELDAFFLHMLMK 12 0 O76038 O76038 SCGN Secretagogin 0 ; 124.1 0.00023366 0 185239 218297 126914 158729 183329 165925 194362 231678 156934 FALSE TRUE 160759.1968 216862.9926 188290.0349 194770.8455 179681.1116 172308.2421 175512.8032 182135.4626 138381.4413 1.161710669 1.567139283 1.360659588 1.407492534 1.298448043 1.24516872 1.268326168 1.316184171 1 17.07829095 0.641733917 1.347265989 7.23E-33 1.346031289 0.468472179 0.108511221 5.123567969 2.472412381 14.25531431 0.030907131 4.382621015 -0.641733917 1.346031289 ELDALDANDELTPLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELDALDANDELTPLGR 16 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;; 225.72 1.54E-14 215149000 581556 504222 341935 399065 515736 497666 467938 611939 569877 FALSE TRUE 504701.9011 500909.7325 507295.9097 489678.8076 505473.8626 516811.5331 422557.4448 481080.607 502506.7903 1.004368321 0.996821819 1.009530457 0.974472021 1.005904542 1.028466765 0.840898975 0.957361405 1 18.93878357 ELDALGHELPVLAPQWEGYDELQTDGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 290.72 3.73E-71 2030295000 564653 602968 402665.8 472073.7 586303 620841 645796 700229 644555 FALSE TRUE 490032.6754 599007.0635 597396.3277 579265.2488 574636.7174 644725.155 583166.8033 550490.4775 568356.4422 0.862192524 1.053928519 1.051094495 1.019193601 1.011049888 1.134367638 1.026058227 0.968565563 1 19.11643647 4.743540846 24.70071073 1.030280647 0.862192442 0.60268757 0.043541531 346.7369597 1719662.411 0.011453388 0.092259938 55403.96502 -4.743540846 -0.168088206 ELDAVEVFFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELDAVEVFFSR 11 0 Q6PCB6-2;Q6PCB6 Q6PCB6-2 ABHD17C Alpha/beta hydrolase domain-containing protein 17C 0 78.934 0.038989 0 13496 11257 7316.3 9409.9 13713 11510 12702 12331 10207 FALSE TRUE 11712.46941 11183.05203 10854.48715 11546.56162 13440.13813 11952.79715 11470.162 9694.11161 9000.340088 1.301336315 1.242514385 1.206008556 1.282902813 1.493292253 1.328038389 1.274414287 1.077082812 1 13.1357638 1.681835882 2.695502779 1.008113572 1.308749563 0.692362917 0.074819048 0.144506792 2.315887971 0.073223216 0.02257454 48.06576762 -1.681835882 0.300635991 ELDCQLCGAWFETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELDCQLCGAWFETR 14 0 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3 M0QXA7 WIZ Protein Wiz 0 134.13 9.43E-05 29150000 24755 20990 19079 15063 21634 20762 15898 21038 17724 FALSE TRUE 21483.56403 20852.11531 28305.66822 18483.28437 21203.52573 21560.72757 14356.21441 16539.18742 15628.68891 1.374623563 1.334220383 1.811135174 1.182650987 1.356705341 1.379560864 0.918580854 1.05825815 1 13.93190914 2.266783796 9.310428184 1.002996268 1.409637351 0.59477781 0.161076875 0.195917492 60.63164443 0.05973309 0.045659193 184.8348232 -2.266783796 0.406641083 ELDDLEQWIQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ELDDLEQWIQER 12 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 ;;;; 289.62 1.02E-35 292847000 334803 325302 241823 287971 348369 393065 314455 384608 406953 FALSE TRUE 290557.9353 323165.0697 358769.4116 353359.2169 341437.1385 408186.4649 283959.2025 302362.5722 358843.4799 0.809706603 0.900573893 0.999793592 0.984716838 0.951493221 1.137505591 0.791317715 0.842602943 1 18.45299518 ELDDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ELDDTR 6 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 114.54 0.058621 5036500000 16593900 16038000 10435500 12183200 11899900 15841600 15619900 17041900 17143000 FALSE TRUE 14400974.07 15932645.32 15482142.7 14949581.77 11663115.27 16451036.6 14105084.5 13397622.31 15116374.07 0.952673836 1.053999144 1.02419685 0.988966117 0.771555084 1.088292505 0.933099726 0.886298675 1 23.84960879 3.462327112 24.99928979 0.931906736 1.013314354 0.148242663 0.08322548 394.5531984 666717.3422 0.022956195 0.029648018 2899.526695 -3.462327112 0.081407618 ELDEEGS(ph)DPPLPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ELDEEGSDPPLPGR 14 0 C9JQV0;Q9BRJ6;H7C0T1;H7C2R9 C9JQV0 C7orf50 Uncharacterized protein C7orf50 1 ELDEEGS(1)DPPLPGR;ELDEEGS(1)DPPLPGR;ELDEEGS(1)DPPLPGR;ELDEEGS(1)DPPLPGR;ELDEEGS(1)DPPLPGR;ELDEEGS(1)DPPLPGR 218.16 5.76E-12 2988940000 4976610 5415350 3725170 3816000 5488810 4681180 5430360 5870150 5397150 TRUE FALSE 4318938.379 5379776.209 5526674.672 4682481.124 5379593.42 4861268.024 4903724.523 4614864.104 4759105.075 0.907510616 1.130417615 1.16128444 0.983899504 1.130379207 1.02146684 1.03038795 0.969691577 1 22.18225888 2.181441423 1.891314958 0.985180347 1.067186437 0.126095832 0.075474022 0.616214508 4.408288969 0.045700481 0.022845417 151.8593102 -2.181441423 0.08200609 ELDEETER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELDEETER 8 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 ; 176.09 0.00061035 150470000 405270 397510 265160 328480 386610 445720 335280 429140 819080 FALSE TRUE 351712.5427 394898.7306 393392.2629 403066.4045 378917.2174 462867.1368 302764.5972 337371.7506 722249.2955 0.486968343 0.546762362 0.544676562 0.558071025 0.524634942 0.640868935 0.419196805 0.467112606 1 19.46213737 1.234539615 24.99987486 1.000000692 0.522167255 0.86545125 0.05903839 42.83824443 266301.6611 0.112112247 0.015063498 17.16088239 -1.234539615 -0.477833437 ELDEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELDEGR 6 0 O15541 O15541 RNF113A RING finger protein 113A 0 119.22 0.049314 2203500000 2712500 2654400 1856100 2229500 1710400 2730300 2565200 3072300 3082000 FALSE TRUE 2354036.252 2636963.072 2753716.168 2735742.051 1676366.386 2835336.408 2316427.299 2415312.554 2717649.471 0.866203047 0.970310226 1.013271284 1.006657437 0.616844227 1.043304679 0.852364267 0.888750584 1 21.37392796 5.159032202 7.723784685 0.91742725 0.000125614 0.01865298 0.123834263 24719.3503 39073.00654 0.028992091 368370.1382 144222.2287 -5.159032202 -0.917301636 ELDFVSHHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ELDFVSHHVR 10 0 Q02818;H7BZI1;C9JKZ2;C9JBD3;C9J3C1 Q02818 NUCB1 Nucleobindin-1 0 ;; 123.79 0.00026176 569271000 470680 612370 229482 398509 634762 692640 541871 644760 603030 FALSE TRUE 408478.4454 608347.3011 340460.2628 488996.5593 622131.4781 719286.309 489320.4338 506883.0915 531740.4804 0.768191365 1.144068063 0.640275238 0.91961507 1.169990815 1.352701808 0.920224154 0.953252781 1 19.02036277 3.419564021 7.808039635 1.064152704 0.863746813 0.272755951 0.17297356 0.369756057 43.50637855 0.051406689 0.066542048 2627.628846 -3.419564021 -0.200405891 ELDFWQEGWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELDFWQEGWR 10 0 Q5JRX3-3;Q5JRX3;Q5JRX3-2 Q5JRX3-3 PITRM1 "Presequence protease, mitochondrial" 0 ; 91.855 0.02295 68591000 95210 87574 61799 88539 96675 90649 90082 106675 99911 FALSE TRUE 82627.75727 86998.72063 91685.20311 108643.1332 94751.35664 94136.32569 81345.86151 83863.3814 88099.6354 0.937889889 0.987503753 1.040699007 1.233184822 1.075502256 1.068521172 0.923339366 0.951915193 1 16.42684843 2.247203908 24.89965082 0.955601778 1.06212695 0.263954625 0.077437336 236.4268196 681101.1811 0.031440728 0.023962461 176.6867196 -2.247203908 0.106525172 ELDGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELDGER 6 0 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A590UJB9;A0A590UK79;A0A5F9UKJ4 P67936 TPM4 Tropomyosin alpha-4 chain 0 ; 124.32 0.042818 3286200000 9547600 9905200 6496200 7888900 6447300 9191300 9300200 10547000 11117000 FALSE TRUE 8285860.469 9840132.089 9637784.048 9680195.319 6319011.344 9544895.259 8398268.035 8291606.127 9802760.925 0.845257834 1.00381231 0.983170366 0.987496828 0.64461547 0.973694588 0.856724764 0.845843961 1 23.22475671 ELDGERER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELDGERER 8 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A590UJB9;A0A590UK79;A0A5F9UKJ4 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;;; 143.03 0.00055443 1729316000 2664390 2888750 1123372 1092030 2174850 2586080 2756930 2912510 244126 FALSE TRUE 2312284.111 2869773.611 1666638.457 1339992.102 2131574.74 2685568.171 2489563.353 2289692.402 215265.7024 10.74153516 13.33130907 7.742238722 6.224828606 9.902063898 12.47559709 11.56507203 10.63658714 1 17.71575895 4.237808166 24.99999917 8.970740237 12.03642229 0.153465853 3.309790469 40.18739208 1335430.332 0.851644531 1.959509538 17290.52443 -4.237808166 3.065682054 ELDGHVLK ddPTM_MDA-MB-175_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 87.616 0.018317 0 184280 158970 94467 122770 150800 145050 164070 181360 179900 FALSE TRUE 159926.9311 157925.7156 140151.5572 150646.8049 147799.375 150630.1674 148158.5167 142577.5753 158632.4269 1.008160401 0.995544976 0.883498789 0.949659586 0.931709726 0.949554705 0.933973712 0.89879212 1 17.27532818 4.373549856 8.146723975 0.932951788 1.004916928 0.443192626 0.031059851 0.183348054 12.62650983 0.00727819 0.019396703 23634.68702 -4.373549856 0.07196514 ELDGLWSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELDGLWSFR 9 0 F8WBK6;F2Z3L6;P08236-3;P08236-2;P08236 F8WBK6 GUSB Beta-glucuronidase 0 84.498 0.035947 29891000 47192 52205 34613 38654 47934 59733 40797 47227 47504 FALSE TRUE 40955.45763 51862.06192 51351.96257 47430.98149 46980.20718 62030.96716 36840.51322 37127.87357 41888.13124 0.97773418 1.238108753 1.225931094 1.132325078 1.121563693 1.480872155 0.879497656 0.886357841 1 15.3542539 2.185901568 24.99999916 0.912766698 1.193071086 0.499116593 0.129325313 75.09689955 35651.78584 0.050449656 0.034013183 153.4269204 -2.185901568 0.280304388 ELDLFLAYYVQEQDSGQS(ph)GSPSHNDPAK ddPTM_MDA-MB-175_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(0.093)GQS(0.468)GS(0.35)PS(0.089)HNDPAK 154.51 1.72E-08 34372000 44882 31273 23316 31629 29384 27361 39468 46991 55259 TRUE FALSE 38950.72998 31067.5656 34591.69559 38810.84787 28799.31589 28413.59537 35640.39943 36942.34033 48726.34397 0.799377232 0.63759279 0.709917732 0.796506463 0.591042002 0.583125945 0.731440049 0.758159495 1 15.57241436 1.123019408 1.838488677 1.185836377 0.6868018 0.627375824 0.074094956 0.811909536 2.010735804 0.786790237 0.020490346 13.27453778 -1.123019408 -0.499034577 ELDQDMVT(ph)EDEDDPGSHKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELDQDMVTEDEDDPGSHKR 19 1 Q9NRL2;Q9NRL2-2;A0A087WWN7 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 1 ELDQDMVT(1)EDEDDPGSHKR 130.83 1.28E-05 378190000 500320 424310 350110 380060 387770 332060 370190 510940 638700 TRUE FALSE 434201.4444 421522.6797 519424.367 466358.4319 380054.1357 344834.5631 334289.0308 401679.4571 563193.6136 0.770963011 0.748450745 0.922283837 0.828060583 0.674819683 0.612284221 0.593559697 0.713217351 1 19.10327145 4.740907884 20.67568568 0.749651869 0.770962944 0 0.128576531 334.10605 2940387.433 0.033079157 0.209473976 55069.08793 -4.740907884 0.021311075 ELDRYS(ph)LDSEDLYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELDRYSLDSEDLYSR 15 1 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;A0A590UJF3 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 ELDRYS(0.998)LDS(0.002)EDLYSR;ELDRYS(0.994)LDS(0.005)EDLYSR;ELDRYS(1)LDSEDLYSR;ELDRYS(0.994)LDS(0.006)EDLYSR 263.31 2.86E-25 743680000 753600 631497 394365 467019 553896 461657 690530 695602 624161 TRUE FALSE 654009.8506 627348.6546 585081.2331 573062.8019 542874.5533 479417.2435 623562.5069 546852.9255 550373.3976 1.188302075 1.139860061 1.063062342 1.041225474 0.986374988 0.871076338 1.132980826 0.993603484 1 19.07005121 4.210572744 1.379230182 1.002487923 1.198770161 0.533075766 0.062773351 0.462134079 1.449375307 0.018959295 0.097961345 16239.50338 -4.210572744 0.196282238 ELDTVTLEDIKEHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ELDTVTLEDIKEHVK 15 1 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;; 258.61 4.75E-25 940692000 2693290 2073230 1624560 1547260 1854300 1420460 2732440 3149510 1437780 FALSE TRUE 2337364.903 2059610.816 2410202.65 1898589.031 1817403.058 1475106.015 2467448.389 2476011.796 1267807.286 1.843627914 1.624545653 1.901079664 1.497537561 1.433501036 1.163509653 1.946233009 1.952987511 1 20.27390403 3.726975285 24.4110134 1.557505635 1.773230539 0.150185514 0.304766209 1375.70224 2898690.696 0.089091431 0.133471961 5333.045453 -3.726975285 0.215724904 ELDYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELDYER 6 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ;;; 144.58 0.026183 4037240000 4068130 4436810 2826230 3257440 4197140 4239640 4101660 4681480 4390070 FALSE TRUE 3530516.313 4407664.303 4193004.281 3997091.539 4113625.126 4402741.694 3703881.645 3680381.933 3871080.926 0.912023381 1.13861332 1.083161102 1.03255179 1.06265542 1.137341683 0.956808115 0.950737534 1 21.88430504 2.21146604 24.99941206 0.964823666 1.064364633 0.312248192 0.064044008 231.3323003 213442.208 0.024661125 0.016631546 162.7294062 -2.21146604 0.099540967 ELEAELEDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELEAELEDER 10 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 123.75 0.0010558 103680000 158630 127480 77279 94880 109840 124260 115210 139210 122570 FALSE TRUE 137666.6436 126642.5755 114651.3829 116423.9542 107654.3989 129040.3626 104036.9519 109441.0248 108079.9142 1.273748638 1.171749408 1.060801942 1.077202503 0.996062956 1.193934724 0.962592843 1.012593557 1 16.72173891 8 0.499421083 1.018553481 9.353921151 0.616293676 0.062285868 74.73528275 0.819656132 0.037808002 651.804889 100000000 -8 8.33536767 ELEAIFGRPVVDGEEGEPHSIS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 ELEAIFGRPVVDGEEGEPHSISPR 24 1 P36507;G5E9C7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 ELEAIFGRPVVDGEEGEPHS(0.193)IS(0.807)PR;ELEAIFGRPVVDGEEGEPHS(0.01)IS(0.99)PR;ELEAIFGRPVVDGEEGEPHSIS(1)PR;ELEAIFGRPVVDGEEGEPHSIS(1)PR;ELEAIFGRPVVDGEEGEPHS(0.005)IS(0.995)PR;ELEAIFGRPVVDGEEGEPHS(0.006)IS(0.994)PR;ELEAIFGRPVVDGEEGEPHS(0.028)IS(0.972)PR;ELEAIFGRPVVDGEEGEPHS(0.001)IS(0.999)PR;ELEAIFGRPVVDGEEGEPHS(0.001)IS(0.999)PR;ELEAIFGRPVVDGEEGEPHS(0.015)IS(0.985)PR 242.11 7.84E-38 10560510000 1918181 2233155 1798167 2261594 2685096 2862634 2703240 3089610 3299628 TRUE FALSE 1664688.521 2218485.258 2667766.576 2775123.484 2631667.843 2972761.382 2441080.201 2428920.945 2909549.737 0.572146439 0.762484047 0.916900145 0.953798263 0.904493163 1.021725577 0.838988992 0.834809907 1 21.47236448 4.567324604 2.178006561 0.916502324 0.540745103 0.784367892 0.060494159 0.219500154 1.545732723 0.016833007 0.138883632 36925.34856 -4.567324604 -0.375757221 ELEAMGLGT(ph)PSEAIEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELEAMGLGTPSEAIEIR 17 0 O95359-3;E9PBC6;E7EMZ9;O95359-2;Q4VXL4;H0Y911 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 ELEAMGLGT(0.891)PS(0.109)EAIEIR 88.133 0.048865 14783000 34299 38738 26717 32353 31115 39503 33370 40292 40773 TRUE FALSE 29766.30025 38483.52753 39637.43056 39699.24313 30495.87238 41022.70597 30133.78254 31675.86935 35952.86239 0.827925741 1.070388419 1.102483305 1.104202572 0.848218204 1.141013629 0.838146966 0.881038873 1 15.13381902 2.21861495 24.99978123 0.898269025 1.018544958 0.174767019 0.111393633 376.6345779 472068.0858 0.0438285 0.02959361 165.430259 -2.21861495 0.120275933 ELEAVLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELEAVLSR 8 0 Q96DP5 Q96DP5 MTFMT "Methionyl-tRNA formyltransferase, mitochondrial" 0 69.905 0.052711 615540000 1504100 1871000 1082800 1197700 1741100 2642500 1357600 1442500 1444300 FALSE TRUE 1305329.374 1858709.278 1606445.702 1469656.091 1706455.516 2744158.685 1225940.161 1134032.601 1273556.499 1.024948147 1.459463541 1.2613855 1.153977928 1.339913476 2.154720805 0.962611523 0.890445458 1 20.28043153 2.047280508 24.99999584 0.934128577 1.396471048 0.333163276 0.298782167 128.1414062 67755.35292 0.121700747 0.0820506 111.5014481 -2.047280508 0.462342472 ELECIREIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELECIREIK 9 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 59.8 0.091116 362280000 813730 910880 370650 542800 907880 917240 772130 959840 563050 FALSE TRUE 706193.5188 904896.3693 549897.5797 666051.0362 889814.9642 952526.8163 697248.9514 754585.6855 496486.8704 1.422381055 1.82259879 1.107577285 1.341527996 1.792222549 1.918533748 1.404365338 1.519850233 1 18.92139604 1.071313915 2.295751329 0.615830137 1.553010625 0.319569276 0.246862288 1.542677774 5.507050762 3.562029516 0.067177392 11.78457475 -1.071313915 0.937180487 ELEDATETADAMNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELEDATETADAMNR 14 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 247.3 1.91E-17 2334600000 1049130 942740 550730 615550 909680 821340 1080470 929910 869690 FALSE TRUE 910484.8123 936547.0789 817064.8701 755320.0356 891579.1478 852937.4813 975686.1857 731055.9831 766876.239 1.187264341 1.221249312 1.065445542 0.984930811 1.162611517 1.112223118 1.272286369 0.953290695 1 19.54863424 1.641838616 9.916907625 0.976733073 1.136636652 0.421826484 0.080803955 0.102867159 19.54632049 0.047144634 0.02134282 43.83677697 -1.641838616 0.159903579 ELEDDEQFVSLYGTEEYLHPDMYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELEDDEQFVSLYGTEEYLHPDMYER 25 0 A0A494C0X2;A0A494C167;A0A494C045;Q9UHD2;A0A494C1I2;A0A494C079;A0A494C0R4;A0A494C0A8;A0A494C1M6;A0A494C148 A0A494C0X2 TBK1 Serine/threonine-protein kinase TBK1 0 137.89 1.51E-05 36348000 33641 28004 23186 22745 26216 27606 28507 35433 23701 FALSE TRUE 29195.25661 27820.03988 34398.82715 27909.59989 25694.35289 28668.02068 25742.39553 27855.92869 20899.09478 1.396962736 1.331160042 1.645948186 1.335445395 1.229448125 1.371735043 1.231746915 1.332877284 1 14.35115283 -0.031623841 0.513157985 6.25E-29 1.413854202 0.493893801 0.114652004 14.82569323 1.129809615 16.70290094 0.076745792 0.929771348 0.031623841 1.413854202 ELEDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELEDFK 6 0 P00367;P00367-2;P00367-3;P49448;A6NF36 P00367 GLUD1;GLUD2;CCDC182 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial;Coiled-coil domain-containing protein 182" 0 97.071 0.096521 161340000 621430 625170 555330 776840 763240 715260 662830 886070 934260 FALSE TRUE 539306.451 621063.2171 823889.4455 953233.3953 748053.0173 742776.515 598548.8486 696590.8259 823812.8471 0.654646808 0.753888725 1.00009298 1.157099454 0.908037572 0.901632595 0.726559255 0.845569268 1 19.6519571 4.410191313 4.87841747 0.920366492 0.675656972 0.428596177 0.112174859 0.202141626 9.073058746 0.031664671 0.092207947 25715.28326 -4.410191313 -0.24470952 ELEDLLS(ph)PLEELVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELEDLLSPLEELVK 14 0 P37198;M0QXN5 P37198 NUP62 Nuclear pore glycoprotein p62 1 ELEDLLS(1)PLEELVK 77.42 0.025929 242320000 50160 61834 32671 48077 56581 41515 47822 63720 68069 TRUE FALSE 43531.22891 61427.80838 48470.80488 58993.61766 55455.1488 43112.10891 43184.2298 50093.97387 60021.96036 0.725255034 1.023422228 0.807551179 0.982867226 0.923914322 0.718272257 0.719473832 0.834594098 1 15.87320282 2.775083152 24.98098713 0.811419728 0.900159487 0.093607258 0.113037119 1207.291457 825771.498 0.035323794 0.035322592 595.7762023 -2.775083152 0.08873976 ELEEEEENS(ph)DEDELDSHTMVK ddPTM_MDA-MB-175_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 340.57 9.02E-81 3123720000 1902430 1518860 1206951 1416170 1455960 1317648 1677191 2108050 2052140 TRUE FALSE 1651019.055 1508882.509 1790636.541 1737733.043 1426989.245 1368338.771 1514537.275 1657259.912 1809538.347 0.912397937 0.833849424 0.989554349 0.96031844 0.788592984 0.756181141 0.836974401 0.915846804 1 20.78719025 5.449494277 22.15281336 0.884853372 0.912549727 0 0.083234419 0 0 0.019661027 0 281510.2918 -5.449494277 0.027696355 ELEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELEEER 6 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1;Q9ULV0;A0A0A0MR36;Q9ULV0-2 Q14980;Q9ULV0 NUMA1;MYO5B Nuclear mitotic apparatus protein 1;Unconventional myosin-Vb 0 ; 143.37 0.02654 1070860000 1898400 1932240 1167600 1445500 1591900 1909800 1826500 2101320 1902100 FALSE TRUE 1647521.63 1919546.988 1732255.265 1773722.868 1560224.304 1983271.242 1649366.311 1651969.07 1677235.905 0.982283783 1.144470484 1.032803591 1.057527366 0.930235455 1.182464098 0.983383617 0.984935432 1 20.67765419 ELEEETNAFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELEEETNAFNR 11 0 A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599;Q92599-3 A0A087X142 8-Sep Septin-8 0 156.48 0.0031559 0 119830 113840 93586 88633 95243 106820 112670 112880 109790 FALSE TRUE 103994.1619 113092.1775 138844.5026 108758.4773 93347.85064 110929.4345 101743.2807 88741.49043 96810.75127 1.074200546 1.168177873 1.434184745 1.123413215 0.964230206 1.145837968 1.050950224 0.916649125 1 16.56287965 3.476140512 11.57707879 1.015154026 1.229623774 0.453047842 0.10575822 0.080496247 438.5990133 0.031052185 0.04142503 2993.232914 -3.476140512 0.214469748 ELEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELEELR 6 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5;P06727;Q9BT92;F5GWH6;A0A499FI31;Q15020-4;Q15020;P61129;O94964-2 Q14980;A0A499FI31;P61129;O94964-2 NUMA1;APOA4;TCHP;SART3;ZC3H6;SOGA1 Nuclear mitotic apparatus protein 1;Apolipoprotein A-IV;Trichoplein keratin filament-binding protein;Squamous cell carcinoma antigen recognized by T-cells 3;Zinc finger CCCH domain-containing protein 6;Protein SOGA1;N-terminal form;C-terminal 80 kDa form 0 ; 120.9 0.046264 396610000 1330200 1261590 851620 1042310 1308280 1324280 1227320 1565730 1340770 FALSE TRUE 1154410.7 1253302.532 1263466.28 1278982.416 1282247.788 1375225.909 1108294.695 1230910.824 1182265.698 0.976439308 1.060085338 1.068682177 1.081806246 1.084568206 1.163212221 0.937432844 1.04114568 1 20.17312287 2.224699217 24.99997367 1.000609713 1.072705583 0.347179705 0.051090911 288.0155806 519451.7347 0.020630217 0.013986989 167.7641719 -2.224699217 0.07209587 ELEELRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELEELRK 7 1 P61129 P61129 ZC3H6 Zinc finger CCCH domain-containing protein 6 0 91.906 0.025751 590230000 841550 740330 478790 585690 635420 604150 813460 905670 838360 FALSE TRUE 730337.0353 735466.7235 710334.4455 718679.8662 622776.3852 627392.0414 734570.7744 711999.5184 739250.0359 0.987943185 0.994882229 0.960885236 0.972174273 0.842443497 0.848687198 0.993670259 0.963137618 1 19.49570288 3.448561439 24.99760097 0.932066827 0.979922931 0.178788903 0.052715521 430.8692372 377126.2857 0.016825807 0.021722369 2809.062739 -3.448561439 0.047856104 ELEEQLENETLHK ddPTM_MDA-MB-175_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 ; 200.16 1.12E-07 143601000 337620 315280 234050 272200 301010 249530 344930 389220 483630 FALSE TRUE 293002.6616 313208.9049 347237.3629 334007.1703 295020.4899 259129.5806 311478.7417 305988.3319 426455.8124 0.687064528 0.734446327 0.814239958 0.783216363 0.691796152 0.607635242 0.730389252 0.717514741 1 18.70203674 1.238006545 24.95374733 1.000000323 0.721940536 0.714305324 0.055489735 7.877532835 354447.9765 0.084181064 0.014596981 17.29842429 -1.238006545 -0.278059786 ELEEWYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ELEEWYAR 8 0 P09496-2;F8WF69;P09496-4;P09496-3;P09496;P09496-5;C9J8P9 P09496-2 CLTA Clathrin light chain A 0 ;;;;;;; 208.67 0.00012422 11423100000 7881850 7877410 5099930 5895770 7466390 7759320 7285850 8407700 7905520 FALSE TRUE 6840243.552 7825662.775 7566273.206 7234494.69 7317823.447 8057826.061 6579269.388 6609778.784 6970938.432 0.981251466 1.122612522 1.085402386 1.037807859 1.049761595 1.155916975 0.943814015 0.94819067 1 22.73292145 2.21453274 24.9905343 0.959866422 1.072447415 0.518238678 0.049088934 166.7123415 173390.2243 0.019088889 0.012876972 163.8825601 -2.21453274 0.112580992 ELEFYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 ELEFYLR 7 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ;;;;;;;;; 198.39 0.00093189 10876193000 5040716 5236649 3408210 3963909 4914003 5116512 4749838 5562331 5503979 FALSE TRUE 4374572.609 5202249.108 5056431.756 4863975.123 4816223.954 5313347.527 4289199.442 4372869.802 4853304.873 0.901359532 1.071898272 1.041853312 1.002198553 0.992359656 1.094789564 0.883768804 0.901008677 1 22.21053606 2.224139799 24.99892797 0.920728206 1.019167576 0.329666195 0.059570781 238.71061 413808.8327 0.023153473 0.015690759 167.5482126 -2.224139799 0.09843937 ELEIEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELEIEER 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 118.05 0.011849 717800000 1150310 1044700 740650 917150 1046460 1075620 1065960 1174020 1276290 FALSE TRUE 998293.619 1037837.297 1098830.817 1125402.925 1025637.493 1116999.797 962583.3633 922964.9592 1125408.45 0.887050047 0.922187226 0.976384012 0.999995091 0.911346892 0.992528355 0.855319118 0.82011554 1 20.10201727 2.227083931 24.98904983 0.875354355 0.949017643 0.155304908 0.057935811 297.4344359 647621.0154 0.023325159 0.015877228 168.6878997 -2.227083931 0.073663287 ELEKPIQSKPQS(ph)PVIQAAAVS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELEKPIQSKPQSPVIQAAAVSPK 23 2 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 2 ELEKPIQS(0.005)KPQS(0.995)PVIQAAAVS(1)PK 148.31 5.77E-08 286280000 273580 194660 178790 151650 208890 133260 318410 345420 281660 TRUE FALSE 237425.7098 193381.2656 265253.442 186084.4503 204733.4977 138386.5984 287530.6472 271554.6211 248362.4757 0.9559645 0.778625133 1.068009333 0.749245432 0.824333455 0.557196082 1.157705674 1.093380231 1 17.92208769 2.202641395 24.99998795 1.088796925 0.828196657 0.447227338 0.136884482 156.7122315 109071.5697 0.054749406 0.036913385 159.4561943 -2.202641395 -0.260600268 ELEKPIQSKPQSPVIQAAAVS(ph)PK ddPTM_MDA-MB-175_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 179.54 2.52E-17 7243800000 7670100 4351700 4571900 3808700 4858200 3529300 7215700 7861000 6408500 TRUE FALSE 6656476.851 4323113.396 6782886.132 4673523.547 4761531.325 3665074.455 6515922.525 6179986.324 5650894.431 1.177951019 0.765031704 1.200320801 0.827041383 0.842615516 0.648583069 1.153078084 1.093629761 1 22.43004781 ELELAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELELAHR 7 0 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 0 117.17 0.01512 0 640050 561180 376490 459120 451280 637850 558830 684550 733950 FALSE TRUE 555465.7708 557493.5716 558561.8233 563370.2132 442300.4109 662388.5022 504634.7526 538164.3097 647183.2671 0.858282034 0.861415305 0.863065922 0.870495641 0.683423743 1.023494481 0.779740111 0.831548554 1 19.30381478 1.235558977 24.74396375 1.000000242 0.844788289 0.247015445 0.084218274 101.7732665 838790.6786 0.12872309 0.01889484 17.20120918 -1.235558977 -0.155211954 ELELELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELELELDR 8 0 O94992 O94992 HEXIM1 Protein HEXIM1 0 ; 164.77 0.00076339 148503000 300040 321160 207238 268420 331560 313730 293680 342670 418100 FALSE TRUE 260388.9538 319050.2788 307458.99 329368.8635 324962.6047 325799.3961 265198.9588 269392.6872 368672.6943 0.706287604 0.86540252 0.833961925 0.893390991 0.881439308 0.883709049 0.71933442 0.730709628 1 18.49198104 4.746182453 23.85201822 0.838191266 0.70628748 0.224961225 0.081383135 880.7407425 2756088.063 0.020913062 0.209595329 55741.9879 -4.746182453 -0.131903786 ELELLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELELLDR 7 0 G3V1A6;P57764 G3V1A6 GSDMD Gasdermin-D 0 101.33 0.021265 35866000 62535 57811 44855 61249 65677 71806 77811 72425 84835 FALSE TRUE 54270.84131 57431.23573 66547.02803 75156.52158 64370.15619 74568.42328 70264.9012 56937.47736 74805.90294 0.725488754 0.767736682 0.889595946 1.004687045 0.860495678 0.996825389 0.939296211 0.761136155 1 16.1908645 4.261303309 3.578908686 0.913195207 0.735866652 0.493343073 0.074320771 0.204196553 5.430161466 0.019994891 0.056319251 18251.69945 -4.261303309 -0.177328555 ELELVEDVWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELELVEDVWR 10 0 A0A1B0GVV3;Q5EBL4-2;Q5EBL4 A0A1B0GVV3 RILPL1 RILP-like protein 1 0 ;;; 166.07 1.32E-05 101614000 276699 278818 183350 222363 266415 255105 269285 326247 307816 FALSE TRUE 240132.5261 276986.4262 272018.6733 272853.9178 261113.8627 264919.0544 243169.7821 256481.6179 271426.3431 0.884706043 1.020484685 1.002182287 1.005259529 0.962006339 0.976025582 0.895896026 0.944940034 1 18.05020122 2.438023272 24.96406665 0.943194818 0.979493827 0.075620126 0.044242356 318.1892451 203162.0475 0.016038022 0.012423024 274.1721084 -2.438023272 0.036299009 ELENAEFIPMPDSPS(ph)PLSAAFSESEKDTLPYEELQGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELENAEFIPMPDSPSPLSAAFSESEKDTLPYEELQGLK 38 1 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 ELENAEFIPMPDS(0.357)PS(0.42)PLS(0.051)AAFS(0.051)ES(0.06)EKDT(0.06)LPY(0.001)EELQGLK 95.323 0.00017917 12909000 51067 45718 46460 49334 59713 48531 75701 101550 78142 TRUE FALSE 44318.36656 45417.67545 68928.2114 60536.03872 58524.82813 50398.01897 68359.52867 79834.32276 68904.14178 0.643188717 0.659142894 1.00034932 0.878554426 0.849365896 0.7314222 0.992096076 1.158628795 1 16.07230308 -1.999999678 0.069519214 2.847717641 6.73E-10 0.504659266 0.11658325 491.5377159 3.280817965 147.0949705 30.11797175 0.010000007 1.999999678 -2.847717641 ELENFFQELEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ELENFFQELEK 11 0 P22676;A6NER6;H3BN14 P22676 CALB2 Calretinin 0 ;; 150.06 7.93E-05 83405000 147941 157408 114154 122953 148666 121527 153854 184754 182614 FALSE TRUE 128390.222 156373.9765 169359.2562 150871.3579 145707.8375 126202.2223 138933.2628 145245.7949 161025.581 0.797328109 0.971112637 1.051753735 0.936940311 0.90487385 0.783740208 0.862802431 0.902004477 1 17.29693037 3.196780201 4.183979885 0.883463167 0.950221835 0.076802756 0.080746707 0.463778353 17.31940464 0.025402958 0.0301894 1573.186462 -3.196780201 0.066758668 ELEQHIQTS(ph)DPENFQSEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELEQHIQTSDPENFQSEER 19 0 Q96K76-2;Q96K76-4;Q96K76 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 1 ELEQHIQT(0.048)S(0.952)DPENFQSEER;ELEQHIQT(0.204)S(0.796)DPENFQSEER;ELEQHIQT(0.038)S(0.962)DPENFQSEER;ELEQHIQT(0.043)S(0.957)DPENFQSEER 211.5 8.14E-17 1417060000 546770 504600 333707 418428 521670 515770 494030 580020 546450 TRUE FALSE 474512.9592 501285.2494 495088.8214 513438.4727 511289.7876 535612.0056 446119.0466 455987.2367 481849.3035 0.984774608 1.04033615 1.02747647 1.065558192 1.061098945 1.11157576 0.925847653 0.946327479 1 18.87822249 2.225020407 24.99999022 0.953772314 1.04849683 0.580310918 0.036469254 158.8586666 293306.4845 0.015049589 0.010209151 167.8882904 -2.225020407 0.094724516 ELESPLT(ph)PGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELESPLTPGK 10 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 ELES(0.001)PLT(0.999)PGK 163.45 7.22E-05 227900000 600100 446310 366210 484190 519350 442500 583300 681000 934440 TRUE FALSE 520795.2645 443378.1602 543310.3809 594132.7399 509015.9511 459523.2613 526731.6558 535373.4495 823971.5677 0.632054897 0.538098859 0.65938001 0.721059759 0.617759121 0.557693104 0.639259504 0.64974748 1 19.65223503 1.228175214 4.137583911 1.043137452 0.624206428 0.844471338 0.050423666 0.096019949 2.981919017 0.122957854 0.013288043 16.9112307 -1.228175214 -0.418931024 ELESQISELQEDLESER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ELESQISELQEDLESER 17 0 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;; 444.58 3.93E-182 1320762000 778122 674980 505298 787448 645806 665788 612884 768016 1531752 FALSE TRUE 675291.2062 670546.0119 749661.8029 966250.1038 632955.7241 691401.2952 553446.604 603781.7551 1350670.024 0.499967568 0.496454352 0.55502957 0.715385762 0.468623508 0.511895047 0.409757079 0.44702388 1 20.36524383 1.234006743 24.99979993 1.000000732 0.510780297 0.777849867 0.081780603 69.9830022 384142.9944 0.168113075 0.021569178 17.13983919 -1.234006743 -0.489220435 ELEVQHPAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELEVQHPAAK 10 0 P50990-2;P50990;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;; 102.53 0.0029347 2698770000 6494300 5484300 3778970 4961800 5199200 4491000 6325000 7133200 6709300 FALSE TRUE 5636061.801 5448273.272 5606492.532 6088452.526 5095746.092 4663771.676 5711602.474 5607820.691 5916134.197 0.95265956 0.920917797 0.947661487 1.029126846 0.861330376 0.788314044 0.965428147 0.947885985 1 22.49622335 1.491893954 2.086017344 0.999115388 0.920762363 0.127607327 0.063646687 0.958674174 6.961872007 0.125528212 0.018643939 31.0380161 -1.491893954 -0.078353025 RRES(ph)EKS(ph)LENETLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRESEKSLENETLNK 15 3 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 RRES(0.954)EKS(0.906)LENET(0.14)LNK 145.77 5.75E-06 323790000 228130 131260 201110 202880 157600 159180 277840 284080 565890 TRUE FALSE 197982.0425 130397.7444 298367.4687 248947.0048 154464.0683 165303.7576 250895.1196 223331.7027 498991.1289 0.396764654 0.261322771 0.597941429 0.498900663 0.309552734 0.331275945 0.50280477 0.447566479 1 18.92865464 1.206116016 3.554489994 1.110128297 0.414623176 0.766987175 0.100752863 0.175758735 3.112804722 0.346559966 0.026226998 16.07370582 -1.206116016 -0.69550512 TCEESSFCKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TCEESSFCKR 10 1 Q14697;Q14697-2 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 94.363 0.013076 633490000 869380 624210 345657 452230 653030 717680 693330 687450 248933 FALSE TRUE 754489.2303 620109.5234 512817.8814 554915.7334 640035.9806 745289.614 626090.9633 540444.1672 219504.4243 3.437239284 2.825043392 2.336253052 2.528038945 2.915822688 3.395328437 2.852293138 2.462110588 1 17.74389049 1.2065664 2.329600369 0.381027354 2.876680749 0.75940855 0.334578501 0.350795603 1.855074032 1.874531032 0.094723467 16.09038367 -1.2065664 2.495653396 ELFEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ELFEER 6 0 Q9H307 Q9H307 PNN Pinin 0 ;;;; 122.78 0.044374 1599020000 3289710 2928250 1945050 2307430 2854120 2951140 2802630 3159600 3113130 FALSE TRUE 2854966.488 2909014.133 2885682.686 2831367.248 2797328.596 3064672.265 2530831.374 2483944.128 2745099.318 1.040023022 1.059711798 1.051212489 1.03142616 1.019026371 1.116415805 0.921945285 0.904864939 1 21.38842692 2.221200536 24.99999361 0.933630426 1.050673808 0.682964607 0.035368516 124.1194936 178741.2923 0.013951979 0.009430816 166.4180911 -2.221200536 0.117043382 ELFEMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELFEMAR 7 0 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 100.19 0.023212 204270000 861650 991410 550100 739780 1031300 1341600 717280 872000 848930 FALSE TRUE 747780.7694 984897.3624 816130.2 907758.3558 1010779.148 1393212.22 647718.296 685529.5859 748570.4625 0.998945065 1.315704281 1.090251674 1.212655857 1.35027923 1.861163765 0.86527365 0.91578498 1 19.5137786 ELFGDDS(ph)EDEGASHHSGSDNHSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELFGDDSEDEGASHHSGSDNHSER 24 0 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 ELFGDDS(1)EDEGASHHSGSDNHSER 124.09 0.00018124 150600000 98368 84520 69492 59192 86954 75355 117160 110600 94786 TRUE FALSE 85368.41957 83964.78255 103098.5636 72632.44829 85223.78552 78253.95561 105797.8412 86949.05069 83580.50706 1.021391501 1.004597669 1.233524027 0.869011817 1.019661025 0.93627041 1.265819567 1.040302981 1 16.35087889 ELFGKDEQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ELFGKDEQQR 10 1 G3XA94;Q9NPL8 G3XA94 TIMMDC1 "Complex I assembly factor TIMMDC1, mitochondrial" 0 ;;;;; 52.79 0.088821 81423100000 41816200 56720200 23862540 31285300 45648700 50382600 59489300 44797000 32845100 FALSE TRUE 36290083.22 56347601.27 35402544.16 38389105.53 44740380.18 52320851.22 53720036.84 35217510.16 28962189.7 1.253015867 1.945557358 1.222371117 1.325490439 1.544785828 1.806522634 1.854833402 1.215982304 1 24.78766735 1.544582031 5.263841977 1.047515864 1.565571622 0.379212103 0.25017598 0.144094423 8.309293086 0.182646375 0.064215366 35.04144696 -1.544582031 0.518055758 ELFGPELFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELFGPELFR 9 0 P35249;C9J8M3;C9JZI1;P35249-2;C9JXZ7;C9JTT7 P35249 RFC4 Replication factor C subunit 4 0 78.334 0.069943 36524000 35521 33757 26864 25221 29604 39474 30329 40751 34680 FALSE TRUE 30826.80985 33535.24804 39855.52025 30947.81353 29014.93832 40992.59032 27387.69825 32036.71577 30580.16991 1.008065356 1.096633804 1.303312584 1.012022288 0.948815471 1.340495833 0.895603207 1.047630405 1 14.9003088 ELFLAEHS(ph)DLEEGGLDLTVSLKPVSFYISDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELFLAEHSDLEEGGLDLTVSLKPVSFYISDKK 32 2 Q9H8G2;A0A3B3ISJ3 Q9H8G2 CAAP1 Caspase activity and apoptosis inhibitor 1 1 ELFLAEHS(1)DLEEGGLDLTVSLKPVSFYISDKK 230.67 6.10E-37 124000000 259340 193710 161110 174860 184310 135320 285610 303930 157680 TRUE FALSE 225067.5619 192437.5063 239023.3349 214564.6356 180642.5916 140525.848 257911.5862 238936.9347 139039.25 1.618734004 1.38405167 1.719106906 1.543194713 1.299220124 1.01069193 1.854955245 1.718485497 1 17.08513268 3.450848891 24.48511025 1.435536843 1.567669321 0.08231914 0.279681548 660.3299261 615406.3279 0.085409785 0.110267163 2823.897251 -3.450848891 0.132132478 ELFLAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELFLAGR 7 0 Q7Z4W1;J3KS22;J3KRZ4 Q7Z4W1 DCXR L-xylulose reductase 0 ; 126.24 0.0092382 151785000 306930 225540 129404 196589 241650 263010 211390 241540 244210 FALSE TRUE 266368.4228 224058.4129 191984.2072 241227.5371 236841.6378 273128.1649 190889.4303 189888.5507 215339.772 1.236968073 1.040487834 0.891540868 1.120218225 1.09985088 1.268359125 0.886456917 0.881809008 1 17.71625528 2.201186468 24.99988321 0.912712196 1.096562575 0.396487096 0.107620756 174.616522 116801.2994 0.044979468 0.030325984 158.922895 -2.201186468 0.183850378 ELFQETLESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ELFQETLESLR 11 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 ;; 174.4 2.57E-05 95946000 136890 120199 89717 92629 118724 129651 116314 126342 117700 FALSE TRUE 118799.6397 119409.4049 133104.4413 113661.8302 116361.6247 134638.7579 105033.8862 99324.74649 103785.6401 1.144663554 1.150538791 1.282493813 1.095159505 1.121172684 1.297277328 1.012027156 0.9570182 1 16.66324732 2.099067168 7.214056109 0.97824785 1.177924515 0.66134104 0.065083317 0.123653517 7.817287766 0.026004636 0.017465134 125.6224235 -2.099067168 0.199676664 ELFQT(ph)PGHTEEAVAAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELFQTPGHTEEAVAAGK 17 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 ELFQT(1)PGHTEEAVAAGK;ELFQT(1)PGHTEEAVAAGK 251.12 3.98E-21 199950000 495960 453870 304740 356900 372840 324300 458010 566550 568970 TRUE FALSE 430417.6294 450888.4981 452113.2833 437939.5999 365421.2134 336776.0309 413592.2607 445397.6914 501707.0148 0.857906341 0.898708778 0.901150014 0.872899096 0.728355799 0.671260359 0.824370098 0.887764528 1 18.93648558 1.367611306 2.449910438 1.016875748 0.821389115 0.380069518 0.072779082 0.514146395 4.227780526 0.19085827 0.022099029 23.31370548 -1.367611306 -0.195486633 ELFS(ph)PLHALNFGIGGDTTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELFSPLHALNFGIGGDTTR 19 0 P68402;P68402-3;P68402-2;P68402-4 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 1 ELFS(1)PLHALNFGIGGDTTR 64.152 0.020972 31388000 14599 12605 6931.2 9202.6 13494 16507 9579.9 10691 11629 TRUE FALSE 12669.70516 12522.19693 10283.1515 11292.19098 13225.4958 17142.03497 8650.842772 8404.812847 10254.23287 1.235558557 1.22117345 1.002820166 1.101222405 1.289759651 1.671703305 0.84363627 0.819643259 1 13.32393195 ELFSPLHALNFGIGGDGTQHVLWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ELFSPLHALNFGIGGDGTQHVLWR 24 0 M0R1K3;Q15102;M0R389;M0QZT2;M0QXS6;M0R323 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ;; 329.12 5.17E-87 3607540000 2579700 2478880 1068910 1941110 2473540 2440090 2306030 2851200 2596740 FALSE TRUE 2238786.109 2462596.074 1585838.451 2381868.694 2424321.393 2533961.841 2082391.566 2241493.068 2289756.355 0.977739882 1.075483891 0.692579561 1.040228008 1.058768278 1.106651297 0.909438055 0.978922086 1 21.12676266 ELFSPLHALNFGIGGDTTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELFSPLHALNFGIGGDTTR 19 0 P68402;P68402-3;P68402-2;P68402-4 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 ; 217.67 3.54E-19 1823880000 1411470 1262730 534240 869430 1249560 1321320 1254580 1468260 1335600 FALSE TRUE 1224940.663 1254435.043 792600.2509 1066847.37 1224696.201 1372152.035 1132911.025 1154284.025 1177706.89 1.040106561 1.065150467 0.673002984 0.905868327 1.039898986 1.165104873 0.961963486 0.980111465 1 20.16754909 3.240812509 24.89197852 1.024978266 0.913609873 0.172861969 0.117086614 106.4485001 1176649.012 0.036025265 0.044255069 1741.055072 -3.240812509 -0.111368393 ELGDVLFQMAEVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELGDVLFQMAEVHR 14 0 Q9UQB8;Q9UQB8-2;Q9UQB8-4;Q9UQB8-5;Q9UQB8-3;I3L4C2;Q9UQB8-6;I3L3J7;I3L125;I3L0M4;I3L526;I3L327;I3L1C8;I3L113;I3L2M4;I3L3C5;I3L2J6 Q9UQB8 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 0 ; 159.02 4.98E-06 130670000 198713 159321 116750 164956 170802 181497 127531 195463 182217 FALSE TRUE 172452.5736 158274.4099 173210.6905 202411.781 167403.3744 188479.307 115163.0632 153664.7585 160675.5138 1.073297166 0.985056192 1.078015476 1.259754994 1.041872345 1.173043126 0.716743084 0.956366996 1 17.29379056 2.25910353 24.99990182 0.897384839 1.099900781 0.482190915 0.102895205 203.5926955 247763.6047 0.038233874 0.029581869 181.5948511 -2.25910353 0.202515941 ELGELIPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELGELIPLR 9 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 155.1 0.00017241 95742000 205917 219639 134025 158882 223051 213559 210536 228090 208351 FALSE TRUE 178704.5467 218196.1769 198839.9383 194958.5865 218612.7215 221774.7529 190118.2511 179314.7285 183719.9821 0.972700654 1.187656206 1.08229892 1.061172466 1.189923485 1.207134631 1.034826201 0.976021913 1 17.48714902 2.022665757 13.0375645 0.992027521 1.119418476 0.380753558 0.069871162 1.053757722 604.4394744 0.027970697 0.018799648 105.3575729 -2.022665757 0.127390955 ELGELSPHWDNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ELGELSPHWDNLR 13 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3;E9PG59 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 ;;;; 220.69 2.04E-11 2164495000 2204003 2148952 1357819 1758998 2117468 2320427 2168561 2391394 2916270 FALSE TRUE 1912738.419 2134835.393 2014464.81 2158405.381 2075334.53 2409695.328 1958254.288 1880013.003 2571511.883 0.74381862 0.830186867 0.783377601 0.839352676 0.807048392 0.937073379 0.761518662 0.731092481 1 21.29418539 5.951840667 1.021654794 0.82870206 5.05E-10 0.108342331 0.080188757 53.02594791 6.296481061 0.02460927 83.81352247 895036.3369 -5.951840667 -0.828702059 ELGENLDQILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELGENLDQILR 11 0 Q96P70 Q96P70 IPO9 Importin-9 0 ; 232.41 8.24E-13 180120000 404270 380900 299920 370930 412560 413260 381560 457070 560830 FALSE TRUE 350844.6952 378397.8428 444962.3152 455155.3258 404350.8632 429158.3796 344556.3699 359329.1374 494529.3163 0.709451763 0.765167666 0.899769337 0.920380877 0.817647913 0.867811807 0.696735984 0.726608364 1 18.91569652 4.456086648 8.889727585 0.830716622 0.723111045 0.202007926 0.089435916 0.350191464 133.7525885 0.023696418 0.064624488 28581.60732 -4.456086648 -0.107605578 ELGFSSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELGFSSHR 8 0 Q9H0A0;E9PMU0;E9PJN6 Q9H0A0 NAT10 N-acetyltransferase 10 0 124.08 0.0033259 0 201860 225730 75581 138550 235730 252300 181370 205060 198610 FALSE TRUE 175183.6896 224247.1648 112132.2244 170009.8951 231039.4342 262006.1443 163780.7653 161209.5148 175130.5521 1.000303416 1.280457134 0.640277913 0.970760916 1.319241169 1.496061887 0.935192423 0.920510516 1 17.41807126 ELGHLTHQQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELGHLTHQQAR 11 0 Q9HD20;Q9HD20-2 Q9HD20 ATP13A1 Manganese-transporting ATPase 13A1 0 55.721 0.07144 58507000 29105 33748 22709 24573 39292 53729 27246 34692 34128 FALSE TRUE 25258.70051 33526.30717 33691.14836 30152.67522 38510.16607 55795.9894 24603.68711 27273.38577 30093.42672 0.839342782 1.114074096 1.119551744 1.001968819 1.279686971 1.854092255 0.817576787 0.906290468 1 14.87716077 ELGIIPTIIRDEELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELGIIPTIIRDEELK 15 1 Q8NDH3-3;Q8NDH3-2;Q8NDH3;Q8NDH3-5;Q8NDH3-4;H0YEP3 Q8NDH3-3 NPEPL1 Probable aminopeptidase NPEPL1 0 171.46 9.87E-07 65930000 137360 110650 69148 72963 89867 86826 124310 144770 60509 FALSE TRUE 119207.528 109923.1329 102588.2041 89530.36432 88078.82252 90166.2524 112254.4353 113812.0621 53355.69495 2.234204392 2.060194942 1.922722667 1.677990782 1.65078578 1.689908687 2.103888543 2.133081805 1 15.70335465 4.280363283 1.988523921 1.776160948 2.2189912 0.241014399 0.312174641 0.639732755 4.653408741 0.087572071 0.371617658 19070.55284 -4.280363283 0.442830252 ELGITALHIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELGITALHIK 10 0 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ; 155.42 1.27E-05 2801100000 4490000 4406800 3043200 4072600 4223400 3253300 4424100 4947900 6537600 FALSE TRUE 3896635.124 4377851.441 4514901.699 4997346.076 4139362.603 3378456.556 3995051.463 3889830.09 5764732.376 0.675943803 0.759419719 0.783193634 0.86688258 0.718049396 0.586056097 0.693015946 0.674763343 1 22.4588222 2.924884663 0.005452253 1.483809989 7.52E-05 0.013359248 0.114522376 109725.3499 819.8994443 111661.9851 111446.1171 841.1717194 -2.924884663 -1.483734795 ELGLPEELVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELGLPEELVSR 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ; 167.67 4.41E-05 102188000 146401 129364 81498 94737 125871 126812 117949 132913 127422 FALSE TRUE 127053.7369 128514.1994 120910.7054 116248.4838 123366.4134 131690.5397 106510.3241 104490.5893 112358.3163 1.13079068 1.143788939 1.076117099 1.034622871 1.09797314 1.172058678 0.947952298 0.92997646 1 16.77774739 2.223612604 24.99485499 0.952725235 1.105388918 0.745634349 0.041176502 117.8890906 197123.0239 0.017629208 0.011939487 167.3449473 -2.223612604 0.152663683 ELGMEERPYSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELGMEERPYSSR 12 1 Q9NX46 Q9NX46 ADPRHL2 Poly(ADP-ribose) glycohydrolase ARH3 0 87.719 0.0094758 311750000 245700 220860 198360 227170 245270 219360 231640 266650 437450 FALSE TRUE 213230.1225 219409.1561 294287.5595 278752.4206 240389.6069 227798.9211 209175.5885 209628.9726 385735.1593 0.552788921 0.568807771 0.76292646 0.722652353 0.623198589 0.590557836 0.542277735 0.543453112 1 18.55725113 1.232245049 24.99692346 1.000000642 0.613022731 0.724540681 0.074926559 128.9696458 510410.2495 0.187411202 0.020527108 17.07045312 -1.232245049 -0.386977911 ELGNDAYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELGNDAYK 8 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 81.972 0.049969 346240000 307090 197210 131320 167440 172910 175550 212150 245250 230840 FALSE TRUE 266507.2784 195914.5145 194826.7912 205459.8112 169469.4293 182303.5221 191575.7257 192805.196 203550.3582 1.309294078 0.96248671 0.957142955 1.00938074 0.832567581 0.895618773 0.941171155 0.947211284 1 17.63502623 4.743025401 4.216725272 0.939041356 1.340021786 0.84279552 0.049773365 0.085657229 3.463962885 0.012580994 0.104378894 55338.24749 -4.743025401 0.400980431 ELGPQDLLWMLDHQEDGGEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ELGPQDLLWMLDHQEDGGEALR 22 0 Q8N0W3-2;Q8N0W3 Q8N0W3-2 FUK L-fucose kinase 0 ;; 171.15 6.35E-12 119874000 93925 82899 49669 59424 76853 82571 73467 84694 82378 FALSE TRUE 81512.57327 82354.43101 73689.09453 72917.12744 75323.77566 85747.5598 66342.18165 66582.84719 72639.36669 1.122154239 1.133743792 1.014451225 1.003823832 1.036955292 1.180455774 0.913308922 0.916622077 1 16.148464 -1.999988643 0.068902488 0.15665172 1.429998944 0.312156168 0.073113694 688.8359247 4.559951082 91.61495329 19.01942877 0.010000261 1.999988643 1.273347225 ELGSEEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELGSEEVR 8 0 J3QLI2;O43829 J3QLI2 ZBTB14 Zinc finger and BTB domain-containing protein 14 0 96.253 0.0090721 882460000 512360 545270 308460 324750 477000 745280 391650 395190 435950 FALSE TRUE 444650.3278 541688.0855 457632.2877 398489.451 467508.6332 773951.4039 353667.8433 310681.6939 384412.4876 1.156701049 1.409132385 1.19047196 1.036619423 1.216164012 2.013335749 0.920021734 0.808198755 1 18.55229568 2.041413884 24.9999871 0.882509002 1.327209275 0.362345646 0.266947923 146.77348 88600.97532 0.109226573 0.073640464 110.0053695 -2.041413884 0.444700272 ELGTVMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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" 0 103.02 0.044249 0 642570 646650 572610 684720 697570 803720 646310 711840 1234500 FALSE TRUE 557652.7464 642402.1136 849526.1113 840196.1413 683689.7218 834639.6285 583630.9557 559618.5555 1088558.816 0.512285361 0.590140013 0.780413606 0.771842668 0.628068701 0.766738201 0.536150134 0.514091244 1 20.05398793 4.449290727 7.290857345 0.687561937 0.530794754 0.180899211 0.140050728 0.293913392 57.17698727 0.03545342 0.097999475 28137.83811 -4.449290727 -0.156767183 ELGYPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELGYPR 6 0 Q9UD71;J3KSJ8;Q9UD71-2;J3KT77 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 0 ; 114.67 0.058367 777360000 683670 747810 572970 614620 722680 748030 674470 855410 848630 FALSE TRUE 593321.2773 742897.5869 850060.2085 754178.8649 708300.0819 776807.1981 609060.0032 672487.2283 748305.9282 0.792885977 0.992772553 1.135979519 1.00784831 0.946538114 1.038087724 0.813918453 0.898679541 1 19.51326868 2.254288416 24.99985139 0.899287642 0.992067046 0.136141212 0.095600737 419.6240017 667005.3875 0.036070496 0.027840758 179.5925911 -2.254288416 0.092779404 ELHAAEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELHAAEVR 8 0 A0A0J9YW36;Q9NZ72-2;Q9NZ72 A0A0J9YW36 STMN3 Stathmin-3 0 74.173 0.041664 317310000 123840 124780 68786 74143 111650 152470 81556 97683 97187 FALSE TRUE 107474.2302 123960.312 102051.1397 90978.30135 109428.3834 158335.6196 73646.71167 76794.25062 85697.66358 1.254109222 1.446484149 1.190827561 1.06161939 1.276912099 1.847607192 0.859378291 0.896106701 1 16.38696825 ELHCPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELHCPDR 7 0 Q17RN3;Q17RN3-2;K7EQL1;K7EQT7 Q17RN3 FAM98C Protein FAM98C 0 62.464 0.085299 233920000 217810 252880 128510 171170 248910 313250 212910 261670 227520 FALSE TRUE 189025.8566 251218.8146 190657.8658 210036.7647 243957.178 325300.9302 192262.021 205713.9068 200622.8448 0.942195077 1.252194459 0.950329789 1.046923469 1.215998997 1.621455077 0.958325664 1.025376283 1 17.61412637 ELHEVCHLLEQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELHEVCHLLEQER 13 0 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 ; 236.92 5.75E-17 528860000 178066 177750 121440 119251 160278 181112 150448 174204 171734 FALSE TRUE 154534.1269 176582.3485 180168.7902 146328.7622 157088.7814 188079.4958 135857.5761 136951.8303 151431.8022 1.020486613 1.16608497 1.189768514 0.966301398 1.037356613 1.242007908 0.897153532 0.904379584 1 17.20830869 2.212275055 24.99999699 0.926176997 1.101160477 0.460079809 0.086562845 191.3786603 182017.3284 0.035278622 0.023793033 163.0328255 -2.212275055 0.174983479 ELHINLIPNK ddPTM_MDA-MB-175_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 ; 137.46 9.06E-05 5416700000 8533800 8120300 6908300 9053100 7875600 7287300 8731600 10603500 22327500 FALSE TRUE 7406036.708 8066957.215 10249176.99 11108744.72 7718890.968 7567647.147 7884810.776 8336024.042 19687968.39 0.376170693 0.40974046 0.520580732 0.564240276 0.392061325 0.384379282 0.400488797 0.423407021 1 24.23081091 1.237847487 24.99966153 1.000000651 0.435001577 0.893771703 0.061334865 5.698863445 199638.5837 0.093916541 0.01614996 17.29208998 -1.237847487 -0.564999075 ELHINLIPNKQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ELHINLIPNKQDR 13 1 P07900;P07900-2;G3V2J8 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;; 139.42 2.33E-05 46283058300 13129703 11576693 7255336 8792413 10798452 9678522 12704453 14733222 8263669 FALSE TRUE 11394579.48 11500644.94 10764040.76 10788864.76 10583583.93 10050861 11472377.1 11582637.13 7286747.465 1.563740137 1.578296077 1.477207878 1.48061461 1.452442806 1.37933434 1.574416728 1.589548312 1 22.79684356 1.233296746 24.98939371 0.999999196 1.512520198 0.85244127 0.066938791 66.83995101 317276.2038 0.149477046 0.018001036 17.11184139 -1.233296746 0.512521002 ELHSEFSEVMNEIWASDQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 155.28 3.17E-08 205604000 122718 98693 75671.8 131317 118771 140675 98409 129856 120750 FALSE TRUE 106500.5054 98044.67918 112266.9356 161134.5319 116407.6895 146086.8583 88865.31033 102087.3049 106475.0726 1.000238862 0.920822845 1.054396422 1.513354516 1.093285843 1.372028727 0.834611409 0.958790659 1 16.70015619 2.218346106 24.99994776 0.932874045 1.156556493 0.268384264 0.177329517 347.3419471 429565.9605 0.075246079 0.050800789 165.3278835 -2.218346106 0.223682448 ELHWHPQCPGLLVSTALSGFTIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELHWHPQCPGLLVSTALSGFTIFR 24 0 Q9BQ67 Q9BQ67 GRWD1 Glutamate-rich WD repeat-containing protein 1 0 ; 91.128 0.0053809 153258000 111327 105744 62853 82690 78139 94249 88066 142990 82259 FALSE TRUE 96614.85488 105049.3607 93248.92103 101466.0283 76584.18678 97874.82002 79525.37287 112412.7012 72534.43473 1.331986046 1.448268827 1.285581412 1.398867017 1.055832131 1.349356625 1.096380956 1.549783929 1 16.14637844 ELHYLPFPS(ph)P ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELHYLPFPSP 10 0 Q8N565 Q8N565 MREG Melanoregulin 1 ELHYLPFPS(1)P;ELHYLPFPS(1)P;ELHYLPFPS(1)P;ELHYLPFPS(1)P 119.53 0.00071367 398014000 319833 389721 307246 418538 481712 670235 390403 581567 525635 TRUE FALSE 277566.2587 387160.8971 455831.1933 513573.4499 472126.8737 696019.3741 352541.7771 457203.4228 463495.0291 0.598854877 0.83530755 0.983465118 1.108045216 1.018623381 1.501676028 0.760616091 0.986425731 1 18.82219434 4.552849647 1.686810425 1.052354242 0.530307922 0.406333954 0.182467176 0.69510583 2.589294444 0.05040853 0.524597619 35714.91712 -4.552849647 -0.52204632 ELIFEETAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELIFEETAR 9 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 ; 183.65 0.00010452 168609000 239540 220170 171950 193264 194424 228670 216760 247020 372900 FALSE TRUE 207884.1821 218723.6888 255105.5951 237147.5451 190555.3428 237467.0829 195738.6486 194196.6953 328816.1868 0.632220038 0.665185285 0.775830404 0.721216152 0.57951935 0.722187935 0.595282886 0.590593478 1 18.3269218 1.231491453 24.99970386 1.00000059 0.659026878 0.733233889 0.064398351 139.0816398 491810.4834 0.163689142 0.016655311 17.04085783 -1.231491453 -0.340973711 ELIIGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ELIIGDR 7 0 P25705;P25705-2;P25705-3;K7EK77;K7ENJ4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;;;;; 126.67 0.0091423 2915640000 2654460 2701490 2024470 3159230 3227460 3523380 2477540 3202530 2847760 FALSE TRUE 2303666.385 2683743.734 3003510.463 3876581.457 3163239.86 3658926.709 2237268.552 2517693.882 2511101.057 0.917392942 1.068751784 1.196093027 1.543777558 1.259702333 1.457100541 0.890951221 1.002625472 1 21.25988866 2.220241055 24.99931142 0.969397396 1.245308186 0.349169883 0.177471271 289.4437854 394978.9906 0.076819279 0.051901507 166.0508315 -2.220241055 0.27591079 ELIKPPTILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELIKPPTILR 10 1 Q9Y2T2;H0YBA0;E7ER80;E5RJ52;P53677-2;P53677 Q9Y2T2 AP3M1;AP3M2 AP-3 complex subunit mu-1;AP-3 complex subunit mu-2 0 102.4 0.0044718 0 494600 495730 348610 359510 521260 452660 536200 605660 586600 FALSE TRUE 429237.3568 492473.517 517198.962 441142.2403 510887.9458 470074.1231 484199.4065 476144.3223 517252.8163 0.829840541 0.952094414 0.999895884 0.85285614 0.987694856 0.908789877 0.936098154 0.920525336 1 18.98051007 3.68505558 0.010659608 1.847484019 1.50E-05 0.127847655 0.054032251 10894.82709 75.19596412 6406.283571 6625.189058 4842.343351 -3.68505558 -1.847468991 ELILGSETPSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ELILGSETPSSPR 13 0 R4GNJ5;A0A590TQL1;Q96AP0-2;Q96AP0 R4GNJ5 ACD Adrenocortical dysplasia protein homolog 1 ELILGSET(0.002)PS(0.113)S(0.885)PR;ELILGSETPSS(1)PR;ELILGSETPS(0.054)S(0.946)PR 342.97 3.22E-63 349658000 995990 961440 582530 744670 914050 950700 852570 1033910 935650 TRUE FALSE 864367.398 955124.2373 864243.4564 913758.7051 895862.1933 987274.0442 769887.8926 812816.3924 825038.5229 1.047669138 1.157672291 1.047518913 1.107534593 1.085842865 1.196639935 0.933153873 0.985185988 1 19.65410196 2.224626703 24.99999866 0.973713441 1.105781912 0.636787809 0.047828187 139.0111469 249409.5014 0.018185636 0.012330957 167.7361623 -2.224626703 0.132068471 ELINQDES(ph)VIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELINQDESVIR 11 0 A0A494C0Q2 A0A494C0Q2 1 ELINQDES(1)VIR 58.487 0.068285 22654000 2570.1 2540.3 2139.3 2531.1 2783.3 3093.9 1998.8 2797.7 3554.3 TRUE FALSE 2230.454773 2523.612602 3173.872636 3105.82494 2727.917775 3212.924335 1804.956684 2199.433627 3134.114703 0.711669797 0.80520748 1.012685538 0.990973603 0.870395003 1.02514574 0.57590639 0.701771899 1 11.61384227 1.197483367 23.30870423 1.000004088 0.834443503 0.108537442 0.146932745 10027.50164 5689056.654 12.90525538 0.039164283 15.75735672 -1.197483367 -0.165560586 ELIPQES(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELIPQESPR 9 0 Q96DF8 Q96DF8 DGCR14 Protein DGCR14 1 ELIPQES(1)PR 97.463 0.0070007 342550000 352610 319560 188440 218110 315210 367380 301890 340770 390880 TRUE FALSE 306011.6951 317460.7893 279570.2143 267635.2091 308937.9377 381513.3463 272612.7543 267898.9874 344670.6117 0.887838083 0.921055578 0.811122866 0.776495587 0.896328051 1.106892591 0.790937043 0.777260893 1 18.39485877 3.061396605 24.9997566 0.897671338 0.849658554 0.079291953 0.101941488 267.5507147 108939.6456 0.033356139 0.037822304 1151.851798 -3.061396605 -0.048012784 ELISDNQYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELISDNQYR 9 0 P25205;P25205-2 P25205 MCM3 DNA replication licensing factor MCM3 0 134.77 0.0028531 0 247340 238720 111360 184230 255100 214990 188010 226530 236690 FALSE TRUE 214653.3923 237151.8326 165214.0685 226062.2373 250024.0091 223260.8044 169776.8191 178088.3224 208708.7778 1.02848282 1.136281066 0.791600958 1.083146764 1.197956366 1.069724075 0.813462763 0.853286212 1 17.67113175 2.248166741 24.9389413 0.878349484 1.051389174 0.307819977 0.114350939 221.6358787 575400.7172 0.043988622 0.033625636 177.0788697 -2.248166741 0.173039691 ELISNASDALDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ELISNASDALDK 12 0 P08238;P14625;Q96GW1;A0A1W2PRR1;F8W026 P08238;P14625 HSP90AB1;HSP90B1 Heat shock protein HSP 90-beta;Endoplasmin 0 ;; 177.1 5.51E-05 353865000 673040 462150 409730 534280 503840 454990 556710 650010 751680 FALSE TRUE 584096.0587 459114.1062 607876.7985 655596.44 493814.5697 472493.7597 502720.3499 511010.4199 662817.2467 0.881232439 0.69267073 0.917110714 0.989105886 0.745023718 0.712856767 0.758459971 0.770967295 1 19.33825162 ELISNASDALDKIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELISNASDALDKIR 14 1 P08238;P14625;Q96GW1;A0A1W2PRR1;F8W026 P08238;P14625 HSP90AB1;HSP90B1 Heat shock protein HSP 90-beta;Endoplasmin 0 ; 254.58 2.68E-24 5224500000 4096500 3065200 1142780 1425560 2703060 2614930 3584600 3674200 221200 FALSE TRUE 3555137.146 3045064.499 1695432.23 1749255.186 2649274.394 2715528.049 3236966.044 2888500.923 195049.988 18.22680013 15.61171334 8.692296 8.96824042 13.58254067 13.92221593 16.59557161 14.80902897 1 17.57348438 1.235584479 24.99424328 0.999982669 13.72216078 0.641824168 3.004788706 58.98335852 495263.5618 5.432760138 0.794397437 17.20221928 -1.235584479 12.72217811 ELISNSSDALDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 234.3 1.19E-15 723580000 1082690 904820 811330 951810 866570 763570 1075820 1291780 1531330 FALSE TRUE 939609.7733 898876.1778 1203691.902 1167933.008 849326.9524 792945.032 971487.142 1015542.9 1350297.912 0.695853682 0.665687305 0.891426915 0.864944689 0.628992273 0.587237102 0.719461338 0.752088032 1 20.36484631 1.228004057 3.670456202 1.040458189 0.723795627 0.458379168 0.094209543 0.30359884 6.270495545 0.270454744 0.026029232 16.90456725 -1.228004057 -0.316662562 ELISNSSDALDKIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELISNSSDALDKIR 14 1 P07900;P07900-2;G3V2J8 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;; 233.02 3.23E-17 5188280000 3688960 2829330 1284340 1458590 2785740 2474350 3477010 3867660 190459 FALSE TRUE 3201454.589 2810743.945 1905451.12 1789785.153 2730309.224 2569539.846 3139810.105 3040591.007 167943.154 19.06272756 16.73628176 11.34581002 10.65708908 16.2573416 15.3000571 18.6956719 18.10488213 1 17.35761346 1.232963752 25 0.999976659 15.7492814 0.729329818 2.827722524 107.0968459 478327.5044 6.516723938 0.762724427 17.09872595 -1.232963752 14.74930474 ELKAPR ddPTM_MDA-MB-175_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 76.592 0.068081 161750000 419630 373380 287590 497230 390810 431330 424240 532720 474800 FALSE TRUE 364174.8323 370927.2422 426669.4859 610133.6712 383033.6456 447923.5442 383097.2701 418801.9736 418669.6849 0.869838074 0.885966325 1.019107667 1.457315142 0.914882685 1.069873364 0.915034654 1.000315974 1 18.67545293 4.212056655 5.201524803 1.052715882 0.87555697 0.190318286 0.152010852 0.292188335 20.72368087 0.039679625 0.092244615 16295.08592 -4.212056655 -0.177158913 ELKDDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELKDDLK 7 1 P12429;D6RA82;D6RFG5;D6RCA8;D6RAZ8 P12429 ANXA3 Annexin A3;Annexin 0 ; 81.594 0.024421 501990000 656750 418160 447670 445330 368370 262650 560100 620570 667030 FALSE TRUE 569958.8235 415413.0794 664164.7094 546448.9829 361040.1577 272754.3155 505781.5882 487865.9348 588174.4733 0.969030193 0.706275261 1.12919676 0.929059331 0.613831735 0.463730284 0.859917611 0.829457851 1 19.16588465 3.313207945 13.82913819 0.756418168 0.931290631 0.208797637 0.174038037 1.906846203 349.4422489 0.052568901 0.067863807 2056.875216 -3.313207945 0.174872463 ELKENGELLPILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELKENGELLPILR 13 1 O76003 O76003 GLRX3 Glutaredoxin-3 0 92.457 0.0028142 0 269320 263660 221570 154020 209150 231850 279750 297050 136950 FALSE TRUE 233728.6796 261928.0001 328721.9931 188992.595 204988.3242 240769.4195 252619.8881 233528.1691 120759.927 1.935482121 2.168997668 2.722111558 1.565027404 1.697486321 1.993785732 2.091918191 1.933821715 1 16.88178226 1.235253423 4.179942229 0.89324844 2.024736381 0.523040618 0.30535863 0.197068627 6.403776012 0.679698802 0.079637996 17.18911129 -1.235253423 1.131487941 ELKPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELKPAR 6 1 P36542-2;P36542 P36542-2 ATP5C1 "ATP synthase subunit gamma, mitochondrial" 0 83.801 0.051597 182480000 382630 363620 284440 506640 364170 444450 356180 500890 458750 FALSE TRUE 332064.476 361231.3563 421996.1354 621680.3555 356923.7295 461548.2791 321637.7184 393778.5714 404517.0976 0.820891077 0.892994038 1.043209639 1.536845684 0.882345225 1.140985837 0.795115263 0.973453468 1 18.62584116 2.252922353 24.99606383 0.928074748 1.059418581 0.081804803 0.204317515 629.2602479 1095203.166 0.078049948 0.060173685 179.0285741 -2.252922353 0.131343833 ELKTDS(ph)SPNQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELKTDSSPNQAR 12 1 A6NLN1;P26599;P26599-2;P26599-3;K7ES59;A0A087WU68 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 1 ELKT(0.001)DS(0.499)S(0.499)PNQAR 112.34 0.00077795 572540000 491380 426400 145890 149650 318100 289330 446050 487610 35400 TRUE FALSE 426442.888 423598.9503 216442.892 183630.3198 311770.4324 300460.7123 402792.1397 383338.3961 31215.05233 13.66145036 13.57034247 6.93392693 5.882749061 9.987823473 9.625507245 12.90377909 12.28056234 1 14.92995426 4.255821836 24.43393882 8.978435909 13.61590276 0.276477759 3.418459945 279.3461955 395416.4874 0.873596725 2.298134699 18022.78225 -4.255821836 4.637466853 ELKTDSS(ph)PNQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELKTDSSPNQAR 12 1 A6NLN1;P26599;P26599-2;P26599-3;K7ES59;A0A087WU68 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 1 ELKTDS(0.012)S(0.988)PNQAR;ELKTDS(0.126)S(0.873)PNQAR 156.5 4.44E-05 982880000 1135860 964480 312690 318550 829320 746100 1039430 1198470 72774 TRUE FALSE 985753.2231 958144.2674 463907.9299 390881.6462 812818.1545 774802.9498 938626.2386 942186.517 64170.74062 15.36141259 14.93117047 7.229274984 6.091275283 12.66649172 12.07408458 14.62701271 14.68249404 1 15.96962801 4.290716743 11.24940655 10 15.16123233 0.219398552 4.200439462 1.060601286 223.3860461 1.096355084 2.899405992 19530.65205 -4.290716743 5.16123233 ELLACSHPFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELLACSHPFSK 11 0 P25098;E9PRV7 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 0 68.132 0.060943 0 528410 532360 337700 454240 521320 519330 637560 701330 596250 FALSE TRUE 458579.2797 528862.8921 501012.8495 557382.1346 510946.7519 539308.9612 575729.5293 551356.0373 525762.0043 0.872218373 1.005897893 0.952927076 1.060141528 0.971821371 1.025766329 1.095038296 1.048679883 1 19.00405036 6.380911227 0.557788599 1.042798111 4.02E-11 0.585683773 0.040104814 15.85447612 0.891511346 0.020958604 15.9093336 2403871.378 -6.380911227 -1.042798111 ELLDLAMQNAWFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELLDLAMQNAWFR 13 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 137.17 0.00014855 104730000 98471 99511 59125 67312 86853 91792 91582 107140 78032 FALSE TRUE 85457.80786 98857.30569 87718.04776 82596.2184 85124.79523 95323.29764 82700.39174 84228.94476 68807.14585 1.241990302 1.436730218 1.274839214 1.200401752 1.237150505 1.385369157 1.201915742 1.224130775 1 16.07027078 0.507092388 1.095307345 8.44E-11 1.292610699 0.587947348 0.074654183 5.356115637 1.591085817 11.94237848 0.023492464 3.214344255 -0.507092388 1.292610699 ELLDMMIAEEESLKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELLDMMIAEEESLKER 16 1 O43663-2;O43663-4;O43663;H0YLA0 O43663-2 PRC1 Protein regulator of cytokinesis 1 0 63.134 0.064865 18616000 31607 22782 19940 22037 21967 20650 29526 34745 21146 FALSE TRUE 27430.05487 22632.34354 29583.0507 27040.83766 21529.89968 21444.41886 26662.57306 27315.05214 18646.14397 1.47108458 1.213781443 1.586550589 1.450210709 1.154656947 1.150072578 1.42992423 1.464916938 1 14.18658969 3.26658974 24.99626639 1.277798117 1.426086789 0.234001649 0.163378961 420.4916506 374990.099 0.048917819 0.063138578 1847.522516 -3.26658974 0.148288672 ELLDTS(ph)FEDLSKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELLDTSFEDLSKPK 14 1 P78345 P78345 RPP38 Ribonuclease P protein subunit p38 1 ELLDT(0.159)S(0.841)FEDLSKPK 189.42 4.36E-07 98781000 160210 129440 110390 129400 110970 83095 158140 198960 197260 TRUE FALSE 139037.8426 128589.7001 163774.9732 158782.2478 108761.9141 86291.71842 142803.6071 156413.9523 173940.1475 0.799343019 0.739275561 0.941559356 0.912855658 0.625283557 0.496100065 0.820992791 0.899240081 1 17.40823144 1.641804336 2.735540955 0.980791048 0.757022907 0.286955397 0.128833661 0.335258029 5.638718503 0.133480512 0.03839014 43.83331695 -1.641804336 -0.223768141 ELLEIVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELLEIVKK 8 1 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 80.239 0.041594 0 268050 224030 109490 151970 189040 154670 277580 303380 112930 FALSE TRUE 232626.5133 222558.3322 162439.7302 186477.1112 185278.4739 160620.255 250660.3343 238504.5479 99579.54405 2.336087352 2.23498043 1.631256015 1.872644758 1.860607775 1.612984439 2.517187006 2.395115886 1 16.60356179 4.410850777 9.294533167 1.920872284 2.311015258 0.141996912 0.42345106 0.639435157 82.97016283 0.108226365 0.28761036 25754.36086 -4.410850777 0.390142974 ELLGPDFGYVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ELLGPDFGYVTR 12 0 Q9Y2J8;Q9Y2J8-2 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ;; 212.28 5.15E-08 347206000 710990 732580 418304 490442 770820 760040 655370 788620 707290 FALSE TRUE 617030.8701 727767.6337 620597.2135 601804.352 755482.1901 789279.2306 591812.3183 619979.75 623674.9819 0.989346836 1.16690208 0.995065108 0.964932648 1.211339579 1.265529729 0.948911429 0.994075068 1 19.25043486 ELLHSVHPES(ph)PNLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ELLHSVHPESPNLK 14 0 Q9Y217 Q9Y217 MTMR6 Myotubularin-related protein 6 1 ELLHSVHPES(1)PNLK;ELLHSVHPES(1)PNLK;ELLHSVHPES(1)PNLK 261.74 2.67E-24 3089470000 837780 1017990 429812 900760 1303680 1139830 1358830 1686360 1567190 TRUE FALSE 727065.2503 1011302.757 637670.5208 1105291.325 1277739.319 1183679.998 1227050.876 1325745.037 1381918.584 0.526127414 0.731810664 0.46143856 0.799823766 0.924612588 0.856548289 0.887932828 0.959351045 1 20.39824119 3.517653598 4.140407951 0.921066342 0.589916817 0.808589323 0.077967368 0.089581549 3.320244965 0.021432706 0.031232037 3293.469134 -3.517653598 -0.331149525 ELLKPNASVALHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELLKPNASVALHK 13 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ; 116.51 0.00034822 1446310000 2530000 2073830 1350360 2005510 2099100 1771710 2423800 3067400 2948000 FALSE TRUE 2195654.09 2060206.874 2003398.613 2460891.698 2057332.017 1839868.83 2188740.249 2411460.381 2599490.798 0.844647764 0.792542476 0.770688865 0.946682212 0.791436545 0.707780474 0.841988073 0.927666442 1 21.30979762 1.623917521 2.556381921 0.991789196 0.810011083 0.532815317 0.060769402 0.202587839 2.899245005 0.064616945 0.016973031 42.06467338 -1.623917521 -0.181778113 ELLLPDTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELLLPDTER 9 0 Q8TEX9;Q8TEX9-2;H0YN14;H0YK93;H0YLV0;H0YL92;H0YKG5 Q8TEX9 IPO4 Importin-4 0 114.84 0.0036589 55738000 126830 119720 77283 92546 139740 143300 117920 155330 139400 FALSE TRUE 110069.0942 118933.5514 114657.3173 113559.9838 136959.4474 148812.8437 106484.1365 122113.8883 122920.2908 0.895450974 0.967566467 0.932777791 0.923850595 1.1142135 1.210645067 0.866286077 0.993439631 1 16.90736356 3.279166345 24.98260288 1.027371401 0.932805716 0.2582885 0.089233607 258.2403049 158880.2572 0.027401595 0.035374868 1901.806576 -3.279166345 -0.094565685 ELLLYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELLLYGR 7 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 0 ; 124.89 0.0095448 245640000 480760 516780 235460 296020 461560 453390 411830 484400 489010 FALSE TRUE 417226.3479 513385.2382 349329.2436 363235.8654 452375.859 470832.2067 371890.79 380814.8296 431199.7949 0.967594031 1.19059713 0.810133139 0.842384133 1.049109634 1.091911945 0.86245586 0.883151695 1 18.71799697 4.241071143 25 0.93222886 1.079095541 0.248234679 0.104814267 90.40762866 900234.4753 0.026977608 0.064867235 17420.92229 -4.241071143 0.146866681 ELLNPVVEFVSHPSTTCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELLNPVVEFVSHPSTTCR 18 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 197.09 1.88E-15 1309810000 683460 697490 261190 388440 759640 759690 720680 753350 732420 FALSE TRUE 593139.0293 692908.1423 387502.3576 476641.2389 744524.6502 788915.7659 650788.5645 592251.9651 645834.142 0.91840767 1.072888683 0.600002899 0.73802422 1.152810918 1.221545463 1.007671354 0.917034153 1 19.30080419 3.240481289 24.99994251 1.046141178 0.832918712 0.374418037 0.145514963 65.40237656 851285.2184 0.046885237 0.057481934 1739.727744 -3.240481289 -0.213222466 ELLPLIYHHLLR ddPTM_MDA-MB-175_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 0 102.4 0.0013639 303000000 242610 223990 142200 166620 225240 235280 203640 246410 184690 FALSE TRUE 210548.4738 222518.5949 210968.3956 204453.6176 220758.1647 244331.3738 183891.0241 193717.1391 162856.1586 1.292849319 1.366350507 1.295427802 1.255424538 1.355540783 1.500289433 1.129162236 1.189498394 1 17.31323875 1.678214107 1.557836955 1.018941485 1.33449463 0.601475485 0.086762532 0.329533231 1.378585697 0.135394119 0.025742573 47.66659245 -1.678214107 0.315553145 ELLQHPFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELLQHPFLK 9 0 Q13177;A0A087X294;O75914-2;O75914;O75914-4;O75914-3 Q13177 PAK2;PAK3 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34;Non-specific serine/threonine protein kinase;Serine/threonine-protein kinase PAK 3 0 ; 74.162 0.041871 735140000 1313960 1095980 716500 859640 1013530 977860 1112620 1309890 1105060 FALSE TRUE 1140316.857 1088780.435 1063001.797 1054834.401 993362.7359 1015478.907 1004718.284 1029780.217 974421.0657 1.170250621 1.117361348 1.09090601 1.082524217 1.019438897 1.042135626 1.031092532 1.056812351 1 19.8941858 4.75225863 0.609276108 1.02964615 1.263755765 0.87491035 0.017788076 1.253113825 0.360701988 0.009610843 0.208678071 56527.35045 -4.75225863 0.234109615 ELLQTELSGFLDAQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELLQTELSGFLDAQK 15 0 P23297;Q5T7Y6 P23297 S100A1 Protein S100-A1;Protein S100 0 217.93 1.77E-11 0 118050 121230 77024 83154 92328 79804 96276 117820 120160 FALSE TRUE 102449.3934 120433.6321 114273.064 102035.3866 90490.85344 82874.11152 86939.16834 92625.10988 105954.8217 0.966915821 1.136650794 1.078507445 0.963008431 0.854051302 0.782164608 0.820530552 0.874194382 1 16.69308972 3.479041679 2.96256981 0.859840135 1.067135153 0.622789147 0.068996779 0.162472174 2.902725082 0.020925673 0.030400769 3013.295196 -3.479041679 0.207295018 ELLQTELSGFLDAQKDVDAVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELLQTELSGFLDAQKDVDAVDK 22 1 P23297;Q5T7Y6 P23297 S100A1 Protein S100-A1;Protein S100 0 180.37 4.87E-17 119740000 161530 166520 74176 66143 118050 83766 184560 192700 20264 FALSE TRUE 140183.4012 165426.1192 110047.7617 81161.77908 115701.036 86988.53222 166661.3996 151492.6046 17868.413 7.845319067 9.258019675 6.15878767 4.542192922 6.47517135 4.868285292 9.327151749 8.478235003 1 14.12512389 4.228299165 24.58752913 6.200765188 8.551669243 0.181277531 2.300009909 287.8616956 689753.8176 0.598643811 1.269502569 16916.05798 -4.228299165 2.350904055 ELLS(ph)PLSEPDDRYPLIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELLSPLSEPDDRYPLIVK 18 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 ELLS(0.802)PLS(0.198)EPDDRYPLIVK 237.15 4.65E-24 42985000 136050 115390 73940 90692 113020 107490 113930 156370 142610 TRUE FALSE 118070.6478 114631.9955 109697.6313 111285.0047 110771.1231 111625.2099 102881.0861 122931.4924 125750.8083 0.938925558 0.911580586 0.872341362 0.884964528 0.880878021 0.88766992 0.818134591 0.977580137 1 16.94020815 1.60015511 6.756692699 0.993861129 0.885514375 0.670194101 0.030449554 0.067629042 6.538377333 0.019950818 0.007787597 39.82493817 -1.60015511 -0.108346755 ELLSHSAERPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELLSHSAERPER 12 1 P52735-3;P52735-2;P52735 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 0 70.438 0.028409 289190000 136820 129560 88007 101930 110160 128020 134370 146100 137290 FALSE TRUE 118738.8903 128708.9118 130567.4796 125074.7644 107968.0315 132945.0122 121338.8181 114857.652 121059.7326 0.980828949 1.063185165 1.07853765 1.033165708 0.891857509 1.098176986 1.002305354 0.948768426 1 16.88535954 3.453905854 24.985161 0.987359278 1.045212052 0.16490514 0.056619972 371.6326026 399961.8843 0.015976404 0.02062663 2843.844555 -3.453905854 0.057852774 ELLSPLS(ph)EPDDRYPLIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELLSPLSEPDDRYPLIVK 18 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 ELLS(0.004)PLS(0.996)EPDDRYPLIVK;ELLSPLS(1)EPDDRYPLIVK;ELLSPLS(1)EPDDRYPLIVK;ELLS(0.006)PLS(0.994)EPDDRYPLIVK 311.65 2.16E-61 1582730000 977900 797620 548137 675360 781230 708290 889670 1047210 989480 TRUE FALSE 848668.0373 792380.3817 813217.8866 828710.8102 765685.0515 735538.3746 803389.9403 823272.2909 872504.8016 0.972680077 0.908167359 0.932049755 0.94980659 0.877571161 0.843019286 0.920785695 0.943573364 1 19.73480355 1.344215794 2.244765426 1.012250686 0.912721829 0.363605196 0.035797702 0.580489044 3.708794344 0.106925108 0.010138434 22.09102128 -1.344215794 -0.099528857 ELLTLDEKDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELLTLDEKDPR 11 1 P46781;B5MCT8;C9JM19;F2Z3C0;A8MXK4 P46781 RPS9 40S ribosomal protein S9 0 ;;; 93.096 0.0086686 12407000000 16495100 15670600 11160200 12570900 14557500 12016500 18673100 20915000 17448900 FALSE TRUE 14315230.74 15567658.8 16557310.05 15425314.98 14267834.23 12478782.53 16862185.64 16442490.01 15386110.92 0.930399554 1.011799465 1.076120544 1.002548016 0.927319081 0.811042023 1.095935531 1.068657967 1 23.87512528 ELLTTMGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ELLTTMGDR 9 0 J3QRS3;P19105;O14950;P24844-2;P24844 J3QRS3;P24844 MYL12A;MYL12B;MYL9 Myosin regulatory light chain 12A;Myosin regulatory light chain 12B;Myosin regulatory light polypeptide 9 0 ;;;;; 183.65 0.00010452 3089250000 1833290 1862950 1255850 1459630 1764920 1922350 1750800 1975230 2080680 FALSE TRUE 1591016.082 1850712.159 1863183.261 1791061.301 1729801.545 1996304.048 1581007.685 1552842.436 1834704.381 0.867178439 1.00872499 1.015522326 0.976212473 0.942823031 1.088079404 0.861723394 0.846372011 1 20.80711619 2.198811682 24.99999903 0.88925643 0.983586835 0.224797348 0.068878976 189.8825736 119424.9362 0.027059632 0.018243905 158.056253 -2.198811682 0.094330406 ELLTTMGDRFT(ph)DEEVDELYR ddPTM_MDA-MB-175_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;ELLTTMGDRFT(1)DEEVDELYR 177.41 1.06E-16 121556000 107788 109395 75498 78811 97751 99327 116937 116623 105747 TRUE FALSE 93543.5427 108676.377 112009.0853 96706.2421 95805.94635 103148.174 105596.4677 91684.07901 93245.71013 1.003194062 1.165483934 1.201225077 1.03711197 1.027456879 1.106197527 1.132453896 0.983252515 1 16.50874973 1.69566212 7.006785294 0.992277029 1.098211312 0.328785938 0.061824085 0.142931155 14.92175073 0.037532668 0.016342876 49.62061242 -1.69566212 0.105934283 ELLTTMGDRFTDEEVDELYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ELLTTMGDRFTDEEVDELYR 20 1 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ;;;;; 228.63 2.15E-26 335651000 773643 803268 259074.5 259282.8 703191 750955 758271 887607 99655.3 FALSE TRUE 671404.1174 797991.2796 384363.7948 318156.9226 689198.8749 779844.7248 684733.9951 697799.1504 87874.16396 7.64051784 9.081068242 4.374025054 3.620596866 7.843020563 8.874562097 7.792210637 7.940890917 1 16.42315144 4.261590437 24.98366544 6.293379404 8.360793585 0.133272836 2.447444053 560.7611374 608325.3351 0.624157968 1.649030989 18263.77033 -4.261590437 2.067414181 ELLVHLDDPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELLVHLDDPER 11 0 Q86Y56;H0Y650;Q86Y56-2;E9PGY2;Q86Y56-3 Q86Y56 DNAAF5 "Dynein assembly factor 5, axonemal" 0 ; 130.01 0.00023316 166330000 165914 168637 121930 129810 166015 194867 169738 171706 180308 FALSE TRUE 143988.0445 167529.2124 180895.7558 159285.3445 162711.6263 202363.6596 153276.8349 134988.0081 158992.1936 0.905629649 1.053694578 1.137765017 1.001843807 1.023393807 1.272789908 0.964052583 0.849022867 1 17.27859641 2.01191985 24.99978511 0.911570417 1.068287089 0.268171238 0.100819461 240.7510094 504930.8738 0.040275133 0.02713126 102.7826592 -2.01191985 0.156716671 ELLVSALQELESS(ph)TSNSPSNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELLVSALQELESSTSNSPSNK 21 0 A0A087WVI0;E9PBL8;Q8WTW3 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 1 ELLVSALQELES(0.004)S(0.867)T(0.111)S(0.015)NS(0.003)PSNK 129.78 1.03E-05 35455000 86399 86455 72648 79447 95933 80319 114630 123440 137340 TRUE FALSE 74981.15324 85887.07141 107780.8158 97486.65562 94024.12099 83408.9239 103513.2002 97043.31661 121103.8217 0.619147705 0.709201991 0.889986908 0.804984139 0.776392683 0.688738991 0.854747594 0.801323321 1 16.88588487 -0.616218596 0.979261121 10 0.759561077 0.482091387 0.07760893 65.02621772 2.042631968 1255.733409 0.026170122 0.241981076 0.616218596 -9.240438923 ELLVSALQELESST(ph)SNSPSNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELLVSALQELESSTSNSPSNK 21 0 A0A087WVI0;E9PBL8;Q8WTW3 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 1 ELLVSALQELES(0.001)S(0.09)T(0.769)S(0.06)NS(0.08)PSNK 197.12 3.41E-21 37725000 59069 58525 49527 53066 64486 56535 73197 84557 89191 TRUE FALSE 51262.88199 58140.54542 73478.42286 65115.44636 63202.85476 58709.93803 66098.36621 66475.14357 78646.94159 0.651810241 0.739260094 0.934282012 0.827946326 0.803627624 0.746499951 0.840444204 0.845234948 1 16.26310304 -1.999954701 0.034904631 2.040785867 9.82E-07 0.381540349 0.077340884 3028.068429 10.4399059 454.6122852 203.90089 0.010001043 1.999954701 -2.040784885 ELLVSQHTVQLVGGLS(ph)PLS(ph)SPSDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELLVSQHTVQLVGGLSPLSSPSDTK 25 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 2 ELLVSQHTVQLVGGLS(0.998)PLS(0.618)S(0.322)PS(0.058)DT(0.004)K 80.36 1.66E-05 0 50598 42593 25103 42042 55849 44879 43572 65908 89577 TRUE FALSE 43911.3461 42313.20378 37242.89476 51588.27867 54737.71417 46605.52417 39346.39415 51814.0871 78987.30911 0.555929131 0.535696231 0.471504792 0.653121106 0.692993783 0.59003813 0.498135645 0.6559799 1 16.26933325 1.252284501 3.252376885 1.063141679 0.574499265 0.805239969 0.065875099 0.147524 2.138488909 0.180629423 0.018125925 17.87658263 -1.252284501 -0.488642415 ELLVSQHTVQLVGGLS(ph)PLSSPSDT(ph)KAESPAEKVPEESVLPLVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELLVSQHTVQLVGGLSPLSSPSDTKAESPAEKVPEESVLPLVQK 44 2 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 2 ELLVSQHTVQLVGGLS(0.862)PLS(0.183)S(0.174)PS(0.158)DT(0.389)KAES(0.233)PAEKVPEES(0.001)VLPLVQK 109.69 4.23E-05 279580000 262090 182210 55732 115560 177360 139660 261970 313150 126540 TRUE FALSE 227454.1424 181013.0505 82684.18161 141799.6642 173830.883 145032.8106 236564.1897 246185.3094 111580.5854 2.038474182 1.622262959 0.741026598 1.270827391 1.557895421 1.299803278 2.120119633 2.206345384 1 16.7677265 2.249075301 24.99797034 1.879609877 1.399221855 0.102446722 0.457222685 342.4534522 814161.013 0.174517339 0.133718253 177.4497128 -2.249075301 -0.480388022 ELLVSQHTVQLVGGLS(ph)PLSSPSDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELLVSQHTVQLVGGLSPLSSPSDTK 25 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 ELLVSQHTVQLVGGLS(1)PLSSPSDTK;ELLVSQHTVQLVGGLS(1)PLSSPSDTK;ELLVSQHTVQLVGGLS(0.999)PLS(0.001)SPSDTK;ELLVSQHTVQLVGGLS(0.993)PLS(0.007)SPSDTK 266.61 1.16E-45 4993830000 5231110 4576240 1835408 4439980 4877440 4054980 5034110 6496170 9599150 TRUE FALSE 4539805.56 4546178.378 2723017.448 5448145.32 4780388.487 4210977.705 4545902.787 5107014.599 8464349.422 0.536344299 0.5370972 0.321704281 0.643657894 0.564767385 0.497495731 0.537064641 0.603355833 1 23.01296775 1.146609626 2.221900584 1.230492542 0.51810591 0.775557248 0.080567898 0.408090632 1.660923777 0.640657401 0.02115457 14.01553325 -1.146609626 -0.712386633 ELLVSQHTVQLVGGLS(ph)PLSSPSDTKAESPAEKVPEESVLPLVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELLVSQHTVQLVGGLSPLSSPSDTKAESPAEKVPEESVLPLVQK 44 2 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 ELLVSQHTVQLVGGLS(0.989)PLS(0.003)S(0.003)PS(0.003)DT(0.001)KAES(0.001)PAEKVPEESVLPLVQK 132.28 8.74E-10 197890000 297490 224130 63276 112180 197290 128570 329190 385620 42497 TRUE FALSE 258175.9428 222657.6753 93876.48525 137652.1836 193364.315 133516.1711 297265.2045 303158.1639 37473.05307 6.889642599 5.9418077 2.505173119 3.673364519 5.160089695 3.562991541 7.932772488 8.090031077 1 15.1935659 2.252682051 24.99429324 6.271656727 4.567256636 0.023113469 2.298556668 535.1866812 947255.4764 0.865589502 0.667152067 178.9295424 -2.252682051 -1.704400091 ELMETMHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELMETMHR 8 0 E9PM90;Q9UK41;Q9UK41-2 E9PM90 VPS28 Vacuolar protein sorting-associated protein 28 homolog 0 140.5 0.00064854 70234000 56112 44257 30932 37745 44774 50612 42506 47529 40406 FALSE TRUE 48696.65703 43966.27285 45890.81866 46315.57915 43883.085 52559.07639 38383.77466 37365.29322 35629.24871 1.366760703 1.233993824 1.28800972 1.2999314 1.231659005 1.475166564 1.077310806 1.048725263 1 15.12077444 2.104573629 7.538500367 1.03847085 1.305920218 0.769684704 0.070803592 0.100286383 6.441901359 0.027496132 0.018486056 127.2253427 -2.104573629 0.267449367 ELMWLNEKEEEEVGFDWSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELMWLNEKEEEEVGFDWSDR 20 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 138.04 2.29E-06 131316000 154638 131724 108423 126136 116206 100305 152882 166937 137387 FALSE TRUE 134202.1965 130858.6964 160856.7255 154777.1067 113893.728 104163.7983 138055.5272 131238.8217 121145.2654 1.107779129 1.08018003 1.327800347 1.277615813 0.940141801 0.859825582 1.13958665 1.083317794 1 16.8863785 3.23831198 24.99999998 1.017305773 1.199150456 0.463662534 0.103050327 7.071952345 711082.5638 0.033375757 0.0402724 1731.059437 -3.23831198 0.181844683 ELNEDKLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELNEDKLEK 9 1 O00567;A0A494C128;Q5JXT2 O00567 NOP56 Nucleolar protein 56 0 ; 94.616 0.0078445 667190000 675090 494480 458030 493900 466720 356830 628850 783940 697340 FALSE TRUE 585875.146 491231.7283 679534.84 606047.5438 457433.1851 370557.481 567864.2238 616300.5316 614901.2596 0.952795489 0.798879041 1.105112129 0.985601402 0.743913235 0.602629244 0.923504733 1.002275604 1 19.22999524 1.998244402 24.99900352 0.989777325 0.863601326 0.143451572 0.136645704 138.1729159 1967536.499 0.061277585 0.040619988 99.59657465 -1.998244402 -0.126175999 ELNHMLSDTGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 ELNHMLSDTGNR 12 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;;;;;;; 206.32 9.16E-08 15597800000 7658850 7687930 5007880 7088010 8150010 9442490 6511690 8101850 9258340 FALSE TRUE 6646713.567 7637427.482 7429707.518 8697451.004 7987840.746 9805748.7 5880187.306 6369332.426 8163829.592 0.814166133 0.935520199 0.910076262 1.065364105 0.978442856 1.201121188 0.720273156 0.780189292 1 22.96081464 2.205467437 24.99998128 0.817666483 0.981976575 0.248858963 0.122299396 246.2865314 186053.5471 0.050053249 0.033748234 160.4971914 -2.205467437 0.164310092 ELNHMLSDTGNRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 ELNHMLSDTGNRK 13 1 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;;;;;;;;;; 126.95 0.00011855 9194416000 10647400 9625400 6211667 8570310 9809080 9616010 9699230 12718200 9913020 FALSE TRUE 9240319.113 9562170.114 9215649.938 10516329.87 9613898.499 9985944.127 8758600.167 9998511.903 8741114.069 1.057110002 1.093930366 1.054287802 1.203088049 1.099848191 1.142410916 1.002000443 1.143848693 1 23.05938573 1.222213986 24.93637395 0.999999705 1.10005976 0.239862673 0.05569652 1402.223241 2138932.739 0.341882391 0.012851234 16.68068904 -1.222213986 0.100060056 ELNHYLEAEKSCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELNHYLEAEKSCR 13 1 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 66.498 0.050805 1547600000 9648.8 13409 10906 9634.5 8900.6 19665 12539 9134.2 15410 FALSE TRUE 8373.686633 13320.9154 16180.17808 11822.16048 8723.495474 20421.52527 11322.96971 7180.922412 13588.24736 0.61624479 0.980326237 1.190747979 0.870028354 0.641988275 1.502881478 0.833291404 0.528465682 1 13.73007177 2.003365081 24.99935964 0.715649766 0.976079763 0.082988575 0.277260145 180.4159489 1340311.551 0.110583092 0.074139619 100.7778481 -2.003365081 0.260429997 ELNLQDFSHLDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELNLQDFSHLDHR 13 0 Q5VZK9;Q5VZK9-2;Q5VZK9-3;A0A0U1RR91;Q5VZK9-4 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 0 ; 130.07 8.46E-05 377680000 224280 225460 131381 157322 219690 232480 204380 218950 219910 FALSE TRUE 194640.8297 223978.9384 194917.291 193044.3646 215318.5988 241423.656 184559.2591 172129.2464 193912.4903 1.003756021 1.155051632 1.005181723 0.995523106 1.11039056 1.245013437 0.95176571 0.887664565 1 17.56504621 2.032105293 24.99342897 0.930980235 1.08365322 0.395792349 0.080827642 171.3129641 133363.5898 0.033125293 0.022332891 107.6726231 -2.032105293 0.152672984 ELNLVLSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELNLVLSVR 9 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 126.31 0.0011097 358160000 652790 638890 415770 441240 642830 626280 628090 742970 773550 FALSE TRUE 566522.1475 634693.0895 616837.7627 541430.2859 630038.9407 650373.3969 567177.9285 584091.6473 682101.8002 0.830553661 0.930496136 0.904319212 0.793767566 0.923672889 0.953484358 0.831515073 0.856311546 1 19.37962754 ELNNYEIRPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELNNYEIRPGR 11 1 B7Z8Z7;A0AV96;A0AV96-2;D6R9D6;D6RBS9;D6REZ6;D6R9M7 B7Z8Z7 RBM47 RNA-binding protein 47 0 ;;; 159.44 2.61E-05 3369610000 1991180 1724590 1079070 1379870 1721310 1861110 1629830 1869890 1769480 FALSE TRUE 1728040.518 1713261.055 1600911.861 1693190.573 1687059.299 1932708.106 1471769.337 1470028.575 1560294.09 1.107509494 1.098037265 1.026032125 1.085173996 1.081244433 1.238681937 0.943264059 0.942148396 1 20.57338655 2.191747127 24.9999975 0.956936391 1.100024171 0.599799201 0.055371614 81.72759552 43644.69094 0.022521841 0.015184266 155.5059917 -2.191747127 0.14308778 ELNS(ph)NHDGADETSEKEQQEAIEHIDEVQNEIDR ddPTM_MDA-MB-175_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 142.46 2.15E-10 338130000 293220 148030 489420 248430 84430 123840 146400 163480 199640 TRUE FALSE 254470.2341 147057.5812 726105.149 304839.8285 82750.00818 128604.2049 132202.1505 128521.0742 176038.7866 1.445535038 0.835370341 4.124688445 1.731662859 0.470066908 0.730544713 0.750983082 0.730072484 1 17.42553381 3.364071283 5.378370546 0.742628739 2.144614982 0.378727479 0.836227376 0.219174333 9.4762975 0.243736135 0.316193594 2312.444313 -3.364071283 1.401986243 ELNSNHDGADET(ph)SEKEQQEAIEHIDEVQNEIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 33 1 Q01105-2 Q01105-2 SET Protein SET 1 ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;ELNS(0.086)NHDGADET(0.457)S(0.457)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.822)S(0.178)EKEQQEAIEHIDEVQNEIDR 210.06 9.57E-28 6062030000 910163 624433 720001 703185 591701 605984 670691 700486 955823 TRUE FALSE 789882.6535 620331.0585 1068195.892 862853.9018 579927.3077 629296.5966 605647.49 550692.5201 842826.6938 0.937182768 0.736012591 1.267396844 1.023761953 0.688074206 0.746650054 0.718590778 0.653387611 1 19.68487648 3.242019343 24.99811324 0.743905649 0.992605172 0.341798875 0.157386998 97.17787744 702352.7264 0.04610338 0.057124252 1745.89991 -3.242019343 0.248699523 ELNSNHDGADET(ph)SEKEQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK 44 2 Q01105-2 Q01105-2 SET Protein SET 1 ELNS(0.01)NHDGADET(0.495)S(0.495)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK 136.39 7.69E-10 365380000 264488 189770 93404 135183 158453 165267 250233 285040 157589 TRUE FALSE 229535.2407 188523.3884 138574.4868 165878.3663 155300.0953 171624.9284 225965.4422 224086.4142 138959.0079 1.6518198 1.356683465 0.997232845 1.193721578 1.11759646 1.235075948 1.62613022 1.612608045 1 17.08429983 2.269694017 24.40806243 1.463400013 1.241891868 0.068195173 0.240918616 284.1093394 222735.7843 0.091352477 0.070752653 186.0775661 -2.269694017 -0.221508145 ELNSNHDGADETS(ph)EKEQQEAIEHIDEVQNEIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 33 1 Q01105-2 Q01105-2 SET Protein SET 1 ELNSNHDGADET(0.367)S(0.633)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.379)S(0.621)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.168)S(0.832)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.407)S(0.593)EKEQQEAIEHIDEVQNEIDR 415.9 6.23E-187 3890420000 763576 537186 391727 515674 612010 665696 689170 829322 1074535 TRUE FALSE 662667.4969 533657.1898 581167.4874 632765.6633 599832.1984 691305.7559 622334.3995 651977.9441 947504.6964 0.699381754 0.563223794 0.61336634 0.667823247 0.633065145 0.72960668 0.656814053 0.68809996 1 19.85377357 1.211951544 3.248258196 1.072478154 0.650669339 0.851616222 0.045278734 0.143160272 1.942978421 0.160155899 0.011833114 16.29114257 -1.211951544 -0.421808815 ELNSNHDGADETS(ph)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK 44 2 Q01105-2 Q01105-2 SET Protein SET 1 ELNSNHDGADET(0.414)S(0.586)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK 204.23 3.40E-36 511350000 663630 445100 285080 284790 443980 411990 674030 728870 409000 TRUE FALSE 575929.6141 442176.1088 422945.6415 349455.9222 435145.6666 427839.5219 608662.6743 573006.8226 360648.4859 1.596927858 1.226058409 1.172736496 0.968965449 1.206564518 1.186306164 1.687689532 1.588823591 1 18.46023384 2.27185098 24.90697837 1.470453771 1.211227201 0.127553216 0.233887368 274.3344446 205248.8899 0.087791925 0.067998922 187.0040363 -2.27185098 -0.25922657 STAQQELDGKPAS(ph)PTPVIVASHTANK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 STAQQELDGKPASPTPVIVASHTANK 26 1 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 1 STAQQELDGKPAS(0.981)PT(0.019)PVIVASHTANK;STAQQELDGKPAS(0.999)PT(0.001)PVIVASHTANK;STAQQELDGKPAS(0.975)PT(0.025)PVIVASHTANK;STAQQELDGKPAS(1)PTPVIVASHTANK;S(0.003)T(0.003)AQQELDGKPAS(0.88)PT(0.092)PVIVAS(0.017)HT(0.005)ANK 311.78 5.44E-82 6837910000 1906200 1357010 1478910 1521980 1628150 1165722 1974330 2373760 4173230 TRUE FALSE 1654290.84 1348095.712 2194115.823 1867568.821 1595753 1210568.08 1782859.78 1866149.897 3679875.504 0.449550763 0.36634275 0.596247297 0.507508697 0.433643203 0.328969847 0.484489157 0.507123106 1 21.81122553 1.207840721 3.231409446 1.117999233 0.453090369 0.84438474 0.073249882 0.155186498 2.053092656 0.27421566 0.019447701 16.13766592 -1.207840721 -0.664908864 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 33 1 Q01105-2 Q01105-2 SET Protein SET 0 177.86 9.63E-20 398490000 153120 111200 50587 110370 127070 108090 118730 138040 184390 FALSE TRUE 132884.804 110469.5199 75051.0424 135431.1954 124541.5556 112248.2922 107215.5829 108521.2202 162591.6243 0.817291817 0.67942934 0.461592304 0.832953087 0.765977683 0.690369462 0.659416396 0.66744656 1 17.31089341 1.235782494 24.9794452 1.000000417 0.692001432 0.459358907 0.10325339 70.07457054 629949.9831 0.167827021 0.024934164 17.21006436 -1.235782494 -0.307998985 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK 44 2 Q01105-2 Q01105-2 SET Protein SET 0 ; 131.01 6.99E-10 166710000 334950 214757 96974 154114 197710 148135 282170 359030 102939 FALSE TRUE 290685.5088 213346.2471 143870.9508 189107.9392 193775.9578 153833.8493 254805.1968 282254.2285 90769.66869 3.20245202 2.350413417 1.585011302 2.083382499 2.134809575 1.694771519 2.807162354 3.109565481 1 16.46992267 1.217135358 24.91742777 0.999994623 2.363318211 0.38736453 0.541755572 1983.22992 2306355.679 6.735988928 0.143654307 16.48676159 -1.217135358 1.363323588 ELNYFAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ELNYFAK 7 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;; 112.17 0.014922 1823650000 3396660 3261980 1605950 1727810 2537660 2454150 2612630 3106560 3073140 FALSE TRUE 2947782.775 3240551.839 2382592.792 2120135.668 2487165.531 2548562.739 2359257.545 2442246.319 2709836.89 1.087808195 1.195847562 0.879238452 0.782384975 0.917828501 0.940485661 0.870627141 0.901252148 1 21.36977459 4.233197353 24.99697992 0.895543578 1.141827906 0.735596854 0.060541979 56.37764751 262768.5295 0.015381873 0.033591607 17107.92562 -4.233197353 0.246284328 ELPDVLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELPDVLER 8 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 96.253 0.021106 70404000 165720 151240 91515 100790 150960 153980 126770 158370 164390 FALSE TRUE 143819.6821 150246.4945 135771.9601 123675.91 147956.1913 159903.7102 114475.8649 124503.8079 144956.0015 0.992160936 1.036497233 0.936642559 0.853196202 1.020697245 1.103118937 0.789728357 0.858907577 1 17.14525554 2.227700501 24.99994241 0.874003439 0.985180583 0.271889244 0.082215293 285.880696 658090.5021 0.034532052 0.02354038 168.9275569 -2.227700501 0.111177144 ELPDVQGESDSIS(ph)PLLLHLEDDDFSENEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELPDVQGESDSISPLLLHLEDDDFSENEK 29 0 Q8IWI9-3;Q8IWI9 Q8IWI9-3 MGA MAX gene-associated protein 1 ELPDVQGESDS(0.001)IS(0.999)PLLLHLEDDDFSENEK 203.33 1.74E-25 39418000 52382 36039 28579 32618 39930 28832 42671 52744 43800 TRUE FALSE 45459.58598 35802.25744 42399.89999 40024.41543 39135.47112 29941.1857 38532.77299 41465.10605 38622.0139 1.177038207 0.926990952 1.097816911 1.036310938 1.013294419 0.775236262 0.997689377 1.073613255 1 15.23713577 3.128691496 4.40896742 0.974397942 1.052695887 0.174147582 0.097035288 0.48843652 16.56138956 0.030912409 0.035602075 1344.904653 -3.128691496 0.078297945 ELPEPLLTFDLYPHVVGFLNIDESQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELPEPLLTFDLYPHVVGFLNIDESQR 26 0 Q07960;H0YE29 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 218.93 3.36E-34 896270000 357650 334100 248240 293767 342460 347049 439040 434910 352360 FALSE TRUE 310385.6463 331905.2751 368289.6943 360471.2873 335645.716 360400.1996 396461.9684 341907.881 310704.4022 0.998974086 1.068234865 1.18533787 1.16017438 1.080273448 1.159945585 1.276010142 1.100428184 1 18.24518316 4.470320463 4.199353591 1.141005795 1.009747479 0.288303621 0.071815919 0.245860119 10.14434933 0.018399824 0.065300613 29533.87709 -4.470320463 -0.131258316 ELPEQLQEHAIEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELPEQLQEHAIEDK 14 0 Q15424;Q15424-3;Q15424-4 Q15424 SAFB Scaffold attachment factor B1 0 ; 183.01 1.46E-06 318650000 458620 322100 309340 398970 348510 302730 361100 470910 856260 FALSE TRUE 398012.205 319984.1039 458937.8587 489562.2364 341575.3328 314376.219 326080.5776 370209.5611 755033.9183 0.527144802 0.423800966 0.607837406 0.648397674 0.452397336 0.416373638 0.431875403 0.490321762 1 19.52618193 1.238049876 24.99999988 1.000000568 0.497704647 0.803982085 0.077618425 5.688606279 278172.8545 0.11643201 0.020246914 17.3001503 -1.238049876 -0.502295921 ELPESGIQLGT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELPESGIQLGTPR 13 0 A0A087WTA5;E7ERK9;Q9UI10-3;Q9UI10;Q9UI10-2;A0A087WW69;F8W8L6 A0A087WTA5 EIF2B4 Translation initiation factor eIF-2B subunit delta 1 ELPESGIQLGT(1)PR 132.84 0.0012764 47163000 56750 61770 38922 50831 52862 71342 54733 60532 64145 TRUE FALSE 49250.34371 61364.2288 57744.80939 62372.95545 51810.14962 74086.5729 49425.00208 47587.70286 56561.85117 0.870734297 1.084904888 1.020914418 1.102738934 0.915991053 1.309832889 0.873822215 0.841339204 1 15.78754172 ELPGFLQSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELPGFLQSGK 10 0 P25815 P25815 S100P Protein S100-P 0 ; 177.78 5.32E-06 629310000 929260 875990 649890 763950 792020 702620 937200 1097140 1564590 FALSE TRUE 806455.9366 870235.564 964178.9778 937416.5237 776260.3516 729650.2461 846310.4882 862525.149 1379625.953 0.584546801 0.630776452 0.698869847 0.679471506 0.562660009 0.528875413 0.613434741 0.62518768 1 20.39584574 1.23803357 6.509517474 1.010854556 0.615789195 0.853674688 0.050047144 0.048022159 9.534862075 0.083918108 0.013580119 17.29950076 -1.23803357 -0.395065362 ELPGHTGYLSCCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 214 1.42E-09 1308580000 903210 912980 508750 797470 1017150 1230830 748060 1093550 932740 FALSE TRUE 783848.5101 906982.5743 754783.2017 978547.7521 996910.705 1278180.827 675513.2563 859702.8425 822472.5398 0.953039125 1.102751193 0.917700185 1.189763432 1.212089957 1.554071127 0.821320134 1.045266317 1 19.64960799 3.732062603 24.83799768 1.128284997 1.00232227 0.112498988 0.191296446 1303.780031 4983564.966 0.054986116 0.083866595 5395.883981 -3.732062603 -0.125962727 ELPLTQPPSAHSSITSGSCPGT(ph)PEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELPLTQPPSAHSSITSGSCPGTPEMR 26 0 Q9HCD6;Q9HCD6-2;Q9HCD6-3;Q9HCD6-4;J3KRP9 Q9HCD6 TANC2 Protein TANC2 1 ELPLTQPPSAHSSIT(0.003)S(0.01)GS(0.315)CPGT(0.672)PEMR 139.41 1.23E-06 303050000 56565 85128 19483 35381 102050 109660 60328 85703 68908 TRUE FALSE 49089.79193 84568.78856 28905.04397 43414.79681 100019.4047 113878.6912 54477.39985 67376.08039 60761.77474 0.807905828 1.39180906 0.475710989 0.714508373 1.646090903 1.874183097 0.896573546 1.10885636 1 15.89087639 3.259123341 24.9999297 1.27841492 0.859808724 0.278235927 0.364623888 383.0680705 465726.9229 0.111826445 0.144200762 1816.031347 -3.259123341 -0.418606196 ELPPAAAIGATSLVAAPHS(ph)SSSSPSKDSSR ddPTM_MDA-MB-175_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(0.196)S(0.196)S(0.196)S(0.196)S(0.196)PS(0.013)KDS(0.003)S(0.003)R 99.774 0.00031355 144830000 74036 73442 15808 59564 109230 101710 88984 105830 70091 TRUE FALSE 64251.95502 72959.55467 23452.80167 73088.91658 107056.5367 105622.8495 80354.34538 83199.07807 61804.92183 1.039592853 1.180481303 0.379464952 1.182574371 1.732168467 1.708971493 1.300128582 1.34615619 1 15.91543411 3.481572371 24.88398463 1.418253305 0.87842814 0.433788443 0.287386984 170.0254018 950530.5396 0.083504779 0.110670639 3030.905324 -3.481572371 -0.539825165 ELPPAAAIGATSLVAAPHSS(ph)SSSPSKDSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELPPAAAIGATSLVAAPHSSSSSPSKDSSR 30 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 ELPPAAAIGATSLVAAPHS(0.031)S(0.231)S(0.231)S(0.231)S(0.231)PS(0.044)KDSSR;ELPPAAAIGATSLVAAPHS(0.047)S(0.226)S(0.226)S(0.226)S(0.226)PS(0.047)KDSSR 220.94 7.57E-35 538040000 480040 531030 129995 287726 745180 611870 634610 774850 437800 TRUE FALSE 416601.4977 527541.629 192861.0168 353058.5859 730352.3759 635409.0348 573065.6199 609154.3574 386043.7827 1.079156086 1.366533156 0.499583274 0.914555814 1.89189001 1.645950701 1.484457581 1.577941116 1 18.55840495 3.26017235 24.99013094 1.530910421 0.960399845 0.453816697 0.302448781 217.1613409 251106.8999 0.087621474 0.113015976 1820.423151 -3.26017235 -0.570510575 ELPPS(ph)PEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 107.09 0.0017336 480520000 1142670 915330 834500 935310 929000 634060 1171470 1473240 1538560 TRUE FALSE 991663.2643 909317.137 1238066.991 1147686.431 910514.7176 658452.6985 1057861.02 1158199.091 1356673.19 0.730952209 0.670255109 0.912575704 0.845956447 0.671137843 0.485343636 0.779746388 0.853705299 1 20.3716418 1.495454209 2.283109417 1.003103004 0.725521012 0.384916269 0.113451053 0.418426159 3.815120409 0.202488247 0.033433682 31.293505 -1.495454209 -0.277581992 ELPQLVASVIESESEILHHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELPQLVASVIESESEILHHEK 21 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 0 ; 170.91 4.39E-12 39637000 64503 52686 38293 44190 58182 54844 67188 72970 78222 FALSE TRUE 55978.76512 52339.9022 56811.62288 54224.0149 57024.29203 56953.88417 60672.1181 57365.93335 68974.68427 0.811584217 0.758827717 0.823659049 0.78614372 0.826742342 0.825721564 0.879628791 0.831695483 1 16.07377933 -1.221848551 0.766317125 10 0.802844899 0.788647153 0.029933387 49.33142668 0.763658003 751.9053682 0.011375895 0.060000028 1.221848551 -9.197155101 ELPSFLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELPSFLGK 8 0 P26447 P26447 S100A4 Protein S100-A4 0 ; 148.38 0.0012147 938490000 2287700 2098490 1676500 1879260 1857670 1937520 2287700 2362300 2827100 FALSE TRUE 1985374.649 2084704.881 2487261.008 2305974.706 1820706.001 2012057.648 2065839.206 1857140.528 2492883.459 0.796416953 0.836262471 0.997744599 0.925023068 0.73036146 0.807120622 0.828694658 0.744976875 1 21.24938401 3.263639276 24.99892016 0.81230323 0.892882031 0.115459108 0.089015245 427.4084275 426046.4629 0.025471757 0.032869688 1835.013552 -3.263639276 0.080578801 ELPSLS(ph)PAPDTGLSPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELPSLSPAPDTGLSPSK 17 0 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;A0A0A0MSL0 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 ELPS(0.001)LS(0.999)PAPDTGLSPSK 132.59 2.42E-05 70228000 55479 51353 45644 53875 59001 43004 54584 72368 119510 TRUE FALSE 48147.30958 51015.65876 67717.59107 66108.14218 57826.99553 44658.39171 49290.45208 56892.66637 105381.6639 0.456885076 0.484103751 0.642593678 0.627321108 0.548738683 0.423777629 0.467732718 0.539872538 1 16.68526434 1.239256462 6.507041053 1.013169235 0.524358833 0.818694787 0.070455801 0.053301657 10.60936983 0.115535291 0.019045153 17.34828154 -1.239256462 -0.488810402 ELPSLSPAPDTGLS(ph)PSKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELPSLSPAPDTGLSPSKR 18 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;A0A0A0MSL0 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 ELPSLSPAPDT(0.226)GLS(0.62)PS(0.154)KR 129.43 1.30E-05 373240000 261490 215340 156130 168530 235810 192590 249810 276550 247690 TRUE FALSE 226933.434 213925.4174 231634.9902 206797.3123 231117.8424 199999.0619 225583.4646 217411.9346 218408.3704 1.039032678 0.979474445 1.060559125 0.946837852 1.058191323 0.915711525 1.032851737 0.99543774 1 17.73666862 3.749490044 24.99589698 0.994119388 1.021667312 0.116447767 0.04424607 1844.042412 4217372.636 0.010622585 0.018184099 5616.814013 -3.749490044 0.027547924 ELPTAFDYVEFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELPTAFDYVEFTR 13 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 146.16 9.81E-05 419921000 267168 249553 179035 208509 273338 258793 250643 302271 275247 FALSE TRUE 231861.0719 247913.6699 265616.9248 255854.1553 267899.1086 268748.9342 226335.6804 237632.6989 242707.6132 0.955310255 1.021449911 1.094390577 1.054166171 1.103793594 1.107295031 0.932544626 0.97909042 1 17.88885984 2.234262683 24.99972109 0.970741957 1.058318949 0.420227172 0.047305047 106.8485746 621494.5406 0.019695507 0.01380673 171.4994308 -2.234262683 0.087576992 ELPVNAQNYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELPVNAQNYVR 11 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 96.618 0.016 61196000 22569 24586 15695 19772 23165 26060 26341 21801 22475 FALSE TRUE 19586.44947 24424.49295 23285.1545 24261.5348 22704.06182 27062.54506 23786.45387 17139.02581 19818.0311 0.988314599 1.232437916 1.174947924 1.224215194 1.145626511 1.365551649 1.200243039 0.864819806 1 14.27452602 1.759990642 10.43073101 0.934642896 1.197625588 0.54379427 0.097949638 0.115333355 49.74388943 0.05100531 0.02409753 57.54275386 -1.759990642 0.262982692 ELQAHGADELLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELQAHGADELLK 12 0 O15144;C9JTV5;G5E9J0 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;; 167.98 4.77E-05 1519660000 3453840 2682900 2451280 3146440 2734120 2328920 3018920 3647650 5509900 FALSE TRUE 2997406.293 2665275.853 3636727.207 3860887.292 2679716.361 2418515.059 2726145.603 2867628.434 4858525.899 0.616937391 0.54857706 0.748524817 0.794662285 0.551549259 0.497787829 0.5611055 0.590226026 1 22.21208723 1.23657239 24.99817749 1.000000492 0.612381513 0.636352713 0.091775953 37.40182124 470131.1919 0.154103003 0.024283755 17.24139453 -1.23657239 -0.387618979 ELQDAFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELQDAFSR 8 0 H7C2Q8;Q99848 H7C2Q8 EBNA1BP2 Probable rRNA-processing protein EBP2 0 78.264 0.072295 44635000 120870 76498 64751 99575 87021 92378 56804 89805 146720 FALSE TRUE 104896.7233 75995.4796 96064.80018 122185.0257 85289.45235 95931.84144 51295.15682 70600.89961 129374.9287 0.810796375 0.587404997 0.742530265 0.944425839 0.659242507 0.741502564 0.396484522 0.545707737 1 16.98119854 2.416196283 24.99999734 0.609076535 0.745420152 0.05333895 0.175851316 155.4332931 63778.97613 0.065407405 0.050664338 260.733169 -2.416196283 0.136343617 ELQELVQYPVEHPDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ELQELVQYPVEHPDK 15 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;;; 223.06 1.32E-12 14907357000 14904910 8573740 7320741 8726730 8440830 7159780 9865040 11889220 13881760 FALSE TRUE 12935188.38 8517418.537 10861075.83 10708267.43 8272873.997 7435221.37 8908329.939 9346802.825 12240674.15 1.056738234 0.695829203 0.887293927 0.874810268 0.675851174 0.607419271 0.72776465 0.763585625 1 23.54517968 6.292082183 9.38971065 0.794713776 1.091223976 0 0.145381734 0 0 0.031866753 0 1959215.388 -6.292082183 0.296510201 ELQEMDKDDESLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 ELQEMDKDDESLIK 14 1 P52566;F5H3P3;H0YGX7;F5H2R5;F5H6Q0 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ;;;;;;;;;;; 240.2 1.98E-17 11363139000 12403851 10570431 10381291 9852151 9488456 6177332 14036805 17012448 14362212 FALSE TRUE 10764650.66 10500993.14 15401718.05 12089232.47 9299654.289 6414977.959 12675517.81 13374468.39 12664327.66 0.849997801 0.829178889 1.216149682 0.954589362 0.734318832 0.506539165 1.000883596 1.056074096 1 23.59426715 2.027450569 24.99989408 1.030973814 0.854749217 0.173279499 0.175941243 391.6042076 356641.7812 0.077973205 0.052568281 106.5247611 -2.027450569 -0.176224596 ELQEQMSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELQEQMSR 8 0 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;C9IZ80;H0Y503 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 ; 163.69 0.0007781 517360000 363580 355390 210760 264950 362320 403680 351870 381540 369630 FALSE TRUE 315531.9818 353055.4197 312684.2409 325110.947 355110.5409 419209.8308 317745.7016 299950.6401 325932.7625 0.968089183 1.083215498 0.95935198 0.997478574 1.089520851 1.286185002 0.974881135 0.920283797 1 18.31421485 2.023965098 24.99990754 0.952388029 1.064256499 0.200235983 0.093249948 333.2500287 347638.1614 0.039550546 0.026663643 105.6732583 -2.023965098 0.11186847 ELQHAALGGTATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELQHAALGGTATR 13 0 O14828;O14828-2 O14828 SCAMP3 Secretory carrier-associated membrane protein 3 0 100.41 0.0024143 455310000 289630 297890 196120 247270 331030 365430 260460 313990 347950 FALSE TRUE 251354.6617 295933.141 290964.288 303416.4328 324443.1506 379488.3286 235200.6293 246845.682 306815.7474 0.819236509 0.964530483 0.948335574 0.988920665 1.057452733 1.236860662 0.766585911 0.804540458 1 18.22701301 ELQNAGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELQNAGDR 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 154.28 0.00099468 251300000 493740 501330 307220 308820 357040 500180 431160 447730 460070 FALSE TRUE 428491.008 498036.7302 455792.6196 378942.301 349935.6025 519422.2483 389346.1696 351986.4237 405681.0487 1.056226337 1.227655893 1.123524555 0.934089236 0.862587995 1.280370996 0.959734675 0.86764325 1 18.62998638 4.943873885 0.178676122 0.83972648 1.43920437 0.145179788 0.13090433 59.26871628 2.800216455 2.079601712 9.387303438 87876.72932 -4.943873885 0.599477889 ELQNTVANLHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ELQNTVANLHVR 12 0 H3BV04;H3BN93;H3BUB6;H3BPL9;O15127 H3BV04 SCAMP2 Secretory carrier-associated membrane protein 2 0 ;; 183.79 1.52E-05 905840000 675050 621400 441726 555780 729790 739280 487370 756610 761000 FALSE TRUE 585840.4321 617317.9825 655346.1711 681978.3436 715268.6068 767720.58 440104.9324 594814.8394 671035.4469 0.873039472 0.919948395 0.976619304 1.016307479 1.065917769 1.144083496 0.65585944 0.886413441 1 19.35602945 2.249523665 24.99995738 0.847565128 0.998479087 0.295610453 0.110525645 272.6579465 621765.1411 0.042739653 0.032780071 177.6330059 -2.249523665 0.150913959 ELQQAELPNRS(ph)PGFGIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELQQAELPNRSPGFGIK 17 1 F8VU11;Q6NWY9-2;Q6NWY9-3;Q6NWY9 F8VU11 PRPF40B Pre-mRNA-processing factor 40 homolog B 1 ELQQAELPNRS(1)PGFGIK;ELQQAELPNRS(1)PGFGIK;ELQQAELPNRS(1)PGFGIK;ELQQAELPNRS(1)PGFGIK 228.57 8.40E-16 2301890000 2709080 2405190 1737240 2133630 2441680 2231090 2884440 3349200 1942370 TRUE FALSE 2351068.214 2389390.149 2577375.075 2618103.302 2393095.345 2316921.476 2604707.453 2632999.644 1712745.231 1.372689978 1.395064546 1.504821048 1.52860055 1.397227855 1.352753132 1.520779276 1.537297898 1 20.70787914 1.232303053 24.99979376 0.999999247 1.456040188 0.806973969 0.06930688 96.86866672 386965.2245 0.166723053 0.018316178 17.07273316 -1.232303053 0.456040941 ELQQAVLHMEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ELQQAVLHMEQR 12 0 Q02818 Q02818 NUCB1 Nucleobindin-1 0 ;; 212.83 1.57E-08 765710000 599710 746110 466184 484252 714840 855910 563288 729900 706960 FALSE TRUE 520456.804 741208.7543 691632.1417 594208.8179 700616.0826 888837.4115 508660.4165 573816.5651 623383.9942 0.834889585 1.189008318 1.109480109 0.953198708 1.123891677 1.425826489 0.815966437 0.920486523 1 19.24976159 ELQQELQEYEVVTESEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ELQQELQEYEVVTESEKR 18 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 ;;;; 238.94 1.08E-23 627097000 653243 534314 452468 573211 524752 475337 603512 789547 806013 FALSE TRUE 566915.2824 530804.0562 671283.0382 703367.3185 514310.4619 493623.522 544983.4991 620708.5183 710727.0614 0.797655406 0.746846553 0.94450187 0.989644769 0.723639903 0.694533174 0.76679717 0.87334302 1 19.43893611 1.332354945 3.010144168 1.014830336 0.811602383 0.298962763 0.092773431 0.455343882 5.696650085 0.198322927 0.026278394 21.49586593 -1.332354945 -0.203227953 ELQTLHNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ELQTLHNLR 9 0 P33176;O60282;O60282-2;Q12840;J3KNA1;A0A0G2JMZ6 P33176;Q12840 KIF5B;KIF5C;KIF5A Kinesin-1 heavy chain;Kinesin heavy chain isoform 5C;Kinesin heavy chain isoform 5A;Kinesin-like protein 0 ;;;;; 187.97 3.99E-05 3302060000 2331710 2468640 1579250 1640490 2267740 2556880 2187220 2436350 2478350 FALSE TRUE 2023568.616 2452423.341 2342980.582 2012988.328 2222616.411 2655244.828 1975103.741 1915355.512 2185362.286 0.925964829 1.122204477 1.072124561 0.921123395 1.017047116 1.215013568 0.903787785 0.876447591 1 21.05944104 ELRAPS(ph)PPVEHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELRAPSPPVEHPR 13 1 Q86WR7;Q86WR7-2 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 ELRAPS(1)PPVEHPR;ELRAPS(1)PPVEHPR 93.495 0.0033745 158007000 159586 158118 90964 77238 146558 172653 144315 153693 48455 TRUE FALSE 138496.3058 157079.3124 134954.4947 94776.06841 143641.7825 179295.0726 130319.3535 120826.948 42726.7051 3.241445963 3.676373174 3.15855141 2.218192772 3.361873615 4.196323405 3.050067942 2.827902309 1 15.38285045 3.999906376 24.19894426 2.867033833 3.44854805 0.102374161 0.819791 6.08776152 1576326.972 0.215841294 0.441394689 9997.844466 -3.999906376 0.581514217 KDS(ph)EGYSESPDLEFEYADTDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDSEGYSESPDLEFEYADTDK 21 1 Q5VSL9;Q5VSL9-4 Q5VSL9 STRIP1 Striatin-interacting protein 1 1 KDS(0.275)EGY(0.174)S(0.275)ES(0.275)PDLEFEYADTDK;KDS(0.972)EGYS(0.026)ES(0.001)PDLEFEYADTDK 224.88 1.85E-25 444590000 244734 152897 229147.1 248567 181473 144830 282074 327830 647065 TRUE FALSE 212391.7818 151892.6095 339963.404 305007.9365 177862.0423 150401.7038 254718.5069 257726.1057 570569.7128 0.372245104 0.266212184 0.595831493 0.534567345 0.311727101 0.263599172 0.44642837 0.451699591 1 19.12204364 1.209110099 3.362951332 1.120431986 0.400171639 0.751772812 0.107694441 0.198713064 2.981403892 0.389805051 0.028998052 16.18490294 -1.209110099 -0.720260347 ELS(ph)APAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELSAPAR 7 0 F5H672;F5H5N2;B4DNC9;B3KQ30;Q9H1K1 F5H672 ISCU "Iron-sulfur cluster assembly enzyme ISCU, mitochondrial" 1 ELS(1)APAR;ELS(1)APAR 93.649 0.015504 825150000 1491660 1199920 903660 1079790 1246490 1472580 1269890 1385900 1514320 TRUE FALSE 1294533.352 1192037.647 1340672.999 1324972.823 1221687.288 1529231.105 1146736.263 1089536.07 1335298.815 0.969470906 0.892712278 1.004024705 0.992266906 0.914916777 1.145235125 0.858786251 0.815949253 1 20.3487312 ELS(ph)NS(ph)PLRENSFGSPLEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 ELS(0.996)NS(0.916)PLRENS(0.086)FGS(0.002)PLEFR 152.23 3.29E-08 85948000 281360 194950 153780 181160 215320 233780 202470 232090 213340 TRUE FALSE 244177.5631 193669.3606 228148.5224 222295.1469 211035.5533 242773.6679 182834.4906 182459.3596 188119.1882 1.297993923 1.029503489 1.212787087 1.181671838 1.121818328 1.290531126 0.971907716 0.969913603 1 17.52128749 2.218486288 24.98803584 0.978016708 1.179486272 0.615647727 0.077384638 148.554519 184915.6649 0.02912916 0.019666473 165.3812569 -2.218486288 0.201469564 ELS(ph)NSPLRENS(ph)FGSPLEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 ELS(0.553)NS(0.447)PLRENS(1)FGSPLEFR 155.8 1.27E-08 198800000 328510 220820 172670 186920 226870 254840 233130 260840 226680 TRUE FALSE 285096.5712 219369.4189 256173.7895 229363.0429 222355.7309 264643.8597 210521.0885 205061.3959 199882.1486 1.426323327 1.0974938 1.281624154 1.147491382 1.112434164 1.323999474 1.053226063 1.025911505 1 17.60879011 -1.188575365 0.214523201 2.25E-13 1.326668288 0.451194381 0.102956438 63.09177488 1.330312889 26.02366868 0.550988934 0.064777567 1.188575365 1.326668288 ELS(ph)PAALEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ELSPAALEK 9 0 O75683 O75683 SURF6 Surfeit locus protein 6 1 ELS(1)PAALEK;ELS(1)PAALEK;ELS(1)PAALEK;ELS(1)PAALEK;ELS(1)PAALEK;ELS(1)PAALEK 181.31 5.00E-05 1945680000 4525960 3383250 2609880 3055440 3483040 3058580 3815910 4601320 4474160 TRUE FALSE 3927842.919 3361025.208 3872026.698 3749224.351 3413734.318 3176245.552 3445843.636 3617363.526 3945229.902 0.99559291 0.851921255 0.981445136 0.950318345 0.865281467 0.805085035 0.873420237 0.916895495 1 21.91167794 4.763348575 22.88312417 0.904300004 0.995593263 0.181490903 0.060045674 4256.114752 3928850.889 0.015186785 0.832930169 57989.39459 -4.763348575 0.091293259 ELS(ph)PAGSISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELSPAGSISK 10 0 A0A494C0Q6;A0A494C0K5;A0A494C0W0;O95453-2;O95453-3;O95453;O95453-4 A0A494C0Q6 PARN Poly(A)-specific ribonuclease PARN 1 ELS(1)PAGSISK;ELS(1)PAGSISK 170.23 4.61E-06 1684420000 4235600 3436200 2251900 2896000 3578500 2769900 3860500 4736500 4112100 TRUE FALSE 3675854.728 3413627.376 3340926.372 3553581.063 3507294.851 2876459.845 3486109.304 3723636.334 3625972.223 1.013757002 0.941437818 0.921387746 0.980035379 0.967270193 0.793293403 0.961427471 1.0269346 1 21.78993644 1.990380013 24.9153061 1.009028168 0.934016536 0.229161855 0.057736751 618.7714871 1602587.873 0.025101373 0.01586498 97.8092689 -1.990380013 -0.075011632 ELS(ph)PQHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELSPQHK 7 0 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 ELS(1)PQHK;ELS(1)PQHK;ELS(1)PQHK;ELS(1)PQHK 76.221 0.026631 1275040000 1404560 1228160 957326 1224345 984784 1116896 1329370 1591850 2411560 TRUE FALSE 1218943.837 1220092.136 1420292.056 1502351.245 965188.7251 1159863.712 1200447.902 1251445.265 2126468.124 0.573224599 0.573764602 0.667911284 0.706500713 0.453892872 0.545441382 0.564526639 0.588508829 1 21.0200278 1.238651062 8.402311457 1.004108475 0.584043856 0.789147884 0.06754638 0.041260533 30.75132797 0.098792476 0.017231934 17.32411517 -1.238651062 -0.420064619 ELS(ph)PQHKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELSPQHKR 8 1 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 ELS(1)PQHKR 55.314 0.076388 125530000 497630 405220 225860 248100 351890 352000 450860 521550 162980 TRUE FALSE 431866.9347 402558.0831 335086.6515 304434.897 344888.0775 365541.6678 407135.6666 410020.5912 143712.6901 3.005071678 2.801131083 2.331642747 2.118357793 2.399844282 2.543558732 2.832983409 2.85305766 1 17.13282793 4.359534734 3.846293687 2.381554962 2.964209401 0.180559993 0.520477687 0.417251426 11.1742083 0.131665377 0.403539547 22884.14728 -4.359534734 0.582654438 ELSAEYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELSAEYLR 8 0 Q9H3K6;H3BV85;Q9H3K6-2;H3BPT9 Q9H3K6 BOLA2;BOLA2B BolA-like protein 2 0 147.06 0.0012641 422860000 776980 1068300 756710 593110 892930 1179400 923630 918810 788210 FALSE TRUE 674300.1244 1061282.267 1122657.487 727784.6906 875162.44 1224772.281 834056.5048 722329.6317 695028.7117 0.970175927 1.526961763 1.615267784 1.047128958 1.259174514 1.762189476 1.200031726 1.039280276 1 19.40671305 2.002666737 24.97861198 1.051608848 1.373060392 0.257931739 0.239931506 104.8884391 982455.3249 0.097576079 0.065357107 100.615928 -2.002666737 0.321451544 ELSDDCFQQWGVRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELSDDCFQQWGVRPR 15 1 P42785;P42785-2 P42785 PRCP Lysosomal Pro-X carboxypeptidase 0 ; 99.566 0.0033596 132800000 141512 137624 79396 113138 136003 135292 142773 150919 163058 FALSE TRUE 122810.8307 136719.9389 117792.1712 138827.7121 133296.8064 140496.7708 128926.8964 118646.1463 143781.469 0.854149227 0.950887064 0.819244455 0.965546625 0.92707918 0.977154927 0.89668646 0.825183851 1 17.13351822 4.772366724 21.00060264 0.911948808 0.854148275 0.091789712 0.060532718 4278.506595 2657435.333 0.014613991 1.533393386 59206.13681 -4.772366724 -0.057800533 ELSDFISYLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELSDFISYLQR 11 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 290.58 4.55E-35 11181169000 2750070 3186240 1552750 1887010 3097430 3755360 2607000 2747010 1632540 FALSE TRUE 2386641.282 3165309.38 2303665.094 2315484.462 3035797.203 3899831.129 2354173.541 2159583.289 1439542.981 1.657915959 2.198829366 1.600275312 1.608485813 2.108861801 2.709075853 1.635361759 1.500186738 1 20.45717943 1.550589531 2.053397108 1.006394985 1.962047128 0.447222679 0.344384555 0.362051276 2.791839742 0.564456814 0.099460079 35.52953561 -1.550589531 0.955652143 ELSDFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ELSDFLR 7 0 E7ETZ4;Q9Y6E2;Q75MG1;B5MCH7;B5MCE7;E9PFD4 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 ;;;;; 139.27 0.0062933 1312475000 2570620 2600280 1823280 1998240 2530180 2735010 2559480 2747210 2944970 FALSE TRUE 2230906.054 2583198.589 2705024.307 2451970.933 2479834.368 2840227.604 2311262.024 2159740.52 2596819.002 0.859091855 0.994754963 1.041668405 0.944220961 0.954950794 1.093733373 0.890035856 0.831686967 1 21.30831403 2.099680079 24.99843769 0.890735479 0.982694784 0.172180999 0.073716427 16.16732674 4031.434808 0.029228012 0.019705552 125.7998371 -2.099680079 0.091959305 ELSDIAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 20 ELSDIAHR 8 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;;;;;;;;;;;;;; 214.64 8.75E-06 1.17518E+11 71090511.6 69199121.6 38920753 48710635.2 65399092.1 68495888.7 65275378.7 72756794.6 67544848.7 FALSE TRUE 61695720.37 68744548.01 57742959.33 59771129.42 64097778.12 71130969.86 58944982.52 57198320.27 59559773.63 1.035862237 1.154211036 0.96949595 1.003548633 1.07619244 1.194278714 0.989677746 0.960351539 1 25.82783493 2.031663521 24.99988145 0.976644827 1.070340507 0.288360352 0.065878386 233.8310467 184620.0376 0.027378618 0.0184585 107.5631522 -2.031663521 0.09369568 ELSDLAR ddPTM_MDA-MB-175_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 ;;; 121.29 0.010358 969230000 2155350 2023260 1390620 1588960 1980530 2144830 1889710 2087340 2327780 FALSE TRUE 1870515.037 2009969.072 2063128.483 1949757.654 1941121.328 2227342.998 1706446.215 1640978.585 2052592.5 0.911293906 0.979234345 1.005133013 0.949900018 0.945692497 1.085136479 0.83136142 0.799466326 1 20.96901581 2.210222361 24.9999882 0.858902425 0.977687815 0.318960729 0.068883624 209.7420039 185032.7442 0.027379786 0.018463373 162.2640686 -2.210222361 0.11878539 ELSDQATAS(ph)PIVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELSDQATASPIVAR 14 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 ELSDQAT(0.002)AS(0.998)PIVAR;ELSDQATAS(1)PIVAR;ELSDQATAS(1)PIVAR;ELSDQAT(0.001)AS(0.999)PIVAR 326.02 2.93E-57 1606730000 2365640 2155720 1384710 1532680 1833060 1716440 2017020 2483700 2460760 TRUE FALSE 2053014.68 2141558.933 2054360.388 1880698.42 1796585.692 1782472.557 1821409.711 1952580.083 2169851.756 0.946154351 0.986960942 0.946774535 0.866740511 0.827976237 0.821472044 0.839416659 0.899867965 1 21.04916505 3.816463527 4.194142125 0.87178448 0.966122796 0.374932523 0.05128626 0.243257763 8.057461292 0.014709772 0.026347518 6553.352466 -3.816463527 0.094338316 ELSEALTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELSEALTR 8 0 P41250 P41250 GARS Glycine--tRNA ligase 0 99.802 0.015249 122560000 257130 229040 156820 176260 215200 247970 202280 224270 236100 FALSE TRUE 223149.619 227535.4212 232658.6765 216282.527 210917.941 257509.5664 182662.9167 176311.6058 208188.527 1.071863192 1.092929685 1.117538415 1.038878223 1.0131103 1.236905655 0.87739185 0.846884352 1 17.66753104 2.210630268 24.99760105 0.894061139 1.089824253 0.606469584 0.070663829 130.2050816 116532.2978 0.02780307 0.018749233 162.416545 -2.210630268 0.195763114 ELSEPMEFQYLPDTDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELSEPMEFQYLPDTDDR 17 0 Q04206;Q04206-4;Q04206-2;A0A087X0W8;E9PKH5;Q2TAM5;Q04206-3 Q04206 RELA Transcription factor p65 0 ; 303.15 3.51E-46 198248000 168959 163258 108454 122602 154082 161457 152109 176481 177731 FALSE TRUE 146630.6401 162185.5474 160902.7172 150440.658 151016.0697 167668.3553 137357.4926 138741.9115 156719.8437 0.93562268 1.034875633 1.026690133 0.959933691 0.963605285 1.069860404 0.876452461 0.885286179 1 17.25782834 2.222761407 24.99202361 0.91138813 0.998039477 0.334378468 0.051233157 241.9791455 382772.4004 0.020395937 0.013802489 167.0172803 -2.222761407 0.086651347 ELSEQIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ELSEQIQR 8 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;; 176.09 0.00061035 1139120000 1014380 1005240 642240 874030 1002230 990520 882240 1042020 1000500 FALSE TRUE 880327.1129 998636.5123 952829.4122 1072491.87 982287.5838 1028625.945 796680.5006 819192.132 882222.0298 0.997852109 1.131955991 1.080033574 1.215671151 1.113424456 1.165949059 0.903038548 0.928555516 1 19.75078226 2.236781592 24.99969625 0.938974166 1.120715653 0.644927503 0.060659979 26.75301736 375933.2239 0.023320374 0.016639725 172.4970179 -2.236781592 0.181741487 ELSESVQQQSTPVPLIS(ph)PKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 113.31 8.62E-05 116740000 161530 169100 68274 81857 160440 133470 200910 211220 21290 TRUE FALSE 140183.4012 167989.171 101291.5348 100443.883 157247.5579 138604.6773 181425.7791 166052.2467 18773.12045 7.46724028 8.948388276 5.395561969 5.35040955 8.376207796 7.383145365 9.664124809 8.845212874 1 14.19638085 4.26892093 24.99477338 6.991532807 8.207813355 0.050704995 2.469488218 820.2527444 675277.4019 0.615713791 1.628595673 18574.66246 -4.26892093 1.216280548 ELSEYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ELSEYVR 7 0 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;C9IZ80 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 ;; 132.96 0.0077193 1386360000 1708180 1893860 1142420 1363790 1837830 2099490 1628310 1862190 1731390 FALSE TRUE 1482439.685 1881419.109 1694898.133 1673459.364 1801260.779 2180258.739 1470396.747 1463975.16 1526707.047 0.971004679 1.232338 1.11016592 1.096123429 1.179833933 1.428079306 0.9631165 0.958910331 1 20.54199183 ELSFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ELSFGR 6 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;;;; 185.89 0.0048112 2167860000 2019690 1803880 1210542 1390805 1520100 2119510 1405273 1410929 1494920 FALSE TRUE 1752782.849 1792030.194 1795964.16 1706608.532 1489852.984 2201048.921 1268989.841 1109212.813 1318192.261 1.3296868 1.359460412 1.362444777 1.294658286 1.130224345 1.669748023 0.962674322 0.841465123 1 20.33012937 2.09589026 8.875898721 0.907351936 1.344324096 0.680253402 0.136635009 0.137463556 11.39167129 0.052305326 0.03522727 124.7068359 -2.09589026 0.436972159 ELSLAGNELGDEGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELSLAGNELGDEGAR 15 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 ; 208.51 6.63E-09 178963000 161481 147193 117418 125235 155057 165187 158017 157910 173465 FALSE TRUE 140140.8767 146226.0795 174201.7375 153671.5208 151971.6691 171541.8508 142692.5357 124142.1754 152958.1653 0.91620396 0.955987405 1.138884852 1.00466373 0.993550549 1.121495217 0.93288603 0.811608685 1 17.2227776 2.011676627 24.34121714 0.886317672 1.022492736 0.277971198 0.080780572 161.2468719 336135.121 0.032446293 0.021854635 102.725113 -2.011676627 0.136175064 ELSNS(ph)PLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ELSNSPLR 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ELSNS(1)PLR;ELS(0.019)NS(0.981)PLR;ELS(0.001)NS(0.999)PLR;ELSNS(1)PLR;ELS(0.003)NS(0.997)PLR;ELSNS(1)PLR;ELS(0.001)NS(0.999)PLR 190.53 0.00019508 23221070000 14946290 12741380 9777680 12720060 12175000 12338190 11544070 13371740 22359600 TRUE FALSE 12971099.91 12657681.04 14506198.75 15608344.04 11932741.32 12812848.15 10424527.87 10512297.46 19716273.56 0.657888006 0.641991551 0.735747488 0.791647772 0.605222954 0.649861553 0.528727086 0.533178718 1 24.23288357 3.197449419 24.99958417 0.636343493 0.704255074 0.00294871 0.137548981 500.8471479 304561.8176 0.041617328 0.047190097 1575.612505 -3.197449419 0.067911581 ELSNS(ph)PLRENS(ph)FGSPLEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 ELS(0.026)NS(0.974)PLRENS(1)FGSPLEFR;ELS(0.308)NS(0.713)PLRENS(0.675)FGS(0.304)PLEFR 194.19 2.08E-15 296227000 585940 443480 322110 388470 442010 482740 435720 500000 433550 TRUE FALSE 508506.5444 440566.7507 477883.4734 476678.0509 433214.8658 501311.3202 393463.9415 393078.891 382296.2129 1.330137541 1.152422482 1.250034547 1.246881436 1.133191623 1.311316469 1.02921224 1.028205035 1 18.54433138 2.222498334 24.79400907 1.021447426 1.229749186 0.740129256 0.060832002 102.3741194 158025.0786 0.022748819 0.015392927 166.9161404 -2.222498334 0.20830176 EPPSS(ph)PLQPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EPPSSPLQPQK 11 0 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 EPPS(0.074)S(0.926)PLQPQK;EPPS(0.017)S(0.983)PLQPQK;EPPS(0.022)S(0.978)PLQPQK;EPPS(0.098)S(0.902)PLQPQK 177.83 8.19E-06 1461710000 1535250 1619860 1494170 2102230 1962700 1571660 2218940 2762160 4763570 TRUE FALSE 1332362.823 1609219.033 2216755.61 2579573.452 1923646.11 1632122.777 2003747.54 2171493.579 4200426.181 0.317197057 0.383108514 0.527745403 0.614121839 0.457964508 0.388561233 0.477034342 0.516969823 1 22.00210428 1.209263898 3.177896588 1.118631956 0.458011654 0.812811636 0.081857439 0.184174979 2.324120194 0.3192175 0.022564429 16.1906356 -1.209263898 -0.660620301 LTISPDYAYGATGHPGIIPPHATLVFDVELLK ddPTM_MDA-MB-175_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 0 252.43 2.61E-59 310760000 105190 79963 44725 75060 81254 78108 91327 130360 276180 FALSE TRUE 91288.87498 79437.71779 66354.1596 92103.52022 79637.20437 81112.8653 82470.1216 102483.5285 243530.315 0.374856309 0.326192317 0.272467761 0.378201458 0.327011462 0.333070917 0.338644171 0.420824522 1 17.89374185 1.209386346 3.028720464 1.155964172 0.335501227 0.979384848 0.030024817 0.055175543 0.603368905 0.11506404 0.007767588 16.19520113 -1.209386346 -0.820462945 ELSNSVSTYRPFGLGS(ph)ESPYKQPSDGMERPSSLMDSSQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELSNSVSTYRPFGLGSESPYKQPSDGMERPSSLMDSSQEK 40 3 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 ELSNS(0.001)VS(0.001)T(0.001)YRPFGLGS(0.499)ES(0.499)PYKQPSDGMERPSSLMDSSQEK 122.75 1.09E-08 472760000 195190 128220 103790 123410 123290 101830 178700 197390 138780 TRUE FALSE 169395.147 127377.7144 153983.1912 151432.1267 120836.7702 105747.466 161369.7015 155179.6846 122373.5865 1.384245995 1.040892222 1.258304145 1.237457617 0.987441601 0.864136363 1.318664478 1.268081528 1 16.90093267 4.753950077 23.58516035 1.13813982 1.384246394 0.227927401 0.149110345 2250.562322 3448976.741 0.038089007 0.819040316 56747.9369 -4.753950077 0.246106574 ELSNSVSTYRPFGLGSES(ph)PYKQPSDGMERPSSLMDSSQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELSNSVSTYRPFGLGSESPYKQPSDGMERPSSLMDSSQEK 40 3 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 ELSNSVSTYRPFGLGS(0.02)ES(0.979)PYKQPSDGMERPSSLMDSSQEK;ELSNSVSTYRPFGLGS(0.392)ES(0.608)PYKQPSDGMERPSSLMDSSQEK 189.19 1.78E-24 268680000 351490 234800 205933 205904 222870 172574 305120 360080 260190 TRUE FALSE 305039.7059 233257.5833 305522.8876 252657.6502 218435.323 179213.0335 275529.5094 283079.6941 229430.6346 1.329550897 1.016680199 1.3316569 1.101237638 0.952075661 0.781120768 1.200927286 1.233835641 1 17.80769851 7.999971664 0.76343173 1.074635095 44.2646072 0.194012545 0.156851206 880.5350333 3.595195848 0.061691373 65506.51207 99993475.52 -7.999971664 43.1899721 ELSPLISLPS(ph)PVPPLS(ph)PIHSNQQTLPR ddPTM_MDA-MB-175_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(0.088)LPS(0.912)PVPPLS(0.997)PIHS(0.003)NQQTLPR;ELS(0.002)PLIS(0.138)LPS(0.86)PVPPLS(0.852)PIHS(0.082)NQQT(0.066)LPR 120.33 7.17E-05 159629000 62742 59862 35842 39475 60801 53187 52780 62003 48783 TRUE FALSE 54450.48573 59468.76258 53175.31108 48438.40209 59591.17906 55233.13831 47661.40372 48744.14096 43015.92931 1.265821443 1.382482339 1.236177201 1.12605732 1.38532818 1.284015926 1.107994282 1.133164893 1 15.39258339 1.904842512 1.425838088 1.032538055 1.281188863 0.569776228 0.080960463 0.369454617 1.332854478 0.097301072 0.026473379 80.32347934 -1.904842512 0.248650808 ELSSTEAQLHDAQELLQEETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELSSTEAQLHDAQELLQEETR 21 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 ;;; 307.34 2.40E-56 671240000 658280 684440 389194 490570 640310 682090 628400 745200 705100 FALSE TRUE 571286.6301 679943.8686 577409.5202 601961.4164 627569.0837 708330.4437 567457.8647 585844.7792 621743.8813 0.918845601 1.093607656 0.928693531 0.968182293 1.009369135 1.139264036 0.912687494 0.942260627 1 19.24596088 ELST(ph)PDKVLIPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELSTPDKVLIPER 13 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 ELS(0.155)T(0.845)PDKVLIPER 151.04 7.20E-05 177920000 291790 253460 232650 309550 289610 263330 358710 385290 443770 TRUE FALSE 253229.2122 251795.0046 345160.3182 379838.0587 283847.3276 273460.4755 323922.3594 302898.7318 391308.0161 0.647135253 0.643470091 0.8820681 0.970688161 0.725380815 0.698836886 0.827793825 0.77406728 1 18.57794514 4.248659037 24.72953238 0.828866785 0.645302531 0.411861057 0.095950363 189.1785931 463259.3811 0.02449924 0.063177463 17727.97117 -4.248659037 -0.183564254 ELSTS(ph)PCNPIVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELSTSPCNPIVR 12 0 H3BSS6;Q9H2Y7;H3BNX5 H3BSS6 ZNF106 Zinc finger protein 106 1 ELST(0.003)S(0.997)PCNPIVR 162.67 6.51E-05 163130000 302250 281570 194540 235910 272940 287900 284140 325900 283470 TRUE FALSE 262306.8967 279720.3481 288620.1947 289476.9712 267509.028 298975.6993 256584.1465 256208.8212 249958.4995 1.049401789 1.11906716 1.154672457 1.158100131 1.070213769 1.196101352 1.026506988 1.025005437 1 17.93132906 2.131857614 8.521185377 1.017908897 1.124639872 0.588544721 0.04238986 0.170148159 12.40447137 0.016650199 0.011214377 135.4745179 -2.131857614 0.106730974 ELSVEEQIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELSVEEQIKR 10 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 76.332 0.058229 227010000 460850 441790 262770 275200 402710 361720 425250 458630 333990 FALSE TRUE 399947.5049 438887.8524 389846.4509 337688.3662 394696.8589 375635.6025 384009.3205 360555.5436 294506.0827 1.358027995 1.490250552 1.323729708 1.146626118 1.340199344 1.275476551 1.303909641 1.224271975 1 18.16793791 0.522331748 1.032485995 3.10E-17 1.327413475 0.59915537 0.083180343 5.458276178 1.571766329 11.52317147 0.028870516 3.329137619 -0.522331748 1.327413475 ELSVQDQPSLS(ph)PTSLQNSSSHTTTAK ddPTM_MDA-MB-175_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 ELSVQDQPSLS(0.961)PT(0.039)SLQNSSSHTTTAK;ELSVQDQPSLS(0.999)PT(0.001)SLQNSSSHTTTAK;ELSVQDQPSLS(0.8)PT(0.189)S(0.011)LQNSSSHTTTAK;ELSVQDQPSLS(0.656)PT(0.329)S(0.015)LQNSSSHTTTAK 247.99 9.31E-46 1996610000 1312100 1679270 427600 1288950 2190500 1854850 2123120 2748340 2403700 TRUE FALSE 1138702.661 1668238.765 634388.7902 1581625.798 2146913.336 1926207.28 1917220.149 2160628.879 2119537.324 0.537241146 0.787076852 0.299305317 0.746212761 1.012916032 0.908786676 0.904546538 1.01938704 1 21.01531794 3.440844372 4.759412253 0.964539065 0.558164051 0.719104963 0.122269521 0.098946594 5.305330027 0.033813237 0.045294752 2759.588792 -3.440844372 -0.406375013 ELTDEEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ELTDEEAER 9 0 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 ;; 186.76 9.61E-05 1669540000 1799180 1630690 1167730 1341420 1609730 1627200 1589470 1853150 1991680 FALSE TRUE 1561413.804 1619977.89 1732448.134 1646009.913 1577699.522 1689799.437 1435323.444 1456868.294 1756225.859 0.889073462 0.922420019 0.986460895 0.937242727 0.898346596 0.962176606 0.817277252 0.829544951 1 20.74404696 2.251104978 24.99434365 0.868580625 0.933255961 0.136903111 0.056172474 329.9283064 657374.2522 0.020978476 0.016136909 178.2809659 -2.251104978 0.064675336 ELTFCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELTFCR 6 0 H3BQR2;Q9Y5Y2;B7Z6P0;H3BRE1;H3BNF0;H3BNS4 H3BQR2 NUBP2 Cytosolic Fe-S cluster assembly factor NUBP2 0 ; 109.88 0.067884 142738000 258112 262929 161320 212624 261237 300460 234222 248221 250803 FALSE TRUE 224001.8452 261201.8021 239334.8916 260903.529 256038.8948 312018.8906 211507.1865 195140.8708 221153.3551 1.012880158 1.181089032 1.082212348 1.179740316 1.15774366 1.41087116 0.956382445 0.882378071 1 17.7546876 2.035409615 24.99807066 0.928765108 1.168402185 0.506490041 0.104369149 124.9328407 88198.14375 0.041502986 0.027981201 108.4949728 -2.035409615 0.239637077 ELTGEDVLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELTGEDVLVR 10 0 Q16401-2;Q16401 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 129.1 0.007895 0 84314 70236 45214 61354 69716 69615 63253 77214 79871 FALSE TRUE 73171.69128 69774.61509 67079.64163 75285.36344 68328.788 72293.1341 57118.7338 60702.38698 70428.74137 1.038946456 0.990712225 0.952446974 1.068957956 0.97018329 1.026472044 0.811014547 0.861897938 1 16.10387668 2.253329828 24.99993608 0.881582458 1.005702622 0.480688856 0.057009067 179.1578638 303261.3561 0.020847845 0.016079068 179.196626 -2.253329828 0.124120164 ELTHIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELTHIYR 7 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 ;;; 162.31 0.0012769 1694620000 2151830 2080480 1293110 1458230 1957760 2117160 1846760 2102710 2010410 FALSE TRUE 1867460.213 2066813.19 1918462.321 1789343.409 1918804.406 2198608.515 1667661.499 1653061.83 1772741.62 1.053430569 1.165885184 1.082200756 1.009365036 1.082393725 1.240230663 0.940724514 0.93248887 1 20.75755085 2.19509047 24.99999684 0.951768434 1.101834807 0.535645016 0.0647499 102.8917997 59173.09454 0.026412485 0.017807403 156.7077482 -2.19509047 0.150066373 ELTIGS(ph)KLQDAEIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELTIGSKLQDAEIAR 15 1 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 1 ELT(0.007)IGS(0.993)KLQDAEIAR;ELT(0.11)IGS(0.89)KLQDAEIAR 93.006 0.0030422 200176000 385340 351680 266790 365900 411520 408400 404880 481620 286910 TRUE FALSE 334416.3427 349369.7909 395810.5364 448983.1874 403331.5571 424111.4123 365614.7999 378629.311 252991.8266 1.321846429 1.380952877 1.564519066 1.774694437 1.594247381 1.67638385 1.445164473 1.49660689 1 17.94873125 0.994964262 1.967540099 0.430372254 1.549865535 0.606905502 0.13411963 1.328757636 2.75133714 3.478408339 0.038884165 9.884717506 -0.994964262 1.119493281 ELTIGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ELTIGSK 7 0 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;; 126.28 0.0092303 7140070000 12497000 11346410 8088010 9439360 9830650 9237620 11166900 13400700 13770300 FALSE TRUE 10845489.79 11271874.69 11999398.69 11582710.96 9635039.298 9592997.219 10083935.76 10535064.59 12142390.82 0.893192284 0.928307683 0.988223725 0.953906947 0.793504297 0.790041876 0.830473661 0.867626874 1 23.53354918 3.25929152 24.91054833 0.852487978 0.943387417 0.312723027 0.062111118 282.3152317 339231.7401 0.018698886 0.024112846 1816.734738 -3.25929152 0.090899438 ELTNDGELILTMTADDVVCTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELTNDGELILTMTADDVVCTR 21 0 P29373 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 ;;; 196.64 2.22E-21 140350000 166051 153095 115622 118738 144590 161983 152353 175530 167664 FALSE TRUE 144106.9396 152089.3089 171537.1859 145699.2777 141712.9419 168214.5908 137577.8295 137994.2755 147842.9529 0.974729852 1.028722072 1.160266232 0.985500322 0.958537009 1.137792418 0.930567381 0.933384194 1 17.17370595 2.190548113 24.99999876 0.949216426 1.039530878 0.264079399 0.067663501 150.4457104 78335.60513 0.027327661 0.018424354 155.0772579 -2.190548113 0.090314452 ELTNRHS(ph)LPFSLPSQMEPRPDVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELTNRHSLPFSLPSQMEPRPDVPR 24 2 P22681;A0A0U1RR39;A0A1B0GW38;A0A0U1RQX8 P22681 CBL E3 ubiquitin-protein ligase CBL 1 ELT(0.032)NRHS(0.968)LPFSLPSQMEPRPDVPR 129.51 3.65E-05 82522000 51428 51968 28426 32921 50513 54397 53877 61172 45403 TRUE FALSE 44631.6595 51626.61879 42172.90868 40396.21622 49507.89013 56489.68779 48652.01683 48090.84384 40035.50906 1.114801848 1.289520728 1.053387597 1.009009681 1.236599491 1.410989622 1.215221636 1.201204755 1 15.28899253 ELTPAS(ph)PTCTNSVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ELTPASPTCTNSVSK 15 0 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;A0A090HNM7 R4GMW8 BIVM-ERCC5;ERCC5;ERCC5-201 DNA repair protein complementing XP-G cells 1 ELTPAS(0.706)PT(0.294)CTNSVSK;ELTPAS(1)PTCTNSVSK;ELTPAS(0.876)PT(0.124)CTNSVSK;ELTPAS(0.996)PT(0.003)CTNSVSK;ELTPAS(0.988)PT(0.012)CTNSVSK;ELTPAS(0.998)PT(0.002)CTNSVSK 375.27 9.27E-98 3059920000 5020540 4433980 2986340 3730830 4335710 3600270 4744550 5585860 5100380 TRUE FALSE 4357062.919 4404852.893 4430544.013 4577971.974 4249437.854 3738774.717 4284424.271 4391367.308 4497418.887 0.968791884 0.979417974 0.985130388 1.017910959 0.944861477 0.831315653 0.952640699 0.976419457 1 22.10066583 3.129159265 8.731200511 0.940516368 0.986916179 0.210636296 0.045032869 0.469758701 34.64487201 0.014794497 0.016798091 1346.353999 -3.129159265 0.046399811 ELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGS(ph)SPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGSSPQR 38 1 O00139-1;O00139-5;O00139;O00139-4;O00139-2;H0Y8H2 O00139-1 KIF2A Kinesin-like protein KIF2A 1 ELTVDPTAAGDVRPIMHHPPNQIDDLET(0.003)QWGVGS(0.499)S(0.499)PQR;ELTVDPTAAGDVRPIMHHPPNQIDDLET(0.005)QWGVGS(0.806)S(0.188)PQR 128.8 7.63E-09 336650000 102656 87910 76899 109959 101962 99414 93587 113590 276237 TRUE FALSE 89089.7495 87332.51342 114087.6136 134926.8716 99933.15569 103238.5209 84510.94714 89299.66246 243580.5766 0.365750631 0.358536443 0.468377303 0.553931161 0.410267342 0.423837247 0.346952735 0.366612411 1 17.89403957 1.235905011 24.99846342 1.000000782 0.411502881 0.898469423 0.062142144 23.47374064 220924.2392 0.111088437 0.016662498 17.21492008 -1.235905011 -0.588497901 ELVEFAQDDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELVEFAQDDDR 11 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 120.86 0.0009858 340000000 133790 99067 81513 109600 123060 106850 93508 132520 335890 FALSE TRUE 116109.3125 98416.22235 120932.9594 134486.3551 120611.3468 110960.5886 84439.60855 104181.6293 296181.4668 0.392020857 0.332283527 0.408306977 0.454067422 0.407221114 0.374637177 0.285094167 0.351749319 1 18.17612184 1.237361193 24.99999371 1.00000075 0.373372562 0.947550179 0.046159304 6.856146378 142843.4713 0.074882239 0.012463756 17.27273831 -1.237361193 -0.626628188 ELVEFAQDDDRLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ELVEFAQDDDRLR 13 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ;;;; 253.69 7.90E-24 2522700000 2701240 2279300 1303340 1331350 1937440 2174130 1719250 2202660 2117300 FALSE TRUE 2344264.29 2264327.128 1933639.583 1633653.366 1898888.735 2257770.188 1552517.4 1731638.3 1866995.206 1.255634874 1.21281893 1.035696062 0.87501744 1.017082812 1.209306902 0.831559393 0.927500132 1 20.83228679 4.204205438 3.31039415 0.972724108 1.246190296 0.523577698 0.100418872 0.18429715 4.101658795 0.027169353 0.072623754 16003.14858 -4.204205438 0.273466188 ELVGPPLAETVFT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELVGPPLAETVFTPK 15 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 ELVGPPLAETVFT(1)PK;ELVGPPLAETVFT(1)PK 176.08 9.16E-06 98581000 138319 120843 103131 106367 108212 99563 106429 143122 251770 TRUE FALSE 120039.7937 120049.1744 153005.4966 130519.2531 106058.7929 103393.253 96107.53196 112516.4741 222006.0374 0.540705087 0.540747341 0.689195205 0.587908575 0.477729318 0.465722708 0.432905038 0.506817181 1 17.76023939 1.237000085 24.99993402 1.00000058 0.528002407 0.810713063 0.07133189 18.95739276 303598.1892 0.120355753 0.019528835 17.25838231 -1.237000085 -0.471998173 ELVGPPLAETVFT(ph)PKTS(ph)PENVQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELVGPPLAETVFTPKTSPENVQDR 24 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 2 ELVGPPLAET(0.054)VFT(0.945)PKT(0.236)S(0.765)PENVQDR 69.444 0.074689 76300000 45561 38552 24436 25265 36488 33366 40222 52170 25585 TRUE FALSE 39539.99841 38298.74937 36253.33133 31001.8044 35761.96019 34649.61161 36321.27663 41013.85149 22560.37045 1.752630725 1.697611724 1.60694752 1.374170893 1.585167241 1.53586182 1.60995923 1.817960019 1 14.46150314 4.175178598 3.235545943 1.533138479 1.733572471 0.157521543 0.211140177 0.510520731 10.63767609 0.054671826 0.142247627 14968.5109 -4.175178598 0.200433992 ELVLDNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELVLDNSR 8 0 P39687;H0YN26;H7BZ09 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;;; 157.91 0.0008592 1400300000 2711320 2614980 1594920 1815370 2525820 2707010 2292890 2761640 2418690 FALSE TRUE 2353012.192 2597802.024 2366228.647 2227577.505 2475561.124 2811150.426 2070525.881 2171084.777 2132755.224 1.10327344 1.218049777 1.109470332 1.044459992 1.160733823 1.318083949 0.970822089 1.017971848 1 21.02428697 2.191912288 24.99999487 0.999726621 1.1543155 0.519828118 0.073618048 102.9407783 55167.74393 0.030463178 0.020538344 155.5651412 -2.191912288 0.154588879 ELVSDANQHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELVSDANQHVK 11 0 P30153;B3KQV6;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ; 166.29 2.06E-05 1306650000 2805400 2272200 1409900 2054820 2357600 2173600 2529900 2845100 2706600 FALSE TRUE 2434659.282 2257273.769 2091732.356 2521398.287 2310688.373 2257219.799 2284550.687 2236697.506 2386628.831 1.02012481 0.945800092 0.876438065 1.056468544 0.968180868 0.945777479 0.95722915 0.937178616 1 21.18654279 4.746523367 23.84734766 0.958964802 1.020124867 0.140448038 0.045839492 1037.956377 3108391.459 0.010839922 0.112287816 55785.76168 -4.746523367 0.061160065 ELWAVLNGWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELWAVLNGWR 10 0 C9J0K6;P30626-3;P30626-2;P30626 C9J0K6 SRI Sorcin 0 ; 192.14 1.66E-06 1147000000 866930 937440 641500 657850 817740 769780 870260 961870 1105120 FALSE TRUE 752363.004 931281.8949 951731.5457 807224.8971 801468.5739 799393.9347 785862.3191 756181.5858 974473.9726 0.772070907 0.95567652 0.976661843 0.82836989 0.822462781 0.820333798 0.806447726 0.775989515 1 19.89426413 3.688954005 24.41086974 0.831385507 0.906890503 0.097099052 0.080108778 491.85903 242038.0598 0.021423573 0.031776384 4886.006102 -3.688954005 0.075504995 ELWDSIMTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELWDSIMTR 9 0 A0A499FI31;Q15020-4;Q15020 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 107.69 0.0063561 36381000 92038 79745 59871 63045 87358 87316 69160 85398 100120 FALSE TRUE 79874.94511 79221.14984 88824.81586 77360.33083 85619.74671 90675.10302 62452.87384 67136.30227 88283.92766 0.904750697 0.897345099 1.006126689 0.876267435 0.969822582 1.027085059 0.707409327 0.760458943 1 16.42986319 2.242426661 24.99999903 0.804871405 0.945170654 0.301751707 0.087717085 105.1579384 680016.156 0.033360804 0.024843518 174.7538133 -2.242426661 0.140299249 ELWNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELWNLR 6 0 Q92466-4;Q92466 Q92466-4 DDB2 DNA damage-binding protein 2 0 126.16 0.040975 58712000 80179 77827 53187 60128 71864 69533 70853 81834 77329 FALSE TRUE 69583.142 77315.74931 78908.4111 73780.9814 70434.047 72207.9795 63981.68697 64334.43593 68187.25371 1.020471396 1.13387393 1.157231107 1.082034799 1.032950341 1.058965944 0.938323271 0.94349651 1 16.05721446 2.638303967 1.290092577 0.954624159 1.103870403 0.613668146 0.044608991 0.270189697 0.937427283 0.025320508 0.018518831 434.8144487 -2.638303967 0.149246243 ELYDHAEATIVVMLVGNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ELYDHAEATIVVMLVGNK 18 0 P57735 P57735 RAB25 Ras-related protein Rab-25 0 ;; 139.65 1.33E-07 103095000 166224 149841 127854 163420 142563 129187 179285 220719 263116 FALSE TRUE 144257.0772 148856.6846 189684.622 200527.0087 139726.2752 134156.9075 161897.9683 173519.9595 232010.7262 0.621769 0.641593977 0.81756833 0.864300595 0.602240584 0.578235798 0.697803808 0.747896282 1 17.82383198 1.20483376 2.566719783 1.092080015 0.692075639 0.533481574 0.090740505 0.510072155 3.463995984 0.467386277 0.025780764 16.02631815 -1.20483376 -0.400004376 ELYLFDVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELYLFDVLR 9 0 P08243-2;P08243;P08243-3 P08243-2 ASNS Asparagine synthetase [glutamine-hydrolyzing] 0 79.906 0.059594 12414000 25884 24368 14092 12510 22698 22728 23874 25872 23566 FALSE TRUE 22463.36382 24207.925 20906.93833 15350.5867 22246.35421 23602.36087 21558.70315 20339.47414 20780.05433 1.08100602 1.164959659 1.006106048 0.738717352 1.070562851 1.135818054 1.037470972 0.978797929 1 14.34291181 4.188122053 8.315509053 0.994385804 1.122726218 0.207343237 0.103783735 0.384339914 57.05844844 0.027795682 0.058625595 15421.3379 -4.188122053 0.128340414 ELYLLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELYLLFR 7 0 H0YBU9;B4E3T4;Q93062-4;Q93062-5;Q93062;Q93062-2;Q6ZRY4;Q93062-3 H0YBU9 RBPMS;RBPMS2 RNA-binding protein with multiple splicing;RNA-binding protein with multiple splicing 2 0 86.113 0.020315 380130000 217710 198130 110810 166220 194560 220640 217180 230250 135720 FALSE TRUE 188939.0719 196828.471 164398.0866 203962.7915 190688.6367 229128.1636 196117.917 181012.8293 119675.3362 1.578763661 1.644687011 1.373700646 1.704300969 1.59338292 1.914581323 1.638749664 1.512532449 1 16.86876633 1.21865594 2.617029402 0.830026788 1.635788379 0.693191328 0.132017122 0.309996489 2.286630393 0.570447148 0.035213467 16.54458735 -1.21865594 0.805761591 ELYLLFRPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELYLLFRPFK 10 1 H0YBU9;B4E3T4;Q93062-4;Q93062-5;Q93062;Q93062-2;Q6ZRY4;Q93062-3 H0YBU9 RBPMS;RBPMS2 RNA-binding protein with multiple splicing;RNA-binding protein with multiple splicing 2 0 122.26 0.0030633 0 88873 93060 56275 64624 81088 75969 99695 112970 78280 FALSE TRUE 77128.20787 92448.68273 83489.77823 79297.86692 79474.50745 78891.57659 90026.59424 88812.24463 69025.82758 1.117381864 1.339334652 1.209544038 1.148814432 1.151373482 1.14292837 1.304245054 1.28665237 1 16.07484866 4.007237358 24.94194403 1.189526914 1.239878508 0.03427226 0.099272702 651.5534314 2245382.89 0.025515002 0.052949237 10168.04262 -4.007237358 0.050351594 ELYPVEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ELYPVEFR 8 0 Q5BJF2;J3KT68 Q5BJF2 TMEM97 Transmembrane protein 97 0 75.38 0.089662 70784000 182370 186750 107790 166480 198690 189890 154990 239850 221280 FALSE TRUE 158269.3424 185523.227 159917.6045 204281.8285 194736.4577 197195.1912 139959.0937 188559.944 195120.5305 0.811136286 0.950813461 0.819583691 1.046951994 0.998031613 1.010632713 0.717295578 0.96637675 1 17.57400606 5.690615287 1.194535283 0.938495186 1.12E-15 0.13728003 0.099248406 29.3752205 6.231895594 0.028907725 58.42787229 490473.2058 -5.690615287 -0.938495186 ELYVAADEASIAPILAEAQAHFGR ddPTM_MDA-MB-175_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 83.064 0.013747 21623000 17269 16969 9389.8 12920 13471 14574 13342 17263 15147 FALSE TRUE 14986.8579 16857.52952 13930.73869 15853.68347 13202.95346 15134.67121 12048.09489 13571.44179 13356.33892 1.122078287 1.262136999 1.04300578 1.186978226 0.988515905 1.133145191 0.902050702 1.016104928 1 13.70523699 3.149519919 0.766506403 0.979580966 1.181157381 0.428839186 0.079908183 0.583210752 0.859884678 0.053100396 0.069298461 1410.976949 -3.149519919 0.201576416 EMADRYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EMADRYDR 8 1 P17812;B4E1E0;P17812-2;A0A3B3IRI2;A0A3B3IRQ8;A0A3B3ITF6;A0A3B3ITB8;A0A3B3ISY3 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ; 110.87 0.0030483 392520000 392230 377460 258970 302140 329790 362700 326430 357310 298130 FALSE TRUE 340395.8117 374980.4404 384208.7582 370745.5049 323227.8242 376653.3037 294772.8688 280902.0371 262885.411 1.294844816 1.426402625 1.461506581 1.41029319 1.229538843 1.432766095 1.121297936 1.068534142 1 18.00407456 2.134376148 4.256239103 1.053492565 1.376988627 0.809584178 0.072017544 0.089911229 2.921097584 0.031880161 0.020729431 136.2624359 -2.134376148 0.323496061 EMANLRPEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EMANLRPEGR 10 1 Q15042-4;Q15042;Q15042-3 Q15042-4 RAB3GAP1 Rab3 GTPase-activating protein catalytic subunit 0 75.416 0.035624 119980000 133380 167290 80512 142070 165910 174400 187990 191120 190390 FALSE TRUE 115753.4951 166191.061 119447.8725 174329.1649 162608.7156 181109.2809 169758.7587 150250.4753 167882.3111 0.689491908 0.989925978 0.711497666 1.038401031 0.968587545 1.078787156 1.011177161 0.894975023 1 17.3570907 3.726748707 24.98352277 0.990723409 0.81626726 0.507824792 0.092734126 635.7432399 1344668.455 0.024261265 0.036313844 5330.263842 -3.726748707 -0.17445615 EMDEEDKAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EMDEEDKAFK 10 1 Q9Y2S6 Q9Y2S6 TMA7 Translation machinery-associated protein 7 0 ;;; 146.16 2.66E-05 4576170000 5624690 4725410 3840740 4156760 4123810 2814760 6904800 7292010 4207400 FALSE TRUE 4881372.965 4694368.471 5698134.711 5100615.89 4041754.249 2923045.639 6235173.559 5732670.408 3710005.965 1.315731837 1.265326394 1.535882897 1.37482687 1.089419879 0.787881655 1.680637071 1.545191696 1 21.82299008 EMDEQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EMDEQIR 7 0 P06753-2;A0A087WWU8;P06753-6;P06753-3;J3KN67;A0A2R2Y2Q3;A0A494C0P6 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;;; 205.95 0.00053279 4451130000 5887050 5915180 3912510 4773970 5309130 5569660 5372850 6228880 6991810 FALSE TRUE 5109061.427 5876322.793 5804612.923 5857972.854 5203488.7 5783928.424 4851791.834 4896882.485 6165246.187 0.828687334 0.953136763 0.941505456 0.950160412 0.844003393 0.93815044 0.786958328 0.794272011 1 22.55572707 2.255084668 24.9594126 0.843570831 0.91162443 0.07743841 0.071772337 413.5553059 624670.0655 0.02636431 0.020363031 179.9221649 -2.255084668 0.068053598 EMDRETLIDVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 EMDRETLIDVAR 12 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;;;;;;;;; 218.5 3.12E-11 6184800000 7525800 7054710 3766052 4226746 6635260 6943440 6967880 7911430 2409944 FALSE TRUE 6531246.462 7008367.145 5587327.344 5186493.281 6503231.308 7210558.63 6292136.07 6219632.261 2125043.166 3.073465315 3.297988134 2.629277106 2.440653143 3.06028198 3.393135135 2.960945063 2.926826317 1 21.01906072 1.237922338 6.539396048 0.945066403 2.972671298 0.831472484 0.279209149 0.050475278 10.234664 0.454486673 0.073543541 17.29507054 -1.237922338 2.027604895 EMDT(ph)ARTPLSEAEFEEIMNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EMDTARTPLSEAEFEEIMNR 20 1 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 1 EMDT(0.587)ART(0.413)PLSEAEFEEIMNR 78.717 0.023357 48714000 48857 44105 31943 37016 42439 49841 50255 48859 49243 TRUE FALSE 42400.42366 43815.27135 47390.74164 45421.04855 41594.54693 51758.41552 45381.27784 38410.88307 43421.54864 0.976483451 1.00906745 1.091410673 1.046048563 0.957924078 1.191998377 1.045132642 0.884604172 1 15.40612356 1.758154644 25 0.937908765 1.04810179 0.271879889 0.069981352 9.836264189 12564.76524 0.036387872 0.017474431 57.3000029 -1.758154644 0.110193026 EMDTART(ph)PLSEAEFEEIMNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EMDTARTPLSEAEFEEIMNR 20 1 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 1 EMDT(0.004)ART(0.996)PLSEAEFEEIMNR;EMDT(0.002)ART(0.997)PLS(0.001)EAEFEEIMNR;EMDT(0.004)ART(0.977)PLS(0.019)EAEFEEIMNR;EMDT(0.161)ART(0.838)PLS(0.001)EAEFEEIMNR;EMDT(0.43)ART(0.569)PLS(0.001)EAEFEEIMNR 308.35 5.40E-66 776364000 764950 627743 482336 506597 587137 597570 620985 680309 595464 TRUE FALSE 663859.9194 623619.3149 715595.3029 621627.5917 575454.1224 620558.9046 560761.9703 534830.2145 525068.9243 1.264329098 1.187690389 1.36285975 1.183897128 1.095959208 1.181861801 1.06797783 1.018590493 1 19.00214729 2.407191928 0.552803023 0.950784429 1.276498743 0.728231319 0.057989286 0.718727616 0.477572915 0.14843566 0.059954643 255.3829668 -2.407191928 0.325714314 EMEADERDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EMEADERDR 9 1 P49756 P49756 RBM25 RNA-binding protein 25 0 90.696 0.011812 97316000 167940 151370 65319 68683 115030 138430 126940 147390 38319 FALSE TRUE 145746.3035 150375.6405 96907.48688 84278.5249 112741.1281 143755.4917 114629.3783 115871.7955 33788.97147 4.313428232 4.45043557 2.868021211 2.494261329 3.336625033 4.25450925 3.39250866 3.429278562 1 15.04426482 4.242231053 24.97225156 3.074034494 4.381932453 0.322116764 0.841934432 114.0548242 775953.302 0.212627723 0.518887042 17467.51212 -4.242231053 1.307897959 EMEAELEDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 EMEAELEDER 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;; 237.65 8.19E-12 7792430000 6414220 6381390 4121570 4759070 5644410 6022130 6272940 6507600 6087940 FALSE TRUE 5566564.575 6339470.229 6114775.038 5839689.581 5532097.284 6253805.238 5664591.244 5116000.382 5368230.669 1.036945862 1.180923589 1.139067118 1.087823892 1.030525256 1.164965819 1.055206379 0.953014261 1 22.35601523 1.945301783 4.60804718 0.978420089 1.107682593 0.535244117 0.049697212 0.152718557 6.664413285 0.025305035 0.013204551 88.16613103 -1.945301783 0.129262504 EMEAELEDERK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 EMEAELEDERK 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;;;; 191.53 2.87E-06 6924560000 5460360 4529217 3747155 4111058 4336133 3580285 5696800 6444210 5680400 FALSE TRUE 4738759.591 4499464.275 5559291.691 5044536.552 4249852.437 3718020.881 5144325.213 5066165.84 5008869.583 0.946073662 0.898299347 1.109889487 1.007120762 0.848465381 0.74228742 1.027043154 1.01143896 1 22.25605362 EMEEQMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EMEEQMR 7 0 P23246;P23246-2;H0Y9K7;H0Y9U2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 137.18 0.019715 0 776330 642350 410770 526270 574020 594110 547130 656280 711520 FALSE TRUE 673736.0235 638130.3606 609419.7459 645767.647 562598.1251 616965.7961 494069.4168 515939.6292 627404.9162 1.073845624 1.017094932 0.97133403 1.029267751 0.896706593 0.983361431 0.787480946 0.822339156 1 19.25903731 3.065522052 1.03686218 0.864039326 1.032630922 0.427187728 0.069380143 0.444863827 1.078192113 0.03602383 0.041899211 1162.845596 -3.065522052 0.168591596 EMEHNTVCAAGTS(ph)PVGEIGEEK ddPTM_MDA-MB-175_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(0.061)S(0.939)PVGEIGEEK;EMEHNTVCAAGTS(1)PVGEIGEEK;EMEHNTVCAAGT(0.002)S(0.998)PVGEIGEEK;EMEHNTVCAAGT(0.032)S(0.968)PVGEIGEEK;EMEHNTVCAAGT(0.04)S(0.96)PVGEIGEEK;EMEHNTVCAAGT(0.084)S(0.916)PVGEIGEEK;EMEHNTVCAAGT(0.013)S(0.987)PVGEIGEEK;EMEHNTVCAAGT(0.014)S(0.986)PVGEIGEEK;EMEHNTVCAAGT(0.09)S(0.91)PVGEIGEEK;EMEHNTVCAAGT(0.04)S(0.96)PVGEIGEEK;EMEHNTVCAAGT(0.249)S(0.751)PVGEIGEEK;EMEHNTVCAAGT(0.053)S(0.947)PVGEIGEEK 276.79 1.13E-45 14086420000 10890220 8789460 4447900 7227390 8989900 8353910 10579260 12225620 11196110 TRUE FALSE 9451049.835 8731721.459 6598919.317 8868479.363 8811018.578 8675290.323 9553284.994 9611266.303 9872518.63 0.957308888 0.8844472 0.668412952 0.898299582 0.892479306 0.878731218 0.967664418 0.973537419 1 23.23498675 2.300773339 1.125613192 0.997900883 0.845851997 0.358275117 0.074388776 0.604717535 1.516283312 0.07104348 0.03034296 199.8818402 -2.300773339 -0.152048886 EMFEDTVEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 EMFEDTVEER 10 0 Q16576;E9PC52 Q16576 RBBP7 Histone-binding protein RBBP7 0 ;;;;;;; 197.96 7.11E-07 3036060000 2624502 2285707 1453212 1697298 2108004 2107244 2047597 2517285 2171862 FALSE TRUE 2277667.411 2270692.04 2155990.184 2082695.452 2066058.845 2188311.04 1849021.358 1978983.192 1915106.949 1.189316039 1.185673752 1.125780566 1.087508692 1.078821653 1.142657355 0.96549248 1.033353878 1 20.86899353 7.999993508 0.096177328 0.785000679 1.995537262 0.728094028 0.038870972 158.4050826 1.41373221 2.940854667 25.94895883 99998505.16 -7.999993508 1.210536583 EMFEVTGLHDVDQGWMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EMFEVTGLHDVDQGWMR 17 0 Q9BWS9-3;Q9BWS9;Q9BWS9-2 Q9BWS9-3 CHID1 Chitinase domain-containing protein 1 0 ; 193.69 1.16E-10 199941000 124173 128899 104449 130833 135470 179784 140563 131634 114804 FALSE TRUE 107763.2234 128052.254 154960.8858 160540.6323 132774.412 186700.4068 126931.2219 103485.0935 101232.0019 1.06451736 1.264938474 1.530749989 1.585868394 1.311585364 1.844282473 1.253864583 1.022256713 1 16.62730591 1.898342401 4.057996448 1.023930874 1.439069439 0.406513026 0.207633563 0.224612169 6.121479296 0.117830951 0.057095111 79.13022507 -1.898342401 0.415138565 EMFPYEAS(ph)TPTGISASCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EMFPYEASTPTGISASCR 18 0 P42167;G5E972;H0YJH7;P42167-2 P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 EMFPYEAS(0.512)T(0.483)PT(0.005)GISASCR;EMFPY(0.002)EAS(0.55)T(0.441)PT(0.007)GISASCR 105.39 0.0018736 205004000 252425 244624 167044 214468 265825 261113 198740 346430 285143 TRUE FALSE 219066.3967 243017.0488 247827.0371 263166.2373 260535.6026 271158.1861 179466.2254 272348.6404 251433.7194 0.871268966 0.966525291 0.985655535 1.046662468 1.036199931 1.078447977 0.713771509 1.083182642 1 17.93981861 4.745260577 2.449848883 0.991647257 0.842840434 0.115681124 0.104477801 1.283836935 9.403228805 0.026018131 0.40481954 55623.79005 -4.745260577 -0.148806823 EMFPYEAST(ph)PTGISASCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EMFPYEASTPTGISASCR 18 0 P42167;G5E972;H0YJH7;P42167-2 P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 EMFPYEAS(0.142)T(0.854)PT(0.004)GISASCR;EMFPY(0.004)EAS(0.317)T(0.609)PT(0.069)GISASCR 270.94 6.77E-38 421420000 349000 331370 237753 293360 360090 398010 256390 469860 394110 TRUE FALSE 302878.7657 329193.2087 352731.146 359971.8717 352924.9135 413321.7022 231525.3373 369384.0955 347518.7648 0.871546508 0.947267434 1.014998848 1.035834344 1.015556423 1.189350746 0.666223988 1.062918417 1 18.40673135 4.59611188 2.883109154 0.994487406 0.866666064 0.087981981 0.130465413 0.843783731 11.33905037 0.031765571 0.210139216 39455.89327 -4.59611188 -0.127821342 EMKPVIFLDVFLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EMKPVIFLDVFLPR 14 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 119.56 0.00016457 456030000 972140 833280 519730 734860 800030 599740 983020 1035130 965240 FALSE TRUE 843669.2359 827806.1288 771073.1664 901721.1946 784110.9682 622812.3859 887686.8717 813775.5049 851130.4268 0.991233787 0.972596094 0.905940079 1.059439501 0.921258298 0.731747293 1.042950462 0.956111401 1 19.6990207 EMLFEFIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EMLFEFIDR 9 0 O60942-2;O60942 O60942-2 RNGTT mRNA-capping enzyme;Polynucleotide 5-triphosphatase;mRNA guanylyltransferase 0 105.52 0.007176 17418000 46703 38546 27996 28168 33398 37223 37853 41586 38958 FALSE TRUE 40531.08022 38292.78879 41534.95924 34563.97492 32733.44514 38654.9929 34182.02189 32693.15752 34352.42962 1.179860658 1.114703944 1.209083599 1.006158088 0.952871325 1.125247714 0.995039427 0.951698552 1 15.06812452 3.726805672 24.21848687 1.001790398 1.162564852 0.67895506 0.0526684 276.4806613 569628.0275 0.014714523 0.022044122 5330.963045 -3.726805672 0.160774453 EMLMEDVGS(ph)EEEQEEEDEAPFQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EMLMEDVGSEEEQEEEDEAPFQEK 24 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 EMLMEDVGS(1)EEEQEEEDEAPFQEK;EMLMEDVGS(1)EEEQEEEDEAPFQEK;EMLMEDVGS(1)EEEQEEEDEAPFQEK;EMLMEDVGS(1)EEEQEEEDEAPFQEK;EMLMEDVGS(1)EEEQEEEDEAPFQEK 180.48 2.27E-17 452894000 761634 559902 581407 797592 585490 526384 715831 834951 1874760 TRUE FALSE 660982.1372 556223.9669 862577.3699 978697.454 573839.8945 546634.3331 646409.8198 656403.2262 1653128.009 0.399837238 0.336467572 0.521784983 0.592027628 0.34712369 0.33066667 0.391022242 0.397067392 1 20.65676701 1.237536909 24.99994081 1.000000692 0.414318629 0.831493486 0.082833944 10.67722177 260617.3558 0.127554876 0.021471046 17.2797283 -1.237536909 -0.585682062 EMLNLYIENEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EMLNLYIENEGK 12 0 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 134.98 0.00031615 33708000 172590 116990 104670 113930 102210 87276 141460 187470 137300 FALSE TRUE 149781.7942 116221.485 155288.7621 139799.5478 100176.221 90633.5642 127741.231 147380.9994 121068.5504 1.237165174 0.95996429 1.282651536 1.154713981 0.827433885 0.748613607 1.055114896 1.217335129 1 16.88546462 3.367036007 23.74923464 0.995545488 1.153346342 0.271908357 0.150237212 10.5868885 2233.469516 0.048457173 0.062557913 2328.284285 -3.367036007 0.157800854 EMLQQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EMLQQSK 7 0 P08238;Q58FF7;P07900;P07900-2 P08238;P07900 HSP90AB1;HSP90AB3P;HSP90AA1 Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Heat shock protein HSP 90-alpha 0 ; 131.03 0.0081555 484220000 969330 833870 560530 710250 691940 662710 896300 976280 918310 FALSE TRUE 841230.5845 828392.2531 831604.1829 871523.118 678171.7478 688204.8825 809376.964 767510.1194 809748.4379 1.038878922 1.023024206 1.026990784 1.07628873 0.837509177 0.849899611 0.999541248 0.947837728 1 19.62711425 3.258702865 24.9999159 0.931158426 1.038968792 0.518677441 0.054627294 224.1952827 278262.3106 0.016802508 0.021663765 1814.273953 -3.258702865 0.107810366 EMNDAAMFYTNR ddPTM_MDA-MB-175_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 ;; 234.3 1.19E-15 1059780000 1212970 1211080 655104 717720 968030 1091700 957060 1172460 1203510 FALSE TRUE 1052672.941 1203124.336 971914.4856 880689.2957 948768.0969 1133698.405 864244.4685 921738.5531 1061232.419 0.991934399 1.133704846 0.915835653 0.829874097 0.894024796 1.068284746 0.814378126 0.868554839 1 20.01730922 4.180523305 9.068985814 0.905360458 1.062496211 0.361045542 0.082397095 0.281749644 41.04842765 0.020784176 0.043569493 15153.86121 -4.180523305 0.157135753 EMNPALGIDCLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EMNPALGIDCLHK 13 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;;;; 157.38 4.21E-05 2168300000 2415260 1858480 1149146 1481620 1732410 1590790 1892280 2269200 2024360 FALSE TRUE 2096077.272 1846271.523 1704876.849 1818044.466 1697938.43 1651988.721 1708766.977 1783949.239 1785042.467 1.174245045 1.034301176 0.955090358 1.018488075 0.951203381 0.925461859 0.95726965 0.999387562 1 20.76752697 4.696163968 2.307152827 0.972998665 1.21341983 0.839007416 0.02793773 0.208586221 1.417550726 0.007602933 0.097574326 49677.98455 -4.696163968 0.240421164 EMPQDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EMPQDLR 7 0 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 0 ; 104.75 0.018802 474340000 1110910 1153550 820370 988290 1076370 1163070 981340 1221300 1393470 FALSE TRUE 964100.4288 1145972.254 1217103.676 1212696.35 1054952.343 1207814.056 886169.7978 960134.4992 1228735.564 0.784628082 0.932643514 0.990533449 0.986946569 0.858567436 0.98297314 0.721204646 0.781400431 1 20.22874304 2.252316776 24.99992411 0.818493194 0.926253065 0.15743061 0.093984839 339.8401077 617612.2089 0.034928171 0.026907976 178.7791119 -2.252316776 0.107759871 EMPQDLRS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EMPQDLRSPAR 11 1 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 EMPQDLRS(1)PAR;EMPQDLRS(1)PAR;EMPQDLRS(1)PAR;EMPQDLRS(1)PAR 155.56 1.91E-05 3506590000 3944350 4335580 2669110 3028130 4435330 4949710 4290730 4952210 2532770 TRUE FALSE 3423094.154 4307099.29 3959900.524 3715713.199 4347075.611 5140128.547 3874615.665 3893218.43 2233348.816 1.5327181 1.928538551 1.773077495 1.663740645 1.946438272 2.30153414 1.734890509 1.743220048 1 21.09077717 1.142438746 2.369219259 0.603002109 1.854045605 0.619858894 0.204576543 0.567948636 2.678757577 1.651006773 0.054785895 13.88157508 -1.142438746 1.251043496 EMPQDLRS(ph)PART(ph)PPSEEDSAEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EMPQDLRSPARTPPSEEDSAEAER 24 2 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 2 EMPQDLRS(0.995)PART(0.52)PPS(0.456)EEDS(0.029)AEAER 95.302 0.0077898 589500000 335290 326710 176450 172830 311380 324530 306710 344790 141580 TRUE FALSE 290980.577 324563.8205 261781.8102 212073.693 305184.1472 337014.8791 276965.3114 271059.3417 124842.5737 2.330780025 2.59978476 2.096895334 1.698728941 2.444551872 2.699518835 2.218516514 2.171209177 1 16.92975048 1.210105755 3.294863665 0.733544283 2.295574678 0.683060556 0.27560357 0.242053568 3.417302197 1.014679286 0.074763006 16.22205071 -1.210105755 1.562030395 EMPQDLRSPART(ph)PPS(ph)EEDSAEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EMPQDLRSPARTPPSEEDSAEAER 24 2 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 2 EMPQDLRS(0.046)PART(0.955)PPS(0.986)EEDS(0.013)AEAER 93.147 0.0090696 246120000 113670 122710 75427 77035 113800 137270 118710 127850 74377 TRUE FALSE 98648.2215 121903.9099 111903.7495 94526.97416 111535.6026 142550.8657 107197.5225 100510.2724 65584.23579 1.504145323 1.85873798 1.706259868 1.441306329 1.700646524 2.173553812 1.634501358 1.532537068 1 16.00106146 1.220452663 2.024237244 0.746713704 1.726923996 0.561542924 0.199246629 0.615318876 2.370716619 1.156839186 0.055000808 16.61317589 -1.220452663 0.980210292 EMPSVFQNVLGSAVLS(ph)PAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EMPSVFQNVLGSAVLSPAHK 20 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 EMPSVFQNVLGSAVLS(1)PAHK 172.66 3.88E-12 403970000 199760 171690 158970 187330 185300 179510 202930 261440 311380 TRUE FALSE 173361.2099 170562.1571 235848.4237 229866.1397 181612.8925 186415.8659 183249.8798 205533.0905 274569.0111 0.63139394 0.62119959 0.858976848 0.837188941 0.66144716 0.678939932 0.667409185 0.748566234 1 18.06680928 1.242208342 3.902612475 1.032402941 0.712365256 0.563223928 0.080075825 0.202957997 5.21689762 0.186301121 0.021650076 17.4665987 -1.242208342 -0.320037686 EMQNLSQHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EMQNLSQHGR 10 0 A0A087WXB0;O15126-2;O15126;A0A087WU14 A0A087WXB0 SCAMP1 Secretory carrier-associated membrane protein 1 0 ;; 138.76 5.61E-05 186786000 207867 234425 100000 164723 240371 283057 196652 230060 230976 FALSE TRUE 180396.8493 232885.0467 148360.3345 202125.8748 235588.0874 293946.386 177580.7193 180863.4593 203670.2804 0.885729862 1.143441479 0.728433889 0.992417128 1.156713129 1.443246336 0.871902955 0.888020869 1 17.63587595 4.836940715 19.07454925 1.016288755 0.885642128 0.047451253 0.194129142 94882.588 18358108.54 0.049525121 1120.040319 68697.46549 -4.836940715 -0.130646627 EMQPTHPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 23 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 ;;;;;;;;;;;;;;;;;;;;;; 160.33 5.05E-05 47565166000 13766186 11438961 7420153 9170194 11093200 11635362 10728500 11846434 11896035 FALSE TRUE 11946949.64 11363817.71 11008563.81 11252426.71 10872467.02 12082981.91 9688051.721 9313166.278 10489699.29 1.138922033 1.083331123 1.049464193 1.072712038 1.036489867 1.151890208 0.92357764 0.887839205 1 23.32246999 2.223140344 24.96636341 0.926303044 1.083655705 0.714900589 0.044897423 114.5511011 185463.7689 0.017789681 0.012042349 167.1630723 -2.223140344 0.157352661 EMSGSNETSS(ph)PVSEKPSASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EMSGSNETSSPVSEKPSASR 20 1 A0A087X165;Q9C0H9 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 EMSGSNETS(0.019)S(0.981)PVSEKPSASR;EMSGSNET(0.003)S(0.026)S(0.97)PVSEKPSASR 232.59 1.22E-26 1083690000 641200 312830 270140 278590 342340 332080 394400 471510 478940 TRUE FALSE 556463.7954 310774.9991 400780.6076 341848.1175 335528.1038 344855.3325 356151.1487 370681.2558 422320.2588 1.317634624 0.735875186 0.948996879 0.80945233 0.794487351 0.816573028 0.843320066 0.877725489 1 18.68797793 4.747558383 24.97542323 0.85337795 1.317634867 0.786918802 0.07593422 520.2617512 1444078.407 0.017697148 0.211304764 55918.86951 -4.747558383 0.464256917 EMSLWESLGESWMRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EMSLWESLGESWMRPR 16 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 ; 198.81 3.63E-11 849200000 467470 483430 269840 376020 436730 460670 429440 503440 384240 FALSE TRUE 405692.6551 480254.3165 400335.5266 461401.0881 428039.9274 478392.273 387792.9749 395783.2738 338815.5849 1.19738487 1.417450489 1.18157353 1.361805975 1.263341908 1.411954746 1.144554714 1.168137746 1 18.37014071 1.501925349 1.271571582 0.957649151 1.302744119 0.536004417 0.088965133 0.617610352 1.270687925 0.260068734 0.025477489 31.76328044 -1.501925349 0.345094968 EMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGR 37 1 P00367;P00367-2;P00367-3;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 35.965 0.06401 15044000 20016 20446 6952.1 20913 20784 20450 17171 27426 16667 FALSE TRUE 17370.83489 20311.68888 10314.15881 25661.61629 20370.43906 21236.72473 15505.75906 21561.16333 14696.64625 1.181959108 1.382062856 0.701803571 1.746086546 1.386060379 1.445004825 1.055054249 1.467080514 1 13.84319935 4.837646613 17.85819929 1.283709082 1.181840651 0.008315762 0.29154216 66338.14243 11915788.43 0.066716467 921.3430958 68809.21646 -4.837646613 -0.101868431 EMTLDEWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EMTLDEWK 8 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;; 171.38 0.00067401 614827000 1566980 1285850 912110 1147590 1147560 965370 1479720 1682780 1498510 FALSE TRUE 1359899.623 1277403.167 1353209.447 1408167.849 1124725.801 1002508.409 1336216.982 1322930.592 1321357.855 1.029168304 0.966735213 1.024105197 1.065697566 0.851189401 0.758695614 1.011245347 1.001190243 1 20.3335898 3.252762002 24.99986619 0.932275039 1.017711366 0.263632162 0.079826475 422.2526924 743321.6178 0.025781681 0.033123511 1789.62485 -3.252762002 0.085436327 EMTNHQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EMTNHQK 7 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ;; 89.369 0.017923 289197000 367700 320231 211188 248671 154234 261330 336904 389943 451133 FALSE TRUE 319107.5134 318127.3815 313319.2232 305135.5512 151165.0452 271383.5342 304231.1019 306556.724 397800.5707 0.802179627 0.799715749 0.787628893 0.767056595 0.380002082 0.682210017 0.76478297 0.770629171 1 18.60168582 -0.20052944 14.19893973 4.153721627 0.743135648 0 0.153485821 0 0 0 0.035338059 0.630188625 0.20052944 -3.410585979 EMVANWDSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EMVANWDSLR 10 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ;; 147.75 6.13E-05 528904000 450398 491900 315603 338351 504641 479850 440411 496125 532248 FALSE TRUE 390876.7631 488668.6765 468229.6664 415178.7659 494599.6314 498310.14 397700.009 390032.5296 469326.2478 0.832846586 1.041213183 0.997663499 0.884627203 1.053850352 1.061756385 0.847384971 0.831047766 1 18.84023162 2.220424738 24.99880158 0.878050825 0.981510281 0.177592232 0.084987856 341.1390169 470228.2737 0.033922937 0.022921846 166.121077 -2.220424738 0.103459456 EMVELPLRHPALFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EMVELPLRHPALFK 14 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 167.32 2.20E-06 1389850000 4121700 2584400 1074170 1278740 2390100 2234900 2897200 3288500 336060 FALSE TRUE 3577006.902 2567422.906 1593642.205 1569097.461 2342541.686 2320878.049 2616229.99 2585279.866 296331.3696 12.07096942 8.664026726 5.377905845 5.29507714 7.905142439 7.832036318 8.828731137 8.724286832 1 18.17685183 4.61908608 3.149410265 6.824276291 12.2646611 0.370081577 2.322116336 0.333232277 5.329550356 0.582833495 3.733387706 41599.3055 -4.61908608 5.440384812 EMVHADVELMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EMVHADVELMR 11 0 O60547;O60547-2 O60547 GMDS "GDP-mannose 4,6 dehydratase" 0 108.37 0.0015249 0 186640 175900 110680 119160 166920 196650 160850 175720 161540 FALSE TRUE 161975.0511 174744.5013 164205.2182 146217.0992 163598.6186 204215.2527 145250.7918 138143.6455 142442.9252 1.137122471 1.226768553 1.152779037 1.026496044 1.148520492 1.433663711 1.019712222 0.969817527 1 17.12002444 2.027555587 24.9990921 0.986356239 1.182666334 0.439528891 0.102158353 190.2702286 172616.901 0.042337871 0.028543613 106.5505232 -2.027555587 0.196310096 EMVQNLMVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EMVQNLMVLR 10 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 153.05 3.94E-05 842280000 440340 448030 348850 356780 469600 501270 480140 470240 447810 FALSE TRUE 382147.9533 445086.8614 517555.0268 437792.352 460255.8788 520554.1813 433576.0967 369682.8354 394870.4119 0.967780674 1.127171973 1.310695892 1.1086988 1.165587152 1.31829118 1.098021233 0.936213057 1 18.59101974 1.918013315 4.828051914 0.972230137 1.171383484 0.391935973 0.100509221 0.211960217 8.469618468 0.052704004 0.027074818 82.79675479 -1.918013315 0.199153347 ENAEVDGDDDAEEMEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ENAEVDGDDDAEEMEAK 17 0 P05198 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ; 276.75 2.13E-35 519740000 637500 515030 440290 495850 516800 434790 599500 741590 687170 FALSE TRUE 553252.7598 511646.734 653215.7167 608440.3211 506516.6911 451516.6526 541360.5823 583006.7496 605933.5454 0.913058476 0.844394138 1.078031942 1.004137047 0.835927793 0.745158699 0.893432269 0.962162854 1 19.20880005 1.581219078 3.744406764 0.992691713 0.902194517 0.122101077 0.090700699 0.433814921 13.54293731 0.082189657 0.025938528 38.12580992 -1.581219078 -0.090497196 ENALSSGTLQEEQRT(ph)PPPGQDTQQFHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ENALSSGTLQEEQRTPPPGQDTQQFHEK 28 1 Q12802-2;Q12802;Q12802-4;H0YMW2 Q12802-2 AKAP13 A-kinase anchor protein 13 1 ENALSSGT(0.001)LQEEQRT(0.998)PPPGQDTQQFHEK;ENALS(0.017)S(0.014)GT(0.062)LQEEQRT(0.907)PPPGQDTQQFHEK 121.75 7.04E-05 373550000 218487 209331 141909 150962 193024 175190 213550 241163 172249 TRUE FALSE 189613.3894 207955.8909 210536.6671 185240.2294 189183.2 181929.6727 192839.9539 189592.1692 151885.9194 1.248393466 1.369158455 1.386149999 1.219601067 1.245561147 1.19780473 1.269636807 1.248253754 1 17.21262861 0.652205966 1.568720594 1.90E-09 1.281277578 0.672284373 0.059985708 3.828903519 2.218781747 12.17171744 0.018305054 4.489582596 -0.652205966 1.281277576 ENALVQMADGNQAQLAMSHLNGHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ENALVQMADGNQAQLAMSHLNGHK 24 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20;K7EK45 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 209.76 2.85E-25 1605200000 934160 822870 508730 805180 919830 745020 959860 1177000 1093800 FALSE TRUE 810708.3891 817464.5128 754753.5296 988008.4254 901527.1826 773681.4015 866772.9249 925307.7094 964492.2101 0.840554626 0.847559477 0.782539788 1.024381965 0.934716914 0.80216449 0.898683178 0.959372922 1 19.87941006 -2 0.446041037 4.021062414 0.861418347 0.286029419 0.068901754 131.7566449 1.711652603 375.8775906 0.057808352 0.01 2 -3.159644067 ENAS(ph)PAPGTTAEEAMSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 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(0.998)PAPGT(0.001)TAEEAMSR;ENAS(0.999)PAPGTT(0.001)AEEAMSR;ENAS(0.961)PAPGT(0.014)T(0.025)AEEAMSR;ENAS(0.994)PAPGT(0.003)T(0.003)AEEAMSR;ENAS(1)PAPGTTAEEAMSR;ENAS(1)PAPGTTAEEAMSR;ENAS(1)PAPGTTAEEAMSR;ENAS(1)PAPGTTAEEAMSR;ENAS(1)PAPGTTAEEAMSR 351.95 1.09E-87 7443850000 4284870 3558676 3025583 3771459 3837267 3832153 3568690 4203100 7276220 TRUE FALSE 3718613.573 3535298.823 4488765.059 4627826.409 3760912.894 3979578.406 3222598.993 3304299.774 6416033.561 0.579581378 0.551010027 0.69961683 0.721290867 0.586174131 0.620255235 0.502272777 0.515006622 1 22.61325026 1.231640513 24.99992533 1.000000695 0.59468405 0.763246285 0.070545787 132.1329095 477306.9628 0.187666376 0.019388335 17.04670765 -1.231640513 -0.405316645 ENDFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ENDFDR 6 0 O14579;M0QXB4;O14579-3;O14579-2 O14579 COPE Coatomer subunit epsilon 0 ;;; 156.16 0.022768 5701100000 9372200 8385700 5391480 6865390 7106000 8204200 8762100 9858800 9109400 FALSE TRUE 8133640.024 8330613.785 7998817.761 8424281.73 6964604.503 8519820.883 7912352.891 7750572.341 8032497.109 1.012591715 1.037113823 0.995807114 1.048774947 0.867053471 1.060669026 0.985042731 0.964901977 1 22.93741713 ENDHLFLSLTEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ENDHLFLSLTEQR 13 0 Q13137;Q13137-3;Q13137-4;Q13137-5;Q13137-2;D6REB0 Q13137 CALCOCO2 Calcium-binding and coiled-coil domain-containing protein 2 0 89.541 0.0074024 110570000 65904 54816 38506 46176 52141 54468 59796 62595 55769 FALSE TRUE 57194.61942 54455.91009 57127.63039 56660.96656 51103.49611 56563.41921 53996.99312 49209.54636 49176.05235 1.163058373 1.107366441 1.161696144 1.152206488 1.039194764 1.150222852 1.098034318 1.000681104 1 15.58566831 1.801200081 3.24528462 0.997351047 1.126467752 0.674469939 0.036367466 0.130404095 2.537656458 0.023948199 0.009759158 63.27032735 -1.801200081 0.129116705 ENDPMDSHQSQES(ph)PNLENIANPLEENVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ENDPMDSHQSQESPNLENIANPLEENVTK 29 0 Q96JQ2 Q96JQ2 CLMN Calmin 1 ENDPMDS(0.002)HQS(0.006)QES(0.992)PNLENIANPLEENVTK;ENDPMDS(0.354)HQS(0.178)QES(0.468)PNLENIANPLEENVTK;ENDPMDS(0.188)HQS(0.143)QES(0.669)PNLENIANPLEENVTK 215.7 1.78E-34 287641000 234558 243892 85674 216729 308956 272458 249780 394428 344351 TRUE FALSE 203560.566 242289.8574 127106.233 265940.6319 302808.3801 282939.6356 225556.374 310082.6416 303642.2171 0.670396126 0.797945226 0.418605272 0.875835497 0.997253883 0.93181916 0.742836013 1.02121057 1 18.21201287 3.525294175 12.36423157 0.934167983 0.645991127 0.586406186 0.119207431 1.127523763 288.3273313 0.031884224 0.04720509 3351.92409 -3.525294175 -0.288176856 ENEFSFEDNAIR ddPTM_MDA-MB-175_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 ; 142.08 0.00014206 192590000 291230 272270 179162 211327 293590 246840 272740 322490 247670 FALSE TRUE 252743.2176 270481.4404 265805.3425 259312.0253 287748.1334 256336.0945 246289.7168 253528.0231 218390.7347 1.157298261 1.238520676 1.217109063 1.187376496 1.31758398 1.173749861 1.127748011 1.160891846 1 17.73655213 0.129754553 0.79067438 1.01E-08 1.218350928 0.644971711 0.048512309 8.150315462 1.023029374 13.15438422 0.01836425 1.348200714 -0.129754553 1.218350918 ENFMTVDQDGSGTVEHHELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ENFMTVDQDGSGTVEHHELR 20 0 H7C2Z6;H7BXD5;P28676;C9JIZ3 H7C2Z6 GCA Grancalcin 0 133.09 6.58E-06 141490000 17381 14231 11924 17623 16910 19008 14364 18791 16207 FALSE TRUE 15084.05681 14137.51562 17690.48628 21624.5715 16573.52408 19739.25006 12970.98149 14772.69088 14291.02692 1.055491456 0.989258204 1.237873694 1.513157285 1.159715406 1.381233845 0.90763117 1.033703943 1 13.80282197 2.226695766 24.99979538 0.988506714 1.22319066 0.364027554 0.150873851 263.6412643 555499.6808 0.064756641 0.044043147 168.5371968 -2.226695766 0.234683946 ENFQNWLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ENFQNWLK 8 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ; 140.5 0.0015088 891440000 963290 811390 446300 436310 660390 653900 652950 831810 1105140 FALSE TRUE 835988.7858 806059.9257 662132.1728 535380.8541 647249.531 679055.9561 589627.0095 653933.9047 974491.6082 0.857871714 0.827159433 0.679464212 0.549395038 0.664192001 0.696830994 0.605061146 0.671051345 1 19.89429024 -0.778645264 19.13355634 5.99666813 0.712648356 0 0.133512354 0 0 0 0.030124007 0.16647719 0.778645264 -5.284019774 ENFS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ENFSPER 7 0 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 ENFS(1)PER;ENFS(1)PER;ENFS(1)PER;ENFS(1)PER 115.82 0.0058681 4792900000 4266470 3484560 2370620 2828860 3316730 3424560 3383940 3826230 3902850 TRUE FALSE 3702645.18 3461669.696 3517059.761 3471195.899 3250733.562 3556305.039 3055766.02 3008020.49 3441459.519 1.075893864 1.00587256 1.021967494 1.008640631 0.944579921 1.033371167 0.887927347 0.874053719 1 21.71458911 3.071647364 0.638402272 0.909626891 1.050694592 0.419172901 0.048557986 0.734401914 0.836320967 0.052115089 0.059688224 1179.362635 -3.071647364 0.141067701 ENFSCLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ENFSCLTR 8 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;C9JF79;C9JRL4 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic;Malate dehydrogenase" 0 ;;; 162.59 0.00079298 1610550000 1122180 1036320 566230 642540 979850 1023690 964070 1068850 1078330 FALSE TRUE 973881.0698 1029512.346 840060.7219 788438.5276 960352.902 1063072.017 870574.6398 840284.7453 950851.0558 1.024220422 1.082727247 0.883482977 0.829192462 1.009992991 1.118021598 0.915574142 0.88371858 1 19.85885985 4.249215521 24.99472934 0.944993318 1.053473862 0.219045147 0.082134351 336.1573743 788556.3055 0.021925994 0.056717563 17750.70149 -4.249215521 0.108480544 ENFTAGS(ph)DCVTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ENFTAGSDCVTLK 13 0 Q1W6H9 Q1W6H9 FAM110C Protein FAM110C 1 ENFTAGS(0.999)DCVT(0.001)LK;ENFTAGS(1)DCVTLK;ENFTAGS(1)DCVTLK;ENFTAGS(1)DCVTLK;ENFTAGS(1)DCVTLK 314.51 1.11E-50 1897440000 5335320 4426180 3211692 3491840 3825250 3229460 5058300 4837870 5524350 TRUE FALSE 4630243.944 4397104.132 4764876.994 4284715.641 3749135.009 3353699.416 4567746.845 3803329.149 4871267.636 0.950521361 0.902661168 0.978159557 0.879589454 0.769642584 0.68846544 0.937691621 0.780767848 1 22.21586582 3.486240492 7.568983544 0.828347593 0.938149648 0.237620619 0.088012238 0.194058711 74.82489846 0.024177436 0.033502508 3063.659473 -3.486240492 0.109802055 ENGEEGCHQNGLALPVVEEGEVLS(ph)HSLEAEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ENGEEGCHQNGLALPVVEEGEVLSHSLEAEHR 32 0 Q9HC44 Q9HC44 GPBP1L1 Vasculin-like protein 1 1 ENGEEGCHQNGLALPVVEEGEVLS(0.5)HS(0.5)LEAEHR 65.301 0.0021411 48912000 32820 25507 20915 25591 32548 35876 35403 33939 33665 TRUE FALSE 28482.75384 25339.44284 31029.56396 31401.82768 31900.35848 37256.17293 31969.62251 26681.40896 29685.16205 0.959494639 0.85360635 1.045288683 1.057829081 1.07462302 1.25504361 1.076956307 0.89881298 1 14.85745437 4.22188768 22.88023654 1.052700946 0.906550597 0.324518304 0.090773073 105.7406027 145109.2309 0.026352678 0.055184341 16668.16076 -4.22188768 -0.146150349 ENGFTQHVYHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ENGFTQHVYHK 11 0 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 0 77.74 0.018383 184260000 280140 232730 127820 154000 219020 218620 275530 269560 140930 FALSE TRUE 243118.7892 231201.1813 189634.1795 188968.0537 214661.9305 227030.4529 248809.143 211916.6917 124269.4159 1.956384742 1.860483366 1.525992362 1.520632026 1.727391481 1.82692138 2.002175202 1.705300456 1 16.92311175 1.243985349 5.35563489 0.962697735 1.765891068 0.700400829 0.157875964 0.091674044 7.677607479 0.270043307 0.042557153 17.53821335 -1.243985349 0.803193332 ENGSGHEASLQLRPPPEPS(ph)TPVSGQDDLIQHQDMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ENGSGHEASLQLRPPPEPSTPVSGQDDLIQHQDMR 35 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 ENGSGHEASLQLRPPPEPS(0.481)T(0.442)PVS(0.076)GQDDLIQHQDMR;ENGSGHEASLQLRPPPEPS(0.5)T(0.5)PVSGQDDLIQHQDMR;ENGSGHEASLQLRPPPEPS(0.488)T(0.488)PVS(0.024)GQDDLIQHQDMR 201.25 8.16E-28 724486000 194809 182457 80187 130003 189021 201094 176856 204896 184906 TRUE FALSE 169064.4971 181258.428 118965.7014 159522.1681 185259.8519 208830.2163 159704.5323 161080.5849 163046.6233 1.036908914 1.111696914 0.729642227 0.978383758 1.136238507 1.28080062 0.979502237 0.987941864 1 17.31492504 ENGSGHEASLQLRPPPEPST(ph)PVSGQDDLIQHQDMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ENGSGHEASLQLRPPPEPSTPVSGQDDLIQHQDMR 35 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 ENGSGHEASLQLRPPPEPS(0.389)T(0.605)PVS(0.006)GQDDLIQHQDMR;ENGSGHEASLQLRPPPEPS(0.134)T(0.86)PVS(0.006)GQDDLIQHQDMR 167.82 1.33E-14 235249000 115265 99319 55518 89281 117523 120070 102783 127047 109427 TRUE FALSE 100032.4382 98666.56695 82366.6905 109553.6156 115184.5222 124689.1706 92815.12048 99878.98773 96490.66472 1.036705867 1.022550391 0.853623413 1.135380463 1.193737473 1.292240767 0.961907774 1.035115553 1 16.55810175 3.708344934 24.95208972 1.098823959 0.976118877 0.25549686 0.106017722 1058.419913 874042.4364 0.031699973 0.047024685 5109.106245 -3.708344934 -0.122705082 ENGVTHPIDYHTTDYVDEIKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ENGVTHPIDYHTTDYVDEIKK 21 1 Q99536-3;Q99536;K7ENX2;K7EM19;Q99536-2 Q99536-3 VAT1 Synaptic vesicle membrane protein VAT-1 homolog 0 ; 139.83 6.95E-08 250115000 241490 186328 131254 173892 184455 169842 225363 264540 259480 FALSE TRUE 209576.4846 185103.9991 194728.8734 213376.8364 180784.7064 176375.9316 203507.3309 207970.1797 228804.57 0.915962844 0.809004816 0.851070734 0.932572441 0.790127166 0.77085843 0.889437352 0.90894242 1 17.80375634 1.395175618 1.736519848 1.024431915 0.846094351 0.46745809 0.051572442 0.607555913 2.324985058 0.168868408 0.014765048 24.84137427 -1.395175618 -0.178337564 ENHGQADHS(ph)PSMTATHFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ENHGQADHSPSMTATHFPR 19 0 Q9Y3L3;Q6ZT62-2;Q6ZT62;Q9Y3L3-2 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 ENHGQADHS(0.976)PS(0.024)MTATHFPR;ENHGQADHS(0.999)PS(0.001)MTATHFPR;ENHGQADHS(0.999)PS(0.001)MTATHFPR;ENHGQADHS(1)PSMTATHFPR;ENHGQADHS(1)PSMTATHFPR;ENHGQADHS(0.958)PS(0.042)MTATHFPR;ENHGQADHS(0.951)PS(0.049)MTATHFPR;ENHGQADHS(0.993)PS(0.007)MTATHFPR 340 1.75E-75 19324820000 2127590 2183449 1387470 1575504 2165179 2388772 2124752 2249015 2198410 TRUE FALSE 1846423.591 2169105.78 2058455.133 1933246.263 2122096.174 2480669.605 1918693.878 1768080.644 1938516.474 0.952493113 1.118951429 1.061871364 0.997281317 1.09470113 1.279674244 0.989774347 0.912079246 1 20.88652157 2.015345364 24.99714199 0.95010967 1.085715488 0.288983553 0.087482108 260.5674352 424455.0457 0.035708866 0.0240661 103.596567 -2.015345364 0.135605817 ENIAEWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ENIAEWK 7 0 P11908;P11908-2;H7C540;D3YTJ7 P11908 PRPS2 Ribose-phosphate pyrophosphokinase 2 0 79.906 0.072942 196990000 808320 761830 511790 614060 693990 587350 824810 844260 825820 FALSE TRUE 701498.464 756825.4886 759293.3558 753491.7083 680180.9568 609945.7346 744820.0532 663721.569 728192.5004 0.963342061 1.03932063 1.042709662 1.034742473 0.934067512 0.837616062 1.022834007 0.911464439 1 19.47396036 3.235514998 24.871176 0.938423701 1.023026777 0.344142057 0.05393116 77.89495794 636108.6218 0.015473461 0.018309901 1719.946739 -3.235514998 0.084603076 S(ph)LDNFFAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLDNFFAK 8 0 Q9UKY7;Q9UKY7-2 Q9UKY7 CDV3 Protein CDV3 homolog 1 S(1)LDNFFAK;S(1)LDNFFAK 108.9 0.0039033 75977000 179207 128014 100434 125715 111421 73721 140910 229640 554720 TRUE FALSE 155524.3409 127173.0676 149004.2183 154260.5122 109203.9401 76557.09457 127244.5699 180533.2731 489141.6335 0.317953595 0.259992319 0.304623872 0.315369827 0.223256277 0.156513143 0.260138498 0.369081797 1 18.89989274 1.209738531 2.900725686 1.18340679 0.262020231 0.957397348 0.048477719 0.093045102 0.897951065 0.2117218 0.013718092 16.20833971 -1.209738531 -0.921386559 ENIKPNETS(ph)PSFSK ddPTM_MDA-MB-175_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(0.158)S(0.826)PS(0.015)FS(0.001)K 84.208 0.0049808 724880000 671610 527890 631740 704670 579650 374070 753950 810540 1542800 TRUE FALSE 582855.0369 524422.2558 937251.577 864676.0937 568116.0991 388460.715 680832.045 637212.3286 1360411.942 0.428440106 0.385487836 0.688946891 0.635598724 0.417605934 0.285546387 0.500460209 0.4683966 1 20.37561214 1.237917001 24.9895741 1.000000601 0.478059938 0.667108587 0.116253943 10.26948235 398414.944 0.17420549 0.030060915 17.294858 -1.237917001 -0.521940663 ENIQS(ph)S(ph)LLETLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ENIQSSLLETLYR 13 0 A0A494C0J1;O14830 A0A494C0J1 PPEF2 Serine/threonine-protein phosphatase with EF-hands 2 2 ENIQS(0.667)S(0.667)LLET(0.667)LYR;ENIQS(0.667)S(0.667)LLET(0.667)LYR 51.211 0.076529 19092000 15684.7 11177.9 11263.8 10757.2 17110.1 14022 13356.6 18571 9696.6 TRUE FALSE 13611.92716 11104.47164 16711.01136 13199.78667 16769.64249 14561.43541 12061.27899 14599.73617 8550.278994 1.591986316 1.298726234 1.954440477 1.543784324 1.961297695 1.70303629 1.410629875 1.707515764 1 13.06175578 1.235205829 24.99693799 0.999999101 1.6453986 0.487193792 0.208421649 82.7094041 616175.9217 0.345323365 0.048990466 17.18722764 -1.235205829 0.645399498 ENISEWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ENISEWR 7 0 B1ALA9;P60891;A0A2R8Y7H4;P60891-2 B1ALA9 PRPS1 Ribose-phosphate pyrophosphokinase 1 0 ; 96.492 0.029528 636160000 1251050 1229680 760440 919470 1245550 1170900 1162330 1351310 1295860 FALSE TRUE 1085720.573 1221602.151 1128191.328 1128249.717 1220765.992 1215945.281 1049607.416 1062342.872 1142664.907 0.950165325 1.069081709 0.987333487 0.987384586 1.068349946 1.064131114 0.918560996 0.929706396 1 20.12397096 2.231211042 24.9992218 0.944029049 1.022340376 0.365048105 0.044336146 163.9757063 557749.1579 0.01755448 0.012104247 170.298586 -2.231211042 0.078311326 ENIVEAIIHSPELIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ENIVEAIIHSPELIR 15 0 O95373;E9PLB2 O95373 IPO7 Importin-7 0 ;;; 144.97 4.14E-06 284835000 209029 192645 136067 167554 191248 193869 199122 220094 239168 FALSE TRUE 181405.288 191379.5023 201869.4563 205599.6966 187442.539 201327.2659 179811.1791 173028.6109 210893.8315 0.860173514 0.907468469 0.957208918 0.974896682 0.888800481 0.954638002 0.852614692 0.820453636 1 17.68615737 1.196627332 23.89735085 1.000001969 0.901293081 0.277694324 0.049642472 8716.282049 4966703.42 5.386903052 0.013538666 15.72632808 -1.196627332 -0.098708888 ENKGS(ph)GTPSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ENKGSGTPSPK 11 1 A0A0C4DG97 A0A0C4DG97 FSD1L 1 ENKGS(0.851)GT(0.075)PS(0.075)PK 50.675 0.093916 187160000 152520 238450 122910 155680 362990 448700 257650 293100 150500 TRUE FALSE 132364.0956 236883.6062 182349.6871 191029.5234 355767.2092 465961.7793 232663.1427 230422.8459 132708.0615 0.997408101 1.784997864 1.374066391 1.439471885 2.680825907 3.511179157 1.753195248 1.736313856 1 17.01789649 3.323105039 11.82416573 2.12613958 1.423256972 0.227189492 0.674950863 0.952876243 128.2898812 0.21036284 0.27156124 2104.287325 -3.323105039 -0.702882608 ENKPSIIFIDEIDSLCGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ENKPSIIFIDEIDSLCGSR 19 1 O75351 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 0 82.037 0.0045836 54694000 48760 32585 26716 30989 36495 30812 36543 48327 43969 FALSE TRUE 42316.24246 32370.94699 39635.94696 38025.52609 35768.8209 31997.35758 32999.06548 37992.64713 38771.03491 1.09143959 0.834926049 1.022308201 0.980771501 0.922565544 0.825290263 0.851126764 0.979923472 1 15.24269162 3.196902402 6.245706335 0.914015761 0.974711655 0.140208855 0.081016505 0.435531518 42.91666582 0.024665145 0.028524614 1573.629188 -3.196902402 0.060695895 ENLATVEGNFASIDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ENLATVEGNFASIDER 16 0 Q13561;Q13561-3;Q13561-2;H0YI98 Q13561 DCTN2 Dynactin subunit 2 0 ;;; 265.99 8.86E-27 353421000 119236 119316 81308 92165 113733 118448 112730 132860 121320 FALSE TRUE 103478.6605 118532.2053 120628.8208 113092.4719 111469.9358 123004.7712 101797.462 104448.9229 106977.6878 0.96729199 1.108008668 1.127607291 1.057159434 1.041992383 1.149817067 0.951576577 0.976361754 1 16.7069504 2.220098624 24.99905966 0.975042279 1.076836296 0.454640386 0.051264157 206.2167633 279232.4162 0.020163864 0.013622386 165.9963827 -2.220098624 0.101794016 ENLPSHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ENLPSHFK 8 0 Q8TBX8;F8VNT5;Q8TBX8-2;F8VU68 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 ;; 135.71 0.00082207 692340000 1411920 1316070 848060 974730 1253010 1140240 1351370 1522220 1455450 FALSE TRUE 1225331.195 1307424.65 1258184.653 1196057.344 1228077.552 1184105.771 1220314.345 1196705.099 1283388.359 0.954762591 1.018728774 0.98036159 0.931952776 0.956902518 0.922640261 0.950853525 0.932457499 1 20.29152637 3.868422803 5.495792239 0.946850441 0.989581875 0.291404898 0.025895312 0.233758064 9.433238674 0.00641816 0.011373464 7386.22959 -3.868422803 0.042731435 ENLSAAFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ENLSAAFSR 9 0 P15170-2;P15170-3 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ; 97.472 0.015513 403750000 395180 447890 266380 327810 419800 419170 352980 407580 379710 FALSE TRUE 342955.9617 444947.7811 395202.259 402244.2708 411446.8013 435295.7411 318748.0539 320422.1888 334821.1164 1.024296094 1.328911945 1.180338514 1.201370676 1.228855592 1.300084492 0.951995075 0.956995163 1 18.35303099 2.22839945 24.99888127 0.96628794 1.215047667 0.660605599 0.081371662 109.1641073 268567.1395 0.030475283 0.020810619 169.199646 -2.22839945 0.248759728 ENLSDEDKLNNAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ENLSDEDKLNNAK 13 1 Q14651 Q14651 PLS1 Plastin-1 0 128.96 0.0001452 167340000 221920 161700 169090 166040 162660 121930 260210 270150 234210 FALSE TRUE 192592.7097 160637.7821 250862.4896 203741.9198 159423.3842 126620.726 234974.8743 212380.5248 206521.9606 0.932553173 0.777824216 1.214701278 0.986538764 0.77194398 0.613110226 1.137771855 1.028367754 1 17.65593567 ENLVRPGIDHLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ENLVRPGIDHLGR 13 1 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 0 ; 146.59 2.55E-05 192565000 221540 218759 138382 164992 208240 208273 215200 241350 193946 FALSE TRUE 192262.9277 217321.9577 205303.9981 202455.9553 204096.4314 216285.3971 194329.9371 189739.1807 171017.9248 1.124226761 1.270755437 1.200482337 1.183828862 1.193421284 1.264694314 1.136313268 1.109469553 1 17.38378802 1.411837176 1.369637326 0.953614634 1.206358371 0.68707396 0.044258913 0.489951802 1.071846329 0.163907643 0.012645773 25.8129224 -1.411837176 0.252743736 ENPDKEEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ENPDKEEFR 9 1 G3XAH6;P51003 G3XAH6 PAPOLA Poly(A) polymerase alpha 0 77.744 0.028942 206970000 288130 281730 193030 235940 291960 299330 344650 373680 372810 FALSE TRUE 250052.8905 279879.2971 286379.9536 289513.7831 286150.5672 310845.4188 311225.896 293771.44 328736.8265 0.760647638 0.851377985 0.871152638 0.880685581 0.870454857 0.945575286 0.946732678 0.893637148 1 18.32657356 7.298638563 0.280344919 0.961011964 3.73E-14 0.773881989 0.030676758 27.56572233 0.634012952 0.076035838 11.73379305 19890173.13 -7.298638563 -0.961011964 ENPEDVLS(ph)PTSVATYLSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ENPEDVLSPTSVATYLSSK 19 0 Q5JTU8;B1AMJ5;A0A0A0MRG9;Q96SN8-3;Q96SN8-2;Q96SN8;Q96SN8-4 Q5JTU8 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 1 ENPEDVLS(0.675)PT(0.132)S(0.182)VAT(0.01)YLSSK;ENPEDVLS(0.832)PT(0.142)S(0.025)VAT(0.001)YLSSK;ENPEDVLS(0.958)PT(0.017)S(0.025)VATYLSSK 141.97 1.68E-07 71002000 168424 182178 133275 188167 213468 187328 236130 311181 266318 TRUE FALSE 146166.3417 180981.2607 197727.2358 230893.1933 209220.4044 194534.6294 213230.1489 244637.3648 234834.1894 0.6224236 0.770676796 0.841986579 0.983217963 0.890928212 0.828391427 0.908003002 1.041745094 1 17.84128294 5.516605788 0.547988409 0.967455239 3.57E-25 0.755316549 0.060449256 5.099679907 0.636438241 0.039743587 3.771791527 328553.2658 -5.516605788 -0.967455239 ENPEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ENPEKR 6 1 Q1KMD3;H3BQZ7;Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;Q7Z6E9-4 Q1KMD3;Q7Z6E9 HNRNPUL2;HNRNPUL2-BSCL2;RBBP6 Heterogeneous nuclear ribonucleoprotein U-like protein 2;E3 ubiquitin-protein ligase RBBP6 0 ; 129.39 0.025998 268300000 524340 353160 227994 301390 201359 314540 406800 493190 412570 FALSE TRUE 455047.1405 350840.0687 338252.661 369825.206 197352.3499 326640.5573 367348.5986 387725.1565 363796.4446 1.250828993 0.964385645 0.929785505 1.016571798 0.54248015 0.897866272 1.009764125 1.065775002 1 18.47277192 4.747115329 3.401497772 0.929776316 1.295437684 0.331943348 0.144682116 0.43142145 8.325178501 0.0385266 0.414675874 55861.85194 -4.747115329 0.365661368 ENPSATLEDLEKPGVDEEPQHVLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ENPSATLEDLEKPGVDEEPQHVLLR 25 1 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 ; 209.16 1.46E-25 523310000 439630 360200 258020 302730 324570 271770 412170 491880 480180 FALSE TRUE 381531.7816 357833.8225 382799.335 371469.4734 318111.692 282225.1678 372197.8168 386695.2898 423413.6674 0.901085182 0.845116372 0.904078835 0.87732046 0.75130237 0.666547137 0.87904063 0.913280131 1 18.69170831 1.570386128 2.293411409 0.993656242 0.826556765 0.369316846 0.073070185 0.367447756 3.84882401 0.105297611 0.021897514 37.1865705 -1.570386128 -0.167099477 ENPVYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ENPVYEK 7 0 P46777;A0A2R8Y6J3;A0A2R8Y4A2 P46777 RPL5 60S ribosomal protein L5 0 ;; 93.374 0.034855 562790000 900780 813980 535940 655510 704160 708010 900120 998880 926800 FALSE TRUE 781739.6407 808632.9118 795122.3766 804353.5643 690148.5937 735247.6028 812826.5009 785277.2853 817234.7598 0.956566802 0.989474447 0.972942434 0.984238072 0.844492461 0.89967735 0.994605884 0.960895601 1 19.64039104 2.204584276 24.99977429 0.980503876 0.942423667 0.178106104 0.044064184 407.0237908 299485.1803 0.01967191 0.013263526 160.1711436 -2.204584276 -0.038080209 ENPYYDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ENPYYDSR 8 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;; 191.85 0.00041646 11852740000 14292220 12657120 8881530 8857370 12341650 13040620 13296370 14040380 13319140 FALSE TRUE 12403466.92 12573974.55 13176667.61 10868571.23 12096075.31 13542301.09 12006890.08 11037954 11744566.44 1.05610258 1.070620581 1.121937338 0.925412725 1.029929489 1.153069477 1.022335745 0.939834949 1 23.48549012 1.993436288 24.85242995 0.970259569 1.058105078 0.267530089 0.060977881 344.1156708 1302937.403 0.026100195 0.016874338 98.50001296 -1.993436288 0.087845509 ENQPENSQT(ph)PTKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ENQPENSQTPTKK 13 1 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 ENQPENS(0.023)QT(0.975)PT(0.002)KK 93.754 0.0024283 0 140750 97456 81837 89876 88035 66996 124420 151620 121320 TRUE FALSE 122149.5309 96815.80512 121413.6469 110283.7195 86283.27574 69573.37947 112353.7676 119197.2429 106977.6878 1.1418225 0.905009326 1.134943645 1.030903936 0.806553941 0.650354115 1.050254215 1.114225268 1 16.7069504 4.753613884 23.31141251 0.970638549 1.141822819 0.128032953 0.146157851 2708.920229 4194835.478 0.038995872 0.794128278 56704.02455 -4.753613884 0.171184269 ENQRS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 ENQRSPVR 8 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR 101.71 0.0031496 5533331000 3195912 2752612 1655324 2072218 1946332 2662042 2647669 2956900 2176556 TRUE FALSE 2773564.132 2734529.911 2455844.223 2542746.769 1907603.801 2764452.478 2390898.468 2324589.946 1919246.029 1.445132145 1.424793835 1.279588018 1.324867542 0.993933957 1.440384628 1.245748816 1.21119956 1 20.87210823 8 0.233191495 1.117166799 3.123729578 0.371381906 0.129327827 104.7862313 1.639471615 0.519991695 78.1804244 100000000 -8 2.006562779 ENRPYYFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ENRPYYFNR 9 1 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 0 65.465 0.076413 0 101590 91542 60907 78484 115500 107820 88931 114400 111990 FALSE TRUE 88164.6241 90940.65457 90361.82892 96304.99175 113201.776 111967.9052 80306.48531 89936.45026 98750.66978 0.892800265 0.920911775 0.915050289 0.975233808 1.146339323 1.133844514 0.813224715 0.910742686 1 16.59150291 3.718785456 5.12193192 0.988546413 0.910114528 0.151116153 0.096286599 0.458946809 36.74493606 0.030156746 0.047783936 5233.418386 -3.718785456 -0.078431885 ENS(ph)IRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ENSIRR 6 1 Q96NY8-2;Q96NY8 Q96NY8-2 PVRL4 Nectin-4;Processed poliovirus receptor-related protein 4 1 ENS(1)IRR 59.245 0.083203 60424000 77795 74210 71184 88078 74666 90556 74158 97115 132500 TRUE FALSE 67514.19364 73722.50962 105608.8205 108077.4561 73180.29268 94039.74792 66966.16857 76347.713 116836.0009 0.577854369 0.630991381 0.903906498 0.925035565 0.626350543 0.80488674 0.57316382 0.653460512 1 16.83412536 4.455378789 23.69391587 0.761499368 0.591138523 0.218138754 0.137990837 184.1899284 200721.2946 0.035367197 0.093595926 28535.05994 -4.455378789 -0.170360845 ENS(ph)REALAEAALESPRPALVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ENSREALAEAALESPRPALVR 21 2 O14745;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 ENS(0.978)REALAEAALES(0.022)PRPALVR;ENS(0.965)REALAEAALES(0.035)PRPALVR 134.11 6.92E-06 634100000 323110 297520 198925 194463 293700 327100 332440 349240 168845 TRUE FALSE 280410.1948 295565.5715 295125.7954 238618.7963 287855.9446 339683.7487 300200.02 274557.7438 148884.3364 1.883409642 1.985202598 1.982248787 1.602712562 1.933419938 2.281527774 2.016330442 1.844100933 1 17.18383246 1.23327065 3.69061201 0.868334118 1.953836404 0.767163179 0.164012229 0.143013103 3.029656792 0.43489915 0.044093363 17.11081319 -1.23327065 1.085502285 ENSFGS(ph)PLEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ENSFGSPLEFR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ENS(0.001)FGS(0.999)PLEFR;ENSFGS(1)PLEFR;ENS(0.018)FGS(0.982)PLEFR;ENS(0.001)FGS(0.999)PLEFR;ENSFGS(1)PLEFR;ENSFGS(1)PLEFR 257.47 1.66E-20 5549740000 7892730 6504230 5259820 6350750 6341560 6082780 5565740 7161460 12340960 TRUE FALSE 6849685.733 6461503.285 7803486.545 7792784.853 6215375.363 6316788.483 5025975.391 5630037.51 10882025.77 0.629449505 0.593777613 0.717098701 0.716115273 0.571159773 0.580479096 0.461860273 0.517370353 1 23.37544381 1.231918713 24.99999481 1.000000686 0.594043998 0.721204361 0.078426613 141.4907648 532518.607 0.20736336 0.022002504 17.05763092 -1.231918713 -0.405956687 ENSQLDTS(ph)PPCLGGNKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ENSQLDTSPPCLGGNKK 17 1 Q9Y3E2 Q9Y3E2 BOLA1 BolA-like protein 1 1 ENSQLDT(0.031)S(0.969)PPCLGGNKK 114.02 0.00023511 346890000 471180 432160 305070 360740 408820 288290 529170 633920 464160 TRUE FALSE 408912.3692 429321.1125 452602.8724 442651.5306 400685.2818 299380.7028 477851.1748 498361.1412 409287.5336 0.999083372 1.048947445 1.105831073 1.081517257 0.978982375 0.731467925 1.167519496 1.217630884 1 18.6427552 ENSS(ph)PSVTSANLDHTKPCWYWDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ENSSPSVTSANLDHTKPCWYWDK 23 1 O75909;G3V5E1;O75909-1;O75909-4;G3V2Q3;O75909-2;G3V235 O75909 CCNK Cyclin-K 1 ENS(0.137)S(0.856)PS(0.007)VTSANLDHTKPCWYWDK 211.89 2.44E-25 264150000 169550 123250 108310 142200 130910 114500 147500 169170 320630 TRUE FALSE 147143.5379 122440.3626 160689.0783 174488.6834 128305.1471 118904.8891 133195.4727 132994.312 282725.4867 0.520446669 0.433071543 0.568357244 0.617166445 0.453815284 0.420566573 0.471112365 0.47040086 1 18.10904242 1.237024195 24.99994789 1.000000623 0.492814281 0.872465704 0.060751729 13.92012196 226424.8514 0.096278195 0.015680876 17.25934042 -1.237024195 -0.507186341 ENTEGEYSGIEHVIVDGVVQSIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ENTEGEYSGIEHVIVDGVVQSIK 23 0 H0YL72;P50213;P50213-2;H0YLI6;H0YMU3 H0YL72 IDH3A "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial" 0 ; 231.29 2.48E-33 123770000 160827 151129 98889 221710 192559 162823 167726 239820 215532 FALSE TRUE 139573.3045 150136.2236 146712.0512 272052.6441 188727.4526 169086.9062 151459.9583 188536.3593 190052.0525 0.734395144 0.789974229 0.771957205 1.431463857 0.993030331 0.889687346 0.796939346 0.992024852 1 17.53603508 3.93395632 24.9999994 1.002732616 0.766865498 0.34270335 0.163552635 231.2838072 87549.27926 0.044929955 0.07782104 8589.271281 -3.93395632 -0.235867118 ENTHQTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ENTHQTLK 8 0 C9JRZ6;Q9NX63 C9JRZ6 CHCHD3 MICOS complex subunit MIC19 0 ; 98.582 0.0074202 207460000 416570 355730 157038 340840 323160 424620 304960 479740 452070 FALSE TRUE 361519.219 353393.1862 232982.1021 418232.9314 316729.7483 440955.4062 275385.0261 377151.3343 398626.7996 0.906911476 0.886526412 0.584461713 1.049184179 0.794552069 1.106186053 0.6908342 0.946126389 1 18.60467918 3.704951393 24.99966042 0.919289725 0.802022168 0.162351039 0.1461597 1241.211594 923254.3656 0.037923128 0.056252488 5069.339682 -3.704951393 -0.117267557 ENVEYIEREES(ph)DGEYDEFGR ddPTM_MDA-MB-175_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 257.53 1.93E-36 21153660000 10081360 8577530 5290600 6495110 8489260 7925910 8278340 9241900 6044170 TRUE FALSE 8749082.733 8521183.641 7849151.856 7969923.997 8320340.335 8230824.886 7475507.861 7265591.606 5329635.108 1.64159132 1.598830589 1.472737194 1.495397684 1.561146339 1.544350545 1.402630332 1.363243723 1 22.34560533 0.695723854 0.927411255 2.93E-13 1.551861493 0.907031193 0.055189565 1.528553054 0.508073306 3.061109617 0.019887845 4.962766634 -0.695723854 1.551861493 ENVEYIEREES(ph)DGEYDEFGRK ddPTM_MDA-MB-175_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 160.52 1.10E-11 1477360000 2169830 1466870 1219560 1351780 1631040 1187940 1781460 2353820 1711080 TRUE FALSE 1883081.468 1457234.034 1809343.295 1658722.31 1598585.495 1233640.82 1608694.283 1850473.91 1508798.072 1.248067255 0.965824428 1.199195127 1.099366669 1.059509238 0.817631493 1.066209133 1.226455644 1 20.52496831 3.316617714 4.318723283 1.04958534 1.124056789 0.123565957 0.122064405 0.664742069 23.33887301 0.038352478 0.049434657 2073.087885 -3.316617714 0.074471448 ENVFQEHQTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ENVFQEHQTLK 11 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;; 180.09 6.82E-06 7796090000 8278280 7984310 4000810 7210450 8076090 6939210 8812350 10510380 13181830 FALSE TRUE 7184284.324 7931860.542 5935615.098 8847692.877 7915391.61 7206165.899 7957729.653 8262817.029 11623489.07 0.618083286 0.682399277 0.510656917 0.761190794 0.680982411 0.619965817 0.684624866 0.710872353 1 23.47053986 0.995345717 1.76353583 1.361730415 0.649537285 0.742103713 0.064153721 0.944389371 1.581459208 1.414924566 0.016958388 9.893403384 -0.995345717 -0.712193129 ENVPENSRPATGYPLPPQIFNESQYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ENVPENSRPATGYPLPPQIFNESQYR 26 1 O75368 O75368 SH3BGRL SH3 domain-binding glutamic acid-rich-like protein 0 ;;; 178.95 2.16E-17 1319340000 284455 252494 169797 214245 256514 253603 299517 337704 328667 FALSE TRUE 246863.551 250835.3503 251911.3971 262892.6018 251409.8733 263359.2715 270469.8874 265488.6276 289812.3617 0.851804766 0.865509493 0.869222402 0.907113141 0.86749189 0.908723389 0.933258629 0.91607075 1 18.14475961 -2 0.331605746 2.169337211 0.858612578 0.825594064 0.01813245 31.34918147 0.495869827 24.82954781 0.027405859 0.01 2 -1.310724633 ENYSHHTQDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ENYSHHTQDDR 11 0 Q92804-2;Q92804;A0A075B7D9;A0A075B7E4;A0A075B7F2 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;;;;; 222.94 4.23E-12 1677970000 1813306 1831559 669250 1475351 1947773 2121594 1795184 2187070 4567255 FALSE TRUE 1573673.018 1819527.368 992901.5385 1810351.994 1909016.128 2203213.094 1621087.332 1719382.1 4027319.317 0.390749502 0.451796152 0.246541548 0.449517868 0.47401658 0.5470669 0.402522672 0.426929668 1 21.94138843 1.238610315 9.999200989 1.002367226 0.424235763 0.849941669 0.076108478 0.027267505 58.61542135 0.107019912 0.019014784 17.32248981 -1.238610315 -0.578131463 ENYSHHTQDDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ENYSHHTQDDRR 12 1 Q92804-2;Q92804;A0A075B7D9;A0A075B7E4;A0A075B7F2 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;; 130.1 0.00014444 415683000 379401 239826 902920 277312 14920.2 138445 112172 101494 74121 FALSE TRUE 329262.1966 238250.5672 1339575.132 340279.928 14623.31721 143771.0687 101293.5767 79790.29793 65358.49982 5.037786936 3.645288186 20.49580599 5.206360749 0.223740099 2.199730244 1.549814898 1.220809813 1 15.99608725 3.480497375 23.70995299 1.435854864 9.74034066 0.433118932 4.437787727 65.3779 459142.0884 1.254328764 1.656969678 3023.412294 -3.480497375 8.304485797 ENYTWSQDYTDLEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ENYTWSQDYTDLEVR 15 0 Q8IVD9 Q8IVD9 NUDCD3 NudC domain-containing protein 3 0 192.65 2.92E-07 90131000 72700 65456 39101 42061 64975 63242 73176 76193 73786 FALSE TRUE 63092.5108 65026.01523 58010.37438 51611.59291 63682.12462 65674.96066 66079.40278 59899.71988 65063.10314 0.969712598 0.99942997 0.891601716 0.793254401 0.978774782 1.009404063 1.015620215 0.920640378 1 15.98955201 3.061869917 24.99994283 0.980571097 0.914066012 0.262801631 0.059172623 109.0713718 44071.54973 0.0192042 0.021775515 1153.107819 -3.061869917 -0.066505084 ENYVWNVLLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ENYVWNVLLHR 11 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 0 ; 155.15 3.17E-05 492320000 946050 956590 652720 678230 988010 1040450 969180 1022560 1013320 FALSE TRUE 821027.0955 950306.0973 968377.5752 832232.4876 968350.534 1080476.785 875189.0728 803893.5016 893526.464 0.918861532 1.063545553 1.083770447 0.93140217 1.083740183 1.209227514 0.979477506 0.899686281 1 19.76915093 2.011099627 24.99759091 0.941749043 1.050950232 0.200861887 0.084501349 290.1831938 653522.2916 0.034601475 0.023304761 102.5887238 -2.011099627 0.109201189 EPAAAISRPR ddPTM_MDA-MB-175_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 ;;; 141.89 3.35E-05 1073690000 693850 662290 444010 490160 636440 681010 647020 687070 560720 FALSE TRUE 602155.9645 657939.3734 658734.7211 601458.3196 623776.0892 707208.8954 584272.1 540145.4273 494432.3204 1.217873387 1.330696531 1.332305139 1.216462385 1.261600554 1.430345198 1.181702886 1.092455742 1 18.91541353 1.772111601 2.331571006 1.022196786 1.295586346 0.707987543 0.066481235 0.146308258 1.558615997 0.056123692 0.018324472 59.17136681 -1.772111601 0.27338956 EPAESAAVAHERPPGGTGSADPERPPGAT(ph)CPESPGPGPPHPLGVVESGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPAESAAVAHERPPGGTGSADPERPPGATCPESPGPGPPHPLGVVESGK 49 2 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 EPAESAAVAHERPPGGTGSADPERPPGAT(0.5)CPES(0.5)PGPGPPHPLGVVESGK 78.147 0.00015042 148760000 72916 61204 47710 67999 61025 60444 70298 84993 93651 TRUE FALSE 63279.96585 60801.94689 70782.71558 83439.21225 59810.72189 62769.31979 63480.51078 66817.90837 82579.68547 0.766289742 0.736282132 0.857144408 1.010408453 0.724278877 0.760106065 0.768718244 0.809132512 1 16.3334993 1.23946418 7.491128071 1.003132897 0.804524387 0.359007086 0.082308578 0.119521938 48.03291202 0.121409553 0.021000853 17.35658101 -1.23946418 -0.19860851 EPAESAAVAHERPPGGTGSADPERPPGATCPES(ph)PGPGPPHPLGVVESGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPAESAAVAHERPPGGTGSADPERPPGATCPESPGPGPPHPLGVVESGK 49 2 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 EPAES(0.032)AAVAHERPPGGT(0.026)GS(0.026)ADPERPPGAT(0.21)CPES(0.706)PGPGPPHPLGVVESGK 54.346 0.0038436 288830000 169880 132010 88853 115590 121570 113250 149510 171040 182830 TRUE FALSE 147429.9276 131142.8176 131822.608 141836.4762 119150.9948 117606.8008 135010.5432 134464.427 161216.0457 0.914486687 0.813460081 0.817676723 0.879791311 0.739076525 0.729498111 0.837451028 0.834063548 1 17.29863582 1.173386032 2.746976122 1.062659782 0.81496211 0.506865672 0.055575213 0.518571995 3.917651549 0.319939508 0.014791546 14.90685516 -1.173386032 -0.247697672 EPAHLMSLFGGKPMIIYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPAHLMSLFGGKPMIIYK 18 1 P06396-2;A0A0A0MS51;A0A0A0MT01;P06396-4;P06396-3;P06396 P06396-2 GSN Gelsolin 0 141 7.39E-08 255270000 1063200 697090 385260 527950 627180 553630 782870 974880 647050 FALSE TRUE 922695.4262 692510.7699 571573.0246 647829.1167 614700.3451 574928.5043 706947.3879 766409.4985 570556.4861 1.617185062 1.213746205 1.001781661 1.135433796 1.077369831 1.007662726 1.239048902 1.343266648 1 19.1220102 4.717265168 3.767453291 1.136032339 1.656974609 0.663322502 0.110899527 0.163983259 4.486945461 0.030307492 0.229378765 52151.30357 -4.717265168 0.52094227 EPAITSQNS(ph)PEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 EPAITSQNSPEAR 13 0 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;E5RIS7 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 1 EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR 307.7 3.41E-43 8157963000 2602213 2339897 1864687 2288042 2302289 2324718 2230674 2544893 4989700 TRUE FALSE 2258323.959 2324526.063 2766455.87 2807576.907 2256477.953 2414151.406 2014343.579 2000687.436 4399823.35 0.513276052 0.528322589 0.628765214 0.638111279 0.512856488 0.548692803 0.457823739 0.454719946 1 22.06901417 1.232632537 24.99833595 1.000000757 0.533539623 0.853107734 0.060593251 80.94580866 341308.3935 0.148888429 0.016898618 17.08569057 -1.232632537 -0.466461134 EPALPLEPDSGGNTS(ph)PGVTANGEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EPALPLEPDSGGNTSPGVTANGEAR 25 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;Q5VY93 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 EPALPLEPDSGGNT(0.081)S(0.893)PGVT(0.025)ANGEAR;EPALPLEPDSGGNT(0.02)S(0.98)PGVTANGEAR 173.89 2.50E-12 244820000 472550 481560 369700 463440 534500 565010 539300 608710 565730 TRUE FALSE 410101.3202 478396.6007 548488.1566 568671.1352 523864.4957 586746.3003 486998.769 478542.1035 498850.0439 0.822093383 0.958998814 1.099505078 1.139964088 1.050144231 1.176197752 0.976242811 0.959290491 1 18.92824668 4.577681041 3.066814438 1.050790707 0.818787998 0.544107074 0.069335973 0.258533485 4.070324796 0.019772167 0.116688298 37816.4747 -4.577681041 -0.232002709 EPCHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPCHSK 6 0 B1AN48;Q9UBC9 B1AN48 SPRR3 Small proline-rich protein 3 0 72.021 0.086696 139010000 410250 421730 285270 331810 280610 350450 474370 535810 570930 FALSE TRUE 356034.4231 418959.6279 423227.5262 407152.5319 275026.41 363932.0383 428365.6704 421231.2012 503435.3058 0.707209882 0.832201522 0.840679073 0.808748467 0.546299409 0.72289733 0.850885239 0.836713668 1 18.94144687 1.226801065 1.286975786 1.112278433 0.751421327 0.446492686 0.087782677 1.534508202 2.138070961 0.754328564 0.0286458 16.85780653 -1.226801065 -0.360857106 EPCLHPLEPDEVEYEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EPCLHPLEPDEVEYEPR 17 0 Q9UIQ6-3;Q9UIQ6-2;Q9UIQ6 Q9UIQ6-3 LNPEP "Leucyl-cystinyl aminopeptidase;Leucyl-cystinyl aminopeptidase, pregnancy serum form" 0 ; 148.56 3.58E-07 270120000 403370 355070 262790 311020 369130 396420 312170 403290 387150 FALSE TRUE 350063.6325 352737.5218 389876.123 381641.8446 361785.0352 411670.5339 281895.8014 317049.5719 341381.568 1.025432142 1.033264695 1.142053817 1.117933364 1.059767337 1.205895609 0.825749917 0.928724927 1 18.38102564 2.234783793 24.99999886 0.916509321 1.095730004 0.614621436 0.066890977 62.41562308 413141.3126 0.026365706 0.018546301 171.7053366 -2.234783793 0.179220683 EPDCFKDIVNMLMHHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EPDCFKDIVNMLMHHDR 17 1 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ; 212.9 7.43E-13 657980000 1658000 1314630 697040 689210 1182760 1057050 1515600 1694570 259581 FALSE TRUE 1438891.099 1305994.109 1034130.875 845705.6644 1159225.39 1097715.398 1368617.345 1332199.393 228893.6299 6.286287215 5.705681323 4.517953933 3.694754043 5.064472046 4.795744635 5.979272319 5.820168055 1 17.80431779 4.371578924 3.706493814 4.632311043 6.177745232 0.174097658 1.396746361 0.433703018 10.98470811 0.353834646 1.117938681 23527.6702 -4.371578924 1.545434189 EPDPDS(ph)DWEPEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EPDPDSDWEPEER 13 0 Q9NPE2-3;Q9NPE2 Q9NPE2-3 NGRN Neugrin 1 EPDPDS(1)DWEPEER;EPDPDS(1)DWEPEER 162.94 4.15E-05 359150000 194147 248730 175262 233190 252750 250020 239010 296360 283730 TRUE FALSE 168489.982 247096.0763 260019.2894 286139.3536 247720.7695 259638.4312 215830.847 232985.7203 250187.7626 0.67345413 0.987642536 1.039296593 1.143698439 0.990139433 1.037774304 0.862675475 0.93124347 1 17.9326517 4.738073371 6.695077434 0.994446548 0.667802854 0.664232051 0.072704915 0.078917508 23.67970157 0.01979654 0.117438934 54710.83847 -4.738073371 -0.326643694 EPEAAS(ph)SRGSPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPEAASSRGSPVR 13 1 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EPEAAS(0.516)S(0.092)RGS(0.393)PVR 83.087 0.011507 0 166570 149550 56771 52910 122540 116940 144120 143190 49898 TRUE FALSE 144557.3525 148567.5962 84225.64549 64924.02418 120101.6937 121438.7575 130143.2646 112569.9328 43999.11528 3.285460436 3.376604171 1.914257706 1.475575674 2.729638834 2.760027257 2.957860942 2.558459007 1 15.42518689 4.249818694 24.82602127 2.285201397 3.331033049 0.363414679 0.614556279 240.0723457 529390.0188 0.159347974 0.413257008 17775.37184 -4.249818694 1.045831652 EPEAASSRGS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPEAASSRGSPVR 13 1 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EPEAAS(0.001)S(0.008)RGS(0.99)PVR 107.34 0.00078906 673650000 1200700 1001800 290870 262520 844910 837830 1005900 991860 30956 TRUE FALSE 1042024.453 995219.1098 431535.7049 322129.1784 828097.944 870061.8622 908347.9728 779758.4577 27296.41695 38.17440417 36.45969769 15.8092436 11.80115247 30.33723971 31.87458134 33.27718706 28.56633012 1 14.73642397 8 0.062971637 7.08E-11 79.52121277 0.147987564 11.07636294 2176.75638 13.25186083 4043.307854 17044.78253 99999999.99 -8 79.52121277 EPEDEEEEEEEEEEDEDEDLEELEVLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EPEDEEEEEEEEEEDEDEDLEELEVLER 28 0 Q9NQC3-5;Q9NQC3;Q9NQC3-4;Q9NQC3-2;F8W914 Q9NQC3-5;Q9NQC3-2 RTN4 Reticulon-4;Reticulon 0 ; 142.21 1.20E-07 104024000 142761 89217 74742 117675 110279 107668 62625 130121 163813 FALSE TRUE 123894.7721 88630.92765 110887.4812 144394.9073 108084.6637 111810.0576 56551.63714 102295.6368 144447.2138 0.857716594 0.613586966 0.767667844 0.999637885 0.748264095 0.774054789 0.391503828 0.708186985 1 17.14018285 2.448326203 24.9990481 0.673632241 0.793191864 0.055523106 0.172889716 530.2140167 460313.5689 0.065165315 0.050477619 280.7541622 -2.448326203 0.119559624 EPEDEGEDDD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPEDEGEDDD 10 0 P39687 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 211.39 1.39E-07 157590000 288790 267870 194680 228950 225910 260980 265860 293840 324560 FALSE TRUE 250625.6698 266110.3443 288827.8992 280936.5968 221414.833 271020.0695 240076.9381 231004.6027 286190.8865 0.875729038 0.929835144 1.009214174 0.981640611 0.773661369 0.946990565 0.838869962 0.807169667 1 18.12661821 3.271008034 24.99880056 0.866164595 0.952021895 0.207226372 0.072792028 273.9883746 211089.9351 0.020516127 0.026484066 1866.414218 -3.271008034 0.085857301 EPELGLEELLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPELGLEELLR 11 0 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 0 82.749 0.042076 18441000 19180 15177 12259 12500 14795 15141 16038 18214 28043 FALSE TRUE 16645.3144 15077.30129 18187.4934 15338.31605 14500.60845 15723.48407 14482.63723 14319.07784 24727.78849 0.673142057 0.609731084 0.735508289 0.620286608 0.586409434 0.635862931 0.585682672 0.579068276 1 14.5938456 1.234243893 24.9999982 1.000000552 0.625374951 0.859768351 0.047175552 47.34585074 274163.6394 0.091328447 0.011958115 17.14920108 -1.234243893 -0.374625601 EPEQLR ddPTM_MDA-MB-175_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 ; 130.05 0.037058 2214700000 923280 873670 767450 939040 812870 818980 813070 1022990 2190660 FALSE TRUE 801266.2087 867930.8042 1138591.387 1152263.384 796695.4774 850486.6906 734218.5965 804231.5494 1931682.67 0.414802193 0.449313346 0.589429829 0.596507595 0.412436002 0.440282818 0.380092759 0.416337301 1 20.88142668 1.235611351 24.9866049 1.000000734 0.461881859 0.841350285 0.073365339 34.30258421 290562.2137 0.135324573 0.019833805 17.20328368 -1.235611351 -0.538118875 EPEQLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 92.47 0.025087 2259200000 3016700 2491000 2111600 2575000 2333700 2117500 2544300 3180300 3563100 FALSE TRUE 2618035.452 2474636.457 3132776.823 3159693.106 2287263.936 2198961.595 2297554.178 2500217.594 3141874.377 0.833271843 0.787630618 0.997104418 1.005671369 0.72799344 0.699888452 0.731268632 0.795772617 1 21.58319407 3.224322475 24.98635009 0.782549619 0.903983578 0.229249898 0.104055863 354.2400508 621650.2161 0.033119288 0.037726179 1676.187028 -3.224322475 0.121433959 EPFFHGHDNYDQLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EPFFHGHDNYDQLVR 15 0 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2 P68400 CSNK2A1 Casein kinase II subunit alpha 0 ;; 242.41 3.66E-18 942810000 414529 340492 258654 331815 346009 359402 277455 371923 565718 FALSE TRUE 359747.9424 338255.2856 383739.9395 407158.6672 339124.0979 373228.4275 250547.4568 292390.1608 498839.4625 0.721169774 0.678084456 0.769265402 0.816211823 0.679826123 0.748193468 0.502260698 0.586140798 1 18.92821607 EPFGTEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPFGTEGR 8 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 107.29 0.0093769 770230000 564550 573190 410990 521750 534340 586700 536550 598390 888650 FALSE TRUE 489943.2871 569424.6771 609746.1387 640221.3119 523707.6794 609270.7286 484515.4636 470428.9552 783594.8094 0.625250807 0.726682554 0.778139584 0.817031078 0.668339904 0.77753288 0.618323983 0.600347207 1 19.57974832 3.310745771 0.007741228 1.441052892 7.62E-07 0.022934752 0.118306735 52133.54207 425.9486534 39421.88349 39861.45763 2045.247034 -3.310745771 -1.44105213 EPFHSILSVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPFHSILSVLK 11 0 Q8NCW5-2;Q8NCW5;Q5T3I4 Q8NCW5-2 APOA1BP NAD(P)H-hydrate epimerase 0 126.67 0.00030261 524950000 1032200 1059500 622180 864430 1045600 908470 1083300 1278100 1327700 FALSE TRUE 895792.1547 1052540.075 923068.3291 1060712.043 1024794.606 943419.4288 978241.7327 1004788.261 1170740.819 0.765149844 0.89903765 0.788448062 0.906017819 0.87533858 0.805831157 0.835574977 0.85824996 1 20.15899029 1.23208672 3.864143383 1.020042008 0.842638739 0.547167859 0.045486986 0.1970683 4.860791404 0.101262197 0.010658759 17.06423093 -1.23208672 -0.17740327 EPGFEAGPEAS(ph)DDDLWTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPGFEAGPEASDDDLWTR 18 0 H9KVB4;O15417;O15417-2;H7C177 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 EPGFEAGPEAS(1)DDDLWTR 329.6 2.10E-52 0 67761 63346 41742 51248 64530 62102 65026 75927 89729 TRUE FALSE 58806.21217 62929.87596 61928.57082 62884.64168 63245.97925 64491.10413 58719.78853 59690.60191 79121.33984 0.743240854 0.795359079 0.782703768 0.794787371 0.79935425 0.815091153 0.742148561 0.754418492 1 16.27177924 1.234760155 24.99950127 1.000000317 0.778545517 0.888367939 0.024688396 36.66911824 241174.2634 0.046834527 0.006402842 17.16959912 -1.234760155 -0.2214548 EPHSFQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPHSFQSR 8 0 F8VR84;Q9HB07;F8VQQ3;H3BPH3 F8VR84 C12orf10 "UPF0160 protein MYG1, mitochondrial" 0 81.95 0.025051 0 29227 34265 19819 24996 29695 35562 36685 40087 28874 FALSE TRUE 25364.5779 34039.91096 29403.53469 30671.72384 29104.1276 36930.09315 33127.29435 31514.70701 25460.54861 0.996230611 1.336966908 1.154866501 1.20467647 1.143106853 1.450483009 1.301122566 1.237785858 1 14.63597589 4.755476366 23.82751821 1.233947053 0.996230246 0.265590292 0.121161909 2514.137222 3541301.454 0.029094667 0.763738081 56947.72322 -4.755476366 -0.237716807 EPLGPALAHELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EPLGPALAHELR 12 0 Q13228;Q13228-4;Q13228-2;Q13228-3 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 153.75 6.79E-05 257510000 170386 173598 118049 158695 170611 171154 148867 183191 359610 FALSE TRUE 147869.0584 172457.6233 175137.8913 194729.1253 167216.1749 177738.4051 134429.9013 144017.0302 317097.3155 0.466320751 0.543863397 0.552315907 0.61409894 0.527333934 0.560516903 0.423938945 0.454172972 1 18.27456614 1.234017965 24.9992344 1.000000723 0.516968179 0.878528554 0.056346181 50.1862326 276150.9335 0.119337549 0.015324863 17.14028209 -1.234017965 -0.483032543 EPLIPAS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EPLIPASPK 9 0 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 EPLIPAS(1)PK;EPLIPAS(1)PK;EPLIPAS(1)PK;EPLIPAS(1)PK 97.214 0.0071775 1022770000 1738000 1954720 1752440 1754950 2965060 2269750 3045160 3413500 3162230 TRUE FALSE 1508318.896 1941879.316 2599925.846 2153438.22 2906061.107 2357068.751 2749840.852 2683549.589 2788394.772 0.540927315 0.696414774 0.932409525 0.772285991 1.042198593 0.845313861 0.986173436 0.962399448 1 21.4110034 5.151927532 0.697155888 0.963666222 4.68E-16 0.762505327 0.076324887 2.2154174 0.553625096 0.02956551 1.914747157 141882.0751 -5.151927532 -0.963666222 EPLPVEQDDDIEVIVDETSDHTEET(ph)SPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPLPVEQDDDIEVIVDETSDHTEETSPVR 29 0 Q676U5-3;Q676U5;E7EVC7;Q676U5-2;Q676U5-4;Q676U5-5;C9J1B2;C9JAY7;C9JK97 Q676U5-3 ATG16L1 Autophagy-related protein 16-1 1 EPLPVEQDDDIEVIVDETSDHTEET(0.581)S(0.419)PVR 168.31 1.30E-11 63652000 23885 25319 17131 26250 26018 28060 26323 30580 47689 TRUE FALSE 20728.53673 25152.67782 25415.6089 32210.46371 25500.2927 29139.48636 23770.19951 24040.70497 42051.26075 0.492934965 0.598143251 0.604395884 0.765980927 0.606409707 0.692951551 0.565267226 0.571699981 1 15.35986143 1.23467868 24.99990417 1.000000554 0.614583818 0.733395514 0.073464361 61.32679844 394890.7452 0.133634117 0.018151902 17.16637834 -1.23467868 -0.385416735 EPNEDCKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 90.108 0.010628 445125000 889460 785070 557753 715980 747970 866940 667790 850650 874080 FALSE TRUE 771915.6074 779912.8235 827484.2164 878554.2021 733086.8604 900291.7428 603027.8286 668745.1173 770747.2582 1.001515866 1.011891791 1.073612923 1.139873276 0.951137812 1.168076478 0.782393738 0.86765812 1 19.55589833 2.234792477 24.99999933 0.875874818 1.05522001 0.502203219 0.081682991 73.80923864 489684.3648 0.031249792 0.021981954 171.7087701 -2.234792477 0.179345192 EPPAAAPSAGGAAPCS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPPAAAPSAGGAAPCSPR 18 0 A6NEL2 A6NEL2 SOWAHB Ankyrin repeat domain-containing protein SOWAHB 1 EPPAAAPSAGGAAPCS(1)PR 98.889 0.0011654 0 54075 53683 37628 40179 54963 56853 54441 59859 55224 TRUE FALSE 46928.85174 53330.35284 55825.02666 49302.25605 53869.34383 59040.1717 49161.3202 47058.61867 48695.48163 0.963720866 1.095180724 1.146410812 1.01246059 1.106249328 1.212436344 1.009566361 0.966385732 1 15.57150029 2.019494442 24.99701256 0.982947064 1.091320024 0.321436372 0.067500932 248.8850894 319134.9871 0.027242481 0.018364376 104.5910306 -2.019494442 0.10837296 EPPKPEQVESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPPKPEQVESR 11 1 O60664-4;O60664;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 0 104.17 0.002074 0 256730 241460 222280 264830 211940 218890 252200 279960 656410 FALSE TRUE 222802.48 239873.8334 329775.3515 324963.6992 207722.8087 227310.8399 227741.6828 220092.7327 578809.9576 0.384932009 0.414425893 0.569747198 0.561434189 0.358879121 0.392721025 0.393465385 0.380250425 1 19.14273022 1.235381495 24.98425705 1.000000787 0.432042067 0.853304499 0.074015209 35.25737702 277034.1055 0.137110758 0.019719595 17.19418105 -1.235381495 -0.56795872 EPPLSLTIHLTSPVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EPPLSLTIHLTSPVVR 16 0 Q12906;Q12906-5;Q12906-2;Q12906-3;K7EKJ9;K7EKY0;K7EQR9;K7EPG3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ; 177.84 2.88E-09 494170000 348670 303370 169474 218064 299500 316770 316260 361890 296710 FALSE TRUE 302592.3761 301377.1425 251432.1933 267578.7641 293540.536 328956.3469 285589.1539 284502.6397 261633.2818 1.156551544 1.151906747 0.961009974 1.022724488 1.12195411 1.257318429 1.091562786 1.087409972 1 17.99718655 KTST(ph)SPPPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KTSTSPPPEK 10 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KT(0.007)S(0.07)T(0.54)S(0.382)PPPEK;KT(0.053)S(0.116)T(0.415)S(0.415)PPPEK 105.03 0.0050351 606521000 1425840 1014830 958580 1334970 929574 701835 1378970 1718570 3276160 TRUE FALSE 1237411.631 1008163.515 1422152.494 1638095.342 911077.2961 728835.0466 1245237.702 1351067.179 2888856.097 0.428339658 0.34898364 0.492289144 0.56703944 0.31537649 0.252291918 0.431048713 0.467682409 1 21.46206691 1.209988838 3.21577964 1.127159812 0.405045111 0.815150446 0.088278132 0.176057471 2.306845715 0.3358367 0.024160032 16.21768415 -1.209988838 -0.722114701 EPQLAFHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EPQLAFHQR 9 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;;; 134.23 0.0002548 1595870000 1753480 1633350 1225270 1348900 1561490 1584340 1631050 1799740 1747760 FALSE TRUE 1521753.175 1622620.416 1817814.67 1655188.362 1530419.404 1645290.585 1472871.022 1414879.607 1541141.804 0.987419309 1.052868991 1.1795246 1.074001339 0.993042561 1.067578974 0.955701168 0.918072304 1 20.55556818 2.224558077 7.457635163 0.949084492 1.062042316 0.419039747 0.05575758 0.135770589 38.56482177 0.023294509 0.016304887 167.7096596 -2.224558077 0.112957824 EPRPNS(ph)SPSPSPGQASETPHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPRPNSSPSPSPGQASETPHPR 22 1 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 1 EPRPNS(0.493)S(0.493)PS(0.014)PSPGQASETPHPR 172.32 3.04E-12 212380000 72281 61080 39355 59904 91241 77801 64072 80161 149360 TRUE FALSE 62728.88271 60678.76146 58387.20963 73506.11878 89425.48261 80794.05481 57858.3073 63019.19396 131702.831 0.476291073 0.460724808 0.443325396 0.558121023 0.678994384 0.613457237 0.439309519 0.478495363 1 17.00692683 1.235702934 24.99996358 1.000000648 0.518046435 0.789305135 0.078166328 39.81385487 348238.6396 0.143874054 0.021228665 17.20691187 -1.235702934 -0.481954213 EPRPNS(ph)SPSPSPGQASETPHPRPS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPRPNSSPSPSPGQASETPHPRPS 24 2 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 1 EPRPNS(0.493)S(0.493)PS(0.014)PSPGQASETPHPRPS 125.52 5.13E-05 49383000 20666 22156 10970 14699 20883 20448 23677 24864 19445 TRUE FALSE 17934.93574 22010.45578 16275.12869 18036.63261 20467.46916 21234.64779 21380.80818 19547.02709 17146.23425 1.045998525 1.283690369 0.949195517 1.051929674 1.193700544 1.238443817 1.24696816 1.140018666 1 14.06560414 3.233216876 24.99810793 1.170816819 1.087523437 0.123251119 0.106265045 288.7588747 1350814.538 0.032251101 0.037618172 1710.869466 -3.233216876 -0.083293383 EPRPNSS(ph)PSPSPGQASETPHPRPS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EPRPNSSPSPSPGQASETPHPRPS 24 2 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 1 EPRPNS(0.319)S(0.394)PS(0.282)PS(0.004)PGQASETPHPRPS;EPRPNS(0.312)S(0.487)PS(0.201)PSPGQASETPHPRPS 210.8 1.96E-25 330210000 81128 77099 43237 55461 75185 86535 72571 81342 67164 TRUE FALSE 70406.72925 76592.53159 64146.55782 68054.26772 73688.9656 89864.05745 65533.07559 63947.6463 59223.94843 1.18882194 1.293269591 1.083118561 1.149100482 1.244242702 1.517360119 1.106529999 1.079759928 1 15.85389306 2.018578898 24.99897939 1.059847324 1.24255674 0.369230288 0.115041915 265.900349 357782.929 0.048747937 0.032860596 104.3707725 -2.018578898 0.182709416 EPRPNSSPS(ph)PSPGQASETPHPRPS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 EPRPNSSPSPSPGQASETPHPRPS 24 2 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 1 EPRPNS(0.007)S(0.079)PS(0.912)PS(0.002)PGQASETPHPRPS;EPRPNS(0.005)S(0.055)PS(0.935)PS(0.005)PGQASETPHPRPS;EPRPNS(0.001)S(0.016)PS(0.949)PS(0.033)PGQASETPHPRPS;EPRPNSS(0.002)PS(0.997)PS(0.001)PGQASETPHPRPS;EPRPNS(0.016)S(0.061)PS(0.921)PS(0.001)PGQASETPHPRPS;EPRPNS(0.001)S(0.001)PS(0.997)PS(0.001)PGQASETPHPRPS;EPRPNS(0.086)S(0.086)PS(0.822)PS(0.005)PGQASETPHPRPS 270.46 3.65E-52 12558290000 1169743 1243644 516698 818563 1316375 1359371 1140014 1359030 952565 TRUE FALSE 1015158.499 1235474.421 766574.8811 1004430.24 1290181.713 1411666.882 1029455.618 1068412.01 839953.8509 1.208588422 1.470883691 0.912639284 1.195815983 1.536014998 1.680648146 1.225609736 1.271988942 1 19.67995054 1.129076169 2.020012523 0.823479693 1.324697437 0.180449834 0.211455582 2.051086751 6.37632376 2.141896871 0.060085584 13.46096419 -1.129076169 0.501217744 EPRPNSSPSPSPGQASETPHPRPS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EPRPNSSPSPSPGQASETPHPRPS 24 2 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 ; 160.67 1.14E-11 395060000 159847 143073 69079 84193 155812 145812 149043 168068 96133 FALSE TRUE 138722.8139 142133.144 102485.8355 103310.3075 152711.646 151421.482 134588.8328 132127.9661 84768.26626 1.636494647 1.676725859 1.209011815 1.218738002 1.801519045 1.78629915 1.587726619 1.558696101 1 16.37123666 1.238476497 23.48180338 0.999999398 1.557423838 0.42947658 0.202613605 1.006412961 277082.5751 0.295443602 0.052818853 17.31715313 -1.238476497 0.55742444 EPS(ph)PALGPNLDGSGLLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 211.26 3.38E-16 1258463000 165958 158612 158294 169770 194860 201917 185120 241920 336859 TRUE FALSE 144026.2298 157570.0673 234845.5079 208318.8733 190982.6672 209684.8776 167167.0909 190187.2906 297035.9128 0.48487817 0.530474803 0.790630014 0.701325545 0.642961538 0.70592433 0.562784107 0.640283826 1 18.18027784 -1.999999959 0.048836944 1.821524233 5.30E-07 0.296430731 0.122664644 2052.016242 9.807939703 318.5904294 104.023911 0.010000001 1.999999959 -1.821523704 EPS(ph)PALGPNLDGSGLLPRPIFYCSFPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EPSPALGPNLDGSGLLPRPIFYCSFPTR 28 1 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 1 EPS(1)PALGPNLDGSGLLPRPIFYCSFPTR;EPS(1)PALGPNLDGSGLLPRPIFYCSFPTR 51.9 0.057169 157240000 36062 32685 17516 20553.8 42640 30180 31255 40822 15324.1 TRUE FALSE 31296.31533 32470.29008 25986.79619 25220.85444 41791.54742 31341.04413 28223.89491 32092.53298 13512.50236 2.316100638 2.402981271 1.92316682 1.866482889 3.092805931 2.319410817 2.088724514 2.375025153 1 13.72200725 1.236423679 24.99796593 0.999998338 2.29545526 0.594872677 0.33665267 41.00159595 479518.4876 0.526629138 0.082158371 17.23549175 -1.236423679 1.295456922 EPS(ph)PEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EPSPEK 6 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 EPS(1)PEK;EPS(1)PEK;EPS(1)PEK;EPS(1)PEK 98.933 0.041299 7806600000 17156700 12651890 12307350 13806980 8286500 10097310 15324500 18200700 31090700 TRUE FALSE 14889398.63 12568778.9 18259225.63 16942065.84 8121614.862 10485760.05 13838332.35 14308621.94 27415192.86 0.543107564 0.458460349 0.666025795 0.61798091 0.296245038 0.382479894 0.50476874 0.521923082 1 24.70847229 1.234145861 4.793315597 1.038309799 0.495132674 0.690402386 0.105590636 0.117585191 6.328569149 0.216472598 0.028148745 17.14533048 -1.234145861 -0.543177125 EPS(ph)PEKNSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 102.73 0.002142 3365650000 7981000 5147620 3185750 2959470 3767030 3413900 7585300 8305200 657810 TRUE FALSE 6926290.629 5113804.945 4726389.356 3631462.896 3692073.473 3545234.942 6849678.773 6529197.611 580044.4512 11.94096524 8.816229403 8.148322678 6.260663107 6.365156094 6.112005614 11.80888596 11.25637457 1 19.14580394 4.747767393 2.10687897 7.765917614 13.15349814 0.182851869 3.006936014 1.45153578 7.033834491 0.812434604 15.00127388 55945.78768 -4.747767393 5.387580525 EPS(ph)PLPELALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EPSPLPELALR 11 0 Q13207 Q13207 TBX2 T-box transcription factor TBX2 1 EPS(1)PLPELALR;EPS(1)PLPELALR 135.5 0.00012451 58860000 84135 66199 61763 75091 77802 87210 93703 106514 121001 TRUE FALSE 73016.34658 65764.13441 91631.79338 92141.55924 76253.89242 90565.02513 84615.69748 83736.80999 106696.3996 0.684337493 0.61636695 0.858808673 0.863586396 0.714681027 0.848810508 0.793051104 0.78481383 1 16.70315197 6.122936716 0.450531887 0.847194675 2.62E-14 0.372769468 0.085299114 20.92551269 1.301591165 0.068369012 12.23905497 1327201.049 -6.122936716 -0.847194675 EPSEVPT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EPSEVPTPK 9 0 P17096;P17096-3;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 1 EPSEVPT(1)PK;EPS(0.001)EVPT(0.999)PK;EPSEVPT(1)PK 119.27 0.0095435 1443850000 2097870 2147050 1906640 2134940 2070600 1558760 2118750 2578460 4647400 TRUE FALSE 1820631.164 2132945.887 2828697.481 2619710.758 2029399.111 1618726.506 1913273.951 2027076.395 4097989.666 0.44427422 0.520485912 0.690264669 0.639267292 0.495218211 0.395005024 0.466881107 0.494651417 1 21.96648492 1.236770073 24.99903898 1.000000601 0.519396333 0.750334605 0.087329209 26.0980143 364265.6702 0.147569831 0.023571387 17.24924429 -1.236770073 -0.480604268 EPSTAS(ph)GGGQLNR ddPTM_MDA-MB-175_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(0.245)AS(0.753)GGGQLNR 127.07 0.00019007 242780000 155610 143560 115020 176850 146760 203170 84594 127560 322820 TRUE FALSE 135045.7442 142616.9449 170644.0567 217006.4955 143839.7631 210986.0814 76390.0869 100282.2867 284656.5874 0.474416368 0.501014033 0.599473416 0.762344892 0.5053098 0.741195148 0.268358753 0.352292169 1 18.11886296 4.366360117 5.392618327 0.570456083 0.481094442 0.032830721 0.209372019 0.96703078 40.82898492 0.053668375 0.148805782 23246.63607 -4.366360117 -0.089361642 EPSVPASCAVSATYERS(ph)PS(ph)PAHLPDDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EPSVPASCAVSATYERSPSPAHLPDDPK 28 1 Q92615;H0Y4V9;H0Y641 Q92615 LARP4B La-related protein 4B 2 EPSVPASCAVSATYERS(1)PS(1)PAHLPDDPK;EPS(0.005)VPAS(0.026)CAVS(0.064)AT(0.063)Y(0.018)ERS(0.857)PS(0.967)PAHLPDDPK 191.72 4.92E-18 505610000 368510 317350 270310 267690 311480 255451 371770 422160 319380 TRUE FALSE 319810.4698 315265.307 401032.8201 328473.1059 305282.1574 265278.3653 335715.8026 331884.3693 281623.2602 1.135596788 1.119457628 1.424004607 1.166356449 1.084009031 0.941961843 1.192074129 1.17846931 1 18.10340697 3.473087952 13.0240737 1.096169837 1.22890752 0.270496414 0.109492037 0.492918106 1553.044882 0.032338729 0.042647258 2972.267906 -3.473087952 0.132737683 EPTEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EPTEEER 7 0 Q15056;Q15056-2 Q15056;Q15056-2;REV__B4E135 EIF4H Eukaryotic translation initiation factor 4H 0 ;;; 158.36 0.003312 2220680000 2412330 2176840 1664400 2002920 1797500 2046900 2052800 2426300 3118280 FALSE TRUE 2093534.478 2162540.195 2469309.407 2457713.599 1761733.267 2125645.568 1853719.772 1907454.626 2749640.491 0.761384801 0.78648107 0.898048096 0.893830887 0.64071404 0.773063088 0.674168051 0.693710553 1 21.39081157 4.747824633 19.37541369 0.782225995 0.761384555 0 0.112019408 743.9764696 1555099.087 0.027720202 0.275369032 55953.16187 -4.747824633 -0.02084144 EPTGVEENKTDSLFVLPSRDDAT(ph)PVRDEPMDAESITFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EPTGVEENKTDSLFVLPSRDDATPVRDEPMDAESITFK 38 3 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 EPTGVEENKTDSLFVLPS(0.05)RDDAT(0.95)PVRDEPMDAESITFK;EPTGVEENKT(0.003)DS(0.011)LFVLPS(0.264)RDDAT(0.721)PVRDEPMDAES(0.001)ITFK 101.55 1.96E-05 326418000 286086 198237 140160 158160 198320 170715 247768 268995 162610 TRUE FALSE 248279.0103 196934.7681 207941.8448 194072.6453 194373.82 177282.5165 223739.4975 211472.5126 143386.431 1.731537695 1.373454703 1.450219824 1.353493799 1.35559424 1.236396744 1.560395191 1.474843268 1 17.12954898 7.068294691 1.291384853 1.361606767 175.4010963 0.378113865 0.15212571 830.3139702 3.863019925 0.042888492 425726.4792 11702932.26 -7.068294691 174.0394895 EPTPSIAS(ph)DIS(ph)LPIATQELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EPTPSIASDISLPIATQELR 20 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5 A0A499FIX8 ESYT2 Extended synaptotagmin-2 2 EPTPS(0.015)IAS(0.986)DIS(0.999)LPIATQELR;EPT(0.001)PS(0.096)IAS(0.906)DIS(0.998)LPIATQELR;EPTPS(0.01)IAS(0.991)DIS(0.999)LPIATQELR 78.661 0.012459 35663000 85262 96889 62664 80188 118881 108042 68089 112776 128445 TRUE FALSE 73994.41067 96252.52978 92968.52 98395.911 116515.5007 112198.4457 61485.73926 88659.73002 113260.3784 0.653312409 0.849834082 0.820838861 0.868758452 1.028740168 0.990623969 0.542870685 0.782795637 1 16.78928373 7.410475047 8.982640113 0.831760917 0.045681369 0 0.153426228 0 0 0.035186621 0 25732089.11 -7.410475047 -0.786079548 EPTPSIAS(ph)DISLPIATQELR ddPTM_MDA-MB-175_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;EPTPS(0.001)IAS(0.999)DISLPIATQELR 244.1 7.45E-30 767750000 237453 234878 149323 230878 325003 338745 180647 349008 285947 TRUE FALSE 206072.9844 233335.071 221536.1023 283302.3786 318536.0762 351776.7393 163127.8817 274375.3552 252142.6714 0.817287226 0.925408895 0.878614084 1.123579666 1.263316813 1.395149569 0.64696658 1.088175015 1 17.94388077 3.74694737 23.15668918 1.079204864 0.878933893 0.21162186 0.192882102 408.5454773 1128025.348 0.053313691 0.090195844 5584.025209 -3.74694737 -0.20027097 EPTPSIASDIS(ph)LPIATQELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EPTPSIASDISLPIATQELR 20 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5 A0A499FIX8 ESYT2 Extended synaptotagmin-2 1 EPTPSIASDIS(1)LPIATQELR;EPTPSIASDIS(1)LPIATQELR 280.32 1.10E-44 85179000 67549 73656 49478 69138 78652 81371 51328 89247 88157 TRUE FALSE 58622.2285 73172.14889 73405.72629 84836.83961 77086.97908 84501.39502 46350.21846 70162.22357 77735.17989 0.754127392 0.941300309 0.944305093 1.091357089 0.991661423 1.087041866 0.596257943 0.902580063 1 16.24628003 1.233918468 23.55722375 1.000000263 0.913431757 0.032802404 0.147475974 326.6565889 1657216.235 0.281824408 0.036760457 17.1363557 -1.233918468 -0.086568505 EPVS(ph)PMELTGPEDGAASSGAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPVSPMELTGPEDGAASSGAGR 22 0 A0A0C4DFL8;F5GX28;O94953;K7EQ54 A0A0C4DFL8 KDM4B Lysine-specific demethylase 4B 1 EPVS(1)PMELTGPEDGAASSGAGR 190.57 3.00E-24 0 56879 47761 39498 49554 43233 54380 48065 50227 102840 TRUE FALSE 49362.29604 47447.25485 58599.36491 60805.99309 42372.74788 56472.03379 43403.6637 39486.34692 90682.37236 0.544342795 0.523224675 0.646204586 0.670538182 0.467265542 0.622745439 0.478633968 0.435435751 1 16.46853451 1.229942374 24.99539195 1.000000857 0.545820492 0.767273789 0.078124855 170.0271847 493089.6225 0.233691008 0.02042814 16.98018331 -1.229942374 -0.454180365 EPWLLPSQHNDIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EPWLLPSQHNDIIR 14 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 148.7 7.69E-06 342100000 574950 553030 240260 425030 602160 762430 452080 479290 558720 FALSE TRUE 498968.9008 549397.1095 356450.5396 521539.5577 590178.1941 791761.1755 408237.3512 376797.5633 492668.7581 1.012787786 1.115145015 0.723509526 1.058600833 1.197920884 1.607086227 0.828624394 0.764809128 1 18.91025846 EPWMILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPWMILR 7 0 Q86YE8;K7EQQ2;K7EM14;A0A0A0MRV5 Q86YE8 ZNF573 Zinc finger protein 573 0 106.84 0.027051 265390000 15691 12936 11340 12234 14966 14644 12314 13768 18102 FALSE TRUE 13617.39459 12851.02256 16824.06193 15011.91668 14668.20588 15207.36416 11119.79018 10823.82034 15962.00218 0.85311319 0.805100915 1.054006994 0.940478301 0.918945237 0.952722847 0.696641314 0.678099164 1 13.96235401 2.246823694 24.99701378 0.763982496 0.92234701 0.228684367 0.107884919 211.6796473 640363.2566 0.040934577 0.031161707 176.5321027 -2.246823694 0.158364514 EPYGHLGPAELLEAS(ph)PAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EPYGHLGPAELLEASPAAR 19 0 Q9H6W3 Q9H6W3 NO66 Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66 1 EPYGHLGPAELLEAS(1)PAAR 155.97 1.33E-08 74079000 47142 42200 32195 29961 34173 42778 32412 38247 40248 TRUE FALSE 40912.06526 41922.78542 47764.60969 36764.10298 33493.02416 44423.69734 29268.68923 30068.17669 35489.92729 1.15277963 1.181258701 1.345863836 1.03590246 0.943733243 1.251726919 0.824704119 0.847231285 1 15.115122 2.798905817 0.724469654 0.871711966 1.218815832 0.413978504 0.13009219 0.676130539 0.897583938 0.139103479 0.105521707 629.3696799 -2.798905817 0.347103866 EQAAEHYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQAAEHYK 8 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 87.308 0.015416 673540000 1586470 1544930 1081830 1292550 1360060 1335260 1616400 2093680 1801520 FALSE TRUE 1376813.97 1534781.253 1605006.607 1586043.233 1332997.467 1386628.316 1459641.777 1645962.825 1588546.358 0.86671312 0.966154526 1.010361831 0.998424267 0.839130354 0.872891313 0.918853749 1.03614403 1 20.59927576 1.748769525 8.889647385 1.016697836 0.927079246 0.320705514 0.05638689 0.143048027 47.17625156 0.033964437 0.015720499 56.07503139 -1.748769525 -0.089618589 EQAEAEVASLNR ddPTM_MDA-MB-175_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 ; 219.92 7.17E-11 1190330000 766640 724620 448730 632230 706530 670210 611870 777590 972630 FALSE TRUE 665326.5816 719859.9235 665737.3289 775787.4845 692471.4353 695993.4124 552530.9416 611308.4297 857646.7894 0.775758261 0.83934311 0.776237184 0.904553593 0.807408649 0.811515208 0.644240669 0.712774113 1 19.71002409 2.449976396 24.99985729 0.759346851 0.822448085 0.002519704 0.09712576 573.403291 528089.0377 0.035848611 0.027768901 281.8229754 -2.449976396 0.063101235 EQAEAEVASLNRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EQAEAEVASLNRR 13 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;P06753-3;P06753-4 P06753-2;P06753-3 TPM3 Tropomyosin alpha-3 chain 0 ;; 210.14 5.18E-08 2386570000 2064340 1896120 785000 826360 1698110 1768430 1816740 2006630 274759 FALSE TRUE 1791532.239 1883664.263 1164628.626 1013997.668 1664320.933 1836462.646 1640552.834 1577527.79 242277.304 7.394552477 7.77482757 4.807006708 4.185277165 6.86948759 7.580002815 6.77138472 6.511248738 1 17.88629974 4.250841833 24.92419248 5.651542489 7.584691199 0.180906091 1.878764998 419.4128358 851163.5289 0.47164909 1.228230895 17817.29755 -4.250841833 1.93314871 EQAEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQAEEER 7 0 Q9UII2;A0A0B4J230;Q9UII2-3;Q9UII2-2 Q9UII2 ATPIF1 "ATPase inhibitor, mitochondrial" 0 ; 163.67 0.0028529 859090000 1206660 1242120 901960 1444290 853050 1488120 1095200 1396070 1470930 FALSE TRUE 1047196.824 1233960.432 1338150.873 1772238.119 836075.974 1545368.939 988987.6726 1097531.295 1297038.331 0.807375386 0.951367745 1.031697245 1.366372972 0.644603906 1.19145973 0.762496874 0.846182621 1 20.30678969 2.209394937 24.99871954 0.860228697 0.998758112 0.082858674 0.201919392 508.3924221 435753.7909 0.078932156 0.053225751 161.9552152 -2.209394937 0.138529415 EQAIGEYEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQAIGEYEDLR 11 0 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 ; 129.89 0.0005481 541030000 268700 242970 205130 258610 253140 258460 240390 303200 604140 FALSE TRUE 233190.6142 241373.9141 304331.5541 317331.3531 248103.0093 268403.1234 217077.0148 238363.0395 532719.2574 0.437736408 0.453097782 0.571279431 0.595682151 0.46572938 0.503835969 0.407488582 0.447445885 1 19.02301591 1.236024994 24.99982384 1.000000678 0.484966013 0.88337231 0.05877543 23.94557056 236039.7636 0.103567339 0.015678787 17.21967674 -1.236024994 -0.515034664 EQALQEAMEQLEQLELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQALQEAMEQLEQLELER 18 0 Q9UH65;E7EMB1 Q9UH65 SWAP70 Switch-associated protein 70 0 ; 159.31 1.01E-10 39110000 30384 33449 19261 22970 26895 26228 22824 30214 34496 FALSE TRUE 26368.67742 33229.27132 28575.68402 28185.68957 26359.84212 27237.00813 20610.53199 23752.97123 30417.92218 0.86687964 1.092424102 0.939435766 0.92661456 0.866589176 0.89542632 0.677578563 0.780887369 1 14.89263399 3.180043516 1.380297278 0.812589999 0.978760786 0.245833305 0.098105364 0.481576338 1.94443211 0.038316769 0.049816322 1513.712913 -3.180043516 0.166170787 EQCCYNCGKPGHLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 183.01 3.14E-07 5128430000 3497130 2426410 1767100 1974960 2311630 2052220 2744860 3159380 2329050 FALSE TRUE 3034975.41 2410470.753 2621675.471 2423404.853 2265633.086 2131170.231 2478663.9 2483771.173 2053712.362 1.47779965 1.173713903 1.27655436 1.180011816 1.103189097 1.037716026 1.206918722 1.209405572 1 20.9698027 7.9999999 0.768293818 1.133786691 66.63568994 0.640423191 0.079439804 295.1625214 1.179141418 0.029316026 33533.92487 99999976.93 -7.9999999 65.50190325 EQDDLLVLLADQDQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQDDLLVLLADQDQK 15 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ; 171.87 1.36E-08 14519000 91399 61982 49373 56724 58456 54264 70373 78431 76845 FALSE TRUE 79320.39057 61574.83616 73249.94794 69604.05117 57292.83997 56351.57119 63548.23729 61659.141 67760.47164 1.170599741 0.908713217 1.081012959 1.027207301 0.845520088 0.831628969 0.937836407 0.909957376 1 16.0481563 3.317066848 7.391236092 0.904609708 1.040771127 0.447927461 0.078218926 0.221761132 17.6915366 0.021680508 0.027969471 2075.232918 -3.317066848 0.13616142 EQDFFFELDAMDHLQSFIADCDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EQDFFFELDAMDHLQSFIADCDR 23 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ;; 193.54 5.82E-18 104057000 85459 72387 50428 62343 67437 57563 80260 97994 111451 FALSE TRUE 74165.37662 71911.48503 74815.14947 76498.931 66095.13564 59777.48586 72476.39755 77038.74569 98275.38975 0.754668863 0.731734417 0.761280618 0.778413916 0.672550227 0.60826506 0.737482677 0.783906794 1 16.58454256 1.195462822 2.164328529 1.105522963 0.719132371 0.761503202 0.048972249 0.409366615 1.755543403 0.325356837 0.014341355 15.68421626 -1.195462822 -0.386390593 EQDFFFELDAMDHLQSFIADCDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EQDFFFELDAMDHLQSFIADCDRR 24 1 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ;;;;; 243.87 6.84E-38 1405155000 1112733 1011160 543689 680023 840696 901158 942137 1130210 554101 FALSE TRUE 965682.5147 1004517.623 806618.8189 834432.6157 823967.7944 935826.1314 850768.6987 888523.3868 488595.811 1.976444523 2.055927621 1.650891802 1.707817785 1.686399629 1.915338016 1.741252544 1.818524365 1 18.89828197 1.238321556 24.99717184 0.999999097 1.812932212 0.793877197 0.13113008 2.650004084 276512.5555 0.187211477 0.033139407 17.31097607 -1.238321556 0.812933114 EQDLPLAEAVRPKT(ph)PPVVIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQDLPLAEAVRPKTPPVVIK 20 2 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 1 EQDLPLAEAVRPKT(1)PPVVIK;EQDLPLAEAVRPKT(1)PPVVIK 98.565 0.037243 7241900000 1628620 1289130 828100 754500 1308930 909440 1703160 1979570 335370 TRUE FALSE 1413393.741 1280661.62 1228571.93 925820.7568 1282884.854 944426.7453 1537987.805 1556254.361 295722.9407 4.779452475 4.33061303 4.154469474 3.130703201 4.338130992 3.193620161 5.20077273 5.262541882 1 18.17388664 4.470051838 2.220437476 3.941752063 4.784708648 0.060674638 1.219771584 1.447543624 11.95123323 0.32133361 1.920399663 29515.61507 -4.470051838 0.842956586 EQDLQLEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQDLQLEELR 10 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ; 135.8 0.0094751 429710000 709180 749620 601053 481947 579880 942810 568120 585950 644330 FALSE TRUE 615460.0662 744695.6969 891724.2412 591380.4324 568341.5225 979080.5108 513023.8098 460649.1524 568158.0414 1.083255048 1.310719276 1.569500344 1.040873119 1.00032294 1.723253812 0.902959692 0.810776437 1 19.11593277 2.049696509 24.99988501 0.881368821 1.280475641 0.381443439 0.229576899 102.0687518 51345.30966 0.091500631 0.061689697 112.1234646 -2.049696509 0.39910682 EQDVVTGVS(ph)PLLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQDVVTGVSPLLFR 14 0 Q6P0Q8;Q6P0Q8-2 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 EQDVVTGVS(1)PLLFR;EQDVVT(0.001)GVS(0.999)PLLFR 185.33 1.25E-06 105762000 532740 418180 219680 248010 378020 348340 321890 432280 354040 TRUE FALSE 462337.0592 415432.948 325917.9828 304324.4611 370498.1416 361740.8652 290673.1573 339840.286 312185.7945 1.48096764 1.33072342 1.04398723 0.974818414 1.186787317 1.158735828 0.931090275 1.08858344 1 18.25204537 4.371900138 3.234581405 1.05599933 1.459323262 0.781958861 0.078922981 0.107661901 2.138621557 0.020546125 0.07035994 23545.07823 -4.371900138 0.403323932 EQDYLCHVYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQDYLCHVYVR 11 0 O15498;O15498-2 O15498 YKT6 Synaptobrevin homolog YKT6 0 ; 196.27 6.11E-08 972820000 1700470 1631290 1143110 1294350 1634180 1542940 1459240 1813280 2145700 FALSE TRUE 1475748.581 1620573.949 1695921.819 1588251.95 1601663.015 1602297.9 1317723.129 1425524.183 1892037.79 0.779978386 0.856523034 0.896346695 0.839439867 0.846528026 0.846863582 0.696457088 0.753433251 1 20.85150947 2.397425021 24.95793073 0.794628736 0.84713322 0.00046188 0.082051221 82.33937921 25780.32445 0.030458475 0.023593034 249.7037251 -2.397425021 0.052504484 EQEAGLLQFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EQEAGLLQFLR 11 0 Q9NZL4;Q9NZL4-3;K7EN20 Q9NZL4 HSPBP1 Hsp70-binding protein 1 0 ;;; 169.65 3.87E-05 146890000 190770 192838 122738 149279 184759 192414 172799 209537 212155 FALSE TRUE 165559.2612 191571.2345 182094.5073 183175.0785 181082.6574 199816.2911 156040.9796 164729.1432 187074.2776 0.884992118 1.02403835 0.973380786 0.979156947 0.967971972 1.068112055 0.834112426 0.880554747 1 17.51325168 2.229614917 24.99974809 0.896870401 0.983522947 0.262359953 0.061200404 227.3792461 635430.3712 0.023762959 0.016286161 169.6738512 -2.229614917 0.086652546 EQEELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQEELER 7 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 ; 114.99 0.01345 479340000 542080 486410 377210 444020 491130 532800 498380 602430 544560 FALSE TRUE 470442.7545 483214.7407 559630.0177 544841.5274 481357.4739 553297.1608 450047.1843 473605.0326 480182.7372 0.979716092 1.00631427 1.16545218 1.13465455 1.002446437 1.152263749 0.937241491 0.986301664 1 18.87322401 2.223657913 24.99999975 0.975417025 1.074154978 0.334599118 0.065777177 281.3615126 471993.8588 0.027167268 0.018401494 167.3624068 -2.223657913 0.098737952 EQEELRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQEELRR 7 1 Q8WXF1;Q8WXF1-2;A0A0U1RQF9 Q8WXF1 PSPC1 Paraspeckle component 1 0 91.853 0.025813 155060000 123010 112580 63956 82333 93583 103880 100750 114130 120840 FALSE TRUE 106753.9168 111840.4546 94885.33552 101027.966 91720.88139 107876.3308 90979.28051 89724.18766 106554.4329 1.001872132 1.049608651 0.890486984 0.948134801 0.860788978 1.012405847 0.853829147 0.842050258 1 16.70123109 4.236746437 24.99999413 0.90822453 1.025740414 0.368047118 0.059545833 43.27347151 596360.1537 0.014884035 0.033777538 17248.30555 -4.236746437 0.117515884 EQEKGEGSDSKES(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQEKGEGSDSKESPK 15 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBM7;E5RHK4 Q6PKG0 LARP1 La-related protein 1 1 EQEKGEGSDS(0.005)KES(0.995)PK 102.07 0.00082467 188940000 393910 223830 284320 212290 191530 149810 348750 399880 444990 TRUE FALSE 341853.7955 222359.646 421818.103 260493.6891 187718.9277 155573.2876 314928.2787 314368.7739 392383.7891 0.871223035 0.566689176 1.075014093 0.663874748 0.47840643 0.396482454 0.802602675 0.801176763 1 18.58190591 -0.436059542 9.837851825 6.326896341 0.732047804 0 0.217939822 0 0 0 0.049712155 0.366387339 0.436059542 -5.594848538 EQELQQTLQQEQSVLDQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQELQQTLQQEQSVLDQLR 19 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 150.05 1.85E-07 13124000 27146 26725 17153 26916 26203 23155 23609 28840 32880 FALSE TRUE 23558.58732 26549.44172 25448.24817 33027.68919 25681.61157 24045.78783 21319.40281 22672.79043 28992.96386 0.812562228 0.915720167 0.877738761 1.139162224 0.885787727 0.829366323 0.735330231 0.782010095 1 14.8234152 2.875940247 4.461028628 0.819389412 0.938725326 0.14848839 0.106620631 0.366729415 11.67502285 0.03531818 0.035557499 751.5194879 -2.875940247 0.119335915 EQELQQTLQQEQSVLDQLRGEAEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQELQQTLQQEQSVLDQLRGEAEAAR 26 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 184.59 1.42E-17 141958000 79532 80737 31512 33103 68053 71582 81772 79834 13739.6 FALSE TRUE 69021.64469 80206.63333 46751.3086 40619.5421 66698.87844 74335.80586 73841.76403 62762.12037 12115.32014 5.69705496 6.620265284 3.858858706 3.352741952 5.505333551 6.13568647 6.094908197 5.18039306 1 13.56454491 4.246568655 24.97650799 4.659674006 6.158660365 0.165446693 1.541772122 361.9987062 1129022.034 0.393978914 1.003453045 17642.84648 -4.246568655 1.498986359 EQELSEEDKQLQDELEMLVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EQELSEEDKQLQDELEMLVER 21 1 Q13200;C9JPC0 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;;; 159.78 2.01E-11 96074000 133118 92273 105374 117953 100263 86214 109575 136374 242601 FALSE TRUE 115526.119 91666.85259 156333.2189 144736.0314 98267.96246 89530.70837 98948.43337 107211.4814 213920.9862 0.540041074 0.428507994 0.730798888 0.676586407 0.459365695 0.418522324 0.46254664 0.501173276 1 17.7067185 1.236787237 24.99703755 1.000000594 0.525374603 0.676589486 0.102724041 29.7032231 418563.6023 0.16772433 0.026810535 17.24992603 -1.236787237 -0.474625991 EQEPMPTVDSHEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQEPMPTVDSHEPR 14 0 A6NGP5;Q9H910;Q9H910-3;Q9H910-2;H3BU16 A6NGP5;Q9H910-2 HN1L Hematological and neurological expressed 1-like protein 0 101.04 0.0015462 166930000 95090 89215 48423 64775 80060 75692 76323 80009 103410 FALSE TRUE 82523.61557 88628.94079 71840.52477 79483.15377 78466.96263 78603.92022 68921.20721 62899.69798 91184.98761 0.90501318 0.971968557 0.787854741 0.871669294 0.860525013 0.862026988 0.75583941 0.689803219 1 16.4765087 4.230481499 0.593760621 0.799844436 0.978217218 0.092763243 0.089343879 3.97088152 1.712994536 0.059315498 0.459416314 17001.27526 -4.230481499 0.178372783 EQESIIQQLQTSLHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQESIIQQLQTSLHDR 16 0 Q5VU43-13;Q5VU43-2;E9PQG4;Q5VU43-6;Q5VU43-7;A0A087WX83;A0A075B749;Q5VU43-3;Q5VU43;Q5VU43-4 Q5VU43-13;A0A087WX83 PDE4DIP Myomegalin 0 ; 94.882 0.0039415 143375000 56787 65204 26542 41321 54133 62757 60023 66442 66479 FALSE TRUE 49282.45407 64775.67063 39377.79998 50703.5646 53055.85921 65171.3024 54201.9787 52233.89535 58619.92835 0.840711605 1.105011085 0.671747665 0.864954394 0.905082294 1.111760185 0.924633998 0.891060375 1 15.83910358 2.986977564 23.89492608 0.967433778 0.874629324 0.162476397 0.11786816 758.226352 1391277.889 0.036922408 0.038677281 970.4598302 -2.986977564 -0.092804454 EQEVAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQEVAEER 8 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 165.15 0.00075827 366230000 527630 494440 383220 487810 457940 576360 475130 561580 691390 FALSE TRUE 457902.3587 491191.9911 568546.4738 598574.7162 448827.8899 598532.9422 429051.9657 441490.4872 609654.6618 0.751084815 0.805688895 0.932571355 0.981825866 0.73620021 0.981757345 0.703762298 0.724164867 1 19.21763274 1.214848482 24.54373256 1.000000937 0.825971928 0.210977086 0.105040368 2941.042807 3043984.198 1.554725053 0.026465027 16.40017497 -1.214848482 -0.174029009 EQEVAEERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQEVAEERR 9 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 94.465 0.013955 118030000 69555 68558 30057 37372 65868 78558 63540 81081 12289 FALSE TRUE 60363.13052 68107.63798 44592.66573 45857.8838 64557.35567 81580.17709 57377.90058 63742.45912 10836.20842 5.570502909 6.285190848 4.115153936 4.231912309 5.957559431 7.528479883 5.295016334 5.882358169 1 13.40357243 1.236495934 24.99620009 0.999994115 5.608840213 0.687860684 0.975583618 33.74505784 408431.2501 1.594470726 0.249840219 17.23835952 -1.236495934 4.608846098 EQFAWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 ;;;;;;; 153.88 0.023438 17706900000 9383880 8680250 6132300 7533770 8890540 8957010 8755040 9895190 9868140 FALSE TRUE 8143776.482 8623228.866 9097900.791 9244427.625 8713635.648 9301591.971 7905977.568 7779180.623 8701539.731 0.935900626 0.991000344 1.045550681 1.062389866 1.001390089 1.068959317 0.908572254 0.894000472 1 23.05283928 2.225474355 24.99986883 0.924750434 1.018904718 0.405574573 0.047083055 203.2464473 388277.0799 0.019362917 0.013143965 168.0638682 -2.225474355 0.094154284 EQFLDGDGWTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EQFLDGDGWTSR 12 0 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;;;;; 274.49 1.98E-27 33650500000 33719000 32062300 22847100 28100800 33040800 41374900 28577000 29874200 25770400 FALSE TRUE 29262948.72 31851680.64 33896033.98 34481516.13 32383352.72 42966619.18 25805606.94 23485834.81 22723852.67 1.287763529 1.401684877 1.491649962 1.517415054 1.42508197 1.890815778 1.135617596 1.03353226 1 24.43770412 2.022948129 24.87416199 1.038785314 1.496062599 0.653643792 0.154621859 123.0872185 133417.3194 0.062188941 0.041925018 105.4260972 -2.022948129 0.457277285 EQFNEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EQFNEFR 7 0 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 ;;; 177.78 0.0016874 2468350000 5160000 4630360 3104130 3898670 4813890 5696900 4011620 4319760 4042140 FALSE TRUE 4478092.926 4599942.86 4605297.651 4783922.611 4718103.007 5916063.429 3622573.71 3396012.94 3564282.814 1.256379799 1.290566181 1.292068529 1.342183789 1.323717352 1.659818746 1.016354172 0.952789977 1 21.76518038 2.091001025 10.21239195 0.97651963 1.351741318 0.708871354 0.112213259 0.177174022 18.37272888 0.045466024 0.030641466 123.3107745 -2.091001025 0.375221688 EQFVEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQFVEFR 7 0 O43852;O43852-3;O43852-15;H0Y875;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ; 113.26 0.014355 423910000 1365620 1181580 788350 979140 1190170 1543400 1062730 1142410 1071820 FALSE TRUE 1185149.857 1173818.123 1169598.697 1201468.702 1166487.946 1602775.597 959666.6082 898114.5117 945110.6606 1.25397999 1.241990142 1.237525663 1.271246588 1.234234248 1.695860245 1.015401316 0.950274448 1 19.85012374 2.034643599 24.99998489 0.974960635 1.312532198 0.567902344 0.137453977 120.2815483 86798.74496 0.054995267 0.037077632 108.3037761 -2.034643599 0.337571563 EQFYHSCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQFYHSCK 8 0 J3QQY1;Q96JB5;J3QS62;Q96JB5-4;J3QL86;Q96JB5-2 J3QQY1 CDK5RAP3 CDK5 regulatory subunit-associated protein 3 0 102.07 0.0050364 196510000 688060 663500 375660 501600 577900 556620 486730 686610 562130 FALSE TRUE 597131.1277 659141.4248 557330.4325 615495.9465 566400.9206 578033.5316 439526.9995 539783.7947 495675.6318 1.204681226 1.329783799 1.124385378 1.2417313 1.142684619 1.166152811 0.886723033 1.088985942 1 18.91903681 2.394731235 6.908242725 1.008188398 1.206945556 0.645154096 0.073552729 0.137769382 9.582386036 0.026682752 0.020592867 248.1596884 -2.394731235 0.198757159 EQGDGAEDEEWDD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQGDGAEDEEWDD 13 0 Q7Z6K5;H0YMP5 Q7Z6K5 ARPIN Arpin 0 ; 199.82 2.67E-07 1452920000 3415800 3410200 2323100 2736600 3353900 3292400 3457500 4047700 3675800 FALSE TRUE 2964393.375 3387798.172 3446558.93 3357986.856 3287163.952 3419060.758 3122192.182 3182130.854 3241251.111 0.914583065 1.045213115 1.063342151 1.036015644 1.01416516 1.054858337 0.963267601 0.98176005 1 21.62811937 2.228349321 24.99969655 0.980926406 1.024694024 0.162662998 0.041984641 339.866521 832066.1805 0.016626883 0.011347801 169.1801169 -2.228349321 0.043767618 EQGVEEHETLLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQGVEEHETLLLR 13 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 197.14 4.72E-07 0 129320 134340 67764 99520 141850 128510 137650 145200 143700 FALSE TRUE 112230.0343 133457.5117 100534.8971 122117.5371 139027.4625 133453.8629 124300.7242 114150.1099 126711.9497 0.885709948 1.053235405 0.793412912 0.963741284 1.097192987 1.053206609 0.980970812 0.900863022 1 16.95119306 3.482915943 24.99319739 0.997020678 0.917288699 0.224234328 0.079950022 470.0684672 2027464.05 0.023728018 0.031678823 3040.296521 -3.482915943 -0.079731979 EQGVLSFWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 191.45 8.35E-05 4177730000 1802040 2139078 1513471 2207023 2670014 2723120 1590840 2502639 2761058 FALSE TRUE 1563895.848 2125026.256 2245390.638 2708161.304 2616885.945 2827880.188 1436560.582 1967469.125 2434648.869 0.64234965 0.872826584 0.922264671 1.112341635 1.074851482 1.161514592 0.590048364 0.808112065 1 21.21528229 4.733601873 2.489811763 0.937233779 0.579242884 0.25858201 0.163724862 0.871493979 6.83066752 0.04633519 0.660513896 54150.42541 -4.733601873 -0.357990895 EQGVTFPS(ph)GDIQEQLIR ddPTM_MDA-MB-175_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 1 EQGVTFPS(1)GDIQEQLIR;EQGVTFPS(1)GDIQEQLIR 183.06 7.48E-10 109974000 142102 151843 109657 115360 154314 177309 135682 163042 192482 TRUE FALSE 123322.8607 150845.5333 162687.492 141554.2512 151243.4533 184130.192 122523.5805 128176.7371 169726.9972 0.726595431 0.888753915 0.95852454 0.834011403 0.891098386 1.084860953 0.72188622 0.755193571 1 17.37285654 EQGVTFPSGDIQEQLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EQGVTFPSGDIQEQLIR 17 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 295.44 9.41E-46 1145070000 796270 696711 567256 639139 781061 902800 753480 815963 1074720 FALSE TRUE 691040.902 692134.2596 841582.899 784265.2786 765519.4142 937531.3002 680407.6256 641475.6623 947667.8259 0.729201607 0.730355342 0.888056844 0.827574027 0.807792977 0.989303714 0.71798114 0.676899273 1 19.85402193 4.268135459 23.17039581 0.825596926 0.729778013 0.158500479 0.102811206 204.9660992 160573.2807 0.026545969 0.070197424 18541.09841 -4.268135459 -0.095818913 EQHDAQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQHDAQVR 8 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ; 152.34 0.00045865 207540000 250390 221542 122315 178533 173324 223525 190738 255000 204924 FALSE TRUE 217300.3271 220086.676 181466.9431 219071.6464 169875.1915 232124.1514 172240.2581 200470.2344 180698.1182 1.20255999 1.217979901 1.004254748 1.212362633 0.940104929 1.284596396 0.953193425 1.109420709 1 17.46322196 8 0.368702556 1.05370368 3.276855533 0.163611471 0.113018711 142.2708321 2.113722854 0.118920491 221.5403967 99999999.99 -8 2.223151854 EQHGLQLQSEINQLHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQHGLQLQSEINQLHSK 17 0 Q15075 Q15075 EEA1 Early endosome antigen 1 0 165.17 1.45E-09 86056000 151650 119380 77472 105530 108620 105010 112360 131380 200590 FALSE TRUE 131609.0683 118595.7849 114937.7183 129492.1994 106458.6745 109049.8027 101463.3445 103285.4094 176876.4787 0.744073317 0.670500599 0.649819123 0.732105254 0.601881467 0.616530832 0.573639555 0.583940896 1 17.43238268 1.232945559 24.99999102 1.000000571 0.641396276 0.788310904 0.057504141 87.95222064 391548.9695 0.129731657 0.015163024 17.09800968 -1.232945559 -0.358604295 EQHGVAASCLEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EQHGVAASCLEDLR 14 0 O00273;O00273-2;K7ERT1 O00273 DFFA DNA fragmentation factor subunit alpha 0 ;; 191.96 4.28E-07 656410000 211855 200044 133063 151955 189665 209965 186741 199796 182745 FALSE TRUE 183857.825 198729.8978 197412.7119 186458.7052 185891.0376 218042.4894 168630.8866 157071.1802 161141.0943 1.140974162 1.233266403 1.225092288 1.157114553 1.153591754 1.353115358 1.046479716 0.974743165 1 17.29796493 2.055849141 8.510326361 0.992955008 1.207076227 0.723554587 0.060057244 0.128445969 17.79421106 0.023635878 0.015887333 113.7232181 -2.055849141 0.214121219 EQHLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EQHLTK 6 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;; 77.058 0.073422 658420000 2459290 1996510 1054490 1602050 1331750 1797290 2299000 2495410 2386380 FALSE TRUE 2134288.595 1983394.794 1564444.891 1965819.938 1305250.781 1866432.909 2076043.334 1961785.991 2104264.875 1.014268033 0.942559474 0.743463862 0.934207457 0.620288252 0.886976222 0.986588408 0.932290423 1 21.00488489 2.39884288 5.908840936 0.963279627 0.845285155 0.19939441 0.110523016 0.339711017 19.66623931 0.041638957 0.032077925 250.520275 -2.39884288 -0.117994472 EQHTEDTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQHTEDTVK 9 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 108.7 0.0025694 162300000 243260 184560 151200 203270 167490 185750 207260 253250 267960 FALSE TRUE 211112.5747 183347.6132 224320.8257 249425.5603 164157.2767 192895.9227 187159.9571 199094.4583 236282.0741 0.893476898 0.775969205 0.94937725 1.055626252 0.694751294 0.816379844 0.79210392 0.84261347 1 17.85015066 4.266226278 24.99526705 0.868357357 0.834723231 0.021030599 0.108107848 1403.703295 1268188.975 0.027383006 0.072409623 18459.76967 -4.266226278 -0.033634127 EQHVQDIIPINSHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EQHVQDIIPINSHFR 15 0 Q01968-2;Q01968;A0A2R8YF88 Q01968-2 OCRL Inositol polyphosphate 5-phosphatase OCRL-1 0 ;; 218.63 1.11E-12 351985000 265484 252607 189078 171239 220635 278180 227837 250280 268503 FALSE TRUE 230399.6167 250947.608 280516.7532 210121.4322 216244.7952 288881.7646 205741.4028 196759.5697 236760.8812 0.973132114 1.059920062 1.184810395 0.887483739 0.913346808 1.220141449 0.868983937 0.831047632 1 17.85307121 EQIDFLAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQIDFLAAR 9 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 75.294 0.089959 51484000 76320 75841 61233 78255 76658 88370 63096 71486 130810 FALSE TRUE 66234.11863 75342.79548 90845.48361 96023.9938 75132.65578 91769.65108 56976.95963 56199.2752 115345.7908 0.574222242 0.653190679 0.787592533 0.832488062 0.651368856 0.795604681 0.493966526 0.487224326 1 16.81560583 2.255765589 24.99530065 0.617384649 0.71854731 0.002277717 0.160509619 643.5659449 934968.3579 0.059896398 0.046279547 180.2044822 -2.255765589 0.101162661 EQIS(ph)DIDDAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQISDIDDAVR 11 0 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 1 EQIS(1)DIDDAVR 157.35 0.0013376 0 159230 117150 79966 83370 117780 111760 116870 135220 113450 TRUE FALSE 138187.3521 116380.4339 118637.8251 102300.4327 115436.4084 116059.4795 105535.9654 106304.2553 100038.0702 1.381347638 1.163361445 1.185926766 1.022615015 1.153924782 1.160153122 1.054958029 1.062638004 1 16.61018961 8 0.630748141 1.070837873 24.46525563 0.741721676 0.055535915 106.0060336 0.743765846 0.02463794 3445.05377 99999999.91 -8 23.39441776 EQISDIDDAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQISDIDDAVR 11 0 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 ; 252.68 5.04E-20 2200820000 1690050 1306460 825812 976220 1228750 1214660 1216810 1403330 1416090 FALSE TRUE 1466705.61 1297877.778 1225177.445 1197885.672 1204300.279 1261388.756 1098803.953 1103238.8 1248681.453 1.174603504 1.039398619 0.981176938 0.959320464 0.964457569 1.010176577 0.879971389 0.883523013 1 20.25197405 8 0.580083362 0.929771086 14.423873 0.744477053 0.041991878 81.7405271 0.690087658 0.021966015 1387.95529 100000000 -8 13.49410192 EQIVKQSTELVCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQIVKQSTELVCR 13 1 Q9Y2V7 Q9Y2V7 COG6 Conserved oligomeric Golgi complex subunit 6 0 53.967 0.08466 1367300000 2927700 3026300 1411400 1945300 3045000 3499200 2559200 2704300 2365100 FALSE TRUE 2540797.027 3006420.036 2093957.761 2387010.097 2984410.457 3633816.488 2311009.178 2126006.49 2085500.572 1.218315191 1.441581976 1.004055232 1.144574175 1.431028357 1.74241932 1.108131644 1.019422636 1 20.99196228 2.01711873 24.99870457 1.026902029 1.325738075 0.330806643 0.196284561 283.2342215 413609.0528 0.084691738 0.05708522 104.0204504 -2.01711873 0.298836046 EQIVPKPEEEVAQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQIVPKPEEEVAQK 14 1 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 0 ; 126.63 7.69E-05 768340000 728280 640430 447160 473350 548230 475950 635910 805920 681880 FALSE TRUE 632035.9528 636222.9732 663408.0717 580831.3522 537321.2956 494260.1045 574239.5461 633580.2797 601268.9232 1.051170164 1.058133804 1.103346682 0.966009268 0.893645547 0.822028356 0.95504611 1.053738611 1 19.19765087 3.666781697 6.171665018 0.951522978 1.069332705 0.464129622 0.062059713 0.251032479 17.13811911 0.020303288 0.030429507 4642.8184 -3.666781697 0.117809726 EQIVPKPEEEVAQKK ddPTM_MDA-MB-175_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 0 133.71 2.23E-05 85866000 236080 195030 153300 160900 159920 122850 321630 344850 143750 FALSE TRUE 204881.4298 193748.8351 227436.3928 197434.8042 156737.9049 127576.119 290438.3721 271106.5111 126756.0388 1.61634453 1.528517592 1.794284477 1.55759683 1.236532053 1.006469753 2.291317833 2.138805486 1 16.95169495 2.232785225 24.99984735 1.898586762 1.469825763 0.136371951 0.398108886 232.0081461 1004277.45 0.162869701 0.113156712 170.9169858 -2.232785225 -0.428760999 EQIVVDLSHPGVSEDDQVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 EQIVVDLSHPGVSEDDQVSR 20 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ;;;;;; 269.11 3.00E-37 5932500000 4817320 4748350 2880321 3612561 4715250 4770250 4494620 5336850 4733280 FALSE TRUE 4180698.956 4717157.776 4273253.87 4432848.19 4621425.75 4953764.604 4058732.444 4195606.159 4173717.031 1.001672832 1.13020546 1.023848488 1.062086423 1.107268585 1.186895175 0.972450316 1.005244517 1 21.99290136 2.1887583 24.99998448 0.994368269 1.084516106 0.409830899 0.052455068 108.4191528 54423.90403 0.021014108 0.01416774 154.4394692 -2.1887583 0.090147837 EQIYDVYR ddPTM_MDA-MB-175_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 ;;;;; 164.96 0.00076093 7196890000 4539770 4707360 2928800 3611150 4512990 4523260 4031880 4760670 4826210 FALSE TRUE 3939827.892 4676437.042 4345177.476 4431116.8 4423190.329 4697272.739 3640868.898 3742637.768 4255660.952 0.925785192 1.098874439 1.021034694 1.041228813 1.039366241 1.103770435 0.855535471 0.879449235 1 22.02095179 2.234457273 24.99999661 0.90261207 1.040485622 0.489506036 0.060724989 76.10987731 463699.3334 0.022973135 0.016122683 171.5762902 -2.234457273 0.137873552 EQLEEEEEAKHNLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 EQLEEEEEAKHNLEK 15 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;; 318.32 1.17E-56 11472810000 9141740 6841470 6578390 6260680 6281660 4559010 9661790 10396730 6861530 FALSE TRUE 7933635.897 6796527.933 9759721.407 7682263.083 6156667.256 4734398.065 8724791.093 8173470.197 6050367.74 1.311265073 1.123324767 1.613079044 1.269718373 1.0175691 0.782497572 1.442026579 1.350904697 1 22.5285914 3.469664999 24.422114 1.154049081 1.345760732 0.186289897 0.217106832 281.0149778 920426.021 0.066725766 0.086338859 2948.933638 -3.469664999 0.191711651 EQLEWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EQLEWER 7 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;A0A0U1RQP7;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 ;;; 155 0.0038174 2042740000 2569710 2444620 1575380 1931670 2364890 2470950 2340560 2607400 2382310 FALSE TRUE 2230116.313 2428561.13 2337239.037 2370285.197 2317833.316 2566009.045 2113572.851 2049827.801 2100676.026 1.061618396 1.156085517 1.112612801 1.128344004 1.103374955 1.221515843 1.006139369 0.975794352 1 21.00242225 2.109290745 7.829953343 0.987729425 1.129365111 0.713204983 0.040935096 0.110398613 7.226649289 0.015622853 0.010510575 128.6147401 -2.109290745 0.141635686 EQLLELPEQQEGHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EQLLELPEQQEGHLK 15 0 P07476 P07476 IVL Involucrin 0 ;;; 219.77 1.76E-12 1060830000 933810 854570 674060 794020 873320 831230 1087100 1208390 1163320 FALSE TRUE 810404.6425 848956.2734 1000037.671 974314.3768 855942.6406 863207.956 981673.2093 949985.2022 1025793.635 0.790026975 0.827609223 0.974891671 0.949815191 0.834419918 0.841502547 0.956988985 0.926097774 1 19.96830909 7.999953557 0.035223259 1.500154332 7.04E-06 0.341305057 0.058697734 3100.993343 10.78897623 152.9392292 343.4360387 99989306.75 -7.999953557 -1.500147295 EQLQDLHDQIAGQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQLQDLHDQIAGQK 14 0 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 0 110.38 0.00071275 318910000 666740 555210 458350 496910 571990 484760 647010 756100 596310 FALSE TRUE 578628.6197 551562.789 680009.5931 609741.0103 560608.5181 503409.0309 584263.0698 594413.899 525814.9111 1.100441633 1.048967569 1.293248972 1.159611486 1.066170826 0.957388275 1.111157286 1.130462234 1 19.00419553 3.233178875 17.75112035 1.062290011 1.153502199 0.272338785 0.078347049 5.549175257 18302.87376 0.0245046 0.028845607 1710.719771 -3.233178875 0.091212187 EQLQLLEEQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EQLQLLEEQHR 11 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 218.06 1.09E-11 2408460000 2809080 2628740 1866290 2199030 2609830 2911100 2533020 2837570 4082510 FALSE TRUE 2437852.961 2611471.634 2768834.086 2698353.372 2557899.489 3023091.901 2287368.11 2230777.737 3599880.319 0.677203892 0.725432904 0.76914615 0.749567522 0.710551258 0.839775668 0.635401154 0.619681084 1 21.77951751 2.763207042 0.011977205 1.473977229 2.60E-06 0.046666866 0.107176249 11260.63182 157.1436591 9730.088611 9603.685553 579.704994 -2.763207042 -1.473974633 EQLRQEQALLEEIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EQLRQEQALLEEIER 15 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 308.98 3.82E-56 567200000 664790 685140 301288 322723 637510 666450 650790 695450 116824 FALSE TRUE 576936.3171 680639.2702 446991.8845 396002.1897 624824.7983 692088.7628 587676.486 546733.4295 103013.1998 5.60060573 6.607301506 4.339170955 3.844188807 6.065482865 6.718447384 5.704865853 5.307411385 1 16.65246969 4.240430461 24.99952731 4.90688028 6.103953671 0.108264482 1.586168795 123.9790624 1657460.335 0.404249718 0.963772584 17395.24145 -4.240430461 1.19707339 EQLSAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQLSAER 7 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ; 80.462 0.069435 2034000000 1820460 1708560 1123350 1287750 1404150 1672970 1663270 1723630 1779820 FALSE TRUE 1579881.599 1697336.357 1666605.817 1580153.32 1376210.162 1737330.238 1501966.331 1355045.138 1569411.707 1.00667122 1.081511212 1.061930282 1.006844356 0.876895563 1.10699457 0.957025059 0.863409602 1 20.58179244 2.9492467 0.516414892 0.917223207 1.064439481 0.180535157 0.072363181 1.545347193 1.31906713 0.133067106 0.124483645 889.7063701 -2.9492467 0.147216274 EQLSAQELMESGLQIQKS(ph)PEPEVLSTQEDLFDQSNK ddPTM_MDA-MB-175_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 246.16 2.98E-50 47403000 136250 111490 74463 78170 98366 72830 151390 165440 66238 TRUE FALSE 118244.2173 110757.6148 110473.5559 95919.69325 96408.70905 75631.81723 136708.2211 130061.9435 58407.4191 2.02447256 1.896293597 1.891430191 1.64225187 1.650624365 1.29490086 2.340596849 2.226805181 1 15.83386402 4.237568639 2.137199477 1.772139423 1.993877363 0.056789275 0.393666675 1.441348764 12.57062726 0.113078969 0.41561949 17280.9908 -4.237568639 0.22173794 EQMMNSSISSGSGS(ph)LR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EQMMNSSISSGSGSLR 16 0 A0A590UJD9;A0A0C4DFT3;A0A590UJ18;A0A590UK02;E7EQD7;A0A590UK70;A0A590UJ08;Q12959-4;Q12959-2;A0A590UJC5;A0A590UJL2;A0A590UJ25;Q12959;Q12959-3;Q12959-5;Q12959-7;Q12959-6;A0A590UKA8;A0A590UJR5;A0A590UJ68;A0A590UJS9;A0A590UK48;A0A590UJ81;C9JUA9;Q12959-8;A0A590UJX2;A0A590UJ64;A0A590UK81;A0A590UJ29;Q12959-9;A0A590UJR4 A0A590UJD9;A0A590UJ08;Q12959 DLG1 Disks large homolog 1 1 EQMMNSSISSGSGS(1)LR;EQMMNSSISSGSGS(1)LR;EQMMNSSIS(0.005)S(0.061)GS(0.209)GS(0.725)LR 267.33 2.76E-27 1079480000 650640 584990 385211 474640 575170 693540 543220 612580 595590 TRUE FALSE 564656.2755 581147.1622 571500.3281 582414.2664 563725.2423 720220.9326 490538.608 481584.5341 525180.0287 1.075167075 1.10656752 1.088198897 1.108980225 1.073394287 1.371379133 0.93403896 0.916989428 1 19.00245253 EQMQPTHPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 EQMQPTHPIR 10 0 Q04917;A2IDB2 Q04917 YWHAH 14-3-3 protein eta 0 ;;;;;;; 132.03 0.00017787 2377625000 1298306 1218203 761519 1024486 1298648 1463543 1271080 1347072 1370155 FALSE TRUE 1126731.573 1210200.544 1129792.136 1257111.205 1272807.446 1519846.446 1147810.857 1059011.136 1208176.837 0.932588292 1.001675009 0.9351215 1.040502654 1.053494329 1.25796688 0.950035477 0.876536533 1 20.2044002 2.021479647 24.99812249 0.92460024 1.037618397 0.181436944 0.094067308 344.3512743 400756.1915 0.03991687 0.026909524 105.0702214 -2.021479647 0.113018157 EQNFYGSQESIIALCTHLQQLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQNFYGSQESIIALCTHLQQLIR 23 0 Q9H993;F5GZY1 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 ; 126.46 5.00E-05 868890000 467650 354520 284836 374015 414170 364960 434000 479280 604680 FALSE TRUE 405848.8676 352191.1348 422583.6423 458940.8222 405928.8273 379000.2474 391910.7468 376789.7018 533195.4193 0.761163455 0.660529183 0.792549274 0.860736619 0.761313418 0.710809271 0.735022719 0.706663426 1 19.02430486 1.232917047 24.99471304 1.000000404 0.747338403 0.683856398 0.053713205 115.0565037 509517.62 0.119267052 0.013909396 17.09688723 -1.232917047 -0.252662001 EQNYCESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQNYCESR 8 0 Q7L5D6;Q7L5D6-2;C9JPA8;C9JY46 Q7L5D6 GET4 Golgi to ER traffic protein 4 homolog 0 ; 197.66 0.00027553 194190000 342770 301300 197891 225610 256140 282960 266640 295600 328870 FALSE TRUE 297472.076 299320.7405 293591.7495 276838.1987 251043.3151 293845.6543 240781.2938 232388.2404 289991.3632 1.02579633 1.032171224 1.012415495 0.954642909 0.865692386 1.013291055 0.830305052 0.801362626 1 18.14565041 3.509781875 0.862496416 0.875217205 1.046251856 0.375521387 0.067889677 0.653637689 1.033641214 0.034545935 0.076730718 3234.311727 -3.509781875 0.171034651 EQNYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQNYQR 6 0 Q9BVK6 Q9BVK6 TMED9 Transmembrane emp24 domain-containing protein 9 0 ; 170.31 0.013437 157129000 244250 265360 185960 196663 185339 305510 211295 256560 301850 FALSE TRUE 211971.7436 263616.8327 275890.878 241318.34 181651.1165 317263.1674 190803.6434 201696.6406 266165.6369 0.796390346 0.990423992 1.036538305 0.90664724 0.682473961 1.191976437 0.716860545 0.757786178 1 18.0219648 EQPFGEGVPLDGDDPEHIQWIFQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EQPFGEGVPLDGDDPEHIQWIFQK 24 0 Q8TBC4;F8W8D4;Q8TBC4-2 Q8TBC4 UBA3 NEDD8-activating enzyme E1 catalytic subunit 0 ;; 198.05 1.80E-24 520340000 350121 285286 206980 261091 282103 228816 296812 389290 333993 FALSE TRUE 303851.6228 283411.9375 307076.2203 320375.7021 276489.7022 237618.6996 268027.2179 306043.363 294508.728 1.03172366 0.962321013 1.042672733 1.087830925 0.938816666 0.806830756 0.910082427 1.039165681 1 18.16795086 3.209896704 24.81623933 0.942727713 1.027045631 0.317478911 0.066899274 292.4014756 253150.4148 0.022932656 0.026007815 1621.4244 -3.209896704 0.084317917 EQPGSYSDAPEYLWS(ph)GTL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQPGSYSDAPEYLWSGTL 18 0 Q96A59-2 Q96A59-2 1 EQPGSYSDAPEYLWS(0.5)GT(0.5)L 104.98 0.00051527 24612000 46863 38500 37365 46032 54678 64596 27295 61189 55263 TRUE FALSE 40669.93581 38247.09096 55434.83898 56484.26916 53590.01478 67081.04992 24647.9351 48104.20852 48729.8711 0.8345997 0.784879789 1.137594616 1.159130281 1.099736436 1.376589932 0.505807517 0.987160595 1 15.57251879 2.243405944 24.99999481 0.849975826 1.061769633 0.212168101 0.211826721 211.7465847 1092536.773 0.082928317 0.062147295 175.148307 -2.243405944 0.211793807 EQPGSYSDAPEYLWSGT(ph)L ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQPGSYSDAPEYLWSGTL 18 0 Q96A59-2 Q96A59-2 1 EQPGSYSDAPEYLWS(0.092)GT(0.908)L 130.07 0.00022186 21294000 68886 62210 46280 66096 80400 89666 39181 86322 81965 TRUE FALSE 59782.54057 61801.33841 68661.1628 81104.10701 78800.1973 93115.50904 35381.23265 67862.71206 72275.19107 0.827151609 0.855083708 0.949996282 1.122156937 1.090280027 1.288346771 0.489534958 0.938948912 1 16.1412129 2.25038559 24.99998317 0.823132527 1.018934594 0.223187379 0.186396064 365.0805655 771841.8035 0.071791117 0.055154373 177.9858962 -2.25038559 0.195802067 EQPLDEELKDAFQNAYLELGGLGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EQPLDEELKDAFQNAYLELGGLGER 25 1 P05023-4;P05023;P05023-3;P05023-2 P05023-4 ATP1A1 Sodium/potassium-transporting ATPase subunit alpha-1 0 ;; 171.79 6.13E-12 273337000 236183 196580 161302 274067 245654 214213 164859 380026 246773 FALSE TRUE 204970.8181 195288.653 239308.1867 336298.1012 240765.966 222453.9127 148870.9996 298760.3973 217599.7771 0.941962445 0.897467156 1.099763014 1.545489181 1.106462374 1.022307632 0.684150515 1.372981173 1 17.73131755 4.196107043 6.286905857 1.130520072 0.919478217 0.116923673 0.226344251 0.364747393 36.16873789 0.059237791 0.129417918 15707.49907 -4.196107043 -0.211041854 EQQAQVEKEDFSDMVAEHAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQQAQVEKEDFSDMVAEHAAK 21 1 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 143.95 7.95E-08 507430000 878070 679820 538330 556980 590940 460080 865170 987510 584140 FALSE TRUE 762030.8248 675354.2177 798668.1886 683450.8219 579181.4502 477779.5753 781265.9466 776338.6713 515083.6347 1.479431249 1.311154485 1.55056021 1.326873494 1.124441569 0.927576695 1.516774935 1.507208964 1 18.97444718 3.484762478 24.31678475 1.256821953 1.434335524 0.207132094 0.198009287 531.2237192 1690523.383 0.061131782 0.082622432 3053.250787 -3.484762478 0.177513571 EQQEAIEHIDEVQNEIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EQQEAIEHIDEVQNEIDR 18 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;; 243.17 4.48E-24 6769700000 3093110 2458520 2280660 3170660 2567540 2531170 2236930 2770700 8512200 FALSE TRUE 2684347.677 2442369.82 3383594.804 3890606.814 2516450.977 2628545.748 2019992.873 2178207.367 7505897.413 0.35763181 0.325393445 0.450791507 0.518339993 0.335263172 0.350197399 0.269120768 0.290199459 1 22.83959314 1.234775628 25 1.000000914 0.359680556 0.882028942 0.073309648 39.51305209 260946.5055 0.146222339 0.020047422 17.17021084 -1.234775628 -0.640320358 EQQEAIEHIDEVQNEIDRLNEQAS(ph)EEILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQQEAIEHIDEVQNEIDRLNEQASEEILK 29 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 1 EQQEAIEHIDEVQNEIDRLNEQAS(1)EEILK 332.02 2.16E-105 42357000 39105 27503 24371 24686 29175 27513 29420 35314 42580 TRUE FALSE 33937.17517 27322.33098 36156.89712 30291.3336 28594.47458 28571.44291 26566.85293 27762.37591 37546.24091 0.903876776 0.727698175 0.962996461 0.80677407 0.761580225 0.760966803 0.707576905 0.739418254 1 15.19638085 3.487915354 24.29839116 0.779448108 0.856765243 0.088416502 0.097885813 779.9162703 1755653.221 0.026746447 0.037009428 3075.497331 -3.487915354 0.077317135 EQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EQQEAIEHIDEVQNEIDRLNEQASEEILK 29 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 0 ;;;;; 330.27 2.44E-105 1975980000 552212 375331 306868 363138 394458 347650 451906 563332 427941 FALSE TRUE 479235.7851 372865.4259 455270.3912 445594.0331 386609.0575 361024.3205 408080.2257 442867.8357 377350.3025 1.270002387 0.988114819 1.206492716 1.18084981 1.024536233 0.956735209 1.081436063 1.17362523 1 18.52554491 3.241590126 24.99980296 1.061097527 1.152213344 0.2729863 0.090434853 137.5154822 1134782.324 0.027056493 0.033416836 1744.175276 -3.241590126 0.091115817 EQQEAIEHIDEVQNEIDRLNEQASEEILKVEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQQEAIEHIDEVQNEIDRLNEQASEEILKVEQK 33 2 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 0 ; 84.58 0.00026072 159537000 42762 26800 16608.1 18001.4 25766 23040.3 37242 39107 7734.1 FALSE TRUE 37110.89335 26623.94904 24639.83271 22088.893 25253.30701 23926.67525 33630.27657 30744.27238 6819.783509 5.441652702 3.903928769 3.612993386 3.238943432 3.702948485 3.508421524 4.931282134 4.50810093 1 12.73551023 4.739966243 3.292129353 3.667500658 5.688710044 0.244872408 1.034597274 0.522871106 9.209802622 0.255380143 2.695542833 54949.81602 -4.739966243 2.021209387 EQQEVADRLETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQQEVADRLETK 12 1 O75884 O75884 RBBP9 Putative hydrolase RBBP9 0 ; 110.25 0.0013771 390090000 550320 519410 336100 374310 467970 428120 544100 587230 390070 FALSE TRUE 477593.8177 515997.9615 498639.0842 459302.8065 458658.3126 444590.0534 491333.2657 461655.4343 343956.369 1.388530235 1.500184349 1.449716095 1.335351945 1.333478179 1.292576889 1.428475557 1.342191848 1 18.39186604 1.236392377 3.769385852 0.950106771 1.388158254 0.801372816 0.060488277 0.126864485 2.891943892 0.157165342 0.016744116 17.23424953 -1.236392377 0.438051484 EQQHVMEELFQSSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQQHVMEELFQSSFR 15 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 193.64 8.44E-08 587780000 614500 575170 333880 400570 574240 485490 630490 668020 603330 FALSE TRUE 533292.2681 571391.6704 495345.4848 491525.5408 562813.7475 504167.1145 569345.1768 525169.1215 532005.0147 1.002419626 1.074034369 0.931091759 0.923911481 1.057910606 0.947673613 1.070187613 0.987150698 1 19.02108032 2.258786858 24.99991246 1.014582189 0.990821504 0.061793773 0.053253354 896.6587342 1108278.137 0.019760661 0.015287783 181.4624868 -2.258786858 -0.023760685 EQQTRPIWTAEDQLDGSLEDNLDLPHHGLADSS(ph)ADLSCDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQQTRPIWTAEDQLDGSLEDNLDLPHHGLADSSADLSCDSR 41 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 EQQTRPIWTAEDQLDGSLEDNLDLPHHGLADS(0.388)S(0.555)ADLS(0.04)CDS(0.017)R 205.76 9.20E-36 316100000 108060 117990 51926 68608 104300 125390 101670 124930 61512 TRUE FALSE 93779.59721 117214.9159 77037.58728 84186.49501 102224.6341 130213.8344 91810.05905 98214.69171 54240.12143 1.728971004 2.161037122 1.42030632 1.552107421 1.884668237 2.400692163 1.692659541 1.810738787 1 15.72707279 1.228260115 4.743577915 0.930033276 1.836561218 0.462642252 0.281498179 0.195205901 9.971684343 0.597645683 0.071831039 16.91453701 -1.228260115 0.906527942 EQQTRPIWTAEDQLDGSLEDNLDLPHHGLADSSADLS(ph)CDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQQTRPIWTAEDQLDGSLEDNLDLPHHGLADSSADLSCDSR 41 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 EQQTRPIWTAEDQLDGSLEDNLDLPHHGLADS(0.194)S(0.194)ADLS(0.474)CDS(0.138)R 75.504 0.00099547 276440000 30866 30442 16467 20016 29842 31522 28384 29607 22427 TRUE FALSE 26786.9799 30242.0245 24430.49628 24560.93873 29248.20258 32734.67174 25631.32405 23275.77345 19775.70561 1.354539779 1.52925135 1.235379246 1.241975341 1.478996662 1.655297282 1.296101619 1.176988266 1 14.27144155 1.617001377 2.244740995 1.015270672 1.40903082 0.530216013 0.12893535 0.249935087 2.596815112 0.163214691 0.037729242 41.40009873 -1.617001377 0.393760148 EQRPFFPILYVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQRPFFPILYVIR 13 1 O95486 O95486 SEC24A Protein transport protein Sec24A 0 75.483 0.014654 0 52378 78085 47094 68763 72325 70208 64777 73475 71447 FALSE TRUE 45456.11459 77572.05449 69868.81592 84376.69013 70885.874 72908.94719 58494.93651 57762.94303 63000.61705 0.721518562 1.231290392 1.109017962 1.339299424 1.125161583 1.157273541 0.928481962 0.916863131 1 15.94307834 2.235807172 24.99385474 0.941036139 1.129793362 0.190017419 0.158573388 100.9047058 915921.8781 0.060410579 0.042797021 172.110423 -2.235807172 0.188757223 EQS(ph)AEEDAEAEVDNSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQSAEEDAEAEVDNSK 16 0 Q8NEZ4;Q8NEZ4-3;H0YMU7;C9J4Z5 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 EQS(1)AEEDAEAEVDNSK 166.91 2.12E-09 0 51689 42233 39580 42343 40878 34810 44997 56919 89544 TRUE FALSE 44858.16769 41955.56864 58721.02039 51957.62532 40064.60778 36149.16323 40633.19787 44747.31479 78958.21033 0.568125436 0.53136423 0.743697459 0.658039552 0.507415348 0.457826527 0.5146165 0.566721492 1 16.26880167 1.23848575 24.03745471 1.000000698 0.567617762 0.737268953 0.080954802 0.621096278 197148.5253 0.120157464 0.02148784 17.31752207 -1.23848575 -0.432382937 EQS(ph)PSQHGKDPASLLASELVQLHMQLEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQSPSQHGKDPASLLASELVQLHMQLEEK 29 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 EQS(0.855)PS(0.145)QHGKDPASLLASELVQLHMQLEEK 145.79 2.99E-08 33461000 51780 43469 21636 29777 36705 30330 55987 64516 37966 TRUE FALSE 44937.14181 43183.44928 32099.24197 36538.32296 35974.64231 31496.81473 50557.38936 50719.75546 33477.70273 1.34230064 1.289916743 0.958824512 1.091422648 1.074585153 0.940829632 1.510180963 1.515030941 1 15.03091291 2.232355276 24.99976586 1.384858626 1.11401759 0.230829163 0.188551476 184.0360089 741426.6052 0.077037745 0.053399392 170.7478626 -2.232355276 -0.270841036 EQSEVSVS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EQSEVSVSPR 10 0 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 EQSEVSVS(1)PR;EQSEVSVS(1)PR;EQSEVSVS(1)PR 192.4 7.20E-07 10340800000 3307980 2722760 1739300 2118180 2497790 2825420 2417520 2951080 2919950 TRUE FALSE 2870822.062 2704874.01 2580431.298 2599145.143 2448088.866 2934115.736 2183069.282 2320014.507 2574756.837 1.114987645 1.050535713 1.002203882 1.009472081 0.950803909 1.139570034 0.847873963 0.901061597 1 21.29600476 7.999999981 0.18621855 0.883768598 1.857096864 0.295211128 0.074392717 135.6780705 1.943527622 0.618458684 36.52022592 99999995.6 -7.999999981 0.973328266 EQSSDLTPSGDVS(ph)PVKPLSR ddPTM_MDA-MB-175_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 261.46 1.34E-36 3096740000 2092430 1892130 1557440 2022010 2460650 1966830 2572400 3187470 2878570 TRUE FALSE 1815910.074 1879700.473 2310623.193 2481138.275 2411687.879 2042495.223 2322929.044 2505854.345 2538268.734 0.715412852 0.740544312 0.910314642 0.977492352 0.950131027 0.804680448 0.915162769 0.987229726 1 21.27541339 4.229464679 3.919465306 0.937990889 0.720236892 0.719807862 0.054084643 0.114364984 3.84632663 0.015186114 0.039454818 16961.5165 -4.229464679 -0.217753997 EQST(ph)PPKS(ph)PQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EQSTPPKSPQ 10 1 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 2 EQS(0.004)T(0.996)PPKS(1)PQ;EQST(1)PPKS(1)PQ;EQS(0.002)T(0.998)PPKS(1)PQ 164.13 0.00015679 1489790000 5612550 4476010 3420320 3625250 4105090 3886770 5676620 6340750 5758350 TRUE FALSE 4870837.297 4446606.796 5074398.192 4448418.421 4023406.74 4036296.557 5126102.266 4984829.956 5077604.423 0.959278607 0.875729266 0.999368554 0.876086054 0.792382865 0.794921428 1.009551324 0.981728694 1 22.27571657 2.210887633 24.99817783 0.994411523 0.883493931 0.420622989 0.063116337 229.5507575 207361.2985 0.027620101 0.018626204 162.5128226 -2.210887633 -0.110917592 EQSTCNFQAIVISLKEEFYTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQSTCNFQAIVISLKEEFYTK 21 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 174.71 2.42E-12 82194000 79886 58622 43879 59350 49665 45832 76540 94630 32924 FALSE TRUE 69328.86269 58236.90822 65099.03117 72826.32461 48676.76367 47595.1867 69117.16258 74394.11091 29031.76223 2.388034944 2.00597221 2.242338259 2.508505134 1.676672718 1.639417763 2.380742927 2.562507585 1 14.82534453 1.226792541 24.99415271 0.999997367 2.178136127 0.572429482 0.31927661 439.875684 934189.5619 1.337399192 0.083590277 16.85747566 -1.226792541 1.178138761 EQSTPPKS(ph)PQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EQSTPPKSPQ 10 1 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 EQSTPPKS(1)PQ;EQS(0.001)T(0.09)PPKS(0.909)PQ;EQSTPPKS(1)PQ;EQST(0.002)PPKS(0.998)PQ;EQST(0.001)PPKS(0.999)PQ;EQSTPPKS(1)PQ 158.01 2.14E-05 3614770000 7048360 6295910 4476910 5641660 6860720 5669030 8163320 10044730 8211430 TRUE FALSE 6116901.368 6254551.753 6641958.65 6922685.13 6724205.095 5887121.252 7371642.483 7896742.658 7240684.1 0.844796056 0.863806743 0.917310928 0.95608164 0.928669861 0.813061469 1.018086465 1.090607262 1 22.78769458 2.092270882 6.458998373 1.05246652 0.893044924 0.692919333 0.046795547 0.111323729 6.468930387 0.019742463 0.013208007 123.6718571 -2.092270882 -0.159421596 EQTLS(ph)PTITSGLHNIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EQTLSPTITSGLHNIAR 17 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;O94979-7;H7BXG7;H0Y8W8 D6REX3 SEC31A Protein transport protein Sec31A 1 EQT(0.001)LS(0.499)PT(0.499)ITSGLHNIAR;EQTLS(0.498)PT(0.498)IT(0.004)SGLHNIAR;EQTLS(0.943)PT(0.037)IT(0.019)S(0.001)GLHNIAR;EQT(0.001)LS(0.995)PT(0.003)IT(0.001)SGLHNIAR;EQT(0.167)LS(0.796)PT(0.036)IT(0.001)SGLHNIAR;EQT(0.024)LS(0.674)PT(0.213)IT(0.085)S(0.004)GLHNIAR 249.85 2.57E-21 6533410000 2944157 2857654 1293537 1972183 2821987 3074015 2548562 3223248 3084367 TRUE FALSE 2555079.193 2838881.883 1919095.82 2419997.293 2765834.98 3192274.346 2301402.85 2533981.499 2719736.647 0.93945831 1.043807637 0.705618252 0.889791038 1.016949558 1.173743917 0.846185917 0.931701053 1 21.37503553 3.251019181 24.4373528 0.983900834 0.891817933 0.151599337 0.115049228 385.5169454 756182.195 0.034558135 0.044277309 1782.45749 -3.251019181 -0.092082901 EQTLSPT(ph)ITSGLHNIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQTLSPTITSGLHNIAR 17 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;O94979-7;H7BXG7;H0Y8W8 D6REX3 SEC31A Protein transport protein Sec31A 1 EQT(0.014)LS(0.202)PT(0.769)IT(0.008)S(0.008)GLHNIAR 282.1 5.77E-35 496850000 248190 244300 111230 177400 240290 248090 232390 272820 254100 TRUE FALSE 215391.0627 242695.1772 165021.2 217681.3814 235508.6991 257634.1828 209852.8536 214479.5661 224060.5875 0.96130723 1.083167638 0.736502577 0.971529102 1.051093821 1.149841593 0.936589768 0.957239149 1 17.77352937 3.478634104 24.9296374 1.011579103 0.927844315 0.147052507 0.10068929 119.4234352 1967954.022 0.029582526 0.038746894 3010.468614 -3.478634104 -0.083734788 EQTLSPTIT(ph)SGLHNIAR ddPTM_MDA-MB-175_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(0.085)PT(0.085)IT(0.809)S(0.02)GLHNIAR 218.14 5.30E-14 578490000 264190 279040 123050 194100 275050 271350 253950 308730 307060 TRUE FALSE 229276.6221 277206.9679 182557.3916 238173.3716 269577.0431 281789.0101 229321.9681 242710.492 270759.7166 0.846790006 1.023811708 0.674241331 0.879648474 0.995632018 1.040734617 0.846957483 0.896405474 1 18.04665359 3.457430638 17.85100662 0.943940072 0.851019947 0.201051304 0.098868421 16.5337533 14986.84789 0.028645751 0.037016869 2867.01944 -3.457430638 -0.092920125 EQTLSPTITSGLHNIAR ddPTM_MDA-MB-175_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 0 ; 191.64 2.31E-10 788740000 744080 727160 397940 533450 708470 723570 688550 788630 694320 FALSE TRUE 645747.9427 722383.2381 590385.115 654577.9758 694372.8331 751406.2061 621774.527 619987.6116 612238.2806 1.05473304 1.179905375 0.96430611 1.069155583 1.134154552 1.227310069 1.015576037 1.012657378 1 19.22373373 2.045795922 24.99981609 1.00929719 1.103295984 0.288123915 0.070821045 160.2597495 87484.44749 0.029321088 0.019768267 111.1209439 -2.045795922 0.093998794 EQVANSAFVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EQVANSAFVER 11 0 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ;;;;; 275.57 8.65E-27 3529280000 2969701 2415345 1516632 2020432 2507445 2342310 2560757 2842961 2542669 FALSE TRUE 2577247.489 2399478.44 2250080.308 2479201.966 2457551.75 2432420.181 2312415.18 2235015.914 2242077.567 1.149490779 1.070203134 1.003569342 1.105761015 1.096104696 1.084895642 1.031371623 0.996850397 1 21.09640476 2.062708546 2.879064343 0.999705027 1.082277468 0.507393923 0.036033054 0.227334902 3.736723504 0.01994549 0.010650886 115.5336638 -2.062708546 0.082572441 EQVEPTPEDEDDDIELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQVEPTPEDEDDDIELR 17 0 A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7;B4DSP0;A0A087WZG9;Q86TG7-2 A0A087WXK2;B4DSP0 PEG10 Retrotransposon-derived protein PEG10 0 ; 350.76 2.66E-87 1326530000 358760 293230 171799 212520 272070 293000 292950 286680 273770 FALSE TRUE 311348.957 291303.7528 254881.571 260775.9142 266656.3393 304271.8996 264539.7541 225375.7129 241405.2225 1.289735797 1.206700294 1.055824594 1.080241394 1.104600541 1.260419706 1.095832772 0.93359916 1 17.88109736 -0.927762532 0.299314188 9.89E-22 1.207917139 0.423024218 0.084507663 42.86058976 1.243378749 23.90907814 0.196101326 0.11809662 0.927762532 1.207917139 EQVNDLFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 132.01 0.0026942 0 267020 244020 148050 171520 216420 241540 232740 249550 233370 FALSE TRUE 231732.6305 242417.0166 219647.4752 210466.2375 212113.6654 250832.2001 210168.9106 196185.6745 205781.2645 1.126111413 1.178032496 1.067383252 1.022766762 1.030772485 1.218926323 1.021321893 0.953369953 1 17.65075211 -1.954709466 0.246937323 7.00E-10 1.145074243 0.313372669 0.068571909 98.38844714 1.602275796 45.07225412 0.247789864 0.011099171 1.954709466 1.145074243 EQWDTIEELIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EQWDTIEELIR 11 0 Q16698-2;Q16698 Q16698-2 DECR1 "2,4-dienoyl-CoA reductase, mitochondrial" 0 ;;;;; 208.56 4.46E-08 591707000 283501 265047 203300 327365 309981 318381 261167 321546 325875 FALSE TRUE 246035.6245 263305.8888 301616.56 401698.2267 303812.9846 330629.3231 235839.0645 252785.8902 287350.4287 0.856221533 0.916323285 1.049647155 1.397938498 1.057290869 1.150613641 0.820736776 0.879712939 1 18.13245168 2.238325173 24.99999747 0.892583316 1.077513856 0.224552699 0.149450742 9.413459161 999311.5435 0.062197157 0.044941448 173.1112025 -2.238325173 0.18493054 EQWIQDAEECDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQWIQDAEECDR 12 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ; 202.18 3.25E-07 710490000 892040 795850 511630 561210 718800 754720 703820 870900 735760 FALSE TRUE 774154.6539 790622.0089 759055.9793 688641.3081 704497.2863 783754.5668 635563.6447 684664.8124 648779.291 1.193248096 1.218630157 1.16997566 1.061441568 1.085881279 1.208044982 0.979629981 1.055312372 1 19.30736824 7.230830923 0.03387095 1.79E-07 2.650529889 0.553932738 0.057596473 1473.505701 5.845380864 164.1863488 317.1439616 17014959.64 -7.230830923 2.65052971 EQWWLSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EQWWLSLR 8 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ; 160.63 0.00081944 1641930000 1004990 1033530 806580 1017130 1067560 1050760 893560 1022160 1492890 FALSE TRUE 872178.0252 1026740.673 1196644.786 1248084.912 1046317.645 1091183.417 806902.6887 803579.0385 1316402.245 0.662546747 0.77995968 0.909026698 0.948102996 0.794831252 0.828913367 0.612960584 0.610435786 1 20.32816896 2.276958007 24.33678488 0.708563236 0.827366632 0.055648451 0.131412773 229.6263176 145539.1896 0.049718364 0.038510718 189.2160653 -2.276958007 0.118803396 EQYAQEHGLNFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EQYAQEHGLNFQR 13 0 Q15126 Q15126 PMVK Phosphomevalonate kinase 0 ;;; 167.32 3.21E-05 2458040000 1945280 1872010 1246460 1447720 1898440 1935550 1691460 2002380 2201160 FALSE TRUE 1688206.319 1859712.643 1849252.225 1776446.953 1860664.758 2010011.861 1527422.47 1574186.62 1940941.372 0.869787384 0.958149828 0.952760476 0.915250186 0.958640371 1.035586077 0.786949308 0.811042849 1 20.88832511 2.230018352 24.99975628 0.851254869 0.947969269 0.231068659 0.06910337 231.3793421 677146.9858 0.027655243 0.018975983 169.8315418 -2.230018352 0.0967144 EQYELVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQYELVHR 8 0 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 0 116.3 0.0022971 269090000 260280 287250 173430 211320 273630 304040 267970 295490 300770 FALSE TRUE 225883.3385 285363.0358 257301.3281 259303.4358 268185.2983 315736.6155 241982.3106 232301.763 265213.3132 0.851704373 1.075975532 0.970167466 0.977716513 1.011206018 1.190500626 0.912406348 0.875905361 1 18.01679367 EQYLGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQYLGYR 7 0 Q5JRG1;H7BYF2;Q9BVL2-2;Q9BVL2-3;Q9BVL2 Q5JRG1 NUPL1 Nucleoporin p58/p45 0 126.28 0.0092303 254670000 170510 169160 121190 150080 160770 176560 149430 186470 201570 FALSE TRUE 147976.6715 168048.7768 179797.8894 184157.9578 157570.9915 183352.3774 134938.3016 146594.8416 177740.6242 0.832542769 0.945471963 1.011574535 1.036105047 0.886522101 1.03157271 0.759186608 0.824768351 1 17.43941393 2.244381243 24.99924533 0.849448255 0.959592766 0.211885134 0.086178044 186.052761 799089.2154 0.03247207 0.024459584 175.5420814 -2.244381243 0.110144511 EQYPGIEIESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EQYPGIEIESR 11 0 Q9BRT3;J3KTI2 Q9BRT3 MIEN1 Migration and invasion enhancer 1 0 103.34 0.0048398 0 107710 74665 69543 76292 82320 89633 71631 90437 82836 FALSE TRUE 93475.8506 74174.5207 103174.2274 93615.26465 80681.99306 93081.23951 64684.23665 71097.75133 73043.22245 1.279733389 1.015488066 1.412509251 1.28164204 1.104578773 1.274330956 0.885561103 0.973365481 1 16.15646279 2.240902491 24.9999053 0.95441448 1.223593908 0.580126825 0.110269953 42.28172931 451371.9118 0.041360466 0.03047851 174.141584 -2.240902491 0.269179428 EQYVPPRS(ph)PK ddPTM_MDA-MB-175_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 85.457 0.0086156 3837140000 3717800 3048070 2380590 2703280 3375810 2993220 4052410 4295920 3883210 TRUE FALSE 3226483.31 3028047.027 3531851.287 3317101.041 3308637.986 3108371.11 3659407.902 3377270.939 3424141.338 0.942275155 0.884323026 1.031456046 0.968739522 0.966267937 0.907781194 1.068708193 0.98631178 1 21.70731082 8 0.192405275 1.024766992 0.551576944 0.18776603 0.049003141 175.3064091 2.551880446 0.35738531 23.91807801 100000000 -8 -0.473190048 ERAS(ph)LDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ERASLDK 7 1 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 1 ERAS(1)LDK;ERAS(1)LDK;ERAS(1)LDK;ERAS(1)LDK;ERAS(1)LDK 123.96 0.0025395 3679720000 3946390 2877430 2472190 2802870 2399080 2439950 3644940 3939890 4076780 TRUE FALSE 3424864.563 2858527.973 3667749.353 3439304.473 2351343.002 2533816.455 3291454.28 3097375.184 3594827.713 0.952720085 0.795178017 1.020285156 0.956736942 0.654090596 0.704850596 0.915608353 0.861619925 1 21.7774912 4.777002693 21.43889245 0.862141713 0.952721577 0.05209362 0.119411227 10663.65927 5946282.967 0.030177662 5.372583258 59841.53058 -4.777002693 0.090579864 ERASS(ph)PPDRIDIFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERASSPPDRIDIFGR 15 2 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 ERAS(0.107)S(0.893)PPDRIDIFGR 147.49 1.93E-06 72238000 16872 13337 6433.7 9734.8 11824 10820 10524 13942 8975.1 TRUE FALSE 14642.32245 13249.38837 9545.058839 11945.23513 11588.72553 11236.2524 9503.3841 10960.6118 7914.073902 1.850162461 1.67415525 1.206086645 1.509366134 1.464318589 1.419781081 1.200820743 1.384951914 1 12.95020482 8 0.392726884 1.248434804 10.48678704 0.599458171 0.153649023 61.67767489 0.879078677 0.153062334 434.9375117 100000000 -8 9.238352237 ERAVELLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERAVELLR 8 1 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 ; 163.16 0.00030782 579820000 294310 174965 114028 91738 392490 395330 441650 384740 87669 FALSE TRUE 255416.1878 173815.6434 169172.3222 112568.515 384680.2169 410538.6009 398818.851 302466.3451 77304.87069 3.304011578 2.248443621 2.188378568 1.456163292 4.976144626 5.310643395 5.159039106 3.912642791 1 16.2382717 3.237636933 24.99988444 4.195310974 2.287700917 0.317988655 1.28271015 29.44574427 796968.0447 0.393402675 0.472387859 1728.370849 -3.237636933 -1.907610057 ERDAEQS(ph)GSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERDAEQSGSPR 11 1 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5 P08651-3 NFIC Nuclear factor 1 C-type 1 ERDAEQS(0.807)GS(0.193)PR;ERDAEQS(0.798)GS(0.202)PR 83.729 0.043381 26467300 75014 62914 40122.4 45113.6 46165.8 61335 65357 69301 60736 TRUE FALSE 65100.70984 62500.71379 59525.72684 55357.3324 45247.1909 63694.59714 59018.6882 54481.52045 53555.85927 1.215566527 1.167019158 1.111469924 1.033637274 0.844859769 1.189311459 1.102002451 1.017284032 1 15.7087568 4.094015528 2.25765048 1.033903826 1.200909464 0.375119464 0.086184417 0.347992023 3.506502849 0.02429779 0.068609622 12416.96702 -4.094015528 0.167005637 ERDAEQSGS(ph)PR ddPTM_MDA-MB-175_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(0.001)GS(0.999)PR;ERDAEQS(0.013)GS(0.987)PR;ERDAEQS(0.002)GS(0.998)PR;ERDAEQS(0.003)GS(0.997)PR 187.74 9.09E-06 2032830000 3809090 3250420 2162440 2550400 2512380 3075530 3247730 3447610 3182060 TRUE FALSE 3305709.105 3229067.777 3208203.217 3129507.3 2462388.553 3193847.629 2932765.644 2710365.431 2805880.492 1.178136102 1.150821564 1.143385553 1.115338771 0.877581408 1.138269302 1.045221154 0.96595897 1 21.42002213 3.458692359 24.98773596 1.00886411 1.152214653 0.546118034 0.064956331 179.8591153 243870.1345 0.018304091 0.023634533 2875.360875 -3.458692359 0.143350542 ERDFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERDFLK 6 1 E9PFR3;Q14738;H0Y8C4;Q14738-2;Q14738-3;H0YJZ3;E9PNH9;E9PNS4;C9J979;H0YJ75;Q13362-3;Q13362;Q13362-4;Q13362-5;Q96B13;Q13362-2;G3V2U3;Q15172;Q15172-2;C9IYS7;A0A087WYI0;Q5TA45-2;Q5TA45-4;Q5TA45-3;Q5TA45;Q5TA45-5 E9PFR3;H0YJ75;Q15172;C9IYS7 PPP2R5D;PPP2R5C;CPSF3L;PPP2R5A Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform;Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform;Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform;Integrator complex subunit 11 0 64.776 0.096479 141650000 519500 439620 338100 394100 406380 457150 497860 460130 478400 FALSE TRUE 450846.7588 436732.1073 501606.2909 483586.4284 398293.8331 474736.8563 449577.6138 361734.7802 421844.097 1.068752086 1.035292684 1.189079791 1.146362914 0.944173063 1.125384614 1.065743522 0.857508219 1 18.68635039 1.830866688 7.030931973 0.924444013 1.084114833 0.427653146 0.073886743 0.206928422 13.31984141 0.036065981 0.019330938 67.74335287 -1.830866688 0.15967082 ERDFTSLENTVEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERDFTSLENTVEER 14 1 Q07065 Q07065 CKAP4 Cytoskeleton-associated protein 4 0 ; 160.04 4.39E-06 184872000 80328 70159 40534 72915 86155 99950 58924 129325 85242 FALSE TRUE 69712.45127 69698.12091 60136.37798 89471.46519 84440.68406 103795.1412 53209.55955 101669.8552 75164.78787 0.927461558 0.927270906 0.800060503 1.190337493 1.123407469 1.380901139 0.707905404 1.352626117 1 16.19776935 3.73388596 24.93990428 1.13388604 0.889164978 0.264019552 0.189268633 473.9834276 2528764.617 0.048077873 0.07403098 5418.585872 -3.73388596 -0.244721062 ERDFYFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ERDFYFGK 8 1 Q15691;Q15555-4;Q15555-5;Q15555-3;Q15555 Q15691;Q15555-4 MAPRE1;MAPRE2 Microtubule-associated protein RP/EB family member 1;Microtubule-associated protein RP/EB family member 2 0 ;; 123.35 0.0012323 1213120000 1484140 1319770 844469 1016210 1318820 1122980 1293480 1587010 1351500 FALSE TRUE 1288007.139 1311100.344 1252857.033 1246956.012 1292578.062 1166181.767 1168038.509 1247640.262 1191727.21 1.080790241 1.100168171 1.051295148 1.046343494 1.084625787 0.978564354 0.98012238 1.04691766 1 20.18462261 2.746651023 24.97263994 1.006518181 1.071526409 0.679239548 0.024207452 408.0909017 1259653.769 0.008449827 0.008300544 558.0216166 -2.746651023 0.065008228 ERDHS(ph)PT(ph)PSVFNSDEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERDHSPTPSVFNSDEER 17 1 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 2 ERDHS(0.999)PT(0.827)PS(0.108)VFNS(0.066)DEER 84.107 0.012294 598910000 243870 216840 156950 181940 199100 224050 189090 207110 292180 TRUE FALSE 211641.9616 215415.5638 232851.545 223252.2578 195138.2995 232669.3485 170752.0809 162821.1382 257638.8133 0.821467693 0.836114563 0.903790629 0.866531929 0.757410334 0.903083451 0.662757598 0.631974415 1 17.97499043 2.242822809 24.9999429 0.73295924 0.846774692 0.095409515 0.106452346 170.5588955 1000422.383 0.040132001 0.029970134 174.9132902 -2.242822809 0.113815452 ERDHS(ph)PTPS(ph)VFNSDEERYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERDHSPTPSVFNSDEERYR 19 2 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 2 ERDHS(0.999)PT(0.034)PS(0.582)VFNS(0.384)DEERY(0.001)R 51.857 0.07086 593100000 165120 147050 72076 117710 137970 123590 157760 174380 182720 TRUE FALSE 143298.9736 146084.0189 106932.1947 144437.8546 135224.6669 128344.5873 142460.4595 137090.194 161119.0498 0.889398081 0.906683717 0.663684368 0.896466649 0.839284164 0.796582325 0.884193767 0.850862727 1 17.29776755 -0.393647777 1.244228019 9.999997937 0.83367666 0.33165652 0.070859679 94.71882401 3.337755551 2350.781592 0.020400825 0.403972891 0.393647777 -9.166321277 ERDHS(ph)PTPSVFNS(ph)DEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERDHSPTPSVFNSDEER 17 1 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 2 ERDHS(0.49)PT(0.196)PS(0.315)VFNS(1)DEER 126.32 5.84E-05 122960000 118720 93096 71436 101380 105020 99280 108880 104080 162860 TRUE FALSE 103030.8512 92484.44625 105982.6885 124399.8785 102930.3075 103099.3658 98320.83436 81823.30195 143606.8763 0.717450681 0.644011266 0.738005667 0.866252938 0.716750549 0.717927779 0.684652691 0.569772869 1 17.13176531 4.210814587 23.40988468 0.736872543 0.680730993 0.049434372 0.115511577 369.7624641 311976.459 0.029874774 0.062221469 16248.54909 -4.210814587 -0.05614155 ERDHS(ph)PTPSVFNS(ph)DEERYR ddPTM_MDA-MB-175_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(0.372)PS(0.172)VFNS(0.456)DEERYR 69.435 0.012294 621050000 166240 139460 103010 117070 142870 122820 166150 174040 191950 TRUE FALSE 144270.9628 138543.8781 152825.9805 143652.5328 140027.1665 127544.9649 150036.7986 136822.9004 169257.8897 0.852373636 0.818537194 0.902917913 0.848719862 0.827300676 0.75355403 0.886439024 0.80836941 1 17.36886356 1.232362101 24.99795565 1.000000269 0.837121171 0.604787413 0.04133948 142.1568593 573247.0256 0.088195422 0.009784204 17.07505458 -1.232362101 -0.162879098 ERDHS(ph)PTPSVFNSDEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ERDHSPTPSVFNSDEER 17 1 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 ERDHS(0.987)PT(0.01)PS(0.003)VFNSDEER;ERDHS(0.736)PT(0.263)PS(0.001)VFNSDEER;ERDHS(0.787)PT(0.213)PSVFNSDEER;ERDHS(0.956)PT(0.044)PSVFNSDEER 232.54 6.71E-17 4060590000 1726440 1628090 1047510 1339510 1577010 1512230 1563330 1693820 1611550 TRUE FALSE 1498286.58 1617394.97 1554089.34 1643666.219 1545630.586 1570406.467 1411718.497 1331609.774 1421034.395 1.054363346 1.138181437 1.093632459 1.156668849 1.087679927 1.105115029 0.993444284 0.937070756 1 20.43851004 2.186143862 3.763398466 0.964237716 1.109246796 0.790383406 0.031457133 0.083003143 2.41524753 0.012783495 0.008406372 153.5125416 -2.186143862 0.14500908 ERDHS(ph)PTPSVFNSDEERYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERDHSPTPSVFNSDEERYR 19 2 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 ERDHS(1)PTPSVFNSDEERYR 136.34 3.14E-06 267570000 43614 43065 12930 15967 38626 38660 37679 43744 8720.9 TRUE FALSE 37850.2994 42782.10318 19182.99125 19592.55139 37857.41817 40147.27522 34024.89638 34389.68602 7689.925137 4.922063443 5.563396576 2.494561508 2.547820823 4.92298917 5.220762817 4.424606973 4.472044318 1 12.90875384 4.265879268 24.99397894 3.777033492 5.242731335 0.207326454 1.306957166 393.8720614 360348.9998 0.33294835 0.880427919 18445.02585 -4.265879268 1.465697844 ERDLFFELDAMDHLESFIAECDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERDLFFELDAMDHLESFIAECDRR 24 2 Q9NQ29-3;Q9NQ29;Q9NQ29-2;A8MYV2 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 0 ; 175.61 8.58E-13 45821000 29176 27901 10797 13950.1 24085 24726.1 26393 31347 5037.3 FALSE TRUE 25320.31768 27717.71649 16018.46531 17117.68342 23605.75562 25677.32907 23833.41092 24643.68799 4441.796133 5.700468216 6.240204563 3.606303584 3.853775119 5.314461744 5.780843672 5.365714727 5.548135767 1 12.11692746 1.23538874 24.99985258 0.999994292 5.168627873 0.714986501 0.828638357 52.89049745 416795.797 1.498917439 0.215996147 17.19446786 -1.23538874 4.168633581 ERDLS(ph)R ddPTM_MDA-MB-175_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 784540000 343190 314743 242300 271814 246056 339207 346123 381390 525830 TRUE FALSE 297836.572 312675.4325 359477.0904 333533.5231 241159.967 352256.5128 312556.0447 299832.7165 463666.9764 0.642350193 0.674353466 0.775291553 0.719338534 0.520114607 0.759718787 0.67409598 0.646655319 1 18.82272945 1.235277592 24.97731178 1.000000452 0.677053088 0.673750978 0.070747222 54.8927795 417553.9179 0.118186296 0.01686297 17.19006791 -1.235277592 -0.322947365 ERDLS(ph)RDR ddPTM_MDA-MB-175_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 97.734 0.0063176 709410000 460230 452150 255020 260620 407550 395950 434470 500180 127651 TRUE FALSE 399409.4394 449179.7969 378348.525 319797.7543 399440.5524 411182.4527 392335.1663 393220.3994 112560.2442 3.548405943 3.990572338 3.361298011 2.841125271 3.548682354 3.65299894 3.48555717 3.493421698 1 16.78033784 1.238490706 24.9990175 0.999997279 3.488416742 0.884238007 0.283167964 0.548709464 194796.9425 0.402968654 0.072084757 17.31771971 -1.238490706 2.488419463 ERDPQQEQER ddPTM_MDA-MB-175_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 0 153.54 1.47E-05 164700000 135170 121050 87629 99535 104190 125050 98937 142370 117560 FALSE TRUE 117306.942 120254.8146 130006.6775 122135.943 102116.8228 129860.7544 89342.10497 111925.2834 103662.1907 1.131627078 1.160064376 1.254137855 1.178211093 0.985092271 1.252730176 0.86185816 1.079711731 1 16.66153026 2.739550449 1.008064805 1.004054995 1.181387877 0.307651243 0.103084648 0.634747025 1.429147069 0.066498252 0.050316487 548.9723221 -2.739550449 0.177332881 ERDQGGFGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERDQGGFGDR 10 1 A0A087WTP3;Q92945;M0R0I5 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ; 142.1 3.32E-05 674570000 662910 612170 439700 477870 537410 598390 547470 652570 750320 FALSE TRUE 575304.7639 608148.615 652340.3907 586377.6873 526716.5924 621410.4505 494376.4437 513022.9838 661618.0244 0.869542157 0.919183868 0.985977357 0.886278284 0.796103753 0.939228418 0.747223361 0.775406602 1 19.33563901 3.473521682 20.47061244 0.838856613 0.926295818 0.140080751 0.079669804 17.36050465 98720.42462 0.022795862 0.029690056 2975.23779 -3.473521682 0.087439205 ERDQGGFGDRNEYGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERDQGGFGDRNEYGSR 16 2 A0A087WTP3;Q92945;M0R0I5 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ; 203.99 1.48E-11 448490000 347930 323990 111308 130017 302640 292620 298270 331020 40966 FALSE TRUE 301950.169 321861.6884 165136.9211 159539.347 296618.0561 303877.2808 269343.8213 260233.949 36123.04615 8.358934286 8.910148027 4.571511506 4.416552978 8.211324562 8.412282826 7.456287607 7.204097571 1 15.14063194 4.260890392 24.96116228 6.21610725 8.634543563 0.197026791 2.226632813 430.6766477 481419.9244 0.561491979 1.483117825 18234.35443 -4.260890392 2.418436313 ERDQRPS(ph)SPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ERDQRPSSPIR 11 2 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 ERDQRPS(0.967)S(0.033)PIR;ERDQRPS(0.5)S(0.5)PIR;ERDQRPS(0.5)S(0.5)PIR 143.64 2.92E-05 2644970000 1975720 1622490 1021624 1290233 1596733 1686840 1562830 1865560 1505329 TRUE FALSE 1714623.596 1611831.756 1515684.784 1583200.123 1564961.137 1751733.826 1411266.987 1466624.512 1327370.72 1.291744326 1.214304136 1.141869984 1.19273395 1.178993263 1.319702024 1.06320485 1.104909495 1 20.34013993 2.210043221 24.95291236 1.06651813 1.215724742 0.649298231 0.05757519 139.0128241 121636.137 0.023387015 0.015770721 162.1971506 -2.210043221 0.149206612 ERDQRPSS(ph)PIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERDQRPSSPIR 11 2 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 ERDQRPS(0.367)S(0.633)PIR 88.282 0.010313 134090000 165590 142920 91579 111760 151140 136540 156910 168640 144440 TRUE FALSE 143706.8619 141981.1491 135866.9107 137136.8161 148132.6097 141792.7822 141692.8924 132577.6484 127364.4677 1.128312036 1.114762631 1.06675679 1.076727431 1.163060721 1.113283671 1.112499387 1.040931201 1 16.95860332 1.581099296 2.739007923 1.002727162 1.1104177 0.680988683 0.026416219 0.150187968 2.437667863 0.029934514 0.007515638 38.11529592 -1.581099296 0.107690538 ERDSASFNPELLTHILDGS(ph)PEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERDSASFNPELLTHILDGSPEK 22 1 Q15067-2;Q15067;I3L0T4;I3L2U4;K7ELT1 Q15067-2;K7ELT1 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 1 ERDSASFNPELLTHILDGS(1)PEK 96.887 0.00084313 22804000 27340 20974 21063 22879 25120 34587 23017 31150 25561 TRUE FALSE 23726.94973 20836.22041 31249.13725 28074.02663 24620.16115 35917.58427 20784.81488 24488.81491 22539.2077 1.052696707 0.924443339 1.386434593 1.245564041 1.092325936 1.593560197 0.922162623 1.08649848 1 14.46014918 ERDVIMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 2059250000 540050 461150 323940 355600 423980 478090 501030 591870 597640 FALSE TRUE 468681.0242 458120.6753 480598.4675 436344.415 415543.6275 496482.4317 452440.1877 465303.2064 526987.68 0.889358598 0.869319517 0.911972871 0.827997374 0.788526266 0.942113925 0.858540351 0.882948927 1 19.00740971 1.234754834 3.924209789 1.015693747 0.86944417 0.483512943 0.041998685 0.225599013 5.881745591 0.096201125 0.010540382 17.16938874 -1.234754834 -0.146249577 ERDVYEELLTQAEIQGNINK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ERDVYEELLTQAEIQGNINK 20 1 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;; 259.18 2.53E-36 1028730000 1693590 1429190 1229020 1586060 1465260 1184250 1569160 1940190 2545770 FALSE TRUE 1469777.79 1419801.557 1823378.183 1946199.164 1436104.193 1229808.864 1416983.105 1525295.467 2244811.971 0.654744277 0.632481284 0.812263213 0.866976473 0.639743645 0.547844933 0.631225743 0.679475826 1 21.09816318 1.238161783 24.99999955 1.000000354 0.683113357 0.537746845 0.092338615 8.491267791 531582.8873 0.14016842 0.024593862 17.30460867 -1.238161783 -0.316886996 ERECSPSS(ph)PLPPLPEDEEGSEVTNSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERECSPSSPLPPLPEDEEGSEVTNSK 26 1 Q96GY3 Q96GY3 LIN37 Protein lin-37 homolog 1 ERECS(0.001)PS(0.085)S(0.914)PLPPLPEDEEGSEVTNSK 189.2 5.43E-18 164540000 200900 166650 107400 126550 149470 118270 188990 215170 163220 TRUE FALSE 174350.556 165555.2652 159338.9992 155285.1117 146495.8394 122819.9234 170661.7789 169157.57 143924.3175 1.211404431 1.150293905 1.107102691 1.07893589 1.017867181 0.85336464 1.185774453 1.175323065 1 17.13495085 4.342375935 1.565795858 1.063938974 1.216843355 0.250699471 0.093249018 0.96231529 3.750904448 0.029448788 0.181487646 21997.63215 -4.342375935 0.152904381 EREDEIATMECINNGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EREDEIATMECINNGK 16 1 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ;;; 267.51 2.25E-27 2061120000 2031690 1550250 1334110 1580430 1580790 1278090 2000490 2253170 1991200 FALSE TRUE 1763197.019 1540066.306 1979290.058 1939290.787 1549335.372 1327258.949 1806482.788 1771347.13 1755802.604 1.004211416 0.877129526 1.127285068 1.104503879 0.882408631 0.755927202 1.028864397 1.008853231 1 20.74369923 5.088663189 19.98313557 0.97564151 2.693914925 0.007242907 0.110956281 4412.11361 1085089.456 0.027409686 31279.62801 122648.7676 -5.088663189 1.718273416 EREDLYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EREDLYAK 8 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ; 109.29 0.0033258 330210000 558400 484850 362230 398310 444000 466040 496000 620360 547910 FALSE TRUE 484606.0252 481664.9884 537405.6396 488752.3733 435165.2687 483968.8604 447897.9963 487700.8416 483136.704 1.003041212 0.996953832 1.112326253 1.011623355 0.900708361 1.001722404 0.927062657 1.009446887 1 18.88207193 3.469395355 24.99923771 0.970231188 1.038155617 0.335049068 0.045392837 205.6375623 665393.5134 0.012802617 0.016558711 2947.103276 -3.469395355 0.067924429 EREEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EREEAER 7 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 100.84 0.0086653 160580000 71128 68405 48732 51899 46490 66723 61007 75818 72516 FALSE TRUE 61728.25458 67955.64305 72298.9582 63683.46118 45564.93996 69289.87699 55090.55053 59604.91072 63943.24109 0.965360115 1.06274943 1.130673969 0.995937336 0.712584148 1.083615341 0.861553928 0.932153418 1 15.96450425 3.472328164 24.99995918 0.917480539 1.055475964 0.27104088 0.101960969 159.9281389 834153.1029 0.027644092 0.0358264 2967.072538 -3.472328164 0.137995425 EREEIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EREEIEK 7 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ;;;; 135.83 0.0027717 5559340000 5039830 4058040 3083270 3388840 3503670 3171130 4852290 5442790 4876720 FALSE TRUE 4373803.696 4031382.468 4574349.685 4158327.917 3433953.822 3293125.423 4381715.663 4278891.714 4300199.717 1.017116409 0.937487264 1.063752845 0.96700809 0.798556822 0.765807553 1.018956316 0.995044881 1 22.03597223 3.472693689 24.99660976 0.921932543 1.00194316 0.182821425 0.087340561 262.6505251 1482830.135 0.028068429 0.036388069 2969.570832 -3.472693689 0.080010617 EREELWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EREELWK 7 1 Q16537-2;Q16537;Q16537-3 Q16537-2 PPP2R5E Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform 0 107.01 0.0069077 212090000 321210 301830 201760 250430 218950 276220 252770 303470 313380 FALSE TRUE 278761.2847 299847.2589 299331.8108 307293.9591 214593.3234 286846.3621 228256.4043 238575.3021 276332.5734 1.008789088 1.085095598 1.08323028 1.112043923 0.776576285 1.038047591 0.826020623 0.863362937 1 18.07604611 3.256215054 24.99999516 0.897375393 1.073985936 0.533559718 0.079630557 177.8544458 251853.6481 0.021666849 0.027909313 1803.91078 -3.256215054 0.176610543 EREES(ph)EDELEEANGNNPIDIEVDQNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EREESEDELEEANGNNPIDIEVDQNK 26 1 Q9UKL0 Q9UKL0 RCOR1 REST corepressor 1 1 EREES(1)EDELEEANGNNPIDIEVDQNK;EREES(1)EDELEEANGNNPIDIEVDQNK;EREES(1)EDELEEANGNNPIDIEVDQNK;EREES(1)EDELEEANGNNPIDIEVDQNK;EREES(1)EDELEEANGNNPIDIEVDQNK;EREES(1)EDELEEANGNNPIDIEVDQNK 331.91 3.24E-95 3779340000 1926980 1513904 1229174 1457551 1475770 1170775 1818508 2143160 2157810 TRUE FALSE 1672324.711 1503959.065 1823606.658 1788510.232 1446405.064 1215815.472 1642149.374 1684861.912 1902716.16 0.878914441 0.790427441 0.958422857 0.939977423 0.760179103 0.638989408 0.863055357 0.885503549 1 20.85962893 1.327651981 2.183077488 1.027326748 0.830753755 0.252901995 0.091239753 0.854024792 4.937168485 0.309738651 0.026520365 21.2643436 -1.327651981 -0.196572993 EREKEPS(ph)RER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EREKEPSRER 10 3 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477 Q8NI27 THOC2 THO complex subunit 2 1 EREKEPS(1)RER;EREKEPS(1)RER 124.47 0.0024023 1994900000 1308080 785510 644850 716290 878200 734200 1078300 1129570 701530 TRUE FALSE 1135213.914 780349.9331 956701.6169 878934.5923 860725.5382 762445.1491 973726.632 888020.2458 618595.9226 1.835146131 1.261485737 1.546569549 1.420854164 1.391418059 1.232541504 1.574091578 1.435541706 1 19.2386378 8 0.036153702 1.88E-06 3.570724584 0.298932711 0.187034683 3514.228266 12.54282567 407.901649 935.6704218 99999999.96 -8 3.570722703 ERELEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERELEEAR 8 1 Q9Y490;Q9Y4G6;H0YMT1;A0A1B0GVU7 Q9Y490;Q9Y4G6 TLN1;TLN2 Talin-1;Talin-2 0 ; 128.27 0.0010404 169085000 225101 211728 136222 161421 199367 214565 213193 212110 227748 FALSE TRUE 195353.3325 210337.1448 202099.4148 198074.1052 195399.9868 222819.4544 192517.5757 166751.9271 200823.8909 0.972759424 1.047371126 1.006351455 0.986307477 0.972991739 1.109526628 0.958638809 0.830339092 1 17.61557138 1.999546316 24.99999686 0.900482312 1.015296288 0.349205614 0.05701015 13.42245789 739659.777 0.022174901 0.01476089 99.89558995 -1.999546316 0.114813976 ERELSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERELSWR 7 1 Q96KN1 Q96KN1 FAM84B Protein FAM84B 0 ; 123.16 0.0038953 450460000 552660 561430 472930 503580 543440 614190 542870 585940 782490 FALSE TRUE 479624.5807 557741.9294 701640.5299 617925.5357 532626.6072 637818.2867 490222.551 460641.2908 689984.9236 0.695123276 0.808339299 1.016892552 0.895563823 0.771939486 0.924394526 0.710482989 0.667610661 1 19.39620531 2.232586136 24.9963712 0.763212432 0.855886093 0.031118868 0.122624853 333.8799391 1396888.636 0.049472552 0.034333385 170.8386522 -2.232586136 0.092673661 ERENMDTDDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ERENMDTDDER 11 1 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 0 ;; 88.441 0.013618 407450000 476030 408863 262538 319732 444050 412390 394660 447950 465190 FALSE TRUE 413121.4294 406177.152 389502.2549 392332.0374 435214.2738 428254.9102 356385.9339 352159.3785 410195.7681 1.007132354 0.990203175 0.949552105 0.956450719 1.060991623 1.044025666 0.868819139 0.858515387 1 18.64595308 2.232817171 24.9998573 0.896891791 0.999193845 0.416880008 0.050723792 125.6730083 547017.8899 0.021142409 0.014694161 170.9295585 -2.232817171 0.102302054 EREPEAASSRGS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EREPEAASSRGSPVR 15 2 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EREPEAAS(0.352)S(0.014)RGS(0.635)PVR 135.18 2.41E-05 394130000 269740 251390 78031 65532 231420 214970 246080 229670 22223 TRUE FALSE 234093.1756 249738.6025 115767.0526 80412.04219 226815.1948 223240.035 222215.1995 180556.8578 19595.82226 11.94607567 12.74448192 5.907741512 4.103529882 11.57467096 11.39222596 11.33992728 9.214048557 1 14.25825849 4.256334381 24.9741674 8.239709661 12.34528207 0.224017184 3.446402471 413.887247 581548.6359 0.88731498 2.336652657 18044.06493 -4.256334381 4.105572407 EREQPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EREQPPR 7 1 Q15233;Q15233-2;H7C367;Q8WXF1;Q8WXF1-2 Q15233;Q8WXF1 NONO;PSPC1 Non-POU domain-containing octamer-binding protein;Paraspeckle component 1 0 119.41 0.0043674 52955000 63651 53096 36624 40386 43197 49976 53348 56547 46640 FALSE TRUE 55239.35908 52747.20888 54335.4889 49556.25856 42337.46421 51898.60906 48174.31917 44454.8641 41126.27233 1.343164745 1.282567223 1.321186819 1.204978126 1.029450563 1.261933215 1.171375776 1.080935898 1 15.32777269 8 0.04208167 1.89E-10 3.120739828 0.634420191 0.072312382 1053.497287 4.360608161 99.42571387 261.098713 100000000 -8 3.120739828 ERESLQQMAEVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERESLQQMAEVTR 13 1 K7ELL7;P14314-2;P14314;K7EPW7;K7EKX1;K7EJ70 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 59.421 0.090767 220230000 244560 241900 128200 126040 245110 293540 188580 186660 152590 FALSE TRUE 212240.7764 240310.943 190197.9488 154659.3084 240232.7905 304832.6737 170291.5406 146744.2116 134550.984 1.577400402 1.786021445 1.413575309 1.14944762 1.785440607 2.265555142 1.265628355 1.090621616 1 17.03779342 2.013572793 24.99716548 1.089685996 1.649916306 0.457233866 0.28587713 214.4688338 394988.1655 0.123935547 0.083511137 103.1745999 -2.013572793 0.56023031 ERESSANNSVS(ph)PSESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERESSANNSVSPSESLR 17 1 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 ERESSANNS(0.008)VS(0.852)PS(0.139)ESLR 99.11 0.0010064 205350000 83804 53839 33215 32832 83690 64992 43372 62994 40763 TRUE FALSE 72729.08907 53485.32806 49277.8851 40287.00741 82024.73274 67492.2843 39165.79012 49523.22332 35944.04458 2.023397476 1.488016407 1.37096105 1.120825658 2.282011769 1.877704223 1.089632249 1.37778661 1 15.13346514 2.231253156 24.97200559 1.199294871 1.670480218 0.351799692 0.341596266 218.4081238 746364.4569 0.143198065 0.098756169 170.3151009 -2.231253156 0.471185347 EREVDEDS(ph)EPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EREVDEDSEPER 12 1 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EREVDEDS(1)EPER;EREVDEDS(1)EPER;EREVDEDS(1)EPER 239.19 2.22E-16 2345600000 899200 793870 598850 689960 791860 770390 752520 807930 1030910 TRUE FALSE 780368.4417 788655.0157 888455.863 846625.9634 776103.5352 800027.4018 679540.7262 635160.4568 909036.9942 0.858456198 0.86757197 0.977359413 0.931343794 0.853764522 0.880082336 0.747539133 0.698717941 1 19.79397948 2.353973283 5.583266808 0.788753508 0.898918101 0.137852958 0.085885702 0.287788627 12.95213506 0.032736758 0.025067291 225.9296776 -2.353973283 0.110164594 EREVDEDS(ph)EPEREVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EREVDEDSEPEREVR 15 2 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EREVDEDS(1)EPEREVR;EREVDEDS(1)EPEREVR 221.51 1.20E-12 1262380000 680690 579370 279800 282020 529560 546820 566360 599100 152099 TRUE FALSE 590735.0919 575564.0803 415112.2159 346056.9514 519022.7921 567856.5192 511434.4944 470987.1272 134118.0295 4.404591195 4.291474327 3.095126117 2.580241842 3.869895748 4.234005833 3.813316497 3.51173611 1 17.03314367 4.246687433 23.02225966 3.267729426 4.348034883 0.224867915 0.900920801 110.9799418 314370.9459 0.227145162 0.576258183 17647.67237 -4.246687433 1.080305457 EREVEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EREVEER 7 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;; 172.21 0.00082886 2295398000 2991350 2944889 1864463 2289390 2283934 2900903 2835767 3253203 3151655 FALSE TRUE 2596035.518 2925543.83 2766123.543 2809230.991 2238488.182 3012502.616 2560754.753 2557530.855 2779069.936 0.934138247 1.052706084 0.995341465 1.010852931 0.805481054 1.083996691 0.921443077 0.920283013 1 21.40617071 ERFS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ERFSPPR 7 1 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 ERFS(1)PPR;ERFS(1)PPR;ERFS(1)PPR;ERFS(1)PPR;ERFS(1)PPR 85.533 0.012561 5998980000 802240 669552 526753 685686 675118 710355 638906 729974 1255869 TRUE FALSE 696221.9514 665153.6688 781492.5127 841381.4864 661684.4726 737682.8165 576944.9945 573874.7408 1107401.598 0.628698706 0.600643588 0.705699282 0.75977991 0.597510853 0.66613848 0.520989852 0.518217368 1 20.07874708 1.228852536 24.98418546 1.000000763 0.621300534 0.71426237 0.074569833 244.8041337 629968.9548 0.263351459 0.020534011 16.9376259 -1.228852536 -0.378700229 ERFS(ph)PPRHELS(ph)PPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERFSPPRHELSPPQK 15 2 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 2 ERFS(1)PPRHELS(1)PPQK;ERFS(1)PPRHELS(1)PPQK 92.913 0.0027133 467290000 258252 221286 140941 179085 217922 208680 239976 262001 211024 TRUE FALSE 224123.3439 219832.3577 209100.539 219748.9864 213585.7786 216708.0546 216703.1645 205974.125 186076.9831 1.204465701 1.181405427 1.123731348 1.18095738 1.147835562 1.164615048 1.164588768 1.106929624 1 17.50554009 1.213227993 1.709077149 0.928361491 1.166389073 0.861390026 0.021406832 0.364362749 0.931825368 0.148088127 0.005928307 16.33909481 -1.213227993 0.238027582 ERFS(ph)PPRHELS(ph)PPQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ERFSPPRHELSPPQKR 16 3 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 2 ERFS(1)PPRHELS(1)PPQKR;ERFS(1)PPRHELS(1)PPQKR;ERFS(1)PPRHELS(1)PPQKR;ERFS(1)PPRHELS(1)PPQKR 107.75 0.0015847 7067700000 1647670 1301660 679510 762510 1215480 1058520 1484210 1627290 523810 TRUE FALSE 1429926.235 1293109.31 1008123.309 935649.5497 1191294.326 1099241.949 1340271.543 1279306.697 461885.7785 3.095843824 2.79963006 2.1826247 2.025716299 2.579196809 2.379899968 2.901738059 2.769746887 1 18.8171766 4.416291103 4.244723556 2.350759233 3.040789319 0.221850061 0.526837656 0.325207905 11.56799484 0.132438435 0.412329515 26079.01011 -4.416291103 0.690030086 ERFS(ph)PPRHELSPPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERFSPPRHELSPPQK 15 2 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 ERFS(1)PPRHELSPPQK;ERFS(1)PPRHELSPPQK 108.49 0.00056078 1184690000 1073230 868720 608000 804870 905260 726050 882560 1127020 1102210 TRUE FALSE 931399.9363 863013.3211 902030.8336 987628.0352 887247.0971 753981.6133 796969.467 886015.5435 971907.9894 0.958321103 0.887957842 0.928103116 1.016174418 0.912892071 0.775774684 0.820005058 0.91162492 1 19.89046021 2.996260405 24.96930231 0.873330589 0.944799807 0.204536461 0.065539904 261.9705907 1749195.523 0.021161797 0.023488277 991.4262308 -2.996260405 0.071469218 ERFS(ph)PPRHELSPPQKR ddPTM_MDA-MB-175_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 1 ERFS(1)PPRHELSPPQKR;ERFS(1)PPRHELSPPQKR;ERFS(1)PPRHELSPPQKR 178.03 2.04E-09 2042220000 1309930 989800 518670 677890 911200 871550 1040080 1225870 581087 TRUE FALSE 1136819.432 983297.9386 769500.5468 831815.2854 893068.9027 905079.0925 939213.2017 963727.2402 512391.5568 2.218653716 1.919036185 1.501782253 1.623397721 1.742942269 1.766381745 1.832998981 1.880841375 1 18.96688718 8 0.039180475 7.92E-13 4.477033117 0.283733283 0.268364232 3404.269794 13.1439204 477.5298914 1173.755506 99999999.94 -8 4.477033117 ERFTEHEVQIYVGEIVLALEHLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERFTEHEVQIYVGEIVLALEHLHK 24 1 O75582-3;O75582;O75582-2;A0A3B3ISL8;G3V2D1 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 0 159.98 7.10E-12 64353000 282190 222060 155970 178020 207300 220160 279360 297340 168020 FALSE TRUE 244897.8765 220601.2732 231397.6137 218442.1619 203175.1356 228629.6977 252267.7102 233756.1549 148156.867 1.652963386 1.488970965 1.561841974 1.474397821 1.371351458 1.543159641 1.702706836 1.577761191 1 17.17676597 1.236553753 24.99849348 0.999999306 1.546246393 0.777197674 0.091981449 26.37634307 328470.0986 0.15178728 0.023882043 17.24065467 -1.236553753 0.546247087 ERGDYVLAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ERGDYVLAVK 10 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;A0A0A0MT44 O75369-8 FLNB Filamin-B 0 ;;; 100.72 0.0034837 1863240000 3790300 3643640 2318560 2912920 3424140 3251390 3970150 4382670 3938650 FALSE TRUE 3289402.252 3619704.689 3439823.371 3574343.007 3356006.313 3376473.077 3585125.464 3445470.126 3473027.284 0.947128249 1.042233301 0.99043949 1.029172165 0.966305773 0.972198834 1.032276792 0.992065378 1 21.72776231 2.252984679 24.99907012 1.005777376 0.994117471 0.05957686 0.029707863 960.2121176 1664187.515 0.01064264 0.008211827 179.0542684 -2.252984679 -0.011659905 ERGT(ph)PPVDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERGTPPVDPK 10 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 ERGT(1)PPVDPK 78.814 0.046682 541820000 1488700 924250 737770 801780 904780 823580 1163700 1307700 1257300 TRUE FALSE 1291964.523 918178.5409 1094558.04 983836.4034 886776.6482 855263.6555 1050844.553 1028058.532 1108663.426 1.165335207 0.828185109 0.987277125 0.887407648 0.79986101 0.7714367 0.947848128 0.927295433 1 20.08039002 4.74734239 24.87051307 0.89481021 1.165335355 0.556790809 0.076167516 877.409197 2484818.022 0.019265559 0.223837577 55891.06556 -4.74734239 0.270525145 ERGTGDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERGTGDVK 8 1 P43487;F6WQW2;P43487-2;C9JXG8;C9JJ34;C9JGV6;C9JDM3;C9JIC6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ; 93.598 0.0099914 242650000 401540 289100 192121 272480 223440 274080 370980 456120 295180 FALSE TRUE 348475.4716 287200.8831 285031.3582 334350.7486 218993.9812 284624.035 335002.4167 358582.2875 260284.1567 1.338827058 1.10341285 1.095077633 1.284560508 0.841365006 1.093512715 1.287064188 1.377656989 1 17.98972797 0.979123616 17.26570037 0.591519067 1.178151005 0.112274446 0.157013772 7128148.879 152479281.1 112768190.9 0.040419085 9.530674035 -0.979123616 0.586631937 ERHAS(ph)EMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERHASEMR 8 1 P49754-2;P49754-3;P49754 P49754-2 VPS41 Vacuolar protein sorting-associated protein 41 homolog 1 ERHAS(1)EMR;ERHAS(1)EMR 66.92 0.0366 1022720000 230950 280510 195232 193752 330140 306160 262060 285250 274070 TRUE FALSE 200429.3723 278667.3113 289646.8482 237746.3529 323570.8599 317938.1733 236645.4615 224251.5073 241669.7568 0.829352315 1.153091371 1.198523357 0.983765433 1.338896783 1.315589412 0.979210078 0.927925406 1 17.88267742 2.035354218 24.65857679 0.957240407 1.142780659 0.220498107 0.148229881 204.9979762 142979.4419 0.060851143 0.041025655 108.4811343 -2.035354218 0.185540252 ERHPGSFDVVHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ERHPGSFDVVHVK 13 1 P62701;C9JEH7;P22090 P62701 RPS4X;RPS4Y1 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1" 0 ;;;;; 198.78 7.94E-08 3085511000 2994235 2906263 1367733 2073345 2938873 2639081 3041373 3693245 2704326 FALSE TRUE 2598539.258 2887171.567 2029173.254 2544129.671 2880395.177 2740608.154 2746421.115 2903473.298 2384623.661 1.089706229 1.210745165 0.850940669 1.066889385 1.207903463 1.149283301 1.151720986 1.21758135 1 21.18533017 3.358427376 7.182846572 1.154673101 1.049180898 0.155350307 0.104270038 0.37721051 22.17747616 0.029695635 0.038369385 2282.587194 -3.358427376 -0.105492203 ERHPS(ph)WR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 ERHPSWR 7 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR 123.75 0.0025517 1.31397E+11 15568171 16171472 13295390 14371554 18362114 19605510 18382694 19800990 19728590 TRUE FALSE 13510797.76 16065240.54 19725085.07 17634834.99 17996743.86 20359746.66 16599943.17 15566702.38 17396298.57 0.776647843 0.923486136 1.133866782 1.013711907 1.034515692 1.170349346 0.95422271 0.894828421 1 24.05227704 4.576404535 3.708322046 1.01825031 0.782178297 0.504384962 0.079972909 0.233246078 5.383724537 0.022107747 0.110988392 37705.48527 -4.576404535 -0.236072014 ERHPS(ph)WRS(ph)EETQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERHPSWRSEETQER 14 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 ERHPS(0.998)WRS(0.638)EET(0.365)QER 88.176 0.0035665 166120000 59231 51516 30462 44786 66039 65674 58150 62328 42685 TRUE FALSE 51403.47328 51177.588 45193.52509 54955.34581 64724.9531 68200.52128 52510.62195 48999.64224 37638.82793 1.365703347 1.359701957 1.200715526 1.460070593 1.719632536 1.811972504 1.395118415 1.301837622 1 15.19993408 1.361271738 2.045630487 0.929518853 1.480095383 0.426147542 0.176331806 0.623932745 3.310878597 0.598420463 0.054350937 22.97585796 -1.361271738 0.55057653 ERHPS(ph)WRSEET(ph)QER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERHPSWRSEETQER 14 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 ERHPS(0.998)WRS(0.368)EET(0.634)QER 83.395 0.0094325 636130000 319280 307040 175250 290670 379780 404170 373110 398830 229420 TRUE FALSE 277086.339 305023.034 260001.4862 356671.0661 372223.121 419718.6814 336925.8496 313543.3082 202298.229 1.369692362 1.507788949 1.285238568 1.763095347 1.839972218 2.07475213 1.665490852 1.549906343 1 17.62612416 3.736389908 24.98256278 1.665307383 1.399594857 0.163255561 0.27675584 369.9365499 4257591.93 0.079399466 0.124607524 5449.917246 -3.736389908 -0.265712526 ERKS(ph)ESDKDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ERKSESDKDVK 11 3 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 ERKS(1)ESDKDVK;ERKS(0.809)ES(0.191)DKDVK;ERKS(0.992)ES(0.008)DKDVK 130.24 0.001262 861670000 2334610 751090 978150 797440 596370 582950 1606930 1636620 1230350 TRUE FALSE 2026085.373 746156.0403 1451186.612 978510.9401 584503.4038 605376.4637 1451090.176 1286641.549 1084899.425 1.867532904 0.687765173 1.337623174 0.901937007 0.538762756 0.558002383 1.337534285 1.185954679 1 20.04912987 4.749841573 24.71111128 0.967195372 1.867533524 0.499307744 0.289948815 1388.923903 3042391.926 0.0751871 1.123606352 56213.62251 -4.749841573 0.900338152 GGGFGDRDR ddPTM_MDA-MB-175_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 ;;; 107.08 0.0025827 2485610000 3303390 3272850 1605510 1600530 2613710 3262700 2943430 3138300 682260 FALSE TRUE 2866838.642 3251350.433 2381940.006 1963954.799 2561702.285 3388218.18 2657976.612 2467198.967 601604 4.7653251 5.404469439 3.95931544 3.264530819 4.258120432 5.631974156 4.418149832 4.101034845 1 19.19845463 1.211295212 3.136398708 0.228137333 4.513669789 0.727893643 0.67217863 0.234683911 2.859768696 2.609087943 0.185232182 16.26654099 -1.211295212 4.285532456 ERLEQEQLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ERLEQEQLER 10 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;A0A0U1RQP7;A0A075B6E5;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 ;;; 181.87 1.68E-06 1663900000 2130010 2047055 1331864 1533918 1936520 2016320 2003301 2342184 1909683 FALSE TRUE 1848523.782 2033607.761 1975957.885 1882217.526 1897987.041 2093889.135 1809021.177 1841326.178 1683922.451 1.097748759 1.207661172 1.173425702 1.117757843 1.127122594 1.243459361 1.074290076 1.093474451 1 20.68339427 1.439749706 1.311770282 0.971252927 1.158356586 0.510587284 0.048462461 0.735467508 1.505722371 0.175037243 0.014420377 27.52641834 -1.439749706 0.187103659 ERLEQQVPVNQVFGQDEMIDVIGVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERLEQQVPVNQVFGQDEMIDVIGVTK 26 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 231.68 2.65E-35 129430000 55958 45579 29694 35087 43257 44906 54165 63289 39973 FALSE TRUE 48563.00852 45279.58855 44054.11772 43054.03962 42396.27033 46633.56288 48912.08664 49755.13987 35247.43748 1.377774159 1.284620721 1.249853064 1.221479991 1.202818513 1.323034133 1.387677804 1.411595946 1 15.10523076 ERLNS(ph)SENGEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERLNSSENGEDR 12 1 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 ERLNS(0.5)S(0.5)ENGEDR;ERLNS(0.5)S(0.5)ENGEDR 179.55 5.41E-05 1009440000 923210 787590 535350 665940 867240 907160 891390 1035000 952450 TRUE FALSE 801205.4594 782416.2694 794247.0506 817151.8553 849983.6207 942059.0322 804943.135 813673.3044 839852.446 0.953983599 0.931611586 0.945698324 0.972970739 1.012063041 1.121695884 0.958433995 0.96882888 1 19.67977636 3.47950842 3.120501848 1.007884747 0.943142035 0.337641553 0.04383753 0.341427307 6.832153898 0.014142015 0.020420908 3016.535354 -3.47950842 -0.064742712 ERLNSS(ph)ENGEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERLNSSENGEDR 12 1 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 ERLNS(0.37)S(0.63)ENGEDR 200.26 9.82E-08 868400000 589020 540750 420450 447090 590120 597670 582160 659050 689580 TRUE FALSE 511179.5146 537197.7776 623781.0263 548608.6178 578377.7666 620662.7516 525702.2128 518117.2862 608058.638 0.840674703 0.883463772 1.025856698 0.902229791 0.951187485 1.020728451 0.864558416 0.852084411 1 19.21385093 4.468775141 24.99850852 0.935348357 0.851371931 0.247496897 0.060615 252.1522842 755255.2236 0.015889907 0.042195158 29428.97533 -4.468775141 -0.083976426 ERNHKPS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ERNHKPSR 8 2 P84103 P84103 SRSF3 Serine/arginine-rich splicing factor 3 1 ERNHKPS(1)R;ERNHKPS(1)R;ERNHKPS(1)R;ERNHKPS(1)R;ERNHKPS(1)R 80.979 0.0072684 755543000 424507 260380 217910 246250 250557 269011 406546 505777 372520 TRUE FALSE 368407.3244 258669.5466 323292.0049 302164.8262 245571.4059 279360.0272 367119.2315 397620.5245 328481.11 1.121547977 0.787471604 0.984202729 0.91988494 0.747596737 0.850459947 1.117626616 1.210482163 1 18.32545088 2.229311188 23.03820382 1.130779002 0.894211266 0.415189884 0.114925903 61.27003496 152605.7474 0.044786653 0.030737433 169.5552291 -2.229311188 -0.236567736 ERPAYAVHGNMLHYVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERPAYAVHGNMLHYVK 16 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 93.153 0.0029216 1228190000 802230 724290 362010 509850 642590 601430 659000 707150 576890 FALSE TRUE 696213.2729 719532.0913 537079.2469 625619.2351 629803.7162 624567.4013 595090.2814 555931.4755 508690.7214 1.368637649 1.414478505 1.055807044 1.229861699 1.238087682 1.227793972 1.169846935 1.09286734 1 18.95642925 7.999999996 0.041092103 2.73E-09 3.127635183 0.535527362 0.088198583 1373.358424 5.554514352 131.4799156 337.5751089 99999999.15 -7.999999996 3.12763518 ERPDLEAPAPGS(ph)PFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ERPDLEAPAPGSPFR 15 1 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 ERPDLEAPAPGS(1)PFR;ERPDLEAPAPGS(1)PFR;ERPDLEAPAPGS(1)PFR;ERPDLEAPAPGS(1)PFR;ERPDLEAPAPGS(1)PFR;ERPDLEAPAPGS(1)PFR;ERPDLEAPAPGS(1)PFR;ERPDLEAPAPGS(1)PFR 180.12 5.12E-07 40870130000 6671600 6849200 3785710 4651100 6341830 6396980 5105820 6599590 5856150 TRUE FALSE 5789931.156 6804207.154 5616492.018 5707203.343 6215639.991 6643075.96 4610658.362 5188319.037 5163842.618 1.121244698 1.317663542 1.087657474 1.105224106 1.203685017 1.286459803 0.892873525 1.004739962 1 22.3000136 2.23482955 24.99994464 0.97092725 1.185456096 0.634739848 0.079034935 60.95135581 408396.4402 0.031132698 0.021903914 171.7234281 -2.23482955 0.214528846 ERPDLEAPAPGSPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERPDLEAPAPGSPFR 15 1 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 0 ; 207.92 2.87E-09 1241370000 353090 326380 214130 252410 351840 313280 344870 368170 356030 FALSE TRUE 306428.2619 324235.9883 317683.9842 309723.5483 344839.0724 325332.0843 311424.5605 289439.7106 313940.539 0.976071019 1.032794265 1.011924058 0.98656755 1.09842161 1.036285678 0.991985812 0.921957105 1 18.26013181 1.999099589 5.724817428 0.955488883 1.024669874 0.322032328 0.037612925 0.156749336 19.06931934 0.016939475 0.010231631 99.79288746 -1.999099589 0.069180991 ERPDLPPIQYEPVLCSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERPDLPPIQYEPVLCSR 17 1 F5H365;Q15436;G3V4V1;G3V1W4;G3V3G5;G3V2R6;G3V5X8;G3V4Q2 F5H365 SEC23A Protein transport protein Sec23A 0 ; 147.06 3.77E-07 760530000 242150 220810 141916 169801 216780 213609 222120 254160 262020 FALSE TRUE 210149.264 219359.4846 210547.0523 208356.9123 212466.5021 221826.6765 200578.8366 199809.8619 231044.2941 0.909562665 0.949426107 0.911284363 0.901805055 0.919592076 0.960104543 0.868140187 0.86481193 1 17.81780994 2.232579324 24.99995403 0.899579701 0.924428728 0.000989329 0.040971686 413.6519174 1728913.018 0.016276899 0.011297839 170.8359724 -2.232579324 0.024849027 ERPDLPPVQYEPVLCSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERPDLPPVQYEPVLCSR 17 1 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ; 162.37 2.60E-09 221910000 72662 71862 60060 75427 81840 74756 88194 90803 126576 FALSE TRUE 63059.5326 71389.93379 89105.21689 92553.85318 80211.54412 77631.91169 79640.95945 71385.48508 111612.3295 0.564987156 0.639624082 0.798345643 0.829243988 0.718662038 0.695549605 0.713549837 0.639584223 1 16.76813688 4.416944376 4.336999153 0.753093746 0.579121008 0.334092511 0.099006425 0.237234856 8.835769648 0.02476887 0.076368946 26118.26814 -4.416944376 -0.173972738 ERPEIS(ph)PPSDFEHTIHVGFDAVTGEFTGMPEQWAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERPEISPPSDFEHTIHVGFDAVTGEFTGMPEQWAR 35 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 ERPEIS(0.464)PPS(0.464)DFEHT(0.07)IHVGFDAVT(0.002)GEFTGMPEQWAR;ERPEIS(0.96)PPS(0.031)DFEHT(0.009)IHVGFDAVTGEFTGMPEQWAR 133.25 1.01E-08 151632000 51377 38608 29306 38361 42869 45223 38759 41766 50324 TRUE FALSE 44587.39928 38354.38151 43478.47962 47071.45136 42015.99077 46962.75807 35000.15815 32834.66592 44374.75405 1.004792032 0.864328881 0.979802154 1.06077098 0.946844477 1.058321541 0.78874033 0.739940235 1 15.4374515 2.228395061 24.99935295 0.819188505 0.981651216 0.3663742 0.086636817 190.6494826 468845.1113 0.034736721 0.023719461 169.197936 -2.228395061 0.16246271 ERPES(ph)PMVPSEQVVEEAVPLPPQALTTSQDGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 ERPESPMVPSEQVVEEAVPLPPQALTTSQDGHR 33 1 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 ERPES(0.999)PMVPS(0.001)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.995)PMVPS(0.005)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.996)PMVPS(0.004)EQVVEEAVPLPPQALTTSQDGHR;ERPES(1)PMVPSEQVVEEAVPLPPQALTTSQDGHR;ERPES(1)PMVPSEQVVEEAVPLPPQALTTSQDGHR;ERPES(0.999)PMVPS(0.001)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.996)PMVPS(0.004)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.999)PMVPS(0.001)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.999)PMVPS(0.001)EQVVEEAVPLPPQALTTSQDGHR 160.45 3.34E-14 3166480000 1335588 1439477 616124 996938 1471130 1517726 1387988 1713504 1787638 TRUE FALSE 1159086.662 1430020.981 914083.6272 1223308.01 1441857.391 1576113.901 1253381.137 1347084.504 1576305.472 0.735318555 0.907197879 0.579889903 0.776060245 0.914706836 0.999878468 0.79513848 0.854583409 1 20.58811571 3.301164378 5.333442919 0.901102112 0.745965329 0.403977993 0.098392654 0.222962864 12.35832716 0.028716026 0.036842494 2000.61895 -3.301164378 -0.155136783 ERPES(ph)PMVPSEQVVEEAVPLPPQALTTSQDGHRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ERPESPMVPSEQVVEEAVPLPPQALTTSQDGHRR 34 2 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 ERPES(1)PMVPSEQVVEEAVPLPPQALTTSQDGHRR;ERPES(0.999)PMVPS(0.001)EQVVEEAVPLPPQALTTSQDGHRR;ERPES(1)PMVPSEQVVEEAVPLPPQALTTSQDGHRR;ERPES(1)PMVPSEQVVEEAVPLPPQALTTSQDGHRR;ERPES(1)PMVPSEQVVEEAVPLPPQALTTSQDGHRR 169.82 7.92E-15 566656000 221500 249968 82691 136191.7 258546 272846 245337 271162 115920 TRUE FALSE 192228.2138 248325.9437 122680.6442 167116.107 253401.4404 283342.5622 221544.2555 213176.1165 102216.0697 1.880606586 2.429421759 1.200208975 1.634929885 2.479076346 2.771996254 2.167411213 2.085544056 1 16.6412625 3.259388026 24.98508931 2.137452983 1.790366602 0.075578468 0.538075255 655.3012609 786110.8599 0.160022755 0.206365783 1817.138484 -3.259388026 -0.347086381 ERPFYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ERPFYGR 7 1 Q13232 Q13232 NME3 Nucleoside diphosphate kinase 3 0 ;; 100.45 0.0089232 461140000 290615 308159 160406 204371 312362 372314 302855 352198 182059 FALSE TRUE 252209.4914 306134.6832 237978.8781 250776.5592 306146.6073 386637.1605 273484.1687 276883.1985 160536.1924 1.571044433 1.90695119 1.482400165 1.562118519 1.907025467 2.408411179 1.703567056 1.724740037 1 17.29253906 3.253338202 24.79567416 1.775342183 1.639778185 0.023371002 0.354947457 1005.423778 1687014.055 0.105864654 0.136064269 1792.000812 -3.253338202 -0.135563998 ERPGLGSENMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERPGLGSENMDR 12 1 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 125.29 0.00028073 390700000 562200 490220 314240 386140 448690 537110 479990 514800 486300 FALSE TRUE 487903.8456 486999.7125 466207.5151 473818.9888 439761.9468 557772.9693 433440.6437 404714.0262 428810.168 1.13780848 1.135700011 1.087211894 1.104962112 1.025539923 1.30074567 1.010798428 0.943806972 1 18.70997959 2.018444461 24.99999707 0.970713542 1.126702619 0.498795836 0.070192588 173.7710918 235532.0147 0.027183246 0.01832365 104.3384692 -2.018444461 0.155989077 ERPGSEEPPAEPVSFYTQPFSHYGQALCVSFPQPCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERPGSEEPPAEPVSFYTQPFSHYGQALCVSFPQPCR 36 1 Q9H4A4;A6NKB8;A0A087WU27;A0A087WUS4 Q9H4A4 RNPEP Aminopeptidase B 0 ; 193.58 4.82E-24 708680000 126035 108437 85721 85394 107359 132996 100047 126927 203041 FALSE TRUE 109379.1554 107724.6702 127175.9623 104784.0129 105222.7659 138112.4422 90344.45734 99784.6488 179037.7243 0.610927981 0.601686994 0.710330534 0.585262203 0.587712821 0.771415313 0.504611292 0.557338679 1 17.44990408 1.233458974 24.99989853 1.000000597 0.613662186 0.719937633 0.075222705 87.51517131 428806.6217 0.150421253 0.018423729 17.11823459 -1.233458974 -0.386338411 ERPIS(ph)LGIFPLPAGDGLLTPDAQK ddPTM_MDA-MB-175_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 216.8 7.89E-33 1255523000 1297670 1344000 1068989 1047021 1350440 1378620 1646380 1858660 1949510 TRUE FALSE 1126179.622 1335171.176 1585955.656 1284763.121 1323568.886 1431656.403 1486714.321 1461200.023 1719041.149 0.655120805 0.776695297 0.922581555 0.747371941 0.769946017 0.832822649 0.864850921 0.850008753 1 20.71317265 -2 0.493295685 7.03596109 0.774277272 0.511402268 0.066991933 100.2770627 1.149546199 645.7278787 0.045483357 0.01 2 -6.261683818 ERPISLGIFPLPAGDGLLT(ph)PDAQK ddPTM_MDA-MB-175_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 ERPISLGIFPLPAGDGLLT(1)PDAQK;ERPISLGIFPLPAGDGLLT(1)PDAQK;ERPISLGIFPLPAGDGLLT(1)PDAQK;ERPISLGIFPLPAGDGLLT(1)PDAQK 234.39 3.79E-37 3818650000 3891124 3420599 3155414 3786730 4008397 3964290 5651090 5691490 5711230 TRUE FALSE 3376902.105 3398128.86 4681382.765 4646564.923 3928637.742 4116798.802 5103048.162 4474409.155 5036054.896 0.670545134 0.674760091 0.929573418 0.922659705 0.780102247 0.817465037 1.013302727 0.888475056 1 22.26386258 5.721532727 0.503378087 0.931392403 1.21E-20 0.552475078 0.080669919 9.472161765 0.899636796 0.055116173 6.412088354 526662.9009 -5.721532727 -0.931392403 ERPLLLEEQPLLLQDLLDQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERPLLLEEQPLLLQDLLDQER 21 1 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 0 98.816 0.00084669 9898200 14803 14044 9118.5 9967.9 13203 12980 11721 14174 12964 FALSE TRUE 12846.74604 13951.74404 13528.2371 12231.26404 12940.28613 13479.349 10584.29922 11143.0004 11431.41069 1.123811085 1.220474395 1.183426741 1.069969786 1.131993809 1.179150095 0.925896157 0.974770368 1 13.48071583 2.241057436 24.99999571 0.966822782 1.151470127 0.798693943 0.043683912 27.71811471 277538.2453 0.017486045 0.012899795 174.2037246 -2.241057436 0.184647345 ERPLQQVS(ph)PVASVPWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERPLQQVSPVASVPWR 16 1 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 ERPLQQVS(1)PVASVPWR 127.16 4.10E-05 662470000 430720 503350 306020 414810 462340 557120 508440 546620 513530 TRUE FALSE 373799.2607 500043.4607 454012.2956 508998.9505 453140.3386 578552.7669 459131.5671 429729.5668 452821.0684 0.825489993 1.104284883 1.00263068 1.124061988 1.000705069 1.277663093 1.013935965 0.94900524 1 18.78858156 7.278061147 11.55709286 1.036002595 0.226036471 0 0.118717004 0 0 0.025828697 0 18969729.88 -7.278061147 -0.809966125 ERPMYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERPMYGR 7 1 P50402;Q5HY57 P50402 EMD Emerin 0 108.46 0.0066099 93367000 110620 107140 73793 89064 107450 135010 90425 121700 98543 FALSE TRUE 96001.28672 106436.1903 109479.5416 109287.3425 105311.9552 140203.9221 81655.59742 95675.40207 86893.3588 1.104817308 1.224905928 1.259929909 1.257718012 1.211967827 1.61351712 0.93972196 1.10106691 1 16.4069583 ERPPLDVDEMLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERPPLDVDEMLER 13 1 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-5;A0A0G2JMG8;F5H5B1;K7ELX1;K7EPE6;F5GYZ4 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 0 83.966 0.0090841 110630000 93203 73318 52578 56446 82486 86270 79246 82357 88245 FALSE TRUE 80885.9874 72836.36923 78004.89666 69262.92702 80844.68998 89588.86272 71560.73512 64745.59645 77812.77663 1.039494938 0.936046397 1.002469004 0.890122805 1.03896421 1.151338721 0.919652764 0.832068964 1 16.24771944 2.021938502 24.99973878 0.895585761 1.004745934 0.221624619 0.079350011 290.9251145 331518.5927 0.032714271 0.022054121 105.1812922 -2.021938502 0.109160173 ERPQDVDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERPQDVDQR 9 1 P31749;G3V4I6 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 0 64.73 0.06253 841090000 886260 865430 890300 604370 797330 1154200 802770 908550 822370 FALSE TRUE 769138.4955 859744.9333 1320852.058 741601.4457 781464.6929 1198602.821 724917.489 714263.6528 725150.3554 1.060660716 1.185609201 1.821487155 1.022686454 1.077658843 1.65290248 0.999678871 0.984986972 1 19.46792063 2.062961882 24.99996733 0.991686909 1.300960773 0.24303256 0.256747851 87.87817624 34892.54379 0.103392091 0.069706925 115.6010775 -2.062961882 0.309273865 ERPQLAECEEPSIYS(ph)PAFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERPQLAECEEPSIYSPAFPR 20 1 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 1 ERPQLAECEEPS(0.004)IYS(0.996)PAFPR;ERPQLAECEEPSIYS(1)PAFPR 161.68 1.34E-11 337520000 196184 208809 140830 168087 218253 238410 209481 233510 231167 TRUE FALSE 170257.7873 207437.3199 208935.859 206253.7224 213910.1923 247581.787 189165.5649 183575.7037 203838.7006 0.835257421 1.01765425 1.025005842 1.01184771 1.049409124 1.214596572 0.928015947 0.900592984 1 17.63706846 4.739735373 23.40543044 1.012054159 0.835257292 0.321454944 0.083166026 59.02444112 1175606.14 0.022353305 0.133404281 54920.61265 -4.739735373 -0.176796867 ERPS(ph)SAIYPSDSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERPSSAIYPSDSFR 14 1 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 ERPS(0.499)S(0.499)AIYPS(0.001)DS(0.001)FR 106.28 0.0026666 0 108940 123700 87410 97772 115690 148260 125020 140480 154790 TRUE FALSE 94543.30298 122887.4066 129681.7684 119972.627 113387.9953 153963.6581 112895.5796 110439.4452 136490.9025 0.692671095 0.900334046 0.950112908 0.878978926 0.830736652 1.128014067 0.82712897 0.809134112 1 17.05844527 4.737396709 6.08258093 0.907388284 0.6872634 0.347893554 0.095369917 0.154295108 28.91247356 0.023193805 0.141098504 54625.66146 -4.737396709 -0.220124884 ERPS(ph)SREDTPSR ddPTM_MDA-MB-175_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(0.5)S(0.5)REDTPSR;ERPS(0.752)S(0.248)REDTPSR;ERPS(0.616)S(0.302)REDT(0.067)PS(0.015)R;ERPS(0.492)S(0.492)REDT(0.005)PS(0.012)R;ERPS(0.736)S(0.253)REDT(0.004)PS(0.008)R 123.4 0.00026894 7750043000 1545152 1640229 936486 1029917 1560081 1606693 1584699 1786795 781539 TRUE FALSE 1340956.248 1629454.228 1389373.762 1263775.396 1529038.44 1668503.519 1431015.135 1404702.794 689146.3498 1.945822174 2.364453107 2.016079404 1.833827309 2.218742711 2.421116385 2.076503975 2.038322912 1 19.39445087 1.2218464 3.730644506 0.830161977 2.129555759 0.794723086 0.178397321 0.133439178 2.875740427 0.497458339 0.04592583 16.6665765 -1.2218464 1.299393782 ERPSQPEGLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ERPSQPEGLRK 11 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;; 127.52 0.00016026 1140980000 941830 913260 591390 721940 858270 799060 1061700 1219020 758600 FALSE TRUE 817364.7792 907260.7349 877388.1821 885867.5112 841192.1062 829800.3553 958736.4974 958342.0594 668919.1722 1.221918601 1.356308464 1.311650523 1.324326687 1.257539238 1.240509152 1.4332621 1.432672435 1 19.35147237 4.761298457 21.91017511 1.31045017 1.221918073 0.019132421 0.123102784 3813.747821 3674602.103 0.029333407 1.158023959 57716.29669 -4.761298457 -0.088532097 ERPSS(ph)AIYPSDSFR ddPTM_MDA-MB-175_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(0.203)S(0.797)AIYPSDSFR;ERPS(0.001)S(0.999)AIYPSDSFR;ERPS(0.033)S(0.967)AIYPSDSFR;ERPS(0.072)S(0.829)AIYPS(0.03)DS(0.069)FR 233.65 2.07E-17 3221020000 1615730 1724740 1124030 1470460 1666230 1870000 1728870 2014610 2081730 TRUE FALSE 1402207.187 1713410.069 1667614.668 1804350.418 1633075.283 1941940.11 1561204.454 1583801.329 1835630.251 0.763883242 0.933417865 0.908469811 0.982959622 0.889653721 1.057914637 0.850500504 0.86281065 1 20.80784406 4.739532167 23.74262345 0.929029867 0.763883141 0.410994986 0.064205192 43.29097109 1057608.118 0.015458095 0.091319252 54894.92132 -4.739532167 -0.165146726 ERPSS(ph)REDT(ph)PSR ddPTM_MDA-MB-175_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(0.319)S(0.681)REDT(0.625)PS(0.376)R 78.166 0.029203 420030000 443240 438340 250420 283170 366880 374590 373190 414360 301210 TRUE FALSE 384664.711 435460.5157 371523.9496 347468.0765 359579.8058 389000.7197 336998.0912 325752.3386 265601.2969 1.448278737 1.639527068 1.398803221 1.308231852 1.353833019 1.464603992 1.268811919 1.226471189 1 18.01890267 0.142422778 0.443077815 4.65E-22 1.485672132 0.728791178 0.087646069 8.131981038 0.621285142 7.75398022 0.082048303 1.388106469 -0.142422778 1.485672132 ERPSS(ph)REDTPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ERPSSREDTPSR 12 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 ERPS(0.383)S(0.612)REDT(0.004)PS(0.001)R;ERPS(0.033)S(0.967)REDTPSR;ERPS(0.469)S(0.5)REDT(0.026)PS(0.005)R 128.74 0.00019425 6247318000 633163 643369 357262 399095 592680 623570 608188 654284 317951 TRUE FALSE 549488.9053 639142.6667 530035.0982 489715.6195 580886.8276 647559.1414 549206.0214 514370.4582 280363.195 1.959918117 2.279695331 1.890530239 1.746718643 2.071908289 2.30971523 1.958909126 1.834657571 1 18.09693744 1.150322307 2.130319916 0.500716499 2.036237136 0.78631362 0.167824262 0.433442983 1.608216657 1.415051254 0.046712741 14.13586234 -1.150322307 1.535520638 ERPT(ph)SPAPHRPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ERPTSPAPHRPPK 13 2 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 ERPT(0.888)S(0.112)PAPHRPPK;ERPT(0.9)S(0.1)PAPHRPPK;ERPT(0.9)S(0.1)PAPHRPPK 124.92 0.0098245 1677470000 878700 818400 658030 820970 823420 740590 901290 1185880 1626890 TRUE FALSE 762577.5687 813023.8765 976255.509 1007383.786 807035.553 769080.9765 813883.0345 932288.7905 1434560.918 0.531575592 0.566740573 0.680525656 0.702224474 0.562566248 0.53610897 0.567339473 0.64987745 1 20.4521778 1.232085511 3.438746227 1.064374561 0.596361686 0.83314966 0.056836953 0.136136305 2.291883208 0.170578202 0.015841839 17.06418343 -1.232085511 -0.468012875 ERPT(ph)SPAPHRPPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERPTSPAPHRPPKR 14 3 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 ERPT(0.897)S(0.103)PAPHRPPKR;ERPT(0.897)S(0.103)PAPHRPPKR 138.05 9.37E-06 2917500000 58115 45991 37337 39952 48554 48323 56271 66985 42789 TRUE FALSE 50434.95551 45688.88209 55393.29808 49023.71223 47587.87039 50182.01708 50813.84708 52660.77903 37730.53317 1.336714625 1.21092596 1.468129216 1.299311409 1.26125624 1.330010813 1.346756667 1.395707259 1 15.20344487 1.231832763 24.99815626 0.999999436 1.332180195 0.69101649 0.069577096 132.3824185 491837.1648 0.157619759 0.016610683 17.05425543 -1.231832763 0.332180759 ERPTPSLNNNCTT(ph)SEDSLVLYNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERPTPSLNNNCTTSEDSLVLYNR 23 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 ERPTPSLNNNCT(0.002)T(0.568)S(0.43)EDSLVLYNR 118.75 0.00040894 199530000 41365 28547 15352 24560 27776 23229 38851 30919 30257 TRUE FALSE 35898.51044 28359.47288 22776.27855 30136.72338 27223.31194 24122.63466 35083.236 24307.21246 26680.05193 1.345518762 1.06294669 0.853681942 1.129560147 1.02036203 0.904144967 1.314961309 0.911063162 1 14.70347385 4.722009896 4.512401744 1.021557311 1.362764381 0.378091556 0.130269346 0.183418713 9.390987775 0.030062722 0.192491375 52724.18754 -4.722009896 0.34120707 ERPTPSLNNNCTTS(ph)EDSLVLYNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERPTPSLNNNCTTSEDSLVLYNR 23 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 ERPTPSLNNNCTT(0.027)S(0.972)EDSLVLYNR 177.12 3.36E-17 178750000 72779 45621 21202 36914 37089 25750 48632 40616 49242 TRUE FALSE 63161.07075 45321.31265 31455.35812 45295.8879 36351.00146 26740.61916 43915.67613 31930.58447 43420.66686 1.454631523 1.043772837 0.724432866 1.043187292 0.837182017 0.615850034 1.011400315 0.73537757 1 15.40609426 4.652921539 2.791039672 0.848449764 1.511574782 0.652443892 0.13880835 0.198473128 2.349413791 0.032669555 0.271324399 44969.86037 -4.652921539 0.663125018 ERPTPSLNNNCTTSEDSLVLYNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ERPTPSLNNNCTTSEDSLVLYNR 23 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;; 280.55 5.67E-52 1674970000 406392 391057 219066 263395 390378 409015 363023 415542 365605 FALSE TRUE 352686.2675 388488.1208 325007.0503 323202.8605 382610.2416 424750.0717 327817.0853 326681.5771 322383.5934 1.093995708 1.205049292 1.008137687 1.00254128 1.186816728 1.317530049 1.016854121 1.013331893 1 18.2984188 2.048696638 24.99994828 1.009858598 1.132464301 0.29224214 0.092134132 149.8235073 76915.9177 0.039738437 0.026791644 111.8656211 -2.048696638 0.122605702 ERPTS(ph)PAPHRPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERPTSPAPHRPPK 13 2 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 ERPT(0.072)S(0.928)PAPHRPPK 53.193 0.076582 164730000 95323 78464 74589 91018 93158 74550 99442 104090 172690 TRUE FALSE 82725.82403 77948.56482 110660.4899 111685.028 91304.33806 77417.98674 89798.13015 81831.16353 152274.7849 0.543266727 0.511894105 0.726715785 0.733444004 0.599602476 0.508409759 0.589711095 0.537391424 1 17.21631754 1.233640142 24.99639814 1.000000622 0.594438303 0.720274715 0.079551732 90.27427852 458545.8206 0.168486737 0.020958064 17.12537706 -1.233640142 -0.405562319 ERPTS(ph)PAPHRPPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ERPTSPAPHRPPKR 14 3 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 ERPT(0.121)S(0.879)PAPHRPPKR;ERPT(0.195)S(0.805)PAPHRPPKR;ERPT(0.192)S(0.808)PAPHRPPKR 168.42 2.49E-06 1134271000 360130.6 287517.7 180180.5 224391.3 276030.8 251673 274565.7 351390 257194 TRUE FALSE 312538.4288 285628.9773 267316.3925 275342.7743 270538.3271 261355.0232 247938.3607 276247.983 226788.8183 1.378103343 1.259449118 1.178701818 1.214093253 1.19290858 1.152415825 1.093256548 1.21808467 1 17.79098999 8 0.370224239 1.117117188 4.461945156 0.662634066 0.057605137 52.24820777 0.774390437 0.064323128 123.1011832 100000000 -8 3.344827968 ERQELGS(ph)PEER ddPTM_MDA-MB-175_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 133.86 9.26E-05 735000000 382150 349650 273676 306011 386810 425430 421580 400200 441560 TRUE FALSE 331647.9093 347353.1261 406026.629 375495.4746 379113.2378 441796.5674 380695.2365 314620.3444 389359.2798 0.851778618 0.892114672 1.042807119 0.964393284 0.973684865 1.134675839 0.977747947 0.808046349 1 18.57074249 6.962479408 13.32930252 0.956388482 0.336003269 0 0.093722836 0 0 0.022379956 0 9172324.431 -6.962479408 -0.620385213 ERQEQEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERQEQEEAR 9 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ; 215.87 5.69E-07 1964590000 1635190 1656660 985090 1266340 1241230 1482770 1478180 1797870 1968520 FALSE TRUE 1419095.498 1645777.291 1461482.819 1553881.852 1216531.951 1539813.121 1334826.331 1413409.492 1735803.808 0.817543718 0.948135546 0.841963137 0.895194402 0.700846458 0.887089379 0.768996084 0.814267998 1 20.72717246 5.069315094 14.87949068 0.848512184 0.484814006 0.012047234 0.085559812 4790537.392 22722025.82 0.020038376 53406332 117304.6137 -5.069315094 -0.363698178 FLQDYFDGNLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLQDYFDGNLKR 12 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 180.28 3.15E-05 13988700000 7546700 6768700 4394500 5016100 7089300 7502900 7532200 7389000 2777000 FALSE TRUE 6549384.474 6724235.964 6519694.899 6155082.171 6948236.8 7791541.418 6801728.403 5808919.851 2448706.224 2.67463055 2.746036213 2.662505954 2.513605802 2.837513432 3.18190126 2.777682491 2.372240408 1 21.22358827 1.213381561 2.361533758 0.446144047 2.771300764 0.911939769 0.172242226 0.187831536 1.044218103 0.937151022 0.05004855 16.34487339 -1.213381561 2.325156717 ERQEQLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ERQEQLER 8 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;A0A0U1RQP7;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 ;; 179.1 0.00022446 1693250000 918031 916240 565109 601774 765422 856987 862781 872214 723266 FALSE TRUE 796710.8774 910221.1591 838397.6026 738415.9842 750191.5997 889955.8444 779108.6314 685697.8237 637762.3174 1.249228522 1.42721063 1.314592568 1.157823164 1.17628712 1.395434977 1.221628513 1.075162023 1 19.28265933 1.713274792 2.616347889 1.012216277 1.28491463 0.596325326 0.084320634 0.175943646 2.55984056 0.076280913 0.024427116 51.67432259 -1.713274792 0.272698353 ERRPDS(ph)PTRPTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERRPDSPTRPTLR 13 3 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 ERRPDS(0.955)PT(0.045)RPTLR 91.317 0.036401 101310000 43261 38869 25565 21670 33761 36677 33956 38276 30858 TRUE FALSE 37543.94924 38613.66698 37928.31951 26590.50471 33089.22215 38087.98792 30662.95235 30090.97526 27210.00239 1.379784856 1.419098257 1.393910921 0.977232722 1.216068329 1.399778926 1.126900024 1.105879185 1 14.73184946 8 0.047146377 2.41E-13 3.33417847 0.427827807 0.127726716 1282.704215 5.927158777 121.5506294 358.1932222 100000000 -8 3.33417847 ERRT(ph)PPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERRTPPGR 8 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 ERRT(1)PPGR;ERRT(1)PPGR 77.541 0.052975 3196000000 126651 98161 41853 44619 101271 100239 97266 97810 9235.3 TRUE FALSE 109913.7495 97516.17393 62093.25079 54750.42591 99255.90523 104095.2592 87833.15829 76894.09266 8143.513355 13.49709206 11.97470547 7.62487247 6.72319471 12.18833947 12.78259821 10.78565902 9.442373249 1 12.99143564 4.398445474 5.091429398 9.049989562 13.15940801 0.205932149 3.323695169 0.324050527 14.47056969 0.850555781 2.421385128 25029.11385 -4.398445474 4.109418443 ERRT(ph)PS(ph)DDEEDNLFAPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERRTPSDDEEDNLFAPPK 18 2 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 2 ERRT(1)PS(1)DDEEDNLFAPPK;ERRT(1)PS(1)DDEEDNLFAPPK 149.85 8.54E-09 0 429700 360170 253268 276670 325380 305830 402340 437930 312490 TRUE FALSE 372914.0563 357804.0196 375749.2519 339492.1521 318905.5746 317595.478 363321.1287 344282.0775 275547.7882 1.353355288 1.298518932 1.363644595 1.232062701 1.157351241 1.152596724 1.318541263 1.249445984 1 18.07194302 8 0.028538467 1.31E-08 2.974130397 0.43359189 0.083135381 4062.068088 11.48922391 430.5649715 829.723402 99999999.98 -8 2.974130384 ERS(ph)HERPDRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ERSHERPDRK 10 3 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 ERS(1)HERPDRK;ERS(1)HERPDRK;ERS(1)HERPDRK;ERS(1)HERPDRK;ERS(1)HERPDRK 93.823 0.0060825 1953800000 702973 660923 445779 431036 561206 490164 718519 887603 361509 TRUE FALSE 610073.3369 656581.3533 661359.2154 528909.3118 550039.0986 509020.9263 648837.138 697796.0058 318771.8179 1.913824569 2.059722085 2.07471043 1.659209761 1.725494751 1.596819097 2.03542817 2.189014106 1 18.28216456 3.746756262 24.01573556 1.769412042 2.020449352 0.159427252 0.315971598 822.3213264 2409639.061 0.085649833 0.144979813 5581.568535 -3.746756262 0.251037309 ERS(ph)KDAS(ph)PINRWS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERSKDASPINRWSPTR 16 3 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 3 ERS(1)KDAS(0.999)PINRWS(0.982)PT(0.018)R 79.172 0.03723 196110000 214430 160900 95971 114590 177490 146900 224460 241320 121430 TRUE FALSE 186092.5322 159843.0373 142382.8966 140609.4109 173958.2963 152551.3381 202691.9037 189715.596 107074.6837 1.737969478 1.492818206 1.329753137 1.313190065 1.624644502 1.424719016 1.892995587 1.77180627 1 16.70825789 ERS(ph)PALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 ERSPALK 7 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 ERS(1)PALK;ERS(1)PALK;ERS(1)PALK;ERS(1)PALK;ERS(1)PALK;ERS(1)PALK;ERS(1)PALK;ERS(1)PALK;ERS(1)PALK 93.096 0.0091971 45858139500 33644878 24563045 20200928 23800229 20071431.3 19338555.6 28005109 31819043 37836111 TRUE FALSE 29198622.13 24401688.74 29970164.35 29204434.76 19672049.09 20082522.35 25289177.84 25014788.27 33363169.06 0.875175319 0.73139601 0.898300887 0.875349542 0.589633708 0.601936894 0.757996874 0.749772548 1 24.991753 ERS(ph)PALKS(ph)PLQSVVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERSPALKSPLQSVVVR 16 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 ERS(1)PALKS(0.999)PLQS(0.001)VVVR;ERS(1)PALKS(0.979)PLQS(0.021)VVVR 147.1 5.21E-06 1197070000 1621500 1417530 901750 1127280 1556330 1114460 1583680 2077450 1573410 TRUE FALSE 1407214.667 1408218.152 1337839.316 1383246.153 1525362.078 1157333.997 1430094.957 1633203.484 1387403.262 1.014279485 1.015002768 0.964275746 0.997003677 1.09943671 0.834172752 1.030770935 1.177165665 1 20.40395575 1.991104912 24.9974872 1.102056771 0.988049005 0.22006964 0.077604374 488.8467405 1373784.349 0.031546966 0.020038771 97.97266288 -1.991104912 -0.114007766 ERS(ph)PALKSPLQSVVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ERSPALKSPLQSVVVR 16 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 ERS(1)PALKSPLQSVVVR;ERS(1)PALKSPLQSVVVR;ERS(1)PALKSPLQSVVVR;ERS(1)PALKSPLQSVVVR;ERS(1)PALKSPLQSVVVR 199.6 1.97E-11 14576850000 14003410 10642040 4236170 4539650 9485760 8109380 12347040 13731290 1064249 TRUE FALSE 12152823.89 10572131.74 6284795.981 5570446.917 9297011.935 8421353.096 11149625.96 10794960.49 938434.6956 12.95010079 11.26570851 6.697105308 5.935891909 9.90693543 8.97382965 11.88108881 11.50315578 1 19.83989683 4.423410236 5.739892776 8.545887343 12.57174443 0.221872492 3.149524288 0.284990129 19.80877652 0.79918637 2.245741849 26510.03105 -4.423410236 4.025857089 ERS(ph)PAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ERSPAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR 40 3 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 ERS(1)PAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR;ERS(1)PAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR;ERS(1)PAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR;ERS(1)PAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR 150.76 1.21E-13 2885511000 299307 242243 214109.9 229354.8 257747 299176 228590 264535 299044 TRUE FALSE 259752.8216 240651.6898 317654.1638 281433.3128 252618.339 310685.4943 206421.377 207966.2489 263691.359 0.985063836 0.912626378 1.204643812 1.067283031 0.958007649 1.17821644 0.782814339 0.788672976 1 18.00849077 2.225842445 24.99991486 0.839795933 1.048185659 0.416837725 0.1073781 203.2966396 399613.7932 0.043186631 0.029333142 168.2063726 -2.225842445 0.208389726 ERS(ph)PQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERSPQR 6 1 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6;F5H3E1 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 1 ERS(1)PQR 78.334 0.042427 147090000 53109 46675 23778 34413 27338 40668 38738 47858 51436 TRUE FALSE 46090.51109 46368.38885 35277.12033 42226.99762 26794.02729 42232.52428 34981.19472 37623.93913 45355.29468 1.016210156 1.022336845 0.777794976 0.931026861 0.590758532 0.931148713 0.771270366 0.829537971 1 15.46898336 4.247301514 24.86513374 0.827796315 1.019273625 0.322476984 0.112000207 188.8006699 537066.399 0.026067041 0.066715043 17672.64337 -4.247301514 0.19147731 ERS(ph)PS(ph)PLR ddPTM_MDA-MB-175_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 99.539 0.0062235 10304330000 2912110 2838240 2393615 2574670 2693280 2913700 2676390 3296100 4847670 TRUE FALSE 2527267.285 2819595.415 3551175.22 3159288.175 2639688.997 3025791.924 2416834.11 2591254.665 4274583.975 0.59123117 0.659618674 0.830765109 0.739086703 0.617531206 0.70785647 0.565396334 0.606200435 1 22.02735259 1.232455997 24.99936523 1.00000055 0.664540982 0.641247473 0.07881451 143.7292508 588534.6471 0.185677307 0.020736785 17.07874667 -1.232455997 -0.335459568 LLEQALVIEEQLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLEQALVIEEQLRR 14 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y4X2;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;Q12873-3;Q12873;Q12873-2;H7C0J3;I3L229;H7C3H7 Q14839-2;Q12873-3;H7C0J3 CHD4;CHD3 Chromodomain-helicase-DNA-binding protein 4;Chromodomain-helicase-DNA-binding protein 3 0 ; 188.59 1.31E-06 354590000 350410 315880 196148 178495 274840 290610 318290 319230 102889 FALSE TRUE 304102.4307 313804.9635 291005.8289 219025.0179 269371.2217 301789.9547 287422.2848 250965.1488 90725.57963 3.351892949 3.458836689 3.207538933 2.414148455 2.969076889 3.326404262 3.168040215 2.766200555 1 16.46922175 1.213726769 2.808329222 0.465862993 3.114269207 0.841059072 0.288474435 0.197432843 1.752405625 1.257921161 0.081131052 16.35787062 -1.213726769 2.648406214 ERS(ph)PS(ph)PLRGNVVPS(ph)PLPTRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ERSPSPLRGNVVPSPLPTRR 20 3 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 3 ERS(1)PS(1)PLRGNVVPS(1)PLPTRR;ERS(1)PS(1)PLRGNVVPS(0.999)PLPT(0.001)RR;ERS(1)PS(1)PLRGNVVPS(0.998)PLPT(0.002)RR;ERS(1)PS(1)PLRGNVVPS(1)PLPTRR;ERS(1)PS(1)PLRGNVVPS(1)PLPTRR 103.73 0.00054809 5184550000 1171530 1265850 495329 502488 1143510 1239810 1337230 1468860 255078 TRUE FALSE 1016709.342 1257534.548 734871.7612 616585.5804 1120756.388 1287506.293 1207545.64 1154755.72 224922.9694 4.520255734 5.590956545 3.267215274 2.74131887 4.982845421 5.724209921 5.368707534 5.134005311 1 17.77907147 4.260299158 24.98256115 4.249690849 5.055605554 0.063582262 1.457550126 868.9911365 998652.0658 0.37137138 0.980723204 18209.54768 -4.260299158 0.805914705 KVTHAVVTVPAYFNDAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVTHAVVTVPAYFNDAQR 18 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 163.45 2.15E-11 1302750000 1930680 1705590 1056620 1344750 1806380 2115260 1573670 1789200 847170 FALSE TRUE 1675535.746 1694385.867 1567604.966 1650096.041 1770436.572 2196635.421 1421055.726 1406593.504 747018.5277 2.242964109 2.268197915 2.098482043 2.208909123 2.370003563 2.940536733 1.902303186 1.882943262 1 19.5107845 1.214035107 1.48200179 0.406880104 2.319276646 0.723077684 0.256375064 0.69592446 1.294921721 2.038485015 0.076162051 16.36948844 -1.214035107 1.912396542 ERS(ph)PS(ph)PPTIQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ERSPSPPTIQSK 12 1 Q14687;Q14687-2;Q14687-3;H0Y613;H7C3B5 Q14687 GSE1 Genetic suppressor element 1 2 ERS(1)PS(0.997)PPT(0.003)IQSK;ERS(1)PS(0.986)PPT(0.014)IQSK;ERS(1)PS(0.986)PPT(0.014)IQSK;ERS(1)PS(0.998)PPT(0.003)IQSK 118.48 0.00035339 1661670000 2066970 1627810 1065870 1357010 1662340 1350280 1756970 2228760 1887340 TRUE FALSE 1793814.677 1617116.809 1581328.297 1665139.861 1629262.686 1402226.145 1586579.32 1752157.018 1664220.815 1.077870593 0.97169606 0.950191394 1.000552238 0.978994297 0.842572171 0.953346638 1.052839264 1 20.66641544 1.747146029 25 1.026811048 0.964218301 0.144379507 0.058708579 3.523996727 10293.42023 0.031904872 0.015321412 55.86580082 -1.747146029 -0.062592747 ERS(ph)PSPSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ERSPSPSFR 9 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 ERS(0.983)PS(0.013)PS(0.004)FR;ERS(0.998)PS(0.002)PSFR;ERS(0.959)PS(0.04)PS(0.001)FR 87.719 0.008876 1114480000 851772 774220 506152 657160 612189 569641 886682 936445 729945 TRUE FALSE 739208.1721 769134.0978 750928.8002 806378.2221 600007.6366 591555.4579 800691.7161 736193.5242 643651.7337 1.148459848 1.19495382 1.166669428 1.252817603 0.932192994 0.919061391 1.243982847 1.143776185 1 19.29592076 3.262478637 24.99969072 1.068075728 1.189308941 0.329369774 0.099008448 353.6548574 369646.1371 0.031116516 0.040149214 1830.116079 -3.262478637 0.121233212 ERS(ph)PYKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERSPYKR 7 2 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8W6A0;F8VWU8;F8VPY7;Q8NEY8-6;F8WF16;B7Z8L1;Q8NEY8-3;Q8NEY8-5 F8W0Q9;Q8NEY8-6 PPHLN1 Periphilin-1 1 ERS(0.993)PY(0.007)KR 61.78 0.04666 91823000 137070 136410 75807 82383 118810 168850 120560 146280 89142 TRUE FALSE 118955.8522 135513.9137 112467.5188 101089.3193 116445.9134 175345.7688 108868.1098 114999.1604 78603.73431 1.513361334 1.724013686 1.430816484 1.286062554 1.481429788 2.230756214 1.385024652 1.463024134 1 16.26231023 1.149870882 1.822276908 0.696156916 1.586777633 0.329123391 0.258988246 1.435347867 3.703394071 2.408137901 0.072607013 14.12117653 -1.149870882 0.890620717 ERSDS(ph)GGS(ph)SSEPFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERSDSGGSSSEPFDR 15 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 2 ERS(0.277)DS(0.715)GGS(0.56)S(0.251)S(0.197)EPFDR;ERS(0.23)DS(0.848)GGS(0.857)S(0.05)S(0.016)EPFDR 128 0.00089313 623440000 885410 730420 562950 573690 891950 968630 821430 891960 843360 TRUE FALSE 768400.8252 725621.8229 835194.503 703955.0828 874201.9401 1005893.823 741767.845 701221.2952 743658.9416 1.033270471 0.975745442 1.123088094 0.946610124 1.17554149 1.352627887 0.997457038 0.942933993 1 19.5042816 2.021746282 24.99995961 0.968232049 1.099655012 0.205094244 0.113105439 359.9862046 413845.6478 0.048593424 0.032758908 105.1347489 -2.021746282 0.131422963 ERSDS(ph)GGSSSEPFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ERSDSGGSSSEPFDR 15 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 ERS(0.016)DS(0.981)GGS(0.002)S(0.001)SEPFDR;ERS(0.046)DS(0.682)GGS(0.129)S(0.129)S(0.014)EPFDR;ERS(0.001)DS(0.999)GGSSSEPFDR 150.1 1.96E-06 1194560000 677510 570940 424612 521140 644030 729490 705440 729270 577480 TRUE FALSE 587975.3369 567189.4575 629955.7834 639472.8021 631215.063 757553.9523 637026.5374 573321.2857 509210.9723 1.154679237 1.113859458 1.237121385 1.255811121 1.239594387 1.487701549 1.251007092 1.12590128 1 18.95790398 1.500953599 2.800550521 1.005504462 1.25143632 0.417226306 0.097204455 0.29142733 4.325202196 0.135433722 0.028017523 31.69228837 -1.500953599 0.245931858 ERSDTFINLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERSDTFINLR 10 1 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ; 105.13 0.0038893 143300000 199350 153264 112850 125179 181558 182313 175954 195892 140049 FALSE TRUE 173005.3924 152257.1987 167424.6375 153602.8052 177945.351 189326.6991 158890.0082 154002.0202 123492.5668 1.4009377 1.232926019 1.355746681 1.243822274 1.440939772 1.533101984 1.286636211 1.247054979 1 16.91406468 1.232892413 1.767693622 0.867978217 1.35793471 0.615530681 0.0896035 0.681962233 1.962850498 0.576716212 0.025938523 17.09591749 -1.232892413 0.489956493 ERSDYDRS(ph)R ddPTM_MDA-MB-175_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;ERSDYDRS(1)R 117.25 0.00093085 1310574000 635052 483434 266356 284857 438560 515134 531467 609729 180201 TRUE FALSE 551128.2692 480258.2902 395166.6525 349538.1356 429833.514 534951.5383 479925.4121 479343.1983 158897.8431 3.468443992 3.022434295 2.486922698 2.199766396 2.705093447 3.366638137 3.020339376 3.016675299 1 17.27774002 4.517467528 3.208382139 2.634833242 3.447643426 0.176555916 0.643607485 0.519011682 9.953720415 0.163136703 0.789647321 32920.58379 -4.517467528 0.812810184 ERSLS(ph)R ddPTM_MDA-MB-175_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 133.68 0.037777 2726400000 2757800 1942870 1326640 1768750 1552330 1954820 2336040 2641810 1651250 TRUE FALSE 2393349.743 1930107.159 1968207.541 2170371.721 1521441.67 2030023.19 2109491.2 2076879.49 1456041.106 1.643737758 1.325585625 1.351752731 1.490597835 1.044916702 1.394207335 1.448785471 1.426387951 1 20.47361965 4.738744123 22.60067014 1.327103858 1.643737867 0.284288222 0.16436183 5.387544867 661357.6536 0.038563255 0.216757594 54795.40269 -4.738744123 0.316634008 ERTESEVPPRPAS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ERTESEVPPRPASPK 15 2 Q9Y3L3;Q6ZT62-2;Q6ZT62;A0A2R8Y5V0;A0A3B3IU28 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 ERTESEVPPRPAS(1)PK;ERTESEVPPRPAS(1)PK;ERTESEVPPRPAS(1)PK 138.28 6.01E-06 669100000 766910 636600 534017 572024 714010 607650 772380 931430 982310 TRUE FALSE 665560.9004 632418.1327 792269.4074 701910.792 699802.5979 631026.6887 697474.7065 732250.9429 866182.4309 0.768384207 0.730121173 0.914668064 0.810349837 0.807915946 0.728514763 0.805228416 0.845377275 1 19.72431138 1.200774764 2.145450438 1.075323813 0.795884283 0.605970864 0.051877624 0.553279325 2.350193248 0.314443707 0.014179574 15.87723101 -1.200774764 -0.279439529 ERVDDSTGTVIS(ph)DVEEDAGELSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERVDDSTGTVISDVEEDAGELSR 23 1 S4R403;Q9Y2D8-2;Q9Y2D8-3;Q9Y2D8 S4R403 SSX2IP Afadin- and alpha-actinin-binding protein 1 ERVDDSTGTVIS(1)DVEEDAGELSR 163.94 9.01E-12 30704000 13326 12080 6975.4 9852.4 13148 11583 12536 15361 11606 TRUE FALSE 11564.93534 12000.64568 10348.72677 12089.538 12886.38052 12028.60551 11320.26065 12076.16969 10233.9519 1.130055666 1.172630651 1.011215107 1.181316672 1.259179313 1.175362716 1.106147533 1.180010401 1 13.32107574 1.232157688 24.85484346 0.999999725 1.152396739 0.359962901 0.063690759 240.6377657 934008.8551 0.146326992 0.01581108 17.06701961 -1.232157688 0.152397013 ERVEAVNMAEGIIHDTETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ERVEAVNMAEGIIHDTETK 19 1 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;; 248.35 4.43E-25 263090000 433610 426250 254830 553470 504410 413890 409150 592720 542710 FALSE TRUE 376307.3399 423449.9357 378066.6404 679143.8228 494373.2279 429812.6161 369470.696 465971.4406 478551.4421 0.786346685 0.884857715 0.790022988 1.419165764 1.033061829 0.898153424 0.772060563 0.973712332 1 18.86831449 ERVEFILEQMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERVEFILEQMR 11 1 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 ; 227.57 3.56E-12 365400000 104283 121598 72520 81410 110124 113942 112772 123629 89736 FALSE TRUE 90501.73733 120799.2147 107590.9146 99895.38477 107932.7479 118325.4225 101835.3888 97191.90043 79127.51231 1.143745515 1.526639865 1.359715621 1.262460829 1.364035652 1.495376501 1.286978269 1.228294655 1 16.27189178 1.271792875 1.621439976 0.877746612 1.361164811 0.513002569 0.108665118 0.764513532 1.951241606 0.585161013 0.029411076 18.6979018 -1.271792875 0.483418198 ERVPYTDDGLEAIIFTAQGDMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERVPYTDDGLEAIIFTAQGDMR 22 1 P35250;P35250-2;H7C5P4;A0A087WVY3 P35250 RFC2 Replication factor C subunit 2 0 85.945 0.0027924 33852000 25751 29620 18275 20647 26541 26969 24004 32817 21461 FALSE TRUE 22347.94011 29425.42427 27112.85113 25335.21692 26012.88603 28006.51488 21676.09577 25799.33993 18923.90503 1.180937025 1.554934049 1.432730247 1.338794339 1.374604554 1.479954314 1.14543461 1.363320091 1 14.20792221 0.498469564 0.950740179 3.05E-13 1.389148661 0.438960185 0.125062409 6.846871917 1.738547426 13.81769646 0.039733962 3.151153537 -0.498469564 1.389148661 ERWET(ph)FQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ERWETFQK 8 1 A0A0M3HER2;Q7Z7K6-3;Q7Z7K6 A0A0M3HER2 CENPV Centromere protein V 1 ERWET(1)FQK 95.502 0.061174 7212800 57405 35042 22284 31164 44890 37713 51843 52939 45708 TRUE FALSE 49818.7838 34811.80679 33060.61694 38240.26251 43996.77683 39163.84351 46815.27384 41618.40682 40304.45231 1.23606155 0.863721123 0.82027208 0.948785068 1.091610835 0.971700179 1.161541 1.032600729 1 15.2986516 3.252169809 24.20376261 1.053393581 0.949322279 0.100742542 0.119867829 307.8001385 547413.59 0.03381159 0.043386915 1787.186227 -3.252169809 -0.104071302 ES(ph)EELLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ESEELLK 7 0 O43303-2;O43303 O43303-2 CCP110 Centriolar coiled-coil protein of 110 kDa 1 ES(1)EELLK;ES(1)EELLK;ES(1)EELLK;ES(1)EELLK;ES(1)EELLK 130.75 0.0037061 2914690000 4088930 3020270 2026810 2611670 2752120 1515140 4301160 3894100 3537130 TRUE FALSE 3548567.54 3000429.648 3006982.095 3204689.59 2697358.196 1573428.416 3884034.165 3061377.019 3118974.521 1.137735341 0.961992356 0.96409319 1.027481811 0.864822133 0.504469788 1.245292047 0.981533193 1 21.57264034 5.79318128 1.281065584 0.942961545 3.174953915 0.100333547 0.183251699 49.12195719 8.284490763 0.052786047 265.940258 621128.2464 -5.79318128 2.23199237 ES(ph)KS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESKSSPR 7 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 2 ES(0.748)KS(0.853)S(0.399)PR 52.579 0.082427 255590000 199990 182920 114800 129160 132690 197240 130570 170170 143540 TRUE FALSE 173560.8148 181718.3865 170317.664 158487.7521 130049.7286 204827.9504 117907.3415 133780.4698 126570.8647 1.371254081 1.435704709 1.345630879 1.252166148 1.027485503 1.618286727 0.931551995 1.056961016 1 16.94958582 -0.187041521 0.229011172 9.28E-15 1.488189128 0.36607426 0.17598819 41.3903566 1.397176187 19.29235935 0.885670861 0.650067538 0.187041521 1.488189128 ES(ph)PEGSYTDDANQEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESPEGSYTDDANQEVR 16 0 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 ES(1)PEGSYTDDANQEVR;ES(0.999)PEGS(0.001)YTDDANQEVR 326.03 3.33E-59 340650000 301750 150221 145390 139410 135137 153706 150640 162315 258990 TRUE FALSE 261872.973 149234.1884 215701.0903 171065.1712 132448.0381 159619.1693 136030.956 127605.2004 228372.4972 1.146692251 0.653468304 0.944514304 0.749062051 0.579964924 0.698942172 0.595653845 0.558759053 1 17.80102939 7.999999949 0.817449621 0.680425149 119.8551061 0.395634413 0.154496491 567.0832144 1.822377749 0.05247546 125347.7835 99999988.21 -7.999999949 119.174681 ES(ph)PGAAATSSSGPQAQQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESPGAAATSSSGPQAQQHR 19 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 ES(1)PGAAATSSSGPQAQQHR 233.7 2.62E-24 772300000 358380 224880 177330 291200 264820 251200 244250 304570 584300 TRUE FALSE 311019.175 223402.7485 263087.3811 357321.4107 259550.6001 260863.8265 220562.6726 239440.0757 515224.7196 0.603657323 0.433602543 0.510626473 0.693525363 0.503761932 0.506310774 0.428090237 0.464729402 1 18.97484229 1.235095513 24.998862 1.000000682 0.513124003 0.784166135 0.079426921 46.45836314 335118.2693 0.141889928 0.019960367 17.18286243 -1.235095513 -0.486876679 ES(ph)PHFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ESPHFYR 7 0 Q9HDC5 Q9HDC5 JPH1 Junctophilin-1 1 ES(1)PHFYR;ES(1)PHFYR;ES(1)PHFYR 86.136 0.013075 877290000 1231680 1081520 885360 1112510 1307080 1335690 941550 1536230 1476290 TRUE FALSE 1068910.367 1074415.424 1313523.057 1365122.399 1281071.665 1387074.859 850238.6259 1207719.169 1301764.678 0.821124114 0.825353032 1.009032646 1.048670641 0.984103876 1.065534257 0.653143107 0.927755369 1 20.31203724 4.260830101 23.68314413 0.945076107 0.823238255 0.18129254 0.115183943 255.0221346 271201.9079 0.030052717 0.079336485 18231.8232 -4.260830101 -0.121837851 ES(ph)PSLASR ddPTM_MDA-MB-175_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(0.991)PS(0.009)LASR;ES(0.999)PS(0.001)LASR 182.24 0.00024085 550180000 706910 630330 548230 714770 620870 663290 590930 725890 1634660 TRUE FALSE 613490.0524 626189.3207 813355.8617 877069.4531 608515.9017 688807.1955 533621.6996 570664.0724 1441412.357 0.425617312 0.434427607 0.564277015 0.608479211 0.422166425 0.477869634 0.370207524 0.395906189 1 20.45905169 1.234341225 25 1.00000079 0.461038833 0.840796917 0.073519927 53.02434294 314127.9857 0.149966159 0.019812422 17.15304492 -1.234341225 -0.538961957 ES(ph)PSPAPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESPSPAPKPR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 ES(0.998)PS(0.002)PAPKPR 125.97 0.0033797 0 414380 308380 208720 260430 299800 291880 363290 393830 365490 TRUE FALSE 359618.6331 306354.2315 309657.6901 319564.6119 293834.5665 303108.8125 328058.1917 309612.5193 322282.1886 1.115850164 0.950577607 0.960827812 0.991567711 0.911730704 0.940507491 1.017922192 0.960687653 1 18.29796493 4.74237609 24.72039675 0.966709362 1.115850232 0.702043596 0.030530927 182.2671556 1180850.45 0.007366691 0.053710701 55255.5734 -4.74237609 0.14914087 ES(ph)PVSAPLEGLICR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESPVSAPLEGLICR 14 0 O75376;O75376-2;A0A088AWL3 O75376 NCOR1 Nuclear receptor corepressor 1 1 ES(1)PVSAPLEGLICR;ES(1)PVSAPLEGLICR 134.91 3.77E-05 71585000 36256 24509 29155 31708 34284 27918 30554 37407 58896 TRUE FALSE 31464.67774 24347.99877 43254.45552 38907.78603 33601.81548 28992.02353 27590.87778 29407.80415 51933.38197 0.605866141 0.468831373 0.832883472 0.749186449 0.647017664 0.558254102 0.531274428 0.56626014 1 15.66437456 1.233808504 24.99985279 1.000000578 0.618162371 0.561152083 0.105613773 120.5237273 633971.9239 0.217813975 0.027463008 17.13201728 -1.233808504 -0.381838207 ES(ph)SPSHGLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESSPSHGLLK 10 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 1 ES(0.604)S(0.374)PS(0.022)HGLLK 153.34 1.06E-05 371690000 667060 611400 372580 482360 608630 523080 682780 776210 897170 TRUE FALSE 578906.3309 607383.6731 552760.9342 591887.2104 596519.4538 543203.2261 616564.1007 610223.532 791107.5847 0.731766882 0.767763683 0.698717779 0.748175371 0.754030761 0.686636352 0.779368208 0.771353409 1 19.59351438 0.904706297 1.703697288 1.388786532 0.735452687 0.890296404 0.028622739 0.750817985 0.941145817 1.084150029 0.00741896 8.029829007 -0.904706297 -0.653333845 ESAAHDYTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ESAAHDYTLR 10 0 Q06124;Q06124-1;Q06124-3;A0A0U1RRI0 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ;;; 155.15 1.32E-05 1602760000 1500280 1387270 655556 968440 1386510 1579660 1276300 1364790 1391730 FALSE TRUE 1302014.197 1378156.932 972585.0743 1188339.104 1358921.164 1640430.542 1152524.622 1072940.279 1227201.265 1.060962235 1.123008077 0.792522875 0.968332691 1.107333575 1.336724944 0.939148822 0.874298544 1 20.22694044 2.033612196 24.99921396 0.921735697 1.059738487 0.156000496 0.137891308 328.4334284 244272.4757 0.059652568 0.040217537 108.0468713 -2.033612196 0.13800279 ESAAPAAAPTAEAPPPSVVTRPEPQALPS(ph)PAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ESAAPAAAPTAEAPPPSVVTRPEPQALPSPAIR 33 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 1 ESAAPAAAPTAEAPPPSVVTRPEPQALPS(0.999)PAIR;ESAAPAAAPTAEAPPPSVVTRPEPQALPS(1)PAIR;ESAAPAAAPTAEAPPPSVVTRPEPQALPS(1)PAIR;ESAAPAAAPTAEAPPPSVVTRPEPQALPS(1)PAIR 321.14 7.79E-105 2394340000 743090 628018 495431 480583 650490 829340 742910 771910 767580 TRUE FALSE 644888.7737 623892.5084 735023.0887 589706.7154 637546.5217 861245.2465 670862.7025 606843.0535 676837.5668 0.952796957 0.921775828 1.085966744 0.871267708 0.941949077 1.272454853 0.991172381 0.896585951 1 19.36845012 ESADPLGAWLQDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 234.63 7.53E-17 315766000 387067 333037 230100 260942 324817 365561 342451 386344 358390 FALSE TRUE 335915.1152 330849.258 341377.1296 320192.8693 318353.7772 379624.3682 309240.1547 303727.3421 316021.5425 1.062950053 1.046919952 1.08023373 1.013199502 1.007379986 1.201261045 0.978541375 0.961096955 1 18.26966338 2.057386857 24.99997533 0.975380544 1.065140446 0.376134862 0.053683931 78.2767559 34099.93427 0.02127934 0.014346525 114.126594 -2.057386857 0.089759902 ESAGADTRPTVRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESAGADTRPTVRPR 14 2 O75489;E9PS48;O75489-2;G3V194 O75489 NDUFS3 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial" 0 ; 122.97 5.94E-05 562700000 522830 596640 400990 590570 622570 729290 531250 611060 605050 FALSE TRUE 453736.6908 592720.6326 594910.1052 724667.9448 610182.075 757346.2582 479729.4568 480389.5743 533521.6783 0.85045596 1.110958855 1.115062667 1.358272727 1.143687501 1.419522934 0.899175191 0.900412474 1 19.02518737 2.183491962 24.99999744 0.924947656 1.16917704 0.336449729 0.154157276 98.05727432 44515.00833 0.063056694 0.042512844 152.5780154 -2.183491962 0.244229384 ESAS(ph)PTIPNLDLLEAHTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ESASPTIPNLDLLEAHTK 18 0 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 ES(0.003)AS(0.995)PT(0.002)IPNLDLLEAHTK;ES(0.001)AS(0.991)PT(0.009)IPNLDLLEAHTK;ES(0.003)AS(0.997)PTIPNLDLLEAHTK;ES(0.004)AS(0.9)PT(0.097)IPNLDLLEAHTK 299.94 1.08E-49 1204470000 3116840 2557380 1955120 2415570 2722710 2014440 2880800 3464990 3017590 TRUE FALSE 2704941.697 2540580.402 2900622.571 2964062.088 2668533.398 2091936.81 2601420.459 2724028.853 2660853.948 1.016569023 0.954798892 1.090109652 1.113951441 1.002886085 0.786190017 0.977663754 1.023742342 1 21.34345789 2.99667674 24.98609983 0.954317554 1.043002076 0.265826685 0.075608674 218.5154863 1642941.955 0.02488559 0.027662427 992.3771142 -2.99667674 0.088684522 ESAWS(ph)PPPIEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESAWSPPPIEIR 12 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 ESAWS(1)PPPIEIR 153.81 7.44E-05 45260000 176800 171200 118720 132420 160580 142660 162200 194730 184400 TRUE FALSE 153435.432 170075.3759 176133.3891 162487.9849 157384.7722 148148.2225 146469.869 153088.5049 162600.4421 0.943634778 1.045971178 1.08322823 0.999308383 0.967923397 0.911118203 0.900796253 0.94150116 1 17.31097165 3.203051179 2.734405229 0.935944188 1.027440341 0.429291827 0.043376465 0.235020877 3.595473653 0.014022843 0.017234008 1596.067223 -3.203051179 0.091496153 ESCDSALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESCDSALR 8 0 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 75.972 0.086092 227150000 455460 403630 224640 298540 343330 371220 378790 439770 391160 FALSE TRUE 395269.807 400978.528 333276.6554 366328.0699 336498.4047 385501.0736 342055.0041 345728.6078 344917.5104 1.145983591 1.162534565 0.966250322 1.062074435 0.975590959 1.117661649 0.991700896 1.002351569 1 18.39589185 4.249937325 24.99569677 1.017701672 1.154259163 0.624447692 0.044401562 130.9673791 287742.1862 0.010383748 0.026959502 17780.22796 -4.249937325 0.136557492 ESCFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESCFYR 6 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;H0YFJ7 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 110.23 0.067187 328930000 327090 257030 138560 202610 244870 243420 244960 245060 285760 FALSE TRUE 283864.2278 255341.553 205568.0795 248615.6972 239997.5661 252784.5249 221203.8169 192655.8261 251977.7783 1.126544688 1.013349489 0.815818287 0.986657232 0.952455283 1.003201658 0.877870336 0.764574667 1 17.94293698 4.479997552 4.689172559 0.90597061 1.106770639 0.431097219 0.079283188 0.169718774 9.933031691 0.021299163 0.074054243 30199.34695 -4.479997552 0.200800028 ESCSS(ph)PSTVGSSLTTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESCSSPSTVGSSLTTR 16 0 Q7Z589-4;E9PMC9;Q7Z589-6;Q7Z589-7;Q7Z589;Q7Z589-5;H0YEP9 Q7Z589-4;Q7Z589-7 EMSY;C11orf30 Protein EMSY 1 ESCS(0.005)S(0.923)PS(0.055)T(0.017)VGSSLTTR;ESCS(0.023)S(0.973)PS(0.001)T(0.003)VGSSLTTR 377.05 1.26E-104 559270000 1041260 883190 535310 614740 825310 826800 833330 917530 890990 TRUE FALSE 903654.8528 877388.2667 794187.7065 754326.1127 808887.9457 858607.531 752513.7849 721323.3497 785658.1772 1.150188312 1.116755724 1.01085654 0.960119979 1.029567271 1.092851263 0.957813215 0.918113463 1 19.58354224 8 0.403986475 0.966395047 4.282495437 0.557269445 0.049433067 67.78406981 0.945109447 0.051581132 178.2485681 100000000 -8 3.31610039 ESDFYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ESDFYLR 7 0 P61326;P61326-2 P61326 MAGOH Protein mago nashi homolog 0 ;;; 197.62 0.00097263 1652960000 2690980 2292310 1541820 1754280 2377980 2402420 2340400 2772180 2484760 FALSE TRUE 2335360.175 2277251.665 2287449.309 2152616.086 2330662.85 2494842.652 2113428.368 2179370.88 2191014.503 1.065880747 1.039359466 1.044013769 0.982474595 1.063736843 1.138670076 0.964588945 0.994685739 1 21.0631676 ESDHIHIIALAQALSVSIQVEYMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESDHIHIIALAQALSVSIQVEYMDR 25 0 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5H3F0;Q96FW1-2 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 167.57 7.19E-12 30477000 30262 22822.5 13363.8 22064.6 18253.5 19426.2 21965 25811.1 26242 FALSE TRUE 26262.80003 22672.57749 19826.57838 27074.70467 17890.29106 20173.53848 19834.83768 20291.59713 23139.70065 1.134967147 0.979812913 0.856820867 1.170054231 0.773142718 0.871815015 0.857177799 0.876917011 1 14.49808258 3.225962086 24.99998706 0.874351614 1.018685693 0.380081508 0.100268488 256.5796669 509144.6066 0.029343843 0.03349543 1682.527171 -3.225962086 0.144334079 ESDQTLAALLS(ph)PK ddPTM_MDA-MB-175_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 258.12 6.66E-24 4877414000 4788659 3775767 2991487 3398503 4522593 3365816 4651214 5772583 5370987 TRUE FALSE 4155825.58 3750963.738 4438180.119 4170185.049 4432602.248 3495301.119 4200139.982 4538161.048 4736035.036 0.877490464 0.792005065 0.937108802 0.880522424 0.935931051 0.738022648 0.886847321 0.958219484 1 22.17524832 1.683524245 3.133778357 0.990154265 0.861689155 0.400110568 0.060015313 0.20529795 4.584091896 0.046991904 0.015865346 48.25299166 -1.683524245 -0.128465109 ESDSAEGDEAES(ph)PEQQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ESDSAEGDEAESPEQQVR 18 0 Q8TEH3;Q8TEH3-7;Q8TEH3-6 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 ESDSAEGDEAES(1)PEQQVR;ESDSAEGDEAES(1)PEQQVR;ESDSAEGDEAES(1)PEQQVR 375.69 1.67E-92 193710000 510570 440580 280376 282320 372780 419260 381870 408200 423920 TRUE FALSE 443096.8809 437685.801 415966.7714 346425.071 365362.4073 435389.2035 344836.3062 320909.6066 373804.6605 1.185370135 1.170894446 1.112791828 0.926754285 0.977415335 1.164750602 0.922504031 0.858495467 1 18.51192503 8 0.23720544 0.885536988 2.856578231 0.484361697 0.084297784 74.82397869 1.175727956 0.345197984 56.12326095 100000000 -8 1.971041242 ESDTKNEVNGTSEDIKSEGDT(ph)QSN ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESDTKNEVNGTSEDIKSEGDTQSN 24 2 O95232 O95232 LUC7L3 Luc7-like protein 3 1 ESDTKNEVNGTSEDIKSEGDT(0.595)QS(0.405)N 199.04 2.71E-24 242610000 155090 97602 69625 68506 90499 61548 128170 146500 52650 TRUE FALSE 134594.4636 96960.84604 103295.8829 84061.33435 88698.24696 63915.79139 115740.0931 115172.1151 46425.77698 2.89913217 2.088513157 2.224968317 1.810660797 1.910538772 1.376730677 2.493013594 2.480779484 1 15.50263843 5.776332641 1.123682834 1.947187604 10.00877951 0.316810434 0.45809138 20.00088191 3.451519966 0.138244034 327.0612536 597492.7516 -5.776332641 8.061591907 ESDTKNEVNGTSEDIKSEGDTQS(ph)N ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESDTKNEVNGTSEDIKSEGDTQSN 24 2 O95232 O95232 LUC7L3 Luc7-like protein 3 1 ESDTKNEVNGTSEDIKSEGDT(0.002)QS(0.998)N;ESDTKNEVNGTSEDIKSEGDT(0.111)QS(0.889)N 286.34 7.96E-53 771160000 1065120 622520 559210 514050 569670 375120 891180 1033970 316410 TRUE FALSE 924361.6933 618430.6251 829645.8264 630772.9093 558334.6815 389551.1091 804753.5008 812863.5619 279004.3703 3.313072453 2.216562502 2.973594377 2.260799387 2.001168229 1.396218664 2.884375969 2.913443833 1 18.08992819 8 0.705155261 2.205038884 134.1999169 0.237327209 0.637444632 542.0671193 2.831835332 0.25699465 112883.6157 100000000 -8 131.994878 ESDVPLKTEEFEVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ESDVPLKTEEFEVTK 15 1 Q969H8;M0QXF7;M0QYN0 Q969H8 MYDGF Myeloid-derived growth factor 0 ;;; 236.43 9.52E-18 1278800000 2393740 1952100 1684600 1834880 1605470 1454750 2366620 2662470 2166460 FALSE TRUE 2077401.194 1939276.527 2499278.195 2251517.548 1573524.288 1510715.174 2137105.557 2093121.51 1910343.567 1.087448996 1.015145422 1.308287283 1.178592996 0.823686543 0.790808104 1.118702203 1.095678048 1 20.86540069 3.276800461 24.99983274 0.98473382 1.149418487 0.3348018 0.125606367 236.164431 154394.2172 0.040143729 0.051824301 1891.474369 -3.276800461 0.164684667 ESEDAELLWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ESEDAELLWR 10 0 E5RH53;Q96DB5-3;Q96DB5-2;Q96DB5;H0YB83;E5RGC8 E5RH53 RMDN1 Regulator of microtubule dynamics protein 1 0 ;; 194.22 1.13E-06 581623000 601420 523880 379113 419285 493160 560400 425395 580410 544930 FALSE TRUE 521940.8232 520438.5978 562453.3149 514490.0676 483347.0809 581958.9506 384140.2584 456293.8383 480508.9962 1.086224873 1.083098552 1.170536492 1.070718908 1.005906413 1.211130187 0.799444467 0.949605193 1 18.87420392 2.240169004 25 0.918407023 1.100595751 0.58958033 0.073984878 28.87947163 448901.2452 0.027671356 0.020282471 173.847722 -2.240169004 0.182188728 ESEDDPES(ph)EPDDHEK ddPTM_MDA-MB-175_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 110.74 0.0005783 425030000 1148770 907630 753650 729350 961440 794460 1053730 1146640 966090 TRUE FALSE 996957.1339 901667.7188 1118117.661 894960.0649 942309.225 825023.3903 951539.4268 901439.9592 851879.9408 1.170302394 1.058444595 1.312529627 1.050570652 1.106152616 0.968473785 1.116987713 1.058177234 1 19.70029059 ESEDKPEIEDVGS(ph)DEEEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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;ESEDKPEIEDVGS(1)DEEEEK;ESEDKPEIEDVGS(1)DEEEEK 326.81 2.25E-75 17585090000 15309662 8068383 13611391 13077547 8189931 7095358 12832703 15541502 37620050 TRUE FALSE 13286451.38 8015381.261 20193905.21 16047003.92 8026967.396 7368321.014 11588189.44 12218072.74 33172650.55 0.400524262 0.241626193 0.608751634 0.483741988 0.241975461 0.222120358 0.349329621 0.368317651 1 24.98349095 1.238563205 8.67693286 1.005422697 0.362879338 0.740487002 0.118225241 0.045713923 40.90410502 0.172553239 0.030185861 17.32061088 -1.238563205 -0.642543359 ESEDKPEIEDVGS(ph)DEEEEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ESEDKPEIEDVGSDEEEEKK 20 2 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK 323.8 3.85E-67 15363330000 8165530 3816919 7542570 5335930 3209049 2669857 6407250 7446060 15387920 TRUE FALSE 7086434.522 3791845.408 11190182.08 6547534.461 3145195.203 2772568.126 5785875.881 5853778.014 13568777.63 0.522260348 0.279453722 0.824700823 0.482544164 0.231796503 0.204334407 0.426410989 0.431415281 1 23.69378742 1.238190159 7.1493291 1.011474318 0.421648047 0.511951096 0.176319112 0.093733186 29.34475695 0.267494529 0.044716865 17.30573939 -1.238190159 -0.589826271 ESEDKPEIEDVGS(ph)DEEEEKKDGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 ESEDKPEIEDVGSDEEEEKKDGDK 24 3 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK 233.49 1.37E-36 49686330000 19740250 8306160 20535560 10197580 5845017 4729608 15409350 17072950 19135730 TRUE FALSE 17131525.95 8251596.288 30466625.5 12513096.4 5728712.597 4911559.08 13914953.61 13422032.5 16873525.8 1.015290233 0.489026205 1.805587396 0.741581608 0.339508925 0.291080782 0.824661886 0.795449194 1 24.00825813 3.50036201 24.91954538 0.652267629 1.080492221 0.233146883 0.377014419 1147.895151 1230810.312 0.104479865 0.153793624 3164.9147 -3.50036201 0.428224591 ESEDSETQPFDTHLEAYGPCLS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 225.05 5.00E-34 809450000 772190 615830 418027 448193 555390 518010 563480 658350 595590 TRUE FALSE 670143.135 611784.5722 620186.2554 549962.0709 544338.8256 537938.1799 508833.7963 517566.9758 525180.0287 1.27602555 1.164904488 1.180902208 1.047187709 1.036480437 1.02429291 0.968874992 0.985503918 1 19.00245253 4.163030668 0.638920623 0.979075998 1.339819777 0.939207215 0.024577383 0.391335355 0.207446838 0.013645182 0.095579926 14555.61863 -4.163030668 0.360743779 ESEEQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ESEEQKR 7 1 P00367 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ;; 125.5 0.0064823 1546108000 1398020 1339576 1065100 1714610 881280 1235621 1420646 1789400 1828540 FALSE TRUE 1213268.115 1330776.237 1580185.923 2103938.407 863744.2522 1283156.139 1282871.97 1406750.735 1612372.084 0.752474027 0.825353062 0.980038006 1.304871516 0.535697846 0.795818876 0.795642632 0.872472768 1 20.62075328 3.219067756 24.99990518 0.808468215 0.956686098 0.1692844 0.181426086 509.5236468 653470.4539 0.056406752 0.064050494 1656.028309 -3.219067756 0.148217883 ESEIIDFFLGASLKDEVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESEIIDFFLGASLKDEVLK 19 1 P15880;E9PQD7;E9PPT0;E9PMM9;I3L404 P15880 RPS2 40S ribosomal protein S2 0 ; 200.99 5.66E-16 468930000 675270 528990 435830 571180 496860 344770 680890 917440 504670 FALSE TRUE 586031.3586 525515.0299 646598.8458 700875.1489 486973.4581 358033.525 614857.3926 721252.5955 445008.4875 1.316899284 1.180910128 1.453003401 1.574970295 1.094301506 0.804554374 1.381675653 1.620761437 1 18.76347333 3.22105551 24.99990489 1.23164257 1.372233174 0.128945145 0.23947657 779.0141999 1112545.942 0.081615218 0.09274637 1663.625276 -3.22105551 0.140590605 ESEITDEDIDGILER ddPTM_MDA-MB-175_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 ;; 317.15 5.19E-56 419755000 832610 745600 526780 620740 770020 758460 712630 883170 793210 FALSE TRUE 722578.4789 740702.1045 781532.57 761688.5044 754698.1085 787638.447 643519.2523 694310.9683 699437.6174 1.033084954 1.058996665 1.117372801 1.089001343 1.079007033 1.126102496 0.920052391 0.992670327 1 19.41583586 2.24216973 24.99997247 0.973322511 1.084321535 0.716952949 0.033463862 47.91111554 331878.2655 0.012820997 0.009535193 174.6504586 -2.24216973 0.110999024 ESENSGDSGYPS(ph)EK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESENSGDSGYPSEK 14 0 O00418 O00418 EEF2K Eukaryotic elongation factor 2 kinase 1 ESENSGDSGYPS(1)EK 205.78 1.18E-07 0 451740 327250 201630 221580 305150 187790 393510 396320 370170 TRUE FALSE 392041.4144 325100.2732 299138.9424 271893.1256 299078.112 195014.4028 355347.4608 311570.0522 326408.9243 1.201074435 0.995990762 0.916454546 0.832983125 0.916268183 0.597454262 1.088657308 0.954539012 1 18.31632098 4.701893724 2.064481034 0.902710218 1.271114966 0.360453417 0.126980031 0.750710578 3.75771542 0.033626508 0.503708128 50337.74126 -4.701893724 0.368404748 ESENVVCHFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESENVVCHFYR 11 0 F8WCJ3;B8ZZX4;O14530-2;O14530 F8WCJ3 TXNDC9 Thioredoxin domain-containing protein 9 0 67.519 0.059751 262380000 356660 299600 187560 260050 323550 312500 350640 380060 332960 FALSE TRUE 309526.4773 297631.9079 278264.6434 319098.3271 317111.988 324522.0772 316634.9868 298787.1266 293597.8481 1.054253222 1.013740086 0.947774805 1.086855129 1.080089619 1.105328528 1.078464944 1.017674784 1 18.16348187 5.113619956 18.10141998 1.042344392 2.411347702 0.006708972 0.048121205 2522.279016 378127.3865 0.012185093 8418.446516 129903.2319 -5.113619956 1.36900331 ESESALMEDRDES(ph)EVS(ph)DEGGSPISSEGQEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESESALMEDRDESEVSDEGGSPISSEGQEPR 31 1 O14976-2;O14976 O14976-2 GAK Cyclin-G-associated kinase 2 ESESALMEDRDES(1)EVS(0.985)DEGGS(0.015)PISSEGQEPR 83.343 0.00043713 323770000 122470 102710 52393 71377 112440 120800 106730 121860 108800 TRUE FALSE 106285.2792 102035.2912 77730.43004 87584.23878 110202.664 125447.2542 96379.34103 95801.18732 95937.78795 1.107856263 1.063556847 0.810217034 0.912927436 1.148688815 1.307589604 1.004602494 0.998576154 1 16.54981155 3.241188681 24.9951803 1.084465246 0.968389046 0.189330648 0.120830892 135.1173826 1285071.887 0.039000801 0.048036306 1742.563773 -3.241188681 -0.1160762 ESESVDKVMDQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ESESVDKVMDQK 12 1 Q14103-3;Q14103;H0Y8G5;H0YA96;D6RAF8;D6RF44;Q14103-2;Q14103-4;D6RBQ9 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;;; 154.36 5.51E-05 2130610000 5134300 3120530 1887600 1937160 2581300 1819120 4364970 4794390 540862 FALSE TRUE 4455789.246 3100031.033 2800449.674 2377021.786 2529937.18 1889102.724 3941655.881 3769147.008 476921.9105 9.342806753 6.500080966 5.871924967 4.984090127 5.304719965 3.961031527 8.264782545 7.903069508 1 18.86339354 4.775693227 2.089897315 5.648587995 10.60039655 0.271788346 2.027021056 1.20575749 5.395838514 0.53680898 11.66305993 59661.37075 -4.775693227 4.951808554 ESEVAHVDQLFDDASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESEVAHVDQLFDDASR 16 0 E9PRF4;Q15047-3;Q15047;E9PAP1;X6RHV1;B0QZE6;E9PS59;X6R732;E9PQM8;Q15047-2 E9PRF4 SETDB1 Histone-lysine N-methyltransferase SETDB1 0 160.25 8.85E-09 66765000 91272 80097 44073 67506 78888 82970 73429 90805 80376 FALSE TRUE 79210.17395 79570.83753 65386.85022 82834.26906 77318.28314 86161.90959 66307.86688 71387.0574 70874.04084 1.11761899 1.122707787 0.922578273 1.168753299 1.090925284 1.215704771 0.935573393 1.007238427 1 16.11296969 2.216277219 24.99997649 0.984526514 1.100901405 0.368371057 0.077164378 269.3734503 302210.453 0.030986012 0.02090827 164.5421694 -2.216277219 0.116374892 ESFDGSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESFDGSVR 8 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 157.58 0.00087158 1117290000 1386530 1131910 905930 1243000 1087190 1111640 1093060 1257110 2291500 FALSE TRUE 1203296.547 1124474.409 1344040.778 1525242.148 1065557.046 1154405.51 987055.2094 988286.8093 2020601.48 0.595514038 0.556504793 0.665168659 0.754845606 0.527346464 0.571317759 0.488495737 0.489105258 1 20.94635338 1.231161519 24.99993867 1.000000744 0.577702486 0.728278343 0.080402093 156.8503207 529917.273 0.221117042 0.02178879 17.02791679 -1.231161519 -0.422298257 ESFESQFLADTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESFESQFLADTER 13 0 A0A590UJ56;A0A590UJR3;A0A590UJ21;A0A0C4DGX4;Q13616;A0A590UJC4;A0A590UJ50 A0A590UJ56 CUL1 Cullin-1 0 ; 213.77 7.55E-09 96461000 247614 226456 147424 189467 269300 260433 236067 280300 246396 FALSE TRUE 214891.1825 224968.3956 218718.7395 232488.3782 263941.4569 270452.026 213173.2587 220360.0263 217267.3456 0.989063414 1.035445041 1.006680221 1.070056697 1.214823407 1.244789111 0.981156455 1.014234448 1 17.72911183 3.675143965 5.327141268 1.08570643 1.012897927 0.152481699 0.08602077 0.508099519 29.16746989 0.027185345 0.04124925 4733.081312 -3.675143965 -0.072808503 ESFQIFLDELHEHGQLHSMSSWMELYPTISSDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESFQIFLDELHEHGQLHSMSSWMELYPTISSDIR 34 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 108.04 4.68E-06 541600000 254090 206300 98464 169270 194490 217580 195340 255720 205550 FALSE TRUE 220511.3627 204944.8017 146081.5197 207705.3406 190620.0295 225950.4434 176395.9569 201036.268 181250.1132 1.216613655 1.130729235 0.805966502 1.145959785 1.051696058 1.246622358 0.973218465 1.109164924 1 17.46762237 2.075496073 0.007238637 1.98E-07 2.132550177 0.020821436 0.126774084 94321.80928 344.497424 51528.7757 49963.8683 118.9860571 -2.075496073 2.132549979 ESGADGASTS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESGADGASTSPR 12 0 O75528-2;O75528 O75528-2 TADA3 Transcriptional adapter 3 1 ESGADGAS(0.008)T(0.031)S(0.96)PR 71.806 0.045729 91817000 87502 73520 45679 54827 69469 70175 72191 83251 67191 TRUE FALSE 75938.389 73037.04228 67769.51719 67276.30833 68086.70281 72874.67766 65189.92793 65448.42151 59247.75652 1.281709105 1.232739374 1.14383263 1.135508115 1.149186177 1.229998939 1.10029361 1.104656536 1 15.85447291 -1.651644359 0.264427817 6.20E-34 1.240605812 0.654277142 0.047112715 47.33280997 0.903975577 24.99214285 0.141759324 0.022302607 1.651644359 1.240605812 ESGCSWHGGPDGLYEYLRPSGTPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESGCSWHGGPDGLYEYLRPSGTPAR 25 1 Q8IZ83;F5H4B6;Q8IZ83-3;M0QY06 Q8IZ83 ALDH16A1 Aldehyde dehydrogenase family 16 member A1 0 ; 118.22 0.00048896 948790000 413080 337790 152776 263010 352200 373830 414450 442990 396000 FALSE TRUE 358490.4314 335571.0352 226658.9846 322730.4404 345191.9091 388211.482 374256.7028 348260.0359 349185.3311 1.026648027 0.961011261 0.649107979 0.924238253 0.988563603 1.111763432 1.071799613 0.997350131 1 18.41363343 3.21432437 3.365521146 1.039959517 0.874735365 0.340882313 0.101548685 0.270700452 6.379681163 0.032511179 0.039665683 1638.0395 -3.21432437 -0.165224152 ESGGS(ph)GFRSPHLWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESGGSGFRSPHLWK 14 1 P00519-2;P00519 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 ES(0.053)GGS(0.655)GFRS(0.292)PHLWK 93.153 0.0028232 225560000 872760 756000 384970 404280 627970 547820 747940 885720 381920 TRUE FALSE 757422.5547 751033.7862 571142.7796 496077.953 615474.6256 568894.9899 675404.8939 696315.6707 336769.8527 2.249080637 2.230109911 1.695943907 1.473047391 1.827582311 1.689269349 2.005538467 2.067630654 1 18.36140347 4.241617888 24.42813761 1.730154239 2.239595603 0.369480116 0.298416202 66.04160223 527649.2239 0.075387412 0.182392173 17442.86775 -4.241617888 0.509441364 ESGGSGFRS(ph)PHLWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESGGSGFRSPHLWK 14 1 P00519-2;P00519 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 ES(0.133)GGS(0.157)GFRS(0.71)PHLWK 78.234 0.013594 139330000 136610 121590 53999 79934 103450 90797 115810 117350 70228 TRUE FALSE 118556.6424 120791.2673 80113.09702 98084.23641 101391.5474 94290.01934 104578.764 92255.61572 61925.72584 1.91449742 1.950582987 1.293696536 1.58390128 1.637308986 1.52263083 1.688777364 1.489778512 1 15.91825125 1.21214552 2.316966932 0.790996656 1.645167815 0.550254429 0.185959736 0.541459328 2.859095726 0.980980979 0.050977655 16.29842055 -1.21214552 0.854171159 ESGLQAAHPNSIFLIDHAWTCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ESGLQAAHPNSIFLIDHAWTCR 22 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ;; 226.16 3.18E-26 2047210000 841409 758530 364078 505818 758828 829502 755567 761604 636950 FALSE TRUE 730214.6688 753547.1665 540147.3386 620671.7078 743728.8074 861413.4787 682292.2286 598740.9114 561650.4966 1.300122893 1.341665628 0.961714343 1.105085301 1.324184367 1.533718004 1.214798585 1.066038248 1 19.09931313 1.697987913 3.532519278 1.018575776 1.255554789 0.280960378 0.14972339 0.276293477 7.877402064 0.119294775 0.043471759 49.88706028 -1.697987913 0.236979013 ESGLQHTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESGLQHTR 8 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 0 84.213 0.017612 35518000 154800 148920 104630 131680 119480 152800 115510 137790 172530 FALSE TRUE 134342.7878 147941.7347 155229.418 161579.9566 117102.5818 158678.3149 104307.858 108324.6808 152133.6999 0.883057389 0.972445518 1.020348667 1.062091809 0.76973466 1.043018838 0.685632822 0.712036063 1 17.21498024 2.239652155 24.99999167 0.776326101 0.958032332 0.281173138 0.11813738 32.01569802 733300.5453 0.044961423 0.032819933 173.6409505 -2.239652155 0.181706231 ESGPPHMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ESGPPHMK 8 0 O95793-2;O95793-3;O95793;Q5JW30;A0A087X1A5;Q5JW28;E7EVI1;E7EPX0;E7EVJ4;Q9NUL3-4;Q9NUL3-6;Q9NUL3-8;Q9NUL3-3;Q9NUL3-7;Q9NUL3-2;Q9NUL3;E5RJN7 O95793-2;E7EPX0 STAU1;STAU2 Double-stranded RNA-binding protein Staufen homolog 1;Double-stranded RNA-binding protein Staufen homolog 2 0 ;;; 108.46 0.0038063 478240000 1707630 1401670 893002 1197130 1322550 1331110 1565830 1855730 1737460 FALSE TRUE 1481962.369 1392462.337 1324860.754 1468956.663 1296233.843 1382318.663 1413976.048 1458896.581 1532059.458 0.967300819 0.9088827 0.864758053 0.958811785 0.846072805 0.90226176 0.922925047 0.952245406 1 20.54704086 1.435397701 1.639947221 1.014813584 0.906081138 0.400076932 0.036457015 0.653950284 2.339050178 0.10537761 0.010148728 27.25195741 -1.435397701 -0.108732446 ESGS(ph)PYSVLVDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESGSPYSVLVDTK 13 0 Q9Y2D9;D6RF85 Q9Y2D9 ZNF652 Zinc finger protein 652 1 ES(0.012)GS(0.988)PYSVLVDTK 123.18 0.0002375 99595000 197310 149340 92691 132750 155700 124900 133680 198770 186790 TRUE FALSE 171234.9836 148358.9757 137516.6776 162892.9165 152601.8746 129704.9838 120715.7342 156264.5823 164707.899 1.039628243 0.900739895 0.834912463 0.988980598 0.926500038 0.787484903 0.732907984 0.948737634 1 17.32955022 2.963265624 24.64027156 0.866254571 0.933994811 0.131041985 0.090543009 1153.690679 773859.2621 0.030614846 0.030624669 918.8944411 -2.963265624 0.06774024 ESGYSDDEIMELWSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ESGYSDDEIMELWSTR 16 0 Q7Z3K3-5;Q7Z3K3-7;Q7Z3K3-2;Q7Z3K3-3;Q7Z3K3-6;Q7Z3K3 Q7Z3K3-5 POGZ Pogo transposable element with ZNF domain 0 ;; 329.77 3.81E-71 136156000 157110 150671 95610 110853 144794 136004 136119 161856 146931 FALSE TRUE 136347.5154 149681.2323 141847.3158 136023.8679 141912.8827 141236.1619 122918.2003 127244.354 129560.9846 1.052380976 1.155295576 1.094830487 1.049882944 1.095336556 1.090113373 0.948728514 0.982119381 1 16.98327181 2.247664313 24.99745022 0.976850532 1.09131208 0.744502592 0.031109867 88.26688363 242368.6034 0.011590271 0.008846864 176.8741284 -2.247664313 0.114461547 ESHPHGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESHPHGVK 8 0 E9PM92;O00193;E9PQA1;E9PRZ9 E9PM92 C11orf58;SMAP Small acidic protein 0 ; 86.794 0.015781 71941700 202271 179351 106713 162177 129288.4 168192 163750 208299 199383 FALSE TRUE 175540.3749 178172.8315 158319.7637 199001.7666 126715.8138 174662.4551 147869.5502 163755.8798 175812.1689 0.998454066 1.013427185 0.900505151 1.131899844 0.72074541 0.993460556 0.841065503 0.931425173 1 17.4236754 3.258715491 24.99963462 0.902185469 1.003342125 0.255687385 0.095822848 363.5805449 450973.9514 0.025587004 0.032990461 1814.326696 -3.258715491 0.101156655 ESIESEIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ESIESEIRR 9 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;; 179.51 7.97E-05 11627370000 8566000 5563700 3198680 3710740 5395110 5458660 5533470 6052720 2896210 FALSE TRUE 7433981.397 5527151.688 4745572.347 4553320.232 5287757.866 5668658.182 4996834.931 4758392.93 2553823.353 2.910922319 2.164265466 1.85822263 1.782942515 2.070526084 2.21967513 1.95660946 1.863242782 1 21.28422731 8 0.068410952 1.52E-09 6.352102063 0.500915118 0.332565377 642.8766612 4.228126077 89.10527162 424.4687883 100000000 -8 6.352102061 ESIPSLPQS(ph)PMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESIPSLPQSPMR 12 0 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37;H0Y765 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 ESIPS(0.001)LPQS(0.999)PMR 104.09 0.0085047 297910000 297630 282820 197300 272520 309170 332420 297990 331670 512520 TRUE FALSE 258297.4414 280962.1368 292714.9399 334399.8312 303018.1219 345208.4125 269090.9757 260744.9516 451930.4695 0.571542436 0.621693282 0.647699059 0.739936459 0.670497217 0.763852928 0.59542561 0.576958115 1 18.7857413 1.231338128 24.99989048 1.000000613 0.648908428 0.749429248 0.063882997 140.0092134 484584.6265 0.166828916 0.016750962 17.0348427 -1.231338128 -0.351092184 ESIWLPFMETELHCDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESIWLPFMETELHCDEK 17 0 O75884;O75884-2 O75884 RBBP9 Putative hydrolase RBBP9 0 ; 231.06 5.86E-16 157880000 347130 335620 237972 257050 278350 250082 378830 415830 427730 FALSE TRUE 301255.891 333415.2901 353056.0552 315417.1313 272811.3796 259702.8164 342091.1249 326907.9905 377164.2467 0.798739259 0.884005557 0.93608039 0.836285873 0.723322483 0.688566901 0.90700836 0.866752332 1 18.5248334 1.186670936 1.531186189 1.084064701 0.821744402 0.350835385 0.075730269 1.694996793 3.21422894 0.710400841 0.023792925 15.36989626 -1.186670936 -0.262320299 ESKGS(ph)PVFLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ESKGSPVFLPR 11 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 ES(0.498)KGS(0.502)PVFLPR;ES(0.001)KGS(0.999)PVFLPR;ES(0.01)KGS(0.99)PVFLPR 154.19 1.95E-05 2990520000 4008240 2437000 1493100 1740250 2341110 2045610 2770020 3126320 1668200 TRUE FALSE 3478540.928 2420991.187 2215168.154 2135400.361 2294526.491 2124305.94 2501383.887 2457780.797 1470987.296 2.364766125 1.645827393 1.5059057 1.451678315 1.559854729 1.444136156 1.700479598 1.670837541 1 20.48835336 4.752641205 2.770304187 1.507198339 2.542755097 0.674483961 0.191929719 0.28026689 2.863591991 0.047275764 0.671581519 56577.16803 -4.752641205 1.035556757 ESLCDS(ph)PHQNLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ESLCDSPHQNLSR 13 0 O15042-2;O15042;E7ET15;E7EW00;H0Y8D9;C9JDJ7;C9J5L1;U3KPT1 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 ESLCDS(1)PHQNLSR;ESLCDS(1)PHQNLSR;ESLCDS(1)PHQNLSR;ESLCDS(1)PHQNLSR 215.15 1.91E-11 1799870000 1034100 921000 711720 861270 870610 904350 859980 919180 1698810 TRUE FALSE 897441.0649 914949.8904 1055910.173 1056834.517 853286.5643 939140.9297 776579.272 722620.5101 1497978.617 0.599101385 0.610789687 0.704890017 0.705507078 0.56962533 0.626938809 0.518418129 0.48239708 1 20.5145856 1.228141601 24.99792247 1.000000833 0.59912426 0.759882029 0.070255398 251.8902692 604308.6325 0.274645585 0.019845501 16.90992187 -1.228141601 -0.400876572 ESLCDS(ph)PHQNLSRPLLENK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ESLCDSPHQNLSRPLLENK 19 1 O15042-2;O15042;E7ET15;E7EW00;H0Y8D9;C9JDJ7;C9J5L1;U3KPT1 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 ESLCDS(1)PHQNLSRPLLENK;ESLCDS(1)PHQNLSRPLLENK;ESLCDS(1)PHQNLSRPLLENK;ESLCDS(1)PHQNLSRPLLENK;ESLCDS(1)PHQNLSRPLLENK 253.66 4.22E-31 2532150000 2582470 2130980 1158280 1319210 1723050 1521260 2210890 2441040 956697 TRUE FALSE 2241190.046 2116981.452 1718428.082 1618756.793 1688764.676 1579783.857 1996478.228 1919042.592 843597.3705 2.656705823 2.509469003 2.037023991 1.918873683 2.001861 1.872675179 2.366624527 2.274832354 1 19.68619507 4.272617121 3.256340375 1.974356978 2.631068792 0.356872789 0.366497726 0.282378929 6.021868752 0.094337175 0.280564705 18733.42221 -4.272617121 0.656711814 ESLIDGIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ESLIDGIKR 9 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;;; 125.71 0.00079186 3637590000 5992710 5761530 3328030 4132730 5524460 4842230 6815600 7218810 2837230 FALSE TRUE 5200758.19 5723682.13 4937476.44 5071129.511 5414534.054 5028513.721 6154624.161 5675123.658 2501815.902 2.078793322 2.287811076 1.973557062 2.026979486 2.164241602 2.009945543 2.460062772 2.268401786 1 21.2545442 1.235554387 24.99477799 0.999998409 2.167644097 0.856202402 0.149194985 31.30824357 260259.3704 0.262189527 0.038230063 17.20102738 -1.235554387 1.167645687 ESLKEEDES(ph)DDDNM ddPTM_MDA-MB-175_Pertuzumab_2h_R1 25 ESLKEEDESDDDNM 14 1 P25788-2;P25788;G3V4X5;H0YJ03 P25788-2 PSMA3 Proteasome subunit alpha type-3 1 ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM 220.93 1.58E-11 78180350000 54990390 42136320 33540840 35876960 41431640 33243410 52750430 59845360 52086700 TRUE FALSE 47723270.63 41859523.74 49761302.41 44023372.11 40607231.42 34522305.49 47634701.42 47047895.48 45929069.66 1.039064605 0.911394985 1.083438066 0.958507813 0.884129196 0.75164391 1.037136214 1.024359862 1 25.45290422 ESLLGDMEWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ESLLGDMEWR 10 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4;Q63HN8-5 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 ;; 144.5 7.47E-05 158566000 283350 293419 193656 224872 301144 315186 283036 324021 328933 FALSE TRUE 245904.5796 291491.5113 287308.6893 275932.6246 295151.8236 327311.4094 255587.2123 254731.6307 290046.9155 0.84780967 1.004980559 0.990559368 0.951337904 1.017600284 1.12847747 0.881192658 0.878242854 1 18.14592675 ESLLVSVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ESLLVSVQR 9 0 J3QRZ1;A6NIZ0;Q9GZM8-3;Q9GZM8;Q9GZM8-2 J3QRZ1 NDEL1 Nuclear distribution protein nudE-like 1 0 ;;; 101.46 0.0039682 2720270000 3131540 4217760 1885150 1991720 4238320 5753770 2730830 2791440 1188990 FALSE TRUE 2717699.055 4190053.257 2796814.845 2443970.468 4153985.724 5975121.255 2465994.527 2194512.279 1048428.957 2.592163291 3.996506611 2.667624571 2.331078755 3.962105107 5.699118874 2.352085481 2.093143522 1 19.99979767 2.013320179 24.98600281 1.804041157 3.531429721 0.412930429 0.994425553 235.0871068 440974.9343 0.422898495 0.284950232 103.1146042 -2.013320179 1.727388563 ESNCYDPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ESNCYDPER 9 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 158.57 0.00015521 5644540000 7616400 6631620 4246900 4490950 6367270 6929720 6663490 7032970 6850820 FALSE TRUE 6609873.443 6588056.452 6300715.045 5510688.837 6240573.784 7196310.813 6017265.765 5529024.096 6040923.864 1.094182544 1.090571012 1.043005207 0.91222617 1.033049567 1.191259975 0.996083695 0.915261344 1 22.52633777 2.005832409 24.99995967 0.952806273 1.056628294 0.271757596 0.07142868 190.05334 814638.2353 0.030637165 0.020588422 101.35202 -2.005832409 0.103822021 ESNEEEQVWHFLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESNEEEQVWHFLGK 14 0 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;Q9H2U2-4;H0YAK2 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 ; 146.47 8.30E-06 283400000 131728 114358 97514 142100 138413 107295 103668 153269 250304 FALSE TRUE 114319.811 113606.7748 144672.0966 174365.9769 135658.8521 111422.7081 93614.29332 120493.6171 220713.3463 0.517956041 0.514725442 0.655475072 0.790011025 0.614638192 0.504829952 0.424144235 0.545928097 1 17.75181434 1.236619131 24.99994932 1.000000543 0.569934739 0.646224989 0.099760164 36.74812615 473065.7311 0.17185123 0.027165403 17.24325024 -1.236619131 -0.430065804 ESNRLS(ph)APSYLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESNRLSAPSYLAR 13 1 H0YJH0;Q9H4B6 H0YJH0 SAV1 Protein salvador homolog 1 1 ESNRLS(1)APSYLAR;ESNRLS(1)APSYLAR 175.39 1.11E-05 945390000 587560 622850 444060 467540 671710 718970 542500 733600 778770 TRUE FALSE 509912.4573 618758.4573 658808.9013 573702.1029 658344.2852 746629.2411 489888.4335 576725.3489 686704.6978 0.742549831 0.901054645 0.959377304 0.835442228 0.958700716 1.087263919 0.713390246 0.83984477 1 19.38933031 5.769729335 11.78076863 0.889566863 0.648065693 0 0.115045175 17069002.97 1671937.248 0.026225488 0 588476.7845 -5.769729335 -0.24150117 ESNTAGNDVFHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ESNTAGNDVFHK 12 0 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 ;; 151.7 6.38E-05 772650000 988520 975380 755020 878470 860510 816190 895700 1109420 1331360 FALSE TRUE 857884.5774 968972.6646 1120150.197 1077940.04 843387.5346 847589.3574 808835.1519 872179.1665 1173968.137 0.73075627 0.825382422 0.95415724 0.918202126 0.718407517 0.72198668 0.688975387 0.742932571 1 20.16296182 3.233913331 24.99968673 0.761484382 0.861788132 0.129165161 0.103342175 208.670802 1122525.702 0.031659615 0.037086228 1713.615301 -3.233913331 0.100303751 ESPFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESPFFR 6 0 P25098 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 0 135.25 0.031826 142990000 180690 186460 114450 123040 180140 220470 177360 189660 178740 FALSE TRUE 156811.3587 185235.132 169798.4028 150978.1125 176555.5664 228951.6236 160159.6545 149102.6849 157609.5608 0.994935573 1.175278524 1.077335676 0.957924835 1.120208479 1.452650603 1.016179816 0.946025635 1 17.26599553 2.016825314 24.99988888 0.97274091 1.130607437 0.208650708 0.132638282 352.1921132 523302.5579 0.055659889 0.037516408 103.9501965 -2.016825314 0.157866527 ESPFS(ph)TSASPLLSGSQHFDVPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESPFSTSASPLLSGSQHFDVPPR 23 0 O14980 O14980 XPO1 Exportin-1 1 ES(0.054)PFS(0.326)T(0.256)S(0.069)AS(0.289)PLLS(0.003)GS(0.003)QHFDVPPR 63.625 0.023609 238340000 93792 84873 39295 58795 94067 98667 82578 102600 109530 TRUE FALSE 81397.14956 84315.46367 58298.19343 72145.30338 92195.25074 102462.7833 74569.59827 80659.78843 96581.48818 0.842782101 0.872998183 0.603616641 0.746988939 0.954585112 1.060894642 0.77208997 0.8351475 1 16.55945907 3.245859885 24.99653363 0.908752504 0.762555145 0.347113495 0.106356899 223.1834863 764293.2672 0.032817833 0.041488472 1761.407678 -3.245859885 -0.146197359 ESPRPLQLPGAEGPAIS(ph)DGEEGGGEPGAGGGAAGAAGAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ESPRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR 40 1 Q6PKG0;A0A0B4J210 Q6PKG0 LARP1 La-related protein 1 1 ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR 367.18 2.96E-162 10883800000 2225650 2461460 1528990 1978530 2413460 2403900 2327600 2855300 2401950 TRUE FALSE 1931524.713 2445290.507 2268414.678 2427785.476 2365436.868 2496379.589 2101869.71 2244716.315 2117994.207 0.911959394 1.154531254 1.071020247 1.146266344 1.116828771 1.178652699 0.992386902 1.059831187 1 21.01426721 2.215159066 24.9999849 1.025202138 1.101201072 0.193961179 0.075094344 380.52918 406518.1051 0.029016062 0.019575942 164.1190771 -2.215159066 0.075998934 ESPSTRPS(ph)TPSLEGSQSSAEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESPSTRPSTPSLEGSQSSAEGR 22 1 Q3KR16-2;Q3KR16;Q3KR16-3 Q3KR16-2 PLEKHG6 Pleckstrin homology domain-containing family G member 6 1 ES(0.019)PS(0.098)T(0.098)RPS(0.39)T(0.39)PS(0.004)LEGSQSSAEGR 51.956 0.073107 416720000 119230 102810 87757 99180 131700 117730 123730 141940 143600 TRUE FALSE 103473.4534 102134.6343 130196.5787 121700.3349 129079.4277 122259.1493 111730.6836 111587.2356 126623.7716 0.817172416 0.806599212 1.028215927 0.961117595 1.019393326 0.965530783 0.88238316 0.881250291 1 16.95018875 4.257399042 24.99862442 0.953086262 0.811885673 0.604677336 0.050195844 192.3695854 255270.4517 0.014032257 0.036990338 18088.3537 -4.257399042 -0.141200589 ESQFLKEELVAAVEDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ESQFLKEELVAAVEDVR 17 1 P35221-2;P35221;G3XAM7;E5RIB1;E5RJL0;E5RHV7;E5RG03;E5RIE0;E5RGY6 P35221-2 CTNNA1 Catenin alpha-1 0 ;; 175.21 1.15E-09 111328000 316928 263341 181858 260265 281313 277445 266674 380422 221034 FALSE TRUE 275045.1618 261611.0956 269805.1371 319362.1462 275715.4217 288118.4887 240811.9965 299071.7157 194903.6123 1.411185552 1.342258835 1.384300341 1.638564531 1.414624482 1.47826141 1.23554404 1.534459583 1 17.5724013 1.229849579 24.99926051 0.999999188 1.429081607 0.610207163 0.107979395 229.0940904 657412.0336 0.29521414 0.025519497 16.97655554 -1.229849579 0.429082418 ESQLAHIKDEPPPLS(ph)PAPLTPATPSSLDPFFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ESQLAHIKDEPPPLSPAPLTPATPSSLDPFFSR 33 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 ES(0.095)QLAHIKDEPPPLS(0.905)PAPLTPATPSSLDPFFSR;ES(0.005)QLAHIKDEPPPLS(0.995)PAPLTPATPSSLDPFFSR;ES(0.003)QLAHIKDEPPPLS(0.997)PAPLTPATPSSLDPFFSR;ESQLAHIKDEPPPLS(0.961)PAPLT(0.039)PATPSSLDPFFSR;ES(0.001)QLAHIKDEPPPLS(0.999)PAPLTPATPSSLDPFFSR 183.75 5.99E-20 4071480000 1503498 1573312 739781 958368 1902582 1615537 2323788 2495254 435027 TRUE FALSE 1304806.93 1562976.81 1097541.566 1175980.102 1864724.341 1677687.754 2098427.397 1961663.35 383598.6036 3.401490301 4.074511208 2.861171953 3.065652719 4.861134328 4.373550211 5.470372878 5.113843824 1 18.54923794 3.244327589 24.99511478 4.391021159 3.367440042 0.078221038 1.258583974 293.7819034 1273297.07 0.364451356 0.457474915 1755.203955 -3.244327589 -1.023581116 ESQQQHGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ESQQQHGLR 9 0 Q9UHB9;Q9UHB9-4;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;;; 202.2 2.02E-05 649408000 659194 581782 295550 384040 562137 642418 602927 653513 557265 FALSE TRUE 572079.8427 577960.2357 438478.9686 471242.1517 550951.5735 667132.2362 544455.2323 513764.3306 491385.7665 1.164217366 1.176184324 0.89233144 0.959006515 1.12122005 1.357654783 1.107999599 1.045541743 1 18.90649654 1.56418308 0.004666261 0.606448379 1.567405532 0.002865868 0.129839246 1353678.949 2146.726857 224459.8226 217664.0907 36.65920819 -1.56418308 0.960957153 ESQSHPGDFVLSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESQSHPGDFVLSVR 14 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 109.79 0.00074703 878110000 315290 309360 102020 218450 284770 325250 308790 325380 317970 FALSE TRUE 273623.6277 307327.7938 151357.2132 268052.4113 279103.6341 337762.578 278843.5933 255800.0191 280379.9488 0.97590298 1.096111883 0.539828949 0.956032742 0.99544791 1.204660245 0.994520452 0.912333497 1 18.09702365 3.485057066 24.82892269 1.011347375 0.868958772 0.161382154 0.156062792 669.9445585 2096070.046 0.045115913 0.061076676 3055.322553 -3.485057066 -0.142388604 ESRPSEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESRPSEER 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 120.31 0.0013928 263480000 195560 167680 111890 139030 134960 194090 173470 204480 238060 FALSE TRUE 169716.2505 166578.499 166000.3782 170598.8864 132274.56 201556.7679 156646.9061 160753.5433 209916.818 0.808492869 0.793545275 0.790791228 0.812697563 0.630128454 0.960174463 0.746233235 0.765796399 1 17.67945823 1.235101702 24.87539706 1.000000319 0.786842488 0.407077241 0.080203258 90.17588401 648404.5123 0.128399516 0.018089902 17.1831073 -1.235101702 -0.213157831 ESS(ph)KVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESSKVPR 7 1 E5RJ29;Q9NYI0-2;Q9NYI0 E5RJ29 PSD3 PH and SEC7 domain-containing protein 3 1 ES(0.196)S(0.804)KVPR 52.255 0.088909 57112000 135720 127880 97408 92960 132870 125450 143670 157640 141890 TRUE FALSE 117784.2581 127039.9479 144514.8346 114067.9888 130226.147 130276.1427 129736.9055 123929.9128 125115.9258 0.941401003 1.015377915 1.155047478 0.911698395 1.04084389 1.041243485 1.036933585 0.990520686 1 16.93290591 1.691675423 8.204297645 0.99557754 1.022725926 0.024342021 0.064488733 0.508390317 64.39706126 0.035566085 0.015962833 49.1671939 -1.691675423 0.027148386 ESS(ph)PIPS(ph)PTSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESSPIPSPTSDR 12 0 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 2 ESS(1)PIPS(0.993)PT(0.007)SDR;ES(0.133)S(0.867)PIPS(0.988)PT(0.011)S(0.001)DR 214.61 6.34E-11 396930000 477760 485410 420020 491370 623260 590000 547850 671440 971900 TRUE FALSE 414622.8055 482221.3097 623143.0769 602943.0686 610858.3454 612697.6818 494719.5913 527857.7812 857003.0892 0.483805497 0.562683281 0.727118822 0.703548302 0.712784298 0.714930541 0.577266987 0.615934514 1 19.70894088 4.385959772 3.586690204 0.70328259 0.496550992 0.351805154 0.11205154 0.266925828 6.461249066 0.02835839 0.092904684 24319.78728 -4.385959772 -0.206731598 ESS(ph)PIPSPTSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESSPIPSPTSDR 12 0 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 ES(0.043)S(0.956)PIPSPTSDR 89.189 0.010032 231610000 249120 219850 158190 214940 264770 239380 264350 295630 381640 TRUE FALSE 216198.1608 218405.7909 234691.2131 263745.4122 259501.595 248589.1035 238713.3777 232411.8251 336522.954 0.642446996 0.649007113 0.697400312 0.783736768 0.771125987 0.738698804 0.709352438 0.690626961 1 18.36034539 1.235964692 24.99987931 1.000000381 0.712097619 0.798317533 0.045753333 34.78107043 334886.7574 0.082411542 0.012390668 17.21728593 -1.235964692 -0.287902762 ESS(ph)PLS(ph)SRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESSPLSSRK 9 1 A0A0A0MS66;Q14693-6;Q14693;Q14693-2;Q14693-4;Q14693-3;Q14693-5;Q14693-7 A0A0A0MS66 LPIN1 Phosphatidate phosphatase LPIN1 2 ESS(1)PLS(0.622)S(0.378)RK 94.409 0.0058424 195640000 159130 142900 95001 108190 137590 153470 128500 147540 168690 TRUE FALSE 138100.5673 141961.2805 140943.8014 132756.1931 134852.2282 159374.0902 116038.0898 115989.7192 148747.6604 0.928421778 0.954376561 0.947536257 0.892492647 0.906583861 1.071439307 0.780100268 0.779775083 1 17.18250745 2.212137103 24.99975469 0.834926166 0.945615578 0.246588686 0.077352125 265.8725466 251544.8008 0.031077595 0.020959506 162.981047 -2.212137103 0.110689412 ESSANNSVS(ph)PSESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ESSANNSVSPSESLR 15 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 ESSANNSVS(1)PSESLR;ESSANNS(0.001)VS(0.994)PS(0.006)ESLR;ESSANNS(0.003)VS(0.997)PSESLR;ESSANNS(0.298)VS(0.702)PSESLR;ESSANNS(0.02)VS(0.969)PS(0.011)ESLR;ESSANNS(0.053)VS(0.947)PSESLR;ESSANNS(0.095)VS(0.905)PSESLR 431.41 1.73E-153 5276290000 4912299 3164327 2040635 2401059 3108321 3208421 3116804 3756447 3591603 TRUE FALSE 4263126.241 3143540.328 3027492.912 2946256.144 3046471.493 3331851.032 2814536.828 2953160.042 3167007.785 1.346105387 0.992590022 0.955947417 0.930296464 0.961940008 1.052050155 0.888705371 0.932476407 1 21.59468898 4.742386949 3.769095513 0.956772272 1.387889994 0.885223616 0.043348407 0.082569123 2.252897767 0.010817114 0.099735886 55256.95503 -4.742386949 0.431117722 ESSGFPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESSGFPSR 8 0 J3KPH2;Q9BYJ1;Q9BYJ1-2 J3KPH2 ALOXE3 Hydroperoxide isomerase ALOXE3 0 79.454 0.065131 525380000 256900 318950 309770 386180 503650 509580 536990 544650 649140 FALSE TRUE 222950.0141 316854.7964 459575.8081 473868.0714 493628.3504 529183.8723 484912.7925 428180.836 572399.4087 0.389500776 0.553555422 0.802893576 0.827862615 0.862384452 0.924501081 0.847158095 0.74804556 1 19.12666266 4.389500171 1.817694661 0.858273676 0.361448163 0.867751879 0.065022215 0.16018619 0.86974022 0.018224496 0.108456145 24518.85421 -4.389500171 -0.496825513 ESSIIAPAPAEDVDT(ph)PPR ddPTM_MDA-MB-175_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 298 2.34E-48 836410000 582030 508360 352030 476560 525630 489200 482310 602940 738170 TRUE FALSE 505113.2608 505020.5497 522272.8855 584770.2318 515170.9914 508019.8406 435535.6504 474005.9731 650904.3835 0.776017605 0.775875171 0.802380348 0.898396518 0.791469537 0.780483053 0.669123855 0.728226734 1 19.3120861 3.004396584 24.99255753 0.773872554 0.814133147 0 0.090913917 501.6268747 2851475.406 0.028049038 0.031678413 1010.174924 -3.004396584 0.040260593 ESSPLS(ph)S(ph)RK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESSPLSSRK 9 1 A0A0A0MS66;Q14693-6;Q14693;Q14693-2;Q14693-4;Q14693-3;Q14693-5;Q14693-7 A0A0A0MS66 LPIN1 Phosphatidate phosphatase LPIN1 2 ES(0.001)S(0.262)PLS(0.892)S(0.846)RK 66.962 0.041603 9099300000 1708500 1748100 1211100 1396300 1600900 1889100 1691700 1785900 2113600 TRUE FALSE 1482717.396 1736616.616 1796792.011 1713351.256 1569045.222 1961774.899 1527639.194 1403999.183 1863732.616 0.795563368 0.931794937 0.964082506 0.91931173 0.841883223 1.052605338 0.819666502 0.753326508 1 20.82976346 ESSPS(ph)HGLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESSPSHGLLK 10 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 1 ES(0.212)S(0.375)PS(0.413)HGLLK 154.15 9.66E-06 278920000 621930 514500 326160 466120 502050 436280 563870 680670 799010 TRUE FALSE 539740.3747 511120.2156 483892.0669 571959.6702 492060.1872 453063.9739 509185.9742 535114.0175 704551.948 0.766076052 0.725454265 0.686808217 0.811806243 0.698401571 0.643052617 0.722708915 0.75950967 1 19.42634656 1.211730836 2.977907978 1.06586521 0.721023525 0.788055802 0.044912885 0.20155169 2.108271112 0.174185195 0.011774669 16.28286553 -1.211730836 -0.344841685 ESSPSHPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESSPSHPTR 9 0 Q13144;A0A3B3IUB1;A0A3B3ITG6;A0A3B3IRP4;A0A3B3ISX3;A0A3B3ISM8;A0A3B3IUF2;A0A3B3ITQ2;A0A3B3ISV1;A0A3B3IS56;A0A3B3ISS1;A0A3B3ISI2;A0A3B3IST9;A0A3B3ITK8 Q13144 EIF2B5 Translation initiation factor eIF-2B subunit epsilon 0 67.993 0.05933 35719000 20097 19143 13676 12970 12503 15560 16489 19170 13269 FALSE TRUE 17441.13053 19017.24837 20289.75934 15915.03673 12254.21476 16158.60327 14889.89932 15070.64468 11700.35394 1.490649824 1.625356675 1.734115007 1.360218402 1.0473371 1.381035425 1.27260247 1.288050324 1 13.51426455 3.54218778 5.072744475 1.221729818 1.61304838 0.695184106 0.125882042 0.122210493 6.178135253 0.034563637 0.051052802 3484.879612 -3.54218778 0.391318562 ESSSCGKDT(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ESSSCGKDTPSK 12 1 O43148;O43148-2;K7EPP5 O43148 RNMT mRNA cap guanine-N7 methyltransferase 1 ESS(0.001)S(0.006)CGKDT(0.992)PS(0.002)K;ES(0.001)S(0.004)S(0.075)CGKDT(0.919)PS(0.001)K;ESS(0.001)S(0.001)CGKDT(0.995)PS(0.003)K 91.657 0.013216 522920000 1424700 790379 696129 728017 523756 560024 1004180 1273450 1246590 TRUE FALSE 1236422.285 785186.9483 1032779.313 893324.3869 513334.2803 581568.4857 906794.7782 1001132.627 1099219.55 1.124818318 0.714313122 0.9395569 0.812689682 0.466998863 0.529074001 0.824944187 0.910766759 1 20.06804814 ESSTSEGADQKMS(ph)S(ph)PEDDSDTKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ESSTSEGADQKMSSPEDDSDTKR 23 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 2 ESST(0.001)S(0.004)EGADQKMS(0.995)S(1)PEDDSDTKR;ES(0.016)S(0.016)T(0.016)S(0.016)EGADQKMS(0.957)S(0.978)PEDDS(0.001)DTKR;ES(0.024)S(0.026)T(0.028)S(0.03)EGADQKMS(0.908)S(0.984)PEDDSDTKR 114.03 0.00038005 1013020000 1099320 696460 689660 630650 755480 548601 1119770 1217480 933110 TRUE FALSE 954042.0767 691884.9084 1023181.883 773848.7214 740447.4261 569706.0355 1011174.878 957131.3764 822798.7988 1.159508349 0.840891977 1.243538377 0.94050784 0.89991311 0.692400179 1.228945496 1.163262972 1 19.65018016 0.922862397 20.60122584 4.97E-05 1.025756797 0.000763609 0.180713876 2769.162538 1012706.479 48511.81257 0.043463793 8.372639594 -0.922862397 1.025707056 ESSTVFELKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ESSTVFELKR 10 1 B8ZZU8;Q15370;Q15370-2;I3L0M9;A0A0B4J296 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 ;;; 178.54 3.54E-06 1804250000 1668490 1448390 868310 1148480 1528400 1342490 1939520 2113970 750090 FALSE TRUE 1447994.819 1438875.431 1288227.62 1409259.937 1497987.83 1394136.459 1751425.649 1661913.966 661415.2147 2.18923724 2.175449549 1.947683681 2.130673601 2.264822152 2.107808269 2.647997219 2.512663648 1 19.33519671 3.461141141 20.67127186 2.198038046 2.099243308 0 0.4454992 240.6096929 311232.6238 0.127953069 0.165330521 2891.619478 -3.461141141 -0.098794738 ESSYACYYDEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESSYACYYDEKR 12 1 Q99538-3;Q99538-2;Q99538 Q99538-3 LGMN Legumain 0 129.54 0.00037273 338100000 103720 96768 64208 79471 89221 95560 92115 125480 56519 FALSE TRUE 90013.13921 96132.32464 95259.20356 97516.10519 87445.67666 99236.25504 83181.70148 98647.07849 49837.38821 1.806136767 1.928919795 1.911400396 1.956685707 1.754619971 1.991200956 1.669062214 1.979378977 1 15.60494084 1.234406949 24.99964929 0.999998722 1.875240746 0.875226916 0.103788384 36.63503974 220464.7415 0.170692795 0.022700477 17.15564097 -1.234406949 0.875242024 ESSYDIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESSYDIYR 8 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 0 ; 110.12 0.0081123 384240000 541600 609540 385970 437940 596860 616180 538290 654080 696610 FALSE TRUE 470026.1878 605535.8916 572626.383 537380.9705 584983.6537 639884.8433 486086.7187 514210.0821 614257.5594 0.765193982 0.985801285 0.932225211 0.874846328 0.95234262 1.041720747 0.791340231 0.837124548 1 19.22848418 2.211273261 24.99982908 0.864489737 0.927345879 0.058735996 0.088606193 521.7748032 478030.2833 0.035231791 0.023759645 162.6571884 -2.211273261 0.062856141 ESSYDIYRVPS(ph)SQS(ph)MEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ESSYDIYRVPSSQSMEDR 18 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 ESSYDIYRVPS(0.97)S(0.036)QS(0.994)MEDR;ESSYDIYRVPS(0.666)S(0.334)QS(1)MEDR;ESSYDIYRVPS(0.711)S(0.289)QS(1)MEDR 122.34 2.07E-05 809700000 1244850 1332480 636430 641820 1277650 1316770 1301230 1398330 373040 TRUE FALSE 1080339.918 1323726.851 944209.6767 787555.0406 1252227.265 1367426.994 1175036.915 1099308.011 328939.6362 3.284310553 4.024224221 2.870464891 2.394223602 3.806860369 4.157075778 3.572196189 3.341974911 1 18.32746333 4.23085747 24.99200722 3.1249921 3.654267423 0.07109701 0.892272322 511.0185699 1657961.721 0.230981802 0.495602501 17015.99972 -4.23085747 0.529275324 LLREELQLLQEQGSYVGEVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLREELQLLQEQGSYVGEVVR 21 1 P62195-2;P62195;J3QSA9;J3KRP2;J3QQM1;J3QLH6;J3QSE0 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ; 168.78 9.45E-12 146413000 111784 100775 54110 65109 99566 102371 93675 112619 36118 FALSE TRUE 97011.46118 100113.0024 80277.77699 79892.99358 97584.8314 106309.2786 84590.41292 88536.30325 31848.17119 3.046060655 3.143445877 2.520640087 2.508558282 3.064063893 3.338002612 2.656052444 2.779949365 1 14.95892291 1.216685316 3.819470402 0.714969951 2.889276629 0.826143971 0.271524976 0.126996552 2.924106189 0.810242249 0.072489138 16.46968587 -1.216685316 2.174306678 ESSYGPEIDSHDFVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ESSYGPEIDSHDFVLR 16 0 E5RGL4;E5RHV6;Q11201 E5RGL4 ST3GAL1 "CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase 1" 0 ;; 266.42 3.43E-27 559596000 441079 475069 314213 335510 488098 548191 350532 539214 518590 FALSE TRUE 382789.2926 471948.2405 466167.4578 411692.6734 478385.8047 569280.2625 316537.4606 423907.2823 457282.881 0.837095174 1.032070651 1.019429061 0.900301959 1.04614851 1.244919253 0.692213669 0.927013234 1 18.80272739 2.225080636 24.99997193 0.876776836 1.010811139 0.206636853 0.129418548 387.8441021 719289.8643 0.052039017 0.035302456 167.9115751 -2.225080636 0.134034303 ESTAEKDEL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESTAEKDEL 9 1 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ; 107.57 0.0049449 0 581590 418100 391100 493400 472890 455640 506370 529960 509890 FALSE TRUE 504731.4079 415353.4736 580237.2682 605434.0111 463480.4142 473168.7656 457262.3153 416632.1782 449611.3851 1.122594811 0.923805507 1.290530639 1.346571798 1.030846704 1.052394982 1.017016763 0.926649529 1 18.77831904 3.023065293 24.97312418 0.995198537 1.165141492 0.344165162 0.114096529 282.3138682 305663.0691 0.036964176 0.041911029 1054.545428 -3.023065293 0.169942955 ESTLHLVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ESTLHLVLR 9 0 M0R2S1;P62987;P0CG48;Q96C32;Q5PY61;J3QKN0;F5GXK7;F5H747;F5H388;B4DV12;F5H265;F5H2Z3;F5GYU3;F5H6Q2;M0R1M6;J3QTR3;J3QS39;P0CG47;P62979;A0A2R8Y422 M0R2S1;P62979 UBA52;UBC;UBB;RPS27A Ubiquitin-60S ribosomal protein L40;Ubiquitin;60S ribosomal protein L40;Polyubiquitin-C;Ubiquitin;Polyubiquitin-B;Ubiquitin;Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ;; 179.37 4.99E-05 2136530000 2030420 2119240 951800 1462550 1877820 1995990 1573190 2060800 3466460 FALSE TRUE 1762094.853 2105318.573 1412093.664 1794644.331 1840455.056 2072777.027 1420622.276 1620113.957 3056659.048 0.576477397 0.688764609 0.461972906 0.587126108 0.602113297 0.678118493 0.464763081 0.530027698 1 21.54352421 1.235214339 24.99999981 1.000000595 0.571199119 0.758427277 0.075604766 46.81592236 349703.276 0.129870209 0.018448674 17.18756444 -1.235214339 -0.428801476 ESTQLS(ph)PADLTEGKPTDPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ESTQLSPADLTEGKPTDPSK 20 1 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 ES(0.002)T(0.012)QLS(0.975)PADLT(0.011)EGKPTDPSK;ES(0.034)T(0.034)QLS(0.93)PADLT(0.001)EGKPTDPSK;EST(0.001)QLS(0.99)PADLT(0.009)EGKPTDPSK;ESTQLS(0.999)PADLTEGKPTDPSK 161.2 1.39E-11 966840000 2245084 1272275 1490556 1793277 1251630 943870 1744029 2186097 4348680 TRUE FALSE 1948390.461 1263917.342 2211393.867 2200467.951 1226725.012 980181.2897 1574893.336 1718617.169 3834584.004 0.508109995 0.329610028 0.576697202 0.573847893 0.319910846 0.255616069 0.410707741 0.448188687 1 21.87063864 1.237205994 5.437999378 1.02965396 0.423163232 0.742349808 0.106013214 0.082752987 7.406770142 0.188442243 0.027667901 17.26656684 -1.237205994 -0.606490728 ESTQLS(ph)PADLTEGKPTDPSKLESPSFTGTGDTEIAHATEDLENNGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESTQLSPADLTEGKPTDPSKLESPSFTGTGDTEIAHATEDLENNGSK 47 2 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 ES(0.001)T(0.005)QLS(0.72)PADLT(0.274)EGKPTDPSKLESPSFTGTGDTEIAHATEDLENNGSK;ES(0.013)T(0.013)QLS(0.948)PADLT(0.016)EGKPT(0.002)DPS(0.002)KLES(0.002)PS(0.002)FT(0.002)GT(0.002)GDTEIAHATEDLENNGSK 218.5 5.34E-50 281237000 310570 182487 167279 180414 151711 115582 285610 332510 224652 TRUE FALSE 269527.3876 181288.2309 248175.6839 221379.7562 148692.2479 120028.5143 257911.5862 261405.3241 198093.8965 1.3606042 0.915163133 1.252818428 1.117549607 0.750614989 0.605917277 1.301966344 1.319603121 1 17.5958249 0.95974068 18.24835287 0.558744474 1.081374437 0.009137599 0.253239493 17622275.63 204157272.6 318433928.8 0.065648106 9.114664344 -0.95974068 0.522629963 ESTSS(ph)KSPPRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESTSSKSPPRK 11 2 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 ES(0.013)T(0.011)S(0.076)S(0.564)KS(0.335)PPRK 54.524 0.068416 3233000000 514440 351690 282010 328820 314200 260950 445810 567120 379930 TRUE FALSE 446455.4506 349379.7252 418390.9793 403483.6067 307948.0347 270988.9154 402575.4148 445845.8013 335015.1082 1.332642736 1.04287752 1.248871973 1.20437436 0.919206409 0.808885655 1.201663462 1.33082297 1 18.35386663 4.750676456 23.19477459 1.111906192 1.332643116 0.172874716 0.159698859 1494.333715 2860629.898 0.042576333 0.647653358 56321.79087 -4.750676456 0.220736924 ESTSSKS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ESTSSKSPPR 10 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 ESTSSKS(1)PPR;ESTS(0.006)S(0.032)KS(0.962)PPR;EST(0.001)S(0.01)S(0.08)KS(0.909)PPR;ESTSS(0.005)KS(0.994)PPR;ESTSS(0.001)KS(0.998)PPR 116.82 0.00062969 9585604000 5709270 4315140 2680877 3231725 3536628 3431053 4639930 5638190 4110570 TRUE FALSE 4954775.504 4286793.561 3977358.084 3965537.555 3466256.022 3563047.829 4189950.303 4432506.945 3624623.097 1.366976751 1.182686709 1.097316322 1.094055147 0.956307988 0.983011953 1.155968549 1.222887684 1 21.78939956 4.709331128 1.789067268 1.082498541 1.451029255 0.579928319 0.080229474 0.720031671 2.450209173 0.024702134 0.441010807 51207.21163 -4.709331128 0.368530714 ESTSSKS(ph)PPRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ESTSSKSPPRK 11 2 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 ES(0.01)T(0.342)S(0.043)S(0.043)KS(0.562)PPRK;ESTS(0.019)S(0.127)KS(0.855)PPRK;ES(0.016)T(0.016)S(0.012)S(0.045)KS(0.911)PPRK;ES(0.001)T(0.001)S(0.001)S(0.007)KS(0.989)PPRK;ES(0.002)T(0.002)S(0.012)S(0.205)KS(0.779)PPRK 83.877 0.0085468 6058960000 4301230 2688800 2216870 2416250 2325520 1972300 3833690 4375190 2987890 TRUE FALSE 3732811.558 2671137.096 3288955.747 2964896.493 2279246.702 2048175.657 3461899.334 3439589.666 2634665.048 1.416806877 1.013843144 1.248339234 1.125340959 0.865099229 0.777395084 1.313980818 1.305513074 1 21.32918813 4.748631106 24.04957616 1.099983222 1.416807171 0.252959856 0.178680467 1424.237549 3401136.838 0.047678103 0.613618508 56057.16191 -4.748631106 0.316823949 ESVASMGADS(ph)GDDFASDGSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESVASMGADSGDDFASDGSSSR 22 0 Q92805;Q5T165 Q92805 GOLGA1 Golgin subfamily A member 1 1 ESVASMGADS(1)GDDFASDGSSSR;ESVASMGADS(1)GDDFASDGSSSR 318.69 2.74E-66 0 364670 343650 239180 311560 341580 335350 304590 388130 438500 TRUE FALSE 316477.9355 341392.5405 354848.248 382304.4599 334783.2263 348251.1315 275050.9087 305131.4199 386661.0295 0.818489352 0.882924615 0.917724366 0.988732845 0.865831311 0.900662609 0.711348928 0.789144487 1 18.56070984 ESVDHLTIPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESVDHLTIPSR 11 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 130.1 0.00023125 486860000 460290 401870 208810 286990 383200 375390 404600 501120 481450 FALSE TRUE 399461.5103 399230.0895 309791.2144 352155.4659 375575.0697 389831.4962 365361.9543 393959.3877 424533.5295 0.940942193 0.940397075 0.729721431 0.82951155 0.884677048 0.918258439 0.860619784 0.927981797 1 18.69551898 0.24564427 0.846045395 1.599192675 0.864735701 0.311863519 0.061620554 14.33340264 2.225265097 14.62358697 0.023662375 1.760533405 -0.24564427 -0.734456975 ESVFTVEGGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ESVFTVEGGHR 11 0 Q99623-2;Q99623;F5GY37;J3KPX7;F5H0C5;F5H3X6;F5H2D2;F5GWA7 Q99623-2 PHB2 Prohibitin-2 0 ;;;;; 199.09 5.14E-08 1746810000 1335830 1169300 866278 1583880 1532260 1939610 1050790 1494370 1572730 FALSE TRUE 1159296.681 1161618.791 1285212.938 1943524.162 1501771.024 2014228.052 948884.5475 1174810.605 1386803.651 0.83594868 0.837623113 0.926744703 1.401441481 1.082900974 1.452424826 0.684224149 0.8471355 1 20.40333211 2.192502582 24.99995766 0.837835999 1.084546724 0.217554588 0.2194474 202.5437024 109937.7324 0.093655645 0.06314287 155.7767297 -2.192502582 0.246710725 PIS(ph)PGLSYASHTVGFT(ph)PPTSLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 PISPGLSYASHTVGFTPPTSLTR 23 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 PIS(0.999)PGLS(0.001)YASHTVGFT(1)PPTSLTR;PIS(1)PGLSYASHTVGFT(0.972)PPT(0.021)S(0.005)LT(0.001)R 171.4 1.10E-11 327140000 129815 138661 156863 202840 199025 215387 249660 287420 622130 TRUE FALSE 112659.6188 137750.1268 232722.4715 248897.9222 195064.7919 223673.0773 225448.0116 225957.4697 548582.5001 0.205364952 0.251101934 0.42422511 0.453711014 0.355579684 0.407729151 0.410964644 0.411893324 1 19.06534908 1.217533639 3.679282885 1.10190436 0.364920896 0.86855273 0.077797411 0.115386853 2.353329798 0.243096045 0.021244089 16.50188813 -1.217533639 -0.736983464 ESVPSAS(ph)PTGIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESVPSASPTGIPK 13 0 Q5THJ4-2;Q5THJ4;H3BLS7;A0A2R8YD87 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 ESVPS(0.008)AS(0.969)PT(0.023)GIPK;ESVPSAS(0.975)PT(0.025)GIPK 160.07 4.67E-05 547700000 554730 478360 413130 506180 542540 459160 575190 672920 903880 TRUE FALSE 481421.025 475217.6217 612921.0498 621115.9055 531744.5155 476824.1823 519408.1623 529021.2947 797024.3361 0.604022993 0.596239789 0.769011713 0.779293526 0.667162207 0.598255487 0.651684194 0.663745473 1 19.60426425 1.238130457 24.9848594 1.000000377 0.667854771 0.728128599 0.064098398 5.946906575 345005.2338 0.096126423 0.016816592 17.30336056 -1.238130457 -0.332145606 ESVQVPDDQDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ESVQVPDDQDFR 12 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5H1Z6;F5GWK5;F5H3G8;F5H5A8 Q9Y365 STARD10 PCTP-like protein 0 ;;;; 274.53 1.97E-27 4494840000 5909760 4767420 3030700 3747475 4856310 4783360 4859860 5547520 5238420 FALSE TRUE 5128770.243 4736102.504 4496356.657 4598396.475 4759678.932 4967378.954 4388551.525 4361226.019 4619139.955 1.110330125 1.025321283 0.97341858 0.995509233 1.030425356 1.075390441 0.950079791 0.944164078 1 22.13919283 4.680102041 2.837711413 0.992717473 1.123788171 0.472234434 0.037937127 0.347141475 4.198510503 0.010774767 0.097962838 47874.25641 -4.680102041 0.131070698 ESVSTEDLSPPS(ph)PPLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESVSTEDLSPPSPPLPK 17 0 Q13127-4;Q13127 Q13127-4 REST RE1-silencing transcription factor 1 ESVSTEDLSPPS(1)PPLPK 189.37 3.76E-10 193340000 264710 208820 136580 179520 216840 148160 222980 302200 243810 TRUE FALSE 229727.9028 207448.2477 202630.5448 220282.7598 212525.3082 153859.8111 201355.4339 237576.8817 214987.0595 1.068566189 0.964933648 0.942524379 1.024632647 0.988549305 0.715670103 0.936593274 1.105075265 1 17.7138903 1.752425359 25 1.055146616 0.944642957 0.168247303 0.095525839 7.189348329 12986.55265 0.052445706 0.025184819 56.54905588 -1.752425359 -0.110503659 S(ph)PPHHSGFQQYQQADASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPPHHSGFQQYQQADASK 18 0 E9PD50;B1ALB4;Q92540-2;Q92540;Q92540-5;Q92540-4 E9PD50 SMG7 Protein SMG7 1 S(0.495)PPHHS(0.495)GFQQY(0.01)QQADASK 142.39 1.89E-07 325690000 242540 261140 115730 285970 358390 359820 359370 430560 942620 TRUE FALSE 210487.7245 259424.5541 171697.4151 350903.8593 351258.7402 373662.5082 324518.3527 338488.0946 831184.5374 0.253238258 0.312114269 0.206569549 0.422173228 0.422600186 0.44955421 0.390428765 0.407235793 1 19.66480929 1.218237868 3.636437605 1.104966558 0.355581808 0.871957609 0.077533646 0.116314599 2.286937326 0.247002002 0.021505606 16.52866846 -1.218237868 -0.74938475 ESYDYLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESYDYLK 7 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 77.058 0.090912 374230000 803690 725160 472790 526870 710840 542600 812450 998210 831480 FALSE TRUE 697480.3302 720396.3762 701432.8254 646503.8862 696695.6747 563474.1731 733658.724 784750.5596 733183.3816 0.951304063 0.982559608 0.956694932 0.881776514 0.95023386 0.768531021 1.000648327 1.070333261 1 19.48381456 2.013596633 24.99989087 1.03878058 0.917239336 0.416986145 0.061412816 199.9526349 367647.8518 0.025024347 0.016862428 103.1802637 -2.013596633 -0.121541244 ESYELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ESYELR 6 0 P35268;K7ERI7;K7EMH1 P35268 RPL22 60S ribosomal protein L22 0 ;; 110.23 0.067187 3281040000 7311440 7149210 4845510 5423170 7035440 7501510 7288260 7700800 7485430 FALSE TRUE 6345214.679 7102246.369 7188814.843 6654583.636 6895448.509 7790097.944 6581445.667 6054043.848 6600510.993 0.961321735 1.076014626 1.089130046 1.008192191 1.044684043 1.180226493 0.997111538 0.917208358 1 22.65414629 2.006961368 24.99249373 0.954031309 1.061419435 0.343615287 0.059346279 159.1285221 571296.1229 0.023653309 0.015908358 101.6158297 -2.006961368 0.107388126 ESYPHIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ESYPHIK 7 0 O60664-4;O60664;O60664-3;K7ER39;K7EL96 O60664-4 PLIN3 Perilipin-3 0 96.964 0.012345 215970000 536540 486470 281850 377070 477370 445770 530390 582460 462620 FALSE TRUE 465634.8796 483274.3465 418153.6027 462689.5067 467871.271 462919.0604 478952.8594 457905.4617 407929.5906 1.141458944 1.184700394 1.025063178 1.134238646 1.146941241 1.134801375 1.174106685 1.122511022 1 18.63796064 1.244412241 5.186915352 0.99287222 1.133861414 0.492956012 0.042533926 0.134712783 9.890286117 0.067647585 0.010464546 17.55546112 -1.244412241 0.140989194 ESYPVFYLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESYPVFYLFR 10 0 P30040;F8VY02 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 ; 132.76 0.00050056 1222470000 456210 481090 338520 363050 458770 540000 446540 499300 392360 FALSE TRUE 395920.6926 477929.6881 502229.4043 445486.0514 449641.3746 560774.1494 403234.6195 392528.5806 345975.6478 1.144360001 1.381396902 1.451632239 1.287622566 1.299633016 1.620848615 1.165500006 1.134555519 1 18.40031097 2.019110583 24.92297195 1.098830468 1.36512978 0.501482258 0.126147906 181.3730383 236535.8125 0.050260802 0.03388021 104.4986266 -2.019110583 0.266299312 ESYSIYVYK ddPTM_MDA-MB-175_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 ; 200.16 5.48E-05 1822110000 2334700 1949930 1143640 1670420 1764300 1560280 1695550 2404400 2038600 FALSE TRUE 2026163.48 1937120.781 1696708.129 2049714.392 1729193.882 1620304.981 1531115.822 1890237.771 1797599.03 1.127149851 1.077615613 0.943874635 1.140251167 0.961946381 0.901371749 0.851756035 1.051534708 1 20.77763982 3.135071968 9.198495424 0.954779831 1.06328753 0.386747429 0.074051658 0.338672914 27.43664481 0.023251385 0.026393391 1364.809284 -3.135071968 0.108507699 ESYSVYVYK ddPTM_MDA-MB-175_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 ;;;;;;; 205.7 3.38E-05 13080900000 11121000 8902750 5625575 7785280 8226890 7314850 8604710 11225900 9786980 FALSE TRUE 9651331.673 8844267.249 8346121.886 9553046.815 8063190.985 7596257.013 7770226.549 8825328.645 8629974.374 1.118349981 1.02483123 0.967108536 1.106961203 0.934323862 0.880217795 0.900376549 1.022636715 1 23.04092484 3.22074757 24.99972959 0.95000194 1.045978052 0.446989212 0.05866872 265.2735825 372297.4168 0.018939641 0.021519871 1662.446085 -3.22074757 0.095976112 ESYTEEIVS(ph)EAESHVSGISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ESYTEEIVSEAESHVSGISR 20 0 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 ESYTEEIVS(1)EAESHVSGISR;ESYTEEIVS(1)EAESHVSGISR;ESYTEEIVS(1)EAESHVSGISR;ESYTEEIVS(1)EAESHVSGISR 366.6 3.40E-112 542880000 677310 726480 291043 455362 849490 839940 756520 828570 830300 TRUE FALSE 587801.7674 721707.705 431792.3683 558758.9019 832586.811 872253.0353 683152.8068 651386.7534 732142.8799 0.80285117 0.985747079 0.589765168 0.763182867 1.137191707 1.191369962 0.933086732 0.889698953 1 19.4817657 3.255153734 24.99945067 1.013464477 0.785725005 0.470925751 0.128291838 254.3137804 383150.9026 0.040125666 0.051656973 1799.507802 -3.255153734 -0.227739472 ET(ph)ERASPIKMDLAPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETERASPIKMDLAPSK 16 2 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 ET(0.627)ERAS(0.373)PIKMDLAPSK;ET(0.679)ERAS(0.321)PIKMDLAPSK 112.37 0.00099921 923990000 990570 818410 532490 586670 775870 493080 932970 1187270 485140 TRUE FALSE 859663.6647 813033.8108 790003.9451 719882.3902 760431.705 512049.1067 842490.713 933381.5498 427787.3019 2.009558631 1.900556205 1.846721353 1.682804485 1.777592981 1.196971262 1.969414962 2.181882318 1 18.70653413 4.121652679 1.627751104 1.698906583 1.992991406 0.121695243 0.342764136 1.200971108 5.866388692 0.103389902 0.387189287 13232.82834 -4.121652679 0.294084823 ET(ph)RHSWDSPAFNNDVVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETRHSWDSPAFNNDVVQR 18 1 A0A1W2PR28;Q5JU85-3;Q5JU85;A0A1W2PRJ5 A0A1W2PR28 IQSEC2 IQ motif and SEC7 domain-containing protein 2 1 ET(0.369)RHS(0.369)WDS(0.261)PAFNNDVVQR 82.482 0.0076446 95794000 118130 136470 86230 98008 190670 205640 128660 131350 117060 TRUE FALSE 102518.8212 135573.5196 127931.1164 120262.2144 186876.04 213551.1039 116182.573 103261.8247 103221.3002 0.993194438 1.313425808 1.239386795 1.165091063 1.810440672 2.068866635 1.125567812 1.000392598 1 16.65538118 2.018652005 24.99880016 1.019050789 1.437249803 0.266025162 0.309956987 325.9957325 436921.9177 0.136785258 0.092204855 104.3883434 -2.018652005 0.418199015 ETAAVIFLHGLGDTGHSWADALSTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETAAVIFLHGLGDTGHSWADALSTIR 26 0 O95372;Q5QPQ3;Q5QPQ2;Q5QPN5;Q5QPN9 O95372 LYPLA2 Acyl-protein thioesterase 2 0 ; 257.2 6.80E-53 981300000 526730 414890 208553 348010 407010 479310 463620 471570 461400 FALSE TRUE 457121.2959 412164.5603 309409.9284 427030.9895 398911.2973 497749.3659 418658.2038 370728.4253 406853.8176 1.123551694 1.013053196 0.760494101 1.049593173 0.980478196 1.223410828 1.029013827 0.911207931 1 18.634151 ETAENYLGHTAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETAENYLGHTAK 12 0 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ; 158.58 7.31E-05 660770000 434210 425050 354930 663400 482200 466650 430370 541630 870020 FALSE TRUE 376828.0484 422257.8186 526575.3352 814035.1094 472605.1634 484602.3275 388632.7836 425806.6395 767167.2267 0.491194143 0.550411701 0.686389247 1.061092134 0.616039303 0.631677567 0.506581577 0.555037578 1 19.54918156 4.291036652 4.21771499 0.701409545 0.509056753 0.174678123 0.179709368 0.419266159 15.14681576 0.047864134 0.133807377 19545.04399 -4.291036652 -0.192352792 ETAIELGYLTAEQFDEWVKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETAIELGYLTAEQFDEWVKPK 21 1 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 ; 246.31 2.51E-30 545600000 804340 631840 520810 671570 587270 432780 791900 957900 794620 FALSE TRUE 698044.4311 627689.4014 772675.458 824060.2328 575584.476 449429.3266 715101.6599 753060.5394 700680.9288 0.996237235 0.895827724 1.102749377 1.176084861 0.821464453 0.641417952 1.020581024 1.074755296 1 19.4183981 5.116112928 18.01312118 0.972064223 3.98099422 0.002573058 0.152825981 3558.640116 557728.7999 0.038733815 4517.071213 130651.0572 -5.116112928 3.008929998 ETAIQTEDSAISES(ph)PEEPLPNLKPKPNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETAIQTEDSAISESPEEPLPNLKPKPNLR 29 2 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 ETAIQTEDSAISES(1)PEEPLPNLKPKPNLR;ETAIQTEDSAISES(1)PEEPLPNLKPKPNLR 206.41 1.01E-25 350000000 369680 292760 201315 270300 259230 225030 378380 416660 242240 TRUE FALSE 320825.8514 290836.8403 298671.6074 331675.7463 254071.8302 233687.0497 341684.7658 327560.5015 213602.6632 1.50197496 1.361578718 1.398257882 1.552769714 1.18946003 1.094026855 1.599627836 1.533503827 1 17.70457011 3.247815752 24.99971988 1.328854182 1.443112849 0.142807872 0.189170338 597.5442677 1614060.589 0.05840567 0.0743635 1769.358154 -3.247815752 0.114258667 ETCAWFTDNYEQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ETCAWFTDNYEQAR 14 0 Q13630 Q13630 TSTA3 GDP-L-fucose synthase 0 ;;;;; 332.69 4.11E-68 4097430000 1908457 2087989 1197285 1440871 1893739 1885916 1716452 2111080 1995282 FALSE TRUE 1656249.572 2074272.863 1776296.031 1768042.783 1856057.299 1958468.409 1549990.749 1659641.97 1759402.035 0.941370727 1.178964683 1.009602124 1.004911184 1.054936428 1.113144335 0.880975876 0.943298881 1 20.74665376 2.23787874 24.9999989 0.939296619 1.05260013 0.35454247 0.069311183 18.32132735 671673.277 0.025750932 0.018544891 172.9333443 -2.23787874 0.113303511 ETCSTLAES(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ETCSTLAESPR 11 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 ETCSTLAES(1)PR;ETCSTLAES(1)PR;ETCSTLAES(1)PR;ETCSTLAES(1)PR 222.55 7.97E-12 2651980000 1286830 1250830 860664 969010 1180430 1375010 1257140 1371640 1350210 TRUE FALSE 1116772.155 1242613.215 1276883.989 1189038.531 1156941.752 1427907.524 1135222.756 1078325.46 1190589.712 0.937999165 1.043695576 1.072480281 0.998697132 0.971738409 1.199327955 0.953496192 0.90570702 1 20.1832449 2.033421331 24.99999767 0.941162898 1.037968805 0.225191434 0.072955234 226.8473121 169686.619 0.028755031 0.019386508 107.9993972 -2.033421331 0.096805907 TS(ph)PAPWKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSPAPWKR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.199)S(0.801)PAPWKR 70.1 0.031976 406810000 642560 502430 311180 327940 452630 524670 518750 508090 235790 TRUE FALSE 557644.068 499129.5042 461667.6888 402403.7892 443623.5486 544854.3944 468441.7048 399438.9075 207915.1748 2.682074882 2.400640091 2.22046173 1.935422894 2.133675663 2.620560981 2.253042402 1.921162839 1 17.66563553 1.219208116 1.951751784 0.517241459 2.310742994 0.786272226 0.217954935 0.411790308 1.450639532 1.382203648 0.06314433 16.56563606 -1.219208116 1.793501535 ETDEFFKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETDEFFKK 8 1 O14745;O14745-2;J3QRA3 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 90.657 0.020911 664310000 1767700 1335100 1120100 1397000 1228200 1050300 1693200 2188800 1328400 FALSE TRUE 1534093.966 1326329.64 1661784.107 1714210.202 1203761.223 1090705.721 1528993.725 1720742.153 1171358.065 1.309671237 1.132300771 1.418681576 1.463438254 1.027662897 0.931146293 1.30531711 1.469014646 1 20.15975072 3.243755697 24.99981988 1.188054076 1.323089808 0.189604965 0.178012738 324.73169 1562668.695 0.058062784 0.072683547 1752.894173 -3.243755697 0.135035732 ETDLLLDDSLVSIFGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETDLLLDDSLVSIFGNR 17 0 P30044-2;P30044;P30044-3;P30044-4 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 ; 235.73 8.42E-20 93413000 113726 63260 54522.1 58599 59950 62500 67042 78396 95598 FALSE TRUE 98696.82096 62844.44089 80889.16993 71904.79858 58757.11229 64904.41544 60540.27716 61631.62548 84296.51335 1.17082922 0.745516492 0.959579071 0.85299849 0.697028975 0.769953737 0.718182458 0.731129 1 16.36318534 6.870270598 1.459356431 0.794052289 199.979687 0.516169678 0.106169452 650.7460963 3.307407573 0.0288955 432026.9253 7417722.772 -6.870270598 199.1856347 ETDLLLDDSLVSIFGNRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ETDLLLDDSLVSIFGNRR 18 1 P30044-2;P30044;P30044-3;P30044-4 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 ;;;; 243.99 6.48E-24 1186259000 1859190 947406 488763 630857 845096 891776 877902 998180 347203 FALSE TRUE 1613493.331 941182.4276 725130.4216 774102.7239 828280.243 926083.1998 792763.1992 784726.9748 306157.0569 5.270149078 3.07418172 2.368491613 2.528449717 2.705409607 3.024863151 2.589400379 2.563151681 1 18.22391241 4.741450242 2.475903282 2.460257512 5.913102369 0.739441593 0.533632314 0.274878876 2.089207243 0.134268568 2.017678332 55137.90262 -4.741450242 3.452844856 ETDLQELFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETDLQELFR 9 0 O75821;K7ENA8;K7ER90;K7EL20;K7EP16 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 ; 93.649 0.021534 66151000 68446 61021 59050 74992 62225 62855 63334 70006 191844 FALSE TRUE 59400.68768 60620.14903 87606.77751 92020.07978 60986.84424 65273.07252 57191.87843 55035.76169 169164.4209 0.351141732 0.358350466 0.517879452 0.543968284 0.360518151 0.385855797 0.338084558 0.325338871 1 17.36806664 1.234409702 24.99999283 1.00000088 0.397034956 0.866081379 0.074438248 47.20320401 284254.8628 0.151591234 0.020129389 17.15574972 -1.234409702 -0.602965924 ETDLQELFRPFGS(ph)ISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETDLQELFRPFGSISR 16 1 O75821;K7ENA8;K7EP16 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 1 ETDLQELFRPFGS(0.996)IS(0.004)R;ETDLQELFRPFGS(0.999)IS(0.001)R 154.84 1.92E-07 77105000 59870 47920 31403.3 39772 49199 44780 47682 54204 55569 TRUE FALSE 51958.02781 47605.21036 46590.04092 48802.84048 48220.03616 46502.71558 43057.80698 42612.89642 48999.69612 1.06037449 0.97154093 0.950823058 0.995982513 0.984088473 0.949040897 0.878736204 0.86965634 1 15.58048518 2.515134797 3.325170098 0.905153192 0.988944575 0.369965535 0.044751037 0.236070455 5.327647103 0.017014537 0.013899653 327.4423111 -2.515134797 0.083791383 ETDLQELFRPFGSISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETDLQELFRPFGSISR 16 1 O75821;K7ENA8;K7EP16 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 ; 228.51 3.68E-15 2869600000 1728500 1613830 1244370 1252340 1732940 1710360 1511990 1908140 1412390 FALSE TRUE 1500074.346 1603228.644 1846151.494 1536702.938 1698457.884 1776158.656 1365357.443 1500099.11 1245418.863 1.204473764 1.287300756 1.482353888 1.233884425 1.363764381 1.426153649 1.096303808 1.204493648 1 20.2481996 2.227404572 24.99163394 1.12181481 1.334595276 0.563835294 0.09586039 165.919224 371686.9252 0.038086881 0.02594466 168.8124887 -2.227404572 0.212780466 ETDPS(ph)PEER ddPTM_MDA-MB-175_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 158.47 7.26E-05 1051300000 2520700 2306120 1688690 2384600 2244360 2673600 2223160 2560800 2486100 TRUE FALSE 2187583.108 2290970.946 2505346.132 2926059.876 2199701.627 2776455.122 2007558.285 2013192.848 2192196.09 0.997895726 1.045057491 1.142847642 1.334761926 1.003423752 1.266517687 0.915774959 0.918345242 1 21.06394542 2.215482605 24.99983823 0.938009166 1.131709265 0.396887752 0.108588657 225.9475099 244761.4202 0.043713259 0.029492197 164.2413873 -2.215482605 0.1937001 ETDPVKS(ph)PPLPEHQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETDPVKSPPLPEHQK 15 1 Q96JM3;A0A2R8Y4S6;S4R3K0;A0A2R8Y735 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 ET(0.001)DPVKS(0.999)PPLPEHQK;ET(0.002)DPVKS(0.998)PPLPEHQK 150.98 1.86E-06 1255760000 1456240 1100040 986680 950960 1117550 807010 1533400 1827630 1602730 TRUE FALSE 1263794.194 1092813.765 1463841.748 1166890.003 1095312.941 838056.1969 1384691.104 1436805.547 1413257.085 0.894242249 0.773259003 1.035792966 0.825674263 0.775027384 0.592996282 0.97978713 1.016662546 1 20.4305925 2.031348839 24.99398846 1.006132742 0.819729665 0.383524523 0.109536977 198.4869733 158250.115 0.045930304 0.030965924 107.4852421 -2.031348839 -0.186403076 ETEAAPTS(ph)PPIVPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETEAAPTSPPIVPLK 15 0 A0A1W2PRB5;A0A0J9YVS1;A0A0G2JNB1;A0A0G2JNT7;Q7Z3B3;A0A3B3IT55;Q7Z3B3-4;Q7Z3B3-2 A0A1W2PRB5;Q7Z3B3-4 KANSL1 KAT8 regulatory NSL complex subunit 1 1 ETEAAPT(0.18)S(0.82)PPIVPLK;ETEAAPT(0.24)S(0.76)PPIVPLK 167.61 1.36E-06 158278000 481410 422180 268130 352110 446050 328700 468630 568150 455040 TRUE FALSE 417790.4488 419406.6718 397798.5648 432061.9572 437174.4777 341345.3017 423182.3347 446655.5438 401245.6896 1.041233488 1.045261501 0.991408943 1.076801492 1.089543113 0.850713941 1.054671354 1.113172192 1 18.61412637 2.015401788 24.99997085 1.07044549 1.016387012 0.058896316 0.070955711 528.7112997 858193.3183 0.028835535 0.019433781 103.6100273 -2.015401788 -0.054058478 ETEAVIHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETEAVIHK 8 0 Q86Y56;H0Y650;E9PGY2;Q86Y56-3 Q86Y56 DNAAF5 "Dynein assembly factor 5, axonemal" 0 63.565 0.072507 78414000 110410 101780 78008 82455 109580 118820 115710 132710 134160 FALSE TRUE 95819.03876 101111.4005 115732.9297 101177.668 107399.5724 123391.0823 104488.462 104330.9993 118299.7576 0.809968175 0.854705052 0.97830234 0.855265218 0.907859615 1.04303749 0.8832517 0.881920651 1 16.85208759 4.422842861 5.766765029 0.927857828 0.820024682 0.355238389 0.058620399 0.194292764 13.54159623 0.014575129 0.040890445 26475.42016 -4.422842861 -0.107833147 ETEDGHESPLFDFIESCLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ETEDGHESPLFDFIESCLR 19 0 Q9UBF2;Q9UBF2-2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 ;; 182.17 2.98E-14 159984000 127206 133929 39986.4 92335 130257 140942 134953 153090 180651 FALSE TRUE 110395.4048 133049.2116 59323.95679 113301.073 127665.1405 146364.1299 121865.2788 120352.8948 159294.6446 0.693026467 0.835239703 0.372416517 0.711267308 0.801440255 0.918826432 0.765030608 0.755536353 1 17.28133824 3.301650532 3.82576057 0.835349604 0.639278444 0.353072024 0.133330573 0.271353762 7.949268484 0.039756783 0.050995349 2002.859719 -3.301650532 -0.19607116 ETEEILADVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETEEILADVLK 11 0 P56537 P56537 EIF6 Eukaryotic translation initiation factor 6 0 120.06 0.0011689 10835000 32120 25399 19932 24935 21819 19610 28624 33466 56781 FALSE TRUE 27875.26062 25232.1523 29571.18187 30596.87286 21384.84459 20364.40939 25848.04889 26309.55633 50068.41487 0.556743422 0.503953488 0.5906155 0.611101289 0.427112475 0.406731658 0.516254588 0.525472125 1 15.61161316 1.23808334 6.761111578 1.011920374 0.515285103 0.851064807 0.063477206 0.045011615 10.70476953 0.102498965 0.016820432 17.30148339 -1.23808334 -0.496635271 ETEEILADVLKVEVFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETEEILADVLKVEVFR 16 1 P56537 P56537 EIF6 Eukaryotic translation initiation factor 6 0 66.965 0.048429 13655000 31862 28769 12696 13475 23867 20345 34023 33317 7772.9 FALSE TRUE 27651.35597 28580.01454 18835.82807 16534.7047 23392.09339 21127.68531 30723.4547 26192.41882 6853.996617 4.034340476 4.169832018 2.748152519 2.412417984 3.412912889 3.082535125 4.482560528 3.821481143 1 12.74272976 4.251144932 24.76346944 3.145199655 4.102086948 0.186586679 0.920577398 392.2807725 771915.4695 0.234070162 0.609964652 17829.73677 -4.251144932 0.956887293 ETEELMAWMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETEELMAWMR 10 0 Q12931-2;Q12931;I3L0K7 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ; 161.79 1.62E-05 63647000 67831 64303 58781 106780 79850 89632 63154 80152 128906 FALSE TRUE 58866.96149 63880.58936 87207.68821 131026.031 78261.14122 93080.20104 57029.3348 63012.11854 113666.8795 0.517890187 0.561998267 0.767221627 1.152719522 0.68851315 0.818885866 0.501723414 0.554357776 1 16.79445241 4.271569966 5.672224202 0.759117864 0.53411705 0.211161531 0.191584512 0.325749181 27.76679534 0.05182858 0.135672499 18688.30728 -4.271569966 -0.225000814 ETEELVASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETEELVASR 9 0 Q8TEV9 Q8TEV9 SMCR8 Smith-Magenis syndrome chromosomal region candidate gene 8 protein 0 66.27 0.064204 261890000 419350 389840 255680 375420 393940 486470 289710 385500 646350 FALSE TRUE 363931.835 387279.1154 379327.7032 460664.8489 386101.3647 505184.8157 261613.9688 303063.825 569939.2393 0.638544971 0.679509479 0.665558146 0.808270105 0.677443029 0.886383637 0.459020806 0.531747604 1 19.1204486 4.629846038 2.044721878 0.695329543 0.631339066 0.011756251 0.158397011 4.349443901 23.86299297 0.042721668 0.475735593 42642.8319 -4.629846038 -0.063990478 ETEFKDDSLPIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETEFKDDSLPIKR 13 2 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 0 87.18 0.0047729 140960000 270670 172600 160370 173290 170330 146660 265680 269880 228250 FALSE TRUE 234900.2737 171466.1792 237925.4684 212638.1431 166940.7662 152302.1051 239914.3945 212168.2622 201266.545 1.167110379 0.851935821 1.182141167 1.05650019 0.829451145 0.756718436 1.192023217 1.05416557 1 17.61874786 0.903967407 19.01032125 0.271118784 1.010892142 0.000522773 0.153942174 2747.843819 845017.9444 48522.59697 0.036434953 8.016179007 -0.903967407 0.739773358 ETEGSLS(ph)DSDFKEPPSEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETEGSLSDSDFKEPPSEGR 19 1 P78411-3;P78411-2;P78411 P78411-3 IRX5 Iroquois-class homeodomain protein IRX-5 1 ETEGS(0.019)LS(0.98)DSDFKEPPSEGR 207.86 1.80E-16 126740000 131390 130590 96377 115160 134040 101240 146630 181140 166450 TRUE FALSE 114026.4786 129732.1457 142985.2396 141308.8381 131372.8662 105134.7683 132409.8452 142404.6206 146772.4706 0.77689282 0.88389972 0.974196584 0.962774814 0.895078387 0.716311226 0.902143601 0.970240673 1 17.16322187 1.725856253 3.605037695 0.99030449 0.874719331 0.274963469 0.076962849 0.286873683 8.224066996 0.057386633 0.021972622 53.19321655 -1.725856253 -0.115585159 ETELELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETELELR 7 0 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 104.37 0.019001 210460000 564650 524210 365930 403230 519210 548530 545670 577670 560520 FALSE TRUE 490030.0719 520766.43 542894.972 494789.5345 508878.7368 569632.304 492751.0074 454139.7659 494255.9641 0.991449992 1.053637119 1.09840854 1.001079543 1.029585425 1.152504664 0.996955107 0.918835176 1 18.91489885 2.005501011 24.99917593 0.9549026 1.054673599 0.394079794 0.049797741 123.119649 559510.3836 0.019836643 0.013329115 101.2747106 -2.005501011 0.099770999 ETERAS(ph)PIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ETERASPIK 9 1 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 ET(0.071)ERAS(0.929)PIK;ET(0.001)ERAS(0.999)PIK;ETERAS(1)PIK 111.94 0.0012378 1898620000 4765000 4053300 3640900 4341600 3754900 3191820 4439700 5710700 8436300 TRUE FALSE 4135293.177 4026673.605 5401651.418 5327426.637 3680184.836 3314611.381 4009138.577 4489511.246 7438970.225 0.555895917 0.541294492 0.72612892 0.71615109 0.494716974 0.445573955 0.538937307 0.603512463 1 22.82667149 1.238270734 4.932397377 1.028316423 0.575975374 0.698273502 0.087424174 0.110274796 6.65652224 0.1721692 0.023979889 17.3089504 -1.238270734 -0.45234105 ETERAS(ph)PIKMDLAPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ETERASPIKMDLAPSK 16 2 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 ET(0.024)ERAS(0.976)PIKMDLAPSK;ET(0.085)ERAS(0.915)PIKMDLAPSK;ET(0.058)ERAS(0.942)PIKMDLAPSK;ET(0.1)ERAS(0.9)PIKMDLAPSK;ET(0.235)ERAS(0.765)PIKMDLAPSK 120.23 0.00010447 3192520000 3711760 2941790 2013450 2119240 2615960 1970470 3738920 4331080 1543970 TRUE FALSE 3221241.512 2922465.188 2987161.155 2600445.833 2563907.514 2046275.256 3376320.114 3404912.247 1361443.625 2.3660484 2.146592876 2.194112998 1.91006501 1.883227088 1.50301872 2.479955872 2.500957207 1 20.37670581 3.846478567 4.136410667 1.966518803 2.238738493 0.107671377 0.438930469 0.720977886 21.16760045 0.122795277 0.223106668 7022.286866 -3.846478567 0.27221969 ETES(ph)APGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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;ET(0.001)ES(0.999)APGS(1)PR;ETES(1)APGS(1)PR;ET(0.001)ES(0.999)APGS(1)PR;ETES(1)APGS(1)PR 183.52 2.43E-06 7561810000 8193790 7643660 4839350 5263640 6760640 7382590 7179820 7905320 7809670 TRUE FALSE 7110959.891 7593448.294 7179675.847 6458829.912 6626116.491 7666603.014 6483522.161 6214828.837 6886419.709 1.03260623 1.102669982 1.042584703 0.937908258 0.9622005 1.113293023 0.941493902 0.902476047 1 22.71532268 4.456714909 0.243799602 0.913741594 1.182530349 0.210872777 0.062347179 19.56035392 1.788341546 0.42367628 1.840754902 28622.98409 -4.456714909 0.268788754 ETESAPGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ETESAPGSPR 10 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 1 ETESAPGS(1)PR;ETESAPGS(1)PR;ETESAPGS(1)PR;ETESAPGS(1)PR;ETESAPGS(1)PR 198.97 3.01E-07 11360920000 10509240 9140080 6294410 7929730 8806520 9668120 10207450 11296280 9242840 TRUE FALSE 9120417.307 9080038.213 9338407.73 9730296.395 8631287.482 10040058.83 9217533.07 8880658.43 8150161.985 1.119047367 1.114092975 1.145794126 1.193877669 1.05903263 1.231884575 1.130963174 1.089629684 1 22.9583973 1.344778181 2.101530263 0.976686369 1.143268872 0.494530645 0.046096855 0.455176167 2.489030559 0.135400931 0.011880678 22.11964645 -1.344778181 0.166582504 ETFLTSPEELYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ETFLTSPEELYR 12 0 O95433;O95433-2;G3V438;H0YJ63;H0YJG7 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ;;; 285.16 5.26E-28 644994000 557433 498071 316258 369163 523411 536377 507734 579969 578392 FALSE TRUE 483766.8167 494799.1388 469201.4266 452987.1015 512996.1451 557011.7703 458494.0348 455947.1427 510015.1567 0.948534196 0.970165558 0.919975457 0.888183607 1.005844902 1.092147484 0.898981195 0.893987437 1 18.9601806 5.17618886 12.98947537 0.953416087 0.000735242 0 0.063521004 2701156.36 440332.873 0.016398848 76404840.69 150033.714 -5.17618886 -0.952680845 ETGANLAICQWGFDDEANHLLLQNNLPAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ETGANLAICQWGFDDEANHLLLQNNLPAVR 30 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;; 255.7 4.01E-58 1071570000 375545 330328 236623 280181 339994 322815 327092 378187 347307 FALSE TRUE 325915.7767 328158.0536 351054.6743 343800.3783 333228.7846 335233.9019 295370.6682 297314.6531 306248.7621 1.064219083 1.071540833 1.146305611 1.122618018 1.088098389 1.094645737 0.96447955 0.970827281 1 18.22434449 2.243412667 24.4337089 0.976269026 1.099583928 0.83490214 0.025030293 33.50671855 168732.909 0.010144411 0.007596407 175.1510183 -2.243412667 0.123314902 ETGEAGWWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETGEAGWWR 9 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 0 ; 168.23 0.00013814 513130000 601980 581960 365970 437460 527810 578980 540320 656560 584110 FALSE TRUE 522426.8178 578137.0664 542954.3161 536791.9792 517307.6136 601253.7352 487919.8496 516159.7534 515057.1812 1.014308385 1.122471616 1.05416318 1.042198806 1.004369287 1.167353368 0.947312002 1.002140679 1 18.97437308 2.200516108 24.99994264 0.985613814 1.065354692 0.385483073 0.050110603 168.9260075 111004.107 0.019267389 0.012990346 158.6777771 -2.200516108 0.079740878 ETGEHLVHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ETGEHLVHVK 10 0 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 0 ;;; 158.79 4.56E-06 2341930000 2759890 2071190 1526710 2001710 1940120 1871220 2187260 2562330 2713700 FALSE TRUE 2395163.544 2057584.217 2265032.063 2456228.85 1901515.408 1943207.044 1975139.862 2014395.67 2392889.477 1.000950343 0.859874322 0.946567773 1.026469828 0.794652417 0.812075552 0.82542043 0.841825621 1 21.19032233 3.231029634 24.99996052 0.848834619 0.950573495 0.346315257 0.070139352 199.3887779 661892.7765 0.021068283 0.024346977 1702.274658 -3.231029634 0.101738876 ETGENVLHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETGENVLHVR 10 0 Q9Y223-5;Q9Y223-3;Q9Y223;Q9Y223-2;Q9Y223-4 Q9Y223-5 GNE Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase;UDP-N-acetylglucosamine 2-epimerase (hydrolyzing);N-acetylmannosamine kinase 0 93.058 0.0090448 105970000 85421 88792 44400 57764 80165 81080 75631 79660 83206 FALSE TRUE 74132.39842 88208.71951 65871.98851 70880.19907 78569.87334 84199.20007 68296.31726 62625.32891 73369.48147 1.010398287 1.202253549 0.897811831 0.966071964 1.070879496 1.147605222 0.930854572 0.853561013 1 16.16289247 2.081463477 9.040957944 0.909134895 1.046285714 0.272794374 0.092084295 0.340077356 34.22883496 0.037823954 0.025472997 120.6322637 -2.081463477 0.137150819 ETGEPYRLS(ph)PEPTPLAEPILEVEVTLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ETGEPYRLSPEPTPLAEPILEVEVTLSK 28 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JWW9;C9JSU8;C9J556 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 ETGEPYRLS(1)PEPTPLAEPILEVEVTLSK;ETGEPYRLS(0.995)PEPT(0.005)PLAEPILEVEVTLSK;ETGEPYRLS(1)PEPTPLAEPILEVEVTLSK;ET(0.01)GEPY(0.001)RLS(0.979)PEPT(0.009)PLAEPILEVEVTLSK;ETGEPYRLS(1)PEPTPLAEPILEVEVTLSK 329.84 4.47E-96 2295870000 761840 593415 575757 791260 544791 528594 653401 847550 1962950 TRUE FALSE 661160.9137 589516.8178 854195.011 970927.6767 533950.725 548929.3532 590034.2716 666308.0281 1730892.287 0.381976925 0.340585502 0.493499808 0.560940553 0.30848293 0.317136634 0.340884454 0.384950602 1 20.72308452 1.238246479 24.99999925 1.000000676 0.390461531 0.852949897 0.079459903 2.91504316 231616.5902 0.117428873 0.020689516 17.30798376 -1.238246479 -0.609539145 ETGLMYSIMVHALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETGLMYSIMVHALR 14 0 P78527;P78527-2;H0YG84 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 166.38 3.81E-06 306090000 325570 294660 128350 192660 281950 247360 331290 354320 181880 FALSE TRUE 282545.0996 292724.3591 190420.4893 236406.3976 276339.7466 256876.0993 299161.5468 278551.4253 160378.3536 1.761740866 1.825211149 1.18732039 1.474054274 1.723048905 1.601688093 1.865348659 1.736839287 1 17.29111991 1.233775269 24.99841548 0.999999015 1.648136256 0.515408397 0.197128331 132.0963255 689980.598 0.402809028 0.050702384 17.1307063 -1.233775269 0.64813724 ETGLSHLCEFIEDCEFTVLATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ETGLSHLCEFIEDCEFTVLATR 22 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ;;;;; 258.37 3.55E-37 1464224000 1043182 1010964 674762 780005 989424 943969 978836 1127487 1220117 FALSE TRUE 905322.8556 1004322.911 1001079.16 957117.0569 969736.3982 980284.0983 883908.6354 886382.6792 1075876.158 0.841474968 0.933493045 0.93047806 0.889616383 0.901345746 0.911149569 0.821570985 0.823870547 1 20.03708059 ETGYVVERPSTTK ddPTM_MDA-MB-175_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 ; 94.09 0.0048471 373190000 370010 276400 217110 231000 313560 244900 307530 358230 393880 FALSE TRUE 321112.241 274584.3102 322105.1222 283452.0806 307320.7695 254321.4615 277705.7879 281625.3022 347315.9551 0.92455367 0.790589393 0.927412396 0.81612168 0.884844952 0.732248138 0.799576823 0.810861978 1 18.40588916 3.649078637 24.984129 0.832273886 0.87185361 0.044671432 0.078285369 215.6568863 60205.69705 0.020935296 0.031052064 4457.3695 -3.649078637 0.039579724 ETHADLWPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ETHADLWPAK 10 0 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 0 ;; 127.76 0.00034743 2166600000 1924760 1568350 1142060 1359000 1615980 1490010 1822880 2015790 1946920 FALSE TRUE 1670398.089 1558047.406 1694364.036 1667581.721 1583825.16 1547331.649 1646097.378 1584728.995 1716757.336 0.97299604 0.907552496 0.986956048 0.971355524 0.922567871 0.901310638 0.958841034 0.923094349 1 20.7112547 3.242544892 24.99989121 0.938237487 0.957934917 0.067085286 0.033107776 285.9548889 1794260.071 0.009443659 0.011740756 1748.013943 -3.242544892 0.01969743 ETHPDSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETHPDSLR 8 0 P56597 P56597 NME5 Nucleoside diphosphate kinase homolog 5 0 83.265 0.018284 595170000 573380 427740 343100 376020 356910 442390 459410 508730 464390 FALSE TRUE 497606.3802 424930.1478 509024.3076 461401.0881 349808.1893 459409.0296 414856.4889 399942.0484 409490.3432 1.215184652 1.03770493 1.243067916 1.126769155 0.854252597 1.121904429 1.01310445 0.976682491 1 18.6434699 3.452352798 24.82847992 0.998278163 1.157951234 0.490931653 0.082795371 170.2197845 170631.6217 0.022191598 0.028650264 2833.693004 -3.452352798 0.159673071 ETHQQVVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ETHQQVVSR 9 0 O14745;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;;; 135.55 0.00021771 3049890000 2253260 2063960 1377250 1785880 1983980 2109800 1985150 2276200 2478440 FALSE TRUE 1955485.982 2050401.711 2043292.707 2191391.349 1944502.68 2190965.371 1792630.459 1789452.343 2185441.647 0.894778401 0.938209315 0.934956424 1.002722426 0.889752734 1.00252751 0.820260043 0.818805822 1 21.05949343 2.231928196 24.99997579 0.86452852 0.943385516 0.178182528 0.062145365 208.1653525 784641.1449 0.02418211 0.016729143 170.5800339 -2.231928196 0.078856996 ETHSLFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETHSLFFR 8 0 A0A0C4DGS1;P39656-2;P39656-3;P39656;U3KQ84 A0A0C4DGS1 DDOST Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit 0 126.41 0.0012203 331840000 35719 34688 24008 46095 45327 49878 29587 51641 54665 FALSE TRUE 30998.64365 34460.13224 35618.3491 56561.57427 44425.08138 51796.83894 26717.65729 40597.97402 48202.56597 0.643091151 0.714902444 0.738930561 1.173414177 0.921633122 1.074566009 0.554278735 0.842236781 1 15.55682233 3.97818521 24.79270927 0.905536177 0.690976633 0.302090702 0.163219791 937.2770612 1065228.136 0.045035875 0.07895304 9510.102757 -3.97818521 -0.214559544 ETHVMDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 ETHVMDYR 8 0 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;;;;;;; 138.78 0.00066361 15084556000 11200950 11611080 7275235 8133477 10967990 11830320 10655468 11778480 11558624 FALSE TRUE 9720716.078 11534806.05 10793562.98 9980307.265 10749748.46 12285440.07 9622102.353 9259743.712 10192176.64 0.953742897 1.131731372 1.059004702 0.979212549 1.054705863 1.20537943 0.944067464 0.908514838 1 23.28095885 2.065193242 24.99992716 0.94128886 1.063560044 0.342707326 0.073450404 57.15152498 21915.49861 0.029192933 0.019681869 116.1965521 -2.065193242 0.122271184 ETIEDVEEMLNNLPGVTSVHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ETIEDVEEMLNNLPGVTSVHSR 22 0 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2;H0YD73;E9PL38 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ;;;; 219.22 1.12E-25 568190000 562220 627650 204965.4 397459 630486 614618 584421 690088 612851 FALSE TRUE 487921.2025 623526.9258 304087.353 487708.1407 617940.5621 638262.7522 527743.9414 542518.0515 540400.4529 0.902888219 1.15382384 0.562707435 0.902493953 1.143486388 1.181092186 0.976579384 1.003918573 1 19.04366936 3.35432294 7.206311233 1.053013369 0.874128295 0.25523507 0.153422077 0.336385709 19.89367316 0.044788499 0.057863541 2261.116504 -3.35432294 -0.178885073 ETIELS(ph)PTGRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETIELSPTGRPK 12 1 A0A0B4J1V9;Q9NRZ9-4;Q9NRZ9-3;Q9NRZ9-2;Q9NRZ9;A0A087WSW7;F6XU50;Q9NRZ9-6;Q9NRZ9-5 A0A0B4J1V9 HELLS Lymphoid-specific helicase 1 ETIELS(0.973)PT(0.027)GRPK 72.175 0.0258 166090000 234510 191340 127200 174530 195920 134460 213310 256840 258170 TRUE FALSE 203518.9093 190083.0749 188714.3455 214159.704 192021.5753 139632.7632 192623.229 201916.7647 227649.4367 0.894001375 0.83498153 0.828969086 0.940743395 0.843496817 0.613367488 0.846139713 0.886963604 1 17.79645436 1.355203409 2.358110895 1.019474032 0.826602339 0.295387163 0.084216233 0.615491641 4.516559958 0.223440012 0.023529204 22.65705241 -1.355203409 -0.192871693 ETIFELEDEVEQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETIFELEDEVEQHR 14 0 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1;C9J8U1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 0 ; 233.52 3.45E-17 171207000 299600 290910 216290 260210 285770 304810 290080 348630 349250 FALSE TRUE 260007.1009 288998.9931 320888.5674 319294.6576 280083.7361 316536.2379 261948.0862 274078.1875 307962.0629 0.844282892 0.938424007 1.041974341 1.036798671 0.909474802 1.02784166 0.850585568 0.889973866 1 18.23239311 1.170792048 22.063564 1.000009049 0.943231903 0.057707225 0.073057776 44010.0902 14319605.9 76.14622809 0.018649802 14.81808385 -1.170792048 -0.056777146 ETIFELEDQVEQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETIFELEDQVEQHR 14 0 Q5M775-4;Q5M775;J3KSG2;Q5M775-5;Q5M775-3;Q5M775-2;J3KRN9;J3QQM0 Q5M775-4 SPECC1 Cytospin-B 0 96.734 0.003254 24461000 27165 24604 19857 22960 26200 29852 26815 30726 34609 FALSE TRUE 23575.07642 24442.3747 29459.91162 28173.41892 25678.67126 31000.42576 24214.48543 24155.48401 30517.56345 0.772508476 0.80092812 0.965342848 0.923187035 0.841439105 1.01582244 0.79346064 0.791527281 1 14.89735216 4.398230662 7.942459488 0.89065879 0.779536858 0.268528529 0.078891769 0.32402053 27.82290994 0.02024696 0.054085095 25016.73695 -4.398230662 -0.111121932 ETKPEPMEEDLPENKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETKPEPMEEDLPENKK 16 2 P31948;P31948-2;P31948-3;F5H783 P31948 STIP1 Stress-induced-phosphoprotein 1 0 147.56 5.71E-07 312410000 629960 285280 325300 298610 230450 159200 441770 427760 419580 FALSE TRUE 546709.1899 283405.9769 482616.1681 366413.9645 225864.4959 165324.527 398927.2134 336286.8528 369977.7304 1.477681344 0.766008204 1.304446534 0.99036762 0.610481327 0.446849941 1.078246555 0.908938093 1 18.49707891 3.475235666 24.75394779 0.821407322 1.142102572 0.311144403 0.251820489 73.20938372 961074.7507 0.072360244 0.094099451 2987.003048 -3.475235666 0.320695249 ETLAQLQQEFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETLAQLQQEFQR 12 0 O15212 O15212 PFDN6 Prefoldin subunit 6 0 124.21 0.00076099 98250000 76087 74587 40860 55907 79063 74908 68728 82401 68281 FALSE TRUE 66031.91017 74097.03309 60620.03267 68601.53883 77489.80098 77789.75923 62062.76914 64780.1874 60208.89797 1.096713483 1.230665825 1.006828471 1.139392036 1.287015767 1.291997726 1.030790651 1.075923818 1 15.87768909 2.199368347 24.99840769 1.043778846 1.173715652 0.363411469 0.087017419 192.8230574 122989.0431 0.037209315 0.025086967 158.2589744 -2.199368347 0.129936806 ETLAVNYEKEEEFLTNELSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETLAVNYEKEEEFLTNELSR 20 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 188.26 2.39E-17 240390000 180780 179648 138189 150720 150479 138342 189027 228770 254080 FALSE TRUE 156889.465 178467.8805 205017.6626 184943.2796 147484.7623 143664.1063 170695.1906 179849.3158 224042.9518 0.700265122 0.796578866 0.915081956 0.825481356 0.658287891 0.641234661 0.76188601 0.802744805 1 17.77341582 1.214658532 2.677075932 1.064031305 0.759687318 0.472575211 0.08011503 0.531149874 4.133401366 0.376462995 0.02320332 16.39300353 -1.214658532 -0.304343986 ETLEQQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ETLEQQKR 8 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITI7 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;; 124.08 0.0021167 1125480000 1278930 1050960 586790 729150 873610 828160 1093410 1291050 609640 FALSE TRUE 1109916.16 1044056.175 870563.6067 894714.6519 856226.8702 860019.8511 987371.2665 1014969.004 537569.0537 2.064695042 1.942180576 1.619445168 1.664371574 1.592775597 1.599831399 1.836733829 1.888071863 1 19.03609056 4.336364473 3.635122845 1.639668045 2.041630721 0.323926635 0.239575729 0.286072605 7.064389386 0.060408503 0.185566833 21695.2407 -4.336364473 0.401962676 ETLIAEIEELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETLIAEIEELDR 12 0 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 ; 88.681 0.022914 27278700 61782 48720 44115 45525 46097 44235 60001 62744 73272 FALSE TRUE 53617.35216 48399.95511 65449.16156 55862.14706 45179.75989 45936.74907 54182.11226 49326.68387 64609.86763 0.82986321 0.749110885 1.012990182 0.86460705 0.699270275 0.710986584 0.838604291 0.76345434 1 15.9794669 3.417695881 24.99998442 0.794470434 0.866885535 0.076593058 0.104228867 178.5230975 75102.61348 0.029936608 0.038648001 2616.350241 -3.417695881 0.072415101 ETLIDVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETLIDVAR 8 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ; 107.01 0.0095055 180080000 440140 393600 310780 411350 426650 434450 378230 461880 827630 FALSE TRUE 381974.3838 391014.4157 461074.2475 504753.3046 418160.4997 451163.5726 341549.3128 363110.5564 729788.5242 0.523404207 0.535791401 0.631791584 0.691643247 0.572988593 0.618211383 0.468011351 0.497555859 1 19.47711894 1.233020254 24.9992732 1.000000688 0.566155299 0.806515985 0.066583001 85.52243718 385853.4544 0.154434836 0.018150039 17.10095068 -1.233020254 -0.433845389 ETLLNGVGYLHEGLSPMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETLLNGVGYLHEGLSPMER 19 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 83.167 0.0034219 69599000 49601 44465 33137 37439 45096 43697 50191 56906 52565 FALSE TRUE 43046.10218 44172.90649 49162.16404 45940.09717 44198.67783 45378.05187 45323.48455 44737.09474 46350.82558 0.928701952 0.953012291 1.060653471 0.991138703 0.953568297 0.979012807 0.97783554 0.965184421 1 15.50030742 4.466485856 24.99872294 0.986642655 0.934779493 0.344809542 0.028680848 212.3939243 499236.6629 0.007372052 0.019544935 29274.2553 -4.466485856 -0.051863162 ETLNPPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETLNPPGR 8 0 Q9H6W3;Q9H6W3-2 Q9H6W3 NO66 Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66 0 67.169 0.05979 172520000 385200 528390 312410 340080 425430 976940 293040 289000 279280 FALSE TRUE 334294.844 524918.9713 463492.5209 417300.3618 416964.7753 1014523.514 264621.0259 227199.599 246263.8366 1.357466239 2.131530876 1.882097377 1.694525545 1.693162834 4.119660963 1.074542773 0.922586126 1 17.90984526 2.039998708 24.99992257 0.968593688 2.134619001 0.345601434 0.745341351 161.026366 100643.7692 0.2998366 0.202149506 109.6474934 -2.039998708 1.166025313 ETLQQHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ETLQQHK 7 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;; 134.06 0.0032115 5086320000 8516000 8291950 5988280 7650160 6927700 8929700 8951360 8892730 7838770 FALSE TRUE 7390589.023 8237479.634 8884232.238 9387245.753 6789852.324 9273231.337 8083258.485 6991088.893 6912079.541 1.069228006 1.191751279 1.285319734 1.358092843 0.982316868 1.341597891 1.169439448 1.01143062 1 22.72068839 1.766531004 3.899114045 1.002183053 1.207955165 0.335678895 0.11410793 0.216125047 6.663813985 0.07082137 0.029603325 58.41589082 -1.766531004 0.205772112 ETLVYLTHLDYVDTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ETLVYLTHLDYVDTER 16 0 O14980 O14980 XPO1 Exportin-1 0 ;;;;; 216.99 1.47E-14 2000800000 1791730 1620750 1008808 1217150 1467960 1492250 1610770 1820280 1626410 FALSE TRUE 1554948.341 1610103.187 1496670.923 1493522.51 1438750.468 1549657.823 1454557.773 1431027.287 1434137.663 1.084239248 1.122697792 1.043603388 1.041408053 1.003216431 1.080550259 1.014238599 0.997831188 1 20.45175208 8 0.17831896 0.969522928 1.564112202 0.565515342 0.027587046 84.00241099 1.176184219 0.260126181 13.07882175 100000000 -8 0.594589273 ETMQSLNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 18 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 ;;;;;;;;;;;;;;;;; 275.17 8.12E-21 44101850000 14172133 13709085 9702822 11720436 13240682 14131039 13894696 14645321 16030879 FALSE TRUE 12299249.72 13619029.12 14395139.17 14381740.13 12977218.33 14674669.21 12547190.52 11513533.07 14135726.75 0.870082588 0.963447396 1.018351545 1.01740366 0.918043944 1.038126265 0.887622599 0.814498843 1 23.75284272 2.131137427 9.253089193 0.881304429 0.972352782 0.177526528 0.067098499 0.35153285 27.92076985 0.026781726 0.018046014 135.2500477 -2.131137427 0.091048353 ETNGNEDEEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETNGNEDEEGR 11 0 Q9BUQ8;H0YIL9 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 ; 125.17 0.00077669 109638000 137942 122368 90060 105856 94310 112769 103954 145402 174116 FALSE TRUE 119712.6152 121564.1566 133613.3172 129892.2227 92433.41551 117107.2964 93872.55708 114308.9138 153532.2048 0.779723155 0.791782784 0.870262479 0.846025906 0.602045777 0.762753955 0.611419325 0.744527273 1 17.22818178 ETPEHPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETPEHPLK 8 0 Q8N163-2;Q8N163;H0YB24;G3V119;E5RHJ4 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ; 94.302 0.010456 788620000 2678400 2282350 1559560 1937620 1954810 1891460 2493300 2701100 2432400 FALSE TRUE 2324442.654 2267357.093 2313768.432 2377586.236 1915913.106 1964225.69 2251500.15 2123490.785 2144844.443 1.083734842 1.057119597 1.078758154 1.108512202 0.893264363 0.915789346 1.049726546 0.990044193 1 21.03244159 3.258376305 24.99937909 0.97559813 1.080018029 0.607084866 0.044729789 190.8122409 240726.3667 0.01382683 0.01782609 1812.910252 -3.258376305 0.104419899 ETPHS(ph)PGVEDAPIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 ETPHSPGVEDAPIAK 15 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 ETPHS(1)PGVEDAPIAK;ET(0.133)PHS(0.867)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK;ET(0.126)PHS(0.874)PGVEDAPIAK;ET(0.143)PHS(0.857)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK;ET(0.147)PHS(0.853)PGVEDAPIAK;ET(0.002)PHS(0.998)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK;ET(0.02)PHS(0.98)PGVEDAPIAK;ET(0.203)PHS(0.797)PGVEDAPIAK;ET(0.04)PHS(0.96)PGVEDAPIAK;ET(0.028)PHS(0.972)PGVEDAPIAK;ET(0.021)PHS(0.979)PGVEDAPIAK 346.06 3.36E-82 60367317000 26603816 22762774 16649978 20122496 21619712 18895033 27247571 29878807 28027372 TRUE FALSE 23088054.31 22613243.84 24701963.05 24691616.27 21189522.03 19621937.15 24605105.76 23489456.64 24714008.01 0.934209227 0.914997026 0.999512626 0.999093966 0.857389138 0.793960135 0.995593501 0.950451122 1 24.55882566 ETPPNGNLS(ph)PAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETPPNGNLSPAPR 13 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 ETPPNGNLS(1)PAPR;ETPPNGNLS(1)PAPR 254.38 8.71E-24 1247660000 536570 510910 300070 398100 561820 542580 551750 626840 594810 TRUE FALSE 465660.915 507553.7986 445184.8557 488494.6896 550640.8812 563453.4037 498241.3699 492795.1441 524492.2394 0.88783185 0.967705069 0.848792074 0.931366859 1.049855155 1.074283586 0.949949937 0.939566131 1 19.0005619 3.436606999 9.480976044 0.99421853 0.905077388 0.475412248 0.049299942 0.360954094 80.49226229 0.015434236 0.019970491 2732.794652 -3.436606999 -0.089141142 ETQS(ph)PEQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ETQSPEQVK 9 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 ETQS(1)PEQVK;ETQS(1)PEQVK;ETQS(1)PEQVK;ETQS(1)PEQVK;ET(0.001)QS(0.999)PEQVK;ETQS(1)PEQVK;ETQS(1)PEQVK;ETQS(1)PEQVK 231.52 5.28E-08 16180190000 18664960 13965320 11269770 13452970 11950940 11119640 16445350 18817520 21859870 TRUE FALSE 16198338.25 13873580.89 16719868.47 16507672.45 11713139.68 11547419.75 14850482.49 14793539.79 19275621.07 0.840353636 0.719747542 0.867410103 0.856401586 0.607666006 0.599068622 0.770428223 0.767474092 1 24.20027401 1.216763517 3.640617113 1.041357363 0.748662973 0.40993132 0.092967449 0.352600186 6.935172098 0.293247594 0.025194439 16.47265176 -1.216763517 -0.29269439 ETQS(ph)PEQVKSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ETQSPEQVKSEK 12 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 ETQS(1)PEQVKSEK;ETQS(1)PEQVKSEK;ET(0.001)QS(0.999)PEQVKSEK;ET(0.004)QS(0.996)PEQVKSEK 183.36 9.51E-06 3958190000 5621000 3954310 2180780 2139470 3377370 2700050 5476900 5611800 956560 TRUE FALSE 4878170.608 3928333.877 3235412.502 2625269.363 3310166.945 2803922.671 4945751.081 4411760.241 843476.5665 5.783409761 4.657312406 3.835806033 3.112439002 3.924432612 3.324244895 5.863531101 5.230447906 1 19.68598846 4.604498958 2.636911854 3.971830269 5.902544562 0.192247757 1.299548882 0.695223244 7.514055866 0.339890544 2.55298984 40225.26906 -4.604498958 1.930714293 ETRHS(ph)WDSPAFNNDVVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETRHSWDSPAFNNDVVQR 18 1 A0A1W2PR28;Q5JU85-3;Q5JU85;A0A1W2PRJ5 A0A1W2PR28 IQSEC2 IQ motif and SEC7 domain-containing protein 2 1 ET(0.1)RHS(0.898)WDS(0.001)PAFNNDVVQR;ET(0.081)RHS(0.919)WDSPAFNNDVVQR 223.68 3.04E-19 427830000 148278 166918 110787 144785 237910 242850 212700 223500 167414 TRUE FALSE 128682.6866 165821.5047 164363.9638 177660.6472 233176.0565 252192.5966 192072.3867 175706.2643 147622.5076 0.871700994 1.123280639 1.113407206 1.203479402 1.579542715 1.708361419 1.301105027 1.190240344 1 17.17155318 4.079319099 1.449079676 1.341910226 0.93711937 0.34976523 0.201961889 0.633653048 2.394806105 0.068411824 0.26256843 12003.80963 -4.079319099 -0.404790856 ETSFGS(ph)SENITMTSLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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(0.984)S(0.016)ENITMTSLSK;ETSFGS(0.937)S(0.063)ENITMTSLSK;ETSFGS(0.936)S(0.064)ENITMTSLSK;ETSFGS(0.545)S(0.455)ENITMTSLSK;ETSFGS(0.923)S(0.077)ENITMTSLSK;ET(0.001)S(0.002)FGS(0.854)S(0.143)ENITMTSLSK;ETSFGS(0.984)S(0.015)ENITMTSLSK;ETSFGS(0.987)S(0.013)ENITMTSLSK 374.68 6.27E-105 2538412000 5048540 3402780 2405274 2994058 3519880 3122476 4112040 4767510 4886200 TRUE FALSE 4381362.648 3380426.914 3568472.552 3673904.63 3449841.275 3242599.672 3713254.994 3748015.087 4308559.002 1.016897447 0.784584106 0.828228777 0.852699157 0.800694913 0.752594933 0.861832225 0.86989991 1 22.03877401 1.138005039 1.943133365 1.088640808 0.835202046 0.324182908 0.070418951 1.238979189 3.598837642 0.628984609 0.018300727 13.74057917 -1.138005039 -0.253438761 ETSMVHELNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETSMVHELNR 10 0 B4DR61;P61619-3;P61619 B4DR61 SEC61A1 Protein transport protein Sec61 subunit alpha isoform 1 0 104.52 0.0026705 241810000 208380 192400 112960 196730 268080 266940 164560 284020 206060 FALSE TRUE 180842.055 191136.1117 167587.8338 241400.5533 262745.7325 277209.3545 148600.9965 223284.5332 181699.8215 0.995279211 1.051933404 0.922333508 1.328567916 1.446042876 1.525644616 0.817837878 1.228864901 1 17.47119748 3.743791788 24.90272803 1.221311714 0.996057172 0.226702325 0.204127282 700.6591076 3335442.053 0.057116329 0.095235328 5543.598745 -3.743791788 -0.225254542 ETSSALTHAGAHLDLSAFSSWEELASLGLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ETSSALTHAGAHLDLSAFSSWEELASLGLDR 31 0 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ;; 208.11 2.70E-26 213791000 434261 410037 203349 282319 397381 400377 409309 490785 377468 FALSE TRUE 376872.3086 407343.4399 301689.2566 346423.8439 389473.8956 415779.7623 369614.2762 385834.447 332844.1631 1.132278557 1.223826298 0.906397918 1.040798915 1.170138878 1.249172461 1.110472459 1.159204486 1 18.34448734 3.234882099 24.99261441 1.143992862 1.074294948 0.085731921 0.099369371 232.2154391 1577719.136 0.030371698 0.035781108 1717.442079 -3.234882099 -0.069697914 ETSVSKEDT(ph)DHEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETSVSKEDTDHEEK 14 1 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 ETSVSKEDT(1)DHEEK 106.16 0.0014045 340680000 391830 361600 340310 312910 345530 255120 371880 439250 443570 TRUE FALSE 340048.6727 359224.6258 504885.0543 383960.998 338654.629 264934.6315 335815.1348 345319.8057 391131.6599 0.869396951 0.918423801 1.290831467 0.981666885 0.865832822 0.677354095 0.858573133 0.882873572 1 18.57729479 3.29465441 4.510583961 0.850720584 1.032275859 0.259028696 0.133593387 0.279161411 11.59381081 0.040874262 0.052200959 1970.853803 -3.29465441 0.181555275 ETTEAACR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETTEAACR 8 0 Q9Y2Q3-3;Q9Y2Q3;Q9Y2Q3-2;E9PFN5;Q9Y2Q3-4 Q9Y2Q3-3 GSTK1 Glutathione S-transferase kappa 1 0 93.195 0.02615 206340000 154870 137710 105200 119690 112860 168250 122200 150230 148150 FALSE TRUE 134403.5371 136805.3739 156075.0719 146867.4438 110614.3068 174722.6864 110349.0628 118104.4836 130635.8758 1.028840939 1.047226676 1.194733613 1.124250463 0.846737591 1.337478586 0.844707184 0.904073884 1 16.99519162 ETVAYLQAHALTTEGIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ETVAYLQAHALTTEGIFR 18 0 Q07960;H0YE29 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ;; 195.77 2.03E-15 868805000 804640 811070 423331 412489 742109 781850 707494 846900 227882 FALSE TRUE 698304.7853 805742.0278 628055.2876 506150.9319 727342.4828 811928.2754 638881.3408 665797.0256 200942.0496 3.475155085 4.009822879 3.125554302 2.518890063 3.619662905 4.040609107 3.179430797 3.313378295 1 17.61641997 4.166487738 7.395759428 3.054978246 3.739450663 0.127174555 0.818454764 0.479352096 41.17224776 0.208549081 0.440694907 14671.94662 -4.166487738 0.684472417 ETVQTTEDQILKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ETVQTTEDQILKR 13 1 P18206;P18206-2 P18206 VCL Vinculin 0 ; 223.06 2.63E-11 1063100000 409620 367310 218020 269610 319360 297980 410710 439570 218550 FALSE TRUE 355487.6792 364897.1164 323455.2012 330829.0712 313005.3608 309443.4834 370879.4074 345571.3762 192713.268 1.844645586 1.893471686 1.678427254 1.716690681 1.624202444 1.605719662 1.924514131 1.793189332 1 17.55609638 1.237068686 24.99978974 0.99999907 1.76055158 0.831703684 0.1074558 16.00540568 268103.5381 0.17119365 0.02791083 17.26110866 -1.237068686 0.76055251 ETVQTTQS(ph)PTPVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETVQTTQSPTPVEK 14 0 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 1 ETVQTTQS(1)PTPVEK 353.26 5.59E-82 211930000 300110 242830 227380 277450 252020 181620 246710 310610 704560 TRUE FALSE 260449.7031 241234.8337 337341.7285 340449.2631 247005.2951 188607.0389 222784.1022 244188.4687 621267.7194 0.419222977 0.388294492 0.542989307 0.547991232 0.397582696 0.30358416 0.358595973 0.393048699 1 19.24485557 1.237097728 24.99989788 1.000000711 0.417557391 0.854580593 0.075329855 14.9870491 256028.54 0.1251328 0.020447703 17.26226297 -1.237097728 -0.582443321 ETVSEAPPLLFS(ph)DEEEKEAQLGVK ddPTM_MDA-MB-175_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 ETVS(0.001)EAPPLLFS(0.999)DEEEKEAQLGVK 71.974 0.017619 39720000 45605 40361 35866 36527 36876 26124 56632 61714 73952 TRUE FALSE 39578.1837 40095.86593 53210.91756 44821.01363 36142.23975 27129.00718 51139.83736 48516.94136 65209.47881 0.60693912 0.614877878 0.815999737 0.687338934 0.554248254 0.416028585 0.784239321 0.744016702 1 15.99279407 1.21573233 1.460634009 1.161556515 0.632049341 0.522813724 0.110380032 1.130125345 2.042760545 0.905435255 0.03389981 16.43358556 -1.21573233 -0.529507174 ETVVEVPQVTWEDIGGLEDVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ETVVEVPQVTWEDIGGLEDVKR 22 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 191.22 2.41E-17 2049680000 2273210 1321470 863515 1064800 1185535 1017175 1564520 1825960 1496449 FALSE TRUE 1972799.539 1312789.177 1281113.742 1306579.114 1161945.173 1056306.38 1412793.091 1435492.664 1319540.504 1.495065542 0.994883577 0.97087868 0.990177346 0.880568023 0.800510767 1.0706705 1.087873134 1 20.3316042 4.73865398 5.729951465 0.97875787 1.511490565 0.794327617 0.083274393 0.070395861 9.958343729 0.023090086 0.14687687 54784.03042 -4.73865398 0.532732695 ETVYCLNDDDETEVLKEDIIQGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ETVYCLNDDDETEVLKEDIIQGFR 24 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;;; 352.93 4.95E-102 4782428000 2370443 1925701 1384067 1441663 1614607 1479518 2094738 2614746 1861548 FALSE TRUE 2057182.952 1913050.943 2053406.431 1769014.619 1582479.48 1536436.015 1891590.631 2055602.916 1641477.916 1.253250459 1.165444216 1.250949775 1.077696265 0.964057734 0.936007728 1.152370442 1.25228789 1 20.64656391 3.729836958 23.33736526 1.079441694 1.217437758 0.379738676 0.094577504 350.981064 938939.0448 0.030135378 0.045563781 5368.302222 -3.729836958 0.137996063 ETWYLSWALDTNQEER ddPTM_MDA-MB-175_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 ;;; 244.18 1.13E-19 475017000 479716 421044 346552 394942 400631 436865 470625 509447 571539 FALSE TRUE 416320.3152 418278.1342 514145.7063 484619.6174 392659.2269 453671.4792 424983.8599 400505.7236 503972.3105 0.826077756 0.829962531 1.020186418 0.96159969 0.779128573 0.90019128 0.843268273 0.794697874 1 18.94298495 3.255957722 24.99966096 0.85518479 0.911687699 0.066571101 0.082228349 613.3724647 881411.3908 0.023965598 0.030868055 1802.842228 -3.255957722 0.056502909 EVAALCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EVAALCR 7 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;; 110.61 0.015737 430410000 816050 782380 517700 610490 776330 748670 799580 860610 758420 FALSE TRUE 708206.9249 777240.4943 768061.4516 749111.0853 760882.5519 777471.8194 722036.8547 676575.2488 668760.4516 1.058984459 1.162210613 1.148485156 1.120148602 1.13775052 1.162556514 1.079664404 1.011685495 1 19.35113001 1.883516775 2.686574567 1.003360279 1.133434803 0.749153056 0.029781771 0.121335442 1.57262738 0.01950797 0.007980798 76.47452266 -1.883516775 0.130074525 EVAATEEDVTRLPS(ph)PT(ph)SPFSSLSQDQAATSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVAATEEDVTRLPSPTSPFSSLSQDQAATSK 31 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 2 EVAAT(0.002)EEDVT(0.011)RLPS(0.961)PT(0.647)S(0.366)PFS(0.01)S(0.002)LSQDQAATSK;EVAATEEDVT(0.001)RLPS(0.953)PT(0.632)S(0.413)PFS(0.001)SLSQDQAATSK 132.67 7.21E-06 413655000 340589 350617 236748 340112 389533 334444 427165 570383 448631 TRUE FALSE 295579.3007 348313.7738 351240.1247 417339.6279 381782.0554 347310.2771 385738.604 448411.0342 395594.3543 0.747177753 0.880482166 0.887879518 1.054968615 0.965084692 0.877945485 0.975086221 1.133512219 1 18.59366231 6.164972239 0.390774669 1.04236212 1.05E-14 0.588013148 0.068660954 15.98205971 0.861446788 0.084256741 9.693268518 1462083.713 -6.164972239 -1.04236212 EVAATEEDVTRLPS(ph)PTS(ph)PFSSLSQDQAATSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EVAATEEDVTRLPSPTSPFSSLSQDQAATSK 31 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 2 EVAATEEDVTRLPS(0.697)PT(0.471)S(0.823)PFS(0.008)S(0.001)LSQDQAATSK;EVAATEEDVT(0.003)RLPS(0.935)PT(0.067)S(0.994)PFS(0.002)SLSQDQAATSK;EVAATEEDVTRLPS(0.998)PT(0.011)S(0.991)PFS(0.001)SLSQDQAATSK;EVAATEEDVTRLPS(0.999)PT(0.016)S(0.936)PFS(0.045)S(0.004)LSQDQAATSK 354.77 6.85E-121 2084094000 698470 770050 524439 707200 824540 721340 957010 1174280 953670 TRUE FALSE 606165.4198 764991.4908 778059.4545 867780.5689 808133.2672 749090.4166 864199.3175 923169.3603 840928.219 0.720828967 0.909698918 0.925238846 1.031931798 0.961001485 0.890789962 1.027673109 1.097798051 1 19.68162313 5.628434293 0.678138207 1.017414018 5.29E-13 0.712728561 0.055196342 5.600982105 0.809338739 0.02603638 5.773282822 425044.3947 -5.628434293 -1.017414018 EVAATEEDVTRLPS(ph)PTSPFSSLSQDQAATSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 EVAATEEDVTRLPSPTSPFSSLSQDQAATSK 31 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 EVAATEEDVTRLPS(0.874)PT(0.123)S(0.003)PFSSLSQDQAATSK;EVAATEEDVTRLPS(0.996)PT(0.004)SPFSSLSQDQAATSK;EVAATEEDVTRLPS(0.999)PTSPFSSLSQDQAATSK;EVAATEEDVTRLPS(0.992)PT(0.006)S(0.001)PFSSLSQDQAATSK;EVAATEEDVTRLPS(1)PTSPFSSLSQDQAATSK;EVAAT(0.004)EEDVT(0.003)RLPS(0.314)PT(0.314)S(0.314)PFS(0.026)S(0.026)LSQDQAATSK;EVAATEEDVT(0.01)RLPS(0.763)PT(0.206)S(0.021)PFSSLSQDQAATSK;EVAATEEDVT(0.002)RLPS(0.991)PT(0.002)S(0.005)PFSSLSQDQAATSK 374.48 1.97E-137 8569238000 2316219 2087561 1332120 1641273 1871640 1620539 2139885 2707041 1888409 TRUE FALSE 2010124.791 2073847.674 1976337.688 2013949.12 1834398.026 1682882.184 1932359.282 2128161.348 1665163.439 1.207163659 1.245431905 1.186873097 1.209460328 1.101632418 1.010640844 1.160462232 1.278049528 1 20.66723236 3.253664694 23.13170261 1.129940667 1.212792375 0.27257393 0.079278775 175.9301061 269430.535 0.024918682 0.032005284 1793.348501 -3.253664694 0.082851708 EVAATEEDVTRLPSPTSPFSS(ph)LSQDQAATSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVAATEEDVTRLPSPTSPFSSLSQDQAATSK 31 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 EVAAT(0.001)EEDVT(0.01)RLPS(0.165)PT(0.165)S(0.165)PFS(0.203)S(0.23)LS(0.062)QDQAATSK 59.598 0.019179 298240000 60066 76594 48909 62787 80492 68710 98341 124060 53356 TRUE FALSE 52128.12591 76090.84897 72561.55599 77043.74799 78890.36668 71353.31816 88803.90496 97530.73444 47048.31446 1.107970105 1.61729171 1.542277483 1.637545338 1.67679475 1.516596694 1.887504493 2.072991042 1 15.52185542 5.257925432 1.202141661 1.685455912 2.16E-12 0.221711466 0.281054258 6.559361793 3.39888313 0.081922589 18.67544559 181102.9115 -5.257925432 -1.685455912 EVADIFNAPS(ph)DDEEFVGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EVADIFNAPSDDEEFVGFR 19 0 Q96GN5-5;Q96GN5-2;Q96GN5 Q96GN5-5 CDCA7L Cell division cycle-associated 7-like protein 1 EVADIFNAPS(1)DDEEFVGFR;EVADIFNAPS(1)DDEEFVGFR;EVADIFNAPS(1)DDEEFVGFR 232.54 8.42E-21 75591000 110880 111654 85055 127423 118023 107390 96125 133368 236418 TRUE FALSE 96226.92707 110920.5375 126187.8825 156356.3397 115674.5732 111521.3628 86802.8123 104848.2911 208468.9334 0.461588811 0.532072265 0.605307853 0.750022256 0.554876793 0.53495435 0.416382484 0.502944441 1 17.66947288 1.235363815 24.99422806 1.000000629 0.544708471 0.720935559 0.089009957 53.81703456 420696.0773 0.166098986 0.023852444 17.19348106 -1.235363815 -0.455292157 EVAWVIFDEIHYMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVAWVIFDEIHYMR 14 0 P42285 P42285 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 ; 176.91 2.16E-06 163743000 398860 388540 225147 275980 330830 332120 340700 414160 324240 FALSE TRUE 346149.6404 385987.6552 334028.8423 338645.4771 324247.1303 344896.8713 307658.9664 325595.107 285908.7166 1.210699851 1.350038081 1.168305906 1.18445314 1.134093196 1.20631814 1.076074105 1.138807907 1 18.12519508 -2 0.113518965 0.221349733 1.432862592 0.598469949 0.057910474 158.829529 1.627644665 30.38386778 2.362168203 0.01 2 1.211512859 EVCGFAPYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 EVCGFAPYER 10 0 Q9Y3U8;J3QSB5 Q9Y3U8 RPL36 60S ribosomal protein L36 0 ;;;;;; 220.39 1.36E-08 9831990000 4898480 5198420 3085370 3439170 4731690 5097540 4733700 5026220 4849800 FALSE TRUE 4251133.457 5164271.237 4577465.252 4220086.113 4637538.626 5293645.662 4274626.503 3951401.967 4276462.169 0.994077181 1.20760363 1.070386004 0.986817127 1.084433451 1.237856306 0.999570751 0.923988524 1 22.02798635 2.014890983 24.95842552 0.95812927 1.0970912 0.344890006 0.08068609 225.8051769 378465.3517 0.032449618 0.021868369 103.4882358 -2.014890983 0.138961931 EVDDFFEQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVDDFFEQEK 10 0 Q9Y5X3;Q5QPE5;A0A087WUY5;Q5QPE4 Q9Y5X3 SNX5 Sorting nexin-5 0 129.16 0.00072253 75700000 75780 69943 62125 74019 67546 57500 81468 96351 106530 FALSE TRUE 65765.481 69483.53983 92168.8578 90826.14526 66201.96675 59712.06221 73567.2459 75747.08845 93936.14476 0.700108368 0.739689073 0.981186294 0.966892409 0.70475499 0.63566652 0.783162286 0.806367865 1 16.51939276 1.235364298 4.483961051 1.018433985 0.791234983 0.264864069 0.110378053 0.330347917 13.84458387 0.241101164 0.030132821 17.19350018 -1.235364298 -0.227199002 EVDDLEQWIAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EVDDLEQWIAER 12 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;;; 351.42 3.53E-71 1139030000 896090 847470 547268 664440 855340 893710 830780 948090 854430 FALSE TRUE 777669.4361 841902.9138 811928.6353 815311.2573 838320.4074 928091.602 750211.0835 745348.3315 753420.2588 1.03218546 1.1174413 1.077657026 1.082146714 1.11268631 1.231837864 0.995740524 0.989286289 1 19.5230953 2.067514338 24.99999684 0.993465274 1.107474353 0.531920392 0.05038952 38.79947639 14366.57388 0.020397784 0.013752181 116.8192297 -2.067514338 0.114009079 EVDEDFDGKLSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVDEDFDGKLSFR 13 1 Q9BUP0;A0A087X1Z2;Q9BUP0-2;Q8WYH2;C9JTV4 Q9BUP0 EFHD1;PP1187 EF-hand domain-containing protein D1 0 79.466 0.018634 95918000 178660 143340 86861 101090 128840 120100 127850 183690 89596 FALSE TRUE 155049.6283 142398.3901 128867.2701 124044.0296 126276.3361 124720.3247 115451.1267 144409.323 79004.06295 1.96255259 1.802418569 1.631147378 1.57009684 1.598352431 1.578657098 1.461331511 1.827872107 1 16.26963923 8 0.383372971 1.485614658 8.558245487 0.399385465 0.201063589 95.79671979 1.388866689 0.207455911 500.5301185 100000000 -8 7.072630829 EVDEDS(ph)EPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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;EVDEDS(1)EPER 196.7 3.45E-07 2162044000 1161445 959676 787913 918382 921458 907079 957879 1008395 1438702 TRUE FALSE 1007957.101 953371.8252 1168950.362 1126914.67 903122.7886 941974.9161 864984.042 792757.5766 1268620.289 0.794530176 0.751502899 0.92143439 0.888299423 0.711893698 0.742519196 0.681830529 0.624897445 1 20.27482889 3.228276699 24.98284889 0.730546547 0.838588427 0.119803911 0.10826464 348.12625 845705.8006 0.03266533 0.037445895 1691.518295 -3.228276699 0.10804188 EVDEDS(ph)EPEREVR ddPTM_MDA-MB-175_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 131.56 7.82E-05 1317280000 1718180 1501720 703560 771900 1423010 1390350 1396630 1464250 405420 TRUE FALSE 1491118.16 1491855.102 1043803.969 947171.6928 1394694.885 1443837.664 1261185.038 1151131.532 357491.7095 4.171056615 4.173118042 2.919799094 2.649492751 3.901334907 4.038800414 3.527872127 3.220023016 1 18.44755026 4.245806075 24.71875473 3.132266444 4.172088029 0.232662457 0.843422308 231.4255843 789513.5084 0.213610913 0.54044408 17611.8945 -4.245806075 1.039821585 EVDEQMLNVQNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EVDEQMLNVQNK 12 0 Q5JP53;P07437;Q5ST81;P68371;Q13885;Q9BVA1 Q5JP53;P68371;Q13885;Q9BVA1 TUBB;TUBB4B;TUBB2A;TUBB2B Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-2B chain 0 ;;;;; 278.83 1.05E-15 1418760000 2381200 1796278 1342585 1614067 1713414 1579778 2067049 2334350 2276890 FALSE TRUE 2066518.387 1784478.132 1991863.597 1980565.582 1679320.414 1640553.082 1866586.906 1835167.418 2007718.658 1.029286837 0.88880886 0.992102947 0.986475657 0.83643214 0.817122994 0.929705414 0.914056066 1 20.93712569 3.265877268 24.99968174 0.899438521 0.969352503 0.272402405 0.060441175 330.2173056 302206.2879 0.017797812 0.022971342 1844.494092 -3.265877268 0.069913982 EVDETRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVDETRK 7 1 Q9UHV9 Q9UHV9 PFDN2 Prefoldin subunit 2 0 88.029 0.030318 293050000 685170 560710 386970 437380 377950 508560 692570 787210 662390 FALSE TRUE 594623.0485 557026.6591 574109.9863 536693.8139 370429.5344 528124.6323 625404.668 618871.2676 584083.0088 1.018045448 0.953677218 0.982925334 0.918865651 0.634207003 0.90419448 1.07074621 1.05956047 1 19.15581389 2.246344363 22.72465247 1.047932874 0.896609934 0.289119512 0.104251279 71.14107406 207697.8508 0.04222566 0.031998137 176.3373717 -2.246344363 -0.15132294 EVDGEGKPYYEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EVDGEGKPYYEVR 13 1 G3V1D3;G3V180;Q9NY33-4;Q9NY33;E9PQ14 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ;;; 109.84 0.0010085 2944760000 2452180 1923500 1357960 1573590 1803540 1469350 2212960 2363700 2190460 FALSE TRUE 2128118.2 1910864.402 2014673.998 1930897.66 1767653.083 1525876.845 1998347.48 1858241.149 1931506.314 1.101791997 0.98931305 1.043058458 0.999684881 0.915168162 0.789993196 1.034605719 0.962068379 1 20.88129496 3.446490945 4.30776938 0.942935905 1.037430078 0.3242382 0.068922259 0.276472153 11.78529151 0.020752897 0.028196538 2795.702434 -3.446490945 0.094494172 EVDGLLTSEPMGS(ph)PVSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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(0.999)PVSSK;EVDGLLTSEPMGS(0.998)PVS(0.002)SK;EVDGLLTSEPMGS(1)PVSSK;EVDGLLTSEPMGS(0.956)PVS(0.035)S(0.009)K 322.83 1.35E-61 3613180000 5709730 4815160 3528400 4484360 4828210 4340020 5807470 6672440 6512590 TRUE FALSE 4955174.714 4783528.897 5234746.042 5502602.477 4732138.067 4506983.378 5244262.453 5245590.631 5742679.029 0.86286813 0.832978628 0.911551214 0.958194329 0.824029698 0.784822442 0.913208352 0.913439634 1 22.4532925 1.315247719 1.643457007 1.034348712 0.867359676 0.421668304 0.049217051 0.938055436 2.691016237 0.24448501 0.014882948 20.66558574 -1.315247719 -0.166989035 EVDILNHVFDDVESFVSR ddPTM_MDA-MB-175_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 0 242.98 4.58E-24 634190000 453160 479760 319410 360160 497500 434970 409740 456670 443690 FALSE TRUE 393273.7578 476608.425 473877.7444 441939.8327 487600.7233 451703.5774 370003.4779 359014.6743 391237.4737 1.005204727 1.218207501 1.211227902 1.129594843 1.246303732 1.1545509 0.945726069 0.917638771 1 18.57768504 2.249091686 6.317037498 0.945544907 1.169000405 0.666474081 0.068623495 0.07794719 12.28530186 0.025627445 0.018725282 177.4564077 -2.249091686 0.223455498 EVDRNEGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVDRNEGLK 9 1 H0Y6T8;Q9NP72;Q9NP72-2;Q5W0J0;A0A087X163;Q9NP72-3 H0Y6T8 RAB18 Ras-related protein Rab-18 0 ; 157.66 6.20E-05 511720000 795050 663530 445700 633600 722080 619650 708480 945350 675760 FALSE TRUE 689982.1281 659171.2277 661242.0108 777468.564 707712.0207 643488.3365 639771.7186 743194.2592 595872.4226 1.157935998 1.106228788 1.109704 1.304756747 1.187690509 1.079909578 1.073672307 1.247237212 1 19.18464395 1.216207575 24.59865678 0.99999923 1.158470595 0.314516857 0.073487127 2015.331549 2217650.585 0.929939698 0.018422477 16.45157853 -1.216207575 0.158471365 EVDRPGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 EVDRPGSK 8 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ;;;;;;; 112.41 0.0027782 8617300000 6720080 5786080 3988620 4686280 4291000 4852360 6480130 7222980 6971190 FALSE TRUE 5832004.401 5748070.859 5917529.973 5750371.499 4205617.495 5039033.429 5851687.99 5678401.936 6147063.86 0.94874635 0.935092101 0.96265959 0.935466367 0.684166879 0.819746393 0.951948462 0.92375841 1 22.55146604 1.506007485 1.702076677 1.002039244 0.884507311 0.147777195 0.084080168 1.197489823 5.305684887 0.208821319 0.026541755 32.06324581 -1.506007485 -0.117531933 EVDWSQNTATFS(ph)PAISPTHPGEGLVLRPLCTADLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVDWSQNTATFSPAISPTHPGEGLVLRPLCTADLNR 36 1 Q96EK6;G3V4W4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 1 EVDWSQNTATFS(1)PAISPTHPGEGLVLRPLCTADLNR 252.14 4.20E-62 189760000 8587.2 8951.9 4305.5 6944.3 15018 8259.9 12573 9431.3 7244.8 TRUE FALSE 7452.379763 8893.094379 6387.654201 8521.109452 14719.17118 8577.663698 11353.6724 7414.489889 6388.327997 1.166561856 1.392084812 0.999894527 1.333855972 2.304072551 1.342708718 1.777252577 1.160630746 1 12.64122267 3.471971518 24.99457265 1.513731141 1.200121462 0.148531032 0.363623483 287.0966214 1393432.44 0.107390296 0.139113355 2964.636959 -3.471971518 -0.313609678 EVDWSQNTATFSPAIS(ph)PTHPGEGLVLRPLCTADLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVDWSQNTATFSPAISPTHPGEGLVLRPLCTADLNR 36 1 Q96EK6;G3V4W4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 1 EVDWSQNTATFS(0.002)PAIS(0.737)PT(0.21)HPGEGLVLRPLCT(0.051)ADLNR 107.38 1.34E-05 162760000 0 0 0 0 0 0 0 0 5543.5 TRUE FALSE 0 0 0 0 0 0 0 0 4888.153745 0 0 0 0 0 0 0 0 1 12.25507395 1.23856059 24.99997459 1.000001086 1.11E-17 1 3.62E-07 2.50E-08 0.502528732 4.17E-07 7.50E-08 17.32050657 -1.23856059 -1.000001086 EVDWSQNTATFSPAISPTHPGEGLVLRPLCTADLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVDWSQNTATFSPAISPTHPGEGLVLRPLCTADLNR 36 1 Q96EK6;G3V4W4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 0 ; 282.06 1.16E-76 2276700000 0 61202 0 0 24940 0 18317 18381 15596 FALSE TRUE 0 60799.96003 0 0 24443.74279 0 16540.62016 14450.36619 13752.25865 0 4.421089044 0 0 1.777434778 0 1.202756622 1.050763119 1 13.74738096 EVDYSGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EVDYSGLR 8 0 Q9UKY7;Q9UKY7-2;H0Y8K3 Q9UKY7 CDV3 Protein CDV3 homolog 0 ;; 183.74 0.00051576 1478670000 709030 729520 432610 522290 695710 700160 627520 706910 668550 FALSE TRUE 615329.889 724727.7351 641821.643 640883.9272 681866.7321 727095.6083 566663.207 555742.7977 589514.7806 1.043790435 1.229363129 1.08872867 1.087138013 1.156657567 1.233379776 0.96123664 0.942712237 1 19.16916846 2.218529644 24.96191715 0.962437025 1.139957271 0.638006145 0.060977112 137.1203964 170873.5055 0.023978012 0.016189979 165.3977679 -2.218529644 0.177520246 EVEDKES(ph)EGEEEDEDEDLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 EVEDKESEGEEEDEDEDLSK 20 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 EVEDKES(1)EGEEEDEDEDLSK;EVEDKES(1)EGEEEDEDEDLSK;EVEDKES(1)EGEEEDEDEDLSK;EVEDKES(1)EGEEEDEDEDLSK;EVEDKES(1)EGEEEDEDEDLSK;EVEDKES(1)EGEEEDEDEDLSK;EVEDKES(1)EGEEEDEDEDLSK 335.77 3.16E-80 5189190000 5586910 3108522 3385156 2700655 2986538 2499288 4421140 5118540 4999480 TRUE FALSE 4848585.688 3088101.914 5022228.764 3313879.995 2927111.737 2595437.227 3992378.523 4023980.054 4408447.17 1.099839808 0.700496523 1.139228524 0.7517114 0.663977955 0.588741824 0.905620135 0.912788539 1 22.07183914 4.760076056 23.10835944 0.836617383 1.09984057 0.204679518 0.165265916 3354.252789 3602425.703 0.04131938 1.638014732 57554.07208 -4.760076056 0.263223188 EVEEDEYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EVEEDEYK 8 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;; 168.72 0.00071006 1686550000 2290840 1833220 1731270 1849440 1760980 1873700 2246600 2177060 1874380 FALSE TRUE 1988099.69 1821177.457 2568517.963 2269383.619 1725939.943 1945782.451 2028725.078 1711512.661 1652792.932 1.202872817 1.101878779 1.55404704 1.373059852 1.04425661 1.177269345 1.227452658 1.035527578 1 20.65647456 3.237982751 24.99999871 1.103039282 1.310821533 0.384730516 0.132481205 17.76463794 768554.1319 0.041293465 0.049705014 1729.747658 -3.237982751 0.20778225 EVEELEQLTQQLMQDMEHPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 EVEELEQLTQQLMQDMEHPQR 21 0 Q15942;Q15942-2;H0Y2Y8;C9JJK5 Q15942 ZYX Zyxin 0 ;;;;;;; 245.66 3.09E-30 1501537000 2361510 2264456 1486168.2 1748125.6 2256937 2221080 2297284.9 2416099 2192151.4 FALSE TRUE 2049430.47 2249580.639 2204884.112 2145064.236 2212028.369 2306526.385 2074494.564 1899435.031 1932997.759 1.060234271 1.163778193 1.140655287 1.1097086 1.144351233 1.193238003 1.073200708 0.982636955 1 20.88240853 1.938923463 3.811733118 0.994273704 1.136288894 0.739313836 0.035058423 0.106332299 2.925983471 0.018804405 0.009309084 86.88073029 -1.938923463 0.14201519 EVEERPAPTPWGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EVEERPAPTPWGSK 14 1 A0A1W2PNV4;C9JEY1;C9K057;O15143 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 ;;; 214.45 6.27E-12 3786670000 2775410 2572400 1704540 2259840 2499010 2198110 2821390 3217250 3054610 FALSE TRUE 2408632.537 2555501.735 2528861.245 2772971.211 2449284.59 2282672.714 2547772.032 2529266.124 2693497.486 0.894239757 0.948767077 0.938876408 1.029505773 0.909332421 0.847475346 0.945897312 0.939026726 1 21.36104929 1.160495727 2.571694608 1.026604263 0.931783903 0.179655139 0.046099522 1.371467426 8.380047423 0.314154669 0.012534293 14.47090614 -1.160495727 -0.09482036 EVEERPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVEERPEK 8 1 Q32MZ4-3 Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 86.67 0.014472 207700000 641220 539690 514240 555530 463750 634580 588370 647720 882240 FALSE TRUE 556481.1524 536144.7409 762928.184 681671.5772 454522.2823 658992.7032 531309.968 509210.1186 777942.5923 0.715324187 0.689182912 0.980699851 0.876249204 0.584261984 0.847096829 0.682968092 0.65456002 1 19.56930417 EVEERS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVEERSR 7 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;Q9UKE5-6;Q9UKE5-2;Q9UKE5-4;Q9UKE5 Q04637-9;Q9UKE5-6 EIF4G1;TNIK Eukaryotic translation initiation factor 4 gamma 1;TRAF2 and NCK-interacting protein kinase 1 EVEERS(1)R;EVEERS(1)R 69.915 0.035395 161565000 246594 304800 89531 87355 194047 360510 332640 346200 12022.3 TRUE FALSE 214005.9781 302797.7487 132828.4911 107190.2879 190185.8443 374379.053 300380.624 272167.8241 10601.03739 20.18726755 28.56302997 12.52976347 10.11130175 17.94030502 35.31532238 28.33502165 25.67369722 1 13.37191783 -1.168554626 9.19E-16 7.047776354 34.62520282 0 10.19416845 0 0.125001088 176010953.3 176010951.1 0.067833679 1.168554626 27.57742647 EVEGERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EVEGERR 7 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;Q5VU61;P06753-3;P06753-4 P06753-2;P06753-3 TPM3 Tropomyosin alpha-3 chain 0 ;;; 143.11 0.0039189 1103370000 3175340 2949740 1363516 1415100 1860290 2717300 2671530 3139770 480079 FALSE TRUE 2755710.774 2930362.964 2022916.898 1736420.083 1823273.869 2821836.289 2412445.432 2468354.619 423324.6075 6.509687187 6.92225992 4.778642352 4.101864273 4.307034923 6.665892412 5.698807461 5.83087913 1 18.69140483 4.235757259 24.91299129 4.833912763 6.71597395 0.238743722 1.516526752 100.3717169 892023.4222 0.383510411 0.859607427 17209.06436 -4.235757259 1.882061186 EVELVS(ph)E ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVELVSE 7 0 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 EVELVS(1)E;EVELVS(1)E 117.04 0.0055819 283670000 559530 556530 343700 416470 522780 575990 468670 610880 610960 TRUE FALSE 485586.6928 552874.1178 509914.4696 511035.8788 512377.7008 598148.708 423218.4555 480248.0659 538733.0048 0.901349441 1.026248834 0.946506832 0.9485884 0.951079099 1.110287847 0.78558108 0.891439844 1 19.03921093 2.226715275 24.99851024 0.887704464 0.978391133 0.23206689 0.075518035 312.9133857 660369.5165 0.029690094 0.020198465 168.5447679 -2.226715275 0.090686669 EVEPEPTEDKDLEADEEDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EVEPEPTEDKDLEADEEDTR 20 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;;;;; 253.11 3.91E-36 6938650000 7898710 6453520 6025590 6542730 6580280 5288670 7578100 8819410 8468640 FALSE TRUE 6854875.461 6411126.402 8939585.478 8028356.846 6449345.302 5492128.557 6843177.028 6933447.804 7467487.027 0.917962822 0.858538673 1.197134384 1.075108242 0.863656713 0.735472126 0.916396239 0.928484747 1 22.8321914 3.228245258 24.82254298 0.888165376 1.014421819 0.235886135 0.110310753 299.6308132 721020.232 0.035543467 0.040746318 1691.395841 -3.228245258 0.126256443 EVESPYEVHDYIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVESPYEVHDYIR 13 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;Q6Y7W6-4;Q6Y7W6-5 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 0 83.692 0.010087 447870000 107950 146900 58323 72456 127330 145640 116750 96787 91348 FALSE TRUE 93684.13399 145935.0042 86528.19788 88908.24222 124796.3821 151242.865 105427.603 76089.85325 80548.9435 1.163070922 1.811755659 1.07423132 1.103779123 1.549323637 1.877651754 1.308863883 0.944641232 1 16.29757805 1.826586644 4.400622582 0.975287535 1.432856523 0.315618133 0.273034454 0.254208751 7.973776427 0.159067569 0.074835922 67.07900997 -1.826586644 0.457568988 EVFEDAAEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EVFEDAAEIR 10 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;;;; 196.79 7.61E-07 6138090000 6997400 6063900 3453460 4260130 5579540 5274780 5304100 6194820 5546450 FALSE TRUE 6072675.861 6024065.842 5123564.807 5227457.629 5468518.07 5477704.2 4789709.198 4870105.951 4890755 1.241664295 1.231725131 1.047602018 1.068844714 1.118133718 1.120011982 0.979339427 0.995777943 1 22.22162576 8 0.242874226 0.963850877 2.745128182 0.711743875 0.049416274 49.30684389 0.778894077 0.190176176 34.51664 100000000 -8 1.781277306 EVFEFRPELVNDDDEEADDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EVFEFRPELVNDDDEEADDTR 21 1 Q8WU90;Q8WU90-2 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 0 ;;;; 226.12 2.32E-25 2166730000 1446080 1296620 1072570 1174920 1300730 1353770 1263850 1531570 1796940 FALSE TRUE 1254976.864 1288102.418 1591268.44 1441703.544 1274848.018 1405850.408 1141282.022 1204055.674 1584507.8 0.792029464 0.812935359 1.004266713 0.90987469 0.804570364 0.887247389 0.72027542 0.759892551 1 20.59560333 3.232319016 24.73006788 0.819167448 0.883894341 0.040428513 0.093974191 328.7552622 1302570.782 0.028970504 0.033671428 1707.33607 -3.232319016 0.064726893 EVFESMNLTAYDLSVDTLDVHADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVFESMNLTAYDLSVDTLDVHADR 24 0 A0A5F9UK94;H0Y360;Q01433-2;Q01433;A0A590UK85;Q01433-5;A0A590UJY6;Q01433-3;Q01433-4;A0A590UJX5 A0A5F9UK94 AMPD2 AMP deaminase 2 0 54.521 0.051129 0 13757 9895.4 7920.8 8626 9301.2 9434.8 10210 12863 17570 FALSE TRUE 11938.97759 9830.396466 11751.32537 10584.66514 9116.124317 9797.762861 9219.835771 10112.34755 15492.89462 0.770609876 0.634509994 0.758497728 0.683194807 0.588406785 0.632403634 0.595100916 0.652708729 1 13.91931909 1.237830951 24.97614571 1.000000397 0.659844505 0.750122367 0.060816213 8.88104009 303779.9094 0.087170527 0.014974438 17.2914316 -1.237830951 -0.340155892 EVFLPSTPGLGMHVEVKDPDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVFLPSTPGLGMHVEVKDPDGK 22 1 Q7Z7H5-3;Q7Z7H5;F8W7F7 Q7Z7H5-3 TMED4 Transmembrane emp24 domain-containing protein 4 0 151.45 2.92E-08 248220000 249330 160330 157350 153450 198870 132320 213150 309090 190900 FALSE TRUE 216380.4088 159276.7817 233444.9863 188293.1678 194912.8761 137410.436 192478.7458 242993.5088 168332.0195 1.285438204 0.946206088 1.386812723 1.118582005 1.157907311 0.816305991 1.143447019 1.443537062 1 17.3609501 1.976012752 24.91146641 1.26546246 1.112625759 0.035502211 0.189973776 1576.14201 1636867.342 0.083643106 0.048579591 94.62649453 -1.976012752 -0.152836701 EVFQIASNDHDAAINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVFQIASNDHDAAINR 16 0 Q9UKG1;C9JAB0 Q9UKG1 APPL1 DCC-interacting protein 13-alpha 0 ; 227 5.43E-15 851740000 783750 887210 475090 557560 760150 821680 830050 842120 855660 FALSE TRUE 680175.4517 881381.8591 704845.1131 684162.5198 745024.5022 853290.5613 749551.8788 662039.1914 754504.8496 0.901485858 1.168159303 0.934182349 0.906770209 0.987435008 1.130927868 0.993435469 0.877448557 1 19.52517065 1.973709307 23.15096214 0.931611962 1.008657977 0.077668243 0.091812134 617.4165327 543679.357 0.041271797 0.023951393 94.12593574 -1.973709307 0.077046015 EVGGQGAGNTGGLEPVHPASLPDSSLATSAPLCCTLCHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVGGQGAGNTGGLEPVHPASLPDSSLATSAPLCCTLCHER 40 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 0 ; 260.93 1.93E-63 747450000 80819 76438 55943 56752 74810 72958 67747 82405 65841 FALSE TRUE 70138.56438 75935.87374 82997.22192 69638.409 73321.42736 75764.74147 61176.90637 64783.33203 58057.35199 1.208090999 1.30794587 1.429572984 1.199476149 1.262913737 1.304998228 1.053732288 1.115850617 1 15.82519115 2.238271016 24.99999998 1.068770082 1.288131956 0.70937735 0.068925921 4.226149184 364757.3049 0.026945349 0.019455286 173.0896166 -2.238271016 0.219361874 EVGKGNEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVGKGNEGK 9 1 Q9NZW4 Q9NZW4 DSPP Dentin sialophosphoprotein;Dentin phosphoprotein;Dentin sialoprotein 0 69.954 0.049048 2005500000 2514300 2523100 1041600 1540500 3154300 4139400 2277600 2321100 2346600 FALSE TRUE 2182028.885 2506525.59 1545321.244 1890294.07 3091535.601 4298645.397 2056718.703 1824750.828 2069187.621 1.05453409 1.211357329 0.746825096 0.913544065 1.494081817 2.077455593 0.993974003 0.881868231 1 20.98063304 3.263871403 24.96703842 1.255761414 0.981211643 0.154301818 0.353330186 555.8097418 548257.3658 0.114925346 0.148309708 1835.994613 -3.263871403 -0.274549771 EVGVYEALKDDSWLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EVGVYEALKDDSWLK 15 1 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 0 ;;; 168.41 1.07E-08 1591199000 3071430 2373090 1899201 1927460 1985810 1591618 2997030 3452100 2974130 FALSE TRUE 2665532.743 2357501.016 2817660.956 2365119.252 1946296.266 1652848.574 2706378.492 2713895.279 2622531.74 1.016396753 0.89894089 1.074404902 0.901845807 0.742144027 0.630249217 1.031971683 1.034837916 1 21.3225288 EVHDELEDLPS(ph)PPPPLS(ph)PPPTTSPHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EVHDELEDLPSPPPPLSPPPTTSPHK 26 0 F5H039;Q9NQX3;Q9NQX3-2;H0YJ30;G3V582 F5H039 GPHN Gephyrin;Molybdopterin adenylyltransferase;Molybdopterin molybdenumtransferase 2 EVHDELEDLPS(0.974)PPPPLS(0.869)PPPT(0.052)T(0.052)S(0.052)PHK;EVHDELEDLPS(1)PPPPLS(0.993)PPPT(0.002)T(0.002)S(0.002)PHK;EVHDELEDLPS(0.999)PPPPLS(0.823)PPPT(0.064)T(0.059)S(0.055)PHK 140.27 1.51E-07 469600000 324937 301731 199404 269708 358356 325742 371351 439886 555561 TRUE FALSE 281995.7522 299748.9092 295836.4414 330949.3236 351225.4167 338273.5055 335337.4372 345819.8021 489883.2115 0.575638735 0.611878305 0.603891773 0.6755678 0.716957447 0.690518674 0.684525269 0.705922951 1 18.90207833 -0.202980428 1.169772943 10 0.646064563 0.864142961 0.043191064 15.99427684 1.014588728 363.8686236 0.01468234 0.626642105 0.202980428 -9.353935437 EVHELYK ddPTM_MDA-MB-175_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 ; 117.16 0.0052935 928530000 2783600 2326400 1683050 1997090 2172500 1988700 2625100 2871100 2785300 FALSE TRUE 2415740.207 2311117.725 2496978.609 2450559.808 2129271.5 2065206.576 2370518.206 2257137.608 2456025.007 0.983597561 0.940999265 1.01667475 0.997774779 0.866958396 0.840873595 0.965184882 0.919020613 1 21.22789382 3.260906133 24.98789681 0.918115732 0.98391524 0.321814694 0.047856198 303.9487926 339888.7509 0.014257978 0.018392749 1823.501536 -3.260906133 0.065799508 EVIEIEDAS(ph)PTKCPITTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVIEIEDASPTKCPITTK 18 1 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 EVIEIEDAS(0.999)PT(0.001)KCPITTK;EVIEIEDAS(0.982)PT(0.018)KCPITTK 171.15 8.48E-12 223660000 841310 513860 430920 507620 575100 434540 637150 805770 798880 TRUE FALSE 730128.7519 510484.4198 639314.3533 622882.8795 563656.6352 451257.035 575359.2911 633462.356 704437.3165 1.036470861 0.724669758 0.907553218 0.884227546 0.800151585 0.640592178 0.816764356 0.899245882 1 19.42611181 1.431311441 2.72677236 1.003478695 0.823394408 0.210790101 0.105502606 0.491394982 5.875682848 0.168572251 0.027486113 26.99674726 -1.431311441 -0.180084287 EVIITPNSAWGGEGSLGCGIGYGYLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVIITPNSAWGGEGSLGCGIGYGYLHR 27 0 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 0 199.75 5.13E-25 400620000 188740 218440 114010 97439 168580 164890 148960 182710 133660 FALSE TRUE 163797.5308 217005.0533 169145.6173 119564.0142 165225.5878 171233.425 134513.8821 143638.8884 117858.8671 1.389776899 1.841228061 1.435153939 1.014467704 1.401893569 1.452868412 1.141313212 1.218736375 1 16.84670078 8 0.059622025 1.66E-09 3.967378719 0.379628819 0.195075941 835.1240779 4.829230573 80.69450544 315.4358161 99999999.99 -8 3.967378718 EVIKPYDWTYTTDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVIKPYDWTYTTDYK 15 1 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 ; 173.58 8.77E-07 1217080000 1353520 1018680 874330 971780 993450 713000 1352890 1860410 1467700 FALSE TRUE 1174648.903 1011988.224 1297158.912 1192437.502 973682.2887 740429.5714 1221686.936 1462575.799 1294190.178 0.907632373 0.781947075 1.002293894 0.921377339 0.752348693 0.572118058 0.943977907 1.13010887 1 20.3036182 2.000048221 24.99999996 1.063156597 0.824467299 0.41766391 0.118832678 1.55671839 806690.4446 0.051562618 0.034366384 100.0111039 -2.000048221 -0.238689298 EVIKS(ph)PTASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVIKSPTASR 10 1 O94885 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 EVIKS(0.969)PT(0.031)ASR 104.41 0.0016264 333410000 396630 324790 217330 232810 339730 274900 342730 444420 357310 TRUE FALSE 344214.3406 322656.4331 322431.5149 285673.0688 332970.0377 285475.5809 309492.0974 349384.2415 315069.2188 1.092503869 1.024081103 1.023367234 0.906699391 1.056815511 0.906072583 0.982298742 1.108912647 1 18.26530929 0.900703095 18.77295865 0.000193196 1.013676948 0.00317215 0.067785687 1070.989862 264998.1934 14291.10615 0.016287564 7.956152433 -0.900703095 1.013483751 EVIKSPTAS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVIKSPTASR 10 1 O94885 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 EVIKS(0.135)PT(0.111)AS(0.754)R 69.815 0.066838 0 101660 86368 57213 57480 85471 70355 97185 110270 92383 TRUE FALSE 88225.37343 85800.64292 84881.39817 70531.71253 83770.29432 73061.60238 87760.01366 86689.61862 81461.58698 1.083030379 1.053265055 1.04198066 0.865827872 1.028341055 0.896884103 1.077317751 1.064177876 1 16.3138323 -0.826917766 17.56429714 0.436143672 1.013755398 0 0.074298725 0 0 0 0.016857267 0.148964312 0.826917766 0.577611725 EVLAELEALER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EVLAELEALER 11 0 Q16822;Q16822-3;H0YML5 Q16822 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 0 ;;; 164.43 5.30E-05 84509000 178645 202611 124211 180873 201913 215566 196707 228616 179627 FALSE TRUE 155036.6106 201280.035 184279.8551 221942.9791 197895.3263 223858.9635 177630.3854 179728.2475 158391.7007 0.978817766 1.270773873 1.163443882 1.401228588 1.249404643 1.413325083 1.121462707 1.13470748 1 17.27313722 1.620074965 1.81021417 1.010291004 1.247666415 0.262310213 0.125984365 0.53337278 3.1925496 0.186533599 0.035478971 41.69413466 -1.620074965 0.237375411 EVLAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVLAGR 6 0 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 101.33 0.085259 197330000 369690 301180 243960 290140 287760 285480 292420 331380 442930 FALSE TRUE 320834.5298 299201.5287 361939.872 356020.7215 282034.139 296462.6003 264061.1534 260516.9658 390567.32 0.821457693 0.766069032 0.92670291 0.911547647 0.722114024 0.75905634 0.676096386 0.667021925 1 18.57521171 3.227740994 24.98920297 0.745681076 0.855007417 0.151827067 0.102097116 334.6192971 772841.5159 0.030954192 0.035438918 1689.433083 -3.227740994 0.109326341 EVLAGRPLFPHVLCHNCAVEFNFGQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 106.43 0.00194 581755000 286068 239783 117430 123186 218273 194699 247495 286418 68026 FALSE TRUE 248263.389 238207.8497 174219.5408 151157.2641 213929.7943 202189.1965 223492.973 225169.7396 59984.04378 4.138823817 3.971186914 2.904431409 2.519957885 3.566445022 3.37071634 3.725873731 3.753827275 1 15.87229116 4.28820394 6.671295848 3.105822683 4.07472519 0.222522391 0.810807133 0.334198781 33.29958138 0.200422209 0.53154826 19417.97511 -4.28820394 0.968902507 EVLAS(ph)PDRLWGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EVLASPDRLWGSR 13 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 EVLAS(1)PDRLWGSR;EVLAS(1)PDRLWGSR;EVLAS(1)PDRLWGSR 207.79 3.09E-08 441298000 251504 237207 134536 197808 250680 240503 231594 275290 260706 TRUE FALSE 218267.1092 235648.7716 199598.0596 242723.3297 245691.9584 249755.306 209134.0495 216421.3758 229885.6337 0.949459545 1.025069587 0.868249383 1.055843838 1.06875734 1.086432858 0.909730835 0.941430625 1 17.81055678 4.799218635 20.23560285 0.989499971 0.949456286 0.034526991 0.070577109 28782.98502 9598248.962 0.018011553 20.01631599 62982.31716 -4.799218635 -0.040043685 EVLASHDSSVVPLDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EVLASHDSSVVPLDAR 16 0 Q9Y2V7;Q9Y2V7-2 Q9Y2V7 COG6 Conserved oligomeric Golgi complex subunit 6 0 ;; 150.05 2.47E-08 253920000 232087 276689 83640 137589 340810 352599 255098 272021 289238 FALSE TRUE 201416.1149 274871.4117 124088.5838 168830.6854 334028.5478 366163.7117 230358.6352 213851.426 255044.6131 0.789728951 1.077738551 0.486536776 0.661965306 1.309686739 1.435684946 0.903209177 0.838486347 1 17.9603901 3.256402448 24.99976952 1.067395859 0.758013108 0.356712406 0.227155313 340.4765725 477069.0638 0.072726856 0.093685028 1804.689319 -3.256402448 -0.309382751 EVLDEDT(ph)DEEKETLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EVLDEDTDEEKETLK 15 1 Q9Y3P9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 1 EVLDEDT(1)DEEKETLK;EVLDEDT(1)DEEKETLK;EVLDEDT(1)DEEKETLK;EVLDEDT(1)DEEKETLK 215.57 3.76E-12 900920000 633880 404456 405816 401047 414772 332211 615450 722690 678070 TRUE FALSE 550111.152 401799.1019 602069.975 492110.851 406518.8487 344991.3721 555763.7537 568148.3675 597909.3371 0.920057805 0.672006736 1.006958643 0.823052628 0.679900486 0.576996128 0.929511749 0.950224946 1 19.18956721 2.026575203 24.89566557 0.962050621 0.780222599 0.32408001 0.12358251 243.0854745 227721.5486 0.051399278 0.034652268 106.3102655 -2.026575203 -0.181828022 EVLDQVCYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVLDQVCYR 9 0 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 ; 126.07 0.0011258 865200000 385380 373010 249910 292940 362370 336550 380950 458640 374040 FALSE TRUE 334451.0566 370559.6727 370767.3119 359456.5043 355159.546 349497.2963 344005.5276 360563.4051 329821.4173 1.014036806 1.123516101 1.124145651 1.089851918 1.076823782 1.059656159 1.043005425 1.093207979 1 18.33132556 2.91670017 2.329985779 1.05489221 1.092871801 0.183260762 0.03767242 0.538897044 5.787822219 0.013137636 0.013564606 825.4678638 -2.91670017 0.037979591 EVLEALGEVMVSRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVLEALGEVMVSRPR 15 1 Q8NE71;Q8NE71-2;H0YGW7;A0A0G2JIC2 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 178.23 6.57E-07 133600000 161670 137270 100030 121320 139450 137020 130010 153870 118470 FALSE TRUE 140304.8999 136368.2643 148404.8426 148867.5603 136675.2178 142291.2481 117401.6502 120966.0979 104464.6116 1.343085451 1.305401535 1.420623122 1.425052542 1.308339885 1.362100006 1.123841351 1.157962454 1 16.67265477 1.96455815 1.133071711 1.02138746 1.371915974 0.827171737 0.057146279 0.247746963 0.542213212 0.080930041 0.020176638 92.16332837 -1.96455815 0.350528514 EVLEGLDYLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EVLEGLDYLHR 11 0 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 0 ;;; 240.37 1.11E-15 2223680000 2083330 2188180 1636540 1861140 2193050 2310480 2028150 2498760 2840040 FALSE TRUE 1808012.662 2173805.702 2427976.218 2283740.283 2149412.596 2399365.661 1831460.325 1964419.619 2504293.707 0.721965102 0.868031452 0.969525344 0.911929889 0.858290938 0.958100743 0.731328087 0.784420619 1 21.25597234 1.221318906 24.56988411 1.000000554 0.851571192 0.234163653 0.084974733 1445.738516 2060074.134 0.618603841 0.021851935 16.64634558 -1.221318906 -0.148429362 EVLEGLEYLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVLEGLEYLHK 11 0 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 0 ; 212.82 4.64E-09 356540000 599630 488350 358520 456860 475260 450460 526490 631030 621670 FALSE TRUE 520387.3762 485141.9967 531901.4712 560597.0457 465803.2558 467789.4877 475431.0808 496089.1452 548176.8808 0.949305588 0.885009955 0.970309931 1.022657221 0.849731669 0.85335501 0.867295024 0.904980058 1 19.06428196 3.221459807 24.99964758 0.892141659 0.952654887 0.246783983 0.053247549 373.1265206 545471.6107 0.016810629 0.019108791 1665.174713 -3.221459807 0.060513228 EVLHGNQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 EVLHGNQR 8 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;;;;;; 147.19 0.00054134 11979693000 9570183 9519895 6013531 6668615 7357088 8573064 9288860 9340716 8912566 FALSE TRUE 8305459.069 9457358.183 8921694.706 8182825.959 7210696.343 8902875.32 8388027.787 7343276.573 7858932.601 1.056817699 1.203389654 1.135229828 1.041213403 0.917515992 1.132835179 1.067324052 0.934385997 1 22.90590195 3.674586442 4.154812084 1.009261547 1.139704784 0.383951188 0.069875137 0.219145932 7.574990218 0.019813399 0.030936671 4727.009139 -3.674586442 0.130443237 EVLLLHNNDQDNALEDLMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVLLLHNNDQDNALEDLMAR 20 0 A0A0D9SG79;Q9NZ09-2;Q9NZ09;Q9NZ09-3;Q9NZ09-4 A0A0D9SG79 UBAP1 Ubiquitin-associated protein 1 0 205.02 9.06E-22 56410000 115680 115080 111310 113790 135640 141420 147560 175930 140350 FALSE TRUE 100392.5949 114324.0319 165139.8883 139627.7587 132941.0294 146860.5189 133249.6539 138308.7386 123757.9829 0.811200963 0.92377097 1.334377666 1.12823234 1.07420165 1.186675118 1.076695424 1.11757428 1 16.91716206 4.450174461 14.14641648 1.127002461 0.839322857 0.622344257 0.087492823 0.970488785 509.3108908 0.021091018 0.055943221 28195.15333 -4.450174461 -0.287679604 EVLSEPWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVLSEPWR 8 0 P50416;P50416-2 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 ; 111.01 0.007715 639620000 986580 1002180 692740 1022980 1422840 1639170 774500 1413790 1429260 FALSE TRUE 856200.9533 995596.6136 1027751.381 1255263.244 1394528.268 1702229.931 699389.1092 1111462.011 1260294.511 0.679365772 0.789971395 0.815485089 0.996007864 1.106509832 1.350660433 0.55494101 0.881906571 1 20.26532948 4.008751326 2.431678105 0.964312086 0.727873092 0.218534069 0.198033434 0.53510618 6.290118434 0.05847835 0.142444368 10203.55068 -4.008751326 -0.236438993 EVLT(ph)PESDISIAHVLAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVLTPESDISIAHVLAAR 18 0 Q17RN3 Q17RN3 FAM98C Protein FAM98C 1 EVLT(0.978)PES(0.022)DISIAHVLAAR 178.77 3.20E-13 16882000 23059 25277 11869 18947 23127 29871 25012 25430 25284 TRUE FALSE 20011.69473 25110.95372 17608.8881 23249.20594 22666.81795 31020.1567 22586.34009 19991.9924 22294.95432 0.897588505 1.126306579 0.789814944 1.042801237 1.016679273 1.391353229 1.013069583 0.896704793 1 14.44442962 4.782054376 20.92833192 1.026006347 0.897585005 0.068971617 0.155369279 9984.562651 4803485.397 0.038900771 10.20071414 60541.66718 -4.782054376 -0.128421341 EVLTPESDISIAHVLAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EVLTPESDISIAHVLAAR 18 0 Q17RN3 Q17RN3 FAM98C Protein FAM98C 0 ;; 200.94 1.46E-15 219358000 66869 54922 37646 50429 54058 52479 57756 65345 56834 FALSE TRUE 58032.09223 54561.21377 55851.73152 61879.67521 52982.35156 54497.90109 52154.83201 51371.48027 50115.14927 1.157975045 1.088716976 1.114468027 1.234749893 1.057212287 1.087453632 1.040699924 1.025068887 1 15.61295916 2.483073757 1.217011287 1.013018017 1.138491515 0.57784292 0.044385456 0.350830871 1.077058342 0.030535206 0.017807895 304.1401506 -2.483073757 0.125473498 EVLYDS(ph)EGLS(ph)GEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVLYDSEGLSGEER 14 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 EVLY(0.009)DS(0.991)EGLS(1)GEER;EVLY(0.002)DS(0.998)EGLS(1)GEER 75.968 0.042064 1425520000 416290 367290 252050 289930 357480 365630 344100 328440 375660 TRUE FALSE 361276.2218 364877.2478 373942.2231 355763.0378 350366.8474 379696.0227 310729.235 258205.6619 331249.9028 1.090645518 1.101516543 1.128882514 1.074001939 1.057711548 1.14625248 0.938050796 0.77948902 1 18.33756051 2.098055193 4.855133864 0.869784211 1.097383194 0.70780116 0.058845868 0.091801771 3.624733641 0.023769173 0.015551041 125.3300442 -2.098055193 0.227598983 EVMNADDPDLQRPDEEAIKEITEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVMNADDPDLQRPDEEAIKEITEK 24 2 Q13573;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 0 156.28 1.66E-08 65473000 124820 93355 75893 79661 73969 52876 116420 152410 63798 FALSE TRUE 108324.7207 92741.74486 112595.1086 97749.24759 72497.16162 54910.17394 105129.6063 119818.3076 56255.87312 1.925571762 1.648570002 2.001481844 1.737582979 1.288703874 0.976078957 1.868775658 2.129880862 1 15.7797161 3.466038873 24.28748026 1.541843107 1.842875511 0.191360305 0.365176527 352.728475 773013.9164 0.115541164 0.149316473 2924.414128 -3.466038873 0.301032405 EVMS(ph)PTGSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVMSPTGSAR 10 0 H0YHB7;O43347 H0YHB7 MSI1 RNA-binding protein Musashi homolog 1 1 EVMS(0.965)PT(0.035)GSAR;EVMS(0.99)PT(0.01)GS(0.001)AR 108.24 0.003109 0 253610 223823 150724 155727 207358 217199 218990 239970 213249 TRUE FALSE 220094.7959 222352.692 223614.6305 191087.1955 203231.9815 225554.7861 197752.3835 188654.2829 188038.9462 1.170474524 1.182482122 1.18919317 1.016210734 1.08079728 1.199511009 1.051656519 1.00327239 1 17.52067197 -2 0.176663259 0.186500655 1.23030702 0.496363913 0.057316323 103.8080312 1.449014615 28.05108859 0.581927923 0.01 2 1.043806365 EVMSLHEASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVMSLHEASR 10 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 128.51 0.0003276 198490000 206840 241580 97190 155490 217540 251500 210490 208740 180210 FALSE TRUE 179505.5699 239993.0451 144191.4091 190796.381 213211.3796 261175.3677 190076.7122 164102.5754 158905.7791 1.129635253 1.510285192 0.90740192 1.200688748 1.341747171 1.643586339 1.196159846 1.032703633 1 17.27781207 1.805324366 3.88875105 1.015426693 1.288510213 0.232701451 0.199915603 0.317209245 8.561852934 0.124409262 0.054746102 63.87403707 -1.805324366 0.27308352 EVMVDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVMVDDR 7 0 P51149;C9J592;C9J8S3;C9IZZ0;C9J4V0;C9J7D1 P51149 RAB7A Ras-related protein Rab-7a 0 ; 86.953 0.045825 458619000 989530 972410 660690 850100 992600 1144440 827280 1077010 1447580 FALSE TRUE 858761.1034 966022.1747 980201.8939 1043128.198 972849.202 1188467.347 747050.5129 846699.7928 1276448.741 0.672773669 0.756804518 0.767913244 0.817211192 0.762152972 0.931073304 0.585256962 0.663324555 1 20.28370417 4.755310643 2.764626938 0.772225979 0.651733115 0.07433149 0.118356459 1.568006427 15.83346777 0.030176798 0.437823499 56925.99668 -4.755310643 -0.120492864 EVNKFQMAYSNLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVNKFQMAYSNLLR 14 1 P37108 P37108 SRP14 Signal recognition particle 14 kDa protein 0 ; 251.87 3.14E-24 1497890000 1915040 1603880 967710 1054010 1815230 1531380 1859690 2266750 668040 FALSE TRUE 1661962.612 1593344.007 1435697.793 1293339.08 1779110.474 1590293.18 1679337.55 1782023.152 589065.0722 2.82135657 2.704869261 2.43724821 2.195579302 3.020227405 2.699690161 2.850852358 3.025171982 1 19.16806749 1.232404135 24.99969325 0.999997163 2.723019926 0.822678302 0.250859186 89.57382623 363697.3471 0.590448353 0.065618476 17.07670733 -1.232404135 1.723022763 EVPAESVTVWIDPLDATQEYTEDLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVPAESVTVWIDPLDATQEYTEDLRK 26 1 Q9NX62;H0YB38 Q9NX62 IMPAD1 Inositol monophosphatase 3 0 ; 167.99 1.57E-11 115466000 87129 85604 71750 71737 77796 77944 84409 105651 94621 FALSE TRUE 75614.68189 85041.66169 106448.54 88025.98228 76248.01181 80942.55612 76223.02817 83058.35583 83435.01317 0.90627039 1.019256286 1.275825771 1.055024491 0.913861087 0.970126965 0.913561648 0.99548562 1 16.34836531 3.356059599 6.513586025 0.96085056 1.07862551 0.23419186 0.093978882 0.305774312 16.23425393 0.027914287 0.036089156 2270.176369 -3.356059599 0.11777495 EVPAHSTEVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EVPAHSTEVGR 11 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ;;;; 169.65 1.66E-05 2050090000 948219 881197 434216 603487 914835 1006090 844326 901088 913595 FALSE TRUE 822909.4567 875408.3589 644204.31 740517.9471 896631.5733 1044794.933 762443.3945 708397.3435 805590.8399 1.021498031 1.086666228 0.799666876 0.919223395 1.113011133 1.296930007 0.94644 0.879351289 1 19.61968775 2.02540639 24.99892796 0.92560886 1.036371828 0.10787981 0.130784682 478.1069037 470437.1058 0.057520441 0.038778785 106.0245384 -2.02540639 0.110762968 EVPCYVFDEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVPCYVFDEELR 12 0 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 0 121.9 0.00085632 60152000 25248 24351 14803 17842 24425 26878 21577 26355 23142 FALSE TRUE 21911.41283 24191.03668 21961.78031 21893.2988 23938.99029 27912.01405 19484.46586 20719.18834 20406.17912 1.073763623 1.185476053 1.07623187 1.072875949 1.173124579 1.367821672 0.954831659 1.015338943 1 14.31671846 EVPENETPVDTNLIELDTNDDDIVFEDFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EVPENETPVDTNLIELDTNDDDIVFEDFAR 30 0 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 0 ;;;; 288.7 5.78E-73 189216000 231610 210221 149729 190044 202431 228786 201121 244906 249183 FALSE TRUE 201002.1517 208840.0444 222138.4452 233196.3948 198403.0191 237587.5455 181616.3164 192534.7578 219724.8696 0.914790174 0.950461569 1.010984535 1.061310881 0.902961142 1.081295649 0.826562404 0.876253826 1 17.74533865 2.227304841 24.99995593 0.892697059 0.985960463 0.245833401 0.07052587 278.8481017 619338.0669 0.027803089 0.018937734 168.773727 -2.227304841 0.093263404 EVPIPEHIDIYHLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EVPIPEHIDIYHLTR 15 0 Q9UG63;Q9UG63-2;C9JHK9;C9JZV3 Q9UG63 ABCF2 ATP-binding cassette sub-family F member 2 0 ;; 180.49 3.63E-07 1030220000 924334 939696 526910 755219 906215 941183 915777 1061356 988895 FALSE TRUE 802180.9199 933523.0751 781725.4384 926703.0167 888183.0945 977390.919 826965.0875 834393.2789 871988.9597 0.919943895 1.07056754 0.896485477 1.062746273 1.018571491 1.120875337 0.948366465 0.956885141 1 19.73395034 4.779813214 22.33394717 1.004279189 0.919942893 0.151513296 0.065508017 12524.1878 6779949.266 0.01573227 4.16058969 60230.04859 -4.779813214 -0.084336296 EVPTADPTGVDRDDGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVPTADPTGVDRDDGPR 17 1 Q96KN1 Q96KN1 FAM84B Protein FAM84B 0 107.63 0.00063359 1249400000 861120 839280 533970 617670 795460 858980 732550 901300 769740 FALSE TRUE 747320.8102 833766.7144 792199.678 757921.414 779631.9023 892025.5164 661507.4138 708564.0089 678742.2141 1.101037765 1.228399674 1.167158402 1.116655776 1.14864213 1.314233148 0.974607738 1.04393685 1 19.37250422 2.214181175 24.9999496 1.012731587 1.176783531 0.634967967 0.061809142 145.5573219 149260.9537 0.024314218 0.016401537 163.7499497 -2.214181175 0.164051944 EVPVY(ph)IGEDS(ph)T(ph)IARESY(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVPVYIGEDSTIARESYR 18 1 H0YL34;A0A075B7B1;O15061-2;O15061 H0YL34 SYNM Synemin 4 EVPVY(0.814)IGEDS(0.814)T(0.831)IARES(0.726)Y(0.814)R 49.089 0.066054 572000000 21468 20444 13960 7831.1 20949 21019 24352 23001 18938 TRUE FALSE 18630.94941 20309.70202 20711.10269 9609.270946 20532.15589 21827.61453 21990.34679 18082.41514 16699.17121 1.115681082 1.216210179 1.240247341 0.575434003 1.229531431 1.307107655 1.316852585 1.082833089 1 14.02748888 EVPWS(ph)PSAEK ddPTM_MDA-MB-175_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(0.976)PS(0.024)AEK;EVPWS(0.994)PS(0.006)AEK 194.39 4.91E-07 778300000 1101280 945920 758510 899510 1096490 950360 1243750 1458210 1429540 TRUE FALSE 955743.0577 939706.1892 1125327.973 1103757.494 1074671.994 986920.9642 1123131.316 1146383.139 1260541.41 0.758200445 0.745478238 0.89273384 0.875621765 0.85254795 0.782934187 0.89099121 0.909437112 1 20.26561208 -2 0.414718824 4.23956641 0.802720749 0.605586254 0.048501662 65.49209492 0.912797103 184.5464712 0.048085886 0.01 2 -3.436845661 EVPWSPSAEKAS(ph)PQENGPAVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVPWSPSAEKASPQENGPAVHK 22 1 Q5JSZ5;Q5JT00;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 EVPWSPSAEKAS(1)PQENGPAVHK;EVPWSPSAEKAS(1)PQENGPAVHK 256.75 2.43E-37 174789000 255040 174951 139249 171038 169474 150789 232140 254780 221240 TRUE FALSE 221335.8178 173801.7354 206590.2822 209874.7921 166101.799 156589.9504 209627.0985 200297.2797 195085.2592 1.134559416 0.890901425 1.058974332 1.075810612 0.851431828 0.802674436 1.074540944 1.026716629 1 17.57374525 5.565148493 3.8256521 0.979393474 23.79845021 0.21437403 0.096066221 1286.143448 113.4870431 0.024965656 253428.1819 367407.9021 -5.565148493 22.81905674 EVQAEQPSSSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EVQAEQPSSSSPR 13 0 A0A1W2PP04;Q9Y388 A0A1W2PP04 RBMX2 "RNA-binding motif protein, X-linked 2" 1 EVQAEQPSSSS(1)PR;EVQAEQPSSSS(1)PR;EVQAEQPSSSS(1)PR;EVQAEQPSSS(0.003)S(0.997)PR;EVQAEQPSSS(0.003)S(0.997)PR;EVQAEQPSSS(0.003)S(0.997)PR 296.95 1.05E-40 3734580000 5916650 5251900 3138160 3884640 4903940 5014660 4601000 5261740 5215570 TRUE FALSE 5134749.712 5217399.923 4655784.673 4766706.885 4806361.188 5207577.215 4154795.728 4136557.848 4598991.256 1.116494776 1.134466154 1.012349103 1.036467916 1.045090308 1.132330314 0.903414574 0.899448948 1 22.13288602 2.230395788 24.99985342 0.925743322 1.075453147 0.660429807 0.04891021 106.9893113 327586.8142 0.020394444 0.014016147 169.9792026 -2.230395788 0.149709826 EVQDEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EVQDEEK 7 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ;; 114.89 0.013499 1598610000 2102160 1916060 1454380 1700140 1063050 1465150 2449050 2618180 2809190 FALSE TRUE 1824354.23 1903473.276 2157723.033 2086182.772 1041897.385 1521515.269 2211541.508 2058302.582 2477090.758 0.736490669 0.768430979 0.871071448 0.842190689 0.420613327 0.614234769 0.892797933 0.830935473 1 21.2402153 1.742878716 1.78356598 0.958725089 0.718157103 0.299691031 0.13503387 0.538321712 3.207525419 0.171966599 0.042865267 55.31955982 -1.742878716 -0.240567986 EVQDLFEAQGNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVQDLFEAQGNDR 13 0 Q9H3U1;A0A1W2PNX8;Q9H3U1-3;Q9H3U1-2 Q9H3U1;Q9H3U1-2 UNC45A Protein unc-45 homolog A 0 124.38 0.00049436 104810000 87329 80770 59516 60540 80288 93413 79517 96126 111830 FALSE TRUE 75788.25139 80239.41655 88298.13667 74286.5323 78690.42588 97006.65856 71805.45358 75570.20295 98609.5848 0.768568811 0.813708086 0.895431584 0.753339875 0.797999769 0.983744722 0.728179251 0.766357582 1 16.58944026 EVQQGEEFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EVQQGEEFER 10 0 P00568;Q5T9B7;H0YID2 P00568 AK1 Adenylate kinase isoenzyme 1 0 ;;; 218.6 1.56E-08 2186600000 805810 726890 506450 622100 743550 755660 727230 758450 944040 FALSE TRUE 699320.1668 722115.0117 751370.914 763357.3132 728754.8097 784730.7292 656703.3465 596261.3698 832436.6667 0.840088135 0.867471413 0.902616312 0.917015485 0.875447753 0.942691211 0.788892865 0.716284366 1 19.66698099 2.224152612 24.99286234 0.808390737 0.890842817 0.072506709 0.07633917 374.5814899 649762.841 0.030525743 0.020683284 167.5531559 -2.224152612 0.08245208 EVQQGEEFERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVQQGEEFERR 11 1 P00568;Q5T9B7;H0YID2 P00568 AK1 Adenylate kinase isoenzyme 1 0 ; 200.93 9.42E-06 766940000 1017290 846850 436250 504420 860410 888480 863060 833450 404530 FALSE TRUE 882852.549 841286.9866 647221.9592 618956.2706 843289.5244 922660.4005 779360.574 655223.2034 356706.9242 2.475008162 2.358482355 1.814436209 1.735195558 2.364096313 2.586606365 2.184876494 1.836867072 1 18.4443797 1.26364116 2.143512029 0.683364324 2.206855491 0.674988232 0.267542446 0.429260504 2.082887836 1.255785989 0.078867482 18.35021511 -1.26364116 1.523491167 EVRPDTQYTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVRPDTQYTGR 11 1 O43709;O43709-3;H7C0G4 O43709 WBSCR22 Probable 18S rRNA (guanine-N(7))-methyltransferase 0 ; 157.47 2.79E-05 487090000 187001 159652 100617 120571 166303 144521 148742 173956 158507 FALSE TRUE 162288.344 158603.2355 149275.7177 147948.4884 162993.8957 150080.8164 134317.0237 136756.8631 139768.483 1.161122597 1.134756793 1.068021306 1.058525393 1.1661706 1.073781536 0.960996505 0.978452797 1 17.09267955 2.364378673 4.384636488 0.979154751 1.113259291 0.753849051 0.03584176 0.1064813 3.582833146 0.014334574 0.010858808 231.4081618 -2.364378673 0.13410454 EVS(ph)DSEAGGGPQGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EVSDSEAGGGPQGER 15 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 EVS(0.952)DS(0.048)EAGGGPQGER;EVS(0.849)DS(0.151)EAGGGPQGER;EVS(0.97)DS(0.03)EAGGGPQGER;EVS(0.967)DS(0.033)EAGGGPQGER 343.87 6.87E-70 2102860000 1643490 1234310 1076320 1413700 1266200 1257990 1243270 1368480 2484310 TRUE FALSE 1426298.632 1226201.736 1596831.952 1734702.192 1241005.097 1306385.689 1122697.867 1075841.202 2190617.702 0.65109427 0.559751588 0.728941408 0.791878104 0.566509207 0.596354941 0.512502873 0.491113169 1 21.0629063 EVS(ph)PAPAVAGQSK ddPTM_MDA-MB-175_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 241.83 6.95E-17 2415530000 5038520 3818110 2575620 3248560 3722060 3106550 4127530 4969290 4929150 TRUE FALSE 4372666.816 3793028.584 3821198.447 3986195.199 3647998.288 3226060.989 3727242.776 3906646.005 4346431.502 1.006036058 0.872676489 0.879157637 0.917119066 0.839308818 0.742232102 0.857540899 0.898816881 1 22.05139998 4.738612622 23.8775268 0.872866459 1.006036132 0.286917126 0.064343344 3.143837376 1435811.729 0.016349491 0.091695114 54778.81356 -4.738612622 0.133169673 EVS(ph)PEVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EVSPEVVR 8 0 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 EVS(1)PEVVR;EVS(1)PEVVR;EVS(1)PEVVR;EVS(1)PEVVR;EVS(1)PEVVR 200.78 0.0001228 4990020000 5213710 4301210 2847010 3283500 4350630 4309650 4086140 4964750 4551780 TRUE FALSE 4524705.014 4272955.068 4223833.559 4029068.86 4264060.975 4475445.024 3689866.772 3903076.848 4013673.754 1.127322571 1.064599499 1.052360959 1.003835665 1.062383551 1.115049528 0.91932404 0.972444969 1 21.93649192 7.999976316 0.046265475 0.54253676 1.864770792 0.403143178 0.049097208 1298.064605 5.889913379 49.31178102 142.4335072 99994546.71 -7.999976316 1.322234031 EVS(ph)PGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVSPGSR 7 0 Q96RL1-2;Q96RL1-3;Q96RL1;Q96RL1-4 Q96RL1-2 UIMC1 BRCA1-A complex subunit RAP80 1 EVS(1)PGSR 97.857 0.012262 80128000 170880 125290 91135 110620 94825 125010 119210 132530 125160 TRUE FALSE 148297.775 124466.9617 135208.1908 135737.9617 92938.16802 129819.2156 107649.0325 104189.4908 110363.7274 1.343718435 1.127788674 1.225114393 1.229914619 0.842107912 1.176285168 0.975402291 0.944055564 1 16.75190656 4.448805452 0.369765515 0.933677661 1.516620245 0.508874533 0.108248967 5.190407669 0.833270878 0.19452919 1.405303575 28106.41486 -4.448805452 0.582942584 EVS(ph)PLLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EVSPLLPK 8 0 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 EVS(1)PLLPK;EVS(1)PLLPK;EVS(1)PLLPK;EVS(1)PLLPK 123.75 0.0013996 704820000 2943200 2076640 1552050 1915370 2070190 1748090 2348670 2918420 2876640 TRUE FALSE 2554248.663 2062998.415 2302626.571 2350284.033 2028997.269 1815340.153 2120896.345 2294338.594 2536566.896 1.006970747 0.813303374 0.907772854 0.926561029 0.799898979 0.715668156 0.836128686 0.904505455 1 21.27444578 4.751245628 23.77004571 0.861777291 1.006970932 0.249411608 0.078477257 1601.217995 3000363.923 0.020190225 0.329666038 56395.65275 -4.751245628 0.14519364 EVS(ph)PPGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVSPPGAR 8 0 H0Y9Y2;Q8NFC6 H0Y9Y2;Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 EVS(1)PPGAR;EVS(1)PPGAR 89.913 0.014233 792490000 356090 326080 200828 267361 307950 285842 305420 380440 394460 TRUE FALSE 309031.8043 323937.959 297949.0925 328069.4014 301822.3975 296838.5267 275800.4154 299085.8666 347827.3882 0.888463114 0.931318148 0.856600436 0.943196001 0.867736147 0.853407572 0.792923228 0.85986865 1 18.40801201 3.048127567 24.9928529 0.86548875 0.903599064 0.052870902 0.05608605 288.4943915 149814.3546 0.01701009 0.019287627 1117.191355 -3.048127567 0.038110314 EVS(ph)PSDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVSPSDVR 8 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 EVS(0.995)PS(0.005)DVR 101.82 0.0053764 627020000 1400100 1261100 897370 1163900 1287700 1052500 1234200 1374600 1702500 TRUE FALSE 1215073.238 1252815.751 1331341.134 1428181.284 1262077.289 1092990.356 1114507.474 1080652.487 1501232.389 0.809383841 0.834524861 0.886832141 0.951339242 0.840694151 0.728062067 0.742395036 0.719843573 1 20.51771589 2.98853596 24.05620103 0.780714417 0.872476913 0.123098514 0.086845012 551.4451625 1157160.458 0.027194713 0.028774823 973.9484263 -2.98853596 0.091762496 EVS(ph)SRPS(ph)TPGLSVVSGISATSEDIPNKIEDLR ddPTM_MDA-MB-175_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(0.533)T(0.467)PGLSVVSGISATSEDIPNKIEDLR;EVS(0.5)S(0.5)RPS(0.528)T(0.473)PGLSVVSGISATSEDIPNKIEDLR 156.26 3.60E-11 3577400000 225123 210809 144525 157778 202126 189141 231978 268122 216476 TRUE FALSE 195372.4252 209424.1818 214417.7734 193603.9064 198104.0881 196417.3767 209480.8093 210786.1968 190884.4539 1.023511455 1.097125395 1.123285679 1.01424659 1.037822012 1.028985717 1.097422053 1.10426068 1 17.54234009 1.218036925 24.83792171 0.999999734 1.068249004 0.221238491 0.03858023 2362.703495 2859197.629 0.413712238 0.009875421 16.52102259 -1.218036925 0.068249271 EVSAYIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVSAYIK 7 0 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 78.496 0.081838 69100000 164830 119010 92010 107420 119070 115380 138400 143740 143480 FALSE TRUE 143047.2979 118228.2155 136506.3438 131811.3528 116700.74 119818.7433 124977.9893 113002.3196 126517.9579 1.130648173 0.934477741 1.078948365 1.04183908 0.92240455 0.947049299 0.987828063 0.893172175 1 16.94898265 3.246844044 24.93567367 0.945654204 1.04079761 0.414323621 0.056629951 168.1540338 506192.398 0.015215266 0.019305681 1765.403747 -3.246844044 0.095143406 EVSEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVSEDR 6 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 97.596 0.095131 130930000 299700 306790 200350 235800 147420 299100 294720 296440 347310 FALSE TRUE 260093.8857 304774.6763 297239.9301 289341.994 144486.6304 310606.5705 266138.0998 233048.6129 306251.4075 0.849282254 0.995178043 0.970574903 0.944785842 0.471790911 1.014220875 0.869018373 0.760971565 1 18.22435695 3.405648671 24.99999599 0.817489635 0.946380664 0.125001256 0.152667103 85.05012424 29747.4153 0.042218505 0.054503863 2544.770791 -3.405648671 0.128891029 EVSEDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EVSEDRR 7 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 168.45 0.0016814 638124000 1488950 1438170 1007166 1205770 990340 1588740 1388110 1520660 1446670 FALSE TRUE 1292181.485 1428722.567 1494234.846 1479558.508 970634.1716 1649859.856 1253491.306 1195478.693 1275646.321 1.012962186 1.119998971 1.171355118 1.159850096 0.760895991 1.293352106 0.982632322 0.937155286 1 20.28279696 2.028559469 24.99961262 0.962829945 1.08513867 0.131156181 0.137423397 379.7203581 332387.7591 0.053776157 0.036255276 106.7971023 -2.028559469 0.122308725 EVSGHSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVSGHSVR 8 0 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 0 123.16 0.0013597 32373000 77342 77611 49412 53571 37506 63588 60135 66472 57959 FALSE TRUE 67121.05874 77101.16823 73307.80847 65735.11433 36759.70398 66034.27151 54303.11696 52257.48009 51107.15305 1.313339811 1.508617946 1.434394289 1.286221408 0.7192673 1.292074936 1.062534571 1.022508142 1 15.64123761 3.465611738 24.9969801 1.033490428 1.416524184 0.623898088 0.144197211 134.9913364 293180.2433 0.039299353 0.050775366 2921.539336 -3.465611738 0.383033756 EVSHLNALEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVSHLNALEER 11 0 A0A087WYJ2;M0R2B7;P28340;M0R3H8 A0A087WYJ2 POLD1 DNA polymerase;DNA polymerase delta catalytic subunit 0 ; 147.87 3.51E-05 228380000 168986 148996 86277 110619 146056 163836 139011 157937 137764 FALSE TRUE 146654.0719 148017.2355 128000.8458 135736.7347 143149.7714 170138.8769 125529.7346 124163.4016 121477.6969 1.207251008 1.21847252 1.053698326 1.117379883 1.178403732 1.400577072 1.033356228 1.022108624 1 16.89033194 2.039275957 24.99999957 1.017162611 1.188718238 0.473941672 0.088102145 138.8875167 88404.38415 0.037164942 0.025056559 109.4651703 -2.039275957 0.171555627 EVSMDDHK ddPTM_MDA-MB-175_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 91.853 0.012192 100320000 119680 115280 78968 147100 140910 148130 79458 233540 174770 FALSE TRUE 103863.9848 114522.7181 117157.1889 180501.3033 138106.1667 153828.657 71752.17539 183599.2884 154108.8897 0.673964915 0.743128565 0.760223431 1.171258216 0.896159637 0.998181593 0.465594006 1.191360789 1 17.23359056 3.972079258 23.77951625 0.948856909 0.719328946 0.230232203 0.197839263 560.2440625 477150.1919 0.051590556 0.089687334 9377.331249 -3.972079258 -0.229527964 EVSQVDTICECLLEHEEQVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EVSQVDTICECLLEHEEQVLR 21 0 Q8WUM0 Q8WUM0 NUP133 Nuclear pore complex protein Nup133 0 ;;; 252.01 2.51E-36 254135000 239744 223580 138140 174014 216298 207985 188065 227777 218230 FALSE TRUE 208061.223 222111.2883 204944.9661 213526.5383 211994.093 215986.3175 169826.4852 179068.6611 192431.098 1.081224527 1.154238013 1.065030383 1.109625942 1.101662336 1.122408591 0.882531394 0.930559889 1 17.55398244 2.24572946 24.99999992 0.9339116 1.106051206 0.825304245 0.036422678 57.54132088 200665.1691 0.013307096 0.010088309 176.0878779 -2.24572946 0.172139606 EVSS(ph)RPS(ph)TPGLSVVSGISATSEDIPNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EVSSRPSTPGLSVVSGISATSEDIPNK 27 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 2 EVS(0.462)S(0.538)RPS(0.538)T(0.461)PGLSVVSGISATSEDIPNK;EVS(0.463)S(0.537)RPS(0.536)T(0.462)PGLS(0.001)VVSGISATSEDIPNK;EVS(0.093)S(0.905)RPS(0.532)T(0.453)PGLS(0.017)VVSGISATSEDIPNK;EVS(0.15)S(0.85)RPS(0.55)T(0.45)PGLSVVSGISATSEDIPNK 217.58 1.95E-34 1197000000 873920 751849 739811 896281 797444 780594 862480 1077697 2583530 TRUE FALSE 758429.2578 746910.0544 1097586.074 1099795.3 781576.4246 810623.9563 778836.8223 847239.8832 2278108.027 0.332920673 0.327864195 0.481797202 0.482766966 0.343081371 0.355832097 0.341878793 0.371905052 1 21.11940473 1.23807824 24.99974458 1.000000701 0.380504856 0.921008312 0.057084903 3.201691533 165757.5406 0.085482526 0.014901038 17.30128023 -1.23807824 -0.619495845 EVSS(ph)RPS(ph)TPGLSVVSGISATSEDIPNKIEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.475)S(0.525)RPS(0.525)T(0.475)PGLSVVSGISATSEDIPNKIEDLR;EVS(0.48)S(0.52)RPS(0.52)T(0.48)PGLSVVSGISATSEDIPNKIEDLR;EVS(0.107)S(0.893)RPS(0.542)T(0.458)PGLSVVSGISATSEDIPNKIEDLR 189.42 3.75E-20 1617880000 230003 180237 150996 146010 171043 175894 208849 259263 202314 TRUE FALSE 199607.5208 179053.0113 224018.1707 179163.8021 167639.5789 182660.756 188594.8561 203821.625 178396.6694 1.118897127 1.003679115 1.255730678 1.004300152 0.939701282 1.023902277 1.057165791 1.142519228 1 17.44472916 EVSS(ph)RPST(ph)PGLSVVSGISATSEDIPNKIEDLR ddPTM_MDA-MB-175_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 2 EVS(0.144)S(0.856)RPS(0.291)T(0.709)PGLSVVSGISATSEDIPNKIEDLR 178.36 3.74E-19 709030000 179280 146930 123900 127400 167000 151620 181040 213880 167360 TRUE FALSE 155587.6938 145964.8072 183818.4544 156328.1172 163677.0267 157452.9195 163482.7687 168143.4264 147574.8915 1.054296515 0.989089714 1.245594373 1.059313787 1.109111619 1.066935696 1.107795283 1.139376928 1 17.17108776 EVSS(ph)RPSTPGLSVVSGISATSEDIPNKIEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVSSRPSTPGLSVVSGISATSEDIPNKIEDLR 32 2 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 EVS(0.141)S(0.848)RPS(0.006)T(0.006)PGLSVVSGISATSEDIPNKIEDLR 184.5 6.62E-20 403750000 148000 142420 86651 101030 130220 107530 169150 185780 118160 TRUE FALSE 128441.425 141484.4336 128555.7134 123970.4056 127628.8768 111666.7487 152745.859 146052.3927 104191.2594 1.232746641 1.357929969 1.23384355 1.189834986 1.224948019 1.071747758 1.466014135 1.401772026 1 16.66887473 2.236070162 24.99998674 1.320066254 1.224532254 0.038627505 0.138610321 165.6756509 1663059.143 0.055024317 0.039016703 172.2146773 -2.236070162 -0.095534 EVSSEDIADMHSNLSNYHQYIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVSSEDIADMHSNLSNYHQYIVK 23 0 Q8TBX8;Q8TBX8-3;F8VNT5 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 254.4 9.33E-44 190850000 286530 227350 116090 182770 227160 219190 275370 300930 287540 FALSE TRUE 248664.3345 225856.5229 172231.5123 224270.722 222639.9604 227622.3811 248664.6598 236578.4613 253547.3488 0.980741214 0.890786372 0.679287372 0.884531915 0.878100132 0.897750981 0.980742496 0.933074088 1 17.95189566 2.527026789 1.61296547 0.967045173 0.851158544 0.290056334 0.076188168 0.501215594 2.667682884 0.040014038 0.028271842 336.5323274 -2.527026789 -0.115886628 ESVPEFPLS(ph)PPK ddPTM_MDA-MB-175_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 218.11 3.68E-11 1957647000 1502158 1119272 1016136 1278091 1342326 1115578 1471253 1897663 3107110 TRUE FALSE 1303644.014 1111919.429 1507542.768 1568301.096 1315616.339 1158495.008 1328571.111 1491862.535 2739790.995 0.475818782 0.405840968 0.550240062 0.572416326 0.480188577 0.422840651 0.484916956 0.544516913 1 21.38563441 1.220106827 3.348086328 1.09499996 0.486241114 0.911994462 0.049893407 0.102600834 1.556013942 0.167132429 0.013654123 16.5999518 -1.220106827 -0.608758847 EVSTYIKK ddPTM_MDA-MB-175_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 ; 140.5 0.0010399 5760200000 4425000 3461650 1295480 1433270 2723500 2534600 4442600 4709300 309220 FALSE TRUE 3840225.038 3438910.193 1921978.461 1758715.86 2669307.678 2632107.702 4011757.336 3702252.843 272664.3639 14.08407386 12.61224659 7.048880293 6.450112639 9.789719641 9.653288258 14.71317072 13.57805908 1 18.05676663 4.41945443 7.433205668 9.596810513 13.7280434 0.176282652 3.837094887 0.390796707 41.87853297 0.996846729 2.684355149 26269.65869 -4.41945443 4.131232885 EVTSLFNKDDEQHLLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVTSLFNKDDEQHLLER 17 1 Q86YL5;Q86YL5-2 Q86YL5 TDRP Testis development-related protein 0 ; 160.13 1.88E-09 274360000 264337 220291 154573 171201 217010 223737 252847 294290 233818 FALSE TRUE 229404.1957 218843.8939 229325.0198 210074.8037 212691.9256 232344.3072 228325.9369 231358.3737 206176.3024 1.112660345 1.06144058 1.112276324 1.018908581 1.031602192 1.126920526 1.107430554 1.122138534 1 17.653519 2.733362065 24.97097973 1.095997561 1.06684942 0.043940495 0.045604602 1164.75621 5594848.105 0.01530813 0.013973659 541.2053301 -2.733362065 -0.029148141 EVTWEVLEGEVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVTWEVLEGEVEK 13 0 P05455 P05455 SSB Lupus La protein 0 ; 236.57 2.37E-16 71115000 197492 149986 152817 174783 127346 125985 159404 186781 416160 FALSE TRUE 171392.9318 149000.7321 226719.8123 214470.1515 124812.0637 130831.7245 143945.0246 146839.3367 366962.0389 0.467059024 0.406038544 0.617829062 0.584447787 0.340122548 0.35652659 0.39226135 0.400148574 1 18.4852713 1.235859308 24.99938277 1.000000741 0.443339971 0.784667583 0.091272982 36.79781006 340478.5837 0.162059263 0.02420619 17.21310856 -1.235859308 -0.55666077 EVTYELDHPGFQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EVTYELDHPGFQIR 14 0 A5YKK6-3;A5YKK6-2;A5YKK6;A5YKK6-4 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 ;;; 220.32 4.68E-12 850610000 858050 821470 535052 572540 807650 815920 783890 907090 859920 FALSE TRUE 744656.5185 816073.7095 793804.9368 702543.9577 791579.3451 847308.9704 707868.4685 713115.8625 758261.2372 0.982058006 1.076243476 1.046875269 0.926519678 1.043940144 1.117436747 0.933541679 0.940461977 1 19.53233545 2.19252425 24.99963978 0.95332797 1.030582136 0.295914818 0.053739627 152.7424987 82944.36647 0.022107423 0.014904869 155.7845021 -2.19252425 0.077254166 EVVAGSHELGQDYEHVTMLQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVVAGSHELGQDYEHVTMLQER 22 0 Q01082;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 229.15 1.77E-26 398400000 141360 143680 74833 111620 153490 154320 135880 172820 159860 FALSE TRUE 122678.9178 142736.1566 111022.4891 136965.027 150435.8493 160256.7903 122702.3785 135863.7879 140961.5329 0.870300679 1.012589418 0.787608412 0.971648252 1.06721207 1.136883141 0.870467112 0.963835914 1 17.10494199 3.493702341 24.52435077 1.000283124 0.898611791 0.274095941 0.086560122 867.7591354 1283461.949 0.024605759 0.035410154 3116.752677 -3.493702341 -0.101671333 EVVEEAENGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 EVVEEAENGR 10 0 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;;;; 278.02 1.42E-23 27620660000 14475000 13487420 8384950 9550000 12409300 12084070 12488840 14558880 13484710 FALSE TRUE 12562092.08 13398820.25 12439939.87 11718473.46 12162379.21 12548951.99 11277674.22 11445576.81 11890562.95 1.056475806 1.126844903 1.046202768 0.985527222 1.022859831 1.055370721 0.94845587 0.962576529 1 23.50331368 3.753851069 0.514368537 0.968076719 1.119954523 0.507912769 0.036697774 1.446748467 0.731452224 0.040872771 0.133437899 5673.50013 -3.753851069 0.151877804 EVVEFYRDPQLEGSLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EVVEFYRDPQLEGSLSR 17 1 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 ;; 202.34 9.74E-12 565690000 557820 558710 336999 397673 531670 587470 483880 528360 497280 FALSE TRUE 484102.6737 555039.7972 499972.8436 487970.7327 521090.8072 610070.351 436953.3921 415374.3257 438492.1249 1.104016803 1.265791939 1.140209402 1.112838076 1.188369819 1.391291465 0.996490854 0.947278873 1 18.74219141 2.070830651 12.49754425 0.970475991 1.196089225 0.604609378 0.083641512 0.463425027 80.41804529 0.033595425 0.022648102 117.7146867 -2.070830651 0.225613233 EVVESCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EVVESCR 7 0 O60701-2;O60701;E7ER95;E7ER83;E7ETF4;E7EV97 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ;; 124.34 0.0096679 1115150000 944450 957130 609121 655720 782300 881420 891750 970810 920930 FALSE TRUE 819638.5396 950842.55 903693.953 804611.2481 766733.7605 915328.7978 805268.2223 763209.8364 812058.7045 1.009334097 1.17090371 1.112843133 0.990828919 0.944185139 1.127170724 0.991637942 0.939845644 1 19.6312245 3.737516833 24.77944034 0.995392997 1.105014658 0.344329081 0.063845909 84.20876916 1999120.308 0.017370725 0.027523003 5464.077277 -3.737516833 0.109621662 EVVETPLLHPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EVVETPLLHPER 12 0 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ;;;; 213.06 1.31E-08 2611410000 1854260 1866550 1320980 1624210 1865280 2038240 1780090 2007970 2352300 FALSE TRUE 1609214.843 1854288.51 1959810.346 1993011.705 1828164.577 2116652.412 1607457.146 1578581.242 2074213.774 0.775819187 0.893971747 0.94484492 0.960851639 0.881377127 1.020460108 0.774971783 0.761050409 1 20.98413316 1.17523214 23.12077849 1.000010787 0.87642439 0.168720382 0.086031812 34907.0254 12739909.46 76.81389134 0.02270931 14.97035639 -1.17523214 -0.123586397 EVVHTVSLHEIDVINSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVVHTVSLHEIDVINSR 17 0 Q9Y230;Q9Y230-2;M0R0Y3 Q9Y230 RUVBL2 RuvB-like 2 0 ; 234.77 2.22E-20 738720000 187247 185676 72071 143220 181279 197842 167095 187351 195071 FALSE TRUE 162501.8345 184456.2821 106924.7767 175740.29 177671.9026 205453.1098 150890.1526 147287.4466 172009.9286 0.944723574 1.072358344 0.621619796 1.021686896 1.032916553 1.194425877 0.877217692 0.856272936 1 17.39213232 5.550278128 10.33972203 0.95175504 0.875688454 0 0.153097968 27549936.95 4823208.156 0.036412693 49466231.1 355040.6891 -5.550278128 -0.076066586 EVVKGPGAPAAS(ph)SPTQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVVKGPGAPAASSPTQK 17 1 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 EVVKGPGAPAAS(0.499)S(0.499)PT(0.002)QK 88.79 0.002549 544010000 211290 193780 122710 156730 272220 184670 316600 365760 99782 TRUE FALSE 183367.4912 192507.0464 182052.9664 192317.942 266803.3546 191774.3744 285896.1807 287545.0703 87985.88563 2.084055753 2.187930996 2.069115576 2.185781737 3.032342661 2.179603842 3.249341399 3.268081787 1 16.42498449 3.362515368 8.035128853 2.669714149 2.122673468 0.073764612 0.655132576 0.491012732 32.5697447 0.186734649 0.241176614 2304.17451 -3.362515368 -0.547040681 EVVKPVPITS(ph)PAVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVVKPVPITSPAVSK 15 1 Q96HC4;A0A0D9SFR4 Q96HC4 PDLIM5 PDZ and LIM domain protein 5 1 EVVKPVPIT(0.075)S(0.925)PAVSK;EVVKPVPIT(0.05)S(0.95)PAVSK 89.483 0.0039753 581360000 577880 484610 380120 383780 460350 394520 623530 691750 714900 TRUE FALSE 501511.6938 481426.565 563947.3034 470923.1147 451189.9357 409697.4397 563060.1566 543824.6457 630385.3364 0.795563705 0.763702036 0.894607268 0.747040084 0.715736724 0.649915878 0.893199959 0.862686066 1 19.26587445 1.532237397 1.531245871 1.010842073 0.768953695 0.514805898 0.07106105 0.52389849 1.825415511 0.174204724 0.021831745 34.05943167 -1.532237397 -0.241888377 EVVNKDVLDVYIEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVVNKDVLDVYIEHR 15 1 P33993;P33993-2 P33993 MCM7 DNA replication licensing factor MCM7 0 109.35 0.00060491 19862000 257260 229420 137930 169870 225470 200880 246960 333610 153690 FALSE TRUE 223262.4392 227912.9249 204633.4093 208441.5798 220983.5881 208607.9836 223009.8572 262270.0977 135520.9433 1.647438645 1.681754269 1.509976277 1.538076512 1.630623155 1.539304395 1.64557486 1.935273555 1 17.0481563 1.221762121 24.99609873 0.999998107 1.645470989 0.742374373 0.118645239 597.83849 889532.3693 0.911530509 0.03256771 16.66334249 -1.221762121 0.645472882 LRAETEQGEQQR ddPTM_MDA-MB-175_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 ;;; 217.91 3.24E-11 1208560000 625110 576069 294923 262540 518570 580260 539950 576810 119695 FALSE TRUE 542500.1297 572284.7648 437548.7493 322153.7197 508251.4716 602582.9777 487585.7321 453463.6702 105544.7935 5.13999897 5.42219797 4.145621351 3.052293809 4.815504914 5.709262939 4.619704261 4.296409661 1 16.68749589 1.220265932 3.449233792 0.354780278 4.675600882 0.714012047 0.729816431 0.201800116 3.362023841 2.378942682 0.200598665 16.60603437 -1.220265932 4.320820604 KLVGYLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLVGYLDR 8 1 P07602;C9JIZ6;P07602-2;P07602-3;Q5BJH1 P07602 PSAP Prosaposin;Saposin-A;Saposin-B-Val;Saposin-B;Saposin-C;Saposin-D 0 ; 91.584 0.019856 3833400000 6903800 7018600 3589000 4357200 7150400 7077600 6945700 7608000 3241400 FALSE TRUE 5991445.338 6972494.354 5324652.404 5346568.856 7008121.03 7349879.852 6272107.083 5981088.406 2858205.385 2.096226314 2.439465824 1.862935545 1.870603451 2.451930525 2.571501646 2.194421408 2.092602735 1 21.44667816 1.221414456 3.511710974 0.795506518 2.213786201 0.723217577 0.233825026 0.185944332 3.287862632 0.726982846 0.063054729 16.65000838 -1.221414456 1.418279683 ESWHGKPLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ESWHGKPLPK 10 1 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 93.258 0.0053527 7485200000 6277900 6924700 1959390 5094710 6852200 5178930 6809600 7727800 12975200 FALSE TRUE 5448259.609 6879211.19 2906957.558 6251541.773 6715854.626 5378166.788 6149206.04 6075270.108 11441286.64 0.476192913 0.601262027 0.254076106 0.546401989 0.586984212 0.470066607 0.537457564 0.530995359 1 23.44774596 1.221452016 3.88394932 1.070196232 0.497628469 0.727023223 0.096357545 0.147045601 3.62256955 0.248382198 0.023685301 16.65144839 -1.221452016 -0.572567763 EVWALVQAGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 155.42 7.34E-05 627289000 410089 412613 363358 347701 478557 476635 481301 495969 575785 FALSE TRUE 355894.6996 409902.518 539079.1442 426651.8263 469034.652 494971.4569 434624.5031 389909.889 507716.3532 0.700971512 0.80734551 1.061772269 0.840335009 0.923812379 0.974897605 0.856038023 0.767967954 1 18.9536632 4.473989485 24.99958957 0.902886987 0.727564955 0.408231469 0.085190508 83.6055508 667394.6028 0.021820867 0.058403978 29784.44313 -4.473989485 -0.175322032 EVWEELDGLDPNRFNPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVWEELDGLDPNRFNPK 17 1 Q02818;H7BZI1 Q02818 NUCB1 Nucleobindin-1 0 182.1 6.99E-10 124190000 186250 179210 100380 102870 161510 152360 178370 229300 76717 FALSE TRUE 161636.5906 178032.7577 148924.1038 126228.2058 158296.267 158221.3878 161071.7049 180265.9794 67647.60366 2.389391226 2.631767396 2.20146902 1.865967144 2.340012926 2.338906025 2.381040808 2.664779973 1 16.04575121 4.218315834 19.43708331 2.184102911 2.510577373 0.10208615 0.45351611 42.77204114 41067.83108 0.11335522 0.23723788 16531.636 -4.218315834 0.326474462 EVWEETDGLDPNDFDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVWEETDGLDPNDFDPK 17 0 P80303-2;P80303;E9PKG6;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 150.49 6.65E-07 43869000 74479 61195 62811 66514 64458 60487 79019 104640 118480 FALSE TRUE 64636.41144 60793.00602 93186.60969 81617.0203 63175.41191 62813.97403 71355.74954 82263.55031 104473.4294 0.618687563 0.58189921 0.891964687 0.781222755 0.604703151 0.601243535 0.683003803 0.787411218 1 16.67277654 1.287092819 2.162031337 1.071950027 0.682964977 0.535078121 0.094758324 0.522725439 2.718291106 0.384931739 0.02728112 19.36835867 -1.287092819 -0.38898505 EVWEMELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVWEMELDR 9 0 Q8ND24;E9PN76;Q8ND24-2 Q8ND24 RNF214 RING finger protein 214 0 ; 102.61 0.0082748 72241000 72066 67728 42324 51372 66336 66482 65523 74770 63969 FALSE TRUE 62542.29551 67283.09031 62792.02797 63036.79777 65016.04338 69039.60556 59168.58955 58781.01736 56406.65769 1.108775064 1.192821788 1.113202422 1.1175418 1.152630665 1.223962 1.048964643 1.042093607 1 15.78357783 2.101992093 7.351331949 1.030484187 1.149929676 0.703155571 0.037289341 0.12200682 7.734320958 0.015177279 0.01019843 126.4713322 -2.101992093 0.119445489 EVWYFGLHYVDNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVWYFGLHYVDNK 13 0 P15311;E7EQR4 P15311 EZR Ezrin 0 185.87 8.29E-06 38143000 239800 208820 197020 242920 173870 148120 246350 290240 279120 FALSE TRUE 208109.8224 207448.2477 292299.531 298078.6988 170410.3272 153818.2722 222459.0149 228174.4347 246122.7516 0.845552965 0.842864978 1.187616866 1.211097702 0.692379417 0.624965678 0.903853924 0.927075751 1 17.9090185 3.229778816 24.99999118 0.83716304 1.020848541 0.261000054 0.160364553 308.8752775 879302.8782 0.053215796 0.061248579 1697.378966 -3.229778816 0.183685501 EVYELLDS(ph)PGKVLLQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVYELLDSPGKVLLQSK 17 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 1 EVYELLDS(1)PGKVLLQSK;EVYELLDS(1)PGKVLLQSK 131.18 1.68E-05 61251000 101972 84611 49790 60893 82776 56635 91266 123445 30119 TRUE FALSE 88496.14184 84055.18477 73868.61054 74719.68634 81128.91955 58813.7851 82415.03737 97047.2474 26558.36613 3.332138031 3.164923036 2.781368785 2.813414273 3.05474061 2.214510667 3.103166699 3.654112114 1 14.69687877 1.227170928 24.98317035 0.999995548 3.016249927 0.738622177 0.376665483 285.123763 625375.0193 1.510939791 0.098613673 16.87216944 -1.227170928 2.016254379 EVYFAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EVYFAER 7 0 P50238 P50238 CRIP1 Cysteine-rich protein 1 0 ;;;;; 158.03 0.0033409 33855520000 21921950 18973470 11627080 13250480 16495940 16876250 16116050 18310630 17389260 FALSE TRUE 19024908.76 18848832.03 17249974.78 16259204 16167703.07 17525490.26 14553117.95 14395044.27 15333521.49 1.240739694 1.229256569 1.12498455 1.060369858 1.054402479 1.14295273 0.949104741 0.938795715 1 23.87018573 8 0.166303187 0.845604168 2.539754277 0.769700644 0.050221649 60.36514768 0.812144228 0.6255696 24.57608936 100000000 -8 1.694150109 EVYLFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVYLFER 7 0 A0A2R8YE10;Q9NRW7;B7Z7G7;A0A2R8YF01;A0A1B0GXI6;A0A2R8YD95;Q9NRW7-2;A0A2R8Y7W9 A0A2R8YE10 VPS45 Vacuolar protein sorting-associated protein 45 0 ; 89.752 0.041043 267060000 396950 389590 271320 320080 400600 416910 339270 437520 430260 FALSE TRUE 344492.0518 387030.7576 402531.2595 392759.0561 392628.8438 432948.7975 306367.6476 343959.7528 379395.153 0.908003302 1.020125731 1.060981555 1.035224233 1.034881022 1.141155321 0.807515977 0.906600282 1 18.53334172 2.235045838 24.99999938 0.901050639 1.034196635 0.413835843 0.072151407 84.79221779 603101.1745 0.028449621 0.020049503 171.8089717 -2.235045838 0.133145996 EVYPEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVYPEAR 7 0 O00422;O00422-2;H7BZW6;U3KPY7 O00422 SAP18 Histone deacetylase complex subunit SAP18 0 ; 117.17 0.017459 443610000 862760 776030 460560 581000 731910 775740 736840 843440 783850 FALSE TRUE 748744.08 770932.2078 683288.3565 712924.93 717346.423 805583.2198 665381.3702 663076.9197 691184.146 1.083277278 1.115378893 0.988576431 1.031454402 1.037851385 1.165511716 0.962668739 0.959334677 1 19.3987106 2.165323053 24.99997218 0.970472471 1.065431326 0.458502876 0.049112133 37.81840627 12908.35034 0.020231072 0.013639788 146.326523 -2.165323053 0.094958855 EVYQQQQYGSGGR ddPTM_MDA-MB-175_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 ;;; 311.49 3.09E-50 1650800000 712107 602852 393094 467328 564149 616708 527670 581831 563299 FALSE TRUE 618000.2557 598891.8255 583195.5732 573441.9651 552923.5386 640433.1558 476496.6446 457410.9685 496706.4339 1.244196196 1.205725927 1.174125265 1.1544887 1.113179739 1.289359493 0.959312407 0.920887948 1 18.92203391 2.221908119 24.99038792 0.95187297 1.190488423 0.82455237 0.051385469 88.98251787 133534.9734 0.020535904 0.013887552 166.6894521 -2.221908119 0.238615452 EWAHATIIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EWAHATIIPK 10 0 P30153;B3KQV6;E9PH38 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ; 147.12 2.75E-05 1877070000 6054700 5350900 2413000 4838500 5663300 5231900 6148500 7613800 8158500 FALSE TRUE 5254556.054 5315749.586 3579934.871 5937155.377 5550611.41 5433174.578 5552219.416 5985648.121 7194011.424 0.730406966 0.738913142 0.497627076 0.825291347 0.771559994 0.755235745 0.771783514 0.832032057 1 22.77836502 -1.999999951 0.500554021 9.999983581 0.69444393 0.547246595 0.082939957 88.94315663 0.998399895 867.0874731 0.054247828 0.010000001 1.999999951 -9.305539651 EWAMNVGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EWAMNVGDK 9 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ;;; 154.05 0.00017824 855120000 1066440 935106 759778 943981 962041 849241 1102330 1191280 1985330 FALSE TRUE 925507.252 928963.2271 1127209.182 1158326.314 942898.2663 881911.8508 995426.2063 936534.0426 1750626.549 0.528672007 0.530646144 0.643889002 0.661663857 0.538606173 0.503769265 0.568611396 0.534970775 1 20.73943992 1.236194639 24.99999107 1.000000567 0.564576028 0.878332571 0.05101373 22.2987685 235565.5293 0.087101392 0.013364306 17.22640444 -1.236194639 -0.435424538 EWAMNVGDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EWAMNVGDKK 10 1 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ; 106.01 0.0039663 7202800000 4857500 4674400 3037100 4851800 4881500 4441900 7801200 8823100 7645900 FALSE TRUE 4215569.068 4643693.559 4505851.718 5953475.345 4784367.7 4612782.767 7044640.825 6936348.726 6742010.412 0.625268846 0.688769859 0.668324645 0.883041553 0.709635169 0.684185055 1.044887266 1.02882498 1 22.68474742 2.237208285 24.99967076 1.026303623 0.714883915 0.827795833 0.067635587 13.97786618 258388.9957 0.027409923 0.019624534 172.6665791 -2.237208285 -0.311419708 EWDFDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EWDFDLK 7 0 Q96EY4;H0Y9X1 Q96EY4 TMA16 Translation machinery-associated protein 16 0 ;; 119.21 0.011243 208524000 830060 681777 482768 606671 667984 526556 780370 921210 885470 FALSE TRUE 720365.4679 677298.362 716236.2196 744424.9229 654692.4253 546812.95 704689.8375 724216.4104 780790.7453 0.922610152 0.867451831 0.917321605 0.953424368 0.838499213 0.700332264 0.902533543 0.927542257 1 19.57457643 1.504101225 2.374688426 0.998569643 0.868655106 0.269660865 0.068953213 0.491614048 5.011323809 0.113092002 0.019989785 31.92281819 -1.504101225 -0.129914537 EWDRDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EWDRDK 6 1 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 ; 94.163 0.040853 713300000 840260 671800 404600 454270 503260 480480 676870 849430 338060 FALSE TRUE 729217.5121 667386.9016 600265.9133 557418.9466 493246.1106 498964.3765 611227.2516 667786.0048 298094.9319 2.446259342 2.238840148 2.013673662 1.869937684 1.654661176 1.673843877 2.050444963 2.240178994 1 18.18541232 4.264255236 1.505166079 1.8088352 2.470545828 0.36402243 0.324033955 0.670971801 2.52103251 0.096344131 0.514602282 18376.17999 -4.264255236 0.661710628 EWEEAER ddPTM_MDA-MB-175_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 ; 113.5 0.014228 384750000 828500 695640 494360 605890 718790 760750 655020 849350 827020 FALSE TRUE 719011.6258 691070.295 733434.1495 743466.5849 704487.4853 790016.5448 591496.2612 667723.1121 729250.6377 0.985959543 0.947644416 1.005736727 1.019493911 0.966043016 1.083326505 0.811101466 0.91562911 1 19.47605522 2.242404368 24.99998267 0.90623461 0.99834228 0.366483451 0.057175939 102.3745261 665856.0834 0.02144261 0.015962016 174.7448432 -2.242404368 0.09210767 EWFLQAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EWFLQAAK 8 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7ERC6 P06744 GPI Glucose-6-phosphate isomerase 0 ; 157.54 0.0008731 1090810000 2322900 1984590 1611990 1971820 1926520 1613690 2242900 2452700 2909300 FALSE TRUE 2015922.88 1971553.098 2391553.756 2419551.868 1888186.021 1675769.698 2025383.903 1928209.192 2565365.868 0.785822757 0.768527064 0.932246657 0.943160544 0.736029915 0.653228344 0.789510739 0.751631265 1 21.29073316 EWGSGSDTLR ddPTM_MDA-MB-175_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 0 126.82 0.00086619 223110000 198830 187060 126810 164350 240170 270790 177800 217010 239390 FALSE TRUE 172554.1117 185831.1905 188135.7402 201668.1794 235391.0869 281207.4665 160556.9834 170604.1003 211089.5869 0.817444926 0.880342765 0.891260165 0.95536773 1.115124106 1.332171192 0.760610628 0.808207088 1 17.68749589 3.862500779 2.624530963 0.980589812 0.852514536 0.136753818 0.157213548 0.771260559 10.29217711 0.050021073 0.101477278 7286.194822 -3.862500779 -0.128075276 EWHGPPSQGPSYHDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EWHGPPSQGPSYHDTR 16 0 Q9NWH9;Q9NWH9-3;H7C3F4;H0YKH2 Q9NWH9 SLTM SAFB-like transcription modulator 0 103.39 0.0008343 72061000 116720 108240 73731 95081 96316 90638 112670 128690 88983 FALSE TRUE 101295.1563 107528.9643 109387.5582 116670.5943 94399.50004 94124.90251 101743.2807 101170.645 78463.53111 1.290983911 1.370432388 1.394119748 1.486940399 1.203100328 1.199600645 1.296695156 1.289397043 1 16.25973464 3.218350603 24.9793782 1.216725726 1.385141538 0.493479842 0.093482531 223.3400578 276045.3836 0.028505494 0.032361364 1653.295955 -3.218350603 0.168415812 EWLEVLEDTKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EWLEVLEDTKR 11 1 Q8IYI6 Q8IYI6 EXOC8 Exocyst complex component 8 0 90.653 0.018161 23951000 30222 30761 22677 25966 27501 28391 28849 39728 30614 FALSE TRUE 26228.08613 30558.92897 33643.67305 31861.97717 26953.7839 29483.22014 26051.22842 31232.47636 26994.8478 0.971596 1.1320282 1.246299787 1.180298456 0.998478825 1.092179529 0.965044464 1.156979161 1 14.72039646 3.244757451 24.9987514 1.053512002 1.140642522 0.203004622 0.086478207 253.0365886 1020773.665 0.025246058 0.031766007 1756.942106 -3.244757451 0.087130519 EWLLAHEGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EWLLAHEGHR 10 0 B4DEE8;P16455 B4DEE8 MGMT Methylated-DNA--protein-cysteine methyltransferase 0 ;;; 97.813 0.0033556 688302000 337258 363551 278999 280726 349076 356813 341845 373887 345566 FALSE TRUE 292688.5008 361162.8095 413923.8496 344469.1289 342130.0706 370539.827 308692.9245 293934.1746 304713.5812 0.960536448 1.185253405 1.358403022 1.130468578 1.122792326 1.216026623 1.013059291 0.964624463 1 18.21709428 2.152150861 5.5604691 0.983201895 1.168696978 0.400303907 0.097952973 0.196460832 9.763655858 0.04117155 0.027536195 141.9550547 -2.152150861 0.185495084 EWLTNFMEDR ddPTM_MDA-MB-175_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 ; 114.83 0.0030314 115376000 139029 136332 81555 122883 135161 129505 107392 138024 137211 FALSE TRUE 120655.9654 135436.4261 120995.2708 150785.4633 132471.5605 134487.1412 96977.14037 108508.6417 120990.0719 0.997238563 1.119401154 1.00004297 1.24626311 1.094896122 1.11155518 0.801529736 0.89683922 1 16.88452914 2.253044819 24.99563525 0.894830819 1.098581616 0.550840841 0.083116495 157.6527038 272063.7699 0.030282139 0.023349464 179.0790652 -2.253044819 0.203750797 EWNGVVSESDS(ph)PVK ddPTM_MDA-MB-175_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(0.001)DS(0.999)PVK;EWNGVVSESDS(1)PVK 240.78 2.17E-17 458040000 794790 640400 580950 764790 672960 545780 723240 872180 1660060 TRUE FALSE 689756.4878 636193.1702 861899.3632 938447.2586 659569.4126 566776.5098 653100.2961 685671.0943 1463809.598 0.471206425 0.434614701 0.588805651 0.641099266 0.450584156 0.387192781 0.446164786 0.468415493 1 20.48129648 1.237401154 24.9993595 1.000000614 0.485575494 0.823303803 0.074832272 12.84880903 276911.9813 0.119131485 0.019885507 17.27432769 -1.237401154 -0.51442512 EWNGVVSESDS(ph)PVKRPGR ddPTM_MDA-MB-175_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(0.001)DS(0.999)PVKRPGR;EWNGVVSESDS(1)PVKRPGR;EWNGVVSESDS(1)PVKRPGR;EWNGVVS(0.01)ES(0.215)DS(0.775)PVKRPGR 278.52 1.83E-39 3654720000 3212700 2941480 2002850 2435310 2922920 2380860 2975400 3834630 2596020 TRUE FALSE 2788133.555 2922157.224 2971434.959 2988284.357 2864759.611 2472453.225 2686846.166 3014624.216 2289121.473 1.217992836 1.276540917 1.298067837 1.305428476 1.251466838 1.080088258 1.17374556 1.316935012 1 21.12636259 2.978477826 23.21590349 1.172045388 1.27659966 0.34044013 0.084181266 432.4904991 466526.7895 0.027404067 0.027705032 951.6512577 -2.978477826 0.104554272 EWQELDDAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EWQELDDAEK 10 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 116.55 0.002503 315760000 527070 428630 328460 358720 375440 340160 488500 614170 531200 FALSE TRUE 457416.3641 425814.3013 487304.3546 440172.8587 367969.4785 353246.1753 441125.3452 482834.525 468402.1411 0.976546271 0.909078469 1.040354669 0.939732807 0.785584536 0.754151496 0.941766287 1.030811951 1 18.83738815 1.926049832 5.594068444 1.011109908 0.89992914 0.23941534 0.083169077 0.346840721 19.26150986 0.046366192 0.02463046 84.3431529 -1.926049832 -0.111180768 EWSGLLEELAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EWSGLLEELAR 11 0 Q01813;Q01813-2;Q5VSR5;V9GYV7 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ;;;; 171.85 3.27E-05 468984000 897938 747252 600348 602726 625166 539682 872937 973311 763051 FALSE TRUE 779273.2182 742343.2524 890678.3008 739584.1504 612726.4197 560443.9158 788279.7041 765176.017 672843.9801 1.158178183 1.10329181 1.323751608 1.099191153 0.910651559 0.832947804 1.17156388 1.137226519 1 19.35991248 3.481240922 24.79466767 1.027289624 1.190158291 0.360227006 0.111272825 204.5859289 1231327.836 0.034896757 0.046175348 3028.593056 -3.481240922 0.162868667 EWSLESS(ph)PAQNWTPPQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EWSLESSPAQNWTPPQPR 18 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;F8W1U7;E5RHT6;E5RHC5;Q8N6T3-3 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 EWSLES(0.001)S(0.998)PAQNWT(0.001)PPQPR 208.39 6.69E-16 325970000 214450 204960 123000 153480 200240 215320 205410 233890 196270 TRUE FALSE 186109.8892 203613.6043 182483.2114 188329.9798 196255.6158 223603.4997 185489.3698 183874.4436 173067.1842 1.075362091 1.176500359 1.054406774 1.088190004 1.133985144 1.292004032 1.071776667 1.062445457 1 17.40097267 1.707180137 2.536055296 1.017061952 1.133625949 0.286182136 0.068158619 0.333215151 4.553034641 0.061665177 0.01913111 50.95421754 -1.707180137 0.116563997 EWSLESSPAQNWT(ph)PPQPR ddPTM_MDA-MB-175_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(0.011)S(0.011)PAQNWT(0.977)PPQPR;EWSLES(0.234)S(0.234)PAQNWT(0.532)PPQPR 288.82 7.51E-40 578900000 630410 634750 360430 415840 622520 576720 548210 665230 566670 TRUE FALSE 547099.7212 630580.2855 534735.1536 510262.8277 610133.0699 598906.7916 495044.6786 522975.7413 499678.9182 1.094902549 1.261970963 1.070157523 1.021181421 1.221050254 1.19858327 0.990725565 1.046623586 1 18.93064183 2.231211635 24.97862479 1.018664082 1.144449916 0.422103818 0.072792945 171.1726508 581796.1186 0.029838901 0.020571507 170.2988186 -2.231211635 0.125785834 EWSQHINGASHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EWSQHINGASHSR 13 0 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 235.22 6.42E-17 2057650000 573450 532530 205149 450340 520810 609960 473530 568250 861760 FALSE TRUE 497667.1296 529031.7754 304359.7426 552596.58 510446.8999 633425.5559 427607.1335 446734.1596 759883.7145 0.654925379 0.696200965 0.40053463 0.727212032 0.671743439 0.833582223 0.562727066 0.587898057 1 19.53541913 EWTDGLFTHVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EWTDGLFTHVLR 12 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 162.49 6.25E-05 3359130000 7049337 6795081 4466337 5146358 7323757 7445367 7997686 10178674 8896028 FALSE TRUE 6117749.255 6750443.665 6626272.512 6314917.241 7178028.564 7731795.086 7222071.643 8002043.776 7844349.704 0.779892469 0.860548537 0.844719162 0.805027501 0.915057186 0.985651504 0.92067181 1.020102886 1 22.90322242 3.014975147 2.874187826 0.981910278 0.826615959 0.8327551 0.033491535 0.103315168 1.740946727 0.011142376 0.0122231 1035.082932 -3.014975147 -0.155294319 EWVESMGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EWVESMGGK 9 0 P50502;Q3KNR6;Q8NFI4 P50502 ST13;ST13P5 Hsc70-interacting protein;Putative protein FAM10A5 0 ; 88.177 0.046057 219765000 395920 360420 288160 334530 377540 344790 404690 450440 451530 FALSE TRUE 343598.1689 358052.3773 427515.1398 410490.1495 370027.6926 358054.2944 365443.2261 354116.9113 398150.6378 0.862985353 0.89928872 1.073752242 1.030992068 0.929366068 0.899293535 0.917851666 0.889404355 1 18.60295484 3.024765835 24.97123205 0.91936646 0.970903407 0.076367491 0.06563215 513.3785377 517632.7453 0.020958936 0.023764348 1058.682746 -3.024765835 0.051536947 EWVLDCHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EWVLDCHR 8 0 F5H8D7;P18887 F5H8D7 XRCC1 DNA repair protein XRCC1 0 116.52 0.0022553 278170000 135780 153360 90842 100290 150470 159280 131670 136640 126130 FALSE TRUE 117836.329 152352.5681 134773.495 123062.3773 147475.9414 165407.6047 118900.6637 107420.5993 111219.0551 1.059497663 1.369842317 1.211784212 1.106486449 1.325995274 1.487223611 1.069067379 0.965847078 1 16.76304446 2.015751668 24.93985275 0.991575966 1.260537045 0.487505958 0.122418871 178.4086732 282476.0305 0.049659388 0.033468769 103.6935321 -2.015751668 0.268961079 EWVSMAGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EWVSMAGPR 9 0 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 98.933 0.013211 118370000 79904 104700 78146 73110 95011 114190 100500 108680 84982 FALSE TRUE 69344.48395 104012.2188 115937.667 89710.74292 93120.46699 118582.9632 90753.52547 85439.62775 74935.52477 0.925388648 1.388022825 1.547165611 1.197172412 1.242674516 1.582466574 1.211088142 1.140175211 1 16.1933622 1.647838491 2.312488479 1.020429591 1.320942356 0.227376179 0.185806233 0.400956522 4.534079791 0.19790412 0.050616452 44.44659449 -1.647838491 0.300512764 EYAENIGDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EYAENIGDGR 10 0 A0A087WUB9;Q8WYA6;Q8WYA6-4;Q8WYA6-3;Q8WYA6-2 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 80.986 0.046001 0 153240 126040 87743 111400 109400 142970 135280 170770 158300 FALSE TRUE 132988.9457 125212.0349 130175.8083 136695.0726 107223.154 148470.1484 122160.5664 134252.1644 139585.9543 0.952738736 0.897024601 0.932585294 0.979289595 0.768151456 1.063646762 0.875163744 0.961788491 1 17.09079425 1.484971622 5.259227772 0.992832275 0.92442221 0.10033297 0.075225238 0.338810573 20.34361585 0.055185166 0.01752501 30.54721501 -1.484971622 -0.068410065 EYAENIGDGRS(ph)PEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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;EYAENIGDGRS(1)PEFR;EYAENIGDGRS(1)PEFR 209.31 6.44E-09 1091070000 889235 727266 558684 627966 699165 755034 682277 713292 772397 TRUE FALSE 771720.3417 722488.5418 828865.4511 770555.2782 685252.9844 784080.6466 616109.8816 560760.0566 681085.1066 1.133074757 1.060790399 1.216977795 1.131364158 1.006119467 1.151222716 0.904600432 0.823333312 1 19.37747556 2.229839946 22.87703054 0.891202646 1.114268173 0.660021173 0.069713298 35.71010332 93676.06451 0.02768104 0.019037132 169.7617901 -2.229839946 0.223065527 EYATEVDVDFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EYATEVDVDFVR 12 0 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1;K7EJ01;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7;H7C034 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 ;;; 301.79 3.33E-36 1311060000 1314690 1117290 927610 1097300 1195300 1250730 1092370 1333450 1749930 FALSE TRUE 1140950.385 1109950.448 1376205.299 1346458.736 1171515.869 1298846.392 986432.1255 1048302.094 1543055.269 0.739409928 0.719319956 0.891870386 0.872592682 0.759218346 0.841736792 0.639272063 0.67936782 1 20.55735831 EYATEVDVDFVRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EYATEVDVDFVRK 13 1 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1;K7EJ01;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7;H7C034 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 78.486 0.037037 355880000 231730 198110 83844 107780 170040 131870 204510 250390 69949 FALSE TRUE 201106.2934 196808.6024 124391.2388 132253.0963 166656.5367 136943.1242 184676.6517 196846.047 61679.70891 3.260493555 3.190816005 2.016728695 2.144191318 2.701966978 2.220229743 2.994123269 3.191423088 1 15.91250834 4.29786946 10.15640007 2.441025357 3.229918337 0.259633374 0.608537605 0.664524977 108.6439397 0.152108158 0.402671247 19854.98028 -4.29786946 0.78889298 EYCIQAFESFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EYCIQAFESFVR 12 0 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 138.63 0.00016539 208701000 303110 257320 200340 239480 318490 329440 269990 310540 352610 FALSE TRUE 263053.2455 255629.648 297225.0941 293857.5942 312152.6721 342113.77 243806.4114 244133.4376 310924.8475 0.846034814 0.822158956 0.955938699 0.945108108 1.003948943 1.100310164 0.784132929 0.785184715 1 18.24620639 7.538400939 20.4556486 0.908196612 0.147693918 0 0.105375543 0 0 0.02555426 0 34546252.21 -7.538400939 -0.760502694 EYDQCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EYDQCR 6 0 A0A087WTZ5;Q04323;E9PJ81;E9PRQ7;Q04323-2;E9PS08 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 0 ; 122.79 0.04436 408330000 800120 770180 484580 546250 556770 763380 678630 796550 774800 FALSE TRUE 694382.1148 765120.6369 718924.5088 670284.4114 545691.3663 792747.7226 612816.5671 626213.9813 683204.0267 1.016361274 1.119900655 1.05228377 0.981089668 0.798723873 1.160338188 0.896974466 0.916584149 1 19.38195695 3.713882266 4.054002533 0.951115543 1.070468875 0.215312646 0.093913062 0.297668097 11.35740075 0.025050194 0.040666685 5174.665316 -3.713882266 0.119353332 EYDSISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 EYDSISR 7 0 P54920;M0R0Y2;M0R213 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;;; 166.17 0.0026368 870920000 1999000 1945470 1452150 1666940 1797750 1975390 1737730 1985510 2570280 FALSE TRUE 1734827.085 1932690.079 2154414.597 2045444.205 1761978.292 2051384.532 1569205.212 1560924.138 2266424.426 0.765446694 0.852748522 0.950578617 0.902498306 0.777426448 0.905119318 0.692370411 0.688716606 1 21.11198662 2.250628772 24.99839104 0.767603134 0.861122981 0.064368156 0.102073217 409.7284668 848725.6461 0.03818467 0.029343768 178.085587 -2.250628772 0.093519846 EYEEDGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EYEEDGAR 8 0 P61163 P61163 ACTR1A Alpha-centractin 0 ; 93.195 0.023925 270610000 1011580 1053020 680580 763060 855960 1089330 937750 1054530 1043600 FALSE TRUE 877897.14 1046102.642 1009710.764 936324.4356 838928.0707 1131237.23 846807.1493 829026.9659 920226.7969 0.954000843 1.13678785 1.09724121 1.017493121 0.911653598 1.229302639 0.920215704 0.90089418 1 19.81162994 EYEEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EYEEEER 7 0 Q16543;K7EKQ2;K7EQA9;K7EL68;K7EIU0 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;; 180.7 0.001588 1911100000 2351070 2215520 1740030 2000070 1851500 2053370 2036620 2533490 3190460 FALSE TRUE 2040370.143 2200966.103 2581514.328 2454216.463 1814658.772 2132364.473 1839108.906 1991722.879 2813287.453 0.725261878 0.782346681 0.917614844 0.87236605 0.64503141 0.757961818 0.653722357 0.707969915 1 21.42382554 4.740519106 20.41550525 0.779828807 0.725261688 0.023325092 0.113404325 79.08019703 823346.6434 0.028332904 0.174936242 55019.81249 -4.740519106 -0.054567119 EYELESLFEHYCYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EYELESLFEHYCYSR 15 0 K7ES25;A0A494C165;P12955-3;P12955 K7ES25 PEPD Xaa-Pro dipeptidase 0 116.96 0.00040748 27604000 40716 41172 25498 25402 38361 36388 40081 36885 39185 FALSE TRUE 35335.27744 40901.53842 37828.91809 31169.91235 37597.69115 37787.86991 36193.95079 28997.42979 34552.59394 1.022651946 1.183747261 1.094821366 0.902100502 1.088129337 1.093633374 1.047503144 0.839225843 1 15.0765064 1.848108352 7.167531776 0.913609385 1.064825869 0.353122732 0.080106905 0.244230101 13.95391755 0.039190969 0.021262965 70.48689044 -1.848108352 0.151216484 EYELFEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EYELFEFR 8 0 A0A2R8YE10;Q9NRW7;B7Z7G7;A0A2R8YF01;A0A087WU65;A0A1B0GXI6;A0A2R8YD95;Q9NRW7-2 A0A2R8YE10 VPS45 Vacuolar protein sorting-associated protein 45 0 ;;;;; 160.75 0.00081788 707275000 1154162 1108418 755802 921579 1105219 1197082 1006187 1295685 1287874 FALSE TRUE 1001636.567 1101136.729 1121310.375 1130837.597 1083227.304 1243134.519 908607.1396 1018612.846 1135623.003 0.882015039 0.969632287 0.987396673 0.995786097 0.953861714 1.094671837 0.800095751 0.896963907 1 20.11505255 2.230077034 24.99999934 0.894469758 0.979853083 0.231629569 0.069837716 259.4758059 764633.1352 0.027576244 0.01892989 169.8544908 -2.230077034 0.085383325 EYFDDST(ph)EER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EYFDDSTEER 10 0 Q8NEF9 Q8NEF9 SRFBP1 Serum response factor-binding protein 1 1 EYFDDS(0.357)T(0.643)EER;EYFDDS(0.237)T(0.763)EER 182.23 2.01E-05 309560000 328950 292480 260940 362050 339240 342780 272920 354150 743560 TRUE FALSE 285478.424 290558.6796 387131.4568 444258.9861 332489.7877 355966.9684 246452.2604 278417.7785 655657.1839 0.435408062 0.443156404 0.590447975 0.677578157 0.507109197 0.542916294 0.375885854 0.424639256 1 19.32258216 1.23340235 24.99957279 1.000000778 0.49854434 0.760441419 0.088256414 88.85877895 430605.4044 0.196647414 0.023945665 17.11600286 -1.23340235 -0.501456438 EYFLIGHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EYFLIGHDR 9 0 Q5SXH7-4;Q5SXH7-3;Q5SXH7-2;Q5SXH7-1;Q5SXH7;A0A494C040 Q5SXH7-4 PLEKHS1 Pleckstrin homology domain-containing family S member 1 0 ;;;; 108.67 0.0025742 2120140000 1870740 2019310 1318000 1475160 1845560 1780990 2256200 2108370 2032330 FALSE TRUE 1623516.969 2006045.02 1955389.208 1810117.624 1808836.967 1849505.838 2037394.071 1657511.483 1792070.263 0.90594493 1.119400875 1.091134231 1.010070678 1.009356053 1.032049846 1.136894079 0.924914339 1 20.77319577 1.675236265 11.73567373 0.963240689 1.04516102 0.199035533 0.067460764 0.16827723 29.11011647 0.034979711 0.016423428 47.34087324 -1.675236265 0.081920331 EYFSWEGAFQHVGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EYFSWEGAFQHVGK 14 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 231.69 4.44E-13 5916300000 5558000 4993100 2084600 1976120 2785400 2847400 2995400 4109200 4726900 FALSE TRUE 4823496.218 4960299.997 3092719.533 2424828.249 2729975.99 2956941.321 2704906.569 3230479.558 4168091.267 1.157243426 1.190065111 0.741998995 0.581759874 0.6549703 0.709423362 0.648955696 0.775050101 1 21.99095544 4.229142188 8.07246321 0.720695301 1.174875206 0.73366709 0.110947461 0.05961308 27.45168767 0.029084194 0.065793867 16948.92618 -4.229142188 0.454179905 EYGEQIDPSTHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EYGEQIDPSTHR 12 0 Q9Y2B0;F8VXJ7;F8W031;F8W1K5 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 119.39 0.00022899 0 344310 289040 190320 282960 336720 360440 253920 297250 395720 FALSE TRUE 298808.5611 287141.2772 282359.3886 347210.3928 330019.9308 374306.36 229294.8775 233685.4007 348938.4324 0.856336056 0.822899545 0.809195441 0.995047723 0.945782694 1.072700297 0.657121303 0.669703819 1 18.41261298 2.223100455 24.99925113 0.748607985 0.912673244 0.220475236 0.12166668 319.2392749 516209.3547 0.050877039 0.034438072 167.1477192 -2.223100455 0.164065259 EYGS(ph)PLK ddPTM_MDA-MB-175_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 140.88 0.0027215 10668440000 12462920 9538370 7928720 9382900 9964450 8262810 11884430 13534150 15786280 TRUE FALSE 10815913.54 9475711.819 11763075.51 11513430.85 9766176.94 8580685.647 10731879.81 10639977.35 13920043.96 0.777002829 0.680724274 0.845045859 0.827111673 0.701590955 0.61642662 0.770965942 0.764363775 1 23.73066043 1.208510118 3.418047628 1.050193762 0.744567188 0.579259601 0.067615262 0.286070229 4.508252677 0.240862919 0.018073899 16.1625588 -1.208510118 -0.305626574 EYGS(ph)PLKAYT(ph)PVVVTLWYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EYGSPLKAYTPVVVTLWYR 19 1 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12 P21127-2 CDK11B Cyclin-dependent kinase 11B 2 EYGS(0.999)PLKAY(0.02)T(0.943)PVVVT(0.037)LWYR;EY(0.002)GS(0.998)PLKAY(0.214)T(0.783)PVVVT(0.003)LWYR 87.792 0.0060952 720520000 1308720 1039950 506350 516290 1013810 803680 1283970 1404180 275290 TRUE FALSE 1135769.336 1033118.5 751222.5536 633521.5355 993637.1645 834598.0897 1159450.787 1103907.034 242745.5298 4.678847586 4.255973326 3.094691607 2.609817515 4.093328373 3.43816049 4.776404278 4.547589549 1 17.8890852 1.231220546 24.99992758 0.999994848 3.936325042 0.631505497 0.705035992 191.6307515 652628.5512 1.888499155 0.187372175 17.0302313 -1.231220546 2.936330193 EYGS(ph)TSSIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EYGSTSSIDR 10 0 Q9P2F8 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 EYGS(0.695)T(0.257)S(0.047)S(0.001)IDR;EYGS(0.729)T(0.262)S(0.01)SIDR 90.689 0.011182 733260000 460550 523970 385570 362940 507520 578610 568600 622260 604360 TRUE FALSE 399687.1506 520528.0066 572032.9417 445351.0742 497421.3449 600869.5011 513457.2595 489194.5414 532913.2493 0.750004154 0.976759364 1.073407243 0.835691503 0.933400222 1.127518413 0.963491263 0.917962806 1 19.02354118 2.974196343 24.92529062 0.990443329 0.920427795 0.160481158 0.098692093 1748.48455 1688966.143 0.032152407 0.032267911 942.3155186 -2.974196343 -0.070015535 EYGSCSHHYQQLLQSLEQGAQEESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 298.23 2.55E-63 1000680000 367614 366064 167061 273256 431234 453859 371492 450961 403724 FALSE TRUE 319032.8785 363659.3015 247852.2584 335302.9513 422653.2871 471319.2494 335464.763 354526.4995 355996.2086 0.896169315 1.021525771 0.696221624 0.941872253 1.187240979 1.323944576 0.942326786 0.99587156 1 18.44150235 3.442587711 9.242275657 1.077742663 0.875166254 0.370301608 0.132320381 0.374004014 94.27381501 0.040552443 0.052557496 2770.688554 -3.442587711 -0.202576409 EYHPDKNPNAGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EYHPDKNPNAGDK 13 1 O60884;I3L320 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ;; 158.81 2.80E-05 415560000 385605 282081 299548 362047 240717 247796 322624 419730 1370130 FALSE TRUE 334646.3223 280227.9913 444410.4147 444255.3049 235927.2027 257328.8725 291335.9741 329974.0058 1208154.792 0.276989608 0.231947092 0.367842281 0.367713895 0.195278953 0.212993297 0.241141264 0.273122292 1 20.20437388 1.238610412 10.2534335 1.00260976 0.270086556 0.93977494 0.058007063 0.016642573 42.23145983 0.084912818 0.01511314 17.32249371 -1.238610412 -0.732523204 EYHTMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EYHTMR 6 0 Q9Y3P9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 0 80.555 0.048701 19005000 19468 24131 10658 14535 14371 26925 20040 16523 16801 FALSE TRUE 16895.25447 23972.48187 15812.24445 17835.3939 14085.04522 27960.82217 18096.52388 12989.68503 14814.80492 1.140430439 1.618143607 1.067327213 1.203889893 0.950741187 1.887356757 1.221516178 0.876804325 1 13.85475201 1.834770797 5.303684697 0.941140592 1.311662261 0.235691859 0.272196635 0.294126922 12.02420373 0.141210927 0.070952061 68.35508011 -1.834770797 0.370521669 EYIDHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EYIDHLK 7 0 M0R3F6;M0R2Z9;Q8IX01-4;Q8IX01-3;Q8IX01 M0R3F6 SUGP2 SURP and G-patch domain-containing protein 2 0 71.296 0.054702 1157000000 3117900 2143000 1705400 1712900 2369000 2369000 3041400 3266900 1689700 FALSE TRUE 2705861.615 2128922.492 2530137.144 2101840.125 2321861.535 2460136.963 2746445.496 2568298.858 1489945.591 1.816080823 1.428859218 1.69814063 1.410682469 1.558353237 1.651158927 1.843319322 1.723753454 1 20.50682822 1.234004792 24.99946679 0.99999904 1.640276515 0.661941754 0.144025781 88.95530172 488068.2255 0.279617413 0.035897609 17.13976219 -1.234004792 0.640277475 EYIPGQPPLSQS(ph)SDS(ph)SPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 2 EYIPGQPPLS(0.01)QS(0.951)S(0.04)DS(0.538)S(0.407)PT(0.055)R;EYIPGQPPLS(0.091)QS(0.749)S(0.16)DS(0.378)S(0.311)PT(0.311)R;EYIPGQPPLS(0.335)QS(0.47)S(0.192)DS(0.409)S(0.346)PT(0.248)R 120.9 5.29E-05 531860000 580218 485861 360775 360067 455845 483611 410284 445391 497092 TRUE FALSE 503540.7212 482669.3471 535246.9967 441825.7156 446774.5763 502215.8281 370494.7208 350147.6007 438326.35 1.148780403 1.101164343 1.221115264 1.007983471 1.019273827 1.145757785 0.845248571 0.798828546 1 18.74164588 2.234998333 24.99997823 0.862660535 1.103716474 0.638773168 0.079667674 53.27545347 373878.4026 0.031890905 0.022467518 171.7901792 -2.234998333 0.241055939 EYIPGQPPLSQS(ph)SDSS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 2 EYIPGQPPLSQS(1)SDS(0.101)S(0.896)PT(0.003)R;EYIPGQPPLSQS(0.997)S(0.002)DS(0.102)S(0.893)PT(0.005)R;EYIPGQPPLS(0.048)QS(0.949)S(0.004)DS(0.124)S(0.868)PT(0.007)R 279.47 2.00E-39 1068781000 1107690 865250 558880 583810 716030 771450 704680 757730 794520 TRUE FALSE 961305.96 859566.1158 829156.2373 716372.9835 701782.4039 801128.1807 636340.2421 595695.3362 700592.7507 1.372132325 1.226912661 1.183506733 1.022524117 1.001698067 1.143500528 0.908288362 0.850273337 1 19.41821653 8 0.258924993 0.859430253 4.376610514 0.788460349 0.071868686 36.65573801 0.585126386 0.223776022 55.32131695 100000000 -8 3.517180261 EYIPGQPPLSQSSDS(ph)SPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 EYIPGQPPLSQS(0.001)S(0.012)DS(0.579)S(0.408)PTR 208.62 2.75E-16 3634800000 857450 933600 570070 688320 928050 1020400 818860 989420 935760 TRUE FALSE 744135.81 927467.1201 845757.7588 844613.5763 909583.6207 1059655.448 739447.0832 777840.2327 825135.5188 0.90183466 1.124017933 1.024992549 1.023605889 1.102344524 1.284219894 0.896152288 0.942681796 1 19.65427156 EYIPGQPPLSQSSDSS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 EYIPGQPPLSQS(0.001)S(0.001)DS(0.413)S(0.578)PT(0.007)R;EYIPGQPPLSQSSDS(0.058)S(0.939)PT(0.004)R;EYIPGQPPLSQSS(0.001)DS(0.247)S(0.741)PT(0.011)R;EYIPGQPPLSQSSDS(0.043)S(0.952)PT(0.005)R;EYIPGQPPLSQSSDS(0.014)S(0.986)PTR;EYIPGQPPLSQSSDS(0.155)S(0.841)PT(0.003)R;EYIPGQPPLSQSSDS(0.26)S(0.728)PT(0.011)R;EYIPGQPPLSQSSDS(0.211)S(0.783)PT(0.007)R 272.63 2.46E-39 35368280000 4725700 4669820 3045010 3679623 4845430 5163890 4632620 5220570 5051320 TRUE FALSE 4101186.772 4639143.645 4517587.021 4515137.642 4749015.423 5362548.19 4183349.225 4104191.732 4454158.704 0.920754523 1.041530837 1.014240246 1.013690338 1.066198072 1.203941877 0.939200757 0.921429164 1 22.08672153 EYISLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EYISLR 6 0 K7ESG5;K9J957;P61289;P61289-2;A0A087WTV2;B3KQ25;P61289-3 K7ESG5 PSME3 Proteasome activator complex subunit 3 0 118.06 0.05163 231680000 274560 261670 187490 248020 290280 344070 251600 266480 368910 FALSE TRUE 238276.2004 259951.0725 278160.7911 304336.7317 284503.9959 357306.5955 227199.8707 209495.3257 325297.8801 0.732486176 0.79911702 0.855095616 0.935563219 0.874595297 1.098398168 0.698436371 0.644010732 1 18.31140189 EYKPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EYKPKPR 7 2 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 0 71.342 0.030695 319310000 766150 764530 487670 705320 663470 659860 1008200 1085700 878310 FALSE TRUE 664901.3363 759507.7521 723508.8432 865473.6861 650268.2451 685245.2412 910424.9192 853531.5039 774477.1924 0.858516355 0.980671554 0.934189993 1.117494091 0.839622201 0.884784275 1.175534836 1.102074422 1 19.56286323 2.243171819 24.99999955 1.097981774 0.94171878 0.415298094 0.087362943 110.1244662 597052.1439 0.033249023 0.024871387 175.0539115 -2.243171819 -0.156262994 EYLQTHWEEEECQQDVSLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EYLQTHWEEEECQQDVSLLR 20 0 Q9UHY7 Q9UHY7 ENOPH1 Enolase-phosphatase E1 0 ; 213.18 9.95E-23 176782000 172730 177562 95363 117495 158375 138827 133183 168970 214240 FALSE TRUE 149903.2929 176395.5835 141480.8658 144174.0355 155223.6474 144167.7645 120266.9332 132837.0804 188912.7913 0.793505256 0.933740814 0.748921578 0.763177732 0.821668275 0.763144536 0.636626733 0.703166152 1 17.52736086 4.216740845 24.94966156 0.76324859 0.863623072 0.105367866 0.099524081 383.8560637 438918.3171 0.025384644 0.052913283 16471.79184 -4.216740845 0.100374482 EYLSEEVQAVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EYLSEEVQAVHK 12 0 Q53GS9;B9A018;A0A087X1B2;Q53GS9-2 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 0 74.392 0.036627 127770000 229040 203280 121520 160670 208960 171460 201210 210360 179440 FALSE TRUE 198771.7837 201944.6403 180287.4785 197152.5792 204802.1048 178056.1771 181696.6852 165376.151 158226.8076 1.256245934 1.276298519 1.139424357 1.246012494 1.294357814 1.12532244 1.148330602 1.045184147 1 17.27163452 1.85377174 0.964029756 0.967978279 1.238890404 0.759257795 0.048478606 0.430074538 0.60007371 0.104519792 0.018944715 71.41208932 -1.85377174 0.270912125 EYNEFAEVFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EYNEFAEVFLK 11 0 O95373 O95373 IPO7 Importin-7 0 162.38 5.86E-05 54572000 126790 121780 72334 91050 115960 101400 125610 145000 140000 FALSE TRUE 110034.3803 120980.0192 107314.9643 111724.2941 113652.6229 105300.9236 113428.3615 113992.8784 123449.3595 0.891332128 0.979997139 0.869303533 0.905021254 0.920641657 0.852988821 0.918825031 0.923397893 1 16.91355983 1.142873739 2.081553378 1.047705983 0.905632561 0.434169483 0.033716556 0.941780251 3.247524946 0.28155625 0.008746372 13.89548595 -1.142873739 -0.142073422 EYPDFNFVGR ddPTM_MDA-MB-175_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 95.775 0.012923 0 58589 66643 49650 56199 65696 60658 44701 69235 80541 FALSE TRUE 50846.3152 66205.21774 73660.90607 68959.8419 64388.77813 62991.55251 40365.9039 54429.63404 71019.53473 0.715948301 0.93221137 1.03719218 0.970998221 0.90663475 0.886960929 0.568377476 0.766403698 1 16.11592829 2.454504516 24.97767773 0.761419947 0.921147649 0.178528146 0.130214307 330.4231259 364913.1664 0.048871441 0.03785822 284.7767414 -2.454504516 0.159727703 EYRPCDPQLVSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EYRPCDPQLVSER 13 1 O15020;O15020-2;A4QPE4 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 ; 115.83 0.00057781 314600000 321850 318490 215870 285630 348900 401420 294870 347840 358180 FALSE TRUE 279316.707 316397.8182 320265.454 350486.6571 341957.5726 416862.8872 266273.5528 273457.1229 315836.3684 0.884371576 1.00177766 1.014023355 1.109709622 1.082704865 1.319869809 0.843074387 0.865818982 1 18.26881778 EYS(ph)PPYAPSHQQYPPSHATPLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 EYSPPYAPSHQQYPPSHATPLPK 23 0 Q9UPT8 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 EYS(1)PPYAPSHQQYPPSHATPLPK;EY(0.001)S(0.815)PPY(0.005)APS(0.178)HQQY(0.001)PPSHATPLPK;EYS(1)PPYAPSHQQYPPSHATPLPK;EYS(1)PPYAPSHQQYPPSHATPLPK;EYS(1)PPYAPSHQQYPPSHATPLPK;EYS(0.999)PPYAPS(0.001)HQQYPPSHATPLPK 237.5 6.25E-37 4143160000 4636843 3595069 1688846 2883197 3975238 3148871 4104050 4739354 5059551 TRUE FALSE 4024072.449 3571452.755 2505577.574 3537870.946 3896138.541 3270010.105 3706039.863 3725880.029 4461416.645 0.9019719 0.800519889 0.561610308 0.792992726 0.873296276 0.732953312 0.830686788 0.835133843 1 22.08907045 -0.836819909 0.871664792 9.999999995 0.77150396 0.35311527 0.091886253 90.60615932 2.209544346 1558.017765 0.033073069 0.145606275 0.836819909 -9.228496034 EYSGFAGVSRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EYSGFAGVSRPR 12 1 E9PK91;Q9NYF8-3;H0YF63;Q9NYF8;Q9NYF8-2;H0YF14;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 106.79 0.00077655 0 159210 119560 68768 95911 125280 131980 117150 144820 106220 FALSE TRUE 138169.9951 118774.6025 102024.4348 117689.0585 122787.1731 137057.356 105788.811 113851.37 93662.79261 1.475185517 1.268108703 1.089273894 1.256518786 1.310949308 1.463306316 1.129464626 1.215545328 1 16.51518843 1.005549724 1.184385984 0.734088165 1.288513718 0.371069616 0.11944118 3.032983313 2.449176658 2.394687157 0.037759101 10.12860708 -1.005549724 0.554425554 EYSSELNAPSQESDSHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EYSSELNAPSQESDSHPR 18 0 P49756;P49756-2;P49756-3;E9PQU5 P49756 RBM25 RNA-binding protein 25 0 ; 163.56 3.28E-11 1125840000 534300 480860 205280 285510 464220 469590 437370 462050 500540 FALSE TRUE 463690.9013 477701.199 304554.0946 350339.4092 454982.9302 487655.4312 394953.9247 363244.2032 441366.7314 1.050579639 1.082322624 0.690025036 0.793760346 1.03085008 1.104875824 0.894842988 0.822998603 1 18.75161836 2.541089596 0.011185882 3.76E-07 1.852937458 0.000916398 0.137822297 20387.52877 195.7948185 16405.57253 16021.95859 347.6078661 -2.541089596 1.852937083 EYTAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EYTAGR 6 0 P07237;I3L3P5 P07237 P4HB Protein disulfide-isomerase 0 ; 152.78 0.023762 1585400000 1312270 1216190 793540 893900 816740 1495000 996060 988840 975140 FALSE TRUE 1138850.195 1208200.768 1177298.598 1096873.657 800488.4719 1552513.617 899462.2545 777384.2612 859860.0601 1.32445993 1.405113255 1.369174652 1.275642059 0.930952034 1.805542192 1.046056558 0.9040823 1 19.71374236 2.020209675 24.99989444 0.954153549 1.340213934 0.40992673 0.210318034 208.7435247 258220.1291 0.081609171 0.055014395 104.7634218 -2.020209675 0.386060385 EYTINIHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EYTINIHK 8 0 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2;B8ZZK4 H7C2W9 RPL31 60S ribosomal protein L31 0 ;;;; 164.53 0.00032954 5047930000 4890520 4587800 3527090 4288160 4483280 4208370 4875880 5625810 7338100 FALSE TRUE 4244225.391 4557662.44 5232802.521 5261852.268 4394071.499 4370268.717 4403017.908 4422774.312 6470598.178 0.655924734 0.704364931 0.808704602 0.813194101 0.679082734 0.675404128 0.680465358 0.683518616 1 22.62546766 1.234925295 24.99974016 1.000000405 0.713396992 0.730954341 0.054798411 61.37891369 422031.5285 0.105460799 0.014649979 17.17612906 -1.234925295 -0.286603414 EYTINIHKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EYTINIHKR 9 1 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2;B8ZZK4 H7C2W9 RPL31 60S ribosomal protein L31 0 145.9 6.24E-05 411830000 558100 475760 263830 334080 433510 451820 555730 672940 284990 FALSE TRUE 484345.671 472634.7012 391419.0705 409937.9701 424883.9991 469201.8078 501835.3901 529037.0178 251298.8069 1.927369561 1.880767788 1.557584277 1.631277025 1.690752155 1.867107185 1.996966863 2.105211021 1 17.9390443 2.740631207 24.09276558 1.822895812 1.729604532 0 0.314791799 645.6396167 7512505.768 0.103943591 0.099055412 550.3401611 -2.740631207 -0.09329128 EYTLDVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EYTLDVYR 8 0 P54577;A0A0C4DGZ5 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed;Tyrosine--tRNA ligase" 0 107.29 0.0093769 247960000 345290 396490 226760 318850 381990 381020 363270 438220 655370 FALSE TRUE 299659.0516 393885.4311 336421.8945 391249.7658 374389.1464 395678.086 328040.1313 344510.0632 577892.9052 0.518537343 0.681588972 0.582152664 0.677028152 0.647852124 0.684691026 0.567648657 0.596148629 1 19.14044263 1.236235905 24.99570951 1.000000493 0.621435969 0.826199969 0.054844971 23.91680483 257098.1337 0.082950536 0.012731375 17.22804135 -1.236235905 -0.378564524 EYVAYSHTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EYVAYSHTGR 10 0 Q969X5;Q969X5-2 Q969X5 ERGIC1 Endoplasmic reticulum-Golgi intermediate compartment protein 1 0 ;; 164.64 6.10E-06 2136190000 1907910 1977360 1236990 1266530 2073070 2018910 1470750 1972680 1932660 FALSE TRUE 1655774.859 1964370.592 1835202.501 1554114.994 2031819.963 2096578.774 1328116.891 1550837.733 1704183.136 0.97159444 1.15267576 1.076881036 0.911941305 1.19225447 1.230254384 0.779327563 0.910018237 1 20.70064895 2.233692658 24.99994151 0.89439558 1.088207124 0.415457136 0.107802822 118.6231587 609193.5111 0.043361262 0.030289152 171.2744801 -2.233692658 0.193811544 EYVDLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EYVDLER 7 0 Q13951-2;A0A494C0A9;Q13951 Q13951-2 CBFB Core-binding factor subunit beta 0 ; 92.187 0.036883 878270000 1577260 1465530 948800 1140470 1440030 1544710 1347170 1547220 1515510 FALSE TRUE 1368821.095 1455902.837 1407642.854 1399431.144 1411376.22 1604135.993 1216521.661 1216359.043 1336348.134 1.024299776 1.08946374 1.053350409 1.047205521 1.056144117 1.200387797 0.910332891 0.910211203 1 20.34986446 2.207084842 24.9998095 0.93269379 1.075396336 0.5974689 0.053352767 125.3508568 99559.76823 0.021203454 0.014296922 161.0960314 -2.207084842 0.142702546 EYVEHTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EYVEHTVK 8 0 O75937 O75937 DNAJC8 DnaJ homolog subfamily C member 8 0 ; 81.548 0.022576 520560000 1305740 1081720 733940 980470 853910 948790 1245920 1508120 1438630 FALSE TRUE 1133183.151 1074614.11 1088875.839 1203100.699 836918.8616 985290.5652 1125090.87 1185620.274 1268556.8 0.893285307 0.847115486 0.858357969 0.948401127 0.659740945 0.77670197 0.886906183 0.934621354 1 20.27475669 1.686846376 2.166374318 0.990784916 0.831311243 0.35546464 0.076423394 0.347186995 3.335727752 0.0848323 0.022399277 48.62351779 -1.686846376 -0.159473673 EYVEPELHINDLWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EYVEPELHINDLWR 14 0 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ;; 148.72 7.68E-06 227462000 310448 298314 211270 254162 298524 302398 273878 345403 383296 FALSE TRUE 269421.5102 296354.3557 313440.8787 311873.3667 292583.9565 314031.4467 247317.3537 271541.2564 337983.1835 0.79714472 0.876831659 0.927386018 0.922748178 0.865676077 0.929133348 0.731744553 0.80341647 1 18.36659194 1.225249319 24.86376161 1.000000375 0.855836249 0.329502991 0.064202765 840.1328867 1569156.72 0.318659316 0.017039088 16.79768061 -1.225249319 -0.144164126 EYVESQLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EYVESQLQR 9 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;; 186.76 9.61E-05 551588000 658436 602034 400695 456734 592667 745345 521639 564856 486572 FALSE TRUE 571422.0143 598079.199 594472.4422 560442.4354 580874.0862 774018.9045 471050.5301 444065.9401 429050.0125 1.331830784 1.3939615 1.385555122 1.306240343 1.353861017 1.804029558 1.097891892 1.034998082 1 18.7107863 2.028102343 24.95914861 1.033932543 1.41949908 0.630392868 0.139698974 124.940857 110965.9506 0.056211047 0.037896698 106.6847497 -2.028102343 0.385566538 EYVSNDAAQS(ph)DDEEKLQSQPTDTDGGR ddPTM_MDA-MB-175_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(0.999)DDEEKLQS(0.001)QPTDTDGGR;EYVS(0.002)NDAAQS(0.996)DDEEKLQS(0.002)QPTDTDGGR 334.86 1.39E-95 3275010000 1723840 1412830 1316590 1285310 1499640 1206700 1805660 1933610 2361940 TRUE FALSE 1496030.176 1403549.027 1953297.328 1577159.28 1469800.098 1253122.53 1630547.371 1520122.549 2082714.144 0.718307974 0.673903824 0.93786146 0.757261521 0.705713793 0.601677639 0.782895423 0.72987575 1 20.99003341 1.23725616 24.94825738 1.000000322 0.739627084 0.477510672 0.085977578 29.87838285 571203.688 0.128216887 0.021207329 17.26856144 -1.23725616 -0.260373238 EYVTCHTCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 EYVTCHTCR 9 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;;;; 244.8 1.41E-10 4274629000 2976299 3196323 1951886 2379804 3042404 3008413 2776180 3047571 2953799 FALSE TRUE 2582973.546 3175326.144 2895824.598 2920174.871 2981866.113 3124148.595 2506946.491 2395871.658 2604604.247 0.991695206 1.219120389 1.111809827 1.121158761 1.144844218 1.199471512 0.962505722 0.919860152 1 21.31263275 2.22210319 23.09953242 0.952333142 1.134601465 0.616572704 0.063253422 55.51707508 77921.82601 0.023904608 0.016184922 166.7643403 -2.22210319 0.182268323 EYWDYEAHVPSWGNQDDYQLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EYWDYEAHVPSWGNQDDYQLVR 22 0 P19784;H3BNI9 P19784 CSNK2A2 Casein kinase II subunit alpha 0 ; 114.37 0.00023027 563010000 254145 200977 128899 177084 210592 200694 193957 223079 216240 FALSE TRUE 220559.0943 199656.7689 191234.9875 217293.6288 206401.6312 208414.828 175147.08 175375.2919 190676.3535 1.156719699 1.047097687 1.00292975 1.139594002 1.082471043 1.093029231 0.918556899 0.919753753 1 17.54076642 2.24131783 24.99901853 0.939466218 1.083528048 0.653833269 0.048195417 41.23562046 373879.4727 0.018444517 0.013633835 174.3082048 -2.24131783 0.144061829 EYWDYESHVVEWGNQDDYQLVR ddPTM_MDA-MB-175_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 ;;; 335.98 6.07E-81 1433860000 1171030 1015850 686120 880360 877220 988260 984590 1111350 1125060 FALSE TRUE 1016275.418 1009176.814 1017929.927 1080259.193 859765.0383 1026279.002 889104.6133 873696.451 992056.6885 1.024412647 1.017257205 1.026080403 1.088908735 0.866649102 1.034496328 0.896223597 0.880692062 1 19.92006304 3.242461882 24.9999998 0.930737257 1.036665326 0.469761965 0.054502317 86.72069621 555717.4891 0.015663114 0.019466994 1747.679863 -3.242461882 0.105928068 EYWMDPEGEMKPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EYWMDPEGEMKPGR 14 1 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 60.401 0.097846 192630000 376200 263050 220400 246090 230920 195140 292880 319180 413130 FALSE TRUE 326484.2168 261322.0072 326986.1772 301968.4958 226325.1438 202647.1621 264476.5427 250925.8409 364290.242 0.896220044 0.717345614 0.897597958 0.828922823 0.621276987 0.556279413 0.726005015 0.688807472 1 18.47472883 3.276421469 20.40950097 0.707220907 0.831087373 0.175873109 0.123912598 41.39119253 22310.80091 0.035625814 0.045987593 1889.824476 -3.276421469 0.123866466 EYWNDPELDEGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EYWNDPELDEGER 13 0 A0A494C108;Q8N9T8;H0YFD2;F8WFC1 A0A494C108 KRI1 Protein KRI1 homolog 0 ; 155.15 2.79E-06 0 293988 231715 204303 188481 230259 236090 225942 250462 230101 FALSE TRUE 255136.7409 230192.8489 303104.6142 231278.4918 225677.2964 245172.5351 204030.1796 196902.6504 202898.7219 1.257458591 1.134520941 1.493871481 1.139871605 1.112265737 1.208349332 1.005576465 0.970447958 1 17.63040025 2.482310385 0.839264382 0.95130549 1.269217399 0.525348305 0.105358477 0.548561187 0.822915066 0.118249611 0.05726285 303.6060244 -2.482310385 0.317911908 EYYDHLPELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EYYDHLPELK 10 0 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 102.52 0.0029357 954520000 2492800 1899300 1395900 1584200 1833200 1639600 1948600 2576700 2308900 FALSE TRUE 2163370.164 1886823.373 2070961.909 1943916.823 1796722.907 1702676.473 1759625.072 2025692.757 2035944.472 1.062588 0.926755812 1.017199603 0.954798547 0.882500938 0.836307913 0.864279501 0.994964639 1 20.95726678 7.99999002 0.746773606 0.925021852 23.15643856 0.31156201 0.060020038 543.8867985 2.386318062 0.024652792 20329.56604 99997702.15 -7.99999002 22.2314167 EYYS(ph)TESEPLTNGGQKPSSSDTFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EYYSTESEPLTNGGQKPSSSDTFFR 25 1 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 EYYS(0.87)T(0.112)ES(0.019)EPLTNGGQKPSSSDTFFR 202.14 3.53E-25 197620000 150920 104950 62889 104610 98325 61477 186560 144320 115220 TRUE FALSE 130975.5396 104260.5765 93302.33075 128363.2994 96368.52487 63842.05997 168467.4399 113458.2911 101598.8229 1.289144263 1.026198667 0.918340667 1.263432939 0.948520093 0.628374012 1.658163305 1.116728402 1 16.63252416 2.242206554 25 1.245464759 1.017205729 0.180218198 0.246641415 170.6441917 1170110.151 0.093185977 0.069292654 174.6652676 -2.242206554 -0.228259031 EYYSEADASHCIQQILESVNHCHLNGIVHR ddPTM_MDA-MB-175_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 64.315 0.0028696 214580000 74521 90279 57493 60787 95406 97981 66821 99541 83208 FALSE TRUE 64672.86104 89685.9513 85296.8071 74589.61742 93507.60726 101750.3925 60340.7097 78254.93178 73371.24503 0.881446962 1.222358313 1.162537273 1.016605584 1.274444876 1.386788413 0.822402696 1.066561318 1 16.16292715 2.22413883 24.9998275 0.978708133 1.15947688 0.273012768 0.14876064 335.4350665 581464.2316 0.059697575 0.040454043 167.5478389 -2.22413883 0.180768746 FAAFFGNVPIFHIPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FAAFFGNVPIFHIPGR 16 0 Q92620;J3KTG2 Q92620 DHX38 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 0 105 0.0013175 138070000 63213 70637 34516 51537 47774 72524 64641 72915 57447 FALSE TRUE 54859.24189 70172.9809 51208.05305 63239.26354 46823.39087 75314.04521 58372.12577 57322.69468 50655.6811 1.082983008 1.385293404 1.010904442 1.248414041 0.924346289 1.486783784 1.152331278 1.131614331 1 15.62843646 1.310299136 2.265018651 0.9677863 1.188250176 0.110592465 0.164998318 1.167828122 7.123023349 0.491381897 0.040911579 20.43144752 -1.310299136 0.220463876 FAAQAAHQGTASQYFMLLLLTDGAVTDVEATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FAAQAAHQGTASQYFMLLLLTDGAVTDVEATR 32 0 Q99829;B0QZ18;A6PVH9;H0Y524 Q99829 CPNE1 Copine-1 0 ;;; 316.02 3.45E-104 881668000 686541 718528 353940 572957 685497 710340 696304 872810 786844 FALSE TRUE 595812.8674 713807.9423 525106.5679 703055.6439 671856.9509 737667.2395 628776.5453 686166.3737 693824.1987 0.858737514 1.028802316 0.756829423 1.013305165 0.968338885 1.063190417 0.906247644 0.988962874 1 19.40421063 FACFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FACFER 6 0 F8VVM2;Q00325-2;Q00325 F8VVM2 SLC25A3 "Phosphate carrier protein, mitochondrial" 0 ; 116.87 0.053984 897020000 643080 670420 424750 649290 926560 1052970 525910 858620 904020 FALSE TRUE 558095.3486 666015.9669 630160.5207 796721.2183 908123.2688 1093478.437 474907.3291 675010.7948 797147.7855 0.700115285 0.835498736 0.790519063 0.999464883 1.139215695 1.371738663 0.595758199 0.8467825 1 19.60448769 3.74625323 20.3526339 0.974184491 0.781389492 0.205417224 0.19878647 93.31958425 246885.435 0.057653145 0.096776177 5575.107291 -3.74625323 -0.192794999 FACHSASLTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FACHSASLTVR 11 0 Q15233;Q15233-2;C9JYS8;C9IZL7 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ; 167.12 1.96E-05 1950210000 1335280 1305220 618970 985770 1420430 1211420 1333770 1451190 1447050 FALSE TRUE 1158819.365 1296645.924 918305.9623 1209604.145 1392166.222 1258024.111 1204421.191 1140864.312 1275981.397 0.908178887 1.016195006 0.719686011 0.947979451 1.091055265 0.985926687 0.943917516 0.894107323 1 20.28317587 3.492786488 24.98502427 0.973687565 0.884670018 0.220395064 0.086221807 1228.363245 1959156.04 0.024533419 0.035149088 3110.186902 -3.492786488 -0.089017547 FACNGTVIEHPEYGEVIQLQGDQR ddPTM_MDA-MB-175_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 ;;; 292.44 7.57E-62 3487380000 1734233 1732415 1094944 1500397 1890480 1993750 1774295 2057860 2241080 FALSE TRUE 1505049.715 1721034.652 1624462.581 1841085.071 1852863.147 2070450.853 1602224.144 1617802.653 1976142.075 0.761610075 0.870906335 0.822037343 0.931656227 0.937616364 1.047723683 0.810783882 0.818667177 1 20.91425524 4.780740446 1.065519931 0.908660912 0.691578321 0.294071397 0.076083641 3.037005067 2.671147213 0.025628728 0.764280198 60358.77899 -4.780740446 -0.21708259 FADDQLIIDFDNFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FADDQLIIDFDNFVR 15 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 155.02 5.53E-06 31199000 45744 46879 22191 36992 42559 40871 46143 52387 52755 FALSE TRUE 39698.8145 46571.04876 32922.64182 45391.59899 41712.15917 42443.33382 41668.05896 41184.44773 46518.364 0.853400917 1.001132558 0.707734301 0.97577806 0.896681559 0.912399538 0.895733542 0.885337406 1 15.50551274 FADGSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FADGSIR 7 0 P31040;D6RFM5;P31040-2;A0A087X1I3;P31040-3;H0Y8X1 P31040 SDHA "Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial" 0 95.957 0.030441 139350000 111280 133720 77279 87529 105890 134220 103030 109350 130510 FALSE TRUE 96574.06605 132841.5845 114651.3829 107403.7972 103782.9962 139383.5303 93038.16646 85966.35346 115081.2565 0.83918154 1.15432859 0.996264608 0.933286623 0.901823627 1.211174908 0.808456297 0.747005691 1 16.81229335 FADQDDIGNVS(ph)FDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FADQDDIGNVSFDR 14 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 FADQDDIGNVS(1)FDR;FADQDDIGNVS(1)FDR;FADQDDIGNVS(1)FDR 202.35 1.74E-08 405500000 400367 436730 340707 368420 454700 399040 435870 527980 677120 TRUE FALSE 347457.4865 433861.0919 505474.0448 452075.3919 445652.3596 414391.327 393599.3945 415075.5857 597071.645 0.581936003 0.726648293 0.846588595 0.757154348 0.746396791 0.694039535 0.659216357 0.69518556 1 19.18754453 1.235960081 24.99723321 1.000000376 0.716372702 0.63507998 0.068243116 49.5218254 475921.6299 0.115177112 0.017364829 17.21710314 -1.235960081 -0.283627674 FADQDDIGNVSFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FADQDDIGNVSFDR 14 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 ;;; 381.34 9.82E-98 2952770000 2765660 2938040 1909320 2501250 2799960 2830980 2826900 3191110 3874980 FALSE TRUE 2400171.024 2918739.822 2832673.538 3069197.042 2744246.274 2939889.632 2552747.673 2508715.96 3416884.279 0.70244434 0.854210908 0.82902238 0.898244363 0.803142878 0.860400702 0.747098077 0.734211567 1 21.70424996 4.746069761 23.42542742 0.828936844 0.70244419 0.233938086 0.076034122 619.8230321 1933473.487 0.018533704 0.180744301 55727.5257 -4.746069761 -0.126492654 FAEAFEAIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FAEAFEAIPR 10 0 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;; 158.76 1.84E-05 519064000 571801 568222 311037 396043 528668 558288 514474 610065 568111 FALSE TRUE 496236.0491 564489.3123 461455.5336 485970.6163 518148.5411 579765.7006 464580.3907 479607.3473 500949.5648 0.990590838 1.126838612 0.921161662 0.970098889 1.03433275 1.157333475 0.927399529 0.957396475 1 18.93430584 FAEEDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FAEEDKK 7 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 87.616 0.030803 755670000 1383200 1244000 961290 1449700 1149000 1199300 1966700 2195900 2433800 FALSE TRUE 1200406.615 1235828.082 1426173.059 1778876.542 1126137.148 1245437.847 1775969.737 1726323.874 2146078.937 0.559348771 0.575853973 0.664548277 0.828896138 0.524741718 0.580331798 0.827541665 0.804408377 1 21.03327171 1.468024404 1.044305215 1.08891001 0.627516604 0.622595293 0.094905248 0.871205964 1.04589454 0.428058435 0.033840792 29.37814732 -1.468024404 -0.461393406 FAEFEDFPETSEPVWILGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FAEFEDFPETSEPVWILGR 19 0 Q9Y4P1;H0Y2Y0;F2Z2K8;C9JIK8;Q9Y4P1-6;Q9Y4P1-2 Q9Y4P1 ATG4B Cysteine protease ATG4B 0 90.731 0.005094 13643000 27169 28568 20750 18031 29239 29782 26908 30901 30198 FALSE TRUE 23578.54781 28380.33493 30784.7694 22125.21414 28657.20111 30927.73281 24298.4663 24293.06162 26628.02684 0.885478596 1.065806907 1.15610404 0.830899498 1.076204455 1.161472947 0.912514714 0.912311745 1 14.70065791 FAELETILGDIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FAELETILGDIDR 13 0 Q5JY65;Q9BZJ0-2;Q9BZJ0-3;Q9BZJ0 Q5JY65 CRNKL1 Crooked neck-like protein 1 0 ;;; 178.53 3.38E-05 157106000 207416 207317 123589 139400 214280 199795 213212 231347 208323 FALSE TRUE 180005.4501 205955.121 183357.0538 171052.9006 210016.2472 207481.2429 192534.7331 181875.2444 183695.2923 0.979913246 1.121178003 0.998158698 0.931177378 1.143285953 1.129485902 1.048120127 0.990092028 1 17.48695513 1.762935238 5.919667457 0.995457307 1.053150172 0.100269866 0.068244735 0.383040675 34.03814198 0.04023055 0.018388 57.93422985 -1.762935238 0.057692865 FAELPEFRPEEVLPS(ph)PTLQSLAT(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 2 FAELPEFRPEEVLPS(0.994)PT(0.006)LQSLAT(0.592)S(0.407)PR;FAELPEFRPEEVLPS(1)PTLQSLAT(0.558)S(0.442)PR 211.37 2.50E-25 1090703000 178618 216308 173526 226035 302327 322578 302454 319566 315928 TRUE FALSE 155013.1787 214887.0585 257443.754 277359.7015 296311.2842 334987.7844 273122.0576 251229.2978 278579.3517 0.556441738 0.771367501 0.924130781 0.995621893 1.06365128 1.20248605 0.980410271 0.901823111 1 18.0877288 4.524157042 1.388606821 1.018466031 0.466391846 0.80623792 0.076146407 0.420983244 0.988367668 0.025573576 0.292485077 33431.59075 -4.524157042 -0.552074185 FAELPEFRPEEVLPS(ph)PTLQSLATS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 2 FAELPEFRPEEVLPS(0.998)PT(0.002)LQSLAT(0.056)S(0.944)PR;FAELPEFRPEEVLPS(0.998)PT(0.002)LQSLAT(0.053)S(0.947)PR 242.07 2.17E-45 1131333000 233770 279250 216667 307730 401470 450110 416000 461620 427780 TRUE FALSE 202876.7022 277415.5884 321447.8859 377604.7999 393481.5325 467426.023 375656.384 362906.1553 377208.3357 0.537837272 0.73544395 0.852175987 1.001051048 1.043141138 1.23917204 0.995885691 0.962084135 1 18.52500203 4.3211448 1.221222034 1.042880024 0.488616488 0.835883942 0.076556351 0.330697288 0.697727369 0.026327571 0.194843949 20948.1078 -4.3211448 -0.554263536 FAELPEFRPEEVLPSPTLQSLAT(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 1 FAELPEFRPEEVLPSPTLQSLAT(0.5)S(0.5)PR;FAELPEFRPEEVLPSPTLQS(0.003)LAT(0.498)S(0.498)PR 235.86 1.02E-44 476260000 341195 279303 129812 173347 218963 207338 207550 232037 194583 TRUE FALSE 296105.2163 277468.2402 192589.5174 212708.0858 214606.0647 215314.427 187421.8329 182417.6933 171579.6194 1.725759838 1.617139851 1.122449846 1.239704847 1.250766644 1.25489512 1.092331558 1.063166441 1 17.38851867 8 0.416759594 1.065029311 14.09577153 0.813692663 0.101564277 36.926814 0.501281719 0.092360177 397.8330429 100000000 -8 13.03074222 FAELPEFRPEEVLPSPTLQSLATS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 1 FAELPEFRPEEVLPSPTLQS(0.005)LAT(0.21)S(0.785)PR 96.707 0.0041861 203310000 89813 75128 45072 39384 63493 53888 57787 55741 52218 TRUE FALSE 77943.98449 74634.47922 66868.96996 48326.73915 62229.61352 55961.10623 52182.82563 43821.22093 46044.84753 1.692784072 1.62090838 1.452257387 1.049558023 1.351500045 1.215360876 1.133304342 0.951707374 1 15.49075211 8 0.213807532 0.846581975 5.556478139 0.821379547 0.107849167 38.94101472 0.592760341 0.591113433 60.69780254 99999999.96 -8 4.709896164 FAEMEER ddPTM_MDA-MB-175_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 ; 89.296 0.041823 624170000 1985980 1844960 1165140 1404160 1788660 1722700 2013260 2142300 1849780 FALSE TRUE 1723527.711 1832840.336 1728605.601 1722995.989 1753069.165 1788973.384 1818014.355 1684185.816 1631101.116 1.056665154 1.123682841 1.059778321 1.056339164 1.074776511 1.096788768 1.114593288 1.032545316 1 20.63741479 1.546728035 4.535467423 1.006369313 1.082939932 0.600025815 0.023435394 0.104372595 4.584147624 0.018234848 0.006051182 35.21502771 -1.546728035 0.076570619 FAEQTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FAEQTLR 7 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 121.62 0.010284 367890000 963850 739810 701930 747000 694940 704060 971910 966440 1182730 FALSE TRUE 836474.7804 734950.1394 1041385.696 916617.7672 681112.0536 731145.6438 877654.3178 759774.3268 1042909.007 0.802059216 0.704711662 0.998539364 0.878904834 0.653088668 0.701063697 0.84154448 0.728514494 1 19.99218186 1.228534244 24.98990784 1.000000433 0.788021123 0.301906359 0.101044258 566.6979784 1412348.122 0.334605039 0.025258533 16.92521694 -1.228534244 -0.21197931 FAESTEISELSHNFVMVNLEDEEEPKDEDFSPDGGYIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FAESTEISELSHNFVMVNLEDEEEPKDEDFSPDGGYIPR 39 1 O95881 O95881 TXNDC12 Thioredoxin domain-containing protein 12 0 161.01 3.40E-18 37863000 25895 23858 17221 16619 21732 23852 20019 26536 23100 FALSE TRUE 22472.91014 23701.27523 25549.1332 20392.59796 21299.57572 24769.60187 18077.56046 20861.4829 20369.14432 1.103281993 1.163587182 1.25430567 1.00115143 1.045678473 1.216035465 0.887497294 1.024170804 1 14.31409776 2.714297553 0.646803018 0.970118323 1.163288854 0.296800817 0.092842403 1.071115387 1.151995908 0.128889879 0.084444665 517.9615875 -2.714297553 0.193170531 FAGHSEAGGGSGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FAGHSEAGGGSGDR 14 0 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ; 178.58 1.97E-06 686220000 420630 452870 205730 288210 453330 495480 385620 441170 435220 FALSE TRUE 365042.6798 449895.0672 305221.7161 353652.4855 444309.6199 514541.4362 348222.6318 346829.2287 383768.7874 0.951204714 1.172307603 0.795327098 0.921524879 1.157753404 1.340758949 0.907376116 0.903745276 1 18.54987785 FAGVDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FAGVDIR 7 0 P62249;M0R210;M0R3H0;M0R1M5;Q6IPX4;M0QX76 P62249 RPS16 40S ribosomal protein S16 0 ; 101.21 0.021463 630300000 2902140 3159280 1962950 2428940 3158070 3034160 3138870 3347040 3327630 FALSE TRUE 2518614.846 3138526.482 2912239.186 2980467.951 3095230.586 3150886.099 2834462.871 2631301.543 2934241.372 0.858352987 1.069621099 0.992501576 1.015754184 1.054865702 1.073833301 0.965995128 0.896757018 1 21.48455612 2.010184615 24.3169999 0.938115622 1.015306579 0.1397431 0.065519528 209.0194492 499056.3132 0.025436214 0.017125794 102.3728079 -2.010184615 0.077190957 FAHIDGDHLTLLNVYHAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FAHIDGDHLTLLNVYHAFK 19 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 324.25 7.88E-63 2044440000 3268600 2619300 1020780 1941600 2529900 2268000 2921500 3456200 3176300 FALSE TRUE 2836646.228 2602093.646 1514432.622 2382469.955 2479559.94 2355251.428 2638173.38 2717118.526 2800801.432 1.01279805 0.92905324 0.540714027 0.850638652 0.885303724 0.840920531 0.941935172 0.9701218 1 21.41740827 2.096296725 1.33035399 0.99871692 0.828787 0.200512145 0.120566278 0.800072896 2.649875244 0.123433398 0.043085165 124.8236061 -2.096296725 -0.16992992 FAHTNVESLVNEYDDNGEGIILFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FAHTNVESLVNEYDDNGEGIILFR 24 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 372.72 8.04E-119 3380520000 1046396 952694 883033 1143050 1186950 1369220 947389 984140 1714640 FALSE TRUE 908112.1174 946435.6904 1310070.712 1402596.973 1163332.017 1421894.779 855511.3606 773689.3196 1511937.213 0.600628194 0.625975525 0.866484866 0.927682024 0.769431434 0.940445653 0.565837889 0.511720535 1 20.5279668 4.354770776 7.695144583 0.768021256 0.607609634 0.172182592 0.158258679 0.480042525 29.84689795 0.043435589 0.115971802 22634.49327 -4.354770776 -0.160411621 FAHTNVESLVNEYDDNGEGIILFRPSHLTNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FAHTNVESLVNEYDDNGEGIILFRPSHLTNK 31 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;; 306.4 1.74E-82 4286090000 2435760 1989460 1010355 1908620 2560080 2565140 2502930 2473380 1258377 FALSE TRUE 2113868.145 1976391.106 1498966.057 2342001.342 2509139.417 2663822.596 2260196.234 1944466.935 1109613.105 1.905049729 1.781153357 1.35089073 2.110646795 2.261274138 2.400676943 2.036922802 1.752382814 1 20.0816253 3.709629963 24.92995307 1.949333436 1.689243228 0.076508648 0.400588158 1878.448856 1618685.852 0.116898637 0.17342256 5124.245911 -3.709629963 -0.260090208 FAIHGDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FAIHGDPK 8 0 Q9BW30 Q9BW30 TPPP3 Tubulin polymerization-promoting protein family member 3 0 ; 100.15 0.0063088 312250000 675140 665780 433500 486640 687420 570100 731680 902400 825270 FALSE TRUE 585918.5384 661406.4473 643142.05 597139.0498 673741.6869 592032.1159 660721.7862 709428.7825 727707.5208 0.805156635 0.908890493 0.883791952 0.82057562 0.925841314 0.813557781 0.907949646 0.974881752 1 19.4729992 1.79825463 2.649574494 0.99412217 0.863966096 0.626495647 0.04026397 0.156318762 2.08633207 0.028184183 0.010348364 62.84267024 -1.79825463 -0.130156074 FAIQDIS(ph)VEETSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FAIQDISVEETSAK 14 0 O43707;P12814-3;P12814;P12814-2;P12814-4;H9KV75;P35609-2;P35609;G3V2N5;A0A494C1A0;G3V2W4;Q08043;A0A494C166;A0A494C033;A0A087WSZ2;G3V5M4;G3V2X9;G3V2E8 O43707;P12814-3 ACTN4;ACTN1;ACTN2;ACTN3 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2;Alpha-actinin-3 1 FAIQDIS(1)VEETSAK 198.85 2.25E-08 197340000 265050 222850 179300 233980 241330 183080 275280 286740 384220 TRUE FALSE 230022.9709 221386.0837 266010.0797 287108.7352 236528.0052 190123.2061 248583.388 225422.8824 338797.9493 0.678938498 0.653445761 0.785158471 0.847433509 0.698138834 0.561169884 0.733721643 0.665360823 1 18.37006562 1.234056212 24.99085675 1.000000445 0.703564755 0.596118815 0.076846786 103.4257435 573741.8045 0.152566356 0.01968406 17.14179163 -1.234056212 -0.29643569 FAMEPEEFDSDTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FAMEPEEFDSDTLR 14 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;; 320.96 8.34E-56 1091380000 1219580 1079910 851584 918913 1042800 1357920 974430 972360 844230 FALSE TRUE 1058409.413 1072816 1263412.871 1127566.241 1022050.32 1410160.061 879929.9286 764428.3809 744426.0911 1.42177904 1.441131649 1.697163608 1.514678562 1.372937263 1.894291559 1.182024568 1.02686941 1 19.5057691 2.047218037 8.720022149 1.041701023 1.547880463 0.707526839 0.150300884 0.141466089 24.08970642 0.059333108 0.039855815 111.4854105 -2.047218037 0.506179439 FAPPLS(ph)PLSSDMLIMPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FAPPLSPLSSDMLIMPK 17 0 Q5H9M0 Q5H9M0 MUM1L1 PWWP domain-containing protein MUM1L1 1 FAPPLS(1)PLSSDMLIMPK;FAPPLS(0.962)PLS(0.019)S(0.019)DMLIMPK 200.77 1.27E-11 238090000 201401 235410 118724 158720 241780 188553 216155 285930 222887 TRUE FALSE 174785.3476 233863.5762 176139.3235 194759.8019 236969.051 195806.7559 195192.3214 224786.0946 196537.5528 0.889322906 1.189918023 0.896212052 0.99095465 1.205718946 0.996281643 0.993155347 1.143731014 1 17.58444547 FAQFFLCPLFDESCKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FAQFFLCPLFDESCKDR 17 1 A0A3B3ISG5;P14735;Q5T5N3 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 205.78 6.91E-12 599220000 643100 691260 399320 398370 613800 542330 728950 807930 475810 FALSE TRUE 558112.7056 686719.0675 592432.4876 488825.9972 601586.5809 563193.786 658256.5412 635160.4568 419560.2838 1.330232453 1.636758993 1.412031859 1.165091206 1.433850162 1.342342943 1.568920049 1.51387174 1 18.67851859 4.010685548 24.9615385 1.367830912 1.493720675 0.086653222 0.179618197 570.1112012 1331762.902 0.045618495 0.094809467 10249.09568 -4.010685548 0.125889763 FAQHGTFEYEYSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FAQHGTFEYEYSQR 14 0 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 213.32 1.21E-09 4083600000 1647900 1483400 609250 992830 1487830 1426100 1375760 1638750 1434040 FALSE TRUE 1430125.84 1473655.448 903885.3378 1218267.226 1458225.094 1480962.99 1242339.007 1288316.065 1264509.425 1.130972859 1.165396966 0.714811072 0.96343072 1.153194326 1.171175921 0.982467179 1.01882678 1 20.27014636 1.610553118 0.003017832 0.000101138 2.05115653 0.002892725 0.137477171 2104264.476 2293.828182 786757.9528 772272.6004 40.78994483 -1.610553118 2.051055392 FAQPGSFEYEYAMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FAQPGSFEYEYAMR 14 0 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;; 176.18 5.27E-06 2019300000 1708410 1631282 1052579 1127177 1494193 1430430 1674520 1943780 1366915 FALSE TRUE 1482639.29 1620566.001 1561609.725 1383119.766 1464461.483 1485459.568 1512125.308 1528117.774 1205319.866 1.230079527 1.344511152 1.295597766 1.147512627 1.214998213 1.232419385 1.254542757 1.267810991 1 20.20098463 1.235991458 24.99488346 0.99999967 1.249405855 0.697657847 0.051393924 42.27007868 411151.7368 0.087720153 0.01321626 17.21834709 -1.235991458 0.249406186 FAQPGTFEFEYASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FAQPGTFEFEYASR 14 0 Q8WXF1;Q8WXF1-2 Q8WXF1 PSPC1 Paraspeckle component 1 0 ; 174.05 3.02E-07 117000000 122669 111109 58644 76758 100535 113507 106838 120661 110908 FALSE TRUE 106457.9808 110379.1177 87004.43455 94187.07707 98534.55019 117873.6877 96476.8672 94858.58413 97796.58259 1.088565449 1.128660274 0.889646982 0.963091701 1.007545945 1.205294547 0.986505506 0.969958066 1 16.57749643 FAQQHQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FAQQHQAR 8 0 B4DE93;G3V0I5;P49821-2;P49821 B4DE93 NDUFV1 "NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial" 0 ; 98.523 0.007462 129549000 74834 95909 59199 90323 113578 127877 94686 108890 114564 FALSE TRUE 64944.49729 95278.96746 87827.83441 110832.2177 111318.02 132796.5109 85503.36629 85604.72088 101020.3744 0.642885137 0.943165851 0.869407136 1.097127369 1.101936324 1.314551759 0.846397242 0.84740055 1 16.62428677 5.162362684 1.240295999 1.009737584 0.067362157 0.407613059 0.140716749 4.418677918 2.875547643 0.04519672 6.860277226 145332.4797 -5.162362684 -0.942375427 FAQSAPGS(ph)PLSSQPVLITVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FAQSAPGSPLSSQPVLITVQR 21 0 Q01167;Q01167-2 Q01167 FOXK2 Forkhead box protein K2 1 FAQSAPGS(1)PLSSQPVLITVQR;FAQSAPGS(0.827)PLS(0.147)S(0.026)QPVLITVQR;FAQSAPGS(1)PLSSQPVLITVQR 427.65 6.18E-174 469970000 680020 555040 320400 439440 579350 651790 616690 602870 621550 TRUE FALSE 590153.634 551393.9057 475346.5117 539221.5684 567822.0685 676864.7831 556883.4987 473950.942 548071.0671 1.076783048 1.006062788 0.867308165 0.983853374 1.0360373 1.234994554 1.016078994 0.864761836 1 19.06400345 1.883859014 7.964705092 0.926405776 1.03136036 0.157535899 0.095802695 0.508171826 31.84703952 0.049080951 0.027203054 76.53481106 -1.883859014 0.104954583 FAQSAPGSPLS(ph)SQPVLITVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FAQSAPGSPLSSQPVLITVQR 21 0 Q01167;Q01167-2 Q01167 FOXK2 Forkhead box protein K2 1 FAQSAPGS(0.045)PLS(0.808)S(0.146)QPVLITVQR 130.72 1.51E-05 278440000 251070 201120 132600 164590 221930 228950 217620 252550 226370 TRUE FALSE 217890.4634 199798.8295 196725.8035 201962.6751 217514.0272 237757.8547 196515.2459 198544.1478 199608.7965 1.091587481 1.000952027 0.985556784 1.011792459 1.089701612 1.191119123 0.984501933 0.994666324 1 17.60681577 FARPDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FARPDFR 7 1 F8WF90;C9JQU6;F8WF33;O75915 F8WF90 ARL6IP5 PRA1 family protein 3 0 ; 91.906 0.014647 1115760000 1697650 1744140 1128750 1658200 2449700 2658600 1484260 2689400 2151500 FALSE TRUE 1473301.251 1732682.629 1674617.275 2034719.654 2400955.763 2760878.062 1340316.694 2114292.739 1897152.121 0.776585723 0.913307167 0.882700579 1.072512653 1.265557852 1.455275005 0.706488783 1.114456092 1 20.85540393 3.740927176 3.974858964 1.102197567 0.85785719 0.269637942 0.191014604 0.321980772 12.02392545 0.054378639 0.091413951 5507.153422 -3.740927176 -0.244340376 FAS(ph)AENIPDLPYDYSSSLESVADETSPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FASAENIPDLPYDYSSSLESVADETSPER 29 0 P50747 P50747 HLCS Biotin--protein ligase;Biotin--[methylmalonyl-CoA-carboxytransferase] ligase;Biotin--[propionyl-CoA-carboxylase [ATP-hydrolyzing]] ligase;Biotin--[methylcrotonoyl-CoA-carboxylase] ligase;Biotin--[acetyl-CoA-carboxylase] ligase 1 FAS(1)AENIPDLPYDYSSSLESVADETSPER;FAS(0.996)AENIPDLPY(0.001)DY(0.001)S(0.001)S(0.001)S(0.001)LESVADETSPER;FAS(1)AENIPDLPYDYSSSLESVADETSPER 174.06 7.25E-13 111812000 267134 251657 175983 184628 265874 274331 260021 279612 279516 TRUE FALSE 231831.5651 250003.8486 261088.9674 226550.6093 260583.6276 284884.6911 234804.2034 219819.1497 246471.9369 0.940600248 1.014329874 1.05930505 0.919174053 1.057254756 1.155850417 0.952661006 0.891862792 1 17.91106387 2.022989845 24.99947676 0.933423595 1.024921606 0.205189698 0.069868564 299.8748334 326086.6318 0.028649269 0.019314043 105.4362242 -2.022989845 0.091498011 FAS(ph)DDEHDEHDENGATGPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 FASDDEHDEHDENGATGPVK 20 0 P05455 P05455 SSB Lupus La protein 1 FAS(1)DDEHDEHDENGATGPVK;FAS(1)DDEHDEHDENGATGPVK;FAS(1)DDEHDEHDENGATGPVK;FAS(1)DDEHDEHDENGATGPVK;FAS(1)DDEHDEHDENGATGPVK;FAS(1)DDEHDEHDENGATGPVK;FAS(1)DDEHDEHDENGATGPVK;FAS(1)DDEHDEHDENGATGPVK 168.12 2.12E-11 17348150000 5367220 3942420 3682640 4039770 4197110 3278660 4445080 5026850 10144440 TRUE FALSE 4657928.278 3916521.983 5463577.022 4957061.523 4113595.723 3404792.172 4013996.826 3951897.246 8945175.86 0.520719587 0.43783622 0.610784752 0.554160321 0.459867507 0.380628869 0.448733137 0.441790895 1 23.09267841 1.236042061 24.9992047 1.000000685 0.479457088 0.860222539 0.065638681 25.8320866 256354.6147 0.113805986 0.017228225 17.22035346 -1.236042061 -0.520543597 FAS(ph)DDEHDEHDENGATGPVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FASDDEHDEHDENGATGPVKR 21 1 P05455 P05455 SSB Lupus La protein 1 FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR 181.38 2.38E-17 2430820000 3413860 2545590 1847790 1871690 2650300 2230210 3011620 3250970 1843760 TRUE FALSE 2962709.751 2528867.852 2741387.424 2296685.821 2597564.215 2316007.622 2719553.556 2555775.365 1625792.793 1.822316942 1.5554675 1.686185002 1.412655925 1.597721571 1.424540465 1.672755327 1.572017895 1 20.63271197 1.239352569 7.065876092 0.988066352 1.587586213 0.705591737 0.120371737 0.05691394 16.92828589 0.164262039 0.027901549 17.35212108 -1.239352569 0.599519861 FAS(ph)ENDLPEWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FASENDLPEWK 11 0 P43487;F6WQW2;P43487-2;C9JXG8;C9JJ34;C9JGV6;C9JDM3;C9JIC6 P43487 RANBP1 Ran-specific GTPase-activating protein 1 FAS(1)ENDLPEWK;FAS(1)ENDLPEWK;FAS(1)ENDLPEWK;FAS(1)ENDLPEWK 247.73 4.01E-16 341274000 1675580 1170336 460283 1415214 1083346 471621 1375786 1475031 1186622 TRUE FALSE 1454147.858 1162647.986 682877.3984 1736559.969 1061789.534 489764.565 1242362.485 1159607.099 1046340.899 1.389745788 1.111156017 0.652633763 1.659650283 1.014764438 0.468073613 1.187340079 1.108249807 1 19.99692153 3.019989368 24.99873136 0.962525549 1.179860063 0.135039543 0.311733981 592.4475177 740910.6018 0.094742157 0.107415444 1047.102913 -3.019989368 0.217334514 FASAENIPDLPYDYSSSLESVADET(ph)SPEREGR ddPTM_MDA-MB-175_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 FASAENIPDLPYDYS(0.006)S(0.006)S(0.006)LES(0.003)VADET(0.615)S(0.364)PEREGR 150.56 4.55E-10 59088000 56534 65136 29571 31658 63612 60168 67523 68329 16531 TRUE FALSE 49062.88866 64708.11733 43871.63451 38846.43276 62346.24565 62482.70189 60974.62985 53717.37509 14576.72401 3.365837799 4.439139911 3.009704682 2.664963179 4.277109562 4.286470804 4.183013262 3.685147297 1 13.8313789 4.229807834 24.97771495 3.429827152 3.902488945 0.045701454 1.017937625 699.1601578 1995204.257 0.262634371 0.560327192 16974.92383 -4.229807834 0.472661793 ILEFFGLKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILEFFGLKK 9 1 P07237;H7BZ94;H0Y3Z3;I3L398;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ; 110.14 0.0043469 0 392050 334160 210723 261420 291990 294640 350780 371860 121416 FALSE TRUE 340239.5992 331964.881 312629.3476 320779.4066 286179.9703 305974.9915 316761.4096 292340.6328 107062.3388 3.177957842 3.100669056 2.920068356 2.99619278 2.673021844 2.857914323 2.958663272 2.730564605 1 16.70809155 1.222037157 3.443124382 0.66302374 2.941619316 0.952308064 0.136326381 0.070715462 1.175596236 0.438030107 0.037448241 16.67389863 -1.222037157 2.278595576 FATHAAALSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FATHAAALSVR 11 0 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;; 129.82 0.00023706 2775050000 1041845 1199684 590678 790401 1273220 1239950 1068784 1305610 1048496 FALSE TRUE 904162.5436 1191803.197 876331.8565 969873.6276 1247885.413 1287651.679 965133.4922 1026415.462 924543.9973 0.977955128 1.28907137 0.947853059 1.049029176 1.349730696 1.392742457 1.043902178 1.110185632 1 19.81838245 FATLAELVQYYMEHHGQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FATLAELVQYYMEHHGQLK 19 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 227.04 7.88E-20 516720000 1236900 1074300 744060 930930 942470 935980 1324400 1389400 1410200 FALSE TRUE 1073440.531 1067242.853 1103889.905 1142311.885 923716.6909 971987.7563 1195959.892 1092287.622 1243487.763 0.863249775 0.858265666 0.887736846 0.918635405 0.742843411 0.781662502 0.961778578 0.878406411 1 20.24596088 0.970991138 1.083805062 1.141881371 0.850914466 0.354303897 0.060958509 3.567463892 2.313511846 1.382089662 0.020374551 9.35386586 -0.970991138 -0.290966906 FATVEVTDKPVDEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FATVEVTDKPVDEALR 16 1 Q9NRV9;A0A3B3IRV5;F5GWX2 Q9NRV9 HEBP1 Heme-binding protein 1 0 ;;; 295.12 1.09E-45 1754030000 2982760 2588390 1678890 2000600 2429780 2223510 2796310 3548330 3263050 FALSE TRUE 2588580.709 2571386.696 2490806.82 2454866.807 2381432.132 2309049.869 2525124.287 2789547.243 2877295.946 0.899657441 0.893681687 0.865676269 0.85318537 0.827663256 0.802506906 0.877603254 0.969503066 1 21.45628219 1.71169917 3.141245144 0.993781491 0.856439373 0.774592023 0.028363954 0.103898776 2.256772718 0.024213963 0.008569041 51.48718757 -1.71169917 -0.137342118 FAVLHGEAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FAVLHGEAPR 10 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;; 152.28 1.83E-05 1801690000 2041890 2105740 1413140 1489950 2042190 2183880 1968450 2173410 2175200 FALSE TRUE 1772049.063 2091907.255 2096539.231 1828265.92 2001554.414 2267895.277 1777550.022 1708643.185 1918050.334 0.923880376 1.090642523 1.093057462 0.953189751 1.043535917 1.182396122 0.926748371 0.890822913 1 20.87120915 FAVQDVNDVLDLEWDQHLEQK ddPTM_MDA-MB-175_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 0 158.73 2.34E-11 46866000 46664 39501 20804 33367 33705 29362 39367 54648 45360 FALSE TRUE 40497.23417 39241.51533 30864.88399 40943.48733 33034.33644 30491.57514 35549.1944 42961.95047 39997.59247 1.012491794 0.981096934 0.771668545 1.023648795 0.825908121 0.762335262 0.888783354 1.074113411 1 15.28762554 1.759541056 10.40713781 1.035772111 0.890833035 0.284873041 0.093264449 0.203639999 88.61557807 0.050958368 0.024061162 57.48321581 -1.759541056 -0.144939076 FAYLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FAYLGR 6 0 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 123.06 0.044092 3627600000 241030 253120 165080 191890 262460 305800 268480 300900 244030 FALSE TRUE 209177.2748 251457.2381 244913.2402 235461.5574 257237.5595 317564.3239 242442.8509 236554.8766 215181.0514 0.972098953 1.168584485 1.138172895 1.094248568 1.19544708 1.475800596 1.12669238 1.099329495 1 17.71519152 4.739509979 23.54803254 1.163651817 0.972098824 0.190880322 0.123028179 66.2766283 1643340.564 0.031343073 0.184795898 54892.11684 -4.739509979 -0.191552993 FCDS(ph)PTSDLEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FCDSPTSDLEMR 12 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 FCDS(0.68)PT(0.269)S(0.051)DLEMR;FCDS(0.804)PT(0.181)S(0.015)DLEMR;FCDS(0.489)PT(0.489)S(0.021)DLEMR;FCDS(0.933)PT(0.06)S(0.007)DLEMR 338.34 1.85E-58 852250000 1477160 1359790 800570 865610 1364430 1362470 1299960 1391260 1107340 TRUE FALSE 1281949.563 1350857.45 1187728.33 1062159.981 1337280.512 1414885.103 1173890.079 1093749.876 976431.5267 1.312892434 1.383463574 1.216396949 1.087797712 1.369558925 1.449036685 1.20222468 1.120150104 1 19.89715935 1.658273929 2.195970727 1.014097566 1.295921275 0.500122538 0.100942136 0.26877982 2.679483591 0.120257372 0.030149816 45.52751318 -1.658273929 0.281823709 FCFSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FCFSNR 6 0 Q15363;E7EQ72;F5GX39 Q15363 TMED2 Transmembrane emp24 domain-containing protein 2 0 ;; 124.94 0.042201 3927760000 2720470 2916750 1764256 2015960 3057700 3391580 2343320 2797390 3052760 FALSE TRUE 2360952.997 2897589.677 2617456.103 2473714.53 2996857.752 3522056.277 2116065.187 2199189.918 2691866.191 0.877069226 1.076424113 0.972357434 0.918958951 1.11330116 1.308406892 0.786095979 0.816975942 1 21.36017527 FCFTPHTEEGCLSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 FCFTPHTEEGCLSER 15 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;;;;;; 301.57 2.41E-44 1.53177E+11 16649740 17440610 11122740 11345850 18487120 21159250 18613280 18800250 18453460 FALSE TRUE 14449434.67 17326041.48 16501734.27 13922098.65 18119262.48 21973260.04 16808166.97 14779962.84 16271912.98 0.887998522 1.064782088 1.014123803 0.855590776 1.113529952 1.350379643 1.032955805 0.908311325 1 23.95588053 4.745945457 22.5246644 1.036651763 0.887998226 0.118168093 0.131759727 574.1925606 1751170.638 0.034648587 0.32577296 55711.57759 -4.745945457 -0.148653537 FCHNNKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FCHNNKK 7 1 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 100.82 0.0061748 866330000 1168700 1032000 667240 828580 631460 836650 1307800 1422200 964460 FALSE TRUE 1014253.334 1025220.724 989919.4958 1016721.753 618895.1814 868836.4669 1180969.757 1118073.598 850442.6375 1.19261816 1.205514257 1.164005016 1.195520671 0.727733011 1.021628536 1.388653044 1.314696075 1 19.6978544 0.974402129 12.92043348 0.665215499 1.156341263 0.065748989 0.178333448 141328.0059 2354227.619 1361211.77 0.047748024 9.427621291 -0.974402129 0.491125764 FCIWTESAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FCIWTESAFR 10 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;; 229.44 3.77E-09 10729830000 1954526 2306752 1293375 1615652 2024231 2201242 2048155 2213510 2390827 FALSE TRUE 1696230.437 2291598.794 1918855.476 1982510.48 1983952.763 2285925.204 1849525.243 1740168.112 2108186.156 0.804592342 1.08700021 0.910192618 0.940386823 0.941070957 1.084308991 0.877306417 0.825433801 1 21.00757083 FCLDNGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FCLDNGAK 8 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 101.54 0.017807 85341000 848520 779020 388330 500550 705760 770420 701990 804530 669700 FALSE TRUE 736385.9321 773902.5663 576127.6869 614207.5279 691716.7568 800058.5559 633911.1178 632487.5204 590528.8289 1.246994043 1.310524615 0.975613143 1.040097448 1.171351377 1.354817101 1.073463456 1.07105274 1 19.17164797 2.025692075 24.99968946 1.050098361 1.176002529 0.239252303 0.113874834 360.2946797 350583.3107 0.0495375 0.033397112 106.0943057 -2.025692075 0.125904168 FCLESER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FCLESER 7 0 Q9H074;Q9H074-3;Q9H074-2 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 0 ; 157.86 0.0033668 921820000 1153410 1111570 686840 852480 1095300 1102300 1124720 1263440 1214810 FALSE TRUE 1000983.946 1104268.023 1018998.121 1046048.613 1073505.673 1144706.194 1015644.828 993263.1881 1071196.546 0.934454046 1.030873398 0.951270918 0.976523512 1.002155652 1.068623866 0.948140499 0.927246444 1 20.03079178 FCLQYTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FCLQYTR 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 125.25 0.0094623 213300000 156600 246920 129970 144520 218230 244460 232340 219680 189340 FALSE TRUE 135904.9132 245297.9663 192823.9267 177335.4748 213887.65 253864.5344 209807.7026 172703.1416 166956.4409 0.814014197 1.469233322 1.154935537 1.062166119 1.281098524 1.52054352 1.256661327 1.034420359 1 17.34911223 1.679140869 4.879780335 1.010319911 1.236999096 0.154206033 0.198125684 0.258225221 14.0697276 0.127021175 0.049987266 47.76841911 -1.679140869 0.226679185 FCLSS(ph)PTEALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FCLSSPTEALK 11 0 E7EWD6;Q76L83;Q76L83-2 E7EWD6 ASXL2 Putative Polycomb group protein ASXL2 1 FCLS(0.127)S(0.87)PT(0.003)EALK;FCLS(0.125)S(0.75)PT(0.125)EALK;FCLS(0.001)S(0.985)PT(0.014)EALK 173.6 1.26E-05 210247000 882100 745400 574720 708870 835220 750460 907950 1126640 1133220 TRUE FALSE 765528.25 740503.4183 852656.5143 869829.7679 818600.7561 779330.6818 819897.1487 885716.8035 999252.0226 0.766101277 0.741057713 0.85329476 0.870480868 0.819213509 0.77991404 0.820510872 0.886379796 1 19.93048906 1.307650647 1.731432709 1.05379092 0.807091622 0.727285445 0.038324161 0.479405161 1.532247847 0.191915243 0.011814384 20.30722811 -1.307650647 -0.246699298 FCNVDDDELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FCNVDDDELR 10 0 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;;;;; 290.22 9.98E-32 5309990000 3817010 3343000 2397750 2716140 3607540 3744380 3497800 3595240 4324520 FALSE TRUE 3312582.457 3321039.613 3557309.92 3332881.101 3535757.012 3888428.722 3158583.894 2826425.904 3813280.172 0.868696321 0.870914138 0.932873998 0.874019466 0.927221933 1.019707062 0.82831152 0.741205937 1 21.8626011 FCNVDDDELREYCIQAFESFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FCNVDDDELREYCIQAFESFVR 22 1 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 84.181 0.0030373 49862000 31184 43464 5157.4 4758.9 29496 36147 30410 37306 3214.1 FALSE TRUE 27062.95539 43178.48212 7651.53589 5839.48098 28909.08731 37537.59848 27460.84288 29328.40222 2834.13276 9.548937077 15.23516567 2.699780335 2.060411941 10.20032926 13.24482714 9.689328345 10.34828101 1 11.46869162 4.254892727 24.99969128 7.629968273 12.39204964 0.203326818 4.284513027 450.2886479 689248.4403 1.113772003 2.927738888 17984.26638 -4.254892727 4.762081364 FCPFAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FCPFAER 7 0 Q5TA02;P78417-3;P78417;Q5TA01;P78417-2 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 ;; 128.82 0.0086565 1513600000 702600 821470 495840 556090 797690 813380 730610 822420 748850 FALSE TRUE 609749.6298 816073.7095 735629.8825 682358.7338 781817.5297 844671.2549 659755.5547 646551.8831 660321.8061 0.923412833 1.235872724 1.114047538 1.033373012 1.183994717 1.279181222 0.999142461 0.979146648 1 19.33280976 2.043622294 24.99984042 0.988401771 1.131469217 0.292431806 0.099393646 151.7949826 86992.74044 0.039178658 0.026414228 110.5661771 -2.043622294 0.143067447 FCQLLWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FCQLLWR 7 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ; 114.54 0.013684 1158160000 749870 1016770 560950 662080 930450 1019770 842750 907220 1092910 FALSE TRUE 650772.7796 1010090.771 832227.2963 812415.3833 911935.8654 1059001.212 761020.2347 713218.063 963707.4248 0.675280446 1.048130112 0.863568418 0.843010402 0.946278758 1.098882487 0.789679746 0.740077377 1 19.87823569 FCSNSGRLS(ph)GPAELR ddPTM_MDA-MB-175_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;FCSNSGRLS(1)GPAELR;FCSNSGRLS(1)GPAELR;FCSNSGRLS(1)GPAELR 169.51 7.22E-07 6481890000 4133490 4358350 2302620 3183820 5323210 5416070 3318770 5615840 2567090 TRUE FALSE 3587238.824 4329719.712 3416174.734 3906754.993 5217288.536 5624429.718 2996916.196 4414936.319 2263611.545 1.584741354 1.912748555 1.509170044 1.725894623 2.304851532 2.48471507 1.323953398 1.950394859 1 21.11019497 0.972663422 2.402823028 1.30E-12 1.86109132 0.353128274 0.354044888 2.36145483 6.671109282 12.83813072 0.094848184 9.389953079 -0.972663422 1.86109132 FCYHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FCYHER 6 0 P28331-4;P28331;P28331-2;F8WDL5;C9JPQ5 P28331-4 NDUFS1 "NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial" 0 118.42 0.02188 113290000 175940 212240 226400 172550 202530 292920 149360 190170 135180 FALSE TRUE 152689.0832 210845.7815 335887.7973 211730.1148 198500.0492 304188.8219 134875.0902 149503.6254 119199.1744 1.280957557 1.7688527 2.817870165 1.776271655 1.665280404 2.551937322 1.131510272 1.254233732 1 16.86301472 2.210802153 24.81329351 1.154880192 1.982353824 0.452658137 0.43937625 183.0923237 163664.8058 0.178608813 0.120448742 162.4808388 -2.210802153 0.827473632 FDASFFGVHPK ddPTM_MDA-MB-175_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 ;;; 152.54 3.29E-05 43217135000 23191970 21921140 15468950 16961080 23409600 22701040 27187200 30027510 30301110 FALSE TRUE 20127092.4 21777138.59 22949785.96 20812352.45 22943794.76 23574363.7 24550589.53 23606360.66 26718947.29 0.753289124 0.815044783 0.858933015 0.778936094 0.858708785 0.882308851 0.918845689 0.88350639 1 24.67135983 -2 0.180357027 1.745393074 0.735581734 0.764617252 0.033955688 58.64568152 0.828011359 15.73234033 0.30286749 0.01 2 -1.009811339 FDDAVVQSDMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FDDAVVQSDMK 11 0 P11142;E9PKE3;E9PNE6;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 156.51 7.22E-05 130802000 314670 279920 222890 245440 271490 241880 301710 347070 528190 FALSE TRUE 273085.5622 278081.1871 330680.3495 301170.9033 266087.8802 251185.2801 272450.2106 272851.7814 465747.9799 0.58633762 0.597063646 0.709998462 0.646639205 0.57131301 0.539315877 0.584973467 0.585835673 1 18.82918999 1.237088905 24.99860045 1.000000486 0.602655441 0.878842733 0.046361447 13.3995123 227524.5187 0.075931753 0.012400777 17.26191227 -1.237088905 -0.397345045 FDDDKVSIVTPEDILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FDDDKVSIVTPEDILR 16 1 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 ;; 260.29 8.05E-27 461460000 949318 628442 555877 658931 596983 502322 759233 874199 1224036 FALSE TRUE 823863.221 624313.7231 824700.9765 808551.3547 585104.2063 521646.6524 685602.7005 687258.3469 1079331.859 0.763308536 0.578426105 0.764084716 0.749122106 0.542098523 0.483305156 0.635210288 0.636744243 1 20.04170708 1.238240385 24.9723431 1.000000401 0.640058334 0.583004212 0.094556724 5.703607587 444069.8388 0.135008527 0.0237831 17.30774088 -1.238240385 -0.359942067 FDDDVVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FDDDVVSR 8 0 Q93009;A0A669KBL1;Q93009-3;H3BND8;F5H2X1 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 133.86 0.0037102 0 380990 355610 225860 261220 334550 354780 316650 401460 328250 FALSE TRUE 330641.2062 353273.9745 335086.6515 320533.9935 327893.1095 368428.6162 285941.3317 315610.9032 289444.6589 1.142329616 1.220523384 1.157688149 1.107410289 1.132835239 1.272881032 0.987896383 1.090401545 1 18.14292801 2.223416462 24.99999451 1.037903812 1.169066387 0.618383203 0.053828217 167.5513853 276591.7704 0.021416968 0.014500826 167.2693857 -2.223416462 0.131162575 FDDGAGGDNEVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FDDGAGGDNEVQR 13 0 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ;; 234.65 2.67E-16 571980000 760990 754450 470720 556700 722070 732090 704420 799910 734860 FALSE TRUE 660423.2434 749493.9683 698361.7665 683107.2436 707702.2197 760253.976 636105.4568 628855.4714 647985.688 1.019194182 1.156652041 1.077742579 1.054201129 1.092157177 1.173257358 0.981665905 0.970477409 1 19.30560242 2.209162358 24.77388063 0.981121241 1.095471185 0.578268644 0.044858381 123.2481008 103860.0392 0.017522383 0.011815696 161.8685058 -2.209162358 0.114349944 FDDKPDYSYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FDDKPDYSYLR 11 1 P48730-2;H7BYT1;P48730;H0Y645;B0QY35;B0QY34;A0A669KBC0;P49674 P48730-2;P49674 CSNK1D;CSNK1E Casein kinase I isoform delta;Casein kinase I isoform epsilon 0 ; 100.04 0.0039473 701390000 856880 779030 484630 596720 777290 706860 866910 927720 856930 FALSE TRUE 743641.1369 773912.5006 718998.689 732214.3963 761823.4497 734053.3616 782837.2016 729334.2975 755624.7116 0.984140838 1.024202211 0.951528818 0.969018595 1.008203461 0.971452297 1.036013235 0.965207048 1 19.52731036 3.238993596 24.99998222 0.994055893 0.983028747 0.061455704 0.026297665 45.47940181 2625734.255 0.007576119 0.009187609 1733.778432 -3.238993596 -0.011027146 FDDMS(ph)SPGLELPSCELSR ddPTM_MDA-MB-175_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(0.553)S(0.447)PGLELPSCELSR 82.362 0.0056795 32580000 60473 50403 38691 59190 49379 42479 39301 61520 135350 TRUE FALSE 52481.33983 50071.89937 57402.09701 72629.99416 48396.45451 44113.19462 35489.59507 48364.42675 119349.0772 0.43972975 0.419541571 0.480959705 0.608550949 0.405503383 0.369614878 0.29735961 0.405235029 1 16.86482789 1.23733107 24.99139058 1.000000692 0.425548313 0.835532748 0.079702869 13.13886073 266943.4632 0.128935124 0.021416739 17.27154027 -1.23733107 -0.574452379 FDDTNPEKEEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FDDTNPEKEEAK 12 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RQT0;A0A0U1RR66 P47897 QARS Glutamine--tRNA ligase 0 ; 111.39 0.0012651 463940000 481750 357630 333390 344960 346010 249960 532780 538390 519140 FALSE TRUE 418085.5169 355280.705 494618.5191 423288.4404 339125.078 259576.1229 481111.0776 423259.4883 457767.8606 0.913313391 0.776115441 1.080500755 0.924679246 0.740823258 0.567047504 1.050993569 0.924616 1 18.80425665 FDDTNPEKEKEDFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FDDTNPEKEKEDFEK 15 2 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 105.28 0.00074676 154302000 688660 402200 468110 342810 343350 238416 705360 739440 235178 FALSE TRUE 597651.8362 399557.9217 694489.5617 420650.25 336518.0068 247588.0178 636954.2958 581316.5103 207375.5248 2.881978656 1.926736157 3.348946615 2.028446947 1.622746981 1.193911471 3.071501791 2.803206941 1 17.66188611 FDEDDDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FDEDDDK 7 0 Q13136-2;A0A2R8Y7R9;Q13136 Q13136-2 PPFIA1 Liprin-alpha-1 0 ;; 102.71 0.019865 5757000000 7987800 6472800 7293800 7627900 4602200 4116330 9352300 8529100 16333700 FALSE TRUE 6932191.991 6430279.751 10821106.08 9359931.28 4510625.224 4274687.879 8445315.385 6705218.339 14402748.59 0.481310352 0.446461987 0.751322291 0.649871184 0.313178085 0.296796674 0.586368312 0.465551301 1 23.77984082 1.236143592 24.99401359 1.000000655 0.500252796 0.562404848 0.13891855 52.99415745 547880.7953 0.233683867 0.035691695 17.22437977 -1.236143592 -0.499747859 FDEFDEAIDEAIEDDIKEADGGGVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FDEFDEAIDEAIEDDIKEADGGGVGR 26 1 Q96T23-2;Q96T23;Q96T23-3;H0YDG9 Q96T23-2 RSF1 Remodeling and spacing factor 1 0 219.07 3.03E-34 26558000 42226 30489 24262 19548 29574 23718 40015 47203 17906 FALSE TRUE 36645.72711 30288.71575 35995.18435 23986.67217 28985.53526 24630.44681 36134.35146 37109.00578 15789.17308 2.320940237 1.918321853 2.279738411 1.519184827 1.835785517 1.559957997 2.288552496 2.350281778 1 13.94664799 4.894837104 1.081894526 1.868713368 2.605005542 0.123255865 0.412906857 6.282666565 4.877730867 0.129410799 5.729574477 78494.11615 -4.894837104 0.736292174 FDEILEASDGIMVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FDEILEASDGIMVAR 15 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;; 258.01 1.93E-24 521558000 590784 462817 385225 528511 484163 488875 494337 571434 1160466 FALSE TRUE 512710.3975 459776.7247 571521.0985 648517.5003 474529.1035 507682.3376 446396.2738 449237.286 1023277.031 0.501047499 0.449317937 0.558520402 0.633765325 0.463734736 0.496133815 0.436241858 0.439018245 1 19.96476535 1.234674331 24.99870268 1.000000726 0.495240664 0.872024567 0.060526682 41.42288134 266415.8386 0.118106785 0.016055658 17.16620646 -1.234674331 -0.504760061 FDEVLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FDEVLIR 7 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 140.12 0.0061558 110437000 214190 194359 151028 196735 213720 230570 202360 251530 291530 FALSE TRUE 185884.2488 193082.2429 224065.646 241406.6887 209467.3901 239440.1771 182735.1583 197742.2669 257065.6555 0.723100285 0.751100891 0.871628089 0.93908573 0.814840044 0.931435888 0.710850144 0.769228649 1 17.97177735 4.317735336 5.306640271 0.849394861 0.731412156 0.265049823 0.084966124 0.302924571 14.47557006 0.021997513 0.060301551 20784.29685 -4.317735336 -0.117982705 FDFLCQYHKPASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FDFLCQYHKPASK 13 1 J3KQ32;Q9NTK5;Q9NTK5-3;C9JTK6 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 145.29 2.51E-05 1247000000 6068500 4814100 3322320 4135800 4614100 3831300 5647400 6718200 6201400 FALSE TRUE 5266532.349 4782475.86 4929005.064 5074896.602 4522288.437 3978692.59 5099716.017 5281565.211 5468277.557 0.963106261 0.874585427 0.901381653 0.928061268 0.827004187 0.727595216 0.932600067 0.965855364 1 22.38265504 2.008718381 24.97605715 0.971110491 0.869017911 0.354310045 0.063284978 216.5665481 620408.3191 0.027231306 0.018328736 102.0277667 -2.008718381 -0.10209258 FDGGEEVLISGEFNDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FDGGEEVLISGEFNDLR 17 0 Q16698-2;Q16698 Q16698-2 DECR1 "2,4-dienoyl-CoA reductase, mitochondrial" 0 ; 142.85 1.33E-06 21653100 36846 38573 26688 38703 40763 42362 34784 44943 53182 FALSE TRUE 31976.70774 38319.61142 39594.40607 47491.10769 39951.89605 43991.69355 31410.65303 35332.2892 46894.88455 0.681880509 0.817138411 0.844322498 1.012714034 0.851945717 0.938091521 0.669809796 0.753435893 1 15.51714294 4.727771996 2.633812819 0.853083056 0.649670912 0.230367646 0.104289478 0.815098891 7.557667718 0.028106316 0.361687355 53428.37876 -4.727771996 -0.203412144 FDGILGMAYPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FDGILGMAYPR 11 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;A0A1B0GU92;A0A1B0GU03;C9JH19;H7C469;F8WD96;F8W787 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ;;; 177.36 1.86E-05 5882230000 2352000 2789870 1631560 2007930 2864910 3058430 2598480 2965670 2424060 FALSE TRUE 2041177.241 2771543.16 2420587.873 2463861.196 2807903.896 3176089.781 2346479.81 2331484.549 2137490.388 0.954941015 1.29663421 1.132443863 1.152688784 1.313645157 1.485896638 1.097773268 1.09075791 1 21.0274865 2.02383763 24.99622244 1.064582621 1.228659629 0.23127256 0.138572462 326.8746326 342760.3667 0.056864765 0.038336347 105.642247 -2.02383763 0.164077008 FDHSEIYTYIGSVVISVNPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FDHSEIYTYIGSVVISVNPYR 21 0 E9PDF6;O43795;O43795-2;E7EQD9;C9JUP5;C9JYW1;C9K0I9 E9PDF6 MYO1B Unconventional myosin-Ib 0 122.57 2.79E-05 19200000 36969 31988 24898 30445 37089 28305 31886 39375 39477 FALSE TRUE 32083.45298 31777.86872 36938.75608 37358.00257 36351.00146 29393.91167 28793.70063 30954.96267 34810.07403 0.921671495 0.91289288 1.061151322 1.073195149 1.044266709 0.844408192 0.827165739 0.889252997 1 15.08721726 2.738645097 24.9999947 0.884147617 1.004820669 0.393434718 0.069155788 8.164681848 2416541.139 0.024827812 0.023363857 547.8290992 -2.738645097 0.120673052 FDIYDPFHPTDEAYS(ph)PPPAPEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 FDIYDPFHPTDEAYSPPPAPEQK 23 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 FDIYDPFHPT(0.01)DEAY(0.029)S(0.961)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPT(0.132)DEAYS(0.868)PPPAPEQK;FDIYDPFHPT(0.005)DEAYS(0.995)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK 276.9 5.73E-52 9833532000 5694775 4719768 2890678 3548743 4350353 3684940 5082827 6045654 5541273 TRUE FALSE 4942196.055 4688763.533 4288619.55 4354539.337 4263789.487 3826702.026 4589895.22 4752837.939 4886190.019 1.011462108 0.959595005 0.877702163 0.891193204 0.872620481 0.783166846 0.93936077 0.972708372 1 22.22027854 1.818211605 3.369113428 0.987429894 0.897599944 0.257703383 0.059543896 0.329483543 6.651225408 0.040966477 0.017295116 65.79783518 -1.818211605 -0.08982995 FDKDHDVMLFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FDKDHDVMLFLK 12 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 100.93 0.0017761 219120000 1251500 970300 646820 828470 909170 689200 1150100 1453100 1161700 FALSE TRUE 1086111.104 963926.0354 959624.3155 1016586.776 891079.2958 715713.97 1038563.479 1142365.873 1024365.149 1.06027729 0.940998467 0.936799066 0.99240664 0.869884432 0.698690277 1.013860614 1.115194004 1 19.96629865 2.011377561 24.99979218 1.065435846 0.914575333 0.283288959 0.096517245 248.516601 546060.7089 0.040673877 0.02739755 102.6543981 -2.011377561 -0.150860513 FDKEEEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FDKEEEIR 8 1 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 118.18 0.0017663 245850000 1084660 872330 852640 839910 1073830 935050 1249920 1310850 1774870 FALSE TRUE 941319.4328 866599.6068 1264979.556 1030624.403 1052462.884 971021.9786 1128702.951 1030534.929 1565046.891 0.601464045 0.553721177 0.808269429 0.658526213 0.672480096 0.620442738 0.721194335 0.658469043 1 20.57777445 1.237927052 24.99059154 1.000000386 0.664582353 0.70648258 0.068483369 8.527183978 336080.4561 0.094237766 0.016313963 17.29525829 -1.237927052 -0.335418033 FDLGQDVIDFTGHALALYR ddPTM_MDA-MB-175_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 ; 253.2 7.18E-31 2561900000 1568760 1463690 1077310 1441300 1391620 1489950 1427720 1859110 2369570 FALSE TRUE 1361444.391 1454074.924 1598300.719 1768569.194 1363929.485 1547269.341 1289259.934 1461553.794 2089442.134 0.651582721 0.695915384 0.764941366 0.846431287 0.652772078 0.740517919 0.617035482 0.699494746 1 20.99468637 1.237450492 24.99817213 1.000000347 0.708795181 0.664064906 0.065137899 17.69581875 398295.8498 0.096913295 0.016247011 17.27629025 -1.237450492 -0.291205166 FDLHSSSHIDTLLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FDLHSSSHIDTLLER 15 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PNN8;E9PKG4;E9PJD8 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 ;;; 217.48 1.20E-12 452199000 443071 484680 198990 314892 552456 503023 494494 582110 550682 FALSE TRUE 384518.0448 481496.1052 295222.2296 386393.0414 541463.2065 522374.6203 446538.048 457630.3065 485581.0013 0.791872095 0.991587611 0.607977307 0.795733442 1.115083179 1.075772361 0.919595385 0.942438656 1 18.88935245 3.261525864 24.59424427 0.998496526 0.797219592 0.495766054 0.106748162 181.9047225 194806.2331 0.031530917 0.040676509 1826.105498 -3.261525864 -0.201276934 FDLLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FDLLKR 6 1 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;H0Y961;H0Y9G8;O15519-11;C9JV51;F8WBH9;C9J408;O15519-5;E9PAP3;O15519-14;O15519-8;O15519-6;O15519-10;O15519-12;O15519-9;O15519-2;O15519-13;O15519 D6RGI3 SEPT11;CFLAR Septin-11;CASP8 and FADD-like apoptosis regulator;CASP8 and FADD-like apoptosis regulator subunit p43;CASP8 and FADD-like apoptosis regulator subunit p12 0 ; 107.74 0.049715 381100000 1312990 1176540 527310 672140 1131110 1010930 1232990 1411730 333330 FALSE TRUE 1139475.045 1168811.231 782318.8797 824759.66 1108603.124 1049821.131 1113414.82 1109842.526 293924.1071 3.876766203 3.976574915 2.661635643 2.806029312 3.771732556 3.57174218 3.788103094 3.775949297 1 18.16508417 4.266256547 24.62478069 3.19275381 3.926671896 0.140616775 0.84447219 412.8364148 367049.6119 0.207574789 0.548893417 18461.05632 -4.266256547 0.733918086 FDLLWLIQDRPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FDLLWLIQDRPDR 13 1 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 193.06 1.99E-06 1361690000 1348470 1259230 823190 1231580 1256800 1255110 1328780 1612060 1700160 FALSE TRUE 1170266.273 1250958.035 1221287.437 1511229.063 1231792.139 1303394.894 1199915.12 1267333.514 1499169.022 0.780609962 0.834434288 0.814642925 1.008044484 0.821649941 0.869411571 0.800386816 0.845357325 1 20.51573162 7.999982621 0.019227629 1.547941929 2.25E-05 0.146712242 0.072686602 20883.35663 39.93643112 1287.605132 2004.019006 99995998.41 -7.999982621 -1.547919469 FDLLWLIQDRPDRDNDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FDLLWLIQDRPDRDNDLR 18 2 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 116.29 9.26E-05 492610000 1096240 972230 360880 436040 851690 830490 951070 1142270 330110 FALSE TRUE 951369.1065 965843.3571 535402.7751 535049.5465 834743.0353 862439.4877 858835.3778 898004.4497 291084.7719 3.268357532 3.318082739 1.839336258 1.838122768 2.867697372 2.962846466 2.950464816 3.085027238 1 18.15107984 FDLMYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FDLMYAK 7 0 P68363;P68363-2;P68366-2;P68366;Q9BQE3;F5H5D3;A6NHL2-2;A6NHL2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA4A;TUBA1C;TUBAL3 Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain;Tubulin alpha chain-like 3 0 91.906 0.037363 907640000 625310 692380 476010 531250 596710 774600 767880 776010 989830 FALSE TRUE 542673.6992 687831.7102 706210.0282 651878.4321 584836.6384 804399.3632 693411.1158 610066.3004 872813.425 0.621752237 0.788062707 0.809119117 0.746870309 0.670059169 0.921616625 0.794455145 0.698965303 1 19.73531377 -1.999999353 0.031021142 1.883586663 7.77E-11 0.253355215 0.097362475 5526.44155 16.96850183 734.3883388 359.9946498 0.010000015 1.999999353 -1.883586663 FDLSQNHPLGMAIFLK ddPTM_MDA-MB-175_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 ;; 212.7 3.82E-12 13467640000 9079010 8271160 5319960 7732720 8871960 9479460 11424970 11190950 13999920 FALSE TRUE 7879195.825 8216826.205 7892710.45 9488552.263 8695425.354 9844140.96 10316978.17 8797852.431 12344865.41 0.638256924 0.665606788 0.639351681 0.768623387 0.704375873 0.79742797 0.835730308 0.712673014 1 23.55740777 -2 0.203665868 2.064752126 0.597579883 0.639836315 0.065667479 72.93622863 1.09295668 33.21782375 0.401490677 0.01 2 -1.467172243 FDMIWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FDMIWDR 7 0 P51580 P51580 TPMT Thiopurine S-methyltransferase 0 ;;; 128.57 0.0087129 385957000 975404 995350 604560 740900 991610 1020620 1042570 1126890 1049410 FALSE TRUE 846501.89 988811.4803 896927.2381 909132.6689 971878.9011 1059883.912 941461.7219 885913.343 925349.9453 0.914791095 1.068581119 0.969284369 0.98247444 1.050282551 1.145387123 1.01741155 0.957381959 1 19.81963954 3.252445541 24.89887212 1.028817445 0.988804173 0.142598364 0.059977955 620.1363535 1112040.919 0.018635853 0.02393332 1788.321264 -3.252445541 -0.040013272 FDNLYGCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FDNLYGCR 8 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 155.82 0.00093732 564200000 492910 591180 409810 465480 607330 620360 542990 568070 1028470 FALSE TRUE 427770.6946 587296.4997 607995.4867 571174.3484 595245.3212 644225.6506 490330.9134 446592.6512 906885.4482 0.471692092 0.647597225 0.670421483 0.62981973 0.656362193 0.710371582 0.540675688 0.492446595 1 19.79056081 1.228516854 24.98575233 1.000000811 0.603825482 0.718685337 0.078167421 246.2696142 612598.6699 0.271927592 0.020464931 16.92453923 -1.228516854 -0.396175329 FDNSYSLWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FDNSYSLWR 9 0 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 ;; 156.46 0.00016491 3824370000 2480900 2391580 1770170 2028270 2612720 2516460 2666670 2798340 2666320 FALSE TRUE 2153042.779 2375869.554 2626230.133 2488819.704 2560731.984 2613269.845 2408056.754 2199936.768 2351110.687 0.915755601 1.010530711 1.117016799 1.058571899 1.089158413 1.111504388 1.024220921 0.935701062 1 21.16491103 1.951340093 6.495523507 0.967298375 1.054927345 0.242198203 0.059312583 0.29445832 30.3286827 0.029652092 0.016382851 89.40052982 -1.951340093 0.087628971 YWCDAEYDAYRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YWCDAEYDAYRR 12 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 ;;;; 209.19 9.32E-08 1530220000 1531850 1590890 745017 811611 1395140 1423030 1397470 1570610 546128 FALSE TRUE 1329412.141 1580439.339 1105309.713 995899.6822 1367379.444 1477774.885 1261943.574 1234747.274 481565.37 2.760605775 3.281879133 2.29524335 2.068046717 2.839447204 3.068690103 2.620503161 2.564028377 1 18.87737212 1.22234077 3.759693807 0.749337385 2.699350938 0.703941469 0.344843811 0.175498344 3.884674682 0.986360477 0.092163262 16.68555933 -1.22234077 1.950013554 KPIKS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPIKSPSK 8 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 KPIKS(0.968)PS(0.032)K 72.652 0.056709 0 1421900 1134900 1308400 1272200 902740 757800 1600400 1763300 3323000 TRUE FALSE 1233992.312 1127444.767 1941146.616 1561072.454 884777.2402 786953.0564 1445193.454 1386232.017 2930158.726 0.421134972 0.384772592 0.66247149 0.532760373 0.301955397 0.268570112 0.493213368 0.473091101 1 21.48254739 1.222401601 3.992920535 1.07345282 0.439395332 0.710024814 0.112147886 0.161767526 4.387871055 0.308025952 0.03037828 16.68789662 -1.222401601 -0.634057488 QTDDLRGEIAVLEATVQNNQDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QTDDLRGEIAVLEATVQNNQDER 23 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ;;; 239.32 2.97E-37 291993000 218446 203155 117788 128804 199321 216301 205145 228996 80432 FALSE TRUE 189577.8076 201820.4614 174750.6708 158050.9168 195354.9021 224622.2394 185250.0695 180026.9874 70923.42059 2.672993012 2.845610939 2.463934612 2.228472845 2.754448396 3.167109504 2.611973139 2.538329172 1 16.1139745 1.22391484 3.793398997 0.760785596 2.674163634 0.82354349 0.242240778 0.123783933 2.831619318 0.685333354 0.065570155 16.74614473 -1.22391484 1.913378039 FDQLFDDES(ph)DPFEVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FDQLFDDESDPFEVLK 16 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 FDQLFDDES(1)DPFEVLK;FDQLFDDES(1)DPFEVLK 167.05 6.78E-09 95844000 252997 179778 133046 166883 189385 147983 211522 252495 235606 TRUE FALSE 219562.8054 178597.0265 197387.4906 204776.3358 185616.609 153676.0018 191008.629 198500.9092 207752.9271 1.056845786 0.859660699 0.950106905 0.985672446 0.893448827 0.739705591 0.919402829 0.955466245 1 17.66450928 4.753031251 24.02239986 0.913971697 1.056845958 0.271644342 0.074040879 2249.438098 3734134.828 0.018931693 0.38224627 56628.00366 -4.753031251 0.142874261 FDQLFDDESDPFEVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FDQLFDDESDPFEVLK 16 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 178.23 6.56E-09 66410000 257310 219200 164420 186360 213110 188140 242600 315240 300360 FALSE TRUE 223305.8316 217760.0608 243934.062 228675.8863 208869.5279 195377.8675 219072.6893 247828.3792 264851.783 0.843135089 0.82219594 0.92102103 0.863410787 0.788627985 0.737687568 0.827152028 0.935724791 1 18.0148257 1.592669831 3.123856943 0.990885971 0.82843798 0.611374161 0.047347379 0.155135712 3.406711003 0.048978808 0.013997382 39.14441715 -1.592669831 -0.162447991 FDQLLAEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FDQLLAEEK 9 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4;P35749;P35749-2;P35749-4;P35749-3;Q7Z406;Q7Z406-6;Q7Z406-2;A0A0C4DFM8;A1L2Z2 P35579;P35580;P35749;Q7Z406 MYH9;MYH10;MYH11;MYH14 Myosin-9;Myosin-10;Myosin-11;Myosin-14 0 118.4 0.0023148 44846000 129790 105440 83473 95638 122080 113150 127490 153270 151780 FALSE TRUE 112637.9227 104747.3577 123840.822 117354.0696 119650.8468 117502.9537 115126.0394 120494.4032 133836.7413 0.841606883 0.78265024 0.925312592 0.876844942 0.894005978 0.877957372 0.860197568 0.900308854 1 17.0301147 1.205688243 2.195902627 1.047380866 0.86650754 0.568347546 0.036809818 0.573957859 2.610488809 0.213593394 0.010127813 16.05788128 -1.205688243 -0.180873325 FDREVDIGIPDATGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FDREVDIGIPDATGR 15 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 175.26 7.90E-07 355910000 477080 319440 153120 165394 335510 321000 322690 348940 97941 FALSE TRUE 414032.6692 317341.5776 227169.3442 202949.2356 328834.0074 333349.0777 291395.5735 274321.8965 86362.52655 4.794124092 3.674528644 2.630415682 2.349968715 3.807600594 3.859881027 3.374097367 3.176399619 1 16.39811783 4.598470737 2.970582865 2.989272433 4.857015975 0.352177317 0.826359937 0.369652954 5.297569054 0.211150636 1.361710294 39670.77975 -4.598470737 1.867743542 FDRPPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FDRPPAR 7 1 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2;F8WEA1 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ;;; 113.5 0.0055777 1530940000 2209760 1850840 1062530 1330790 2024190 2030970 1779860 2061800 2243900 FALSE TRUE 1917734.617 1838681.71 1576373.062 1632966.209 1983912.579 2109102.73 1607249.451 1620900.115 1978628.698 0.969224099 0.929270718 0.796699787 0.825301994 1.002670476 1.065941645 0.81230473 0.819203783 1 20.91606948 1.485373918 0.003973374 0.179753455 1.619081887 0 0.096429093 1119591.455 1424.018161 261527.4358 254347.5068 30.57552467 -1.485373918 1.439328432 FDSEYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FDSEYER 7 0 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 158.12 0.0033328 4322110000 3203740 2828990 1988970 2437550 2937360 2826550 2710670 3067320 4225840 FALSE TRUE 2780357.642 2810406.178 2950842.545 2991032.983 2878912.283 2935289.208 2447789.641 2411397.488 3726266.009 0.746151143 0.754215124 0.791903352 0.802689066 0.772599776 0.787729378 0.656901476 0.64713509 1 21.82929924 FDSLTDLVEHYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FDSLTDLVEHYK 12 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4;H0YF12 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ; 290.61 4.13E-36 506640000 1236370 1069860 810170 1030840 1119990 962390 1212160 1453980 1766180 FALSE TRUE 1072980.572 1062832.019 1201970.922 1264907.977 1097704.39 999413.766 1094604.91 1143057.692 1557384.212 0.688963304 0.682446894 0.771788305 0.812200334 0.704838524 0.641725888 0.702848341 0.733959984 1 20.57069348 1.236877879 4.882457914 1.019793504 0.716723047 0.780468023 0.047207415 0.090870337 5.267434572 0.094439451 0.012848892 17.25352664 -1.236877879 -0.303070457 FDSPDLLLEAGDPAT(ph)SPCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FDSPDLLLEAGDPATSPCR 19 0 A0A096LNM2;Q969U6-2;Q969U6 A0A096LNM2 FBXW5 F-box/WD repeat-containing protein 5 1 FDSPDLLLEAGDPAT(0.63)S(0.37)PCR 138.66 1.66E-05 31817000 53042 53601 38139 46982 60458 61591 60090 68509 66416 TRUE FALSE 46032.36531 53248.8915 56583.14797 57649.98117 59255.00408 63960.44562 54262.48105 53858.88349 58564.37614 0.786013074 0.909236895 0.96617008 0.984386499 1.011792629 1.09213911 0.926544166 0.919652646 1 15.83773574 4.712502416 1.642446269 0.983017455 0.721050299 0.648790554 0.047474413 0.688174579 1.874168285 0.014533358 0.282569227 51582.50342 -4.712502416 -0.261967156 FDSSLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FDSSLDR 7 0 Q02790;F5H1U3 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ;;;;; 183.9 0.0014795 4410400000 2869010 2725630 2201560 2824440 2479650 2726280 2333260 2725570 7456330 FALSE TRUE 2489863.059 2707725.157 3266241.78 3465772.271 2430309.816 2831161.756 2106980.804 2142728.066 6574851.162 0.378694969 0.411830639 0.496778056 0.527125586 0.369637237 0.430604691 0.320460609 0.325897577 1 22.64852681 1.233853754 24.99998861 1.000000897 0.405893782 0.887954317 0.066127476 50.60744614 268762.729 0.143448439 0.018164096 17.13380239 -1.233853754 -0.594107114 FDSSLDRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FDSSLDRK 8 1 Q02790;F5H1U3 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ;;;;; 166.52 0.0005099 13137320000 8750250 7622820 5495390 7194880 7705250 6673650 9494130 10878600 8323380 FALSE TRUE 7593882.292 7572745.194 8152978.985 8828587.471 7551930.6 6930389.634 8573390.734 8552296.047 7339399.498 1.034673517 1.031793568 1.110850961 1.202903245 1.02895756 0.944272026 1.168132452 1.165258282 1 22.8072306 4.245864345 24.56084327 1.096521457 1.033233499 0.069074416 0.080581646 349.5228382 1175332.141 0.021129172 0.053471556 17614.25765 -4.245864345 -0.063287959 FDSSYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FDSSYDR 7 0 O95302;Q96AY3;C9JPC3;K7ELI6;K7ESG6 O95302;Q96AY3 FKBP9;FKBP10 Peptidyl-prolyl cis-trans isomerase FKBP9;Peptidyl-prolyl cis-trans isomerase FKBP10;Peptidyl-prolyl cis-trans isomerase 0 108 0.017104 245240000 589570 593120 308630 424480 577300 608560 535780 620170 550010 FALSE TRUE 511656.8307 589223.7557 457884.5003 520864.6718 565812.8595 631971.697 483820.1381 487551.4717 484988.4444 1.054987674 1.214923288 0.944114248 1.073973365 1.166652249 1.303065474 0.997591064 1.005284718 1 18.88759085 FDVNTSAVQVLIEHIGNLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FDVNTSAVQVLIEHIGNLDR 20 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 261.26 2.26E-36 889730000 701980 644570 478120 642500 745570 679710 616530 753770 1576920 FALSE TRUE 609211.5644 640335.7772 709340.4312 788389.445 730734.6157 705858.8835 556739.0155 592582.1513 1390498.314 0.438124634 0.460508129 0.510133974 0.566983388 0.525519958 0.507630161 0.400388127 0.426165315 1 20.40717056 1.235050574 24.99963269 1.000000732 0.478655194 0.913940564 0.050201428 31.07947341 221322.6699 0.100409146 0.014065145 17.18108453 -1.235050574 -0.521345538 FDVPGDENAEMDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FDVPGDENAEMDAR 14 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 198.32 5.17E-08 932860000 240610 270550 210630 269900 235650 248920 203377 281910 499320 FALSE TRUE 208812.7789 268772.7392 312491.3725 331184.9202 230961.026 258496.1135 183653.5298 221625.7403 440290.9584 0.474260883 0.610443467 0.709738337 0.752195597 0.524564544 0.587102934 0.417118558 0.503362007 1 18.74809769 1.232948488 24.99806543 1.000000682 0.571910138 0.63448138 0.10200839 132.919621 591999.6564 0.234626175 0.027409778 17.09812501 -1.232948488 -0.428090545 FDYDWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FDYDWER 7 0 Q93008;Q93008-3;O00507;O00507-2 Q93008 USP9X;USP9Y Probable ubiquitin carboxyl-terminal hydrolase FAF-X;Probable ubiquitin carboxyl-terminal hydrolase FAF-Y 0 ; 89.55 0.041389 101692000 489840 454290 302120 343730 502700 524480 458730 528530 556130 FALSE TRUE 425106.4029 451305.7391 448226.2425 421779.1501 492697.2535 544657.085 414242.4352 415507.9725 490384.9449 0.866883063 0.920309124 0.91402937 0.860098081 1.004715293 1.110672525 0.844729104 0.847309806 1 18.90355516 4.761189625 0.946930708 0.93661961 0.83768108 0.077576988 0.082527683 8.216075807 5.713197952 0.030423651 0.846828971 57701.83512 -4.761189625 -0.09893853 FEAFEHENK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FEAFEHENK 9 0 Q9UBQ0;F8VXU5;Q9UBQ0-2;Q05DG7 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ; 132.88 0.00029277 1042300000 1476650 1125000 1112630 1391470 1222940 1088690 1333200 1585690 2813800 FALSE TRUE 1281506.961 1117609.801 1650701.59 1707424.531 1198605.887 1130572.609 1203906.469 1246602.533 2481155.769 0.516495972 0.450439192 0.665295428 0.688156927 0.483083691 0.455663696 0.485220027 0.502428162 1 21.24258088 1.236509079 24.99973681 1.000000598 0.530139368 0.764337055 0.081868129 28.3606331 345509.2897 0.137143346 0.021541742 17.23888129 -1.236509079 -0.469861231 FEDEDS(ph)DDVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FEDEDSDDVPR 11 0 P49756 P49756 RBM25 RNA-binding protein 25 1 FEDEDS(1)DDVPR;FEDEDS(1)DDVPR 210.31 1.38E-08 299420000 804570 681910 548520 756280 738640 703570 699630 797380 1469040 TRUE FALSE 698244.036 677430.4883 813786.1067 928004.933 723942.5091 730636.7932 631779.9903 626866.4922 1295371.765 0.539029841 0.522962216 0.628225911 0.716400464 0.558868526 0.564036374 0.487720983 0.483927865 1 20.30493477 1.232398334 24.99909237 1.000000722 0.560983845 0.802183171 0.068249834 100.6384325 408228.5785 0.169045332 0.018769071 17.07647921 -1.232398334 -0.439016877 FEDEDSDDVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FEDEDSDDVPR 11 0 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 221.68 1.92E-11 738360000 951880 747720 670540 838080 821100 815700 791330 890840 1980800 FALSE TRUE 826086.6462 742808.1781 994815.3868 1028378.873 804761.7165 847080.5068 714586.9384 700340.7985 1746632.081 0.472959735 0.425280279 0.569562072 0.588778189 0.460750564 0.484979359 0.409122761 0.400966412 1 20.73614431 1.233672277 24.99980027 1.000000802 0.474427559 0.875895444 0.061917483 55.79322611 285301.9605 0.135407996 0.01688264 17.12664426 -1.233672277 -0.525573244 FEDENFILK ddPTM_MDA-MB-175_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 5201349000 6633610 5027351 4306530 5393679 4682859 3915235 5222659 6413860 13944570 FALSE TRUE 5756961.631 4994326 6389182.312 6618396.254 4589679.268 4065856.624 4716166.334 5042305.952 12296058.82 0.468195681 0.406172911 0.519612211 0.538253464 0.373264258 0.330663401 0.383551055 0.41007497 1 23.55169264 1.2375657 24.99989921 1.000000676 0.426492752 0.885667391 0.064501344 8.464681566 212587.8677 0.10186032 0.01718504 17.28087387 -1.2375657 -0.573507924 FEDMAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FEDMAK 6 0 P26583;D6R9A6;P09429;Q5T7C4;B2RPK0;P23497 P26583;P09429;P23497 HMGB2;HMGB1;HMGB1P1;SP100 High mobility group protein B2;High mobility group protein B1;Putative high mobility group protein B1-like 1;Nuclear autoantigen Sp-100 0 ; 103.29 0.080996 208880000 535580 433040 317640 377890 419430 384700 476530 560350 696340 FALSE TRUE 464801.746 430195.3317 471251.7664 463695.7002 411084.1636 399499.6579 430316.1939 440523.5131 614019.4785 0.756982087 0.700621636 0.767486673 0.755180766 0.669496943 0.650630268 0.700818474 0.717442245 1 19.2279249 1.238613299 7.656062286 1.004274596 0.713039339 0.849892675 0.037661922 0.038144203 17.059543 0.057667882 0.009877571 17.32260885 -1.238613299 -0.291235257 FEDRFDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FEDRFDK 7 1 Q9HD45;Q5TB53 Q9HD45 TM9SF3 Transmembrane 9 superfamily member 3 0 ;;; 113.71 0.0055352 2983180000 4172770 3332770 2961170 3109700 3510100 3835400 3265960 4449040 4997650 FALSE TRUE 3621327.872 3310876.814 4393201.717 3815804.914 3440255.877 3982950.32 2949227.702 3497647.418 4406833.51 0.821752822 0.751305173 0.996906669 0.865883611 0.78066391 0.903812298 0.669239647 0.793687216 1 22.07131096 3.269685956 24.4278494 0.816704929 0.861125513 0.011198663 0.103724763 623.4743523 489311.0484 0.029963595 0.038678299 1860.741125 -3.269685956 0.044420584 FEDYLNAESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FEDYLNAESR 10 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1;A0A5F9ZGZ7 E7EPK1 7-Sep Septin-7 0 ;;; 253.32 1.03E-16 3282090000 3791190 3394490 2457700 3219860 3587650 3513990 3367470 3961110 4512720 FALSE TRUE 3290174.636 3372191.372 3646251.941 3950978.425 3516262.784 3649175.469 3040893.278 3114057.452 3979231.383 0.826836723 0.847447923 0.916320663 0.992899896 0.883653763 0.91705536 0.764191118 0.782577627 1 21.92405836 1.21390121 24.80172411 1.000000674 0.864702506 0.279897224 0.067311511 3362.920008 3382129.506 1.246354997 0.018649578 16.36444234 -1.21390121 -0.135298168 FEEAKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FEEAKR 6 1 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 94.163 0.071825 246330000 391780 249630 165460 198630 208540 206550 278560 327810 221460 FALSE TRUE 340005.2804 247990.1641 245477.0094 243731.9774 204390.462 214496.1122 251545.2941 257710.3825 195279.2511 1.741123435 1.269925825 1.257056283 1.248120197 1.046657343 1.098407081 1.28813119 1.319701817 1 17.57517914 5.417873549 1.29834456 1.186010214 3.696061719 0.737981143 0.104452188 3.876731395 1.597137677 0.031262524 19.88276862 261742.0799 -5.417873549 2.510051505 FEEESKEPVADEEEEDS(ph)DDDVEPITEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 FEEESKEPVADEEEEDSDDDVEPITEFR 28 1 P54105;E9PJF4 P54105 CLNS1A Methylosome subunit pICln 1 FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR 367.2 1.24E-127 21275310000 9201340 6886180 5402038 7441220 7032610 5749680 6539180 10285890 10538720 TRUE FALSE 7985359.606 6840944.23 8014481.646 9130862.733 6892674.82 5970873.91 5905011.33 8086332.468 9292844.527 0.85930197 0.7361518 0.862435783 0.982569191 0.741718513 0.642523814 0.635436363 0.870167627 1 23.14768884 1.409054696 4.221675157 0.990221362 0.780793621 0.315206054 0.104360002 0.287489846 8.131869364 0.128307268 0.028840504 25.64807031 -1.409054696 -0.209427741 FEEHVQSVDIAAFNKI ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FEEHVQSVDIAAFNKI 16 1 P29692;P29692-2;E9PRY8;P29692-4;E9PQZ1;H0YE72;P29692-3 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 135.09 3.97E-05 426080000 400960 395220 209110 360670 344300 325500 393380 535690 656130 FALSE TRUE 347972.1201 392623.7738 310236.2954 442565.636 337449.1036 338022.1956 355230.0681 421136.8622 578563.0589 0.601441995 0.678618809 0.536218638 0.764939325 0.583253802 0.584244345 0.613986778 0.727901403 1 19.14211468 1.236537986 2.226738942 1.110252222 0.624649715 0.784472927 0.062198249 0.279893049 1.409399973 0.274080684 0.015655456 17.24002876 -1.236537986 -0.485602506 FEELCSDLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 FEELCSDLFR 10 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;P17066;P48741 A0A0G2JIW1;P17066 HSPA1B;HSPA1A;HSPA6;HSPA7 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 6;Putative heat shock 70 kDa protein 7 0 ;;;;;;; 276.39 1.63E-23 8511680000 3007572 2921980 2229874 2802671 3017649 3069838 2938514 3358715 6443920 FALSE TRUE 2610113.74 2902785.321 3308248.525 3439060.287 2957603.689 3187936.654 2653537.365 2640479.935 5682127.119 0.459355042 0.510862439 0.582220083 0.605241702 0.520509948 0.561046345 0.466997184 0.464699201 1 22.43799968 1.23441091 24.99926829 1.000000699 0.521569389 0.900753869 0.049929694 39.71111154 239200.6459 0.101212128 0.013453609 17.15579744 -1.23441091 -0.478431311 FEELNADLFR ddPTM_MDA-MB-175_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 ;;;;;;;;; 290.22 9.98E-32 12786641000 3979877 3575005 2809398 3625103 3983764 4004327 3529093 4424138 7628245 FALSE TRUE 3453926.171 3551520.557 4168032.27 4448238.042 3904494.891 4158376.051 3186842.104 3478070.517 6726442.566 0.513484823 0.527993887 0.619648831 0.661306181 0.58046952 0.618213269 0.473778238 0.51707429 1 22.68141227 1.23484335 24.90613194 1.000000653 0.563431784 0.84936188 0.057704617 41.85755971 280406.1019 0.112655809 0.015527746 17.17288849 -1.23484335 -0.43656887 FEELNMDLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FEELNMDLFR 10 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;; 232.79 1.12E-10 409589000 1319788 1182568 742137 1160547 1441791 1298580 1172288 1418105 1511560 FALSE TRUE 1145374.672 1174799.633 1101036.935 1424066.934 1413102.18 1348537.213 1058599.69 1114854.281 1332865.099 0.859332781 0.881409254 0.826067797 1.068425406 1.060198951 1.011758215 0.794228682 0.836434447 1 20.34609934 7.519029175 9.467945298 0.920662649 0.044860385 0 0.101777172 0 0 0.024822471 0 33039173.53 -7.519029175 -0.875802264 FEEPAPLSYDSRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FEEPAPLSYDSRPR 14 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 0 ; 162.32 4.06E-06 470450000 274470 282860 173649 195304 273390 293700 248230 295330 256560 FALSE TRUE 238198.0941 281001.874 257626.2372 239650.7582 267950.0739 304998.829 224156.6928 232175.9778 226229.7691 1.052903405 1.242108301 1.13878133 1.059324594 1.184415627 1.348181675 0.990836413 1.026283936 1 17.78742926 2.140536086 23.32093644 1.009363365 1.168432986 0.456802602 0.084881865 7.74226178 1832.350645 0.03431153 0.023132841 138.208924 -2.140536086 0.159069621 FEETTADGRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FEETTADGRK 10 1 Q01469;I6L8B7 Q01469 FABP5 "Fatty acid-binding protein, epidermal" 0 77.192 0.054096 774810000 733120 530340 1452100 624930 298690 297110 564710 584140 460320 FALSE TRUE 636236.3345 526856.1616 2154340.417 766829.908 292746.6534 308540.014 509944.5111 459226.2068 405901.494 1.567464875 1.297990201 5.307544931 1.889201984 0.721225858 0.760135202 1.25632578 1.131373532 1 18.63077012 3.477210745 23.14288486 1.031393055 2.751143931 0.360174121 1.06871152 1.329185479 343751.9442 0.306325106 0.400609164 3000.61824 -3.477210745 1.719750876 FEGAIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FEGAIYR 7 0 P22102;P22102-2 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ; 110.61 0.015737 352110000 726940 698840 477960 620300 702120 720050 673170 735220 942790 FALSE TRUE 630873.0372 694249.274 709103.0547 761148.5957 688149.1857 747750.7894 607886.077 577998.9245 831334.4402 0.75886792 0.835102265 0.85296966 0.915574477 0.827764558 0.899458453 0.731217243 0.695266425 1 19.66506945 1.212389488 24.63327631 1.000001103 0.813101821 0.411106248 0.069744109 2632.128484 2477300.454 1.493234437 0.019255955 16.30757888 -1.212389488 -0.186899282 FEGDFDFESANAQFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FEGDFDFESANAQFNR 16 0 Q9BX40;Q9BX40-2;Q5TBQ0;Q5TBP9;Q9BX40-3 Q9BX40 LSM14B Protein LSM14 homolog B 0 ; 264.55 1.18E-26 155028000 151139 145419 104569 126489 149982 154528 125790 168566 246250 FALSE TRUE 131165.5982 144463.733 155138.9182 155210.2607 146997.6516 160472.7922 113590.9052 132519.4727 217138.6055 0.604063924 0.665306534 0.714469533 0.714798091 0.676976124 0.739033908 0.523126253 0.610298995 1 17.72825672 1.234051094 24.99647976 1.000000516 0.654841932 0.741056105 0.063900475 76.01331011 421291.1546 0.130059195 0.016792379 17.14158965 -1.234051094 -0.345158584 FEGGDRDLEHLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FEGGDRDLEHLSK 13 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;;; 171.73 1.48E-05 3132020000 3949550 3649633 1076251 2882124 4305360 4179230 3973920 3909530 2045882 FALSE TRUE 3427606.961 3625658.321 1596729.583 3536554.305 4219691.759 4340007.682 3588529.85 3073507.433 1804020.161 1.899982625 2.009765966 0.885095199 1.960374048 2.339049115 2.40574234 1.989185004 1.70369905 1 20.78278403 FEGKPLLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FEGKPLLQR 9 1 Q9H3K6;A0A087WZT3;H3BV85;Q9H3K6-2;H3BTW0;A0A0B4J295;H3BVE0 Q9H3K6 BOLA2;BOLA2B BolA-like protein 2 0 ; 157.66 6.20E-05 5045900000 5375000 5777000 3132000 4210100 5908800 5074900 5952800 6562200 5875600 FALSE TRUE 4664680.131 5739050.507 4646645.676 5166067.552 5791226.44 5270134.687 5375498.372 5158924.597 5180993.262 0.900344759 1.107712405 0.896863872 0.997119141 1.117783048 1.01720547 1.037542051 0.995740457 1 22.30479728 3.468579008 24.97184899 1.031026586 0.976371532 0.167403548 0.066097471 377.9539502 1104881.843 0.01803499 0.023322081 2941.568784 -3.468579008 -0.054655054 FEGLS(ph)PLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FEGLSPLQR 9 0 Q9Y3E2 Q9Y3E2 BOLA1 BolA-like protein 1 1 FEGLS(1)PLQR;FEGLS(1)PLQR;FEGLS(1)PLQR;FEGLS(1)PLQR;FEGLS(1)PLQR;FEGLS(1)PLQR 136.94 0.00018736 1305372000 2524101 2261489 1251841 1376816 1935205 2041244 1986988 2109202 1997649 TRUE FALSE 2190534.658 2246633.13 1857235.495 1689443.116 1896698.207 2119771.978 1794290.21 1658165.566 1761489.211 1.243569727 1.275416912 1.054355305 0.959099327 1.076758345 1.20339765 1.018621175 0.941343016 1 20.74836421 8 0.384901787 0.996566027 5.353714575 0.486814815 0.084269832 74.00559085 1.070033076 0.09664323 239.5054963 100000000 -8 4.357148548 FEHCNFNDVTTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FEHCNFNDVTTR 12 0 E9PNW4;A0A2U3TZL5;P13987;P13987-2 E9PNW4 CD59 CD59 glycoprotein 0 ;;; 155.98 6.42E-05 2502890000 2058630 2008400 1291320 1861300 2053110 2372120 1764120 2406320 2589760 FALSE TRUE 1786576.83 1995206.688 1915806.671 2283936.613 2012257.128 2463376.991 1593035.914 1891747.194 2283601.523 0.782350516 0.873710526 0.83894088 1.000146738 0.881176995 1.078724535 0.697598026 0.82840512 1 21.1228795 4.866211965 1.550854752 0.895210962 0.715294489 0.112063384 0.106566585 4.023484192 7.193981454 0.02963468 1.204857089 73487.24483 -4.866211965 -0.179916474 FEHLLED ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FEHLLED 7 0 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 0 ;;; 163.34 0.0028812 727680000 1752520 1858420 1224390 1310650 1937830 2223380 1690250 2066130 2012800 FALSE TRUE 1520920.042 1846211.917 1816509.099 1608253.115 1899270.974 2308914.867 1526329.815 1624304.178 1774849.077 0.856929224 1.040207835 1.023472431 0.906135139 1.070102804 1.300907721 0.859977243 0.91517876 1 20.75926492 FEHQEWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FEHQEWK 7 0 Q9UHB9;Q9UHB9-4;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;; 130.22 0.0035843 768420000 2813460 2390730 1748070 2047730 2520140 2535200 2751750 3085040 3191630 FALSE TRUE 2441654.133 2375025.137 2593442.499 2512698.394 2469994.145 2632730.784 2484885.709 2425328.204 2814319.137 0.867582535 0.843907539 0.921516847 0.892826389 0.877652471 0.935476986 0.882943827 0.861781513 1 21.42435451 FEIGEGENLDLPYGLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FEIGEGENLDLPYGLER 17 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;;; 383.98 2.46E-121 2672820000 2684140 2327201 1619101 2019052 2408700 2556080 2582500 2957020 2808170 FALSE TRUE 2329424.098 2311913.463 2402103.659 2477508.616 2360771.583 2654414.052 2332049.547 2324684.285 2476191.342 0.940728634 0.933657034 0.970079985 1.000531976 0.95338819 1.071974531 0.941788911 0.938814479 1 21.23969137 4.156545826 4.544710678 0.979712565 0.937105398 0.194910939 0.038306962 0.365002032 13.56836632 0.010170373 0.023055844 14339.89021 -4.156545826 -0.042607167 FEIWDTAGQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FEIWDTAGQER 11 0 P20339-2;P20339;P51148;P51148-2;K7ERI8;K7ERQ8;F8VVK3;K7ENY4;F8VWU4;F8VVZ0;F8VUA5;P61020;P61020-2 P20339-2;P51148;P61020 RAB5A;RAB5C;RAB5B Ras-related protein Rab-5A;Ras-related protein Rab-5C;Ras-related protein Rab-5B 0 ;;;;; 192.12 3.57E-06 1274524000 1790040 1540210 1231108 1782990 1702920 1695200 1272070 1780790 3641260 FALSE TRUE 1553481.679 1530092.259 1826475.947 2187845.131 1669035.224 1760415.441 1148704.847 1399981.917 3210794.391 0.483830943 0.476546322 0.568854845 0.681403062 0.519820026 0.54828034 0.35776344 0.436023534 1 21.61449885 1.233577062 24.99967157 1.000000758 0.506348506 0.767423067 0.08492434 83.42995776 418471.5712 0.187183281 0.023150348 17.12288982 -1.233577062 -0.493652252 FEKEAAEMGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FEKEAAEMGK 10 1 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;A0A2R8YDN5;P68104;A0A087WVQ9;Q5VTE0;A0A087WV01;A6PW80;Q5JR01 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 76.522 0.032598 161260000 283060 215290 112590 117460 201990 170390 303050 317770 102380 FALSE TRUE 245652.9038 213875.7458 167038.9006 144131.0883 197970.7942 176945.0136 273660.2576 249817.3584 90276.75303 2.721109207 2.369112076 1.850298055 1.5965471 2.192932151 1.960028552 3.031348032 2.767239073 1 16.46206691 FELAVDAVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FELAVDAVHR 10 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7;H3BSK9;H3BUE3;H3BSQ5 Q8WWM7 ATXN2L Ataxin-2-like protein 0 ; 151.22 2.02E-05 330820000 275110 295160 157461 198759 264880 299510 264240 293250 300670 FALSE TRUE 238753.5165 293221.0745 233609.6663 243890.2688 259609.4062 311032.3435 238614.0455 230540.7696 265125.1351 0.900531428 1.105972372 0.881129834 0.91990625 0.979195753 1.173152984 0.900005371 0.869554558 1 18.01631393 FELDTSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FELDTSER 8 0 P04844-2;P04844 P04844-2 RPN2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 0 175.38 0.00061997 132190000 256240 243730 172570 293680 345350 352710 194860 367410 407480 FALSE TRUE 222377.2348 242128.9216 256025.4292 360364.5326 338478.2107 366278.9819 175962.5072 288842.2307 359308.1786 0.618903905 0.673875342 0.712551076 1.002939967 0.942027571 1.019400625 0.489725861 0.803884375 1 18.45486225 3.953880101 8.661872794 0.853842047 0.657730816 0.285249103 0.154786054 0.545798659 98.25690914 0.043529852 0.076422978 8992.492853 -3.953880101 -0.196111231 FELSENCSERPGLR ddPTM_MDA-MB-175_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 ; 217.2 5.33E-12 853520000 325204 331849 235481 267940 366380 371708 339560 373020 436340 FALSE TRUE 282227.4674 329669.0621 349360.3992 328779.8722 359089.7548 386007.8473 306629.5235 293252.5758 384756.3823 0.73352251 0.856825454 0.908004169 0.854514408 0.933291224 1.003252617 0.796944606 0.762177288 1 18.55358573 4.72140897 3.479282065 0.881088301 0.718063794 0.283775274 0.077805722 0.424459636 9.042531934 0.020684681 0.178051462 52651.28438 -4.72140897 -0.163024507 FENAFLSHVVSQHQALLGTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FENAFLSHVVSQHQALLGTIR 21 0 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 166.01 8.07E-12 892490000 128620 110820 62175 90816 140190 153040 108980 130940 124850 FALSE TRUE 111622.5411 110092.0161 92243.03796 111437.1608 137400.4933 158927.5478 98411.13637 102939.5 110090.3752 1.013917346 1.000014905 0.837884672 1.012233455 1.248069988 1.44360983 0.893912262 0.935045409 1 16.74832882 3.473478993 24.94638611 1.088377622 0.950465302 0.154933477 0.163294364 241.2132082 1652092.84 0.052764002 0.068441938 2974.945353 -3.473478993 -0.13791232 FENLCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 110.36 0.066925 2732710000 3725580 3122680 2046630 2474910 3027020 2702790 3693190 4225540 3921010 FALSE TRUE 3233235.164 3102166.909 3036387.114 3036876.142 2966788.224 2806768.08 3335025.002 3321941.154 3457472.665 0.9351441 0.897235412 0.878210013 0.878351454 0.858080023 0.81179762 0.964584633 0.96080041 1 21.72128641 2.126568791 8.42581359 0.973005245 0.876855755 0.677318035 0.032135613 0.152639903 10.72169195 0.013713724 0.009235302 133.8347188 -2.126568791 -0.096149491 FENYGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FENYGDK 7 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;M0R3F1;M0QYZ0 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 84.743 0.049602 156010000 197770 143300 126850 163850 143500 163080 155590 187420 249800 FALSE TRUE 171634.1934 142358.6529 188195.0843 201054.6468 140644.6308 169353.7931 140500.9057 147341.6915 220268.9286 0.779202925 0.646294753 0.854387795 0.912768987 0.638513256 0.768850124 0.637860758 0.668917275 1 17.74890648 3.218914709 24.99990245 0.727017981 0.791331957 0.038151077 0.122625373 771.1955947 981362.8055 0.037153452 0.042185335 1655.444819 -3.218914709 0.064313976 FEPES(ph)PGFESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FEPESPGFESR 11 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 FEPES(1)PGFESR;FEPES(1)PGFESR;FEPES(1)PGFESR;FEPES(1)PGFESR;FEPES(1)PGFESR;FEPES(1)PGFESR 217.09 1.22E-11 3325360000 3829120 3225750 2112750 2543670 3297830 3013540 3053630 3442900 3152120 TRUE FALSE 3323092.09 3204559.836 3134482.967 3121249.151 3232209.635 3129472.834 2757489.433 2706662.628 2779479.965 1.195580516 1.152935037 1.127722814 1.122961558 1.162882869 1.125920271 0.992088257 0.973801813 1 21.40638355 2.264486979 4.083765272 0.983548369 1.14894053 0.929142 0.020845898 0.04901815 1.808337134 0.008721516 0.006223336 183.8598829 -2.264486979 0.16539216 FEREPVIVASDRPVPGPS(ph)PGPPEPVMLPQPTSQPPVPQLPEGEASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FEREPVIVASDRPVPGPSPGPPEPVMLPQPTSQPPVPQLPEGEASR 46 2 P98174 P98174 FGD1 "FYVE, RhoGEF and PH domain-containing protein 1" 1 FEREPVIVAS(0.092)DRPVPGPS(0.907)PGPPEPVMLPQPT(0.001)S(0.001)QPPVPQLPEGEASR 54.632 0.007343 47322000 24602 22238 12582 14327 26384 23643 19234 30148 21830 TRUE FALSE 21350.78337 22091.91711 18666.69728 17580.16432 25859.01002 24552.56151 17368.68964 23701.08481 19249.28227 1.109172959 1.147674849 0.969734717 0.913289341 1.343375283 1.275505298 0.902303234 1.231271093 1 14.23251703 FESDPATHNEPGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FESDPATHNEPGVR 14 0 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;D6R9Y6;D6RDP1 D6RGI3 11-Sep Septin-11 0 ;; 126.71 8.38E-05 1864760000 2194940 1847000 937850 1492430 1884090 1993230 1829860 2004610 2088930 FALSE TRUE 1904873.118 1834866.935 1391397.397 1831309.042 1846600.295 2069910.848 1652400.459 1575939.751 1841979.075 1.034144819 0.99613886 0.755381761 0.994207299 1.002508834 1.123742868 0.897078844 0.855568759 1 20.81282524 FESILPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FESILPR 7 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 120.65 0.010504 173980000 122120 117610 79185 78787 122950 110840 119390 128560 127020 FALSE TRUE 105981.5326 116837.4122 117479.1309 96676.79253 120503.5355 115104.0865 107811.5762 101068.4445 112003.8403 0.946231239 1.043155412 1.048884847 0.863156051 1.075887534 1.027679821 0.962570354 0.902365885 1 16.77318867 2.040325307 7.054773736 0.940705304 1.001745827 0.098023402 0.064450923 0.353363515 47.81577384 0.026022043 0.017286272 109.7299816 -2.040325307 0.061040523 FESPATGILS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 160.52 6.25E-05 2670372000 2180671 1996316 1547458 1564854 2194628 2711214 2273441 2357573 2474492 TRUE FALSE 1892489.802 1983202.069 2295813.865 1920178.018 2150959.197 2815516.157 2052963.042 1853424.361 2181960.375 0.867334634 0.90890838 1.052179449 0.880024239 0.985792053 1.29036081 0.940880075 0.849430806 1 21.05719347 4.41907009 6.831980563 0.988694191 0.87722928 0.130256324 0.119618186 0.432498003 39.69319695 0.031836064 0.086483673 26246.42094 -4.41907009 -0.111464911 FESPEVAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FESPEVAER 9 0 A0A087X0X3;P52272-2;P52272 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;; 166.52 0.00014117 3164130000 2599980 2278520 1430227 1630210 2244720 2221090 2402340 2416840 2254010 FALSE TRUE 2256386.055 2263552.252 2121889.561 2000374.097 2200054.464 2306536.77 2169361.437 1900017.574 1987543.506 1.135263731 1.138869285 1.06759402 1.006455502 1.106921412 1.160496242 1.091478718 0.955962759 1 20.92255501 1.773318542 6.929073806 0.978717965 1.100338422 0.576288003 0.043850503 0.129495652 16.38914865 0.025833665 0.012335779 59.33603769 -1.773318542 0.121620458 FEVGDIMLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FEVGDIMLIR 10 0 P00491;G3V5M2;G3V393 P00491 PNP Purine nucleoside phosphorylase 0 114.89 0.0030127 241030000 266470 293200 201750 195050 321680 259110 306780 318460 267250 FALSE TRUE 231255.3144 291273.9499 299316.9748 239339.0837 315279.1974 269078.1294 277028.5228 250359.8073 235656.0095 0.981325768 1.236013249 1.270143611 1.015629027 1.337878877 1.141825876 1.175563159 1.062395174 1 17.84632295 1.578598381 2.47199584 1.000244331 1.173286345 0.220864812 0.107172497 0.392182105 4.986386082 0.120211649 0.027410811 37.89643712 -1.578598381 0.173042014 FEWELPLDEAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FEWELPLDEAQR 12 0 Q9BSJ8-2;Q9BSJ8 Q9BSJ8-2 ESYT1 Extended synaptotagmin-1 0 ;;;; 177.57 5.37E-05 176723900 439606 337475 219745 354227 444220 447114 264608 509974 462816 FALSE TRUE 381510.9533 335258.1045 326014.417 434659.6544 435380.8911 464314.7649 238946.3569 400920.0287 408102.4197 0.934841194 0.821504819 0.798854408 1.065074926 1.066842219 1.137740779 0.585505857 0.982400518 1 18.63857174 5.125352228 18.69355093 0.927437957 2.571162423 0 0.161783124 17302.87484 2692656.643 0.038525671 53043.08529 133460.3403 -5.125352228 1.643724466 FFALPYVDHFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FFALPYVDHFLR 12 0 Q9HD33-3;Q9HD33-2;Q9HD33 Q9HD33-3 MRPL47 "39S ribosomal protein L47, mitochondrial" 0 147.37 6.55E-05 71280000 103740 146270 74942 124740 158970 169100 102380 134730 141280 FALSE TRUE 90030.49616 145309.1427 111184.2019 153064.1235 155806.808 175605.3864 92451.20336 105919.038 124578.0393 0.722683521 1.166410577 0.892486368 1.22866056 1.250676354 1.409601462 0.742114773 0.850222387 1 16.92669025 2.208988546 24.99995321 0.85613539 1.115899868 0.254744235 0.199431802 278.5429455 235475.6764 0.081802289 0.055160219 161.8037365 -2.208988546 0.259764477 FFDANYDGKDYDPVAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FFDANYDGKDYDPVAAR 17 1 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ;; 143.46 5.00E-07 2765890000 8483600 7430300 4395010 4771400 7008000 6396900 8327400 9635100 2869080 FALSE TRUE 7362470.765 7381489.87 6520451.536 5854819.296 6868554.511 6642992.882 7519810.03 7574708.845 2529900.631 2.910181797 2.917699525 2.577354801 2.31424872 2.714950314 2.625792018 2.972373673 2.994073662 1 21.27064929 4.220261061 5.669659448 2.541045779 2.917630202 0.088198483 0.563269599 0.450746145 44.99720433 0.141311554 0.327604351 16605.84812 -4.220261061 0.376584424 FFDEESYSLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FFDEESYSLLR 11 0 A6NLM8;P51571 A6NLM8 SSR4 Translocon-associated protein subunit delta 0 ; 265.94 1.25E-20 522940000 362780 409340 291440 395810 550030 754270 342090 557500 556270 FALSE TRUE 314837.7038 406651.0186 432381.3588 485684.7101 539085.4791 783287.255 308914.1645 438282.9635 490508.3943 0.641859971 0.829039876 0.881496349 0.99016595 1.099034156 1.596888584 0.629783645 0.893527957 1 18.9039183 4.387319766 1.397161005 1.018819619 0.618261035 0.226608106 0.239010053 1.202790799 3.358453271 0.073937411 0.571092212 24396.06411 -4.387319766 -0.400558584 FFDHSGTLVMDAYEPEISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FFDHSGTLVMDAYEPEISR 19 0 E9PL01;A0A087WUC6;E9PI68;Q15005;E9PRB9 E9PL01 SPCS2 Signal peptidase complex subunit 2 0 ; 193.9 4.29E-15 394730000 450430 431930 277959 436620 524900 529060 433459 581830 649910 FALSE TRUE 390904.5343 429092.6234 412380.9021 535761.2443 514455.5169 549413.2805 391422.2129 457410.1823 573078.3802 0.68211356 0.748750325 0.719589006 0.934883016 0.897705331 0.9587053 0.68301689 0.798163389 1 19.12837294 3.758941739 23.85369123 0.862240255 0.720010849 0.409210295 0.090251007 545.1405063 638018.9576 0.025286316 0.043715531 5740.394491 -3.758941739 -0.142229406 FFDQYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FFDQYR 6 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 114.94 0.057818 436065000 854040 835450 543300 615260 920210 893120 754140 886060 913700 FALSE TRUE 741176.4501 829961.8739 806041.6972 754964.1867 901899.6214 927478.9043 681003.6189 696582.9643 805683.4269 0.919935083 1.030133978 1.000444679 0.937048177 1.119421836 1.151170389 0.84524963 0.864586438 1 19.61985355 2.215096038 24.99460452 0.892799908 1.025523287 0.337644419 0.080815285 254.2929178 270872.2332 0.033961231 0.022911682 164.0952607 -2.215096038 0.132723379 FFDS(ph)EDEDFEILSL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FFDSEDEDFEILSL 14 0 Q9Y4P1;Q9Y4P1-4 Q9Y4P1 ATG4B Cysteine protease ATG4B 1 FFDS(1)EDEDFEILSL;FFDS(1)EDEDFEILSL;FFDS(1)EDEDFEILSL;FFDS(1)EDEDFEILSL;FFDS(1)EDEDFEILSL;FFDS(1)EDEDFEILSL 155.02 6.25E-06 795295000 1255462 1200039 774185 898568 1198749 1262690 1159100 1307337 1245508 TRUE FALSE 1089549.516 1192155.865 1148583.455 1102601.598 1174896.24 1311266.501 1046690.66 1027773.156 1098265.463 0.992063897 1.085489715 1.045815874 1.003948167 1.069774367 1.193943127 0.953039766 0.935814874 1 20.06679538 FFEDLEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FFEDLEQR 8 0 Q5VV41;Q5VV41-2;B0QZD3 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 0 ;;; 110.12 0.0081123 246629000 890960 841720 550514 632329 848160 907240 798900 901710 867500 FALSE TRUE 773217.3786 836190.6859 816744.4118 775908.964 831283.2754 942142.1099 721422.801 708886.3336 764945.1383 1.010814162 1.093138114 1.067716325 1.014332826 1.086722738 1.231646641 0.943103976 0.926715261 1 19.54499676 FFEEVLLFEDELHDHGVSSLSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FFEEVLLFEDELHDHGVSSLSVK 23 0 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 ;;; 198.98 1.56E-24 616158000 327097 286944 158776.2 258962 291917 271167 326624 399181 397528 FALSE TRUE 283870.3027 285059.046 235560.9014 317763.2801 286108.4228 281598.97 294948.0548 313819.2496 350532.6927 0.80982547 0.813216718 0.672008364 0.906515388 0.816210381 0.80334581 0.841428092 0.895263854 1 18.41918948 -1.759115808 0.595347099 10 0.793464519 0.570270521 0.055640689 88.89314806 0.997829486 1043.670391 0.027554822 0.017413425 1.759115808 -9.206535481 FFEHFIEGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 FFEHFIEGGR 10 0 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8;F5H3F0;Q96FW1-2 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ;;;;;;; 228.64 2.00E-09 5496683000 5508033 4049083 2294555 2769372 4042141 4168778 3745310 4342240 4191597 FALSE TRUE 4780132.483 4022484.307 3404209.473 3398200.24 3961710.302 4329153.587 3382090.413 3413685.767 3696071.178 1.293300982 1.08831354 0.921034609 0.919408766 1.071870673 1.171285232 0.91505013 0.923598492 1 21.81756111 4.636963758 2.96777041 0.986464879 1.312958595 0.579674945 0.081965673 0.240176652 3.333174588 0.022385789 0.162372456 43347.47032 -4.636963758 0.326493716 FFEHHPIPQEEASLAETALTSGSSPSAPAS(ph)DSIGPQILTSPSPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FFEHHPIPQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSK 45 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5 P15056 BRAF Serine/threonine-protein kinase B-raf 1 FFEHHPIPQEEASLAETALTSGSS(0.001)PS(0.012)APAS(0.742)DS(0.201)IGPQILT(0.021)S(0.021)PS(0.001)PSK 121.61 3.00E-09 177790000 28094 20560 16746 19673 26091 25557 29536 33635 32221 TRUE FALSE 24381.30672 20424.94001 24844.42161 24140.05533 25571.84015 26540.19433 26671.60327 26442.417 28411.87009 0.858138047 0.718887562 0.874438097 0.849646829 0.900040725 0.934123458 0.9387486 0.930682032 1 14.79420617 3.313609173 0.758628546 0.960393146 0.786183309 0.672149652 0.04282314 0.40145767 0.553876703 0.026507102 0.044509985 2058.776359 -3.313609173 -0.174209836 FFEHHPIPQEEASLAETALTSGSSPSAPASDSIGPQILTS(ph)PSPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FFEHHPIPQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSK 45 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5 P15056 BRAF Serine/threonine-protein kinase B-raf 1 FFEHHPIPQEEASLAETALTSGSSPSAPASDSIGPQILT(0.096)S(0.866)PS(0.035)PS(0.002)K 208.51 2.40E-36 167750000 21111 25578 14908 14248 27515 22893 25826 32356 29917 TRUE FALSE 18321.12786 25409.97643 22117.55866 17483.22617 26967.50533 23773.70852 23321.3985 25436.92119 26380.24634 0.694501773 0.963219831 0.838413652 0.662739307 1.022261316 0.901193576 0.884047791 0.964241231 1 14.68717042 3.220374033 24.99990402 0.947654995 0.805589734 0.445415771 0.090343335 254.1449195 349355.4875 0.026865977 0.030520501 1661.01683 -3.220374033 -0.142065261 FFEVILIDPFHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FFEVILIDPFHK 12 0 P61313;A0A2R8YEM3;E7EQV9;E7ENU7 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 184.03 1.48E-05 2459600000 3533180 3233070 2295340 3114000 2732100 2659810 3868640 4595200 4202010 FALSE TRUE 3066261.311 3211831.75 3405374.101 3821081.295 2677736.555 2762134.612 3493459.888 3612552.24 3705253.165 0.827544347 0.86683193 0.919066512 1.031260517 0.722686531 0.745464477 0.942839729 0.974981217 1 21.82114069 2.015896207 24.66277342 0.977665656 0.856946336 0.312109544 0.08574282 262.6757015 407536.422 0.037380312 0.025192921 103.7280485 -2.015896207 -0.12071932 FFFDPSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FFFDPSAR 8 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 90.777 0.030141 197410000 901910 902400 545900 659320 927670 1040500 855720 936960 907460 FALSE TRUE 782720.3084 896472.075 809899.0659 809028.6831 909211.182 1080528.708 772732.4061 736598.3954 800181.1126 0.978178935 1.12033646 1.012144692 1.01105696 1.136256739 1.350355177 0.965696883 0.920539593 1 19.60996705 2.038716177 24.99999098 0.951150236 1.1008681 0.282531881 0.104450414 191.33302 123547.6793 0.043889146 0.02958999 109.3241669 -2.038716177 0.149717863 FFGNSWAETYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FFGNSWAETYR 11 0 O43488;H3BLU7 O43488 AKR7A2 Aflatoxin B1 aldehyde reductase member 2 0 ; 194.12 1.52E-06 1098810000 376090 370190 236960 253690 368790 329110 343860 404470 385090 FALSE TRUE 326388.7536 367758.1975 351554.6486 311294.1919 361451.8005 341771.0747 310512.5101 317977.2381 339565.0989 0.961196409 1.08302708 1.035308545 0.916743779 1.064455098 1.006496474 0.91444177 0.936424972 1 18.37332866 2.327881545 7.288759551 0.946115588 1.014201125 0.234159128 0.051683151 0.29111186 20.22428311 0.018967162 0.014616351 212.7558669 -2.327881545 0.068085538 FFGYCNDVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FFGYCNDVDR 10 0 H3BQQ1;H3BNN8;H3BTB6;Q9NRP2 H3BQQ1 CMC2 COX assembly mitochondrial protein 2 homolog 0 100.71 0.0089076 168450000 157990 138910 78128 118190 144480 154840 105460 152720 145790 FALSE TRUE 137111.2212 137997.4911 115910.9621 145026.8459 141605.1307 160796.795 95232.50543 120062.0165 128554.8723 1.066557951 1.073452049 0.901645811 1.12813185 1.101515082 1.250802806 0.740792657 0.933935948 1 16.97202476 2.235387785 25 0.894118533 1.080502785 0.43159085 0.10554167 81.85782971 644977.7996 0.042192156 0.029805501 171.9443006 -2.235387785 0.186384252 FFHLAFEEEFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FFHLAFEEEFGR 12 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ;;; 169.52 4.36E-05 3460229000 4132353 3710502 2322113 2928306 3391893 3776161 3541335 4093894 3869982 FALSE TRUE 3586252.081 3686127.468 3445094.614 3593222.634 3324400.965 3921432.357 3197896.877 3218446.627 3412477.137 1.050923402 1.080191111 1.009558299 1.052966068 0.97418996 1.149145386 0.937118916 0.943140862 1 21.70238795 2.190208428 24.99999914 0.955599085 1.048538109 0.451812048 0.04791698 96.48752874 49887.11895 0.018263851 0.012313507 154.956011 -2.190208428 0.092939024 FFHPEEWADLFQAAGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FFHPEEWADLFQAAGAK 17 0 P04066 P04066 FUCA1 Tissue alpha-L-fucosidase 0 146.16 4.47E-07 159440000 208800 225010 118320 124220 176180 200780 200250 264610 225100 FALSE TRUE 181206.551 223531.8945 175539.9478 152426.0496 172674.3627 208504.1365 180829.7858 208025.2107 198488.9344 0.912930242 1.126168041 0.884381531 0.767932228 0.86994453 1.050457231 0.911032075 1.048044372 1 17.59869906 2.74051876 24.99612177 1.000953755 0.914586196 0.180194383 0.095415553 352.4139167 4498652.552 0.033577084 0.031988945 550.1976866 -2.74051876 -0.086367559 FFHVSSGVDGDTTSS(ph)DDFDWPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FFHVSSGVDGDTTSSDDFDWPR 22 0 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 1 FFHVSSGVDGDTT(0.006)S(0.078)S(0.916)DDFDWPR 122.51 1.65E-05 56723000 56702 62720 25113 39082 62461 52725 52060 60812 59241 TRUE FALSE 49208.68704 62307.98819 37257.7308 47956.16543 61218.1483 54753.36487 47011.22921 47807.82704 52237.59647 0.942016677 1.192780534 0.713235932 0.91803928 1.171917401 1.04816011 0.899950082 0.915199593 1 15.6728009 2.228696441 24.97921177 0.931951924 0.997928319 0.039677748 0.13632325 737.2975416 1867054.648 0.056061289 0.038313447 169.3153923 -2.228696441 0.065976395 FFIEEMIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FFIEEMIR 8 0 Q14376;Q14376-2;Q5QPP4;Q5QPP3;Q5QPP1 Q14376 GALE UDP-glucose 4-epimerase 0 101.33 0.012733 69823000 203870 209170 147630 178270 182110 209350 220940 223890 253340 FALSE TRUE 176928.063 207795.9485 219024.3618 218748.9282 178486.3673 217403.83 199513.2728 176012.8658 223390.4338 0.79201271 0.930191795 0.980455421 0.979222451 0.798988409 0.973201163 0.893114667 0.78791586 1 17.76920788 1.995671097 24.97219206 0.867320923 0.913224572 0 0.084598334 571.4665466 3296627.557 0.034378477 0.022528272 99.00818453 -1.995671097 0.04590365 FFIGQFSDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FFIGQFSDDR 10 0 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;P52701-4 P52701 MSH6 DNA mismatch repair protein Msh6 0 85.744 0.032642 287190000 625150 561860 297360 360440 483300 520710 588170 639170 217280 FALSE TRUE 542534.8436 558169.1047 441164.2906 442283.411 473683.2756 540742.0506 531129.3639 502488.4695 191593.4059 2.831698935 2.913300184 2.302606859 2.30844798 2.472336004 2.822341656 2.772169331 2.622681439 1 17.54768838 4.242821062 24.87984815 2.400708311 2.872499749 0.152569948 0.511382627 207.6236467 1212418.513 0.127073359 0.312287074 17491.25865 -4.242821062 0.471791437 FFLEETLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FFLEETLVR 9 0 Q9NZT2-2;Q9NZT2;A0A0A0MRN5;A0A087X028 Q9NZT2-2 OGFR Opioid growth factor receptor 0 117.04 0.0028307 13504000 23206 24145 12506 19265 21719 21858 19695 25829 21487 FALSE TRUE 20139.2683 23986.38991 18553.94343 23639.4127 21286.83439 22698.8914 17784.98193 20305.66935 18946.83134 1.062935957 1.265984242 0.979263662 1.247671037 1.123503662 1.198031006 0.938678432 1.071718484 1 14.20966897 2.245441765 24.99988145 1.014985511 1.147663244 0.359406526 0.089396215 166.394369 604529.0019 0.030690208 0.023237116 175.9712684 -2.245441765 0.132677733 FFMPAWNLEIIGTYAQTEMGHGTHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FFMPAWNLEIIGTYAQTEMGHGTHLR 26 0 Q15067-2;Q15067-3 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ; 157.88 1.65E-09 444470000 207677 180216 91249 185647 194643 262547 170290 265380 205119 FALSE TRUE 180231.9583 179032.1492 135377.3216 227800.9888 190769.9851 272647.353 153775.302 208630.5522 180870.0655 0.996472013 0.989838472 0.748478314 1.259473137 1.054734981 1.507421099 0.850197635 1.153483036 1 17.46459413 3.731184177 24.97679223 1.133212071 0.919420485 0.253070709 0.182727284 790.787185 2677623.067 0.047832742 0.072605937 5384.981024 -3.731184177 -0.213791586 FFPASADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 FFPASADR 8 0 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ;;;;;;;; 161.6 0.00080627 5845710000 3912440 4389980 2844510 3099590 4265710 5182340 3843300 3763280 3474200 FALSE TRUE 3395401.141 4361141.932 4220124.55 3803399.284 4180830.717 5381707.973 3470577.358 2958531.858 3063484.034 1.108346283 1.423588922 1.37755722 1.241527373 1.364730702 1.756727933 1.132885734 0.96574091 1 21.5467419 2.01092045 24.96121088 1.001090291 1.379768919 0.51555815 0.162713474 154.6014622 353375.9196 0.065748578 0.044283163 102.5464075 -2.01092045 0.378678628 FFQGS(ph)QEFLASASASAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FFQGSQEFLASASASAER 18 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 FFQGS(0.982)QEFLAS(0.018)ASASAER;FFQGS(1)QEFLASASASAER;FFQGS(1)QEFLASASASAER;FFQGS(1)QEFLASASASAER;FFQGS(0.999)QEFLASASASAER 246.9 2.62E-24 348954000 212457 168404 115884.7 140098.8 172694 184166 168366 216151 202729 TRUE FALSE 184380.2692 167297.743 171926.9285 171910.3738 169257.7273 191250.9852 152037.8912 169928.7907 178762.6086 1.031425255 0.935865416 0.961761131 0.961668523 0.946829589 1.069860116 0.850501637 0.950583526 1 17.44768548 2.232249173 24.99999363 0.933747133 0.978561578 0.159526651 0.053882836 304.783898 1207252.334 0.020918572 0.014491142 170.7061521 -2.232249173 0.044814445 FFQPTEMAAQDFFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FFQPTEMAAQDFFQR 15 0 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 185.95 9.35E-07 80705000 85624 89201 71068 57157 73721 90687 74996 101370 70051 FALSE TRUE 74308.57146 88615.03276 105436.7225 70135.37044 72254.09633 94175.78757 67722.89946 79692.81436 61769.65058 1.202994849 1.434604728 1.706934093 1.135434146 1.169734581 1.524628789 1.096378219 1.290161327 1 15.91461055 -0.13547279 0.458663994 9.23E-13 1.388834609 0.236713413 0.188066655 27.77972577 1.773519079 27.27251382 0.151788518 0.732027185 0.13547279 1.388834609 FFQTSGLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FFQTSGLSK 9 0 P0CE72;P0CE71 P0CE72 OCM;OCM2 Oncomodulin-1;Putative oncomodulin-2 0 ; 59.153 0.060226 1213200000 3807600 4389400 1502620 2037900 3485200 5444700 3257360 3682650 1000090 FALSE TRUE 3304416.013 4360565.742 2229292.058 2500636.342 3415851.339 5654161.132 2941461.729 2895143.956 881860.4995 3.747096071 4.944734167 2.527941845 2.835637092 3.873459964 6.411627616 3.33551818 3.282995392 1 19.75019093 4.250730626 24.9428164 3.433322437 4.34591473 0.083513001 1.370780736 666.7959559 1366592.497 0.352304662 0.917063378 17812.73576 -4.250730626 0.912592293 FFSDCK ddPTM_MDA-MB-175_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 98.133 0.093712 735190000 2444000 2195100 1176300 1376900 1870900 1704000 2169500 2480100 2164400 FALSE TRUE 2121019.208 2180680.244 1745162.614 1689546.19 1833672.75 1769553.983 1959102.224 1949749.915 1908527.098 1.111338272 1.142598523 0.914402848 0.885261829 0.960778997 0.927183054 1.026499559 1.021599283 1 20.86402824 4.246718812 24.99914761 0.96693386 1.126968474 0.686927661 0.04614736 118.1081169 361910.161 0.013363646 0.03406541 17648.94752 -4.246718812 0.160034614 FFSGYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FFSGYGR 7 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ; 117.6 0.012086 1817310000 1766120 1869570 1164900 1246980 1812010 1969450 1799580 1802000 1674200 FALSE TRUE 1532722.767 1857288.672 1728249.536 1530125.868 1775954.546 2045216.016 1625057.009 1416656.323 1476277.983 1.038234523 1.258088715 1.170680289 1.036475437 1.202994671 1.38538679 1.100779817 0.959613528 1 20.49353298 1.995606605 24.96065874 0.992904381 1.184582788 0.40490618 0.100426798 170.9902192 971465.4082 0.042417262 0.027800727 98.99348313 -1.995606605 0.191678408 FFSLSSVDKLEQIYECTDTEDVCIVER ddPTM_MDA-MB-175_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 0 251.44 4.61E-47 30498000 98390 84139 59269 74588 71160 74057 115540 106310 80486 FALSE TRUE 85387.51221 83586.28537 87931.68664 91524.34541 69744.05522 76906.02071 104334.9486 83576.43381 70971.03677 1.203131814 1.177752069 1.23897988 1.289601358 0.982711517 1.083625437 1.470106023 1.177613258 1 16.11494276 1.257471487 6.029181312 0.994694919 1.207502367 0.204200364 0.126441385 0.204129037 25.36533422 0.163727131 0.031800588 18.09137131 -1.257471487 0.212807448 FFT(ph)TPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FFTTPSK 7 0 O76021;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 FFT(0.914)T(0.086)PSK;FFT(0.875)T(0.125)PSK;FFT(0.86)T(0.14)PSK 151.44 0.021027 1015360000 4067500 4072300 2282670 2769720 3322700 2753790 3827900 4258500 4132600 TRUE FALSE 3529969.569 4045548.793 3386576.847 3398627.259 3256584.771 2859730.083 3456670.847 3347852.915 3644048.736 0.968694391 1.110179662 0.929344554 0.932651428 0.893672123 0.784767244 0.948579752 0.918717931 1 21.79711082 4.11565437 7.023192293 0.911380516 1.038538466 0.399898794 0.063379043 0.19879039 11.34132546 0.016073968 0.033924525 13051.31795 -4.11565437 0.127157951 FFTESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FFTESR 6 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;; 149.94 0.024602 2718320000 3462850 3528270 2059660 2478260 3435950 3716780 3345050 3620710 3539570 FALSE TRUE 3005225.599 3505092.562 3055718.465 3040986.811 3367581.317 3859766.932 3020647.566 2846449.343 3121126.067 0.962865816 1.123021783 0.979043589 0.974323608 1.078963568 1.236658452 0.967806971 0.911994351 1 21.5736352 2.025542911 24.99995326 0.946767761 1.059352024 0.237632434 0.083604722 281.4375982 275453.9774 0.034486622 0.023250131 106.0578724 -2.025542911 0.112584263 FFTGDVFGYHGYTFANLGEHEFVEEK ddPTM_MDA-MB-175_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" 0 144.76 1.38E-07 183320000 99762 76588 60365 73322 90801 84947 99317 102040 86115 FALSE TRUE 86578.19894 76084.88839 89557.71591 89970.88076 88994.23775 88214.96606 89685.25263 80219.54008 75934.5828 1.140168231 1.001979409 1.179406176 1.184847239 1.171985602 1.161723194 1.181085736 1.056429589 1 16.21246946 1.555183376 3.912005308 1.009513553 1.144498845 0.468735324 0.053608404 0.164153806 5.454555772 0.047418766 0.014703823 35.90735178 -1.555183376 0.134985291 FFTNFESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FFTNFESR 8 0 J3QQZ9;Q9NVS9-3;Q9NVS9;Q9NVS9-4;J3QQV6;A0A286YFL3 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 ;;;; 156.01 0.00093025 1576800000 1766912 2208099 1266216 1457873 2091500 2267260 1978543 2021745 2035140 FALSE TRUE 1533410.102 2193593.852 1878562.293 1788905.347 2049883.242 2354482.959 1786664.204 1589410.565 1794548.068 0.854482602 1.222365615 1.046816369 0.996855631 1.142283831 1.312020002 0.99560677 0.885688488 1 20.77518914 2.010165351 24.96281872 0.936469639 1.101684187 0.211860088 0.125687643 261.1266216 641240.0398 0.049862318 0.033577402 102.368267 -2.010165351 0.165214547 FFTT(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FFTTPSK 7 0 O76021;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 FFT(0.349)T(0.651)PSK 110.41 0.076129 159630000 849270 845680 484490 584660 687830 565800 799640 899320 870750 TRUE FALSE 737036.8177 840124.6724 718790.9845 717415.989 674143.5287 587566.6921 722091.0359 707007.4165 767810.927 0.959919678 1.094181709 0.936156232 0.934365433 0.878007209 0.765249193 0.940454232 0.920809267 1 19.55039157 4.069900007 6.226237319 0.90531288 1.026579847 0.348195269 0.067256596 0.218761501 14.85184368 0.017552293 0.037163457 11746.27074 -4.069900007 0.121266967 FFTVEPQHIPCVLMAFLDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FFTVEPQHIPCVLMAFLDHR 20 0 O43592 O43592 XPOT Exportin-T 0 134.07 5.56E-06 80494000 142290 131630 89722 121060 131500 131890 132120 147310 159950 FALSE TRUE 123486.016 130765.3139 133111.8593 148548.5233 128883.4073 136963.8936 119307.0227 115808.9029 141040.8932 0.875533423 0.92714468 0.943782021 1.053230165 0.913801695 0.971093493 0.845903766 0.821101598 1 17.10575399 2.241146061 24.99711251 0.873060161 0.949623412 0.136901979 0.06502833 99.00938409 957278.3589 0.025007634 0.018467983 174.2392771 -2.241146061 0.076563252 FFWHLTLPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FFWHLTLPER 10 0 P55212;D6RBM3;D6RHU3 P55212 CASP6 Caspase-6;Caspase-6 subunit p18;Caspase-6 subunit p11 0 99.815 0.0044381 162060000 194260 162660 93105 125960 152000 160770 165940 172400 192770 FALSE TRUE 168588.0488 161591.4757 138130.8894 154561.1432 148975.4974 166954.9259 149847.1643 135533.6016 169980.9502 0.991805544 0.95064462 0.812625705 0.909285087 0.876424665 0.982197862 0.881552693 0.797345829 1 17.37501355 4.464508291 24.63620429 0.887505555 0.981515343 0.211032478 0.063329702 221.3187668 432289.9993 0.015630914 0.041413333 29141.25766 -4.464508291 0.094009788 FFYSDQNVDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FFYSDQNVDSR 11 0 Q9Y490;Q9Y4G6 Q9Y490;Q9Y4G6 TLN1;TLN2 Talin-1;Talin-2 0 106.29 0.00547 132260000 123280 120560 87992 121440 120330 129990 135250 130150 310750 FALSE TRUE 106988.2356 119768.0334 130545.2255 149014.8081 117935.6684 134990.7994 122133.4758 102318.4353 274013.489 0.390448792 0.437088093 0.476418975 0.543822892 0.430400959 0.492642898 0.44572067 0.373406564 1 18.06388739 1.233738768 24.99994492 1.000000837 0.449341053 0.92693569 0.048638651 38.96132059 201979.1763 0.100234691 0.012574887 17.12926657 -1.233738768 -0.550659784 FGAVFLWDSGSSVGEITGHNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FGAVFLWDSGSSVGEITGHNK 21 0 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ;; 257.83 1.71E-36 456415000 980290 823577 499712 716281 798813 767806 914420 1075150 894690 FALSE TRUE 850742.1928 818166.8685 741374.3946 878923.5487 782918.1842 797343.9937 825739.6891 845237.5393 788920.7674 1.07836202 1.037071024 0.939732385 1.114083423 0.992391399 1.010676898 1.046669987 1.071384573 1 19.58952089 2.192139261 23.7762438 1.046330091 1.02728316 0.003039559 0.049633993 329.8679311 168948.0236 0.019485184 0.01313697 155.6464649 -2.192139261 -0.019046931 FGAVWTGDNTAEWDHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FGAVWTGDNTAEWDHLK 17 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 247.5 9.34E-21 1357460000 1442600 945800 877600 1015170 1117930 1189410 1167300 1198010 1039280 FALSE TRUE 1251956.755 939586.9775 1302010.295 1245679.864 1095685.38 1235167.372 1054095.426 941824.8844 916417.5024 1.366142344 1.025282663 1.420761053 1.359292965 1.19561813 1.347821674 1.150234934 1.02772468 1 19.80564549 1.921907823 2.664291027 1.011152212 1.279317376 0.501926026 0.111663814 0.225501624 2.907603192 0.07173895 0.030556203 83.54256834 -1.921907823 0.268165164 FGCRDPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FGCRDPVR 8 1 P11216;P11217;P11217-2 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form" 0 ;;;; 147.29 0.00049219 1908350000 2361720 3489130 1708240 1697410 3520000 3689330 3153070 3231930 2223200 FALSE TRUE 2049612.718 3466209.675 2534350.578 2082832.884 3449958.887 3831260.912 2847285.757 2540806.92 1960375.829 1.045520297 1.768135285 1.292788118 1.062466112 1.759845656 1.95435021 1.452418314 1.296081539 1 20.90269883 3.240277067 24.99981782 1.488063401 1.326260986 0.084701042 0.318398608 163.0023112 2374078.252 0.099200702 0.121466711 1738.909847 -3.240277067 -0.161802415 FGDES(ph)PLLTMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FGDESPLLTMR 11 0 H0YJ41;Q9P203-5;Q9P203 H0YJ41 BTBD7 BTB/POZ domain-containing protein 7 1 FGDES(1)PLLTMR;FGDES(1)PLLTMR 153.15 3.42E-05 77040000 119343 124705 71399 89521 128474 111180 112642 136861 124070 TRUE FALSE 103571.5202 123885.8046 105927.7952 109848.1113 125917.6188 115457.1665 101717.9962 107594.3402 109402.5859 0.946700842 1.13238461 0.968238495 1.004072348 1.150956512 1.055342207 0.929758609 0.983471636 1 16.73928731 2.255412533 24.91938314 0.971937425 1.046760788 0.20815424 0.065795542 332.927495 492307.9419 0.023812231 0.018395625 180.0580459 -2.255412533 0.074823363 FGDILHVINASDDEWWQAR ddPTM_MDA-MB-175_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 ; 197.09 8.04E-16 495470000 848490 836140 502610 715510 833210 838010 753390 974770 840200 FALSE TRUE 736359.8967 830647.3413 745673.8771 877977.4814 816630.7511 870248.787 680326.3538 766323.0212 740872.5132 0.993909051 1.121174462 1.006480688 1.185058786 1.102255431 1.174626905 0.918277223 1.034352075 1 19.49886578 2.237724172 24.99999601 0.991908899 1.098431148 0.385095624 0.067090592 23.36791645 698381.7156 0.025155901 0.018085882 172.8718073 -2.237724172 0.106522248 FGDRFPAMSDAYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FGDRFPAMSDAYDR 14 1 P00491;G3V5M2 P00491 PNP Purine nucleoside phosphorylase 0 142.91 8.46E-06 525520000 330160 353350 111800 101330 316200 340080 303230 344350 63982 FALSE TRUE 286528.5195 351028.8206 165866.8539 124338.5252 309908.2386 353163.0977 273822.8013 270713.4322 56418.12085 5.078661167 6.221916209 2.939957082 2.203875694 5.493062051 6.259745847 4.853454832 4.798341883 1 15.78387099 4.253893405 24.99630025 4.138501029 5.650288851 0.157273608 1.59736094 517.6229975 843840.6014 0.410919841 1.078422814 17942.93176 -4.253893405 1.511787822 FGDSHHSHAGGHCGGCCH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FGDSHHSHAGGHCGGCCH 18 0 F5H2C9;Q86UY6-4;Q86UY6-3;Q86UY6 F5H2C9 NAA40 N-alpha-acetyltransferase 40 0 63.29 0.015507 26211000 22758 17764 22639 16427 5300.2 12655 11265 11445 8989.5 FALSE TRUE 19750.47264 17647.30711 33587.29612 20157.00142 5194.73639 13141.84604 10172.52203 8997.575815 7926.771551 2.491616229 2.226291877 4.23719744 2.542901772 0.655340747 1.657906495 1.283312124 1.13508706 1 12.95251768 3.364707091 5.508893414 1.187341269 2.981309008 0.694545063 0.574172688 0.11564555 5.142622525 0.164700027 0.213564332 2315.832216 -3.364707091 1.79396774 FGDYNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FGDYNK 6 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 113.08 0.061517 2212950000 2900690 2590010 1793640 2455590 2616500 2183820 2920360 3350060 3101320 FALSE TRUE 2517356.467 2572996.054 2661050.303 3013169.241 2564436.769 2267832.969 2637143.937 2633675.739 2734685.483 0.920528698 0.94087458 0.97307362 1.101833926 0.937744682 0.829284751 0.964331713 0.963063488 1 21.38294349 FGEEIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FGEEIAR 7 0 Q8WUM4;Q8WUM4-2;F8WDK9 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 104.45 0.018959 517980000 715420 713060 423790 512260 731970 691840 753940 801560 674870 FALSE TRUE 620875.4344 708375.8619 628736.2615 628576.4624 717405.2291 718455.5325 680823.0148 630152.6317 595087.6374 1.043334452 1.190372337 1.056543981 1.056275451 1.20554551 1.207310465 1.144071851 1.058924085 1 19.18274262 1.531142131 3.128926603 1.005669883 1.131550452 0.331304439 0.061575803 0.271823376 5.489596649 0.067203548 0.016718978 33.97364396 -1.531142131 0.125880569 FGESEEVEMEVES(ph)DEEDDKQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FGESEEVEMEVESDEEDDKQEK 22 1 Q15459;Q15459-2;H7C1L2 Q15459 SF3A1 Splicing factor 3A subunit 1 1 FGES(0.003)EEVEMEVES(0.997)DEEDDKQEK 65.071 0.035467 115610000 211590 125220 130980 115400 122500 110410 168190 208330 191440 TRUE FALSE 183627.8454 124397.4216 194322.3661 141603.3338 120062.4897 114657.5441 151878.9597 163780.2507 168808.1813 1.087789964 0.736915833 1.151143058 0.838841653 0.711236202 0.679217934 0.899713263 0.970215125 1 17.3650253 4.769173811 23.39299225 0.87866863 1.087790723 0.178274161 0.144253443 10445.27674 7981403.222 0.036344556 4.009702648 58772.45209 -4.769173811 0.209122094 FGEYHKDDPSSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FGEYHKDDPSSFR 13 1 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ;;; 167.32 1.93E-05 1710460000 4255430 3808520 2433760 2608260 4290150 3562990 4432320 5040030 3086250 FALSE TRUE 3693064.144 3783501.581 3610734.476 3200505.298 4204784.409 3700060.531 4002474.289 3962258.806 2721397.041 1.357047167 1.390279156 1.326794445 1.176052318 1.545083038 1.359618047 1.4707425 1.455964987 1 21.37591602 1.232458475 24.96295677 0.999999351 1.388519795 0.603476529 0.098094568 142.0275492 580954.404 0.21634728 0.02417645 17.07884414 -1.232458475 0.388520445 FGGEHVPNS(ph)PFQVTALAGDQPSVQPPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FGGEHVPNSPFQVTALAGDQPSVQPPLR 28 0 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5F3 Q60FE5 FLNA Filamin-A 1 FGGEHVPNS(0.999)PFQVT(0.001)ALAGDQPSVQPPLR;FGGEHVPNS(1)PFQVTALAGDQPSVQPPLR;FGGEHVPNS(1)PFQVTALAGDQPSVQPPLR 241.61 1.64E-45 999270000 481477 498781 281771 363920 464476 521621 465663 520008 586223 TRUE FALSE 417848.5945 495504.4748 418036.3981 446553.5982 455233.8363 541688.0974 420503.0739 408808.3359 516920.3848 0.808342265 0.958570196 0.808705577 0.863873067 0.880665282 1.047913979 0.813477445 0.790853578 1 18.97958257 3.004315777 24.00686079 0.893481334 0.864392943 0.057109902 0.086436318 405.2973921 2254446.109 0.027225685 0.030730364 1009.986985 -3.004315777 -0.029088392 FGGPVHHQAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FGGPVHHQAQR 11 0 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 0 ; 196.88 3.41E-08 850060000 719750 1063030 628630 692870 1122700 1247840 995000 1043220 1235810 FALSE TRUE 624633.2139 1056046.886 932637.5706 850196.7234 1100360.467 1295845.212 898505.0531 820135.5213 1089713.95 0.573208422 0.969104678 0.855855402 0.780201743 1.009770011 1.189160892 0.824532946 0.75261542 1 20.05551805 4.74500385 24.25401733 0.909282793 0.573208189 0.414215502 0.129735337 558.0287798 2100478.582 0.033848666 0.307222433 55590.91856 -4.74500385 -0.336074604 FGHEFLEFEFRPDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FGHEFLEFEFRPDGK 15 1 P61326;Q96A72;F5H6N1;P61326-2 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ;;; 214.18 1.51E-12 1177732000 3696403 2946030 2378720 3015740 2853309 2379956 3554616 4009983 4950975 FALSE TRUE 3207913.978 2926677.335 3529076.948 3700509.86 2796533.733 2471514.447 3209889.887 3152479.341 4365676.376 0.734803431 0.670383483 0.808368886 0.847637237 0.640572844 0.566124063 0.735256032 0.722105596 1 22.05777376 1.236267794 5.887705635 1.011648384 0.714651562 0.558597079 0.079455205 0.115928512 14.52661492 0.138546574 0.020944814 17.22930637 -1.236267794 -0.296996822 FGHGSDYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FGHGSDYSR 9 0 Q9NWH9;Q9NWH9-3;H7C3F4;H0YMM0 Q9NWH9 SLTM SAFB-like transcription modulator 0 ; 120.99 0.00062649 436270000 336960 380830 121263 217130 406610 427350 306670 360560 341800 FALSE TRUE 292429.8823 378328.3027 179906.1924 266432.6851 398519.2565 443790.431 276929.1906 283457.0499 301392.7934 0.970261694 1.255266586 0.596916039 0.88400483 1.322258744 1.472465304 0.918831494 0.94049047 1 18.2012854 3.300012142 24.99998889 1.108209276 0.926537354 0.159549612 0.229646334 161.1198004 65545.62591 0.071518544 0.092330012 1995.318101 -3.300012142 -0.181671922 FGHLGLAINLITYDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FGHLGLAINLITYDDR 16 0 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ; 153.23 4.71E-07 322150000 225746 245200 185409 269480 232640 253070 274560 308250 576310 FALSE TRUE 195913.0941 243589.2651 275073.4126 330669.5527 228010.9192 262805.7667 247933.2135 242333.1363 508179.2883 0.385519636 0.479337255 0.541292057 0.650694667 0.448682039 0.517151668 0.487885318 0.476865433 1 18.95497805 1.236845519 24.99998612 1.00000062 0.501455225 0.843075127 0.067994985 17.05585486 248537.2697 0.104254971 0.016749016 17.2522411 -1.236845519 -0.498545395 FGIDDQDYLVSLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FGIDDQDYLVSLTR 14 0 Q8TBX8;Q8TBX8-3;F8VNT5;F8VU68 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 ; 260.28 4.36E-24 179262000 332130 312570 187150 248670 281370 290200 320920 318280 323820 FALSE TRUE 288238.179 310516.7071 277656.366 305134.3242 275771.2875 301364.1818 289797.2278 250218.2989 285538.3685 1.009455158 1.087478046 0.972395995 1.0686281 0.965794156 1.055424472 1.014915191 0.876303595 1 18.12332509 1.8768106 7.602324947 0.932402128 1.02664062 0.358866029 0.048261903 0.22758592 13.12098015 0.021060387 0.01159715 75.30270906 -1.8768106 0.094238493 FGIGDGNLQYYLYNWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FGIGDGNLQYYLYNWK 16 0 P30419;P30419-2 P30419 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 0 ; 229.54 7.18E-15 159170000 193187 214560 127727 153668 192403 189429 225890 263390 230240 FALSE TRUE 167656.8485 213150.5412 189496.2044 188560.6681 188574.5567 196716.4562 203983.2226 207066.0982 203021.2895 0.825809199 1.049892559 0.933380952 0.928772882 0.928841291 0.968944965 1.00473809 1.019923077 1 17.6312715 2.380212669 2.713195604 1.011647076 0.939762835 0.286778227 0.053389347 0.348448541 5.244890509 0.021420021 0.015437946 240.0007889 -2.380212669 -0.071884241 FGINIPS(ph)PEHSNTIDVCNTVDIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FGINIPSPEHSNTIDVCNTVDIK 23 0 C9IZ03;Q9HCI7-2;Q9HCI7 C9IZ03 MSL2 E3 ubiquitin-protein ligase MSL2 1 FGINIPS(0.954)PEHS(0.029)NT(0.017)IDVCNTVDIK;FGINIPS(0.999)PEHS(0.001)NTIDVCNTVDIK 284.27 2.24E-52 297520000 245408 201025 136182 161258 221453 183620 218590 263612 244408 TRUE FALSE 212976.711 199704.4535 202040.0707 197874.0936 217046.5186 190683.9802 197391.1754 207240.6252 215514.3647 0.98822513 0.926641033 0.937478441 0.91814805 1.007109289 0.884785478 0.91590728 0.961609337 1 17.71742451 1.372389274 3.378698691 1.001187261 0.938832784 0.22872137 0.035224375 0.383469766 6.467489244 0.050697206 0.008722052 23.57161148 -1.372389274 -0.062354477 FGKPNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FGKPNKR 7 2 P51858;P51858-2;P51858-3;Q5TGJ6 P51858 HDGF;HDGFL1 Hepatoma-derived growth factor;Hepatoma-derived growth factor-like protein 1 0 ; 81.635 0.014999 3979000000 7394100 6546200 3924000 5098000 6369200 5536200 7839500 8727300 6607700 FALSE TRUE 6416950.951 6503197.581 5821659.525 6255578.818 6242465.381 5749181.196 7079226.497 6861034.811 5826545.234 1.101330324 1.116132686 0.999161474 1.073634301 1.071383664 0.986722143 1.214995544 1.177547678 1 22.47420928 2.237862781 24.99999981 1.144083041 1.059336637 0.196489 0.067610933 25.65965489 919184.6412 0.026338758 0.018961926 172.9269895 -2.237862781 -0.084746404 FGLGS(ph)PLPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FGLGSPLPSPR 11 0 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;Q14934-12;Q14934-13;Q14934-18;G3V5H0 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 2 FGLGS(1)PLPS(1)PR;FGLGS(1)PLPS(1)PR;FGLGS(1)PLPS(1)PR;FGLGS(1)PLPS(1)PR 158.52 4.35E-05 275654000 562550 743500 498254 576490 803040 1022770 502333 733370 764350 TRUE FALSE 488207.5922 738615.8995 739211.301 707390.8656 787061.0751 1062116.624 453616.823 576544.5326 673989.4138 0.724354986 1.0958865 1.096769899 1.049557829 1.167764744 1.57586544 0.673032564 0.855420754 1 19.36236641 FGLGS(ph)PLPSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FGLGSPLPSPR 11 0 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;Q14934-12;Q14934-13;Q14934-18;G3V5H0 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 FGLGS(1)PLPSPR;FGLGS(1)PLPSPR;FGLGS(0.994)PLPS(0.006)PR;FGLGS(1)PLPSPR 151.79 3.49E-05 566270000 728550 794470 461145 528293 796350 750400 918280 881310 621780 TRUE FALSE 632270.2716 789251.0743 684156.2644 648250.0001 780504.193 779268.3736 829225.3469 692848.7149 548273.8767 1.153201526 1.439519751 1.247836699 1.182347049 1.423566262 1.421312243 1.512429065 1.263690911 1 19.06453721 1.283566139 3.883860402 0.976052693 1.343259197 0.452949279 0.116596525 0.205741037 4.959692599 0.197296081 0.029698483 19.21171518 -1.283566139 0.367206504 FGLGT(ph)PEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FGLGTPEK 8 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 FGLGT(1)PEK 97.813 0.08904 118950000 408090 421730 326310 364130 388850 324320 398380 484680 636380 TRUE FALSE 354159.8725 418959.6279 484114.6074 446811.2819 381112.6458 336796.8003 359745.1689 381034.9538 561147.8814 0.631134651 0.746611797 0.862721973 0.796245155 0.679166149 0.60019259 0.641087993 0.679027697 1 19.09802149 1.235438406 24.99955109 1.000000403 0.705427339 0.577354298 0.079446383 73.61143097 589303.0876 0.14981427 0.021626429 17.19643435 -1.235438406 -0.294573065 FGLSVGHHLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FGLSVGHHLGK 11 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ; 135.86 6.43E-05 34359000000 37406000 45180000 10055700 29232000 46681000 44217000 48561000 55057000 51599000 FALSE TRUE 32462702.33 44883209.61 14918670.15 35869572.38 45752139.43 45918056.6 43851561.69 43283489 45499025 0.713481274 0.986465306 0.327889887 0.788359144 1.005563074 1.009209683 0.963791239 0.951305858 1 25.43933229 3.369662249 4.806995755 0.979953088 0.685351626 0.451137455 0.157718725 0.19464852 7.415705444 0.044910043 0.058507466 2342.406415 -3.369662249 -0.294601462 FGMFEFLSNHMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FGMFEFLSNHMR 12 0 P53007 P53007 SLC25A1 "Tricarboxylate transport protein, mitochondrial" 0 ; 236.57 4.44E-16 439340000 403020 631750 188464 533850 876980 994260 446650 784390 775350 FALSE TRUE 349759.8859 627599.9927 279605.8208 655068.8019 859529.8138 1032509.826 403333.9517 616654.3026 683689.0063 0.511577461 0.917961218 0.408966384 0.958138563 1.257194142 1.510203932 0.589937747 0.901951468 1 19.3829807 3.575275233 7.087202342 1.028915072 0.645600605 0.359215155 0.267037092 0.336870885 21.12462209 0.077140204 0.114567599 3760.756661 -3.575275233 -0.383314467 FGNDVQHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FGNDVQHFK 9 0 P62993;J3KT38 P62993 GRB2 Growth factor receptor-bound protein 2 0 ; 75.294 0.038668 1087740000 1976980 1792460 1283680 1502910 1588040 1521730 1914350 2116500 2079670 FALSE TRUE 1715717.084 1780685.212 1904471.942 1844168.686 1556441.111 1580271.938 1728696.632 1663902.946 1833813.782 0.935600496 0.971028373 1.038530717 1.00564665 0.848745454 0.861740681 0.942678395 0.907345643 1 20.80641571 3.262452966 24.99497978 0.911282627 0.990141299 0.374592079 0.048487383 251.3309061 262928.0349 0.014391536 0.018569317 1830.007904 -3.262452966 0.078858672 FGQAATMEGIGAIGGT(ph)PPAFNR ddPTM_MDA-MB-175_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 203.32 1.36E-21 3632150000 5069660 5064230 2958670 3370460 4551910 5020090 4530940 5469060 5245240 TRUE FALSE 4399691.586 5030962.74 4389492.708 4135774.457 4461335.897 5213216.111 4091530.136 4299544.079 4625153.703 0.951253054 1.087739579 0.949047965 0.894191788 0.964581111 1.127144403 0.884625766 0.929600259 1 22.14106988 4.170318721 24.99999956 0.960158086 1.019506683 0.085191681 0.074475671 108.3844882 39704.37561 0.019096438 0.039752429 14801.94278 -4.170318721 0.059348598 FGQYNKEDPTSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FGQYNKEDPTSFR 13 1 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ; 96.313 0.0039168 966270000 2261000 2057690 866440 1077230 1978010 1779120 2249000 2492600 593570 FALSE TRUE 1962203.121 2044172.899 1285453.282 1321831.536 1938651.471 1847563.898 2030892.326 1959576.887 523398.8308 3.748963517 3.905574064 2.455972781 2.525476669 3.703965995 3.529935088 3.880200349 3.743945863 1 18.99755118 1.234189198 24.99945125 0.999996386 3.438726541 0.680263315 0.525013656 85.91831856 491288.7801 1.065966373 0.139039421 17.14704148 -1.234189198 2.438730155 FGTFGGLGS(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FGTFGGLGSK 10 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 FGTFGGLGS(1)K 81.92 0.019156 0 364530 267350 140580 253710 357750 222060 406700 429390 432780 TRUE FALSE 316356.4369 265593.7602 208564.9582 311318.7332 350631.4749 230602.7919 367258.2966 337568.29 381617.2414 0.828988847 0.695968975 0.54652918 0.815787914 0.918804071 0.604277708 0.962373438 0.884572953 1 18.54176683 1.411433834 0.547380972 1.153896582 0.709958848 0.363129953 0.119479589 3.913108881 1.090197416 1.11177702 0.085069957 25.78896031 -1.411433834 -0.443937734 FGTLNGFQILHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FGTLNGFQILHDR 13 0 Q93008;Q93008-3;O00507;O00507-2 Q93008 USP9X;USP9Y Probable ubiquitin carboxyl-terminal hydrolase FAF-X;Probable ubiquitin carboxyl-terminal hydrolase FAF-Y 0 160.78 4.33E-05 206320000 154830 131500 103760 117870 161980 150550 153190 143040 232890 FALSE TRUE 134368.8232 130636.1678 153938.6831 144634.185 158756.9149 156341.7559 138333.6574 112452.0091 205358.0095 0.654314986 0.636138654 0.749611293 0.704302624 0.773073888 0.761313164 0.673621924 0.547590081 1 17.64778169 4.24661951 24.5378901 0.723094168 0.645226778 0.095261572 0.113091 402.3343877 1224999.316 0.028162584 0.071705321 17644.91253 -4.24661951 -0.07786739 FGTVLTEHVAAAELGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FGTVLTEHVAAAELGAR 17 0 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ;;;; 202.63 1.04E-11 2493782000 1878084 1918011 1083875 1274517 1854489 1915733 1798116 1884106 1991567 FALSE TRUE 1629890.441 1905411.459 1608040.575 1563915.565 1817588.297 1989432.488 1623734.987 1481204.594 1756126.218 0.928116911 1.085008264 0.91567483 0.890548497 1.034998668 1.132852791 0.924611779 0.843449963 1 20.74396511 2.020847349 24.99520652 0.902589171 0.99772062 0.143135314 0.083876799 357.6793197 428842.6489 0.034682687 0.023380421 104.9173588 -2.020847349 0.095131449 FGVEQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FGVEQDR 7 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;; 166.05 0.002647 10103310000 7718940 7864630 4719480 5792790 7537210 7749680 7549150 8245060 7743850 FALSE TRUE 6698862.522 7812966.728 7001836.314 7108131.507 7387234.267 8047815.204 6817034.595 6481918.082 6828380.875 0.981032348 1.144190236 1.025402133 1.040968809 1.081842739 1.178583233 0.998338365 0.949261355 1 22.7031121 2.018743221 24.93579269 0.971844473 1.076057687 0.374879026 0.057073792 207.3644217 275874.4957 0.022309511 0.015038547 104.4102706 -2.018743221 0.104213214 FGVEQDVDMVFASFIR ddPTM_MDA-MB-175_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 0 142.57 3.65E-05 0 242450 269240 182300 156850 188970 203750 194690 254120 248660 FALSE TRUE 210409.6182 267471.3447 270460.8898 192465.1898 185209.8667 211588.3943 175808.9938 199778.4156 219263.6981 0.959619034 1.219861505 1.233495978 0.877779548 0.844690062 0.9649951 0.801815327 0.911133112 1 17.74230745 3.72855808 24.90832733 0.895478339 1.145879106 0.598516785 0.091597443 396.8571869 988254.2766 0.024342363 0.036587012 5352.5173 -3.72855808 0.250400767 FGVLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FGVLFR 6 0 Q9P1F3 Q9P1F3 ABRACL Costars family protein ABRACL 0 97.908 0.094307 713290000 483690 526870 262690 292080 449330 488170 407700 474590 624980 FALSE TRUE 419769.141 523408.9563 389727.7626 358401.2282 440389.2121 506950.2158 368161.3168 373102.6218 551095.5764 0.761699348 0.949760765 0.707187245 0.650343141 0.799115854 0.919895273 0.668053478 0.677019809 1 19.07194302 4.22298528 24.96547929 0.761743878 0.855730129 0.06452027 0.121198048 508.7962089 815545.3478 0.030762004 0.064391644 16710.33976 -4.22298528 0.093986251 FGVPVIADGGIQNVGHIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FGVPVIADGGIQNVGHIAK 19 0 P12268;H0Y4R1 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 190.24 1.23E-14 205410000 256180 235880 151240 172640 236410 203090 220670 260060 181460 FALSE TRUE 222325.1639 234330.4887 224380.1699 211840.5506 231705.9035 210903.0037 199269.4574 204448.1928 160008.0055 1.389462753 1.46449228 1.402305898 1.323937199 1.448089443 1.318077824 1.245371797 1.277737274 1 17.28778456 0.27628647 0.63318104 1.21E-18 1.408263239 0.837222122 0.05356633 4.052142799 0.504104373 5.460734722 0.025906581 1.889237119 -0.27628647 1.408263239 FGVQMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 FGVQMDR 7 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;;; 155.51 0.0037367 5152800000 4258300 4307140 2357649 3166380 4446990 4420700 4111820 4672270 4282120 FALSE TRUE 3695554.866 4278846.114 3497815.942 3885354.974 4358503.599 4590767.19 3713056.329 3673141.42 3775892.652 0.978723498 1.133201208 0.92635471 1.028989787 1.15429754 1.215809773 0.983358552 0.972787565 1 21.84838632 2.077040681 24.99999984 0.982497788 1.073089507 0.194438829 0.083903861 56.0843752 18197.03342 0.035516549 0.023945249 119.4099952 -2.077040681 0.090591718 FGVQSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 FGVQSER 7 0 Q14247 Q14247 CTTN Src substrate cortactin 0 ;;;;;; 153.73 0.004017 3481450000 3367160 3520740 1988150 2317400 3430620 3555850 3264190 3692580 3328370 FALSE TRUE 2922181.275 3497612.027 2949625.99 2843601.089 3362357.374 3692645.85 2947629.356 2902950.503 2934893.89 0.995668458 1.191733725 1.005019636 0.968894003 1.145648701 1.258187174 1.004339328 0.989115999 1 21.48487691 2.038775972 24.99990474 0.994664001 1.094553254 0.204565539 0.08973716 244.282792 157494.6622 0.037481334 0.025269868 109.3392202 -2.038775972 0.099889253 FGVQTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 FGVQTDR 7 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;;; 137.18 0.0067653 6006940000 5243100 5272370 3108980 3918370 5342780 5452830 5110160 5687690 5288760 FALSE TRUE 4550211.051 5237735.454 4612493.127 4808095.797 5236469.131 5662603.899 4614577.47 4471421.755 4663528.818 0.975701283 1.123127069 0.989056422 1.030999482 1.122855532 1.214231566 0.989503368 0.958806503 1 22.1529906 2.032081336 24.9984887 0.975768857 1.076570339 0.28342958 0.069956563 227.7282106 177449.9985 0.02899065 0.019545321 107.6666836 -2.032081336 0.100801482 FGWDCHGLPVEYEIDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FGWDCHGLPVEYEIDK 16 0 A0A0A0MSX9;P41252;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;; 180.74 2.42E-09 1013100000 1131860 992300 708580 789140 943820 765760 1082360 1238390 1136770 FALSE TRUE 982281.8332 985781.516 1051251.658 968326.2982 925039.8286 795219.2827 977392.8938 973569.9357 1002382.346 0.97994726 0.983438625 1.048753166 0.966024893 0.922841302 0.793329298 0.97506994 0.971256068 1 19.93500148 3.481858467 6.353675484 0.934312552 1.003045755 0.240448321 0.058082863 0.237574152 44.16015593 0.017715118 0.024436048 3032.902628 -3.481858467 0.068733204 FGYTVSEENYMCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FGYTVSEENYMCR 13 0 Q96EK6;G3V5E4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 0 ; 313.89 3.74E-32 265010000 200626 211040 115085 140078 182793 205194 169972 209482 198018 FALSE TRUE 174112.7658 209653.6643 170740.4909 171884.8509 179155.7769 213087.946 153488.1416 164685.9045 174608.5376 0.997160667 1.200706834 0.977847322 0.984401182 1.02604248 1.220375297 0.879041447 0.943172119 1 17.41376458 2.202985582 24.99995652 0.938674312 1.064027572 0.314427419 0.088282727 212.9301973 149632.9442 0.035417028 0.023879169 159.5826167 -2.202985582 0.125353259 FGYVDFESAEDLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FGYVDFESAEDLEK 14 0 P19338 P19338 NCL Nucleolin 0 ;; 281.99 5.48E-33 403903000 708470 498370 390052 458615 475842 416570 600240 689160 816950 FALSE TRUE 614843.8945 495096.1747 578682.4518 562750.5452 466373.6752 432595.7175 542028.8172 541788.497 720371.1017 0.853509938 0.687279339 0.803311586 0.781195337 0.647407529 0.600517867 0.752429985 0.752096379 1 19.45838078 1.204788487 3.251260363 1.059532647 0.727918646 0.558844315 0.074104234 0.315335201 4.218226299 0.280129741 0.019437851 16.02464759 -1.204788487 -0.331614001 FHCPHCDTVIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FHCPHCDTVIAR 12 0 A0A2R8Y595;A0A2R8YFL0;P49711-2;P49711 A0A2R8Y595 CTCF Transcriptional repressor CTCF 0 101.35 0.0015733 76941000 71028 73474 33699 48851 74399 85337 57402 54287 48667 FALSE TRUE 61641.46984 72991.34446 49995.94912 59943.36619 72918.60546 88619.96961 51835.16288 42678.14751 42913.6427 1.436407304 1.700889038 1.165036244 1.396837053 1.699194029 2.065076839 1.20789473 0.994512347 1 15.38914875 2.012075036 24.96635902 1.028165914 1.567718794 0.525943322 0.234024564 172.0108508 355648.4847 0.100343576 0.067596958 102.819393 -2.012075036 0.53955288 FHDEVGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FHDEVGK 7 0 B0QYR6;Q9UJY5-4;Q9UJY5-3;Q9UJY5;Q9UJY5-6;B0QYR8;B0QYR9;B0QYS0;B0QYS1;B0QYS2;B0QYS3;B0QYR5;B0QYS5 B0QYR6 GGA1 ADP-ribosylation factor-binding protein GGA1 0 ; 85.265 0.020938 325390000 605000 593940 394560 489270 540410 498880 603010 651190 685640 FALSE TRUE 525047.7171 590038.369 585370.5357 600366.2315 529656.8983 518072.2364 544530.183 511938.0861 604584.4203 0.868444008 0.975940413 0.968219683 0.993022995 0.876067726 0.856906363 0.900668566 0.846760302 1 19.20558428 3.223837724 24.99975848 0.888300932 0.954360103 0.205296979 0.052730692 307.3921381 521956.5105 0.015370475 0.017500704 1674.317143 -3.223837724 0.066059171 FHDFLGDSWGILFSHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FHDFLGDSWGILFSHPR 17 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;; 244.05 9.95E-21 19683730400 5195400 5698144.1 2538594.8 3781995.5 4547660.4 4470192.5 4607876.8 4694347.5 4098779.7 FALSE TRUE 4508814.727 5660712.616 3766267.736 4640755.382 4457170.855 4642163.698 4161005.617 3690497.819 3614226.633 1.247518538 1.566230674 1.042067396 1.284024455 1.233229487 1.284414114 1.151285196 1.021103044 1 21.78525554 -0.284663076 0.321807806 8.42E-11 1.350775182 0.419437604 0.127217876 24.2481685 1.050746528 15.2763055 0.228163577 0.519202678 0.284663076 1.350775182 FHDIDDVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FHDIDDVKK 9 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;H0Y9D8;D6R967 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 129.38 0.00025371 51695000 240660 156370 147270 188790 167310 132640 202580 247280 203660 FALSE TRUE 208856.1712 155342.7952 218490.2646 231657.655 163980.8583 137742.7466 182933.8228 194401.0963 179583.5468 1.163002819 0.865016857 1.216649679 1.289971487 0.913117383 0.767012062 1.018655807 1.082510619 1 17.45429565 3.204460354 24.99996162 0.967257968 1.120399616 0.293645861 0.135433786 291.9272607 214019.9849 0.044040135 0.049939166 1601.254465 -3.204460354 0.153141648 FHDIISDAEIEIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FHDIISDAEIEIVK 14 0 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ; 109.22 0.00078023 91922000 189799 154445 107697 137793 155368 167889 170103 162706 146303 FALSE TRUE 164716.5813 153430.4406 159779.6294 169081.0067 152276.4808 174347.7985 153606.4372 127912.5881 129007.226 1.276801202 1.18931664 1.238532401 1.310632062 1.180371716 1.351457619 1.190680879 0.99151491 1 16.97709235 1.811763979 3.6388592 0.993250318 1.253792653 0.810160066 0.051565536 0.082392785 1.934175941 0.030267877 0.013086808 64.82820231 -1.811763979 0.260542335 FHDLLSQLDDQYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 116.58 0.0010918 0 72181 74647 33922 43600 70594 88434 75571 69228 60430 FALSE TRUE 62642.09797 74156.63894 50326.79266 53500.04638 69189.31751 91836.1132 68242.13605 54424.13093 53286.03424 1.175581911 1.391671195 0.944464969 1.00401629 1.298451245 1.723455583 1.280675829 1.021358255 1 15.70146985 3.206259678 24.99472859 1.258484409 1.134523991 0.080897956 0.226641226 655.8802278 507523.1577 0.07648103 0.086727834 1607.902378 -3.206259678 -0.123960418 FHDPDSAVVAQHLTNTVFVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FHDPDSAVVAQHLTNTVFVDR 21 0 Q05519-2;Q05519;B4DWT1;Q5T760 Q05519-2;Q5T760 SRSF11 Serine/arginine-rich splicing factor 11 0 176.67 5.67E-14 517260000 217080 190780 169840 152430 188280 210230 180430 210100 144890 FALSE TRUE 188392.328 189526.7536 251975.1921 187041.5612 184533.5964 218317.6841 162931.9264 165171.75 127761.2693 1.47456525 1.483444511 1.972234571 1.463992666 1.444362579 1.708793951 1.275284187 1.292815506 1 16.96309102 1.260038156 0.79638552 0.663928864 1.605769294 0.560852183 0.170948171 1.830162387 0.936969233 1.560488748 0.069714506 18.19860741 -1.260038156 0.94184043 FHDTS(ph)SPLMVTPPSAEAHWAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FHDTSSPLMVTPPSAEAHWAVR 22 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 FHDT(0.002)S(0.499)S(0.499)PLMVTPPSAEAHWAVR 164.79 2.27E-11 842750000 53264 53403 15794 30287 41606 50562 41448 49519 53908 TRUE FALSE 46225.02745 53052.19218 23432.03123 37164.12626 40778.122 52507.15286 37428.37934 38929.74721 47535.05765 0.972440757 1.116064538 0.492942102 0.781825627 0.857853635 1.104598489 0.787384747 0.81896918 1 15.53670429 2.987576314 24.67996248 0.906878292 0.833656545 0.04574528 0.178748662 2210.274427 4390777.397 0.058321872 0.061308933 971.7987011 -2.987576314 -0.073221747 FHDTSS(ph)PLMVTPPSAEAHWAVR ddPTM_MDA-MB-175_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 FHDT(0.001)S(0.173)S(0.826)PLMVTPPSAEAHWAVR;FHDT(0.069)S(0.458)S(0.473)PLMVTPPSAEAHWAVR;FHDTS(0.04)S(0.96)PLMVTPPSAEAHWAVR;FHDTS(0.001)S(0.999)PLMVTPPSAEAHWAVR;FHDT(0.022)S(0.167)S(0.811)PLMVTPPSAEAHWAVR;FHDT(0.012)S(0.373)S(0.615)PLMVTPPSAEAHWAVR;FHDT(0.001)S(0.006)S(0.994)PLMVTPPSAEAHWAVR;FHDT(0.02)S(0.129)S(0.85)PLMVTPPSAEAHWAVR;FHDT(0.005)S(0.034)S(0.961)PLMVTPPSAEAHWAVR;FHDTS(0.025)S(0.975)PLMVTPPSAEAHWAVR 274.11 3.58E-45 8143214000 1322933 1465266 549257 721938 1179456 1379260 891777 1235801 1445121 TRUE FALSE 1148104.052 1455640.571 814879.5224 885865.057 1155987.133 1432321.025 805292.6038 971534.5732 1274280.442 0.900982244 1.14232356 0.639482092 0.695188459 0.907168544 1.124023392 0.631958694 0.762418178 1 20.28125139 4.248346922 24.99987157 0.816467204 1.021652856 0.197442284 0.16620661 324.6216082 829253.6827 0.041882906 0.10788896 17715.23519 -4.248346922 0.205185652 FHEVFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FHEVFK 6 0 Q09161 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 74.743 0.079523 237160000 675450 568630 378300 459310 531900 447520 573430 678360 677800 FALSE TRUE 586187.5711 564894.6321 561247.1453 563603.3556 521316.2306 464736.384 517818.8469 533297.993 597671.2562 0.980785951 0.945159444 0.939056613 0.942998931 0.872245779 0.777578609 0.866394095 0.892293192 1 19.18899264 3.272525938 5.745628254 0.87657949 0.951390627 0.291199004 0.054255973 0.242404203 21.2682966 0.016719669 0.021159663 1872.948942 -3.272525938 0.074811137 FHFFEDQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FHFFEDQLR 9 0 Q56VL3 Q56VL3 OCIAD2 OCIA domain-containing protein 2 0 113.22 0.0022445 0 124990 163950 116690 185420 205310 247770 100110 187550 243340 FALSE TRUE 108472.2548 162873.0017 173121.6743 227522.445 201224.7327 257301.8722 90401.34761 147443.892 214572.6224 0.505527003 0.759057702 0.806820891 1.0603517 0.937793137 1.199136541 0.421308863 0.687151466 1 17.71110649 7.76430924 12.72419192 0.812345662 0.004026366 0 0.242133247 0 0 0.055650508 0 58117809.96 -7.76430924 -0.808319296 FHFPPLDT(ph)HSPTNDVQPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FHFPPLDTHSPTNDVQPGR 19 0 P41162 P41162 ETV3 ETS translocation variant 3 1 FHFPPLDT(0.66)HS(0.339)PT(0.001)NDVQPGR;FHFPPLDT(0.583)HS(0.413)PT(0.004)NDVQPGR 161.66 5.43E-11 294660000 222410 291700 165741 257580 332310 345380 281490 348650 315350 TRUE FALSE 193017.955 289783.8035 245893.902 316067.4759 325697.6812 358666.9921 254191.1431 274093.9107 278069.6822 0.694135202 1.042126568 0.884288787 1.136648459 1.171280805 1.289845729 0.914127499 0.985702247 1 18.08508693 5.238271229 1.26173221 1.062683012 2.70E-11 0.464748903 0.121143224 4.504195584 2.604024107 0.037072067 8.437369156 173089.7015 -5.238271229 -1.062683012 FHFPPLDTHS(ph)PTNDVQPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FHFPPLDTHSPTNDVQPGR 19 0 P41162 P41162 ETV3 ETS translocation variant 3 1 FHFPPLDT(0.006)HS(0.991)PT(0.003)NDVQPGR;FHFPPLDTHS(0.997)PT(0.003)NDVQPGR;FHFPPLDT(0.466)HS(0.524)PT(0.011)NDVQPGR;FHFPPLDT(0.115)HS(0.872)PT(0.013)NDVQPGR 256.06 3.85E-31 636020000 609550 731720 437344 538203 769910 805430 828990 885420 577731 TRUE FALSE 528996.4231 726913.2831 648845.0212 660410.2171 754590.2973 836415.4133 748594.6774 696079.8233 509432.2993 1.038403776 1.42690851 1.273662903 1.296365028 1.481237641 1.641857837 1.469468423 1.366383373 1 18.95853091 4.743484893 23.98444114 1.380654242 1.03840352 0.276751911 0.167340271 407.4587161 1984470.014 0.041748912 0.330077432 55396.82734 -4.743484893 -0.342250722 FHGILDQGEGVLIIFDEPPVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FHGILDQGEGVLIIFDEPPVDK 22 0 O00231 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 ;; 122 2.64E-05 176823000 396826 381806 286761.1 372124.6 329924.5 317794.5 380388 493195 595522 FALSE TRUE 344384.4387 379297.8912 425439.7271 456621.178 323359.6479 330020.2601 343498.0303 387729.0873 525120.0676 0.655820373 0.722306982 0.810176098 0.869555757 0.615782309 0.628466289 0.654132362 0.738362731 1 19.0022878 1.242741993 4.62060196 1.021652955 0.711081664 0.565409935 0.079783205 0.155308065 7.284778426 0.15662191 0.021661192 17.48807444 -1.242741993 -0.310571292 FHGTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 FHGTVK 6 0 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;; 130.84 0.015589 37713751000 30102712 27723009 22670295 23137473 17686630 21529268 24941188 27088257 26024432 FALSE TRUE 26124562.34 27540894.73 33633725.49 28391189.88 17334700.67 22357512.87 22522395.43 21295644.04 22947853.3 1.138431643 1.200151246 1.465658903 1.23720461 0.755395306 0.974274699 0.981459797 0.928001577 1 24.45185586 3.337792977 7.459299118 0.934843408 1.275066226 0.708008668 0.106085416 0.124310068 8.196476295 0.030576763 0.039481333 2176.671933 -3.337792977 0.340222818 FHHTIGGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FHHTIGGSR 9 0 P61313;E7ERA2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;;; 128.36 0.0004195 1075266000 765814 784385 320768 537206 651076 780571 575597 671039 578672 FALSE TRUE 664609.7396 779232.3233 475892.4777 659186.833 638120.8614 810600.0715 519775.6915 527542.5319 510262.0554 1.30248709 1.527121829 0.932643281 1.291859401 1.250574787 1.58859563 1.018644608 1.033865886 1 18.96087884 2.132957797 24.99999619 1.020937951 1.303773797 0.393638663 0.173951093 10.1162517 2368.406459 0.069836485 0.047083758 135.8181459 -2.132957797 0.282835846 FHKPGENYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FHKPGENYK 9 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RQT0;C9J165;A0A0U1RR66;A0A0U1RQJ6 P47897 QARS Glutamine--tRNA ligase 0 ; 144.65 5.95E-05 1046200000 1516540 1327380 887890 1236240 1355880 1021100 1615230 1856740 1800070 FALSE TRUE 1316125.397 1318660.353 1317276.574 1516947.187 1328900.641 1060382.378 1458585.243 1459690.6 1587267.775 0.829176663 0.830773719 0.82990192 0.955697086 0.837225238 0.668055129 0.918928278 0.919624668 1 20.5981141 1.748139928 2.399760236 0.975479718 0.832078478 0.364355462 0.073064667 0.310029259 3.596057256 0.065152262 0.020888903 55.99379822 -1.748139928 -0.143401241 FHLGLFTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FHLGLFTDR 9 0 Q8TEQ6 Q8TEQ6 GEMIN5 Gem-associated protein 5 0 111.46 0.002122 170650000 69532 85573 45063 52014 62133 70175 64396 73468 62247 FALSE TRUE 60343.17003 85010.86533 66855.61753 63824.57368 60896.67486 72874.67766 58150.88583 57757.43993 54888.23057 1.09938268 1.548799523 1.218031932 1.162809823 1.109466897 1.327692237 1.059441801 1.052273672 1 15.74420921 0.565469769 0.288862099 0.528718298 1.339951365 0.326068007 0.132397992 20.13800778 1.249260453 6.235534862 0.37201111 3.676797984 -0.565469769 0.811233066 FHMVDGNVSGEFTDLVPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FHMVDGNVSGEFTDLVPEK 19 0 O95433;O95433-2;G3V438;H0YJ63 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 56.149 0.097366 576270000 350780 274670 188020 201150 281390 225840 310530 369620 364800 FALSE TRUE 304423.5342 272865.6747 278947.1009 246824.1819 275790.8895 234528.2109 280414.8484 290579.6394 321673.7596 0.946373539 0.848268367 0.867173938 0.767312143 0.857362098 0.72908717 0.871736783 0.903336473 1 18.29523873 1.406926172 1.926983283 1.019835051 0.835242479 0.434075521 0.058656581 0.52282163 2.64035866 0.159097997 0.016118737 25.5226739 -1.406926172 -0.184592573 FHMYEGYPLWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FHMYEGYPLWK 11 0 P00491;G3V5M2;G3V393 P00491 PNP Purine nucleoside phosphorylase 0 ; 130.94 0.0002137 2287100000 4279900 4403300 2661800 3203800 3985000 3566100 4097100 4543800 4301800 FALSE TRUE 3714300.371 4374374.432 3949055.383 3931271.757 3905706.297 3703290.175 3699763.873 3572143.73 3793246.105 0.979187817 1.153200797 1.041075447 1.036387213 1.029647481 0.976285238 0.975355611 0.941711566 1 21.85500155 2.959069877 1.297597606 0.96424744 1.06496581 0.41296994 0.044529324 0.35755023 1.275519951 0.018913924 0.019673346 910.0596878 -2.959069877 0.10071837 FHNLEGFLEEFADIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FHNLEGFLEEFADIAK 16 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 123.03 9.01E-05 162400000 240670 238350 196190 249740 200290 174340 264210 292090 317490 FALSE TRUE 208864.8497 236784.2632 291068.1402 306447.284 196304.6209 181046.9726 238586.9549 229628.8265 279956.6939 0.746061281 0.845788896 1.039689876 1.094623886 0.701196382 0.646696352 0.852228077 0.820229813 1 18.09484415 3.221133443 24.99987406 0.801833273 0.933140836 0.187417075 0.131825667 432.9884317 621134.9184 0.042314634 0.048087546 1663.923837 -3.221133443 0.131307564 FHNWFDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FHNWFDDR 8 0 P46977;A0A0C4DH80;E9PN73;E9PI32 P46977 STT3A Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A 0 129.1 0.0023729 0 97507 100090 73193 99462 135430 129640 66796 142560 128670 FALSE TRUE 84621.2029 99432.5022 108589.3796 122046.3673 132735.208 134627.3347 60318.1342 112074.6534 113458.7792 0.74583213 0.876375569 0.957082214 1.075689058 1.16989808 1.186574857 0.531630383 0.987800629 1 16.79180872 7.544993597 10.15462697 0.947922658 0.049613068 0 0.196128427 0 0 0.044771306 0 35074670.24 -7.544993597 -0.898309589 FHPEPYGLEDDQR ddPTM_MDA-MB-175_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 ;;;;; 186.13 8.07E-06 3786410000 3058420 2732590 1596310 2219370 2764540 3025690 2348210 3024780 2504150 FALSE TRUE 2654242.048 2714639.436 2368290.855 2723311.879 2709531.063 3142090.252 2120480.956 2377954.336 2208112.24 1.202041273 1.229393772 1.072540975 1.23332131 1.227080315 1.422975787 0.960313936 1.076917329 1 21.07438208 2.209862883 24.99997328 1.023678615 1.22383636 0.573930457 0.08854596 163.6357872 142549.8349 0.036262701 0.024453109 162.1298134 -2.209862883 0.200157745 FHPIQGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FHPIQGHR 8 0 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 108.09 0.0038781 75818000 60987 67469 72817 58621 54646 66511 50279 60096 66963 FALSE TRUE 52927.41343 67025.7917 108031.5448 71931.79402 53558.65151 69069.72121 45402.95032 47244.93807 59046.71042 0.89636515 1.135131682 1.829594638 1.218218483 0.907055637 1.16974715 0.768932765 0.800128199 1 15.84956907 3.296484059 4.726192766 0.912011545 1.30865379 0.306097929 0.254065133 0.239293791 10.82425459 0.077563927 0.099182231 1979.174375 -3.296484059 0.396642245 FHPLQEHVVKEELLNALYCEFINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FHPLQEHVVKEELLNALYCEFINR 24 1 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 78.916 0.012572 77918000 104570 98602 37303 48618 103630 85501 104720 116690 11363 FALSE TRUE 90750.80955 97954.27697 55342.85557 59657.45998 101567.9657 88790.2788 94564.27052 91736.75158 10019.67908 9.057257102 9.776189052 5.52341598 5.954029014 10.13684819 8.861589083 9.437854218 9.155657662 1 13.29054868 4.29433042 24.99997472 7.578789222 9.416732981 0.094086282 2.677793824 249.4191761 111802.527 0.663228625 1.754736376 19693.84069 -4.29433042 1.837943759 FHQLDIDDLQSIR ddPTM_MDA-MB-175_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 ;;;;; 212.87 1.04E-08 3642344000 2804744 2939360 1610922 2150805 2660455 2786223 2508341 2762985 2599291 FALSE TRUE 2434089.974 2920051.151 2389969.267 2639178.148 2607517.151 2893410.802 2265082.476 2172142.159 2292005.779 1.061991203 1.274015614 1.042741379 1.151470983 1.137657319 1.262392455 0.988253388 0.947703614 1 21.12817925 2.134714784 7.79298136 0.969969369 1.154114186 0.560691263 0.073607376 0.154193319 10.35901807 0.028061339 0.018886671 136.3687263 -2.134714784 0.184144817 FHQLLDDESDPFDILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FHQLLDDESDPFDILR 16 0 Q5JVS0;Q5JVS0-2 Q5JVS0 HABP4 Intracellular hyaluronan-binding protein 4 0 123.36 8.83E-05 23790000 30447 33097 21618 18140 25288 34192 27832 34094 18460 FALSE TRUE 26423.35181 32879.58363 32072.53711 22258.96425 24784.81828 35507.38837 25132.85692 26803.26342 16277.67983 1.623287353 2.019918316 1.970338368 1.367453131 1.522625984 2.181354391 1.544007327 1.646626774 1 13.99060746 0.924732611 1.595979401 4.54E-13 1.762330822 0.463525537 0.25044368 2.372813465 2.791492562 8.477502693 0.070716747 8.408772655 -0.924732611 1.762330822 FHS(ph)PSTTWS(ph)PNKDTPQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FHSPSTTWSPNKDTPQEK 18 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 2 FHS(0.986)PS(0.014)T(0.001)T(0.001)WS(0.998)PNKDTPQEK;FHS(0.808)PS(0.218)T(0.038)T(0.002)WS(0.934)PNKDTPQEK 166.06 3.53E-11 845050000 750960 496970 394230 389400 495080 375220 636850 650760 616720 TRUE FALSE 651718.7333 493705.3713 584880.9466 477819.2216 485228.8766 389654.9562 575088.385 511600.0382 543812.0642 1.198426398 0.907860277 1.075520359 0.878647704 0.892273101 0.716525031 1.057513106 0.940766254 1 19.05274863 7.351397953 1.223574802 0.927415252 199.9995953 0.386635819 0.102709332 1256.307625 3.336527671 0.029782917 700256.0156 22459389.83 -7.351397953 199.0721801 FHS(ph)PSTTWSPNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FHSPSTTWSPNK 12 0 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 FHS(0.953)PS(0.046)T(0.001)TWSPNK;FHS(0.916)PS(0.078)T(0.005)TWSPNK 143.91 4.03E-05 550500000 1976460 1715280 1193250 1648720 1886110 1386470 1723220 2111400 3430700 TRUE FALSE 1715265.803 1704012.213 1770309.691 2023087.075 1848580.101 1439808.398 1556102.39 1659893.541 3025126.554 0.567006296 0.563286257 0.585201862 0.668761137 0.611075295 0.475949806 0.514392493 0.548702182 1 21.52856407 1.23720099 24.99971908 1.000000526 0.5656888 0.874009654 0.051688239 12.63377054 232210.8231 0.084552353 0.013917404 17.2663679 -1.23720099 -0.434311726 FHS(ph)PSTTWSPNKDTPQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FHSPSTTWSPNKDTPQEK 18 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 FHS(0.903)PS(0.073)T(0.02)T(0.003)WSPNKDTPQEK;FHS(0.981)PS(0.018)TTWSPNKDTPQEK;FHS(0.681)PS(0.254)T(0.058)T(0.007)WSPNKDTPQEK 181.26 4.49E-14 1444160000 1571570 1149220 644370 812294 1185472 805125 1407430 1631730 529395 TRUE FALSE 1363883.043 1141670.698 955989.4873 996737.7678 1161883.427 836098.6797 1270937.655 1282797.238 466810.5262 2.921705845 2.445683279 2.047917589 2.135208424 2.48898292 1.791087889 2.722598536 2.748004095 1 18.83247757 4.64377295 3.047249513 2.220811282 2.966322946 0.184733519 0.507636063 0.569680913 8.382807213 0.124917782 0.896712851 44032.46004 -4.64377295 0.745511664 FHSEDYIDFLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FHSEDYIDFLQR 12 0 O15379;O15379-2 O15379 HDAC3 Histone deacetylase 3 0 ; 242.82 2.59E-16 168389000 274440 250920 152662 183110 247610 277740 203488 264700 223980 FALSE TRUE 238172.0587 249271.69 226489.8538 224687.9242 242683.0454 288424.8375 183753.7651 208095.9649 197501.3396 1.205926295 1.262126579 1.146776292 1.137652659 1.228766579 1.460369019 0.9303925 1.053643309 1 17.59150291 2.209777861 24.99999786 1.004284265 1.231826282 0.606379921 0.09300365 151.6703966 131736.1461 0.038300373 0.02582692 162.0980762 -2.209777861 0.227542017 FHSGWEPPVDVLQEAPWEVEGLASAPIEEVS(ph)PVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FHSGWEPPVDVLQEAPWEVEGLASAPIEEVSPVSR 35 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 FHSGWEPPVDVLQEAPWEVEGLASAPIEEVS(0.952)PVS(0.048)R 168.5 1.40E-14 21413000 17502 18029 10932 14970 15836 18180 17412 19495 16125 TRUE FALSE 15189.06636 17910.56631 16218.75177 18369.1673 15520.89458 18879.39636 15723.38692 15326.14596 14218.72087 1.068244218 1.259646805 1.140661802 1.291900127 1.091581636 1.327784443 1.105822884 1.077885001 1 13.79550406 1.764419913 2.256666458 1.020601311 1.196314053 0.365457235 0.085457377 0.27958236 2.801214477 0.069092787 0.021774107 58.13262222 -1.764419913 0.175712742 FHSMNQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 FHSMNQR 7 0 Q9H6S3;Q9H6S3-3;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 ;;;;;;; 122.98 0.0032528 514179000 199374.4 240332.1 131748.7 155950.8 202025.5 240943 226926 230585 236276 FALSE TRUE 173026.5679 238753.3426 195462.812 191361.8127 198005.5878 250212.2331 204918.7514 181276.1922 208343.7204 0.830486119 1.145958909 0.938174722 0.918490907 0.950379437 1.200958841 0.983560968 0.870082342 1 17.66860609 1.981540491 24.57234173 0.926079413 1.003786258 0.046199146 0.111632041 1518.438652 2021263.14 0.048853703 0.028895814 95.83860662 -1.981540491 0.077706845 FHSQLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FHSQLMR 7 0 P49458 P49458 SRP9 Signal recognition particle 9 kDa protein 0 ; 162.5 0.0012696 2446100000 1036160 1532900 790930 867690 1331190 1368340 1141840 1355170 1318190 FALSE TRUE 899228.8307 1522830.279 1173426.394 1064712.276 1304701.923 1420980.925 1031104.533 1065377.441 1162355.08 0.773626619 1.310124854 1.009524898 0.915995718 1.122464164 1.222501583 0.887082227 0.916567975 1 20.14861942 2.194200777 24.99986518 0.928825858 1.064583537 0.130128798 0.15103467 244.9016273 138017.3807 0.058668278 0.039554342 156.3870462 -2.194200777 0.135757679 FHTEALTALLSDDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FHTEALTALLSDDSK 15 0 B7Z7P8;P62495-2;P62495;I3L492;D6RJE8 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 210.14 2.03E-09 821820000 927490 721070 653550 822110 752860 616940 824480 1072800 1270500 FALSE TRUE 804919.8465 716333.2437 969608.966 1008782.641 737879.5589 640674.081 744522.0565 843390.0685 1120302.937 0.718484099 0.639410306 0.865488194 0.900455231 0.658642885 0.571875749 0.664572083 0.752823223 1 20.09545747 1.244644199 4.104709268 1.027583197 0.718383242 0.440368947 0.099440386 0.238776609 7.296301109 0.218431369 0.027360841 17.56484003 -1.244644199 -0.309199955 FHTVSGSK ddPTM_MDA-MB-175_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 ; 114.5 0.0026447 1700990000 4279200 3860200 1953660 2907200 3307800 3213600 5010400 5370600 4162000 FALSE TRUE 3713692.878 3834842.092 2898456.511 3567324.194 3241981.252 3337229.271 4524492.179 4222138.984 3669973.101 1.011912833 1.04492376 0.789775955 0.972030065 0.883380113 0.909333442 1.232840692 1.150455022 1 21.80733806 2.251453262 24.9985274 1.136870423 0.932917168 0.506578752 0.08940763 168.6768648 327060.3166 0.033486269 0.025768096 178.4239961 -2.251453262 -0.203953255 FHVDISLTDFIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FHVDISLTDFIQK 13 0 Q15046;Q15046-2;H3BVA8 Q15046 KARS Lysine--tRNA ligase 0 ;; 218.01 2.49E-11 336872000 489467 419330 269230 413640 385309 364887 473285 530027 539599 FALSE TRUE 424782.6958 416575.3936 399430.5285 507563.2841 377642.1047 378924.439 427385.8935 416684.8507 475808.2209 0.892760312 0.875511131 0.839477989 1.066739207 0.79368554 0.796380605 0.898231419 0.875741176 1 18.86002067 1.237428688 24.83216182 1.000000155 0.879635477 0.199585601 0.075637617 44.39509067 973453.9809 0.107371522 0.018023263 17.2754229 -1.237428688 -0.120364678 FHVEEEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FHVEEEGK 8 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ;;;; 179.21 0.00024555 4646260000 6605690 5638710 3667150 3812690 4152600 3917940 5106140 6114880 8462970 FALSE TRUE 5732731.33 5601668.943 5440596.006 4678419.538 4069971.384 4068665.687 4610947.329 4807260.498 7462487.328 0.768206508 0.750643679 0.729059329 0.626924956 0.545390726 0.545215758 0.617883438 0.644190105 1 22.83122515 -0.150110038 11.46241575 3.726926466 0.678252177 0 0.134257334 0 0 0 0.030386963 0.707766433 0.150110038 -3.048674289 FHVEEEGKGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FHVEEEGKGK 10 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 121.83 0.00030322 803300000 1342870 1018260 461700 437010 760980 644730 1071870 1233540 208426 FALSE TRUE 1165406.327 1011570.983 684979.6643 536239.7998 745837.9868 669533.1803 967920.2124 969757.0704 183786.1157 6.341101027 5.504066393 3.727047942 2.91773836 4.058184613 3.643001963 5.26655786 5.276552402 1 17.48766826 4.368801942 3.699156328 3.906396013 6.185654154 0.364854385 1.21793239 0.263432865 6.640446397 0.316597506 0.998202699 23377.70864 -4.368801942 2.279258141 FHVGS(ph)AESMLHVRPGGYTPQR ddPTM_MDA-MB-175_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(0.999)AES(0.001)MLHVRPGGYTPQR 54.658 0.061862 149140000 54282 57190 42633 42053 75101 68351 61994 64904 55776 TRUE FALSE 47108.49617 56814.31512 63250.4614 51601.77639 73606.63703 70980.5072 55981.83142 51024.78468 49182.22482 0.95783581 1.155179851 1.286043111 1.049195651 1.49661056 1.443214646 1.138253335 1.037463939 1 15.58584938 1.872157419 3.647012625 1.022397155 1.237116498 0.220738422 0.161694552 0.363579214 8.018964795 0.100466818 0.046049859 74.50019664 -1.872157419 0.214719343 FHVLVASQDFVESVLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FHVLVASQDFVESVLVR 17 0 O60784;O60784-4;O60784-2;O60784-3;V9GYF4;B0QY02;V9GZ68;Q6UW50;B0QY01;H7BYN7 O60784 TOM1 Target of Myb protein 1 0 ;; 217.37 4.99E-15 240206000 240695 240470 144494 200514 200122 218328 196465 248629 257942 FALSE TRUE 208886.5459 238890.3367 214371.7817 246043.7684 196139.9637 226727.2194 177411.8545 195461.6232 227448.3906 0.91839096 1.050305681 0.942507358 1.081756471 0.862349315 0.996829298 0.780009276 0.859366921 1 17.7951797 3.218657967 24.99469474 0.890546232 0.997978202 0.272650534 0.079183321 287.1785854 360651.5275 0.023134922 0.026266055 1654.466459 -3.218657967 0.10743197 FICEQDHQNFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FICEQDHQNFLR 12 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;;;; 291.5 3.91E-36 8667810000 3656050 3406770 2056118 2686950 3621440 3773500 3297180 3812530 3647900 FALSE TRUE 3172893.729 3384390.704 3050463.542 3297063.065 3549380.429 3918668.987 2977419.991 2997250.129 3216649.418 0.986397122 1.05214783 0.94833572 1.024999195 1.103440247 1.218245596 0.925627759 0.931792601 1 21.61712727 FICVTPTTCSNTIDLPMS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 194.49 1.18E-17 519079000 174154 255994 146281 230307 323622 327190 314090 386633 294017 TRUE FALSE 151139.1076 254312.3586 217022.9809 282601.7244 317182.5554 339777.211 283629.6001 303954.5417 259258.6452 0.58296651 0.980921421 0.837090623 1.090037804 1.223421325 1.310572347 1.094002477 1.172398866 1 17.98403257 4.977422233 0.75296044 1.162581908 0.111850362 0.713664622 0.110591102 2.083507965 0.71496128 0.044488463 2.003692109 94934.09911 -4.977422233 -1.050731546 FIDFFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FIDFFK 6 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 118.06 0.05163 186816000 977460 704320 475400 566250 658890 612430 746920 886150 937360 FALSE TRUE 848286.1844 699693.2755 705305.0301 694825.7171 645779.3781 635990.5784 674483.8134 696653.7185 826546.3686 1.026301992 0.846526344 0.853315745 0.840637311 0.781298428 0.769455414 0.816026588 0.842848925 1 19.65673623 4.742045323 4.627110856 0.837563295 1.038457147 0.456826807 0.062309686 0.178856314 10.2668727 0.015436328 0.117143799 55213.50571 -4.742045323 0.200893852 FIDFFKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FIDFFKR 7 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 117.17 0.0084845 401840000 3015800 2329470 871840 973450 2153880 2064780 2569540 2874130 208078 FALSE TRUE 2617254.389 2314167.558 1293464.74 1194486.701 2111022.002 2144213.423 2320346.406 2259519.666 183479.2559 14.26457926 12.61269317 7.049651111 6.510200268 11.50550776 11.68640789 12.64636918 12.31485083 1 17.48525744 4.423032283 7.023602011 9.561215644 13.86992621 0.206872456 3.566631667 0.318513021 32.81979507 0.902255771 2.447111264 26486.97021 -4.423032283 4.308710569 FIEEHATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FIEEHATK 8 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;; 152.63 0.00045401 6093590000 9257130 7893440 4848650 6993980 8032970 8892410 8657500 8543110 7144890 FALSE TRUE 8033776.816 7841587.473 7193473.358 8582070.055 7873129.613 9234506.767 7817896.983 6716232.409 6300229.244 1.275156269 1.244651134 1.141779621 1.362183775 1.249657641 1.46574139 1.240890876 1.066029846 1 22.58697289 1.709140516 3.275581233 1.015922581 1.287082457 0.613831178 0.083709526 0.135274523 3.230030823 0.063507181 0.022817541 51.1847417 -1.709140516 0.271159876 FIEIAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 158.38 0.0033101 1169800000 1587420 1746280 1143520 1190940 1705950 2098800 1547160 1686310 1458010 FALSE TRUE 1377638.425 1734808.572 1696530.097 1461361.129 1672004.933 2179542.194 1397116.661 1325705.729 1285645.719 1.071553699 1.349367517 1.319593782 1.13667483 1.300517637 1.695289894 1.086704246 1.031159448 1 20.29406171 2.024069966 24.999977 1.030143055 1.312797538 0.389579544 0.16260456 220.6962838 229222.5242 0.06618273 0.044618335 105.6987778 -2.024069966 0.282654483 FIESDKFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FIESDKFTR 9 1 P25098;E9PRV7 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 0 133.75 0.00024455 370120000 631800 520960 397070 441500 580050 579490 686330 744460 546280 FALSE TRUE 548306.0292 517537.7795 589094.3801 541749.3229 568508.1398 601783.3553 619769.8222 585263.0224 481699.4007 1.138274261 1.074399882 1.222950203 1.124662647 1.180213509 1.249292306 1.286631915 1.214996368 1 18.8777736 4.238422209 24.99999979 1.191351719 1.106337064 0.129854222 0.079735614 6.397762612 1156554.069 0.020362966 0.047247353 17314.98857 -4.238422209 -0.085014656 FIGEGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FIGEGAR 7 0 P62195-2;P62195;J3QSA9;J3KRP2;J3QQM1 P62195-2 PSMC5 26S protease regulatory subunit 8 0 103.28 0.043984 0 252420 195660 185360 180710 201180 210010 224880 277100 275620 FALSE TRUE 219062.0574 194374.6966 275000.716 221742.9675 197176.9116 218089.2206 203071.1722 217844.3214 243036.5176 0.901354494 0.799775682 1.131520147 0.912385388 0.811305698 0.897351652 0.83555827 0.896343988 1 17.89081358 3.479301157 24.99411677 0.883496313 0.945136009 0.068240109 0.093823224 224.3012749 2571790.918 0.026663392 0.035006929 3015.096086 -3.479301157 0.061639696 FIGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FIGSPR 6 0 P23443-5;P23443;P23443-3;P23443-2;P23443-4;K7ERJ3 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 1 FIGS(1)PR;FIGS(1)PR;FIGS(1)PR;FIGS(1)PR 96.492 0.044211 1721520000 2965200 1861090 1657700 2257880 2524080 3025200 2630050 2907370 3630660 TRUE FALSE 2573341.307 1848864.377 2459369.265 2770566.164 2473855.746 3141581.402 2374988.156 2285651.551 3201447.511 0.803805559 0.577508883 0.7682054 0.86541046 0.772730378 0.9813003 0.741848226 0.713943159 1 21.61029293 4.005722221 24.79921903 0.827345173 0.686207161 0.254284713 0.107371658 193.8486695 840085.8899 0.026743842 0.055411374 10132.63086 -4.005722221 -0.141138012 FIHQQPQS(ph)SSPVYGSSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FIHQQPQSSSPVYGSSAK 18 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 FIHQQPQS(0.449)S(0.449)S(0.103)PVYGSSAK 233.14 1.03E-23 215590000 77558 73774 42264 57235 77065 78520 85112 103070 90900 TRUE FALSE 67308.51379 73289.37374 62703.01176 70231.08153 75531.55728 81540.71521 76857.85134 81029.28259 80153.90555 0.839740913 0.914358112 0.782282676 0.876202863 0.94233159 1.017301835 0.958878433 1.010921203 1 16.2904852 3.140845018 2.628415213 0.994969979 0.849686891 0.78711951 0.035431605 0.116745798 1.640204308 0.010986926 0.013039881 1383.072728 -3.140845018 -0.145283088 FIHQQPQSS(ph)SPVYGSSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FIHQQPQSSSPVYGSSAK 18 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 FIHQQPQS(0.089)S(0.6)S(0.311)PVYGSSAK 219.04 4.86E-19 451620000 719880 646660 387480 541420 721210 605850 715000 975250 867880 TRUE FALSE 624746.0341 642412.0479 574866.624 664357.6861 706859.332 629157.4415 645659.41 766700.3769 765280.2151 0.816362454 0.839446826 0.751184485 0.868123431 0.923660795 0.822126888 0.84369019 1.001855741 1 19.54562858 1.735909111 4.764265254 1.002552591 0.837758799 0.713686951 0.042930127 0.090314618 4.862640418 0.028251046 0.01185116 54.43887108 -1.735909111 -0.164793792 FIHQQPQSSS(ph)PVYGSSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FIHQQPQSSSPVYGSSAK 18 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 FIHQQPQS(0.035)S(0.149)S(0.817)PVYGSSAK;FIHQQPQSS(0.001)S(0.999)PVYGSSAK;FIHQQPQSS(0.008)S(0.992)PVYGSSAK;FIHQQPQSS(0.043)S(0.957)PVYGSSAK 251.55 1.53E-26 12856470000 8792780 8703860 5261990 7552120 8937880 8195320 10421650 12227710 10783850 TRUE FALSE 7630791.845 8646683.771 7806705.964 9266944.273 8760033.675 8510599.263 9410959.987 9612909.373 9508995.538 0.802481378 0.909316209 0.820981137 0.974545023 0.92123649 0.895005075 0.989690231 1.010927951 1 23.18086152 8 0.067647669 1.354535883 0.000922924 0.659935936 0.041979002 357.5850686 2.327443698 10.66332397 49.93409822 100000000 -8 -1.353612959 FIIGSVSEDNS(ph)EDEISNLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FIIGSVSEDNSEDEISNLVK 20 0 Q13085;Q13085-4;A0A0C4DGT1;A0A087X2F8;A0A087X126;A0A087WYK6 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 1 FIIGSVSEDNS(1)EDEISNLVK;FIIGSVS(0.002)EDNS(0.998)EDEISNLVK;FIIGS(0.002)VS(0.011)EDNS(0.987)EDEISNLVK 138.35 1.26E-06 355570000 572662 433989 394628 417705 496170 440328 595493 751048 719422 TRUE FALSE 496983.2658 431138.0977 585471.4208 512551.3045 486297.1877 457267.7031 537742.1805 590442.2299 634372.7507 0.783424675 0.679628968 0.922913886 0.807965512 0.766579566 0.720818639 0.847675408 0.930749672 1 19.27497128 1.711728357 2.155406657 0.992252401 0.783020805 0.590363648 0.063715318 0.211910093 1.991494051 0.065856665 0.018222245 51.49064798 -1.711728357 -0.209231595 FIIHAPPGEFNEVFNDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FIIHAPPGEFNEVFNDVR 18 0 P47755;F8W9N7;C9JUG7;A0A0D9SET8;P47755-2 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 ;;;; 220.64 6.67E-19 3445645000 2108337 2124176 1216359 1485732 1957898 2176935 1859333 2286604 2116673 FALSE TRUE 1829714.924 2110222.148 1804594.281 1823090.159 1918939.66 2260683.098 1679015.172 1797631.529 1866442.329 0.980322239 1.130612029 0.966863135 0.976772831 1.028126951 1.211225797 0.899580526 0.963132641 1 20.8318595 FIILFS(ph)LDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FIILFSLDLK 10 0 Q5T6F7;F1DAM0;Q13285 Q5T6F7 NR5A1 Steroidogenic factor 1 1 FIILFS(1)LDLK 74.92 0.026117 687340000 836260 818770 551230 592420 621340 569940 1182500 930830 870280 TRUE FALSE 725746.1222 813391.446 817806.6718 726938.0156 608976.5496 591865.9606 1067821.332 731779.2482 767396.4898 0.9457251 1.059936365 1.065689878 0.947278265 0.793561813 0.771264879 1.391485818 0.953586911 1 19.54961264 0.883100175 17.20622088 1.320036642 0.996897599 0 0.17114588 814504653.1 389239864.1 10293476018 0.042136831 7.640119916 -0.883100175 -0.323139043 FIIQSEKPPHYLESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FIIQSEKPPHYLESR 15 1 A0A3B3ISG5;P14735;P14735-2 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 199.68 4.39E-09 1737450000 2177300 2187700 1226700 1850450 2129500 2218200 2309200 2454300 2382400 FALSE TRUE 1889564.288 2173328.855 1819936.223 2270622.955 2087127.116 2303535.589 2085254.139 1929467.044 2100755.386 0.899468972 1.034546368 0.866324673 1.080860232 0.993512681 1.09652728 0.992621108 0.918463452 1 21.00247675 4.756319016 23.5029132 0.992840078 0.899468793 0.16729221 0.068172816 3225.741432 4269049.02 0.016475179 0.453240261 57058.3247 -4.756319016 -0.093371284 FIKDNWEELYNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FIKDNWEELYNR 12 1 E9PLK3;P55786;P55786-2;H0YDG0 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ; 167.98 4.35E-05 3738700000 3482000 2828300 1915130 2152300 2931900 2855100 3285600 3677400 2037300 FALSE TRUE 3021844.878 2809720.711 2841293.274 2641012.611 2873560.926 2964937.544 2966963.018 2891016.628 1796452.715 1.682117683 1.564038223 1.58161317 1.470126427 1.599575042 1.65044007 1.651567555 1.609291802 1 20.77671953 1.23799191 24.99866126 0.999999316 1.599481034 0.913154289 0.058255171 3.891817279 170920.2562 0.08540799 0.014813979 17.29784138 -1.23799191 0.599481717 FILHAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FILHAK 6 0 P61221 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 72.054 0.086609 328790000 726940 698770 506920 649600 707560 690310 850020 918920 1007500 FALSE TRUE 630873.0372 694179.7339 752068.2075 797101.6085 693480.9403 716866.6724 767585.1912 722416.109 888394.4977 0.710127132 0.7813868 0.846547575 0.897238345 0.78060022 0.806923809 0.864013896 0.8131704 1 19.76084093 -1.999975524 0.028539906 1.979700565 1.74E-05 0.415404562 0.059629476 4201.122845 11.88150978 571.155764 296.3527498 0.010000564 1.999975524 -1.979683117 FIMLNLMHETTDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FIMLNLMHETTDK 13 0 Q8TD06;B5MC62;H7C040 Q8TD06 AGR3 Anterior gradient protein 3 homolog 0 ; 207.66 5.21E-08 404820000 1054500 1016470 669440 1029300 983470 954920 1026350 1207830 1637300 FALSE TRUE 915145.1532 1009792.742 993183.4231 1263018.297 963900.8711 991656.3903 926814.735 949544.9538 1443740.259 0.633871049 0.699428263 0.687923895 0.87482377 0.667641471 0.686866203 0.641953931 0.657697912 1 20.46137978 1.234383721 24.99898796 1.000000447 0.694274392 0.669466994 0.067620687 78.87871144 472029.5589 0.127796111 0.016936929 17.15472343 -1.234383721 -0.305726056 FIMLNLMHETTDKNLSPDGQYVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FIMLNLMHETTDKNLSPDGQYVPR 24 1 Q8TD06;B5MC62;H7C040 Q8TD06 AGR3 Anterior gradient protein 3 homolog 0 172.91 2.91E-12 325230000 184900 187770 88541 108980 169220 193920 196080 219640 45950 FALSE TRUE 160464.9965 186536.5265 131359.7238 133725.5747 165852.8531 201380.2279 177064.1918 172671.6952 40517.84335 3.960353841 4.60381183 3.242021611 3.300411957 4.09332875 4.97016157 4.37003002 4.261621078 1 15.30626977 4.252317422 24.99602948 3.760204399 4.282082656 0.049285919 1.080326347 949.9327699 1725990.084 0.268147013 0.701468045 17877.93779 -4.252317422 0.521878256 FINDQYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FINDQYEK 8 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4;K7EL40;K7EK18;K7EIE4;K7EQD7;K7ER52;K7ELJ9 Q9UHD8 9-Sep Septin-9 0 ;;; 176.79 0.00060086 730730000 1037770 957360 650520 779560 950610 804010 1035910 1198310 1101180 FALSE TRUE 900626.0651 951071.0391 965113.6479 956571.0128 931694.7208 834940.785 935447.6076 942060.7318 970999.7549 0.927524503 0.979476086 0.993938096 0.985140324 0.959521067 0.859877442 0.963386039 0.970196673 1 19.88911141 1.398274702 2.472394312 1.002444212 0.953622094 0.138318241 0.037843172 0.901333645 8.05521203 0.082220718 0.010741543 25.01927391 -1.398274702 -0.048822118 FINYVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FINYVK 6 0 P06748;P06748-2 P06748 NPM1 Nucleophosmin 0 ; 130.84 0.036268 1133120000 1986310 1742170 1082540 1321450 1602300 1407510 1624230 1968330 1716180 FALSE TRUE 1723814.101 1730725.571 1606059.965 1621505.42 1570417.365 1461657.82 1466712.425 1547417.947 1513295.155 1.139112945 1.14368011 1.061299879 1.071506384 1.037746906 0.965877552 0.969217683 1.022548669 1 20.52926197 3.778495984 0.890158804 0.992668974 1.156069548 0.849003782 0.023934305 0.29738312 0.431861532 0.010948444 0.036479593 6004.764563 -3.778495984 0.163400574 FIPHENGVHTIDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FIPHENGVHTIDVK 14 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;;;;; 198.16 1.30E-08 3392030000 4087500 3777550 2369877 3143950 3538100 3384790 4071490 4634730 4204060 FALSE TRUE 3547326.519 3752735.025 3515957.444 3857831.9 3467698.732 3515005.062 3676637.526 3643629.057 3707060.816 0.956910797 1.012320869 0.948448817 1.040671327 0.935430764 0.948191906 0.991793151 0.982888935 1 21.82184435 1.418341795 1.772515539 1.00189786 0.976250395 0.053188093 0.032106459 2.226795496 9.371496228 0.089321558 0.008682103 26.20244364 -1.418341795 -0.025647464 FIQENIFGICPHMTEDNKDLIQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FIQENIFGICPHMTEDNKDLIQGK 24 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 230.86 9.86E-34 1977120000 1380200 1158630 636630 699940 1024920 958930 1427120 1393640 298965 FALSE TRUE 1197803.073 1151018.883 944506.3974 858872.0749 1004526.097 995820.6576 1288718.122 1095620.931 263621.6983 4.543643717 4.366176573 3.582809775 3.257971861 3.81048337 3.7774609 4.888513087 4.156034721 1 18.0081096 1.237319302 24.99875845 0.999996338 4.047219115 0.802267151 0.475533487 14.7524449 296974.8293 0.757383131 0.125737565 17.27107228 -1.237319302 3.047222777 FISADVHGIWSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FISADVHGIWSR 12 0 A0AVT1;A0AVT1-4;A0AVT1-3 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ; 171.32 3.88E-05 660020000 1042860 1042880 485620 751600 1013300 1115430 969810 1079420 1111420 FALSE TRUE 905043.4087 1036029.253 720467.4563 922262.2675 993137.3125 1158341.314 875757.9755 848594.4331 980029.1937 0.923486172 1.057141215 0.735148974 0.941055913 1.013375233 1.181945723 0.893603967 0.865886892 1 19.9024652 5.072077951 14.47764484 0.953580795 0.591101687 0.006296368 0.119146125 5310113.066 23825892.89 0.029805134 57527662.93 118053.251 -5.072077951 -0.362479108 FISDKDASIVGFFDDSFSEAHSEFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FISDKDASIVGFFDDSFSEAHSEFLK 26 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;; 314.05 4.57E-82 8231105000 5266950 4217276 2870993 3775469 3934509 3963794 5264337 5506206 2689300 FALSE TRUE 4570909.213 4189572.436 4259414.818 4632746.941 3856219.969 4116283.72 4753802.408 4328746.696 2371374.018 1.927536179 1.766727815 1.796180099 1.953612929 1.626154263 1.735822224 2.00466159 1.825417106 1 21.17729179 1.238769226 11.43941929 0.998462469 1.829224266 0.846538483 0.110995588 0.022492268 125.6950533 0.14912927 0.026802912 17.32882938 -1.238769226 0.830761797 FISETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FISETLR 7 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 134.06 0.0074714 128900000 175420 191900 115990 119170 186960 251300 141770 140770 217860 FALSE TRUE 152237.8025 190639.3963 172083.152 146229.3699 183239.8618 260967.6736 128021.1672 110667.431 192104.839 0.792472503 0.992371651 0.895777289 0.761195661 0.953853441 1.358464862 0.666413027 0.57607831 1 17.55153433 FITHAPPGEFNEVFNDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FITHAPPGEFNEVFNDVR 18 0 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 ;;;; 244.1 3.98E-24 3227390000 1757430 1646210 1020540 1232350 1602940 1678900 1478340 1826810 1642850 FALSE TRUE 1525181.173 1635395.938 1514076.558 1512173.903 1571044.63 1743488.369 1334970.814 1436160.898 1448634.145 1.052840828 1.128922678 1.045175252 1.043861839 1.084500622 1.203539469 0.921537587 0.99138965 1 20.46626185 2.218033357 24.99999993 0.973168719 1.089953788 0.557047945 0.051288639 182.6994202 222506.5726 0.02072773 0.013992509 165.2088686 -2.218033357 0.116785069 FITIFGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FITIFGTR 8 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ; 178.99 0.00057395 418060000 457600 596950 251430 296270 314100 353680 246410 373040 820340 FALSE TRUE 397127.0006 593028.5961 373022.389 363542.6317 307850.0245 367286.2985 222513.1961 293268.299 723360.3397 0.549003006 0.819824593 0.515679902 0.502574736 0.425583223 0.507750119 0.307610445 0.405424908 1 19.46435497 1.232064193 24.99637527 1.000000842 0.498166192 0.582138742 0.131928988 178.6840857 687459.4741 0.329932904 0.035481772 17.06334582 -1.232064193 -0.501834651 FITLLLPGGAQTAVRPGS(ph)PSTSTMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FITLLLPGGAQTAVRPGSPSTSTMR 25 1 H0Y4W2;F2Z2U4;Q9Y4A5-2;Q9Y4A5 H0Y4W2 TRRAP Transformation/transcription domain-associated protein 1 FITLLLPGGAQTAVRPGS(0.46)PS(0.446)T(0.067)S(0.011)T(0.015)MR 151.41 8.94E-08 236290000 282740 219600 156180 164550 218950 199240 210870 257540 239740 TRUE FALSE 245375.1926 218157.4331 231709.1704 201913.5925 214593.3234 206904.8917 190419.8599 202467.0752 211398.2103 1.160725023 1.031973889 1.096079149 0.955133878 1.015114192 0.978744765 0.900763822 0.957752078 1 17.68960364 5.968148813 0.438709088 0.94778065 1.668237843 0.687737981 0.041392527 9.070393967 0.619916102 0.034781885 4.234402331 929284.7551 -5.968148813 0.720457193 FITLLLPGGAQTAVRPGSPS(ph)TSTMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FITLLLPGGAQTAVRPGSPSTSTMR 25 1 H0Y4W2;F2Z2U4;Q9Y4A5-2;Q9Y4A5 H0Y4W2 TRRAP Transformation/transcription domain-associated protein 1 FITLLLPGGAQTAVRPGS(0.134)PS(0.698)T(0.134)S(0.027)T(0.008)MR 122.89 0.00010168 374480000 266120 231750 111130 191160 216740 194670 260940 229850 274720 TRUE FALSE 230951.5677 230227.619 164872.8397 234565.7997 212427.298 202159.0809 235634.079 180698.3662 242242.9146 0.95338833 0.950399806 0.680609544 0.968308196 0.87691852 0.834530419 0.972718147 0.745938706 1 17.88609494 4.4142129 24.9999995 0.862392048 0.952676789 0.105313424 0.099955594 110.7058759 43994.02594 0.022881895 0.060539824 25954.51395 -4.4142129 0.090284741 FIVLNSLNQNAKPEGPEQAELGRLS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FIVLNSLNQNAKPEGPEQAELGRLSPR 27 2 P41182-2;P41182 P41182-2 BCL6 B-cell lymphoma 6 protein 1 FIVLNSLNQNAKPEGPEQAELGRLS(1)PR;FIVLNSLNQNAKPEGPEQAELGRLS(1)PR 268.3 5.20E-54 970240000 1448340 1353880 821880 1018980 1345300 1097890 1480340 1720100 953320 TRUE FALSE 1256938.199 1344986.273 1219343.917 1250354.983 1318531.162 1140126.539 1336776.855 1352270.001 840619.5956 1.495252081 1.599993957 1.45052997 1.487420695 1.568522991 1.356293078 1.590228043 1.60865867 1 19.68109356 1.232807953 24.99999645 0.99999916 1.522868424 0.813698695 0.078123438 78.70339454 341994.375 0.166106097 0.019158041 17.09259307 -1.232807953 0.522869264 FIVS(ph)PVPESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 96.334 0.0071447 66622000 362010 441290 173840 202980 411820 502300 296170 343210 94104 TRUE FALSE 314169.4613 438391.1369 257909.6055 249069.7114 403625.5877 521623.806 267447.479 269817.2124 82979.13232 3.786126132 5.283149205 3.108126082 3.00159455 4.86418183 6.286204633 3.22306912 3.251627304 1 16.34046095 4.229296999 24.9374273 3.618573746 4.534637807 0.079029419 1.397519946 519.9639122 1399742.191 0.374175331 0.796491692 16954.96894 -4.229296999 0.916064061 FKAEAPLPS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FKAEAPLPSPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 FKAEAPLPS(1)PK;FKAEAPLPS(1)PK 94.017 0.0053402 3353500000 10012400 4033100 3089800 5590100 7065600 4608300 5882200 10032700 7021900 TRUE FALSE 8689235.972 4006606.301 4584037.615 6859417.644 6925008.384 4785584.283 5311745.149 7887285.18 6191778.981 1.403350475 0.647084838 0.740342578 1.10782663 1.118419828 0.772893267 0.8578706 1.273831835 1 22.56192254 1.74716966 25 1.145157121 0.935766225 0.100760291 0.229335422 3.920431464 11419.86012 0.11824413 0.056782169 55.86884073 -1.74716966 -0.209390896 FKDHVEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FKDHVEGK 8 1 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 94.692 0.0061163 687640000 2892000 2422000 1660900 1872200 2347600 1766700 2991800 3280800 2896400 FALSE TRUE 2509814.873 2406089.723 2464116.795 2297311.625 2300887.353 1834666.092 2701655.696 2579226.451 2553990.892 0.982703142 0.942090174 0.96481033 0.899498754 0.900898809 0.718352637 1.057817279 1.009880834 1 21.28432195 FKDIFQEIFDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FKDIFQEIFDK 11 1 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 180.09 6.22E-06 2072500000 4199000 3828500 3082500 5117700 4627100 3692600 4563700 6170200 4903300 FALSE TRUE 3644091.511 3803350.331 4573207.31 6279752.004 4535029.763 3834656.711 4121113.076 4850750.747 4323637.46 0.842830035 0.879664488 1.057722196 1.45242335 1.048892236 0.886905238 0.953158796 1.121914312 1 22.04381413 4.244199889 5.134520476 1.07890188 0.855965559 0.26129475 0.149650202 0.24076239 18.05840077 0.04050409 0.101230092 17546.87933 -4.244199889 -0.222936321 FKDIFQEIYDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FKDIFQEIYDK 11 1 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 204.85 2.90E-08 3790100000 7567500 5597200 4461300 4825900 4987600 4239700 7619600 8046500 6841200 FALSE TRUE 6567435.701 5560431.625 6618799.602 5921694.354 4888356.518 4402804.002 6880652.365 6325818.593 6032441.13 1.088686248 0.92175481 1.097200861 0.981641466 0.81034467 0.72985445 1.140608291 1.048633291 1 22.5243105 FKDLEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FKDLEDK 7 1 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 78.905 0.031071 287770000 842580 523780 451170 457600 448180 337520 689900 817300 718300 FALSE TRUE 731230.9182 520339.2547 669357.3211 561505.074 439262.0948 350504.6128 622993.6042 642526.7552 633383.3923 1.154483883 0.821523363 1.056796451 0.886516888 0.693516913 0.553384596 0.983596368 1.014435748 1 19.27271951 6.782845639 1.606254464 0.878701618 199.5345804 0.225659346 0.157437806 1791.579309 8.052961907 0.046208848 1308256.17 6065207.166 -6.782845639 198.6558788 FKDPNAPK ddPTM_MDA-MB-175_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 ; 88.819 0.013082 6574400000 27493000 20119300 14795200 17031700 18502800 13186400 25923000 28885000 25822000 FALSE TRUE 23859730.39 19987134.99 21950208.21 20899007.8 18134630.48 13693689.34 23408991.45 22708167.53 22769352.58 1.047887959 0.877808665 0.964024257 0.917856919 0.796449105 0.601408815 1.028092098 0.997312833 1 24.44058993 FKDPNCVGTVLASRPHTLDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FKDPNCVGTVLASRPHTLDGR 21 2 K7EQ55;K7EK33;Q96EP5;Q96EP5-2;K7EQ02 K7EQ55 DAZAP1 DAZ-associated protein 1 0 ; 188.86 1.42E-17 3620200000 2271290 1995390 1064970 1311030 1913800 1768160 2072740 2173770 1448080 FALSE TRUE 1971133.272 1982282.152 1579993.054 1608719.399 1875719.124 1836182.259 1871725.994 1708926.202 1276889.632 1.543699019 1.552430298 1.237376367 1.259873492 1.468975139 1.438011723 1.465847906 1.338350754 1 20.2842024 1.241866693 3.038344889 0.92384249 1.417020094 0.618534007 0.103882431 0.276626282 3.241772586 0.332780249 0.028605421 17.45286354 -1.241866693 0.493177604 FKEANNFLWPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FKEANNFLWPFK 12 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 95.508 0.0054791 1319220000 4900500 4316800 2101230 2271780 4217600 3579500 5461700 6180700 1084880 FALSE TRUE 4252886.509 4288442.657 3117391.856 2787622.371 4133678.012 3717205.681 4932025.175 4859005.403 956626.7223 4.445711592 4.482879849 3.258733823 2.914012651 4.321098204 3.885743096 5.155642279 5.079311805 1 19.86759657 4.338689419 24.78913924 3.871132281 4.464364073 0.051240736 1.194782912 46.62239876 11491.79607 0.300972096 0.796297333 21811.69512 -4.338689419 0.593231792 FKEIAEAYDVLSDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FKEIAEAYDVLSDPR 15 1 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 72.175 0.037871 41818000 109890 103860 57896 64982 87936 89416 96568 124640 77873 FALSE TRUE 95367.75807 103177.7368 85894.69925 79737.15629 86186.24564 92855.89138 87202.85022 97986.70595 68666.94265 1.388845264 1.502582361 1.250888651 1.161216055 1.255134455 1.352264828 1.269939317 1.426985128 1 16.06732811 4.230016065 24.99676847 1.263938281 1.445713819 0.331152487 0.116119203 201.4482205 589335.4381 0.029239284 0.062460861 16983.06472 -4.230016065 0.181775539 FKELSTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FKELSTLR 8 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3;A0A0D9SFF6 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 92.538 0.010676 1475320000 1843550 1916490 1089440 1359990 1980500 1986090 1938910 2110400 1355450 FALSE TRUE 1599920.197 1903900.451 1616296.828 1668796.516 1941091.925 2062496.167 1750874.807 1659107.383 1195210.245 1.338609841 1.592941877 1.352311725 1.39623679 1.624058974 1.725634612 1.46490947 1.388130155 1 20.18883299 1.194195552 2.132399953 0.806358276 1.505851269 0.618972871 0.122592707 0.554287275 2.285391959 0.790081374 0.034114544 15.63851648 -1.194195552 0.699492993 FKEYCPQVFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FKEYCPQVFR 10 1 Q8TBX8;F8VNT5;Q8TBX8-2;F8VU68 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 122.51 0.0004438 606440000 607080 590950 332160 377770 679860 665470 710540 749290 395690 FALSE TRUE 526852.8399 587068.0105 492793.687 463548.4524 666332.1161 691071.0615 641631.9402 589060.1645 348911.979 1.509987824 1.682567656 1.412372509 1.328554135 1.909742733 1.980645845 1.838950735 1.688277273 1 18.4125036 3.244207344 24.99942248 1.710630742 1.492527644 0.107714542 0.279731595 313.8045171 1389280.784 0.084037439 0.105472226 1754.71805 -3.244207344 -0.218103099 FKFPGR ddPTM_MDA-MB-175_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 90.285 0.044874 5217000000 4594100 4099700 3383700 3373000 3789600 3555400 4114700 4944700 4455000 FALSE TRUE 3986978.045 4072768.801 5020068.638 4138891.203 3714194.374 3692178.539 3715657.027 3887314.385 3928334.975 1.014928225 1.036767187 1.277912568 1.053599357 0.945488202 0.939883834 0.945860537 0.989557767 1 21.90548653 3.41313338 5.292369314 0.96599007 1.112218589 0.468537468 0.071546147 0.174194043 9.507341088 0.02113808 0.027684826 2589.007927 -3.41313338 0.146228518 FKGPEFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FKGPEFVR 8 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 102.61 0.0044983 711060000 1289210 1072410 586250 821650 1052800 915650 1093960 1287580 1065560 FALSE TRUE 1118837.632 1065365.268 869762.4609 1008218.191 1031851.34 950875.648 987867.9276 1012241.037 939590.7107 1.190771279 1.133861006 0.925682269 1.07303976 1.09819236 1.012010482 1.051381113 1.077321248 1 19.84167292 4.463587055 24.98821119 1.040868062 1.176543753 0.5514107 0.049141067 139.8016428 258116.048 0.011849808 0.031384451 29079.50806 -4.463587055 0.135675691 FKGPGDTSNFDDYEEEEIRVS(ph)INEK ddPTM_MDA-MB-175_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 304.89 6.89E-64 2093740000 1598899 1239575 1123458 974680 1190418 946978 1787044 1843382 1805539 TRUE FALSE 1387600.446 1231432.15 1666766.047 1195995.991 1166731.011 983408.8564 1613736.748 1449189.105 1592090.236 0.871558919 0.773468816 1.046904257 0.751211184 0.7328297 0.61768412 1.013596284 0.91024307 1 20.60249068 2.194677573 24.99999657 0.962827111 0.80388037 0.349590376 0.112438517 170.918197 97370.20277 0.047152299 0.031790267 156.5588322 -2.194677573 -0.158946741 FKIPGSPPESMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FKIPGSPPESMGR 13 1 P50395;P50395-2;Q5SX87;V9GYF8;Q5SX90;V9GYJ7;Q5SX86 P50395;Q5SX86 GDI2 Rab GDP dissociation inhibitor beta 0 ; 128.22 0.00015304 4380500000 2824900 2479900 1263990 1750310 2407200 2187000 2682000 3142700 1659160 FALSE TRUE 2451582.308 2463609.374 1875259.792 2147744.637 2359301.43 2271135.305 2421900.053 2470658.062 1463015.995 1.675704378 1.683925112 1.281776685 1.468025397 1.612628596 1.552365328 1.655415977 1.688743028 1 20.48051411 1.231761563 24.99978283 0.999999018 1.577209794 0.677979108 0.125041771 152.1443595 559375.8776 0.311700574 0.032579996 17.05145969 -1.231761563 0.577210776 FKLDLDFPNLPYLLDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FKLDLDFPNLPYLLDGK 17 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 158.65 3.02E-09 2451340000 5796000 4887000 3672100 4901100 4264200 3503600 7061400 7463900 6118200 FALSE TRUE 5030043.915 4854896.975 5447939.842 6013969.664 4179350.763 3638385.759 6376586.515 5867803.069 5394913.366 0.932367876 0.899902676 1.009828976 1.114748144 0.774683573 0.674410414 1.181962727 1.087654735 1 22.36316836 2.200385633 24.99999728 1.093247543 0.909862422 0.331472971 0.126000542 207.1044446 135626.9756 0.05454063 0.036772095 158.6301127 -2.200385633 -0.18338512 FKMPEMHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FKMPEMHFK 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 113.22 0.0011031 1208440000 3830800 2870600 1698940 2738700 2992900 2485900 2827600 4297500 2417300 FALSE TRUE 3324550.074 2851742.84 2520553.067 3360563.693 2933347.146 2581534.182 2553379.787 3378513.068 2131529.548 1.559701613 1.337885671 1.18250909 1.576597283 1.37617006 1.211118178 1.197909637 1.585018172 1 21.02345762 2.979949174 23.93271833 1.296046429 1.402702666 0.13747515 0.181220018 1285.737602 1534661.685 0.057770871 0.0585788 954.8808279 -2.979949174 0.106656237 FKMPEMNIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FKMPEMNIK 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 90.149 0.010603 649630000 900530 807900 456910 582040 767910 746190 674750 961560 559630 FALSE TRUE 781522.6788 802592.8517 677873.2043 714201.0779 752630.0934 774896.4121 609312.8489 755937.8769 493471.1789 1.583725073 1.626422952 1.373683476 1.447300488 1.525175381 1.570297203 1.234748603 1.531878475 1 18.9126063 0.850494497 2.100557767 3.29E-15 1.487212157 0.617670636 0.117999731 2.283931346 3.395190708 10.01149469 0.03107024 7.087523262 -0.850494497 1.487212157 FKNEEEVFAWNNEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FKNEEEVFAWNNEVK 15 1 P49419;P49419-2;A0A1B0GW77;A0A1B0GW82;A0A1B0GTG2;A0A1B0GUA1;A0A1B0GV49;A0A1B0GTJ4;A0A1B0GTY9;P49419-4 P49419 ALDH7A1 Alpha-aminoadipic semialdehyde dehydrogenase 0 ; 154.46 2.26E-06 939670000 1447680 1264460 1020700 1241150 1246220 1084280 1562750 1946250 1600960 FALSE TRUE 1256365.42 1256153.679 1514313.934 1522972.077 1221422.66 1125992.953 1411194.746 1530059.583 1411696.333 0.889968608 0.889818617 1.072690988 1.078824137 0.865216288 0.797616971 0.999644692 1.083844697 1 20.42899836 2.005233424 24.97809475 1.046061308 0.936925772 0.213193669 0.088875581 214.2125221 1022388.693 0.039508319 0.026542687 101.2123303 -2.005233424 -0.109135536 FKNELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FKNELER 7 1 P41091;Q2VIR3;Q2VIR3-2;H7BZU1 P41091 EIF2S3;EIF2S3L Eukaryotic translation initiation factor 2 subunit 3;Putative eukaryotic translation initiation factor 2 subunit 3-like protein 0 ;;; 127.02 0.0035526 2262130000 3130320 2886210 2034100 2610390 2899950 2500930 3335840 3496570 3237490 FALSE TRUE 2716640.281 2867250.296 3017797.564 3203118.947 2842246.669 2597142.395 3012330.75 2748855.716 2854757.62 0.951618541 1.00437609 1.057111659 1.122028338 0.995617508 0.909759335 1.055196675 0.962903364 1 21.44493683 3.019336862 24.98555821 0.982167109 1.036533593 0.167302053 0.055017963 420.0202219 542713.0518 0.016814476 0.019063545 1045.530875 -3.019336862 0.054366485 FKPNQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FKPNQTR 7 1 Q9NZJ9;A0A024RBG1;Q9NZJ9-2 Q9NZJ9 NUDT4 Diphosphoinositol polyphosphate phosphohydrolase 2 0 ; 105.57 0.0072026 2632500000 2266700 2233800 1407130 1791650 2093500 2168600 2618600 2873600 2825300 FALSE TRUE 1967149.852 2219126.021 2087622.775 2198471.516 2051843.446 2252027.445 2364648.575 2259103.002 2491296.253 0.789608964 0.890751559 0.837966489 0.882460893 0.823604757 0.903958107 0.949163943 0.906798218 1 21.24846516 -1.999999974 0.267521158 1.982181952 0.821124564 0.673210633 0.034749246 48.35839499 0.780777302 25.18822433 0.08940008 0.010000001 1.999999974 -1.161057388 FKVLANQYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FKVLANQYK 9 1 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 119.86 0.00069141 328070000 643710 978810 487770 553180 865610 905490 1133500 1228000 460890 FALSE TRUE 558642.0925 972380.1327 723657.2035 678787.9738 848386.0545 940324.7862 1023573.344 965401.7563 406404.1092 1.374597549 2.392643456 1.780634563 1.67022911 2.087543003 2.313767909 2.518609731 2.375472428 1 18.63255546 3.084199644 7.212423076 2.152100063 1.846151644 0.044612795 0.482370413 0.608291562 44.02204519 0.144500013 0.164150001 1213.946769 -3.084199644 -0.305948419 FKYDDAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FKYDDAER 8 1 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;E9PPR1;E9PL12;E9PMW7;E9PK06;H0YCK7;E9PIZ1;E9PK72;E9PKK3;E9PJD0;E9PNW6;P29692-3;E9PL71;E9PN91 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 ;;;; 128.86 0.0010174 4329450000 6029700 5398610 3479600 4545850 5384170 4734450 6032210 7175490 7741120 FALSE TRUE 5232859.868 5363146.175 5162346.199 5578054.721 5277035.551 4916587.355 5447207.203 5641067.303 6825973.612 0.766610035 0.785696881 0.756279835 0.817180821 0.773081739 0.720276349 0.798011758 0.826412117 1 22.70260341 1.099477995 1.769247359 1.152201566 0.77261153 0.886971638 0.025332134 0.426311615 0.919953282 0.310681199 0.006997731 12.57413141 -1.099477995 -0.379590036 FKYDDAERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 115.78 0.00079882 231710000 1007000 900130 413670 478620 812590 756390 960890 1114700 218490 FALSE TRUE 873922.3986 894216.9868 613722.1956 587297.9862 796421.0488 785488.8127 867703.0357 876330.0796 192660.3611 4.53607786 4.641416541 3.185513575 3.04835921 4.133808554 4.077064988 4.503796374 4.548574884 1 17.55570025 1.233286854 24.99998698 0.999995172 4.084017442 0.751946038 0.556727273 92.95444267 440596.0408 1.241253438 0.149533929 17.11145163 -1.233286854 3.08402227 FLAAGTHLGGTNLDFQMEQYIYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FLAAGTHLGGTNLDFQMEQYIYK 23 0 C9J9K3;A0A0C4DG17;P08865;F8WD59 C9J9K3 RPSA 40S ribosomal protein SA 0 ;; 333.28 1.29E-86 4344200000 1727468 1510841 975401 1434222 1510129 1377940 1640802 1985994 1985570 FALSE TRUE 1499178.727 1500916.186 1447108.186 1759884.026 1480080.387 1430950.243 1481677.275 1561304.638 1750838.177 0.856263444 0.857255802 0.826523094 1.005166582 0.845355332 0.817294404 0.846267402 0.89174697 1 20.73961432 1.25101551 3.19310452 1.02075532 0.866082546 0.397278774 0.051976842 0.361575237 4.957512945 0.138835305 0.013495144 17.82442421 -1.25101551 -0.154672774 FLALLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLALLR 6 0 I3L0N3;P46459;P46459-2;K7EQD6 I3L0N3 NSF Vesicle-fusing ATPase 0 ; 123.07 0.044078 75549000 115866 149934 87992 89918 142476 153499 125254 133113 163631 FALSE TRUE 100554.0145 148949.0737 130545.2255 110335.2562 139641.0063 159404.2059 113106.8864 104647.8208 144286.7296 0.696904108 1.032313049 0.904762523 0.764694415 0.967802145 1.104773851 0.783903597 0.725276823 1 17.13857909 FLATEGAPDFLCPEELEHVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FLATEGAPDFLCPEELEHVSR 21 0 A0A494C1T9;Q6ZRV2 A0A494C1T9 FAM83H Protein FAM83H 0 ;; 230.99 7.13E-26 405178000 653432 634486 225392 434219 683509 744987 621273 717568 687432 FALSE TRUE 567079.3056 630318.0197 334392.3251 532815.0606 669908.5082 773647.132 561022.0401 564121.6673 606164.5721 0.935520371 1.039846353 0.551652704 0.878994064 1.105159455 1.276298826 0.925527597 0.930641105 1 19.20935001 3.352136234 6.301183023 1.034491884 0.839153818 0.279247433 0.156299213 0.313398591 16.13028156 0.047838933 0.061854129 2249.760225 -3.352136234 -0.195338066 FLCADYAEQDELDYHR ddPTM_MDA-MB-175_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 ;;; 226.7 5.71E-15 993610000 852930 784630 431011 535589 720060 787020 693120 819970 727292 FALSE TRUE 740213.1395 779475.7139 639449.3612 657202.6684 705732.2148 817297.1687 625901.3291 644625.7965 641312.3683 1.154216223 1.215438455 0.997095008 1.024777785 1.10045003 1.274413545 0.975969528 1.005166637 1 19.29066771 FLDAGHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FLDAGHK 7 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 134.44 0.0031745 6753060000 14009790 12528500 9235620 11951880 12805830 14413590 13421830 13590620 13011470 FALSE TRUE 12158360.76 12446199.46 13701996.72 14665737.03 12551019.04 14968090.13 12120182.99 10684371.68 11473268.84 1.059712008 1.084799775 1.194253958 1.278252714 1.093935757 1.304605544 1.056384467 0.931240418 1 23.45177315 2.004830712 24.60431177 0.970639879 1.169121336 0.530423171 0.080308439 76.47141319 389490.1927 0.032784095 0.022010611 101.1185218 -2.004830712 0.198481457 FLDAYAEHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLDAYAEHK 9 0 P04062-4;P04062-5;P04062-2;P04062;A0A0G2JNZ5;A0A0G2JNZ0;A0A0G2JLB3;P04062-3 P04062-4 GBA Glucosylceramidase 0 87.913 0.013139 223710000 549720 416240 312070 384580 444700 420760 432550 515260 543560 FALSE TRUE 477073.1092 413505.692 462988.0958 471904.7669 435851.34 436946.9095 390601.3676 405075.6588 479300.956 0.995351883 0.862726616 0.965965308 0.9845688 0.909347946 0.911633712 0.81493968 0.845138433 1 18.87057229 2.770499849 2.503866507 0.87574738 0.945696518 0.151381944 0.060215975 0.456826805 5.66663505 0.022057765 0.02076438 589.5217725 -2.770499849 0.069949138 FLDFWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLDFWR 6 0 Q8TAT6;Q8TAT6-2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 106.76 0.074087 565710000 1065700 752300 460060 565280 769270 820590 756330 809650 775120 FALSE TRUE 924865.0449 747358.0918 682546.5548 693635.4638 753963.0321 852158.6283 682981.233 636512.6482 683486.1966 1.353158337 1.093450161 0.998625222 1.014849264 1.103113766 1.246782499 0.999261194 0.931273596 1 19.38255268 4.722913673 3.243961481 1.038429756 1.392134096 0.567796982 0.084590799 0.25844719 4.434479734 0.02368701 0.225664492 52834.02207 -4.722913673 0.35370434 FLDGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLDGDR 6 0 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 114.02 0.059648 287870000 580790 612470 403610 508340 586360 635230 584240 657300 907160 FALSE TRUE 504037.13 608446.6442 598797.146 623766.3665 574692.5832 659667.7091 527580.4947 516741.5101 799916.5782 0.630112119 0.760637622 0.748574492 0.779789272 0.718440646 0.824670631 0.659544394 0.64599425 1 19.60949003 FLDGIYVSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLDGIYVSEK 10 0 A0A2R8Y5Y7;P32969;D6RAN4;H0Y9R4;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 112.36 0.0037955 67352000 153692 141431 87149 116724 130042 123950 139252 166869 184311 FALSE TRUE 133381.2128 140501.9304 129294.5479 143227.9682 127454.4186 128718.4367 125747.3625 131185.3629 162521.9635 0.820696538 0.864510417 0.795551229 0.881283767 0.784228887 0.792006409 0.773725346 0.807185442 1 17.31027517 1.237296102 24.99973451 1.000000224 0.813953458 0.743528917 0.03416109 16.5535442 327133.1245 0.051037616 0.008437234 17.27014968 -1.237296102 -0.186046766 FLEDTFGNDGRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLEDTFGNDGRPR 13 1 O00754;O00754-2;M0R2P5 O00754;M0R2P5 MAN2B1 Lysosomal alpha-mannosidase;Lysosomal alpha-mannosidase A peptide;Lysosomal alpha-mannosidase B peptide;Lysosomal alpha-mannosidase C peptide;Lysosomal alpha-mannosidase D peptide;Lysosomal alpha-mannosidase E peptide 0 ; 186.51 7.07E-06 563380000 742760 698230 414680 552140 646960 752810 571330 720120 632720 FALSE TRUE 644602.3841 693643.2812 615220.635 677511.8259 634086.7618 781771.0878 515922.5045 566127.942 557920.5624 1.155365885 1.24326531 1.102702923 1.214351776 1.136518 1.401222935 0.924723947 1.01471066 1 19.0897002 2.212444367 24.99998763 0.9847868 1.202596392 0.625887306 0.083369997 139.5071786 133543.3134 0.031909348 0.021520979 163.0963969 -2.212444367 0.217809592 FLEEHPGGEEVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FLEEHPGGEEVLR 13 0 P00167-2;P00167;P00167-3 P00167-2 CYB5A Cytochrome b5 0 ;;; 184.98 9.05E-06 1304930000 1649320 1506700 960310 1481840 1902240 2078070 1130320 2119500 2038470 FALSE TRUE 1431358.183 1496802.388 1424719.128 1818314.421 1864389.146 2158014.698 1020701.74 1666261.419 1797484.399 0.796311881 0.832720656 0.792618355 1.01158843 1.037221323 1.200574925 0.567850125 0.926996318 1 20.77754782 3.753144093 24.01196029 0.94332315 0.809767314 0.163153726 0.158154747 1050.234802 1729222.118 0.043463195 0.074795303 5664.27191 -3.753144093 -0.133555836 FLEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FLEELR 6 0 Q5T508;D6R9F0;Q92535;Q9HBX8-1;O75473-3;O75473-2;O75473;Q9HBX8-2;Q9HBX8 REV__Q8IYE1 LGR6;PIGC;LGR5 Phosphatidylinositol N-acetylglucosaminyltransferase subunit C;Leucine-rich repeat-containing G-protein coupled receptor 6;Leucine-rich repeat-containing G-protein coupled receptor 5 0 ;;; 132.94 0.034151 310386000 896640 847410 560953 585198 874310 962910 809450 896950 919500 FALSE TRUE 778146.7522 841843.3079 832231.7471 718076.1501 856912.9416 999953.7708 730949.6636 705144.2226 810797.7575 0.959729778 1.038290129 1.026435679 0.88564151 1.056876309 1.233296172 0.901519099 0.869691876 1 19.62898257 FLEESVSMS(ph)PEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLEESVSMSPEER 13 0 A0A087WTB8;P15374;Q5TBK7 A0A087WTB8;Q5TBK7 UCHL3 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L3 1 FLEESVSMS(1)PEER;FLEESVSMS(1)PEER 251.68 1.02E-23 189449000 594570 545520 392180 461090 560750 612010 585700 636120 637330 TRUE FALSE 515996.0681 541936.4432 581839.5598 565787.5318 549592.1721 635554.4207 528898.9041 500090.6883 561985.5734 0.918166039 0.964324475 1.035328285 1.006765224 0.977947118 1.130908783 0.941125412 0.889863925 1 19.10017357 2.031721241 24.99998291 0.930593724 1.006529968 0.179490457 0.060719851 258.9795322 204104.5527 0.024575779 0.016568847 107.5774487 -2.031721241 0.075936244 FLEFQYLTGGLVDPEVHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLEFQYLTGGLVDPEVHGR 19 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 226.44 1.50E-19 845570000 758980 643190 388550 460570 640360 614310 600130 759950 622820 FALSE TRUE 658678.87 638964.8425 576454.0796 565149.4579 627618.0888 637942.9032 541929.485 597440.6064 549190.9291 1.199362253 1.163465761 1.04964239 1.029058253 1.142804907 1.161604953 0.986777924 1.087855925 1 19.06694827 4.34021554 4.515282301 1.068178646 1.190630723 0.431457789 0.055841737 0.197279864 6.787637155 0.014183196 0.040520282 21888.4768 -4.34021554 0.122452076 FLEGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FLEGVR 6 0 F8VWS0;P05388;F8VU65;F8VW21;Q8NHW5;F8VZS0 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 0 ;;;;; 145 0.026058 4450660000 5715350 5584300 3195730 4220720 5533540 5916590 5063520 5606230 5753030 FALSE TRUE 4960052.017 5547616.366 4741195.717 5179098.986 5423433.38 6144205.046 4572460.61 4407381.342 5072913.347 0.977752167 1.093576016 0.934610034 1.020931885 1.069096397 1.211178789 0.901348061 0.868806747 1 22.27438309 FLEHLSGAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLEHLSGAGK 10 0 Q01813 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 87.298 0.012971 319230000 563900 653200 219670 388810 806010 709910 628780 755430 793550 FALSE TRUE 489379.1863 648909.0862 325903.1468 477095.2531 789971.9779 737220.6971 567801.0124 593887.1733 699737.423 0.699375466 0.927360843 0.465750632 0.681820405 1.128954879 1.053567628 0.811448686 0.848728614 1 19.41645413 3.267211514 24.99259624 0.946033094 0.69400221 0.475881865 0.142302481 213.6842053 186398.4462 0.042891272 0.055362526 1850.169484 -3.267211514 -0.252030884 FLEIGKFDLSQNHPLGMAIFLK ddPTM_MDA-MB-175_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 ; 194.24 2.60E-18 1584090000 4002500 3944700 1121250 1467210 3148100 3053800 5588100 5626900 401410 FALSE TRUE 3473559.484 3918787.006 1663490.25 1800362.455 3085458.969 3171281.662 5046166.922 4423631.224 353955.7671 9.813541145 11.07140318 4.699712238 5.086405203 8.717075002 8.959542285 14.25649019 12.49769501 1 18.43320956 FLELGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLELGK 6 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 0 ; 102.98 0.081604 1979740000 3481800 3212200 3091900 3225100 3362200 3211800 4041100 4257800 5745000 FALSE TRUE 3021671.308 3191098.847 4587153.182 3957408.248 3295298.798 3335360.024 3649194.744 3347302.604 5065832.645 0.596480681 0.629925833 0.905508236 0.78119601 0.650494998 0.658403121 0.720354382 0.660760597 1 22.27236799 1.233527656 24.93635137 1.000000473 0.703330375 0.530145957 0.088604043 132.3303386 655565.8395 0.182587748 0.022491367 17.120942 -1.233527656 -0.296670098 FLEMCNDLLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLEMCNDLLAR 11 0 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 136.02 0.0002509 305420000 253090 241870 153924 184448 247970 265370 229200 264290 252860 FALSE TRUE 219643.5153 240281.14 228362.1612 226329.7375 243035.8821 275578.9556 206972.2193 207773.6402 222967.1789 0.985093485 1.07765251 1.024196307 1.015080958 1.090007432 1.235961979 0.928263166 0.93185751 1 17.76647183 FLEMHQL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLEMHQL 7 0 Q9Y617;Q9Y617-2 Q9Y617 PSAT1 Phosphoserine aminotransferase 0 114.59 0.033087 0 85011 118070 62567 66473 105010 108000 91567 105050 110090 FALSE TRUE 73776.58096 117294.3904 92824.61047 81566.71063 102920.5064 112154.8299 82686.84643 82585.875 97075.28561 0.759993447 1.208282723 0.956212592 0.840241778 1.060213275 1.155338655 0.851780614 0.850740479 1 16.56681643 FLENGS(ph)QEDLLHGNPGSTYLASNSTSAPNWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLENGSQEDLLHGNPGSTYLASNSTSAPNWK 31 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 FLENGS(1)QEDLLHGNPGSTYLASNSTSAPNWK;FLENGS(1)QEDLLHGNPGSTYLASNSTSAPNWK 364.27 4.73E-137 1308790000 1426380 1027110 606480 794470 947950 843770 1106050 1220720 1037470 TRUE FALSE 1237880.269 1020362.847 899775.7566 974866.5562 929087.6496 876230.3779 998785.4412 959678.5277 914821.4785 1.353138616 1.115368267 0.983553379 1.065635842 1.015594486 0.957815703 1.091781801 1.049033664 1 19.80313071 4.690754014 2.742167764 1.028362621 1.396958615 0.870881324 0.039919473 0.126986521 1.387088639 0.010017794 0.100276304 49062.99028 -4.690754014 0.368595994 FLENHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLENHEK 7 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ; 119.27 0.0048185 494290000 1144060 969000 587020 684540 955050 896930 991310 1101260 952900 FALSE TRUE 992869.5723 962634.5752 870904.8355 839975.2695 936046.3735 931435.4775 895172.9088 865764.119 840249.2475 1.181636967 1.1456536 1.036483922 0.999673932 1.114010368 1.108522834 1.065365915 1.030365837 1 19.68045782 4.338850096 4.408941997 1.052184482 1.17295935 0.598563193 0.038869097 0.150849036 5.031520688 0.010599732 0.030455451 21819.76636 -4.338850096 0.120774868 FLEPTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLEPTLR 7 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ; 158.38 0.0033101 147549000 308560 265000 161543 196263 266730 283250 246320 291750 284780 FALSE TRUE 267783.0142 263259.1976 239665.7351 240827.5138 261422.5948 294146.8108 222431.9243 229361.5329 251113.6328 1.066381826 1.048366807 0.954411485 0.959037991 1.041052976 1.171369342 0.885781954 0.913377463 1 17.93798083 2.184007903 24.99998632 0.926984317 1.032944458 0.363344483 0.066187435 102.8404596 47127.97986 0.028115366 0.018955387 152.7593858 -2.184007903 0.105960142 FLESAAADFS(ph)DEDEDDDVDGREK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLESAAADFSDEDEDDDVDGREK 23 1 O43815-2;O43815 O43815-2 STRN Striatin 1 FLESAAADFS(1)DEDEDDDVDGREK 263.18 7.21E-44 0 240520 211810 98188 95065 204330 138960 251360 261030 41458 TRUE FALSE 208734.6726 210418.6062 145672.0452 116650.9612 200264.2328 144305.8811 226983.1459 205210.7658 36556.88247 5.709859772 5.755923152 3.984804923 3.190943903 5.478154023 3.947434009 6.20904001 5.613464606 1 15.15785542 4.250811688 24.39651422 4.436974237 5.732892758 0.14363502 1.468898085 373.3277228 743417.1692 0.364267093 0.947613112 17816.06089 -4.250811688 1.295918521 FLEVDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLEVDER 7 0 Q92696;H0YLH3 Q92696 RABGGTA Geranylgeranyl transferase type-2 subunit alpha 0 ; 116.88 0.012459 134066000 843780 786150 541830 621080 837080 905190 826460 914240 890430 FALSE TRUE 732272.3351 780985.7289 803860.8003 762105.7066 820423.7457 940013.245 746310.0364 718736.8906 785164.3798 0.932635705 0.994677992 1.02381211 0.970632044 1.044906986 1.197218403 0.950514384 0.915396711 1 19.5826352 2.049493804 24.9999998 0.94604238 1.028058799 0.179565895 0.071713261 164.9780553 83331.88808 0.030162119 0.020335292 112.0711438 -2.049493804 0.08201642 FLEVQYLTGGLIEPDTPGRVPLDEALQR ddPTM_MDA-MB-175_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 ; 219.67 2.50E-34 400520000 90755 77527 49475 66909 77651 81051 99449 107466 44728.4 FALSE TRUE 78761.49681 77017.72003 73401.27548 82101.71109 76105.89702 84169.08442 89804.45129 84485.2322 39440.65951 1.996961962 1.952749295 1.861055986 2.081651578 1.929630437 2.134068889 2.276951055 2.142084672 1 15.26739606 1.235633519 25 0.999998579 2.05353665 0.881599373 0.120550198 29.21180616 249448.0039 0.225742273 0.033121438 17.20416183 -1.235633519 1.053538072 FLFEGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLFEGQR 7 0 B8ZZN6;P63165;B8ZZ67;P63165-2;G2XKQ0 B8ZZN6;G2XKQ0 SUMO1 Small ubiquitin-related modifier 1;Small ubiquitin-related modifier 0 92.677 0.036046 168390000 395370 420820 290940 288480 411920 494610 377140 433630 363140 FALSE TRUE 343120.8528 418055.6057 431639.5571 353983.7931 403723.5979 513637.9668 340565.0208 340901.599 320210.0029 1.071549451 1.305566978 1.347988986 1.105473876 1.260808826 1.604065963 1.063567714 1.064618831 1 18.28865885 2.04290161 24.99999342 1.045073945 1.282243246 0.381633177 0.144125232 139.3227711 81186.78301 0.058153359 0.039206955 110.3828518 -2.04290161 0.237169301 FLFENQTPAHVYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLFENQTPAHVYYR 14 0 O15042-2;O15042;E7ET15;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 ; 148.72 7.68E-06 1432860000 889310 853660 505600 643740 890300 854320 776750 894650 787200 FALSE TRUE 771785.4303 848052.2513 750109.8511 789911.0059 872584.7718 887186.2432 701420.9046 703336.0597 694138.1128 1.111861481 1.22173417 1.080634873 1.137973829 1.25707659 1.278111988 1.010491848 1.013250889 1 19.40486322 2.215337531 24.90866516 1.009133319 1.179981726 0.640632836 0.061185952 146.3589272 156980.6849 0.026092998 0.017604306 164.1865324 -2.215337531 0.170848406 FLGDIEVWDQAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLGDIEVWDQAEK 13 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 197.3 9.71E-07 0 74741 52613 41457 64757 57607 63045 39909 72417 89935 FALSE TRUE 64863.78748 52267.38174 61505.74387 79461.0666 56460.73341 65470.38195 36038.63132 56931.1881 79302.98675 0.817923639 0.659084656 0.77557916 1.001993366 0.711962257 0.825572713 0.454442295 0.717894627 1 16.27508758 FLGEVHCGTNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FLGEVHCGTNVR 12 0 Q9Y2J8 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ;;; 215.72 4.08E-11 3418280000 3067400 3409050 1782700 2074810 3285710 3289690 2938370 3287920 2337090 FALSE TRUE 2662035.318 3386655.726 2644819.683 2545927.322 3220330.799 3416246.503 2653407.33 2584823.895 2060801.883 1.291747324 1.643367931 1.283393472 1.235406151 1.562659092 1.657726796 1.28756061 1.254280635 1 20.97477439 1.428977816 1.661048535 0.940501965 1.438826615 0.453391929 0.152321163 0.625744116 2.284864921 0.466879947 0.044436272 26.85207282 -1.428977816 0.49832465 FLGMHPCER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FLGMHPCER 9 0 Q9Y678;H0Y8X7 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ;;; 117.89 0.0010783 1882990000 1687670 1646090 1029921 1175136 1816860 1994240 1678520 1866130 1600225 FALSE TRUE 1464640.133 1635276.726 1527994.24 1441968.59 1780708.041 2070959.703 1515737.389 1467072.622 1411048.223 1.037980212 1.158909171 1.082878824 1.021913047 1.261975325 1.467674647 1.074192479 1.039704099 1 20.42833586 2.015253751 24.9996351 1.032965997 1.173397361 0.205100737 0.127045989 393.2739082 644540.9014 0.055617546 0.037483543 103.574716 -2.015253751 0.140431364 FLGQNLS(ph)VRT(ph)GRYRS(ph)ILQLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLGQNLSVRTGRYRSILQLVK 21 3 O43692 O43692 PI15 Peptidase inhibitor 15 3 FLGQNLS(0.758)VRT(0.758)GRY(0.725)RS(0.758)ILQLVK 62.203 0.033876 250260000 161150 151750 78831 142230 156750 150440 125510 196410 180230 TRUE FALSE 139853.6192 150753.1443 116953.9353 174525.4953 153630.9817 156227.5241 113338.0595 154409.25 158923.4147 0.880006382 0.948589889 0.735913808 1.09817358 0.966698217 0.983036543 0.713161492 0.971595345 1 17.27797217 3.750509483 24.99646901 0.943602543 0.864212038 0.151874765 0.108973768 1862.217643 3895661.707 0.029085891 0.049864915 5630.01411 -3.750509483 -0.079390505 FLGTEPEPDAVGLDSGHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLGTEPEPDAVGLDSGHIR 19 0 Q16762 Q16762 TST Thiosulfate sulfurtransferase 0 ; 122.29 3.35E-05 182826000 193731 242089 102543 195958 256112 288004 178869 262907 221958 FALSE TRUE 168128.9575 240498.7014 152133.1378 240453.2589 251015.8723 299083.7002 161522.3119 206686.384 195718.3781 0.859035105 1.228799788 0.777306348 1.228567604 1.282536033 1.528132939 0.825279228 1.056039734 1 17.57841971 4.758388627 23.00459558 1.108579556 0.859034415 0.116888514 0.221029641 3715.107887 4310085.232 0.054472638 1.803771716 57330.88244 -4.758388627 -0.249545141 FLHKHDLDLICR ddPTM_MDA-MB-175_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 65.563 0.038977 246820000 899470 842670 286490 314990 774680 715140 860630 1000600 74772 FALSE TRUE 780602.7605 837134.4453 425037.5223 386513.2938 759265.3836 742651.8986 777166.2351 786629.4767 65932.53934 11.83941599 12.69683306 6.44655168 5.86225402 11.51579161 11.26381459 11.78729415 11.9308233 1 16.00870303 4.269911617 24.98056899 9.12747923 12.26812935 0.14915966 3.487659324 439.6147831 350279.3409 0.879452403 2.32630761 18617.08223 -4.269911617 3.140650123 FLHNPDAAQGFVGCALSSTIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLHNPDAAQGFVGCALSSTIQR 22 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 215.79 1.40E-25 720260000 423150 408340 190377 261790 377210 404720 357910 431160 364260 FALSE TRUE 367229.6554 405657.5877 282443.954 321233.4207 369704.259 420289.8403 323199.9433 338959.7893 321197.5978 1.143313829 1.262953367 0.879346408 1.000111529 1.151018132 1.308508666 1.006233999 1.055299889 1 18.29310158 FLIDGFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLIDGFPR 8 0 P30085;P30085-3;A0A494BXC7;P30085-2;Q5T0D2 P30085 CMPK1 UMP-CMP kinase 0 77.923 0.07435 326890000 595290 552860 317570 368400 534950 555510 516520 598720 502660 FALSE TRUE 516620.9182 549228.2263 471147.9142 452050.8506 524305.5416 576880.8292 466427.9699 470688.3872 443236.1074 1.165565958 1.239132411 1.062972773 1.019887241 1.182903497 1.301520385 1.052323947 1.061936019 1 18.75771589 2.040147195 24.99271247 1.04191296 1.157278694 0.345038951 0.08038701 187.8266798 116926.472 0.034853634 0.023498267 109.6849888 -2.040147195 0.115365734 FLISYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FLISYDR 7 0 Q8TBX8;Q8TBX8-3;F8VNT5;F8VU68 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 ;; 108.92 0.016619 1130210000 1994430 1873350 1196380 1401210 1773460 2072150 1820720 2082470 1696420 FALSE TRUE 1730861.022 1861043.841 1774953.37 1719376.147 1738171.616 2151866.951 1644146.855 1637149.996 1495871.16 1.157092314 1.24412041 1.186568347 1.149414597 1.161979495 1.438537629 1.099123306 1.094445859 1 20.51255449 2.023001909 24.9941327 1.066813564 1.220536771 0.433222581 0.086264792 216.7935657 235569.2805 0.034881697 0.023515784 105.4391531 -2.023001909 0.153723208 FLKNEVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLKNEVER 8 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 69.276 0.049557 1419240000 2199790 2103400 1370620 1226320 2051150 2052060 2446720 2844500 607700 FALSE TRUE 1909082.178 2089582.627 2033456.416 1504774.699 2010336.128 2131004.076 2209437.471 2236225.811 535858.3983 3.562661673 3.89950523 3.794764481 2.808157349 3.751618216 3.976804475 4.123174103 4.173165557 1 19.03149229 FLKPDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLKPDVR 7 1 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-6;B4DWJ1 E7ESA6 PTK2 Focal adhesion kinase 1 0 69.344 0.054714 638720000 1462300 1514000 908840 1146000 1456800 1368700 1585200 1794700 1832500 FALSE TRUE 1269053.35 1504054.434 1348358.064 1406216.816 1427812.53 1421354.775 1431467.548 1410917.371 1615863.938 0.785371417 0.930805125 0.834450248 0.870256946 0.883621756 0.879625284 0.885883715 0.873165951 1 20.62387429 1.235761466 5.991198769 1.005037749 0.870496895 0.549436029 0.037533705 0.099497269 13.42898718 0.054643523 0.008264145 17.20923107 -1.235761466 -0.134540854 FLKPDVRLS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLKPDVRLSR 10 2 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-6;B4DWJ1 E7ESA6 PTK2 Focal adhesion kinase 1 1 FLKPDVRLS(1)R 58.32 0.088099 360260000 790850 920350 271230 246830 911440 978130 1099400 1151300 31269 TRUE FALSE 686337.1687 914304.1603 402397.7352 302876.5241 893304.1272 1015759.294 992780.3572 905103.4544 27572.41444 24.89216787 33.16010508 14.59421467 10.98476612 32.39847309 36.83969339 36.00629025 32.82641266 1 14.75093799 -1.975782029 1.84E-13 8.639114582 43.14749739 0 12.18332362 0 0.113384762 11.35415671 11.35415702 0.010573481 1.975782029 34.50838281 FLKPVELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLKPVELR 8 1 A0A087X0K9;G5E9E7;Q07157-2;H0Y3R8;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 0 76.827 0.031733 345780000 568170 527360 309230 413510 532200 515620 470770 631860 559940 FALSE TRUE 493084.8949 523895.7374 458774.6623 507403.7656 521610.2612 535456.2351 425114.7979 496741.6561 493744.5311 0.998664013 1.061066411 0.929174165 1.027664579 1.056437547 1.084480336 0.861001532 1.006070194 1 18.91340524 2.26638653 24.99998416 0.96224071 1.024854687 0.250894367 0.057066039 324.4999021 291543.4508 0.021074179 0.016320463 184.6658247 -2.26638653 0.062613977 FLLDHQGELFPSPDPSGL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLLDHQGELFPSPDPSGL 18 0 Q07960 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 84.289 0.0090832 0 32450 25405 22241 26721 30779 28998 37136 32550 28818 FALSE TRUE 28161.65028 25238.11288 32996.82199 32788.41145 30166.55812 30113.57182 33534.55644 25589.4358 25411.16887 1.108239075 0.993189767 1.298516497 1.290314964 1.187137761 1.185052603 1.31967784 1.007015298 1 14.63317512 1.627675029 7.649390742 0.999831113 1.1957504 0.410617552 0.096517505 0.112520978 14.1600085 0.061952081 0.025914704 42.43019515 -1.627675029 0.195919287 FLLESFNNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLLESFNNDR 10 0 Q13618;Q13618-2;Q13618-3 Q13618 CUL3 Cullin-3 0 ; 147.4 6.27E-05 993320000 455150 387370 232680 314230 382570 417470 428700 413800 399620 FALSE TRUE 395000.7743 384825.341 345204.8263 385580.7242 374957.6055 433530.341 387124.74 325312.0902 352377.3788 1.120959511 1.092082988 0.979645252 1.094226665 1.064079671 1.230301282 1.098608376 0.923192321 1 18.42676179 1.75880335 12.03518908 0.962419995 1.096166901 0.441050397 0.063417646 0.199962888 115.5354899 0.035339039 0.016771276 57.38565596 -1.75880335 0.133746906 FLLSLPEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLLSLPEHR 9 0 Q15008;Q15008-4;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 149.72 8.70E-05 3085500000 3313300 3781000 1906390 2577700 3574900 3752800 3436200 3837500 3563500 FALSE TRUE 2875439.01 3756162.362 2828326.58 3163006.183 3503766.484 3897172.644 3102957.853 3016880.488 3142227.09 0.915095863 1.19538221 0.900102539 1.006612855 1.115058328 1.240258114 0.987502738 0.960108994 1 21.58335602 2.033441808 24.99699317 0.97618485 1.065101927 0.108011274 0.107559527 372.357455 278327.3277 0.043454484 0.02929682 108.0044895 -2.033441808 0.088917077 FLMECRNS(ph)PVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLMECRNSPVTK 12 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 FLMECRNS(0.989)PVT(0.011)K;FLMECRNS(0.974)PVT(0.026)K 137.93 5.05E-05 829080000 359420 327520 141094 143403 367920 365380 536210 548400 51672 TRUE FALSE 311921.7363 325368.4996 209327.5303 175964.8429 360599.1118 379436.405 484208.4367 431128.9277 45563.39502 6.845884425 7.141006489 4.59420397 3.861978301 7.914228332 8.327658745 10.6271369 9.462177422 1 15.47558763 6.087049385 17.22301187 6.965501352 6.67921087 0 2.853530858 0 0 0.663835168 0 1221938.602 -6.087049385 -0.286290483 FLMPEAYPS(ph)SPR ddPTM_MDA-MB-175_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(0.5)S(0.5)PR;FLMPEAYPS(0.608)S(0.392)PR;FLMPEAYPS(0.5)S(0.5)PR 172.09 3.85E-05 476956000 1138150 1141360 716490 909040 1119240 1212460 1038310 1190620 1377220 TRUE FALSE 987740.5938 1133862.331 1062986.961 1115451.426 1096969.314 1259104.121 937614.856 936015.1784 1214406.621 0.813352445 0.933676012 0.875313871 0.9185156 0.903296553 1.036806041 0.772076535 0.770759285 1 20.21182013 2.1994689 24.99996534 0.828453721 0.912440652 0.10704739 0.083779036 268.8588164 171938.9202 0.033400965 0.022519352 158.2956206 -2.1994689 0.083986931 FLMPEAYPSS(ph)PR ddPTM_MDA-MB-175_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(0.012)S(0.988)PR 163.51 6.27E-05 102290000 344120 348110 218480 285680 348240 362140 323820 354260 402280 TRUE FALSE 298643.6701 345823.2425 324137.6588 350548.0103 341310.7053 376071.7601 292415.9862 278504.2559 354722.9167 0.841906897 0.974910913 0.913777045 0.988230514 0.962189611 1.060184562 0.824350423 0.785131839 1 18.43633301 2.207206007 24.99980023 0.850287576 0.957395843 0.204676159 0.077759035 244.889615 195254.8252 0.030973879 0.020884823 161.1409825 -2.207206007 0.107108267 FLNDTTKPVGLLLSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLNDTTKPVGLLLSER 16 1 Q9P287-4;Q9P287-3;Q9P287;Q9P287-2 Q9P287-4 BCCIP BRCA2 and CDKN1A-interacting protein 0 93.152 0.0041303 374000000 195910 210450 126810 165110 233870 187060 197890 297270 251610 FALSE TRUE 170019.9971 209067.5401 188135.7402 202600.749 229216.4446 194256.3192 178698.6583 233701.1239 221864.9524 0.766322014 0.94231891 0.847974131 0.913171489 1.033134986 0.875561088 0.805438878 1.053348541 1 17.75932226 7.999965336 0.045840557 1.460928588 1.46E-06 0.269951295 0.081171725 1959.203521 8.810887698 82.66489773 236.4751464 99992018.6 -7.999965336 -1.460927124 FLNEHPGGEEVLLEQAGVDASESFEDVGHSSDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLNEHPGGEEVLLEQAGVDASESFEDVGHSSDAR 34 0 D6RFH4;H3BUX2;O43169 D6RFH4 CYB5B Cytochrome b5 type B 0 ; 157.26 7.96E-12 112733000 91486 93710 34293 76888 144987 140880 66373 130202 149168 FALSE TRUE 79395.8933 93094.41284 50877.2095 94346.59556 142102.0424 146299.7448 59936.15668 102359.3155 131533.529 0.603617146 0.707761843 0.386800308 0.717281717 1.080348436 1.112261991 0.45567208 0.778199417 1 17.00507108 3.47757476 24.99993854 0.855379306 0.575531796 0.345369148 0.199201383 21.45309181 1182674.104 0.060300336 0.078765969 3003.134341 -3.47757476 -0.279847511 FLPLFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLPLFDR 7 0 P61604;B8ZZL8;S4R3N1 P61604;S4R3N1 HSPE1;HSPE1-MOB4 "10 kDa heat shock protein, mitochondrial" 0 ; 139.27 0.0062933 2159630000 1014670 1061680 735960 1234720 1285070 1422700 919720 1210610 1127940 FALSE TRUE 880578.7887 1054705.754 1091872.718 1515082.048 1259499.621 1477432.19 830525.696 951730.4725 994596.2182 0.885363098 1.06043612 1.097805016 1.523313702 1.266342661 1.485459288 0.835038059 0.956901359 1 19.92375142 2.216115228 24.99969328 0.932132507 1.222911784 0.335058811 0.191976561 287.1113709 319782.52 0.082678942 0.055788638 164.480807 -2.216115228 0.290779276 FLPLNIRNS(ph)PFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLPLNIRNSPFTR 13 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 FLPLNIRNS(0.999)PFT(0.001)R 121.62 0.0001481 638770000 634420 564980 238200 223250 513110 574960 469520 503740 83625 TRUE FALSE 550579.7896 561268.6092 353394.3167 273942.3247 502900.1149 597079.0832 423986.0227 396019.1211 73738.94777 7.466607624 7.611562494 4.792505554 3.715028936 6.82000666 8.097201023 5.749824693 5.37055563 1 16.17013921 4.244685077 24.93475872 5.261383182 7.539086247 0.225785009 1.870906381 231.4138996 942137.8713 0.481367862 1.207035838 17566.49339 -4.244685077 2.277703065 FLPSELRDEH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLPSELRDEH 10 1 Q9Y490 Q9Y490 TLN1 Talin-1 0 166.86 4.94E-06 105460000 170760 214950 70313 68196 158050 183780 169560 190410 9382.9 FALSE TRUE 148193.6333 213537.9793 104316.602 83680.94411 154905.1142 190850.1355 153116.0973 149692.3033 8273.664251 17.91148744 25.80936001 12.60827111 10.11413342 18.72267348 23.06718399 18.50644317 18.09262483 1 13.0143107 1.238575192 12.16577753 0.978583406 18.11752399 0.592793818 4.45507863 0.044681338 385.2418072 6.324718662 1.132885384 17.32108895 -1.238575192 17.13894059 FLQDYFDGNLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLQDYFDGNLK 11 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 149.31 8.01E-05 489400000 1075820 976040 816360 1112290 1022750 1082270 1028790 1093520 1685440 FALSE TRUE 933647.6612 969628.329 1211154.427 1364852.445 1002399.276 1123905.627 929018.1041 859679.2578 1486189.203 0.628215882 0.6524259 0.814939594 0.918357126 0.67447622 0.756233207 0.62510083 0.578445366 1 20.50318636 4.383383279 7.650767057 0.743977476 0.634309791 0.127045229 0.12804518 0.521468526 35.98995298 0.033197376 0.088767563 24175.93498 -4.383383279 -0.109667685 ISHQSQDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISHQSQDK 8 0 Q9NRX4;Q9NRX4-2 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 98.582 0.009553 0 119720 115080 47822 90033 71403 90682 114330 131200 243890 FALSE TRUE 103898.6987 114324.0319 70948.87915 110476.3687 69982.22 94170.59522 103242.2942 103143.901 215057.602 0.483120325 0.53159726 0.329906399 0.513705945 0.325411515 0.437885452 0.480068099 0.479610579 1 17.7143636 1.224092114 3.984579908 1.072136868 0.44268947 0.864007684 0.068971183 0.088666021 2.396721388 0.16700917 0.016735732 16.75298168 -1.224092114 -0.629447398 FLQEHGS(ph)DSFLAEHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLQEHGSDSFLAEHK 15 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 1 FLQEHGS(0.573)DS(0.427)FLAEHK 117.66 0.00058942 131870000 94193 92897 48232 67158 91196 85701 91814 111480 104490 TRUE FALSE 81745.1564 92286.75349 71557.15653 82407.25035 89381.37802 88997.97293 82909.89241 87640.86954 92137.31124 0.887210136 1.001621952 0.77663604 0.894396084 0.970088847 0.965927611 0.899851442 0.951198471 1 16.49149788 3.269622417 10.43578665 0.952738092 0.889773885 0.244826152 0.058543203 0.726700775 237.5633984 0.01672616 0.021449519 1860.46891 -3.269622417 -0.062964207 FLQEHGSDS(ph)FLAEHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLQEHGSDSFLAEHK 15 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 1 FLQEHGS(0.001)DS(0.999)FLAEHK;FLQEHGSDS(1)FLAEHK 204.31 8.30E-09 402020000 517770 473070 236928 361370 468500 415290 500430 600470 603930 TRUE FALSE 449345.3826 469962.372 351507.1733 443424.5817 459177.7666 431266.475 451898.3756 472064.1634 532534.0834 0.843787086 0.882501959 0.660065119 0.832668923 0.862250475 0.809838259 0.848581133 0.886448733 1 19.02251434 -1.296306495 0.729117103 9.999999985 0.809414978 0.492237292 0.059618712 92.59992104 1.39348851 1336.97283 0.024258002 0.050546781 1.296306495 -9.190585007 FLQEHGSDSFLAEHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FLQEHGSDSFLAEHK 15 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ;;;;; 270.26 2.11E-27 2277960000 2162370 2245708 547704 1541359 2683900 2065024 2518169 2954323 2413260 FALSE TRUE 1876607.326 2230955.796 812575.4864 1891348.119 2630495.641 2144466.81 2273957.358 2322564.017 2127967.152 0.881877958 1.048397666 0.381855277 0.888805129 1.236154251 1.007753718 1.068605479 1.091447307 1 21.02104445 3.468286581 22.93371012 1.076187531 0.771287614 0.400744281 0.17545027 69.37280512 180080.7388 0.049320933 0.063812042 2939.588779 -3.468286581 -0.304899916 FLQHGTLVGLLPVPHPILIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLQHGTLVGLLPVPHPILIR 20 0 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 0 ; 229.6 1.30E-25 279650000 272390 283920 130051 192162 284030 294350 302580 334770 308540 FALSE TRUE 236392.9714 282054.9108 192944.0986 235795.3191 278378.3587 305673.835 273235.8382 263182.0407 272064.7527 0.868884959 1.036719781 0.709184474 0.866688231 1.023206262 1.123533394 1.004304437 0.967350743 1 18.05359053 3.23832314 24.99857117 1.020177587 0.870738306 0.434814774 0.086801622 6.443220381 678274.072 0.02616693 0.031575648 1731.103923 -3.23832314 -0.14943928 FLQPVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLQPVHK 7 0 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ; 83.614 0.02215 1394400000 2299400 2148800 1253540 1626940 2202520 2094370 2239690 2575100 2554400 FALSE TRUE 1995528.464 2134684.391 1859756.137 1996361.593 2158694.161 2174941.769 2022485.209 2024434.904 2252421.742 0.885947967 0.94772855 0.82566959 0.886317849 0.958388086 0.965601481 0.897915861 0.898781461 1 21.10304555 3.255907531 24.07619704 0.936074476 0.886456395 0.310047403 0.041836526 233.0998229 323521.5774 0.012350036 0.01589981 1802.633888 -3.255907531 -0.04961808 FLRPHYGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLRPHYGK 8 1 Q13200;C9JPC0;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 127.12 0.00071504 2274900000 4202400 4100900 2395600 3161100 4380600 3856500 4517500 4882200 4806600 FALSE TRUE 3647042.192 4073960.918 3554120.173 3878876.069 4293434.63 4004862.05 4079393.545 3838179.523 4238369.224 0.860482417 0.961209537 0.838558414 0.915181256 1.012992121 0.944906364 0.96249131 0.905579321 1 22.01507784 3.467287578 24.98180835 0.957212388 0.891308355 0.412804455 0.042695833 219.5014463 557626.7154 0.01181475 0.015272426 2932.834646 -3.467287578 -0.065904034 FLRT(ph)AEADGGLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FLRTAEADGGLAR 13 1 Q8NC60 Q8NC60 NOA1 Nitric oxide-associated protein 1 1 FLRT(1)AEADGGLAR;FLRT(1)AEADGGLAR;FLRT(1)AEADGGLAR;FLRT(1)AEADGGLAR 87.001 0.013852 560921000 27006.1 29108.5 22828.2 17320.7 30625.7 36009.6 25275 26432.6 26055.8 TRUE FALSE 23437.17546 28917.28435 33867.99388 21253.62967 30016.30849 37394.91261 22823.83439 20780.19419 22975.51301 1.020093673 1.258613217 1.474090866 0.925055717 1.306447803 1.627598592 0.993398249 0.904449628 1 14.48780945 2.030656012 24.99966218 0.946456708 1.267537789 0.340455792 0.199180441 205.8852569 167896.4719 0.080444045 0.054234776 107.3139084 -2.030656012 0.321081081 FLSAIVSSVDKIPYGMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLSAIVSSVDKIPYGMR 17 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 243.83 1.61E-20 879200000 891880 909110 438690 571000 837540 803390 997710 1073640 280370 FALSE TRUE 774015.7983 903137.9966 650841.9513 700654.2772 820874.5926 834296.9332 900952.2378 844050.4411 247224.978 3.130815521 3.653101737 2.632589784 2.834075597 3.320354599 3.374646607 3.644260564 3.414098559 1 17.91546499 1.236236351 24.9999425 0.999997063 3.262941853 0.827993187 0.322314414 26.27661592 282567.6379 0.54286569 0.083483073 17.22805904 -1.236236351 2.26294479 FLSAQSHSTS(ph)PQGLDSPLPLEGSGAHQVLHNESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNESK 34 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 FLS(0.002)AQS(0.013)HS(0.071)T(0.41)S(0.503)PQGLDSPLPLEGSGAHQVLHNESK;FLSAQSHS(0.024)T(0.161)S(0.815)PQGLDSPLPLEGSGAHQVLHNESK;FLSAQS(0.001)HS(0.002)T(0.01)S(0.987)PQGLDSPLPLEGSGAHQVLHNESK;FLSAQS(0.012)HS(0.056)T(0.2)S(0.732)PQGLDSPLPLEGSGAHQVLHNESK 248.02 6.57E-48 1249257000 600596 515084 190461 413048 571996 540805 630110 699088 670711 TRUE FALSE 521225.7169 511700.3793 282568.5767 506836.8614 560614.3987 561610.1183 569002.0292 549593.4715 591420.3097 0.881311833 0.865205964 0.47777963 0.85698251 0.947911983 0.949595591 0.962094165 0.929277305 1 19.17382426 3.482619298 18.98003378 0.949430963 0.739405151 0.449313989 0.109309628 9.507317217 32820.64863 0.030981371 0.041637298 3038.220557 -3.482619298 -0.210025812 FLSCTVEADGIHLVTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLSCTVEADGIHLVTER 17 0 Q8IZE3;Q8IZE3-2;X6RHX1 Q8IZE3 SCYL3 Protein-associating with the carboxyl-terminal domain of ezrin 0 ; 205.12 8.17E-12 128936000 86979 75410 49647 57931 90106 80460 83286 86682 73467 FALSE TRUE 75484.50477 74914.62674 73656.45526 71085.11897 88313.06689 83555.34826 75208.93654 68145.72886 64781.81495 1.16521133 1.156414447 1.13699277 1.097300516 1.363238541 1.289796347 1.16095754 1.051926824 1 15.98330127 1.709174605 2.913198655 1.010881188 1.200449141 0.469351449 0.076746727 0.213533123 3.951157586 0.067216728 0.022793324 51.18875948 -1.709174605 0.189567953 FLSDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLSDFR 6 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 110.24 0.067171 633070000 1166560 1210290 734900 922140 1200310 1390490 1104230 1288050 1261100 FALSE TRUE 1012396.14 1202339.525 1090300.098 1131525.981 1176426.179 1443983.05 997141.9446 1012610.531 1112014.195 0.910416562 1.081226778 0.980473184 1.017546347 1.057923707 1.298529333 0.896698935 0.910609357 1 20.08474377 FLSDLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLSDLRR 7 1 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4;P53992;G5EA31 A0A0A0MTR7;P53992 RNF213;SEC24C E3 ubiquitin-protein ligase RNF213;Protein transport protein Sec24C 0 ; 130.77 0.0056624 739960000 1156930 1427070 784460 790850 1556170 1821700 1492070 1565260 538650 FALSE TRUE 1004038.769 1417695.483 1163827.48 970424.5799 1525205.262 1891781.978 1347369.281 1230541.33 474971.4106 2.113893061 2.98480172 2.450310595 2.043122087 3.211151719 3.982938626 2.836737645 2.59076926 1 18.85748115 4.762600463 21.92447018 2.678720193 2.113889508 0.040973669 0.773528525 4509.841052 4112641.503 0.191932244 8.75558782 57889.58858 -4.762600463 -0.564830684 FLSDPQVHTVLVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FLSDPQVHTVLVER 14 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 220.14 4.75E-12 1362780000 2347120 2335290 1164960 1645140 2493860 2739840 2234290 2579440 2751520 FALSE TRUE 2036942.145 2319949.326 1728338.553 2018694.181 2444237.065 2845243.418 2017608.9 2027846.829 2426238.44 0.839547388 0.95619181 0.712353132 0.832026296 1.007418325 1.172697362 0.831578985 0.835798657 1 21.21028991 3.255270593 24.62314456 0.952602118 0.834921432 0.257510638 0.11142622 358.4643792 528214.8679 0.034914008 0.044942383 1799.992076 -3.255270593 -0.117680686 FLSHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLSHFK 6 0 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 0 113.07 0.026452 204780000 556740 614260 427010 463870 602270 582070 663560 712910 765860 FALSE TRUE 483165.3984 610224.8856 633513.4643 569198.7733 590286.0053 604462.6095 599208.0533 560459.7444 675320.9033 0.715460452 0.903607282 0.938092485 0.842856738 0.874082236 0.895074633 0.887293804 0.82991618 1 19.36521369 4.741368024 24.85561962 0.889643981 0.715460383 0.580578545 0.048021203 177.9010531 1574972.352 0.011210662 0.075333622 55127.46523 -4.741368024 -0.174183598 FLSHS(ph)TDSLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FLSHSTDSLNK 11 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;A0A087WY36 Q12802-2 AKAP13 A-kinase anchor protein 13 1 FLS(0.153)HS(0.844)T(0.003)DSLNK;FLS(0.003)HS(0.996)T(0.001)DSLNK;FLS(0.063)HS(0.935)T(0.003)DSLNK;FLS(0.007)HS(0.968)T(0.024)DSLNK;FLS(0.004)HS(0.963)T(0.033)DSLNK 184.21 3.23E-06 3171790000 3309260 3176990 1633910 2186810 3295430 2820180 3307780 3776290 3590540 TRUE FALSE 2871932.906 3156120.144 2424074.341 2683358.634 3229857.39 2928674.149 2986992.005 2968759.771 3166070.452 0.907096968 0.996857206 0.765641314 0.847535983 1.020147037 0.925018629 0.943438262 0.93767963 1 21.59426193 3.252507535 24.9987912 0.958161297 0.879563779 0.310904153 0.063111331 330.6628384 592684.6403 0.018556084 0.023830844 1788.576559 -3.252507535 -0.078597518 FLSLYGDQIDMHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FLSLYGDQIDMHR 13 0 Q96CN7;D6RGE2 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 ;; 184.21 9.70E-06 1078369000 1112110 1058390 673440 946960 1098020 1213910 984160 1200580 1610450 FALSE TRUE 965141.8458 1051437.366 999117.8365 1161981.741 1076171.55 1260609.903 888716.3147 943845.3099 1420064.436 0.679646516 0.740415252 0.703572184 0.818259871 0.757832901 0.887713171 0.625828161 0.664649636 1 20.43752496 3.768153903 23.14553196 0.771198494 0.711131675 0.101144145 0.10682821 914.2354788 715036.146 0.028776933 0.049829394 5863.459137 -3.768153903 -0.060066819 FLSNGHVTIPGQQDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLSNGHVTIPGQQDK 15 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 119.56 0.000203 1631540000 1836700 1801940 879320 1917680 1940130 1730640 2095480 2374690 5792300 FALSE TRUE 1593975.441 1790102.937 1304562.093 2353118.554 1901525.209 1797218.841 1892260.672 1866881.023 5107540.893 0.312082757 0.350482351 0.255418825 0.460714579 0.372297599 0.351875566 0.370483705 0.36551465 1 22.28419742 1.238126787 7.266026143 1.012004041 0.355776246 0.94021585 0.05113117 0.022760907 7.726462544 0.073357014 0.012302353 17.30321431 -1.238126787 -0.656227795 FLSNGHVTIPGQQDKDMFQETMEAMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FLSNGHVTIPGQQDKDMFQETMEAMR 26 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 169.01 5.21E-12 2925530000 4210320 3922410 1556901 3040440 4107130 3897420 4591230 5158880 3470900 FALSE TRUE 3653915.544 3896643.43 2309823.531 3730818.372 4025406.148 4047356.269 4145973.221 4055693.658 3060574.156 1.193866039 1.273173997 0.754702684 1.218992967 1.315245422 1.322417319 1.354639035 1.325141445 1 21.54537089 3.492164434 24.72319915 1.279718099 1.076008154 0.213941161 0.16499364 841.0517493 1382251.759 0.0452755 0.064615311 3105.735269 -3.492164434 -0.203709944 FLSPVVPNYDNVHPNYHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLSPVVPNYDNVHPNYHK 18 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ; 123.97 1.90E-05 888610000 1624270 1499040 1070020 1390630 1584780 1463810 1538510 1914370 2661950 FALSE TRUE 1409618.604 1489192.708 1587485.251 1706393.796 1553245.979 1520123.718 1389305.537 1504996.873 2347257.304 0.600538595 0.634439482 0.676314969 0.726973474 0.661728042 0.647616994 0.591884637 0.641172517 1 21.16254457 1.237878218 24.99987469 1.000000405 0.648083254 0.895665519 0.037800337 5.416101524 198272.9456 0.058107172 0.010016698 17.29331364 -1.237878218 -0.351917151 FLSQIESDR ddPTM_MDA-MB-175_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 ;;;;; 191.17 8.42E-05 1887320000 2366330 2280900 1439110 2125880 2423180 2770400 1880350 2399730 2768810 FALSE TRUE 2053613.495 2265916.618 2135068.41 2608593.546 2374963.459 2876979.081 1697993.946 1886566.414 2441484.436 0.84113315 0.928089725 0.874496015 1.068445699 0.97275388 1.178372894 0.695476048 0.772712857 1 21.21932715 2.216898846 24.99997961 0.807007293 0.974257352 0.263483267 0.120740475 301.2230148 347640.664 0.049462516 0.033380475 164.7778555 -2.216898846 0.16725006 FLSQPFQVAEVFTGHMGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FLSQPFQVAEVFTGHMGK 18 0 P06576 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 ;;; 296.16 2.48E-49 2052870000 2380690 2316860 1621040 2860800 2712990 2540680 2342520 3172110 2645240 FALSE TRUE 2066075.785 2301640.394 2404980.366 3510388.365 2659006.807 2638421.604 2115342.771 2493778.962 2332522.741 0.885768764 0.986760109 1.03106406 1.50497498 1.139970368 1.131145072 0.906890524 1.069133826 1 21.15345972 2.273175761 24.70283001 1.004529333 1.122810063 0.104539534 0.164403664 392.7204252 280260.3327 0.064910257 0.050276701 187.5753479 -2.273175761 0.11828073 FLSVLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLSVLER 7 0 P07099 P07099 EPHX1 Epoxide hydrolase 1 0 77.058 0.090912 106740000 63016 61117 52898 57377 83762 83609 54600 87212 78064 FALSE TRUE 54688.27594 60715.5184 78479.64973 70405.3248 82095.30008 86825.49233 49304.9004 68562.39248 68835.36285 0.794479373 0.882039636 1.140106574 1.022807491 1.192632634 1.261350108 0.716272834 0.996034446 1 16.07086229 7.420803918 6.324572952 1.002238919 0.004972607 0 0.170701474 0 0 0.039059923 0 26351413.61 -7.420803918 -0.997266312 FLTAFLVQISAHSDQNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLTAFLVQISAHSDQNK 17 0 Q07960 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 138.55 3.29E-06 25327000 73403 72954 29486 53766 60209 51654 85079 101510 78810 FALSE TRUE 63702.60757 72474.76037 43745.52822 65974.39206 59010.9587 53641.1628 76828.05167 79802.87645 69493.17158 0.916674345 1.042904774 0.629493909 0.949365104 0.849161973 0.771891131 1.105548213 1.148355653 1 16.0845836 2.225898785 24.92844157 1.098781326 0.861336343 0.459798069 0.114474264 180.2427384 354856.4178 0.04525285 0.030739408 168.2281948 -2.225898785 -0.237444983 FLTAVNLEHPEMLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLTAVNLEHPEMLEK 15 0 Q9Y2Q3-3;Q9Y2Q3;Q9Y2Q3-2;E9PFN5;Q9Y2Q3-4;C9JNT3 Q9Y2Q3-3 GSTK1 Glutathione S-transferase kappa 1 0 ; 133.87 3.87E-05 1118010000 1035680 983310 676270 906210 1074380 954300 979980 1259990 1135700 FALSE TRUE 898812.2639 976850.5719 1003316.434 1111978.831 1053001.94 991012.5385 884941.6904 990550.9438 1001438.84 0.897520875 0.97544706 1.001874897 1.11038117 1.051489016 0.989588679 0.883670231 0.989127747 1 19.93364288 4.69777622 2.772597355 1.000634847 0.88338619 0.25881251 0.05636063 0.637349451 7.120067169 0.015915168 0.162486265 49862.74923 -4.69777622 -0.117248657 FLTLPPVLHLQLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLTLPPVLHLQLMR 14 0 Q93009;A0A669KBL1;Q93009-3;H3BND8;F5H2X1 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 148.68 7.69E-06 102767000 177840 246220 123407 163866 251310 224290 226546 238030 223894 FALSE TRUE 154337.9934 244602.5646 183087.038 201074.2798 246309.4227 232918.5814 204575.6038 187129.1369 197425.5064 0.781753058 1.238961313 0.927372766 1.018481773 1.247606893 1.179779582 1.036216685 0.947846812 1 17.59094887 4.764411021 23.98679664 1.065186885 0.781752418 0.392937995 0.113840778 5832.038413 5411441.098 0.029008784 2.065997741 58131.43188 -4.764411021 -0.283434468 FLTPIYHPNIDSAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FLTPIYHPNIDSAGR 15 0 Q9NPD8 Q9NPD8 UBE2T Ubiquitin-conjugating enzyme E2 T 0 168.41 1.26E-06 549270000 269490 298240 147280 212890 299560 306210 246770 316810 251530 FALSE TRUE 233876.2137 296280.8418 218505.1006 261229.9283 293599.3421 317990.0968 222838.2834 249062.6469 221794.4099 1.054472986 1.335835479 0.985169557 1.177802129 1.323745455 1.433715561 1.004706491 1.122943752 1 17.75886348 FLTWILNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLTWILNR 8 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 170.32 0.00068835 618210000 603360 564180 274760 386250 501510 561120 574960 555860 532160 FALSE TRUE 523624.4473 560473.8644 407634.855 473953.966 491530.9322 582706.6495 519200.4677 436993.6647 469248.651 1.115878428 1.194406981 0.868696914 1.010027338 1.047485019 1.24178652 1.106450635 0.931262485 1 18.83999307 1.745106854 11.39773946 0.967119094 1.081405815 0.186373708 0.102295128 0.154921458 128.5568017 0.058464441 0.027527963 55.60410485 -1.745106854 0.114286721 FLVHNVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLVHNVK 7 0 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ; 99.171 0.010725 4590300000 8813500 8217000 5287000 6669200 7670800 7334400 8978900 10075400 9698700 FALSE TRUE 7648773.644 8163021.986 7843810.884 8183543.792 7518166.088 7616559.114 8108127.66 7920854.117 8552130.735 0.894370524 0.954501543 0.917176213 0.956901157 0.879098592 0.890603681 0.948082754 0.926184873 1 23.02785248 0.441768711 1.419310791 1.501218809 0.919498281 0.459593594 0.027000616 9.49708534 2.935705564 13.78300769 0.007634883 2.76546847 -0.441768711 -0.581720528 FLVYVANFDEKDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLVYVANFDEKDPR 14 1 P50395;P50395-2;Q5SX87;Q5SX86 P50395;Q5SX86 GDI2 Rab GDP dissociation inhibitor beta 0 ; 84.892 0.0072533 8526900000 4040600 3204290 2357920 2883920 2932380 2414020 3656600 4463800 3814900 FALSE TRUE 3506624.472 3183240.808 3498217.999 3538758.114 2874031.375 2506888.911 3301983.495 3509251.107 3363906.868 1.042426146 0.946292788 1.039927125 1.051978623 0.854373051 0.745231366 0.981591829 1.043206975 1 21.68170633 3.260142854 24.98591161 0.934942275 1.016292426 0.223730691 0.086939706 498.8928215 577567.9742 0.02872677 0.037051397 1820.299517 -3.260142854 0.081350151 FLWESYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLWESYR 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 149.4 0.004697 1312400000 753270 1354970 729710 860240 1460470 1428360 1295010 1474870 1522800 FALSE TRUE 653723.461 1346069.113 1082600.197 1055570.64 1431409.504 1483309.933 1169420.13 1159480.528 1342776.319 0.486844646 1.002452228 0.806240162 0.786110557 1.066007409 1.104658991 0.870897195 0.863494919 1 20.35678757 4.74443356 24.8029131 0.928990146 0.486844431 0.635465549 0.107092337 416.1544322 1757468.274 0.02736443 0.23916828 55517.96768 -4.74443356 -0.442145716 FLYDDNQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLYDDNQR 8 0 Q02880;Q02880-2;E9PCY5;P11388;P11388-2;P11388-3;P11388-4 Q02880;P11388 TOP2B;TOP2A DNA topoisomerase 2-beta;DNA topoisomerase 2;DNA topoisomerase 2-alpha 0 ; 138.55 0.0016298 800250000 1190550 1101150 598760 921510 1104930 1018700 810790 1089390 902770 FALSE TRUE 1033215.801 1093916.473 888322.3387 1130752.93 1082944.055 1057890.048 732159.7106 856432.4261 796045.559 1.297935513 1.374188274 1.115918968 1.420462582 1.360404618 1.328931537 0.91974599 1.075858557 1 19.60249148 2.247795318 24.99574584 1.011361083 1.316568182 0.743568177 0.087862433 92.31494215 249870.9991 0.032140936 0.024543588 176.9274906 -2.247795318 0.305207099 FLYQLHETEKEDLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLYQLHETEKEDLIR 15 1 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 148.91 2.07E-06 315970000 511550 442740 257160 307350 398610 350630 419680 526380 507200 FALSE TRUE 443947.3714 439831.6118 381523.4361 377138.5151 390678.4409 364118.963 378979.4982 413817.7333 447239.3938 0.992639239 0.983436651 0.853063128 0.843258712 0.87353316 0.814147788 0.847375038 0.925271206 1 18.77068774 4.248336825 24.49345988 0.878040262 0.988038051 0.432416265 0.051665395 154.9819292 388283.4152 0.013754275 0.035391478 17714.8233 -4.248336825 0.109997788 FLYTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FLYTGR 6 0 U3KQ56;Q9UBQ7;Q9UBQ7-2 U3KQ56 GRHPR Glyoxylate reductase/hydroxypyruvate reductase 0 ; 126.05 0.041086 426780000 467890 439780 274190 335010 448780 449850 364760 442910 381720 FALSE TRUE 406057.151 436891.0562 406789.2011 411079.1408 439850.156 467156.0206 329385.6313 348197.1432 336593.4965 1.206372539 1.297978306 1.208547418 1.221292583 1.306769622 1.387893781 0.978585846 1.03447377 1 18.36064778 2.226330513 24.99995469 1.009554611 1.269143214 0.836250991 0.055699576 86.14816708 176096.8452 0.023097461 0.015700325 168.3955121 -2.226330513 0.259588604 FMELLEPLNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FMELLEPLNER 11 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 100.48 0.0093063 26793000 31782 32300 20306 21776 31060 33121 27804 30624 28478 FALSE TRUE 27581.92817 32087.81917 30126.04952 26720.57363 30441.96677 34395.1863 25107.57236 24075.29592 25111.36328 1.09838434 1.277820675 1.199697889 1.064082954 1.212278538 1.369706054 0.999849036 0.958741094 1 14.61605273 2.106705307 9.087580234 0.977396484 1.200686307 0.59438283 0.084768334 0.178765061 13.92188216 0.034540226 0.023268322 127.8513468 -2.106705307 0.223289822 FMEQSRS(ph)PSVSPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FMEQSRSPSVSPSK 14 1 Q96JG6;Q96JG6-3;H0Y7Q2 Q96JG6 CCDC132 Coiled-coil domain-containing protein 132 1 FMEQS(0.04)RS(0.959)PS(0.001)VSPSK;FMEQS(0.029)RS(0.672)PS(0.299)VSPSK 117.26 0.00019007 578570000 607470 552990 292350 351050 532230 476060 597130 665190 215810 TRUE FALSE 527191.3004 549357.3723 433731.4379 430761.268 521639.6643 494374.3363 539220.4245 522944.295 190297.1877 2.770357812 2.886839154 2.279231991 2.263623931 2.741184306 2.597906687 2.833570118 2.74804006 1 17.53789472 1.23628462 24.9954437 0.999997873 2.640733312 0.85335368 0.213669245 23.55155849 258586.9095 0.360816292 0.055659364 17.22997391 -1.23628462 1.640735439 FMERDPDELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FMERDPDELR 10 1 A0A087WTB8;P15374;Q5TBK7 A0A087WTB8;Q5TBK7 UCHL3 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L3 0 ;;; 186.87 1.18E-06 1728820000 2617420 2510640 1319330 1610490 2434790 2527510 2243990 2665620 1468650 FALSE TRUE 2271521.315 2494147.441 1957362.401 1976176.369 2386342.443 2624744.945 2026368.195 2095597.907 1295027.87 1.754032765 1.925941131 1.511444229 1.525972077 1.84269582 2.026786454 1.56472941 1.618187496 1 20.30455172 0.920090229 1.581229659 4.70E-08 1.744841664 0.650834263 0.168371484 1.707705393 1.955620256 6.006109759 0.049178674 8.319365968 -0.920090229 1.744841617 FMFNIADGGFTELHSLWQNEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FMFNIADGGFTELHSLWQNEER 22 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y4X2;A0A2R8Y7I0;A0A2R8Y7M9 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 270.47 2.66E-45 63953000 38215 35420 23787 28155 34519 34237 40593 42777 34937 FALSE TRUE 33164.79093 35187.32369 35290.47276 34548.02307 33832.13944 35554.11954 36656.29711 33629.47144 30806.78766 1.076541679 1.142193859 1.145542117 1.121441919 1.098204065 1.154100192 1.189877293 1.091625385 1 14.91096063 1.323567366 3.44815484 0.992478518 1.132860133 0.646095434 0.030946921 0.162433674 2.77197993 0.052155473 0.007942933 21.06528631 -1.323567366 0.140381615 FMGVQMETFMLHYQDLLQLQYEGVAVMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FMGVQMETFMLHYQDLLQLQYEGVAVMK 28 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 147.28 6.17E-08 28235000 18523 18223 12541 14255 14327 10387 19873 24363 18995 FALSE TRUE 16075.13862 18103.29191 18605.86955 17491.81562 14041.92073 10786.59461 17945.71952 19153.16204 16749.43274 0.959742271 1.080830151 1.110835802 1.044322867 0.838352018 0.643997608 1.071422525 1.143511087 1 14.03182462 3.444496883 24.94242268 0.95838331 1.057517932 0.123796127 0.139433107 504.0859122 385388.8463 0.046201314 0.059645998 2782.895402 -3.444496883 0.099134621 FMHVLYPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FMHVLYPR 8 0 B1AV70;Q96EC8-2;Q96EC8 B1AV70 YIPF6 Protein YIPF;Protein YIPF6 0 78.496 0.029156 0 51151 92027 45297 58764 84624 106200 62864 85868 98557 FALSE TRUE 44391.26575 91422.46858 67202.78071 72107.26435 82940.14796 110285.5827 56767.45896 67505.79643 86905.70374 0.51079807 1.051973169 0.773283891 0.829718433 0.954369442 1.269025829 0.653207517 0.776770609 1 16.40716325 4.754140829 23.93548074 0.896036934 0.510797552 0.343974786 0.173302846 2053.025698 3153914.901 0.042854242 0.967511766 56772.8673 -4.754140829 -0.385239382 FMKPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FMKPGK 6 1 P61353;K7EQQ9;K7ERY7 P61353 RPL27 60S ribosomal protein L27 0 65.619 0.094454 1221700000 1343500 1104200 843360 1105000 1111200 995460 1434300 1591400 1858600 FALSE TRUE 1165953.071 1096946.437 1251211.717 1355907.139 1089089.294 1033755.99 1295201.807 1251091.494 1638878.425 0.711433535 0.669327523 0.763456091 0.827338452 0.664533304 0.630770394 0.790297674 0.763382735 1 20.64427741 0.774829274 1.458504854 1.602690789 0.718491396 0.680157338 0.05944311 2.473449491 1.783158645 4.52875781 0.017612763 5.95428028 -0.774829274 -0.884199394 FMLLFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FMLLFSR 7 0 A0A2R8YGH5;H7C1E4;P61966;P61966-2 A0A2R8YGH5 AP1S1 AP-1 complex subunit sigma-1A 0 ; 126.24 0.023473 34046000 113930 232520 107417 107399 211890 205379 234880 233400 143389 FALSE TRUE 98873.86184 230992.5608 159364.2205 131785.5844 207673.8036 213280.063 212101.3738 183489.2263 126437.7158 0.781996584 1.826927665 1.260416795 1.042296467 1.642498856 1.686838945 1.677516653 1.45122225 1 16.94806735 3.223207993 24.994744 1.510269963 1.273018285 0.133144126 0.323488638 537.2617458 874683.6825 0.096160017 0.10942294 1671.891129 -3.223207993 -0.237251678 FMQDPMEIFVDDETKLTLHGLQQYYVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FMQDPMEIFVDDETKLTLHGLQQYYVK 27 1 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;H0YCC6 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 82.342 0.0060777 157590000 110300 107670 55844 71222 102120 81602 112370 126330 25899 FALSE TRUE 95723.57554 106962.7087 82850.34519 87394.04366 100088.0118 84741.28174 101472.3747 99315.3126 22837.24972 4.191554442 4.683694839 3.627860018 3.826819986 4.382664857 3.710660555 4.443283492 4.34882982 1 14.4791013 1.236462194 24.99998289 0.999995963 4.158311849 0.894940241 0.339383658 16.57831598 197459.061 0.527119208 0.082367224 17.23702034 -1.236462194 3.158315886 FMRDPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 FMRDPIR 7 1 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3KTB5;Q14240;Q14240-2;E7EQG2;J3KTN0 P60842;Q14240;J3KTN0 EIF4A1;EIF4A2 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ;;;;;;; 101.64 0.0081246 4007630000 2776757 4568748 2380782 2912583 4653144 4784060 4166951 4338560 3544967 FALSE TRUE 2409801.527 4538735.594 3532136.138 3573929.486 4560555.538 4968105.884 3762840.733 3410792.707 3125885.04 0.770918155 1.45198417 1.129963544 1.143333629 1.458964575 1.589343761 1.203768112 1.09114464 1 21.57583329 1.6923692 3.125954195 1.024600917 1.271889437 0.12642966 0.225968377 0.405177532 8.922789517 0.175773636 0.060143652 49.24580037 -1.6923692 0.247288521 FMSAYEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FMSAYEQR 8 0 Q15428 Q15428 SF3A2 Splicing factor 3A subunit 2 0 ; 98.299 0.017729 463760000 414640 515710 281350 349350 528260 538460 459080 496340 489160 FALSE TRUE 359844.2734 512322.2671 417411.8011 428675.257 517748.6595 559174.9046 414558.4923 390201.5535 431332.0621 0.834262753 1.187767644 0.967727275 0.993840465 1.200348189 1.296390771 0.961112166 0.904643053 1 18.71843943 2.03226163 24.99977384 0.941720115 1.085341604 0.162947339 0.132613386 296.2729843 229582.9153 0.053998948 0.0364058 107.7113899 -2.03226163 0.143621489 FMSVQRPGPYDRPGTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FMSVQRPGPYDRPGTAR 17 2 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 191.36 1.39E-10 8810700000 1786950 1651410 952320 1172850 1656410 1670740 1614840 1965580 1367530 FALSE TRUE 1550800.03 1640561.779 1412865.137 1439163.518 1623450.682 1735014.449 1458233.065 1545256.013 1205862.161 1.286050827 1.360488646 1.171663879 1.193472658 1.346298718 1.438816562 1.209286693 1.281453273 1 20.20163358 1.223856645 4.676695735 0.97392185 1.286175417 0.546134437 0.081821508 0.179944288 8.595710305 0.188163049 0.021181917 16.74390092 -1.223856645 0.312253568 FNADEFEDMVAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 FNADEFEDMVAEK 13 0 P27635;X1WI28;A0A087WV22;F8W7C6 P27635;F8W7C6 RPL10 60S ribosomal protein L10 0 ;;;;;; 223.31 3.72E-11 874652000 1121232 954988 810319 991851 976093 830793 1168594 1347693 1773038 FALSE TRUE 973058.3504 948714.6209 1202191.979 1217065.929 956670.659 862754.1443 1055263.934 1059499.34 1563431.467 0.622386315 0.606815611 0.768944468 0.778458125 0.611904442 0.551833683 0.674966544 0.677675588 1 20.57628455 1.233908976 4.892498496 1.024423856 0.661549572 0.696510075 0.070274122 0.114716828 6.679928048 0.143437466 0.018875916 17.13598114 -1.233908976 -0.362874284 FNADEFEDMVAEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FNADEFEDMVAEKR 14 1 P27635;X1WI28;A0A087WV22;F8W7C6 P27635;F8W7C6 RPL10 60S ribosomal protein L10 0 ;;;;; 200.77 3.01E-08 4637730000 3968610 3677754 1801930 2097119 3246354 2963305 3803660 4497620 1371617 FALSE TRUE 3444148.133 3653594.592 2673349.375 2573301.921 3181757.907 3077305.261 3434781.639 3535838.964 1209466.001 2.84766015 3.020832822 2.210355126 2.127634774 2.63071298 2.544350365 2.839915828 2.923471153 1 20.20593878 4.246854327 24.99163883 2.417877509 2.934246681 0.163333922 0.542393185 369.5742871 1113622.068 0.133986306 0.342087381 17654.45548 -4.246854327 0.516369171 FNAHGDANTIVCNSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FNAHGDANTIVCNSK 15 0 P09382 P09382 LGALS1 Galectin-1 0 ;; 212.02 1.09E-09 2572370000 3388600 3241400 2065880 2922490 3599400 3336900 3676800 4709300 4024000 FALSE TRUE 2940787.924 3220107.03 3064946.478 3586086.022 3527778.982 3465272.702 3320224.502 3702252.843 3548287.304 0.828790814 0.907510231 0.863781936 1.010652666 0.994220219 0.976604318 0.935725948 1.043391508 1 21.7586914 3.741181706 24.97634588 0.99436151 0.87077591 0.769328654 0.032686521 109.0776907 1039397.018 0.008849779 0.014464523 5510.381992 -3.741181706 -0.123585601 FNAHHGDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FNAHHGDTK 9 0 P53602 P53602 MVD Diphosphomevalonate decarboxylase 0 132.88 0.0001693 132510000 325280 215590 175240 224340 184010 217970 266980 284600 297650 FALSE TRUE 282293.4238 214173.7751 259986.6501 275279.8258 180348.561 226355.4469 241088.3207 223740.5048 262462.1561 1.07555858 0.816017739 0.990568141 1.048836259 0.6871412 0.862430799 0.918564125 0.852467678 1 18.00174989 4.755662433 23.60604468 0.894564678 1.075558897 0.226336186 0.103659613 2503.250969 3455173.648 0.024808981 0.651126867 56972.12686 -4.755662433 0.180994219 FNALFVRPHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FNALFVRPHIR 11 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 83.862 0.0098487 274910000 168660 196290 98144 111730 182480 188840 185700 195120 98693 FALSE TRUE 146371.1537 195000.5581 145606.7667 137100.0042 178849.005 196104.797 167690.8426 153395.1064 87025.62597 1.681931638 2.240725716 1.673148168 1.575398081 2.055130348 2.25341438 1.926913374 1.762642954 1 16.40915267 1.214361864 2.739097397 0.760837252 1.921467761 0.60926622 0.228514756 0.351076981 2.909174304 0.96363425 0.060768637 16.38180923 -1.214361864 1.160630508 FNDEHIPESPYLVPVIAPSDDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 FNDEHIPESPYLVPVIAPSDDAR 23 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;;;;;;; 166.79 1.16E-11 8658250000 10094530 9987140 5980980 7732070 10215700 10605420 9666750 11031790 10982270 FALSE TRUE 8760512.284 9921533.82 8873401.933 9487754.671 10012427.56 11013417.37 8729270.073 8672727.558 9683958.552 0.904641654 1.024532867 0.916299041 0.979739289 1.033918878 1.137284646 0.901415472 0.895576691 1 23.20716547 FNDFDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FNDFDHR 7 0 Q9NWH9;Q9NWH9-3;H7C3F4;H0YMM0 Q9NWH9 SLTM SAFB-like transcription modulator 0 ;;; 141.93 0.0025235 1066180000 2435680 2121690 1193440 1543170 2120730 2100590 1998430 2285260 2100370 FALSE TRUE 2113798.717 2107752.479 1770591.576 1893570.334 2078531.622 2181401.057 1804622.566 1796574.933 1852066.651 1.141318924 1.138054334 0.956008562 1.02240939 1.122276901 1.177819953 0.974383165 0.970037947 1 20.82070459 2.200356283 24.96132339 0.978795652 1.086927908 0.400053576 0.064058591 177.6787259 116087.6135 0.028079507 0.018931609 158.6193927 -2.200356283 0.108132256 FNDILGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FNDILGR 7 0 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2;A0A087WY74 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 ;;; 149.4 0.0046968 835790000 1585000 1517740 903930 1166810 1521080 1510590 1424650 1682300 1573390 FALSE TRUE 1375538.234 1507769.866 1341073.571 1431752.044 1490813.484 1568703.375 1286487.662 1322553.237 1387385.627 0.991460635 1.086770568 0.966619191 1.031978432 1.074548745 1.130690231 0.927274752 0.953270101 1 20.40393741 2.213322966 24.99986026 0.957370582 1.045732787 0.407609272 0.049290189 220.780685 218698.6761 0.020171075 0.013605301 163.4266828 -2.213322966 0.088362205 FNDPHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FNDPHVK 7 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 62.2 0.086891 186770000 639810 514010 318630 394140 525780 482820 576320 609040 602270 FALSE TRUE 555257.4874 510633.4345 472720.5338 483635.5111 515318.0067 501394.3978 520428.5751 478801.5356 531070.3267 1.045544177 0.961517541 0.890127936 0.910680727 0.970338542 0.944120529 0.97996169 0.9015784 1 19.0185434 4.699349205 3.866224453 0.939996494 1.052034793 0.454948865 0.035028275 0.189030316 5.406368601 0.008376496 0.055244166 50043.67611 -4.699349205 0.112038299 FNDS(ph)EGDDT(ph)EETEDYR ddPTM_MDA-MB-175_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 344.46 3.95E-72 778680000 1257000 1086870 855480 957230 1206410 1182010 1152450 1307690 1617280 TRUE FALSE 1090884.265 1079730.279 1269192.989 1174583.702 1182404.801 1227482.69 1040685.576 1028050.67 1426087.001 0.764949309 0.757127916 0.889982861 0.823640985 0.829125292 0.860734786 0.72974901 0.720889167 1 20.44363057 FNDS(ph)EGDDTEETEDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 FNDSEGDDTEETEDYR 16 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 FNDS(0.994)EGDDT(0.006)EETEDYR;FNDS(1)EGDDTEETEDYR;FNDS(1)EGDDTEETEDYR;FNDS(1)EGDDTEETEDYR;FNDS(1)EGDDTEETEDYR;FNDS(1)EGDDTEETEDYR;FNDS(1)EGDDTEETEDYR 440.58 6.66E-182 17468480000 4933987 4175981 2830066 3443638 3763176 4022377 3984092 4331820 5270562 TRUE FALSE 4281948.117 4148548.706 4198695.384 4225568.641 3688296.16 4177120.446 3597715.371 3405494.003 4647482.165 0.92134794 0.892644352 0.903434426 0.909216752 0.793611687 0.898792141 0.774121394 0.73276107 1 22.1480179 3.25081165 24.67706191 0.82448679 0.905429256 0.152101587 0.073533751 301.1398768 606577.0212 0.021244929 0.027215562 1781.605932 -3.25081165 0.080942466 FNDYFEFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FNDYFEFPR 9 0 Q93008;Q93008-3;O00507;O00507-2 Q93008 USP9X;USP9Y Probable ubiquitin carboxyl-terminal hydrolase FAF-X;Probable ubiquitin carboxyl-terminal hydrolase FAF-Y 0 83.862 0.036949 79115000 241600 237060 106820 140390 277420 265510 243160 284970 162610 FALSE TRUE 209671.9479 235502.7373 158478.5093 172267.6952 271899.8848 275724.3415 219578.3806 224031.3831 143386.431 1.462285841 1.642433915 1.105254578 1.201422575 1.896273467 1.922945843 1.531374894 1.562430849 1 17.12954898 3.26408158 24.99984087 1.593258301 1.355848588 0.136644887 0.286230781 486.7381243 476795.9413 0.08605084 0.111049009 1836.883358 -3.26408158 -0.237409713 FNEEHIPDSPFVVPVAS(ph)PSGDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FNEEHIPDSPFVVPVASPSGDAR 23 0 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5C6 Q60FE5 FLNA Filamin-A 1 FNEEHIPDSPFVVPVAS(0.902)PS(0.098)GDAR;FNEEHIPDSPFVVPVAS(0.911)PS(0.089)GDAR;FNEEHIPDSPFVVPVAS(0.963)PS(0.037)GDAR;FNEEHIPDSPFVVPVAS(0.989)PS(0.011)GDAR;FNEEHIPDSPFVVPVAS(0.961)PS(0.039)GDAR 165.98 8.05E-12 1728990000 548332 560515 370152 444100 559763 598599 557939 657524 598609 TRUE FALSE 475868.5369 556832.9401 549158.7453 544939.6926 548624.8115 621627.4909 503830.1617 516917.6095 527842.126 0.901535731 1.054923267 1.04038446 1.03239144 1.039372919 1.177676923 0.954509193 0.979303439 1 19.00974697 4.745161567 24.07252822 1.031422909 0.90153563 0.331157726 0.05935441 613.5889441 2237550.877 0.015192331 0.140782021 55611.11042 -4.745161567 -0.129887279 FNEEHIPDSPFVVPVASPSGDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FNEEHIPDSPFVVPVASPSGDAR 23 0 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5C6 Q60FE5 FLNA Filamin-A 0 ;;;;; 187.21 2.50E-17 2985670000 2032440 1664930 996473 1286310 1699460 1753700 1631160 1869850 1680350 FALSE TRUE 1763847.904 1653992.965 1478370.676 1578386.346 1665644.071 1821165.974 1472970.354 1469997.129 1481700.937 1.190420995 1.116279894 0.997752406 1.065252984 1.124143226 1.229104962 0.994107729 0.992101099 1 20.49882286 2.151648522 24.99826278 0.994657949 1.112378156 0.467000311 0.06259634 21.99187604 6321.479296 0.026991517 0.018197682 141.7909531 -2.151648522 0.117720207 FNEGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FNEGER 6 0 P35579 P35579 MYH9 Myosin-9 0 ;;;;; 138.25 0.028816 13892460000 9485430 9457810 5667860 6896870 8331990 9279540 9651000 10069940 9610790 FALSE TRUE 8231906.392 9395681.023 8408856.054 8462909.746 8166199.7 9636529.908 8715047.505 7916561.695 8474613.355 0.971360704 1.108685509 0.992240672 0.99861898 0.963607348 1.137105553 1.028371106 0.934150192 1 23.01471612 1.757630208 25 0.964731293 1.030778025 0.162334813 0.057851964 12.7198265 16695.71881 0.029869925 0.014344525 57.23085153 -1.757630208 0.066046732 FNENNRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FNENNRR 7 1 P17931;G3V3R6 P17931 LGALS3 Galectin-3;Galectin 0 ;;;;; 119.41 0.0076786 4280880000 2384920 2279720 1273137 1553781 1942130 2182900 1766058 2361890 2092380 FALSE TRUE 2069746.779 2264744.369 1888830.312 1906590.724 1903485.413 2266877.576 1594785.967 1856818.204 1845021.22 1.12180107 1.227489605 1.023744492 1.033370621 1.031687545 1.228645801 0.864372696 1.006393956 1 20.81520598 7.999999938 0.130515475 0.86653777 1.886372399 0.246284311 0.095050933 252.3385937 2.881062552 2.527739938 46.88281362 99999985.84 -7.999999938 1.019834629 FNEVAAQYSEDKAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FNEVAAQYSEDKAR 14 1 Q9Y237;Q9Y237-2;H0Y4T6;J3KMW3;H0Y610;H0Y8P6;A0A494C021;Q9Y237-3 Q9Y237 PIN4 Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4 0 146.2 7.63E-06 126380000 212550 174160 83265 102890 183260 148370 212000 238140 57185 FALSE TRUE 184460.979 173015.9315 123532.2325 126252.7471 179613.4845 154077.8899 191440.2726 187215.6142 50424.65445 3.658150581 3.431177336 2.449837959 2.50379003 3.562017162 3.055606263 3.796560923 3.712779319 1 15.62184167 1.231768153 24.96987319 0.999996059 3.274256216 0.691984018 0.476212266 148.0977345 544373.2885 1.214204352 0.126976219 17.05171845 -1.231768153 2.274260158 FNEYWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FNEYWR 6 0 Q99584 Q99584 S100A13 Protein S100-A13 0 ;;;;; 128.48 0.038633 10463470000 11700030 13707160 9076990 11182700 14313480 14019010 11923930 13794350 19929850 FALSE TRUE 10153841.39 13617116.76 13466652.72 13721902.95 14028669.75 14558330.39 10767549.1 10844535.6 17573765.84 0.577784038 0.774854797 0.766292942 0.780817446 0.798273397 0.828412676 0.612705848 0.617086611 1 24.06692004 4.742582946 23.81999688 0.755340718 0.577783903 0.225439192 0.109366668 362.1403634 2144403.102 0.02724936 0.199770967 55281.89811 -4.742582946 -0.177556815 FNFESFPES(ph)PGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FNFESFPESPGEK 13 0 H0YBR0;Q96Q05-3;Q96Q05;Q96Q05-2 H0YBR0 TRAPPC9 Trafficking protein particle complex subunit 9 1 FNFESFPES(1)PGEK;FNFESFPES(1)PGEK;FNFESFPES(1)PGEK;FNFESFPES(1)PGEK 257.46 7.02E-24 295278000 386840 329361 323962 416415 390249 320610 397903 454981 1029128 TRUE FALSE 335718.1139 327197.4059 480631.1068 510968.3903 382483.8084 332944.0742 359314.4283 357686.8538 907465.6602 0.369951315 0.360561749 0.529641096 0.563071874 0.42148571 0.366894406 0.395953747 0.394160208 1 19.79148352 1.236631357 24.99949913 1.000000725 0.425999536 0.873874643 0.068624765 18.4233974 238666.2875 0.115719176 0.018292371 17.24373566 -1.236631357 -0.574001189 FNFLNPNDPYHAYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FNFLNPNDPYHAYYR 15 0 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 ; 206.43 3.90E-09 1904330000 928550 883970 481840 606770 826800 856130 745690 933190 920640 FALSE TRUE 805839.7649 878163.1429 714859.4357 744546.4024 810348.2976 889065.8751 673373.0986 733634.5806 811802.988 0.992654347 1.081744162 0.880582415 0.917151591 0.998208075 1.095174431 0.829478468 0.903710126 1 19.63077012 4.244958509 24.99906184 0.9423908 1.037199251 0.195386056 0.07633874 243.4896699 951383.2201 0.019737207 0.049620427 17577.55678 -4.244958509 0.094808451 FNGGHS(ph)PTHSPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FNGGHSPTHSPEK 13 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 FNGGHS(0.974)PT(0.026)HSPEK;FNGGHS(0.5)PT(0.5)HSPEK 155.92 3.02E-05 1721590000 1348710 1077840 725300 928520 1310910 1072640 1420440 1519510 1488740 TRUE FALSE 1170474.556 1070759.598 1076057.506 1139354.658 1284825.456 1113905.155 1282685.947 1194574.611 1312742.853 0.89162516 0.815665913 0.819701668 0.867919147 0.978733537 0.848532637 0.977103737 0.90998371 1 20.32415291 3.40724473 5.830863437 0.936299406 0.840210324 0.503780822 0.046692466 0.159649203 9.76265487 0.012612625 0.016418555 2554.140188 -3.40724473 -0.096089082 FNGGHSPT(ph)HS(ph)PEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FNGGHSPTHSPEK 13 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 2 FNGGHS(0.369)PT(0.631)HS(1)PEK 113.33 0.0014736 490240000 595940 494000 361900 364540 550950 500950 636390 646680 650130 TRUE FALSE 517185.0191 490754.8815 536916.0505 447314.3786 539987.1729 520221.8707 574672.9958 508392.5145 573272.372 0.902162819 0.856058839 0.936581068 0.780282463 0.941938247 0.907460216 1.002443208 0.886825424 1 19.12886123 3.085104213 25 0.942261733 0.87125634 0.35397009 0.052672604 28.19661805 8278.963074 0.014667613 0.01663151 1216.47787 -3.085104213 -0.071005393 FNGGHSPT(ph)HSPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FNGGHSPTHSPEK 13 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 FNGGHS(0.319)PT(0.681)HSPEK;FNGGHS(0.352)PT(0.648)HSPEK 152.37 0.00015725 1708210000 1884550 1697700 1025300 1490510 1687270 1644160 2029460 2106990 2350000 TRUE FALSE 1635501.943 1686547.697 1521138.509 1828953.077 1653696.628 1707411.899 1832643.282 1656426.585 2072185.677 0.789264186 0.813897961 0.734074425 0.882620267 0.798044618 0.823966654 0.884401095 0.799362047 1 20.98272185 0.05224532 1.777287373 9.999999998 0.814622126 0.613451196 0.045120641 41.69394288 3.189737824 1475.533256 0.011920248 1.127834357 -0.05224532 -9.185377872 FNGS(ph)TEALDKLDADAVSPTVSQLSAVFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FNGSTEALDKLDADAVSPTVSQLSAVFEK 29 1 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 1 FNGS(0.557)T(0.443)EALDKLDADAVSPTVSQLSAVFEK;FNGS(0.998)T(0.002)EALDKLDADAVSPTVSQLSAVFEK;FNGS(0.968)T(0.032)EALDKLDADAVSPTVSQLSAVFEK 349.7 3.90E-120 2905377000 3887700 2199672 1741311 1853625 1982494 1545861 2878740 3319670 2855010 TRUE FALSE 3373930.595 2185222.21 2583414.824 2274518.887 1943046.248 1605331.273 2599560.238 2609784.404 2517493.97 1.340194112 0.868014873 1.026185109 0.903485337 0.771817637 0.637670355 1.032598397 1.036659644 1 21.26355689 4.742571738 24.54456594 0.915906221 1.340194326 0.526339358 0.128260256 288.7797689 1766990.572 0.034336128 0.254338654 55280.47148 -4.742571738 0.424288106 FNGSHVVGSPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FNGSHVVGSPFK 12 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ; 135.02 0.00013516 2046470000 8625100 11500700 6357800 8396000 11481200 10890200 12053600 13676500 13679200 FALSE TRUE 7485271.182 11425151.14 9432453.346 10302440.12 11252746.58 11309153.04 10884643.73 10751886.91 12062060.56 0.620563223 0.947197296 0.781993532 0.854119416 0.932904169 0.937580522 0.902386758 0.891380611 1 23.52397305 4.744341234 24.99412307 0.900978633 0.620563102 0.701316535 0.058450059 370.2868801 1600993.591 0.014242998 0.123318044 55506.16654 -4.744341234 -0.280415531 FNHDGEEEEEDDDYGSR ddPTM_MDA-MB-175_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 ; 221.79 3.57E-15 515490000 365560 310150 203065 239810 308140 320860 311830 325400 318900 FALSE TRUE 317250.3198 308112.6042 301267.9132 294262.5258 302008.6169 333203.6918 281588.7746 255815.7423 281200.0053 1.128201685 1.095706253 1.071365247 1.046452775 1.073999329 1.18493487 1.001382537 0.909728796 1 18.1012371 2.027709405 9.530723916 0.950499307 1.094942636 0.676861903 0.043031135 0.16060455 52.47280637 0.017503096 0.011713018 106.5882679 -2.027709405 0.144443328 FNHPEIVQLVSELEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FNHPEIVQLVSELEAER 17 0 Q7Z4H3-2;Q7Z4H3 Q7Z4H3-2 HDDC2 HD domain-containing protein 2 0 ;; 185.33 5.85E-10 123244000 210668 173579 101768 126727 173958 173786 160613 188423 179323 FALSE TRUE 182827.69 172438.7481 150983.3452 155502.3023 170496.5761 180471.6599 145036.776 148130.2078 158123.6392 1.156232496 1.090531112 0.954843602 0.983422232 1.078248496 1.141332572 0.917236516 0.93679989 1 17.27069354 FNHSVEDLLQEGEEADDDDIYNVLSTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FNHSVEDLLQEGEEADDDDIYNVLSTLK 28 0 Q8WVM7;Q68DW7;Q8WVM7-2 Q8WVM7 STAG1;DKFZp781D1416 Cohesin subunit SA-1 0 241.94 2.47E-45 34620000 25283 23131 16677 22955 21074 21252 26747 28049 38318 FALSE TRUE 21941.78749 22979.05094 24742.05298 28167.2836 20654.66863 22069.57819 24153.08006 22050.93963 33788.08969 0.649394141 0.680093227 0.732271437 0.833645342 0.611300278 0.653176264 0.71484006 0.652624633 1 15.04422717 1.234095136 24.99764028 1.000000459 0.691991232 0.715665517 0.061222642 76.10497503 425978.6602 0.116950651 0.015142368 17.14332804 -1.234095136 -0.308009227 FNHWELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FNHWELK 7 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 112.17 0.0064142 3666700000 10213100 8896700 6005400 7344000 9106300 8121700 10087800 12461600 10867600 FALSE TRUE 8863412.958 8838256.992 8909631.527 9011567.446 8925102.446 8434147.054 9109486.709 9796783.816 9582844.708 0.924925033 0.922299929 0.929748086 0.94038542 0.931362525 0.880129785 0.950603603 1.022325219 1 23.19202256 1.882869497 4.207531157 1.010296147 0.92266346 0.820869694 0.017047129 0.085091275 2.373747642 0.009495037 0.004599159 76.36062899 -1.882869497 -0.087632687 FNIDMPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FNIDMPHR 8 0 Q05655;Q05655-2;A0A494C1T7 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 0 ;;; 93.551 0.0083352 624560000 1026310 1164830 692376 780950 1179230 1379320 893500 1033440 1062220 FALSE TRUE 890680.5332 1157178.155 1027211.349 958276.6336 1155765.63 1432383.333 806848.5075 812446.8982 936645.5617 0.95092591 1.235449355 1.096691632 1.023094191 1.233941287 1.529269333 0.86142351 0.867400574 1 19.83714369 FNKVPEWQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FNKVPEWQR 9 1 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 86.624 0.012779 699120000 407910 458710 229430 302830 503030 439640 468050 519930 388680 FALSE TRUE 354003.66 455696.7038 340383.1154 371592.18 493020.6872 456553.2353 422658.583 408747.0156 342730.6932 1.032891617 1.32960576 0.993150372 1.084210394 1.438507542 1.332104899 1.233209022 1.192618647 1 18.38671587 4.776245663 22.22981795 1.202798523 1.03288984 0.116682498 0.14473352 10682.1105 6300676.78 0.035972117 6.841514098 59737.31009 -4.776245663 -0.169908683 FNLLAHLADDLGHVVPNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FNLLAHLADDLGHVVPNSR 19 0 Q8N5N7;Q8N5N7-2 Q8N5N7 MRPL50 "39S ribosomal protein L50, mitochondrial" 0 112.32 0.00011502 90441000 72709 73902 37044 51904 75495 81615 61696 80556 30200 FALSE TRUE 63100.32143 73416.5329 54958.6023 63689.5965 73992.7972 84754.78186 55712.73142 63329.72629 26629.7904 2.369538794 2.756932435 2.063801535 2.391667209 2.778572271 3.182705556 2.092120538 2.378153389 1 14.70075345 1.084747365 1.995390651 9.36E-16 2.54213423 0.665435542 0.334749853 0.792763277 2.146580166 4.344846938 0.091077944 12.15478736 -1.084747365 2.54213423 FNNDSHS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FNNDSHSPK 9 0 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 FNNDS(0.001)HS(0.999)PK 72.705 0.029627 283490000 145310 130020 90048 96214 116660 116220 149690 161410 158670 TRUE FALSE 126106.9153 129165.8901 133595.514 118060.8592 114338.6942 120691.0586 135173.0868 126893.7276 139912.2134 0.901328857 0.923192386 0.954852409 0.843820967 0.817217393 0.862619894 0.966127857 0.906952471 1 17.09416238 0.688440177 1.00988151 1.212137368 0.889395839 0.348635806 0.045601168 6.694870397 2.475925103 3.082709344 0.016327127 4.880228725 -0.688440177 -0.322741529 FNPFVTSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FNPFVTSDR 9 0 P61254;E5RIT6;J3QRI7;J3QQQ9;J3QQV1;J3QRC4;J3KSS0;E5RHH1;Q9UNX3 P61254;Q9UNX3 RPL26;RPL26L1 60S ribosomal protein L26;60S ribosomal protein L26-like 1 0 ;;;;; 176.44 0.00012365 3839815000 2781990 3094430 1914974 2218690 3103670 3075420 2809710 3036120 3473900 FALSE TRUE 2414342.973 3074102.486 2841061.832 2722477.475 3041913.039 3193733.397 2537224.757 2386869.365 3063219.499 0.788171717 1.003552793 0.927475759 0.888763432 0.993044423 1.042606773 0.828286957 0.77920285 1 21.54661732 2.195924315 24.99996245 0.848718227 0.942894859 0.111100393 0.089056842 226.3699366 132731.3263 0.035436418 0.023891421 157.0089158 -2.195924315 0.094176632 FNPNFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FNPNFYR 7 0 Q9H832-2;Q9H832;I3L4C5 Q9H832-2 UBE2Z Ubiquitin-conjugating enzyme E2 Z 0 ; 134.12 0.0074573 1072880000 1222140 929880 585140 624660 990740 995800 1052960 1020800 961220 FALSE TRUE 1060631.102 923771.5571 868115.6612 766498.6003 971026.2123 1034109.07 950844.1013 802509.8639 847585.6666 1.251355638 1.08988577 1.024221734 0.904331716 1.14563784 1.220064368 1.121826547 0.946818588 1 19.69299967 5.836874772 0.020943115 1.57E-07 2.303479364 0.123656121 0.104995411 9543.939267 34.94897221 1675.004378 2201.509466 686870.3538 -5.836874772 2.303479207 FNQTYQLAHGTAEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FNQTYQLAHGTAEEK 15 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 203.04 5.61E-09 648920000 416040 329420 179869 264223 370970 308430 397730 456690 384090 FALSE TRUE 361059.2599 327256.0183 266854.25 324218.8705 363588.4228 320295.5017 359158.2058 359030.3975 338683.3178 1.066067447 0.966259633 0.787916723 0.957292118 1.07353508 0.945707937 1.060454374 1.060077006 1 18.3695774 3.398214056 6.864566079 1.029716426 0.931423142 0.230303187 0.075790182 0.294244409 21.00008155 0.02220699 0.028751975 2501.578042 -3.398214056 -0.098293285 FNVLYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FNVLYDR 7 0 Q7L5N1;E7EM64 Q7L5N1 COPS6 COP9 signalosome complex subunit 6 0 79.809 0.096446 0 2201700 1699200 1054500 1277500 1545100 1413700 1745500 1978100 1547300 FALSE TRUE 1910739.767 1688037.843 1564459.727 1567575.9 1514355.533 1468085.954 1576221.679 1555098.709 1364379.957 1.400445497 1.237219761 1.146645199 1.148929147 1.109922149 1.076009616 1.155265929 1.139784194 1 20.37981404 6.153292147 0.724300616 1.102813948 3.468863396 0.836455465 0.042542253 7.3883502 0.591478425 0.016518931 22.50592295 1423285.902 -6.153292147 2.366049447 FNVWDTAGQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FNVWDTAGQEK 11 0 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ;; 234.67 3.89E-15 1453570000 1887300 1599070 1150554 1393645 1593710 1286553 1730610 1950290 2431740 FALSE TRUE 1637888.523 1588565.604 1706965.763 1710093.398 1561998.289 1336047.526 1562775.709 1533235.661 2144262.467 0.763847033 0.740844756 0.796061951 0.797520557 0.728454801 0.623080218 0.728817359 0.715041038 1 21.03205008 1.235881994 24.99777676 1.000000352 0.73539852 0.741298952 0.048875742 40.80191709 380699.6101 0.086197685 0.01290389 17.21400775 -1.235881994 -0.264601832 FNVWDVGGQDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FNVWDVGGQDK 11 0 P62330 P62330 ARF6 ADP-ribosylation factor 6 0 134.57 0.0027653 0 385180 352900 205080 280120 323370 266570 377160 407680 372080 FALSE TRUE 334277.4871 350581.7767 304257.374 343725.5274 316935.5697 276825.1204 340583.0813 320500.8046 328093.1263 1.018849407 1.068543498 0.92735065 1.047646232 0.965992715 0.84373947 1.038068323 0.976859248 1 18.32374584 4.249386706 24.99836995 0.973414245 1.043696461 0.20923107 0.058344238 341.401043 788308.7741 0.014242449 0.03687654 17757.69964 -4.249386706 0.070282216 (ac)ASLEVS(ph)RSPRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASLEVSRSPRR 11 2 Q5QPJ9;Q5QPK2;O60762 Q5QPJ9 DPM1 Dolichol-phosphate mannosyltransferase subunit 1 1 ASLEVS(0.601)RS(0.399)PRR;ASLEVS(0.5)RS(0.5)PRR 63.185 0.013238 545180000 125213 127513 70136 81800 111543 118819 123951 120527 55690 TRUE FALSE 108665.7848 126675.3587 104054.0042 100373.9402 109323.5125 123390.0438 111930.2511 94753.23899 49106.39164 2.212864378 2.579610402 2.118950318 2.044009687 2.226258311 2.512708421 2.2793418 1.92955002 1 15.5836232 1.224184976 2.120025837 0.574373728 2.284452407 0.861110197 0.162149652 0.265776405 1.154574254 0.897023663 0.045515775 16.75656424 -1.224184976 1.710078678 FNYSGS(ph)GGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FNYSGSGGR 9 0 Q12906;Q12906-7 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 FNYS(0.008)GS(0.992)GGR;FNYS(0.003)GS(0.997)GGR 104.94 0.0033337 207960000 742700 563310 537530 428520 534290 509230 642310 735670 637140 TRUE FALSE 644550.3132 559609.5795 797481.3059 525822.0155 523658.6743 528820.4076 580018.8751 578352.6955 561818.035 1.147258139 0.996069091 1.419465479 0.935929398 0.93207879 0.941266344 1.032396326 1.029430633 1 19.09974341 FPAMSDAYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FPAMSDAYDR 10 0 P00491;G3V5M2 P00491 PNP Purine nucleoside phosphorylase 0 ;;; 122.33 0.0011433 1267830000 658090 739450 448530 537940 688960 771150 641120 683150 798390 FALSE TRUE 571121.7391 734592.5043 665440.6082 660087.4989 675251.0439 800816.6395 578944.2811 537063.6888 704005.2437 0.811246428 1.04344749 0.945221096 0.937617304 0.95915627 1.137515163 0.82235791 0.762868876 1 19.42522665 FPDELAHVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FPDELAHVEK 10 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 77.379 0.02688 0 110410 126550 102350 104030 140630 155770 134010 115890 180440 FALSE TRUE 95819.03876 125718.6847 151846.8023 127651.6015 137831.7381 161762.5727 121013.7308 91107.82536 159108.5888 0.602224176 0.790143924 0.954359557 0.802292337 0.866274657 1.016680331 0.760573215 0.572614125 1 17.27965219 7.965072918 22.29194018 0.808267581 0.004053377 0 0.151118144 0 0 0.034967227 0 92272633.98 -7.965072918 -0.804214204 FPDSVEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FPDSVEELR 9 0 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 ;; 168.27 0.00013809 322310000 508377 415918 259704 306857 429699 463820 399775 446500 429995 FALSE TRUE 441193.6914 413185.8073 385297.7231 376533.5719 421148.8306 481663.4555 361004.882 351019.4497 379161.481 1.163603672 1.089735714 1.016183717 0.993069156 1.110737382 1.270338575 0.952113809 0.925778243 1 18.53245288 2.091741935 24.99963807 0.951892156 1.098468119 0.440240581 0.078091911 16.68921922 4540.599195 0.033388711 0.02251066 123.521323 -2.091741935 0.146575964 FPEFCSSPS(ph)PPVEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FPEFCSSPSPPVEVK 15 0 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 FPEFCSSPS(1)PPVEVK;FPEFCS(0.012)S(0.009)PS(0.978)PPVEVK 193.96 7.49E-08 120330000 576200 461124 322122 341404 406469 352671 481703 543286 550112 TRUE FALSE 500053.7101 458094.8461 477901.2766 418924.9962 398381.0621 366238.4816 434987.5172 427108.5168 485078.386 1.030871967 0.944372826 0.985204228 0.863623299 0.821271517 0.755008865 0.896736548 0.880493811 1 18.88785837 3.738361382 24.99999961 0.865584241 0.982571994 0.423516781 0.064337415 18.03503965 2263085.743 0.018056553 0.028797503 5474.713312 -3.738361382 0.116987753 FPEHELTFDPQR ddPTM_MDA-MB-175_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 ;;; 165.7 5.39E-05 1385410000 1424570 1426940 938510 1199130 1396210 1876540 1157520 1243000 1135810 FALSE TRUE 1236309.465 1417566.337 1392376.575 1471410.794 1368428.153 1948731.708 1045263.889 977194.123 1001535.836 1.234413609 1.415392527 1.390241393 1.469154414 1.366329695 1.945743366 1.043660997 0.975695615 1 19.93378261 2.03674628 24.99998771 0.993181248 1.462264775 0.587911982 0.183380396 107.0698152 72843.52175 0.072407857 0.048817231 108.8294114 -2.03674628 0.469083527 FPELGPDGHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FPELGPDGHQR 11 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 0 65.879 0.064238 192820000 1164500 1259700 891720 767370 887860 746740 1753400 1315300 707740 FALSE TRUE 1010608.375 1251424.948 1322958.775 941613.087 870193.3231 775467.571 1583355.538 1034033.331 624071.7835 1.619378413 2.005258018 2.119882375 1.508821761 1.394380176 1.242593547 2.53713688 1.656914089 1 19.25135246 3.7274586 24.67483799 1.608520982 1.923881451 0.13325858 0.416656926 1419.339121 3154558.75 0.118419189 0.177518619 5338.983763 -3.7274586 0.315360469 FPGDQVVNGAGPELSTGPSPGS(ph)PTLDIDQSIEQLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FPGDQVVNGAGPELSTGPSPGSPTLDIDQSIEQLNR 36 0 Q68CZ2;E9PCX8;Q68CZ2-2 Q68CZ2 TNS3 Tensin-3 1 FPGDQVVNGAGPELST(0.001)GPS(0.021)PGS(0.802)PT(0.174)LDIDQS(0.003)IEQLNR 246.41 7.86E-50 78653000 17725 15061 8582.7 10962 16613 19085 16636 18390 18033 TRUE FALSE 15382.59634 14962.0633 12733.32243 13451.08964 16282.4338 19819.2123 15022.64328 14457.44161 15901.15928 0.967388356 0.940941665 0.800779503 0.845918804 1.023977781 1.246400463 0.944751449 0.909206766 1 13.95684433 3.229809122 24.90996617 1.015477719 0.886200438 0.315171158 0.099129703 260.1575123 740502.1109 0.033025992 0.038018704 1697.497415 -3.229809122 -0.129277281 FPGLALRPSS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FPGLALRPSSR 11 1 B4DF95;Q15735;B5MCL8;B5MBZ3;A0A087WVS7;Q15735-3;Q15735-2 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 FPGLALRPS(0.168)S(0.832)R;FPGLALRPS(0.16)S(0.84)R;FPGLALRPS(0.378)S(0.622)R;FPGLALRPS(0.135)S(0.865)R 90.412 0.0069683 1985440000 1417736 1331098 970070 1074260 1062586 1314384 1299180 1382430 1171339 TRUE FALSE 1230378.596 1322353.93 1439199.097 1318187.152 1041442.618 1364949.203 1173185.724 1086808.103 1032864.638 1.191229277 1.280278055 1.393405335 1.27624386 1.008305038 1.321517993 1.13585622 1.052227042 1 19.97821976 0.701843572 0.432758171 0.591085339 1.287899453 0.450650749 0.10035579 8.584100525 0.953594232 3.392701461 0.102785181 5.033192861 -0.701843572 0.696814114 FPGQLNADLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 143.03 8.07E-05 4854550000 2133440 2354790 1566010 1781040 2312810 2458150 2061240 2402060 2817470 FALSE TRUE 1851500.499 2339321.229 2323337.674 2185452.353 2266789.606 2552716.621 1861341.262 1888398.162 2484391.906 0.745252991 0.941607169 0.93517358 0.879672949 0.912412249 1.027501585 0.749214026 0.760104779 1 21.24446134 2.216826497 24.9998305 0.816902153 0.908805862 0.093757325 0.09707021 429.6007557 494147.7579 0.038754106 0.026153899 164.7504075 -2.216826497 0.091903709 FPGQLNADLRK ddPTM_MDA-MB-175_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 ; 117.98 0.0012547 5638300000 2130950 1757910 919690 1114090 1600060 1493680 2073620 2107670 532230 FALSE TRUE 1849339.558 1746362.173 1364455.16 1367061.162 1568221.936 1551142.836 1872520.652 1656961.172 469310.3757 3.940546926 3.721124151 2.907362016 2.912914849 3.34154542 3.305153511 3.989940876 3.530629746 1 18.84018283 1.23742429 24.99834175 0.999997078 3.450519151 0.813686361 0.369352691 12.87820397 283182.1784 0.580640812 0.097020086 17.27524797 -1.23742429 2.450522074 FPHHDNELAQSEAYFENDCWVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FPHHDNELAQSEAYFENDCWVR 22 0 P49589-3;P49589;B4DKY1;P49589-2 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 0 146.89 4.75E-08 126630000 150400 159170 177180 117000 141290 182360 165600 159430 142950 FALSE TRUE 130524.2589 158124.4018 262864.8406 143566.6382 138478.6054 189375.5072 149540.1375 125337.1352 126050.6138 1.035490863 1.25445166 2.085391198 1.138960247 1.098595248 1.502376715 1.186349935 0.994339745 1 16.94364362 1.948798165 3.467133415 1.004419183 1.360546272 0.196565366 0.294953479 0.394307897 9.035414939 0.171004662 0.083346009 88.8787965 -1.948798165 0.356127089 FPHLFTGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FPHLFTGK 8 0 O75351;I3L4J1;Q9UN37 O75351;I3L4J1 VPS4B;VPS4A Vacuolar protein sorting-associated protein 4B;Vacuolar protein sorting-associated protein 4A 0 154.31 0.0004271 177020000 290380 274800 212760 284190 263310 238040 280120 346010 712870 FALSE TRUE 252005.5473 272994.8207 315651.4476 348719.6831 258070.6462 247197.5528 252954.0055 272018.4542 628595.3207 0.400902678 0.434293434 0.502153671 0.554760227 0.410551332 0.393253886 0.402411531 0.432740183 1 19.26177201 1.237990026 24.99994996 1.000000636 0.44190437 0.923125379 0.050661236 3.811607535 166854.0214 0.077511451 0.013443712 17.29776633 -1.237990026 -0.558096266 FPLDYYSIPFPTPTT(ph)PLTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FPLDYYSIPFPTPTTPLTGR 20 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5;H0Y5H6;H7C2T8 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 FPLDYYSIPFPT(0.001)PT(0.052)T(0.563)PLT(0.385)GR;FPLDYYSIPFPTPT(0.189)T(0.808)PLT(0.003)GR 275.74 1.79E-43 997630000 281240 459090 261440 369570 640510 693760 543590 650950 620610 TRUE FALSE 244073.4214 456074.2076 387873.2585 453486.517 627765.1041 720449.3961 490872.7255 511749.4082 547242.1928 0.446006219 0.833404685 0.708778058 0.828676083 1.147143098 1.316509227 0.896993565 0.935142456 1 19.06181994 3.466359106 3.532749624 1.043544695 0.684903605 0.593636846 0.149949026 0.187304326 4.998773684 0.046630718 0.065746221 2926.571279 -3.466359106 -0.35864109 FPPEDFRHS(ph)PEDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 FPPEDFRHSPEDFR 14 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR 163.79 2.55E-06 2613215000 1758707 1560404 1037046 1216336 1635833 1596364 1509064 1776288 1470391 TRUE FALSE 1526289.414 1550153.603 1538564.914 1492523.679 1603283.124 1657777.156 1362715.206 1396442.634 1296563.051 1.177181019 1.195586749 1.186648743 1.151138526 1.236563947 1.278593551 1.051021163 1.077034112 1 20.30626093 2.219067408 24.99190611 1.050188386 1.20213979 0.790648863 0.039125798 112.1968988 143844.6107 0.016517234 0.011154053 165.602698 -2.219067408 0.151951404 FPQGPPSQMGS(ph)PMGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 FPQGPPSQMGSPMGSR 16 0 Q8WXF1 Q8WXF1 PSPC1 Paraspeckle component 1 1 FPQGPPS(0.059)QMGS(0.935)PMGS(0.006)R;FPQGPPS(0.003)QMGS(0.997)PMGSR;FPQGPPS(0.003)QMGS(0.996)PMGS(0.001)R;FPQGPPS(0.035)QMGS(0.963)PMGS(0.002)R;FPQGPPSQMGS(0.999)PMGSR;FPQGPPSQMGS(1)PMGSR;FPQGPPS(0.001)QMGS(0.999)PMGSR;FPQGPPS(0.09)QMGS(0.909)PMGSR 174.68 3.97E-09 2464380000 885380 771223 701859 859615 800656 827579 804893 860208 2075900 TRUE FALSE 768374.7897 766156.7853 1041280.36 1054803.724 784724.5121 859416.4996 726834.6007 676259.2133 1830489.467 0.419764661 0.41855296 0.568853511 0.576241351 0.428696546 0.469500926 0.397071174 0.36944174 1 20.80379804 1.233070236 24.99996492 1.000000862 0.454874464 0.862838912 0.068160233 68.80026425 313241.8784 0.157312664 0.01858168 17.10291887 -1.233070236 -0.545126397 FPQLDS(ph)TSFANSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FPQLDSTSFANSR 13 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 FPQLDS(0.895)T(0.05)S(0.05)FANS(0.004)R 123.28 0.00023632 120210000 85391 102970 75169 75477 101510 104960 98815 98002 119770 TRUE FALSE 74106.363 102293.5833 111520.9798 92615.20644 99490.1496 108997.8791 89231.93651 77045.03495 105610.927 0.701692193 0.96858901 1.055960618 0.876947197 0.942044089 1.032070091 0.844911971 0.729517647 1 16.68839959 2.030231961 24.08705628 0.827971472 0.935518104 0.058048304 0.116598569 239.8074209 191063.1235 0.046366053 0.031259452 107.2091767 -2.030231961 0.107546632 FPQLDSTSFANSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FPQLDSTSFANSR 13 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 180.24 1.05E-06 0 182025 158845 117266 122806 208330 183664 188422 202092 194861 FALSE TRUE 157969.9351 157801.5367 173976.2298 150690.9793 204184.6406 190729.6729 170148.8634 158876.1985 171824.7546 0.919366569 0.91838651 1.012521335 0.877003897 1.188330757 1.110024416 0.990246509 0.924640916 1 17.39057837 4.239327015 24.86207844 1.010022665 0.918876529 0.173530705 0.086459005 35.83662074 1162321.478 0.023373667 0.054888313 17351.1001 -4.239327015 -0.091146137 FPQS(ph)PHSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FPQSPHSGR 9 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 FPQS(1)PHSGR 71.085 0.03258 136650000 111320 101300 69870 82516 102290 143110 90645 111910 112160 TRUE FALSE 96608.77995 100634.5536 103659.3657 101252.519 100254.6291 148615.5343 81854.26185 87978.91738 98900.57257 0.976827307 1.017532568 1.048116942 1.023780918 1.013691089 1.502676177 0.827641941 0.889569343 1 16.59369125 FPSHFSSDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FPSHFSSDLK 10 0 P22694-2;P22694-4;A0A0A0MS54;P22694-9;P22694-6;P22694-7;P22694-5;P22694;P22694-3;P22694-10;A0A087WVC4;P17612-2;P17612 P22694-2;P17612-2 PRKACB;PRKACA cAMP-dependent protein kinase catalytic subunit beta;cAMP-dependent protein kinase catalytic subunit alpha 0 ; 121.83 0.00050465 821550000 1555990 1562090 645260 1268650 1865200 1548070 1944500 2287820 2832400 FALSE TRUE 1350361.979 1551828.528 957309.8943 1556716.373 1828086.169 1607625.255 1755922.689 1798587.497 2497556.899 0.540673159 0.621338608 0.383298533 0.623295659 0.731949759 0.643679131 0.703056131 0.720138748 1 21.25208611 -2 0.420899816 8.179056111 0.543829331 0.701380162 0.085452148 52.7926604 0.72628795 337.0731183 0.07909834 0.01 2 -7.635226781 FPSLLTHNENMVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FPSLLTHNENMVAK 14 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ; 190.03 6.50E-07 2224000000 1662880 1669620 1055330 1580610 1614150 1377760 1798800 2035690 3360000 FALSE TRUE 1443126.195 1658652.156 1565691.118 1939511.659 1582031.573 1430763.319 1624352.653 1600373.535 2962784.628 0.487084407 0.559828798 0.528452559 0.654624585 0.533967794 0.482911686 0.548252019 0.540158579 1 21.49852233 1.23829131 24.99993134 1.000000507 0.543695051 0.903914701 0.04693408 1.829205414 169490.0742 0.064264929 0.011365025 17.3097705 -1.23829131 -0.456305456 FPSS(ph)PLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FPSSPLR 7 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 FPS(0.307)S(0.693)PLR;FPS(0.021)S(0.979)PLR 124.08 0.0043859 204410000 595650 712030 491000 690150 727370 656590 668250 779560 1113260 TRUE FALSE 516933.3433 707352.628 728449.2423 846859.1058 712896.7601 681849.4422 603443.2179 612857.1605 981651.671 0.526595491 0.720573956 0.742064893 0.862687989 0.726221715 0.694594083 0.614722346 0.624312247 1 19.90485166 4.738458265 4.533118454 0.734178922 0.513062978 0.268339313 0.113142063 0.295254614 15.73765949 0.028153016 0.208827913 54759.34759 -4.738458265 -0.221115944 FPVIQHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FPVIQHFK 8 0 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;Q15257-4;Q68CR8;B7ZBQ0 Q15257 PPP2R4;DKFZp781M17165 Serine/threonine-protein phosphatase 2A activator 0 ; 127.84 0.001159 1442150000 2326800 2172610 1535580 2028530 2130840 1894510 2257000 2832500 3334500 FALSE TRUE 2019307.485 2158337.982 2278191.624 2489138.741 2088440.453 1967393.026 2038116.487 2226791.918 2940299.209 0.686769387 0.734053859 0.774816256 0.846559674 0.710281609 0.669113204 0.693166356 0.757335142 1 21.48753154 1.240697255 4.534540294 1.021506447 0.733304437 0.734052224 0.050539813 0.111352858 4.873469403 0.103082991 0.013739773 17.40593088 -1.240697255 -0.28820201 FQAPS(ph)PSTLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FQAPSPSTLLR 11 0 Q6P9B9 Q6P9B9 INTS5 Integrator complex subunit 5 1 FQAPS(0.927)PS(0.068)T(0.005)LLR;FQAPS(0.926)PS(0.066)T(0.009)LLR 128.21 0.00028373 106275000 184173 152728 87004 101005 152217 163693 147403 158817 152421 TRUE FALSE 159834.0714 151724.7197 129079.4254 123939.729 149188.1795 169990.3756 133107.8797 124855.2205 134401.963 1.189224233 1.128887676 0.960398364 0.922157134 1.110014885 1.264790869 0.990371545 0.928968727 1 17.03619468 -1.999999949 0.032879111 4.11E-07 1.7687751 0.122883204 0.108231555 6088.517586 19.79496416 775.1682946 364.1604844 0.010000001 1.999999949 1.768774689 FQDADPLEQDELHTFTDTMLPGCFHLLDELPDTVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FQDADPLEQDELHTFTDTMLPGCFHLLDELPDTVYR 36 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ; 289.18 4.36E-92 209070000 151036 119570 82498 97358 140006 139890 122728 139621 149881 FALSE TRUE 131076.2099 118784.5368 122394.3087 119464.6219 137220.1545 145271.6588 110825.8574 109764.1357 132162.2389 0.991782607 0.898778182 0.926091369 0.903924017 1.038270505 1.099191872 0.838559171 0.830525698 1 17.01195051 2.16535251 25 0.875237112 0.97007013 0.21360618 0.076083142 60.89287664 20792.60879 0.032487975 0.021903393 146.3364483 -2.16535251 0.094833019 FQDNFEFVQWFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FQDNFEFVQWFK 12 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ; 221.28 6.41E-11 900090000 633430 549610 445820 553640 543760 480020 573970 692350 916250 FALSE TRUE 549720.6206 545999.5757 661420.0432 679352.4239 532940.2398 498486.68 518306.4777 544296.3404 807931.9688 0.680404591 0.675798949 0.818658091 0.8408535 0.659635044 0.616990909 0.641522427 0.673690807 1 19.62387429 1.235476325 24.99986783 1.000000409 0.700231841 0.625876673 0.072661852 64.87979001 525792.4963 0.135555109 0.019685388 17.19793586 -1.235476325 -0.299768568 FQDNLDFIQWFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FQDNLDFIQWFK 12 0 Q15555-4;Q15555-5;Q15555-3;Q15555;K7EL66;K7ERD8;Q15555-2;M0QX52 Q15555-4 MAPRE2 Microtubule-associated protein RP/EB family member 2 0 158.4 0.00017111 56882000 89562 96497 59596 63592 85840 76665 100870 100760 88180 FALSE TRUE 77726.15478 95863.10485 88416.82494 78031.53554 84131.95194 79614.35216 91087.64293 79213.25812 77755.46085 0.999623099 1.232879386 1.137114023 1.00355055 1.082006987 1.023906891 1.171462968 1.018748487 1 16.24665638 3.764314087 23.55749036 1.054541967 1.134172932 0.16986303 0.074591297 586.2639418 536269.7721 0.018691443 0.032355348 5811.845847 -3.764314087 0.079630965 FQEHCPDLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FQEHCPDLER 10 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 ; 109.24 0.0020454 709830000 868630 782550 594930 684920 775880 982920 841480 893550 941170 FALSE TRUE 753838.3447 777409.3775 882640.1379 840441.5543 760441.506 1020733.568 759873.3991 702471.2861 829905.9548 0.908341891 0.936743944 1.06354236 1.012694932 0.916298409 1.229938841 0.915613865 0.846446856 1 19.66258833 2.035085446 24.99999665 0.902887096 1.011563047 0.150239699 0.099070901 264.7680963 188658.4296 0.039509802 0.026637386 108.4140193 -2.035085446 0.108675951 EEDCHS(ph)PTSKPPKPDQPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EEDCHSPTSKPPKPDQPLK 19 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 EEDCHS(0.985)PT(0.014)S(0.002)KPPKPDQPLK;EEDCHS(0.995)PT(0.002)S(0.002)KPPKPDQPLK;EEDCHS(0.994)PT(0.006)S(0.001)KPPKPDQPLK 165.66 1.02E-11 1818240000 1452620 1050830 1376480 1532060 1047860 715180 1680220 2005900 4901900 TRUE FALSE 1260652.587 1043927.029 2042150.332 1879937.639 1027009.636 742693.4374 1517272.523 1576953.895 4322402.966 0.291655497 0.241515434 0.472457184 0.434928824 0.237601548 0.171824201 0.351025236 0.364832688 1 22.04340215 1.225762995 3.997908319 1.086382968 0.316786457 0.848835726 0.090280636 0.103709263 2.845284104 0.238878034 0.024426093 16.81756036 -1.225762995 -0.769596511 FQEHLQLQNLGINPANIGFSTLTMESDKFICIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FQEHLQLQNLGINPANIGFSTLTMESDKFICIR 33 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;J3KSQ2;J3QL20 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 285.48 2.14E-74 3852520000 2994400 2359490 1416438 1602427 2219630 2044950 2779070 3086680 1602910 FALSE TRUE 2598682.453 2343990.355 2101432.155 1966282.542 2175463.706 2123620.55 2509556.219 2426617.503 1413415.806 1.838583128 1.658386969 1.486775615 1.391156469 1.539153373 1.502474036 1.775525793 1.716846163 1 20.43075452 4.556619729 2.812201513 1.522869391 1.84489565 0.221306722 0.209576177 0.546061849 7.273273086 0.053935548 0.326418317 36026.30562 -4.556619729 0.322026259 FQEKPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FQEKPDR 7 1 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 ;;;; 136.8 0.002686 2604840000 5560920 4869480 3338550 4178690 4574000 4594170 5658770 6342270 7342400 FALSE TRUE 4826030.332 4837492.065 4953083.947 5127525.432 4482986.349 4770910.693 5109983.356 4986024.916 6474389.836 0.745403112 0.747173431 0.765027141 0.79197045 0.692418353 0.736889624 0.789260994 0.770115029 1 22.62631281 1.161175163 2.815195463 1.088742346 0.752050484 0.879543034 0.028507007 0.20521308 1.5997609 0.177740564 0.00750412 14.493563 -1.161175163 -0.336691861 FQEKPDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FQEKPDRR 8 2 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 85.676 0.0093218 163580000 341690 314780 186470 189210 279270 280030 378900 404460 167500 FALSE TRUE 296534.8008 312712.1895 276647.5157 232173.0224 273713.0734 290802.9353 342154.3363 317969.3765 147698.3408 2.0077057 2.117235629 1.873057708 1.571940626 1.8531899 1.96889778 2.316575355 2.152829712 1 17.17229409 4.227605397 23.41415305 1.873587038 2.062470621 0.058717235 0.356504462 325.3627654 695396.7318 0.093187275 0.197500776 16889.05681 -4.227605397 0.188883582 FQELIFEDFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 FQELIFEDFAR 11 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ;;;;;; 218.07 2.53E-11 1333966000 1956578 1880320 1144234 1511041 1815485 1815248 1999546 2184759 2046314 FALSE TRUE 1698011.26 1867968.054 1697589.39 1854145.954 1779360.4 1885081.765 1805630.337 1717565.29 1804401.09 0.941038702 1.035228844 0.940804901 1.027568629 0.986122437 1.044713271 1.000681249 0.951875555 1 20.78308863 3.722980706 24.81202763 0.997684575 0.978644611 0.117337968 0.035588809 2346.254059 3736559.073 0.009748694 0.014510729 5284.217757 -3.722980706 -0.019039965 FQESEERPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FQESEERPK 9 1 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;; 182.46 4.22E-05 3296020000 3773000 3161130 2144100 2529100 2918130 2602650 3689400 4007400 4001300 FALSE TRUE 3274388.49 3140364.329 3180993.932 3103370.81 2860064.922 2702775.63 3331602.556 3150448.696 3528270.872 0.928043398 0.890057607 0.90157305 0.879572721 0.810613761 0.766034051 0.944259292 0.892915768 1 21.75052989 1.009554486 1.379165562 1.120963263 0.868658009 0.365100435 0.052054746 2.646523544 2.861622452 1.09692398 0.016034985 10.22243801 -1.009554486 -0.252305254 FQETEFLS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FQETEFLSPPR 11 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 FQET(0.001)EFLS(0.999)PPR;FQETEFLS(1)PPR 148.48 3.65E-05 361740000 491370 472810 326215 317537 436493 515000 461790 494560 465780 TRUE FALSE 426434.2095 469704.08 483973.6651 389638.6291 427807.6433 534812.3832 417005.6769 388802.1927 410716.019 1.038270215 1.143622499 1.17836569 0.948681354 1.041614214 1.302146394 1.015313885 0.946644822 1 18.64778169 2.013568837 24.99959389 0.972951677 1.107826882 0.277198053 0.094275207 278.4327336 512990.1683 0.038672413 0.026058759 103.1736599 -2.013568837 0.134875205 FQEYIDAHPETIVLDPLPAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FQEYIDAHPETIVLDPLPAIR 21 0 Q13572-2;Q13572;G3V588;G3V5A3 Q13572-2 ITPK1 Inositol-tetrakisphosphate 1-kinase 0 74.579 0.013229 51368000 75775 56353 39610 38604 53927 49079 70572 74717 42303 FALSE TRUE 65761.14176 55982.81343 58765.52849 47369.62823 52853.95821 50967.10089 63727.9383 58739.351 37301.98753 1.762939353 1.500799747 1.575399392 1.269895557 1.416920698 1.366337406 1.708432781 1.57469762 1 15.18696488 5.067486554 1.26770507 1.434825231 2.154885342 0.245077636 0.192081562 4.845833798 3.90286638 0.05575955 5.534269634 116811.7563 -5.067486554 0.720060111 FQGEDTVVIASKPYAFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FQGEDTVVIASKPYAFDR 18 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 156.67 9.05E-09 1957350000 1470290 1255540 856920 990920 1274350 1234750 1375310 1552230 1239080 FALSE TRUE 1275987.451 1247292.275 1271329.378 1215923.531 1248992.928 1282251.631 1241932.648 1220297.694 1092597.374 1.167847811 1.141584544 1.163584508 1.112874294 1.143141067 1.173581103 1.136679144 1.116877748 1 20.05933043 1.110799067 1.911243925 0.908067649 1.148454561 0.876907434 0.01740743 0.391179835 1.026327718 0.190636092 0.004678299 12.90622009 -1.110799067 0.240386912 FQGIKHECQANGPEDLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FQGIKHECQANGPEDLNR 18 1 P60981;P60981-2 P60981 DSTN Destrin 0 ;;; 302.14 7.22E-50 2442130000 2208500 2007120 619820 628649 1780150 1705500 2392720 2400400 167650 FALSE TRUE 1916641.129 1993935.097 919567.0252 771393.3637 1744728.498 1771111.689 2160674.383 1887093.14 147830.608 12.965117 13.48797197 6.220410223 5.218089638 11.80221418 11.98068325 14.6158797 12.76523966 1 17.17358548 4.303191577 24.99968959 9.773017472 13.22658815 0.133332635 4.107839759 148.3364232 57373.72164 1.06533996 2.818623895 20099.79262 -4.303191577 3.453570679 FQNDRTEDEQFNDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FQNDRTEDEQFNDEK 15 1 Q9Y376;A0A087X0K1 Q9Y376 CAB39 Calcium-binding protein 39 0 165.58 1.29E-06 194830000 360540 276740 195420 214840 288060 213150 350260 381070 179780 FALSE TRUE 312893.7255 274922.0767 289925.7656 263622.7056 282328.1696 221350.0184 316291.8391 299581.146 158526.6132 1.973761498 1.734232954 1.828877561 1.662955514 1.780951248 1.396295637 1.995197101 1.88978456 1 17.27436553 1.233729666 24.99950976 0.999998811 1.781779822 0.675803663 0.170380594 90.55802941 468568.8273 0.330303626 0.041405 17.12890757 -1.233729666 0.781781012 FQNVADLHLYLYSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FQNVADLHLYLYSAK 15 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;;; 157.91 1.87E-06 1332326000 2642947 2010659 1217064 1776092 1801448 1658592 2235129 2633323 2475048 FALSE TRUE 2293674.858 1997450.849 1805640.221 2179380.834 1765602.709 1722399.107 2018366.534 2070207.369 2182450.645 1.050962991 0.915232999 0.827345271 0.998593411 0.809000063 0.789204151 0.924816576 0.948570074 1 21.0575176 1.578437068 2.423960706 0.994855984 0.895083939 0.133787668 0.081240385 0.570654278 6.91785389 0.099952752 0.022378285 37.8823636 -1.578437068 -0.099772045 FQPGETLTEILETPATSEQEAEHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 FQPGETLTEILETPATSEQEAEHQR 25 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;;;;; 272.18 5.95E-53 3948298000 1495705 1418055 953321 1207709 1443801 1428707 1537749 1731377 1676494 FALSE TRUE 1298043.795 1408739.703 1414350.224 1481937.787 1415072.185 1483670.283 1388618.339 1361135.502 1478300.789 0.878064738 0.952945242 0.956740492 1.002460256 0.957228864 1.003632206 0.939334098 0.92074327 1 20.49550841 4.776681056 2.640298111 0.964673365 0.85555082 0.506962728 0.027657966 0.525021745 4.415366094 0.007409902 0.131624416 59797.22849 -4.776681056 -0.109122545 FQPGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FQPGYR 6 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 ; 107.15 0.073319 538530000 606100 689050 389180 436020 616990 665760 648000 676190 580980 FALSE TRUE 526002.3493 684523.5852 577388.7497 535025.0051 604713.1061 691372.218 585157.0597 531592.0306 512297.2063 1.026752328 1.336184498 1.127058166 1.044364479 1.180395089 1.349552973 1.142221844 1.037663341 1 18.9666215 1.734849766 3.502083663 1.011547976 1.18072326 0.276029825 0.104679455 0.256139084 6.769040808 0.072669301 0.02790584 54.30624389 -1.734849766 0.169175284 FQPISEHQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FQPISEHQTR 10 0 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;A0A0A0MRE9;A0A6I8PUA5;A0A6I8PUD8 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 0 73.273 0.045482 124130000 373220 340960 200250 273550 273210 385570 411970 443800 612570 FALSE TRUE 323898.0314 338720.2113 297091.5698 335663.7084 267773.6555 400403.1274 372017.2128 348896.8237 540152.6724 0.599641634 0.627082358 0.55001407 0.621423767 0.495736982 0.741277694 0.688726043 0.645922609 1 19.04300771 -0.177895793 1.16322316 9.999999998 0.605818994 0.757635846 0.067346615 18.92567741 1.284177238 427.0704992 0.020477502 0.663902352 0.177895793 -9.394181004 FQPLDQVVVDNVFPNCILLLK ddPTM_MDA-MB-175_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 ; 70.335 0.010501 1607270000 861200 1200590 740480 505290 855450 1297590 609110 581000 692010 FALSE TRUE 747390.238 1192703.245 1098578.605 620023.8174 838428.2187 1347509.127 550038.606 456757.6713 610201.3661 1.224825573 1.95460599 1.80035422 1.016097065 1.374018914 2.208302376 0.901405071 0.74853597 1 19.21892588 2.104115338 10.6544272 0.847073587 1.58510182 0.479335246 0.350009877 0.284059246 26.87625411 0.14248037 0.096037552 127.0911583 -2.104115338 0.738028233 FQPQLNPDVVAPLPTHTAHEDFTFGES(ph)RPELGSEGLGSAAHGSQPDLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGSAAHGSQPDLRR 49 2 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 FQPQLNPDVVAPLPT(0.001)HT(0.001)AHEDFT(0.012)FGES(0.246)RPELGS(0.246)EGLGS(0.246)AAHGS(0.246)QPDLRR 112.68 2.56E-08 1044700000 127820 106770 32102 39733 123970 167340 87772 96488 38329 TRUE FALSE 110928.2631 106068.6208 47626.63457 48754.98493 121503.2395 173777.6781 79259.88495 75854.79207 33797.78928 3.282115946 3.138330142 1.409164196 1.442549527 3.595005535 5.141687719 2.345120395 2.244371412 1 15.04464126 4.446583631 24.99457942 2.512968002 3.246174015 0.06377087 1.194237649 592.9971632 485358.5987 0.318902032 0.843754525 27962.99149 -4.446583631 0.733206013 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGS(ph)EGLGSAAHGSQPDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGSAAHGSQPDLR 48 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 FQPQLNPDVVAPLPT(0.037)HT(0.037)AHEDFT(0.01)FGES(0.075)RPELGS(0.295)EGLGS(0.295)AAHGS(0.25)QPDLR 83.434 9.57E-06 630110000 10481 9265.6 6126.9 4957.8 10692 8589.2 6276.7 8694.7 15358 TRUE FALSE 9095.909295 9204.733664 9089.889333 6083.544265 10479.25012 8919.632082 5667.9866 6835.406067 13542.39474 0.671661805 0.679697634 0.671217278 0.449222193 0.773810712 0.658645111 0.418536508 0.504741311 1 13.72519526 -0.770339492 8.988836029 6.277008266 0.627912462 0 0.169342054 0 0 0 0.037126084 0.169691664 0.770339492 -5.649095804 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGS(ph)AAHGSQPDLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGSAAHGSQPDLRR 49 2 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 FQPQLNPDVVAPLPTHTAHEDFTFGES(0.006)RPELGS(0.025)EGLGS(0.485)AAHGS(0.485)QPDLRR 182.3 2.36E-29 2256300000 570150 415110 175430 243770 447400 556710 429010 491590 140880 TRUE FALSE 494803.2329 412383.1151 260268.5348 299121.7043 438497.6153 578126.9939 387404.6762 386467.3041 124225.3269 3.983110734 3.319637995 2.095132621 2.407896294 3.529856804 4.653857699 3.118564353 3.111018612 1 16.92259981 4.600771664 4.147818827 2.944649333 3.954489631 0.122347569 0.951040697 0.552833462 14.69010952 0.241660279 1.163959432 39881.51645 -4.600771664 1.009840298 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGSAAHGS(ph)QPDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGSAAHGSQPDLR 48 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGSAAHGS(1)QPDLR;FQPQLNPDVVAPLPT(0.013)HT(0.064)AHEDFT(0.064)FGES(0.064)RPELGS(0.064)EGLGS(0.064)AAHGS(0.666)QPDLR 263.29 2.01E-73 3035600000 255031 225867 94204 155040 227925 252550 197230 213921 314990 TRUE FALSE 221328.0072 224383.2648 139761.3695 190244.2016 223389.7384 262265.7619 178102.665 168175.6589 277752.241 0.796854082 0.807854021 0.503187189 0.684942094 0.804276997 0.944243549 0.641228543 0.605488036 1 18.08343903 3.251393338 24.21763981 0.770275891 0.692110924 0.088694491 0.144573478 525.9750617 992600.249 0.044009595 0.056409288 1783.993789 -3.251393338 -0.078164967 LS(ph)PDAIPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSPDAIPGK 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 1 LS(1)PDAIPGK 89.171 0.010812 0 310870 252950 202920 276750 260390 227000 301640 387820 635570 TRUE FALSE 269787.7419 251288.3548 301052.7907 339590.3174 255208.7484 235732.8369 272386.9992 304887.711 560433.6386 0.481391057 0.448381998 0.537178303 0.605942067 0.455377284 0.420625781 0.486028997 0.544021076 1 19.09618403 1.226314206 3.634389873 1.07694166 0.492537731 0.905452181 0.051304405 0.0914214 1.822963178 0.149666132 0.014044465 16.83891894 -1.226314206 -0.584403929 FQQDDAHIFCAMEQIEDEIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FQQDDAHIFCAMEQIEDEIK 20 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 213.45 7.26E-23 73170000 69050 53570 42868 73792 45397 53987 48198 73603 111650 FALSE TRUE 59924.86755 53218.09514 63599.10818 90547.60144 44493.68852 56063.91482 43523.76538 57863.57123 98450.86419 0.608677923 0.540554881 0.645998476 0.919723785 0.451938019 0.56946087 0.442086169 0.587740613 1 16.58711625 1.238124273 24.93307137 1.00000045 0.592842425 0.482324425 0.131578439 9.282444474 529771.956 0.186299947 0.032591507 17.30311417 -1.238124273 -0.407158024 FQQENLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FQQENLK 7 0 Q6ZUJ8-3;Q6ZUJ8-2;Q6ZUJ8 Q6ZUJ8-3 PIK3AP1 Phosphoinositide 3-kinase adapter protein 1 0 98.133 0.026723 31299000 107620 110150 140080 121410 52747 94076 66709 81024 100700 FALSE TRUE 93397.74433 109426.4174 207823.1565 148977.9961 51697.4379 97695.1646 60239.57145 63697.64813 88795.36072 1.051831352 1.232343858 2.340473138 1.67776779 0.582208772 1.100228253 0.678408995 0.717353335 1 16.43819668 3.245303358 24.9997548 0.807291139 1.605719112 0.518203928 0.363557426 128.0881166 474903.6911 0.109066283 0.137574784 1759.151968 -3.245303358 0.798427973 FQSGDFHVINGVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FQSGDFHVINGVLR 14 0 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 ; 192.68 3.46E-07 5276900000 9472900 8024900 3923100 5641500 9017300 9297400 8040600 9024500 9282300 FALSE TRUE 8221032.264 7972183.904 5820324.282 6922488.8 8837873.372 9655076.994 7260823.85 7094680.904 8184957.068 1.0044075 0.974004364 0.71110016 0.845757497 1.079770278 1.179612417 0.8870937 0.866795127 1 22.96454342 4.467043585 24.99525105 0.933275378 0.996806889 0.027147103 0.129196756 801.6399519 1988280.21 0.034907072 0.092582943 29311.87399 -4.467043585 0.063531511 FQSPQIQATIS(ph)PPLQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FQSPQIQATISPPLQPK 17 0 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 1 FQSPQIQAT(0.008)IS(0.992)PPLQPK;FQSPQIQAT(0.008)IS(0.992)PPLQPK;FQSPQIQATIS(1)PPLQPK 214.24 6.30E-15 1117012000 1228080 1069050 646677 861430 1075910 901500 1242240 1492340 1170740 TRUE FALSE 1065786.116 1062027.34 959412.1602 1057030.848 1054501.496 936181.2883 1121767.756 1173214.704 1032336.451 1.032401903 1.028760865 0.929359958 1.02392088 1.021470757 0.906856759 1.086629998 1.136465445 1 19.97748181 2.140460702 13.56481634 1.088010453 0.992365125 0.340523635 0.053899125 0.637835476 84.76578415 0.021379164 0.014413664 138.1849361 -2.140460702 -0.095645328 FQSSHHPTDITSLDQYVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FQSSHHPTDITSLDQYVER 19 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;; 229.6 4.43E-20 5224760000 1603360 2032850 338637 1117518 2616950 3432300 1926010 1820200 1661200 FALSE TRUE 1391471.914 2019496.074 502402.9859 1371267.542 2564877.815 3564342.802 1739225.847 1430964.395 1464814.828 0.949930248 1.378669874 0.342980543 0.936137125 1.75099116 2.433306062 1.187334954 0.976890981 1 20.48228687 3.328874077 8.364762069 1.434388595 0.891579862 0.252936372 0.48299597 0.440837487 36.20685905 0.153896222 0.198655854 2132.426528 -3.328874077 -0.542808734 FQVWDLGGQTSIRPYWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FQVWDLGGQTSIRPYWR 17 1 B4DZG7;F8VYN9;P40616-2;P40616 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ; 171.78 1.53E-09 1831940000 1003920 1074670 519630 683890 977430 878490 972620 1159630 821460 FALSE TRUE 871249.4284 1067610.422 770924.8061 839177.6771 957981.0553 912286.0788 878295.4621 911652.1488 724347.9346 1.202805153 1.473891718 1.064301794 1.158528432 1.322542675 1.259458383 1.212532569 1.25858321 1 19.46632333 1.236641845 24.92021433 0.999999677 1.245104028 0.342235276 0.106334467 56.19912621 729680.4334 0.157693686 0.024996322 17.24415209 -1.236641845 0.245104351 FQVWDYEEGEVEALLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FQVWDYEEGEVEALLDR 17 0 O43598;H0Y8X4 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ;;; 212.39 3.75E-12 1183030000 242377 234598 151417 196194 213712 218392 243670 257743 251904 FALSE TRUE 210346.2653 233056.9103 224642.7677 240742.8463 209459.5493 226793.6816 220038.9209 202626.6652 222124.1961 0.946975922 1.049218925 1.011338574 1.083820901 0.942983939 1.021021958 0.990612121 0.912222391 1 17.76100703 1.966552001 8.709139541 0.950186763 1.01107517 0.175935334 0.046564163 0.467453885 114.1166177 0.020371902 0.011708235 92.58742404 -1.966552001 0.060888407 FQWDLNAWTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FQWDLNAWTK 10 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 179.09 4.99E-06 1283190000 2866880 2310510 1410510 1739920 2192630 1918910 2317700 2561390 2465780 FALSE TRUE 2488014.544 2295332.108 2092637.354 2134995.429 2149000.953 1992731.709 2092929.811 2013656.681 2174278.297 1.14429443 1.055675398 0.962451475 0.981932916 0.988374375 0.916502598 0.962585982 0.926126469 1 21.05210518 4.714092738 1.241712608 0.955124788 1.230943591 0.83596162 0.026727385 0.503546207 0.690642756 0.007657522 0.17661218 51771.73718 -4.714092738 0.275818803 FRADNLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FRADNLNK 8 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 116.73 0.0044014 0 319680 230780 137560 165580 194630 204050 234660 248550 176220 FALSE TRUE 277433.478 229263.991 204084.4761 203177.4697 190757.2438 211899.9355 211902.7093 195399.5167 155387.4724 1.78543015 1.4754342 1.313390797 1.307553734 1.227623057 1.363687383 1.363705234 1.257498521 1 17.24551067 7.999995021 0.713262651 1.249203845 76.68409988 0.747048424 0.099822654 163.1051508 0.82375307 0.039531507 19661.27856 99998853.53 -7.999995021 75.43489604 FRAPELLFRPDLIGEESEGIHEVLVFAIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FRAPELLFRPDLIGEESEGIHEVLVFAIQK 30 2 P61163;R4GMT0 P61163 ACTR1A Alpha-centractin 0 149.44 1.61E-08 169370000 143060 128840 56842 66305 126170 121300 190330 191870 35353 FALSE TRUE 124154.2585 127993.6416 84330.98133 81360.56366 123659.4638 125966.4895 171871.8259 150840.0936 31173.60861 3.982672012 4.105833339 2.70520434 2.609918045 3.966799782 4.040805511 5.513376011 4.838711344 1 14.92803755 3.022722801 24.07508594 4.141840533 3.349914408 0.018658999 1.255350761 423.2806543 448466.2705 0.387183078 0.438990339 1053.714123 -3.022722801 -0.791926125 FRDGPPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 FRDGPPLR 8 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;;;;;; 133.13 0.00085038 6129340000 4387920 4368520 2321560 2698400 4454540 5066360 3782000 4220020 2539550 FALSE TRUE 3808045.254 4339822.904 3444274.181 3311112.962 4365903.369 5261266.148 3415222.222 3317601.563 2239327.292 1.7005309 1.938002953 1.538084314 1.478619483 1.949649515 2.349485118 1.525110793 1.48151705 1 21.09463397 1.419090439 1.769311359 0.901183631 1.802100441 0.500346503 0.255034599 0.554395599 2.326086945 0.78009292 0.075903619 26.24765075 -1.419090439 0.90091681 FRDQDLASCDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FRDQDLASCDR 11 1 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ;;;; 230.81 1.39E-12 4123130000 2915910 2655990 1673590 1945630 2636720 2675680 2595150 2749610 2573830 FALSE TRUE 2530565.106 2638542.627 2482943.722 2387415.029 2584254.431 2778615.141 2343472.752 2161627.299 2269554.75 1.115005093 1.162581615 1.094022395 1.051931014 1.138661419 1.224299674 1.032569385 0.95244554 1 21.11397786 2.024927152 9.815950445 0.978659699 1.127742709 0.674598272 0.045761017 0.182208151 68.71351832 0.019469389 0.013020139 105.9076062 -2.024927152 0.14908301 FRDQDLASCDRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FRDQDLASCDRDR 13 2 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ;;;;; 207.97 2.79E-08 1749101000 971216 799192 395208 478328 740815 768718 732980 846615 367352 FALSE TRUE 842867.3449 793942.0551 586331.9107 586939.6832 726074.2309 798291.0789 661895.7124 665572.9706 323924.065 2.602052258 2.451012879 1.810090617 1.811966898 2.241495181 2.464438938 2.043366899 2.054719122 1 18.30529613 1.120673958 2.332363628 0.366601028 2.193768401 0.667153393 0.264430239 0.618810602 2.645744269 2.661634309 0.074445647 13.20304059 -1.120673958 1.827167373 FRDQDLASCDRDRSS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FRDQDLASCDRDRSSR 16 3 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 1 FRDQDLASCDRDRS(0.271)S(0.729)R;FRDQDLASCDRDRS(0.005)S(0.995)R 144.57 7.20E-06 1410730000 526570 550040 127291 85682 435490 493070 433790 501920 87197 TRUE FALSE 456982.4403 546426.751 188849.3534 105137.4077 426824.601 512038.722 391721.1126 394588.3139 76888.67 5.943430162 7.106726531 2.456140201 1.367397923 5.551202811 6.659482106 5.094653251 5.131943549 1 16.2304834 4.255858449 24.98501239 4.136870576 6.525079395 0.248666791 1.864369228 393.2436982 567991.8424 0.488434323 1.285537669 18024.30174 -4.255858449 2.388208819 FRDSILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FRDSILR 7 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 123.98 0.0038219 6299200000 2848950 2770050 1342760 1460530 3353670 4032540 3488390 3644990 764500 FALSE TRUE 2472454.039 2751853.359 1992123.227 1792165.659 3286938.528 4187674.423 3150086.475 2865537.254 674121.6809 3.667667291 4.082131516 2.955138937 2.658519537 4.875883125 6.212045305 4.672875185 4.250771537 1 19.3626495 3.232235436 24.98747997 4.344150571 3.366260156 0.086408266 1.347637068 363.2992629 1435202.844 0.419210733 0.486964235 1707.007526 -3.232235436 -0.977890415 FREDHNCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FREDHNCK 8 1 Q86SF2;H0YAK0;H0YAH3 Q86SF2 GALNT7 N-acetylgalactosaminyltransferase 7;Polypeptide N-acetylgalactosaminyltransferase 0 ; 90.601 0.0078595 186826000 375860 370990 262990 268550 274040 332610 343890 428390 432090 FALSE TRUE 326189.1487 368552.9423 390172.8436 329528.382 268587.1402 345405.7219 310539.6007 336782.1322 381008.8124 0.856119696 0.967308184 1.024052019 0.864883885 0.704936819 0.90655573 0.815045717 0.883922159 1 18.53946484 3.597825578 9.064371564 0.856479541 0.950704613 0.190251965 0.083764072 0.5202052 36.55945126 0.02308812 0.034262116 3961.189128 -3.597825578 0.094225071 FREGERPSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FREGERPSLR 10 2 Q7L2H7;J3KNJ2;E9PN86;E7ESM3 Q7L2H7 EIF3M Eukaryotic translation initiation factor 3 subunit M 0 59.198 0.059705 24344000 25144 28138 15924 16677 30161 40488 21333 22129 31865 FALSE TRUE 21821.15669 27953.15963 23624.89966 20463.76774 29560.85511 42045.59956 19264.12894 17396.88556 28097.956 0.77661011 0.994846729 0.840804921 0.728300939 1.052064254 1.49639353 0.685606061 0.619151285 1 14.77817756 FRELAEEAAR ddPTM_MDA-MB-175_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 ;;; 205.56 1.52E-07 1925180000 1429620 1357100 732000 863140 1455150 1575820 1439300 1517450 671510 FALSE TRUE 1240692.095 1348185.121 1085997.648 1059129.129 1426195.362 1636442.815 1299716.908 1192955.126 592124.8528 2.09532177 2.276859541 1.834068682 1.78869224 2.408605812 2.763678652 2.195004823 2.014702002 1 19.17554188 1.216185561 2.929912733 0.720722246 2.194968312 0.646359961 0.275422284 0.311861565 3.14126579 1.133573091 0.077919592 16.45074463 -1.216185561 1.474246066 FRGTEPEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FRGTEPEPR 9 1 P25325-2;P25325;B1AH49 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase 0 ; 63.816 0.067112 398580000 461550 446380 268340 298030 456410 517410 487820 520020 339060 FALSE TRUE 400554.9981 443447.7004 398110.1215 365702.2666 447328.334 537315.0975 440511.2915 408817.7698 298976.7131 1.339753167 1.483218194 1.331575685 1.223179768 1.496197912 1.797180429 1.473396663 1.367390007 1 18.18967359 1.237561343 2.94259103 0.910704457 1.45102037 0.46656125 0.149898022 0.401772807 4.263598596 0.522060255 0.041912167 17.28070049 -1.237561343 0.540315913 FRHENIIGINDIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FRHENIIGINDIIR 14 1 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 76.262 0.016795 170980000 178270 214770 116430 143070 206570 222470 188490 249670 118390 FALSE TRUE 154711.1678 213359.1617 172735.9374 175556.2302 202459.6611 231028.5649 170210.2688 196280.0134 104394.0691 1.481991929 2.043786238 1.654652788 1.681668621 1.93937896 2.21304301 1.630459185 1.88018357 1 16.67168022 1.236195425 24.98945996 0.99999892 1.824187121 0.584755176 0.215900955 43.91991812 463930.7012 0.326569649 0.050059597 17.22643562 -1.236195425 0.824188201 FRIDELEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FRIDELEPR 9 1 Q14697;F5H6X6;Q14697-2 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;; 141.95 9.62E-05 1932740000 2569588 2059385 1329477 1634619 2239411 2909460 1900574 1851906 1521447 FALSE TRUE 2230010.435 2045856.764 1972416.524 2005784.228 2194851.102 3021388.809 1716256.626 1455890.313 1341583.269 1.662222903 1.524956976 1.470215506 1.49508739 1.63601556 2.252106805 1.279277005 1.085203093 1 20.35550517 2.011910844 24.99987641 1.088753131 1.657478163 0.592382735 0.2213484 154.5873185 324464.746 0.093891445 0.06325087 102.7805279 -2.011910844 0.568725032 FRKVQHELDEAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FRKVQHELDEAEER 14 2 P13533;P12883 P13533 MYH6;MYH7 Myosin-6;Myosin-7 0 ;; 60.157 0.053531 1644770000 716270 750380 315017 343740 746560 1019380 570190 599420 217047 FALSE TRUE 621613.1047 745450.7044 467360.2749 421791.4207 731704.9166 1058596.208 514893.0616 471238.6977 191387.9509 3.247921835 3.894971971 2.441952446 2.20385567 3.823150376 5.531153885 2.690310749 2.462217164 1 17.54614048 4.248123864 24.97748237 2.935967473 3.571446803 0.05451043 1.18059398 765.2339525 1998611.116 0.313704148 0.807202816 17706.1388 -4.248123864 0.63547933 FRLS(ph)LFSDLPEDTELQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FRLSLFSDLPEDTELQR 17 1 Q9BST9 Q9BST9 RTKN Rhotekin 1 FRLS(0.999)LFS(0.001)DLPEDTELQR;FRLS(1)LFSDLPEDTELQR;FRLS(1)LFSDLPEDTELQR;FRLS(0.999)LFS(0.001)DLPEDTELQR 110.75 0.00032896 126085000 100326 108950 67007 111647 100627 108140 105130 115741 131987 TRUE FALSE 87067.66491 108234.3003 99411.80932 136998.1578 98624.71957 112300.2158 94934.50878 90990.68785 116383.6472 0.748109094 0.929978591 0.854173346 1.17712549 0.847410456 0.964914045 0.81570316 0.781816776 1 16.82852884 0.948890267 15.85839127 1.701716202 0.891451485 0.076343093 0.120242632 6136564.666 53159228.64 152848656.4 0.029843924 8.889764712 -0.948890267 -0.810264717 FRNS(ph)VEGLNQEIEIIIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FRNSVEGLNQEIEIIIK 17 1 Q6P1L5 Q6P1L5 FAM117B Protein FAM117B 1 FRNS(1)VEGLNQEIEIIIK;FRNS(1)VEGLNQEIEIIIK 264.63 1.06E-27 222586000 450140 364950 233257 301380 358250 312090 390650 484300 370680 TRUE FALSE 390652.8585 362552.6194 346060.8654 369812.9353 351121.5259 324096.3042 352764.8231 380736.2138 326858.6327 1.195173752 1.109203133 1.058747822 1.131415537 1.074230541 0.991548859 1.079258089 1.164834506 1 18.31830728 4.695191385 2.837466194 1.079541689 1.210270164 0.351311594 0.052248865 0.462434584 5.51958098 0.01359191 0.132743307 49566.85736 -4.695191385 0.130728475 FRPAGAAPRPPPKPM ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FRPAGAAPRPPPKPM 15 3 P62854;Q5JNZ5 P62854 RPS26;RPS26P11 40S ribosomal protein S26;Putative 40S ribosomal protein S26-like 1 0 ; 149.57 4.08E-06 1640790000 2175130 2079920 1334840 1477000 2072840 2089530 2143450 2461820 2263590 FALSE TRUE 1887681.059 2066256.869 1980373.089 1812375.425 2031594.539 2169915.571 1935578.549 1935378.951 1995990.969 0.945736273 1.035203516 0.992175375 0.908007828 1.017837541 1.087136969 0.96973312 0.96963312 1 20.92867376 4.011346519 24.84602948 0.990034069 0.996274756 0 0.04935984 3135.670111 6866203.336 0.01301799 0.027069839 10264.70609 -4.011346519 0.006240686 FRPAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FRPAIK 6 1 Q96CN7;D6RGE2 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 85.306 0.050036 322100000 820620 752440 494150 538750 543700 679430 675310 783670 635080 FALSE TRUE 712172.9878 747497.1721 733122.5928 661081.4218 532881.4337 705568.1117 609818.5401 616088.269 560001.5659 1.271733922 1.334812646 1.309143827 1.180499238 0.951571328 1.259939534 1.088958634 1.100154547 1 19.09507134 3.573757249 3.892096897 1.090380299 1.306728756 0.611934228 0.081224812 0.154662552 4.212202006 0.022154721 0.033402499 3747.634675 -3.573757249 0.216348457 FRPDMEEEEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FRPDMEEEEAK 11 1 Q99436 Q99436 PSMB7 Proteasome subunit beta type-7 0 ;;; 212.9 3.97E-09 3248440000 3284400 2579760 2140840 2545780 2549980 2112160 3134320 3428270 3808830 FALSE TRUE 2850358.218 2562813.387 3176157.385 3123838.259 2499240.387 2193416.162 2830354.129 2695161.139 3358554.456 0.848686021 0.763070368 0.945691793 0.930113922 0.744141689 0.6530834 0.842729861 0.802476534 1 21.67940899 1.236102321 24.84571389 1.000000262 0.815434101 0.311516609 0.085841908 83.60373371 844773.4099 0.144107053 0.022002578 17.22274298 -1.236102321 -0.184566161 FRPLNESEVNRGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FRPLNESEVNRGDK 14 2 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 143.38 5.14E-06 704070000 718290 593560 322253 335607 590690 508600 646000 701840 241351 FALSE TRUE 623366.1566 589660.8653 478095.6287 411811.6988 578936.4247 528166.1711 583351.0194 551756.9777 212818.7597 2.929094021 2.770718456 2.246491941 1.935034765 2.720326091 2.481765103 2.741069538 2.592614384 1 17.6992658 4.327012744 4.623055076 2.317470276 2.887547194 0.187658384 0.509510177 0.37502866 13.85459988 0.127035992 0.358325477 21233.06766 -4.327012744 0.570076919 FRPPETTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FRPPETTER 9 1 Q96P70 Q96P70 IPO9 Importin-9 0 ; 94.309 0.008034 1261460000 1345670 1450030 810960 966110 1557720 1776580 1313270 1592530 1505060 FALSE TRUE 1167836.3 1440504.657 1203142.968 1185480.042 1526724.42 1844926.182 1185909.278 1251979.853 1327133.521 0.879968957 1.085425569 0.906572661 0.893263581 1.150392478 1.390158678 0.893587012 0.943371434 1 20.3398821 4.755285595 22.50735336 1.025859704 0.879968505 0.089039213 0.152224429 2430.256642 3270256.692 0.039157543 0.905578771 56922.7135 -4.755285595 -0.145891198 FRPSDEHHPEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FRPSDEHHPEVK 12 1 Q9H008 Q9H008 LHPP Phospholysine phosphohistidine inorganic pyrophosphate phosphatase 0 ;; 86.291 0.0072217 210010000 353599 363208 164683 247190 340644 292304 367730 445930 405259 FALSE TRUE 306869.9962 360822.0627 244324.2496 303318.2676 333865.8509 303549.124 332067.6012 350571.3397 357349.7427 0.85873854 1.009716867 0.683711839 0.848799457 0.934283171 0.849445481 0.929250987 0.98103146 1 18.44697722 1.892473394 1.397477362 1.009083071 0.861702552 0.293054893 0.081370266 0.639046945 2.195855509 0.099928297 0.026174514 78.06806121 -1.892473394 -0.147380519 FRPSLEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FRPSLEER 8 1 P35221-2;P35221;G3XAM7;P26232;P26232-5;P26232-2;P26232-3;H0YBB8 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 0 ;;;; 177.7 0.00023119 2397330000 2188563 2485004 1515793 2034161 2684527 3328001 1864267 2786019 2611520 FALSE TRUE 1899338.854 2468679.845 2248835.565 2496048.345 2631110.165 3456031.352 1683470.673 2190250.518 2302789.081 0.824799314 1.072039062 0.976570361 1.083923997 1.142575404 1.500802388 0.731057259 0.951129453 1 21.13495085 FRQS(ph)LPLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FRQSLPLSR 9 1 A0A087X165;Q9C0H9;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 FRQS(1)LPLSR;FRQS(1)LPLSR 165.35 3.73E-05 1235570000 443830 312430 153275 248450 290440 251950 358680 302460 301020 TRUE FALSE 385176.741 310377.6268 227399.3027 304864.3698 284660.8122 261642.6795 323895.2688 237781.2827 265433.7585 1.451121904 1.169322352 0.856708295 1.148551607 1.072436354 0.98571742 1.220248964 0.895821557 1 18.01799234 4.63085102 3.371664325 1.028264715 1.464684633 0.606595257 0.108334768 0.169552714 3.116898086 0.025783096 0.157905384 42741.62409 -4.63085102 0.436419918 FRRS(ph)ET(ph)PPHWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FRRSETPPHWR 11 2 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 FRRS(1)ET(1)PPHWR;FRRS(1)ET(1)PPHWR;FRRS(1)ET(1)PPHWR;FRRS(1)ET(1)PPHWR 86.641 0.027065 3947620000 1185950 1089960 571740 727288 1068370 1155460 989490 1114330 638192 TRUE FALSE 1029223.703 1082799.981 848235.3764 892429.8563 1047111.527 1199911.294 893529.4121 876039.2012 562745.6688 1.828932251 1.924137388 1.507315691 1.585849356 1.860718945 2.132244388 1.587803268 1.556723134 1 19.10212352 1.145712683 1.560228992 0.548360056 1.784587176 0.648714115 0.181252601 0.947858055 1.724875166 1.953563188 0.054352757 13.986617 -1.145712683 1.23622712 FRYS(ph)GR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 FRY(0.001)S(0.999)GR;FRYS(1)GR;FRYS(1)GR;FRYS(1)GR 94.302 0.027032 1356580000 1033280 992720 502229 934330 825110 796360 1120240 1040340 901150 TRUE FALSE 896729.43 986198.757 745108.6243 1146483.907 808691.9253 826996.4845 1011599.297 817871.3869 794617.0736 1.128505112 1.241099379 0.937695211 1.442813079 1.017712748 1.040748446 1.273065141 1.029264805 1 19.59990027 1.587354444 8.309756932 1.008897364 1.151364049 0.142785667 0.143061033 0.1998621 30.24807818 0.086373327 0.033657474 38.66824341 -1.587354444 0.142466685 FS(ph)GGFGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FSGGFGAR 8 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8Y7T2;A0A087WVZ1;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 1 FS(1)GGFGAR;FS(1)GGFGAR;FS(1)GGFGAR;FS(1)GGFGAR;FS(1)GGFGAR;FS(1)GGFGAR 159.79 0.00037459 3448460000 2230280 2458740 1421522 2323690 3076350 2487750 3132380 3218390 3968030 TRUE FALSE 1935542.847 2442588.375 2108974.794 2851319.33 3015136.654 2583455.352 2828602.27 2530162.344 3498934.014 0.553180723 0.69809501 0.602747804 0.814910861 0.86173007 0.73835498 0.808418295 0.723123767 1 21.73848403 3.734897242 24.71374402 0.810838999 0.626016556 0.573585498 0.083255911 202.640828 1367051.487 0.02170734 0.033671802 5431.218091 -3.734897242 -0.184822443 FS(ph)LCSDNLEGISEGPSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSLCSDNLEGISEGPSNR 18 0 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-5;Q14C86;C9IZ08;H0Y7I9;B4DGD8;A0A0A0MQV8 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 FS(0.577)LCS(0.423)DNLEGISEGPSNR;FS(0.938)LCS(0.062)DNLEGISEGPSNR 159.95 4.38E-11 117516000 129828 124177 93287 111550 150803 138449 145920 163104 244950 TRUE FALSE 112670.9009 123361.2731 138400.9052 136879.1324 147802.3153 143775.2226 131768.7009 128225.4789 215992.29 0.521643161 0.571137391 0.640767803 0.633722307 0.684294404 0.66564979 0.610062057 0.593657666 1 17.72062029 1.236380115 24.9999913 1.000000491 0.617623576 0.870673583 0.046608422 21.15003934 242431.2006 0.078492138 0.012189083 17.23376294 -1.236380115 -0.382376915 FS(ph)PDSQYIDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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;FS(1)PDSQYIDNR 196.84 6.20E-08 371130000 339710 349170 224800 288720 401650 386940 365110 411190 495960 TRUE FALSE 294816.4628 346876.2793 333514.0319 354278.2888 393657.9508 401825.8322 329701.6884 323260.2184 437328.1738 0.674130963 0.793171582 0.762617302 0.810097108 0.900143129 0.918819907 0.75389995 0.739170805 1 18.73835677 5.41571371 0.79692264 0.839021419 0.340594987 0.326948104 0.079630901 9.570121048 2.171339487 0.030521591 5.430560685 260443.6122 -5.41571371 -0.498426431 ERS(ph)PS(ph)PLRGNVVPS(ph)PLPTR ddPTM_MDA-MB-175_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(0.997)PLPT(0.003)R;ERS(1)PS(1)PLRGNVVPS(0.996)PLPT(0.004)R;ERS(1)PS(1)PLRGNVVPS(0.715)PLPT(0.285)R;ERS(1)PS(1)PLRGNVVPS(0.981)PLPT(0.019)R;ERS(1)PS(1)PLRGNVVPS(0.977)PLPT(0.023)R 154.14 2.56E-08 11203110000 3229390 3367250 1853040 1952040 3332460 3353750 3204330 3653880 1278670 TRUE FALSE 2802617.929 3345130.313 2749176.342 2395280.517 3266150.566 3482770.933 2893574.57 2872526.197 1127507.089 2.485676548 2.966837499 2.438278542 2.124403953 2.896789383 3.088912669 2.566347119 2.547679056 1 20.10470507 1.227572086 4.154435948 0.810523532 2.654841547 0.771155358 0.281095275 0.120271745 3.784675884 0.680530464 0.073337522 16.88776147 -1.227572086 1.844318016 FS(ph)PPRHELS(ph)PPQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FSPPRHELSPPQKR 14 2 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 2 FS(1)PPRHELS(1)PPQKR 55.383 0.071409 505500000 619500 506660 325540 360640 598370 499560 505870 628430 398950 TRUE FALSE 537631.5054 503331.7171 482972.2329 442528.824 586463.6077 518778.3965 456810.8053 494045.1349 351786.5855 1.528288819 1.430787125 1.372912592 1.257946841 1.667100543 1.474696358 1.298545266 1.404388784 1 18.42434094 0.761370635 1.533049373 1.38E-14 1.438488439 0.57804735 0.115088557 3.153369004 2.355301056 10.06231933 0.032607458 5.772588971 -0.761370635 1.438488439 FS(ph)PTMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FSPTMGR 7 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 FS(0.993)PT(0.007)MGR;FS(0.995)PT(0.005)MGR;FS(0.991)PT(0.009)MGR;FS(0.999)PT(0.001)MGR;FS(0.979)PT(0.021)MGR;FS(1)PTMGR 180.45 0.00071991 6411910000 4851000 4332520 3429250 4010930 4744560 4405670 4234970 4761010 9625700 TRUE FALSE 4209928.059 4304059.391 5087646.77 4921672.96 4650152.539 4575158.976 3824263.261 3742905.062 8487760.712 0.495999852 0.507090096 0.599409779 0.579855291 0.54786565 0.539030155 0.450562097 0.440976742 1 23.01695255 1.232915104 24.99998429 1.000000768 0.518528996 0.899557528 0.050393863 62.69861889 277618.3218 0.123790272 0.014406847 17.09681075 -1.232915104 -0.481471772 FS(ph)PVLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 167.23 0.0011476 5472923000 4423360 4221830 2709326 3112139 4965960 4621460 4231730 5033280 4746520 TRUE FALSE 3838801.769 4194096.521 4019565.116 3818797.726 4867147.112 4799250.557 3821337.476 3956952.241 4185391.813 0.917190538 1.002079783 0.960379648 0.912411047 1.162889242 1.146666972 0.91301786 0.945419788 1 21.99693126 5.664117998 0.874851149 1.007090375 0.602040792 0.098204551 0.086408154 30.45522604 5.474418506 0.031941244 17.32145016 461442.9319 -5.664117998 -0.405049583 FS(ph)PVTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FSPVTPK 7 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 FS(1)PVTPK;FS(1)PVTPK;FS(1)PVTPK;FS(1)PVTPK;FS(1)PVTPK;FS(1)PVTPK 138.26 0.0029403 9108110000 9172800 8609570 7217560 8846480 9815900 7364810 11013200 13004500 17155600 TRUE FALSE 7960591.239 8553013.168 10707996.16 10855208.49 9620582.794 7648139.006 9945141.559 10223588.88 15127484.51 0.52623364 0.565395599 0.707850413 0.717581861 0.635967122 0.505579034 0.657422029 0.675828745 1 23.85066877 1.135595723 2.259931943 1.190458928 0.61875808 0.74457588 0.069954687 0.494823713 2.040268547 0.639085159 0.019719742 13.66456224 -1.135595723 -0.571700848 FS(ph)QIQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSQIQPK 7 0 Q86V21;Q86V21-2 Q86V21 AACS Acetoacetyl-CoA synthetase 1 FS(1)QIQPK;FS(1)QIQPK 55.567 0.08171 1167220000 1474330 1507220 711850 1091840 1249270 1570200 1169950 1321280 1455230 TRUE FALSE 1279493.555 1497318.973 1056103.041 1339758.96 1224411.971 1630606.61 1056488.429 1038734.554 1283194.367 0.997115938 1.166868411 0.823026556 1.044081079 0.954190575 1.270740156 0.823326891 0.809491205 1 20.29130828 FS(ph)RS(ph)PIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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;FS(1)RS(1)PIR 70.942 0.031672 333040000 71268 72705 58996 66480 69561 78566 66797 72591 147521 TRUE FALSE 61849.75323 72227.39607 87526.66293 81575.30008 68176.87219 81588.48486 60319.03722 57067.97955 130081.2354 0.475470217 0.555248386 0.672861559 0.627110435 0.524109968 0.627211793 0.463702832 0.438710313 1 16.98905334 1.230061344 24.99965475 1.000000847 0.547294947 0.773836403 0.076784048 170.534583 501568.9797 0.235191326 0.020747868 16.98483544 -1.230061344 -0.4527059 FSALQQAVPTESTDNRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FSALQQAVPTESTDNRR 17 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C044 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;;; 164.01 4.24E-09 2650970000 1532590 1460890 773621 957544 1524360 1583300 1354980 1562910 1232350 FALSE TRUE 1330054.348 1451293.317 1147746.703 1174969 1494028.218 1644210.576 1223574.248 1228693.859 1086662.987 1.223980539 1.33555052 1.056212199 1.081263478 1.374877249 1.51308234 1.125992385 1.130703699 1 20.05147315 1.684424638 2.279063324 1.029832347 1.254135955 0.260693377 0.138171834 0.427534481 4.64000225 0.150581478 0.041252175 48.35313515 -1.684424638 0.224303608 FSASS(ph)GGGGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FSASSGGGGSR 11 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77;H0YEC5;H0YD99;H0YEN8;H0YDC0;H0YCF8 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 FSAS(0.095)S(0.905)GGGGSR 131.49 0.0011087 0 474200 370510 241460 266310 405800 467790 417980 484170 443740 TRUE FALSE 411533.2685 368076.0954 358230.8636 326779.7558 397725.3739 485786.184 377444.3639 380634.0133 391281.5627 1.051757373 0.940693686 0.915532184 0.83515245 1.016468477 1.241525874 0.964636211 0.972788011 1 18.57784761 3.023925257 24.95432824 1.037431622 0.93357832 0.23955692 0.092233876 359.0213769 374460.8716 0.029336849 0.033263593 1056.635644 -3.023925257 -0.103853302 FSAVKDELPQS(ph)PGLIHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSAVKDELPQSPGLIHGR 18 1 A0A0U1RR07;Q9HCH5-13;Q9HCH5;Q9HCH5-14;Q9HCH5-15;Q9HCH5-6 A0A0U1RR07 SYTL2 Synaptotagmin-like protein 2 1 FSAVKDELPQS(1)PGLIHGR;FSAVKDELPQS(1)PGLIHGR 150.36 3.35E-08 490290000 590440 680580 422280 635790 834440 749470 998340 1158710 823780 TRUE FALSE 512411.858 676109.2252 626496.0204 780155.8369 817836.2766 778302.5959 901521.1405 910928.8836 726393.6669 0.70541895 0.93077522 0.862474508 1.074012443 1.125885747 1.071461153 1.241091686 1.254042987 1 19.4703921 4.186008173 0.667031137 1.183347492 0.628334598 0.731953482 0.086592876 0.888835268 0.504917979 0.046778063 0.344172625 15346.45862 -4.186008173 -0.555012895 FSCPETDSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FSCPETDSHR 10 0 P50416 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 ;;; 158.79 7.88E-06 1701420000 1482730 1520140 964160 1517860 2222370 2506140 1220370 2241170 2108710 FALSE TRUE 1286783.474 1510154.1 1430431.001 1862513.312 2178149.185 2602552.827 1102018.705 1761913.236 1859420.706 0.692034605 0.812163754 0.769288519 1.001663209 1.171412784 1.399657871 0.59266776 0.947560297 1 20.8264218 3.739696393 6.468685246 1.007394772 0.762196111 0.271327168 0.201061412 0.222285213 51.52388646 0.057714238 0.093405555 5491.568348 -3.739696393 -0.245198661 FSDAGQPMSFVLEFHFEPNEYFTNEVLTK ddPTM_MDA-MB-175_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 0 311.14 4.74E-92 207690000 213450 200750 139730 171850 178610 155460 220560 282950 216380 FALSE TRUE 185242.0417 199431.26 207303.8954 210871.1691 175056.0104 161440.6468 199170.1251 222443.3444 190799.8029 0.970871242 1.045238292 1.086499526 1.105195948 0.917485279 0.846125857 1.043869659 1.165846825 1 17.54170016 1.997083283 24.99970987 1.097796216 0.99827763 0.150166208 0.085663161 189.7366224 1626266.792 0.038096763 0.025155024 99.33065137 -1.997083283 -0.099518586 FSDFLGLHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSDFLGLHSK 10 0 O60749;O60749-2;D6RC15 O60749 SNX2 Sorting nexin-2 0 ; 123.51 0.00046005 8354100000 2663700 2852500 1654240 1608750 2661600 3767700 2096220 2235100 2274700 FALSE TRUE 2311685.296 2833761.74 2454235.997 1974041.276 2608639.367 3912645.857 1892928.907 1757141.259 2005787.557 1.152507546 1.412792561 1.223577237 0.98417266 1.300556162 1.950678098 0.943733498 0.876035576 1 20.93573738 2.051016827 24.99999446 0.923370431 1.328682068 0.358574513 0.250250675 108.5106837 53173.42523 0.103830357 0.070002398 112.4648548 -2.051016827 0.405311638 FSDHVALLSVFQAWDDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FSDHVALLSVFQAWDDAR 18 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;; 264.38 5.83E-31 1088793000 962484 915113 285091 584202 939119 892362 873782 1058823 911395 FALSE TRUE 835289.3008 909101.5624 422961.9612 716853.9931 920432.3693 926691.7436 789042.7561 832401.9412 803650.9214 1.039368311 1.131214484 0.526300599 0.891996729 1.145313649 1.153102322 0.981822748 1.035775508 1 19.61620945 3.261359531 22.86366306 1.05816584 0.887439368 0.202388259 0.163051199 149.9188014 150341.8175 0.048379641 0.062389706 1825.406239 -3.261359531 -0.170726472 FSDIQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FSDIQIR 7 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ;;; 115.69 0.013082 598770000 1406540 1494800 898160 1133660 1551770 1644890 1493960 1664880 1721380 FALSE TRUE 1220662.175 1484980.56 1332513.18 1391074.83 1520892.813 1708169.983 1349075.989 1308858.368 1517880.417 0.804188631 0.978325132 0.877877575 0.916458776 1.001984607 1.125365321 0.888789376 0.862293467 1 20.53362671 3.431595897 7.807406787 0.962370862 0.896112592 0.190697208 0.082006694 0.536297409 79.12503496 0.02555902 0.033145799 2701.443552 -3.431595897 -0.06625827 FSDPGQPMSFVLEFHFEPNDYFTNSVLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSDPGQPMSFVLEFHFEPNDYFTNSVLTK 29 0 Q99733;Q99733-2;C9JZI7;E9PP22;H0YCI4 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 ; 235.86 2.96E-45 281548000 258690 248170 165055 210558 214630 197815 276410 330430 287980 FALSE TRUE 224503.4611 246539.7549 244876.1501 258368.4121 210359.2829 205425.0711 249603.8007 259770.1159 253935.3325 0.884096982 0.970876138 0.964324845 1.017457514 0.82839706 0.808966082 0.982942383 1.022977438 1 17.95410162 2.015565203 24.99589617 1.010078979 0.916471653 0.31382989 0.063314539 295.4675298 474484.4466 0.027894624 0.018799921 103.6490206 -2.015565203 -0.093607327 FSEAEHWLDYFPPLAIQDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FSEAEHWLDYFPPLAIQDLK 20 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRU9 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 172.84 5.76E-12 136420000 321360 244430 176840 278470 247610 217360 299250 366160 469500 FALSE TRUE 278891.4618 242824.3232 262360.4155 341700.8696 242683.0454 225721.9799 270228.7811 287859.5335 413996.2449 0.673656984 0.586537502 0.633726559 0.825371906 0.586196248 0.545227119 0.652732445 0.69531919 1 18.65925816 1.198568042 2.740739863 1.103028567 0.642634748 0.687315925 0.07495291 0.320490553 2.567105875 0.355829752 0.020031708 15.7967608 -1.198568042 -0.460393819 FSEAEHWLDYFPPLAIQDLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FSEAEHWLDYFPPLAIQDLKR 21 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRU9 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 65.784 0.015221 124690000 461350 327960 176320 203760 380840 315820 395200 436380 85884 FALSE TRUE 400381.4286 325805.6092 261588.9418 250026.8223 373262.0291 327969.7998 356873.5648 343063.5329 75730.89136 5.286897083 4.302149405 3.454190715 3.301516961 4.928794874 4.330726786 4.71239092 4.530034267 1 16.20859429 4.664267927 3.361789602 3.917217094 5.367664338 0.147840817 1.121808608 0.567068048 10.54701393 0.274136841 1.862957718 46160.22603 -4.664267927 1.450447243 FSEEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FSEEQR 6 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;; 153.88 0.023438 3617100000 5916310 5264060 3211840 4055780 4809510 5415350 5142090 5617920 5388860 FALSE TRUE 5134454.643 5229480.043 4765096.567 4976706.838 4713810.161 5623682.019 4643410.903 4416571.527 4751795.11 1.080529468 1.100527258 1.002799249 1.04733195 0.99200619 1.183485796 0.977190892 0.929453275 1 22.1800412 2.02591283 24.99992516 0.957777862 1.063474239 0.412597075 0.055479007 188.0689213 181442.4863 0.021771102 0.014677624 106.1482478 -2.02591283 0.105696377 FSEGEATLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FSEGEATLR 9 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A1B0GTT3;A0A0U1RQQ5 P47897 QARS Glutamine--tRNA ligase 0 82.563 0.040558 0 61006 56092 44055 41497 59641 66374 59342 56124 58907 FALSE TRUE 52943.90253 55723.52796 65360.14536 50919.52809 58454.26079 68927.45073 53587.02197 44122.31936 51943.08157 1.019267647 1.072780557 1.258303192 0.98029471 1.125352194 1.326980392 1.031648881 0.849435922 1 15.66464399 1.998278465 24.99419819 0.921937063 1.131012337 0.385098505 0.107797307 58.25348323 845759.2258 0.04391593 0.029123588 99.60438644 -1.998278465 0.209075274 FSEGVLQS(ph)PSQDQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FSEGVLQSPSQDQEK 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 FSEGVLQS(0.994)PS(0.006)QDQEK;FSEGVLQS(0.5)PS(0.5)QDQEK;FSEGVLQS(0.994)PS(0.006)QDQEK 311.54 3.75E-56 291938000 613520 553740 363470 515580 606800 502740 678640 872860 812350 TRUE FALSE 532441.7775 550102.4455 539245.3077 632650.3191 594725.8672 522080.7331 612825.5973 686205.6816 716314.9084 0.743306849 0.767961743 0.752804809 0.883201385 0.830257559 0.728842478 0.855525398 0.957966494 1 19.45023444 1.78967169 2.467801321 0.992215344 0.788683117 0.750106217 0.045948403 0.136919321 1.606967494 0.038590715 0.013424756 61.61290562 -1.78967169 -0.203532226 FSELTAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FSELTAEK 8 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 80.455 0.059104 73263000 721540 550940 271860 233850 440910 294770 824470 846520 86864 FALSE TRUE 626186.6609 547320.8389 403332.4053 286949.2167 432136.7536 306109.9926 744513.0263 665498.2856 76595.03688 8.175290285 7.14564365 5.265777285 3.746316059 5.64183753 3.996472946 9.720120998 8.688530129 1 16.22496329 4.44242731 4.2752621 5.857207988 7.994926727 0.111817869 2.470179348 0.512695068 20.69613514 0.656073504 2.135553776 27696.65425 -4.44242731 2.13771874 FSESES(ph)RSPLEDETDNTWMFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FSESESRSPLEDETDNTWMFK 21 1 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 FSESES(0.642)RS(0.358)PLEDETDNTWMFK 239.47 3.82E-30 44117000 48495 41743 36695 35934 50474 42607 54834 66529 45412 TRUE FALSE 42086.26288 41468.78748 54440.82474 44093.36392 49469.66615 44246.11886 49516.20712 52302.29108 40043.44509 1.051015036 1.035594899 1.359543981 1.101138122 1.235399852 1.104952852 1.236562114 1.306138644 1 15.28927848 4.312226311 24.99999431 1.199748851 1.043301424 0.256897401 0.104460793 50.91586733 17277.20079 0.02444031 0.064662971 20522.31317 -4.312226311 -0.156447426 FSESESRS(ph)PLEDETDNTWMFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FSESESRSPLEDETDNTWMFK 21 1 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 FSESES(0.262)RS(0.738)PLEDETDNTWMFK 215.46 3.97E-25 51156000 37769 36063 27899 28187 35023 34457 38312 50062 39336 TRUE FALSE 32777.73096 35826.09978 41391.04972 34587.28916 34326.11082 35782.58309 34596.50814 39356.63088 34685.74289 0.944991464 1.032876819 1.193315935 0.99716155 0.989631703 1.03162222 0.997427336 1.134663052 1 15.08205516 1.761222192 25 1.075583681 1.030987977 0.046754238 0.072214103 35.52605542 39230.16358 0.038543588 0.018509646 57.70616218 -1.761222192 -0.044595703 FSETHADPHNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FSETHADPHNSR 12 0 O00767 O00767 SCD Acyl-CoA desaturase 0 ;;; 138.75 3.98E-05 1270010000 1512530 1972310 388754 1431410 3312470 3189790 1485760 2715860 2953310 FALSE TRUE 1312645.328 1959353.766 576756.7347 1756433.518 3246558.328 3312503.285 1341671.224 2135094.474 2604173.056 0.504054569 0.75239 0.221474043 0.674468816 1.246675339 1.271998141 0.515200486 0.819874266 1 21.31239389 3.469410963 24.90591135 0.935312485 0.506840706 0.442772429 0.246316183 181.8455667 587397.5982 0.074647434 0.096558451 2947.209194 -3.469410963 -0.42847178 FSFHS(ph)PSAQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FSFHSPSAQQR 11 0 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 1 FSFHS(0.998)PS(0.002)AQQR;FSFHS(1)PSAQQR;FSFHS(1)PSAQQR;FSFHS(1)PSAQQR;FSFHS(0.999)PSAQQR 193 7.38E-07 1311500000 1037570 1315080 396109 765383 1331880 1384540 1097620 1294960 1109220 TRUE FALSE 900452.4956 1306441.153 587668.6373 939174.9083 1305378.194 1437804.15 991172.9813 1018042.881 978089.2752 0.920624035 1.335707472 0.600833331 0.960213891 1.334620701 1.470013204 1.013376802 1.040848629 1 19.89960663 3.33892909 12.55585591 1.158399131 0.955807307 0.184746289 0.225996631 1.036751305 123.0711932 0.067544631 0.087197202 2182.373555 -3.33892909 -0.202591825 FSFSGNTLVSSSADPEGHFETPIWIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FSFSGNTLVSSSADPEGHFETPIWIER 27 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 117.04 0.00055979 412020000 147370 116800 62663 77152 131250 164120 112030 125020 106150 FALSE TRUE 127894.6811 116032.7331 92967.0364 94670.54079 128638.3818 170433.8026 101165.3478 98285.44591 93601.06793 1.366380576 1.239651808 0.993226236 1.011425862 1.374326005 1.820853184 1.080814034 1.050046202 1 16.51423737 2.028159527 24.99970401 1.03964661 1.289078624 0.222836173 0.227246708 351.5813696 312128.4572 0.100628084 0.06784214 106.698798 -2.028159527 0.249432014 FSFSPEPTLEDIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FSFSPEPTLEDIRR 14 1 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 ;; 207.04 1.60E-08 1089362000 737150 808910 436580 492430 780910 820300 742090 819600 503700 FALSE TRUE 639733.7598 803596.2169 647711.5483 604243.7578 765371.4188 851857.4718 670122.226 644334.9181 444153.1598 1.440344948 1.809277271 1.458306744 1.360440074 1.723215071 1.917936309 1.508763838 1.450704344 1 18.76069773 1.181972464 1.843123116 0.72256795 1.612536703 0.544407064 0.173441905 0.822816287 2.338685861 1.35499318 0.048824685 15.20451124 -1.181972464 0.889968753 FSFWDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FSFWDK 6 0 P78406;E9PQ57 P78406 RAE1 mRNA export factor 0 100.74 0.086812 279920000 926310 576380 481120 606010 657460 588360 637250 750500 1039200 FALSE TRUE 803895.7865 572593.7218 713791.2412 743613.8328 644377.8323 610994.5899 575449.5931 590011.4154 916346.9599 0.877283193 0.624865632 0.77895303 0.811498117 0.703202892 0.666772103 0.627982214 0.643873381 1 19.80553443 3.199499915 24.32939432 0.707195967 0.762972819 0.013423347 0.121298227 426.9929932 265955.3493 0.036096468 0.040930343 1583.069258 -3.199499915 0.055776851 FSFWDKDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSFWDKDAR 9 1 P78406;E9PQ57 P78406 RAE1 mRNA export factor 0 ; 121.5 0.00055821 871560000 7124400 5329600 2411000 2686800 5001400 4468300 5391500 6265100 1391800 FALSE TRUE 6182892.489 5294589.507 3576967.664 3296879.005 4901881.925 4640198.392 4868633.16 4925357.12 1227262.99 5.037952372 4.314144199 2.914589371 2.686367171 3.994157704 3.780932393 3.967065903 4.013285793 1 20.22701301 4.433903149 4.253056414 3.343115687 4.909697511 0.314489247 0.918775184 0.246490976 9.486754237 0.229963268 0.737185223 27158.3355 -4.433903149 1.566581823 FSGDLDDQTCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FSGDLDDQTCR 11 0 P05455 P05455 SSB Lupus La protein 0 ;;;;; 280.25 5.64E-27 4826160000 8422770 7157840 4276380 4814990 6777020 6673700 6573460 7486000 6952280 FALSE TRUE 7309679.604 7110819.678 6344451.672 5908307.072 6642170.561 6930441.557 5935966.861 5885177.156 6130389.378 1.192367915 1.159929531 1.034918221 0.96377354 1.083482655 1.130505932 0.968285454 0.960000547 1 22.54754728 8 0.422219127 0.992973735 5.084606406 0.53761318 0.057648795 74.62508954 1.000958146 0.054302263 256.8656958 100000000 -8 4.091632671 FSGEEGEIEDDES(ph)GTENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSGEEGEIEDDESGTENR 18 0 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 FSGEEGEIEDDES(1)GTENR;FSGEEGEIEDDES(1)GTENR 367.31 1.72E-107 3199000000 1380380 1068280 1028390 1333080 1068040 1040380 1008960 1235390 2910600 TRUE FALSE 1197959.286 1061262.398 1525722.844 1635776.189 1046788.094 1080404.092 911111.2145 971211.4623 2566512.184 0.466765478 0.413503745 0.594473252 0.637353759 0.407864066 0.420961996 0.354999762 0.378416852 1 21.29137768 1.233558946 24.9986545 1.000000837 0.456165563 0.778912586 0.090518472 81.04483582 405019.5059 0.199638425 0.024651396 17.12217557 -1.233558946 -0.543835274 FSGEEGEIEDDES(ph)GTENREEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FSGEEGEIEDDESGTENREEK 21 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 FSGEEGEIEDDES(0.993)GT(0.007)ENREEK;FSGEEGEIEDDES(1)GTENREEK;FSGEEGEIEDDES(0.997)GT(0.003)ENREEK 284.88 1.66E-45 1146870000 1079310 752770 723063 843390 783720 756410 881510 1024620 1586240 TRUE FALSE 936676.4489 747825.0043 1072738.685 1034894.59 768125.5053 785509.5822 796021.2959 805512.9866 1398716.514 0.669668542 0.534650872 0.766945035 0.739888733 0.549164536 0.561593128 0.569108385 0.575894385 1 20.41567216 1.23473293 24.99983358 1.000000547 0.617827715 0.684900906 0.080794452 69.20713223 451947.2844 0.151330326 0.02068017 17.16852283 -1.23473293 -0.382172832 FSGEEGEIEDDES(ph)GTENREEKDNIQPTTE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FSGEEGEIEDDESGTENREEKDNIQPTTE 29 2 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 FSGEEGEIEDDES(0.975)GT(0.025)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.977)GT(0.023)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.994)GT(0.006)ENREEKDNIQPTTE 242.34 1.37E-45 1634110000 1571510 1114510 949810 907280 1177280 982000 1385950 1588580 883750 TRUE FALSE 1363830.972 1107188.71 1409141.293 1113291.791 1153854.431 1019778.175 1251540.782 1248874.529 779274.0818 1.75013003 1.420794989 1.808274298 1.42862674 1.480678568 1.308625809 1.606034143 1.602612686 1 19.57177131 1.234956807 24.99937315 0.999999229 1.546165721 0.565138462 0.151774649 77.31044488 536213.8718 0.255335477 0.035499948 17.1773754 -1.234956807 0.546166492 FSGFSAKPNNSGEAPSS(ph)PTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FSGFSAKPNNSGEAPSSPTPK 21 1 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 FSGFSAKPNNSGEAPS(0.21)S(0.762)PT(0.028)PK 107.47 0.00020741 401240000 610110 414310 352680 418850 410170 341720 566410 586620 766250 TRUE FALSE 529482.4177 411588.3703 523237.2276 513956.2942 402008.4195 354866.1895 511479.6454 461175.8781 675664.7979 0.783646594 0.609160595 0.774403564 0.760667562 0.59498204 0.525210416 0.757002062 0.682551288 1 19.36594817 1.238405596 24.91843589 1.000000348 0.683957059 0.562892233 0.086956047 2.70396821 433172.5811 0.118936029 0.021162424 17.31432623 -1.238405596 -0.316043288 FSGWYDADLS(ph)PAGHEEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSGWYDADLSPAGHEEAK 18 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 1 FSGWYDADLS(1)PAGHEEAK;FSGWYDADLS(1)PAGHEEAK 195.36 1.65E-15 301240000 613230 532950 420350 509540 533420 453070 612990 728370 860410 TRUE FALSE 532190.1018 529449.0164 623632.666 625238.8448 522805.9856 470499.8961 553542.3241 572613.7437 758693.31 0.701456168 0.697843265 0.821982556 0.824099589 0.689087381 0.620145044 0.729599585 0.754736777 1 19.53315729 1.224619232 3.615121866 1.042278238 0.727985721 0.66571178 0.060449868 0.207679125 4.057843971 0.182634745 0.016786881 16.77332772 -1.224619232 -0.314292517 FSGWYDADLSPAGHEEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FSGWYDADLSPAGHEEAK 18 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;; 308.36 4.36E-61 8482600000 8268600 7179200 3646630 6190020 7461600 6306560 8531400 10185400 13653000 FALSE TRUE 7175883.56 7132039.362 5410152.465 7595558.65 7313128.758 6549177.444 7704026.141 8007331.473 12038957.89 0.596055209 0.592413349 0.449387108 0.630914961 0.607455298 0.5439987 0.639924669 0.665118322 1 23.52120718 -0.202002762 1.096581019 9.99999999 0.56987685 0.864131236 0.052270704 11.96382133 0.810847501 252.765715 0.016042759 0.628054364 0.202002762 -9.43012314 FSGWYDADLSPAGHEEAKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FSGWYDADLSPAGHEEAKR 19 1 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;; 180.88 2.12E-14 6078180000 5856530 4572570 2000120 3531430 4946740 4255250 5954700 6584890 3138190 FALSE TRUE 5082574.722 4542532.487 2967384.722 4333295.156 4848309.552 4418952.221 5377214.111 5176762.517 2767196.753 1.836723289 1.641564692 1.072343236 1.565951229 1.752065352 1.596905683 1.943199053 1.870760549 1 21.3999938 3.467043402 20.62675975 1.681610222 1.494313231 0.013230921 0.315862867 73.66523338 150767.6399 0.091348847 0.118242814 2931.186163 -3.467043402 -0.187296991 FSHDADPEVSYNSIFAMGMVGSGTNNAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FSHDADPEVSYNSIFAMGMVGSGTNNAR 28 0 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 122.04 4.72E-05 30352000 22697 25107 15269 16658 25001 22042 22750 29830 23690 FALSE TRUE 19697.53394 24942.07046 22653.13947 20440.4535 24503.52901 22889.97 20543.7085 23451.08664 20889.39519 0.942944196 1.194006348 1.08443252 0.978508632 1.173012851 1.095769877 0.98345157 1.122631193 1 14.3504831 1.211780933 23.98281416 0.999999381 1.075285178 0.067879702 0.082800702 4667.681113 4179813.258 1.441312615 0.018667012 16.2847439 -1.211780933 0.075285797 FSHEEIAMATVTALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 FSHEEIAMATVTALR 15 0 P04075;J3KPS3;P04075-2;H3BQN4;H3BU78;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;;;;;;; 242.91 5.98E-18 13392828000 6138458 5820869 4317061 5033062 5832951 6035077 5640492 6270574 8968986 FALSE TRUE 5327245.222 5782631.328 6404806.139 6175895.653 5716886.687 6267250.317 5093477.954 4929660.548 7908682.693 0.673594507 0.731175033 0.809844874 0.780900675 0.722862063 0.792451861 0.644036201 0.623322586 1 22.91500598 4.68526207 4.152587996 0.749007861 0.670759021 0.056013251 0.103916352 0.723859847 23.88802848 0.025575034 0.145833223 48446.46235 -4.68526207 -0.07824884 ENIKPNET(ph)SPSFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.346)S(0.307)PS(0.346)FS(0.001)K;ENIKPNET(0.542)S(0.344)PS(0.113)FS(0.002)K 98.816 0.0039249 1019090000 1475500 1074270 1214310 1508900 1111660 826720 1540280 1864010 3428380 TRUE FALSE 1280508.937 1067213.05 1801554.378 1851518.807 1089540.141 858524.4534 1390903.883 1465405.967 3023080.822 0.423577473 0.353021673 0.595933249 0.612460902 0.360407215 0.283989911 0.460094839 0.484739262 1 21.52758812 1.227663413 4.024651127 1.068100456 0.443405812 0.745813991 0.101761241 0.140419979 3.955957264 0.263101892 0.027594826 16.89131312 -1.227663413 -0.624694644 FSHQGVQLIDFSPCER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FSHQGVQLIDFSPCER 16 0 P55884;P55884-2;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;; 190.46 8.53E-10 1780930000 1555360 1480130 887386 935030 1534090 1569570 1348960 1603870 1510800 FALSE TRUE 1349815.235 1470406.929 1316528.838 1147342.853 1503564.61 1629952.374 1218138.067 1260894.882 1332194.945 1.01322651 1.103747566 0.988240379 0.861242461 1.128637078 1.223508901 0.914384243 0.946479257 1 20.34537378 FSHVDSPNSECKGEDATDDQFES(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSHVDSPNSECKGEDATDDQFESPK 25 1 Q5T5P2;Q5T5P2-3;A0A0U1RRK8 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 FSHVDSPNSECKGEDATDDQFES(1)PK;FSHVDSPNSECKGEDATDDQFES(1)PK 298.5 2.58E-63 333970000 237233 208244 193928 231039 277856 181611 331460 410150 486190 TRUE FALSE 205882.058 206876.0315 287712.2295 283499.9362 272327.2092 188597.6927 299315.0602 322442.6143 428713.1721 0.480232639 0.482551144 0.671106577 0.661281142 0.635220065 0.439915787 0.698170898 0.752117349 1 18.70965322 1.247685328 1.281109236 1.193393515 0.571937145 0.726749953 0.084815869 0.787267021 1.12461067 0.657670035 0.027053568 17.68826874 -1.247685328 -0.621456369 FSLCS(ph)DNLEGISEGPSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSLCSDNLEGISEGPSNR 18 0 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-5;Q14C86;C9IZ08;H0Y7I9;B4DGD8;A0A0A0MQV8 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 FS(0.137)LCS(0.854)DNLEGIS(0.008)EGPSNR;FS(0.138)LCS(0.862)DNLEGISEGPSNR 304.79 6.63E-50 314510000 248550 243510 191353 243210 310430 301550 302590 346360 508200 TRUE FALSE 215703.4878 241910.3668 283891.9508 298434.5477 304253.0503 313150.8236 273244.8684 272293.6094 448121.1749 0.481350804 0.539832483 0.633516037 0.665968413 0.67895263 0.698808361 0.609756654 0.607633883 1 18.77352937 1.237574574 24.99489532 1.00000045 0.6184569 0.777491776 0.0647842 12.46058077 315695.2071 0.100700955 0.017009424 17.28122698 -1.237574574 -0.38154355 FSLDVCEAMEYLEGNNFVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSLDVCEAMEYLEGNNFVHR 20 0 P41240 P41240 CSK Tyrosine-protein kinase CSK 0 ; 211.06 3.09E-22 363050000 541960 532040 346640 369122 508730 539080 602470 624880 568450 FALSE TRUE 470338.6128 528544.9942 514276.2634 452936.7918 498607.2683 559818.7564 544042.5521 491254.2748 501248.4886 0.938334227 1.054457033 1.025990652 0.903617272 0.994730717 1.116848767 1.085374948 0.980061359 1 18.93516646 2.97430825 24.87173162 1.040925032 0.98412457 0.232575459 0.056171422 1238.419982 1198892.992 0.019096958 0.019170336 942.5583607 -2.97430825 -0.056800462 FSLYFLAYEDKNDIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSLYFLAYEDKNDIPK 16 1 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 ; 211.7 5.84E-12 458100000 925610 556010 458000 566190 356400 283910 612430 796020 940680 FALSE TRUE 803288.2933 552357.5337 679490.3319 694752.0932 349308.3373 294832.2014 553036.6329 625797.3176 829473.882 0.968431087 0.665913112 0.819182311 0.837581638 0.421120357 0.355444828 0.666731822 0.754450901 1 19.66183703 7.999984479 0.910567092 0.669152842 153.1546561 0.166944805 0.190715024 2056.124243 4.275322864 0.066691584 651880.227 99996426.18 -7.999984479 152.4855033 FSPDDKYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSPDDKYSR 9 1 Q9NPE3 Q9NPE3 NOP10 H/ACA ribonucleoprotein complex subunit 3 0 ; 77.379 0.029885 340900000 995470 821930 565510 735050 868230 824140 935190 1163440 961660 FALSE TRUE 863916.1173 816530.6877 838992.5275 901954.337 850953.9217 855845.1991 844495.4177 914647.4099 847973.6503 1.018800663 0.962919882 0.989408724 1.063658448 1.00351458 1.009282775 0.995898183 1.07862716 1 19.69365991 3.892226995 11.55591981 1.027329004 0.987197684 0.224674837 0.030124009 0.757561364 76.89451515 0.00793374 0.013751714 7802.378145 -3.892226995 -0.04013132 FSPDGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FSPDGNR 7 0 O75083;O75083-3;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 93.262 0.055144 0 418250 395270 225180 252210 356530 402920 390950 378230 390290 FALSE TRUE 362977.2028 392673.4453 334077.8012 309478.1353 349435.7505 418420.5931 353035.7292 297348.4579 344150.3608 1.05470528 1.140993851 0.970732096 0.899252683 1.015357792 1.21580751 1.025818274 0.864007398 1 18.3926795 1.893668944 7.312576734 0.92703014 1.047970506 0.214904765 0.091499999 0.390477496 23.71738693 0.046674292 0.025619058 78.28326731 -1.893668944 0.120940366 FSPFLQTAEDNTQDEVAGAPADHHGPS(ph)DEEQGSPPEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FSPFLQTAEDNTQDEVAGAPADHHGPSDEEQGSPPEDK 38 0 Q92766;Q92766-2;Q92766-5;Q92766-3;A0A087X055 Q92766 RREB1 Ras-responsive element-binding protein 1 1 FSPFLQTAEDNTQDEVAGAPADHHGPS(1)DEEQGSPPEDK 121.94 3.49E-08 65834000 62730 51408 34544 38587 60676 42259 54988 60753 57185 TRUE FALSE 54440.07156 51070.29746 51249.59394 47348.76812 59468.66631 43884.73108 49655.27222 47761.44373 50424.65445 1.079632021 1.012804114 1.016359844 0.939000349 1.179356943 0.87030306 0.984741944 0.947184354 1 15.62184167 2.706428395 24.99900517 0.95323514 1.036090333 0.31304379 0.069019486 876.0840135 681596.3813 0.022275803 0.019646702 508.6609461 -2.706428395 0.082855193 FSPPS(ph)PLPQAVFSTSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FSPPSPLPQAVFSTSSR 17 0 Q99594;A0A1X7SBS4 Q99594 TEAD3 Transcriptional enhancer factor TEF-5 1 FSPPS(1)PLPQAVFSTSSR;FSPPS(1)PLPQAVFSTSSR;FS(0.001)PPS(0.999)PLPQAVFSTSSR;FSPPS(1)PLPQAVFSTSSR 159.44 3.37E-09 1675510000 1059211 749516 539555 665708 773130 728491 970366 1050628 869181 TRUE FALSE 919233.5827 744592.38 800485.6027 816867.1761 757746.2256 756516.5202 876260.0547 825959.3782 766427.4124 1.199374615 0.971510632 1.044437594 1.065811534 0.988673178 0.987068714 1.143304689 1.07767463 1 19.54778964 1.224912027 24.25877927 0.999999796 1.056954291 0.064302699 0.070907856 1575.970841 2800858.239 0.313312282 0.016680884 16.78463986 -1.224912027 0.056954495 FSPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSPSPR 6 0 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 FSPS(1)PR;FSPS(1)PR 122.18 0.02028 740130000 919720 930510 435290 627560 917150 795780 795460 1026620 826620 TRUE FALSE 798176.6717 924397.4185 645797.7 770057.0897 898900.5094 826394.1715 718316.4116 807085.3022 728897.9253 1.095045882 1.268212443 0.885991958 1.056467666 1.233232361 1.133758436 0.985482859 1.107267937 1 19.47535727 -0.459095115 0.712397954 1.17E-15 1.104694539 0.070311988 0.109493922 93.39786568 5.02806001 139.3716403 0.046135967 0.347460056 0.459095115 1.104694539 FSQTVLGADSEALT(ph)DSWEALSLDTEYWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FSQTVLGADSEALTDSWEALSLDTEYWK 28 0 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 1 FSQTVLGADS(0.003)EALT(0.448)DS(0.448)WEALS(0.1)LDT(0.001)EYWK 78.921 0.024588 14051000 46102 36139 23918 25592 26992 28332 35253 40905 40182 TRUE FALSE 40009.50389 35901.60053 35484.8248 31403.05475 26454.91201 29421.95037 31834.16949 32157.78407 35431.72974 1.12919985 1.0132613 1.001498517 0.886297536 0.746644666 0.830384251 0.898465012 0.907598481 1 15.11275428 4.12108855 1.670279893 0.875831058 1.101793879 0.602553297 0.067562358 0.310810953 1.6115978 0.021206548 0.077635135 13215.65066 -4.12108855 0.225962821 FSS(ph)PIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSSPIVK 7 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 FS(0.012)S(0.988)PIVK;FS(0.01)S(0.99)PIVK 91.783 0.016942 318300000 1516540 1409730 865800 1109010 1318970 1158120 1494980 1805840 1535010 TRUE FALSE 1316125.397 1400469.391 1284503.776 1360827.671 1292725.078 1202673.626 1349997.07 1419675.169 1353542.866 0.972355903 1.034669404 0.948993791 1.005382027 0.955067704 0.888537523 0.997380359 1.048858669 1 20.36830915 1.999842527 25 1.026479331 0.968543746 0.266875629 0.039314945 6.789981482 1078005.025 0.016547355 0.011025664 99.96374702 -1.999842527 -0.057935585 FSS(ph)PTEELDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FSSPTEELDYR 11 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;O95359-2;Q4VXL4;H0Y911 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 FSS(0.999)PTEELDYR;FS(0.001)S(0.999)PTEELDYR;FSS(1)PTEELDYR 237.08 1.50E-15 1810680000 1424830 1560960 1028250 1229210 1651470 1761150 1659430 1836800 1667420 TRUE FALSE 1236535.105 1550705.951 1525515.139 1508320.918 1618608.978 1828902.58 1498498.734 1444014.614 1470299.507 0.841008991 1.054687119 1.037554003 1.025859636 1.100870245 1.243897975 1.01917924 0.982122763 1 20.48767864 4.738658604 8.397347855 1.055860296 0.839635776 0.462939376 0.073425967 0.091349398 96.05595407 0.019539057 0.11171543 54784.61377 -4.738658604 -0.21622452 FSSETWQNLGTLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSSETWQNLGTLHR 14 0 F8W9U3;Q96IU4;B4DQI4 F8W9U3 ABHD14B Alpha/beta hydrolase domain-containing protein 14B 0 ; 238.43 2.51E-17 3490500000 3339500 3094500 1812120 2448100 3229200 3398700 3056800 3441700 3368400 FALSE TRUE 2898176.614 3074172.026 2688467.293 3003978.522 3164945.238 3529450.188 2760352.006 2705719.238 2970191.589 0.975754098 1.03500799 0.905149453 1.011375338 1.065569389 1.188290412 0.929351499 0.910957814 1 21.50212456 FSSVSS(ph)PQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FSSVSSPQPR 10 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 FS(0.004)S(0.018)VS(0.061)S(0.917)PQPR;FS(0.001)S(0.009)VS(0.05)S(0.94)PQPR;FS(0.047)S(0.194)VS(0.078)S(0.681)PQPR;FS(0.002)S(0.078)VS(0.048)S(0.872)PQPR 106.11 0.0025801 1922110000 4794280 4439020 2275590 3127280 4539040 4346770 3490540 4392880 3614940 TRUE FALSE 4160703.751 4409859.785 3376072.935 3837376.721 4448721.984 4513993.055 3152027.968 3453496.797 3187585.911 1.305283643 1.383448135 1.05913159 1.203850446 1.395639869 1.416116516 0.988844867 1.083420775 1 21.6040328 2.226850069 24.9998439 1.034980887 1.287840034 0.585719387 0.106761081 172.602254 368470.646 0.045933627 0.031251288 168.5970878 -2.226850069 0.252859147 FSTELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FSTELER 7 0 Q9UH65;E7EMB1 Q9UH65 SWAP70 Switch-associated protein 70 0 95.352 0.031474 208470000 151340 154220 97612 97864 145860 187660 119500 146950 150960 FALSE TRUE 131340.0356 153206.9187 144817.4897 120085.517 142957.6714 194879.4016 107910.9084 115525.8861 133113.6808 0.98667571 1.150947955 1.087923411 0.902127537 1.073951757 1.464007309 0.810667302 0.867873876 1 17.02229933 FSTLTDDPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSTLTDDPSPR 11 0 Q14C86-2;Q14C86-6;Q14C86-4;Q14C86-5;Q14C86 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 FSTLTDDPS(1)PR;FSTLTDDPS(1)PR 109.72 0.0019832 556600000 1042080 1253960 834710 1001400 1480950 1652690 1523880 1735240 1673420 TRUE FALSE 904366.4877 1245722.654 1238378.548 1228783.175 1451481.992 1716270.054 1376094.352 1364172.43 1475590.194 0.612884588 0.844219933 0.839242869 0.832740134 0.983661994 1.163107522 0.932572172 0.924492745 1 20.49286068 5.436635808 0.592034387 0.990489433 1.52E-15 0.683033145 0.079957029 5.269788744 0.781185945 0.044646273 4.266473651 273297.594 -5.436635808 -0.990489433 FSTWTNTEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSTWTNTEFR 10 0 P07099 P07099 EPHX1 Epoxide hydrolase 1 0 ; 132.88 0.00049334 411370000 198995 214160 108634 194187 233310 294600 175450 291760 262712 FALSE TRUE 172697.3066 212753.1689 161169.7658 238280.1263 228667.5875 305933.4526 158434.886 229369.3945 231654.4866 0.745495194 0.918407288 0.695733409 1.028601387 0.987106232 1.320645488 0.683927552 0.990135774 1 17.8216151 3.725579761 24.83739143 0.993342997 0.799731494 0.283182901 0.160569344 977.4299112 1870201.091 0.043315091 0.064716069 5315.936211 -3.725579761 -0.193611503 FSTYSQS(ph)PPDTPSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FSTYSQSPPDTPSLR 15 0 A0A0A0MTL6;Q6ZS17-2;Q6ZS17;Q6ZS17-3;Q6ZS17-4;H3BMG9;H3BSV5 A0A0A0MTL6 FAM65A Protein FAM65A 1 FSTYS(0.189)QS(0.811)PPDTPSLR;FSTYS(0.08)QS(0.92)PPDTPSLR;FSTYS(0.001)QS(0.969)PPDT(0.03)PS(0.001)LR 323.02 8.63E-57 1021470000 1623040 1182860 650150 889990 1136890 1101290 1028480 1223890 1006160 TRUE FALSE 1408551.152 1175089.715 964564.7146 1092075.832 1114268.113 1143657.339 928738.1679 962170.6478 887212.911 1.587613451 1.32447319 1.087185165 1.230906154 1.255919633 1.289044968 1.046804162 1.084486752 1 19.75892083 8 0.660976062 1.120145226 45.52996337 0.68927545 0.095836652 149.9586915 0.93618175 0.043731961 9764.796342 100000000 -8 44.40981814 FSVCVLGDQQHCDEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 FSVCVLGDQQHCDEAK 16 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;;;;; 250.41 7.80E-21 4565770000 5443930 4659455 3109636 3553996 4470576 3394476 5717827 6271110 5485384 FALSE TRUE 4724500.857 4628846.733 4613466.371 4360985.111 4381620.284 3525063.688 5163313.018 4930081.928 4836908.152 0.976760507 0.956984625 0.953804833 0.901605938 0.905872129 0.7287845 1.06748213 1.019263086 1 22.20565371 FSVLLLHGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSVLLLHGIR 10 0 F8W9U3;Q96IU4;B4DQI4 F8W9U3 ABHD14B Alpha/beta hydrolase domain-containing protein 14B 0 ; 153.97 1.53E-05 818880000 533370 1002470 562120 688980 881670 906870 982370 1020910 1163680 FALSE TRUE 462883.8031 995884.7086 833963.1122 845423.4394 864126.492 941757.8757 887099.9086 802596.3412 1026111.076 0.451104967 0.970542792 0.812741556 0.823910256 0.842137379 0.917793305 0.864526199 0.782172963 1 19.96875548 4.747612155 24.9221366 0.865321174 0.451104743 0.78470432 0.069836747 521.9431313 1437065.051 0.016192341 0.194198496 55925.79351 -4.747612155 -0.41421643 FSWFAGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSWFAGEK 8 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 134.48 0.0020353 2007820000 2128350 2349430 1598370 1876160 2419080 2242380 2764600 2885600 3144700 FALSE TRUE 1847083.155 2333996.44 2371347.078 2302170.803 2370945.041 2328645.81 2496489.518 2268536.896 2772937.148 0.666110718 0.841705497 0.855175199 0.830228267 0.855030213 0.839775907 0.900305122 0.818098923 1 21.40298349 5.375469715 1.375323642 0.867407588 1.68E-14 0.606594189 0.051327012 4.320519561 2.08067472 0.013395721 8.008010339 237393.9872 -5.375469715 -0.867407588 FSWGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FSWGYR 6 0 P04066 P04066 FUCA1 Tissue alpha-L-fucosidase 0 ; 126.68 0.040453 552070000 817580 1059620 725700 665210 982480 1066400 1116470 1181320 1289710 FALSE TRUE 709534.7315 1052659.286 1076650.947 816256.0976 962930.5702 1107425.098 1008194.911 928703.911 1137241.953 0.623908333 0.925624739 0.946721095 0.717750603 0.846724453 0.973781432 0.886526309 0.816628254 1 20.1171078 2.989120008 24.80254024 0.901259671 0.817427203 0.202348641 0.104454776 1023.774307 2333850.417 0.032307474 0.03433376 975.2590932 -2.989120008 -0.083832467 FSWMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FSWMGR 6 0 Q9H223 Q9H223 EHD4 EH domain-containing protein 4 0 133.82 0.033265 306110000 549280 511900 305640 341650 498570 621350 486960 502570 458520 FALSE TRUE 476691.2563 508537.2952 453448.5263 419226.8543 488649.4324 645253.7366 439734.6942 395099.3165 404314.2879 1.179011651 1.257777205 1.121524863 1.0368836 1.208588089 1.595921183 1.08760612 0.977208395 1 18.62511766 2.008494418 24.99996836 1.000605458 1.229475858 0.338268867 0.14428331 218.3621173 642660.1961 0.061804998 0.041594781 101.9751654 -2.008494418 0.2288704 FSWNVWPSSR ddPTM_MDA-MB-175_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 ; 147.75 6.13E-05 2350300000 1087290 1167770 721210 799240 1136540 1171230 1120910 1297310 1185080 FALSE TRUE 943601.8717 1160098.842 1069989.568 980719.6576 1113925.078 1216287.976 1012204.321 1019890.352 1044981.192 0.90298455 1.110162413 1.023931891 0.938504602 1.065976197 1.163932887 0.968634008 0.975989194 1 19.99504555 FT(ph)DTRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FTDTRK 6 1 P13639 P13639 EEF2 Elongation factor 2 1 FT(1)DTRK;FT(1)DTRK 92.439 0.027398 1593550000 1418840 1079520 603340 528230 637150 432810 1135230 1239450 1506380 TRUE FALSE 1231336.699 1072428.562 895117.2421 648172.695 624471.9616 449460.4808 1025135.569 974403.2629 1328297.472 0.927003721 0.807370777 0.673883118 0.487972543 0.470129602 0.338373361 0.771766559 0.733573076 1 20.34114684 1.265053695 1.663855924 1.120601239 0.621973459 0.300561169 0.173578533 1.335000769 3.568758754 1.077651614 0.053572215 18.40999605 -1.265053695 -0.498627781 FT(ph)GSFDDDPDPHRDPYGEEVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FTGSFDDDPDPHRDPYGEEVDR 22 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 FT(0.5)GS(0.5)FDDDPDPHRDPYGEEVDR;FT(0.564)GS(0.436)FDDDPDPHRDPYGEEVDR;FT(0.57)GS(0.43)FDDDPDPHRDPYGEEVDR 116.65 0.0002531 493439000 257655 244997 162050 221949 225850 214004 272954 267774 522128 TRUE FALSE 223605.2389 243387.5986 240417.922 272345.9127 221356.0269 222236.8724 246482.9631 210512.6139 460402.6227 0.485673252 0.528640774 0.522190601 0.591538578 0.480787936 0.482701143 0.535363942 0.457235914 1 18.81253653 1.234737181 24.99998717 1.0000007 0.510848584 0.943467823 0.037655107 24.14863226 157875.3814 0.067647032 0.009250168 17.16869087 -1.234737181 -0.489152116 FT(ph)GSFDDDPDPHRDPYGEEVDRR ddPTM_MDA-MB-175_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(0.5)GS(0.5)FDDDPDPHRDPYGEEVDRR;FT(0.5)GS(0.5)FDDDPDPHRDPYGEEVDRR 118.01 0.0020102 3190800000 401718 377424 165395 206454 340431 255821 385337 382176 214632 TRUE FALSE 348629.9485 374944.6769 245380.5752 253332.5362 333657.0891 265662.5994 347967.077 300450.6365 189258.4495 1.84208393 1.981125165 1.296536963 1.338553374 1.762970637 1.403702715 1.838581464 1.587515048 1 17.52999819 7.999999992 0.038766897 3.52E-05 4.049301623 0.212562202 0.269957461 3878.578819 14.82089626 494.5626936 1204.206564 99999998.2 -7.999999992 4.049266469 FTDALELLRPWAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FTDALELLRPWAK 13 1 Q5VTQ0-2;Q5VTQ0-3;Q5VTQ0-4;Q5VTQ0 Q5VTQ0-2 TTC39B Tetratricopeptide repeat protein 39B 0 ; 104.87 0.0013661 147563000 217657 227115 168496 171724 227604 206196 245870 289520 262630 FALSE TRUE 188893.076 225623.0666 249981.2292 210716.5588 223075.1257 214128.4935 222025.5652 227608.401 231582.1806 0.815663258 0.974267822 1.079449328 0.909899709 0.963265503 0.924632858 0.958733374 0.982840737 1 17.82116472 4.738739679 23.81159268 0.973491168 0.815663205 0.543180758 0.045669382 5.949489449 789906.8505 0.011052812 0.062298104 54794.84206 -4.738739679 -0.157827964 FTDDDKTDHLSWEWNLTIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FTDDDKTDHLSWEWNLTIK 19 1 P52565;J3KRE2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;; 218.37 2.03E-19 1869090000 7680755 6070898 2209854 5232936 5784692 4310387 8221313 9615760 8506403 FALSE TRUE 6665723.766 6031017.871 3278546.786 6421154.099 5669587.947 4476210.377 7424011.331 7559504.554 7500785.728 0.888670068 0.804051481 0.43709378 0.856064195 0.755865872 0.596765531 0.989764486 1.007828357 1 22.8386103 2.219232806 23.77550581 1.000602957 0.721300416 0.502939987 0.129386927 109.7303078 134979.4436 0.052202229 0.035267957 165.6657788 -2.219232806 -0.279302541 FTDEESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FTDEESR 7 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ; 149.48 0.0046838 686180000 1782570 1500060 993180 1153170 1390010 1631630 1487830 1731940 1727470 FALSE TRUE 1546998.858 1490206.007 1473485.17 1415014.874 1362351.521 1694399.862 1343540.476 1361578.109 1523250.465 1.015590603 0.978306616 0.967329539 0.928944324 0.894371315 1.112358014 0.882022036 0.893863577 1 20.53872175 4.511029861 1.594894699 0.946299051 1.023841489 0.076064733 0.067131472 1.719154463 5.856214209 0.018878085 0.181908378 32436.19192 -4.511029861 0.077542438 FTDEEVDELYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 FTDEEVDELYR 11 0 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ;;;;;;;;; 346.43 2.34E-70 41281930000 25483540 24192460 17162670 20643280 24670970 25956710 24171360 27397460 30864890 FALSE TRUE 22115825.62 24033538.14 25462594.62 25330652.24 24180065.96 26955281.43 21827225.23 21538726.39 27216077.87 0.812601497 0.883063984 0.935571788 0.93072383 0.888447854 0.99041756 0.801997457 0.791397147 1 24.69795584 1.206275254 24.46717203 1.000001089 0.878780643 0.262401355 0.063603939 5638.027427 4272401.653 2.555553988 0.016917727 16.07960048 -1.206275254 -0.121220446 FTDFDEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FTDFDEVR 8 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4;E5RHK8;Q9UQ16-5;Q9UQ16-2;Q9UQ16-3;Q9UQ16;Q9UQ16-4 P50570-2 DNM2;DNM3 Dynamin-2;Dynamin-3 0 ;;; 169.06 0.00070539 691800000 1686720 1442560 1006640 1234990 1561220 1616080 1476540 1626510 1871970 FALSE TRUE 1463815.678 1433083.728 1493454.471 1515413.355 1530154.776 1678251.643 1333345.378 1278693.494 1650667.839 0.886802083 0.868184195 0.90475772 0.91806075 0.926991331 1.016710693 0.807761166 0.774652213 1 20.65461841 2.19287266 24.99999912 0.840645916 0.917387629 0.115749057 0.070161798 202.5763816 110846.2809 0.028743722 0.019379091 155.9095292 -2.19287266 0.076741713 FTDKDQQPS(ph)GS(ph)EGEDDDAEAALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FTDKDQQPSGSEGEDDDAEAALK 23 1 Q9NXG2;H3BNW0 Q9NXG2 THUMPD1 THUMP domain-containing protein 1 2 FTDKDQQPS(1)GS(1)EGEDDDAEAALK 104.9 0.00090613 142010000 319820 241470 216070 200080 217800 188650 348040 316240 432820 TRUE FALSE 277554.9767 239883.7677 320562.1747 245511.222 213466.2061 195907.4876 314287.1344 248614.537 381652.5127 0.727245249 0.628539731 0.839932043 0.6432847 0.559320846 0.513313763 0.82349028 0.651415958 1 18.54190016 1.236191153 24.99798389 1.000000426 0.673636802 0.499100512 0.102850716 55.87058033 589303.884 0.163885571 0.025087185 17.22626614 -1.236191153 -0.326363624 FTDKDQQPS(ph)GS(ph)EGEDDDAEAALKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FTDKDQQPSGSEGEDDDAEAALKK 24 2 Q9NXG2;H3BNW0 Q9NXG2 THUMPD1 THUMP domain-containing protein 1 2 FTDKDQQPS(1)GS(1)EGEDDDAEAALKK 96.46 0.0034511 379530000 504770 272980 293570 302450 275070 193510 406380 526710 422540 TRUE FALSE 438063.3656 271186.7764 435541.4339 371125.8952 269596.6452 200954.4549 366969.3301 414077.1654 372587.8026 1.175731901 0.72784663 1.168963211 0.996076341 0.723578827 0.539347916 0.984920407 1.111354592 1 18.50722092 2.005944507 24.99678628 1.058983148 0.880640345 0.110754507 0.19839666 304.1626365 1279005.302 0.083165542 0.055889908 101.3781838 -2.005944507 -0.178342803 FTDKDQQPS(ph)GSEGEDDDAEAALKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FTDKDQQPSGSEGEDDDAEAALKK 24 2 Q9NXG2;H3BNW0 Q9NXG2 THUMPD1 THUMP domain-containing protein 1 1 FTDKDQQPS(1)GSEGEDDDAEAALKK;FTDKDQQPS(0.834)GS(0.166)EGEDDDAEAALKK 180.48 1.84E-17 483200000 535920 265140 285930 287530 231020 165173 400590 476210 352610 TRUE FALSE 465096.8142 263398.2779 424206.7044 352818.0811 226423.154 171527.3122 361740.8435 374376.1974 310924.8475 1.495849617 0.847144511 1.364338385 1.13473749 0.728224701 0.551668075 1.163434979 1.204072947 1 18.24620639 4.751961962 23.84452418 1.016098966 1.495850222 0.294501852 0.240314698 1754.495255 3121602.796 0.062609508 1.124464873 56488.74972 -4.751961962 0.479751256 FTDLLQLVEFHQLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FTDLLQLVEFHQLNR 15 0 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ; 226.24 8.91E-13 415310000 711260 374890 218484 270990 343420 358140 353030 418080 363860 FALSE TRUE 617265.1889 372427.3229 324143.5932 332522.4213 336586.6139 371917.8775 318793.2049 328676.8455 320844.8853 1.923874175 1.16077064 1.010281317 1.036396204 1.049063361 1.159182816 0.993605382 1.024410426 1 18.29151646 4.741604706 3.223165908 1.04069453 2.053845838 0.97234463 0.046524863 0.051155448 0.841214287 0.011914853 0.1306472 55157.51687 -4.741604706 1.013151308 FTDYQLR ddPTM_MDA-MB-175_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 ;; 107.74 0.017236 1180880000 1572500 1597050 1378940 1580590 1695380 1743630 1423530 1656540 3955760 FALSE TRUE 1364690.141 1586558.873 2045799.996 1939487.117 1661645.255 1810708.574 1285476.28 1302301.812 3488114.559 0.391240058 0.454847123 0.586505965 0.556027356 0.476373475 0.519108115 0.368530407 0.373354083 1 21.73401599 1.232540725 24.99992422 1.000000872 0.465114006 0.837147274 0.074052912 86.92965063 360972.4399 0.181187499 0.020369674 17.08207898 -1.232540725 -0.534886866 FTFPALEEDVIYDDVPCES(ph)PDAHQPGAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FTFPALEEDVIYDDVPCESPDAHQPGAER 29 0 Q9HCE6-5;Q9HCE6-3;Q9HCE6-2;Q9HCE6 Q9HCE6-5 ARHGEF10L Rho guanine nucleotide exchange factor 10-like protein 1 FTFPALEEDVIYDDVPCES(1)PDAHQPGAER 163.15 3.67E-12 42133000 7135 8951.6 6709.9 8895.1 11017 11105 11385 13492 12518 TRUE FALSE 6192.091672 8892.79635 9954.830083 10914.86841 10797.78325 11532.21654 10280.88445 10606.84079 11038.1363 0.560972569 0.805642919 0.901857869 0.988832545 0.978225215 1.044761201 0.931396766 0.960926782 1 13.43020898 4.818869067 1.190448493 0.981825051 0.308179263 0.951650497 0.030479157 0.366041138 0.390541737 0.009392524 0.319440167 65897.51952 -4.818869067 -0.673645789 FTGS(ph)FDDDPDPHRDPYGEEVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FTGSFDDDPDPHRDPYGEEVDR 22 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 FT(0.105)GS(0.895)FDDDPDPHRDPYGEEVDR;FT(0.14)GS(0.86)FDDDPDPHRDPYGEEVDR;FT(0.022)GS(0.978)FDDDPDPHRDPYGEEVDR 214.08 7.57E-25 1953970000 1515674 1437851 942949 1244786 1331948 1108584 1612190 1551936 2908500 TRUE FALSE 1315373.841 1428405.662 1398962.29 1527433.687 1305444.841 1151231.944 1455840.062 1220066.564 2564660.443 0.512884208 0.556957029 0.545476612 0.595569558 0.50901274 0.448882793 0.567654118 0.475722455 1 21.2903364 1.234796025 24.99982761 1.000000674 0.52679505 0.922049653 0.043264864 28.04063413 186183.9486 0.077085166 0.010583695 17.17101728 -1.234796025 -0.473205624 FTGS(ph)FDDDPDPHRDPYGEEVDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 FTGSFDDDPDPHRDPYGEEVDRR 23 2 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 FT(0.185)GS(0.815)FDDDPDPHRDPYGEEVDRR;FT(0.169)GS(0.831)FDDDPDPHRDPYGEEVDRR;FTGS(1)FDDDPDPHRDPYGEEVDRR;FT(0.186)GS(0.814)FDDDPDPHRDPYGEEVDRR;FT(0.049)GS(0.951)FDDDPDPHRDPYGEEVDRR;FT(0.163)GS(0.837)FDDDPDPHRDPYGEEVDRR;FT(0.168)GS(0.832)FDDDPDPHRDPYGEEVDRR 223.09 7.92E-33 26315310000 3817420 3503360 1800341 2147712 3240130 2850340 4034190 3785006 2347216 TRUE FALSE 3312938.275 3480346.197 2670991.929 2635382.835 3175657.752 2959994.424 3642954.875 2975611.922 2069730.798 1.600661437 1.681545349 1.290502094 1.273297396 1.534333718 1.430134985 1.760110483 1.437680651 1 20.9810117 1.254163381 4.852816007 0.971723619 1.504481519 0.516416159 0.153603402 0.14228101 7.811979796 0.248113282 0.039741245 17.95408931 -1.254163381 0.5327579 FTGSFDDDPDPHRDPYGEEVDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FTGSFDDDPDPHRDPYGEEVDRR 23 2 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 ;;; 250.81 1.26E-38 3558270000 1289710 1263279 707809 899384 1292218 1392431 1005475 1337896 1028184 FALSE TRUE 1119271.556 1254980.437 1050107.8 1103602.883 1266505.39 1445998.722 907964.1893 1051797.352 906633.2588 1.234536175 1.384220604 1.15824981 1.217253915 1.396932417 1.594910299 1.001467992 1.160113355 1 19.79015956 2.200596282 24.9999995 1.073813296 1.323408099 0.507843047 0.12797219 150.4414467 99066.60259 0.05358534 0.036128102 158.7070728 -2.200596282 0.249594803 FTLDCTHPVEDGIMDAANFEQFLQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 FTLDCTHPVEDGIMDAANFEQFLQER 26 0 P35268 P35268 RPL22 60S ribosomal protein L22 0 ;;;;;;;;;; 384.72 8.45E-145 8305790000 2386751 2480386 1537117 1808387 2443608 2528221 2383476 2682231 2581240 FALSE TRUE 2071335.808 2464092.181 2280471.923 2219008.908 2394984.982 2625483.298 2152326.864 2108656.774 2276088.748 0.910041759 1.082599342 1.001925749 0.974921962 1.052237082 1.153506558 0.945625194 0.926438732 1 21.11812538 FTLRDEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FTLRDEGK 8 1 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ;; 133.57 0.00083321 1406000000 1805500 1588720 878530 1089830 1394450 1352770 1803920 2063580 615620 FALSE TRUE 1566898.6 1578283.594 1303390.047 1337292.559 1366703.173 1404811.937 1628976.116 1622299.476 542842.1049 2.886472118 2.907445055 2.401048177 2.463501903 2.517680852 2.587883152 3.000828604 2.988529189 1 19.0501731 1.233152601 24.99976325 0.99999729 2.722555134 0.856591618 0.221062441 70.63720547 326500.3334 0.51651539 0.061465639 17.10616281 -1.233152601 1.722557844 FTLTQSEADADILFNFSHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FTLTQSEADADILFNFSHFK 20 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 245.12 6.14E-30 1101030000 1315430 1122920 768680 872320 1255950 992180 1319730 1483870 1239840 FALSE TRUE 1141592.593 1115543.465 1140416.219 1070393.589 1230959.052 1030349.807 1191742.788 1166555.948 1093267.528 1.044202415 1.020375559 1.043126399 0.979077455 1.12594495 0.94244984 1.090074257 1.067036127 1 20.06021505 FTMDCVAPTIHVYEHHENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FTMDCVAPTIHVYEHHENR 19 0 M0R1B0;O43402 M0R1B0 EMC8 ER membrane protein complex subunit 8 0 ; 99.569 0.00026952 190993000 71383 67809 38194 48872 63904 75933 57847 73540 66517 FALSE TRUE 61949.55569 67363.55821 56664.74615 59969.13456 62632.43543 78854.19165 52237.00684 57814.04329 58653.43604 1.056196531 1.148501482 0.96609423 1.022431738 1.067839152 1.344408733 0.890604377 0.985688942 1 15.83992801 FTPGTFTNQIQAAFREPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FTPGTFTNQIQAAFREPR 18 1 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 84.829 0.0034166 383770000 215620 193900 48916 62792 156110 180200 209350 197930 30312 FALSE TRUE 187125.2707 192626.2581 72571.94121 77049.88332 153003.7164 187132.4106 189047.2692 155604.2098 26728.54989 7.000951097 7.206760521 2.715146969 2.882681014 5.724355307 7.001218224 7.072859171 5.821648029 1 14.70609395 4.302796661 24.99821726 4.908036499 7.103884797 0.207035375 1.965641168 115.0141481 44756.20593 0.516816392 1.367367319 20081.52365 -4.302796661 2.195848299 FTPVASKFS(ph)PGAPGGSGSQPNQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FTPVASKFSPGAPGGSGSQPNQK 23 1 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 FTPVAS(0.028)KFS(0.972)PGAPGGSGSQPNQK;FTPVAS(0.003)KFS(0.997)PGAPGGSGSQPNQK 222.63 9.63E-33 2576100000 3247300 3015100 2038330 2283800 3048100 2458900 4057900 5002100 2043260 TRUE FALSE 2818161.077 2995293.61 3024073.206 2802371.696 2987448.774 2553495.474 3664365.483 3932439.841 1801708.13 1.564160715 1.662474381 1.678447888 1.555397152 1.658120271 1.417263668 2.033828577 2.182617581 1 20.78093389 2.239871648 24.99999941 1.843566374 1.598274192 0.012232925 0.318443763 77.05473085 1469402.223 0.121489655 0.08883286 173.7287312 -2.239871648 -0.245292181 FTSGAFLS(ph)PSVSVQECR ddPTM_MDA-MB-175_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(0.999)PS(0.001)VSVQECR;FTSGAFLS(1)PSVSVQECR 303.45 1.48E-46 358400000 905910 876820 567010 640770 891940 977890 827850 934780 1028310 TRUE FALSE 786191.6982 871060.1117 841217.9325 786266.6221 874192.1391 1015510.061 747565.2344 734884.5715 906744.3633 0.867048895 0.960645742 0.927734394 0.867131525 0.964099888 1.119951887 0.824449828 0.810465001 1 19.79033635 FTVHTK ddPTM_MDA-MB-175_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 74.517 0.080118 393430000 1005600 868150 573440 761040 814390 813100 926680 1100100 1025900 FALSE TRUE 872707.4121 862447.0655 850757.502 933845.7638 798185.2323 844380.4831 836810.7162 864852.176 904619.2707 0.964723437 0.953381266 0.940459185 1.032308059 0.88234383 0.93340979 0.925041886 0.956039965 1 19.7869512 1.261133466 4.201337584 1.004016028 0.947130154 0.161698379 0.037313701 0.383616127 12.41064371 0.063168562 0.009194896 18.24456301 -1.261133466 -0.056885873 FTVWLHGVLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FTVWLHGVLDK 11 0 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;G3V3Y4;A0A3B3IT62;G3V473;G3V240;G3V572;G3V3R9;Q6PJT7-9;Q6PJT7-2;Q6PJT7-3;Q6PJT7-11 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 0 ; 120.96 0.00042157 235290000 547410 604120 373731 478310 527530 461690 677360 765410 747450 FALSE TRUE 475068.3815 600151.4959 554468.5617 586917.596 517033.1851 479451.5131 611669.7315 601733.0279 659087.3125 0.72079734 0.910579652 0.841267236 0.890500522 0.784468424 0.727447645 0.928055691 0.912979231 1 19.33011007 2.099231368 9.176095463 0.94135085 0.820635664 0.488085469 0.064643277 0.259566737 21.66078096 0.026368233 0.017763229 125.6699286 -2.099231368 -0.120715186 FTYCSQVLGLHCYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FTYCSQVLGLHCYK 14 0 Q14258 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 176.91 2.16E-06 322130000 196350 204150 105960 142100 174470 155190 206630 206440 221380 FALSE TRUE 170401.85 202808.9252 157202.6104 174365.9769 170998.3883 161160.2597 186591.0544 162294.4125 195208.7086 0.872921353 1.038933799 0.805305314 0.893228474 0.875977253 0.825579252 0.955854151 0.831389202 1 17.57465789 5.120658012 12.90565403 0.897146048 0.000385773 0.00977678 0.076356838 1025204.933 1333172.487 0.017286242 26259975.37 132025.5582 -5.120658012 -0.896760275 FTYFSSLS(ph)PMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FTYFSSLSPMAR 12 0 Q9H425 Q9H425 C1orf198 Uncharacterized protein C1orf198 1 FTYFSSLS(1)PMAR 167.71 5.09E-05 133300000 171020 153760 102180 117060 153510 162590 140240 170030 164560 TRUE FALSE 148419.2737 152749.9404 151594.5898 143640.2622 150455.4513 168844.9425 126639.5464 133670.4077 145105.9043 1.022834146 1.052679015 1.044716895 0.9898995 1.036866502 1.163598017 0.872738756 0.921192066 1 17.1467467 2.219107725 24.99999787 0.926761834 1.047997496 0.527686547 0.053584852 186.0245343 239068.7862 0.021742988 0.014683239 165.6180721 -2.219107725 0.121235662 FTYHNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FTYHNVR 7 0 Q8TE77;Q8TE77-2;Q8TE77-3;A0A087WWG1;Q8TE77-5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ;;;;; 113.1 0.006205 2618740000 5009460 5069000 2770370 3356970 4383350 4745990 4283170 4692410 6747730 FALSE TRUE 4347447.169 5035701.405 4110130.198 4119221.347 4296129.911 4928571.306 3867788.833 3688974.638 5950021.046 0.730660805 0.846333377 0.690775741 0.69230366 0.722036086 0.828328382 0.650046244 0.619993544 1 22.50446334 1.22564447 24.96653028 1.000000678 0.719570956 0.60648482 0.070196547 470.1848221 908796.9449 0.332936508 0.01846166 16.81297124 -1.22564447 -0.280429722 FVADGIFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FVADGIFK 8 0 P23396;P23396-2;E9PPU1;E9PL09;F2Z2S8;H0YCJ7;E9PQ96;E9PJH4;E9PK82;E9PQX2 P23396 RPS3 40S ribosomal protein S3 0 101.99 0.011752 144380000 454920 418540 251470 347480 454010 393480 477170 497140 488840 FALSE TRUE 394801.1694 415790.5832 373081.7331 426380.6449 444976.0893 408617.4302 430894.1268 390830.4797 431049.8921 0.91590597 0.964599669 0.865518679 0.989167734 1.032307622 0.947958549 0.999638638 0.906694299 1 18.71749534 3.705778767 24.96017778 0.973906687 0.920267226 0.343536918 0.041040856 816.5848534 621749.4772 0.011393601 0.016901022 5079.006483 -3.705778767 -0.053639461 FVCYCEGEESGEGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FVCYCEGEESGEGDR 15 0 Q9BUH6;Q9BUH6-2 Q9BUH6 C9orf142 Protein PAXX 0 215.08 2.42E-11 0 71767 77242 55197 61248 79835 83965 68986 72842 108190 FALSE TRUE 62282.80912 76734.59222 81890.45382 75155.29452 78246.43969 87195.18788 62295.74834 57265.30516 95399.90145 0.652860309 0.804346661 0.858391388 0.787792161 0.820194135 0.913996624 0.65299594 0.600265873 1 16.54170016 4.74356272 23.024072 0.786702542 0.652860132 0.12896308 0.115906648 438.9317869 2020132.549 0.029826561 0.233229836 55406.75554 -4.74356272 -0.13384241 FVDGEWYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 FVDGEWYR 8 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;;;; 183.89 0.00051388 7041820000 7988220 7941350 5288600 6100060 7858570 8217930 7564760 8117990 7975690 FALSE TRUE 6932556.487 7889182.749 7846184.649 7485171.857 7702199.832 8534079.085 6831130.74 6382021.013 7032813.014 0.985744463 1.121767738 1.115653812 1.064321182 1.095180523 1.213465944 0.971322674 0.907463486 1 22.74567043 2.075612872 9.108841744 0.944814901 1.099172157 0.546961158 0.059990783 0.195303509 21.54439615 0.023632582 0.015914902 119.0180615 -2.075612872 0.154357256 FVDGLMIHSGDPVNYYVDTAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 FVDGLMIHSGDPVNYYVDTAVR 22 0 P23396;P23396-2;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 0 ;;;;;;; 281.96 1.01E-45 11737370000 8569110 7862140 4884460 6247700 8036540 8127730 7738500 8643690 7558900 FALSE TRUE 7436680.402 7810493.085 7246601.194 7666335.775 7876628.577 8440409.032 6988021.461 6795304.159 6665295.453 1.115731546 1.171814984 1.087213799 1.150186939 1.181737349 1.266321815 1.04841886 1.019505318 1 22.6682374 2.056071838 9.991184518 1.017954382 1.159537087 0.669662293 0.046678852 0.236535674 40.5144934 0.019682309 0.013256361 113.7815481 -2.056071838 0.141582705 FVDILGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FVDILGLR 8 0 A0A087WUB9;Q8WYA6;Q8WYA6-4;Q8WYA6-3;Q8WYA6-2 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 109.86 0.012882 0 97457 101840 68112 72369 98154 105170 99545 94620 91098 FALSE TRUE 84577.81053 101171.0063 101051.191 88801.48754 96200.92744 109215.958 89891.14122 74386.24933 80328.49822 1.052899188 1.259465925 1.257974359 1.105479245 1.197593999 1.359616579 1.119044215 0.926025644 1 16.29362428 1.917288516 4.631363757 0.96747612 1.207940459 0.570356268 0.085826694 0.147654691 5.45283014 0.044547895 0.022660786 82.65868966 -1.917288516 0.240464339 FVDILTNWYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FVDILTNWYVR 11 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 119.53 0.0019994 0 172390 173690 146000 142400 173910 171010 189790 180250 155930 FALSE TRUE 149608.2247 172549.019 216606.0883 174734.0964 170449.5312 177588.8654 171384.195 141704.9402 137496.133 1.088090417 1.254937249 1.575361311 1.270829169 1.239667818 1.291591708 1.246465564 1.030610368 1 17.06903152 1.758601489 2.695775258 0.997479191 1.295345276 0.466926977 0.118713275 0.21814691 3.18223285 0.096538133 0.033878259 57.35898913 -1.758601489 0.297866086 FVDKYSISLS(ph)PPEQQKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FVDKYSISLSPPEQQKK 17 2 Q15057;A0A0U1RQT1;A0A087X1H5;H7C3K3 Q15057 ACAP2 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2" 1 FVDKYS(0.052)IS(0.273)LS(0.675)PPEQQKK;FVDKYS(0.008)IS(0.008)LS(0.985)PPEQQKK 116.48 0.0001378 378820000 957100 803000 489690 455120 647180 498400 1119870 1200330 185130 TRUE FALSE 830616.81 797725.0401 726505.7219 558461.9521 634302.3842 517573.7705 1011265.18 943648.7705 163244.1423 5.088187535 4.886699326 4.450424448 3.421022918 3.885605788 3.170550338 6.194802248 5.780598049 1 17.3166717 4.197194822 3.559491966 4.199138597 5.019453025 0.065661705 1.433912905 0.827943384 21.41491068 0.387993775 0.996378943 15746.89104 -4.197194822 0.820314428 FVEGLPINDFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FVEGLPINDFSR 12 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 0 ;;;; 231.42 8.10E-12 841623000 906395 882587 521754 542235 789503 895430 821920 861333 908461 FALSE TRUE 786612.6042 876789.2279 774075.9796 665357.7443 773793.4349 929877.7715 742210.3249 677143.6409 801063.7755 0.981960024 1.094531116 0.966310053 0.830592725 0.965957341 1.160803671 0.92653088 0.845305532 1 19.61155758 FVEIHFNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FVEIHFNEK 9 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ; 91.085 0.010992 451380000 1749560 1450380 962070 1349780 1464480 1331840 1606280 1902440 1872330 FALSE TRUE 1518351.213 1440852.358 1427330.27 1656268.179 1435339.713 1383076.747 1450503.213 1495618.011 1650985.28 0.919663689 0.872722716 0.864532402 1.003199846 0.869383713 0.837728091 0.878568228 0.905894213 1 20.65489583 1.240047797 3.72461762 1.013741239 0.891783662 0.361868378 0.044597385 0.311171871 6.837736902 0.10581881 0.011469179 17.37992096 -1.240047797 -0.121957576 FVEVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FVEVGR 6 0 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ;;;;; 172.15 0.012125 2249030000 2606360 2887920 1969940 1818520 2695600 2796790 3136500 2721630 2872430 FALSE TRUE 2261922.922 2868949.063 2922609.573 2231442.76 2641962.834 2904384.321 2832322.713 2139630.604 2532854.598 0.893033072 1.132693944 1.153879728 0.880999155 1.043077181 1.146684189 1.118233441 0.844750664 1 21.27233283 1.741980238 25 0.920049243 1.056274669 0.213330774 0.103808013 0.813406595 5990.729895 0.05439445 0.026120813 55.20523188 -1.741980238 0.136225426 FVEVLDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FVEVLDER 8 0 Q96HU1;Q96HU1-2 Q96HU1 SGSM3 Small G protein signaling modulator 3 0 ;; 128.69 0.0026123 197964000 511760 572980 312552 361357 541340 573270 499210 595960 552160 FALSE TRUE 444129.6194 569216.0567 463703.1926 443408.6298 530568.3931 595324.0679 450796.691 468518.5918 486884.2738 0.912187235 1.169099286 0.95238893 0.910706412 1.089721771 1.222721907 0.925880574 0.962279164 1 18.89321938 FVEWLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FVEWLK 6 0 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;H0Y503 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 101.52 0.084748 182100000 588140 597950 365270 431640 557990 517140 594490 698210 628490 FALSE TRUE 510415.8088 594022.0271 541915.7938 529650.4592 546887.0907 537034.7104 536836.4513 548903.225 554190.6282 0.92101126 1.071873101 0.977850881 0.955718903 0.986821254 0.969043291 0.968685546 0.990459234 1 19.08002279 1.48599541 5.446507466 0.998139697 0.981203302 0.031810886 0.037779018 0.684359074 44.7735324 0.02816321 0.009128194 30.61931073 -1.48599541 -0.016936395 FVEWTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FVEWTR 6 0 A0A2R8YD12;A0A024QZX5;A0A087X1N8;P35237 A0A2R8YD12 SERPINB6 Serpin B6 0 ; 114.02 0.059648 181302000 341930 323040 207936 223050 300650 326090 306220 326400 340390 FALSE TRUE 296743.0842 320917.929 308494.5451 273696.9116 294667.6532 338634.8933 276522.8315 256601.9 300149.482 0.988650996 1.069193679 1.027803024 0.911868679 0.981736338 1.128220815 0.921283721 0.854913686 1 18.19532165 2.034483646 24.99924078 0.908394975 1.015105342 0.292437837 0.066336474 188.2184476 136449.9518 0.027109483 0.01827714 108.2638945 -2.034483646 0.106710367 FVFDRPLPVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FVFDRPLPVSR 11 1 P25786;P25786-2;F5GX11;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ; 197.07 5.32E-08 6532500000 2161600 2096200 1114810 1618810 1925710 1998580 1876830 2161800 2004700 FALSE TRUE 1875939.083 2082429.924 1653935.845 1986385.552 1887392.139 2075466.666 1694815.315 1699515.893 1767706.65 1.061227599 1.178040443 0.935639318 1.123707688 1.067706646 1.174101295 0.958765028 0.961424167 1 20.75344745 2.212239114 24.99954511 0.970292467 1.087561971 0.391321957 0.068511338 214.0194127 203269.047 0.026465056 0.017848943 163.0193338 -2.212239114 0.117269504 FVFDVFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FVFDVFR 7 0 Q3KQV9;Q3KQV9-2 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 ; 110.63 0.036673 89237000 425750 833880 478230 530020 861330 867400 780290 807050 891750 FALSE TRUE 369486.0588 828402.1874 709503.6276 650369.1418 844191.2182 900769.4393 704617.5959 634468.638 786328.3309 0.469887761 1.053506728 0.902299459 0.827096159 1.073586166 1.14553858 0.896085729 0.806874957 1 19.58477231 4.7462221 24.59825822 0.950774992 0.469887469 0.667035404 0.109207672 516.4270778 1658011.175 0.0286595 0.296290836 55747.07687 -4.7462221 -0.480887523 FVFHNTTFCIVNSHLAAHVEDFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FVFHNTTFCIVNSHLAAHVEDFER 24 0 Q01968-2;Q01968;A0A2R8YCN4;A0A2R8YG38 Q01968-2 OCRL Inositol polyphosphate 5-phosphatase OCRL-1 0 136.57 6.91E-06 9967300 3126.8 3583.4 1223.3 3267.5 4453.1 3057.9 2877.2 4066.9 3303 FALSE TRUE 2713.585458 3559.860409 1814.891972 4009.435816 4364.492022 3175.539392 2598.169587 3197.225084 2912.523103 0.931695771 1.222259973 0.623133932 1.376619403 1.498526147 1.090305306 0.892068318 1.097750978 1 11.50805378 4.78016445 21.20406395 1.096032999 0.9316922 0.045075993 0.24293482 12712.26187 6478005.746 0.059855594 13.97851042 60278.77947 -4.78016445 -0.164340799 FVFLLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FVFLLDR 7 0 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 0 ; 124.37 0.009661 291340000 610620 732920 428620 463020 681500 761950 688050 720210 723610 FALSE TRUE 529925.0199 728105.4003 635902.0656 568155.7678 667939.4833 791262.7095 621323.0169 566198.6962 638065.6501 0.830518019 1.141113614 0.996609151 0.890434656 1.046819372 1.240096077 0.973760328 0.887367461 1 19.28334534 2.006146212 24.99970798 0.934116115 1.030233563 0.07591846 0.117235995 329.6431753 1340816.631 0.047604638 0.031998082 101.4252793 -2.006146212 0.096117448 FVHFIDAPSLALIMPIVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FVHFIDAPSLALIMPIVQR 19 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 152.71 5.30E-08 265890000 186925 177658 125891 197102 183319 203905 184761 225850 220209 FALSE TRUE 162222.3876 176490.9529 186772.3087 241857.0216 179671.3106 211749.3573 166842.9067 177553.7351 194176.1429 0.835439335 0.908921922 0.961870526 1.245554773 0.925300647 1.090501408 0.859234838 0.914395211 1 17.56700643 4.388732009 2.881067768 0.994018367 0.846389897 0.213116054 0.106857286 0.464947712 7.328426548 0.028636582 0.109839981 24475.5246 -4.388732009 -0.14762847 FVHLLDQSDQDFQEELDLMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FVHLLDQSDQDFQEELDLMK 20 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;;;; 322.71 6.91E-67 1162833000 611426 561200 442290 602500 553604 482922 669860 756003 1042984 FALSE TRUE 530624.5049 557513.4402 656182.9234 739306.8336 542588.3635 501500.3218 604897.0803 594337.6417 919683.6197 0.576964179 0.606201337 0.71348767 0.803870829 0.589972847 0.545296568 0.657723012 0.646241413 1 19.81077812 1.2384387 9.412542548 1.002025388 0.644680479 0.697841141 0.073923788 0.047994315 69.60082444 0.108631584 0.019128818 17.31564608 -1.2384387 -0.357344909 FVHSENQHLVSPEALDFLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FVHSENQHLVSPEALDFLDK 20 0 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2;A0A087WY74 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 ; 111.95 9.29E-05 804640000 1143310 911620 507650 842390 880870 843940 911680 1300800 1089800 FALSE TRUE 992218.6867 905631.5082 753151.238 1033667.525 863342.4104 876406.9179 823265.4139 1022634.043 960965.0855 1.032523139 0.942418743 0.783744643 1.075655651 0.89841184 0.912007035 0.856706894 1.064173983 1 19.87412449 1.699476744 9.674223678 1.030561107 0.92765284 0.210143781 0.083062407 0.163109647 28.57616338 0.044289677 0.020426005 50.05837462 -1.699476744 -0.102908267 FVIFPIEYHDIWQMYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FVIFPIEYHDIWQMYK 16 0 P31350;P31350-2;A0A286YFD6;C9JXC1 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 0 192.51 5.23E-10 465760000 272670 256980 171280 193330 194040 184720 281980 295550 242760 FALSE TRUE 236635.9686 255291.8815 254111.5809 237228.5314 190178.9836 191826.2979 254633.623 232348.9325 214061.1894 1.105459469 1.192611712 1.187097865 1.108227662 0.888432808 0.896128338 1.189536617 1.085432316 1 17.70766372 3.469695792 24.97925481 1.025875662 1.161953717 0.373064477 0.089125442 220.0406235 740212.594 0.028215456 0.036500433 2949.142732 -3.469695792 0.136078054 FVIHCNSPVWGADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FVIHCNSPVWGADK 14 0 O75367-2;O75367-3;O75367;B4DJC3 O75367-2 H2AFY Core histone macro-H2A.1;Histone H2A 0 ; 181.26 1.66E-06 971820000 944920 678020 583530 1185690 1059600 1290640 652900 1056950 2146500 FALSE TRUE 820046.4279 673566.042 865727.0598 1454919.037 1038516.033 1340291.756 589581.8585 830929.4677 1892743.215 0.433258152 0.35586763 0.457392769 0.768682738 0.548683004 0.708121284 0.311495957 0.439008029 1 20.85204727 3.984929931 23.23846211 0.591369897 0.397579617 0.211495168 0.188098045 469.9408327 724671.3734 0.050046674 0.090882244 9658.950283 -3.984929931 -0.19379028 FVIKPIDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FVIKPIDK 8 1 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 120.15 0.0037951 0 3173100 2877000 2054400 2802300 2525500 2037100 3006100 3983200 4145300 FALSE TRUE 2753766.795 2858100.798 3047914.712 3438605.045 2475247.491 2115468.555 2714568.885 3131423.677 3655247.356 0.753373582 0.781917205 0.833846362 0.940731149 0.677176467 0.578748399 0.742649846 0.856692686 1 21.80153761 1.396473946 2.659790794 1.012454719 0.760079362 0.409106912 0.093746488 0.396977306 4.170588601 0.192864233 0.027323113 24.91574894 -1.396473946 -0.252375357 FVIKPIDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FVIKPIDKK 9 2 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 ; 68.657 0.032312 2066270000 2859500 2156080 1640850 2350550 2332200 1613050 3162300 3886100 2410130 FALSE TRUE 2481609.83 2141916.569 2434370.548 2884278.303 2285793.783 1675105.077 2855620.633 3055087.757 2125207.177 1.167702545 1.007862476 1.145474462 1.357175119 1.0755628 0.788207896 1.343690471 1.437548202 1 21.01917206 FVINYDYPNSSEDYIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FVINYDYPNSSEDYIHR 17 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;;; 231.71 3.78E-16 6978320000 4745880 4145570 2221900 3322870 4062590 4406640 3918650 4718630 4205470 FALSE TRUE 4118699.933 4118337.478 3296418.272 4077378.42 3981752.407 4576166.292 3538619.926 3709587.695 3708304.127 1.110669404 1.110571662 0.888928782 1.099526436 1.073739443 1.23403209 0.954242102 1.000346133 1 21.82232814 FVINYDYPNSSEDYVHR ddPTM_MDA-MB-175_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 ;;; 289.01 1.25E-38 4975510000 4575750 4091650 2339390 3226240 4319710 4921600 4071160 4863840 4435260 FALSE TRUE 3971053.044 4064771.682 3470726.829 3958807.102 4233756.222 5110937.137 3676339.53 3823745.666 3910928.615 1.015373441 1.03933671 0.887443155 1.01224223 1.082545001 1.306834678 0.940017037 0.977707865 1 21.89907977 3.471852989 21.51912604 1.053510579 0.980456867 0.109019711 0.105326934 67.69862292 276515.731 0.032514928 0.042212055 2963.827947 -3.471852989 -0.073053712 FVKEPAFEDITLESER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FVKEPAFEDITLESER 16 1 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 92.633 0.0038472 0 269170 276030 180900 179760 239290 298050 260770 292220 266500 FALSE TRUE 233598.5025 274216.7408 268383.8451 220577.2555 234528.5972 309516.1764 235480.5655 229731.0271 234994.6736 0.994058712 1.166906196 1.142084801 0.938647894 0.998016651 1.317119965 1.002067672 0.977600996 1 17.84226853 2.032428487 24.99999558 0.987990093 1.093139388 0.164950343 0.105929538 324.1454353 249891.1336 0.043402996 0.029262068 107.7527808 -2.032428487 0.105149294 FVLCPECENPETDLHVNPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FVLCPECENPETDLHVNPK 19 0 P55010;H0YLZ1;H0YN40 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 203.89 4.84E-16 406450000 415900 404450 257730 318250 366540 320140 434790 516110 484940 FALSE TRUE 360937.7612 401793.1413 382369.0901 390513.5266 359246.5711 332455.993 392624.1327 405743.8929 427610.9456 0.844079799 0.939623144 0.894198556 0.913244927 0.840124826 0.777473066 0.918180736 0.948862271 1 18.70593926 1.690893434 2.435349727 0.989457962 0.872909609 0.476128172 0.045876174 0.246256238 3.110232562 0.045926721 0.013421246 49.07874335 -1.690893434 -0.116548353 FVLDHEDGLNLNEDLENFLQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FVLDHEDGLNLNEDLENFLQK 21 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5;F5H763;F5H0Z7;F5H3L6;F5H2F3 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;; 320.08 6.45E-67 162127000 203058 210998 142191 165080 205817 178773 220348 263203 240680 FALSE TRUE 176223.3708 209611.9402 210955.0432 202563.9371 201721.6444 185650.513 198978.6849 206919.0867 212227.0846 0.83035288 0.987677613 0.994006225 0.954467887 0.95049906 0.874772951 0.937574416 0.974989065 1 17.69524926 0.882420559 0.009268137 1.93741318 7.32E-08 0.113477273 0.050992941 45362.59466 97.764217 10689.59837 9764.454595 7.628173443 -0.882420559 -1.937413106 FVLKPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FVLKPQR 7 1 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2;A0A2R8Y6Q7 A0A2R8Y430 GSS Glutathione synthetase 0 ; 129.29 0.0033519 2078430000 2264600 3110700 1533490 2015720 2870600 2634700 2696800 2821800 3445600 FALSE TRUE 1965327.372 3090265.607 2275090.893 2473420.034 2813480.676 2736058.614 2435264.751 2218380.029 3038265.093 0.646858425 1.0171152 0.748812504 0.814089607 0.926015535 0.900533209 0.80153136 0.730146963 1 21.53481632 4.781491281 23.02457803 0.850995251 0.646856538 0.321327453 0.098169149 14620.19745 7840608.592 0.023390485 8.970853288 60463.22128 -4.781491281 -0.204138714 FVLMAT(ph)PNLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FVLMATPNLSR 11 0 A0A087X1U1;F5GXM9;E7EUN2;Q9UPQ3-2;Q9UPQ3 A0A087X1U1 AGAP1 "Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1" 1 FVLMAT(1)PNLSR;FVLMAT(0.999)PNLS(0.001)R;FVLMAT(1)PNLSR;FVLMAT(1)PNLSR 147.26 0.00039553 412092000 561082 657276 441661 439839 680716 860457 442682 593388 653727 TRUE FALSE 486933.5921 652958.3107 655249.7369 539711.1675 667171.0834 893559.3376 399750.7678 466496.594 576444.1388 0.844719478 1.132734756 1.136709861 0.936276616 1.157390697 1.550123034 0.693477027 0.809265916 1 19.13682128 FVMEEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 FVMEEGR 7 0 P09467 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;;;;;; 196.68 0.0010226 6159860000 5653550 5940920 3948540 4411680 5535750 6430430 5739540 6172740 7139140 FALSE TRUE 4906419.043 5901893.705 5858067.151 5413419.372 5425599.406 6677812.803 5182920.294 4852747.587 6295159.002 0.779395571 0.937528933 0.930566988 0.8599337 0.861868525 1.060785407 0.823318409 0.770869741 1 22.58581139 FVMEEGRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FVMEEGRK 8 1 P09467 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;;;; 124.23 0.0021064 2668920000 2685450 2500220 1639970 1843660 2283430 2323040 2924230 2977590 1934270 FALSE TRUE 2330560.978 2483795.89 2433064.977 2262291.182 2237994.21 2412408.852 2640638.625 2340855.55 1705602.804 1.366414837 1.456256922 1.426513237 1.326388052 1.312142666 1.414402489 1.548214284 1.372450576 1 20.70185028 1.245218178 5.279678296 0.979648265 1.407734531 0.783618832 0.066738395 0.071512364 5.631650486 0.110513753 0.017468913 17.58806969 -1.245218178 0.428086266 FVMQEEFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 FVMQEEFSR 9 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;;;;;;;;; 282.35 3.91E-21 9362726000 2791916 2872592 1921244 2310917 2884694 3623196 2569045 2518641 2145104 FALSE TRUE 2422957.227 2853721.754 2850364.025 2835646.025 2827294.233 3762582.695 2319899.411 1980049.222 1891512.249 1.280963012 1.508698532 1.506923376 1.499142301 1.494726896 1.989192878 1.226478662 1.046807507 1 20.85110869 2.011213826 24.98101768 1.059715853 1.544337707 0.612565784 0.175805702 134.0486798 298618.8452 0.07148222 0.04814664 102.6157032 -2.011213826 0.484621854 FVNDYDKDNDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FVNDYDKDNDGR 12 1 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 ;;; 142.38 5.59E-05 1219390000 2524730 2000070 2362920 2944150 2184540 2478930 2479370 2378010 4513350 FALSE TRUE 2191080.534 1986931.408 3505636.015 3612664.256 2141071.928 2574296.041 2238921.079 1869491.067 3979786.905 0.550552225 0.499255728 0.880860232 0.907753189 0.537986575 0.646842684 0.562573106 0.469746525 1 21.92425975 FVPAENDSILMNPAQDGEVQLS(ph)QNDDK ddPTM_MDA-MB-175_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 152.19 4.76E-08 51041000 37688 35012 25426 25147 32045 53730 18447 23340 34210 TRUE FALSE 32707.43531 34782.00387 37722.09864 30857.0107 31407.36719 55797.02787 16658.01278 18348.92263 30165.73277 1.084257941 1.153030299 1.250495021 1.022916 1.041160426 1.849682495 0.552216414 0.60827041 1 14.88062301 2.173025333 24.9999994 0.689851803 1.212399661 0.459170109 0.261310876 49.0234018 18700.38503 0.103525411 0.069796835 148.9447958 -2.173025333 0.522547858 FVPDKEFSGSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FVPDKEFSGSDR 12 1 Q13573;G3V4X8 Q13573 SNW1 SNW domain-containing protein 1 0 74.46 0.033238 163360000 207640 186960 120260 166090 197340 168620 181080 236070 246740 FALSE TRUE 180199.8479 185731.8474 178418.1382 203803.273 193413.3201 175106.9205 163518.8895 185588.2676 217570.6783 0.828235906 0.853662124 0.820046799 0.936722148 0.888967767 0.804827755 0.751566759 0.853002202 1 17.73112461 3.209926605 0.00691891 1.705690824 2.65E-07 0.042954021 0.068262785 32421.68283 270.6160156 33242.33424 33465.54325 1621.536039 -3.209926605 -1.705690559 FVPYLIAGIQHSCQDIGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FVPYLIAGIQHSCQDIGAK 19 0 P12268;H0Y4R1 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 228.76 9.61E-20 284740000 328910 298980 191850 178470 261550 255770 325190 347060 180400 FALSE TRUE 285443.7101 297015.9807 284629.3017 218994.3412 256345.6667 265609.6374 293653.1239 272843.9198 159073.3175 1.794416025 1.867164056 1.78929632 1.376688087 1.611493811 1.669730924 1.846023761 1.715208585 1 17.27933234 1.238222581 24.98603411 0.999999204 1.708321497 0.713772701 0.141049659 4.766739919 351806.9118 0.208750458 0.036769688 17.30703138 -1.238222581 0.708322293 FVQSCIDWNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FVQSCIDWNR 10 0 Q9ULW8 Q9ULW8 PADI3 Protein-arginine deiminase type-3 0 128.81 0.0078458 0 131170 139560 103110 105900 128600 142120 136890 135750 125730 FALSE TRUE 113835.5522 138643.2212 152974.3409 129946.2136 126041.1116 147587.4484 123614.4289 106720.9189 110866.3426 1.026781884 1.250543834 1.379808671 1.172097956 1.136874444 1.331219601 1.114986081 0.962608817 1 16.75846193 1.948717648 4.152524844 0.987400086 1.220384064 0.489856248 0.098272266 0.176444478 6.130238401 0.052062287 0.026675074 88.86232005 -1.948717648 0.232983978 LDNTPAS(ph)PPRS(ph)PAEPNDIPIAK ddPTM_MDA-MB-175_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 2 LDNT(0.018)PAS(0.982)PPRS(1)PAEPNDIPIAK;LDNT(0.001)PAS(0.999)PPRS(1)PAEPNDIPIAK;LDNT(0.003)PAS(0.997)PPRS(1)PAEPNDIPIAK;LDNTPAS(1)PPRS(1)PAEPNDIPIAK;LDNTPAS(1)PPRS(1)PAEPNDIPIAK;LDNTPAS(1)PPRS(1)PAEPNDIPIAK 248.92 1.72E-31 8098720000 4309530 4525120 4578570 6181390 5471730 4728820 6463080 7748120 14025420 TRUE FALSE 3740014.692 4495394.189 6792781.766 7584969.076 5362853.278 4910740.765 5836291.496 6091244.834 12367350.83 0.302410334 0.363488855 0.549251158 0.613305888 0.433629914 0.397072973 0.47191121 0.492526243 1 23.56003316 1.228187414 4.101295734 1.06386419 0.453998626 0.792942848 0.088063324 0.119575318 3.600564321 0.221511063 0.023756549 16.91170578 -1.228187414 -0.609865564 FVSEDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FVSEDDR 7 0 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 146.21 0.020296 0 438170 455030 352230 413310 429590 484430 415480 476360 991340 FALSE TRUE 380264.7243 452040.878 522569.6061 507158.3525 421041.9995 503066.3356 375186.8135 374494.121 874144.9145 0.435013369 0.5171235 0.597806608 0.580176518 0.481661556 0.575495352 0.429204366 0.428411943 1 19.73751294 1.233106641 24.99991573 1.00000078 0.505417727 0.856393636 0.063623928 68.39234708 313462.4549 0.142497939 0.016896242 17.10435262 -1.233106641 -0.494583053 FVSEDDRNS(ph)FTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FVSEDDRNSFTLK 13 1 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 1 FVSEDDRNS(0.997)FT(0.003)LK 147.64 2.60E-05 386260000 955390 727390 599540 650790 755870 701820 889960 943750 929780 TRUE FALSE 829132.7909 722611.7272 889479.5493 798561.8162 740829.6658 728819.4695 803651.8162 741936.4068 819862.4676 1.011307169 0.881381641 1.084913122 0.974019238 0.903602366 0.888953329 0.980227597 0.904952277 1 19.64502239 3.42237111 8.491499182 0.933133461 0.98932982 0.166028301 0.059236853 0.47765932 67.27803388 0.016287622 0.021065701 2644.66769 -3.42237111 0.056196359 FVSEDDRNSFTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FVSEDDRNSFTLK 13 1 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;; 161.76 3.79E-05 4038470000 4589900 4155200 2580250 3061870 3873110 3437490 4736200 5385400 3108760 FALSE TRUE 3983333.086 4127904.218 3828067.53 3757114.381 3796042.689 3569732.465 4276884.053 4233774.119 2741245.934 1.45311044 1.505849645 1.396469935 1.370586394 1.384787348 1.302229917 1.560197135 1.544470734 1 21.38640034 1.230439604 24.99978772 0.999999189 1.442813431 0.745360907 0.080752028 172.2673611 530266.3148 0.239231876 0.021930384 16.9996353 -1.230439604 0.442814242 FVSEEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FVSEEHR 7 0 Q6NXG1;Q6NXG1-2;Q6NXG1-4;Q6NXG1-3;A0A2U3TZN9;Q6NXG1-5;H0YBR2;H0YBB3 Q6NXG1 ESRP1 Epithelial splicing regulatory protein 1 0 ;; 168.45 0.0010486 1166030000 3337140 3501130 2085200 2598660 3095800 4002250 4429180 5073480 4407750 FALSE TRUE 2896128.494 3478130.847 3093609.695 3188725.471 3034199.637 4156219.147 3999638.805 3988555.784 3886670.816 0.745143757 0.894886912 0.795953617 0.820425918 0.780668027 1.069351984 1.029065489 1.026213943 1 21.89010349 2.739752501 24.99998803 1.030189213 0.812361169 0.880161116 0.041000769 32.65791579 685012.7807 0.012729838 0.012063545 549.227787 -2.739752501 -0.217828044 FVSELWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FVSELWK 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 137.77 0.0066323 830450000 715610 675340 521730 694100 618590 538280 750360 787810 1444000 FALSE TRUE 621040.3254 670903.6471 774040.3731 851706.0137 606281.2693 558987.9799 677590.2027 619342.9622 1273291.965 0.48774385 0.526904799 0.607904859 0.6689008 0.476152592 0.439010058 0.532156191 0.486410799 1 20.28013184 1.235424666 24.99855977 1.000000646 0.528821089 0.831104469 0.066847558 37.38640594 297977.3219 0.121179931 0.017509599 17.1958903 -1.235424666 -0.471179558 FVVGSHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FVVGSHVR 8 0 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 130.22 0.0010572 229460000 276350 325750 193460 221370 322280 342160 264490 317270 317040 FALSE TRUE 239829.6473 323610.1268 287017.9031 271635.4419 315867.2585 355323.1166 238839.8005 249424.2795 279559.8924 0.857882886 1.157569936 1.026677685 0.971653836 1.129873301 1.271008919 0.854342154 0.892203375 1 18.09279787 2.184538867 24.99996538 0.908109467 1.069537855 0.281874789 0.115366531 113.4300917 52491.68638 0.046268884 0.031194501 152.9462618 -2.184538867 0.161428389 FVYVWDTTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FVYVWDTTSR 10 0 Q96DI7;Q96DI7-2;Q9NSS8 Q96DI7 SNRNP40;DKFZp434D199 U5 small nuclear ribonucleoprotein 40 kDa protein 0 ; 131.22 0.00059518 271810000 342730 325690 206310 351310 352720 363030 344390 393200 359680 FALSE TRUE 297437.3621 323550.5209 306082.2061 431080.3049 345701.5621 376995.999 310991.1108 309117.2399 317159.0401 0.937817702 1.02015229 0.965074828 1.359192867 1.089994351 1.188665468 0.980552567 0.974644266 1 18.27484694 2.200372589 24.6874286 0.982706252 1.096232138 0.156694898 0.118408619 267.5061437 172932.7569 0.049775508 0.033559409 158.6253482 -2.200372589 0.113525886 FWAWDPEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FWAWDPEEER 10 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;H0Y8P3 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 0 ;;; 161.92 1.61E-05 336754000 1089150 1088240 676560 791470 1070400 1135520 1034330 1139220 1193630 FALSE TRUE 945216.0679 1081091.28 1003746.679 971185.3604 1049101.134 1179204.189 934020.8358 895606.6684 1052520.421 0.898050099 1.027145182 0.953660051 0.922723532 0.996751334 1.12036229 0.887413505 0.850916192 1 20.00541679 FWEGDFHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FWEGDFHR 8 0 P49589-3;P49589;B4DKY1;P49589-2 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 0 ;;;;; 135.83 0.00081697 2160680000 1501670 1566200 887100 1131570 1496410 1597680 1397930 1637340 1562620 FALSE TRUE 1303220.505 1555911.529 1316104.527 1388510.263 1466634.369 1659143.783 1262358.964 1287207.583 1377888.844 0.945809606 1.129199598 0.955160159 1.007708474 1.064406883 1.204120195 0.916154427 0.934188261 1 20.39402808 FWETLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FWETLDR 7 0 A0A1B0GUB2;Q6P1J9 A0A1B0GUB2 CDC73 Parafibromin 0 ; 116.88 0.012459 273230000 496050 460190 295250 344850 524120 539900 470650 546550 521430 FALSE TRUE 430495.7357 457166.9816 438033.8876 423153.4632 513691.0374 560670.3024 425006.4354 429674.5358 459787.1394 0.936293556 0.994301368 0.952688429 0.920324704 1.117236637 1.219412755 0.92435477 0.934507512 1 18.81060659 3.275614676 24.9988672 1.026437692 0.95412957 0.194426111 0.087006797 394.8826282 266408.608 0.028407646 0.036673121 1886.316987 -3.275614676 -0.072308121 FWEVISDEHGIDPSGNYVGDSDLQLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FWEVISDEHGIDPSGNYVGDSDLQLER 27 0 Q13509;G3V5W4;G3V2R8;G3V3R4;G3V2N6;G3V3J6;G3V3W7 Q13509 TUBB3 Tubulin beta-3 chain 0 ;;; 206.03 2.90E-25 492409000 810434 159705 102545.1 148154 163198 168983 163102 199469 170530 FALSE TRUE 703333.0935 158655.8873 152136.2534 181794.6301 159950.6791 175483.8854 147284.3931 156814.1066 150370.1377 4.677345545 1.055102361 1.011745122 1.208980938 1.063713059 1.167012866 0.979479007 1.042854047 1 17.19815856 4.738666225 24.99990537 1.066077055 4.677346606 0.996039538 0.071563708 0.466908074 110389.0321 0.017330558 0.097197272 54785.57506 -4.738666225 3.611269551 FWEVISDEHGIDPTGSYHGDSDLQLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FWEVISDEHGIDPTGSYHGDSDLQLER 27 0 Q13885;Q9BVA1 Q13885;Q9BVA1 TUBB2A;TUBB2B Tubulin beta-2A chain;Tubulin beta-2B chain 0 ;;; 345.69 2.76E-110 1490910000 959830 813370 285239 472606 957310 1046220 778870 960730 954140 FALSE TRUE 832986.0336 808026.9189 423181.5345 579918.4156 938261.4039 1086468.76 703335.3073 755285.3659 841342.6562 0.990067516 0.960401702 0.502983572 0.689277325 1.115195333 1.291351095 0.835967726 0.897714338 1 19.68233397 3.24095329 24.99997527 1.010513704 0.777969679 0.303934997 0.181009252 91.82301504 959408.8067 0.057862422 0.071182185 1741.619546 -3.24095329 -0.232544025 FWEVISDEHGIDPTGTYHGDSDLQLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 18 FWEVISDEHGIDPTGTYHGDSDLQLDR 27 0 Q5JP53;P07437 Q5JP53 TUBB Tubulin beta chain 0 ;;;;;;;;;;;;;;;;; 316.22 2.00E-82 66455040000 2692608 2213121.9 1039762.8 1607146.1 2251630 2428730.9 2178571 2519830 2407699 FALSE TRUE 2336773.031 2198583.757 1542595.568 1972073.186 2206826.968 2522165.749 1967293.52 1980983.964 2123063.567 1.100660888 1.035571327 0.72658944 0.928880895 1.039454024 1.187984095 0.926629589 0.933078027 1 21.01771614 3.249681926 24.52333283 1.008603038 0.938376298 0.073207352 0.11848771 531.5827926 1172171.78 0.036613242 0.046798609 1776.97749 -3.249681926 -0.07022674 FWEVISDEHGIDPTGTYHGDSDLQLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 FWEVISDEHGIDPTGTYHGDSDLQLER 27 0 P68371;M0R2D3;M0QY85;M0R0X0;M0QY37;M0QX14;M0QZL7;P04350;M0QYM7;M0R278 P68371;P04350 TUBB4B;TUBB4A Tubulin beta-4B chain;Tubulin beta-4A chain 0 ;;;;;;;;;;; 368.93 4.86E-127 66026057000 4038424.6 4085384.7 1984123.4 2951266.2 4326143.4 4748424.7 3953759.94 4744721.5 4391406.7 FALSE TRUE 3504736.557 4058547.539 2943652.113 3621396.298 4240061.61 4931099.671 3570324.91 3730099.731 3872259.603 0.905088222 1.048108328 0.760189764 0.935215267 1.09498382 1.273442428 0.922026227 0.963287618 1 21.88474425 3.363537738 6.371792115 1.0407763 0.9076952 0.261991281 0.115679243 0.341363442 17.77387272 0.035465961 0.045878679 2309.605145 -3.363537738 -0.133081101 FWQIYIEGQDEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FWQIYIEGQDEPR 13 0 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 137.16 0.00014881 41674000 46483 45624 28395 39894 50741 53030 40443 45786 48660 FALSE TRUE 40340.15378 45324.29294 42126.91698 48952.54244 49731.35337 55070.09841 36520.84408 35995.02021 42907.47023 0.940166212 1.056326385 0.981808453 1.140886241 1.159037182 1.283461787 0.851153514 0.838898682 1 15.38894122 2.203591216 24.9999525 0.882748144 1.09196002 0.443229343 0.103644501 161.715616 115610.8907 0.04411315 0.029742456 159.8053136 -2.203591216 0.209211875 FWSFFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FWSFFLR 7 0 Q6PKG0;Q6PKG0-3;Q659C4-7;A0A3B3ISF0;Q659C4;Q659C4-9;Q659C4-2;Q659C4-6;Q659C4-5 Q6PKG0;A0A3B3ISF0 LARP1;LARP1B La-related protein 1;La-related protein 1B 0 ; 114.19 0.013869 90206000 170508 252380 144452 166473 244640 237500 253380 220710 201795 FALSE TRUE 147974.9358 250722.0992 214309.4704 204273.239 239772.1426 246636.7787 228807.2466 173512.8841 177939.025 0.831604735 1.409033792 1.204398363 1.14799572 1.347496102 1.386074689 1.285874454 0.975125519 1 17.44102343 1.71082501 6.409033805 0.988808549 1.243459914 0.271246457 0.163822572 0.153573501 15.27477175 0.093354189 0.040228867 51.38365702 -1.71082501 0.254651365 FWTHWNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FWTHWNR 7 0 Q15428 Q15428 SF3A2 Splicing factor 3A subunit 2 0 ; 141.78 0.0025335 2525800000 1656220 1892470 1053390 1001510 1795210 1928460 1834160 1795600 1915270 FALSE TRUE 1437346.331 1880038.24 1562812.927 1228918.153 1759488.833 2002649.104 1656283.446 1411624.913 1688848.962 0.851080447 1.113206854 0.925371636 0.727666109 1.041827228 1.185807108 0.98071733 0.835850301 1 20.68760888 FWYFVSQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FWYFVSQLK 9 0 Q02543;M0R3D6;M0R1A7;M0R117 Q02543 RPL18A 60S ribosomal protein L18a 0 190.51 8.60E-05 245940000 254320 329180 269730 302400 294250 235630 394470 323020 763830 FALSE TRUE 220710.9676 327017.5949 400172.3302 371064.5419 288395.0007 244694.8386 356214.3601 253944.6867 673530.8876 0.327692422 0.485527243 0.594141022 0.550924314 0.428183779 0.363301584 0.528876057 0.377034953 1 19.36138458 1.233113122 24.99892335 1.000000851 0.46087463 0.797672222 0.085930642 79.03667796 362665.0027 0.179827692 0.021333005 17.10460788 -1.233113122 -0.53912622 FYAFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FYAFGR 6 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;; 143.79 0.026415 24190200000 15221090 15581110 9812004 11710940 15018540 17773980 14511954 15579390 14340541 FALSE TRUE 13209584.39 15478756.66 14557121.95 14370087.92 14719700.44 18457756.51 13104586.93 12247858.69 12645218.58 1.044630768 1.224079803 1.151195755 1.136404865 1.164052669 1.459662907 1.036327435 0.968576273 1 23.59208864 2.020864187 24.99022586 0.988165934 1.196325182 0.436950391 0.105578142 198.8146288 238130.6706 0.042322468 0.028530859 104.9214267 -2.020864187 0.208159248 FYAGGSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FYAGGSER 8 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ;; 108.09 0.0090221 1593340000 1238240 1383050 790650 862690 1306740 1518860 1213860 1226780 1106100 FALSE TRUE 1074603.447 1373964.653 1173010.985 1058576.95 1280738.431 1577291.527 1096140.044 964442.6438 975338.1181 1.101775299 1.408705994 1.202671118 1.085343565 1.313122503 1.617174083 1.123856459 0.988829029 1 19.89554292 2.006841495 24.99791344 1.012434378 1.289052149 0.396302844 0.151768736 163.153131 596137.2573 0.063123767 0.042446853 101.5877858 -2.006841495 0.276617771 FYALSASFEPFSNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FYALSASFEPFSNK 14 0 P27797 P27797 CALR Calreticulin 0 ; 215.08 1.54E-11 300320000 823590 738710 601310 764070 778920 860940 776290 793150 802810 FALSE TRUE 714750.4948 733857.3654 892105.5273 937563.7716 763421.0159 894060.9189 701005.5153 623541.0448 707902.7164 1.009673333 1.036664147 1.260209216 1.324424599 1.078426454 1.262971448 0.990256852 0.880828722 1 19.43319159 2.087621759 5.897132044 0.932916872 1.163670336 0.461498666 0.105196925 0.171894286 9.192504597 0.045424916 0.03022354 122.3550107 -2.087621759 0.230753464 FYCDYCDTYLTHDS(ph)PSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FYCDYCDTYLTHDSPSVR 18 0 A0A0A0MRR7;P09234 A0A0A0MRR7 SNRPC U1 small nuclear ribonucleoprotein C 1 FYCDYCDTYLTHDS(1)PSVR;FYCDYCDTYLTHDS(0.999)PS(0.001)VR 232.29 2.10E-20 709880000 1028560 1095320 603240 642570 904220 1015290 860490 1089310 915530 TRUE FALSE 892633.19 1088124.771 894968.8817 788475.3396 886227.7911 1054348.863 777039.8122 856369.5335 807297.0864 1.105705948 1.347861635 1.108599172 0.976685477 1.097771571 1.306023372 0.962520273 1.060786107 1 19.62274016 -1.999999852 0.094652942 0.299861082 1.387718944 0.172242747 0.117124504 566.9666749 4.990963261 82.31681356 9.649912086 0.010000003 1.999999852 1.087857862 FYCDYCDTYLTHDSPSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FYCDYCDTYLTHDSPSVR 18 0 A0A0A0MRR7;P09234 A0A0A0MRR7 SNRPC U1 small nuclear ribonucleoprotein C 0 ;;; 304.59 6.76E-50 4383690000 1195440 1386810 294365 653460 1717900 1806920 1247660 1437640 1414360 FALSE TRUE 1037459.575 1377699.954 436720.8986 801838.0805 1683717.151 1876433.382 1126662.125 1130211.874 1247155.972 0.831860327 1.104673341 0.350173441 0.642933281 1.350045374 1.504569936 0.903385102 0.906231377 1 20.25021047 3.253950475 24.942193 1.105896096 0.731697643 0.365141103 0.261028716 305.2013367 494633.8862 0.082133799 0.105638339 1794.528976 -3.253950475 -0.374198453 FYDLSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FYDLSSK 7 0 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2;H0YD73;E9PL38 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 97.798 0.027295 215730000 307390 289140 207720 219520 277980 241240 337880 375480 343250 FALSE TRUE 266767.6327 287240.6203 308174.0868 269365.3712 272448.7419 250520.6589 305112.4496 295186.524 302671.376 0.881377143 0.94901812 1.01818048 0.889959846 0.900147035 0.827698549 1.008065096 0.975270697 1 18.20739272 2.173401179 24.99999998 0.991018366 0.916199187 0.38300962 0.049539823 71.07122466 27267.1492 0.021150669 0.014259781 149.0737507 -2.173401179 -0.074819179 FYEAFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FYEAFSK 7 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 126.67 0.0091423 5328500000 5215500 4078300 2592700 3176000 3912800 3367500 4338400 4886100 3810900 FALSE TRUE 4526258.461 4051509.379 3846538.392 3897159.342 3834942.935 3497049.904 3917662.636 3841245.539 3360379.743 1.346948502 1.205670099 1.144673723 1.15973778 1.141223084 1.040671046 1.165839261 1.143098647 1 21.68019284 8 0.613114942 1.104068169 17.84446501 0.706646098 0.050045532 107.7238175 0.807362374 0.022810696 2423.42327 100000000 -8 16.74039684 FYEDDENGWQAFGDFSPTDVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FYEDDENGWQAFGDFSPTDVHK 22 0 Q00653;Q00653-4;Q00653-3 Q00653 NFKB2 Nuclear factor NF-kappa-B p100 subunit;Nuclear factor NF-kappa-B p52 subunit 0 162.65 1.60E-11 33756000 31949 30164 24053 29491 27249 30242 34548 45308 40725 FALSE TRUE 27726.8587 29965.8507 35685.11125 36187.38229 26706.79821 31405.42931 31197.54028 35619.23679 35910.53689 0.772109278 0.834458443 0.993722577 1.007709308 0.743703674 0.87454636 0.868757278 0.991888172 1 15.1321196 1.705109762 4.816042839 0.998343462 0.874380056 0.283598887 0.082504014 0.217345049 11.98052669 0.055869269 0.022524171 50.71188597 -1.705109762 -0.123963406 FYEEEENGGVWEGFGDFSPTDVHR ddPTM_MDA-MB-175_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 ; 209.76 4.92E-25 114645000 80366 72702 44486 56819 68792 70165 63290 80950 75283 FALSE TRUE 69745.42948 72224.41577 65999.5784 69720.62237 67423.17379 72864.29295 57152.14554 63639.47245 66383.1295 1.050649917 1.087993536 0.99422216 1.050276221 1.015667298 1.097632689 0.860943827 0.958669363 1 16.01852902 2.248279088 24.99991368 0.940498733 1.047158393 0.567946998 0.045006908 139.2732924 358268.8476 0.01638428 0.012530694 177.1246838 -2.248279088 0.10665966 FYEEVHDLER ddPTM_MDA-MB-175_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 ;;;;;; 246.5 1.29E-12 20508680000 6556580 6930360 4269559 4990232 6999740 7240650 6439400 7364520 7112330 FALSE TRUE 5690111.341 6884834.009 6334332.013 6123340.447 6860458.869 7519202.491 5814907.979 5789674.709 6271518.45 0.907294045 1.09779379 1.010015687 0.976372867 1.093907149 1.19894449 0.927192996 0.923169525 1 22.58038336 FYEQFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FYEQFSK 7 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;; 157.34 0.0034487 7225130000 4342200 4090410 2345270 3150460 3930280 3440310 4453430 5076930 4080130 FALSE TRUE 3768367.268 4063539.827 3479450.416 3865820.095 3852075.117 3572660.952 4021537.044 3991268.028 3597781.679 1.047414102 1.129457035 0.967109938 1.074501023 1.07068062 0.993017718 1.117782401 1.109369157 1 21.77867621 2.210949777 24.99993571 1.084480697 1.049467652 0.049824771 0.054071975 563.7340318 510422.8777 0.021365292 0.014408126 162.5360782 -2.210949777 -0.035013045 FYFHDGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FYFHDGVR 8 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ;;;; 182.39 0.00022882 3818390000 2979790 3280720 1996760 2006610 3448360 3922920 3186670 3465310 3750770 FALSE TRUE 2586003.202 3259168.734 2962399.815 2462241.47 3379744.383 4073837.271 2877627.234 2724280.424 3307358.243 0.78189389 0.985429607 0.895699709 0.744473773 1.021886392 1.231749623 0.8700682 0.823702854 1 21.65724789 3.211450648 24.99829042 0.971916511 0.864544148 0.221801993 0.124709114 464.8577366 428647.1943 0.041422295 0.04698042 1627.236391 -3.211450648 -0.107372363 FYFHLGDAMQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FYFHLGDAMQR 11 0 Q12797;Q12797-10 Q12797 ASPH Aspartyl/asparaginyl beta-hydroxylase 0 107.83 0.0016151 0 143270 147450 104870 150060 184770 214730 125990 207610 226200 FALSE TRUE 124336.5065 146481.3912 155585.4828 184133.4165 181093.4385 222990.802 113771.5092 163214.2171 199458.8937 0.623369077 0.734393882 0.780037831 0.923164734 0.907923608 1.117978737 0.570400783 0.818284981 1 17.60573193 4.31894943 1.744412776 0.871229053 0.626690692 0.282844543 0.140701281 0.678239708 3.525387051 0.040587039 0.212287874 20842.48175 -4.31894943 -0.244538361 FYGDEEKDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 FYGDEEKDK 9 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;;;; 166.19 5.56E-05 11351350000 14743390 10922110 12912120 12497290 10824860 9438820 15379570 16124230 13245350 FALSE TRUE 12795013.66 10850361.94 19156464.42 15334990.7 10609466.46 9801937.513 13888061.67 12676188.89 11679499.81 1.095510412 0.929009128 1.640178495 1.312983514 0.908383632 0.839242919 1.189097298 1.085336624 1 23.47747515 3.246063413 24.99692349 1.020120588 1.250159469 0.25942345 0.200424171 269.3262726 897304.1009 0.061155298 0.077376285 1762.233339 -3.246063413 0.230038881 FYGDEEKDKGLQTSQDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FYGDEEKDKGLQTSQDAR 18 2 P27797 P27797 CALR Calreticulin 0 ;;; 156.73 5.34E-09 3000470000 6483300 4768230 2974080 2881150 5094000 4457450 7881000 7083400 175200 FALSE TRUE 5626515.478 4736907.183 4412355.036 3535359.143 4992639.366 4628930.986 7116701.833 5568670.033 154488.0556 36.42039158 30.6619639 28.56114033 22.88435264 32.31731636 29.9630348 46.06635643 36.04595845 1 17.23713577 1.235255326 24.99999754 0.999955823 33.00993324 0.732874043 6.045332867 54.09365572 409075.9191 11.328185 1.614199225 17.1891866 -1.235255326 32.00997742 FYGPEGPYGVFAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FYGPEGPYGVFAGR 14 0 O00264 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 0 ; 177.57 4.84E-06 495820000 211930 201667 177196 244680 290280 278280 204737 294080 336820 FALSE TRUE 183922.9135 200342.2362 262888.5783 300238.3337 284503.9959 288985.6117 184881.6373 231193.2805 297001.5233 0.619265893 0.674549524 0.885142188 1.010898296 0.957920999 0.973010537 0.622493902 0.778424561 1 18.1801108 4.291956848 4.686385949 0.87553651 0.635454379 0.42301229 0.11753348 0.221469258 9.979772378 0.033102702 0.090756232 19586.50052 -4.291956848 -0.240082131 FYHDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FYHDAK 6 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 124.12 0.018491 330490000 1025100 955400 574310 754190 821650 910010 986340 1116700 1135200 FALSE TRUE 889630.4377 949123.9145 852048.237 925440.3666 805300.7725 945018.6736 890684.8986 877902.3952 1000997.949 0.888743517 0.948177681 0.851198784 0.924517745 0.804497924 0.944076533 0.889796926 0.877027167 1 19.93300759 1.234125356 24.91017332 1.000000171 0.890837923 0.390548008 0.042789659 127.9610421 718581.7651 0.073489669 0.009548137 17.14452101 -1.234125356 -0.109162248 FYHDWNDKEIEVLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FYHDWNDKEIEVLNK 15 1 J3KQ32;Q9NTK5;Q9NTK5-3;Q9NTK5-2;C9JCJ9 J3KQ32 OLA1 Obg-like ATPase 1 0 214.18 1.51E-12 1309500000 962160 646530 502490 640350 661090 438800 904960 999250 783400 FALSE TRUE 835008.1182 642282.9019 745495.8447 785751.2546 647935.6024 455680.9199 817197.1185 785568.1637 690787.3445 1.208777383 0.929783829 1.079197311 1.137471989 0.937966811 0.659654413 1.182993761 1.137206942 1 19.39788213 FYIGEMVLAIDSIHQLHYVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FYIGEMVLAIDSIHQLHYVHR 21 0 Q9Y5S2;A0A0U1RRC3 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 0 ;; 147.06 3.58E-08 541956000 148728.9 143072.8 62500.4 109371.6 128647.3 133623.5 138108.4 154006.6 143105.3 FALSE TRUE 129073.999 142132.9454 92725.80249 134206.0934 126087.4704 138764.0825 124714.6686 121073.4871 126187.5545 1.022874241 1.126362627 0.73482526 1.06354461 0.999206863 1.09966536 0.988327804 0.95947249 1 16.9452101 FYLAEMVIAIDSVHQLHYVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FYLAEMVIAIDSVHQLHYVHR 21 0 Q5VT25-2;A0A0A0MRJ0;Q5VT25;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-6 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 0 76.768 0.0037144 15109000 0 0 0 1034.9 0 0 0 842.06 0 FALSE TRUE 0 0 0 1269.889862 0 0 0 661.9920219 0 0 FYLDLYPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FYLDLYPR 8 0 P52888;K7EP46;K7EMU4 P52888 THOP1 Thimet oligopeptidase 0 73.975 0.081003 0 175530 224460 136760 134830 217440 234540 172890 192310 188050 FALSE TRUE 152333.2658 222985.5075 202897.5934 165445.2122 213113.3694 243562.9056 156123.1544 151186.0031 165818.9432 0.918672275 1.344752916 1.223609254 0.99774615 1.285217269 1.468848497 0.941527858 0.911753507 1 17.3392493 2.157387733 24.99936032 0.942494219 1.207631324 0.36645208 0.158153806 29.73509907 9155.363496 0.063266218 0.042654083 143.6771593 -2.157387733 0.265137105 FYNELTEILVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FYNELTEILVR 11 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 97.734 0.014065 244060000 241390 238140 125850 168840 223370 245290 221450 252840 243760 FALSE TRUE 209489.6999 236575.6427 186711.4809 207177.7026 218925.374 254726.465 199973.8131 198772.1336 214942.9705 0.974629221 1.100643776 0.868655907 0.963872892 1.018527722 1.185088605 0.930357539 0.924766849 1 17.7135944 FYQDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FYQDLK 6 0 P55145;H7C2D6 P55145 MANF Mesencephalic astrocyte-derived neurotrophic factor 0 97.068 0.09653 305560000 608740 524080 396350 503110 555240 599230 582800 602260 573130 FALSE TRUE 528293.4666 520637.284 588026.1857 617348.8151 544191.8103 622282.7659 526280.1457 473471.3858 505375.2243 1.045348963 1.030199462 1.163543754 1.221565256 1.076807457 1.231328201 1.041365149 0.936870988 1 18.94699541 2.003801001 24.50748916 0.971483798 1.127966208 0.490621389 0.06808706 66.64088562 429673.1097 0.028549252 0.019143198 100.879054 -2.003801001 0.156482411 FYQHKFPEVEDVVMVNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FYQHKFPEVEDVVMVNVR 18 1 P05198;G3V4T5 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 133.54 7.48E-06 339800000 526580 402700 227460 294540 452500 417100 496310 596030 267160 FALSE TRUE 456991.1188 400054.6372 337460.4168 361419.8088 443496.1353 433146.1069 448177.9326 468573.6228 235576.6491 1.939882923 1.698193088 1.4324867 1.534191993 1.882598029 1.838663163 1.902471804 1.989049528 1 17.84583702 3.239248816 24.9994431 1.775167104 1.638924579 0 0.302963809 69.63236996 2529399.358 0.088821673 0.107928909 1734.797612 -3.239248816 -0.136242524 FYQLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FYQLER 6 0 Q9Y3P9;A0A0U1RQX4;Q5R372-4;Q5R372;Q5R372-3 Q9Y3P9;Q5R372-4 RABGAP1;RABGAP1L Rab GTPase-activating protein 1;Rab GTPase-activating protein 1-like 0 ;; 117.7 0.05234 501140000 571900 569670 344821 394233 563600 633360 514810 545170 605880 FALSE TRUE 496321.966 565927.8003 511577.589 483749.6281 552385.4627 657725.769 464883.8054 428589.638 534253.5566 0.929000771 1.059286912 0.957555795 0.905468241 1.033938765 1.231111634 0.870155752 0.802221404 1 19.02716508 2.09357601 24.20358115 0.871352627 1.016943802 0.255490571 0.101636908 15.3257508 3953.702643 0.041821362 0.028195951 124.0440707 -2.09357601 0.145591175 FYS(ph)TSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FYSTSLK 7 0 A0A0C4DH43 A0A0C4DH43 1 FYS(0.333)T(0.333)S(0.333)LK;FYS(0.333)T(0.333)S(0.333)LK;FYS(0.333)T(0.333)S(0.333)LK 73.616 0.050779 244714000 602810 684430 427539 450468 508586 786570 473536 567750 586130 TRUE FALSE 523147.1312 679933.9343 634298.2904 552753.6444 498466.1336 816829.8569 427612.5516 446341.0807 516838.3791 1.012206431 1.31556394 1.227266233 1.069490322 0.964452629 1.580435761 0.827362226 0.863598948 1 18.97935368 FYSTS(ph)LK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FYSTSLK 7 0 A0A0C4DH43 A0A0C4DH43 1 FY(0.001)S(0.271)T(0.271)S(0.457)LK 73.616 0.050779 138480000 376630 430730 275120 287880 322390 542090 296480 333980 361020 TRUE FALSE 326857.3912 427900.5063 408168.9522 353247.554 315975.0697 562944.5531 267727.4152 262560.976 318340.6269 1.026753621 1.344159275 1.282176756 1.109652756 0.992569101 1.768371692 0.841009261 0.824779981 1 18.28021176 FYTEDGNWDLVGNNTPIFFIRDPILFPSFIHSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FYTEDGNWDLVGNNTPIFFIRDPILFPSFIHSQK 34 1 P04040 P04040 CAT Catalase 0 142.37 1.67E-10 160560000 122750 106660 48776 75824 100930 115200 122470 159580 49918 FALSE TRUE 106528.2765 105959.3434 72364.23675 93040.9981 98921.69047 119631.8185 110592.8783 125455.0589 44016.75091 2.420175826 2.40725045 1.644015863 2.113763424 2.247364661 2.717870267 2.512517984 2.850166272 1 15.42576504 2.99447721 21.50719358 2.394504948 2.13550029 0 0.544434594 142.304396 554193.0692 0.165133906 0.180927636 987.3638221 -2.99447721 -0.259004658 FYTLIPHDFGMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FYTLIPHDFGMK 12 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 158.05 6.32E-05 838120000 3286800 2931200 1781210 2169420 2816100 2557950 2993500 3683800 3273500 FALSE TRUE 2852441.052 2911944.754 2642609.114 2662019.969 2760065.12 2656355.992 2703190.831 2896048.037 2886510.559 0.988196992 1.008811399 0.915503013 0.922227691 0.956194361 0.920265468 0.936490886 1.003304155 1 21.46089507 1.695643904 6.348080508 1.001652788 0.948747259 0.342084774 0.029854112 0.153182658 13.71121099 0.019375802 0.008251816 49.61853118 -1.695643904 -0.052905529 FYTQQWEDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FYTQQWEDYR 10 0 A0A590UJ56;A0A590UJR3;A0A590UJ21;A0A0C4DGX4;Q13616;A0A590UJC4;A0A590UK34;A0A590UJ50;A0A590UJM8;A0A590UJA0 A0A590UJ56 CUL1 Cullin-1 0 ;;; 199.81 6.32E-07 1106060000 1004850 1035640 619000 809270 1116230 1082470 1011680 1153810 1146390 FALSE TRUE 872056.5265 1028836.813 918350.4704 993027.1224 1094019.207 1124113.321 913567.4293 907076.7105 1010865.08 0.862683402 1.017778567 0.908479765 0.98235377 1.082260361 1.112031015 0.903748133 0.897327179 1 19.94715902 4.750865061 22.58440457 0.981125043 0.86268311 0.222880816 0.072535502 912.7486722 1675197.055 0.019524338 0.291837355 56346.25561 -4.750865061 -0.118441933 FYVHNDIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FYVHNDIFR 9 0 Q13283;E5RIZ6 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ;;; 193.82 3.31E-05 5015870000 2921530 5784610 3125440 3495750 5470410 6102940 4819400 5580290 5900450 FALSE TRUE 2535442.408 5746610.516 4636913.238 4289513.467 5361559.544 6337724.051 4352015.33 4386988.409 5202905.523 0.48731279 1.104500263 0.891216113 0.824445773 1.03049335 1.218112461 0.83645865 0.843180486 1 22.31088608 4.750113006 24.81759388 0.955379004 0.487312482 0.581938277 0.127754185 1286.988887 2764736.291 0.032378649 0.505566227 56248.76692 -4.750113006 -0.468066522 FYVHNDMFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FYVHNDMFR 9 0 Q9UN86-2;Q9UN86;D6RB17;D6RAC7 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ;;; 185.6 4.27E-05 2276710000 1492050 2252950 1198630 1473780 2155850 2397750 1935860 2087880 2140690 FALSE TRUE 1294871.812 2238150.223 1778291.477 1808424.274 2112952.803 2489992.994 1748120.595 1641403.11 1887620.067 0.685981165 1.185699528 0.942081253 0.958044633 1.119373988 1.319117675 0.926097696 0.869562227 1 20.84813698 4.756939105 23.84564214 1.026925015 0.685980607 0.397575727 0.136108558 2504.84986 3249882.137 0.035587315 1.075954562 57139.85122 -4.756939105 -0.340944408 FYWGHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FYWGHK 6 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 118.11 0.022144 5662700000 7634200 7234400 4837800 6447200 7041400 7160400 8726000 9321100 9528800 FALSE TRUE 6625321.127 7186876.75 7177376.261 7911135.299 6901289.916 7435865.221 7879753.863 7327855.302 8402316.119 0.788511291 0.855344723 0.854214024 0.941542211 0.821355662 0.884978037 0.937807356 0.872123257 1 23.00235563 -1.999999999 0.024573981 2.050109632 2.65E-14 0.476508546 0.044832146 4480.629384 10.92932372 604.0460764 343.2551294 0.01 1.999999999 -2.050109632 GAAAADLLSS(ph)SPESQHGGTQSPGGGQPLLQPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 33 0 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 GAAAADLLS(0.099)S(0.801)S(0.099)PESQHGGTQSPGGGQPLLQPTK;GAAAADLLS(0.073)S(0.501)S(0.426)PESQHGGTQSPGGGQPLLQPTK 216.53 4.06E-36 2810200000 667200 609420 317060 590350 765550 819450 757880 917710 1230870 TRUE FALSE 579027.8295 605416.6799 470391.2765 724397.9904 750317.0528 850974.7718 684380.9142 721464.8581 1085357.951 0.533490199 0.557803699 0.433397365 0.667427727 0.691308386 0.784049881 0.630557793 0.664725271 1 20.04973949 3.531622535 3.535894748 0.733367669 0.513706905 0.523189633 0.105641693 0.209440139 5.229810517 0.030314573 0.044957054 3401.124544 -3.531622535 -0.219660764 GAAAADLLSS(ph)SPESQHGGTQSPGGGQPLLQPTKVDAAEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GAAAADLLSSSPESQHGGTQSPGGGQPLLQPTKVDAAEGR 40 1 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 GAAAADLLS(0.095)S(0.444)S(0.444)PES(0.018)QHGGTQSPGGGQPLLQPTKVDAAEGR;GAAAADLLS(0.057)S(0.471)S(0.471)PESQHGGTQSPGGGQPLLQPTKVDAAEGR 280.01 1.41E-77 1229400000 314380 286000 86921 127598 317980 318960 384970 403040 35847 TRUE FALSE 272833.8865 284121.2472 128956.2863 156571.0761 311652.8201 331230.5976 347635.6687 316853.0325 31609.2085 8.631468469 8.988559369 4.079706278 4.953337447 9.859557861 10.47892729 10.99792387 10.0240736 1 14.94805729 GAAAADLLSSS(ph)PESQHGGTQSPGGGQPLLQPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 33 0 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 GAAAADLLS(0.012)S(0.058)S(0.93)PESQHGGTQSPGGGQPLLQPTK;GAAAADLLS(0.016)S(0.116)S(0.869)PESQHGGTQSPGGGQPLLQPTK 317.44 1.40E-104 2412830000 1083570 929450 488200 921870 1138520 1123100 1158130 1375910 1967200 TRUE FALSE 940373.4791 923344.3818 724295.1529 1131194.673 1115865.679 1166306.384 1045814.731 1081682.354 1734639.857 0.542114535 0.532297455 0.417547856 0.652120767 0.643283777 0.672362265 0.602900208 0.623577482 1 20.72620473 0.036917033 1.373194456 9.999999997 0.574624974 0.756144382 0.074074872 16.72225602 1.709191894 443.3948577 0.023392386 1.088722085 -0.036917033 -9.425375023 GAAAHPDSEEQQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GAAAHPDSEEQQQR 14 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;;; 210.41 5.28E-09 1445800000 1981467 2211530 1418206 1559988 1990277 2415064 2025910 2116025 2016570 FALSE TRUE 1719611.116 2197002.314 2104055.165 1914207.118 1950674.382 2507973.075 1829437.56 1663529.521 1778173.392 0.967066048 1.235538853 1.183267714 1.076501947 1.097010219 1.410420989 1.028829679 0.93552717 1 20.76196458 2.014145702 24.99991097 0.968864327 1.164207792 0.344498341 0.115096979 226.8945941 400992.7989 0.045335086 0.030550033 103.3107946 -2.014145702 0.195343465 GAAEEAELEDS(ph)DDEEKPVKQDDFPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GAAEEAELEDSDDEEKPVKQDDFPK 25 2 Q9UBB9;F6XM96 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 GAAEEAELEDS(1)DDEEKPVKQDDFPK 263.59 1.71E-45 284330000 851870 510190 681780 461460 421020 303230 810570 907750 714980 TRUE FALSE 739293.2211 506838.5283 1011491.088 566241.546 412642.5257 314895.4543 731961.0462 713634.7266 630455.8789 1.172632766 0.803923867 1.604380453 0.898146191 0.654514518 0.499472627 1.161002809 1.131934447 1 19.26603588 4.823062561 19.31745806 0.983999501 1.172696224 0.040907898 0.302116266 56790.07072 12966744.86 0.076562793 562.6073506 66536.89969 -4.823062561 0.188696722 GAAGRPLELSDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GAAGRPLELSDFR 13 1 P42167;G5E972;H0YJH7;P42167-2 P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 0 88.163 0.0058097 0 804370 726780 514880 799670 892990 813370 538280 1005700 678060 FALSE TRUE 698070.4665 722005.7343 763877.6902 981247.2957 875221.2461 844660.8702 486077.6884 790638.8814 597900.5192 1.167536144 1.207568335 1.277599978 1.641154781 1.463824195 1.412711384 0.812974187 1.32235858 1 19.18954594 2.283110181 24.99998099 1.09319718 1.368242586 0.392148896 0.1824633 150.1204306 84242.79153 0.069938188 0.054173617 191.915557 -2.283110181 0.275045406 GAAS(ph)PVLQEDHCDSLPSVLQVEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GAASPVLQEDHCDSLPSVLQVEEK 24 0 Q8N9B5-2;Q8N9B5 Q8N9B5-2 JMY Junction-mediating and -regulatory protein 1 GAAS(1)PVLQEDHCDSLPSVLQVEEK;GAAS(1)PVLQEDHCDSLPSVLQVEEK 237.32 1.25E-37 384320000 291370 226427 177338 227685 217695 199870 266640 300070 393990 TRUE FALSE 252864.7163 224939.5861 263099.25 279384.3592 213363.2954 207559.1282 240781.2938 235902.3656 347412.951 0.727850575 0.647470353 0.75730985 0.804185216 0.614148939 0.597442115 0.693069424 0.679025825 1 18.40629201 1.237473971 24.99895468 1.00000037 0.688756427 0.707627878 0.062604706 15.86527045 364818.2609 0.094837935 0.015910613 17.27722429 -1.237473971 -0.311243943 GAASTLVPGVSETSASPGS(ph)PSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GAASTLVPGVSETSASPGSPSVR 23 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 GAASTLVPGVSETSASPGS(1)PSVR 308.77 4.29E-73 300330000 223860 205220 143030 161190 166760 230490 195480 209380 200200 TRUE FALSE 194276.3338 203871.8963 212199.7864 197790.6531 163441.8023 239357.0994 176522.3797 164605.7164 176532.5841 1.100512604 1.154868363 1.202043167 1.120420087 0.925844954 1.355880563 0.999942195 0.932438152 1 17.42957497 2.022956507 24.99999639 0.962832191 1.139071219 0.355480025 0.105844027 223.3761469 243259.0995 0.041086788 0.027698953 105.4281309 -2.022956507 0.176239028 GAAVDEYFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GAAVDEYFR 9 0 K7EQA8;Q86X55-2;Q86X55-1;Q86X55 K7EQA8 CARM1 Histone-arginine methyltransferase CARM1 0 104.06 0.0077283 238260000 780150 519200 272200 311920 410920 474920 478650 682000 281790 FALSE TRUE 677051.2009 515789.341 403836.8305 382746.2034 402743.496 493190.4797 432230.5967 536159.6073 248477.1072 2.724803136 2.075802261 1.625247633 1.540368075 1.620847492 1.984852791 1.739518789 2.157782716 1 17.92275341 4.632905899 2.564037227 1.721089095 2.822371578 0.547964504 0.305578435 0.309138106 3.020336747 0.076803966 0.659136514 42944.33666 -4.632905899 1.101282483 GAAYGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GAAYGFR 7 0 K7EJE6;A0A0A0MR62;K7EK60;O95466;O95466-2;O95466-3 K7EJE6 FMNL1 Formin-like protein 1 0 113.97 0.033593 0 151580 170440 89392 102890 179400 196760 111690 151170 145590 FALSE TRUE 131548.3189 169320.3684 132622.2702 126252.7471 175830.291 204329.4845 100858.321 118843.4719 128378.5161 1.02469107 1.31891514 1.033056576 0.983441396 1.369623956 1.591617436 0.785632395 0.925727104 1 16.97004426 2.195294123 24.99997974 0.903434233 1.212232282 0.38197107 0.189563107 152.3400642 88023.1304 0.079932311 0.053890756 156.7812502 -2.195294123 0.308798049 GACS(ph)TPDMPQFEPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GACSTPDMPQFEPVK 15 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 GACS(0.5)T(0.5)PDMPQFEPVK;GACS(0.5)T(0.5)PDMPQFEPVK 166.38 1.44E-06 145981000 129014 121592 113962 164734 117311 114455 113397 145679 357390 TRUE FALSE 111964.473 120793.2541 169074.4044 202139.3725 114976.7406 118858.1579 102399.7764 114526.6795 315139.7613 0.355285136 0.383300583 0.5365061 0.641427701 0.364843649 0.377160144 0.324934486 0.363415518 1 18.26563227 1.235291646 24.99999811 1.000000804 0.41801195 0.779155657 0.097316764 47.30594409 361718.9082 0.182112394 0.026014154 17.1906242 -1.235291646 -0.581988854 GACST(ph)PDMPQFEPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GACSTPDMPQFEPVK 15 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 GACS(0.158)T(0.842)PDMPQFEPVK;GACS(0.019)T(0.981)PDMPQFEPVK 335.1 5.71E-68 573500000 821990 734650 794660 1192480 728550 685990 792780 974550 2588500 TRUE FALSE 713361.9388 729824.0358 1178960.234 1463250.81 714053.2804 712380.4792 715896.3176 766150.0665 2282490.479 0.312536655 0.319748995 0.516523615 0.641076413 0.312839544 0.31210666 0.313647012 0.33566408 1 21.12217741 1.235865596 24.99991223 1.000000821 0.38339656 0.753997552 0.110753904 39.99323752 370915.9323 0.195525427 0.029226073 17.21335779 -1.235865596 -0.616604261 GADDDRPSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GADDDRPSWR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 128.81 0.00029159 3879100000 4842500 4617000 3673570 4057990 4730500 5145700 4147090 4880200 6130500 FALSE TRUE 4202551.356 4586670.623 5450120.739 4979418.652 4636372.305 5343658.409 3744905.85 3836607.208 5405759.274 0.777421106 0.848478519 1.008206334 0.921132148 0.857672728 0.988512092 0.69276223 0.709725871 1 22.36606584 2.237968648 24.99977781 0.777346684 0.9018072 0.152219804 0.105818144 23.34824151 985944.9435 0.041443141 0.029859399 172.9691486 -2.237968648 0.124460516 GADFLVTEVENGGSLGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GADFLVTEVENGGSLGSK 18 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 140.1 3.01E-07 68623000 73358 67816 50073 62581 55131 58385 71239 85144 90032 FALSE TRUE 63663.55443 67370.51223 74288.47028 76790.97254 54034.00096 60631.10873 64330.25274 66936.61819 79388.51952 0.801923941 0.848617818 0.935758353 0.967280572 0.680627392 0.763726406 0.810321859 0.843152368 1 16.27664277 1.239520866 4.930856096 1.011092985 0.83127768 0.303546989 0.080467239 0.245221548 14.78620387 0.151867665 0.02144408 17.35884662 -1.239520866 -0.179815305 GADIMYTGTVDCWR ddPTM_MDA-MB-175_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" 0 248.21 3.37E-12 0 39643 45968 38378 62979 58356 48203 36328 54290 57629 FALSE TRUE 34404.07711 45666.03318 56937.72917 77279.34452 57194.82977 50057.4006 32804.91615 42680.50599 50816.16527 0.677030172 0.898651697 1.120464893 1.520763011 1.125524318 0.985068439 0.64556064 0.839900173 1 15.63299989 2.466525028 20.4963386 0.822109447 1.083888861 0.189359448 0.225316612 39.90176469 77174.94204 0.089918461 0.069821583 292.7689587 -2.466525028 0.261779413 GADNDGS(ph)GSESGYTTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 GADNDGS(1)GSESGYTTPK;GADNDGS(0.992)GS(0.008)ESGYTTPK;GADNDGS(0.993)GS(0.007)ESGYTTPK;GADNDGS(0.995)GS(0.005)ESGYTTPK;GADNDGS(1)GSESGYTTPK;GADNDGS(0.997)GS(0.003)ESGYTTPK 366.52 1.27E-104 4005270000 4346280 3583850 2393140 3134450 3404360 2960070 3920070 4877800 4011130 TRUE FALSE 3771908.086 3560307.453 3550470.509 3846174.78 3336619.897 3073945.808 3539902.215 3834720.429 3536938.781 1.066432958 1.006607033 1.00382583 1.087430407 0.943363768 0.869097827 1.000837853 1.084191915 1 21.75406982 7.999982611 0.905829145 0.99997988 34.24318836 0.104067443 0.062407309 2954.490155 6.262264497 0.022424086 203104.0378 99995996.13 -7.999982611 33.24320848 GADS(ph)GEEKEEGINR ddPTM_MDA-MB-175_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 224.86 1.81E-12 8721580000 7567970 5137970 4827750 5293680 5212660 4787110 5778150 6651920 10110400 TRUE FALSE 6567843.59 5104218.337 7162466.048 6495690.953 5108938.264 4971273.219 5217785.902 5229458.673 8915160.03 0.73670507 0.572532441 0.80340297 0.728611818 0.573061868 0.557620189 0.585271143 0.58658046 1 23.08782926 1.233556275 24.96837556 1.000000566 0.638261383 0.632679773 0.085426571 106.2060634 529835.3099 0.176877555 0.021834895 17.12207026 -1.233556275 -0.361739183 GADS(ph)GEEKEEGINREDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GADSGEEKEEGINREDK 17 2 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 1 GADS(1)GEEKEEGINREDK;GADS(1)GEEKEEGINREDK;GADS(1)GEEKEEGINREDK 241.76 1.17E-20 2469330000 2755710 1606550 1651430 1566130 1428980 1423170 2365470 2533080 2503690 TRUE FALSE 2391535.941 1595996.467 2450067.072 1921743.753 1400546.094 1477920.271 2136067.083 1991400.554 2207706.62 1.083267097 0.722920542 1.109779284 0.870470621 0.634389588 0.669436898 0.967550246 0.902022278 1 21.07411704 4.766679903 23.25883169 0.863130191 1.083267925 0.18046232 0.149643003 7467.731415 6176660.577 0.037497281 3.067424203 58435.92233 -4.766679903 0.220137735 GADSGEEKEEGINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GADSGEEKEEGINR 14 1 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 0 77.078 0.012993 0 72024 67664 42608 55613 56728 60037 62255 70629 73807 FALSE TRUE 62505.84591 67219.51073 63213.37132 68240.78164 55599.22379 62346.66224 56217.51968 55525.53799 65081.62054 0.960422396 1.032849369 0.971293751 1.048541525 0.854299929 0.957976487 0.863800244 0.853167723 1 15.98996255 3.238220999 24.9999986 0.898716464 1.003104591 0.456410745 0.052514284 7.544503368 555378.3045 0.014902589 0.017962785 1730.696832 -3.238220999 0.104388127 GADSLEDFLYHEGYACTSIHGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GADSLEDFLYHEGYACTSIHGDR 23 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;;; 293.67 7.83E-62 1316680000 513410 529520 232210 408712 575810 612030 488490 588580 825040 FALSE TRUE 445561.5677 526041.5483 344507.5327 501516.3064 564352.5076 635575.1901 441116.315 462716.7473 727504.7111 0.612451797 0.723076484 0.473546807 0.689365029 0.775737255 0.873637216 0.606341524 0.636032647 1 19.47259706 3.48285821 20.14455155 0.750617484 0.609434416 0.274246669 0.126179238 31.81397313 111711.2338 0.036345514 0.048818741 3039.89239 -3.48285821 -0.141183067 GADYMDCLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GADYMDCLYR 10 0 A0A0A0MTN0;Q13617;Q13617-2;Q5T2B5 A0A0A0MTN0 CUL2 Cullin-2 0 102.61 0.0068034 114700000 169890 154460 108780 110390 136450 153060 127060 125410 156100 FALSE TRUE 147438.6061 153445.3421 161386.3718 135455.7367 133734.912 158948.3172 114737.7408 98592.04744 137646.0358 1.071143133 1.114782138 1.172473808 0.984087452 0.971585641 1.154761314 0.833570978 0.716272335 1 17.07060354 2.224952541 24.24771396 0.821416184 1.074974053 0.5610629 0.093995428 105.3720433 187756.2662 0.038273842 0.025975917 167.8620571 -2.224952541 0.253557869 GAEDDELEEEADWIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GAEDDELEEEADWIYR 16 0 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ; 247.67 5.98E-20 114569000 84044 84409 45144 60141 63942 76056 77657 72926 73280 FALSE TRUE 72937.37246 83854.51172 66975.7894 73796.93325 62669.6793 78981.92353 70125.83609 57331.34241 64616.92188 1.128765815 1.297717522 1.036505414 1.142068225 0.96986482 1.222310213 1.085254977 0.887249667 1 15.97962441 -1.539700913 0.195521788 1.14E-12 1.240647924 0.312033932 0.100149049 95.67756132 1.664030002 33.79508096 0.71722518 0.028860183 1.539700913 1.240647924 GAEDDRGPWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GAEDDRGPWR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 105.86 0.0022734 2146490000 3605620 3898720 3042390 3309570 3571080 4464350 3142300 3770830 5616550 FALSE TRUE 3129128.182 3873109.052 4513699.98 4061058.452 3500022.495 4636096.433 2837560.23 2964467.349 4952567.857 0.631819345 0.782040582 0.911385792 0.819990471 0.70670864 0.936099528 0.572947269 0.598571778 1 22.23974531 2.23260427 24.99942065 0.691455061 0.799284478 0.040369653 0.143951169 331.4206875 1390989.99 0.057017631 0.039580244 170.8457857 -2.23260427 0.107829417 GAEEMETVIPVDVMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GAEEMETVIPVDVMR 15 0 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ;;; 236.57 2.41E-17 274280000 349849 340207 230837 253623 323506 334935 306049 362211 326810 FALSE TRUE 303615.5682 337972.1578 342470.5453 311211.9785 317068.8635 347820.1662 276368.4151 284754.9964 288174.8941 1.053580914 1.172802228 1.188412149 1.07994133 1.100265394 1.206975949 0.959030161 0.988132562 1 18.13658513 2.226784435 24.99988593 0.982611185 1.133970684 0.683345959 0.048543465 121.3595445 257634.2591 0.019288468 0.013122843 168.5716101 -2.226784435 0.151359499 GAEETSWS(ph)GEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GAEETSWSGEER 12 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 GAEET(0.007)S(0.005)WS(0.988)GEER;GAEETSWS(1)GEER;GAEETSWS(1)GEER 280.05 5.50E-28 2349800000 2256810 2017950 1526780 1520550 1929410 1866900 1816660 2288690 1896470 TRUE FALSE 1958566.84 2004693.954 2265135.915 1865814.118 1891018.516 1938720.851 1640480.593 1799271.454 1672271.477 1.171201487 1.198784995 1.354526431 1.115736376 1.13080833 1.159333803 0.9809894 1.075944593 1 20.67337764 2.787823518 0.940656565 1.021876853 1.229963427 0.583740841 0.067973553 0.399335833 0.805638683 0.047924222 0.037930788 613.5126444 -2.787823518 0.208086574 GAEFLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GAEFLLR 7 0 Q9BXT2 Q9BXT2 CACNG6 Voltage-dependent calcium channel gamma-6 subunit 0 ;;; 142.11 0.0058425 411006000 571895 462367 339690 369558 473597 564482 412583 399572 386929 FALSE TRUE 496317.6268 459329.6807 503965.2202 453471.7922 464173.3463 586197.9878 372570.7642 314126.6373 341186.6944 1.454680487 1.34627079 1.477095175 1.329101632 1.360467316 1.71811503 1.091985034 0.920688416 1 18.38020186 2.060544825 7.363392953 0.969648884 1.434363954 0.784781021 0.110855816 0.089847474 9.152692784 0.044107918 0.029552102 114.9594891 -2.060544825 0.46471507 GAEILEVLHSLPAVR ddPTM_MDA-MB-175_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 ; 216.46 2.20E-12 1061530000 1121910 1161200 904100 909100 1096690 1228000 1066000 1290610 1414710 FALSE TRUE 973646.7509 1153572.001 1341325.784 1115525.05 1074868.015 1275241.955 962619.4841 1014623.095 1247464.595 0.780500508 0.924733259 1.075241565 0.894233835 0.861642101 1.022267052 0.771660765 0.813348209 1 20.25056744 2.230983256 24.99999839 0.847852346 0.928713898 0.081249041 0.098903846 367.4348047 1212265.905 0.039696832 0.027346094 170.2092884 -2.230983256 0.080861553 GAELVEGCDGILGDNFRPTQPLSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GAELVEGCDGILGDNFRPTQPLSDR 25 1 P35219 P35219 CA8 Carbonic anhydrase-related protein 0 ;;; 245.09 7.59E-39 2660890000 863920 923480 674980 592358 868910 966540 851350 978500 910930 FALSE TRUE 749750.7831 917413.5991 1001402.586 726861.9375 851620.391 1003723.419 768786.208 769255.3897 803240.8931 0.933407138 1.142140057 1.246702694 0.90491152 1.060230372 1.249592031 0.957105415 0.957689525 1 19.61547319 GAEQDNPNQYSWGENYAGSSGLMSAS(ph)PELGPAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GAEQDNPNQYSWGENYAGSSGLMSASPELGPAQR 34 0 H0YA26;E9PHT6;Q9NVE7;H0YA31 H0YA26 PANK4 Pantothenate kinase 4 1 GAEQDNPNQYSWGENYAGSSGLMS(0.021)AS(0.979)PELGPAQR;GAEQDNPNQYSWGENYAGS(0.001)S(0.001)GLMS(0.004)AS(0.994)PELGPAQR 164.17 1.77E-14 247140000 70773 63211 48272 54407 65951 75803 63070 69464 77879 TRUE FALSE 61420.16873 62795.76278 71616.50066 66760.94091 64638.70413 78719.19046 56953.48111 54609.66417 68672.23334 0.89439597 0.914427269 1.042874204 0.972167901 0.941264045 1.146303049 0.829352394 0.795221904 1 16.06743926 GAES(ph)ENEEESPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GAESENEEESPR 12 0 Q9UEG4 Q9UEG4 ZNF629 Zinc finger protein 629 1 GAES(1)ENEEESPR;GAES(1)ENEEESPR 188.39 9.71E-06 343950000 346470 292250 247680 302390 289860 302870 288450 334980 442960 TRUE FALSE 300683.1117 290330.1905 367458.8764 371052.2712 284092.3531 314521.6049 260476.1634 263347.1338 390593.7734 0.769810305 0.743304708 0.940769929 0.949969755 0.727334567 0.805239679 0.666872288 0.67422256 1 18.57530943 3.203490389 24.98965027 0.755605562 0.849688715 0.088891742 0.112318229 363.7543879 259195.7917 0.034814786 0.039477851 1597.682171 -3.203490389 0.094083152 GAFGKPQGTVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GAFGKPQGTVAR 12 1 P27635;X1WI28;A0A087WV22;H7C123;H7C2C5;Q96L21;F8W7C6 P27635;F8W7C6 RPL10;RPL10L 60S ribosomal protein L10;60S ribosomal protein L10-like 0 66.023 0.053966 2006100000 4126600 3399900 2096200 2335500 3545700 3533200 3518300 4439000 2748600 FALSE TRUE 3581259.355 3377565.833 3109929.331 2865810.971 3475147.507 3669124.49 3177095.808 3489754.394 2423663.639 1.477622264 1.393578621 1.2831522 1.182429329 1.433840674 1.513875288 1.310864988 1.439867454 1 21.20875806 1.232624397 24.99996079 0.99999939 1.376208359 0.594022403 0.098540577 147.966225 623085.3399 0.219121945 0.02482168 17.08537036 -1.232624397 0.376208969 KTSTS(ph)PPPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTSTSPPPEK 10 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KT(0.039)S(0.027)T(0.105)S(0.83)PPPEK 82.908 0.010171 647770000 1284800 856070 832280 1053000 751050 627340 1130300 1387300 2736800 TRUE FALSE 1115010.425 850446.4198 1234773.392 1292099.744 736105.5744 651474.1757 1020683.68 1090636.691 2413258.622 0.462035198 0.352405835 0.511662273 0.535417022 0.305025565 0.26995622 0.42294832 0.451935272 1 21.2025511 1.228293917 4.053963478 1.070885068 0.40802163 0.829402447 0.08372886 0.105788479 3.059604058 0.211224224 0.022443257 16.91585356 -1.228293917 -0.662863437 GAGATSGS(ph)PPAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GAGATSGSPPAGR 13 0 B4DEE8;P16455 B4DEE8 MGMT Methylated-DNA--protein-cysteine methyltransferase 1 GAGATS(0.005)GS(0.995)PPAGR;GAGATSGS(1)PPAGR;GAGATS(0.018)GS(0.982)PPAGR 185.99 8.59E-06 1911400000 626220 657140 611720 648070 626040 738150 620920 690330 1285560 TRUE FALSE 543463.4404 652823.2041 907549.8381 795224.1986 613583.0288 766547.1081 560703.274 542708.3017 1133582.561 0.479421137 0.575893831 0.800603211 0.701514143 0.541277759 0.676216391 0.49462941 0.478754985 1 20.11245804 1.228447627 24.9994354 1.000000828 0.59376608 0.593952882 0.105616809 332.9595787 823022.7515 0.373044852 0.027884518 16.92184167 -1.228447627 -0.406234748 GAGDGS(ph)DEEVDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GAGDGSDEEVDGK 13 0 P35579;P35579-2 P35579 MYH9 Myosin-9 1 GAGDGS(1)DEEVDGK;GAGDGS(1)DEEVDGK;GAGDGS(1)DEEVDGK;GAGDGS(1)DEEVDGK;GAGDGS(1)DEEVDGK;GAGDGS(1)DEEVDGK 215.87 2.98E-11 5375710000 8414730 6803190 7085180 8044570 6313500 5912760 8215580 9111080 20803500 TRUE FALSE 7302702.11 6758499.397 10511596.75 9871212.572 6187873.702 6140227.703 7418834.316 7162746.445 18344133.93 0.398094679 0.368428372 0.573022242 0.538112762 0.33732166 0.334724317 0.404425433 0.390465228 1 24.12881546 1.236912124 24.99851868 1.000000721 0.418054014 0.843854057 0.078668642 17.18983687 260591.9901 0.127629301 0.020594789 17.25488719 -1.236912124 -0.581946707 GAGDGS(ph)DEEVDGKADGAEAKPAE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GAGDGSDEEVDGKADGAEAKPAE 23 2 P35579;P35579-2 P35579 MYH9 Myosin-9 1 GAGDGS(1)DEEVDGKADGAEAKPAE;GAGDGS(1)DEEVDGKADGAEAKPAE;GAGDGS(1)DEEVDGKADGAEAKPAE;GAGDGS(1)DEEVDGKADGAEAKPAE;GAGDGS(1)DEEVDGKADGAEAKPAE;GAGDGS(1)DEEVDGKADGAEAKPAE;GAGDGS(1)DEEVDGKADGAEAKPAE 205.87 1.16E-24 7791350000 16108080 12032100 11144880 9737300 10351990 7951900 17541390 18589720 9174580 TRUE FALSE 13979356.42 11953060.34 16534581.25 11948302.79 10146005.65 8257814.739 15840228.7 14614453.04 8089971.604 1.727985845 1.477515735 2.043836747 1.476927655 1.254146015 1.020747061 1.958007948 1.80649003 1 22.94770321 3.537773656 24.97290802 1.469236838 1.728858238 0.170628233 0.330422716 563.5868998 232048.2527 0.096612315 0.143298988 3449.639054 -3.537773656 0.2596214 GAGFGPQHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GAGFGPQHNR 10 0 Q56VL3 Q56VL3 OCIAD2 OCIA domain-containing protein 2 0 105.52 0.0025382 105510000 123220 140530 101640 134500 161490 212120 82260 159730 172900 FALSE TRUE 106936.1648 139606.8492 150793.444 165040.2807 158276.6649 220280.3937 74282.43786 125572.9825 152459.959 0.701404917 0.915695177 0.989069163 1.082515579 1.038152352 1.444840961 0.487225881 0.823645653 1 17.21807087 2.217531202 24.99999784 0.76961204 1.024566925 0.235278445 0.219459054 361.9921866 430337.0543 0.090011925 0.060755543 165.0179555 -2.217531202 0.254954885 GAGGEENKENERPSAGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GAGGEENKENERPSAGSK 18 2 Q9UHB9;Q9UHB9-4;Q9UHB9-2;K7EN53;K7EQC2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;;; 192.85 8.63E-15 627410000 1302880 946230 882740 835490 885880 793720 1279400 1430410 1216340 FALSE TRUE 1130701.107 940014.1528 1309636.017 1025200.774 868252.7212 824254.922 1155323.985 1124527.953 1072545.671 1.054221874 0.876432751 1.221053846 0.955857454 0.809525174 0.768503332 1.077179291 1.048466264 1 20.03260765 GAGGS(ph)PVGVEEGLVNVGTGQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GAGGSPVGVEEGLVNVGTGQK 21 0 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 GAGGS(1)PVGVEEGLVNVGTGQK;GAGGS(1)PVGVEEGLVNVGTGQK 292.53 9.61E-55 340500000 403470 377130 238890 283300 337090 253810 336940 449420 357650 TRUE FALSE 350150.4172 374652.6082 354418.003 347627.595 330382.5685 263574.2349 304263.6107 353315.0304 315369.0244 1.110287917 1.187981632 1.123819956 1.102288329 1.047606274 0.8357645 0.964785972 1.120322552 1 18.26668144 3.241102943 2.928203036 0.996425888 1.140137188 0.487089527 0.072118223 0.261927301 4.618229731 0.025203055 0.031553948 1742.219792 -3.241102943 0.1437113 GAGHPCYLDKPEEWHTGLLDFLQGLQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GAGHPCYLDKPEEWHTGLLDFLQGLQ 26 1 F8W9U3;Q96IU4;Q96IU4-2 F8W9U3 ABHD14B Alpha/beta hydrolase domain-containing protein 14B 0 164.82 8.02E-12 658350000 935830 837230 579530 643110 766800 763580 915960 1118900 947400 FALSE TRUE 812157.6944 831730.181 859792.6464 789137.9548 751542.1802 792955.4167 827130.3402 879631.9423 835399.4513 0.97217887 0.995607766 1.029199439 0.944623502 0.899620151 0.949193126 0.990101608 1.052947714 1 19.67210667 1.965880896 5.782142306 1.028369479 0.965671562 0.332901706 0.035695432 0.22528552 21.65157278 0.01904762 0.010621464 92.44446129 -1.965880896 -0.062697917 GAGSVFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GAGSVFR 7 0 P62917;E9PKZ0;G3V1A1;E9PKU4;E9PP36 P62917 RPL8 60S ribosomal protein L8 0 92.677 0.036046 830240000 360580 384950 286950 279770 325940 386410 368760 354990 419120 FALSE TRUE 312928.4394 382421.2381 425719.9798 343296.0545 319454.4317 401275.4427 332997.712 279078.151 369572.1111 0.846731747 1.034767578 1.151926693 0.928901409 0.864389985 1.085783886 0.901035825 0.755138558 1 18.49549637 2.009690591 24.14464271 0.850481572 0.987679583 0.147879317 0.109942605 184.5791787 459886.5869 0.044471829 0.029935607 102.2564217 -2.009690591 0.137198012 GAGTDDHTLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GAGTDDHTLIR 11 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;;; 199.09 5.14E-08 5939350000 6709400 6903900 3310130 3439520 4305890 4755270 3410110 4839680 8531800 FALSE TRUE 5822735.791 6858547.826 4910919.94 4220515.586 4220211.213 4938208.314 3079398.057 3804752.094 7523180.323 0.773972647 0.911655381 0.652771797 0.561001519 0.560961061 0.656399036 0.409321314 0.505737192 1 22.84291124 4.106780185 4.969879297 0.591766391 0.840482932 0.248390008 0.157568255 0.245853948 9.682511241 0.039999957 0.087267963 12787.33919 -4.106780185 0.248716541 GAGTNEDALIEILTTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GAGTNEDALIEILTTR 16 0 P12429;D6RA82;D6RFG5;D6RCA8 P12429 ANXA3 Annexin A3;Annexin 0 94.532 0.0094459 11361000 31786 27256 15669 17615 30625 26592 32171 35685 30532 FALSE TRUE 27585.39956 27076.95354 23246.58081 21614.75498 30015.62242 27615.01145 29051.06137 28054.04045 26922.54174 1.024620923 1.005735409 0.863461594 0.802849716 1.114888137 1.025720815 1.079060872 1.04202793 1 14.716527 3.220700672 24.99996917 1.051723755 0.925657087 0.457145471 0.069393351 235.4956536 329640.9383 0.022050067 0.025053704 1662.266575 -3.220700672 -0.126066668 GAGYTFGQDISETFNHANGLTLVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 367.99 1.11E-119 946229000 665450 599835 429513 516341 608597 674998 582009 708840 609605 FALSE TRUE 577509.0965 595894.6444 637226.9234 633584.1158 596487.1104 700965.6098 525565.8568 557260.0822 537538.1914 1.074359191 1.108562431 1.185454231 1.178677396 1.109664615 1.304029409 0.977727472 1.036689283 1 19.03600773 2.202739052 24.99967536 1.010319656 1.157482024 0.570920156 0.063386865 127.4472579 88943.89983 0.025087026 0.016914347 159.4920545 -2.202739052 0.147162368 GAHGIIVVYDVTDQESYANVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GAHGIIVVYDVTDQESYANVK 21 0 Q9H0U4 Q9H0U4 RAB1B Ras-related protein Rab-1B 0 ;; 246.95 2.42E-30 415110000 460410 356903 300712 305129 383377 341257 388515 483350 405523 FALSE TRUE 399565.652 354558.4807 446137.329 374413.2031 375748.5478 354385.3776 350836.8751 379989.3639 357582.5329 1.117408193 0.991543065 1.247648551 1.047067931 1.050802299 0.991058972 0.981135382 1.062661984 1 18.44791674 3.493750654 24.7997006 1.0215574 1.113004915 0.333653352 0.065383437 792.6519565 1182093.287 0.017404003 0.02507331 3117.099416 -3.493750654 0.091447515 GAHLTALEMLTAFASHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GAHLTALEMLTAFASHIR 18 0 Q96EL3 Q96EL3 MRPL53 "39S ribosomal protein L53, mitochondrial" 0 198.95 9.70E-16 28731000 24638 27728 16387 21837 29586 39569 18964 26348 23204 FALSE TRUE 21382.02588 27545.85294 24311.80801 26795.42461 28997.29648 41091.24503 17124.8742 20713.68524 20460.84955 1.045021411 1.346271222 1.188211073 1.309594919 1.417208822 2.008286358 0.836958121 1.012357047 1 14.32057843 GAHNGQGLGNAFLSHISACDGIFHLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GAHNGQGLGNAFLSHISACDGIFHLTR 27 0 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 424.61 1.30E-187 1383290000 106153 102410 42003 81788 137747 126559 103628 99457 100171 FALSE TRUE 92124.61209 101737.262 62315.79129 100359.2155 135006.1042 131427.8066 93578.17251 78188.89453 88328.8985 1.0429725 1.151800415 0.705497208 1.136199105 1.528447728 1.487936665 1.059428727 0.885201739 1 16.4305979 2.000464225 24.99999766 0.945775225 1.176161274 0.152248954 0.22836945 30.76581118 1656784.213 0.104130699 0.069470217 100.1069489 -2.000464225 0.230386048 GAHSVGLMWWMLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GAHSVGLMWWMLAR 14 0 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;; 230.59 8.54E-13 789363000 451662 589568 284824 383954 458814 448517 513620 505136 382645 FALSE TRUE 391973.7223 585695.089 422565.8391 471136.6241 449684.4991 465771.7392 463809.2115 397116.5974 337409.144 1.161716359 1.735860155 1.252384076 1.396336265 1.332757298 1.38043603 1.374619567 1.176958611 1 18.36413955 1.454824963 1.797918175 0.947938804 1.388801286 0.423601356 0.147025453 0.495713506 2.315348468 0.340403933 0.038272999 28.49869433 -1.454824963 0.440862482 GAHVTINAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GAHVTINAR 9 0 Q9UJU6-2;Q9UJU6-3;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ;;; 131.22 0.00033917 707180000 807700 838000 448681 550150 756760 885480 742490 817160 750670 FALSE TRUE 700960.3985 832495.1228 665664.6323 675069.966 741701.9566 919544.9886 670483.4341 642416.6931 661926.6478 1.058969904 1.257684859 1.005647128 1.019856155 1.120519863 1.389194697 1.012927091 0.970525504 1 19.33631183 2.02678649 24.99991801 0.985727799 1.140060325 0.275310365 0.113437064 272.9147369 254711.0155 0.046945086 0.031649483 106.3619987 -2.02678649 0.154332527 GAILSEEELAAMS(ph)PTAAAVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GAILSEEELAAMSPTAAAVAK 21 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 1 GAILSEEELAAMS(1)PTAAAVAK;GAILSEEELAAMS(0.999)PT(0.001)AAAVAK;GAILSEEELAAMS(0.997)PT(0.003)AAAVAK;GAILSEEELAAMS(1)PTAAAVAK 342.97 7.00E-81 421892000 1266450 1051800 736380 896630 914670 878410 1150010 1390680 1367750 TRUE FALSE 1099085.424 1044890.657 1092495.831 1100223.546 896469.8565 912203.0011 1038482.207 1093293.904 1206056.153 0.911305349 0.866369824 0.905841596 0.912249022 0.743306897 0.756352015 0.861056265 0.906503318 1 20.20186565 1.369522914 2.214363199 1.018188683 0.848514896 0.396280972 0.059030786 0.554916655 3.615414158 0.170179745 0.017517598 23.41655018 -1.369522914 -0.169673786 GAKEEHGGLIRS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 GAKEEHGGLIRSPR 14 2 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 1 GAKEEHGGLIRS(1)PR;GAKEEHGGLIRS(1)PR;GAKEEHGGLIRS(1)PR;GAKEEHGGLIRS(1)PR;GAKEEHGGLIRS(1)PR;GAKEEHGGLIRS(1)PR;GAKEEHGGLIRS(1)PR;GAKEEHGGLIRS(1)PR;GAKEEHGGLIRS(1)PR 139.9 5.27E-06 31155380000 27017430 21866810 8771850 8953780 18478430 17922740 24463080 25335480 2017258 TRUE FALSE 23447008.17 21723165.49 13013946 10986872.6 18110745.4 18612239.41 22090654.27 19917684.76 1778780.057 13.1815106 12.21239545 7.31621987 6.176633561 10.18155411 10.46348554 12.41899142 11.19738479 1 20.7624567 4.355655357 5.996726896 8.926314089 12.9238674 0.223109871 3.239395822 0.333716734 15.81557895 0.82317272 2.241404651 22680.6427 -4.355655357 3.997553308 GALAEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GALAEAR 7 0 P18206;P18206-2 P18206 VCL Vinculin 0 80.377 0.094703 0 108610 99669 66591 64542 80751 93374 96744 107010 74249 FALSE TRUE 94256.91332 99014.26778 98794.63033 79197.24756 79144.21309 96966.1582 87361.78177 84126.74425 65471.3678 1.43966617 1.512329299 1.508974589 1.20964706 1.208837019 1.481046776 1.334350949 1.284939464 1 15.9985765 0.659515823 1.196763277 6.31E-09 1.390392427 0.553675011 0.109146664 4.567318708 1.996504013 11.23649986 0.035927342 4.565788844 -0.659515823 1.390392421 GALALEEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GALALEEKR 9 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 136.57 0.00030327 772930000 1443940 1633670 485790 680420 1493200 1449330 2018510 2191870 165519 FALSE TRUE 1253119.671 1622938.314 720719.6689 834919.7606 1463488.241 1505086.663 1822755.211 1723155.658 145951.5324 8.58586169 11.11970726 4.938075381 5.720527541 10.0272208 10.31223611 12.48877063 11.80635537 1 17.15512983 5.067863935 18.04859248 8.8585681 4.008083037 0 3.612234221 3949.846924 1071667.606 0.864187478 15159.11527 116913.3044 -5.067863935 -4.850485063 GALHTVS(ph)HEDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 GALHTVSHEDIR 12 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2;H0YD72 Q13136-2 PPFIA1 Liprin-alpha-1 1 GALHT(0.004)VS(0.996)HEDIR;GALHT(0.019)VS(0.981)HEDIR;GALHT(0.004)VS(0.996)HEDIR;GALHTVS(1)HEDIR;GALHT(0.003)VS(0.997)HEDIR;GALHTVS(1)HEDIR;GALHT(0.005)VS(0.995)HEDIR;GALHT(0.001)VS(0.999)HEDIR 214.65 2.79E-11 20364590000 12647710 13615960 10252110 9968770 13635640 15912800 12173710 12893590 12226680 TRUE FALSE 10976283.08 13526515.86 15210064.69 12232331.59 13364317.44 16524975.71 10993105.48 10136396.12 10781255.82 1.018089475 1.254632678 1.410787847 1.134592463 1.239588195 1.532750543 1.019649813 0.940186958 1 23.3620219 2.027987133 24.81663488 0.970050228 1.265138681 0.474651601 0.138827399 151.6804677 134496.798 0.055514566 0.03742711 106.6564521 -2.027987133 0.295088454 GALKEEVASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GALKEEVASR 10 1 Q9P2M7;Q9P2M7-2 Q9P2M7 CGN Cingulin 0 ;;; 121.83 0.00030322 444080000 1260180 1445210 551420 812930 1242620 1484440 1206930 1368350 566270 FALSE TRUE 1093644.02 1435716.32 818088.5564 997518.1814 1217894.293 1541547.367 1089882.114 1075739.001 499326.2057 2.190239582 2.875307372 1.638384982 1.997728479 2.439075457 3.087255084 2.182705618 2.154381222 1 18.9296231 4.252271188 24.99902254 2.131523609 2.532773152 0.098879239 0.55650149 649.1331208 1183568.408 0.14054937 0.367540928 17876.03465 -4.252271188 0.401249543 GALLVFAEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GALLVFAEHR 10 0 Q9UHL4;R4GNE8;R4GN05 Q9UHL4 DPP7 Dipeptidyl peptidase 2 0 ; 154.56 1.43E-05 422810000 667770 959780 727430 727310 906480 1146280 849440 975240 977160 FALSE TRUE 579522.5026 953475.142 1079217.581 892456.8517 888442.8215 1190378.133 767061.4395 766692.5153 861641.258 0.672579797 1.106580184 1.252513817 1.035763833 1.031105246 1.381524065 0.890232951 0.889804786 1 19.71672781 GALQEELAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GALQEELAR 9 0 P11309;P11309-2 P11309 PIM1 Serine/threonine-protein kinase pim-1 0 113.26 0.0042572 114550000 200330 215750 112700 130540 178060 230660 187390 195890 180960 FALSE TRUE 173855.8829 214332.724 167202.097 160181.1022 174516.9544 239533.6395 169216.9466 154000.4479 159567.115 1.089547072 1.343213632 1.047848092 1.003847831 1.093689978 1.501146646 1.060475065 0.965113946 1 17.28380383 2.008953969 24.99933354 0.989883858 1.178670863 0.243529151 0.147053781 269.5124276 752471.129 0.061211638 0.041204999 102.0831279 -2.008953969 0.188787005 GALQNIIPAS(ph)TGAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GALQNIIPASTGAAK 15 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 GALQNIIPAS(0.5)T(0.5)GAAK;GALQNIIPAS(0.936)T(0.064)GAAK;GALQNIIPAS(0.928)T(0.072)GAAK;GALQNIIPAS(0.5)T(0.5)GAAK;GALQNIIPAS(0.732)T(0.268)GAAK 258.12 8.63E-25 4433740000 6101910 8244020 5259640 4868930 6842080 5190890 7130150 7782110 8966510 TRUE FALSE 5295527.133 8189864.49 7803219.496 5974494.973 6705935.994 5390586.897 6438669.15 6117966.337 7906499.402 0.669768865 1.035839513 0.986937341 0.755643512 0.848154873 0.681791855 0.814351437 0.773789515 1 22.91460765 3.729626502 24.87754456 0.804464219 0.911347669 0.089514864 0.123911314 1140.410379 3175536.974 0.032470482 0.048941347 5365.701418 -3.729626502 0.10688345 GALQNIIPASTGAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GALQNIIPASTGAAK 15 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 246.3 8.49E-18 1696190000 1275550 1229110 868590 928030 1105010 1010350 1329320 1549770 1389650 FALSE TRUE 1106982.836 1221035.895 1288643.029 1138753.396 1083022.463 1049218.818 1200402.751 1218363.746 1225367.16 0.903388692 0.996465333 1.051638294 0.929316072 0.883835064 0.856248521 0.979626997 0.99428464 1 20.22478266 2.017865211 24.99738428 0.993800641 0.939991925 0.181574549 0.055088963 463.0348127 647885.6616 0.024958962 0.016823314 104.1993983 -2.017865211 -0.053808716 GALSALREEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GALSALREEHR 11 1 O14964-2;O14964;I3L1E3 O14964-2 HGS Hepatocyte growth factor-regulated tyrosine kinase substrate 0 54.776 0.077826 38810000 188130 45716 37591 66920 46768 51102 71210 78174 17957 FALSE TRUE 163268.1438 45415.68859 55770.13333 82115.20881 45837.4083 53067.92701 64304.06516 61457.09845 15834.14392 10.31114437 2.868212442 3.522143895 5.18595822 2.894846008 3.351486969 4.061101472 3.881302253 1 13.95075125 4.741640729 24.87686044 3.470140443 10.31114706 0.807160635 1.068434972 114.5282 924951.398 0.250249288 1.720754031 55162.09214 -4.741640729 6.841006618 GANDFMCDEMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GANDFMCDEMER 12 0 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;;; 264.17 3.72E-21 3447730000 2498660 2377980 1651140 1849110 2248600 2464430 2197470 2469710 2277480 FALSE TRUE 2168455.75 2362358.893 2449636.827 2268978.687 2203857.259 2559238.217 1984359.698 1941581.736 2008238.909 1.079779772 1.176333594 1.219793529 1.12983504 1.097407908 1.274369402 0.988109377 0.966808146 1 20.93749948 2.170373558 10.46420345 0.980801296 1.161564867 0.687560204 0.056523302 0.232628803 34.27112691 0.022173667 0.014950583 148.038119 -2.170373558 0.180763571 GANLKDYYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GANLKDYYSR 10 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 84.309 0.013688 718420000 757310 690350 241380 242210 613200 602270 705840 743650 169927 FALSE TRUE 657229.5647 685815.0454 358112.1754 297207.4824 600998.5197 625439.7166 637387.7454 584626.2346 149838.4236 4.386255199 4.577030569 2.389988941 1.983519816 4.010977325 4.174094344 4.253833763 3.901711059 1 17.1930481 GAPGS(ph)PTQERPAGGLGEAPNGAPSVCAEEGSLGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GAPGSPTQERPAGGLGEAPNGAPSVCAEEGSLGPR 35 1 A0A0J9YWL0;A0A494C1M5 A0A0J9YWL0 1 GAPGS(0.847)PT(0.153)QERPAGGLGEAPNGAPSVCAEEGSLGPR 172.03 2.91E-15 280330000 35636 34297 23386 19697 43377 32569 30953 34830 42386 TRUE FALSE 30926.61231 34071.70075 34695.54782 24169.5049 42513.88257 33821.9505 27951.18282 27381.87555 37375.17537 0.827464005 0.911613134 0.928304616 0.646672682 1.137489849 0.904930885 0.747854225 0.732621995 1 15.18979273 2.258313792 24.57907601 0.803909224 0.895159381 0.039276985 0.138721468 494.4510315 615249.0474 0.050581401 0.0391198 181.2649319 -2.258313792 0.091250157 GAPHSS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GAPHSSPAR 9 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 GAPHS(0.001)S(0.999)PAR;GAPHS(0.009)S(0.991)PAR;GAPHS(0.121)S(0.879)PAR;GAPHS(0.158)S(0.842)PAR;GAPHS(0.024)S(0.976)PAR;GAPHS(0.159)S(0.841)PAR;GAPHS(0.249)S(0.751)PAR 165.63 3.95E-05 1130717000 827054 846776 660774 652922.9 518025.2 979945 737027 857257 811807 TRUE FALSE 717756.7184 841213.4727 980326.5166 801179.0237 507717.512 1017644.118 665550.235 673939.2617 715836.1013 1.00268304 1.175148154 1.3694846 1.119221317 0.709265027 1.421616088 0.929752263 0.941471463 1 19.44926978 3.468612436 24.99338435 1.000214734 1.192150164 0.159316797 0.193873089 324.0932985 951971.4844 0.054047328 0.06988812 2941.795209 -3.468612436 0.19193543 GAPQHYPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GAPQHYPK 8 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77;H0YEC5;H0YD99;H0YEN8;H0YDC0;H0YCF8 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 ; 63.486 0.073008 186746000 805210 739950 501300 528070 667900 700590 814260 837600 815400 FALSE TRUE 698799.4584 735089.2197 743730.3567 647976.3645 654610.0967 727542.1506 735293.1905 658485.7582 719004.3409 0.971898803 1.022371045 1.034389244 0.901213425 0.9104397 1.01187449 1.022654731 0.915830018 1 19.45564096 3.767523316 24.97164389 0.959662836 1.010834832 0.20919283 0.045074755 1156.628659 997241.322 0.012293723 0.021289367 5854.951691 -3.767523316 0.051171996 GAPS(ph)PGVLGPHASEPQLAPPACTPAAPAVPGPPGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GAPSPGVLGPHASEPQLAPPACTPAAPAVPGPPGPR 36 0 O96013;O96013-4;O96013-3;M0R0L9 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 GAPS(1)PGVLGPHASEPQLAPPACTPAAPAVPGPPGPR 235.19 9.57E-50 561430000 151400 200440 76749 112010 238430 265700 183020 194960 203840 TRUE FALSE 131392.1064 199123.2964 113865.0731 137443.5825 233685.7095 275921.6509 165270.7486 153269.3212 179742.2674 0.731002831 1.107826775 0.633490802 0.76467035 1.300115509 1.535096085 0.919487391 0.85271719 1 17.45557018 3.260399486 24.98506932 1.09341848 0.818020619 0.31439885 0.22685685 370.2615294 423600.2406 0.072458446 0.093460727 1821.375483 -3.260399486 -0.275397861 GAPS(ph)SPATGVLPSPQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GAPSSPATGVLPSPQGK 17 0 Q5SRE5;Q5SRE5-2 Q5SRE5 NUP188 Nucleoporin NUP188 homolog 1 GAPS(0.5)S(0.5)PATGVLPSPQGK 138.73 2.82E-06 108770000 211570 157670 130030 144190 196850 185650 217380 260950 248520 TRUE FALSE 183610.4884 156634.2554 192912.9429 176930.5433 192933.0701 192792.0756 196298.5211 205147.8732 219140.2487 0.837867482 0.71476717 0.880317258 0.807384971 0.880409104 0.879765706 0.895766625 0.936148765 1 17.74149496 -2 0.200793541 1.942879097 0.7454788 0.688608416 0.04212972 52.83431109 0.786796892 19.27772592 0.246619256 0.01 2 -1.197400298 GAPSS(ph)PATGVLPSPQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GAPSSPATGVLPSPQGK 17 0 Q5SRE5;Q5SRE5-2 Q5SRE5 NUP188 Nucleoporin NUP188 homolog 1 GAPS(0.001)S(0.999)PATGVLPSPQGK;GAPS(0.031)S(0.969)PATGVLPSPQGK 276.14 1.01E-35 644210000 500880 447900 322030 403760 488680 440950 548090 597220 619600 TRUE FALSE 434687.4389 444957.7154 477764.7851 495439.8791 478956.2241 457913.6318 494936.3162 469509.1506 546351.5939 0.795618506 0.814416432 0.874463972 0.906815107 0.876644691 0.838129946 0.905893424 0.859353493 1 19.05947014 1.764742912 0.025106176 1.806017856 1.79E-06 0.489124555 0.040690951 1140.667575 11.14661741 430.0235238 372.8437583 58.17587339 -1.764742912 -1.806016067 GAPVGGHILSYLLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GAPVGGHILSYLLEK 15 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 167.98 1.28E-06 482960000 639360 582540 368680 495210 552880 575670 653680 658070 633190 FALSE TRUE 554866.9561 578713.2564 546974.8812 607654.9993 541878.7697 597816.3974 590286.2142 517346.8516 558334.9995 0.993788597 1.036498262 0.97965358 1.088334064 0.970526243 1.07071274 1.057225885 0.926588611 1 19.09077147 1.742139972 25 0.962276549 1.028305584 0.291198479 0.042030242 0.672410511 4730.079229 0.020626593 0.009905139 55.2255401 -1.742139972 0.066029035 GAPVNIS(ph)SSDLTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GAPVNISSSDLTGR 14 0 P48730-2;H7BYT1;P48730;J3KRM8 P48730-2 CSNK1D Casein kinase I isoform delta 1 GAPVNIS(0.922)S(0.051)S(0.028)DLTGR;GAPVNIS(0.48)S(0.48)S(0.04)DLTGR;GAPVNIS(0.759)S(0.221)S(0.019)DLTGR;GAPVNIS(0.76)S(0.224)S(0.016)DLTGR;GAPVNIS(0.897)S(0.094)S(0.009)DLTGR 320.78 3.88E-56 2786270000 2357670 1806170 1441698 1236707 1601940 1946470 1740440 1556400 1564266 TRUE FALSE 2046097.936 1794305.15 2138907.975 1517520.226 1570064.528 2021351.96 1571652.397 1223575.972 1379340.255 1.483388836 1.300843025 1.550674655 1.100178306 1.138272099 1.465448393 1.139423279 0.887073343 1 20.39554695 0.25843912 0.262435845 7.31E-13 1.50095067 0.514402601 0.152576494 20.81415059 0.990031348 11.01199228 0.573111059 1.813172483 -0.25843912 1.50095067 GAPVNISS(ph)SDLTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GAPVNISSSDLTGR 14 0 P48730-2;H7BYT1;P48730;J3KRM8 P48730-2 CSNK1D Casein kinase I isoform delta 1 GAPVNIS(0.408)S(0.546)S(0.046)DLTGR 307.06 7.62E-45 1432900000 1232000 855680 698700 602620 880750 1040600 817830 823200 875620 TRUE FALSE 1069188.079 850058.9817 1036593.657 739454.0815 863224.7982 1080632.555 738516.9725 647165.0861 772105.2011 1.384769947 1.100962642 1.342554947 0.957711566 1.118014484 1.399592379 0.95649786 0.838182524 1 19.55843791 2.085860337 7.996566502 0.904558625 1.200875546 0.469720076 0.142579659 0.196964031 15.97360432 0.056241601 0.037828458 121.8597653 -2.085860337 0.296316921 GAPVNISSS(ph)DLTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GAPVNISSSDLTGR 14 0 P48730-2;H7BYT1;P48730;J3KRM8 P48730-2 CSNK1D Casein kinase I isoform delta 1 GAPVNISS(0.004)S(0.996)DLTGR;GAPVNIS(0.001)S(0.039)S(0.96)DLTGR;GAPVNIS(0.087)S(0.24)S(0.673)DLTGR;GAPVNIS(0.296)S(0.169)S(0.535)DLTGR 234.29 3.46E-17 511350000 942890 1001070 724070 677690 979270 1091670 815740 899440 980670 TRUE FALSE 818284.6975 994493.9053 1074232.674 831569.8723 959784.4429 1133667.251 736629.6604 707101.7554 864736.3098 0.946282339 1.150054524 1.242266182 0.961645606 1.109915742 1.310997628 0.851854666 0.81770795 1 19.72190074 2.209003486 24.99097087 0.873240222 1.119425866 0.452662213 0.118930713 170.4912523 144151.5428 0.047626296 0.032114873 161.8093027 -2.209003486 0.246185644 GAQAS(ph)PPPIAPYPSPTRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GAQASPPPIAPYPSPTRK 18 1 Q14164-2;Q14164 Q14164-2 IKBKE Inhibitor of nuclear factor kappa-B kinase subunit epsilon 1 GAQAS(0.999)PPPIAPYPSPTRK 77.287 0.0027628 0 120850 124350 45290 61954 114630 110040 115360 137780 26144 TRUE FALSE 104879.3663 123533.1367 67192.39549 76021.60261 112349.0873 114273.31 104172.405 108316.8192 23053.2861 4.549432382 5.358591227 2.914655862 3.297647124 4.873452174 4.956920653 4.518765979 4.698541402 1 14.49268479 4.263671748 24.99790898 3.944016383 4.954011964 0.130480636 1.213875938 539.032032 536592.0109 0.300564065 0.794518072 18351.50761 -4.263671748 1.009995581 GAQASS(ph)GSPALPR ddPTM_MDA-MB-175_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(0.179)S(0.677)GS(0.143)PALPR 169.04 3.06E-05 101790000 170560 170320 118720 109240 161680 169670 148290 156730 155570 TRUE FALSE 148020.0639 169201.1567 176133.3891 134044.6116 158462.8843 176197.3147 133908.8586 123214.5092 137178.6918 1.079031021 1.233436144 1.283970468 0.977153302 1.155156695 1.28443647 0.976163695 0.898204433 1 17.06569688 2.116615853 6.80377268 0.940865342 1.167168199 0.522407914 0.095058123 0.159950107 8.881620963 0.039072433 0.026223214 130.8024421 -2.116615853 0.226302857 GAQASSGS(ph)PALPR ddPTM_MDA-MB-175_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 GAQASS(0.002)GS(0.998)PALPR;GAQAS(0.032)S(0.37)GS(0.598)PALPR 194 1.46E-06 849570000 501490 515740 347810 386090 491280 562650 472360 523560 505840 TRUE FALSE 435216.8259 512352.07 516012.0794 473757.6355 481504.4892 584295.5096 426550.5999 411600.7683 446040.1715 0.975734595 1.148667996 1.156873556 1.062141183 1.079509246 1.309961629 0.956305345 0.922788562 1 18.76681412 2.059597113 24.99926087 0.950977054 1.121338891 0.438805342 0.086436019 60.125688 25220.5558 0.033927528 0.022873931 114.7088993 -2.059597113 0.170361838 GAQEVGER ddPTM_MDA-MB-175_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 ; 125.98 0.0028818 365000000 808610 734780 514880 516830 538700 879970 683140 725240 652800 FALSE TRUE 701750.1397 729953.1818 763877.6902 634184.1508 527980.9239 913823.0153 616889.1879 570153.0698 575626.7277 1.219106247 1.268101613 1.327036521 1.101728117 0.917227951 1.587527075 1.071682669 0.99049096 1 19.13477406 2.015227502 24.99984912 1.005522295 1.230645268 0.276543707 0.167762566 296.780828 487239.8934 0.067438262 0.045449978 103.568456 -2.015227502 0.225122973 GAQGGDYFYSFGGCHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GAQGGDYFYSFGGCHR 16 0 Q9BYN0 Q9BYN0 SRXN1 Sulfiredoxin-1 0 ; 153.23 4.71E-07 561250000 433090 489920 293291 375400 465040 503090 415350 494710 445250 FALSE TRUE 375856.0592 486701.6833 435127.5086 460640.3076 455786.6138 522444.1978 375069.4209 388920.1163 392613.0522 0.957319317 1.239647232 1.108285897 1.173267942 1.160905404 1.330684741 0.955315721 0.990593955 1 18.58274861 2.202653913 24.99994066 0.982655806 1.16329279 0.445072708 0.094585357 150.0525693 104472.6449 0.036333809 0.024497141 159.4607904 -2.202653913 0.180636984 GAQPGRHS(ph)VTGYGDCAVGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GAQPGRHSVTGYGDCAVGAR 20 1 Q96IF1;H0YJL9 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 GAQPGRHS(0.451)VT(0.451)GY(0.098)GDCAVGAR 89.859 0.0012194 154430000 102680 83699 55089 55565 73379 82909 81057 84857 85289 TRUE FALSE 89110.57784 83149.17576 81730.22466 68181.88251 71918.90146 86098.56288 73196.10462 66710.99091 75206.23158 1.184882901 1.105615506 1.086748039 0.906598843 0.956289126 1.144832829 0.973271803 0.887040735 1 16.19856459 3.986022554 3.161415212 0.974472987 1.143723015 0.493770474 0.071646917 0.219492537 4.500647434 0.020764631 0.044677336 9683.281437 -3.986022554 0.169250028 GAS(ph)PEAASGGLPQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GASPEAASGGLPQAR 15 0 P17861-2;B1AHH2;P17861 P17861-2 XBP1 "X-box-binding protein 1;X-box-binding protein 1, cytoplasmic form;X-box-binding protein 1, luminal form" 1 GAS(1)PEAASGGLPQAR;GAS(1)PEAASGGLPQAR 211.7 1.31E-09 736190000 280190 235560 187451 208051 282890 318720 269570 297410 284230 TRUE FALSE 243162.1816 234012.5908 278102.9306 255292.1594 277261.0425 330981.3646 243427.1429 233811.1859 250628.6532 0.970209026 0.933702463 1.109621454 1.018607235 1.106262348 1.320604649 0.971266213 0.932898864 1 17.93519184 4.250078573 24.99472763 1.057585823 0.951955698 0.160480337 0.106851799 479.4324081 1040380.41 0.029344786 0.076178976 17786.01167 -4.250078573 -0.105630125 GAS(ph)PPISAIEEFSIIPEAPMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 GASPPISAIEEFSIIPEAPMR 21 0 A0A2R8YF49;C9J591;A0A2R8YFR7;Q12774;A0A5F9ZH52 A0A2R8YF49;A0A2R8YFR7;A0A5F9ZH52 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 GAS(1)PPISAIEEFSIIPEAPMR;GAS(0.999)PPIS(0.001)AIEEFSIIPEAPMR;GAS(0.999)PPIS(0.001)AIEEFSIIPEAPMR;GAS(0.926)PPIS(0.074)AIEEFSIIPEAPMR;GAS(1)PPISAIEEFSIIPEAPMR;GAS(0.882)PPIS(0.117)AIEEFSIIPEAPMR;GAS(1)PPISAIEEFSIIPEAPMR;GAS(0.97)PPIS(0.03)AIEEFSIIPEAPMR;GAS(0.945)PPIS(0.055)AIEEFSIIPEAPMR;GAS(0.899)PPIS(0.1)AIEEFS(0.001)IIPEAPMR 342.97 7.00E-81 1186206000 292462 254461 177065.3 198911.7 250015.6 265580.5 247163.1 290627 254685.7 TRUE FALSE 253812.4057 252789.4289 262694.6713 244077.6417 245040.7787 275797.5537 223193.2606 228478.6777 224577.0467 1.13017964 1.125624514 1.169730724 1.086832538 1.091121209 1.228075432 0.993838257 1.01737324 1 17.77685096 2.212921652 24.99993975 1.006165479 1.134909156 0.713779703 0.04020147 118.2446499 115296.5909 0.015832564 0.010678655 163.2757367 -2.212921652 0.128743677 YPDVAS(ph)PTLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YPDVASPTLRR 11 1 Q8IVL1-9;Q8IVL1-13;A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-5;Q8IVL1-4;Q8IVL1-10;Q8IVL1-8;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1;E9PNV5 Q8IVL1-9 NAV2 Neuron navigator 2 1 YPDVAS(1)PTLRR;YPDVAS(0.997)PT(0.003)LRR;YPDVAS(0.999)PT(0.001)LRR 143.94 2.26E-05 1326840000 1775280 1737520 950350 1093090 1753980 1856830 1749710 1952000 705660 TRUE FALSE 1540672.25 1726106.117 1409942.439 1341292.791 1719079.23 1928263.452 1580023.394 1534579.99 622237.6787 2.476018896 2.774030207 2.265922632 2.155595582 2.762737276 3.098917854 2.539260234 2.466228007 1 19.24710623 1.228598922 4.084479769 0.814184042 2.581633621 0.776050472 0.265217679 0.124339797 3.693249432 0.665226019 0.071384192 16.92773775 -1.228598922 1.767449578 GASDEEIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GASDEEIKR 9 1 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ;; 150.27 0.00013733 1378770000 2338140 2023830 1279550 1590970 1541840 1676280 1918440 2458630 3137650 FALSE TRUE 2029148.875 2010535.327 1898344.66 1952224.055 1511160.401 1740767.576 1732389.984 1932871.108 2766720.591 0.733413009 0.726685352 0.686135299 0.705609399 0.546191909 0.629180837 0.62615285 0.698614495 1 21.39974552 1.238275518 4.080415423 1.035804221 0.663611509 0.781376921 0.055297361 0.115215219 3.446371705 0.127810575 0.015046709 17.30914108 -1.238275518 -0.372192713 GASFLFPPAES(ph)LSPEEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GASFLFPPAESLSPEEPR 18 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 GASFLFPPAES(0.536)LS(0.464)PEEPR 66.965 0.03245 27239000 34387 34656 24111 28342 51400 39704 34307 48842 47353 TRUE FALSE 29842.67082 34428.34245 35771.16025 34777.48428 50377.24056 41231.43857 30979.91242 38397.51839 41754.98228 0.71470922 0.82453256 0.856692023 0.832894241 1.206496514 0.987461527 0.74194529 0.919591299 1 15.34966073 4.220570977 1.377702241 0.943831699 0.723560104 0.300700654 0.119352647 0.846290665 2.629146513 0.038285146 0.202250203 16617.70239 -4.220570977 -0.220271595 GASFLFPPAESLS(ph)PEEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GASFLFPPAESLSPEEPR 18 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 GASFLFPPAES(0.032)LS(0.968)PEEPR;GASFLFPPAES(0.005)LS(0.995)PEEPR 151.44 5.00E-08 187671000 542180 501690 359660 378210 499660 535330 521010 594420 612210 TRUE FALSE 470529.5393 498394.3654 533592.779 464088.3611 489717.7436 555924.4915 470482.5304 467307.9088 539835.2312 0.871616953 0.923234232 0.988436375 0.859685204 0.90716151 1.02980402 0.871529873 0.865649149 1 19.04215961 3.725202419 24.86336236 0.91707803 0.927309704 0 0.061958591 7705.909658 14342858.36 0.017304672 0.025821554 5311.319406 -3.725202419 0.010231674 GASIVEDKLVEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GASIVEDKLVEDLR 14 1 P00367 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ;;;; 150.22 6.63E-06 764368000 3060830 3044610 1382264 1974028 3279790 3040430 3180430 4173070 289046 FALSE TRUE 2656333.56 3024609.756 2050731.494 2422261.229 3214528.596 3157397.31 2871992.388 3280691.455 254875.3112 10.4220905 11.86701742 8.046018598 9.503710726 12.61216154 12.38800767 11.26822514 12.87175066 1 17.95943211 1.232707589 24.99999848 0.999992539 11.17386979 0.819519948 1.492687852 84.35178509 360253.9931 3.416625249 0.390245905 17.08864346 -1.232707589 10.17387725 GATKES(ph)SEKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GATKESSEKDR 11 2 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BUL0;H3BTY0;H3BUG0;H3BNU7;H3BNI3;H3BTR6;H3BP82 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 1 GAT(0.007)KES(0.852)S(0.141)EKDR;GAT(0.016)KES(0.657)S(0.328)EKDR;GAT(0.018)KES(0.491)S(0.491)EKDR;GAT(0.003)KES(0.877)S(0.12)EKDR 155.98 1.63E-05 677981000 1811190 1125900 1101160 1047570 804470 825570 1628270 1876280 1722360 TRUE FALSE 1571836.653 1118503.889 1633684.659 1285436.78 788462.6209 857330.2121 1470360.626 1475052.123 1518744.563 1.03495788 0.736466102 1.075680993 0.846381157 0.519154202 0.56449928 0.96814215 0.971231212 1 20.53444781 2.047625956 24.99888275 0.979399926 0.793405765 0.198713955 0.173902411 194.7935228 102246.3282 0.075400914 0.05083527 111.5901742 -2.047625956 -0.185994161 GATQQILDEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GATQQILDEAER 12 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;; 201.6 3.41E-07 658780000 929640 863960 649381 731060 865660 947280 868530 1004260 943610 FALSE TRUE 806785.7186 858284.5899 963423.8236 897058.3466 848435.0596 983722.4746 784300.0943 789506.8142 832057.5008 0.969627361 1.031520765 1.157881304 1.078120618 1.019683206 1.182277035 0.942603238 0.948860882 1 19.66632371 2.198951796 24.99991517 0.959820379 1.07293364 0.395728297 0.063642052 150.9280484 95260.29281 0.025669788 0.017306823 158.1072542 -2.198951796 0.113113261 GATYGKPVHHGVNQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GATYGKPVHHGVNQLK 16 1 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 149.3 5.48E-07 2958000000 5351800 4125700 3018800 3729900 3930600 3606900 5014600 5628700 5220800 FALSE TRUE 4644546.07 4098598.005 4478701.777 4576830.803 3852388.75 3745659.777 4528284.864 4425046.308 4603602.972 1.008893708 0.890302233 0.972868817 0.994184518 0.836820372 0.81363658 0.983639313 0.961213713 1 22.13433199 GAVAAEGAS(ph)DTEREEPTESQGLAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GAVAAEGASDTEREEPTESQGLAAR 25 1 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 GAVAAEGAS(1)DTEREEPTESQGLAAR;GAVAAEGAS(0.994)DT(0.006)EREEPTESQGLAAR;GAVAAEGAS(0.997)DT(0.003)EREEPTESQGLAAR;GAVAAEGAS(0.999)DT(0.001)EREEPTESQGLAAR;GAVAAEGAS(0.999)DT(0.001)EREEPTESQGLAAR;GAVAAEGAS(0.997)DT(0.003)EREEPTESQGLAAR 339.82 1.69E-88 11706000000 4027210 4511600 3166260 3282250 4156770 4571240 3949520 4596700 3777600 TRUE FALSE 3495003.995 4481963.003 4697473.927 4027535.029 4074058.41 4747098.561 3566496.158 3613731.477 3331016.431 1.049230488 1.345524135 1.410222382 1.209100919 1.223067641 1.425120127 1.070693055 1.084873507 1 21.66753104 2.150081111 9.11961399 1.057932508 1.280489444 0.484011252 0.109551932 0.245836016 22.97987971 0.04358866 0.029374067 141.2801382 -2.150081111 0.222556936 GAVAAEGASDT(ph)ER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GAVAAEGASDTER 13 0 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 GAVAAEGAS(0.386)DT(0.614)ER 129.29 0.00011636 0 143080 141590 110240 123070 145180 149350 129100 147380 305260 TRUE FALSE 124171.6155 140659.886 163552.4327 151014.9245 142291.202 155095.5911 116579.9019 115863.9339 269172.5106 0.46130868 0.522564082 0.607611945 0.561033979 0.528624568 0.576194021 0.433104783 0.430444898 1 18.03817156 1.232511127 24.99996619 1.000000793 0.514187927 0.869270019 0.059094632 76.99840154 318169.5904 0.14515417 0.016275863 17.08091484 -1.232511127 -0.485812866 GAVDGGLSIPHSTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GAVDGGLSIPHSTK 14 0 P46777;A0A2R8Y6J3;Q5T7N0 P46777 RPL5 60S ribosomal protein L5 0 ;;;;; 186.51 1.06E-06 3674020000 5132280 4888360 2194140 3694520 4847470 4509860 5186760 5921120 5784720 FALSE TRUE 4454036.194 4856248.041 3255233.443 4533417.233 4751014.831 4683357.232 4683748.814 4654934.566 5100856.992 0.873193701 0.952045519 0.63817383 0.888755995 0.931415023 0.918151056 0.918227824 0.91257892 1 22.28230822 3.485975271 24.48892483 0.929010456 0.82243455 0.294107811 0.080881939 421.5155407 1165851.386 0.022417116 0.030559354 3061.789092 -3.485975271 -0.106575906 GAVEALAAALAHISGATSVDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GAVEALAAALAHISGATSVDQR 22 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 187.06 2.97E-17 204819000 158529 183303 70643.5 109708.6 208698 184895 180940 175663 73060.3 FALSE TRUE 137578.991 182098.8705 104806.9329 134619.6144 204545.3181 192008.0303 163392.4666 138098.8345 64423.19456 2.135550587 2.826604172 1.626850913 2.08961408 3.175026006 2.980417714 2.536236642 2.143619785 1 15.97529258 GAVEKGEELSCEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GAVEKGEELSCEER 14 1 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ;; 157.8 4.74E-06 951190000 881350 786920 373892 365444 717570 681420 935660 944790 156085 FALSE TRUE 764877.3644 781750.6707 554707.4218 448423.6457 703291.7609 707634.6683 844919.8372 742754.0109 137632.8091 5.557376685 5.679973225 4.030342949 3.258115914 5.109913584 5.141467888 6.138942035 5.396634826 1 17.0704649 4.253131087 24.14834131 4.515562487 5.618676237 0.115011622 1.427506225 409.2453276 678243.0588 0.359901617 0.942097715 17911.46412 -4.253131087 1.10311375 GAVIVVSHDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GAVIVVSHDAR 11 0 Q8NE71;Q8NE71-2;H0YGW7;A0A0G2JIC2 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 ;;; 171.85 1.40E-05 890730000 1426060 1334580 877690 978760 1192880 1255980 1195340 1379100 1187380 FALSE TRUE 1237602.558 1325813.056 1302143.82 1201002.417 1169144.022 1304298.363 1079416.111 1084190.197 1047009.289 1.182035891 1.266285858 1.243679338 1.147079047 1.11665105 1.245737146 1.0309518 1.035511536 1 19.99784281 1.837009856 0.565858908 0.909549771 1.230004746 0.680352665 0.054177142 1.276736116 0.540273729 0.259695871 0.04135932 68.70840326 -1.837009856 0.320454975 GAWSNVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GAWSNVLR 8 0 P05141;P12236;P12235 P05141;P12236;P12235 SLC25A5;SLC25A6;SLC25A4 "ADP/ATP translocase 2;ADP/ATP translocase 2, N-terminally processed;ADP/ATP translocase 3;ADP/ATP translocase 3, N-terminally processed;ADP/ATP translocase 1" 0 ; 108.09 0.0090221 1139510000 1021950 1357300 1067380 1294840 1617910 1756500 1020870 1522130 1465360 FALSE TRUE 886896.7182 1348383.807 1583568.538 1588853.212 1585716.756 1824073.692 921866.1845 1196634.345 1292126.81 0.686385199 1.043538294 1.225551955 1.229641859 1.227214499 1.411683186 0.713448693 0.926096677 1 20.30131623 2.225069127 24.99977396 0.88255023 1.145363294 0.270513765 0.199018306 316.4504327 586378.9324 0.083314764 0.05652148 167.9071254 -2.225069127 0.262813065 GCCFDDTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GCCFDDTVR 9 0 P04155 P04155 TFF1 Trefoil factor 1 0 ; 174.16 0.00012768 433980000 958730 966650 727960 742680 983250 1090040 813630 886310 854160 FALSE TRUE 832031.4014 960300.0125 1080003.891 911316.8452 963685.2487 1131974.544 734724.2878 696779.5038 753182.1779 1.104688116 1.274990355 1.433921198 1.209955402 1.279484933 1.502922636 0.975493459 0.925114168 1 19.52263934 2.16407659 9.323399088 0.956779972 1.300510881 0.670699255 0.110315691 0.179261943 20.76545017 0.044297483 0.029861149 145.9071554 -2.16407659 0.343730909 GCCFDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GCCFDSR 7 0 X6R3S7;Q07654 X6R3S7 TFF3 Trefoil factor 3 0 ;;;;; 129.67 0.0084638 13047300000 20965000 24460800 16447700 15697700 21156100 22664500 19138200 21052600 18421600 FALSE TRUE 18194422.13 24300115.39 24401862.73 19262102.71 20735135 23536417.98 17282180.31 16550665.32 16243819.43 1.120082762 1.495960694 1.502224451 1.185811181 1.276493813 1.448946048 1.063923444 1.018890009 1 23.95338756 2.154749724 6.211720361 1.021401564 1.342615694 0.580494484 0.124740268 0.143878943 8.499030646 0.051263634 0.034416231 142.807075 -2.154749724 0.321214129 GCGDLCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GCGDLCR 7 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 ; 122.98 0.0099764 553850000 1254250 1277050 1046790 918700 1095580 1445900 1227650 1218970 1363410 FALSE TRUE 1088497.685 1268660.974 1553021.145 1127304.876 1073780.101 1501524.709 1108592.692 958302.7515 1202229.223 0.905399456 1.055257142 1.291784558 0.937678818 0.893157545 1.248950433 0.922114245 0.797104856 1 20.19728056 2.018804576 24.99344756 0.876724748 1.056067804 0.197851549 0.140459375 314.2320184 417649.0096 0.056641 0.038180821 104.425022 -2.018804576 0.179343056 GCHLLVATPGR ddPTM_MDA-MB-175_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 ;; 123.79 0.00036257 1225540000 1863230 1693564 1084951 1182557 1665001 1652731 1740128 1949682 1120309 FALSE TRUE 1616999.435 1682438.867 1609636.933 1451074.641 1631870.738 1716312.631 1571370.654 1532757.677 987867.3463 1.636858877 1.703102014 1.629405951 1.468896251 1.651912824 1.737391804 1.590669699 1.55158249 1 19.9139578 1.179376127 2.685516603 0.788929165 1.631361992 0.883538414 0.071356389 0.198292949 1.431245562 0.406652787 0.019408896 15.11388547 -1.179376127 0.842432826 GCLDEETSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GCLDEETSR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 160.11 0.00015249 513570000 1116510 995160 691170 876530 936710 1071610 993210 1210950 1111950 FALSE TRUE 968960.3746 988622.7284 1025422.124 1075559.533 918071.3036 1112835.53 896888.6471 951997.7661 980496.5377 0.988234366 1.008287832 1.04581922 1.096953933 0.93633304 1.134971402 0.91472903 0.970934348 1 19.90315301 2.202359412 24.99993787 0.961807586 1.032690899 0.260209142 0.058098126 231.0708657 159572.173 0.022136602 0.014924998 159.3526949 -2.202359412 0.070883313 GCLDFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GCLDFLR 7 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 78.616 0.081085 35073000 165350 177860 141300 186950 194840 244690 149700 178040 323400 FALSE TRUE 143498.5786 176691.6259 209633.1526 229399.8549 190963.0652 254103.3826 135182.117 139967.5315 285168.0204 0.503207121 0.619605332 0.735121534 0.804437519 0.669651053 0.891065493 0.474043747 0.490824782 1 18.12145268 4.580678984 3.069291002 0.696002209 0.500184768 0.15055344 0.162033639 0.659624253 10.36228543 0.042419625 0.252125876 38078.42567 -4.580678984 -0.195817441 GCPHVLGYEGPGDPAS(ph)DEGDGLPGDRPWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GCPHVLGYEGPGDPASDEGDGLPGDRPWLR 30 1 Q96C34;Q96C34-2;K7EQS2 Q96C34 RUNDC1 RUN domain-containing protein 1 1 GCPHVLGYEGPGDPAS(1)DEGDGLPGDRPWLR 152.95 9.61E-09 106670000 35660 36023 22002 27746 34239 45000 28873 45240 30794 TRUE FALSE 30947.44065 35786.36254 32642.24079 34046.15337 33557.71089 46731.17912 26072.9009 35565.77806 27153.5684 1.139719104 1.317924849 1.202134479 1.25383717 1.23584902 1.720995872 0.96020164 1.309801258 1 14.72885418 0.550668315 1.305995878 4.13E-17 1.279565677 0.151077758 0.191760292 13.94431546 5.315932305 37.53911185 0.053537181 3.553598147 -0.550668315 1.279565677 GCPNPPS(ph)SPAHLPTQAAICPASAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GCPNPPSSPAHLPTQAAICPASAK 24 0 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 GCPNPPS(0.5)S(0.5)PAHLPTQAAICPASAK 181.21 2.16E-17 181350000 68846 93202 52312 78928 105170 89649 109450 132140 125150 TRUE FALSE 59747.82667 92589.74993 77610.25817 96849.80874 103077.3228 93097.85504 98835.55585 103882.8893 110354.9096 0.541415211 0.839017949 0.703278708 0.877621205 0.934052895 0.843622231 0.895615394 0.941352675 1 16.75179129 5.560279596 0.461405831 0.945791312 2.71E-15 0.747960245 0.066319825 5.71532086 0.558176573 0.051799774 3.432377338 363311.8772 -5.560279596 -0.945791312 GCQLLVYPGAFNLTTGPAHWELLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GCQLLVYPGAFNLTTGPAHWELLQR 25 0 Q9NQR4 Q9NQR4 NIT2 Omega-amidase NIT2 0 ; 264.97 2.61E-45 788310000 1534360 1323230 930020 1110170 1307050 1366030 1170690 1419700 1305720 FALSE TRUE 1331590.438 1314537.615 1379780.783 1362251.066 1281042.262 1418582.058 1057156.664 1116108.203 1151359.269 1.156537733 1.141726697 1.198392908 1.183167672 1.112634689 1.232093315 0.918181399 0.969383088 1 20.13490665 2.235261022 24.99999076 0.962103464 1.168617325 0.87355801 0.037340643 25.64031571 194264.8842 0.014098312 0.009947351 171.8941204 -2.235261022 0.206513861 GCRLS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GCRLSPR 7 1 P17812;B4E1E0;P17812-2;A0A3B3IRI2 P17812 CTPS1 CTP synthase 1;CTP synthase 1 GCRLS(1)PR;GCRLS(1)PR;GCRLS(1)PR;GCRLS(1)PR;GCRLS(1)PR;GCRLS(1)PR 88.392 0.011289 12341500000 2342360 2821530 1918470 1948200 2513660 2883500 2680870 2796760 1888410 TRUE FALSE 2032811.191 2802995.184 2846248.509 2390568.586 2463643.084 2994430.111 2420879.64 2198694.638 1665164.321 1.220787141 1.683314462 1.709289872 1.435635244 1.4795195 1.798279048 1.453838285 1.320407008 1 20.66723312 1.384241616 1.781968969 0.903679379 1.559345518 0.536722651 0.162913112 0.497540136 1.985104662 0.518857787 0.044587065 24.22376339 -1.384241616 0.655666139 GCVNYEGADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GCVNYEGADR 10 0 Q7Z5L9;Q7Z5L9-2;Q9H1B7 Q7Z5L9;Q9H1B7 IRF2BP2;IRF2BPL Interferon regulatory factor 2-binding protein 2;Interferon regulatory factor 2-binding protein-like 0 ; 116.12 0.002636 197560000 199776 198086 181291 165006 183966 206338 183454 189726 323320 FALSE TRUE 173375.0954 196784.76 268963.934 202473.1343 180305.4365 214275.9564 165662.6593 149154.5713 285097.4779 0.608125672 0.690236762 0.943410429 0.710189146 0.632434344 0.751588397 0.581073745 0.523170434 1 18.12109575 3.479298131 24.73306846 0.669934049 0.755762894 0.00281972 0.151933803 228.8015767 2599600.313 0.043537851 0.057146453 3015.075076 -3.479298131 0.085828845 GCWDSIHVVEVQEK ddPTM_MDA-MB-175_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 2252180000 2858440 2440660 1158250 2233530 2523630 2258910 2829490 3311860 3623600 FALSE TRUE 2480689.912 2424627.144 1718383.574 2740687.124 2473414.7 2345811.729 2555086.495 2603644.512 3195222.136 0.776374789 0.758828977 0.537797843 0.857745411 0.774097886 0.73416233 0.799658486 0.814855557 1 21.6074848 -1.013640871 0.766685617 10 0.733318265 0.49810671 0.080837196 65.94736584 1.439551099 992.501451 0.031008282 0.096907888 1.013640871 -9.266681735 GCWVLYEEPEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GCWVLYEEPEFR 12 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 0 ;; 159.4 0.0001532 62552000 124671 120815 89730 97003 122339 136451 119439 140954 137020 FALSE TRUE 108195.4115 120021.3583 133123.7281 119029.0137 119904.6933 141700.3583 107855.8242 110812.084 120821.6517 0.895496875 0.993376242 1.101820131 0.985162941 0.992410645 1.172806002 0.892686225 0.917154189 1 16.88251949 GDAASS(ph)PAPAASVGSSQGGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GDAASSPAPAASVGSSQGGAR 21 0 E7EXA6;A0A0D9SF58;Q8WVB6;Q8WVB6-2;F8WCC1 E7EXA6 CHTF18 Chromosome transmission fidelity protein 18 homolog 1 GDAASS(1)PAPAASVGSSQGGAR 175.33 9.24E-18 0 56867 50365 29474 33476 43095 46974 37829 43314 43056 TRUE FALSE 49351.88187 50034.149 43727.72498 41077.23745 42237.49381 48781.12018 34160.3494 34051.63817 37965.96873 1.29989787 1.317868361 1.151761076 1.081948883 1.112509314 1.284864362 0.899762354 0.896898968 1 15.2124192 3.386988735 0.075493832 5.07E-10 2.298057472 0.58817917 0.09889873 33.78345036 2.447799428 34.47094834 39.36921289 2437.747584 -3.386988735 2.298057471 LS(ph)PTSLVHPVMSTLPELSCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSPTSLVHPVMSTLPELSCK 20 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 LS(0.707)PT(0.146)S(0.146)LVHPVMSTLPELSCK;LS(0.833)PT(0.136)S(0.031)LVHPVMSTLPELSCK 196.1 1.15E-21 1570810000 2135880 1996590 1455000 2244540 2096880 1605660 2332510 2972490 5650200 TRUE FALSE 1853618.046 1983474.269 2158642.867 2754197.113 2055156.19 1667430.779 2106303.539 2336846.145 4982239.793 0.372045129 0.398108953 0.433267558 0.552803002 0.412496443 0.334674935 0.422762377 0.469035262 1 22.24836303 1.22896955 3.969218839 1.071931092 0.421337352 0.913260325 0.055939853 0.074310832 2.000010689 0.143340235 0.015037093 16.94219006 -1.22896955 -0.65059374 GDDALEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDDALEKR 8 1 Q9Y617 Q9Y617 PSAT1 Phosphoserine aminotransferase 0 ; 85.676 0.026575 866240000 909910 770470 465210 512920 586380 580020 695380 799460 471250 FALSE TRUE 789663.0881 765408.7318 690187.112 629386.3255 574712.1852 602333.7447 627942.1546 628501.7004 415539.3618 1.900332822 1.841964449 1.660942802 1.514625047 1.383051133 1.449522717 1.511149634 1.512496187 1 18.66462562 8 0.236162546 1.235099789 5.468795958 0.701559347 0.136450549 55.32637769 0.868425126 0.556158344 88.60461124 100000000 -8 4.233696169 GDDDEES(ph)DEEAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDDDEESDEEAVK 13 0 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 GDDDEES(1)DEEAVK;GDDDEES(1)DEEAVK 299.64 7.85E-41 313910000 584410 419190 448950 511340 425370 386570 514520 579430 1257410 TRUE FALSE 507178.7378 416436.3133 666063.7216 627447.5623 416905.9692 401441.598 464621.9296 455523.4036 1108760.422 0.457428609 0.375587282 0.600728262 0.565900036 0.376010868 0.362063427 0.419046279 0.410840245 1 20.08051624 1.236444317 24.99710619 1.000000712 0.444622932 0.826376584 0.079809547 23.9302681 282586.2945 0.132943324 0.02075675 17.23631083 -1.236444317 -0.55537778 GDDDEES(ph)DEEAVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GDDDEESDEEAVKK 14 1 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 GDDDEES(1)DEEAVKK;GDDDEES(1)DEEAVKK;GDDDEES(1)DEEAVKK;GDDDEES(1)DEEAVKK;GDDDEES(1)DEEAVKK;GDDDEES(1)DEEAVKK 212.55 1.40E-09 2710590000 2934920 1984670 2308490 2455640 2020140 1551743 2831880 3137350 4984690 TRUE FALSE 2547062.886 1971632.572 3424883.485 3013230.594 1979943.166 1611439.557 2557244.713 2466452.117 4395405.627 0.579483011 0.448566694 0.779196228 0.68554096 0.45045744 0.366619078 0.581799481 0.561143232 1 22.06756488 1.237963918 7.448875465 1.007511561 0.555838681 0.580381411 0.118492835 0.080179132 30.84081386 0.181813797 0.030588764 17.29672648 -1.237963918 -0.45167288 GDDGIFDDNFIEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 GDDGIFDDNFIEER 14 0 O60493-4;O60493;O60493-2 O60493-4 SNX3 Sorting nexin-3 0 ;;;;;;; 298.51 2.30E-43 4304640000 3362810 3245700 2204563 2462492 2853410 3313640 2941600 3345320 3503450 FALSE TRUE 2918406.138 3224378.783 3270697.041 3021638.445 2796632.724 3441117.875 2656324.085 2629949.351 3089276.132 0.94468931 1.043732786 1.058726025 0.978105652 0.905271204 1.113891322 0.859853238 0.851315725 1 21.5588374 2.210014372 24.99939558 0.890976858 1.005413005 0.31821257 0.070685095 222.4674837 194824.4864 0.028104071 0.018951678 162.1863768 -2.210014372 0.114436147 GDDLLPAGTEDYIHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GDDLLPAGTEDYIHIR 16 0 K7EM18;P41567;O60739 K7EM18 EIF1;EIF1B Eukaryotic translation initiation factor 1;Eukaryotic translation initiation factor 1b 0 ;;;;; 208.51 1.47E-11 4185469000 4051911 4100665 3551923 4166580 4177783 4447926 3764963 4614472 7775870 FALSE TRUE 3516440.695 4073727.462 5269644.843 5112665.671 4094653.292 4619040.591 3399837.468 3627703.073 6856615.507 0.512853709 0.594130947 0.768548978 0.745654422 0.597182865 0.673661894 0.495847764 0.529080721 1 22.70906519 GDDQLELIKDDEKEAEEGEDDRDS(ph)ANGEDDS ddPTM_MDA-MB-175_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 157.45 4.65E-09 1262100000 910260 501720 707860 681180 602610 561260 644520 917560 1298100 TRUE FALSE 789966.8347 498424.1683 1050183.464 835852.3302 590619.24 582852.0354 582014.5496 721346.9345 1144640.097 0.690144297 0.435441821 0.917479185 0.730231566 0.515986852 0.509201134 0.508469475 0.630195409 1 20.12646262 1.241034668 6.39570122 1.011056064 0.612479049 0.42684501 0.139480901 0.120181622 22.10013631 0.209043201 0.035107362 17.4194592 -1.241034668 -0.398577014 GDDSFGDKYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDDSFGDKYR 10 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 161.67 6.39E-06 927470000 1098050 1005870 710390 903550 924210 877990 1016850 1230340 1332130 FALSE TRUE 952939.9104 999262.3737 1053936.98 1108714.837 905820.0292 911766.8434 918236.0435 967241.3655 1174647.109 0.811256337 0.850691553 0.897237112 0.943870571 0.771142262 0.776204901 0.781712258 0.823431444 1 20.16379597 3.227378221 24.99992624 0.823241239 0.875506825 0.082376285 0.072865796 520.8569132 1164451.312 0.022563718 0.025811477 1688.02246 -3.227378221 0.052265586 GDDTPLHLAASHGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GDDTPLHLAASHGHR 15 0 A0A0A0MTH3;Q13418;Q13418-2;A0A087WWY6 A0A0A0MTH3 ILK Integrin-linked protein kinase 0 37.77 0.091076 44378000 44211 43815 21887 30996 39170 45101 37445 47457 39072 FALSE TRUE 38368.40433 43527.17638 32471.62641 38034.11554 38390.59363 46836.06465 33813.58966 37308.68986 34452.95267 1.113646331 1.263380146 0.94249183 1.103943569 1.114290377 1.359420921 0.981442432 1.082888025 1 15.07234001 GDEASEEGQNGSS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GDEASEEGQNGSSPK 15 0 P35611;P35611-3;E7EV99;E7ENY0;P35611-2;P35611-6;P35611-4;H0Y9H2;P35611-5 P35611 ADD1 Alpha-adducin 1 GDEASEEGQNGSS(1)PK 285.9 3.99E-34 198000000 506150 359400 264320 292610 335800 304610 411570 470260 478350 TRUE FALSE 439260.9951 357039.0777 392146.0361 359051.5728 329118.237 316328.5438 371656.0047 369698.5586 421800.0079 1.041396365 0.846465318 0.929696607 0.851236524 0.780270817 0.749949118 0.881119008 0.876478311 1 18.6861996 GDEELDSLIK ddPTM_MDA-MB-175_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 ;;;;; 214.13 2.25E-08 826039000 3404250 2847540 2144370 2582750 2689230 2194960 2820330 3423990 3320480 FALSE TRUE 2954369.737 2828834.322 3181394.504 3169202.862 2635719.584 2279401.532 2546814.831 2691796.384 2927936.637 1.009027893 0.966152849 1.086565353 1.08240145 0.900196934 0.778500977 0.869832632 0.919349261 1 21.4814529 3.194713393 8.980313483 0.888966093 1.034574919 0.553748516 0.063474256 0.243485895 46.53498604 0.020515315 0.023383293 1565.717456 -3.194713393 0.145608827 GDEGIFEESFIEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GDEGIFEESFIEER 14 0 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 0 ;;;;; 265.26 2.19E-24 1005421000 795704 783936 591352 619750 732517 818965 746562 887670 924811 FALSE TRUE 690549.7003 778786.2728 877331.8052 760473.7098 717941.3448 850471.1135 674160.5321 697848.6784 815480.8971 0.846800585 0.955002472 1.075845931 0.93254632 0.880390144 1.042907463 0.826703034 0.855751104 1 19.63729156 2.223601101 24.99998215 0.883340999 0.956557456 0.110833277 0.080063487 453.3921642 757691.8631 0.032428588 0.021962275 167.3405149 -2.223601101 0.073216456 GDFCIQVGR ddPTM_MDA-MB-175_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 ;;;;;;; 170.24 0.0001346 15768370000 8996340 9323100 6339830 5947440 8129450 9411320 9502360 9629090 9053320 FALSE TRUE 7807450.875 9261855.942 9405792.993 7297897.153 7967689.85 9773379.57 8580822.59 7569984.037 7983046.823 0.978003894 1.160190607 1.178220948 0.914174414 0.998076302 1.224266848 1.074880654 0.948257502 1 22.92850804 1.766356468 9.521171125 0.974740886 1.07921942 0.160594787 0.095932868 0.3444301 104.3171074 0.052864424 0.025158735 58.39241913 -1.766356468 0.104478534 GDFDENLNYPEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GDFDENLNYPEQK 13 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 147.71 9.98E-05 119080000 150640 118630 89158 107860 115760 111450 138720 173340 153600 FALSE TRUE 130732.5423 117850.7117 132275.107 132351.2615 113456.6025 115737.5536 125266.9558 136272.5899 135441.583 0.965231943 0.870122079 0.976621095 0.977183363 0.837679241 0.85452009 0.924878113 1.006135538 1 17.04731121 1.770161256 4.647874852 1.003347459 0.91223633 0.354570905 0.049357349 0.207048484 9.424684754 0.030904045 0.013674765 58.90623364 -1.770161256 -0.091111128 GDFHSPIVLGRPPNTEDRES(ph)PSVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GDFHSPIVLGRPPNTEDRESPSVKR 25 3 Q02078-8;Q02078-7;Q02078-4;Q02078-6;Q02078-3;Q02078-5;Q02078-2;Q02078 Q02078-8 MEF2A Myocyte-specific enhancer factor 2A 1 GDFHSPIVLGRPPNT(0.096)EDRES(0.816)PS(0.088)VKR 111.03 0.0019173 278610000 148140 137070 101570 103740 139000 118090 143370 147910 90603 TRUE FALSE 128562.9237 136169.5781 150689.5917 127295.7526 136234.1719 122632.9987 129465.9995 116280.5975 79892.01656 1.609208644 1.704420342 1.88616583 1.593347597 1.705228855 1.534984395 1.62051235 1.455472055 1 16.28576372 0.830341341 1.081132636 2.22E-16 1.687659292 0.845849535 0.09068547 1.44355605 0.743069848 3.483731486 0.029190653 6.766145627 -0.830341341 1.687659292 GDFIALDLGGSSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GDFIALDLGGSSFR 14 0 P19367-4;P19367-2;P19367;P19367-3;B1AR62 P19367-4 HK1 Hexokinase-1 0 ;; 241.39 4.53E-17 270432000 636500 612110 445570 481020 599260 678230 485010 619220 577670 FALSE TRUE 552384.9123 608089.0091 661049.1423 590242.9429 587335.8984 704321.947 437973.8049 486804.6218 509378.5107 1.084429164 1.193786146 1.297756243 1.158751165 1.153044124 1.382708403 0.859819949 0.955683468 1 18.95837857 2.225991163 24.99999991 0.938802373 1.209761986 0.681723079 0.088005369 125.1179725 248851.214 0.034713202 0.023580932 168.2639824 -2.225991163 0.270959613 GDFIHVMDNSDPNWWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GDFIHVMDNSDPNWWK 16 0 P62993;P62993-2 P62993 GRB2 Growth factor receptor-bound protein 2 0 183.6 1.96E-09 359590000 607570 515650 423830 533080 496580 496430 530340 650150 935850 FALSE TRUE 527278.0851 512262.6612 628795.6056 654123.9616 486699.0295 515527.9833 478907.7084 511120.482 825214.8791 0.638958529 0.620762754 0.761978027 0.79267107 0.589784603 0.62471969 0.580343036 0.619378655 1 19.65441031 1.235252085 24.97628421 1.000000488 0.652352729 0.70873426 0.069789633 56.47382235 426251.8445 0.129926959 0.018530159 17.18905831 -1.235252085 -0.347647759 GDFILVGDLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GDFILVGDLMR 11 0 Q16531;F5GY55;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 93.111 0.022087 10632000 22803 25579 20156 20461 23749 25998 18838 21229 36742 FALSE TRUE 19789.52577 25410.96986 29903.50902 25106.98278 23276.44136 26998.15988 17011.09366 16689.34355 32398.40262 0.610817947 0.784327862 0.922993315 0.774945082 0.718444105 0.833317624 0.525059641 0.515128593 1 14.98363506 2.25444713 24.99973497 0.639242966 0.778874921 0.055407716 0.154294894 444.5335258 699537.2415 0.057391251 0.044307371 179.6582355 -2.25444713 0.139631954 GDFVTSFYWPWQTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GDFVTSFYWPWQTK 14 0 G3V3Y1;Q8N8N7;Q8N8N7-2 G3V3Y1 PTGR2 Prostaglandin reductase 2 0 204.49 3.16E-08 47239000 153920 118610 82350 92068 118370 113700 145730 168440 147970 FALSE TRUE 133579.082 117830.8431 122174.7354 112973.4466 116014.6686 118074.1126 131597.127 132420.4168 130477.1552 1.023773716 0.903076427 0.936368786 0.865848481 0.889156944 0.904940887 1.008583662 1.014893501 1 16.99343771 2.233837907 24.62200965 1.009329785 0.916543012 0.491781335 0.04169457 76.17706726 397144.7204 0.016522323 0.01155706 171.3317723 -2.233837907 -0.092786773 GDHRYPSSNPESPVVIFYSEIGSEEFSNFHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GDHRYPSSNPESPVVIFYSEIGSEEFSNFHR 31 1 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ;; 157.16 8.14E-10 223449000 237603 219134 123829.9 153072 219181 276186 194502 209776 89373.9 FALSE TRUE 206203.1615 217694.4943 183714.4538 187829.3372 214819.7269 286811.0541 175639.226 164917.0349 78808.21936 2.61651847 2.762332357 2.331158543 2.383372429 2.725854342 3.639354581 2.22869172 2.092637497 1 16.26605848 1.299724355 1.661129779 0.518563318 2.698669367 0.666295745 0.380541956 0.56172731 1.602872254 1.941175466 0.111745889 19.9399633 -1.299724355 2.180106049 GDHSPVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDHSPVTR 8 0 Q9H3U1;A0A1W2PNX8;Q9H3U1-3;Q9H3U1-2 Q9H3U1;Q9H3U1-2 UNC45A Protein unc-45 homolog A 0 ; 97.431 0.0082369 253820000 164437 144569 123534 119387 141365 176221 140368 154595 160279 FALSE TRUE 142706.2338 143619.3167 183275.4556 146495.6431 138552.1131 183000.3359 126755.133 121536.0623 141330.9992 1.009730594 1.016191193 1.296781715 1.036542895 0.980337745 1.294835082 0.896867168 0.859939171 1 17.10871841 2.177531469 24.99994681 0.905723964 1.101506024 0.363353506 0.116033913 70.36108495 28821.84753 0.046123535 0.03109649 150.4982565 -2.177531469 0.19578206 GDHWTTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GDHWTTR 7 0 O75821;K7ENA8;K7ER90;K7EL20 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 ;; 111.01 0.0066756 453430000 880100 790050 671260 1036260 769040 1047350 763900 960670 2248010 FALSE TRUE 763792.5551 784860.1095 995883.5812 1271558.671 753737.6086 1087642.232 689817.0956 755238.1964 1982252.819 0.385315409 0.395943495 0.502399881 0.641471491 0.380242924 0.548689966 0.347996527 0.380999936 1 20.91870955 1.234377528 24.99999096 1.000000809 0.447231899 0.78038697 0.092046084 59.57524082 355999.4132 0.174125484 0.023069087 17.1544788 -1.234377528 -0.55276891 GDIFLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDIFLVR 7 0 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 131.3 0.0080945 231880000 444710 396120 245590 259210 348570 427790 328940 379540 408470 FALSE TRUE 385940.4467 393517.8616 364358.1454 318067.5923 341634.139 444247.3581 297039.4494 298378.3246 360181.1419 1.071517639 1.092555428 1.011596952 0.88307675 0.948506457 1.233399827 0.824694618 0.828411846 1 18.45836312 7.999998576 0.106008596 0.736982074 1.78626454 0.133818398 0.117533312 481.5312787 4.665353131 6.827600077 74.6917964 99999672.1 -7.999998576 1.049282466 GDIYFCTGYDPPMKPYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDIYFCTGYDPPMKPYGR 18 1 Q9NRV9;A0A3B3IRV5 Q9NRV9 HEBP1 Heme-binding protein 1 0 ; 124.78 2.84E-05 1319510000 1423670 1294520 759030 885610 1124410 1149840 1191260 1357200 1231260 FALSE TRUE 1235528.402 1286016.213 1126099.447 1086701.286 1102036.441 1194075.089 1075731.789 1066973.342 1085701.845 1.137999726 1.184502189 1.037208743 1.000920548 1.015045194 1.099818605 0.990816948 0.982749865 1 20.05019654 4.168573256 5.205148416 1.01424036 1.16112206 0.752822217 0.034219364 0.091204253 4.520804784 0.009329828 0.02064895 14742.57196 -4.168573256 0.1468817 GDKEEVAYEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GDKEEVAYEER 11 1 Q9NRV9;F5GWX2 Q9NRV9 HEBP1 Heme-binding protein 1 0 ;;; 126.95 0.00027072 4120220000 8057300 6986900 4749750 5382330 6199000 5697700 7174600 8486900 7744500 FALSE TRUE 6992507.39 6941002.594 7046744.987 6604470.29 6075652.028 5916894.206 6478808.396 6672042.48 6828954.033 1.023949987 1.016407866 1.031892286 0.967127654 0.889689988 0.866442237 0.948726315 0.977022608 1 22.70323319 3.590047441 4.204978541 0.938135104 1.022763978 0.520142425 0.03827086 0.216710252 6.432510314 0.01231421 0.018581389 3890.876452 -3.590047441 0.084628874 GDKSELNEIKENQRS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GDKSELNEIKENQRSPVR 18 3 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 GDKSELNEIKENQRS(1)PVR;GDKSELNEIKENQRS(1)PVR;GDKSELNEIKENQRS(1)PVR 186.55 3.38E-14 1758140000 2032430 1468280 795147 745003 1221120 936789 1813810 2074810 352576 TRUE FALSE 1763839.226 1458634.772 1179682.749 914167.3178 1196822.101 972827.879 1637906.985 1631128.028 310894.8669 5.673426658 4.691729993 3.794474835 2.940438763 3.849603928 3.129121714 5.268362908 5.246558246 1 18.24606727 4.514601296 2.576427063 3.808620876 5.701322425 0.232667404 1.216912745 0.572218372 6.501794247 0.321862657 1.876251308 32704.03177 -4.514601296 1.892701549 GDLAGR ddPTM_MDA-MB-175_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" 0 110.23 0.067187 279120000 277250 290900 225710 230750 167340 350140 233690 282360 297500 FALSE TRUE 240610.71 288989.0587 334864.111 283145.3143 164010.2614 363610.1124 211026.7798 221979.5113 262329.8889 0.917206617 1.101624599 1.27650003 1.07934828 0.625206156 1.386079619 0.804432848 0.846184597 1 18.00102267 3.450364991 24.99972869 0.927202468 1.111955849 0.127214246 0.209182152 401.0983638 374765.1437 0.058149511 0.075072579 2820.752559 -3.450364991 0.184753381 GDLEEYGQDLLHTVFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GDLEEYGQDLLHTVFK 16 0 P43490 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 121.79 9.68E-05 29853000 27218 20735 21026 27728 20406 19922 22262 24686 72416 FALSE TRUE 23621.07234 20598.79042 31194.24393 34024.0662 19999.96052 20688.41223 20103.03467 19407.09101 63855.06298 0.369916984 0.322586643 0.488516376 0.532832709 0.313208688 0.323990163 0.314822877 0.303924076 1 15.96251339 1.234943528 24.99553043 1.000000893 0.369332807 0.863437475 0.078583336 39.73769332 274560.7895 0.151413961 0.021031193 17.17685021 -1.234943528 -0.630668086 GDLGIEIPAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GDLGIEIPAEK 11 0 P14618;P14618-3;B4DNK4;P30613;P30613-2;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM;PKLR Pyruvate kinase PKM;Pyruvate kinase;Pyruvate kinase PKLR 0 ;;;; 192.1 3.59E-06 1259972000 4104580 3016310 2371840 2659470 2839320 2706040 3697220 3832900 3991130 FALSE TRUE 3562149.353 2996495.661 3518869.757 3263343.311 2782823.087 2810143.11 3338664.173 3013264.163 3519303.158 1.012174625 0.851445734 0.99987685 0.927269736 0.790731279 0.798494186 0.948671945 0.856210456 1 21.74685836 4.751869783 24.33541173 0.893687709 1.012174737 0.192357739 0.074222054 2655.340712 4855085.847 0.018044552 0.326928997 56476.76121 -4.751869783 0.118487028 GDLPFVVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDLPFVVPR 9 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 105.14 0.0073212 139785000 150425 227220 110873 198878 160789 190417 160613 165048 156597 FALSE TRUE 130545.9551 225727.3769 164491.5536 244036.2896 157589.6135 197742.4652 145036.776 129753.7696 138084.2811 0.945407791 1.634707261 1.191240251 1.767299563 1.141256719 1.43204182 1.050349648 0.93967082 1 17.07518957 2.148810129 4.694254229 0.974323216 1.366725055 0.337062176 0.235515186 0.207797268 8.010660952 0.091066354 0.060223605 140.86728 -2.148810129 0.392401839 GDLS(ph)DVEEEEEEEMDVDEATGAVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDLSDVEEEEEEEMDVDEATGAVKK 25 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 GDLS(1)DVEEEEEEEMDVDEATGAVKK;GDLS(1)DVEEEEEEEMDVDEATGAVKK 285.22 8.23E-54 269970000 313690 205010 158991 173065 186383 161865 246820 288470 137160 TRUE FALSE 272235.0717 203663.2758 235879.5794 212362.0534 182674.343 168092.0513 222883.4344 226782.9354 120945.1011 2.250897881 1.683931586 1.950302884 1.755854942 1.510390593 1.389821083 1.842847974 1.875089883 1 16.88399281 8 0.500226182 1.578304445 20.79227719 0.382558658 0.267440104 145.9083972 1.596463106 0.16827269 2939.333919 99999999.98 -8 19.21397274 GDLSSIR ddPTM_MDA-MB-175_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 6340410000 6823490 7390950 6117990 5356460 7542590 9333360 7671120 7393570 8368700 FALSE TRUE 5921748.508 7342398.363 9076670.427 6572726.111 7392507.216 9692420.399 6927175.963 5812512.592 7379361.82 0.80247434 0.994990968 1.230007506 0.890690316 1.001781373 1.313449677 0.938722905 0.787671446 1 22.81506462 2.00855492 24.99435458 0.874027678 1.044576047 0.136430708 0.155130196 298.335089 871622.7543 0.062725133 0.042214865 101.9893726 -2.00855492 0.170548369 GDLSYLDQGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDLSYLDQGHR 11 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 0 ; 153.95 3.22E-05 689970000 608870 627840 435090 468580 622920 656490 576050 635200 666770 FALSE TRUE 528406.2868 623715.6777 645500.9793 574978.2508 610525.1107 681745.5951 520184.7597 499367.4231 587945.2102 0.898733892 1.060839797 1.097893083 0.977945293 1.03840477 1.15953933 0.8847504 0.849343467 1 19.16532219 2.204565115 24.99916654 0.897334474 1.03977966 0.367808519 0.078091189 172.1184407 126569.0022 0.031109957 0.020975545 160.164077 -2.204565115 0.142445186 GDMEQNDSDNRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 GDMEQNDSDNRR 12 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ;;;;;;;;;; 198.14 3.00E-07 4904659800 3551078.8 2719473.6 1909262.3 1959239.4 2340453.4 3000173.5 2446981.8 2722955.5 2443429.8 FALSE TRUE 3081794.739 2701609.199 2832587.934 2404114.651 2293882.956 3115592.116 2209673.882 2140672.656 2154570.313 1.430352364 1.253896976 1.314688092 1.11582093 1.064659131 1.446038729 1.025575201 0.993549685 1 21.03896875 0.184179761 0.096876649 2.79E-12 1.815060978 0.470541941 0.124957366 150.0410657 2.550677509 43.46806327 12.66164013 1.528198473 -0.184179761 1.815060978 GDMS(ph)DEDDENEFFDAPEIITMPENLGHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 32 GDMSDEDDENEFFDAPEIITMPENLGHK 28 0 P22059 P22059 OSBP Oxysterol-binding protein 1 1 GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK 263.66 4.58E-54 7156875700 4861546 3973763.3 3260688.5 3705724 4076066.3 3728412.5 4591526 5455343 5631460 TRUE FALSE 4219080.379 3947659.387 4837568.365 4547165.273 3994960.555 3871846.941 4146240.515 4288760.353 4965715.214 0.849642035 0.794983042 0.974193677 0.915712053 0.804508592 0.779715867 0.83497348 0.863674248 1 22.24357009 1.238713807 4.493841594 1.012574857 0.851095558 0.394754894 0.057741316 0.230340644 9.749589105 0.119057198 0.015432871 17.32661825 -1.238713807 -0.161479299 GDMS(ph)DEDDENEFFDAPEIITMPENLGHKR ddPTM_MDA-MB-175_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 210.06 4.83E-26 494182000 537025 472486 152797 131334 384567 349606 483263 550857 53845.1 TRUE FALSE 466055.7856 469382.2084 226690.1403 161155.392 376914.8691 363055.569 436396.2286 433060.5173 47479.59362 9.815917747 9.885977798 4.774475159 3.394203272 7.938460302 7.646560161 9.191237654 9.12098197 1 15.53501997 4.260457491 24.54008121 6.598796258 9.850952934 0.246078893 2.601735007 316.9893133 355245.9076 0.671101467 1.772003012 18216.18763 -4.260457491 3.252156675 GDNIYEWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 83.647 0.041905 172420000 714720 541460 397560 449650 508750 599610 528060 559920 610600 FALSE TRUE 620267.9411 537903.1136 589821.3458 551749.905 498626.8704 622677.3847 476848.8225 440185.4653 538415.5636 1.152024538 0.999048226 1.095476033 1.024765891 0.926100403 1.156499601 0.885652003 0.817557097 1 19.03836059 2.210850087 24.32034326 0.883028621 1.050324276 0.445326569 0.081883773 129.5549223 113703.5061 0.031791171 0.02143989 162.4987734 -2.210850087 0.167295655 GDNRLDLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDNRLDLLK 9 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 140.07 0.00010029 912060000 2382000 2050400 1275060 1515700 2045600 1872630 2317600 2532500 1394420 FALSE TRUE 2067212.665 2036930.787 1891683.281 1859862.851 2004896.562 1944671.288 2092839.509 1990944.583 1229573.256 1.681244004 1.656616047 1.538487659 1.512608413 1.630562923 1.581582291 1.702086068 1.619215913 1 20.22972626 1.238302883 24.99979158 0.999999318 1.614656923 0.914602774 0.059087168 1.72880795 167366.0429 0.085483119 0.015122038 17.31023177 -1.238302883 0.614657606 GDPIVQHRPMLEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 88.311 0.0039633 216900000 91439 96819 69999 69355 90234 96056 91939 113040 60845 FALSE TRUE 79355.10447 96182.98961 103850.7505 85103.11277 88438.51994 99751.33648 83022.76993 88867.27568 53651.97341 1.479071494 1.792720444 1.935637106 1.586206571 1.648374036 1.859229589 1.547431803 1.656365461 1 15.71134362 0.921298527 1.860568835 3.02E-12 1.709307358 0.694986287 0.142462915 1.33908316 2.039533408 5.464533227 0.037595281 8.342544397 -0.921298527 1.709307358 GDQCCYSHS(ph)PPTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDQCCYSHSPPTPR 14 0 Q9NXH9-2;Q9NXH9 Q9NXH9-2 TRMT1 tRNA (guanine(26)-N(2))-dimethyltransferase 1 GDQCCYS(0.003)HS(0.994)PPT(0.004)PR;GDQCCYS(0.001)HS(0.964)PPT(0.036)PR 152.01 4.37E-06 546310000 272820 223150 166346 176197 207680 233510 243030 248090 242840 TRUE FALSE 236766.1458 221684.113 246791.482 216205.2219 203547.5743 242493.2808 219460.988 195037.8841 214131.7318 1.105703222 1.03526979 1.152521767 1.009683245 0.950571746 1.132449071 1.024887746 0.910831302 1 17.70813908 0.138739673 0.20535861 0.688627489 1.129996181 0.264740975 0.065687079 52.74731392 1.852582664 6.472893529 0.524760621 1.376384182 -0.138739673 0.441368692 GDQENVHPDVMLVQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GDQENVHPDVMLVQPR 16 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;;;;; 190.81 7.97E-10 3984270000 3136090 2889710 2642840 2749700 2993950 3460230 2848090 3102680 4704130 FALSE TRUE 2721647.761 2870727.305 3920926.264 3374061.412 2934376.253 3593347.287 2571882.67 2439196.027 4148013.11 0.656132873 0.692072862 0.945254067 0.813416284 0.707417304 0.866281565 0.620027614 0.588039614 1 21.98398902 2.236794627 24.99904203 0.700359563 0.781812965 0.000298585 0.138677727 139.0126185 1967772.672 0.054671139 0.03901536 172.5021957 -2.236794627 0.081453402 GDQFVFYEDWGENMVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GDQFVFYEDWGENMVSK 17 0 C9JIF9;P13798;H7C1U0;C9JLK2 C9JIF9 APEH Acylamino-acid-releasing enzyme 0 142.1 2.23E-05 0 50256 49741 28288 38768 36348 35380 41605 46727 53221 FALSE TRUE 43614.54227 49414.2481 41968.17142 47570.86693 35624.74591 36741.09149 37570.1535 36734.79468 46929.27401 0.929367504 1.052951471 0.894285546 1.013671486 0.759115641 0.782903471 0.800569672 0.782769294 1 15.51820052 3.242064853 24.99999603 0.815837768 0.972718945 0.462498858 0.078662416 74.85196575 534006.9462 0.022108361 0.027400564 1746.082875 -3.242064853 0.156881177 GDQPAASGDS(ph)DDDEPPPLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GDQPAASGDSDDDEPPPLPR 20 0 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 1 GDQPAASGDS(1)DDDEPPPLPR;GDQPAASGDS(1)DDDEPPPLPR;GDQPAASGDS(1)DDDEPPPLPR;GDQPAASGDS(1)DDDEPPPLPR 351.8 4.05E-95 1066310000 690023 593020 595642 758149 772471 654697 481931 751297 1318348 TRUE FALSE 598834.7123 589124.4126 883696.4635 930298.318 757100.3384 679883.6172 435193.4058 590637.9831 1162494.401 0.515129115 0.506776129 0.760172662 0.800260472 0.651272245 0.584848939 0.374361722 0.508078131 1 20.14879234 -0.646455011 0.010368756 1.290200043 4.04E-07 0.013693231 0.179440688 298737.848 422.3911167 28664.11764 24082.58407 0.22570698 0.646455011 -1.290199639 GDQVLNFS(ph)DAEDLIDDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GDQVLNFSDAEDLIDDSK 18 0 F8W126;Q96EZ8-4;Q96EZ8-3;Q96EZ8;Q96EZ8-2 F8W126 MCRS1 Microspherule protein 1 1 GDQVLNFS(1)DAEDLIDDSK;GDQVLNFS(1)DAEDLIDDSK;GDQVLNFS(1)DAEDLIDDSK;GDQVLNFS(1)DAEDLIDDSK;GDQVLNFS(1)DAEDLIDDSK;GDQVLNFS(1)DAEDLIDDSK 200.23 1.61E-15 324040000 502112 398431 314574 371141 395646 346591 434851 528739 536826 TRUE FALSE 435756.627 395813.6805 466703.0386 455414.2366 387773.4187 359924.58 392679.217 415672.2795 473363.0418 0.920554814 0.836173604 0.985930454 0.962082369 0.819188201 0.760356319 0.829551913 0.878125757 1 18.85258755 3.236518993 24.99999338 0.853083258 0.924023413 0.185778479 0.071120506 97.58136075 1194899.521 0.022326648 0.026581145 1723.92748 -3.236518993 0.070940155 GDRDESDDGGVAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDRDESDDGGVAQR 14 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 0 ; 184 1.23E-06 120690000 130760 114791 70570 78949 111121 120039 104846 119219 112091 FALSE TRUE 113479.7347 114036.9304 104697.888 96875.57711 108909.9095 124656.978 94678.05106 93724.94461 98839.72967 1.148118627 1.153755992 1.059269267 0.980127904 1.101883927 1.261203146 0.957894678 0.94825173 1 16.59280344 2.139987816 24.475266 0.963993007 1.109513466 0.480287115 0.072543459 10.31812107 2550.45641 0.03103828 0.020926007 138.0345538 -2.139987816 0.145520459 FSHEEIAMATVTALRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FSHEEIAMATVTALRR 16 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BU78;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;; 235.93 6.65E-20 6163090000 3384320 3206890 1710680 1832130 3136220 3227620 3117640 3466970 932284 FALSE TRUE 2937073.537 3185823.728 2537970.57 2248143.119 3073815.358 3351788.63 2815291.753 2725585.445 822070.4476 3.572775966 3.875365837 3.087290849 2.734732924 3.73911429 4.077252308 3.424635639 3.315513231 1 19.64890251 1.228995343 4.13180631 0.715449889 3.49258826 0.808128732 0.380417948 0.111123912 3.438919138 0.941355618 0.102477834 16.94319633 -1.228995343 2.777138371 GDRYDALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GDRYDALR 8 1 A0AVT1 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ;;; 132.76 0.00086507 1318940000 1410300 1232250 869800 903380 1155840 1413660 1232620 1340190 993610 FALSE TRUE 1223925.282 1224155.269 1290438.189 1108506.236 1132841.045 1468044.415 1113080.702 1053600.798 876146.5577 1.396941266 1.397203764 1.472856542 1.265206405 1.29298122 1.67556946 1.270427524 1.202539448 1 19.74081269 1.55684048 1.936115754 0.9960148 1.405759589 0.56594281 0.116845316 0.299176753 1.999716929 0.1932037 0.032738549 36.04462237 -1.55684048 0.409744789 GDS(ph)ES(ph)EEDEDLEVPVPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 332.56 8.72E-75 1891050000 990590 870900 732037 872820 945670 894570 766430 950290 2166780 TRUE FALSE 859681.0217 865179.0006 1086052.542 1071007.121 926853.0172 928984.6868 692101.7366 747077.8787 1910625.737 0.449947368 0.452824948 0.568427673 0.560553069 0.485104434 0.486220126 0.362238257 0.391012151 1 20.86561377 1.233554261 24.99969877 1.000000819 0.467249672 0.871212193 0.064090429 60.93537459 304250.8081 0.146805488 0.018128531 17.12199087 -1.233554261 -0.532751147 GDS(ph)LILEHQWELEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GDSLILEHQWELEK 14 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4;A0A0U1RQL3 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 GDS(1)LILEHQWELEK;GDS(1)LILEHQWELEK;GDS(1)LILEHQWELEK 284.38 1.00E-33 776680000 1103060 951380 882350 1118180 1032370 931760 1168840 1451230 1817560 TRUE FALSE 957287.8262 945130.3221 1309057.411 1372079.859 1011827.857 967605.4101 1055486.077 1140895.758 1602690.127 0.597300632 0.589714946 0.816787593 0.856110508 0.631330935 0.603738298 0.658571522 0.711862972 1 20.61206408 1.236388106 4.215975053 1.031959425 0.683256341 0.550561045 0.090364373 0.192657673 6.460046071 0.205703614 0.024568422 17.23408005 -1.236388106 -0.348703085 GDS(ph)PENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 GDSPENR 7 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 GDS(1)PENR;GDS(1)PENR;GDS(1)PENR;GDS(1)PENR;GDS(1)PENR;GDS(1)PENR;GDS(1)PENR;GDS(1)PENR;GDS(1)PENR 162.49 0.0013321 1139474000 2241943 2402555 1544919 1765404 1779884 2520955 2305093 2669348 2802706 TRUE FALSE 1945664.552 2386772.458 2292046.996 2166265.961 1744467.791 2617937.77 2081545.436 2098528.703 2471373.29 0.787280724 0.965767684 0.927438605 0.876543406 0.705869809 1.059304874 0.842262658 0.849134654 1 21.23688151 2.728616517 24.9943212 0.914896054 0.864358349 0.13806981 0.096129425 2252.991066 5662842.015 0.032947772 0.0293794 535.3237569 -2.728616517 -0.050537704 GDS(ph)RS(ph)PSHKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDSRSPSHKR 10 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GDS(0.989)RS(0.899)PS(0.112)HKR;GDS(0.999)RS(0.891)PS(0.11)HKR 103.83 0.0014812 3605380000 1323960 872590 561030 685090 545370 679680 911380 990460 964740 TRUE FALSE 1148995.332 866857.8988 832345.9845 840650.1554 534518.204 705827.7294 822994.5079 778657.8368 850689.5362 1.350663529 1.019006185 0.978436843 0.988198537 0.628335228 0.829712485 0.967444024 0.915325514 1 19.69827318 5.187919251 1.102444221 0.88680609 2.093998252 0.64272209 0.106870723 2.715783076 1.390759171 0.033869021 4.8304364 154141.3829 -5.187919251 1.207192161 GDS(ph)VSDSGSDALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GDSVSDSGSDALR 13 0 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 1 GDS(0.991)VS(0.009)DS(0.001)GSDALR;GDS(0.998)VS(0.002)DSGSDALR;GDS(0.992)VS(0.008)DSGSDALR;GDS(0.999)VS(0.001)DSGSDALR 336.67 1.25E-62 1499320000 372722 588150 616770 721700 866170 1091360 819550 1038500 2107680 TRUE FALSE 323465.8433 584286.4039 915042.035 885573.0155 848934.9116 1133345.325 740070.1671 816424.8566 1858512.471 0.17404556 0.314383903 0.49235184 0.4764956 0.456781929 0.60981314 0.39820565 0.439289415 1 20.82571694 1.238606974 7.015615136 1.012137433 0.426952291 0.715882468 0.114755561 0.062732325 17.92960026 0.174852425 0.029276572 17.32235657 -1.238606974 -0.585185141 GDSFFIR ddPTM_MDA-MB-175_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 ; 100.67 0.022387 208186000 445380 481290 316450 360500 426170 483460 500280 479090 455350 FALSE TRUE 386521.9046 478128.3743 469486.2785 442357.0349 417690.0508 502059.019 451762.9226 376640.3318 401519.0417 0.962649001 1.190798753 1.169275251 1.101708733 1.040274576 1.250399027 1.125134491 0.93803853 1 18.61510888 1.760109394 8.452452118 0.970749035 1.125993936 0.376995604 0.080371425 0.136323334 34.84312898 0.042555615 0.01991549 57.55849019 -1.760109394 0.155244901 GDSGAAPDVDDKLCLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GDSGAAPDVDDKLCLR 16 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 0 116.35 0.00039654 321840000 152640 167430 101290 103860 139960 137430 153670 183080 120280 FALSE TRUE 132468.2373 166330.1413 150274.1828 127443.0004 137175.0698 142717.021 138767.1071 143929.7667 106060.6354 1.248985891 1.568255184 1.416870474 1.2016051 1.293364586 1.345617254 1.308375219 1.357051711 1 16.69452977 1.237360076 24.99756939 0.999999586 1.345132184 0.539547953 0.099413651 24.49216728 509754.0986 0.147473725 0.024565803 17.27269385 -1.237360076 0.345132597 GDT(ph)PGHATPGHGGATSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GDTPGHATPGHGGATSSAR 19 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 GDT(1)PGHATPGHGGATSSAR;GDT(0.907)PGHAT(0.093)PGHGGATSSAR;GDT(0.983)PGHAT(0.017)PGHGGATSSAR 125.04 0.00010339 226468000 93016.9 78293.4 43443 78396.6 83959 80179.3 70605.5 84964.5 140345 TRUE FALSE 80724.48099 77779.0855 64452.18011 96197.74625 82288.38016 83263.84955 63758.18948 66795.50287 123753.574 0.652300199 0.628499711 0.520810656 0.777333075 0.664937404 0.672819757 0.515202813 0.539746051 1 16.91711067 1.231391619 24.99923151 1.000000665 0.617555398 0.686745917 0.080308449 157.6631564 549743.3776 0.205874169 0.020756971 17.03694097 -1.231391619 -0.382445267 GDTHPLTLDEILDETQHLDIGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDTHPLTLDEILDETQHLDIGLK 23 0 P29084;E5RH41;E5RIW4 P29084 GTF2E2 Transcription initiation factor IIE subunit beta 0 ; 234.74 2.59E-37 52041000 87416 80324 54490 67891 70192 63089 85288 94391 81564 FALSE TRUE 75863.75412 79796.34636 80841.54626 83306.6892 68795.31653 65516.07465 77016.78289 74206.2192 71921.59684 1.054811871 1.109490749 1.124023239 1.158298659 0.956532107 0.910937431 1.070843617 1.031765457 1 16.13413743 3.237908327 24.99999921 1.000342614 1.112384828 0.587658405 0.048804743 14.06938057 539236.5047 0.015633423 0.018817383 1729.45126 -3.237908327 0.112042214 GDTNIKPILQVINIRPITTGNS(ph)PPR ddPTM_MDA-MB-175_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(0.313)T(0.313)GNS(0.373)PPR 60.728 0.037499 111080000 121640 92384 67466 71402 83923 81096 92247 117020 77155 TRUE FALSE 105564.9658 91777.12342 100092.7833 87614.91541 82253.09649 84215.8156 83300.90014 91996.18365 68033.8238 1.551654161 1.348992579 1.471220897 1.287814068 1.209002992 1.237852158 1.224404208 1.352212451 1 16.05396456 8 0.268962124 1.162176298 3.810777296 0.595560427 0.096155175 64.1422314 1.027275495 0.256670663 76.83371298 100000000 -8 2.648600998 GDTPGHAT(ph)PGHGGATSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GDTPGHATPGHGGATSSAR 19 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 GDT(0.019)PGHAT(0.981)PGHGGATSSAR 189.45 2.61E-14 341070000 263310 231280 129890 238530 259820 274920 226950 272250 358610 TRUE FALSE 228512.9164 229760.7065 192705.2385 292691.8822 254650.0903 285496.3503 204940.4239 214031.4562 316215.5343 0.722649243 0.726595254 0.609411043 0.925608803 0.805305441 0.902853653 0.648103593 0.676853073 1 18.27054872 3.752558973 24.99555616 0.802025874 0.690256197 0.240240498 0.112006736 1496.337276 2671862.857 0.03095523 0.053273574 5656.645637 -3.752558973 -0.111769677 GDTPGHATPGHGGATSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GDTPGHATPGHGGATSSAR 19 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;;; 232.01 1.18E-20 764340000 600738 562969 201626 388569 644570 658898 515321 601483 679422 FALSE TRUE 521348.9512 559270.8196 299133.008 476799.5304 631744.3181 684246.2324 465345.2487 472860.5412 599101.5052 0.870218063 0.933515965 0.499302715 0.795857674 1.054486281 1.142120703 0.776738574 0.789282846 1 19.19244093 3.446113736 18.86513145 0.928123011 0.761482867 0.236052168 0.156091138 23.66734319 14397.92142 0.048274783 0.062328577 2793.275268 -3.446113736 -0.166640144 GDTSGDYKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDTSGDYKK 9 1 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ; 125.75 0.00079034 1743090000 6023600 4975700 2561710 2752500 1711640 2168010 3392800 4950000 7044500 FALSE TRUE 5227565.998 4943014.299 3800561.524 3377497.194 1677581.713 2251414.748 3063766.778 3891481.021 6211707.235 0.841566706 0.79575777 0.611838482 0.543730905 0.270067736 0.362447015 0.493224594 0.626475279 1 22.5665584 4.188031217 2.593057821 0.535752988 0.837539909 0.249713064 0.190437525 0.404057136 5.386170357 0.054296562 0.160979038 15418.11273 -4.188031217 0.301786921 GDTVEGLSWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GDTVEGLSWLR 11 0 H0YB70;J9JIE9;F6UJY1;Q5T013-4;Q5T013 H0YB70 HYI Putative hydroxypyruvate isomerase 0 91.867 0.012169 0 97041 87570 107870 56759 51187 92166 56056 54292 47101 FALSE TRUE 84216.78598 86994.7469 160036.2928 69646.99846 50168.47885 95711.68566 50619.69775 42682.0783 41532.77344 2.027718811 2.094604807 3.853253216 1.67691663 1.207925084 2.304485777 1.218789249 1.02767224 1 15.34196259 2.672942389 0.699750743 0.892937843 2.551790922 0.408049849 0.656060942 0.812429676 0.97066555 0.847143134 0.52543363 470.914853 -2.672942389 1.65885308 GDVAEGDLIEHFSQFGTVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GDVAEGDLIEHFSQFGTVEK 20 0 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ;;;;; 318.1 1.54E-66 1936879000 3234790 2859704 1049486 1983055 2875419 2637085 2988613 3514439 3348974 FALSE TRUE 2807304.306 2840918.416 1557020.94 2433337.947 2818203.788 2738535.366 2698777.771 2762903.569 2953062.109 0.950641809 0.962024607 0.527256415 0.824005001 0.954332718 0.927354477 0.913891301 0.935606319 1 21.49378027 3.277898314 6.324342159 0.941607467 0.804559208 0.225568974 0.119177834 0.292158704 30.66106962 0.035667525 0.045430125 1896.261878 -3.277898314 -0.137048259 GDVDMSEVEHFMPILMEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GDVDMSEVEHFMPILMEK 18 0 E7ENJ6;Q9BXS5;Q9BXS5-2;K7ENA7 E7ENJ6 AP1M1 AP-1 complex subunit mu-1 0 71.085 0.024106 24960000 37541 30217 26440 37369 34341 30264 37114 47893 64979 FALSE TRUE 32579.86173 30018.50254 39226.47244 45854.2026 33657.68129 31428.27566 33514.68999 37651.45465 57297.25664 0.568611198 0.523908199 0.684613448 0.800286179 0.587422213 0.548512747 0.584926608 0.657124911 1 15.80617844 1.235948245 3.958754407 1.044590771 0.617235192 0.700054777 0.078748503 0.15332487 4.123673198 0.191866037 0.021442683 17.21663391 -1.235948245 -0.427355579 GDVEEDEAVPDSEQDIKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GDVEEDEAVPDSEQDIKPR 19 1 O14787-2;O14787;A0A075B780 O14787-2 TNPO2 Transportin-2 0 168.09 1.53E-11 190070000 288430 217870 165550 178640 203600 180000 242080 267490 287980 FALSE TRUE 250313.2447 216438.7976 245610.5337 219202.9423 199548.7583 186924.7165 218603.1189 210289.3451 253935.3325 0.98573618 0.852338253 0.967216855 0.863223484 0.785825101 0.736111492 0.860861373 0.828121644 1 17.95410162 3.541395483 6.224241216 0.835448256 0.925861975 0.237771014 0.075148977 0.338263531 25.6005069 0.020685582 0.030565572 3478.527837 -3.541395483 0.090413719 GDVEEDETIPDSEQDIRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GDVEEDETIPDSEQDIRPR 19 1 Q92973-2;Q92973;Q92973-3 Q92973-2 TNPO1 Transportin-1 0 ;;;;; 280.65 1.09E-39 4027860000 1837850 1772660 1285690 1226322 1648520 1891080 1613450 1755070 1817060 FALSE TRUE 1594973.466 1761015.28 1907453.984 1504777.153 1615717.677 1963831.071 1456977.867 1379761.938 1602249.237 0.995459027 1.09908948 1.190485188 0.939165467 1.008405958 1.225671404 0.909332852 0.861140643 1 20.61166715 2.180783322 24.8603262 0.909910677 1.073271651 0.376604803 0.092118905 73.5010295 31625.11758 0.037116002 0.025023616 151.6293669 -2.180783322 0.163360974 GDVEGSQS(ph)QDEGEGSGESER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDVEGSQSQDEGEGSGESER 20 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 1 GDVEGSQS(1)QDEGEGSGESER;GDVEGSQS(1)QDEGEGSGESER 401.68 3.66E-151 507860000 243660 271500 187827 238310 256920 297380 248800 280760 248510 TRUE FALSE 211459.7136 269716.4986 278660.7654 292421.9278 251807.7947 308820.401 224671.4143 220721.6589 219131.4309 0.964990338 1.230843506 1.271660411 1.334459081 1.149117649 1.409293043 1.025281555 1.00725696 1 17.74143691 2.109681128 9.895495614 1.007864015 1.2301843 0.434297196 0.116263315 0.265733726 22.29631578 0.045968428 0.0309791 128.7304027 -2.109681128 0.222320285 GDVEHTIR ddPTM_MDA-MB-175_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 0 135.83 0.00081697 103280000 140460 145200 116670 141960 129570 150310 127070 151210 277230 FALSE TRUE 121897.8551 144246.1716 173092.0022 174194.1877 126991.8105 156092.523 114746.771 118874.9182 244456.1852 0.498649093 0.590069634 0.708069637 0.712578361 0.519487001 0.638529652 0.469396063 0.486283127 1 17.89921638 1.230967493 24.99971274 1.000000753 0.57723252 0.697252111 0.087413084 173.2446792 570345.1601 0.24017545 0.023269664 17.02031108 -1.230967493 -0.422768233 GDVPTKRPPVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDVPTKRPPVLR 12 2 P62424;Q5T8U2;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 ; 95.401 0.0034128 1463100000 913170 878390 359950 373260 769300 689030 979020 1018240 66961 FALSE TRUE 792492.2708 872619.7983 534023.024 458014.3879 753992.4351 715537.43 884074.7911 800497.3 59044.94686 13.42184747 14.77890733 9.044347609 7.757046323 12.76980462 12.11852102 14.97291196 13.55742265 1 15.84952598 1.234778182 24.99968639 0.999983776 12.32895527 0.704507466 2.300385753 67.9762541 449216.5335 4.458235354 0.610975967 17.1703118 -1.234778182 11.32897149 GDVTAEEAAGAS(ph)PAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GDVTAEEAAGASPAK 15 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 GDVTAEEAAGAS(1)PAK;GDVTAEEAAGAS(1)PAK;GDVTAEEAAGAS(1)PAK 183.73 5.18E-07 1552340000 2139620 1815600 1425950 1724750 1946820 1648090 1980330 2563030 3169900 TRUE FALSE 1856863.796 1803673.204 2115544.19 2116380.849 1908082.091 1711493.089 1788277.901 2014945.98 2795158.033 0.664314423 0.645284876 0.756860315 0.757159639 0.682638358 0.612306377 0.639777029 0.720870146 1 21.41449842 1.240203201 3.859916416 1.037455066 0.681859139 0.820727726 0.046650032 0.113505733 2.809125539 0.115292454 0.013017963 17.38614116 -1.240203201 -0.355595927 GDVTDTEQLAQEMLIISHHPSLVAVQSGLWPALLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDVTDTEQLAQEMLIISHHPSLVAVQSGLWPALLAR 36 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 273.54 2.49E-76 544780000 328760 343350 142971 198030 399300 499810 326960 393460 448820 FALSE TRUE 285313.533 341094.5112 212112.2538 242995.7382 391354.7112 519038.0141 295251.4695 309321.6409 395761.0109 0.720923803 0.861869921 0.535960461 0.613996153 0.988866261 1.311493552 0.746034757 0.781586949 1 18.59426996 3.235047887 24.99951468 0.943422903 0.685434372 0.396731918 0.171830007 111.707707 795005.0774 0.055746348 0.065739381 1718.097822 -3.235047887 -0.257988531 GDVVIVLTGWRPGSGFTNTMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GDVVIVLTGWRPGSGFTNTMR 21 1 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 126.23 1.99E-05 305120000 584690 489800 399890 553800 500800 568600 484330 523330 967570 FALSE TRUE 507421.7351 486582.4715 593278.1416 679548.7543 490835.0598 590474.4099 437359.7511 411419.9521 853184.9769 0.594738244 0.570312986 0.695368716 0.796484669 0.575297354 0.692082521 0.51262008 0.482216592 1 19.70249904 1.226492037 24.99537525 1.000000882 0.611848903 0.629616433 0.092801061 416.478669 862519.0611 0.412799161 0.024959086 16.84581539 -1.226492037 -0.388151979 GDVVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDVVPK 6 0 P68363;P68363-2;P68366-2;P68366;Q9BQE3;F5H5D3;A0A1W2PQM2;A6NHL2-2;A6NHL2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA4A;TUBA1C;TUBAL3 Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain;Tubulin alpha chain-like 3 0 ; 102.98 0.081604 814270000 2410700 1885070 1459430 1687010 1507360 1692680 2245200 2329700 2322700 FALSE TRUE 2092119.887 1872686.851 2165215.23 2070071.405 1477366.485 1757798.495 2027460.85 1831511.785 2048113.052 1.021486526 0.914347403 1.057175641 1.01072126 0.721330536 0.85825267 0.989916473 0.8942435 1 20.96586392 GDYDAFFEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 GDYDAFFEAR 10 0 O75368 O75368 SH3BGRL SH3 domain-binding glutamic acid-rich-like protein 0 ;;;;;;;;; 252.77 1.07E-16 13687776000 6565036 6149047 4988242 4592672 5814632 6330643 5503822 6247875 7961582 FALSE TRUE 5697449.859 6108653.505 7400572.516 5635508.372 5698932.199 6574186.933 4970062.19 4911815.552 7020372.846 0.811559441 0.870132348 1.054156621 0.802736336 0.811770589 0.936444129 0.707948466 0.699651665 1 22.74311622 2.949140362 1.216626683 0.793417245 0.897473246 0.031026007 0.113567554 1.020303481 3.244158513 0.05552666 0.05678383 889.48855 -2.949140362 0.104056 GDYGPPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GDYGPPGR 8 0 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 0 ; 124.59 0.006025 87782000 311980 294480 205134 200966 288520 289070 255010 303060 278590 FALSE TRUE 270751.0525 292545.5415 304337.4885 246598.4019 282779.0165 300190.71 230279.1695 238252.9774 245655.4076 1.102157918 1.190877679 1.238879663 1.003838687 1.151120666 1.221999194 0.937407288 0.96986661 1 17.90627647 2.230631791 24.99986134 0.967932621 1.150515372 0.62235979 0.066969355 114.3773678 360632.0366 0.027055018 0.018606931 170.0715973 -2.230631791 0.182582751 GDYPLEAVR ddPTM_MDA-MB-175_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 ;;;;;;; 251.33 1.28E-11 14250390000 7107020 6734050 5662810 5640730 6364270 7442430 6553630 6685080 7828140 FALSE TRUE 6167809.3 6689813.582 8401363.857 6921543.96 6237633.478 7728745.098 5918059.971 5255527.665 6902706.207 0.893534958 0.969158093 1.217111609 1.002729039 0.903650437 1.119668847 0.857353593 0.761372063 1 22.71873065 2.164796729 9.46975016 0.848214836 1.018541024 0.263901677 0.111460768 0.384371217 45.91525945 0.045445418 0.030636154 146.1492966 -2.164796729 0.170326188 GEAAAERPGEAAVAS(ph)SPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GEAAAERPGEAAVASSPSK 19 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 GEAAAERPGEAAVAS(0.493)S(0.493)PS(0.014)K 185.62 1.35E-14 981460000 1101500 874490 779570 985930 955560 700170 882180 1238600 2153900 TRUE FALSE 955933.9842 868745.4176 1156572.66 1209800.475 936546.2255 727105.993 796626.3194 973735.0288 1899268.396 0.503316954 0.457410558 0.608956934 0.636982366 0.49310894 0.382834777 0.419438517 0.512689534 1 20.85701236 1.23941692 7.232103672 1.009253508 0.500000574 0.807143439 0.076547834 0.048419327 16.20830574 0.121582529 0.020815867 17.35469237 -1.23941692 -0.509252934 GEAAAERPGEAAVAS(ph)SPSKANGQENGHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GEAAAERPGEAAVASSPSKANGQENGHVK 29 2 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 GEAAAERPGEAAVAS(0.5)S(0.5)PSKANGQENGHVK 167.01 1.94E-12 321090000 402490 287040 184840 226560 262790 181960 335350 431190 154520 TRUE FALSE 349299.9267 285154.4153 274229.2423 278003.9108 257560.9931 188960.1189 302827.8086 338983.374 136252.8216 2.563616096 2.092833102 2.012650006 2.040353421 1.890316766 1.386834538 2.222543394 2.487899847 1 17.05592658 6.36557021 0.886888077 1.910109537 13.23578416 0.222295472 0.415038396 61.35491703 3.465363982 0.139677408 1228.519329 2320439.29 -6.36557021 11.32567462 GEAAAERPGEAAVASS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GEAAAERPGEAAVASSPSK 19 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 GEAAAERPGEAAVAS(0.027)S(0.97)PS(0.003)K;GEAAAERPGEAAVAS(0.287)S(0.712)PS(0.001)K;GEAAAERPGEAAVAS(0.037)S(0.953)PS(0.01)K;GEAAAERPGEAAVAS(0.032)S(0.967)PS(0.001)K;GEAAAERPGEAAVAS(0.007)S(0.989)PS(0.005)K 229.89 4.23E-20 4436010000 3023010 2570040 2149100 2786390 2629740 2054420 2558720 3454720 5757700 TRUE FALSE 2623511.569 2553157.238 3188411.948 3419082.437 2577413.319 2133454.867 2310575.728 2715955.013 5077031.265 0.516741267 0.502883891 0.628007153 0.673441281 0.507661502 0.420217004 0.455103703 0.534949436 1 22.27555371 1.239013318 8.697056009 1.003923099 0.528926035 0.799573669 0.073976019 0.040259044 36.93206994 0.113851457 0.020107596 17.33857167 -1.239013318 -0.474997064 GEAAAERPGEAAVASS(ph)PSKANGQENGHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GEAAAERPGEAAVASSPSKANGQENGHVK 29 2 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 GEAAAERPGEAAVAS(0.191)S(0.78)PS(0.029)KANGQENGHVK;GEAAAERPGEAAVAS(0.22)S(0.777)PS(0.004)KANGQENGHVK 219.04 1.16E-34 537190000 468520 336720 204721 271968 347900 240778 374360 511100 163039 TRUE FALSE 406603.8949 334508.0641 303724.7604 333722.4912 340977.4707 250040.8855 338054.6248 401805.2424 143764.7152 2.828259316 2.326774437 2.112651634 2.321310141 2.371774397 1.739236816 2.351443638 2.794880802 1 17.13335011 4.719710627 2.702323027 2.179305037 2.940173376 0.17486169 0.477940679 0.8329623 8.414365479 0.117148552 1.392572064 52445.78945 -4.719710627 0.760868339 GEADRDTYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GEADRDTYR 9 1 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ; 180.09 4.47E-05 16395700000 8835500 8869000 6636100 6739900 8053800 9380500 8531700 8459800 7947500 FALSE TRUE 7667866.289 8810738.955 9845340.156 8270297.308 7893545.137 9741373.905 7704297.047 6650737.604 7007955.604 1.094165934 1.257248112 1.404880498 1.180129809 1.12636917 1.390045037 1.09936442 0.949026789 1 22.7405622 2.011180443 6.492775006 0.985407588 1.242923476 0.556674046 0.099648081 0.100519196 18.97243646 0.042726421 0.027111688 102.6078159 -2.011180443 0.257515888 GEADRDTYRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GEADRDTYRR 10 2 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;;;;;; 183.08 9.61E-07 6967969000 3869574 4118352 1841494.2 1833027 3414502 3841233 3581118 3725363 532252.5 FALSE TRUE 3358199.992 4091298.275 2732046.955 2249243.796 3346560.091 3989007.719 3233821.728 2928723.113 469330.2158 7.155303193 8.717312751 5.821161439 4.792454695 7.130502103 8.499362677 6.890290927 6.240218538 1 18.84024382 4.226952995 24.610348 5.981438031 7.93630794 0.162604097 2.000758445 319.5643024 677541.9673 0.517294165 1.091982586 16863.70496 -4.226952995 1.954869909 GEAEAPHHGTGHPESAGEHALEPPAPAGAS(ph)ASTPPPPAPEAQLPPFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GEAEAPHHGTGHPESAGEHALEPPAPAGASASTPPPPAPEAQLPPFPR 48 0 Q9H6Z4;Q9H6Z4-2;K7EPW1;K7EMT3 Q9H6Z4 RANBP3 Ran-binding protein 3 1 GEAEAPHHGT(0.001)GHPES(0.001)AGEHALEPPAPAGAS(0.81)AS(0.111)T(0.077)PPPPAPEAQLPPFPR 79.542 7.19E-05 353250000 33706 34828 13450 25243 39758 40350 29309 36388 41101 TRUE FALSE 29251.6667 34599.21257 19954.46499 30974.80897 38966.89359 41902.29061 26466.61769 28606.70937 36242.0866 0.807118724 0.954669441 0.550588193 0.854664062 1.075183502 1.156177653 0.730273011 0.789322913 1 15.1453784 5.042660074 13.20867263 0.876465072 0.553442208 0.016855001 0.174719408 1911169.579 20011437.8 0.044408813 14248259.14 110321.4786 -5.042660074 -0.323022864 GEAEAPHHGTGHPESAGEHALEPPAPAGASAST(ph)PPPPAPEAQLPPFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GEAEAPHHGTGHPESAGEHALEPPAPAGASASTPPPPAPEAQLPPFPR 48 0 Q9H6Z4;Q9H6Z4-2;K7EPW1;K7EMT3 Q9H6Z4 RANBP3 Ran-binding protein 3 1 GEAEAPHHGTGHPESAGEHALEPPAPAGAS(0.023)AS(0.093)T(0.884)PPPPAPEAQLPPFPR;GEAEAPHHGTGHPESAGEHALEPPAPAGAS(0.05)AS(0.305)T(0.645)PPPPAPEAQLPPFPR 86.822 7.80E-06 786010000 274854 296060 154822 206881 312586 303748 243367 316271 321228 TRUE FALSE 238531.3475 294115.1624 229694.437 253856.493 306366.1502 315433.3821 219765.3058 248638.9079 283252.7918 0.842114727 1.03834868 0.810916763 0.896218856 1.081599755 1.11361085 0.775862806 0.877798613 1 18.11173065 5.029736736 13.69915388 0.938948198 0.5947207 0.076444527 0.112060624 1152817.237 16461811.13 0.028280422 8717366.897 107086.9961 -5.029736736 -0.344227497 GEAERGS(ph)GGS(ph)S(ph)GDELREDDEPVK ddPTM_MDA-MB-175_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 97.063 0.0022563 505260000 316370 277540 185690 216470 288520 245350 259740 326390 324590 TRUE FALSE 274560.9029 275716.8215 275490.3051 265622.822 282779.0165 254788.7733 234550.4548 256594.0385 286217.34 0.959274176 0.96331278 0.962521366 0.928045876 0.987987019 0.890193352 0.819483735 0.896500675 1 18.12675155 2.723437764 24.44353601 0.893063154 0.958739092 0.282234124 0.045585693 724.8175951 1171543.087 0.015905579 0.014085091 528.9781873 -2.723437764 0.065675939 GEAGVPAEFSIWTR ddPTM_MDA-MB-175_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 1077100000 1663530 1626970 1086390 1210550 1534290 1567990 1514880 1547880 1472080 FALSE TRUE 1443690.296 1616282.327 1611771.838 1485423.88 1503760.631 1628311.59 1367967.171 1216877.908 1298052.379 1.112197257 1.245159558 1.241684745 1.144348181 1.158474538 1.254426721 1.053861302 0.93746441 1 20.30791717 2.050426703 4.492338414 0.971208986 1.192920995 0.791791721 0.048639077 0.079282165 3.433060269 0.02129385 0.013300395 112.3121401 -2.050426703 0.221712009 GEAHLAVNDFELAR ddPTM_MDA-MB-175_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 ;;;;; 232.53 1.31E-13 9791170000 4110570 3525700 3900170 4425030 4010690 4373750 3665950 4124020 9056130 FALSE TRUE 3567347.76 3502539.445 5786305.257 5429800.694 3930885.116 4542010.993 3310426.733 3242130.416 7985524.628 0.446726787 0.438611063 0.724599263 0.679955413 0.49225133 0.568780538 0.414553444 0.406000929 1 22.92895576 1.230120182 24.99970525 1.000000895 0.520295793 0.656106867 0.108882195 224.1719099 663922.1214 0.328651307 0.029239358 16.98713671 -1.230120182 -0.479705102 GEASEDLCEMALDPELLLLRDDGEEEFAGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GEASEDLCEMALDPELLLLRDDGEEEFAGAK 31 1 Q8N163-2;Q8N163;H0YB24;G3V119;A0A087X2B6 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ; 172.18 5.22E-13 83195000 253202 231186 124772 136539 188676 168928 254257 279578 80890 FALSE TRUE 219740.7142 229667.3239 185112.1565 167542.2668 184921.7167 175426.7695 229599.1953 219792.4204 71327.27635 3.08073889 3.219908788 2.595250597 2.348922816 2.592580654 2.459462613 3.218953632 3.081463805 1 16.12216626 4.231153548 20.17707574 2.56510457 3.150324498 0.169536342 0.597489239 27.63844767 75302.33109 0.151574886 0.329222909 17027.60427 -4.231153548 0.585219928 GEAVLRPGLDAEPELS(ph)PEEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GEAVLRPGLDAEPELSPEEQR 21 1 C9JQV0;Q9BRJ6 C9JQV0 C7orf50 Uncharacterized protein C7orf50 1 GEAVLRPGLDAEPELS(1)PEEQR;GEAVLRPGLDAEPELS(1)PEEQR 219.51 3.05E-25 326010000 369130 356490 334560 313740 351140 396080 373600 396490 499570 TRUE FALSE 320348.5352 354148.1937 496354.335 384979.4622 344153.001 411317.4539 337368.3295 311703.699 440511.4037 0.727219619 0.803947845 1.126768412 0.873937562 0.78125787 0.933727142 0.765856063 0.707595073 1 18.74881984 2.22818966 24.99248522 0.797689092 0.878476687 0.017685863 0.13024197 594.5047388 1432656.286 0.053497588 0.036507943 169.1179324 -2.22818966 0.080787595 GEAVLRPGLDAEPELSPEEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GEAVLRPGLDAEPELSPEEQR 21 1 C9JQV0;Q9BRJ6 C9JQV0 C7orf50 Uncharacterized protein C7orf50 0 ; 220.52 4.24E-25 420040000 219710 254150 204077 194062 235620 241330 220620 243960 320120 FALSE TRUE 190674.7668 252480.4719 302769.3198 238126.7432 230931.623 250614.1213 199224.3064 191791.0525 282275.7783 0.675491068 0.89444611 1.072601134 0.843596091 0.818106408 0.887834311 0.705778964 0.67944566 1 18.10674581 2.255254305 24.63216231 0.767264785 0.872953436 0.04612852 0.128695342 418.0937879 616912.0081 0.048387231 0.037369878 179.992457 -2.255254305 0.105688651 GECEESWIHFI ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GECEESWIHFI 11 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 0 ;;;; 201.97 9.68E-08 587817000 1344360 1493060 911910 1098860 1373270 1647540 1237720 1533720 1423730 FALSE TRUE 1166699.42 1483251.991 1352912.726 1348372.958 1345944.614 1710921.93 1117686.105 1205745.913 1255418.261 0.929331248 1.181480337 1.077658951 1.074042811 1.07210852 1.362830208 0.890289826 0.960433626 1 20.25973667 GEDEEENNLEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GEDEEENNLEVR 12 0 P04843;F8WF32 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ; 229.16 2.06E-11 506600000 243830 231810 192858 252520 297610 288170 183161 365570 332280 FALSE TRUE 211607.2477 230287.2248 286124.7739 309858.5255 291688.1433 299256.0864 165398.0744 287395.7004 292998.2369 0.722213382 0.785967954 0.976540941 1.057543993 0.995528664 1.021357976 0.564501944 0.9808786 1 18.16053246 4.363302206 4.659892346 0.934008813 0.737063713 0.2456819 0.138309918 0.305892289 10.77642593 0.03596973 0.103063104 23083.5291 -4.363302206 -0.196945101 GEDIFLDMFEDEY(ph)RS(ph)MT(ph)MK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GEDIFLDMFEDEYRSMTMK 19 1 Q2KHT3;Q2KHT3-2 Q2KHT3 CLEC16A Protein CLEC16A 3 GEDIFLDMFEDEY(1)RS(1)MT(1)MK 43.233 0.078481 228850000 328670 330580 153080 179300 349000 292090 383430 428820 106560 TRUE FALSE 285235.4268 328408.3982 227110 220012.8054 342055.5828 303326.8913 346245.0176 337120.1801 93962.59819 3.035627284 3.495097034 2.417025544 2.34149342 3.640337638 3.228166283 3.684923834 3.587812455 1 16.51979899 3.23668691 24.99966839 3.157440099 2.841418114 0.001490403 0.833416478 223.4840564 2981811.451 0.247211896 0.294755328 1724.594155 -3.23668691 -0.316021986 GEDIFLDMFEDEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GEDIFLDMFEDEYR 14 0 Q2KHT3;Q2KHT3-2 Q2KHT3 CLEC16A Protein CLEC16A 0 ;; 174.84 5.77E-06 38818600 52882 48852 33587.9 38958.3 40087 46882.3 42855 49753 48409 FALSE TRUE 45893.50971 48531.088 49831.12078 47804.37746 39289.34713 48685.89242 38698.9287 39113.70813 42686.14317 1.075138354 1.136928389 1.167384005 1.119903882 0.920423918 1.140554962 0.9065923 0.916309257 1 15.3814802 2.890149282 0.901026494 0.938778748 1.133728361 0.443240708 0.075558768 0.488810192 0.932439189 0.051763976 0.046826421 776.5139855 -2.890149282 0.194949613 GEDLTEEEDGGIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GEDLTEEEDGGIIR 14 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;; 318.59 1.19E-55 1370830000 890890 742740 835860 1058310 736460 777950 690350 842120 2629640 FALSE TRUE 773156.6293 737860.892 1240084.692 1298615.461 721805.8869 807878.2399 623399.9633 662039.1914 2318766.955 0.333434383 0.318212613 0.534803504 0.560045699 0.311288672 0.348408553 0.26884977 0.285513467 1 21.1449264 1.233980199 24.99996899 1.000000947 0.368311665 0.799221303 0.099221338 67.93689031 370753.5518 0.209453858 0.026845551 17.13879166 -1.233980199 -0.631689282 KAYS(ph)FCGTVEYMAPEVVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAYSFCGTVEYMAPEVVNR 19 1 E9PGT3;Q15418-4;Q15418;Q15418-2;Q15418-3;B4DG22;B1AXG1;B7ZB17;P51812;Q9UK32-2;Q9UK32 E9PGT3;B4DG22;Q9UK32-2 RPS6KA1;RPS6KA3;RPS6KA6 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1;Ribosomal protein S6 kinase alpha-3;Ribosomal protein S6 kinase alpha-6 1 KAYS(1)FCGTVEYMAPEVVNR 172.06 5.56E-12 190480000 331970 338150 174300 172310 298640 257170 302490 333990 137030 TRUE FALSE 288099.3234 335928.6704 258592.063 211435.6191 292697.6483 267063.4963 273154.5664 262568.8376 120830.4695 2.384326773 2.780165233 2.140122968 1.749853493 2.422382777 2.210233043 2.260643093 2.173034986 1 16.88262478 1.229357745 4.063956072 0.850213159 2.270918817 0.70864654 0.255687364 0.146127945 4.270084779 0.625522923 0.067334767 16.95734066 -1.229357745 1.420705657 GEDVDQLVACIESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GEDVDQLVACIESK 14 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 134.08 9.50E-05 12602000 27487 23144 11207 17809 27329 25123 24386 29460 27628 FALSE TRUE 23854.52331 22991.96554 16626.74269 21852.80564 26785.20637 26089.49807 22021.04947 23160.20826 24361.84931 0.97917539 0.943769303 0.682490991 0.89700931 1.099473444 1.070916158 0.903915347 0.950675294 1 14.57233603 3.459172828 24.48119657 0.994313722 0.861631386 0.317666871 0.094097777 238.796233 325710.4987 0.028460102 0.036749804 2878.543708 -3.459172828 -0.132682336 GEDVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GEDVNR 6 0 P58546 P58546 MTPN Myotrophin 0 97.071 0.096521 209600000 219190 207140 150680 151660 105200 208420 177430 193640 269370 FALSE TRUE 190223.4861 205779.2837 223549.352 186096.721 103106.7258 216438.0523 160222.8659 152231.5929 237525.3855 0.800855394 0.866346489 0.941159832 0.783481398 0.434087184 0.911220718 0.674550493 0.640906624 1 17.85772218 3.480722392 24.99969458 0.714780773 0.868006095 0.135597724 0.154799819 251.9476794 1749069.577 0.042459524 0.056046784 3024.979195 -3.480722392 0.153225322 GEDVPS(ph)EEEEEEENGFEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GEDVPSEEEEEEENGFEDR 19 0 Q9ULX3 Q9ULX3 NOB1 RNA-binding protein NOB1 1 GEDVPS(1)EEEEEEENGFEDR;GEDVPS(1)EEEEEEENGFEDR 302.9 4.66E-50 3553700000 492690 513490 397930 390260 522820 576510 478040 587530 676740 TRUE FALSE 427579.7682 510116.8504 590370.279 478874.4978 512416.9049 598688.7128 431679.7544 461891.2817 596736.5681 0.716530193 0.854844294 0.989331492 0.802488943 0.858698683 1.003271367 0.723400873 0.774028786 1 19.18673466 4.731145689 5.739334796 0.86573521 0.712367081 0.204291602 0.097167228 0.232761654 32.99154335 0.024011535 0.139023101 53845.0382 -4.731145689 -0.153368129 GEEAAGGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GEEAAGGDR 9 0 O43598;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ; 180.87 0.000112 416760000 564140 538640 368010 382680 265950 521240 474980 544330 597200 FALSE TRUE 489587.4697 535101.6384 545980.8669 469573.3429 260658.1153 541292.4401 428916.5127 427929.2655 526599.6963 0.929714683 1.016144981 1.036804371 0.891708343 0.494983414 1.027901163 0.814502013 0.812627255 1 19.00634716 3.483666813 24.99257032 0.82354346 0.991054179 0.211575193 0.144351715 437.1547192 1669167.142 0.039805488 0.0533584 3045.557571 -3.483666813 0.16751072 GEEDTGQEEGGSRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GEEDTGQEEGGSRR 14 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 104.95 0.001648 98567000 128900 111810 76690 70332 97069 113720 105860 109370 91742 FALSE TRUE 111865.5384 111075.5127 113777.5405 86301.95556 95137.51681 118094.882 95593.71349 85982.07662 80896.36527 1.382825273 1.373059375 1.406460477 1.066821176 1.176041921 1.459829272 1.181681194 1.062866994 1 16.30378726 -0.103720985 0.402963803 2.75E-28 1.349375773 0.46668561 0.119332873 18.18196202 1.066212025 14.66944664 0.136141381 0.787551594 0.103720985 1.349375773 GEEDWLYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GEEDWLYER 9 0 J3QQZ9;Q9NVS9-3;Q9NVS9;Q9NVS9-4 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 ;;;;; 206.03 3.25E-05 4101420000 3413100 3550000 2429850 2793490 3297690 3745620 3411750 3737550 3507330 FALSE TRUE 2962050.187 3526679.816 3604933.587 3427794.6 3232072.421 3889716.425 3080879.01 2938304.018 3092697.443 0.957756212 1.140324872 1.165627629 1.108351096 1.04506583 1.257709975 0.9961786 0.95007807 1 21.56043427 2.027516752 24.98510432 0.97196966 1.114073586 0.386137483 0.077798345 186.6720923 169496.7544 0.030193573 0.020356051 106.5409958 -2.027516752 0.142103926 GEEGHDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GEEGHDPK 8 0 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 88.948 0.014253 786460000 2319800 1702740 1760770 2215600 882680 1424670 1901820 2276800 6441300 FALSE TRUE 2013232.552 1691554.589 2612284.261 2718685.843 865116.3949 1479477.977 1717381.789 1789924.038 5679816.852 0.35445378 0.297818509 0.459924031 0.478657308 0.152314136 0.260479874 0.302365698 0.315137633 1 22.43741298 1.237989102 24.99116332 1.000000771 0.326215638 0.837482318 0.093079815 5.556395328 242752.9784 0.136853919 0.02372626 17.29772951 -1.237989102 -0.673785133 GEEGHDPKEPEQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GEEGHDPKEPEQLR 14 1 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 152.89 3.93E-06 721590000 2804100 2304600 1812900 2023800 2221700 2308100 2577300 2919500 2159400 FALSE TRUE 2433531.08 2289460.931 2689624.504 2483334.722 2177492.517 2396894.101 2327353.843 2295187.645 1904118.192 1.278035728 1.20237333 1.412530228 1.304191479 1.14357004 1.258794811 1.222273834 1.205380871 1 20.8606916 0.425903897 1.028493997 4.34E-17 1.268812514 0.584472631 0.06914499 6.55411817 1.587606388 13.7766747 0.022985348 2.666268594 -0.425903897 1.268812514 GEEGHDPKEPEQLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GEEGHDPKEPEQLRK 15 2 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 124.09 5.93E-05 202180000 252030 199060 142960 151550 181280 134750 267760 288420 75121 FALSE TRUE 218723.5969 197752.3618 212095.9342 185961.7438 177672.8827 139933.9197 241792.6764 226743.6275 66240.28096 3.301972663 2.985379272 3.201917792 2.807381568 2.682248325 2.112520021 3.650236275 3.42304749 1 16.01542117 3.660082839 4.507495096 2.738612535 3.145670971 0.097046534 0.728198101 0.724811457 27.15925053 0.207036141 0.317312012 4571.753844 -3.660082839 0.407058436 GEEGRPGK ddPTM_MDA-MB-175_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 ;; 78.516 0.027746 410360000 1160680 1032810 766290 937120 608000 835900 1108060 1278480 1702150 FALSE TRUE 1007293.197 1026025.403 1136870.407 1149907.419 595901.9895 868057.6139 1000600.512 1005087.001 1500923.766 0.671115496 0.683595947 0.757447135 0.766133127 0.397023488 0.578348903 0.666656451 0.669645603 1 20.51741927 1.22512366 4.002925007 1.044983089 0.645564381 0.534062165 0.103285262 0.227190984 6.25211651 0.272054518 0.027666509 16.79282107 -1.22512366 -0.399418708 GEEGRPGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GEEGRPGKK 9 2 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ;; 56.563 0.068121 346240000 754580 638510 416360 503820 371650 436030 744290 823390 456300 FALSE TRUE 654860.3411 634315.5858 617713.0886 618220.0314 364254.8921 452804.3562 672108.8704 647314.4561 402356.7338 1.62756153 1.576500484 1.535237357 1.536497291 0.905303333 1.125380336 1.670430277 1.608807314 1 18.61811565 3.445738136 24.99228258 1.319300362 1.572178449 0.270961091 0.240949128 347.3367048 276604.1793 0.076952187 0.099345727 2790.860544 -3.445738136 0.252878087 GEEGS(ph)DDDETENGPKPK ddPTM_MDA-MB-175_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 282.62 2.89E-36 3805423000 2570417 1672296 1804073 1752456 1638246 1321154 2371205 2604367 2765250 TRUE FALSE 2230729.881 1661310.577 2676528.737 2150377.919 1605648.11 1371979.649 2141245.904 2047443.384 2438345.295 0.914853973 0.681327038 1.097682409 0.881900494 0.65849907 0.562668319 0.878155325 0.83968558 1 21.21747101 5.067357527 19.80922529 0.82391565 2.87871191 0.030426327 0.159321874 1162.370242 416852.4461 0.0384473 22846.93991 116777.0571 -5.067357527 2.05479626 GEEHCGHLIEAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GEEHCGHLIEAHK 13 0 H7C4E5;C9J8T6;Q14061 H7C4E5 COX17 Cytochrome c oxidase copper chaperone 0 ;;; 200.21 3.88E-08 1809700000 1924380 1584320 1479380 1876180 1722440 1618560 1395550 1941800 3018190 FALSE TRUE 1670068.307 1573912.498 2194813.116 2302195.345 1688166.814 1680827.051 1260209.776 1526561.181 2661383.017 0.627518962 0.591388946 0.824688932 0.865037212 0.634319376 0.6315615 0.473516877 0.57359695 1 21.34374472 GEEKPAGHRTS(ph)PVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GEEKPAGHRTSPVAK 15 2 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 GEEKPAGHRT(0.024)S(0.976)PVAK;GEEKPAGHRT(0.046)S(0.954)PVAK 122.19 5.76E-05 1171350000 2810700 2147400 1549050 2041570 2039130 1487760 2851000 3381000 2295300 TRUE FALSE 2439258.874 2133293.588 2298175.761 2505139.672 1998555.302 1544995.09 2574510.459 2657999.461 2023952.249 1.205195861 1.054023675 1.135489122 1.237746431 0.987451806 0.763355504 1.272021344 1.313271824 1 20.94874382 GEEKPSMY ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GEEKPSMY 8 1 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 101.54 0.043395 143260000 189120 176940 117310 137380 173610 156690 189980 200690 188740 FALSE TRUE 164127.3128 175777.6695 174041.5084 168574.2287 170155.5007 162717.9657 171555.7688 157774.0053 166427.3722 0.986179801 1.056182449 1.045750504 1.01289966 1.022400933 0.97771156 1.030814622 0.948005146 1 17.34453321 2.584919928 0.934366133 0.977154085 1.030824698 0.267329931 0.027880396 0.665123861 1.265635555 0.023143775 0.013673812 384.5208804 -2.584919928 0.053670613 GEELLSPLNLEQAAYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GEELLSPLNLEQAAYAR 17 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 93.959 0.0068239 29434000 11852 10786 8624.3 8997.2 9806 11188 8984.1 12034 9036.2 FALSE TRUE 10285.72817 10715.14606 12795.04033 11040.15177 9610.879785 11618.4096 8112.823365 9460.622749 7967.95073 1.290887522 1.344780662 1.605813183 1.385569784 1.20619217 1.458142751 1.018181919 1.187334494 1 12.95999301 2.217548528 1.111933489 1.046476747 1.40141156 0.519725744 0.129502146 0.462966355 1.095365766 0.132860727 0.049480736 165.024539 -2.217548528 0.354934814 GEFGDVMLGDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GEFGDVMLGDYR 12 0 P41240 P41240 CSK Tyrosine-protein kinase CSK 0 130.98 0.00048112 263990000 155930 153020 111780 131100 157490 171500 142070 159230 164900 FALSE TRUE 135323.4554 152014.8015 165837.1819 160868.2587 154356.2571 178097.716 128292.0733 125179.9036 145405.7099 0.930661221 1.045452766 1.140513547 1.106340727 1.061555679 1.224833029 0.882304233 0.86090088 1 17.1497244 2.21151834 24.99940253 0.901918183 1.085542465 0.487118168 0.082134183 169.959981 157119.3208 0.03338349 0.02251355 162.749004 -2.21151834 0.183624282 GEFKDEEETVTTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GEFKDEEETVTTK 13 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ;;; 184 1.18E-06 815570000 1403150 967000 857460 889430 910300 687660 1337370 1479910 1318650 FALSE TRUE 1217720.172 960647.7133 1272130.524 1091388.676 892186.811 714114.7252 1207672.063 1163442.763 1162760.699 1.047266366 0.826178348 1.094060476 0.938618476 0.767300453 0.614154508 1.03862477 1.00058659 1 20.14912278 -0.8829043 8.756098902 9.13532332 0.924446829 0 0.148783741 0 0 0 0.034537246 0.130947044 0.8829043 -8.210876491 GEFSAS(ph)PMLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 GEFSASPMLK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GEFSAS(1)PMLK;GEFSAS(1)PMLK;GEFSAS(1)PMLK;GEFS(0.014)AS(0.986)PMLK;GEFSAS(1)PMLK;GEFSAS(1)PMLK;GEFS(0.002)AS(0.998)PMLK;GEFS(0.001)AS(0.999)PMLK 250.26 3.54E-13 20169510000 26976250 20766230 13863698 16561290 19444990 17069810 21327310 25363830 23093780 TRUE FALSE 23411270.21 20629815.27 20568228.72 20321784.02 19058072.74 17726496.64 19258990.76 19939972.34 20363659.64 1.149659277 1.013070128 1.010045792 0.99794361 0.935886431 0.870496608 0.94575293 0.979193951 1 24.27949352 6.223629516 0.738003402 0.950890961 2.711670761 0.725921511 0.037372967 12.37502089 0.904000816 0.015653803 29.28297025 1673514.639 -6.223629516 1.7607798 GEGDAPFSEPGTTSTQRPS(ph)S(ph)PETATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GEGDAPFSEPGTTSTQRPSSPETATK 26 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GEGDAPFSEPGTTST(0.001)QRPS(0.999)S(0.989)PET(0.011)ATK;GEGDAPFSEPGTTSTQRPS(1)S(0.999)PET(0.001)ATK 192.07 2.76E-18 490850000 858830 591260 471320 613750 615310 511930 626430 764970 928200 TRUE FALSE 745333.4395 587375.9741 699251.9285 753111.3181 603066.5348 531624.2784 565678.915 601387.1185 818469.2534 0.910643175 0.71765185 0.854341108 0.920146132 0.736822467 0.649534819 0.691142535 0.734770568 1 19.6425687 3.206836007 24.98995657 0.747999264 0.841452895 0.133619602 0.107085099 376.389547 296486.6025 0.032637228 0.037010459 1610.037556 -3.206836007 0.09345363 GEGDAPFSEPGTTSTQRPSS(ph)PETATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GEGDAPFSEPGTTSTQRPSSPETATK 26 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GEGDAPFSEPGTTSTQRPS(0.011)S(0.989)PETATK;GEGDAPFSEPGTTSTQRPS(0.023)S(0.977)PETATK;GEGDAPFSEPGTTSTQRPS(0.25)S(0.75)PETATK;GEGDAPFSEPGTTSTQRPS(0.209)S(0.791)PETATK;GEGDAPFSEPGTTSTQRPS(0.041)S(0.895)PET(0.062)AT(0.002)K;GEGDAPFSEPGTTSTQRPS(0.008)S(0.992)PETATK;GEGDAPFSEPGTTST(0.002)QRPS(0.239)S(0.735)PET(0.022)AT(0.001)K 310.71 5.85E-82 22067550000 12310250 8655900 6822385 8431090 8832350 7503736 9778140 11728400 12340000 TRUE FALSE 10683419.27 8599038.823 10121713.21 10345497.85 8656603.515 7792409.579 8829857.488 9220372.931 10881179.26 0.981825501 0.790267178 0.9302037 0.950769912 0.795557477 0.716136495 0.811479829 0.847368903 1 23.37533158 3.232923623 24.99594197 0.82817033 0.905690697 0.170994158 0.085335876 261.6182184 1160083.979 0.02612457 0.030442858 1709.714612 -3.232923623 0.077520367 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(ph)PVAPAPVPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPSPVAPAPVPSR 42 1 Q9UK76;Q9UK76-3 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(1)PVAPAPVPSR;GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(1)PVAPAPVPSR;GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(1)PVAPAPVPSR;GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(1)PVAPAPVPSR;GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(1)PVAPAPVPSR 249.61 1.27E-55 4147240000 472018 440698 413334 592133 487000 440515 489268 686878 1150927 TRUE FALSE 409639.6254 437803.0258 613223.7049 726585.8478 477309.6528 457461.8971 441818.8647 539994.485 1014865.721 0.403639237 0.431390101 0.604241223 0.715942841 0.470318036 0.45076101 0.435347116 0.532084663 1 19.95285742 1.239858193 5.619722447 1.022090958 0.506199358 0.733765415 0.093757013 0.08114649 8.36058508 0.161564268 0.025016893 17.37233491 -1.239858193 -0.515891601 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPSPVAPAPVPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPSPVAPAPVPSR 42 1 Q9UK76;Q9UK76-3 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 0 189.02 3.63E-28 173140000 55457 42926 44777 52824 48682 42911 56618 61179 111740 FALSE TRUE 48128.21694 42644.01628 66431.30697 64818.49656 47713.32344 44561.81394 51127.19507 48096.34695 98530.22449 0.488461456 0.432801371 0.674222629 0.657853942 0.484250632 0.452265426 0.518898595 0.488138002 1 16.58827872 1.235852262 24.99887374 1.000000633 0.525082012 0.775658018 0.080346938 37.23775865 343646.1424 0.139463823 0.020836052 17.21282929 -1.235852262 -0.474918621 GEGERPAQNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GEGERPAQNEK 11 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;; 178.32 6.92E-06 6952080000 9173340 7649520 4834310 6105810 6613890 6715370 8492140 9880730 8324110 FALSE TRUE 7961059.877 7599269.799 7172198.486 7492227.482 6482286.529 6973714.629 7668573.57 7767812.781 7340043.199 1.084606679 1.035316768 0.977133007 1.020733432 0.883140106 0.950091769 1.044758643 1.058278892 1 22.80735712 -1.433936006 20.43985708 0.219969188 1.006706338 0 0.058295097 0 0 0 0.014017802 0.036818322 1.433936006 0.786737151 GEGLY(ph)ADPYGLLHEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GEGLYADPYGLLHEGR 16 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 GEGLY(1)ADPYGLLHEGR;GEGLY(1)ADPYGLLHEGR;GEGLY(1)ADPYGLLHEGR;GEGLY(1)ADPYGLLHEGR 207.39 1.02E-10 606180000 1201920 974330 814470 781760 975640 1394410 879320 1040030 1091080 TRUE FALSE 1043083.227 967929.5621 1208350.416 959270.5565 956226.6728 1448053.855 794043.6817 817627.678 962093.7654 1.084180424 1.006065726 1.255959096 0.997065557 0.993901746 1.505106786 0.825328788 0.849841988 1 19.87581798 GEGLYADPYGLLHEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GEGLYADPYGLLHEGR 16 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 0 145.55 1.21E-06 154370000 374460 227520 168770 182370 218700 246760 219430 242390 260660 FALSE TRUE 324974.1622 226025.4061 250387.7365 223779.8959 214348.2979 256253.0169 198149.7124 190556.7848 229845.0717 1.413883534 0.983381564 1.089376138 0.973611895 0.932577306 1.114894546 0.862101201 0.82906622 1 17.81030221 8 0.880986204 0.939658129 199.1830818 0.695451082 0.090464166 474.9522088 1.139561061 0.031057397 189095.9241 100000000 -8 198.2434237 GEGPAIPGDT(ph)PPPTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GEGPAIPGDTPPPTPR 16 0 O75145-2;O75145 O75145-2 PPFIA3 Liprin-alpha-3 1 GEGPAIPGDT(1)PPPTPR;GEGPAIPGDT(1)PPPTPR;GEGPAIPGDT(1)PPPTPR;GEGPAIPGDT(1)PPPTPR;GEGPAIPGDT(1)PPPTPR;GEGPAIPGDT(1)PPPTPR 287.03 4.76E-35 6092930000 4931460 5038930 3442190 3581610 4656800 5329340 4479350 4837600 4727640 TRUE FALSE 4279755.066 5005828.937 5106844.597 4394869.292 4564138.791 5534363.158 4044943.326 3803116.886 4168743.785 1.026629433 1.200800336 1.225032015 1.054243081 1.094847519 1.327585346 0.970302694 0.912293267 1 21.99118127 2.079021146 11.40358475 0.947312499 1.152766599 0.514173363 0.088861698 0.35923659 49.89889182 0.035161723 0.023701927 119.9557708 -2.079021146 0.2054541 GEGPGEAGGPLT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GEGPGEAGGPLTPR 14 0 P50548;P50548-2 P50548 ERF ETS domain-containing transcription factor ERF 1 GEGPGEAGGPLT(1)PR;GEGPGEAGGPLT(1)PR;GEGPGEAGGPLT(1)PR;GEGPGEAGGPLT(1)PR;GEGPGEAGGPLT(1)PR;GEGPGEAGGPLT(1)PR 240.82 2.30E-16 3541890000 1096386 1438650 1394420 1582120 2067160 2267740 1882360 2273650 2422630 TRUE FALSE 951495.8122 1429199.413 2068766.176 1941364.527 2026027.56 2354981.425 1699809.017 1787447.641 2136229.441 0.445408997 0.669028984 0.968419467 0.908780906 0.9484129 1.102400978 0.795705267 0.836730178 1 21.02663518 4.471966786 2.75821662 0.926377038 0.449953342 0.78544511 0.086363338 0.140821396 1.961529601 0.023696173 0.114728031 29646.0465 -4.471966786 -0.476423697 GEGQLGPAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GEGQLGPAER 10 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;; 203.78 4.63E-07 3189380000 2205420 2319250 1756570 1836450 2273750 2373190 2254160 2468270 2351700 FALSE TRUE 1913968.159 2304014.694 2606053.127 2253444.041 2228506.824 2464488.155 2035551.91 1940449.669 2073684.705 0.922979349 1.111072811 1.256725828 1.086685953 1.074660395 1.188458472 0.981611093 0.935749617 1 20.98376512 2.129271437 7.059260746 0.962319109 1.111104349 0.350079986 0.086101222 0.224986537 13.21028204 0.035363137 0.023764286 134.6701787 -2.129271437 0.14878524 GEGS(ph)PSEATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GEGSPSEATR 10 0 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 GEGS(0.62)PS(0.38)EATR 150.33 2.28E-05 145750000 193660 211110 138210 189710 182330 209140 172950 212840 299830 TRUE FALSE 168067.3403 209723.2045 205048.8183 232786.555 178701.9897 217185.7511 156177.3356 167325.8223 264384.439 0.635693012 0.793250939 0.775570677 0.880485084 0.6759172 0.821477058 0.590720605 0.632888316 1 18.01227774 GEGSPS(ph)EATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GEGSPSEATR 10 0 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 GEGS(0.224)PS(0.776)EATR 136.94 0.00010946 118380000 157720 146920 117680 154980 146930 167680 136720 164220 226110 TRUE FALSE 136876.9024 145954.8728 174590.4416 190170.5777 144006.3805 174130.7581 123460.9154 129102.831 199379.5334 0.686514308 0.732045413 0.875668824 0.953811931 0.722272633 0.873363254 0.619225621 0.647522987 1 17.6051578 2.25960111 24.99673474 0.727388736 0.809764883 0.019063486 0.129279323 632.8345061 751824.3908 0.048608649 0.037613781 181.8030271 -2.25960111 0.082376146 GEGYAKPNEGAIVEVALEGYYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GEGYAKPNEGAIVEVALEGYYK 22 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;; 230.86 1.51E-26 1316014000 2706438 2139649 1900264 2361296 1961202 1605128 2824405 3277892 3167220 FALSE TRUE 2348775.361 2125593.505 2819238.026 2897464.347 1922177.917 1666878.313 2550494.638 2576940.304 2792794.86 0.841012491 0.761099047 1.009468353 1.037478402 0.688263196 0.596849535 0.913240953 0.9227102 1 21.41327818 1.769502394 2.911362097 0.970073262 0.8291211 0.151076839 0.133515472 0.51155798 8.564427564 0.106904013 0.039739839 58.81693561 -1.769502394 -0.140952162 GEHSIVYLKPSYAFGSVGK ddPTM_MDA-MB-175_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" 0 274.95 1.84E-39 714960000 322400 273280 216660 272780 261840 239610 323150 365120 468160 FALSE TRUE 279794.0231 271484.8057 321437.5007 334718.8682 256629.8963 248827.9517 291810.9627 287041.9294 412814.6581 0.677771532 0.657643328 0.778648467 0.81082118 0.621658876 0.602759487 0.706881301 0.695328821 1 18.65513467 1.238485374 10.42066102 1.000999523 0.694603305 0.697403785 0.063356602 0.043182823 120.791658 0.09265034 0.016455815 17.3175071 -1.238485374 -0.306396218 GEHVPGFCLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GEHVPGFCLPK 11 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 78.096 0.019892 0 589010 571540 450670 405330 560660 583410 577360 677740 720340 FALSE TRUE 511170.8361 567785.5161 668615.5194 497366.3716 549503.9629 605854.1602 521367.7161 532810.5752 635182.2258 0.8047625 0.893893899 1.052635751 0.783029423 0.86511231 0.95382732 0.820815972 0.838831053 1 19.27681102 GEIPS(ph)PQLTRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GEIPSPQLTRPK 12 1 Q8IWZ3-6;H7C0V5 Q8IWZ3-6 ANKHD1;ANKHD1-EIF4EBP3 Ankyrin repeat and KH domain-containing protein 1 1 GEIPS(1)PQLTRPK;GEIPS(1)PQLTRPK 108.34 0.0010397 952110000 1143620 956830 684380 924620 866700 766230 870520 1038820 1362360 TRUE FALSE 992487.7194 950544.5207 1015348.457 1134569.103 849454.3657 795707.3639 786097.1044 816676.4271 1201303.353 0.826175767 0.791261024 0.845205713 0.944448461 0.707110626 0.662370052 0.654370191 0.679825312 1 20.19616908 3.211078666 24.98650737 0.72272581 0.846981443 0.203838881 0.105578413 307.2157408 279318.6572 0.032085837 0.036390372 1625.843225 -3.211078666 0.124255633 GEKPNPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GEKPNPLR 8 1 P68402;J3KNE3 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 ;; 82.279 0.018864 1488060000 2905660 2511940 1733070 2106100 2445600 2560190 3017800 3253880 3227240 FALSE TRUE 2521669.669 2495438.901 2571188.449 2584322.195 2396937.345 2658682.166 2725134.22 2558063.084 2845719.364 0.886127319 0.876909696 0.903528465 0.908143729 0.842295757 0.934274194 0.957625778 0.898916146 1 21.44036196 -2 0.478971505 3.520666985 0.885868133 0.522893497 0.030317922 92.15667178 1.099721742 240.4755794 0.021425654 0.01 2 -2.634798852 GELGCFLSHYNIWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GELGCFLSHYNIWK 14 0 Q8NBJ5;M0QX72 Q8NBJ5 COLGALT1 Procollagen galactosyltransferase 1 0 171.73 2.97E-06 169280000 321230 296220 238950 294610 325000 353910 313670 319700 271110 FALSE TRUE 278778.6416 294274.1113 354507.0192 361505.7033 318533.1359 367525.1467 283250.3317 251334.6429 239059.6846 1.166146613 1.230965028 1.482922642 1.512198528 1.332441881 1.537378196 1.184851942 1.051346835 1 17.86701133 1.99600536 3.98568599 1.044461405 1.379705482 0.601349181 0.118895079 0.151357179 5.42503311 0.063371671 0.034809843 99.08441736 -1.99600536 0.335244077 GELQYRPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GELQYRPSR 9 1 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 0 156.16 6.53E-05 113700000 139440 128950 88687 106960 135100 133770 117980 129310 109560 FALSE TRUE 121012.6507 128102.919 131576.3298 131246.9028 132411.7743 138916.2185 106538.3178 101658.0628 96607.94161 1.252615972 1.326008161 1.361961839 1.358551902 1.370609622 1.437937877 1.102790474 1.05227439 1 16.55985417 2.130069334 5.199624243 1.043936606 1.351191647 0.895204344 0.04864429 0.061941847 2.591156749 0.021398745 0.014204471 134.9178259 -2.130069334 0.307255041 GELS(ph)EEELPYYVELPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GELSEEELPYYVELPDR 17 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 GELS(1)EEELPYYVELPDR;GELS(1)EEELPYYVELPDR;GELS(1)EEELPYYVELPDR 270.51 1.45E-35 186453000 276837 266273 198025 229882 270724 235340 253121 307387 361274 TRUE FALSE 240252.289 264523.8351 293790.5524 282080.2216 265337.1221 244393.6821 228573.3644 241654.6821 318564.5993 0.754171335 0.830361678 0.922232266 0.885472593 0.832914651 0.767171502 0.717510247 0.75857356 1 18.28122643 2.954171373 6.818399045 0.794334922 0.852995874 0.023518311 0.085860008 0.598011945 72.06538369 0.02809295 0.028532033 899.8525931 -2.954171373 0.058660952 GELS(ph)PSFLNPPLPPSIDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GELSPSFLNPPLPPSIDDR 19 0 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 GELS(0.964)PS(0.036)FLNPPLPPSIDDR;GELS(0.974)PS(0.026)FLNPPLPPSIDDR 90.385 0.0023548 227400000 97801 115112 61426 91219 108522 115533 91205 111726 121144 TRUE FALSE 84876.35005 114355.8217 91131.81906 111931.6681 106362.6245 119977.6293 82359.95314 87834.26435 106822.4943 0.794555029 1.07052192 0.853114502 1.047828632 0.99569501 1.123149483 0.770998221 0.822245023 1 16.70485595 2.221513573 24.99992892 0.851736809 0.982807028 0.189924462 0.112256313 345.5209087 506711.4168 0.043540352 0.029436958 166.5380875 -2.221513573 0.131070219 GELSEEELPYYVELPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GELSEEELPYYVELPDR 17 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 0 179.02 2.18E-09 43419000 44276 44509 35979 35919 38883 49264 37185 39103 53954 FALSE TRUE 38424.81442 44216.61745 53378.56474 44074.95794 38109.30437 51159.21796 33578.80442 30741.12775 47575.61958 0.807657677 0.929396566 1.121973086 0.926419 0.801025918 1.075324261 0.705798573 0.646152967 1 15.53793482 2.221954544 24.9999961 0.752011318 0.943827474 0.226816326 0.134706732 294.3287933 443100.7097 0.05436486 0.036767007 166.7072715 -2.221954544 0.191816156 GEMMDLQHGSLFLQTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GEMMDLQHGSLFLQTPK 17 0 A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50;C9J7H8;F5H793 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 ;; 216.19 5.37E-15 2109310000 2587270 2751090 1684070 2259950 2514150 2577070 2764090 3124760 4294980 FALSE TRUE 2245355.714 2733017.909 2498491.885 2773106.189 2464123.334 2676211.55 2496028.977 2456554.391 3787232.357 0.592875087 0.721639881 0.659714443 0.732224994 0.650639597 0.706640443 0.659064124 0.648641055 1 21.85271251 1.235927944 24.9892074 1.000000436 0.673335485 0.865576071 0.040686502 22.7118537 215535.1634 0.060502119 0.009073203 17.21582915 -1.235927944 -0.32666495 GEMMDLQHGSLFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 GEMMDLQHGSLFLR 14 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2;F5H5J4;F5H6W8 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;;;;;;;;; 211.51 3.74E-09 13758474000 11058370 10571030 4269922 8170569 13363360 13874540 9762600 11605460 18453640 FALSE TRUE 9596978.386 10501588.21 6334870.561 10025821.57 13097455.28 14408302.53 8815824.555 9123722.693 16272071.7 0.589782209 0.645374996 0.389309406 0.616136762 0.80490398 0.885462085 0.541776408 0.560698285 1 23.95589461 3.462263786 11.46780801 0.722755506 0.543689654 0.293281951 0.151070341 0.721398313 547.6308141 0.045319291 0.059066882 2899.103941 -3.462263786 -0.179065852 GENLEHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GENLEHLR 8 0 C9JXZ5;Q9BV40;B8ZZT4 C9JXZ5 VAMP8 Vesicle-associated membrane protein 8 0 ;;;;; 177.97 0.00025206 3300740000 4862160 4933310 3601050 3987370 5272250 6222030 4248230 5557270 5317910 FALSE TRUE 4219613.237 4900902.762 5342529.825 4892763.302 5167342.54 6461395.52 3836237.308 4368891.057 4689232.738 0.899851526 1.045139586 1.139318546 1.043403809 1.101959069 1.377921695 0.818094883 0.931685694 1 22.16092045 GEPAAAAAPEAGAS(ph)PVEK ddPTM_MDA-MB-175_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 328.48 8.28E-75 3328980000 2893920 2854890 2506720 3956240 3823590 2738670 3782610 5110700 6936800 TRUE FALSE 2511481.14 2836136.04 3718978.176 4854564.759 3747508.04 2844028.407 3415773.064 4017816.577 6116739.406 0.410591489 0.463667953 0.608000101 0.793652375 0.612664328 0.464958243 0.558430372 0.656855934 1 22.54433138 1.214998758 2.478898848 1.127376567 0.565307162 0.62924166 0.105896716 0.428975723 2.71551011 0.533519201 0.030308857 16.40585081 -1.214998758 -0.562069405 GEPGRPALYFCGSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GEPGRPALYFCGSIR 15 1 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ; 136.26 2.19E-05 3112200000 942170 902780 758880 749990 892760 1101420 849090 998110 832330 FALSE TRUE 817659.8473 896849.5787 1125876.906 920286.6924 874995.8227 1143792.34 766745.3825 784671.9438 733932.8956 1.114079846 1.221977628 1.534032489 1.25391122 1.192201396 1.558442668 1.044707748 1.069133089 1 19.48528864 2.177067689 23.90634525 1.044723189 1.310275339 0.458666862 0.140498252 41.59627304 16170.4156 0.056303955 0.03796014 150.3376264 -2.177067689 0.265552149 GEPNVS(ph)YICSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GEPNVSYICSR 11 0 A0A3B3ITW1;P49841;P49841-2;P49840;A8MT37 A0A3B3ITW1;P49840 GSK3B;GSK3A Glycogen synthase kinase-3 beta;Glycogen synthase kinase-3 alpha 1 GEPNVS(0.82)Y(0.18)ICSR;GEPNVS(0.875)Y(0.123)ICS(0.001)R;GEPNVS(0.654)Y(0.346)ICSR;GEPNVS(0.53)Y(0.47)ICSR;GEPNVS(0.588)Y(0.411)ICSR;GEPNVS(0.599)Y(0.401)ICSR 246.73 5.04E-16 10173480000 1371235 1259600 889086 971951 1276135 1228799 1271594 1436919 1326445 TRUE FALSE 1190022.82 1251325.605 1319050.963 1192647.33 1250742.41 1276071.693 1148275.01 1129645.054 1169634.183 1.017431636 1.069843565 1.127746592 1.019675508 1.069344953 1.091000683 0.981738586 0.965810567 1 20.15762595 2.227557561 24.89879358 0.979003562 1.066897245 0.590545286 0.032655469 130.4345885 295157.6727 0.013007407 0.008866018 168.8719666 -2.227557561 0.087893683 GEPNVSY(ph)ICSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GEPNVSYICSR 11 0 A0A3B3ITW1;P49841;P49841-2;P49840;A8MT37 A0A3B3ITW1;P49840 GSK3B;GSK3A Glycogen synthase kinase-3 beta;Glycogen synthase kinase-3 alpha 1 GEPNVS(0.197)Y(0.803)ICSR;GEPNVS(0.083)Y(0.917)ICSR;GEPNVS(0.121)Y(0.879)ICSR;GEPNVS(0.472)Y(0.528)ICSR;GEPNVS(0.461)Y(0.539)ICSR 205.32 3.11E-07 26033250000 1279350 1185740 867990 820882 1144230 1227470 1097290 1187280 1140580 TRUE FALSE 1110280.656 1177950.796 1287752.867 1007275.804 1121462.062 1274691.565 990874.9847 933389.4114 1005741.932 1.103941897 1.171225698 1.280400893 1.001525116 1.115059466 1.26741416 0.985217931 0.928060551 1 19.93982873 2.116089064 7.325810213 0.958525832 1.153566814 0.537947329 0.081088253 0.162797319 9.770118891 0.033092636 0.022244419 130.6438781 -2.116089064 0.195040982 GEPPHSELHPMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GEPPHSELHPMK 12 0 B4DR80;Q9Y6E0-2;H0Y630;Q9Y6E0;Q5JV98 B4DR80 STK24 Serine/threonine-protein kinase 24;Serine/threonine-protein kinase 24 36 kDa subunit;Serine/threonine-protein kinase 24 12 kDa subunit 0 ;;; 117.79 0.00040209 510102000 673590 619810 385805 494681 571160 588480 566120 659400 677290 FALSE TRUE 584573.3748 615738.4273 572381.5884 607005.8818 559795.0335 611119.2064 511217.7695 518392.4415 597221.5478 0.97882164 1.031005043 0.958407463 1.016383089 0.937332277 1.023270524 0.855993511 0.868006929 1 19.18790669 2.24164382 24.99999973 0.897501281 0.989944911 0.395486966 0.047703656 68.43928028 554943.3189 0.017654216 0.013079466 174.439093 -2.24164382 0.09244363 GEQVSQNGLPAEQGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GEQVSQNGLPAEQGSPR 17 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 GEQVSQNGLPAEQGS(1)PR;GEQVSQNGLPAEQGS(1)PR;GEQVSQNGLPAEQGS(1)PR;GEQVSQNGLPAEQGS(1)PR 382.07 4.07E-106 3771750000 2631650 2698340 2282180 2701200 3016150 3022040 2435760 3149530 4334980 TRUE FALSE 2283870.785 2680614.427 3385849.881 3314548.745 2956134.516 3138299.834 2199540.37 2476027.519 3822503.603 0.597480348 0.701271916 0.88576761 0.867114616 0.773350354 0.821006377 0.575418783 0.647750212 1 21.86608643 4.490594791 6.593194348 0.77480959 0.620665299 0.21224846 0.120258494 0.270577183 53.78919867 0.03166253 0.105136314 30945.30666 -4.490594791 -0.154144291 GES(ph)ENAGTNQETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GESENAGTNQETR 13 0 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 GES(1)ENAGTNQETR;GES(1)ENAGTNQETR 278.68 2.68E-32 577900000 612780 422580 354140 440180 458240 487210 449850 518000 785120 TRUE FALSE 531799.5704 419804.0442 525403.2885 540129.5967 449121.9205 505953.284 406223.6162 407229.7311 692304.008 0.768159023 0.606386846 0.7589199 0.780191347 0.648735115 0.730825299 0.586770568 0.588223853 1 19.40104617 3.215936173 24.94956681 0.68726029 0.721877084 0 0.125320644 1381.923705 1523940.668 0.037619886 0.042689175 1644.130073 -3.215936173 0.034616794 GES(ph)LDNLDSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GESLDNLDSPR 11 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 GES(1)LDNLDSPR;GES(1)LDNLDSPR;GES(1)LDNLDSPR 240.42 1.16E-15 1445920000 1333330 1376440 960960 1273340 1441540 1417450 1394530 1495620 2087370 TRUE FALSE 1157127.062 1367398.075 1425683.47 1562471.309 1412856.174 1471980.219 1259288.695 1175793.302 1840603.497 0.628667209 0.742907464 0.774573923 0.848890764 0.767604852 0.799726949 0.68417163 0.638808578 1 20.81174744 4.726716138 2.866743763 0.770454358 0.605672891 0.195794157 0.096908572 0.748772762 8.862869285 0.024697104 0.283502825 53298.64128 -4.726716138 -0.164781467 GESAEDKEHEEGRDS(ph)EEGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 GESAEDKEHEEGRDSEEGPR 20 2 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;K7EPS6;A0A087WX58 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 1 GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR 306.39 7.74E-56 6727579000 3447866 2658644 2577999 2908686 2675198 2474938 3003867 3573943 5165113 TRUE FALSE 2992221.772 2641179.193 3824727.939 3569147.613 2621966.794 2570150.466 2712552.441 2809683.102 4554499.225 0.656981509 0.579905509 0.839769149 0.783653139 0.575687175 0.564310221 0.595576441 0.616902751 1 22.11886101 1.23526371 24.99876116 1.000000485 0.650012539 0.587447091 0.091748241 73.5909467 557908.7986 0.169357464 0.024109556 17.18951844 -1.23526371 -0.349987947 GESDPAYQQYQDAANNLREDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GESDPAYQQYQDAANNLREDYK 22 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 178.22 5.57E-17 127070000 382860 321180 154780 178100 295030 320300 323120 308210 38033 FALSE TRUE 332264.081 319070.1474 229632.1257 218540.3271 289159.4802 332622.1483 291783.8721 242301.69 33536.78207 9.907452668 9.514035866 6.847172315 6.516436987 8.622159384 9.918129521 8.700413521 7.224953471 1 15.03345665 4.274226645 7.060105943 7.237617047 9.746134609 0.17990479 2.377957164 0.371645724 53.66799122 0.603868277 1.576846603 18802.9783 -4.274226645 2.508517562 GESEDDFWWCIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 ;;;;;; 285.83 1.83E-32 1099761000 826689 833833 609742 635059 707878 827230 803387 881743 840075 FALSE TRUE 717439.9541 828355.4961 904615.2707 779258.8522 693792.6127 859054.0734 725474.6524 693189.1212 740762.2905 0.968515762 1.118247387 1.221195088 1.051968846 0.93659278 1.159689261 0.979362289 0.93577809 1 19.49865113 2.087914159 8.552915154 0.961615227 1.076970465 0.254953767 0.084057132 0.338293749 29.21434058 0.03492331 0.023510476 122.437417 -2.087914159 0.115355237 GESFYQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GESFYQDR 8 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 166.52 0.00073982 665960000 1534900 1477200 976400 1035700 1358300 1480100 1246500 1392800 1348300 FALSE TRUE 1332059.076 1467496.176 1448590.306 1270871.515 1331272.487 1537040.405 1125614.622 1094960.559 1188905.51 1.120407858 1.234325322 1.21842341 1.068942405 1.119746251 1.29281965 0.946765418 0.920981987 1 20.18120263 2.218153766 24.92274363 0.948256521 1.172974174 0.706681587 0.066695915 120.3003611 146920.8359 0.027192363 0.018357656 165.2546794 -2.218153766 0.224717653 GESGQSWPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GESGQSWPR 9 0 A0A087WYT3;Q15185-4;Q15185;Q15185-3;B4DDC6 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 112.11 0.0046906 82227000 295140 259010 207410 256130 245650 281430 270890 337920 311910 FALSE TRUE 256136.5012 257308.5463 307714.1697 314288.2312 240762.0456 292256.7942 244619.1295 265658.4377 275036.3551 0.931282343 0.935543762 1.11881271 1.142715228 0.875382622 1.062611501 0.889406527 0.96590299 1 18.06926281 3.224746142 24.99966453 0.959569515 1.031387079 0.158566675 0.084028302 469.5705473 849766.7092 0.025944017 0.029564287 1677.822992 -3.224746142 0.071817565 GESLDNLDS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GESLDNLDSPR 11 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 GESLDNLDS(1)PR;GESLDNLDS(1)PR 91.812 0.0053884 83236000 261175 312518 221166 271061 402030 384290 389721 463460 384231 TRUE FALSE 226660.062 310465.0487 328122.6174 332609.543 394030.3896 399073.885 351925.9174 364352.6856 338807.6489 0.668993344 0.916346044 0.968462838 0.981706122 1.162991423 1.177877437 1.038718927 1.075396871 1 18.37010692 5.204354558 0.830611221 1.083278416 0.07404243 0.815975379 0.061216148 2.051071978 0.644238229 0.023076603 2.270918464 160086.444 -5.204354558 -1.009235986 GESLSLPGPS(ph)PPPDGTEQVIISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GESLSLPGPSPPPDGTEQVIISR 23 0 Q9BZQ8 Q9BZQ8 FAM129A Protein Niban 1 GESLS(0.002)LPGPS(0.997)PPPDGT(0.001)EQVIISR 110.08 0.00070306 80402000 77591 97866 67952 85317 113440 99012 87584 123730 109520 TRUE FALSE 67337.15276 97223.1118 100813.8145 104689.5288 111182.7659 102821.0557 79090.11716 97271.30237 96572.67037 0.697269243 1.006735254 1.043916608 1.084049229 1.151286027 1.064701383 0.818969972 1.007234262 1 16.55932735 4.738000396 5.389838621 1.020251608 0.684783249 0.591542989 0.084900098 0.118396076 12.78678053 0.022584164 0.147186929 54701.64617 -4.738000396 -0.335468359 GETDEEYLWCIEQTLYFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GETDEEYLWCIEQTLYFK 18 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 96.163 0.0016437 39530000 78459 82899 48895 68118 61501 60147 75630 89787 83467 FALSE TRUE 68090.44436 82354.43101 72540.78554 83585.23302 60277.25042 62460.89401 68295.41424 70586.74877 73599.62635 0.925146604 1.118951754 0.985613503 1.135674692 0.818988539 0.84865776 0.927931535 0.959063956 1 16.16741082 3.239472298 24.99998053 0.915107022 1.042908912 0.408912206 0.077814985 25.29494057 693621.4998 0.022750175 0.027684601 1735.690545 -3.239472298 0.12780189 GEVPPKET(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GEVPPKETPK 10 1 P49006 P49006 MARCKSL1 MARCKS-related protein 1 GEVPPKET(1)PK;GEVPPKET(1)PK 105.65 0.0040752 1089900000 3030940 2091660 1871010 1996470 2126890 1522910 2794020 3292860 2912600 TRUE FALSE 2630393.6 2077919.748 2775836.694 2449799.028 2084569.05 1581497.333 2523056.37 2588707.514 2568275.746 1.024186598 0.809071904 1.080817236 0.95386916 0.811660918 0.61578175 0.982393099 1.007955442 1 21.29236868 2.028808493 24.99862145 1.001734955 0.880823227 0.152909642 0.127413036 383.8053279 333046.2158 0.054089636 0.036466706 106.8583571 -2.028808493 -0.120911727 GEVQFGSWFDHIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GEVQFGSWFDHIK 13 0 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 ; 137.8 5.65E-05 786210000 1103060 943730 978480 989990 471140 607590 812430 980620 1225910 FALSE TRUE 957287.8262 937530.5755 1451676.201 1214782.361 461765.2358 630964.3805 733640.6636 770922.0442 1080984.316 0.885570504 0.867293411 1.342920687 1.12377427 0.427171078 0.583694297 0.678678361 0.713166725 1 20.04391416 3.257590084 24.99999699 0.679637973 1.062063738 0.486499059 0.191042761 216.6390017 284608.1388 0.057301504 0.073852909 1809.631235 -3.257590084 0.382425764 GEVQVSDKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GEVQVSDKER 10 1 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ;;;; 188.96 9.70E-07 3252990000 2902440 2574860 1695890 1850400 2424550 2294480 2814730 3133360 2065460 FALSE TRUE 2518875.2 2557945.575 2516028.076 2270561.602 2376306.199 2382750.13 2541757.918 2463315.348 1821283.672 1.383021898 1.404474006 1.381458647 1.246682017 1.304742493 1.308280619 1.395585958 1.352516023 1 20.79652421 1.237989243 24.99297014 0.999999603 1.346814888 0.832615839 0.048908536 5.848264238 255586.3835 0.074099368 0.012845684 17.29773512 -1.237989243 0.346815285 GEVRPELGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GEVRPELGSR 10 1 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 103.91 0.0025097 313400000 119320 123170 59035 72620 118040 145840 78680 90501 69544 FALSE TRUE 103551.5597 122360.8882 87584.52346 89109.48093 115691.2349 151450.5592 71049.62571 71148.06543 61322.58754 1.688636501 1.995364075 1.42825877 1.453126564 1.886600673 2.4697353 1.158620804 1.160226081 1 15.90413095 2.045473 24.99296327 1.111916805 1.798203806 0.566229948 0.294475524 93.94739569 51635.15014 0.124458959 0.083910178 111.03835 -2.045473 0.686287001 GEVWGPGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GEVWGPGYR 9 0 Q15654 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 ; 141.39 0.00024853 376830000 421230 399010 286670 319720 393520 446010 383260 435620 400900 FALSE TRUE 365563.3882 396388.877 425304.5709 392317.3126 385689.7219 463168.2933 346091.5042 342466.053 353506.0587 1.034107844 1.121307167 1.20310405 1.109789501 1.091041334 1.310213169 0.979025665 0.968769967 1 18.43137542 2.110804633 24.92154081 0.979522165 1.142640756 0.521771174 0.073218168 5.62581969 1237.617225 0.028861717 0.019458566 129.063855 -2.110804633 0.163118591 GEWIKPGAIVIDCGINYVPDDKKPNGR ddPTM_MDA-MB-175_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 ; 236.94 2.10E-45 1402290000 848710 673900 546280 592460 540670 461810 889490 1038190 584720 FALSE TRUE 736550.8231 669473.1065 810462.8352 726987.0982 529911.7248 479576.1295 803227.3967 816181.1477 515595.0677 1.42854513 1.298447461 1.57189796 1.409996223 1.02776725 0.930141034 1.55786478 1.582988665 1 18.97587894 3.444614215 24.99665932 1.270838995 1.431418181 0.151237529 0.227488214 504.7565638 388136.8323 0.073010666 0.094256953 2783.647351 -3.444614215 0.160579186 GEWKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GEWKPR 6 1 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ;;;;; 118.06 0.02024 21118650000 29163400 26718900 21548800 25151000 24375500 30431600 26163400 26628900 24570000 FALSE TRUE 25309382.8 26543381.79 31969871.76 30861918.96 23890475.24 31602323.34 23626077.49 20934516.96 21665362.59 1.168195671 1.225152899 1.475621358 1.424481997 1.102703688 1.458656564 1.090499981 0.966266633 1 24.36888705 2.058396124 5.876777859 0.993741505 1.308104824 0.567049944 0.122041121 0.133422659 9.384801243 0.05104856 0.033685654 114.392124 -2.058396124 0.314363319 GEYWECK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GEYWECK 7 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 ; 88.942 0.042427 825180000 471470 433290 311190 341720 408890 362510 437290 556530 491700 FALSE TRUE 409164.0449 430443.6895 461682.5249 419312.7489 400753.889 376455.9943 394881.6831 437520.3904 433571.7861 0.943705421 0.992785285 1.064835258 0.967112626 0.924308043 0.868266816 0.910764251 1.009107152 1 18.72591135 5.076663615 12.2876469 0.96651455 0.74414557 0.017134892 0.055612727 1669250.746 7811196.504 0.015003654 9149887.827 119306.3654 -5.076663615 -0.222368979 GFAFVEYESHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 138.25 6.15E-05 409320000 378520 353190 259710 268360 342510 389750 323940 373460 354700 FALSE TRUE 328497.623 350869.8716 385306.6247 329295.2396 335694.7211 404743.9347 292524.3487 293598.4853 312767.7701 1.050292435 1.12182234 1.231925606 1.052842624 1.073303432 1.294071747 0.935276511 0.938710805 1 18.25473233 2.201855149 24.99999116 0.953031219 1.13421231 0.537065566 0.078426425 125.1226053 85219.83563 0.031126965 0.020986433 159.1677764 -2.201855149 0.181181091 GFAFVQYVNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GFAFVQYVNER 11 0 B4DY08;G3V4W0;G3V5X6;G3V3K6;G3V251;B4DSU6;G3V4M8;P07910;G3V2Q1;G3V576;G3V555;G3V575;P07910-2;G3V4C1;B2R5W2;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ;; 244.61 1.60E-15 5396631000 1250826 1150701 964633 923393 1180508 1622349 1125383 1333434 1351167 FALSE TRUE 1085526.175 1143141.969 1431132.745 1133063.494 1157018.2 1684761.816 1016243.53 1048289.516 1191433.577 0.911109269 0.959467646 1.201185508 0.95100853 0.971114314 1.41406273 0.852958612 0.87985561 1 20.18426709 GFAFVR ddPTM_MDA-MB-175_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 ; 130.16 0.036949 3230000000 2561000 2662800 1730280 1731520 2443700 2705800 2088270 2470200 2278300 FALSE TRUE 2222557.361 2645307.891 2567049.195 2124688.081 2395075.151 2809893.877 1885749.897 1941966.953 2008961.969 1.106321272 1.316753593 1.277798801 1.057604929 1.192195366 1.398679477 0.938668788 0.966651924 1 20.93801882 2.215561484 24.99993596 0.966827063 1.222382429 0.603236129 0.098027243 155.8209433 169375.2864 0.039725231 0.026801811 164.2712205 -2.215561484 0.255555366 GFAFVTFDDHDSVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 16 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 ;;;;;;;;;;;;;;; 276.51 1.52E-33 13510041000 14832560 11425684 15649789 13778576 8640385 8094154 10524675 12793353 16358439 FALSE TRUE 12872399.62 11350627.93 23218079.31 16907212.27 8468458.243 8405541.342 9503993.638 10057594.02 14424562.98 0.892394427 0.786895793 1.609620988 1.172112618 0.587085949 0.58272416 0.658875673 0.697254678 1 23.78202427 3.243618557 24.9962464 0.694599773 1.12711352 0.415398815 0.241363625 124.6172135 615851.8944 0.072846369 0.091131147 1752.340737 -3.243618557 0.432513747 GFAFVTFDDHDSVDKIVIQK ddPTM_MDA-MB-175_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 ;;; 270.42 1.35E-44 1550764000 1792219 1613009 304299.4 643641 1533967 1231933 2028265 2359656 130840.6 FALSE TRUE 1555372.718 1602413.038 451459.6077 789789.5265 1503444.058 1279326.26 1831564.172 1855061.927 115372.7733 13.48128049 13.88900511 3.913051534 6.845545129 13.03118591 11.08863229 15.87518545 16.07885356 1 16.81594328 -1.324488511 1.31E-13 9.785983885 12.34654662 0 5.123214793 0 0.661793089 198475718.2 198475720.5 0.047370884 1.324488511 2.560562738 GFAFVTFDDHDTVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 GFAFVTFDDHDTVDK 15 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;;;;;; 303.02 1.84E-44 10179549000 7012460 5914530 4248480 5634404 5479734 4754026 6320540 7500600 8902450 FALSE TRUE 6085745.644 5875677.063 6303059.138 6913781.545 5370698.014 4936916.456 5707575.004 5896655.06 7850012.503 0.775252987 0.748492701 0.802936191 0.8807351 0.684164262 0.628905553 0.72707846 0.751165053 1 22.90426352 1.238773757 8.734138433 1.002063297 0.748571572 0.5812804 0.066720885 0.066604903 62.28451159 0.100396462 0.01765517 17.32901019 -1.238773757 -0.253491725 GFAFVTFDDHDTVDKIVVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFAFVTFDDHDTVDKIVVQK 20 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 286.28 1.99E-45 987720000 1592970 1459620 452758 732617 1167730 1013790 1367470 1768560 368653 FALSE TRUE 1382454.978 1450031.66 671713.2832 898968.8872 1144494.458 1052791.157 1234852.97 1390367.207 325071.2623 4.252775126 4.460657795 2.066357015 2.765451738 3.520749418 3.238647273 3.798714661 4.277115107 1 18.3103965 4.27642446 24.99935267 3.139885663 4.356719651 0.26626051 0.929488691 251.2367204 165873.5387 0.232491433 0.615085537 18898.37489 -4.27642446 1.216833989 GFAFVTFES(ph)PADAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFAFVTFESPADAK 14 0 P38159;H3BT71;H0Y6E7;H3BR27;P38159-3;O75526;Q8N7X1;Q96E39;A0A1B0GUK8 P38159;Q96E39 RBMX;RBMXL2;RBMXL3;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA-binding motif protein, X-linked-like-2;RNA-binding motif protein, X-linked-like-3;RNA binding motif protein, X-linked-like-1" 1 GFAFVTFES(1)PADAK;GFAFVTFES(1)PADAK 171.21 3.20E-06 92251000 324280 277570 221470 254120 280910 235800 305260 375500 368330 TRUE FALSE 281425.5764 275746.6244 328573.6328 311821.83 275320.4406 244871.3786 275655.9322 295202.2471 324786.447 0.866494212 0.849009024 1.011660541 0.960082642 0.847696827 0.753945803 0.848729788 0.90891184 1 18.30913191 1.28645775 3.247978845 1.012999001 0.878422119 0.239005942 0.068970549 0.505905211 7.429512854 0.161423729 0.019572924 19.34005701 -1.28645775 -0.134576882 GFAVLEYETAEMAEEAQQQADGLSLGGSHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GFAVLEYETAEMAEEAQQQADGLSLGGSHLR 31 0 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 0 ;;; 235.57 9.79E-46 269907000 128290 107348 69824 86941 116910 118308 102676 129041 121367 FALSE TRUE 111336.1515 106642.8239 103591.1199 106682.2829 114583.7197 122859.3853 92718.49732 101446.5863 107019.1315 1.040338768 0.996483735 0.967968236 0.996852444 1.070684448 1.14801329 0.866373105 0.947929449 1 16.7075092 2.220178848 24.999998 0.937159855 1.03150057 0.385622299 0.05843079 276.7478391 376385.9362 0.025079901 0.016945584 166.0270488 -2.220178848 0.094340715 GFAVSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFAVSER 7 0 Q96CN7;D6RGE2 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 ; 124.34 0.0096679 387090000 975540 906460 689340 717700 884740 1110390 820240 972920 950740 FALSE TRUE 846619.9173 900505.4046 1022707.13 880664.7544 867135.405 1153107.422 740693.251 764868.6293 838344.6003 1.009871021 1.07414708 1.219912586 1.050480619 1.034342447 1.375457564 0.883518843 0.912355884 1 19.67718386 GFAYVQFEDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 168.74 4.12E-05 945250000 1063834 1048762 792607 798818 1017630 1102435 944120 1114524 1185953 FALSE TRUE 923245.6415 1041872.613 1175914.396 980201.8361 997381.154 1144846.388 852559.3877 876191.7158 1045750.987 0.882854191 0.996291303 1.124468837 0.937318585 0.953746318 1.094760035 0.815260419 0.837858846 1 19.99610793 2.227526819 24.99998383 0.871802927 0.999097409 0.281247642 0.085014264 248.6621792 563404.9238 0.034144271 0.023263836 168.8600134 -2.227526819 0.127294482 GFAYVQFEDVRDAEDALHNLDR ddPTM_MDA-MB-175_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 ;;; 286.38 2.28E-46 411014000 311634 302006 105993 76056.5 245993 283704 264817 277081 13826 FALSE TRUE 270450.7773 300022.1027 157251.5693 93326.29078 241098.2206 294618.2765 239135.0881 217829.3844 12191.50603 22.18354128 24.60910916 12.89845315 7.655025601 19.77591776 24.16586398 19.61489315 17.86730728 1 13.57358873 1.238419125 5.893212347 0.309736304 18.54050807 0.540065626 5.107214779 0.118912498 15.04062968 8.745121096 1.363298342 17.31486562 -1.238419125 18.23077177 GFAYVQFEDVRDAEDALHNLDRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 82.975 0.0048488 23804000 59787 50228 9198.5 8675 32101 34083 48014 54320 2660.8 FALSE TRUE 51885.99647 49898.04896 13646.92537 10644.79134 31462.2529 35394.19506 43357.60967 42704.09072 2346.243255 22.1145 21.2672104 5.816500628 4.53695128 13.40962956 15.08547547 18.47958841 18.20104997 1 11.19613688 4.25339212 24.39899624 10 21.69087041 0.362915879 5.824792057 200.5936448 329984.4051 1.650253986 4.323793801 17922.23305 -4.25339212 11.69087041 GFCFITYTDEEPVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFCFITYTDEEPVKK 15 1 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 ; 217.93 3.22E-12 1093650000 1182280 935020 759170 776670 794070 715170 1190580 1302200 1187510 FALSE TRUE 1026038.702 928877.7921 1126307.151 953024.7942 778269.5606 742683.0527 1075117.735 1023734.664 1047123.921 0.979863684 0.887075325 1.075619732 0.910135635 0.743244945 0.709259943 1.026734003 0.977663334 1 19.99800076 GFCFLEYEDHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GFCFLEYEDHK 11 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5;O43390;O43390-3;B4DT28;O43390-2;O43390-4 O60506-2;O43390;O43390-2 SYNCRIP;HNRNPR Heterogeneous nuclear ribonucleoprotein Q;Heterogeneous nuclear ribonucleoprotein R 0 ;;;;; 220.25 9.28E-12 14114640000 10032730 7906510 5514450 6336880 7508400 6861650 8429490 10102040 8773270 FALSE TRUE 8706879.311 7854571.615 8181256.465 7775765.457 7358997.53 7125622.116 7611999.357 7941797.36 7736104.015 1.125486329 1.0153136 1.057542201 1.005126798 0.951253695 0.921086648 0.983957731 1.026588751 1 22.88317576 5.651140293 0.75895585 0.983704135 1.539637646 0.614885004 0.034649901 7.440608743 1.183504332 0.014658722 4.843415096 447857.9555 -5.651140293 0.555933511 GFCYVEFDEVDSLKEALTYDGALLGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GFCYVEFDEVDSLKEALTYDGALLGDR 27 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;; 246.31 1.58E-45 2065040000 1077683 1073094 503439 558799 824902 752786 1122109 1351360 230753 FALSE TRUE 935264.461 1066044.775 746903.7843 685682.8537 808488.0641 781746.1645 1013287.042 1062382.18 203473.6432 4.596489483 5.239227833 3.670764294 3.369885371 3.973428948 3.8420021 4.979942492 5.221227494 1 17.6344824 4.236184392 24.99909617 3.924287494 4.917858771 0.139674778 1.151583316 130.3718269 1371642.027 0.293137231 0.66046913 17225.99796 -4.236184392 0.993571277 GFDEYMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GFDEYMK 7 0 Q01469 Q01469 FABP5 "Fatty acid-binding protein, epidermal" 0 ;;; 135.87 0.0070624 799300000 2087780 2108040 1533200 1646120 1881600 1807900 2146700 2482030 2337960 FALSE TRUE 1811874.583 2094192.146 2274660.648 2019896.705 1844159.841 1877451.083 1938513.364 1951267.2 2061569.032 0.878881354 1.01582441 1.103363803 0.979786111 0.894541882 0.910690379 0.940309703 0.946496173 1 20.97531134 3.470009396 24.37002294 0.93808352 1.00776525 0.178996366 0.059972892 191.0693795 654727.9912 0.017426251 0.022551685 2951.273077 -3.470009396 0.069681729 GFDQTINLILDESHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GFDQTINLILDESHER 16 0 F2Z2Y6;C9JIZ0;C9JNV3;O95777 F2Z2Y6 LSM8 U6 snRNA-associated Sm-like protein LSm8 0 ;;; 258.2 1.07E-26 842380000 1309710 1198430 757024 851604 1067720 1127900 1011610 1217480 1012550 FALSE TRUE 1136628.505 1190557.434 1123123.338 1044973.704 1046474.461 1171291.043 913504.2179 957131.3764 892847.4925 1.273037685 1.333438739 1.257911735 1.170383199 1.172064064 1.311860147 1.023135783 1.071998728 1 19.76805424 -0.897175621 0.23246011 1.70E-10 1.353339696 0.679902766 0.06653761 30.42344683 0.76396056 13.7876627 0.296186831 0.126713935 0.897175621 1.353339696 GFEDEVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFEDEVKK 8 1 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;C9IZ80;C9JFN4;C9J188;C9JWF5 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 87.476 0.024528 330760000 1268400 837840 921930 1173600 950790 662180 1332000 1379800 1693100 FALSE TRUE 1100777.726 832336.1739 1367778.432 1440083.817 931871.1392 687654.4931 1202822.845 1084740.508 1492943.647 0.737320346 0.557513457 0.91616213 0.964593553 0.624183733 0.460603114 0.805671967 0.726578334 1 20.50972828 1.227364427 5.066619282 1.01973763 0.723817275 0.244324271 0.152340111 0.305816693 20.01629136 0.32076119 0.039627528 16.87968848 -1.227364427 -0.295920355 GFEEQWYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFEEQWYR 8 0 F8WBK6;F2Z3L6;P08236-3;P08236-2;P08236 F8WBK6 GUSB Beta-glucuronidase 0 91.069 0.0291 0 106010 108770 91247 98161 100420 120070 109940 119430 125840 FALSE TRUE 92000.5099 108055.4827 135374.3544 120449.9553 98421.83847 124689.1706 99278.03572 93890.82391 110963.3386 0.829107263 0.973794445 1.219991721 1.085493253 0.886976183 1.123697 0.89469222 0.846142745 1 16.75972357 2.203006778 24.71645651 0.898767137 1.023792524 0.149164269 0.117585391 260.2320027 180907.0934 0.048719567 0.032848199 159.5904054 -2.203006778 0.125025387 GFEGSFEELCR ddPTM_MDA-MB-175_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 ;;; 237.44 3.25E-15 855360000 1040590 853820 680840 642670 847120 1090150 758260 854300 874800 FALSE TRUE 903073.395 848211.2002 1010096.501 788598.0461 830263.9694 1132088.776 684724.0619 671614.5932 771382.1406 1.170721161 1.09959922 1.309463168 1.022318258 1.076332891 1.46761082 0.887658692 0.870663913 1 19.55708622 2.1543315 24.99999997 0.90794941 1.179388784 0.49042557 0.129957779 20.4330625 6062.239455 0.051120293 0.034465302 142.6696186 -2.1543315 0.271439374 GFEKPTENSSAVLLQWHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFEKPTENSSAVLLQWHEK 19 1 Q9BPX5 Q9BPX5 ARPC5L Actin-related protein 2/3 complex subunit 5-like protein 0 116.65 6.87E-05 511840000 541150 416360 373780 347450 348970 335540 472750 599070 508800 FALSE TRUE 469635.6564 413624.9037 554541.2582 426343.8329 342026.1797 348448.4409 426902.7778 470963.5425 448650.2436 1.046774549 0.921931749 1.236021302 0.950281069 0.762344799 0.776659427 0.951526905 1.049734284 1 18.77523167 3.497660073 24.91039604 0.916441251 1.060201421 0.285972447 0.11521776 1140.561979 1383321.948 0.034862242 0.051009988 3145.285501 -3.497660073 0.14376017 GFENVIHDKLPLQES(ph)EEEEREER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFENVIHDKLPLQESEEEEREER 23 2 P23497;P23497-2;P23497-3;P23497-4;E9PHV6;P23497-7;P23497-6;P23497-5;C9JBL0 P23497 SP100 Nuclear autoantigen Sp-100 1 GFENVIHDKLPLQES(1)EEEEREER;GFENVIHDKLPLQES(1)EEEEREER 192.87 3.73E-18 243450000 317050 267330 178020 193588 252490 242170 326280 299230 195230 TRUE FALSE 275151.0392 265573.8916 264111.0674 237545.1142 247465.943 251486.4366 294637.4158 235241.9931 172150.1318 1.598320235 1.542687704 1.53419033 1.379871811 1.437500747 1.460855324 1.71151432 1.36649325 1 17.39330776 1.307623056 3.365594273 0.960202464 1.514584159 0.763184436 0.09186071 0.133498968 2.152755963 0.172261287 0.024013661 20.30593801 -1.307623056 0.554381695 GFESPSDNSSAMLLQWHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GFESPSDNSSAMLLQWHEK 19 0 B1ALC0;O15511;O15511-2 B1ALC0 ARPC5 Actin-related protein 2/3 complex subunit 5 0 ;;; 334.03 2.25E-75 2442300000 2819410 2366780 1668610 2166790 2346950 2211640 2620250 3084030 2865170 FALSE TRUE 2446817.825 2351232.466 2475555.377 2658792.787 2300250.287 2296723.222 2366138.558 2424534.184 2526452.867 0.968479506 0.930645688 0.97985417 1.05238171 0.910466337 0.909070283 0.936545696 0.959659377 1 21.26868183 GFFDPNTEENLTYLQLMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFFDPNTEENLTYLQLMER 19 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 162.87 6.23E-11 131528000 31211 28075 11468.8 23382.5 21683.9 28096 22267 26666 23360 FALSE TRUE 27086.38727 27890.57348 17015.15004 28691.854 21252.43281 29176.8713 20107.54977 20963.68342 20598.40741 1.314974829 1.354016013 0.826042019 1.392916133 1.031751261 1.416462483 0.976170117 1.017733216 1 14.33024518 2.19200832 24.99999358 1.001176927 1.209692032 0.257658511 0.178882403 172.1503855 92448.71377 0.068479033 0.04616871 155.5995439 -2.19200832 0.208515105 GFFDPNTHENLTYLQLLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GFFDPNTHENLTYLQLLER 19 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 Q15149-3;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 PLEC;EPPK1 Plectin;Epiplakin 0 ;;; 271.72 2.48E-39 4268850000 3746970 3640490 2698790 2703530 3493450 3827320 3238320 3793210 3588150 FALSE TRUE 3251798.421 3616575.381 4003933.871 3317407.807 3423937.18 3974559.477 2924268.225 2982061.56 3163962.995 1.027761205 1.143052364 1.265480626 1.048497664 1.082167265 1.256196575 0.924242233 0.942508356 1 21.5933013 2.219591019 24.99563985 0.95155358 1.136757511 0.53757304 0.079372453 178.6477824 235396.7694 0.031892561 0.021540779 165.8024788 -2.219591019 0.185203931 GFFDPNTHENLTYLQLLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFFDPNTHENLTYLQLLQR 19 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 253.71 6.97E-31 770280000 776600 808780 580320 626150 744940 855680 709700 916080 760420 FALSE TRUE 673970.3423 803467.0709 860964.6931 768326.9276 730117.1515 888598.5633 640873.4032 720183.4209 670524.0139 1.005139754 1.198267406 1.284017687 1.145860419 1.088875471 1.325230036 0.955779942 1.074060594 1 19.35492948 2.217192175 24.99999034 1.021046917 1.175417934 0.403313597 0.094063137 244.9730034 286603.7963 0.037039437 0.024997997 164.8891863 -2.217192175 0.154371017 GFFDPNTHENLTYR ddPTM_MDA-MB-175_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 ;;; 139.77 1.01E-05 2315100000 4737280 4587470 3283620 3215560 4293880 4960700 3948200 4573670 4640910 FALSE TRUE 4111236.445 4557334.608 4871589.615 3945702.045 4208440.189 5151541.339 3565304.172 3595626.263 4092266.907 1.00463546 1.113645496 1.190437898 0.964184921 1.028388491 1.258847836 0.871229627 0.878639235 1 21.96446881 2.206389654 24.99999904 0.906818167 1.089867265 0.447058423 0.092386863 167.9749091 130531.8331 0.037109072 0.025021198 160.8383666 -2.206389654 0.183049098 GFFDPNTHENLTYVQLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GFFDPNTHENLTYVQLLR 18 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 270.96 6.05E-39 3250227000 4273255 4390247 3290125 3377427 3976736 4621764 3856244 4289473 4347500 FALSE TRUE 3708533.525 4361407.178 4881240.455 4144323.421 3897606.734 4799566.252 3482266.05 3372202.58 3833543.503 0.967390489 1.137696018 1.273297264 1.081068577 1.016711231 1.251992119 0.908367428 0.879656792 1 21.87024712 2.215143127 24.93682307 0.918116397 1.122420008 0.46328529 0.097173278 185.6335909 197675.9917 0.039144253 0.026408418 164.1130537 -2.215143127 0.204303612 GFFNIYHPLDPVAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFFNIYHPLDPVAYR 15 0 Q9Y6Y8;Q9Y6Y8-2 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 ; 105.46 0.0013133 1376430000 1806220 1941990 1381350 1364110 1904380 2008030 1824730 2094380 1867240 FALSE TRUE 1567523.451 1929232.94 2049375.48 1673852.025 1866486.564 2085280.213 1647767.965 1646513.135 1646497.014 0.952035404 1.171719671 1.244688246 1.016614066 1.133610658 1.266494986 1.000771912 1.000009791 1 20.65096847 2.091330735 24.99940377 1.000114999 1.132893474 0.303886654 0.093146235 20.89548536 5711.131719 0.037159056 0.025052629 123.4044258 -2.091330735 0.132778475 GFGDGYNGYGGGPGGGNFGGS(ph)PGYGGGR ddPTM_MDA-MB-175_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 264.09 4.29E-54 1778200000 1176040 1207060 849678 824027 1131850 1222130 1099990 1374120 1253490 TRUE FALSE 1020623.334 1199130.743 1260585.123 1011134.925 1109328.399 1269146.132 993313.1391 1080275.131 1105303.84 0.923387124 1.084887883 1.140487418 0.914802689 1.003641134 1.148232808 0.898678809 0.977355811 1 20.07601158 2.210304811 24.99998739 0.960069453 1.035915429 0.165807493 0.081638413 395.2525614 349706.1781 0.032891234 0.022180282 162.2948771 -2.210304811 0.075845976 GFGDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GFGDLK 6 0 P24534;C9JZW3;F2Z2G2;F8WF65;F8WFC9 P24534 EEF1B2 Elongation factor 1-beta 0 ;; 116.35 0.055015 1016090000 3169690 2756930 1885140 2291400 2441750 2321910 2966410 3439360 3161400 FALSE TRUE 2750807.436 2738819.545 2796800.009 2811697.392 2393163.952 2411235.38 2678728.015 2703879.629 2787662.893 0.986779084 0.982478747 1.003277698 1.008621738 0.858483986 0.864966631 0.960922506 0.96994498 1 21.41062468 GFGDSFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GFGDSFGR 8 0 A0A0A0MQW0;A0A0A0MR39;A0A087WUT0;H0YN19;A0A0C4DGV1 A0A0A0MQW0 MYEF2 0 ;;;; 194.25 0.00038703 1396278000 3129980 2920110 2013590 2133540 2781620 3113150 2674700 2983860 2820580 FALSE TRUE 2716345.213 2900927.605 2987368.859 2617992.866 2726271.204 3232914.895 2415308.006 2345784.759 2487134.246 1.092158663 1.166373552 1.201128915 1.052614217 1.096149598 1.299855406 0.971120883 0.94316773 1 21.24605295 2.132025226 11.19133186 0.964538403 1.14726173 0.600870128 0.069025831 0.245019404 24.11007947 0.027569897 0.018585409 135.5268132 -2.132025226 0.182723327 GFGEYSRS(ph)PTF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFGEYSRSPTF 11 1 D6REL5;Q6UWZ7-2;Q6UWZ7 D6REL5 FAM175A BRCA1-A complex subunit Abraxas 1 GFGEYS(0.001)RS(0.999)PTF;GFGEYS(0.001)RS(0.999)PTF 120.55 0.001149 296140000 804710 589600 238230 250680 526890 581360 564830 553910 83650 TRUE FALSE 698365.5346 585726.8788 353438.8248 307600.7254 516405.9198 603725.2954 510052.8735 435460.657 73760.99229 9.467952001 7.940875801 4.791676655 4.170235728 7.001070671 8.184885759 6.914940508 5.903671351 1 16.17057044 4.418751601 4.236776528 5.664353071 9.186842775 0.332790577 1.963674159 0.245160643 8.776286884 0.509621384 1.594048086 26227.18024 -4.418751601 3.522489704 GFGFGQGAGALVHS(ph)E ddPTM_MDA-MB-175_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 230.55 3.28E-13 12366340000 6166510 7160440 4546680 5065930 6763410 6565860 6242800 7662030 6390160 TRUE FALSE 5351590.08 7113402.598 6745469.656 6216226.834 6628831.373 6818452.883 5637374.217 6023564.51 5634722.564 0.949752187 1.262422864 1.197125427 1.10320016 1.176425511 1.210077835 1.000470591 1.069008179 1 22.42591315 2.23218121 24.99922833 1.03176599 1.156190271 0.327066105 0.085032349 171.0122345 670144.5427 0.032207557 0.022300974 170.6794405 -2.23218121 0.124424281 GFGFGQGAGALVHSE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFGFGQGAGALVHSE 15 0 P21291;E9PP21 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ; 149.94 7.60E-06 159608000 306410 320140 211718 225543 315490 313850 285540 315050 291320 FALSE TRUE 265917.1422 318036.9793 314105.533 276755.9854 309212.3662 325924.0126 257848.3747 247679.0092 256880.4815 1.035178464 1.238073743 1.222769169 1.077372573 1.203720752 1.268776867 1.003767874 0.964179948 1 17.97073775 2.143646732 7.082951314 0.981620852 1.176004317 0.599520005 0.071336166 0.140107421 8.964775136 0.028484862 0.019153962 139.2024028 -2.143646732 0.194383465 GFGFILFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFGFILFK 8 0 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ; 168.43 0.00071391 126110000 729200 646750 456590 552120 583760 513920 730080 842170 726140 FALSE TRUE 632834.3724 642501.4567 677398.4512 677487.2846 572144.3181 533690.835 659276.954 662078.4993 640296.5564 0.988345738 1.003443561 1.057944861 1.058083599 0.893561448 0.833505709 1.029643135 1.034018523 1 19.28838073 5.177672921 10.41401045 0.991029105 0.799291307 0 0.07215825 7835369.375 4312962.907 0.019156196 35189669.02 150547.2828 -5.177672921 -0.191737797 GFGFITFTNPEHASVAMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFGFITFTNPEHASVAMR 18 0 P98179 P98179 RBM3 RNA-binding protein 3 0 137.44 3.15E-06 1063400000 426450 624800 195350 273610 567840 715740 370390 530630 395240 FALSE TRUE 370093.552 620695.6477 289821.9134 335737.3324 556541.095 743274.9809 334469.6348 417158.9039 348515.1775 1.061915165 1.780971641 0.831590508 0.963336331 1.596891989 2.132690422 0.959698907 1.196960508 1 18.41086196 3.242154754 24.99992027 1.361168261 1.18042885 0.063368665 0.410001508 380.6514679 2647698.429 0.126176426 0.156492666 1746.444361 -3.242154754 -0.18073941 GFGFVDFNSEEDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GFGFVDFNSEEDAK 14 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;; 293.94 3.43E-43 789940000 1261562 936724 662994 785701 866182 762212 1069666 1205534 1020444 FALSE TRUE 1094843.385 930570.5984 983620.116 964106.4207 848946.6729 791534.7889 965929.956 947739.9356 899808.2728 1.216751855 1.034187645 1.093144113 1.071457609 0.94347507 0.879670495 1.073484191 1.053268751 1 19.77925811 8 0.786139301 1.007859802 46.61078102 0.504300675 0.063411141 452.5784718 1.670131729 0.024519198 36703.01827 100000000 -8 45.60292122 GFGFVEFEDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFGFVEFEDPR 11 0 Q13243;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ; 117.89 0.0018472 607371000 492840 420880 345480 396830 423950 426260 368430 459840 644520 FALSE TRUE 427709.9453 418115.2116 512555.2836 486936.3167 415514.2244 442658.498 332699.7153 361506.7945 568325.5798 0.752579086 0.735696626 0.901869108 0.856791132 0.731120047 0.778881883 0.58540338 0.636091014 1 19.11635813 3.140638901 6.895867311 0.721144768 0.812489715 0.048316124 0.118430085 0.501638704 30.41267527 0.036793355 0.041895481 1382.416475 -3.140638901 0.091344948 GFGFVEFEDPRDADDAVYELDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFGFVEFEDPRDADDAVYELDGK 23 1 Q13243;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 118.35 0.00026595 272320000 661470 584280 258740 250340 472810 407320 601200 636040 90853 FALSE TRUE 574055.0635 580441.8262 383867.5294 307183.5232 463402.006 422989.864 542895.7165 500027.7957 80112.46184 7.165615066 7.245337528 4.791608204 3.834403739 5.784393531 5.279950887 6.776669997 6.241573211 1 16.28973906 4.242349166 24.99999388 5.064052949 7.205477275 0.268821886 1.598300569 137.2476426 905637.7501 0.401059529 0.980234749 17472.26332 -4.242349166 2.141424326 GFGFVLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFGFVLFK 8 0 Q14103-3;Q14103;H0Y8G5;H0YA96;D6RAF8;D6RF44;Q14103-2;Q14103-4;D6RBQ9;A0A087WUK2;O14979;O14979-2;O14979-3 Q14103-3;Q14103-2;A0A087WUK2;O14979-2 HNRNPD;HNRNPDL Heterogeneous nuclear ribonucleoprotein D0;Heterogeneous nuclear ribonucleoprotein D-like 0 135.36 0.0019477 236890000 171850 187580 121020 135450 153210 136870 157790 208880 179020 FALSE TRUE 149139.5871 186347.7746 179545.6768 166205.9927 150161.4208 142135.4775 142487.5501 164212.6375 157856.4595 0.944779754 1.18048875 1.137398351 1.052893199 0.951252937 0.900409637 0.902639971 1.040265555 1 17.26825377 3.372555488 4.033640478 0.962139867 1.096762234 0.408215281 0.072232143 0.217515593 6.530352704 0.021782213 0.028655019 2358.063457 -3.372555488 0.134622367 GFGFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFGFVR 6 0 Q13148;A0A087WYY0;A0A087X260;G3V162;B1AKP7;K7EN94;A0A0A0N0M3;A0A087WXQ5;Q13148-4;A0A087WV68;A0A087WXV3;K7EJM5;A0A087WX29;Q5JQF3;Q96DU9-2;Q96DU9 Q13148 TARDBP;TDP43;PABPC5 TAR DNA-binding protein 43;Polyadenylate-binding protein 5 0 118.11 0.051516 731380000 1567300 1543400 1031200 1099500 1491600 1624300 1263600 1548800 1547500 FALSE TRUE 1360177.334 1533261.304 1529891.769 1349158.28 1461920.078 1686787.872 1141056.266 1217601.173 1364556.313 0.996790914 1.123633586 1.12116426 0.988715722 1.071351958 1.236143834 0.836210463 0.892305551 1 20.3800005 2.221875068 24.99999973 0.90286808 1.087193951 0.532695495 0.079427845 179.6652084 269190.8108 0.031889145 0.021564328 166.6767671 -2.221875068 0.184325871 GFGFVSFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GFGFVSFER 9 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YAP2 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ;;;;; 141.52 0.00024782 4167613000 1801633 1913240 1300538 1333770 1705197 1985762 1683791 1914406 1684811 FALSE TRUE 1563542.634 1900671.8 1929482.527 1636622.864 1671266.916 2062155.549 1520497.208 1505025.175 1485634.563 1.052440939 1.279366978 1.298759853 1.101632195 1.124951558 1.388063795 1.023466501 1.013052074 1 20.50264785 2.074499309 15.51839437 1.010698372 1.206374891 0.464167535 0.099045541 1.457706555 302.0582386 0.039295444 0.026492871 118.7132812 -2.074499309 0.195676519 GFGFVTFDDHDPVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 GFGFVTFDDHDPVDK 15 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;; 240.46 7.67E-18 56474818000 60819240 42448340 34955280 39580120 40374330 36154500 48259630 58772580 59888150 FALSE TRUE 52781823.34 42169494.06 51859770.33 48567391.19 39570959.82 37545387.01 43579418.51 46204521.14 52808241.13 0.999499741 0.798540022 0.982039341 0.919693407 0.749333039 0.710975905 0.82523897 0.874949064 1 25.65425976 4.753995117 23.41441583 0.855299441 0.9995 0.186838799 0.092926121 2220.173576 3367905.377 0.023764971 0.516233346 56753.82249 -4.753995117 0.144200559 GFGFVTFDDHDPVDKIVLQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFGFVTFDDHDPVDKIVLQK 20 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ; 268.23 3.11E-37 2044190000 4366800 2938300 1064400 1086530 2462900 1923680 3798900 4140700 90825 FALSE TRUE 3789716.316 2918998.114 1579147.4 1333243.243 2413893.109 1997685.214 3430483.263 3255243.528 80087.77197 47.31953734 36.44748808 19.71770923 16.64727599 30.14059512 24.94369821 42.83404543 40.64594941 1 16.28929436 7.999999996 0.062176096 10 70.5856043 0.090831896 13.32782157 3534.552568 21.26269536 5051.983149 20918.78534 99999999.04 -7.999999996 60.5856043 GFGFVTFENIDDAKDAMMAMNGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFGFVTFENIDDAKDAMMAMNGK 23 1 Q14011;K7EMY9;K7EPM4;K7EQR7;D6W5Y5;Q14011-2;K7EJV1;K7ENX8;K7ELV6;K7EJV5;K7ELT6;K7ER40 Q14011 CIRBP Cold-inducible RNA-binding protein 0 ; 256.11 1.31E-43 744330000 1008710 682770 507960 561040 611930 437940 776990 949130 311220 FALSE TRUE 875406.4178 678284.8389 753611.155 688432.707 599753.7902 454787.8352 701637.6294 746165.9356 274427.9261 3.18993198 2.471631982 2.746116861 2.508610245 2.185469236 1.657221412 2.556728243 2.718986898 1 18.06606777 8 0.271280856 1.958657365 9.990144784 0.370018151 0.488509939 111.7644474 1.790741382 1.313328557 410.8253838 100000000 -8 8.031487419 GFGFVTFSSMAEVDAAMAARPHS(ph)IDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GFGFVTFSSMAEVDAAMAARPHSIDGR 27 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 GFGFVTFSSMAEVDAAMAARPHS(0.999)IDGR;GFGFVTFSSMAEVDAAMAARPHS(0.999)IDGR;GFGFVTFSSMAEVDAAMAARPHS(1)IDGR;GFGFVTFSSMAEVDAAMAARPHS(1)IDGR;GFGFVTFSSMAEVDAAMAARPHS(1)IDGR 163.72 6.73E-12 206086000 136290.6 151917.9 86843.9 80567.7 128347.3 127617.1 133460.1 158199.2 85427.3 TRUE FALSE 118279.4519 150919.9413 128841.9005 98861.82769 125793.4398 132526.6124 120517.16 124369.5322 75328.18191 1.570188592 2.003499055 1.710407675 1.312414891 1.669938616 1.759323125 1.599894714 1.651035894 1 16.20090209 1.236907613 6.478297928 0.980582269 1.66264578 0.595166406 0.170963032 0.090418379 17.45498386 0.270532769 0.042939166 17.25470795 -1.236907613 0.682063511 GFGFVTFSSMAEVDAAMAARPHSIDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GFGFVTFSSMAEVDAAMAARPHSIDGR 27 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;; 263.18 2.12E-53 2122223000 694443 625967 261350.8 330008.5 550912 570247 563679 632644 178789 FALSE TRUE 602670.5981 621854.9816 387740.921 404941.9738 539949.929 592184.7711 509013.4973 497358.0038 157652.7681 3.822772066 3.944459644 2.459461548 2.568568752 3.424931484 3.756259901 3.228700032 3.154768609 1 17.26639098 4.25290576 24.85817789 2.90206439 3.883616626 0.255867887 0.753212416 336.4895931 583079.4789 0.188336716 0.493194296 17902.17341 -4.25290576 0.981552237 GFGFVTYATVEEVDAAMNAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 247.58 8.85E-30 143184000 136803 133236 109174 110163 135507 131294 127532 150326 193483 FALSE TRUE 118724.1369 132360.7639 161970.9116 135177.1929 132810.6758 136344.9651 115163.9663 118179.9547 170609.6602 0.69588168 0.775810489 0.949365419 0.792318517 0.778447573 0.799163219 0.675014335 0.692692047 1 17.38033981 2.439210664 24.98832273 0.760466724 0.803529019 0 0.107316243 704.7142646 464500.2004 0.040207825 0.031144896 274.9227404 -2.439210664 0.043062295 GFGFVTYATVEEVDAAMNARPHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 289.14 1.08E-61 5564873000 4655245 4337992 2211484 2481986 3907291 3420015 4508410 5185965 1285254 FALSE TRUE 4040042.578 4309495.445 3280965.059 3045558.856 3829543.554 3551585.19 4071185.092 4076986.742 1133312.736 3.564808238 3.802565088 2.895021784 2.687306653 3.379070429 3.133808592 3.592287426 3.597406622 1 20.1121146 4.238649102 24.99999998 3.01560132 3.68368682 0.146517271 0.747616734 4.779707322 1348376.679 0.185336875 0.431180592 17324.03696 -4.238649102 0.6680855 GFGFVTYSCVEEVDAAMCARPHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GFGFVTYSCVEEVDAAMCARPHK 23 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 261.28 5.50E-44 1313666000 1832450 1824280 769735 772241 1383500 1345630 1792270 2051710 218130 FALSE TRUE 1590287.09 1812296.185 1141981.421 947590.122 1355971.057 1397397.257 1618455.931 1612967.783 192342.9199 8.267978309 9.422214166 5.937215787 4.926566169 7.049758096 7.265134883 8.414429458 8.385896314 1 17.5533212 4.238225039 24.99999625 6.491601554 8.845096664 0.201131636 2.154478934 15.05921315 1122294.47 0.546242962 1.264110606 17307.12932 -4.238225039 2.353495111 GFGFVYFQNHDAADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFGFVYFQNHDAADK 15 0 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ; 225.09 1.05E-12 3450200000 3949300 2950300 2474000 2529500 2680100 2504900 3392200 3928800 3654800 FALSE TRUE 3427389.999 2930919.285 3670434.675 3103861.636 2626771.254 2601265.124 3063224.966 3088656.694 3222733.708 1.063503941 0.909451277 1.138919628 0.963114523 0.815075489 0.80716105 0.950505144 0.958396496 1 21.61985355 3.480561846 24.96740261 0.909114293 1.028925836 0.35091557 0.081109227 170.5920277 1237943.948 0.023986256 0.031635116 3023.861156 -3.480561846 0.119811543 GFGGIGGILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFGGIGGILR 10 0 B7Z7P8;P62495-2;P62495 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 ; 83.614 0.039422 120340000 196123 246050 194591 159407 233800 254590 191440 221598 260080 FALSE TRUE 170204.8486 244433.6813 288695.8585 195602.7957 229147.8374 264384.242 172874.1783 174210.9922 229333.6387 0.742171317 1.065843122 1.258846544 0.852918032 0.999189821 1.15283673 0.75381082 0.759639943 1 17.80708846 2.225692956 24.99964814 0.818029776 1.01782793 0.210143382 0.157338533 310.6785455 603589.9938 0.063079362 0.042835146 168.1484841 -2.225692956 0.199798154 GFGQEVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFGQEVHR 8 0 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 0 105.57 0.0043629 87630000 135570 129380 91508 98367 137300 136660 106430 124980 126840 FALSE TRUE 117654.081 128530.0943 135761.5749 120702.7308 134567.9986 141917.3986 96108.43498 98253.9996 111845.1197 1.051937548 1.149179281 1.213835483 1.079195329 1.203163795 1.268874306 0.859299317 0.878482672 1 16.77114278 2.229778074 24.99998657 0.903266809 1.161087782 0.724515369 0.072139823 92.77325641 264081.5942 0.029087392 0.01994353 169.7376065 -2.229778074 0.257820973 GFGS(ph)EEGSR ddPTM_MDA-MB-175_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 214.81 6.95E-07 4390890000 4982010 4424980 2950550 3457720 4306200 4499480 4084230 4665160 4615890 TRUE FALSE 4323624.756 4395912.015 4377445.849 4242848.174 4220515.045 4672577.907 3688142.003 3667551.838 4070204.743 1.062262227 1.080022331 1.075485418 1.0424164 1.03692942 1.14799579 0.906131813 0.901073059 1 21.95666994 2.224457746 24.99999725 0.927280224 1.071372199 0.724301238 0.040128841 111.524001 197695.6818 0.01591935 0.010791451 167.6709197 -2.224457746 0.144091976 GFGS(ph)FR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFGSFR 6 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 1 GFGS(1)FR 71.715 0.091786 141280000 332190 295310 175210 221140 250290 252540 256560 254780 335780 TRUE FALSE 288290.2498 293370.0892 259942.142 271353.2169 245309.7187 262255.3772 231678.8507 200297.2797 296084.4709 0.973675684 0.990832408 0.877932373 0.916472303 0.828512613 0.885745127 0.782475521 0.676486947 1 18.1756493 3.665455354 0.714155264 0.797009381 1.002182177 0.272908278 0.085454058 1.087160742 1.091092331 0.051678861 0.152746612 4628.66078 -3.665455354 0.205172797 GFGS(ph)VEELCTNSSLGMEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFGSVEELCTNSSLGMEK 18 0 Q2NKX8;B5MDQ0 Q2NKX8 ERCC6L DNA excision repair protein ERCC-6-like 1 GFGS(1)VEELCTNSSLGMEK 187.75 4.34E-14 72087000 110840 99984 55970 75555 102880 87075 105780 125260 96459 TRUE FALSE 96192.21317 99327.19852 83037.27921 92710.91754 100832.8893 90424.8316 95521.47188 98474.12377 85055.72691 1.130931645 1.167789661 0.976269115 1.09000206 1.185492064 1.063124552 1.123045741 1.157760063 1 16.37612076 3.431767034 24.99995771 1.113902455 1.088251877 0.002799588 0.069420048 570.920694 314698.6695 0.019763629 0.025514762 2702.508283 -3.431767034 -0.025650578 GFGSDKEAILDIITSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFGSDKEAILDIITSR 16 1 E5RK69;P08133;P08133-2;E7EMC6;E5RFF0;E5RJF5;E5RK63;E5RIU8;E5RJR0;E5RI05 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 100.11 0.0019747 200840000 223060 184620 116310 198890 220910 244050 129760 264180 124550 FALSE TRUE 193582.0558 183407.2191 172557.905 244051.0143 216514.3232 253438.7614 117175.8952 207687.1629 109825.8409 1.762627577 1.669982379 1.571195846 2.222163858 1.97143333 2.307642349 1.066924635 1.891059164 1 16.74485802 1.234531555 24.94532121 0.999998806 1.799015055 0.348833725 0.346696858 138.4572661 857112.7966 0.621590578 0.083453004 17.16056393 -1.234531555 0.799016249 GFGSEEGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFGSEEGSR 9 0 Q9Y5S9 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ; 217.81 1.29E-06 1903680000 2313900 2147460 1418480 1555410 1989870 2165200 1864950 2103190 2016650 FALSE TRUE 2008112.252 2133353.194 2104461.673 1908589.613 1950275.48 2248496.645 1684087.436 1653439.186 1778243.934 1.129267033 1.199696595 1.183449375 1.073300224 1.096742377 1.264447808 0.947050854 0.929815732 1 20.76202181 2.218568375 24.9999576 0.952388599 1.154268122 0.735633517 0.056124678 117.1053444 146437.1294 0.022873596 0.015443409 165.4125188 -2.218568375 0.201879522 GFGSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GFGSFR 6 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;; 112.27 0.06314 2764450000 3882510 3008100 1986220 2102090 2716610 2866080 2809050 3113360 2540650 FALSE TRUE 3369426.466 2988339.593 2946762.636 2579401.663 2662554.776 2976339.952 2536628.763 2447592.192 2240297.251 1.50400866 1.333903165 1.315344486 1.151365812 1.188482812 1.328546893 1.132273301 1.092530105 1 21.09525874 8 0.150514032 0.900485376 2.964255959 0.748892468 0.073203779 82.38224007 1.040437887 1.283032987 36.30334786 100000000 -8 2.063770583 GFGSSAPEGLEPDS(ph)MASAASALHLLSPRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GFGSSAPEGLEPDSMASAASALHLLSPRPR 30 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDS(0.25)MAS(0.25)AAS(0.25)ALHLLS(0.25)PRPR;GFGSSAPEGLEPDS(0.25)MAS(0.25)AAS(0.25)ALHLLS(0.25)PRPR;GFGSSAPEGLEPDS(0.25)MAS(0.25)AAS(0.25)ALHLLS(0.25)PRPR 99.866 0.00064764 1785070000 363059 391142 278323 322248 470391 604200 400569 501364 333779 TRUE FALSE 315079.8333 388572.5624 412920.9337 395419.3337 461031.1394 627443.965 361721.88 394151.2102 294320.0269 1.070534807 1.320238268 1.402965806 1.343501283 1.566428028 2.131842578 1.229008722 1.339192628 1 18.16702619 1.292114611 1.850415585 0.891039186 1.458339643 0.194523481 0.27904801 1.353676805 4.903392273 1.313878483 0.080420161 19.59361684 -1.292114611 0.567300457 GFGSSAPEGLEPDSMAS(ph)AASALHLLSPRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GFGSSAPEGLEPDSMASAASALHLLSPRPR 30 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDS(0.003)MAS(0.332)AAS(0.332)ALHLLS(0.332)PRPR;GFGSSAPEGLEPDS(0.001)MAS(0.368)AAS(0.368)ALHLLS(0.263)PRPR;GFGSSAPEGLEPDS(0.007)MAS(0.331)AAS(0.331)ALHLLS(0.331)PRPR;GFGSSAPEGLEPDS(0.046)MAS(0.318)AAS(0.318)ALHLLS(0.318)PRPR 144.4 2.58E-08 1532072000 487851 535758 351078 400228 689649 784665 535769 665676 521036 TRUE FALSE 423380.2543 532238.5704 520860.4951 491105.8845 675926.3342 814851.5703 483810.2048 523326.3677 459439.7176 0.921514266 1.15845137 1.13368626 1.068923442 1.471197 1.773576683 1.053043928 1.13905339 1 18.80951605 4.88417233 1.009772986 1.251957408 0.702348413 0.164763619 0.229589785 5.207316831 3.552723649 0.079624083 3.31618225 76590.04593 -4.88417233 -0.549608995 GFGSSAPEGLEPDSMASAAS(ph)ALHLLSPRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFGSSAPEGLEPDSMASAASALHLLSPRPR 30 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDS(0.003)MAS(0.153)AAS(0.514)ALHLLS(0.33)PRPR;GFGSSAPEGLEPDS(0.002)MAS(0.073)AAS(0.462)ALHLLS(0.462)PRPR 144.4 5.38E-08 233419000 128355 145784 96623 121567 181298 219323 153276 188741 137763 TRUE FALSE 111392.5615 144826.3353 143350.206 149170.6454 177690.5245 227760.4977 138411.3171 148380.2059 121476.8151 0.916986188 1.1922138 1.180062269 1.227976263 1.462752579 1.874929776 1.139405219 1.221469347 1 16.89032146 4.845552631 1.090625554 1.322367351 0.668535057 0.223071144 0.233359505 3.596598276 3.046060626 0.076916785 2.864452725 70073.30978 -4.845552631 -0.653832295 GFGSSAPEGLEPDSMASAASALHLLS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 GFGSSAPEGLEPDSMASAASALHLLSPR 28 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR 263.36 4.79E-54 4612268000 1607509 1722065 1270727 1616405 2188487 2638395 1762537 2213076 3097805 TRUE FALSE 1395072.613 1710752.642 1885254.828 1983434.46 2144940.39 2739895.763 1591606.433 1739826.92 2731586.022 0.510718902 0.626285472 0.690168573 0.726110928 0.78523626 1.003042094 0.582667513 0.636929207 1 21.38130743 4.459723138 1.149269873 0.771103797 0.460062387 0.330181234 0.134011299 1.440680736 2.260610393 0.043791622 0.483286384 28821.93522 -4.459723138 -0.31104141 GFGSSAPEGLEPDSMASAASALHLLS(ph)PRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFGSSAPEGLEPDSMASAASALHLLSPRPR 30 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDSMASAAS(0.002)ALHLLS(0.998)PRPR 118.74 8.61E-05 232850000 124070 141050 96118 110560 184900 217220 140360 176940 133670 TRUE FALSE 107673.8351 140123.4333 142600.9863 135664.3378 181220.8518 225576.594 126747.9088 139102.7579 117867.6849 0.913514465 1.188819764 1.209839545 1.150988398 1.537493944 1.913812036 1.075340616 1.180160263 1 16.84680871 4.966893074 1.116255239 1.309763567 0.56630256 0.182587446 0.260794003 5.088309053 3.787406792 0.0851758 5.001370559 92660.16599 -4.966893074 -0.743461008 GFHLDVEDYLSGVLILASELSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GFHLDVEDYLSGVLILASELSR 22 0 E9PGT1;Q15631;H7C1D4 E9PGT1 TSN Translin 0 ;;; 235.7 1.80E-30 1726521000 786872 830068 627402 691420.5 661336 700499 760593 883746 729616 FALSE TRUE 682884.8715 824615.2287 930815.7057 848418.0922 648176.7075 727447.6498 686830.8079 694763.7952 643361.6277 1.061432392 1.281728958 1.44680016 1.318726601 1.007484251 1.130697913 1.067565702 1.079896228 1 19.29527037 3.242880189 24.98790061 1.064435958 1.289613852 0.543253364 0.099843783 84.49958129 488810.4313 0.029722942 0.037030329 1749.364017 -3.242880189 0.225177894 GFHQVPFAPIVFIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFHQVPFAPIVFIER 15 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A0U1RQX5;A0A0U1RRC8 P47897 QARS Glutamine--tRNA ligase 0 ; 69.431 0.049679 1061090000 1378430 1506290 961260 960400 1254450 1500370 1117540 1349790 1072100 FALSE TRUE 1196266.983 1496395.082 1426128.551 1178473.499 1229488.899 1558090.205 1009161.143 1061147.913 945357.5593 1.265412194 1.582887942 1.508559949 1.246590232 1.300554364 1.648149094 1.067491483 1.12248313 1 19.85050057 2.212934885 24.95382646 1.07582285 1.422502436 0.616802053 0.134385584 147.3624927 143497.5319 0.054270345 0.036603662 163.280712 -2.212934885 0.346679586 GFIYVHKPPVHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFIYVHKPPVHIR 13 1 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 0 135.99 5.01E-05 589430000 122420 91187 62093 74452 78316 80316 89205 104340 103050 FALSE TRUE 106241.8868 90587.98659 92121.38249 91357.46453 76757.66482 83405.80849 80553.91283 82027.70297 90867.54639 1.169195065 0.996923436 1.013798503 1.005391563 0.844720342 0.917883357 0.886498162 0.902717265 1 16.4714775 7.026501166 0.575028891 0.910695781 4.797447092 0.698058348 0.049953588 26.15008199 0.728528629 0.025066391 114.5963789 10629214.36 -7.026501166 3.88675131 GFKDQIYDIFQK ddPTM_MDA-MB-175_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 ; 189.24 7.45E-06 6376900000 9071900 6814400 4650700 5234100 6358400 5120600 8439600 9427500 3990800 FALSE TRUE 7873025.43 6769635.758 6899794.076 6422582.403 6231880.28 5317592.795 7621128.891 7411502.49 3519012.17 2.237282808 1.92373184 1.960719015 1.82510946 1.770917513 1.511103838 2.165701203 2.106131531 1 21.74673907 7.999998035 0.606398128 1.778723512 31.29826226 0.192127115 0.324723664 371.767156 2.856263274 0.152268424 14557.81597 99999547.64 -7.999998035 29.51953875 GFKDQIYEIFQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFKDQIYEIFQK 12 1 Q14240;Q14240-2;E7EQG2 Q14240 EIF4A2 "Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ; 119.01 0.00021041 381660000 1706830 1296030 875790 1000310 1082860 943870 1670980 1795030 933900 FALSE TRUE 1481268.091 1287516.294 1299324.973 1227445.674 1061313.205 980181.2897 1508928.617 1411176.803 823495.4059 1.798756958 1.563477203 1.577816906 1.490531296 1.288790681 1.190269287 1.832346126 1.713642594 1 19.65140108 4.954497544 1.150051945 1.466594827 2.080232909 0.182470322 0.242212582 5.238742787 4.221073842 0.076391881 4.340862447 90052.86693 -4.954497544 0.613638082 GFLSDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFLSDLR 7 0 Q9GZT8-2;Q9GZT8 Q9GZT8-2 NIF3L1 NIF3-like protein 1 0 98.415 0.026241 57174000 169290 176900 123600 131140 184150 192260 156450 176500 189540 FALSE TRUE 146917.8976 175737.9323 183373.3734 160917.3413 180485.7753 199656.3666 141277.5031 138756.8485 167132.7971 0.879048877 1.051486813 1.09717169 0.962811274 1.079894422 1.194597171 0.845300896 0.830219149 1 17.35063534 2.20819826 24.99758588 0.877063101 1.04483622 0.366819099 0.093672561 195.634358 161066.0813 0.037855764 0.025525764 161.5095698 -2.20819826 0.167773119 GFNGCDS(ph)PEPDGEDSLEQSPLLEDKYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GFNGCDSPEPDGEDSLEQSPLLEDKYR 27 1 Q14814-4;Q14814;Q05BX2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 GFNGCDS(1)PEPDGEDSLEQSPLLEDKYR;GFNGCDS(0.999)PEPDGEDS(0.001)LEQSPLLEDKYR;GFNGCDS(1)PEPDGEDSLEQSPLLEDKYR;GFNGCDS(1)PEPDGEDSLEQSPLLEDKYR 162.49 7.38E-12 606190000 735970 872526 488079 618891 792322 708271 883222 1100125 553672 TRUE FALSE 638709.6998 866794.3193 724115.6369 759419.6607 776556.3424 735518.6437 797567.2664 864871.8299 488217.5269 1.308248198 1.775426468 1.483182387 1.555494465 1.59059497 1.506538793 1.633630958 1.771488696 1 18.89716456 1.227545587 24.99158561 0.99999873 1.590397851 0.637447958 0.136728814 299.0304797 678413.6999 0.469070727 0.03190138 16.88673106 -1.227545587 0.590399121 GFNLPYQDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFNLPYQDAR 10 0 Q8NE71;Q8NE71-2;H0YGW7;A0A0G2JIC2 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 ; 111.46 0.0040738 217770000 278300 280330 178129 199018 256430 254770 263040 273970 277630 FALSE TRUE 241521.9499 278488.4938 264272.7802 244208.0787 251327.5447 264571.1668 237530.4213 215383.6475 244808.8977 0.986573414 1.137575049 1.079506434 0.997545763 1.026627492 1.080725289 0.970268742 0.879803184 1 17.90129647 2.080911242 4.899631023 0.929438563 1.052540123 0.460848018 0.052033371 0.153142412 6.573354462 0.021917353 0.01426604 120.4789688 -2.080911242 0.12310156 GFNS(ph)RS(ph)NLRSHMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GFNSRSNLRSHMR 13 2 Q9H4Q4 Q9H4Q4 PRDM12 PR domain zinc finger protein 12 2 GFNS(0.992)RS(0.994)NLRS(0.014)HMR;GFNS(0.999)RS(0.999)NLRS(0.001)HMR;GFNS(0.994)RS(0.996)NLRS(0.009)HMR 69.229 0.027378 366410000 64933 76130 37894.6 52273 65929 70698 56841 78003 89797 TRUE FALSE 56351.93953 75629.89702 56220.55531 64142.38359 64617.14189 73417.79781 51328.56857 61322.66547 79181.30096 0.711682416 0.955148452 0.710023132 0.810069837 0.816065676 0.92721131 0.648241036 0.774458928 1 16.27287215 1.235230947 24.96263567 1.000000292 0.794102202 0.320419946 0.094230772 112.3758687 842341.8815 0.153376665 0.021819881 17.18822171 -1.235230947 -0.20589809 GFPTDATLDDIKEWLEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFPTDATLDDIKEWLEDK 18 1 P05455;E7ERC4;E9PGX9 P05455 SSB Lupus La protein 0 ; 200.99 1.32E-15 730470000 1163130 826600 917060 835940 676660 533170 980960 1105340 2031270 FALSE TRUE 1009419.424 821170.0102 1360553.283 1025752.954 663195.7899 553681.3949 885826.6502 868971.6428 1791135.575 0.563563941 0.458463347 0.759603741 0.572683033 0.370265545 0.309123108 0.494561474 0.485151239 1 20.77244311 1.237572453 24.97876721 1.000000596 0.499373537 0.625775086 0.121095755 17.45503013 440996.0117 0.18642803 0.03147177 17.28114254 -1.237572453 -0.500627059 GFPTIYFSPANKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFPTIYFSPANKK 13 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 178.58 2.32E-05 1926630000 2111040 1767520 1392000 1711330 1815920 1658270 1971460 2020670 1189710 FALSE TRUE 1832060.715 1755909.045 2065175.856 2099913.633 1779786.745 1722064.72 1780268.113 1588565.445 1049063.839 1.746376767 1.673786646 1.968589307 2.001702427 1.696547606 1.641525192 1.697006461 1.514269567 1 20.00067104 0.874630846 1.009524154 6.62E-18 1.80700205 0.827004538 0.114287338 1.597420103 0.789089457 3.754276526 0.041332684 7.492570643 -0.874630846 1.80700205 GFPTWLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFPTWLK 7 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 138.07 0.0065628 1154910000 1502480 1548160 1168250 1462310 1610640 1422930 1616320 1814270 1762510 FALSE TRUE 1303923.461 1537990.035 1733219.608 1794349.836 1578591.415 1477671.038 1459569.535 1426302.479 1554148.076 0.838995641 0.989603281 1.115221667 1.15455526 1.015727806 0.950791666 0.939144447 0.917739115 1 20.56769254 2.771895061 4.566095853 0.944881228 1.034461727 0.139280229 0.08505953 0.365560728 18.72985746 0.030230911 0.02928249 591.4187115 -2.771895061 0.089580499 GFQQILAGEYDHLPEQAFYMVGPIEEAVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFQQILAGEYDHLPEQAFYMVGPIEEAVAK 30 0 P06576 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 ; 234.53 2.11E-45 155877000 150355 125277 102088 173019 140486 148932 130777 175990 174009 FALSE TRUE 130485.2058 124454.0471 151458.0983 212305.6084 137690.6035 154661.5104 118094.2667 138355.9081 153437.8543 0.850410783 0.811103934 0.987097343 1.383658612 0.897370497 1.00797493 0.769655358 0.901706484 1 17.22729492 1.021923423 14.22443021 1.024020213 0.950669606 0.008106852 0.169844737 300837.3803 12846042.74 252524.6421 0.043250641 10.51776404 -1.021923423 -0.073350607 GFRDDFLGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GFRDDFLGGR 10 1 Q15056-2 Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;; 152.54 1.63E-05 852200000 563041 483767 257809 259962 465116 458970 500836 562443 146477 FALSE TRUE 488633.7053 480589.1027 382486.2947 318990.3454 455861.1016 476626.8729 452265.0018 442168.9414 129160.6559 3.783146669 3.720862977 2.961322022 2.469717602 3.529411478 3.690186222 3.50156941 3.423402724 1 16.97880715 4.24486991 22.28426216 3.043821518 3.752006677 0.146884745 0.783350892 81.97337733 289492.693 0.194822858 0.486017326 17573.97117 -4.24486991 0.708185159 GFS(ph)IAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFSIAK 6 0 O76070;F8W754 O76070 SNCG Gamma-synuclein 1 GFS(1)IAK 88.294 0.053987 309890000 569360 707000 411810 421690 609680 436070 688560 612860 679440 TRUE FALSE 494117.6334 702355.6704 610962.6934 517441.1596 597548.5608 452845.8951 621783.5572 481804.6583 599117.3772 0.824742617 1.172317307 1.019771278 0.863672428 0.997381454 0.75585505 1.03783262 0.804190759 1 19.19247915 3.753081977 22.71953604 0.904052476 1.022281152 0.116823802 0.120608349 398.278275 623123.6038 0.028980614 0.049817964 5663.461815 -3.753081977 0.118228676 GFS(ph)LEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFSLEELR 8 0 P26373;P26373-2;J3QSB4 P26373 RPL13 60S ribosomal protein L13 1 GFS(1)LEELR;GFS(1)LEELR 133.99 0.00093948 68356000 332130 260560 108632 379610 216350 137127 241180 333270 354590 TRUE FALSE 288238.179 258848.3642 161166.7986 465806.2525 212045.0583 142402.3644 217790.4007 262002.804 312670.7742 0.921858398 0.827862357 0.515452073 1.489765885 0.67817358 0.455438679 0.696548634 0.837951052 1 18.25428485 GFSDEDNTWEPEENLDCPDLIAEFLQSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GFSDEDNTWEPEENLDCPDLIAEFLQSQK 29 0 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 0 ;;; 220.55 1.99E-34 127660000 245353 214319 167865 215206 197369 189595 230703 276600 348085 FALSE TRUE 212928.9794 212911.1244 249045.0755 264071.8115 193441.743 196888.8423 208329.4586 217451.2425 306934.7878 0.693727097 0.693668925 0.811394098 0.860351521 0.630237271 0.641467993 0.678741762 0.708460726 1 18.22757264 1.237793347 24.97272745 1.000000334 0.714752224 0.615003541 0.07092646 13.83018581 449834.9589 0.108622758 0.018595085 17.28993445 -1.237793347 -0.28524811 GFSEEHNTWEPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GFSEEHNTWEPEK 13 0 P45973;F8VNY3 P45973 CBX5 Chromobox protein homolog 5 0 ;;;; 170.79 2.62E-05 1671080000 3729250 2868660 1835815 3114610 2988430 2709200 3157460 4224030 6055100 FALSE TRUE 3236420.164 2849815.584 2723621.274 3821829.804 2928966.09 2813424.677 2851250.015 3320754.056 5339272.976 0.606153718 0.533745998 0.510110887 0.715795919 0.548570209 0.526930294 0.534014655 0.621948732 1 22.34821188 1.233690123 3.588202483 1.062709944 0.568277732 0.839885019 0.058810729 0.111458313 2.154788098 0.151389954 0.014938041 17.12734806 -1.233690123 -0.494432212 GFSESER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFSESER 7 0 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;C9IZ80;C9JFN4;C9J188;C9JWF5 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 119.56 0.011062 575440000 943600 853860 642030 750760 862650 905560 899970 915330 1131800 FALSE TRUE 818900.8692 848250.9374 952517.8555 921231.5326 845484.9527 940397.4792 812691.0479 719593.8026 997999.8934 0.820542041 0.84995093 0.954426811 0.923077787 0.847179402 0.942282144 0.814319774 0.721035951 1 19.92868014 2.21036119 24.84390866 0.817984682 0.890318743 0.028764083 0.080818462 382.9629153 337390.2733 0.032533564 0.021939172 162.315947 -2.21036119 0.072334061 GFSLEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 GFSLEELR 8 0 P26373;P26373-2;J3QSB4 P26373 RPL13 60S ribosomal protein L13 0 ;;;;;;;;; 194.25 0.00038703 8140415000 7208440 9350370 6665430 6631280 8851650 9866100 8688320 9271560 9040200 FALSE TRUE 6255826.39 9288946.804 9888854.243 8137013.477 8675519.483 10245655.25 7845728.064 7288909.045 7971477.855 0.784776237 1.165272861 1.240529601 1.020765989 1.088320088 1.285289307 0.984225034 0.914373618 1 22.92641578 2.022306835 24.98749229 0.950539157 1.105802742 0.169995181 0.136728718 336.1851689 376583.6345 0.054227774 0.036557777 105.2705363 -2.022306835 0.155263585 GFSNLKK ddPTM_MDA-MB-175_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 81.548 0.043137 519960000 680410 483520 352120 409730 433680 360090 497150 590980 337960 FALSE TRUE 590492.0946 480343.7253 522406.4098 502765.4588 425050.6165 373942.8953 448936.4695 464603.526 298006.7538 1.981472188 1.611855165 1.753001914 1.687094176 1.426312025 1.254813492 1.506464078 1.559036901 1 18.1849855 7.999999997 0.170096413 1.109268937 4.395466173 0.620307808 0.166067248 100.1353412 1.365272188 1.913396099 81.28093743 99999999.32 -7.999999997 3.286197235 GFSQYGVS(ph)GSPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFSQYGVSGSPTK 13 0 Q9NXC5 Q9NXC5 MIOS WD repeat-containing protein mio 1 GFSQYGVS(0.721)GS(0.278)PTK 191.89 3.34E-06 400520000 985250 821010 526650 628040 793410 736740 827470 1013700 925210 TRUE FALSE 855046.7162 815616.7313 781339.7015 770646.081 777622.6933 765082.8645 747222.0868 796928.1436 815832.7278 1.048066211 0.999735244 0.957720468 0.944612854 0.953164376 0.937793788 0.915901093 0.976827867 1 19.63791386 4.530306305 2.037879103 0.953378343 1.056116962 0.65445558 0.022311907 0.303865452 1.894016758 0.006280886 0.049423382 33908.32247 -4.530306305 0.102738619 GFSQYGVSGS(ph)PTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GFSQYGVSGSPTK 13 0 Q9NXC5 Q9NXC5 MIOS WD repeat-containing protein mio 1 GFSQYGVS(0.004)GS(0.995)PT(0.001)K;GFSQYGVS(0.001)GS(0.997)PT(0.002)K;GFSQYGVS(0.001)GS(0.994)PT(0.006)K 199.07 1.27E-07 759480000 2237600 1834480 1267820 1524450 1868770 1569850 2014980 2399680 2141670 TRUE FALSE 1941895.491 1822429.18 1880941.993 1870599.672 1831585.133 1630243.145 1819567.55 1886527.106 1888484.212 1.028282618 0.965022195 0.996006204 0.990529685 0.969870503 0.863254845 0.96350689 0.998963663 1 20.84879729 4.740985602 23.19843096 0.96886852 1.028282673 0.182432662 0.039832065 160.0203485 1530544.572 0.010349683 0.066919486 55078.94356 -4.740985602 0.059414153 GFSVLHTYQDHLWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFSVLHTYQDHLWR 14 0 Q5SY38;P41214 Q5SY38 EIF2D Eukaryotic translation initiation factor 2D 0 ; 218.5 3.10E-12 518360000 330850 477190 202525 373420 356960 364540 345730 378250 349780 FALSE TRUE 287127.3342 474055.3075 300466.7674 458210.7184 349857.1944 378564.0897 312201.1578 297364.181 308429.4069 0.930933717 1.53699776 0.974183268 1.48562591 1.13431854 1.227392983 1.012228895 0.96412396 1 18.2345808 2.208504788 4.334675198 0.981841716 1.228581927 0.233083538 0.189808784 0.254331053 10.7743513 0.071308593 0.04849557 161.6236046 -2.208504788 0.246740211 GFSVVADT(ph)PELQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 GFSVVADTPELQR 13 0 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 1 GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR 320.62 5.78E-50 9166491000 25898810 15840920 9879962 9833792 13569550 14651500 11888520 14383640 15141790 TRUE FALSE 22476216.64 15736859.95 14657944.67 12066704.77 13299542.5 15215152.69 10735573.16 11307810.52 13351744.84 1.683391715 1.178636961 1.097829898 0.903754897 0.996090224 1.139562872 0.804057694 0.846916314 1 23.67052495 8 0.74263406 0.924913565 129.3946833 0.851477541 0.095452662 135.6349695 0.605267417 0.037499197 29118.76955 100000000 -8 128.4697698 GFTDADNTWEPEENLDCPELIEAFLNSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFTDADNTWEPEENLDCPELIEAFLNSQK 29 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 0 ; 165.31 4.79E-12 92162000 187965 147733 111454 144724 129511 126988 147766 184568 210680 FALSE TRUE 163124.949 146762.5322 165353.5272 177585.7962 126933.9845 131873.3105 133435.6761 145099.5695 185773.6504 0.878084425 0.790007258 0.890080627 0.955925643 0.683272274 0.709860146 0.718270195 0.781055705 1 17.50318636 3.240157821 24.99999024 0.770863989 0.873027255 0.21256806 0.094779252 69.41890129 1086556.86 0.028612982 0.035002701 1738.432452 -3.240157821 0.102163266 GFTECEMTKSS(ph)PLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFTECEMTKSSPLK 14 1 Q9NQW6 Q9NQW6 ANLN Actin-binding protein anillin 1 GFTECEMTKS(0.006)S(0.994)PLK 145.69 5.16E-06 399970000 378380 318740 201990 194950 285420 223240 409730 498520 77386 TRUE FALSE 328376.1243 316646.176 299673.0396 239216.3771 279740.7004 231828.1873 369994.4477 391915.3775 68237.51524 4.812252075 4.640353255 4.391617112 3.505643139 4.099514753 3.397371467 5.422155927 5.743400476 1 16.05827749 4.144299305 3.546731591 4.134943633 4.739982867 0.047503549 1.292659253 0.998268999 24.15181691 0.344463027 0.83581735 13941.17262 -4.144299305 0.605039234 GFTGIDSDYEKPETPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFTGIDSDYEKPETPER 17 1 O95340;O95340-2 O95340 PAPSS2 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 2;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 233.52 3.76E-20 489160000 559450 565110 385500 417200 520320 448520 544280 669600 645470 FALSE TRUE 485517.265 561397.7552 571929.0894 511931.6365 509966.65 465774.8546 491495.8094 526411.2508 569163.2719 0.853036886 0.986356258 1.004859445 0.899446014 0.895993602 0.81835016 0.86354098 0.924886191 1 19.11848304 5.042347501 13.44079514 0.918997586 0.608435528 0.116079427 0.060205485 780293.0007 8235843.889 0.015818844 5710461.829 110242.106 -5.042347501 -0.310562059 GFTGSVADLAFAHLNSPQLACLDEAGNLFVWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFTGSVADLAFAHLNSPQLACLDEAGNLFVWR 32 0 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 189.23 7.21E-20 100320000 40945 42738 24132 26813 36110 42361 37400 44512 35804 FALSE TRUE 35534.01451 42457.25126 35802.31592 32901.30146 35391.48165 43990.65508 33772.95376 34993.45519 31571.29191 1.125516644 1.344805635 1.134014915 1.042127182 1.121002009 1.393375197 1.069736198 1.108394781 1 14.94632568 1.697913852 2.06936479 1.025400369 1.186125511 0.213404714 0.111078507 0.513864195 4.408715334 0.122541104 0.031846632 49.87855365 -1.697913852 0.160725143 GFTIPEAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GFTIPEAFR 9 0 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ;;; 159.46 0.00015364 4007040000 5014980 4249020 3090510 3453890 4184960 4148870 4236600 4773550 4443340 FALSE TRUE 4352237.687 4221107.908 4585090.973 4238148.514 4101687.484 4308479.714 3825735.184 3752763.48 3918053.407 1.110816325 1.077348231 1.170247186 1.081697484 1.046868702 1.099648031 0.976437732 0.957813253 1 21.90170563 2.235052073 10.74708745 0.973726472 1.09711809 0.747725406 0.03273841 0.059012275 125.1598323 0.013161527 0.009407981 171.8114381 -2.235052073 0.123391619 GFVEFAAKPPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFVEFAAKPPAR 12 1 Q8WXF1;Q8WXF1-2;X6RDA4 Q8WXF1 PSPC1 Paraspeckle component 1 0 ; 158.42 6.70E-05 2056760000 3056700 2620400 1955520 2303640 2403200 2468200 2611100 3227700 2973800 FALSE TRUE 2652749.35 2603186.42 2901216.013 2826716.671 2355381.022 2563153.251 2357875.924 2537481.473 2622240.752 1.011634553 0.992733569 1.106388119 1.077977554 0.898232178 0.97746679 0.899183617 0.967676775 1 21.32236872 3.245675825 24.99997753 0.94865561 1.047523084 0.552823238 0.044096608 128.1212799 450163.9696 0.01300857 0.016434003 1760.661325 -3.245675825 0.098867474 GFVEPDHYVVVGAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFVEPDHYVVVGAQR 15 0 P02786;G3V0E5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ; 170.79 1.12E-06 1943140000 1460150 1206410 791120 893690 1220520 1258160 963320 1174130 1254140 FALSE TRUE 1267187.478 1198485.013 1173708.278 1096615.974 1196234.04 1306562.229 869897.3747 923051.4366 1105876.998 1.145866566 1.083741696 1.061337093 0.991625629 1.081706231 1.181471567 0.786613137 0.834678213 1 20.0767595 2.235151774 24.99999999 0.861989665 1.084348049 0.661992967 0.072897398 51.16416668 375224.392 0.029390019 0.020719411 171.8508854 -2.235151774 0.222358384 GFVLHK ddPTM_MDA-MB-175_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 ; 104.03 0.034176 2407200000 5754400 5198700 3526300 4033800 4727100 4578700 5291000 5896600 5507000 FALSE TRUE 4993941.46 5164549.397 5231630.475 4949735.943 4633039.958 4754845.552 4777879.634 4635657.977 4855968.734 1.028413018 1.063546674 1.077360824 1.019309681 0.954091802 0.979175487 0.983918945 0.954630936 1 22.2113277 3.45284128 4.336348103 0.973169674 1.056515445 0.81457039 0.017959655 0.076248456 3.378539302 0.005081587 0.006937118 2836.882053 -3.45284128 0.083345771 GFVPSPTSQPGGHESLVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GFVPSPTSQPGGHESLVDR 19 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ; 157.98 5.46E-10 1458660000 943870 879920 378030 429690 920510 959320 822970 977630 523360 FALSE TRUE 819135.188 874139.7476 560846.5724 527257.6819 902193.6519 996225.6612 743158.4961 768571.4324 461488.977 1.774983215 1.89417254 1.215297874 1.14251414 1.954962517 2.158720383 1.610349397 1.665416664 1 18.81593666 3.213755709 24.99993087 1.695306471 1.513597498 0.049638835 0.367208955 812.3551981 818739.6029 0.117276527 0.133034351 1635.896069 -3.213755709 -0.181708973 GFVQVDDGRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GFVQVDDGRK 10 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;; 113.22 0.0024315 832560000 1117260 845140 586930 659440 825650 764100 920410 1078510 840130 FALSE TRUE 969611.2602 839588.2197 870771.3112 809175.9309 809221.1804 793495.4214 831148.7799 847879.0295 740810.7885 1.30885143 1.133336923 1.175430116 1.092284215 1.092345296 1.071117529 1.121944757 1.144528458 1 19.49874558 7.999999705 0.800953302 1.095122883 53.55334644 0.70227486 0.04359268 294.8532028 1.019752581 0.015044983 28066.73751 99999932.14 -7.999999705 52.45822356 GFWYDAEISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GFWYDAEISR 10 0 A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2 A0A087WVR3 UHRF1 E3 ubiquitin-protein ligase UHRF1 0 161.79 1.62E-05 99644000 193640 230770 185660 154290 228210 238580 193210 212860 206220 FALSE TRUE 168049.9834 229254.0567 275445.797 189323.9027 223669.0675 247758.327 174472.5239 167341.5455 181840.9065 0.924159402 1.260739737 1.51476256 1.041151335 1.230026135 1.362500505 0.95947896 0.92026348 1 17.47231726 2.218172284 23.82690911 0.95163514 1.229395358 0.371315722 0.160597488 139.3006965 162792.1611 0.064549187 0.04359038 165.261726 -2.218172284 0.277760218 GGAAGGGYSQVIPMEEFNLHLTGDIHAITAANNLVAAAIDAR ddPTM_MDA-MB-175_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 ;;; 286.35 1.09E-81 1385318000 300679 303964 184430 201571 263759 308417 286885 285932 264082 FALSE TRUE 260943.5083 301967.2405 273620.9649 247340.7764 258510.7119 320282.0016 259062.9369 224787.6669 232862.5268 1.120590384 1.296761847 1.17503219 1.062175094 1.110143034 1.375412377 1.112514497 0.965323489 1 17.82911897 1.899464913 4.540036721 0.9877297 1.188774179 0.46075276 0.091330904 0.197458115 6.47768703 0.049859639 0.024942152 79.33501579 -1.899464913 0.20104448 GGAARPNGPAAGNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGAARPNGPAAGNK 14 1 P51148;P51148-2;K7ERI8;K7ERQ8;F8VVK3;F8VWU4;F8VSF8 P51148 RAB5C Ras-related protein Rab-5C 0 ; 142.76 8.81E-06 0 99835 91322 86388 90227 73350 80140 86828 104702 101060 FALSE TRUE 86641.5518 90722.09977 128165.5258 110714.4194 71890.47851 83223.03766 78407.43392 82312.29209 89112.80193 0.972268293 1.018059109 1.438239209 1.242407566 0.806735698 0.933906643 0.879867227 0.9236865 1 16.44334508 3.243414562 24.99999381 0.90977559 1.176372944 0.481492346 0.133368571 109.6476796 564731.122 0.040821602 0.051003936 1751.517826 -3.243414562 0.266597354 GGAAVDPDSGLEHSAHVLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GGAAVDPDSGLEHSAHVLEK 20 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;;;; 222.6 4.07E-25 4760600000 10174490 8076330 3807360 6514070 8328100 7238400 8812080 10781400 8923160 FALSE TRUE 8829905.368 8023276.056 5648612.031 7993189.155 8162387.104 7516865.932 7957485.838 8475881.511 7868274.19 1.122216277 1.019699602 0.717897203 1.015875777 1.037379596 0.955338585 1.011338147 1.077222439 1 22.9076158 3.522806152 24.9991781 1.021022835 0.944409377 0.072475462 0.103745302 1031.45967 564420.6808 0.028953924 0.042943348 3332.776207 -3.522806152 -0.076613459 GGAEGELQALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGAEGELQALR 11 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 112.3 0.0035945 184926000 323410 300800 217300 236260 286200 319540 275770 283030 301380 FALSE TRUE 280670.5491 298824.025 322387.0068 289906.444 280505.1799 331832.9106 249025.8678 222506.237 265751.1997 1.05614029 1.124450333 1.213115904 1.090894206 1.055518019 1.248660066 0.937063946 0.837272747 1 18.01971668 2.115921694 6.889765522 0.901566424 1.129026689 0.640647774 0.072719572 0.117842398 6.634263424 0.028791337 0.019328544 130.5935399 -2.115921694 0.227460265 GGAEQFMEETER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GGAEQFMEETER 12 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;; 199.82 3.89E-07 2042130000 1496510 1362500 987780 1127970 1304560 1454400 1289850 1456320 1271620 FALSE TRUE 1298742.412 1353549.648 1465473.712 1384092.828 1278601.808 1510351.709 1164760.546 1144897.301 1121290.532 1.158256825 1.207135536 1.306952721 1.234374846 1.14029484 1.346976244 1.038767841 1.021053213 1 20.09672871 2.140814318 7.61005771 1.018032476 1.23016663 0.727838032 0.06130514 0.11441215 7.805855161 0.024247528 0.016318054 138.2974963 -2.140814318 0.212134154 GGAESHTFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GGAESHTFK 9 0 P50238;K4DIB9;H3BRQ4 P50238 CRIP1 Cysteine-rich protein 1 0 ;;;;; 167.23 0.00010981 6783614000 15380810 13395410 8366519 9949677 11243450 10680050 13303350 15121330 13811210 FALSE TRUE 13348196.99 13307414.67 12412595.57 12208903.23 11019727.34 11090918.43 12013193.16 11887751.25 12178464.49 1.09604926 1.092700536 1.019225009 1.002499391 0.904853592 0.910699247 0.986429215 0.976128909 1 23.53782891 3.989377133 1.759374203 0.959589601 1.100433596 0.741214795 0.032156476 0.204699603 1.217782557 0.010287966 0.029427097 9758.366687 -3.989377133 0.140843995 GGAGGS(ph)PGSSSGSGSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GGAGGSPGSSSGSGSSR 17 0 Q8TAE6 Q8TAE6 PPP1R14C Protein phosphatase 1 regulatory subunit 14C 1 GGAGGS(1)PGSSSGSGSSR;GGAGGS(0.999)PGS(0.001)S(0.001)SGSGSSR;GGAGGS(0.987)PGS(0.013)SSGSGSSR;GGAGGS(1)PGSSSGSGSSR 384.29 1.09E-121 780788000 809691 877408 597988 639013 573112 898380 779094 901889 915977 TRUE FALSE 702688.2829 871644.2491 887176.9969 784110.6684 561708.1925 932941.2599 703537.5838 709027.0559 807691.2425 0.869996164 1.079180017 1.098411064 0.970804965 0.695449155 1.155071655 0.871047681 0.877844179 1 19.62344437 3.476244694 24.99993523 0.914579366 1.024263168 0.103231811 0.128542183 57.98616683 1653749.382 0.035313952 0.045999313 2993.951036 -3.476244694 0.109683802 GGAPDPSPGATATPGAPAQPS(ph)SPDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGAPDPSPGATATPGAPAQPSSPDAR 26 0 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 GGAPDPSPGATATPGAPAQPS(0.536)S(0.464)PDAR 96.598 0.0044928 395140000 58730 75476 65448 71051 66794 83140 57192 70457 75208 TRUE FALSE 50968.6817 74980.19319 97098.87171 87184.2155 65464.93008 86338.4496 51645.52864 55390.31885 66316.99592 0.768561377 1.130633138 1.464162699 1.314658698 0.987151622 1.301905317 0.778767613 0.835235645 1 16.01709104 2.233174467 24.99993587 0.859956856 1.172628402 0.323987306 0.196674526 148.2549128 688119.641 0.080236174 0.055860539 171.070241 -2.233174467 0.312671545 GGAPDPSPGATATPGAPAQPSS(ph)PDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGAPDPSPGATATPGAPAQPSSPDAR 26 0 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 GGAPDPSPGATATPGAPAQPS(0.19)S(0.81)PDAR 202.85 2.84E-25 368570000 212340 197930 208900 224040 269240 349740 184580 256360 284730 TRUE FALSE 184278.731 196629.7848 309924.7387 274911.7062 263882.6508 363194.7241 166679.46 201539.409 251069.5438 0.733974851 0.783168607 1.234417899 1.094962384 1.051034095 1.446590131 0.663877655 0.802723445 1 17.93772751 GGAVERPLT(ph)PAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GGAVERPLTPAPR 13 1 H9KVB4;O15417 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 GGAVERPLT(1)PAPR;GGAVERPLT(1)PAPR;GGAVERPLT(1)PAPR;GGAVERPLT(1)PAPR 130.01 0.00023777 2804440000 1972700 1951600 1345800 1357080 1774160 1767240 1542940 1875770 1709300 TRUE FALSE 1712002.697 1938779.811 1996633.381 1665225.756 1738857.687 1835226.866 1393305.916 1474651.183 1507228.501 1.135861414 1.286321092 1.324705166 1.104826345 1.153678879 1.217616881 0.92441585 0.978385946 1 20.52346672 2.243302141 24.99984805 0.968048165 1.206298248 0.728368801 0.067995303 60.16102664 317203.2189 0.027033857 0.020248052 175.1064488 -2.243302141 0.238250083 GGCGS(ph)PGLQCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGCGSPGLQCK 11 0 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 GGCGS(1)PGLQCK 89.193 0.0077711 0 389260 388670 235570 278630 330230 311420 334590 418240 412960 TRUE FALSE 337818.3047 386116.8012 349492.4399 341897.2001 323659.0691 323400.5289 302141.5133 328802.6307 364140.3392 0.927714588 1.060351627 0.959774027 0.938916026 0.88883058 0.888120579 0.829739199 0.902955798 1 18.47413504 3.638282787 2.167401791 0.896412118 0.99444919 0.324971031 0.052692018 0.326438593 2.998685782 0.015656686 0.027429275 4347.932435 -3.638282787 0.098037072 GGCWPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GGCWPR 6 0 Q9Y4W6 Q9Y4W6 AFG3L2 AFG3-like protein 2 0 ;;; 118.11 0.051516 3351150000 2632560 2510810 1435980 1658280 2988730 2763320 2894940 3259440 2861500 FALSE TRUE 2284660.526 2494316.324 2130424.731 2034817.819 2929260.12 2869626.709 2614189.164 2562434.121 2523216.73 0.905455524 0.988546205 0.84432887 0.806437987 1.160922915 1.137289031 1.03605415 1.015542617 1 21.2668327 3.24114209 24.99999981 1.063982647 0.890512918 0.64577222 0.067516988 49.6853293 481168.0509 0.021710817 0.026734596 1742.37684 -3.24114209 -0.173469729 GGDAKS(ph)PVLQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GGDAKSPVLQEK 12 1 A6NFI3 A6NFI3 ZNF316 Zinc finger protein 316 1 GGDAKS(1)PVLQEK;GGDAKS(1)PVLQEK;GGDAKS(1)PVLQEK;GGDAKS(1)PVLQEK 127.94 0.00015795 3876310000 8086850 5367730 4139620 4578800 5151880 3379670 6957020 7327560 5029490 TRUE FALSE 7018152.283 5332469.028 6141554.078 5618486.523 5049367.667 3509688.092 6282329.271 5760618.317 4434909.422 1.582479283 1.202385104 1.384820634 1.266877401 1.138550348 0.791377626 1.416563152 1.298925811 1 22.08047321 8 0.717203615 1.171947678 55.1834393 0.329733514 0.181744995 441.4529094 2.194040264 0.072690701 38336.0321 100000000 -8 54.01149162 GGDEYDNHCGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GGDEYDNHCGK 11 0 P20645;F5GX30;F5H4U1;H0YGE9 P20645 M6PR Cation-dependent mannose-6-phosphate receptor 0 ;; 151.79 3.33E-05 2040610000 3629930 3080350 2201680 2560460 2669450 2884060 3112980 3910910 3759400 FALSE TRUE 3150225.553 3060114.978 3266419.812 3141851.577 2616333.168 2995011.654 2811083.679 3074592.331 3314968.015 0.950303454 0.923120514 0.98535485 0.947777343 0.78924839 0.903481313 0.847997225 0.927487782 1 21.66056352 3.435191929 24.99995367 0.892539374 0.952716307 0.21408866 0.055265964 223.0284546 132977.7718 0.016091524 0.020774089 2723.904823 -3.435191929 0.060176933 GGDISVCEWYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GGDISVCEWYQR 12 0 P14854 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 0 ;;;;; 276.57 1.69E-27 6799680000 2173240 1850750 1455096 1824330 1935290 2638850 1276671 2056350 1955120 FALSE TRUE 1886040.828 1838592.301 2158785.293 2238572.01 1896781.515 2740368.267 1152859.643 1616615.555 1723987.941 1.093998852 1.066476312 1.252204404 1.298484726 1.100228993 1.589551877 0.668716767 0.937718598 1 20.71731825 2.221366607 24.99992679 0.874830141 1.223646913 0.505853335 0.169689772 199.8504662 290578.4897 0.067053837 0.045330423 166.4817403 -2.221366607 0.348816771 GGDLMAYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 GGDLMAYDR 9 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;;;; 201.07 5.13E-05 10480660000 7721560 7653050 5838300 6171820 7158020 7917150 6571970 7452240 10812350 FALSE TRUE 6701136.282 7602776.611 8661721.408 7573226.061 7015589.406 8221727.884 5934621.361 5858636.469 9534126.3 0.702857931 0.797427721 0.908496608 0.794328271 0.735839781 0.86234728 0.622460955 0.614491175 1 23.18466931 2.250896867 24.99324294 0.713192879 0.801817496 0.021007785 0.119952938 508.9242729 1031080.268 0.044649109 0.034330747 178.1955552 -2.250896867 0.088624617 GGDLMAYDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 GGDLMAYDRR 10 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;;;;;;; 142.83 5.62E-05 24255700000 8607520 8716460 4627541 4441893 7912900 8388920 7453380 8117210 3218641 FALSE TRUE 7470014.423 8659201 6865435.306 5450492.696 7755448.771 8711647.181 6730552.355 6381407.81 2838136.928 2.6320134 3.051015938 2.418993685 1.920447404 2.732584427 3.069495025 2.371468511 2.248449589 1 21.43651276 1.112476323 1.789568181 5.93E-11 2.610834367 0.696857587 0.330753389 0.787488538 1.794212951 3.940715506 0.095818737 12.95616062 -1.112476323 2.610834367 GGDS(ph)PEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 152.17 0.00048396 2257250000 3974449 3898464 2903780 3316819 5109610 3771771 4961236 5386149 5362854 TRUE FALSE 3449215.495 3872854.733 4308057.721 4069953.448 5007938.758 3916873.471 4480096.096 4234362.951 4728863.51 0.729396289 0.818982135 0.911013336 0.860662068 1.059015289 0.828290659 0.947393827 0.895429302 1 22.17306207 4.613731194 1.238566015 0.931192936 0.66257793 0.52581221 0.064824657 0.908212921 1.423038607 0.017912669 0.295406461 41089.53189 -4.613731194 -0.268615006 GGDSIGET(ph)PT(ph)PGASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGDSIGETPTPGASK 15 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 GGDSIGET(1)PT(1)PGASK 309.73 6.24E-56 354630000 1024400 913450 727030 771860 1016800 895690 1057000 1204100 1357400 TRUE FALSE 889022.9445 907449.4868 1078624.14 947122.6101 996567.6693 930147.7739 954492.3027 946612.5853 1196929.718 0.742752837 0.758147678 0.901159127 0.79129342 0.83260333 0.777111437 0.797450584 0.790867309 1 20.19090701 1.236876165 24.99832566 1.000000248 0.800529646 0.678420137 0.043494533 26.06375653 386682.5974 0.064782199 0.010442535 17.25345856 -1.236876165 -0.199470602 GGDSIGET(ph)PTPGASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GGDSIGETPTPGASK 15 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 GGDSIGET(1)PTPGASK;GGDSIGET(0.995)PT(0.005)PGASK;GGDSIGET(0.997)PT(0.003)PGASK 236.26 1.18E-16 544140000 934760 813300 643020 765300 830050 702850 928410 1175340 1282820 TRUE FALSE 811229.0976 807957.3787 953986.6228 939073.0619 813533.629 729889.0943 838372.9411 924002.6875 1131166.481 0.717161542 0.714269201 0.843365357 0.830181125 0.719198847 0.645253468 0.741157871 0.816858264 1 20.10937984 1.261625964 2.364787097 1.059016763 0.746192161 0.664618454 0.057238045 0.373962314 2.305437424 0.239255746 0.016735602 18.26526444 -1.261625964 -0.312824602 GGDVAVELPFTLMHPKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGDVAVELPFTLMHPKPK 18 1 P49407-2;H0YET9 P49407-2 ARRB1 Beta-arrestin-1 0 128.69 1.37E-05 292620000 982210 806320 625510 682500 704150 680520 1145700 1123100 661730 FALSE TRUE 852408.4599 801023.2308 928008.7282 837472.0564 690138.7926 706700.0448 1034590.19 882933.805 583501.0332 1.460851672 1.372788025 1.590414884 1.435253768 1.182755048 1.211137606 1.77307345 1.513165795 1 19.15437569 3.469545574 24.74457884 1.377821235 1.472551736 0.067105459 0.212683126 652.0434186 2129769.469 0.064743567 0.083765394 2948.122831 -3.469545574 0.094730501 GGDVS(ph)PSPYSSSSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 GGDVSPSPYSSSSWR 15 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YFE7 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 GGDVS(0.992)PS(0.008)PYSSSSWR;GGDVS(0.991)PS(0.009)PYSSSSWR;GGDVS(0.711)PS(0.289)PYSSSSWR;GGDVS(0.968)PS(0.032)PYSSSSWR;GGDVS(0.997)PS(0.003)PYSSSSWR;GGDVS(0.702)PS(0.298)PYSSSSWR;GGDVS(0.955)PS(0.045)PYSSSSWR;GGDVS(0.997)PS(0.003)PYSSSSWR 371.23 1.44E-97 6580540000 3944250 3141870 2099878 2335442 3047270 3152820 2758280 3341580 2881840 TRUE FALSE 3423007.369 3121230.849 3115386.024 2865739.801 2986635.289 3274111.026 2490782.43 2627009.121 2541152.158 1.347029676 1.228273891 1.225973822 1.12773247 1.175307539 1.288435647 0.98017839 1.033786628 1 21.27705133 -1.255665935 0.143458348 1.17E-15 1.451601742 0.648180116 0.0727815 81.05137266 1.237164078 23.35413422 1.551229425 0.05550525 1.255665935 1.451601742 GGEFDEFVNDDT(ph)DDDLPISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGEFDEFVNDDTDDDLPISK 20 0 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 GGEFDEFVNDDT(1)DDDLPISK;GGEFDEFVNDDT(1)DDDLPISK 133.68 3.80E-05 172229000 466410 409270 303250 357350 379610 349990 455830 526060 528900 TRUE FALSE 404772.7368 406581.4784 449902.7143 438491.7793 372056.5037 363454.3418 411623.6768 413566.1628 466374.0445 0.867914374 0.871792681 0.964682146 0.940214801 0.797764172 0.779319403 0.882604171 0.886769252 1 18.83112797 1.200636176 2.987858554 1.032455626 0.872311804 0.341991733 0.055282613 0.621042981 6.392766801 0.253370865 0.015718851 15.87216524 -1.200636176 -0.160143822 GGEHGPQVPLSQPPEDELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GGEHGPQVPLSQPPEDELDR 20 0 Q15654;H7BZE2 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 ;;; 150.13 9.10E-08 1445700000 734071 800971 645856 682582 743907 895320 766180 779533 1045230 FALSE TRUE 637061.6575 795709.3688 958194.1219 837572.6757 729104.7061 929763.5397 691875.9815 612835.9343 921664.1001 0.691208063 0.863339875 1.039634854 0.908761311 0.791074217 1.008787843 0.750681275 0.664923299 1 19.81388153 2.191705969 24.99910096 0.773705043 0.88687453 0.058417718 0.129214552 239.2463006 127647.0529 0.052241169 0.035221112 155.4912551 -2.191705969 0.113169487 GGET(ph)PGSEQWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGETPGSEQWK 11 0 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9;D6RHI8 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 GGET(1)PGSEQWK;GGET(1)PGSEQWK 210.31 1.47E-07 728290000 1407290 1167870 1256340 1435300 1398370 1816230 1991960 1723760 2144700 TRUE FALSE 1221313.061 1160198.185 1863910.226 1761206.802 1370545.173 1886101.543 1798780.026 1355147.338 1891156.009 0.645802385 0.613486238 0.985593054 0.931285834 0.724712909 0.997327314 0.951153695 0.716570887 1 20.85083695 4.250416596 24.99587186 0.885407674 0.629644148 0.537742118 0.10380149 176.8327302 372808.012 0.025798658 0.067090057 17799.86037 -4.250416596 -0.255763526 GGFCNFMHLKPISR ddPTM_MDA-MB-175_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 ; 180.48 1.05E-06 2120490000 2991300 2566800 1602950 1842680 2473700 2305040 2333100 2969000 2289830 FALSE TRUE 2595992.126 2549938.522 2378141.982 2261088.658 2424478.21 2393716.38 2106836.321 2334102.455 2019128.906 1.285699055 1.262890405 1.177805921 1.119833732 1.200754544 1.185519346 1.043438245 1.15599477 1 20.94530159 7.999999999 0.097346736 0.857137114 2.082233099 0.650874217 0.052044428 207.8751107 1.874536257 3.8474892 34.83139601 99999999.83 -7.999999999 1.225095985 GGFDGEYQDDSLDLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GGFDGEYQDDSLDLLR 16 0 Q5F1R6;Q5F1R6-3;Q5F1R6-2 Q5F1R6 DNAJC21 DnaJ homolog subfamily C member 21 0 ;;; 244.72 1.05E-19 136908000 198401 193650 135648 139964 178983 201224 173229 201755 188618 FALSE TRUE 172181.8052 192377.9004 201247.8265 171744.9654 175421.5885 208965.2175 156429.2782 158611.2633 166319.7949 1.035245415 1.156674709 1.210005259 1.03261891 1.054724656 1.256406176 0.940533136 0.95365235 1 17.34360036 2.208185022 24.9996665 0.961412705 1.122320458 0.509141003 0.073809553 159.6009571 131353.3674 0.029591207 0.01995313 161.5046467 -2.208185022 0.160907754 GGFDS(ph)PFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GGFDSPFYR 9 0 A0A2R8YFV7;A0A2R8Y5N2;A0A2R8Y5S3;Q92574-2;Q92574;A0A2R8Y6S1;A0A2R8YEH9 A0A2R8YFV7 TSC1 Hamartin 1 GGFDS(1)PFYR;GGFDS(1)PFYR;GGFDS(1)PFYR;GGFDS(1)PFYR;GGFDS(1)PFYR;GGFDS(1)PFYR 162 6.72E-05 2866680000 3938260 3796330 2842750 2836730 3773810 4270520 3695500 3998210 3993010 TRUE FALSE 3417808.963 3771391.658 4217513.408 3480852.903 3698718.564 4434809.668 3337110.979 3143223.906 3520960.907 0.970703468 1.071125684 1.197830229 0.98860879 1.050485553 1.259545273 0.947784161 0.892717638 1 21.74753778 2.039364234 24.99928429 0.933162021 1.088761637 0.356987544 0.09000647 147.3607999 93584.72364 0.035872531 0.024185217 109.487423 -2.039364234 0.155599615 GGFGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GGFGFR 6 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;; 117.67 0.052398 5560100000 5293830 5380650 3845820 3607330 4931580 5251840 4650210 5245720 4890710 FALSE TRUE 4594236.953 5345304.156 5705671.415 4426429.411 4833451.206 5453881.683 4199233.35 4123963.6 4312535.835 1.065321455 1.239480519 1.323043247 1.026409885 1.120790966 1.264657708 0.973727178 0.956273468 1 22.04010501 2.221312344 24.80657163 0.972295653 1.174037987 0.517010499 0.089549563 172.9152217 248685.7115 0.036736885 0.024836282 166.4609404 -2.221312344 0.201742334 GGGAPWPGGAQTYS(ph)PSSTCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GGGAPWPGGAQTYSPSSTCR 20 0 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 GGGAPWPGGAQTYS(1)PSSTCR;GGGAPWPGGAQTYS(0.999)PS(0.001)STCR;GGGAPWPGGAQTYS(0.971)PS(0.022)S(0.005)T(0.001)CR 250.94 6.50E-31 876546000 695920 646080 421847 472190 603490 700900 611040 661140 616400 TRUE FALSE 603952.4088 641835.8579 625853.6202 579407.9565 591481.7297 727864.0765 551781.4348 519760.356 543529.8942 1.111166865 1.18086579 1.151461266 1.066009363 1.088222996 1.339142675 1.015181392 0.956268204 1 19.05199986 2.022757687 24.99831383 0.978224643 1.152145471 0.527320284 0.074486605 164.6608684 180871.9504 0.029811222 0.020097385 105.379877 -2.022757687 0.173920828 GGGDRYEDRYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GGGDRYEDRYDR 12 2 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;; 180.2 1.11E-05 3239030000 2598720 2529080 1079660 1004840 2124090 2419800 2134690 2407120 313059 FALSE TRUE 2255292.568 2512466.307 1601787.187 1233004.28 2081824.765 2512891.272 1927668.092 1892376.12 276049.5217 8.169883991 9.101505744 5.802535638 4.466605385 7.541490209 9.103045195 6.983051739 6.855205214 1 18.07456758 4.237774139 24.98598056 6.213554576 8.63569534 0.202687391 2.159019686 34.21545115 1087171.524 0.552723373 1.270914775 17289.16979 -4.237774139 2.422140765 GGGEAAQS(ph)PGPLPQSKPDGGETLYVTADLTLEDNRR ddPTM_MDA-MB-175_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(0.898)PGPLPQS(0.071)KPDGGET(0.01)LY(0.01)VT(0.01)ADLT(0.001)LEDNRR 40.777 0.075381 68644000 36384 31042 18764 30542 32961 30054 37105 47240 33340 TRUE FALSE 31575.76221 30838.08306 27838.33316 37477.02791 32305.14059 31210.19683 33506.56281 37138.09362 29398.58318 1.074057278 1.048964941 0.946927714 1.274790274 1.098867261 1.061622481 1.139733932 1.263261341 1 14.84345901 3.753115583 24.9963018 1.147627917 1.025881482 0.275374771 0.088355139 1045.412857 1795358.315 0.023304124 0.040146644 5663.900076 -3.753115583 -0.121746435 GGGEYGETWHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GGGEYGETWHK 11 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ;; 122.69 0.00038551 1218620000 1739300 1526890 979520 1129210 1428000 1451950 1631520 1823570 1875900 FALSE TRUE 1509447.098 1516859.759 1453219.148 1385614.389 1399585.594 1507807.456 1473295.442 1433613.747 1654133.239 0.91253054 0.917011836 0.878538146 0.837667944 0.846114183 0.911539301 0.890675193 0.866685774 1 20.65764402 1.2341807 24.9943515 1.000000176 0.881537547 0.649346777 0.027103759 90.41223229 515876.555 0.054711642 0.007097126 17.14670593 -1.2341807 -0.118462629 EKTPSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKTPSPK 7 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 58.815 0.097845 235020000 323000 238670 223070 314970 193810 201270 314140 384720 754790 FALSE TRUE 280314.7316 237102.1611 330947.3981 386488.7525 189953.5602 209012.9871 283674.7512 302450.6219 665559.5861 0.421171504 0.356244829 0.497246836 0.580697447 0.285404289 0.314040984 0.426219916 0.45443057 1 19.34420831 1.229483306 4.156941314 1.065832404 0.412741904 0.823789019 0.084945292 0.102418513 3.240534216 0.204788618 0.022527562 16.96224401 -1.229483306 -0.6530905 GGGGEGGGEAS(ph)PDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GGGGEGGGEASPDR 14 0 A0A0D9SGD0;A0A0D9SGA5 A0A0D9SGD0 SLC12A5 1 GGGGEGGGEAS(1)PDR;GGGGEGGGEAS(1)PDR;GGGGEGGGEAS(1)PDR 199.33 2.18E-08 577410000 460153 482577 430283 438697 377855 543904 474504 520202 818990 TRUE FALSE 399342.6152 479406.9199 638369.298 538309.8589 370336.4248 564828.3388 428486.6751 408960.8505 722169.9352 0.552975963 0.663842257 0.883959948 0.745406078 0.512810637 0.782126632 0.593332198 0.566294484 1 19.46197883 1.228238899 24.99763659 1.000000696 0.663432194 0.460226412 0.114832226 428.9173004 1038700.76 0.394663031 0.028782338 16.91371072 -1.228238899 -0.336568502 GGGGEGGGEAS(ph)PDRQGSLPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGGGEGGGEASPDRQGSLPSR 21 1 A0A0D9SGD0;A0A0D9SGA5 A0A0D9SGD0 SLC12A5 1 GGGGEGGGEAS(1)PDRQGSLPSR;GGGGEGGGEAS(1)PDRQGSLPSR 267.19 2.59E-37 1580160000 645160 627510 337030 320190 568740 629990 590460 564100 124284 TRUE FALSE 559900.4714 623387.8455 500018.8353 392894.0333 557423.1867 654226.123 533197.2801 443471.6048 109591.2871 5.108987093 5.688297509 4.562578363 3.585084578 5.086382334 5.969691024 4.865325467 4.04659546 1 16.74177358 4.099593752 5.192255803 4.242941787 5.383692228 0.137477232 1.301626965 0.459966602 19.51917133 0.345844168 0.748629947 12577.48338 -4.099593752 1.140750441 GGGGGGQGAEGPPGT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGGGGGQGAEGPPGTPR 17 0 Q8TER5;Q8TER5-4;Q8TER5-3;G3V485;G3V3N2;G3V5C1 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 GGGGGGQGAEGPPGT(1)PR 105.2 0.0090895 270530000 277350 267100 204310 229680 271690 337280 266940 318460 340090 TRUE FALSE 240697.4948 265345.4025 303114.9994 281832.3544 266283.9006 350255.3798 241052.1999 250359.8073 299884.9476 0.802632799 0.884824012 1.01077097 0.939801603 0.887953539 1.167965857 0.803815603 0.834852864 1 18.19404958 7.246407967 10.63570313 0.921721065 0.200811738 0 0.112127069 0 0 0.025016358 0 17636319.85 -7.246407967 -0.720909327 GGGGGQDNGLEGLGNDS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGGGGQDNGLEGLGNDSR 18 0 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 1 GGGGGQDNGLEGLGNDS(1)R;GGGGGQDNGLEGLGNDS(1)R 288.57 1.58E-40 1634110000 2080100 1108690 1204470 1111840 976010 1616390 1427790 1067550 2009420 TRUE FALSE 1805209.515 1101406.942 1786955.721 1364300.265 956589.3105 1678573.569 1289323.146 839262.7402 1771868.657 1.018816777 0.621607554 1.008514776 0.769978215 0.53987597 0.947346499 0.727662934 0.47365968 1 20.75684023 3.484455443 24.54448185 0.709021799 0.862243169 0.095000171 0.191379868 568.6799201 1903136.693 0.05251417 0.070807097 3051.092983 -3.484455443 0.153221369 GGGGNFGPGPGSNFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGGGNFGPGPGSNFR 15 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ; 273.44 4.41E-33 682130000 494370 424030 307240 308170 377230 404670 372970 463570 425410 FALSE TRUE 429037.7519 421244.519 455822.2917 378144.7086 369723.861 420237.9168 336799.4268 364439.163 375118.5144 1.143739206 1.122963818 1.215142079 1.008067302 0.985618803 1.120280393 0.89784805 0.971530727 1 18.51698695 3.665828623 6.591008849 0.992137118 1.156471009 0.634099024 0.058441186 0.151490394 11.38364142 0.016255684 0.024292084 4632.640748 -3.665828623 0.164333891 GGGGYTCQS(ph)GSGWDEFTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GGGGYTCQSGSGWDEFTK 18 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 GGGGYTCQS(0.998)GS(0.002)GWDEFTK;GGGGYTCQS(0.997)GS(0.003)GWDEFTK;GGGGYTCQS(0.999)GS(0.001)GWDEFTK;GGGGYTCQS(0.998)GS(0.002)GWDEFTK 289.68 4.06E-49 530229000 1097160 880363 614354 654940 865010 748097 937310 1072350 1149030 TRUE FALSE 952167.5262 874579.8375 911457.6493 803654.1371 847797.9934 776876.7757 846409.8205 843036.2975 1013192.982 0.939769168 0.863191764 0.899589382 0.793189601 0.836758651 0.766760912 0.835388554 0.832058958 1 19.95047756 4.865264225 1.209487021 0.84148484 1.000175147 0.155179159 0.063195466 3.488929467 3.591732125 0.018350396 0.745090705 73327.05195 -4.865264225 0.158690307 GGGHVAQIYAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GGGHVAQIYAIR 12 0 P62249;M0R210;M0R3H0;M0R1M5;M0QX76 P62249 RPS16 40S ribosomal protein S16 0 ;;;; 154.35 5.96E-05 5173500000 3909450 4130020 3215040 3410950 3902400 3754480 3627170 4200190 4557500 FALSE TRUE 3392806.277 4102889.627 4769844.098 4185458.331 3824749.875 3898917.275 3275407.612 3302012.054 4018717.542 0.844250993 1.020945011 1.186907029 1.041491045 0.951733939 0.970189428 0.815038026 0.821658158 1 21.93830375 2.662918449 1.877671534 0.867650077 1.029169851 0.248821392 0.098882012 0.410530948 2.889118322 0.04341569 0.036531953 460.1701559 -2.662918449 0.161519775 GGGPGKS(ph)PTQGST ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGGPGKSPTQGST 13 1 Q6P582 Q6P582 MZT2A Mitotic-spindle organizing protein 2A 1 GGGPGKS(0.698)PT(0.231)QGS(0.008)T(0.062) 130.1 3.46E-05 0 256170 234130 159020 183090 214860 219590 258620 307590 213860 TRUE FALSE 222316.4854 232591.9846 235922.6039 224663.3829 210584.7064 228037.7694 233539.0722 241814.2722 188577.7144 1.178911761 1.233401228 1.251063015 1.191357014 1.116699855 1.209250892 1.238423495 1.282305669 1 17.52479967 1.227355432 24.99331391 0.999999533 1.215222015 0.687122076 0.045072591 320.8341442 715577.5094 0.181876788 0.012123613 16.87933885 -1.227355432 0.215222482 GGGPGKS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GGGPGKSPTR 10 1 H7BZ50;H7C173;A0A494C0V9;B8ZZ87;Q6NZ67 H7BZ50 MZT2B Mitotic-spindle organizing protein 2B 1 GGGPGKS(0.536)PT(0.464)R;GGGPGKS(0.89)PT(0.11)R;GGGPGKS(0.754)PT(0.246)R;GGGPGKS(0.895)PT(0.105)R 84.169 0.0091476 5182450000 2870750 2409680 1572540 1896060 1614640 2147710 2750740 3084490 2418870 TRUE FALSE 2491373.114 2393850.653 2333025.604 2326589.402 1582511.823 2230333.793 2483973.658 2424895.817 2132913.944 1.168060775 1.122338133 1.093820785 1.090803222 0.741948276 1.045674533 1.164591598 1.136893415 1 21.02439433 4.009136181 2.213645991 1.039259844 1.147978453 0.151390584 0.114649529 0.756039556 7.30764356 0.035350003 0.090260481 10212.59669 -4.009136181 0.10871861 GGGPGKSPT(ph)QGST ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGGPGKSPTQGST 13 1 Q6P582 Q6P582 MZT2A Mitotic-spindle organizing protein 2A 1 GGGPGKS(0.118)PT(0.875)QGS(0.007)T 93.478 0.0099681 0 260660 241400 169850 187920 209190 205960 274800 330270 220080 TRUE FALSE 226213.1206 239814.2275 251990.0281 230590.1082 205027.5283 213883.4145 248149.9383 259644.3307 194062.3931 1.165672117 1.235758375 1.298500055 1.188226655 1.056503143 1.102137364 1.278712142 1.337942537 1 17.56616104 3.506419171 23.95235836 1.178894424 1.235189745 0.08183085 0.103803011 1476.546265 1207137.576 0.031251086 0.046250105 3209.365433 -3.506419171 0.056295321 GGGPGKSPT(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGGPGKSPTR 10 1 H7BZ50;H7C173;A0A494C0V9;B8ZZ87;Q6NZ67 H7BZ50 MZT2B Mitotic-spindle organizing protein 2B 1 GGGPGKS(0.434)PT(0.566)R 72.705 0.076285 2243200000 207580 176340 127190 137460 115740 160050 215200 206040 177880 TRUE FALSE 180147.7771 175181.6109 188699.5094 168672.3939 113437.0004 166207.2271 194329.9371 161979.9494 156851.229 1.148526398 1.116864764 1.203047694 1.075365459 0.723213972 1.059648867 1.238944306 1.032697993 1 17.25903731 3.482636398 24.99963121 1.02099571 1.150049563 0.215379964 0.125680254 445.2209418 2018148.151 0.038151959 0.050839442 3038.340186 -3.482636398 0.129053853 GGGPVTLQDYRLPDS(ph)DDDEDEETAIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGGPVTLQDYRLPDSDDDEDEETAIQR 27 1 Q96K21-3 Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 GGGPVTLQDYRLPDS(1)DDDEDEETAIQR 159.75 8.80E-12 188970000 71206 90825 32332 27020 75942 86688 72421 90107 15774 TRUE FALSE 61795.94669 90228.36459 47967.86334 33155.30397 74430.90278 90022.94345 65397.62257 70838.31926 13909.21569 4.442805983 6.486948409 3.448638975 2.38369328 5.35119337 6.472179702 4.701747678 5.092905369 1 13.76375345 6.072297874 12.49580641 4.501909331 3.511975329 0 1.725492535 0 0 0.380789597 0 1181130.471 -6.072297874 -0.989934002 GGGQEERPFVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GGGQEERPFVAR 12 1 Q9HA64;I3L2G3 Q9HA64 FN3KRP Ketosamine-3-kinase 0 ;;; 196.24 1.91E-07 2153000000 2034590 1876130 1275610 1328470 1678420 2040790 1642750 1820110 1596490 FALSE TRUE 1765713.777 1863805.578 1892499.263 1630119.418 1645022.726 2119300.512 1483436.358 1430893.641 1407754.771 1.254276535 1.323956144 1.344338731 1.157956948 1.168543527 1.505447224 1.05376049 1.016436719 1 20.42496461 2.072757041 10.97629232 1.017090552 1.284398668 0.632366619 0.096973166 0.291618472 42.40965276 0.038970458 0.026266598 118.2379906 -2.072757041 0.267308116 GGGSQHYPEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGGSQHYPEER 11 0 Q9NWH9;Q9NWH9-3;H7C3F4;H0YKH2 Q9NWH9 SLTM SAFB-like transcription modulator 0 ; 84.289 0.016073 1031740000 463500 406890 167385 265160 449720 481530 390180 410810 376170 FALSE TRUE 402247.3006 404217.1128 248332.9459 325368.6307 440771.4519 500054.7707 352340.4037 322961.4784 331699.6111 1.212685475 1.218624018 0.748668185 0.980913513 1.328827159 1.507553081 1.062227364 0.973656488 1 18.3395178 2.006457179 24.99661906 0.994845104 1.159942793 0.124948347 0.199235744 373.6991018 1446634.249 0.089749035 0.060339618 101.4979286 -2.006457179 0.165097689 GGGT(ph)PDANSLAPPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GGGTPDANSLAPPGK 15 0 Q9BRQ0;Q5T171 Q9BRQ0 PYGO2 Pygopus homolog 2 1 GGGT(0.993)PDANS(0.007)LAPPGK;GGGT(0.996)PDANS(0.004)LAPPGK;GGGT(1)PDANSLAPPGK;GGGT(1)PDANSLAPPGK;GGGT(1)PDANSLAPPGK;GGGT(1)PDANSLAPPGK 261.56 6.60E-24 6142230000 10328450 9284940 5816750 7373070 8610380 7637200 9627160 11174300 10241060 TRUE FALSE 8963519.164 9223946.618 8629749.756 9047238.234 8439050.284 7931008.026 8693519.505 8784762.903 9030373.553 0.992596719 1.021435776 0.955635966 1.001867551 0.934518404 0.878259131 0.962697662 0.972801718 1 23.10635424 3.243383032 24.99679126 0.949957032 0.992262846 0.276656081 0.034724942 181.7928554 942310.1903 0.010873818 0.013582575 1751.390671 -3.243383032 0.042305814 GGGTSSGGSSTNS(ph)LTGSRPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GGGTSSGGSSTNSLTGSRPPK 21 1 Q5T9C2-3;Q5T9C2;Q5T9C2-2 Q5T9C2-3 FAM102A Protein FAM102A 1 GGGTSSGGSSTNS(1)LTGSRPPK;GGGTSSGGSST(0.001)NS(0.999)LTGSRPPK;GGGTSSGGSST(0.001)NS(0.999)LTGSRPPK;GGGTSSGGSSTNS(1)LTGSRPPK;GGGTSSGGSST(0.001)NS(0.997)LT(0.001)GS(0.001)RPPK;GGGTSSGGSST(0.001)NS(0.999)LTGSRPPK 302.83 1.79E-55 1818090000 852208 844743 687356 758847 880356 858711 1116660 1035944 1189010 TRUE FALSE 739586.5536 839193.8276 1019763.661 931154.8096 862838.638 891746.1678 1008366.485 814415.4373 1048446.592 0.705411758 0.800416381 0.972642448 0.888128033 0.822968613 0.850540385 0.961771913 0.77678295 1 19.99982194 4.478508987 5.547308708 0.884930016 0.724898607 0.44321552 0.069955693 0.138506438 14.85591568 0.016648547 0.054131808 30096.0145 -4.478508987 -0.160031409 GGHDILVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGHDILVR 8 0 Q9Y678;H0Y8X7 Q9Y678 COPG1 Coatomer subunit gamma-1 0 130.27 0.001055 410480000 277580 293400 223470 205000 251320 334870 228130 241740 250190 FALSE TRUE 240897.0997 291472.6361 331540.8395 251548.3832 246319.2237 347752.6656 206005.9877 190045.7822 220612.8232 1.091945138 1.32119535 1.502817627 1.140225575 1.116522694 1.576303048 0.933789726 0.861444858 1 17.75115713 2.131978164 10.00124941 0.914297246 1.2874019 0.528498851 0.159963267 0.228221255 19.84790609 0.063774034 0.042983072 135.5121277 -2.131978164 0.373104654 GGHFAAFEEPELLAQDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGHFAAFEEPELLAQDIR 18 0 P07099 P07099 EPHX1 Epoxide hydrolase 1 0 ; 248.97 1.40E-24 520710000 286520 280900 236450 338250 389970 417590 199735 406010 438090 FALSE TRUE 248655.6561 279054.7494 350798.0109 415054.8323 382210.36 433654.9575 180364.7304 319187.9211 386299.4993 0.643686198 0.722379268 0.908098539 1.074437925 0.989414588 1.122587418 0.466903868 0.826270605 1 18.55936028 7.313442143 8.534536764 0.856785703 0.049554128 0 0.204171037 0 0 0.047192128 0 20579847.06 -7.313442143 -0.807231575 GGHGQQDLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGHGQQDLFR 10 0 B5MD46;Q9BXI6;Q9BXI6-2;H0Y2U5;H7C1Q1;F8W9Y7;H7C471;H0Y5R9;F8WCD1 B5MD46 TBC1D10A TBC1 domain family member 10A 0 141.95 3.66E-05 140660000 59742 69986 60858 55921 61219 70559 54917 62598 74917 FALSE TRUE 51846.94333 69526.25736 90289.13236 68618.71775 60000.86167 73273.45039 49591.15779 49211.90484 66060.39761 0.784841527 1.052465015 1.366766408 1.038726987 0.90827279 1.109188758 0.750694207 0.744953204 1 16.01149803 2.238940557 24.99999942 0.810389341 1.052137088 0.268768202 0.162743136 12.1184581 797492.6642 0.064836922 0.04707018 173.3566702 -2.238940557 0.241747748 GGHHRPDSSTLHTDDGYMPMS(ph)PGVAPVPSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGHHRPDSSTLHTDDGYMPMSPGVAPVPSGR 31 1 P35568 P35568 IRS1 Insulin receptor substrate 1 1 GGHHRPDS(0.007)S(0.007)T(0.007)LHT(0.007)DDGY(0.013)MPMS(0.957)PGVAPVPSGR 49.479 0.042168 80421000 14145 13791 10269 23969 24485 35062 22530 29636 34649 TRUE FALSE 12275.70241 13700.40601 15235.12275 29411.52779 23997.7964 36410.85783 20345.04407 23298.57203 30552.83469 0.401786038 0.448416854 0.49864842 0.962644812 0.78545237 1.191734194 0.665897102 0.762566625 1 14.89901862 3.814563436 5.063743452 0.874232434 0.438909992 0.673675746 0.145839017 0.136755936 6.383870124 0.039364797 0.069482107 6524.743387 -3.814563436 -0.435322442 GGHMDDGGYSMNFNMSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GGHMDDGGYSMNFNMSSSR 19 0 P38159;P38159-2;H3BT71;H0Y6E7;Q96E39;A0A1B0GUK8 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;;;;;; 270.55 2.64E-39 2558840000 1753634 1601859 969658 1134589 1626616 1607118 1489331 1636721 1460959 FALSE TRUE 1521886.824 1591336.283 1438587.852 1392214.774 1594249.524 1668944.869 1344895.909 1286720.951 1288246.091 1.181363432 1.235273519 1.116702672 1.080705607 1.23753492 1.295517123 1.043974376 0.998816111 1 20.29697678 2.080916696 7.128705004 1.005809358 1.186555105 0.657917415 0.060642354 0.138611373 10.19111171 0.026654709 0.017879 120.4804819 -2.080916696 0.180745747 GGHPPAIQSLINLLADNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGHPPAIQSLINLLADNR 18 0 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 0 105.9 0.00073551 0 105760 91840 72315 67948 103380 99666 81299 119680 93094 FALSE TRUE 91783.54804 91236.69699 107286.7759 83376.63192 101322.9403 103500.2155 73414.63549 94087.36335 82088.53337 1.118104372 1.111442649 1.306964219 1.015691577 1.234312956 1.260836456 0.894334842 1.146169379 1 16.32489309 2.253098225 24.9983937 1.036175247 1.17320308 0.347509051 0.102465331 283.5193608 487530.3972 0.036469296 0.028120943 179.1010883 -2.253098225 0.137027833 GGHSGQLGPSSVAPSFRPEDELEHLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGHSGQLGPSSVAPSFRPEDELEHLTK 27 1 Q93052;A0A087WZF1;C9JUT4;C9JXK9 Q93052 LPP Lipoma-preferred partner 0 267.75 8.16E-54 279660000 255250 208250 109870 173830 208910 198290 225560 272450 269140 FALSE TRUE 221518.0658 206881.992 163003.4995 213300.7583 204753.0997 205918.3446 203685.2259 214188.6877 237322.5758 0.933404945 0.871733299 0.68684363 0.898779889 0.862762841 0.867672803 0.858263169 0.902521334 1 17.85648982 -1.10057013 0.83984896 10 0.845954006 0.344068809 0.064028269 133.1592577 2.128568729 2230.024545 0.023253477 0.079328615 1.10057013 -9.154045994 GGIDNPAITS(ph)DQELDDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GGIDNPAITSDQELDDKK 18 1 Q13017-2;Q13017;H0YK04;A0A0A0MSK6 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 1 GGIDNPAIT(0.033)S(0.967)DQELDDKK;GGIDNPAIT(0.005)S(0.995)DQELDDKK;GGIDNPAIT(0.047)S(0.953)DQELDDKK 244.78 2.22E-24 1224350000 1154810 844850 937800 814520 773160 578314 1323270 1456570 1259730 TRUE FALSE 1002198.933 839300.1247 1391323.217 999469.2152 757775.6287 600562.1138 1194939.479 1145093.841 1110806.154 0.902226665 0.755577489 1.252534667 0.899769245 0.682185299 0.540654291 1.07574078 1.030867389 1 20.08317564 GGKNIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGKNIR 6 1 Q9NYT6 Q9NYT6 ZNF226 Zinc finger protein 226 0 ; 92.075 0.043018 1041550000 2698100 2482100 1404380 1930700 1550180 2389400 2914400 3521400 3721500 FALSE TRUE 2341539.249 2465794.922 2083542.865 2369094.944 1519334.451 2481321.764 2631761.937 2768376.014 3281548.51 0.713547047 0.751411998 0.63492673 0.721944209 0.462993141 0.756143558 0.80198782 0.843618799 1 21.64594533 1.583970763 1.13870075 1.041709935 0.667230911 0.619316263 0.085119251 0.618030009 1.048585854 0.254182625 0.02883119 38.3681415 -1.583970763 -0.374479025 GGLLTSEEDSGFSTS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GGLLTSEEDSGFSTSPK 17 0 Q9UQR1 Q9UQR1 ZNF148 Zinc finger protein 148 1 GGLLTSEEDSGFSTS(1)PK;GGLLTSEEDSGFST(0.119)S(0.88)PK;GGLLTSEEDSGFSTS(1)PK 285.18 3.01E-36 411209000 807230 664860 508751 733370 800840 570240 672170 912080 1015290 TRUE FALSE 700552.5102 660492.4909 754784.6853 899892.8674 784904.8508 592177.5018 606983.0569 717038.7898 895263.5728 0.78250979 0.737763169 0.843086559 1.005170873 0.876730468 0.661456045 0.677993694 0.800924791 1 19.77195296 4.14911427 0.003085567 1.620660983 1.55E-05 0.004348967 0.117250854 1979800.085 2551.024216 664506.2222 675398.0414 14096.59654 -4.14911427 -1.620645454 GGLNTPLHESDFSGVT(ph)PQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGLNTPLHESDFSGVTPQR 19 0 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 1 GGLNTPLHESDFSGVT(1)PQR 225.17 6.62E-19 283230000 153650 165650 59183 102860 193860 224560 172780 182930 211470 TRUE FALSE 133344.7632 164561.8342 87804.09676 126215.9351 190002.5653 233198.9685 156023.8222 143811.8431 186470.2575 0.715099367 0.882509825 0.47087454 0.676868991 1.018943009 1.250596056 0.836722297 0.771232072 1 17.50858601 3.246141077 24.95535696 0.953312003 0.684960116 0.446317069 0.158970179 187.6759076 617837.2392 0.050301847 0.063671384 1762.548503 -3.246141077 -0.268351886 GGLRPGS(ph)LDAEIDLLSSTLAELNGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GGLRPGSLDAEIDLLSSTLAELNGGR 26 1 Q15654 Q15654 TRIP6 Thyroid receptor-interacting protein 6 1 GGLRPGS(1)LDAEIDLLSSTLAELNGGR;GGLRPGS(1)LDAEIDLLSSTLAELNGGR;GGLRPGS(1)LDAEIDLLSSTLAELNGGR 187.49 6.92E-18 21208950000 1669690 1916290 1602872 1805143 2142100 2514200 2172890 2535700 2376480 TRUE FALSE 1449036.236 1903701.765 2378026.26 2215028.308 2099476.401 2610922.901 1962163.462 1993460.288 2095535.242 0.69148741 0.908456096 1.134806141 1.057022695 1.001880741 1.245945594 0.936354313 0.951289317 1 20.99888735 4.602184003 3.133178958 1.037993843 0.682307197 0.606388522 0.091471225 0.206241139 3.303879965 0.023961816 0.147546118 40011.42351 -4.602184003 -0.355686647 GGLS(ph)PANDTGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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;GGLS(1)PANDTGAK;GGLS(1)PANDTGAK 256.4 3.80E-21 10880380000 18472300 16060190 12860480 14645250 14801000 13988190 19229910 21080040 21009800 TRUE FALSE 16031138.75 15954689.55 19079851.14 17970677.85 14506489.06 14526324.72 17364996.29 16572237.49 18526045.38 0.865329779 0.8612032 1.029893361 0.970022338 0.783032145 0.784102836 0.937328822 0.894537239 1 24.14305162 0.927402835 1.887331966 1.152203777 0.889576322 0.166833833 0.076336821 4.989088217 7.923426385 3.155516196 0.022298541 8.460632574 -0.927402835 -0.262627455 GGLS(ph)PANDTGAKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGLSPANDTGAKK 13 1 P30419;B7Z8J4;K7EN42 P30419 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 1 GGLS(0.999)PANDT(0.001)GAKK 70.783 0.026981 293530000 422980 364060 182090 180660 257900 223360 413450 482230 52009 TRUE FALSE 367082.1213 361668.4659 270149.3331 221681.6142 252768.2946 231952.8037 373353.6826 379108.8672 45860.55527 8.00431044 7.886264433 5.890668603 4.8338188 5.511671045 5.057784459 8.141063283 8.266556412 1 15.4849662 4.242177196 7.061795072 5.868180442 7.961259903 0.185041092 2.013129495 0.244688868 66.45995468 0.520623627 1.249276173 17465.34609 -4.242177196 2.09307946 GGLWDDDDAPRPSQFEEDLALMEEMEAEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGLWDDDDAPRPSQFEEDLALMEEMEAEHR 30 1 A0A087WYJ2;M0R2B7;P28340;M0QZR8;A0A2R8Y7K6;M0R2J2 A0A087WYJ2 POLD1 DNA polymerase;DNA polymerase delta catalytic subunit 0 ; 230.69 1.38E-35 145355000 100086 105196 74034 76015 93283 107909 94518 106487 100039 FALSE TRUE 86859.38151 104504.9605 109837.09 93275.36757 91426.85081 112060.3291 85351.65891 83715.58373 88212.50338 0.984660657 1.184695554 1.245141968 1.057393952 1.036438683 1.270345186 0.967568719 0.949021743 1 16.42869554 2.18996163 23.42900233 0.967174881 1.129986221 0.406161928 0.089754034 57.49464498 27716.62605 0.035853806 0.024172744 154.8679787 -2.18996163 0.162811341 GGNFGFGDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 GGNFGFGDSR 10 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;; 251.98 1.11E-16 43513910000 22170800 18222380 12412970 13012610 17320030 18434090 16680760 19376220 16923880 FALSE TRUE 19240872.61 18102675.99 18415923.81 15967321.99 16975395.29 19143261.37 15063062.46 15232766.14 14923158.19 1.289329803 1.213059311 1.23405003 1.069969358 1.137520294 1.28278888 1.009374978 1.020746812 1 23.83104955 -1.671630512 0.157490094 4.97E-11 1.361888634 0.574407955 0.072991011 92.98682796 1.340490309 28.10880657 1.088601497 0.021299504 1.671630512 1.361888634 GGNFGGR ddPTM_MDA-MB-175_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 ;;;;; 151.7 0.0043358 6457160000 6344660 6164690 4129770 4343960 3852370 5875750 5434860 5992210 5700340 FALSE TRUE 5506197.106 6124193.745 6126940.585 5330322.511 3775715.374 6101793.905 4907788.114 4710822.523 5026452.299 1.095444019 1.21839289 1.218939367 1.060454212 0.751169045 1.213936499 0.97639206 0.937206253 1 22.26110907 3.482351682 24.94844208 0.975876145 1.174676303 0.390340209 0.11517702 218.847785 1043876.658 0.031685121 0.042165054 3036.348955 -3.482351682 0.198800159 GGNIGDGGGAADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GGNIGDGGGAADR 13 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 182.25 2.64E-05 2076390000 3880250 2705440 1882410 1998600 2357470 2785210 2374200 2553950 2542330 FALSE TRUE 3367465.131 2687667.787 2792749.772 2452412.677 2310560.959 2892358.831 2143950.449 2007807.667 2241778.644 1.502139893 1.198899719 1.2457741 1.093958444 1.030682028 1.290207148 0.95636135 0.895631544 1 21.0962124 8 0.243163218 0.894873997 4.235112689 0.669518388 0.104120607 53.20328736 0.840653476 0.383272582 69.95381688 100000000 -8 3.340238692 GGNRFEPYANPTKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGNRFEPYANPTKR 14 2 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 140.1 5.65E-06 849910000 1259840 960580 405420 468470 898020 845430 1043780 1138540 200366 FALSE TRUE 1093348.952 954269.8867 601482.468 574843.2736 880151.1589 877954.2392 942554.3763 895072.0811 176678.9597 6.188337047 5.40115183 3.404380855 3.253603454 4.981641053 4.969206523 5.334842234 5.066093226 1 17.43077072 4.428576929 5.608069421 4.213643959 6.014530306 0.247182668 1.29489866 0.256861522 18.0733399 0.326277784 0.927187107 26827.29771 -4.428576929 1.800886347 GGNVGINSFGFGGSNVHIILRPNTQPPPAPAPHATLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 307 1.03E-93 5869880000 534840 665077 256299 371800 645645 747310 626883 600897 537267 FALSE TRUE 464159.5389 660708.0654 380246.0537 456222.8726 632797.9277 776059.4993 566087.9831 472399.8527 473751.9073 0.979752338 1.394628824 0.802626961 0.962999548 1.335715842 1.63811372 1.194903861 0.99714607 1 18.85377223 3.245233804 24.9990707 1.221048661 1.044091344 0.152613127 0.230619285 384.0205657 1438607.849 0.073073432 0.092151839 1758.870255 -3.245233804 -0.176957317 GGPAS(ph)PGGLQGLETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GGPASPGGLQGLETR 15 0 C9JWC4;Q8NCD3-3;Q8NCD3-2;Q8NCD3 C9JWC4 HJURP Holliday junction recognition protein 1 GGPAS(1)PGGLQGLETR;GGPAS(1)PGGLQGLETR;GGPAS(1)PGGLQGLETR 279.32 1.24E-33 970310000 787840 740380 446480 542610 662600 715010 644120 759410 673730 TRUE FALSE 683724.9479 735516.395 662399.2214 665817.8938 649415.5564 742516.8974 581653.3415 597016.0812 594082.4069 1.150892435 1.238071329 1.114995519 1.120750061 1.093140529 1.249855052 0.97907855 1.004938161 1 19.18030354 2.221081065 24.99377126 0.996161172 1.157730558 0.709141483 0.050263363 130.3144367 186333.4073 0.02027367 0.013702688 166.3723171 -2.221081065 0.161569386 GGPASVPSS(ph)SPGTSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGPASVPSSSPGTSVK 16 0 O43237;O43237-2;J3KRI4;J3KRZ2 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 GGPASVPS(0.14)S(0.574)S(0.278)PGT(0.008)SVK 162.37 7.52E-09 0 419730 380100 244340 268230 312350 268950 342610 396530 400860 TRUE FALSE 364261.617 377603.0981 362503.6413 329135.7211 306134.8461 279296.6805 309383.7349 311735.1453 353470.7875 1.030528208 1.068272433 1.025554739 0.931153953 0.866082451 0.790154916 0.875273844 0.881926191 1 18.43123146 3.655629216 2.533496699 0.878018588 1.049394229 0.666109975 0.051365182 0.170600992 2.137444491 0.01556255 0.026449603 4525.110783 -3.655629216 0.171375641 GGPASVPSSS(ph)PGTSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGPASVPSSSPGTSVK 16 0 O43237;O43237-2;J3KRI4;J3KRZ2 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 GGPASVPS(0.001)S(0.154)S(0.845)PGTSVK;GGPASVPS(0.001)S(0.033)S(0.966)PGTSVK 326.43 1.35E-60 844770000 1807450 1574840 947970 1100270 1346400 1189880 1575200 1844140 1650590 TRUE FALSE 1568590.903 1564494.772 1406411.463 1350103.12 1319609.274 1235655.454 1422437.346 1449785.012 1455459.131 1.077729268 1.074914946 0.966300897 0.927613213 0.906661854 0.848979836 0.977311775 0.996101492 1 20.4730429 4.202395181 4.055815264 0.945244024 1.07930004 0.601523174 0.044379598 0.155770841 5.455483395 0.013170041 0.032435325 15936.58199 -4.202395181 0.134056016 GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(ph)PGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GGPEGVAAQAVASAASAGPADAEMEEIFDDASPGK 35 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 1 GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(1)PGK;GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(1)PGK;GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(1)PGK;GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(1)PGK;GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(1)PGK 161.04 1.03E-14 221099000 246034 192570 177472 211981 241533 206334 220001 294581 408598 TRUE FALSE 213519.9835 191304.995 263298.0528 260114.526 236726.9659 214271.8025 198665.3369 231587.1456 360294.0099 0.59262707 0.530969124 0.730786651 0.721950737 0.657038306 0.594713752 0.551397835 0.642772678 1 18.45881514 1.240317022 6.319176598 1.011244474 0.627038383 0.765157436 0.064865424 0.062790945 10.91326367 0.104041937 0.017206972 17.39069836 -1.240317022 -0.384206091 GGPEVQQVPAGERPLWFICSGMGTQWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 337.29 1.60E-95 16810340000 2112600 2187197 1772289 1554634 2362250 2573730 2058810 2330360 2166149 FALSE TRUE 1833414.557 2172829.159 2629373.888 1907637.411 2315245.847 2672743.059 1859146.923 1832030.649 1910069.333 0.959868066 1.137565596 1.376585574 0.998726789 1.2121266 1.399291121 0.97334002 0.959143533 1 20.86519358 2.101453937 24.98638243 0.97339815 1.181261464 0.324498072 0.1381608 12.53002904 3062.92146 0.055628971 0.037505046 126.3147123 -2.101453937 0.207863314 GGPGAAPGGASPASSSSAAS(ph)SPSSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGPGAAPGGASPASSSSAASSPSSGR 26 0 Q9BXK1 Q9BXK1 KLF16 Krueppel-like factor 16 1 GGPGAAPGGAS(0.001)PAS(0.074)S(0.009)S(0.009)S(0.013)AAS(0.528)S(0.359)PS(0.003)S(0.003)GR 153.86 7.86E-08 141930000 100450 98869 72581 76017 93783 101110 95268 93981 95197 TRUE FALSE 87175.27799 98219.52303 107681.4144 93277.8217 91916.90178 104999.7671 86028.92402 73883.89451 83942.91911 1.038506629 1.170075142 1.282793302 1.111205361 1.094992916 1.250847221 1.024850278 0.880168277 1 16.35712101 2.031693229 5.817242591 0.936757046 1.15867841 0.595302864 0.076086287 0.104741465 10.16222972 0.031985555 0.020649451 107.5705102 -2.031693229 0.221921364 GGPGAAPGGASPASSSSAASS(ph)PSSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGPGAAPGGASPASSSSAASSPSSGR 26 0 Q9BXK1 Q9BXK1 KLF16 Krueppel-like factor 16 1 GGPGAAPGGASPASSSSAAS(0.445)S(0.543)PS(0.006)S(0.006)GR 341.39 1.60E-95 151030000 136050 124140 94900 109830 116770 135290 110780 128330 129240 TRUE FALSE 118070.6478 123324.5162 140793.9574 134768.5801 114446.5055 140494.6938 100036.5727 100887.6282 113961.3944 1.036058293 1.08216047 1.235453095 1.182581003 1.004256801 1.232827086 0.877811062 0.88527899 1 16.79818565 2.22683044 24.99991829 0.911781045 1.128384622 0.585398959 0.082338483 145.1301579 309305.6678 0.033026401 0.022471119 168.5894681 -2.22683044 0.216603576 GGPGGGFRPFVPHIPFDFYLCEMAFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGPGGGFRPFVPHIPFDFYLCEMAFPR 27 1 Q12905;A0A0A0MRL0 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 155.44 1.97E-08 229630000 288570 266400 174790 198090 236730 295990 227570 279370 237340 FALSE TRUE 250434.7434 264650.0009 259319.0286 243069.3621 232019.5362 307376.9268 205500.2964 219628.8996 209281.9356 1.196638127 1.264562085 1.239089403 1.161444543 1.108645787 1.468721732 0.981930408 1.049440311 1 17.67508826 2.177361965 24.99999996 1.017388973 1.231415217 0.563025226 0.095007135 51.1812089 20907.20351 0.036932066 0.024899602 150.4395288 -2.177361965 0.214026244 GGPGKLS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 94.82 0.017233 7625910000 5647300 4990910 3303160 4100860 4630730 4483100 5556610 6267470 5003910 TRUE FALSE 4900994.997 4958124.384 4900579.224 5032022.941 4538587.533 4655567.758 5017730.817 4927220.314 4412353.46 1.110743969 1.123691569 1.11064974 1.140439674 1.028609239 1.055121218 1.137200558 1.116687581 1 22.07311693 3.269098381 24.99981811 1.078274774 1.120779726 0.285579948 0.040381268 347.7621182 284694.0459 0.012257241 0.0158223 1858.225352 -3.269098381 0.042504952 GGPNYQEGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGPNYQEGLR 10 0 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 84.615 0.034433 164630000 40802 36875 29215 34595 38141 36943 37355 38329 47864 FALSE TRUE 35409.91232 36632.7657 43343.47172 42450.3235 37382.06872 38364.22112 33732.31785 30132.64163 42205.57245 0.838986661 0.867960404 1.026960878 1.005799022 0.885714055 0.908984736 0.799238487 0.713949364 1 15.36514587 2.312706637 4.489257505 0.810259508 0.92877173 0.139449831 0.091106489 0.294279816 11.20058161 0.036446771 0.027208173 205.4502324 -2.312706637 0.118512222 GGPPFAFVEFEDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGPPFAFVEFEDPR 14 0 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 111.06 0.0015673 125770000 111980 87288 79304 95653 91670 99875 77427 101190 164420 FALSE TRUE 97181.55928 86714.59938 117655.6797 117372.4756 89845.94635 103717.2559 69918.14146 79551.30596 144982.4549 0.670298757 0.598104091 0.811516674 0.809563307 0.619702201 0.715377981 0.482252432 0.548696089 1 17.1455188 3.193711957 24.9976685 0.64542912 0.719862791 0.007352094 0.149438796 443.3905936 247134.559 0.045928738 0.052078512 1562.111238 -3.193711957 0.074433671 GGPPFAFVEFEDPRDAEDAVYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GGPPFAFVEFEDPRDAEDAVYGR 23 1 J3KTL2;Q07955;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;;;;; 164.98 1.25E-11 3376901000 1121263 1059012 564717 539973 867035 986497 916363 1042665 264832.6 FALSE TRUE 973085.2536 1052055.28 837816.0301 662582.1226 849782.6998 1024448.178 827494.2573 819699.2038 233524.3917 4.166953381 4.505119455 3.58770244 2.837314414 3.638946208 4.386900102 3.543502463 3.510122423 1 17.83321372 4.108016813 4.56023573 3.281150849 4.327318663 0.224220924 0.878245104 0.339799475 11.96390503 0.22743418 0.503634095 12823.80228 -4.108016813 1.046167814 GGQGDPAVPAQQPADPST(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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(0.015)T(0.985)PER;GGQGDPAVPAQQPADPS(0.027)T(0.973)PER;GGQGDPAVPAQQPADPS(0.006)T(0.994)PER;GGQGDPAVPAQQPADPS(0.34)T(0.66)PER;GGQGDPAVPAQQPADPS(0.155)T(0.845)PER;GGQGDPAVPAQQPADPS(0.185)T(0.815)PER;GGQGDPAVPAQQPADPS(0.001)T(0.999)PER;GGQGDPAVPAQQPADPS(0.008)T(0.992)PER 266.92 5.19E-36 6264970000 5093300 4991530 4206640 4144210 4746800 5288620 4309550 4918620 6129060 TRUE FALSE 4420207.5 4958740.311 6240985.174 5085216.221 4652347.967 5492076.634 3891610.504 3866811.39 5404489.509 0.817876969 0.917522423 1.154777924 0.940924432 0.860830234 1.016206364 0.720069953 0.715481339 1 22.36572692 2.239844127 24.99948625 0.787949344 0.954475916 0.225317068 0.119133111 42.55910168 828971.9512 0.046595986 0.034061787 173.7177224 -2.239844127 0.166526571 RNS(ph)CNVGGGGGGFK ddPTM_MDA-MB-175_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 163.79 2.59E-06 2012600000 1977620 1321760 1339380 1517530 1760180 1853810 2248940 2435760 4847900 TRUE FALSE 1716272.506 1313077.272 1987108.648 1862108.38 1725155.862 1925127.27 2030838.145 1914891.679 4274786.785 0.401487277 0.307167898 0.46484392 0.435602633 0.403565359 0.450344629 0.475073553 0.44795022 1 22.02742103 1.230069735 4.614439149 1.050671443 0.421684064 0.937253944 0.046931422 0.049532114 2.291745598 0.102938763 0.012406453 16.98516361 -1.230069735 -0.628987379 GGQGDPAVPAQQPADPST(ph)PERQSS(ph)PSGSEQLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGQGDPAVPAQQPADPSTPERQSSPSGSEQLVR 33 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;H7BZT5;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 2 GGQGDPAVPAQQPADPS(0.104)T(0.895)PERQS(0.2)S(0.444)PS(0.284)GS(0.073)EQLVR 81.831 0.0018891 377590000 114450 110930 51515 40277 91117 111770 90009 94406 11343 TRUE FALSE 99325.14252 110201.2935 76427.82631 49422.50845 89303.94997 116069.8642 81279.94103 74218.01157 10002.04346 9.930484995 11.01787789 7.641221176 4.941241121 8.928570477 11.60461506 8.126333518 7.42028485 1 13.28800716 4.19894794 7.055424543 7.318465939 10.47347867 0.204433864 2.746137467 0.306635732 41.81203196 0.719934099 1.552162338 15810.58504 -4.19894794 3.155012735 GGQGDPAVPTQQPADPS(ph)TPEQQNSPSGSEQFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGQGDPAVPTQQPADPSTPEQQNSPSGSEQFVR 33 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 GGQGDPAVPTQQPADPS(0.568)T(0.431)PEQQNSPSGSEQFVR 139.3 4.48E-10 89784000 81977 87104 68718 73969 82557 92077 76497 92956 89180 TRUE FALSE 71143.53175 86531.80809 101950.2546 90764.792 80914.27722 95619.26177 69078.33271 73078.08278 78637.24199 0.904705327 1.100392205 1.296462745 1.154221457 1.028956194 1.215953909 0.878442974 0.929306279 1 16.2629251 2.231060573 24.99831398 0.932144559 1.121914008 0.385122872 0.107566427 171.1933939 570596.9066 0.043790542 0.030170969 170.2395933 -2.231060573 0.189769449 GGQS(ph)DDDEDEGVPASYHTVSLQLLDLMHTLHTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 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;GGQS(1)DDDEDEGVPASYHTVSLQLLDLMHTLHTR;GGQS(1)DDDEDEGVPASYHTVSLQLLDLMHTLHTR;GGQS(1)DDDEDEGVPASYHTVSLQLLDLMHTLHTR 307.76 7.57E-104 6346809000 991167.8 1119434.8 442743.4 582367.4 962537 1126641.4 1011495 1170844 584377.7 TRUE FALSE 860182.4639 1112081.159 656855.5891 714602.8191 943384.3969 1169984.024 913400.3706 920468.1221 515293.234 1.669306731 2.158152069 1.274721936 1.386788671 1.830771946 2.270520834 1.772583667 1.786299647 1 18.97503412 GGQS(ph)DDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GGQSDDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR 37 0 A0A669KBG8;A0A669KB10;Q92538 A0A669KBG8 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 GGQS(1)DDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR;GGQS(1)DDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR;GGQS(1)DDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR;GGQS(1)DDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR;GGQS(1)DDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR;GGQS(1)DDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR;GGQS(1)DDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR 260.14 4.97E-62 2468639000 412334.2 429161 176937 253895.1 413940 431680.2 490193.09 505975 211083.1 TRUE FALSE 357843.1907 426341.8131 262504.325 311545.863 405703.4039 448287.2166 442654.2396 397776.1838 186129.0964 1.922553742 2.290570477 1.410334709 1.673816018 2.179688247 2.408474684 2.378210866 2.137098345 1 17.50594407 3.230747956 24.97922151 2.081447667 1.828052138 0.036012803 0.447017632 530.8717303 1697339.355 0.137303241 0.158540275 1701.170942 -3.230747956 -0.253395529 GGQVSLTVHGTQQVHS(ph)PPEQSPVQANSSSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGQVSLTVHGTQQVHSPPEQSPVQANSSSSK 31 0 P22670 P22670 RFX1 MHC class II regulatory factor RFX1 1 GGQVSLTVHGT(0.001)QQVHS(0.998)PPEQSPVQANSSSSK 155.88 5.22E-09 94453000 128970 71226 22918 64123 90235 71964 77366 100760 81219 TRUE FALSE 111926.2877 70758.11172 34001.22146 78683.10721 88439.50004 74732.50165 69863.05723 79213.25812 71617.38234 1.562836899 0.988001926 0.474762137 1.098659357 1.234888754 1.043496693 0.975504199 1.106061902 1 16.12802217 GGREGFES(ph)DTDSEFTFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GGREGFESDTDSEFTFK 17 1 E9PMS6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 GGREGFES(0.968)DT(0.032)DSEFTFK;GGREGFES(0.996)DT(0.004)DSEFTFK;GGREGFES(0.988)DT(0.012)DSEFTFK 130.17 1.89E-05 342494000 494210 451300 222798 239248 424360 398400 494070 579770 127692 TRUE FALSE 428898.8963 448335.3806 330543.858 293572.9151 415916.0662 413726.7058 446155.1674 455790.6973 112596.3972 3.809170692 3.981791528 2.935652171 2.607302918 3.693866558 3.674422237 3.962428447 4.048004275 1 16.78080114 1.232435479 24.99784097 0.999995727 3.59520633 0.752271688 0.466914525 113.8354797 464537.7327 1.135892265 0.126482312 17.07793984 -1.232435479 2.595210603 GGRS(ph)PDEVTLTSIVPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GGRSPDEVTLTSIVPTR 17 1 A0A0C4DGG1;Q9UKS6;H0YDM6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 GGRS(1)PDEVTLTSIVPTR;GGRS(1)PDEVTLTSIVPTR;GGRS(1)PDEVTLTSIVPTR;GGRS(1)PDEVTLTSIVPTR 185.16 3.60E-10 2150570000 822040 719576 505683 576383 727484 697690 646150 821800 707470 TRUE FALSE 713405.3312 714849.0579 750232.9902 707259.5696 713008.4917 724530.5858 583486.4725 646064.4653 623833.7026 1.143582542 1.145896823 1.202616959 1.133730939 1.142946411 1.161416228 0.935323741 1.035635719 1 19.25080197 2.251450453 24.99806797 0.997469133 1.155261887 0.864992193 0.030632047 71.76131171 139171.1535 0.011019214 0.008479653 178.4228421 -2.251450453 0.157792755 GGRSPDEVT(ph)LTSIVPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGRSPDEVTLTSIVPTR 17 1 A0A0C4DGG1;Q9UKS6;H0YDM6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 GGRS(0.051)PDEVT(0.691)LT(0.243)S(0.012)IVPT(0.002)R 128.59 0.00023206 229930000 233100 208790 134450 161890 189670 228880 188260 200700 168570 TRUE FALSE 202295.2444 207418.4447 199470.4697 198649.5988 185895.9381 237685.1617 170002.5742 157781.8668 148641.8466 1.360957557 1.3954243 1.341953657 1.336431182 1.250629902 1.599046077 1.143706016 1.061490222 1 17.1814808 2.041325426 9.885296542 1.055240024 1.371972257 0.736589825 0.089579202 0.184666322 42.6542804 0.035117248 0.02361902 109.9829657 -2.041325426 0.316732233 GGRT(ph)PPQQGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGRTPPQQGGR 11 1 A0A2R8Y4Z8;M0QYB4;Q9Y3X0 A0A2R8Y4Z8;Q9Y3X0 CCDC9 Coiled-coil domain-containing protein 9 1 GGRT(1)PPQQGGR 72.891 0.072839 360850000 147310 146440 81501 105720 134510 131830 127000 136340 100850 TRUE FALSE 127842.6103 145478.026 120915.1562 129725.3418 131833.5142 136901.5854 114683.5595 107184.752 88927.62789 1.437602838 1.635914838 1.35970293 1.458774342 1.482480949 1.539471913 1.289628007 1.205303172 1 16.44034408 1.584601743 1.24445657 0.935396087 1.48746929 0.808291469 0.07919419 0.313264528 0.670135104 0.202400396 0.024632762 38.42392654 -1.584601743 0.552073203 GGS(ph)DGYGSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGSDGYGSGR 10 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 GGS(0.999)DGYGS(0.001)GR;GGS(0.985)DGYGS(0.015)GR 108.3 0.0022758 461900000 976070 870310 518890 625080 586180 869220 810990 909400 829760 TRUE FALSE 847079.8765 864592.8763 769826.9396 767013.9677 574516.1648 902659.4559 732340.3146 714931.887 731666.7181 1.157740069 1.18167583 1.052155197 1.048310588 0.78521566 1.233703042 1.000920633 0.977127795 1 19.48082711 4.094002545 2.641865975 1.005051536 1.173072971 0.272609475 0.10750977 0.352700943 4.913256551 0.028094611 0.072986531 12416.59584 -4.094002545 0.168021434 GGS(ph)GAPILLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GGSGAPILLR 10 0 M0QXB5;O95571;M0QX80;M0QY80 M0QXB5 ETHE1 "Persulfide dioxygenase ETHE1, mitochondrial" 1 GGS(1)GAPILLR;GGS(1)GAPILLR;GGS(1)GAPILLR 125.3 0.00043301 332551000 302322 353125 240074 257951 334618 388439 348565 355235 370829 TRUE FALSE 262369.3817 350805.2986 356174.5894 316522.7171 327959.7565 403382.4997 314761.2199 279270.7597 326990.0181 0.802377342 1.072831827 1.089252178 0.967988928 1.002965651 1.233623283 0.962601922 0.854065091 1 18.31888707 2.006931636 24.9998209 0.914126054 1.034849219 0.123926546 0.112755969 268.2419017 967444.3192 0.044924076 0.030211884 101.6088734 -2.006931636 0.120723165 GGS(ph)GGGGGGGGGGYNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGSGGGGGGGGGGYNR 16 0 P35637-2;P35637;H3BPE7;H3BNZ4 P35637-2 FUS RNA-binding protein FUS 1 GGS(1)GGGGGGGGGGYNR 175.27 2.46E-12 0 50506 51841 32970 39733 31635 51329 44583 53286 53207 TRUE FALSE 43831.50413 51500.45306 48914.40228 48754.98493 31005.52539 53303.65984 40259.34752 41891.20357 46916.92907 0.934236426 1.097694459 1.042574679 1.039176815 0.660860078 1.136128491 0.858098523 0.89288034 1 15.51782097 GGS(ph)LESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGSLESR 7 0 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 GGS(0.996)LES(0.004)R;GGS(0.999)LES(0.001)R 109.11 0.0079678 193610000 921680 878560 538690 683720 512820 784270 841130 864870 852570 TRUE FALSE 799877.6528 872788.6815 799202.2858 838969.076 502615.8853 814441.3744 759557.3421 679924.2809 751780.1459 1.063978155 1.160962665 1.063079798 1.115976633 0.66856765 1.08335047 1.010345041 0.904419044 1 19.51995129 GGS(ph)PAPLPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GGSPAPLPAK 10 0 A0A087WWH3;Q9NZM4-2;Q9NZM4 A0A087WWH3 GLTSCR1 Glioma tumor suppressor candidate region gene 1 protein 1 GGS(1)PAPLPAK;GGS(1)PAPLPAK;GGS(1)PAPLPAK 133.81 0.00019653 526500000 1551780 1373540 1095420 1336940 1315880 1250840 1317030 1527950 2759750 TRUE FALSE 1346708.341 1364517.125 1625168.776 1640512.661 1289696.562 1298960.624 1189304.633 1201209.783 2433495.499 0.553404903 0.560723094 0.667833073 0.674138358 0.529976966 0.533783861 0.488722759 0.49361496 1 21.21459868 1.233200376 24.99738063 1.00000069 0.56082986 0.826179364 0.063020593 78.5026928 366055.188 0.147560395 0.017633161 17.10804468 -1.233200376 -0.43917083 GGS(ph)PAPLPAKVDEATSGLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGSPAPLPAKVDEATSGLIR 20 1 A0A087WWH3;Q9NZM4-2;Q9NZM4 A0A087WWH3 GLTSCR1 Glioma tumor suppressor candidate region gene 1 protein 1 GGS(1)PAPLPAKVDEATSGLIR;GGS(1)PAPLPAKVDEATSGLIR 151.47 4.58E-08 203155000 371520 307220 154867 192695 268540 271159 327430 397090 93353 TRUE FALSE 322422.6907 305201.8516 229761.1992 236449.3449 263196.5794 281590.6622 295675.889 312175.3937 82316.91469 3.916846154 3.707644446 2.79117846 2.872427202 3.197357194 3.420811667 3.591921419 3.792360232 1 16.32890129 4.363009677 5.690854117 3.085858741 3.863697916 0.16229525 0.772445445 0.392141735 17.53734541 0.189688161 0.520815066 23067.98588 -4.363009677 0.777839175 GGS(ph)PDLWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGSPDLWK 8 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 GGS(1)PDLWK;GGS(1)PDLWK 137.98 0.00076059 6149470000 11637170 9802770 6545300 8193800 9268700 8235000 10517010 12680100 11517080 TRUE FALSE 10099288.5 9738374.958 9710628.973 10054327.52 9084271.004 8551805.779 9497071.989 9968559.292 10155543.92 0.994460619 0.958922046 0.956189944 0.990033385 0.894513487 0.842082496 0.935161333 0.981587926 1 23.27576418 3.258934346 24.99769679 0.932941487 0.972423569 0.194107955 0.0445245 528.1454082 648007.5737 0.014546165 0.018755529 1815.241223 -3.258934346 0.039482082 GGS(ph)PLAAPQGGSPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGSPLAAPQGGSPTK 15 0 E7EPC8;Q9UQB3-2;Q9UQB3 E7EPC8 CTNND2 Catenin delta-2 1 GGS(1)PLAAPQGGSPTK 144.73 4.39E-06 88156000 365190 276520 150830 223560 271000 221570 265150 383260 211630 TRUE FALSE 316929.2162 274703.5219 223771.8925 274322.7149 265607.6302 230093.9413 239435.7938 301302.8315 186611.3425 1.69833844 1.472062299 1.199133394 1.470021657 1.423319862 1.233011553 1.283072029 1.614600846 1 17.50967715 4.614575263 3.41618055 1.347719676 1.704528773 0.335765553 0.168098682 0.315121719 5.959044246 0.040393186 0.234557088 41169.46874 -4.614575263 0.356809097 GGS(ph)PQMDDIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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 137.84 8.46E-05 4556888000 10881540 7344300 6576120 7955910 7200660 6328290 8433130 9727270 14179370 TRUE FALSE 9443516.919 7296054.81 9756353.628 9762420.964 7057380.954 6571743.411 7615286.351 7647169.008 12503101.03 0.755293978 0.583539619 0.780314708 0.780799974 0.564450446 0.525609078 0.609071808 0.611621788 1 23.57578262 1.235087436 24.99765827 1.000000495 0.646808062 0.587728225 0.09170244 75.39105462 542527.8548 0.166670848 0.023428766 17.18254286 -1.235087436 -0.353192433 GGS(ph)PVLGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGSPVLGAR 9 0 A0A0A0MRC1;A0A0A0MQV3;K7EJS8;Q6UWL6-3;Q6UWL6-2;Q6UWL6 A0A0A0MRC1 KIRREL2 Kin of IRRE-like protein 2 1 GGS(1)PVLGAR 68.422 0.058944 0 15707 13299 16849 18472 20308 23133 21905 23166 23840 TRUE FALSE 13631.28015 13211.63799 24997.23276 22666.34993 19903.91053 24022.94148 19780.65647 18212.13118 21021.66236 0.648439687 0.628477319 1.189117793 1.07823775 0.946828571 1.142770779 0.940965378 0.866350666 1 14.35958914 4.255898168 24.98674229 1.008499086 0.638458152 0.73080754 0.096814411 136.2996952 196430.651 0.026210333 0.06899134 18025.95023 -4.255898168 -0.370040934 GGS(ph)PYNQFDIIPGDTLGGHTGPAGDSWLPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GGSPYNQFDIIPGDTLGGHTGPAGDSWLPAK 31 0 Q9UPQ9-1;Q9UPQ9;H0Y720;Q9UPQ9-2 Q9UPQ9-1 TNRC6B Trinucleotide repeat-containing gene 6B protein 1 GGS(1)PYNQFDIIPGDTLGGHTGPAGDSWLPAK;GGS(1)PYNQFDIIPGDTLGGHTGPAGDSWLPAK;GGS(1)PYNQFDIIPGDTLGGHTGPAGDSWLPAK;GGS(1)PYNQFDIIPGDTLGGHTGPAGDSWLPAK 241.67 3.90E-46 1696860000 923630 848890 393738 651748 827840 701899 872660 1023150 1079740 TRUE FALSE 801569.9553 843313.5857 584151.0138 799737.3447 811367.6036 728901.5087 788029.5675 804357.3347 952094.3672 0.841901793 0.885745799 0.613543188 0.839976973 0.852192421 0.765576957 0.827680107 0.844829423 1 19.86074505 0.795347035 1.381240451 1.38792052 0.799575459 0.404604958 0.074532215 3.925896644 2.74281074 4.425387521 0.021342056 6.242334473 -0.795347035 -0.588345061 GGS(ph)REYDTGGGSSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGSREYDTGGGSSSSR 16 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 GGS(1)REYDTGGGSSSSR 86.439 0.0041234 391780000 126170 117510 60648 52896 91444 127250 97023 114520 20064 TRUE FALSE 109496.3148 116738.0691 89977.57566 64906.84526 89624.44331 132145.3898 87613.72439 90030.7892 17692.05678 6.189009916 6.598332265 5.085761186 3.668699806 5.065801248 7.469193181 4.952150307 5.08876895 1 14.11081416 1.209020198 3.040511089 1.08E-11 5.552221569 0.655733801 1.032288069 0.293019779 3.238542109 4.147733157 0.280254348 16.18155294 -1.209020198 5.552221569 GGS(ph)SKDLLDNQSQEEQRR ddPTM_MDA-MB-175_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(0.963)S(0.037)KDLLDNQSQEEQRR 136.77 2.90E-06 256440000 218680 154800 92674 95467 149270 104030 267740 248560 98259 TRUE FALSE 189780.8839 153783.1086 137491.4564 117144.2415 146299.819 108032.1014 241774.616 195407.3783 86642.93296 2.190379266 1.774906543 1.586874448 1.35203458 1.688537242 1.246865702 2.79047128 2.255318139 1 16.40279446 2.266130734 24.9999813 2.09757645 1.632779555 0.103007942 0.502631161 391.1856931 354717.4518 0.18748632 0.145192539 184.5570902 -2.266130734 -0.464796895 GGS(ph)TEDASQYYCDKNDNGDSYLVLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.948)T(0.018)EDAS(0.034)QYYCDKNDNGDSYLVLIR;GGS(0.984)T(0.016)EDASQYYCDKNDNGDSYLVLIR 280.94 4.65E-61 821940000 375780 388840 269010 374610 398730 369890 356760 552920 381510 TRUE FALSE 326119.7209 386285.6844 399104.1358 459670.9261 390796.0531 384119.9077 322161.4701 434682.3608 336408.3224 0.969416329 1.148264352 1.1863682 1.366407712 1.161671775 1.141826412 0.957650119 1.292127251 1 18.35985387 1.191722508 23.35890188 0.999994766 1.157825004 0.129705664 0.123957221 12888.75903 6426658.232 18.51473996 0.029991153 15.54971768 -1.191722508 0.157830237 GGS(ph)TVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGSTVPK 7 0 Q92504;A2AAT0 Q92504 SLC39A7 Zinc transporter SLC39A7 1 GGS(0.988)T(0.012)VPK 66.073 0.072234 270940000 551990 436220 465700 666160 1215600 860190 1053900 1165600 1952600 TRUE FALSE 479043.1229 433354.4421 690914.0777 817421.8096 1191411.938 893282.0659 951692.9402 916345.5107 1721765.852 0.278227799 0.251691855 0.401282251 0.474757824 0.691970942 0.51881739 0.552742371 0.532212617 1 20.71545753 -1.999999997 0.12796255 2.630548246 4.37E-11 0.666637047 0.122891751 139.4326609 1.569254976 65.44517714 3.73354397 0.01 1.999999997 -2.630548246 GGS(ph)WIQEINVAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGSWIQEINVAEK 13 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 1 GGS(1)WIQEINVAEK 117.37 0.0002535 0 35228 28511 23681 23376 30418 27479 30391 37317 33301 TRUE FALSE 30572.53054 28323.70936 35133.21081 28683.87808 29812.74131 28536.13491 27443.6855 29337.04995 29364.19372 1.041150009 0.964566221 1.196464345 0.976831796 1.015275325 0.97180039 0.934596937 0.999075617 1 14.8417704 GGSDDSSKDPIDVNYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GGSDDSSKDPIDVNYEK 17 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;; 139.46 6.36E-07 2660100000 5090700 3509130 2794800 3165920 3032780 2238040 4206010 4849010 4142550 FALSE TRUE 4417951.097 3486078.294 4146374.628 3884790.524 2972433.612 2324138.847 3798111.798 3812086.947 3652822.458 1.209462312 0.954351966 1.135115291 1.063503789 0.81373613 0.636258366 1.039774542 1.043600391 1 21.8005802 3.372203738 7.746466162 0.920586859 1.087321522 0.31444502 0.134510263 0.356815346 23.62134918 0.042367004 0.05473553 2356.154354 -3.372203738 0.166734663 GGSDGYGSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GGSDGYGSGR 10 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;; 206.38 3.52E-07 10375201000 4448500 3676651 2410101 2649556 2375975 3750977 3326292 3598532 3428120 FALSE TRUE 3860619.454 3652498.837 3575633.905 3251178.186 2328697.746 3895279.512 3003708.714 2829013.936 3022851.559 1.277144901 1.208295798 1.182867844 1.075533523 0.770364572 1.288610915 0.993667289 0.935875904 1 21.5274787 3.719091818 3.050009532 0.999453842 1.230133564 0.393717344 0.127132662 0.262378044 4.963448079 0.035335812 0.060683898 5237.111473 -3.719091818 0.230679722 GGSFGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGSFGGR 7 0 P51991;H7C1J8;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 85.89 0.047643 652940000 831290 783080 503530 604280 493360 725280 715510 882970 688710 FALSE TRUE 721432.9203 777935.8959 747038.7922 741491.0098 483543.1012 753181.9909 646119.9503 694153.7368 607291.4884 1.187951641 1.280992589 1.230115696 1.220980409 0.796229011 1.24023143 1.063937109 1.143032218 1 19.21202962 3.436268211 24.99999435 1.065509782 1.235773512 0.37866085 0.114361623 158.3539679 96904.11817 0.031166239 0.040235465 2730.663659 -3.436268211 0.17026373 DSGSDTASAIIPSTTPSVDS(ph)DDESVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DSGSDTASAIIPSTTPSVDSDDESVVK 27 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 DSGSDTASAIIPSTT(0.001)PS(0.08)VDS(0.84)DDES(0.08)VVK;DSGSDTASAIIPSTT(0.001)PS(0.181)VDS(0.679)DDES(0.139)VVK;DSGSDTASAIIPSTT(0.001)PS(0.051)VDS(0.915)DDES(0.034)VVK;DSGSDTASAIIPSTT(0.009)PS(0.263)VDS(0.707)DDES(0.021)VVK 175.71 5.71E-13 414929000 990720 781120 804030 933250 892290 766260 995100 1336820 2238430 TRUE FALSE 859793.8418 775988.7713 1192861.597 1145158.676 874535.1747 795738.518 898595.3552 1050951.446 1973805.355 0.435602143 0.393143513 0.604346114 0.580178118 0.443070626 0.403149437 0.455260369 0.532449384 1 20.9125483 1.230142559 3.696734208 1.074157435 0.476737631 0.849908713 0.068960977 0.11344638 2.40659417 0.190985573 0.018874193 16.98801199 -1.230142559 -0.597419804 GGSGSHNWGTVK ddPTM_MDA-MB-175_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 0 ;; 104.24 0.0011024 664110000 1630620 1699910 837620 1517340 1935140 1795030 1879820 2096110 3042160 FALSE TRUE 1415129.436 1688743.179 1242695.834 1861875.238 1896634.5 1864085.966 1697515.346 1647873.188 2682519.31 0.527537465 0.629536262 0.463256995 0.694077105 0.707034798 0.694901229 0.632806384 0.614300588 1 21.35515713 1.237717698 24.99272999 1.00000044 0.623431831 0.710513218 0.076120027 11.91893539 353184.0081 0.111406107 0.018990023 17.28692303 -1.237717698 -0.376568609 GGSGSHNWGTVKDELTES(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGSGSHNWGTVKDELTESPK 20 1 Q8NC51;Q8NC51-2 Q8NC51 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 GGSGSHNWGTVKDELT(0.006)ES(0.994)PK 165.96 9.60E-12 474010000 423430 368860 125160 263980 522930 351690 561530 614750 172010 TRUE FALSE 367472.6527 366436.9344 185687.7946 323920.6937 512524.7161 365219.7419 507072.907 483290.4965 151675.1738 2.422760717 2.415932188 1.224246461 2.135621049 3.379094307 2.407907193 3.343150329 3.186352021 1 17.21062544 3.433614713 15.13517296 2.766113524 1.997063649 0.134742993 0.751790573 4.313737277 1499.027564 0.212772291 0.274707824 2714.030429 -3.433614713 -0.769049875 GGSGYHS(ph)RS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(1)PAR;GGS(0.002)GY(0.001)HS(0.998)RS(0.999)PAR 57.595 0.063783 2052500000 1157930 1041370 584180 756110 925190 1065220 914960 975400 819100 TRUE FALSE 1004906.617 1034529.172 866691.402 927796.3319 906780.5291 1106199.703 826227.32 766818.3006 722266.9311 1.391323032 1.432336339 1.199959966 1.284561555 1.255464552 1.531566316 1.143936244 1.061682693 1 19.46217259 2.039296811 8.514255313 1.055185675 1.339336649 0.67010803 0.09479443 0.153022574 30.10480757 0.039444372 0.026429668 109.4704268 -2.039296811 0.284150974 GGSGYVNQLSAGYESVDS(ph)PTGSENSLTHQSNDTDSSHDPQEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGSGYVNQLSAGYESVDSPTGSENSLTHQSNDTDSSHDPQEEK 43 0 Q15007 Q15007 WTAP Pre-mRNA-splicing regulator WTAP 1 GGSGYVNQLSAGYESVDS(0.949)PT(0.034)GS(0.007)ENS(0.007)LT(0.002)HQSNDTDSSHDPQEEK 119.68 5.15E-07 101440000 32730 38600 10647 25206 39928 37252 40581 46681 41048 TRUE FALSE 28404.64757 38346.43406 15795.92481 30929.40755 39133.51092 38685.10855 36645.46087 36698.63142 36195.3522 0.78475953 1.059429781 0.436407545 0.854513236 1.081175028 1.068786631 1.012435538 1.013904526 1 15.14351683 3.382078062 5.324175897 1.031048387 0.768236002 0.420042995 0.149674144 0.2019388 9.07269338 0.042418989 0.055173635 2410.338632 -3.382078062 -0.262812385 GGSISVQVNSIKFDS(ph)E ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 GGSISVQVNSIKFDSE 16 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 GGSISVQVNSIKFDS(1)E;GGSISVQVNSIKFDS(1)E;GGSISVQVNS(0.168)IKFDS(0.832)E;GGSISVQVNS(0.282)IKFDS(0.718)E;GGSISVQVNS(0.005)IKFDS(0.995)E;GGSISVQVNSIKFDS(1)E;GGSISVQVNSIKFDS(1)E;GGSISVQVNS(0.039)IKFDS(0.961)E;GGSISVQVNS(0.357)IKFDS(0.643)E 256.67 3.16E-26 5058347000 7837208 6986709 4240742 4871201 7289047 5986009 8122475 9709795 4252212 TRUE FALSE 6801501.106 6940812.849 6291579.016 5977281.639 7144009.225 6216294.64 7334758.625 7633430.901 3749520.341 1.813965651 1.851120201 1.677969031 1.594145676 1.905312833 1.65789063 1.956185847 2.035841976 1 21.83827462 1.229033648 24.99507402 0.999998381 1.817242989 0.774305546 0.137666418 198.3447872 520341.9672 0.462546961 0.0367653 16.94469077 -1.229033648 0.817244607 GGSSVEAPCPSDVT(ph)PEDDRSFQTVWATVFEHHVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGSSVEAPCPSDVTPEDDRSFQTVWATVFEHHVER 35 1 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 GGSSVEAPCPS(0.008)DVT(0.966)PEDDRS(0.013)FQT(0.013)VWAT(0.001)VFEHHVER;GGSSVEAPCPS(0.027)DVT(0.973)PEDDRSFQTVWATVFEHHVER 181.47 5.22E-20 216730000 105117.2 106600 67147 69200 97435 106390 87583 92189 56315 TRUE FALSE 91225.69569 105899.7376 99619.51379 84912.91766 95496.23413 110482.8921 79089.21414 72475.09977 49657.50485 1.837097856 2.132602874 2.006132086 1.709971492 1.923097715 2.224898179 1.592694083 1.459499425 1 15.59972415 1.534827263 1.410655351 0.888446682 1.96367954 0.784430042 0.165696112 0.306760151 0.863211663 0.428549652 0.050342575 34.26314807 -1.534827263 1.075232858 GGTLGGGTLGPPS(ph)PPGAPS(ph)PPEPGGEIELVFRPHPLLVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGTLGGGTLGPPSPPGAPSPPEPGGEIELVFRPHPLLVEK 40 1 Q06587;Q06587-2 Q06587 RING1 E3 ubiquitin-protein ligase RING1 2 GGTLGGGTLGPPS(1)PPGAPS(1)PPEPGGEIELVFRPHPLLVEK 109.65 1.09E-05 200520000 147560 98049 74752 93318 106240 90130 102110 118970 137530 TRUE FALSE 128059.5721 97404.90966 110902.3172 114507.2782 104126.0319 93597.35942 92207.38792 93529.19133 121271.3601 1.055975393 0.803197965 0.914497184 0.944223583 0.858620137 0.77180102 0.760339357 0.771238908 1 16.88787935 3.028894343 4.790198547 0.811223319 0.91861137 0.215483811 0.090862774 0.279515443 15.98049089 0.027611036 0.030671987 1068.794827 -3.028894343 0.107388051 GGTLGGGTLGPPS(ph)PPGAPSPPEPGGEIELVFRPHPLLVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGTLGGGTLGPPSPPGAPSPPEPGGEIELVFRPHPLLVEK 40 1 Q06587;Q06587-2 Q06587 RING1 E3 ubiquitin-protein ligase RING1 1 GGTLGGGTLGPPS(1)PPGAPSPPEPGGEIELVFRPHPLLVEK 181.76 3.29E-24 677170000 646130 445930 347430 460180 449880 393030 485770 616520 627950 TRUE FALSE 560742.2834 443000.6565 515448.3101 564670.9024 440928.2682 408150.1184 438660.1002 484681.9958 553714.4664 1.012692132 0.800052524 0.930891897 1.019787159 0.796309822 0.737112976 0.792213545 0.875328396 1 19.07878269 3.217943062 24.99995358 0.835832423 0.930086873 0.230033678 0.090369906 398.7058434 483452.1431 0.028280312 0.03210122 1651.745234 -3.217943062 0.09425445 GGTPAFLPSSLS(ph)PQSSLPASR ddPTM_MDA-MB-175_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 GGTPAFLPS(0.008)S(0.078)LS(0.906)PQS(0.007)S(0.001)LPASR;GGTPAFLPS(0.003)S(0.362)LS(0.635)PQSSLPASR;GGTPAFLPS(0.003)S(0.051)LS(0.945)PQSSLPASR;GGTPAFLPS(0.004)S(0.056)LS(0.938)PQS(0.002)S(0.001)LPASR 325.11 3.59E-66 323900000 620719 617077 474746 469250 630759 715497 597431 664436 619530 TRUE FALSE 538689.4114 613023.3806 704334.7535 575800.3845 618208.13 743022.6326 539492.2336 522351.532 546289.8692 0.986087134 1.122157695 1.289305904 1.054019884 1.131648535 1.360125227 0.987556724 0.956180155 1 19.05930714 2.043940746 24.99986857 0.974032025 1.157285465 0.379228494 0.106160388 127.4440441 72508.11625 0.042598856 0.028720128 110.6472809 -2.043940746 0.18325344 GGVDHAAAFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GGVDHAAAFGR 11 0 Q9HC38-2;F6TLX2;Q9HC38;I3L3Q4 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 ;;;; 195.58 6.34E-08 4280140000 2730410 2954890 2138410 2211320 2435100 2715900 2408900 2630020 3640410 FALSE TRUE 2369579.401 2935479.133 3172552.229 2713434.004 2386646.274 2820382.43 2175285.249 2067610.69 3210044.877 0.738176409 0.914466696 0.988320211 0.845294726 0.743493118 0.878611527 0.677649482 0.644106475 1 21.61416204 3.400317083 5.048639392 0.767516175 0.888770537 0.098634441 0.117222211 0.352419332 16.18287701 0.034521525 0.045168659 2513.721058 -3.400317083 0.121254362 GGVGAPGS(ph)PSTPPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGVGAPGSPSTPPTR 15 0 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 GGVGAPGS(0.744)PS(0.038)T(0.218)PPTR;GGVGAPGS(0.702)PS(0.198)T(0.1)PPTR 189.33 2.75E-07 330775000 360160 318450 230307 241808 325967 363920 307415 336680 316976 TRUE FALSE 312563.9435 316358.081 341684.2355 296714.2022 319480.8944 377920.2379 277601.9406 264683.602 279503.4584 1.11828292 1.131857483 1.222468722 1.061576139 1.143030202 1.352112922 0.993196801 0.946977914 1 18.09250661 2.034813844 24.97761995 0.969817295 1.166342934 0.575668956 0.077539812 114.8629109 82409.33922 0.031030904 0.02092094 108.34624 -2.034813844 0.196525639 GGVGAPGSPST(ph)PPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGVGAPGSPSTPPTR 15 0 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 GGVGAPGS(0.138)PS(0.067)T(0.794)PPT(0.001)R 184.98 4.94E-06 183120000 293560 290850 160820 181380 247160 300380 239990 260900 240770 TRUE FALSE 254765.3022 288939.3872 238593.0899 222565.1012 242241.9996 311935.813 216715.8067 205108.5653 212306.4449 1.199988547 1.360954385 1.123814635 1.048320042 1.141001629 1.46927152 1.020768855 0.966096745 1 17.69578864 2.029262629 24.99984813 0.984468353 1.216424388 0.449854861 0.119347163 182.4777178 155894.8478 0.049797449 0.033572935 106.970156 -2.029262629 0.231956035 GGVILVSHDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GGVILVSHDER 11 0 Q9NUQ8-2;Q9NUQ8 Q9NUQ8-2 ABCF3 ATP-binding cassette sub-family F member 3 0 ;; 111.27 0.0016834 725970000 981660 836230 639240 660330 868810 897900 916040 911430 880990 FALSE TRUE 851931.1438 830736.7501 948378.6021 810268.019 851522.3808 932442.794 827202.5818 716527.7873 776840.3658 1.096661787 1.06937897 1.220815297 1.043030273 1.0961356 1.200301677 1.064829556 0.922361683 1 19.56725864 1.927377623 5.022003394 0.962335458 1.119713471 0.566308209 0.057156536 0.14454584 6.641070929 0.028396136 0.014804432 84.60141432 -1.927377623 0.157378013 GGVTEISAADKAEEFRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGVTEISAADKAEEFRR 17 2 Q9NQW7-4;Q9NQW7-3;Q5T6H7;Q9NQW7-2;Q9NQW7 Q9NQW7-4 XPNPEP1 Xaa-Pro aminopeptidase 1 0 150.39 1.63E-07 290530000 195890 216770 106260 123680 194180 185450 217490 203730 136420 FALSE TRUE 170002.6402 215346.0236 157647.6914 151763.4343 190316.1979 192584.3815 196397.8533 160163.9249 120292.583 1.413242911 1.790185381 1.310535425 1.261619217 1.582110826 1.600966383 1.63266802 1.331453037 1 16.87618817 1.344766403 2.896116358 0.960140061 1.51135754 0.522029916 0.156364485 0.275594611 3.202448724 0.315940123 0.041661302 22.11904659 -1.344766403 0.551217479 GGVTGS(ph)PEASISGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GGVTGSPEASISGSK 15 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK 342.28 1.54E-69 7045130000 11936450 7384490 5510000 8835790 7849860 7164790 7224470 10671730 12609600 TRUE FALSE 10359017.89 7335980.799 8174654.43 10842091.17 7693663.144 7440424.108 6523842.011 8389663.587 11118907.45 0.931657893 0.659775327 0.735203028 0.975104003 0.691944166 0.669168634 0.586734087 0.754540284 1 23.4065117 1.697932099 0.008186708 2.33E-07 1.511040183 0 0.143760035 146779.3872 444.9970848 42082.56986 40065.35604 49.8806494 -1.697932099 1.51103995 GGWDHGDTQSIQSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGWDHGDTQSIQSSR 15 0 Q9P206-2;Q9P206;Q9P206-3;Q9P206-4 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 0 135.47 2.88E-05 118840000 129830 137440 53975 88003 137640 141210 105630 131000 96429 FALSE TRUE 112672.6366 136537.1476 80077.49054 107985.4262 134901.2333 146642.4401 95386.01886 102986.6694 85029.27347 1.325104072 1.605766367 0.941763786 1.269979406 1.586526943 1.724611232 1.121802115 1.211190749 1 16.37567199 GGYDKDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GGYDKDGR 8 1 Q92804-2;Q92804;A0A075B7D9;A0A075B7E4;A0A075B7F2 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;; 81.548 0.02059 963670000 4974720 4280280 2653450 3072080 2700510 3645620 4555600 5313050 3101390 FALSE TRUE 4317298.148 4252162.559 3936667.295 3769642.718 2646775.134 3785869.36 4113798.613 4176895.604 2734747.207 1.578682716 1.554864942 1.439499521 1.378424561 0.967831735 1.384358068 1.504270158 1.527342488 1 21.38297605 4.005189848 2.358286238 1.322110536 1.570718373 0.266611604 0.18593357 0.488001727 5.379494091 0.054882786 0.135055807 10120.21755 -4.005189848 0.248607837 GGYFDEFGIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 GGYFDEFGIIR 11 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;;;; 268 6.60E-21 9142223000 8692936 9162681 7526555 7279896 9170721 10977132 9553357 9373944 10348399 FALSE TRUE 7544142.483 9102490.745 11166422.17 8932907.653 8988241.594 11399429.37 8626873.909 7369399.024 9125023.059 0.826753251 0.997530712 1.223714406 0.97894631 0.985010288 1.249249377 0.94540845 0.807603332 1 23.12139677 2.009575477 24.98324622 0.885993063 1.048478029 0.175328345 0.129434571 273.7046868 714116.2756 0.052135237 0.035102279 102.2293212 -2.009575477 0.162484967 GGYIGSTYFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GGYIGSTYFER 11 0 P61081 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ;;; 220.39 2.13E-11 2018800000 1068820 1018400 718660 718950 960490 1063640 951860 1010550 1026930 FALSE TRUE 927572.729 1011710.063 1066206.38 882198.586 941378.1282 1104558.919 859548.7637 794451.7466 905527.5053 1.024345173 1.117260445 1.17744229 0.974237205 1.039590871 1.2197961 0.949224357 0.877335853 1 19.78839894 2.075072187 10.18128817 0.924931659 1.089276336 0.455036326 0.077038645 0.30403346 38.99521502 0.030958291 0.020861739 118.8699793 -2.075072187 0.164344678 GGYVLHIGTIYGDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GGYVLHIGTIYGDLK 15 0 P49588;P49588-2;H3BPK7 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 204.13 5.06E-09 1415840000 2964200 1944650 1325740 1724640 1727890 1461230 2168730 2666200 2409400 FALSE TRUE 2572473.46 1931875.466 1966872.298 2116245.871 1693508.37 1517444.464 1958406.898 2096053.878 2124563.477 1.210824477 0.909304658 0.92577714 0.996085029 0.797108859 0.714238233 0.921792603 0.986580962 1 21.01873502 4.73865439 8.066012917 0.907195081 1.213192986 0.531172179 0.089892557 0.082815982 68.49641903 0.023977536 0.137837544 54784.08215 -4.73865439 0.305997905 GHAAFTSDPKPTIEVSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GHAAFTSDPKPTIEVSGK 18 1 P00390-5;P00390-4;P00390-2;P00390-3;P00390 P00390-5 GSR "Glutathione reductase, mitochondrial" 0 ; 227.22 1.86E-19 1149220000 1600520 1372790 1073190 1389360 1328330 1002190 1681720 1946930 1978060 FALSE TRUE 1389007.227 1363772.052 1592188.274 1704835.423 1301898.832 1040744.898 1518627.053 1530594.171 1744216 0.796350467 0.781882549 0.912838934 0.97742219 0.746409178 0.596683494 0.870664558 0.877525588 1 20.73414728 1.383381164 2.019272665 1.022182615 0.810328121 0.262649772 0.101352997 0.849479703 4.575441136 0.307652686 0.029999614 24.17581725 -1.383381164 -0.211854494 GHAAPILYAVWAEAGFLAEAELLNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GHAAPILYAVWAEAGFLAEAELLNLR 26 0 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 ;; 197.31 6.56E-25 1512970000 445254 503864 396241.6 397462.6 361995 350744 447624 494965 478141.8 FALSE TRUE 386412.5558 500554.0842 587865.3631 487712.5582 354792.0077 364237.3486 404213.4934 389120.5866 421616.4211 0.916502623 1.187226254 1.394313252 1.156768413 0.841504244 0.863906932 0.958723316 0.922925596 1 18.68557153 3.293066776 7.417100043 0.91873171 1.183672788 0.499819023 0.121784795 0.184680864 20.9560318 0.035855619 0.046113892 1963.662182 -3.293066776 0.264941078 GHALLIDCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GHALLIDCR 9 0 P51570;P51570-2 P51570 GALK1 Galactokinase 0 ;;; 102.61 0.0035568 970910000 420017 707428 465256 385316 608498 674210 579552 630348 644899 FALSE TRUE 364510.6893 702780.8589 690255.3578 472807.887 596390.0803 700147.295 523347.1362 495552.9856 568659.7749 0.640999602 1.235854706 1.213828353 0.831442469 1.048764317 1.231223529 0.920316786 0.871440196 1 19.11720623 2.064517696 24.99952573 0.917328508 1.045323958 0.059071061 0.187803081 142.6025106 55254.5736 0.074112981 0.04996782 116.0159489 -2.064517696 0.12799545 GHAVGDIPGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GHAVGDIPGVR 11 0 D6RD47;P62266 D6RD47 RPS23 40S ribosomal protein S23 0 ;;;;; 154.24 3.21E-05 5852430000 1055100 970320 885831 939728 976392 1140511 926075 1062460 1717570 FALSE TRUE 915665.8617 963945.904 1314221.835 1153107.605 956963.7095 1184387.196 836264.389 835261.1971 1514520.831 0.604591131 0.636469228 0.867747612 0.76136794 0.63185906 0.782021067 0.552164336 0.551501954 1 20.53042999 3.243445979 24.98227584 0.677083087 0.722481744 0 0.146294417 680.393885 3479301.138 0.043227132 0.054049769 1751.644536 -3.243445979 0.045398658 GHDDIVNFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GHDDIVNFER 10 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 0 ; 131.43 0.00025026 171700000 141298 152530 102634 117141 158187 159920 152284 171856 148865 FALSE TRUE 122625.1113 151528.0204 152268.1457 143739.6544 155039.3882 166072.2259 137515.5211 135105.9318 131266.3493 0.934170196 1.15435541 1.159993757 1.095022869 1.181105356 1.265154602 1.047606808 1.029250318 1 17.0021376 2.022448718 24.99797535 1.023228634 1.136360246 0.267900098 0.083425219 288.0212623 320727.4454 0.033804163 0.022789111 105.3049335 -2.022448718 0.113131611 GHDGGHSHGGDMSNRPVCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GHDGGHSHGGDMSNRPVCR 19 1 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 0 ;;;;; 159.26 2.18E-11 288680500 60338.9 51803.5 26530.2 34942.5 48078.3 64234.9 44866.4 45341.22 45483.1 FALSE TRUE 52364.96149 51463.1994 39360.29346 42876.72869 47121.63589 66706.05817 40515.26343 35645.35295 40106.13973 1.305659478 1.283175088 0.98140319 1.069081417 1.174923246 1.663238063 1.010201024 0.888775464 1 15.29153549 2.020237269 24.98284626 0.94035642 1.233935994 0.351652706 0.180283517 254.9193154 314695.8593 0.076350863 0.051469349 104.7700784 -2.020237269 0.293579574 GHDGTPESDCFAFTESHYNAELFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GHDGTPESDCFAFTESHYNAELFR 24 0 Q9Y3P9;Q9Y3P9-2;Q9Y3P9-3;Q9Y3P9-4 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 0 ;; 181.69 1.88E-17 470479000 440810 380740 257551 281545 410230 380860 387390 447770 418760 FALSE TRUE 382555.8416 378238.8939 382103.5251 345474.0954 402067.2256 395511.9306 349820.9774 352017.8701 369254.6699 1.036021675 1.024330698 1.03479673 0.935598446 1.088861586 1.071108812 0.94737049 0.953320022 1 18.49425664 2.224582483 24.99949322 0.963254724 1.029806426 0.345067486 0.041983183 262.2421487 469008.4067 0.017326788 0.011744637 167.7190846 -2.224582483 0.066551702 GHDLNEDGLVSWEEYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GHDLNEDGLVSWEEYK 16 0 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-13;O43852-14;O43852-11 O43852 CALU Calumenin 0 ;; 195.27 7.94E-11 718385000 2386380 1518534 1505238 1902200 1656202 1745370 1707680 1911430 2240250 FALSE TRUE 2071013.837 1508558.65 2233176.132 2334123.583 1623246.821 1812515.513 1542069.456 1502685.569 1975410.197 1.048396854 0.763668555 1.130487296 1.181589316 0.821726456 0.917538806 0.780632528 0.76069546 1 20.91372083 3.199948461 24.96804521 0.841600162 1.019041806 0.311855943 0.127555591 194.579708 125821.7555 0.039469516 0.044755048 1584.705121 -3.199948461 0.177441643 GHEDDSYEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHEDDSYEAR 10 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 210.64 7.35E-08 85307000 61953 63922 49269 53746 67990 66021 64102 77793 86659 FALSE TRUE 53765.75408 63502.09217 73095.65319 65949.85076 66637.13202 68560.87059 57885.39791 61157.57234 76414.27174 0.7036088 0.831023979 0.956570697 0.86305672 0.872050868 0.89722599 0.757520769 0.800342278 1 16.22155449 4.694344811 3.924822238 0.866024492 0.694750837 0.373483137 0.069528213 0.251340205 7.390891167 0.017648261 0.111522746 49470.33047 -4.694344811 -0.171273654 GHEFYNPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHEFYNPQK 9 0 P78406 P78406 RAE1 mRNA export factor 0 138.4 0.00013778 208150000 497320 335270 226640 311460 313130 324820 304640 361790 556640 FALSE TRUE 431597.902 333067.5893 336243.8621 382181.7534 306899.3256 337316.0356 275096.0597 284424.024 490834.6533 0.879314244 0.678573909 0.685045075 0.778636453 0.625260102 0.687229464 0.560465847 0.579470137 1 18.90487758 4.739367762 23.12378785 0.682799622 0.879314406 0.160855635 0.124184734 40.34465774 1155199.101 0.029406623 0.171660907 54874.14445 -4.739367762 0.196514783 GHEFYNPQKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHEFYNPQKK 10 1 P78406 P78406 RAE1 mRNA export factor 0 86.882 0.0086048 346260000 706890 535030 394190 351240 453680 532250 622450 597900 303980 FALSE TRUE 613472.6955 531515.3527 584821.6025 430994.4104 444652.6556 552726.0019 562084.8948 470043.7379 268043.8307 2.288702911 1.982941936 2.181813329 1.607925126 1.658880395 2.062073208 2.09698874 1.753607746 1 18.0321094 1.253116909 2.913426669 0.826632513 1.965336672 0.679026591 0.211400429 0.244802886 2.585702094 0.652769211 0.05705357 17.91087937 -1.253116909 1.138704158 GHEGPVWQVAWAHPMYGNILASCSYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GHEGPVWQVAWAHPMYGNILASCSYDR 27 0 P55735;P55735-4;P55735-3;P55735-2;A8MXL6;E7ERC8 P55735 SEC13 Protein SEC13 homolog 0 ; 186.71 6.11E-18 2096400000 745640 737910 497340 573910 665090 670450 664360 710360 935240 FALSE TRUE 647101.7848 733062.6206 737855.2875 704225.0372 651856.0102 696242.6453 599930.4695 558455.042 824676.9926 0.784673018 0.888908781 0.89472035 0.853940444 0.790437973 0.844261028 0.727473271 0.677180335 1 19.65346963 3.07384331 1.772984926 0.78144295 0.861623325 0.018850015 0.090309767 0.753172271 4.865685675 0.033253194 0.038484335 1185.341011 -3.07384331 0.080180375 GHEYTNIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHEYTNIK 8 0 Q06124;Q06124-1 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 128.69 0.0011229 101690000 190140 182490 155460 172740 166750 173100 200400 215670 284170 FALSE TRUE 165012.5172 181291.2112 230640.976 211963.2572 163432.0012 179759.269 180965.2388 169550.6488 250575.7463 0.658533476 0.723498638 0.920444135 0.845904922 0.652225938 0.717384949 0.722197745 0.676644294 1 17.93488725 1.229762624 24.99599094 1.000000494 0.740881997 0.487916884 0.083827501 330.1150932 937818.6737 0.255403719 0.02190499 16.97315682 -1.229762624 -0.259118497 GHFDYQSLLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GHFDYQSLLMR 11 0 Q9H832-2;Q9H832 Q9H832-2 UBE2Z Ubiquitin-conjugating enzyme E2 Z 0 ; 96.604 0.0068882 1287180000 787070 711720 361570 449230 629960 776730 549670 585560 516860 FALSE TRUE 683056.7053 707044.6645 536426.4614 551234.5376 617425.0285 806611.3057 496363.088 460342.5508 455757.3996 1.498728723 1.551361898 1.177000004 1.209491142 1.354722993 1.769826022 1.089094962 1.010060509 1 18.79790655 2.026413306 24.97837007 1.018897426 1.409787202 0.550504673 0.168443067 163.9964057 155086.395 0.071596328 0.048268839 106.2706424 -2.026413306 0.390889777 GHFEEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 1263150000 1940860 1723700 1450510 1534180 1517370 1495060 1864890 2490600 2326200 FALSE TRUE 1684370.433 1712376.901 2151981.488 1882539.017 1487177.306 1552575.926 1684033.255 1958004.572 2051199.286 0.821163719 0.834817423 1.049133306 0.917774801 0.72502819 0.756911304 0.820999337 0.954565744 1 20.96803623 1.608632353 4.240881235 0.989831266 0.848761635 0.278349639 0.088631674 0.237746148 9.481504553 0.072970499 0.025462149 40.60994053 -1.608632353 -0.141069631 GHFGPINSVAFHPDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GHFGPINSVAFHPDGK 16 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ; 215.23 9.43E-15 2772700000 3131300 2661200 1735890 2408100 2639400 2343800 2790700 3321700 3313100 FALSE TRUE 2717490.771 2643718.402 2575372.21 2954895.911 2586881.104 2433967.503 2520058.344 2611380.304 2921429.092 0.930192274 0.904940123 0.881545343 1.011455633 0.885484817 0.833142762 0.862611504 0.89387085 1 21.47824284 GHGFITPADGGPDIFLHISDVEGEYVPVEGDEVTYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GHGFITPADGGPDIFLHISDVEGEYVPVEGDEVTYK 36 0 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 0 ;; 207.76 1.12E-30 447530000 218280 220073 67227 172136 206318 183840 208079 274879 326483 FALSE TRUE 189433.7449 218627.326 99738.20206 211222.1097 202212.6755 190912.4438 187899.5306 216098.265 287886.5517 0.658015263 0.759421809 0.346449674 0.73369912 0.702404035 0.663151657 0.65268603 0.750636887 1 18.13514087 -0.417406141 0.979568 10 0.636268555 0.499476118 0.112473897 37.85697692 1.798148894 718.459205 0.036259977 0.382466903 0.417406141 -9.363731445 GHHEAEIKPLAQSHATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHHEAEIKPLAQSHATK 17 1 B0QYF8;P02144;Q8WVH6;F2Z2F1;B0QYF7 B0QYF8 MB Myoglobin 0 83.418 0.001861 151380000 146200 155100 86763 138800 132100 113650 123020 158670 194930 FALSE TRUE 126879.2996 154081.1379 128721.877 170316.6614 129471.4684 118022.189 111089.5393 124739.6553 171885.5975 0.73816132 0.896416804 0.74888111 0.990872208 0.7532421 0.686632218 0.646299288 0.725713248 1 17.39108914 3.040584531 24.99819584 0.744418567 0.844525468 0.096209314 0.117004115 291.8811669 179783.5405 0.034667735 0.03930947 1097.954975 -3.040584531 0.100106901 GHIVLLQEAETLIQIEEDSTHIICDNDEMLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GHIVLLQEAETLIQIEEDSTHIICDNDEMLR 31 0 Q9NV88-3;Q9NV88-2;Q9NV88;H0YBK3 Q9NV88-3 INTS9 Integrator complex subunit 9 0 ;; 197.14 9.18E-26 109155000 34388.4 34863.7 25506.3 26975.8 33050.1 34294.8 38691.1 31786.7 30228 FALSE TRUE 29843.88581 34634.67806 37841.23199 33101.06769 32392.46767 35614.14315 34938.84308 24989.36157 26654.48028 1.11965739 1.299394237 1.419694986 1.241857554 1.215272905 1.336140971 1.31080564 0.9375295 1 14.70209043 1.734412881 6.915483908 0.972499237 1.282465354 0.717350523 0.080349601 0.062060769 8.673285787 0.046681611 0.020748531 54.25164119 -1.734412881 0.309966116 GHKGS(ph)FKDDPQLYQEIQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHKGSFKDDPQLYQEIQER 19 2 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 GHKGS(1)FKDDPQLYQEIQER 63.573 0.019436 327880000 441590 286430 143330 270600 270600 107060 559030 462370 303750 TRUE FALSE 383232.7627 284548.4225 212644.8674 332043.8659 265215.5894 111178.6675 504815.3566 363495.7737 267841.021 1.430821766 1.062378053 0.793921956 1.239705048 0.990197799 0.415092009 1.884757438 1.357132572 1 18.03101741 2.228832831 24.9999997 1.421739807 0.994661447 0.260164016 0.337887173 275.4852507 707978.8794 0.135039139 0.092318059 169.368574 -2.228832831 -0.42707836 GHKHEDGTQS(ph)DSEDPLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHKHEDGTQSDSEDPLAK 18 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 GHKHEDGT(0.015)QS(0.985)DSEDPLAK 185.71 3.12E-14 433860000 412210 279160 257430 248980 290610 229710 369480 392570 352660 TRUE FALSE 357735.4041 277326.1796 381924.0091 305514.7144 284827.4296 238547.0923 333647.8865 308621.9605 310968.9366 1.150389515 0.891813127 1.228174149 0.982460556 0.915935311 0.767109072 1.072929953 0.992452699 1 18.24641095 4.762567626 23.34360899 0.985525954 1.150389993 0.164681591 0.119310693 5525.858374 5372945.554 0.029067184 1.533604224 57885.21174 -4.762567626 0.164864038 GHLENNPALEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 215.72 1.26E-11 9933010000 21201300 17973500 12584060 15646800 16937000 15916500 19598000 22539100 21151700 FALSE TRUE 18399494.49 17855430.9 18669753.51 19199645.09 16599986.84 16528818.05 17697388.98 17719288.86 18651170.12 0.986506175 0.957335694 1.000996366 1.029407 0.890023882 0.886208101 0.948862128 0.950036311 1 24.15276281 3.24328754 24.99999957 0.935499168 0.991504834 0.39229707 0.036158687 140.5751336 743476.0827 0.011304761 0.014120399 1751.005619 -3.24328754 0.056005667 GHLLDSFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHLLDSFAR 9 0 Q9NQW7-4;Q9NQW7-3;Q5T6H7;Q9NQW7-2;Q9NQW7 Q9NQW7-4 XPNPEP1 Xaa-Pro aminopeptidase 1 0 129.42 0.00038974 473480000 679490 821250 498710 566640 733260 751570 604160 773100 983220 FALSE TRUE 589693.6749 815855.1547 739887.8241 695304.2726 718669.5606 780483.3842 545568.6562 607778.5813 866984.8517 0.680166065 0.941025847 0.853403405 0.801979725 0.828929778 0.900227245 0.629271267 0.701025606 1 19.72564726 2.273373147 24.99994758 0.754840265 0.838297007 0.040673899 0.115371781 405.902017 291489.2658 0.041934618 0.032480948 187.6606201 -2.273373147 0.083456743 GHLSGLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHLSGLAK 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 73.931 0.04229 164590000 574690 644190 351640 517530 543110 660670 756520 958820 996510 FALSE TRUE 498743.2604 639958.2735 521694.2802 635043.0965 532303.1736 686086.4024 683152.8068 753783.8045 878703.723 0.567589789 0.728298125 0.593708968 0.722704456 0.605782313 0.780793781 0.777455232 0.857836134 1 19.74501728 -2 0.382995392 6.240972629 0.621638896 0.815468238 0.056202065 29.91422091 0.442479356 123.8019916 0.0555102 0.01 2 -5.619333733 GHLSRPEAQSLS(ph)PYTTSANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GHLSRPEAQSLSPYTTSANR 20 1 O94776;O94776-2 O94776 MTA2 Metastasis-associated protein MTA2 1 GHLSRPEAQSLS(1)PYTTSANR;GHLSRPEAQSLS(1)PYTTSANR;GHLSRPEAQS(0.006)LS(0.936)PY(0.014)T(0.034)T(0.007)S(0.002)ANR;GHLSRPEAQSLS(1)PYTTSANR;GHLSRPEAQSLS(1)PYTTSANR 200.95 7.89E-22 3053610000 1071754 1258073 636994 782205 1407626 1458000 1181174 1303057 1271854 TRUE FALSE 930118.9934 1249808.636 945046.429 959816.6005 1379616.997 1514090.203 1066623.927 1024408.401 1121496.869 0.829354962 1.114411168 0.842665241 0.855835292 1.230156797 1.350061909 0.951071694 0.913429568 1 20.09699416 3.26503947 24.99991005 1.06972029 0.92027688 0.251487543 0.150490975 424.1977492 400501.7843 0.048059742 0.062026496 1840.939302 -3.26503947 -0.14944341 GHMLADVVAIIGTQDIVFGEVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GHMLADVVAIIGTQDIVFGEVDR 23 0 O75306 O75306 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" 0 ;; 186.63 2.68E-17 76615000 127994 118651 86430 121411 139148 158616 115548 157588 108822 FALSE TRUE 111079.2686 117871.5738 128227.8371 148979.2232 136379.227 164718.0602 104342.1727 123889.0326 95957.18713 1.157591963 1.228376709 1.336302584 1.552559299 1.42125078 1.716578665 1.08738257 1.291086538 1 16.55010325 GHNCPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GHNCPK 6 0 P17844;J3KTA4;J3QRQ7;J3KRX8;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ; 71.995 0.086763 70054000 161726 136247 124673 151579 110247 138822 146462 172571 315880 FALSE TRUE 140353.4993 135351.9845 184965.2798 185997.3287 108053.3004 144162.5722 132258.1378 135668.0346 278537.0263 0.503895303 0.48593893 0.664059936 0.667765184 0.38793155 0.517570587 0.474831442 0.487073609 1 18.08750959 1.23594539 24.99994827 1.000000631 0.522916335 0.757769568 0.084641855 36.78870844 351604.5272 0.143133595 0.021533371 17.21652073 -1.23594539 -0.477084297 GHNGWVTQIATTPQFPDMILSASR ddPTM_MDA-MB-175_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 ; 250.05 2.11E-38 2587800000 765680 694200 484200 586220 716940 719830 672220 771410 705250 FALSE TRUE 664493.448 689639.7545 718360.7396 719330.2108 702674.2967 747522.3259 607028.2079 606449.9746 621876.1484 1.068530204 1.108966401 1.155150815 1.156709761 1.129926431 1.202043731 0.976123959 0.975194138 1 19.24626776 2.224515346 24.94003289 0.981666739 1.137033426 0.811598109 0.034771374 90.82752774 161280.1483 0.014383093 0.0097513 167.6931589 -2.224515346 0.155366687 GHNSSNS(ph)PSLQAGGAEGAGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHNSSNSPSLQAGGAEGAGDR 21 0 Q8IWZ3-6;H7C0V5 Q8IWZ3-6 ANKHD1;ANKHD1-EIF4EBP3 Ankyrin repeat and KH domain-containing protein 1 1 GHNS(0.043)S(0.03)NS(0.919)PS(0.008)LQAGGAEGAGDR 153.27 4.12E-13 0 37129 41081 19034 25877 49066 50135 41398 43564 36774 TRUE FALSE 32222.30858 40811.13621 28238.90606 31752.76836 48089.6826 52063.72589 37383.22833 34248.17762 32426.61961 0.99369928 1.258568938 0.870855686 0.979219195 1.483031015 1.605585982 1.152856165 1.056174773 1 14.98489101 3.28699222 24.99997933 1.243414013 1.031175016 0.243904291 0.203472356 209.7055325 108246.6646 0.065205619 0.08417993 1936.387277 -3.28699222 -0.212238997 GHNTLPSPWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GHNTLPSPWR 10 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RQQ5 P47897 QARS Glutamine--tRNA ligase 0 ;; 76.143 0.028392 762240000 190894 173389 91693 129111 201937 226038 181159 205202 180749 FALSE TRUE 165666.8742 172249.9962 136036.0415 158427.6259 197918.8488 234733.8281 163590.2281 161321.1492 159381.0591 1.039438909 1.080743202 0.853527027 0.994017901 1.241796546 1.472783713 1.026409468 1.012172651 1 17.28212066 3.314380091 10.42797538 1.140043578 0.987941399 0.217371752 0.148811121 0.773869609 101.2878514 0.047565315 0.061395396 2062.434149 -3.314380091 -0.152102178 GHPEFSTNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GHPEFSTNR 9 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;;;;; 144.5 9.94E-05 2811650000 391948 338785 217373 269631.3 265840 427968 268091 308148 390121 FALSE TRUE 340151.0787 336559.499 322495.3099 330855.2077 260550.3041 444432.2059 242091.5761 242252.9482 344001.3398 0.988807424 0.978366826 0.937482715 0.961784649 0.757410725 1.291949055 0.703751841 0.704220944 1 18.39205466 GHPETLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GHPETLEK 8 0 B0QYF8;P02144;F2Z2F1;F2Z337 B0QYF8 MB Myoglobin 0 ;; 134.48 0.00087486 1186340000 3129730 3170540 2328780 2814560 2828900 2752120 2643880 3671570 4592040 FALSE TRUE 2716128.251 3149712.514 3454985.797 3453648.866 2772610.425 2857995.837 2387476.925 2886433.328 4049174.262 0.670785714 0.777865389 0.85325688 0.852926706 0.684734774 0.705821892 0.58962069 0.712844926 1 21.9491963 3.226951439 24.9961179 0.722571609 0.792544748 0.03441182 0.114901867 617.7142833 1330017.819 0.035378134 0.040440691 1686.364453 -3.226951439 0.069973139 GHPFYDCQTDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHPFYDCQTDFR 12 0 O95149;H3BUB4;H3BRI5 O95149 SNUPN Snurportin-1 0 123.64 0.00033718 158410000 111530 122590 101400 103730 117910 132960 111520 126320 125670 FALSE TRUE 96791.02792 121784.6982 150437.3792 127283.4819 115563.8217 138075.0572 100704.8076 99307.45102 110813.4358 0.873459317 1.099006609 1.357573458 1.148628603 1.042868321 1.246013683 0.908777955 0.896167963 1 16.75777329 2.22138865 24.8589355 0.925803796 1.134123953 0.334996709 0.127732155 246.1544135 356341.7164 0.052697136 0.035625677 166.4901906 -2.22138865 0.208320157 GHPHSASSPS(ph)ER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GHPHSASSPSER 12 0 C9J470;E9PHA2;Q15003;C9JZP1 C9J470 NCAPH Condensin complex subunit 2 1 GHPHSAS(0.052)S(0.197)PS(0.751)ER;GHPHSAS(0.245)S(0.169)PS(0.586)ER 119.62 0.00032101 564450000 78077 89991 59326 56785 79864 105467 79016 102799 78292 TRUE FALSE 67758.92663 89399.8432 88016.25203 69678.90215 78274.86265 109524.3837 71353.04048 80816.23383 69036.40895 0.981495528 1.294966592 1.274925121 1.009306585 1.133820021 1.586472782 1.033556663 1.170632063 1 16.0750698 GHPVSTLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GHPVSTLSR 9 0 Q8IZH2-2;Q8IZH2;H7C5E4 Q8IZH2-2 XRN1 5-3 exoribonuclease 1 0 ; 63.216 0.07752 105739000 151133 170477 92486 116437 148228 176174 158230 172892 169399 FALSE TRUE 131160.3911 169357.1254 137212.5389 142875.8005 145278.5528 182951.5278 142884.879 135920.3912 149372.8432 0.878073874 1.133787921 0.91859093 0.956504525 0.972590129 1.224797787 0.956565303 0.909940444 1 17.18855836 2.027307444 24.99992956 0.943951668 1.017327965 0.064049912 0.103143102 496.7277422 454751.585 0.041030774 0.027662276 106.4896608 -2.027307444 0.073376297 GHQAFDVGQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHQAFDVGQPR 11 0 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 0 122.33 0.00039312 165070000 87199 93703 55716 63508 91807 110140 62392 71448 84725 FALSE TRUE 75675.43122 93087.45882 82660.44396 77928.46206 89980.22032 114377.1571 56341.23344 56169.40121 74708.90702 1.012937202 1.246002151 1.106433587 1.043094661 1.204410878 1.530970826 0.754143457 0.751843434 1 16.18899264 2.202308432 24.99996215 0.814553064 1.183249859 0.530730477 0.156992193 127.9065954 88205.14308 0.063862824 0.043057816 159.3339902 -2.202308432 0.368696794 GHQFSCVCLHGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GHQFSCVCLHGDR 13 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ;; 194.48 5.70E-07 2481750000 192472 175859 111889 115511 181879 167962 176190 165683 210761 FALSE TRUE 167036.3375 174703.7706 165998.8946 141739.538 178259.9637 174423.6068 159103.1209 130252.9798 185845.0747 0.898793459 0.940050582 0.89321116 0.762675784 0.959185838 0.938543069 0.856106201 0.700868613 1 17.50374093 1.999433644 24.99871708 0.813893669 0.896964688 0.022014208 0.090010987 37.91173897 1673443.379 0.036347763 0.024182115 99.8696768 -1.999433644 0.083071019 GHQQLYWSHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 GHQQLYWSHPR 11 0 A0A2R8Y851;P62273;P62273-2 A0A2R8Y851 RPS29 40S ribosomal protein S29 0 ;;;;;;; 220.1 5.43E-12 11076760000 3588970 4104859 2633343 2756041 3806037 4199452 3649724 4039290 3585303 FALSE TRUE 3114678.521 4077893.911 3906836.483 3381842.232 3730304.31 4361007.636 3295774.328 3175519.267 3161452.564 0.985204889 1.289879835 1.235772609 1.069711522 1.179933665 1.379431621 1.042487357 1.004449443 1 21.59215614 2.025952227 24.9902342 1.008820213 1.19237585 0.37121227 0.107805493 210.8578606 203040.9704 0.042587817 0.028711835 106.1578777 -2.025952227 0.183555638 GHS(ph)PAQKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GHSPAQKPK 9 1 Q14966;Q14966-3;Q14966-4;A0A096LPI0;Q14966-2;Q14966-6;A0A096LPB4 Q14966 ZNF638 Zinc finger protein 638 1 GHS(1)PAQKPK;GHS(1)PAQKPK;GHS(1)PAQKPK 130.01 0.00022609 537605000 1077140 659120 733350 813340 430892 494494 875610 990940 2173870 TRUE FALSE 934793.2199 654790.1973 1088000.513 998021.2781 422318.0922 513517.5042 790693.477 779035.1925 1916877.565 0.487664542 0.341592081 0.567589987 0.520649465 0.220315632 0.267892699 0.412490339 0.406408425 1 20.87032676 1.238325253 7.972144962 1.007558337 0.400117301 0.753450982 0.107306064 0.049149849 27.19022298 0.160636639 0.027593553 17.31112343 -1.238325253 -0.607441036 GHSAQIAKPIRPGQHPAAS(ph)PTHPSAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHSAQIAKPIRPGQHPAASPTHPSAIR 27 2 P33176 P33176 KIF5B Kinesin-1 heavy chain 1 GHSAQIAKPIRPGQHPAAS(0.962)PT(0.038)HPSAIR 152.82 4.11E-08 1871700000 1062400 1140400 459110 884240 1363300 1362600 1227800 1483300 1575000 TRUE FALSE 922001.1482 1132908.637 681137.1316 1085020.207 1336172.997 1415020.104 1108728.145 1166107.838 1388805.294 0.663880784 0.815743317 0.490448254 0.781261572 0.962102465 1.018875799 0.798332315 0.83964818 1 20.40541292 3.465357611 6.525181575 0.906229331 0.666283965 0.586682209 0.102211142 0.111996857 21.15397072 0.029456051 0.039473891 2919.8303 -3.465357611 -0.239945366 GHTAS(ph)ESDEQQWPEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GHTASESDEQQWPEEK 16 0 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 GHTAS(0.886)ES(0.113)DEQQWPEEK;GHT(0.015)AS(0.699)ES(0.286)DEQQWPEEK;GHT(0.011)AS(0.788)ES(0.201)DEQQWPEEK;GHT(0.056)AS(0.79)ES(0.154)DEQQWPEEK 378.76 8.71E-105 2417040000 2157160 1811210 1910880 2397790 2539010 2433700 3172860 3094960 4079770 TRUE FALSE 1872085.84 1799312.042 2834987.96 2942244.867 2488488.668 2527326.014 2865156.526 2433126.889 3597464.238 0.520390396 0.500161203 0.788051742 0.817866328 0.691734095 0.702529851 0.796437806 0.676344983 1 21.77854891 4.239839216 24.98050121 0.76844801 0.510275704 0.59842667 0.091980706 21.31479365 416391.3158 0.022170946 0.052427807 17371.57581 -4.239839216 -0.258172306 GHTDSVQDISFDHSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GHTDSVQDISFDHSGK 16 0 P43034 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ;;; 312.04 6.29E-58 1603330000 1407374 1323415 661352 991666 1267860 1229012 1334379 1567761 1529950 FALSE TRUE 1221385.96 1314721.4 981184.0393 1216838.922 1242632.067 1276292.887 1204971.13 1232507.51 1349081.054 0.905346611 0.974531068 0.727298064 0.90197614 0.921095188 0.946046113 0.893179195 0.913590408 1 20.3635456 3.481422564 24.83036343 0.927936148 0.868777718 0.167017385 0.066264924 324.7370169 1874630.661 0.018749881 0.024827005 3029.860017 -3.481422564 -0.05915843 GHTDTEGRPPS(ph)PPPTSTPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 GHTDTEGRPPSPPPTSTPEK 20 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 1 GHTDTEGRPPS(0.999)PPPTSTPEK;GHTDTEGRPPS(1)PPPTSTPEK;GHTDT(0.003)EGRPPS(0.988)PPPT(0.003)S(0.002)T(0.003)PEK;GHT(0.003)DT(0.015)EGRPPS(0.982)PPPTSTPEK;GHTDTEGRPPS(1)PPPTSTPEK;GHT(0.036)DT(0.036)EGRPPS(0.925)PPPT(0.002)STPEK;GHTDTEGRPPS(1)PPPTSTPEK;GHT(0.002)DT(0.008)EGRPPS(0.99)PPPT(0.001)STPEK 174.99 1.57E-12 8314920000 2992720 2290950 1823415 1786512 2134971 1881510 2598890 2835120 2929630 TRUE FALSE 2597224.469 2275900.599 2705224.593 2192166.855 2092489.254 1953892.907 2346850.048 2228851.651 2583292.479 1.005393114 0.881007713 1.047200274 0.848594138 0.81000865 0.756357603 0.90847245 0.862794929 1 21.30077956 3.712747442 24.63242331 0.860197721 0.968181111 0.334242135 0.074941604 728.6789308 695347.4098 0.020503993 0.030425215 5161.161419 -3.712747442 0.10798339 GHTGGHHS(ph)PVK ddPTM_MDA-MB-175_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 206.45 4.40E-08 1338750000 1769450 1661930 999970 1411570 1115730 1235940 1232490 1308480 1113660 TRUE FALSE 1535612.699 1651012.672 1483558.837 1732088.543 1093529.156 1283487.412 1112963.309 1028671.735 982004.3835 1.563753406 1.681268129 1.510745636 1.763829747 1.113568508 1.307007823 1.1333588 1.047522549 1 19.90536994 3.229320844 24.99723236 1.121511177 1.625057468 0.859791397 0.102249484 68.38584562 185010.3523 0.031460316 0.036158779 1695.589989 -3.229320844 0.503546291 GHVDILAPTVQELAALEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GHVDILAPTVQELAALEK 18 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ; 99.891 0.0009522 426470000 515360 401890 306590 374450 343960 291440 426290 504540 434890 FALSE TRUE 447253.8702 399249.9581 454857.9495 459474.5956 337115.8689 302651.8854 384948.4614 396648.0473 383477.7996 1.166309681 1.041129261 1.186138937 1.198177824 0.879101396 0.789229222 1.003835064 1.034344225 1 18.54878353 3.241406946 24.99999729 0.9500186 1.143038251 0.614558149 0.081112222 60.19973371 528744.246 0.026622211 0.032854459 1743.439759 -3.241406946 0.193019651 GHVQPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GHVQPIR 7 0 P62854;Q5JNZ5 P62854 RPS26;RPS26P11 40S ribosomal protein S26;Putative 40S ribosomal protein S26-like 1 0 ;;; 126.68 0.0091404 190282000 224114 207948 152311 159447 190095 227622 191996 224878 205514 FALSE TRUE 194496.7671 206581.9759 225969.109 195651.8783 186312.4814 236378.7656 173376.2575 176789.5897 181218.369 1.073272914 1.139961567 1.24694373 1.079647054 1.028110353 1.304386343 0.956725625 0.97556109 1 17.46736967 2.192493481 24.99998546 0.97617682 1.141438033 0.484438241 0.081608776 104.1520242 56521.07946 0.032267013 0.021754499 155.7734652 -2.192493481 0.165261214 GHVS(ph)PAEDQTIQAPPVSVSALAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHVSPAEDQTIQAPPVSVSALAR 23 0 E9PEM3;H7C357;H0Y6E6;Q92622-3;Q92622-2;Q92622 E9PEM3 KIAA0226 Run domain Beclin-1 interacting and cysteine-rich containing protein 1 GHVS(0.997)PAEDQT(0.003)IQAPPVSVSALAR 94.588 0.0027066 94811000 108580 105950 81233 79604 106910 138770 130900 137040 134190 TRUE FALSE 94230.87789 105254.0075 120517.5505 97679.30487 104782.7002 144108.5717 118205.3381 107735.0624 118326.2111 0.79636521 0.889524024 1.018519476 0.8255086 0.885540906 1.217892218 0.998978477 0.910491948 1 16.85241016 GHVSELEADLAEQQHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHVSELEADLAEQQHLR 17 0 O00291-3;O00291-4;O00291 O00291-3 HIP1 Huntingtin-interacting protein 1 0 240.92 1.41E-20 88979000 62178 60992 41863 60986 63518 71396 61386 66150 85563 FALSE TRUE 53961.01976 60591.33954 62108.08682 74833.80341 62254.11607 74142.65032 55432.79517 52004.33728 75447.83961 0.715209608 0.803089125 0.823192382 0.991861448 0.825127882 0.982700773 0.734716798 0.689275366 1 16.20319197 4.629981759 2.201734064 0.8484702 0.698320789 0.161181104 0.10587173 1.117720317 7.429034287 0.029290524 0.299375593 42656.16021 -4.629981759 -0.15014941 GHWDDVFLDSTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GHWDDVFLDSTQR 13 0 Q9H6T3;Q9H6T3-3 Q9H6T3 RPAP3 RNA polymerase II-associated protein 3 0 ; 198.14 1.28E-07 291560000 473840 457630 324720 351390 426790 469500 403730 474010 448810 FALSE TRUE 411220.8434 454623.7984 481755.6781 431178.4702 418297.714 487561.9688 364576.3267 372646.6502 395752.1931 1.039086708 1.148758759 1.217316509 1.089516313 1.056968783 1.23198804 0.921223769 0.941616134 1 18.59423782 2.223643082 24.98883681 0.950264277 1.130157537 0.626721304 0.064123292 144.7565462 242484.4265 0.025581644 0.017324529 167.3566916 -2.223643082 0.17989326 GHYAYDCHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHYAYDCHR 9 0 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2;F8WEA1 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 102.61 0.0035568 112270000 43899 48968 38899 46878 48816 46210 50922 47192 73137 FALSE TRUE 38097.63592 48646.32598 57710.68651 57522.36639 47844.65711 47987.7286 45983.59228 37100.35805 64490.82718 0.590745034 0.754313879 0.894866589 0.891946481 0.741883136 0.744101614 0.713025314 0.575281163 1 15.97680635 3.021796254 24.72555451 0.727274949 0.79241413 0 0.133538385 739.5416358 838925.8704 0.040954708 0.04643462 1051.46847 -3.021796254 0.065139181 GHYEVT(ph)GSDDETGKLQGSGVSLASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GHYEVTGSDDETGKLQGSGVSLASK 25 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GHYEVT(0.486)GS(0.486)DDET(0.028)GKLQGSGVSLASK;GHY(0.004)EVT(0.498)GS(0.498)DDETGKLQGSGVSLASK;GHYEVT(0.546)GS(0.453)DDET(0.001)GKLQGSGVSLASK;GHYEVT(0.572)GS(0.428)DDETGKLQGSGVSLASK 220.33 1.82E-33 2625430000 2605360 1414180 1255250 1830070 1597640 1223900 1588660 2495480 2125420 TRUE FALSE 2261055.075 1404890.158 1862293.099 2245615.364 1565850.09 1270984.225 1434591.998 1961841.022 1874155.269 1.206439569 0.749612469 0.993670658 1.198201345 0.835496458 0.678163782 0.76546059 1.046786813 1 20.83780905 GHYEVTGS(ph)DDETGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GHYEVTGSDDETGK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GHYEVT(0.001)GS(0.999)DDETGK;GHYEVTGS(1)DDETGK 237.06 1.79E-17 437980000 544630 390520 315490 413280 394590 356170 364460 522430 1059390 TRUE FALSE 472655.7656 387954.6484 468062.0193 507121.5406 386738.431 369872.0904 329114.7253 410712.4101 934150.1211 0.505974099 0.415302251 0.501056531 0.542869427 0.414000301 0.395945022 0.352314599 0.439664248 1 19.83329489 1.238386753 24.99923104 1.000000615 0.442453752 0.902736714 0.057150041 1.258936529 180496.0553 0.083609903 0.014869829 17.313575 -1.238386753 -0.557546863 GHYEVTGS(ph)DDETGKLQGSGVSLASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHYEVTGSDDETGKLQGSGVSLASK 25 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GHYEVT(0.024)GS(0.842)DDET(0.134)GKLQGSGVSLASK 273.75 3.27E-53 429700000 214170 115990 100330 141350 123930 100250 128240 203020 174770 TRUE FALSE 185866.8919 115228.0541 148849.9236 173445.6779 121464.0355 104106.6824 115803.3045 159605.7529 154108.8897 1.206075083 0.747705433 0.965874998 1.12547484 0.788170207 0.67553976 0.751438186 1.035668696 1 17.23359056 3.219041241 24.99370393 0.857215975 0.989212323 0.197367445 0.158346445 510.387475 653526.9897 0.050491758 0.057332189 1655.927205 -3.219041241 0.131996348 GHYNNVSCAVFHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GHYNNVSCAVFHPR 14 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;;; 208.15 4.88E-09 2054450000 1157632 1074640 540771 603805 1095490 1034174 964361 1127934 1071028 FALSE TRUE 1004647.998 1067580.619 802289.6644 740908.1538 1073691.892 1073959.343 870837.4187 886734.0917 944412.29 1.063781157 1.130417965 0.849512096 0.784517696 1.136888945 1.137172138 0.922094543 0.938926887 1 19.84905729 1.354327357 0.011029315 6.82E-07 1.942628273 0.011838849 0.122807133 52174.66988 170.8052395 15680.60155 14422.85021 22.61139501 -1.354327357 1.942627592 GHYT(ph)EGAELVDSVLDVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHYTEGAELVDSVLDVVR 18 0 Q13509;A0A0B4J269;Q13509-2;G3V2A3;Q5JP53;P07437;Q5ST81;P68371;Q13885;Q9BVA1 Q13509;Q5JP53;P68371;Q13885;Q9BVA1 TUBB3;TUBB;TUBB4B;TUBB2A;TUBB2B Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-2B chain 1 GHY(0.454)T(0.546)EGAELVDSVLDVVR 75.574 0.061317 6487100 15161 12419 11280 8613.7 12337 11627 15512 15164 14913 TRUE FALSE 13157.43544 12337.41877 16735.04573 10569.57224 12091.51784 12074.29821 14007.64863 11921.29661 13150.00213 1.00056527 0.938206599 1.272626846 0.803769622 0.919506911 0.918197434 1.065220255 0.906562333 1 13.68277541 3.709932266 24.99982981 0.939237949 1.057240471 0.256848474 0.107283338 1052.445076 919051.9582 0.028516215 0.042303818 5127.814022 -3.709932266 0.118002523 GHYTEGAELVDAVLDVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GHYTEGAELVDAVLDVVR 18 0 P04350;M0R278;M0R1I1;K7ES63;K7ESM5;Q9BUF5;K7EL29 P04350;K7ESM5 TUBB4A;TUBB6 Tubulin beta-4A chain;Tubulin beta-6 chain 0 ;; 155.92 1.53E-08 57137500 70185 62717 40030 47707.2 61291 65949.8 53209.1 72254 66959.8 FALSE TRUE 60909.87442 62305.0079 59388.64189 58539.84892 60071.42901 68486.93148 48048.88967 56803.04438 59043.88872 1.031603367 1.05523212 1.005838931 0.991463303 1.017402991 1.159932602 0.813782607 0.962047819 1 15.84950012 2.236487328 24.9999989 0.928291872 1.038834413 0.421640139 0.065125453 55.29785418 666771.1918 0.02528068 0.018001017 172.3801792 -2.236487328 0.110542541 GHYTEGAELVDSVLDVVR ddPTM_MDA-MB-175_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 ;;;;;;;;;;;;;;; 415.56 1.07E-147 56751160000 14821203 14353819 8692383.6 10694618.8 13465910 15060591 12579164 14750474 14783967 FALSE TRUE 12862543.47 14259527.82 12896049.38 13122995.46 13197964.74 15639981.68 11359238.61 11596199.92 13036223.26 0.986677139 1.093838877 0.989247355 1.006656237 1.012407081 1.199732573 0.871359625 0.889536769 1 23.63602263 2.191957531 24.99999992 0.911850782 1.04399299 0.416481644 0.070962612 111.2722363 59690.65745 0.028105171 0.018948548 155.5813484 -2.191957531 0.132142209 GHYTEGAELVDSVLDVVRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 320.73 3.83E-62 1328740000 4029500 3247800 768710 1118230 2824900 2773100 3783100 4140800 338620 FALSE TRUE 3496991.366 3226464.988 1140460.727 1372141.213 2768690.017 2879782.951 3416215.544 3255322.144 298588.7294 11.71173263 10.80571593 3.819503602 4.595421989 9.272587156 9.644647196 11.44120728 10.90236109 1 18.18780018 4.451398796 24.99441816 7.819425011 11.48523402 0.186342398 3.350196408 361.9486355 351703.9231 0.875802348 2.317311394 28274.75146 -4.451398796 3.665809006 GHYTIGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GHYTIGK 7 0 P68363;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;F8VWV9;P68366-2;P68366;C9JEV8;C9JQ00;C9JJQ8;C9JDL2;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA1A;TUBA1C;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 ;;;; 111.73 0.0065139 20804500000 44987900 36302500 22581300 36505100 35625100 36822200 43636700 47077200 61317900 FALSE TRUE 39042635.03 36064026.49 33501692.21 44794140.9 34916230.21 38238773.86 39404819.55 37010107.14 54068967.72 0.722089522 0.667000463 0.619610354 0.828463031 0.645772089 0.707222192 0.728788087 0.684498127 1 25.68829748 1.236769769 24.99600373 1.000000376 0.699947767 0.736055993 0.056376159 22.78494018 317930.4665 0.080481219 0.012862609 17.24923223 -1.236769769 -0.300052609 GHYTIGKEIIDLVLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHYTIGKEIIDLVLDR 16 1 P68363;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;Q9BQE3 TUBA1B;TUBA1A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 274.47 1.87E-35 148120000 283020 251860 83368 96097 217350 210900 281000 284590 54535 FALSE TRUE 245618.1899 250205.5151 123685.0436 117917.2926 213025.1602 219013.4595 253748.6633 223732.6432 48087.93443 5.107688505 5.20308302 2.572059813 2.452118063 4.429908724 4.554436827 5.276763626 4.652573371 1 15.55338734 4.281346588 24.89289649 3.778450386 5.155391395 0.194696544 1.289894949 259.929089 151222.6129 0.334035457 0.883761116 19113.78024 -4.281346588 1.376941009 GHYTIGKEIIDLVLDRIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GHYTIGKEIIDLVLDRIR 18 2 P68363;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;Q9BQE3 TUBA1B;TUBA1A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 202.5 7.72E-16 84318000 187670 197500 69448 63475 153260 158080 225730 225020 48906 FALSE TRUE 162868.934 196202.6095 103033.2851 77887.9689 150210.4258 164161.4399 203838.7393 176901.2241 43124.38839 3.776724496 4.549690252 2.389211509 1.806123444 3.483189709 3.806696072 4.726762441 4.102115548 1 15.39621638 3.014835479 24.98770872 3.641224811 3.112091718 0 1.207881371 967.1252298 1628937.617 0.379808645 0.430500631 1034.750105 -3.014835479 -0.529133093 GIAPAS(ph)PMLGNASNPNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GIAPASPMLGNASNPNK 17 0 H0YIY6;P27448-6;P27448-7;H0YKP9;J3KNR0;P27448-8;P27448-3;P27448-4;P27448-2;P27448 H0YIY6;J3KNR0 MARK3 MAP/microtubule affinity-regulating kinase 3 1 GIAPAS(1)PMLGNASNPNK;GIAPAS(1)PMLGNASNPNK;GIAPAS(1)PMLGNASNPNK;GIAPAS(1)PMLGNASNPNK;GIAPAS(1)PMLGNASNPNK 346.63 1.58E-87 1196702000 1987890 1741780 1288470 1602190 1659470 1421020 1648200 1960540 2845340 TRUE FALSE 1725185.3 1730338.132 1911578.402 1965991.727 1626449.794 1475687.559 1488357.818 1541293.778 2508967.147 0.687607768 0.689661535 0.761898538 0.783586078 0.648254719 0.588165358 0.593215347 0.614314053 1 21.25866215 1.23286492 24.99797262 1.000000531 0.668217822 0.715570689 0.065200249 117.7990998 516956.6671 0.158996135 0.018433692 17.09483527 -1.23286492 -0.33178271 GSEEDS(ph)PKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GSEEDSPKK 9 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 GSEEDS(1)PKK;GSEEDS(1)PKK;GSEEDS(1)PKK 138.42 8.39E-05 1379040000 3737600 2609330 3288380 3514000 1801400 1857700 3737200 4530000 10539900 TRUE FALSE 3243666.69 2592189.139 4878651.567 4311907.408 1765555.664 1929166.921 3374766.919 3561294.752 9293885.029 0.349010847 0.278913407 0.524931345 0.463951017 0.189969605 0.207573788 0.363116921 0.383186874 1 23.14785037 1.230278594 4.306892026 1.067713958 0.340959642 0.802469983 0.102305205 0.105720462 3.800172915 0.241114095 0.027580831 16.99333402 -1.230278594 -0.726754316 GIAYIEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIAYIEFK 8 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 129.4 0.0025415 793100000 1576300 1410190 939620 1188650 1270070 1126480 1407450 1611980 1599130 FALSE TRUE 1367987.961 1400926.369 1394023.375 1458551.15 1244798.092 1169816.415 1270955.716 1267270.621 1410082.673 0.970147345 0.993506548 0.988611095 1.034372791 0.882783765 0.829608389 0.901334184 0.898720795 1 20.42734832 3.230210143 24.99989865 0.898287641 0.995859358 0.528295509 0.044114193 143.3096115 429043.5984 0.013555874 0.015622163 1699.065583 -3.230210143 0.097571717 GICFIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GICFIR 6 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 135.18 0.031903 2835500000 2713000 3110200 2129720 1541670 2688700 2676300 2362500 2112010 2727900 FALSE TRUE 2354470.176 3089768.891 3159659.715 1891729.736 2635200.13 2779258.993 2133385.114 1660373.097 2405410.77 0.978822497 1.284507798 1.313563469 0.786447687 1.095530195 1.155419701 0.886910935 0.690265928 1 21.19785185 2.129134347 4.87471061 0.814133068 1.105015312 0.321121186 0.165530849 0.216919956 8.380656404 0.070648407 0.046632464 134.6276754 -2.129134347 0.290882244 GIDDNLDEIPDGEMPQVDHLVFVVHGIGPVCDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GIDDNLDEIPDGEMPQVDHLVFVVHGIGPVCDLR 34 0 Q9Y6Y8;Q9Y6Y8-2;H7C0V8;A0A0C4DH82 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 ;; 201.01 2.06E-27 647011000 328550 381078 251180 274176 344117 357069 338839 426513 336950 FALSE TRUE 285131.2851 378574.6735 372651.4881 336431.8513 337269.745 370805.6755 305978.4459 335306.5141 297116.1549 0.959662679 1.274163883 1.254228294 1.132324331 1.135144419 1.248015867 1.029827698 1.128536798 1 18.18066752 2.225744731 24.9992371 1.067612437 1.173021795 0.238855892 0.094734924 343.2730732 669597.7038 0.036859091 0.025035519 168.168531 -2.225744731 0.105409358 GIDLLKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GIDLLKK 7 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 101.28 0.034484 0 561390 429970 330390 298770 369260 436320 507520 556680 261420 FALSE TRUE 487200.8891 427145.4988 490167.7091 366610.2949 361912.4484 453105.5127 458300.7885 437638.3141 230515.2254 2.113530194 1.85300341 2.12640058 1.590395143 1.570015377 1.965620761 1.988158429 1.898522379 1 17.81450252 1.237945203 24.99810153 0.999998989 1.882887408 0.689968932 0.187082787 9.011941819 365763.2361 0.269222828 0.046592483 17.29598115 -1.237945203 0.882888419 GIEEEEILPGFILCDPNNLCHSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GIEEEEILPGFILCDPNNLCHSGR 24 0 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ;;;;; 312.56 1.65E-73 2250883000 1765358 1763278 1395118 1572443 1596911 1737990 1633925 1825321 2435266 FALSE TRUE 1532061.467 1751694.911 2069801.731 1929490.216 1565135.595 1804851.6 1475467.205 1434990.309 2147371.628 0.713458932 0.815739059 0.963876818 0.898535769 0.728861076 0.840493362 0.6871038 0.668254293 1 21.03414046 3.235509956 24.98753149 0.765796119 0.853889115 0.057127677 0.111936946 173.5743565 1421723.787 0.033879759 0.040077854 1719.926771 -3.235509956 0.088092996 GIEFEDES(ph)SDRDARPALETQPQQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GIEFEDESSDRDARPALETQPQQEK 25 2 D6RB01;Q9Y6X4 D6RB01 FAM169A Soluble lamin-associated protein of 75 kDa 1 GIEFEDES(0.5)S(0.5)DRDARPALETQPQQEK 150.95 8.24E-08 197930000 106290 99435 71867 65725 95085 78454 96666 119090 114940 TRUE FALSE 92243.5072 98781.80494 106622.1216 80648.86579 93192.99453 81472.17615 87291.3462 93623.53026 101351.9241 0.910130794 0.974641634 1.051998988 0.795730979 0.919499016 0.803854262 0.861269748 0.923746945 1 16.62901395 3.744418698 24.99944243 0.884872005 0.978495582 0.304563548 0.067596159 615.8518943 2628148.85 0.018149108 0.030370035 5551.606787 -3.744418698 0.093623577 GIEFEDESS(ph)DRDARPALETQPQQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GIEFEDESSDRDARPALETQPQQEK 25 2 D6RB01;Q9Y6X4 D6RB01 FAM169A Soluble lamin-associated protein of 75 kDa 1 GIEFEDES(0.125)S(0.875)DRDARPALETQPQQEK 148.89 1.06E-07 131970000 90310 100160 67651 66213 85767 92569 107870 114400 97672 TRUE FALSE 78375.30468 99502.04237 100367.2499 81247.67365 84060.4045 96130.18933 97408.784 89936.45026 86125.32743 0.910014592 1.155316854 1.165362767 0.943365629 0.976024208 1.116166315 1.13101206 1.044250895 1 16.39414994 2.713071381 24.95741467 1.073839561 1.039683165 0.048548404 0.088630321 3431.705083 3360098.326 0.031505216 0.027798755 516.501255 -2.713071381 -0.034156396 GIEGHS(ph)PGNLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIEGHSPGNLPK 12 0 Q96GY0;H0YAP0 Q96GY0 ZC2HC1A Zinc finger C2HC domain-containing protein 1A 1 GIEGHS(1)PGNLPK;GIEGHS(1)PGNLPK 119.32 0.00034189 627250000 1304890 1507250 1117300 1268880 1495760 1099870 1674560 1803720 1681530 TRUE FALSE 1132445.48 1497348.776 1657630.017 1556998.598 1465997.302 1142182.711 1512161.429 1418008.515 1482741.439 0.763751151 1.009851574 1.117949478 1.05008099 0.988707312 0.770318196 1.019841618 0.956342406 1 20.49983561 2.973725732 24.97223954 0.939952824 0.999468105 0.039738993 0.111206618 2341.259126 2225238.339 0.036076685 0.036191734 941.2949574 -2.973725732 0.059515281 GIEGMIMKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GIEGMIMKR 9 1 Q13393-3;Q13393-4;Q13393-2;Q13393 Q13393-3 PLD1 Phospholipase D1 0 ;; 68.735 0.034717 814350000 893260 952810 502440 642220 1100800 1359320 695570 708400 776540 FALSE TRUE 775213.4278 946550.9284 745421.6646 788045.8667 1078896.234 1411613.92 628113.7285 556914.1728 684738.3258 1.132130916 1.382354241 1.08862267 1.150871562 1.575632899 2.061537768 0.917304764 0.813324086 1 19.38519324 2.046538558 24.99999406 0.884919352 1.389574313 0.398300613 0.28252871 120.2059237 64572.75064 0.121309203 0.081786614 111.3111213 -2.046538558 0.50465496 GIEHQDSQHSFLAFLNTPTDALDQFETVDS(ph)TPLSVHTPTLR ddPTM_MDA-MB-175_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(0.022)VDS(0.331)T(0.331)PLS(0.17)VHT(0.122)PT(0.024)LR 181.05 7.81E-28 113210000 21831 31656 11237 20327 31961 47716 21393 33671 32585 TRUE FALSE 18945.97804 31448.04965 16671.25079 24942.55603 31325.03863 49551.6654 19318.31015 26470.71868 28732.83842 0.659384143 1.094498538 0.580215938 0.868085348 1.090217338 1.724565623 0.67234256 0.921270579 1 14.8104129 3.340096597 4.967484757 1.062326484 0.797858912 0.187323094 0.292641668 0.422140779 16.94268837 0.088049714 0.114010341 2188.248285 -3.340096597 -0.264467572 GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLSVHT(ph)PTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLSVHTPTLR 41 0 Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha 1 GIEHQDSQHSFLAFLNTPTDALDQFET(0.001)VDS(0.027)T(0.027)PLS(0.07)VHT(0.843)PT(0.031)LR;GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLS(0.01)VHT(0.987)PT(0.003)LR 263.64 1.13E-66 772680000 92494 123849 38785 76494 126897 187963 107417 118360 119854 TRUE FALSE 80270.68355 123035.4278 57541.55573 93863.13184 124371.998 195194.0582 96999.71587 93049.63508 105684.9967 0.759527711 1.164171185 0.544462862 0.888140557 1.17681792 1.846941992 0.91781917 0.880443185 1 16.68941106 3.292775162 5.81436508 1.144449871 0.837045353 0.219090385 0.304826436 0.364788421 26.01506726 0.095079767 0.121780058 1962.344091 -3.292775162 -0.307404518 GIEILTDMSRPVELSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 GIEILTDMSRPVELSDR 17 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;;;;;;;;;; 306.53 3.61E-47 8509681000 5431031 4936897 4309351 4499901 4717246 5349490 4778319 5500668 6249575 FALSE TRUE 4713306.493 4904466.199 6393367.558 5521672.299 4623382.034 5555288.342 4314918.359 4324392.954 5510757.363 0.855291965 0.889980428 1.160161324 1.00198066 0.838973979 1.008080737 0.782999155 0.784718446 1 22.39381918 2.240962355 24.9999904 0.838037371 0.961568352 0.159691171 0.108928437 97.96839798 1019781.992 0.042950901 0.031663214 174.16559 -2.240962355 0.12353098 GIFEALRPLETLPVEGLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIFEALRPLETLPVEGLIR 19 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 170.5 1.10E-11 1074050000 363950 379140 255140 229070 332850 353760 357800 414270 356230 FALSE TRUE 315853.0854 376649.4044 378526.5574 281083.8446 326226.9362 367369.3761 323100.6111 325681.5844 314116.8952 1.00552721 1.199074008 1.205049977 0.894838351 1.038552657 1.169530776 1.028599913 1.036816514 1 18.26094202 -1.99999979 0.167692424 0.618121999 1.138766666 0.070658982 0.095350521 354.5060129 4.801019342 44.81547838 1.11602271 0.010000005 1.99999979 0.520644666 GIFEPFGR ddPTM_MDA-MB-175_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 ; 168.45 0.00071364 977700000 1467360 1420480 949370 980090 1220970 1407550 1082030 1381170 1338930 FALSE TRUE 1273444.658 1411148.773 1408488.507 1202634.414 1196675.086 1461699.359 977094.8971 1085817.544 1180643.221 1.07860244 1.195237264 1.19298403 1.018626451 1.013578924 1.238053405 0.827595399 0.919683038 1 20.17114163 2.232945081 24.99998563 0.912903379 1.119621557 0.575650899 0.08377406 98.05754887 436540.1665 0.033965558 0.023616255 170.9799089 -2.232945081 0.206718178 GIFFSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIFFSHR 7 0 P23381;P23381-2;G3V277;G3V5U1;G3V3Y5;G3V3H8;G3V456;G3V423;G3V3P2;G3V227;G3V2Y7 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ; 151.51 0.0018764 2216290000 2482100 4197100 2855400 2626100 3829800 4133800 3699300 3652700 4113100 FALSE TRUE 2154084.196 4169528.974 4236280.991 3222396.142 3753594.473 4292829.961 3340542.455 2871598.53 3626854.004 0.59392636 1.149626913 1.16803185 0.888482453 1.034945015 1.183623591 0.921057879 0.791760167 1 21.79028724 2.01224071 24.89588413 0.873626736 1.01673652 0.058636773 0.178457232 440.5239398 895960.0333 0.070148246 0.047258352 102.8586239 -2.01224071 0.143109784 GIFGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIFGFR 6 0 Q9UHB9;Q9UHB9-4;Q9UHB9-2;Q9UHB9-3 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ; 139.13 0.027931 834580000 860780 836560 591560 586690 786390 1037080 710340 762350 848000 FALSE TRUE 747025.7421 831064.5823 877640.3946 719906.9315 770742.3775 1076977.139 641451.3361 599327.3851 747750.406 0.999030875 1.111419767 1.17370768 0.962763678 1.03074819 1.440289607 0.857841508 0.801507268 1 19.51219726 GIFLGDDEWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GIFLGDDEWR 10 0 Q8TB72-3;Q8TB72;Q8TB72-2;C9JW01 Q8TB72-3 PUM2 Pumilio homolog 2 0 ;;; 164.57 1.42E-05 325136000 594470 532667 350617 425133 487500 527143 470042 546020 499039 FALSE TRUE 515909.2833 529167.8754 520176.5539 521665.9454 477799.7038 547422.5323 424457.3992 429257.8721 440043.1779 1.172406048 1.202536255 1.182103439 1.185488087 1.085801866 1.244020041 0.964581251 0.975490347 1 18.74728557 2.228795983 24.99990408 0.978435885 1.176045313 0.846853676 0.039820416 67.58834947 173041.473 0.015300345 0.010458031 169.3542045 -2.228795983 0.197609428 GIFPVLCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GIFPVLCK 8 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 102.98 0.016956 0 280710 291590 242710 250550 290320 305640 255970 286310 469240 FALSE TRUE 243613.4623 289674.5261 360085.3678 307441.2069 284543.2 317398.1686 231146.0688 225084.8346 413766.9818 0.588769701 0.700090966 0.870261243 0.743029822 0.687689479 0.767093999 0.558638265 0.543989358 1 18.658459 GIFPVLCKDPVQEAWAEDVDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GIFPVLCKDPVQEAWAEDVDLR 22 1 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;; 238.63 1.34E-30 28244479000 13679062 10865964 6768566 6974875 9704232 9403236 12124744 12857498 5498454 FALSE TRUE 11871339.3 10794584.77 10041867.16 8558626.973 9511136.769 9764984.574 10948888.19 10108022.11 4848433.032 2.448489898 2.226406902 2.071157236 1.765235679 1.961692924 2.014049593 2.258232324 2.084801841 1 22.20908713 1.238906308 9.240210361 0.993216419 2.095563991 0.781624391 0.183312451 0.038385636 50.63102859 0.268057296 0.047601849 17.33429997 -1.238906308 1.102347571 GIGIENIHYLNDGLWHMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIGIENIHYLNDGLWHMK 18 0 Q9ULC4-2;Q9ULC4;Q9ULC4-3;A0A3B3IRV3 Q9ULC4-2 MCTS1 Malignant T-cell-amplified sequence 1 0 ; 232.84 1.47E-21 1565690000 2788400 2746200 1615550 1766560 2507900 2189400 2928900 3357600 1463530 FALSE TRUE 2419905.875 2728160.031 2396835.384 2167684.448 2457997.697 2273627.635 2644855.729 2639603.369 1290513.151 1.875150109 2.114011802 1.857273118 1.679707368 1.904666911 1.761801213 2.049460501 2.045390524 1 20.29951341 1.233631657 24.98945143 0.999998591 1.916316325 0.822941832 0.132768136 65.46508186 331863.3976 0.276512352 0.034366097 17.12504248 -1.233631657 0.916317734 GIGLDESELDS(ph)EAELMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIGLDESELDSEAELMR 17 0 Q96RS0 Q96RS0 TGS1 Trimethylguanosine synthase 1 GIGLDESELDS(1)EAELMR;GIGLDESELDS(1)EAELMR 274.52 8.79E-27 319130000 253820 249870 183983 181031 273190 257300 216318 256300 279430 TRUE FALSE 220277.0439 248228.5875 272957.7942 222136.8554 267754.0535 267198.4975 195339.5137 201492.2395 246396.1037 0.893995646 1.007437146 1.107800773 0.901543702 1.086681362 1.084426634 0.792786536 0.81775741 1 17.91061992 2.237406123 24.9999921 0.85603488 1.015869037 0.359076453 0.089661087 29.61066137 641173.1341 0.034690996 0.024874772 172.7452534 -2.237406123 0.159834157 GIGQVLPTHLMEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GIGQVLPTHLMEER 14 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-6;B4DWJ1;E5RJQ2;E5RG80 E7ESA6 PTK2 Focal adhesion kinase 1 0 88.73 0.005598 0 160650 181780 144130 124500 180580 171150 176940 204060 188130 FALSE TRUE 139419.6955 180585.8752 213831.7501 152769.6279 176986.8113 177734.2512 159780.386 160423.357 165889.4857 0.840437203 1.088591446 1.289001224 0.920912059 1.066895895 1.071401545 0.963173678 0.967049577 1 17.33986292 2.235946333 24.89464868 0.974156701 1.054414491 0.07080088 0.115994034 162.3535085 1545987.546 0.04542358 0.03219073 172.1655813 -2.235946333 0.08025779 GIGT(ph)PQPDVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIGTPQPDVAK 11 0 Q9Y6X8;H0YKA3 Q9Y6X8 ZHX2 Zinc fingers and homeoboxes protein 2 1 GIGT(1)PQPDVAK;GIGT(1)PQPDVAK 115.24 0.012852 170890000 816730 594600 442840 483990 558870 671940 593480 666640 804550 TRUE FALSE 708797.0612 590694.0334 656998.9052 593887.3268 547749.5804 697789.9666 535924.4009 524084.2238 709437.0155 0.999097941 0.832623645 0.926084897 0.83712481 0.772090501 0.983582688 0.755422101 0.738732562 1 19.43631508 7.999999995 0.872904053 0.836633589 63.22641525 0.163432162 0.092480743 1336.304712 3.332964635 0.030543063 165815.2058 99999998.88 -7.999999995 62.38978166 GIGTDEFTLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GIGTDEFTLNR 11 0 P12429;D6RA82 P12429 ANXA3 Annexin A3;Annexin 0 185.6 1.02E-05 80873000 192510 141000 72187 104380 132170 100200 199160 173180 106290 FALSE TRUE 167069.3157 140073.7617 107096.8747 128081.0743 129540.0756 104054.7588 179845.4939 136146.8047 93724.51729 1.782557228 1.494526361 1.14267726 1.366569581 1.382136493 1.110219203 1.918873514 1.45262743 1 16.51613887 4.652271194 3.686720973 1.372112292 1.795367899 0.230929232 0.251232133 0.381686849 8.582972808 0.062588821 0.366877347 44902.56958 -4.652271194 0.423255607 GIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK 33 1 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;; 290.54 1.37E-89 2648730000 1636730 1453560 919767 1122432 1221752 1123486 1491390 1722850 1296787 FALSE TRUE 1420431.984 1444011.469 1364569.398 1377297.341 1197441.526 1166707.233 1346755.227 1354431.935 1143482.318 1.242198468 1.262819237 1.193345429 1.204476291 1.047188493 1.02031069 1.177766552 1.184479999 1 20.12500263 3.373038552 5.675620819 1.102211036 1.229992831 0.546364985 0.062657839 0.195737464 9.180315189 0.019905879 0.025816651 2360.68778 -3.373038552 0.127781795 GIHNFRAS(ph)GDYDNDCTNPITPLCTQPDQVIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GIHNFRASGDYDNDCTNPITPLCTQPDQVIK 31 1 Q8TAF3-4;Q8TAF3-3;Q8TAF3 Q8TAF3-4 WDR48 WD repeat-containing protein 48 1 GIHNFRAS(0.889)GDY(0.108)DNDCT(0.002)NPITPLCTQPDQVIK 100.75 0.0001327 150370000 76575 94154 23865 24592 75982 68421 89253 93776 6769.6 TRUE FALSE 66455.41973 93535.49617 35406.19382 30175.98947 74470.10686 71053.20014 80597.2578 73722.73217 5969.3056 11.13285601 15.66940988 5.93137564 5.055192595 12.47550584 11.90309307 13.50194867 12.35030288 1 12.5433474 4.25119079 24.99971102 9.543382789 13.40113188 0.156820706 4.139037372 493.4850468 976768.4599 1.056095907 2.753506454 17831.61958 -4.25119079 3.857749096 GIHNSIGDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIHNSIGDYR 10 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 151.15 2.03E-05 670320000 605690 625130 292780 372660 800430 836880 554870 608020 648160 FALSE TRUE 525646.5319 621023.4799 434369.3873 457278.1488 784503.009 869075.3151 501058.7928 477999.6546 571535.2632 0.919709711 1.086588212 0.760004527 0.800087376 1.372623982 1.52059789 0.8766892 0.836343241 1 19.12448299 GIHPTIISESFQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIHPTIISESFQK 13 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ; 263.29 3.66E-24 2507500000 5730600 5602000 2264800 4340200 5336800 4639900 5708000 6856000 6122300 FALSE TRUE 4973286.691 5565200.093 3360064.855 5325708.746 5230608.121 4818399.955 5154439.039 5389897.753 5398528.669 0.921230023 1.030873491 0.622403818 0.986511154 0.968895127 0.892539477 0.954785897 0.998401247 1 22.36413483 2.018528456 0.747405147 1.026093518 0.889965288 0.119214057 0.10889452 2.593890054 2.277204388 0.261755686 0.056805074 104.3586508 -2.018528456 -0.136128231 GIHYWEVELQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GIHYWEVELQK 11 0 Q14258 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 128.44 0.00026569 209300000 535340 449000 337700 419890 494700 419840 526140 657980 593470 FALSE TRUE 464593.4626 446050.4894 501012.8495 515232.4421 484856.4379 435991.5165 475115.0238 517276.0974 523310.6527 0.887796685 0.852362716 0.957390886 0.98456326 0.926517424 0.833140916 0.90790245 0.988468503 1 18.9973081 1.701043567 4.558558221 0.996642322 0.907647346 0.399954336 0.044441907 0.176815437 8.662003912 0.03198903 0.012665693 50.23929851 -1.701043567 -0.088994976 GIINDDEDDEDLMMASGRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GIINDDEDDEDLMMASGRPR 20 1 O75717;O75717-2 O75717 WDHD1 WD repeat and HMG-box DNA-binding protein 1 0 252.55 4.04E-36 131010000 112960 106460 74927 81973 115010 102420 111560 136850 95277 FALSE TRUE 98032.0498 105760.6573 111161.9478 100586.2225 112721.526 106360.1637 100740.9284 107585.6925 84013.4616 1.166861214 1.258853703 1.323144478 1.19726316 1.34170791 1.265989541 1.199104601 1.280576832 1 16.35833289 1.235282064 24.97818526 0.999999641 1.2564683 0.678336604 0.054989244 51.77531928 394391.0864 0.088608257 0.012649031 17.19024489 -1.235282064 0.256468658 GIIRPGTAFELLEAQAATGYVIDPIK ddPTM_MDA-MB-175_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 0 120.85 0.00013529 109780000 188200 132060 100970 123780 116840 120390 166940 162720 166600 FALSE TRUE 163328.8932 131192.4892 149799.4297 151886.1409 114515.1126 125021.4812 150750.1845 127923.5943 146904.7378 1.1118014 0.893044643 1.019704551 1.03390907 0.779519533 0.851037775 1.026176465 0.870792843 1 17.1645214 6.813756374 1.64630629 0.929911089 174.836013 0.277110287 0.087174601 1958.702178 6.933320909 0.023026439 1285062.382 6512629.532 -6.813756374 173.9061019 GIISILDEECLRPGEATDLTFLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIISILDEECLRPGEATDLTFLEK 24 1 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 194.25 4.40E-28 98597000 183535 158786 106418 123664 148892 125455 155409 217554 166281 FALSE TRUE 159280.3847 157742.9243 157882.1007 151743.8013 145929.3405 130281.335 140337.4591 171031.7701 146623.4496 1.086322721 1.075836946 1.076786156 1.034921779 0.995266043 0.88854365 0.957128341 1.166469419 1 17.16175633 3.633150276 3.237262644 1.013282334 1.080006233 0.200433949 0.068956549 0.562755451 11.15119866 0.022861627 0.036242434 4296.850826 -3.633150276 0.066723899 GIITDS(ph)FGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 173.28 5.83E-05 1187630000 1911840 1880120 1351090 1347260 1794230 2173440 1720440 1805440 1833220 TRUE FALSE 1659185.5 1867769.368 2004481.643 1653175.975 1758528.333 2257053.643 1553591.994 1419360.706 1616498.82 1.026406874 1.15544122 1.240014294 1.022689255 1.087862429 1.396260619 0.961084521 0.878046237 1 20.62444102 2.030010535 24.97508474 0.927087919 1.152057436 0.437335163 0.111429849 162.3893105 135141.4439 0.044268463 0.029845399 107.1545298 -2.030010535 0.224969517 GILAADES(ph)TGSIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GILAADESTGSIAK 14 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 GILAADES(0.929)T(0.071)GSIAK;GILAADES(0.8)T(0.195)GS(0.005)IAK;GILAADES(0.882)T(0.118)GSIAK;GILAADES(0.931)T(0.069)GSIAK;GILAADES(0.5)T(0.5)GSIAK;GILAADES(0.987)T(0.013)GSIAK 338.78 9.48E-69 1805210000 3184160 3450320 2287850 2398220 2766580 2474480 3102920 3361680 4785410 TRUE FALSE 2763365.188 3427654.621 3394261.912 2942772.505 2711530.471 2569674.847 2801999.296 2642810.893 4219684.281 0.654874868 0.812301204 0.804387648 0.697391632 0.642590841 0.608973249 0.664030555 0.626305362 1 22.00870363 1.231521233 24.99849948 1.000000538 0.688553575 0.667499597 0.06901306 171.5826467 609275.4876 0.184954797 0.018872373 17.04202638 -1.231521233 -0.311446964 GILAADESTGS(ph)IAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GILAADESTGSIAK 14 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 GILAADESTGS(1)IAK;GILAADES(0.005)T(0.005)GS(0.989)IAK;GILAADEST(0.001)GS(0.999)IAK;GILAADES(0.001)T(0.084)GS(0.915)IAK 218.78 5.51E-12 311244000 805610 877440 610318 583528 763930 658460 804850 833670 1433920 TRUE FALSE 699146.5973 871676.0389 905469.8262 716026.9511 748729.2876 683791.3823 726795.7709 655396.1581 1264403.611 0.552945745 0.689396986 0.716124043 0.566296193 0.592160036 0.54080151 0.574813109 0.518344105 1 20.27002563 1.232045315 24.99999261 1.000000681 0.593661236 0.805546436 0.062710483 104.3193372 400247.7717 0.155361564 0.016691664 17.06260413 -1.232045315 -0.406339445 GILAADESTGSIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GILAADESTGSIAK 14 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 184.24 1.92E-07 0 90499 85685 61734 60231 81906 71996 91428 103430 107030 FALSE TRUE 78539.32785 85122.12959 91588.76889 73907.36912 80276.23085 74765.73271 82561.32663 81312.29939 94377.03533 0.832186851 0.901936889 0.970456092 0.783107552 0.850590724 0.792202599 0.874803138 0.861568697 1 16.52614823 1.236650375 6.420454061 1.004276876 0.859190221 0.411196002 0.053263348 0.133876807 24.75994403 0.084444346 0.013305904 17.2444908 -1.236650375 -0.145086655 GILADEDSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GILADEDSSR 10 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 179.37 0.0064717 228460000 497320 527550 571860 560940 550720 645450 509320 546080 1687910 FALSE TRUE 431597.902 524084.4893 848413.4088 688310.0004 539761.7495 670280.8792 459926.2248 429305.0416 1488367.203 0.289980793 0.352120423 0.570029632 0.462459801 0.362653617 0.450346445 0.309013948 0.288440273 1 20.50529907 1.232999294 24.99972294 1.000000975 0.385903925 0.826948901 0.088324146 78.01851699 350677.6779 0.198728786 0.023336949 17.10012536 -1.232999294 -0.61409705 GILADEDSSRPVWLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 229.17 4.54E-13 86548470000 24514870 23243500 18271020 18168290 23812470 23059690 26005480 27726960 27576860 FALSE TRUE 21275167.82 23090811.92 27106946.38 22293677.93 23338648.44 23946811.2 23483472.55 21797765.38 24316755.03 0.874918047 0.949584428 1.114743573 0.916803163 0.959776434 0.984786464 0.965732168 0.896409301 1 24.53544738 1.9684734 24.15074809 0.937884934 0.970552618 0.00582806 0.065965403 1577.948387 1208772.984 0.029909167 0.017295679 92.99795532 -1.9684734 0.032667684 GILGYTEHQVVSSDFNSDTHSSTFDAGAGIALNDHFVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 58 GILGYTEHQVVSSDFNSDTHSSTFDAGAGIALNDHFVK 38 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 420.03 1.25E-220 25847522300 7316121.3 8465059.6 3029078.45 5178969.4 9043526 8437754.1 8446493.8 9573929 8494107.8 FALSE TRUE 6349277.334 8409452.066 4493950.92 6354933.558 8863577.526 8762359.96 7627354.131 7526618.788 7489944.052 0.847706911 1.122765672 0.599997929 0.848462086 1.183397027 1.169883233 1.018345942 1.00489653 1 22.83652351 3.258530988 24.88464929 1.066960577 0.855682854 0.385644667 0.138111615 261.5317302 325886.8708 0.040485971 0.052197106 1813.556073 -3.258530988 -0.211277723 GILHLS(ph)PDVYQEMEASR ddPTM_MDA-MB-175_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 231.37 3.14E-16 350550000 320129 319995 209121 242491 302210 326424 274083 360586 319318 TRUE FALSE 277823.1415 317892.9318 310252.6151 297552.2878 296196.6123 338981.7425 247502.4728 283477.49 281568.5898 0.986697919 1.129007081 1.101872248 1.056766623 1.051951897 1.203904678 0.879013078 1.006779521 1 18.10312688 2.230491166 24.99994545 0.967819453 1.087736331 0.454234554 0.065223288 162.2304101 502600.5027 0.024956985 0.017157279 170.016537 -2.230491166 0.119916878 GILLEDGSES(ph)PAKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GILLEDGSESPAKR 14 1 Q08999;Q08999-2 Q08999 RBL2 Retinoblastoma-like protein 2 1 GILLEDGS(0.175)ES(0.825)PAKR;GILLEDGS(0.003)ES(0.997)PAKR 116 0.00023703 511290000 502290 403220 249492 263795 360070 343970 374080 501770 375560 TRUE FALSE 435911.1039 400571.2213 370147.1657 323693.6866 352905.3115 357202.7485 337801.7792 394470.3903 331161.7246 1.316308835 1.209593958 1.11772327 0.97744897 1.065658514 1.078635367 1.020050791 1.191171446 1 18.33717641 4.388495318 2.153197581 1.068020013 1.314649129 0.684621416 0.059143426 0.225772736 1.850888239 0.016300656 0.081330998 24462.18902 -4.388495318 0.246629116 GILQVLPDEITFPLS(ph)PLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GILQVLPDEITFPLSPLRK 19 1 A0A0U1RR07;Q9HCH5-7;Q9HCH5-8;A0A0U1RQP0;A0A0U1RRJ3;Q9HCH5-11 A0A0U1RR07 SYTL2 Synaptotagmin-like protein 2 1 GILQVLPDEIT(0.005)FPLS(0.995)PLRK;GILQVLPDEITFPLS(1)PLRK 166.91 1.16E-11 1224840000 569520 759480 715580 923400 1064470 1042960 1242570 1573240 1071090 TRUE FALSE 494256.489 754490.9259 1061636.881 1133072.083 1043289.13 1083083.346 1122065.753 1236814.869 944466.9604 0.523317924 0.7988537 1.124059312 1.199694781 1.104632743 1.146766792 1.188041297 1.309537465 1 19.8491408 4.447900863 1.977580725 1.17572342 0.487762848 0.878883767 0.079469359 0.136749143 0.866322217 0.021784117 0.138496365 28047.93313 -4.447900863 -0.687960572 GILRT(ph)PDTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GILRTPDTIR 10 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 1 GILRT(0.931)PDT(0.069)IR 69.352 0.092532 640910000 1018800 1047700 490990 470480 952200 1242600 834960 997530 347500 TRUE FALSE 884162.9987 1040817.59 728434.4063 577309.6748 933253.0829 1290403.626 753985.7077 784215.9723 306418.9459 2.885471054 3.396714217 2.377249893 1.884053459 3.045676827 4.211239688 2.460636713 2.559293356 1 18.22514598 1.137030594 1.959966361 6.01E-11 2.908233913 0.474791443 0.622232156 1.038416863 3.069424637 6.096333748 0.177088629 13.70978343 -1.137030594 2.908233913 GILSGTSDLLLTFDEAEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GILSGTSDLLLTFDEAEVR 19 0 P18206;P18206-2;P18206-3 P18206 VCL Vinculin 0 ; 236.3 8.08E-24 16398100 38547 34035 26247 30335 34063 35431 34451 38056 48312 FALSE TRUE 33452.91628 33811.42184 38940.13699 37223.02539 33385.21294 36794.0535 31109.94732 29918.02055 42600.6104 0.785268473 0.793683976 0.914074625 0.873767419 0.783679216 0.8636978 0.73026999 0.702290889 1 15.37858648 2.259208432 24.99690586 0.784878697 0.836714531 0 0.089117096 690.462451 835894.1221 0.033177343 0.025670425 181.6387198 -2.259208432 0.051835834 GILSLPHQAS(ph)PVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GILSLPHQASPVSR 14 0 O75925;O75925-2 O75925 PIAS1 E3 SUMO-protein ligase PIAS1 1 GILSLPHQAS(0.998)PVS(0.002)R;GILSLPHQAS(1)PVSR;GILSLPHQAS(0.998)PVS(0.002)R;GILSLPHQAS(1)PVSR 225.17 1.85E-12 2750220000 1798550 1775730 1128590 1189820 1602010 1703810 1472560 1695570 1525480 TRUE FALSE 1560867.061 1764065.113 1674379.899 1459986.816 1570133.135 1769356.673 1329751.358 1332985.55 1345139.492 1.160375611 1.311436563 1.244763022 1.08537949 1.167264172 1.315370401 0.988560194 0.990964549 1 20.35932436 2.221573029 24.99837567 0.992522038 1.211936858 0.697004125 0.068654764 135.7825837 199811.6307 0.028680762 0.019391 166.5608885 -2.221573029 0.21941482 GILTLK ddPTM_MDA-MB-175_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 ; 124.32 0.042818 4410600000 5818600 4733800 3358100 4080300 4469800 4451000 5005300 5960200 5247500 FALSE TRUE 5049657.268 4702703.356 4982088.392 5006794.478 4380859.725 4622232.85 4519886.776 4685657.612 4627146.528 1.091311295 1.016329033 1.076708585 1.082047964 0.946773503 0.998938076 0.976819461 1.012645176 1 22.14169135 3.250824845 24.99994855 0.99006544 1.0637306 0.69123887 0.026349105 134.7562815 274691.6377 0.007421384 0.00950919 1781.660063 -3.250824845 0.07366516 GIMVLAGDTLPIEVYCHLPVMCEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GIMVLAGDTLPIEVYCHLPVMCEDR 25 0 D6RC52;D6RCB9;Q9NX24;H0YC83 D6RC52 NHP2 H/ACA ribonucleoprotein complex subunit 2 0 194.37 1.87E-18 204850000 139020 129130 117960 102910 122600 128490 123730 163180 144440 FALSE TRUE 120648.1548 128281.7365 175005.8506 126277.2884 120160.4999 133433.0934 111730.6836 128285.2269 127364.4677 0.94726698 1.007201921 1.374055525 0.991464029 0.943438166 1.047647714 0.877251604 1.007229325 1 16.95860332 3.51156862 24.98681378 0.974690857 1.113191225 0.218989465 0.117524426 897.7650643 651202.5241 0.031850524 0.047213357 3247.645519 -3.51156862 0.138500368 GINLPTPPGLS(ph)PGDLDVFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GINLPTPPGLSPGDLDVFVR 20 0 Q6P1N0-2;Q6P1N0;K7EMP1 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 GINLPTPPGLS(1)PGDLDVFVR;GINLPTPPGLS(1)PGDLDVFVR 177.64 6.79E-17 167973000 238473 222792 189208 200950 229494 260184 231273 250252 230792 TRUE FALSE 206958.1888 221328.4647 280709.6217 246578.7688 224927.5184 270193.4468 208844.1801 196737.5573 203508.0327 1.016953415 1.087566234 1.379354014 1.211641455 1.105251304 1.327679519 1.026220819 0.966731164 1 17.63472621 2.074872946 8.099652294 0.985573307 1.189246182 0.41595388 0.107227442 0.23304057 22.13140661 0.044502071 0.029926277 118.815458 -2.074872946 0.203672875 GIPDDRDGLFDTIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIPDDRDGLFDTIQR 15 1 Q93008;Q93008-3;O00507;H7C2M9 Q93008 USP9X;USP9Y Probable ubiquitin carboxyl-terminal hydrolase FAF-X;Probable ubiquitin carboxyl-terminal hydrolase FAF-Y 0 ; 157.03 1.84E-06 496350000 331680 274345 232388 200248 308481 354300 296471 351850 219054 FALSE TRUE 287847.6476 272542.8096 344771.6141 245717.369 302342.8316 367930.1503 267719.2881 276609.6156 193157.6857 1.490221042 1.4109861 1.784923095 1.272107647 1.56526431 1.904817554 1.386014163 1.432040432 1 17.55941956 1.058432594 1.593934933 0.558648237 1.554424236 0.462654986 0.184434482 1.572870336 2.493068664 2.839216879 0.050796616 11.44017305 -1.058432594 0.995775999 GIPHLVTHDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 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 ;;;;;;;; 187.97 1.94E-06 11007310000 4747385 4800695 3396955 3515878 4568269 4973712 4168096 4940418 4386392 FALSE TRUE 4120006.044 4769158.918 5039733.8 4314211.837 4477369.385 5165053.919 3763874.691 3883948.057 3867837.735 1.065196197 1.23302973 1.302984806 1.115406626 1.157589768 1.335385369 0.973121147 1.004165201 1 21.88309584 2.217430564 24.99986492 0.994069286 1.201717664 0.602549999 0.080078772 157.4311371 186262.1014 0.031890211 0.021524292 164.9797209 -2.217430564 0.207648378 GIPLATGDT(ph)SPEPELLPGAPLPPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIPLATGDTSPEPELLPGAPLPPPK 25 0 O75821;K7ENA8;K7ER90;K7EL20;K7EL60 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 1 GIPLAT(0.07)GDT(0.465)S(0.465)PEPELLPGAPLPPPK;GIPLAT(0.078)GDT(0.461)S(0.461)PEPELLPGAPLPPPK 141.37 1.37E-06 163441000 316210 285060 229580 264500 286430 281170 308460 388120 421430 TRUE FALSE 274422.0473 283187.4221 340605.6559 324558.7676 280730.6034 291986.7918 278545.5967 305123.5584 371609.0255 0.738469812 0.762057438 0.916569923 0.873387742 0.755446139 0.785736545 0.749566285 0.821087588 1 18.50342602 1.245284167 4.623837274 1.014463664 0.800327372 0.5531534 0.056733649 0.153797632 7.213816067 0.106414993 0.015087691 17.59074232 -1.245284167 -0.214136292 GIPLATGDTS(ph)PEPELLPGAPLPPPK ddPTM_MDA-MB-175_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(0.158)S(0.79)PEPELLPGAPLPPPK;GIPLAT(0.004)GDT(0.167)S(0.828)PEPELLPGAPLPPPK 217.21 1.00E-33 309250000 744340 645880 479850 582530 616230 560470 707000 866140 788490 TRUE FALSE 645973.5831 641637.1718 711907.065 714802.3399 603968.2286 582031.6436 638435.2488 680922.7013 695275.6105 0.929089951 0.922852984 1.023920664 1.028084876 0.868674551 0.837123631 0.918247727 0.979356519 1 19.40722546 1.600083795 4.515496074 0.995149683 0.933418175 0.143963089 0.058725942 0.345829681 15.32442321 0.047897113 0.016965278 39.8183991 -1.600083795 -0.061731508 GIPNERPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIPNERPTR 9 1 Q96F86;H3BPW9;H3BSQ0;H3BPN4 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 0 ; 97.277 0.0062014 253310000 309630 267730 197185 189591 280320 299940 324080 358550 308230 FALSE TRUE 268711.611 265971.264 292544.3255 232640.5343 274742.1804 311478.8859 292650.7715 281876.8727 271791.4005 0.988668554 0.978586017 1.076356077 0.85595252 1.010856782 1.146021858 1.076747722 1.0371074 1 18.05214028 2.992671653 24.99461247 1.063577764 0.976277561 0.309314038 0.06356622 432.8989012 1476483.443 0.019452011 0.021186914 983.267429 -2.992671653 -0.087300203 GIPNMLLS(ph)EEETES ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GIPNMLLSEEETES 14 0 F5GYQ2;Q9UI30;Q9UI30-2 F5GYQ2 TRMT112 Multifunctional methyltransferase subunit TRM112-like protein 1 GIPNMLLS(0.999)EEET(0.001)ES 80.96 0.015567 12219000 14355 13699 6039.9 9467.4 12923 11809 11629 13421 11771 TRUE FALSE 12457.95038 13609.01037 8960.815842 11617.11787 12665.85758 12263.29987 10501.22137 10551.02359 10379.44579 1.200251982 1.311150002 0.863323151 1.119242598 1.220282647 1.181498523 1.011732378 1.016530536 1 13.34144179 -1.412249035 0.289202945 2.89E-10 1.178636856 0.185927182 0.119101784 99.38895991 2.199198798 54.79011419 0.277725763 0.038703565 1.412249035 1.178636856 GIPVVEHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 83.265 0.018284 131120000 263180 226680 150440 202740 244080 201700 206810 272860 246610 FALSE TRUE 228400.0962 225190.9242 223193.2872 248775.2157 239223.2855 209459.5295 186753.598 214511.0124 217456.0467 1.050327639 1.035569843 1.026383449 1.144025284 1.100099487 0.963226972 0.858810784 0.986456875 1 17.7303643 2.677130226 6.287588492 0.947775932 1.070729756 0.587702199 0.049601634 0.170847729 13.81620113 0.018057725 0.015954429 475.4777801 -2.677130226 0.122953824 GIQFLQEQGMLGTSVEDIAQFLHQEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GIQFLQEQGMLGTSVEDIAQFLHQEER 27 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 0 161.84 2.51E-17 0 51527 38570 31291 23139 36102 41265 38963 37964 31938 FALSE TRUE 44717.5764 38316.63113 46423.43226 28393.06361 35383.64083 42852.49125 35184.37426 29845.69404 28162.32602 1.587850959 1.360563438 1.648423224 1.008193129 1.256417556 1.521624713 1.249341913 1.059773756 1 14.78147888 -0.233513281 0.203233297 1.46E-24 1.614617082 0.424228267 0.177838621 51.54006093 1.528854961 23.06050728 1.375238239 0.584099345 0.233513281 1.614617082 GIQLS(ph)PGVGSSAGPPGDLEDDEGLKHLQQEAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIQLSPGVGSSAGPPGDLEDDEGLKHLQQEAEK 33 1 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 GIQLS(0.97)PGVGS(0.015)S(0.015)AGPPGDLEDDEGLKHLQQEAEK;GIQLS(0.994)PGVGS(0.003)S(0.003)AGPPGDLEDDEGLKHLQQEAEK 156.85 1.99E-11 178745000 205864 177871 149894 141142 184852 129181 268480 294114 107873 TRUE FALSE 178658.5508 176702.5537 222383.2398 173190.4483 181173.8069 134150.6767 242442.8509 231220.0099 95120.37683 1.878236365 1.857672978 2.33791378 1.820750233 1.904679238 1.410325328 2.548800362 2.430814696 1 16.53746681 GIQLYDTPYEPEGQS(ph)VDSDSESTVSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GIQLYDTPYEPEGQSVDSDSESTVSPR 27 0 Q15464 Q15464 SHB SH2 domain-containing adapter protein B 1 GIQLYDTPYEPEGQS(0.359)VDS(0.252)DS(0.3)ES(0.041)T(0.048)VS(0.001)PR 81.683 0.0069034 90498000 64007 53014 38081 45141 48346 67447 64157 60762 62883 TRUE FALSE 55548.31278 52665.74754 56497.09897 55390.95399 47384.00919 70041.72973 57935.06401 47768.51915 55449.04338 1.001790282 0.949804439 1.018901239 0.998952382 0.854550526 1.263172915 1.044834329 0.861485 1 15.75887495 1.753134064 25 0.924886417 1.018515516 0.104887872 0.106708349 10.02192437 17221.063 0.056570186 0.027165899 56.64141104 -1.753134064 0.093629099 GIRPAINVGLSVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GIRPAINVGLSVSR 14 1 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 157.23 4.88E-06 449300000 264500 237830 165430 286400 276970 333760 231890 273320 276490 FALSE TRUE 229545.6548 236267.6791 245432.5013 351431.4973 271458.8389 346599.9632 209401.3435 214872.645 243803.6672 0.941518466 0.969089931 1.006680926 1.441452876 1.11343214 1.421635561 0.85889333 0.881334754 1 17.8953603 2.174295299 24.9999945 0.904454558 1.146011216 0.291829456 0.172751446 78.72046171 30622.11132 0.072841428 0.049109694 149.3809784 -2.174295299 0.241556658 GIRPFPSEETTENDDDVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIRPFPSEETTENDDDVYR 19 1 P52735-3;P52735-2;P52735 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 0 ; 237.16 2.99E-24 839720000 647922 637220 490049 586241 636960 718120 543510 685320 1166350 FALSE TRUE 562297.4661 633034.0599 727038.3355 719355.9792 624285.7422 745746.5411 490800.4839 538769.6512 1028465.432 0.546734434 0.615513211 0.706915676 0.699445948 0.607007025 0.725106083 0.477216315 0.523857812 1 19.97206187 1.230610058 24.9976376 1.000000707 0.611280892 0.690696981 0.081441076 187.6800573 590043.1575 0.232174514 0.02165595 17.0063087 -1.230610058 -0.388719815 GIS(ph)HASSSIVSLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GISHASSSIVSLAR 14 0 Q6GQQ9;Q6GQQ9-2;Q5SZ59 Q6GQQ9 OTUD7B OTU domain-containing protein 7B 1 GIS(0.978)HAS(0.013)S(0.004)S(0.004)IVSLAR 103.67 0.0024381 0 104600 106780 53371 58435 112960 131380 88733 92217 93454 TRUE FALSE 90776.84498 106078.5551 79181.39412 71703.55987 110712.317 136434.2736 80127.68732 72497.11218 82405.97458 1.101580868 1.28726777 0.960869579 0.870125743 1.343498667 1.655635702 0.972352887 0.879755534 1 16.33046132 2.028927168 24.99985538 0.929717765 1.197778562 0.233696061 0.215779692 300.1533767 259401.6553 0.093951661 0.06334111 106.8875612 -2.028927168 0.268060797 GIS(ph)PIVFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 GISPIVFDR 9 0 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 GIS(1)PIVFDR;GIS(1)PIVFDR;GIS(1)PIVFDR;GIS(1)PIVFDR;GIS(1)PIVFDR;GIS(1)PIVFDR;GIS(1)PIVFDR;GIS(1)PIVFDR;GIS(1)PIVFDR;GIS(1)PIVFDR 209.8 8.22E-06 19653110000 7916010 6575840 5572040 6545540 6422670 6674330 6289780 7217780 12284870 TRUE FALSE 6869889.222 6532642.874 8266697.181 8031804.899 6294871.433 6931095.794 5679798.104 5674313.916 10832566.66 0.634188502 0.603055866 0.763133746 0.741449847 0.58110618 0.639838739 0.524326162 0.523819893 1 23.36887178 1.229205575 24.98888218 1.000000743 0.622923758 0.689623708 0.078744903 245.9279425 656866.1969 0.268325174 0.021720476 16.9514001 -1.229205575 -0.377076985 GIS(ph)PVVSEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GISPVVSEHR 10 0 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 1 GIS(1)PVVSEHR 136.93 6.74E-05 124360000 119580 129040 71794 109120 124760 138470 106830 133130 203850 TRUE FALSE 103777.2 128192.3277 106513.8185 133897.3638 122277.5201 143797.0305 96469.64304 104661.1855 179751.0852 0.577338378 0.713165807 0.592562868 0.744904342 0.680260261 0.79997865 0.536684621 0.582256209 1 17.45564096 1.231396801 24.99829189 1.000000604 0.652835514 0.631453509 0.083216415 172.1856928 600792.695 0.204237831 0.020644339 17.03714428 -1.231396801 -0.347165091 GIS(ph)SLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GISSLPR 7 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 GIS(0.772)S(0.228)LPR 98.458 0.011799 352740000 862510 933950 509700 534380 828440 793740 656350 794130 773870 TRUE FALSE 748527.1182 927814.821 756192.6248 655719.1465 811955.6648 824275.6914 592697.278 624311.4794 682383.9702 1.096929516 1.359666788 1.108162937 0.960924018 1.189880918 1.207935308 0.868568583 0.914897633 1 19.38022423 2.238591887 24.99999994 0.922660563 1.154051518 0.510131877 0.104402752 0.673264697 538543.0992 0.041959825 0.030373375 173.2175483 -2.238591887 0.231390954 GISCLVDAFLGISRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GISCLVDAFLGISRPR 16 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 0 ; 148.7 8.27E-07 98993000 88475 102277 70694 74550 95446 113632 119624 98507 75530 FALSE TRUE 76782.80458 101605.1357 104881.8549 91477.71693 93546.81134 118003.4966 108022.8829 77442.04463 66600.92944 1.152878875 1.525581347 1.574780648 1.373520125 1.404587175 1.771799546 1.621942573 1.162777236 1 16.02325469 1.587941506 4.365646869 1.035028772 1.496125618 0.524253542 0.16449127 0.122753703 5.095226119 0.125867145 0.043367471 38.72054901 -1.587941506 0.461096846 GISDLAQHYLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GISDLAQHYLMR 12 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;; 172.11 3.66E-05 6202610000 5689600 6193600 3979070 4812700 5962300 6520900 5683900 6091200 6125200 FALSE TRUE 4937704.944 6152913.834 5903361.561 5905497.093 5843661.895 6771763.243 5132676.253 4788644.282 5401085.834 0.914205976 1.139199417 1.092995324 1.093390713 1.081942053 1.25377812 0.950304515 0.886607699 1 22.36481805 2.034623276 24.95226689 0.930179856 1.097422813 0.401632433 0.086158495 144.6399326 104238.3917 0.033451488 0.022552881 108.2987081 -2.034623276 0.167242958 GISEETTTGVHNLYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GISEETTTGVHNLYK 15 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;;; 269.4 6.17E-26 12866900000 8842700 9126400 5513340 7327700 8835000 8045700 9873800 11083500 10671900 FALSE TRUE 7674114.79 9066448.077 8179609.665 8991566.282 8659200.785 8355223.285 8916240.396 8713379.777 9410280.139 0.81550333 0.96346208 0.869220634 0.955504634 0.920185229 0.887882524 0.947499996 0.925942655 1 23.16580624 2.487097892 0.017823336 1.859999641 2.00E-07 0.330132866 0.043022077 1442.704257 20.56318747 1095.095066 1049.947331 306.9713839 -2.487097892 -1.859999441 GISHVIVDEIHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 GISHVIVDEIHER 13 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;;;; 242.48 3.57E-17 11158700000 2888817 2688470 1783568 1906625 2464769 2677877 2498921 2760272 2663089 FALSE TRUE 2507052.514 2670809.264 2646107.45 2339553.347 2415724.919 2780896.661 2256576.026 2170009.313 2348261.652 1.0676206 1.137355908 1.126836717 0.996291595 1.028729025 1.184236287 0.960955958 0.92409179 1 21.16316174 2.134260137 9.364649659 0.952620677 1.086819931 0.533374758 0.056431092 0.213231962 17.54022263 0.023359629 0.015741173 136.2260415 -2.134260137 0.134199255 GISQEQMQEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GISQEQMQEFR 11 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;;;;; 338.37 1.94E-57 2713510000 1524540 1385706 1213721 1433720 1243280 1456620 1024360 1347617 2433260 FALSE TRUE 1323068.176 1376603.206 1800680.535 1759268.039 1218541.16 1512657.114 925017.7249 1059439.592 2145602.775 0.616641716 0.64159276 0.839242266 0.819941165 0.567924862 0.705003336 0.431122543 0.493772475 1 21.03295158 3.224114963 24.98645962 0.608979393 0.730934927 0.050369174 0.166468705 545.7195067 943921.6126 0.051065174 0.058155355 1675.386312 -3.224114963 0.121955534 GISS(ph)LPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GISSLPR 7 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 GIS(0.262)S(0.738)LPR;GIS(0.074)S(0.926)LPR;GIS(0.148)S(0.852)LPR 113.94 0.0063108 1001870000 2302840 2617820 1471860 1442960 2221220 2254820 1917400 2336020 2163130 TRUE FALSE 1998513.859 2600623.368 2183656.419 1770606.122 2177022.068 2341564.384 1731450.843 1836480.302 1907407.236 1.047764642 1.363433733 1.144829682 0.928279021 1.141351478 1.22761639 0.907751009 0.962815002 1 20.86318146 2.344611698 0.415639935 0.881675322 1.206392627 0.231041977 0.125366376 3.346443758 1.305903738 0.619983801 0.246329616 221.1116871 -2.344611698 0.324717305 GISTKPVYIPEVELNHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GISTKPVYIPEVELNHK 17 1 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 ; 132.59 1.39E-05 1337900000 2205900 2027060 1332670 1532730 1916070 1464630 1964290 2537100 2229870 FALSE TRUE 1914384.726 2013744.109 1977153.67 1880759.773 1877943.956 1520975.264 1773793.458 1994560.909 1966257.309 0.973618619 1.024150858 1.005541676 0.956517626 0.955085556 0.773538263 0.902116651 1.014394657 1 20.9070207 3.52551318 2.60266395 0.930369465 1.00334992 0.199049783 0.066003444 0.534791294 7.175182966 0.022093233 0.033855233 3353.614816 -3.52551318 0.072980455 GITGVEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GITGVEDK 8 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 87.476 0.035587 222060000 608850 593520 409700 544810 552690 477170 716900 707340 1177000 FALSE TRUE 528388.9299 589621.128 607832.2904 668517.4374 541692.5503 495527.0387 647375.1483 556080.8455 1037856.401 0.509115644 0.568114363 0.585661263 0.644132885 0.521934007 0.477452409 0.623761773 0.535797481 1 19.98517541 1.236609526 24.99995444 1.000000556 0.560454456 0.881467107 0.050903808 16.34969254 209437.2334 0.077703115 0.012289451 17.2428689 -1.236609526 -0.4395461 GITGVEDKESWHGKPLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GITGVEDKESWHGKPLPK 18 2 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 209.7 2.96E-16 4818100000 5558600 4716900 1555860 2417500 4202300 3081600 6199900 6834100 1096160 FALSE TRUE 4824016.926 4685914.373 2308279.1 2966430.324 4118682.452 3200151.146 5598634.652 5372680.898 966573.2135 4.990844831 4.847966308 2.388105803 3.069017724 4.261117931 3.310821261 5.792250989 5.558483126 1 19.88251949 GITPLPKPPPGVGLLPTPPEHFPFS(ph)DPEDDFQTDFSDDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GITPLPKPPPGVGLLPTPPEHFPFSDPEDDFQTDFSDDFR 40 1 P61129 P61129 ZC3H6 Zinc finger CCCH domain-containing protein 6 1 GITPLPKPPPGVGLLPT(0.001)PPEHFPFS(0.999)DPEDDFQTDFSDDFR 86.227 0.00024798 106780000 45638 34995 24990 32107 34713 31655 37286 50359 45292 TRUE FALSE 39606.82267 34765.11554 37075.24759 39397.38507 34022.27921 32872.78833 33670.00946 39590.11974 39937.63136 0.991716868 0.870485163 0.928328655 0.986472751 0.851885254 0.823103104 0.843064757 0.991298642 1 15.28546115 1.62831246 6.925589309 0.998201067 0.898120677 0.331792106 0.056836527 0.13903742 13.96571502 0.037182936 0.015217257 42.49251731 -1.62831246 -0.100080391 GIVDQSQQAYQEAFEISKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIVDQSQQAYQEAFEISKK 19 1 B7Z2E6;H0YB80;P63104-2;P63104;B0AZS6 B7Z2E6;P63104 YWHAZ 14-3-3 protein zeta/delta 0 ; 312.76 2.26E-61 2144500000 2987100 2265800 1117450 1231530 1950400 1500510 2799500 3277900 451760 FALSE TRUE 2592347.167 2250915.811 1657852.558 1511167.709 1911590.856 1558235.591 2528004.921 2576946.594 398353.4474 6.50765591 5.650549343 4.161762797 3.79353491 4.798730545 3.911690989 6.346135416 6.468995336 1 18.60368953 4.451434729 4.078208471 4.633320379 6.370907621 0.173109448 1.528538573 0.396770973 14.57593935 0.391547247 1.338385572 28277.091 -4.451434729 1.737587243 GIVEFASKPAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIVEFASKPAAR 12 1 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 151.78 6.32E-05 2558100000 4380000 3263300 2040950 2283000 2948000 3003000 3436100 3939600 2026820 FALSE TRUE 3801171.902 3241863.167 3027960.247 2801390.043 2889340.568 3118527.353 3102867.551 3097147.198 1787211.649 2.126872833 1.813922358 1.694237081 1.567464069 1.616675098 1.744912168 1.736150026 1.732949313 1 20.76927906 8 0.046828148 2.80E-12 4.580494721 0.441814717 0.209287913 1554.245433 7.13510584 203.1291783 594.2804288 100000000 -8 4.580494721 GIVEFSGKPAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GIVEFSGKPAAR 12 1 Q15233;Q15233-2;H7C367;C9IZL7 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 197.43 1.78E-07 1599300000 1489400 1207900 838360 898330 1118300 1086100 1243700 1555800 881550 FALSE TRUE 1292572.016 1199965.225 1243793.7 1102309.557 1096048.018 1127882.97 1123086.165 1223104.277 777334.1633 1.662826719 1.543692896 1.600075951 1.418063953 1.410008809 1.45096282 1.444791981 1.573460083 1 19.5681754 1.234072792 24.99980646 0.999999242 1.50818227 0.787862815 0.083621728 65.50025199 364827.7117 0.165511443 0.02134365 17.14244609 -1.234072792 0.508183028 GIVVYTGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GIVVYTGDR 9 0 P05023-4;P05023;P05023-3;P05023-2 P05023-4 ATP1A1 Sodium/potassium-transporting ATPase subunit alpha-1 0 ; 111.74 0.0048295 150210000 396570 362150 253730 351360 442880 518580 299570 456210 372700 FALSE TRUE 344162.2697 359771.0128 376434.6767 431141.6582 434067.5545 538530.1082 270517.7475 358653.0417 328639.8306 1.047232373 1.094727356 1.145432299 1.311897153 1.320800202 1.63866354 0.823143522 1.091325544 1 18.32614782 2.196490978 24.99999538 0.99027458 1.252234589 0.375559261 0.174505373 173.8653209 103318.7112 0.074269752 0.050073144 157.2139132 -2.196490978 0.261960009 GIWHNNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GIWHNNEK 8 0 P12532;P12532-2;F8WCN3 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ;;; 188.98 0.00019413 4239500000 7698300 7212400 5313530 6592500 6956200 7190600 6550900 8856200 8333200 FALSE TRUE 6680950.15 7165021.27 7883170.881 8089427.885 6817785.23 7467227.035 5915594.726 6962370.549 7348058.589 0.909212967 0.975090384 1.072823629 1.100893221 0.927834903 1.016217678 0.805055465 0.947511573 1 22.8089317 GIYAYGFEKPSAIQQR ddPTM_MDA-MB-175_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 ; 246.34 3.13E-20 11281300000 3186900 2592300 1934740 1922360 2295410 2269800 2749400 3075300 2373600 FALSE TRUE 2765743.09 2575271.011 2870386.735 2358861.219 2249735.832 2357120.675 2482763.611 2417671.027 2092995.712 1.321427977 1.230423453 1.371425043 1.127026303 1.074887932 1.126194698 1.186224891 1.155124692 1 20.99713793 3.72144225 23.71508808 1.119858608 1.300025274 0.701333414 0.060118927 233.0330397 322834.4644 0.016379709 0.024375336 5265.53192 -3.72144225 0.180166665 GIYKGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GIYKGDR 7 1 Q15363;E7EQ72 Q15363 TMED2 Transmembrane emp24 domain-containing protein 2 0 ;;; 108.09 0.0066864 2805120000 6640300 6960870 3835140 3969760 6360520 7070080 6157300 7832470 2341410 FALSE TRUE 5762767.531 6915143.587 5689826.532 4871154.682 6233958.096 7342070.553 5560165.994 6157557.243 2064611.177 2.791212018 3.349368473 2.755882848 2.359356927 3.019434441 3.556151702 2.693081417 2.982429482 1 20.97743868 1.237797171 24.99630374 0.999997751 2.939819263 0.767894872 0.334910173 9.039629475 295772.7521 0.479164466 0.082078895 17.2900867 -1.237797171 1.939821513 GIYLWDVEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GIYLWDVEGR 10 0 P04181 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 ;;;; 189.7 2.28E-06 853660000 627594 840891 630522 882020 902645 1028506 670627 881775 882145 FALSE TRUE 544655.8628 835367.1317 935444.5482 1082296.122 884684.1305 1068073.291 605589.6968 693214.2782 777858.823 0.700198862 1.07393155 1.202589108 1.391378602 1.137332514 1.373094011 0.7785342 0.891182638 1 19.56914881 2.22362774 24.98730267 0.885531173 1.156400291 0.275605411 0.19555403 305.1448884 510597.3733 0.081264219 0.05503766 167.3507798 -2.22362774 0.270869118 GKAEEQAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GKAEEQAVR 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;;; 145.89 8.76E-05 1598780000 3855810 3357180 2276450 2665130 2634630 2902400 3545730 3775190 3087790 FALSE TRUE 3346254.939 3335126.464 3377348.834 3270288.5 2582206.018 3014057.206 3201865.65 2967894.997 2722754.984 1.228995983 1.224908772 1.240415996 1.201095405 0.94837987 1.106988041 1.175965399 1.090033813 1 21.37663573 3.450698534 24.36532573 1.07770888 1.229115221 0.626696572 0.061076997 115.0988597 106136.1724 0.018028996 0.023276111 2822.919759 -3.450698534 0.151406341 GKAS(ph)PFEEDQNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GKASPFEEDQNR 12 1 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;C9JW01;A0A0C4DG68 Q8TB72-3 PUM2 Pumilio homolog 2 1 GKAS(1)PFEEDQNR;GKAS(1)PFEEDQNR;GKAS(1)PFEEDQNR;GKAS(1)PFEEDQNR;GKAS(1)PFEEDQNR;GKAS(1)PFEEDQNR 161.24 3.81E-05 6755930000 7448630 5662040 4023810 4350470 5672650 5151860 6187090 6771790 6609950 TRUE FALSE 6464274.673 5624845.686 5969737.975 5338310.706 5559775.363 5350055.388 5587066.964 5323695.407 5828529.241 1.109074761 0.965054039 1.024227164 0.91589327 0.953889932 0.917908304 0.958572349 0.913385725 1 22.47470045 7.999999997 0.807448215 0.942244587 43.53427546 0.655279683 0.035203846 296.6687855 0.997829143 0.011302294 23128.32972 99999999.34 -7.999999997 42.59203087 GKDETDSPTVHLGLDS(ph)DS(ph)ESELVIDLGEDHSGR ddPTM_MDA-MB-175_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(1)DS(0.997)ES(0.003)ELVIDLGEDHSGR;GKDETDSPTVHLGLDS(0.996)DS(0.903)ES(0.101)ELVIDLGEDHSGR;GKDETDSPTVHLGLDS(1)DS(0.984)ES(0.016)ELVIDLGEDHSGR 255.35 3.68E-59 534000000 219387 184363 137092 165416 174673 171290 209682 246602 219564 TRUE FALSE 190394.4521 183151.9073 203390.1497 202976.231 171197.349 177879.6371 189347.0719 193868.0814 193607.394 0.983404859 0.945996449 1.050528833 1.048390905 0.884250056 0.918764689 0.977995044 1.001346474 1 17.56277453 3.276234489 24.99985748 0.961809265 1.005820538 0.225435707 0.046000553 327.2285912 217142.2026 0.014622988 0.018877735 1889.011007 -3.276234489 0.044011273 GKDETDSPTVHLGLDS(ph)DSESELVIDLGEDHSGR ddPTM_MDA-MB-175_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 1 GKDETDSPTVHLGLDS(0.964)DS(0.03)ES(0.006)ELVIDLGEDHSGR 124.91 6.54E-08 35928000 84142 65828 43094 50255 61757 51535 68833 79457 64425 TRUE FALSE 73022.42151 65395.57153 63934.40254 61666.16585 60528.15653 53517.5848 62157.58625 62465.73889 56808.74989 1.285407999 1.151153153 1.125432309 1.085504715 1.065472425 0.942065877 1.09415515 1.099579537 1 15.79382554 5.259707974 0.74958827 1.047562117 1.646155248 0.729740469 0.047052726 3.145892611 0.785954039 0.019281472 1.889966141 181847.7675 -5.259707974 0.598593131 GKDILYIGDHIFGDILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GKDILYIGDHIFGDILK 17 1 P49902-2;P49902;Q5JUV6 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;; 218.43 2.80E-15 3291381000 7784100 8221790 4239047 5203681 7329987 5598364 9457430 11888460 3013849 FALSE TRUE 6755411.463 8167780.52 6289064.308 6385256.304 7184134.6 5813736.686 8540249.894 9346205.345 2657555.205 2.541964679 3.073418948 2.366484917 2.402680589 2.703287061 2.187625934 3.213573844 3.516843349 1 21.34166823 1.223138214 24.9939244 0.999995153 2.776461244 0.63808917 0.413962 633.7187683 1026961.9 2.689156352 0.112429888 16.71622521 -1.223138214 1.776466091 GKDNFLFITYEELQQDLQGSVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GKDNFLFITYEELQQDLQGSVER 23 1 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 ; 251.55 1.08E-39 337130000 596480 543470 374210 437900 503620 480620 628930 717550 459590 FALSE TRUE 517653.6567 539899.9098 555179.2077 537331.8879 493598.9473 499109.7624 567936.4654 564107.5165 405257.7938 1.277344112 1.33223819 1.369940853 1.325901429 1.21798755 1.231585845 1.401420217 1.391972036 1 18.62848041 1.230926194 24.99856915 0.999999425 1.322278533 0.722357766 0.062026441 165.9961127 543500.6741 0.17486653 0.016792886 17.0186926 -1.230926194 0.322279108 GKDQTSSHNSSDDKNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GKDQTSSHNSSDDKNR 16 2 K7EMM8;Q49A26-4;Q49A26-2;Q49A26-3;Q49A26 K7EMM8 GLYR1 Putative oxidoreductase GLYR1 0 76.151 0.016522 10136000 18036 18346 2684.2 9524.7 15173 18703 16432 22480 9804.1 FALSE TRUE 15652.4969 18225.48392 3982.288098 11687.42871 14871.08699 19422.51651 14838.42717 17672.82694 8645.070467 1.810569036 2.108193795 0.460642642 1.35191827 1.720181119 2.246657975 1.716403264 2.044266384 1 13.07766201 3.147757192 5.398551717 1.812336262 1.413043852 0.074850494 0.523441517 0.47773601 22.25392874 0.161255332 0.184950008 1405.261643 -3.147757192 -0.39929241 GKDSLYAQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GKDSLYAQGK 10 1 H0Y5B4;H7BZ11;J3KQN4;P83881;H7BY91;H0Y3V9 H0Y5B4 RPL36A;RPL36A-HNRNPH2 60S ribosomal protein L36a 0 ; 109.6 0.0018215 1326270000 2586600 2235800 1429340 1623430 2016290 1943840 2910400 3281100 1351650 FALSE TRUE 2244774.256 2221112.883 2120573.605 1992054.594 1976169.774 2018620.783 2628149.856 2579462.299 1191859.477 1.883421913 1.863569427 1.779214451 1.671383777 1.658056014 1.693673476 2.205083659 2.164233577 1 20.18478272 1.226570134 24.97329488 0.999997995 1.874243173 0.672598644 0.189523677 394.5255946 821649.1761 0.891813839 0.05449457 16.84884494 -1.226570134 0.874245179 GKDSLYAQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GKDSLYAQGR 10 1 Q969Q0 Q969Q0 RPL36AL 60S ribosomal protein L36a-like 0 ;;;;; 160.91 6.60E-06 1901560000 2657970 2776420 1626650 1789930 2515770 2627690 3096270 3231920 1444110 FALSE TRUE 2306712.53 2758181.514 2413303.381 2196360.964 2465711.099 2728778.935 2795994.212 2540799.059 1273388.961 1.811475206 2.166016511 1.895181641 1.724815458 1.936337737 2.142926489 2.19571105 1.995304763 1 20.28024173 1.238457078 24.9999873 0.999998956 1.992347192 0.802775084 0.153140051 1.102249919 264856.1318 0.218238926 0.038976127 17.31637883 -1.238457078 0.992348236 GKDYYQTLGLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GKDYYQTLGLAR 12 1 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 210.64 3.76E-08 2556300000 3136000 3405500 1950850 2146790 3087800 3088000 2925000 3804900 3400000 FALSE TRUE 2721569.654 3383129.046 2894287.585 2634251.481 3026358.821 3206797.358 2641333.95 2991251.745 2998055.873 0.907778163 1.128440959 0.965388141 0.878653231 1.009440434 1.069625615 0.881015585 0.997730486 1 21.51559584 GKEDALVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GKEDALVTK 9 1 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ; 81.475 0.019314 461780000 1399210 1048980 794980 955090 945370 749310 1168550 1342850 1296620 FALSE TRUE 1214300.853 1042089.181 1179434.987 1171957.782 926558.9866 778136.4406 1055224.201 1055691.978 1143335.061 1.062069113 0.911446886 1.031574232 1.025034412 0.810400222 0.68058478 0.922935224 0.923344358 1 20.12481682 3.248259809 24.98469569 0.869257111 1.002385383 0.366501452 0.091383685 253.3171974 652530.3319 0.028348981 0.036129516 1771.168213 -3.248259809 0.133128272 GKEDKENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GKEDKENR 8 2 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ; 52.482 0.080223 59065000 164594 118971 88401 104016 84694 96039 156690 180453 137488 FALSE TRUE 142842.4859 118189.4717 131152.0193 127634.4226 83008.7551 99733.68248 141494.2279 141864.5302 121234.3253 1.178234675 0.974884559 1.08180599 1.052791132 0.684696804 0.822652184 1.167113584 1.170168019 1 16.8874387 0.925295197 21.01516926 0.246633965 1.020292966 0.000574471 0.159008378 180.8871837 1500540.637 201051.6055 0.040977491 8.419672468 -0.925295197 0.773659001 GKEGTHATCASEEGGTESSESGSSLQPLSADSTPDVNQS(ph)PR ddPTM_MDA-MB-175_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 197.35 2.22E-35 185580000 239520 252010 90793 144930 247570 234350 284610 325940 100310 TRUE FALSE 207866.8251 250354.5297 134700.7985 177838.5716 242643.8414 243365.5961 257008.566 256240.2675 88451.46607 2.350066476 2.83041696 1.522878076 2.010577998 2.743242731 2.751402627 2.905645066 2.896958963 1 16.43259844 3.239773423 24.9963386 2.562200788 2.1782224 0.032493493 0.636965993 92.08569348 1897897.255 0.18772066 0.228923041 1736.894431 -3.239773423 -0.383978388 GKEKCSEKSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GKEKCSEKSR 10 3 Q5VUJ6-2;Q5VUJ6 Q5VUJ6-2 LRCH2 Leucine-rich repeat and calponin homology domain-containing protein 2 0 72.006 0.060265 1513100000 1987000 2069400 797180 1003400 1888100 1855200 1617700 1799200 1100800 FALSE TRUE 1724412.916 2055805.975 1182698.914 1231237.306 1850530.504 1926570.744 1460815.703 1414455.081 970664.678 1.776527935 2.117936319 1.218442312 1.268447625 1.906457035 1.984795355 1.504964316 1.457202588 1 19.88861347 1.239503244 1.571690178 0.72915962 1.690657489 0.365760003 0.288771384 1.345135764 2.999784059 2.04025768 0.087493542 17.3581423 -1.239503244 0.961497869 GKELNEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GKELNEFR 8 1 Q9UHV9 Q9UHV9 PFDN2 Prefoldin subunit 2 0 ;;; 96.331 0.0082232 2144680000 4699000 4345190 2396480 2742110 4090260 3822230 4446150 5210130 1612400 FALSE TRUE 4078015.244 4316646.161 3555425.744 3364747.986 4008871.828 3969273.661 4014963.057 4095984.245 1421783.909 2.868238428 3.036077518 2.500679408 2.366567778 2.819606976 2.791755932 2.823891192 2.880876777 1 20.43927078 1.236180499 24.9999919 0.999997708 2.760466382 0.89214956 0.192417403 20.87010041 219163.4331 0.327960113 0.050184257 17.22584358 -1.236180499 1.760468674 GKELSDQAT(ph)ASPIVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GKELSDQATASPIVAR 16 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 GKELSDQAT(0.654)AS(0.346)PIVAR 172.81 7.18E-09 413960000 466460 455910 223980 213010 442560 388400 470730 566220 111900 TRUE FALSE 404816.1291 452915.0972 332297.4772 261377.1762 433753.9219 403341.9993 425078.6771 445138.2593 98671.30948 4.10267312 4.590139723 3.367721366 2.648968353 4.39594776 4.087733318 4.308027119 4.511324129 1 16.59034303 4.23980525 24.99999475 3.636863082 4.346406484 0.089817565 1.060129427 91.20584724 1831786.521 0.265114614 0.626838156 17370.21725 -4.23980525 0.709543403 GKFDGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GKFDGAK 7 1 O15347;E7ES08;E7EQU1 O15347 HMGB3 High mobility group protein B3 0 ; 64.42 0.067044 2972600000 5194200 3992300 3257800 3459900 2608300 2621200 5373400 6115500 6174900 FALSE TRUE 4507773.31 3966074.318 4833282.977 4245523.176 2556399.933 2722039.26 4852288.495 4807747.916 5444910.356 0.827887516 0.728400297 0.88766989 0.779723246 0.469502667 0.499923613 0.891160401 0.882980178 1 22.37647687 2.03399117 24.37290728 0.919313251 0.701487399 0.391274728 0.133233871 157.528936 112953.208 0.059775189 0.040300145 108.1411964 -2.03399117 -0.217825852 GKFEDMAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GKFEDMAK 8 1 P09429;Q5T7C4;B2RPK0;P23497 P09429;P23497 HMGB1;HMGB1P1;SP100 High mobility group protein B1;Putative high mobility group protein B1-like 1;Nuclear autoantigen Sp-100 0 ;; 113.62 0.0025657 9712670000 15584100 12751200 10387300 10940400 10753700 8926370 15423500 16711100 16275200 FALSE TRUE 13524621.7 12667436.53 15410633.02 13424585.03 10539722.41 9269773.23 13927731.34 13137561.31 14351164.4 0.942405879 0.882676567 1.073824576 0.935435248 0.734415837 0.645924817 0.970494864 0.915435218 1 23.77466446 3.460523254 24.82343752 0.857223551 0.965721484 0.179679352 0.113264365 423.3164032 633096.1445 0.035190044 0.045442095 2887.508388 -3.460523254 0.108497933 GKFGHEFLEFEFRPDGK ddPTM_MDA-MB-175_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 ; 158.98 1.96E-09 1150070000 3353100 2555100 1652170 1980330 2404500 1923720 3080200 3616800 1347850 FALSE TRUE 2909979.339 2538315.38 2451164.938 2429994.194 2356655.154 1997726.753 2781482.678 2843375.466 1188508.708 2.448429127 2.135714582 2.062387024 2.04457416 1.982867385 1.680868419 2.34031325 2.392389257 1 20.18072104 7.999988022 0.703398628 1.967643611 63.71523611 0.159032644 0.386230642 668.8544986 3.519432479 0.151881388 64976.93752 99997241.96 -7.999988022 61.7475925 GKFNTSDVSAIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GKFNTSDVSAIEK 13 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 139.65 3.55E-05 457750000 1321800 1016800 644260 884230 884620 785790 1088600 1427600 971680 FALSE TRUE 1147120.781 1010120.574 955826.2909 1085007.936 867017.7927 816019.8498 983027.7396 1122318.85 856809.0973 1.3388289 1.178933063 1.115565059 1.266335686 1.011914784 0.952394007 1.147312444 1.309882041 1 19.70861427 5.755914578 1.071409416 1.125438371 2.733339426 0.281787075 0.112041263 20.71575607 3.662218109 0.036470966 62.96040261 570052.1364 -5.755914578 1.607901055 GKFQDNFEFVQWFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GKFQDNFEFVQWFK 14 1 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ; 123.76 9.21E-05 655240000 2990400 2759400 1501240 1662670 2299800 1998130 3092600 3607300 631230 FALSE TRUE 2595211.063 2741273.32 2227244.685 2040204.636 2254038.479 2074999.354 2792680.128 2835906.967 556606.7085 4.662558003 4.924973555 4.001469352 3.665433069 4.049607101 3.727945284 5.017331062 5.094992431 1 19.08629877 4.230940817 21.90210407 3.97774221 4.793765955 0.103706672 1.12526719 88.18953594 253506.8187 0.284076647 0.613713327 17019.26565 -4.230940817 0.816023745 GKGAYQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GKGAYQDR 8 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ; 95.502 0.0087598 803740000 2127310 1940990 799570 901700 1228880 1763960 2036420 2302500 265266 FALSE TRUE 1846180.594 1928239.509 1186244.726 1106444.767 1204427.692 1831820.683 1838928.302 1810128.293 233906.5557 7.892812531 8.24363175 5.071447113 4.730285406 5.149183138 7.831420874 7.861807449 7.73868132 1 17.83557277 4.250946961 24.90547962 5.964242147 8.068223471 0.182683049 2.05277696 423.9170838 852362.0824 0.521998601 1.35969895 17821.61107 -4.250946961 2.103981323 GKGGVTGS(ph)PEASISGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GKGGVTGSPEASISGSK 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GKGGVTGS(0.534)PEAS(0.466)ISGSK;GKGGVT(0.005)GS(0.995)PEASISGSK 300.5 6.26E-46 709620000 2044690 1136100 834792 1209880 1186310 921220 1271040 1906880 936950 TRUE FALSE 1774479.036 1128636.884 1238500.203 1484601.746 1162704.752 956659.9295 1147774.736 1499108.551 826184.8384 2.14779908 1.366082784 1.499059467 1.796936565 1.407317949 1.157924819 1.389246913 1.814495355 1 19.65610506 4.743534051 24.50003442 1.461704341 2.147799459 0.445521769 0.249675773 399.1571684 1966233.988 0.060440367 0.482419382 55403.09813 -4.743534051 0.686095119 GKGGVTGSPEAS(ph)ISGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GKGGVTGSPEASISGSK 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GKGGVT(0.021)GS(0.303)PEAS(0.671)IS(0.003)GS(0.001)K 250.35 7.50E-21 99727000 395360 218950 155790 224940 229990 173760 239090 362970 180480 TRUE FALSE 343112.1743 217511.703 231130.5651 276016.065 225413.649 180444.6596 215903.0886 285351.6901 159143.86 2.155987509 1.366761514 1.452337307 1.734380861 1.416414362 1.133846192 1.356653587 1.793042409 1 17.27997197 4.742057186 24.71312939 1.437964799 2.155987828 0.490343423 0.238186744 266.41216 1882857.333 0.057696 0.409294574 55215.01395 -4.742057186 0.718023029 GKGS(ph)PRPQAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GKGSPRPQAPK 11 2 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 GKGS(1)PRPQAPK;GKGS(1)PRPQAPK;GKGS(1)PRPQAPK;GKGS(1)PRPQAPK 99.011 0.0040115 7165800000 7291900 6140200 4323440 5448200 5361490 4012550 7250600 8627800 6917500 TRUE FALSE 6328256.94 6099864.622 6414270.045 6685297.081 5254806.839 4166915.395 6547437.928 6782812.112 6099721.03 1.037466617 1.000023541 1.051567771 1.096000464 0.861483142 0.683132126 1.073399569 1.111987266 1 22.54031183 GKHQPWQS(ph)PERPLSR ddPTM_MDA-MB-175_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 144.27 2.23E-06 445770000 707240 420890 249944 359610 417410 413870 514180 543370 166646 TRUE FALSE 613776.4421 418125.1459 370817.7544 441264.9468 409104.3576 429791.8467 464314.9027 427174.554 146945.2997 4.176904217 2.845447569 2.523508783 3.002919778 2.784058819 2.924842424 3.159780569 2.907031084 1 17.16491969 1.238193303 5.285201632 0.889045273 3.01347076 0.685070937 0.435117573 0.09198278 7.325084999 0.715235522 0.104458449 17.30586466 -1.238193303 2.124425487 GKHSYNS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GKHSYNSR 8 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 GKHS(0.003)Y(0.001)NS(0.997)R;GKHS(0.003)Y(0.001)NS(0.996)R;GKHSYNS(1)R 61.344 0.052423 220304000 501670 394317 186554 219583 252247 335725 406693 467040 113037 TRUE FALSE 435373.0384 391726.7057 276772.1384 269442.6763 247227.7782 348640.558 367251.9755 367167.1305 99673.89463 4.367974584 3.930083269 2.776776601 2.703242181 2.48036639 3.497812133 3.684535222 3.683683996 1 16.60492808 4.359242523 4.140318563 2.961500286 4.274948138 0.323538035 0.784477119 0.270506149 8.098566993 0.20083269 0.596895285 22868.75505 -4.359242523 1.313447852 GKLDDYQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GKLDDYQER 9 1 Q14444-2;Q14444;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ; 129.89 0.00034347 1448010000 2804500 2442800 1543200 1991270 2225900 2051860 2503800 2899900 2406600 FALSE TRUE 2433878.219 2426753.086 2289496.682 2443418.288 2181608.945 2130796.382 2260981.861 2279778.952 2122094.49 1.146922642 1.143565048 1.078885362 1.151418233 1.028045149 1.004100615 1.065448251 1.074306052 1 21.01705747 3.233839998 24.999822 1.040186907 1.127487452 0.705402488 0.030619437 72.89494059 386042.1677 0.00951472 0.011139254 1713.325972 -3.233839998 0.087300545 GKLDGNQDLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GKLDGNQDLIR 11 1 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;;; 152.85 2.99E-05 4310430000 5782260 5801420 3997250 6799300 6545710 6312450 5588080 6893900 6121670 FALSE TRUE 5018119.691 5763310.09 5930333.47 8343184.986 6415463.177 6555294.036 5046148.862 5419693.133 5397973.146 0.929630355 1.067680393 1.098622262 1.545614393 1.18849483 1.214399157 0.934822891 1.00402373 1 22.36398637 2.241512325 24.95444459 0.982834205 1.183351655 0.254261804 0.156420687 106.438975 899871.6749 0.063480381 0.046984037 174.3862846 -2.241512325 0.20051745 GKLEAIIT(ph)PPPAK ddPTM_MDA-MB-175_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 123.4 0.00036196 1830710000 4078700 3255000 2881300 4207200 3727700 4060900 2635000 5027000 5278500 TRUE FALSE 3539689.461 3233617.691 4274706.317 5162509.063 3653526.063 4217125.451 2379458.106 3952015.17 4654481.743 0.760490567 0.69473206 0.918406506 1.109147988 0.784947984 0.906035448 0.5112187 0.849077381 1 22.15018911 1.267253106 5.871782099 1.004153669 0.813345468 0.122984366 0.155176736 0.297424824 29.30094194 0.194020525 0.039614688 18.50346685 -1.267253106 -0.190808201 GKLEEQRPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GKLEEQRPER 10 2 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;E9PJF7;P13693-2 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 ;;;;;; 162.26 3.84E-06 8632220000 12142420 10448110 7359050 8318590 9927770 9616070 11806100 12884460 10647450 FALSE TRUE 10537768.43 10379475.68 10917911.19 10207453 9730226.8 9986006.435 10661146.24 10129218.5 9388720.591 1.122385988 1.105526102 1.162875292 1.087203832 1.036374094 1.063617384 1.135527055 1.078871013 1 23.16249714 3.493021334 22.47814777 1.069583274 1.127330647 0.40425627 0.036785304 217.8635188 307995.3082 0.010527003 0.015069542 3111.869198 -3.493021334 0.057747374 GKLPES(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GKLPESPK 8 1 E9PKP7;P17480-2;P17480;E9PLT2 E9PKP7 UBTF Nucleolar transcription factor 1 1 GKLPES(1)PK 96.229 0.0055042 310760000 447170 325070 294550 326280 379770 252370 400960 549250 504030 TRUE FALSE 388075.3515 322934.5938 436995.3652 400366.8609 372213.32 262078.8372 362074.9609 431797.1618 444444.1476 0.873170124 0.726603321 0.983240228 0.900826039 0.837480529 0.589677778 0.814669206 0.971544263 1 18.7616426 1.691635815 4.588055264 0.991236591 0.815786772 0.309323997 0.104499713 0.200842534 9.895051087 0.073048333 0.028653743 49.1627101 -1.691635815 -0.175449819 GKLPIVNEDDELVAIIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GKLPIVNEDDELVAIIAR 18 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 284.38 1.42E-39 270250000 438900 426220 262990 316090 406650 392520 425880 526690 359260 FALSE TRUE 380898.253 423420.1328 390172.8436 387863.0656 398558.4606 407620.4984 384578.2231 414061.4422 316788.6921 1.202373262 1.336601158 1.231650161 1.224358935 1.258120857 1.286726795 1.213989744 1.307058783 1 18.27316131 1.232108352 24.99999877 0.999999567 1.259427185 0.78350215 0.042547544 92.40521693 357999.6661 0.088389692 0.009557415 17.06508094 -1.232108352 0.259427618 GKMLVQQEHRS(ph)LK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GKMLVQQEHRSLK 13 2 Q9NWF6 Q9NWF6 SPATA6L 1 GKMLVQQEHRS(1)LK 50.675 0.086546 53137000 44298 45931 26524 33785 46466 43651 44460 42449 42155 TRUE FALSE 38443.90706 45629.27624 39351.09512 41456.40062 45541.41751 45330.28222 40148.27604 33371.61169 37171.48392 1.034231163 1.227534427 1.058636647 1.115274298 1.225170822 1.219490788 1.080082682 0.897774535 1 15.18190866 1.928088571 4.795651655 0.94939953 1.148882401 0.566622905 0.070622972 0.143110561 6.041978813 0.035915741 0.01856334 84.74002176 -1.928088571 0.199482872 GKNDGTVQGR ddPTM_MDA-MB-175_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 ; 159.09 7.11E-06 298150000 548900 512850 329670 403480 327130 502420 565500 623530 503730 FALSE TRUE 476361.4743 509481.0546 489099.5147 495096.3008 320620.753 521748.4225 510657.897 490192.9618 444179.6133 1.072452359 1.147015845 1.101130039 1.114630852 0.721826809 1.17463388 1.14966532 1.103591762 1 18.76078365 GKNENESEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GKNENESEKR 10 2 P47813;O14602;A6NJH9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 ;;;; 199.08 1.60E-07 1861980000 2039460 1558580 1097440 1343570 818400 957390 1962300 2276670 1591620 FALSE TRUE 1769940.194 1548341.585 1628165.655 1648648.104 802115.4412 994221.4128 1771996.448 1789821.838 1403460.497 1.261125766 1.103231326 1.160107932 1.174702179 0.57152691 0.708407123 1.262590897 1.275291924 1 20.42055703 GKPDAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GKPDAAK 7 1 P09429 P09429 HMGB1 High mobility group protein B1 0 ;;; 79.906 0.028595 871834000 1967070 1582440 1171970 1436480 1081170 1076080 1940190 2237300 2878690 FALSE TRUE 1707116.716 1572044.847 1738738.612 1762654.739 1059656.832 1117477.494 1752030.672 1758870.806 2538374.548 0.672523571 0.619311618 0.684981109 0.694402936 0.417454876 0.440233493 0.690217554 0.692912245 1 21.27547353 1.089037823 1.629939977 1.286238249 0.595391936 0.615130814 0.098797366 1.140979428 2.022609839 1.422533535 0.029943139 12.27546134 -1.089037823 -0.690846313 GKPELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GKPELR 6 1 J3KTJ3;P62829;J3KT29;J3QQT9;C9JD32;B9ZVP7 J3KTJ3 RPL23 60S ribosomal protein L23 0 ;;; 100.82 0.033949 4445700000 13308200 12421300 8766200 10311500 10626500 10559000 13395400 14743700 14770000 FALSE TRUE 11549487.65 12339703.66 13005563.64 12652883.68 10415053.44 10965211.56 12096316.17 11590874.49 13023907.43 0.886791289 0.947465554 0.99859153 0.971512102 0.799687306 0.841929477 0.928777806 0.889969048 1 23.63465901 4.839933917 17.72326649 0.917612696 0.886749102 0.024492701 0.064691368 58009.4565 10103364.98 0.016598803 273.2858473 69172.57095 -4.839933917 -0.030863594 GKPLISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GKPLISR 7 1 Q9Y6Q5;K7EMG5;Q9Y6Q5-2 Q9Y6Q5;Q9Y6Q5-2 AP1M2 AP-1 complex subunit mu-2 0 ; 109.86 0.0063228 1091170000 1396390 1275680 881350 967230 1237050 1364870 1376830 1530560 1538980 FALSE TRUE 1211853.523 1267299.974 1307573.808 1186854.355 1212435.125 1417377.432 1243305.239 1203261.655 1357043.538 0.893010055 0.933868324 0.963545952 0.874588266 0.893438635 1.044459808 0.916186699 0.886678741 1 20.37203558 GKPQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GKPQER 6 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 77.748 0.065301 114350000 204510 189550 140010 156450 109400 148180 197880 217270 286400 FALSE TRUE 177483.4853 188304.8336 207719.3043 191974.3637 107223.154 153880.5805 178689.6281 170808.5013 252542.1183 0.702787664 0.745637341 0.822513511 0.76016771 0.424575333 0.609326403 0.70756367 0.676356492 1 17.94616449 1.238079367 24.99999983 1.000000361 0.680777633 0.468444354 0.106752572 11.57667356 600753.4876 0.159584554 0.027829092 17.30132509 -1.238079367 -0.319222728 GKPSEQLT(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GKPSEQLTPTR 11 1 Q14687;Q14687-2;Q14687-3;H0Y613 Q14687 GSE1 Genetic suppressor element 1 1 GKPSEQLT(0.891)PT(0.109)R;GKPSEQLT(0.991)PT(0.009)R;GKPSEQLT(0.941)PT(0.059)R;GKPSEQLT(0.92)PT(0.08)R 145.69 5.84E-05 1577500000 2927040 2603130 1902470 2254870 2408720 2453320 2697160 3154680 3042750 TRUE FALSE 2540224.248 2586029.868 2822510.855 2766872.697 2360791.185 2547700.808 2435589.838 2480076.232 2683039.561 0.946771074 0.963843361 1.051982571 1.031245583 0.879894288 0.949557675 0.907772615 0.92435321 1 21.3554369 3.248318005 24.99997484 0.930341646 0.999810978 0.375451228 0.042332839 215.6581198 552547.319 0.012456934 0.015881369 1771.405565 -3.248318005 0.069469332 GKPVDSQTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GKPVDSQTSR 10 1 Q9Y450;Q9Y450-4;E9PN23 Q9Y450 HBS1L HBS1-like protein 0 ; 122.7 0.00043924 164551000 108980 128777 77446 99871 114800 121605 128921 156907 155062 FALSE TRUE 94578.01688 127931.0554 114899.1446 122548.237 112515.7046 126283.223 116418.2613 123353.6591 136730.747 0.691709941 0.935642189 0.840331434 0.896274171 0.822899802 0.92359053 0.851441712 0.902164742 1 17.06097818 7.999999998 0.040547235 1.421947169 9.19E-09 0.370738937 0.06525726 2128.686137 8.498233576 93.27001387 236.5150315 99999999.56 -7.999999998 -1.42194716 GKQS(ph)PPGPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GKQSPPGPGK 10 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 GKQS(1)PPGPGK 51.726 0.093715 266110000 745990 635310 453810 539020 550290 490360 726140 857580 729420 TRUE FALSE 647405.5314 631136.6068 673274.0339 661412.7294 539340.3056 509224.4665 655719.0546 674193.1907 643188.7986 1.00655598 0.981261813 1.046775123 1.028333719 0.838541198 0.791718493 1.019481459 1.048204185 1 19.29488276 2.033898591 24.99963443 1.029434997 0.949402959 0.156368104 0.080530381 342.6724483 252713.7144 0.036386579 0.024531681 108.1181462 -2.033898591 -0.080032038 GKS(ph)EEELEASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GKSEEELEASK 11 1 Q7RTP6;J3QR21;A0A5F9ZHV5 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 GKS(1)EEELEASK 164.01 1.41E-05 162240000 585550 407580 403790 333320 323640 254410 552210 647440 524880 TRUE FALSE 508168.0839 404902.5801 599064.1946 409005.4005 317200.1972 264197.3173 498656.7592 508989.9944 462829.2843 1.097960093 0.87484218 1.294352399 0.883706832 0.685350318 0.57083103 1.077409697 1.099735932 1 18.82012062 GKT(ph)PEEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GKTPEEIR 8 1 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2 E5RJR5 SKP1 S-phase kinase-associated protein 1 1 GKT(1)PEEIR 98.156 0.012484 280090000 753310 666150 495340 502610 584270 540340 624260 772430 1139500 TRUE FALSE 653758.1749 661774.0168 734888.0808 616735.2824 572644.1701 561127.2294 563719.3613 607251.8556 1004789.608 0.650641855 0.658619488 0.731385033 0.613795443 0.569914503 0.558452461 0.561032237 0.604357221 1 19.93846202 1.2374693 24.99869804 1.000000456 0.61640141 0.838471044 0.052612556 11.74558388 268928.2167 0.086210584 0.014461196 17.27703845 -1.2374693 -0.383599045 GKT(ph)PEEIRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GKTPEEIRK 9 2 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2 E5RJR5 SKP1 S-phase kinase-associated protein 1 1 GKT(1)PEEIRK 99.844 0.008139 1759000000 2621400 2216700 1617000 1661600 1801800 1391800 2449600 2856700 2220600 TRUE FALSE 2274975.348 2202138.352 2398986.609 2038891.676 1765947.705 1445343.447 2212038.169 2245816.936 1958083.198 1.16183794 1.124639829 1.225170928 1.041269175 0.901875726 0.738141999 1.1296957 1.146946636 1 20.90101063 3.585611698 5.457692063 1.000005283 1.164509389 0.344515538 0.11646639 0.329341686 13.8844877 0.036963981 0.055140521 3851.338564 -3.585611698 0.164504106 GKTPATPTSQFVFSFPVSVGVHSAPSSLPYLHS(ph)PITTSPSC ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GKTPATPTSQFVFSFPVSVGVHSAPSSLPYLHSPITTSPSC 41 1 Q13115-2;Q13115 Q13115-2 DUSP4 Dual specificity protein phosphatase 4 1 GKTPATPTSQFVFSFPVSVGVHSAPSS(0.001)LPYLHS(0.999)PITTSPSC 217.97 3.49E-44 217810000 70721 127350 35792 79656 153250 122000 146600 186770 71859 TRUE FALSE 61375.04067 126513.4295 53101.13092 97743.11227 150200.6248 126693.4189 132382.7546 146830.6889 63363.91088 0.96861194 1.996616492 0.838034303 1.542567542 2.370444354 1.99945706 2.089245325 2.317260518 1 15.95137376 3.434674449 7.807731087 2.009698439 1.315750283 0.300334105 0.478796831 0.257205972 40.50439255 0.130470168 0.169322438 2720.661113 -3.434674449 -0.693948156 GKTPEEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GKTPEEIR 8 1 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ;; 85.731 0.01508 771370000 3009350 2586610 1955620 2567050 2613300 2499220 2580820 3249840 3429030 FALSE TRUE 2611656.773 2569618.389 2901364.373 3149937.937 2561300.443 2595366.611 2330532.474 2554887.006 3023653.98 0.863741946 0.849838773 0.959555687 1.041765347 0.847087815 0.858354371 0.770766923 0.844966727 1 21.52786162 GKVEYLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GKVEYLLK 8 1 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 0 80.688 0.024749 0 1108700 1043100 789460 1006400 1113100 871470 1184500 1429600 1514800 FALSE TRUE 962182.4859 1036247.807 1171245.497 1234918.502 1090951.488 904996.0148 1069627.372 1123891.165 1335722.07 0.720346326 0.775795977 0.876863176 0.924532528 0.816750365 0.677533175 0.800785879 0.841410942 1 20.34918842 1.227767487 2.686683969 1.047921071 0.802564511 0.447769425 0.06973571 0.518128307 4.183183531 0.292167261 0.019715452 16.89536142 -1.227767487 -0.245356559 QWKT(ph)WQGHMKAT(ph)QSY(ph)LQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QWKTWQGHMKATQSYLQEK 19 2 P49750;H0YIQ2;F8VU51 P49750 YLPM1 YLP motif-containing protein 1 3 QWKT(0.989)WQGHMKAT(0.621)QS(0.52)Y(0.871)LQEK 63.63 0.012927 1041400000 683230 499750 534550 667990 528330 393950 680400 855800 1648400 TRUE FALSE 592939.4244 496467.1093 793060.168 819667.3391 517817.2667 409105.5114 614414.9127 672793.8298 1453528.03 0.407931194 0.341560052 0.545610509 0.563915743 0.356248559 0.281456912 0.422705927 0.462869526 1 20.47112746 1.230406361 4.134706498 1.065258303 0.419016172 0.8181949 0.085747874 0.1069994 3.326849632 0.210624425 0.02327827 16.99833409 -1.230406361 -0.646242131 GKYS(ph)PTVQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 GKYSPTVQTR 10 1 O60437;K7EKI8 O60437 PPL Periplakin 1 GKYS(0.797)PT(0.199)VQT(0.004)R;GKYS(0.704)PT(0.296)VQTR;GKY(0.001)S(0.499)PT(0.499)VQT(0.001)R;GKYS(0.697)PT(0.303)VQTR;GKYS(0.897)PT(0.103)VQTR;GKYS(0.846)PT(0.153)VQTR;GKY(0.003)S(0.834)PT(0.162)VQT(0.001)R;GKYS(0.789)PT(0.211)VQTR 136.93 6.33E-05 16712910000 6732010 5790320 3968710 4596270 5494670 5379810 6108390 6851970 6572610 TRUE FALSE 5842357.822 5752283.007 5887991.431 5639923.353 5385336.817 5586774.772 5515999.278 5386729.538 5795603.533 1.008067199 0.992525278 1.015941031 0.973138228 0.9292107 0.963967728 0.9517558 0.929451007 1 22.46652748 3.523632091 4.793350551 0.951743036 1.003533886 0.554687135 0.020538355 0.142061157 7.329701452 0.00555298 0.008110248 3339.120496 -3.523632091 0.05179085 GLAAHYFFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLAAHYFFPR 10 0 O00203;O00203-3 O00203 AP3B1 AP-3 complex subunit beta-1 0 ; 121.96 0.0005013 1448320000 791580 1047290 690510 636680 959070 1094840 818060 889320 1001000 FALSE TRUE 686970.6974 1040410.283 1024442.946 781247.925 939986.3834 1136959.203 738724.6671 699145.8387 882662.9203 0.778293368 1.178717559 1.160627599 0.88510337 1.064943776 1.288101241 0.836927269 0.792087016 1 19.75150307 2.141827607 23.83677167 0.857132277 1.061823437 0.237450614 0.15322856 13.00615826 3192.472635 0.060748211 0.040956453 138.6205465 -2.141827607 0.20469116 GLAEDIENEVVQITWNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLAEDIENEVVQITWNR 17 0 Q15029;Q15029-3;Q15029-2;K7EP67 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 169.79 4.49E-09 23925000 52630 48420 40906 44755 45213 51896 43536 53488 77440 FALSE TRUE 45674.81215 48101.92583 60688.27842 54917.30679 44313.34976 53892.4727 39313.88542 42050.00744 68285.13142 0.668883712 0.704427521 0.888748065 0.804235207 0.648945808 0.789227048 0.57573127 0.615800344 1 16.05928386 3.250304231 24.9983812 0.704071906 0.770861361 0.007862069 0.12993627 745.0800423 1586026.764 0.037769778 0.048359476 1779.525561 -3.250304231 0.066789455 GLAGPPAS(ph)PGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GLAGPPASPGK 11 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 GLAGPPAS(1)PGK;GLAGPPAS(1)PGK;GLAGPPAS(1)PGK;GLAGPPAS(1)PGK;GLAGPPAS(1)PGK;GLAGPPAS(1)PGK 162.23 2.66E-05 4081090000 5297510 4471920 3341470 4370820 4926590 3934290 4889160 6271790 5570480 TRUE FALSE 4597430.631 4442543.663 4957416.069 5363281.485 4828560.498 4085644.682 4415010.016 4930616.516 4911944.2 0.935969637 0.904436916 1.009257407 1.09188567 0.983024298 0.831777503 0.898831468 1.00380141 1 22.22786274 4.336277839 0.003260495 1.170220885 0.75282646 0.000956513 0.072748019 4501981.525 5300.369178 335881.7313 342668.6348 21690.91334 -4.336277839 -0.417394425 GLAHPPSYSNPPVYHGNS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLAHPPSYSNPPVYHGNSPK 20 0 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 GLAHPPSYSNPPVYHGNS(1)PK;GLAHPPSYSNPPVYHGNS(1)PK 199.85 2.37E-21 323670000 648120 594130 412240 560580 732370 657150 536420 882860 720020 TRUE FALSE 562469.2999 590227.1209 611600.6429 687868.2569 717797.2699 682430.9857 484398.071 694067.2594 634900.0558 0.885917862 0.929637847 0.963302235 1.083427621 1.130567344 1.074863641 0.762951691 1.093191366 1 19.27616998 4.120238532 2.870551024 1.021526664 0.903013831 0.184494345 0.101258946 0.469214846 7.678556731 0.02770536 0.071442918 13189.80978 -4.120238532 -0.118512833 GLAHQLAS(ph)PGLTTLPEASDVGSITLALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLAHQLASPGLTTLPEASDVGSITLALR 28 0 P42345 P42345 MTOR Serine/threonine-protein kinase mTOR 1 GLAHQLAS(0.995)PGLT(0.002)T(0.003)LPEASDVGSITLALR 139.73 8.92E-08 225650000 119220 124230 102120 101680 167170 179290 141440 178580 153340 TRUE FALSE 103464.7749 123413.925 151505.5736 124767.9981 163843.6441 186187.4023 127723.1706 140392.0567 135212.3199 0.765202276 0.912741717 1.120501251 0.922756138 1.211750854 1.37700028 0.944611931 1.038308172 1 17.04486708 4.552379311 1.833617695 1.087763855 0.716847125 0.395050882 0.133514341 0.634880136 2.934511086 0.037602936 0.357545498 35676.25925 -4.552379311 -0.37091673 GLALEAESELERQDEALDGVAAAVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLALEAESELERQDEALDGVAAAVDR 26 1 A0A087X0B7;Q5SQN1-4;Q5SQN1 A0A087X0B7 SNAP47 Synaptosomal-associated protein 47 0 67.614 0.031205 27282000 19693 21793 11501 14476 18863 23393 19620 22181 11078 FALSE TRUE 17090.52015 21649.84035 17062.92207 17762.99705 18487.6632 24292.94385 17717.25542 17437.76576 9768.37146 1.749577217 2.216320339 1.746751968 1.81841949 1.892604441 2.486898041 1.813736864 1.78512517 1 13.25390235 1.117710751 1.949550439 0.424877063 1.973649792 0.627649282 0.230949796 0.755106078 2.10593562 2.394087363 0.061693818 13.11326239 -1.117710751 1.548772729 GLALHDILTEIHLFVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLALHDILTEIHLFVHR 17 0 P40937-2;P40937 P40937-2 RFC5 Replication factor C subunit 5 0 ; 272.16 4.37E-36 242480000 149571 125154 82392 126373 114903 117419 123635 141513 141299 FALSE TRUE 129804.8134 124331.8551 122237.0468 155067.9211 112616.6551 121936.1849 111644.8967 111251.5462 124594.7932 1.041815714 0.997889655 0.981076686 1.244577861 0.903863253 0.978661963 0.896063903 0.892906865 1 16.92688425 GLALWEAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLALWEAYR 9 0 A0A499FI31;Q15020-4;Q15020;Q15020-2;A0A494C0L2;F8W667;F8VVK9;F8VZM2 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 ; 155.75 0.0001688 485320000 409130 935250 595140 539000 820000 973050 797490 750840 888410 FALSE TRUE 355062.4339 929106.2812 882951.6946 661388.1881 803683.6043 1010483.863 720149.5425 590278.709 783383.1819 0.453242349 1.186017651 1.127100651 0.84427162 1.025913784 1.289897315 0.919281342 0.753499338 1 19.57935863 2.0047214 24.99809075 0.852316795 1.007158839 0.032465123 0.233714034 329.2360993 1743176.237 0.092170175 0.061891776 101.0930735 -2.0047214 0.154842044 GLAPDLPEDLYHLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GLAPDLPEDLYHLIK 15 0 P62277;J3KMX5 P62277 RPS13 40S ribosomal protein S13 0 ;;; 217.93 2.01E-12 5437500000 5300330 4790250 3524770 4065430 4698930 4259610 5408720 6062160 5563020 FALSE TRUE 4599877.961 4758782.532 5229360.562 4988548.018 4605430.486 4423479.953 4884183.167 4765814.26 4905366.113 0.93772368 0.970117708 1.066048984 1.016957329 0.938855608 0.901763467 0.995681679 0.971551185 1 22.22592939 3.24517748 24.99955632 0.962385988 1.000622129 0.149743723 0.042518541 315.5875667 1192333.934 0.013115779 0.016550608 1758.642158 -3.24517748 0.038236141 GLAPNT(ph)PGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GLAPNTPGK 9 0 O43663-2;O43663-4;O43663;O43663-3;H0YL53;G3V3N7 O43663-2 PRC1 Protein regulator of cytokinesis 1 1 GLAPNT(1)PGK;GLAPNT(1)PGK;GLAPNT(1)PGK;GLAPNT(1)PGK 132.03 0.0035386 1515090000 6063570 7037960 4258310 4079300 5880930 5384060 6145350 6612260 7505400 TRUE FALSE 5262253.861 6991727.177 6317642.959 5005567.413 5763910.999 5591188.272 5549374.903 5198279.656 6618120.162 0.795128183 1.056452135 0.954597802 0.756342782 0.870928732 0.844830274 0.838512261 0.785461661 1 22.65799006 3.773254856 24.74656503 0.842725353 0.947498693 0.164903488 0.089089238 776.63727 553954.0161 0.022056815 0.038200745 5932.733712 -3.773254856 0.10477334 GLAVFISDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLAVFISDIR 10 0 O95782-2;O95782;M0R2D9;E9PR62;O94973-3;O94973;O94973-2 O95782-2;O94973-3 AP2A1;AP2A2 AP-2 complex subunit alpha-1;AP-2 complex subunit alpha-2 0 75.38 0.091125 84599000 168430 190830 156190 148380 170990 213410 183860 222310 199620 FALSE TRUE 146171.5488 189576.4252 231724.0064 182071.9468 167587.6335 221620.0208 166029.2855 174770.7365 176021.151 0.830420367 1.077009348 1.316455466 1.034375391 0.952088045 1.259053355 0.943234859 0.992896226 1 17.42538927 GLCAIAQAESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLCAIAQAESLR 12 0 P23396;P23396-2;F2Z2S8;H0YCJ7;H0YF32 P23396 RPS3 40S ribosomal protein S3 0 ; 162.36 0.00014632 1208810000 630042 595549 202748 371211 644473 889970 578506 491860 755248 FALSE TRUE 546780.3534 591636.7994 300797.611 455500.1312 631649.2482 924207.7218 522402.5772 386679.5667 665963.4418 0.82103659 0.888392308 0.451672858 0.683971676 0.948474358 1.38777546 0.784431313 0.580631822 1 19.34508346 3.242225885 24.98248188 0.905997051 0.705377502 0.188727292 0.229755377 204.9490433 1396923.301 0.07480771 0.092821559 1746.730426 -3.242225885 -0.200619549 GLCDLCPSLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLCDLCPSLEK 11 0 C9J5L0;C9J7Q8;C9JBX7;C9J0A8;C9J471;A0A0U1RQR1;H0Y329;G8JLI5;C9JYH8;A0A0U1RR06;Q9Y484;Q9Y484-3 C9J5L0 WDR45 WD repeat domain phosphoinositide-interacting protein 4 0 73.067 0.034093 0 172100 212830 184440 174070 128100 192130 161940 132480 274660 FALSE TRUE 149356.549 211431.9057 273635.8009 213595.254 125551.0606 199521.3654 146235.0837 104150.183 242190.0077 0.616691623 0.87300012 1.12983935 0.881932562 0.518399012 0.823821624 0.603803126 0.430035012 1 17.88577982 3.289382095 11.1776643 0.646696328 0.893680747 0.190870732 0.198464501 0.846022781 182.737579 0.057212101 0.073798501 1947.072373 -3.289382095 0.24698442 GLCNFLMSDEEYDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLCNFLMSDEEYDDR 15 0 Q9UKN8 Q9UKN8 GTF3C4 General transcription factor 3C polypeptide 4 0 ; 262.64 1.21E-24 164723000 149619 133862 89225 104360 131965 136325 125346 131214 124468 FALSE TRUE 129846.4701 132982.6517 132374.5084 128056.533 129339.1547 141569.511 113189.9642 103154.9072 109753.5348 1.18307324 1.211648007 1.206107016 1.166764544 1.178450925 1.289885662 1.031310421 0.939877767 1 16.74390788 2.088435414 5.437499358 0.971145721 1.202502791 0.887077798 0.036669676 0.055893233 2.669537999 0.014925077 0.009866736 122.5844589 -2.088435414 0.23135707 GLDDDRGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GLDDDRGPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 107.15 0.0025715 3742760000 6036840 5970860 4766140 5075090 5856630 7121280 5545750 6530800 7508540 FALSE TRUE 5239056.299 5931637.028 7071061.246 6227466.752 5740094.521 7395240.25 5007924.019 5134239.243 6620888.955 0.791291975 0.895897374 1.067992726 0.940578644 0.866967345 1.116955789 0.756382421 0.775460709 1 22.6585935 2.195499964 24.99994221 0.826031087 0.94593222 0.149421204 0.112794176 224.2446443 130189.2892 0.045364397 0.030584902 156.8555768 -2.195499964 0.119901133 GLDDDRGPWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GLDDDRGPWR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;; 120.09 0.00055254 4215320000 1440170 1525720 1157290 1138840 1467390 1689570 1449980 1568940 1550810 FALSE TRUE 1249847.886 1515697.445 1716959.315 1397431.028 1438191.81 1754568.851 1309361.163 1233434.391 1367475.008 0.91398225 1.108391331 1.255569063 1.021906082 1.051713414 1.283071969 0.95750281 0.901979475 1 20.38308304 2.037093446 24.9679805 0.939713931 1.107585818 0.304767771 0.108371 174.5493867 117490.3049 0.043266587 0.029170246 108.916442 -2.037093446 0.167871886 GLDEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLDEDR 6 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 107.49 0.07263 265930000 870100 862140 639300 687480 637110 961080 786130 881440 958500 FALSE TRUE 755114.0804 856476.5456 948467.6183 843582.8415 624432.7575 998053.3695 709891.2336 692950.9154 845187.2219 0.893428179 1.013357187 1.122198246 0.998101745 0.738809983 1.18086661 0.839921872 0.819878599 1 19.68891143 3.45112097 24.99240787 0.907535847 1.018384145 0.106222977 0.129271384 424.3508525 407899.9189 0.036499578 0.047122098 2825.666935 -3.45112097 0.110848298 GLDFSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GLDFSDR 7 0 Q13561;Q13561-3;Q13561-2;F8W1I6;F8VW18;F8VX93;F8VRV7;H0YHL1 Q13561 DCTN2 Dynactin subunit 2 0 ;;; 186.67 0.0013852 4365560000 4763720 4848140 3490660 3595460 4648870 5264940 4375600 4882920 4658660 FALSE TRUE 4134182.332 4816292.249 5178754.852 4411864.146 4556366.582 5467485.649 3951254.985 3838745.557 4107918.522 1.006393459 1.172441036 1.260676137 1.073990178 1.109166737 1.330962535 0.961863037 0.93447461 1 21.96997614 2.143283578 12.83620936 0.95836583 1.15802483 0.497767782 0.091531276 0.458115048 59.17483728 0.036330687 0.024493572 139.0860515 -2.143283578 0.199658999 GLDGIPFTVDATSQIHCIEDFHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GLDGIPFTVDATSQIHCIEDFHR 23 0 Q15654;H7BZE2 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 ;; 215.58 1.55E-32 539547000 525985 615674 360965 365395 525064 603083 516962 617851 382279 FALSE TRUE 456474.7496 611629.597 535528.8814 448363.5195 514616.2537 626283.9933 466827.1048 485728.3718 337086.4121 1.354177247 1.814459364 1.588699105 1.330114485 1.526659738 1.857933072 1.384888527 1.440960995 1 18.36275895 0.90623379 1.365598771 0.241797681 1.569269815 0.491738352 0.175903258 2.467804498 2.134718188 5.72696475 0.050458474 8.058121111 -0.90623379 1.327472134 GLDGPRPNQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLDGPRPNQK 10 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 123.75 0.00041389 1259950000 948430 852930 577720 688910 797030 746160 913530 1008440 881580 FALSE TRUE 823092.5725 847327.0467 857107.3244 845337.5448 781170.6624 774865.258 824936.0012 792792.9537 777360.6167 1.058829782 1.090005113 1.102586504 1.087445809 1.004901259 0.99678996 1.061201177 1.019852224 1 19.56822449 3.245570369 24.99994658 1.019322806 1.086370962 0.725981513 0.020760496 89.06875053 317656.9624 0.006202692 0.007835539 1760.233853 -3.245570369 0.067048156 GLDHDFGPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GLDHDFGPSR 10 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6 Q9UDY2-7 TJP2 Tight junction protein ZO-2 0 ;;;;; 170.99 4.16E-06 2898000000 1602650 1777080 1168904 1309490 1788370 1979170 1614930 1830630 1764630 FALSE TRUE 1390855.742 1765406.244 1734189.884 1606829.719 1752784.936 2055309.951 1458314.337 1439164.02 1556017.452 0.893856133 1.134567124 1.11450542 1.032655332 1.126455834 1.32087847 0.9372095 0.924902236 1 20.56942681 GLDHLLDENRVPDLAQMYQLFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLDHLLDENRVPDLAQMYQLFSR 23 1 Q13619;A0A0A0MR50;Q13619-2 Q13619 CUL4A Cullin-4A 0 ; 112.47 0.00051658 437320000 127639 126699 68396 80628 118841 129850 105966 129833 73424 FALSE TRUE 110771.1828 125866.7059 101472.5344 98935.81972 116476.2966 134845.4135 95689.43363 102069.2233 64743.89836 1.710913083 1.944070547 1.56729108 1.528110327 1.799031253 2.082750914 1.477968365 1.576507221 1 15.98245662 0.896384843 1.300113804 4.38E-12 1.748334613 0.616812376 0.181755465 2.117723928 1.654148035 6.189962257 0.054777839 7.877435264 -0.896384843 1.748334613 GLDIPEVDLVIQSSPPKDVESYIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLDIPEVDLVIQSSPPKDVESYIHR 25 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 143.98 1.88E-07 309370000 681570 588530 275240 386840 559590 457180 615460 713080 198941 FALSE TRUE 591498.7976 584663.9077 408346.9846 474677.9345 548455.2538 474768.0104 555772.7839 560593.3912 175422.4216 3.371854021 3.332891556 2.327792427 2.705913703 3.126483199 2.706427183 3.168196966 3.195676961 1 17.42047363 1.234878099 24.99997417 0.999997181 2.985969666 0.786734924 0.32591118 50.63105375 343673.1277 0.595962842 0.082407728 17.17426261 -1.234878099 1.985972485 GLDIYVWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLDIYVWR 8 0 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 0 ; 113.89 0.0064252 310900000 1311070 1378180 993570 1034820 1277310 1345150 1280120 1377030 1308160 FALSE TRUE 1137808.778 1369126.645 1474063.775 1269791.697 1251894.03 1396898.791 1155974.159 1082562.851 1153510.815 0.986387611 1.186921377 1.277893329 1.100806062 1.085290241 1.210997567 1.002135519 0.938493889 1 20.1376001 2.117120221 5.735305919 0.966722831 1.144783905 0.480729267 0.079280122 0.164196577 7.597191371 0.032872845 0.021917999 130.9544379 -2.117120221 0.178061073 GLDQDHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 120.12 0.0015631 201813000 732250 728920 572240 593470 613590 826950 658910 762810 787470 FALSE TRUE 635481.3072 724131.6765 848977.178 728226.4341 601380.7595 858763.3016 595009.0096 599689.0177 694376.1937 0.915183028 1.042852107 1.222647299 1.048749137 0.866073412 1.236740703 0.856897191 0.863637065 1 19.40535796 2.184463429 24.99997979 0.895761684 1.053504611 0.251733055 0.12018157 120.1513402 55524.56699 0.048035349 0.032385453 152.9196969 -2.184463429 0.157742928 GLDVDSLVIEHIQVNK ddPTM_MDA-MB-175_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 ;;;;; 258.36 1.05E-26 1758700000 2152592 2018383 1521270 1787736 1965776 1815502 2367886 2536980 2437911 FALSE TRUE 1868121.513 2005124.109 2256961.26 2193668.783 1926660.904 1885345.537 2138248.78 1994466.57 2149703.939 0.869013393 0.932744306 1.049893997 1.020451581 0.896244766 0.87702567 0.994671285 0.927786629 1 21.03570655 3.073770878 0.003201049 1.902142736 0.001802243 0.020045696 0.061703941 229322.847 1018.932359 302312.2477 302576.552 1185.143333 -3.073770878 -1.900340493 GLDYLHSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLDYLHSEK 9 0 B4DR80;Q9Y6E0-2;H0Y630;Q9Y6E0;Q9P289-2;Q8NBY1;B4E0Y9;Q9P289-3;Q9P289 B4DR80;Q8NBY1 STK24;STK26 Serine/threonine-protein kinase 24;Serine/threonine-protein kinase 24 36 kDa subunit;Serine/threonine-protein kinase 24 12 kDa subunit;Serine/threonine-protein kinase 26 0 ; 81.594 0.020839 556580000 863840 723130 651370 902590 811410 730200 839640 913090 1340300 FALSE TRUE 749681.3553 718379.7114 966374.7107 1107536.855 795264.5285 758291.2665 758211.842 717832.8092 1181851.261 0.634328007 0.607842742 0.817678791 0.937120339 0.672897305 0.641613113 0.641545909 0.607379992 1 20.17261705 4.260583624 24.80072114 0.738825219 0.621085251 0.147917903 0.13108083 499.7423857 562762.9221 0.034022946 0.089849807 18221.47898 -4.260583624 -0.117739968 GLECSDWKPEAGLS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLECSDWKPEAGLSPPR 17 1 S4R3M9;O75764;S4R419;O75764-2 S4R3M9 TCEA3 Transcription elongation factor A protein 3 1 GLECSDWKPEAGLS(1)PPR;GLECSDWKPEAGLS(1)PPR 106.69 0.00044855 986080000 2515080 2643310 1733740 2164580 2617050 2187910 2620470 3426540 3371850 TRUE FALSE 2182705.806 2625945.923 2572182.463 2656080.973 2564975.825 2272080.313 2366337.223 2693801.086 2973233.734 0.734118472 0.883195254 0.865112767 0.8933307 0.862688929 0.76417817 0.795879986 0.906017262 1 21.50360145 1.42191263 3.034381685 1.001481316 0.83364411 0.535908324 0.051980907 0.236696794 3.500209436 0.078606324 0.013951732 26.4187722 -1.42191263 -0.167837206 GLECSDWKPEAGLS(ph)PPRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLECSDWKPEAGLSPPRK 18 2 S4R3M9;O75764;S4R419;O75764-2 S4R3M9 TCEA3 Transcription elongation factor A protein 3 1 GLECSDWKPEAGLS(1)PPRK 78.413 0.00624 282630000 158060 173900 120570 128160 153900 105940 190470 221530 197300 TRUE FALSE 137171.9705 172757.6394 178878.0553 157260.6868 150837.6911 110015.5804 171998.2487 174157.5334 173975.4188 0.788456045 0.993000279 1.028180053 0.903924749 0.867005765 0.632362785 0.988635348 1.001046784 1 17.40852395 2.041460242 24.99999533 0.99887275 0.877162435 0.235548707 0.107933002 228.110562 137546.8126 0.046524669 0.03136689 110.0171125 -2.041460242 -0.121710316 GLEDSYEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLEDSYEGR 9 0 Q8NHP8-2;Q8NHP8 Q8NHP8-2 PLBD2 Putative phospholipase B-like 2;Putative phospholipase B-like 2 32 kDa form;Putative phospholipase B-like 2 45 kDa form 0 ; 135.83 0.00048809 174910000 520910 419040 296290 331310 383570 476250 379730 467400 431270 FALSE TRUE 452070.4237 416287.2986 439576.835 406538.9993 375937.7074 494571.6457 342903.843 367450.1473 380285.7519 1.188765084 1.094669723 1.155911924 1.06903558 0.988566376 1.300526363 0.901700475 0.966247474 1 18.53672436 2.205490176 24.99999974 0.955859336 1.122755164 0.493075847 0.084149425 158.3770353 119725.9586 0.032678724 0.022033532 160.5055949 -2.205490176 0.166895828 GLEDVRPSVESLLDELESSVPS(ph)PVPAITVNQGEMSSPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GLEDVRPSVESLLDELESSVPSPVPAITVNQGEMSSPQR 39 1 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;P49023-3;P49023-4 F5GZ78;P49023-3;P49023-4 PXN Paxillin 1 GLEDVRPSVESLLDELES(0.001)SVPS(0.999)PVPAITVNQGEMSSPQR;GLEDVRPSVESLLDELES(0.001)S(0.001)VPS(0.997)PVPAITVNQGEMSSPQR;GLEDVRPSVESLLDELES(0.039)S(0.171)VPS(0.781)PVPAIT(0.008)VNQGEMSSPQR 169.2 3.42E-18 132491000 99574 116351 90928 109433 123534 145141 141475 164081 142534 TRUE FALSE 86415.04361 115586.6826 134901.0849 134281.4352 121075.9151 150724.6682 127754.7763 128993.555 125683.7929 0.687559164 0.919662591 1.073337157 1.068406929 0.963337534 1.199237107 1.016477728 1.026334041 1 16.9394391 4.644318533 2.347730652 1.048710463 0.639456642 0.770605459 0.063037542 0.205530305 1.580697195 0.015735533 0.157471272 44087.81063 -4.644318533 -0.409253821 GLEFPMTDLDMLS(ph)PIHTPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLEFPMTDLDMLSPIHTPQR 20 0 O60784;O60784-4;O60784-2;V9GYF4;B0QY02;B0QY01 O60784 TOM1 Target of Myb protein 1 1 GLEFPMTDLDMLS(1)PIHTPQR;GLEFPMTDLDMLS(1)PIHTPQR 277.94 8.60E-45 90275000 77144 71503 57717 70489 76452 93692 81838 97309 105598 TRUE FALSE 66949.22494 71033.29208 85629.13425 86494.60481 74930.75478 97296.39187 73901.36336 76500.22761 93114.32474 0.719000273 0.762861056 0.919612901 0.92890761 0.804717802 1.044913252 0.793662668 0.821573134 1 16.50671551 4.334037176 4.77625296 0.891404141 0.73029819 0.401030095 0.081581984 0.208779808 7.894421361 0.020134336 0.05658744 21579.29124 -4.334037176 -0.161105951 GLEFPMTDLDMLSPIHT(ph)PQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLEFPMTDLDMLSPIHTPQR 20 0 O60784;O60784-4;O60784-2;V9GYF4;B0QY02;B0QY01 O60784 TOM1 Target of Myb protein 1 1 GLEFPMTDLDMLS(0.001)PIHT(0.999)PQR;GLEFPMTDLDMLSPIHT(1)PQR 176.48 1.46E-12 29472000 29685.5 36067 28143.2 33188 41732.5 51034 45090 55652 48087 TRUE FALSE 25762.48596 35830.0735 41753.34565 40723.84265 40902.1049 52997.311 40717.17874 43751.25288 42402.20964 0.607574138 0.845004867 0.984697402 0.960417936 0.964622015 1.249871444 0.960260776 1.0318154 1 15.37185183 5.165236641 0.900222525 1.039021522 8.93E-15 0.733570854 0.082281674 2.184366051 0.824482363 0.027332774 2.666467337 146297.4111 -5.165236641 -1.039021522 GLEGERPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GLEGERPAR 9 1 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;;;;; 162.88 5.79E-05 17447900000 4541510 4575900 2974300 3081250 4228200 4509340 4028220 4731840 3891250 FALSE TRUE 3941337.947 4545840.612 4412681.428 3780894.906 4144067.092 4682817.228 3637563.844 3719972.839 3431230.858 1.148665919 1.324842542 1.286034549 1.101906302 1.207749424 1.36476309 1.060133811 1.084151138 1 21.71029476 2.175313078 12.72240651 1.055924166 1.237359958 0.55924307 0.079781618 0.689983018 137.2499398 0.032508669 0.02191905 149.7314663 -2.175313078 0.181435792 GLEGGVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLEGGVLR 8 0 Q86XI8;Q86XI8-2 Q86XI8 C19orf68 Uncharacterized protein C19orf68 0 78.616 0.070178 237880000 409980 521880 367660 342670 523560 567350 478780 512480 544900 FALSE TRUE 355800.1042 518451.7359 545461.6057 420478.4609 513142.1803 589176.3216 432347.9893 402890.1401 480482.5428 0.740505789 1.079023044 1.135237094 0.875117041 1.067972579 1.226217956 0.899820391 0.838511505 1 18.87412449 2.06137654 24.99995858 0.896145292 1.027317207 0.1125588 0.139470307 119.2891855 48588.0144 0.055745704 0.03758374 115.1798585 -2.06137654 0.131171915 GLEGKS(ph)PDTGPDWLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLEGKSPDTGPDWLK 15 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 GLEGKS(0.994)PDT(0.006)GPDWLK 109.89 0.0020312 0 172180 141850 115720 127730 137430 123860 183010 188050 161660 TRUE FALSE 149425.9768 140918.178 171682.5791 156733.0487 134695.4119 128624.9743 165261.7184 147836.9709 142548.739 1.048244817 0.988561379 1.204378098 1.099504982 0.944907776 0.902322779 1.159334832 1.037097711 1 17.12109575 3.287066654 24.99891943 1.018252564 1.086786342 0.16249145 0.084679057 253.8510117 130827.0968 0.02556501 0.033004219 1936.71918 -3.287066654 0.068533778 GLEGWEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GLEGWEK 7 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ;;; 132.69 0.0077809 895810000 2408690 2210730 1688060 1988880 2176950 2114600 2500800 2773030 2755900 FALSE TRUE 2090375.514 2196207.569 2504411.462 2440485.602 2133632.954 2195950.03 2258272.801 2180039.114 2430100.642 0.860201211 0.903751693 1.030579318 1.004273469 0.878001889 0.903645714 0.929291883 0.897098283 1 21.21258463 4.012571299 0.003445779 1.300542413 0.561645099 0.009583519 0.057862453 1278706.782 2071.049274 220295.3375 223814.4521 10293.69507 -4.012571299 -0.738897314 GLEHPLFPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLEHPLFPK 9 0 B7ZM87;O75044;A0A075B7B5;Q5VZB4 B7ZM87 SRGAP2 SLIT-ROBO Rho GTPase-activating protein 2 0 63.159 0.094731 0 247280 258090 219950 255530 197980 223960 225950 276260 257680 FALSE TRUE 214601.3215 256394.5898 326318.5557 313551.992 194040.5853 232575.8861 204037.4038 217183.9489 227217.364 0.944475888 1.128411074 1.43615149 1.379964922 0.853986605 1.023583242 0.897983324 0.955842217 1 17.79371356 3.231672003 24.99953677 0.947717484 1.230826628 0.488774888 0.140119163 141.494968 513500.0389 0.044194755 0.051207754 1704.794373 -3.231672003 0.283109143 GLEHVTVDDLVAEITPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLEHVTVDDLVAEITPK 17 0 E5RHX8;Q9NPA8-2;Q9NPA8 E5RHX8 ENY2 Transcription and mRNA export factor ENY2 0 126.88 4.21E-05 34806000 112050 79645 46038 63580 76230 63855 88261 95699 87837 FALSE TRUE 97242.3086 79121.80675 68302.13079 78016.81076 74713.17214 66311.54317 79701.4618 75234.51358 77453.00992 1.255500705 1.021545926 0.881852505 1.007279263 0.964625806 0.85615192 1.029029884 0.971356874 1 16.24103368 4.70421881 3.439058486 0.961286191 1.282098291 0.747557958 0.053840072 0.127681796 2.613565231 0.012891099 0.101455158 50607.95748 -4.70421881 0.3208121 GLEPGVFTLAEEDDEAEGAPGS(ph)PEREPPAILFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLEPGVFTLAEEDDEAEGAPGSPEREPPAILFR 33 1 Q9HCE9-2;Q9HCE9 Q9HCE9-2 ANO8 Anoctamin-8 1 GLEPGVFTLAEEDDEAEGAPGS(1)PEREPPAILFR;GLEPGVFTLAEEDDEAEGAPGS(1)PEREPPAILFR 97.003 8.01E-05 52758000 29032.2 30419.6 26383.5 29345 37324 46889 23497.7 40413 35230.8 TRUE FALSE 25195.52121 30219.77164 39142.64885 36008.23076 36581.32542 48692.85017 21218.89667 31770.99444 31065.85496 0.811035822 0.972764847 1.259989429 1.159093507 1.177541242 1.567407375 0.683029542 1.022698216 1 14.92304214 2.204944614 24.99985251 0.917953969 1.155132238 0.242965013 0.212403481 295.1745924 219516.094 0.087872636 0.05924745 160.304094 -2.204944614 0.237178269 GLESDVAELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLESDVAELR 10 0 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 124.92 0.00098346 151104000 447010 447280 284660 351400 461770 531830 357900 512650 460050 FALSE TRUE 387936.4959 444341.7882 422322.5281 431190.7408 452581.6804 552289.8442 323190.9131 403023.7869 405663.4131 0.956301415 1.095345979 1.041066348 1.06292736 1.115658119 1.361448497 0.796697219 0.993493063 1 18.62992367 2.205877734 24.99991829 0.937721177 1.100602433 0.336002208 0.115930519 235.7690885 180343.8474 0.04697272 0.03167144 160.6488917 -2.205877734 0.162881256 GLESTTLADKDGEIYCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GLESTTLADKDGEIYCK 17 1 P21291;E9PP21;E9PND2 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ;; 234.48 3.56E-20 2789760000 3347360 3025260 2370540 2591600 2438990 1831860 3624930 4023890 3318660 FALSE TRUE 2904997.895 3005386.868 3516941.073 3180062.39 2390458.871 1902332.84 3273384.847 3163412.437 2926331.795 0.992709678 1.027015075 1.201825807 1.086706024 0.816878959 0.650074213 1.118596617 1.081016323 1 21.48066192 5.166513556 11.91842646 1.002999666 0.000780639 0 0.158384509 700789.9432 353098.5902 0.041744925 18943266.06 146728.1884 -5.166513556 -1.002219026 GLEVTAYSPLGSSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLEVTAYSPLGSSDR 15 0 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 90.689 0.013766 61761000 60064 61466 27895 43908 58571 54510 62994 57521 70645 FALSE TRUE 52126.39022 61062.2258 41385.1153 53877.98249 57405.55169 56607.03497 56884.85158 45220.58178 62293.42858 0.836787947 0.980235431 0.664357642 0.864906359 0.921534631 0.908715996 0.913175802 0.725928606 1 15.92679236 GLEWLWSPQIVGLYNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLEWLWSPQIVGLYNR 16 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 164.13 1.74E-08 74961000 132380 137680 86826 112160 141310 133630 149140 141950 114500 FALSE TRUE 114885.6476 136775.571 128815.344 137627.6423 138498.2075 138770.8326 134676.4258 111595.0972 100963.9404 1.137887914 1.354697236 1.275854958 1.363136598 1.371759134 1.374459356 1.333906196 1.105296571 1 16.6234806 1.612943476 3.196766802 1.015425924 1.322744362 0.711732056 0.070979736 0.10287936 2.408950171 0.061369139 0.018534193 41.0150718 -1.612943476 0.307318438 GLEYLYLNVHDEDRDDQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GLEYLYLNVHDEDRDDQTR 19 1 Q9Y6G9;C9JGM7;C9JLW1 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 ;;;;; 264.96 1.35E-31 3135830000 2095298 2228940 1608336 1691238 2087053 2342530 2074662 2395560 2238770 FALSE TRUE 1818399.06 2214297.946 2386132.669 2075259.437 2045524.729 2432648.645 1873461.599 1883288.136 1974105.161 0.921125731 1.121671728 1.208716089 1.051240571 1.036178198 1.232279158 0.949018135 0.953995853 1 20.91276741 2.186279091 24.99997895 0.964044681 1.09688428 0.317715133 0.088022623 111.6041424 53365.92567 0.035023651 0.023612966 153.5603491 -2.186279091 0.132839599 GLEYLYLSVHDEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLEYLYLSVHDEDR 14 0 O43237;O43237-2;H3BUM4 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 ; 159.52 4.90E-06 153501000 213817 182181 118438 182284 184869 189789 175396 198286 501360 FALSE TRUE 185560.5417 180984.241 175715.013 223674.3682 181190.4686 197090.3056 158386.1229 155884.082 442089.792 0.419734961 0.409383443 0.397464534 0.505947824 0.409849926 0.445815102 0.358266863 0.352607287 1 18.7539799 1.235145689 24.99999999 1.000000822 0.410374411 0.948397615 0.043073787 21.56326343 157834.6456 0.080801776 0.011402279 17.18484776 -1.235145689 -0.589626411 GLEYLYLSVHDEDRDDHTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GLEYLYLSVHDEDRDDHTR 19 1 O43237 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 ;;; 150.59 4.78E-08 1342320000 690710 691335 298097 436418 650223 730576 616283 712950 471152 FALSE TRUE 599430.9235 686793.5749 442257.7063 535513.3771 637284.8344 758681.7315 556515.9695 560491.1907 415452.9473 1.442837095 1.653119997 1.064519362 1.288986829 1.533951892 1.826155613 1.339540309 1.349108712 1 18.66432557 1.170405235 1.887464927 0.78898352 1.45327306 0.323252006 0.204363693 1.34296426 3.929577503 1.697234579 0.058394734 14.80489169 -1.170405235 0.66428954 GLFDDEDEESDLFTEAPQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GLFDDEDEESDLFTEAPQDR 20 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6 Q641Q2 FAM21A WASH complex subunit FAM21A 0 ;; 364.17 1.42E-111 258687000 360327 329735 238738 266368 327022 345222 317592 365972 346015 FALSE TRUE 312708.874 327568.9491 354192.4953 326850.9256 320514.902 358502.9137 286791.9767 287711.7358 305109.5009 1.024907035 1.073611107 1.160870095 1.071257777 1.050491385 1.174997542 0.939964098 0.942978619 1 18.21896758 2.219902785 24.99956325 0.956354676 1.092028877 0.622747378 0.048277873 147.7692301 197993.9106 0.019274621 0.013020319 165.9215456 -2.219902785 0.135674201 GLFDEYGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLFDEYGSK 9 0 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ; 179.68 0.00011522 466130000 1121620 988970 811900 1019040 1035470 1098130 1054610 1044410 944230 FALSE TRUE 973395.0752 982473.391 1204537.556 1250428.607 1014866.173 1140375.772 952334.0845 821071.0491 832604.2051 1.169096996 1.180000515 1.446710872 1.501828359 1.218905894 1.369649306 1.143801675 0.986148093 1 19.66727132 1.998996863 2.941950634 0.996096233 1.318585111 0.60178627 0.108519616 0.182709106 3.076602062 0.066564866 0.032770333 99.76928573 -1.998996863 0.322488877 GLFIIDDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GLFIIDDK 8 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5;Q13162;H7C3T4 Q06830;Q13162 PRDX1;PRDX4 Peroxiredoxin-1;Peroxiredoxin-4 0 ;;;;; 161.11 0.00081293 2970588000 7530077 5814293 4747390 5565766 5398434 4930998 6822257 7629556 6969350 FALSE TRUE 6534958.246 5776098.526 7043243.683 6829558.238 5291015.725 5120696.684 6160635.566 5998034.823 6145441.383 1.063383057 0.939899702 1.146092403 1.111321028 0.860965941 0.833251245 1.002472432 0.976013674 1 22.5510852 3.247105266 24.99991321 0.939755194 1.062005766 0.426082729 0.075161148 211.4581628 618680.081 0.023305566 0.029601495 1766.465933 -3.247105266 0.122250571 GLFIIDDKGILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLFIIDDKGILR 12 1 Q06830;A0A0A0MSI0;A0A0A0MRQ5;Q13162;H7C3T4 Q06830;Q13162 PRDX1;PRDX4 Peroxiredoxin-1;Peroxiredoxin-4 0 ; 161.99 5.83E-05 1596610000 2730600 2216050 648080 782290 1738770 1767810 2540800 2842500 214847 FALSE TRUE 2369744.292 2201492.622 961493.6557 959920.9011 1704171.879 1835818.795 2294393.607 2234653.495 189448.0324 12.50867724 11.62056208 5.075236958 5.066935184 8.995458317 9.690355562 12.11093923 11.7956015 1 17.53144263 4.417002492 11.5783218 8.307988553 12.2871661 0.210094853 3.389865407 0.982401606 185.7045955 0.883811957 2.340916421 26121.76344 -4.417002492 3.979177548 GLFIKPTVFSEVTDNMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLFIKPTVFSEVTDNMR 17 1 H0Y2X5;P47895 H0Y2X5 ALDH1A3 Aldehyde dehydrogenase family 1 member A3 0 198.42 1.30E-11 158360000 169960 133380 117220 105570 133210 167110 148000 160570 136030 FALSE TRUE 147499.3554 132503.818 173907.9841 129541.282 130559.3816 173538.8298 133646.9828 126233.3551 119948.6884 1.229687105 1.104670837 1.449853153 1.079972477 1.088460269 1.446775552 1.114201286 1.052394626 1 16.87205786 2.00899272 24.86678234 1.04594719 1.228424663 0.301970502 0.131573844 223.6352601 618396.3942 0.052238439 0.035165063 102.092237 -2.00899272 0.182477473 GLFLPEDENLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLFLPEDENLR 11 0 Q12797;Q12797-10 Q12797 ASPH Aspartyl/asparaginyl beta-hydroxylase 0 125.56 0.0007577 29733000 82073 78115 60027 70537 87707 82421 81091 106460 104710 FALSE TRUE 71226.8451 77601.85742 89056.25798 86553.50394 85961.8023 85591.7892 73226.8073 83694.35747 92331.30309 0.771426837 0.84047181 0.964529417 0.937423182 0.93101472 0.92700727 0.793087554 0.906457016 1 16.49453223 4.463406788 4.531525598 0.915234271 0.783552427 0.470917329 0.053512737 0.170202952 8.727512243 0.014047207 0.046892546 29067.44021 -4.463406788 -0.131681844 GLFS(ph)DEEDSEDLFSSQSASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLFSDEEDSEDLFSSQSASK 20 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6 Q641Q2 FAM21A WASH complex subunit FAM21A 1 GLFS(0.999)DEEDS(0.001)EDLFSSQSASK;GLFS(0.993)DEEDS(0.007)EDLFSSQSASK 211.29 1.84E-22 138322000 261340 232730 171514 204915 232440 192743 259310 308920 268380 TRUE FALSE 226803.2568 231201.1813 254458.7441 251444.0827 227814.8988 200157.9479 234162.1561 242859.862 236652.4221 0.958381304 0.976965202 1.075242509 1.062503736 0.962656104 0.845788715 0.989477116 1.026230198 1 17.85241016 3.205945727 24.89369382 0.968401786 1.019391887 0.171384196 0.05807463 386.6946263 295148.1178 0.019546033 0.022164547 1606.740449 -3.205945727 0.050990102 GLGACTLLGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GLGACTLLGSPR 12 0 O95644-6;O95644;K7ER53;O95644-8;O95644-11;O95644-3;O95644-10;O95644-2;O95644-5;O95644-4 O95644-6 NFATC1 "Nuclear factor of activated T-cells, cytoplasmic 1" 1 GLGACTLLGS(1)PR;GLGACT(0.001)LLGS(0.999)PR;GLGACTLLGS(1)PR;GLGACTLLGS(1)PR;GLGACTLLGS(1)PR;GLGACTLLGS(1)PR 181.67 1.87E-05 1612800000 1106120 1061280 839541 915610 1006390 1123160 900120 1081660 1115440 TRUE FALSE 959943.4394 1054308.382 1245545.836 1123513.245 986364.808 1166368.692 812826.5009 850355.4265 983573.9539 0.975974847 1.071915719 1.266346908 1.142276328 1.002837462 1.185847477 0.826401002 0.864556674 1 19.90767401 2.236215543 24.99999498 0.887288748 1.109953309 0.527718484 0.093726854 45.80997313 488352.3753 0.037508314 0.026656209 172.2723362 -2.236215543 0.222664561 GLGAFVIDSDHLGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLGAFVIDSDHLGHR 15 0 Q13057;Q13057-2;K7EQ60 Q13057 COASY Bifunctional coenzyme A synthase;Phosphopantetheine adenylyltransferase;Dephospho-CoA kinase 0 77.078 0.015588 120840000 120010 113090 82790 96482 128170 131660 111780 145770 134080 FALSE TRUE 104150.3744 112347.1043 122827.5209 118389.7127 125619.6678 136725.0454 100939.5928 114598.2199 118229.2151 0.880919105 0.950248246 1.038893143 1.001357512 1.06250953 1.156440438 0.853761845 0.969288511 1 16.85122705 7.050451586 10.70901203 0.990376886 0.298880586 0 0.086952688 0 0 0.019862532 0 11231857.52 -7.050451586 -0.6914963 GLGFCHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLGFCHSR 8 0 Q00535 Q00535 CDK5 Cyclin-dependent-like kinase 5 0 63.673 0.071824 39131000 164010 190370 126580 93331 142670 288800 141540 132980 138130 FALSE TRUE 142335.663 189119.4469 187794.5114 114523.23 139831.1461 299910.3229 127813.4726 104543.2619 121800.4288 1.168597388 1.552699353 1.541821431 0.940253094 1.148034925 2.462309254 1.049368002 0.858316041 1 16.89415969 2.021553698 24.99963819 0.929478246 1.463984639 0.255627153 0.405790157 302.9557452 351389.9732 0.165984658 0.111896872 105.0881382 -2.021553698 0.534506393 GLGGEVPGSHQGPDPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GLGGEVPGSHQGPDPYR 17 0 K7EM09;K7EPR0;K7ELQ9;Q6UW68 K7EM09 TMEM205 Transmembrane protein 205 0 ;;;;; 159.88 3.16E-09 7226300000 5612670 5459190 4370890 5350300 7437090 8061940 4107780 7887570 7187300 FALSE TRUE 4870941.439 5423328.221 6484667.024 6565167.389 7289106.459 8372088.049 3709408.128 6200874.537 6337625.582 0.768575135 0.855735031 1.023201346 1.035903321 1.150132075 1.321013358 0.585299349 0.978422353 1 22.595511 7.529119896 13.15802826 0.968467665 0.034267238 0 0.201497389 0 0 0.04562454 0 33815817.89 -7.529119896 -0.934200427 GLGHPPSS(ph)PLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GLGHPPSSPLLK 12 0 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 1 GLGHPPS(0.095)S(0.905)PLLK;GLGHPPS(0.006)S(0.994)PLLK;GLGHPPS(0.098)S(0.902)PLLK;GLGHPPS(0.164)S(0.836)PLLK 137.68 5.66E-05 1456360000 3483300 2880910 2219850 2833160 3403330 3038530 3714040 4587080 4828100 TRUE FALSE 3022973.079 2861985.113 3293376.885 3476472.28 3335610.392 3155424.215 3353852.972 3606168.639 4257327.518 0.710063547 0.672249222 0.773578465 0.816585585 0.783498657 0.741174881 0.787783641 0.847049851 1 22.02151665 -1.116777784 0.732420822 10 0.744063087 0.808183682 0.038890125 38.32193958 0.759381673 550.626119 0.017512355 0.076422672 1.116777784 -9.255936913 GLGKPGGQGDAIQLS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLGKPGGQGDAIQLSPK 17 1 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 GLGKPGGQGDAIQLS(1)PK 177.93 6.06E-10 555280000 1437500 1042000 836360 846880 1131300 824190 1371000 1579500 1225400 TRUE FALSE 1247530.733 1035155.033 1240826.493 1039177.048 1108789.343 855897.1226 1238040.631 1241736.217 1080534.608 1.154549538 0.958002664 1.148344981 0.961724909 1.026148848 0.792105238 1.145766755 1.1491869 1 20.04331385 GLGLDDALEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLGLDDALEPR 11 0 Q9Y230;X6R2L4;M0R0Z0;A0A1W2PS48 Q9Y230 RUVBL2 RuvB-like 2 0 101.38 0.0077377 111060000 204690 191750 144380 168370 199660 211050 205620 214000 206500 FALSE TRUE 177639.6979 190490.3816 214202.6509 206600.9819 195687.1566 219169.2301 185679.004 168237.7653 182087.8052 0.975571635 1.046145739 1.176370107 1.134622835 1.074685679 1.203645844 1.019722347 0.923937576 1 17.47427478 2.006280286 24.86730182 0.961124007 1.103679936 0.440902804 0.066408891 122.3348934 484392.7874 0.027488859 0.018479115 101.4565957 -2.006280286 0.142555929 GLGMEVFPVDLIYRPWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLGMEVFPVDLIYRPWK 17 1 A5YKK6-3;A5YKK6-2;A5YKK6;A5YKK6-4 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 114.69 0.00032026 146720000 127540 124800 88510 94615 110400 106980 131450 142450 122760 FALSE TRUE 110685.2659 123980.1806 131313.732 116098.7818 108203.256 111095.5898 118701.9992 111988.176 108247.4526 1.022520744 1.145340399 1.213088427 1.072531307 0.999591707 1.026311355 1.09658007 1.034557149 1 16.72397355 3.485677027 24.56218392 1.036400819 1.131150743 0.403239086 0.052833361 319.6923675 917783.1335 0.014955677 0.020330535 3059.687179 -3.485677027 0.094749924 GLGPPS(ph)PPAPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GLGPPSPPAPPR 12 0 Q13425;Q13425-2;A0A140TA73 Q13425 SNTB2 Beta-2-syntrophin 1 GLGPPS(1)PPAPPR;GLGPPS(1)PPAPPR;GLGPPS(1)PPAPPR;GLGPPS(1)PPAPPR;GLGPPS(1)PPAPPR;GLGPPS(1)PPAPPR 159.77 7.33E-05 3663970000 1095533 943840 684617 743862 1013503 1074747 773312 914986 823619 TRUE FALSE 950755.5383 937639.8529 1015700.071 912767.2363 993336.2732 1116093.213 698316.3213 719323.3643 726251.7001 1.309126764 1.291067343 1.398551041 1.256819414 1.367757587 1.53678568 0.961534852 0.990460145 1 19.47011011 2.222517067 24.99992593 0.984408416 1.354296309 0.845126381 0.075854406 86.40688545 134642.8416 0.030886466 0.020897277 166.9233404 -2.222517067 0.369887893 GLGS(ph)SPDLELLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GLGSSPDLELLLR 13 0 Q9NQQ7-2;Q9NQQ7;Q9NQQ7-3 Q9NQQ7-2 SLC35C2 Solute carrier family 35 member C2 1 GLGS(0.5)S(0.5)PDLELLLR;GLGS(0.946)S(0.054)PDLELLLR;GLGS(0.93)S(0.07)PDLELLLR 184.98 9.49E-06 218658000 299408 240583 130436 172412 228190 210231 214988 357211 279577 TRUE FALSE 259840.4742 239002.5944 193515.2859 211560.7798 223649.4654 218318.7226 194138.4969 280824.2075 246525.7256 1.054009571 0.969483383 0.784969948 0.85816918 0.907205384 0.885581909 0.787497923 1.139127395 1 17.91137868 1.7241729 11.52042261 1.067149169 0.890271916 0.425287591 0.085521357 0.08797059 41.36428942 0.046921024 0.0220632 52.98743543 -1.7241729 -0.176877253 GLGSS(ph)PDLELLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GLGSSPDLELLLR 13 0 Q9NQQ7-2;Q9NQQ7;Q9NQQ7-3 Q9NQQ7-2 SLC35C2 Solute carrier family 35 member C2 1 GLGS(0.002)S(0.998)PDLELLLR;GLGS(0.362)S(0.638)PDLELLLR;GLGS(0.021)S(0.979)PDLELLLR 247.14 3.17E-17 157458000 330158 265620 158302 197611 257770 279089 240343 373958 293786 TRUE FALSE 286526.7838 263875.1247 234857.3767 242481.5978 252640.8813 289825.7344 217034.5729 293989.9918 259054.9538 1.106046341 1.018606751 0.90659288 0.936023783 0.975240495 1.1187809 0.837793563 1.134855704 1 17.98289865 GLGTDEDS(ph)LIEIICSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLGTDEDSLIEIICSR 16 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;A6NMY6;H0YL33;H0YNP5;H0YN28;H0YKS4;H0YNA0;H0YMM1;H0YN52;H0YLE2 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 1 GLGTDEDS(1)LIEIICSR 147.64 5.06E-06 0 31262 22411 16505 22463 25303 27587 23863 28916 29492 TRUE FALSE 27130.64749 22263.78067 24486.87321 27563.56748 24799.5198 28648.28974 21548.76993 22732.53842 26005.48936 1.043266178 0.856118505 0.941604016 1.059913432 0.953626346 1.101624713 0.828623897 0.874143844 1 14.66652857 2.21639204 24.99850403 0.892331265 0.985441969 0.219364034 0.08029712 353.1366435 398213.1874 0.032457948 0.021901705 164.5856777 -2.21639204 0.093110705 GLGTDEDSLIEIICSR ddPTM_MDA-MB-175_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 ;;; 228.78 8.81E-15 247799000 398084 362216 255837 363184 365282 387796 178072 403159 476915 FALSE TRUE 345476.1908 359836.5792 379560.6289 445650.4781 358013.6029 402714.7631 160802.6048 316946.5852 420534.652 0.821516584 0.855664515 0.902566833 1.059723559 0.851329614 0.957625635 0.382376587 0.753675312 1 18.68186516 GLGTDEDTIIDIITHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GLGTDEDTIIDIITHR 16 0 E5RK69;P08133;P08133-2 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ;;;;; 234.66 1.11E-19 1065571000 858013 847530 723467 1014198 1028243 1265884 433826 973699 1433068 FALSE TRUE 744624.4081 841962.5196 1073338.061 1244487.157 1007782.976 1314583.377 391753.6213 765481.0462 1263652.334 0.589263667 0.666292854 0.849393486 0.984833505 0.797516017 1.040304633 0.310016933 0.605768712 1 20.26916816 4.439808299 5.881237485 0.770048237 0.606428742 0.091758696 0.215531276 0.47065856 43.06956291 0.057472836 0.16364837 27530.13231 -4.439808299 -0.163619495 GLGTDEDTLIEILASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GLGTDEDTLIEILASR 16 0 P04083;Q5T3N1 P04083 ANXA1 Annexin A1;Annexin 0 ;;;; 177.1 6.99E-09 178381000 164398 158419 115292 148924 150932 169670 103005 180703 180223 FALSE TRUE 142672.3878 157378.3352 171047.5968 182739.4704 147928.7485 176197.3147 93015.59095 142061.0697 158917.2423 0.897777898 0.990316299 1.076331268 1.149903357 0.930853987 1.108736297 0.585308363 0.893931128 1 17.27791614 2.280027463 24.99993056 0.83043168 1.027689222 0.354559653 0.12666366 154.4354876 93106.95146 0.046414036 0.035951813 190.5581217 -2.280027463 0.197257541 GLGTDEESILTLLTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLGTDEESILTLLTSR 16 0 P08758;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 ; 263.44 1.41E-26 55934000 71530 70769 38142 34619 49016 50920 40919 56042 78702 FALSE TRUE 62077.12927 70304.11378 56587.59878 42479.77307 48040.6775 52878.92535 36950.68168 44057.85442 69397.93922 0.894509692 1.013057658 0.815407481 0.612118653 0.692249338 0.761966795 0.532446382 0.634858253 1 16.0826052 4.009424416 4.548427515 0.689902643 0.95026583 0.393329574 0.12591235 0.17369747 9.278643227 0.032681454 0.06714303 10219.37688 -4.009424416 0.260363188 GLHQSIEEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 175.15 2.89E-06 3262400000 2013220 2283840 920380 1299630 2434200 2911570 1978690 2212650 2203270 FALSE TRUE 1747167.876 2268837.305 1365478.846 1594730.855 2385764.182 3023579.982 1786796.948 1739492.016 1942801.931 0.89930314 1.167817094 0.702839968 0.820840679 1.228001756 1.556298629 0.919701036 0.895352217 1 20.88970739 3.247107287 24.99870611 1.098614588 0.903075692 0.201135267 0.217619822 394.3589399 1153479.68 0.069564496 0.088358823 1766.474151 -3.247107287 -0.195538896 GLHSENREDEGWQVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GLHSENREDEGWQVYR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 ;; 229.23 2.03E-15 1164100000 511300 577740 360058 386680 513534 617730 466902 533550 305135 FALSE TRUE 443730.4095 573944.7879 534183.2531 474481.604 503315.6781 641494.4728 421621.9159 419454.4846 269062.2879 1.649173554 2.133129813 1.985351635 1.763463798 1.87062885 2.38418575 1.567004872 1.558949371 1 18.03758067 1.375599086 1.40364011 0.77274863 1.949849601 0.638602876 0.224831495 0.588754681 1.290577847 0.945291894 0.065170456 23.74647147 -1.375599086 1.177100971 GLHVVEVTYDDVPIPNS(ph)PFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLHVVEVTYDDVPIPNSPFK 20 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 1 GLHVVEVTYDDVPIPNS(1)PFK 123.63 1.83E-05 101530000 194890 180260 146320 157840 190720 184710 214860 249310 231270 TRUE FALSE 169134.7927 179075.8602 217080.8414 193679.9844 186925.0451 191815.9132 194022.9103 195996.9966 203929.5241 0.829378647 0.878126211 1.064489521 0.949739795 0.916615904 0.940599033 0.951421385 0.961101623 1 17.63771113 4.462060376 24.7497992 0.964378634 0.8415655 0.595287031 0.040386003 118.7616881 195163.2369 0.010012887 0.02651286 28977.46409 -4.462060376 -0.122813133 GLIAEAAQLGPVGGVFNLAVVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GLIAEAAQLGPVGGVFNLAVVLR 23 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;; 170.49 5.19E-19 488303000 304782.7 309203.2 279215.7 212619.7 270881.4 310991.7 334531 360307.2 331289.7 FALSE TRUE 264504.894 307172.0238 414245.3464 260898.2526 265491.3901 322955.7519 302088.2351 283258.3092 292125.0091 0.905451042 1.051508821 1.418041364 0.893104816 0.908828008 1.105539553 1.034106036 0.969647584 1 18.15622635 GLIHPDDSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GLIHPDDSVK 10 0 Q16401-2;Q16401 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ;; 125.48 0.00040796 1103750000 2286150 2005090 1443980 1663100 2105180 2188140 2077770 2412250 2309960 FALSE TRUE 1984029.485 1991918.432 2142293.558 2040732.274 2063291.037 2272319.162 1876268.185 1896409.11 2036879.16 0.974053603 0.977926659 1.051752897 1.001891675 1.012966835 1.115588596 0.921148501 0.93103663 1 20.95792896 2.176027298 25 0.945393264 1.020324963 0.35844671 0.044933803 68.42364146 27353.99647 0.018271047 0.01231834 149.9779103 -2.176027298 0.074931698 GLKPSCTIIPLMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 140.1 3.57E-05 739990000 2160400 1960000 1471000 1610800 1861400 1853100 2394600 2721600 2366200 FALSE TRUE 1874897.666 1947124.631 2182380.52 1976556.76 1824361.782 1924389.956 2162372.061 2139607.02 2086470.532 0.898597722 0.933214537 1.045967574 0.947320717 0.87437697 0.922318301 1.036377954 1.025467164 1 20.99263311 2.237318705 24.99956833 1.022282698 0.93937578 0.431950243 0.045150228 33.45760764 673470.215 0.019025776 0.013635274 172.7104856 -2.237318705 -0.082906917 GLKYELISETGGSHDKR ddPTM_MDA-MB-175_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 0 131.82 1.54E-05 606020000 1543600 1229100 518170 700170 1125900 919720 1519000 1645100 436400 FALSE TRUE 1339609.349 1221025.961 768758.7452 859154.2999 1103496.793 955102.2235 1371687.614 1293308.167 384809.2891 3.48122924 3.173067791 1.99776556 2.232675572 2.867645932 2.482014469 3.564590701 3.360906827 1 18.5537841 GLLAQGLRPES(ph)PPPAGPLLNGAPAGES(ph)PQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GLLAQGLRPESPPPAGPLLNGAPAGESPQPK 31 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 2 GLLAQGLRPES(1)PPPAGPLLNGAPAGES(1)PQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGES(1)PQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGES(1)PQPK 133.71 1.51E-06 541950000 498190 498570 343530 446090 523100 409680 551310 711000 583140 TRUE FALSE 432352.9292 495294.8608 509662.257 547381.5526 512691.3334 425440.6547 497844.0411 558958.183 514201.8535 0.840823358 0.963230407 0.991171567 1.064526603 0.997062399 0.827380632 0.968187955 1.087040389 1 18.97197529 GLLAQGLRPES(ph)PPPAGPLLNGAPAGESPQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GLLAQGLRPESPPPAGPLLNGAPAGESPQPK 31 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK 225.51 2.27E-35 15368070000 4259930 3844950 2769500 3341410 3836330 3139220 4380890 5355020 4611440 TRUE FALSE 3696969.457 3819692.27 4108839.463 4100128.211 3759994.539 3259987.825 3956031.962 4209890.646 4066280.817 0.909177114 0.939357718 1.010466234 1.00832392 0.924676555 0.801712418 0.972887053 1.035317243 1 21.95527842 1.998043316 24.99968896 1.015357558 0.934940247 0.270297102 0.057986428 103.5860955 1323479.337 0.025988171 0.017223211 99.55047033 -1.998043316 -0.080417311 GLLASDLNTDGDMRVT(ph)PEPGAGPTQGLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GLLASDLNTDGDMRVTPEPGAGPTQGLLR 29 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JHD7;C9JJK9;C9JMI3;C9JGN4;V9GYX5;C9JVY3;V9GY85;H7C3H1 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 1 GLLASDLNTDGDMRVT(1)PEPGAGPTQGLLR;GLLASDLNTDGDMRVT(1)PEPGAGPTQGLLR;GLLASDLNTDGDMRVT(1)PEPGAGPTQGLLR;GLLASDLNTDGDMRVT(1)PEPGAGPTQGLLR;GLLASDLNTDGDMRVT(1)PEPGAGPTQGLLR;GLLASDLNTDGDMRVT(1)PEPGAGPTQGLLR 217.93 3.89E-34 3686130000 2147980 1969700 1369870 1472330 1876390 2196670 1796350 2067520 1804720 TRUE FALSE 1864119.001 1956760.911 2032343.714 1806645.03 1839053.51 2281177.316 1622140.253 1625396.937 1591368.058 1.171394004 1.229609267 1.277104755 1.135277927 1.155643097 1.433469338 1.019336945 1.021383413 1 20.60183612 2.099540121 16.56725301 1.014662277 1.227501855 0.609557759 0.082975714 0.842170048 136.4925618 0.032761746 0.022087973 125.7593028 -2.099540121 0.212839579 GLLDAAHFCYLMAQAGFGVYTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLLDAAHFCYLMAQAGFGVYTK 22 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 0 167.24 1.08E-11 36453000 94081 85892 47546 74471 76905 68105 85219 110020 98025 FALSE TRUE 81647.95748 85327.7698 70539.40463 91380.77877 75374.74096 70725.04342 76954.4745 86493.07918 86436.59617 0.944599407 0.987171795 0.816082629 1.057200108 0.872023475 0.818230316 0.890299687 1.000653462 1 16.39935464 1.685030284 6.123546846 1.000904683 0.911945055 0.200353526 0.07297165 0.210668793 17.04682473 0.044435842 0.018629881 48.42061312 -1.685030284 -0.088959628 GLLDDLRNDLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GLLDDLRNDLDR 12 1 Q07065 Q07065 CKAP4 Cytoskeleton-associated protein 4 0 ;;;; 103.97 0.0019955 323589500 461695 442648 238315 287084 516950 572785 317330 594375 125454.4 FALSE TRUE 400680.836 439740.2161 353564.9311 352270.81 506663.7064 594820.4096 286555.3854 467272.5317 110623.3238 3.622028541 3.975113034 3.196115603 3.184417156 4.580080305 5.376989132 2.590370419 4.223996494 1 16.75529607 4.287532913 24.98769816 3.57295819 3.798569849 0.006554159 1.184791417 1131.958395 577552.8696 0.28598067 0.756631003 19387.99561 -4.287532913 0.225611659 GLLDKFPLFTAVYQICYESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLLDKFPLFTAVYQICYESR 20 1 Q8N335 Q8N335 GPD1L Glycerol-3-phosphate dehydrogenase 1-like protein 0 115.76 9.56E-05 139820000 104980 108570 81953 91854 97137 73559 122400 118400 156870 FALSE TRUE 91106.62701 107856.7965 121585.7449 112710.8546 95204.16375 76388.86233 110529.6668 93081.08139 138325.0073 0.658641765 0.779734616 0.878986 0.814826305 0.688264296 0.552241882 0.799057734 0.672915789 1 17.07770247 1.230603506 24.992729 1.000000487 0.733000578 0.451359623 0.093315052 299.0671075 939271.7254 0.25412687 0.023708067 17.00605214 -1.230603506 -0.26699991 GLLEFEHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GLLEFEHQR 9 0 Q14697;F5H6X6;Q14697-2;E9PKU7;E9PNH1 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;; 257.93 4.92E-15 4005460000 4367130 3894190 3086000 3053270 3865230 5249760 3206060 3068870 2965250 FALSE TRUE 3790002.706 3868608.809 4578399.922 3746561.62 3788319.485 5451721.664 2895136.795 2412616.032 2614701.523 1.449497265 1.479560392 1.751022012 1.432883098 1.448853512 2.085026385 1.107253264 0.922711832 1 21.31821484 2.026053515 21.52623458 0.973579331 1.593548303 0.675077643 0.197238734 24.20255256 19996.48755 0.077697662 0.052378261 106.1826392 -2.026053515 0.619968972 GLLEPLGLECTFIDDISAYHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLLEPLGLECTFIDDISAYHK 21 0 Q9Y2J8 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 182.34 4.71E-17 564850000 1612200 1574100 809260 1183300 1464700 1374200 1560000 1916600 1581400 FALSE TRUE 1399143.685 1563759.633 1200620.843 1451986.351 1435555.336 1427066.363 1408711.44 1506750.005 1394448.694 1.003366916 1.121417834 0.861000371 1.041261939 1.029478777 1.023391086 1.010228233 1.08053456 1 20.41126342 GLLHSFDLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLLHSFDLLK 10 0 F8WAE5;Q9BY44-4;Q9BY44-3;Q9BY44;H7C5Q3;C9IZE1 F8WAE5 EIF2A "Eukaryotic translation initiation factor 2A;Eukaryotic translation initiation factor 2A, N-terminally processed" 0 ; 195.79 3.45E-07 300300000 568510 977930 624540 740610 898450 798100 984500 1068140 1133140 FALSE TRUE 493379.9631 971505.9134 926569.633 908776.82 880572.6028 828803.4234 889023.3415 839726.5733 999181.4801 0.493784135 0.972301762 0.92732867 0.909521281 0.881293959 0.829482371 0.889751621 0.840414469 1 19.93038721 4.745028994 24.9981875 0.897924136 0.493783953 0.856301482 0.053004859 274.6266149 1061315.168 0.012964709 0.120139236 55594.13712 -4.745028994 -0.404140182 GLLPGGTQVLDGTSGFS(ph)PAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GLLPGGTQVLDGTSGFSPAPK 21 0 Q96S94;Q96S94-3 Q96S94 CCNL2 Cyclin-L2 1 GLLPGGTQVLDGTSGFS(1)PAPK;GLLPGGTQVLDGTSGFS(1)PAPK;GLLPGGTQVLDGTSGFS(1)PAPK 273.42 1.08E-44 316728000 736383 617862 439574 526578 578065 518870 668735 798711 773554 TRUE FALSE 639068.1208 613803.2238 652153.4567 646145.5831 566562.6375 538831.2647 603881.1826 627912.8682 682105.3274 0.936905336 0.899865753 0.956089083 0.947281244 0.830608727 0.789953169 0.885319552 0.920551186 1 19.379635 3.280564764 24.99993292 0.884930243 0.934027114 0.16250959 0.05609439 307.4507682 182985.8143 0.01761531 0.022741084 1907.940222 -3.280564764 0.049096872 GLLPGLLPAPADKLT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLLPGLLPAPADKLTPK 17 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GLLPGLLPAPADKLT(1)PK 102.33 0.001541 146230000 206780 197130 168700 170880 166370 110540 254420 270890 230450 TRUE FALSE 179453.4991 195835.0401 250283.8843 209680.9157 163059.5625 114792.5453 229746.3876 212962.2816 203206.4635 0.883109208 0.963724464 1.231672851 1.031861448 0.802432953 0.564905975 1.130605708 1.048009388 1 17.63258677 GLLS(ph)CLS(ph)KS(ph)NNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLLSCLSKSNNR 12 1 Q8N4B4 Q8N4B4 FBXO39 F-box only protein 39 3 GLLS(1)CLS(1)KS(1)NNR 65.563 0.049259 117210000 73335 79345 48642 57171 79366 74115 59273 64033 68484 TRUE FALSE 63643.59394 78823.77747 72165.4339 70152.54935 77786.77188 76966.25201 53524.71358 50340.04126 60387.89954 1.053913026 1.305290929 1.195031363 1.161698782 1.288118522 1.274531034 0.886348325 0.833611396 1 15.88197187 2.232905367 24.99802101 0.890590067 1.21754049 0.752246874 0.082706544 58.22083105 257351.473 0.031730328 0.022059565 170.9642742 -2.232905367 0.326950423 GLLS(ph)ILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLLSILR 7 0 P36405 P36405 ARL3 ADP-ribosylation factor-like protein 3 1 GLLS(1)ILR;GLLS(1)ILR 64.567 0.076518 18667900 47439 56960 30895 40146 50321 24648 60884 55684 70477 TRUE FALSE 41169.81595 56585.82601 45835.92534 49261.76289 49319.71055 25596.22451 54979.47905 43776.40993 62145.28935 0.662476857 0.910540873 0.737560736 0.792686999 0.793619453 0.411877148 0.884692623 0.704420406 1 15.92335742 1.233499593 24.68213478 1.000000474 0.741361868 0.264035033 0.137716508 189.9532725 926256.5538 0.258762152 0.031896421 17.11983573 -1.233499593 -0.258638606 GLLS(ph)PPMGQSGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GLLSPPMGQSGLR 13 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 GLLS(0.946)PPMGQS(0.054)GLR;GLLS(1)PPMGQSGLR;GLLS(1)PPMGQSGLR;GLLS(1)PPMGQSGLR 150.05 4.62E-05 1440913000 874970 907870 569270 685770 920860 933590 830360 970830 822590 TRUE FALSE 759340.4976 901906.1422 844570.8761 841484.5598 902536.6876 969505.8114 749831.815 763225.5595 725344.3473 1.046868981 1.243417896 1.164372314 1.160117347 1.244287201 1.336614554 1.033759783 1.052225143 1 19.46830653 2.197519681 24.62259 1.033782748 1.199964965 0.53614622 0.074759006 98.20019604 58914.62677 0.030064291 0.020269613 157.5867434 -2.197519681 0.166182218 GLLSDS(ph)MTDVPVDTGVAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLLSDSMTDVPVDTGVAAR 19 0 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;A0A087WZ51;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 1 GLLS(0.017)DS(0.975)MT(0.008)DVPVDTGVAAR;GLLS(0.002)DS(0.947)MT(0.051)DVPVDTGVAAR 127.29 9.27E-05 285760000 509450 420410 217919 224980 273530 237239 243650 299340 379890 TRUE FALSE 442124.8917 417648.299 323305.3573 276065.1476 268087.2882 246365.7378 220020.8605 235328.4705 334979.837 1.319855236 1.246786382 0.965148709 0.82412467 0.800308731 0.735464379 0.656818221 0.702515329 1 18.35371473 4.133130997 1.440509741 0.757819541 1.360799218 0.832122371 0.091532003 0.186833968 0.680842314 0.027927492 0.11884449 13587.23217 -4.133130997 0.602979678 GLLSGQT(ph)SPTNAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLLSGQTSPTNAK 13 0 G3V1P3;Q969J3 G3V1P3 LOH12CR1 Loss of heterozygosity 12 chromosomal region 1 protein 1 GLLSGQT(0.771)S(0.229)PTNAK;GLLSGQT(0.677)S(0.323)PTNAK 225.21 1.43E-10 144260000 705270 633000 446000 555740 675300 571770 682030 937930 758600 TRUE FALSE 612066.7826 628841.7813 661687.0918 681929.261 661862.8512 593766.3619 615886.8356 737360.9685 668919.1722 0.915008581 0.940086347 0.989188409 1.019449418 0.98945116 0.887650387 0.920719365 1.10231699 1 19.35147237 1.744333682 25 1.052606353 0.954249396 0.443668338 0.046247699 1.034531046 4500.979418 0.025769764 0.012374995 55.50520131 -1.744333682 -0.098356957 GLLSNHTGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GLLSNHTGSPR 11 0 Q13111 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 GLLSNHT(0.001)GS(0.999)PR;GLLSNHT(0.01)GS(0.99)PR;GLLSNHT(0.152)GS(0.848)PR;GLLSNHT(0.079)GS(0.921)PR 121.45 0.00026498 1597840000 1572830 1797390 764800 1332950 1934300 1945040 1590620 1951910 2234970 TRUE FALSE 1364976.53 1785582.827 1134659.838 1635616.67 1895811.214 2019866.947 1436361.917 1534509.236 1970754.393 0.692616257 0.906040262 0.575748983 0.82994445 0.96197234 1.024920688 0.728838623 0.778640526 1 20.91031656 3.488398082 24.85697603 0.879082428 0.736245844 0.292263932 0.121067153 777.3317864 1713434.757 0.034902049 0.048487118 3078.917715 -3.488398082 -0.142836584 GLLYDS(ph)DEEDEERPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 GLLYDSDEEDEERPAR 16 1 P49736 P49736 MCM2 DNA replication licensing factor MCM2 1 GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR 359.6 2.81E-87 67752580000 8982530 8537510 6108496 6819469 8229130 8524400 7823340 9102820 9681150 TRUE FALSE 7795465.902 8481426.535 9062585.097 8367933.666 8065386.413 8852339.184 7064633.691 7156252.781 8536655.476 0.913175649 0.993530377 1.061608393 0.980235607 0.944794649 1.036979788 0.827564579 0.838297012 1 23.02523953 2.238757342 25 0.875592463 0.989597384 0.359418367 0.061964365 4.922786558 625722.3434 0.024024075 0.017415687 173.283552 -2.238757342 0.114004922 GLLYDS(ph)DEEDEERPARK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GLLYDSDEEDEERPARK 17 2 P49736 P49736 MCM2 DNA replication licensing factor MCM2 1 GLLY(0.003)DS(0.997)DEEDEERPARK;GLLYDS(1)DEEDEERPARK;GLLYDS(1)DEEDEERPARK;GLLYDS(1)DEEDEERPARK;GLLYDS(1)DEEDEERPARK;GLLYDS(1)DEEDEERPARK 247.89 4.41E-21 3076480000 1872490 1701720 817312 931790 1571530 1462750 1794230 2035160 684431 TRUE FALSE 1625035.702 1690541.289 1212566.817 1143367.161 1540259.628 1519022.939 1620225.851 1599956.872 603518.3469 2.692603648 2.80114316 2.00916314 1.894502739 2.552133892 2.516945751 2.684633962 2.651049268 1 19.2030381 4.254679474 24.87444573 2.269408664 2.746873757 0.161511489 0.503856349 475.9575452 734478.9699 0.125433215 0.329582965 17975.43768 -4.254679474 0.477465093 GLMAGGRPEGQYS(ph)EDEDT(ph)DTDEYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLMAGGRPEGQYSEDEDTDTDEYK 24 1 Q9NPQ8-4;Q9NPQ8;Q9NPQ8-3;Q9NPQ8-2;H0YE35;H0YC88 Q9NPQ8-4 RIC8A Synembryn-A 2 GLMAGGRPEGQYS(1)EDEDT(0.994)DT(0.006)DEYK;GLMAGGRPEGQYS(1)EDEDT(0.998)DT(0.002)DEYK 209.05 1.31E-24 513830000 683070 542660 550080 591740 558890 530400 617670 729110 1403690 TRUE FALSE 592800.5688 539095.2307 816100.5279 726103.6112 547769.1824 550804.8312 557768.4585 573195.5004 1237747.367 0.478935027 0.435545447 0.659343376 0.586633129 0.4425533 0.44500586 0.450631909 0.463095714 1 20.23928545 1.236397208 24.99931509 1.000000649 0.49452822 0.826822004 0.072601072 24.70959884 285461.6342 0.122341367 0.01901232 17.23444124 -1.236397208 -0.505472429 GLMAGGRPEGQYS(ph)EDEDT(ph)DTDEYKEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLMAGGRPEGQYSEDEDTDTDEYKEAK 27 2 Q9NPQ8-4;Q9NPQ8;Q9NPQ8-3;Q9NPQ8-2;H0YE35;H0YC88 Q9NPQ8-4 RIC8A Synembryn-A 2 GLMAGGRPEGQYS(1)EDEDT(0.988)DT(0.012)DEYKEAK;GLMAGGRPEGQYS(1)EDEDT(1)DTDEYKEAK 224.57 3.51E-34 468310000 396130 316600 283190 227860 297180 238590 455890 482690 243670 TRUE FALSE 343780.4168 314520.2338 420141.6312 279599.0956 291266.6994 247768.7117 411677.858 379470.4998 214863.6102 1.599993673 1.463813409 1.955387563 1.301286409 1.355588781 1.153144134 1.915996188 1.766099431 1 17.71306164 3.705614983 24.99677612 1.469763389 1.652140159 0.127358294 0.294284409 1827.340701 1386454.662 0.085452279 0.126755109 5077.091411 -3.705614983 0.18237677 GLMAGGRPEGQYS(ph)EDEDTDTDEYKEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLMAGGRPEGQYSEDEDTDTDEYKEAK 27 2 Q9NPQ8-4;Q9NPQ8;Q9NPQ8-3;Q9NPQ8-2;H0YE35;H0YC88 Q9NPQ8-4 RIC8A Synembryn-A 1 GLMAGGRPEGQYS(1)EDEDTDTDEYKEAK;GLMAGGRPEGQYS(1)EDEDTDTDEYKEAK 253.26 4.40E-53 389050000 467870 359820 272040 259900 345590 242180 515300 588210 166791 TRUE FALSE 406039.7941 357456.3187 403599.4539 318914.2673 338713.4351 251496.8213 465326.2853 462425.869 147073.158 2.760801492 2.430466059 2.744208797 2.168405654 2.303026873 1.710011703 3.16391034 3.144189431 1 17.16617444 3.752512074 23.8988945 2.378667054 2.623689471 0.054508286 0.638665766 2146.094274 3676247.398 0.175057403 0.300929633 5656.034815 -3.752512074 0.245022416 GLNPDGTPALSTLGGFS(ph)PASKPS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLNPDGTPALSTLGGFSPASKPSSPR 26 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 2 GLNPDGT(0.009)PALS(0.032)T(0.014)LGGFS(0.923)PAS(0.027)KPS(0.524)S(0.472)PR 77.308 0.012557 1068600000 207070 153060 137370 177330 259050 183180 260790 292960 233250 TRUE FALSE 179705.1749 152054.5388 203802.5915 217595.4868 253895.4118 190227.0531 235498.6259 230312.7838 205675.4507 0.873731766 0.739293573 0.990894104 1.057955561 1.234446848 0.924889443 1.145001142 1.119787427 1 17.65001008 4.048826859 3.503924646 1.086339768 0.807441308 0.609704784 0.088965576 0.137555638 3.487764378 0.022381516 0.050266195 11189.91685 -4.048826859 -0.27889846 GLNPDGTPALSTLGGFSPASKPSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLNPDGTPALSTLGGFSPASKPSSPR 26 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 1 GLNPDGTPALSTLGGFSPAS(0.003)KPS(0.197)S(0.8)PR;GLNPDGTPALSTLGGFSPAS(0.007)KPS(0.183)S(0.81)PR 179.2 1.41E-17 793090000 607580 650950 501850 706550 883070 747610 973330 1032440 914470 TRUE FALSE 527286.7636 646673.8666 744546.3386 866982.9764 865498.6347 776371.0405 878936.6064 811660.7405 806362.3984 0.653907926 0.801964313 0.923339605 1.075177833 1.073337046 0.962806602 1.090001975 1.006570671 1 19.62106884 4.340356719 1.667058881 1.033780174 0.641251592 0.90367187 0.042213206 0.134356295 0.613896611 0.011636529 0.066997163 21895.59338 -4.340356719 -0.392528582 GLNSSFETS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GLNSSFETSPK 11 0 M0QXD7;M0R025;M0QYG0;M0QYA8;Q8IV63-2;Q8IV63;M0QZ79 M0QXD7 VRK3 Inactive serine/threonine-protein kinase VRK3 1 GLNSSFET(0.05)S(0.95)PK;GLNSSFET(0.045)S(0.955)PK;GLNSSFET(0.137)S(0.863)PK;GLNSSFET(0.051)S(0.949)PK 144.97 3.83E-05 590712000 1661290 1558340 1131600 1260210 1762280 1442430 1777750 2099900 1821110 TRUE FALSE 1441746.317 1548103.162 1678845.545 1546359.942 1727214.076 1497921.215 1605344.079 1650852.726 1605820.45 0.897825356 0.964057446 1.045475255 0.962971882 1.075596014 0.93280741 0.999703347 1.028043158 1 20.61487916 4.58778186 3.318494728 1.006325808 0.897182436 0.430095057 0.039958472 0.237676963 4.351127522 0.009246434 0.051978234 38706.31798 -4.58778186 -0.109143371 GLNTS(ph)QESDDDILDESSSPEGTQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLNTSQESDDDILDESSSPEGTQK 24 0 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 GLNT(0.189)S(0.518)QES(0.293)DDDILDESSSPEGTQK 54.537 0.024645 0 412240 222610 183790 207410 262090 238380 275920 314740 320950 TRUE FALSE 357761.4395 221147.6603 272671.4587 254505.6106 256874.9218 247550.6329 249161.3209 247435.3003 283007.6566 1.264140496 0.781419354 0.963477321 0.899288781 0.907660679 0.874713553 0.880404876 0.874306029 1 18.11048156 4.749845467 24.99997401 0.896728891 1.26414071 0.80025797 0.057538941 686.2026432 1520155.201 0.012813105 0.19394877 56214.12658 -4.749845467 0.367411819 GLNVIGASDQS(ph)PLQS(ph)PSNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLNVIGASDQSPLQSPSNLR 20 0 Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;A0JP02;B4DJX4;Q9HAU0-5;Q9HAU0-8;H0YGJ6 Q9HAU0 PLEKHA5 Pleckstrin homology domain-containing family A member 5 2 GLNVIGAS(0.007)DQS(0.993)PLQS(0.999)PS(0.001)NLR;GLNVIGAS(0.001)DQS(0.999)PLQS(1)PSNLR 173.03 8.01E-12 121162000 234810 212663 167335 187809 235590 251770 227852 276700 261850 TRUE FALSE 203779.2636 211266.0028 248258.7657 230453.9039 230902.2199 261455.7548 205754.9481 217529.8583 230894.3913 0.882564806 0.914989756 1.075204834 0.998092256 1.000033906 1.132360788 0.891121464 0.942118416 1 17.8168736 4.419948672 9.260984489 0.997795604 0.89058697 0.314985962 0.065536897 0.371465918 56.30478762 0.017081512 0.045433363 26299.57146 -4.419948672 -0.107208634 GLNVIGASDQS(ph)PLQSPSNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLNVIGASDQSPLQSPSNLR 20 0 Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;A0JP02;B4DJX4;Q9HAU0-5;Q9HAU0-8;H0YGJ6 Q9HAU0 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 GLNVIGASDQS(1)PLQSPSNLR 239.09 3.09E-27 0 65141 65557 46235 61618 71192 71084 57419 68925 67085 TRUE FALSE 56532.4518 65126.35175 68594.40065 75609.30867 69775.41848 73818.64748 51850.51422 54185.92512 59154.28772 0.955678007 1.100957416 1.159584593 1.27817123 1.179549635 1.2479002 0.876530108 0.916010102 1 15.85219512 2.232442963 24.99999533 0.925492544 1.158353919 0.568329616 0.091430633 105.3575883 430541.9992 0.038391234 0.026624943 170.7823414 -2.232442963 0.232861375 GLPLGSAVSS(ph)PVLFS(ph)PVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLPLGSAVSSPVLFSPVGR 19 0 Q8WUM0 Q8WUM0 NUP133 Nuclear pore complex protein Nup133 2 GLPLGSAVS(0.068)S(0.932)PVLFS(1)PVGR;GLPLGSAVS(0.089)S(0.911)PVLFS(1)PVGR 293.83 1.87E-49 91661000 135999 141677 110199 131162 136131 141802 121430 157854 233770 TRUE FALSE 118026.3876 140746.3145 163491.605 160944.3368 133422.2594 147257.2147 109653.7373 124098.1505 206133.9769 0.572571244 0.682790467 0.793132736 0.780775393 0.64725991 0.714376237 0.531953727 0.602026664 1 17.6532228 1.231894519 24.99815531 1.000000566 0.665436384 0.611678547 0.08373137 175.1818788 656878.2536 0.211158797 0.022379271 17.05668067 -1.231894519 -0.334564182 GLPPS(ph)MER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 GLPPSMER 8 0 P38159;P38159-2;H3BUY5 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 1 GLPPS(1)MER;GLPPS(1)MER;GLPPS(1)MER;GLPPS(1)MER;GLPPS(1)MER;GLPPS(1)MER;GLPPS(1)MER;GLPPS(1)MER;GLPPS(1)MER;GLPPS(1)MER;GLPPS(1)MER 134.23 0.00092897 8839400000 6713650 6531910 4958450 4914530 6527770 7625290 6223530 6680170 7237970 TRUE FALSE 5826424.142 6489001.453 7356373.005 6030449.15 6397880.148 7918639.841 5619973.018 5251667.631 6382305.432 0.912902744 1.016717473 1.152620018 0.944870034 1.002440296 1.240717782 0.880555323 0.822848058 1 22.60564622 2.104830317 20.19960936 0.883776807 1.043717724 0.294047426 0.103936299 3.061821694 576.9672534 0.041469068 0.027958458 127.300561 -2.104830317 0.159940918 GLPRPDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLPRPDNR 8 1 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 75.213 0.035543 168240000 248310 251060 174080 202370 235130 294270 296400 334010 321270 FALSE TRUE 215495.2044 249410.7703 258265.6703 248321.2015 230451.373 305590.7573 267655.1736 262584.5608 283289.8266 0.760688116 0.880408497 0.911665884 0.876562369 0.8134827 1.078721255 0.944810397 0.926911368 1 18.11191927 2.758974845 24.99762657 0.974113954 0.855392189 0.586078833 0.057412307 673.1163046 824243.3011 0.018663229 0.018640853 574.0832098 -2.758974845 -0.118721765 GLPSPYNMSS(ph)APGS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 GLPSPYNMSSAPGSR 15 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 2 GLPSPYNMS(0.003)S(0.997)APGS(1)R;GLPSPYNMS(0.006)S(0.994)APGS(1)R;GLPSPYNMS(0.063)S(0.937)APGS(1)R;GLPSPYNMS(0.005)S(0.995)APGS(1)R;GLPSPYNMS(0.003)S(0.997)APGS(1)R;GLPSPYNMS(0.004)S(0.996)APGS(1)R;GLPSPYNMS(0.005)S(0.995)APGS(1)R;GLPSPYNMS(0.015)S(0.985)APGS(1)R;GLPSPYNMS(0.144)S(0.856)APGS(1)R 214.81 5.41E-12 3344010000 7916640 6375310 3936701 3244593 5126350 6380650 4509240 4856710 4465180 TRUE FALSE 6870435.966 6333430.169 5840502.771 3981327.431 5024345.665 6626117.734 4071934.599 3818140.361 3937311.507 1.744956159 1.608567206 1.483373302 1.011179183 1.276085383 1.682904114 1.034191628 0.969732863 1 21.90877943 8 0.128205006 0.56631315 4.413581709 0.534699554 0.20662404 162.9963018 1.836258862 6.348858384 112.0914744 100000000 -8 3.847268559 GLPSPYNMSS(ph)APGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GLPSPYNMSSAPGSR 15 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 GLPSPYNMS(0.036)S(0.599)APGS(0.366)R;GLPSPYNMS(0.188)S(0.648)APGS(0.164)R;GLPSPYNMS(0.042)S(0.855)APGS(0.103)R;GLPSPYNMS(0.091)S(0.908)APGS(0.001)R;GLPSPYNMS(0.028)S(0.972)APGSR 142.62 4.78E-06 6125090000 3579300 2735670 1737590 1621520 2312870 2395870 2289210 2558890 1979780 TRUE FALSE 3106286.436 2717699.204 2577894.336 1989710.899 2266848.412 2488040.669 2067202.767 2011691.287 1745732.664 1.77935975 1.556767116 1.476683337 1.139756929 1.298508334 1.425212875 1.184146238 1.152347853 1 20.73540122 8 0.308489399 1.092831243 7.373996259 0.784143941 0.10759053 37.71752729 0.599068498 0.206666795 129.6537869 100000000 -8 6.281165016 GLPSPYNMSSAPGS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GLPSPYNMSSAPGSR 15 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 GLPSPYNMSSAPGS(1)R;GLPSPYNMS(0.007)S(0.034)APGS(0.959)R;GLPSPYNMSS(0.001)APGS(0.999)R;GLPSPYNMSSAPGS(1)R;GLPSPYNMSSAPGS(1)R;GLPSPYNMSSAPGS(1)R;GLPSPYNMS(0.002)S(0.144)APGS(0.854)R 142.21 4.92E-06 2956990000 3266840 2515840 1526742 1577571 2289080 2465190 2120850 2335730 1801070 TRUE FALSE 2835118.817 2499313.281 2265079.538 1935782.607 2243531.787 2560027.454 1915170.293 1836252.316 1588149.556 1.78517118 1.57372665 1.426238183 1.218891885 1.412670348 1.611956156 1.205913061 1.156221282 1 20.59891535 7.081675832 0.067815853 2.35E-25 3.965679921 0.640647228 0.142608715 354.724612 2.879316608 44.35889118 156.8862012 12069126.29 -7.081675832 3.965679921 GLPSTAS(ph)GR ddPTM_MDA-MB-175_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 140.17 0.00011511 1159880000 1801470 1612970 1141770 1047040 1526230 1701470 1393340 1409730 1545130 TRUE FALSE 1563401.175 1602374.294 1693933.791 1284786.435 1495861.009 1766926.652 1258214.101 1108270.21 1362466.492 1.147478624 1.176083451 1.243284735 0.942985712 1.097906641 1.296858795 0.923482602 0.813429333 1 20.37778932 2.111264882 7.397540036 0.886340452 1.143748056 0.541865624 0.102858816 0.158247014 9.68636368 0.042260079 0.028407821 129.2007047 -2.111264882 0.257407605 GLPTGDS(ph)PLGPMTHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GLPTGDSPLGPMTHR 15 0 J3QQZ9;Q9NVS9-3;Q9NVS9;Q9NVS9-4 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 1 GLPTGDS(1)PLGPMTHR;GLPTGDS(1)PLGPMTHR;GLPT(0.012)GDS(0.988)PLGPMTHR 182.7 1.48E-11 772940000 638020 677810 511530 512650 640360 751990 656310 693210 794550 TRUE FALSE 553704.0405 673357.4215 758907.619 629055.0179 627618.0888 780919.5419 592661.1572 544972.4361 700619.2042 0.790306685 0.961089016 1.083195571 0.897855803 0.895804861 1.114613384 0.845910523 0.777843988 1 19.41827101 GLPTGDSPLGPMTHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLPTGDSPLGPMTHR 15 0 J3QQZ9;Q9NVS9-3;Q9NVS9;Q9NVS9-4 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 ; 122.78 8.10E-05 368840000 247841 257910 181208 169209 244900 243840 246518 279440 245620 FALSE TRUE 215088.1839 256215.7722 268840.7949 207630.4896 240026.9691 253220.6826 222610.7223 219683.9306 216583.0834 0.993097801 1.182990694 1.241282517 0.95866439 1.108244307 1.169161869 1.027830608 1.014317126 1 17.72456104 2.105153078 7.088793249 1.012071484 1.11123602 0.224329776 0.083558095 0.324645271 19.42981685 0.034217664 0.022977285 127.395204 -2.105153078 0.099164537 GLPVTCEVAPHHLFLSHDDLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLPVTCEVAPHHLFLSHDDLER 22 0 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 ; 225.9 1.98E-26 590280000 231216 224429 173900 138406 230933 278182 204150 228520 201210 FALSE TRUE 200660.2198 222954.7111 257998.6217 169833.1977 226337.8851 288883.8415 184351.5644 179652.7763 177423.183 1.130969563 1.256626712 1.454142673 0.957221006 1.275695099 1.628219248 1.039050034 1.012566528 1 17.43683501 2.038485362 24.99982212 1.012768109 1.279982531 0.338630497 0.175975811 175.6569504 114104.8216 0.071393251 0.048133244 109.2660798 -2.038485362 0.267214421 GLPWQSSDQDIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GLPWQSSDQDIAR 13 0 Q6NXG1;Q6NXG1-2;Q6NXG1-4;Q6NXG1-3;A0A2U3TZN9;Q6NXG1-5;H0YBR2;H0YBB3 Q6NXG1 ESRP1 Epithelial splicing regulatory protein 1 0 ;; 179.94 3.10E-05 369863000 237459 265666 159223 181906 218914 245641 251706 270813 189881 FALSE TRUE 206078.1915 263920.8226 236223.7754 223210.5376 214558.0397 255090.9682 227295.5909 212901.7474 167433.4845 1.230806324 1.576272652 1.410851456 1.33312962 1.281452395 1.523536161 1.357527687 1.271560155 1 17.35322855 1.211255982 1.796278482 0.837870847 1.395795726 0.588660118 0.10250518 0.672234957 1.918301947 0.665334576 0.027305101 16.26507171 -1.211255982 0.557924879 GLPWSCS(ph)VEDVQNFLSDCTIHDGAAGVHFIYTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR 33 0 P52597;A0A1B0GW42 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 1 GLPWS(0.128)CS(0.872)VEDVQNFLSDCTIHDGAAGVHFIYTR 146.23 5.44E-10 281530000 60068 43587 26506 33421 39198 53602 37477 51118 32930 TRUE FALSE 52129.86161 43300.67413 39324.39026 41009.74886 38418.03649 55664.10363 33842.48631 40186.8135 29037.05291 1.79528762 1.49122138 1.354283108 1.412324762 1.323069411 1.917002521 1.165493151 1.383983892 1 14.82560742 0.66986946 0.944268751 0.005470838 1.509621054 0.358457188 0.215042548 6.270413363 2.056711928 12.56990609 0.071409421 4.675945708 -0.66986946 1.504150216 GLPWSCSADEVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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" 0 180.19 3.05E-05 278750000 185260 141730 99826 108160 140360 131400 152760 182020 119560 FALSE TRUE 160777.4216 140798.9663 148102.1875 132719.3811 137567.1106 136455.043 137945.3587 143096.4395 105425.753 1.525029863 1.335527253 1.404800851 1.258889572 1.304871976 1.294323627 1.308459791 1.357319587 1 16.6858678 -1.99999866 0.053493334 7.61E-10 2.034696171 0.481059292 0.095176362 1055.671579 5.506147827 192.1052247 56.43909161 0.010000031 1.99999866 2.03469617 GLQDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GLQDLK 6 0 Q15847;Q5TBU2;O15350-6;O15350-5;O15350-13;O15350-11;O15350-8;O15350 Q15847 ADIRF;TP73 Adipogenesis regulatory factor;Tumor protein p73 0 ;;; 110.61 0.066431 4008390000 8570700 8460100 5855500 6842000 7125000 6713300 9196100 10443200 9126600 FALSE TRUE 7438060.28 8404525.046 8687239.385 8395580.673 6983226.44 6971564.995 8304263.637 8210002.949 8047663.745 0.924250878 1.044343466 1.079473455 1.043232041 0.867733377 0.86628433 1.031885017 1.020172215 1 22.9401386 4.773835275 22.1857035 0.994198523 0.924250221 0.085105881 0.072014391 11173.00548 7026586.394 0.01922068 2.840829558 59406.67906 -4.773835275 -0.069948302 GLQDVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GLQDVLR 7 0 P40227;P40227-2;Q92526-3;Q92526;Q92526-2 P40227 CCT6A;CCT6B T-complex protein 1 subunit zeta;T-complex protein 1 subunit zeta-2 0 ;; 116.3 0.012765 615850000 1613270 2250230 1388980 1433210 2131850 2373380 1833610 1990280 2374300 FALSE TRUE 1400072.282 2235448.091 2060695.374 1758642.236 2089430.356 2464685.464 1655786.784 1564674.11 2093612.959 0.66873501 1.067746587 0.984277139 0.840003511 0.998002208 1.17724026 0.790875304 0.747355954 1 20.99756333 GLQEFLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLQEFLDR 8 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ; 177.97 0.0005864 353340000 582040 557670 411070 398420 517730 581070 527940 565980 525950 FALSE TRUE 505121.9393 554006.6291 609864.8269 488887.3505 507428.1859 603424.1389 476740.4601 444949.5815 463772.7902 1.089158204 1.194564754 1.315007779 1.054152725 1.094130998 1.301120186 1.027961256 0.959412865 1 18.82305865 2.059663836 8.30652182 0.98176961 1.172651056 0.500893067 0.085164728 0.203030359 25.35026077 0.034730355 0.023342551 114.726524 -2.059663836 0.190881446 GLQEVGLPLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLQEVGLPLHR 11 0 P11172-2;P11172-3;P11172 P11172-2 UMPS Uridine 5-monophosphate synthase;Orotate phosphoribosyltransferase;Orotidine 5-phosphate decarboxylase 0 ; 131.37 0.00020478 361320000 377330 373210 233250 264660 343590 363520 305290 351680 326610 FALSE TRUE 327464.8845 370758.3589 346050.4802 324755.0981 336753.2312 377504.8496 275683.0228 276475.9688 287998.5379 1.137036621 1.287361949 1.201570267 1.127627593 1.169287989 1.310787383 0.957237578 0.959990876 1 18.13570196 2.223667458 24.9991957 0.969190021 1.203948324 0.777802089 0.058744474 102.5253668 172094.5696 0.023543937 0.015945871 167.3660851 -2.223667458 0.234758304 GLQLT(ph)PGIGGMQQHFFDDEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GLQLTPGIGGMQQHFFDDEDR 21 0 P12270 P12270 TPR Nucleoprotein TPR 1 GLQLT(1)PGIGGMQQHFFDDEDR;GLQLT(1)PGIGGMQQHFFDDEDR;GLQLT(1)PGIGGMQQHFFDDEDR;GLQLT(1)PGIGGMQQHFFDDEDR;GLQLT(1)PGIGGMQQHFFDDEDR;GLQLT(1)PGIGGMQQHFFDDEDR;GLQLT(1)PGIGGMQQHFFDDEDR 276.46 3.06E-44 2268397000 367312 682958 911272 935267 1147880 1426534 1208347 1472324 2188655 TRUE FALSE 318770.7885 678471.6039 1351966.187 1147633.667 1125039.434 1481413.686 1091161.694 1157478.97 1929914.699 0.165173512 0.351555229 0.700531577 0.594655125 0.582947751 0.767605784 0.565393742 0.599756544 1 20.88010565 4.394995794 2.974028829 0.670103392 0.182253362 0.662636169 0.129867799 0.15579657 2.624749709 0.032598842 0.123420791 24831.09059 -4.394995794 -0.48785003 GLQLTPGIGGMQQHFFDDEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLQLTPGIGGMQQHFFDDEDR 21 0 P12270 P12270 TPR Nucleoprotein TPR 0 215.58 6.51E-25 126970000 56181 55182 50394 51472 59036 55864 50466 56584 82219 FALSE TRUE 48756.53851 54819.50581 74764.70696 63159.5043 57861.2991 58013.12423 45571.81509 44483.95194 72499.16348 0.672511739 0.756139839 1.031249236 0.871175628 0.798096093 0.800190257 0.628584013 0.61357883 1 16.14567673 2.430361367 8.92743628 0.714234051 0.832280905 0.044492289 0.138534468 0.645233824 114.3520315 0.052680346 0.040812372 269.3775306 -2.430361367 0.118046854 GLQPS(ph)TPPPKPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLQPSTPPPKPPR 13 1 A0A1B0GTL5 A0A1B0GTL5 1 GLQPS(0.577)T(0.423)PPPKPPR 55.173 0.079787 205290000 514700 411100 349770 444580 447880 465020 473000 613460 614460 TRUE FALSE 446681.0909 408399.457 518919.9419 545528.684 438968.0643 482909.6203 427128.5328 482276.353 541819.2388 0.824409801 0.753755917 0.957736279 1.006846278 0.810174377 0.891274406 0.788322935 0.890105626 1 19.0474521 5.37442059 0.016810164 1.675570377 8.38E-06 0.095239335 0.083327588 16159.63256 56.57951234 2570.90909 3089.300453 236821.2068 -5.37442059 -1.675561994 GLQSIFQEQGMAESVHTWQDHGYLATYTNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLQSIFQEQGMAESVHTWQDHGYLATYTNK 30 0 P52788;H7C2R7;P52788-2 P52788 SMS Spermine synthase 0 ; 258.44 1.89E-58 536102000 401964 278768 122846 210606 284651 271629 318855 359753 361234 FALSE TRUE 348843.439 276936.7547 182254.7365 258427.3112 278987.002 282078.7434 287932.4912 282822.6206 318529.328 1.095168979 0.869423096 0.572175685 0.811314025 0.875859701 0.885566002 0.903943423 0.887901351 1 18.28106669 2.737561185 1.838338332 0.919840612 0.824161569 0.080618992 0.128216161 0.923353573 6.216847512 0.055513491 0.049495964 546.4635328 -2.737561185 -0.095679043 GLQTSQDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GLQTSQDAR 9 0 P27797 P27797 CALR Calreticulin 0 ;; 159.79 0.00015304 802090000 1353840 1318260 1135720 1246780 1243860 1815130 1157040 1212740 1300950 FALSE TRUE 1174926.614 1309600.263 1684957.991 1529880.455 1219109.62 1884959.226 1044830.439 953404.9886 1147153.173 1.024210752 1.141608892 1.46881692 1.333632239 1.062726102 1.643162631 0.910802902 0.831105219 1 20.12962661 2.05339511 24.87305884 0.893728016 1.274301703 0.455330358 0.18783773 71.83657368 33463.24646 0.074262824 0.050067976 113.0824242 -2.05339511 0.380573688 GLS(ph)GEEEDDEPDCCNDER ddPTM_MDA-MB-175_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 449.36 7.06E-191 1169760000 957560 1084750 724210 728100 947610 958960 945900 1019310 1013890 TRUE FALSE 831016.0199 1077624.206 1074440.378 893426.2333 928754.415 995851.8117 854166.7636 801338.4888 894029.0792 0.929517886 1.205356997 1.201795784 0.999325698 1.038841394 1.113891969 0.95541273 0.896322622 1 19.76996223 2.186644471 6.23278912 0.93759878 1.086847848 0.329736022 0.087241737 0.205151596 17.36978819 0.035839163 0.024241854 153.6895968 -2.186644471 0.149249068 GLS(ph)LEHQK ddPTM_MDA-MB-175_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 133.23 0.00059804 2262500000 4133770 3281160 1930670 3058800 2960980 1789810 5723100 4412940 3668390 TRUE FALSE 3587481.821 3259605.844 2864348.47 3753347.291 2902062.291 1858665.149 5168074.643 3469267.123 3234717.113 1.109055814 1.007694253 0.885501999 1.160332468 0.897161078 0.574598978 1.597689833 1.072510208 1 21.62520812 2.240815901 24.99982755 1.20755998 0.947896589 0.269941992 0.219599804 85.5222413 948030.7083 0.083640606 0.061608518 174.106867 -2.240815901 -0.259663391 GLS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLSPGR 6 0 Q96FF7;A0A044PY82 Q96FF7 LOC113230 Uncharacterized protein LOC113230 1 GLS(1)PGR 79.451 0.0704 900670000 1060700 1032600 790260 854500 789460 1141100 1021700 1077600 1213100 TRUE FALSE 920525.8075 1025816.783 1172432.379 1048527.285 773751.2906 1184998.855 922615.6913 847163.6259 1069688.7 0.860554858 0.958986276 1.096050074 0.980217221 0.723342493 1.107797863 0.862508589 0.791972119 1 20.02875957 3.408311699 24.99999355 0.888268711 0.981853651 0.090045824 0.118364481 104.5820326 37995.28299 0.033591625 0.043366608 2560.422876 -3.408311699 0.09358494 GLS(ph)PMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLSPMR 6 0 Q3KR16-2;Q3KR16;F5H731 Q3KR16-2 PLEKHG6 Pleckstrin homology domain-containing family G member 6 1 GLS(1)PMR;GLS(1)PMR 86.794 0.055776 613810000 580960 696880 516000 624130 787440 1128970 484590 658880 928210 TRUE FALSE 504184.664 692302.1494 765539.3259 765848.2557 771771.4846 1172402.206 437594.5364 517983.6394 818478.0712 0.616002654 0.845840803 0.935320509 0.935697953 0.942934834 1.43241737 0.534644179 0.632861964 1 19.64258424 GLSAS(ph)LPDLDSENWIEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 GLSASLPDLDSENWIEVK 18 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 1 GLSAS(1)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK;GLS(0.006)AS(0.993)LPDLDS(0.001)ENWIEVK;GLSAS(1)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK;GLS(0.001)AS(0.999)LPDLDSENWIEVK 396.21 6.09E-127 10111900000 8589500 7152000 5285810 6419610 6846230 5966510 8081840 9968870 8805100 TRUE FALSE 7454375.812 7105018.041 7842045.396 7877280.568 6710003.417 6196045.501 7298064.401 7837104.728 7764171.109 0.960099373 0.915103228 1.010029955 1.014568131 0.864226628 0.798030519 0.939966971 1.009393613 1 22.88840048 -0.140229919 8.812270037 1.003685686 0.946381656 0 0.071111108 0 0 0 0.017343552 0.72405254 0.140229919 -0.05730403 GLSAS(ph)LPDLDSENWIEVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLSASLPDLDSENWIEVKK 19 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 1 GLS(0.059)AS(0.941)LPDLDSENWIEVKK 56.882 0.020306 0 128340 78941 48522 63859 72101 67538 96128 106040 45974 TRUE FALSE 111379.5438 78422.43137 71987.4015 78359.16197 70666.33116 70136.23056 86805.52136 83364.1712 40539.00609 2.747466072 1.934493194 1.775756449 1.93293249 1.743168814 1.730092504 2.141283907 2.056394057 1 15.3070231 4.74014374 3.399621319 1.818506146 2.869080418 0.489013652 0.309016611 0.278111216 5.421368898 0.074853013 0.761272037 54972.27875 -4.74014374 1.050574272 GLSDHVS(ph)LDGQELGTR ddPTM_MDA-MB-175_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 333.98 1.25E-71 1955410000 2242270 2211490 1224992 1532971 2022020 2096960 2404250 2119260 2231220 TRUE FALSE 1945948.338 2196962.577 1817402.229 1881055.496 1981785.758 2177631.408 2171086.205 1666072.741 1967447.713 0.989072454 1.116656144 0.923735973 0.956089192 1.007287637 1.106830638 1.10350389 0.846819323 1 20.90789386 1.737819808 24.99999995 0.920293652 1.027697628 0.259132319 0.074175538 0.144138575 4393.182675 0.039952427 0.019185595 54.67890496 -1.737819808 0.107403976 GLSEDTTEETLKESFDGSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GLSEDTTEETLKESFDGSVR 20 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;; 261.66 1.97E-36 2051735000 4796600 3777540 2165476 2456593 3329969 2946848 4221680 4980120 1593013 FALSE TRUE 4162717.157 3752725.091 3212707.437 3014399.987 3263709.132 3060215.149 3812262.123 3915160.093 1404688.818 2.963444361 2.671570417 2.287131068 2.145955708 2.323439249 2.178571589 2.713954916 2.78720813 1 20.42181913 4.430295387 2.652798614 2.28368823 2.951254584 0.214515797 0.485507383 0.519781382 6.75629503 0.124960202 0.563602094 26933.66081 -4.430295387 0.667566354 GLSFHPK ddPTM_MDA-MB-175_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 79.597 0.032193 820040000 2165800 2480900 667160 1639100 2748700 2314200 2409700 2733100 3161700 FALSE TRUE 1879584.043 2464602.805 989800.8075 2011282.707 2694006.248 2403228.771 2176007.665 2148647.834 2787927.428 0.674186861 0.884026887 0.355031052 0.721425776 0.966311469 0.862012672 0.780510871 0.77069719 1 21.41076158 3.467479041 22.85359008 0.853902668 0.641684897 0.363743829 0.144649728 83.60919586 198164.5528 0.04110528 0.05316655 2934.127898 -3.467479041 -0.212217771 GLSLVDKENT(ph)PPALSGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLSLVDKENTPPALSGTR 18 1 P31350;P31350-2;A0A286YFD6 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 GLSLVDKENT(1)PPALSGTR 96.128 0.0026678 496120000 241200 203820 144140 148490 220440 184050 237350 322350 282920 TRUE FALSE 209324.8089 202481.093 213846.5861 182206.924 216053.6753 191130.5226 214331.8335 253417.961 249473.5199 0.839066242 0.811633608 0.857191522 0.730365788 0.866038509 0.766135511 0.859136607 1.015811061 1 17.92852716 1.82229248 3.591245552 1.00959219 0.812522643 0.792329307 0.040848089 0.085693157 1.921063574 0.023314843 0.010144111 66.41902249 -1.82229248 -0.197069547 GLSSAGGGS(ph)PHREDAQPEHSASAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GLSSAGGGSPHREDAQPEHSASAR 24 1 Q92994-9;Q92994-3;Q92994-7;Q92994-8;Q92994-5;Q92994 Q92994-9 BRF1 Transcription factor IIIB 90 kDa subunit 1 GLSS(0.001)AGGGS(0.999)PHREDAQPEHSASAR;GLSSAGGGS(1)PHREDAQPEHSASAR;GLSSAGGGS(1)PHREDAQPEHSASAR;GLS(0.002)S(0.004)AGGGS(0.994)PHREDAQPEHSASAR;GLS(0.027)S(0.203)AGGGS(0.77)PHREDAQPEHSASAR;GLS(0.03)S(0.09)AGGGS(0.88)PHREDAQPEHSASAR 251.33 2.20E-39 6066300000 4249684 3772107 1999720 2628100 3535585 3922801 3270378 3699036 3301276 TRUE FALSE 3688077.492 3747327.781 2966791.281 3224850.273 3465233.776 4073713.693 2953217.245 2908025.937 2911002.912 1.266943938 1.287297847 1.019164656 1.107814169 1.190391724 1.399419312 1.014501646 0.998977337 1 21.47308485 2.046456386 24.99425122 1.00161252 1.201320426 0.478894028 0.101650193 108.6423571 58450.79674 0.043358904 0.029232558 111.2900623 -2.046456386 0.199707906 GLSTS(ph)LPDLDSEPWIEVK ddPTM_MDA-MB-175_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 GLST(0.012)S(0.987)LPDLDSEPWIEVK;GLST(0.012)S(0.988)LPDLDSEPWIEVK;GLST(0.003)S(0.997)LPDLDSEPWIEVK;GLS(0.007)T(0.062)S(0.932)LPDLDSEPWIEVK 300.03 1.74E-49 600060000 1393810 1432140 941620 1034620 1303590 1096750 1457180 1769050 1521750 TRUE FALSE 1209614.477 1422732.178 1396990.582 1269546.284 1277651.109 1138942.682 1315862.908 1390752.424 1341850.449 0.901452526 1.060276262 1.041092607 0.946116078 0.952156115 0.848785111 0.980633057 1.036443685 1 20.35579246 1.988469932 24.55609185 1.017139001 0.961612315 0.138383881 0.060916006 923.3224357 1966436.994 0.028170648 0.017441163 97.38003628 -1.988469932 -0.055526686 GLTDESEILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLTDESEILR 10 0 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 0 ; 138.54 0.00014393 139251000 298920 303170 224710 208931 281770 315610 276790 316770 294150 FALSE TRUE 259416.9646 301178.4563 333380.5076 256371.9769 276163.3283 327751.7209 249946.9484 249031.2006 259375.9221 1.000158236 1.161165824 1.28531787 0.988418566 1.0647223 1.2636166 0.96364746 0.960116878 1 17.98468503 2.197201339 24.99972101 0.971117137 1.126810197 0.353710877 0.0972282 158.6435356 95891.37514 0.039337305 0.026521497 157.4712733 -2.197201339 0.155693059 GLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSR 33 0 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;; 295.41 4.37E-90 16164530000 4414733 4406892 1728681 2631869 3964312 4227468 3630172 4301683 3514257 FALSE TRUE 3831314.849 4377942.836 2564676.914 3229475.082 3885429.947 4390101.429 3278118.478 3381801.566 3098805.541 1.236384406 1.412783984 0.827634029 1.042167712 1.253847618 1.416707622 1.057865179 1.091324228 1 21.56328079 GLTLAPGLS(ph)PARPLFGSDFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLTLAPGLSPARPLFGSDFEK 21 1 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 GLTLAPGLS(1)PARPLFGSDFEK 131.27 8.16E-06 287030000 349740 305320 256660 272110 289820 242060 323700 378990 417300 TRUE FALSE 303520.9729 303314.3328 380781.6345 333896.7344 284053.149 251372.2048 292307.6238 297945.9378 367967.2694 0.824858617 0.824297045 1.034824742 0.907408789 0.771952216 0.683137403 0.794384849 0.809707717 1 18.48921792 3.248297361 24.92723911 0.803826526 0.902377838 0.160528985 0.096530329 340.073038 870622.8763 0.028902397 0.036834763 1771.321364 -3.248297361 0.098551311 GLTMLDHEQVTPEDPGAQFLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLTMLDHEQVTPEDPGAQFLIR 22 0 Q9UBE0;M0QX65;B3KNJ4;Q9UBE0-2;Q9UBE0-3;A0A590UK93;A0A590UKC5;M0QZS6;A0A590UKA0 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 ; 163.95 1.45E-11 338280000 486630 396900 314990 315030 408720 435580 381220 420460 391260 FALSE TRUE 422320.6125 394292.7378 467320.2176 386562.3764 400587.2716 452337.0445 344249.3431 330547.901 345005.6885 1.224097534 1.142858657 1.354529021 1.120452182 1.161103382 1.31110025 0.99780773 0.958094061 1 18.39626062 2.174474702 7.956062623 0.978424199 1.214399836 0.698753079 0.072284638 0.130425171 14.16421739 0.028303186 0.019088176 149.4426989 -2.174474702 0.235975637 GLVAAYSGDS(ph)DNEEELVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLVAAYSGDSDNEEELVER 19 0 P52756 P52756 RBM5 RNA-binding protein 5 1 GLVAAYSGDS(1)DNEEELVER 135.26 5.38E-07 0 253850 250360 126500 225900 208480 219020 244000 311830 253850 TRUE FALSE 220303.0793 248715.3687 187675.8231 277194.0477 204331.6559 227445.8411 220336.9176 245147.5812 223840.1422 0.984198264 1.111129426 0.838436847 1.238357182 0.912846346 1.016108366 0.984349435 1.095190428 1 17.77210926 1.750521521 25 1.052565012 1.01435199 0.017117559 0.109131025 16.1866164 33904.48687 0.052827401 0.025368272 56.30170168 -1.750521521 -0.038213022 GLVAAYSGES(ph)DS(ph)EEEQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GLVAAYSGESDSEEEQER 18 0 P98175-5;P98175-2;P98175;P98175-4;P98175-3 P98175-5 RBM10 RNA-binding protein 10 2 GLVAAYSGES(1)DS(1)EEEQER;GLVAAYS(0.043)GES(0.957)DS(1)EEEQER;GLVAAYSGES(1)DS(1)EEEQER 256.68 1.96E-30 330691000 744900 659770 467550 517127 667320 701180 608250 683290 672850 TRUE FALSE 646459.5777 655435.9274 693658.7439 634548.5891 654041.6376 728154.8483 549262.0086 537173.7509 593306.4395 1.089588001 1.104717367 1.169140764 1.069512392 1.102367333 1.227282901 0.925764448 0.905390057 1 19.17841792 2.219676916 24.99991564 0.934984981 1.124252912 0.745412474 0.050416874 110.0928816 145749.6392 0.020048256 0.013541671 165.8352752 -2.219676916 0.189267931 GLVDRPLALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLVDRPLALR 10 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 144.77 2.88E-05 521240000 794030 821320 587790 705670 869230 889570 746080 871530 723050 FALSE TRUE 689096.9237 815924.6948 872047.21 865903.159 851934.0236 923792.3335 673725.2764 685160.0918 637571.8527 1.080814532 1.279737635 1.367763031 1.35812639 1.336216491 1.448922705 1.056704862 1.074639805 1 19.28222841 2.217986392 24.46950087 1.05074861 1.316208423 0.635459745 0.095655925 120.5267401 143344.4233 0.039721285 0.026817713 165.1910037 -2.217986392 0.265459814 GLVEDTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLVEDTLR 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 122.13 0.0032656 103040000 236600 238590 171700 180630 232080 276160 198310 255310 259670 FALSE TRUE 205332.7105 237022.6866 254734.6943 221644.8023 227462.0621 286784.0539 179077.9267 200713.9433 228972.1084 0.896758614 1.035159646 1.112514079 0.967999132 0.993405108 1.252484662 0.782094937 0.876586868 1 17.80481235 2.207433274 24.99996927 0.87988006 1.040184036 0.323942425 0.106614575 225.316149 180961.5 0.042426877 0.028607349 161.2253297 -2.207433274 0.160303976 GLVETAAHLGYSVVAINHIVDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLVETAAHLGYSVVAINHIVDFK 23 0 P78346;P78346-2 P78346 RPP30 Ribonuclease P protein subunit p30 0 107.39 0.00078141 15608000 45046 44106 24760 36369 35671 33104 38647 51062 45217 FALSE TRUE 39093.05697 43816.26478 36734.01882 44627.13732 34961.21689 34377.5323 34899.01989 40142.78866 39871.49777 0.980476259 1.098937016 0.921310231 1.119274163 0.876847343 0.862208199 0.875287407 1.006804131 1 15.28307018 3.223242618 24.99980258 0.927779549 1.027160045 0.339736866 0.073128755 299.4016925 488638.6 0.022423283 0.025518602 1672.024427 -3.223242618 0.099380496 GLVGEIIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLVGEIIKR 9 1 Q32Q12;P22392-2;J3KPD9;P22392;E7ERL0;E5RHP0;F6XY72;C9K028;P15531;P15531-2 Q32Q12;P15531 NME1-NME2;NME2;NME1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Nucleoside diphosphate kinase A 0 ; 191.17 5.80E-05 9480200000 8832200 7987000 5074400 5285600 7881900 7018500 9254400 10959500 4629800 FALSE TRUE 7665002.392 7934532.871 7528396.813 6485776.265 7725065.611 7288506.237 8356909.712 8615896.212 4082470.318 1.877540262 1.94356168 1.844078763 1.588689142 1.892252731 1.785317631 2.047022773 2.110461446 1 21.96101097 1.229894951 24.99794199 0.999998312 1.892403115 0.794596822 0.141554771 165.5451424 477512.9961 0.445209037 0.038659689 16.97832925 -1.229894951 0.892404803 GLVGPELHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GLVGPELHDR 10 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;; 185.61 1.43E-06 2788290000 3378410 2994450 2332510 2241680 2905530 3591030 2851810 3189560 3387820 FALSE TRUE 2931944.559 2974779.261 3460519.638 2750687.706 2847715.638 3729179.248 2575241.905 2507497.415 2987315.779 0.981464557 0.995803417 1.158404365 0.920789066 0.953269038 1.248337813 0.862058817 0.839381438 1 21.51041832 GLVLDHGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GLVLDHGAR 9 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;;; 208.37 1.02E-05 6399930000 6501880 5819460 4573100 4786000 5997370 6463990 5591710 6004280 5950140 FALSE TRUE 5642640.084 5781231.584 6784666.456 5872734.449 5878034.071 6712663.878 5049426.825 4720311.447 5246721.228 1.075460243 1.10187512 1.293125013 1.119315129 1.120325212 1.279401666 0.962396629 0.899668811 1 22.32298471 2.145552781 7.535595207 0.940095525 1.163435434 0.634721261 0.075293808 0.13559615 9.514149132 0.030319405 0.020405139 139.8146825 -2.145552781 0.223339909 GLVQALQTK ddPTM_MDA-MB-175_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 0 159.37 0.00015379 210260000 317200 289520 255310 239270 320700 297100 316160 383020 400260 FALSE TRUE 275281.2163 287618.1241 378778.77 293599.9105 314318.6974 308529.6292 285498.8519 301114.1537 352941.7188 0.779962248 0.814916766 1.073204866 0.831865135 0.890568274 0.87416594 0.808912171 0.853155458 1 18.42907045 6.805832141 0.007801769 1.696857335 1.66E-05 0.038473199 0.08903707 262053.0864 267.3567768 27149.83168 31127.62515 6394876.192 -6.805832141 -1.696840782 GLVRPGS(ph)SR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLVRPGSSR 9 1 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 1 GLVRPGS(0.614)S(0.386)R 54.259 0.082492 167320000 102070 94262 93315 87139 74741 107430 100930 91470 79221 TRUE FALSE 88581.19089 93642.78672 138442.4461 106925.2418 73253.80033 111562.9016 91141.82413 71909.85232 69855.58363 1.268061711 1.34051971 1.981837942 1.530661348 1.048646315 1.597050598 1.304717811 1.029407366 1 16.09208782 1.846925327 2.763434168 1.001925292 1.464577633 0.364269533 0.24031352 0.290271874 3.999163361 0.174215772 0.069362904 70.29514441 -1.846925327 0.462652341 GLVSSDELAKDVTGAEALLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLVSSDELAKDVTGAEALLER 21 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 66.874 0.020229 32057000 47180 34164 17261 20274 33917 34162 38918 45899 7975.8 FALSE TRUE 40945.04346 33939.57443 25608.47733 24877.52157 33242.11806 35476.23425 35143.73835 36083.85604 7032.91001 5.821920571 4.825822367 3.641234894 3.537301278 4.726651985 5.044317956 4.997040812 5.13071488 1 12.77990604 4.588886575 3.405173769 4.209036746 5.822508035 0.174289645 1.227019205 0.513256341 9.870709047 0.303204454 1.669638493 38804.90058 -4.588886575 1.61347129 GLVVDMDGFEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GLVVDMDGFEEER 13 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;; 289.22 3.98E-40 732060000 1683540 1166560 823080 887650 1042350 1216990 1060840 1171450 1179400 FALSE TRUE 1461055.923 1158896.791 1221124.241 1089204.499 1021609.274 1263808.393 957959.9001 920944.5337 1039972.676 1.404898376 1.114353115 1.174188774 1.047339536 0.982342419 1.215232306 0.92113949 0.885546857 1 19.98811419 8 0.327284615 0.932743194 5.248781832 0.638325308 0.092709455 51.01395926 0.79858567 0.147755812 130.8284212 100000000 -8 4.316038637 GLVVDMDGFEEERK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLVVDMDGFEEERK 14 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 208.15 1.35E-08 252820000 507380 342880 239605 276659 315654 280641 369880 461700 373100 FALSE TRUE 440328.4475 340627.5987 355478.7794 339478.6544 309373.103 291437.4409 334009.0945 362969.048 328992.543 1.338414675 1.035365712 1.080507103 1.031873401 0.940365092 0.885848166 1.015248222 1.103274392 1 18.32769536 GLVYETSVLDPDEGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 155.99 4.80E-07 67593000 131994 145367 104351 148195 149723 170338 114582 152479 144469 FALSE TRUE 114550.6585 144412.0746 154815.4926 181844.9398 146743.8052 176891.0131 103469.8553 119872.5524 127390.0394 0.89921205 1.133621398 1.215287265 1.42746592 1.151925268 1.388578055 0.812228772 0.940988424 1 16.95889295 2.229413279 24.99999919 0.918186404 1.208025904 0.44379985 0.15029439 178.2743268 487225.3735 0.061391348 0.042044704 169.5950917 -2.229413279 0.289839501 GLVYIQQTDDSLIHFCWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GLVYIQQTDDSLIHFCWK 18 0 Q16186;A0A087WX59;A0A087WUX6 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 0 ;; 147.64 7.51E-08 79222000 99537 93824 68056 82717 88086 82134 104152 117657 117879 FALSE TRUE 86382.93326 93207.66397 100968.1092 101499.1591 86333.26094 85293.74813 94051.35507 92496.96616 103943.4789 0.831056784 0.896714878 0.971375119 0.976484145 0.830578905 0.820578155 0.904831703 0.889877529 1 16.66543973 1.237790141 24.92271325 1.00000013 0.892258953 0.289480219 0.053980575 26.96227338 871551.7932 0.081634505 0.013959282 17.28980681 -1.237790141 -0.107741177 GLWEDVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLWEDVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIK 39 0 A0A1W2PR36;Q14353;Q14353-2;K7EM34 A0A1W2PR36 GAMT Guanidinoacetate N-methyltransferase 0 217.1 6.62E-40 183740000 134520 127900 73355 86388 102710 103250 110910 142690 126320 FALSE TRUE 116742.8412 127059.8165 108829.7234 106003.7158 100666.2719 107222.0943 100153.9653 112176.8539 111386.5935 1.048087005 1.140710138 0.977045082 0.951673917 0.903755728 0.962612204 0.899156372 1.007094753 1 16.76521607 4.139905575 5.883490728 0.955313884 1.093369707 0.663066432 0.040822224 0.112698428 5.550898662 0.010513253 0.022579698 13800.84171 -4.139905575 0.138055823 GLWHEEMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLWHEEMK 8 0 P23921;E9PL69 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ; 114.5 0.0020061 426130000 663600 712900 472250 591500 725180 564490 730830 932200 743800 FALSE TRUE 575903.5787 708216.913 700631.6796 725809.1155 710750.3368 586206.2956 659954.2191 732856.2844 655868.8113 0.878077397 1.079814897 1.068249728 1.106637643 1.083677596 0.8937859 1.006229001 1.117382427 1 19.32304775 4.745513968 24.04996029 1.047577564 0.878077261 0.387642436 0.065621657 541.6253494 1873267.409 0.016673751 0.158614485 55656.25343 -4.745513968 -0.169500303 GLYDGPVCEVSVT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLYDGPVCEVSVTPK 15 0 A0A1C7CYX9;Q16555-2;Q16555 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 1 GLYDGPVCEVSVT(1)PK;GLYDGPVCEVSVT(1)PK 222.45 1.57E-11 385250000 1117240 822250 505940 428440 504620 425690 568970 668030 603320 TRUE FALSE 969593.9033 816848.5856 750614.2763 525723.8503 494579.0493 442066.5698 513791.377 525176.9831 531996.1969 1.82255796 1.535440649 1.410939177 0.988209791 0.929666513 0.830958139 0.965780169 0.987181837 1 19.02105641 4.047882279 1.435036417 0.936874301 1.785531962 0.953025666 0.069551753 0.095337213 0.356088343 0.02208653 0.080952538 11165.60549 -4.047882279 0.848657661 GLYGGSSYVDFLCCVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GLYGGSSYVDFLCCVHK 17 0 O94855;O94855-2;E9PDM8 O94855 SEC24D Protein transport protein Sec24D 0 162.37 2.85E-09 164010000 171980 169200 118960 112880 153050 144410 143540 188130 160090 FALSE TRUE 149252.4073 168088.5141 176489.4539 138511.1293 150004.6044 149965.5461 129619.5129 147899.8635 141164.3426 1.05729538 1.190729266 1.250241036 0.981204791 1.062623901 1.062347215 0.918217097 1.047714039 1 17.10701619 3.727192126 24.99902894 1.014079287 1.168552633 0.569676543 0.063095317 496.0602465 1090824.111 0.016964317 0.025418324 5335.708873 -3.727192126 0.154473346 GLYGIKDDVFLSVPCILGQNGISDLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GLYGIKDDVFLSVPCILGQNGISDLVK 27 1 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 215.34 3.57E-34 907280000 1381690 981190 788510 846230 959600 760540 1266160 1469810 985720 FALSE TRUE 1199096.166 974744.4983 1169836.073 1038379.455 940505.8374 789798.4659 1143367.998 1155502.57 869189.3045 1.379556973 1.121440972 1.345893314 1.194652822 1.082049483 0.90866105 1.315441863 1.329402655 1 19.7293109 7.999987671 0.946738753 1.169610767 130.6253226 0.168589013 0.144781613 2779.402373 4.949742161 0.049790228 779046.26 99997161.25 -7.999987671 129.4557119 GMAFLHTLEPLIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GMAFLHTLEPLIPR 14 0 A0A0A0MTH3;Q13418;Q13418-3;Q13418-2 A0A0A0MTH3 ILK Integrin-linked protein kinase 0 ; 180.24 1.77E-06 171729000 254410 249140 176312 170994 223190 243720 206090 236230 209691 FALSE TRUE 220789.0739 247503.3829 261577.0729 209820.8012 218748.9557 253096.0661 186103.4235 185714.0528 184901.5689 1.194089781 1.338568323 1.41468282 1.134770259 1.183056245 1.368815136 1.00649997 1.004394143 1 17.49639794 2.224833038 24.82258005 1.003909683 1.271501143 0.683051019 0.086282238 123.5314444 223370.9814 0.035879608 0.024335135 167.8158737 -2.224833038 0.26759146 GMAYGHIDSYGADDS(ph)EEEGAGPVERPPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GMAYGHIDSYGADDSEEEGAGPVERPPVR 29 1 Q8NG27-3;Q8NG27;K7EPI8 Q8NG27-3 PJA1 E3 ubiquitin-protein ligase Praja-1 1 GMAYGHIDSYGADDS(1)EEEGAGPVERPPVR 115.84 0.00010821 91764000 32475 20266 19300 23015 24357 31514 22848 33292 32586 TRUE FALSE 28183.34647 20132.87131 28633.54455 28240.90751 23872.34335 32726.36397 20632.20448 26172.76488 28733.7202 0.98084572 0.700670542 0.996513655 0.982848977 0.830812828 1.138953249 0.718048493 0.910872824 1 14.81045717 GMDDDRGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GMDDDRGPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;;; 131.5 0.00030212 4168660000 7258170 6902240 5219367 5589091 6344780 7734130 6558680 7224170 7693230 FALSE TRUE 6298984.445 6856898.731 7743470.339 6858179.535 6218531.291 8031666.986 5922620.223 5679337.464 6783745.114 0.928540849 1.010783662 1.141474246 1.010972467 0.916681153 1.183957659 0.873060548 0.837197944 1 22.69365053 2.159952303 24.99999981 0.888356531 1.029882809 0.300737793 0.09147845 35.79554939 11382.12681 0.036215111 0.024416228 144.5281031 -2.159952303 0.141526278 GMDDRLFYIYT(ph)SGT(ph)TGLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GMDDRLFYIYTSGTTGLPK 19 1 Q6PCB7-2;Q6PCB7 Q6PCB7-2 SLC27A1 Long-chain fatty acid transport protein 1 2 GMDDRLFY(0.25)IY(0.25)T(0.283)S(0.283)GT(0.467)T(0.467)GLPK 58.09 0.090937 3696400000 367780 498060 252330 154430 331300 325520 475840 415830 91816 TRUE FALSE 319176.9412 494788.2111 374357.632 189495.6918 324707.7782 338042.965 429693.11 326907.9905 80961.61708 3.942324186 6.111392397 4.623890252 2.340562092 4.010638496 4.175348483 5.307368177 4.037814489 1 16.30495049 3.988246687 24.14960233 3.685431583 5.112054223 0.209320335 1.268761076 575.7627218 1183036.564 0.330617092 0.6176803 9732.99919 -3.988246687 1.426622639 GMFTAEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GMFTAEDLR 9 0 Q16864;Q16864-2 Q16864 ATP6V1F V-type proton ATPase subunit F 0 ; 129.47 0.00090379 210540000 528730 532770 380250 387740 545130 588770 430430 524390 509860 FALSE TRUE 458856.9909 529270.1988 564140.1719 475782.2932 534282.9795 611420.3629 388686.9648 412253.2793 449584.9316 1.020623599 1.177241855 1.254802223 1.058270106 1.188391652 1.359966315 0.864546246 0.916964183 1 18.77823416 2.21941261 24.99998432 0.922434505 1.175299716 0.586560087 0.098666505 163.083549 212923.2194 0.039703752 0.026814178 165.7343806 -2.21941261 0.252865211 GMGGAFVLVLYDELKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GMGGAFVLVLYDELKK 16 1 P12236 P12236 SLC25A6 "ADP/ATP translocase 3;ADP/ATP translocase 3, N-terminally processed" 0 169.79 5.43E-12 0 115370 105280 95216 131620 100400 75368 118300 183420 108650 FALSE TRUE 100123.5622 104588.4087 141262.7761 161506.3327 98402.23643 78267.45573 106827.2842 144197.0604 95805.52077 1.045070904 1.091674132 1.474474278 1.685772713 1.027104029 0.816940977 1.115043093 1.505101785 1 16.54782117 GMGLSLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GMGLSLMR 8 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 153.15 0.0010369 1296360000 1168250 1961820 1393770 1281240 1961220 2301700 1810830 1802440 2520200 FALSE TRUE 1013862.803 1948932.675 2067801.834 1572165.125 1922195.559 2390247.888 1635215.985 1417002.233 2222264.827 0.456229514 0.87700289 0.930492986 0.707460742 0.864971418 1.075590928 0.735833086 0.63763878 1 21.08359932 4.742366194 24.49626507 0.836354227 0.45622932 0.460666792 0.133979008 291.186994 1874248.615 0.034134553 0.24789073 55254.31439 -4.742366194 -0.380124907 GMGPGT(ph)PAGYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GMGPGTPAGYGR 12 0 P23246 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 1 GMGPGT(1)PAGYGR;GMGPGT(1)PAGYGR 159.5 0.00078917 324030000 445890 401910 329040 302230 353490 504930 417740 403020 461400 TRUE FALSE 386964.5068 399269.8267 488164.8446 370855.9408 346456.2406 524354.9838 377227.6391 316837.3093 406853.8176 0.951114356 0.981359421 1.199853174 0.911521349 0.851549686 1.288804384 0.927182253 0.778749751 1 18.634151 2.009366619 24.999131 0.867389646 1.029703217 0.15856868 0.139740206 291.9426252 779180.0843 0.055765223 0.037544266 102.1801695 -2.009366619 0.162313571 GMGS(ph)LDAMDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GMGSLDAMDK 10 0 P12268;H0Y4R1 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 1 GMGS(1)LDAMDK;GMGS(1)LDAMDK;GMGS(1)LDAMDK;GMGS(1)LDAMDK;GMGS(1)LDAMDK 151.13 2.13E-05 702800000 1669200 1470960 1064078 1217494 1501920 1293520 1582140 1800670 1844260 TRUE FALSE 1448610.991 1461297.167 1578669.68 1493944.621 1472034.73 1343282.551 1428704.306 1415610.733 1626233.684 0.890776649 0.898577604 0.970752049 0.918653104 0.905180323 0.826008319 0.878535675 0.870484204 1 20.63310315 2.995978346 22.89055441 0.886127082 0.920590113 0.050759686 0.048047432 137.719956 783900.6988 0.01471223 0.016267966 990.7825421 -2.995978346 0.034463031 GMKDDKEEEEDGT(ph)GSPQLNNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GMKDDKEEEEDGTGSPQLNNR 21 2 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 GMKDDKEEEEDGT(0.583)GS(0.417)PQLNNR 143.67 2.17E-07 616090000 303520 233220 218220 226140 239570 178160 296320 335500 342090 TRUE FALSE 263409.063 231687.9625 323751.9219 277488.5433 234803.0257 185013.9305 267582.932 263755.9359 301648.5099 0.873231772 0.768072624 1.073275389 0.919906892 0.778399422 0.613342763 0.887068635 0.874381697 1 18.20250893 5.9349491 13.18118417 0.86201455 0.866856515 0 0.127184626 0 0 0.029233549 0 860892.8484 -5.9349491 0.004841965 GMKDDKEEEEDGTGS(ph)PQLNNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 16 GMKDDKEEEEDGTGSPQLNNR 21 2 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 GMKDDKEEEEDGT(0.001)GS(0.999)PQLNNR;GMKDDKEEEEDGT(0.294)GS(0.706)PQLNNR;GMKDDKEEEEDGTGS(1)PQLNNR;GMKDDKEEEEDGTGS(1)PQLNNR;GMKDDKEEEEDGTGS(1)PQLNNR;GMKDDKEEEEDGT(0.001)GS(0.999)PQLNNR;GMKDDKEEEEDGTGS(1)PQLNNR;GMKDDKEEEEDGT(0.09)GS(0.91)PQLNNR;GMKDDKEEEEDGT(0.414)GS(0.586)PQLNNR;GMKDDKEEEEDGT(0.225)GS(0.775)PQLNNR;GMKDDKEEEEDGT(0.005)GS(0.995)PQLNNR;GMKDDKEEEEDGT(0.145)GS(0.855)PQLNNR;GMKDDKEEEEDGT(0.205)GS(0.795)PQLNNR;GMKDDKEEEEDGT(0.016)GS(0.984)PQLNNR;GMKDDKEEEEDGT(0.047)GS(0.953)PQLNNR;GMKDDKEEEEDGT(0.153)GS(0.847)PQLNNR 256.75 9.69E-37 24333064000 8933603 6377564 7832910 6479618 6026480 4610352 9634039 9979790 10228886 TRUE FALSE 7753004.729 6335669.362 11620931.48 7950914.302 5906564.839 4787715.225 8699731.381 7845689.571 9019638.75 0.859569318 0.702430501 1.288403205 0.881511391 0.654856032 0.530810086 0.964532131 0.869845211 1 23.10463822 GMKDDKEEEEDGTGSPQLNNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GMKDDKEEEEDGTGSPQLNNR 21 2 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 0 ;; 197.68 5.05E-22 914370000 267192 198473 221535 185406 205288 179233 283216 298110 305995 FALSE TRUE 231881.9002 197169.2178 328670.067 227505.2661 201203.1704 186128.2095 255749.7559 234361.4964 269820.6197 0.859392809 0.730741846 1.218105819 0.843172276 0.745692344 0.689822037 0.947851043 0.868582604 1 18.04164108 0.861558633 1.593957127 1.231246062 0.859423326 0.078449222 0.147225297 9.333347404 9.42533562 7.413743553 0.042017044 7.270405493 -0.861558633 -0.371822736 GMLHQDHITFAMLLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GMLHQDHITFAMLLAR 16 0 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 125.54 4.42E-05 13935000 8043.8 12203 4837.9 6707.3 8567.2 10118 9639.7 11300 9964.7 FALSE TRUE 6980.79145 12122.83769 7177.524622 8230.29498 8396.729481 10507.24601 8704.843378 8883.582937 8786.684518 0.794473892 1.379682822 0.816863813 0.936678102 0.955619775 1.195814643 0.990685777 1.01102787 1 13.10110318 GMLPHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GMLPHK 6 0 P40429;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ; 104.64 0.033659 2262500000 2817800 2585200 1845210 2242470 2523500 2657700 2903200 3353800 3206900 FALSE TRUE 2445420.591 2568217.651 2737559.728 2751657.088 2473287.287 2759943.439 2621648.111 2636615.969 2827783.935 0.864783395 0.908208587 0.96809367 0.973078973 0.874638001 0.976009307 0.927103404 0.932396544 1 21.43124046 GMPTFPWDEDPEEDGS(ph)PDPEPSPEPEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GMPTFPWDEDPEEDGSPDPEPSPEPEPK 28 0 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 1 GMPTFPWDEDPEEDGS(0.992)PDPEPS(0.008)PEPEPK 72.707 0.0066531 18317000 31145 23487 23113 28074 24824 24869 30594 32582 68059 TRUE FALSE 27029.10934 23332.71235 34290.52411 34448.63078 24330.05097 25825.72652 27626.99859 25614.59285 60013.14255 0.450386502 0.388793377 0.571383578 0.574018112 0.405412047 0.430334514 0.46034914 0.42681639 1 15.87299086 1.236200401 24.99993899 1.000000698 0.463224066 0.878370862 0.062748444 21.63481286 229108.8177 0.104525664 0.016015319 17.22663297 -1.236200401 -0.536776633 GMPTFPWDEDPEEDGS(ph)PDPEPSPEPEPKPSLEPNTSLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GMPTFPWDEDPEEDGSPDPEPSPEPEPKPSLEPNTSLER 39 1 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 1 GMPTFPWDEDPEEDGS(0.971)PDPEPS(0.028)PEPEPKPSLEPNTSLER;GMPTFPWDEDPEEDGS(0.871)PDPEPS(0.128)PEPEPKPSLEPNTSLER 106.66 8.19E-06 58343000 88880 82419 63320 60437 71530 68321 90203 98718 81863 TRUE FALSE 77134.28281 81877.58416 93941.76379 74160.14457 70106.69295 70949.35308 81455.12694 77607.92392 72185.2494 1.068560176 1.134270295 1.301398341 1.027358708 0.971205247 0.982878825 1.128417892 1.075121643 1 16.13941644 3.642585723 24.99999881 1.037060251 1.164726904 0.441130965 0.072564061 49.25680026 12825.75965 0.020767985 0.0308039 4391.22533 -3.642585723 0.127666653 GMTPGEAEIHFLENAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GMTPGEAEIHFLENAK 16 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;Q4VXN0 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 0 118.33 0.0002802 59064000 109470 102030 81843 108900 103890 99768 104510 141830 153080 FALSE TRUE 95003.26214 101359.7582 121422.5485 133627.4094 101822.7923 103606.1395 94374.63629 111500.7582 134983.0568 0.7038162 0.750907267 0.899539182 0.989956907 0.754337579 0.767549217 0.699159128 0.826035214 1 17.0424188 0.295738233 0.015646251 1.716913962 4.47E-06 0.078339944 0.10495742 28764.55131 82.47631811 4985.660059 4103.237839 1.975778398 -0.295738233 -1.71690949 GMWSEGNGSHTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GMWSEGNGSHTIR 13 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 230.23 4.43E-12 2014360000 1295808 1270410 883343 1098560 1330571 1497212 1240528 1354580 1664230 FALSE TRUE 1124563.69 1262064.593 1310530.629 1348004.838 1304095.24 1554810.714 1120221.785 1064913.608 1467486.625 0.76631955 0.860017782 0.893044343 0.918580664 0.88865903 1.059505884 0.763360814 0.725671764 1 20.48491592 GNAEGS(ph)S(ph)DEEGKLVIDEPAK ddPTM_MDA-MB-175_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 204.05 5.70E-22 9429880000 15825920 10613420 13112830 13068910 11237590 8245940 14173540 17699890 30332000 TRUE FALSE 13734484.57 10543699.75 19454238.45 16036405.76 11013983.94 8563166.648 12798992.27 13914906.26 26746185.51 0.513511901 0.394213214 0.727364971 0.599577302 0.411796439 0.320164034 0.478535239 0.520257599 1 24.67282982 1.236507687 5.010215282 1.033228428 0.492704867 0.667093043 0.112129647 0.113496841 7.27896197 0.214979876 0.029674856 17.23882602 -1.236507687 -0.540523561 GNAEGS(ph)S(ph)DEEGKLVIDEPAKEK ddPTM_MDA-MB-175_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 170.1 3.71E-11 2955530000 3175870 1933440 2091310 1578717 1762757 1283144 3101240 3367190 1380492 TRUE FALSE 2756170.733 1920739.105 3102674.511 1937188.824 1727681.584 1332507.38 2800482.222 2647142.622 1217291.808 2.264182437 1.577878938 2.548833804 1.591392311 1.419283012 1.094649098 2.300584135 2.174616311 1 20.21524362 3.662952252 24.99905647 1.672621371 2.075084776 0.207224471 0.472698787 260.0342099 85976.20571 0.135974911 0.20168341 4602.059744 -3.662952252 0.402463405 GNAEGS(ph)SDEEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GNAEGSSDEEGK 12 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.847)S(0.153)DEEGK 136.81 0.00024938 0 139630 110580 127660 193110 99954 119000 134310 187160 576300 TRUE FALSE 121177.5417 109853.5927 189396.803 236958.577 97965.11096 123578.007 121284.6369 147137.2905 508170.4705 0.238458448 0.216174688 0.372703284 0.466297415 0.192780015 0.243182188 0.238669195 0.289543173 1 18.95495302 1.238696501 8.715683278 1.005958288 0.282622979 0.884551236 0.081497637 0.027799293 25.62260743 0.119073814 0.020900338 17.32592784 -1.238696501 -0.723335309 GNAEGS(ph)SDEEGKLVIDEPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GNAEGSSDEEGKLVIDEPAK 20 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.618)S(0.382)DEEGKLVIDEPAK 174.4 2.10E-12 784340000 895600 611480 902630 856830 586770 458010 883060 1020400 1820900 TRUE FALSE 777244.1908 607463.1476 1339144.887 1051386.347 575094.425 475629.9411 797420.9771 802195.4008 1605635.276 0.484072692 0.378331964 0.834028068 0.654810194 0.358172515 0.296225393 0.496638925 0.499612467 1 20.61471279 1.238485289 24.51582894 1.000000534 0.500675651 0.511238749 0.153568445 1.267242693 408854.3151 0.221231777 0.039562565 17.31750371 -1.238485289 -0.499324883 GNAEGS(ph)SDEEGKLVIDEPAKEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GNAEGSSDEEGKLVIDEPAKEK 22 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.5)S(0.5)DEEGKLVIDEPAKEK;GNAEGS(0.859)S(0.141)DEEGKLVIDEPAKEK 212.77 8.83E-24 1282530000 2097000 1289200 1422150 1113800 1140920 716040 2126900 2212200 797960 TRUE FALSE 1819876.137 1280731.16 2109906.497 1366705.313 1118217.924 743586.5221 1920633.565 1739138.245 703626.0778 2.586425083 1.820187171 2.998618959 1.942374446 1.589221832 1.056792159 2.729622488 2.471679632 1 19.42444943 3.513284335 24.70401087 1.881998511 2.4147397 0.203330849 0.608703438 1060.519555 724467.6937 0.174249728 0.25834227 3260.500983 -3.513284335 0.53274119 GNAEGSS(ph)DEEGKLVIDEPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GNAEGSSDEEGKLVIDEPAK 20 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.089)S(0.911)DEEGKLVIDEPAK;GNAEGS(0.087)S(0.913)DEEGKLVIDEPAK;GNAEGS(0.358)S(0.642)DEEGKLVIDEPAK 272.91 1.18E-44 2468610000 3667740 2492650 3535970 3621390 2518990 1949250 3496240 4392190 7908400 TRUE FALSE 3183038.866 2476275.618 5245976.919 4443681.949 2468867.027 2024238.909 3157175.183 3452954.349 6973477.961 0.456449262 0.355099081 0.752275543 0.637226069 0.354036686 0.290276806 0.452740397 0.495155268 1 22.73344694 1.23774459 5.574374287 1.024959652 0.472829581 0.595769537 0.136256133 0.113818464 11.31223393 0.241093426 0.036161455 17.28799348 -1.23774459 -0.552130071 GNAEGSS(ph)DEEGKLVIDEPAKEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GNAEGSSDEEGKLVIDEPAKEK 22 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.098)S(0.902)DEEGKLVIDEPAKEK 245.2 3.77E-31 812340000 1321400 831830 899080 754060 696790 420050 1381200 1502900 491600 TRUE FALSE 1146773.642 826365.654 1333878.095 925280.8481 682925.2422 436209.5953 1247251.437 1181516.531 433483.608 2.645483291 1.906336569 3.077113115 2.134523269 1.575434987 1.006288559 2.877274742 2.725631393 1 18.72561791 3.491880471 24.00564629 1.972732996 2.500397704 0.168691291 0.677387213 966.6416026 1572225.537 0.200288731 0.285133483 3103.705249 -3.491880471 0.527664709 GNAGQSNYGFANSAMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 GNAGQSNYGFANSAMER 17 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;; 438.46 7.10E-162 3548000000 1341822 1245553 881253 940819 1278119 1546366 1285331 1417865 1325893 FALSE TRUE 1164496.823 1237370.88 1307429.898 1154446.333 1252686.932 1605855.701 1160679.797 1114665.604 1169147.44 0.996022215 1.058353154 1.118276321 0.987425789 1.071453343 1.373527107 0.992757421 0.953400371 1 20.15702545 2.029746463 24.99996675 0.973283263 1.100706928 0.217133257 0.106609238 291.6150053 245082.2266 0.044233125 0.02982157 107.0893945 -2.029746463 0.127423665 GNAMVEEGHFAAEDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GNAMVEEGHFAAEDVK 16 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 165.8 6.90E-09 888170000 1240210 1069280 818990 951500 1015930 1034510 1159110 1475300 1328510 FALSE TRUE 1076313.106 1062255.829 1215056.303 1167552.618 995714.9806 1074308.269 1046699.691 1159818.576 1171455.061 0.918783094 0.906783251 1.037219731 0.996668721 0.849981372 0.917071687 0.893503921 0.990066639 1 20.15987018 1.609792677 7.091236165 0.997328642 0.933461196 0.20420845 0.052216032 0.20007181 21.87944108 0.035542075 0.014187111 40.7185849 -1.609792677 -0.063867447 GNDPLTSS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 GNDPLTSSPGR 11 0 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 GNDPLTS(0.007)S(0.993)PGR;GNDPLTS(0.001)S(0.999)PGR;GNDPLTSS(1)PGR;GNDPLTSS(1)PGR;GNDPLTS(0.001)S(0.999)PGR;GNDPLTS(0.001)S(0.999)PGR;GNDPLTSS(1)PGR;GNDPLTSS(1)PGR 212.78 5.01E-09 26464620000 12506410 12290290 8168460 9104310 11674890 12388230 10657720 12532950 11625370 TRUE FALSE 10853656.23 12209554.28 12118754.58 11171582.74 11442582.53 12864813.22 9624135.955 9852876.174 10251032 1.058786689 1.191056108 1.182198492 1.089800786 1.116237129 1.254977374 0.938845567 0.96115944 1 23.28926582 2.222036363 24.99989538 0.964361307 1.148111926 0.697683353 0.05652234 125.7826123 190297.7235 0.022286648 0.01507325 166.7386817 -2.222036363 0.183750619 GNDS(ph)DGEGESDDPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GNDSDGEGESDDPEK 15 0 O75351;K7EKZ3 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 1 GNDS(1)DGEGESDDPEK;GNDS(1)DGEGESDDPEK 281.49 9.60E-34 649090000 1355540 949170 1152750 1272710 995610 908770 1143370 1342270 3810500 TRUE FALSE 1176401.954 942934.8398 1710223.756 1561698.258 975799.3089 943730.97 1032486.153 1055236.006 3360027.031 0.350116813 0.280633111 0.508991071 0.464787409 0.290414125 0.280870053 0.307285074 0.314055809 1 21.68004141 1.236726958 24.99966213 1.000000817 0.34841145 0.872936934 0.077976672 17.12640654 233430.1945 0.128147532 0.020426608 17.24753196 -1.236726958 -0.651589367 GNDVAFHFNPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 GNDVAFHFNPR 11 0 P17931;G3V3R6 P17931 LGALS3 Galectin-3;Galectin 0 ;;;;;;; 146.07 3.59E-05 14897120000 12680590 12612420 8505430 9361390 10488300 12085170 9061250 12229290 15919400 FALSE TRUE 11004817.9 12529568.18 12618684.4 11487036.68 10279603.35 12550094.31 8182491.37 9614151.502 14037426.67 0.783962628 0.892582984 0.898931456 0.818314991 0.732299701 0.894045227 0.582905369 0.684894157 1 23.74277515 3.440555516 4.722080404 0.758585431 0.861895902 0.074534863 0.116461064 0.395453351 20.74434013 0.034188849 0.045821599 2757.753952 -3.440555516 0.103310471 GNEFFCEVDEDYIQDKFNLTGLNEQVPHYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GNEFFCEVDEDYIQDKFNLTGLNEQVPHYR 30 1 P67870;Q5SRQ3;Q5SRQ6;N0E472;A0A0G2JM12;N0E644;A0A0G2JM58 P67870 CSNK2B;CSNK2B-LY6G5B-1181;CSNK2B-LY6G5B--991;CSNK2B-LY6G5B-562 Casein kinase II subunit beta 0 ; 331.52 1.43E-105 795750000 806190 705890 397410 506440 598650 588260 696720 879730 428460 FALSE TRUE 699649.9489 701252.9621 589598.8053 621434.9425 586738.0362 610890.7429 629152.2016 691606.5856 377807.9469 1.851866681 1.856109613 1.560578093 1.644843491 1.553006074 1.616934604 1.665269899 1.830577126 1 18.52729352 1.231642065 24.99996981 0.99999881 1.694149984 0.787396056 0.11387539 118.6943713 428859.4557 0.288659383 0.02980972 17.04676856 -1.231642065 0.694151174 GNEFLFSHLWPLIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GNEFLFSHLWPLIEK 15 0 H7C5G1;Q2TAA2-2;Q2TAA2 H7C5G1 IAH1 Isoamyl acetate-hydrolyzing esterase 1 homolog 0 84.859 0.0081658 102020000 280720 276710 178460 164670 206620 205480 233200 297050 266920 FALSE TRUE 243622.1407 274892.2738 264763.8529 202060.8403 202508.6662 213384.9486 210584.2999 233528.1691 235365.0217 1.035082184 1.167940214 1.124907393 0.858499869 0.860402556 0.906612831 0.89471366 0.992195729 1 17.84454041 3.748562353 24.79617672 0.921952047 1.11517298 0.713421984 0.056873231 352.0844181 872880.5292 0.016292542 0.027792159 5604.828823 -3.748562353 0.193220933 GNEPGSDRS(ph)PS(ph)PSKNDSFFTPDSNHNSLSQSTTGHLSLPQK ddPTM_MDA-MB-175_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(0.178)DRS(0.819)PS(0.922)PS(0.052)KNDS(0.014)FFT(0.013)PDS(0.001)NHNSLSQSTTGHLSLPQK 108.64 1.23E-05 464640000 55754 68034 11934 41801 130530 91334 92659 121500 104350 TRUE FALSE 48385.96764 67587.08017 17705.32232 51292.55594 127932.7084 94847.67808 83672.94444 95518.17051 92013.86188 0.525855199 0.734531502 0.192420163 0.55744379 1.390363428 1.03079771 0.909351512 1.038084573 1 16.4895636 3.354677668 7.627397323 1.053636125 0.488179264 0.715781644 0.178974334 0.125570475 7.876015316 0.051149721 0.066066375 2262.964122 -3.354677668 -0.565456861 GNEPGSDRSPS(ph)PS(ph)KNDSFFTPDSNHNSLSQSTTGHLSLPQK ddPTM_MDA-MB-175_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(0.08)DRS(0.428)PS(0.499)PS(0.928)KNDS(0.034)FFT(0.028)PDS(0.002)NHNSLSQSTTGHLSLPQK 81.09 0.0012755 477740000 80700 106740 16177 47771 195740 134350 141130 181580 145190 TRUE FALSE 70035.29053 106038.8179 24000.25131 58618.13568 191845.157 139518.5314 127443.2343 142750.5301 128025.8036 0.547040429 0.828261295 0.187464172 0.457861884 1.498488208 1.08976884 0.995449595 1.11501374 1 16.96607509 3.259068507 24.99936595 1.123331946 0.505543224 0.700069817 0.206241414 138.1781363 168439.7694 0.059525476 0.076757107 1815.80207 -3.259068507 -0.617788721 GNETSFVPS(ph)RR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GNETSFVPSRR 11 1 P35749;P35749-2 P35749 MYH11 Myosin-11 1 GNETSFVPS(1)RR;GNETSFVPS(0.999)RR 54.259 0.081342 989160000 36051 33816 14803 30232 50849 38752 37593 49443 35570 TRUE FALSE 31286.76901 33593.86047 21961.78031 37096.63767 49837.20438 40242.81452 33947.23665 38869.99922 31364.95512 0.997507214 1.071063559 0.700201235 1.182741615 1.588945503 1.283050282 1.082330152 1.2392812 1 14.93686588 3.502043091 24.25012225 1.243511658 0.938360105 0.400361771 0.177642394 538.2646992 523755.3534 0.04985179 0.073519654 3177.189297 -3.502043091 -0.305151553 GNFGGSFAGSFGGAGGHAPGVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GNFGGSFAGSFGGAGGHAPGVAR 23 0 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 255.2 1.53E-43 2102040000 964770 825500 427410 577400 862660 887920 736350 883090 953890 FALSE TRUE 837273.2001 820077.2361 634106.9056 708507.495 845494.7538 922078.857 664938.8903 694248.0757 841122.2109 0.995423958 0.974979885 0.753882013 0.842335972 1.005198463 1.096248375 0.790537786 0.825383121 1 19.68195591 GNFNYIEFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GNFNYIEFTR 10 0 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ;;; 262.63 4.66E-17 10772500000 3510590 3534270 2392430 2528300 3208200 3797130 3161310 3560160 3306310 FALSE TRUE 3046656.637 3511053.148 3549417.15 3102389.158 3144363.097 3943208.048 2854726.643 2798847.489 2915441.798 1.045006845 1.2042954 1.217454299 1.064123166 1.078520277 1.352525045 0.97917463 0.960008013 1 21.47528309 2.064662345 24.99999179 0.97487752 1.157578451 0.473983864 0.089616751 47.37240905 18314.78926 0.035357195 0.023837822 116.0545964 -2.064662345 0.182700931 GNFTLPEVAECFDEITYVELQKEEAQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GNFTLPEVAECFDEITYVELQKEEAQK 27 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 214.02 4.99E-27 79237000 104121 80736 54333 41897 64750 45848 95173 103608 19094.1 FALSE TRUE 90361.14604 80205.6399 80608.62053 51410.35421 63461.60168 47611.80223 85943.13711 81452.23548 16836.81725 5.366878116 4.763705557 4.787640047 3.05344849 3.769216042 2.82783863 5.104476448 4.837745416 1 14.03933182 3.870629828 5.663791979 3.674607881 4.996445342 0.271736281 1.148119955 0.366907186 15.30031183 0.310512637 0.549119374 7423.860937 -3.870629828 1.321837461 GNHECASINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 157.49 0.0056673 43221000 180202 176704 116374 118641.6 164870 196259 141462 159094 162244 FALSE TRUE 156387.8491 175543.2198 172652.8556 145580.9886 161589.4096 203809.2107 127743.037 125072.9862 143063.6991 1.093134387 1.227028385 1.206825048 1.017595585 1.12949274 1.424604648 0.892910206 0.874246835 1 17.12629812 2.192503977 24.99984315 0.911128026 1.176226889 0.553698094 0.11007643 89.45418832 48555.66376 0.044440554 0.029961926 155.7772298 -2.192503977 0.265098863 GNICIPYEEDIPSLGLSEVSDT(ph)KEDENGSPLNHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GNICIPYEEDIPSLGLSEVSDTKEDENGSPLNHR 34 1 O15055 O15055 PER2 Period circadian protein homolog 2 1 GNICIPYEEDIPSLGLS(0.027)EVS(0.106)DT(0.433)KEDENGS(0.433)PLNHR;GNICIPYEEDIPSLGLS(0.006)EVS(0.025)DT(0.526)KEDENGS(0.443)PLNHR 78.915 0.0027611 134464000 106370 116219 83012 97003 114248 93601 116307 157382 125494 TRUE FALSE 92312.93499 115455.5497 123156.8809 119029.0137 111974.6883 97201.89104 105027.565 123727.084 110658.2423 0.834216531 1.043352464 1.112948103 1.07564526 1.011896502 0.878397208 0.949116513 1.118100934 1 16.75575139 GNICIPYEEDIPSLGLSEVSDTKEDENGS(ph)PLNHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GNICIPYEEDIPSLGLSEVSDTKEDENGSPLNHR 34 1 O15055 O15055 PER2 Period circadian protein homolog 2 1 GNICIPYEEDIPSLGLS(0.001)EVS(0.017)DT(0.064)KEDENGS(0.917)PLNHR 87.226 0.0003396 62212000 47358 44516 28958 37551 44304 36078 45054 60813 41606 TRUE FALSE 41099.52031 44223.57146 42962.18566 46077.52848 43422.43708 37465.94401 40684.67001 47808.6132 36687.38608 1.120262976 1.205416253 1.171034251 1.255950162 1.183579473 1.021221406 1.108955267 1.3031349 1 15.1629965 2.969641224 24.92712008 1.1347781 1.192123229 0.135885273 0.088147801 1800.988581 1478764.065 0.029508375 0.029550237 932.4836459 -2.969641224 0.057345129 GNIETTS(ph)EDGQVFSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GNIETTSEDGQVFSPK 16 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 GNIET(0.002)T(0.037)S(0.961)EDGQVFSPK 195.48 5.07E-11 147380000 885930 723090 459900 604690 681060 627020 811530 905700 832070 TRUE FALSE 768852.1058 718339.9742 682309.1783 741994.1066 667508.2385 651141.8651 732827.9455 712023.1032 733703.6325 1.047905546 0.97906013 0.929952024 1.011299486 0.909779111 0.887472593 0.998806484 0.970450563 1 19.4848379 4.694550351 3.421053077 0.958914483 1.055255617 0.326432395 0.040230418 0.32711721 6.548504249 0.010135163 0.07638009 49493.74898 -4.694550351 0.096341134 GNIETTSEDGQVFS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GNIETTSEDGQVFSPK 16 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 GNIETTSEDGQVFS(1)PK 226 6.67E-15 246920000 451100 360640 234680 267680 386720 360930 437440 476020 427760 TRUE FALSE 391485.9921 358270.9321 348172.033 328460.8352 379025.0286 374815.2107 395017.1361 374226.8274 377190.7001 1.037899375 0.949840312 0.923066324 0.870808414 1.004863133 0.993702153 1.04726107 0.992142243 1 18.52493458 3.05017906 24.9999974 1.008285154 0.94333871 0.339357262 0.043097599 122.2013053 60881.72766 0.013218469 0.014988333 1122.481159 -3.05017906 -0.064946443 NMDPLNDNIATLLHQSSDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NMDPLNDNIATLLHQSSDK 19 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 308.54 1.85E-61 1972100000 1905600 1975840 726230 1760370 2346240 2044310 2298440 2598340 4826150 FALSE TRUE 1653770.132 1962860.577 1077437.257 2160088.914 2299554.414 2122955.929 2075537.643 2042705.211 4255608.045 0.388609598 0.461240922 0.253180567 0.507586434 0.540358602 0.498860775 0.487718235 0.480003137 1 22.02093385 1.230557838 4.537419108 1.04974826 0.451704719 0.821313312 0.080393732 0.08991018 3.911463422 0.175343216 0.020985578 17.00426398 -1.230557838 -0.598043541 GNKHDDGTQS(ph)DSENAGAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GNKHDDGTQSDSENAGAHR 19 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 GNKHDDGTQS(1)DSENAGAHR;GNKHDDGT(0.21)QS(0.789)DSENAGAHR;GNKHDDGT(0.001)QS(0.999)DSENAGAHR 319.95 4.04E-62 726306000 435449 266338 241795 226631 256189 250857 298897 318275 361927 TRUE FALSE 377903.3114 264588.4081 358727.8708 278091.0324 251091.3401 260507.6311 269910.0149 250214.3681 319140.4024 1.184128705 0.829065847 1.124044051 0.871375201 0.786773903 0.816279071 0.845740661 0.784025984 1 18.28383174 3.586481954 6.239551119 0.836497275 1.023045137 0.411758556 0.108699553 0.225241881 11.10802778 0.027537571 0.040977836 3859.063756 -3.586481954 0.186547861 GNKHDDGTQS(ph)DSENAGAHRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GNKHDDGTQSDSENAGAHRR 20 2 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 GNKHDDGT(0.004)QS(0.989)DS(0.007)ENAGAHRR 54.235 0.051559 62725000 26304 17855 13360 11209 15070 19369 18679 19285 8324.7 TRUE FALSE 22827.85975 17737.70933 19820.94069 13754.17477 14770.13648 20114.13796 16867.51345 15161.05283 7340.56345 3.109823914 2.41639616 2.70019336 1.873721937 2.012125716 2.740135427 2.297849964 2.065379985 1 12.84167509 1.093550634 1.687257951 2.66E-10 2.43669161 0.624748626 0.3540727 1.023527136 1.970016343 4.620803802 0.099959418 12.40368231 -1.093550634 2.43669161 GNKPWISLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GNKPWISLPR 10 1 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ; 152.07 1.70E-05 7796100000 7593100 8526300 5464800 6015500 8012100 7971600 8171000 9164300 8356000 FALSE TRUE 6589652.597 8470290.174 8107595.559 7381411.216 7852674.885 8278272.61 7378577.678 7204585.762 7368163.199 0.894341292 1.14957961 1.100355046 1.001798008 1.065757459 1.123519171 1.001413443 0.977799428 1 22.81287359 2.026770859 24.01537012 0.988001684 1.06035315 0.149472871 0.070567031 218.7955036 196273.6926 0.027376536 0.018456607 106.3581707 -2.026770859 0.072351466 GNLELRPGGAHPGTCS(ph)PSRPGS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GNLELRPGGAHPGTCSPSRPGS 22 2 Q5JTU8;B1AMJ5;A0A0A0MRG9;Q96SN8-3;Q96SN8-2;Q96SN8;Q96SN8-4 Q5JTU8 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 1 GNLELRPGGAHPGT(0.007)CS(0.982)PS(0.01)RPGS;GNLELRPGGAHPGT(0.023)CS(0.853)PS(0.124)RPGS 131.94 5.92E-06 1307750000 969870 895850 622600 709320 883440 1002150 881650 962130 914630 TRUE FALSE 841699.2222 889965.1024 923691.4425 870381.9473 865861.2724 1040703.359 796147.7187 756385.9868 806503.4833 1.043639909 1.103485751 1.145303723 1.079204201 1.073598925 1.290389168 0.987159678 0.937858301 1 19.62132124 2.030297886 24.99999848 0.963895884 1.12025033 0.512548048 0.067960532 141.8551691 117049.821 0.026758983 0.01804066 107.225452 -2.030297886 0.156354446 GNPS(ph)PPAAGEGQRPPPPLCVPGGGGGAPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GNPSPPAAGEGQRPPPPLCVPGGGGGAPAR 30 1 Q92623 Q92623 TTC9 Tetratricopeptide repeat protein 9A 1 GNPS(1)PPAAGEGQRPPPPLCVPGGGGGAPAR;GNPS(1)PPAAGEGQRPPPPLCVPGGGGGAPAR;GNPS(1)PPAAGEGQRPPPPLCVPGGGGGAPAR;GNPS(1)PPAAGEGQRPPPPLCVPGGGGGAPAR;GNPS(1)PPAAGEGQRPPPPLCVPGGGGGAPAR;GNPS(1)PPAAGEGQRPPPPLCVPGGGGGAPAR 247.66 2.95E-46 7433320000 250467 224679 159323 185783 247540 251798 237220 266451 247452 TRUE FALSE 217367.1513 223203.0689 236372.1357 227967.8697 242614.4383 261484.832 214214.4409 209472.5272 218198.5065 0.996189914 1.022935823 1.08328943 1.044772823 1.111897795 1.198380485 0.981741096 0.960008987 1 17.7352817 2.046444805 24.99996817 0.975265448 1.075642437 0.400524168 0.055101661 117.9789706 63504.33929 0.023606245 0.01591532 111.2870948 -2.046444805 0.100376989 GNPTVEVDLFTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GNPTVEVDLFTSK 13 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 131.79 0.00029383 125740000 124140 129160 76994 83573 137600 120830 110520 126270 133230 FALSE TRUE 107734.5845 128311.5395 114228.5559 102549.527 134862.0292 125478.4083 99801.78741 99268.14313 117479.7012 0.917048506 1.092201786 0.972325898 0.872912733 1.147960268 1.068085865 0.849523674 0.844981236 1 16.84205198 2.233369515 24.99921137 0.885060792 1.013500268 0.254315382 0.090735536 158.3615931 762624.0923 0.036278318 0.025283772 171.1470883 -2.233369515 0.128439476 GNRGS(ph)GGGGGGGGQGSTNYGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GNRGSGGGGGGGGQGSTNYGK 21 1 Q99729-3;Q99729-4 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 1 GNRGS(1)GGGGGGGGQGSTNYGK;GNRGS(1)GGGGGGGGQGSTNYGK;GNRGS(1)GGGGGGGGQGSTNYGK;GNRGS(1)GGGGGGGGQGSTNYGK 171.45 4.17E-12 451261000 490044 404340 210820 247894 346150 336995 417923 503394 154706 TRUE FALSE 425283.4438 401683.8639 312773.2572 304182.1215 339262.2922 349959.4157 377392.8918 395747.1105 136416.8329 3.117529081 2.944532983 2.292776122 2.229799029 2.486953296 2.565368278 2.766468651 2.901013768 1 17.05766215 4.328276865 4.886160508 2.408059361 3.071311342 0.232973749 0.52033922 0.321536048 12.82666668 0.128654294 0.359000349 21294.96178 -4.328276865 0.663251981 GNRPVILTYHDIGLNHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GNRPVILTYHDIGLNHK 17 1 Q5TH30;Q9UGV2;Q9UGV2-2;Q5TH29 Q5TH30 NDRG3 Protein NDRG3 0 207.79 3.72E-12 807990000 263360 263250 165650 193900 254020 230420 273610 313430 294450 FALSE TRUE 228556.3087 261520.6934 245758.8941 237927.9586 248965.499 239284.4065 247075.3443 246405.4336 259640.4564 0.88028003 1.007241695 0.946535441 0.916374751 0.958885616 0.921599083 0.951605723 0.949025576 1 17.98615567 1.07621745 2.129361948 1.040266208 0.942228329 0.24352538 0.032583808 1.808551696 5.531652838 0.407590464 0.008064107 11.9183861 -1.07621745 -0.098037879 GNS(ph)PPSSGEACR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 GNSPPSSGEACR 12 0 P41227-2;P41227 P41227-2 NAA10 N-alpha-acetyltransferase 10 1 GNS(1)PPSSGEACR;GNS(0.99)PPS(0.008)S(0.002)GEACR;GNS(0.992)PPS(0.004)S(0.004)GEACR;GNS(1)PPSSGEACR;GNS(0.986)PPS(0.007)S(0.007)GEACR;GNS(0.966)PPS(0.013)S(0.02)GEACR;GNS(0.985)PPS(0.008)S(0.008)GEACR;GNS(0.995)PPS(0.001)S(0.003)GEACR 189.11 8.75E-06 3347989000 2192258 2146211 1674156 1954622 2158945 2416003 2011427 2420687 2792299 TRUE FALSE 1902545.551 2132112.399 2483783.441 2398448.8 2115986.218 2508948.199 1816359.119 1903041.923 2462196.593 0.772702536 0.865939139 1.008767313 0.974109381 0.85938963 1.018987763 0.737698657 0.772904133 1 21.23151453 1.194236401 23.15583516 1.000003907 0.875768558 0.133168162 0.099164966 10315.6066 5388072.983 11.6906874 0.025962564 15.63998748 -1.194236401 -0.124235349 GNS(ph)PPSSGEACREEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GNSPPSSGEACREEK 15 1 P41227-2;P41227 P41227-2 NAA10 N-alpha-acetyltransferase 10 1 GNS(0.949)PPS(0.049)S(0.002)GEACREEK;GNS(0.826)PPS(0.15)S(0.023)GEACREEK 151.96 1.76E-06 895360000 960340 991760 378605 379516 816840 694660 1154380 1169460 89161 TRUE FALSE 833428.6358 985245.0633 561699.6444 465690.9083 800586.4821 721384.0197 1042428.405 919380.0797 78620.48815 10.60065455 12.53165792 7.144443612 5.923276735 10.18292434 9.175522013 13.25899177 11.69389941 1 16.2626177 4.249407088 24.9879753 8.912218944 11.56615648 0.117049261 3.413089471 546.93719 1260002.211 0.867928343 2.247870376 17758.53305 -4.249407088 2.653937535 GNS(ph)RPGTPSAEGGS(ph)TSSTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 2 GNS(0.57)RPGT(0.43)PS(0.108)AEGGS(0.83)T(0.011)S(0.05)S(0.001)TLR 220.55 1.01E-23 1002800000 968780 796040 547310 726080 738950 757590 699880 798540 1198500 TRUE FALSE 840753.2684 790810.7608 811990.9466 890947.5614 724246.3407 786734.9775 632005.7453 627778.4352 1056814.695 0.795554104 0.748296522 0.768338054 0.843049936 0.685310626 0.744439854 0.598028915 0.594028866 1 20.011291 3.218379959 24.93265457 0.699598991 0.784453615 0.048655629 0.115007713 530.2804889 655145.2624 0.034776008 0.039480865 1653.407712 -3.218379959 0.084854624 GNSRPGT(ph)PS(ph)AEGGSTSSTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 2 GNS(0.058)RPGT(0.942)PS(0.937)AEGGS(0.051)T(0.011)SSTLR;GNS(0.374)RPGT(0.627)PS(0.94)AEGGS(0.018)T(0.003)S(0.018)S(0.012)T(0.008)LR 251.56 9.86E-31 1156350000 1392660 1186790 914700 1063460 1113990 1122240 967250 1182110 1897280 TRUE FALSE 1208616.452 1178993.898 1357051.979 1304934.847 1091823.778 1165413.299 873446.2439 929324.9757 1672985.72 0.722430824 0.704724424 0.811155746 0.780003578 0.652619903 0.696606842 0.522088284 0.555488887 1 20.6739937 3.231193696 24.65637579 0.657443644 0.755058852 0.041729929 0.131227105 325.5753884 1089667.313 0.039703876 0.045934349 1702.917843 -3.231193696 0.097615209 GNSRPGT(ph)PSAEGGSTSSTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 GNS(0.001)RPGT(0.992)PS(0.007)AEGGSTSSTLR;GNSRPGT(0.993)PS(0.007)AEGGSTSSTLR;GNSRPGT(0.994)PS(0.006)AEGGSTSSTLR 201.97 1.95E-21 3174300000 419817 401004 438692 505729 665619 715893 665076 711820 812459 TRUE FALSE 364337.1198 398369.7783 650844.9185 620562.499 652374.4842 743433.867 600577.0319 559602.8324 716411.0226 0.508558786 0.556063162 0.908479767 0.86621015 0.910614806 1.03771975 0.8383135 0.781119797 1 19.45042801 4.259726565 5.984044553 0.895257765 0.525570651 0.81376736 0.074246236 0.069554996 8.008033247 0.019973754 0.050933811 18185.55522 -4.259726565 -0.369687114 GNTSGSHIVNHLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GNTSGSHIVNHLVR 14 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 180.11 1.04E-06 221290000 74940 65590 25004 39299 60861 70338 61460 74132 61527 FALSE TRUE 65036.48913 65159.13497 37096.01803 48222.4386 59649.98517 73043.94837 55499.61866 58279.4487 54253.34815 1.198755309 1.201015922 0.683755368 0.888838021 1.099471041 1.346349135 1.022971311 1.074209255 1 15.72742455 3.108145203 9.717110405 1.110801219 0.986066697 0.098939613 0.172917968 0.749725179 62.51535056 0.055419162 0.062884712 1282.759392 -3.108145203 -0.124734522 GNVAGDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GNVAGDSK 8 0 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ; 112.84 0.0068939 126624000 431870 376150 325190 417460 314470 385300 451580 514590 904290 FALSE TRUE 374797.2853 373679.0459 482452.9717 512250.6735 308212.6623 400122.7403 407785.8411 404548.933 797385.8664 0.470032516 0.468630135 0.605043295 0.642412532 0.386528875 0.501793118 0.511403397 0.507343998 1 19.60491851 1.238165865 24.99963871 1.000000547 0.512877864 0.824286826 0.070857466 3.908207405 247190.4254 0.100131058 0.017559533 17.30477132 -1.238165865 -0.487122683 GNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK 49 1 P68104;A0A087WVQ9;A0A087WV01 P68104 EEF1A1 Elongation factor 1-alpha 1;Elongation factor 1-alpha 0 ; 308.99 5.69E-120 2237070000 3064700 2511300 1119800 1315790 2004040 1716870 3162000 3226800 644040 FALSE TRUE 2659692.13 2494803.105 1661339.026 1614560.23 1964163.525 1782919.1 2855349.727 2536773.931 567902.3249 4.683361933 4.393014424 2.925395711 2.843024512 3.458629132 3.139481953 5.027888779 4.466919433 1 19.11528329 4.368212458 6.213838061 3.457200021 4.609069268 0.18204802 1.069657734 0.383648459 19.08918856 0.27498554 0.746915605 23345.99875 -4.368212458 1.151869247 GNVS(ph)S(ph)YIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GNVSSYIR 8 0 Q5HYW3 Q5HYW3 RGAG4 Retrotransposon gag domain-containing protein 4 2 GNVS(0.667)S(0.667)Y(0.667)IR 70.028 0.076593 103230000 286790 228180 196810 299200 228250 250610 302470 279900 525390 TRUE FALSE 248889.9749 226681.0706 291987.9743 367137.933 223708.2716 260251.1289 273136.506 220045.5632 463278.9927 0.537235616 0.489297106 0.630263791 0.792476971 0.482880241 0.561758968 0.589572396 0.474974188 1 18.82152174 1.230789498 24.99908191 1.000000774 0.569652333 0.678956173 0.092966477 176.269914 566999.3388 0.24497476 0.02327951 17.01333672 -1.230789498 -0.430348441 GNVVPS(ph)PLPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GNVVPSPLPTR 11 0 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 GNVVPS(0.999)PLPT(0.001)R;GNVVPS(1)PLPTR;GNVVPS(0.993)PLPT(0.007)R;GNVVPS(1)PLPTR;GNVVPS(0.962)PLPT(0.038)R;GNVVPS(0.999)PLPT(0.001)R 116.98 0.00096087 41901982600 2883857 2832483 2777581 3042688 2860200 3322757 2645862 3011317 6206067 TRUE FALSE 2502747.991 2813876.233 4120828.462 3733576.815 2803287.616 3450585.612 2389266.71 2367370.294 5472392.829 0.457340704 0.514194854 0.753021318 0.682256726 0.512259939 0.63054421 0.436603655 0.432602404 1 22.38374037 1.22909005 24.94835553 1.000000909 0.551642424 0.633404326 0.10702527 272.2342252 717094.2316 0.357503143 0.028629908 16.94689156 -1.22909005 -0.448358485 DSLHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 DSLHEK 6 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;; 97.068 0.041493 1160470000 2591450 2467170 1189790 2786960 1363030 2070690 2672070 3260920 7989600 FALSE TRUE 2248983.317 2450962.998 1765176.424 3419781.864 1335908.37 2150350.784 2412933.063 2563597.635 7045078.59 0.31922757 0.347897183 0.25055454 0.485414296 0.189622919 0.305227366 0.342499098 0.363884888 1 22.74818437 1.231058078 4.387998856 1.066201452 0.321818322 0.888500381 0.075221018 0.063835088 2.457968786 0.151038332 0.017697931 17.02386151 -1.231058078 -0.74438313 GNWDEQFDKENTEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GNWDEQFDKENTEER 15 1 A0A2R8YD12;A0A024QZX5;A0A087X1N8;P35237;A0A2R8Y6A7 A0A2R8YD12 SERPINB6 Serpin B6 0 ; 115.56 0.00047249 1030170000 672850 584560 431780 529020 582090 591640 680180 759280 661810 FALSE TRUE 583931.1677 580719.9869 640590.2522 649142.0766 570507.5478 614400.7736 614216.2483 596913.8807 583571.5757 1.000616192 0.995113558 1.097706398 1.112360683 0.977613667 1.052828478 1.052512278 1.022863185 1 19.15455009 1.440879691 3.082558984 1.000153232 1.042298421 0.089823964 0.042640329 0.725973692 11.59929811 0.060296835 0.011493814 27.59813223 -1.440879691 0.042145189 GNWEQPQNQNQTQHK ddPTM_MDA-MB-175_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 ;;; 241.8 6.75E-18 1212970000 972706 782594 561895 700325 778722 758985 836568 990341 1010790 FALSE TRUE 844160.4376 777453.0885 833629.3014 859344.495 763226.9557 788183.6441 755437.7641 778564.284 891295.5577 0.947116173 0.872273043 0.935300635 0.964152113 0.856311859 0.884312322 0.84757268 0.873519763 1 19.76554439 3.231270026 24.99802556 0.886231036 0.926007113 0.12314934 0.047577563 336.3328338 1153218.285 0.014240651 0.016472077 1703.217168 -3.231270026 0.039776077 GNYAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 111.73 0.064213 1915720000 2006270 1992740 1308920 1448650 1132290 1952930 1478730 1851740 1715330 FALSE TRUE 1741136.336 1979649.56 1941918.09 1777588.124 1109759.644 2028060.481 1335322.992 1455759.811 1512545.642 1.151129783 1.308819718 1.283874044 1.175229411 0.733703244 1.340825973 0.882831536 0.962456782 1 20.52854725 3.461128504 24.92082894 0.988163612 1.249949532 0.39071136 0.154703487 217.0963312 338290.88 0.04171183 0.0538655 2891.535338 -3.461128504 0.261785919 GNYDEGFGHRPHK ddPTM_MDA-MB-175_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 ; 187.57 4.11E-06 495360000 558560 502970 340730 408200 475880 481850 520220 601800 632100 FALSE TRUE 484744.8808 499665.957 505508.1677 500888.0489 466410.919 500387.0813 469769.1445 473109.7532 557373.8581 0.869694324 0.896464643 0.906946317 0.898657233 0.836800851 0.897758433 0.842825937 0.848819417 1 19.08828581 1.231515352 24.97463841 1.000000221 0.873999904 0.707241879 0.025321856 146.1378823 517994.5076 0.064464541 0.006566242 17.04179559 -1.231515352 -0.126000317 GPAAEEALNVFYYCTYEGAVDLDHVTDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GPAAEEALNVFYYCTYEGAVDLDHVTDER 29 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7;H7C408 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 0 ;; 247.57 7.57E-46 121425000 59101 62240 47367 49170 58568 61134 60899 72326 63367 FALSE TRUE 51290.65311 61831.14134 70273.83963 60334.80002 57402.61139 63485.86454 54993.02435 56859.64774 55875.82545 0.917939962 1.10658126 1.257678774 1.079801498 1.027324624 1.136195556 0.984200661 1.017607298 1 15.76993662 2.229074096 24.96041995 1.003461856 1.093088691 0.187004862 0.084912876 327.6255789 862022.182 0.034900738 0.023874482 169.4626899 -2.229074096 0.089626836 GPAGEAGAS(ph)PPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPAGEAGASPPVR 13 0 Q13425;Q13425-2;A0A140TA73 Q13425 SNTB2 Beta-2-syntrophin 1 GPAGEAGAS(1)PPVR;GPAGEAGAS(1)PPVR 131.08 0.00014116 1763600000 1043660 980530 807810 889200 1004170 1153450 816290 1009370 1496140 TRUE FALSE 905737.6867 974088.8339 1198469.618 1091106.451 984188.9816 1197823.968 737126.3214 793524.0804 1319268.034 0.686545617 0.738355519 0.908435274 0.827054414 0.746011392 0.907945874 0.558738863 0.601488144 1 20.33130627 2.246233935 24.99918353 0.688647562 0.80285911 0.0602583 0.135445605 347.3206624 1131551.835 0.050994675 0.038735983 176.2925401 -2.246233935 0.114211548 GPAGEAGAS(ph)PPVRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GPAGEAGASPPVRR 14 1 Q13425;Q13425-2;A0A140TA73 Q13425 SNTB2 Beta-2-syntrophin 1 GPAGEAGAS(1)PPVRR;GPAGEAGAS(1)PPVRR;GPAGEAGAS(1)PPVRR;GPAGEAGAS(1)PPVRR;GPAGEAGAS(1)PPVRR;GPAGEAGAS(1)PPVRR 128.64 4.44E-05 4135170000 2613820 2319970 1508840 1766960 2117330 2643210 1966300 2284010 1551820 TRUE FALSE 2268397.064 2304729.964 2238520.071 2168175.274 2075199.275 2744895.999 1775608.529 1795592.236 1368365.607 1.657741946 1.684293987 1.635907873 1.584499978 1.516553225 2.005966815 1.297612655 1.312216725 1 20.38402232 1.761647334 1.830112155 1.065023595 1.662110516 0.657403982 0.158833464 0.212183928 1.339127106 0.166861163 0.04413026 57.76267984 -1.761647334 0.597086921 GPAGNNDCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPAGNNDCR 9 0 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ; 103.83 0.0078128 167665000 514760 476070 317890 311060 248620 458140 415130 464690 446350 FALSE TRUE 446733.1618 472942.6648 471622.6673 381690.9273 243672.9484 475764.9423 374870.7565 365319.6597 393583.0115 1.13504178 1.201633838 1.198280041 0.969785067 0.619114498 1.208804568 0.95245665 0.928189604 1 18.58630842 3.707680894 6.258381324 0.941326317 1.18100412 0.371080024 0.142393958 0.192675633 25.57417809 0.038286811 0.058652047 5101.300343 -3.707680894 0.239677803 GPALTPIRDEEWGGHS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GPALTPIRDEEWGGHSPR 18 1 S4R3V8;Q86X29-6;Q86X29-5;Q86X29-2;Q86X29-3;Q86X29-4;Q86X29 S4R3V8 LSR Lipolysis-stimulated lipoprotein receptor 1 GPALTPIRDEEWGGHS(1)PR;GPALTPIRDEEWGGHS(1)PR;GPALTPIRDEEWGGHS(1)PR;GPALTPIRDEEWGGHS(1)PR;GPALTPIRDEEWGGHS(1)PR 209.41 3.17E-16 3140420000 1751680 1637140 1303990 1995080 2052660 2391390 914239 2234620 1806340 TRUE FALSE 1520191.05 1626385.52 1934603.926 2448093.407 2011816.082 2483388.321 825576.2425 1756763.903 1592796.543 0.954416342 1.021088052 1.214595759 1.536978102 1.263071602 1.559137187 0.518318706 1.102943066 1 20.60313056 2.247399324 24.99995958 0.906691827 1.258345154 0.361331087 0.23962178 224.4487059 634846.0121 0.092229398 0.070348998 176.7662401 -2.247399324 0.351653327 GPANGT(ph)PPPLPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPANGTPPPLPAR 13 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 GPANGT(1)PPPLPAR;GPANGT(1)PPPLPAR 106.66 0.015166 346420000 940510 934050 798350 938030 912230 987350 832650 975070 1758910 TRUE FALSE 816219.2206 927914.164 1184434.73 1151024.048 894078.4077 1025333.993 751899.7312 766558.8685 1550973.664 0.526262463 0.598278479 0.763671723 0.742129976 0.576462663 0.661090525 0.484792069 0.49424364 1 20.56474276 1.22858392 24.99752134 1.000000802 0.604718174 0.630520361 0.094814536 310.6572536 778324.9591 0.3418577 0.025885689 16.927153 -1.22858392 -0.395282628 GPAPAPQQCS(ph)EPETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPAPAPQQCSEPETK 15 0 Q3YEC7;Q3YEC7-2;G3V154 Q3YEC7 RABL6 Rab-like protein 6 1 GPAPAPQQCS(0.901)EPET(0.099)K 164.59 3.48E-09 0 143520 145210 103900 111680 146550 129870 158070 169890 173180 TRUE FALSE 124553.4684 144256.1059 154146.3875 137038.6509 143633.9417 134866.1829 142740.3957 133560.3456 152706.8577 0.815637688 0.9446603 1.009426753 0.897396836 0.940586061 0.883170442 0.93473468 0.874619173 1 17.22040533 5.564270966 0.003977994 1.795259234 0.025724093 0.039285161 0.056983339 803035.9775 620.4486435 134807.2802 141254.1514 366666.2742 -5.564270966 -1.769535141 GPAPAPQQCSEPET(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPAPAPQQCSEPETK 15 0 Q3YEC7;Q3YEC7-2;G3V154 Q3YEC7 RABL6 Rab-like protein 6 1 GPAPAPQQCS(0.118)EPET(0.882)K 200.09 4.55E-11 0 168490 157730 112740 121820 155660 146700 153010 201800 208010 TRUE FALSE 146223.6196 156693.8612 167261.4411 149481.0929 152562.6705 152343.6439 138171.1138 158646.6404 183419.2948 0.797209584 0.854293227 0.911907558 0.814969293 0.83177002 0.83057589 0.753307409 0.864939758 1 17.48478589 1.272176783 3.976057471 1.012931967 0.830418121 0.639684007 0.040335574 0.143720084 3.803773681 0.071347504 0.010419633 18.71443771 -1.272176783 -0.182513846 GPAS(ph)DS(ph)ETEDASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPASDSETEDASR 13 0 Q96ST2;Q96ST2-3 Q96ST2 IWS1 Protein IWS1 homolog 2 GPAS(1)DS(0.958)ET(0.042)EDASR;GPAS(1)DS(0.972)ET(0.028)EDASR 199.13 1.76E-07 357890000 799770 645990 571090 692090 698950 725280 610490 712540 1521650 TRUE FALSE 694078.3681 641746.4492 847271.0342 849239.6124 685042.2625 753181.9909 551284.7738 560168.866 1341762.27 0.517288631 0.478286253 0.631461365 0.632928523 0.510554125 0.561337882 0.410866206 0.417487418 1 20.35569765 1.231316068 24.99985894 1.000000844 0.51680405 0.799842279 0.075442444 127.281616 439191.4627 0.208275042 0.020865085 17.03397744 -1.231316068 -0.483196794 GPASQFYITPSTSLS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GPASQFYITPSTSLSPR 17 0 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 1 GPASQFYITPSTS(0.004)LS(0.996)PR;GPASQFYITPSTSLS(1)PR;GPASQFYITPSTSLS(1)PR;GPASQFYITPSTSLS(1)PR 309.59 4.66E-58 1182040000 1359470 1088260 830300 810000 987860 1223310 1022710 1056540 1062630 TRUE FALSE 1179812.595 1081111.148 1231835.857 993922.8801 968203.5187 1270371.527 923527.7416 830607.143 937007.092 1.259128778 1.153791852 1.314649449 1.06074211 1.033293693 1.355775787 0.985614463 0.886447019 1 19.83770044 2.074094061 8.18891916 0.93536747 1.185760726 0.540313122 0.104036337 0.18001341 17.55252707 0.041622206 0.027993642 118.6025593 -2.074094061 0.250393256 GPASSHRES(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPASSHRESPR 11 1 C9JAV3;A4D2B0 C9JAV3 MBLAC1 Metallo-beta-lactamase domain-containing protein 1 1 GPASSHRES(1)PR;GPASS(0.002)HRES(0.998)PR 83.087 0.010394 682320000 641950 668840 381179 549330 535950 746680 616860 668730 799320 TRUE FALSE 557114.681 664446.346 565518.4394 674063.7725 525285.6436 775405.2628 557037.0121 525727.2936 704825.3002 0.790429459 0.942710691 0.802352639 0.956355812 0.745270698 1.100138236 0.790319264 0.745897307 1 19.42690619 GPASTPTYS(ph)PAPTQPAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPASTPTYSPAPTQPAPR 18 0 Q6P1N0-2;Q6P1N0;K7EJY5 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 GPASTPT(0.001)YS(0.998)PAPTQPAPR;GPASTPT(0.002)YS(0.998)PAPTQPAPR 241.8 5.46E-24 534710000 353370 391450 284670 302510 393480 443670 395400 429650 408720 TRUE FALSE 306671.2592 388878.5392 422337.3642 371199.5191 385650.5178 460738.272 357054.1689 337772.691 360401.5872 0.850915396 1.079014502 1.17185212 1.029960833 1.070057768 1.27840245 0.990711977 0.937211996 1 18.45924584 2.022114308 24.99998826 0.964073257 1.085858706 0.171382767 0.108063594 347.1771868 392478.4128 0.043620208 0.029406632 105.2238791 -2.022114308 0.121785448 GPAVGIDLGTTYSCVGVFQHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GPAVGIDLGTTYSCVGVFQHGK 22 0 P11142;E9PKE3;E9PNE6;P11142-2;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;; 297.67 1.32E-55 3214470000 4448190 3931030 2680100 3427100 3910610 3684260 4468440 5013340 4580830 FALSE TRUE 3860350.421 3905206.805 3976205.324 4205275.435 3832796.512 3825995.866 4035091.377 3941276.255 4039289.496 0.955700359 0.966805377 0.984382359 1.041092855 0.948878885 0.94719526 0.998960679 0.975735029 1 21.94567012 3.075916993 0.002978486 1.959013391 2.13E-05 0.040906095 0.027964521 124157.4587 513.4545411 168775.0196 168925.2353 1191.014346 -3.075916993 -1.958992062 GPAWVGSHGVLQHTQGLPADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPAWVGSHGVLQHTQGLPADR 21 0 Q15654 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 ; 274.95 5.38E-45 1247100000 499690 584110 394810 498990 592490 558700 457990 607590 677650 FALSE TRUE 433654.7004 580272.9429 585741.4366 612293.3061 580700.6082 580193.5505 413574.2003 477661.6068 597538.989 0.725734569 0.971104737 0.980256431 1.024691807 0.971820448 0.970971872 0.69212923 0.799381489 1 19.18867333 2.276431604 24.99632869 0.818253918 0.949164301 0.179212915 0.109218195 227.8013058 150356.9388 0.040522717 0.031388085 188.9868575 -2.276431604 0.130910383 GPCAPAASS(ph)PTQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GPCAPAASSPTQK 13 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 GPCAPAASS(1)PTQK;GPCAPAAS(0.002)S(0.998)PTQK;GPCAPAAS(0.021)S(0.977)PT(0.003)QK;GPCAPAAS(0.019)S(0.963)PT(0.018)QK 292.95 1.43E-40 1489760000 2475660 2623450 2252070 2802990 2762720 2501120 3056430 3616380 4871080 TRUE FALSE 2148495.258 2606216.384 3341178.585 3439451.721 2707747.277 2597339.705 2760017.889 2843045.28 4295226.472 0.50020535 0.606770423 0.77788182 0.800761437 0.6304085 0.604703785 0.642577966 0.66190812 1 22.03430277 1.23863574 8.074532638 1.00405051 0.657624625 0.617740868 0.085689821 0.06766036 40.34685834 0.128337098 0.022228295 17.32350396 -1.23863574 -0.346425885 GPEDSWLLLSAPGPTPASPRPAS(ph)PCGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPEDSWLLLSAPGPTPASPRPASPCGK 27 1 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;Q14934-12;Q14934-13;Q14934-18 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 GPEDSWLLLSAPGPT(0.023)PAS(0.064)PRPAS(0.912)PCGK;GPEDSWLLLSAPGPT(0.332)PAS(0.062)PRPAS(0.606)PCGK 223.4 1.28E-34 333590000 305200 286000 162778 190066 303990 233330 324190 409120 174977 TRUE FALSE 264867.0467 284121.2472 241497.9853 233223.3903 297941.1937 242306.3561 292750.1037 321632.8718 154291.4184 1.716667391 1.841458521 1.565206852 1.5115772 1.931028938 1.570446099 1.897384227 2.084580433 1 17.2352983 3.248016257 24.99810217 1.753914644 1.665099738 0 0.303800067 1154.370514 3051819.406 0.086834697 0.110574938 1770.175221 -3.248016257 -0.088814906 GPEEEHPSVTLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 1351150000 2181200 2401190 917430 1743180 2505520 2663180 2185000 2457690 2938460 FALSE TRUE 1892948.894 2385416.425 1361102.217 2138995.662 2455665.054 2765634.258 1973099.036 1932132.119 2591078.606 0.730564055 0.920626807 0.525303329 0.825523261 0.947738539 1.067367949 0.761497174 0.745686416 1 21.30512135 3.485549158 24.79526613 0.882452822 0.733411332 0.259840956 0.134979492 591.8609643 1741281.601 0.039607077 0.053801739 3058.786452 -3.485549158 -0.149041491 GPEENYSRPEAPNEFYDGDHDNDKES(ph)DVEI ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPEENYSRPEAPNEFYDGDHDNDKESDVEI 30 2 O15379;O15379-2 O15379 HDAC3 Histone deacetylase 3 1 GPEENYSRPEAPNEFYDGDHDNDKES(1)DVEI;GPEENYSRPEAPNEFYDGDHDNDKES(1)DVEI 110.13 0.00012012 437270000 251910 170887 175423 197098 184626 214531 223802 256720 373180 TRUE FALSE 218619.4552 169764.432 260258.1496 241852.1134 180952.3038 222784.1464 202097.7165 201822.4258 329063.0855 0.664369432 0.515902389 0.79090655 0.734971876 0.549901559 0.677025641 0.614161009 0.613324419 1 18.32800467 1.235613919 24.99994922 1.000000482 0.643488259 0.656926853 0.080601057 50.72884611 430306.522 0.131626225 0.019318277 17.20338542 -1.235613919 -0.356512223 GPELLTMWFGESEANVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPELLTMWFGESEANVR 17 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 130.1 0.00011162 265390000 439590 346400 235720 290976 324472 353266 352826 384410 339237 FALSE TRUE 381497.0677 344124.4756 349714.9804 357046.5481 318015.642 366856.3716 318608.9888 302206.913 299132.7883 1.275343535 1.150407073 1.169096114 1.193605522 1.063125322 1.226399733 1.065108879 1.010276789 1 18.19042653 -1.345451472 0.246202149 8.41E-15 1.242754981 0.634806871 0.055639847 38.1027164 0.814984847 17.76005242 0.192871799 0.045138646 1.345451472 1.242754981 GPESESEDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GPESESEDHR 10 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;; 200.71 2.55E-07 2420714000 2107856 1914864 979749 1379248 1775956 1666823 1915703 1974099 1809298 FALSE TRUE 1829297.489 1902285.132 1453558.893 1692427.339 1740617.95 1730946.759 1729918.418 1551953.291 1595404.852 1.14660394 1.192352606 0.911090932 1.06081371 1.091019592 1.084957688 1.084313124 0.972764555 1 20.60549114 GPGAPAAS(ph)SPTQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPGAPAASSPTQK 13 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 GPGAPAAS(0.715)S(0.281)PT(0.004)QK 122.42 0.00024672 261270000 376000 468130 459920 549550 550320 486280 623440 770950 1029300 TRUE FALSE 326310.6473 465054.8232 682338.8503 674333.7268 539369.7087 504987.5063 562978.8848 606088.342 907617.3266 0.35952448 0.512390861 0.751791345 0.742971412 0.594269956 0.556388129 0.620282214 0.667779607 1 19.79172463 -2 0.068265063 2.027527846 1.01E-09 0.409560904 0.130015092 806.0815889 5.29032404 169.6350459 35.72343072 0.01 2 -2.027527845 GPGAPAAS(ph)SPTRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPGAPAASSPTRK 13 1 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 GPGAPAAS(0.453)S(0.453)PT(0.093)RK;GPGAPAAS(0.497)S(0.497)PT(0.005)RK 107.65 0.0013545 17133000 179359 224876 176589 232056 239086 204007 273054 326175 373200 TRUE FALSE 155656.2537 223398.7747 261988.0311 284747.8616 234328.6564 211855.2813 246573.2651 256425.0145 329080.7212 0.473003259 0.678857072 0.796120873 0.86528272 0.712070447 0.643779072 0.749278974 0.779216156 1 18.32808198 4.654792365 2.398885129 0.782944982 0.431009926 0.536984493 0.094334369 0.375806912 3.01296646 0.024893228 0.253078754 45163.99653 -4.654792365 -0.351935056 GPGAPAASS(ph)PTQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GPGAPAASSPTQK 13 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 GPGAPAAS(0.077)S(0.923)PTQK;GPGAPAAS(0.255)S(0.744)PTQK;GPGAPAAS(0.34)S(0.66)PTQK;GPGAPAAS(0.03)S(0.97)PTQK;GPGAPAAS(0.138)S(0.861)PT(0.002)QK 317.41 8.42E-51 3441850000 3170870 3843720 3345610 4318150 4437510 3953970 5067610 6069140 7806800 TRUE FALSE 2751831.496 3818470.35 4963558.186 5298651.956 4349212.233 4106081.784 4576153.962 4771301.641 6883888.998 0.399749545 0.554696677 0.721039835 0.769717809 0.631795811 0.596477047 0.664762893 0.693111357 1 22.7147924 -2 0.066158266 2.07533254 1.17E-09 0.475582557 0.111980888 732.586376 4.669900584 154.5423543 34.12100379 0.01 2 -2.075332539 GPGAPAASS(ph)PTRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GPGAPAASSPTRK 13 1 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 GPGAPAAS(0.487)S(0.507)PT(0.006)RK;GPGAPAAS(0.097)S(0.785)PT(0.118)RK;GPGAPAAS(0.36)S(0.544)PT(0.097)RK;GPGAPAAS(0.306)S(0.678)PT(0.017)RK 105.83 0.00041726 950120000 665819 728554 589175 748832 769689 699327 894072 1075543 1218860 TRUE FALSE 577829.3322 723768.0808 874102.0007 918865.7508 754373.6948 726230.5622 807365.0351 845546.4993 1074767.759 0.537631807 0.673418117 0.813293842 0.854943538 0.701894608 0.675709292 0.751199529 0.786724845 1 20.03559352 -2 0.046855967 2.036077749 3.87E-12 0.414468712 0.094562189 1629.65813 7.484446116 277.0424439 94.62240794 0.01 2 -2.036077749 GPGAPAS(ph)PSASHPQGLDTTPKPH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GPGAPASPSASHPQGLDTTPKPH 23 1 P98171-2;P98171;E7EQN5;E9PCM6 P98171-2 ARHGAP4 Rho GTPase-activating protein 4 1 GPGAPAS(0.983)PS(0.017)ASHPQGLDTTPKPH;GPGAPAS(0.972)PS(0.028)ASHPQGLDTTPKPH;GPGAPAS(0.996)PS(0.004)ASHPQGLDTTPKPH;GPGAPAS(0.877)PS(0.123)ASHPQGLDTTPKPH;GPGAPAS(0.997)PS(0.003)ASHPQGLDTTPKPH;GPGAPAS(0.997)PS(0.003)ASHPQGLDTTPKPH 240.8 1.73E-37 4241120000 2108078 2247799 1323441 1898015 2529850 2256200 2809670 3149040 2891810 TRUE FALSE 1829490.151 2233033.06 1963461.494 2328988.315 2479510.935 2342997.474 2537188.636 2475642.302 2549943.516 0.71746301 0.875718637 0.770001956 0.913348982 0.972378768 0.918842892 0.994997975 0.970861623 1 21.28203386 4.645845601 0.414599551 1.005140978 0.565493034 0.787972045 0.043548831 2.687124065 0.441602072 0.053189715 0.598700263 44243.10532 -4.645845601 -0.439647944 GPGAPGLAHLQESQAGS(ph)DTDVEEGKAPQAVPLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPGAPGLAHLQESQAGSDTDVEEGKAPQAVPLEK 34 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 GPGAPGLAHLQESQAGS(0.956)DT(0.044)DVEEGKAPQAVPLEK 247.42 1.02E-47 433990000 1899500 570110 500720 620260 548660 494870 724210 895740 788000 TRUE FALSE 1648476.262 566364.9099 742869.8668 761099.5131 537742.7394 513907.9691 653976.2257 704192.9717 694843.5377 2.372442389 0.815097039 1.069118192 1.095353805 0.773904786 0.73960243 0.941184871 1.013455452 1 19.40632863 4.741504586 24.99411789 0.936454511 2.372442912 0.932942559 0.121444576 69.27714349 588129.1299 0.031291879 0.213605284 55144.80254 -4.741504586 1.4359884 GPGASVHDR ddPTM_MDA-MB-175_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 ; 147.4 9.25E-05 390660000 680530 714340 288770 442960 683690 852730 678080 715950 709560 FALSE TRUE 590596.2363 709647.4535 428420.1379 543540.8382 670085.9066 885535.0749 612319.906 562849.664 625676.6251 0.943932077 1.134208032 0.684730931 0.868724859 1.07097801 1.41532389 0.97865236 0.899585571 1 19.25505768 3.231560334 24.37663437 1.061294323 0.908123329 0.183617021 0.171923787 244.8111916 852488.6558 0.055835926 0.064715088 1704.356079 -3.231560334 -0.153170994 GPGDLMGPQGLS(ph)PEEMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 174.02 7.21E-12 57301000 124080 139670 100270 108160 143700 135890 122690 165330 141930 TRUE FALSE 107682.5136 138752.4986 148760.9074 132719.3811 140840.6511 141117.7762 110791.5427 129975.4661 125151.1971 0.860419366 1.108678956 1.188649496 1.060472326 1.125363995 1.127578317 0.88526155 1.038547526 1 16.93331257 2.260770719 24.99928551 0.98420216 1.086211464 0.210013663 0.093618211 355.6804915 400346.6175 0.034216096 0.026482719 182.2933049 -2.260770719 0.102009304 GPGGSQGSQGPS(ph)PQGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GPGGSQGSQGPSPQGAR 17 0 Q96MG7 Q96MG7 NDNL2 Melanoma-associated antigen G1 1 GPGGSQGSQGPS(1)PQGAR;GPGGSQGSQGPS(1)PQGAR;GPGGSQGSQGPS(1)PQGAR;GPGGSQGS(0.049)QGPS(0.951)PQGAR 251.97 5.91E-27 930706000 1043139 1046959 715310 778069 1002862 1114842 993251 1104451 956471 TRUE FALSE 905285.5382 1040081.457 1061236.309 954741.4585 982907.0083 1157730.693 896925.6709 868272.7485 843398.088 1.073378694 1.23320348 1.258286358 1.132017575 1.165412896 1.372697792 1.063466569 1.02949338 1 19.68585423 2.02302546 24.9944351 1.025741301 1.205419846 0.524482631 0.079336637 166.9829863 181261.4646 0.03144838 0.021201226 105.4448711 -2.02302546 0.179678545 GPGLLES(ph)PSIFNFTADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GPGLLESPSIFNFTADR 17 0 Q92615 Q92615 LARP4B La-related protein 4B 1 GPGLLES(0.987)PS(0.005)IFNFT(0.007)ADR;GPGLLES(0.965)PS(0.032)IFNFT(0.003)ADR;GPGLLES(0.898)PS(0.078)IFNFT(0.024)ADR;GPGLLES(0.5)PS(0.5)IFNFTADR 118.5 0.0001737 144791000 113755.9 132365.7 88041.2 93814.7 121980.3 136615.9 127122 142217.1 143191.4 TRUE FALSE 98722.76959 131496.181 130618.2188 115116.7615 119553.1307 141871.6021 114793.728 111805.0799 126263.4758 0.781879074 1.041442746 1.034489332 0.911718617 0.946854424 1.123615528 0.909160209 0.885490275 1 16.94607785 4.751878813 24.16607883 0.973514289 0.781878873 0.421301524 0.073016924 1559.358601 2829401.25 0.018674418 0.336924548 56477.93545 -4.751878813 -0.191635416 GPGLLESPS(ph)IFNFTADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPGLLESPSIFNFTADR 17 0 Q92615 Q92615 LARP4B La-related protein 4B 1 GPGLLES(0.276)PS(0.724)IFNFTADR;GPGLLES(0.356)PS(0.644)IFNFTADR 164.57 2.70E-09 143104000 147169 149280 115713 121921 145961 174322 146145 164995 161924 TRUE FALSE 127720.2438 148299.3699 171672.1938 149605.0265 143056.6617 181028.2801 131971.8804 129712.1032 142781.5292 0.894515169 1.038645339 1.202341751 1.047789776 1.001926947 1.267869039 0.924292387 0.90846557 1 17.12344983 GPGPTVKPSGHLFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPGPTVKPSGHLFFR 15 1 F5GXQ0;Q5VW32-2;Q5VW32 F5GXQ0 BROX BRO1 domain-containing protein BROX 0 ; 150.05 1.95E-06 1584610000 520430 460380 306960 400970 478310 463110 483770 542090 584030 FALSE TRUE 451653.8569 457355.7335 455406.8827 492016.3669 468792.5668 480926.1414 436854.0599 426168.272 514986.6387 0.877020534 0.888092426 0.884308152 0.955396373 0.910300446 0.933861396 0.848282318 0.827532678 1 18.97417548 3.94716008 24.99351238 0.901970805 0.883466831 0.045836298 0.049482709 1567.793248 741571.9094 0.013989863 0.024231364 8854.419222 -3.94716008 -0.018503974 DGLPRTPS(ph)RR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 DGLPRTPSRR 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DGLPRT(0.296)PS(0.704)RR;DGLPRT(0.042)PS(0.958)RR;DGLPRT(0.338)PS(0.662)RR;DGLPRT(0.06)PS(0.94)RR;DGLPRT(0.113)PS(0.887)RR 88.101 0.0064827 2867689000 1746140 1415770 752506 830578 1346670 1363130 1385750 1566620 501115 TRUE FALSE 1515383.175 1406469.714 1116420.419 1019173.429 1319873.902 1415570.493 1251360.178 1231610.504 441873.7556 3.429448243 3.182967298 2.526559689 2.306481018 2.986993197 3.203563179 2.831940486 2.787245201 1 18.75327472 1.231265083 4.44299425 0.820218949 2.900467109 0.771961572 0.326257569 0.110522471 4.455207969 0.737427558 0.08749473 17.03197781 -1.231265083 2.08024816 GPGQPSS(ph)PQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPGQPSSPQR 10 0 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 GPGQPS(0.005)S(0.995)PQR;GPGQPS(0.002)S(0.998)PQR 110.08 0.0020286 318270000 781740 696510 647210 679580 624930 732580 615520 712240 1472080 TRUE FALSE 678431.0783 691934.5799 960202.9208 833889.0257 612495.1157 760762.8266 555826.9651 559933.0187 1298052.379 0.522653083 0.533055978 0.739725866 0.642415544 0.471857011 0.586080222 0.428200721 0.431363963 1 20.30791717 1.230042738 24.98808394 1.000000864 0.541516835 0.692982011 0.095281716 208.4317871 611408.3199 0.292461219 0.025786427 16.98410783 -1.230042738 -0.458484029 GPGQVPTATSALSLELQEVEPLGLPQAS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GPGQVPTATSALSLELQEVEPLGLPQASPSR 31 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GPGQVPTATSALSLELQEVEPLGLPQAS(0.834)PS(0.166)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.835)PS(0.165)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.806)PS(0.194)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.811)PS(0.189)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.5)PS(0.5)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.924)PS(0.076)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.783)PS(0.217)R 227.62 1.72E-35 3229298000 1498491 1374261.2 1031360.4 1028523.5 1404103 1629225 1291239.8 1507636 1420896 TRUE FALSE 1300461.618 1365233.588 1530129.739 1262065.481 1376164.097 1691902.34 1166015.563 1185239.774 1252919.294 1.037945241 1.089642082 1.221251638 1.007299901 1.098366115 1.350368175 0.930639004 0.945982538 1 20.25686206 GPGRPVS(ph)SPHELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPGRPVSSPHELR 13 1 Q68D10;Q68D10-2 Q68D10 SPTY2D1 Protein SPT2 homolog 1 GPGRPVS(0.5)S(0.5)PHELR 69.331 0.029069 97473000 61838 73548 37922 45283 75348 60321 65338 64744 65429 TRUE FALSE 53665.95162 73064.85835 56261.20604 55565.19726 73848.72222 62641.5879 59001.53082 50898.99944 57694.05816 0.930181605 1.26641912 0.97516465 0.963100864 1.280005681 1.08575458 1.022662172 0.882222556 1 15.81613512 1.997244453 4.064497108 0.93574402 1.089146259 0.190916449 0.119820802 0.299749021 11.36972489 0.057893944 0.0320728 99.36752039 -1.997244453 0.153402239 GPGS(ph)PPRT(ph)PPAPGPPSFEEQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GPGSPPRTPPAPGPPSFEEQLR 22 1 A0A6E1YH78;Q6ZTN6-2;Q6ZTN6;Q6ZTN6-3 A0A6E1YH78 ANKRD13D Ankyrin repeat domain-containing protein 13D 2 GPGS(1)PPRT(1)PPAPGPPSFEEQLR;GPGS(1)PPRT(0.996)PPAPGPPS(0.004)FEEQLR;GPGS(1)PPRT(1)PPAPGPPSFEEQLR;GPGS(1)PPRT(1)PPAPGPPSFEEQLR 151.41 1.12E-07 4613540000 1110360 1142790 827200 904270 1255910 1349830 1216730 1363570 1325870 TRUE FALSE 963623.1127 1135282.937 1227236.687 1109598.324 1230919.848 1401758.834 1098731.712 1071981.167 1169127.159 0.824224384 0.971051719 1.049703343 0.949082669 1.052853694 1.198978933 0.939788032 0.916907249 1 20.15700042 4.708383434 3.314492397 1.008237472 0.80521814 0.359155461 0.079454485 0.366098245 6.735114315 0.021452673 0.181639785 51095.59185 -4.708383434 -0.203019332 GPHHLDNSS(ph)PGPGSEAR ddPTM_MDA-MB-175_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(0.225)S(0.775)PGPGSEAR;GPHHLDNS(0.169)S(0.831)PGPGSEAR;GPHHLDNS(0.084)S(0.914)PGPGS(0.002)EAR 160.52 1.98E-09 1276200000 656788 652699 494987 547699 633778 730056 569381 631524 662806 TRUE FALSE 569991.8017 648411.3773 734364.3688 672062.429 621167.0578 758141.7267 514162.5183 496477.5071 584449.8298 0.975262157 1.109438902 1.256505403 1.149906108 1.062823576 1.29718872 0.879737647 0.849478401 1 19.15671966 2.216439604 24.99362845 0.895934277 1.142365848 0.555860003 0.097547609 160.3258063 181144.2163 0.039081116 0.026371416 164.6037042 -2.216439604 0.246431572 GPHHLDNSSPGPGSEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GPHHLDNSSPGPGSEAR 17 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 0 ;; 125.45 2.71E-05 307509000 219859 211935 142481 189291 200038 224616 188372 225717 245529 FALSE TRUE 190804.0761 210542.785 211385.2882 232272.4147 196057.6352 233257.1229 170103.7124 177449.1761 216502.8413 0.881300564 0.972471233 0.976362651 1.07283772 0.905566107 1.077385966 0.785688129 0.819615923 1 17.72402643 2.230983394 24.99985455 0.854816344 0.981136841 0.290415564 0.08201976 188.639172 622378.7009 0.031912745 0.02198329 170.2093425 -2.230983394 0.126320496 GPIAFWAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPIAFWAR 8 0 Q5H909;Q9UNF1-2;Q9UNF1 Q5H909 MAGED2 Melanoma-associated antigen D2 0 ; 103.28 0.011172 323710000 242240 531190 316640 340000 481740 532480 419430 468180 438560 FALSE TRUE 210227.3702 527700.5779 469768.1631 417202.1966 472154.3165 552964.8502 378753.7432 368063.3504 386713.9364 0.543625017 1.364576055 1.214769158 1.078839311 1.220939491 1.429906704 0.97941581 0.951771622 1 18.56090723 2.052018986 24.99882119 0.970382879 1.160267416 0.093385964 0.237861034 198.371332 95330.51939 0.09244135 0.062323932 112.7246735 -2.052018986 0.189884537 GPIAQWADGAIS(ph)PNGHRPQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPIAQWADGAISPNGHRPQLR 21 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;Q5SRD0 Q641Q2;A0A0A0MR88 FAM21A;FAM21C;FAM21D WASH complex subunit FAM21A;WASH complex subunit FAM21C;Putative WASH complex subunit FAM21 1 GPIAQWADGAIS(1)PNGHRPQLR;GPIAQWADGAIS(1)PNGHRPQLR 201.15 4.28E-22 979330000 778890 730900 576020 631910 818500 931800 824160 981910 878430 TRUE FALSE 675957.713 726098.6698 854585.1987 775394.8236 802213.4514 967646.949 744233.0901 771936.1877 774583.0061 0.872673048 0.937405887 1.103284208 1.00104807 1.035671381 1.249248875 0.960817736 0.996582912 1 19.56306032 4.414986017 5.03776121 1.044625608 0.886417561 0.366123727 0.08093843 0.200440208 9.887373909 0.020778707 0.060126938 26000.75849 -4.414986017 -0.158208046 GPIKFNVWDTAGQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPIKFNVWDTAGQEK 15 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 213.51 3.08E-10 1938850000 3281600 2348700 1128550 1226920 2199500 1745390 3140800 3459600 301400 FALSE TRUE 2847928.245 2333271.235 1674320.555 1505510.938 2155734.253 1812536.283 2836205.699 2719791.463 265768.8354 10.71580963 8.779325958 6.299913052 5.664738442 8.111313166 6.819973005 10.67170158 10.23367341 1 18.01981242 4.564076873 3.527420248 7.449470282 10.6474518 0.156288931 2.692546178 0.546042669 11.77111197 0.680988206 3.45898409 36650.24422 -4.564076873 3.19798152 GPIVESYIGFIESYRDPFGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPIVESYIGFIESYRDPFGSR 21 1 G3V1D3;G3V180;Q9NY33-4;Q9NY33 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ; 150.7 6.28E-08 382090000 777760 664770 486940 501920 685570 760820 665160 746590 403540 FALSE TRUE 674977.0454 660403.0821 722425.8127 615888.6074 671928.4983 790089.2377 600652.8856 586937.5385 355833.9609 1.896887649 1.855930447 2.030232895 1.730831441 1.888320318 2.220387384 1.6880145 1.649470267 1 18.44084468 1.028653976 1.364666475 0.171489066 1.919232508 0.801371821 0.142774225 0.910811228 1.001655363 2.555913014 0.041141619 10.68203449 -1.028653976 1.747743442 GPKPEPPGS(ph)GSPAPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPKPEPPGSGSPAPPR 16 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 GPKPEPPGS(0.5)GS(0.5)PAPPR;GPKPEPPGS(0.882)GS(0.118)PAPPR 152.13 3.50E-07 1805080000 1675610 1372770 989250 1104430 1309380 1207800 1499330 1690190 1710790 TRUE FALSE 1454173.893 1363752.183 1467654.609 1355207.712 1283325.9 1254264.848 1353925.207 1328756.022 1508542.355 0.963959605 0.904019817 0.972895858 0.898355758 0.850705912 0.831441586 0.897505597 0.880821156 1 20.52472377 3.575309047 6.631030836 0.886894311 0.942261524 0.21751174 0.047382961 0.374174835 21.52517112 0.013055845 0.01940019 3761.049483 -3.575309047 0.055367213 GPKPEPPGSGS(ph)PAPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPKPEPPGSGSPAPPR 16 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 GPKPEPPGS(0.005)GS(0.995)PAPPR 122.53 5.62E-05 299380000 391670 305180 212290 245700 317060 281750 298960 387190 376450 TRUE FALSE 339909.8171 303175.2525 314954.1541 301489.9403 310751.1263 292589.1048 269966.9052 304392.4316 331946.5099 1.02398973 0.913325622 0.948809958 0.908248562 0.936148196 0.881434497 0.813284361 0.916992415 1 18.34059126 8 0.88922642 0.904734678 53.69458401 0.324774741 0.048180793 1044.607017 2.411022271 0.016388668 111838.6939 100000000 -8 52.78984933 GPKPEPPGSGS(ph)PAPPRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPKPEPPGSGSPAPPRR 17 2 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 GPKPEPPGS(0.012)GS(0.988)PAPPRR 133.09 1.12E-05 166280000 241180 198960 111270 140700 193790 164940 201490 212930 134640 TRUE FALSE 209307.4519 197653.0187 165080.5442 172648.0855 189933.9581 171285.3485 181949.5308 167396.5765 118723.0126 1.76298973 1.664824825 1.390467952 1.454209102 1.599807434 1.442730814 1.532554867 1.409975816 1 16.85724008 0.811001994 1.362059755 9.97E-12 1.549127175 0.715737582 0.10901979 2.139819037 1.514237746 6.182160513 0.033211225 6.471455869 -0.811001994 1.549127175 GPLLVQDVVFTDEMAHFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GPLLVQDVVFTDEMAHFDR 19 0 P04040 P04040 CAT Catalase 0 ;;;;; 227.25 1.31E-19 1151406000 1224518 1003120 841334 1014836 1099188 1608010 931247 1276820 1012869 FALSE TRUE 1062694.844 996530.4387 1248205.936 1245270.025 1077316.309 1669871.185 840934.8093 1003781.979 893128.7807 1.18985623 1.115774634 1.397565461 1.39427824 1.206227291 1.869686904 0.941560531 1.12389389 1 19.76850869 GPLMVNSNYYAMDLLYILPTHIQAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPLMVNSNYYAMDLLYILPTHIQAAR 26 0 P50416;P50416-2 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 ; 171.52 5.85E-12 555500000 214700 203902 178472 205477 260494 302400 148464 329070 271210 FALSE TRUE 186326.851 202562.5543 264781.6562 252133.6934 255310.679 314033.5237 134065.9841 258700.9413 239147.8628 0.77912823 0.847018041 1.107188051 1.054300425 1.067585033 1.313135397 0.560598713 1.081761461 1 17.86754337 4.379244206 5.60946113 1.018562185 0.795486334 0.187197482 0.186472808 0.322347956 14.80258438 0.045485738 0.125650048 23946.61908 -4.379244206 -0.22307585 GPLPLSSQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GPLPLSSQHR 10 0 P43243;A0A0R4J2E8;D6REM6;D6R991;D6R8Z5;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;; 135.55 0.00014123 1972030000 2073430 2664690 1118800 1672600 2528840 2763580 2319170 2362510 2641440 FALSE TRUE 1799420.972 2647185.476 1659855.422 2052389.394 2478521.032 2869896.711 2094257.25 1857305.622 2329171.972 0.772558228 1.136535004 0.712637556 0.881166963 1.064121096 1.232153205 0.899142388 0.797410257 1 21.15138573 4.996427516 18.91708582 0.95032115 0.620430611 0.125935226 0.155206 52623060.29 2066897319 0.039235243 351310986.6 99180.77919 -4.996427516 -0.329890539 GPLS(ph)PFNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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;GPLS(1)PFNSR 142.19 0.00011005 2501218000 2730070 2783690 1956908 2118677 2727490 2873990 2565220 3013650 2690210 TRUE FALSE 2369284.332 2765403.757 2903275.254 2599754.995 2673218.285 2984554.255 2316445.359 2369204.4 2372176.438 0.998780822 1.165766472 1.223886726 1.095936606 1.126905335 1.258150198 0.976506352 0.998747126 1 21.17777989 2.213254992 24.998337 0.992573359 1.146398817 0.516291069 0.069870362 174.4768119 172356.8007 0.027767246 0.018728366 163.4011062 -2.213254992 0.153825458 GPMDSDDSHGSVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPMDSDDSHGSVLR 14 0 Q8IW45-2;Q8IW45;Q8IW45-4 Q8IW45-2 CARKD ATP-dependent (S)-NAD(P)H-hydrate dehydratase 0 ; 210.38 5.32E-09 632060000 529110 621390 198710 340800 609340 687040 525050 595310 583110 FALSE TRUE 459186.7729 617308.0482 294806.8206 418183.8488 597215.3262 713470.8734 474130.7318 468007.5892 514175.4001 0.89305473 1.200578729 0.57335847 0.813309716 1.161501165 1.387602116 0.922118662 0.910209997 1 18.97190106 3.246652672 24.9996678 1.05953005 0.87248871 0.20370973 0.201052432 355.8010804 1099208.878 0.062281724 0.078976392 1764.625991 -3.246652672 -0.18704134 GPNGESSVIHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPNGESSVIHDR 12 0 O60437;K7EKI8 O60437 PPL Periplakin 0 119.25 0.00053749 192930000 93675 88896 53577 47998 79672 98246 66255 86266 84410 FALSE TRUE 81295.61141 88312.03632 79487.0164 58896.6795 78086.68308 102025.5872 59829.6003 67818.68722 74431.14596 1.092225712 1.186493036 1.067926812 0.791290779 1.049113003 1.370737826 0.80382479 0.911160057 1 16.18361883 6.347123571 0.033730542 3.54E-06 2.354084841 0.076347654 0.166285351 3998.799695 19.99435634 537.1112736 902.2375915 2223942.583 -6.347123571 2.354081306 GPNGYGFHLHGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPNGYGFHLHGEK 13 0 O14745;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ; 162.93 2.29E-05 1486780000 2547600 2520500 1782080 2322100 2434500 2227000 2785700 3156800 2904800 FALSE TRUE 2210928.205 2503942.67 2643899.849 2849368.296 2386058.213 2312674.131 2515543.243 2481742.886 2561397.853 0.863172507 0.977568817 1.032209754 1.112427065 0.931545332 0.902895319 0.982097818 0.968901759 1 21.28849993 4.731519439 4.904368723 0.987906863 0.857264843 0.330643136 0.056201051 0.215491881 15.61505386 0.014704033 0.095115323 53891.39672 -4.731519439 -0.130642021 GPPASS(ph)PAPAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 GPPASSPAPAPK 12 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 GPPAS(0.003)S(0.997)PAPAPK;GPPASS(1)PAPAPK;GPPAS(0.478)S(0.522)PAPAPK;GPPAS(0.001)S(0.999)PAPAPK;GPPAS(0.002)S(0.998)PAPAPK;GPPASS(1)PAPAPK;GPPASS(1)PAPAPK;GPPAS(0.007)S(0.993)PAPAPK 207.25 8.47E-08 17615998000 24441500 23344290 15967190 17900930 20674250 19961010 22768240 26664260 26446850 TRUE FALSE 21211493.85 23190939.82 23688976.49 21965609.76 20262872.87 20728922.97 20560179.59 20962315.5 23320333.52 0.909570776 0.994451464 1.015807791 0.941908045 0.868892928 0.888877638 0.881641747 0.898885751 1 24.47508509 3.473089227 12.09943768 0.903819355 0.97597756 0.314750153 0.044155809 0.236586096 666.1484858 0.012529651 0.016566025 2972.276633 -3.473089227 0.072158205 GPPASSPAPAPKFS(ph)PVTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPPASSPAPAPKFSPVTPK 19 1 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 GPPASSPAPAPKFS(0.995)PVT(0.005)PK;GPPASSPAPAPKFS(0.86)PVT(0.14)PK 172.8 4.63E-12 1591360000 1869660 1648090 939620 968510 1678560 1255230 2491500 2756900 340870 TRUE FALSE 1622579.694 1637263.588 1394023.375 1188424.998 1645159.94 1303519.51 2249874.713 2167358.389 300572.7369 5.398292974 5.447146022 4.637890279 3.95386824 5.47341704 4.336785577 7.485292035 7.210761733 1 18.19735463 GPPDFS(ph)S(ph)DEEREPTPVLGSGAAAAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GPPDFSSDEEREPTPVLGSGAAAAGR 26 1 P42166;P42167;G5E972;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 2 GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR;GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR;GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR;GPPDFS(0.999)S(0.999)DEEREPT(0.001)PVLGSGAAAAGR 163.06 8.72E-12 4536740000 2908020 2893120 1911990 2426640 3364360 3143700 2469550 3541350 2998690 TRUE FALSE 2523717.789 2874114.904 2836634.759 2977645.701 3297415.818 3264640.173 2230053.421 2784059.861 2644188.284 0.954439517 1.086955464 1.072780927 1.126109558 1.247042746 1.234647394 0.843379208 1.052897737 1 21.33439348 2.244205602 24.99957049 0.978563735 1.122673417 0.35997625 0.096807586 164.0344788 726452.3493 0.038359208 0.028873234 175.4711013 -2.244205602 0.144109682 GPPDFS(ph)SDEEREPT(ph)PVLGSGAAAAGR ddPTM_MDA-MB-175_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" 2 GPPDFS(0.538)S(0.462)DEEREPT(1)PVLGSGAAAAGR 112.74 0.0039766 90667000 227200 198080 163300 207120 245060 199420 183980 299240 262990 TRUE FALSE 197174.9443 196778.7994 242272.4262 254149.7616 240183.7855 207091.8164 166137.6479 235249.8547 231899.6218 0.850259879 0.848551619 1.044729717 1.095947288 1.035723058 0.89302352 0.716420521 1.01444691 1 17.82314094 4.267788308 24.30569089 0.96558267 0.849405436 0.187937074 0.104933419 300.2983957 249720.9625 0.028432396 0.075194544 18526.28362 -4.267788308 -0.116177233 GPPDFS(ph)SDEEREPTPVLGSGAAAAGR ddPTM_MDA-MB-175_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(0.592)S(0.408)DEEREPTPVLGSGAAAAGR;GPPDFS(0.941)S(0.059)DEEREPTPVLGSGAAAAGR;GPPDFS(0.948)S(0.052)DEEREPTPVLGSGAAAAGR;GPPDFS(0.948)S(0.052)DEEREPTPVLGSGAAAAGR;GPPDFS(0.99)S(0.01)DEEREPTPVLGSGAAAAGR;GPPDFS(0.939)S(0.061)DEEREPTPVLGSGAAAAGR 303.68 4.52E-71 8777810000 1218780 1143490 716394 970300 1206290 1129260 1025410 1433090 1147650 TRUE FALSE 1057715.135 1135978.339 1062844.535 1190621.445 1182287.189 1172703.363 925965.896 1126634.856 1011976.124 1.045197717 1.122534723 1.050266413 1.176531162 1.168295536 1.158825129 0.915007651 1.113301815 1 19.94874382 2.276127127 24.99999918 1.027140082 1.121935464 0.381700793 0.065192422 187.0692769 124491.3956 0.02382865 0.018457204 188.8544085 -2.276127127 0.094795382 GPPDFSSDEEREPT(ph)PVLGSGAAAAGR ddPTM_MDA-MB-175_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(1)PVLGSGAAAAGR;GPPDFSSDEEREPT(0.991)PVLGS(0.009)GAAAAGR;GPPDFSSDEEREPT(1)PVLGSGAAAAGR;GPPDFSSDEEREPT(1)PVLGSGAAAAGR;GPPDFSSDEEREPT(1)PVLGSGAAAAGR 287.61 2.18E-61 11242200000 7612340 5872840 4511560 6428770 7782650 8103780 4519220 8376750 7533280 TRUE FALSE 6606349.982 5834260.927 6693365.506 7888520.486 7627790.491 8415537.66 4080946.74 6585447.2 6642704.22 0.994527193 0.878296057 1.007626606 1.187546551 1.148295971 1.266884296 0.614350211 0.991380465 1 22.66333925 2.2535683 24.99999821 0.883568072 1.075967905 0.30578326 0.149876206 325.1802888 541689.1719 0.058397195 0.045048814 179.2950503 -2.2535683 0.192399834 GPPDFSSDEEREPTPVLGSGAAAAGR ddPTM_MDA-MB-175_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" 0 238.72 4.71E-45 242900000 112270 104050 58862 81228 90537 110390 79401 102550 89789 FALSE TRUE 97433.23504 103366.4887 87327.86008 99672.05889 88735.49083 114636.7747 71700.70324 80620.48054 79174.24671 1.230617772 1.305556958 1.102983151 1.258894944 1.120762047 1.447904836 0.905606384 1.018266468 1 16.27274362 2.217735625 24.99999938 0.980840607 1.23583443 0.620505131 0.099282618 151.7778277 182204.9818 0.037668917 0.025426927 165.0956478 -2.217735625 0.254993822 GPPHSDSCPGLTLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GPPHSDSCPGLTLHR 15 0 Q9BVJ7 Q9BVJ7 DUSP23 Dual specificity protein phosphatase 23 0 ;;; 220.21 9.84E-13 1021350000 538730 492010 334606 428100 489277 568150 505530 564950 622590 FALSE TRUE 467535.4655 488777.9539 496422.5808 525306.6481 479541.345 590007.0981 456503.7784 444139.8389 548988.1195 0.851631299 0.890325194 0.904250134 0.956863417 0.873500405 1.074717425 0.831536717 0.809015393 1 19.0664154 6.1053689 15.6651572 0.904028336 0.601397963 0 0.081161427 0 0 0.018211326 0 1274585.284 -6.1053689 -0.302630373 GPPNHHMGPMSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPPNHHMGPMSER 13 0 Q9C0J8 Q9C0J8 WDR33 pre-mRNA 3 end processing protein WDR33 0 62.732 0.052084 13577000 42977 28112 29098 28348 11363 19346 23937 26279 23850 FALSE TRUE 37297.48056 27927.33042 43169.89013 34784.84667 11136.89853 20090.25314 21615.59342 20659.44035 21030.48017 1.773496385 1.327945448 2.052729647 1.654020564 0.529559879 0.955292175 1.027822154 0.982357045 1 14.36019417 3.303332672 9.061820771 0.922450474 1.703542761 0.762362696 0.222610144 0.152217559 19.7240729 0.062570776 0.080712412 2010.632378 -3.303332672 0.781092287 GPPNS(ph)PDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPPNSPDLK 9 0 M0QZS0;A0A590UK10;A0A3B3IPE9;A0A087WZG4;Q6ZSZ5-2;Q6ZSZ5-1;Q6ZSZ5-6;Q6ZSZ5-5;Q6ZSZ5 M0QZS0 ARHGEF18 Rho guanine nucleotide exchange factor 18 1 GPPNS(1)PDLK 107.85 0.0028398 184550000 791490 764950 587250 759950 815750 716830 909010 1090000 1181500 TRUE FALSE 686892.5911 759924.9931 871246.0642 932508.2626 799518.171 744406.914 820854.3501 856911.9824 1041824.416 0.659317041 0.729417531 0.836269578 0.895072383 0.767421226 0.714522431 0.787900857 0.822510943 1 19.99068072 1.163650565 2.094018828 1.103269288 0.773609284 0.554498476 0.064533146 0.767145492 2.820238017 0.523752912 0.018585888 14.57640963 -1.163650565 -0.329660004 GPPPSWGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GPPPSWGR 8 0 P84103;P84103-2 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;; 129.39 0.002542 831920000 395736 349822 255851 304233 387221 361298 338575 376529 472220 FALSE TRUE 343438.4849 347523.9962 379581.3994 373313.7526 379516.0597 375197.3679 305740.0486 296011.2035 416394.6896 0.824790742 0.834602374 0.911590395 0.896538217 0.911433477 0.901061847 0.734255398 0.710890919 1 18.66759214 2.253103154 24.98697676 0.789982822 0.881555266 0.096393 0.082526024 357.2367752 613803.3929 0.030932391 0.023851068 179.103121 -2.253103154 0.091572444 GPPQEEEEEEDEEEEATKEDAEAPGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 GPPQEEEEEEDEEEEATKEDAEAPGIR 27 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;;;;;;; 311.34 4.66E-82 9136130000 4255380 3360684 2778956 2891651 3289068 2883080 4040253 4468840 4075170 FALSE TRUE 3693020.751 3338607.446 4122868.417 3548244.556 3223621.982 2993993.953 3648429.886 3513213.343 3593408.045 1.027720956 0.929092217 1.147342123 0.987431572 0.897093217 0.833190641 1.015311882 0.977682829 1 21.77692134 3.478972564 24.99441858 0.947942085 1.031360983 0.241144034 0.072885378 111.9219181 1511069.178 0.021436841 0.02810953 3012.815691 -3.478972564 0.083418897 GPPQRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPPQRPK 7 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 82.386 0.022464 228360000 531710 475550 394140 487270 370230 444720 521280 601490 870660 FALSE TRUE 461443.1763 472426.0807 584747.4223 597912.101 362863.1473 461828.6662 470726.3458 472866.0443 767731.5667 0.601047549 0.615353206 0.761656089 0.778803591 0.472643256 0.601549664 0.613139235 0.615926275 1 19.55024244 1.236949222 24.99747451 1.000000454 0.632936251 0.643394282 0.085979562 28.07141977 435328.4553 0.134508764 0.021780944 17.25636116 -1.236949222 -0.367064202 GPPQS(ph)PVFEGVYNNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 294.22 1.34E-45 18925980000 4133190 3961507 3151494 3417701 3935400 4142460 3927634 4713520 5910320 TRUE FALSE 3586978.469 3935483.6 4675567.04 4193742.248 3857093.239 4301823.117 3546732.659 3705570.429 5211608.703 0.688267035 0.755137967 0.897144683 0.804692464 0.740096477 0.825430949 0.680544696 0.711022381 1 22.31329734 GPPS(ph)PPAPVMHS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 GPPSPPAPVMHSPSR 15 0 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 2 GPPS(1)PPAPVMHS(0.995)PS(0.005)R;GPPS(1)PPAPVMHS(0.939)PS(0.061)R;GPPS(1)PPAPVMHS(0.5)PS(0.5)R;GPPS(1)PPAPVMHS(0.976)PS(0.024)R;GPPS(1)PPAPVMHS(0.997)PS(0.003)R;GPPS(1)PPAPVMHS(0.976)PS(0.024)R;GPPS(1)PPAPVMHS(0.974)PS(0.026)R;GPPS(1)PPAPVMHS(0.595)PS(0.406)R;GPPS(1)PPAPVMHS(0.928)PS(0.072)R;GPPS(1)PPAPVMHS(0.774)PS(0.226)R 187.52 1.78E-07 9419010000 4127570 3819460 2570010 2982060 3876160 4097580 3602480 4048470 4363440 TRUE FALSE 3582101.167 3794369.716 3812875.432 3659182.301 3799032 4255216.554 3253112.044 3182736.196 3847599.094 0.930996468 0.98616556 0.990975239 0.951030035 0.987377299 1.105940731 0.845491426 0.827200578 1 21.87552705 2.204369601 24.99985765 0.8757352 0.989682146 0.346906377 0.064278472 178.4832979 130502.6027 0.025934868 0.017486292 160.0919893 -2.204369601 0.113946946 GPPS(ph)PPAPVMHS(ph)PSRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GPPSPPAPVMHSPSRK 16 1 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 2 GPPS(1)PPAPVMHS(0.891)PS(0.109)RK;GPPS(1)PPAPVMHS(0.941)PS(0.059)RK;GPPS(1)PPAPVMHS(0.861)PS(0.139)RK;GPPS(1)PPAPVMHS(0.965)PS(0.035)RK 118.16 0.00014278 1176400000 1384320 1151220 674980 843870 1132360 973280 1213900 1442120 889530 TRUE FALSE 1201378.605 1143657.56 1001402.586 1035483.581 1109828.251 1010722.711 1096176.165 1133733.861 784370.7768 1.531646308 1.458057329 1.276695429 1.320145538 1.414928098 1.288577725 1.397522954 1.445405533 1 19.58117626 -1.999999999 0.036912116 1.05E-05 2.25252365 0.292515858 0.12309436 3609.688963 13.14607598 611.1673005 261.8300618 0.01 1.999999999 2.252513119 GPPS(ph)PPAPVMHSPS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPPSPPAPVMHSPSR 15 0 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 2 GPPS(1)PPAPVMHS(0.248)PS(0.752)R;GPPS(1)PPAPVMHS(0.002)PS(0.998)R 200.27 1.02E-08 825050000 1346970 1232690 815740 899850 1154220 1249530 1153550 1191240 1282540 TRUE FALSE 1168964.502 1224592.378 1210234.592 1104174.696 1131253.28 1297600.228 1041678.899 936502.5962 1130919.582 1.033640694 1.082828874 1.070133201 0.976351204 1.000295068 1.147385055 0.92109016 0.828089469 1 20.10906491 2.088594268 7.820661494 0.893750251 1.047931782 0.506491127 0.062208851 0.163981337 12.53588829 0.024971344 0.016791382 122.6293054 -2.088594268 0.154181532 GPPS(ph)PPAPVMHSPS(ph)RK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPPSPPAPVMHSPSRK 16 1 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 2 GPPS(1)PPAPVMHS(0.143)PS(0.857)RK 67.251 0.025394 151180000 205700 180400 102080 127860 160230 156330 187780 229410 134230 TRUE FALSE 178516.2238 179214.9405 151446.2294 156892.5672 157041.7365 162344.1163 169569.1245 180352.4568 118361.4823 1.508229031 1.514132275 1.27952292 1.325537364 1.326797649 1.371595836 1.432637723 1.523742802 1 16.85284014 4.2537453 24.71256283 1.348633837 1.511180814 0.233773936 0.135645221 341.0467816 555030.8097 0.033451264 0.087730004 17936.8138 -4.2537453 0.162546977 GPPS(ph)PPAPVMHSPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPPSPPAPVMHSPSR 15 0 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 1 GPPS(1)PPAPVMHSPSR;GPPS(1)PPAPVMHSPSR 90.581 0.019959 479690000 441460 416050 239210 327280 427160 400900 358280 437270 455060 TRUE FALSE 383119.9425 413316.9402 354892.7561 401593.9262 418660.3517 416322.8824 323534.0607 343763.2133 401263.3252 0.954784348 1.030039164 0.884438556 1.0008239 1.043355636 1.03753036 0.80628864 0.856702299 1 18.61418978 2.246474329 24.99901787 0.877822736 0.991435145 0.350452469 0.066400292 177.2480057 559918.9759 0.025298849 0.01923483 176.3901499 -2.246474329 0.113612409 GPPS(ph)PRPAGPTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPPSPRPAGPTPR 13 1 Q14681 Q14681 KCTD2 BTB/POZ domain-containing protein KCTD2 1 GPPS(1)PRPAGPTPR 97.129 0.0023739 209120000 139280 158860 120800 119510 152490 165280 129330 152500 107800 TRUE FALSE 120873.7951 157816.4382 179219.2841 146646.5721 149455.7473 171638.4286 116787.5965 119889.0618 95056.00681 1.271606069 1.660246874 1.885407246 1.542738613 1.572291456 1.805655785 1.228618795 1.261246562 1 16.53649018 2.15815118 6.796182859 1.179992042 1.629996154 0.60437137 0.17532659 0.148760126 10.30163522 0.071498724 0.048095043 143.9299519 -2.15815118 0.450004113 GPQES(ph)PQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPQESPQK 8 0 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 GPQES(1)PQK;GPQES(1)PQK 131.12 0.0010687 532540000 1229630 1028370 839660 929180 711980 870840 1312040 1434380 1517180 TRUE FALSE 1067131.28 1021614.57 1245722.384 1140164.521 697812.991 904341.7783 1184798.563 1127648.999 1337820.709 0.797663897 0.76364087 0.931157947 0.852255099 0.521604268 0.675981297 0.885618346 0.842899943 1 20.35145335 1.359306258 1.457264541 1.050636162 0.766023012 0.293343968 0.113045979 1.352871233 3.159614563 0.542566525 0.036068143 22.87211142 -1.359306258 -0.28461315 GPQGS(ph)PLLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPQGSPLLSR 10 0 Q8TEP8;H0Y966;A0A0A0MR42;K7ENP4;Q8TEP8-1;K7EPA2 Q8TEP8 CEP192 Centrosomal protein of 192 kDa 1 GPQGS(1)PLLSR 80.815 0.023997 139650000 67370 72225 66706 66422 79133 76806 66177 78924 87460 TRUE FALSE 58466.88381 71750.54922 98965.24472 81504.1303 77558.40812 79760.77652 59759.16473 62046.71679 77120.57843 0.758122994 0.930368401 1.283253403 1.056840236 1.00567721 1.034234677 0.774879623 0.804541642 1 16.23482825 2.250384175 24.75595795 0.844754811 1.021892307 0.200028378 0.140830022 272.4044625 570355.6784 0.054641749 0.041969681 177.9853164 -2.250384175 0.177137496 GPQLFHMDPSGTFVQCDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GPQLFHMDPSGTFVQCDAR 19 0 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ;; 149.53 8.47E-08 2700430000 1818720 1573870 1212810 1344520 1465920 1587820 1440050 1753320 1867260 FALSE TRUE 1578371.544 1563531.144 1799328.973 1649813.816 1436751.06 1648904.463 1300394.173 1378386.162 1646514.65 0.958613726 0.949600506 1.092810788 1.002003727 0.872601443 1.001451437 0.789785972 0.837153901 1 20.65098392 3.024047418 1.599715189 0.878841661 1.002547218 0.246695775 0.07788809 0.459554732 2.425177864 0.030650338 0.034150621 1056.932902 -3.024047418 0.123705557 GPQPPTVS(ph)PIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GPQPPTVSPIR 11 0 P46087-2;P46087;P46087-4 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 GPQPPTVS(1)PIR;GPQPPTVS(1)PIR;GPQPPT(0.001)VS(0.999)PIR 166.45 2.14E-05 2425610000 1446730 1427150 964460 943900 1273440 1259740 1203090 1195600 1159010 TRUE FALSE 1255540.965 1417774.958 1430876.082 1158226.922 1248101.035 1308203.013 1086414.517 939930.2442 1021993.158 1.228521889 1.387264627 1.400083817 1.133302031 1.221242066 1.280050656 1.06303502 0.919703069 1 19.96295411 2.116626624 3.041500454 0.958845908 1.278858567 0.740024855 0.079981568 0.127563787 2.350385845 0.041990786 0.02454487 130.8056865 -2.116626624 0.32001266 MQES(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MQESPK 6 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 MQES(1)PK;MQES(1)PK 87.639 0.054767 281090000 487770 533870 583770 843370 541550 708190 881170 1019790 2612800 TRUE FALSE 423309.9586 530362.9728 866083.1246 1034870.049 530774.2145 735434.5276 795714.269 801715.8445 2303917.761 0.183734839 0.230200479 0.375917552 0.449178381 0.230378976 0.319210408 0.345374424 0.347979367 1 21.13565779 1.231523381 4.568330945 1.060819003 0.311022663 0.887010432 0.077469497 0.067583019 3.020430513 0.165924105 0.020184538 17.04211065 -1.231523381 -0.74979634 GPRT(ph)PPITTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPRTPPITTK 10 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 GPRT(1)PPITTK 94.616 0.012905 328330000 1087400 753600 538090 658280 797680 679420 819530 1080900 718040 TRUE FALSE 943697.3349 748649.552 798312.1238 807752.5352 781807.7286 705557.727 740052.1067 849757.9466 633154.1292 1.490470158 1.182412808 1.260849589 1.275759721 1.234782642 1.114353827 1.168834053 1.342102827 1 19.27219721 4.742063642 24.82168939 1.210360632 1.490470275 0.481554904 0.09472361 278.5729279 1973812.406 0.022217905 0.157661737 55215.83475 -4.742063642 0.280109643 GPS(ph)PAPAS(ph)SPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPSPAPASSPKR 12 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 GPS(0.999)PAPAS(0.914)S(0.088)PKR 74.475 0.024331 137160000 648070 518980 364840 403920 495650 462960 553400 654630 498050 TRUE FALSE 562425.9075 515570.7862 541277.8443 495636.2095 485787.5347 480770.3708 499731.3532 514642.4688 439171.0964 1.280653286 1.173963383 1.232498789 1.128572016 1.106146417 1.09472225 1.137896727 1.171849589 1 18.74442358 8 0.355315953 1.096334844 3.279264 0.582832518 0.049541247 64.57677777 0.978528642 0.063922704 93.84760505 99999999.98 -8 2.182929157 GPS(ph)PAPASS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPSPAPASSPK 11 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 GPS(1)PAPAS(0.02)S(0.98)PK 120.21 0.00070609 354870000 1070200 822950 607850 662520 829040 746570 944020 1054800 1147400 TRUE FALSE 928770.3585 817543.9873 901808.2931 812955.292 812543.726 775291.031 852469.0857 829239.2285 1011755.679 0.917978893 0.808044871 0.891330102 0.803509492 0.803102708 0.766282856 0.842564172 0.819604224 1 19.94842952 1.236684652 24.99938248 1.000000215 0.828836697 0.586038198 0.04444026 34.23020621 456028.3152 0.065724766 0.010450836 17.24585189 -1.236684652 -0.171163518 GPS(ph)PAPASS(ph)PKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPSPAPASSPKR 12 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 GPS(0.997)PAPAS(0.414)S(0.589)PKR 76.196 0.021233 216560000 862630 652490 500970 555770 696710 691900 796130 918260 735160 TRUE FALSE 748631.2599 648203.7502 743240.7676 681966.0729 682846.8341 718517.8407 718921.4351 721897.2449 648250.2223 1.154849214 0.999928312 1.146533764 1.05201055 1.053369225 1.108395826 1.109018417 1.113608943 1 19.30619127 5.129283477 18.01708519 1.079742034 17.18806539 0.206692971 0.048853331 958908.0553 4134509.601 0.011142956 657549701 134673.9126 -5.129283477 16.10832335 GPS(ph)PGEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPSPGEEK 8 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 GPS(1)PGEEK 70.908 0.050886 0 290990 253330 248900 289860 242980 282730 294950 336620 742530 TRUE FALSE 252534.9342 251665.8585 369268.8725 355677.1432 238145.1734 293606.8061 266345.7944 264636.4326 654748.9493 0.385697349 0.384370007 0.563985437 0.543226749 0.363719825 0.44842654 0.406790717 0.404180003 1 19.32058231 1.236456191 24.99995529 1.000000718 0.438167927 0.874642823 0.066918096 19.37347564 230092.8689 0.109442125 0.017086835 17.23678208 -1.236456191 -0.561832792 GPS(ph)PRPPATAYDAPASAFGSSLLGSGGSAFAPPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLR 35 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 GPS(0.977)PRPPAT(0.023)AYDAPASAFGSSLLGSGGSAFAPPLR;GPS(0.98)PRPPAT(0.02)AYDAPASAFGSSLLGSGGSAFAPPLR 171.29 3.36E-15 1229910000 176780 205620 147180 200893 182893 234770 132715 170056 250770 TRUE FALSE 153418.0751 204269.2687 218356.7403 246508.8261 179253.7871 243801.7538 119844.3197 133690.8478 221124.2563 0.693809344 0.923775944 0.98748434 1.114797762 0.810647326 1.10255545 0.541977265 0.604596031 1 17.75449777 2.236288347 24.99999978 0.685183226 0.942541628 0.269223664 0.170953037 67.97542903 747861.0495 0.066266639 0.04712095 172.301218 -2.236288347 0.257358401 GPS(ph)PTPEDVSMKEENLCQAFSDALLCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPSPTPEDVSMKEENLCQAFSDALLCK 27 1 H1UBN3;O95067 H1UBN3 CCNB2V;CCNB2 G2/mitotic-specific cyclin-B2 1 GPS(0.495)PT(0.495)PEDVS(0.011)MKEENLCQAFSDALLCK 159.75 8.80E-12 38550000 79626 68505 51308 52808 64986 51140 79200 98840 69850 TRUE FALSE 69103.22235 68054.98614 76120.72041 64798.86352 63692.90574 53107.38889 71519.19619 77703.83517 61592.41257 1.12194375 1.104924832 1.235878207 1.052059187 1.034103116 0.862239141 1.161168936 1.261581288 1 15.91046502 3.695254746 24.97812235 1.079395993 1.149316767 0.124716522 0.108704843 1352.420735 780053.6466 0.033800202 0.050134148 4957.40894 -3.695254746 0.069920774 GPS(ph)WDPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 GPSWDPFR 8 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR 121.8 0.0014873 39431989000 33615317 28800364 24525334 38064541 28422909 30320656 37464528 34732473 62604506 TRUE FALSE 29172967.69 28611172.51 36385867.55 46707676.81 27857348.72 31487111.26 33831223.84 27305203.94 55203472.62 0.528462546 0.518285737 0.659122802 0.846100337 0.504630368 0.5703828 0.612845936 0.494628375 1 25.71825569 1.230038266 24.99837092 1.000000765 0.592597192 0.605322988 0.103582786 238.7844774 700364.8864 0.29616549 0.026099876 16.98393291 -1.230038266 -0.407403572 GPS(ph)WDPFRDWYPHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 GPSWDPFRDWYPHSR 15 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 GPS(1)WDPFRDWYPHSR;GPS(1)WDPFRDWYPHSR;GPS(1)WDPFRDWYPHSR;GPS(1)WDPFRDWYPHSR;GPS(1)WDPFRDWYPHSR;GPS(1)WDPFRDWYPHSR;GPS(1)WDPFRDWYPHSR;GPS(1)WDPFRDWYPHSR;GPS(1)WDPFRDWYPHSR 150.23 1.95E-06 13583867000 10338880 9067386 3942492 5333273 8132392 8361282 10487567 9561606 1981794 TRUE FALSE 8972570.813 9007821.744 5849094.318 6544274.149 7970573.31 8682945.929 9470484.367 7516930.965 1747508.571 5.134493164 5.154665273 3.347104795 3.744916767 4.561106848 4.968757277 5.419420839 4.301513074 1 20.7368681 4.268150422 24.11506012 4.078076998 5.144582379 0.143587409 1.201657858 317.3542812 258629.4979 0.302260067 0.799385737 18541.73721 -4.268150422 1.066505381 GPSFPEPLREEQDLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPSFPEPLREEQDLER 16 1 A0A1B0GVZ4;A0A494C085;P06132;A0A1B0GVN9;H0Y5R6;Q5T446;A0A494BZY8;A0A494C0Q8;A0A494C1D8;A0A494C0S8 A0A1B0GVZ4 UROD Uroporphyrinogen decarboxylase 0 70.334 0.039868 197440000 294440 324820 232990 298040 262690 314170 230440 290620 353610 FALSE TRUE 255529.008 322686.236 345664.7433 365714.5373 257462.9829 326256.3232 208091.9643 228473.1746 311806.6286 0.819511147 1.034892162 1.108586898 1.172888911 0.825713629 1.046341845 0.66737505 0.732739954 1 18.25029207 2.250366664 24.99968526 0.780490195 1.007540273 0.31717238 0.138033773 227.164461 481028.1469 0.051810311 0.039800637 177.9781402 -2.250366664 0.227050078 GPSHPLDLGTS(ph)SPNTSQIHWTPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPSHPLDLGTSSPNTSQIHWTPYR 24 0 O60504-2;O60504;H0YAZ3 O60504-2 SORBS3 Vinexin 1 GPSHPLDLGT(0.004)S(0.965)S(0.03)PNTSQIHWTPYR 138.34 1.22E-05 165050000 103310 122120 50652 79641 153570 157600 145530 167900 125130 TRUE FALSE 89657.32175 121317.7857 75147.47662 97724.70629 150514.2575 163662.974 131416.523 131995.8916 110337.2739 0.812575103 1.0995177 0.681070629 0.885690781 1.364128839 1.483297241 1.191043772 1.19629466 1 16.75156072 3.251213292 24.56067822 1.248244639 0.87265347 0.580795753 0.159243277 137.8744274 267632.3422 0.047243223 0.0605505 1783.254351 -3.251213292 -0.375591169 GPSHPLDLGTSS(ph)PNTSQIHWTPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GPSHPLDLGTSSPNTSQIHWTPYR 24 0 O60504-2;O60504;H0YAZ3 O60504-2 SORBS3 Vinexin 1 GPSHPLDLGT(0.004)S(0.066)S(0.931)PNTSQIHWTPYR;GPSHPLDLGTS(0.032)S(0.968)PNTSQIHWTPYR;GPSHPLDLGTS(0.009)S(0.99)PNT(0.001)SQIHWTPYR 246.57 1.15E-37 1605060000 762150 1058040 540792 872210 1374880 1443740 1230970 1518550 1296700 TRUE FALSE 661429.9465 1051089.666 802320.82 1070258.611 1347522.578 1499281.612 1111590.719 1193819.9 1143405.603 0.578473592 0.919262301 0.701693973 0.936027083 1.178516682 1.311242142 0.972175329 1.04409135 1 20.12490583 3.505776312 3.897559358 1.094059576 0.754896832 0.638419248 0.125887355 0.152702068 5.043734253 0.036898134 0.053381222 3204.618329 -3.505776312 -0.339162744 GPSLNPVLDYDHGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GPSLNPVLDYDHGSR 15 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 183.36 5.09E-07 1861310000 1694360 1735380 860840 1423000 1918830 2003100 1524880 1704040 3911550 FALSE TRUE 1470446.033 1723980.175 1277145.103 1746113.899 1880649.037 2080160.553 1376997.372 1339644.307 3449131.015 0.426323624 0.499830296 0.370280253 0.506247484 0.545253001 0.603096996 0.399230231 0.388400528 1 21.7178015 1.233451547 24.99990068 1.000000825 0.466316905 0.837174381 0.073825207 66.43441056 325041.9181 0.157784855 0.019287975 17.11794184 -1.233451547 -0.53368392 GPSPAAAS(ph)PEGSPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPSPAAASPEGSPLR 15 0 Q9P107;Q9P107-2 Q9P107 GMIP GEM-interacting protein 1 GPSPAAAS(0.999)PEGS(0.001)PLR 152.77 2.91E-06 93086000 105100 106230 103590 113820 132780 154090 121560 121970 214190 TRUE FALSE 91210.76871 105532.1681 153686.4705 139664.5706 130137.9378 160017.942 109771.1299 95887.66467 188868.7022 0.482932152 0.558759429 0.813721218 0.739479697 0.689039191 0.847244356 0.58120339 0.507694835 1 17.52702412 4.406745517 6.000465967 0.712154967 0.500611263 0.293834758 0.138292487 0.252627354 15.71837058 0.035509067 0.097826617 25512.05939 -4.406745517 -0.211543704 GPSPAPAS(ph)SPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPSPAPASSPKR 12 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 GPS(0.005)PAPAS(0.643)S(0.352)PKR 64.65 0.066599 33505000 155660 123290 76682 96808 115730 100360 132610 152460 110210 TRUE FALSE 135089.1366 122480.0999 113765.6717 118789.736 113427.1994 104220.9141 119749.5026 119857.6154 97181.09935 1.390076234 1.260328404 1.170656356 1.222354314 1.167173454 1.072440164 1.232230376 1.233342864 1 16.56838813 GPSPAPASS(ph)PKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPSPAPASSPKR 12 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 GPSPAPAS(0.253)S(0.747)PKR 62.494 0.047392 289740000 274740 229110 164730 190410 240650 181180 221560 298440 251270 TRUE FALSE 238432.4129 227604.9613 244393.979 233645.5007 235861.5358 188150.1118 200073.1453 234620.9285 221565.1468 1.076127795 1.027259768 1.103034401 1.054522808 1.064524539 0.849186411 0.902999177 1.05892525 1 17.75737143 2.897698034 24.99999074 0.963824283 1.064543235 0.476166526 0.05802367 39.20457307 9570.441193 0.020308129 0.020308139 790.1290581 -2.897698034 0.100718952 GPSQEEEDNHS(ph)DEEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPSQEEEDNHSDEEDR 16 0 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 GPSQEEEDNHS(1)DEEDR;GPSQEEEDNHS(1)DEEDR 268.09 1.26E-27 440610000 220950 190322 172606 208108 200800 200815 160412 211501 424590 TRUE FALSE 191750.8977 189071.7623 256078.8389 255362.1021 196804.4729 208540.483 144855.2689 166273.1571 374395.4539 0.512161394 0.505005497 0.683979563 0.682065179 0.525659355 0.557005917 0.386904455 0.444111047 1 18.51420339 1.231765223 24.99994383 1.000000793 0.534091117 0.714574777 0.091921661 147.2879505 541815.8541 0.243592027 0.025473825 17.05160339 -1.231765223 -0.465909676 GPSQEEEDNHS(ph)DEEDRASEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPSQEEEDNHSDEEDRASEPK 21 1 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 GPSQEEEDNHS(1)DEEDRASEPK;GPSQEEEDNHS(1)DEEDRASEPK 353.53 1.10E-95 710340000 572110 450480 306730 363120 442080 370120 526400 629540 433190 TRUE FALSE 496504.214 447520.7672 455065.654 445571.9459 433283.4729 384358.7559 475349.809 494917.7701 381978.7717 1.299821484 1.17158544 1.19133755 1.16648353 1.134312965 1.006230671 1.244440383 1.295668259 1 18.54313294 6.01516338 1.245217816 1.159897947 3.884716106 0.200220209 0.092173909 60.78032221 5.902561648 0.027713072 416.583458 1035531.656 -6.01516338 2.72481816 GPSS(ph)VEDIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPSSVEDIK 9 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 GPS(0.076)S(0.924)VEDIK 100.69 0.0047115 451080000 1097300 910910 617980 744750 808700 669440 966730 1142700 1121800 TRUE FALSE 952289.0248 904926.1722 916837.195 913856.8703 792608.4522 695193.79 872976.6734 898342.4975 989182.082 0.962703472 0.914822649 0.926863933 0.923851015 0.801276597 0.702796586 0.882523743 0.908166973 1 19.91587658 3.38118658 9.689311312 0.859117036 0.931553416 0.187073437 0.07590734 0.607847489 55.99856172 0.023943002 0.030914426 2405.395978 -3.38118658 0.07243638 GPSSEAMHVGHLIPFIFTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPSSEAMHVGHLIPFIFTK 19 0 P23381;P23381-2;G3V277;G3V5U1;G3V3Y5;G3V3H8;G3V456;G3V423 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 117.01 6.20E-05 268750000 281470 273360 120870 157120 236940 242710 291070 317580 181960 FALSE TRUE 244273.0263 271564.2802 179323.1363 192796.4974 232225.3576 252047.2108 262842.0762 249667.9884 160448.8961 1.52243507 1.692528193 1.117633967 1.20160688 1.447347805 1.570887784 1.638166934 1.556059247 1 17.29175434 1.23216461 24.91411294 0.999999179 1.470666931 0.397973375 0.181004637 241.4976858 940601.6378 0.44075427 0.047938891 17.06729167 -1.23216461 0.470667752 GPSSHEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPSSHEMR 8 0 Q9H0L4 Q9H0L4 CSTF2T Cleavage stimulation factor subunit 2 tau variant 0 81.296 0.023227 32626000 50052 44172 35223 37437 47593 58096 56072 75460 118050 FALSE TRUE 43437.50138 43881.83122 52256.96061 45937.64304 46645.99241 60330.99071 50634.14607 59323.46623 104094.2635 0.417290059 0.421558593 0.502015758 0.441308113 0.448112997 0.57958036 0.486425903 0.569901397 1 16.66753104 -0.010324337 1.208456142 9.999999999 0.463697977 0.926066881 0.046713675 6.935531247 0.687905929 160.0209281 0.014668424 0.976507681 0.010324337 -9.536302022 GPSWDPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 GPSWDPFR 8 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;;;;; 159.2 0.00083884 3.05006E+11 146330360 183527440 146983820 158982280 167450590 190237340 168114910 179672590 290438940 FALSE TRUE 126992432.2 182321836.2 218065687 195081636.6 164118650.9 197555893.6 151811151.9 141251004.8 256103579.4 0.495863558 0.71190663 0.851474577 0.761729442 0.640829196 0.771390599 0.592772472 0.551538581 1 27.93215218 4.737158947 7.365730642 0.716997093 0.493316207 0.241390378 0.129850473 0.160799024 80.97097061 0.032001248 0.182258339 54595.7639 -4.737158947 -0.223680886 GPSWDPFRDWYPHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 GPSWDPFRDWYPHSR 15 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;; 182.7 3.22E-07 53205159000 2099369 2745938 890457 1111013 1795464 2320279 1846669 2024806 262592 FALSE TRUE 1821932.068 2727899.752 1321084.984 1363285.482 1759737.779 2409541.635 1667579.325 1591816.994 231548.6729 7.868462577 11.78110726 5.705431031 5.887684284 7.599861217 10.40619929 7.201852223 6.874653929 1 17.82095596 4.227001093 24.9950945 6.639649971 9.824785351 0.241712149 2.502853497 292.339096 632127.0997 0.640558041 1.351502576 16865.5727 -4.227001093 3.185135379 GPTEADELMKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GPTEADELMKR 11 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;; 145.41 5.81E-05 1834000000 2085200 1889220 759002 763447 1622060 1565200 2258110 2229380 176283 FALSE TRUE 1809635.537 1876809.589 1126057.906 936799.3099 1589784.18 1625414.257 2039118.84 1752644.436 155443.0246 11.64179314 12.07393895 7.244184222 6.026641032 10.22743982 10.45665614 13.11811093 11.27515655 1 17.24602635 4.260249639 24.81006382 9.022155694 11.85786933 0.13342339 3.365610721 526.2036154 601912.6298 0.856253067 2.260961143 18207.47149 -4.260249639 2.835713632 GPTEQLVSPEPEVHDIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GPTEQLVSPEPEVHDIER 18 0 P35813;P35813-3;P35813-2 P35813 PPM1A Protein phosphatase 1A 0 ;;; 175.21 3.91E-12 1978120000 1179410 1132480 817894 806777 1037170 1161470 1079320 1195600 1134310 FALSE TRUE 1023547.98 1125040.664 1213430.274 989968.0487 1016532.346 1206152.502 974647.7125 939930.2442 1000213.164 1.023329843 1.124800897 1.21317167 0.989757068 1.016315704 1.205895449 0.974439997 0.939729928 1 19.93187607 2.092172325 11.10458404 0.963030737 1.093761874 0.373777315 0.075632783 0.407557451 46.0464759 0.030821397 0.020775956 123.6437945 -2.092172325 0.130731137 GPTSS(ph)PCEEEGDEGEEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPTSSPCEEEGDEGEEDR 18 0 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 GPTSS(1)PCEEEGDEGEEDR 334.51 5.29E-75 188750000 92989 82727 63377 71451 88908 72585 82479 85089 166810 TRUE FALSE 80700.26805 82183.56089 94026.32918 87675.04161 87138.90475 75377.39192 74480.19927 66893.37951 147089.9118 0.548645839 0.558730098 0.639243902 0.596064275 0.592419315 0.512457931 0.506358311 0.45477884 1 17.16633878 1.231197469 24.99992228 1.000000793 0.548959894 0.880217614 0.052038149 99.44209752 337604.1689 0.150208578 0.014884838 17.02932639 -1.231197469 -0.451040899 GPTSS(ph)PCEEEGDEGEEDRT(ph)SDLRDEAS(ph)SVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPTSSPCEEEGDEGEEDRTSDLRDEASSVTR 31 2 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 3 GPT(0.017)S(0.12)S(0.862)PCEEEGDEGEEDRT(0.5)S(0.5)DLRDEAS(0.523)S(0.465)VT(0.012)R;GPT(0.032)S(0.147)S(0.821)PCEEEGDEGEEDRT(0.5)S(0.5)DLRDEAS(0.821)S(0.147)VT(0.032)R 134.61 1.47E-05 441030000 154126 142396 100571 95389 144039 153287 147276 130789 133178 TRUE FALSE 133757.8586 141460.5913 149207.472 117048.5304 141172.9057 159184.0501 132993.1962 102820.7902 117433.8486 1.139006004 1.204598104 1.270566143 0.996718849 1.202148337 1.355521019 1.132494573 0.875563489 1 16.84148878 1.865437941 5.103221899 0.938212054 1.193679631 0.543720233 0.095759384 0.158124539 5.662505452 0.050647305 0.025670803 73.35638829 -1.865437941 0.255467577 GPTSS(ph)PCEEEGDEGEEDRTSDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPTSSPCEEEGDEGEEDRTSDLR 23 1 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 GPT(0.002)S(0.037)S(0.962)PCEEEGDEGEEDRTSDLR;GPTS(0.005)S(0.995)PCEEEGDEGEEDRTSDLR 221.5 1.07E-32 582030000 431060 412940 309690 340610 394400 402910 375200 406080 383380 TRUE FALSE 374094.3288 410227.37 459457.1199 417950.7064 386552.2116 418410.2084 338813.1617 319242.9521 338057.2531 1.10660051 1.213484894 1.359110374 1.236331132 1.143451909 1.237690375 1.002236037 0.944345815 1 18.36690808 2.196321628 5.18090511 0.970861381 1.220544313 0.728848639 0.067267081 0.096111986 5.952844614 0.028945807 0.019653617 157.1526207 -2.196321628 0.249682932 GPTSTSIDNIDGT(ph)PVRDER ddPTM_MDA-MB-175_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 244.78 2.50E-24 5631750000 6014100 4790550 3540430 3428680 4480360 5198630 4429010 4438490 4283260 TRUE FALSE 5219321.447 4759080.562 5252593.79 4207214.198 4391209.602 5398624.66 3999485.292 3489353.454 3776897.882 1.381906954 1.260050102 1.39071639 1.113933797 1.162649809 1.429380626 1.058933923 0.923867566 1 21.84877035 2.061866848 6.066686713 0.96609137 1.278479352 0.666151765 0.100067901 0.111419611 7.973138837 0.041586097 0.027561228 115.309967 -2.061866848 0.312387982 GPVEGYEENEEFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GPVEGYEENEEFLR 14 0 F5GYQ2;Q9UI30;Q9UI30-2;F5GX77 F5GYQ2 TRMT112 Multifunctional methyltransferase subunit TRM112-like protein 0 ;; 232.17 6.22E-13 886090000 539043 434287 325699 335876 419353 457899 418923 461900 484673 FALSE TRUE 467807.1018 431434.1401 483208.1258 412141.7793 411008.6958 475514.6708 378295.9119 363126.2795 427375.5101 1.094604372 1.009496637 1.130640653 0.964355162 0.961703902 1.112639025 0.885160481 0.849665624 1 18.70514471 2.223011748 24.99458308 0.897601832 1.040296164 0.454482826 0.068455548 196.4158133 315733.1473 0.027296296 0.018474838 167.113582 -2.223011748 0.142694332 GPVS(ph)GTEPEPVYSMEAADYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPVSGTEPEPVYSMEAADYR 20 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 GPVS(0.5)GT(0.5)EPEPVYSMEAADYR 289.61 2.09E-54 142300000 58109 81898 82533 86812 121500 174870 144380 122420 140260 TRUE FALSE 50429.74842 81360.00665 122446.2349 106523.9914 119082.3877 181597.3621 130378.0498 96241.43567 123678.6226 0.407748303 0.657834029 0.990035564 0.861296716 0.962837273 1.468300328 1.054168029 0.778157402 1 16.91623663 4.6004588 1.257827485 1.022425522 0.20747602 0.576622857 0.179558069 0.922175952 1.527707454 0.058426009 0.914802263 39852.79635 -4.6004588 -0.814949502 GPVS(ph)PSVSFQPLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GPVSPSVSFQPLAR 14 0 Q7Z434;Q7Z434-4 Q7Z434 MAVS Mitochondrial antiviral-signaling protein 1 GPVS(0.943)PS(0.057)VSFQPLAR;GPVS(0.992)PS(0.008)VSFQPLAR;GPVS(0.987)PS(0.013)VSFQPLAR;GPVS(0.955)PS(0.045)VSFQPLAR;GPVS(1)PSVSFQPLAR;GPVS(1)PSVSFQPLAR;GPVS(0.999)PS(0.001)VSFQPLAR 252.52 3.48E-24 7266615000 1466501 1654366 1354669 1736667 2425503 2950593 1501314 2454298 2506498 TRUE FALSE 1272699.177 1643498.361 2009791.459 2131003.786 2377240.236 3064104.222 1355716.799 1929465.472 2210182.662 0.575834387 0.743602956 0.909332742 0.964175415 1.075585415 1.386357913 0.613395817 0.872989145 1 21.07573418 4.429300487 1.810305726 0.970408087 0.552331088 0.347165354 0.189259765 0.6241938 3.229380298 0.054816554 0.363957722 26872.03072 -4.429300487 -0.418076999 LGHEEQQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LGHEEQQKR 9 1 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 ;; 122.28 0.00038314 332579000 559890 461733 344543 349943 423591 513668 547466 551280 210793 FALSE TRUE 485899.1179 458699.8455 511165.1472 429402.9067 415162.3678 533429.1403 494372.8316 433393.0621 185873.2917 2.614141674 2.467809341 2.750073142 2.310191544 2.233577315 2.869853627 2.659730331 2.331658616 1 17.50395996 1.231769256 3.339110895 0.738913023 2.549290573 0.867358422 0.189905519 0.116224671 1.783518486 0.552860531 0.049534726 17.05176174 -1.231769256 1.81037755 GPVSGTEPEPVYS(ph)MEAADYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GPVSGTEPEPVYSMEAADYR 20 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 GPVSGTEPEPVY(0.104)S(0.896)MEAADYR;GPVSGTEPEPVYS(1)MEAADYR;GPVSGTEPEPVYS(1)MEAADYR;GPVSGTEPEPVYS(1)MEAADYR 267.6 7.10E-37 994940000 410596 624700 607060 587760 854320 1163460 910070 868950 1030150 TRUE FALSE 356334.6983 620596.3046 900636.2465 721219.8913 837320.7034 1208219.059 821811.5515 683131.8047 908366.8406 0.39228061 0.683200087 0.991489568 0.793974261 0.921786954 1.330100357 0.904713288 0.75204397 1 19.79291552 4.569501571 2.12716048 0.943927732 0.333302218 0.584196815 0.156427036 0.368668161 2.437923897 0.043943566 0.375195306 37110.90717 -4.569501571 -0.610625515 GPVSGTEPEPVYSMEAADYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPVSGTEPEPVYSMEAADYR 20 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 130.61 3.68E-05 76401000 43218 48986 29303 32265 43728 53531 41676 51014 48355 FALSE TRUE 37506.6318 48664.20774 43474.02881 39591.26139 42857.89835 55590.37221 37634.26793 40105.05309 42638.52699 0.879641827 1.141320097 1.019594997 0.928532578 1.00514491 1.303759209 0.882635274 0.940582518 1 15.37986998 GPVTIPYPLFQSHVEDLYVEGLPEGIPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPVTIPYPLFQSHVEDLYVEGLPEGIPFR 29 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 ; 242.45 1.72E-45 353420000 206578 183192 146373 130957 189325 177513 158354 198158 194837 FALSE TRUE 179278.1939 181988.5997 217159.4724 160692.7884 185557.8029 184342.04 142996.8535 155783.4538 171803.5918 1.043506669 1.059282858 1.263998442 0.935328457 1.080057762 1.072981292 0.832327496 0.906753183 1 17.39040067 2.256976035 24.42825724 0.908357424 1.077460704 0.428251629 0.088625 159.6302948 211750.9093 0.032368718 0.025020628 180.7074406 -2.256976035 0.16910328 GPWALEEESLVGREPEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GPWALEEESLVGREPEER 18 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63 O00515 LAD1 Ladinin-1 0 ;;; 234.48 8.29E-24 675890000 850050 898040 592760 573590 844470 920000 834980 915270 514140 FALSE TRUE 737713.7387 892140.7161 879420.7187 703832.3763 827666.6992 955392.9953 754003.7681 719546.6331 453358.9549 1.62721775 1.967846243 1.939789011 1.552483675 1.825632184 2.107365444 1.663149608 1.587145518 1 18.79029426 1.106591467 1.523603193 0.436644725 1.830026544 0.706337505 0.165754754 0.876524405 1.401096913 2.051880303 0.047048317 12.7817838 -1.106591467 1.393381819 GPWWDDWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GPWWDDWER 9 0 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 ; 121.96 0.0013943 153204000 214170 199043 157885 172860 199711 205090 196125 220260 271440 FALSE TRUE 185866.8919 197735.4734 234238.7141 212110.505 195737.1418 212979.945 177104.8277 173159.1131 239350.6724 0.776546353 0.826132935 0.97864239 0.88619139 0.817783965 0.889823884 0.73993871 0.723453631 1 17.86876633 2.256960751 24.94482313 0.797398346 0.865186977 0.02198003 0.091509922 538.1040801 729499.7848 0.034373603 0.026573173 180.701081 -2.256960751 0.067788631 GQAALDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQAALDR 7 0 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ; 88.942 0.042427 819110000 662390 679700 480820 483990 481610 774080 616460 696040 756000 FALSE TRUE 574853.4832 675235.0059 713346.1602 593887.3268 472026.9033 803859.3585 556675.8041 547197.2626 666626.5412 0.862332127 1.012913474 1.070083647 0.890884611 0.708082973 1.205861616 0.835063967 0.820845299 1 19.34651923 3.687616811 24.75905669 0.900036183 0.984890328 0.052434074 0.139047575 855.7542085 415902.1485 0.037652393 0.055847574 4870.985211 -3.687616811 0.084854146 GQASLEWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQASLEWK 8 0 A0A494C1U9 A0A494C1U9 0 ; 60.436 0.092303 624400000 820600 928290 459210 656440 947310 1192630 715000 884100 862490 FALSE TRUE 712155.6309 922192.0019 681285.492 805494.7351 928460.3844 1238511.248 645659.41 695042.0951 760527.4148 0.936397054 1.212569046 0.895806619 1.059126495 1.220811198 1.628489945 0.848962703 0.91389486 1 19.53664073 GQDHCGIESEVVAGIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GQDHCGIESEVVAGIPR 17 0 P07858;R4GMQ5 P07858 CTSB Cathepsin B;Cathepsin B light chain;Cathepsin B heavy chain 0 ;;; 244.86 1.36E-21 2274000000 960070 924050 700840 739110 883580 1170260 778580 930120 923670 FALSE TRUE 833194.317 917979.8547 1039768.568 906936.2221 865998.4867 1215280.659 703073.4314 731221.0762 814474.7848 1.022983563 1.127081982 1.276612349 1.113522774 1.063260033 1.492103478 0.863223079 0.897782338 1 19.63551051 GQDMETEAHQNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GQDMETEAHQNK 12 0 Q15363;F5GX39 Q15363 TMED2 Transmembrane emp24 domain-containing protein 2 0 85.271 0.0089262 87356000 278680 279990 188480 233430 233090 273830 275810 330920 410740 FALSE TRUE 241851.7319 278150.7273 279629.5584 286433.8493 228451.965 284364.4173 249061.9887 260155.3332 362182.7851 0.667761533 0.767984395 0.772067503 0.7908544 0.630764284 0.785140622 0.687669318 0.71829845 1 18.46635845 1.237232082 24.99975547 1.000000328 0.728668247 0.720657313 0.053300788 17.49739886 329129.6887 0.074697373 0.012339526 17.26760406 -1.237232082 -0.271332081 GQDS(ph)PLLQRPQHLMDQGQMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GQDSPLLQRPQHLMDQGQMR 20 1 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 GQDS(1)PLLQRPQHLMDQGQMR;GQDS(1)PLLQRPQHLMDQGQMR;GQDS(1)PLLQRPQHLMDQGQMR;GQDS(1)PLLQRPQHLMDQGQMR;GQDS(1)PLLQRPQHLMDQGQMR 231.4 6.14E-26 1931289000 902279 853949 493538 532460 797747 715949 612998 819311 639971 TRUE FALSE 783040.5441 848339.3528 732214.6276 653363.1811 781873.3955 743492.0213 553549.5483 644107.7185 564314.3574 1.387596353 1.503309887 1.29752968 1.157800032 1.385528093 1.31751392 0.980924091 1.141398779 1 19.10613953 -0.340078395 0.154180802 2.47E-10 1.644780629 0.619706809 0.105377718 55.48998966 1.224178939 19.43266484 2.005043153 0.457005688 0.340078395 1.644780629 GQDSIPHHSDYDEEEWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQDSIPHHSDYDEEEWDR 18 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 ; 188.84 2.07E-14 557350000 201875 209660 117797 194166 241194 260766 198162 207052 424250 FALSE TRUE 175196.7073 208282.7297 174764.0232 238254.3579 236394.7113 270797.8368 178944.2797 162775.5411 374095.6483 0.468320624 0.556763305 0.46716401 0.636880859 0.631909813 0.723873261 0.478338309 0.435117441 1 18.51304766 1.229547996 24.99804867 1.000000868 0.549433678 0.702209131 0.09213677 219.4560132 608653.0466 0.291005584 0.024385077 16.96477077 -1.229547996 -0.45056719 GQDTPKPAGQHGSLS(ph)PAAAHTAS(ph)PEPPTQSGPLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GQDTPKPAGQHGSLSPAAAHTASPEPPTQSGPLTR 35 1 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 2 GQDT(0.001)PKPAGQHGS(0.17)LS(0.828)PAAAHTAS(0.999)PEPPT(0.001)QSGPLTR;GQDTPKPAGQHGS(0.006)LS(0.988)PAAAHT(0.24)AS(0.766)PEPPTQSGPLTR;GQDTPKPAGQHGS(0.063)LS(0.937)PAAAHTAS(1)PEPPTQSGPLTR;GQDTPKPAGQHGS(0.101)LS(0.898)PAAAHT(0.009)AS(0.989)PEPPT(0.002)QSGPLTR 257.29 9.64E-60 925770000 391995 353760 141323 301897 427884 354546 402264 502593 490594 TRUE FALSE 340191.8676 351436.1273 209667.2755 370447.3281 419369.9455 368185.614 363252.4992 395117.3981 432596.5362 0.786395265 0.812387751 0.484671647 0.856334476 0.969425112 0.851106246 0.839702746 0.913362371 1 18.72266259 3.497163624 24.63347296 0.906391621 0.70031313 0.51196791 0.098183685 523.7282844 643697.2487 0.026570098 0.038803805 3141.692127 -3.497163624 -0.206078492 GQDTPKPAGQHGSLS(ph)PAAAHTASPEPPTQSGPLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GQDTPKPAGQHGSLSPAAAHTASPEPPTQSGPLTR 35 1 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 GQDT(0.02)PKPAGQHGS(0.45)LS(0.53)PAAAHTASPEPPTQSGPLTR 76.716 0.0016868 87878000 30355 33396 11048 19710 34210 28542 33245 44349 39103 TRUE FALSE 26343.50984 33176.61948 16390.84975 24185.45675 33529.28793 29640.02921 30020.90502 34865.31147 34480.28789 0.764016528 0.962190907 0.475368704 0.701428504 0.972419025 0.85962244 0.87066863 1.011166484 1 15.0734842 3.239735255 24.99997027 0.941758582 0.724755224 0.424981423 0.125434649 31.84589852 677770.7452 0.037854756 0.046160961 1736.741791 -3.239735255 -0.217003358 GQEETPSWEHILFTCCHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GQEETPSWEHILFTCCHNR 19 0 Q8TCD5;J3KSY6 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 0 ;;; 286 2.51E-40 967830000 544035 620725 338461 426315 531945 586617 552182 606568 459831 FALSE TRUE 472139.3963 616647.4166 502141.8717 523116.3366 521360.3352 609184.5356 498631.4746 476858.1535 405470.303 1.164424109 1.520820174 1.23841837 1.290147102 1.285816326 1.50241468 1.229760776 1.176061847 1 18.62923673 1.485195707 1.739812039 0.971631517 1.332557611 0.471935028 0.111796637 0.454918017 2.062288781 0.24845968 0.030073938 30.56298069 -1.485195707 0.360926094 GQELAFPLS(ph)PDWQVDYESYTWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GQELAFPLSPDWQVDYESYTWR 22 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 1 GQELAFPLS(1)PDWQVDYESYTWR 98 0.00079007 14096000 37503 48203 29506 32277 37812 40310 38817 43100 43200 TRUE FALSE 32546.88353 47886.35132 43775.20029 39605.98617 37059.61518 41860.75178 35052.53331 33883.4004 38092.94521 0.854407118 1.257092384 1.149168174 1.039719716 0.972873454 1.098910876 0.920184384 0.889492798 1 15.21723622 2.532059949 1.044119454 0.921504311 1.089482999 0.169531133 0.112249911 0.772211258 1.780689984 0.086733899 0.049963926 340.4551824 -2.532059949 0.167978689 GQETSTNPIASIFAWTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQETSTNPIASIFAWTR 17 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 238.02 7.20E-20 83059000 145743 132185 81578 100435 113279 134989 127997 149834 114343 FALSE TRUE 126482.6933 131316.668 121029.3937 123240.3018 111024.9695 140182.1142 115583.8706 117793.1651 100825.5008 1.254471263 1.302415232 1.200384751 1.222312816 1.101159614 1.390343842 1.146375369 1.168287429 1 16.62150105 0.969870452 1.237828823 0.748302659 1.236443567 0.47284633 0.07797818 2.343820021 1.927899808 1.736345581 0.02268915 9.329759571 -0.969870452 0.488140907 GQFETYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GQFETYLR 8 0 A0A1B0GV06;A0A1B0GTP7;A0A1B0GUE3;A0A1B0GUG1;A0A1B0GUW4;E7EMM4;A0A1B0GW68;A0A1B0GUA4;A0A1B0GTM3;A0A1B0GTZ5;A0A1B0GUH5;Q13510-3;Q13510;Q13510-2 A0A1B0GV06 ASAH1 Acid ceramidase;Acid ceramidase subunit alpha;Acid ceramidase subunit beta 0 101.64 0.017746 0 147140 173400 105410 120340 154820 174940 116950 137950 154500 FALSE TRUE 127695.0762 172260.924 156386.6286 147665.0363 151739.3849 181670.055 105608.207 108450.466 136235.186 0.937313479 1.264437837 1.147916578 1.083897931 1.113804659 1.333503189 0.77519039 0.796053275 1 17.05573984 2.224226479 24.99999567 0.840954881 1.147849014 0.563822341 0.119847601 153.976229 268545.9501 0.046581515 0.03156846 167.5816565 -2.224226479 0.306894133 GQFHEYQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GQFHEYQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQER 39 1 P51148;P51148-2;K7ERI8;K7ERQ8;F8VVK3;F8VWU4 P51148 RAB5C Ras-related protein Rab-5C 0 71.359 0.0019078 18610000 10474 10853 7376.5 5907.5 7377.4 8682.8 8745.8 12147 7940.3 FALSE TRUE 9089.834362 10781.70593 10943.80007 7248.888165 7230.604174 9016.832935 7897.633662 9549.458578 7001.60678 1.298249766 1.539890238 1.56304123 1.035317805 1.032706406 1.287823384 1.127974465 1.3638953 1 12.77347032 3.743220981 24.99470462 1.165224241 1.474343403 0.564775616 0.133664877 308.3329489 1653662.075 0.036243824 0.060212469 5536.317401 -3.743220981 0.309119162 GQFQGRPVSVWDVLFSSYLSEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GQFQGRPVSVWDVLFSSYLSEAR 23 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 208.4 9.33E-25 1834420000 1065030 1021931 713111 632665 938442 999425 958145 962849 527536 FALSE TRUE 924283.5871 1015217.868 1057973.865 776321.2579 919768.8402 1037873.526 865224.2454 756951.2342 465171.2951 1.986974684 2.182460265 2.274374786 1.668893301 1.977269126 2.23116417 1.860012117 1.627252675 1 18.82740255 1.171321636 1.326959917 0.390251407 2.049917447 0.786388761 0.173828777 0.734887435 0.993854607 1.751887229 0.053363387 14.83616437 -1.171321636 1.65966604 GQFSTDELVAEVEKR ddPTM_MDA-MB-175_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 ;;;;; 298.78 5.61E-44 6472670000 6162870 4693530 3726520 3836280 4706880 4108930 5711720 6444150 4195460 FALSE TRUE 5348431.115 4662697.892 5528677.536 4707366.008 4613222.297 4267003.196 5157798.274 5066118.671 3699477.498 1.445726084 1.260366604 1.494448213 1.272440773 1.246992933 1.153406987 1.394196417 1.369414647 1 21.81889009 3.565864151 10.16464208 1.258164867 1.386110013 0.260382795 0.1246029 0.870820186 95.54560887 0.03411819 0.050608917 3680.138395 -3.565864151 0.127945147 GQGESDPLDHEPAVS(ph)PLLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GQGESDPLDHEPAVSPLLPR 20 0 P00519-2;P00519 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 GQGESDPLDHEPAVS(1)PLLPR;GQGESDPLDHEPAVS(1)PLLPR;GQGESDPLDHEPAVS(1)PLLPR;GQGESDPLDHEPAVS(1)PLLPR 236.94 8.95E-30 4627940000 2661740 2419030 1455440 1763490 2351040 2353080 2065790 2596950 2522370 TRUE FALSE 2309984.315 2403139.233 2159295.652 2163917.358 2304258.904 2443604.51 1865450.004 2041612.452 2224178.292 1.038578752 1.080461598 0.97082849 0.972906428 1.036004583 1.098654959 0.838714239 0.917917623 1 21.08484101 2.240882094 24.99979052 0.915337234 1.029659338 0.487903505 0.054963227 51.99377806 559926.4874 0.021729101 0.016008611 174.1334057 -2.240882094 0.114322104 GQGPRS(ph)PHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GQGPRSPHK 9 1 Q86U38;Q86U38-2 Q86U38 NOP9 Nucleolar protein 9 1 GQGPRS(1)PHK 54.776 0.080217 127290000 166680 126930 84306 97831 108390 119880 130880 166990 69824 TRUE FALSE 144652.8157 126096.1885 125076.6636 120045.0238 106233.2511 124491.8612 118187.2777 131280.488 61569.48626 2.349423789 2.048030544 2.031471613 1.949748668 1.725420456 2.021973363 1.919575506 2.132232961 1 15.90992791 1.234418004 24.99980953 0.999998523 2.012124659 0.805133763 0.157977797 54.1116305 326507.5127 0.292044897 0.038832166 17.15607767 -1.234418004 1.012126137 GQGSS(ph)PVAMQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 GQGSSPVAMQK 11 0 P18206;P18206-2 P18206 VCL Vinculin 1 GQGS(0.044)S(0.956)PVAMQK;GQGS(0.089)S(0.911)PVAMQK;GQGS(0.206)S(0.794)PVAMQK;GQGS(0.024)S(0.976)PVAMQK;GQGS(0.011)S(0.989)PVAMQK;GQGS(0.031)S(0.969)PVAMQK;GQGS(0.153)S(0.847)PVAMQK;GQGS(0.003)S(0.997)PVAMQK;GQGS(0.06)S(0.94)PVAMQK 245.72 6.09E-16 3390810000 5301660 4766590 4249677 5641350 4228390 4512840 4639660 6078720 19513640 TRUE FALSE 4601032.198 4735277.956 6304835.012 6922304.74 4144253.312 4686451.875 4189706.487 4778833.033 17206759.71 0.267396783 0.275198703 0.366416171 0.402301471 0.240850304 0.272361093 0.243491893 0.27772998 1 24.03647211 1.237809736 24.99949273 1.000000818 0.293006199 0.948440288 0.051789037 4.038957252 134379.9816 0.079198987 0.013578977 17.29058693 -1.237809736 -0.706994618 GQGTLQHS(ph)PVGPAGPASIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GQGTLQHSPVGPAGPASIER 20 0 E7EWR4 E7EWR4 CSTF2 1 GQGTLQHS(1)PVGPAGPASIER 144.18 1.03E-07 230130000 125100 113310 79379 89180 119060 127570 120490 133070 126040 TRUE FALSE 108567.718 112565.6591 117766.9499 109429.682 116690.9389 132477.7004 108804.8983 104614.0161 111139.6948 0.976858163 1.012830379 1.059629956 0.984613843 1.049948348 1.19199266 0.978992236 0.941283996 1 16.76201466 2.026681065 24.99996621 0.964554847 1.046067809 0.241595067 0.06051835 277.8806178 260370.9283 0.025213358 0.016998326 106.3361826 -2.026681065 0.081512961 GQHFYAVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GQHFYAVER 9 0 Q15654;H7BZE2 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 ;;; 132.78 0.00029547 2463710000 1343310 1975950 1352880 1362560 1756350 2109540 1705720 1779380 1749470 FALSE TRUE 1165788.18 1962969.854 2007137.293 1671950.073 1721402.071 2190695.369 1540299.537 1398873.434 1542649.65 0.755705082 1.272466405 1.301097299 1.083817103 1.115873634 1.420086129 0.998476574 0.906799178 1 20.55697902 2.021252888 24.99847299 0.948510926 1.168289793 0.208259568 0.175243393 306.0923781 360036.3073 0.068820594 0.046394505 105.0153751 -2.021252888 0.219778867 GQHHQQQQAAGGSESHPVPPTAPLT(ph)PLLHGEGASQQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GQHHQQQQAAGGSESHPVPPTAPLTPLLHGEGASQQPR 38 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 GQHHQQQQAAGGSESHPVPPT(0.158)APLT(0.842)PLLHGEGASQQPR;GQHHQQQQAAGGSESHPVPPT(0.053)APLT(0.947)PLLHGEGASQQPR;GQHHQQQQAAGGSESHPVPPT(0.001)APLT(0.999)PLLHGEGASQQPR 262.02 1.37E-62 2034190000 369438 278415 130605 200255 303429 311337 309725 327954 402615 TRUE FALSE 320615.8323 276586.0735 193766.0148 245725.9585 297391.3565 323314.3359 279687.9172 257823.5892 355018.3134 0.903096601 0.77907551 0.545791604 0.692150093 0.837678918 0.910697628 0.787812647 0.726226168 1 18.43753392 3.23061493 24.58509574 0.834761429 0.720372038 0.214118086 0.113123272 252.32222 780719.6496 0.035466687 0.040945084 1700.649947 -3.23061493 -0.114389391 GQHPNPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GQHPNPLR 8 0 M0R1K3;Q15102;M0R389;M0QZT2 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ;;;;; 96.492 0.0089028 5234450000 2964650 3036620 2173310 2234630 2742120 3196430 2731390 3025400 2848320 FALSE TRUE 2572863.991 3016672.243 3224329.985 2742036.896 2687557.177 3319398.73 2466500.218 2378441.754 2511594.854 1.024394514 1.201098273 1.283777907 1.091751279 1.070059995 1.32162985 0.982045418 0.946984642 1 21.26017233 2.115730151 9.904954838 0.968261519 1.164636376 0.486145645 0.0916349 0.237650625 19.51718761 0.036502001 0.024600045 130.5359552 -2.115730151 0.196374858 GQICWYQKPGVGLDAINDANLLEACIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQICWYQKPGVGLDAINDANLLEACIYR 28 1 P14324-2;P14324;A0A087WVN4;A0A087X090 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 ; 325.56 5.94E-84 638270000 1039620 1064320 658080 702470 998810 910940 1164780 1215410 641010 FALSE TRUE 902231.5829 1057328.412 976329.6891 861976.5501 978935.6351 945984.4513 1051819.815 955504.0298 565230.528 1.596218778 1.870614483 1.727312381 1.524999991 1.731922794 1.6736259 1.86086873 1.69046784 1 19.10847986 1.240060956 6.632750206 0.981758544 1.716512694 0.820449027 0.104337349 0.044893948 9.806754064 0.149248596 0.025084261 17.38044759 -1.240060956 0.73475415 GQKPALDCSQVS(ph)PPRPATSPENNASLSDTSPMDSSPSGIPK ddPTM_MDA-MB-175_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(0.085)QVS(0.543)PPRPAT(0.085)S(0.085)PENNAS(0.085)LS(0.095)DT(0.018)S(0.003)PMDSSPSGIPK 64.273 0.0034229 151870000 51599 34008 23501 27362 29309 22843 41107 47373 42837 TRUE FALSE 44780.06141 33784.59921 34866.16221 33574.9603 28725.80824 23721.78499 37120.44947 37242.65261 37772.85866 1.185508934 0.894414678 0.923048015 0.88886469 0.760488066 0.628011377 0.982728096 0.985963306 1 15.20506235 4.741240834 5.116211861 0.88442917 1.19986884 0.412594829 0.113509237 0.193000285 16.59468972 0.030732836 0.215326083 55111.32261 -4.741240834 0.315439671 GQKPEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQKPEQR 7 1 Q92522 Q92522 H1FX Histone H1x 0 ; 80.18 0.027919 86311000 267710 239670 161952 188549 139253 207976 263110 292210 309370 FALSE TRUE 232331.4452 238095.592 240272.5289 231361.9322 136482.1377 215976.9713 237593.6327 229723.1655 272796.631 0.851665376 0.872795207 0.880775279 0.848111398 0.50030727 0.791714218 0.870955157 0.842104115 1 18.0574663 0.963343855 1.328130665 1.222078553 0.795277401 0.240398937 0.111036421 4.186312766 3.861237437 2.919208792 0.035001928 9.190599783 -0.963343855 -0.426801151 GQLCELSCSTDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GQLCELSCSTDYR 13 0 E9PKG1;Q99873-2;Q99873-3;Q99873;Q99873-5 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ;; 248.32 5.16E-17 1188340000 689250 615580 516070 465200 603660 673060 591820 637060 727170 FALSE TRUE 598163.8662 611536.2144 765643.1782 570830.7701 591648.347 698953.0537 534425.3875 500829.6766 641204.791 0.932874917 0.953729952 1.194069647 0.890247201 0.922713547 1.09006212 0.833470671 0.781076005 1 19.29042568 2.218159375 24.9829875 0.851088719 0.995993303 0.23698358 0.104239167 296.4899089 363073.4559 0.041986813 0.028344664 165.2568137 -2.218159375 0.144904584 GQLGHGDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GQLGHGDTK 9 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;;; 119.16 0.00087304 1009430000 2744740 1880310 1347116 1572280 1283882 1603970 2025430 2295680 2323650 FALSE TRUE 2382015.655 1867958.12 1998585.803 1929290.205 1258335.26 1665675.764 1829004.11 1804766.697 2048950.744 1.162553888 0.911665703 0.975419155 0.941599114 0.614136413 0.812940852 0.892654016 0.880824833 1 20.96645387 5.941220056 0.911218428 0.857025907 3.320328576 0.430881513 0.105277654 16.53770928 1.959522604 0.035840044 66.63317547 873413.8137 -5.941220056 2.463302668 GQMQKPFEDASFALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQMQKPFEDASFALR 15 1 K7EN45;Q13526 K7EN45 PIN1 Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 0 ; 163.7 1.39E-06 2256100000 1543050 1661990 1197380 1426170 1607800 1597290 1720270 1845610 1746530 FALSE TRUE 1339132.033 1651072.278 1776436.973 1750003.696 1575807.926 1658738.78 1553438.48 1450940.664 1540057.213 0.869533951 1.072085027 1.153487648 1.136323821 1.023213886 1.077063089 1.008688812 0.942134261 1 20.55455252 2.044292064 4.17767721 0.968437116 1.062408409 0.165557059 0.077864806 0.324819158 12.25840943 0.036553975 0.022172492 110.736824 -2.044292064 0.093971293 GQNHNVQGFHPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQNHNVQGFHPYR 13 0 K7EQ55;K7EK33;Q96EP5 K7EQ55 DAZAP1 DAZ-associated protein 1 0 ; 172.13 1.38E-05 324530000 357560 319500 260460 269620 298850 377960 331470 341470 396470 FALSE TRUE 310307.5401 317401.1835 386419.3272 330841.3419 292903.4697 392500.3658 299324.0904 268449.2978 349599.7683 0.887607968 0.907898724 1.105319174 0.946343138 0.837825125 1.122713461 0.856190758 0.767876075 1 18.4153447 2.052290105 24.99963093 0.850758397 0.966642341 0.136338494 0.105111143 145.2226147 69429.41043 0.041720871 0.0281282 112.7950665 -2.052290105 0.115883944 GQNQDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQNQDYR 7 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 131.27 0.008102 1841440000 3581600 3039700 2008140 2212990 1951740 3128950 2744700 3043950 2929380 FALSE TRUE 3108282.485 3019732.011 2979283.221 2715483.203 1912904.193 3249322.731 2478519.416 2393024.981 2583072.034 1.203327838 1.169046767 1.153387587 1.051261122 0.740553948 1.257929585 0.959523925 0.926425957 1 21.30065645 3.657216 3.755684064 0.977718567 1.176644182 0.338954615 0.125168632 0.262421605 7.026789087 0.034183695 0.053628788 4541.67444 -3.657216 0.198925614 GQPEGPLPSSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GQPEGPLPSSSPR 13 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;H3BQK4 P49815 TSC2 Tuberin 1 GQPEGPLPSS(0.009)S(0.991)PR;GQPEGPLPSS(0.001)S(0.999)PR;GQPEGPLPSS(0.108)S(0.892)PR 194.67 8.64E-07 931000000 1199780 1018480 852750 792320 1106520 1294410 1075560 1142200 1419480 TRUE FALSE 1041226.033 1011789.538 1265142.752 972228.3659 1084502.417 1344206.79 971252.3567 897949.4186 1251670.691 0.831868989 0.808351226 1.010763263 0.776744532 0.866443885 1.073930068 0.775964767 0.717400691 1 20.25542362 GQPGDIYHQTWAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQPGDIYHQTWAR 13 0 P04062-4;P04062-5;P04062-2;P04062;A0A0G2JNZ5;A0A0G2JNZ0;A0A0G2JLB3;P04062-3 P04062-4 GBA Glucosylceramidase 0 ; 177.38 1.55E-05 1062180000 1155830 1051160 600050 821380 1141410 1376130 976130 1154880 1196660 FALSE TRUE 1003084.137 1044254.861 890236.187 1007886.883 1118698.174 1429070.612 881465.0628 907917.8993 1055192.218 0.950617451 0.989634725 0.843672055 0.955168988 1.060184254 1.354322546 0.835359708 0.860428919 1 20.0090744 4.75714288 19.55464122 0.9785554 0.950617073 0.002872364 0.149683427 2613.220673 2749003.362 0.038624968 0.837728101 57166.66801 -4.75714288 -0.027938327 GQPIYIQFSNHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GQPIYIQFSNHK 12 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;K7ES59;K7EKJ7 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ;; 279.86 5.35E-28 9459400000 8042200 8222220 1959236 5251473 8774050 7662140 8536040 9855020 7769850 FALSE TRUE 6979402.894 8168207.695 2906729.083 6443900.208 8599463.571 7956907.484 7708216.155 7747600.665 6851307.184 1.018696536 1.19221157 0.424259051 0.940535877 1.25515662 1.161370709 1.125072332 1.130820799 1 22.70794784 3.402309548 7.249665835 1.133013238 0.872913397 0.268122606 0.199488005 0.299815779 24.31759571 0.057782304 0.0747708 2525.280054 -3.402309548 -0.260099841 GQPSNKEDVDDLVSQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GQPSNKEDVDDLVSQLR 17 1 P12270 P12270 TPR Nucleoprotein TPR 0 ;;; 199.76 1.19E-11 1030960000 1440080 1247130 783000 969980 1177340 1005520 1205820 1523020 1184320 FALSE TRUE 1249769.779 1238937.521 1161661.419 1190228.784 1153913.237 1044203.005 1088879.762 1197334.025 1044311.039 1.196740945 1.186368309 1.1123711 1.139726327 1.104951681 0.99989655 1.042677633 1.146530086 1 19.99412004 3.905227708 0.859943751 1.063328487 1.211054033 0.565541149 0.046061171 0.768048493 0.953139396 0.0207974 0.086984521 8039.475352 -3.905227708 0.147725546 GQPVAPYNTTQFLMDDHDQEEPDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQPVAPYNTTQFLMDDHDQEEPDLK 25 0 O94992 O94992 HEXIM1 Protein HEXIM1 0 ; 221.6 1.12E-33 399050000 107611 102626 66190 76054 88224 86555 104067 125345 109224 FALSE TRUE 93389.9337 101951.843 98199.70539 93323.22311 86468.51501 89884.82686 93974.59836 98540.94719 96311.66315 0.969663804 1.058561754 1.019603464 0.968971151 0.897799001 0.933270426 0.975734353 1.023146564 1 16.5554229 5.102440021 17.49439308 0.98531167 0.000172276 0.010235623 0.045842998 1034.157585 195142.5216 0.012099732 4237.844614 126601.8411 -5.102440021 -0.985139394 GQQQET(ph)ET(ph)FY(ph)LT(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GQQQETETFYLTK 13 0 P98171-2;P98171;E7EQN5;E9PCM6;A0A0B4J1X7;H7C120 P98171-2 ARHGAP4 Rho GTPase-activating protein 4 4 GQQQET(1)ET(1)FY(1)LT(1)K 45.598 0.064452 1080500000 0 0 0 0 0 0 0 0 0 TRUE FALSE 0 0 0 0 0 0 0 0 0 0 GQRDS(ph)SYYWEIEASEVMLSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQRDSSYYWEIEASEVMLSTR 21 1 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 GQRDS(0.826)S(0.174)YYWEIEASEVMLSTR;GQRDS(0.842)S(0.158)YYWEIEASEVMLSTR 184.25 2.44E-17 68028000 25392.2 30356 23313 32709 34775 48691 37364 39496 31147 TRUE FALSE 22036.55643 30156.58944 34587.24478 40136.07838 34083.04554 50564.17428 33740.44503 31050.08776 27464.83714 0.802355256 1.098007218 1.259328231 1.461362329 1.24097024 1.841051306 1.22849609 1.130539664 1 14.74529812 4.593044678 1.945687118 1.312901013 0.731756259 0.354626635 0.222596228 0.682272734 3.473793908 0.062428159 0.640488768 39178.21794 -4.593044678 -0.581144754 GQRPETLHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GQRPETLHER 10 1 Q5BJF2;Q86XC5;J3KTD1 Q5BJF2 TMEM97 Transmembrane protein 97 0 ;;; 95.498 0.0044348 312579000 332490 358232 345685 366405 398390 459851 247836 427654 468611 FALSE TRUE 288550.6041 355878.7504 512859.4222 449602.8554 390462.8184 477541.7655 223800.9029 336203.5201 413212.3414 0.698310711 0.861249084 1.241152238 1.088067345 0.944944716 1.155681275 0.541612339 0.813633782 1 18.65652382 2.253053699 24.99875618 0.780885666 1.004710402 0.226081038 0.185596533 336.0240535 579598.9837 0.070792604 0.054583859 179.082727 -2.253053699 0.223824736 GQS(ph)PLAPLLETLEDPSASHGGQTDAYLTLTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GQSPLAPLLETLEDPSASHGGQTDAYLTLTSR 32 0 Q5UIP0-2;Q5UIP0 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 GQS(1)PLAPLLETLEDPSASHGGQTDAYLTLTSR;GQS(1)PLAPLLETLEDPSASHGGQTDAYLTLTSR;GQS(0.999)PLAPLLET(0.001)LEDPSASHGGQTDAYLTLTSR;GQS(0.844)PLAPLLET(0.155)LEDPSASHGGQTDAYLTLTSR 121.01 1.14E-07 252272000 60942.2 51304.8 27231.3 35252.2 52424.5 41223.1 45485.7 57967.6 47403.8 TRUE FALSE 52888.53386 50967.77539 40400.44776 43256.75081 51381.35502 42808.97933 41074.50381 45571.67984 41799.77677 1.265282687 1.219331282 0.966523051 1.034856024 1.229225584 1.024143731 0.98264888 1.090237398 1 15.35120762 4.354989127 6.190087286 1.052911448 1.252989569 0.548794814 0.073950906 0.150965234 7.4143352 0.018558531 0.050346404 22645.87611 -4.354989127 0.200078121 GQS(ph)TDSLPQTICR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GQSTDSLPQTICR 13 0 Q96NE9-3;Q96NE9-2;Q96NE9 Q96NE9-3 FRMD6 FERM domain-containing protein 6 1 GQS(0.937)T(0.057)DS(0.006)LPQTICR 85.469 0.009725 87618000 145880 144880 103730 124760 167720 165750 187070 220230 195050 TRUE FALSE 126601.5884 143928.2737 153894.175 153088.6648 164382.7001 172126.5098 168927.9802 173135.5283 171991.4112 0.736092503 0.836834076 0.894778256 0.890094824 0.955761099 1.000785496 0.982188465 1.006652176 1 17.391977 6.206945246 0.357810063 1.021762726 5.89E-20 0.964062706 0.016452639 3.932054901 0.192163496 0.023419126 2.109934561 1610442.585 -6.206945246 -1.021762726 GQSLGSLYTHLQGCTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GQSLGSLYTHLQGCTR 16 0 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 84.41 0.0060853 0 107730 82292 69551 59735 68594 93439 86497 91683 83673 FALSE TRUE 93493.20755 81751.41843 103186.0962 73298.74474 67229.1136 97033.65879 78108.53425 72077.30393 73781.27326 1.267167174 1.108023958 1.398540465 0.993460014 0.911194814 1.315152945 1.058649855 0.976905124 1 16.17096707 7.999999763 0.094583839 0.729680773 2.228625246 0.236529728 0.141322206 499.1017954 4.39081255 11.71049295 99.77426461 99999945.44 -7.999999763 1.498944473 GQSQLS(ph)NPTDDSWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQSQLSNPTDDSWK 14 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 GQSQLS(0.998)NPT(0.002)DDSWK;GQSQLS(1)NPTDDSWK 246.03 1.12E-17 359740000 1525910 1207560 925380 985630 1198700 1053050 1415270 1625220 1465630 TRUE FALSE 1324257.127 1199627.459 1372896.863 1209432.356 1174848.215 1093561.515 1278017.333 1277679.35 1292364.891 1.024677424 0.928242068 1.062313649 0.935828855 0.909068502 0.846170863 0.988898214 0.988636692 1 20.30158203 6.046422925 2.578752396 0.958917931 33.83321733 0.110546675 0.058675864 2881.201604 41.76989821 0.015572791 558036.8008 1112814.882 -6.046422925 32.8742994 GQSQTS(ph)PDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GQSQTSPDHR 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GQS(0.001)QT(0.108)S(0.892)PDHR;GQS(0.015)QT(0.006)S(0.978)PDHR;GQSQT(0.017)S(0.983)PDHR;GQSQT(0.005)S(0.995)PDHR 125.03 0.00044036 608999000 646791 530497 370295 393999 322853 533526 463091 554405 655609 TRUE FALSE 561315.9306 527012.1303 549370.9006 483462.4948 316428.857 554051.0905 418180.5061 435849.8051 578103.6509 0.970960709 0.911622214 0.950298272 0.836290333 0.547356614 0.958394035 0.723365966 0.753930207 1 19.14096866 3.628357071 4.749027516 0.786237484 0.940279477 0.221115185 0.124735667 0.31449378 11.08252627 0.033361702 0.050392615 4249.688236 -3.628357071 0.154041993 GQSQTS(ph)PDHRS(ph)DT(ph)SSPEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GQSQTSPDHRSDTSSPEVR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 GQS(0.318)QT(0.318)S(0.365)PDHRS(0.934)DT(0.505)S(0.15)S(0.41)PEVR 74.287 0.020111 458290000 171450 169920 93755 128750 157910 161560 141060 145810 133110 TRUE FALSE 148792.4481 168803.7843 139095.2316 157984.6553 154767.8999 167775.3177 127380.0229 114629.6662 117373.8874 1.267679305 1.438171539 1.185061129 1.345994912 1.318588856 1.429409227 1.085250099 0.976619832 1 16.84075196 2.094518497 4.914705516 0.998451964 1.328303359 0.803614852 0.073241197 0.078713208 3.195302272 0.029673622 0.019423739 124.3135581 -2.094518497 0.329851396 GQSQTS(ph)PDHRS(ph)DTS(ph)SPEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQSQTSPDHRSDTSSPEVR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 GQS(0.321)QT(0.321)S(0.357)PDHRS(0.539)DT(0.437)S(0.595)S(0.429)PEVR;GQS(0.116)QT(0.413)S(0.473)PDHRS(0.774)DT(0.379)S(0.672)S(0.173)PEVR 67.532 0.043115 745830000 342870 284700 160362 208957 269480 316400 264800 275470 225400 TRUE FALSE 297558.8608 282829.787 237913.5996 256403.8806 264117.8752 328572.1127 239119.7368 216562.8842 198753.4688 1.497125371 1.423018117 1.197028666 1.290059903 1.328871777 1.653164167 1.203097175 1.089605558 1 17.60062051 2.006842673 24.98820465 1.079747591 1.385960184 0.581465874 0.124604657 123.5154648 451054.0046 0.053161157 0.035748874 101.5880615 -2.006842673 0.306212593 GQSS(ph)PPPAPPICLR ddPTM_MDA-MB-175_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(0.01)S(0.99)PPPAPPICLR;GQS(0.002)S(0.998)PPPAPPICLR;GQS(0.002)S(0.998)PPPAPPICLR;GQS(0.019)S(0.981)PPPAPPICLR 200.63 1.99E-08 918350000 1034740 1085910 858530 965630 1086860 1282280 1038230 1138840 1658850 TRUE FALSE 897996.4873 1078776.586 1273717.98 1184891.05 1065233.612 1331610.141 937542.6144 895307.9285 1462742.643 0.613912838 0.737502657 0.870773807 0.81004752 0.728244041 0.910351625 0.64094844 0.612074812 1 20.48024453 4.686963194 3.911533156 0.774924033 0.606030998 0.174644191 0.118495711 0.430450914 12.22709702 0.029967193 0.184029182 48636.59853 -4.686963194 -0.168893035 GQSSLFPMEDGFLDDGRGDQPLHSGLGS(ph)PHCFSHQNGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GQSSLFPMEDGFLDDGRGDQPLHSGLGSPHCFSHQNGER 39 1 E5RJM0;B7ZLQ8;Q17RY0-2;Q17RY0;Q17RY0-3 E5RJM0 CPEB4 Cytoplasmic polyadenylation element-binding protein 4 1 GQSSLFPMEDGFLDDGRGDQPLHS(0.072)GLGS(0.825)PHCFS(0.103)HQNGER 43.469 0.04144 187500000 29102 29832 17864 20140 29719 31468 30289 30012 24768 TRUE FALSE 25256.09696 29636.03163 26503.09015 24713.09482 29127.65004 32678.59432 27351.57744 23594.16735 21839.95526 1.156417065 1.356963935 1.21351394 1.131554279 1.333686342 1.496275699 1.25236417 1.080321231 1 14.41468228 1.67217056 3.310930936 1.018151954 1.284146869 0.479122553 0.104500961 0.173718907 4.398010264 0.085620543 0.029159262 47.00786861 -1.67217056 0.265994914 GQSSWGTGESFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQSSWGTGESFR 12 0 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 259.35 6.64E-21 871270000 304000 268190 185371 236480 281640 318840 267540 318540 320660 FALSE TRUE 263825.6298 266428.2422 275017.0356 290176.3984 276035.915 331105.9811 241594.012 250422.6999 282751.9401 0.933063906 0.942268485 0.972644204 1.026257851 0.976247643 1.171012234 0.854438035 0.885662181 1 18.1091774 GQTEHDEGMLEYLEDIIGCGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQTEHDEGMLEYLEDIIGCGR 21 0 Q9NTJ3;E9PD53;Q9NTJ3-2;C9JR83;C9J578 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 0 ; 195.03 1.56E-18 119057000 127232 136958 100271 105992 125132 139000 119486 144880 136585 FALSE TRUE 110417.9688 136058.3139 148762.391 130059.1036 122642.118 144347.4199 107898.2661 113898.5395 120438.0769 0.916802822 1.129695171 1.235177403 1.079883596 1.018300202 1.198519801 0.895881675 0.945702077 1 16.87793205 2.227016475 24.9978453 0.944745592 1.099917886 0.372204581 0.091250451 222.763823 482371.5217 0.036639502 0.024938027 168.6617004 -2.227016475 0.155172295 GQVCLPVISAENWKPATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GQVCLPVISAENWKPATK 18 1 P68036-2;P68036;P68036-3;A0A1B0GUS4 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 156.15 1.25E-08 191850000 361890 323970 207530 278860 268550 216640 329310 435740 423920 FALSE TRUE 314065.3196 321841.8197 307892.2021 342179.4251 263206.3804 224974.281 297373.5669 342560.3919 373804.6605 0.840185671 0.860989318 0.823671384 0.915396359 0.70412814 0.601849856 0.795531994 0.916415519 1 18.51192503 1.588368224 3.131356986 0.987352628 0.78968705 0.405561219 0.086709452 0.23254555 5.110727067 0.089565898 0.025416446 38.75861272 -1.588368224 -0.197665578 GQVLFDLVCEHLNLLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GQVLFDLVCEHLNLLEK 17 0 Q9H4G0-2;A0A1B0GTW6;A0A0C4DH22;Q9H4G0;Q9H4G0-4;Q4VXN0;Q4VXN1;Q4VXN5;Q4VXN6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 0 148.56 3.58E-07 228850000 386670 364710 358190 401380 296810 312510 401220 465040 401960 FALSE TRUE 335570.5798 362314.196 531411.8821 492519.4637 290904.0617 324532.4619 362309.7462 365594.8149 354440.7467 0.946760729 1.022213725 1.499296813 1.389567843 0.820741025 0.915618379 1.02220117 1.031469486 1 18.43518494 3.235878759 25 0.969884211 1.221073413 0.364556943 0.167735464 86.47772246 806136.638 0.053968045 0.063992686 1721.387951 -3.235878759 0.251189202 GQVLNSDELQELYEGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GQVLNSDELQELYEGLR 17 0 O00764;F2Z2Y4;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;;;;; 308.84 1.08E-57 1034772000 690730 701995 529447 534493 635643 699211 616581 707561 689363 FALSE TRUE 599448.2804 697383.5486 785489.3401 655857.8049 622994.9479 726110.0996 556785.0695 556254.5864 607867.2915 0.986149919 1.147262829 1.292205307 1.078948998 1.024886446 1.194520761 0.915964845 0.91509215 1 19.21339687 2.228928202 24.98878216 0.936573602 1.123419381 0.473079129 0.087908398 166.2338918 431246.2803 0.03603321 0.024645048 169.4057715 -2.228928202 0.18684578 GQVQEVGWHDVAGWLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQVQEVGWHDVAGWLGR 17 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ; 204.78 8.48E-12 3629300000 2996300 2847150 2225870 2096880 2690420 2898600 2702350 3375600 2878240 FALSE TRUE 2600331.363 2828446.884 3302308.177 2573008.653 2636885.906 3010111.018 2440276.513 2653754.209 2537977.746 1.024568229 1.114449048 1.301157263 1.013802685 1.038971248 1.186027349 0.961504299 1.045617604 1 21.27524799 2.251573105 0.91844958 0.996886647 1.121501545 0.169689793 0.09211467 1.272884493 2.036846347 0.120115487 0.04210683 178.473239 -2.251573105 0.124614898 GQYFGELALVTNKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQYFGELALVTNKPR 15 1 P13861-2;P13861;H7C330;P31323 P13861-2;P31323 PRKAR2A;PRKAR2B cAMP-dependent protein kinase type II-alpha regulatory subunit;cAMP-dependent protein kinase type II-beta regulatory subunit 0 ; 152.94 2.50E-06 1767470000 917580 807240 549270 759760 900740 795700 824230 954190 956630 FALSE TRUE 796319.4781 801937.1873 814898.8092 932275.1202 882817.0363 826311.0939 744296.3015 750143.894 843538.2912 0.944022917 0.950682614 0.966048391 1.10519597 1.04656427 0.979577457 0.882350344 0.889282564 1 19.68609403 0.94077926 22.4376805 1.698551156 0.967234533 0.01718157 0.066311471 146.9518862 886990.1696 79186.55176 0.018106231 8.72527773 -0.94077926 -0.731316623 GQYHTLQAGFSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GQYHTLQAGFSSR 13 0 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 0 139.3 3.91E-05 632250000 232510 242340 132010 149300 223650 255080 223100 277270 211950 FALSE TRUE 201783.2144 240748.0526 195850.4775 183200.8469 219199.8026 264893.0927 201463.7963 217977.9682 186893.5125 1.079669442 1.288156284 1.0479255 0.980241874 1.172859345 1.417347714 1.077960351 1.166321748 1 17.51185696 1.235989474 24.39564829 0.999999717 1.15513753 0.130012934 0.124998659 116.1793698 1102017.984 0.202681305 0.030631899 17.21826842 -1.235989474 0.155137813 ERQEQEEARR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ERQEQEEARR 10 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ; 77.593 0.018298 210886000 169846 152521 77510 101283 150643 163970 158979 171066 48596.9 FALSE TRUE 147400.4208 151519.0795 114994.0953 124280.8532 147645.499 170278.032 143561.241 134484.8671 42851.82984 3.43976958 3.535883533 2.683528234 2.900246118 3.445488782 3.973646694 3.350177614 3.138369298 1 15.38706919 1.231809618 4.151422886 0.745283335 3.321761649 0.814208354 0.347650018 0.107595921 3.399984927 0.845195783 0.095097986 17.05334655 -1.231809618 2.576478314 GQYISPFHDIPIYADKDVFHMVVEVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQYISPFHDIPIYADKDVFHMVVEVPR 27 1 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 266.36 1.26E-53 11283000000 4455400 5498500 1476820 3224200 5267600 4911900 5542500 6302100 4116700 FALSE TRUE 3866607.601 5462379.991 2191015.092 3956303.889 5162785.066 5100863.971 5004989.203 4954444.958 3630028.416 1.065172819 1.504776097 0.6035807 1.089882347 1.422243706 1.405185687 1.378774111 1.364850186 1 21.79154941 3.29847485 7.754140352 1.32967609 1.062447121 0.203247199 0.24343629 0.378430482 42.25337872 0.06926993 0.089223215 1988.267667 -3.29847485 -0.267228969 GQYTHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 273720000 305240 282620 193090 239350 151360 223770 319670 356580 379920 FALSE TRUE 264901.7606 280763.4506 286468.9698 293698.0757 148348.2321 232378.5767 288668.4526 280328.1419 335006.2904 0.790736676 0.838084116 0.855115196 0.876694212 0.442822229 0.693654368 0.861680693 0.836784711 1 18.35382866 1.303511993 1.476087555 1.071040558 0.757319644 0.26517705 0.126016152 1.59834829 3.483336431 0.730445124 0.039466674 20.11462742 -1.303511993 -0.313720914 GRAEGEWEDQEALDYFS(ph)DKESGK ddPTM_MDA-MB-175_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(1)DKESGK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(0.996)DKES(0.004)GK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(0.996)DKES(0.004)GK;GRAEGEWEDQEALDYFS(1)DKESGK 268.99 7.01E-45 3668977000 3705430 2269679 2022020 1850700 2267056 1866178 3193201 3629370 2312062 TRUE FALSE 3215748.037 2254769.329 2999875.635 2270929.721 2221946.021 1937971.075 2883524.859 2853257.469 2038732.664 1.57732698 1.105966157 1.471441395 1.113892842 1.089866298 0.95057636 1.414371246 1.399525067 1 20.95924118 4.749660034 24.33093767 1.215095768 1.577327289 0.302548842 0.180588056 1613.960169 3537849.423 0.045210694 0.648655994 56190.12964 -4.749660034 0.362231521 GRAEGSEKEESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRAEGSEKEESR 12 2 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 73.466 0.022004 55729000 80695 71257 33913 29361 57481 59825 66013 81980 20163 FALSE TRUE 70030.95129 70788.90808 50313.44023 36027.8638 56337.24056 62126.50646 59611.06942 64449.21497 17779.35311 3.938891976 3.981523267 2.829880251 2.026387776 3.168688996 3.49430635 3.352825553 3.624947127 1 14.11791521 4.240251676 24.97117956 2.902574848 3.960208045 0.270221299 0.784516736 61.33140189 905581.0511 0.198341945 0.471688761 17388.08184 -4.240251676 1.057633197 GRAS(ph)PGGVSTSSSDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GRASPGGVSTSSSDGK 16 1 P54259 P54259 ATN1 Atrophin-1 1 GRAS(1)PGGVSTSSSDGK;GRAS(1)PGGVSTSSSDGK;GRAS(1)PGGVSTSSSDGK;GRAS(1)PGGVSTSSSDGK 152.51 3.27E-07 1578850000 1988330 1636940 1316230 1519880 1646120 1472180 1932830 2177180 2183780 TRUE FALSE 1725567.153 1626186.833 1952763.231 1864991.984 1613365.433 1528815.717 1745384.444 1711607 1925616.016 0.896111758 0.844502133 1.014097938 0.968517071 0.837843796 0.793935917 0.906403161 0.88886205 1 20.87688862 1.236910057 24.63763984 1.000000152 0.893831749 0.218931987 0.06304939 61.8312592 922589.7526 0.100423282 0.016208969 17.25480506 -1.236910057 -0.106168403 GRAS(ph)PGGVSTSSSDGKAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRASPGGVSTSSSDGKAEK 19 2 P54259 P54259 ATN1 Atrophin-1 1 GRAS(1)PGGVSTSSSDGKAEK 97.542 0.00057382 88776000 163080 132990 56775 58095 105560 83485 161300 179980 21219 TRUE FALSE 141528.5648 132116.3799 84231.5799 71286.35768 103459.5625 86696.72197 145657.1508 141492.6776 18710.51399 7.564119557 7.061076996 4.501831427 3.809962554 5.529487996 4.633583129 7.784775495 7.562201533 1 14.19156157 4.352653329 5.969247126 5.326392282 7.428999915 0.188074189 1.923787637 0.384143373 18.18097149 0.497369779 1.354439199 22524.40508 -4.352653329 2.102607633 MYS(ph)FDDVLEEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 MYSFDDVLEEGK 12 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;E9PJ10;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 MYS(1)FDDVLEEGK;MYS(1)FDDVLEEGK;MYS(1)FDDVLEEGK;MYS(1)FDDVLEEGK;MYS(1)FDDVLEEGK;MYS(1)FDDVLEEGK;MY(0.001)S(0.999)FDDVLEEGK;MYS(1)FDDVLEEGK;MY(0.001)S(0.999)FDDVLEEGK;MYS(1)FDDVLEEGK;MYS(1)FDDVLEEGK 234.82 5.20E-16 1001656000 2230665 2477635 2556539 3201020 3483273 2471544 3689418 4377071 10030300 TRUE FALSE 1935876.968 2461359.253 3792889.812 3927860.516 3413962.682 2566625.897 3331618.81 3441068.429 8844529.361 0.21887846 0.278291716 0.428840208 0.444100568 0.3859971 0.290193609 0.376686952 0.38906179 1 23.07635394 1.231941311 4.545208545 1.057582459 0.352488554 0.896378478 0.069399361 0.066208407 2.905701578 0.152199956 0.018529493 17.05851851 -1.231941311 -0.705093905 GRAS(ph)SHSSQTQGGGSVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.613)S(0.048)HS(0.287)S(0.048)QT(0.003)QGGGSVTK;GRAS(0.887)S(0.086)HS(0.027)S(0.001)QTQGGGSVTK;GRAS(0.344)S(0.344)HS(0.176)S(0.134)QT(0.002)QGGGSVTK 215.39 5.77E-19 491638000 385966 380456 68148.3 116006.4 259292.7 245128.6 233883 264609.7 228000.2 TRUE FALSE 334959.6152 377956.7595 101105.0458 142347.4262 254133.2826 254558.8559 211201.0627 208024.9748 201046.2761 1.666082166 1.879949069 0.502894397 0.70803314 1.264053667 1.26617046 1.050509697 1.034711903 1 17.61716809 4.257480831 24.99994338 0.995711448 1.773016205 0.664601529 0.235276598 154.7003724 204407.5175 0.062070605 0.163630326 18091.76053 -4.257480831 0.777304757 GRASS(ph)HS(ph)SQTQGGGSVTKKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRASSHSSQTQGGGSVTKKR 20 3 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(0.414)S(0.586)HS(0.527)S(0.469)QT(0.003)QGGGSVTKKR 78.202 0.013043 47085000 0 1544.4 963.73 937.58 0 0 1188.5 3.4356 1037.6 TRUE FALSE 0 1534.254735 1429.793051 1150.471869 0 0 1073.239453 2.700923676 914.93611 0 1.67689822 1.562724474 1.257434105 0 0 1.173021199 0.002952035 1 9.837527193 3.255470646 24.99777843 0.41474158 1.195056919 0.242290387 0.599120666 306.8079635 453545.7667 0.165756247 0.213423188 1800.821412 -3.255470646 0.780315339 GRASSHS(ph)SQTQGGGSVTK ddPTM_MDA-MB-175_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(0.25)S(0.25)HS(0.492)S(0.008)QTQGGGSVTK 216.15 5.52E-19 165220000 144900 146340 27381 42401 92746 101210 86658 101690 89543 TRUE FALSE 125751.0979 145378.6829 40622.54318 52028.79511 90900.53605 105103.6142 78253.9205 79944.38485 78957.32855 1.592646309 1.841231024 0.514487305 0.658948271 1.151261545 1.331144507 0.991091289 1.012501136 1 16.26878556 4.255049004 24.99999858 0.969198056 1.716939113 0.644644024 0.236025037 161.3964182 244707.9519 0.062607227 0.164611409 17990.73906 -4.255049004 0.747741057 GRASSHSS(ph)QTQGGGSVTK ddPTM_MDA-MB-175_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(0.194)S(0.257)HS(0.194)S(0.342)QT(0.013)QGGGSVTK 99.366 0.00063561 171160000 120680 103430 17348 35270 71375 76450 73610 86229 68114 TRUE FALSE 104731.8322 102750.5615 25737.55083 43278.59257 69954.77714 79391.08097 66471.31353 67789.59938 60061.64052 1.743739121 1.710751832 0.428518945 0.720569605 1.16471639 1.321826715 1.106718247 1.128667129 1 15.87415626 4.335302805 11.14792151 1.010970786 1.733489941 0.602311518 0.251057666 0.295844579 31.97121885 0.067202987 0.177972648 21642.26969 -4.335302805 0.722519155 GRDDCGTFEDTGPLLQFDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRDDCGTFEDTGPLLQFDYK 20 1 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 0 152.81 5.48E-08 86479000 77114 76063 50933 59072 65170 62439 65860 81363 74174 FALSE TRUE 66923.18952 75563.33714 75564.36916 72485.20046 63873.2445 64841.06873 59472.90734 63964.15562 65405.23422 1.023208468 1.155310245 1.155326023 1.108247701 0.976576955 0.991374307 0.909298897 0.977966922 1 15.99711848 3.23878297 4.863690316 0.967245307 1.118384204 0.718155614 0.043353284 0.092077125 5.777857489 0.012830112 0.015671182 1732.937781 -3.23878297 0.151138897 GRDEVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GRDEVSK 7 1 Q9UKY7;H0Y8K3;D6R9V8 Q9UKY7 CDV3 Protein CDV3 homolog 0 ; 82.426 0.022365 165871000 552620 506880 437550 468950 244640 466420 396730 519850 549030 FALSE TRUE 479589.8668 503550.2719 649150.6435 575432.265 239772.1426 484363.4792 358255.1857 408684.123 484124.2989 0.990633744 1.040126003 1.34087598 1.188604386 0.495269796 1.000494047 0.740006619 0.844171887 1 18.88501798 3.286880241 24.9999995 0.823036904 1.147266479 0.479556443 0.167592697 98.57300236 50999.76709 0.046638408 0.060209796 1935.888058 -3.286880241 0.324229575 GRDIVVLGVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRDIVVLGVEK 11 1 O14818;O14818-4 O14818 PSMA7 Proteasome subunit alpha type-7 0 76.357 0.032443 127430000 242180 304940 118780 167100 222510 186000 301120 272860 240780 FALSE TRUE 210175.2994 302936.8291 176222.4053 205042.609 218082.4863 193155.5404 271917.4287 214511.0124 212315.2627 0.989920822 1.426825492 0.830003472 0.965745968 1.027163491 0.909758149 1.28072483 1.010341931 1 17.69584856 4.232493196 24.9999982 1.015029425 1.20837315 0.231208644 0.154264442 192.8489554 794620.7319 0.037442179 0.081277051 17080.20962 -4.232493196 0.193343725 GRDPSSDTYEEDSELLLQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GRDPSSDTYEEDSELLLQIR 20 1 Q9UBE0;M0QZS6 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 ;;; 230.67 1.38E-25 371954000 394806 320197 217101 265164 314663 363607 300060 358087 290768 FALSE TRUE 342631.3868 318093.6048 322091.7698 325373.539 308401.8219 377595.1966 270960.2274 281512.8817 256393.7383 1.336348497 1.240644982 1.25623883 1.269038554 1.202844594 1.47271614 1.056812967 1.097970971 1 17.9680015 2.199677927 24.9883246 1.061473443 1.286466464 0.693202516 0.076463231 88.81179185 57075.13366 0.029500133 0.019889362 158.3718271 -2.199677927 0.224993021 GRDQVDQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GRDQVDQLR 9 1 Q9P2M7 Q9P2M7 CGN Cingulin 0 ; 155.15 6.75E-05 354320000 225640 223090 153732 163597 191971 235770 224410 223640 144691 FALSE TRUE 195821.1023 221624.5071 228077.3094 200744.1993 188151.1527 244840.2245 202646.7527 175816.3264 127585.7948 1.534819002 1.737062558 1.787638739 1.573405563 1.474702987 1.919024174 1.588317516 1.378024306 1 16.96110819 1.386868005 1.877735775 0.893969853 1.669959657 0.733992433 0.129503592 0.308652397 1.405645019 0.392475829 0.035883987 24.37070005 -1.386868005 0.775989804 GRDS(ph)PYQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 GRDSPYQSR 9 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR 145.81 5.83E-05 72374490000 1244204 1202976 1008286 1037190 1030776 1348972 1183972 1151177 1571547 TRUE FALSE 1079779.289 1195073.571 1495896.482 1272699.842 1010265.574 1400867.826 1069150.578 905006.757 1385760.504 0.779196178 0.862395463 1.079476921 0.918412553 0.729033315 1.010901827 0.77152623 0.653075877 1 20.40224651 2.185440388 24.99386477 0.774354478 0.89670771 0.072580398 0.131508086 177.8826398 83694.90557 0.05323698 0.035892397 153.2640819 -2.185440388 0.122353232 GRDSPYQS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRDSPYQSR 9 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 GRDS(0.003)PYQS(0.997)R 137.78 0.000408 14434000000 3003000 2665700 2145400 2164400 2463500 2844900 2666500 2703600 3665700 TRUE FALSE 2606145.941 2648188.841 3182922.616 2655860.101 2414481.17 2954345.144 2407903.24 2125456.179 3232345.122 0.80627094 0.819277874 0.984710016 0.821651154 0.746975053 0.913994339 0.74494002 0.657558552 1 21.62414981 3.486533724 24.57653711 0.792469577 0.871367959 0.040854308 0.105495845 851.9098737 2224389.39 0.029996405 0.041056173 3065.728729 -3.486533724 0.078898382 GRDSPYQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GRDSPYQSR 9 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 ; 99.568 0.0048868 0 260060 219300 168015 211620 204102 238950 206931 236330 257780 FALSE TRUE 225692.4121 217859.4039 249267.616 259671.5554 200040.7695 248142.5611 186862.8635 185792.6686 227305.5421 0.992903253 0.958442992 1.096619175 1.1423899 0.880052319 1.091669648 0.822077903 0.817369726 1 17.79427333 2.233411051 24.99999451 0.864400495 1.025624378 0.371125159 0.089568111 121.6444989 590548.7488 0.035365847 0.02465988 171.1634577 -2.233411051 0.161223883 GRDVIAQSQSGTGK ddPTM_MDA-MB-175_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 ; 184.51 1.17E-06 358520000 379810 311920 211287 210180 327750 296720 333830 396780 162092 FALSE TRUE 329617.1462 309870.977 313466.0999 257904.5814 321228.4162 308135.0104 301455.218 311931.6847 142929.6684 2.30614924 2.167996193 2.193149284 1.804416006 2.247457927 2.155850593 2.109115772 2.182413828 1 17.12494589 1.237292843 24.99970656 0.999998627 2.140806655 0.880531115 0.132628235 10.05826854 198261.6512 0.189441873 0.031385838 17.27002008 -1.237292843 1.140808028 GRDWNVDLIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GRDWNVDLIPK 11 1 P50395;P50395-2;Q5SX87;V9GYF8;Q5SX90;V9GYJ7;Q5SX86;G5E9U5;P31150 P50395;Q5SX86;G5E9U5;P31150 GDI2;GDI1 Rab GDP dissociation inhibitor beta;Rab GDP dissociation inhibitor alpha 0 ; 142.97 3.41E-05 499470000 2091000 1771390 1106040 1322030 1747150 1510180 2013600 2379800 1008900 FALSE TRUE 1814669.052 1759753.622 1640924.643 1622217.117 1712385.133 1568277.602 1818321.382 1870898.29 889628.9913 2.039804311 1.978075849 1.844504461 1.823476003 1.924830632 1.762844531 2.043909764 2.103009578 1 19.76284428 1.232523497 24.99999188 0.999998467 1.94110864 0.883975367 0.107030888 70.26538893 290942.8495 0.256999374 0.028837059 17.08140134 -1.232523497 0.941110173 GRECS(ph)PTSSLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.606)PT(0.131)S(0.131)S(0.131)LER 117.08 0.0020314 258700000 456220 514650 287830 254770 434360 457220 404050 443590 252330 TRUE FALSE 395929.3711 511269.2303 427025.5507 312619.4224 425717.0858 474809.5493 364865.2932 348731.7305 222499.8349 1.779459168 2.297840943 1.919217383 1.405032155 1.913336637 2.133977086 1.639845231 1.567334784 1 17.76344474 0.996532492 1.128011018 0.107532217 1.901479649 0.582793431 0.238762765 2.023626299 1.470711263 4.958269736 0.0781601 9.920475561 -0.996532492 1.793947433 GREDVSNFDDEFTSEAPILT(ph)PPREPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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;GREDVSNFDDEFT(0.006)S(0.006)EAPILT(0.989)PPREPR;GREDVSNFDDEFT(0.012)S(0.003)EAPILT(0.985)PPREPR 184.82 2.45E-17 4755390000 704278 683910 521841 514777 686334 749262 625825 694473 612118 TRUE FALSE 611205.8779 679417.3502 774205.0531 631664.9857 672677.2962 778086.594 565132.5878 545965.3533 539754.1074 1.132378373 1.25875346 1.43436621 1.17028287 1.246266192 1.441557523 1.047018596 1.011507547 1 19.04194279 2.117453235 7.532964113 1.013691863 1.279561515 0.615405489 0.097593786 0.144594573 8.923043177 0.03939556 0.026494097 131.0548916 -2.117453235 0.265869653 GREETVAEDVCIDLTCDSGSQAVPS(ph)PATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GREETVAEDVCIDLTCDSGSQAVPSPATR 29 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 GREETVAEDVCIDLTCDSGSQAVPS(0.873)PAT(0.127)R;GREETVAEDVCIDLTCDSGSQAVPS(0.996)PAT(0.004)R 182.53 5.78E-18 399690000 342410 365180 245410 187848 286790 336640 294380 345500 278720 TRUE FALSE 297159.6509 362781.1085 364091.0968 230501.7595 281083.4401 349590.7586 265831.0729 271617.5137 245770.0391 1.209096324 1.476099812 1.48142995 0.937875749 1.143684727 1.422430333 1.081625221 1.105169347 1 17.90694953 -1.288774641 0.141544366 8.00E-17 1.527301568 0.258778051 0.167216924 187.3321147 2.799553244 56.04825191 3.771254621 0.051431046 1.288774641 1.527301568 GREEYEGPNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GREEYEGPNK 10 1 P23246 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 164.65 5.56E-06 162460000 287370 218100 206310 211880 202800 207490 258480 315680 453700 FALSE TRUE 249393.3264 216667.2867 306082.2061 259990.5924 198764.6768 215472.2746 233412.6494 248174.2886 400064.1029 0.623383414 0.541581425 0.765082905 0.649872334 0.496832071 0.538594373 0.583438123 0.620336308 1 18.60987166 1.237287786 5.207040462 1.02329893 0.599938443 0.7443306 0.073328733 0.08715212 6.526830479 0.133445008 0.019088243 17.26981901 -1.237287786 -0.423360487 GREEYEGPNKKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GREEYEGPNKKPR 13 3 P23246 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 110.38 0.00046572 710340000 512140 353510 303170 321040 252320 227620 363360 421150 246872 FALSE TRUE 444459.4014 351187.7695 449784.026 393937.0388 247299.3257 236376.6887 328121.4031 331090.3499 217687.0734 2.041735389 1.613268827 2.066195383 1.809648284 1.136031285 1.085855421 1.507307706 1.520946305 1 17.73189621 3.306648579 6.39862346 1.295714136 1.883810637 0.69501716 0.207327711 0.132331428 9.587139693 0.061990641 0.079812434 2026.042631 -3.306648579 0.588096501 GREFGVTTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GREFGVTTGR 10 1 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ; 165.63 5.28E-06 817720000 743060 722300 320170 326770 674350 833780 758320 758390 167442 FALSE TRUE 644862.7383 717555.1637 475005.2829 400968.1229 660931.7543 865856.0561 684778.2431 596214.2003 147647.1975 4.367592133 4.859930807 3.217164233 2.715717803 4.476426004 5.864358218 4.637935936 4.038100352 1 17.17179445 4.258503401 24.95006414 3.855634314 4.613761707 0.069516734 1.29308181 827.6828606 1035481.178 0.333013935 0.878498762 18134.40878 -4.258503401 0.758127394 GREGS(ph)LTGTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GREGSLTGTK 10 1 Q9Y6D6;E5RIF2;E5RHL7 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 GREGS(1)LTGTK;GREGS(1)LTGTK;GREGS(0.999)LT(0.001)GTK;GREGS(0.999)LT(0.001)GTK 117.03 0.00061278 1618010000 1936490 1480030 1016660 1041520 1174240 1138030 1961990 1731200 1377420 TRUE FALSE 1680577.94 1470307.585 1508320.177 1278013.035 1150874.921 1181810.751 1771716.512 1360996.352 1214582.977 1.383666635 1.210545194 1.241842019 1.052223734 0.947547383 0.973017713 1.45870356 1.120546211 1 20.21202962 4.535779754 1.403273505 1.112313732 1.421233701 0.274173053 0.146761407 1.337744661 3.178291415 0.044829843 0.526600181 34338.37617 -4.535779754 0.308919969 GRES(ph)PAAGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GRESPAAGPR 10 1 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9;A0A0C4DGI9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 GRES(1)PAAGPR;GRES(1)PAAGPR;GRES(1)PAAGPR;GRES(1)PAAGPR 135.04 9.37E-05 3250520000 716055 759415 541567 551529 668010 799115 652122 736991 731208 TRUE FALSE 621426.5175 754426.3529 803470.6126 676762.089 654717.9079 829857.4711 588879.3088 579391.2099 644765.4232 0.963802486 1.1700788 1.246144076 1.049625282 1.015435823 1.287068818 0.913323338 0.898607756 1 19.29841485 2.202459226 24.9999543 0.928247628 1.121715978 0.422749132 0.101566511 155.0102827 107342.4805 0.040430936 0.027259517 159.389323 -2.202459226 0.19346835 GRFPESSAVQSSSFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GRFPESSAVQSSSFER 16 1 Q9NWH9;Q9NWH9-3;H7C3F4;H0YMM0 Q9NWH9 SLTM SAFB-like transcription modulator 0 ; 150.91 6.33E-07 354030000 94916 93746 64621 83068 96354 96576 94994 111053 75391 FALSE TRUE 82372.61011 93130.17635 95871.93174 101929.859 94436.74391 100291.3412 85781.4965 87305.18017 66478.36187 1.239089048 1.400909615 1.44215244 1.533278741 1.420563643 1.508631356 1.290367183 1.313287177 1 16.02059721 0.661085538 1.113658533 1.26E-07 1.423443662 0.688430517 0.086177331 3.08672111 1.238406039 7.128112154 0.027122257 4.582321301 -0.661085538 1.423443536 GRGDSVPAAASEADPFLHRLRPMLS(ph)SAFGQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRGDSVPAAASEADPFLHRLRPMLSSAFGQDR 32 3 Q9NZU7 Q9NZU7 CABP1 Calcium-binding protein 1 1 GRGDSVPAAASEADPFLHRLRPMLS(0.5)S(0.5)AFGQDR 50.294 0.054151 195320000 5341.6 4461.3 0 2357.8 9767.9 3854.9 4107.7 4843.2 4131.3 TRUE FALSE 4635.694026 4431.993427 0 2893.174527 9573.537901 4003.200497 3709.335886 3807.51937 3642.90242 1.272527642 1.216610525 0 0.794194901 2.627997348 1.098904125 1.018236411 1.045188405 1 11.83087264 GRGEYFAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRGEYFAIK 9 1 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 0 85.29 0.015475 0 294150 285140 165280 179890 316640 311930 261580 295950 187990 FALSE TRUE 255277.3322 283266.8966 245209.9608 220736.7739 310339.4835 323930.1489 236212.0119 232663.3956 165766.0364 1.53998574 1.708835554 1.479253327 1.331616408 1.872153611 1.954140643 1.424972311 1.403564932 1 17.33878892 1.321011899 1.616850045 0.836508223 1.631354939 0.524643909 0.189312768 0.759476036 2.119777991 0.929133197 0.057184519 20.94169834 -1.321011899 0.794846716 GRKDDDS(ph)DDESQSSHTGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GRKDDDSDDESQSSHTGK 18 2 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 GRKDDDS(0.99)DDES(0.01)QSSHTGK;GRKDDDS(1)DDESQSSHTGK;GRKDDDS(0.941)DDES(0.058)QSSHTGK;GRKDDDS(1)DDESQSSHTGK;GRKDDDS(0.999)DDES(0.001)QSSHTGK 272.18 2.94E-39 1553330000 2271700 1647230 795200 1256860 1499660 1306510 1687500 2570200 1094300 TRUE FALSE 1971489.089 1636409.238 1179761.38 1542249.273 1469819.7 1356772.285 1523846.51 2020582.731 964933.1006 2.043135517 1.695878436 1.222635413 1.598296578 1.523234822 1.40607912 1.579225035 2.094013284 1 19.8800694 4.650260789 3.80549 1.545943364 2.055076218 0.260861372 0.28509469 0.348867002 8.334221325 0.071739506 0.404259159 44695.19013 -4.650260789 0.509132854 GRLGS(ph)VDSFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GRLGSVDSFER 11 1 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 GRLGS(1)VDSFER;GRLGS(1)VDSFER;GRLGS(0.999)VDS(0.001)FER 178.68 4.50E-06 553666000 375725 367453 240729 270864 436688 496230 463590 503450 232765 TRUE FALSE 326071.9893 365039.177 357146.3496 332367.8111 427998.7632 515320.2892 418631.1132 395791.1354 205247.7869 1.588674812 1.778529175 1.740074059 1.619349062 2.085278335 2.510722756 2.039637647 1.928357628 1 17.64700714 3.246372081 24.96507578 1.954153124 1.692748875 0.079432066 0.375819366 441.0839445 1409675.496 0.112331081 0.1423243 1763.486264 -3.246372081 -0.261404249 GRLPLLAVCDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GRLPLLAVCDYK 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 ; 122.39 0.0003277 959940000 1623910 1650480 1185750 1337580 1562270 1472960 1953260 2127600 1691950 FALSE TRUE 1409306.179 1639637.888 1759182.666 1641297.983 1531183.884 1529625.724 1763833.146 1672629.297 1491929.598 0.94461976 1.099004866 1.179132493 1.100117582 1.026311084 1.025266692 1.182249583 1.121118114 1 20.50874803 4.739016397 24.00978493 1.097081214 0.944619695 0.357120215 0.061614622 24.86673366 1309209.497 0.01541114 0.088332832 54829.76653 -4.739016397 -0.152461519 GRLPLLLVANAGTAAVGHTDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GRLPLLLVANAGTAAVGHTDK 21 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q86XE2;Q6P996-2;J3KNK7;H3BNL6;Q6P474;Q6P996-4 H3BND4;Q6P996-4 PDXDC1;PDXDC2P Pyridoxal-dependent decarboxylase domain-containing protein 1;Putative pyridoxal-dependent decarboxylase domain-containing protein 2 0 ; 302.74 1.81E-55 1366180000 669300 596780 392100 489810 682060 560960 639900 768730 632180 FALSE TRUE 580850.3092 592859.7129 581720.8715 601028.8468 668488.3404 582540.4942 577842.5965 604343.0718 557444.4006 1.04198788 1.06353156 1.043549583 1.078186176 1.199201821 1.045019904 1.036592342 1.084131567 1 19.08846839 0.311937166 1.636221425 1.35E-11 1.076209647 0.184271417 0.047570456 35.31030259 7.505492612 121.8920249 0.013628968 2.050865436 -0.311937166 1.076209647 EELRSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 EELRSPK 7 1 P50454;E9PKH2;H0YEP8 P50454 SERPINH1 Serpin H1 0 ;; 109.01 0.0064969 362853000 833360 731770 444744 553296 782840 857160 864750 855450 283065 FALSE TRUE 723229.3645 726962.9547 659823.686 678930.3134 767263.0156 890135.4999 780886.6781 672518.6746 249601.3782 2.897537545 2.912495756 2.643509787 2.720058352 3.073953442 3.566228305 3.128535122 2.694370839 1 17.92926637 1.232290248 3.2752778 0.655385327 2.986562843 0.859155994 0.251412587 0.136065781 1.968604348 0.822456739 0.072357631 17.0722298 -1.232290248 2.331177516 GRLPNNSSRPS(ph)TPTINVLESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GRLPNNSSRPSTPTINVLESK 21 2 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 1 GRLPNNS(0.084)S(0.084)RPS(0.416)T(0.416)PTINVLESK;GRLPNNS(0.096)S(0.096)RPS(0.404)T(0.404)PTINVLESK 100.62 0.00034568 644650000 1123950 824890 790864 863720 923090 966000 1336320 1577910 1054270 TRUE FALSE 975417.1598 819471.2433 1173328.476 1059840.827 904722.315 1003162.645 1206723.892 1240486.226 929635.4016 1.049247004 0.881497458 1.262138333 1.140060743 0.973201229 1.07909256 1.298061466 1.334379289 1 19.82630548 2.291140468 7.995838063 1.239988458 1.063625595 0.205098628 0.132024751 0.320199945 42.78921934 0.049831223 0.038334668 195.4971668 -2.291140468 -0.176362863 GRLPNNSSRPST(ph)PTINVLESK ddPTM_MDA-MB-175_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(0.002)S(0.002)RPS(0.099)T(0.896)PTINVLESK 200.95 3.43E-20 267140000 185440 142120 102930 143170 210180 191050 241150 290040 183130 TRUE FALSE 160933.6342 141186.4044 152707.2923 175678.9367 205997.8292 198399.8171 217763.3101 228017.2031 161480.58 0.996612931 0.874324357 0.945669704 1.087926094 1.275681752 1.228629579 1.348541788 1.412041021 1 17.30100115 3.451559394 2.160842857 1.282660998 0.928652703 0.618402155 0.111662161 0.186781265 1.756773945 0.034919014 0.052513793 2828.520915 -3.451559394 -0.354008295 GRLS(ph)PVPVPR ddPTM_MDA-MB-175_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 128.21 0.00020321 1.47271E+11 7978646 7822233 5943513 6326559 8097602 10594811 6135670 8237670 8450190 TRUE FALSE 6924247.716 7770848.236 8817815.767 7763100.916 7936475.563 11002400.23 5540633.668 6476108.376 7451218.165 0.929277276 1.042896351 1.183405931 1.041856613 1.065124573 1.476590806 0.743587632 0.869134178 1 22.82904487 2.174422098 25 0.865232861 1.115961969 0.370213093 0.154863839 64.96779634 25322.31313 0.062066301 0.041845103 149.4245985 -2.174422098 0.250729109 GRLSPVPVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GRLSPVPVPR 10 1 Q9UKM9;Q9UKM9-2;Q5QPM1;Q5QPL9;Q5QPM0 Q9UKM9 RALY RNA-binding protein Raly 0 ; 97.813 0.0052921 645400000 200141 183969 139961 140369 206732 264350 148548 204682 189113 FALSE TRUE 173691.8598 182760.4955 207646.6077 172241.9269 202618.4377 274519.7156 134141.8378 160912.3471 166756.2766 1.041591137 1.095973713 1.245210147 1.032896215 1.215057339 1.64623318 0.804418524 0.964955265 1 17.34738154 GRLT(ph)PS(ph)PDIIVLSDNEASSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 GRLT(1)PS(1)PDIIVLSDNEASSPR;GRLT(1)PS(1)PDIIVLSDNEASSPR 189.39 4.99E-17 504920000 555190 581740 397290 420510 557690 555470 505230 617990 556270 TRUE FALSE 481820.2348 577918.5116 589420.7729 515993.2226 546593.0601 576839.2903 456232.8724 485837.6477 490508.3943 0.98228744 1.178203102 1.201652774 1.051955947 1.11433987 1.176002892 0.930122456 0.990477744 1 18.9039183 2.236174614 24.99946141 0.975254672 1.120885356 0.509787681 0.06644225 48.5786788 508973.1226 0.025547216 0.018144965 172.2561014 -2.236174614 0.145630685 GRLT(ph)PSPDIIVLS(ph)DNEAS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 3 GRLT(0.994)PS(0.006)PDIIVLS(0.998)DNEAS(0.772)S(0.23)PR 93.191 0.0014707 54765000 189450 173890 139660 145710 162390 174940 180400 197550 217380 TRUE FALSE 164413.7025 172747.7051 207200.0431 178795.6825 159158.7567 181670.055 162904.8358 155305.4698 191681.584 0.857743864 0.901222233 1.080959572 0.932774442 0.830328889 0.94777 0.849872128 0.810226348 1 17.54835221 3.453532405 18.29220404 0.878446375 0.952894113 0.104249251 0.078521841 20.30517667 15743.95972 0.022713186 0.029335365 2841.400187 -3.453532405 0.074447738 GRLT(ph)PSPDIIVLS(ph)DNEASSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 GRLT(1)PSPDIIVLS(1)DNEASSPR;GRLT(1)PSPDIIVLS(1)DNEASSPR 235.07 1.97E-29 254332000 360880 332630 217841 262450 335720 348840 299560 377490 330660 TRUE FALSE 313188.7936 330444.9316 323189.6362 322043.2838 329039.8288 362260.1005 270508.7173 296766.7011 291569.7515 1.074147068 1.133330635 1.108447068 1.104515411 1.128511538 1.242447472 0.927766738 1.017824036 1 18.15348153 2.224803368 24.99999424 0.987101312 1.129500115 0.675871337 0.048916132 137.8807144 250558.0433 0.019514602 0.013233699 167.8044092 -2.224803368 0.142398803 GRLT(ph)PSPDIIVLSDNEASS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 GRLT(0.999)PS(0.001)PDIIVLSDNEAS(0.05)S(0.95)PR 197.08 2.13E-21 107400000 309360 252500 175580 182370 226730 255670 223640 261610 248760 TRUE FALSE 268477.2922 250841.3109 260491.0753 223779.8959 222218.5166 265505.7903 201951.4272 205666.7374 219351.8762 1.223957127 1.143556715 1.187548882 1.020186833 1.013068684 1.210410392 0.920673352 0.937611024 1 17.74288752 8 0.111014475 0.733768824 2.238967397 0.513660536 0.07814705 195.0310477 1.962504765 3.718083791 45.34812736 100000000 -8 1.505198573 GRLT(ph)PSPDIIVLSDNEASSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 GRLT(0.973)PS(0.027)PDIIVLSDNEASSPR;GRLT(0.914)PS(0.086)PDIIVLSDNEASSPR;GRLT(0.996)PS(0.004)PDIIVLSDNEASSPR;GRLT(0.97)PS(0.03)PDIIVLSDNEASSPR;GRLT(0.99)PS(0.01)PDIIVLSDNEASSPR;GRLT(0.996)PS(0.004)PDIIVLSDNEASSPR 280.97 8.62E-45 1557762000 1527389 1315000 942354 957910 1194113 1370461 1202523 1368939 1273753 TRUE FALSE 1325540.674 1306361.678 1398079.546 1175418.106 1170352.488 1423183.521 1085902.505 1076202.048 1123171.371 1.180176692 1.16310094 1.244760668 1.046517153 1.04200705 1.267111643 0.966818183 0.958181517 1 20.09914664 2.213377195 24.96614512 0.97115503 1.151245824 0.584413607 0.07231707 157.6136427 156252.5887 0.029753116 0.020068569 163.4470909 -2.213377195 0.180090794 GRNDS(ph)GEENVPLDLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GRNDSGEENVPLDLTR 16 1 Q6R327-3;Q6R327;Q6R327-4 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 GRNDS(1)GEENVPLDLTR;GRNDS(1)GEENVPLDLTR 173.77 4.64E-09 669900000 258591 257786 201948 222903 292940 318840 303140 352070 312050 TRUE FALSE 224417.5442 256092.5868 299610.7283 273516.533 287111.0671 331105.9811 273741.5295 276782.5703 275159.8045 0.815589852 0.930704931 1.088860812 0.994027938 1.043433897 1.20332249 0.994845631 1.00589754 1 18.06991021 4.501319279 3.108940407 1.044109076 0.820544474 0.591583361 0.063685316 0.193769785 3.518445129 0.016720807 0.079244947 31718.9848 -4.501319279 -0.223564602 GRPITMFIPSDVDNYDDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRPITMFIPSDVDNYDDIR 19 1 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 178.32 3.49E-14 190790000 229590 231860 172350 194250 222490 277370 197360 232230 256040 FALSE TRUE 199249.0998 230336.8964 255699.0365 238357.4314 218062.8843 288040.6034 178220.0576 182569.4217 225771.2429 0.882526478 1.020222476 1.132558041 1.055747527 0.96585766 1.275807316 0.789383339 0.808647813 1 17.78450221 2.200830379 24.9999963 0.850866939 1.053297907 0.369022116 0.116191831 160.4315195 106300.6102 0.04601495 0.031024057 158.7926437 -2.200830379 0.202430968 GRPPAEKLS(ph)PNPPNLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 102.8 0.00048523 513510000 1066000 622950 486220 658300 528080 407930 712570 876050 1020300 TRUE FALSE 925125.3991 618857.8004 721357.6183 807777.0765 517572.2412 423623.3311 643465.0711 688713.5249 899681.2963 1.02828124 0.687863361 0.801792392 0.897848027 0.575283985 0.470859329 0.715214458 0.765508328 1 19.77905451 4.74415422 24.30216665 0.733608931 1.028281429 0.269866526 0.149123514 604.3430709 2625530.654 0.037829813 0.318620056 55482.26983 -4.74415422 0.294672498 GRPS(ph)KTPS(ph)PSQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRPSKTPSPSQPK 13 2 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 GRPS(0.742)KT(0.258)PS(0.992)PS(0.008)QPK 143.14 2.18E-05 229810000 531530 414350 360400 365570 446720 277270 604530 696910 494530 TRUE FALSE 461286.9638 411628.1076 534690.6455 448578.2559 437831.146 287936.7563 545902.7736 547881.2199 436067.2268 1.057834516 0.943955616 1.226165629 1.028690597 1.004045063 0.660303592 1.251877555 1.256414576 1 18.73419104 GRPS(ph)LTGENLEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GRPSLTGENLEAK 13 1 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 GRPS(0.998)LT(0.002)GENLEAK;GRPS(1)LTGENLEAK 208.07 2.96E-08 239723000 384440 289889 209790 258645 267867 222149 405170 347950 312876 TRUE FALSE 333635.28 287984.7001 311245.1457 317374.3004 262536.9708 230695.2158 365876.6758 273543.6002 275888.1557 1.209313532 1.043845827 1.12815697 1.150373055 0.951606531 0.836191083 1.32617754 0.99150179 1 18.073724 7.999996981 0.694823277 1.044785981 18.94120799 0.122400753 0.130743253 700.3524077 3.81716549 0.051831229 19449.49667 99999304.78 -7.999996981 17.89642201 GRPS(ph)S(ph)PRTPLYLQPDAYGSLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRPSSPRTPLYLQPDAYGSLDR 22 2 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 2 GRPS(0.764)S(0.786)PRT(0.428)PLY(0.021)LQPDAYGSLDR 52.669 0.061788 97475000 62519 77803 41926 63679 85021 79212 82761 101150 63334 TRUE FALSE 54256.95575 77291.90697 62201.55383 78138.29022 83329.24844 82259.3369 74734.85096 79519.85965 55846.72667 0.97153332 1.384000667 1.113790504 1.399156135 1.492106224 1.472948225 1.338213632 1.423894727 1 15.7691851 4.742771263 24.01078454 1.341168402 0.971533059 0.33619988 0.156451733 280.4250916 1598987.201 0.037357538 0.277689486 55305.87436 -4.742771263 -0.369635344 GRPSKT(ph)PS(ph)PSQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GRPSKTPSPSQPK 13 2 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 GRPS(0.079)KT(0.922)PS(0.654)PS(0.345)QPK;GRPS(0.417)KT(0.584)PS(0.877)PS(0.122)QPK 76.85 0.030402 272586000 339520 255750 242540 242060 306810 215705 377660 444200 342690 TRUE FALSE 294651.5718 254069.9614 359833.1552 297023.4227 300705.0813 224003.3109 341034.5913 349211.2868 302177.5786 0.975094092 0.840796867 1.190800313 0.982943288 0.995127046 0.741296929 1.128589993 1.155649232 1 18.20503709 GRPSKT(ph)PSPS(ph)QPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRPSKTPSPSQPK 13 2 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 GRPS(0.088)KT(0.912)PS(0.391)PS(0.609)QPK 159.81 4.96E-05 112260000 236630 159360 165720 166420 187440 127860 262080 284500 213120 TRUE FALSE 205358.746 158313.1537 245862.7463 204208.2046 183710.3107 132778.8569 236663.5219 223661.889 187925.1964 1.092768558 0.842426437 1.308301127 1.086646221 0.977571471 0.706551647 1.259349606 1.190164455 1 17.51979899 GRPSS(ph)PRT(ph)PLYLQPDAYGSLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRPSSPRTPLYLQPDAYGSLDR 22 2 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 2 GRPS(0.458)S(0.553)PRT(0.986)PLY(0.003)LQPDAYGSLDR 106.33 0.00092658 85221000 37622 74945 47044 59912 87312 98476 80463 93450 58172 TRUE FALSE 32650.15738 74452.68136 69794.63575 73515.9353 85574.66202 102264.4354 72659.71064 73466.44473 51294.97243 0.63651769 1.451461573 1.360652564 1.433199626 1.668285564 1.993654165 1.416507451 1.432234803 1 15.64652981 4.743715288 4.64104503 1.485445224 0.581182451 0.526648486 0.247972133 0.164960964 9.544498626 0.063175049 0.48771164 55426.22338 -4.743715288 -0.904262773 GRPTSTNPIASIFAWTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GRPTSTNPIASIFAWTR 17 1 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 175.33 1.13E-09 987710000 567320 550820 369090 522240 642600 637050 514510 641880 414500 FALSE TRUE 492347.2246 547201.6272 547583.1585 640822.5739 629813.5172 661557.7257 464612.8994 504618.9571 365498.2822 1.347057561 1.497138711 1.498182578 1.753284776 1.723164097 1.810015964 1.271176698 1.38063291 1 18.4795051 1.389632352 1.292714591 0.870436154 1.594030273 0.551902422 0.164685759 0.835313148 1.530528922 0.773365004 0.053413398 24.52631782 -1.389632352 0.723594119 GRPVSLWELLFSEAISSEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRPVSLWELLFSEAISSEQR 20 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 133.26 1.01E-05 231280000 188270 232440 162840 148830 178510 199800 167170 212340 205570 FALSE TRUE 163389.6425 230913.0863 241589.9687 182624.1262 174958.0002 207486.4353 150957.8791 166932.7434 181267.7488 0.90137183 1.273878491 1.33277966 1.007482729 0.965191003 1.144640658 0.832789507 0.920918059 1 17.46776274 3.556272155 7.762603318 0.966231646 1.17951165 0.310718653 0.134417649 0.333899545 29.41350246 0.036853828 0.054654294 3599.748465 -3.556272155 0.213280004 GRPYDYNGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GRPYDYNGPR 10 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;;; 136.96 9.47E-05 3601620000 2531130 2432890 1722200 1910690 2252250 2643880 2249070 2314500 1886620 FALSE TRUE 2196634.757 2416908.185 2555061.68 2344541.368 2207434.631 2745591.774 2030955.538 1819562.186 1663585.933 1.320421575 1.452830381 1.535875983 1.409329883 1.326913499 1.650405741 1.220829954 1.09375906 1 20.66586496 2.023010592 5.186205241 1.079614754 1.446872412 0.741508068 0.099250444 0.085343259 6.436034847 0.043237482 0.026958504 105.4412613 -2.023010592 0.367257658 GRRPS(ph)GPDGAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GRRPSGPDGAAR 12 2 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;H7C528 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 GRRPS(1)GPDGAAR;GRRPS(1)GPDGAAR 89.506 0.0073908 301900000 312240 292290 190242 152501 275490 361100 297080 292150 93393 TRUE FALSE 270976.6929 290369.9277 282243.6675 187128.6829 270008.288 374991.7507 268269.2273 229675.996 82352.18593 3.290461447 3.525952887 3.427275965 2.272297702 3.278702137 4.553513017 3.257584778 2.788948386 1 16.32951932 3.900766316 23.47069314 2.955522798 3.426134894 0.07332593 0.88795984 84.79035322 20032.23553 0.245202242 0.424703316 7957.310697 -3.900766316 0.470612096 GRRT(ph)PPVQPPPTREDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRRTPPVQPPPTREDR 16 3 Q9Y6R9 Q9Y6R9 CCDC61 Coiled-coil domain-containing protein 61 1 GRRT(1)PPVQPPPTREDR 70.414 0.044735 116360000 76429 57939 15268 21907 59099 46322 55777 74640 7435.7 TRUE FALSE 66328.714 57558.39489 22651.65587 26881.31918 57923.04553 48104.03731 50367.75512 58678.81685 6556.660017 10.11623507 8.77861514 3.454755289 4.099849483 8.834230443 7.336667936 7.681922655 8.949498174 1 12.67874537 4.461330037 24.32350539 6.349049953 9.781831762 0.246328831 2.535314955 223.2094861 343813.8041 0.638751274 1.691285219 28928.77452 -4.461330037 3.432781809 GRS(ph)FAGNLNTYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRSFAGNLNTYK 12 1 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 1 GRS(1)FAGNLNTYK 132.5 0.00010892 327580000 204120 250840 134710 136470 204050 158600 181300 217310 169940 TRUE FALSE 177145.0248 249192.2155 199856.2066 167457.5993 199989.8042 164701.4446 163717.5539 170839.9476 149849.8868 1.182149874 1.662945637 1.333709426 1.117502341 1.33460097 1.09910957 1.092543728 1.140073918 1 17.19315847 3.360818468 0.842322366 1.081145567 1.433773419 0.429096465 0.142433026 0.591871098 0.956923552 0.075865724 0.135414287 2295.189077 -3.360818468 0.352627851 GRS(ph)IDQDYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GRSIDQDYER 10 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 GRS(1)IDQDYER;GRS(1)IDQDYER;GRS(1)IDQDYER;GRS(1)IDQDYER;GRS(1)IDQDYER;GRS(1)IDQDYER;GRS(1)IDQDYER 211.94 3.01E-08 9874340000 3710417 3777940 2430222 2351043 3577010 3947560 3841705 4036400 2430510 TRUE FALSE 3220075.992 3753122.463 3605485.488 2884883.247 3505834.499 4099425.188 3469137.04 3173247.271 2143177.877 1.502477245 1.751195038 1.682308094 1.346077373 1.635811258 1.912778791 1.61868834 1.480627113 1 21.03132016 1.223493404 2.244382163 0.800993813 1.6400129 0.64727659 0.147188655 0.437406744 2.184625848 0.753291299 0.040412084 16.72990228 -1.223493404 0.839019087 GRS(ph)KDRDPNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRSKDRDPNR 10 3 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 1 GRS(1)KDRDPNR 98.531 0.029363 207420000 232070 205790 113150 111100 131300 155010 220210 263000 56930 TRUE FALSE 201401.3615 204438.1519 167869.7185 136326.9531 128687.3869 160973.335 198854.0681 206759.4967 50199.80025 4.011995277 4.072489351 3.344031602 2.715687161 2.563503963 3.206652899 3.961252178 4.118731461 1 15.615394 4.156571786 4.088965872 3.108012934 4.050117933 0.200980785 0.860501148 0.392801824 12.29739833 0.229872708 0.537087039 14340.74739 -4.156571786 0.942104999 GRS(ph)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 GRSPQPPAEEDEDDFDDTLVAIDTYNCDLHFK 32 1 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;M0QYZ0;M0R0K8;M0QYI8 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 1 GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(0.999)PQPPAEEDEDDFDDT(0.001)LVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK 366.61 3.79E-148 23109082000 1170458 938779 756066.2 949239.3 935366 1026328.2 746545.9 1112675 1195355 TRUE FALSE 1015779.01 932612.0989 1121702.343 1164778.591 916754.0466 1065811.71 674145.9935 874738.1101 1054041.494 0.963699262 0.884796381 1.064191827 1.105059524 0.869751383 1.011166749 0.639582026 0.829889635 1 20.00750023 2.289303832 24.99999075 0.816909097 0.982718128 0.31647549 0.110685959 117.3680231 57823.89394 0.041332344 0.032015851 194.6721529 -2.289303832 0.165809031 GRS(ph)RT(ph)PPTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRSRTPPTSR 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GRS(1)RT(1)PPTSR 80.287 0.026993 2329400000 1277900 961140 612230 706250 776410 1010600 874110 938980 618610 TRUE FALSE 1109022.277 954826.2081 908306.4758 866614.8569 760960.96 1049478.436 789338.9467 738186.4342 545478.6305 2.033117734 1.750437423 1.665155012 1.588723753 1.395033494 1.923958845 1.447057506 1.35328204 1 19.05716315 0.741142204 0.657058663 5.87E-31 1.739535944 0.637415741 0.179441376 3.977331714 0.836925609 6.034191238 0.087371488 5.509880808 -0.741142204 1.739535944 GRST(ph)DEY(ph)S(ph)EADEEEEEEEGKPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRSTDEYSEADEEEEEEEGKPSR 23 2 Q96T23-2;Q96T23;Q96T23-3 Q96T23-2 RSF1 Remodeling and spacing factor 1 3 GRS(0.664)T(0.705)DEY(0.747)S(0.884)EADEEEEEEEGKPSR 57.896 0.083575 241980000 182430 114410 117210 111560 151520 121890 132290 165820 171690 TRUE FALSE 158321.4133 113658.4332 173893.148 136891.4031 148505.0484 126579.1872 119460.5362 130360.6834 151393.0038 1.045764397 0.750750896 1.148620766 0.904212214 0.980924116 0.836096676 0.789075672 0.861074687 1 17.20793901 2.740690624 24.71277982 0.862190082 0.96080006 0.143783426 0.113158087 302.7978344 3513139.238 0.03532286 0.033724625 550.4154607 -2.740690624 0.098609978 GRVEDVVVSDECR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GRVEDVVVSDECR 13 1 Q96EK6;G3V5E4;G3V4W4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 0 ;; 181.71 1.08E-05 2403640000 1231670 1320660 855670 956840 1211910 1276640 1317860 1424730 1128200 FALSE TRUE 1068901.689 1311984.498 1269474.874 1174105.146 1187795.362 1325753.167 1190054.14 1120062.577 994825.4812 1.07446151 1.318808698 1.276077963 1.180212176 1.193973601 1.332648984 1.196244128 1.125888508 1 19.92408394 1.433650774 1.925373416 0.97504403 1.232784351 0.494951655 0.07417494 0.422989172 2.249332656 0.177807686 0.019852436 27.14255796 -1.433650774 0.257740321 GRWES(ph)QQDVSQTTVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GRWESQQDVSQTTVSR 16 1 Q9NQT8;H0YBA8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 GRWES(0.673)QQDVS(0.162)QT(0.162)T(0.002)VSR;GRWES(0.607)QQDVS(0.34)QT(0.008)T(0.001)VS(0.045)R;GRWES(0.909)QQDVS(0.024)QT(0.006)T(0.003)VS(0.058)R;GRWES(1)QQDVSQTTVSR;GRWES(0.95)QQDVS(0.039)QT(0.01)TVSR;GRWES(0.976)QQDVS(0.02)QT(0.003)TVSR 317.97 1.68E-57 7722640000 4868010 5376320 3260110 2933150 4686330 5336310 4035490 4244530 3736530 TRUE FALSE 4224690.145 5341002.6 4836710.1 3599166.538 4593081.202 5541601.299 3644128.801 3336870.29 3294801.68 1.282228964 1.621039176 1.467982164 1.092377292 1.394038746 1.681922567 1.106023717 1.012768177 1 21.6517602 2.072168328 7.926995763 1.022685182 1.417462174 0.556516034 0.163024828 0.179674584 17.19242058 0.068195323 0.045835042 118.0778203 -2.072168328 0.394776992 GRYPDHS(ph)VDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRYPDHSVDRR 11 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 GRYPDHS(1)VDRR 97.45 0.0032651 85902000 26555 25667 15851 22011 30061 26705 21101 36539 29943 TRUE FALSE 23045.68947 25498.39179 23516.59662 27008.93397 29462.84491 27732.35863 19054.62827 28725.4192 26403.17265 0.872837889 0.965732116 0.890673137 1.022942747 1.11588275 1.050341904 0.721679494 1.087953314 1 14.68842368 3.738445315 24.71144265 0.998542826 0.915346154 0.131268001 0.108858359 20.710037 4439026.807 0.029836854 0.047630235 5475.771473 -3.738445315 -0.083196672 PTRPDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 PTRPDK 6 1 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 76.847 0.067468 475590000 446320 320850 340600 393930 218549 285920 443490 502490 954540 FALSE TRUE 387337.6812 318742.3152 505315.2992 483377.8273 214200.3025 296919.5274 400480.4081 395036.4239 841695.3686 0.460187493 0.378690827 0.60035414 0.574290706 0.254486731 0.352763646 0.475802081 0.469334202 1 19.68293865 1.232642623 4.785002142 1.043239668 0.443069371 0.749745664 0.100728016 0.101889139 5.434350726 0.207273015 0.026444997 17.0860874 -1.232642623 -0.600170297 GS(ph)AGEEEESLAILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSAGEEEESLAILR 14 0 O15068-4;O15068-10;O15068;H7BYP9;O15068-5;O15068-3;O15068-6;O15068-8;O15068-2;O15068-9 O15068-4 MCF2L Guanine nucleotide exchange factor DBS 1 GS(1)AGEEEESLAILR 149.35 1.04E-06 0 16168 10482 5982.8 11894 15169 17314 14217 16344 18017 TRUE FALSE 14031.35784 10413.14305 8876.102091 14594.71449 14867.16658 17980.08078 12838.23753 12848.96279 15887.05079 0.883194623 0.655448465 0.558700429 0.918654739 0.935804057 1.131744402 0.808094448 0.808769542 1 13.95556371 3.711776069 23.10065318 0.921284055 0.694747941 0.453199649 0.120988723 269.0133006 232013.4745 0.034727147 0.051534035 5149.63051 -3.711776069 -0.226536114 GS(ph)DESIGK ddPTM_MDA-MB-175_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 294750000 847280 889030 567840 663050 786230 999960 703320 756320 839500 TRUE FALSE 735309.8013 883189.9034 842449.3233 813605.6366 770585.5612 1038429.108 635112.1347 594586.8537 740255.2664 0.993319244 1.193088308 1.138052455 1.099087941 1.040972751 1.402798677 0.857963683 0.803218674 1 19.49766332 2.180601863 24.99992619 0.868380027 1.139689861 0.509378082 0.118592094 57.10072854 24629.2367 0.045770233 0.030858298 151.5660256 -2.180601863 0.271309834 GS(ph)FGAMDDPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GSFGAMDDPFK 11 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R3I1 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 GS(1)FGAMDDPFK;GS(1)FGAMDDPFK;GS(1)FGAMDDPFK 160.22 2.91E-05 268551000 1014940 1040480 1221120 1514280 1213140 1109120 1538350 1690880 3003670 TRUE FALSE 880813.1075 1033645.018 1811657.716 1858120.418 1189000.887 1151788.564 1389161.054 1329298.47 2648579.554 0.332560563 0.390263912 0.684011063 0.701553561 0.448920209 0.434870292 0.524492856 0.501891087 1 21.33678741 1.238131665 24.99999994 1.000000554 0.507965143 0.642751397 0.116537174 7.185253868 418275.4492 0.171187974 0.029957007 17.30340868 -1.238131665 -0.492035411 GS(ph)FKDDPQLYQEIQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSFKDDPQLYQEIQER 16 1 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 GS(1)FKDDPQLYQEIQER;GS(1)FKDDPQLYQEIQER 146.06 7.03E-07 206980000 608080 512650 245050 456890 493850 234967 802950 650530 720890 TRUE FALSE 527720.6873 509282.3684 363556.9996 560633.8576 484023.3512 244006.3325 725080.0326 511419.2219 635667.2054 0.830183912 0.801177667 0.571929772 0.881961273 0.761441438 0.383858614 1.140659808 0.804539258 1 19.27791214 2.214828013 24.99985643 0.951439472 0.714007399 0.38387336 0.163462861 268.8090113 283160.4767 0.064355772 0.043415106 163.9940206 -2.214828013 -0.237432073 GS(ph)FSSENYWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSFSSENYWR 10 0 Q6P6C2-3;Q6P6C2;Q6P6C2-1;K7ER58 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 GS(0.959)FS(0.041)SENYWR 185.25 1.54E-06 165300000 132130 129080 127150 171620 180800 189690 159330 171220 419950 TRUE FALSE 114668.6857 128232.065 188640.1653 210588.944 177202.4337 196987.497 143878.2011 134605.9354 370303.9894 0.309660952 0.34628864 0.509419749 0.568692075 0.478532338 0.531961585 0.388540781 0.363501175 1 18.49835057 1.233845516 24.99936898 1.000000848 0.439148397 0.811178836 0.085348076 67.30949793 356829.6429 0.179756817 0.022760006 17.1334774 -1.233845516 -0.560852451 GS(ph)GDTSSLIDPDTSLSELR ddPTM_MDA-MB-175_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(0.995)GDT(0.001)S(0.002)S(0.002)LIDPDTSLSELR 97.235 0.001205 55904000 63200 55847 48929 55702 55410 60304 48631 63379 153730 TRUE FALSE 54847.95987 55480.13738 72591.22806 68349.99045 54307.44941 62623.9339 43914.77311 49825.89407 135556.2145 0.40461413 0.409277712 0.535506456 0.50421879 0.400626778 0.461977594 0.323959866 0.367566284 1 17.04853173 1.235136941 24.99995464 1.000000803 0.424129334 0.894236314 0.062038356 32.52847623 237487.0341 0.118689188 0.016754841 17.18450159 -1.235136941 -0.575871469 GS(ph)GFSLDVIDGPISQR ddPTM_MDA-MB-175_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 133.25 3.64E-05 99960000 273560 261190 242110 248000 237940 274600 204260 247410 565300 TRUE FALSE 237408.3529 259474.2257 359195.2058 304312.1904 233205.4595 285164.0397 184450.8966 194503.2968 498470.878 0.476273266 0.520540391 0.720594164 0.610491413 0.467841693 0.572077632 0.370033446 0.39019992 1 18.9271497 1.22960516 24.99635854 1.000000935 0.513001596 0.686500331 0.102769623 232.287908 648310.0014 0.334691252 0.028169486 16.96700393 -1.22960516 -0.486999339 GS(ph)GGGGGGGGQGSTNYGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 318.13 2.11E-61 245539000 511350 451190 323853 406738 377773 391907 481080 573370 670480 TRUE FALSE 443773.8019 448226.1032 480469.394 499094.0795 370256.0564 406983.9159 434424.9356 450759.2875 591216.6182 0.750611177 0.758141922 0.812679108 0.844181412 0.626261247 0.688383755 0.734798249 0.762426619 1 19.1733273 1.236031152 4.669541303 1.020168278 0.745546938 0.640454743 0.059664532 0.134655659 6.572228163 0.122484044 0.015945771 17.21992088 -1.236031152 -0.27462134 GS(ph)GGLFSPSTAHVPDGALGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GSGGLFSPSTAHVPDGALGQR 21 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 GS(1)GGLFSPSTAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(0.999)GGLFS(0.001)PSTAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR 260.18 8.93E-37 11766100000 4510700 4919691 3233072 4511728 5715328 6151266 5286355 5792974 7796692 TRUE FALSE 3914599.566 4887373.226 4796596.433 5536184.8 5601604.155 6387909.183 4773685.106 4554191.591 6874975.954 0.569398292 0.710893137 0.697689194 0.80526606 0.814781636 0.929153677 0.694356626 0.662430185 1 22.71292324 4.752294994 1.018145521 0.797244447 0.457636405 0.374842821 0.101220795 2.469797254 2.037213276 0.033982402 0.9250227 56532.08382 -4.752294994 -0.339608042 GS(ph)GVFCANCLTTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSGVFCANCLTTK 13 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 GS(1)GVFCANCLTTK;GS(1)GVFCANCLTTK;GS(1)GVFCANCLTTK;GS(1)GVFCANCLTTK 216.23 2.92E-11 648061000 670653 827570 472690 622262 874365 801661 961159 1130063 838461 TRUE FALSE 582024.5068 822133.6382 701284.4651 763556.0978 856966.8472 832501.4174 867945.9481 888407.8216 739339.0958 0.787222683 1.111984532 0.948528854 1.032754932 1.159098514 1.126007568 1.173948399 1.201624298 1 19.49587668 5.858718998 0.541480287 1.144648815 2.52E-14 0.549752178 0.084016282 9.972964995 0.906325097 0.047509831 9.362467313 722302.2997 -5.858718998 -1.144648815 GS(ph)IDEVDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSIDEVDKR 9 1 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 1 GS(1)IDEVDKR;GS(1)IDEVDKR 57.836 0.069076 1056080000 2215570 1656820 1303680 1746650 1777700 1540040 1977710 2280410 3785300 TRUE FALSE 1922776.811 1645936.24 1934144.009 2143253.578 1742327.248 1599286.335 1785911.989 1792762.068 3337806.146 0.576060061 0.493119183 0.57946565 0.642114456 0.521997735 0.479142966 0.535055635 0.537107905 1 21.67046874 1.238015404 24.99999987 1.000000518 0.544258599 0.904819494 0.046324104 3.877344425 177625.4158 0.067382215 0.011698678 17.29877716 -1.238015404 -0.455741919 GS(ph)KSPSPRPNMPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSKSPSPRPNMPVR 14 2 Q9H6S0 Q9H6S0 YTHDC2 Probable ATP-dependent RNA helicase YTHDC2 1 GS(0.876)KS(0.109)PS(0.015)PRPNMPVR 82.259 0.0058501 280850000 325940 296830 194800 205710 313370 315870 345270 354920 229700 TRUE FALSE 282866.2032 294880.1042 289005.9316 252419.5996 307134.5501 328021.7233 311785.7685 279023.12 202545.1277 1.396558912 1.4558736 1.426871803 1.246238813 1.516375899 1.619499452 1.539339762 1.377584952 1 17.62788386 1.250736395 3.466833596 0.939475448 1.456436875 0.680543332 0.097730816 0.185077506 3.252813214 0.250038976 0.026933194 17.81297242 -1.250736395 0.516961427 GS(ph)LAS(ph)LDSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GSLASLDSLR 10 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 2 GS(1)LAS(1)LDSLR;GS(1)LAS(1)LDSLR;GS(1)LAS(1)LDSLR;GS(1)LAS(0.998)LDS(0.002)LR;GS(1)LAS(0.999)LDS(0.001)LR;GS(1)LAS(1)LDSLR;GS(1)LAS(1)LDSLR 158.86 1.15E-05 4349178000 3778620 3436400 2576230 2926850 3654350 3968330 2948030 3641550 3798720 TRUE FALSE 3279265.793 3413826.062 3822103.445 3591436.027 3581635.585 4120994.223 2662130.504 2862832.871 3349639.649 0.978990619 1.019162185 1.141049141 1.072185788 1.069259968 1.230279867 0.794751312 0.854668911 1 21.67557447 2.226859432 24.99993383 0.873525706 1.083383638 0.564232004 0.083538292 153.5581825 328079.0255 0.033914826 0.023078325 168.6007229 -2.226859432 0.209857932 GS(ph)LAS(ph)LDSLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSLASLDSLRK 11 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 2 GS(1)LAS(0.999)LDS(0.001)LRK;GS(1)LAS(0.997)LDS(0.003)LRK 125.28 0.0011605 186235000 1021720 922060 619450 743620 937690 926430 899230 1067050 835390 TRUE FALSE 886697.1133 916002.9271 919018.0919 912470.2865 919031.8036 962070.3616 812022.813 838869.6613 736631.1459 1.203719281 1.243502847 1.247596028 1.238707176 1.247614642 1.306040841 1.102346565 1.138792007 1 19.49058287 1.522606632 1.14159768 0.964739318 1.245405666 0.759716785 0.043811208 0.458745221 0.733268012 0.144320549 0.013928864 33.31245441 -1.522606632 0.280666348 GS(ph)LASLDSLR ddPTM_MDA-MB-175_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 GS(0.92)LAS(0.08)LDSLR;GS(0.912)LAS(0.088)LDSLR;GS(0.998)LAS(0.002)LDSLR 229.86 1.50E-09 4019020000 3710220 2678610 2189980 3026270 3306460 3501710 2648020 3368630 3050700 TRUE FALSE 3219905.027 2661014.035 3249061.653 3713430.857 3240667.915 3636423.05 2391215.428 2648274.689 2690049.721 1.196968592 0.989206264 1.207807286 1.380432052 1.204686995 1.351805143 0.888911238 0.984470535 1 21.35920141 2.229822817 24.99999026 0.96048141 1.217038714 0.570905105 0.107841031 146.8053704 420025.2867 0.045956424 0.031516921 169.7550947 -2.229822817 0.256557304 GS(ph)LDESSLGFGYPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GSLDESSLGFGYPK 14 0 Q9BUZ4;Q2KJU6 Q9BUZ4 TRAF4 TNF receptor-associated factor 4 1 GS(1)LDESSLGFGYPK;GS(1)LDESSLGFGYPK;GS(0.658)LDES(0.324)S(0.018)LGFGYPK;GS(0.979)LDES(0.02)SLGFGYPK;GS(0.997)LDES(0.003)SLGFGYPK;GS(1)LDESSLGFGYPK;GS(1)LDESSLGFGYPK 321.78 3.20E-56 4346087000 3554139 3138498 2328131 2801782 3002492 2884890 3618667 4146702 4103145 TRUE FALSE 3084450.526 3117881 3454022.939 3437969.426 2942748.283 2995873.585 3267729.231 3259962.047 3618075.872 0.852511289 0.861751138 0.954657409 0.950220379 0.813346206 0.828029508 0.903167691 0.901020919 1 21.78679123 1.085224233 1.929198079 1.082018925 0.88077601 0.393631358 0.04627914 1.530468742 3.852391684 0.644925593 0.013513314 12.16814098 -1.085224233 -0.201242915 GS(ph)LTLTISGESPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSLTLTISGESPK 13 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(1)LTLTISGESPK 265.41 2.68E-24 95715000 328380 275840 195360 230190 272520 215090 299040 326210 303150 TRUE FALSE 284983.751 274027.9889 289836.7494 282458.1577 267097.3852 223364.6515 270039.1468 256452.5301 267311.9523 1.066109272 1.025124341 1.084264085 1.05666116 0.999197315 0.835595451 1.010202292 0.959375471 1 18.02816482 3.077310951 4.599075661 0.954207268 1.056625051 0.512953172 0.048768003 0.173424569 6.857803074 0.014828145 0.016849349 1194.843294 -3.077310951 0.102417782 GS(ph)LTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GSLTQR 6 0 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;Q9BV36-3;Q9BV36 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 GS(0.999)LT(0.001)QR;GS(0.988)LT(0.012)QR;GS(0.998)LT(0.002)QR;GS(1)LTQR;GS(1)LTQR 124.98 0.019007 2022159000 1717350 2140580 1497756 1333512 1104077 2241570 1658562 1908634 3433280 TRUE FALSE 1490397.846 2126518.389 2222075.811 1636306.281 1082108.028 2327804.648 1497714.913 1500487.472 3027401.55 0.492302663 0.702423631 0.733987803 0.540498594 0.357437892 0.768911758 0.49471961 0.495635431 1 21.52964861 1.232162478 24.99952678 1.000000711 0.573329505 0.523765408 0.127887599 180.8475625 706559.6217 0.287120493 0.0311726 17.06720789 -1.232162478 -0.426671206 GS(ph)PDGSLQTGKPSAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GSPDGSLQTGKPSAPK 16 1 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 GS(0.903)PDGS(0.095)LQT(0.002)GKPSAPK;GS(0.972)PDGS(0.026)LQT(0.001)GKPSAPK;GS(0.926)PDGS(0.074)LQTGKPSAPK;GS(0.992)PDGS(0.008)LQTGKPSAPK;GS(0.993)PDGS(0.007)LQTGKPSAPK;GS(0.886)PDGS(0.114)LQTGKPSAPK 201.4 8.69E-11 4409350000 4997480 3573640 3104920 3873370 3492790 2670690 4411730 5366910 6668750 TRUE FALSE 4337050.356 3550164.524 4606469.697 4752877.859 3423290.313 2773433.172 3983881.104 4219238.062 5880377.972 0.737546188 0.603730668 0.783362859 0.808260605 0.582154809 0.471641991 0.67748725 0.717511371 1 22.48747746 1.204107682 2.703912504 1.094693005 0.664233557 0.524733315 0.09896133 0.465758603 3.639866122 0.475951372 0.027537594 15.99954683 -1.204107682 -0.430459448 GS(ph)PEEELPLPAFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GSPEEELPLPAFEK 14 0 Q5JTD0-4;Q5JTD0-2;Q5JTD0 Q5JTD0-4 TJAP1 Tight junction-associated protein 1 1 GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK 267.07 6.35E-25 2179760000 1767080 1367780 1010882 1211570 1306830 1251380 1593690 1689360 1665940 TRUE FALSE 1533555.901 1358794.963 1499747.916 1486675.486 1280826.64 1299521.398 1439134.189 1328103.511 1468994.471 1.043949403 0.924983034 1.020935031 1.012036135 0.871907053 0.884633281 0.979672979 0.904090204 1 20.48639754 3.260757024 24.99993922 0.926763926 0.99654494 0.348388386 0.049062783 275.7266621 310550.4887 0.013639373 0.017594697 1822.875569 -3.260757024 0.069781014 GS(ph)PEPSALPPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSPEPSALPPQR 12 0 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 1 GS(0.997)PEPS(0.003)ALPPQR 108.56 0.00057894 0 244320 276640 198620 222850 237370 305000 228000 266200 305310 TRUE FALSE 212032.493 274822.7336 294673.2963 273451.4985 232646.8014 316733.5474 205888.5951 209275.2016 269216.5996 0.787590711 1.020823879 1.094558422 1.015730453 0.864162172 1.176500809 0.764769317 0.777348803 1 18.03840784 2.207481853 24.99986756 0.829342559 0.994244493 0.2288379 0.124754301 254.4191631 204653.9335 0.049204576 0.033177438 161.2433652 -2.207481853 0.164901934 GS(ph)PHPGVGVPTYYNHPEALKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSPHPGVGVPTYYNHPEALKR 21 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 GS(1)PHPGVGVPTYYNHPEALKR 72.532 0.0073388 87113000 92337 78107 49143 59341 64811 64875 82952 76568 55455 TRUE FALSE 80134.4315 77593.90997 72908.71917 72815.28102 63521.3879 67370.78323 74907.32781 60194.52905 48899.17307 1.638768643 1.586814359 1.491001066 1.489090233 1.299027855 1.377748927 1.531873099 1.230992781 1 15.57752245 0.471187192 0.632442285 5.44E-82 1.521209053 0.73755794 0.097282036 4.824239748 0.732955253 6.631370505 0.052430169 2.959287719 -0.471187192 1.521209053 GS(ph)PHYFS(ph)PFRPY ddPTM_MDA-MB-175_Pertuzumab_2h_R1 48 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(0.001)FS(0.999)PFRPY;GS(1)PHY(0.037)FS(0.963)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHY(0.001)FS(0.999)PFRPY;GS(1)PHY(0.001)FS(0.999)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHY(0.012)FS(0.988)PFRPY;GS(1)PHY(0.002)FS(0.998)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHY(0.01)FS(0.99)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHY(0.001)FS(0.999)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHY(0.001)FS(0.999)PFRPY;GS(0.999)PHY(0.188)FS(0.814)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHY(0.001)FS(1)PFRPY;GS(0.999)PHY(0.05)FS(0.951)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY 196.22 1.19E-07 24660028600 3844455.4 3744601.9 2712173.3 2723111.6 3433484.3 4025750.5 3513087.8 3803662.3 3849476.7 TRUE FALSE 3336400.878 3720003.364 4023789.38 3341435.709 3365164.68 4180623.727 3172389.086 2990278.717 3394395.95 0.982914465 1.095924995 1.185421335 0.984397742 0.991388374 1.23162524 0.934596061 0.880945759 1 21.69472343 2.046287243 24.99960575 0.924709283 1.076598938 0.361778253 0.087159869 115.3811855 62316.53293 0.034747006 0.023426418 111.2467271 -2.046287243 0.151889655 GS(ph)PHYFSPFRPY ddPTM_MDA-MB-175_Pertuzumab_2h_R1 39 GSPHYFSPFRPY 12 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(0.999)PHYFS(0.001)PFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY 203.93 3.14E-07 1.33075E+11 11552596.2 12328274 7393445.9 7353616.6 10975243.8 11933849.4 9974465.3 11054435.3 10227095.6 TRUE FALSE 10025891.34 12247288.76 10968941.07 9023367.642 10756857.92 12392952.31 9007143.19 8690530.337 9018060.009 1.111757 1.358084637 1.216330459 1.000588556 1.192812857 1.374237064 0.998789449 0.963680695 1 23.10438568 2.117798094 9.124249653 0.980033833 1.205666111 0.486795329 0.10724318 0.227698451 17.13313255 0.044566177 0.030025182 131.1589992 -2.117798094 0.225632278 GS(ph)PIPYGLGHHPPVTIGQPQNQHQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GSPIPYGLGHHPPVTIGQPQNQHQEK 26 0 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 GS(0.998)PIPY(0.002)GLGHHPPVTIGQPQNQHQEK;GS(1)PIPYGLGHHPPVTIGQPQNQHQEK;GS(1)PIPYGLGHHPPVTIGQPQNQHQEK 221.05 4.76E-34 497270000 494920 438460 340759 427810 428310 370407 425790 502210 539730 TRUE FALSE 429515.068 435579.7274 505551.1922 524950.7992 419787.469 384656.797 384496.9513 394816.2997 475923.7343 0.902487178 0.915230101 1.062252533 1.103014541 0.882047771 0.808232011 0.807896147 0.829578925 1 18.86037088 3.051021209 10.90490916 0.850729875 0.994631072 0.3950865 0.079920162 0.552107829 115.5137847 0.025260205 0.028642827 1124.659896 -3.051021209 0.143901197 GS(ph)PLAEGPQAFFPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GSPLAEGPQAFFPER 15 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 GS(1)PLAEGPQAFFPER;GS(1)PLAEGPQAFFPER;GS(1)PLAEGPQAFFPER;GS(1)PLAEGPQAFFPER;GS(1)PLAEGPQAFFPER;GS(1)PLAEGPQAFFPER;GS(1)PLAEGPQAFFPER 238.58 9.40E-18 2267008000 264972 357474 278709 335708 429420 402953 364881 450979 454677 TRUE FALSE 229955.2788 355125.7298 413493.6046 411935.6324 420875.3821 418454.8627 329494.8968 354540.6504 400925.603 0.573560973 0.885764658 1.031347466 1.027461527 1.049759304 1.043721976 0.821835508 0.884305337 1 18.61297503 4.708425121 3.130970586 0.969106603 0.527131211 0.744345763 0.074317712 0.187781768 2.926711378 0.021447825 0.19628096 51100.49668 -4.708425121 -0.441975392 GS(ph)PLNAAPYGIESMSQDTEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSPLNAAPYGIESMSQDTEVR 21 0 P18031;B4DSN5 P18031 PTPN1 Tyrosine-protein phosphatase non-receptor type 1;Tyrosine-protein phosphatase non-receptor type 1 GS(1)PLNAAPYGIESMSQDTEVR;GS(1)PLNAAPYGIESMSQDTEVR 207.07 4.06E-22 85589000 41680 42145 40614 49420 53308 52650 35987 64634 92029 TRUE FALSE 36171.8824 41868.14672 60255.06625 60641.56634 52247.2751 54675.47957 32496.98628 50812.52208 81149.43646 0.445744098 0.515938847 0.742519836 0.747282655 0.64384027 0.673762899 0.400458558 0.626159888 1 16.30829346 -2 0.043435774 1.672217931 1.42E-16 0.174708686 0.155393711 4004.201516 17.08908029 539.3727851 199.1269941 0.01 2 -1.672217931 GS(ph)PMALLLAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSPMALLLAAR 11 0 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 GS(1)PMALLLAAR;GS(1)PMALLLAAR 119.55 0.0005991 61277000 42040 37977 32900 34392 38594 37823 30939 37040 68630 TRUE FALSE 36484.30748 37727.52659 48810.55004 42201.22925 37826.05491 39278.07528 27938.54054 29119.28425 60516.63958 0.602880592 0.623424018 0.806564118 0.697349184 0.625052137 0.649045875 0.461667084 0.481178143 1 15.88504426 3.089948332 3.332427623 0.606558225 0.686856549 0 0.155977179 0.858060837 18.981568 0.050434135 0.05771186 1230.122414 -3.089948332 0.080298325 GS(ph)PNLTLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSPNLTLPK 9 0 Q12923-3;Q12923;Q12923-4;Q12923-2 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 GS(0.994)PNLT(0.006)LPK;GS(1)PNLTLPK 121.36 0.00064621 1145770000 1559330 1533510 1155760 1221390 1582110 1553500 1669140 1952120 1898090 TRUE FALSE 1353260.59 1523436.272 1714689.402 1498725.267 1550629.106 1613264.15 1507267.06 1534674.329 1673699.963 0.808544315 0.910220652 1.024490315 0.895456355 0.926467791 0.963890892 0.900559893 0.916935152 1 20.67460949 4.686984139 3.93980458 0.941048698 0.802213073 0.514481545 0.041744119 0.172149661 4.984688808 0.00996379 0.060679245 48638.94418 -4.686984139 -0.138835625 GS(ph)PPTSSNIVQGQIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSPPTSSNIVQGQIK 15 0 Q9Y4E6-2;Q9Y4E6;A2RRE0 Q9Y4E6-2 WDR7 WD repeat-containing protein 7 1 GS(0.778)PPT(0.207)S(0.011)S(0.004)NIVQGQIK 108.77 0.0020822 0 63377 48810 44438 44389 55708 44823 52233 60395 84357 TRUE FALSE 55001.56887 48489.3639 65928.36544 54468.20089 54599.51979 46547.36981 47167.4517 47479.99924 74384.41156 0.739423324 0.651875344 0.886319648 0.732252897 0.734018306 0.625767803 0.634103984 0.638305772 1 16.18271269 2.987507405 21.79792102 0.700068871 0.75213009 0 0.121225132 438.2124834 764630.7085 0.03773621 0.03968837 971.6445188 -2.987507405 0.052061219 GS(ph)PQSAAAELSSGLLASAAASSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSPQSAAAELSSGLLASAAASSR 23 0 Q12948 Q12948 FOXC1 Forkhead box protein C1 1 GS(0.998)PQS(0.002)AAAELSSGLLASAAASSR 170.59 7.50E-12 37091000 19604 17097 11350 14569 16619 25268 21220 20074 21635 TRUE FALSE 17013.28173 16984.68868 16838.89796 17877.11412 16288.31441 26240.07631 19162.08767 15781.33132 19077.33495 0.891805998 0.890307201 0.882665111 0.937086557 0.853804499 1.375458175 1.004442587 0.827229346 1 14.21957202 GS(ph)PRPQAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSPRPQAPK 9 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 GS(1)PRPQAPK;GS(1)PRPQAPK;GS(1)PRPQAPK;GS(1)PRPQAPK 106.67 0.007625 3329890000 5373920 4732060 3172510 4003840 4176280 4033780 4999040 5846120 5666920 TRUE FALSE 4663742.856 4700974.786 4706746.447 4912973.067 4093180.199 4188962.127 4514233.87 4595972.733 4996983.173 0.933311699 0.940762581 0.94191761 0.983187835 0.819130275 0.838298225 0.903391849 0.919749491 1 22.25262593 3.279700803 24.99999937 0.896723043 0.948587064 0.223577911 0.04967809 258.8704203 157308.2703 0.015225586 0.019655915 1904.148446 -3.279700803 0.05186402 DFYLATS(ph)PPDSFLDDHHLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DFYLATSPPDSFLDDHHLTR 20 0 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 1 DFYLAT(0.06)S(0.939)PPDS(0.001)FLDDHHLTR;DFYLAT(0.006)S(0.994)PPDSFLDDHHLTR 116.65 0.00015339 234675000 142894 157024 132198 177739 199090 167148 230883 243313 452754 TRUE FALSE 124010.1959 155992.499 196129.395 218097.3565 195128.4985 173578.2917 208492.0022 191282.4084 399229.9379 0.310623488 0.39073347 0.491269257 0.546295094 0.488762189 0.434782754 0.52223539 0.479128418 1 18.60686039 1.232984109 5.152945609 1.034208517 0.461593082 0.863902213 0.067617463 0.064168701 4.573685382 0.132045455 0.017770355 17.09952746 -1.232984109 -0.572615435 GS(ph)PRYS(ph)PRHS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSPRYSPRHSR 11 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 3 GS(1)PRY(0.047)S(0.953)PRHS(1)R;GS(1)PRY(0.028)S(0.973)PRHS(0.999)R;GS(1)PRY(0.06)S(0.942)PRHS(0.999)R;GS(1)PRY(0.221)S(0.78)PRHS(0.999)R 92.439 0.0065998 1922431000 2399140 2199680 612655 580605 1743670 1940330 1763100 1878090 266787 TRUE FALSE 2082087.57 2185230.157 908937.0072 712440.2392 1708974.378 2014975.751 1592114.833 1476475.069 235247.7448 8.850616495 9.289058899 3.863743765 3.028467881 7.264572844 8.565335036 6.767821876 6.276255996 1 17.84382137 4.253742321 24.99516011 5.535690769 9.069840411 0.334498048 2.210694988 307.4646122 506200.7733 0.572423757 1.501863741 17936.69077 -4.253742321 3.534149642 GS(ph)PSFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSPSFLK 7 0 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 GS(0.995)PS(0.005)FLK;GS(0.999)PS(0.001)FLK 117.89 0.01332 135140000 1196480 1121040 815290 1025330 1025670 969350 1044990 1224040 1916370 TRUE FALSE 1038362.137 1113675.814 1209566.971 1258146.848 1005261.174 1006641.522 943647.0306 962288.5715 1689818.922 0.614481305 0.659050387 0.715796797 0.744545366 0.594892838 0.595709699 0.558430858 0.569462538 1 20.68843723 1.232824332 24.98344772 1.000000599 0.629967009 0.786446724 0.060334816 97.01881887 422504.8651 0.146391246 0.016918097 17.09323771 -1.232824332 -0.37003359 GS(ph)PSGGSTAEASDTLSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSPSGGSTAEASDTLSIR 18 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 GS(0.999)PS(0.001)GGSTAEASDTLSIR;GS(0.984)PS(0.016)GGSTAEASDTLSIR 385.07 7.76E-93 0 206049 202257 173004 216193 240080 242520 173456 250740 275110 TRUE FALSE 178819.1026 200928.3604 256669.3131 265282.925 235302.8777 251849.9013 156634.2638 197121.2023 242586.8092 0.737134485 0.828274056 1.0580514 1.093558738 0.969973918 1.038184649 0.645683351 0.812580053 1 17.88814158 1.191458709 22.01090378 1.000006206 0.897680031 0.046381579 0.145446363 11502.30305 5373266.76 18.44581284 0.038686125 15.54027533 -1.191458709 -0.102326175 GS(ph)PSPASVSSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSPSPASVSSGR 12 0 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 GS(0.944)PS(0.056)PASVSSGR;GS(0.861)PS(0.139)PASVSSGR;GS(0.964)PS(0.035)PASVSSGR;GS(0.864)PS(0.136)PASVSSGR 283.73 3.25E-28 3571470000 1042430 1044680 870370 1072180 1310890 1423340 1037860 1347590 1505640 TRUE FALSE 904670.2343 1037817.428 1291283.843 1315634.856 1284805.854 1478096.811 937208.4969 1059418.365 1327644.954 0.681409763 0.781698017 0.972612323 0.990953833 0.967733014 1.113322358 0.70591802 0.797968133 1 20.34043795 4.429213183 4.059885392 0.919955338 0.698434805 0.368339167 0.113214717 0.249226275 8.464926967 0.031501545 0.102700876 26866.62933 -4.429213183 -0.221520533 GS(ph)PSSHLLGADHGLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSPSSHLLGADHGLRK 16 1 F8VU11;Q6NWY9-2;Q6NWY9-3;Q6NWY9 F8VU11 PRPF40B Pre-mRNA-processing factor 40 homolog B 1 GS(0.987)PS(0.008)S(0.006)HLLGADHGLRK 73.928 0.015847 136350000 227640 219610 99604 136960 224690 226430 238560 265850 71660 TRUE FALSE 197556.7972 218167.3674 147772.8276 168058.8613 220219.1086 235140.9086 215424.4879 209000.0463 63188.43644 3.126470734 3.452647031 2.338605541 2.659645827 3.485117231 3.721264869 3.409239096 3.307567937 1 15.94737295 1.236774172 24.99980052 0.999997256 3.194817796 0.73790035 0.409710677 26.17092278 366132.1882 0.676943649 0.108197474 17.2494071 -1.236774172 2.19482054 GS(ph)PSYTQASLGLLTPVSGTQEQTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSPSYTQASLGLLTPVSGTQEQTK 24 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 GS(0.887)PS(0.104)Y(0.009)TQASLGLLTPVSGTQEQTK 305.93 5.76E-63 88090000 267620 235770 186760 220550 212070 222470 262380 302640 341740 TRUE FALSE 232253.3389 234221.2113 277077.7607 270629.2484 207850.2219 231028.5649 236934.428 237922.7911 301339.8865 0.77073547 0.777265878 0.919485847 0.898086382 0.689753435 0.766671042 0.786269719 0.789549614 1 18.20103212 1.23669445 24.9914107 1.000000252 0.800263857 0.478618052 0.06568919 46.78458474 626353.5029 0.106052175 0.016860869 17.24624097 -1.23669445 -0.199736395 GS(ph)PTGGAQLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GSPTGGAQLLK 11 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 GS(0.984)PT(0.016)GGAQLLK;GS(0.988)PT(0.012)GGAQLLK;GS(0.644)PT(0.356)GGAQLLK 117.27 0.00092037 604130000 1016500 1043370 675320 813070 935450 825940 910740 1132560 1198820 TRUE FALSE 882166.9495 1036516.034 1001907.011 997689.9705 916836.3752 857714.4463 822416.575 890370.8576 1057096.865 0.834518556 0.980530799 0.947791109 0.943801844 0.867315385 0.811386803 0.777995472 0.842279347 1 20.01167615 3.139086767 4.733714687 0.847253748 0.931858917 0.18311654 0.068118953 0.300839502 11.40399673 0.021007985 0.024183914 1377.484646 -3.139086767 0.084605169 GS(ph)PTRPNPPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSPTRPNPPVR 11 1 Q14195-2;Q14195;H0YBT4 Q14195-2 DPYSL3 Dihydropyrimidinase-related protein 3 1 GS(0.973)PT(0.027)RPNPPVR;GS(0.904)PT(0.096)RPNPPVR;GS(0.982)PT(0.018)RPNPPVR;GS(0.975)PT(0.025)RPNPPVR 109.44 0.0011677 2110720000 663303 556079 359888 363149 556029 525231 436611 531484 486637 TRUE FALSE 575645.828 552426.0804 533931.0406 445607.5308 544965.1108 545436.9764 394268.5324 417830.2826 429107.3282 1.341496148 1.2873844 1.244283202 1.038452391 1.269997213 1.271096857 0.918810998 0.973719755 1 18.71097901 -0.324273157 0.139466765 8.40E-10 1.554943887 0.57840663 0.099879525 71.70684711 1.448297825 21.78444568 2.777708668 0.473943796 0.324273157 1.554943886 GS(ph)PTSAYPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GSPTSAYPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(0.987)PT(0.012)S(0.001)AYPER;GS(0.839)PT(0.161)SAYPER;GS(0.542)PT(0.457)S(0.001)AYPER;GS(1)PTSAYPER;GS(0.994)PT(0.006)SAYPER;GS(0.951)PT(0.035)S(0.014)AYPER;GS(0.989)PT(0.01)SAYPER 174.87 3.12E-06 7386140000 2425350 2114150 1708301 1860351 2037590 2291600 1918050 2167950 2669070 TRUE FALSE 2104833.852 2100262.009 2534441.078 2282772.128 1997045.945 2379759.335 1732037.806 1704350.764 2353535.585 0.894328459 0.892385916 1.076865416 0.969933126 0.848530168 1.011142279 0.735930154 0.724166133 1 21.16639824 2.238102324 24.99998116 0.796555767 0.948512308 0.265532315 0.098456813 13.73819843 749332.677 0.038421419 0.027705247 173.0223967 -2.238102324 0.151956541 GS(ph)PVFLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GSPVFLPR 8 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 GS(1)PVFLPR;GS(1)PVFLPR;GS(1)PVFLPR;GS(1)PVFLPR;GS(1)PVFLPR;GS(1)PVFLPR 112.11 0.0032567 1384373000 1562860 1133303 863787 1043173 1033173 1153607 1004953 1156176 2088600 TRUE FALSE 1356324.091 1125858.258 1281517.282 1280041.374 1012614.879 1197987.008 907492.8127 908936.7598 1841688.087 0.736457004 0.611318641 0.695838395 0.695037006 0.549829738 0.650483117 0.492750547 0.493534582 1 20.81259731 3.264325013 24.79480008 0.609161938 0.680222179 0.004828045 0.14654421 711.7696061 684978.1867 0.041545291 0.053614037 1837.913267 -3.264325013 0.071060242 GS(ph)PVPPVPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSPVPPVPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(1)PVPPVPER;GS(1)PVPPVPER;GS(1)PVPPVPER;GS(1)PVPPVPER 108.53 0.0022444 1227230000 869760 1026070 643290 627050 901460 1015360 1000720 964650 945260 TRUE FALSE 754819.0123 1019329.679 954387.1957 769431.2864 883522.7097 1054421.556 903670.3284 758367.1044 833512.4396 0.905588179 1.222932772 1.145018539 0.92311914 1.059999429 1.265033977 1.084171376 0.909844975 1 19.66884421 1.752838073 24.99876748 0.954540559 1.093603637 0.183399132 0.114724366 6.928050571 12151.46084 0.060328611 0.028970669 56.60282055 -1.752838073 0.139063077 GS(ph)QHSPTRPPVAAAAASLGSLPGPGAAR ddPTM_MDA-MB-175_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 132.35 1.16E-05 407400000 169930 162740 95321 125710 156610 199280 164250 171450 187280 TRUE FALSE 147473.32 161670.9502 141418.5544 154254.3769 153493.7674 206946.4306 148321.0603 134786.7517 165139.9718 0.893020136 0.978993447 0.85635569 0.934082616 0.929476769 1.25315772 0.898153601 0.816197013 1 17.33332984 4.764024729 20.73158374 0.948751437 0.893019423 0.023798252 0.118067147 3911.754773 3184217.904 0.029968662 1.374239228 58079.74873 -4.764024729 -0.055732014 GS(ph)RGPGNPLDHQITNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSRGPGNPLDHQITNER 17 1 Q96PC5;Q96PC5-11;Q96PC5-10;Q96PC5-9;Q96PC5-13;Q96PC5-6;G3V599;Q96PC5-14;Q96PC5-7;Q96PC5-12;Q96PC5-8;Q96PC5-5 Q96PC5 MIA2 Melanoma inhibitory activity protein 2 1 GS(1)RGPGNPLDHQITNER;GS(1)RGPGNPLDHQITNER;GS(1)RGPGNPLDHQITNER;GS(1)RGPGNPLDHQITNER 215.99 3.29E-15 1338130000 817800 904840 596293 766612 1131190 1184090 640725 1148600 852007 TRUE FALSE 709725.658 898896.0465 884662.2893 940682.9715 1108681.532 1229642.709 578587.5881 902980.8284 751283.7031 0.944683952 1.196480162 1.177534247 1.252100861 1.475716201 1.636722191 0.770131956 1.201917231 1 19.51899828 2.223827374 24.99999922 1.025500695 1.279615733 0.294805158 0.20902834 353.5651457 599939.9069 0.087995301 0.059609372 167.4277243 -2.223827374 0.254115039 GS(ph)SFQSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSSFQSGR 8 0 Q96KP1 Q96KP1 EXOC2 Exocyst complex component 2 1 GS(0.702)S(0.298)FQSGR 78.655 0.031534 36166000 85991 80836 54343 57824 63609 89599 76492 82763 90513 TRUE FALSE 74627.07148 80304.98299 80623.45657 70953.82298 62343.30535 93045.93151 69073.81761 65064.77651 79812.65625 0.935028039 1.00616853 1.010158794 0.889004656 0.781120542 1.16580422 0.865449427 0.815218783 1 16.28432992 3.736989981 24.89084548 0.909705781 0.986023462 0.06821284 0.108103576 329.6657602 5224457.266 0.0294896 0.046505047 5457.452708 -3.736989981 0.076317681 GS(ph)SGEGLPFAEEGNLTIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSSGEGLPFAEEGNLTIK 18 0 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 GS(0.5)S(0.5)GEGLPFAEEGNLTIK 116.35 0.00017098 34817000 130430 95991 90128 121390 106830 118460 122360 157620 205920 TRUE FALSE 113193.345 95360.4288 133714.2023 148953.4548 104704.292 123017.2329 110493.546 123914.1896 181576.3722 0.62339248 0.525180824 0.7364075 0.820335009 0.576640511 0.677495818 0.608523811 0.68243565 1 17.47021696 1.239806042 4.700421815 1.025680407 0.654794032 0.635586406 0.082073935 0.125307942 6.279226558 0.153842304 0.020966801 17.37024891 -1.239806042 -0.370886375 GS(ph)SPQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSSPQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK 38 1 Q27J81-2;Q27J81 Q27J81-2 INF2 Inverted formin-2 1 GS(0.5)S(0.5)PQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK;GS(0.548)S(0.451)PQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK 389.49 1.10E-179 2164500000 428410 354430 258181 307991 315073 256985 446780 519870 452280 TRUE FALSE 371794.533 352101.726 383038.1952 377925.0639 308803.6637 266871.3792 403451.3444 408699.8461 398811.9736 0.932255192 0.882876516 0.960448082 0.947627175 0.774308908 0.669165915 1.011632978 1.024793319 1 18.6053492 2.063533385 24.99997676 1.015389119 0.86442068 0.402288273 0.086702904 64.84033084 25513.60814 0.038140334 0.025714204 115.753301 -2.063533385 -0.150968438 GS(ph)TFSLWQDIPDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSTFSLWQDIPDVR 14 0 Q8IW93-2;Q8IW93 Q8IW93-2 ARHGEF19 Rho guanine nucleotide exchange factor 19 1 GS(0.684)T(0.158)FS(0.158)LWQDIPDVR;GS(0.999)T(0.001)FSLWQDIPDVR 230.86 7.93E-13 35258000 38698 44340 29198 28643 41103 35264 36268 41564 40327 TRUE FALSE 33583.96125 44048.72762 43318.25046 35146.83093 40285.13072 36620.6289 32750.73494 32675.86205 35559.588 0.944441799 1.238729977 1.218187636 0.988392524 1.132890817 1.029838391 0.921009966 0.918904405 1 15.11795099 2.470635415 3.154809732 0.940045574 1.111607136 0.378375528 0.091824842 0.239538715 4.955886687 0.035642579 0.028037923 295.5530295 -2.470635415 0.171561563 GS(ph)VHS(ph)LDAGLLLPSGDPFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSVHSLDAGLLLPSGDPFSK 20 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 2 GS(1)VHS(1)LDAGLLLPSGDPFSK;GS(1)VHS(1)LDAGLLLPS(0.001)GDPFSK 66.827 0.012178 80723000 387900 227680 182020 221447 212942 184526 207359 258280 451980 TRUE FALSE 336638.0322 226184.3551 270045.4808 271729.926 208704.8708 191624.8346 187249.3561 203048.8319 398547.4393 0.844662389 0.567521787 0.677574246 0.681800707 0.523663811 0.480808094 0.46982953 0.509472178 1 18.60439193 1.232335493 24.9938951 1.00000069 0.583322475 0.548539042 0.115244902 167.293979 671619.5188 0.265141623 0.02926701 17.07400848 -1.232335493 -0.416678215 GS(ph)VHSLDAGLLLPSGDPFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GSVHSLDAGLLLPSGDPFSK 20 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 GS(0.5)VHS(0.5)LDAGLLLPSGDPFSK;GS(0.5)VHS(0.5)LDAGLLLPSGDPFSK;GS(0.5)VHS(0.5)LDAGLLLPSGDPFSK 114.39 8.05E-05 688990000 1949030 1418600 538920 912070 1233160 1064800 1224450 1597090 1439030 TRUE FALSE 1691460.747 1409281.123 799543.5146 1119169.434 1208622.529 1105763.545 1105703.027 1255564.732 1268909.513 1.333003441 1.110623814 0.630102861 0.881993099 0.952489139 0.87142821 0.871380517 0.989483268 1 20.27515776 4.472568999 24.97184031 0.893934882 1.277408623 0.668891468 0.104170736 61.42496758 336954.6857 0.026477191 0.070651737 29687.18363 -4.472568999 0.383473741 GS(ph)VSDEEMMELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GSVSDEEMMELR 12 0 P13796;Q5TBN3;Q5TBN5 P13796 LCP1 Plastin-2 1 GS(0.642)VS(0.358)DEEMMELR;GS(1)VSDEEMMELR;GS(0.923)VS(0.077)DEEMMELR;GS(0.533)VS(0.467)DEEMMELR;GS(1)VSDEEMMELR;GS(0.999)VS(0.001)DEEMMELR;GS(1)VSDEEMMELR 237.41 4.40E-16 1756010000 1526003 2196650 1687240 2092070 2796350 2819780 2562460 3065760 2984020 TRUE FALSE 1324337.837 2182220.062 2503194.907 2567106.469 2740708.106 2928258.761 2313953.024 2410171.082 2631252.555 0.503310803 0.829346486 0.951332058 0.975621464 1.041598269 1.112876358 0.879411222 0.915978619 1 21.3273183 4.782035483 1.678324231 0.980557575 0.297844549 0.85243319 0.063435105 0.438317112 1.111652247 0.01907748 0.499649006 60539.03352 -4.782035483 -0.682713027 GS(ph)YGDLGGPIITTQVTIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSYGDLGGPIITTQVTIPK 19 0 P61978;P61978-2;S4R359;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 GS(1)YGDLGGPIITTQVTIPK;GS(1)YGDLGGPIITTQVTIPK;GS(1)YGDLGGPIITTQVTIPK;GS(1)YGDLGGPIITTQVTIPK 330.54 3.10E-75 1514830000 631050 555373 385523 522184 510726 441768 583148 717780 972480 TRUE FALSE 547655.1436 551724.7182 571963.2123 640753.8583 500563.5518 458763.1008 526594.3967 564288.3328 857514.5223 0.638654075 0.643399854 0.667001196 0.747222166 0.583737696 0.53499164 0.614093853 0.658051051 1 19.70980158 1.236612099 4.712636339 1.028170399 0.633590829 0.815703588 0.054516132 0.08515537 4.305791577 0.11201685 0.014784849 17.24297105 -1.236612099 -0.39457957 GS(ph)YGS(ph)DAEEEEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 2 GS(0.996)Y(0.004)GS(1)DAEEEEYR 235.35 9.74E-09 0 235250 271100 269630 365920 326440 317860 287880 336020 899470 TRUE FALSE 204161.1165 269319.1262 400023.9699 449007.7287 319944.4827 330088.2799 259961.4419 264164.7379 793135.6813 0.257410077 0.339562489 0.504357551 0.566117172 0.403391866 0.416181352 0.327764149 0.333063742 1 19.59720816 1.23493931 24.97886996 1.000000864 0.395762398 0.81923132 0.089531834 46.5575819 321092.4465 0.171212219 0.023786076 17.17668338 -1.23493931 -0.604238465 GSAADSEESPAIEAIHLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSAADSEESPAIEAIHLLR 19 0 P13716;P13716-2;B7ZBK6 P13716 ALAD Delta-aminolevulinic acid dehydratase 0 ;;; 254.05 6.83E-31 509485000 602985 594041 422045 458411 579023 650420 589486 651001 647661 FALSE TRUE 523299.0045 590138.7056 626147.3737 562500.2239 567501.5751 675442.0783 532317.7385 511789.5022 571095.2544 0.916307745 1.03334549 1.096397438 0.984949918 0.993707391 1.182713519 0.932099741 0.89615436 1 19.12337187 2.09173145 24.87582111 0.9325125 1.035229333 0.249480705 0.074362834 20.31568268 5500.223491 0.029534849 0.01991239 123.518341 -2.09173145 0.102716833 GSAMQVS(ph)PLMFTDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSAMQVSPLMFTDK 14 0 A0A494C1L5;P50851-2;P50851;E9PEM5;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 GSAMQVS(1)PLMFTDK;GSAMQVS(1)PLMFTDK;GSAMQVS(0.998)PLMFT(0.002)DK;GSAMQVS(1)PLMFTDK 201.4 1.88E-08 875570000 1297980 1412380 1031720 1209740 1443140 1296600 1697350 1996280 1844540 TRUE FALSE 1126448.654 1403101.983 1530663.243 1484429.957 1414424.337 1346481.041 1532741.258 1569391.057 1626480.583 0.692568154 0.862661379 0.941089159 0.912663805 0.86962264 0.827849441 0.942366773 0.964899965 1 20.63332217 4.708045193 2.558346831 0.921760179 0.652475134 0.695336307 0.047829461 0.286979609 2.533583649 0.013543236 0.162118792 51055.81262 -4.708045193 -0.269285045 GSASYS(ph)PPR ddPTM_MDA-MB-175_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;GSASYS(1)PPR 134.84 0.0012537 0 3041150 2850890 1887020 2085900 2873880 2980660 2536800 2839260 2814100 TRUE FALSE 2639254.322 2832162.316 2799589.184 2559535.476 2816695.411 3095327.919 2290781.526 2232106.344 2481420.304 1.063606322 1.141347281 1.128220471 1.031480025 1.135114195 1.247401705 0.923173524 0.899527718 1 21.24273469 2.213529149 24.98471346 0.931542349 1.121712363 0.665735137 0.061196354 126.7497748 126512.0601 0.024987385 0.016854455 163.5042889 -2.213529149 0.190170014 GSAVHQLSEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GSAVHQLSEELR 12 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;; 168.61 4.61E-05 6435350000 5790950 6026120 3036600 4190600 5903700 7055600 5396630 5780040 5730740 FALSE TRUE 5025661.285 5986534.021 4505109.917 5142139.779 5786227.92 7327033.498 4873265.653 4544023.426 5053258.446 0.99453874 1.184687877 0.891525728 1.017588915 1.145048879 1.449962153 0.964380846 0.899226405 1 22.26878254 2.030815435 24.99953637 0.939230928 1.112635452 0.204551638 0.148022114 294.8222364 239178.2949 0.062460577 0.042110486 107.3533089 -2.030815435 0.173404524 GSCFHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 109.7 0.068236 1653570000 2026160 1945470 753670 1232740 1495190 1920630 1500240 1787440 2185770 FALSE TRUE 1758397.822 1932690.079 1118147.333 1512652.458 1465438.644 1994517.879 1354746.956 1405209.866 1927370.761 0.912329822 1.002759884 0.580141276 0.78482692 0.760330433 1.034838714 0.702898987 0.729081241 1 20.87820269 GSCLESGGHSNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSCLESGGHSNDR 13 0 A0A096LP25;Q6ZSR9 A0A096LP25 AAK1 Uncharacterized protein FLJ45252 0 136.3 7.40E-05 185780000 117390 121390 59007 85478 116740 145050 117170 116970 99060 FALSE TRUE 101876.6141 120592.5811 87542.98257 104887.0863 114417.1024 150630.1674 105806.8714 91956.87576 87349.23965 1.166313691 1.380579632 1.002218026 1.20077847 1.30988092 1.724458827 1.211308443 1.052749585 1 16.41450752 1.770516449 3.857034353 1.021673232 1.29556625 0.260218575 0.18468447 0.28779894 8.557283056 0.123809376 0.051866826 58.95443053 -1.770516449 0.273893018 GSDALS(ph)ET(ph)SSVSHIEDLEK ddPTM_MDA-MB-175_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 GSDALS(0.927)ET(0.536)S(0.294)S(0.241)VS(0.003)HIEDLEK 169.06 2.64E-11 166200000 267190 274640 178630 243410 326990 259520 336730 419030 388050 TRUE FALSE 231880.1645 272835.8718 265016.0655 298679.9608 320483.5387 269503.9023 304073.9764 329423.6954 342175.1711 0.67766508 0.797357304 0.774504078 0.87288613 0.936606644 0.78761969 0.888650031 0.962734071 1 18.38437555 6.863299671 0.128103425 1.138877872 1.61E-16 0.718024057 0.052068435 80.30833074 1.255014289 1.786756252 16.33234532 7299610.234 -6.863299671 -1.138877872 GSDALS(ph)ETSSVSHIEDLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSDALSETSSVSHIEDLEK 19 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 GSDALS(0.999)ETSSVSHIEDLEK 269.11 3.25E-32 438930000 324870 320750 172520 291720 380990 318390 386600 519920 407840 TRUE FALSE 281937.6064 318642.9721 255951.249 357959.4847 373409.0444 330638.6693 349107.5915 408739.154 359625.6198 0.783975309 0.886040801 0.711715837 0.995367029 1.038327149 0.91939687 0.970752839 1.136568508 1 18.45613628 3.64325595 6.315259044 1.019825244 0.803898772 0.684772693 0.068935552 0.139177349 7.677902635 0.019897201 0.029698409 4398.007346 -3.64325595 -0.215926472 GSDALSET(ph)SSVSHIEDLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSDALSETSSVSHIEDLEK 19 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 GSDALS(0.143)ET(0.553)S(0.283)S(0.021)VSHIEDLEK 303.45 4.40E-49 112410000 54986 52045 39245 53666 81152 65195 66371 84984 64046 TRUE FALSE 47719.46078 51703.11297 58224.01327 65851.68553 79537.23397 67703.09384 59934.35064 66810.83295 56474.55484 0.844972765 0.915511651 1.030977817 1.166041693 1.408372925 1.198824746 1.061262914 1.183025402 1 15.78531337 4.072041514 2.227236801 1.174489884 0.864934221 0.564844109 0.105576858 0.237784948 2.331217899 0.030807953 0.085099375 11804.33467 -4.072041514 -0.309555664 GSDALSETS(ph)SVSHIEDLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSDALSETSSVSHIEDLEK 19 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 GSDALS(0.001)ET(0.125)S(0.528)S(0.347)VSHIEDLEK 256.53 3.73E-31 242090000 378630 367890 278240 285730 411120 342730 445550 524330 526860 TRUE FALSE 328593.0862 365473.3064 412797.7947 350609.3636 402939.5163 355915.0449 402340.6296 412206.1098 464575.211 0.707297932 0.786682754 0.888548904 0.754688058 0.867328921 0.766108558 0.866039815 0.8872753 1 18.82555265 -1.903384979 0.56631665 10 0.79085 0.608968848 0.053004572 88.62840031 0.908143045 989.7293641 0.027576286 0.012491512 1.903384979 -9.209149999 GSDALSETSS(ph)VSHIEDLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSDALSETSSVSHIEDLEK 19 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 GSDALSETS(0.01)S(0.99)VSHIEDLEK;GSDALSET(0.001)S(0.105)S(0.894)VSHIEDLEK;GSDALSET(0.001)S(0.114)S(0.884)VSHIEDLEK;GS(0.002)DALS(0.236)ET(0.236)S(0.236)S(0.261)VS(0.03)HIEDLEK 340.04 6.67E-76 859562000 903401 880273 638959 726546 1000217 841133 998629 1202646 1291364 TRUE FALSE 784014.2689 874490.4287 947961.7096 891519.3739 980314.6386 873491.9308 901782.1133 945469.5119 1138700.419 0.688516712 0.767972343 0.832494389 0.782927062 0.860906541 0.767095468 0.79193974 0.830305756 1 20.11895681 1.16960631 2.234638883 1.089449866 0.787922195 0.692039625 0.044900899 0.475368048 2.076789706 0.309645479 0.011954851 14.77768177 -1.16960631 -0.301527671 GSDALSETSSVSHIEDLEK ddPTM_MDA-MB-175_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 0 ; 268.55 7.40E-32 402800000 643360 562070 288880 475790 593050 562730 662260 770910 760700 FALSE TRUE 558338.3459 558377.7252 428583.3342 583825.3915 581249.4653 584378.5872 598034.1271 606056.8957 670770.9126 0.832383062 0.832441769 0.638941442 0.870379709 0.866539461 0.871204425 0.891562404 0.903522923 1 19.3554606 0.307319617 0.330664382 1.328049375 0.769124747 0.508806441 0.063134769 15.47289523 0.964271024 3.87517256 0.120701406 2.029175533 -0.307319617 -0.558924629 GSDEPPVFLEIHYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSDEPPVFLEIHYK 14 0 P28838-2;P28838;H0Y9Q1 P28838-2 LAP3 Cytosol aminopeptidase 0 ;;; 186.56 1.05E-06 1256200000 1910690 1776620 1215640 1403510 1578070 1481260 1735590 2116590 1947440 FALSE TRUE 1658187.475 1764949.266 1803527.57 1722198.397 1546669.494 1538245.031 1567272.749 1663973.7 1717215.862 0.965625529 1.027796974 1.050262585 1.002901519 0.900684375 0.895778489 0.912682432 0.968995067 1 20.71163997 3.359118082 6.329940621 0.936331829 1.017454241 0.507463885 0.037269328 0.183559704 9.451208426 0.011634168 0.015047568 2286.220327 -3.359118082 0.081122412 GSDFDCELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 GSDFDCELR 9 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;; 210.26 1.65E-05 28456520000 17951190 16789510 10735740 11672280 15150740 15993560 14363220 16482240 14982650 FALSE TRUE 15578894.76 16679218.6 15927579.77 14322649.57 14849269.92 16608842.6 12970277.14 12957641.24 13211418.19 1.179199276 1.2624851 1.205591977 1.084111439 1.123972439 1.257158192 0.981747527 0.98079109 1 23.65528201 2.225497521 24.99265449 0.985872204 1.182441643 0.751621096 0.053609586 115.8752471 221693.706 0.023106431 0.015684648 168.0728332 -2.225497521 0.196569439 GSDHSASLEPGELAELVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GSDHSASLEPGELAELVR 18 0 Q9NR45;Q5TBR0;Q5TBR1 Q9NR45 NANS Sialic acid synthase 0 ;;;;; 256.45 1.36E-30 15953410000 5920710 6879130 2543170 4395320 6992050 7597170 6062410 7036740 6818810 FALSE TRUE 5138273.172 6833940.542 3773055.518 5393344.584 6852921.885 7889438.046 5474478.411 5531987.911 6012698.05 0.854570299 1.136584689 0.627514551 0.896992422 1.139741565 1.312129427 0.910486169 0.920050843 1 22.51958108 3.353153029 7.92506227 1.040900978 0.877040957 0.218881847 0.165604495 0.437137796 28.60967465 0.050207104 0.064839259 2255.03366 -3.353153029 -0.163860021 GSDIDNPTLTVMDIS(ph)PPSRS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSDIDNPTLTVMDISPPSRSPR 22 1 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 2 GSDIDNPTLTVMDIS(0.941)PPS(0.211)RS(0.847)PR 64.767 0.013495 40937000 48334 43928 31371 28709 40727 46054 35919 47457 37211 TRUE FALSE 41946.53944 43639.43408 46542.12053 35227.81724 39916.61238 47825.72718 32435.58091 37308.68986 32811.95797 1.278391843 1.329985675 1.418449962 1.073627403 1.216526378 1.457570049 0.988529271 1.137045521 1 15.00193407 0.838688209 0.447384998 0.637916871 1.318719149 0.368649378 0.130001229 8.817709352 1.131649787 3.451123367 0.123815418 6.897444405 -0.838688209 0.680802278 GSDIDNPTLTVMDISPPSRS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSDIDNPTLTVMDISPPSRSPR 22 1 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 1 GSDIDNPTLTVMDISPPS(0.067)RS(0.932)PR;GSDIDNPTLTVMDISPPS(0.029)RS(0.971)PR 175.76 6.76E-13 187257000 121740 157369 81139 97043 145186 143856 108434 155731 84297 TRUE FALSE 105651.7506 156335.2327 120378.0918 119078.0964 142297.0827 149390.2334 97918.08737 122429.1375 74331.50469 1.421358965 2.103216305 1.619476052 1.601986894 1.914357623 2.009783524 1.317316093 1.647069275 1 16.18168619 0.837151408 1.087644993 6.43E-13 1.760448462 0.453170425 0.245044143 3.44195156 1.808880819 8.688707255 0.074229422 6.873080143 -0.837151408 1.760448462 GSDRT(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSDRTPER 8 1 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 GSDRT(1)PER;GSDRT(1)PER 107.06 0.0065907 767900000 1016250 933520 612820 671040 578720 945870 920610 995170 919960 TRUE FALSE 881949.9877 927387.6457 909181.8018 823409.8882 567204.6042 982258.231 831329.3839 782360.6399 811203.3768 1.087211928 1.143224587 1.120781579 1.015047412 0.699213811 1.21086556 1.024810063 0.964444506 1 19.62970413 3.684853089 5.132233429 0.982228032 1.119989203 0.203353919 0.123357231 0.325219003 19.04237041 0.033763248 0.051678392 4840.086123 -3.684853089 0.137761171 GSDS(ph)DSEGDNPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GSDSDSEGDNPEK 13 0 I3L4J1;Q9UN37 I3L4J1 VPS4A Vacuolar protein sorting-associated protein 4A 1 GSDS(1)DSEGDNPEK;GSDS(1)DSEGDNPEK;GSDS(1)DSEGDNPEK 404.41 3.04E-126 783520000 2623590 2190730 1835840 2016500 1843320 1949260 2553670 2941570 3526340 TRUE FALSE 2276875.934 2176338.95 2723658.365 2474377.145 1806641.538 2024249.294 2306015.476 2312538.147 3109460.102 0.732241566 0.699908948 0.875926455 0.795757805 0.581014542 0.650997031 0.74161282 0.743710506 1 21.56823268 1.22652376 4.093050864 1.032770687 0.725701671 0.545993367 0.078185502 0.215306959 6.418048932 0.200970975 0.021145698 16.84704592 -1.22652376 -0.307069016 GSDS(ph)DSEGDNPEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GSDSDSEGDNPEKK 14 1 I3L4J1;Q9UN37 I3L4J1 VPS4A Vacuolar protein sorting-associated protein 4A 1 GS(0.115)DS(0.882)DS(0.002)EGDNPEKK;GSDS(1)DSEGDNPEKK;GS(0.001)DS(0.999)DS(0.001)EGDNPEKK 228.9 9.10E-13 1972910000 1777390 1352310 1350300 1357410 1067660 943040 1803430 2001350 2036480 TRUE FALSE 1542503.408 1343426.587 2003309.596 1665630.687 1046415.655 979319.359 1628533.636 1573376.877 1795729.654 0.858984204 0.748122961 1.115596433 0.927550917 0.582724494 0.545360131 0.906892434 0.87617692 1 20.77613874 5.111680896 17.49003323 0.836364521 2.890909952 0.001380884 0.175253656 2902.124829 486337.5373 0.043787205 16638.28547 129324.5263 -5.111680896 2.054545431 GSEEDPLLS(ph)PVETWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSEEDPLLSPVETWK 15 0 Q13017-2;Q13017;H0YK04;A0A0A0MSK6 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 1 GSEEDPLLS(0.998)PVET(0.002)WK;GSEEDPLLS(0.998)PVET(0.002)WK;GSEEDPLLS(0.987)PVET(0.013)WK;GSEEDPLLS(1)PVETWK 171.76 1.12E-06 85995000 218907 211951 190597 243386 248255 254448 320479 325715 456065 TRUE FALSE 189977.8853 210558.6799 282770.3467 298650.5112 243315.2112 264236.7792 289398.9959 256063.382 402149.5153 0.472406103 0.523583075 0.703147302 0.742635512 0.605036689 0.657061041 0.719630349 0.636736766 1 18.61737246 -2 0.063657255 2.035766782 1.72E-08 0.499475473 0.101051203 719.3172635 4.42316872 145.1833679 33.90844139 0.01 2 -2.035766765 TPSS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.367)S(0.633)PSK;T(0.006)PS(0.283)S(0.711)PSK 143.21 0.0025562 861280000 2559570 2180180 2199700 2913270 1732420 2224090 3099030 3608500 8299300 TRUE FALSE 2221316.339 2165858.254 3263482.278 3574772.48 1697948.231 2309652.181 2798486.548 2836850.356 7318166.209 0.303534557 0.295956418 0.445942629 0.488479269 0.232018266 0.315605319 0.382402704 0.387644975 1 22.80305075 1.233165272 4.770811393 1.050106421 0.355398494 0.881072891 0.074394902 0.064399395 3.399050106 0.151219176 0.019371563 17.10666192 -1.233165272 -0.694707927 GSEEDS(ph)PKKESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 174.59 1.56E-05 3241030000 5167455 3426247 3459550 2740641 2198518 1796163 5254238 5978860 2503828 TRUE FALSE 4484562.729 3403739.758 5132599.952 3362945.427 2154771.793 1865262.553 4744682.807 4700327.317 2207828.306 2.031209907 1.541668683 2.32472785 1.523191553 0.975968913 0.844840402 2.149027075 2.128936975 1 21.07419655 3.542182548 22.0441842 1.508463912 1.923537163 0.199868649 0.482604226 134.6548894 45622.24603 0.147089207 0.218167886 3484.83763 -3.542182548 0.415073251 GSEGLYMVNGPPHFTESTVFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSEGLYMVNGPPHFTESTVFPR 22 0 F8WAE5;Q9BY44-4;Q9BY44-3;Q9BY44;H7C5Q3;C9IZE1;F8WF18;F8WAT3 F8WAE5 EIF2A "Eukaryotic translation initiation factor 2A;Eukaryotic translation initiation factor 2A, N-terminally processed" 0 192.18 1.16E-17 102950000 44095 48098 22672 31519 41665 46293 33627 43154 42375 FALSE TRUE 38267.73403 47782.04107 33636.25503 38675.87069 40835.94802 48073.92167 30365.85872 33925.85292 37365.47577 1.024146842 1.278775128 0.900196086 1.03506967 1.092879113 1.286586633 0.812671539 0.907946499 1 15.18941827 2.219379339 24.99999841 0.90317135 1.098176439 0.363378735 0.122197637 261.1311185 340343.8005 0.049035451 0.033117244 165.7216845 -2.219379339 0.195005089 GSEHTVNFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSEHTVNFK 9 0 P35219 P35219 CA8 Carbonic anhydrase-related protein 0 ; 110.87 0.0022166 634100000 852260 911190 436050 729310 896380 831470 961000 1099700 1197540 FALSE TRUE 739631.6816 905204.3329 646925.2385 894910.9823 878543.7917 863457.1889 867802.3679 864537.7129 1055968.185 0.700429892 0.857226899 0.612637054 0.847479114 0.831979414 0.817692428 0.821807304 0.818715682 1 20.01013494 -1.122275096 0.772834211 10 0.773624156 0.456059206 0.074329684 90.25940213 1.624848477 1381.510048 0.02757364 0.075461408 1.122275096 -9.226375844 GSELETAMETLINVFHAHSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSELETAMETLINVFHAHSGK 21 0 P23297;Q5T7Y5;Q5T7Y4 P23297 S100A1 Protein S100-A1 0 231.42 3.19E-26 48978000 163680 182720 104410 124630 150270 141200 190930 182760 161090 FALSE TRUE 142049.2733 181519.7003 154903.0252 152929.1464 147279.921 146632.0554 172413.638 143678.1962 142046.1237 1.000022173 1.27789267 1.09051216 1.076616118 1.036845759 1.032284807 1.213786293 1.011489736 1 17.11599994 4.015016533 24.99787086 1.065335781 1.150268671 0.110073753 0.088253993 440.2551158 732877.6969 0.021211487 0.044126442 10351.81575 -4.015016533 0.08493289 GSEPEEEAPVREDESEVDGDCSLTGPPALVGS(ph)YGTSPEGIGGYIHSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSEPEEEAPVREDESEVDGDCSLTGPPALVGSYGTSPEGIGGYIHSHR 48 1 Q8TBX8;Q8TBX8-3;Q8TBX8-2 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 1 GSEPEEEAPVREDESEVDGDCSLTGPPALVGS(0.235)Y(0.215)GT(0.235)S(0.235)PEGIGGY(0.038)IHS(0.041)HR;GSEPEEEAPVREDESEVDGDCSLTGPPALVGS(0.228)Y(0.214)GT(0.228)S(0.228)PEGIGGY(0.05)IHS(0.053)HR 73.535 0.00018819 133084000 11328.2 10523.6 8109.4 9292.3 12427.9 10047.1 9344.8 12021.9 19928.5 TRUE FALSE 9831.149668 10454.46978 12031.13296 11402.25874 12180.6091 10433.61844 8438.542734 9451.11024 17572.57543 0.559459807 0.594930995 0.684653938 0.648866683 0.693160155 0.59374441 0.480210927 0.537832959 1 14.10103803 1.233368556 24.99920565 1.000000626 0.597531291 0.789128932 0.065123042 84.91845813 408826.5148 0.150128976 0.018215269 17.11467103 -1.233368556 -0.402469335 GSES(ph)PNSFLDQESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSESPNSFLDQESR 14 0 Q5T4Y8;A0A5H1ZRR2;G9CGD6-3;G9CGD6;G9CGD6-2;Q6P9H4 Q5T4Y8 CNKSR3 Connector enhancer of kinase suppressor of ras 3 1 GSES(1)PNSFLDQESR;GSES(1)PNSFLDQESR 260.08 2.00E-24 283590000 443970 401250 248110 282580 378830 397310 360470 395420 395940 TRUE FALSE 385298.2396 398614.1623 368096.8259 346744.108 371292.0242 412594.7728 325511.6749 310862.5102 349132.4243 1.103587673 1.141727707 1.054318649 0.993159282 1.063470472 1.181771569 0.932344441 0.890385678 1 18.41341482 2.211672378 24.54359345 0.93002706 1.084853715 0.59940893 0.057008003 119.0165615 108637.2909 0.024089562 0.016246433 162.8067392 -2.211672378 0.154826655 GSET(ph)PGATPGSK ddPTM_MDA-MB-175_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;GSET(1)PGATPGSK;GSET(1)PGATPGSK 269.57 2.17E-21 5313970000 11928050 10226210 7355680 8622330 9062510 8830970 10689300 12893040 13982190 TRUE FALSE 10351727.97 10159033.35 10912911.45 10580161.81 8882183.782 9170703.13 9652653.331 10135963.73 12329231.43 0.839608538 0.823979452 0.885125039 0.858136363 0.720416665 0.743817908 0.782907952 0.82210832 1 23.55557953 1.239552295 4.738839465 1.014088592 0.807159063 0.59427715 0.049599019 0.145796093 7.53666503 0.10056905 0.013762933 17.36010292 -1.239552295 -0.20692953 GSFAGIEDDADEALEISQAQLLFENRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSFAGIEDDADEALEISQAQLLFENRR 27 1 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 0 122.73 0.00014185 22639000 38462 37926 15966 17359 31614 35755 27973 40885 11219 FALSE TRUE 33379.14925 37676.86161 23687.211 21300.62627 30984.94325 37130.51799 25260.18277 32142.06092 9892.702601 3.374118337 3.808550922 2.394412524 2.153165533 3.132100954 3.753323989 2.553415764 3.249067744 1 13.27214899 4.242168498 24.99990917 2.703494374 3.591334825 0.22421812 0.745406157 145.0312676 1004915.931 0.184029044 0.44870576 17464.9963 -4.242168498 0.88784045 GSFLDKIS(ph)PSVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSFLDKISPSVLR 13 1 Q9BW04;Q9BW04-2 Q9BW04 SARG Specifically androgen-regulated gene protein 1 GS(0.002)FLDKIS(0.976)PS(0.022)VLR;GSFLDKIS(0.934)PS(0.066)VLR 78.249 0.014379 563320000 1063380 938100 624550 717570 921760 925270 1022010 1074030 934050 TRUE FALSE 922851.6387 931937.5593 926584.469 880505.2359 903418.7794 960865.7356 922895.6275 844357.0426 823627.6731 1.12047187 1.131503457 1.125004051 1.069057372 1.096877641 1.166626337 1.120525278 1.025168374 1 19.65163278 1.670683523 3.938465658 1.006016336 1.118649275 0.76119204 0.024833307 0.085031527 3.068484758 0.019114521 0.006980053 46.84718749 -1.670683523 0.112632939 GSFMLGLETHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSFMLGLETHDR 12 0 Q92905 Q92905 COPS5 COP9 signalosome complex subunit 5 0 ; 122.39 0.00035932 272977000 279288 240906 239920 215085 221486 258161 238031 247823 245137 FALSE TRUE 242379.3832 239323.4726 355946.1145 263923.3366 217078.8619 268092.6207 214946.7903 194827.98 216157.1831 1.121310796 1.10717335 1.646700375 1.220978793 1.004263929 1.240266999 0.994400404 0.901325495 1 17.72172125 2.468806432 1.002268767 0.925037805 1.270763392 0.336118584 0.169809756 0.653824264 1.370288715 0.156471814 0.08050658 294.3109577 -2.468806432 0.345725587 GSFS(ph)DTGLGDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GSFSDTGLGDGK 12 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 GSFS(0.994)DT(0.006)GLGDGK;GSFS(0.922)DT(0.078)GLGDGK;GSFS(0.997)DT(0.003)GLGDGK;GSFS(0.999)DT(0.001)GLGDGK;GSFS(0.981)DT(0.019)GLGDGK;GSFS(0.993)DT(0.007)GLGDGK;GSFS(0.998)DT(0.002)GLGDGK 327.29 4.86E-58 4387570000 15456810 13779860 9232970 11440020 13280300 10523350 14721330 18214990 16019650 TRUE FALSE 13414153.4 13689339.19 13698065.17 14037651.39 13016048.01 10928190.08 13293657.68 14319856.14 14125825.23 0.949619097 0.969100139 0.969717872 0.993757969 0.921436292 0.773631976 0.941088925 1.013735899 1 23.75183182 1.77704687 5.769491018 1.006297919 0.929767427 0.216997021 0.059867142 0.294514819 22.17991831 0.036574258 0.017193862 59.84761808 -1.77704687 -0.076530492 GSFS(ph)SENYWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSFSSENYWR 10 0 Q6P6C2-3;Q6P6C2;Q6P6C2-1;K7ER58 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 GS(0.057)FS(0.942)S(0.001)ENYWR 208.03 1.27E-07 221140000 137000 132460 162970 219290 184190 199770 161690 190460 452930 TRUE FALSE 118895.1029 131589.8615 241782.8371 269083.1461 180524.9794 207455.2812 146009.3287 149731.6112 399385.1314 0.297695366 0.329481123 0.605387677 0.673743525 0.452007261 0.519436666 0.365585289 0.374905322 1 18.6074211 -2 0.064313034 1.522111612 4.24E-05 0.187686287 0.189088643 1787.752439 11.09907889 271.5548055 62.49456338 0.01 2 -1.522069219 GSFSEQGINEFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSFSEQGINEFLR 13 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;; 277.1 6.85E-32 961430000 976550 877350 646390 669740 748530 1064060 692955 719280 747990 FALSE TRUE 847496.4432 871586.6301 958986.366 821814.7033 733635.7175 1104995.077 625752.3308 565467.5694 659563.4743 1.28493538 1.32145982 1.453971306 1.245997899 1.11230495 1.675343041 0.948737089 0.857336089 1 19.33115198 2.108526914 9.815647242 0.914029586 1.336788645 0.629685356 0.149289436 0.174395555 14.60149462 0.057903638 0.039021268 128.3887331 -2.108526914 0.422759058 GSFSQADVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSFSQADVHR 10 0 Q04206;Q04206-4;Q04206-2;A0A087X0W8;E9PKH5;Q2TAM5;Q04206-3 Q04206 RELA Transcription factor p65 0 ;;; 168.29 4.98E-06 1353510000 952540 931690 664320 704300 915870 981620 859100 928560 1041590 FALSE TRUE 826659.4256 925569.667 985587.374 864222.0796 897645.9789 1019383.557 775784.6142 729994.6701 918454.4168 0.90005493 1.007746982 1.073093401 0.940952609 0.977344071 1.1098902 0.844663165 0.79480773 1 19.8088486 2.211037163 24.99650831 0.860646872 1.001199282 0.339534608 0.078502556 206.0560042 187136.3925 0.031326118 0.021125404 162.5687861 -2.211037163 0.14055241 GSGDGEMGKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSGDGEMGKPR 11 1 O60547 O60547 GMDS "GDP-mannose 4,6 dehydratase" 0 ; 86.243 0.01333 258430000 602550 482920 338190 382160 413260 412040 529300 594910 543860 FALSE TRUE 522921.4908 479747.6667 501739.8152 468935.2689 405036.9345 427891.4454 477968.5675 467693.1261 479565.4904 1.09040684 1.000379878 1.046238366 0.97783364 0.844591495 0.8922482 0.996670063 0.975243497 1 18.87136832 3.613821415 4.380860002 0.944999827 1.040718356 0.454683549 0.051475831 0.241947055 7.497604358 0.015666133 0.023724222 4109.806881 -3.613821415 0.095718529 GSGEKPVSAPGDDT(ph)ESLHS(ph)QGEEEFDMPQPPHGHVLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSGEKPVSAPGDDTESLHSQGEEEFDMPQPPHGHVLHR 38 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 GSGEKPVSAPGDDT(0.776)ES(0.224)LHS(1)QGEEEFDMPQPPHGHVLHR 157.76 4.97E-15 97586000 77251 70553 41797 45550 81161 64853 74046 85114 59077 TRUE FALSE 67042.08462 70089.5327 62010.169 55892.82369 79546.05489 67347.93688 66865.03032 66913.03346 52092.98436 1.28696955 1.345469713 1.190374669 1.072943399 1.527001301 1.292840825 1.283570737 1.284492226 1 15.66880147 1.238533969 10.23979671 0.998969748 1.285433363 0.383972203 0.113631118 0.078068559 195.1586575 0.154621876 0.02746665 17.31944491 -1.238533969 0.286463615 GSGEKPVSAPGDDTES(ph)LHS(ph)QGEEEFDMPQPPHGHVLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GSGEKPVSAPGDDTESLHSQGEEEFDMPQPPHGHVLHR 38 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 GSGEKPVSAPGDDT(0.123)ES(0.877)LHS(1)QGEEEFDMPQPPHGHVLHR;GSGEKPVSAPGDDT(0.156)ES(0.845)LHS(0.999)QGEEEFDMPQPPHGHVLHR;GS(0.001)GEKPVS(0.004)APGDDT(0.198)ES(0.798)LHS(1)QGEEEFDMPQPPHGHVLHR 134.62 2.54E-09 1194910000 299908 262678 186491 185152 255399 232266 277719 321335 223468 TRUE FALSE 260274.3979 260952.4509 276678.6714 227193.5915 250317.0596 241201.4233 250785.8541 252620.0109 197049.8676 1.320855482 1.324296505 1.404104833 1.152975103 1.270323409 1.224062854 1.272702475 1.282010559 1 17.58820125 1.238318089 24.98479738 0.999999687 1.280057078 0.646715696 0.065359957 3.758041203 386344.8468 0.090645343 0.016055541 17.31083787 -1.238318089 0.280057391 GSGEKPVSAPGDDTES(ph)LHSQGEEEFDMPQPPHGHVLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSGEKPVSAPGDDTESLHSQGEEEFDMPQPPHGHVLHR 38 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 GS(0.001)GEKPVS(0.006)APGDDT(0.185)ES(0.587)LHS(0.22)QGEEEFDMPQPPHGHVLHR 106.19 6.19E-06 245200000 313820 267390 130950 230620 273480 227280 267930 349140 187910 TRUE FALSE 272347.8919 265633.4975 194277.858 282985.7958 268038.2831 236023.6087 241946.1898 274479.128 165695.4939 1.643665048 1.603142556 1.172499345 1.707866576 1.617655838 1.424441928 1.460185695 1.656527414 1 17.33817484 1.230362638 24.98860551 0.999999013 1.533082163 0.540083825 0.155354332 243.0160842 740687.8126 0.405921441 0.036934405 16.99662286 -1.230362638 0.53308315 GSGEQDWVNRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSGEQDWVNRPK 12 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 0 103.97 0.0019955 763820000 1191200 1055600 805770 865210 1102700 970540 1240200 1545500 1344000 FALSE TRUE 1033779.902 1048665.694 1195443.067 1061669.154 1080758.427 1007877.302 1119925.595 1215006.852 1185113.851 0.872304295 0.884864938 1.008715801 0.895837268 0.911944811 0.85044766 0.944994098 1.025223738 1 20.17659423 1.905989924 4.276463593 1.010938153 0.907152065 0.526297119 0.041997318 0.178472623 5.441705198 0.023332524 0.011539679 80.53597559 -1.905989924 -0.103786088 GSGPQRPHS(ph)FSEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSGPQRPHSFSEALR 15 1 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 GSGPQRPHS(0.975)FS(0.025)EALR;GSGPQRPHS(0.992)FS(0.008)EALR 178.43 4.30E-07 776630000 469060 462050 303520 367160 479050 560830 522270 470500 514260 TRUE FALSE 407072.5326 459014.7631 450303.2872 450529.2897 469517.8422 582405.493 471620.3358 369887.2364 453464.7686 0.897693847 1.012239086 0.993028165 0.993526556 1.035400928 1.284345628 1.040037437 0.815691233 1 18.79063094 1.76233068 25 0.898829271 1.041821444 0.199037373 0.106651508 18.81307085 19804.68165 0.058530439 0.028108779 57.8536388 -1.76233068 0.142992173 GSGS(ph)PTHSLSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GSGSPTHSLSQK 12 0 I3L2R2;I3L419;I3L156;Q9BSJ6-2;Q9BSJ6 I3L2R2 FAM64A Protein FAM64A 1 GS(0.005)GS(0.995)PTHSLSQK;GS(0.001)GS(0.999)PTHSLSQK;GSGS(0.993)PT(0.007)HSLSQK 240.18 3.54E-16 497370000 1204730 920230 541580 733100 885120 842210 1000710 1154220 1070320 TRUE FALSE 1045521.878 914184.9485 803489.8995 899561.5597 867507.8437 874610.3637 903661.2982 907399.0352 943787.9889 1.107793159 0.968633803 0.851345757 0.953139445 0.919176609 0.926702156 0.957483364 0.96144372 1 19.84810329 4.70955345 4.118268936 0.939393658 1.1176725 0.654821352 0.038251583 0.124342987 4.454389424 0.009521773 0.061678226 51233.43216 -4.70955345 0.178278843 GSGSSKPT(ph)GS(ph)SRGPRMAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSGSSKPTGSSRGPRMAK 18 3 Q96GE6-4;Q96GE6 Q96GE6-4 CALML4 Calmodulin-like protein 4 2 GS(0.035)GS(0.172)S(0.172)KPT(0.54)GS(0.54)S(0.54)RGPRMAK 41.871 0.087067 242890000 577560 516000 232600 305320 449210 528020 385480 477440 201200 TRUE FALSE 501233.9826 512610.362 345086.138 374647.5725 440271.5999 548333.2711 348096.2089 375343.1714 177414.3652 2.825216448 2.889339662 1.945085662 2.111709343 2.481600627 3.09069263 1.962051993 2.115630101 1 17.4367633 1.096738839 1.375342766 8.12E-16 2.497906909 0.601248344 0.380766745 1.362976905 1.732508884 5.267281988 0.115896137 12.49507419 -1.096738839 2.497906909 GSGTAEVELKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSGTAEVELKK 11 1 P14618;P14618-3;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 134.08 0.00023795 3159660000 6531870 4292250 3815620 4204270 3816690 3305200 5980120 6278170 4914190 FALSE TRUE 5668666.83 4264053.927 5660866.594 5158913.762 3740745.336 3432353.183 5400168.883 4935632.202 4333240.056 1.308182043 0.984033626 1.30638195 1.190544187 0.863267506 0.792098554 1.246219645 1.139016565 1 22.04701473 3.370595599 23.21841497 1.031105927 1.189920704 0.26363322 0.154243763 10.04413709 2151.326031 0.046958707 0.060623429 2347.445935 -3.370595599 0.158814777 GSGTAS(ph)DDEFENLR ddPTM_MDA-MB-175_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 366.96 5.53E-97 14617770000 7318190 6024250 4365240 4503490 6152890 6571930 5781340 6643450 6382860 TRUE FALSE 6351072.65 5984676.305 6476284.665 5526076.236 6030459.527 6824756.4 5220666.537 5222799.917 5628285.562 1.128420472 1.063321368 1.150667391 0.98184006 1.071455856 1.212581758 0.927576698 0.927955744 1 22.4242641 2.210723131 24.9998486 0.945856154 1.095097549 0.552233502 0.063230649 156.0042459 140100.6839 0.025300989 0.017062114 162.4512774 -2.210723131 0.149241395 GSIDEVDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSIDEVDKR 9 1 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ;;; 126.07 0.0007759 3470920000 3663410 3139260 2382830 2830710 2815550 2526540 3698650 3989050 3670660 FALSE TRUE 3179281.087 3118637.994 3535174.558 3473465.97 2759526.064 2623737.629 3339955.492 3136022.7 3236718.756 0.982254353 0.963518374 1.092209371 1.073144203 0.852568997 0.8106165 1.031895492 0.968889464 1 21.62610058 3.255688135 24.999591 0.938629715 1.027793326 0.286184801 0.074226026 375.5068395 548092.4421 0.023233408 0.029917535 1801.723468 -3.255688135 0.089163611 GSKPS(ph)PLSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSKPSPLSVK 10 1 Q96S94;Q96S94-3;A0A0A0MSF3 Q96S94 CCNL2 Cyclin-L2 1 GS(0.001)KPS(0.999)PLS(0.001)VK;GS(0.001)KPS(0.999)PLSVK 84.297 0.0090946 3308700000 7077100 5119300 3958400 4612600 4431400 3521400 6558400 7272700 6398100 TRUE FALSE 6141843.304 5085670.981 5872695.48 5659961.329 4343223.81 3656870.537 5922367.377 5717489.701 5641723.907 1.088646557 0.901439182 1.040939893 1.003232597 0.769839836 0.648183179 1.049744276 1.013429547 1 22.42770463 7.999979036 0.988009094 0.92607383 139.0284375 0.125141202 0.12952014 3975.002694 5.739082106 0.04361587 1242334.451 99995172.89 -7.999979036 138.1023636 GSKS(ph)PLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSKSPLKR 8 2 K7EMM8;Q49A26-4;Q49A26-2;Q49A26-3;Q49A26;K7EPU6 K7EMM8 GLYR1 Putative oxidoreductase GLYR1 1 GS(0.079)KS(0.921)PLKR 93.096 0.0059021 476910000 1096300 782100 572330 733700 657800 669750 913310 1129800 776080 TRUE FALSE 951421.1773 776962.3336 849110.7023 900297.7989 644711.067 695515.7159 824737.3368 888201.0621 684332.7065 1.390290378 1.135357592 1.240786381 1.315584935 0.942101789 1.01634148 1.20517013 1.297908245 1 19.38433837 7.999997209 0.912366215 1.145770921 124.3430798 0.263492039 0.127278594 1656.01124 3.408310711 0.043578077 425075.9472 99999357.46 -7.999997209 123.1973089 GSKS(ph)PSPRPNMPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSKSPSPRPNMPVR 14 2 Q9H6S0 Q9H6S0 YTHDC2 Probable ATP-dependent RNA helicase YTHDC2 1 GS(0.449)KS(0.536)PS(0.015)PRPNMPVR 110.12 0.00037981 257950000 329700 328240 239470 243970 343750 326410 378290 421680 288760 TRUE FALSE 286129.3096 326083.7698 355278.493 299367.1173 336910.0475 338967.2039 341603.494 331507.0135 254623.1218 1.123736555 1.280652627 1.395311198 1.175726365 1.323171459 1.33125068 1.341604375 1.301951729 1 17.95800391 1.237173001 24.99323504 0.999999646 1.290364436 0.55408497 0.07994628 25.99472546 468031.5386 0.11431005 0.018795909 17.26525514 -1.237173001 0.29036479 GSLAEAVGS(ph)PPPAATPTPTPPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSLAEAVGSPPPAATPTPTPPTR 23 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 GSLAEAVGS(1)PPPAATPTPTPPTR 253.53 1.78E-43 271000000 217140 220190 164540 198250 234170 271760 237320 276540 273430 TRUE FALSE 188444.3988 218743.5574 244112.0944 243265.6926 229510.4751 282214.7831 214304.7429 217404.073 241105.4169 0.781585089 0.90725277 1.012470385 1.00895988 0.951909244 1.170503702 0.888842506 0.901697174 1 17.87930454 4.610193986 2.729714819 0.982663701 0.768838015 0.427640765 0.077388458 0.363915659 4.245497422 0.020544448 0.151006225 40756.22825 -4.610193986 -0.213825686 GSLAEAVGSPPPAAT(ph)PTPTPPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSLAEAVGSPPPAATPTPTPPTR 23 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 GSLAEAVGSPPPAAT(1)PTPTPPTR 324.43 5.21E-73 191920000 128990 143350 120200 104270 148410 196320 122250 133900 187860 TRUE FALSE 111943.6447 142408.3244 178329.122 127946.0972 145456.9314 203872.5574 110394.2138 105266.527 165651.4048 0.67577842 0.85968679 1.076532507 0.7723816 0.878090539 1.230732439 0.666424857 0.635470174 1 17.33779091 GSLAPQDS(ph)DSEVSQNR ddPTM_MDA-MB-175_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(0.996)DS(0.004)EVSQNR;GSLAPQDS(1)DSEVSQNR;GSLAPQDS(0.896)DS(0.104)EVSQNR 390.06 2.07E-121 1227860000 945710 918880 652517 732793 878150 1075690 674614 893070 882500 TRUE FALSE 820732.0274 912843.8168 968076.4037 899184.8507 860676.5331 1117072.49 609190.0381 702093.9304 778171.8553 1.05469251 1.173061979 1.244039343 1.155509345 1.106023724 1.435508728 0.782847688 0.90223506 1 19.56972928 2.22142801 24.9999998 0.891854953 1.190233741 0.612304797 0.112400177 153.5482023 224056.7555 0.044051848 0.029781179 166.5052801 -2.22142801 0.298378788 GSLAS(ph)LDSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSLASLDSLR 10 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 1 GS(0.463)LAS(0.537)LDSLR;GSLAS(1)LDSLR 215.72 8.45E-09 2052850000 1562250 1280490 944980 1315250 1409260 1622650 1168310 1536720 1487470 TRUE FALSE 1355794.704 1272078.377 1401975.489 1613897.615 1381218.483 1685074.395 1055007.476 1208104.387 1311622.991 1.033677142 0.969850624 1.068886028 1.230458467 1.053060592 1.284724656 0.804352686 0.921075946 1 20.32292167 2.223372239 24.99999936 0.906762692 1.102010407 0.452716623 0.10268526 221.844308 365151.8679 0.042172987 0.028552658 167.2523538 -2.223372239 0.195247715 GSLAS(ph)LDSLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GSLASLDSLRK 11 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 1 GS(0.101)LAS(0.898)LDS(0.001)LRK;GSLAS(1)LDSLRK;GSLAS(1)LDSLRK;GS(0.002)LAS(0.998)LDSLRK;GS(0.32)LAS(0.68)LDSLRK 189.99 1.51E-06 6000870000 4426950 3244550 2439748 3276780 3424860 3357040 3906110 4822970 2540486 TRUE FALSE 3841917.341 3223236.337 3619618.293 4020822.981 3356711.987 3486187.501 3527296.053 3791615.398 2240152.639 1.715024804 1.438846747 1.61579092 1.794887951 1.49843003 1.556227661 1.574578442 1.69257011 1 21.09516561 1.233712877 24.99999972 0.999999074 1.608249271 0.771863727 0.104349535 69.88974966 360380.921 0.197651122 0.024736635 17.12824541 -1.233712877 0.608250197 GSLDQDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GSLDQDRR 8 1 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2;A0A2R8Y6Q7;A0A2R8Y7I7 A0A2R8Y430 GSS Glutathione synthetase 0 ;;;;; 145.17 0.00091977 3725011000 5992160 6885550 4398510 4040130 5325130 6624740 5306870 5386880 4542680 FALSE TRUE 5200280.874 6840318.369 6525644.148 4957503.266 5219170.331 6879598.035 4792210.564 4234937.633 4005649.545 1.298236607 1.707667706 1.629110104 1.237627808 1.302952311 1.717473772 1.196362914 1.057241175 1 21.93360477 2.04548204 6.421683841 1.059179316 1.479787967 0.563767768 0.169136012 0.137360153 13.83358814 0.072049203 0.047644911 111.0406615 -2.04548204 0.420608651 GSLDYRPLTTADPIDEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSLDYRPLTTADPIDEHR 18 1 O00139-1;O00139-5;O00139;O00139-4;O00139-2;D6R9M0 O00139-1 KIF2A Kinesin-like protein KIF2A 0 75.97 0.0096186 597770000 179260 167130 137670 131090 185320 187610 175210 204970 183470 FALSE TRUE 155570.3368 166032.112 204247.6725 160855.9881 181632.4946 194827.4781 158218.1612 161138.7606 161780.3856 0.961614328 1.026280852 1.262499602 0.994286096 1.122710234 1.204271317 0.97798111 0.996033975 1 17.30367718 2.187571862 24.99984526 0.991759803 1.09639884 0.226628214 0.090495375 155.3615994 76172.69498 0.03655274 0.024643889 154.0181357 -2.187571862 0.104639038 GSLEEEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSLEEEKR 8 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 69.954 0.084315 97792000 184600 171770 128920 138490 142410 143050 161810 212490 163270 FALSE TRUE 160204.6423 170641.6316 191266.1432 169936.2712 139576.3196 148553.2261 146117.6911 167050.6671 143968.4066 1.11277638 1.185271377 1.328528583 1.180371966 0.969492703 1.031846011 1.014928862 1.160328652 1 17.13539273 3.377320429 6.627652655 1.049822564 1.214077211 0.564560767 0.072251776 0.171482571 9.800369708 0.021801666 0.028208188 2384.077832 -3.377320429 0.164254647 GSLEQLSEEEMHAEICYAECLLQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSLEQLSEEEMHAEICYAECLLQK 24 0 Q5VTQ0-2;Q5VTQ0-3;Q5VTQ0-4;Q5VTQ0;Q5VTQ0-5;Q5VTQ0-6 Q5VTQ0-2 TTC39B Tetratricopeptide repeat protein 39B 0 138.43 6.66E-06 19036000 14818 15930 12024 14197 16020 15816 16043 22741 20935 FALSE TRUE 12859.76376 15825.35478 17838.84662 17420.64584 15701.23334 16424.45175 14487.15233 17878.01412 18460.08815 0.696625263 0.857274064 0.966346773 0.943692451 0.850550291 0.889727699 0.784782403 0.968468513 1 14.17212182 4.684812987 3.248947162 0.91057691 0.678456822 0.54033322 0.063017678 0.232818119 4.026248554 0.016241552 0.125367802 48396.39214 -4.684812987 -0.232120088 GSLESPATDVFGSTEEGEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSLESPATDVFGSTEEGEKR 20 1 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 112.68 0.00024049 649070000 263630 230680 183320 231780 203320 178270 244190 308800 278870 FALSE TRUE 228790.6275 229164.6479 271974.1652 284409.1915 199274.3298 185128.1623 220508.4914 242765.5231 245902.3063 0.930412695 0.931933707 1.106025272 1.156594242 0.810380077 0.752852485 0.896732099 0.987243783 1 17.90772574 3.227272378 24.99951332 0.895384284 1.029489785 0.335129004 0.099035465 303.339756 671790.521 0.033573403 0.038401109 1687.61112 -3.227272378 0.134105501 GSLLFTAGPLEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GSLLFTAGPLEEER 14 0 P53004 P53004 BLVRA Biliverdin reductase A 0 ;; 205.97 2.67E-08 257880000 379464 316205 264612 248824 287918 329296 309428 330599 347346 FALSE TRUE 329316.871 314127.8285 392579.2483 305323.2922 282188.9951 341964.2302 279419.7202 259902.9766 306283.1516 1.075204004 1.025612499 1.281752673 0.996866105 0.921333719 1.116497034 0.912292167 0.848570923 1 18.22450648 2.8392193 0.830709765 0.905731397 1.11088007 0.303121707 0.101314072 0.721913785 1.199858169 0.083999952 0.069460862 690.5884334 -2.8392193 0.205148674 GSLLPTS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GSLLPTSPR 9 0 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;Q9H0E9-3 H7C128 BRD8 Bromodomain-containing protein 8 1 GSLLPT(0.029)S(0.971)PR;GSLLPT(0.01)S(0.99)PR;GSLLPT(0.033)S(0.967)PR;GSLLPTS(1)PR;GSLLPT(0.003)S(0.997)PR 113.99 0.0017944 1164139000 2686600 2450110 1550780 1789970 2312170 2602710 1959750 2452430 2231560 TRUE FALSE 2331559.003 2434015.066 2300742.395 2196410.046 2266162.341 2702837.938 1769693.747 1927996.929 1967747.519 1.184887279 1.236954966 1.169226424 1.116205217 1.151653004 1.373569481 0.899350008 0.979798938 1 20.90811369 2.220596411 24.99999965 0.961384882 1.198705878 0.715915828 0.072876798 128.9635284 179471.5878 0.029398808 0.019866194 166.1867561 -2.220596411 0.237320996 GSLPQLVS(ph)PIVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSLPQLVSPIVSR 13 0 F5H1U9;O75970-5;O75970-3;O75970-2;O75970 F5H1U9 MPDZ Multiple PDZ domain protein 1 GSLPQLVS(1)PIVSR;GSLPQLVS(1)PIVSR;GSLPQLVS(1)PIVSR;GSLPQLVS(0.998)PIVS(0.002)R 159.34 4.62E-05 649208000 899230 807320 564674 638340 684370 858770 612610 797010 712790 TRUE FALSE 780394.4771 802016.6618 837752.2351 783284.8534 670752.3759 891807.4376 553199.1765 626575.6138 628524.7782 1.241628817 1.276030301 1.332886569 1.246227485 1.067185255 1.418889865 0.880154921 0.996898827 1 19.2616101 2.229165892 24.99999004 0.96362378 1.257767029 0.703864656 0.09312461 105.2244989 280006.7806 0.036209341 0.024782567 169.4985127 -2.229165892 0.294143249 GSLS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSLSPAR 7 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 GSLS(1)PAR 129.29 0.0038548 703000000 983820 975380 650010 718960 788410 1054500 847220 916420 933430 TRUE FALSE 853805.6943 968972.6646 964357.0102 882210.8566 772722.1835 1095067.297 765056.7348 720450.7146 823080.9688 1.037328922 1.177250722 1.171642945 1.071839698 0.93881673 1.330449055 0.929503614 0.87530965 1 19.65067483 2.053380326 24.99993606 0.920844503 1.116728954 0.405845294 0.105759632 81.32028894 38084.79533 0.041172716 0.027758634 113.0785747 -2.053380326 0.195884451 GSLS(ph)PVTKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSLSPVTKPR 10 1 F5H4N6;Q9Y3R0-3;Q9Y3R0-2;Q9Y3R0;F5H4P8;H0YFK8;F5H4Q7 F5H4N6 GRIP1 Glutamate receptor-interacting protein 1 1 GS(0.004)LS(0.996)PVTKPR;GS(0.003)LS(0.997)PVTKPR 131.49 0.00015067 1228790000 2477000 1996840 1379940 1521700 1884920 1742210 2103800 2358700 2286900 TRUE FALSE 2149658.174 1983722.627 2047283.6 1867225.243 1847413.78 1809233.946 1899773.8 1854310.36 2016545.287 1.066010363 0.983723321 1.015243056 0.925952546 0.916128089 0.8971948 0.942093298 0.919548087 1 20.94345438 4.098060242 1.353959213 0.929959932 1.047736513 0.600349992 0.033560276 0.357635076 1.141790849 0.010083361 0.042460939 12533.15014 -4.098060242 0.117776581 GSLVDNIQQHFLLSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSLVDNIQQHFLLSDR 16 0 O43427-2;O43427;E9PSD3 O43427-2 FIBP Acidic fibroblast growth factor intracellular-binding protein 0 100.77 0.0019406 330930000 96248 132080 127620 184910 167690 206950 208800 197860 409020 FALSE TRUE 83528.58294 131212.3578 189337.4589 226896.6417 164353.2971 214911.5004 188550.6081 155549.1787 360666.1216 0.231595312 0.363805608 0.524966021 0.629104394 0.455693749 0.595873822 0.522784362 0.431283033 1 18.46030439 -2 0.094675714 2.009296928 1.17E-10 0.444272088 0.150546344 405.7219534 3.572279504 108.8233607 12.7508669 0.01 2 -2.009296928 GSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVK ddPTM_MDA-MB-175_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 82.965 0.00023936 22429000 23392 21184 9152.8 18490 22288 19125 23584 26341 27197 FALSE TRUE 20300.68793 21044.84091 13579.12469 22688.4371 21844.51241 19860.75113 21296.82731 20708.18214 23981.80164 0.846503871 0.877533774 0.566226212 0.946068917 0.910878704 0.828159261 0.888041175 0.863495681 1 14.54965243 GSNEEQVNGS(ph)PLER ddPTM_MDA-MB-175_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 337.68 1.11E-68 1488490000 2010570 1999760 1472810 1527900 1888640 2202830 1876990 2060340 2148450 TRUE FALSE 1744868.08 1986623.445 2185065.842 1874833.047 1851059.759 2287574.296 1694959.799 1619752.325 1894462.689 0.921035865 1.048647438 1.153396082 0.989638412 0.977089583 1.207505595 0.894691571 0.854992993 1 20.8533573 GSNMDFREPTEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GSNMDFREPTEEER 14 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;; 220.46 4.22E-12 4249570000 8292900 8676700 3401930 3208880 7357000 7860300 7616700 8129800 687860 FALSE TRUE 7196972.253 8619702.186 5047114.727 3937505.249 7210610.094 8162690.827 6878033.606 6391305.536 606541.9744 11.86557989 14.21122123 8.321130177 6.491727555 11.88806447 13.45775094 11.33974877 10.53728481 1 19.21024796 4.23803204 24.99999759 9.439196262 13.03840101 0.177860211 3.509864625 25.47343973 1205082.85 0.900200305 2.076635982 17299.43979 -4.23803204 3.599204748 GSNYWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GSNYWR 6 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;; 118.01 0.05172 12642750000 9199700 9450800 7499130 7762920 9334600 12106600 8471900 8008600 7490600 FALSE TRUE 7983936.336 9388717.073 11125734.35 9525609.635 9148859.723 12572348.74 7650296.442 6296023.213 6605069.801 1.208758813 1.421441007 1.684423433 1.442166385 1.38512688 1.903439194 1.158246116 0.953210701 1 22.65514238 2.013591793 24.70663572 0.998002747 1.505454691 0.602398442 0.184391711 122.6207255 222894.2658 0.073712395 0.049668104 103.1791136 -2.013591793 0.507451944 GSPHSEGGKRS(ph)PEPNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GSPHSEGGKRSPEPNK 16 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 GSPHSEGGKRS(1)PEPNK;GSPHSEGGKRS(1)PEPNK;GSPHSEGGKRS(1)PEPNK;GSPHSEGGKRS(1)PEPNK;GSPHS(0.015)EGGKRS(0.984)PEPNK 149.53 4.32E-07 1172362000 1421680 1055904 531781 732605 1005228 810313 1440749 1627210 531637 TRUE FALSE 1233801.386 1048967.697 788952.0703 898954.1624 985225.9295 841486.2655 1301025.384 1279243.804 468787.4795 2.631899186 2.237618842 1.682963187 1.917615554 2.101647276 1.795027176 2.775298916 2.728835262 1 18.83857451 1.223946613 24.96119857 0.999996708 2.237618394 0.508049 0.38155699 746.8592795 1275584.938 2.265255447 0.1040566 16.74736992 -1.223946613 1.237621686 GSPQQIDHAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSPQQIDHAK 10 0 A0A087WTP3;Q92945;M0R3J3 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;;; 172.61 3.66E-06 1789710000 2991380 2477870 1655520 2072120 2186690 2044140 2640760 3002170 2802210 FALSE TRUE 2596061.554 2461592.709 2456135.009 2542626.516 2143179.147 2122779.389 2384659.502 2360179.308 2470935.926 1.050638961 0.996218754 0.994009996 1.029013537 0.867355209 0.859099326 0.965083504 0.955176249 1 21.23662617 3.262726063 24.99991093 0.931740386 1.014276638 0.488219106 0.044744689 232.0518527 240063.2492 0.013925699 0.017968504 1831.159029 -3.262726063 0.082536252 GSPSGGSTAEASDTLSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSPSGGSTAEASDTLSIR 18 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 0 65.467 0.033418 516340000 551670 794100 509470 480220 820570 1080400 495920 547380 473720 FALSE TRUE 478765.4117 788883.5048 755851.3961 589261.2907 804242.2624 1121963.687 447825.7547 430327.0467 417717.3613 1.146146788 1.888558097 1.809480443 1.410669858 1.925326398 2.685939803 1.072078387 1.030187123 1 18.67216758 2.048662301 24.99993065 1.027410477 1.807934992 0.465598048 0.392671466 94.69153853 48646.69283 0.159741876 0.107697921 111.8567769 -2.048662301 0.780524516 GSPSSYNSSSSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSPSSYNSSSSSPR 14 0 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 1 GSPSSYNSSSS(0.001)S(0.999)PR;GSPSSYNSSSS(0.001)S(0.999)PR;GSPSSYNSSSSS(1)PR;GSPSSYNSSSSS(1)PR 322.75 2.53E-56 1758960000 1683000 1528050 1091830 1300460 1633610 1790790 1534790 1786260 1804190 TRUE FALSE 1460587.286 1518012.139 1619842.64 1595749.319 1601104.357 1859682.85 1385946.302 1404282.2 1590900.714 0.918088271 0.954184083 1.018192164 1.003047711 1.006413753 1.168949661 0.871170834 0.882696316 1 20.60141237 GSPSVAASS(ph)PPAIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSPSVAASSPPAIPK 15 0 Q92610;H0YM74 Q92610 ZNF592 Zinc finger protein 592 1 GSPSVAAS(0.053)S(0.947)PPAIPK 230.69 3.08E-13 118490000 243020 241070 155160 181410 205600 185770 235620 291740 272950 TRUE FALSE 210904.2913 239486.3953 230195.895 222601.9132 201508.9622 192916.6921 212769.6087 229353.6713 240682.1619 0.876277201 0.99503176 0.956431059 0.924879149 0.837240951 0.801541296 0.884027329 0.95293174 1 17.8767697 5.063536812 14.94680826 0.916353729 0.519393302 0.040954374 0.063848327 3809918.749 21458988.26 0.017075573 45675711.39 115754.2144 -5.063536812 -0.396960427 GSPT(ph)SAYPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSPTSAYPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(0.309)PT(0.69)S(0.001)AYPER 150.06 0.00024854 3878300000 479720 444720 364230 328890 390000 484130 450160 412870 541400 TRUE FALSE 416323.7865 441798.605 540372.8463 403569.5013 382239.763 502754.7944 406503.5525 324580.9635 477396.3088 0.87207165 0.925433643 1.131916683 0.845355303 0.800675992 1.053118311 0.851501248 0.679898352 1 18.86482789 2.009519064 24.75593522 0.801669269 0.937238181 0.098331223 0.123364355 278.1822656 723456.9812 0.049596502 0.033389517 102.2160428 -2.009519064 0.135568911 GSPTDAEGS(ph)PGLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSPTDAEGSPGLSR 14 0 Q8TER5;Q8TER5-4;Q8TER5-3;G3V485;G3V3N2;G3V5C1 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 GSPTDAEGS(1)PGLSR;GSPTDAEGS(1)PGLSR 183.81 1.43E-06 955420000 1400170 1327380 905720 875290 1198330 1418150 1118520 1261490 1256140 TRUE FALSE 1215133.987 1318660.353 1343729.221 1074037.972 1174485.577 1472707.148 1010046.103 991730.1804 1107640.56 1.097047211 1.19051288 1.213145554 0.969662913 1.060349015 1.3295894 0.911889776 0.895353796 1 20.07905836 2.195489521 24.99999529 0.926337951 1.137027059 0.493946763 0.098780696 113.5349883 65898.95709 0.040370199 0.027217786 156.8518052 -2.195489521 0.210689109 GSQGGNFEGPNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSQGGNFEGPNKR 13 1 Q8WXF1 Q8WXF1 PSPC1 Paraspeckle component 1 0 ; 107.74 0.002039 231620000 299440 259329 198638 253418 264640 277138 313904 325118 424350 FALSE TRUE 259868.2453 257625.4507 294700.0012 310960.4302 259374.1818 287799.6782 283461.6384 255594.0458 374183.8264 0.694493527 0.688499696 0.78758081 0.831036534 0.69317315 0.769139813 0.757546474 0.6830708 1 18.51338768 1.231019428 24.99984912 1.000000463 0.73887432 0.736289456 0.049262058 147.248653 488103.4675 0.126815319 0.012338932 17.02234657 -1.231019428 -0.261126143 GSQQYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GSQQYR 6 0 Q13509;A0A0B4J269;Q13509-2;Q5JP53;P07437;Q5ST81;A6NNZ2;P68371;Q13885;Q3ZCM7;A0A075B736;Q5SQY0;Q9BVA1;P04350;K7ESM5;Q9BUF5 Q13509;Q5JP53;P68371;Q13885;Q3ZCM7;Q9BVA1;P04350;K7ESM5 TUBB3;TUBB;TUBB4B;TUBB2A;TUBB8;TUBB2B;TUBB4A;TUBB6 Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-8 chain-like protein LOC260334;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-8 chain;Tubulin beta-2B chain;Tubulin beta-4A chain;Tubulin beta-6 chain 0 ;;;; 127.95 0.039173 3736626000 4989050 4529693 3353614 3193353 2470847 5106757 4077523 4830040 5123270 FALSE TRUE 4329734.402 4499937.148 4975432.948 3918452.606 2421681.979 5303217.246 3682085.447 3797173.533 4517602.857 0.958414128 0.996089584 1.10134359 0.867374298 0.536054641 1.17390072 0.81505293 0.840528407 1 22.10712602 3.710171245 20.28021236 0.863857612 1.016362985 0.152503304 0.161948408 121.2569288 86620.45083 0.043193486 0.06411234 5130.636487 -3.710171245 0.152505373 GSQS(ph)PKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GSQSPKR 7 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 GS(0.006)QS(0.994)PKR;GS(0.001)QS(0.999)PKR;GS(0.001)QS(0.999)PKR;GS(0.001)QS(0.999)PKR;GS(0.001)QS(0.999)PKR 91.265 0.010125 875418000 1595660 1355598 975280 1042309 1934450 1320394 1572360 1914710 1039537 TRUE FALSE 1384789.488 1346692.987 1446928.67 1278981.189 1895958.23 1371190.412 1419872.769 1505264.167 916644.1201 1.5107166 1.469155758 1.578506465 1.395286525 2.068368943 1.495880878 1.548990211 1.642146754 1 19.8060022 1.235562238 24.98169899 0.999999189 1.591283163 0.505632063 0.182900183 68.87984182 573783.0144 0.29459302 0.043010611 17.20133834 -1.235562238 0.591283974 GSRPAS(ph)PAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSRPASPAAK 10 1 A0A590UJ53;Q9P2N6-8;Q9P2N6-6;Q9P2N6-2;Q9P2N6-5;Q9P2N6-4;Q9P2N6-3;Q9P2N6 A0A590UJ53 KANSL3 KAT8 regulatory NSL complex subunit 3 1 GS(0.023)RPAS(0.977)PAAK;GS(0.008)RPAS(0.992)PAAK 65.092 0.042395 364320000 575250 480320 369330 473580 385420 461500 653190 690180 636910 TRUE FALSE 499229.255 477164.7463 547939.2233 581113.5772 377750.8961 479254.2036 589843.7343 542590.378 561615.2254 0.888916882 0.849629292 0.975648805 1.034718346 0.672615127 0.853349735 1.050263076 0.966124766 1 19.09922252 2.245834688 24.99345227 0.999133918 0.879874815 0.280570169 0.095166783 233.7360769 803111.0813 0.03724722 0.028250283 176.1305488 -2.245834688 -0.119259103 GSRPIDTSR ddPTM_MDA-MB-175_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 ;;;;; 109.15 0.0022768 2414690000 1889200 1801960 1289070 1349370 1591740 1932370 1613120 1824990 1707730 FALSE TRUE 1639537.433 1790122.806 1912468.564 1655765.082 1560067.488 2006709.524 1456679.871 1434730.091 1505844.105 1.088782981 1.18878362 1.270030913 1.099559428 1.03600863 1.332614391 0.967351046 0.95277465 1 20.52214099 2.195872366 24.97868769 0.968832024 1.165532842 0.531180832 0.086684442 104.1658508 60951.07848 0.034431917 0.023214179 156.9901361 -2.195872366 0.196700819 GSRPPLILQSQSLPCS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSRPPLILQSQSLPCSSPR 19 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 GSRPPLILQSQSLPCS(0.585)S(0.415)PR;GSRPPLILQSQSLPCS(0.616)S(0.384)PR 158.94 2.08E-11 1232960000 260109 229215 145481 188817 211879 227496 202612 230506 184001 TRUE FALSE 225734.9366 227709.2716 215836.0982 231690.7857 207663.0224 236247.9183 182962.7194 181214.0857 162248.6114 1.391290407 1.403458986 1.330280095 1.427998574 1.279906316 1.456085918 1.127668939 1.116891443 1 17.30784661 2.152331221 5.539626448 1.083908498 1.377257202 0.856699265 0.057997022 0.068715828 3.401050793 0.022781512 0.015234815 142.0140201 -2.152331221 0.293348704 GSRPPLILQSQSLPCSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSRPPLILQSQSLPCSSPR 19 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 GSRPPLILQSQSLPCS(0.181)S(0.819)PR;GSRPPLILQSQSLPCS(0.179)S(0.821)PR 139.47 1.12E-07 590100000 279900 224538 158111 161266 262694 275984 235490 276684 251001 TRUE FALSE 242910.5058 223062.9951 234574.0084 197883.9101 257466.9034 286601.2831 212652.216 217517.2798 221327.9477 1.09751393 1.00783926 1.059848116 0.894075566 1.163282387 1.294916824 0.960801463 0.982782708 1 17.75582611 GSS(ph)FQSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GSSFQSGR 8 0 Q96KP1 Q96KP1 EXOC2 Exocyst complex component 2 1 GS(0.002)S(0.998)FQSGR;GS(0.034)S(0.966)FQSGR;GS(0.001)S(0.999)FQSGR 166.66 0.00033271 1026390000 1165990 1149440 847620 907450 838110 1249380 1113930 1203030 1297400 TRUE FALSE 1011901.467 1141889.253 1257531.867 1113500.392 821433.2507 1297444.457 1005901.24 945771.3965 1144022.85 0.884511588 0.998135005 1.099219187 0.973320063 0.718021717 1.134107118 0.879266738 0.826706736 1 20.12568444 3.461366317 24.99915507 0.903882864 1.00135603 0.093725329 0.118597537 481.5420948 764084.4648 0.033257925 0.042948271 2893.11913 -3.461366317 0.097473166 GSS(ph)GEGLPFAEEGNLTIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSSGEGLPFAEEGNLTIK 18 0 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 GS(0.022)S(0.978)GEGLPFAEEGNLTIK 290.92 3.78E-49 51231000 61080 50047 43152 58003 60494 59989 53997 81905 105190 TRUE FALSE 53008.12324 49718.23796 64020.45153 71173.46767 59290.28775 62296.81565 48760.37925 64390.25314 92754.55803 0.571488069 0.536019351 0.690213537 0.767331215 0.639216972 0.671630774 0.52569254 0.69420042 1 16.50113056 1.2562014 3.879047772 1.036035508 0.633537011 0.715812309 0.072902985 0.134870413 3.382986655 0.150885052 0.019363484 18.03854069 -1.2562014 -0.402498497 GSS(ph)LSGTDDGAQEVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSSLSGTDDGAQEVVK 16 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 GSS(0.999)LSGTDDGAQEVVK 404.11 4.49E-105 0 319070 245620 281070 316040 328640 343580 325910 416730 1042800 TRUE FALSE 276904.0911 244006.506 416996.3921 387801.7124 322100.707 356797.7449 294303.2984 327615.5325 919521.372 0.301139375 0.265362517 0.453492877 0.421743011 0.350291703 0.388025505 0.320061401 0.356289198 1 19.81052358 1.238456707 24.99871883 1.000000704 0.358208028 0.930596551 0.055180126 0.610931685 146267.2777 0.078016735 0.013932875 17.31636402 -1.238456707 -0.641792676 GSS(ph)PGPRPVEGTPASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GSSPGPRPVEGTPASR 16 1 Q13112 Q13112 CHAF1B Chromatin assembly factor 1 subunit B 1 GS(0.055)S(0.945)PGPRPVEGTPASR;GS(0.037)S(0.963)PGPRPVEGTPASR;GS(0.345)S(0.654)PGPRPVEGTPASR;GS(0.047)S(0.953)PGPRPVEGTPASR;GS(0.137)S(0.863)PGPRPVEGTPASR 120.56 6.48E-05 7699160000 6355450 6286470 3874300 4635390 5949230 6568500 5487550 6267360 5377140 TRUE FALSE 5515561.18 6245173.765 5747924.439 5687926.147 5830851.962 6821194.445 4955368.246 4927133.837 4741460.635 1.163262042 1.31714133 1.212268725 1.199614757 1.229758594 1.438627244 1.045114286 1.039159495 1 22.17690013 2.113594776 9.856420046 1.028402466 1.256254349 0.67296347 0.07630639 0.168252938 13.82299357 0.030153606 0.020321168 129.8957003 -2.113594776 0.227851883 GSS(ph)PSHSATSVHTSV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSSPSHSATSVHTSV 15 0 F8WA39;Q13613 F8WA39 MTMR1 Myotubularin-related protein 1 1 GSS(0.874)PS(0.126)HSATSVHTSV 306.66 4.42E-45 755130000 555560 717710 222560 352910 966340 1054600 705710 779920 831220 TRUE FALSE 482141.3384 712995.3158 330190.7604 433043.6094 947111.7246 1095171.144 637270.3528 613140.1773 732954.1185 0.65780562 0.972769369 0.450493083 0.590819532 1.292184191 1.494187858 0.869454631 0.836532822 1 19.48336337 3.251510209 24.99997897 1.068339031 0.674208878 0.461111914 0.229933189 255.8667533 493963.6679 0.073788942 0.094647559 1784.473936 -3.251510209 -0.394130153 GSS(ph)PTPPCS(ph)PVQPSK ddPTM_MDA-MB-175_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(0.005)S(0.959)PT(0.035)PPCS(1)PVQPSK 218.68 2.79E-12 345330000 344080 372580 281240 383550 478750 390430 561050 638590 587900 TRUE FALSE 298608.9562 370132.4974 417248.6047 470640.8897 469223.8117 405450.0947 506639.4574 502032.498 518399.1317 0.576021328 0.713991353 0.804879058 0.907873607 0.905140042 0.782119548 0.977315405 0.968428509 1 18.98370378 5.443456372 0.450281939 0.969295652 4.66E-12 0.830633881 0.054753384 4.331618622 0.447884066 0.050560592 2.53807766 277623.594 -5.443456372 -0.969295652 GSS(ph)PTPPCSPVQPSK ddPTM_MDA-MB-175_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(0.002)S(0.998)PTPPCSPVQPSK;GS(0.003)S(0.979)PT(0.019)PPCSPVQPSK;GS(0.002)S(0.997)PTPPCSPVQPSK;GSS(0.998)PT(0.002)PPCSPVQPSK 330.52 7.80E-69 1150910000 2777720 2083320 1227300 1427690 1585200 1491090 1748760 2080080 1864050 TRUE FALSE 2410637.264 2069634.534 1820826.385 1751868.835 1553657.621 1548453.197 1579165.524 1635271.079 1643684.133 1.466606154 1.259143708 1.107771468 1.065818426 0.945228825 0.942062509 0.960747563 0.994881588 1 20.64850165 4.657970557 0.913145865 0.969558384 1.701660694 0.972859275 0.02732145 0.302149279 0.21858324 0.010397092 0.215589215 45495.72155 -4.657970557 0.73210231 GSSAGFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSSAGFDR 8 0 G3V5Z7;P60900;G3V3I1;G3V295;G3V3U4;G3V4S5;G3V2S7 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ;;; 160.52 0.00082099 2025330000 1814610 1732840 1232740 1228630 1424490 1838810 1619830 1728260 1752310 FALSE TRUE 1574804.691 1721456.86 1828897.187 1507609.22 1396145.436 1909550.211 1462739.136 1358685.048 1545153.908 1.019189534 1.114100577 1.183634315 0.975701652 0.903563994 1.235831719 0.946662419 0.879320203 1 20.55931912 2.030606332 24.97787469 0.925625307 1.068981719 0.272277704 0.099576361 229.4826616 187280.2508 0.040390018 0.027230658 107.3016332 -2.030606332 0.143356411 GSSCFECTHYQSFLEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 GSSCFECTHYQSFLEYR 17 0 P21964-2;P21964 P21964-2 COMT Catechol O-methyltransferase 0 ;;;;;;;;;;; 264 1.94E-27 21052068200 4629312.1 4449503.2 2851806.6 3661779.4 4482959.4 5027197.2 4605250.9 4983205.4 5098481.2 FALSE TRUE 4017536.777 4420274.121 4230949.81 4493242.38 4393757.279 5220596.729 4158634.377 3917585.705 4495744.561 0.893631015 0.983212916 0.941101024 0.999443433 0.977314707 1.161230728 0.925015717 0.871398642 1 22.10012864 4.74208066 22.74640144 0.975664426 0.893630909 0.116622868 0.074746603 259.3450655 1675590.254 0.019496341 0.135392005 55217.99838 -4.74208066 -0.082033517 GSSDGRGS(ph)DS(ph)ESDLPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GSSDGRGSDSESDLPHR 17 1 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3;D6RJ93;D6R8Y0;Q9UPQ0-7;Q6NVB9 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 2 GSSDGRGS(0.999)DS(0.98)ES(0.02)DLPHR;GS(0.001)S(0.001)DGRGS(0.993)DS(0.881)ES(0.123)DLPHR;GSSDGRGS(0.999)DS(0.627)ES(0.373)DLPHR 123.61 3.02E-05 917850000 911840 948340 539300 618760 913490 1002010 866970 948310 929680 TRUE FALSE 791338.0337 942110.2921 800107.2839 759258.9152 895313.3362 1040557.973 782891.3828 745521.2863 819774.2895 0.965312091 1.149231324 0.976009243 0.926180444 1.092146153 1.269322527 0.955008461 0.909422625 1 19.64486722 2.038720838 24.99971285 0.943432776 1.062604324 0.202862246 0.100577154 229.9068909 148436.1331 0.042009614 0.02832282 109.3253403 -2.038720838 0.119171548 GSSDGRGS(ph)DSES(ph)DLPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSSDGRGSDSESDLPHR 17 1 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3;D6RJ93;D6R8Y0;Q9UPQ0-7;Q6NVB9 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 2 GSSDGRGS(1)DS(0.145)ES(0.855)DLPHR 133.48 1.15E-05 276740000 227320 222270 128090 149910 225270 211240 206160 245910 223920 TRUE FALSE 197279.086 220809.8937 190034.7524 183949.3567 220787.5677 219366.5395 186166.6349 193324.0602 197448.4327 0.999142325 1.118316771 0.962452575 0.931632398 1.118203699 1.11100674 0.942862055 0.979111647 1 17.59111639 2.212456893 24.99949404 0.97376094 1.038766824 0.185338468 0.065320278 405.3390619 388189.825 0.027661536 0.018655973 163.101101 -2.212456893 0.065005884 GSSDGRGS(ph)DSESDLPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GSSDGRGSDSESDLPHR 17 1 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3;D6RJ93;D6R8Y0;Q9UPQ0-7;Q6NVB9 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 GS(0.001)S(0.002)DGRGS(0.94)DS(0.055)ES(0.001)DLPHR;GS(0.001)S(0.001)DGRGS(0.992)DS(0.007)ESDLPHR;GSSDGRGS(0.998)DS(0.001)ES(0.002)DLPHR;GSSDGRGS(0.963)DS(0.037)ESDLPHR;GSSDGRGS(0.854)DS(0.142)ES(0.004)DLPHR 164.94 1.53E-09 3275730000 1859950 1809300 1095049 1370200 1783250 1879290 1828140 1897690 1604370 TRUE FALSE 1614152.895 1797414.589 1624618.359 1681324.852 1747766.814 1951587.502 1650847.264 1491883.761 1414703.206 1.140983415 1.27052415 1.148381054 1.188464722 1.235430022 1.379503131 1.166921271 1.054556005 1 20.43206799 1.743759106 3.036742639 1.015043637 1.22663112 0.588262593 0.068254329 0.154213335 2.950418605 0.051398069 0.018805763 55.43181591 -1.743759106 0.211587483 GSSERGS(ph)PIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GSSERGSPIEK 11 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 GS(0.004)S(0.02)ERGS(0.976)PIEK;GS(0.009)S(0.009)ERGS(0.981)PIEK;GS(0.001)S(0.001)ERGS(0.997)PIEK;GS(0.001)S(0.084)ERGS(0.914)PIEK;GS(0.033)S(0.033)ERGS(0.933)PIEK;GS(0.004)S(0.004)ERGS(0.992)PIEK 131.36 0.00053927 7534610000 9941910 10114320 6393130 7292150 8931280 8462010 11339900 13669800 7490510 TRUE FALSE 8628061.404 10047878.37 9484869.052 8947944.111 8753565.002 8787549 10240158.24 10746619.65 6604990.441 1.306294306 1.52125555 1.436015561 1.354724763 1.325295635 1.330440835 1.550366853 1.627045451 1 22.65512504 2.273410743 24.99335059 1.447920045 1.384516927 0 0.175752661 827.1588857 593208.1756 0.06514772 0.050460881 187.6768664 -2.273410743 -0.063403117 GSSGENNNPGS(ph)PTVSNFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSSGENNNPGSPTVSNFR 18 0 D6RD37;D6RAX8;D6RBL1;D6RDZ9;D6RCK9;Q99576-3;D6R8Z7;D6RDZ7 D6RD37 TSC22D3 1 GSSGENNNPGS(1)PTVSNFR;GSSGENNNPGS(0.983)PT(0.017)VSNFR;GSSGENNNPGS(1)PTVSNFR;GSSGENNNPGS(1)PTVSNFR 665.18 0 1959160000 1528743 1666285 1230272 1343550 1890900 2011909 1667097 1953861 1833858 TRUE FALSE 1326715.739 1655339.064 1825235.654 1648623.562 1853274.789 2089308.441 1505422.19 1536043.03 1617061.396 0.820448588 1.023671128 1.12873615 1.019518224 1.146075711 1.292040269 0.930961677 0.94989778 1 20.62494303 4.720290253 3.901587865 1.059154246 0.801774803 0.34448188 0.105524279 0.296645574 9.129069337 0.02850448 0.211107099 52515.83234 -4.720290253 -0.257379443 GSSGENNNPGSPT(ph)VSNFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSSGENNNPGSPTVSNFR 18 0 D6RD37;D6RAX8;D6RBL1;D6RDZ9;D6RCK9;Q99576-3;D6R8Z7;D6RDZ7 D6RD37 TSC22D3 1 GSSGENNNPGS(0.005)PT(0.995)VSNFR 460.43 3.90E-213 710770000 788090 923110 692370 786500 1119400 1104500 950480 1156100 1058300 TRUE FALSE 683941.9097 917046.0296 1027202.448 965086.8459 1097126.13 1146990.83 858302.5959 908877.0118 933188.9796 0.732908258 0.982701307 1.100744298 1.034181572 1.175674117 1.229108846 0.919752177 0.973947434 1 19.83180974 4.707111122 2.955067019 1.055334373 0.690495803 0.557651903 0.091665521 0.30103291 3.980223726 0.025500487 0.250718546 50946.12092 -4.707111122 -0.36483857 GSSGGSGAKPSDAASEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSSGGSGAKPSDAASEAAR 19 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C044 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 105.38 0.00059381 31607000 104426 87873 86592 97584 88107 84175 96098 105252 221820 FALSE TRUE 90625.83952 87295.75648 128468.1808 119741.9387 86353.84308 87413.26672 86778.43075 82744.67887 195596.6923 0.463330123 0.446304871 0.656801397 0.612187953 0.441489281 0.446905649 0.443660011 0.423037209 1 17.57752245 1.233911015 24.99922593 1.000000767 0.490777625 0.803391316 0.079020767 67.86551168 364842.7798 0.166723598 0.021224723 17.13606161 -1.233911015 -0.509223142 GSSGGSGAKPSDAASEAARPATSTLNR ddPTM_MDA-MB-175_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 ;;; 196.22 3.59E-25 1893060000 944540 756518 471606 543229 741935 643498 840705 904037 536853 FALSE TRUE 819716.6458 751548.3834 699676.239 666577.4472 727171.9451 668253.7845 759173.5585 710715.7228 473386.8499 1.73159995 1.587598776 1.478022127 1.408103008 1.53610508 1.411644165 1.603706479 1.501342344 1 18.8526601 1.239810662 5.652538882 0.976763227 1.528522831 0.756700823 0.09496564 0.07150516 7.553320083 0.153086917 0.023770024 17.37043369 -1.239810662 0.551759604 GSSGPQPAKPCSGATPTPLLLVGDRS(ph)PVPSPGS(ph)SSPQLQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSSGPQPAKPCSGATPTPLLLVGDRSPVPSPGSSSPQLQVK 41 2 Q8N3F8 Q8N3F8 MICALL1 MICAL-like protein 1 2 GSSGPQPAKPCSGATPTPLLLVGDRS(1)PVPS(0.186)PGS(0.468)S(0.323)S(0.024)PQLQVK 183.66 7.56E-28 223570000 122190 89027 74202 80563 88016 69026 100330 115320 108480 TRUE FALSE 106042.2819 88442.17578 110086.3354 98856.06048 86264.6538 71681.47489 90600.01204 90659.71542 95655.61798 1.10858394 0.924589456 1.150861159 1.033457967 0.901825273 0.749370255 0.947147841 0.94777199 1 16.54556208 3.276040139 5.682215701 0.908714226 1.053681416 0.415874201 0.0856849 0.194294833 15.90017821 0.025492927 0.032339142 1888.165852 -3.276040139 0.14496719 GSSGPTQINQVVSHPNQPLTITAHDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSSGPTQINQVVSHPNQPLTITAHDDR 27 0 F5GYK2;Q9NRL3;Q9NRL3-3;M0R317 F5GYK2 STRN4 Striatin-4 0 285.36 1.11E-61 805920000 112020 135100 91091 102120 116840 131410 128270 132580 134220 FALSE TRUE 97216.27318 134212.5192 135142.9123 125307.9068 114515.1126 136465.4277 115830.3951 104228.7987 118352.6645 0.821411783 1.13400505 1.141866242 1.058767095 0.967575281 1.153040604 0.978688529 0.880662883 1 16.85273266 2.007750063 24.79833201 0.931167851 1.05266422 0.161483698 0.101484771 228.4244136 730899.7791 0.03977887 0.026761091 101.8005357 -2.007750063 0.121496368 GSSGS(ph)PAHAESYSSGGGGQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSSGSPAHAESYSSGGGGQQK 21 0 P15408 P15408 FOSL2 Fos-related antigen 2 1 GS(0.005)S(0.027)GS(0.968)PAHAESYSSGGGGQQK 313.7 8.32E-67 310050000 311600 282290 145890 234340 296110 256840 334100 409260 328880 TRUE FALSE 270421.2705 280435.6184 216442.892 287550.4787 290217.9903 266720.801 301699.0334 321742.9339 290000.1811 0.932486557 0.96701877 0.746354334 0.991552756 1.000751066 0.919726326 1.040340845 1.1094577 1 18.14569428 2.556092665 0.90903938 1.072650475 0.90125349 0.361566017 0.07562003 0.630468902 1.130498628 0.071121192 0.039802939 359.8261026 -2.556092665 -0.171396985 GSSPS(ph)HSATSVHTSV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GSSPSHSATSVHTSV 15 0 F8WA39;Q13613 F8WA39 MTMR1 Myotubularin-related protein 1 1 GSS(0.075)PS(0.925)HSATSVHTSV;GSS(0.005)PS(0.995)HSATSVHTSV;GSS(0.005)PS(0.989)HS(0.006)ATSVHTSV 242.94 6.26E-18 1492990000 955400 1278300 349067 577920 1668810 1736750 1154090 1226100 1235670 TRUE FALSE 829141.4693 1269902.763 517876.9688 709145.569 1635603.946 1803563.896 1042166.529 963908.0565 1089590.5 0.760966133 1.165486266 0.475295048 0.650836777 1.501118031 1.65526764 0.956475418 0.884651671 1 20.0553546 3.259989752 24.99975488 1.16470752 0.771323789 0.354074296 0.290662773 336.6006227 392684.035 0.093068031 0.120035991 1819.65792 -3.259989752 -0.393383731 GSSPSIRPIQGSQGSSS(ph)PVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSSPSIRPIQGSQGSSSPVEK 21 1 Q92560;F8W6N3;H0Y8E8 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 GSSPSIRPIQGSQGS(0.018)S(0.102)S(0.879)PVEK 153.24 2.73E-08 264150000 180390 153330 118840 151310 146300 136860 146120 203450 203840 TRUE FALSE 156551.0044 152322.7651 176311.4215 185667.2481 143388.9162 142125.0928 131949.3049 159943.8007 179742.2674 0.870974906 0.847451005 0.980912414 1.032963759 0.797747343 0.790716034 0.734102817 0.889850802 1 17.45557018 3.2100209 24.9999743 0.837687409 0.930376552 0.212428171 0.086333294 352.0279935 308365.3992 0.027909626 0.031652108 1621.888148 -3.2100209 0.092689142 GSSPT(ph)PPCS(ph)PVQPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GSSPTPPCSPVQPSK 15 0 E7EPX0;E7EVJ4;Q9NUL3-4;Q9NUL3-6;Q9NUL3-8;Q9NUL3-3;Q9NUL3-7;Q9NUL3-2;Q9NUL3;H0YBY0 E7EPX0 STAU2 Double-stranded RNA-binding protein Staufen homolog 2 2 GS(0.002)S(0.19)PT(0.814)PPCS(0.993)PVQPSK;GSSPT(1)PPCS(1)PVQPSK;GS(0.024)S(0.206)PT(0.77)PPCS(1)PVQPSK 268.08 7.98E-25 625870000 648050 666440 477130 622820 754340 683560 902820 1101110 938360 TRUE FALSE 562408.5506 662062.1118 707871.6639 764240.8002 739330.1098 709856.9955 815264.6554 865646.1953 827428.1498 0.679706813 0.800144535 0.855508317 0.923634034 0.893527867 0.857907718 0.985299637 1.04618896 1 19.65827451 6.357163282 0.20683809 1.099654444 3.39E-17 0.838366163 0.042616003 21.33327477 0.609500911 0.335935824 6.643989189 2275952.959 -6.357163282 -1.099654444 GSSSQGPSQTST(ph)PTDVTAIHL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSSSQGPSQTSTPTDVTAIHL 21 0 Q5T8J1;P30281-4;P30281-2;P30281-3;P30281 Q5T8J1 CCND3 G1/S-specific cyclin-D3 1 GSSSQGPS(0.054)QT(0.21)S(0.138)T(0.536)PT(0.062)DVTAIHL 112.56 0.0024798 49196000 52030 52977 51897 57339 67826 95809 92925 90927 83438 TRUE FALSE 45154.10367 52628.9906 76994.56279 70358.69632 66476.3953 99494.83423 83913.1478 71482.96864 73574.05469 0.613723192 0.71531997 1.046490684 0.95629766 0.903530403 1.3523087 1.140526347 0.971578486 1 16.16690948 4.493816244 1.108898897 1.071738537 0.463444571 0.614526615 0.127288609 0.805066903 1.112024972 0.042115895 0.521775534 31175.70216 -4.493816244 -0.608293966 GSSSS(ph)SPEHSASSDSTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSSSSSPEHSASSDSTK 17 0 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 GS(0.096)S(0.096)S(0.079)S(0.364)S(0.364)PEHSASSDSTK;GS(0.089)S(0.089)S(0.089)S(0.366)S(0.366)PEHSASSDSTK 96.562 0.0012272 168650000 535980 463050 246320 379960 429000 440960 478560 593650 513360 TRUE FALSE 465148.885 460008.1941 365441.1759 466235.7253 420463.7393 457924.0165 432149.3249 466702.5673 452671.1656 1.027564644 1.016208296 0.807299434 1.029965593 0.928850281 1.011604121 0.954665014 1.030996897 1 18.78810389 2.004971893 1.176080578 1.018102566 0.961596846 0.060678604 0.067096487 1.621642862 3.94098579 0.084820612 0.023307885 101.1513987 -2.004971893 -0.056505721 GSSWHETCFICHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSSWHETCFICHR 13 0 Q14192 Q14192 FHL2 Four and a half LIM domains protein 2 0 109.84 0.00063916 127240000 79470 81144 40792 52912 103280 91411 92433 84842 74701 FALSE TRUE 68967.83815 80610.95972 60519.14764 64926.47831 101224.9301 94927.64032 83468.86189 66699.19854 65869.93288 1.047030643 1.223789917 0.91876741 0.985677007 1.536739536 1.441137651 1.267176969 1.012589441 1 16.00733246 4.756921261 21.50023636 1.171006064 1.047029916 0.03665157 0.20305367 2559.07101 2996313.185 0.053839742 1.345163883 57137.50348 -4.756921261 -0.123976148 RRYS(ph)DFEWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRYSDFEWLR 10 2 O60493-4;O60493;O60493-3 O60493-4 SNX3 Sorting nexin-3 1 RRYS(1)DFEWLR 94.09 0.0065691 192930000 62808 60416 40106 40717 62224 65518 62691 72653 28766 TRUE FALSE 54507.76366 60019.12332 59501.39575 49962.41717 60985.86414 68038.51986 56611.23647 57116.72134 25365.31625 2.148909287 2.366188646 2.3457778 1.969713946 2.404301351 2.682344631 2.231836414 2.251764605 1 14.63056953 1.233385963 4.919331105 0.906222252 2.309645524 0.833547233 0.182705004 0.072945843 4.33496771 0.354440004 0.046524894 17.11535704 -1.233385963 1.403423272 GSTDDKGPVAGWINALEAYQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSTDDKGPVAGWINALEAYQK 21 1 Q96KP4;J3QKT2;J3QRH4;A0A087WYZ1;J3KSV5;A0A087WVS2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 129.32 3.50E-06 0 300420 220730 178010 209140 202920 186420 299650 328500 255880 FALSE TRUE 260718.7358 219280.0101 264096.2314 256628.4335 198882.289 193591.698 270589.9891 258252.8314 225630.1579 1.155513688 0.971855944 1.170482855 1.137385338 0.881452599 0.858004532 1.199263395 1.144584721 1 17.78360039 GSTDNLMDDIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSTDNLMDDIER 12 0 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 277.28 1.60E-27 1562130000 1321580 1225870 801480 955450 1145010 1227760 1146720 1230950 1162710 FALSE TRUE 1146929.855 1217817.179 1189078.409 1172399.526 1122226.541 1274992.722 1035511.271 967720.9218 1025255.748 1.118676834 1.187817948 1.159787117 1.143519095 1.094582052 1.243585051 1.010002892 0.943882464 1 19.9675524 2.096203161 6.22154962 0.97063017 1.155382844 0.794394056 0.041845065 0.078182076 4.22905512 0.016209213 0.010829916 124.7967172 -2.096203161 0.184752674 GSTDS(ph)LDSLSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSTDSLDSLSSR 12 0 Q9ULJ8;Q9ULJ8-4;Q9ULJ8-5;Q9ULJ8-3 Q9ULJ8 PPP1R9A Neurabin-1 1 GSTDS(1)LDSLSSR;GST(0.001)DS(0.999)LDSLSSR 271.6 1.07E-27 639340000 609800 546690 384660 499190 596030 623950 526130 632730 576690 TRUE FALSE 529213.385 543098.7574 570682.8626 612538.7191 584170.1691 647953.7602 475105.9936 497425.6134 508514.3652 1.040704887 1.068010649 1.122255145 1.204565222 1.148778106 1.274209353 0.93430201 0.978193828 1 18.955929 2.216521887 24.99522196 0.970843533 1.141780903 0.598477179 0.066505859 168.3968964 190985.8843 0.028451892 0.019199808 164.6348935 -2.216521887 0.170937371 GSTIETEQKEDKGEDSEPVTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSTIETEQKEDKGEDSEPVTSK 22 2 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 ; 131.37 6.87E-06 328330000 406770 274490 316010 262400 223600 151194 409100 463440 290950 FALSE TRUE 353014.3139 272686.8571 468833.493 321981.9305 219150.7975 157010.531 369425.545 364336.9625 256554.2225 1.375983254 1.062881969 1.827424583 1.255024873 0.8542085 0.611997454 1.43995114 1.420116804 1 17.96890424 3.478447201 24.97251302 1.109557768 1.412016741 0.218824933 0.302973466 92.6802562 1745538.472 0.093890545 0.122918795 3009.173311 -3.478447201 0.302458972 GSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNK 40 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 161.3 1.03E-18 600250000 324340 243826 191971 238659 253981 266319 334011 370830 283389 FALSE TRUE 281477.6472 242224.291 284808.8177 292850.1736 248927.275 276564.4643 301618.6646 291530.8903 249887.0753 1.126419391 0.969335011 1.139750095 1.171930054 0.996159064 1.106757778 1.207019868 1.166650536 1 17.93091676 2.473704165 24.93190272 1.139637511 1.07973564 0.0489722 0.080431462 233.7526485 1705475.094 0.029497516 0.022978113 297.64882 -2.473704165 -0.059901871 GSTTATFAAVVLYVENER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSTTATFAAVVLYVENER 18 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 131.53 8.75E-06 0 23797 19129 16069 17924 17261 23391 23721 20687 28560 FALSE TRUE 20652.16616 19003.34034 23840.02215 21993.91815 16917.53987 24290.86691 21420.54107 16263.24604 25183.66934 0.820061838 0.754589813 0.946646092 0.873340491 0.67176628 0.964548358 0.850572678 0.645785402 1 14.62020088 GSVDHENWVSNYNALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSVDHENWVSNYNALR 16 0 Q8WVQ1-3;Q8WVQ1 Q8WVQ1-3 CANT1 Soluble calcium-activated nucleotidase 1 0 142.39 1.51E-06 309080000 248430 234630 153530 235640 291700 263440 225650 325550 244720 FALSE TRUE 215599.3461 233088.7001 227777.6215 289145.6635 285895.7407 273574.7073 203766.4977 255933.6659 215789.4804 0.99911889 1.080167113 1.055554799 1.339943277 1.32488266 1.267785189 0.944283741 1.186034025 1 17.71926501 7.324675647 9.785452459 1.140087578 0.043877875 0 0.141845524 0 0 0.032751684 0 21119111.69 -7.324675647 -1.096209703 GSVFLESDS(ph)SPPSSSDAGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSVFLESDSSPPSSSDAGLR 20 0 Q8TBP0 Q8TBP0 TBC1D16 TBC1 domain family member 16 1 GSVFLES(0.003)DS(0.498)S(0.498)PPSSSDAGLR;GSVFLES(0.003)DS(0.685)S(0.312)PPSSSDAGLR 239.58 1.19E-29 243230000 369210 363900 324200 345290 363740 407890 359970 409260 580230 TRUE FALSE 320417.963 361509.5169 480984.2044 423693.3719 356502.2856 423581.7922 325060.1648 321742.9339 511635.8704 0.626261726 0.706575785 0.940090858 0.828115065 0.696789077 0.827896981 0.635334979 0.628851401 1 18.96475789 2.267731735 24.98480891 0.723529322 0.774943565 0 0.132904179 905.4182549 775480.1914 0.050077569 0.038783459 185.2387046 -2.267731735 0.051414243 GSVHS(ph)LDAGLLLPSGDPFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSVHSLDAGLLLPSGDPFSK 20 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 GS(0.205)VHS(0.795)LDAGLLLPSGDPFSK 86.573 0.0016014 97116000 230040 177110 59733 112660 162610 122070 157400 190890 171650 TRUE FALSE 199639.6312 175946.5527 88620.07859 138241.1749 159374.3791 126766.1119 142135.3722 150069.659 151357.7325 1.318991952 1.162454998 0.585500834 0.913340684 1.052964896 0.837526499 0.939069117 0.991489873 1 17.20760286 4.464048478 24.99853041 0.913293025 1.279857848 0.558052187 0.128463247 138.7783785 265380.3705 0.031839107 0.084339178 29110.42046 -4.464048478 0.366564823 GSVILDSGHLSTASS(ph)SDDLKGEEGSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSVILDSGHLSTASSSDDLKGEEGSFR 27 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 GSVILDSGHLSTAS(0.226)S(0.681)S(0.092)DDLKGEEGSFR 190.23 3.82E-18 614240000 243150 252580 65867 197280 308340 274580 312140 338050 305610 TRUE FALSE 211017.1114 250920.7853 97720.50151 242075.4392 302204.6373 285143.2703 281868.7108 265760.6382 269481.134 0.783049664 0.93112561 0.362624649 0.898301991 1.121431519 1.058119602 1.045968253 0.986193855 1 18.03982475 3.48362316 24.71827423 1.033974121 0.701870994 0.552071948 0.143777835 188.1276039 715205.0583 0.0396365 0.053145456 3045.251461 -3.48362316 -0.332103127 GSVPLSS(ph)SPPATHFPDETEITNPVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GSVPLSSSPPATHFPDETEITNPVPK 26 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 GS(0.001)VPLS(0.014)S(0.689)S(0.296)PPATHFPDETEITNPVPK;GS(0.002)VPLS(0.107)S(0.459)S(0.396)PPAT(0.036)HFPDETEITNPVPK;GSVPLS(0.069)S(0.533)S(0.398)PPATHFPDETEITNPVPK 245.2 1.65E-45 6635120000 1103310 939560 781750 1095760 963800 857780 945220 1286710 1355800 TRUE FALSE 957504.7881 933387.9685 1159806.915 1344569.056 944622.2656 890779.3517 853552.7099 1011557.08 1195518.869 0.800911481 0.780738801 0.97012849 1.124674057 0.790135807 0.74509853 0.713960049 0.846123893 1 20.18920547 GSVPLSSS(ph)PPATHFPDETEITNPVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSVPLSSSPPATHFPDETEITNPVPK 26 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 GSVPLS(0.001)S(0.034)S(0.966)PPATHFPDETEITNPVPK;GS(0.002)VPLS(0.015)S(0.112)S(0.871)PPAT(0.001)HFPDETEITNPVPK 267.24 1.77E-53 6088170000 1080420 864490 723890 1077070 974180 784880 948990 1260520 1269430 TRUE FALSE 937639.7596 858811.1083 1073965.625 1321635.205 954795.724 815074.8415 856957.0959 990967.6074 1119359.432 0.837657443 0.767234441 0.959446622 1.180706722 0.852984034 0.728161856 0.765578126 0.885298841 1 20.09424194 3.029726033 24.99969666 0.83777063 0.937219163 0.109735215 0.126662602 478.2983013 402247.5018 0.041207823 0.046724707 1070.84357 -3.029726033 0.099448533 GSVS(ph)QPSTPSPPKPTGIFQTSANSSFEPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSVSQPSTPSPPKPTGIFQTSANSSFEPVK 30 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 GSVS(0.926)QPS(0.035)T(0.035)PS(0.003)PPKPTGIFQTSANSSFEPVK 215.92 1.08E-34 522390000 296620 321980 227700 314290 406590 253730 434040 586500 455200 TRUE FALSE 257420.9155 319864.8922 337816.4816 385654.3481 398499.6545 263491.1573 391946.8676 461081.5391 401386.7746 0.641328842 0.796899431 0.841623349 0.960804821 0.992807137 0.656452016 0.976481769 1.148721304 1 18.61463356 4.652744456 0.102369828 1.512785723 7.69E-14 0.435187836 0.120007514 85.3974485 2.634343533 13.02026531 27.92351268 44951.52766 -4.652744456 -1.512785723 GSWATHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GSWATHK 7 0 P53582;H0YAI3 P53582 METAP1 Methionine aminopeptidase 1 0 83.614 0.02215 252890000 559370 574040 375030 383470 488070 531750 546370 551060 582990 FALSE TRUE 485447.8372 570269.0934 556395.7624 470542.7245 478358.3619 552206.7666 493383.1215 433220.1074 514069.5863 0.944323201 1.109322762 1.082335499 0.915328852 0.930532314 1.074186805 0.959759407 0.842726586 1 18.97160414 2.78018166 0.549311935 0.90715546 1.044001645 0.116848046 0.078912113 1.757353362 1.532617553 0.149324689 0.107754341 602.8116825 -2.78018166 0.136846185 GSWS(ph)SAPTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSWSSAPTSR 10 0 H7BXC7;Q9H7P9-3;Q9H7P9 H7BXC7 PLEKHG2 Pleckstrin homology domain-containing family G member 2 1 GSWS(0.5)S(0.5)APTSR;GSWS(0.5)S(0.5)APTSR 121.36 0.0005424 236740000 528030 507450 307340 291970 361620 425150 349680 393530 405390 TRUE FALSE 458249.4976 504116.5275 455970.652 358266.251 354424.4695 441505.7956 315768.0874 309376.672 357465.256 1.281941363 1.410253218 1.27556635 1.002240763 0.991493477 1.235101281 0.883353227 0.865473404 1 18.4474435 3.743255408 0.68887105 0.928925266 1.432338024 0.630074465 0.113148242 0.709448101 0.62516333 0.072249332 0.24367687 5536.756288 -3.743255408 0.503412758 GSYGS(ph)DAEEEEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 GS(0.001)YGS(0.999)DAEEEEYR;GSYGS(1)DAEEEEYR;GSYGS(1)DAEEEEYR;GSYGS(1)DAEEEEYR;GS(0.001)YGS(0.999)DAEEEEYR;GSYGS(1)DAEEEEYR;GSYGS(1)DAEEEEYR;GSYGS(1)DAEEEEYR 400.71 2.15E-109 16244617000 5539544 5243145 4432733 4974906 5074568 5628800 4881399 5441224 9105440 TRUE FALSE 4807479.225 5208702.435 6576417.505 6104534.444 4973594.025 5845343.578 4408001.676 4277660.591 8029005.256 0.59876399 0.648735711 0.819082476 0.760310182 0.619453328 0.728028366 0.549009689 0.532775911 1 22.93678983 3.231387221 24.99033043 0.658564237 0.710606805 0 0.141943833 765.1980621 2665756.669 0.043002186 0.049754257 1703.676846 -3.231387221 0.052042569 GSYGS(ph)DAEEEEYRQQLSEHSK ddPTM_MDA-MB-175_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(0.008)YGS(0.992)DAEEEEYRQQLSEHSK;GS(0.004)YGS(0.996)DAEEEEYRQQLSEHSK;GS(0.002)YGS(0.998)DAEEEEYRQQLSEHSK;GSYGS(1)DAEEEEYRQQLSEHSK;GS(0.007)YGS(0.993)DAEEEEYRQQLSEHSK;GS(0.005)YGS(0.995)DAEEEEYRQQLSEHSK;GS(0.002)YGS(0.998)DAEEEEYRQQLSEHSK;GS(0.022)YGS(0.978)DAEEEEYRQQLSEHSK 269.28 8.51E-38 13920150000 5774000 5231510 2118230 3320700 5111840 4747940 5933410 6381740 1875325 TRUE FALSE 5010951.271 5197143.866 3142613.113 4074715.689 5010124.385 4930596.324 5357988.811 5017054.564 1653626.215 3.030280498 3.142877042 1.900437405 2.464109272 3.029780455 2.981687324 3.24014506 3.033971353 1 20.65720173 3.273473881 24.99227861 2.764180232 2.61831645 0 0.708168468 1505.687368 1077820.197 0.205489863 0.265275342 1877.041529 -3.273473881 -0.145863782 GSYSLSHVYTPNDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GSYSLSHVYTPNDVR 15 0 P07686;Q5URX0 P07686 HEXB Beta-hexosaminidase subunit beta;Beta-hexosaminidase subunit beta chain B;Beta-hexosaminidase subunit beta chain A 0 ;;; 157.38 1.96E-06 1716060000 2216810 2167090 1196330 1646510 2313700 2786290 1837300 2362120 2141150 FALSE TRUE 1923852.942 2152854.243 1774879.189 2020375.261 2267661.897 2893480.379 1659118.929 1856999.02 1888025.686 1.018976042 1.140267454 0.940071527 1.070099457 1.201075766 1.53254291 0.878758664 0.983566608 1 20.84844696 GSYVSIHSSGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 199.43 1.72E-07 3678040000 2768360 3414830 1636290 1838950 4670310 5209400 2839620 3360390 3509110 FALSE TRUE 2402514.212 3392397.757 2427605.317 2256511.704 4577379.968 5409808.989 2564234.089 2641796.749 3094267.013 0.776440495 1.096349391 0.784549396 0.729255651 1.479309946 1.748332954 0.828704853 0.853771422 1 21.56116627 3.270638863 24.999877 1.142809346 0.860048828 0.239227534 0.292142741 388.3705633 302670.4012 0.094830981 0.12241599 1864.828352 -3.270638863 -0.282760518 GT(ph)PDTDLEVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTPDTDLEVQR 11 0 P0C7T5 P0C7T5 ATXN1L Ataxin-1-like 1 GT(0.997)PDT(0.003)DLEVQR 134.18 0.0033612 0 157270 122780 68760 88710 136640 132030 129010 120260 88215 TRUE FALSE 136486.371 121973.4501 102012.566 108852.9613 133921.1313 137109.2795 116498.6301 94543.33486 77786.32319 1.75463199 1.568057791 1.311446046 1.399384325 1.72165396 1.762639933 1.49767498 1.215423624 1 16.24722889 1.612129609 2.452816469 1.01539745 1.574196991 0.652884166 0.146464112 0.183488584 2.363451002 0.178001653 0.043926932 40.93828157 -1.612129609 0.55879954 GT(ph)PPPVFTPPLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTPPPVFTPPLPK 13 0 Q6NZY4;Q6NZY4-2 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 GT(1)PPPVFTPPLPK;GT(1)PPPVFTPPLPK 129.71 0.001683 116084000 375820 250880 163475 217629 253930 209743 294480 331710 306400 TRUE FALSE 326154.4348 249231.9528 242532.0568 267044.9907 248877.2898 217811.9489 265921.3749 260776.3979 270177.7411 1.207184698 0.922474042 0.897675937 0.988404854 0.921161339 0.806180213 0.984246052 0.965203117 1 18.0435493 4.740340174 24.7677438 0.936213617 1.207184802 0.69505446 0.05651875 82.50394458 1148179.131 0.014064731 0.088343746 54997.14864 -4.740340174 0.270971185 GT(ph)PS(ph)QSPVVGR ddPTM_MDA-MB-175_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 2 GT(1)PS(0.858)QS(0.142)PVVGR 89.301 0.065441 35328000 64442 49479 39134 42801 52075 52739 46450 49126 82942 TRUE FALSE 55925.82642 49153.96919 58059.3333 52519.62122 51038.80938 54767.90346 41945.28615 38620.7872 73136.69125 0.76467537 0.672083579 0.793846868 0.718102232 0.697855051 0.748843057 0.573519056 0.52806309 1 16.15830774 2.300931962 24.99996178 0.659300916 0.730368583 0 0.129447696 197.9444536 79339.17966 0.047469272 0.036769524 199.9548587 -2.300931962 0.071067668 GT(ph)PSQS(ph)PVVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GTPSQSPVVGR 11 0 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 2 GT(0.998)PS(0.005)QS(0.997)PVVGR;GT(0.999)PS(0.001)QS(1)PVVGR;GT(0.999)PS(0.001)QS(0.999)PVVGR;GT(0.996)PS(0.004)QS(1)PVVGR;GT(1)PS(0.008)QS(0.992)PVVGR;GT(0.991)PS(0.038)QS(0.971)PVVGR;GT(1)PSQS(1)PVVGR 305.67 1.25E-35 8100370000 5421310 4673600 3788951 3857330 3960970 4351770 3867330 4029140 7296320 TRUE FALSE 4704870.148 4642898.814 5621300.377 4733195.732 3882154.447 4519185.408 3492276.932 3167539.766 6433757.362 0.731278767 0.721646552 0.873719673 0.735681417 0.603403925 0.702417756 0.542805197 0.492331244 1 22.6172301 3.380405022 5.260960364 0.639104205 0.775382169 0.089855016 0.141819737 0.377707881 16.59852723 0.041057061 0.053410629 2401.071109 -3.380405022 0.136277964 GT(ph)PSQSPVVGR ddPTM_MDA-MB-175_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(0.997)PS(0.003)QSPVVGR;GT(0.99)PS(0.01)QSPVVGR 151.66 0.00037236 771860000 245770 229970 188515 186547 200604 225350 174597 216549 275850 TRUE FALSE 213290.8718 228459.3119 279681.4845 228905.3475 196612.3729 234019.3603 157664.6098 170241.6815 243239.3272 0.87687659 0.939236737 1.14982017 0.941070468 0.808308324 0.962095081 0.648187164 0.699893736 1 17.89201698 2.966216029 1.45342795 0.778266092 0.986459425 0.23483581 0.127520219 0.487718347 2.139161578 0.054458249 0.057502675 925.1582557 -2.966216029 0.208193334 GT(ph)RESGQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GTRESGQK 8 1 A0A1W2PQW7;A8K830-4;A8K830-2 A0A1W2PQW7 1 GT(0.651)RES(0.349)GQK;GT(0.5)RES(0.5)GQK;GT(0.5)RES(0.5)GQK;GT(0.5)RES(0.5)GQK 73.931 0.068369 6505390000 3766730 3293630 4503000 3786120 1285060 2487080 2295800 2807730 2245690 TRUE FALSE 3268947.087 3271993.928 6680665.862 4645816.413 1259489.82 2582759.577 2073153.669 2207318.789 1980207.086 1.65081072 1.652349368 3.373720813 2.346126547 0.636039447 1.304287614 1.046937809 1.114690885 1 20.91721988 3.248870632 24.99855328 1.048364442 2.292506939 0.602026841 0.49841126 147.4343893 357480.1486 0.148157705 0.189116765 1773.661064 -3.248870632 1.244142497 GT(ph)SPTQIWCNNSQLPVDHILAGSFETAMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTSPTQIWCNNSQLPVDHILAGSFETAMR 29 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 1 GT(0.524)S(0.464)PT(0.011)QIWCNNSQLPVDHILAGSFETAMR;GT(0.5)S(0.5)PTQIWCNNSQLPVDHILAGSFETAMR 132.6 3.96E-05 321850000 23846 28339.6 13287.2 15875 35370 31073 29893 37109 26020.1 TRUE FALSE 20694.69068 28153.4353 19712.93436 19479.66138 34666.2062 32268.39842 26993.98146 29173.52913 22944.03342 0.901963936 1.227048217 0.859174758 0.849007715 1.510902881 1.406396069 1.176514215 1.271508309 1 14.48583141 3.252724344 24.99998546 1.272295163 0.97127191 0.460165496 0.168646781 230.3053341 406502.9903 0.04940273 0.063467344 1789.469677 -3.252724344 -0.301023253 GT(ph)TPPPPSWEPNSQTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTTPPPPSWEPNSQTK 16 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 GT(0.5)T(0.5)PPPPSWEPNSQTK 153.24 5.26E-06 104950000 153080 133950 107130 136100 151510 124750 154300 180210 222830 TRUE FALSE 132850.0901 133070.0736 158938.4263 167003.5852 148495.2474 129549.2132 139336.0097 141673.4939 196487.2912 0.676125613 0.677245194 0.808899269 0.849945989 0.755749883 0.65932617 0.709134972 0.721031335 1 17.58407648 1.236947233 24.9949409 1.00000033 0.733399712 0.662697998 0.060041699 28.34932564 439051.0198 0.098689673 0.015956861 17.25628213 -1.236947233 -0.266600618 GTADVTHDLQEMKEESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTADVTHDLQEMKEESR 17 1 P11166 P11166 SLC2A1 "Solute carrier family 2, facilitated glucose transporter member 1" 0 56.817 0.064678 64604000 115920 103010 74493 76240 101680 95253 108190 133770 92357 FALSE TRUE 100600.8783 102333.3205 110518.064 93551.45726 99656.76693 98917.44455 97697.75045 105164.3265 81438.66067 1.235296326 1.256569296 1.357071237 1.148735213 1.223703412 1.214625139 1.199648295 1.291331729 1 16.31342621 1.231230935 24.99994277 0.999999576 1.241191136 0.652224534 0.055276083 166.0391308 566273.9038 0.134631546 0.013343777 17.03063867 -1.231230935 0.24119156 GTCADRDNLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTCADRDNLTR 11 1 P55212;D6RBM3;D6RHU3 P55212 CASP6 Caspase-6;Caspase-6 subunit p18;Caspase-6 subunit p11 0 ; 132.17 0.00017151 234482000 476822 389903 276837 257419 313741 347480 391231 416024 250264 FALSE TRUE 413808.7646 387341.7015 410716.2992 315869.9184 307498.1679 360847.7804 353289.4778 327060.5051 220678.075 1.875169359 1.755234187 1.86115589 1.431360675 1.39342419 1.635177307 1.600926951 1.482070682 1 17.75158378 -0.151908335 0.138355378 5.48E-25 2.172897958 0.590810142 0.165086731 80.79371485 1.722507874 34.35820665 4.948589398 0.704841821 0.151908335 2.172897958 GTCSGFEPHSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTCSGFEPHSWR 12 0 Q9NZU5;F8WB09;C9IYS1;H7C3D2 Q9NZU5 LMCD1 LIM and cysteine-rich domains protein 1 0 ; 191.29 5.55E-06 1030910000 820640 918540 557720 574090 907100 964450 803200 897060 722840 FALSE TRUE 712190.3448 912506.0503 827435.2575 704445.9089 889050.4847 1001553.016 725305.7876 705230.6999 637386.6787 1.117359946 1.431636526 1.29816842 1.105209651 1.39483694 1.571342874 1.137936847 1.106440915 1 19.28180934 2.019742038 24.97293369 1.079232948 1.320616477 0.399409384 0.139814648 232.5646386 294184.3353 0.057383805 0.038682928 104.650676 -2.019742038 0.241383528 GTDDLNPVTSTPAKPSS(ph)PPPEFSFNTPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTDDLNPVTSTPAKPSSPPPEFSFNTPGK 29 1 B5MCR8;Q6NXT4-4;Q6NXT4-3;Q6NXT4;Q6NXT4-2 B5MCR8 SLC30A6 Zinc transporter 6 1 GTDDLNPVTSTPAKPS(0.213)S(0.787)PPPEFSFNTPGK;GTDDLNPVTSTPAKPS(0.058)S(0.942)PPPEFSFNTPGK 200.86 2.01E-25 360720000 326020 418800 314140 396610 550230 357460 519990 901880 648890 TRUE FALSE 282935.631 416048.8752 466059.1547 486666.3623 539281.4995 371211.7175 469561.4498 709019.9804 572178.9634 0.494487999 0.727130674 0.814533886 0.850549205 0.94250494 0.648768552 0.820654865 1.239157721 1 19.12610693 -2 0.083211034 3.03452428 4.39E-12 0.508957878 0.14115752 350.2607269 2.753294243 127.4977044 19.23886417 0.01 2 -3.03452428 GTDDS(ph)PKDSQEDLQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GTDDSPKDSQEDLQER 16 1 Q969E4;Q5H9L2;Q6IPX3-2;Q6IPX3 Q969E4 TCEAL3;TCEAL5;TCEAL6 Transcription elongation factor A protein-like 3;Transcription elongation factor A protein-like 5;Transcription elongation factor A protein-like 6 1 GTDDS(0.998)PKDS(0.002)QEDLQER;GTDDS(0.999)PKDS(0.001)QEDLQER;GTDDS(1)PKDSQEDLQER 131.09 2.81E-05 1877820000 2240410 1784860 1293060 1527790 1788170 1604230 2151220 2379620 2742240 TRUE FALSE 1944334.142 1773135.137 1918388.141 1874698.07 1752588.915 1665945.766 1942595.016 1870756.781 2418055.511 0.804089953 0.733289674 0.793359843 0.775291577 0.724792672 0.688960927 0.803370728 0.773661635 1 21.20541593 1.135920248 2.639524467 1.107842971 0.757658813 0.79865266 0.037431843 0.333074755 2.026877983 0.295931865 0.009728337 13.67477683 -1.135920248 -0.350184158 GTDIMYTGTLDCWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GTDIMYTGTLDCWR 14 0 P05141 P05141 SLC25A5 "ADP/ATP translocase 2;ADP/ATP translocase 2, N-terminally processed" 0 ;; 231.07 1.57E-12 502500000 254811 268173 241015 394073 384830 392410 201596 356797 428170 FALSE TRUE 221137.0807 266411.3539 357570.6601 483553.2977 377172.6359 407506.2666 182045.2509 280498.7381 377552.2304 0.585712553 0.705627811 0.947076011 1.280758684 0.998994591 1.079337463 0.482172363 0.742940223 1 18.52631671 2.259042089 24.99994532 0.731147672 0.942044442 0.137328009 0.224628129 457.5662379 558510.0522 0.089386101 0.069156318 181.5691618 -2.259042089 0.21089677 GTDLWLGVDALGLNIYEKDDKLTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTDLWLGVDALGLNIYEKDDKLTPK 25 2 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 158.67 1.38E-11 513430000 2129340 1506100 1118250 1127380 1164310 823900 2032930 2359300 503990 FALSE TRUE 1847942.324 1496206.33 1659039.44 1383368.86 1141142.509 855595.9661 1835776.761 1854782.055 444408.8763 4.158203002 3.366733676 3.733137497 3.112829049 2.56777614 1.925244998 4.130828296 4.173593629 1 18.76152811 3.691147871 4.355942221 2.986152993 3.719585211 0.160545273 0.959601042 0.530231121 22.16016647 0.280957082 0.441044678 4910.750522 -3.691147871 0.733432218 GTDTQTPAVLS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GTDTQTPAVLSPSK 14 0 P46087-2;P46087;P46087-4 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 GTDTQTPAVLS(0.997)PS(0.003)K;GTDTQTPAVLS(0.919)PS(0.081)K;GTDTQTPAVLS(0.999)PS(0.001)K;GTDTQTPAVLS(0.636)PS(0.364)K 340.9 6.33E-69 1288720000 2503860 2262790 2039980 2349260 2398310 1753840 2510140 2733660 4743140 TRUE FALSE 2172968.557 2247925.583 3026521.151 2882695.389 2350588.323 1821311.36 2266707.009 2149088.082 4182411.393 0.519549215 0.537471179 0.723630668 0.689242429 0.562017483 0.435469204 0.541961753 0.513839477 1 21.99590355 1.234395216 24.99747879 1.000000636 0.565658643 0.726019231 0.083903437 73.42658493 440588.6289 0.169499961 0.022489596 17.15517751 -1.234395216 -0.434341993 GTDTQTPAVLS(ph)PSKTQATLKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTDTQTPAVLSPSKTQATLKPK 22 2 P46087-2;P46087;P46087-4 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 GTDTQTPAVLS(0.999)PS(0.001)KTQATLKPK 214.11 4.77E-25 506580000 965360 623210 575150 524010 629510 321410 881780 939820 266880 TRUE FALSE 837785.2301 619116.0925 853294.4638 642994.4795 616983.9826 333774.8507 796265.1113 738846.8067 235329.7504 3.560048097 2.63084498 3.625952359 2.732312758 2.621784885 1.418328325 3.383614311 3.139623466 1 17.84432419 3.480706925 3.651140618 2.457787997 3.211282468 0.235355122 0.759996553 0.423343516 12.23881275 0.224072317 0.318718817 3024.871464 -3.480706925 0.753494472 GTEAS(ph)PPQNNS(ph)GSSSPVFTFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTEASPPQNNSGSSSPVFTFR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 2 GT(0.002)EAS(0.998)PPQNNS(1)GSSSPVFTFR;GT(0.005)EAS(0.995)PPQNNS(0.796)GS(0.165)S(0.031)S(0.006)PVFT(0.001)FR 142.23 2.17E-07 112275000 191729 181826 123723 115920 178579 195514 175877 200417 188511 TRUE FALSE 166391.5269 180631.573 183555.8566 142241.4077 175025.6273 203035.5501 158820.4756 157559.3842 166225.4443 1.00099914 1.086666207 1.104258481 0.855713807 1.052941251 1.221446878 0.955452255 0.947865622 1 17.34278171 GTEAS(ph)PPQNNSGSSS(ph)PVFTFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTEASPPQNNSGSSSPVFTFR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 2 GTEAS(0.972)PPQNNS(0.028)GS(0.001)S(0.033)S(0.967)PVFTFR;GTEAS(0.999)PPQNNS(0.001)GSS(0.018)S(0.982)PVFTFR 191.9 1.87E-17 365460000 538920 551250 393750 473390 586270 636210 573350 696820 593030 TRUE FALSE 467700.3566 547628.8025 584168.817 580880.4348 574604.374 660685.4104 517746.6052 547810.4657 522922.669 0.89439679 1.047246247 1.117122763 1.110834296 1.098832405 1.263447637 0.990101665 1.047593647 1 18.99623809 7.261600861 9.500053052 1.068064659 0.183271605 0 0.097228897 0 0 0.021824126 0 18264208.7 -7.261600861 -0.884793054 GTEAS(ph)PPQNNSGSSSPVFTFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GTEASPPQNNSGSSSPVFTFR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 GTEAS(1)PPQNNSGSSSPVFTFR;GTEAS(1)PPQNNSGSSSPVFTFR;GTEAS(1)PPQNNSGSSSPVFTFR;GTEAS(1)PPQNNSGSSSPVFTFR;GTEAS(1)PPQNNSGSSSPVFTFR 483.58 1.62E-249 1209016000 513767 492155 353875 367523 471126 522101 474957 542054 514218 TRUE FALSE 445871.3892 488922.0014 525010.1336 450974.7144 461751.5143 542186.5633 428895.7432 426139.9704 453427.7338 0.983335063 1.078279878 1.157869478 0.994590054 1.018357458 1.195750773 0.945896581 0.939818936 1 18.79051311 2.137775577 23.68824856 0.956628535 1.06984137 0.363698125 0.068109534 8.488930038 1981.016027 0.027161746 0.01831245 137.3332118 -2.137775577 0.113212835 GTEASPPQNNSGSS(ph)SPVFTFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTEASPPQNNSGSSSPVFTFR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 GTEASPPQNNSGS(0.001)S(0.5)S(0.5)PVFTFR 268.01 3.31E-37 136420000 162150 137510 85661 98120 120570 118290 128800 139650 119730 TRUE FALSE 140721.4667 136606.6878 127086.9461 120399.6457 118170.8929 122840.6928 116308.9958 109786.9343 105575.6558 1.332896922 1.293922228 1.203752372 1.140411061 1.119300581 1.163532368 1.101664915 1.039888727 1 16.68791768 8 0.164849094 0.918612441 2.616461145 0.917875776 0.029443191 37.73066361 0.50494514 0.399539228 15.23187452 100000000 -8 1.697848705 GTEASPPQNNSGSSS(ph)PVFTFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GTEASPPQNNSGSSSPVFTFR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 GTEASPPQNNSGSS(0.038)S(0.961)PVFTFR;GTEASPPQNNSGSS(0.041)S(0.959)PVFTFR;GTEASPPQNNSGSS(0.018)S(0.981)PVFTFR;GTEASPPQNNSGS(0.001)S(0.122)S(0.877)PVFTFR 367.85 2.80E-112 803778000 800519 688762 475547 478947 644732 648855 569558 657876 640543 TRUE FALSE 694728.3859 684237.4771 705523.1198 587699.2366 631903.0946 673816.8717 514322.3528 517194.337 564818.7362 1.230002373 1.211428434 1.249114228 1.040509457 1.118771482 1.192978966 0.910597188 0.915681977 1 19.10742842 2.56995985 0.587309258 0.888246642 1.236111109 0.640711708 0.07577455 0.677749688 0.569996289 0.151044913 0.078510472 371.5008824 -2.56995985 0.347864467 GTEDITSPHGIPLDLLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GTEDITSPHGIPLDLLDR 18 0 Q9Y265;H7C4G5;Q9Y265-2;E7ETR0;J3QLR1 Q9Y265 RUVBL1 RuvB-like 1 0 ;;;;; 196.66 1.93E-15 1630894000 1967406 1883540 1114757 1397886 1824180 2023125 1748681 2099101 1838048 FALSE TRUE 1707408.312 1871166.902 1653857.214 1715297.382 1787882.387 2100955.928 1579094.186 1650224.586 1620756.059 1.053464093 1.154502487 1.02042328 1.058331617 1.103116275 1.296281396 0.974294791 1.018181963 1 20.62823554 GTEEGPGTSHTEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTEEGPGTSHTEGR 14 0 Q5JTD0-4;Q5JTD0-2;Q5JTD0 Q5JTD0-4 TJAP1 Tight junction-associated protein 1 0 164.88 2.14E-07 0 149550 124490 174010 112240 97070 142390 106500 129570 144080 FALSE TRUE 129786.5886 123672.217 258161.818 137725.8075 95138.49691 147867.8354 96171.64639 101862.4638 127047.0265 1.02156337 0.973436533 2.03201779 1.084053765 0.748844735 1.163882693 0.756976759 0.801769759 1 16.95500308 3.482322461 24.97773102 0.888685974 1.347546752 0.307690021 0.306830678 261.7222319 1256869.903 0.086616262 0.115196597 3036.144669 -3.482322461 0.458860778 GTELDCGIETDSGVDDDMACHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTELDCGIETDSGVDDDMACHK 22 0 P42574 P42574 CASP3 Caspase-3;Caspase-3 subunit p17;Caspase-3 subunit p12 0 200.99 1.10E-24 0 140670 122650 83016 97013 111520 113030 125650 122330 170130 FALSE TRUE 122080.1031 121844.3041 123162.8153 119041.2844 109300.9702 117378.3372 113464.4823 96170.68147 150017.4252 0.813772819 0.812201009 0.820990062 0.793516381 0.728588496 0.782431355 0.756342019 0.641063405 1 17.19477056 3.457452652 9.212551554 0.7620951 0.814001889 0.003243103 0.089980944 0.703073484 298.7410878 0.025156413 0.032856158 2867.164775 -3.457452652 0.051906789 EKTPS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKTPSPK 7 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 EKT(0.046)PS(0.954)PK 64.439 0.044453 3533800000 642970 413290 526690 529220 315940 311200 538820 709500 1428100 TRUE FALSE 557999.8854 410575.0708 781399.0457 649387.4896 309653.4121 323172.0654 486565.3193 557778.9463 1259271.645 0.443113198 0.326041702 0.620516668 0.515684993 0.24589882 0.256634116 0.386386306 0.442937748 1 20.2641581 1.233800928 4.375853681 1.057228362 0.399351881 0.735449128 0.112498539 0.120746084 4.619644069 0.251054268 0.030221914 17.13171845 -1.233800928 -0.657876481 GTEVQVDDIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTEVQVDDIKR 11 1 Q9Y230;Q9Y230-2 Q9Y230 RUVBL2 RuvB-like 2 0 ; 174.23 1.80E-05 1372860000 900410 783340 520840 671560 697990 663310 896680 942830 887180 FALSE TRUE 781418.5372 778194.188 772719.9661 824047.9622 684101.3646 688827.9649 809720.1116 741213.1416 782298.5911 0.998875041 0.994753406 0.987755794 1.053367565 0.874476028 0.880517967 1.035052499 0.947481115 1 19.57735984 3.258776575 24.99976176 0.950719076 1.006197447 0.263455149 0.05059879 388.324373 480212.6281 0.015006804 0.019348927 1814.5819 -3.258776575 0.055478372 GTFHDDRDDGVDYWAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GTFHDDRDDGVDYWAK 16 1 E9PK91;Q9NYF8-3;H0YF63 E9PK91 BCLAF1 Bcl-2-associated transcription factor 1 0 ;;; 108.14 0.00064505 901453000 1375920 982700 714911 847960 900620 908480 1021720 1234150 1112160 FALSE TRUE 1194088.686 976244.579 1060644.351 1040502.278 882699.424 943429.8135 922633.7517 970236.6267 980681.7118 1.217610843 0.995475461 1.08153781 1.060998962 0.900087575 0.962014283 0.940808563 0.989349159 1 19.90342545 8 0.630406785 0.96847943 18.65722404 0.65967125 0.051579969 130.3994523 0.916020461 0.023018047 3202.236834 100000000 -8 17.6887446 GTFIADSHQNFALFFQLVDVNTGAELTPHQTFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GTFIADSHQNFALFFQLVDVNTGAELTPHQTFVR 34 0 P04844-2;P04844 P04844-2 RPN2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 0 ;; 316.1 9.35E-105 627975000 223414 232206 103174 212922 278049 274104 174947 329692 218640 FALSE TRUE 193889.2738 230680.6235 153069.2915 261269.1944 272516.3689 284648.9582 157980.6669 259189.9315 192792.6283 1.005688213 1.196522012 0.793958218 1.355182492 1.41352069 1.476451464 0.81943313 1.344397521 1 17.55669036 4.741602656 23.25543124 1.182114151 1.005688157 0.046637214 0.238525025 398.689715 3047414.865 0.056937993 0.387034446 55157.25645 -4.741602656 -0.176425994 GTFS(ph)DQELDAQS(ph)LDDEDDNMHHAVYPAVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTFSDQELDAQSLDDEDDNMHHAVYPAVNR 30 0 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 2 GT(0.404)FS(0.596)DQELDAQS(1)LDDEDDNMHHAVYPAVNR;GT(0.461)FS(0.555)DQELDAQS(0.984)LDDEDDNMHHAVYPAVNR 195.92 1.40E-25 300180000 84593 73519 68662 76961 78780 102477 75542 81138 174922 TRUE FALSE 73413.82072 73036.04885 101867.1729 94436.17133 77212.43213 106419.3565 68215.94847 63787.27012 154242.9204 0.475962336 0.473513135 0.660433377 0.612256116 0.500589796 0.689946457 0.442263076 0.413550716 1 17.23484475 1.229565076 24.9988562 1.0000009 0.532062643 0.713853062 0.092803423 208.1994721 578548.5045 0.28655797 0.024094226 16.965438 -1.229565076 -0.467938257 GTFS(ph)DQELDAQSLDDEDDNMHHAVYPAVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GTFSDQELDAQSLDDEDDNMHHAVYPAVNR 30 0 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 GT(0.036)FS(0.964)DQELDAQSLDDEDDNMHHAVYPAVNR;GT(0.004)FS(0.996)DQELDAQSLDDEDDNMHHAVYPAVNR;GT(0.021)FS(0.979)DQELDAQSLDDEDDNMHHAVYPAVNR 240.83 2.22E-45 824060000 143208 143353 113869 138490 163830 143560 137471 164900 252889 TRUE FALSE 124282.7 142411.3047 168936.4293 169936.2712 160570.1035 149082.8461 124139.0836 129637.4183 222992.7505 0.557339643 0.638636478 0.757587091 0.762070833 0.720068716 0.668554676 0.556695602 0.581352613 1 17.76663728 -1.999949376 0.019141359 1.529370511 4.38E-08 0.080932971 0.126588334 38486.3773 73.26206321 3645.136743 2346.559943 0.010001166 1.999949376 -1.529370468 GTGGVDTAATGGVFDISNLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTGGVDTAATGGVFDISNLDR 21 0 P12532;P12532-2 P12532 CKMT1A "Creatine kinase U-type, mitochondrial" 0 68.972 0.04593 48980000 49693 48412 37461 39515 48853 47878 42396 57752 47989 FALSE TRUE 43125.94414 48093.97838 55577.2649 48487.4847 47880.92088 49719.89764 38284.44245 45402.18423 42315.79509 1.019145311 1.13654909 1.313392902 1.145848367 1.131514149 1.17497255 0.904731729 1.072937047 1 15.36890865 2.260196396 24.99903868 1.005642886 1.158707841 0.461121536 0.081519608 212.9605012 246064.3888 0.030504685 0.023607443 182.0523947 -2.260196396 0.153064955 GTGHVSSGYVER ddPTM_MDA-MB-175_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 ; 91.202 0.0084305 210790000 181713 201675 88130 140086 202599 225540 185912 218182 271380 FALSE TRUE 157699.1666 200350.1836 130749.9628 171894.6674 198567.6763 234216.6697 167882.2829 171525.4772 239297.7656 0.659008103 0.837242183 0.546390237 0.718329597 0.829793274 0.978766639 0.701562267 0.71678679 1 17.8684474 3.30324865 4.9676973 0.825263149 0.687521289 0.294863646 0.117665863 0.312079344 14.91654266 0.035180083 0.04513302 2010.243425 -3.30324865 -0.13774186 GTGLVLDGDTSYTYHLVCMGPEASGWGQDEPQTWPTDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GTGLVLDGDTSYTYHLVCMGPEASGWGQDEPQTWPTDHR 39 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 ;; 236.84 2.40E-50 370827000 81707.6 86515 61057.9 70070.4 78502.1 95927.5 74052.3 89001.7 77813.7 FALSE TRUE 70909.73364 85946.67727 90585.70467 85980.95528 76940.0618 99617.893 66870.71934 69969.37907 68614.65303 1.033448841 1.252599459 1.320209324 1.253099032 1.121335726 1.451845759 0.974583655 1.019743976 1 16.06622908 2.201591331 24.99999573 1.001635948 1.2384028 0.51408107 0.110272938 130.6635918 88358.65027 0.042802209 0.028858119 159.0711171 -2.201591331 0.236766852 GTGQS(ph)DDS(ph)DIWDDTALIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTGQSDDSDIWDDTALIK 18 0 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 2 GT(0.203)GQS(0.88)DDS(0.916)DIWDDTALIK;GT(0.003)GQS(0.997)DDS(1)DIWDDTALIK 338.24 4.79E-75 56243000 400967 367816 269876 322403 348099 326480 383181 444373 572090 TRUE FALSE 347978.195 365399.7925 400388.9363 395609.5288 341172.5109 339039.8969 346020.1656 349347.2921 504458.1719 0.689805844 0.724341111 0.793700962 0.784226623 0.676314767 0.672087233 0.685924393 0.692519839 1 18.94437513 1.235834623 25 1.00000038 0.714846843 0.815070168 0.042683381 34.86740024 319704.1075 0.077900363 0.011610331 17.21213022 -1.235834623 -0.285153538 GTGQS(ph)DDSDIWDDTALIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GTGQSDDSDIWDDTALIK 18 0 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 1 GTGQS(1)DDSDIWDDTALIK;GT(0.001)GQS(0.999)DDSDIWDDTALIK;GT(0.007)GQS(0.993)DDSDIWDDTALIK;GT(0.005)GQS(0.995)DDSDIWDDTALIK;GT(0.19)GQS(0.803)DDS(0.007)DIWDDTALIK 352.61 1.99E-90 2014999000 3271090 2681410 2001871 2784050 2645680 2231820 3062480 3922460 4328020 TRUE FALSE 2838807.169 2663795.641 2969982.511 3416211.104 2593036.144 2317679.56 2765481.161 3083672.454 3816366.406 0.743850791 0.697992634 0.77822258 0.895147567 0.679451569 0.607300063 0.724637225 0.808012682 1 21.86376826 1.271170204 2.437980074 1.055720575 0.733052425 0.568290596 0.073515139 0.412562607 2.798168306 0.274684482 0.020958799 18.67111284 -1.271170204 -0.32266815 GTHDLWDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTHDLWDSR 9 0 Q04446;E9PGM4 Q04446 GBE1 "1,4-alpha-glucan-branching enzyme" 0 111.61 0.0020974 127070000 124050 130220 99288 84798 126890 132470 109080 121600 132730 FALSE TRUE 107656.4782 129364.5762 147304.0089 104052.682 124365.1373 137566.2066 98501.43839 95596.78629 117038.8106 0.919835716 1.10531349 1.25859113 0.889044253 1.062597412 1.17538965 0.84161346 0.816795606 1 16.83662749 2.224537023 24.9999934 0.869835189 1.070357332 0.346531887 0.117298138 236.7262769 422010.8135 0.047084617 0.031920819 167.7015293 -2.224537023 0.200522144 GTHHSQNPSPGS(ph)SSPRPSVVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTHHSQNPSPGSSSPRPSVVGR 22 1 J3KT00;A0A1W2PQI7;A0A1W2PPP3;Q86VV8-4;Q86VV8-3;Q86VV8;J3KTD2;Q86VV8-2 J3KT00 RTTN Rotatin 1 GTHHSQNPS(0.064)PGS(0.312)S(0.312)S(0.312)PRPSVVGR 170.65 4.17E-12 76232000 21283 36713 18231 14794 42768 55962 36691 45230 36543 TRUE FALSE 18470.39763 36471.82989 27047.57258 18153.20381 41917.00047 58114.89435 33132.71247 35557.91648 32222.92817 0.573206678 1.131859578 0.839389035 0.563362948 1.300843929 1.803526174 1.028234067 1.10349737 1 14.97579998 3.222911347 24.99976324 1.240646347 0.806764508 0.423873848 0.271383678 262.9341093 420037.125 0.08563482 0.097430146 1670.749526 -3.222911347 -0.433881839 GTHHSQNPSPGSSS(ph)PRPSVVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTHHSQNPSPGSSSPRPSVVGR 22 1 J3KT00;A0A1W2PQI7;A0A1W2PPP3;Q86VV8-4;Q86VV8-3;Q86VV8;J3KTD2;Q86VV8-2 J3KT00 RTTN Rotatin 1 GTHHSQNPS(0.014)PGS(0.026)S(0.373)S(0.587)PRPSVVGR 173.05 2.53E-12 112840000 43112 58494 27054 34541 74952 87284 56421 61205 61076 TRUE FALSE 37414.63997 58109.74906 40137.40489 42384.06198 73460.60184 90641.87196 50949.3001 48116.78705 53855.66486 0.694720603 1.078990469 0.745277307 0.78699357 1.364027388 1.683051768 0.946034187 0.893439663 1 15.71681048 3.25872618 24.97333062 1.149768092 0.838729446 0.328605526 0.247164979 362.8197719 449318.5981 0.079459048 0.102448586 1814.37135 -3.25872618 -0.311038645 GTHQLYSTSHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTHQLYSTSHDR 12 0 O43818 O43818 RRP9 U3 small nucleolar RNA-interacting protein 2 0 68.359 0.03058 130250000 155620 120170 71253 88707 105340 124000 128820 126500 104630 FALSE TRUE 135054.4227 119380.5954 105711.1891 108849.2802 103243.9401 128770.3602 116327.0562 99448.95942 92260.76059 1.463833832 1.293947661 1.145787098 1.179800377 1.11904497 1.395721858 1.260850826 1.077911766 1 16.49342957 7.999999794 0.035941127 1.54E-10 3.049493959 0.377878446 0.112523054 2768.738394 9.825159788 275.169694 628.1425078 99999952.52 -7.999999794 3.049493958 GTHTAVSSNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GTHTAVSSNDR 11 0 Q9NZ08-2;Q9NZ08 Q9NZ08-2 ERAP1 Endoplasmic reticulum aminopeptidase 1 0 ;; 125.72 0.00032242 153109300 54926 44114 37317.3 35504.9 39267 57215 38011.5 41358 37113.7 FALSE TRUE 47667.38994 43824.21223 55364.0711 43566.8302 38485.66352 59416.09807 34325.15058 32513.91355 32726.16067 1.456553075 1.339118654 1.691737435 1.331253936 1.17599079 1.815553577 1.048859685 0.993514451 1 14.99815674 2.097138155 9.876224413 1.003829561 1.452841052 0.584759919 0.180489119 0.208985186 19.40339477 0.070343291 0.047403199 125.0656818 -2.097138155 0.449011491 GTHTGVWVGVSGSETSEALSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 ;;;;;;; 280.32 5.76E-45 6527118000 2461889 2528241 2161939 2282462 2644442 3209086 2898245 2944522 4393757 FALSE TRUE 2136544.131 2511632.818 3207459.932 2800729.882 2591822.778 3332541.615 2617173.646 2314858.885 3874332.053 0.551461285 0.648275053 0.827874299 0.72289361 0.668972804 0.860159008 0.675516092 0.597485929 1 21.88551618 4.470022864 5.248071997 0.74368339 0.570774314 0.267171053 0.114938758 0.223849622 19.14852925 0.028138233 0.090130448 29513.64602 -4.470022864 -0.172909076 GTHTGVWVGVSGSETSEALSRDPETLVGYSMVGCQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTHTGVWVGVSGSETSEALSRDPETLVGYSMVGCQR 36 1 P49327;A0A0U1RQF0;A0A0U1RRG3 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 327.98 4.43E-129 508720000 109500 110330 54841 47472 108970 137880 116810 112310 30539 FALSE TRUE 95029.29756 109605.235 81362.29103 58251.24316 106801.7102 143184.3328 105481.7842 88293.3805 26928.71421 3.528920721 4.070199346 3.021395318 2.163164669 3.966090225 5.317161885 3.917074664 3.278781891 1 14.71685773 4.242172264 24.98002159 3.339642491 3.799559921 0.034390211 1.142412255 453.4650455 3136267.695 0.300723186 0.733241314 17465.14773 -4.242172264 0.45991743 GTINFLHADCDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTINFLHADCDK 12 0 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 99.531 0.001602 0 189380 166910 167570 183190 194340 193770 188580 209120 345000 FALSE TRUE 164352.9532 165813.5572 248607.4125 224786.0894 190473.0142 201224.4573 170291.5406 164401.3154 304214.493 0.540253528 0.545054759 0.817210942 0.738906576 0.626114201 0.661455854 0.559774582 0.540412502 1 18.21472936 -1.999995994 0.023760624 1.517283976 1.47E-08 0.085276671 0.142111497 22725.24338 53.61415721 2247.219679 1301.055674 0.010000092 1.999995994 -1.517283961 GTINFLHADCDKFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTINFLHADCDKFR 14 1 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 105.28 0.0006063 408330000 1136400 1234600 598450 815370 1251500 1497800 1055400 1108600 1003200 FALSE TRUE 986221.8607 1226489.831 887862.4217 1000512.221 1226597.599 1555421.335 953047.4704 871534.5171 884602.8388 1.114875306 1.386486429 1.003684798 1.131029855 1.386608255 1.758327316 1.07737329 0.985226905 1 19.75467035 2.018786421 24.9987907 1.00348055 1.295272743 0.294385311 0.204387826 298.2546083 396881.1274 0.087356276 0.058885948 104.4206569 -2.018786421 0.291792194 GTLDEEDEEADS(ph)DTDDIDHR ddPTM_MDA-MB-175_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 331.34 4.94E-80 13188400000 3842800 3831300 2617700 2931600 3688100 3890200 3534800 4111800 3974400 TRUE FALSE 3334964.244 3806131.938 3883628.476 3597264.587 3614714.026 4039858.511 3191995.64 3232523.568 3504550.96 0.951609573 1.0860541 1.108167215 1.026455209 1.031434289 1.152746403 0.910814446 0.922378817 1 21.74079817 2.217816751 24.99965567 0.938411135 1.060068708 0.466723288 0.057833934 193.0318419 232632.2072 0.022840944 0.015417978 165.1264908 -2.217816751 0.121657574 GTLDEEDEEADSDT(ph)DDIDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTLDEEDEEADSDTDDIDHR 20 0 Q9HCN4-3;Q9HCN4-2;Q9HCN4-4;Q9HCN4;Q9HCN4-5 Q9HCN4-3 GPN1 GPN-loop GTPase 1 1 GTLDEEDEEADS(0.338)DT(0.662)DDIDHR 336.33 5.48E-79 546040000 430310 345280 258750 297780 358470 435950 361850 406210 357310 TRUE FALSE 373443.4432 343011.8329 383882.3655 365395.5003 351337.1483 452721.2786 326757.8427 319345.1526 315069.2188 1.185274285 1.088687223 1.218406441 1.159730873 1.115110989 1.436894662 1.03709859 1.013571411 1 18.26530929 2.032620297 24.99999242 1.013028667 1.194510145 0.464344492 0.093267205 158.6809211 121611.4244 0.036886753 0.024868878 107.8003812 -2.032620297 0.181481478 GTLDPVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTLDPVEK 8 0 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 115.49 0.0057067 404190000 1489890 1265460 913380 1069510 1085000 1062120 1311440 1541970 1404190 FALSE TRUE 1292997.262 1257147.11 1355093.623 1312358.592 1063410.623 1102980.444 1184256.751 1212231.715 1238188.258 1.044265485 1.015311769 1.094416471 1.059902308 0.858844054 0.890801893 0.956443209 0.979036675 1 20.23979925 3.267391616 24.98724982 0.941421786 1.053672677 0.629058071 0.044362543 155.9352668 135144.9592 0.014045889 0.018129889 1850.936912 -3.267391616 0.112250891 GTLIGYSPEGT(ph)PLYNFMGDAFQHSSQSIPRFIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTLIGYSPEGTPLYNFMGDAFQHSSQSIPRFIK 33 1 Q8TAD4-2;Q8TAD4 Q8TAD4-2 SLC30A5 Zinc transporter 5 1 GTLIGYS(0.001)PEGT(0.203)PLY(0.188)NFMGDAFQHS(0.203)S(0.203)QS(0.203)IPRFIK 48.422 0.034308 440770000 0 0 0 0 0 3946.9 0 0 0 TRUE FALSE 0 0 0 0 0 4098.739797 0 0 0 0 GTLS(ph)DSEIETNSATSTIFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 GTLSDSEIETNSATSTIFGK 20 0 A0A0A0MRB5;Q8WXG6-6;Q8WXG6-8;Q8WXG6-5;Q8WXG6-4;Q8WXG6-7;Q8WXG6-3;Q8WXG6-2;Q8WXG6;F8W8U2 A0A0A0MRB5 MADD MAP kinase-activating death domain protein 1 GT(0.003)LS(0.997)DSEIETNSATSTIFGK;GT(0.015)LS(0.983)DS(0.002)EIETNSATSTIFGK;GT(0.001)LS(0.986)DS(0.013)EIETNSATSTIFGK;GTLS(1)DSEIETNSATSTIFGK;GTLS(0.991)DS(0.009)EIETNSATSTIFGK;GT(0.001)LS(0.999)DSEIETNSATSTIFGK;GT(0.021)LS(0.979)DSEIETNSATSTIFGK 420.4 1.86E-173 2454419000 1576140 1400194 985080 1211901 1482703 1309573 1622420 1906520 1728270 TRUE FALSE 1367849.106 1390996.033 1461467.983 1487081.645 1453200.111 1359953.121 1465077.958 1498825.535 1523955.889 0.897564762 0.912753475 0.95899625 0.975803601 0.95357098 0.89238352 0.961365069 0.983509789 1 20.53938971 GTLTLCPYHSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GTLTLCPYHSDR 12 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;;;;; 202.44 1.37E-07 3622380000 4689930 5273330 2726546 2462138 4389272 4994180 4279840 4628788 2068379 FALSE TRUE 4070143.868 5238689.148 4045112.765 3021204.064 4301934.075 5186309.336 3864781.776 3638957.707 1823857.591 2.231612757 2.872312605 2.217888494 1.656491208 2.358700644 2.843593361 2.1190151 1.995198378 1 20.79856166 1.115940921 1.683405767 0.147847346 2.344259895 0.594922801 0.345246018 1.031348778 2.074795244 4.113328788 0.100350072 13.05993216 -1.115940921 2.196412549 GTMTTGHNVADLVVILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTMTTGHNVADLVVILK 17 0 Q12905;B4DY09;A0A0A0MRL0;X6R6Z1 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 130.39 7.61E-05 0 293900 223290 133570 179130 202940 219330 257780 294250 260850 FALSE TRUE 255060.3704 221823.1933 198164.8988 219804.2043 198901.891 227767.767 232780.5353 231326.9274 230012.6102 1.108897335 0.964395792 0.861539281 0.95561806 0.86474342 0.990240348 1.012033797 1.005714109 1 17.81135343 2.496323175 24.65097996 1.005415731 0.945105927 0.123985377 0.067350628 1232.53553 1582301.603 0.023517433 0.020413765 313.5618187 -2.496323175 -0.060309804 GTPGGGGPRPPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTPGGGGPRPPSPR 14 1 Q8TAP9 Q8TAP9 MPLKIP M-phase-specific PLK1-interacting protein 1 GTPGGGGPRPPS(1)PR 59.606 0.060296 155520000 179610 148880 122800 106140 115400 198490 139090 137090 156570 TRUE FALSE 155874.0834 147901.9975 182186.4907 130240.7092 113103.7658 206126.0387 125601.0732 107774.3703 138060.473 1.129027593 1.071284158 1.319613694 0.943359866 0.819233509 1.493012694 0.909754041 0.780631618 1 17.07494081 2.02720815 24.99389484 0.865810083 1.120118886 0.245129472 0.191006176 264.7730578 243224.1487 0.075906692 0.051175019 106.4653167 -2.02720815 0.254308802 GTPGPPPAHGAALQPHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTPGPPPAHGAALQPHPR 18 0 Q15654 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 ; 214.22 5.88E-19 858530000 626490 705590 501940 508830 647780 706480 612090 714980 654270 FALSE TRUE 543697.7592 700954.9328 744679.8629 624367.6285 634890.4454 733658.7428 552729.606 562087.091 576922.9459 0.942409663 1.214988826 1.290778722 1.082237468 1.100477022 1.271675443 0.958064868 0.974284512 1 19.13801912 2.216705122 24.98425729 0.975982565 1.154371985 0.399028323 0.099987879 225.8868907 258222.1159 0.03991763 0.02693803 164.7043701 -2.216705122 0.17838942 GTPLGTPATS(ph)PPPAPLCHSDDYVHISLPQATVTPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTPLGTPATSPPPAPLCHSDDYVHISLPQATVTPPR 36 0 A0A2R8YFV7;A0A2R8Y5N2;A0A2R8Y5S3;Q92574-2;Q92574;A0A2R8Y6W1;Q59IT9 A0A2R8YFV7 TSC1 Hamartin 1 GTPLGTPAT(0.338)S(0.662)PPPAPLCHSDDYVHISLPQATVTPPR 197.26 8.51E-30 238850000 55895 67168 30758 62437 117440 136340 108580 104650 107980 TRUE FALSE 48508.33413 66726.76899 45632.67168 76614.27514 115103.1738 141585.088 98049.92831 82271.41189 95214.72741 0.509462511 0.700803025 0.479260645 0.804647319 1.208879938 1.48700828 1.029776916 0.864061833 1 16.53889712 3.448885393 4.227216965 1.096025554 0.582080378 0.686937658 0.171586363 0.141680659 5.798141574 0.057167435 0.077975854 2811.158892 -3.448885393 -0.513945175 GTPLT(ph)PPACACSSLQVEVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTPLTPPACACSSLQVEVER 20 0 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 GTPLT(1)PPACACSSLQVEVER 180.81 5.95E-16 140520000 44869 47020 31160 35003 52822 61118 52453 55259 48963 TRUE FALSE 38939.44797 46711.12252 46229.08022 42950.96614 51770.94554 63469.24901 47366.11613 43442.29288 43174.64992 0.901905355 1.081910858 1.070745919 0.994819094 1.199105161 1.47005822 1.097081649 1.006199076 1 15.39789686 5.69496808 0.889935369 1.128023768 7.63E-09 0.201643335 0.138543556 20.0449207 3.490272613 0.050874608 32.8340865 495413.7774 -5.69496808 -1.12802376 GTPS(ph)QSPVVGR ddPTM_MDA-MB-175_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(0.03)PS(0.661)QS(0.31)PVVGR 67.519 0.057733 0 55460 57050 32533 36529 53374 53003 58927 60091 43900 TRUE FALSE 48130.82048 56675.23479 48266.06762 44823.46776 52311.96182 55042.05971 53212.26861 47241.00728 38710.19201 1.243363 1.464090769 1.246856838 1.157924191 1.351374382 1.421900974 1.374631999 1.220376465 1 15.24042584 1.313861869 2.72218178 0.959798474 1.32314179 0.562279821 0.090176825 0.297596852 2.857740451 0.226418584 0.024403279 20.59974616 -1.313861869 0.363343316 GTPSQS(ph)PVVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 GTPSQSPVVGR 11 0 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 1 GTPS(0.033)QS(0.967)PVVGR;GTPS(0.007)QS(0.993)PVVGR;GTPSQS(1)PVVGR;GTPS(0.002)QS(0.998)PVVGR;GTPSQS(1)PVVGR;GTPS(0.001)QS(0.999)PVVGR;GT(0.009)PS(0.151)QS(0.84)PVVGR;GTPS(0.077)QS(0.923)PVVGR;GT(0.003)PS(0.067)QS(0.931)PVVGR 240.31 1.17E-15 22915043000 9592720 8358016 6807269 7653224 10036636 10435303 9593120 11365419 9177461 TRUE FALSE 8325017.747 8303111.643 10099287.06 9391005.481 9836926.58 10836755.86 8662780.699 8935012.593 8092512.016 1.028730971 1.026024012 1.247979248 1.160456168 1.215559095 1.339109023 1.070468685 1.104108659 1 22.94815617 1.541255765 1.857516769 1.003173432 1.16585647 0.207525259 0.097526006 0.747761879 4.389718936 0.188179145 0.029169574 34.77408932 -1.541255765 0.162683038 GTQEVAPPTPLT(ph)PT(ph)SHTANTSPRPVSGMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 2 GTQEVAPPT(0.027)PLT(0.959)PT(0.248)S(0.234)HT(0.208)ANT(0.156)S(0.148)PRPVS(0.021)GMER 65.58 0.0099973 123100000 82768 84672 64903 70233 85251 85761 78541 83935 102790 TRUE FALSE 71829.99909 84115.78406 96290.30789 86180.47609 83554.67189 89060.28116 70924.10591 65986.15343 90638.2833 0.792490728 0.928038142 1.062358028 0.950817612 0.921847467 0.982590115 0.78249613 0.728016364 1 16.46783292 2.236262662 24.9999513 0.81190219 0.944431256 0.188355441 0.095772095 76.07081442 827570.6298 0.037810082 0.026878413 172.2910281 -2.236262662 0.132529066 GTQEVAPPTPLT(ph)PTSHT(ph)ANTSPRPVSGMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 2 GTQEVAPPTPLT(0.999)PT(0.004)S(0.022)HT(0.59)ANT(0.203)S(0.181)PRPVS(0.001)GMER 128.54 1.23E-05 95941000 172410 146460 110900 133940 144240 156040 158730 177450 160660 TRUE FALSE 149625.5817 145497.8946 164531.6109 164353.1241 141369.9062 162042.9598 143336.389 139503.6984 141666.9578 1.056178406 1.027041851 1.16139722 1.160137315 0.997903169 1.143830306 1.011784196 0.984729965 1 17.11214378 2.095464476 6.797917887 0.993367607 1.09005188 0.392722183 0.054414999 0.213510311 12.90518686 0.022446265 0.015048587 124.5846326 -2.095464476 0.096684273 GTQEVAPPTPLT(ph)PTSHTANTSPRPVSGMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLT(0.998)PT(0.002)SHTANTSPRPVSGMER;GTQEVAPPTPLT(0.993)PT(0.006)S(0.001)HTANTSPRPVSGMER;GTQEVAPPTPLT(0.971)PT(0.023)S(0.005)HT(0.001)ANTSPRPVSGMER;GTQEVAPPT(0.212)PLT(0.271)PT(0.08)S(0.08)HT(0.102)ANT(0.166)S(0.088)PRPVS(0.002)GMER 133.47 8.83E-06 898550000 158763 151097 109687 121796.8 180280 175365 177134 192881 145491 TRUE FALSE 137782.0673 150104.4339 162732.0001 149452.625 176692.7807 182111.405 159955.5719 151634.8992 128291.2197 1.073978933 1.170028893 1.268457814 1.164948196 1.377278828 1.419515735 1.246816207 1.181958512 1 16.96906291 1.268684491 2.388503212 0.945387477 1.25142735 0.372509516 0.100076667 0.619826509 3.972852244 0.387616148 0.028453846 18.56455276 -1.268684491 0.306039872 GTQEVAPPTPLTPT(ph)SHTANTSPRPVSGMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLT(0.002)PT(0.19)S(0.19)HT(0.19)ANT(0.19)S(0.103)PRPVS(0.137)GMER;GTQEVAPPTPLT(0.001)PT(0.197)S(0.197)HT(0.197)ANT(0.197)S(0.197)PRPVS(0.016)GMER 84.713 0.002042 616649000 43979 36848 23572 23685.6 26513 35822 29838 28387.2 36402 TRUE FALSE 38167.06372 36605.94306 34971.49804 29063.77749 25985.44317 37200.09552 26944.31535 22316.81819 32098.59703 1.18905707 1.140421902 1.089502386 0.905453203 0.809550746 1.158932133 0.839423459 0.695258368 1 14.97022262 4.65447977 0.449919438 0.829643042 1.472730567 0.424157865 0.126294265 5.015833276 0.93005129 0.137110887 1.748834307 45131.50023 -4.65447977 0.643087525 GTQEVAPPTPLTPTSHT(ph)ANTSPRPVSGMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLT(0.001)PT(0.098)S(0.098)HT(0.326)ANT(0.235)S(0.235)PRPVS(0.007)GMER;GTQEVAPPTPLT(0.004)PT(0.123)S(0.123)HT(0.275)ANT(0.204)S(0.204)PRPVS(0.069)GMER;GTQEVAPPTPLTPT(0.025)S(0.025)HT(0.365)ANT(0.365)S(0.218)PRPVS(0.002)GMER;GTQEVAPPTPLTPT(0.072)S(0.072)HT(0.285)ANT(0.285)S(0.285)PRPVS(0.001)GMER 134.42 7.40E-06 5070560000 575259 540641 350309 355318 466433 487593 439858 494034 480846 TRUE FALSE 499237.0656 537089.4937 519719.6041 435998.3826 457151.8959 506351.0182 397200.6389 388388.6737 424000.9337 1.177443317 1.266717715 1.225751084 1.028295808 1.078186059 1.19422147 0.936791897 0.916009006 1 18.69370792 2.767613975 0.452151174 0.882825793 1.262967907 0.598277927 0.077320445 0.938441686 0.619465585 0.225878413 0.161739034 585.617404 -2.767613975 0.380142114 GTQEVAPPTPLTPTSHTANT(ph)SPRPVSGMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLTPT(0.034)S(0.112)HT(0.112)ANT(0.371)S(0.371)PRPVSGMER;GTQEVAPPTPLTPT(0.003)S(0.003)HT(0.041)ANT(0.476)S(0.476)PRPVS(0.001)GMER 159.99 6.62E-12 3098620000 216228 161451 112348 130152 157048 145588 130814 173503 168476 TRUE FALSE 187652.9219 160390.4178 166679.8686 159705.0008 153923.0521 151188.8646 118127.6784 136400.7337 148558.9592 1.263154528 1.079641501 1.121977897 1.075027731 1.036107502 1.017702772 0.795156879 0.918158921 1 17.18067609 3.327371182 0.685332488 0.897545293 1.20071345 0.673072693 0.070263406 0.490014476 0.568914898 0.055283204 0.095061999 2125.059927 -3.327371182 0.303168157 GTQSIPNDS(ph)PAR ddPTM_MDA-MB-175_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 134.02 0.00016029 1545460000 1309770 1049370 907390 1109520 1112410 1201000 901610 1266240 1552470 TRUE FALSE 1136680.576 1042476.619 1346206.839 1361453.474 1090275.217 1247203.247 814172.001 995464.4299 1368938.765 0.83033705 0.761521732 0.98339449 0.994532048 0.796438267 0.911073073 0.594746837 0.727179663 1 20.38462648 GTS(ph)PRPPEGGLGYSQLGDDDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.161)S(0.839)PRPPEGGLGYSQLGDDDLK;GT(0.125)S(0.875)PRPPEGGLGYSQLGDDDLK;GT(0.02)S(0.98)PRPPEGGLGYSQLGDDDLK;GT(0.151)S(0.849)PRPPEGGLGYSQLGDDDLK 187.98 1.61E-17 1356544000 1819230 1584865 1257041 1616822 1319345 1170506 2042431 2044183 3384740 TRUE FALSE 1578814.146 1574453.917 1864950.232 1983946.147 1293092.616 1215536.123 1844356.356 1607050.373 2984599.893 0.528986867 0.527525958 0.624857703 0.664727675 0.433254929 0.407269372 0.617957657 0.538447507 1 21.50910611 1.238104963 24.97688031 1.000000518 0.54441642 0.761778084 0.080332015 5.550026447 303885.5501 0.116666365 0.020379708 17.30234481 -1.238104963 -0.455584098 GTS(ph)PSSSSRPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTSPSSSSRPQR 12 1 H3BVG0;Q8N1F7;Q8N1F7-2 H3BVG0 NUP93 Nuclear pore complex protein Nup93 1 GT(0.051)S(0.946)PS(0.002)SSSRPQR 124.62 0.00019361 1229800000 939690 826520 586880 659670 792260 830090 806680 880610 810170 TRUE FALSE 815507.5856 821090.5357 870697.131 809458.1559 776495.576 862024.0994 728448.2978 692298.4044 714392.6255 1.141539759 1.149354719 1.21879356 1.133071825 1.086931119 1.206653132 1.019674996 0.969072719 1 19.44635766 2.124062451 5.387847225 0.98605275 1.154022029 0.801263335 0.037721158 0.083103848 3.593185898 0.015714138 0.010446792 133.0645748 -2.124062451 0.167969279 GTSDLLAWDPLFGPSLDSSSSSSLTSSSSARPTTPLSVGT(ph)IVPPPRPAS(ph)RPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTSDLLAWDPLFGPSLDSSSSSSLTSSSSARPTTPLSVGTIVPPPRPASRPK 52 3 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 2 GTSDLLAWDPLFGPSLDS(0.005)S(0.005)S(0.027)S(0.027)S(0.027)S(0.027)LT(0.027)S(0.155)S(0.155)S(0.155)S(0.155)ARPT(0.155)T(0.155)PLS(0.158)VGT(0.161)IVPPPRPAS(0.603)RPK 96.875 1.04E-07 108530000 59424 48441 38825 39729 51436 57836 52834 71492 67364 TRUE FALSE 51570.96784 48122.78788 57600.89986 48750.07667 50412.52423 60060.98834 47710.16681 56203.99215 59400.30466 0.868193659 0.810143789 0.969707145 0.820704152 0.848691341 1.011122564 0.803197342 0.946190301 1 15.85818271 1.514509735 5.510802077 0.988674893 0.878648502 0.280704545 0.067295368 0.170462337 11.09410813 0.047013139 0.016195021 32.69713757 -1.514509735 -0.110026391 GTSKEDAMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTSKEDAMK 9 1 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ; 94.616 0.0078445 533010000 1027310 817180 643340 637120 429000 481940 773850 904070 1282890 FALSE TRUE 891548.3806 811811.8908 954461.3758 781787.8338 420463.7393 500480.5437 698802.1461 710741.666 1131228.206 0.78812425 0.717637597 0.843739018 0.691096482 0.371687814 0.442422264 0.617737555 0.62829203 1 20.10945857 3.475562202 24.99840478 0.599225547 0.775081331 0.180055207 0.16544626 86.46182308 1386337.222 0.04921437 0.064017773 2989.249754 -3.475562202 0.175855785 GTSPSSSS(ph)RPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GTSPSSSSRPQR 12 1 H3BVG0;Q8N1F7;Q8N1F7-2 H3BVG0 NUP93 Nuclear pore complex protein Nup93 1 GT(0.005)S(0.372)PS(0.107)S(0.056)S(0.056)S(0.404)RPQR;GTS(0.023)PS(0.033)S(0.009)S(0.009)S(0.926)RPQR;GTS(0.001)PS(0.015)S(0.042)S(0.042)S(0.899)RPQR;GT(0.003)S(0.03)PS(0.01)S(0.014)S(0.014)S(0.93)RPQR 135.13 0.00035014 2177004000 2640860 2433690 1680558 1744635 2328350 2603810 2135040 2441810 2386550 TRUE FALSE 2291863.66 2417702.93 2493281.47 2140781.042 2282020.39 2703980.256 1927984.149 1919647.934 2104414.778 1.089074114 1.148871865 1.184786144 1.017280939 1.084396676 1.284908415 0.916161666 0.912200368 1 21.00498766 2.20869696 24.99929354 0.935305499 1.130149591 0.600536163 0.073704813 133.9357527 112118.5864 0.029719349 0.020039729 161.6951377 -2.20869696 0.194844092 GTSS(ph)PDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GTSSPDYR 8 0 Q66K14-2;Q66K14;G3V133 Q66K14-2 TBC1D9B TBC1 domain family member 9B 1 GT(0.001)S(0.034)S(0.965)PDYR;GT(0.002)S(0.034)S(0.964)PDYR;GT(0.003)S(0.038)S(0.959)PDYR;GT(0.015)S(0.059)S(0.927)PDYR;GT(0.002)S(0.045)S(0.953)PDYR;GT(0.007)S(0.047)S(0.946)PDYR 145.63 0.00059395 2792600000 7583160 7650570 5244180 5464310 6063550 8093250 6758870 8011370 7570060 TRUE FALSE 6581026.193 7600312.902 7780282.989 6705065.102 5942897.218 8404602.565 6103395.828 6298200.87 6675136.131 0.98590142 1.138600435 1.165561696 1.00448365 0.890303524 1.259090811 0.914347769 0.94353145 1 22.67036583 GTSYQSPHGIPIDLLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GTSYQSPHGIPIDLLDR 17 0 Q9Y230;Q9Y230-2;M0R0Y3 Q9Y230 RUVBL2 RuvB-like 2 0 ;;; 190.71 2.83E-10 2916400000 2213260 2162360 1143830 1624530 2179620 2358240 1980330 2318410 2009970 FALSE TRUE 1920772.083 2148155.315 1696990.014 1993404.366 2136249.826 2448963.019 1788277.901 1822636.063 1772353.636 1.083740876 1.212035381 0.957478225 1.124721571 1.205318049 1.38175755 1.008984812 1.028370426 1 20.75723506 GTT(ph)PPPPSWEPNSQTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTTPPPPSWEPNSQTK 16 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 GT(0.025)T(0.975)PPPPSWEPNSQTK;GT(0.025)T(0.975)PPPPSWEPNSQTK 218.2 1.51E-13 221780000 176128 168964 140445 169329 170455 153928 179936 219331 253083 TRUE FALSE 152852.2385 167854.0644 208364.6718 207777.7375 167063.279 159849.7098 162485.8344 172428.7725 223163.8161 0.684932895 0.752156274 0.933684839 0.931054779 0.748612754 0.716288656 0.728101165 0.772655601 1 17.7677436 -1.999980861 0.010569771 1.707958986 2.82E-09 0.050327851 0.105577445 172292.4286 181.6971195 16573.24126 12997.50759 0.010000441 1.999980861 -1.707958983 GTTITLVLKEEASDYLELDTIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GTTITLVLKEEASDYLELDTIK 22 1 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 ;; 215.48 1.30E-25 52756000 123019 101460 55176 54728.7 80715 80647 136205 132206 8190.5 FALSE TRUE 106761.7275 100793.5026 81859.29815 67155.68781 79108.92942 83749.54228 122995.8601 103934.7757 7222.228421 14.78238035 13.95601146 11.33435463 9.29847187 10.95353467 11.59608052 17.03018139 14.3909566 1 12.81822833 1.234339827 24.99970007 0.99998244 12.94675271 0.737841365 2.232469741 73.85207167 437366.0083 4.628795363 0.611717566 17.15298971 -1.234339827 11.94677027 GTTVTPDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTTVTPDKR 9 1 Q16186;A0A087WX59;A0A087WUX6 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 0 74.173 0.06709 254560000 200430 195310 151360 156580 179710 185340 205250 234890 261400 FALSE TRUE 173942.6677 194026.9957 224558.2023 192133.8822 176134.1226 192470.1497 185344.8866 184660.6014 230497.5898 0.754639855 0.84177451 0.974232323 0.83356135 0.764147351 0.835020227 0.804107699 0.801138969 1 17.81439214 1.23318046 24.95169353 1.000000278 0.827577265 0.453398284 0.059993987 169.418931 785629.4566 0.127657206 0.015197883 17.10726018 -1.23318046 -0.172423013 GTVGEPTYDAEFQHFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GTVGEPTYDAEFQHFLR 17 0 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 288.46 4.20E-37 2845690000 1489950 1455640 1158290 1131210 1533270 1595980 1343500 1540200 1654230 FALSE TRUE 1293049.332 1446077.805 1718442.918 1388068.52 1502760.927 1657378.383 1213207.577 1210840.216 1458668.814 0.886458475 0.991368151 1.178089846 0.951599504 1.030227638 1.136226652 0.831722434 0.830099474 1 20.47622093 2.223504206 24.99999958 0.873047941 1.030599826 0.327692013 0.0949483 249.1907546 413758.6129 0.038315226 0.025947691 167.3031841 -2.223504206 0.157551885 GTVLLADNVICPGAPDFLAHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTVLLADNVICPGAPDFLAHVR 22 0 P21964-2;P21964 P21964-2 COMT Catechol O-methyltransferase 0 ; 190.79 1.65E-17 5447300000 1225310 1283060 1098020 1226150 1206780 1362600 1175970 1217290 1871520 FALSE TRUE 1063382.179 1274631.494 1629026.145 1504566.098 1182767.439 1415020.104 1061924.61 956982.0065 1650271.038 0.644368201 0.772377061 0.987126422 0.911708479 0.71671102 0.857447093 0.643484971 0.579893838 1 20.65427156 2.24556303 24.98464455 0.703467789 0.820778997 0.033075631 0.144674993 341.5292155 1218581.893 0.055360299 0.041935449 176.0204108 -2.24556303 0.117311208 GTVQALHATGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GTVQALHATGAR 12 0 Q7Z4W1;J3KS22;J3QS36 Q7Z4W1 DCXR L-xylulose reductase 0 ;;; 148.68 0.0001134 968060000 1925890 1339120 642370 1067550 1354410 1377390 1124690 1442650 1312040 FALSE TRUE 1671378.757 1330323.233 953022.2806 1309953.544 1327459.891 1430379.085 1015617.737 1134150.524 1156932.126 1.444664488 1.14987146 0.823749518 1.132264819 1.147396516 1.23635523 0.87785421 0.98030861 1 20.1418728 4.65797934 3.581286879 1.029379154 1.461838183 0.525875929 0.123998352 0.198447205 4.23458736 0.031804987 0.195886558 45496.64163 -4.65797934 0.432459029 GTVSFHSHSDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GTVSFHSHSDHR 12 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;;; 172.11 2.12E-05 432884000 253501 273161 81233.6 140930.9 453878 399169 302044 374039 300402 FALSE TRUE 220000.2006 271366.5874 120518.4407 172931.4148 444846.7158 414525.2897 272751.8194 294053.6706 264888.8178 0.830537893 1.024454674 0.454977457 0.652845282 1.679371442 1.56490294 1.029684158 1.110102242 1 18.01502742 3.266391532 24.99993487 1.251843537 0.740562469 0.517917116 0.256385321 200.9732653 180528.7901 0.080123439 0.10341628 1846.679517 -3.266391532 -0.511281068 GTVTDFPGFDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GTVTDFPGFDER 12 0 P08758;D6RBE9;E9PHT9;D6RCN3 P08758 ANXA5 Annexin A5;Annexin 0 ;;;;; 207.29 1.87E-07 2345860000 4590710 5312090 2411370 2176010 2913080 3476160 2224000 3415200 5753580 FALSE TRUE 3984036.042 5277194.531 3577516.598 2670106.329 2855115.407 3609890.125 2008316.822 2684886.057 5073398.327 0.785279567 1.040169565 0.705151925 0.526295425 0.562761925 0.711532959 0.395852384 0.529208606 1 22.274521 4.05162552 5.691394778 0.599591295 0.909412601 0.325138541 0.169603761 0.195049589 13.8678733 0.042547974 0.090019572 11262.25924 -4.05162552 0.309821305 GTVTDFPGFDERADAETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTVTDFPGFDERADAETLR 19 1 P08758;D6RBE9;E9PHT9;D6RCN3 P08758 ANXA5 Annexin A5;Annexin 0 142.26 1.43E-07 155360000 182970 99443 81215 83341 143960 161500 126140 170770 47171 FALSE TRUE 158790.0509 98789.75239 120490.8456 102264.8478 141095.4777 167713.0095 113906.9622 134252.1644 41594.49812 3.817573432 2.375067782 2.89679768 2.45861478 3.39216685 4.032096001 2.738510317 3.227642369 1 15.34410509 1.23629089 24.99865808 0.999997293 3.091230716 0.605079934 0.537202695 42.71676964 470369.4971 0.835243117 0.128868804 17.23022269 -1.23629089 2.091233423 GTWERPGGAAPLGYDFWYQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTWERPGGAAPLGYDFWYQPR 21 1 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 172.24 5.34E-12 1853820000 462490 496720 316250 307900 399920 414890 383180 430050 329020 FALSE TRUE 401370.7747 493457.0136 469189.5578 377813.401 391962.3744 430851.0868 346019.2626 338087.1542 290123.6304 1.383447374 1.700850816 1.617205593 1.302249666 1.351018439 1.485060304 1.192661425 1.165320983 1 18.14630828 0.267290047 0.321240538 2.59E-20 1.604345673 0.682801953 0.118323954 10.80309894 0.637847665 7.557884109 0.240193668 1.850504079 -0.267290047 1.604345673 GTYHNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GTYHNK 6 0 P52566;H0YGX7 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ;;; 112.27 0.02714 1370340000 3107930 3529540 2141240 2627700 3122720 3093490 3743090 4549210 4601280 FALSE TRUE 2697209.176 3506354.219 3176750.826 3224359.447 3060583.981 3212498.562 3380085.708 3576396.843 4057321.92 0.664775739 0.864204095 0.782967408 0.794701409 0.754335998 0.791778081 0.833082948 0.88146736 1 21.95209634 0.843217304 0.879619092 1.303961853 0.776859211 0.690950428 0.048852238 2.297597287 0.864588095 1.384899274 0.016576039 6.969751667 -0.843217304 -0.527102641 GTYLATFHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GTYLATFHQR 10 0 P55884;P55884-2;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ; 168.74 4.85E-06 1632440000 1254840 1691640 1105470 1165710 1634520 1667770 1487380 1627240 1706290 FALSE TRUE 1089009.715 1680527.505 1640078.99 1430402.272 1601996.25 1731930.191 1343134.117 1279267.389 1504574.34 0.723799207 1.116945478 1.090061784 0.950702291 1.064750479 1.151109749 0.892700401 0.850252032 1 20.52092396 2.162638917 24.999997 0.900068245 1.023393951 0.125155807 0.12417806 62.29928352 20511.78401 0.048726056 0.032851107 145.424948 -2.162638917 0.123325706 GTYVPSS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GTYVPSSPTR 10 0 Q9Y4P8-4;Q9Y4P8 Q9Y4P8-4 WIPI2 WD repeat domain phosphoinositide-interacting protein 2 1 GTYVPS(0.002)S(0.997)PTR;GTYVPS(0.001)S(0.836)PT(0.163)R;GTYVPS(0.002)S(0.998)PTR;GTYVPS(0.002)S(0.998)PTR 224.09 4.33E-09 16796400000 7323200 7570000 5832800 5589450 8218700 9388500 7878000 8494000 8361100 TRUE FALSE 6355420.565 7520272.172 8653561.59 6858620.052 8055163.95 9749681.67 7113992.773 6677624.2 7372660.283 0.862025418 1.020021523 1.173736651 0.93027751 1.092572239 1.322410269 0.964915309 0.905727912 1 22.81375385 2.02732544 24.99999832 0.942887281 1.071127667 0.141901151 0.126906989 361.4247755 330665.3898 0.052234159 0.035215468 106.4940736 -2.02732544 0.128240386 GTYYFFDCLNWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GTYYFFDCLNWR 12 0 Q9NZN8;Q9NZN8-5;F8VP97;F8VV52;F8VUB4;Q9NZN8-3;Q9NZN8-2;H0YHT6 Q9NZN8 CNOT2 CCR4-NOT transcription complex subunit 2 0 131.82 0.00050046 0 161150 159770 119850 128100 156910 150390 157850 158040 164550 FALSE TRUE 139853.6192 158720.4604 177809.8609 157187.0629 153787.798 156175.6006 142541.7313 124244.3759 145097.0865 0.963862353 1.093891437 1.225454385 1.083323358 1.059895838 1.076352423 0.982388653 0.856284429 1 17.14665902 2.133469006 3.146877759 0.917632705 1.090940894 0.45771518 0.071700241 0.196449038 3.873468704 0.034898464 0.021023119 135.9781118 -2.133469006 0.173308189 GVAINMVTEEDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVAINMVTEEDKR 13 1 P60842 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 ; 188.48 9.74E-06 391020000 326100 245260 233060 224742 252410 240530 277530 358720 325580 FALSE TRUE 283005.0588 243648.8709 345768.5955 275773.1061 247387.5348 249783.3447 250615.1833 282010.5196 287090.3033 0.985770176 0.848683735 1.20438967 0.96057966 0.861706341 0.870051485 0.872948966 0.982305972 1 18.13114508 3.480430638 24.98475498 0.919025635 1.010848644 0.17156981 0.095889284 247.2926049 1866988.101 0.027675056 0.036457642 3022.947731 -3.480430638 0.091823009 GVAPADS(ph)PEAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GVAPADSPEAPR 12 0 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 GVAPADS(1)PEAPR;GVAPADS(1)PEAPR;GVAPADS(1)PEAPR 179.8 2.12E-05 2624150000 1141300 1072350 916180 1006090 1061190 1095650 1092150 1252770 1475920 TRUE FALSE 990474.3133 1065305.662 1359247.712 1234538.112 1040074.395 1137800.364 986233.4611 984874.8846 1301438.419 0.761061222 0.818560177 1.044419538 0.948595103 0.799172961 0.874263698 0.757802633 0.75675873 1 20.31167562 3.226078507 24.83954242 0.823342922 0.898634852 0.058447256 0.101215662 488.9105345 972935.0967 0.031630258 0.036117637 1682.978264 -3.226078507 0.07529193 GVAPADS(ph)PEAPRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GVAPADSPEAPRR 13 1 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 GVAPADS(1)PEAPRR;GVAPADS(1)PEAPRR;GVAPADS(1)PEAPRR 181.75 7.22E-06 3144600000 2531270 2224620 1518011 1646880 2183100 2303130 2101240 2400440 1490170 TRUE FALSE 2196756.256 2210006.325 2252126.197 2020829.275 2139660.581 2391732.901 1897462.068 1887124.586 1314003.8 1.671803579 1.681887316 1.713941921 1.537917375 1.628351897 1.820187203 1.444030883 1.43616372 1 20.32553802 0.817061149 1.016264468 1.38E-10 1.666956934 0.841851892 0.090398769 1.487863494 0.680196128 3.341762459 0.029181496 6.562376582 -0.817061149 1.666956934 GVAPLWMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVAPLWMR 8 0 F8VVM2;Q00325-2;Q00325 F8VVM2 SLC25A3 "Phosphate carrier protein, mitochondrial" 0 ; 142.63 0.0014294 726990000 698240 850080 575190 709200 1016930 1167030 695250 915060 951410 FALSE TRUE 605965.8149 844495.7685 853353.8079 870234.6994 996695.0826 1211926.399 627824.762 719381.54 838935.3936 0.722303314 1.006627894 1.017186561 1.037308363 1.188047483 1.444600393 0.748358892 0.857493372 1 19.67820019 4.74316088 4.066688107 1.028407021 0.694516739 0.222771457 0.1848001 0.432891339 15.36276941 0.049769273 0.427788553 55355.51295 -4.74316088 -0.333890282 GVCLIDEFDKMNDQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVCLIDEFDKMNDQDR 16 1 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 ; 97.836 0.0026796 311660000 321790 266780 159420 199458 254920 224065 280230 339610 177754 FALSE TRUE 279264.6362 265027.5046 236516.0452 244747.9874 249847.5907 232684.9255 253053.3377 266987.0443 156740.1246 1.781704824 1.690872106 1.508969358 1.561489045 1.594024449 1.484526863 1.614477074 1.703373945 1 17.25801502 1.233439821 24.99860672 0.999999051 1.61359287 0.822711174 0.090059898 69.26731421 338108.8675 0.18891304 0.023085008 17.11747967 -1.233439821 0.613593819 GVDDLDFFIGDEAIEKPTYATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GVDDLDFFIGDEAIEKPTYATK 22 1 B4DXW1;P61158;F8WDR7 B4DXW1 ACTR3 Actin-related protein 3 0 ;; 271.94 2.24E-45 1887400000 3737344 3043777 2364923 2798399 2636796 2098800 3557500 4192224 3914322 FALSE TRUE 3243444.521 3023782.228 3508607.673 3433818.264 2584328.918 2179542.194 3212494.198 3295749.522 3451575.312 0.939699768 0.876058598 1.016523574 0.994855378 0.748738963 0.631463027 0.930732754 0.954853718 1 21.71882353 3.273460664 24.99994553 0.860602867 0.955285307 0.176390113 0.110598043 404.0614062 289438.6459 0.035711224 0.046101016 1876.984402 -3.273460664 0.09468244 GVDLDAPGSINGVPLLEVDLDSFEDKPWR ddPTM_MDA-MB-175_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 ; 179.28 1.09E-17 355190000 101583 88033 71902 74040 81432 74432 104522 116163 101856 FALSE TRUE 88158.54917 87454.70543 106674.0477 90851.91363 79811.66252 77295.4472 94385.47253 91322.44643 89814.69971 0.981560362 0.973723741 1.187712569 1.011548376 0.888625835 0.860610206 1.050891144 1.016787305 1 16.45466397 GVDLLLEGVQGES(ph)SPTRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GVDLLLEGVQGESSPTRR 18 1 F5H7T0;F6RJM5;Q96S38-2;Q96S38 F5H7T0 RPS6KC1 Ribosomal protein S6 kinase delta-1 1 GVDLLLEGVQGES(0.408)S(0.408)PT(0.184)RR 93.776 0.001278 71826000 36454 39013 26707 27364 36429 39487 35268 40186 34027 TRUE FALSE 31636.51154 38756.72103 39622.59453 33577.41443 35704.13417 41006.09044 31847.71479 31592.53663 30004.36682 1.054396906 1.29170268 1.320560929 1.119084253 1.189964594 1.366670748 1.061435989 1.052931289 1 14.87288486 2.094467245 9.041119539 1.038331442 1.224772295 0.474399029 0.092436446 0.233606663 20.08411161 0.036883373 0.024843556 124.2988884 -2.094467245 0.186440853 GVDLVLNSLAEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GVDLVLNSLAEEK 13 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 229.54 1.30E-11 607340000 1345380 1301540 1074540 1037700 1209950 1165990 1474930 1655070 1710010 FALSE TRUE 1167584.624 1292990.098 1594191.138 1273325.645 1185874.362 1210846.39 1331891.516 1301146.16 1507854.566 0.774335039 0.857503189 1.057257891 0.844461843 0.786464682 0.80302598 0.883302373 0.86291224 1 20.52406586 1.236824113 6.904104234 1.00322268 0.861529937 0.240874193 0.078707741 0.188867504 49.21866801 0.124166568 0.020082953 17.25139076 -1.236824113 -0.141692743 GVEEEEEDGEMRE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GVEEEEEDGEMRE 13 1 P62306 P62306 SNRPF Small nuclear ribonucleoprotein F 0 ;;; 220.25 4.33E-10 3105300000 1865640 1795310 1241125 1303655 1629710 1633120 1610350 1660473 1807160 FALSE TRUE 1619090.947 1783516.49 1841337.201 1599669.793 1597281.959 1695947.183 1454178.505 1305393.771 1593519.604 1.016047084 1.119230969 1.155515876 1.0038595 1.002361035 1.064277577 0.91255765 0.819189025 1 20.60378534 2.205189426 4.897593953 0.888557874 1.062621896 0.531796248 0.065388261 0.132486017 7.579681226 0.027730583 0.01893155 160.3944831 -2.205189426 0.174064022 GVEFPMADLDALS(ph)PIHT(ph)PQR ddPTM_MDA-MB-175_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 79.426 0.013456 10532000 19172 19527 16725 13078 16192 20861 16277 17328 21957 TRUE FALSE 16638.37162 19398.72585 24813.26594 16047.55978 15869.81088 21663.53617 14698.45905 13622.54205 19361.26847 0.859363716 1.001934655 1.281592989 0.828848575 0.819667931 1.118910995 0.759168185 0.703597601 1 14.24088585 2.686560297 0.915918257 0.806096583 1.013224138 0.096638408 0.166808205 1.091577878 2.061266617 0.138702809 0.094283658 485.91499 -2.686560297 0.207127556 GVEGLIDIENPNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GVEGLIDIENPNR 13 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 146.16 9.81E-05 196030000 299530 306360 226280 226400 281390 309280 267130 313360 357540 FALSE TRUE 259946.3516 304347.501 335709.7649 277807.5803 275790.8895 321178.2017 241223.7737 246350.4026 315272.0285 0.824514477 0.965348884 1.06482572 0.881167865 0.874771196 1.018733578 0.765129006 0.781389975 1 18.26623765 2.234431585 24.99944252 0.831299708 0.939736309 0.160304162 0.093571184 157.2697036 952182.7544 0.037073293 0.026024363 171.5661417 -2.234431585 0.108436601 GVEPS(ph)PSPIKPGDIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GVEPSPSPIKPGDIK 15 1 Q92890;Q92890-1;Q92890-3;C9JNP9 Q92890 UFD1L Ubiquitin fusion degradation protein 1 homolog 1 GVEPS(0.559)PS(0.441)PIKPGDIK 76.713 0.010712 0 138130 102160 108640 114650 76147 61232 135270 159250 241940 TRUE FALSE 119875.7705 101488.9042 161178.6674 140683.0348 74631.82368 63587.63466 122151.5362 125195.6268 213338.1288 0.561905043 0.475718545 0.75550802 0.659436902 0.34982881 0.298060337 0.572572455 0.586841309 1 17.70278231 1.166988859 2.515610166 1.183416166 0.5226939 0.551879112 0.133345079 0.58800262 3.450662888 0.916845555 0.037908719 14.68888596 -1.166988859 -0.660722266 GVEPSPS(ph)PIKPGDIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVEPSPSPIKPGDIK 15 1 Q92890;Q92890-1;Q92890-3;C9JNP9 Q92890 UFD1L Ubiquitin fusion degradation protein 1 homolog 1 GVEPS(0.022)PS(0.978)PIKPGDIK;GVEPS(0.027)PS(0.973)PIKPGDIK 97.32 0.0020345 415960000 622420 531060 550480 624940 460130 340170 642480 789510 1253130 TRUE FALSE 540165.62 527571.4319 816693.9692 766842.1786 450974.3132 353256.56 580172.3885 620679.4305 1104986.399 0.488843682 0.477446087 0.739098662 0.693983364 0.408126574 0.31969313 0.525049348 0.561707756 1 20.07559718 1.230519834 4.092536985 1.054554431 0.524342116 0.599483158 0.121949611 0.191429128 5.74253604 0.306850852 0.033635634 17.00277602 -1.230519834 -0.530212314 GVEPSPS(ph)PIKPGDIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVEPSPSPIKPGDIKR 16 2 Q92890;Q92890-1;Q92890-3 Q92890 UFD1L Ubiquitin fusion degradation protein 1 homolog 1 GVEPS(0.013)PS(0.987)PIKPGDIKR;GVEPS(0.019)PS(0.981)PIKPGDIKR 147.16 5.50E-07 524860000 783740 584480 475340 483740 548280 391490 732600 960840 309820 TRUE FALSE 680166.7733 580640.5124 705216.0139 593580.5605 537370.3007 406550.8736 661552.5648 755371.8433 273193.4325 2.489689327 2.125382397 2.581379821 2.172748279 1.966995677 1.488142924 2.42155369 2.764970725 1 18.05956328 3.501180883 8.601863488 2.049687 2.372849708 0.135453596 0.493548879 0.780682591 253.7815975 0.142358544 0.204209981 3170.887855 -3.501180883 0.323162709 GVESVFDIMEMEDEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GVESVFDIMEMEDEER 16 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;;;;; 248.77 4.30E-20 285659000 218194 191692 179136 178237 184606 192766 178045 199015 252633 FALSE TRUE 189359.1101 190432.7626 265766.7688 218708.435 180932.7018 200181.8328 160778.2233 156457.191 222767.0145 0.850032086 0.854851707 1.193025679 0.981781057 0.812205982 0.898615233 0.72173263 0.702335538 1 17.7651761 3.233337665 9.45190086 0.806969893 0.977744292 0.233520788 0.12546517 0.160239601 169.8500227 0.038622706 0.046073413 1711.345374 -3.233337665 0.170774399 GVGDDQLGEESEERDDHLLPM ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GVGDDQLGEESEERDDHLLPM 21 1 P20645;F5GX30;H0YF90 P20645 M6PR Cation-dependent mannose-6-phosphate receptor 0 ;;;; 179.41 5.25E-17 2917560000 2920230 2854070 1914300 2080240 2817690 3158770 2619190 3248160 2663490 FALSE TRUE 2534314.207 2835321.426 2840061.883 2552590.286 2761623.482 3280289.926 2365181.357 2553566.261 2348615.246 1.079067425 1.207231125 1.20924953 1.086849066 1.175851807 1.396691063 1.007053565 1.087264619 1 21.16337896 GVGDGTVSWGLEDDEDMTLTR ddPTM_MDA-MB-175_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 ; 218.6 1.25E-24 126886000 124743 113649 67037 88759 119982 134623 109140 120081 105419 FALSE TRUE 108257.8965 112902.4322 99456.31743 108913.0875 117594.5929 139802.0339 98555.6196 94402.61262 92956.48591 1.164608316 1.214572938 1.069923378 1.171656679 1.265049897 1.503951366 1.060233922 1.015557029 1 16.50426791 2.02371967 24.99902794 1.017591266 1.227278193 0.440254647 0.110670464 215.0438437 226641.6333 0.04760394 0.032092894 105.6135571 -2.02371967 0.209686927 GVGISVLEMSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVGISVLEMSHR 12 0 Q9Y617;Q9Y617-2 Q9Y617 PSAT1 Phosphoserine aminotransferase 0 ; 115.33 0.00017592 0 781292 797666 494996 571974 779987 790177 625797 736372 802515 FALSE TRUE 678042.2827 792426.0795 734377.7213 701849.4388 764466.7847 820575.6205 565107.3033 578904.5783 707642.5909 0.958170539 1.119811173 1.037780556 0.991813449 1.080300698 1.159590492 0.798577291 0.81807481 1 19.43266136 2.231066094 24.99997753 0.857869311 1.057823031 0.555478773 0.077956058 114.6514657 382446.379 0.030910164 0.021298335 170.2417577 -2.231066094 0.199953719 GVGQADWT(ph)PDLGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVGQADWTPDLGLR 14 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 GVGQADWT(1)PDLGLR;GVGQADWT(1)PDLGLR 190.19 7.07E-06 277450000 780450 819630 556200 563610 666670 784090 620860 722860 838110 TRUE FALSE 677311.5551 814245.7966 825180.1804 691586.2647 653404.5713 814254.4497 560649.0928 568282.0143 739029.5906 0.916487734 1.101776988 1.116572585 0.935803212 0.884138578 1.101788697 0.758628748 0.768957051 1 19.49527261 2.233425125 24.99998179 0.823705355 1.009454309 0.361296368 0.103605528 124.9252284 608137.6699 0.041792102 0.029138652 171.1690047 -2.233425125 0.185748954 GVGSGPHPPDTQQPS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GVGSGPHPPDTQQPSPSK 18 0 Q68CZ2;E9PCX8;Q68CZ2-2 Q68CZ2 TNS3 Tensin-3 1 GVGSGPHPPDTQQPS(0.999)PS(0.001)K;GVGSGPHPPDTQQPS(1)PSK;GVGSGPHPPDTQQPS(0.991)PS(0.009)K;GVGSGPHPPDT(0.001)QQPS(0.997)PS(0.002)K 186.7 3.01E-14 2355630000 2599530 2649330 1733850 2148500 2917610 2551460 3148900 3653650 3252360 TRUE FALSE 2255995.524 2631926.377 2572345.659 2636349.763 2859555.269 2649616.317 2843520.163 2872345.38 2867869.706 0.786645056 0.917728714 0.896953461 0.919271108 0.997100832 0.923897035 0.991509536 1.001560627 1 21.45154805 6.845405688 0.343814094 1.005280692 1.96E-14 0.805487841 0.029324292 15.21493636 0.489550242 0.041221504 8.389203671 7004960.449 -6.845405688 -1.005280692 GVHIHQAGGS(ph)PPASSTSSSSLTNDVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GVHIHQAGGSPPASSTSSSSLTNDVAK 27 0 Q8N122;Q8N122-3;I3L436 Q8N122 RPTOR Regulatory-associated protein of mTOR 1 GVHIHQAGGS(0.794)PPAS(0.015)S(0.015)T(0.055)S(0.055)S(0.055)S(0.011)SLTNDVAK;GVHIHQAGGS(0.973)PPAS(0.011)S(0.011)T(0.002)S(0.002)S(0.001)S(0.001)S(0.001)LTNDVAK;GVHIHQAGGS(0.938)PPAS(0.012)S(0.002)T(0.047)S(0.001)SSSLTNDVAK 294.07 8.93E-71 3600570000 871570 712180 442920 683370 797810 697520 894440 1035150 1003430 TRUE FALSE 756389.8162 707501.6427 657117.5935 838539.6032 781935.1419 724354.0458 807697.3465 813791.228 884805.6485 0.854865492 0.799612484 0.74266885 0.9477105 0.883736607 0.81865893 0.912852837 0.919740091 1 19.75500107 -2 0.318320895 2.550560815 0.810570533 0.498052573 0.053434264 66.28133938 1.059577853 65.84986499 0.092188835 0.01 2 -1.739990282 GVHLRPVNQTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVHLRPVNQTAR 12 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2;A0MZ66-7 A0MZ66 KIAA1598 Shootin-1 0 ; 153.74 4.26E-05 192053000 192630 179461 138890 160589 190523 208844 204290 222178 270780 FALSE TRUE 167173.4574 178282.1089 206057.6686 197053.1869 186731.9651 216878.3638 184477.9872 174666.9637 238768.6969 0.700148133 0.746672873 0.863001186 0.825289033 0.782062169 0.908319921 0.772622164 0.731532089 1 17.86525418 4.406762598 4.713734815 0.826599086 0.709770149 0.285293316 0.076163293 0.257985724 10.66423826 0.018867156 0.055446292 25513.06278 -4.406762598 -0.116828937 GVHPHIVEMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVHPHIVEMDR 11 0 O76041-2;O76041 O76041-2 NEBL Nebulette 0 ; 129.16 0.00014507 326730000 176600 142110 104470 105525 132971 151410 124535 138632 102889 FALSE TRUE 153261.8626 141176.4701 154992.0414 129486.0641 130325.1373 157234.8407 112457.6149 108986.6256 90725.57963 1.689290531 1.556082316 1.708360994 1.427227741 1.436476215 1.733081688 1.239535921 1.20127781 1 16.46922175 2.104958259 5.068758372 1.144114147 1.579935284 0.767093294 0.116490667 0.100429262 4.1095463 0.049660513 0.032723905 127.3380687 -2.104958259 0.435821137 GVIDYDRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GVIDYDRDR 9 1 P49750;P49750-1;H0YIQ2;P49750-3;F8VU51;H0YI23 P49750 YLPM1 YLP motif-containing protein 1 0 66.568 0.057787 269560000 288560 253400 210440 200640 264320 319370 246940 288240 251630 FALSE TRUE 250426.0649 251735.3987 312209.4879 246198.3786 259060.5491 331656.3706 222991.7968 226602.1191 221882.5881 1.128642257 1.134543278 1.407093232 1.109588547 1.167556911 1.494738156 1.00499908 1.021270398 1 17.75943693 GVITDQNS(ph)DGYCQTGTMSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GVITDQNSDGYCQTGTMSR 19 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 GVITDQNS(1)DGYCQTGTMSR 282.72 7.31E-40 0 47135 44587 30550 27045 43506 42664 39249 48157 41362 TRUE FALSE 40905.99033 44294.10506 45324.08218 33185.98061 42640.31572 44305.31169 35442.63802 37859.00031 36472.23148 1.12156533 1.214461064 1.2427011 0.909897181 1.169117271 1.214768329 0.971770484 1.038022593 1 15.15451085 -1.999999905 0.183708946 0.166062114 1.22444573 0.231700453 0.100479232 165.0863721 2.35394198 47.50402609 0.854744744 0.010000002 1.999999905 1.058383616 GVIVDKDFSHPQMPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVIVDKDFSHPQMPK 15 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ; 179.56 4.00E-07 2630700000 7515700 5995500 4547500 5309300 5340700 4505900 7442500 8676300 6077500 FALSE TRUE 6522481.203 5956115.166 6746686.21 6514857.713 5234430.519 4679244.889 6720727.496 6820940.764 5359024.874 1.217102245 1.111417712 1.258939148 1.215679693 0.976750555 0.873152299 1.254095223 1.272795131 1 22.35353908 GVKPAHCEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVKPAHCEK 9 1 Q14894;I3L3Y1 Q14894 CRYM Ketimine reductase mu-crystallin 0 ; 88.681 0.0075825 712870000 1866080 1757420 1265300 1481260 1334220 1268380 1967950 2355970 2106590 FALSE TRUE 1619472.8 1745875.392 1877203.312 1817602.723 1307671.632 1317175.399 1777098.512 1852164.15 1857551.33 0.871832059 0.939880026 1.01057951 0.978493942 0.703976042 0.709092329 0.956688778 0.997099848 1 20.82497065 2.015144226 24.98632717 0.99190829 0.872511344 0.235538908 0.100020265 377.5406694 622898.8648 0.045835518 0.030890686 103.5485987 -2.015144226 -0.119396946 GVKPVFSIGDEEEYDT(ph)DEIDSSSMSDDDRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVKPVFSIGDEEEYDTDEIDSSSMSDDDRK 30 2 Q9NUY8-2;Q9NUY8;E9PGE5 Q9NUY8-2 TBC1D23 TBC1 domain family member 23 1 GVKPVFSIGDEEEYDT(1)DEIDSSSMSDDDRK;GVKPVFSIGDEEEYDT(1)DEIDSSSMSDDDRK 244.49 4.18E-44 477480000 396090 329420 331400 313300 285968 229174 410990 503950 443700 TRUE FALSE 343745.7029 327256.0183 491666.1485 384439.5535 280277.7963 237990.4721 371132.2531 396184.2142 391246.2915 0.878591594 0.836445036 1.256666604 0.982602422 0.716371765 0.608288123 0.94858983 1.012621009 1 18.57771755 GVLCEAQEAAMPEIQEQIHDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GVLCEAQEAAMPEIQEQIHDYR 22 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 0 119.79 1.15E-05 0 27779 28390 21613 20727 29782 33909 29379 28617 29117 FALSE TRUE 24107.93477 28203.50422 32065.11909 25433.38214 29189.39647 35213.50117 26529.8291 22497.47725 25674.82143 0.938971857 1.098488817 1.248893558 0.990596262 1.136888003 1.371518835 1.033301407 0.876246688 1 14.64806662 2.000904497 24.99999804 0.936930859 1.134823286 0.29648908 0.123459741 33.14741356 916166.9466 0.050653093 0.03382497 100.2084852 -2.000904497 0.197892427 GVLRPGTALVLLEAQAATGFVIDPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GVLRPGTALVLLEAQAATGFVIDPVR 26 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;;; 199.1 5.35E-25 1264227000 911855 868909 655752 744239 787988 913805 884218 871422 858226 FALSE TRUE 791351.0514 863201.0796 972875.8606 913229.8399 772308.5805 948959.6697 798466.6745 685075.1867 756767.5 1.045699044 1.140642376 1.285567708 1.206750871 1.020536136 1.253964619 1.055101698 0.905265074 1 19.52949061 1.998708652 5.797100793 0.954333921 1.159848247 0.507123463 0.084495561 0.117169169 14.9942237 0.037983062 0.022967912 99.70309766 -1.998708652 0.205514326 GVLTGPEYEALDALPDAERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GVLTGPEYEALDALPDAERR 20 1 H3BM67;H3BUP2;H3BUN4;O60936;O60936-3;O60936-1;H3BQJ5 H3BM67 NOL3 Nucleolar protein 3 0 ;; 218.14 1.62E-24 311772000 162533 145924 101160 85440 111372 139465 128096 138507 82268 FALSE TRUE 141053.8522 144965.4156 150081.3144 104840.4579 109155.9151 144830.3088 115673.2696 108888.3559 72542.37076 1.944434001 1.998355087 2.068877992 1.445230653 1.504719434 1.996492633 1.594561474 1.501031118 1 16.14653627 0.849351944 0.857001505 8.46E-32 1.833862863 0.60375051 0.21084828 3.232344478 1.174631023 6.582004074 0.083559734 7.06890172 -0.849351944 1.833862863 GVMAVTAVTATAAS(ph)DR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.998)DR;GVMAVTAVTATAAS(1)DR;GVMAVTAVTAT(0.001)AAS(0.999)DR;GVMAVTAVTATAAS(1)DR 208.39 1.57E-11 882800000 794159 735306 790026 991250 752400 756065 787971 836601 2433160 TRUE FALSE 689208.876 730475.7265 1172085.216 1216328.463 737428.712 785151.3098 711553.6937 657700.3866 2145514.597 0.321232434 0.340466445 0.546295615 0.56691689 0.343707152 0.365950113 0.3316471 0.306546685 1 21.03289229 1.233758935 24.99995125 1.000000926 0.390278551 0.81298229 0.091893999 68.82931838 358316.3283 0.196631263 0.024717377 17.13006202 -1.233758935 -0.609722374 GVNCIDYYSGGDKPYLISGADDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GVNCIDYYSGGDKPYLISGADDR 23 1 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ;;;; 257.38 1.20E-43 6300980000 3986270 3401780 2377230 2730590 3286230 3012740 3682490 4367030 3465880 FALSE TRUE 3459474.32 3379433.483 3526866.379 3350612.194 3220840.452 3128642.057 3325362.687 3433174.619 3056147.615 1.131972259 1.105782151 1.15402357 1.096351556 1.053889032 1.023720858 1.088089682 1.123366752 1 21.5432828 3.477850644 5.036188769 1.066941088 1.128062936 0.45804047 0.035513764 0.19658114 14.69900784 0.010728138 0.014868041 3005.042673 -3.477850644 0.061121848 GVNTGAVGSYIYDRDPEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GVNTGAVGSYIYDRDPEGK 19 1 P52943;H0YFA4;H0YHD8;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 ;;; 287.37 2.15E-40 4152120000 4741620 3293120 2210470 2727380 2926010 2646290 3724280 4361790 3479210 FALSE TRUE 4115002.903 3271487.278 3279460.686 3346673.314 2867788.126 2748094.489 3363099.899 3429055.152 3067901.757 1.341308565 1.066359857 1.068958834 1.090867172 0.934771825 0.895757005 1.096221511 1.11772 1 21.54882085 5.593741757 1.30507006 1.030807994 3.207609255 0.651619496 0.071083289 7.925690257 2.18737386 0.022370746 39.18616024 392411.5275 -5.593741757 2.17680126 GVNWAAFHPTMPLIVSGADDR ddPTM_MDA-MB-175_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 ;; 207.43 3.67E-22 7959680000 3497050 3633430 1975700 2289330 3412490 3664220 2812910 3378700 3101760 FALSE TRUE 3034905.982 3609561.759 2931155.128 2809157.367 3344588.125 3805184.914 2540114.421 2656191.298 2735073.466 1.109625032 1.319731189 1.071691552 1.027086622 1.222851293 1.391255102 0.9287189 0.971159031 1 21.38314815 2.202917268 24.99999783 0.965990705 1.184913065 0.480260363 0.109626405 157.271456 110308.0362 0.04577995 0.030866035 159.5575165 -2.202917268 0.21892236 GVPAGNS(ph)DTEGGQPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.882)DT(0.118)EGGQPGR;GVPAGNS(0.999)DT(0.001)EGGQPGR;GVPAGNS(0.995)DT(0.005)EGGQPGR 235.02 1.14E-19 1886700000 843974 761602 456247 575911 697905 653977 736541 853060 716193 TRUE FALSE 732440.6975 756598.9863 676889.5753 706680.3948 684018.0559 679135.9184 665111.3672 670639.7575 631525.4794 1.159795957 1.198049819 1.071832566 1.119005357 1.083120283 1.075389577 1.053182158 1.061936184 1 19.26848142 8 0.144396556 0.958558352 1.766049226 0.741604763 0.028456511 78.06597402 0.958519429 0.515807392 12.83615257 100000000 -8 0.807490873 GVPEKS(ph)PVLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GVPEKSPVLEK 11 1 O00515;E9PDI4;A0A0J9YYF6 O00515 LAD1 Ladinin-1 1 GVPEKS(1)PVLEK;GVPEKS(1)PVLEK;GVPEKS(1)PVLEK;GVPEKS(1)PVLEK;GVPEKS(1)PVLEK;GVPEKS(1)PVLEK 163.8 1.42E-05 9238560000 18329440 16506900 13060120 14975580 16495160 11761780 20742380 24816100 22129670 TRUE FALSE 15907158.06 16398465.09 19376037.72 18376014.33 16166938.59 12214263.29 18730787.18 19509370.13 19513525.62 0.815186265 0.840364033 0.992954225 0.941706521 0.828499109 0.625938312 0.95988739 0.999787046 1 24.21797113 2.020887147 24.99974449 0.993866118 0.846803951 0.349388608 0.094631995 275.7651371 330060.8144 0.041283852 0.027830731 104.9269737 -2.020887147 -0.147062167 GVPHPEDDHS(ph)QVEGPESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GVPHPEDDHSQVEGPESLR 19 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 GVPHPEDDHS(1)QVEGPESLR 102.21 0.00043206 0 147320 147370 87662 82594 153470 120700 163730 177270 102100 TRUE FALSE 127851.2887 146401.9168 130055.6364 101348.2301 150416.2473 125343.4071 147851.4898 139362.19 90029.85431 1.420098807 1.626148547 1.444583437 1.125718028 1.670737428 1.392242696 1.642249573 1.547955299 1 16.45811586 1.234362552 24.9777293 0.999999275 1.489185606 0.47799575 0.158770051 109.5817024 651901.5315 0.285692264 0.037836418 17.15388728 -1.234362552 0.489186331 GVPHPEDDHSQVEGPESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GVPHPEDDHSQVEGPESLR 19 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ;;;; 242.1 1.25E-24 4638090000 1591160 1536200 1034630 1138930 1410240 1593160 1373780 1700470 1488650 FALSE TRUE 1380884.175 1526108.601 1534980.529 1397541.464 1382178.983 1654449.896 1240551.027 1336837.724 1312663.493 1.051971188 1.162604589 1.169363311 1.064660876 1.052957586 1.260376254 0.945064012 1.018416167 1 20.32406569 2.210249659 24.99995842 0.99241772 1.124335914 0.49844695 0.065716075 178.2833132 157431.5963 0.025836668 0.017422829 162.2742682 -2.210249659 0.131918194 GVPLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 5070260000 5951330 5517610 3801960 3269370 4986340 5310240 4960540 5655920 4709040 FALSE TRUE 5164846.662 5481364.457 5640600.573 4011730.428 4887121.59 5514528.369 4479467.594 4446445.522 4152342.656 1.243839223 1.320065542 1.358414042 0.966136651 1.176955274 1.328052337 1.078780815 1.070828178 1 21.98549407 -1.54599171 0.190748224 1.31E-15 1.351658859 0.360263682 0.112198228 105.5833736 1.804367925 39.43616647 0.906860507 0.028445154 1.54599171 1.351658859 GVQDIVVGEGTHFLIPWVQKPIIFDCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVQDIVVGEGTHFLIPWVQKPIIFDCR 27 1 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 ; 210.8 7.21E-26 2445900000 2738500 2251100 1680520 2487920 2331490 3091100 1718190 2524210 2652900 FALSE TRUE 2376600.287 2236312.376 2493225.093 3052840.261 2285097.91 3210016.617 1551560.198 1984427.335 2339277.184 1.015954972 0.955984349 1.065810033 1.30503571 0.97683931 1.372225848 0.663264793 0.848307908 1 21.15763139 2.226075503 24.99999836 0.832260065 1.108146399 0.416555322 0.154970868 216.9639334 434441.6886 0.061481398 0.041774156 168.2966623 -2.226075503 0.275886334 GVQKPAGPSTS(ph)PDGNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GVQKPAGPSTSPDGNSR 17 1 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 GVQKPAGPS(0.047)T(0.213)S(0.725)PDGNS(0.015)R;GVQKPAGPS(0.009)T(0.188)S(0.803)PDGNSR;GVQKPAGPS(0.007)T(0.078)S(0.915)PDGNSR 160.52 1.87E-09 986630000 738850 609030 493110 592600 692410 596040 738230 897310 777780 TRUE FALSE 641209.1005 605029.2418 731579.6454 727158.8873 678632.3957 618970.0445 666636.5682 705427.2394 685831.7344 0.93493647 0.882183211 1.066704278 1.060258444 0.989502762 0.902510067 0.972011843 1.028571884 1 19.38749514 4.254057727 24.99999462 1.001442741 0.908559811 0.400658921 0.047893764 265.6670428 428567.5648 0.012909964 0.033885468 17949.72202 -4.254057727 -0.09288293 GVQVETISPGDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVQVETISPGDGR 13 0 P62942;A0A087WZM5;Q1JUQ3;A0A087WTS4;A0A087WV48 P62942 FKBP1A;FKBP12-Exin Peptidyl-prolyl cis-trans isomerase FKBP1A;Peptidyl-prolyl cis-trans isomerase 0 ; 162.93 9.22E-05 438550000 407210 369020 243300 269080 353750 379650 359290 412800 387770 FALSE TRUE 353396.1668 366595.8833 360960.6938 330178.7266 346711.0671 394255.3812 324446.1111 324525.9324 341928.2723 1.033538889 1.072142648 1.055662029 0.965637396 1.013987714 1.153035338 0.948871846 0.949105291 1 18.38333419 GVQYLNEIKDSVVAGFQWATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVQYLNEIKDSVVAGFQWATK 21 1 P13639 P13639 EEF2 Elongation factor 2 0 ; 311.65 1.37E-66 2064010000 2882100 2521080 1322840 1635240 2208220 1612280 3136100 3750100 830210 FALSE TRUE 2501223.183 2504518.859 1962569.849 2006546.235 2164280.742 1674305.455 2831961.505 2948170.298 732063.5196 3.416675078 3.421176978 2.680873717 2.740945535 2.956411137 2.28710407 3.868464182 4.02720559 1 19.48160931 4.262179471 23.3586922 2.947792346 3.418927473 0.065009392 0.840455524 396.6654889 392280.8133 0.212155221 0.56031507 18288.55828 -4.262179471 0.471135127 GVS(ph)CFR ddPTM_MDA-MB-175_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 107.59 0.032658 2092860000 3300420 2769550 3118560 2813290 2757910 3797540 2539380 2626170 3445020 TRUE FALSE 2864261.135 2751356.644 4626706.047 3452090.493 2703032.987 3943633.821 2293111.318 2064583.982 3037753.66 0.942887889 0.90572079 1.523068216 1.136395797 0.889813095 1.298207249 0.754870728 0.679641674 1 21.53457345 2.2208987 24.86825433 0.781672915 1.115603501 0.322798918 0.206414427 247.6233961 348654.7369 0.084477222 0.0570957 166.3024701 -2.2208987 0.333930586 GVS(ph)MPNMLEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GVSMPNMLEPK 11 0 O14639-3;F8W8M4;O14639-5;O14639-2;O14639;J3QSX6;A0A0A0MRL6;A0A3B3IS55;O14639-4;O14639-6 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 GVS(1)MPNMLEPK;GVS(1)MPNMLEPK;GVS(1)MPNMLEPK;GVS(1)MPNMLEPK;GVS(1)MPNMLEPK 124.3 0.00036919 863619000 3061730 2600370 1819330 2131300 2346880 2067230 2560240 3178100 3066350 TRUE FALSE 2657114.623 2583287.998 2699164.073 2615244.24 2300181.68 2146757.676 2311948.319 2498488.047 2703849.596 0.982715395 0.95541113 0.998267092 0.967229924 0.850706224 0.793963421 0.855058034 0.924048457 1 21.36658347 3.304614595 7.179320504 0.883013808 0.976870157 0.414152327 0.053890195 0.24524958 22.03566503 0.017048489 0.02196413 2016.576002 -3.304614595 0.093856349 GVSFYEVPPHLFAVADTVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVSFYEVPPHLFAVADTVYR 20 0 O00159-3;F5H6E2;O00159-2;O00159;I3L3F5;I3L501;I3L3Y6 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 185.13 3.76E-17 470810000 882360 877360 606270 720880 847770 973020 752380 949910 866370 FALSE TRUE 765753.8904 871596.5644 899464.1999 884566.822 830901.0356 1010452.709 679414.3034 746779.1387 763948.7256 1.00236294 1.140909769 1.17738818 1.157887686 1.087639795 1.322670848 0.889345424 0.97752521 1 19.54311629 2.216121025 24.9999998 0.957424778 1.146836571 0.539574629 0.083823116 174.4876757 194395.6185 0.032719765 0.022077862 164.4830024 -2.216121025 0.189411793 GVSMSLPS(ph)SPLLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GVSMSLPSSPLLPR 14 0 Q9C0D5;Q9C0D5-2 Q9C0D5 TANC1 Protein TANC1 1 GVSMS(0.004)LPS(0.568)S(0.428)PLLPR 92.856 0.018735 95364000 271690 210370 146650 136250 201250 233370 171000 223940 200190 TRUE FALSE 235785.4781 208988.0656 217570.4305 167187.645 197245.5187 242347.8949 154416.4463 176052.1737 176523.7663 1.335715202 1.183908944 1.232527694 0.94711125 1.11738789 1.372891028 0.874762926 0.997328447 1 17.42950291 8 0.129485877 0.801400855 2.441389451 0.329957724 0.135518813 234.2843775 2.659150223 3.825282228 69.40840142 100000000 -8 1.639988596 GVSMSLPSS(ph)PLLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVSMSLPSSPLLPR 14 0 Q9C0D5;Q9C0D5-2 Q9C0D5 TANC1 Protein TANC1 1 GVSMSLPS(0.169)S(0.831)PLLPR;GVSMS(0.001)LPS(0.063)S(0.936)PLLPR 141.54 1.01E-05 226384000 612620 538660 323730 377170 485280 518210 464470 544650 444270 TRUE FALSE 531660.7148 535121.507 480286.9108 462812.2132 475623.8774 538145.874 419425.7709 428180.836 391748.9067 1.357146646 1.365980856 1.226007023 1.18140014 1.214103905 1.373701023 1.070649499 1.092998164 1 18.57956972 -0.614404159 0.285366661 4.19E-12 1.354700832 0.639662668 0.077772392 24.3876408 0.807841898 13.83516081 0.202267887 0.242994163 0.614404159 1.354700832 GVSQEKEAQISS(ph)AIVSSVQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GVSQEKEAQISSAIVSSVQSK 21 1 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 GVS(0.356)QEKEAQIS(0.253)S(0.391)AIVSSVQSK 136.57 2.86E-06 197080000 275590 234970 124960 93305 203100 162840 305380 359490 60724 TRUE FALSE 239170.0832 233426.4666 185391.074 114491.3263 199058.7074 169104.5602 275764.2946 282615.8611 53545.2779 4.466688616 4.359422077 3.4623235 2.138215186 3.717577258 3.1581601 5.150114173 5.278072543 1 15.70847173 GVTDHTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVTDHTQR 8 0 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 141.52 0.00063223 283233000 373113 359731 267019 250339 284756 396317 342163 361286 384589 FALSE TRUE 323805.1717 357367.9034 396150.2815 307182.2961 279089.9127 411563.5714 308980.0849 284027.8004 339123.3265 0.954830135 1.053799239 1.16815993 0.905812936 0.822974685 1.213610328 0.911114219 0.837535428 1 18.3714505 2.265147173 0.550470395 0.883731293 1.034933686 0.047011818 0.126617426 4.114192355 2.394167185 0.390798205 0.126245164 184.1395907 -2.265147173 0.151202393 GVTECYECHPKPTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GVTECYECHPKPTQR 15 1 Q9UBT2;Q9UBT2-2;K7EPL2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 ;;; 283.34 4.15E-34 1503090000 2071390 1584660 1105250 1288420 1516600 1415710 1691100 1918210 1648070 FALSE TRUE 1797650.563 1574250.264 1639752.597 1580975.453 1486422.627 1470173.28 1527097.382 1508015.719 1453237.042 1.236997483 1.083271496 1.128344894 1.087899226 1.022835631 1.011654147 1.050824702 1.037694248 1 20.47083861 8 0.447194378 1.021231685 5.482116615 0.827272346 0.028937593 39.43031029 0.49862912 0.022074364 159.6378533 100000000 -8 4.460884931 GVTIPYRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GVTIPYRPK 9 1 F8VZX2;Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3;Q15366-5;Q15366-4;Q15366-8;Q15366-7;F8VRH0 F8VZX2;Q15366;Q15366-2;Q15366-5 PCBP2 Poly(rC)-binding protein 2 0 65.224 0.061254 355370000 228050 196470 139280 164730 179260 179080 212030 291080 324070 FALSE TRUE 197912.6147 195179.3756 206636.2739 202134.4642 175693.0767 185969.3235 191467.3632 228834.8072 285758.8138 0.692586213 0.683021367 0.723114262 0.707360384 0.614829948 0.650791208 0.670031348 0.800797022 1 18.12443847 1.325270593 2.078264885 1.063133453 0.676720551 0.91950461 0.030663847 0.166206729 0.850117144 0.115444378 0.009227574 21.14806287 -1.325270593 -0.386412901 GVTIPYRPKPSS(ph)SPVIFAGGQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GVTIPYRPKPSSSPVIFAGGQDR 23 2 Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3 Q15366;Q15366-2 PCBP2 Poly(rC)-binding protein 2 1 GVTIPYRPKPS(0.119)S(0.762)S(0.119)PVIFAGGQDR 223.12 1.19E-32 4110200000 1351800 1130300 685080 854190 981430 935770 1137600 1246700 912450 TRUE FALSE 1173156.205 1122874.985 1016386.979 1048146.895 961901.4631 971769.6774 1027275.727 980102.9068 804581.2005 1.458095472 1.395601816 1.263249724 1.302723571 1.195530622 1.207795654 1.276783159 1.21815288 1 19.6178785 8 0.201703947 1.083869503 2.879352002 0.699805867 0.067333458 65.06324771 0.967607185 0.443795631 35.80573332 100000000 -8 1.795482499 GVTIPYRPKPSSS(ph)PVIFAGGQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GVTIPYRPKPSSSPVIFAGGQDR 23 2 Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3 Q15366;Q15366-2 PCBP2 Poly(rC)-binding protein 2 1 GVTIPYRPKPSSS(1)PVIFAGGQDR 241.15 1.45E-37 16585000000 4603100 3703300 2604600 3188300 3569400 3197900 3683900 4425000 3345200 TRUE FALSE 3994788.672 3678972.778 3864193.272 3912252.245 3498375.923 3320925.282 3326635.945 3478748.185 2949734.267 1.354287645 1.247221765 1.310014029 1.326306674 1.185996977 1.125838798 1.127774791 1.179342907 1 21.49215356 3.066339971 3.147914023 1.122334711 1.305288417 0.762321335 0.052676536 0.126756898 2.551416043 0.016645142 0.018824754 1165.037678 -3.066339971 0.182953706 GVTIPYRPKPSSSPVIFAGGQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVTIPYRPKPSSSPVIFAGGQDR 23 2 Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3 Q15366;Q15366-2 PCBP2 Poly(rC)-binding protein 2 0 ; 140.66 1.08E-07 5497400000 3151100 2352100 2135700 2097900 2470200 2267100 2759000 2837400 2401200 FALSE TRUE 2734674.151 2336648.9 3168531.663 2574260.259 2421047.853 2354316.804 2491432.605 2230644.091 2117332.871 1.291565529 1.10358127 1.496473089 1.215803284 1.143442245 1.111925685 1.176684421 1.053516016 1 21.01381667 3.235819949 2.774938124 1.092744678 1.286468778 0.441300292 0.103937119 0.256165866 4.046522747 0.032344723 0.040520826 1721.154868 -3.235819949 0.193724101 GVTLGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVTLGFR 7 0 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 110.36 0.015867 1133710000 596230 782450 477520 533020 621020 768130 612710 701670 693690 FALSE TRUE 517436.6948 777310.0344 708450.2692 654050.3377 608662.917 797680.4581 553289.4785 551623.3309 611682.7585 0.845923296 1.270773164 1.158198853 1.069263975 0.995063059 1.304075433 0.904536659 0.901812783 1 19.22242409 2.17935918 24.99996495 0.927153303 1.110147131 0.272418595 0.132038908 89.15801075 37649.25153 0.050691477 0.034176201 151.1329572 -2.17935918 0.182993828 GVTQYYAYVTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVTQYYAYVTER 12 0 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ; 107.09 0.0035893 101020000 379820 379300 280100 321630 355350 411900 315560 400040 369460 FALSE TRUE 329625.8247 376808.3533 415557.2969 394661.0073 348279.2302 427746.0595 284957.0398 314494.5591 325782.8597 1.011796093 1.156624243 1.275565256 1.211423485 1.069053266 1.312979019 0.874683954 0.965350232 1 18.31355118 2.228085805 24.99999836 0.947568322 1.173863205 0.57056974 0.092515979 146.4919757 349626.1024 0.036593619 0.024965773 169.077495 -2.228085805 0.226294883 GVTSEEFDKFLEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GVTSEEFDKFLEER 14 1 O60784;O60784-3 O60784 TOM1 Target of Myb protein 1 0 73.91 0.03148 82416000 66463 69227 43207 51549 68954 66033 63319 78244 50350 FALSE TRUE 57679.74615 68772.24328 64102.04972 63253.98833 67581.95031 68573.33224 57178.33313 61512.1295 44397.68036 1.299161255 1.549005325 1.443815289 1.42471381 1.522195524 1.544525112 1.287867579 1.385480705 1 15.43819668 0.709225791 1.231926256 1.43E-20 1.457660213 0.700691876 0.089567369 2.565526504 1.282227299 6.645952804 0.025456964 5.119479301 -0.709225791 1.457660213 GVVDSDDLPLNVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GVVDSDDLPLNVSR 14 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;;; 313.05 2.03E-55 3248720000 3716220 3766950 2870860 3147540 3794710 4985770 3147280 3251510 2960030 FALSE TRUE 3225112.111 3742204.657 4259217.498 3862237.064 3719202.695 5177575.798 2842057.27 2556199.89 2610098.625 1.235628447 1.43374071 1.631822436 1.4797284 1.424928031 1.983670558 1.088869686 0.979349924 1 21.31567289 2.028158502 24.89758467 1.001972838 1.525471723 0.616129402 0.190437369 120.6021132 106635.1702 0.075822516 0.051118502 106.6985462 -2.028158502 0.523498884 GVVDSEDLPLNISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GVVDSEDLPLNISR 14 0 P08238;P07900;P07900-2 P08238;P07900 HSP90AB1;HSP90AA1 Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha 0 ;;;;; 371.4 8.78E-97 5199220000 5732810 5232570 3670870 3990260 5120020 5612830 4857000 5821010 5274590 FALSE TRUE 4975204.633 5198196.903 5446115.01 4896309.52 5018141.619 5828759.202 4385968.888 4576232.311 4651033.979 1.069698621 1.117643287 1.170947156 1.052735702 1.078930329 1.253217936 0.943009427 0.983917196 1 22.14912005 2.209048192 24.99991633 0.976006392 1.120444426 0.587526984 0.05849724 142.1682921 120429.5143 0.023186031 0.015634426 161.82596 -2.209048192 0.144438034 GVVEVTHDLQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GVVEVTHDLQK 11 0 P50454;E9PKH2 P50454 SERPINH1 Serpin H1 0 ;;; 178.81 7.38E-06 5307540000 11038500 11040700 9220800 10321500 11503900 13127500 11463100 12084100 11891200 FALSE TRUE 9579734.257 10968172.91 13680009.72 12665154.33 11274994.9 13632523.42 10351410.33 9500009.254 10485435.88 0.913622892 1.046038814 1.30466772 1.207880576 1.075300543 1.300138933 0.987217932 0.906019488 1 23.3218835 2.04375007 13.38108774 0.946390317 1.144382154 0.333701433 0.118406599 1.405581914 428.550667 0.049161499 0.033136219 110.5987121 -2.04375007 0.197991837 GVVHDDMECSHYMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVVHDDMECSHYMK 14 0 F8VQZ7;P50579-3;P50579;F8VRR3;P50579-2 F8VQZ7 METAP2 Methionine aminopeptidase 2 0 ; 135.58 1.85E-05 164063000 295960 260492 150731 182106 245283 247988 240691 265900 229483 FALSE TRUE 256848.1361 258780.8109 223625.0158 223455.9506 240402.3482 257528.2588 217348.8239 209039.3542 202353.7812 1.26930238 1.27885335 1.105119037 1.104283544 1.188029929 1.272663438 1.074103101 1.033039032 1 17.62652028 -0.659505502 0.362283175 1.11E-13 1.229370644 0.542660802 0.068857761 25.32607593 0.953314635 17.78515952 0.098815598 0.219025408 0.659505502 1.229370644 GVVPLAGTNGETTTQGLDGLSER ddPTM_MDA-MB-175_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 ;;; 447.43 5.84E-203 880090000 163114 153209 100804 136149 128496 155267 128106 153069 169247 FALSE TRUE 141558.0716 152202.56 149553.1516 167063.7114 125939.181 161240.222 115682.2998 120336.3855 149238.8125 0.948533892 1.019859093 1.002106283 1.119438761 0.843876864 1.080417482 0.77514889 0.806334381 1 17.18726326 2.236629742 24.99997713 0.845655016 1.001271734 0.335347652 0.093373657 50.96208406 659811.5709 0.035157886 0.025051754 172.4367157 -2.236629742 0.155616717 GVVTEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 86.866 0.019762 724800000 1741800 1837120 839370 1346440 1026070 1948310 1690750 1855350 2290600 FALSE TRUE 1511616.717 1825051.838 1245292.14 1652169.781 1005653.214 2023262.746 1526781.325 1458597.841 2019807.877 0.748396287 0.903576948 0.616539896 0.817983631 0.497895481 1.001710494 0.755904233 0.722146823 1 20.94578664 2.715199317 24.99343294 0.836156715 0.727293107 0.208425508 0.140762641 1692.716375 1810975.309 0.047050522 0.041518273 519.0381935 -2.715199317 -0.108863608 GVWDHGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GVWDHGGR 8 0 Q9Y3S2;D6RBR7;D6R8Y9 Q9Y3S2 ZNF330 Zinc finger protein 330 0 ; 147.34 0.00053893 88264000 272839 258028 171486 196931 221352 270769 219453 248295 257048 FALSE TRUE 236782.6349 256332.9971 254417.2032 241647.1935 216947.5283 281185.6586 198170.4818 195199.0465 226660.0783 1.044659636 1.130913741 1.122461464 1.066121548 0.957149269 1.240561023 0.874306951 0.861197296 1 17.79017079 2.210720462 24.99935253 0.8997215 1.089193048 0.531000287 0.080205709 152.0168727 136503.9951 0.031313136 0.021116449 162.450279 -2.210720462 0.189471548 GVYSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GVYSGR 6 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ;;; 126.68 0.040453 1057128000 1051156 1212571 763593 909811 901456 1374247 1098991 1135295 1131631 FALSE TRUE 912243.0713 1204605.541 1132869.129 1116397.493 883518.7893 1427115.171 992411.022 892520.9991 997850.8723 0.914207821 1.207199968 1.135309053 1.118801941 0.885421673 1.43018883 0.994548434 0.894443272 1 19.9284647 2.01462603 24.99924507 0.941125949 1.118535729 0.187196295 0.151660403 323.5434002 553007.8775 0.058281794 0.039276983 103.4251192 -2.01462603 0.17740978 GWAFGSNS(ph)LPIAGSVGMGVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GWAFGSNSLPIAGSVGMGVAR 21 0 M0QZ22;Q5PRF9;A0A087WZT0 M0QZ22 SAMD4B Protein Smaug homolog 2 1 GWAFGSNS(1)LPIAGSVGMGVAR;GWAFGS(0.097)NS(0.903)LPIAGSVGMGVAR 274.39 1.02E-44 385750000 529120 472350 361510 408220 501960 544760 472680 569980 563260 TRUE FALSE 459195.4514 469247.1017 536337.4452 500912.5903 491971.9781 565717.2697 426839.5664 448094.2126 496672.0445 0.924544589 0.944782592 1.079862358 1.008537919 0.990536882 1.139015727 0.859399217 0.902193344 1 18.92193402 2.206939868 24.99999697 0.914163409 1.012980189 0.28566781 0.069812273 242.5199402 191739.5222 0.028490661 0.019210294 161.0422642 -2.206939868 0.09881678 GWDAEGSPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GWDAEGSPFR 10 0 Q8IVD9 Q8IVD9 NUDCD3 NudC domain-containing protein 3 0 105.1 0.0085576 0 216100 201830 162080 167990 192940 212880 191640 198480 286260 FALSE TRUE 187541.8375 200504.1654 240462.4301 206134.6971 189100.8715 221069.6314 173054.7823 156036.5966 252418.6689 0.742979266 0.79433176 0.952633302 0.81663808 0.749155648 0.875805392 0.685586304 0.618165832 1 17.94545909 2.236608003 24.99854074 0.733288681 0.823063142 0.018383492 0.114976531 114.0355789 1459906.807 0.044985054 0.032055744 172.428084 -2.236608003 0.089774461 GWDDLFNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GWDDLFNK 8 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 148.38 0.0012147 864420000 1607310 1504870 1096280 1112290 1564760 1427260 1722230 2004120 1892070 FALSE TRUE 1394899.911 1494984.41 1626444.675 1364852.445 1533624.337 1482167.616 1555208.4 1575554.534 1668391.64 0.836074623 0.896063235 0.974857843 0.818064783 0.919223221 0.888381109 0.932160269 0.944355328 1 20.67002656 0.321874777 0.636230089 1.300336729 0.887187872 0.424555736 0.042763093 9.714616233 1.27425809 3.812977438 0.020106493 2.098334769 -0.321874777 -0.413148856 GWDEALLTMSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GWDEALLTMSK 11 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 81.771 0.033106 0 162010 135190 119690 112730 181200 164930 126340 160300 132350 FALSE TRUE 140599.968 134301.928 177572.4843 138327.0695 177594.4745 171274.9638 114087.5662 126021.0925 116703.7338 1.204759809 1.150793755 1.521566437 1.185284009 1.521754864 1.467604834 0.977582829 1.079837709 1 16.83249119 2.230329826 24.99515012 1.030053882 1.342485922 0.555599851 0.135983546 138.921287 421869.8911 0.055106015 0.037861011 169.9533877 -2.230329826 0.31243204 GWDLVDAVTPGPQPTLEQLEEGGPRPLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GWDLVDAVTPGPQPTLEQLEEGGPRPLER 29 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 ;; 189.08 4.29E-18 330403000 150188 136624 90646 86567 129060 146050 121176 141690 133092 FALSE TRUE 130340.2753 135726.5079 134482.7088 106223.3604 126491.9585 151668.638 109424.3702 111390.6961 117358.0154 1.11062099 1.156516728 1.145918396 0.905122331 1.077829734 1.292358579 0.932397926 0.949152862 1 16.84055685 GWEEDEDPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GWEEDEDPER 10 0 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 163.32 1.51E-05 203470000 309230 263440 201150 221880 251670 274290 227650 265210 389700 FALSE TRUE 268364.472 261709.4453 298426.8128 272261.2452 246662.2594 284842.1138 205572.538 208496.9054 343630.1099 0.780969025 0.761602193 0.86845362 0.792309048 0.717813289 0.828920707 0.59823785 0.606748068 1 18.39049693 3.286852016 5.302168254 0.724792949 0.804033755 0.019407827 0.116963235 0.512547499 31.78019863 0.034928131 0.044532727 1935.762248 -3.286852016 0.079240807 GWEEGVAQMSVGQR ddPTM_MDA-MB-175_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 ; 225.15 6.71E-12 512650000 272630 195516 181309 188748 220932 268180 192647 254830 363190 FALSE TRUE 236601.2547 194231.6425 268990.6388 231606.1182 216535.8854 278497.0581 173964.1236 200336.5876 320254.0919 0.738792292 0.606492305 0.839928812 0.723194876 0.676137763 0.869612802 0.54320656 0.625555122 1 18.28885748 1.23005123 24.99038778 1.000000569 0.698039707 0.465352736 0.09997298 299.6683445 879997.454 0.276791223 0.024446662 16.98443991 -1.23005123 -0.301960861 GWEFMWNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 GWEFMWNER 9 0 P12532;P12532-2;P17540 P12532 CKMT1A;CKMT2 "Creatine kinase U-type, mitochondrial;Creatine kinase S-type, mitochondrial" 0 ;;;;;;;; 149.72 0.00020229 5834289000 3968290 4201258 2622866 2971692 3963620 4638529 3229321 4062048 3697240 FALSE TRUE 3443870.422 4173659.66 3891292.771 3646460.088 3884751.717 4816976.212 2916141.946 3193410.646 3260156.499 1.056351259 1.280202242 1.19359079 1.118492345 1.191584428 1.477529135 0.894479129 0.979526795 1 21.63650979 2.203073464 24.99998895 0.959839364 1.215324009 0.5434141 0.11299855 132.4235664 93288.85673 0.04478111 0.030192658 159.6149125 -2.203073464 0.255484645 GWEVVESDLYAMNFNPIISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GWEVVESDLYAMNFNPIISR 20 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 331.39 1.78E-79 395070000 179690 176000 140150 174450 177230 174020 185970 195340 300340 FALSE TRUE 155943.5112 174843.8444 207927.0088 214061.5388 173703.4697 180714.662 167934.658 153568.0611 264834.1473 0.588834608 0.660201285 0.785121597 0.808285264 0.65589529 0.682369188 0.634112556 0.579865031 1 18.01472963 GWEWEGEWIVDPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GWEWEGEWIVDPER 14 0 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-2;H0YD14;Q9NZM1-5 Q9NZM1-6 MYOF Myoferlin 0 ;;; 218.54 1.24E-11 222023000 285548 256990 232431 241148 287948 328027 243659 329792 337329 FALSE TRUE 247812.1083 255301.8158 344835.409 295904.3391 282218.3982 340646.411 220028.9877 259268.5472 297450.3499 0.833120917 0.858300607 1.159304096 0.994802458 0.948791616 1.14522108 0.739716688 0.871636383 1 18.18228935 0.939960854 19.58196346 1.861022231 0.94258133 0.017551711 0.131685362 64.33041788 180674.4117 24002.48849 0.031992491 8.708850883 -0.939960854 -0.918440902 GWFVYQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GWFVYQQR 8 0 A0A3B3ISG5;P14735;P14735-2 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 92.319 0.027596 661340000 817880 1069000 694500 694830 936550 914440 970590 1039100 1141900 FALSE TRUE 709795.0858 1061977.669 1030362.523 852601.7713 917914.4873 949619.0985 876462.3312 816896.5513 1006905.883 0.704926943 1.054694075 1.023295762 0.846754186 0.911618954 0.943106118 0.870451098 0.811293851 1 19.94149741 2.226182679 24.43249675 0.87572457 0.922252322 0 0.105857528 662.3624961 1307406.573 0.041674168 0.028341411 168.3381999 -2.226182679 0.046527752 GWGS(ph)PGRPK ddPTM_MDA-MB-175_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 75.819 0.022517 808950000 1500800 1349480 937390 1030470 1254640 1233160 1496180 1543400 1416700 TRUE FALSE 1302465.477 1340615.177 1390714.939 1264453.963 1229675.119 1280600.463 1351080.694 1213355.921 1249219.34 1.04262353 1.073162362 1.113267218 1.012195315 0.984354852 1.025120587 1.081540007 0.971291335 1 20.25259538 3.713531903 23.29197468 1.01181332 1.076032161 0.44761785 0.033475391 291.6375925 271400.4947 0.009441563 0.014013469 5170.492384 -3.713531903 0.064218841 GWIDLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GWIDLQR 7 0 Q13951-2;A0A494C0A9;Q13951;J3KS23;H3BSC0 Q13951-2 CBFB Core-binding factor subunit beta 0 ; 110.61 0.015737 283860000 873280 892960 566990 552840 894230 915530 810160 891540 718490 FALSE TRUE 757873.8354 887094.087 841188.2605 678370.7716 876436.5725 950751.0315 731590.8079 700891.109 633550.9307 1.196231903 1.400193803 1.327735814 1.070743864 1.383371928 1.500670247 1.154746639 1.106290079 1 19.27310108 2.013511608 24.51558072 1.081671501 1.311429421 0.457281134 0.11907474 166.1663067 301492.1674 0.049610181 0.033425843 103.1600653 -2.013511608 0.22975792 GWLRDPSAS(ph)PGDAGEQAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GWLRDPSASPGDAGEQAIR 19 1 P18206;P18206-2 P18206 VCL Vinculin 1 GWLRDPS(0.003)AS(0.997)PGDAGEQAIR;GWLRDPS(0.017)AS(0.983)PGDAGEQAIR;GWLRDPSAS(1)PGDAGEQAIR;GWLRDPSAS(1)PGDAGEQAIR 223.68 1.30E-19 1660350000 788560 814470 578630 643020 713860 877240 620300 771330 1211150 TRUE FALSE 684349.798 809119.6929 858457.4034 789027.5189 699655.5826 910987.9904 560143.4015 606387.082 1067969.227 0.640795428 0.757624539 0.803822228 0.7388111 0.6551271 0.853009588 0.524493953 0.567794527 1 20.02643865 2.251014437 24.99401482 0.663216518 0.741043367 0.002137591 0.13982579 673.0874932 1350842.996 0.051646603 0.039720354 178.2438017 -2.251014437 0.077826849 GWLYYEAGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GWLYYEAGQR 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 ; 154.49 3.35E-05 926140000 1074310 961710 875630 748040 904170 978130 1219780 1100940 884020 FALSE TRUE 932337.2115 955392.4637 1299087.597 917893.9151 886178.786 1015759.294 1101485.923 865512.5485 779512.1627 1.196052167 1.225628681 1.666539227 1.177523532 1.136837664 1.303070488 1.413045205 1.110325906 1 19.57221201 1.560259119 4.599530755 1.02269015 1.302078248 0.327010436 0.151372548 0.181591692 8.201000929 0.116320543 0.03958444 36.32947478 -1.560259119 0.279388098 GWMDWAAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GWMDWAAHK 9 0 Q9UN36;Q9UN36-5;G3V578;H0YJT9;A0A0A0MS87;Q9UN36-2;Q9UN36-3;Q9UN36-6;G3V5H8;G3V4S9;G3V5L7;A0A0U1RR50;G3V2I9;G3V2A6;H0YJ56;G3V5G0;G3V392;G3V383;G3V5B7;G3V5S0 Q9UN36 NDRG2 Protein NDRG2 0 ; 101.9 0.0036728 685690000 1367280 2083000 1356430 1519510 2081080 1813670 1956440 2211460 2395100 FALSE TRUE 1186590.484 2069316.636 2012404.085 1864537.97 2039670.58 1883443.059 1766704.75 1738556.489 2111954.007 0.561844851 0.979811411 0.952863594 0.882849704 0.965774147 0.891801172 0.836526148 0.823198083 1 21.01014699 4.746090508 24.96294978 0.906392058 0.561844683 0.774069692 0.060007697 469.6844382 1557051.298 0.015584028 0.160142343 55730.18793 -4.746090508 -0.344547375 GWNYILEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GWNYILEK 8 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 126.41 0.0028389 464760000 334640 343360 191140 305590 322790 333050 367200 359910 488840 FALSE TRUE 290416.4761 341104.4456 283575.9433 374978.8802 316367.1105 345862.649 331589.0005 282946.0473 431049.8921 0.673742139 0.791334024 0.65787267 0.869919903 0.733945458 0.802372661 0.76925898 0.656411363 1 18.71749534 GWPLYLSTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GWPLYLSTK 9 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 170.22 0.00013465 186790000 575110 632300 444340 478270 651220 610010 603980 686080 648080 FALSE TRUE 499107.7564 628146.3797 659224.3102 586868.5134 638261.9961 633477.4794 545406.1126 539367.1311 571464.7207 0.873383322 1.099186629 1.153569567 1.026954932 1.116887837 1.108515463 0.95440032 0.943832771 1 19.12430491 2.227905566 24.99569078 0.960956747 1.069640555 0.25549416 0.077359319 256.6187013 601996.7345 0.030663945 0.020914165 169.0073399 -2.227905566 0.108683808 GWQDVTATSAYKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GWQDVTATSAYKK 13 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 0 78.373 0.037528 511910000 374120 358390 208390 312750 364870 328180 479690 567330 183220 FALSE TRUE 324679.0941 356035.7125 309168.101 383764.6676 357609.8009 340805.297 433169.7376 446010.8945 161559.9403 2.009650991 2.203737584 1.913643323 2.375370199 2.213480645 2.109466593 2.681170448 2.760652756 1 17.30170999 3.730772178 24.40113345 2.277781525 2.058483327 0 0.484775207 1598.487917 5008060.313 0.132019231 0.200093307 5379.874914 -3.730772178 -0.219298198 GWS(ph)QEGPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 120.86 0.00066109 1691620000 2982240 1362450 689810 1291490 1147360 622754 2068600 1760620 1446130 TRUE FALSE 2588129.428 1353499.976 1023404.423 1584742.544 1124529.781 646711.7494 1867987.49 1384125.114 1275170.159 2.029634563 1.061426953 0.802563028 1.242769471 0.88186645 0.507157217 1.464892726 1.085443464 1 20.28225834 4.736480052 5.468828463 1.012527267 2.066262614 0.616908734 0.253819855 0.098931704 11.40385485 0.06173647 0.391470273 54510.48576 -4.736480052 1.053735347 GWSQEGPVKS(ph)PAECR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GWSQEGPVKSPAECR 15 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR 183.65 3.01E-07 2687290000 1961910 1890140 1607370 2084580 2545580 2123860 2467320 3271530 3220420 TRUE FALSE 1702638.623 1877723.546 2384699.508 2557915.75 2494927.938 2205566.269 2228039.686 2571938.769 2839705.616 0.599582792 0.661238804 0.839769973 0.90076793 0.878586824 0.77668835 0.784602345 0.905706125 1 21.43730995 4.273901944 3.115818065 0.868814019 0.609855961 0.720447945 0.062780013 0.137189913 2.658723343 0.017433799 0.053034743 18788.92548 -4.273901944 -0.258958058 GWVTFDR ddPTM_MDA-MB-175_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 ; 143 0.005702 291840000 502420 461320 339790 354530 439330 479970 450670 487100 523200 FALSE TRUE 436023.924 458289.5585 504113.5805 435031.4552 430588.1925 498434.7565 406964.0928 382937.4556 461347.892 0.945108738 0.993370874 1.092697267 0.942957501 0.933326455 1.080388065 0.882119762 0.830040545 1 18.81549554 2.20718475 24.98947792 0.887720073 0.996631775 0.287253578 0.068119607 211.5449706 168484.6994 0.027353536 0.018443628 161.1330953 -2.20718475 0.108911702 GYADS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.988)PS(0.012)K;GYADS(0.999)PS(0.001)K;GYADS(0.986)PS(0.014)K;GYADS(0.988)PS(0.012)K 134.84 0.00090126 4547170000 11947100 11814300 7902090 9322750 8898070 9247200 11826500 14352100 12998700 TRUE FALSE 10368260.46 11736691.09 11723567.15 11439622.88 8721015.816 9602945.768 10679567.85 11283015.1 11462008.49 0.904576233 1.023964612 1.022819618 0.998046973 0.760862795 0.837806548 0.931736166 0.984383767 1 23.45035653 GYAFIEFASFEDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GYAFIEFASFEDAK 14 0 P19338;H7BY16 P19338 NCL Nucleolin 0 201.46 2.42E-07 0 30665 27406 17213 18927 22148 20269 25754 31656 26930 FALSE TRUE 26612.54255 27225.96818 25537.26437 23224.66463 21707.29813 21048.76155 23256.38104 24886.61075 23746.36608 1.120699583 1.146531983 1.075417783 0.978030262 0.914131369 0.88639927 0.979365894 1.048017649 1 14.53541913 3.8819053 2.893651043 0.970626244 1.131921734 0.717268993 0.044404991 0.172378514 2.767610847 0.014826097 0.029677094 7619.128524 -3.8819053 0.16129549 GYAFIEYEHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GYAFIEYEHER 11 0 P08621;P08621-2;M0QYR1;P08621-3 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;;;;; 171.62 1.43E-05 7421740000 7648960 6814780 4670930 4853910 6142790 6899390 5895160 6889160 6370730 FALSE TRUE 6638130.556 6770013.261 6929807.371 5956064.453 6020560.497 7164813.998 5323448.291 5415966.746 5617589.557 1.181668844 1.205145587 1.233590902 1.060252692 1.071733781 1.275424971 0.947639239 0.964108661 1 22.42151979 2.221793314 24.99978612 0.968277841 1.166098789 0.668701916 0.06652677 145.9009615 217534.3949 0.027792216 0.018794077 166.6453938 -2.221793314 0.197820948 GYAFNHSADFETVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GYAFNHSADFETVR 14 0 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ;;;; 176.89 2.16E-06 3925060000 2756480 2489124 2025029 2247403 2476583 2748051 2464554 2627199 2868646 FALSE TRUE 2392204.184 2472772.781 3004339.798 2757710.201 2427303.844 2853770.3 2225541.932 2065392.939 2529517.938 0.945715446 0.97756681 1.187712391 1.090211759 0.959591473 1.128187414 0.879828484 0.816516423 1 21.27043104 2.220875941 24.62850048 0.880853232 1.049183551 0.386463668 0.087757717 186.8766501 260250.7509 0.035985356 0.024325378 166.2937553 -2.220875941 0.168330318 GYAFVQYSNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GYAFVQYSNER 11 0 Q9UKM9;Q9UKM9-2;Q5QPM1;Q5QPL9;Q5QPM2 Q9UKM9 RALY RNA-binding protein Raly 0 173.37 2.85E-05 263670000 162670 221570 151980 146340 190640 289310 151960 198520 198360 FALSE TRUE 141172.7473 220114.4921 225478.0363 179568.7337 186846.637 300439.9429 137222.9426 156068.0429 174910.1068 0.807116009 1.258443529 1.289108105 1.026634407 1.068243799 1.717682005 0.784534097 0.892275728 1 17.41625413 GYAVLGGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 ;;;;;;; 159.04 0.00015437 17392610000 7992590 10942910 8294930 7309930 11353660 13951810 9956910 10306480 11267300 FALSE TRUE 6936348.981 10871025.3 12306385.89 8969761.332 11127744.38 14488545.16 8991290.401 8102519.457 9935292.63 0.698152459 1.094182699 1.238653591 0.902818031 1.120021804 1.458290732 0.90498496 0.81552902 1 23.24413103 2.038411262 24.99987413 0.884287111 1.09397126 0.145356471 0.201568725 256.5647434 166983.5172 0.081631957 0.055036154 109.2474384 -2.038411262 0.209684149 GYAYTFITEDQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GYAYTFITEDQAR 13 0 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ;; 177.57 3.57E-05 335095000 361170 380680 248800 251826 374730 377440 337800 397720 379240 FALSE TRUE 313440.4694 378179.288 369120.5122 309006.9422 367273.6061 391960.361 305040.208 312670.6731 334406.6792 0.937303256 1.130896335 1.103807236 0.924045366 1.098284302 1.172106855 0.912183359 0.93500128 1 18.35124414 2.210601174 24.99999868 0.944595691 1.061652944 0.298863203 0.080777156 254.7498234 227783.3614 0.03251377 0.021925795 162.4056648 -2.210601174 0.117057253 GYCIYGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GYCIYGDR 8 0 C9IZP5;C9JYI0;C9JYX8;C9J031;F8WAS8;C9IY57;Q9UHC7-4;Q9UHC7-3;Q9UHC7-2;Q9UHC7 C9IZP5 MKRN1 E3 ubiquitin-protein ligase makorin-1 0 83.614 0.041959 123150000 108320 110090 72443 77723 99992 118020 103630 95461 97114 FALSE TRUE 94005.23755 109366.8115 107476.6771 95371.19507 98002.35483 122560.3058 93579.97855 75047.40803 85633.29355 1.097765059 1.277152927 1.255080503 1.113716303 1.1444422 1.431222608 1.092799012 0.876381194 1 16.38588419 1.997459159 24.99279265 0.945929475 1.21968969 0.578238366 0.099341976 62.27242467 612539.5845 0.040176499 0.026555408 99.41665784 -1.997459159 0.273760216 GYDDRDYYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GYDDRDYYSR 10 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 ;;;; 191.52 7.15E-07 21518800000 36411600 33005000 19701400 21199100 31010000 31613300 28423100 33073500 19548900 FALSE TRUE 31599714.8 32788187.98 29229062.94 26012679.66 30392961.67 32829484.11 25666632.14 26000989.4 17237851.31 1.833158567 1.902104119 1.695632617 1.509044207 1.76315256 1.904499784 1.488969343 1.508366033 1 24.03907662 0.855774834 1.010934571 2.67E-20 1.755826433 0.761380845 0.132126941 1.931769109 0.929438143 4.458680672 0.045588215 7.174222379 -0.855774834 1.755826433 GYDFCQVLQWFAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GYDFCQVLQWFAER 14 0 Q9H223 Q9H223 EHD4 EH domain-containing protein 4 0 ; 156.36 1.30E-05 264200000 251337 254292 202941 218901 238080 279506 294090 297420 267972 FALSE TRUE 218122.1786 252621.5391 301083.9464 268605.8177 233342.6738 290258.7767 265569.1971 233819.0475 236292.6554 0.923101813 1.069104491 1.274199343 1.1367506 0.987515559 1.228386791 1.123899499 0.989531592 1 17.85021526 1.720661845 6.23908214 0.995408882 1.112517477 0.167685199 0.102106678 0.226047128 22.58089686 0.061658828 0.026630697 52.56078524 -1.720661845 0.117108596 GYDRYEDYDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GYDRYEDYDYR 11 1 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 0 99.5 0.0043126 505010000 1279100 1066800 511460 419960 808090 994040 922910 1038300 89109 FALSE TRUE 1110063.694 1059792.121 758803.7667 515318.3367 792010.59 1032281.362 833406.3303 816267.6251 78574.63553 14.12750675 13.48771284 9.657108322 6.558329328 10.07972337 13.1375902 10.60655674 10.38843667 1 16.26177605 4.236284043 4.391350349 9.108908315 13.95414981 0.294872473 3.221123477 0.256652168 11.80564631 0.82922625 2.10787842 17229.95104 -4.236284043 4.845241492 GYDS(ph)EDDTWEPEQHLVNCEEYIHDFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GYDSEDDTWEPEQHLVNCEEYIHDFNR 27 0 Q9Y232;Q9Y232-2 Q9Y232 CDYL Chromodomain Y-like protein 1 GYDS(1)EDDTWEPEQHLVNCEEYIHDFNR;GYDS(1)EDDTWEPEQHLVNCEEYIHDFNR;GYDS(1)EDDTWEPEQHLVNCEEYIHDFNR;GYDS(0.984)EDDT(0.016)WEPEQHLVNCEEYIHDFNR 344.94 8.46E-97 1549020000 327183 295588 244147 333524 305701 334871 253576 318442 474032 TRUE FALSE 283944.9376 293646.263 362217.3058 409255.7218 299618.1482 347753.7041 228984.2385 250345.6564 417992.477 0.679306335 0.702515665 0.866564175 0.979098296 0.716802729 0.831961634 0.547819043 0.598923833 1 18.67311745 2.290197304 24.99996234 0.684285104 0.799714975 0.048663377 0.146853295 219.105561 106079.0974 0.055579912 0.043051962 195.0730631 -2.290197304 0.115429871 GYDSGPEGGAAAS(ph)PPPDAELAACHPAAWSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GYDSGPEGGAAASPPPDAELAACHPAAWSR 30 0 Q9H6K5-2;Q9H6K5 Q9H6K5-2 PRR36 Proline-rich protein 36 1 GYDSGPEGGAAAS(1)PPPDAELAACHPAAWSR;GYDSGPEGGAAAS(1)PPPDAELAACHPAAWSR;GYDSGPEGGAAAS(1)PPPDAELAACHPAAWSR;GYDSGPEGGAAAS(1)PPPDAELAACHPAAWSR 282.43 7.65E-72 1420000000 602100 759540 494820 577210 821590 748220 595090 887720 787950 TRUE FALSE 522530.9595 754550.5317 734116.6071 708274.3526 805241.9664 777004.5076 537378.2634 697887.9862 694799.4486 0.752060124 1.085997597 1.05658778 1.019393947 1.158955966 1.118314802 0.773429318 1.004445222 1 19.40623708 2.277757273 24.99979226 0.935953019 1.040675668 0.133021717 0.12529277 308.8887805 197009.3676 0.045734302 0.035425084 189.564615 -2.277757273 0.104722649 GYDVDFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GYDVDFPR 8 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9;O94808 Q06210-2 GFPT1;GFPT2 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1;Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 2 0 ;;;;; 145.34 0.0013282 3054640000 5670080 5370410 3899160 4196870 5607380 5850470 5104930 5849810 5790860 FALSE TRUE 4920764.562 5335131.423 5784806.818 5149833.479 5495804.109 6075541.367 4609854.674 4598873.655 5106271.128 0.963670835 1.044819456 1.132882817 1.008531147 1.076285213 1.18981958 0.902782982 0.900632485 1 22.28383871 2.209344081 24.99999422 0.926101502 1.068661224 0.470350268 0.067265957 170.3211359 145739.1142 0.027231969 0.018363034 161.9362511 -2.209344081 0.142559722 GYDYGPHFQGILEASLEGDSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 30 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 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 344.28 5.86E-82 22294257200 8070853.2 7875777.7 7112316.9 6562199.9 8066421.9 9707164.8 8035685.2 8546321.4 10519168.6 FALSE TRUE 7004269.501 7824041.198 10551857.14 8052247.684 7905915.886 10080605.71 7256385.686 6718757.076 9275604.472 0.755128091 0.84350742 1.137592399 0.86811029 0.852334304 1.08678693 0.782308658 0.724347087 1 23.14500987 GYEENYFFIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GYEENYFFIFR 11 0 B4DGJ5;Q8N7H5-3;Q8N7H5-2;Q8N7H5 B4DGJ5 PAF1 RNA polymerase II-associated factor 1 homolog 0 98.943 0.011968 124370000 35146 46321 18264 28980 38891 47120 43186 45448 25715 FALSE TRUE 30501.36705 46016.7143 27096.53149 35560.35193 38117.14519 48932.73689 38997.82837 35729.29888 22675.00199 1.345153886 2.029402878 1.194995771 1.568262351 1.681020588 2.158003642 1.719859975 1.575713153 1 14.46881506 3.331225817 6.374088769 1.653677366 1.543576564 0.013997011 0.348006389 1.18588726 67.73340947 0.10187011 0.131534191 2144.005115 -3.331225817 -0.110100803 GYEEWLLNEIR ddPTM_MDA-MB-175_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 ;;;;; 302.3 1.44E-35 3344560000 1784450 1569310 1638200 2005490 1350130 1597960 1184968 1555930 4958370 FALSE TRUE 1548630.411 1559001.099 2430438.999 2460867.156 1323265.054 1659434.555 1070049.986 1223206.478 4372197.147 0.354199584 0.356571547 0.555885043 0.562844509 0.30265448 0.379542482 0.244739647 0.279769287 1 22.05992702 1.23311643 24.99998221 1.000000982 0.376652523 0.773881513 0.10539379 91.92324752 422069.9824 0.241779166 0.028700718 17.10473813 -1.23311643 -0.62334846 GYEEWLLNEIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GYEEWLLNEIRR 12 1 O43707;O43707-2;F6THM6;A0A494C060;P12814-3;P12814;P12814-2;P12814-4;H9KV75;P35609-2;P35609;A0A494C1A0 O43707;P12814-3 ACTN4;ACTN2;ACTN1 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2 0 ;;; 211.77 4.49E-08 1329821000 1047743 852315 854928 1074120 857489 939675 761337 938202 1000540 FALSE TRUE 909281.1079 846716.0866 1268374.04 1318015.363 840426.6465 975824.9053 687502.6549 737574.8034 882257.301 1.030630301 0.959715591 1.437646409 1.493912673 0.952586786 1.10605478 0.779254141 0.836008727 1 19.75083994 2.675036925 1.866086622 0.869932309 1.212000784 0.348137677 0.187949738 0.378020479 2.626664175 0.084020745 0.071334121 473.1914897 -2.675036925 0.342068475 GYEVHGIVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GYEVHGIVR 9 0 O60547;O60547-2 O60547 GMDS "GDP-mannose 4,6 dehydratase" 0 ; 135.83 0.0002098 369790000 415190 391080 273210 279940 386530 392110 347820 377630 401880 FALSE TRUE 360321.5895 388510.9697 405335.2698 343504.6556 378838.8092 407194.7254 314088.4699 296876.7632 354370.2042 1.01679426 1.096342088 1.14381871 0.969338425 1.069048144 1.149065922 0.886328665 0.837758817 1 18.43489778 2.224442538 24.99248159 0.892485248 1.07326227 0.577192096 0.066546533 148.7757622 263367.6496 0.026699721 0.018100282 167.6650481 -2.224442538 0.180777022 GYFDEEMNR ddPTM_MDA-MB-175_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 ;;;;;;; 263.91 5.92E-15 11759220000 7667320 8336220 5809650 6076700 7705340 8942570 7797760 8437730 8047900 FALSE TRUE 6654064.235 8281458.822 8619216.172 7456507.612 7552018.809 9286596.455 7041534.435 6633387.102 7096486.43 0.937656163 1.166980153 1.214575164 1.050732314 1.064191256 1.308618927 0.99225645 0.934742449 1 22.75867347 2.026397034 24.98249708 0.962946699 1.126067387 0.329476184 0.100002106 216.8441185 205223.1897 0.039429954 0.026582922 106.2666608 -2.026397034 0.163120688 GYFEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GYFEDR 6 0 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ;; 117.7 0.05234 4622400000 8026600 7985100 6252800 6298200 7177100 9943900 8042000 7748300 8604800 FALSE TRUE 6965864.473 7932645.352 9276674.994 7728302.572 7034289.752 10326448.27 7262088.078 6091386.342 7587550.347 0.918065008 1.045481742 1.222617916 1.018550417 0.927083107 1.360972619 0.957105752 0.802813301 1 22.85520275 2.009813122 24.99802088 0.885113121 1.083755166 0.2373976 0.138972624 240.5663182 612818.0078 0.055075509 0.037083701 102.2852763 -2.009813122 0.198642045 GYFEDRRPS(ph)ANCDPFSVTEALIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GYFEDRRPSANCDPFSVTEALIR 23 2 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 1 GYFEDRRPS(1)ANCDPFSVTEALIR 157.11 5.36E-09 35491000 36137 40333 26321 23850 28789 41520 43112 42047 10946 TRUE FALSE 31361.40389 40068.04987 39049.92364 29265.50702 28216.15522 43117.30127 38931.00488 33055.57626 9651.97635 3.249220963 4.151279325 4.04579562 3.03207405 2.923355197 4.467199225 4.033474955 3.424746918 1 13.23660867 3.741502689 24.83235804 3.276882718 3.849016703 0.091140619 0.935123085 701.2548142 5918870.71 0.255237016 0.418843425 5514.456163 -3.741502689 0.572133985 GYFEHREDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GYFEHREDR 9 1 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;M0QYZ0;M0R0K8;M0QYI8;M0QZV6 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ;;; 153.97 4.62E-05 1010410000 1276560 1106280 583320 579420 1006460 1123070 991180 1079600 261728 FALSE TRUE 1107859.362 1099012.774 865415.5031 710986.1669 986433.4151 1166275.23 895055.5162 848735.9415 230786.814 4.800358142 4.762025849 3.749848131 3.080705325 4.274219129 5.053474284 3.878278402 3.677575537 1 17.81620127 4.221441758 4.992620955 3.620262725 4.800222826 0.197604668 1.038755425 0.305155919 20.15172321 0.270263062 0.64605779 16651.05511 -4.221441758 1.179960101 GYFEYIEENK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GYFEYIEENK 10 0 Q00839;Q5RI18;A0A1W2PRI6;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;; 196.88 7.57E-07 892670000 1852680 1446360 1303460 1603050 1455260 1207220 1512810 1751670 3378740 FALSE TRUE 1607843.644 1436858.766 1933817.616 1967047.004 1426303.173 1253662.535 1366097.919 1377089.002 2979309.206 0.539669948 0.482279168 0.64908255 0.660235936 0.478736202 0.420789669 0.458528412 0.46221755 1 21.50654643 1.234646258 24.99991258 1.000000696 0.516464383 0.783457854 0.079471429 58.63592723 374437.0461 0.159158491 0.021573882 17.16509683 -1.234646258 -0.483536313 GYFEYIEENKYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GYFEYIEENKYSR 13 1 Q00839;Q5RI18;A0A1W2PRI6;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;; 219.35 2.06E-11 10054770000 7772810 5964250 3637350 4272850 6134660 5312910 6494020 7535470 3150230 FALSE TRUE 6745613.465 5925070.449 5396384.626 5243065.899 6012592.268 5517301.086 5864230.94 5924068.382 2777813.398 2.428389707 2.13299801 1.942673554 1.88747952 2.16450546 1.986202921 2.111096067 2.13263727 1 21.40551826 1.237156612 24.99988541 0.999998676 2.088669028 0.844117705 0.148269213 13.60640433 242187.5638 0.220925847 0.036236234 17.26460363 -1.237156612 1.088670353 GYFSEEMNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GYFSEEMNR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 170.66 0.0015124 0 350760 339740 261690 232500 352190 399730 268460 335510 335640 FALSE TRUE 304406.1773 337508.2256 388244.1593 285292.6785 345182.108 415107.8718 242424.7905 263763.7974 295961.0216 1.028534689 1.140380662 1.311808417 0.963953554 1.166309355 1.402576155 0.819110534 0.891211268 1 18.17504766 2.214634094 24.99999801 0.897379003 1.164688297 0.476943682 0.130960542 194.7658466 203502.5866 0.052656218 0.035521456 163.9208111 -2.214634094 0.267309294 GYGFVHFETQEAAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GYGFVHFETQEAAER 15 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;H0YBN4;E5RGH3 P11940-2 PABPC1 Polyadenylate-binding protein 1;Polyadenylate-binding protein 0 ;;;; 253.15 1.16E-24 7232290000 7809170 7285720 5173250 5579660 7038050 7707520 6749800 7697290 7081140 FALSE TRUE 6777168.399 7237859.626 7675051.003 6846607.083 6898006.575 8004033.282 6095205.435 6051284.434 6244015.696 1.085386189 1.15916743 1.229185091 1.096507026 1.104738827 1.281872704 0.976167539 0.969133444 1 22.57404273 2.209540823 24.99184413 0.978901527 1.157280456 0.657538251 0.060431719 119.8452225 103209.8557 0.023940239 0.016143481 162.0096272 -2.209540823 0.17837893 GYGGNRFESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GYGGNRFESR 10 1 Q14011;K7EMY9;K7EPM4;K7EQR7;D6W5Y5;Q14011-2;K7EJV1;Q14011-3 Q14011 CIRBP Cold-inducible RNA-binding protein 0 ; 109.29 0.0018589 401130000 444880 443870 154799 123334 357220 385560 357620 375380 48739 FALSE TRUE 386087.9808 440954.1887 229660.3142 151338.8697 350112.0209 400392.7427 322938.0674 295107.9082 42977.13094 8.983568059 10.26020535 5.343779567 3.521381405 8.146472629 9.31641396 7.514183947 6.866626546 1 15.39128155 4.241147834 24.99579614 6.233881484 9.62188758 0.282961105 2.393461419 92.43820458 893021.0157 0.619529856 1.491250394 17423.99887 -4.241147834 3.388006096 GYHYATCLEGALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GYHYATCLEGALK 13 0 Q06210-2;Q06210;A0A6I8PRN4 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 156.36 4.71E-05 270280000 361010 300160 226400 289220 328590 262880 312580 366010 386620 FALSE TRUE 313301.6138 298188.2292 335887.7973 354891.8215 322051.7019 272993.1637 282266.0397 287741.6098 340914.224 0.91900423 0.874672302 0.985256037 1.041000335 0.944670768 0.80076789 0.827967916 0.844029347 1 18.37904927 2.868975141 7.408171624 0.860901244 0.956345236 0.281000987 0.067017201 0.333562344 18.56841049 0.022472295 0.022503561 739.5629413 -2.868975141 0.095443992 GYIFLEYAS(ph)PAHAVDAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GYIFLEYASPAHAVDAVK 18 0 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 1 GYIFLEYAS(1)PAHAVDAVK 127.5 1.63E-05 53998000 38406 31925 26959 22532 27547 26254 31495 37381 34244 TRUE FALSE 33330.54979 31715.28257 39996.46257 27648.23498 26998.86859 27264.00837 28440.61975 29387.36405 30195.71333 1.103817268 1.050324005 1.324574192 0.915634437 0.894129186 0.902909896 0.941876068 0.973229668 1 14.88205613 3.706394685 24.97669235 0.938594355 1.148647083 0.655695646 0.075561768 384.6469623 298676.455 0.020449597 0.030334335 5086.214652 -3.706394685 0.210052729 GYIWNYGAIPQTWEDPGHNDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GYIWNYGAIPQTWEDPGHNDK 21 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;; 295.21 7.55E-55 8786440000 4193650 3451150 2711060 2995990 3137910 2848150 3634130 4314060 3976640 FALSE TRUE 3639448.527 3428479.168 4022137.684 3676275.32 3075471.73 2957720.173 3281692.632 3391531.841 3506526.149 1.03790714 0.977742364 1.147043402 1.048409498 0.87707081 0.843490123 0.935881409 0.967205632 1 21.74161106 3.255395915 24.09099015 0.926813526 1.054149593 0.538093382 0.058926723 134.1731971 191997.4705 0.01816404 0.023377356 1800.511566 -3.255395915 0.127336067 GYLDDPTVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GYLDDPTVPR 10 0 E7EUI8;P11413;P11413-3;P11413-2 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;; 175.51 6.46E-06 2400450000 8006500 8410900 6792200 7002900 8429200 10384600 8724200 8931200 9779800 FALSE TRUE 6948420.739 8355648.244 10076930.64 8593015.478 8261475.411 10784102.28 7878128.427 7021332.383 8623643.185 0.805740751 0.968923234 1.168523607 0.996448403 0.958002927 1.250527422 0.913549907 0.814195605 1 23.03986606 2.024201995 24.99927948 0.884839879 1.029186447 0.148732073 0.127522392 335.0252599 346060.4545 0.051417027 0.034663851 105.7309161 -2.024201995 0.144346569 GYNDDYYEESYFTTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GYNDDYYEESYFTTR 15 0 P50402;Q5HY57 P50402 EMD Emerin 0 ;;; 246.51 8.15E-18 341934000 268149 258397 187336 260742 309520 331521 192416 346585 318257 FALSE TRUE 232712.4302 256699.5731 277932.3162 319947.4563 303361.1576 344274.8274 173755.5259 272470.4949 280633.02 0.829241086 0.914716212 0.990376386 1.140091983 1.080988821 1.226779469 0.619155671 0.970913882 1 18.09832524 2.252810966 24.99998681 0.875589158 1.030579717 0.217626929 0.14867169 390.116477 684397.2423 0.057050941 0.043977254 178.9826634 -2.252810966 0.154990559 GYNFEDLTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 GYNFEDLTDR 10 0 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y9R3 A0A499FIZ0 WDR26 WD repeat-containing protein 26 0 ;; 200.09 6.20E-07 860440000 1162610 1194000 922750 945690 1165830 1305640 1146330 1261610 1445660 FALSE TRUE 1008968.143 1186156.535 1368994.986 1160423.368 1142632.264 1355868.816 1035159.093 991824.5194 1274755.722 0.791499207 0.930497126 1.073927313 0.910310382 0.896353901 1.063630304 0.812045065 0.778050651 1 20.28178938 2.195830632 24.9998391 0.843452948 0.945897843 0.119508664 0.098781829 233.0514777 136348.7111 0.039815172 0.026843606 156.9750505 -2.195830632 0.102444894 GYNHGQGSYSYSNSYNS(ph)PGGGGGSDYNYESK ddPTM_MDA-MB-175_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 354.21 8.23E-121 2614730000 1517570 1155810 693670 1097830 1288040 1159660 1296520 1458280 1873930 TRUE FALSE 1317019.279 1148217.408 1029131.132 1347109.081 1262410.524 1204272.871 1170783.69 1146438.17 1652396.13 0.797036047 0.694880233 0.622811391 0.815245846 0.763987824 0.728803977 0.708536935 0.693803471 1 20.65612816 1.234581782 24.9996692 1.000000397 0.725142398 0.705038277 0.055231855 65.93680456 414232.8001 0.100124841 0.013508836 17.16254867 -1.234581782 -0.274857999 GYNPGLLVHPDLAYLQAEGGGDR ddPTM_MDA-MB-175_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 ; 230.49 3.72E-33 432970000 596620 583300 414640 426760 551580 646660 522550 631090 559480 FALSE TRUE 517775.1554 579468.2639 615161.2909 523662.3806 540604.6371 671537.4286 471873.1814 496136.3146 493338.9118 1.049532366 1.17458455 1.246934463 1.061465796 1.095807819 1.361209125 0.956488876 1.005670347 1 18.91221956 2.165874425 24.99999814 0.989906929 1.161259424 0.454001042 0.091706785 38.51932614 13247.39697 0.036296021 0.024470777 146.5124142 -2.165874425 0.171352495 GYNS(ph)DDNLCEPSLEFEVPNHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GYNSDDNLCEPSLEFEVPNHR 21 0 Q9P219;Q9P219-2;A0A0A0MR69 Q9P219 CCDC88C Protein Daple 1 GY(0.001)NS(0.999)DDNLCEPSLEFEVPNHR;GY(0.013)NS(0.987)DDNLCEPSLEFEVPNHR 115.55 9.72E-05 112771000 70173 90402 63785 77874 98837 99122 83123 108386 111095 TRUE FALSE 60899.46025 89808.14331 94631.63935 95556.48193 96870.33707 102935.2875 75061.74425 85208.49736 97961.47566 0.621667445 0.916770013 0.966008716 0.975449597 0.988861554 1.050773141 0.766237378 0.869816392 1 16.57992689 4.7372 4.828171217 0.935768529 0.604803876 0.620405853 0.078710625 0.130145766 8.888248237 0.020840141 0.144909388 54600.92497 -4.7372 -0.330964653 GYPHWPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 GYPHWPAR 8 0 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;M0R0J3;H3BPQ6;P51858;O75475;O75475-3;O75475-2;Q9Y3E1 Q7Z4V5-2;P51858;O75475;Q9Y3E1 HDGFRP2;HDGFRP3;HDGF;PSIP1 Hepatoma-derived growth factor-related protein 2;Hepatoma-derived growth factor;PC4 and SFRS1-interacting protein;Hepatoma-derived growth factor-related protein 3 0 ;;;;;;; 135.35 0.00083753 11414390000 6418640 7328130 5689200 5748060 6875950 7935820 6216050 7139820 9927480 FALSE TRUE 5570400.461 7279991.032 8440516.149 7053244.877 6739132.048 8241116.131 5613218.428 5613025.055 8753864.624 0.636336144 0.831631667 0.964204556 0.805729261 0.769846501 0.941426043 0.641227466 0.641205376 1 23.06148864 2.229951563 24.9992223 0.730910509 0.828133391 0.032883164 0.133561294 445.8261204 1294590.519 0.053396235 0.036636332 169.8054256 -2.229951563 0.097222882 GYPTLLLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GYPTLLLFR 9 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 101.33 0.0094406 76125000 85314 154600 115010 87123 140500 174200 126660 116260 121980 FALSE TRUE 74039.53874 153584.4224 170629.2207 106905.6087 137704.3249 180901.5867 114376.5327 91398.70374 107559.6634 0.688357851 1.427899806 1.586368118 0.993919146 1.28025991 1.681872005 1.063377563 0.849748882 1 16.71477762 2.008998426 24.90307507 0.926868448 1.292071984 0.215142804 0.283196931 245.7178097 680019.2811 0.112921441 0.0760108 102.0935784 -2.008998426 0.365203536 GYPTLLWFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GYPTLLWFR 9 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ; 168.23 0.00013814 573310000 116533 660240 414260 323000 562910 741070 505280 379960 461870 FALSE TRUE 101132.8688 655902.84 614597.5216 396342.0867 551709.1923 769579.4424 456278.0234 298708.5109 407268.2548 0.248320039 1.610493409 1.509072987 0.973172061 1.354657982 1.889613132 1.120337807 0.73344413 1 18.63561984 1.994377192 24.93689087 0.871444867 1.300555651 0.11714691 0.439621946 423.5332141 1878350.649 0.17851396 0.116175957 98.71364584 -1.994377192 0.429110784 GYS(ph)PDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GYSPDTR 7 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 GYS(1)PDTR;GYS(1)PDTR;GY(0.001)S(0.999)PDTR;GYS(1)PDTR;GY(0.123)S(0.873)PDT(0.004)R 169.09 0.001075 4477180000 6986080 7813280 5390030 6208740 6970900 8403780 7177620 8175240 7454510 TRUE FALSE 6062851.828 7761954.049 7996666.537 7618529.312 6832192.728 8727078.855 6481535.517 6427028.546 6573246.32 0.922352751 1.180840284 1.216547524 1.159020816 1.039393991 1.327666488 0.986047868 0.977755622 1 22.64817462 2.089642633 24.99998883 0.98558579 1.143626346 0.316758457 0.105885578 20.98477529 5845.809262 0.041084658 0.027699271 122.9256839 -2.089642633 0.158040556 GYSDRDGYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GYSDRDGYGR 10 1 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 0 ;;;;; 162.36 6.19E-06 1686050000 2479370 2107480 788296 802020 1785880 1969310 1908650 2032150 336380 FALSE TRUE 2151714.973 2093635.825 1169518.582 984130.8991 1750344.482 2045070.63 1723549.417 1597590.537 296613.5396 7.254270912 7.05846344 3.942903563 3.317889333 5.901094348 6.894731214 5.810757726 5.386101183 1 18.17822493 4.255420632 23.02470395 4.82341236 7.156374113 0.285920814 1.647313616 136.951886 187017.9774 0.419642159 1.101688495 18006.14039 -4.255420632 2.332961753 GYSFTTTAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 GYSFTTTAER 10 0 P60709;A0A2R8Y793;A0A2R8YEA7;P63261;I3L3I0;I3L1U9;I3L4N8 P60709;P63261 ACTB;ACTG1 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 ;;;;;;;;;;; 230.1 3.05E-09 1.03373E+11 10693080 10147380 7520110 7987230 10031060 10543930 9377820 10249320 10048440 FALSE TRUE 9279962.385 10080721.19 11156860.35 9800852.649 9831461.531 10949561.81 8468360.46 8057582.678 8860524.87 1.047337773 1.137711517 1.259164724 1.106125516 1.109580039 1.235768983 0.955740273 0.909379839 1 23.07896073 2.219368771 23.05344179 0.945556331 1.149983929 0.66486481 0.064892192 53.61656884 64403.4971 0.026081648 0.017626791 165.7176519 -2.219368771 0.204427597 GYSLVSGGTDNHLVLVDLRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GYSLVSGGTDNHLVLVDLRPK 21 1 P34897-3;P34897-2;P34897;H0YIZ0;G3V2Y4 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial;Serine hydroxymethyltransferase" 0 60.093 0.035772 20570000 12365 9788 10024 12019 10945 11448 12886 17650 16063 FALSE TRUE 10730.93392 9723.701984 14871.63993 14748.09765 10727.21591 11888.41197 11636.3177 13875.68485 14164.05044 0.757617601 0.686505744 1.049956719 1.041234477 0.757355105 0.839337026 0.82153885 0.979641022 1 13.78994627 4.256289018 24.98309254 0.920947404 0.722061551 0.428953548 0.098115523 250.5399868 353058.0379 0.025914715 0.068238299 18042.18029 -4.256289018 -0.198885853 GYSYDLEVEQAYDLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GYSYDLEVEQAYDLAR 16 0 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;; 277.82 5.57E-35 806682000 613350 547704 394694 449641 505102 545051 478036 564080 550495 FALSE TRUE 532294.2435 544106.0964 585569.3386 551738.8614 495051.4584 566019.4647 431676.1423 443455.8817 485416.1082 1.096573094 1.120906552 1.206324489 1.136630722 1.019849671 1.166050024 0.88929093 0.913558232 1 18.88886246 2.237940781 24.99998843 0.928090689 1.123759787 0.726233159 0.054977997 8.170418065 329511.8609 0.021822464 0.015716071 172.9580504 -2.237940781 0.195669099 GYT(ph)SDDDTWEPEIHLEDCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GYTSDDDTWEPEIHLEDCK 19 0 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 GYT(0.5)S(0.5)DDDTWEPEIHLEDCK;GYT(0.574)S(0.426)DDDTWEPEIHLEDCK 207.67 1.13E-15 193785000 389730 329510 238760 352980 322830 297500 350470 402920 513620 TRUE FALSE 338226.193 327345.4271 354225.1346 433129.504 316406.3146 308945.0175 316481.4733 316758.6935 452900.4287 0.746800338 0.722775706 0.782125854 0.956345979 0.698622246 0.68214777 0.698788196 0.699400295 1 18.78883438 1.231963041 24.99454162 1.000000427 0.746884978 0.497684883 0.079432295 210.3469791 796812.586 0.193620978 0.020627875 17.05937206 -1.231963041 -0.253115449 GYT(ph)SDSEVYTDHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GYTSDSEVYTDHGR 14 0 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)DSEVYTDHGR 157.58 1.94E-05 380600000 79803 81983 78805 77469 90023 94035 74856 83522 227960 TRUE FALSE 69256.83135 81444.44827 116915.3616 95059.52049 88231.71843 97652.5873 67596.47664 65661.47027 201010.8285 0.344542788 0.405174432 0.581637131 0.472907461 0.438940126 0.485807596 0.336282762 0.326656383 1 17.6169137 1.232661086 24.99561313 1.000000936 0.423585035 0.842520994 0.078261781 81.00084493 343155.6814 0.185095199 0.021074318 17.08681376 -1.232661086 -0.5764159 GYT(ph)SDSEVYTDHGRPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GYTSDSEVYTDHGRPGK 17 1 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 GYT(0.498)S(0.498)DS(0.003)EVYTDHGRPGK;GYT(0.5)S(0.5)DSEVYTDHGRPGK 189.84 4.87E-10 1064170000 864280 875820 582940 679570 881510 778850 951650 1050390 963180 TRUE FALSE 750063.2082 870066.6808 864851.7338 833876.7551 863969.6756 808812.8635 859359.1295 825772.2726 849313.9577 0.883140094 1.02443469 1.018294502 0.981823915 1.017255949 0.952313165 1.011827395 0.972281528 1 19.69593843 4.74777101 24.95688655 0.995400809 0.883140034 0.710318435 0.022879149 650.3650911 1762219.293 0.005339213 0.063959015 55946.25367 -4.74777101 -0.112260775 GYTIPLDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GYTIPLDKR 9 1 Q13573;G3V4X8;G3V3A4;G3V5R3 Q13573 SNW1 SNW domain-containing protein 1 0 ; 100.02 0.0079289 923330000 692460 695650 427710 451130 662170 565890 713640 776070 497110 FALSE TRUE 600949.6565 691080.2293 634551.9866 553565.9616 648994.1125 587660.1545 644431.3026 610113.4699 438342.2221 1.370960008 1.576576918 1.447617762 1.262862516 1.48056491 1.340642368 1.470155669 1.391865623 1 18.74169812 1.239069602 4.853255616 0.970873251 1.421944642 0.706078408 0.084889874 0.096676218 5.479180802 0.148338929 0.020587257 17.34081888 -1.239069602 0.45107139 GYTS(ph)DDDTWEPEIHLEDCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GYTSDDDTWEPEIHLEDCK 19 0 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 GYT(0.121)S(0.879)DDDTWEPEIHLEDCK;GYT(0.133)S(0.867)DDDTWEPEIHLEDCK 331.54 1.77E-75 416160000 818680 711060 558480 760340 694810 617140 751610 873680 1094980 TRUE FALSE 710489.3637 706389 828562.796 932986.8181 680984.6404 640881.7751 678718.9779 686850.331 965532.7118 0.735852193 0.731605456 0.858140574 0.966292293 0.705294219 0.663759775 0.702947678 0.711369302 1 19.88096561 GYTS(ph)DSEVYTDHGRPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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(0.081)S(0.919)DSEVYTDHGRPGK;GYT(0.15)S(0.85)DSEVYTDHGRPGK;GYT(0.214)S(0.786)DSEVYTDHGRPGK;GYT(0.023)S(0.977)DSEVYTDHGRPGK;GYT(0.092)S(0.908)DSEVYTDHGRPGK;GYT(0.104)S(0.896)DSEVYTDHGRPGK;GYT(0.421)S(0.579)DSEVYTDHGRPGK 293.22 2.89E-46 28224700000 8374540 8449640 5842190 6219700 8206070 7208500 9066550 10397700 9556130 TRUE FALSE 7267823.321 8394133.758 8667492.625 7631977.947 8042785.262 7485815.66 8187277.376 8174232.77 8426415.198 0.862504772 0.996169019 1.028609726 0.905720614 0.954472937 0.888374888 0.971620456 0.970072395 1 23.00648757 1.605279086 2.072084231 0.996698472 0.945263996 0.126938927 0.049276388 0.804373127 6.764777576 0.066297699 0.013798791 40.29759109 -1.605279086 -0.051434476 GYWAGLDASAQTTSHELTIPNDLIGCIIGR ddPTM_MDA-MB-175_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 ;; 263.92 1.75E-58 532181000 335055 299471 207866 200364 305440 311660 271566 302989 278046 FALSE TRUE 290776.6328 297503.7553 308390.6929 245859.7086 299362.3416 323649.7619 245229.5711 238197.1602 245175.7186 1.185992783 1.213430747 1.257835379 1.002789795 1.221011376 1.320072655 1.000219649 0.971536503 1 17.90345658 2.150053838 8.475413467 0.98514345 1.195162359 0.601478792 0.080372535 0.179123648 15.25907592 0.033190441 0.022359989 141.2712664 -2.150053838 0.21001891 GYWASLDASTQTTHELTIPNNLIGCIIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GYWASLDASTQTTHELTIPNNLIGCIIGR 29 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ;;; 300.17 5.24E-81 763561000 1036587 989558 612004 745973 915041 1024603 919165 1062422 881724 FALSE TRUE 899599.4016 983057.5283 907971.1814 915357.5711 896833.4743 1064020.14 830024.5198 835231.3231 777487.5932 1.157059495 1.26440285 1.167827229 1.17732756 1.153501975 1.368536488 1.067572688 1.074269648 1 19.56846013 2.037478416 24.99958484 1.050984093 1.21104743 0.584322323 0.066685323 110.0060323 73377.93889 0.025970658 0.017509375 109.0130312 -2.037478416 0.160063337 GYWGGPAFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GYWGGPAFLR 10 0 Q9Y6N5 Q9Y6N5 SQRDL "Sulfide:quinone oxidoreductase, mitochondrial" 0 90.706 0.024772 222280000 238980 206570 187240 233450 230870 242410 194040 251970 248540 FALSE TRUE 207398.1875 205213.0281 277789.8903 286458.3906 226276.1387 251735.6696 175222.0307 198088.1763 219157.8843 0.946341438 0.93637073 1.267533181 1.307086859 1.032480029 1.148649844 0.799524193 0.903860598 1 17.74161106 2.248741087 24.999716 0.897463991 1.111766253 0.361735026 0.128381354 222.1670796 545565.8975 0.051300957 0.039274969 177.3132078 -2.248741087 0.214302262 GYWGLDASAQTTSHELTIPNDLIGCIIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GYWGLDASAQTTSHELTIPNDLIGCIIGR 29 0 Q15366;Q15366-6 Q15366 PCBP2 Poly(rC)-binding protein 2 0 ; 205.77 2.10E-25 171669000 226990 225110 130546 153190 196262 211906 198732 231710 190646 FALSE TRUE 196992.6964 223631.2376 193678.4823 187974.1309 192356.7702 220058.1609 179459.0012 182160.6197 168108.0471 1.171821931 1.330282765 1.152107146 1.118174496 1.144244868 1.309028121 1.067521778 1.083592504 1 17.35902926 2.120133042 9.145729586 1.056200521 1.20086645 0.509003941 0.071210777 0.236118421 17.81174101 0.029517759 0.019887255 131.8660635 -2.120133042 0.144665929 GYWGNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GYWGNK 6 0 P15880;H0YEN5;E9PPT0;E9PMM9;I3L404;E9PM36 P15880 RPS2 40S ribosomal protein S2 0 ; 142.27 0.026864 4294800000 5438600 5112500 3649700 3990900 4983200 4481000 5320500 6090700 5901500 FALSE TRUE 4719875.23 5078915.651 5414707.128 4897094.842 4884044.069 4653386.97 4804518.729 4788251.203 5203831.393 0.90700003 0.975995429 1.040523168 0.941055632 0.938547716 0.89422324 0.923265641 0.920139574 1 22.31114279 3.500006995 24.84006785 0.931254651 0.977344178 0.15760942 0.041203438 1109.36247 1204094.367 0.011297301 0.016614281 3162.328591 -3.500006995 0.046089528 EKT(ph)PSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EKTPSPK 7 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 EKT(0.964)PS(0.036)PK 71.349 0.088201 389640000 1482400 962010 1194600 1351000 729630 772620 1390900 1694500 3949600 TRUE FALSE 1286497.084 955690.493 1772312.556 1657765.199 715111.7905 802343.1914 1256010.732 1332144.362 3482682.787 0.369398295 0.274412156 0.508892904 0.476002352 0.205333599 0.230380784 0.360644597 0.382505225 1 21.73176764 1.233873318 4.749178163 1.050884462 0.347284986 0.819697802 0.095796158 0.083411497 4.331403911 0.197520945 0.025427637 17.13457424 -1.233873318 -0.703599476 SLS(ph)LGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSLGDK 7 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 S(0.001)LS(0.999)LGDK;S(0.001)LS(0.999)LGDK 109.02 0.0074706 800620000 945940 794270 855950 1192110 1134520 1016840 1270100 1529310 3263100 TRUE FALSE 820931.6323 789052.3881 1269890.283 1462796.796 1111945.272 1055958.493 1146925.897 1202278.958 2877340.035 0.285309217 0.274229802 0.441341749 0.508385098 0.386449032 0.366991207 0.398606311 0.417843892 1 21.45630429 1.233941095 4.777160983 1.047171198 0.385285497 0.891056485 0.067689187 0.063294126 3.361758957 0.141640661 0.018328301 17.13724853 -1.233941095 -0.6618857 ESSYDIYRVPS(ph)SQSMEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ESSYDIYRVPSSQSMEDR 18 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 ESSYDIYRVPS(0.932)S(0.027)QS(0.041)MEDR;ESSYDIYRVPS(0.903)S(0.095)QS(0.003)MEDR;ESSYDIYRVPS(0.94)S(0.057)QS(0.004)MEDR 156.89 1.57E-09 481130000 586035 550819 303652 336339 574133 592297 575964 627277 182249 TRUE FALSE 508588.9899 547200.6337 450499.1229 412709.9106 562708.8766 615083.0489 520107.0999 493138.695 160703.7308 3.16476156 3.405027568 2.803289759 2.568141439 3.501529639 3.827434781 3.236434507 3.068620078 1 17.2940439 1.23433595 4.571479442 0.811476862 3.210834446 0.798758568 0.347262626 0.095591531 4.300341718 0.748889276 0.09406926 17.15283656 -1.23433595 2.399357584 EDKYEEEIK ddPTM_MDA-MB-175_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 ;;; 125.74 0.0004497 3100290000 4603530 3370550 4303460 4541470 3153910 2331550 4738610 5684950 11103100 FALSE TRUE 3995161.847 3348408.635 6384627.65 5572680.176 3091153.362 2421246.237 4279060.332 4469267.683 9790504.167 0.408064976 0.342005741 0.652124502 0.56919236 0.315729743 0.247305572 0.437062306 0.456490045 1 23.22295172 1.234386855 4.836725363 1.04238117 0.426594233 0.702445187 0.117054643 0.11393466 6.35085156 0.239441795 0.03143058 17.15484724 -1.234386855 -0.615786937 IS(ph)PVPYEDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ISPVPYEDLK 10 0 Q9Y2I9;F8VZ81;Q9Y2I9-2;Q9Y2I9-3 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 IS(1)PVPYEDLK;IS(1)PVPYEDLK;IS(1)PVPYEDLK 172.11 4.00E-06 182373000 664280 496700 459590 598780 528430 415130 636820 773030 1321340 TRUE FALSE 576493.7149 493437.145 681849.2612 734742.1508 517915.2769 431100.3197 575061.2944 607723.5502 1165132.69 0.494788035 0.423502962 0.585211682 0.630608133 0.444511841 0.370001051 0.49355863 0.521591708 1 20.15206283 1.234713197 4.771144315 1.038661969 0.492984693 0.820076108 0.074386735 0.082913639 4.38709223 0.152688793 0.019916737 17.16774276 -1.234713197 -0.545677275 TSTS(ph)PPPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 TSTSPPPEK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 TST(0.01)S(0.99)PPPEK;TST(0.003)S(0.997)PPPEK;TST(0.006)S(0.994)PPPEK;TST(0.001)S(0.999)PPPEK;TST(0.044)S(0.956)PPPEK;TS(0.001)T(0.133)S(0.866)PPPEK;TST(0.003)S(0.997)PPPEK;TST(0.001)S(0.999)PPPEK;TS(0.001)T(0.149)S(0.851)PPPEK 180.19 5.13E-05 40127420000 14591280 11043150 9126710 13462210 10319440 9731660 13942760 16672060 30144690 TRUE FALSE 12663005.38 10970606.82 13540417.48 16519010.54 10114103.33 10106043.26 12590593.28 13106869.71 26581019.09 0.476392772 0.412723334 0.509401744 0.621458887 0.380500962 0.380197735 0.473668569 0.493091317 1 24.66389308 1.234764594 4.901321347 1.037952323 0.465855172 0.851877142 0.069748012 0.069084668 4.056259082 0.136276449 0.018141081 17.16977461 -1.234764594 -0.572097151 TAQEHDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TAQEHDKR 8 1 A0A087WY55;Q9NP79 A0A087WY55 VTA1 Vacuolar protein sorting-associated protein VTA1 homolog 0 127.4 0.00076474 55659000 71415 63444 48510 67460 35965 59070 72115 85003 158520 FALSE TRUE 61977.32681 63027.23219 71969.59826 82777.82406 35249.36686 61342.46112 65121.2984 66825.76994 139779.9462 0.443392121 0.450903251 0.514877851 0.592201001 0.252177568 0.438850227 0.465884415 0.478078378 1 17.09279787 1.235040311 5.051536928 1.035729774 0.45283615 0.805357098 0.084361198 0.075251136 4.976649339 0.154959182 0.021133636 17.18067851 -1.235040311 -0.582893623 GGQGDPAVPAQQPADPST(ph)PERQS(ph)SPSGSEQLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGQGDPAVPAQQPADPSTPERQSSPSGSEQLVR 33 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;H7BZT5;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 2 GGQGDPAVPAQQPADPS(0.044)T(0.955)PERQS(0.608)S(0.387)PS(0.004)GSEQLVR 136.33 5.25E-08 313560000 122520 119440 64502 52168 100260 107320 108510 120440 19865 TRUE FALSE 106328.6716 118655.3908 95695.38295 64013.54174 98265.02216 111448.6698 97986.7169 94684.84327 17516.58233 6.070172227 6.773889366 5.463130943 3.65445385 5.609828464 6.36246659 5.593940362 5.405440484 1 14.0964337 1.235893023 5.149744232 0.717139349 5.619719606 0.76059628 0.814918815 0.088133951 6.301956609 1.549968038 0.216363102 17.21444489 -1.235893023 4.902580257 S(ph)PDPFGAVAAQK ddPTM_MDA-MB-175_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 183.06 1.69E-05 3410570000 3818170 3994720 4532230 6448200 5667130 4367650 5938700 7423600 15352900 TRUE FALSE 3313589.16 3968478.421 6724031.587 7912362.365 5554365.201 4535676.322 5362765.788 5836120.911 13537897.65 0.244763939 0.293138456 0.496682111 0.5844602 0.4102827 0.335035501 0.396129881 0.431095068 1 23.69050038 1.236129368 5.09151501 1.037706421 0.40140602 0.794250797 0.096259313 0.082299748 5.624545584 0.186045465 0.025849856 17.22381563 -1.236129368 -0.636300401 GYYSPYSVSGS(ph)GSTAGSR ddPTM_MDA-MB-175_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(0.003)VS(0.02)GS(0.244)GS(0.244)T(0.244)AGS(0.244)R 65.172 0.035567 7019500 12755 13096 10033 7578 13738 14182 13652 13733 10783 TRUE FALSE 11069.39443 13009.97151 14884.99236 9298.700722 13464.64068 14727.59072 12328.03114 10796.30482 9508.246024 1.164188895 1.368283013 1.565482458 0.977961729 1.416101418 1.548928233 1.296562069 1.13546755 1 13.21496352 1.607305604 2.648284124 1.015351041 1.343602192 0.309916954 0.171613031 0.299503986 4.612830664 0.177188984 0.046065096 40.4860684 -1.607305604 0.328251151 GYYSPYSVSGSGS(ph)TAGS(ph)R ddPTM_MDA-MB-175_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 2 GYYSPYSVSGSGS(0.996)T(0.004)AGS(1)R;GYYSPYSVSGSGS(0.98)T(0.02)AGS(1)R;GYYSPYSVSGS(0.011)GS(0.961)T(0.038)AGS(0.991)R 281.93 3.47E-39 1042160000 2398380 2516310 1664140 1420660 2022020 2268170 2036620 2231000 2444320 TRUE FALSE 2081428.006 2499780.194 2468923.67 1743242.566 1981785.758 2355427.968 1839108.906 1753918.012 2155355.274 0.965700658 1.159799604 1.145483392 0.808795927 0.919470577 1.092825854 0.853274134 0.813748913 1 21.03949426 3.748149283 24.99437602 0.907955254 1.097275065 0.410450296 0.098896472 652.5276787 1700912.105 0.026942408 0.045915857 5599.500444 -3.748149283 0.189319811 GYYSPYSVSGSGS(ph)TAGSR ddPTM_MDA-MB-175_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(0.962)T(0.037)AGSR 281.61 2.60E-39 940430000 324490 325150 255260 220130 327210 406660 368820 345930 297430 TRUE FALSE 281607.8243 323014.0682 378704.5898 270113.881 320699.1612 422304.4733 333051.8932 271955.5615 262268.1642 1.073740022 1.231617529 1.443959433 1.029914865 1.22279104 1.61020105 1.269890664 1.036936993 1 18.00068317 1.703709318 4.587821498 1.011670141 1.276811844 0.283690835 0.165482669 0.206287273 10.25833855 0.110968848 0.044149668 50.5486217 -1.703709318 0.265141703 GYYSPYSVSGSGSTAGS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 GYYSPYSVSGSGSTAGSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 GYYSPYSVSGSGS(0.029)T(0.006)AGS(0.966)R;GYYSPYSVSGSGS(0.004)T(0.044)AGS(0.953)R;GYYSPYSVSGSGS(0.074)T(0.074)AGS(0.852)R;GYYSPYSVSGSGS(0.158)T(0.158)AGS(0.684)R;GYYSPYSVSGSGSTAGS(1)R;GYYSPYSVSGSGS(0.018)T(0.018)AGS(0.964)R 369.48 1.48E-107 6782820000 1373480 1383886 1059391 975278 1434274 1713037 1351954 1467405 1251901 TRUE FALSE 1191971.138 1374795.162 1571716.031 1196729.776 1405734.754 1778938.642 1220841.709 1153611.86 1103902.69 1.079779177 1.245395246 1.423781322 1.084089918 1.273422709 1.611499508 1.105932362 1.045030391 1 20.07418157 2.017771066 24.98882643 1.040656439 1.287417715 0.352727553 0.153374568 251.9939328 354340.4363 0.062516728 0.04213994 104.1768126 -2.017771066 0.246761276 HAAENPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HAAENPGK 8 0 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;; 130.27 0.0011709 1867076000 4578190 3450580 2369710 3025830 1976483 2947140 3942640 4583260 5610500 FALSE TRUE 3973170.592 3427912.913 3515709.682 3712890.948 1937154.855 3060518.383 3560283.38 3603165.516 4947233.082 0.803109643 0.692894969 0.71064161 0.750498488 0.391563289 0.618632341 0.719651434 0.728319337 1 22.23819044 1.011727608 1.669177374 1.325260631 0.661179869 0.467024192 0.110130638 1.794083134 2.807733374 2.343127761 0.031860835 10.27371722 -1.011727608 -0.664080762 HAASNPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HAASNPSK 8 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;M0QYZ0 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 59.8 0.096332 19476000 38475 30847 17348 26682 25190 37156 31486 42763 58526 FALSE TRUE 33390.43127 30644.36403 25737.55083 32740.55591 24688.76828 38585.41536 28432.49257 33618.46523 51607.12295 0.647012066 0.593801054 0.4987209 0.634419321 0.478398463 0.747676157 0.550941245 0.651430719 1 15.65528258 1.233662535 3.362819126 1.066790702 0.592760751 0.734168235 0.076347773 0.158680671 2.495997772 0.198003431 0.018150348 17.12626009 -1.233662535 -0.474029951 HAASNPSKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HAASNPSKK 9 1 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;M0QYZ0 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 93.111 0.0062453 58456000 193160 138510 91205 117220 90855 127330 147780 196580 142370 FALSE TRUE 167633.4166 137600.1187 135312.0431 143836.5926 89047.16325 132228.4675 133448.3183 154542.8968 125539.1808 1.335307555 1.096073097 1.077847109 1.145750607 0.709317702 1.053284454 1.063001348 1.231033179 1 16.93777817 5.067939759 1.523866393 1.048122855 1.703548642 0.32161876 0.133763339 3.734617185 4.216729402 0.038668032 4.677339925 116933.718 -5.067939759 0.655425787 HAASYS(ph)SDSENQGSYSGVIPPPPGR ddPTM_MDA-MB-175_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(0.084)Y(0.012)S(0.388)S(0.388)DS(0.129)ENQGSYSGVIPPPPGR 163.39 1.17E-11 428130000 300220 293790 158530 212240 370600 329780 300020 362840 329920 TRUE FALSE 260545.1663 291860.0741 235195.6383 260432.3359 363225.7851 342466.85 270924.1066 285249.4896 290917.2334 0.895598942 1.003240924 0.808462378 0.895211098 1.248553689 1.177196847 0.93127555 0.980517676 1 18.15024924 HAASYSS(ph)DSENQGSYSGVIPPPPGR ddPTM_MDA-MB-175_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(0.022)YS(0.11)S(0.724)DS(0.143)ENQGSYSGVIPPPPGR 208.26 1.85E-25 377000000 339980 358390 165700 218390 361330 392550 285530 400370 338600 TRUE FALSE 295050.7816 356035.7125 245833.0742 267978.7874 354140.2399 407651.6525 257839.3445 314753.9912 298571.0937 0.988209468 1.192465446 0.823365287 0.897537615 1.186116966 1.365341994 0.863577721 1.054201153 1 18.18771497 5.058298583 14.8716993 1.045050792 0.569921427 0.012230653 0.166722517 5723802.674 37816260.7 0.041112183 79866037.11 114366.4349 -5.058298583 -0.475129365 HACQLSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HACQLSQR 8 0 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 88.948 0.014253 118470000 28345 38937 21351 26327 37287 39428 29795 41755 38842 FALSE TRUE 24599.13643 38681.22028 31676.41501 32304.94773 36545.06165 40944.82067 26905.48549 32826.01819 34250.14301 0.718219963 1.129373979 0.924854971 0.943206214 1.067004644 1.195464225 0.78555834 0.958419887 1 15.06382239 4.758766855 23.98591136 0.991142622 0.718219508 0.375310969 0.113879256 3273.435643 3885638.376 0.027705917 1.050589547 57380.83387 -4.758766855 -0.272923114 HADGEKEDQFNGS(ph)PPRPQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HADGEKEDQFNGSPPRPQPR 20 2 Q69YN4-3;Q69YN4;Q69YN4-4;Q69YN4-2 Q69YN4-3 KIAA1429 Protein virilizer homolog 1 HADGEKEDQFNGS(1)PPRPQPR;HADGEKEDQFNGS(1)PPRPQPR;HADGEKEDQFNGS(1)PPRPQPR;HADGEKEDQFNGS(1)PPRPQPR;HADGEKEDQFNGS(1)PPRPQPR;HADGEKEDQFNGS(1)PPRPQPR 226.14 2.41E-25 3486560000 1865370 1439196 948259 1064178 1524564 1168141 1600134 1829499 1416876 TRUE FALSE 1618856.628 1429741.827 1406840.224 1305815.88 1494228.159 1213080.14 1444953.251 1438274.876 1249374.533 1.295733653 1.144366072 1.126035617 1.045175682 1.195980964 0.97094995 1.156541303 1.151195929 1 20.2527746 4.921527362 1.564890962 1.09735723 1.44627633 0.451606213 0.070601506 1.618894935 2.642844611 0.01824033 0.986813814 83469.41351 -4.921527362 0.3489191 HADLEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HADLEIR 7 0 Q14764;H3BQK6;H3BP76;H3BRL2;H3BNF6;H3BUK7 Q14764 MVP Major vault protein 0 108.09 0.0073315 131920000 66762 79084 46075 62791 84124 78107 75524 90271 88167 FALSE TRUE 57939.23255 78564.492 68357.02411 77048.65625 82450.09699 81111.82683 68199.6941 70967.24914 77743.9977 0.745256666 1.010553796 0.879257899 0.991056011 1.060533281 1.043319475 0.877234206 0.912832517 1 16.24644367 4.745897278 24.55428778 0.965514402 0.745256532 0.550782045 0.064084456 596.9799121 1997905.267 0.016658823 0.165873701 55705.39752 -4.745897278 -0.22025787 HADNS(ph)SDTEMEDMIAEETLEEMDSELLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HADNSSDTEMEDMIAEETLEEMDSELLK 28 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 HADNS(0.442)S(0.442)DT(0.116)EMEDMIAEETLEEMDSELLK;HADNS(0.298)S(0.298)DT(0.298)EMEDMIAEET(0.106)LEEMDS(0.001)ELLK 134.4 8.73E-06 9484900 17611.8 14067.5 12176.7 12254.6 14983.6 13148.9 15074.7 20277.4 15969.1 TRUE FALSE 15284.35601 13975.08967 18065.39285 15037.19423 14685.45567 13654.74669 13612.75791 15941.23581 14081.25119 1.085440193 0.992460789 1.282939464 1.067887649 1.042908437 0.969711179 0.966729286 1.132089442 1 13.78148791 3.48324643 24.02647291 1.031597238 1.118817422 0.217944441 0.083850946 283.9429289 1113789.547 0.024132273 0.032302109 3042.610992 -3.48324643 0.087220184 HADNSSDT(ph)EMEDMIAEETLEEMDSELLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HADNSSDTEMEDMIAEETLEEMDSELLK 28 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 HADNS(0.242)S(0.242)DT(0.515)EMEDMIAEETLEEMDSELLK 192.25 1.17E-17 76774000 58794 47984 32894 42625 47642 39289 50255 59321 53959 TRUE FALSE 51024.22393 47668.78994 48801.64842 52303.65773 46694.01741 40800.47325 45381.27784 46635.66579 47580.02849 1.072387419 1.001865519 1.025675057 1.099277562 0.981378509 0.857512586 0.95378837 0.98015212 1 15.53806852 3.019150738 15.4991719 0.949684497 1.044118559 0.538243176 0.044646209 2.669943126 2158.854222 0.013990656 0.015834087 1045.082891 -3.019150738 0.094434062 HADYIASYGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HADYIASYGSK 11 0 P53611;Q5T4U8 P53611 RABGGTB Geranylgeranyl transferase type-2 subunit beta 0 149.23 0.0019047 0 162500 143930 82874 112460 152270 123760 156930 196860 183910 FALSE TRUE 141025.2133 142984.5144 122952.1436 137995.7618 149240.1249 128521.1273 141710.9528 154763.021 162168.3693 0.869622195 0.881704089 0.758175864 0.850941293 0.920278878 0.792516616 0.87385076 0.954335433 1 17.30713293 1.678236085 2.530561392 0.994574749 0.845958632 0.594435089 0.045029919 0.171796258 2.389267083 0.042176635 0.012361496 47.66900479 -1.678236085 -0.148616117 HAEATLGSGNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HAEATLGSGNLR 12 0 Q9H8S9;Q7L9L4;Q7L9L4-2;D6RCK3;Q9H8S9-2 Q9H8S9 MOB1A;MOB1B MOB kinase activator 1A;MOB kinase activator 1B 0 ;; 156.36 6.18E-05 960660000 673410 673120 360112 438670 662570 773470 641900 677890 664380 FALSE TRUE 584417.1623 668698.2304 534263.3677 538276.7282 649386.1533 803225.8914 579648.6368 532928.4988 585837.7533 0.997575112 1.141439292 0.911964729 0.918815363 1.108474402 1.371072258 0.989435443 0.909686165 1 19.16014164 2.012818968 24.9999559 0.948742603 1.074551014 0.135921624 0.130943412 431.619362 841754.5085 0.05666371 0.038179204 102.9956703 -2.012818968 0.125808411 HAEELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HAEELER 7 0 Q9UHB9;Q9UHB9-4;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;;;; 136.16 0.0030076 1314449000 773262 727767 480380 538151 627831 785824 765771 766084 838259 FALSE TRUE 671073.4675 722986.2507 712693.3748 660346.4097 615338.3914 816055.1578 691506.6463 602262.8983 739160.976 0.907885412 0.978117452 0.964192372 0.893372934 0.832482249 1.104029006 0.935529159 0.814792607 1 19.49552907 1.976512934 24.80736024 0.8884653 0.947831722 0.025300897 0.082540974 1703.682517 1799449.828 0.036979804 0.021531369 94.73553983 -1.976512934 0.059366422 HAEFESLCAQYSADKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HAEFESLCAQYSADKR 16 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ;; 224.64 4.94E-15 1152750000 1374380 1245750 772180 992270 1278500 1194430 1418870 1566980 1656580 FALSE TRUE 1192752.201 1237566.586 1145608.831 1217580.069 1253060.351 1240380.495 1281268.206 1231893.521 1460741 0.816539141 0.847218355 0.784265541 0.833535904 0.857825139 0.849144712 0.877135787 0.843334665 1 20.47826897 -0.336786472 1.302003708 10 0.834242638 0.796960292 0.025434557 35.97568007 1.360259462 935.0870349 0.007620011 0.460482921 0.336786472 -9.165757361 HAELSGS(ph)PLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HAELSGSPLK 10 0 Q9BTC8;F6RRE2;E7EV10 Q9BTC8 MTA3 Metastasis-associated protein MTA3 1 HAELS(0.001)GS(0.999)PLK 122.46 0.00031432 246510000 814570 741680 463760 552080 849760 699150 813870 1011200 834080 TRUE FALSE 706922.5106 736807.8552 688035.8872 677438.202 832851.4385 726046.7529 734941.0127 794962.7492 735476.0126 0.961176841 1.001810858 0.935497386 0.921088099 1.132397827 0.987179378 0.99927258 1.080881953 1 19.48831876 3.268274957 24.99999448 1.039374524 0.956859124 0.444922308 0.047180838 197.443032 166116.3233 0.013253827 0.017108112 1854.705489 -3.268274957 -0.0825154 HAEMVHTGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 HAEMVHTGLK 10 0 Q01518-2;Q01518;Q5T0R1;Q5T0R9;Q5T0R4;Q5T0R3;Q5T0R2;Q5T0R5;Q5T0R7;Q5T0R6 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 0 ;;;;;; 190.86 4.95E-07 2772020000 4387700 3809430 2210690 2500400 3280740 3104200 3400240 4471800 4647760 FALSE TRUE 3807854.328 3784405.604 3279787.078 3068154.036 3215459.693 3223620.583 3070485.248 3515540.37 4098307.108 0.929128596 0.923407032 0.800278503 0.748639366 0.784582416 0.786573699 0.74920819 0.857803058 1 21.96659667 4.243567548 24.35450784 0.813191821 0.926267901 0.277632666 0.072156103 113.5955929 552521.1816 0.01872864 0.046336113 17521.34932 -4.243567548 0.11307608 HAFEIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HAFEIFR 7 0 Q13618;Q13618-2;Q13618-3;A0A087WTG3 Q13618 CUL3 Cullin-3 0 101.64 0.022281 0 67842 117700 56968 69342 95891 114510 96123 105390 120100 FALSE TRUE 58876.50781 116926.821 84517.91535 85087.16093 93982.95671 118915.2738 86801.00625 82853.16865 105901.9148 0.555953194 1.10410488 0.79807731 0.803452526 0.887452855 1.122881243 0.819635853 0.782357607 1 16.69236915 3.026890518 13.80157472 0.909454036 0.836100608 0.092048893 0.160135741 6.147098562 3147.278964 0.047535437 0.053841203 1063.874791 -3.026890518 -0.073353428 HAFSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HAFSLK 6 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 121.68 0.019546 1053160000 2694300 2427400 1311740 1871880 2370100 2186970 2684100 3163900 2693000 FALSE TRUE 2338241.429 2411454.25 1946101.852 2296918.964 2322939.647 2271104.151 2423796.395 2487324.606 2374636.608 0.984673369 1.015504537 0.819536701 0.967271774 0.978229528 0.956400716 1.020702025 1.047454839 1 21.17927532 2.229790809 4.122862308 1.029253421 0.951381597 0.277064563 0.05245792 0.256402942 9.950185437 0.022144784 0.015296253 169.742584 -2.229790809 -0.077871824 HAHGDQYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HAHGDQYK 8 0 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;;; 158.07 0.00036709 447670000 944584 979852 715131 1172037 775118 1045136 964921 1170627 1089079 FALSE TRUE 819754.8311 973415.2877 1060970.744 1438165.914 759694.6683 1085343.058 871343.1099 920297.5259 960329.3213 0.853618455 1.013626541 1.104798864 1.497575761 0.791077239 1.130177986 0.907337817 0.958314513 1 19.8731697 HAHLTDTEIMTLVDETNMYEGVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HAHLTDTEIMTLVDETNMYEGVGR 24 0 O60925;E5RGS4 O60925 PFDN1 Prefoldin subunit 1 0 ;;; 272.36 3.64E-52 654471000 279680 278545 132620 211573 250499 276441 232413 259694 242768 FALSE TRUE 242719.5794 276715.2196 196755.4756 259613.8833 245514.56 287075.8642 209873.623 204160.459 214068.2436 1.133842065 1.292649554 0.919125006 1.212762243 1.146898558 1.341048347 0.980405218 0.953716701 1 17.70771127 2.116201915 11.59743302 0.971655378 1.168599922 0.406680081 0.111616206 0.369886864 35.72360538 0.043864169 0.0295703 130.6778302 -2.116201915 0.196944544 HAIIVEPEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HAIIVEPEKR 10 1 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;; 127.76 0.00022553 461870000 715370 583460 569870 764550 628050 592720 786800 824660 2139000 FALSE TRUE 620832.042 579627.2128 845461.0381 938152.7629 615553.0338 615522.3219 710496.2571 648312.8765 1886129.857 0.329156574 0.307310343 0.448251765 0.497395638 0.326357717 0.326341434 0.376695303 0.343726533 1 20.84699758 1.237089187 24.99964204 1.000000769 0.370374827 0.91579022 0.060094127 10.55124276 179202.6195 0.094661043 0.015466128 17.26192348 -1.237089187 -0.629625942 HAIVICNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HAIVICNR 8 0 P53621;A0A3B3IT15;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;; 104.45 0.0045784 762200000 786100 784760 408180 540360 820680 873310 709110 805360 842350 FALSE TRUE 682214.8933 779604.8599 605577.2133 663056.9969 804350.0736 906906.8008 640340.6213 633140.0313 742768.3426 0.918475996 1.049593548 0.815297554 0.892683437 1.082908395 1.220982033 0.862100045 0.852405784 1 19.5025528 HALIIYDDLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HALIIYDDLSK 11 0 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;; 143.5 3.72E-05 689860000 1595140 1422220 1064720 1804120 1719970 1571660 1590280 2107540 1968300 FALSE TRUE 1384338.207 1412877.343 1579622.153 2213773.02 1685745.962 1632122.777 1436054.89 1656858.972 1735609.816 0.797609114 0.814052404 0.910125155 1.275501555 0.971270124 0.940374249 0.827406527 0.954626412 1 20.72701122 4.10220912 4.661997996 0.984500083 0.808584408 0.318454155 0.112441135 0.273242022 10.01583677 0.030972162 0.068173057 12653.45487 -4.10220912 -0.175915675 HANAKPFEVPFLKF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HANAKPFEVPFLKF 14 2 A6NFX8;Q9UKK9 A6NFX8 NUDT5 ADP-sugar pyrophosphatase 0 74.678 0.018208 77050000 79615 81716 42377 44124 70299 62889 80563 94030 33653 FALSE TRUE 69093.67603 81179.20222 62870.65894 54143.02859 68900.18744 65308.38052 72750.01266 73922.41624 29674.58068 2.328379187 2.735647829 2.118670509 1.82455918 2.321858839 2.200818985 2.45159362 2.491102302 1 14.85694002 4.219616731 24.32136113 2.124221066 2.532013407 0.156034383 0.437586513 312.2596625 400900.1603 0.109908966 0.229463802 16581.22953 -4.219616731 0.407792341 HAPEHHPGHGDRLS(ph)PGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HAPEHHPGHGDRLSPGER 18 1 C9JPC9;Q9H9J4-2;Q9H9J4 C9JPC9 USP42 Ubiquitin carboxyl-terminal hydrolase 42 1 HAPEHHPGHGDRLS(1)PGER 118.51 5.04E-05 71463000 72784 81931 40689 54228 64539 73325 73300 88614 90994 TRUE FALSE 63165.40999 81392.78987 60366.3365 66541.29622 63254.80017 76145.8602 66191.37728 69664.58569 80236.79298 0.787237471 1.014407317 0.752352309 0.829311513 0.788351551 0.949014254 0.824950435 0.868237415 1 16.29197632 1.24263476 4.289824386 1.013344289 0.852322205 0.263743103 0.078336054 0.29021484 10.36720599 0.143347658 0.018462836 17.48375691 -1.24263476 -0.161022085 HAPHCLS(ph)EEEGEQDRPR ddPTM_MDA-MB-175_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 214.26 3.62E-15 3822080000 1130605 1096347 683810 762047 1067453 1064966 1095231 1197773 1104925 TRUE FALSE 981192.6847 1089145.024 1014502.803 935081.4185 1046212.774 1105935.931 989015.6662 941638.565 974302.0252 1.007072406 1.117872073 1.041261105 0.959744919 1.073807451 1.135105853 1.015101725 0.966475016 1 19.89400954 2.004723707 24.98867245 0.983826506 1.056145191 0.267730761 0.050378889 160.0909084 846884.8644 0.021055584 0.014138364 101.0936104 -2.004723707 0.072318686 HAPS(ph)PEPAVQGTGVAGVPEESGDAAAIPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HAPSPEPAVQGTGVAGVPEESGDAAAIPAK 30 0 P13051 P13051 UNG Uracil-DNA glycosylase 1 HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAK;HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAK;HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAK;HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAK;HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAK 298.87 2.53E-81 3546070000 1501850 1341639 875868 1188446 1474909 1252984 1439032 1905340 1707050 TRUE FALSE 1303376.717 1332825.685 1299440.694 1458300.829 1445561.197 1301187.105 1299474.898 1497897.868 1505244.494 0.865890374 0.885454616 0.863275501 0.968813262 0.960349765 0.864435718 0.863298224 0.995119314 1 20.52156641 1.659556626 6.147610118 0.999326017 0.898543367 0.537960742 0.03903154 0.107193455 8.318064647 0.026233747 0.010791904 45.66217831 -1.659556626 -0.10078265 HAPS(ph)PEPAVQGTGVAGVPEESGDAAAIPAKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HAPSPEPAVQGTGVAGVPEESGDAAAIPAKK 31 1 P13051 P13051 UNG Uracil-DNA glycosylase 1 HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAKK 167.03 5.73E-13 145940000 179170 143160 109170 134350 145850 115330 186970 222830 156520 TRUE FALSE 155492.2305 142219.5725 161964.9772 164856.2209 142947.8704 119766.8197 168837.6782 175179.5386 138016.3839 1.126621537 1.030454273 1.17351993 1.194468484 1.035731167 0.86777248 1.223316199 1.269266254 1 17.07448001 HAPSLHGS(ph)TELLPLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HAPSLHGSTELLPLSR 16 0 Q9H5N1;B4DHR0;Q9H5N1-2;H3BU67;H3BNR2;H3BT64 Q9H5N1 RABEP2 Rab GTPase-binding effector protein 2 1 HAPSLHGS(0.902)T(0.098)ELLPLSR 203.89 1.71E-11 242700000 246350 215800 86858 180090 235090 211950 224380 265400 285370 TRUE FALSE 213794.2233 214382.3956 128862.8193 220982.187 230412.1689 220103.8536 202619.6621 208646.2753 251633.8837 0.849624145 0.851961558 0.512104401 0.878189311 0.91566432 0.87469879 0.805216131 0.829166058 1 17.94096668 HAPTYTIPLS(ph)PVLS(ph)PTLPAEAPTAQVPPSLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HAPTYTIPLSPVLSPTLPAEAPTAQVPPSLPR 32 0 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 2 HAPTYT(0.003)IPLS(0.996)PVLS(0.965)PT(0.036)LPAEAPTAQVPPSLPR;HAPT(0.001)YT(0.001)IPLS(0.997)PVLS(0.992)PT(0.009)LPAEAPTAQVPPSLPR;HAPTYTIPLS(1)PVLS(0.994)PT(0.006)LPAEAPTAQVPPSLPR;HAPTYTIPLS(1)PVLS(0.995)PT(0.005)LPAEAPTAQVPPSLPR;HAPT(0.253)Y(0.109)T(0.26)IPLS(0.543)PVLS(0.506)PT(0.33)LPAEAPT(0.001)AQVPPSLPR 191.21 2.60E-20 1285513000 618222 605391 318036 423391 665807 695678 589525 720178 637746 TRUE FALSE 536522.3963 601414.1467 471839.2734 519528.3977 652558.7433 722441.1828 532352.9562 566173.5391 562352.3944 0.95406795 1.069461342 0.839045549 0.923848467 1.160408935 1.284676993 0.946653667 1.006794929 1 19.10111494 4.7665603 21.50475054 1.026175533 0.954067292 0.034011532 0.12453836 6525.937977 5011598.693 0.032121731 2.08062845 58419.83156 -4.7665603 -0.072108242 HAPTYTIPLS(ph)PVLSPTLPAEAPTAQVPPSLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HAPTYTIPLSPVLSPTLPAEAPTAQVPPSLPR 32 0 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 HAPT(0.003)YT(0.01)IPLS(0.987)PVLS(0.001)PTLPAEAPTAQVPPSLPR;HAPTYT(0.002)IPLS(0.998)PVLSPTLPAEAPTAQVPPSLPR 177.93 1.31E-19 579230000 347352 307102 177082 199697 298029 310600 293187 342056 293695 TRUE FALSE 301448.5531 305084.6267 262719.4475 245041.256 292098.806 322548.983 264753.7699 268909.9863 258974.7117 1.164007679 1.178047944 1.014459851 0.946197621 1.127904744 1.245484476 1.022315145 1.038363879 1 17.9824517 4.183437954 0.01824372 2.32E-06 2.217580215 0.118373405 0.08851345 5362.749036 39.60758698 2289.05475 2528.110832 15255.90423 -4.183437954 2.217577892 HAQGGTWYGVDINNEDIADNFEAFVWEPAMVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HAQGGTWYGVDINNEDIADNFEAFVWEPAMVR 32 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;; 306.4 1.86E-90 569537000 270287 254291 162211 205446 235734 256503 268245 328254 303361 FALSE TRUE 234567.8881 252620.5457 240656.7822 252095.6543 231043.3546 266370.8364 242230.6412 258059.4366 267498.0082 0.876895831 0.944382904 0.899658221 0.942420678 0.863719907 0.995786242 0.90554185 0.964715357 1 18.02916862 -1.999999999 0.472165464 3.26705853 0.910016334 0.378558884 0.036662699 105.7385146 1.285250865 242.3241148 0.024153282 0.01 1.999999999 -2.357042196 HAQPTCPGAQLCTVYYASLNFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 295.87 1.55E-55 3629029000 712345 650019 407273 546888 749608 830609 780958 844803 830938 FALSE TRUE 618206.8034 645748.9824 604231.585 671067.2791 734692.2674 862563.0657 705220.8134 664148.4527 732705.4562 0.843731677 0.881321378 0.824658231 0.915875913 1.00271161 1.177230302 0.962488825 0.906433065 1 19.48287383 3.416587387 3.503505326 1.001298952 0.854203006 0.527264677 0.069406038 0.224842691 5.619633936 0.023119108 0.031471546 2609.680779 -3.416587387 -0.147095946 HAS(ph)APSHVQPSDSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HASAPSHVQPSDSEK 15 0 O60343-2;O60343-3;O60343;A0A3B3IRT3 O60343-2 TBC1D4 TBC1 domain family member 4 1 HAS(0.999)APS(0.001)HVQPSDSEK 144.72 2.70E-06 369510000 602330 425170 355660 452030 661150 543550 726610 796570 933410 TRUE FALSE 522730.5644 422377.0303 527658.3656 554670.3203 647994.4085 564460.7202 656143.474 626229.7044 823063.3331 0.635103695 0.513176828 0.641090842 0.673909647 0.787295925 0.685804722 0.797196823 0.76085239 1 19.65064392 -2 0.211208689 2.58851367 0.521870782 0.745399399 0.065149064 50.5575446 0.769105978 34.02167879 0.354487441 0.01 2 -2.066642888 HAS(ph)PILPITEFSDIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 227.04 3.48E-15 1630493000 704102 688876 426541 572255 888240 821706 531749 1061910 844780 TRUE FALSE 611053.1367 684350.7282 632817.6543 702194.2441 870565.7618 853317.5615 480180.0638 834828.8103 744911.0708 0.820303471 0.918701245 0.849521076 0.942655132 1.16868415 1.14552944 0.644613945 1.120709361 1 19.50670868 3.477187486 25 1.012007897 0.873037884 0.183502252 0.147095232 4.323403004 1632281.259 0.042217091 0.05508897 3000.457542 -3.477187486 -0.138970013 HAS(ph)SSPESPKPAPAPGSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HASSSPESPKPAPAPGSHR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HAS(0.25)S(0.25)S(0.25)PES(0.25)PKPAPAPGSHR;HAS(0.319)S(0.319)S(0.319)PES(0.044)PKPAPAPGSHR 90.534 0.0011138 448650000 688610 417660 322360 449810 185939 207326 326510 424590 334850 TRUE FALSE 597608.4438 414916.364 478254.3742 551946.2354 182239.1777 215301.9654 294845.1105 333794.7327 295264.4145 2.023977203 1.405236607 1.619749454 1.869328671 0.61720671 0.729183589 0.998579903 1.130494283 1 18.17164797 3.244725287 24.99975901 0.923984114 1.698561654 0.788325396 0.214309586 73.88135643 299611.3027 0.065459487 0.082353505 1756.811992 -3.244725287 0.77457754 HAS(ph)TSSPADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HASTSSPADK 10 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5;A0A0A0MSW0 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 HAS(0.95)T(0.046)S(0.001)S(0.003)PADK 101.35 0.0045246 0 91388 83546 65359 70838 84830 90315 112160 111120 145410 TRUE FALSE 79310.84425 82997.18082 96966.83101 86922.85059 83142.04897 93789.47649 101282.7405 87357.85274 128219.7955 0.61855382 0.647303956 0.756254763 0.677920677 0.648433798 0.731474233 0.789915006 0.681313306 1 16.96825949 0.086084731 1.602937724 9.999994019 0.691108528 0.747064453 0.055127689 20.42863614 2.068850858 641.2796427 0.015632013 1.219227448 -0.086084731 -9.308885491 HASNMLGELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HASNMLGELR 10 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 113.69 0.0014551 236480000 41896 56214 13775 27052 69143 82197 44484 52850 59884 FALSE TRUE 36359.33745 55844.72653 20436.63607 33194.57006 67767.18958 85359.17178 40169.94853 41548.43878 52804.58174 0.688564065 1.057573504 0.387023917 0.628630489 1.283358136 1.616510707 0.760728467 0.786833972 1 15.68837549 3.255763218 24.89577681 1.053349134 0.694998005 0.313516915 0.290653231 353.6574583 511813.4464 0.091973348 0.118438121 1802.034985 -3.255763218 -0.358351129 HASS(ph)S(ph)PESPKPAPAPGSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HASSSPESPKPAPAPGSHR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 HAS(0.617)S(0.713)S(0.669)PES(0.002)PKPAPAPGSHR 81.312 0.008038 48689000 69366 49704 34464 37306 52705 50194 51950 71227 68192 TRUE FALSE 60199.10735 49377.49115 51130.90568 45776.89749 51656.27362 52124.99566 46911.897 55995.66034 60130.41944 1.001142315 0.821173237 0.850333428 0.7612935 0.859070568 0.866865659 0.78016913 0.931236816 1 15.8758074 1.517152376 4.392409321 0.988255642 0.845397076 0.385548932 0.064239918 0.160446878 6.540095312 0.051292724 0.015871995 32.89670312 -1.517152376 -0.142858567 HASSSPES(ph)PKPAPAPGSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HASSSPESPKPAPAPGSHR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HASSSPES(0.999)PKPAPAPGSHR;HASSSPES(1)PKPAPAPGSHR;HAS(0.002)S(0.028)S(0.015)PES(0.955)PKPAPAPGSHR;HASSSPES(0.999)PKPAPAPGSHR;HAS(0.233)S(0.233)S(0.233)PES(0.302)PKPAPAPGSHR 146.15 7.14E-08 1533480000 774440 606470 203260 406835 778235 563851 618320 771240 644510 TRUE FALSE 672095.7918 602486.0586 301557.2159 499213.1048 762749.6461 585542.7128 558355.4216 606316.3278 568316.762 1.182607723 1.060123683 0.530614678 0.878406442 1.342120622 1.030310475 0.982472204 1.066863356 1 19.11633574 HAT(ph)RHSPQQEEENTIFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HATRHSPQQEEENTIFK 17 1 O14896;A0A2R8YHF3;B1AJU4 O14896 IRF6 Interferon regulatory factor 6 1 HAT(0.5)RHS(0.5)PQQEEENTIFK 104.86 0.0012166 119980000 288080 273370 96352 160660 321540 268540 307140 356430 142800 TRUE FALSE 250009.4981 271574.2145 142948.1495 197140.3085 315141.9831 278870.9076 277353.6101 280210.2182 125918.3467 1.985489047 2.156748573 1.135244809 1.565620211 2.502748737 2.214696388 2.202646536 2.225332731 1 16.94212898 3.274628147 24.99263838 2.075914454 1.701521417 0.095541361 0.474275509 378.5471813 262308.0503 0.137305498 0.177254821 1882.036954 -3.274628147 -0.374393036 HATAEEVEEEERDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HATAEEVEEEERDR 14 1 Q8TDN6 Q8TDN6 BRIX1 Ribosome biogenesis protein BRX1 homolog 0 182.33 9.23E-07 287770000 50044 47047 33582 26899 50248 47978 45725 49149 39376 FALSE TRUE 43430.5586 46737.94516 49822.36753 33006.82908 49248.16311 49823.74471 41290.59654 38638.86883 34721.01414 1.250843608 1.346099655 1.43493411 0.950629752 1.418396448 1.434973774 1.189210556 1.112838141 1 15.08352147 1.719385562 2.185232099 1.020245881 1.301520295 0.342776511 0.142799876 0.339374614 3.278352326 0.141188203 0.040098263 52.40654904 -1.719385562 0.281274414 HATLQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HATLQK 6 0 Q13263;Q13263-2;M0R3C0 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;; 117.7 0.022498 767490000 3236080 3498300 1403050 2301050 2656720 3382090 3547630 3706710 3797700 FALSE TRUE 2808423.829 3475319.437 2081569.673 2823538.572 2603856.47 3512201.191 3203581.389 2914058.912 3348740.232 0.838650846 1.037799052 0.621597833 0.843164407 0.777562991 1.048812672 0.956652701 0.870195569 1 21.67518704 2.752630192 24.88993197 0.95234068 0.825493704 0.297822141 0.109430082 1090.747919 1929597.645 0.035118879 0.034956001 565.7573334 -2.752630192 -0.126846976 HAVSDPS(ph)ILDSLDLNEDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HAVSDPSILDSLDLNEDER 19 0 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 1 HAVS(0.449)DPS(0.551)ILDSLDLNEDER 134.37 6.35E-06 26047000 20028 18631 14106 20266 19030 18371 15389 17564 38346 TRUE FALSE 17381.24906 18508.61173 20927.70878 24867.70505 18651.34023 19077.74426 13896.57715 13808.07528 33812.77956 0.514043781 0.5473851 0.618928969 0.735452849 0.551606241 0.564216977 0.410985945 0.408368536 1 15.045281 1.228267653 24.99905591 1.000000947 0.540612097 0.698422405 0.094173382 288.7710298 701304.7191 0.362695421 0.026599238 16.91483062 -1.228267653 -0.45938885 HAVSDPSILDSLDLNEDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HAVSDPSILDSLDLNEDER 19 0 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ;;; 356.31 5.44E-91 1905400000 1174740 1049650 711651 1095010 1129230 1154440 924780 1179170 2572500 FALSE TRUE 1019495.133 1042754.78 1055807.804 1343648.757 1106760.532 1198852.054 835094.9779 927013.6718 2268381.981 0.44943715 0.459691 0.465445332 0.592337961 0.487907478 0.528505368 0.368145658 0.408667358 1 21.11323217 1.234661409 24.9999113 1.000000765 0.468109937 0.881918642 0.060941809 40.0694806 256869.7657 0.120021757 0.016288483 17.1656957 -1.234661409 -0.531890827 HAVSDPSILDSLDLNEDEREVLINNINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HAVSDPSILDSLDLNEDEREVLINNINR 28 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ;;;; 355.8 2.75E-111 2123860000 779254 751189 365177 469444 751485 751894 674815 778181 524427 FALSE TRUE 676273.6095 746254.39 541777.8186 576038.4352 736531.9188 780819.8487 609371.5452 611773.049 462429.8375 1.462435065 1.613767818 1.171589233 1.245677481 1.592743069 1.688515285 1.317760005 1.322953234 1 18.81887496 1.166014444 1.610831324 0.767851268 1.447408554 0.425918959 0.162678667 1.372509376 2.789777321 1.573085295 0.048744292 14.65596585 -1.166014444 0.679557286 HAVSDPSILDSLDLNEDEREVLINNINRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HAVSDPSILDSLDLNEDEREVLINNINRR 29 2 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ;; 219.88 1.26E-34 460840000 170937 187985 74007 80540 179450 178324 179407 204109 46688.1 FALSE TRUE 148347.2424 186750.1142 109797.0327 98827.83798 175879.2961 185184.2397 162008.1368 160461.8787 41168.68601 3.603399981 4.536217506 2.667003575 2.400558472 4.272162004 4.498181935 3.935227292 3.897668211 1 15.32925978 4.252096611 24.99673409 3.386796992 4.069808405 0.082787527 1.064761738 724.6438296 1338165.182 0.26833697 0.701476722 17868.8503 -4.252096611 0.683011412 HAVSEGTK ddPTM_MDA-MB-175_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 ;;;;;;;;;;;;;; 199.07 0.00030447 1.24672E+11 79834240 62810870 31603970 50620650 35876180 53616810 62449490 81822590 70452230 FALSE TRUE 69283942.91 62398261.26 46887755.6 62114842.27 35162314.21 55679483.38 56393148.07 64325465.87 62123447.63 1.115262362 1.00442367 0.754751344 0.99986148 0.566007129 0.896271625 0.907759473 1.035445847 1 25.88863456 1.841705509 3.819003092 1.018264936 0.88026775 0.107502774 0.149270948 0.486302282 11.69655754 0.089818324 0.040771773 69.45531876 -1.841705509 -0.137997186 HAVVVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HAVVVGR 7 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 94.95 0.032162 36506000 53592 59394 42429 46374 38572 46881 56469 53100 51869 FALSE TRUE 46509.68142 59003.8369 62947.80632 56903.92548 37804.49266 48684.54241 50992.64507 41744.97822 45737.10591 1.016891657 1.290064942 1.376296227 1.244152299 0.826560665 1.064443004 1.114907558 0.912715778 1 15.48107746 3.265422291 24.40378898 0.988723776 1.246327154 0.52018669 0.117995924 131.5573876 119518.5548 0.033804459 0.043627459 1842.562768 -3.265422291 0.257603378 HAYGDQYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 HAYGDQYR 8 0 O75874;C9J4N6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;;;;;; 164.77 0.00032814 8001830000 4643510 4698050 2808018 3108157 4632874 4929590 4569910 4943340 4780000 FALSE TRUE 4029858.388 4667188.2 4165984.897 3813911.552 4540688.871 5119234.517 4126720.832 3886245.21 4214913.845 0.95609508 1.107303345 0.988391471 0.904861094 1.077291028 1.214552588 0.979075963 0.922022455 1 22.00707171 2.016066218 24.99992209 0.953973667 1.042373295 0.142101983 0.086594678 410.3918469 638589.8432 0.036554152 0.024637142 103.7686623 -2.016066218 0.088399627 HCAPS(ph)PDRS(ph)PELSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HCAPSPDRSPELSSSR 16 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 2 HCAPS(1)PDRS(0.579)PELS(0.408)S(0.011)S(0.002)R;HCAPS(1)PDRS(0.998)PELS(0.002)SSR;HCAPS(1)PDRS(0.999)PELS(0.001)SSR;HCAPS(1)PDRS(1)PELSSSR;HCAPS(1)PDRS(1)PELSSSR 174.71 2.15E-09 5836843000 5740860 4428130 2526787 3269628 4357725 4595010 4007898 4556560 4458364 TRUE FALSE 4982190.806 4399041.322 3748749.645 4012047.011 4271014.798 4771783.008 3619212.669 3582175.103 3931301.287 1.267313401 1.118978425 0.953564576 1.020539185 1.086412484 1.213792243 0.920614424 0.911193226 1 21.9065755 4.56568935 3.009284856 1.010891721 1.27059764 0.460195226 0.087829241 0.290622348 4.462191039 0.024802583 0.144330463 36786.57461 -4.56568935 0.259705919 HCCGVAQMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HCCGVAQMR 9 0 O00170;V9GYQ3 O00170 AIP AH receptor-interacting protein 0 ;;;; 101.54 0.0039126 269463000 123119.5 110652.6 158461.3 99029.4 84554.9 83137.7 99037.8 98820.6 101020.6 FALSE TRUE 106848.9461 109925.7158 235093.7147 121515.5388 82872.42292 86336.06112 89433.1294 77688.58371 89078.05975 1.199497906 1.234038057 2.639187645 1.364146673 0.930334845 0.969218025 1.003986051 0.872140502 1 16.44278251 3.420794559 5.124423083 0.956764859 1.699041247 0.42717175 0.390214111 0.183723604 10.05041881 0.114092035 0.150152968 2635.084576 -3.420794559 0.742276388 HCCPAGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HCCPAGFR 8 0 K7EQ05;P28799-3;P28799-2;P28799 K7EQ05 GRN Granulins;Acrogranin;Paragranulin;Granulin-1;Granulin-2;Granulin-3;Granulin-4;Granulin-5;Granulin-6;Granulin-7 0 ; 81.297 0.023226 203704000 129846 118136 70693 86588 123638 105901 117061 129306 87392 FALSE TRUE 112686.5221 117359.9568 104880.3713 106249.1288 121177.8457 109975.08 105708.4422 101654.9182 77060.61732 1.46231014 1.522956355 1.361011304 1.378773393 1.572500324 1.427124306 1.371757013 1.319155253 1 16.23370612 0.689108751 1.115453988 2.53E-13 1.453379733 0.830609515 0.063615239 2.02929999 0.85788622 4.720126856 0.020305381 4.887747369 -0.689108751 1.453379733 HCDLQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HCDLQVR 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;; 157.21 0.0014914 1108842000 621788 577702 296176 396376 617088 692220 543938 595606 506875 FALSE TRUE 539617.1404 573907.0375 439407.7042 486379.229 604809.1561 718850.1513 491186.9765 468240.2919 446952.8149 1.207324627 1.284043904 0.983118776 1.08821158 1.353183459 1.608335662 1.098968303 1.047628019 1 18.76976301 2.016592263 24.99881856 1.041040493 1.249521478 0.265631206 0.163701896 346.7649924 522453.2909 0.072445642 0.048829538 103.8944295 -2.016592263 0.208480985 HCECAEEGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HCECAEEGTR 10 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;;;; 168.26 7.79E-06 1825617000 724201 670532 436254 496584 560524 690968 643325 670296 861724 FALSE TRUE 628496.003 666127.2311 647227.8936 609340.987 549370.669 717549.9861 580935.4405 526958.4166 759851.9704 0.82712953 0.87665395 0.851781556 0.801920651 0.722996966 0.944328651 0.764537651 0.693501415 1 19.53535886 3.749486079 10.07757566 0.805401023 0.854368924 0.004494655 0.09393184 1.051010665 911.1265621 0.024858126 0.041272624 5616.762737 -3.749486079 0.048967902 HCFECAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HCFECAQR 8 0 O95081;A0A0C4DG34;O95081-2 O95081 AGFG2 Arf-GAP domain and FG repeat-containing protein 2 0 107.01 0.0040859 74887000 56329 56811 37120 49791 50842 61529 47662 48322 103110 FALSE TRUE 48884.97993 56437.8048 55071.35616 61096.80756 49830.34367 63896.06044 43039.74658 37988.71634 90920.45326 0.537667578 0.620738269 0.605709213 0.671980895 0.54806528 0.702768829 0.473378047 0.417823658 1 16.47231726 1.225784979 24.99938464 1.000001015 0.569389392 0.711478886 0.085584485 383.1274836 749658.245 0.412082061 0.023116459 16.81841167 -1.225784979 -0.430611622 HCFTSNEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HCFTSNEAAR 10 0 Q9BV44;H7C0R6;H7C3J3 Q9BV44 THUMPD3 THUMP domain-containing protein 3 0 ;;; 219.5 6.28E-09 415882000 208523 197371 138531 145269 181411 211062 227035 235715 197928 FALSE TRUE 180966.1572 196074.4569 205525.055 178254.5467 177801.276 219181.6917 205017.1806 185309.1816 174529.1773 1.03688197 1.12344801 1.177597111 1.021345253 1.018748147 1.255845556 1.174687143 1.061766201 1 17.41310872 1.464419711 4.296651592 1.008105388 1.116478986 0.199408749 0.075789833 0.326028442 11.52764287 0.075950266 0.020149057 29.13531457 -1.464419711 0.108373598 HCGDFEQQLANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HCGDFEQQLANR 12 0 P83436 P83436 COG7 Conserved oligomeric Golgi complex subunit 7 0 ; 154.36 6.11E-05 497270000 735300 656550 474310 537540 682410 711040 611430 708330 1006030 FALSE TRUE 638128.242 652237.0798 703687.9025 659596.6728 668831.3761 738394.1689 552133.6127 556859.1417 887098.2795 0.719343343 0.735247824 0.793246835 0.743544079 0.75395409 0.832370196 0.622404107 0.627731058 1 19.75873442 1.225595201 24.9675198 1.000000664 0.725534078 0.63600473 0.06451956 464.0949223 893652.9666 0.321018147 0.017706694 16.81106396 -1.225595201 -0.274466586 HCGLSLSST(ph)PPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HCGLSLSSTPPGK 13 0 Q09GN1;Q71F23-3;Q71F23;D6R9S4 Q09GN1 MLF1IP;CENPU Centromere protein U 1 HCGLS(0.001)LS(0.041)S(0.179)T(0.778)PPGK 93.478 0.020588 134200000 385840 359880 185500 261380 375910 292690 367020 438180 321690 TRUE FALSE 334850.2664 357515.9246 275208.4205 320730.3239 368430.1265 303949.9737 331426.4569 344478.6169 283660.1747 1.180462738 1.260367004 0.97020465 1.130685068 1.298843332 1.071528543 1.168392628 1.214405996 1 18.11380409 1.226856377 24.76337811 0.999999592 1.16220301 0.231093168 0.092785445 737.7229679 1560731.791 0.346112699 0.022162257 16.85995367 -1.226856377 0.162203418 HCKDDVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HCKDDVNR 8 1 A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2 A0A087WVR3 UHRF1 E3 ubiquitin-protein ligase UHRF1 0 ;; 149.72 0.00030083 267144000 436925 344818 211656 254182 234554 288072 359549 450360 339867 FALSE TRUE 379184.2542 342552.8679 314013.5495 311897.908 229886.8343 299154.3162 324679.9933 354054.0187 299688.3104 1.265262077 1.143030462 1.04780046 1.040740987 0.767086424 0.998218168 1.083392251 1.181407504 1 18.19310329 4.517741564 1.916454438 1.024338107 1.28669859 0.392446004 0.103285782 0.641957106 3.475092462 0.031639314 0.256057363 32941.36295 -4.517741564 0.262360483 HCLYGLDADLIMLGLTSHEAHFSLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HCLYGLDADLIMLGLTSHEAHFSLLR 26 0 Q8IZH2-2;Q8IZH2;Q8IZH2-3;C9JCZ8 Q8IZH2-2 XRN1 5-3 exoribonuclease 1 0 117.43 0.00027493 11806000 18714 19910 6376.8 10736 18508 18192 20130 22023 17280 FALSE TRUE 16240.89748 19779.2099 9460.641809 13173.77289 18139.72701 18891.85801 18177.7957 17313.55283 15237.17809 1.06587305 1.298088779 0.620891989 0.864580883 1.190491239 1.239852806 1.192989647 1.136270295 1 13.89530812 3.226681595 24.98573841 1.157441275 0.961948915 0.219151702 0.177630783 350.9620495 738194.4098 0.055850674 0.063821937 1685.316976 -3.226681595 -0.195492361 HCNGVDWR ddPTM_MDA-MB-175_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 2450120000 2105150 2046140 1163880 1440090 2008570 2249290 1914050 2041330 2067220 FALSE TRUE 1826949.094 2032698.772 1726736.261 1767084.445 1968603.387 2335821.642 1728425.726 1604807.465 1822835.607 1.002256642 1.115130056 0.9472803 0.969415146 1.079967595 1.281421996 0.948207134 0.880390672 1 20.79775303 2.028986764 24.99979092 0.926445626 1.063659905 0.262461364 0.096645629 253.0137826 218212.0583 0.040576302 0.027356149 106.9022299 -2.028986764 0.137214279 HCNMVLENVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HCNMVLENVK 10 0 P62316;P62316-2 P62316 SNRPD2 Small nuclear ribonucleoprotein Sm D2 0 ; 155.15 1.32E-05 387680000 708890 750300 477340 503810 727790 659700 776750 804530 920690 FALSE TRUE 615208.3904 745371.2299 708183.2206 618207.7608 713308.4029 685079.0859 701420.9046 632487.5204 811847.0771 0.757788514 0.918117772 0.872311105 0.761483016 0.878624094 0.843852377 0.863981561 0.779072239 1 19.63084848 1.22584793 24.99848065 1.000000385 0.836395662 0.486979268 0.053380417 532.925166 1047890.151 0.217813669 0.012383251 16.82084969 -1.22584793 -0.163604723 HCQLEPDHEGVPEETDDFGEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HCQLEPDHEGVPEETDDFGEFR 22 0 E9PFH4;C9J7E5;Q9Y5L0-5;Q9Y5L0-3;Q9Y5L0;Q9Y5L0-1 E9PFH4 TNPO3 Transportin-3 0 ; 209.71 3.10E-23 312860000 236420 228630 129781 159176 233720 258500 214360 257960 257270 FALSE TRUE 205176.498 227128.1145 192543.5257 195319.3437 229069.4293 268444.6623 193571.4002 202797.2614 226855.8337 0.904435626 1.001200237 0.848748399 0.860984443 1.009757719 1.183327129 0.853279358 0.893947747 1 17.79141623 5.056285271 12.0495484 0.949324905 0.690486529 0.02085638 0.102132393 871086.6365 6706738.939 0.025826026 4984925.368 113837.4794 -5.056285271 -0.258838376 HCSQVDSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 HCSQVDSVR 9 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;;;;;; 168.9 5.89E-05 4171801000 963084 1093463 532620 681184 1327137 1463505 971842 1167952 1137586 FALSE TRUE 835810.0093 1086279.97 790196.8135 835857.2384 1300729.57 1519806.984 877592.9124 918194.5538 1003101.879 0.833225445 1.08292088 0.787753298 0.833272528 1.296707341 1.515107305 0.874879143 0.915355233 1 19.93603671 3.268406702 24.99976376 1.096098231 0.891584978 0.250685075 0.200236024 383.9564538 321608.2103 0.064118759 0.082765732 1855.268205 -3.268406702 -0.204513253 HDAATCFVDAGNAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HDAATCFVDAGNAFK 15 0 P54920;M0R2M1;M0R058;M0R0I4 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;; 240.42 7.70E-18 1031580000 1347540 1181930 717240 935660 1177650 975040 1306230 1456400 1427860 FALSE TRUE 1169459.175 1174165.824 1064099.663 1148115.904 1154217.069 1012550.42 1179552.016 1144960.194 1259060.017 0.92883513 0.932573355 0.845154042 0.911883379 0.916729189 0.8042114 0.936851301 0.909376978 1 20.26391563 0.911509911 1.54097201 1.144743462 0.893675419 0.372084773 0.041871021 2.909637935 3.125291839 1.443526998 0.011538366 8.156614003 -0.911509911 -0.251068043 HDADGQATLLNLLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HDADGQATLLNLLLR 15 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;; 220.85 1.61E-12 902262000 983426 871204 547947 645037 907827 868986 852468 1002133 909645 FALSE TRUE 853463.7624 865481.0036 812936.002 791502.5096 889763.0188 902416.4537 769795.7846 787834.6566 802107.8044 1.064026254 1.079008331 1.013499679 0.986778218 1.109281089 1.125056319 0.959716113 0.98220545 1 19.61343662 2.21668472 24.9986358 0.980094676 1.060068971 0.467456132 0.04133301 229.9729236 262798.9808 0.018080853 0.012201756 164.6966327 -2.21668472 0.079974296 HDDFFPYADGPHQFWTGYFSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HDDFFPYADGPHQFWTGYFSSR 22 0 O00754;O00754-2 O00754 MAN2B1 Lysosomal alpha-mannosidase;Lysosomal alpha-mannosidase A peptide;Lysosomal alpha-mannosidase B peptide;Lysosomal alpha-mannosidase C peptide;Lysosomal alpha-mannosidase D peptide;Lysosomal alpha-mannosidase E peptide 0 105.92 0.00029102 206480000 208260 155250 230010 188100 140590 144870 131060 168790 220750 FALSE TRUE 180737.9133 154230.1525 341243.6053 230810.9799 137792.5341 150443.2426 118349.8214 132695.572 194653.1865 0.928512482 0.792333048 1.753085123 1.185754953 0.707887379 0.772878397 0.608003514 0.681702542 1 17.57054644 3.240266405 24.83397126 0.73502774 1.180319724 0.370192833 0.265285721 43.67147838 635789.718 0.079899623 0.097812355 1738.867158 -3.240266405 0.445291985 HDDGTQS(ph)DSENAGAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HDDGTQSDSENAGAHR 16 0 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 HDDGTQS(1)DSENAGAHR 264.96 3.04E-27 64546000 48063 33819 21273 27830 35146 35417 31662 28536 66582 TRUE FALSE 41711.35277 33596.84076 31560.69395 34149.22685 34446.66336 36779.51491 28591.42411 22433.79847 58710.75181 0.710455095 0.572243409 0.537562422 0.581652011 0.586718144 0.626452801 0.486987872 0.382107157 1 15.84133711 1.224704844 24.99988054 1.000001118 0.55190026 0.720228423 0.085931482 426.530467 769540.6346 0.465985704 0.023193591 16.77663453 -1.224704844 -0.448100858 HDDGTQS(ph)DSENAGAHRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HDDGTQSDSENAGAHRR 17 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 HDDGTQS(0.953)DS(0.047)ENAGAHRR 57.009 0.049881 69342000 135200 97680 58617 70252 59103 94600 98000 108670 114310 TRUE FALSE 117332.9774 97038.33365 86964.37726 86203.79033 57926.96593 98239.32321 88495.97508 85431.76617 100796.402 1.164059184 0.962716245 0.862772634 0.855226859 0.574692794 0.974631249 0.877967599 0.847567616 1 16.62108462 4.672883077 1.938322075 0.84957801 1.233708425 0.430666092 0.112940019 0.636100283 2.835832235 0.029644719 0.417489442 47085.05447 -4.672883077 0.384130415 HDDPALTLVAGLTSNKPTDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 177.64 3.89E-17 354190000 610060 447430 399960 423020 468650 350660 635590 833370 674780 FALSE TRUE 529439.0253 444490.8029 593381.9938 519073.1565 459324.7819 364150.1171 573950.5796 655160.3108 595008.2771 0.88980111 0.747032974 0.997266789 0.872379724 0.771963684 0.61200849 0.964609404 1.101094449 1 19.18255021 2.009309332 24.99521965 1.050293387 0.818192451 0.487766613 0.102715598 156.5877477 420430.8435 0.042958065 0.028919002 102.166692 -2.009309332 -0.232100937 HDDSSDNFCEADDIQSPEAEYVDLLLNPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HDDSSDNFCEADDIQSPEAEYVDLLLNPER 30 0 Q96HE7;G3V3E6;G3V5B3 Q96HE7 ERO1L ERO1-like protein alpha 0 ;;; 252.67 4.84E-58 254704000 148484 152582 100856 87554 146560 179844 138717 137155 117295 FALSE TRUE 128861.4632 151579.6788 149630.2989 107434.4739 143643.7427 186762.7151 125264.2467 107825.4706 103428.5187 1.24589876 1.465550127 1.446702523 1.03873163 1.388821425 1.805717778 1.211119024 1.042511987 1 16.65827451 2.003047924 24.99937031 1.055049384 1.397121219 0.39984047 0.191096196 92.23524371 756517.8462 0.080617799 0.054031453 100.7042788 -2.003047924 0.342071836 HDDYLVMLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HDDYLVMLK 9 0 Q9Y224;G3V4C6;H0YJB9 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ;; 89.543 0.0090703 505740000 1217190 1071770 688360 895630 1106620 978860 1166790 1489340 1310680 FALSE TRUE 1056335.258 1064729.472 1021253.198 1098996.48 1084600.427 1016517.378 1053634.885 1170856.231 1155732.904 0.913996006 0.921259115 0.88364119 0.950908706 0.938452495 0.879543513 0.911659504 1.013085487 1 20.14037659 1.738506653 6.241200053 1.005828712 0.914205045 0.756019418 0.021765059 0.064025387 6.901665663 0.012984692 0.005716042 54.76544905 -1.738506653 -0.091623667 HDDYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HDDYYR 6 0 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 0 ;; 114.54 0.025198 339420000 273179 238064 162633 186296 222119 278914 233552 261138 305142 FALSE TRUE 237077.703 236500.1419 241282.8628 228597.3542 217699.2665 289644.0021 210902.163 205295.6709 269068.4604 0.88110551 0.878958989 0.896734097 0.849588071 0.809085042 1.076469541 0.783823428 0.762986753 1 18.03761377 HDEES(ph)HSLSPPGENTVMADSFQIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HDEESHSLSPPGENTVMADSFQIK 24 0 Q96JQ2 Q96JQ2 CLMN Calmin 1 HDEES(0.38)HS(0.306)LS(0.306)PPGENT(0.007)VMADSFQIK 142.04 4.49E-07 119700000 97532 81448 48458 84569 102060 95831 76747 138800 116560 TRUE FALSE 84642.89909 80912.96273 71892.45088 103771.684 100029.2057 99517.68058 69304.08775 109118.7001 102780.4096 0.823531444 0.7872411 0.699476205 1.009644585 0.973232215 0.968255341 0.674292777 1.061668275 1 16.64920578 3.737112712 24.99976923 0.944515709 0.771798733 0.37862346 0.107289299 143.4438862 2476737.912 0.029375654 0.046393791 5458.995193 -3.737112712 -0.172716976 HDEESHSLS(ph)PPGENTVMADSFQIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HDEESHSLSPPGENTVMADSFQIK 24 0 Q96JQ2 Q96JQ2 CLMN Calmin 1 HDEES(0.032)HS(0.22)LS(0.745)PPGENT(0.003)VMADSFQIK 166.69 2.12E-11 137330000 111940 87255 54946 89687 115330 97121 91997 154390 116900 TRUE FALSE 97146.84538 86681.81616 81518.06938 110051.8041 113035.1586 100857.3077 83075.1451 121374.9 103080.2152 0.942439296 0.840916135 0.790821684 1.067632658 1.096574725 0.978435169 0.80592716 1.17748008 1 16.65340793 3.733758704 24.92725034 1.025239594 0.856344747 0.363132747 0.101615981 411.3877014 2135559.694 0.028288912 0.043527883 5416.998359 -3.733758704 -0.168894848 HDELADSLPCAEGEFIFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HDELADSLPCAEGEFIFLR 19 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 173.34 6.61E-12 289230000 368220 315550 202469 265600 336260 331700 305980 362490 428890 FALSE TRUE 319558.794 313477.1313 300383.6856 325908.5394 329569.0839 344460.7136 276306.1067 284974.3344 378187.1128 0.844975366 0.828894271 0.794272664 0.861765323 0.871444512 0.910820866 0.73060688 0.753527354 1 18.52874068 5.679201422 3.758236297 0.833616165 4.946787305 0 0.077791896 34818.11509 1221.266596 0.019533931 1228046.905 477750.7986 -5.679201422 4.113171139 HDELTYF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HDELTYF 7 0 P04080;A0A1W2PQG6 P04080 CSTB Cystatin-B 0 ; 133.99 0.0074869 253370000 923370 925280 507640 683610 913870 949890 698160 1048520 2050200 FALSE TRUE 801344.315 919201.7748 753136.402 838834.0988 895685.775 986432.883 630452.5507 824302.1576 1807827.692 0.443263658 0.508456519 0.416597448 0.464001134 0.495448642 0.545645411 0.348734868 0.45596279 1 20.78582575 1.238398695 24.99103778 1.000000598 0.458485184 0.910408031 0.053258841 1.037951275 159699.3969 0.07210761 0.012840346 17.31405109 -1.238398695 -0.541515414 HDGAFLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HDGAFLIR 8 0 P62993;J3KT38;J3QRL5 P62993 GRB2 Growth factor receptor-bound protein 2 0 ; 114.89 0.0050703 316420000 313970 320930 221060 289290 319330 361190 326820 349070 525920 FALSE TRUE 272478.069 318821.7897 327965.3554 354977.716 312975.9578 375085.213 295125.0467 274424.097 463746.3367 0.587558429 0.68749177 0.707208509 0.765456647 0.674886103 0.808815474 0.636393268 0.591754749 1 18.82297636 -1.917074723 0.025827783 1.649155334 2.42E-06 0.153198816 0.111672274 12382.79702 32.26951233 1377.826937 768.2900389 0.012103899 1.917074723 -1.649152917 HDGITVAVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HDGITVAVHK 10 0 R4GMU8;E9PLX3;A0A0C4DGV4;O43504 R4GMU8 LAMTOR5 Ragulator complex protein LAMTOR5 0 ;; 157.75 4.99E-06 266734000 714410 616510 383412 537480 695300 689660 582830 840480 768310 FALSE TRUE 619998.9084 612460.1052 568831.3256 659523.0489 681464.8903 716191.6665 526307.2363 660749.8926 677481.2671 0.915152844 0.904025152 0.839626648 0.973492672 1.005880049 1.057138701 0.776858729 0.975303562 1 19.36982153 3.719959516 24.61184822 0.959691124 0.888043904 0.194255827 0.074870775 1198.643824 1585972.975 0.021000784 0.031210964 5247.585411 -3.719959516 -0.07164722 HDLDLICR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 HDLDLICR 8 0 F8W0W8;P36873;P36873-2;F8VYE8;F8VR82;P62140;P62136;P62136-2;P62136-3;E9PMD7 F8W0W8;P62140;P62136 PPP1CC;PPP1CB;PPP1CA Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-gamma catalytic subunit;Serine/threonine-protein phosphatase PP1-beta catalytic subunit;Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 ;;;;;; 145.16 0.00057389 7542170000 4844600 4713730 3046830 3752950 4522870 4448910 4007980 4649540 5980940 FALSE TRUE 4204373.835 4682765.197 4520287.179 4605114.658 4432873.736 4620062.447 3619286.716 3655272.054 5273880.087 0.797206946 0.887916509 0.857108449 0.873192902 0.840533661 0.876027208 0.686266403 0.693089716 1 22.33043334 2.268786149 24.99978882 0.76782706 0.857032234 0.075017039 0.089174733 335.4210209 277428.3676 0.032777838 0.025386451 185.6889877 -2.268786149 0.089205174 HDLINQLQHNHALVTLVAENLATYMESMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HDLINQLQHNHALVTLVAENLATYMESMR 29 0 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 152.99 8.55E-09 274900000 104000 101740 46782 51706 79202 97723 92241 98798 96554 FALSE TRUE 90256.1365 101071.6632 69405.93168 63446.63758 77626.03516 101482.467 83295.48202 77670.81655 85139.49611 1.060097142 1.187130155 0.815202519 0.745208046 0.91175117 1.191955223 0.978341261 0.912277146 1 16.37754093 4.250032835 24.99992283 0.937904468 1.123613678 0.292843573 0.120936153 301.8648863 657802.4621 0.032342356 0.083982197 17784.13865 -4.250032835 0.18570921 HDMLAWINESLQLNLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HDMLAWINESLQLNLTK 17 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ;; 260.25 3.09E-27 1768249000 1650400 1342090 941730 1216940 1360270 1225040 1664040 1891490 1862470 FALSE TRUE 1432295.458 1333273.722 1397153.778 1493264.827 1333203.288 1272168.082 1502661.657 1487009.583 1642290.918 0.872132606 0.811837725 0.850734643 0.909257191 0.811794837 0.774630163 0.914978972 0.905448338 1 20.64727828 1.404110793 1.383917363 1.03204746 0.842192062 0.58900202 0.041610328 0.662347084 1.468845459 0.168108406 0.012712163 25.35775448 -1.404110793 -0.189855398 HDNLLHGTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HDNLLHGTK 9 0 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 0 ; 152.07 4.70E-05 207520000 290080 264000 140064 234120 284370 229440 270350 357230 334480 FALSE TRUE 251745.193 262265.7666 207799.4189 287280.5243 278711.5934 238266.7053 244131.4986 280839.1445 294938.1554 0.853552477 0.889222916 0.704552514 0.974036485 0.944983171 0.807853107 0.827737931 0.952196721 1 18.17005295 1.585813436 4.120632308 0.990385385 0.858965459 0.315776544 0.074011466 0.202432869 7.569272724 0.057799637 0.019343823 38.53127999 -1.585813436 -0.131419925 HDS(ph)PDLAPNVTYSLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HDSPDLAPNVTYSLPR 16 0 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 HDS(1)PDLAPNVTYSLPR;HDS(1)PDLAPNVTYSLPR;HDS(1)PDLAPNVTYSLPR 214.82 1.75E-14 956480000 717570 609525 352670 431115 798800 731620 581061 676540 854390 TRUE FALSE 622741.3064 605520.9901 523222.3916 529006.2499 782905.4428 759765.8948 524709.7937 531867.1858 753384.9875 0.826591075 0.803733815 0.694495378 0.70217254 1.039183758 1.00846965 0.69646967 0.705969982 1 19.52302776 5.111058697 14.92307601 0.8186988 1.185638793 0 0.13919342 48999971.98 62581417.7 0.035714541 598770930.6 129139.38 -5.111058697 0.366939993 HDS(ph)PDPS(ph)PPRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HDSPDPSPPRR 11 1 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 HDS(1)PDPS(1)PPRR 85.909 0.052019 155630000 201100 176640 98045 119700 193800 169600 147310 195530 154790 TRUE FALSE 174524.1255 175479.6402 145459.8899 146879.7145 189943.7592 176124.6217 133023.8989 153717.4311 136490.9025 1.278650241 1.285650816 1.065711247 1.076113585 1.39162212 1.29037627 0.974599013 1.126210086 1 17.05844527 2.240928829 24.99998171 1.050437663 1.226521396 0.435562241 0.105445502 67.68930181 714572.8012 0.042930794 0.031636888 174.1521454 -2.240928829 0.176083733 HDS(ph)PDPS(ph)PPRRPQHNS(ph)SGASPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HDSPDPSPPRRPQHNSSGASPR 22 2 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 3 HDS(1)PDPS(0.982)PPRRPQHNS(0.393)S(0.357)GAS(0.268)PR 56.021 0.066012 21383000 20503 22551 4372.7 9063.1 33132 29040 21667 25958 9431.2 TRUE FALSE 17793.4766 22402.861 6487.352346 11121.01538 32472.73802 30157.18759 19565.73767 20407.08371 8316.25428 2.139602278 2.693864358 0.780081047 1.337262546 3.904731256 3.626294552 2.352710369 2.453879237 1 13.02171816 3.29052581 24.99999888 2.665162327 1.737597962 0.203308915 0.914604638 178.6823193 85961.07167 0.277378875 0.358094213 1952.206751 -3.29052581 -0.927564365 HDS(ph)PEDVKR ddPTM_MDA-MB-175_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 117.23 0.00072574 505481000 1310810 958510 635789 715269 1083080 909380 1197050 1414290 1288270 TRUE FALSE 1137583.137 952213.4847 943258.687 877681.7587 1061528.827 944364.437 1080960.275 1111855.09 1135972.188 1.001418124 0.838236618 0.83035368 0.772626098 0.934467268 0.831327075 0.951572835 0.97876964 1 20.11549608 2.096713536 4.433462865 0.982219241 0.863877859 0.405178947 0.062854573 0.201781078 7.06357241 0.0268774 0.017316517 124.943462 -2.096713536 -0.118341383 HDSEQDNSDNNTIFVQGLGENVTIESVADYFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HDSEQDNSDNNTIFVQGLGENVTIESVADYFK 32 0 P35637-2;P35637 P35637-2 FUS RNA-binding protein FUS 0 ;; 157.42 1.35E-11 290777000 264296 166281 317683 242445.8 61481 101193 128542.1 147494 145637.2 FALSE TRUE 229368.614 165188.6892 471315.5614 297496.8244 60257.64839 105085.9602 116076.1069 115953.5559 128420.1361 1.786079823 1.286314546 3.670106384 2.316590166 0.469222742 0.818298153 0.903877775 0.902923478 1 16.97051191 3.246978437 24.87324278 0.835719484 2.295264236 0.58159004 0.609067433 127.5413195 376860.8308 0.180512079 0.229143507 1765.950138 -3.246978437 1.459544752 HDSIPAADTFEDLS(ph)DVEGGGSEPTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 HDSIPAADTFEDLSDVEGGGSEPTQR 26 0 O95671;O95671-2;O95671-3 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 1 HDSIPAADTFEDLS(1)DVEGGGSEPTQR;HDSIPAADTFEDLS(1)DVEGGGSEPTQR;HDS(0.078)IPAADT(0.152)FEDLS(0.77)DVEGGGSEPTQR;HDSIPAADTFEDLS(1)DVEGGGSEPTQR;HDSIPAADTFEDLS(1)DVEGGGSEPTQR;HDSIPAADTFEDLS(1)DVEGGGSEPTQR;HDSIPAADTFEDLS(1)DVEGGGSEPTQR;HDSIPAADTFEDLS(1)DVEGGGSEPTQR 352.67 3.43E-110 4504432000 1252566 1903213 408386 889766 2661980.8 2349104.8 1582700 2100112 2040693 TRUE FALSE 1087036.23 1890710.668 605882.8356 1091800.97 2609012.59 2439476.382 1429209.998 1651019.392 1799444.598 0.604095414 1.050719022 0.336705468 0.606743309 1.449898815 1.355682961 0.794250625 0.917516101 1 20.77912025 3.276757275 24.99714255 1.069645123 0.655872003 0.432468433 0.256712691 183.5739923 120135.6346 0.078393181 0.101203038 1891.286291 -3.276757275 -0.41377312 HDSIPAADTFEDLSDVEGGGSEPTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HDSIPAADTFEDLSDVEGGGSEPTQR 26 0 O95671;O95671-2;O95671-3 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 0 ; 285.4 3.45E-61 206572000 196038 245197 74120 141946 366760 346760 222495 290460 275068 FALSE TRUE 170131.0816 243586.2848 109964.6799 174177.0088 359462.1936 360100.0816 200917.4691 228347.3894 242549.7744 0.701427499 1.004273392 0.453369541 0.718108311 1.482014133 1.484644059 0.828355622 0.941445482 1 17.88792131 3.29592075 24.74277737 1.114508631 0.720653832 0.422406653 0.247041227 86.13029135 37152.11771 0.077308829 0.099805216 1976.608914 -3.29592075 -0.393854799 HDSPEDVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HDSPEDVKR 9 1 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 127.4 0.00028989 182557000 916540 687760 393150 586370 560840 645860 792670 963870 971790 FALSE TRUE 795416.9168 683242.0593 583278.655 719514.2706 549680.3813 670706.6521 715796.9854 757753.9013 856906.0933 0.928242806 0.79733598 0.680679785 0.839665252 0.641470968 0.782707297 0.835327221 0.884290481 1 19.70877759 1.424317687 1.370186633 1.049008199 0.773084225 0.448509097 0.079077021 0.812339305 1.813700087 0.295537818 0.023803427 26.5654812 -1.424317687 -0.275923974 HDWDSFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HDWDSFFR 8 0 Q02040;X6RAJ1;Q02040-2;Q02040-3 Q02040 AKAP17A A-kinase anchor protein 17A 0 156.51 0.00039182 87804000 170380 149620 92514 121600 138230 120920 160040 206300 168830 FALSE TRUE 147863.8513 148637.1364 137254.0798 149211.1385 135479.4934 125571.8706 144519.3454 162184.3504 148871.1097 0.993234024 0.998428349 0.921965854 1.002284048 0.910045567 0.843493885 0.970768242 1.089427967 1 17.18370428 1.916885337 6.614901825 1.046488106 0.94416229 0.37762974 0.052237072 0.243797147 16.19197149 0.02643627 0.014364324 82.58198872 -1.916885337 -0.102325815 HDWDYCEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HDWDYCEHR 9 0 P17568 P17568 NDUFB7 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 0 ; 183.67 2.60E-05 199830000 130558 142582 111863 145625 175499 209850 113604 174377 172782 FALSE TRUE 113304.4295 141645.3695 165960.321 178691.382 172006.9133 217923.0653 102586.7016 137087.8356 152355.9088 0.743682542 0.929700532 1.08929363 1.172854951 1.128980915 1.430355193 0.673335891 0.899786799 1 17.21708593 2.20635243 24.99997158 0.858792121 1.082065856 0.236860546 0.190185491 297.6530154 231036.0214 0.080259325 0.054115642 160.8245814 -2.20635243 0.223273736 HEAMITDLEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HEAMITDLEER 11 0 P35579 P35579 MYH9 Myosin-9 0 ; 160.52 2.74E-05 3624500000 1985670 2036190 1325370 1695370 2146300 2084490 2044240 2365900 2754400 FALSE TRUE 1723258.678 2022814.134 1966323.365 2080329.671 2103592.829 2164681.679 1845989.919 1859970.696 2428777.97 0.709516761 0.832852636 0.809593709 0.85653349 0.866111623 0.891263716 0.760048857 0.765805158 1 21.21179918 5.41710639 1.44192316 0.841087205 0.179874049 0.283520891 0.068280242 11.13565433 5.076983975 0.019066451 17.1598887 261280.1337 -5.41710639 -0.661213155 HEANNPQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HEANNPQLK 9 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 93.111 0.0096207 266080000 336540 226950 182598 259600 238400 202853 252200 310530 657090 FALSE TRUE 292065.3863 225459.1505 270903.0036 318546.1477 233656.3064 210656.8862 227741.6828 244125.576 579409.5688 0.504074151 0.38911879 0.467550103 0.549777161 0.40326622 0.363571638 0.393058201 0.421335078 1 19.14422398 1.237818005 24.99817697 1.000000655 0.433441461 0.906172618 0.056980108 5.279296969 177592.2938 0.084032587 0.014398581 17.29091616 -1.237818005 -0.566559194 HEAPSS(ph)PISGQPCGDDQNASPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HEAPSSPISGQPCGDDQNASPSK 23 0 O75376;O75376-2;A0A088AWL3;E7EVU5;E7EW50;J3KS51;O75376-3 O75376 NCOR1 Nuclear receptor corepressor 1 1 HEAPS(0.417)S(0.583)PISGQPCGDDQNASPSK;HEAPS(0.034)S(0.966)PISGQPCGDDQNASPSK 253.7 1.09E-43 729710000 558230 418630 237904 311930 437810 364170 422090 534030 499230 TRUE FALSE 484458.4911 415879.992 352955.1701 382758.4741 429098.4376 378179.8555 381155.7768 419831.8403 440211.5981 1.100512783 0.944727476 0.801785259 0.869487482 0.974754957 0.859086533 0.865846739 0.953704632 1 18.74783763 4.697989249 3.924175042 0.904181177 1.111821197 0.513156555 0.059751737 0.179331197 5.33422593 0.015154468 0.097488159 49887.21373 -4.697989249 0.20764002 HECQANGPEDLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 HECQANGPEDLNR 13 0 P60981;P60981-2 P60981 DSTN Destrin 0 ;;;;;;;;;;; 273.24 9.07E-32 7945784000 4309522 4063392 2824706 3154664 4204345 4364332 4015863 4493140 4850243 FALSE TRUE 3740007.749 4036699.31 4190743.27 3870978.677 4120686.76 4532230.676 3626405.224 3532316.977 4276852.798 0.874476613 0.943848082 0.979866146 0.905099815 0.963485758 1.059711636 0.847914435 0.825915023 1 22.02811812 HEDEQALLDQNS(ph)QTPPPS(ph)PFSVQAFNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HEDEQALLDQNSQTPPPSPFSVQAFNK 27 0 A0A499FJI4;O75592-2;O75592;A0A087WY34 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 2 HEDEQALLDQNS(0.549)QT(0.453)PPPS(0.977)PFS(0.022)VQAFNK 77.433 3.12E-06 0 29962 32595 19541 29279 36751 42446 39318 51479 49671 TRUE FALSE 26002.44579 32380.8813 28991.09296 35927.24445 36019.727 44078.92509 35504.94641 40470.61646 43798.95097 0.593677365 0.739307234 0.661912953 0.820276369 0.822387893 1.006392256 0.81063463 0.924008808 1 15.4186087 3.605611861 0.824414069 0.932883986 0.618560385 0.750937658 0.0667031 0.383317038 0.528589003 0.03240366 0.084495261 4032.848067 -3.605611861 -0.314323601 HEDGDSNGTFFVYHAIYLEELTAVELTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HEDGDSNGTFFVYHAIYLEELTAVELTEK 29 0 F8VX55;Q12800-2;Q12800-3;Q12800-4;Q12800;F8VWL0 F8VX55 TFCP2 Alpha-globin transcription factor CP2 0 125.78 1.25E-05 41597000 24252 22571 11050 17836 18123 17145 27181 32600 20398 FALSE TRUE 21047.03675 22422.72961 16393.81696 21885.93641 17762.38776 17804.57924 24544.9908 25628.74369 17986.57168 1.170152775 1.246637215 0.911447565 1.216793105 0.987536039 0.989881761 1.364628638 1.424882082 1 14.13463261 2.2329273 24.99798454 1.301087658 1.087716329 0.216028474 0.152536759 168.4338381 747419.7015 0.060123315 0.041800928 170.9729085 -2.2329273 -0.21337133 HEDLVPPAGS(ph)PELS(ph)PPQPLFRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HEDLVPPAGSPELSPPQPLFRPR 23 1 A0A0A0MQV9;Q9UPS6-2;Q9UPS6 A0A0A0MQV9 SETD1B Histone-lysine N-methyltransferase;Histone-lysine N-methyltransferase SETD1B 2 HEDLVPPAGS(1)PELS(1)PPQPLFRPR 65.581 0.038653 138630000 110900 93371 60274 71614 86654 80281 92875 110320 74973 TRUE FALSE 96244.28402 92757.63975 89422.708 87875.05325 84929.75494 83369.46202 83867.99679 86728.92651 66109.77735 1.455825263 1.403085042 1.352639679 1.329229303 1.284677673 1.261076128 1.268617142 1.311892582 1 16.01257604 -1.069385348 0.282473164 1.10E-34 1.425363852 0.705816747 0.065509088 31.93577449 0.834926102 19.82558034 0.171302232 0.08523435 1.069385348 1.425363852 QEAKPQQAAGMLS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 147.9 5.50E-06 427400000 571440 402120 451770 515020 449090 342660 545150 670130 1169410 TRUE FALSE 495922.7562 399478.4472 670247.4831 631963.1626 440153.9876 355842.3519 492281.4369 526827.9145 1031163.682 0.480935049 0.387405466 0.649991359 0.612864062 0.426851716 0.345088135 0.477403777 0.510906196 1 19.97584193 1.23613712 5.040091427 1.033396525 0.484333022 0.755367185 0.091976351 0.091616846 6.013446052 0.177213084 0.024454971 17.22412307 -1.23613712 -0.549063503 HEDTNLASSTLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HEDTNLASSTLLR 13 0 P49407-2;P49407;H0YET9 P49407-2 ARRB1 Beta-arrestin-1 0 ; 179.39 1.38E-05 1131620000 980780 1042440 709850 964370 1093790 1173810 1013800 1094240 2471400 FALSE TRUE 851167.438 1035592.143 1053135.834 1183344.948 1072025.719 1218967.23 915481.832 860245.2914 2179233.907 0.390581036 0.475209265 0.483259659 0.543009607 0.49192779 0.559355848 0.420093423 0.394746653 1 21.05538963 1.233570964 24.99996185 1.000000813 0.470299115 0.897753285 0.056235245 49.89555772 249965.4467 0.119819208 0.014831243 17.12264938 -1.233570964 -0.529701699 HEEAPGHRPTTNPNASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HEEAPGHRPTTNPNASK 17 1 P21291;E9PS42;E9PP21;E9PND2 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ;;;;; 112.34 0.00030046 3372057000 1302240 1217491 871029 1086128 1292453 974721 1296427 1602515 1651194 FALSE TRUE 1130145.685 1209493.221 1292261.538 1332749.963 1266735.714 1012219.148 1170699.709 1259829.638 1455991.726 0.77620337 0.830700614 0.887547308 0.915355451 0.870015736 0.695209409 0.804056567 0.865272525 1 20.47357073 1.260475155 3.101029616 1.025788415 0.828693382 0.441040316 0.061399701 0.364141626 4.628856075 0.172642999 0.017116004 18.21692855 -1.260475155 -0.197095032 HEEEEWT(ph)DDDLVESL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HEEEEWTDDDLVESL 15 0 D6RHI7;P51946 D6RHI7 CCNH Cyclin-H 1 HEEEEWT(1)DDDLVESL;HEEEEWT(1)DDDLVESL 217.88 2.25E-11 296910000 563670 492010 307750 412010 488850 503710 438740 539390 578580 TRUE FALSE 489179.5813 488777.9539 456578.9294 505563.1677 479122.8414 523088.0496 396191.0623 424045.646 510180.9315 0.958835486 0.95804826 0.894935309 0.990948772 0.939123381 1.025299099 0.776569718 0.83116718 1 18.96064945 2.243401588 24.99996266 0.857451127 0.958392114 0.304929927 0.064539142 130.163632 672201.221 0.024248178 0.018167016 175.1465503 -2.243401588 0.100940987 HEEEFDLFMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HEEEFDLFMR 10 0 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YFK5;K7EQF0;A0A2R8Y5K3 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 0 ; 118.4 0.0008296 108042000 115526 87374 58402 65688 89770 93239 85421 98070 88610 FALSE TRUE 100258.9464 86800.03444 86645.40254 80603.46438 87983.75263 96825.96466 77136.88457 77098.49368 78134.62674 1.2831564 1.110903553 1.108924508 1.031597228 1.126053279 1.239219648 0.987230474 0.986739131 1 16.25367443 -1.999999998 0.058943858 3.54E-06 1.64982135 0.416663356 0.078035968 857.5606339 4.904952341 133.770405 34.74431477 0.01 1.999999998 1.64981781 HEENHRPLFHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HEENHRPLFHK 11 1 E5RIA4;E7ETB3;Q9ULA0-2;Q9ULA0;E7EMB6 E5RIA4 DNPEP Aspartyl aminopeptidase 0 106.67 0.0014843 54840000 36408 38658 33087 30847 35584 30750 31578 40727 65033 FALSE TRUE 31596.59055 38404.05305 49087.98387 37851.28282 34875.94802 31932.9724 28515.57042 32017.84799 57344.87283 0.550992425 0.669703343 0.856013475 0.660063942 0.608179011 0.55685837 0.497264516 0.55833846 1 15.80737688 3.477412459 24.99997607 0.619489316 0.701325693 0.004906277 0.154576713 34.61565263 2971936.823 0.044576677 0.058207155 3002.012246 -3.477412459 0.081836376 HEENLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HEENLK 6 0 P42766 P42766 RPL35 60S ribosomal protein L35 0 ;;; 124.89 0.018161 2238190000 3110690 2840890 2402730 2658250 1746010 2502990 3517320 3818770 5600200 FALSE TRUE 2699604.435 2822228.007 3564698.265 3261846.291 1711267.817 2599281.645 3176210.848 3002155.753 4938150.736 0.546683279 0.57151516 0.721869067 0.660540041 0.346540215 0.526367416 0.64319844 0.60795142 1 22.23553944 1.08355675 2.292073428 1.279618249 0.571969854 0.637097533 0.100031324 0.781780598 2.883858783 1.341361614 0.027957454 12.12151073 -1.08355675 -0.707648395 HEERQDEHGYISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HEERQDEHGYISR 13 1 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;; 124.42 0.0001368 1654637000 976520 1049240 119265 169759 724024 822634 1123870 945670 105576 FALSE TRUE 847470.4078 1042347.473 176941.9529 208305.3756 709617.3389 854281.2623 1014877.26 743445.8297 93094.92555 9.103293255 11.19660891 1.90066163 2.237558861 7.62251363 9.176453574 10.90153147 7.985889943 1 16.50641491 4.288942025 24.999998 6.350951216 10.14996193 0.212437368 3.34215561 200.7584859 99615.88211 0.895814134 2.370095151 19451.00407 -4.288942025 3.799010718 HEGALETLLR ddPTM_MDA-MB-175_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 ;; 247.08 1.14E-12 660380000 826270 658740 501760 627870 699730 680260 680830 800420 1346030 FALSE TRUE 717076.326 654412.6936 744412.8143 770437.4799 685806.742 706430.0424 614803.2114 629256.4119 1186903.867 0.604157039 0.551361161 0.627188802 0.649115317 0.577811532 0.595187245 0.517989054 0.530166283 1 20.17877166 1.234501097 24.99996526 1.000000611 0.57911956 0.912040683 0.040825837 36.37678157 223989.7792 0.083227172 0.011142095 17.15936043 -1.234501097 -0.420881051 HEGVFICR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HEGVFICR 8 0 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ;; 113.71 0.0032855 970750000 580080 504360 380672 449880 559360 625630 452965 521858 1005370 FALSE TRUE 503420.9583 501046.826 564766.2525 552032.13 548229.8304 649698.3909 409036.524 410262.7278 886516.3039 0.567864298 0.565186251 0.637062454 0.622698226 0.618409191 0.732866827 0.461397633 0.462780804 1 19.75778764 1.228572979 24.99884323 1.000000852 0.58022774 0.726237813 0.080335394 247.3271076 619010.859 0.288398216 0.021824021 16.92672659 -1.228572979 -0.419773111 HEHQVMLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HEHQVMLMR 9 0 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;; 73.885 0.023642 115810000 162880 151950 115848 111771 125529 145453 129759 144413 132005 FALSE TRUE 141354.9953 150951.8304 171872.4803 137150.3139 123031.2185 151048.671 117174.9922 113531.4038 116399.5193 1.214395009 1.296842387 1.476573798 1.178272167 1.056973596 1.297674354 1.006662166 0.975359731 1 16.82872557 2.467167462 0.666055602 0.929979125 1.319656908 0.550296802 0.108263202 0.728727446 0.706991036 0.187451711 0.083413096 293.2023605 -2.467167462 0.389677783 HEIEGTGLPQAQLLWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HEIEGTGLPQAQLLWR 16 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 246.18 3.54E-20 778050000 936620 875320 541560 735320 967950 927040 875930 987300 1036580 FALSE TRUE 812843.2939 869569.9653 803460.2274 902285.6447 948689.6888 962703.8287 790982.4434 776173.5782 914036.6933 0.889289566 0.951351266 0.879024041 0.987143789 1.03791204 1.053244181 0.865372746 0.849171137 1 19.80189256 4.742902942 21.89007253 0.945249021 0.889289432 0.064951549 0.070739268 297.6734294 1500238.676 0.019212362 0.140274083 55322.64575 -4.742902942 -0.05595959 HEILSVAEVTTCEYEVVILTPLLCSHPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HEILSVAEVTTCEYEVVILTPLLCSHPK 28 0 Q96DZ1;Q96DZ1-3;Q96DZ1-2 Q96DZ1 ERLEC1 Endoplasmic reticulum lectin 1 0 203.72 1.96E-25 57088000 34987 33370 37194 46045 33834 42125 40742 48520 45954 FALSE TRUE 30363.3793 33150.79027 55181.14281 56500.221 33160.7696 43745.57601 36790.84711 38144.37558 40521.37047 0.74931768 0.818106345 1.361778789 1.394331444 0.818352618 1.079568028 0.907936891 0.941339721 1 15.30639535 2.240893218 24.90218807 0.9462623 1.048042451 0.033279651 0.215660681 226.8249375 2421561.095 0.088404126 0.065141196 174.1378661 -2.240893218 0.101780151 HEIS(ph)PGHDGTWNDNQLQEMAQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HEISPGHDGTWNDNQLQEMAQLR 23 0 Q676U5-3;Q676U5;E7EVC7;Q676U5-2;C9J1B2 Q676U5-3 ATG16L1 Autophagy-related protein 16-1 1 HEIS(0.5)PGHDGT(0.5)WNDNQLQEMAQLR 72.876 0.033918 102210000 24841 15734 11755 24978 27433 21833 27960 27152 31102 TRUE FALSE 21558.19891 15630.64232 17439.75732 30649.63666 26887.13697 22672.92964 25248.4435 21345.7561 27425.15699 0.786073856 0.569938116 0.635903646 1.117573791 0.980382245 0.82672014 0.920630774 0.778327581 1 14.74321226 3.768350956 24.94936937 0.916865471 0.654568423 0.586514436 0.107169144 511.7987554 428629.0967 0.029073539 0.050347892 5866.120175 -3.768350956 -0.262297048 HEIVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HEIVPK 6 0 P25788-2;P25788;G3V4X5;H0YJ03 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ; 77.72 0.071677 804370000 3660300 2906400 1938230 2472200 2871600 2569300 3441500 4049100 3763000 FALSE TRUE 3176582.081 2887307.667 2875564.511 3033550.795 2814460.778 2668142.634 3107743.86 3183231.475 3318142.427 0.957337472 0.870157846 0.866618771 0.914231641 0.848203729 0.804107326 0.93659146 0.959341422 1 21.66194438 1.886866244 2.869163449 0.980084567 0.876409062 0.50508936 0.04186837 0.214763983 3.142126862 0.027649318 0.011702346 77.06660793 -1.886866244 -0.103675505 HEKEDGAISTIVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HEKEDGAISTIVLR 14 1 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;; 188.25 5.13E-07 1342070000 2103660 1625070 1152700 1501010 1694770 1528580 1864520 2317960 2023200 FALSE TRUE 1825656.001 1614394.808 1710149.576 1841837.262 1661047.393 1587385.462 1683699.137 1822282.292 1784019.601 1.023338533 0.904919883 0.95859349 1.032408647 0.931070147 0.889780281 0.943767174 1.021447461 1 20.76670004 1.740279207 8.601919669 1.009747614 0.952629774 0.20705854 0.045233769 0.157431385 44.46713331 0.025519399 0.011706799 54.98942861 -1.740279207 -0.05711784 HELIEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 HELIEFR 7 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5;J3KRF5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;;;; 166.78 0.0011106 5425956000 4365874 3680772 2785465 3438953 4090553 4223026 3999364 4086833 7430450 FALSE TRUE 3788912.689 3656592.766 4132525.191 4219819.84 4009158.998 4385488.543 3611506.295 3212895.567 6552030.666 0.578280671 0.558085417 0.630724336 0.644047633 0.61189564 0.669332725 0.55120412 0.490366381 1 22.64351068 1.229948601 24.99216306 1.000000775 0.589945382 0.860859044 0.051577537 131.8591803 382626.9125 0.164184245 0.014311802 16.98042678 -1.229948601 -0.410055393 HELLQPFNVLYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HELLQPFNVLYEK 13 0 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 170.11 2.73E-05 1827570000 2782700 2285900 1499750 1929250 2387300 2090300 2687900 3070200 2630700 FALSE TRUE 2414959.145 2270883.772 2225034.116 2367315.699 2339797.401 2170715.194 2427227.872 2413661.622 2319701.643 1.041064549 0.978955108 0.959189783 1.02052594 1.008663079 0.935773443 1.046353474 1.0405052 1 21.14550783 HELQANCYEEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HELQANCYEEVK 12 0 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;;;; 182.89 1.63E-05 6360820000 7233690 5680550 5848460 7061880 5865310 4903310 6407030 8251000 22099420 FALSE TRUE 6277739.539 5643234.093 8676794.818 8665387.788 5748601.806 5091943.509 5785677.217 6486587.859 19486851.74 0.322152579 0.289591883 0.445264065 0.444678694 0.294999001 0.261301496 0.296901587 0.332869975 1 24.21599769 1.238410259 24.9880533 1.000000733 0.335742778 0.918247607 0.062267345 1.005767401 166589.2553 0.092516665 0.016474242 17.31451215 -1.238410259 -0.664257955 HELQANCYEEVKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 HELQANCYEEVKDR 14 1 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;;;;;;;;;; 292.27 9.95E-44 53304623900 31360529 24427502 19405129.5 21779159.1 24409781.9 19785878.2 28552437.7 33970414 28721539 FALSE TRUE 27216155.64 24267036.13 28789515.03 26724450.05 23924075 20547053.74 25783426.69 26706105.32 25326111.38 1.074628285 0.958182477 1.136752287 1.055213319 0.944640677 0.811299194 1.018057068 1.054488979 1 24.59412224 3.251186016 24.57992519 0.973003253 1.054947452 0.253480131 0.076589913 324.2954912 631354.5474 0.024075248 0.030856922 1783.142357 -3.251186016 0.081944199 HELS(ph)PPQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 152.85 3.74E-05 6218200000 2997150 2330050 1844060 2272240 2550990 2331380 2637240 3118100 4222000 TRUE FALSE 2601069.034 2314743.748 2735853.584 2788186.821 2500230.29 2421069.697 2381480.871 2451318.58 3722879.97 0.698671205 0.621761584 0.734875582 0.748932773 0.671584985 0.650321718 0.639687793 0.658446848 1 21.82798767 1.236621218 24.99828373 1.000000409 0.676485173 0.863741207 0.040184248 18.70145265 240990.4778 0.065775508 0.010401889 17.2433331 -1.236621218 -0.323515236 HEMLPASLIQAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HEMLPASLIQAQR 13 0 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 169.62 2.82E-05 713240000 896590 783270 450470 629610 872310 926400 894820 933610 848200 FALSE TRUE 778103.3598 778124.6478 668318.7987 772572.5735 854952.7376 962039.2075 808040.4941 733964.7669 747926.7623 1.040346995 1.040375458 0.89356182 1.032952172 1.143096866 1.286274614 1.080373821 0.981332403 1 19.51253748 3.470926599 22.86088503 1.091338618 0.99081186 0.223070803 0.09165827 98.18197719 362327.1264 0.029742782 0.038542647 2957.512569 -3.470926599 -0.100526759 HEMLPEFYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HEMLPEFYK 9 0 Q86VP6;Q86VP6-2;A0A0C4DGH5;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 108.98 0.0025238 915100000 1960030 1724360 1064600 1172080 1750550 1586090 1913440 2093860 1985700 FALSE TRUE 1701007.069 1713032.566 1579444.121 1438218.678 1715717.48 1647107.909 1727874.883 1646104.333 1750952.808 0.971475109 0.978343081 0.902048367 0.821392028 0.979876483 0.940692348 0.986819791 0.940119189 1 20.73970877 HEMPPHIYAITDTAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HEMPPHIYAITDTAYR 16 0 P35579;P35579-2;Q5BKV1 P35579 MYH9 Myosin-9 0 ;;;;; 208.47 1.03E-11 2361480000 1387730 1392260 884937 1125540 1456480 1470310 1411400 1601280 1772640 FALSE TRUE 1204337.964 1383114.152 1312895.493 1381111.06 1427498.898 1526873.777 1274522.645 1258858.733 1563080.519 0.770490036 0.884864302 0.839941051 0.883582799 0.913259989 0.976836292 0.815391549 0.805370368 1 20.57596067 5.655716541 1.280920393 0.884538356 2.09E-09 0.254086845 0.063177519 21.17961581 4.999900589 0.018649491 42.81434559 452602.0754 -5.655716541 -0.884538354 HENEALWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HENEALWR 8 0 E9PMQ6;Q00613-2;Q00613;E9PI02 E9PMQ6 HSF1 Heat shock factor protein 1 0 93.649 0.010919 70248000 21200 18773 9025.1 12852 21281 17722 15905 22197 17389 FALSE TRUE 18398.36629 18649.67893 13389.66855 15770.24303 20857.54974 18403.77681 14362.53555 17450.34429 15333.29223 1.19989667 1.216286669 0.873241594 1.028496868 1.360278629 1.200249531 0.936689612 1.138068983 1 13.90437987 2.258154039 24.99609051 1.04481601 1.141529698 0.144088493 0.136400271 602.2878523 768360.7503 0.053740812 0.041567101 181.1982669 -2.258154039 0.096713689 HEPLVLFCESCDTLTCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HEPLVLFCESCDTLTCR 17 0 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;; 339.3 2.18E-72 2225970000 1220080 1145850 709335 787032 1078630 1096390 1026090 1218260 1492270 FALSE TRUE 1058843.337 1138322.836 1052371.779 965739.6446 1057167.373 1138568.833 926579.9497 957744.5795 1315855.541 0.804680532 0.865081919 0.799762395 0.733925279 0.803406864 0.865268867 0.704165405 0.727849334 1 20.32756968 4.066636285 9.720602698 0.791631998 0.834504317 0.003455361 0.085538652 1.356225111 186.3006562 0.021582716 0.045039941 11658.3284 -4.066636285 0.042872319 HEQEYMEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HEQEYMEVR 9 0 Q15363;E7EQ72;F5GX39 Q15363 TMED2 Transmembrane emp24 domain-containing protein 2 0 ; 94.309 0.013191 343470000 386330 353360 231370 255390 363010 433360 400710 359800 338520 FALSE TRUE 335275.5117 351038.7549 343261.3059 313380.2029 355786.8112 450031.6396 361849.2059 282859.57 298500.5512 1.12319897 1.176007057 1.149952 1.049847987 1.191913414 1.5076409 1.212222907 0.9476015 1 18.18737407 1.745083853 7.110097289 0.976825768 1.20431083 0.385614639 0.119279731 0.137801568 21.91811003 0.073571891 0.033195973 55.60116014 -1.745083853 0.227485062 HEQISDLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HEQISDLER 9 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ;; 152.07 8.14E-05 817190000 238251 246980 167755 175467 281236 289109 279457 259225 262257 FALSE TRUE 206765.5267 245357.5721 248881.8791 215309.4642 275639.9538 300231.2103 252355.3032 203791.751 231253.2762 0.894108529 1.060990686 1.076230716 0.931054763 1.19193967 1.298278732 1.091250716 0.881249141 1 17.81911428 4.738732529 20.08140281 1.060327716 0.894108073 0.169765117 0.119057426 2.013087469 231286.6319 0.032286744 0.181191698 54793.93991 -4.738732529 -0.166219643 HEQNIDCGGGYVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HEQNIDCGGGYVK 13 0 P27797 P27797 CALR Calreticulin 0 ;;;;; 233.32 2.88E-16 12076450000 11031280 9865650 7582368 9406535 11276410 11169870 10338740 11020710 10533190 FALSE TRUE 9573468.398 9800841.896 11249226.53 11542432.54 11052031.5 11599582.13 9336090.586 8664016.93 9287968.278 1.030738705 1.05521914 1.21116117 1.24272954 1.189929937 1.248882617 1.005181145 0.932821546 1 23.14693161 2.107318579 5.948601596 0.963973476 1.164650271 0.585242899 0.073332704 0.146812306 7.185202265 0.03312832 0.022108809 128.0320146 -2.107318579 0.200676795 HERGSPS(ph)HSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HERGSPSHSK 10 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 HERGS(0.178)PS(0.822)HSK 101.32 0.0020604 29564000 86569 42764 20249 27817 28168 34264 50381 57941 24737 TRUE FALSE 75128.68731 42483.08047 30041.48413 34133.27501 27607.51191 35582.15825 45495.05837 45550.76805 21812.62004 3.444276165 1.94763767 1.377252438 1.564840672 1.265666933 1.631264753 2.085721857 2.088275868 1 14.41287545 4.721997643 3.324354321 1.637429544 3.654870877 0.74769522 0.337929456 0.163628148 3.026991962 0.090107989 0.826281858 52722.70003 -4.721997643 2.017441334 HERPAGPGT(ph)PPPDSGPLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HERPAGPGTPPPDSGPLAK 19 1 Q9P2K8-2;Q9P2K8;H0YME5 Q9P2K8-2 EIF2AK4 Eukaryotic translation initiation factor 2-alpha kinase 4 1 HERPAGPGT(0.997)PPPDS(0.003)GPLAK;HERPAGPGT(0.993)PPPDS(0.007)GPLAK 111.33 0.00032016 659350000 589610 437580 286530 397580 504660 412380 553310 640680 654070 TRUE FALSE 511691.5446 434705.5082 425096.8664 487856.6156 494618.2534 428244.5254 499650.0814 503675.5678 576746.5897 0.887203416 0.753720119 0.737060043 0.845876897 0.857600655 0.742517655 0.86632516 0.873304804 1 19.13757804 0.650723289 0.954867757 1.422306865 0.802498268 0.569883928 0.052428737 4.037433208 1.305909126 3.408278564 0.017564757 4.474281343 -0.650723289 -0.619808597 HESGASIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HESGASIK 8 0 P61978;P61978-2;S4R359;P61978-3 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;; 150.36 0.00049039 4238035000 6837213 6994650 1275536 3907344 6735167 7786470 7645738 8962443 8956328 FALSE TRUE 5933657.979 6948701.684 1892389.476 4794566.175 6601150.354 8086020.539 6904255.506 7045894.31 7897521.107 0.751331702 0.879858577 0.23961816 0.607097608 0.835850929 1.023868177 0.874230713 0.892165303 1 22.91296846 3.129324347 3.972813322 0.931622153 0.611037117 0.464064988 0.166290016 0.212140869 6.195950782 0.05311808 0.061450937 1346.865868 -3.129324347 -0.320585036 HESQQDYSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 HESQQDYSK 9 0 Q14247 Q14247 CTTN Src substrate cortactin 0 ;;;;;;; 192.12 3.51E-05 3652109000 6040240 6717950 1565540 4061097 6489430 7071800 7698790 8812420 8184970 FALSE TRUE 5242006.98 6673819.344 2322640.38 4983231.144 6360303.039 7343856.722 6952162.531 6927952.561 7217352.171 0.72630611 0.924690827 0.321813364 0.690451432 0.881251585 1.017527834 0.963256658 0.959902246 1 22.78303822 3.148067477 3.389941273 0.976609247 0.657633822 0.517578561 0.146197574 0.198301518 4.502908662 0.046233616 0.05433445 1406.266002 -3.148067477 -0.318975425 HETWSGHVISS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HETWSGHVISS 11 0 Q9Y2V2 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 0 ;;; 182.71 5.67E-06 1664640000 742100 764330 209092 476539 865840 832740 725881 834290 713660 FALSE TRUE 644029.6048 759309.0659 310209.5906 584744.4634 848611.478 864776.0467 655485.1723 655883.576 629291.9278 1.02341946 1.206608622 0.492950214 0.929210177 1.348517978 1.374204894 1.04162336 1.042256458 1 19.26336991 3.39308592 10.59693552 1.147785689 0.899945477 0.249049961 0.21363201 0.612959726 72.84772093 0.064562791 0.083356385 2472.213197 -3.39308592 -0.247840212 HEVININLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HEVININLK 9 0 Q5TA02;P78417-3;P78417;Q5TA01;P78417-2 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 ; 168.8 5.90E-05 2046850000 4039200 3811500 2589520 3151600 3720300 3167000 3955700 4652400 5602400 FALSE TRUE 3505409.486 3786462.006 3841820.533 3867218.949 3646273.309 3288836.539 3572076.823 3657520.465 4940090.654 0.70958404 0.766476219 0.777682193 0.782823478 0.738098461 0.665744167 0.723079205 0.740375171 1 22.23610609 1.238668301 9.390213736 1.001499708 0.738574569 0.851401068 0.034401247 0.030790459 44.47031771 0.051692112 0.009147195 17.32480284 -1.238668301 -0.262925138 HFADLLPGFLQAVNDSCYQNDDSVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HFADLLPGFLQAVNDSCYQNDDSVLK 26 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 86.32 0.012898 244210000 239130 211810 147270 167500 243100 241120 260580 290750 299300 FALSE TRUE 207528.3646 210418.6062 218490.2646 205533.4351 238262.7856 250396.0424 235308.9917 228575.3751 263917.095 0.786339228 0.797290551 0.82787462 0.778780303 0.90279406 0.948767803 0.891601932 0.866087796 1 18.00972528 3.195082273 6.784664215 0.914570186 0.799740494 0.725916353 0.037808717 0.112323866 13.00149706 0.011515053 0.013248138 1567.047905 -3.195082273 -0.114829691 HFCCFDCDSILAGEIYVMVNDKPVCKPCYVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HFCCFDCDSILAGEIYVMVNDKPVCKPCYVK 31 2 Q9UGI8-2;Q9UGI8;H7BYK1 Q9UGI8-2 TES Testin 0 92.819 0.00028201 75966000 73648 67466 46649 61123 52916 42869 79650 96199 64051 FALSE TRUE 63915.2302 67022.8114 69208.61243 75001.91136 51863.07513 44518.19817 71925.55526 75627.59247 56478.96375 1.131664357 1.18668628 1.225387433 1.327961888 0.918272427 0.788226186 1.273492828 1.339040015 1 15.785426 5.131992786 14.05744059 1.147448236 0.000463158 0 0.181382648 8434744.536 5649803.994 0.047484924 306898978.3 135516.6903 -5.131992786 -1.146985078 SASS(ph)DTSEELNSQDSPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASSDTSEELNSQDSPPK 18 0 O14745;O14745-2;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 SAS(0.103)S(0.593)DT(0.304)SEELNSQDSPPK 470.71 1.27E-214 981400000 646890 440950 380670 644490 445110 302390 602510 702000 1501500 TRUE FALSE 561401.8475 438053.3704 564763.2853 790831.3049 436253.1818 314023.139 544078.6729 551882.763 1323994.381 0.424021322 0.330857424 0.426560183 0.597307146 0.329497759 0.237178604 0.410937298 0.416831651 1 20.33646557 1.236140771 5.450194472 1.031419949 0.394063018 0.809259428 0.0921154 0.068617115 6.188333763 0.164572308 0.023861282 17.22426786 -1.236140771 -0.637356931 HFCPNVPIILVGNKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HFCPNVPIILVGNKK 15 1 Q5JR08;P08134;E9PQH6;Q5JR07;C9JNR4;C9JX21;Q5JR05;P61586 Q5JR08;P61586 RHOC;RHOA Rho-related GTP-binding protein RhoC;Transforming protein RhoA 0 ; 203.82 3.39E-09 1352900000 3608900 3194500 1987980 2620300 3238600 2458700 3523900 5244600 2727900 FALSE TRUE 3131974.721 3173515.119 2949373.777 3215279.164 3174158.196 2553287.78 3182152.72 4123083.104 2405410.77 1.302054003 1.319323568 1.22614142 1.33668611 1.319590914 1.061476822 1.322914473 1.714086906 1 21.19785185 1.988538372 24.98433335 1.441184971 1.26174799 0.003044125 0.189852885 995.872825 2170825.544 0.078800164 0.04894322 97.3953835 -1.988538372 -0.179436981 HFDADGNGYIEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HFDADGNGYIEGK 13 0 P22676;A6NER6;H3BN14 P22676 CALB2 Calretinin 0 74.475 0.034007 602680000 1519100 1414100 951190 1131400 1497000 1277700 1679600 1827500 1724000 FALSE TRUE 1318347.086 1404810.684 1411188.666 1388301.662 1467212.629 1326853.946 1516712.651 1436703.347 1520190.684 0.867224816 0.924101627 0.928297141 0.913241791 0.965150388 0.872820732 0.997712107 0.94508101 1 20.53582087 -2 0.171987124 1.350261057 0.871801591 0.429463098 0.034027655 121.4840951 1.669986673 14.55657103 0.332077203 0.01 2 -0.478459467 HFDETVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HFDETVNR 8 0 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ;; 179.68 0.00024309 1420200000 455573 391819 297729 401820 491240 513710 377589 550310 485880 FALSE TRUE 395367.8738 389245.1152 441711.7402 493059.3724 481465.2851 533472.7561 340970.4769 432630.489 428439.8199 0.922808421 0.908517596 1.030977327 1.150825272 1.123764092 1.245152134 0.795842172 1.009781232 1 18.70873305 7.438768164 9.648671886 1.020568264 0.04351507 0 0.129664567 0 0 0.030117423 0 27464276.56 -7.438768164 -0.977053194 HFEALANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HFEALANR 8 0 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ;;;;; 176.09 0.00026235 2271157000 709168 802376 455963 512365 817478 862103 749345 856571 896406 FALSE TRUE 615449.652 797105.1392 676468.2319 628705.3043 801211.7872 895268.6603 676673.6372 673399.9575 790433.9039 0.778622538 1.008439966 0.855818847 0.795392633 1.013635401 1.132629377 0.856078711 0.851937087 1 19.5922853 3.231824879 24.99855599 0.955471586 0.869934339 0.222326114 0.100347408 337.0367385 1250852.452 0.032338958 0.037502446 1705.394581 -3.231824879 -0.085537247 HFEELETIMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HFEELETIMDR 11 0 Q92922;F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 Q92922;F8VXC8 SMARCC1;SMARCC2 SWI/SNF complex subunit SMARCC1;SWI/SNF complex subunit SMARCC2 0 ;; 193.28 1.02E-06 418105000 455716 330099 212050 248842 337831 343180 305322 355057 358204 FALSE TRUE 395491.976 327930.5579 314598.0893 305345.3794 331108.8241 356382.3567 275711.9194 279130.8236 315857.5312 1.252121406 1.038223014 0.996012627 0.966718692 1.048285355 1.128300963 0.872899622 0.883723819 1 18.26891445 7.999999965 0.891312373 0.96886996 133.5744227 0.556798724 0.073853841 709.342884 1.626925439 0.027211094 191233.9962 99999991.91 -7.999999965 132.6055528 HFELGGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HFELGGDK 8 0 H0Y5B4;H7BZ11;J3KQN4;P83881;R4GN19;Q969Q0 H0Y5B4;Q969Q0 RPL36A;RPL36A-HNRNPH2;RPL36AL 60S ribosomal protein L36a;60S ribosomal protein L36a-like 0 ;;;;; 169.12 0.00030285 7806570000 13534200 12401500 9215340 10673800 11873300 10283300 13390700 15341400 18061800 FALSE TRUE 11745621.18 12320033.73 13671909.25 13097449.43 11637044.56 10678905.21 12092071.98 12060761 15926554.58 0.737486637 0.773552978 0.858434835 0.822365526 0.730669305 0.670509441 0.759239666 0.757273705 1 23.92493086 1.23751722 24.97174367 1.000000283 0.764340562 0.682960554 0.05059713 16.783616 401484.5726 0.08008523 0.01350682 17.27894492 -1.23751722 -0.235659721 HFELGGDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HFELGGDKK 9 1 H0Y5B4;H7BZ11;J3KQN4;P83881;R4GN19;Q969Q0 H0Y5B4;Q969Q0 RPL36A;RPL36A-HNRNPH2;RPL36AL 60S ribosomal protein L36a;60S ribosomal protein L36a-like 0 111.65 0.0013568 769340000 1300300 1068800 952040 1072000 1018800 788140 1502700 1571200 1788100 FALSE TRUE 1128462.06 1061778.982 1412449.728 1315413.984 998527.8732 818460.2558 1356968.385 1235211.107 1576712.855 0.715705499 0.673413031 0.895819251 0.834276184 0.633297223 0.519092778 0.860631269 0.783409042 1 20.58848852 1.033631048 1.437773443 1.234159551 0.727575111 0.364210727 0.111235323 2.467343831 3.029554914 2.099976045 0.033905911 10.80515615 -1.033631048 -0.50658444 HFEQMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HFEQMK 6 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 71.029 0.067745 106330000 196350 192270 121530 174210 174470 200640 184990 232030 352320 FALSE TRUE 170401.85 191006.9657 180302.3145 213767.0431 170998.3883 208358.7506 167049.6983 182412.1902 310669.131 0.548499458 0.614824412 0.580367653 0.688085882 0.550419631 0.670677354 0.537709356 0.587159045 1 18.24501937 1.237654173 24.99999714 1.000000471 0.597653286 0.865266769 0.049949685 7.14794206 197031.2403 0.066170887 0.011231567 17.28439461 -1.237654173 -0.402347185 HFESQSDDPHFHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HFESQSDDPHFHEK 14 0 A0A5F9ZHZ6;A0A0A0MRL7;P55210-4;P55210;P55210-3 A0A5F9ZHZ6 CASP7 Caspase-7;Caspase-7 subunit p20;Caspase-7 subunit p11 0 ;; 136.81 8.65E-06 977060000 570074 534654 227148 373308 512360 519320 503089 609581 566012 FALSE TRUE 494737.2765 531141.8227 336997.5326 458073.2871 502165.0384 539298.5764 454299.5062 479226.8469 499098.7062 0.991261389 1.064201963 0.675212194 0.917800991 1.006143739 1.08054493 0.910239799 0.960184511 1 18.92896564 3.303728848 6.851428322 0.985779088 0.905225732 0.118773404 0.10626356 0.508459331 42.83668266 0.031540722 0.04061319 2012.467372 -3.303728848 -0.080553356 HFFHHADEDDEEEDDS(ph)PPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HFFHHADEDDEEEDDSPPER 20 0 A0A087WZV0;O43314-2;O43314;D6RFG4 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 HFFHHADEDDEEEDDS(1)PPER;HFFHHADEDDEEEDDS(1)PPER;HFFHHADEDDEEEDDS(1)PPER;HFFHHADEDDEEEDDS(1)PPER 189.47 3.64E-17 1476940000 801271 756863 320785 500693 656045 660442 534768 572496 583570 TRUE FALSE 695381.0072 751891.1171 475917.699 614382.9983 642990.988 685849.6311 482906.2817 450072.1856 514581.0194 1.351353783 1.461171494 0.924864465 1.193948038 1.249542762 1.332831187 0.938445577 0.87463814 1 18.97303872 2.226666175 24.29789473 0.924588916 1.244120984 0.523508709 0.141155816 125.8036879 256987.9648 0.059014357 0.040166487 168.5257137 -2.226666175 0.319532068 HFGAGGNQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HFGAGGNQR 9 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;;;;; 145.63 9.67E-05 966642000 339043 308472 188159 228388 308640 323340 317481 334095 438286 FALSE TRUE 294237.6085 306445.6271 279153.3218 280246.9861 302498.6678 335779.099 286691.7415 262651.3842 386472.3284 0.761341982 0.79293032 0.722311279 0.725141143 0.782717534 0.868830895 0.741816996 0.679612394 1 18.56000559 3.019107761 18.6133254 0.796337901 0.75176667 0.103029884 0.086083635 43.20245025 42077.57637 0.026523222 0.030050229 1044.979476 -3.019107761 -0.044571231 HFHPLFEYFDYESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HFHPLFEYFDYESR 14 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;; 200.44 1.11E-08 2362526000 1536944 1382260 977048 1056953 1304503 1352359 1179207 1405224 1545135 FALSE TRUE 1333832.956 1373179.843 1449551.681 1296950.333 1278545.943 1404385.126 1064847.687 1104727.783 1362470.901 0.978980876 1.007859942 1.063913864 0.951910483 0.938402385 1.030763391 0.781556279 0.810826699 1 20.37779399 2.246288676 24.99982643 0.849582814 0.994435442 0.456153189 0.066890553 137.4253171 444564.1175 0.025398614 0.019300057 176.3147624 -2.246288676 0.144852628 HFIDVGAGVIDEDYR ddPTM_MDA-MB-175_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 ;;;;; 218.6 1.92E-12 5773860000 4278820 4121670 2504300 3320340 4003600 4263090 3950800 4634340 4394610 FALSE TRUE 3713363.096 4094594.478 3715387.856 4074273.945 3923936.193 4427093.831 3567652.024 3643322.455 3875084.212 0.958266425 1.05664658 0.958788933 1.051402685 1.012606689 1.142450999 0.920664385 0.940191814 1 21.88579623 HFIEITDDQFDFHTYCMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HFIEITDDQFDFHTYCMR 18 0 A0A0B4J1W3;Q9BXJ9 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ;;; 165.9 1.56E-11 385511000 329475 322389 189952 225425 312769 390526 292423 326915 287466 FALSE TRUE 285934.044 320271.2054 281813.4226 276611.1917 306545.5088 405549.7879 264063.8625 257006.7713 253482.097 1.128024612 1.263486492 1.111768547 1.091245476 1.209337908 1.599914916 1.041745613 1.013905023 1 17.95152433 2.033234731 24.99990833 1.013908696 1.230368047 0.338997383 0.142280064 210.8732607 158622.7749 0.059411077 0.040054674 107.9530038 -2.033234731 0.216459351 HFILDECDK ddPTM_MDA-MB-175_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 ;;;;; 178.22 5.12E-05 3655120000 7372030 5937490 4664940 5211000 5908120 5411530 6724300 8105950 8655830 FALSE TRUE 6397797.557 5898486.237 6920920.587 6394237.195 5790559.971 5619715.061 6072178.421 6372555.673 7632547.638 0.838225696 0.772806999 0.906764152 0.837759225 0.758666732 0.736282998 0.795563776 0.834918559 1 22.86373326 1.229507921 3.198287806 1.035795176 0.806203308 0.614309884 0.047774581 0.264346522 3.541094715 0.155583584 0.013038395 16.96320541 -1.229507921 -0.229591868 HFIMQVVCEATQCPDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HFIMQVVCEATQCPDTR 17 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ; 276.12 9.62E-36 3893800000 1568780 1549010 921650 1209880 1734590 1653140 1453210 1571560 1633130 FALSE TRUE 1361461.748 1538834.451 1367363.023 1484601.746 1700075.053 1716737.366 1312277.918 1235494.124 1440063.232 0.945418033 1.068588113 0.94951596 1.030928166 1.180555836 1.192126379 0.911264095 0.857944357 1 20.45770073 2.143562111 12.89720479 0.908656105 1.060478418 0.351786653 0.087659663 0.637670676 83.08821158 0.037780175 0.025470833 139.1752825 -2.143562111 0.151822313 HFKDEDEDEDVAS(ph)PDGLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HFKDEDEDEDVASPDGLGR 19 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 HFKDEDEDEDVAS(1)PDGLGR;HFKDEDEDEDVAS(1)PDGLGR;HFKDEDEDEDVAS(1)PDGLGR;HFKDEDEDEDVAS(1)PDGLGR 322.64 2.38E-62 3543790000 4277500 3504960 3055760 3770160 4135160 4397650 4193730 4665640 4181650 TRUE FALSE 3712217.537 3481935.687 4533535.757 4626232.451 4052878.406 4566830.441 3787022.71 3667929.194 3687300.101 1.006757637 0.944304936 1.229500077 1.254639526 1.099145254 1.238529633 1.027044886 0.994746588 1 21.81413341 2.025674514 23.3015808 1.001167319 1.129658256 0.255151023 0.098812803 143.3937657 130139.5864 0.043093707 0.029052013 106.0900158 -2.025674514 0.128490937 HFLLEEDKPEEPTAHAFVSTLTR ddPTM_MDA-MB-175_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 ;;; 279.73 4.40E-52 14474800000 5783110 5119820 3645620 4402650 5412190 4976870 6501540 7212040 6307000 FALSE TRUE 5018857.361 5086187.565 5408654.026 5402338.973 5304498.008 5168333.409 5871021.651 5669801.37 5561393.645 0.902445984 0.914552698 0.97253573 0.971400213 0.953807327 0.929323428 1.055674535 1.019492906 1 22.40701503 7.999999145 0.108880374 1.123496555 0.4485705 0.569481663 0.031115654 187.0182466 1.85229749 1.643482279 19.13783821 99999803.05 -7.999999145 -0.674926054 HFLPLDFSTQVNSSLTS(ph)PTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HFLPLDFSTQVNSSLTSPTGR 21 0 P19793 P19793 RXRA Retinoic acid receptor RXR-alpha 1 HFLPLDFSTQVNSSLT(0.002)S(0.994)PT(0.004)GR 154.67 2.03E-08 363690000 179600 203100 121890 139720 193390 246370 223450 247040 215210 TRUE FALSE 155865.405 201765.8227 180836.4117 171445.5615 189541.9174 255848.0133 201779.8534 194212.4185 189768.119 0.82134663 1.063222968 0.952933573 0.903447652 0.99880801 1.348213887 1.063296904 1.023419632 1 17.53387811 2.988469427 24.83978791 1.100294864 0.946329017 0.352631243 0.110538468 651.0871902 1402610.84 0.035231135 0.037252729 973.79923 -2.988469427 -0.153965847 HFLQQATQVNAWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HFLQQATQVNAWDR 14 0 P37198 P37198 NUP62 Nuclear pore glycoprotein p62 0 ; 185.62 1.16E-06 1882110000 863580 870110 467950 692090 847990 939310 872060 1008850 825390 FALSE TRUE 749455.715 864394.1901 694252.1852 849239.6124 831116.6581 975445.8635 787487.7554 793115.2784 727813.3345 1.029736169 1.187659183 0.953887697 1.166837116 1.141936564 1.340241814 1.081991382 1.089723478 1 19.47320896 4.778215531 21.37863018 1.119907194 1.029734543 0.067847327 0.105469462 9517.47765 5130329.451 0.025643132 5.05472466 60008.88134 -4.778215531 -0.090172651 HFLVEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HFLVEDK 7 0 P53992;P53992-2 P53992 SEC24C Protein transport protein Sec24C 0 ; 113.89 0.0060283 460120000 1473740 1287540 979950 1111120 1266220 1168790 1568800 1701090 1784720 FALSE TRUE 1278981.525 1279082.065 1453857.098 1363416.778 1241024.699 1213754.108 1416658.017 1337325.141 1573732.435 0.81270583 0.812769717 0.923827371 0.866358695 0.788586847 0.77125824 0.900189884 0.849779233 1 20.58575884 -0.194496536 1.306671009 6.957553828 0.836740738 0.52695409 0.047459262 45.86348169 2.579022993 781.8990447 0.014453346 0.639003834 0.194496536 -6.120813089 HFNALGGWGELQNSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HFNALGGWGELQNSVK 16 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ; 188.9 1.10E-09 983820000 2230200 1926260 1110300 1472420 1705290 1743630 1915370 2247900 2016290 FALSE TRUE 1935473.419 1913606.271 1647244.794 1806755.466 1671358.065 1810708.574 1729617.712 1767204.078 1777926.493 1.088612733 1.076313491 0.926497693 1.016214941 0.940060273 1.018438378 0.972828584 0.993969146 1 20.76176425 4.327039373 8.067344746 0.983057944 1.084546183 0.667415584 0.029736244 0.127869961 10.16825696 0.006609377 0.017597299 21234.36962 -4.327039373 0.101488239 HFPNIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HFPNIDR 7 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 133.12 0.0033029 1153070000 1276120 1220090 681920 800340 1333680 1384720 1204820 1361230 1267370 FALSE TRUE 1107477.509 1212075.148 1011698.793 982069.4294 1307142.377 1437991.074 1087976.742 1070141.558 1117542.962 0.990993229 1.084589308 0.905288501 0.878775548 1.169657383 1.286743439 0.973543549 0.957584266 1 20.09189886 HFRPELEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HFRPELEER 9 1 B4DE93;G3V0I5;P49821-2;P49821 B4DE93 NDUFV1 "NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial" 0 ; 167.09 3.62E-05 282826000 297910 338200 196086 346240 411500 449320 280560 389330 365050 FALSE TRUE 258540.4387 335978.3419 290913.8455 424859.0839 403311.9551 466605.6311 253351.3344 306074.8093 321894.2049 0.803184508 1.043753932 0.903756082 1.319871801 1.252933259 1.449562074 0.787063981 0.950855295 1 18.29622708 HFS(ph)QSEETGNEVFGALNEEQPLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HFSQSEETGNEVFGALNEEQPLPR 24 0 Q6GYQ0-2;A0A1B0GUI1;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5;Q6GYQ0-6;Q6GYQ0-3 Q6GYQ0-2 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 1 HFS(0.976)QS(0.023)EETGNEVFGALNEEQPLPR;HFS(0.837)QS(0.015)EET(0.149)GNEVFGALNEEQPLPR;HFS(0.986)QS(0.014)EETGNEVFGALNEEQPLPR;HFS(0.873)QS(0.046)EET(0.081)GNEVFGALNEEQPLPR;HFS(0.552)QS(0.435)EET(0.013)GNEVFGALNEEQPLPR 316.53 7.60E-74 2439170000 1017141 1368097 914690 976516 1631970 1798200 1516760 1645890 1728250 TRUE FALSE 882723.2397 1359109.881 1357037.143 1198248.883 1599496.99 1867377.918 1369664.849 1293929.232 1523938.254 0.579238193 0.891840517 0.890480398 0.786284405 1.049581232 1.225363241 0.89876663 0.84906933 1 20.53937302 5.229145054 0.996097686 0.965067403 9.47E-15 0.499015223 0.11943346 4.519792261 1.840779955 0.041022796 5.882620748 169490.3803 -5.229145054 -0.965067403 HFSEHPSTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HFSEHPSTSK 10 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 ; 152.04 1.08E-05 262220000 342670 405180 82866 205306 510830 514130 442860 472060 465690 FALSE TRUE 297385.2913 402518.3459 122940.2748 251923.8652 500665.4824 533908.9138 399911.5054 371113.6426 410636.6587 0.724205414 0.980229937 0.299389429 0.613495799 1.219242052 1.300197882 0.973881647 0.903751856 1 18.6475029 3.249072634 24.99892144 1.060581017 0.652255698 0.528157959 0.199201943 188.6893822 448725.0241 0.061652975 0.078736413 1774.486231 -3.249072634 -0.40832532 HFSGLEEAVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HFSGLEEAVYR 11 0 P50990-2;P50990;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;;; 255.19 1.86E-20 8173310000 3792760 5088850 1182293 2422750 6600000 6633440 4496020 5083180 5215380 FALSE TRUE 3291537.156 5055421.009 1754053.849 2972872.417 6468672.913 6888632.729 4059996.672 3996181.514 4598823.718 0.715734579 1.099285669 0.381413587 0.646441916 1.406592927 1.497911891 0.882833725 0.868957316 1 22.13283347 3.264092424 24.999884 1.098172269 0.714951736 0.3818949 0.263969238 290.9681659 284904.2149 0.083092325 0.107231535 1836.929224 -3.264092424 -0.383220533 HFSQS(ph)EETGNEVFGALNEEQPLPR ddPTM_MDA-MB-175_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(0.363)QS(0.613)EET(0.024)GNEVFGALNEEQPLPR 213.16 7.31E-26 790510000 292030 363360 243440 249300 466950 547540 419620 497990 485460 TRUE FALSE 253437.4956 360973.0642 361168.3983 305907.3753 457658.6086 568604.2181 378925.317 391498.7139 428069.4718 0.592047582 0.843258134 0.843714448 0.714620863 1.069122277 1.328298922 0.885195843 0.914568171 1 18.70748543 3.237910481 24.99983756 1.026703458 0.761992522 0.522661663 0.137630328 16.58783916 637865.239 0.043574991 0.052430373 1729.459838 -3.237910481 -0.264710936 HFSTLKDDDLVEFS(ph)DLESEDDERPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HFSTLKDDDLVEFSDLESEDDERPR 25 2 Q9HCK8-2;Q9HCK8;H0YJG4;A0A2R8Y840 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 HFSTLKDDDLVEFS(0.99)DLES(0.01)EDDERPR 61.112 0.036229 30233000 37978 35520 12401 22346 31018 37667 42517 43845 24427 TRUE FALSE 32959.11108 35286.66678 18398.16508 27420.00084 30400.80249 39116.07386 38393.70788 34469.08795 21539.26789 1.530187156 1.638248197 0.854168543 1.273023808 1.41141299 1.816035441 1.782498276 1.600290601 1 14.39468159 2.98808143 21.59776806 1.583244228 1.316483311 0.109055912 0.297990302 188.0278278 340731.3406 0.096008093 0.101324846 972.9296301 -2.98808143 -0.266760917 HFSVEGQLEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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 ;;;;;;;;; 237.76 1.37E-15 4297684000 2441101.5 2516788.9 903695 1677763.6 2871058 2906569 2451613.7 2804284 2689191 FALSE TRUE 2118503.752 2500255.948 1340724.925 2058725.468 2813929.563 3018386.59 2213856.581 2204609.69 2371277.904 0.893401718 1.054391788 0.565401855 0.868192406 1.186672198 1.272894495 0.933613297 0.929713757 1 21.17723332 3.378416117 8.159405045 1.047785334 0.836064405 0.321748015 0.157584895 0.3376059 24.74287917 0.048504359 0.062655246 2390.10025 -3.378416117 -0.211720929 HFTILDAPGHK ddPTM_MDA-MB-175_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 ; 185.77 2.50E-06 1651170000 1838060 1695490 1033440 1468750 1491750 1510310 1754070 1888560 2099600 FALSE TRUE 1595155.714 1684352.215 1533215.041 1802252.136 1462067.094 1568412.603 1583960.561 1484706.141 1851387.68 0.861600048 0.909778234 0.828143699 0.973460154 0.789714175 0.847155147 0.85555315 0.801942325 1 20.8201756 3.215627963 24.99980603 0.850921794 0.889776425 0.0530033 0.066999893 639.6760013 697333.7987 0.019162967 0.021741743 1642.96368 -3.215627963 0.038854631 HFVALSTNTTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HFVALSTNTTK 11 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90 P06744 GPI Glucose-6-phosphate isomerase 0 ; 183.33 5.39E-06 2441500000 3644700 3193100 1631070 2313100 3029200 2595300 3425800 3916300 3666800 FALSE TRUE 3163043.661 3172124.316 2419860.908 2838324.709 2968924.847 2695142.87 3093566.443 3078829.722 3233315.081 0.978266448 0.981074914 0.748414815 0.877837339 0.918229363 0.833554047 0.956778528 0.952220753 1 21.62458267 2.101876039 8.082413657 0.967244525 0.888175206 0.236862048 0.067970573 0.372807579 26.32487307 0.028608563 0.019252079 126.4375405 -2.101876039 -0.079069318 HFVCEGCEQLLSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HFVCEGCEQLLSGR 14 0 Q9NZU5;B4DEY6;Q9NZU5-2 Q9NZU5 LMCD1 LIM and cysteine-rich domains protein 1 0 75.96 0.028794 247090000 138220 127990 81179 88296 136760 134460 160710 159470 152820 FALSE TRUE 119953.8768 127149.2253 120437.4359 108344.9563 134038.7436 139632.7632 145124.3689 125368.5815 134753.7937 0.890170685 0.943566944 0.893759149 0.804021567 0.994693655 1.036206547 1.076959431 0.930352891 1 17.03996636 3.117652289 8.751818033 1.005632011 0.888202387 0.611883922 0.049354083 0.196791823 14.21969614 0.015717828 0.017844549 1311.149726 -3.117652289 -0.117429624 HFVDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HFVDEK 6 0 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;Q15257-4;A6PVN9;H0Y6E5;H0Y562 Q15257 PPP2R4 Serine/threonine-protein phosphatase 2A activator 0 ; 132.94 0.01468 1055800000 4086500 3240200 2262500 2564900 2780000 2742200 3731600 4270300 3810600 FALSE TRUE 3546458.671 3218914.913 3356652.568 3147299.747 2724683.439 2847694.208 3369710.006 3357129.577 3360115.209 1.055457462 0.957977543 0.998969487 0.936664237 0.810889886 0.847498979 1.002855497 0.999111449 1 21.68007927 5.09973769 1.210441271 0.940277897 1.20117621 0.229672551 0.066025598 5.98724589 4.184214688 0.021997779 2.412142619 125816.526 -5.09973769 0.260898313 HFVDSHHQKPVNAIIEHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HFVDSHHQKPVNAIIEHVR 19 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 183.22 9.26E-15 2646600000 879870 832280 358000 674280 969610 944880 998210 1049830 1020040 FALSE TRUE 763592.9502 826812.6979 531129.9974 827385.5797 950316.658 981230.145 901403.7478 825332.0243 899452.0332 0.848953498 0.919240457 0.590503971 0.91987738 1.056550681 1.090919925 1.002169893 0.917594262 1 19.77868682 3.484762722 24.40491157 1.003013335 0.792142958 0.552462686 0.093058833 205.8837857 657541.1167 0.026885074 0.036327492 3053.252504 -3.484762722 -0.210870377 HFVGMLPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HFVGMLPEK 9 0 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;; 99.442 0.0053345 5690560000 5675400 6026800 4843200 6089000 6092500 6131600 7059500 7752700 12012600 FALSE TRUE 4925381.51 5987209.554 7185387.72 7471600.515 5971271.17 6367486.62 6374870.777 6094845.437 10592484.11 0.464988331 0.565231865 0.678347746 0.705368111 0.563727177 0.601132515 0.601829628 0.575393399 1 23.33653763 1.236571002 24.99772161 1.00000051 0.598365551 0.791452631 0.065388781 24.44037087 306989.23 0.104308268 0.016424198 17.24133942 -1.236571002 -0.401634959 HFVGMLPEKDCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HFVGMLPEKDCR 12 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;; 142.08 8.21E-05 11290350000 8713730 8585050 4285640 4789800 8037870 7134930 10167820 10930060 2796140 FALSE TRUE 7562188.503 8528654.241 6358189.839 5877397.298 7877932.113 7409415.374 9181746.381 8592751.727 2465583.515 3.067098907 3.459081467 2.578776911 2.383775387 3.195159307 3.005136646 3.723964866 3.48507835 1 21.23349769 1.232695395 24.99924574 0.999996554 3.129053483 0.729275311 0.404337645 112.8046199 480755.8274 0.954402937 0.108935766 17.08816367 -1.232695395 2.12905693 HFVLDECDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HFVLDECDK 9 0 O00148;O00148-2;O00148-3;K7EQN7;K7EPJ3;A0A0D9SEM9 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ;;; 174.41 5.47E-05 2336960000 3188870 2463530 1999560 2205340 2450580 2237170 2810840 3298700 3551220 FALSE TRUE 2767452.75 2447346.909 2966553.904 2706096.154 2401818.252 2323235.378 2538245.169 2593298.676 3131398.817 0.883775243 0.781550691 0.94735742 0.864181253 0.767011292 0.741916157 0.810578696 0.828159818 1 21.57837583 1.238816669 8.297571578 1.001814338 0.825928413 0.448370762 0.059897118 0.08795443 61.25668669 0.087338231 0.015252704 17.33072251 -1.238816669 -0.175885925 HFWGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HFWGLR 6 0 P62269;J3JS69 P62269 RPS18 40S ribosomal protein S18 0 ; 130.51 0.044092 511810000 613830 724980 436010 456590 713380 840500 643660 674540 514440 FALSE TRUE 532710.8103 720217.5586 646865.8944 560265.738 699185.1337 872834.5789 581237.9523 530294.8703 453623.4893 1.174345736 1.587698996 1.425997352 1.235089786 1.541333618 1.92413885 1.281322432 1.169019865 1 18.79113582 1.771799823 2.813145058 1.058822124 1.479298448 0.372987166 0.209265779 0.258024642 4.018757579 0.159004728 0.058236485 59.12890322 -1.771799823 0.420476324 HFWTAES ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HFWTAES 7 0 Q14157-4;Q14157-1 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 0 ; 111.69 0.015175 234850000 1243640 1147200 775040 897900 1140500 1174790 1112060 1307560 1303300 FALSE TRUE 1079289.823 1139663.968 1149851.936 1101781.919 1117806.281 1219984.931 1004212.592 1027948.469 1149225.359 0.939145499 0.991680143 1.000545217 0.958717026 0.972660647 1.061571538 0.873816945 0.894470751 1 20.1322303 2.220333745 24.99999909 0.914829048 0.986207443 0.306878 0.045239978 264.0164378 362122.5367 0.018107202 0.012234313 166.0862751 -2.220333745 0.071378395 HFYWYLTNEGIQYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HFYWYLTNEGIQYLR 15 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;; 269.36 6.41E-26 1783880000 3048200 2776580 1517650 2522790 2685000 2520450 3169790 3441370 3302470 FALSE TRUE 2645372.647 2758340.463 2251590.616 3095628.028 2631573.753 2617413.342 2862384.254 2705459.806 2912055.759 0.908421015 0.947214165 0.773196258 1.063038721 0.903682474 0.898819789 0.982942804 0.929054946 1 21.47360655 -2 0.222851175 1.369414713 0.892346103 0.110121781 0.071890552 228.0630133 3.538159803 38.04928764 0.315921096 0.01 2 -0.47706861 HGAEVIDTPVFELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HGAEVIDTPVFELK 14 0 B3KWE1;P12081-4;P12081;B4DDD8;E7ETE2 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 132.97 4.73E-05 132340000 268860 252670 163980 227850 264630 222030 300080 374900 336660 FALSE TRUE 233329.4698 251010.1941 243281.2765 279586.825 259364.3807 230571.6378 270978.2878 294730.5525 296860.4383 0.785990451 0.845549496 0.81951397 0.941812343 0.873691295 0.776700456 0.912813743 0.992825296 1 18.17942532 1.908181134 3.327822412 0.99470711 0.845644774 0.651162036 0.046725399 0.15550461 3.03676992 0.028725201 0.013180665 80.9433425 -1.908181134 -0.149062336 HGAGAEISTVHPEQYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HGAGAEISTVHPEQYAK 17 0 Q8TBX8;Q8TBX8-3;Q8TBX8-2 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 138.05 2.86E-06 161950000 218650 186800 108730 132490 219910 186800 230550 271640 215530 FALSE TRUE 189754.8485 185572.8985 161312.1917 162573.8795 215534.2212 193986.3169 208191.2965 213551.8999 190050.2889 0.998445462 0.976441023 0.848786879 0.855425584 1.134090469 1.020710455 1.095453723 1.123659959 1 17.53602169 3.236621693 24.99999947 1.079739244 0.918751762 0.613505884 0.061062119 34.26800151 441844.531 0.018700861 0.022289454 1724.335196 -3.236621693 -0.160987481 HGAVCHTGAPDATLHTVHPDSVSSSYSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HGAVCHTGAPDATLHTVHPDSVSSSYSSR 29 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 0 204.59 7.36E-26 726830000 198730 194730 78549 122200 204630 202580 163780 212250 212260 FALSE TRUE 172467.327 193450.8058 116535.5591 149947.3777 200558.2634 210373.3837 147896.6408 166861.9892 187166.8646 0.921462927 1.033574005 0.622629221 0.801142756 1.071547914 1.123988395 0.790186025 0.891514583 1 17.51396552 3.263681768 24.99624878 0.958488298 0.842330694 0.179021864 0.136425911 486.202543 483781.8186 0.041833854 0.053985695 1835.193102 -3.263681768 -0.116157604 HGAVSVS(ph)LFIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HGAVSVSLFIR 11 0 Q9BT04-2 Q9BT04-2 1 HGAVS(0.285)VS(0.715)LFIR;HGAVS(0.159)VS(0.841)LFIR 67.726 0.038123 374820000 233210 278520 148342 144466 276000 375720 177177 194874 189958 TRUE FALSE 202390.7076 276690.3838 220080.6874 177269.2133 270508.14 390174.1915 159994.4018 153201.7116 167501.3816 1.208292765 1.651869263 1.313903714 1.058314932 1.614960649 2.329378944 0.95518258 0.91462954 1 17.35381347 2.071016265 24.99999991 0.946228354 1.518908868 0.386961525 0.339658738 46.26677677 16286.42572 0.142069704 0.095783363 117.7650076 -2.071016265 0.572680514 HGAWGNSAVSRPLEFWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HGAWGNSAVSRPLEFWR 17 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 168.68 1.24E-09 1198720000 731020 915360 335450 535070 943130 1026450 826720 921970 629530 FALSE TRUE 634413.8548 909346.9399 497674.742 656565.8215 924363.5582 1065938.196 746544.8216 724813.8903 555107.6806 1.142866289 1.638145123 0.896537302 1.182772 1.665196845 1.920236799 1.344864875 1.305717639 1 19.08240813 3.277417185 24.99989208 1.445494187 1.222545838 0.131575078 0.296031892 382.0861015 245827.5137 0.089639499 0.115722012 1894.162286 -3.277417185 -0.222948349 HGDGTTLDIMLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HGDGTTLDIMLK 12 0 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ; 158.41 6.77E-05 573370000 1381850 1246150 781330 959770 1255010 1188720 1506300 1678380 1589980 FALSE TRUE 1199235.021 1237963.959 1159183.801 1177700.448 1230037.756 1234450.828 1360219.258 1319471.498 1402014.376 0.85536571 0.88298949 0.826798799 0.840005971 0.877336051 0.880483716 0.970189237 0.941125513 1 20.41906971 2.335025681 1.589690176 0.972337127 0.853056279 0.844699867 0.022245433 0.143463082 0.741522921 0.013493796 0.007498251 216.2846414 -2.335025681 -0.119280848 HGDLPDIQIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HGDLPDIQIK 10 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 134.68 0.00016435 1175270000 1588180 1306360 793460 1018070 1392920 1046270 1597000 1670340 1476940 FALSE TRUE 1378297.989 1297778.435 1177179.91 1249238.354 1365203.617 1086520.684 1442123.186 1313150.79 1302337.836 1.058325997 0.996499065 0.903897497 0.959227567 1.048271485 0.834284818 1.10733417 1.008302726 1 20.31267231 2.180509791 24.99999997 1.035110804 0.968604083 0.186709604 0.070442668 139.9036126 60249.02491 0.027591156 0.018601962 151.5338965 -2.180509791 -0.06650672 HGEAQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HGEAQVK 7 0 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 0 ;;;;; 128.48 0.0037531 4169640000 10829740 9134830 5906380 7381790 5081620 7717800 10590900 11929110 12270820 FALSE TRUE 9398562.42 9074822.7 8762725.124 9057938.243 4980505.704 8014708.76 9563796.148 9378162.659 10820177.64 0.868614429 0.838694428 0.809850394 0.837133968 0.460297961 0.740718778 0.883885318 0.866729085 1 23.36722085 1.652863999 1.58935852 0.988965127 0.7605966 0.285928775 0.118449859 0.676385854 2.938387818 0.20663384 0.037667007 44.96390265 -1.652863999 -0.228368527 HGEIDYEAIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HGEIDYEAIVK 11 0 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ;; 112.13 0.0015674 1572350000 2797050 2450910 1670550 2052960 2459700 2168150 2937400 3381300 2940560 FALSE TRUE 2427412.756 2434809.811 2478433.568 2519115.946 2410756.782 2251560.133 2652531.4 2658235.308 2592930.347 0.936165817 0.939018595 0.955842709 0.97153244 0.929742207 0.868345784 1.022985983 1.025185776 1 21.30615202 2.203033191 24.99943011 1.018247826 0.93627628 0.669950011 0.027272692 105.9111155 74525.30092 0.011508149 0.007759098 159.6001117 -2.203033191 -0.081971547 HGEKLYTGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HGEKLYTGLR 10 1 Q13618;Q13618-2;A0A087X1R9;H7C1L6 Q13618 CUL3 Cullin-3 0 ; 59.426 0.062893 1626720000 3536900 4076500 2905400 3320600 2523400 3193100 4079400 4068600 4540700 FALSE TRUE 3069489.704 4049721.203 4310461.158 4074592.982 2473189.277 3315940.623 3683780.416 3198561.552 4003903.619 0.766624274 1.011443229 1.076564665 1.017655111 0.617694508 0.828176934 0.920047226 0.798860776 1 21.93297582 HGESAWNLENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 HGESAWNLENR 11 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;;;;;; 212.09 7.11E-09 23628100000 8485700 8264690 4090590 5776140 8902090 8282160 8285350 9183340 8448430 FALSE TRUE 7364293.245 8210398.707 6068813.006 7087700.87 8724955.826 8600780.054 7481838.032 7219554.206 7449666.23 0.988540026 1.102116317 0.81464227 0.951411869 1.171187481 1.154518845 1.004318556 0.969111096 1 22.82874436 5.076396431 13.93339124 1.018046824 0.646515068 0.008769609 0.104278922 2435444.322 10061058.97 0.026790398 26120635.07 119232.989 -5.076396431 -0.371531755 HGEVCPAGWKPGSDTIKPDVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HGEVCPAGWKPGSDTIKPDVQK 22 2 Q06830;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 ;; 139.26 1.35E-07 11814700000 9140020 6021890 5142950 5787630 5035950 3424606 9282570 9762780 8519590 FALSE TRUE 7932143.199 5982331.808 7630097.822 7101799.85 4935744.448 3556352.809 8382347.79 7675085.471 7512413.776 1.055871446 0.796326186 1.015665277 0.945341945 0.657011793 0.473396822 1.115799534 1.021653719 1 22.8408451 HGFCGIPITDTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HGFCGIPITDTGR 13 0 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ;;; 121.01 0.00025159 3488520000 4065970 4402840 2256950 2911370 4341560 4355320 4370310 4608790 4420290 FALSE TRUE 3528641.763 4373917.454 3348418.569 3572441.056 4255171.45 4522871.979 3946478.009 3623236.124 3897728.352 0.905307257 1.122170931 0.859069249 0.91654439 1.091705493 1.160386659 1.012507197 0.929576358 1 21.89420212 HGFELVELSPEELPEEDDDFPESTGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HGFELVELSPEELPEEDDDFPESTGVK 27 0 Q6PD74;Q6PD74-2;H0YL49 Q6PD74 AAGAB Alpha- and gamma-adaptin-binding protein p34 0 ;; 242.64 2.93E-45 164273000 220494 190221 142757 194314 179890 148175 209877 252432 307252 FALSE TRUE 191355.1592 188971.4257 211794.7627 238435.9636 176310.5409 153875.3881 189523.1608 198451.3812 270929.0186 0.706292594 0.697494225 0.781735245 0.880068015 0.650762852 0.567954621 0.699530681 0.732484775 1 18.0475554 1.23625731 4.657461988 1.022829179 0.713047078 0.556425672 0.080293403 0.163343733 7.895969077 0.167207072 0.021776482 17.22889048 -1.23625731 -0.309782101 HGGPGPGGPEPELS(ph)PITEGSEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HGGPGPGGPEPELSPITEGSEAR 23 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 HGGPGPGGPEPELS(1)PITEGSEAR 123.35 4.00E-05 234520000 122350 140380 94497 121260 178820 163490 139130 178780 167750 TRUE FALSE 106181.1375 139457.8345 140196.0653 148793.9363 175261.8319 169779.5661 125637.194 140549.2883 147918.7861 0.717834024 0.94280002 0.947790804 1.005916424 1.184851745 1.147789071 0.849366043 0.950178757 1 17.17444576 5.009848875 1.358822948 1.012215022 0.415635518 0.4903946 0.095091756 2.450857081 2.508272831 0.029946851 2.390013236 102293.697 -5.009848875 -0.596579503 HGGPKDEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HGGPKDEER 9 1 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;; 148.32 5.43E-05 1658780000 2358900 1814500 1178150 1370970 1478250 1455060 2120600 2390370 2002410 FALSE TRUE 2047165.388 1802580.43 1747907.281 1682269.692 1448835.717 1511037.1 1914944.538 1879207.977 1765687.371 1.159415547 1.020894446 0.989930216 0.952756258 0.820550535 0.855778392 1.084532047 1.064292586 1 20.75179849 4.770855173 1.914908865 0.97169301 1.227216473 0.360431182 0.080929553 1.212715502 4.374214612 0.024966943 0.566076543 59000.42951 -4.770855173 0.255523462 HGGS(ph)PQPLAT(ph)TPLSQEPVNPPSEAS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 HGGS(0.999)PQPLAT(0.5)T(0.5)PLSQEPVNPPS(0.045)EAS(0.799)PT(0.156)R;HGGS(1)PQPLAT(0.528)T(0.472)PLSQEPVNPPS(0.168)EAS(0.8)PT(0.031)R 189.3 1.80E-17 614800000 363830 285310 220430 241960 304360 298330 290940 341420 344030 TRUE FALSE 315748.9437 283435.7798 327030.6853 296900.7161 298303.8315 309806.9481 262724.6836 268409.9899 303359.1653 1.040841945 0.934324102 1.078031333 0.978710222 0.983335483 1.021254617 0.866051577 0.884792749 1 18.21066737 2.247712037 24.99928589 0.908128384 1.003813385 0.39615991 0.051442852 169.2201871 462265.9252 0.018517175 0.014138286 176.8935662 -2.247712037 0.095685001 HGGS(ph)PQPLATTPLSQEPVNPPS(ph)EAS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 HGGS(1)PQPLATTPLSQEPVNPPS(1)EAS(0.964)PT(0.036)R;HGGS(1)PQPLATTPLSQEPVNPPS(1)EAS(0.992)PT(0.008)R 225.28 7.43E-35 571670000 230510 198491 136689 167241 227550 211624 176046 231970 287260 TRUE FALSE 200047.5195 197187.0996 202792.2576 205215.6252 223022.2002 219765.3122 158973.086 182365.0207 253300.45 0.789763774 0.778471177 0.800599673 0.81016684 0.880465077 0.867607271 0.627606804 0.719955376 1 17.95049011 4.223551866 20.77288049 0.80066934 0.784117538 0.000285024 0.098432218 339.8532736 470397.1869 0.026463099 0.055694806 16732.15451 -4.223551866 -0.016551802 HGGS(ph)PQPLATTPLSQEPVNPPSEAS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 HGGS(1)PQPLATTPLSQEPVNPPS(0.01)EAS(0.832)PT(0.159)R;HGGS(0.999)PQPLATTPLSQEPVNPPSEAS(0.965)PT(0.035)R;HGGS(1)PQPLATTPLSQEPVNPPS(0.004)EAS(0.992)PT(0.004)R;HGGS(1)PQPLATTPLSQEPVNPPS(0.003)EAS(0.931)PT(0.066)R;HGGS(1)PQPLATTPLSQEPVNPPS(0.021)EAS(0.805)PT(0.174)R;HGGS(0.999)PQPLAT(0.001)TPLSQEPVNPPS(0.058)EAS(0.936)PT(0.006)R;HGGS(0.986)PQPLAT(0.006)T(0.007)PLSQEPVNPPS(0.077)EAS(0.859)PT(0.064)R 238.62 1.75E-45 11515360000 1776651 1358139 929586 1195902 1472978 1397024 1329824 1588757 1917603 TRUE FALSE 1541862.069 1349217.295 1379136.899 1467449.827 1443668.62 1450768.417 1200857.873 1249013.679 1690906.158 0.911855493 0.797925591 0.815620011 0.867848177 0.853783998 0.85798281 0.710185996 0.738665285 1 20.68936516 HGGSDNASTDCER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HGGSDNASTDCER 13 0 O43847;O43847-2;F5H7V1;G3V1R5 O43847 NRD1 Nardilysin 0 79.614 0.01263 0 12165 12473 7087.9 7087.9 10707 12229 12795 13601 13431 FALSE TRUE 10557.36443 12391.06404 10515.63215 8697.316027 10493.95165 12699.45754 11554.14287 10692.53199 11843.20248 0.89142818 1.046259579 0.887904447 0.734371978 0.886073819 1.072299284 0.975592783 0.902841272 1 13.53177163 HGGSPQPLATTPLSQEPVNPPSEAS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HGGSPQPLATTPLSQEPVNPPS(0.004)EAS(0.897)PT(0.1)R;HGGSPQPLATTPLSQEPVNPPS(0.006)EAS(0.909)PT(0.085)R;HGGSPQPLATTPLSQEPVNPPSEAS(0.987)PT(0.013)R;HGGSPQPLATTPLSQEPVNPPS(0.001)EAS(0.992)PT(0.008)R;HGGSPQPLATTPLSQEPVNPPS(0.123)EAS(0.719)PT(0.157)R;HGGSPQPLATTPLSQEPVNPPSEAS(0.929)PT(0.071)R 286.6 1.77E-62 3878780000 1268310 1092934 610975 986750 1236314 1201619 1142920 1334355 1676000 TRUE FALSE 1100699.62 1085754.445 906444.5536 1210806.669 1211713.77 1247846.06 1032079.794 1049013.567 1477865.189 0.744790274 0.734677596 0.613347253 0.819294397 0.819908188 0.844357164 0.698358552 0.709816819 1 20.49508324 3.708949589 24.91880351 0.798397948 0.701312264 0.264224132 0.089598437 1057.451709 889885.5352 0.025127432 0.037275876 5116.224455 -3.708949589 -0.097085685 HGGTIPIVPTAEFQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HGGTIPIVPTAEFQDR 16 0 P00367;P00367-2;P00367-3 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ;;;;; 159.34 9.16E-09 4909240000 4554090 4629240 3047830 4713020 5937210 5693370 4763250 5804560 5312000 FALSE TRUE 3952255.468 4598830.218 4521770.782 5783183.225 5819071.137 5912397.628 4301310.748 4563300.015 4684021.411 0.843773997 0.981812382 0.965360827 1.234661996 1.24232377 1.262248207 0.918294425 0.974226976 1 22.15931624 7.446510289 9.644124616 1.049097889 0.003461087 0 0.147582849 0 0 0.03586035 0 27958269.63 -7.446510289 -1.045636801 HGHFGWPGWEMGPPGNWS(ph)PRPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HGHFGWPGWEMGPPGNWSPRPPR 23 1 Q13501;Q13501-2;E7EMC7;C9JRJ8;E9PFW8 Q13501 SQSTM1 Sequestosome-1 1 HGHFGWPGWEMGPPGNWS(1)PRPPR;HGHFGWPGWEMGPPGNWS(1)PRPPR 100.27 0.0014493 2028210000 689750 559360 340000 357330 450100 463730 408250 510090 383000 TRUE FALSE 598597.7899 555685.5273 504425.1372 438467.2379 441143.8906 481569.9932 368657.9778 401011.223 337722.1763 1.772456273 1.645392474 1.493609756 1.29830751 1.306233116 1.42593536 1.091601333 1.187399736 1 18.36547739 8 0.182660088 0.890463266 4.836894209 0.872600519 0.085120722 38.36812945 0.544168576 0.743905077 40.86388617 100000000 -8 3.946430943 HGINCFINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HGINCFINR 9 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;; 163.2 6.32E-05 4429950000 1416400 2177380 1187240 1441720 2207730 2294340 2113580 2277330 2149350 FALSE TRUE 1229219.151 2163076.647 1761393.235 1769084.561 2163800.492 2382604.744 1908605.337 1790340.702 1895256.292 0.648576742 1.141310891 0.929369417 0.933427616 1.141692816 1.257141187 1.007043399 0.944643059 1 20.85396152 4.74829341 24.43460182 1.037427779 0.648576453 0.57323266 0.107166846 805.2357987 2021522.154 0.02792848 0.351877545 56013.59027 -4.74829341 -0.388851326 HGIVEDWDLMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 HGIVEDWDLMER 12 0 B4DXW1;P61158;F8WDR7 B4DXW1 ACTR3 Actin-related protein 3 0 ;;;;;;;;;;; 253.79 4.30E-21 5148606000 3861550 3601850 2091202 2746344 3703850 3804310 3573400 4026450 3797030 FALSE TRUE 3351236.384 3578189.21 3102514.282 3369943.38 3630150.631 3950664.267 3226852.218 3165425.001 3348149.439 1.000921985 1.068706542 0.926635546 1.00650925 1.084225987 1.179954581 0.963771862 0.945425244 1 21.67493249 HGLAHDEMKS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 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 171.21 2.71E-05 5084881000 6912870 5490040 3521243 4323981 5661600 4769850 6019750 6940040 6329470 TRUE FALSE 5999316.715 5453975.566 5224127.893 5305806.974 5548945.237 4953349.216 5435955.572 5455966.453 5581207.267 1.0749138 0.977203552 0.936021123 0.950655785 0.994219525 0.887504975 0.973974861 0.977560265 1 22.41214579 4.723173525 3.743981819 0.960388344 1.085177661 0.555908107 0.032002749 0.183806486 4.950873802 0.007812146 0.062075055 52865.64373 -4.723173525 0.124789318 HGLEAISIMDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HGLEAISIMDSR 12 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ;;; 199.12 1.75E-07 871210000 1049740 979800 520080 715240 1014200 1034650 949580 1048640 1017560 FALSE TRUE 911014.1993 973363.6293 771592.4276 877646.1738 994019.4042 1074453.655 857489.8778 824396.4965 897265.216 1.01532321 1.084811505 0.859937969 0.978134623 1.107832318 1.197476104 0.955670478 0.918787981 1 19.77517496 2.042851683 24.99999194 0.9486828 1.038100434 0.156562424 0.089336308 247.5767182 144437.0911 0.038871261 0.02620698 110.3701628 -2.042851683 0.089417634 HGLEVIYMIEPIDEYCVQQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HGLEVIYMIEPIDEYCVQQLK 21 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;; 256.66 1.87E-36 3369747000 651666 565906 377285 503568 470351 464305 645040 766761 897949 FALSE TRUE 565546.687 562188.5262 559741.2879 617910.811 460991.9353 482167.1138 582484.1201 602795.1271 791794.4922 0.714259435 0.710018233 0.706927484 0.780392914 0.582211596 0.608954872 0.735650634 0.761302501 1 19.59476651 1.087823468 1.711593665 1.220835524 0.687689885 0.741500256 0.057228239 0.792724821 1.552658436 0.796581794 0.016720723 12.24118519 -1.087823468 -0.533145639 HGLEVSEMAVSELPGNPNAVWTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HGLEVSEMAVSELPGNPNAVWTVR 24 0 Q15393;J3QKV4 Q15393 SF3B3 Splicing factor 3B subunit 3 0 68.634 0.033715 188240000 212610 166780 91215 122790 173800 161900 170560 166960 178140 FALSE TRUE 184513.0498 165684.4112 135326.8791 150671.3462 170341.72 168128.3978 154019.1175 131256.9033 157080.4921 1.174640131 1.05477395 0.861512956 0.959198333 1.084423137 1.070332767 0.98051079 0.835602827 1 17.2611445 4.529217596 4.224818532 0.965297029 1.160390588 0.41298122 0.07820708 0.233685916 8.390362962 0.021657455 0.092181767 33823.42608 -4.529217596 0.195093559 HGLLLPAS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HGLLLPASPVR 11 0 Q96E09 Q96E09 FAM122A Protein FAM122A 1 HGLLLPAS(1)PVR;HGLLLPAS(1)PVR;HGLLLPAS(1)PVR;HGLLLPAS(1)PVR 166.7 2.11E-05 1299250000 978900 1164600 568403 697970 1038810 1073950 972010 1083680 1020720 TRUE FALSE 849535.8848 1156949.666 843284.592 856454.7563 1018139.713 1115265.551 877744.6198 851943.4652 900051.6444 0.943874599 1.285425868 0.936929116 0.951561793 1.131201437 1.239112842 0.975215839 0.946549535 1 19.77964826 2.044405331 24.99984568 0.966883733 1.082656903 0.153145236 0.118857289 223.5450788 125853.1434 0.047987983 0.032353473 110.7657089 -2.044405331 0.11577317 HGLLVPNNTTDQELQHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HGLLVPNNTTDQELQHIR 18 0 P56537;B7ZBH1 P56537 EIF6 Eukaryotic translation initiation factor 6 0 ;; 116.43 9.29E-05 2760010000 1253430 1012280 580890 803940 1115940 1173300 921510 1119430 1107120 FALSE TRUE 1087786.05 1005630.266 861810.347 986486.8645 1093734.977 1218437.61 832142.102 880048.6059 976237.5348 1.114263702 1.030108176 0.882787555 1.010498807 1.120357432 1.248095435 0.85239716 0.901469749 1 19.8968727 2.187083418 24.99999669 0.91178939 1.057369692 0.332716662 0.099115587 129.4649924 62873.80924 0.043173983 0.029107928 153.8450114 -2.187083418 0.145580302 HGLQLGAQS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HGLQLGAQSPGR 12 0 Q8N1G0;A6PVV7 Q8N1G0 ZNF687 Zinc finger protein 687 1 HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR 191.01 6.20E-06 9403540000 4678300 4405540 2512480 3279840 4779980 4724160 4460600 4947300 4781290 TRUE FALSE 4060050.802 4376599.718 3727523.732 4024577.801 4684867.75 4905901.492 4028011.699 3889358.395 4216051.343 0.962998425 1.03808027 0.884126741 0.954584628 1.111197983 1.163624703 0.955399109 0.922512104 1 22.00746101 5.060845835 12.72074355 0.998311894 0.753141711 0.018956916 0.084454726 2526398.346 17119276.49 0.022421284 15026099.88 115039.1951 -5.060845835 -0.245170183 HGLTSGSAS(ph)PPPPALPLYPDPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HGLTSGSASPPPPALPLYPDPVR 23 0 Q92610;H0YM74 Q92610 ZNF592 Zinc finger protein 592 1 HGLT(0.001)S(0.006)GS(0.052)AS(0.941)PPPPALPLYPDPVR;HGLTS(0.003)GS(0.018)AS(0.979)PPPPALPLYPDPVR;HGLTSGS(0.002)AS(0.998)PPPPALPLYPDPVR 189.88 1.09E-17 1596720000 774580 776620 339647 489774 815990 875730 727670 856900 819120 TRUE FALSE 672217.2905 771518.3321 503901.4253 600984.6724 799753.3955 909419.8998 657100.6754 673658.6034 722284.5667 0.930682063 1.068163945 0.697649442 0.832060797 1.107255273 1.259088096 0.909753172 0.932677555 1 19.46220782 3.245263083 24.99988105 1.029086704 0.882248715 0.262390257 0.132034608 264.3597207 986043.1293 0.041582496 0.052438002 1758.988834 -3.245263083 -0.146837989 HGLVPFAFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HGLVPFAFVR 10 0 Q13242;H0YIB4;S4R3G0 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 ; 114.89 0.001295 1291500000 1093490 2221200 846280 890690 1899900 2063300 1859330 1847810 920410 FALSE TRUE 948982.5259 2206608.791 1255543.839 1092934.778 1862095.707 2142676.486 1679012.463 1452670.211 811600.1783 1.169273432 2.718837243 1.546997983 1.346641865 2.294351032 2.64006409 2.068767982 1.789884046 1 19.63040966 1.246395879 2.901710797 0.811845138 1.993251549 0.259428947 0.509798422 0.56017892 5.792749852 1.559649098 0.130180485 17.63582899 -1.246395879 1.181406411 HGLYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HGLYEK 6 0 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4;A0A2R8Y8A0 E7ETK0 RPS24 40S ribosomal protein S24 0 ;;; 114.67 0.025089 7160200000 15385400 13939600 9402200 11108400 12556400 12924500 16257500 18842300 16914700 FALSE TRUE 13352180.41 13848029.85 13949135.37 13630732 12306552.21 13421713.88 14680850.15 14813020.78 14915063.44 0.895214457 0.928459333 0.935238085 0.913890314 0.825108942 0.899876419 0.984296863 0.993158416 1 23.83026678 2.218822523 5.536985363 0.993349205 0.899574998 0.68535028 0.029707288 0.105995002 9.574118928 0.013125676 0.009113789 165.509346 -2.218822523 -0.093774207 HGLYLPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 HGLYLPTR 8 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;;; 111.74 0.0031755 30667100000 8850408 14773417 8691268 9005520 16175429 18135400 14714018 15362020 17678990 FALSE TRUE 7680804.159 14676369.45 12894394.28 11050360.96 15853569.61 18833080.57 13287054.8 12076971.57 15588999.94 0.492706664 0.941456765 0.827146983 0.708856309 1.016971561 1.208100625 0.852335291 0.774711118 1 23.89402504 3.241187482 24.99450405 0.948986862 0.762793124 0.330299608 0.158463387 105.9382421 1007988.829 0.048947392 0.060313088 1742.558963 -3.241187482 -0.186193738 HGNRNS(ph)NSYGIPEPAHAYAQPQTTTPLPAVSGSPGAAITPLPSTQNGPVFAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HGNRNSNSYGIPEPAHAYAQPQTTTPLPAVSGSPGAAITPLPSTQNGPVFAK 52 1 P46109 P46109 CRKL Crk-like protein 1 HGNRNS(0.313)NS(0.313)Y(0.283)GIPEPAHAY(0.055)AQPQT(0.012)T(0.012)T(0.012)PLPAVSGSPGAAITPLPSTQNGPVFAK 117.73 8.71E-11 1464600000 45319 37547 21214 28142 39881 35123 40052 51291 25413 TRUE FALSE 39329.97933 37300.35128 31473.16136 34532.07122 39087.44613 36474.20454 36167.7632 40322.8188 22408.70409 1.755120652 1.664547451 1.40450609 1.541011523 1.744297482 1.627680226 1.614005123 1.799426626 1 14.4517716 1.229886086 24.99996182 0.999998789 1.64231175 0.76033348 0.113595382 174.3787731 502520.0603 0.337131408 0.029264322 16.97798268 -1.229886086 0.642312961 HGQFTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HGQFTLR 7 0 G3V4F7;P61011-2;P61011 G3V4F7 SRP54 Signal recognition particle 54 kDa protein 0 ; 105.57 0.0078976 246280000 203076 188169 116155 140940 197816 221780 181810 198348 220071 FALSE TRUE 176238.9921 186932.9054 172327.9465 172942.5811 193879.8486 230312.0201 164178.0942 155932.8237 194054.4571 0.908193477 0.963301273 0.888039106 0.891206436 0.999100209 1.186842207 0.846041347 0.80355188 1 17.56610204 HGRDDS(ph)FDSLDSFGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HGRDDSFDSLDSFGSR 16 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 HGRDDS(1)FDSLDSFGSR 97.488 0.0018508 127350000 74502 65217 21223 31213 59664 43245 67478 59276 34181 TRUE FALSE 64656.37194 64788.58523 31486.51379 38300.38871 58476.80313 44908.66313 60933.99395 46600.28869 30140.16112 2.14518999 2.149576606 1.044669724 1.270742667 1.940162261 1.48999413 2.021687731 1.546119429 1 14.87939951 4.272919718 24.71412396 1.519244933 2.147385168 0.411951554 0.331293436 172.0199258 123729.0541 0.083672938 0.221352253 18746.47936 -4.272919718 0.628140235 HGS(ph)DPAFAPGPR ddPTM_MDA-MB-175_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 166.7 5.37E-05 3157730000 2854450 2389880 1322506 1574570 2999030 2539250 2296640 2457300 2174630 TRUE FALSE 2477227.2 2374180.721 1962074.325 1932100.184 2939355.171 2636936.591 2073912.206 1931825.518 1917547.719 1.291872518 1.23813384 1.023220599 1.007589102 1.532871981 1.375160871 1.081543988 1.007445864 1 20.87083105 2.048382885 7.5565153 1.015965637 1.236687005 0.315141089 0.152156902 0.29035449 38.2683143 0.068170248 0.045602152 111.7848336 -2.048382885 0.220721368 HGS(ph)FVNKPTR ddPTM_MDA-MB-175_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 92.457 0.0057256 510080000 534600 600830 372350 502280 760600 517490 824570 825170 867150 TRUE FALSE 463951.2555 596883.1082 552419.7054 616330.3509 745465.5481 537398.1752 744603.3283 648713.817 764636.5149 0.606760528 0.780610259 0.722460535 0.806043576 0.974928 0.702815213 0.973800379 0.848395027 1 19.54441457 6.147810281 0.293322408 0.947794472 8.90E-15 0.53320118 0.088551811 22.62208209 0.96672833 0.204122218 8.809095928 1405433.435 -6.147810281 -0.947794472 HGS(ph)GADSDYENTQSGDPLLGLEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HGSGADSDYENTQSGDPLLGLEGK 24 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 HGS(0.999)GADS(0.001)DYENTQSGDPLLGLEGK;HGS(0.957)GADS(0.039)DY(0.003)ENT(0.001)QSGDPLLGLEGK;HGS(0.969)GADS(0.03)DYENTQSGDPLLGLEGK;HGS(0.985)GADS(0.015)DYENTQSGDPLLGLEGK 240.12 1.01E-37 1139540000 434837 389996 256433 336005 486738 400303 499124 549988 577280 TRUE FALSE 377372.1887 387434.0906 380444.8565 412300.0708 477052.8661 415702.9154 450719.0313 432377.3462 509034.616 0.741348774 0.76111541 0.747385039 0.809964701 0.937171758 0.8166496 0.885438862 0.849406568 1 18.95740424 7.097217629 0.077397898 1.238937632 5.80E-11 0.645448051 0.049881731 261.2714652 2.3965947 9.210531496 39.00970817 12508857.03 -7.097217629 -1.238937632 HGS(ph)GPPSSGGGLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HGSGPPSSGGGLYR 14 0 Q9HC52 Q9HC52 CBX8 Chromobox protein homolog 8 1 HGS(1)GPPSSGGGLYR 96.096 0.001866 0 135720 162900 121210 174370 246090 264350 183750 205870 509380 TRUE FALSE 117784.2581 161829.8992 179827.5614 213963.3736 241193.2905 274519.7156 165929.9533 161846.3026 449161.6767 0.262231317 0.360293203 0.400362655 0.476361597 0.536985462 0.611182409 0.36942144 0.360329723 1 18.77687531 1.234612218 24.99977404 1.000000829 0.425353589 0.770430439 0.099117602 60.59326532 383598.6893 0.193966025 0.026203378 17.16375148 -1.234612218 -0.574647239 HGS(ph)PEFCGILGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HGSPEFCGILGER 13 0 Q15464 Q15464 SHB SH2 domain-containing adapter protein B 1 HGS(1)PEFCGILGER;HGS(1)PEFCGILGER 140.81 2.55E-05 162903000 186331 158124 112308 116512 153288 167329 133852 165622 185147 TRUE FALSE 161706.8862 157085.273 166620.5244 142967.8304 150237.8687 173766.2549 120871.0536 130205.0242 163259.1326 0.990492132 0.96218368 1.020589304 0.875711074 0.920241743 1.064358558 0.740363199 0.79753593 1 17.31680417 2.237024979 24.99999343 0.831476579 0.967247963 0.336786885 0.082518756 42.72518724 695535.8256 0.032256899 0.023062031 172.5937159 -2.237024979 0.135771384 HGS(ph)PTAPICLGSPEFTDQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HGSPTAPICLGSPEFTDQGR 20 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 HGS(0.857)PT(0.143)APICLGSPEFTDQGR;HGS(0.998)PT(0.002)APICLGSPEFTDQGR;HGS(0.998)PT(0.002)APICLGSPEFTDQGR;HGS(0.961)PT(0.039)APICLGSPEFTDQGR;HGS(0.952)PT(0.048)APICLGSPEFTDQGR 240.59 6.72E-30 1284039000 1395090 1451490 842190 978980 1637490 1479700 1626770 1678400 1509130 TRUE FALSE 1210725.322 1441955.067 1249475.901 1201272.372 1604907.153 1536625.016 1469006.096 1319487.221 1330722.371 0.909825632 1.083588206 0.93894559 0.902722009 1.206042063 1.15472998 1.103916285 0.991557105 1 20.34377818 3.25814958 24.99981523 1.082911721 0.966269878 0.399702338 0.080079617 308.9977864 394346.5191 0.024975502 0.032196315 1811.964064 -3.25814958 -0.116641844 HGS(ph)VSADEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HGSVSADEAAR 11 0 A0A1B0GU90;A0A1B0GW73;H3BNF1;A0A1B0GTV3;A0A0S2Z5D0;H3BUV4;A0A1B0GUD2;H3BUT1;A0A1B0GTU6;Q9NWW5;Q9NWW5-2 A0A1B0GU90 CLN6 Ceroid-lipofuscinosis neuronal protein 6 1 HGS(0.988)VS(0.012)ADEAAR 73.877 0.027284 48109000 34578 32335 21479 20903 30349 36611 27105 35788 35483 TRUE FALSE 30008.42969 32122.58926 31866.31624 25649.34563 29745.11428 38019.44886 24476.36127 28135.0147 31288.24016 0.959096118 1.02666654 1.018475826 0.819775913 0.950680323 1.21513542 0.782286289 0.899220108 1 14.93333289 HGS(ph)YDSLASDHSGQEDEEWLSQVEIVTHTGPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HGSYDSLASDHSGQEDEEWLSQVEIVTHTGPHR 33 0 K7ESE9;Q9H6U6-6;Q9H6U6-2;Q9H6U6;Q9H6U6-7;Q9H6U6-3;Q9H6U6-8 K7ESE9;Q9H6U6-7 BCAS3 Breast carcinoma-amplified sequence 3 1 HGS(0.487)Y(0.423)DS(0.086)LAS(0.002)DHS(0.002)GQEDEEWLSQVEIVTHTGPHR;HGS(0.657)Y(0.148)DS(0.194)LASDHSGQEDEEWLSQVEIVTHTGPHR;HGS(0.314)Y(0.291)DS(0.073)LAS(0.081)DHS(0.241)GQEDEEWLSQVEIVTHTGPHR 148.45 1.20E-10 230454000 48512.6 46940.7 15161.8 29492.2 55837.7 51846.6 45808.9 48946.9 39108.4 TRUE FALSE 42101.53699 46632.34345 22494.09719 36188.85477 54726.63901 53841.17225 41366.35993 38479.98634 34485.0495 1.220863464 1.352248123 0.652285484 1.04940707 1.5869671 1.56129027 1.199544745 1.115845472 1 15.07368342 HGSGPNIILTGDSS(ph)PGFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HGSGPNIILTGDSSPGFSK 19 0 Q53ET0;Q5T4K5 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 HGSGPNIILTGDS(0.047)S(0.953)PGFSK;HGSGPNIILTGDS(0.004)S(0.996)PGFSK;HGSGPNIILTGDS(0.008)S(0.992)PGFSK 217.7 2.28E-19 1239030000 882670 1226340 252325 741290 1903000 1574920 1634150 2055040 1674360 TRUE FALSE 766022.9231 1218284.092 374350.214 909611.2244 1865134.023 1635508.192 1475670.385 1615585.688 1476419.068 0.518838411 0.825161445 0.253552817 0.616092845 1.263282264 1.107753365 0.999492906 1.094259566 1 20.49367084 3.317431761 6.49800703 1.085924278 0.544061127 0.752680629 0.153944402 0.102057842 6.732596137 0.043151771 0.055648355 2076.97735 -3.317431761 -0.541863151 HGSLGFLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HGSLGFLPR 9 0 P39023;H7C422;H7C3M2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ;; 142.92 0.00010317 944670000 646058 572480 788546 581804 404324 497920 447180 495460 493720 FALSE TRUE 560679.7984 568719.3412 1169889.483 713911.4905 396278.7434 517075.3046 403812.5524 389509.7347 435352.984 1.287874022 1.306340744 2.687220545 1.639845175 0.91024699 1.187715081 0.927552049 0.894698667 1 18.73182609 3.293444202 5.400825851 0.978274992 1.781104672 0.477473835 0.38817711 0.170693409 10.37680843 0.115991457 0.148405145 1965.369453 -3.293444202 0.80282968 HGSNIEAMSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HGSNIEAMSK 10 0 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 73.632 0.037681 0 167370 169290 37362 102020 226080 217730 191880 210900 228990 FALSE TRUE 145251.6304 168177.9228 55430.38817 125185.2003 221581.4503 226106.214 173271.5071 165800.6762 201919.0631 0.719355707 0.832897698 0.274517855 0.619977125 1.097377568 1.119786367 0.858123569 0.821124433 1 17.6234176 3.256063374 23.55940505 0.95745087 0.603403979 0.542741841 0.166915306 106.0880347 142796.9559 0.05102003 0.065674541 1803.280864 -3.256063374 -0.354046891 HGSNIQVDEVRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HGSNIQVDEVRR 12 1 Q6V1X1-5;Q6V1X1-3;Q6V1X1;Q6V1X1-4;Q6V1X1-2;J3KPT0 Q6V1X1-5 DPP8 Dipeptidyl peptidase 8 0 67.456 0.035906 30540000 17529 17601 10683 13583 14016 19095 12047 16063 10921 FALSE TRUE 15212.49824 17485.37787 15849.33453 16667.22775 13737.10902 19829.59701 10878.68379 12628.05245 9629.931821 1.579709859 1.81573226 1.645840783 1.730773183 1.426501171 2.059162762 1.12967402 1.311333526 1 13.23330987 2.214761548 24.99268215 1.180515829 1.69963674 0.686066587 0.178845235 127.616901 134016.3454 0.067055525 0.045236262 163.9689246 -2.214761548 0.519120911 HGSYDS(ph)LASDHSGQEDEEWLSQVEIVTHTGPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HGSYDSLASDHSGQEDEEWLSQVEIVTHTGPHR 33 0 K7ESE9;Q9H6U6-6;Q9H6U6-2;Q9H6U6;Q9H6U6-7;Q9H6U6-3;Q9H6U6-8 K7ESE9;Q9H6U6-7 BCAS3 Breast carcinoma-amplified sequence 3 1 HGS(0.33)Y(0.279)DS(0.39)LASDHSGQEDEEWLSQVEIVTHTGPHR 139.61 2.30E-10 145910000 17472 12796 4625.7 10760 17287 15712 13567 16334 17230 TRUE FALSE 15163.03093 12711.94223 6862.703992 13203.22246 16943.02252 16316.45081 12251.27443 12841.10121 15193.08903 0.998021594 0.836692407 0.451699057 0.869028177 1.115179572 1.073938998 0.806371529 0.845193574 1 13.89112761 3.483584453 24.995875 0.950124508 0.751388234 0.249530901 0.161470536 439.6795139 1700425.83 0.048274432 0.064662146 3044.980058 -3.483584453 -0.198736274 HGTDLWIDNMSSAVPNHS(ph)PEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 HGTDLWIDNMSSAVPNHSPEKK 22 1 Q8N6H7;E9PIY6;H0YF45;E9PJT7;E9PK28;E9PN48 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMS(0.023)S(0.04)AVPNHS(0.936)PEKK;HGTDLWIDNMS(0.001)S(0.003)AVPNHS(0.997)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK 254.95 2.15E-37 15404571000 13637800 11074480 5103070 8101516 11954850 7926500 15133750 17805780 13262130 TRUE FALSE 11835530.18 11001731.01 7570931.721 9941089.032 11716971.87 8231437.584 13666081.25 13998152.51 11694296.1 1.012077176 0.940777531 0.647403799 0.850080154 1.001939046 0.703884827 1.168610846 1.197006848 1 23.47930169 2.221646217 24.99823898 1.139473073 0.85948582 0.488962232 0.126084747 189.7788639 280477.0659 0.051157334 0.034590445 166.5889601 -2.221646217 -0.279987253 HGVESTLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HGVESTLER 9 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 117.53 0.0011373 816030000 648490 585640 305580 408610 566740 595440 465080 593190 640930 FALSE TRUE 562790.4034 581792.8923 453359.5101 501391.1457 555462.9828 618346.9621 419976.6132 466340.9347 565159.9855 0.995807237 1.029430439 0.802179067 0.887166747 0.982842022 1.094109594 0.74311102 0.825148536 1 19.1082998 4.268032784 24.99084547 0.898047368 1.01261899 0.156787779 0.102858472 387.6974654 328740.6792 0.02686962 0.071066773 18536.7155 -4.268032784 0.114571622 HGVIVAADSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HGVIVAADSR 10 0 P28074;H0YJM8;P28074-2 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;;;; 111.06 0.0018039 2882570000 2758260 2434990 1436420 1818170 2446580 2566130 2387660 2643600 2821580 FALSE TRUE 2393748.952 2418994.39 2131077.517 2231013.287 2397897.845 2664850.682 2156105.101 2078286.713 2488016.027 0.962111549 0.972258363 0.856536893 0.896703744 0.963779099 1.071074564 0.866596146 0.835318861 1 21.24656435 HGVVPLATYMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HGVVPLATYMR 11 0 P46778;M0R181;G3V1B3 P46778 RPL21 60S ribosomal protein L21 0 ; 143.96 3.69E-05 2291600000 2183820 3628000 1774440 1908620 3413200 3615300 3184800 3525700 3704900 FALSE TRUE 1895222.654 3604167.429 2632565.119 2342001.342 3345283.998 3754382.93 2875938.586 2771756.492 3266910.943 0.580126819 1.103234062 0.805827023 0.716885579 1.023989958 1.149214961 0.880323534 0.848433441 1 21.6394957 3.226464699 24.99081364 0.964833477 0.823377237 0.245821855 0.152228902 405.1081983 836973.2717 0.046227679 0.052805829 1684.475501 -3.226464699 -0.14145624 HGVYNPNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HGVYNPNK 8 0 P40926;G3XAL0 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 ;;; 128.57 0.001128 1311290000 2712000 2819040 1910410 3490660 3258890 3107030 2895140 3775650 3863890 FALSE TRUE 2353602.329 2800521.541 2834290.666 4283267.704 3194044.465 3226559.455 2614369.768 2968256.63 3407105.326 0.69079236 0.821965062 0.831876445 1.257157409 0.937465725 0.947009014 0.76732872 0.871196029 1 21.70011512 4.311648078 2.449333639 0.942705854 0.718662621 0.308236622 0.128262897 0.422419612 4.833170226 0.03594231 0.135676957 20495.00735 -4.311648078 -0.224043233 HGYIGEFEIIDDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 HGYIGEFEIIDDHR 14 0 P62244;I3L3P7;I3L246;H3BN98 P62244 RPS15A 40S ribosomal protein S15a 0 ;;;;;;;; 234.82 1.85E-17 22936470000 9565380 9543520 5444710 6528760 9128520 9185840 8871360 10356650 9222570 FALSE TRUE 8301290.797 9480827.989 8077789.967 8011214.744 8946880.312 9539225.209 8011016.873 8141960.993 8132288.281 1.020781668 1.165825369 0.993298527 0.985111996 1.100167628 1.173006278 0.985087665 1.001189421 1 22.95522993 HHAISAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HHAISAK 7 0 P27824;P27824-2;P27824-3;H0Y9Q7;D6RDP7;D6RAU8;D6RB85;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 101.64 0.0089085 60284000 82721 77561 50427 72544 71642 91409 53146 113120 169250 FALSE TRUE 71789.21026 77051.49668 74813.66587 89016.22397 70216.46437 94925.56338 47991.9091 88930.1683 149241.4578 0.481027265 0.516287483 0.501292784 0.596457749 0.470489001 0.636053579 0.321572235 0.595881129 1 17.18728883 1.262514802 3.986454861 1.042090461 0.508018093 0.7769163 0.082975091 0.093404084 2.539092715 0.139133033 0.019237115 18.30268486 -1.262514802 -0.534072368 HHAS(ph)SSSHDLSSSWEQTNLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HHASSSSHDLSSSWEQTNLQR 21 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 HHAS(0.245)S(0.245)S(0.245)S(0.245)HDLS(0.006)S(0.006)S(0.006)WEQTNLQR 122.01 4.81E-05 409770000 45072 81896 4127.3 25010 66027 93315 26768 54775 34911 TRUE FALSE 39115.621 81358.01978 6123.276085 30688.90275 64713.19188 96904.88843 24172.04348 43061.79251 30783.86135 1.270653495 2.64287897 0.198911891 0.996915312 2.102179163 3.147912061 0.785218047 1.398843115 1 14.90988659 6.328169506 5.936858155 1.510951904 1.491300266 0 0.891578058 19419879.63 0.823407023 0.204857243 82406134.4 2128969.825 -6.328169506 -0.019651638 HHCAAITPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HHCAAITPGR 10 0 Q92896;Q92896-3;Q92896-2 Q92896 GLG1 Golgi apparatus protein 1 0 ; 121.73 0.00050722 41487000 19633.4 20620.5 11129.7 10656.4 18764.5 26335 12534.2 17781.4 15374.9 FALSE TRUE 17038.79645 20485.04258 16512.06015 13076.09849 18391.12316 27348.12449 11318.63521 13978.98599 13557.29684 1.256798951 1.51099757 1.217946346 0.964506321 1.356547945 2.01722547 0.834874042 1.03110422 1 13.72678193 HHFETLTES(ph)PCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HHFETLTESPCR 12 0 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 HHFETLT(0.001)ES(0.999)PCR;HHFETLTES(1)PCR 208.81 4.03E-08 978900000 524730 565470 307210 436310 557140 605680 559760 595790 551960 TRUE FALSE 455385.601 561755.3903 455777.7836 535380.8541 546054.004 628980.9015 505474.5614 468384.9449 486707.9176 0.93564453 1.154194066 0.936450317 1.100004407 1.121933678 1.29231697 1.038558328 0.962353247 1 18.89269672 2.000743741 24.99999237 0.98507801 1.094378726 0.161431527 0.10242903 41.49314038 1394718.555 0.042296221 0.028233996 100.1713994 -2.000743741 0.109300717 HHGDVMDLQFFDQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HHGDVMDLQFFDQER 15 0 Q8NFH3;B4E301;F5H0E3;B4DVD1;Q8NFH3-2 Q8NFH3 NUP43 Nucleoporin Nup43 0 ; 142.1 2.69E-06 147127000 140788 114782 66162 88109 111783 116755 96307 116717 109110 FALSE TRUE 122182.5091 114027.9895 98158.1645 108115.4951 109558.737 121246.6404 86967.16196 91757.97784 96211.1401 1.269941391 1.18518489 1.020236995 1.123731566 1.138732343 1.260214153 0.903919877 0.953714692 1 16.55391633 2.228900598 24.99998791 0.950762498 1.157364086 0.650110473 0.073737712 129.5905323 335375.3094 0.030855495 0.021101372 169.3950043 -2.228900598 0.206601588 HHGILLGTITLITELCER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HHGILLGTITLITELCER 18 0 O75843 O75843 AP1G2 AP-1 complex subunit gamma-like 2 0 ; 162.87 2.00E-11 155340000 88597 109141 63264.6 62937 73132 76102 79901 95229 89485 FALSE TRUE 76888.68197 108424.0456 93859.57217 77227.80778 71676.81628 79029.69318 72152.21332 74865.01942 78906.18524 0.974431621 1.374088042 1.189508425 0.978729456 0.908380199 1.00156525 0.914405038 0.948785183 1 16.26785077 3.723797999 4.936566247 0.953126549 1.200754241 0.518820624 0.099713442 0.124053206 9.013746884 0.025276146 0.040504103 5294.171414 -3.723797999 0.247627692 HHGT(ph)PTSTKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HHGTPTSTKK 10 1 H0Y9P1;Q9NSY1 H0Y9P1 BMP2K BMP-2-inducible protein kinase 1 HHGT(0.999)PTSTKK;HHGT(0.995)PT(0.002)S(0.002)T(0.002)KK 60.49 0.07451 96570000 237087 204181 76831 97498 97481 109235 157739 170641 68909 TRUE FALSE 205755.3522 202839.7216 113986.7286 119636.4111 95541.31882 113437.3411 142441.4961 134150.7501 60762.65652 3.386213902 3.338229978 1.875933922 1.96891344 1.572369022 1.866892391 2.344227593 2.207782835 1 15.89089732 4.241181877 9.673309113 1.890695501 3.364909318 0.749220842 0.366495711 0.049907153 69.3327175 0.093772038 0.221844508 17425.36474 -4.241181877 1.474213817 HHHHDS(ph)DSNS(ph)PCCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HHHHDSDSNSPCCK 14 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 2 HHHHDS(0.981)DS(0.023)NS(0.996)PCCK 83.418 0.0040384 80092000 42803 40977 19397 21069 36970 23488 23759 31658 26846 TRUE FALSE 37146.4751 40707.81939 28777.45408 25853.03847 36234.36933 24391.59856 21454.85584 24888.18306 23672.29646 1.569196092 1.719639641 1.215659584 1.092122115 1.530665577 1.030385818 0.906327608 1.051363272 1 14.53091205 5.12495488 0.316285428 0.901036569 2.489826867 0.620133444 0.171100618 8.96315169 0.736004984 0.413680122 5.82323824 133338.2897 -5.12495488 1.588790298 HHHHDS(ph)DSNSPCCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HHHHDSDSNSPCCK 14 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 HHHHDS(0.46)DS(0.46)NS(0.08)PCCK 62.891 0.033288 51787000 60864 60073 36674 38592 55711 46149 45563 63510 51143 TRUE FALSE 52820.66819 59678.37651 54409.66907 47354.90344 54602.4601 47924.38189 41144.30727 49928.88074 45096.9328 1.171269639 1.323335597 1.20650487 1.050069273 1.210779907 1.062697148 0.912352675 1.107145822 1 15.46074169 3.332436698 0.81516033 1.019132261 1.257055222 0.526974896 0.081187672 0.534987575 0.826438373 0.047496902 0.081596115 2149.991279 -3.332436698 0.237922961 HHHHDSDSNS(ph)PCCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HHHHDSDSNSPCCK 14 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 HHHHDS(0.002)DS(0.018)NS(0.98)PCCK;HHHHDS(0.032)DS(0.178)NS(0.791)PCCK 139.67 1.70E-05 33949000 35776.4 45671 9325.5 17234.7 38079.1 38727 28129.4 31702.9 27774.8 TRUE FALSE 31048.45809 45370.98419 13835.34299 21148.10205 37321.40041 40216.85275 25401.41512 24923.48155 24491.29479 1.267734449 1.852535139 0.564908598 0.863494651 1.523863917 1.642087652 1.037160973 1.017646546 1 14.57998143 2.041530131 24.99590704 1.015278083 1.276163632 0.106174064 0.365748764 356.0574671 214300.2853 0.156303166 0.105379471 110.0348183 -2.041530131 0.260885549 HHISIAEIYETELVDIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HHISIAEIYETELVDIEK 18 0 P54920;M0R0Y2;M0R2M1;M0R058;M0R0I4;M0R027 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;; 168.07 1.25E-11 315241000 465766 486056 111170 278943 436227 381944 416824 512100 434972 FALSE TRUE 404213.843 482863.0661 164932.1838 342281.2715 427546.9362 396637.6328 376400.4726 402591.4002 383550.1057 1.053874936 1.258930865 0.430014701 0.892403017 1.114709473 1.034122079 0.981359325 1.049644868 1 18.54905553 3.260810745 24.29433691 1.033489022 0.899615346 0.084729871 0.20660689 461.702265 504116.299 0.060541385 0.078088453 1823.101067 -3.260810745 -0.133873676 DHASIQMNVAEVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DHASIQMNVAEVDK 14 0 Q8WVC2;P63220;Q9BYK1 Q8WVC2 RPS21 40S ribosomal protein S21 0 120.66 0.00011908 695800000 772820 820160 234760 743830 980410 740230 875590 1013100 2073500 FALSE TRUE 670689.8789 814772.315 348290.7212 912727.9702 960901.7591 768707.1271 790675.4166 796456.449 1828373.192 0.366823295 0.44562692 0.19049214 0.499202228 0.525550125 0.420432289 0.4324475 0.435609345 1 20.80212914 1.236227335 5.51637204 1.029253119 0.414517663 0.806234024 0.090262784 0.065980227 6.258945689 0.154222102 0.022539423 17.22770136 -1.236227335 -0.614735455 HHPDLIFCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HHPDLIFCR 9 0 Q7RTV0 Q7RTV0 PHF5A PHD finger-like domain-containing protein 5A 0 ;;; 162.49 6.37E-05 2035360000 1965510 2187630 1004300 1328180 2309330 2270200 1846920 2046250 2048080 FALSE TRUE 1705762.874 2173259.314 1489982.839 1629763.569 2263378.851 2357536.063 1667805.983 1608675.361 1805958.316 0.944519516 1.203382878 0.825037226 0.90243698 1.253284105 1.305421085 0.923501926 0.890759962 1 20.78433316 HHPHFLTHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HHPHFLTHK 9 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 57.55 0.066301 97122000 221940 244270 148420 163950 232320 262620 200270 227580 224870 FALSE TRUE 192610.0667 242665.3743 220196.4084 201177.3533 227697.2865 272723.1613 180847.8462 178913.788 198286.1248 0.971374406 1.223814196 1.11049832 1.014581094 1.148326878 1.375402145 0.912054973 0.902301098 1 17.5972242 HHSVEIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HHSVEIK 7 0 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 125.25 0.011864 0 80396 76393 32134 44577 81160 67864 80004 78354 70414 FALSE TRUE 69771.4649 75891.16935 47674.10988 54698.88917 79545.07479 70474.77199 72245.22439 61598.60685 62089.73714 1.123719766 1.22228202 0.767825926 0.880965063 1.281130803 1.135047034 1.163561447 0.992089993 1 15.9220672 1.609340906 25 0.996033508 1.077378429 0.051348126 0.152696266 0.5311901 8768.733086 0.093216801 0.040906756 40.67624982 -1.609340906 0.081344921 HHTAAFEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HHTAAFEER 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 160.36 6.54E-05 1110130000 494660 499330 251165 344021 481230 582040 370767 431942 480695 FALSE TRUE 429289.4277 496049.8684 372629.2341 422136.2261 471654.4645 604431.4554 334810.0734 339574.5647 423867.7847 1.012790882 1.170293866 0.879116667 0.995914861 1.112739589 1.42599055 0.789892711 0.801133223 1 18.6932548 HHVLHDQNVDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HHVLHDQNVDKR 12 1 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;E9PFG7 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 ; 150.69 2.41E-05 67523000 50353 53604 36462 56136 53160 50955 41766 55200 46467 FALSE TRUE 43698.72347 53251.87179 54095.14516 68882.53679 52102.22001 52915.27182 37715.53975 43395.90957 40973.7242 1.066506019 1.299659058 1.320239891 1.68113927 1.271600789 1.291444038 0.920481125 1.059115578 1 15.32241141 2.3185435 5.59022931 1.004634772 1.338680478 0.507325461 0.152318143 0.167704985 8.76183542 0.059545308 0.045359556 208.2300965 -2.3185435 0.334045707 HHYDS(ph)DEKSETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HHYDSDEKSETR 12 1 Q9BQ39 Q9BQ39 DDX50 ATP-dependent RNA helicase DDX50 1 HHYDS(1)DEKSETR;HHYDS(1)DEKSETR 186.77 6.84E-06 2016900000 627930 588720 379590 456540 546400 506680 505580 556700 484700 TRUE FALSE 544947.4595 584852.6596 563160.9937 560204.3848 535527.709 526172.3075 456548.9294 437654.0372 427399.3182 1.275031186 1.368398672 1.31764598 1.310728307 1.252991491 1.231102356 1.068202288 1.023993298 1 18.70522508 2.288767502 1.160570024 0.987722498 1.32213416 0.954219934 0.027802043 0.091150081 0.242635343 0.023841428 0.010193601 194.4318918 -2.288767502 0.334411662 HHYLRPSLFVYPEESLVIGSSTLFSALLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HHYLRPSLFVYPEESLVIGSSTLFSALLIK 30 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 104.3 0.0002243 410630000 223470 208110 73968 131770 112000 83042 205040 219310 111420 FALSE TRUE 193937.8733 206742.9117 109739.1722 161690.3925 109771.4191 86236.67948 185155.2524 172412.2632 98248.05453 1.973961461 2.104295222 1.116960257 1.645736328 1.117288476 0.877744398 1.884569147 1.754866944 1 16.58414122 4.250451313 24.99956444 1.394510246 2.039128712 0.419575813 0.336352035 240.3280788 505267.5812 0.088101184 0.229127111 17801.28333 -4.250451313 0.644618467 HIADLAGNSEVILPVPAFNVINGGSHAGNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HIADLAGNSEVILPVPAFNVINGGSHAGNK 30 0 P06733;A0A2R8Y6G6;P06733-2;K7EM90;A0A2R8YEM5 P06733 ENO1 Alpha-enolase;Enolase 0 ; 174.31 3.80E-13 11083200000 13679000 12416600 7827900 8340200 12255700 11075400 13056000 14843500 15780900 FALSE TRUE 11871285.49 12335034.54 11613498.62 10233969.88 12011835.55 11501477.8 11789831.13 11669333.04 13915299.98 0.853110282 0.88643684 0.834584855 0.735447306 0.863210679 0.826534665 0.847256699 0.838597303 1 23.73016867 1.236739042 6.182367343 1.005698516 0.834933355 0.633316273 0.039307259 0.08856932 13.79998411 0.06359731 0.009890022 17.24801184 -1.236739042 -0.170765161 HIAEDADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 HIAEDADR 8 0 H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;H0YL42;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5 H7BYY1;P09493-3 TPM1 Tropomyosin alpha-1 chain 0 ;;;;;; 157.91 0.00036932 8504720000 5082650 5096950 2899707 3550960 4191150 5178450 4807120 5245840 5015080 FALSE TRUE 4410964.925 5063467.8 4302015.004 4357259.741 4107754.315 5377668.322 4340926.242 4124057.939 4422202.956 0.997458726 1.14501027 0.972821702 0.985314284 0.928893214 1.216060949 0.981620764 0.932579979 1 22.07633381 2.01747049 24.99108835 0.960162004 1.040266594 0.128628524 0.085652943 427.3777643 611350.5038 0.03438766 0.023178624 104.1047367 -2.01747049 0.08010459 HIAEEADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 HIAEEADR 8 0 P06753-2;A0A087WWU8;P06753-6;P06753-5;P06753-7;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;P67936;P67936-2 TPM3;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-4 chain 0 ;;;;;;;;;; 187 0.00020453 44849910000 11655260 12399336 7235748 8763183 10499126 12465694 10837600 12261568 11541533 FALSE TRUE 10114987.86 12317883.95 10734979.93 10752997.64 10290213.93 12945257.31 9786571.22 9639527.103 10177106.12 0.993896275 1.210352315 1.054816547 1.056586962 1.011113947 1.271997871 0.961626135 0.947177615 1 23.27882405 HIAEEADRK ddPTM_MDA-MB-175_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 ;;; 152.97 5.14E-05 1231840000 2866740 2491290 1681020 2049360 2388720 2115080 2998390 3356870 3079350 FALSE TRUE 2487893.046 2474924.552 2493966.895 2514698.511 2341189.145 2196448.496 2707606.599 2639029.474 2715312.751 0.916245484 0.911469425 0.918482371 0.926117446 0.862217122 0.808911789 0.997161965 0.971906265 1 21.37268695 2.201601856 24.99984499 0.986296051 0.893118901 0.636836279 0.035217578 118.4297749 80108.11721 0.015261196 0.010289409 159.0749723 -2.201601856 -0.093177151 HIAELIFYMEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HIAELIFYMEELR 13 0 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 ; 168.61 2.99E-05 216080000 478650 462040 339390 383790 352280 373490 428260 512500 554770 FALSE TRUE 415395.1898 459004.8288 503520.1392 470935.3854 345270.3172 387858.402 386727.4111 402905.8633 489185.7226 0.849156405 0.938303813 1.029302606 0.962692416 0.705806203 0.792865335 0.790553349 0.823625557 1 18.90002277 3.273626004 24.99962867 0.818815467 0.950426705 0.340944124 0.084240889 199.2234158 142033.6968 0.024587647 0.031741126 1877.699125 -3.273626004 0.131611238 HIAFT(ph)PESQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HIAFTPESQR 10 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 HIAFT(1)PESQR;HIAFT(1)PESQR 106.32 0.0089473 501720000 321550 331850 200689 254170 278640 329280 281830 332350 482460 TRUE FALSE 279056.3528 329670.0555 297742.8717 311883.1832 273095.6091 341947.6147 254498.17 261279.5389 425424.1284 0.65594858 0.774920917 0.699873025 0.733111176 0.641937283 0.803780491 0.598222228 0.614162483 1 18.69854233 1.230078235 24.99953048 1.000000582 0.688689639 0.681901507 0.066480171 197.8077063 582939.1114 0.187888311 0.01660859 16.98549605 -1.230078235 -0.311310943 HIAFTPESQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HIAFTPESQR 10 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 ;;; 159.83 7.56E-06 2407250000 1934170 2307150 1305650 1517380 2300520 2432770 1965470 2424930 2410920 FALSE TRUE 1678564.534 2291994.18 1937066.707 1861924.321 2254744.153 2526360.236 1774859.022 1906377.59 2125903.784 0.789576907 1.078126958 0.911173272 0.875827182 1.060604986 1.188369979 0.834872695 0.896737474 1 21.01964487 4.763470367 23.72520402 0.970852051 0.789576459 0.233062975 0.107652626 6540.35591 6229136.096 0.027228264 1.666012377 58005.6592 -4.763470367 -0.181275592 HIANYISGIQTIGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HIANYISGIQTIGHR 15 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ; 216.34 1.28E-12 1573000000 569170 515440 239870 348090 477950 519800 466320 497260 498420 FALSE TRUE 493952.7424 512054.0407 355871.9343 427129.1547 468439.7301 539797.0424 421096.3582 390924.8187 439497.3554 1.123903788 1.165090152 0.809724859 0.971858305 1.065853353 1.22821454 0.958131723 0.889481618 1 18.74549496 3.81261627 0.023722792 3.70E-07 2.081008093 0.063200605 0.122846022 2571.218368 34.41013986 1442.220694 1575.883778 6495.555087 -3.81261627 2.081007723 HICAICGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HICAICGDR 9 0 P19793;A0A5F9ZHH6;P19793-2;A0A087WZ88;P48443 P19793 RXRA;RXRG Retinoic acid receptor RXR-alpha;Retinoic acid receptor RXR-gamma 0 64.841 0.068249 74481000 172090 209230 145050 64341 144850 221130 72793 68719 32264 FALSE TRUE 149347.8705 207855.5544 215196.6652 78950.60744 141967.7684 229637.0142 65733.54606 54023.97662 28449.78668 5.249525144 7.306049663 7.564087127 2.775086096 4.99011715 8.071660319 2.310511035 1.898923786 1 14.79613021 3.737967869 24.99994999 3.51723948 6.766503639 0.355367043 2.030408259 64.64383283 2726470.344 0.604521074 0.961089169 5469.754932 -3.737967869 3.249264159 HIDFSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 HIDFSLR 7 0 P46781 P46781 RPS9 40S ribosomal protein S9 0 ;;;;;;; 157.9 0.0014448 15985690000 1899065 2072231 1308773 1618727 2295870 2269328 2147864 2293080 2391590 FALSE TRUE 1648098.749 2058618.378 1941700 1986283.706 2250186.679 2356630.517 1939564.48 1802722.687 2108858.955 0.78151208 0.976176417 0.920734882 0.941876033 1.067016205 1.117490817 0.919722239 0.854833218 1 21.00803118 4.740266498 24.00227538 0.967416685 0.781511972 0.389415637 0.075543975 109.0105643 1533576.01 0.020691512 0.128262321 54987.81942 -4.740266498 -0.185904713 HIDLVEGDEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HIDLVEGDEGR 11 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;;; 174.84 1.05E-05 5643760000 4745070 4235450 2608840 3465730 4236000 4666550 3443710 4379940 4465920 FALSE TRUE 4117996.977 4207627.05 3870483.75 4252676.967 4151711.888 4846075.198 3109739.534 3443323.916 3937964.025 1.045717267 1.068477778 0.982864172 1.079917678 1.054278775 1.230604233 0.789682058 0.874391918 1 21.9090185 2.225619934 24.99986107 0.881086903 1.071414478 0.556002814 0.079412808 165.5852412 319888.4097 0.031943123 0.021686511 168.120214 -2.225619934 0.190327575 HIDMVEGDEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HIDMVEGDEGR 11 0 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 124.6 0.00034577 312410000 406730 338310 204440 243540 288050 301600 473340 615130 251330 FALSE TRUE 352979.6 336087.6193 303307.8678 298839.4793 282318.3686 313202.7472 427435.5597 483589.2364 221618.0537 1.592738471 1.516517331 1.368606315 1.348443749 1.273896074 1.41325466 1.928703698 2.182084123 1 17.75771589 2.249365597 24.35756594 1.812660458 1.411265039 0.125421651 0.312518105 202.5638851 456638.1008 0.116311693 0.089123938 177.5683656 -2.249365597 -0.401395419 HIDSSPYSPAYLS(ph)PPPESSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HIDSSPYSPAYLSPPPESSWR 21 0 Q53ET0;H0YDQ8 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 HIDSSPYSPAYLS(1)PPPESSWR;HIDSSPYSPAYLS(1)PPPESSWR;HIDSSPYSPAYLS(1)PPPESSWR;HIDSSPYSPAYLS(1)PPPESSWR 208.12 2.13E-22 1467060000 359085 437616 228699 352123 522396 569674 499910 574160 545354 TRUE FALSE 311631.0074 434741.2717 339298.6014 432077.909 512001.3417 591589.7274 451428.8051 451380.3521 480882.8714 0.648039317 0.904048153 0.705574312 0.898509668 1.064711122 1.230215844 0.93875002 0.938649262 1 18.87532601 3.477112632 4.021796158 1.023954284 0.769490801 0.604453892 0.103697454 0.16433347 6.124075528 0.031408669 0.044172867 2999.94044 -3.477112632 -0.254463483 HIEIFTDLSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HIEIFTDLSSR 11 0 P13010;C9JZ81 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;; 186.46 4.02E-06 4418480000 3403120 3022990 1815150 2244770 3081260 3221370 2804600 3196940 3266080 FALSE TRUE 2953389.07 3003131.78 2692962.611 2754479.338 3019948.954 3345298.188 2532610.324 2513299.26 2879967.743 1.025493802 1.042765769 0.935066935 0.956427149 1.048605132 1.161574881 0.879388434 0.872683128 1 21.45762122 2.168489897 24.99998851 0.906467434 1.022402404 0.35833846 0.069188455 51.58975829 18405.14456 0.029350214 0.019787915 147.397425 -2.168489897 0.11593497 HIEPELAGRDS(ph)PIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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;HIEPELAGRDS(1)PIR 207.43 5.73E-09 2082240000 1266300 1069868 825968 1006855 1121185 1198844 1043179 1250450 1873830 TRUE FALSE 1098955.247 1062839.967 1225408.887 1235476.817 1098875.612 1244964.304 942011.6611 983050.9985 1652307.952 0.665103164 0.643245689 0.741634685 0.747727937 0.665054968 0.753469898 0.5701187 0.594956284 1 20.65605117 1.230507564 24.99968323 1.000000602 0.670083736 0.733930681 0.061921962 172.7865185 536350.3013 0.179681479 0.016623065 17.00229565 -1.230507564 -0.329916867 HIEPELAGRDS(ph)PIRAEMPGNLQHYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HIEPELAGRDSPIRAEMPGNLQHYGR 26 2 P86791;P86790 P86791 CCZ1;CCZ1B Vacuolar fusion protein CCZ1 homolog;Vacuolar fusion protein CCZ1 homolog B 1 HIEPELAGRDS(1)PIRAEMPGNLQHYGR 210.81 6.22E-26 1270600000 293630 237840 97173 150860 246690 245320 204710 233730 119730 TRUE FALSE 254826.0515 236277.6134 144166.1878 185115.0688 241781.3516 254757.6191 184857.2557 183748.6584 105575.6558 2.41368192 2.237993329 1.365524909 1.753387818 2.29012408 2.413033736 1.750945844 1.740445342 1 16.68791768 1.090444569 1.448582207 0.252086275 2.036535981 0.497393477 0.330531567 1.657287759 2.312236143 4.808623467 0.102106409 12.3152879 -1.090444569 1.784449706 HIESMIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HIESMIR 7 0 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 104.37 0.0081676 306640000 52055 77388 36678 29480 64135 108290 45187 42245 46096 FALSE TRUE 45175.79986 76879.63313 54415.60348 36173.88457 62858.83898 112455.9864 40804.77169 33211.2355 40646.58339 1.111429205 1.89141686 1.338749753 0.88996126 1.546472882 2.766677467 1.003891798 0.817073238 1 15.31084647 2.029938524 24.99997269 0.899972003 1.586303864 0.272332718 0.502938266 254.7539752 212729.6431 0.209043135 0.140935053 107.1367639 -2.029938524 0.686331861 HIEWESVLTNTAGCLR ddPTM_MDA-MB-175_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 ; 202.82 2.94E-11 1007120000 697080 598060 335410 514760 574560 668210 573490 729180 765730 FALSE TRUE 604959.1118 594131.3045 497615.3979 631644.1256 563127.3801 693916.4711 517873.0281 573250.5315 675206.2717 0.895961926 0.879925631 0.736982784 0.935483203 0.834007923 1.027710346 0.76698492 0.849000602 1 19.36496878 HIGLVYSGMGPDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HIGLVYSGMGPDYR 14 0 A0A024RA52;P25787 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 0 ;; 151.54 5.78E-06 6327540000 4609890 4896410 2627069 3630910 5006240 5194310 4635570 5450710 5692170 FALSE TRUE 4000681.357 4864245.16 3897528.355 4455363.61 4906625.619 5394138.467 4186013.135 4285118.084 5019248.147 0.797067855 0.969118286 0.776516371 0.887655577 0.977561873 1.074690533 0.833992067 0.853737046 1 22.25903984 3.470398274 22.66347912 0.933872009 0.855116486 0.218609512 0.085018442 102.8674467 346764.6445 0.02546666 0.032993848 2953.916904 -3.470398274 -0.078755523 HIGTSALMDLLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HIGTSALMDLLLR 13 0 O75170-6;O75170-2;O75170-4;O75170-3;O75170-5;O75170 O75170-6 PPP6R2 Serine/threonine-protein phosphatase 6 regulatory subunit 2 0 ; 217.09 2.64E-11 346310000 202887 213547 134698 230580 257690 265490 299090 283490 403750 FALSE TRUE 176074.9689 212144.1957 199838.4033 282936.7132 252562.4732 275703.5721 270084.2978 222867.8696 356019.135 0.494566026 0.595878634 0.561313659 0.794723332 0.709407019 0.774406612 0.758622982 0.625999694 1 18.44159526 3.746448668 24.10702038 0.757342762 0.555115324 0.539803371 0.097460978 305.735147 934365.8588 0.02500045 0.042267651 5577.616728 -3.746448668 -0.202227438 HIGYDDSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HIGYDDSSK 9 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ; 142.92 0.00010317 936470000 1567120 1329650 974490 1092850 1120360 1130100 1465280 1732990 1601050 FALSE TRUE 1360021.121 1320915.442 1445756.623 1340998.296 1098067.028 1173575.678 1323177.371 1362403.575 1411775.693 0.963340797 0.935641156 1.024069638 0.9498664 0.777791425 0.831276303 0.937243344 0.965028355 1 20.42907946 3.465808813 24.99921413 0.905063112 0.973227692 0.203718748 0.066149988 407.1121015 899667.4384 0.021266895 0.027476796 2922.865375 -3.465808813 0.06816458 HIHITQATETTTTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HIHITQATETTTTR 14 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 140.31 9.98E-06 203871000 113704 133370 60862 75354 113614 130439 117342 124269 123837 FALSE TRUE 98677.72831 132493.8837 90295.06677 92464.27741 111353.3037 135457.0727 105962.1909 97695.04141 109197.1309 0.903665943 1.213345832 0.826899626 0.846764715 1.01974569 1.240481976 0.970375229 0.894666742 1 16.73657543 2.003854669 24.99421495 0.937622957 1.011263495 0.032857115 0.138168006 375.932681 2437586.829 0.058087062 0.038955948 100.8915209 -2.003854669 0.073640538 HIISATSLST(ph)SPTELGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HIISATSLSTSPTELGSR 18 0 Q5JSZ5;A0A1W2PQP5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 HIISATSLS(0.001)T(0.988)S(0.011)PTELGSR;HIISATS(0.004)LS(0.054)T(0.889)S(0.053)PTELGSR 441.27 1.51E-189 1065840000 547200 492430 302455 350002 493270 558160 509590 596970 593970 TRUE FALSE 474886.1336 489195.1949 448723.2497 429475.3035 483454.8921 579632.7764 460170.0402 469312.6111 523751.5433 0.906701163 0.934021486 0.85674831 0.819998163 0.923061513 1.106694164 0.878603693 0.896059624 1 18.99852306 3.00381271 24.9911147 0.957326817 0.880389793 0.274953451 0.068196871 182.1784618 1194105.398 0.021756037 0.024560335 1008.817739 -3.00381271 -0.076937024 HIISATSLSTS(ph)PTELGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HIISATSLSTSPTELGSR 18 0 Q5JSZ5;A0A1W2PQP5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 HIISATSLST(0.03)S(0.962)PT(0.008)ELGSR;HIISATSLST(0.009)S(0.99)PT(0.001)ELGSR;HIISATSLS(0.004)T(0.194)S(0.793)PT(0.008)ELGSR;HIISATSLS(0.002)T(0.079)S(0.751)PT(0.167)ELGSR;HIISATSLS(0.002)T(0.048)S(0.606)PT(0.344)ELGSR 219.99 4.53E-19 5639000000 1874070 1839340 1173823 1533120 1859310 2152600 2056490 2321090 2064220 TRUE FALSE 1626406.901 1827257.254 1741487.729 1881238.328 1822313.369 2235411.915 1857051.916 1824742.966 1820190.263 0.893536755 1.003882556 0.95676137 1.033539387 1.00116642 1.228119917 1.020251538 1.002501224 1 20.79565783 4.579590511 0.869432831 1.048212142 0.854403885 0.315005015 0.070135823 2.54390371 1.794037308 0.026617923 0.450979508 37983.10907 -4.579590511 -0.193808257 HIKEEPLS(ph)EEEPCTSTAIAS(ph)PEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HIKEEPLSEEEPCTSTAIASPEK 23 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 2 HIKEEPLS(1)EEEPCTSTAIAS(1)PEK;HIKEEPLS(0.994)EEEPCT(0.004)S(0.005)T(0.008)AIAS(0.989)PEK;HIKEEPLS(0.991)EEEPCT(0.01)S(0.004)T(0.006)AIAS(0.988)PEK;HIKEEPLS(1)EEEPCTSTAIAS(1)PEK 156.9 1.67E-08 1448500000 1661590 1198290 885570 1007050 1264670 1009780 1543280 1824080 1355940 TRUE FALSE 1442006.672 1190418.354 1313834.614 1235716.094 1239505.541 1048626.89 1393612.943 1434014.687 1195642.318 1.206051885 0.995630831 1.098852553 1.033516526 1.036685907 0.877040629 1.165576797 1.199367625 1 20.18935443 0.942993336 19.50734582 7.75E-05 1.077255335 0.054685842 0.100041399 1.003748568 98235.01276 12938.59907 0.024599362 8.769873637 -0.942993336 1.077177835 HIKEEPLS(ph)EEEPCTSTAIAS(ph)PEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HIKEEPLSEEEPCTSTAIASPEKK 24 2 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 2 HIKEEPLS(1)EEEPCTSTAIAS(1)PEKK 126.67 4.83E-05 444870000 253990 180880 182370 134590 150190 121100 256480 295480 204200 TRUE FALSE 220424.578 179691.7874 270564.742 165150.7166 147201.5128 125758.7954 231606.6091 232293.9014 180059.7086 1.224174912 0.997956671 1.502639008 0.917199732 0.817515001 0.698428295 1.286276707 1.290093732 1 17.45811586 3.682886564 24.99990557 1.02913057 1.217230802 0.201536765 0.2189205 637.2703199 286159.6057 0.067077239 0.099491686 4818.219311 -3.682886564 0.188100232 HIKEEPLS(ph)EEEPCTSTAIASPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HIKEEPLSEEEPCTSTAIASPEK 23 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 1 HIKEEPLS(0.995)EEEPCT(0.005)STAIASPEK;HIKEEPLS(0.999)EEEPCT(0.001)STAIASPEK;HIKEEPLS(0.636)EEEPCT(0.121)S(0.121)T(0.121)AIASPEK;HIKEEPLS(0.995)EEEPCT(0.005)STAIASPEK;HIKEEPLS(0.988)EEEPCT(0.012)STAIASPEK;HIKEEPLS(0.798)EEEPCT(0.055)S(0.073)T(0.073)AIASPEK 288.48 2.44E-53 7994530000 7552370 5494900 4380160 4700050 5251040 4215240 6714000 7987140 6984680 TRUE FALSE 6554305.169 5458803.64 6498420.027 5767268.188 5146554.577 4377403.01 6062877.313 6279152.267 6158959.087 1.064190406 0.886319192 1.055116609 0.936403069 0.835620842 0.710737472 0.984399673 1.019515177 1 22.55425511 6.081754482 2.279338831 0.932558637 39.57961464 0.145525865 0.100698273 1208.264056 24.87145338 0.028146752 241904.7035 1207131.221 -6.081754482 38.64705601 HILANFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HILANFK 7 0 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;E9PJF7;P13693-2;H0YCX0;Q56UQ5 Q5W0H4 TPT1 Translationally-controlled tumor protein;TPT1-like protein 0 ; 178.02 0.00072178 5692400000 6898800 7530300 5165700 6876600 8071500 6765600 8728000 9757400 10547800 FALSE TRUE 5987106.101 7480832.963 7663849.798 8438037.132 7910892.942 7025877.01 7881559.903 7670855.942 9300851.1 0.643715939 0.804317033 0.823994462 0.907232794 0.85055581 0.755401515 0.847402009 0.824747742 1 23.14893131 4.857767679 1.710502492 0.853577407 0.523437004 0.536917757 0.062764757 1.074146594 2.449538364 0.016603839 0.635941945 72072.18339 -4.857767679 -0.330140403 HILGFDTGDAVLNEAAQILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HILGFDTGDAVLNEAAQILR 20 0 Q9Y224 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ;;; 289.32 2.02E-54 2060102000 1967482 1873334 1111908 1321905 1681219 1833056 1773025 1940321 1852997 FALSE TRUE 1707474.269 1861027.946 1649630.428 1622063.734 1647766.031 1903574.85 1601077.308 1525398.454 1633937.806 1.045005668 1.138983344 1.009604174 0.99273285 1.008463128 1.165022833 0.979888771 0.93357192 1 20.63992164 2.023994125 24.99883515 0.960447818 1.057255485 0.347957356 0.057295048 229.4058294 239010.7647 0.02353983 0.015869822 105.6803213 -2.023994125 0.096807667 HILILQNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HILILQNK 8 0 P41091;Q2VIR3;Q2VIR3-2 P41091 EIF2S3;EIF2S3L Eukaryotic translation initiation factor 2 subunit 3;Putative eukaryotic translation initiation factor 2 subunit 3-like protein 0 178.84 0.00024749 540410000 1571100 1444700 1041600 1422800 1481700 1469000 1818200 1844100 2352800 FALSE TRUE 1363475.154 1435209.671 1545321.244 1745868.486 1452217.069 1525513.381 1641871.244 1449753.566 2074654.664 0.657205837 0.691782442 0.744857094 0.841522455 0.699980143 0.735309547 0.791394959 0.698792715 1 20.98443978 1.233729704 24.99815764 1.000000403 0.735352142 0.71671869 0.052805964 83.40051987 431514.236 0.103022329 0.012921094 17.12890906 -1.233729704 -0.264648261 HILLAVANDEELNQLLK ddPTM_MDA-MB-175_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 ;; 211.57 2.35E-12 938115000 1085852 714552 620286 905136 905132 1235267 655726 1075380 920011 FALSE TRUE 942353.907 709858.0609 920258.3843 1110660.963 887121.6441 1282788.521 592133.7934 845418.3556 811248.3477 1.161609647 0.875019423 1.1343732 1.369076395 1.093526596 1.581252553 0.729904468 1.04212028 1 19.62978411 2.205221443 24.99997454 0.940527519 1.187117696 0.300229917 0.198961039 263.1077571 197294.2783 0.080774899 0.054462256 160.4063081 -2.205221443 0.246590178 HILRPGTALVLLEAQAATGFIIDPVENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HILRPGTALVLLEAQAATGFIIDPVENR 28 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 182.33 7.81E-18 78535000 24346 16808 12863 26232 20407 17989 29588 27403 22817 FALSE TRUE 21128.61442 16697.58714 19083.58982 32188.37653 20000.94063 18681.04847 26718.56031 21543.0817 20119.60025 1.050150806 0.829916446 0.948507405 1.599851693 0.994102287 0.928499982 1.327986639 1.070750981 1 14.29631402 3.96085437 24.99691858 1.150130511 0.92732737 0.196851139 0.200211446 785.6266443 501672.293 0.051826375 0.08978739 9138.067678 -3.96085437 -0.22280314 HIMGQNVADYMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HIMGQNVADYMR 12 0 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;;; 168.83 4.55E-05 7361670000 4693520 5578390 3246968 3652309 5477860 5688060 5038520 6263350 5652640 FALSE TRUE 4073259.44 5541745.189 4817212.585 4481621.58 5368861.303 5906883.349 4549885.106 4923981.344 4984391.339 0.817202977 1.111819842 0.966459545 0.899131163 1.077134787 1.18507616 0.912826621 0.987880166 1 22.24898591 3.23256101 24.99777739 1.025638477 0.961579998 0.140467239 0.100123368 388.5102766 1618753.029 0.030382533 0.035346689 1708.287686 -3.23256101 -0.064058478 HIPGAAFFDIDQCSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HIPGAAFFDIDQCSDR 16 0 P25325-2;P25325;B1AH49 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase 0 ;;;; 285.58 7.37E-36 3561980000 1726360 1919773 1009946 1244429 1725945 1798112 1669580 1920412 1766366 FALSE TRUE 1498217.152 1907161.885 1498359.264 1526995.624 1691602.071 1867286.532 1507664.389 1509746.838 1557548.224 0.961907393 1.224464101 0.961998634 0.980384171 1.086067221 1.198862741 0.967972847 0.969309852 1 20.5708454 HIQDLNWQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HIQDLNWQR 9 0 O75934 O75934 BCAS2 Pre-mRNA-splicing factor SPF27 0 ; 119.53 0.00081249 306530000 144752 131947 96922 89031 106526 112003 111686 155046 153935 FALSE TRUE 125622.6564 131080.2315 143793.8034 109246.8493 104406.341 116311.8279 100854.7089 121890.6195 135736.9797 0.925485868 0.965692855 1.059356144 0.8048422 0.76918126 0.856891233 0.743015714 0.897991246 1 17.05045429 3.728140789 24.981536 0.841722462 0.981729748 0.41255814 0.077645828 674.5944317 1617340.078 0.021905463 0.032878509 5347.376813 -3.728140789 0.140007286 HISDLYEDLR ddPTM_MDA-MB-175_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 ;;;;; 219.5 6.28E-09 3463540000 2595370 2792410 978999 2031120 3542410 3959800 2653910 3016630 4328620 FALSE TRUE 2252385.279 2774066.475 1452446.191 2492316.84 3471922.972 4112136.068 2396534.217 2371547.15 3816895.475 0.590109238 0.726786073 0.380530774 0.652969634 0.90961961 1.077350977 0.627875254 0.621328817 1 21.86396825 3.42530331 6.567619583 0.812536723 0.571327769 0.377240319 0.165464033 0.255331044 24.29129125 0.051196858 0.06662039 2662.583954 -3.42530331 -0.241208955 HISESCPFPSPGGQLAEVHS(ph)VSPEQGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HISESCPFPSPGGQLAEVHSVSPEQGAK 28 0 Q5T1V6;Q5T1V6-2;Q5T1V5 Q5T1V6 DDX59 Probable ATP-dependent RNA helicase DDX59 1 HISESCPFPSPGGQLAEVHS(0.613)VS(0.387)PEQGAK;HISESCPFPSPGGQLAEVHS(0.596)VS(0.404)PEQGAK 188.54 1.15E-17 414577000 217630 244880 52571 146619 280200 243930 250130 321990 282870 TRUE FALSE 188869.6441 243271.3672 77994.51144 179911.0849 274624.5682 253314.1449 225872.4311 253134.9442 249429.4308 0.757206732 0.975311399 0.312691695 0.721290524 1.101011085 1.015574401 0.905556455 1.014855959 1 17.92827218 3.307222677 6.905346179 1.000675313 0.681530811 0.471458559 0.166163362 0.197452153 16.08777296 0.048001604 0.061845808 2028.722647 -3.307222677 -0.319144502 HISFGGNLITFS(ph)PLQPGEF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HISFGGNLITFSPLQPGEF 19 0 Q15398-1;Q15398 Q15398-1 DLGAP5 Disks large-associated protein 5 1 HIS(0.007)FGGNLIT(0.02)FS(0.973)PLQPGEF;HISFGGNLIT(0.165)FS(0.835)PLQPGEF 87.85 0.0027803 104880000 126719 160319 59059 88824 154977 165142 136075 148580 129942 TRUE FALSE 109972.7631 159265.8539 87620.12994 108992.8468 151893.2609 171495.1196 122878.4674 116807.3233 114580.4048 0.959786826 1.389992069 0.764704315 0.951234611 1.325647795 1.496722934 1.072421307 1.019435421 1 16.80600081 2.007929921 24.99064872 1.021552594 1.152707827 0.064281615 0.219439723 555.4925871 1750592.092 0.09361638 0.062992891 101.8427038 -2.007929921 0.131155234 TLHPDLGTDKDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLHPDLGTDKDK 12 1 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 112.43 0.00076587 711740000 2100040 1408810 1491610 1619670 1334220 943710 1875860 2171230 4390300 FALSE TRUE 1822514.393 1399555.434 2212957.585 1987440.829 1307671.632 980015.1344 1693939.386 1706929.361 3871283.735 0.470777788 0.361522309 0.571634046 0.513380306 0.337787598 0.253149911 0.437565289 0.440920759 1 21.88438062 1.236331799 5.55094009 1.028381865 0.420313549 0.80287386 0.089846235 0.069261711 6.746225579 0.161003658 0.023645007 17.23184576 -1.236331799 -0.608068316 HITDSGLAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HITDSGLAAR 10 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 0 ; 160.75 7.28E-06 290940000 352590 331200 229783 280510 357390 339060 311630 373680 394210 FALSE TRUE 305994.3382 329024.3254 340906.8274 344204.0828 350278.6382 352103.8576 281408.1706 293771.44 347606.9429 0.880288338 0.946541294 0.980725024 0.99021061 1.007685967 1.01293678 0.809558544 0.845125352 1 18.40709737 2.246766707 24.99783592 0.873470358 0.971833043 0.295571406 0.060836566 194.3691657 592098.8991 0.023459477 0.017850551 176.5089401 -2.246766707 0.098362685 HITIFSPEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HITIFSPEGR 10 0 G3V5Z7;P60900;G3V3I1;G3V295;G3V3U4;G3V4S5;G3V2S7 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ;;;;; 210.08 8.38E-08 2782040000 2781510 2871820 1220270 1948590 3021520 3212360 2639760 2868880 2544760 FALSE TRUE 2413926.406 2852954.825 1810396.654 2391047.142 2961397.664 3335941.568 2383756.482 2255392.338 2243921.372 1.075762474 1.271414793 0.806800397 1.065566366 1.319742171 1.486657068 1.062317295 1.005112018 1 21.09759069 2.013369259 24.94652536 1.012159083 1.170430307 0.139825172 0.17791194 463.7278195 865295.2158 0.077785393 0.052408631 103.1262579 -2.013369259 0.158271223 HITLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 HITLDK 6 0 Q9NR45;Q5TBR0;Q5TBR1 Q9NR45 NANS Sialic acid synthase 0 ;;;;;; 160.69 0.0087319 9265830000 17880120 17135180 9154950 14003590 16255420 14963350 19946500 22767350 21714710 FALSE TRUE 15517216.84 17022617.87 13582314.44 17183319.14 15931968.95 15538999.76 18012091.5 17898729.38 19147621.72 0.810399175 0.889019959 0.709347335 0.897412712 0.832059938 0.811536805 0.940696018 0.934775589 1 24.19066187 2.19550944 5.696673261 0.954601683 0.826143575 0.580826014 0.053486352 0.132727709 10.27098345 0.020865773 0.014177237 156.8589993 -2.19550944 -0.128458108 HIVDCIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HIVDCIR 7 0 A0A087WVI0;E9PBL8;Q8WTW3 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 0 ; 98.418 0.011277 343640000 274460 276740 180175 195010 284080 291140 284400 275584 291250 FALSE TRUE 238189.4156 274922.0767 267308.2326 239290.001 278427.3638 302340.3442 256818.9318 216652.5062 256818.7568 0.927461135 1.070490645 1.040843885 0.931746591 1.08413952 1.177251802 1.000000681 0.84360079 1 17.97039105 1.98705757 24.31503839 0.913980506 1.041678071 0.258421773 0.080620626 484.0451784 909377.5877 0.035290765 0.021653652 97.0638627 -1.98705757 0.127697565 HIVNHAVVNEDPNAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HIVNHAVVNEDPNAR 15 0 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 0 ;;;; 136.17 1.42E-05 1096339000 470344 459288 300449 357567 503093 528728 455358 513613 460487 FALSE TRUE 408186.8487 456270.9069 445747.1413 438758.0524 493082.4336 549068.5083 411197.4512 403780.8569 406048.7514 1.005265617 1.123685038 1.097767546 1.080555108 1.214342937 1.352223117 1.012680004 0.994414723 1 18.63129343 2.039324334 24.99987591 0.998829361 1.145948888 0.357278059 0.090757866 168.878709 107361.5578 0.038814015 0.026168364 109.4773644 -2.039324334 0.147119527 HIYDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HIYDTK 6 0 B4DDF4;B4DUT8;Q99439;A0A087X1X5;Q99439-2 B4DDF4 CNN2 Calponin;Calponin-2 0 ;;;;; 149.06 0.010686 7825730000 19338800 19904600 12247680 15602100 16745800 16168900 21288200 24979700 22994600 FALSE TRUE 16783128.58 19773845.37 18170699.01 19144795.27 16412591.34 16790928.05 19223673.64 19637985.55 20276204.58 0.827725352 0.975224199 0.896158792 0.944200143 0.809450865 0.828110013 0.948090337 0.968523743 1 24.27328429 2.048776732 7.178991766 0.975141724 0.884858854 0.4153013 0.052341753 0.218216884 25.99836824 0.022224369 0.014832894 111.8862536 -2.048776732 -0.090282869 HIYLLPSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HIYLLPSGR 9 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ; 115.86 0.0014074 2806800000 1631070 1654810 909800 1135450 1728750 1841120 1611570 1792330 1760680 FALSE TRUE 1415519.967 1643939.444 1349782.323 1393271.277 1694351.257 1911949.078 1455280.189 1409054.177 1552534.416 0.911747883 1.058874719 0.869405734 0.897417321 1.091345377 1.231501896 0.937357764 0.907583215 1 20.56619382 4.787905364 21.02145137 0.992035072 0.911745582 0.056904928 0.108448695 18988.72591 8087793.871 0.028275357 13.60144617 61362.82759 -4.787905364 -0.08028949 HIYYITGETK ddPTM_MDA-MB-175_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 ;;;;; 219.54 1.46E-08 11021110000 23830760 20485600 12715450 17298400 20574970 16882970 23496900 27103500 23764590 FALSE TRUE 20681464.69 20351028.74 18864684.15 21226266.11 20165568.35 17532468.78 21218174.25 21307627.44 20955167.24 0.98693866 0.971169951 0.90024021 1.012937089 0.962319609 0.836665658 1.012550938 1.016819727 1 24.3208027 2.093437513 21.34731437 1.011473157 0.946110911 0.282318589 0.048612901 7.07454945 1608.024103 0.019629388 0.013234135 124.0045193 -2.093437513 -0.065362246 HKDAAIYLVTSLASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HKDAAIYLVTSLASK 15 1 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 107.61 0.00068742 310780000 616170 383540 215670 303550 381900 287760 469000 541240 307720 FALSE TRUE 534741.5733 381020.5005 319968.7334 372475.667 374300.9372 298830.3134 423516.4522 425500.0379 271341.6922 1.970731328 1.4042092 1.179209619 1.372718155 1.379444988 1.101306294 1.560823362 1.568133649 1 18.04975121 4.730229396 4.376461502 1.340020867 2.01163269 0.55457559 0.183258223 0.156559634 7.296186336 0.04564811 0.322773781 53731.55335 -4.730229396 0.671611823 HKEAYECSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HKEAYECSSR 10 1 Q9UGR2 Q9UGR2 ZC3H7B Zinc finger CCCH domain-containing protein 7B 0 64.121 0.044548 38305000 101190 108900 54298 74940 106520 116750 93777 123690 113500 FALSE TRUE 87817.48512 108184.6287 80556.69442 91956.27239 104400.4604 121241.448 84682.52097 97239.85606 100082.1593 0.877453941 1.08095818 0.804905639 0.918807838 1.043147561 1.211419187 0.846130035 0.971600301 1 16.6108253 3.252908426 24.65561634 1.00632531 0.923731442 0.147308976 0.111222206 471.5719212 810354.6564 0.032586446 0.04186408 1790.22833 -3.252908426 -0.082593868 HKEEDKNSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HKEEDKNSER 10 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ;; 237.68 2.11E-12 310434000 504880 302748 267906 283523 193758 226444 429530 472370 397450 FALSE TRUE 438158.8288 300759.2285 397466.2377 347901.2305 189902.5949 235155.4472 387874.2467 371357.3515 350463.9138 1.250225235 0.858174598 1.134114589 0.99268774 0.541860624 0.670983339 1.106745178 1.059616517 1 18.41890638 6.83446805 1.523682053 0.924452222 199.9809923 0.218011797 0.19042483 1703.519683 8.205772717 0.057563376 1181159.434 6830744.637 -6.83446805 199.0565401 HKELAPYDENWFYTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HKELAPYDENWFYTR 15 1 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ; 166.92 8.05E-07 4128400000 4969900 4460900 1610960 2346150 4197300 3625100 4172200 4742800 805580 FALSE TRUE 4313115.123 4431596.054 2390025.644 2878879.216 4113781.942 3764559.943 3767580.686 3728589.129 710345.2501 6.071857484 6.238650928 3.364597207 4.052788719 5.791242978 5.299620068 5.303872568 5.248981573 1 19.43816086 4.265522452 24.97552616 4.514472237 6.155256737 0.225759277 1.386844908 360.7497687 334166.7309 0.341705738 0.903548876 18429.87764 -4.265522452 1.640784499 HKGPPVFTQEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HKGPPVFTQEER 12 1 Q99447-3;Q99447;Q99447-4;I3L1R7;I3L2Q1 Q99447-3 PCYT2 Ethanolamine-phosphate cytidylyltransferase 0 ; 155.02 4.33E-05 177149000 333460 258250 138852 189633 275260 238020 285780 322720 287660 FALSE TRUE 289392.4161 256553.5387 206001.2916 232692.071 269782.8645 247176.7834 258065.0996 253708.8394 253653.1625 1.14089812 1.011434418 0.812137683 0.917363177 1.063589596 0.97446758 1.017393582 1.0002195 1 17.95249762 3.246550983 24.99760398 1.008405876 0.962076607 0.050375617 0.083871472 581.6420767 1819638.214 0.025364128 0.032163485 1764.212856 -3.246550983 -0.046329269 HKHEIESGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HKHEIESGR 9 1 O00178;F5H716 O00178 GTPBP1 GTP-binding protein 1 0 ;;; 145.99 5.76E-05 269648000 321265 300680 167144 235641 265407 254046 295007 328446 277904 FALSE TRUE 278809.0163 298704.8133 247975.3975 289146.8906 260125.92 263819.314 266397.2665 258210.3789 245050.5057 1.13776144 1.218952038 1.011935873 1.179948149 1.061519621 1.076591592 1.087111678 1.053702697 1 17.9027196 -1.999997801 0.041653186 0.213093276 1.640870962 0.377223665 0.054849802 1613.58722 6.611741449 182.1230575 70.02332681 0.010000051 1.999997801 1.427777686 HKLDVTSVEDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HKLDVTSVEDYK 12 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;; 149.26 3.80E-05 2448860000 6043640 4776480 3477230 4178180 4691430 3995000 6043710 7309580 6285430 FALSE TRUE 5244957.661 4745102.988 5158830.059 5126899.628 4598079.722 4148690.235 5457591.934 5746483.2 5542373.626 0.9463378 0.856149965 0.930797959 0.925036812 0.829622835 0.748540339 0.984703 1.036827105 1 22.40207254 2.020878476 24.94954165 1.01796038 0.87434613 0.553316329 0.057519131 162.1065573 193714.6753 0.024250554 0.016348051 104.9248788 -2.020878476 -0.14361425 HKMS(ph)PPPSGFGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 HKMSPPPSGFGER 13 1 A0A087WZ13;Q8IY67-2;E9PAU2;K7EQG2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER 126.63 0.0001125 4145637000 1448460 1276387 1036679 984681 1218455 1344889 1243749 1407526 1274271 TRUE FALSE 1257042.341 1268002.33 1538020.432 1208267.871 1194210.129 1396627.75 1123130.413 1106537.518 1123628.134 1.118735196 1.128489303 1.368798435 1.075327178 1.062816152 1.242962603 0.999557042 0.984789794 1 20.09973322 2.218743293 23.66584663 0.992899247 1.16485532 0.457218455 0.088022024 116.773054 139448.3607 0.036024836 0.024334508 165.4791546 -2.218743293 0.171956073 HKPGGGDVK ddPTM_MDA-MB-175_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 82.417 0.011123 229660000 238630 175610 137710 159750 129060 140760 238540 280090 231370 FALSE TRUE 207094.4409 174456.4063 204307.0166 196023.6791 126491.9585 146175.1283 215406.4275 220194.9332 204017.7022 1.015080744 0.85510426 1.001418085 0.960817013 0.620004819 0.716482573 1.055822241 1.079293271 1 17.63833481 2.205509332 24.8809588 1.052624472 0.861093941 0.330888868 0.122886843 216.2724632 162808.0548 0.053890871 0.036335954 160.5126749 -2.205509332 -0.19153053 HKS(ph)DNETNLQQQVVWGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HKSDNETNLQQQVVWGNR 18 1 A0A0U1RR27;Q7Z401;Q7Z401-2 A0A0U1RR27 DENND4A C-myc promoter-binding protein 1 HKS(0.99)DNET(0.01)NLQQQVVWGNR 197.92 1.08E-15 362180000 107020 94585 61315 82739 115960 112500 121060 155810 138730 TRUE FALSE 92877.03585 93963.66491 90967.13909 101526.1545 113652.6229 116827.9478 109319.6198 122491.244 122329.4974 0.759236634 0.768119439 0.743623909 0.829940093 0.929069646 0.955026794 0.893648892 1.001322221 1 16.9004128 3.325158402 1.855512215 0.96339742 0.755583277 0.903008044 0.030331842 0.099542437 0.705341785 0.010616276 0.014920024 2114.260044 -3.325158402 -0.207814144 HKS(ph)ESPCESPYPNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HKSESPCESPYPNEK 15 1 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H0Y594;B7ZBA0;B7ZB98 Q8NI27 THOC2 THO complex subunit 2 1 HKS(0.361)ES(0.361)PCES(0.277)PYPNEK 58.831 0.066843 84010000 65415 42275 26804 40266 55663 47166 58141 68814 108360 TRUE FALSE 56770.24201 41997.29274 39766.50405 49409.01073 54555.4152 48980.50654 52502.49477 54098.66161 95549.80424 0.594142944 0.439533007 0.416186138 0.517102166 0.570963129 0.51261755 0.549477785 0.566182862 1 16.5439653 1.159467495 2.59557268 1.191860636 0.510251449 0.884249505 0.054688225 0.225183008 1.40576587 0.373704011 0.014870895 14.43668548 -1.159467495 -0.681609187 HKSDFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HKSDFGK 7 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 ; 123.72 0.0025333 5039100000 14609300 15656400 3846000 11095700 15425200 20522000 18403200 19526300 12712600 FALSE TRUE 12678643.99 15553552.08 5705938.464 13615148.27 15118268.7 21311494.62 16618460.5 15350752.7 11209730.91 1.131039103 1.3875045 0.509016542 1.214582971 1.34867365 1.901160232 1.482503071 1.369413131 1 23.41824831 3.333417837 3.688074784 1.444682967 1.024869282 0.269398906 0.305134888 0.304771408 7.976273254 0.092486665 0.120486149 2154.853936 -3.333417837 -0.419813685 HKSDSPES(ph)DAEREK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HKSDSPESDAEREK 14 2 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 HKSDS(0.02)PES(0.98)DAEREK 82.707 0.0051989 127510000 300170 269990 67391 142300 294170 190350 277370 405750 129660 TRUE FALSE 260501.774 268216.4179 99981.51301 174611.3899 288316.5925 197672.8877 250470.7001 318983.5201 114331.7425 2.278472874 2.345948833 0.874486042 1.527234573 2.521754556 1.728941441 2.190736313 2.789982144 1 16.80286648 3.255387109 24.98443401 2.134212333 1.735633023 0.040236822 0.622384771 652.5932799 968982.4588 0.181303686 0.233423055 1800.475056 -3.255387109 -0.39857931 HLAAVEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLAAVEER 8 0 Q92922;F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 Q92922;F8VXC8 SMARCC1;SMARCC2 SWI/SNF complex subunit SMARCC1;SWI/SNF complex subunit SMARCC2 0 ; 103.56 0.0047486 542100000 279877 203542 154970 153905 209550 205110 175339 217356 214351 FALSE TRUE 242890.5453 202204.9192 229914.0103 188851.4825 205380.365 213000.7144 158334.6508 170876.1109 189010.669 1.285062619 1.069806907 1.21640758 0.999157791 1.086607259 1.126924293 0.837702187 0.904055373 1 17.52810815 3.770864882 0.296599573 0.840653109 1.381712749 0.546579519 0.090177765 3.913027493 0.830325244 0.413375369 1.014522085 5900.174851 -3.770864882 0.541059641 HLAEVLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLAEVLER 8 0 Q5VTR2 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 0 140.14 0.00065434 114200000 89800 82154 53113 59096 73115 82969 79074 80351 105410 FALSE TRUE 77932.70248 81614.32496 78798.62445 72514.65003 71660.15455 86160.87112 71405.41565 63168.56394 92948.54988 0.838449901 0.878059153 0.847766044 0.780159025 0.770965815 0.926973807 0.768225171 0.679607848 1 16.50414474 3.892890599 5.848773551 0.80545639 0.859329329 0.012157298 0.089732017 0.692117725 31.78332594 0.023996141 0.042444214 7814.309341 -3.892890599 0.05387294 HLAEYTHVEAECPFLTFDDLLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLAEYTHVEAECPFLTFDDLLNR 23 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 214.26 1.67E-32 403400000 180847 114536 94707 119670 127496 120457 117155 148510 201437 FALSE TRUE 156947.6107 113783.6055 140507.622 146842.9025 124959.079 125091.0587 105793.3261 116752.2922 177623.3473 0.883597866 0.640589242 0.791042529 0.826709466 0.703505935 0.704248966 0.595604844 0.657302624 1 17.4384617 3.209166816 24.29088932 0.711144956 0.775532113 0.027349981 0.121353089 474.286549 391945.946 0.03640102 0.041282142 1618.701676 -3.209166816 0.064387157 HLAGEVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HLAGEVAK 8 0 Q13200;Q13200-3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;; 105.57 0.0043629 1023680000 1786120 1586180 989434 1307140 1483470 1372760 1752380 2066770 1931420 FALSE TRUE 1550079.717 1575760.279 1467927.592 1603946.115 1453951.849 1425570.965 1582434.457 1624807.319 1703089.728 0.910157399 0.925236206 0.86192029 0.941786031 0.853714179 0.837049829 0.929155071 0.954035065 1 20.69972302 1.668036508 2.101319397 0.994443952 0.890075575 0.546893666 0.033574925 0.241752251 2.162181691 0.038866142 0.009587915 46.56252339 -1.668036508 -0.104368378 HLAGLGLTEAIDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLAGLGLTEAIDK 13 0 P50454;E9PKH2 P50454 SERPINH1 Serpin H1 0 ; 193.73 1.62E-06 2339800000 4153900 3774200 3181300 4192700 4118400 4533800 4253700 4764100 5190600 FALSE TRUE 3604951.59 3749407.032 4719787.321 5144716.616 4036451.898 4708218.22 3841176.829 3745334.289 4576973.181 0.78762786 0.819189207 1.031202748 1.124043426 0.881904206 1.028675073 0.839239532 0.818299374 1 22.12596241 4.366867389 7.019430359 0.946506938 0.795877172 0.316883529 0.094611072 0.287268504 16.28554101 0.026005125 0.069842717 23273.80486 -4.366867389 -0.150629767 HLAGVEDLLQLHELVEADIAVQAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLAGVEDLLQLHELVEADIAVQAER 25 0 O15020;O15020-2;A4QPE4 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 ; 126.46 7.60E-05 34941000 40924 39346 25825.2 38099 45081 51033 40135 47917 44094 FALSE TRUE 35515.78971 39087.53354 38314.3531 46749.96026 44183.9763 52996.27253 36242.71388 37670.32244 38881.25755 0.913442413 1.005305281 0.985419596 1.202377783 1.136382388 1.363028767 0.932138417 0.968855557 1 15.24678726 3.964580196 22.13042504 1.089073306 0.96837084 0.196341717 0.125398854 291.3673185 182048.2255 0.036583423 0.063430182 9216.800689 -3.964580196 -0.120702466 HLAGYESSSTLMTSELESTSLGDS(ph)DEEDTMSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLAGYESSSTLMTSELESTSLGDSDEEDTMSR 32 0 I3L0M7;I3L2W9;I3L2N2;O14641 I3L0M7 DVL2 Segment polarity protein dishevelled homolog DVL-2 1 HLAGYESSSTLMTSELES(0.01)T(0.032)S(0.092)LGDS(0.842)DEEDT(0.012)MS(0.012)R 50.865 0.047036 33841000 12886 14194 6784.8 10199 11646 12436 11294 15192 14086 TRUE FALSE 11183.08245 14100.75868 10065.95197 12514.83883 11414.26739 12914.42097 10198.70962 11943.30902 12420.76913 0.900353459 1.135256483 0.810412936 1.007573581 0.918966231 1.039744064 0.821101295 0.961559538 1 13.60046689 4.243282563 24.99995906 0.938568133 1.017804881 0.115582622 0.09279428 239.6985842 1269022.371 0.021062658 0.052049522 17509.85552 -4.243282563 0.079236748 HLAQVGDSMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HLAQVGDSMDR 11 0 P55957;P55957-2 P55957 BID BH3-interacting domain death agonist;BH3-interacting domain death agonist p15;BH3-interacting domain death agonist p13;BH3-interacting domain death agonist p11 0 ;;; 136.7 9.38E-05 2494770000 1419350 1464580 797960 1044720 1389890 1527440 1379040 1475540 1413180 FALSE TRUE 1231779.301 1454959.078 1183856.125 1281939.644 1362233.908 1586201.605 1245300.913 1160007.254 1246115.47 0.988495313 1.16759571 0.950037258 1.028748679 1.093184332 1.272917031 0.999346323 0.930898686 1 20.24900633 2.014156783 24.99986951 0.961896164 1.083948511 0.238097316 0.091466181 300.2287835 530180.6806 0.037466749 0.025247588 103.3134307 -2.014156783 0.122052347 HLCEPGADGAETFADGVPR ddPTM_MDA-MB-175_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 ;;; 306.07 1.53E-50 1523590000 874740 887100 484734 591808 897450 871330 787960 919700 828610 FALSE TRUE 759140.8927 881272.5817 719152.9837 726187.0516 879592.5008 904850.6289 711543.7605 723029.3121 730652.6698 1.038990103 1.206144339 0.984261077 0.993888179 1.203844915 1.238414183 0.973846795 0.989566373 1 19.47882623 2.170172426 24.99997738 0.987589039 1.108402046 0.304201317 0.087721436 67.43181297 24649.06782 0.037178709 0.025065886 147.9695749 -2.170172426 0.120813007 HLDGEEDGS(ph)SDQSQASGTTGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLDGEEDGSSDQSQASGTTGGR 22 0 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 1 HLDGEEDGS(0.5)S(0.5)DQSQASGTTGGR 219.34 7.13E-26 572590000 213550 201260 74183 154360 221860 178410 173340 251570 192520 TRUE FALSE 185328.8264 199937.9098 110058.1469 189409.7972 217445.4201 185273.5481 156529.5135 197773.7132 169760.5049 1.091707559 1.17776458 0.648314206 1.115747136 1.280895225 1.091381934 0.922060838 1.165016052 1 17.37314133 HLDGEEDGSS(ph)DQSQASGTTGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLDGEEDGSSDQSQASGTTGGR 22 0 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 1 HLDGEEDGS(0.048)S(0.952)DQSQASGTTGGR 253.77 3.17E-37 585740000 99390 96306 54884 68795 99996 74586 73484 117450 81149 TRUE FALSE 86255.35968 95673.35954 81426.08598 84415.95622 98006.27524 77455.37168 66357.53299 92334.2315 71555.65767 1.205430325 1.337048148 1.137940571 1.179724413 1.36965096 1.082449302 0.927355504 1.290383381 1 16.12677822 2.701053959 24.89056914 1.094847227 1.241338715 0.351172652 0.11393898 701.9476743 465833.395 0.038790869 0.034211103 502.4050067 -2.701053959 0.146491488 HLDHVAALFPGDVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HLDHVAALFPGDVDR 15 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;;;; 134.24 2.10E-05 2210849000 1747649 1468892 865407 1025674 1503463 1559609 1340041 1570719 1553987 FALSE TRUE 1516692.757 1459242.752 1283920.72 1258568.958 1473547.028 1619608.167 1210084.03 1234832.965 1370276.427 1.106851674 1.064925823 0.936979353 0.91847815 1.075364794 1.181957257 0.883094831 0.901156103 1 20.38603553 0.779015389 0.026702942 1.77E-05 1.875224061 0.103504128 0.093598504 3915.267921 23.24686447 934.2009003 711.1753546 6.011950398 -0.779015389 1.875206386 HLDLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLDLEK 6 0 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZHJ1;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZGZ8 P55263-3 ADK Adenosine kinase 0 126.24 0.017575 322630000 623900 571140 387680 549080 571750 465130 618580 726440 843040 FALSE TRUE 541450.0342 567388.1437 575163.3447 673757.0062 560373.2936 483023.8521 558590.2068 571096.4592 743376.7716 0.728365554 0.763257833 0.773717133 0.906346596 0.753821366 0.649769902 0.751422735 0.768246307 1 19.50373408 1.238526666 6.734055662 1.005882172 0.762428502 0.591117029 0.062261132 0.088106882 20.60107722 0.098151154 0.01619974 17.31915369 -1.238526666 -0.243453671 HLDQIIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLDQIIPR 8 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 120.87 0.0014576 559420000 271880 242550 157581 170491 272760 339270 256960 281260 266040 FALSE TRUE 235950.3691 240956.6731 233787.6987 209203.5873 267332.6096 352321.9364 232040.0588 221114.7378 234589.0543 1.005802977 1.027143717 0.996584003 0.891787505 1.13957836 1.501868608 0.989134209 0.942562041 1 17.83977617 3.2204399 24.95515799 1.103070245 0.984834423 0.151217623 0.156619259 586.6171029 807864.272 0.05267892 0.059848434 1661.268767 -3.2204399 -0.118235822 HLDQQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLDQQEK 7 0 P07476 P07476 IVL Involucrin 0 100.15 0.010006 57254000 96391 82078 55169 70118 55845 76981 98189 103250 114750 FALSE TRUE 83652.68513 81538.82421 81848.91293 86039.36359 54733.79376 79942.50888 88666.64589 81170.79099 101184.3857 0.826735119 0.805843942 0.808908532 0.850322537 0.540931225 0.79006764 0.876287831 0.802206688 1 16.62662715 -0.512887494 1.064977795 9.999999869 0.775856312 0.35340037 0.090998964 81.39314007 2.807002768 1713.783909 0.029304765 0.306981714 0.512887494 -9.224143557 HLDRS(ph)PESDRPR ddPTM_MDA-MB-175_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(0.997)PES(0.003)DRPR;HLDRS(1)PESDRPR;HLDRS(0.997)PES(0.003)DRPR;HLDRS(0.999)PES(0.001)DRPR;HLDRS(1)PESDRPR 172.91 1.80E-05 7106760000 3831979 3076149 1503958 1977103 2872412 2943544 2685243 3157083 2033769 TRUE FALSE 3325573.266 3055941.575 2231277.119 2426034.454 2815256.621 3056784.042 2424828.547 2481965.369 1793339.146 1.854402874 1.704051117 1.244202539 1.352802932 1.569840611 1.704520893 1.352130495 1.383991073 1 20.77421692 0.734643592 1.030980526 5.66E-12 1.548829174 0.477465588 0.182549268 4.667940472 1.913890146 10.31707799 0.063236017 5.428046906 -0.734643592 1.548829174 HLDSSSNERPDISSIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HLDSSSNERPDISSIQR 17 1 P49902-2;P49902;Q5JUV6 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;;; 278.34 4.78E-36 16054000000 33921 12560 0 24423 0 0 37146 14950 9995.9 FALSE TRUE 29438.25391 12477.49253 0 29968.61543 0 0 33543.58664 11753.05884 8814.196089 3.339868277 1.415613223 0 3.400039564 0 0 3.805631994 1.3334238 1 13.10561328 4.73856997 15.57476977 1.415809753 3.339999051 0.178163589 1.326719236 0.089080887 12715.35597 0.311885632 1.737651859 54773.43403 -4.73856997 1.924189298 HLDVDLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLDVDLDR 8 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 0 ; 117.89 0.0039768 294890000 186533 171512 109205 127036 169191 198710 161952 189233 213160 FALSE TRUE 161882.1914 170385.3264 162016.9033 155881.4654 165824.4301 206354.5023 146245.92 148766.9956 187960.4676 0.86125659 0.906495544 0.861973293 0.829331122 0.882230355 1.097861188 0.778067441 0.791480238 1 17.52006974 5.123111356 12.94403981 0.883155438 0.000790044 0.000908911 0.096084684 880938.7734 1072830.952 0.023759232 22329904.08 132773.4854 -5.123111356 -0.882365394 HLDVDLDRQS(ph)LSS(ph)IDKNPSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLDVDLDRQSLSSIDKNPSER 21 2 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 2 HLDVDLDRQS(0.989)LS(0.091)S(0.92)IDKNPSER 102.27 0.0002498 447230000 379850 285810 234280 220590 346680 332030 339420 346830 421860 TRUE FALSE 329651.8601 283932.4953 347578.5916 270678.331 339781.7463 344803.409 306503.1006 272663.1035 371988.1914 0.886189045 0.763283625 0.934380713 0.72765302 0.913420786 0.926920308 0.823959222 0.7329886 1 18.5048973 HLDVDLDRQS(ph)LSSIDKNPSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HLDVDLDRQSLSSIDKNPSER 21 2 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 HLDVDLDRQS(0.994)LS(0.005)S(0.001)IDKNPSER;HLDVDLDRQS(0.928)LS(0.063)S(0.009)IDKNPSER;HLDVDLDRQS(0.954)LS(0.039)S(0.007)IDKNPSER 215.46 3.42E-25 1982870000 1506180 1087030 944650 886910 1199290 1134590 1253360 1368030 1409040 TRUE FALSE 1307134.497 1079889.228 1401485.9 1088296.471 1175426.475 1178238.411 1131809.34 1075487.431 1242464.896 1.052049439 0.869150695 1.127988327 0.875917279 0.946044012 0.948307204 0.910938686 0.865607901 1 20.24477366 HLEAADKGHS(ph)PAQKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HLEAADKGHSPAQKPK 16 2 Q14966;Q14966-3;Q14966-4;A0A096LPI0;Q14966-2;Q14966-6;A0A096LPB4 Q14966 ZNF638 Zinc finger protein 638 1 HLEAADKGHS(1)PAQKPK;HLEAADKGHS(1)PAQKPK;HLEAADKGHS(1)PAQKPK 246.22 1.67E-20 1777240000 3478820 2073060 1889140 1646690 1780020 1313920 3218710 3225130 2026570 TRUE FALSE 3019085.123 2059441.932 2802734.423 2020596.133 1744601.085 1364467.353 2906560 2535461.047 1786991.203 1.689479566 1.152463386 1.568409748 1.130725282 0.976278496 0.763555719 1.626510525 1.418843609 1 20.7691011 7.359775153 1.119726294 1.213540852 199.9996195 0.231528225 0.271288472 1266.052481 4.814155534 0.084694388 642469.4914 22896819.11 -7.359775153 198.7860786 HLEEAFTSEHWLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HLEEAFTSEHWLVR 14 0 Q8TCJ2 Q8TCJ2 STT3B Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B 0 ;; 275.85 2.55E-33 256270000 54996 51323 32527 47158 62420 69810 33905 71771 60873 FALSE TRUE 47728.13926 50985.85583 48257.166 57865.94466 61177.96412 72495.63587 30616.89832 56423.33017 53676.66329 0.88917858 0.949870069 0.899034386 1.078046606 1.13974976 1.350598779 0.570394962 1.051170597 1 15.71200737 3.752372693 23.52785749 1.022656233 0.916411903 0.07713215 0.192167468 1193.383087 2032826.938 0.051679141 0.088827134 5654.219883 -3.752372693 -0.10624433 HLEEIVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLEEIVEK 8 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 99.139 0.0070255 220110000 773170 720930 457970 652880 756720 634140 667840 984350 803060 FALSE TRUE 670993.6255 716194.1634 679445.8238 801126.3826 741662.7525 658535.7761 603072.9796 773854.4127 708123.1616 0.947566274 1.011397737 0.95950233 1.131337635 1.047364064 0.929973502 0.851649843 1.092824603 1 19.43364078 4.486858757 0.004776983 1.176844918 0.820281608 0 0.081316975 2080701.947 3249.536063 119301.2362 123271.7324 30680.24032 -4.486858757 -0.356563311 HLEEQEGQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLEEQEGQLK 10 0 P07476 P07476 IVL Involucrin 0 ; 119.27 0.00071409 809980000 1446360 1350440 924650 1143250 1289370 1234310 1582000 1669830 1656450 FALSE TRUE 1255219.861 1341568.871 1371813.833 1402842.386 1263714.06 1281794.704 1428577.883 1312749.849 1460626.368 0.859370944 0.918488739 0.939195583 0.960438903 0.865186393 0.877565086 0.978058397 0.898758148 1 20.47815575 -0.206915008 1.675026892 10 0.912946913 0.313853568 0.039703542 175.8340253 5.712125047 5967.796686 0.010891502 0.620990551 0.206915008 -9.087053087 HLEFSHDQYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 HLEFSHDQYR 10 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;;;;;;; 215.87 4.62E-09 34584870000 1581502 1444973 811674.3 941562 1448627 1414924 1279592 1673094 1292072 FALSE TRUE 1372502.504 1435480.877 1204202.706 1155358.043 1419802.157 1469357.042 1155497.365 1315315.868 1139324.72 1.204663148 1.259940078 1.056944245 1.014072654 1.246178663 1.289673625 1.014194939 1.1544697 1 20.11974756 0.134924556 0.945067603 5.10E-08 1.163054449 0.19693054 0.099338152 26.61342492 3.669281929 51.69381284 0.03469345 1.364346107 -0.134924556 1.163054398 HLEGLSEEAIMELNLPTGIPIVYELDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 HLEGLSEEAIMELNLPTGIPIVYELDK 27 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;;;;;; 216.51 3.66E-34 5021716000 5260653 4378977 2894823 3684776 4236391 3782432 5260726 6089141 5660521 FALSE TRUE 4565444.377 4350211.212 4294769.085 4521460.709 4152095.107 3927944.607 4750541.602 4787025.583 4991340.656 0.914672969 0.871551655 0.860443993 0.905860974 0.831859693 0.786951819 0.951756638 0.959066093 1 22.25099594 2.081858636 8.288700215 0.970300096 0.863000136 0.658452909 0.037053676 0.158845116 14.1817918 0.015673269 0.010546036 120.7420752 -2.081858636 -0.10729996 HLEHPEQQDGQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HLEHPEQQDGQLK 13 0 P07476 P07476 IVL Involucrin 0 ;; 101.39 0.0011367 784850000 446200 431120 296624 393973 436460 401488 534350 572770 561650 FALSE TRUE 387233.5395 428287.9443 440072.3585 483430.5912 427775.2999 416933.5032 482528.8192 450287.5928 495252.3768 0.78189133 0.864787257 0.888582022 0.976129775 0.863752139 0.841860681 0.974308942 0.909208343 1 18.91780437 6.026628531 0.715487602 0.927030068 6.98E-19 0.466993661 0.049525742 14.89919651 1.401122268 0.019500433 16.90043757 1063233.204 -6.026628531 -0.927030068 HLEIIYAINQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLEIIYAINQR 11 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 149.23 3.45E-05 726290000 806530 685890 428170 504670 624860 643710 698260 786110 707230 FALSE TRUE 699945.017 681384.3434 635234.4441 619263.0369 612426.5085 668473.9402 630542.8527 618006.494 623622.0751 1.12238653 1.092623835 1.018620844 0.993010128 0.982047514 1.071921548 1.011097711 0.990995218 1 19.25031247 4.29207549 3.037195264 1.00774787 1.117657037 0.740295032 0.024482833 0.127295352 2.311993286 0.006627528 0.020982151 19591.85192 -4.29207549 0.109909166 HLEINPDHPIVETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 HLEINPDHPIVETLR 15 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;; 244.36 2.88E-18 31653300000 7296410 6206678 3533838 4488501 5827662 6333812 5136024 6720330 8141150 FALSE TRUE 6332170.932 6165905.924 5242813.877 5507683.754 5711702.928 6577477.846 4637933.183 5283239.727 7178712.521 0.882076126 0.858915287 0.730327877 0.767224448 0.795644471 0.916247562 0.646067546 0.735959228 1 22.77529369 4.397630433 7.716354601 0.788052576 0.876358136 0.077695129 0.09893554 0.476762874 38.98846592 0.024353124 0.065153939 24982.18576 -4.397630433 0.08830556 HLEINPDHSIIETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 HLEINPDHSIIETLR 15 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;; 268.93 5.39E-26 46452400000 5757520 4922690 3261534 4203549 5172700 5389700 4943260 5855310 7095850 FALSE TRUE 4996649.144 4890352.525 4838822.752 5158029.048 5069773.39 5597045.247 4463863.406 4603197.523 6256986.697 0.798571163 0.781582695 0.773347138 0.824363116 0.810257978 0.894527273 0.713420632 0.735689198 1 22.57703661 3.490589142 0.01143471 1.598322678 3.29E-07 0.064481428 0.079228768 12558.05851 118.3449982 8162.867147 8376.244804 3094.490418 -3.490589142 -1.598322348 HLEPEPEEEIIAEDYDDDPVDYEATR ddPTM_MDA-MB-175_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 0 179.38 2.31E-17 102250000 66220 59934 35790 47022 62992 68373 50621 59758 63169 FALSE TRUE 57468.85922 59540.28961 53098.16371 57699.06379 61738.58244 71003.35355 45711.78321 46979.21674 55701.23278 1.031734063 1.068922295 0.953267299 1.035866908 1.10838808 1.274717812 0.820660171 0.843414309 1 15.76542164 2.204635254 24.99999163 0.875924008 1.072051792 0.477272486 0.093662668 158.8623547 117066.4718 0.039442447 0.026593685 160.1899458 -2.204635254 0.196127783 HLEQQEGQLEHLEHQEGQLGLPEQQVLQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLEQQEGQLEHLEHQEGQLGLPEQQVLQLK 30 0 P07476 P07476 IVL Involucrin 0 113.6 5.57E-05 338860000 103560 117480 84418 96848 110020 108650 114580 140390 148620 FALSE TRUE 89874.28361 116708.2661 125242.8272 118838.8186 107830.8173 112829.8358 103468.0492 110368.691 131050.3129 0.68579984 0.890560759 0.955685068 0.906818275 0.822819991 0.860965787 0.789529204 0.842185635 1 16.99976127 4.741241049 24.29345161 0.876304415 0.685799737 0.498684918 0.061937345 157.1070055 1423780.689 0.015668541 0.104199482 55111.34989 -4.741241049 -0.190504678 HLEQQEGQLEQLEEQEGQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HLEQQEGQLEQLEEQEGQLK 20 0 P07476 P07476 IVL Involucrin 0 ;;; 256.49 3.45E-36 926590000 718700 618860 476490 577120 611710 550180 822390 843870 819240 FALSE TRUE 623721.974 614794.6679 706922.1578 708163.9167 599538.1678 571345.7806 742634.7444 663414.9675 722390.3805 0.863414008 0.851056 0.978587446 0.980306405 0.829936533 0.790910007 1.028024133 0.918360744 1 19.46241916 2.220823483 24.99630681 0.970755689 0.887387132 0.335615717 0.065264187 350.1689381 493476.8535 0.02810828 0.018996624 166.27367 -2.220823483 -0.083368556 HLEQQEGQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HLEQQEGQLK 10 0 P07476 P07476 IVL Involucrin 0 ;;; 186.74 1.31E-06 2309350000 3574860 3121530 2893490 3429390 3250310 3149000 3948280 4310820 6203670 FALSE TRUE 3102433.193 3101024.464 4292791.442 4208085.414 3185635.19 3270144.068 3565376.413 3388984.69 5470279.2 0.567143482 0.566885958 0.784748143 0.76926337 0.582353308 0.59780204 0.651772292 0.619526822 1 22.38318304 1.236098534 24.90690756 1.00000049 0.644577725 0.677961081 0.077434918 40.59195915 410541.9116 0.130645794 0.019904553 17.22259283 -1.236098534 -0.355422765 HLEQQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HLEQQEK 7 0 P07476 P07476 IVL Involucrin 0 ;; 130.27 0.0035794 793120000 1702860 1480740 1062420 1301740 941980 1341040 1795790 1909290 2030030 FALSE TRUE 1477822.737 1471012.921 1576209.866 1597319.963 923236.441 1392630.677 1621634.562 1501003.192 1790042.166 0.825579846 0.82177557 0.880543428 0.892336501 0.515762398 0.777987638 0.905919756 0.838529516 1 20.77156214 0.952445304 1.158216212 1.217516449 0.793354382 0.250058827 0.109044609 4.545597027 3.220608748 2.767982796 0.035555089 8.962832979 -0.952445304 -0.424162067 HLFLTSKPMVYLVNLSEKDYIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLFLTSKPMVYLVNLSEKDYIR 22 2 J3KQ32;Q9NTK5;Q9NTK5-3;Q9NTK5-2;C9JCJ9 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 253.83 2.94E-37 468510000 869620 738090 290910 421100 584080 460250 834180 1015440 168587 FALSE TRUE 754697.5137 733241.4382 431595.049 516717.1911 572457.9507 477956.1153 753281.352 798296.0582 148656.8369 5.076776348 4.932443427 2.903297675 3.475905998 3.850868636 3.215164033 5.067249967 5.370059492 1 17.18162629 4.354958202 8.826060632 3.794439249 5.037206685 0.179417984 1.208724532 0.490537484 35.30921066 0.3065369 0.81458008 22644.26361 -4.354958202 1.242767437 HLFQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLFQEK 6 0 P25325-2;P25325;F8WB46;F8WBS0;C9JJV8;B4DKT6;Q07001-2;Q07001 P25325-2 MPST;CHRND 3-mercaptopyruvate sulfurtransferase;Acetylcholine receptor subunit delta 0 83.614 0.056787 399260000 494230 485760 326210 383890 488260 476610 588110 627180 539930 FALSE TRUE 428916.2533 482569.0106 483966.2471 471058.0919 478544.5813 494945.4951 531075.1827 493062.4377 476100.0905 0.900895131 1.013587311 1.016522065 0.989409793 1.005134405 1.039582863 1.115469611 1.035627692 1 18.86090538 6.402593106 0.618563979 1.042796066 6.24E-17 0.554643321 0.035233068 19.72075658 1.114080117 0.017255177 22.81263999 2526929.389 -6.402593106 -1.042796066 HLFS(ph)STENLAAGSWK ddPTM_MDA-MB-175_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(0.246)T(0.377)ENLAAGSWK;HLFS(0.599)S(0.381)T(0.02)ENLAAGSWK 257.15 5.72E-25 3246860000 2395430 1832260 1662720 2339260 2316500 2098960 2170280 2848140 4939500 TRUE FALSE 2078867.856 1820223.763 2466816.953 2870424.736 2270406.182 2179708.349 1959806.58 2239087.425 4355557.937 0.477290828 0.417908289 0.566360726 0.659025727 0.52126644 0.50044297 0.449955346 0.514075913 1 22.05442611 1.238613098 13.79637403 1.000248229 0.513422596 0.844779489 0.065565452 0.020419255 502.8033029 0.095688845 0.017198146 17.32260081 -1.238613098 -0.486825634 HLFS(ph)STENLAAGSWKEPAEGGGLSSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.333)S(0.333)T(0.333)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.522)S(0.403)T(0.076)ENLAAGSWKEPAEGGGLSSDR 224.58 1.12E-34 735991000 1129210 988110 447788 566200 927710 1034390 1072480 1316860 269667 TRUE FALSE 979982.0374 981619.0403 664339.7746 694764.3638 909250.386 1074183.653 968471.0547 1035259.737 237787.2745 4.121255183 4.1281395 2.793840739 2.921789509 3.823797502 4.517414378 4.072846442 4.353722205 1 17.85931198 4.37964712 23.43484143 3.52094367 4.125718212 0.072484468 1.017931625 25.23653551 6024.936386 0.253402685 0.670440705 23968.84574 -4.37964712 0.604774541 HLFSS(ph)TENLAAGSWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLFSSTENLAAGSWK 15 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 HLFSS(0.987)T(0.012)ENLAAGSWK 307.02 2.93E-45 976890000 1874000 1383400 1320500 1768800 1711800 1705200 1616100 2109500 3720100 TRUE FALSE 1626346.152 1374312.354 1959098.217 2170433.074 1677738.529 1770800.147 1459370.871 1658399.841 3280314.016 0.495789776 0.418957559 0.597228865 0.661654056 0.511456684 0.539826413 0.444887552 0.505561307 1 21.6454025 1.237419495 24.9987562 1.000000571 0.521277582 0.824928634 0.069214746 12.22026656 267590.6231 0.107050129 0.01789845 17.27505722 -1.237419495 -0.478722989 HLFSS(ph)TENLAAGSWKEPAEGGGLSSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HLFSSTENLAAGSWKEPAEGGGLSSDR 27 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 HLFS(0.005)S(0.968)T(0.027)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.162)S(0.791)T(0.047)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.019)S(0.884)T(0.097)ENLAAGSWKEPAEGGGLSSDR 295.2 7.70E-71 2028980000 2062060 1759720 816195 1011539 1882080 1855460 2027680 2503300 579720 TRUE FALSE 1789553.546 1748160.283 1210909.632 1241224.39 1844630.29 1926840.747 1831035.906 1967988.776 511186.162 3.500786366 3.419811437 2.368823184 2.42812596 3.608529392 3.769352322 3.581935588 3.849847515 1 18.96348926 3.218869411 24.96748531 3.309793329 2.924376449 0.001505737 0.890312803 919.458854 1165825.486 0.269313538 0.305780783 1655.272163 -3.218869411 -0.38541688 HLFSST(ph)ENLAAGSWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLFSSTENLAAGSWK 15 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 HLFS(0.05)S(0.396)T(0.554)ENLAAGSWK 195.97 3.37E-08 592330000 621190 524110 403770 611600 595470 596090 544410 711830 1282500 TRUE FALSE 539098.1676 520667.0869 599034.5225 750473.1277 583621.312 619021.968 491613.202 559610.694 1130884.311 0.476704967 0.46040703 0.529704512 0.663616181 0.516075169 0.547378686 0.434715733 0.49484345 1 20.10901992 1.23711146 24.99988452 1.000000591 0.515058022 0.857618912 0.062049197 13.9795348 241078.9978 0.098104808 0.016050254 17.2628088 -1.23711146 -0.48494257 HLFTGPVLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLFTGPVLSK 10 0 P16930;H0YLC7 P16930 FAH Fumarylacetoacetase 0 ; 185.96 1.39E-06 456940000 1111890 1110100 664550 847730 1138290 990920 1189730 1458780 1395640 FALSE TRUE 964950.9193 1102807.68 985928.6028 1040220.053 1115640.256 1029041.334 1074350.168 1146831.249 1230649.029 0.7840992 0.896118758 0.801145233 0.845261345 0.906546245 0.836177748 0.872994771 0.931891402 1 20.23098795 -2 0.54077743 7.880573555 0.837322208 0.676826081 0.036161112 74.5163258 0.738632577 605.6031986 0.019762259 0.01 2 -7.043251347 HLIEQDFPGMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HLIEQDFPGMR 11 0 A0A024R571;Q9H4M9;C9JC03;C9JIJ3;C9IZH1 A0A024R571 EHD1 EH domain-containing protein 1 0 ;; 149.23 0.00013427 358090000 1036820 915450 538030 690020 887640 918960 919670 982050 962870 FALSE TRUE 899801.61 909436.3487 798223.1076 846699.5873 869977.7006 954312.9858 830480.545 772046.2498 849040.6055 1.05978631 1.071134105 0.940147152 0.997242749 1.02465971 1.123989806 0.978139961 0.90931605 1 19.69547403 2.009699599 24.93452897 0.946844806 1.032758047 0.309053178 0.05234932 213.580768 549044.7934 0.021929276 0.014764985 102.2585426 -2.009699599 0.085913241 HLIPAANTGESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HLIPAANTGESK 12 0 P62258;P62258-2 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;;; 192.68 3.77E-06 5748370000 10179920 8777030 6429370 8889750 8909450 7559410 10113780 12050700 14792100 FALSE TRUE 8834617.779 8719373.112 9538634.837 10908303.61 8732169.376 7850225.394 9132947.172 9473751.584 13043394.79 0.677325031 0.66848955 0.731300017 0.836308629 0.669470603 0.601854465 0.700197097 0.726325603 1 23.63681607 1.227484521 3.817183303 1.041012552 0.699458801 0.716091949 0.059322549 0.163340394 3.840228889 0.161320783 0.016069337 16.88435681 -1.227484521 -0.341553752 HLIPMNPNDDSLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLIPMNPNDDSLFK 14 0 Q14651;C9JAM8 Q14651 PLS1 Plastin-1 0 ; 136.3 2.79E-05 996060000 1030000 1034340 682560 745850 955040 865110 1174910 1252670 1157930 FALSE TRUE 893882.8903 1027545.352 1012648.299 915206.6421 936036.5725 898391.3415 1060967.409 984796.2688 1021040.835 0.87546243 1.006370478 0.991780412 0.896346758 0.916747441 0.879877975 1.039103798 0.964502335 1 19.96160913 2.233846225 24.99997919 0.995135503 0.932318254 0.351887025 0.046468299 155.3080818 823572.6759 0.018934645 0.013237315 171.3350536 -2.233846225 -0.062817248 HLIYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLIYYR 6 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 69.439 0.0935 291000000 316680 368730 199480 246540 338180 405130 300050 388920 346130 FALSE TRUE 274829.9356 366307.7884 295949.1952 302520.6751 331450.8796 420715.6133 270951.1972 305752.4846 305210.9057 0.900459094 1.200179225 0.96965472 0.991185667 1.085973251 1.378442269 0.887750707 1.001774441 1 18.21944699 HLKS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLKSPVR 7 1 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9;A0A0C4DGI9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 HLKS(1)PVR 63.216 0.048914 171430000 100790 130780 95146 118160 130570 118050 122670 171560 215450 TRUE FALSE 87470.34613 129920.8976 141158.9238 144990.034 127971.9125 122591.4599 110773.4823 134873.2291 189979.7464 0.460419322 0.683867096 0.743020909 0.763186796 0.673608186 0.645286996 0.583080483 0.709934778 1 17.5354861 1.249273728 3.852415578 1.036660038 0.659487379 0.623502574 0.084529693 0.169558312 4.17382508 0.179436761 0.021727935 17.75308074 -1.249273728 -0.377172659 HLLIGVSSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLLIGVSSDR 10 0 P36542-2;P36542 P36542-2 ATP5C1 "ATP synthase subunit gamma, mitochondrial" 0 133.23 0.00020274 563820000 189410 165010 91272 166890 199040 235980 159930 190710 187090 FALSE TRUE 164378.9886 163926.0384 135411.4445 204784.9253 195079.4934 245058.3033 144420.0132 149928.1506 164972.4333 0.996402764 0.993657153 0.820812555 1.241328149 1.182497521 1.485450013 0.875419064 0.908807293 1 17.33186545 3.743617501 24.92318192 1.097233352 0.942627471 0.173826733 0.180505604 941.1933846 4638712.246 0.053806645 0.089494735 5541.374492 -3.743617501 -0.154605881 HLLMS(ph)ISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLLMSISK 8 0 Q8TD26 Q8TD26 CHD6 Chromodomain-helicase-DNA-binding protein 6 1 HLLMS(0.5)IS(0.5)K 73.039 0.046782 55331000 119920 148510 79469 112230 147250 202930 107530 122560 141420 TRUE FALSE 104072.2682 147534.428 117900.4742 137713.5368 144320.0131 210736.8484 97101.75715 96351.49776 124701.4887 0.834571177 1.183100776 0.945461641 1.104345572 1.157323899 1.689930494 0.7786736 0.772657157 1 16.92811916 HLLPVETQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HLLPVETQR 9 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 84.213 0.015645 561870000 944290 928950 530827 632260 1002650 1065550 870240 1024200 1061070 FALSE TRUE 819499.684 922847.6663 787536.7127 775824.2965 982699.2267 1106542.398 785844.2587 805182.8003 935631.5134 0.875878668 0.986336665 0.841716746 0.829198552 1.050305823 1.182669013 0.839907856 0.860576828 1 19.83558093 4.777318064 20.1680749 0.94022899 0.875876691 0.034728485 0.113055437 6570.121145 3418008.123 0.029130644 4.275730993 59885.00138 -4.777318064 -0.064352299 HLLQAPLDDAQEILQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HLLQAPLDDAQEILQAR 17 0 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;;; 258.92 3.50E-27 2241739000 1310030 1322908 738370 939840 1320015 1402683 1333203 1564380 1409761 FALSE TRUE 1136906.216 1314217.73 1095448.202 1153245.037 1293749.284 1456645.123 1203909.178 1229849.511 1243100.661 0.914572932 1.057209421 0.881222444 0.927716534 1.040743783 1.171783725 0.968472801 0.989340244 1 20.24551169 3.234033116 24.98422774 1.030443268 0.948613986 0.281757645 0.070292963 170.4322432 940500.2599 0.02184016 0.025594677 1714.088007 -3.234033116 -0.081829282 HLLQAPVDDAQEILHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLLQAPVDDAQEILHSR 17 0 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ; 205.88 4.33E-12 872360000 562900 483920 336960 329950 516230 553320 510010 612570 545310 FALSE TRUE 488511.3388 480741.0977 499914.9831 404870.1905 505958.033 574606.5784 460549.3087 481576.6725 480844.073 1.015945431 0.999785845 1.039661319 0.841998921 1.052228906 1.194995656 0.957793461 1.00152357 1 18.87520961 HLLQEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HLLQEAR 7 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 0 ;;; 125.81 0.0040127 1768390000 1804100 2207550 1115360 1424540 2134430 2170660 1993340 2332720 2466270 FALSE TRUE 1565683.614 2193048.459 1654751.827 1748003.58 2091959.019 2254166.695 1800026.194 1833885.981 2174710.37 0.719950406 1.008432428 0.760906762 0.803786842 0.961948335 1.036536509 0.82770847 0.843278262 1 21.05239184 3.244139717 24.99423364 0.919735481 0.832040602 0.231939988 0.097592164 262.7314686 1177024.455 0.028635971 0.035931083 1754.444835 -3.244139717 -0.087694879 HLLS(ph)PVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLLSPVGR 8 0 H7C0W5;H7C1Q6;Q9NXE4-5;Q9NXE4-9;Q9NXE4-10;Q9NXE4-7;Q9NXE4-8;Q9NXE4-3;Q9NXE4-6;Q9NXE4-2;Q9NXE4;Q9NXE4-4 H7C0W5 SMPD4 Sphingomyelin phosphodiesterase 4 1 HLLS(1)PVGR 87.568 0.0098112 126970000 49288 56661 33202 47518 67768 66547 46465 74410 59134 TRUE FALSE 42774.46592 56288.79016 49258.59825 58307.68817 66419.54939 69107.10615 41958.83145 58498.00056 52143.24589 0.820326107 1.079502996 0.944678403 1.118221299 1.273790081 1.325331881 0.804683919 1.121871099 1 15.67019277 5.438186623 1.131636256 1.094864648 1.10E-15 0.235434524 0.149455938 11.08940223 3.782955679 0.045334313 21.17731077 274275.2521 -5.438186623 -1.094864648 HLLTDLPLPPELPGGDLS(ph)PPDSPEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLLTDLPLPPELPGGDLSPPDSPEPK 26 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 HLLTDLPLPPELPGGDLS(0.992)PPDS(0.008)PEPK;HLLTDLPLPPELPGGDLS(0.974)PPDS(0.026)PEPK 114.06 0.00094744 226430000 250662 149770 93103 132068 161667 140246 178256 202039 179435 TRUE FALSE 217536.3816 148786.151 138127.9222 162056.0579 158450.143 145641.3544 160968.7606 158834.5321 158222.3987 1.374877283 0.940360861 0.872998535 1.024229561 1.001439393 0.920485061 1.017357605 1.003868816 1 17.27159432 4.741569731 24.9951789 0.974908761 1.374877429 0.872856134 0.048244485 98.80098109 820649.2567 0.012152537 0.082950557 55153.07496 -4.741569731 0.399968668 HLLVSNVGGDGEEIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLLVSNVGGDGEEIER 16 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 160.64 8.71E-09 265090000 322190 324030 172540 248930 349330 326560 311520 350230 320500 FALSE TRUE 279611.7752 321901.4256 255980.9211 305453.3612 342379.0165 339122.9745 281308.8383 275336.04 282610.8551 0.989387952 1.13902711 0.905771723 1.080826711 1.211485724 1.199964433 0.995392899 0.974258543 1 18.10845736 2.03825426 24.99543702 0.985150957 1.087994216 0.206569441 0.090498976 248.892269 162625.8741 0.038714933 0.026101545 109.2079513 -2.03825426 0.102843258 HLMEQS(ph)SPGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLMEQSSPGFR 11 0 Q5SXH7-4;Q5SXH7-3;Q5SXH7-2;Q5SXH7-1;Q5SXH7 Q5SXH7-4 PLEKHS1 Pleckstrin homology domain-containing family S member 1 1 HLMEQS(0.78)S(0.22)PGFR 97.551 0.020707 531090000 216420 356670 235730 228090 414030 438780 374100 429740 409510 TRUE FALSE 187819.5487 354327.0113 349729.8165 279881.3206 405791.613 455660.1505 337819.8396 337843.4452 361098.1943 0.520134278 0.981248361 0.968517212 0.775083689 1.123770818 1.261873246 0.935534558 0.93559993 1 18.46203168 4.739435818 5.597994241 0.99531817 0.503570322 0.58497655 0.12646386 0.11233123 14.27996802 0.032526564 0.211547345 54882.74411 -4.739435818 -0.491747848 KYDDVTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KYDDVTEK 8 1 P51572;P51572-2;C9JSP1;C9JQ75;C9J0M4;A0A2R8Y5M6;C9JMD7;C9JM14 P51572 BCAP31 B-cell receptor-associated protein 31 0 78.556 0.044665 0 239050 171630 181120 280230 201410 151020 215730 323570 570650 FALSE TRUE 207458.9368 170502.5512 268710.2378 343860.5045 197402.3351 156829.8371 194808.5378 254377.0735 503188.4071 0.412288785 0.338844355 0.53401516 0.683363328 0.392303027 0.311672199 0.387148303 0.505530473 1 18.94073916 1.236557724 3.79902656 1.070627106 0.440419647 0.733408893 0.105787592 0.150376898 3.519277492 0.26938479 0.028984734 17.24081233 -1.236557724 -0.630207459 HLMLPDFDLLEDIESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 HLMLPDFDLLEDIESK 16 0 P13010;C9JZ81 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;;;;;; 229.17 3.43E-15 7451084000 4320040 3358937.8 2270534.4 2778933.2 3253372.5 2788948 3856592 4621577.1 4099668.6 FALSE TRUE 3749135.768 3336872.716 3368572.43 3409932.456 3188636.752 2896240.634 3482580.301 3633288.802 3615010.448 1.037102333 0.923060324 0.931829238 0.943270429 0.882054643 0.801170751 0.963366594 1.005056238 1 21.78556839 2.005551634 24.99794354 0.99728594 0.916675633 0.26114266 0.057819646 189.2212608 852022.6104 0.024469197 0.016441388 101.2865162 -2.005551634 -0.080610307 HLMQDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLMQDLR 7 0 Q8TDN6 Q8TDN6 BRIX1 Ribosome biogenesis protein BRX1 homolog 0 92.187 0.015854 145740000 117110 166320 98593 112320 182660 203320 137880 141030 167540 FALSE TRUE 101633.6168 165227.433 146272.9046 137823.9727 179025.4234 211141.852 124508.4188 110871.832 147733.6121 0.687951884 1.118414629 0.990112558 0.932922243 1.211812403 1.42920659 0.842790054 0.750484811 1 17.17263858 2.070420205 25 0.839136066 1.068188788 0.175291445 0.198939853 68.51370173 24321.8352 0.082000555 0.055284756 117.6034887 -2.070420205 0.229052722 HLMTLVMDPLQTASVQWFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLMTLVMDPLQTASVQWFER 20 0 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A1B0GTG9;A0A1B0GWF8;P30566-2;A0A096LNY6 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 0 ; 163.45 1.96E-11 429790000 487220 502980 319440 278260 419400 451110 590720 623430 428680 FALSE TRUE 422832.6425 499675.8913 473922.2525 341443.1859 411054.7605 468464.4936 533432.0653 490114.346 378001.9388 1.118599137 1.321887112 1.253756142 0.903284219 1.087440879 1.239317701 1.411188702 1.296592149 1 18.52803411 2.599469608 6.225021109 1.26501869 1.141366219 0.089197591 0.148335715 0.520840785 24.39168626 0.054045502 0.047423645 397.6212696 -2.599469608 -0.123652471 HLNEIDLFHCIDPNDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 HLNEIDLFHCIDPNDSK 17 0 A0A087WYT3;Q15185-4;Q15185;Q15185-3 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ;;;;;;; 254.59 2.79E-27 10599860000 13885980 12566860 7924313 9459890 11389360 9682340 14083710 16570790 13861040 FALSE TRUE 12050912.56 12484307.47 11756537.27 11607902.61 11162734.02 10054825.89 12717873.97 13027255.51 12222403.64 0.98596912 1.021428177 0.961884226 0.949723389 0.913301045 0.822655361 1.04053788 1.065850539 1 23.5430247 2.068933114 24.99999079 1.042306485 0.944766912 0.39574277 0.05389046 49.18597532 17837.50492 0.023506762 0.015848253 117.2014849 -2.068933114 -0.097539573 HLNRPTLDDSSEEEHAIEITTQEITQLFHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HLNRPTLDDSSEEEHAIEITTQEITQLFHR 30 1 H3BU86;O14662;F8W9Z6;B7ZBM8;O14662-6;O14662-2;O14662-5;B7ZBM4;B7ZBM5;Q96NX8;O14662-4 H3BU86;Q96NX8 STX16-NPEPL1;STX16 Syntaxin-16 0 ;;; 248.95 1.10E-46 541723000 230868 182110 95904 146756 201726 226257 140667 246517 205013 FALSE TRUE 200358.2089 180913.7074 142283.4952 180079.1928 197712.0473 234961.2532 127025.136 193801.2579 180776.5967 1.108319398 1.000758454 0.787068115 0.996142178 1.093681654 1.299732695 0.70266361 1.072048382 1 17.46384839 4.730935829 6.591876679 0.992551735 1.110201452 0.046728901 0.162367232 0.401783401 109.7249857 0.038859785 0.209816442 53819.02537 -4.730935829 0.117649717 HLPDNECIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HLPDNECIEK 10 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;;; 166.69 5.47E-06 1010150000 3905780 3219250 2185520 2518250 3128900 2774640 3689690 4072300 4033910 FALSE TRUE 3389621.277 3198102.535 3242444.782 3090057.152 3066641.012 2881382.196 3331864.432 3201470.336 3557025.755 0.952936951 0.899094568 0.91156067 0.868719364 0.862136297 0.810053791 0.936699552 0.900041371 1 21.76223999 0.772133671 1.471159142 1.243420667 0.887175607 0.414958467 0.039986571 4.148506961 3.00765516 3.097580836 0.011659209 5.917437382 -0.772133671 -0.356245061 HLPDYRDPPDGSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLPDYRDPPDGSGR 14 1 Q96HQ2;Q96HQ2-2 Q96HQ2 CDKN2AIPNL CDKN2AIP N-terminal-like protein 0 ; 89.466 0.0036879 432380000 179450 188352 120443 145277 193697 202401 177817 186088 151757 FALSE TRUE 155735.2278 187114.7033 178689.6377 178264.3633 189842.8087 210187.4974 160572.3347 146294.5293 133816.4603 1.163797245 1.398293624 1.335333764 1.332155721 1.418680543 1.57071482 1.199944568 1.093247639 1 17.02989606 1.884608001 2.946786497 1.045633499 1.370378178 0.615834252 0.104677834 0.167641025 2.573236765 0.067984014 0.029038889 76.66691723 -1.884608001 0.32474468 HLPHFKPWLHPEQSPLPSLALSELSVQHADS(ph)LENIDESAVAESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HLPHFKPWLHPEQSPLPSLALSELSVQHADSLENIDESAVAESR 44 1 Q9Y365;F5H8H3;F5GY11 Q9Y365 STARD10 PCTP-like protein 1 HLPHFKPWLHPEQSPLPS(0.002)LALS(0.002)ELS(0.116)VQHADS(0.88)LENIDESAVAESR;HLPHFKPWLHPEQSPLPSLALSELS(0.003)VQHADS(0.997)LENIDESAVAESR;HLPHFKPWLHPEQSPLPSLALSELSVQHADS(1)LENIDESAVAESR;HLPHFKPWLHPEQS(0.042)PLPS(0.188)LALS(0.188)ELS(0.159)VQHADS(0.422)LENIDESAVAESR;HLPHFKPWLHPEQSPLPSLALSELSVQHADS(1)LENIDESAVAESR;HLPHFKPWLHPEQSPLPSLALS(0.008)ELS(0.008)VQHADS(0.983)LENIDESAVAESR 402.33 3.25E-214 73393630000 4976531 3945373 1836245 3143757 3632266 3738104 3808659 4118893 4067198 TRUE FALSE 4318869.819 3919455.585 2724259.224 3857595.076 3559991.013 3881911.28 3439295.836 3238099.785 3586378.486 1.204242619 1.092872824 0.759612861 1.075624085 0.992642307 1.08240424 0.958988531 0.90288847 1 21.77409632 4.470019406 24.9914255 0.967178049 1.176400251 0.430011198 0.091178731 128.4021834 451848.8771 0.022137735 0.058846521 29513.41105 -4.470019406 0.209222203 HLPNLLDETQIFSYFSQFGTVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLPNLLDETQIFSYFSQFGTVTR 23 0 Q9BYG3 Q9BYG3 NIFK MKI67 FHA domain-interacting nucleolar phosphoprotein 0 ; 170.28 7.52E-12 193206000 110887 100326 70266 87946 111130 91243 113317 117417 88203 FALSE TRUE 96233.002 99666.9519 104246.8726 107915.4835 108918.7304 94753.17725 102327.5348 92308.28829 77775.74182 1.237313843 1.281465783 1.34035202 1.387521108 1.400420335 1.218287027 1.315674173 1.186851917 1 16.24703263 0.935634217 1.142477474 0.613855074 1.321334117 0.754174443 0.057516389 1.531504636 1.029624101 1.548891224 0.01878866 8.622520129 -0.935634217 0.707479044 HLPS(ph)PPLTQEVDLHSIAGPPVPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLPSPPLTQEVDLHSIAGPPVPPR 24 0 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 1 HLPS(1)PPLTQEVDLHSIAGPPVPPR;HLPS(1)PPLTQEVDLHSIAGPPVPPR 222.26 1.44E-32 582830000 217936 201955 134765 138856 216540 261014 227867 227774 205371 TRUE FALSE 189135.2054 200628.3443 199937.8048 170385.3771 212231.2777 271055.3775 205768.4934 179066.3026 181092.2743 1.044413441 1.107879091 1.1040659 0.940876013 1.171951031 1.496780459 1.136263235 0.98881249 1 17.46636547 1.748607194 5.810593287 0.995408945 1.147589043 0.16041451 0.141245065 0.294468097 26.12942038 0.089589825 0.039688293 56.05407544 -1.748607194 0.152180098 HLPS(ph)PPTLDSIITEYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HLPSPPTLDSIITEYLR 17 0 Q9Y4B6-3;Q9Y4B6-2;Q9Y4B6 Q9Y4B6-3 VPRBP Protein VPRBP 1 HLPS(0.999)PPT(0.001)LDSIITEYLR;HLPS(0.997)PPT(0.003)LDSIITEYLR;HLPS(0.953)PPT(0.047)LDSIITEYLR;HLPS(0.978)PPT(0.022)LDSIITEYLR 243.97 1.12E-20 3232090000 362259 326798 217898 248760 319439 309809 329456 356438 327085 TRUE FALSE 314385.5553 324651.2424 323274.2016 305244.7601 313082.7889 321727.5527 297505.4078 280216.5075 288417.3839 1.090036776 1.12562994 1.120855467 1.058343835 1.085519828 1.11549293 1.031509973 0.971565943 1 18.1377986 2.050418313 3.664038739 0.986743567 1.098825815 0.840142033 0.020857481 0.082540258 2.28626409 0.010538415 0.006148441 112.3099705 -2.050418313 0.112082248 HLPSTEPDPHVVR ddPTM_MDA-MB-175_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 ; 102.87 0.00095715 598250000 710180 545790 318110 478740 596890 779630 464460 658740 690580 FALSE TRUE 616327.9136 542204.6696 471949.06 587445.2341 585013.0568 809622.8706 419416.7407 517873.5773 608940.4191 1.01213172 0.890406766 0.77503323 0.964700676 0.960706562 1.329560077 0.688764824 0.850450325 1 19.21594155 HLQDIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLQDIK 6 0 Q99733;Q99733-2;C9JZI7;H0YCI4 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 132.96 0.014671 315560000 930940 929590 589170 694320 702230 746070 1016600 1169000 1087800 FALSE TRUE 807913.9203 923483.4621 874094.5827 851975.968 688256.9969 774771.7957 918010.2885 919018.4472 959201.5232 0.842277562 0.962762714 0.911273139 0.888213735 0.717531176 0.807725777 0.957056746 0.958107785 1 19.87147442 2.145577126 6.859017857 0.97012426 0.857890811 0.41602208 0.06526297 0.249071172 15.55033769 0.029733018 0.019984983 139.8225202 -2.145577126 -0.112233448 HLQDLMEGLTAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLQDLMEGLTAK 12 0 P11387 P11387 TOP1 DNA topoisomerase 1 0 101.53 0.0026177 180570000 324640 282320 210030 334840 337930 274460 320560 387140 325710 FALSE TRUE 281738.0015 280465.4213 311601.2105 410870.5397 331205.8541 285018.6538 289472.1405 304353.1237 287204.9349 0.980965044 0.976534131 1.08494379 1.430583148 1.153203911 0.992387732 1.007894035 1.059707153 1 18.13172101 2.740956844 24.43675763 1.02131723 1.131708399 0.158239828 0.125487063 331.777146 3383489.946 0.045248505 0.043253347 550.7529651 -2.740956844 0.110391169 HLQDLSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLQDLSGR 8 0 P30533 P30533 LRPAP1 Alpha-2-macroglobulin receptor-associated protein 0 ; 113.62 0.0028132 354470000 259690 276500 191406 204862 213990 320510 250920 260330 280920 FALSE TRUE 225371.3085 274683.6533 283970.5818 251379.0482 209732.0177 332840.2271 226585.817 204660.4554 247709.9576 0.909819333 1.108892254 1.146383393 1.014812043 0.846683838 1.343669146 0.914722279 0.826210046 1 17.91829234 2.032168223 24.99997035 0.891623273 1.061914305 0.195691437 0.140011034 254.0870417 197466.1745 0.054704628 0.036881589 107.6882262 -2.032168223 0.170291032 HLQEAEQTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLQEAEQTK 9 0 Q96P70 Q96P70 IPO9 Importin-9 0 ; 155.06 7.42E-05 451770000 652000 575180 389690 476950 533090 455920 661970 728810 663050 FALSE TRUE 565836.548 571401.6047 578145.3874 585248.7872 522482.552 473459.5374 597772.2513 572959.6531 584664.9843 0.967796196 0.977314565 0.988849004 1.000998525 0.893644336 0.809796294 1.022418423 0.979979421 1 19.15725067 HLQELVGQETLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLQELVGQETLPR 13 0 A0A5H1ZRP4;Q8WX92;Q8WX92-2 A0A5H1ZRP4 NELFB Negative elongation factor B 0 136.92 6.67E-05 150970000 102190 105600 53815 67688 97564 96502 96943 109850 100650 FALSE TRUE 88685.33258 104906.3066 79840.114 83057.59495 95622.66728 100214.4944 87541.48278 86359.43235 88751.27166 0.999257035 1.182025955 0.899594028 0.935846815 1.077423067 1.129161222 0.986368771 0.973050084 1 16.43748017 2.047626624 24.99910757 0.983131744 1.036681023 0.076259038 0.083056049 312.6492553 164107.5396 0.034850375 0.023496112 111.590346 -2.047626624 0.053549278 HLQGGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HLQGGEK 7 0 Q8N163-2;Q8N163;E5RHH8;E5RGU7;E5RFJ3;H0YC58 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ;;; 147.34 0.0021584 500746000 1616040 1389420 847720 1101170 721220 1144810 1595940 1756020 1774870 FALSE TRUE 1402476.219 1380292.809 1257680.227 1351207.479 706869.133 1188851.581 1441165.984 1380508.788 1565046.891 0.896124089 0.881949811 0.803605461 0.863365492 0.451660035 0.759626813 0.920845243 0.882087813 1 20.57777445 2.235254459 23.89203 0.922870176 0.771344343 0.251813571 0.127916596 75.77027521 547538.3878 0.053453808 0.037761396 171.8915226 -2.235254459 -0.151525833 HLQLAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 HLQLAIR 7 0 A0A0U1RR32;A0A0U1RRH7;P20671;A0A3B3IS11;Q7L7L0;P04908;Q99878;Q96KK5;Q6FI13;P0C0S8;Q16777;Q9BTM1;Q9BTM1-2;Q96QV6;H0YFX9;P16104;Q71UI9;P0C0S5;C9J0D1;A0A494C189;Q71UI9-4;Q71UI9-2;Q71UI9-3;C9J386 A0A0U1RR32;Q7L7L0;Q99878;P16104;Q71UI9 HIST1H2AD;HIST3H2A;HIST1H2AB;HIST1H2AJ;HIST1H2AH;HIST2H2AA3;HIST1H2AG;HIST2H2AC;H2AFJ;HIST1H2AA;H2AFX;H2AFV;H2AFZ Histone H2A type 1-D;Histone H2A type 3;Histone H2A type 1-B/E;Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-A;Histone H2A type 1;Histone H2A type 2-C;Histone H2A.J;Histone H2A type 1-A;Histone H2A;Histone H2AX;Histone H2A.V;Histone H2A.Z 0 ;;;;;;; 181.15 0.00067601 57416240000 15083040 22181730 9975740 16059270 22486160 21598530 16897710 20780850 20246790 FALSE TRUE 13089778.05 22036016.76 14800041.23 19705772.7 22038729.41 22429439.43 15258972.69 16337026.94 17853237.55 0.733187917 1.234286873 0.828983605 1.103764662 1.234438815 1.256323362 0.854689388 0.915073633 1 24.08968238 2.201351551 24.99995474 0.918693127 1.071565423 0.128016534 0.173923402 324.6739497 218139.1803 0.069213254 0.046664898 158.9833161 -2.201351551 0.152872296 HLQQGSES(ph)PMMIGELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLQQGSESPMMIGELR 16 0 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 HLQQGSES(1)PMMIGELR 213.16 1.71E-12 132310000 109360 108140 64029 84158 107160 108860 103370 119920 116220 TRUE FALSE 94907.79892 107429.6212 94993.63856 103267.3602 105027.7257 113047.9146 93345.19331 94276.04122 102480.604 0.926104992 1.048292233 0.92694261 1.007677123 1.024854671 1.103115226 0.910857174 0.919940335 1 16.64499136 HLQTGENHTSVDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLQTGENHTSVDPR 14 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 66.989 0.031133 117280000 94468 104830 29831 61006 120930 136650 95424 102370 111120 FALSE TRUE 81983.81445 104141.3648 44257.37138 74858.34472 118523.7296 141907.0139 86169.79517 80478.97214 97983.52019 0.836710238 1.062845718 0.451681786 0.763989134 1.209629225 1.448274298 0.879431511 0.821352121 1 16.5802515 3.261263132 24.69945746 1.044843162 0.775728991 0.2888234 0.226207992 324.4914851 353031.4852 0.07142342 0.092138223 1825.001104 -3.261263132 -0.269114171 HLS(ph)ASTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLSASTPK 8 0 I3L2J0 I3L2J0 CIC 1 HLS(0.995)AS(0.004)TPK 83.883 0.020437 0 319840 264900 188320 203240 276590 263480 334990 387110 376740 TRUE FALSE 277572.3336 263159.8545 279392.1819 249388.7483 271086.4001 273616.2461 302502.7214 304329.539 332202.2264 0.835552298 0.792167642 0.841030432 0.750713657 0.816028246 0.823643625 0.910598116 0.916097229 1 18.34170222 1.741612744 0.998602937 1.015480628 0.80304954 0.830205011 0.029375323 0.349258869 0.488278828 0.070637099 0.010485236 55.15853766 -1.741612744 -0.212431088 GKYGQFSGLNPGGRPIT(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GKYGQFSGLNPGGRPITPPR 20 2 P62136;P62136-2;P62136-3 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 1 GKYGQFSGLNPGGRPIT(1)PPR;GKYGQFSGLNPGGRPIT(1)PPR 141.21 9.22E-06 765580000 2041490 1675940 985560 1089880 1604660 1606660 1712360 1951960 786830 TRUE FALSE 1771701.924 1664930.64 1462180.113 1337353.912 1572730.405 1668469.25 1546295.591 1534548.544 693811.8538 2.553576902 2.399686069 2.107459111 1.927545493 2.266796678 2.404786313 2.228695838 2.211764668 1 19.40418496 1.23657125 5.594940515 0.940145721 2.25644669 0.843987853 0.170685559 0.060088532 6.053922383 0.304457403 0.045050493 17.24134927 -1.23657125 1.316300969 HLSDAIVEVEEALIQIHDPELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HLSDAIVEVEEALIQIHDPELR 22 0 H7C0I1;B8ZZW5;Q8NBF6-2;Q8NBF6 H7C0I1 AVL9 Late secretory pathway protein AVL9 homolog 0 ;;; 231.06 8.63E-27 258320000 62265.7 78790.7 22076.2 44611.7 90215 94550.8 69514 81971.9 82348.6 FALSE TRUE 54037.12998 78273.1187 32752.32416 54741.46833 88419.898 98188.23046 62772.54298 64442.84709 72613.44232 0.744175297 1.077942543 0.451050427 0.753875131 1.217679471 1.352204596 0.864475515 0.8874782 1 16.14794903 3.263603285 24.37838081 1.041656314 0.757865694 0.352729934 0.205780833 226.8977468 220876.9763 0.062977248 0.081263912 1834.861487 -3.263603285 -0.283790619 HLSPDGQYVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 HLSPDGQYVPR 11 0 O95994;B5MC07;C9J3E2;H7C3Z9 O95994 AGR2 Anterior gradient protein 2 homolog 0 ;;;;;;;;;; 207.29 2.35E-08 37224580000 5413730 6853620 5440990 5105805 7475430 8656248 5050490 5392949 5763559 FALSE TRUE 4698291.864 6808598.119 8072270.963 6265156.063 7326683.568 8989259.462 4560694.257 4239708.824 5082197.621 0.924460679 1.339695665 1.588342596 1.23276514 1.441636889 1.768774088 0.897386249 0.834227462 1 22.27702104 2.199222095 23.38119198 0.894090082 1.385884628 0.500466164 0.222112158 62.57611689 37191.78433 0.09014735 0.060779214 158.2056884 -2.199222095 0.491794546 HLSPNDNENDTSYVIES(ph)DEDLEMEMLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HLSPNDNENDTSYVIESDEDLEMEMLK 27 0 Q14191 Q14191 WRN Werner syndrome ATP-dependent helicase 1 HLSPNDNENDTSYVIES(1)DEDLEMEMLK;HLSPNDNENDTSYVIES(1)DEDLEMEMLK;HLSPNDNENDTSYVIES(1)DEDLEMEMLK 168.61 4.48E-12 96266000 94005 89164 41253.1 65733 101429 90413 91951 120681 105836 TRUE FALSE 81582.00107 88578.27581 61203.23714 80658.68232 99410.76134 93891.24661 83033.60617 94874.30729 93324.18865 0.87417852 0.949145951 0.655813225 0.864284849 1.065219669 1.006076216 0.889732955 1.016610041 1 16.50996344 3.38475571 6.594261666 0.990032206 0.826140567 0.475733833 0.083888532 0.19034936 11.35681422 0.02424838 0.0313883 2425.245512 -3.38475571 -0.163891638 HLSTPSSVS(ph)PEPQDSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLSTPSSVSPEPQDSAK 17 0 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 HLS(0.006)T(0.005)PS(0.025)S(0.166)VS(0.798)PEPQDSAK;HLS(0.014)T(0.012)PS(0.011)S(0.046)VS(0.917)PEPQDSAK 71.535 0.019522 224561000 133579 181406 62870 99651 250110 196098 214028 242760 227080 TRUE FALSE 115926.1967 180214.332 93274.14229 122278.2826 245133.3003 203642.017 193271.5975 190847.6632 200234.8611 0.578951118 0.900014768 0.465823692 0.610674295 1.224228883 1.017015798 0.965224519 0.953119063 1 17.61133365 3.256170094 24.98508383 1.016320755 0.645159162 0.691171289 0.130291707 144.5353171 205071.6916 0.037311919 0.048059998 1803.724043 -3.256170094 -0.371161593 HLSVNDLPVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HLSVNDLPVGR 11 0 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 ;;; 218.55 1.05E-11 2142530000 936480 1234600 361877 988110 1767390 2000090 1023980 1274430 1409200 FALSE TRUE 812721.7953 1226489.831 536881.9276 1212475.478 1732222.397 2077034.757 924674.5772 1001903.062 1242605.981 0.65404626 0.987030362 0.432061277 0.975752166 1.394023868 1.671515177 0.744141418 0.806291839 1 20.24493747 3.491441289 24.19984982 1.091870448 0.717854728 0.301212346 0.297470902 676.9120866 1143932.152 0.091545574 0.129999949 3100.568201 -3.491441289 -0.37401572 HLT(ph)PEPDIVASTK ddPTM_MDA-MB-175_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 173.71 7.80E-05 278860000 1624860 1559430 897930 1048500 1886790 1471190 1791280 2143230 1812480 TRUE FALSE 1410130.634 1549186.002 1332171.951 1286577.95 1849246.57 1527787.631 1617561.941 1684916.943 1598210.679 0.882318365 0.969325272 0.833539638 0.805011484 1.157073091 0.955936318 1.01210808 1.054252086 1 20.60802617 3.250881522 24.99999869 1.032391882 0.876674945 0.603004222 0.065778838 160.7115873 326093.5457 0.018642562 0.023889326 1781.892592 -3.250881522 -0.155716938 HLTASEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLTASEAK 8 0 P39748;P39748-2 P39748 FEN1 Flap endonuclease 1 0 94.806 0.010098 242500000 433450 341100 192270 307560 312560 280580 369590 436280 409780 FALSE TRUE 376168.4843 338859.2916 285252.4151 377396.1988 306340.6675 291374.0942 333747.2187 342984.9171 361336.2752 1.041048215 0.937794832 0.789437526 1.044445921 0.847799373 0.806379304 0.923647144 0.949212522 1 18.46298257 1.480741219 2.422579896 1.000502575 0.907747527 0.096768693 0.085296747 0.813528316 8.284697425 0.135405801 0.022711331 30.25110334 -1.480741219 -0.092755048 HLTDAYFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HLTDAYFK 8 0 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ;;; 160.19 0.0012977 4195510000 9189090 8507510 3567190 6966490 8965050 8066820 9245430 11204200 10125200 FALSE TRUE 7974728.474 8451623.607 5292295.016 8548338.031 8786663.045 8377155.785 8348809.622 8808269.021 8928210.391 0.893205707 0.946620122 0.592761011 0.957452575 0.984146056 0.938279388 0.93510449 0.986566023 1 23.08993959 3.523329524 24.99998755 0.967329209 0.81621614 0.38918434 0.09217577 435.6923081 235720.7264 0.024550805 0.036413287 3336.794982 -3.523329524 -0.151113069 HLTGEFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 HLTGEFEK 8 0 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ;;;;;;; 208.37 5.58E-05 14760150000 17198690 13977710 6999030 12272880 14524350 12559690 16014610 18353060 21632170 FALSE TRUE 14925839.54 13885889.5 10383784.32 15059624.98 14235343.85 13042869.4 14461515.59 14428400.94 19074839.51 0.782488342 0.727968877 0.544370731 0.789502055 0.74628905 0.683773481 0.758146121 0.756410083 1 24.18516758 -0.196437001 1.245399239 9.999535827 0.711390339 0.613988307 0.069377791 31.69902849 1.896173941 773.296626 0.020444302 0.63615508 0.196437001 -9.288145487 HLTGEFEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLTGEFEKK 9 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 205.09 1.01E-05 1498260000 4444900 3276100 1700090 2273600 3072700 2504100 4548400 5049300 1191170 FALSE TRUE 3857495.203 3254579.083 2522259.21 2789855.63 3011559.282 2600434.347 4107296.868 3969546.489 1050351.24 3.672576427 3.098562615 2.401348345 2.656116854 2.867192581 2.475775959 3.910403219 3.779256252 1 20.00244042 4.661449971 3.760763668 2.872281445 3.700554083 0.104458787 0.805656938 0.616348071 14.74145337 0.202401037 1.190416998 45861.68115 -4.661449971 0.828272638 HLTHENVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLTHENVQR 9 0 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ; 82.645 0.017866 74134000 54176 48052 24365 41109 43972 55573 48540 51649 57574 FALSE TRUE 47016.50434 47736.34325 36147.9955 50443.42676 43097.04323 57710.92927 43832.59827 40604.26328 50767.66731 0.926111181 0.940290263 0.712027899 0.993613247 0.848907297 1.136765432 0.863395949 0.799805574 1 15.63162235 HLTSNSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HLTSNSPR 8 0 P14923 P14923 JUP Junction plakoglobin 0 ;;; 131.22 0.0010143 299505000 151179 172348 98871 134764 168077 235023 150032 192437 170090 FALSE TRUE 131200.3121 171215.8346 146685.3463 165364.2259 164732.5965 244064.4869 135481.9197 151285.8451 149982.154 0.874772822 1.141574715 0.978018667 1.102559348 1.098347985 1.627290184 0.903320269 1.008692308 1 17.19443132 4.745174896 23.14272929 1.101948059 0.874772516 0.119915599 0.197616211 651.2193657 2278371.717 0.048644412 0.437034048 55612.81722 -4.745174896 -0.227175543 HLTYENVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 9462540000 4475740 4314640 2163350 3330690 4445240 5011810 3987540 5085430 5371430 FALSE TRUE 3884259.619 4286296.846 3209553.296 4086974.071 4356788.421 5204617.574 3600828.985 3997950.369 4736425.665 0.820082462 0.90496445 0.677631937 0.862881498 0.919847313 1.098849205 0.760241845 0.844085953 1 22.17536731 3.481737613 21.91474923 0.909146847 0.804459578 0.22161855 0.103918747 70.3269792 333858.9021 0.030365003 0.04044747 3032.058759 -3.481737613 -0.104687268 HLVQQEGQLEQQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLVQQEGQLEQQER 14 0 P07476 P07476 IVL Involucrin 0 ; 235.11 3.15E-17 1754050000 596100 632660 369020 490030 621350 735850 656420 655460 679170 FALSE TRUE 517323.8747 628504.0148 547479.3063 601298.8011 608986.3507 764158.6257 592760.4894 515294.9798 598879.2963 0.863819935 1.049466927 0.914173039 1.004040054 1.016876613 1.275981037 0.989782905 0.860432115 1 19.19190573 4.750339405 23.59145277 1.005596357 0.863819743 0.156528525 0.107947743 1834.993916 3675111.211 0.028330581 0.418203659 56278.09713 -4.750339405 -0.141776614 HLVQQEGQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLVQQEGQLK 10 0 P07476 P07476 IVL Involucrin 0 115.7 0.0011882 242390000 530450 484150 318640 410800 474560 492690 585680 570330 605930 FALSE TRUE 460349.6885 480969.5868 472735.3698 504078.4187 465117.1845 511644.1031 528880.8437 448369.3678 534297.6457 0.861597823 0.900190354 0.884779062 0.943441213 0.870520745 0.957601268 0.989861827 0.839175264 1 19.02728413 7.866268802 0.386488279 0.932358176 6.94E-14 0.197656528 0.049196531 148.8056543 2.377103811 0.050635965 102.1401503 73496862.84 -7.866268802 -0.932358176 HLVSLTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLVSLTER 8 0 Q9BVJ7 Q9BVJ7 DUSP23 Dual specificity protein phosphatase 23 0 ; 138.54 0.00070074 533670000 314984 346643 217847 248189 365091 371418 325204 374572 381807 FALSE TRUE 273358.0663 344365.8793 323198.5379 304544.1058 357826.4034 385706.6908 293665.7661 294472.6927 336670.2114 0.811946104 1.022858179 0.959985549 0.904576929 1.062839513 1.145651376 0.872265369 0.874662155 1 18.36097655 4.750802375 23.5028992 0.971769499 0.811945872 0.271927662 0.085583154 1317.918868 2530156.952 0.022608241 0.349432761 56338.12324 -4.750802375 -0.159823627 HLVYESDQNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HLVYESDQNK 10 0 O43852;O43852-3;O43852-15;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;; 204.34 1.89E-07 467590000 1403140 1132720 1001170 1307480 1226970 1182250 1273880 1375910 2225320 FALSE TRUE 1217711.494 1125279.088 1485339.161 1604363.318 1202555.698 1227731.923 1150339.314 1081682.354 1962245.205 0.620570503 0.573465072 0.756958996 0.817616123 0.612846802 0.625677117 0.586236272 0.551247291 1 20.9040739 1.229626952 24.99947262 1.000000687 0.641457623 0.647312783 0.082789284 249.598031 698408.4513 0.264506037 0.022319224 16.96785531 -1.229626952 -0.358543064 HLWDYTFGPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLWDYTFGPEK 11 0 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ; 180.88 6.47E-06 2499400000 2298800 2451200 1587230 1822150 2433200 2117610 2752500 3037100 2933100 FALSE TRUE 1995007.756 2435097.906 2354819.737 2235897.007 2384784.08 2199075.827 2485562.974 2387639.8 2586352.259 0.771359643 0.94151827 0.910479123 0.864498252 0.922064685 0.850261529 0.961030333 0.923168834 1 21.30248735 -2 0.375400796 2.535692024 0.870032606 0.387904318 0.049922917 87.70513904 1.313375125 104.697232 0.053534763 0.01 2 -1.665659418 HLWFQGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HLWFQGIR 8 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 138.9 0.00068575 769280000 465710 641290 369290 396850 585170 633530 571390 565290 678000 FALSE TRUE 404165.2435 637077.3238 547879.8792 486960.858 573526.2619 657902.309 515976.6857 444407.1326 597847.6124 0.676033884 1.065618245 0.916420619 0.81452338 0.959318478 1.100451512 0.863057199 0.743345166 1 19.18941827 0.949093727 21.82982687 2.358331449 0.894870157 0.062274837 0.130959459 308.839099 327978.802 31133.5963 0.030952781 8.893930411 -0.949093727 -1.463461292 HLWNHSIIEEEFVSLVTGCCYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLWNHSIIEEEFVSLVTGCCYR 22 0 Q15021 Q15021 NCAPD2 Condensin complex subunit 1 0 126.69 1.12E-05 166860000 74382 51854 43555 67333 37452 56592 46148 59321 64668 FALSE TRUE 64552.23024 51513.36766 64618.34368 82621.98677 36706.77847 58769.13086 41672.57406 46635.66579 57023.02271 1.132038029 0.903378411 1.133197446 1.448923309 0.643718567 1.030621108 0.730802614 0.817839244 1 15.7992569 3.22405163 24.99999567 0.842018428 1.134942052 0.444093969 0.171601404 229.1936357 394915.6151 0.051049397 0.058137159 1675.142008 -3.22405163 0.292923624 HLYDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HLYDPK 6 0 Q15417;E9PDU6;Q15417-3;Q15417-2;U3KPS3;K7EQ72;K7ER02;B7Z7E1;P51911;P51911-2;B4DDF4;B4DUT8;Q99439;A0A087X1X5;H3BVI6;Q99439-2;H3BQH0 Q15417;P51911-2;B4DDF4 CNN3;CNN2;CNN1 Calponin-3;Calponin;Calponin-1;Calponin-2 0 ;;; 106.76 0.031846 2635340000 6557400 6551300 4337500 5170100 5898900 5287500 7303600 8563000 7665600 FALSE TRUE 5690822.976 6508264.079 6435129.508 6344050.225 5781523.431 5490913.546 6595297.996 6731869.087 6759381.501 0.841914748 0.962849053 0.95202934 0.93855484 0.855333203 0.812339642 0.975725071 0.995929744 1 22.68845981 2.02485692 24.85778469 0.994120145 0.899412201 0.470358668 0.048526438 194.3186623 194324.5121 0.021079974 0.014211496 105.8904808 -2.02485692 -0.094707943 HLYTADMFTHGIQSAAHFVMFFAPWCGHCQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HLYTADMFTHGIQSAAHFVMFFAPWCGHCQR 31 0 Q8NBS9 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 139.4 9.81E-09 124130000 14477 22957 6766.4 10402 18822 14491 17819 18707 9350.8 FALSE TRUE 12563.82777 22806.19396 10038.65367 12763.93308 18447.47902 15048.47815 16090.91612 14706.65363 8245.359076 1.523745376 2.765943089 1.217491389 1.548014218 2.237316635 1.825084633 1.951511872 1.783628037 1 13.00936661 1.235625377 3.922594964 0.895540446 1.876294003 0.291723832 0.421157972 0.321254133 8.370621405 0.917121424 0.101236834 17.20383928 -1.235625377 0.980753557 HLYTLDGGDIINALCFSPNR ddPTM_MDA-MB-175_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 ;; 287.54 1.79E-45 7481240000 2551510 2548350 1309734 1771810 2435190 2680730 2490570 2854030 2503670 FALSE TRUE 2214321.489 2531609.721 1943125.743 2174126.541 2386734.483 2783859.418 2249034.905 2243717.895 2207688.985 1.003004275 1.146723899 0.880162811 0.984797476 1.081100871 1.260983516 1.018728145 1.01631974 1 21.07410551 HMAAASAECQNYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HMAAASAECQNYAK 14 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 186.76 8.04E-08 0 152940 136520 77300 124910 151520 125880 128620 166490 155710 FALSE TRUE 132728.5915 135623.1911 114682.5386 153272.7246 148505.0484 130722.6851 116146.4522 130887.4091 137302.1412 0.966689888 0.987771858 0.835256738 1.116317075 1.081593099 0.952080455 0.845918725 0.953280175 1 17.0669946 1.225011911 23.07144606 1.000000232 0.965266927 0.013167645 0.087127385 1785.695708 3040279.964 0.38236085 0.022061084 16.78850061 -1.225011911 -0.034733305 HMEMYADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HMEMYADR 8 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 82.749 0.019466 172670000 168300 147420 106420 113810 173940 176560 142350 162160 191850 FALSE TRUE 146058.7286 146451.5883 157885.068 139652.3 170478.9343 183352.3774 128544.9189 127483.3459 169169.7116 0.863385811 0.865708093 0.933293948 0.825515979 1.007739108 1.08383691 0.759857765 0.75358257 1 17.36811176 2.182427643 24.99999446 0.817017228 0.92594436 0.147398167 0.100042487 139.6601607 62199.24297 0.041781165 0.028168873 152.2045528 -2.182427643 0.108927132 HMGIGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HMGIGK 6 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ;;; 74.849 0.060109 1134430000 4784350 3966430 2557760 3336960 3636410 3829000 4543280 5265900 5112400 FALSE TRUE 4152086.026 3940374.26 3794701.291 4094667.77 3564052.556 3976304.108 4102673.405 4139828.264 4508017.896 0.921044708 0.874081326 0.841767131 0.90830779 0.790603018 0.882051536 0.910083655 0.918325606 1 22.10406181 1.05769777 1.068402005 1.10819928 0.86813654 0.552730305 0.036618003 1.8681771 1.348731033 0.564666159 0.011722474 11.42083272 -1.05769777 -0.240062741 HMLPSGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HMLPSGFR 8 0 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ;;; 95.741 0.0094349 2633360000 1809580 2099140 1254609 1521670 2164300 2410500 1881410 2177330 2912350 FALSE TRUE 1570439.418 2085350.611 1861342.109 1867188.431 2121234.664 2503233.495 1698951.148 1711724.924 2568055.301 0.61152866 0.812034932 0.724806085 0.727082641 0.826008172 0.974758407 0.661571091 0.666545196 1 21.29224484 4.744651887 23.33018874 0.784056081 0.611528458 0.195674295 0.116002811 499.1202305 1911534.819 0.028486214 0.245553887 55545.88456 -4.744651887 -0.172527622 HMLPSGFRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HMLPSGFRK 9 1 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ; 62.262 0.05438 1407290000 2858400 2841600 1135990 1337050 2730680 2610880 3003700 3439700 395110 FALSE TRUE 2480655.198 2822933.342 1685358.564 1640647.638 2676344.81 2711322.243 2712401.636 2704146.923 348400.5459 7.120124313 8.102551433 4.837416541 4.709084579 7.681804297 7.782198607 7.785296746 7.761603575 1 18.41038736 4.270005204 24.99046072 6.283114925 7.61133845 0.078049313 2.150131064 634.8149922 504506.717 0.535922353 1.417635593 18621.09451 -4.270005204 1.328223525 HMNLILCDCDEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HMNLILCDCDEFR 13 0 P14678-2;P14678;P14678-3;J3QLE5;P63162;P63162-2;J3KRY3;S4R3P3 P14678-2;S4R3P3 SNRPB;SNRPN Small nuclear ribonucleoprotein-associated proteins B and B;Small nuclear ribonucleoprotein-associated protein N 0 ;;; 138.77 4.53E-05 1299860000 1032850 1207150 681914 850700 1008770 1052500 969740 1112080 1543330 FALSE TRUE 896356.2556 1199220.152 1011689.891 1043864.437 988697.4506 1092990.356 875694.7641 874270.3462 1360879.286 0.658659637 0.881209792 0.743408987 0.767051456 0.726513704 0.803150116 0.643477179 0.64243049 1 20.37610767 3.498625642 2.152194528 0.740962246 0.77316973 0 0.113599227 2.095455135 19.37642397 0.034839454 0.054439201 3152.286213 -3.498625642 0.032207483 HMQLYCDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HMQLYCDR 8 0 P33992;B1AHB1;B1AHB2 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ;;;; 138.1 0.00071989 2667025000 1050431 1176335 762712 875135 1131126 1183462 1158399 1317228 1308242 FALSE TRUE 911613.8819 1168607.578 1131562.074 1073847.777 1108618.806 1228990.549 1046057.643 1035549.043 1153583.121 0.79024551 1.013024165 0.980910741 0.930880279 0.961022041 1.065368006 0.906790004 0.897680474 1 20.13769053 4.749146216 24.59377934 0.962799824 0.790245387 0.549076268 0.050721709 1069.025573 2483631.742 0.013010408 0.181972924 56123.68985 -4.749146216 -0.172554437 HMVFLGGAVLADIMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HMVFLGGAVLADIMK 15 0 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 122.35 0.00010944 10271000 36968 39746 26455 33333 37912 32736 40959 56515 41587 FALSE TRUE 32082.58514 39484.90591 39248.72649 40901.76711 37157.62537 33995.3751 36986.80248 44429.70705 36670.63224 0.874884974 1.076744618 1.070304058 1.115382109 1.013280195 0.927046332 1.008621892 1.211588248 1 15.16233752 4.642005286 0.019513533 2.012898232 5.42E-07 0.061485187 0.091498683 6591.615786 38.30589909 1833.936783 2125.201453 43853.60355 -4.642005286 -2.01289769 HMYHSLYLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HMYHSLYLK 9 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ; 103.56 0.0019673 3629100000 3382600 4515900 2575700 2981600 4211800 3844500 4304900 4783500 4533100 FALSE TRUE 2935580.84 4486234.756 3821317.135 3658617.851 4127993.42 3992400.403 3887411.461 3760585.75 3997202.082 0.734408914 1.122343745 0.955997985 0.915294693 1.032720722 0.99879874 0.972533132 0.940804511 1 21.93055908 4.760078876 24.74900621 0.985284487 0.73440862 0.666910569 0.057088587 3120.032972 3588407.969 0.013475159 0.628350476 57554.44578 -4.760078876 -0.250875868 HNAEVAAFHLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HNAEVAAFHLDR 12 0 O75063 O75063 FAM20B Glycosaminoglycan xylosylkinase 0 ; 140.08 3.43E-05 157362000 28759 27509 19328.9 19825.7 25644 30913 21243.8 29282 19928 FALSE TRUE 24958.42528 27328.29157 28676.42069 24327.4282 25133.73457 32102.24311 19183.57955 23020.27217 17572.13454 1.420341122 1.555206142 1.631925855 1.384432161 1.430317672 1.826883526 1.091704568 1.310044156 1 14.10100183 2.214983258 24.99759933 1.168850599 1.534054684 0.625854904 0.147667749 158.0280124 167545.9628 0.05807873 0.039181846 164.0526531 -2.214983258 0.365204084 HNALIQEVISQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HNALIQEVISQSR 13 0 A0A0A0MTN0;Q13617;Q13617-2 A0A0A0MTN0 CUL2 Cullin-2 0 112.42 0.00038864 0 185490 204310 96268 144200 198390 200350 198150 207000 198840 FALSE TRUE 160977.0265 202967.8742 142823.5268 176942.814 194442.4271 208057.5941 178933.4435 162734.6609 175333.3617 0.918119775 1.157611262 0.814582721 1.009179384 1.108987048 1.186640079 1.020532782 0.928144303 1 17.41974101 5.041902718 16.06954215 1.021274287 0.431943763 0.089547374 0.108331371 21284084.63 222483895.2 0.027053537 372455537.6 110129.2592 -5.041902718 -0.589330524 HNAQGQGNGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HNAQGQGNGLR 11 0 P35813;P35813-3;P35813-2;E9PL75;E9PJN3;E9PKB5;E9PP44 P35813 PPM1A Protein phosphatase 1A 0 ;; 128.87 0.001175 114877000 101735 96939 51136 65359 88404 95912 101068 111782 104026 FALSE TRUE 88290.46199 96302.20133 75865.54064 80199.7599 86644.93336 99601.7967 91266.44092 87878.28919 91728.16479 0.962522931 1.049865126 0.827069208 0.8743199 0.944583744 1.08583658 0.994966389 0.958029515 1 16.48507716 2.978796184 24.58490424 1.001913403 0.927323086 0.261339424 0.065095294 986.8996296 1144268.556 0.021995808 0.02223317 952.3491177 -2.978796184 -0.074590316 HNAVFDQLDLVTYEEVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HNAVFDQLDLVTYEEVVK 18 0 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8Y3B3;A0A2R8Y6F8;O14936-3;Q5JS72;O14936-5 A0A2U3TZM1;A0A2R8Y6F8 CASK Peripheral plasma membrane protein CASK 0 106.16 0.00045716 53153000 89493 71760 52612 85211 77181 71995 86368 108910 109800 FALSE TRUE 77666.2733 71288.60384 78055.33918 104559.4599 75645.2491 74764.69424 77992.04465 85620.44404 96819.56908 0.802175366 0.736303668 0.80619383 1.079941389 0.781301237 0.772206435 0.805540093 0.884329943 1 16.56301105 1.317458009 2.643487792 1.02205309 0.828422639 0.257368667 0.093697811 0.610076793 5.484487172 0.242900421 0.025546201 20.77102883 -1.317458009 -0.193630451 HNDDEQYAWESSAGGSFTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 28 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 ;;;;;;;;;;;;;;;;;;;;;;;;;;; 254.26 4.00E-36 2725812900 1943767 1461144.7 994586.5 1362584.3 1731237.5 1663117.6 1612849.5 1835560.4 1764094.7 FALSE TRUE 1686893.266 1451546.344 1475571.858 1671979.891 1696789.261 1727098.81 1456435.604 1443040.093 1555545.434 1.084438441 0.933143007 0.948588081 1.074851209 1.090800194 1.110285031 0.936286123 0.927674667 1 20.5689891 2.206547142 24.99654907 0.948267605 1.035168238 0.298271533 0.061363119 259.0726057 202285.5304 0.027101423 0.018273534 160.896702 -2.206547142 0.086900633 HNDLDDVGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HNDLDDVGK 9 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;; 104.52 0.0032464 2204340000 5662400 3471280 3245620 3657980 3689980 3177280 4242770 4950480 7512600 FALSE TRUE 4914099.493 3448476.933 4815212.688 4488580.268 3616556.617 3299512.018 3831306.818 3891858.377 6624468.986 0.741810325 0.520566545 0.726882819 0.67757586 0.545939097 0.498079472 0.57835682 0.587497411 1 22.65937338 1.237052057 24.95627951 1.000000496 0.604623422 0.685968631 0.082955098 21.91706884 362448.8978 0.123075456 0.02008076 17.26044774 -1.237052057 -0.395377075 HNDLDDVGKDVYHHTFFEMLGSWSFGDYFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HNDLDDVGKDVYHHTFFEMLGSWSFGDYFK 30 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;; 127.63 4.03E-06 834473000 569130 324263 113686 232991 188744 175118 418570 469900 133071 FALSE TRUE 493918.0285 322132.895 168664.9299 285895.1676 184988.3637 181854.9028 377977.1458 369415.5418 117339.498 4.209307497 2.745306572 1.437409677 2.43647853 1.576522542 1.549818313 3.221226887 3.148262504 1 16.8403292 2.224520057 24.9966917 2.632477722 2.27546558 0 0.998971005 1167.833759 2079101.674 0.413591799 0.280366551 167.694978 -2.224520057 -0.357012141 HNESVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HNESVVK 7 0 O00487 O00487 PSMD14 26S proteasome non-ATPase regulatory subunit 14 0 ;;; 86.011 0.02039 983590000 2755800 2536940 1396640 1952740 1912810 2450450 2927210 3289700 3244200 FALSE TRUE 2391614.048 2520274.674 2072059.775 2396139.463 1874748.823 2544720.397 2643329.625 2586223.255 2860674.372 0.836031556 0.881007185 0.724325633 0.837613496 0.655352053 0.889552625 0.924023248 0.904060693 1 21.44792386 2.494123319 23.12274272 0.929999421 0.789542019 0.534555637 0.067253053 219.833388 298973.5792 0.022854737 0.019640647 311.9775326 -2.494123319 -0.140457402 HNGAAEPEPEAETAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HNGAAEPEPEAETAR 15 0 Q9Y446;Q9Y446-2;E9PQ15 Q9Y446 PKP3 Plakophilin-3 0 82.877 0.0097238 520740000 125870 135960 73564 104210 137990 144920 128840 143860 143220 FALSE TRUE 109235.9606 135066.8698 109139.7965 127872.4733 135244.269 150495.1662 116345.1166 113096.6585 126288.6948 0.864970224 1.069508795 0.864208761 1.012540936 1.070913507 1.19167568 0.921263117 0.89554064 1 16.94636597 4.762892668 23.33407611 0.994907479 0.864969838 0.165656667 0.095902896 6230.373992 5974597.165 0.02485047 1.372866244 57928.55129 -4.762892668 -0.129937641 HNGPNDASDGTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HNGPNDASDGTVR 13 0 P31942;P31942-2 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;;; 150.46 0.00010295 458042000 451786 374325 187619 254674 349966 363593 339570 400924 351397 FALSE TRUE 392081.3354 371866.0344 278352.1759 312501.6241 343002.3613 377580.658 306638.5537 315189.5226 309855.247 1.26536936 1.200128247 0.898329716 1.008540689 1.106976127 1.218571129 0.989618722 1.017215379 1 18.24123487 4.413167917 8.048682917 1.03871748 1.249374807 0.503007491 0.083187822 0.186495575 20.43268055 0.021797762 0.058281693 25892.13824 -4.413167917 0.210657327 HNGS(ph)SEILNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HNGSSEILNK 10 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2 Q8TDM6-4 DLG5 Disks large homolog 5 1 HNGS(0.729)S(0.271)EILNK 71.548 0.058894 182090000 370610 292710 193860 225780 314160 278750 338630 386100 349000 TRUE FALSE 321632.9495 290787.1687 287611.3444 277046.7998 307908.8306 289473.6929 305789.7147 303535.5196 307741.6176 1.045139595 0.94490687 0.934587095 0.900257827 1.000543355 0.940638758 0.993657332 0.986332372 1 18.23136003 2.220535256 24.26965485 0.991885748 0.958114349 0.127921808 0.03923459 345.2668821 464868.2677 0.015760238 0.010653344 166.1633563 -2.220535256 -0.033771399 HNGSLS(ph)PGLEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HNGSLSPGLEAR 12 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 HNGSLS(1)PGLEAR;HNGSLS(1)PGLEAR;HNGS(0.001)LS(0.999)PGLEAR;HNGSLS(1)PGLEAR;HNGS(0.002)LS(0.998)PGLEAR 172.2 2.34E-05 3505000000 1796960 1543780 804499 1305790 2073180 1750830 1541880 2174780 1911860 TRUE FALSE 1559487.183 1533638.808 1193557.407 1602289.577 2031927.774 1818185.563 1392348.715 1709720.221 1685842.089 0.925049382 0.909716763 0.707988853 0.950438708 1.205289503 1.078502889 0.82590696 1.01416392 1 20.68503798 3.484248773 24.99746063 1.017276869 0.849700763 0.357447288 0.108212547 389.4155316 1365749.85 0.032040061 0.043101041 3049.641386 -3.484248773 -0.167576105 HNGYDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HNGYDPR 7 0 P12532;P12532-2;F8WCN3;C9JSQ1;P17540;C9J8F6;C9J6W7;C9JT96;D6RHV3;D6R998 P12532 CKMT1A;CKMT1B;CKMT2 "Creatine kinase U-type, mitochondrial;Creatine kinase S-type, mitochondrial" 0 ; 81.191 0.027872 1028650000 817750 815360 454440 643520 860060 983840 661560 935550 868810 FALSE TRUE 709682.2656 810003.8465 674208.704 789641.0516 842946.4887 1021688.961 597402.013 735489.913 766100.2716 0.926356891 1.05730787 0.88005282 1.030728066 1.100308302 1.333623025 0.779796112 0.960043927 1 19.54717371 HNIAGTTHSGAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HNIAGTTHSGAEK 13 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 0 134.88 5.23E-05 49703000 107820 95962 65982 87047 93227 82287 113180 123330 160280 FALSE TRUE 93571.31382 95331.6193 97891.1159 106812.3518 91371.9651 85452.63414 102203.821 96956.83926 141331.881 0.662067986 0.674523106 0.692632938 0.755755538 0.646506397 0.604623907 0.723147674 0.686022422 1 17.10872741 1.236559201 6.510782818 1.009228477 0.681365906 0.858459149 0.040751301 0.045123821 8.896453303 0.065093001 0.01029223 17.24087094 -1.236559201 -0.327862571 HNIAGTTHSGAEKDVDVSEDS(ph)PPPLPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HNIAGTTHSGAEKDVDVSEDSPPPLPER 28 1 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 HNIAGTTHSGAEKDVDVS(0.003)EDS(0.997)PPPLPER 184.1 6.80E-18 306740000 267460 272580 92125 99803 223250 200100 268980 303280 53875 TRUE FALSE 232114.4833 270789.404 136676.9581 122464.7965 218807.7618 207797.9765 242894.361 238425.9321 47505.95887 4.886007752 5.700114479 2.877048719 2.577882848 4.605901385 4.374145505 5.112924078 5.018863692 1 15.53582087 4.253938081 24.9996185 3.874098974 5.29306156 0.205077034 1.286548991 440.4897352 716105.1606 0.327498903 0.859571445 17944.77762 -4.253938081 1.418962586 HNIICLQNDHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HNIICLQNDHK 11 0 F5H169;F5H5V4;F5GX23;J3KN29;O00233-2;O00233 F5H169 PSMD9 26S proteasome non-ATPase regulatory subunit 9 0 ; 99.215 0.0028573 397500000 778360 645890 413670 492480 689850 588960 814040 922270 744490 FALSE TRUE 675497.7539 641647.1061 613722.1956 604305.1111 676123.3347 611617.6723 735094.5261 725049.7376 656477.2403 1.028973607 0.977409523 0.934872008 0.920527132 1.029926543 0.931666225 1.119756301 1.104455255 1 19.32438547 2.238235939 24.9999999 1.082804253 0.969675465 0.506311643 0.048268464 6.376326944 490896.2895 0.018671106 0.013477497 173.0756371 -2.238235939 -0.113128788 HNIMDFAMPYFIQVMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HNIMDFAMPYFIQVMK 16 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5;J3KRF5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 160.81 8.65E-09 1591216000 2326880 1950480 1260258 1419540 1949720 1804870 2422340 2690830 2090650 FALSE TRUE 2019376.912 1937667.168 1869722.984 1741868.253 1910924.387 1874304.517 2187421.84 2115416.945 1843495.739 1.095406336 1.051083074 1.014226909 0.944872406 1.036576514 1.01671215 1.186561918 1.147503029 1 20.81401265 2.261892023 24.9440636 1.122019453 1.023790471 0.303965432 0.059731553 236.1958568 252520.9357 0.022711773 0.017581515 182.7645761 -2.261892023 -0.098228983 HNIQFSSFDIFSDEEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HNIQFSSFDIFSDEEVR 17 0 O76003 O76003 GLRX3 Glutaredoxin-3 0 ;;; 258.82 3.53E-27 773490000 1077370 1082420 488310 734900 1102680 1108400 1084290 1204720 1045750 FALSE TRUE 934992.8248 1075309.512 724458.3493 901770.2772 1080738.825 1151040.865 979135.7227 947100.0031 922122.6263 1.013957144 1.166124202 0.785642092 0.977928804 1.172012045 1.248251406 1.061828107 1.027086828 1 19.81459909 HNKPEVEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HNKPEVEVR 9 1 F8WCF6;P59998;P59998-3;F8WDD7;H7C0A3;A0A0A6YYG9;P59998-2;F8WE39 F8WCF6 ARPC4-TTLL3;ARPC4 Actin-related protein 2/3 complex subunit 4 0 ;;; 141.88 6.35E-05 3729050000 8044600 7365560 4299670 5818150 7238400 6618780 7926540 9006700 8679800 FALSE TRUE 6981485.728 7317175.151 6379004.794 7139249.882 7094370.002 6873408.75 7157825.371 7080687.295 7653683.932 0.912173247 0.956033097 0.833455477 0.932786087 0.926922259 0.898052338 0.935213086 0.925134531 1 22.86772289 -0.843168867 1.089933527 9.999999007 0.911021702 0.411566094 0.032368557 161.4729506 2.422658604 3559.636991 0.009669065 0.143493138 0.843168867 -9.088977305 HNKS(ph)PTLSCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HNKSPTLSCR 10 1 Q5T5U3;A0A087WW76;A0A452Q6Z5 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 HNKS(0.964)PT(0.033)LS(0.003)CR;HNKS(0.97)PT(0.03)LSCR;HNKS(0.971)PT(0.028)LS(0.001)CR 132.06 0.00014152 386000000 499050 434960 244572 322500 457775 394720 469077 538290 455351 TRUE FALSE 433099.2781 432102.7191 362847.8372 395728.5541 448666.1731 409905.1338 423585.9847 423180.8725 401519.9235 1.078649533 1.076167567 0.90368576 0.985576383 1.117419453 1.020883672 1.05495633 1.053947383 1 18.61511205 HNLEIIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HNLEIIK 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 72.485 0.051478 209990000 272670 282260 162130 212910 317840 233130 338630 339940 368660 FALSE TRUE 236635.9686 280405.8155 240536.6103 261254.4696 311515.6058 242098.662 305789.7147 267246.4764 325077.4348 0.727937234 0.862581605 0.739936349 0.803668424 0.958281236 0.744741517 0.940667306 0.822100976 1 18.31042389 -2 0.208360739 1.693477709 0.751649302 0.339122616 0.078229889 125.3123288 1.895928708 37.74811742 0.415934148 0.01 2 -0.941828407 HNLFEDNMALPSESVS(ph)SLTDLKPPTGSNQASPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HNLFEDNMALPSESVSSLTDLKPPTGSNQASPAR 34 1 Q9BZQ8 Q9BZQ8 FAM129A Protein Niban 1 HNLFEDNMALPSESVS(0.851)S(0.145)LT(0.004)DLKPPTGSNQASPAR;HNLFEDNMALPSES(0.001)VS(0.841)S(0.157)LT(0.001)DLKPPTGSNQASPAR 284.47 3.73E-74 692620000 387410 374660 216790 280740 404770 307550 399850 528410 477020 TRUE FALSE 336212.7869 372198.8338 321630.3691 344486.3078 396715.8689 319381.6475 361072.6085 415413.6336 420627.239 0.799312921 0.884866217 0.764644653 0.818982405 0.943153063 0.759298538 0.858414708 0.987605165 1 18.68218275 1.756610268 3.716475251 0.997980846 0.831259658 0.609263795 0.054082405 0.127461218 3.642899815 0.034358813 0.013924693 57.09660271 -1.756610268 -0.166721188 HNLFEDNMALPSESVSS(ph)LTDLKPPTGSNQASPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HNLFEDNMALPSESVSSLTDLKPPTGSNQASPAR 34 1 Q9BZQ8 Q9BZQ8 FAM129A Protein Niban 1 HNLFEDNMALPS(0.013)ES(0.079)VS(0.13)S(0.682)LT(0.096)DLKPPTGSNQASPAR;HNLFEDNMALPS(0.001)ES(0.004)VS(0.212)S(0.572)LT(0.212)DLKPPTGSNQASPAR;HNLFEDNMALPS(0.02)ES(0.142)VS(0.142)S(0.665)LT(0.031)DLKPPTGSNQASPAR 259.77 7.60E-60 998090000 361283 405128 250388 293323 432002 354452 443079 547105 481626 TRUE FALSE 313538.5362 402466.6875 371476.4743 359926.4703 423406.0054 368087.9978 400109.2668 430110.8533 424688.723 0.73827846 0.947674534 0.874702939 0.84750654 0.996979629 0.86672421 0.942123596 1.012767305 1 18.69604627 8 0.065222536 1.35274896 8.72E-10 0.499919459 0.060115917 561.6929345 3.533764368 17.25577655 76.52121394 100000000 -8 -1.352748959 HNMNIGTWDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HNMNIGTWDEK 11 0 A0A024R7W5;A0A087X0Q1;A0A087WY31;Q7Z739 A0A024R7W5 YTHDF3 YTH domain-containing family protein 3 0 87.001 0.0085015 0 204000 173490 110990 138600 164440 154640 204290 226980 198900 FALSE TRUE 177040.8831 172350.3328 164665.1352 170071.2484 161167.9657 160589.1009 184477.9872 178442.0934 175386.2686 1.009434117 0.982690003 0.938871307 0.969695346 0.918931493 0.915630979 1.051838258 1.017423398 1 17.42017627 2.232925795 24.99999985 1.023105217 0.955270358 0.516778328 0.030634193 113.1811907 502144.0301 0.01286777 0.008948166 170.9723162 -2.232925795 -0.067834859 HNNCMASHLTPAVYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HNNCMASHLTPAVYAR 16 0 P12532;P12532-2;F8WCN3;C9JSQ1;C9J8F6;C9J6W7;C9JT96;C9JJX8;C9J995 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ;; 192.24 3.27E-10 1033583000 422083 449464 211007 388470 510214 489316 370487 523620 498584 FALSE TRUE 366303.6621 446511.4414 313050.691 476678.0509 500061.7396 508140.3031 334557.2278 411647.9378 439641.9675 0.833186295 1.015625155 0.712058252 1.084241465 1.137429492 1.155804816 0.76097655 0.936325393 1 18.74596958 4.752505053 22.92301829 0.968099863 0.833185998 0.084451481 0.145349316 2242.644185 3686434.831 0.036398711 0.649658562 56559.43373 -4.752505053 -0.134913865 HNNLDLVIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HNNLDLVIIR 10 0 A0A087X2E5;A0A087WZN1;O43837-2;O43837 A0A087X2E5 IDH3B "Isocitrate dehydrogenase [NAD] subunit, mitochondrial;Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial" 0 120.09 0.0031057 0 35250 33199 23774 33544 43854 48694 31390 39807 38206 FALSE TRUE 30591.62319 32980.91358 35271.18592 41160.67789 42981.3912 50567.28969 28345.80263 31294.58283 33689.3302 0.908050798 0.978972078 1.046954205 1.221771927 1.275816139 1.500988277 0.841388133 0.928916741 1 15.04000413 HNS(ph)SDGFFNNGPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HNSSDGFFNNGPLR 14 0 Q9HC44 Q9HC44 GPBP1L1 Vasculin-like protein 1 1 HNS(0.5)S(0.5)DGFFNNGPLR 88.548 0.0041884 53960000 73425 75373 57429 60084 71346 94354 58020 76543 85082 TRUE FALSE 63721.70021 74877.8698 85201.85649 73726.99053 69926.35419 97983.85944 52393.22933 60174.87511 75023.70289 0.849354241 0.998056173 1.135665839 0.982715964 0.932056823 1.306038701 0.698355684 0.802078181 1 16.19505885 2.206037419 24.99999058 0.821306306 1.030007665 0.307018683 0.14152448 220.7341678 169672.8357 0.056112549 0.03783406 160.7079715 -2.206037419 0.208701359 HNS(ph)TTSSTSSGGYR ddPTM_MDA-MB-175_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(0.48)T(0.48)T(0.04)S(0.001)STSSGGYR;HNS(0.477)T(0.477)T(0.045)SSTSSGGYR;HNS(0.967)T(0.032)T(0.001)SSTSSGGYR;HNS(0.949)T(0.043)T(0.003)S(0.002)S(0.003)T(0.001)SSGGYR 262.83 1.46E-24 892847000 604090 541034 176287.5 323262 621318 576681 593474 587516 739558 TRUE FALSE 524257.9759 537479.912 261540.7246 396663.5779 608954.9874 598866.2912 535918.9828 461880.2755 652128.2957 0.803918461 0.824193515 0.401057164 0.608260032 0.933796296 0.91832588 0.821799922 0.708265963 1 19.31479629 3.24485354 24.99790405 0.853412747 0.652681276 0.372274287 0.138165416 188.1589677 747435.0586 0.042580625 0.053600193 1757.330879 -3.24485354 -0.200731471 HNS(ph)WDTVNTVLPEDPEVADLFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HNSWDTVNTVLPEDPEVADLFSR 23 0 Q8N961 Q8N961 ABTB2 Ankyrin repeat and BTB/POZ domain-containing protein 2 1 HNS(0.714)WDT(0.234)VNT(0.052)VLPEDPEVADLFSR;HNS(0.5)WDT(0.5)VNTVLPEDPEVADLFSR 92.034 0.0032288 231200000 178486 145963 88859 105525 140986 168292 148703 148038 172705 TRUE FALSE 154898.6229 145004.1594 131831.5096 129486.0641 138180.6544 174766.3021 134281.8059 116381.2257 152288.0116 1.017142592 0.952170548 0.865672276 0.850270896 0.907363967 1.147603808 0.881762159 0.764217908 1 17.21644285 2.323788391 0.016023265 4.98E-07 1.819962041 0 0.106081015 7071.378679 74.06720392 4310.423599 4100.628425 210.7600976 -2.323788391 1.819961542 HNS(ph)WSSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HNSWSSSSR 9 0 Q96F86;H3BPW9;H3BQ37 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 1 HNS(0.967)WS(0.033)SSSR;HNS(0.97)WS(0.029)SSSR;HNS(0.939)WS(0.057)S(0.003)S(0.001)SR;HNS(0.87)WS(0.129)S(0.001)SSR 137.55 0.00016947 3260460000 1511680 1692390 931920 1414430 2304360 2547910 2012610 2137210 2508140 TRUE FALSE 1311907.658 1681272.579 1382599.629 1735597.95 2258507.744 2645929.746 1817427.392 1680184.273 2211630.546 0.59318572 0.760195947 0.625149454 0.78475944 1.021195763 1.196370592 0.821759039 0.759703865 1 21.07667897 3.453342106 4.759818604 0.935468467 0.673125594 0.546286505 0.124751212 0.181127966 10.4366423 0.040565187 0.054913524 2840.15542 -3.453342106 -0.262342873 HNST(ph)TSSTSSGGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HNSTTSSTSSGGYR 14 0 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12 A0A0A0MRT6 ABI1 Abl interactor 1 1 HNS(0.148)T(0.744)T(0.091)S(0.008)S(0.008)T(0.001)SSGGYR 187.71 1.03E-05 123880000 117990 92983 33988 66155 107830 105850 116050 110800 138580 TRUE FALSE 102397.3226 92372.18855 50424.71048 81176.50387 105684.394 109922.118 104795.4889 87106.28225 122197.2303 0.837967623 0.755927023 0.412650192 0.664307233 0.864867344 0.899546723 0.857592996 0.712833524 1 16.89885206 3.243764417 21.52554026 0.848627131 0.655794945 0.369521351 0.127669599 26.61291668 110078.8834 0.03850994 0.0480182 1752.929367 -3.243764417 -0.192832186 HNT(ph)PSLLEAALTQEASTPDSQVWPTAPDITR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HNTPSLLEAALTQEASTPDSQVWPTAPDITR 31 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 HNT(0.5)PS(0.5)LLEAALTQEASTPDSQVWPTAPDITR;HNT(0.791)PS(0.207)LLEAALT(0.002)QEASTPDSQVWPTAPDITR;HNT(0.725)PS(0.275)LLEAALTQEASTPDSQVWPTAPDITR 176.78 1.53E-17 501536000 186868 172709 104893 136264 244365 231664 171505 205658 223126 TRUE FALSE 162172.9203 171574.4632 155619.6056 167204.8239 239502.6146 240576.264 154872.4715 161679.6371 196748.2985 0.824265936 0.872050557 0.790957822 0.84984127 1.21730463 1.222761599 0.787160411 0.821758757 1 17.58599163 3.442674948 24.99776845 0.985090998 0.831222244 0.267641045 0.141351912 319.9057525 232155.3943 0.046742653 0.060344757 2771.24516 -3.442674948 -0.153868754 HNTEDFTLFTLDDVDAAFDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HNTEDFTLFTLDDVDAAFDK 20 0 Q9P2I0 Q9P2I0 CPSF2 Cleavage and polyadenylation specificity factor subunit 2 0 114.46 0.00012384 32342000 41779 36913 22575 32355 43539 32833 40873 49053 57613 FALSE TRUE 36257.7993 36670.51607 33492.34551 39701.69727 42672.65908 34096.10676 36909.14275 38563.39768 50802.05677 0.71370731 0.721831327 0.659271448 0.781497833 0.839978965 0.67115603 0.726528513 0.759091268 1 15.63259929 1.228119969 3.696098438 1.038706732 0.732029579 0.728933479 0.051217739 0.15880871 3.356775424 0.137635071 0.013354888 16.90907961 -1.228119969 -0.306677152 HNVEVLGILSDDVETDTVAPGENLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HNVEVLGILSDDVETDTVAPGENLK 25 0 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ; 237.32 1.82E-38 242087000 715320 543320 412547 516910 573130 467530 635250 787030 846600 FALSE TRUE 620788.6496 539750.8951 612056.1091 634282.316 561725.8343 485516.1816 573643.5528 618729.7592 746515.9124 0.831581269 0.723026644 0.81988354 0.849656793 0.75246331 0.650376199 0.768427763 0.828823269 1 19.50981349 1.25033522 2.406555667 1.056090044 0.769247916 0.611707918 0.057334343 0.393862627 2.482668935 0.236227918 0.015915792 17.79652546 -1.25033522 -0.286842128 HNVFQNDEFDVFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HNVFQNDEFDVFSR 14 0 Q9H1I8;H7C3Y4;Q9H1I8-3 Q9H1I8 ASCC2 Activating signal cointegrator 1 complex subunit 2 0 ; 190.44 6.04E-07 258060000 245090 240700 145270 160692 247790 251080 222510 264330 261310 FALSE TRUE 212700.7355 239118.8259 215523.0579 197179.5746 242859.4638 260739.2101 200931.0144 207805.0865 230418.2295 0.923107239 1.037760017 0.935355932 0.855746418 1.053994141 1.131591067 0.872027421 0.901860443 1 17.81389533 HNVGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HNVGVK 6 0 O75874;C9J4N6;C9JLU6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;;; 83.229 0.057225 912210000 5215200 4054460 2578100 3119040 2613800 3732960 4811680 5336800 5084340 FALSE TRUE 4525998.106 4027825.985 3824877.783 3827265.704 2561790.494 3876569.387 4345044.014 4195566.851 4483275.117 1.009529415 0.898411514 0.853143669 0.853676298 0.571410504 0.864673545 0.969167383 0.935826319 1 22.0961216 2.312112539 5.200442955 0.961553026 0.831352736 0.229368004 0.109220979 0.315094532 15.38217764 0.044040826 0.033323699 205.1693766 -2.312112539 -0.13020029 HNVMISTEWAAPNVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HNVMISTEWAAPNVLR 16 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 62.445 0.07683 363830000 393690 383440 238560 295460 372670 364740 400550 494820 456860 FALSE TRUE 341662.869 380921.1574 353928.4139 362548.7088 365254.5961 378771.7838 361704.7227 389006.5937 402850.5313 0.848113239 0.945564491 0.878560127 0.899958373 0.906675225 0.940229079 0.897863338 0.965635052 1 18.61988513 -2 0.499085474 4.376723005 0.894347892 0.614439435 0.027379719 70.97272569 0.800105537 257.9640923 0.016530386 0.01 2 -3.482375114 HNVQTLDIISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HNVQTLDIISR 11 0 Q06203 Q06203 PPAT Amidophosphoribosyltransferase 0 119.39 0.00059317 197940000 106210 109450 50766 72559 109340 111570 104150 129730 92979 FALSE TRUE 92174.0794 108731.0157 75316.6074 89034.62994 107164.3479 115862.1701 94049.54903 101988.2491 81987.12854 1.124250611 1.326196169 0.91863941 1.085958632 1.307087464 1.413175119 1.147125783 1.243954397 1 16.32310981 3.254643577 24.94568763 1.228888914 1.114997841 0.12386743 0.142777611 512.0432145 794206.5055 0.041534478 0.053452338 1797.395198 -3.254643577 -0.113891073 HNYECLVYVQLPFMEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HNYECLVYVQLPFMEDLR 18 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 123.41 3.40E-05 1566710000 1221870 1142810 704180 908970 1029110 981770 1187050 1339650 1191860 FALSE TRUE 1060396.784 1135302.806 1044723.803 1115365.531 1008632.724 1019539.327 1071930.074 1053176.273 1050959.669 1.008979522 1.080253448 0.994066504 1.061282906 0.959725434 0.97010319 1.019953577 1.002109124 1 20.00327588 3.245339228 24.99971994 0.993049017 1.036290503 0.378720849 0.029015994 177.0962546 653131.7833 0.008139043 0.010262812 1759.297268 -3.245339228 0.043241487 HNYPDLVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HNYPDLVER 9 0 Q9NZT2-2;Q9NZT2;A0A087X028;Q4VXW3 Q9NZT2-2 OGFR Opioid growth factor receptor 0 ; 117.52 0.0011383 353640000 212283 214445 128322 166226 216020 210701 205256 216720 286640 FALSE TRUE 184229.2637 213036.2967 190378.9484 203970.1539 211721.6246 218806.8038 185350.3047 170376.1145 252753.7457 0.728888362 0.842861086 0.753219098 0.806991617 0.837659691 0.865691637 0.733323671 0.674079484 1 17.94737295 6.676437962 6.072752894 0.794993091 0.747389226 0 0.091784763 0 0 0.020066777 0 4747204.737 -6.676437962 -0.047603865 HPAKPDPSGECNPDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HPAKPDPSGECNPDLR 16 1 Q16576;E9PC52;Q16576-2;Q5JP01 Q16576 RBBP7 Histone-binding protein RBBP7 0 ;;; 258.14 6.44E-27 3132430000 2764990 2315340 1525980 1999050 2160130 1995420 2271430 2837200 3218560 FALSE TRUE 2399589.566 2300130.379 2263949.032 2452964.856 2117147.639 2072185.099 2051147.068 2230486.859 2838065.503 0.845501826 0.810457115 0.79770852 0.864308753 0.745982655 0.730139983 0.722727177 0.785918033 1 21.43647646 1.238782727 12.07982955 1.000280214 0.784975365 0.675696769 0.046153504 0.036575352 311.3287712 0.067305087 0.01212523 17.32936811 -1.238782727 -0.21530485 HPALFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HPALFK 6 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 84.566 0.055705 1063000000 2622800 1635300 1267800 1483600 1653000 1516800 1704000 2075600 2848400 FALSE TRUE 2276190.335 1624557.607 1880912.321 1820474.055 1620108.534 1575152.278 1538746.342 1631749.092 2511665.397 0.906247439 0.646804948 0.748870579 0.724807555 0.645033585 0.627134601 0.612639862 0.649668182 1 21.26021285 1.234452205 24.9954853 1.000000458 0.686554164 0.549386737 0.086455098 92.11206525 560329.7392 0.155551299 0.020729333 17.15742878 -1.234452205 -0.313446294 HPDASVNFSEFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HPDASVNFSEFSK 13 0 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ; 158.81 4.51E-05 3153900000 5415500 4501600 2898100 4005400 4369700 3738500 4565300 5450800 7279300 FALSE TRUE 4699827.954 4472028.693 4299630.854 4914887.289 4282751.519 3882322.514 4122557.909 4285188.838 6418749.447 0.732203055 0.696713391 0.669854913 0.76570792 0.667225221 0.60484095 0.642268084 0.66760494 1 22.61386082 1.237395176 24.99751402 1.000000385 0.678387712 0.835022731 0.044577248 11.95461085 256300.8437 0.068897282 0.011516992 17.27408991 -1.237395176 -0.321612673 HPDGRPTGDAFALFACEELAQAALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HPDGRPTGDAFALFACEELAQAALR 25 1 Q9H6T0-2;Q9H6T0 Q9H6T0-2 ESRP2 Epithelial splicing regulatory protein 2 0 ; 133.95 3.31E-05 121179000 189028 180820 109228 141683 164773 189349 159395 188848 172533 FALSE TRUE 164047.4709 179632.1815 162051.0261 173854.2906 161494.3397 196633.3786 143936.8974 148464.3248 152136.3453 1.078292439 1.180731542 1.065169706 1.142753169 1.061510577 1.292481282 0.946104609 0.975863621 1 17.21500533 2.196694999 24.99995102 0.973217797 1.132408549 0.557473032 0.068313868 99.63892128 59498.4426 0.025690866 0.01732095 157.2877859 -2.196694999 0.159190752 HPDSHQLFIGNLPHEVDKSELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HPDSHQLFIGNLPHEVDKSELK 22 1 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 120.64 9.58E-06 386410000 590210 466830 328640 427400 430080 355480 597440 638220 536840 FALSE TRUE 512212.2531 463763.363 487571.4032 524447.7024 421522.2494 369155.5456 539500.3608 501741.6196 473375.3868 1.082042429 0.979694712 1.02998892 1.107889673 0.89046085 0.779836797 1.139688239 1.059923337 1 18.85262517 -0.37138557 9.352795515 0.938157535 1.009882959 0 0.106854982 0 0 0 0.024661258 0.425220731 0.37138557 0.071725424 HPDSHQLFIGNLPHEVDKSELKDFFQSYGNVVELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HPDSHQLFIGNLPHEVDKSELKDFFQSYGNVVELR 35 2 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 44.099 0.035204 383530000 278570 255760 103190 127720 204650 179430 309920 348940 40047 FALSE TRUE 241756.2687 254079.8957 153093.0291 156720.7781 200577.8654 186332.7882 279864.0061 274321.8965 35312.68928 6.846158523 7.19514432 4.335354578 4.438086741 5.680050698 5.276652444 7.925309904 7.768366047 1 15.10789908 4.271078365 24.88984948 5.570539891 7.020654047 0.109132056 1.950288065 502.5161109 384629.4588 0.497762514 1.316735538 18667.16497 -4.271078365 1.450114156 HPDVEVDGFSELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HPDVEVDGFSELR 13 0 P09874;Q5VX84;Q5VX85 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;; 242.48 6.18E-17 4259000000 3201980 2656210 1506220 2176900 2703740 2767290 2300010 2842810 2724900 FALSE TRUE 2778830.23 2638761.182 2234633.03 2671198.417 2649940.864 2873749.437 2076955.384 2234897.204 2402765.426 1.156513324 1.098218392 0.930025464 1.111718351 1.102871231 1.196017475 0.86440206 0.93013541 1 21.19626438 2.229953734 24.9998796 0.928429325 1.09222392 0.523221985 0.075254179 154.4262436 448547.6866 0.031151321 0.021369518 169.8062744 -2.229953734 0.163794595 HPDYAILAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HPDYAILAAR 10 0 P23921 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ;;;; 137.98 7.69E-05 2103800000 1239320 1447428 616185 909818 1544847 1546316 1266501 1388273 1429833 FALSE TRUE 1075540.722 1437919.75 914174.127 1116406.083 1514107.567 1605803.777 1143675.928 1091401.623 1260799.772 0.853062275 1.140482242 0.725074788 0.885474528 1.200910407 1.273639013 0.907103534 0.865642307 1 20.26590775 5.028320903 14.85551581 0.988189111 0.497120224 0.067014943 0.167144886 4377015.593 66452829.8 0.043070589 51752106.47 106738.4526 -5.028320903 -0.491068888 HPECNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HPECNLR 7 0 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8;K7EMK2;H0YH35 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 0 ;;; 96.253 0.012868 327611000 294271 283501 139154 189531 188959 294632 245841 276111 276887 FALSE TRUE 255382.3418 281638.6633 206449.3398 232566.9103 185199.0856 305966.6837 221999.3777 217066.8113 244153.7343 1.045989907 1.153530025 0.845571093 0.952542917 0.758534725 1.253172246 0.909260628 0.889057921 1 17.89743032 4.248204085 24.95392518 0.941971576 1.099759989 0.197778464 0.130349697 305.4850646 790471.7213 0.031279619 0.080497925 17709.40971 -4.248204085 0.157788413 HPEHYVDY(ph)T(ph)Y(ph)MAT(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HPEHYVDYTYMATK 14 0 H3BLX4;Q96JM2-2;Q96JM2;Q96JM2-3 H3BLX4 ZNF462 Zinc finger protein 462 4 HPEHY(0.108)VDY(0.976)T(0.969)Y(0.978)MAT(0.969)K 49.049 0.055397 386700000 198770 236480 146820 185460 139190 195060 172460 178970 158030 TRUE FALSE 172502.0409 234926.5473 217822.6431 227571.5276 136420.3913 202564.0844 155734.8557 140698.6582 139347.8734 1.237923742 1.685899767 1.563157282 1.633118052 0.978991555 1.453657522 1.117597649 1.009693616 1 17.08833146 2.522477275 0.731031363 0.953765431 1.539524218 0.479000193 0.196521534 0.67029701 0.796495066 0.25916839 0.128050967 333.0253356 -2.522477275 0.585758787 HPELADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 135.77 0.0030453 7378310000 14957400 12915660 9515190 11702300 11726540 10156140 14906270 16787210 16647760 FALSE TRUE 12980741.69 12830816.18 14116767.71 14359486.07 11493204.8 10546853.28 13460662.23 13197395.78 14679680.78 0.884265938 0.874052806 0.961653589 0.978187897 0.782932883 0.718466119 0.916958784 0.899024712 1 23.80731726 1.183165315 1.944293915 1.053982771 0.872441937 0.210041227 0.076681012 1.724319572 5.561329857 0.602349356 0.022677202 15.24632997 -1.183165315 -0.181540834 HPELTKPPPLMAAEPTAPLSHSASSDPADRLS(ph)PFLAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HPELTKPPPLMAAEPTAPLSHSASSDPADRLSPFLAAR 38 2 Q9ULP9-2;Q9ULP9 Q9ULP9-2 TBC1D24 TBC1 domain family member 24 1 HPELTKPPPLMAAEPTAPLSHSASSDPADRLS(1)PFLAAR;HPELTKPPPLMAAEPTAPLSHSASSDPADRLS(0.999)PFLAAR 246.91 1.08E-50 4517500000 2423300 1937920 1063590 1683610 2063240 1952240 1733470 2328200 2523700 TRUE FALSE 2103054.765 1925189.676 1577945.681 2065899.383 2022185.561 2027343.936 1565358.346 1830332.548 2225351.061 0.945044044 0.865117289 0.709077192 0.92834763 0.908704067 0.911022073 0.703420855 0.822491597 1 21.08560152 1.233860479 24.90783002 1.000000248 0.843462844 0.235209241 0.084934491 212.3024938 1124925.419 0.166193671 0.021035556 17.13406771 -1.233860479 -0.156537404 HPENYDLATLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HPENYDLATLK 11 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;P78347-5 A0A494C1K3 GTF2I General transcription factor II-I 0 ; 160.52 2.74E-05 573880000 903100 764930 454100 604380 678560 644300 829080 917120 912960 FALSE TRUE 783753.0468 759905.1245 673704.2789 741613.7164 665057.9836 669086.6379 748675.9492 721001.025 805030.9088 0.973568888 0.943945277 0.836867593 0.921223904 0.826127266 0.831131613 0.929996527 0.895619059 1 19.61868465 0.793421144 1.72055154 1.250880637 0.89008947 0.294228992 0.050498396 5.103819807 4.837082434 4.555635678 0.014261985 6.21471395 -0.793421144 -0.360791167 HPEPVPEEGS(ph)EDELPPQVHKV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HPEPVPEEGSEDELPPQVHKV 21 1 Q7Z3C6;H7C152;Q7Z3C6-2 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 HPEPVPEEGS(1)EDELPPQVHKV;HPEPVPEEGS(1)EDELPPQVHKV;HPEPVPEEGS(1)EDELPPQVHKV;HPEPVPEEGS(1)EDELPPQVHKV 199.83 3.67E-22 571090000 539028 509924 324176 402273 525114 455721 572569 677980 480459 TRUE FALSE 467794.0841 506574.2757 480948.5979 493615.233 514665.2588 473252.8818 517041.3465 532999.253 423659.6844 1.104174179 1.195710365 1.135223897 1.165122034 1.2148082 1.117059043 1.220416683 1.258083487 1 18.69254632 3.480578812 24.67476508 1.177451145 1.15011513 0 0.074004896 560.6945199 4001439.627 0.020763099 0.027347286 3023.979289 -3.480578812 -0.027336015 HPFAQAVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HPFAQAVGR 9 0 A0A087X2E5;A0A087WZN1;O43837-2;O43837;A0A0D9SG66;O43837-3 A0A087X2E5 IDH3B "Isocitrate dehydrogenase [NAD] subunit, mitochondrial;Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial" 0 104.06 0.003322 287120000 197490 192790 98918 146450 234510 197730 196480 213850 205740 FALSE TRUE 171391.1961 191523.5498 146755.0757 179703.7108 229843.7098 205336.801 177425.3998 168119.8417 181417.6516 0.944732746 1.055705154 0.808934932 0.990552514 1.266931348 1.131845767 0.977994138 0.926700573 1 17.46895531 6.804700622 13.75568516 1.009663996 0.947884655 0 0.12296677 0 0 0.029332119 0 6378236.552 -6.804700622 -0.061779341 HPFFLDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HPFFLDDR 8 0 A0A1B0GV06;A0A1B0GTP7;A0A1B0GUE3;A0A1B0GUG1;A0A1B0GUW4;E7EMM4;A0A1B0GW68;A0A1B0GUA4;A0A1B0GTM3;A0A1B0GTZ5;A0A1B0GUH5;Q13510-3;Q13510;Q13510-2 A0A1B0GV06 ASAH1 Acid ceramidase;Acid ceramidase subunit alpha;Acid ceramidase subunit beta 0 ;;; 126.41 0.0012203 601470000 259726 299605 190101 207890 291464 312328 209195 243454 333732 FALSE TRUE 225402.551 297636.875 282034.4794 255094.6019 285664.4366 324343.4603 188907.3011 191393.2567 294278.5831 0.765949559 1.011411948 0.958392814 0.866847323 0.970727919 1.102164679 0.641933569 0.650381195 1 18.16682302 2.228116211 24.99999934 0.735322006 0.946993771 0.292186701 0.13085714 222.0080056 531399.3319 0.052050741 0.035516967 169.0893329 -2.228116211 0.211671765 HPGAHQGNLASGLHSNAIASPGS(ph)PSLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HPGAHQGNLASGLHSNAIASPGSPSLGR 28 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 HPGAHQGNLASGLHSNAIASPGS(0.815)PS(0.185)LGR;HPGAHQGNLASGLHSNAIASPGS(0.999)PSLGR;HPGAHQGNLASGLHSNAIAS(0.035)PGS(0.954)PS(0.012)LGR;HPGAHQGNLASGLHSNAIAS(0.055)PGS(0.945)PSLGR 253.21 3.05E-53 1541000000 353889 372214 125506 200569 347171 369397 266573 395855 276610 TRUE FALSE 307121.672 369768.9017 186201.1214 246111.257 340262.9763 383607.9416 240720.7915 311204.4888 243909.4809 1.259162501 1.516008727 0.763402557 1.009027021 1.395037926 1.572747153 0.986926751 1.275901567 1 17.89598631 2.020233142 0.011744044 0.000133706 2.374624959 0.01240214 0.256280081 43763.38073 246.4270521 25573.97205 24254.13337 104.7690829 -2.020233142 2.374491253 HPGDFGADAQGAMNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HPGDFGADAQGAMNK 15 0 B0QYF8;P02144;Q8WVH6 B0QYF8 MB Myoglobin 0 ;;; 175.15 6.62E-07 2095160000 2598120 2468930 1871770 2431590 2656080 2345530 2373150 3442210 3956860 FALSE TRUE 2254771.859 2452711.436 2776964.233 2983719.674 2603229.205 2435764.057 2143002.278 2706120.179 3489084.518 0.646235953 0.702967046 0.795900534 0.855158325 0.746106662 0.698109789 0.614201882 0.775596052 1 21.73441711 1.263060578 4.119337608 1.021260208 0.727628122 0.612508069 0.068711967 0.155620115 4.69819075 0.129947549 0.018732339 18.32570024 -1.263060578 -0.293632086 HPGSFDVVHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HPGSFDVVHVK 11 0 P62701;C9JEH7;P22090 P62701 RPS4X;RPS4Y1 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1" 0 ;; 186.87 2.22E-06 2827330000 3284300 3206760 1699530 2801040 3331390 3062980 3574250 4131160 4893080 FALSE TRUE 2850271.434 3185694.582 2521428.393 3437058.943 3265101.857 3180814.823 3227619.785 3247743.583 4314625.657 0.660606889 0.738347851 0.584390998 0.796606523 0.756752061 0.73721687 0.748064848 0.752728937 1 22.04080396 -0.1722178 1.276614376 10 0.714076619 0.69469866 0.058352812 27.00869355 1.669011059 676.0086826 0.017046562 0.672639242 0.1722178 -9.285923381 HPHDIIDDINSGAVECPAS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HPHDIIDDINSGAVECPAS 19 0 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;;;;; 260.65 4.06E-31 7758470000 2979990 2968770 1662230 1816600 2838610 2669710 2242180 2808740 2626010 FALSE TRUE 2586176.771 2949267.954 2466089.988 2229086.795 2782127.215 2772415.471 2024733.729 2208112.809 2315566.089 1.116865886 1.273670386 1.065005227 0.962653066 1.201489013 1.197294901 0.874401183 0.953595243 1 21.1429335 2.239403981 24.99984645 0.942098155 1.134261512 0.51484181 0.088533622 18.69072495 554078.3293 0.035780003 0.026071409 173.5417535 -2.239403981 0.192163357 HPHLSTLSLPRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HPHLSTLSLPRR 12 1 O95140-2 O95140-2 MFN2 Mitofusin-2 0 ;;; 74.962 0.05627 4071210000 5591700 8427720 4708910 3493980 7350210 9496110 3773850 3676130 5980150 FALSE TRUE 4852742.677 8372357.752 6986154.626 4287341.561 7203955.201 9861431.497 3407862.608 2890018.207 5273183.48 0.920268126 1.58772358 1.324845732 0.813046157 1.366149164 1.870109685 0.646262855 0.548059482 1 22.33024277 2.195656053 24.99856538 0.689686137 1.306282001 0.424528766 0.31825342 124.7090426 72661.48521 0.129101399 0.087040796 156.9119622 -2.195656053 0.616595863 HPHTGDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HPHTGDTK 8 0 P51397;B4DQ75 P51397 DAP Death-associated protein 1 0 ; 89.698 0.013721 59626000 150943 112737 87371 114493 64435 87695 110066 135776 242380 FALSE TRUE 130995.5001 111996.4232 129623.9078 140490.3856 63152.86956 91068.6834 99391.81626 106741.359 213726.1125 0.612912941 0.524018436 0.606495417 0.657338422 0.295485043 0.426099938 0.465042924 0.499430593 1 17.70540366 1.238041843 24.91209555 1.00000058 0.506769302 0.686363548 0.10388236 7.352207302 352700.4411 0.151964414 0.026445304 17.29983031 -1.238041843 -0.493231278 HPLLHIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HPLLHIQK 8 0 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 104.45 0.0026476 254650000 192400 270870 178300 230250 280370 287390 261730 301240 314070 FALSE TRUE 166973.8525 269090.6371 264526.4764 282531.7817 274791.1855 298446.0793 236347.4649 236822.1703 276941.0024 0.602922106 0.971653294 0.955172669 1.020187618 0.992237275 1.077652196 0.853421714 0.855135817 1 18.07921914 4.739966324 24.69799073 0.957487619 0.602921969 0.730770433 0.069038869 62.64434089 1100515.908 0.018821662 0.114878079 54949.82627 -4.739966324 -0.35456565 HPLLSSGGPQS(ph)PLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HPLLSSGGPQSPLR 14 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 HPLLSSGGPQS(1)PLR;HPLLSSGGPQS(1)PLR;HPLLSSGGPQS(1)PLR;HPLLSSGGPQS(1)PLR;HPLLSSGGPQS(1)PLR;HPLLSSGGPQS(1)PLR 197.67 1.49E-08 6798590000 2570610 2803500 1542800 2150580 2954620 3136330 2866210 3320900 3155310 TRUE FALSE 2230897.375 2785083.624 2288903.24 2638902.059 2895828.843 3256986.645 2588245.395 2610751.378 2782292.846 0.801819758 1.00100305 0.822667982 0.948463086 1.040806631 1.17061245 0.930256281 0.938345287 1 21.40784285 3.477466953 6.246531122 1.00684095 0.887015391 0.3670348 0.083658906 0.189973652 32.92858685 0.024741148 0.033884136 3002.388953 -3.477466953 -0.11982556 HPNIVSLQDVLMQDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HPNIVSLQDVLMQDSR 16 0 P06493;A0A024QZP7;A0A087WZZ9;E5RIU6;P06493-2 P06493 CDK1;CDC2 Cyclin-dependent kinase 1 0 ; 204.05 2.62E-11 805930000 490920 393060 313180 397850 469770 504120 458290 557770 578070 FALSE TRUE 426043.6782 390477.963 464634.8955 488187.9233 460422.4961 523513.8226 413845.1063 438495.2261 509731.2231 0.83582025 0.766046782 0.911529203 0.957735962 0.903265241 1.027038955 0.811888869 0.860247923 1 18.9593772 4.225603554 24.25610721 0.916843308 0.800933536 0.383119197 0.064631925 154.1265503 288533.0396 0.016856995 0.035471216 16811.38731 -4.225603554 -0.115909772 HPNNLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HPNNLK 6 0 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;;;; 91.26 0.048095 1014625000 939202 854241 756262 994405 516306 683848 853931 930932 2111240 FALSE TRUE 815084.0761 848629.4346 1121992.833 1220199.854 506032.5207 710156.0751 771116.9031 731859.4363 1861651.612 0.437828469 0.455847608 0.602686789 0.65543942 0.27181913 0.381465614 0.414211176 0.393123736 1 20.82815168 1.23491975 24.99427278 1.00000078 0.450485191 0.714846191 0.108858711 61.78611676 424091.5058 0.203935637 0.028280988 17.17590976 -1.23491975 -0.549515589 HPNQATPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HPNQATPK 8 0 Q96F86;H3BPW9;H3BQ37 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 0 ; 71.223 0.049298 59835000 152745 122492 81766 99124 91609 106247 134002 155747 137825 FALSE TRUE 132559.3612 121687.342 121308.3111 121631.6192 89786.16013 110334.3908 121006.5067 122441.7161 121531.4855 1.090740895 1.001282437 0.998163649 1.000823932 0.738789292 0.907866718 0.995680306 1.007489669 1 16.8909706 4.54386572 1.307638743 0.945384277 1.115272006 0.256445385 0.080054392 1.593142123 3.131266411 0.025862119 0.330094582 34983.69836 -4.54386572 0.169887729 HPNYS(ph)PPGS(ph)PIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HPNYSPPGSPIEK 13 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 2 HPNY(0.003)S(0.997)PPGS(1)PIEK;HPNY(0.003)S(0.997)PPGS(1)PIEK;HPNY(0.056)S(0.977)PPGS(0.967)PIEK;HPNY(0.008)S(0.993)PPGS(0.999)PIEK;HPNYS(1)PPGS(1)PIEK;HPNY(0.041)S(0.969)PPGS(0.99)PIEK 145.79 3.54E-06 4375880000 3103840 3268650 2296840 2897320 3996390 3182380 4004950 5101750 4196490 TRUE FALSE 2693659.68 3247178.023 3407599.506 3555200.789 3916869.658 3304808.218 3616550.565 4010780.464 3700385.733 0.72794024 0.877524198 0.920876836 0.960764916 1.05850307 0.893098303 0.977344209 1.083881723 1 21.81924424 5.722291096 0.588310001 1.015682053 2.40E-17 0.74129348 0.051266121 5.69669458 0.639288469 0.027240655 5.072738745 527583.3686 -5.722291096 -1.015682053 RGLLYDS(ph)DEEDEERPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RGLLYDSDEEDEERPAR 17 2 P49736 P49736 MCM2 DNA replication licensing factor MCM2 1 RGLLYDS(1)DEEDEERPAR;RGLLYDS(1)DEEDEERPAR;RGLLYDS(1)DEEDEERPAR;RGLLYDS(1)DEEDEERPAR 238.79 2.30E-20 3984380000 788390 725410 392991 435652 806140 708320 722440 838410 316023 TRUE FALSE 684202.264 720644.7339 583042.7621 534573.4451 790099.3912 735569.5287 652377.88 659122.546 278663.121 2.455302523 2.586078601 2.092285338 1.918350169 2.835320973 2.639637158 2.341098735 2.36530239 1 18.08816256 1.236734997 5.91230663 0.943817676 2.404959965 0.740573383 0.261286869 0.074953065 9.578762176 0.442566422 0.067486845 17.24785123 -1.236734997 1.461142289 HPPEQTNGVHT(ph)PPHVASALAGAVS(ph)PGALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HPPEQTNGVHTPPHVASALAGAVSPGALR 29 0 X6RKU3;Q6P3S6 X6RKU3 FBXO42 F-box only protein 42 2 HPPEQT(0.006)NGVHT(0.994)PPHVASALAGAVS(1)PGALR;HPPEQTNGVHT(1)PPHVASALAGAVS(1)PGALR 200.1 7.46E-25 857150000 210320 203965 101719 157882 235620 225180 173051 222630 205040 TRUE FALSE 182525.6791 202625.1405 150910.6486 193731.5212 230931.623 233842.8203 156268.5407 175022.307 180800.4048 1.009542425 1.120711763 0.834680922 1.071521501 1.277273816 1.293375535 0.864315215 0.968041566 1 17.46403838 2.203590954 24.99999356 0.945777686 1.096614333 0.23652853 0.13284321 296.8757725 212236.0259 0.058377483 0.039359898 159.8052171 -2.203590954 0.150836647 HPPLYSDHSPLCADSLGQEPGAASFQNDS(ph)PPQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HPPLYSDHSPLCADSLGQEPGAASFQNDSPPQVR 34 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 HPPLYSDHSPLCADSLGQEPGAASFQNDS(1)PPQVR;HPPLYSDHSPLCADSLGQEPGAASFQNDS(1)PPQVR;HPPLYSDHSPLCADSLGQEPGAASFQNDS(1)PPQVR 288.85 1.95E-75 1602370000 295063 298853 109260 220406 310184 358094 304848 344216 328985 TRUE FALSE 256069.677 296889.815 162098.5015 270452.551 304011.9453 371870.1079 275283.8879 270608.0871 290092.7681 0.882716514 1.023430597 0.558781601 0.932296771 1.047981814 1.28190065 0.948951226 0.932832931 1 18.1461548 3.479209014 18.6441515 1.029668675 0.825774777 0.319242089 0.146940872 4.011038291 35819.13406 0.043219212 0.057270103 3014.456453 -3.479209014 -0.203893898 HPQGEQMYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 ;;;;;; 115.78 0.0014203 1626817000 115201.3 123689.2 90601.4 120702.8 86141.3 116876.4 123652.1 130257 145253.2 FALSE TRUE 99977.15632 122876.6775 134416.5401 148110.2156 84427.25666 121372.7107 111660.3384 102402.5542 128081.5322 0.780574331 0.959362957 1.049460744 1.156374483 0.659168072 0.947620697 0.871791089 0.79951069 1 16.96670295 3.245864333 24.999995 0.854417782 0.989010029 0.205062454 0.12793648 271.1899464 928254.7907 0.036592197 0.046268137 1761.425717 -3.245864333 0.134592247 HPQHLHQQHHGDAAQHTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HPQHLHQQHHGDAAQHTR 18 0 Q9NR09;A0A3B3IUB9 Q9NR09 BIRC6 Baculoviral IAP repeat-containing protein 6 0 ;;;; 139.9 4.03E-08 518223000 110659 100920 73077.1 76790.8 90994.3 110725 126331 126013 82073.9 FALSE TRUE 96035.13278 100257.0499 108417.43 94227.32481 89183.69146 114984.6624 114079.4391 99066.10058 72371.21704 1.326979657 1.385316621 1.498073881 1.302000003 1.232308853 1.588817587 1.576309529 1.368860503 1 16.14312841 1.249684032 4.799834456 0.974260691 1.417210779 0.560845013 0.114594607 0.134744454 7.208981354 0.19643905 0.029990503 17.76986107 -1.249684032 0.442950088 HPSAVTACNLDLENLVTDSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HPSAVTACNLDLENLVTDSNR 21 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ;;;; 343.92 3.79E-81 1378227000 719370 749910 361829 542423 836820 767331 733230 876230 892550 FALSE TRUE 624303.4318 744983.7918 536810.7146 665588.4326 820168.9192 796850.7201 662121.4675 688855.0333 787033.7558 0.793235903 0.946571588 0.682068222 0.845692358 1.042101324 1.012473371 0.841287254 0.87525475 1 19.58606599 3.458937462 24.1562236 0.939258455 0.811663268 0.378654354 0.087341058 194.2797686 258089.1952 0.025921096 0.033471387 2876.984101 -3.458937462 -0.127595187 HPSGGSS(ph)PPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HPSGGSSPPPR 11 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 HPSGGS(0.245)S(0.755)PPPR;HPSGGS(0.061)S(0.938)PPPR 101.97 0.0018881 203950000 197005 178644 75674 130790 179327 220740 150171 183405 182901 TRUE FALSE 170970.2901 177470.4758 112270.1995 160487.8685 175758.7435 229232.0106 135607.4395 144185.268 161278.6521 1.060092503 1.100396571 0.696125606 0.995096787 1.089783063 1.42134131 0.840826965 0.89401335 1 17.29919596 HPSKPDPSGECNPDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HPSKPDPSGECNPDLR 16 1 Q09028-3;Q09028;Q09028-2;Q09028-4 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 ;;;;; 214.54 1.02E-14 3076640000 2142960 2104810 690511 1561050 2130180 2098250 2110790 2561330 2735800 FALSE TRUE 1859762.406 2090983.365 1024444.429 1915510.262 2087793.586 2178971.035 1906085.911 2013609.512 2412376.841 0.770925328 0.866773105 0.424661857 0.794034427 0.865450849 0.90324654 0.790127761 0.834699404 1 21.20202386 3.484373549 23.82879993 0.864329397 0.689379205 0.334773993 0.122247369 219.1681331 720119.7211 0.034222512 0.046156939 3050.517697 -3.484373549 -0.174950192 HPSS(ph)PSALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HPSSPSALR 9 0 O60504-2;O60504;H0YAZ3;H0YB51 O60504-2 SORBS3 Vinexin 1 HPS(0.004)S(0.996)PSALR;HPS(0.004)S(0.996)PSALR;HPS(0.008)S(0.992)PSALR;HPS(0.014)S(0.986)PSALR 115.33 0.00096234 2495180000 296409 250654 130451 237012 378779 332587 374385 356235 290740 TRUE FALSE 257237.7996 249007.4374 193537.5399 290829.1971 371242.039 345381.8371 338077.2003 280056.9175 256369.0484 1.003388674 0.971285102 0.754917729 1.134416182 1.448076674 1.347205676 1.318713013 1.092397539 1 17.96786257 3.515401907 8.512234977 1.238986526 0.919996502 0.537347011 0.140334321 0.292222765 60.87576173 0.042085187 0.061598569 3276.43764 -3.515401907 -0.318990024 HPSSPCSVKHS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HPSSPCSVKHSPTR 14 1 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 1 HPSSPCSVKHS(0.997)PT(0.003)R;HPSSPCS(0.206)VKHS(0.775)PT(0.018)R 173.87 1.59E-06 65541000 73180 75750 13658.4 38742 98164 80963 73801 99763 32070 TRUE FALSE 63509.07759 75252.39326 20263.64792 47538.96323 96210.72845 84077.699 66643.79038 78429.45881 28278.72113 2.245825661 2.661096055 0.716568752 1.681086037 3.402230532 2.973178971 2.356676247 2.773444331 1 14.78742926 HPTGNSITKS(ph)PPLMAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HPTGNSITKSPPLMAK 16 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 HPTGNSIT(0.003)KS(0.997)PPLMAK;HPTGNSITKS(1)PPLMAK;HPTGNSITKS(1)PPLMAK 241.76 3.88E-20 2803390000 2925740 2991590 826749 1563700 2879880 2184920 3502930 4089170 816490 TRUE FALSE 2539096.046 2971938.048 1226567.582 1918761.985 2822576.022 2268975.286 3163216.388 3214732.817 719965.4823 3.52669136 4.12788963 1.703647761 2.665074968 3.920432426 3.151505651 4.393566727 4.465120754 1 19.45756821 3.239013866 24.99999361 3.584826703 2.992960629 0.010383259 1.142778064 40.50330107 2233986.521 0.339770857 0.412032591 1733.859353 -3.239013866 -0.591866074 HPTLLQDPDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HPTLLQDPDLR 11 0 O60749;O60749-2;D6RC15 O60749 SNX2 Sorting nexin-2 0 ;;;;; 156.36 3.11E-05 2713110000 1162410 1231430 472603 862196 1382880 1427890 1149590 1310910 1366080 FALSE TRUE 1008794.573 1223340.655 701155.3916 1057970.78 1355363.394 1482821.852 1038102.939 1030582.098 1204583.579 0.837463329 1.01557142 0.582072846 0.878287566 1.125171734 1.230982954 0.861794032 0.855550512 1 20.20010307 3.46630637 24.58368281 0.994841276 0.815104552 0.276995532 0.150875105 272.1296897 618584.1295 0.04651082 0.060106499 2926.215929 -3.46630637 -0.179736724 HPTPGSSDPLIQPSSPAVCPEPPS(ph)SPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HPTPGSSDPLIQPSSPAVCPEPPSSPK 27 0 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9 A0A0G2JQJ7 MAPT Microtubule-associated protein tau 1 HPTPGSSDPLIQPSSPAVCPEPPS(0.738)S(0.262)PK 230.79 3.02E-35 692420000 482440 368300 115640 248130 523490 372870 512230 594830 533680 TRUE FALSE 418684.3317 365880.613 171563.8908 304471.7089 513073.5732 387214.5502 462554.0134 467630.2335 470588.9584 0.889702838 0.777495108 0.364572708 0.647001387 1.090279668 0.822829655 0.982925768 0.993712719 1 18.84410794 3.251041114 24.98816145 0.972537172 0.655598754 0.522622594 0.146066857 182.9508062 366297.8147 0.043193981 0.055368445 1782.547509 -3.251041114 -0.316938418 HPTT(ph)PSSTAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HPTTPSSTAK 10 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 1 HPT(0.104)T(0.894)PS(0.002)STAK 88.021 0.045914 61652000 207200 186510 83512 103480 146610 142470 179540 208610 138620 TRUE FALSE 179817.995 185284.8035 123898.6825 126976.7156 143692.7478 147950.9131 162128.2384 164000.3749 122232.5015 1.471114415 1.515839087 1.013631244 1.038813033 1.175569068 1.210405672 1.326392215 1.341708407 1 16.89926842 4.25616978 24.99818082 1.181721644 1.493477018 0.56805484 0.120224885 206.0222293 292466.6452 0.033163235 0.087314691 18037.22736 -4.25616978 0.311755374 HPVSLEQYLMEGSYNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HPVSLEQYLMEGSYNK 16 0 K7EJR3;R4GMR5;P48556;K7EJC1 K7EJR3 PSMD8 26S proteasome non-ATPase regulatory subunit 8 0 159.31 9.18E-09 284560000 228620 190480 131820 173650 211120 179950 213800 243870 216940 FALSE TRUE 198407.2878 189228.7243 195568.5929 213079.8866 206919.125 186872.7929 193065.7089 191720.2983 191293.6003 1.037187273 0.989205724 1.022347808 1.113889258 1.081683468 0.976889936 1.009263815 1.002230592 1 17.54542908 2.729921721 24.98468326 0.999039077 1.047687966 0.365108059 0.03385772 834.1882768 2412558.437 0.012799741 0.011458759 536.9350082 -2.729921721 0.048648889 HPVTGQFLYQDSNWASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HPVTGQFLYQDSNWASK 17 0 P02786;G3V0E5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 221.47 3.67E-15 546320000 250640 182860 105700 161090 177260 173050 175480 221930 196850 FALSE TRUE 217517.289 181658.7806 156816.8735 197667.9466 173732.8728 179707.3455 158461.9766 174471.9966 173578.6173 1.253134127 1.046550454 0.903434283 1.138780512 1.000888678 1.035308083 0.91291185 1.005146828 1 17.40522971 4.708745359 3.800074482 1.000357319 1.271640013 0.597979493 0.064778705 0.151032235 4.192928595 0.01528563 0.108471896 51138.19077 -4.708745359 0.271282694 HPWDDISYVLPEHMSM ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 HPWDDISYVLPEHMSM 16 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;;;;;;;;; 170.79 2.78E-09 1054102000 797322 887465 277327.4 572462.2 926672 980174 831411 931428 862746 FALSE TRUE 691953.8775 881635.184 411443.8582 702448.492 908233.0402 1017881.928 750780.8892 732249.3706 760753.1507 0.909564261 1.158897841 0.540837534 0.923359294 1.193860373 1.337992392 0.986891594 0.962532156 1 19.53706888 3.405581738 7.67426042 1.082259587 0.871496382 0.252788839 0.183031302 0.372388477 34.31625479 0.055137091 0.071310482 2544.378624 -3.405581738 -0.210763205 HPWICQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HPWICQR 7 0 E9PF82;E9PBG7;H0Y9C2;Q13557;D6R938;Q13557-8;Q13557-6;Q13557-11;Q13557-12;Q13557-10;Q13557-3;Q13557-4;Q13557-9;Q13557-5 E9PF82;Q13557 CAMK2D Calcium/calmodulin-dependent protein kinase type II subunit delta 0 88.734 0.01839 328560000 75590 51780 66601 58079 50094 49327 89717 79616 66533 FALSE TRUE 65600.58998 51439.85377 98809.46637 71266.72463 49097.22741 51224.64161 81016.25915 62590.73797 58667.54453 1.118175143 0.876802569 1.684227065 1.214755538 0.836872035 0.873134235 1.380938299 1.066871615 1 15.84027499 3.440389585 24.99181 1.05167248 1.234450281 0.130127693 0.243370573 385.7724761 262474.0708 0.071782592 0.092671206 2756.700502 -3.440389585 0.1827778 HQADACHAYQIIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HQADACHAYQIIHR 14 0 Q99538-3;Q99538-2;Q99538;G3V2T4;G3V4E4;G3V4P5;G3V3Z4 Q99538-3 LGMN Legumain 0 ; 194.77 3.65E-08 568760000 176926 173534 106029 118761 174768 199675 145595 190552 156975 FALSE TRUE 153544.7808 172394.0437 157304.979 145727.5002 171290.4587 207356.6265 131475.2193 149803.9377 138417.5943 1.109286587 1.245463372 1.136452196 1.052810525 1.237490505 1.498051078 0.949844707 1.082260809 1 17.07866781 HQAFEAELHANADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HQAFEAELHANADR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 172.57 1.64E-06 856060000 335190 299473 165088 252134 282658 322220 290241 335050 313837 FALSE TRUE 290893.7922 297505.7421 244925.109 309384.8783 277033.6588 334616.0119 262093.4725 263402.1649 276735.5474 1.051161641 1.075054307 0.88505113 1.117980257 1.001077243 1.209154426 0.947090011 0.951819047 1 18.07814845 HQAFEAELSANQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HQAFEAELSANQSR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 199.37 2.07E-08 576980000 413060 409880 225140 287930 436400 495490 356470 454260 438240 FALSE TRUE 358473.0744 407187.4713 334018.457 353308.9072 427716.4938 514551.8209 321899.5943 357120.0341 386431.7664 0.927649085 1.053711177 0.86436594 0.914285361 1.106835749 1.331546383 0.833005002 0.924147715 1 18.55985417 4.794441765 19.73674924 0.995643779 0.927643551 0.024494652 0.142984513 18404.76077 6497536.578 0.036388537 23.32382251 62293.36127 -4.794441765 -0.068000228 HQALQAEIAGHEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HQALQAEIAGHEPR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 154.69 3.50E-06 435590000 81269 80649 45277 62508 67314 93285 86595 89131 101560 FALSE TRUE 70529.09574 80119.21141 67173.10864 76701.39677 65974.5831 96873.73431 78197.03023 70071.02927 89553.6925 0.787562118 0.894650005 0.750087537 0.856485027 0.736704219 1.08173914 0.873185997 0.782447125 1 16.4504653 HQALWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HQALWDR 7 0 O43427-2;O43427 O43427-2 FIBP Acidic fibroblast growth factor intracellular-binding protein 0 ; 91.069 0.01953 174350000 611960 556760 417750 566150 510650 519890 626820 749470 937100 FALSE TRUE 531087.9355 553102.6069 619775.2973 694703.0106 500489.0641 539890.5047 566031.0929 589201.6729 826317.1055 0.64271686 0.669358777 0.750045344 0.84072205 0.605686438 0.653369634 0.68500469 0.713045475 1 19.65633601 1.236268609 4.866639713 1.021657022 0.695088686 0.688943348 0.064530165 0.111179529 6.36072977 0.124270006 0.016749238 17.22933873 -1.236268609 -0.326568336 HQAS(ph)DS(ph)ENEELPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HQASDSENEELPKPR 15 1 Q96ST2;B8ZZB6 Q96ST2 IWS1 Protein IWS1 homolog 2 HQAS(1)DS(1)ENEELPKPR;HQAS(1)DS(1)ENEELPKPR 97.689 0.0018306 2293610000 2605320 1888430 1164320 1612020 1959450 1619480 1822020 2139520 3726600 TRUE FALSE 2261020.361 1876024.779 1727389.046 1978053.779 1920460.779 1681782.444 1645320.781 1682000.298 3286045.593 0.688067252 0.570906497 0.525674096 0.601955671 0.584429133 0.511795225 0.500699316 0.511861522 1 21.64792107 1.235074117 24.99999975 1.000000622 0.556242734 0.856912236 0.056215554 36.65219966 262773.1877 0.101355168 0.014240633 17.18201592 -1.235074117 -0.443757888 HQAS(ph)DS(ph)ENEEPPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HQASDSENEEPPKPR 15 1 Q96ST2;B8ZZB6 Q96ST2 IWS1 Protein IWS1 homolog 2 HQAS(1)DS(1)ENEEPPKPR;HQAS(1)DS(1)ENEEPPKPR 73.783 0.020909 549370000 999450 696520 448740 621980 743590 610360 643510 803340 1354010 TRUE FALSE 867370.1502 691944.5143 665752.1649 763210.0654 728794.0138 633840.9442 581102.4992 631551.9926 1193940.48 0.726476876 0.579546908 0.557609174 0.639236275 0.610410674 0.530881526 0.486709772 0.528964386 1 20.18729949 1.234722844 24.99945349 1.000000608 0.57564694 0.792655957 0.067028533 51.82143605 337517.9249 0.125715621 0.017151583 17.16812411 -1.234722844 -0.424353667 HQAVQLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HQAVQLPR 8 0 O95758-1;O95758-6;O95758;O95758-5;O95758-4;O95758-2;O95758-7 O95758-1 PTBP3 Polypyrimidine tract-binding protein 3 0 62.546 0.078954 117550000 312200 341600 158660 271240 312630 367070 274530 307060 199320 FALSE TRUE 270941.979 339356.0071 235388.5067 332829.1876 306409.2747 381191.4204 247906.1229 241397.6085 175756.6167 1.541574844 1.930829197 1.339286743 1.893693643 1.743372628 2.168859572 1.410508051 1.373476647 1 17.42321948 1.638259712 1.811448201 1.025180014 1.755148031 0.509815674 0.240102568 0.313185074 1.900965137 0.333332516 0.066549742 43.4770143 -1.638259712 0.729968017 HQDDLQDVIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HQDDLQDVIGR 11 0 E5RG17;Q6P1N9;H0YBX2;G5EA19;U3KQS5;E5RID7 E5RG17 TATDN1 Putative deoxyribonuclease TATDN1 0 ; 139.78 3.89E-05 282520000 353570 288672 165285 230619 300890 306620 265080 301220 273858 FALSE TRUE 306844.8287 286775.6946 245217.3788 282984.5687 294902.8777 318415.8698 239372.5824 236806.4471 241482.8192 1.270669399 1.187561482 1.015465115 1.171862121 1.221216808 1.318586021 0.991261338 0.980634763 1 17.88156102 2.209900876 24.14359904 0.988575194 1.188735801 0.606986066 0.078272204 104.5024387 88034.06239 0.033822488 0.022808866 162.1439975 -2.209900876 0.200160606 HQDFDDLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HQDFDDLER 9 0 A0A0C4DFL8;F5GX28;O94953;K7ES23;O94953-2 A0A0C4DFL8 KDM4B Lysine-specific demethylase 4B 0 68.657 0.05745 70217000 120750 79103 49882 43195 76355 88532 95113 95980 72697 FALSE TRUE 104792.5816 78583.36718 74005.10205 53003.08494 74835.68489 91937.88333 85888.9559 75455.42392 64102.84348 1.634757148 1.225895185 1.15447456 0.826844522 1.167431596 1.434224729 1.339861873 1.177099483 1 15.96810073 4.737670722 3.473932555 1.167941652 1.691842318 0.447621047 0.165104647 0.311217187 6.524634261 0.044201778 0.429561589 54660.13771 -4.737670722 0.523900667 HQDGLPYIDDS(ph)PSSSPHLSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HQDGLPYIDDSPSSSPHLSSK 21 0 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 HQDGLPYIDDS(0.966)PS(0.02)S(0.006)S(0.002)PHLS(0.003)S(0.004)K;HQDGLPYIDDS(0.988)PS(0.009)S(0.002)SPHLSSK;HQDGLPYIDDS(0.991)PS(0.007)S(0.002)SPHLSSK 155.8 2.69E-11 728540000 609729 721019 146031 478609 1028880 911430 798843 978250 1135770 TRUE FALSE 529151.7678 716282.5787 216652.08 587284.4885 1008407.301 946493.3019 721371.3288 769058.8503 1001500.564 0.528358931 0.715209361 0.216327467 0.586404551 1.006896388 0.945075156 0.720290486 0.767906557 1 19.9337318 3.384990936 6.039619779 0.861638731 0.492593749 0.609415403 0.150503764 0.150684955 8.066263156 0.044281826 0.057414513 2426.559449 -3.384990936 -0.369044981 HQDVFNQPTLNSFMGLGQAAWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HQDVFNQPTLNSFMGLGQAAWK 22 0 P16930;H0YLC7 P16930 FAH Fumarylacetoacetase 0 ; 264.71 1.67E-37 517700000 516090 458240 281580 361920 541210 435270 559990 696130 490560 FALSE TRUE 447887.3989 455229.7913 417753.0298 444099.4676 530440.9799 452015.1186 505682.256 547268.0168 432566.5556 1.035418465 1.052392482 0.965754343 1.02666159 1.226264428 1.044960857 1.169027631 1.265164885 1 18.7225626 3.31070046 8.810457049 1.153767052 1.017794256 0.355125724 0.080036348 0.297718437 33.11977385 0.022960415 0.029625349 2045.033656 -3.31070046 -0.135972796 HQDVPSQDDSKPTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HQDVPSQDDSKPTQR 15 1 Q9NRN7 Q9NRN7 AASDHPPT L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase 0 89.866 0.0037461 86891000 225990 164130 103140 128700 178980 160610 199560 230270 210410 FALSE TRUE 196124.8489 163051.8192 153018.849 157923.3021 175418.6482 166788.7706 180206.7019 181028.5525 185535.5695 1.05707412 0.878817036 0.824741312 0.851175343 0.945471796 0.898958464 0.971278458 0.97570807 1 17.50133627 2.125466258 1.587093342 0.992346893 0.900440171 0.219277574 0.06305499 0.59614276 2.89987185 0.050396916 0.020819848 133.4953869 -2.125466258 -0.091906722 HQEGEIFDTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HQEGEIFDTEK 11 0 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ;; 192.15 1.52E-06 4848100000 8556100 6872000 6103200 6796400 7409400 6528800 8598900 9860700 12304400 FALSE TRUE 7425389.707 6826857.38 9054727.934 8339626.496 7261967.436 6779967.161 7764980.002 7752066.041 10849787.85 0.684381097 0.629215748 0.834553455 0.7686442 0.669318842 0.624893985 0.715680353 0.714490103 1 23.3711635 1.23662511 5.753776437 1.012872241 0.705187151 0.689604092 0.06219934 0.088445696 10.04244839 0.107352807 0.016130768 17.24348764 -1.23662511 -0.30768509 HQEGEIFDTEKEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HQEGEIFDTEKEK 13 1 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ; 189.1 3.33E-06 508870000 1674030 1331800 1038130 1028660 1229450 923310 1871610 1981730 883940 FALSE TRUE 1452802.694 1323051.318 1540173.14 1262232.975 1204986.35 958830.3332 1690101.55 1557952.461 779441.6202 1.863901871 1.697434784 1.975995508 1.619406691 1.545961005 1.230150287 2.168349119 1.998805839 1 19.57208144 3.712242212 24.06783417 1.654736168 1.830943185 0.090620082 0.340614805 1595.244714 1458829.603 0.098102002 0.145568318 5155.160749 -3.712242212 0.176207017 HQEGEIFDTEKEKYEITEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HQEGEIFDTEKEKYEITEQR 20 2 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 59.539 0.039496 579560000 511120 379590 184790 169600 349100 300470 528050 547800 52072 FALSE TRUE 443574.197 377096.4483 274155.0621 208110.2722 342153.593 312029.2753 476839.7923 430657.233 45916.10748 9.660535732 8.21272684 5.97078187 4.532402322 7.451711649 6.795638665 10.38502213 9.379219115 1 15.48671272 4.497791367 4.192507819 6.941166221 9.457895468 0.127583308 2.587073666 0.5026337 20.10244809 0.664858744 2.586609862 31462.36517 -4.497791367 2.516729248 HQEHILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HQEHILR 7 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 128.61 0.010513 0 357810 313250 128813 206096 336940 400070 292190 324100 239836 FALSE TRUE 310524.5019 311192.2401 191107.3977 252893.2468 330235.5532 415460.9518 263853.4588 254793.7371 211482.8613 1.468319939 1.471477349 0.903654303 1.195809652 1.561523951 1.964513574 1.247635185 1.20479615 1 17.69018123 1.621325275 2.494061216 1.035857328 1.407971402 0.19683333 0.271541141 0.486534128 6.557796815 0.314757565 0.08054229 41.81434275 -1.621325275 0.372114074 HQEPVYSVAFSPDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HQEPVYSVAFSPDGR 15 0 Q9BZK7;A0A0D9SF63 Q9BZK7 TBL1XR1 F-box-like/WD repeat-containing protein TBL1XR1 0 ; 145.55 4.04E-06 817740000 586160 623500 329070 406400 757250 772260 548970 635630 651070 FALSE TRUE 508697.4709 619404.1874 488209.3527 498679.3314 742182.2065 801969.3419 495730.9739 499705.471 574101.2463 0.886076235 1.078911066 0.850388944 0.868626108 1.292772331 1.396912735 0.863490503 0.870413493 1 19.13094566 4.758399236 22.44587511 1.017016086 0.886075824 0.050304627 0.188364342 4609.939936 5215445.817 0.0498776 1.564939106 57332.283 -4.758399236 -0.130940262 HQERPPESHRVT(ph)PNLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HQERPPESHRVTPNLNR 17 2 Q5TC79;Q5TC79-2;Q5TC79-3 Q5TC79 ZBTB37 Zinc finger and BTB domain-containing protein 37 1 HQERPPES(0.012)HRVT(0.988)PNLNR 82.034 0.0080732 89435000 87526 79433 49213 71829 69848 66989 77246 88573 85400 TRUE FALSE 75959.21734 78911.19939 73012.57141 88138.87229 68458.16146 69566.11018 69754.69481 69632.35323 75304.10929 1.008699499 1.047900309 0.969569551 1.170439079 0.909089319 0.923802311 0.926306618 0.924681985 1 16.20044097 3.180014078 24.9999999 0.933830208 1.043381454 0.498566391 0.055823804 61.60732436 26306.57849 0.01581673 0.017934496 1513.610312 -3.180014078 0.109551246 HQEYLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HQEYLK 6 0 Q9NR28-2;Q9NR28;Q9NR28-3;H7BZK7;A0A2U3TZH2;H7BZQ7;V9GYY5;Q9UGY1 Q9NR28-2;V9GYY5 DIABLO;NOL12 "Diablo homolog, mitochondrial;Nucleolar protein 12" 0 106.42 0.08495 0 997350 845560 594930 794020 867610 865530 832630 1019200 1049100 FALSE TRUE 865547.6705 840005.4607 882640.1379 974314.3768 850346.2585 898827.4992 751881.6708 801252.0114 925076.5931 0.935649736 0.908038823 0.95412655 1.053225629 0.919217138 0.971624951 0.812777749 0.866146671 1 19.8192133 2.274635828 24.99898579 0.884043915 0.957284425 0.196088478 0.060191967 240.4470238 166621.3625 0.022638447 0.01753503 188.2070241 -2.274635828 0.073240511 HQFGTDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HQFGTDK 7 0 O95104-2;O95104-3;O95104 O95104-2 SCAF4 "Splicing factor, arginine/serine-rich 15" 0 ; 136.8 0.0029452 268590000 509980 478630 323400 402100 367080 392770 551580 577740 661210 FALSE TRUE 442584.8509 475485.848 479797.3217 493402.9507 359775.8262 407880.1161 498087.8565 454194.797 583042.5071 0.759095341 0.815525184 0.822919969 0.846255538 0.617066203 0.699571834 0.854290812 0.779008034 1 19.15324154 0.157320641 1.454755757 4.89985612 0.769416696 0.488664924 0.072106452 22.80362316 3.17077361 275.0654072 0.021533695 1.43654965 -0.157320641 -4.130439424 HQGGWTDGGSGGGGGYQDGGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HQGGWTDGGSGGGGGYQDGGYR 22 0 Q8NCA5 Q8NCA5 FAM98A Protein FAM98A 0 ; 280.21 1.27E-45 1002960000 198693 222780 124945 158697 239950 228030 186235 230710 240420 FALSE TRUE 172435.2166 221316.5435 185368.8199 194731.5794 235175.4645 236802.4617 168173.9584 181374.4619 211997.8215 0.813382022 1.043956688 0.874390211 0.918554625 1.109329628 1.117004222 0.79328154 0.855548706 1 17.69368991 2.218406712 24.99999284 0.873500316 0.980731123 0.148668611 0.10803548 431.0761112 534726.0023 0.044752704 0.03021427 165.3509567 -2.218406712 0.107230807 HQGVMVGMGQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 35 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 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 167.09 1.49E-05 82121590000 107205762 94089423 55308905 73653686 92418908 83695173 100749203 116281810 106472038 FALSE TRUE 93038248.93 93471343.39 82056476.46 90377881.13 90579952.55 86914980.46 90978560.8 91415849.84 93885034.96 0.990980607 0.995593637 0.874010182 0.962644165 0.964796494 0.925759686 0.9690422 0.973699907 1 26.48439188 1.468384046 1.640721396 1.005261487 0.952005791 0.157572603 0.034427372 1.188082668 4.503610462 0.092803897 0.010041321 29.40248561 -1.468384046 -0.053255696 TKPSDEEMLFIYGHYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TKPSDEEMLFIYGHYK 16 1 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5;P07108-6 P07108 DBI Acyl-CoA-binding protein 0 ;; 209.67 7.01E-12 6694510000 15702300 12742520 10351020 11667140 10394020 9080470 13575500 17105990 36711020 FALSE TRUE 13627201.27 12658813.55 15356807.89 14316342.46 10187199.34 9429801.557 12258950.1 13448007.16 32371085.04 0.42096832 0.391053112 0.474398924 0.442257108 0.314700583 0.291303228 0.378700624 0.415432697 1 24.94820239 1.236838517 5.322766866 1.033683059 0.387841743 0.926134822 0.054095345 0.043311146 3.546244902 0.103120784 0.014875637 17.25196294 -1.236838517 -0.645841316 HQILEQAVEDYAETVHQLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HQILEQAVEDYAETVHQLSK 20 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 203.77 5.95E-22 138830000 260230 268720 187120 223830 249230 237350 290900 342520 310130 FALSE TRUE 225839.9462 266954.7606 277611.8579 274654.0225 244270.8106 246481.0081 262688.5628 269274.7635 273466.7847 0.8258405 0.976187148 1.015157501 1.004341433 0.893237586 0.901319728 0.960586724 0.984670821 1 18.06100609 5.81713907 0.012081491 1.835720605 5.34E-06 0.123411867 0.056427852 32036.535 68.15682468 4786.512499 5598.303751 656355.4113 -5.81713907 -1.835715267 HQIVEVAGDDKYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HQIVEVAGDDKYGR 14 1 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ;;;;; 162.29 2.68E-06 3976210000 6372080 5727920 3914940 4793300 6038990 5108420 6570270 8101260 6604000 FALSE TRUE 5529993.483 5690292.916 5808218.079 5881692.026 5918825.914 5304944.223 5933086.227 6368868.593 5823282.643 0.949635081 0.977162412 0.997413046 1.010030319 1.016407115 0.910988621 1.01885596 1.093690446 1 22.47340121 2.001646751 24.99930376 1.054358147 0.979823633 0.377055643 0.03759242 45.9369483 697359.4892 0.015066132 0.010075814 100.3798983 -2.001646751 -0.074534514 HQKPVLTGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HQKPVLTGQR 10 1 E7ETZ4;Q9Y6E2;Q75MG1;E9PFE3;C9JF98;F8WDX8;E7EMS9;Q9Y6E2-2 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 139.86 2.42E-05 614680000 829480 821000 556380 607680 908760 826690 918480 1040900 954930 FALSE TRUE 719862.1164 815606.7969 825447.229 745663.0318 890677.454 858493.2992 829405.951 818311.6353 842039.2633 0.854903266 0.968608986 0.980295415 0.885544255 1.057762379 1.019540699 0.984996766 0.971821233 1 19.68352798 5.971765358 0.85720113 0.990699659 4.79E-10 0.472748657 0.043140213 15.37391087 1.697066559 0.014682889 23.22098526 937055.595 -5.971765358 -0.990699659 HQLEETKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HQLEETKK 8 1 P22059;H0YCV6 P22059 OSBP Oxysterol-binding protein 1 0 ; 87.308 0.010008 199787000 407790 313100 249617 298380 248930 301070 367410 448170 551240 FALSE TRUE 353899.5183 311043.2255 370332.6161 366131.7395 243976.78 312652.3577 331778.6348 352332.3332 486073.0352 0.728078895 0.639910472 0.761886773 0.753244292 0.501934406 0.643220946 0.682569513 0.724854719 1 18.89081358 1.175746414 2.447407582 1.12361856 0.670784972 0.656313997 0.073740266 0.445963114 2.491219597 0.462697405 0.019979642 14.98809419 -1.175746414 -0.452833588 HQLILPAFEHEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HQLILPAFEHEYR 13 0 Q9H4Z3;A0A087WWZ2 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 0 85.457 0.0053644 34517000 21332 14360 13640 16184 15294 16956 14624 16984 15975 FALSE TRUE 18512.92215 14265.66821 20236.34962 19858.82456 14989.67932 17608.30829 13205.76673 13352.10377 14086.4537 1.314235829 1.012722472 1.436582269 1.409781694 1.064120157 1.250017121 0.937479866 0.94786836 1 13.78202083 2.240400446 24.98952242 0.957871256 1.24479936 0.509321675 0.132347972 38.52895006 523332.5807 0.051205619 0.037598191 173.9403924 -2.240400446 0.286928104 HQLLEADISAHEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HQLLEADISAHEDR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 193.47 1.47E-07 510861000 191487 189903 96995 157529 185498 227346 147469 176484 388819 FALSE TRUE 166181.5078 188655.5147 143902.1064 193298.3671 181806.9527 236092.1477 133167.4791 138744.27 342853.2608 0.484701553 0.550251482 0.419719229 0.563793288 0.530276283 0.688609895 0.388409545 0.40467537 1 18.38723172 1.231764254 24.99980998 1.00000085 0.501049601 0.754350487 0.088974648 122.5416893 450717.1833 0.216882458 0.022692515 17.05156537 -1.231764254 -0.498951248 HQLSHRPEAPCS(ph)PPSVPSAASEPTVVLLQAEPQLLDTHREEEVSPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HQLSHRPEAPCSPPSVPSAASEPTVVLLQAEPQLLDTHREEEVSPAR 47 2 Q9H9D4 Q9H9D4 ZNF408 Zinc finger protein 408 1 HQLS(0.181)HRPEAPCS(0.595)PPS(0.223)VPS(0.001)AASEPTVVLLQAEPQLLDTHREEEVSPAR 52.721 0.0087907 259140000 23396 20464 9734.1 14166 21108 23898 17448 22243 12881 TRUE FALSE 20304.15932 20329.57064 14441.54332 17382.60681 20687.9921 24817.37152 15755.89565 17486.50755 11358.22285 1.787617621 1.789854883 1.271461522 1.530398464 1.821411004 2.184969589 1.387179654 1.539546087 1 13.4714495 1.042936624 1.441297597 0.420277658 1.692898493 0.42515797 0.250613052 2.105946875 2.647041203 4.483370839 0.075725985 11.03917516 -1.042936624 1.272620835 HQNS(ph)LPELEAAEAGAPGSGPVDLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HQNSLPELEAAEAGAPGSGPVDLFR 25 0 Q96BZ8 Q96BZ8 LENG1 Leukocyte receptor cluster member 1 1 HQNS(1)LPELEAAEAGAPGSGPVDLFR 138.11 8.20E-06 34604000 53025 30787 15805 21206 28551 24428 32663 33929 34645 TRUE FALSE 46017.6119 30584.75817 23448.35086 26021.14641 27982.89096 25367.76097 29495.34729 26673.54739 30549.30757 1.506338951 1.001160439 0.767557524 0.851775326 0.915991006 0.830387429 0.9654997 0.873130997 1 14.89885206 4.714653562 3.380847771 0.886828607 1.571199524 0.8943152 0.066471073 0.079608047 1.553589919 0.015910673 0.136157481 51838.63556 -4.714653562 0.684370917 HQNVQLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 HQNVQLPR 8 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20;K7EK45;A0A087WUW5 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ;;;;;;;; 135.77 0.00081971 5092975000 1204591 1227841 685134 815557 1127449 1188531 1201221 1352825 1257150 FALSE TRUE 1045401.247 1219775.232 1016467.094 1000741.682 1105014.971 1234254.557 1084726.772 1063533.901 1108531.159 0.943050846 1.10035268 0.916949502 0.902763692 0.996828065 1.113414401 0.978526191 0.959408216 1 20.08021789 3.017072467 24.84073778 1.0072555 0.96914026 0.098446938 0.066218637 701.5943426 1020825.063 0.020998775 0.023804848 1040.093703 -3.017072467 -0.038115241 HQPADLLEFALQHFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HQPADLLEFALQHFTR 16 0 P31323 P31323 PRKAR2B cAMP-dependent protein kinase type II-beta regulatory subunit 0 171.71 2.79E-09 44355000 41304 38186 19892 26254 38780 44134 38013 40804 35442 FALSE TRUE 35845.57175 37935.15365 29511.83773 32215.37197 38008.35387 45831.86354 34326.50511 32078.38214 31252.08714 1.146981691 1.213843846 0.944315738 1.030823056 1.216186097 1.466521687 1.098374805 1.026439674 1 14.93166492 1.849603666 4.275607205 1.017008099 1.165380599 0.178513634 0.135400344 0.425144635 12.06188722 0.08307008 0.03949378 70.73000137 -1.849603666 0.1483725 HQPST(ph)PDPFLKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HQPSTPDPFLKPR 13 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 HQPS(0.001)T(0.999)PDPFLKPR;HQPS(0.009)T(0.991)PDPFLKPR;HQPS(0.026)T(0.974)PDPFLKPR 130.29 0.00021069 1595710000 914480 805050 515484 640570 880570 814030 967640 1071640 956100 TRUE FALSE 793629.151 799761.5735 764773.7866 786021.209 863048.3798 845346.2608 873798.4217 842478.1255 843070.9472 0.941355118 0.948629028 0.907128622 0.932331035 1.023696028 1.00269884 1.03644708 0.999296831 1 19.68529452 3.243885383 24.96181313 1.012101397 0.931720629 0.870987949 0.015310906 42.17541866 197711.5426 0.004449441 0.005577413 1753.417688 -3.243885383 -0.080380768 HQPTAIIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HQPTAIIAK 9 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 121.6 0.00060923 3117800000 4629500 5242300 2876000 3189000 4631100 3829400 4594800 4465900 6196600 FALSE TRUE 4017699.845 5207862.986 4266843.22 3913111.191 4538950.171 3976719.496 4149197.003 3510902.039 5464045.007 0.735297722 0.95311495 0.780894596 0.716156471 0.83069414 0.72779772 0.759363621 0.642546325 1 22.38153794 4.023201024 24.97101642 0.762716478 0.849905994 0.044242652 0.106745199 493.6132882 531263.0079 0.025608472 0.053303842 10548.75059 -4.023201024 0.087189516 HQPVPQLQAHS(ph)TPHPDDFANDDIDSYMIAMETTIGNEGSR ddPTM_MDA-MB-175_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 176.86 3.35E-24 31719000 14616 13338 7756.2 8826.4 11496 10747 11103 14813 12545 TRUE FALSE 12684.45857 13250.3818 11507.12426 10830.56902 11267.25209 11160.44404 10026.23277 11645.35522 11061.94439 1.146675315 1.197834787 1.04024427 0.979083662 1.01855982 1.008904371 0.906371648 1.052740351 1 13.43331737 4.126294113 4.258555467 0.997294045 1.171901711 0.772110747 0.039313279 0.091200222 2.903191395 0.009960704 0.022565857 13375.00992 -4.126294113 0.174607666 HQPWQS(ph)PERPLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(0.999)PERPLS(0.001)R;HQPWQS(0.996)PERPLS(0.004)R;HQPWQS(1)PERPLSR 109.87 0.00066805 2406350000 821715 728406 413271 575822 744713 715620 623773 802186 962622 TRUE FALSE 713123.2808 723621.053 613130.2379 706571.186 729894.6683 743150.3645 563279.5905 630644.7665 848821.9238 0.840132966 0.852500428 0.722330822 0.832413921 0.859891395 0.875507976 0.663601604 0.742964748 1 19.69510239 HQQIPLHS(ph)PPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HQQIPLHSPPSK 12 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;C9JAU4 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 HQQIPLHS(1)PPSK;HQQIPLHS(0.992)PPS(0.008)K 149.22 0.00011213 278300000 262760 224720 133610 171151 209659 194370 254260 320250 291950 TRUE FALSE 228035.6003 223243.7995 198224.2429 210013.4504 205487.1961 201847.5397 229601.9043 251767.0297 257436.0036 0.885795293 0.867181732 0.769994252 0.815788963 0.798206907 0.784068805 0.89187954 0.977979095 1 17.97385431 1.876589623 2.550223998 0.993799342 0.819096783 0.788810444 0.035795438 0.125027747 1.472104166 0.027024643 0.010685874 75.26440335 -1.876589623 -0.174702559 HQRPQPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HQRPQPEK 8 1 O95391;A0A0C4DGD2;E5RGM7;E5RK41 O95391 SLU7 Pre-mRNA-splicing factor SLU7 0 67.993 0.034644 23266000 28279 24308 16041 19038 16308 17572 23867 25510 20965 FALSE TRUE 24541.8585 24148.31915 23798.48125 23360.86888 15983.50271 18248.00621 21552.38201 20054.88502 18486.54158 1.327552717 1.306264833 1.287340909 1.263668965 0.864602102 0.987096809 1.165841751 1.084837038 1 14.17418773 3.375867901 7.777194499 1.038201211 1.301683696 0.758494378 0.07723034 0.129092265 8.782055867 0.024097326 0.03113366 2376.117437 -3.375867901 0.263482485 HQS(ph)FGAAVLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HQSFGAAVLSR 11 0 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 HQS(1)FGAAVLSR;HQS(1)FGAAVLSR;HQS(1)FGAAVLSR;HQS(1)FGAAVLSR;HQS(1)FGAAVLSR;HQS(1)FGAAVLSR 162.46 2.03E-05 1934610000 1293580 1787590 792801 763131 1333510 1661100 1174040 1322160 1656410 TRUE FALSE 1122630.125 1775847.204 1176202.215 936411.5573 1306975.76 1725003.592 1060181.782 1039426.373 1460591.097 0.768613562 1.215841455 0.805291925 0.641118215 0.894826596 1.181031156 0.725858034 0.711647754 1 20.47812091 HQS(ph)LGAAASTANLLDDVEGHACDEDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HQSLGAAASTANLLDDVEGHACDEDFR 27 0 Q9NWM3;J3QLQ8;Q9NWM3-2 Q9NWM3 CUEDC1 CUE domain-containing protein 1 1 HQS(1)LGAAASTANLLDDVEGHACDEDFR;HQS(1)LGAAASTANLLDDVEGHACDEDFR;HQS(1)LGAAASTANLLDDVEGHACDEDFR 82.849 0.016131 76627000 49820 41098.8 16416 23478.1 33562 30652.6 38799.8 29762.1 27026.6 TRUE FALSE 43236.16077 40828.81928 24354.83251 28809.16145 32894.18186 31831.82536 35037.00137 23397.70652 23831.54614 1.814240693 1.713225782 1.021957718 1.208866654 1.380278966 1.335701225 1.470194219 0.981795574 1 14.54058493 4.311259485 6.589848434 1.207046024 1.779808469 0.667158358 0.165771704 0.13108872 9.342488265 0.044460235 0.119218254 20476.67727 -4.311259485 0.572762445 HQTLQGVAFPISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HQTLQGVAFPISR 13 0 Q12792;Q12792-3;Q12792-4;F8VS81 Q12792 TWF1 Twinfilin-1 0 ; 145.69 4.19E-05 1014940000 1217340 1248520 432440 698830 1226940 1368930 1093310 1282590 1381400 FALSE TRUE 1056465.435 1240318.39 641569.4304 857510.0324 1202526.294 1421593.623 987280.9645 1008318.11 1218092.466 0.867311361 1.0182465 0.526700106 0.703977782 0.987220862 1.167065443 0.810513974 0.827784539 1 20.21619222 3.232454448 24.99926354 0.94150262 0.778118128 0.241013657 0.15663313 254.6293377 1042476.354 0.050281776 0.05847192 1707.868576 -3.232454448 -0.163384492 HQVEQLSSSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HQVEQLSSSLK 11 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 113.65 0.0008517 0 286120 315090 137930 234760 301010 241360 309390 368060 310160 FALSE TRUE 248308.5171 313020.153 204633.4093 288065.8461 295020.4899 250645.2754 279385.4054 289353.2332 273493.2381 0.907914648 1.144526114 0.748221092 1.053283248 1.07871219 0.916458765 1.021544106 1.057990447 1 18.06114564 HQYHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HQYHIR 6 0 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ; 88.591 0.05113 93474000 61749 64584 39302 40733 53899 68131 62843 66452 71015 FALSE TRUE 53588.7132 64159.74345 58308.57866 49982.05021 52826.51535 70752.04366 56748.49553 52241.75693 62619.6876 0.85578059 1.024593796 0.931154097 0.798184279 0.843608734 1.129868998 0.906240477 0.834270482 1 15.93432869 HQYYNQEWTLWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HQYYNQEWTLWDR 13 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;;; 246.25 3.62E-17 3396860000 1745820 1394071 1088935 1472867 1514719 1498022 1376262 1631058 2911210 FALSE TRUE 1515105.464 1384913.256 1615547.608 1807303.964 1484579.055 1555651.876 1242792.323 1282268.94 2567050.07 0.590212665 0.539496004 0.629340124 0.704039233 0.578321036 0.606007609 0.484132482 0.499510685 1 21.29168001 1.232242582 24.99960187 1.000000703 0.575807751 0.814099054 0.063227162 99.67979494 394380.9134 0.158651121 0.017376664 17.07035614 -1.232242582 -0.424192952 HRADHPPAEVTSHAASGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HRADHPPAEVTSHAASGAK 19 1 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ; 138.75 8.42E-07 124061000 185200 152636 75747 106371 146174 132184 165315 177044 108118 FALSE TRUE 160725.3508 151633.3241 112378.5026 130524.1613 143265.4234 137269.204 149282.7767 139184.5184 95336.41321 1.685875788 1.59050796 1.1787574 1.369090329 1.502735613 1.439840239 1.565852666 1.4599303 1 16.54073973 1.239388758 8.014184559 0.994357655 1.469071543 0.543934787 0.136379689 0.075646716 43.73724067 0.197073395 0.034569769 17.35356706 -1.239388758 0.474713887 HRAEAPPLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HRAEAPPLER 10 1 O75569;G5E9Q4 O75569 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 0 88.338 0.012564 0 61467 36711 27238 30805 36814 39916 45663 43804 32457 FALSE TRUE 53343.98021 36469.84302 40410.38791 37799.74607 36081.47343 41451.59435 41234.60929 34436.85548 28619.97044 1.863872653 1.274279549 1.411964698 1.320747209 1.260709668 1.448345114 1.440763518 1.203245669 1 14.80473456 HRDTHPGS(ph)PGSPGPALRPLPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HRDTHPGSPGSPGPALRPLPAR 22 2 Q8N0Y2-2;Q8N0Y2 Q8N0Y2-2 ZNF444 Zinc finger protein 444 1 HRDTHPGS(0.805)PGS(0.195)PGPALRPLPAR 106.11 0.00023613 204350000 145360 106240 55790 74947 116740 136680 108630 131430 66586 TRUE FALSE 126150.3077 105542.1024 82770.23061 91964.86184 114417.1024 141938.168 98095.07932 103324.7173 58714.27894 2.148545635 1.797554264 1.40971212 1.566311696 1.948709998 2.417438664 1.670719305 1.759788576 1 15.84142378 1.111906998 2.32160736 0.530236694 1.844550688 0.462163336 0.285542046 0.985594961 4.06596907 3.069374523 0.08013686 12.93918726 -1.111906998 1.314313993 HRDTHPGSPGS(ph)PGPALRPLPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HRDTHPGSPGSPGPALRPLPAR 22 2 Q8N0Y2-2;Q8N0Y2 Q8N0Y2-2 ZNF444 Zinc finger protein 444 1 HRDTHPGS(0.006)PGS(0.994)PGPALRPLPAR 87.052 0.001374 225770000 125250 102050 43436 74527 110440 117970 80932 108040 70101 TRUE FALSE 108697.8952 101379.6268 64441.79488 91449.49442 108242.4601 122508.3822 73083.2271 84936.48677 61813.73964 1.758474666 1.640082406 1.042515714 1.479436367 1.751106804 1.981895659 1.182313633 1.374071319 1 15.91563993 1.591651877 1.591160406 1.021425484 1.570695161 0.310280972 0.269659133 0.71325209 2.953758479 0.540422392 0.083768223 39.05277297 -1.591651877 0.549269677 HRDYETATLSDIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HRDYETATLSDIK 13 1 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 ; 131.26 7.96E-05 1436130000 2307260 2177560 1280440 1836790 2207890 1923340 2280570 2748030 2256250 FALSE TRUE 2002349.745 2163255.465 1899665.067 2253861.243 2163957.309 1997332.134 2059400.672 2160385.17 1989518.695 1.006449324 1.08732603 0.9548365 1.132867587 1.087678801 1.003927301 1.035125067 1.085883322 1 20.92398803 4.787728308 21.83504105 1.050301242 1.006448309 0.058341749 0.05257354 23597.28084 10477983.62 0.012153286 6.404616771 61337.816 -4.787728308 -0.043852933 HREELEQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HREELEQSK 9 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 90.15 0.0069846 384790000 489540 496760 297240 406020 411910 401140 513020 601090 517640 FALSE TRUE 424846.0487 493496.7509 440986.2582 498213.0466 403713.7969 416572.1154 463267.3994 472551.5812 456445.1889 0.930771227 1.081174176 0.966131901 1.091506842 0.88447377 0.912644334 1.014946396 1.035286586 1 18.8000821 2.028034988 24.99411222 1.02164968 0.981291007 0.068921707 0.066371715 586.4703661 522854.6083 0.027152573 0.018305771 106.6682053 -2.028034988 -0.040358674 HREQEELRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HREQEELRR 9 2 Q8WXF1;Q8WXF1-2;A0A0U1RQF9 Q8WXF1 PSPC1 Paraspeckle component 1 0 ; 103.26 0.0019415 285900000 132827 115704 70691 80458 119664 136422 115497 133419 66297 FALSE TRUE 115273.5754 114943.9328 104877.404 98727.21862 117282.9205 141670.2426 104296.1187 104888.3851 58459.44419 1.971855481 1.966216655 1.794019863 1.688815554 2.006227089 2.423393595 1.784076468 1.794207704 1 15.83514849 1.08879392 1.963030177 0.358354093 1.95271274 0.69259803 0.196908407 0.770872314 2.033909752 2.60268022 0.055928389 12.2685693 -1.08879392 1.594358647 HRGS(ph)ADYSMEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HRGSADYSMEAK 12 1 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 HRGS(1)ADYSMEAK;HRGS(1)ADYSMEAK;HRGS(1)ADYSMEAK 115.87 0.00054706 417090000 917740 708050 419152 486189 645590 614540 714050 805330 671110 TRUE FALSE 796458.3337 703398.7729 621855.3092 596585.6434 632744.0221 638181.7515 644801.5409 633116.4466 591772.1403 1.345886836 1.188631105 1.05083573 1.008134048 1.069235908 1.078424799 1.089611181 1.069865246 1 19.17468225 4.547324507 2.319339169 1.055398738 1.363571967 0.912376064 0.029863336 0.113674602 0.961254296 0.008304785 0.059783183 35263.42624 -4.547324507 0.308173229 HRGS(ph)EEDPLLSPVETWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HRGSEEDPLLSPVETWK 17 1 Q13017-2;Q13017;H0YK04;A0A0A0MSK6 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 1 HRGS(1)EEDPLLSPVETWK 151.42 1.52E-07 255590000 289020 290050 182090 267990 346640 283760 362260 425850 371150 TRUE FALSE 250825.2747 288144.6425 270149.3331 328841.2255 339742.5422 294676.4308 327128.081 334785.2915 327273.0698 0.766409759 0.880441042 0.825455431 1.004791582 1.038101126 0.900399263 0.999556979 1.022953987 1 18.32013537 3.739606019 24.98719632 0.995526238 0.829735964 0.759268165 0.045136446 44.68682238 1068095.13 0.012035182 0.019404031 5490.425704 -3.739606019 -0.165790274 HRHPLDHDCSGEGHPTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HRHPLDHDCSGEGHPTSR 18 1 A0A087X0D9;E9PFU9;Q8WV99;B8ZZ56;E7EV05;B4DEN4;Q8WV99-2 A0A087X0D9 ZFAND2B AN1-type zinc finger protein 2B 0 ;;; 108.96 0.00024263 1068900000 65458.7 69709.7 32992.6 43174 70291.4 66809.6 51608.5 63548.1 53147.1 FALSE TRUE 56808.16694 69251.77239 48947.93171 52977.31657 68892.73866 69379.80854 46603.51561 49958.83335 46864.11038 1.212189167 1.477714435 1.044465185 1.130445369 1.470053269 1.480446507 0.994439353 1.066036098 1 15.51619588 2.217220645 24.99830225 1.028644569 1.298573658 0.445331158 0.148422692 238.377461 279240.6404 0.062977794 0.042505528 164.899996 -2.217220645 0.269929089 HRHS(ph)PTGPPGFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HRHSPTGPPGFPR 13 1 P98175-5;P98175-2;P98175 P98175-5 RBM10 RNA-binding protein 10 1 HRHS(0.862)PT(0.138)GPPGFPR;HRHS(0.717)PT(0.283)GPPGFPR;HRHS(0.997)PT(0.003)GPPGFPR;HRHS(0.99)PT(0.01)GPPGFPR 132.47 7.15E-05 4061430000 1082011 973186 650227.1 721245.1 849824 956536 898292 981791 923189 TRUE FALSE 939020.5049 966793.0771 964679.1004 885014.8235 832914.1651 993334.5589 811175.7801 771842.635 814050.6481 1.153516071 1.187632587 1.185035726 1.087174153 1.023172412 1.220236801 0.996468441 0.94815063 1 19.63475903 1.962831645 0.476184593 0.876079699 1.18155893 0.525156415 0.065370657 2.103139165 0.719306885 0.365848993 0.077215398 91.79766731 -1.962831645 0.305479231 HRHSPT(ph)GPPGFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HRHSPTGPPGFPR 13 1 P98175-5;P98175-2;P98175 P98175-5 RBM10 RNA-binding protein 10 1 HRHS(0.392)PT(0.608)GPPGFPR;HRHS(0.365)PT(0.635)GPPGFPR 124.86 0.00030333 2297790000 716250 603380 411660 431770 525320 614640 552800 550850 581660 TRUE FALSE 621595.7478 599416.3571 610740.1529 529809.9777 514867.1598 638285.5985 499189.5411 433055.0142 512896.8174 1.21193138 1.168688003 1.190766119 1.032975756 1.003841596 1.244471747 0.973274788 0.844331646 1 18.96830909 1.540831088 0.230449822 0.613345304 1.293587031 0.466202774 0.092946753 13.1110408 1.117569581 3.018407127 0.743161304 34.7401019 -1.540831088 0.680241727 HRMS(ph)PGVAGSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HRMSPGVAGSPR 12 1 Q15596;E7EWM1 Q15596 NCOA2 Nuclear receptor coactivator 2 1 HRMS(1)PGVAGSPR;HRMS(1)PGVAGSPR;HRMS(1)PGVAGSPR;HRMS(1)PGVAGSPR;HRMS(1)PGVAGSPR 130.21 0.0001335 1110820000 397935 381392 222998 232985 399516 440456 390442 388438 296557 TRUE FALSE 345346.8815 378886.6108 330840.5787 285887.8052 391566.4132 457400.6273 352576.9949 305373.5565 261498.3693 1.320646406 1.448906209 1.265172626 1.093268023 1.497395239 1.749152886 1.348295195 1.167783789 1 17.99644242 1.584443101 2.805813831 1.020734803 1.39377284 0.382786613 0.168301157 0.271718478 4.677034895 0.189266079 0.048874521 38.4098933 -1.584443101 0.373038037 HRPDLIDFDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HRPDLIDFDK 10 1 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;P11277-3;P11277;P11277-2;Q01082-3 Q01082;Q01082-3 SPTBN1;SPTB "Spectrin beta chain, non-erythrocytic 1;Spectrin beta chain, erythrocytic" 0 ;; 91.855 0.0059274 287058000 592620 519280 389596 515783 579570 538870 644560 735910 808160 FALSE TRUE 514303.7655 515868.8155 578005.9287 632899.4134 568037.6909 559600.6776 582050.6704 578541.3734 712620.2455 0.721708047 0.723904238 0.811099506 0.888129993 0.797111357 0.785271933 0.816775378 0.81185088 1 19.44277395 HRPELIEYDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HRPELIEYDK 10 1 O43707;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ;;;; 121.9 0.00030212 2870320000 4276690 3758720 2990850 4104680 3656280 3485090 3642440 4379570 8892670 FALSE TRUE 3711514.581 3734028.721 4437235.064 5036710.33 3583527.181 3619163.667 3289196.729 3443033.037 7841388.683 0.473323633 0.476194826 0.565873628 0.642323769 0.457001601 0.461546266 0.4194661 0.439084603 1 22.90267774 1.235044343 24.99983172 1.000000715 0.490475275 0.855130121 0.065728154 40.43503633 287437.5561 0.127329842 0.017844071 17.180838 -1.235044343 -0.50952544 HRPELIEYDKLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HRPELIEYDKLR 12 2 O43707;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ; 131.66 0.00010951 468600000 811700 720810 418020 626270 741770 725850 747200 927270 462720 FALSE TRUE 704431.7884 716074.9516 620175.8702 768474.1754 727010.2282 753773.9192 674736.659 728980.5265 408017.7687 1.726473312 1.755009234 1.519972701 1.883433111 1.781810215 1.84740464 1.653694301 1.786639167 1 18.63827246 1.236572525 24.99988593 0.999999056 1.744107542 0.842362095 0.101189147 19.11109443 240254.4563 0.150947968 0.023788327 17.24139992 -1.236572525 0.744108485 HRPIGIGVQGLADAFILMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HRPIGIGVQGLADAFILMR 19 1 P23921;E9PL69 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 128.69 1.26E-05 14746000 29597 33531 16497 22217 31058 30394 26981 38023 26505 FALSE TRUE 25685.68146 33310.73265 24475.00438 27261.70942 30440.00656 31563.27685 24364.38677 29892.07735 23371.60909 1.099012112 1.425264838 1.047210925 1.16644555 1.302435208 1.350496524 1.042477934 1.278990985 1 14.51246944 1.228039781 24.81162038 0.999999502 1.215970581 0.215590734 0.128262131 632.2547409 1490954.492 0.404816878 0.029155656 16.90595781 -1.228039781 0.215971079 HRPQVAIICGSGLGGLTDKLTQAQIFDYGEIPNFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HRPQVAIICGSGLGGLTDKLTQAQIFDYGEIPNFPR 36 2 P00491;G3V5M2;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 169.27 5.09E-18 849620000 348400 363450 133730 183790 359230 317440 420020 445440 100040 FALSE TRUE 302358.0573 361062.473 198402.2753 225522.3286 352082.0258 329652.1222 379286.525 350186.1224 88213.38517 3.427575721 4.093057673 2.249117579 2.55655452 3.991253993 3.736985284 4.299648226 3.969761752 1 16.42870996 3.230760128 24.99569073 3.55519039 3.094363674 0.010610302 1.032278295 671.1631327 2150654.722 0.313523868 0.361984361 1701.218624 -3.230760128 -0.460826716 HRPS(ph)AGGPDSAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HRPSAGGPDSAGR 13 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 HRPS(1)AGGPDSAGR 88.781 0.004694 111930000 45578 45253 18504 38205 43385 48316 42147 48742 50094 TRUE FALSE 39554.75182 44955.73006 27452.59629 46880.02918 42521.72338 50174.74778 38059.59043 38318.90261 44171.94439 0.895472282 1.01774397 0.621493952 1.061307801 0.96264097 1.135896291 0.861623616 0.867494133 1 15.43084272 HRPS(ph)PPAT(ph)PPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HRPSPPATPPPK 12 1 A9Z1X7;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 HRPS(1)PPAT(1)PPPK;HRPS(1)PPAT(1)PPPK;HRPS(1)PPAT(1)PPPK;HRPS(1)PPAT(1)PPPK;HRPS(1)PPAT(1)PPPK 94.544 0.015009 11769400000 5993680 4797520 3132410 3796960 4731970 4253950 5255830 6070320 5696020 TRUE FALSE 5201600.002 4766004.775 4647253.953 4659117.801 4637813.055 4417602.209 4746120.416 4772229.307 5022643.005 1.035630045 0.948903749 0.925260654 0.927622727 0.923380987 0.879537368 0.944944805 0.950143043 1 22.26001531 4.732263041 3.462492169 0.934887614 1.047450205 0.523373391 0.029669457 0.244210593 5.095282238 0.007664793 0.07172161 53983.74888 -4.732263041 0.112562591 HRPS(ph)PPATPPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HRPSPPATPPPK 12 1 A9Z1X7;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 HRPS(1)PPATPPPK;HRPS(1)PPATPPPK;HRPS(1)PPATPPPK;HRPS(1)PPATPPPK 125.5 0.00021643 501210000 1523200 1195426 703623 982685 1281360 1025475 1289300 1600320 1264200 TRUE FALSE 1321905.261 1187573.168 1043897.436 1205818.649 1255863.443 1064925.687 1164263.884 1258104.022 1114747.716 1.185833567 1.065329088 0.936442767 1.081696451 1.126589833 0.955306453 1.04441917 1.128599775 1 20.08828581 4.718796085 4.769523743 1.04627368 1.19178042 0.332300176 0.064176611 0.20450601 12.64971497 0.015883985 0.094177199 52335.46472 -4.718796085 0.145506739 HRPSAGGPDS(ph)AGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HRPSAGGPDSAGR 13 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 HRPSAGGPDS(1)AGR 94.203 0.0031871 126930000 49117 51572 27715 30504 51035 58881 51746 57911 42851 TRUE FALSE 42626.064 51233.22014 41118.0667 37430.39942 50019.50335 61146.19017 46727.68088 45527.18331 37785.2036 1.128115239 1.355906949 1.088205509 0.990609971 1.323785466 1.618257528 1.236666114 1.204894482 1 15.20553378 3.182360812 24.99999546 1.281815305 1.152326209 0.128352115 0.174682311 203.4802811 90515.18278 0.056199006 0.06372372 1521.811326 -3.182360812 -0.129489096 HRPSAGGPDSAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HRPSAGGPDSAGR 13 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 0 80.706 0.015559 5906000 8150.3 6774 4541.4 5646.7 8213 7971.6 6523.2 8606.1 7928.5 FALSE TRUE 7073.217205 6729.501148 6737.63623 6928.869539 8049.577368 8278.27261 5890.581068 6765.752488 6991.201762 1.011731237 0.962567149 0.963730766 0.991084191 1.151386792 1.184098656 0.842570601 0.967752429 1 12.77132476 2.220298931 24.99999991 0.939303018 1.039207569 0.269290023 0.083045931 383.9740369 525651.2402 0.036809569 0.02486832 166.0729616 -2.220298931 0.099904552 HRS(ph)EPQHPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HRSEPQHPK 9 1 A0A087WZ32;A0A087X038;A8K727;Q9HB19 A0A087WZ32 PLEKHA2 Pleckstrin homology domain-containing family A member 2 1 HRS(1)EPQHPK;HRS(1)EPQHPK;HRS(1)EPQHPK 77.185 0.020121 276890000 393561 348132 251774 256283 324262 300135 411841 450709 464360 TRUE FALSE 341550.9167 345845.098 373532.7485 314475.9722 317809.8206 311681.3877 371900.7232 354328.3878 409463.8898 0.834141728 0.844629054 0.912248327 0.768018817 0.776160801 0.761193833 0.908262566 0.865347096 1 18.6433767 0.87914795 1.148652951 1.233840385 0.822630684 0.531807162 0.051153711 2.887529885 1.779483043 1.762185656 0.016699929 7.570907671 -0.87914795 -0.4112097 HRS(ph)NS(ph)FSDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HRSNSFSDER 10 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 HRS(1)NS(0.971)FS(0.029)DER;HRS(1)NS(0.978)FS(0.022)DER;HRS(1)NS(0.995)FS(0.005)DER;HRS(1)NS(0.994)FS(0.006)DER;HRS(1)NS(0.983)FS(0.017)DER 145.52 1.72E-05 2786887000 2883016 2443231 1500877 2774178 3454730 3517590 2453509 3131190 3543580 TRUE FALSE 2502018.131 2427181.255 2226706.137 3404097.516 3385987.632 3652913.963 2215568.075 2461609.385 3124662.009 0.800732407 0.776782016 0.712623039 1.089429034 1.083633245 1.16905891 0.709058474 0.787800209 1 21.57526871 3.756356448 24.92304947 0.95011334 0.764719431 0.324881017 0.139949105 1235.19656 1729886.857 0.042575563 0.073537457 5706.324282 -3.756356448 -0.185393909 HRS(ph)NSFSDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HRSNSFSDER 10 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 HRS(0.999)NS(0.001)FSDER 127.02 0.00022239 390820000 386830 304790 199510 295290 407730 370350 290470 462710 214690 TRUE FALSE 335709.4354 302787.8144 295993.7033 362340.1077 399616.9707 384597.6041 262300.2641 363763.0673 189309.5928 1.773335574 1.599431967 1.563543078 1.914008173 2.110917703 2.031580114 1.385562455 1.921524747 1 17.53038799 1.232387829 24.99688476 0.999998709 1.783744492 0.552970614 0.222494456 168.1330275 680792.1007 0.503969511 0.055877832 17.07606615 -1.232387829 0.783745783 HRS(ph)PTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HRSPTPK 7 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HRS(0.999)PT(0.001)PK;HRS(0.998)PT(0.002)PK;HRS(0.998)PT(0.002)PK 90.108 0.010526 268907000 548650 323733 194792 251255 221681 276278 390464 524200 438960 TRUE FALSE 476144.5124 321606.3766 288994.0627 308306.2879 217269.9818 286906.5934 352596.8614 412103.9093 387066.6489 1.230135724 0.830881135 0.746626101 0.796519899 0.561324471 0.741233052 0.910946118 1.064684624 1 18.56222248 1.979420808 4.169614534 1.028728666 0.803052657 0.214761372 0.16706133 0.303656961 12.01470139 0.087719653 0.047294526 95.37198204 -1.979420808 -0.225676008 HRSNS(ph)FSDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HRSNSFSDER 10 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 HRS(0.243)NS(0.75)FS(0.007)DER 72.891 0.028238 264650000 604780 427230 82421 159580 548860 566190 416940 549870 99884 TRUE FALSE 524856.7907 424423.498 122280.0713 195815.078 537938.7598 587971.6957 376505.223 432284.5796 88075.82731 5.959146871 4.818842025 1.38834996 2.22325562 6.107677626 6.675744227 4.274784972 4.90809559 1 16.4264585 4.477617037 24.99989099 3.987667076 5.674071507 0.118969954 1.871625812 37.58587679 1895108.373 0.489865046 1.329630773 30034.26695 -4.477617037 1.68640443 HRTPS(ph)LR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HRTPSLR 7 1 P49023-3 P49023-3 PXN Paxillin 1 HRT(0.128)PS(0.872)LR 55.549 0.076888 118270000 23141 22125 10532 13596 20063 30727 21333 20195 12171 TRUE FALSE 20082.85822 21979.65942 15625.31043 16683.1796 19663.78555 31909.08757 19264.12894 15876.45641 10732.15825 1.871278615 2.048018573 1.455933659 1.554503691 1.832230303 2.973221867 1.794991138 1.479334915 1 13.38965261 1.519057391 2.534780576 1.01949928 1.940044132 0.364393885 0.408386627 0.353476235 4.330710815 0.590652604 0.116710323 33.04132011 -1.519057391 0.920544852 HS(ph)FSAGPELLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSFSAGPELLR 11 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 HS(0.999)FS(0.001)AGPELLR 201.09 2.87E-08 140100000 75928 71322 40272 43307 67953 64481 72041 67892 76505 TRUE FALSE 65893.92242 70853.48109 59747.6739 53140.51626 66600.86825 66961.62579 65054.47491 53373.82414 67460.66605 0.97677545 1.050293234 0.885666825 0.787725935 0.987254828 0.9926025 0.964331939 0.791184364 1 16.04175894 4.233723015 24.99946429 0.907797896 1.013534351 0.204695869 0.07916984 163.7800621 846390.4004 0.020827684 0.045700799 17128.64525 -4.233723015 0.105736455 HS(ph)GGDDEGLQEEELIEQVPSTTSVIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HSGGDDEGLQEEELIEQVPSTTSVIER 27 0 Q1W6H9 Q1W6H9 FAM110C Protein FAM110C 1 HS(1)GGDDEGLQEEELIEQVPSTTSVIER;HS(1)GGDDEGLQEEELIEQVPSTTSVIER 167.16 5.28E-12 540170000 367000 308380 249040 284620 368870 331360 339030 388210 613170 TRUE FALSE 318500.0201 306354.2315 369476.577 349247.3211 361530.2087 344107.6336 306150.9228 305194.3126 540681.7411 0.589071159 0.566607318 0.683353161 0.645938811 0.668656219 0.636432873 0.566231296 0.564462029 1 19.04442011 1.234040492 24.99999672 1.000000576 0.614352706 0.886150119 0.043357315 48.05757712 265763.8861 0.091500292 0.01179587 17.14117118 -1.234040492 -0.385647869 HS(ph)LQEIT(ph)S(ph)VTFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSLQEITSVTFK 12 0 H0Y5Q9;Q92835-3;Q92835-2;Q92835 H0Y5Q9 INPP5D "Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1" 3 HS(1)LQEIT(0.667)S(0.667)VT(0.667)FK 52.278 0.078324 0 36469 26506 24213 19041 35813 28952 34041 53437 23573 TRUE FALSE 31649.52925 26331.88034 35922.48779 23364.55007 35100.39137 30065.80217 30739.70906 42009.9134 20786.22679 1.522620222 1.266794623 1.728187041 1.124039986 1.688636986 1.446429045 1.478849883 2.021045657 1 14.34334028 1.96232116 24.85135021 1.633402544 1.460960639 0 0.303670413 1538.049529 1014428.588 0.129769934 0.074946769 91.68982832 -1.96232116 -0.172441905 HS(ph)MLMDWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSMLMDWK 8 0 Q6UWP7-2 Q6UWP7-2 1 HS(1)MLMDWK 57.96 0.071899 155480000 158400 121510 87218 106440 140620 164630 135130 160360 188500 TRUE FALSE 137467.0387 120711.7928 129396.9165 130608.8288 137821.9371 170963.4226 122025.1134 126068.2619 166215.7447 0.827039814 0.72623561 0.778487722 0.785778923 0.829174982 1.028563346 0.734136911 0.758461613 1 17.34269752 3.190870035 4.31621288 0.855207121 0.774794093 0.179312134 0.094542013 0.450041052 17.65172396 0.030061284 0.035512457 1551.922518 -3.190870035 -0.080413027 HS(ph)PAPRPLVQQPEPLPIQVAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HSPAPRPLVQQPEPLPIQVAFR 22 1 A0A0A0MTL6;Q6ZS17-2;Q6ZS17;Q6ZS17-3;Q6ZS17-4;H3BMG9;H3BSV5 A0A0A0MTL6 FAM65A Protein FAM65A 1 HS(1)PAPRPLVQQPEPLPIQVAFR;HS(1)PAPRPLVQQPEPLPIQVAFR 92.819 0.0012171 379310000 396730 384660 219680 276990 477540 450360 344050 450850 257560 TRUE FALSE 344301.1253 382133.1431 325917.9828 339884.813 468037.8883 467685.6406 310684.084 354439.236 227111.5502 1.516000067 1.68257908 1.435056837 1.496554502 2.060828205 2.059277215 1.367980112 1.560639411 1 17.79304155 0.888450214 1.37009013 0.050760292 1.681007356 0.43586697 0.235531533 3.139550615 2.633669927 9.092567281 0.072845912 7.734820051 -0.888450214 1.630247064 HS(ph)PATISSSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSPATISSSTR 11 0 O15119;O15119-2;O15119-3 O15119 TBX3 T-box transcription factor TBX3 1 HS(1)PATISSSTR 124.89 0.00097953 0 131910 108120 67347 103690 148870 121190 116550 139160 215420 TRUE FALSE 114477.7593 107409.7526 99916.23446 127234.3993 145907.7783 125852.2577 105246.9989 109401.7169 189953.293 0.602662673 0.565453491 0.526004224 0.669819392 0.7681245 0.662543174 0.554067778 0.575940091 1 17.5352852 1.235082787 24.99372395 1.000000542 0.614400065 0.746999307 0.070306315 56.02842432 402588.3928 0.135302602 0.019014361 17.18235891 -1.235082787 -0.385600477 HS(ph)PESPSIAVVESELVAEYITTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HSPESPSIAVVESELVAEYITTER 24 0 Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-7 EMSY Protein EMSY 1 HS(0.333)PES(0.333)PS(0.333)IAVVESELVAEYITTER;HS(0.353)PES(0.295)PS(0.353)IAVVESELVAEYITTER;HS(0.367)PES(0.31)PS(0.31)IAVVES(0.014)ELVAEYITTER 136.64 1.25E-05 97060000 72597 58324 38599.5 46473.7 53840 67794 58196 59189 71709 TRUE FALSE 63003.12251 57940.8658 57266.34731 57026.26389 52768.68934 70402.07905 52552.16088 46531.89296 63231.64371 0.996385968 0.916327054 0.905659634 0.901862747 0.834529774 1.113399477 0.831105405 0.735895672 1 15.9483591 7.999999995 0.148900024 0.816379916 1.361544155 0.023482513 0.103676017 442.7163004 5.550986037 1.8607102 50.89855636 99999998.94 -7.999999995 0.54516424 HS(ph)PQQEEENTIFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSPQQEEENTIFK 13 0 O14896;A0A2R8YHF3;B1AJU4 O14896 IRF6 Interferon regulatory factor 6 1 HS(0.997)PQQEEENT(0.003)IFK 79.013 0.013954 109610000 102460 88876 65599 88062 99871 72463 93954 104090 174970 TRUE FALSE 88919.6514 88292.1677 97322.89582 108057.823 97883.76249 75250.6985 84842.35554 81831.16353 154285.2459 0.576332823 0.572265787 0.630798462 0.700376905 0.63443372 0.487737489 0.549905826 0.530388781 1 17.23524058 1.234043694 24.99999614 1.000000621 0.584149164 0.827919831 0.059417473 60.98018465 337466.424 0.125406448 0.016163154 17.14129756 -1.234043694 -0.415851457 HS(ph)PQQPSNGSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HSPQQPSNGSLR 12 0 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 HS(1)PQQPSNGSLR;HS(1)PQQPSNGSLR;HS(1)PQQPSNGSLR;HS(1)PQQPSNGSLR 179.21 2.20E-05 1875960000 1799810 1521550 964191 1331140 1754290 1877820 1519450 1726500 2028620 TRUE FALSE 1561960.548 1511554.838 1430476.993 1633395.682 1719383.061 1950060.951 1372093.973 1357301.411 1788798.855 0.873189596 0.845011072 0.799685772 0.913124289 0.961194187 1.090151051 0.767047658 0.758778108 1 20.77055974 6.809509841 18.91469725 0.88003412 0.876018905 0 0.106155615 0 0 0.025237089 0 6449259.338 -6.809509841 -0.004015216 HS(ph)PS(ph)PRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSPSPRPR 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 HS(1)PS(1)PRPR 67.726 0.033202 149490000 73431 69482 42188 47913 44095 73745 66889 82784 71073 TRUE FALSE 63726.9073 69025.56817 62590.25791 58792.37895 43217.59577 76582.01787 60402.11508 65081.28583 62670.83091 1.016851163 1.101398644 0.998714346 0.938113922 0.689596662 1.221972276 0.963799493 1.03846215 1 15.9355065 4.071716636 7.001434042 0.97871693 1.058229389 0.064272012 0.130061679 0.670411071 53.57499502 0.033010856 0.069494342 11795.50763 -4.071716636 0.079512458 HS(ph)PTLPEPGGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSPTLPEPGGLR 12 0 Q86XN8-2;S4R446;Q86XN8;Q86XN8-3 Q86XN8-2 MEX3D RNA-binding protein MEX3D 1 HS(0.952)PT(0.048)LPEPGGLR 57.414 0.07303 152310000 182150 115650 137520 113550 122850 105430 148690 172750 207630 TRUE FALSE 158078.416 114890.2875 204025.132 139333.263 120405.5254 109485.9603 134270.0667 135808.7568 183084.2179 0.863419129 0.627526986 1.114378586 0.761033718 0.657651035 0.598008728 0.733378705 0.74178298 1 17.48214791 5.076436173 19.76742434 0.772877208 3.800143309 0.0247269 0.161884029 1550.887089 409763.6932 0.037909351 4488.162979 119243.9004 -5.076436173 3.027266101 HS(ph)PTPQQSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HSPTPQQSNR 10 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 HS(0.999)PT(0.001)PQQSNR;HS(0.96)PT(0.039)PQQS(0.001)NR;HS(0.887)PT(0.112)PQQSNR 167.89 3.29E-06 581860000 592734 519539 320050 332119 474378 548259 541777 601857 653962 TRUE FALSE 514402.7001 516126.1141 474827.2505 407531.6951 464938.8059 569350.8785 489235.5499 473154.5642 576651.3574 0.892051486 0.895040144 0.823421717 0.706721123 0.806273669 0.987339874 0.84840787 0.820521027 1 19.13733981 HS(ph)PVQMNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 HSPVQMNR 8 0 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 HS(1)PVQMNR;HS(1)PVQMNR;HS(1)PVQMNR;HS(1)PVQMNR;HS(1)PVQMNR;HS(1)PVQMNR;HS(1)PVQMNR 158.47 0.00023497 3623233000 1211759 1227134 878408 1116340 1366852 1215977 1285005 1478470 1506903 TRUE FALSE 1051621.978 1219072.876 1303209.047 1369822.059 1339654.319 1262756.422 1160385.413 1162310.696 1328758.644 0.7914319 0.917452452 0.98077183 1.030903592 1.008199891 0.950327908 0.873285316 0.87473425 1 20.34164765 4.703720103 3.254684813 0.951399647 0.775017628 0.497438558 0.052550595 0.308740089 5.387112759 0.015453591 0.130678118 50549.87703 -4.703720103 -0.176382019 HS(ph)QPSPEPHSPTEPPAWGSSIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSQPSPEPHSPTEPPAWGSSIVK 23 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 HS(0.315)QPS(0.259)PEPHS(0.213)PT(0.213)EPPAWGSSIVK 72.443 0.034794 400370000 185240 212670 98740 153760 249240 203220 241160 292760 237050 TRUE FALSE 160760.0647 211272.9568 146490.9943 188673.5581 244280.6116 211038.0049 217772.3403 230155.5523 209026.219 0.76909043 1.010748593 0.70082593 0.902631062 1.168660146 1.009624562 1.041842221 1.101084607 1 17.67332439 3.409919356 6.533027005 1.06344304 0.838218941 0.599269821 0.090323138 0.134159743 10.1955562 0.024164717 0.031356117 2569.918529 -3.409919356 -0.225224099 HS(ph)S(ph)ISPVRLPLNSSLGAELSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSSISPVRLPLNSSLGAELSR 21 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 HS(0.74)S(0.78)IS(0.48)PVRLPLNSSLGAELSR 125.05 3.15E-05 138990000 53023 29217 16900 27515 38591 34985 31060 33607 31558 TRUE FALSE 46015.87621 29025.0716 25072.89653 33762.70129 37823.1146 36330.89559 28047.80598 26420.40458 27827.24919 1.653626483 1.043044945 0.901019585 1.213296401 1.35921141 1.305587029 1.007925929 0.949443633 1 14.76421068 2.15676586 6.297113103 0.97476827 1.224315707 0.276011305 0.196745269 0.300948059 18.44366602 0.083026305 0.055770385 143.4715731 -2.15676586 0.249547437 HS(ph)S(ph)PHQS(ph)EDEEDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSSPHQSEDEEDPR 14 0 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 3 HS(1)S(1)PHQS(1)EDEEDPR 68.411 0.023528 72888000 101120 80027 51781 59383 91497 88317 72201 79966 118960 TRUE FALSE 87756.73579 79501.29737 76822.4648 72866.81776 89676.38871 91714.61214 65198.95813 62865.8932 104896.6843 0.836601618 0.757900956 0.732363137 0.694653203 0.854902033 0.874332804 0.621554042 0.599312491 1 16.67860955 2.23686118 24.99993578 0.705971508 0.786003656 0.011755489 0.121141052 119.7336235 1761305.211 0.047999741 0.034276368 172.5286323 -2.23686118 0.080032148 HS(ph)SADNLANEMTYITETEDVFYTYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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(0.344)S(0.344)ADNLANEMT(0.148)Y(0.137)IT(0.007)ET(0.02)EDVFYTYK;HS(0.498)S(0.498)ADNLANEMT(0.002)Y(0.002)ITETEDVFYTYK;HS(0.5)S(0.5)ADNLANEMTYITETEDVFYTYK;HS(0.436)S(0.436)ADNLANEMT(0.068)Y(0.058)IT(0.002)ETEDVFYTYK;HS(0.5)S(0.5)ADNLANEMTYITETEDVFYTYK;HS(0.5)S(0.5)ADNLANEMT(0.001)YITETEDVFYTYK 293.31 4.30E-63 806040000 450457 357057 228563.1 311453 310661.2 313565.4 302092 438555 392634 TRUE FALSE 390927.9661 354711.4691 339096.9797 382173.1639 304479.6499 325628.4638 272795.1643 344773.4261 346217.2558 1.129140618 1.024534344 0.979434081 1.103853599 0.879446777 0.940532161 0.787930583 0.9958297 1 18.40131811 3.235590374 24.99971546 0.921160992 1.051061172 0.477346972 0.071782267 73.47894103 618452.2625 0.021492931 0.025441404 1720.245278 -3.235590374 0.129900179 HS(ph)SNPPLESHVGWVMDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSSNPPLESHVGWVMDSR 18 0 Q6PKG0;Q6PKG0-3;H0YC33;H0YBR8 Q6PKG0 LARP1 La-related protein 1 1 HS(0.503)S(0.497)NPPLESHVGWVMDSR 125.62 3.10E-05 0 60654 63129 39378 54825 84176 86178 87949 67099 70509 TRUE FALSE 52638.42022 62714.30144 58421.33251 67273.8542 82501.06229 89493.32342 79419.71952 52750.40102 62173.50634 0.846637472 1.00869816 0.939649956 1.082034103 1.326948843 1.43941252 1.27738846 0.848438573 1 15.92401232 3.61942637 3.877947104 1.1606436 0.939118878 0.302125469 0.168951353 0.387071799 10.17824756 0.05618506 0.086209231 4163.191324 -3.61942637 -0.221524722 HS(ph)SPTEERDEPAYPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSSPTEERDEPAYPR 15 1 F5H4R1;J3KNB8;F5H538;Q9Y6R4-2;Q9Y6R4 F5H4R1 MAP3K4 Mitogen-activated protein kinase kinase kinase 4 1 HS(0.522)S(0.471)PT(0.007)EERDEPAYPR 173.37 5.90E-07 495970000 187690 210030 97793 109090 233350 235660 154560 173360 151670 TRUE FALSE 162886.291 208650.2991 145086.0219 133860.5518 228706.7915 244725.9927 139570.795 136288.3131 133739.7454 1.217934807 1.560121851 1.084838479 1.000903295 1.710088432 1.829867344 1.043599975 1.019056173 1 17.02906875 2.044761951 24.99977467 1.017019248 1.39336209 0.325282715 0.257970819 158.0241298 88256.58079 0.111631468 0.075261878 110.8567011 -2.044761951 0.376342842 HS(ph)SYPAGTEDDEGMGEEPSPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HSSYPAGTEDDEGMGEEPSPFR 22 0 Q92934 Q92934 BAD Bcl2-associated agonist of cell death 1 HS(0.608)S(0.392)YPAGTEDDEGMGEEPSPFR;HS(0.565)S(0.434)Y(0.001)PAGTEDDEGMGEEPSPFR 353.72 2.49E-96 835320000 476550 253299 226468 223428 299903 346230 304640 322230 338564 TRUE FALSE 413572.7101 251635.0622 335988.6823 274160.7423 293935.5171 359549.6921 275096.0597 253323.6221 298539.3496 1.385320597 0.84288742 1.125441865 0.918340388 0.984578808 1.204362817 0.921473367 0.848543492 1 18.18756158 4.750598076 24.68708791 0.977286787 1.385320894 0.557759604 0.113191271 1237.243028 2537351.239 0.027827497 0.448191524 56311.62705 -4.750598076 0.408034107 HS(ph)YPPALGSPGALAGAGVGAAGPLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSYPPALGSPGALAGAGVGAAGPLER 26 0 Q96IF1;H0YJL9 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 HS(0.564)Y(0.436)PPALGSPGALAGAGVGAAGPLER 209.76 1.11E-25 142030000 128130 109200 54723 84354 113050 125830 100480 119260 133170 TRUE FALSE 111197.2959 108482.658 81187.22584 103507.865 110800.5262 130670.7615 90735.46507 93757.17708 117426.7943 0.94694994 0.923832236 0.691385866 0.881467178 0.943571072 1.112784883 0.772698136 0.798430866 1 16.84140211 4.459850661 24.99910741 0.876972673 0.941170796 0.027059847 0.118657549 792.6054916 1147292.962 0.030662093 0.081162384 28830.39954 -4.459850661 0.064198123 HSAS(ph)PVVFTSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HSASPVVFTSAR 12 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 HS(0.002)AS(0.998)PVVFTSAR;HS(0.001)AS(0.999)PVVFTSAR;HS(0.326)AS(0.674)PVVFTSAR;HS(0.202)AS(0.798)PVVFTSAR 177.39 1.50E-05 1272960000 1570310 1425160 802210 993500 1513690 1491830 1428200 1647170 1419130 TRUE FALSE 1362789.555 1415798.03 1190161.439 1219089.36 1483570.53 1549221.665 1289693.384 1294935.514 1251362.068 1.089044961 1.131405583 0.951092789 0.974209936 1.185564569 1.238028309 1.030631675 1.034820814 1 20.25506785 2.038114886 24.99986103 1.02374546 1.092457121 0.13920733 0.085661722 369.5926669 242417.3329 0.038210633 0.025761573 109.1729098 -2.038114886 0.068711661 HSCDALNR ddPTM_MDA-MB-175_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 ;;; 175.12 0.00026796 1544040000 1738700 2064720 2887560 1145010 1080110 2646770 1041570 978300 1314760 FALSE TRUE 1508926.39 2051156.718 4283993.674 1405002.021 1058617.924 2748592.955 940558.7017 769098.1581 1159330.571 1.301549729 1.76925958 3.695230492 1.211908024 0.91312862 2.370844886 0.811294661 0.663398497 1 20.14486056 2.385884402 0.793520514 0.622917113 2.061546233 0.235927498 0.79979573 1.128221517 1.444544897 1.129844137 0.460469406 243.1556707 -2.385884402 1.43862912 HSCSGS(ph)SPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSCSGSSPPR 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSCS(0.001)GS(0.587)S(0.412)PPR 64.441 0.046415 205210000 9893.7 10102 5602.4 2823.6 5912.9 8481.2 4066.3 5679.9 10165 TRUE FALSE 8586.222478 10035.6393 8311.739379 3464.741536 5795.244858 8807.477252 3671.950852 4465.297586 8963.30528 0.957930385 1.119636003 0.927307407 0.386547309 0.646552212 0.982614892 0.409664821 0.498175332 1 13.12981512 3.93967017 7.124263687 0.636321573 1.035712409 0.383782318 0.210379242 0.237227973 24.2695921 0.055706571 0.098167043 8703.023774 -3.93967017 0.399390836 HSCSGSS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 HSCSGSSPPR 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSCSGS(0.018)S(0.981)PPR;HS(0.001)CS(0.017)GS(0.092)S(0.89)PPR;HSCSGS(0.014)S(0.986)PPR;HSCSGS(0.391)S(0.609)PPR;HSCSGS(0.147)S(0.853)PPR;HSCSGS(0.018)S(0.982)PPR;HSCSGS(0.029)S(0.971)PPR 121.66 0.00032803 9667814000 516311.5 451513.2 198911.3 296649.3 399023.8 467913.3 423966.1 491533.5 434390.2 TRUE FALSE 448079.6271 448547.1801 295105.47 364008.0576 391084.0071 485914.2274 382849.9329 386422.8861 383037.0854 1.169807426 1.171028073 0.770435765 0.950320665 1.021008205 1.268582719 0.999511398 1.008839355 1 18.54712455 3.912853724 0.007101462 2.80E-07 2.088262919 0.011742478 0.137247642 115929.2953 420.0979692 60846.80898 62688.90977 8181.891652 -3.912853724 2.088262639 HSDENDGGQPHKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HSDENDGGQPHKR 13 1 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 ; 63.662 0.027395 76210000 95744 84074 53469 59901 69898 68639 86609 101995 69408 FALSE TRUE 83091.18782 83521.71236 79326.78724 73502.43758 68507.16655 71279.58675 78209.67251 80184.16298 61202.66531 1.357640021 1.364674429 1.296132886 1.200967919 1.119349398 1.164648408 1.277880173 1.310141684 1 15.90130686 3.917334899 2.749259933 1.195342844 1.360034257 0.447381309 0.085020623 0.291960186 4.29666514 0.024756493 0.051988379 8266.751806 -3.917334899 0.164691413 HSDGNLCVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HSDGNLCVK 9 0 P49458;Q6P2S0;Q659G3;E9PE20;P49458-2 P49458 SRP9;DKFZp564M2223 Signal recognition particle 9 kDa protein 0 ; 85.29 0.014915 1130050000 2374000 2087630 1234480 1556500 1854660 1825810 2145880 2739400 2392100 FALSE TRUE 2060269.885 2073916.221 1831478.657 1909927.115 1817755.895 1896050.092 1937772.888 2153600.628 2109308.663 0.976751256 0.983220833 0.868283855 0.905475404 0.861778044 0.898896461 0.918676779 1.020998333 1 21.00833879 1.762072462 5.983386899 1.009910857 0.913440579 0.493607588 0.03962289 0.137446351 12.64598001 0.02439389 0.011144158 57.81925103 -1.762072462 -0.096470277 HSDSGTSEASLS(ph)PPSS(ph)PPSRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSDSGTSEASLSPPSSPPSRPR 22 1 A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4 A0A1B0GV47 KIF21A Kinesin-like protein KIF21A 2 HSDSGTSEAS(0.001)LS(0.999)PPS(0.315)S(0.685)PPSRPR 126.04 1.16E-05 147340000 105330 102040 45061 65209 114580 110840 95762 126770 99065 TRUE FALSE 91410.37363 101369.6925 66852.65032 80015.70011 112300.0822 115104.0865 86475.01598 99661.22203 87353.64856 1.046440248 1.160451729 0.765310338 0.91599723 1.285579756 1.317679209 0.989941661 1.14089364 1 16.41458034 3.258167095 24.99961133 1.142855467 0.970740027 0.271773486 0.142066883 357.543536 455889.9714 0.042653473 0.054986875 1812.037139 -3.258167095 -0.172115441 HSEAATAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSEAATAQR 9 0 Q14103-3;Q14103;H0Y8G5;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 102.07 0.0036447 465060000 36939 35445 12998 18975 21569 25216 27822 27491 28600 FALSE TRUE 32057.41756 35212.15946 19283.87628 23283.56376 21139.8191 26186.07584 25123.82672 21612.26359 25218.94058 1.271164324 1.396258473 0.76465846 0.923257014 0.838251672 1.038349559 0.996228475 0.856985388 1 14.62222005 4.246219194 24.9999979 0.917494856 1.333711562 0.797212649 0.08741309 68.81630205 224632.6584 0.021198112 0.053847461 17628.65563 -4.246219194 0.416216706 HSEAATAQREEWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSEAATAQREEWK 13 1 Q14103-3;Q14103;H0Y8G5;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 166.62 2.00E-05 109400000 274390 227250 33297 43324 205140 150660 224760 215450 12109 FALSE TRUE 238128.6663 225757.1798 49399.54057 53161.37637 201058.1153 156455.9877 202962.8098 169377.6941 10677.48781 22.30193754 21.14328611 4.626513411 4.9788281 18.83009551 14.65288375 19.00847965 15.86306602 1 13.38228463 4.27397416 13.79687693 10 21.72960151 0.310690726 6.244158676 1.986147734 769.8000987 1.714886676 4.523723158 18792.05002 -4.27397416 11.72960151 HSEHVWVEVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HSEHVWVEVVR 11 0 Q9Y2J8;Q9Y2J8-2 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ;;; 137.89 3.98E-05 1437450000 1306885 1514021 605774 943811 1563470 1722430 1387984 1591572 1113050 FALSE TRUE 1134176.836 1504075.296 898728.3326 1158117.713 1532360.006 1788692.997 1253377.525 1251226.713 981466.497 1.155594042 1.532477472 0.915699451 1.179987006 1.561296295 1.822469745 1.277045655 1.274854228 1 19.9045795 3.279758961 24.97310999 1.386608823 1.199960535 0.121261604 0.255645005 361.1071677 218889.1311 0.077422341 0.099950743 1904.403457 -3.279758961 -0.186648288 HSEKS(ph)PPSTENKHEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSEKSPPSTENKHEAK 16 2 H3BQL3;Q6PH81 H3BQL3 C16orf87 UPF0547 protein C16orf87 1 HS(0.074)EKS(0.911)PPS(0.013)T(0.002)ENKHEAK 108.18 0.00050823 34801000 75582 45080 35185 36416 32345 31820 58233 65840 45038 TRUE FALSE 65593.6472 44783.86651 52200.58369 44684.80938 31701.39778 33044.13599 52585.57262 51760.62837 39713.65895 1.651664665 1.127669112 1.31442393 1.125174828 0.798249233 0.832059721 1.324118049 1.303345744 1 15.27734767 7.298915741 1.113855717 1.100187664 199.9999957 0.464743182 0.185595225 626.3847331 2.836244571 0.061394346 315828.4633 19902871.57 -7.298915741 198.8998081 HSETFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HSETFTR 7 0 Q9UNS2-2;Q9UNS2 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 0 ;; 132.08 0.0034032 475990000 205012 216707 132401 155361 178818 228480 196660 212844 224956 FALSE TRUE 177919.1448 215283.4374 196430.5665 190638.0896 175259.8717 237269.7734 177587.9435 167328.967 198361.958 0.896941866 1.085306072 0.990263297 0.961061746 0.883535701 1.196145551 0.895272185 0.843553717 1 17.59777585 HSEVQQANLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HSEVQQANLK 10 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ;;; 172.27 3.77E-06 2468490000 4632090 4222180 2476310 3095510 4152010 3672160 4735540 5456400 4855910 FALSE TRUE 4019947.57 4194444.222 3673861.799 3798392.857 4069393.124 3813430.371 4276288.06 4289591.322 4281849.852 0.938834314 0.979586947 0.858008087 0.887091558 0.950382023 0.890603478 0.998701077 1.001807973 1 22.02980278 2.225912886 24.93941437 1.000449837 0.917663086 0.564071243 0.034292825 163.1112632 321628.1035 0.014254201 0.009682163 168.233657 -2.225912886 -0.082786751 HSGDYFTLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HSGDYFTLLR 10 0 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 ; 152.04 3.31E-05 152110000 246203 231940 129507 148331 217437 239409 211160 230918 231663 FALSE TRUE 213666.6498 230416.3709 192137.0184 182011.8206 213110.4291 248619.2191 190681.7357 181537.9827 204276.0641 1.045970074 1.127965589 0.940575291 0.891009045 1.043247187 1.21707465 0.933451193 0.888689449 1 17.64016064 2.054226196 24.99999283 0.92879289 1.039618764 0.21170348 0.093048646 134.8501153 62169.41551 0.03993592 0.026924788 113.299031 -2.054226196 0.110825874 HSGIDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSGIDFK 7 0 A0A0A0MTH3;Q13418;Q13418-3 A0A0A0MTH3 ILK Integrin-linked protein kinase 0 82.716 0.023735 87400000 183330 171440 113990 131020 173110 154150 185510 217090 194430 FALSE TRUE 159102.476 170313.7994 169115.9453 160770.0935 169665.4497 160080.2502 167519.2688 170666.9929 171444.7069 0.928010429 0.99340366 0.986416836 0.937737282 0.989621976 0.933713575 0.977103766 0.995463762 1 17.38738384 1.836429587 3.484384733 0.997839025 0.963795883 0.279890815 0.023508756 0.303155297 6.310136533 0.013888998 0.006057839 68.61666203 -1.836429587 -0.034043142 HSGNITFDEIVNIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 HSGNITFDEIVNIAR 15 0 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;;;;;; 268.92 9.40E-26 8458528000 4393277 3967102 2171458 2967412 4101054 4160303 3805040 4635790 4116646 FALSE TRUE 3812694.313 3941041.846 3221582.352 3641208.249 4019451.049 4320352.548 3436027.806 3644462.384 3629980.8 1.050334568 1.085692202 0.887492945 1.003092978 1.107292647 1.190186061 0.946569141 1.003989438 1 21.79153049 HSGPNSADSANDGFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HSGPNSADSANDGFVR 16 0 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ;;;;; 289.98 1.67E-45 6928830000 3686730 3773330 1582680 2438180 3411510 3487580 2741920 3470570 5061830 FALSE TRUE 3199519.29 3748542.747 2348069.342 2991806.034 3343627.626 3621749.459 2476009.02 2728415.614 4463426.224 0.716830329 0.839835265 0.526068814 0.670293601 0.749116812 0.8114281 0.554732821 0.611282785 1 22.08972015 1.230870384 24.98377907 1.000000577 0.680766609 0.486168171 0.101708322 254.7131149 827433.7229 0.266346899 0.025517387 17.01650574 -1.230870384 -0.319233968 HSGSRS(ph)DEDRYQNGAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HSGSRSDEDRYQNGAER 17 2 Q9HCG8 Q9HCG8 CWC22 Pre-mRNA-splicing factor CWC22 homolog 1 HS(0.006)GS(0.006)RS(0.987)DEDRYQNGAER;HS(0.001)GS(0.062)RS(0.937)DEDRYQNGAER 190.85 1.44E-10 440760000 174806 166774 71168 75583 164323 153390 163302 169980 48571 TRUE FALSE 151704.9442 165678.4506 105585.0828 92745.27536 161053.2938 159291.0126 147464.9972 133631.0998 42828.99171 3.542108701 3.868371493 2.465271271 2.165478842 3.760380232 3.719233309 3.443111577 3.12010847 1 15.38630009 4.251866402 24.85314166 2.915385052 3.705240454 0.159259585 0.827813869 454.5368125 848987.5176 0.209972368 0.54838852 17859.38097 -4.251866402 0.789855402 HSHEGDYLESIVFIYSMPGYTCSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HSHEGDYLESIVFIYSMPGYTCSIR 25 0 Q12792;Q12792-3;Q12792-4 Q12792 TWF1 Twinfilin-1 0 ; 162.86 1.09E-11 1123880000 538500 528160 314180 539790 466720 471190 494060 509370 535490 FALSE TRUE 467335.8606 524690.4822 466118.4989 662357.5697 457433.1851 489316.9842 446146.1372 400445.1894 472184.9822 0.989730462 1.111196887 0.987152316 1.402750182 0.968758436 1.036282395 0.944854568 0.848068457 1 18.84899263 2.511884814 1.786084042 0.912087701 1.107507405 0.256056692 0.126631411 0.429447581 2.791938266 0.059331462 0.04288054 325.0010871 -2.511884814 0.195419705 HSIS(ph)GPISTSKPLTALSDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSISGPISTSKPLTALSDK 19 1 Q69YQ0-2;Q69YQ0;A0A494C1J1 Q69YQ0-2 SPECC1L Cytospin-A 1 HS(0.394)IS(0.602)GPIS(0.002)T(0.001)SKPLTALSDK 114.4 9.56E-05 300570000 272700 234280 160030 206050 235770 170950 307840 265330 472380 TRUE FALSE 236662.0041 232740.9993 237421.0433 252836.8018 231078.6383 177526.5571 277985.7242 208591.2443 416535.7745 0.568167294 0.558753926 0.569989561 0.606999008 0.554763006 0.426197623 0.667375388 0.500776301 1 18.66808088 1.234115883 24.99982315 1.000000658 0.557124892 0.832109236 0.06258809 49.33921345 277477.1356 0.109537998 0.014207175 17.14414706 -1.234115883 -0.442875766 HSISHS(ph)PNSNSNGSFLAPETEPIVPELCIDHLWTETITNIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSISHSPNSNSNGSFLAPETEPIVPELCIDHLWTETITNIR 41 0 Q9H1A4 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 HS(0.037)IS(0.091)HS(0.611)PNS(0.109)NS(0.109)NGS(0.042)FLAPETEPIVPELCIDHLWTETITNIR 44.604 0.089658 30102000 9390.1 12726 6056.8 7773.3 14263 13509 10140 12359 14111 TRUE FALSE 8149.174494 12642.40207 8985.888739 9538.346572 13979.19421 14028.69997 9156.624361 9716.124028 12442.81366 0.654930205 1.016040457 0.722174983 0.766574734 1.123475332 1.127453996 0.735896608 0.780862295 1 13.60302513 HSLASSEYPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSLASSEYPVR 11 0 P51570;P51570-2 P51570 GALK1 Galactokinase 0 67.548 0.064122 0 92307 114630 49437 72930 114430 101560 84092 97621 73326 FALSE TRUE 80108.39607 113876.988 73344.89856 89489.87117 112153.0669 105467.0789 75936.77078 76745.50884 64657.48381 1.238965567 1.761234451 1.134360545 1.384060528 1.734572091 1.63116584 1.174446735 1.18695477 1 15.98052974 2.144594155 6.533774378 1.130008388 1.484207724 0.410173555 0.203988675 0.217044574 12.66400491 0.083585715 0.056125815 139.5064076 -2.144594155 0.354199335 HSLDS(ph)DEEEDDDDGGSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSLDSDEEEDDDDGGSSK 18 0 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 HSLDS(1)DEEEDDDDGGSSK 357.92 6.46E-91 754890000 790860 557970 458610 687820 528650 466510 691010 782340 1600900 TRUE FALSE 686345.8472 554304.6583 680395.33 844000.0437 518130.8993 484456.9416 623995.9566 615042.6792 1411643.426 0.48620341 0.392666199 0.481988098 0.597884727 0.367040918 0.343186482 0.44203511 0.43569266 1 20.42894429 1.238176784 24.99845565 1.000000626 0.441857805 0.857653798 0.071268531 3.369525523 219163.7761 0.10181989 0.017860735 17.30520641 -1.238176784 -0.558142821 HSLS(ph)LDDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HSLSLDDIR 9 0 Q96NE9-3;Q96NE9-2;Q96NE9 Q96NE9-3 FRMD6 FERM domain-containing protein 6 1 HS(0.002)LS(0.998)LDDIR;HSLS(1)LDDIR;HSLS(1)LDDIR 150.06 5.55E-05 857560000 1701550 1514090 804445 1054930 1548940 1365050 1208950 1520930 1309920 TRUE FALSE 1476685.856 1504143.843 1193477.293 1294467.98 1518119.124 1417564.357 1091706.215 1195690.955 1155062.75 1.278446436 1.302218294 1.033257538 1.120690612 1.314317447 1.227261772 0.945148837 1.035174025 1 20.1395398 2.244738148 24.99991931 1.000123163 1.209048215 0.585662067 0.086839785 110.1746243 445868.8063 0.034785687 0.026247383 175.6864016 -2.244738148 0.208925052 HSLSGRPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HSLSGRPLK 9 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 117.7 0.00066657 2413700000 3639300 3139200 1439500 2268300 3251400 2762100 3449100 3954900 2645000 FALSE TRUE 3158357.284 3118578.389 2135647.015 2783352.184 3186703.501 2868359.774 3114606.813 3109175.412 2332311.113 1.35417495 1.33711938 0.915678446 1.193388038 1.366328653 1.22983583 1.33541653 1.333087766 1 21.15332882 3.427958315 24.99684588 1.269063873 1.18892479 0.020093876 0.154858069 360.9801442 183538.529 0.044915635 0.057985855 2678.911183 -3.427958315 -0.080139082 HSLSGS(ph)SPGMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HSLSGSSPGMK 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSLS(0.002)GS(0.509)S(0.489)PGMK;HSLS(0.006)GS(0.497)S(0.497)PGMK 110.08 0.0072043 209909000 606870 451340 225593 357120 460690 375560 518500 610550 535260 TRUE FALSE 526670.5919 448375.1178 334690.5294 438209.5542 451523.1703 390008.0362 468215.9498 479988.6338 471982.1726 1.115869672 0.949983164 0.709116888 0.92844514 0.956653019 0.826319422 0.992020413 1.016963482 1 18.84837284 2.040149902 17.69747366 1.008133133 0.909235006 0.143212824 0.102220988 13.40504401 5907.51193 0.042313242 0.028526409 109.6856725 -2.040149902 -0.098898127 HSLSGSS(ph)PGMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 HSLSGSSPGMK 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSLSGS(0.003)S(0.997)PGMK;HSLS(0.001)GS(0.017)S(0.982)PGMK;HSLS(0.001)GS(0.347)S(0.652)PGMK;HSLSGS(0.004)S(0.995)PGMK;HSLS(0.012)GS(0.245)S(0.743)PGMK;HSLSGS(0.001)S(0.999)PGMK;HSLS(0.001)GS(0.042)S(0.958)PGMK 248.19 3.53E-16 1384730000 4380060 3325070 1619309 2500680 3404290 2674210 3612750 4349930 4002770 TRUE FALSE 3801223.973 3303227.396 2402412.249 3068497.615 3336551.289 2777088.589 3262386.061 3419731.321 3529567.091 1.076966063 0.935873242 0.680653516 0.869369397 0.945314596 0.78680714 0.92430204 0.968881235 1 21.75105981 1.804873341 2.923059465 0.988584944 0.877132556 0.136525329 0.10319304 0.480091816 7.645372936 0.074504433 0.02905157 63.80773683 -1.804873341 -0.111452388 HSMNILNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSMNILNR 8 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 73.208 0.044162 155500000 549430 457980 275340 305340 432210 379590 545750 575920 242290 FALSE TRUE 476821.4334 454971.4992 408495.345 374672.1138 423609.8666 394193.0729 492823.249 452763.9898 213646.7522 2.231821586 2.129550272 1.912012894 1.753699085 1.982758278 1.845069344 2.30672006 2.119217751 1 17.70486786 1.235709544 24.99980812 0.999998608 2.034517056 0.784470883 0.170510555 38.78800238 340049.9869 0.301476595 0.044565546 17.20717374 -1.235709544 1.034518448 HSMNPFCEIAVEEAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSMNPFCEIAVEEAVR 16 0 P38117-2;P38117;M0QY67 P38117-2 ETFB Electron transfer flavoprotein subunit beta 0 99.569 0.0023496 43125000 34591 33165 19499 31457 38546 36575 23318 31292 36254 FALSE TRUE 30019.71171 32947.13693 28928.78162 38599.79264 37779.01001 37982.06392 21056.62395 24600.44931 31968.09342 0.939052302 1.030625646 0.904926711 1.207447442 1.181772385 1.188124153 0.658676252 0.769531326 1 14.96434508 2.241579789 24.99980004 0.794815759 1.076391737 0.480196898 0.130126312 65.22574128 540098.7096 0.052297288 0.038728311 174.4133763 -2.241579789 0.281575978 HSNASQSLCEIVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HSNASQSLCEIVR 13 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PK08 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 ; 178.67 1.44E-05 676080000 303880 317950 163469 248560 361640 323980 305060 366250 389530 FALSE TRUE 263721.4881 315861.3655 242523.1552 304999.347 354444.0715 336443.7202 275475.3282 287930.2877 343480.2072 0.767792387 0.91959117 0.706076071 0.887967751 1.031919931 0.979514142 0.802012234 0.838273303 1 18.38986744 3.495467914 24.81439638 0.916057374 0.807834476 0.317648586 0.08692373 1018.652905 1377755.663 0.025265754 0.036693786 3129.449254 -3.495467914 -0.108222898 HSNLVQLLGVIVEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSNLVQLLGVIVEEK 15 0 P41240 P41240 CSK Tyrosine-protein kinase CSK 0 107.98 0.0011151 49557000 164930 156380 99811 126160 124550 114760 176710 174150 188090 FALSE TRUE 143134.0826 155352.7295 148079.9334 154806.5562 122071.6987 119174.8915 159572.6914 136909.3777 165854.2145 0.863011429 0.936682435 0.8928319 0.933389343 0.736018069 0.718552084 0.962126238 0.825480246 1 17.33955615 6.338692684 17.27110283 0.870239973 0.534125098 0 0.092660677 0 0 0.020609469 0 2181185.914 -6.338692684 -0.336114876 KGHAVGDIPGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KGHAVGDIPGVR 12 1 D6RD47;P62266 D6RD47 RPS23 40S ribosomal protein S23 0 ;; 97.121 0.0033107 1302060000 2574700 2577470 1379820 1682220 2550470 2251260 2682990 2777570 1231497 FALSE TRUE 2234446.872 2560538.43 2047105.567 2064193.762 2499720.637 2337867.429 2422794.043 2183608.271 1085910.828 2.05767068 2.357963808 1.88515071 1.900886988 2.301957558 2.152909216 2.23111694 2.010854128 1 20.05047421 1.236857522 4.050709657 0.876463176 2.124946375 0.840954887 0.152812995 0.090496571 2.636714132 0.335782086 0.038733509 17.25271793 -1.236857522 1.248483199 HSPEEDFRQS(ph)PQEHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSPEEDFRQSPQEHFR 16 1 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 HSPEEDFRQS(1)PQEHFR 189.11 6.46E-10 202020000 92012 80159 44040 59259 79868 72703 82357 78415 81874 TRUE FALSE 79852.38107 79632.43025 65337.8913 72714.66167 78278.78306 75499.93146 74370.03082 61646.56248 72194.94899 1.106066036 1.103019413 0.905020257 1.00719874 1.084269525 1.045778583 1.030127895 0.853890242 1 16.13961028 -2 0.187180993 0.305124953 1.100120077 0.193525136 0.073539766 167.5405879 2.412308918 37.08172925 0.622246695 0.01 2 0.794995124 HSPES(ph)PSIAVVESELVAEYITTVSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HSPESPSIAVVESELVAEYITTVSHR 26 0 Q7Z589-4;E9PMC9 Q7Z589-4 EMSY;C11orf30 Protein EMSY 1 HS(0.185)PES(0.746)PS(0.068)IAVVESELVAEYITTVSHR;HS(0.037)PES(0.961)PS(0.002)IAVVESELVAEYITTVSHR 140.55 5.25E-07 24746000 15469.5 10945.5 5386.4 8209.6 10959.6 12617.5 9565.5 10549.9 11630.4 TRUE FALSE 13425.16638 10873.59829 7991.281056 10073.71516 10741.5254 13102.90339 8637.839282 8293.885984 10255.46736 1.309074068 1.060273307 0.779221539 0.982277531 1.047395016 1.277650538 0.842266762 0.808728232 1 13.32410562 4.65418925 3.590111898 0.955693598 1.322417745 0.366681202 0.142297167 0.277481158 5.918156771 0.037959092 0.230529823 45101.31971 -4.65418925 0.366724147 HSPESPS(ph)IAVVESELVAEYITTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSPESPSIAVVESELVAEYITTER 24 0 Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-7 EMSY Protein EMSY 1 HS(0.156)PES(0.375)PS(0.469)IAVVES(0.001)ELVAEYITTER 107.39 0.0016216 22044000 14939 13065 7993.3 11619 13306 13520 13225 14520 16125 TRUE FALSE 12964.7733 12979.17515 11858.88662 14257.27154 13041.23663 14040.12315 11942.44154 11415.01099 14218.72087 0.9118101 0.91282298 0.834033295 1.002711261 0.917187752 0.987439255 0.839909697 0.802815605 1 13.79550406 2.213486406 24.97717666 0.862930806 0.925671363 0.075282596 0.067912468 417.9024883 416281.9164 0.027286536 0.018404805 163.4881977 -2.213486406 0.062740557 HSPTSEPTPPGDALPPVS(ph)SPHTHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HSPTSEPTPPGDALPPVSSPHTHR 24 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 HSPTSEPTPPGDALPPVS(0.494)S(0.494)PHT(0.011)HR;HSPTSEPTPPGDALPPVS(0.417)S(0.417)PHT(0.166)HR;HSPTSEPTPPGDALPPVS(0.487)S(0.487)PHT(0.026)HR;HSPTSEPTPPGDALPPVS(0.429)S(0.429)PHT(0.142)HR;HSPTSEPTPPGDALPPVS(0.333)S(0.333)PHT(0.333)HR 179.42 6.32E-17 10658310000 1534024 2022560 629817 1205727 2171259 2218128 1857807 2275193 1993389 TRUE FALSE 1331298.842 2009273.67 934398.6078 1479505.744 2128055.194 2303460.819 1677637.163 1788660.683 1757732.823 0.757395449 1.143105279 0.531593081 0.841712531 1.210681832 1.310472666 0.954432403 1.017595313 1 20.74528437 3.307009977 8.276819693 1.088010611 0.819551839 0.3775821 0.178540611 0.311296362 33.53654284 0.052111576 0.067210759 2027.7293 -3.307009977 -0.268458771 HSPTSEPTPPGDALPPVSSPHT(ph)HR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HSPTSEPTPPGDALPPVSSPHTHR 24 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 HSPTSEPTPPGDALPPVS(0.197)S(0.197)PHT(0.605)HR;HSPTSEPTPPGDALPPVS(0.221)S(0.221)PHT(0.559)HR;HSPTSEPTPPGDALPPVS(0.252)S(0.252)PHT(0.496)HR 134.87 5.95E-05 3812550000 448660 493250 154554 294717 552350 510470 468170 550940 463630 TRUE FALSE 389368.4442 490009.8083 229296.8314 361636.9993 541359.3157 530108.1112 422766.9455 433125.7684 408820.1896 0.952419803 1.198594934 0.560874529 0.884586937 1.324199072 1.296677915 1.034114646 1.059452981 1 18.64110692 3.27367712 24.98145006 1.13199086 0.896349614 0.302178839 0.183638219 246.3974322 175282.5314 0.054963486 0.070954654 1877.92014 -3.27367712 -0.235641246 HSQAVEELAEQLEQTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HSQAVEELAEQLEQTK 16 0 P35579 P35579 MYH9 Myosin-9 0 ;; 171.09 5.05E-09 533490000 334025 283575 233929 262697 305240 249905 332386 378176 684673 FALSE TRUE 289882.7499 281712.1772 347057.8468 322346.3689 299166.3212 259519.0071 300151.2569 297306.0054 603731.7379 0.480151583 0.466618134 0.574854401 0.533923179 0.495528564 0.429858149 0.497159977 0.492447202 1 19.20354812 1.238261688 24.99513045 1.000000562 0.496775491 0.944858314 0.038239682 1.588418679 132592.9471 0.055603755 0.009809282 17.3085899 -1.238261688 -0.503225071 HSQAVEELAEQLEQTKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HSQAVEELAEQLEQTKR 17 1 P35579 P35579 MYH9 Myosin-9 0 ;;;; 280.39 4.18E-36 6189060000 7474070 6816730 4415800 5401250 6976970 6173910 7904610 9254570 6400630 FALSE TRUE 6486352.713 6771950.452 6551295.65 6627686.365 6838141.947 6411424.313 7138022.139 7275552.225 5643954.813 1.14925667 1.199859084 1.160763306 1.174298269 1.211586941 1.135980802 1.26471993 1.289087611 1 22.42827501 3.322094616 8.058431071 1.197961023 1.172156828 0 0.07986141 1.354191481 114.5203789 0.023123778 0.029843303 2099.397212 -3.322094616 -0.025804194 HSQDLAFLSMLNDIAAVPATAMPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 ;;;;;; 217.7 1.14E-33 4511370000 3263702 3259790 1960418 2336892 3475748 3903829 3631955 3805640 3840740 FALSE TRUE 2832395.512 3238376.225 2908482.702 2867519.046 3406587.415 4054011.828 3279728.563 2991833.502 3386692.093 0.836330978 0.956206273 0.8587975 0.846702023 1.005874559 1.19704175 0.968416518 0.883408772 1 21.6914454 3.230442249 24.80558994 1.001120685 0.879222434 0.394655879 0.08338367 210.9090134 644428.8025 0.027930996 0.03221916 1699.973882 -3.230442249 -0.121898251 HSQEELLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSQEELLQR 9 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 118.04 0.0010539 262100000 219530 206930 156410 180070 200420 217530 174790 246640 341270 FALSE TRUE 190518.5543 205570.6632 232050.3992 220957.6457 196432.0341 225898.5199 157838.8927 193897.9554 300925.4494 0.633108814 0.683128209 0.771122548 0.734260416 0.652759793 0.750679347 0.524511613 0.644338841 1 18.1990466 1.235538062 24.98079524 1.00000045 0.672717322 0.67993378 0.07023376 52.40492164 433036.728 0.123038175 0.017950951 17.20038081 -1.235538062 -0.327283128 HSQFIGYPITLFVEK ddPTM_MDA-MB-175_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 ; 133.86 3.87E-05 4720800000 2238070 1847480 1142570 1953350 2063140 1721170 2496060 2648100 2356110 FALSE TRUE 1942303.379 1835343.782 1695120.674 2396887.973 2022087.55 1787384.524 2253992.485 2081824.423 2077573.36 0.934890395 0.883407449 0.815913751 1.153695951 0.973292972 0.860323182 1.084915955 1.002046167 1 20.98646799 3.76509761 24.98854084 1.007872036 0.878604226 0.385207434 0.079849851 818.0161101 770281.6312 0.020893899 0.036173003 5822.340626 -3.76509761 -0.12926781 HSQFLGYPITLYLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HSQFLGYPITLYLEK 15 0 Q58FF8 Q58FF8 HSP90AB2P Putative heat shock protein HSP 90-beta 2 0 ; 188.06 3.15E-07 7819400000 2473600 2082020 1142610 1666140 2017580 1809640 2296800 2765200 2575200 FALSE TRUE 2146707.493 2068343.074 1695180.018 2044462.552 1977434.105 1879258.022 2074056.69 2173883.499 2270762.79 0.945368447 0.910858273 0.746524483 0.900341754 0.870823722 0.827588875 0.913374439 0.957336235 1 21.11474558 1.744360502 2.031709125 0.994608578 0.865361297 0.423246684 0.053823621 0.306570836 2.473137087 0.055323569 0.015509272 55.50862918 -1.744360502 -0.129247281 HSQPS(ph)PEPHS(ph)PTEPPAWGSSIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HSQPSPEPHSPTEPPAWGSSIVK 23 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 2 HS(0.003)QPS(0.997)PEPHS(0.896)PT(0.104)EPPAWGSSIVK;HS(0.066)QPS(0.933)PEPHS(0.908)PT(0.092)EPPAWGSSIVK;HS(0.117)QPS(0.881)PEPHS(0.929)PT(0.072)EPPAWGSSIVK;HSQPS(1)PEPHS(0.861)PT(0.139)EPPAWGSSIVK 239.39 1.71E-37 2543630000 1166270 1206220 743680 960760 1257830 1099560 1277920 1603890 1392810 TRUE FALSE 1012144.465 1198296.261 1103326.135 1178915.242 1232801.644 1141860.785 1153987.515 1260910.605 1228153.588 0.824118802 0.975689256 0.898361692 0.959908641 1.003784588 0.929737775 0.939611728 1.026671759 1 20.22805956 6.603629881 0.510293869 0.985793835 2.11E-36 0.539520586 0.039860244 23.29646612 1.027811841 0.024665044 20.52852945 4014485.38 -6.603629881 -0.985793835 HSQPSPEPHS(ph)PTEPPAWGSSIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSQPSPEPHSPTEPPAWGSSIVK 23 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 HSQPSPEPHS(0.997)PT(0.003)EPPAWGSSIVK 230.8 2.09E-33 198820000 116150 136900 53567 110710 177440 124620 159080 212250 181390 TRUE FALSE 100800.4832 136000.6949 79472.18037 135848.3976 173909.2912 129414.212 143652.4461 166861.9892 159946.2808 0.630214611 0.850289823 0.496867948 0.849337646 1.087298124 0.80911048 0.89812933 1.043237694 1 17.28722792 3.484599327 23.38557957 0.964289197 0.677384328 0.604931431 0.113433456 98.63777435 308462.3586 0.030876964 0.041723442 3052.103993 -3.484599327 -0.286904869 HSS(ph)ETFSSTPSATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HSSETFSSTPSATR 14 0 P35568 P35568 IRS1 Insulin receptor substrate 1 1 HSS(0.989)ET(0.011)FSSTPSATR;HSS(1)ETFSSTPSATR;HSS(0.992)ET(0.008)FSSTPSATR;HSS(0.999)ET(0.001)FSSTPSATR;HS(0.003)S(0.997)ETFSSTPSATR 332.06 1.95E-68 1388290000 1239237 1499850 832708 1068356 1873941 1939570 1599091 1879266 2225632 TRUE FALSE 1075468.691 1489997.387 1235408.374 1310942.559 1836653.24 2014186.513 1444011.401 1477399.59 1962520.32 0.54800385 0.759226476 0.629500934 0.667989292 0.935864572 1.02632645 0.735794369 0.752807283 1 20.90427616 3.25284887 23.70010832 0.868220692 0.65734905 0.551767307 0.105945489 115.6352866 191803.5697 0.032276142 0.041433237 1789.982851 -3.25284887 -0.210871642 HSS(ph)IS(ph)PSTLTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HSSISPSTLTLK 12 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YCQ1 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 2 HS(0.013)S(0.987)IS(0.655)PS(0.14)T(0.205)LTLK;HS(0.016)S(0.983)IS(0.568)PS(0.186)T(0.244)LT(0.003)LK;HS(0.026)S(0.974)IS(0.676)PS(0.136)T(0.185)LT(0.003)LK;HS(0.017)S(0.983)IS(0.476)PS(0.209)T(0.314)LT(0.001)LK 212.02 3.66E-08 368910000 2027080 1527080 893530 1192010 1632790 1390990 1619910 1950200 1716090 TRUE FALSE 1759196.242 1517048.511 1325644.097 1462674.089 1600300.673 1444502.285 1462811.378 1533164.906 1513215.795 1.162554771 1.002532828 0.876044316 0.966599803 1.057549544 0.95459107 0.966690529 1.013183256 1 20.52918631 4.721235226 4.551994356 0.978648797 1.171983123 0.608838299 0.046415054 0.123532021 6.511300484 0.011686478 0.073746527 52630.2249 -4.721235226 0.193334326 HSS(ph)IS(ph)PVRLPLNSSLGAELSR ddPTM_MDA-MB-175_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(0.025)S(0.975)IS(1)PVRLPLNSSLGAELSR;HS(0.095)S(0.905)IS(1)PVRLPLNSSLGAELSR 155.09 1.58E-08 1444180000 2022250 1259850 785640 980980 1439820 1364390 1236430 1492660 1334210 TRUE FALSE 1755004.539 1251573.962 1165578.132 1203726.502 1411170.399 1416878.966 1116521.209 1173466.275 1176481.214 1.491740385 1.06382826 0.990732464 1.023158286 1.199484006 1.204336244 0.949034456 0.997437325 1 20.16604685 4.737769253 6.002523401 1.049803317 1.503497305 0.721684021 0.085548516 0.075576508 13.28586732 0.022847884 0.140522376 54672.54027 -4.737769253 0.453693987 HSS(ph)ISPST(ph)LTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSSISPSTLTLK 12 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YCQ1 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 2 HS(0.017)S(0.977)IS(0.179)PS(0.325)T(0.49)LT(0.012)LK 146.59 0.00034412 200060000 784390 569450 353730 489830 645530 519450 672460 794280 704430 TRUE FALSE 680730.8741 565709.2455 524795.0112 601053.3881 632685.216 539433.5776 607244.9327 624429.4031 621153.0879 1.095914819 0.910740454 0.844872257 0.967641311 1.018565678 0.868439018 0.977609135 1.00527457 1 19.24458935 2.006294391 24.99597573 0.999542397 0.946099521 0.080383186 0.071275257 365.7853073 1452581.481 0.028863017 0.019405522 101.4598909 -2.006294391 -0.053442877 HSS(ph)NPPLESHVGWVMDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HSSNPPLESHVGWVMDSR 18 0 Q6PKG0;Q6PKG0-3;H0YC33;H0YBR8 Q6PKG0 LARP1 La-related protein 1 1 HS(0.204)S(0.796)NPPLESHVGWVMDSR;HS(0.252)S(0.748)NPPLESHVGWVMDSR;HS(0.099)S(0.901)NPPLESHVGWVMDSR;HS(0.064)S(0.936)NPPLESHVGWVMDSR;HS(0.337)S(0.663)NPPLESHVGWVMDSR 280.89 1.75E-39 3021560000 570343 615982 390133 524692 805444 872434 775580 850574 831728 TRUE FALSE 494970.7275 611935.5737 578802.6237 643831.338 789417.2402 905997.1005 700364.371 668685.3693 733402.0633 0.67489683 0.8343794 0.789202339 0.877869548 1.076377174 1.235334813 0.954952823 0.911758233 1 19.4842448 3.467562282 3.315518083 1.023409691 0.775660486 0.630800575 0.09440324 0.188986894 4.3457005 0.031239272 0.044390026 2934.690334 -3.467562282 -0.247749205 HSS(ph)PHQS(ph)EDEEDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HSSPHQSEDEEDPR 14 0 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 2 HS(0.148)S(0.852)PHQS(1)EDEEDPR;HS(0.011)S(0.989)PHQS(1)EDEEDPR;HS(0.455)S(0.546)PHQS(1)EDEEDPR;HS(0.449)S(0.551)PHQS(1)EDEEDPR 176.44 3.25E-06 2719547000 2063846 2180238 1246039 1578540 2792469 2575242 2260137 2720607 2422046 TRUE FALSE 1791103.522 2165915.873 1848627.628 1936971.633 2736904.33 2674313.226 2040949.262 2138826.365 2135714.481 0.838643713 1.014141119 0.865578074 0.906943157 1.281493549 1.25218668 0.955628329 1.001457069 1 21.02628736 HSS(ph)PTEERDEPAYPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSSPTEERDEPAYPR 15 1 F5H4R1;J3KNB8;F5H538;Q9Y6R4-2;Q9Y6R4 F5H4R1 MAP3K4 Mitogen-activated protein kinase kinase kinase 4 1 HS(0.158)S(0.834)PT(0.007)EERDEPAYPR 201.12 3.98E-09 457410000 201230 209790 117600 118490 247540 279210 231500 241280 191210 TRUE FALSE 174636.9456 208411.8757 174471.7533 145394.9655 242614.4383 289951.3894 209049.1656 189684.1496 168605.3716 1.035773321 1.236092739 1.034793564 0.862338869 1.438948451 1.71970434 1.239872512 1.125018425 1 17.36329097 3.230933411 24.9985149 1.298134503 1.055562977 0.28036161 0.208312597 278.2261087 911897.077 0.069460493 0.080256137 1701.897542 -3.230933411 -0.242571527 HSS(ph)YPAGTEDDEGMGEEPSPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSSYPAGTEDDEGMGEEPSPFR 22 0 Q92934 Q92934 BAD Bcl2-associated agonist of cell death 1 HS(0.124)S(0.876)YPAGTEDDEGMGEEPSPFR 299.3 7.11E-56 476720000 365080 196980 161840 204090 254190 246980 233460 208800 261630 TRUE FALSE 316833.753 195686.0254 240106.3653 250431.7538 249132.1163 256481.4804 210819.0851 164149.7449 230700.3994 1.373355893 0.848225776 1.040771346 1.085528046 1.079894603 1.111751349 0.913821934 0.711527788 1 17.81566098 2.089614657 4.626938364 0.828932474 1.075131943 0.327889058 0.144060365 0.207758144 7.89203518 0.05837731 0.037782704 122.9177657 -2.089614657 0.246199469 HSSGILPTFQTNLTFTVPIS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSSGILPTFQTNLTFTVPISPGR 23 0 I3L2J0 I3L2J0 CIC 1 HSSGILPTFQTNLTFTVPIS(1)PGR 148.04 7.12E-08 194150000 169960 196200 77728 112680 264820 281050 174120 246040 221540 TRUE FALSE 147499.3554 194911.1493 115317.5208 138265.7162 259550.6001 291862.1754 157233.8692 193426.2607 195349.7936 0.755052527 0.99775457 0.59031299 0.70778532 1.328645377 1.494049059 0.804883723 0.990153392 1 17.57570021 3.257737095 24.98611208 1.101497669 0.767198746 0.414876228 0.211999493 283.2169321 369016.9923 0.065902961 0.084944197 1810.243909 -3.257737095 -0.334298923 HSSIS(ph)PVRLPLNSSLGAELSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSSISPVRLPLNSSLGAELSR 21 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 HS(0.175)S(0.175)IS(0.649)PVRLPLNS(0.001)SLGAELSR 115.54 9.14E-05 106930000 109160 98734 35376 50350 106510 122530 95702 115970 85510 TRUE FALSE 94734.22942 98085.40985 52483.95193 61782.73705 104390.6594 127243.8084 86420.83477 91170.71798 75401.10521 1.256403725 1.300848437 0.69606343 0.819387685 1.38447121 1.687558929 1.146148117 1.209142992 1 16.20229805 3.225495889 24.99987802 1.285580127 1.015358663 0.221412845 0.249035409 382.0979705 731157.948 0.080832253 0.092207976 1680.722017 -3.225495889 -0.270221464 HSSLAGCQIINYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HSSLAGCQIINYR 13 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 174.72 1.95E-05 3091360000 1512310 1876220 547908 880622 2885440 2803300 1665710 1844920 2100960 FALSE TRUE 1312454.402 1863894.987 812878.1414 1080580.685 2828025.389 2911144.765 1504169.701 1450398.215 1852586.902 0.708444176 1.006103943 0.438780033 0.583282049 1.52652779 1.571394444 0.811929361 0.78290428 1 20.82110979 3.278644731 24.99997729 1.091241956 0.689622191 0.365715449 0.293670046 216.8740338 135260.2766 0.095385038 0.123139975 1899.523763 -3.278644731 -0.401619765 HSSSPLS(ph)PGGPTHLTKPTTTSSSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HSSSPLSPGGPTHLTKPTTTSSSER 25 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 HSSSPLS(1)PGGPTHLTKPTTTSSSER;HS(0.016)S(0.016)S(0.081)PLS(0.886)PGGPTHLTKPTTTSSSER;HSSS(0.001)PLS(0.999)PGGPTHLTKPTTTSSSER;HSSSPLS(1)PGGPTHLTKPTTTSSSER 233.49 1.40E-38 2393090000 625230 789180 166923 467452 1224910 961610 860340 1072310 917220 TRUE FALSE 542604.2714 783995.8246 247647.5211 573594.1212 1200536.687 998603.7589 776904.3592 843004.8512 808787.2965 0.670886244 0.969347353 0.306196106 0.709202684 1.4843664 1.234692685 0.96057933 1.042307236 1 19.62540081 3.384282601 9.465693444 1.121785393 0.652263328 0.554586823 0.21397921 0.240745089 22.31769136 0.062930523 0.081258341 2422.604953 -3.384282601 -0.469522066 HSSVSDSQPCEPPSVGTEYS(ph)QGASPQPQHQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSSVSDSQPCEPPSVGTEYSQGASPQPQHQLK 32 0 A0A2R8YDI1;A0A2R8Y852;P39880-6;P39880-4;P39880-5;P39880-2;P39880;P39880-3 A0A2R8YDI1 CUX1 Homeobox protein cut-like 1 1 HSSVSDSQPCEPPSVGT(0.097)EY(0.001)S(0.557)QGAS(0.345)PQPQHQLK 120.31 4.79E-07 225760000 250820 279620 36223 109350 286560 265610 208010 256270 237910 TRUE FALSE 217673.5015 277783.1578 53740.56396 134179.5888 280858.0166 275828.1886 187837.2222 201468.6548 209784.5508 1.037605013 1.324135437 0.256170265 0.639606626 1.338792659 1.314816499 0.895381578 0.960359826 1 17.67854891 3.250407432 24.9999135 1.079342037 0.810918448 0.179288113 0.303484991 459.2689711 969173.5687 0.093337038 0.119514287 1779.948481 -3.250407432 -0.268423589 HSSVSDSQPCEPPSVGTEYSQGAS(ph)PQPQHQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSSVSDSQPCEPPSVGTEYSQGASPQPQHQLK 32 0 A0A2R8YDI1;A0A2R8Y852;P39880-6;P39880-4;P39880-5;P39880-2;P39880;P39880-3 A0A2R8YDI1 CUX1 Homeobox protein cut-like 1 1 HSSVSDSQPCEPPSVGT(0.002)EY(0.006)S(0.216)QGAS(0.776)PQPQHQLK 148.77 5.84E-10 409500000 125010 163110 23414 61476 158670 133160 134710 151140 141480 TRUE FALSE 108489.6118 162038.5197 34737.08872 75435.0654 155512.7774 138282.7514 121645.8449 118819.8872 124754.3956 0.869625565 1.298860204 0.278443806 0.604668597 1.246551488 1.108439913 0.975082636 0.952430466 1 16.92873112 3.244287587 24.99723498 1.039982677 0.766578488 0.234913772 0.262311544 238.7289305 1042003.983 0.079409409 0.099688414 1755.042296 -3.244287587 -0.273404189 HSSVYPTQEELEAVQNMVSHTER ddPTM_MDA-MB-175_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 ;;; 219.16 1.23E-32 1260670000 950420 1002720 244420 574496 1505610 1579520 948040 1171240 1107420 FALSE TRUE 824819.5889 996133.0663 362622.3295 704944.0974 1475651.307 1640285.156 856099.2267 920779.4406 976502.0692 0.844667528 1.020103385 0.371348245 0.721907428 1.51116045 1.679755945 0.876699859 0.942936497 1 19.89726358 3.273195766 24.88961198 1.169190289 0.733251749 0.37939583 0.292268517 218.9846635 157365.9413 0.092722691 0.1196987 1875.839886 -3.273195766 -0.43593854 HSTENDS(ph)PTNVQQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HSTENDSPTNVQQ 13 0 P49354;P49354-2;B3KVN2 P49354 FNTA Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha 1 HSTENDS(0.999)PTNVQQ;HSTENDS(0.996)PT(0.004)NVQQ;HSTENDS(0.865)PT(0.134)NVQQ;HS(0.001)T(0.002)ENDS(0.99)PT(0.007)NVQQ;HSTENDS(0.999)PT(0.001)NVQQ;HSTENDS(0.974)PT(0.026)NVQQ 203.78 8.72E-08 2204569000 2501370 2438700 1447701 1628314 2493724 2518059 2369673 2607170 2444957 TRUE FALSE 2170807.617 2422680.019 2147814.046 1998047.581 2444103.771 2614930.359 2139862.477 2049646.985 2155916.969 1.006906875 1.123735308 0.996241542 0.926773902 1.133672496 1.212908659 0.992553289 0.950707756 1 21.03987019 2.021961795 24.9943829 0.971772157 1.066108401 0.202308772 0.080606661 355.3530392 404420.2126 0.034580875 0.023312561 105.1869337 -2.021961795 0.094336243 HSTPS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HSTPSPTR 8 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 HST(0.001)PS(0.999)PTR;HS(0.001)T(0.023)PS(0.841)PT(0.135)R 134.51 0.00091634 728127000 236906 202436 81774 145200 192759 220768 196211 221009 221999 TRUE FALSE 205598.2719 201106.1846 121320.1799 178169.8792 188923.473 229261.0878 177182.4874 173747.9452 195754.5311 1.050286145 1.027338593 0.619756688 0.910169886 0.965103959 1.171166187 0.905125855 0.887580708 1 17.57868618 3.260178737 5.300411809 0.977095436 0.88963429 0.081068745 0.137146976 0.517984043 40.06634326 0.042645017 0.053273223 1820.449923 -3.260178737 -0.087461146 HSTPSNSSNPSGPPS(ph)PNS(ph)PHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HSTPSNSSNPSGPPSPNSPHR 21 0 Q9Y5S2 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 2 HSTPSNSSNPS(0.001)GPPS(0.999)PNS(1)PHR;HSTPSNSSNPS(0.002)GPPS(0.998)PNS(1)PHR;HSTPSNSS(0.001)NPS(0.049)GPPS(0.959)PNS(0.991)PHR 212.75 4.13E-23 542335000 271712 302435 74683 160730 383268 379030 256902 303326 274336 TRUE FALSE 235804.5708 300448.2846 110799.9486 197226.2031 375641.7167 393611.5294 231987.6836 238462.0954 241904.3106 0.974784493 1.242012942 0.458032138 0.815306691 1.552852513 1.627137311 0.959005993 0.985770344 1 17.88407695 3.296519341 24.99996949 1.195223147 0.869317194 0.259628565 0.293319847 133.4450683 57559.01076 0.092145854 0.118959731 1979.335169 -3.296519341 -0.325905954 HSTPSNSSNPSGPPS(ph)PNSPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 HSTPSNSSNPSGPPSPNSPHR 21 0 Q9Y5S2 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 1 HSTPSNSSNPS(0.002)GPPS(0.997)PNS(0.001)PHR;HSTPSNSSNPS(0.004)GPPS(0.961)PNS(0.036)PHR;HSTPSNSSNPS(0.001)GPPS(0.996)PNS(0.003)PHR;HSTPSNSSNPSGPPS(1)PNSPHR;HSTPSNSSNPSGPPS(0.995)PNS(0.004)PHR;HSTPSNSSNPSGPPS(0.854)PNS(0.146)PHR;HSTPSNSSNPSGPPS(0.999)PNS(0.001)PHR;HSTPSNSSNPSGPPS(0.999)PNS(0.001)PHR;HSTPSNSSNPS(0.027)GPPS(0.873)PNS(0.1)PHR;HSTPSNSSNPSGPPS(0.993)PNS(0.007)PHR;HSTPSNSSNPS(0.019)GPPS(0.812)PNS(0.169)PHR;HSTPSNSSNPS(0.003)GPPS(0.87)PNS(0.127)PHR 305.81 7.47E-56 5398821000 1614511 1784329 522530.9 1012778.3 2188275.1 2149076 1583778 1830075 1712396 TRUE FALSE 1401149.281 1772607.625 775228.591 1242745.092 2144732.707 2231752.344 1430183.453 1438727.703 1509958.496 0.927938937 1.173944602 0.51341053 0.823032617 1.420391827 1.47802231 0.947167394 0.952825993 1 20.52607746 3.292121933 24.99997735 1.133804793 0.857308957 0.278087846 0.238233446 151.8386781 70870.09064 0.074725322 0.096469892 1959.394717 -3.292121933 -0.276495835 HSTSGT(ph)DEGEDGDEPDDGSNDVVDLLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSTSGTDEGEDGDEPDDGSNDVVDLLPR 28 0 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 1 HS(0.025)T(0.021)S(0.142)GT(0.812)DEGEDGDEPDDGSNDVVDLLPR 202.76 1.36E-24 44858000 22371 20112 5719.3 14129 21320 19599 18884 15301 14714 TRUE FALSE 19414.61567 19979.88295 8485.17261 17337.2054 20895.77371 20352.98621 17052.63259 12029.00022 12974.52768 1.496363964 1.539931428 0.653987013 1.336249444 1.610522882 1.568688026 1.314316251 0.927124325 1 13.6633944 1.775377193 5.299151422 0.964758267 1.358644557 0.270699696 0.270883981 0.254510481 15.58757523 0.163761032 0.075441584 59.61797118 -1.775377193 0.39388629 HSVDELQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HSVDELQK 8 0 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 ;; 137 0.00076673 750890000 965760 939000 571080 709930 930820 845660 969760 1165160 1047770 FALSE TRUE 838132.3691 932831.6472 847256.1981 871130.4571 912298.5031 878193.0874 875712.8245 915999.6013 923903.8242 0.907164087 1.009663152 0.917039389 0.942880021 0.987438821 0.950524356 0.947839809 0.991444756 1 19.81738315 1.659361962 4.509169172 0.99785826 0.953669302 0.273179713 0.029743027 0.201170301 9.287216655 0.019058504 0.007185758 45.64171579 -1.659361962 -0.044188958 HSVGVVIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HSVGVVIGR 9 0 A0A087WTP3;Q92945;M0R0I5 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;;;;; 182.98 4.57E-05 2323390000 2327550 2179120 1065759 1424780 2187330 2277500 2020950 2285960 2135030 FALSE TRUE 2019958.37 2164805.217 1581163.617 1748298.075 2143806.412 2365116.899 1824958.58 1797125.243 1882629.186 1.072945424 1.149884021 0.839869917 0.928647069 1.138730042 1.256283987 0.969366986 0.954582696 1 20.84431744 HSVTAAT(ph)PPPS(ph)PTSGESGDLLSNLLQSPSSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HSVTAATPPPSPTSGESGDLLSNLLQSPSSAK 32 0 Q96QU8;Q96QU8-2 Q96QU8 XPO6 Exportin-6 2 HSVT(0.005)AAT(0.995)PPPS(0.922)PT(0.025)S(0.028)GES(0.025)GDLLSNLLQSPSSAK;HSVT(0.001)AAT(0.999)PPPS(0.967)PT(0.026)S(0.006)GESGDLLSNLLQSPSSAK;HSVT(0.002)AAT(0.998)PPPS(0.982)PT(0.01)S(0.008)GESGDLLSNLLQSPSSAK;HSVT(0.001)AAT(0.999)PPPS(0.886)PT(0.082)S(0.028)GES(0.004)GDLLSNLLQSPSSAK 300.25 1.85E-89 523488000 968620 745940 515046 678249 828650 640539 829490 1113500 1053210 TRUE FALSE 840614.4128 741039.871 764123.9683 832255.8018 812161.4862 665180.9498 749046.1875 875386.6903 928700.7136 0.905151036 0.797931842 0.822788178 0.896150708 0.874513688 0.716248992 0.806552829 0.942592891 1 19.82485422 1.597760649 3.863350515 0.988568553 0.829704469 0.540020481 0.054764859 0.133887408 4.485592745 0.044813957 0.014760463 39.60596957 -1.597760649 -0.158864084 HSVVAGGGGGEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HSVVAGGGGGEGR 13 0 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 0 ; 139.48 3.89E-05 249380000 222778 182218 99951 130740 180019 214740 181853 194695 181302 FALSE TRUE 193337.3229 181020.998 148287.6379 160426.5152 176436.9741 223001.1868 164216.9241 153060.9894 159868.6841 1.209350812 1.132310552 0.927559007 1.003489308 1.10363687 1.394902247 1.027198822 0.957416959 1 17.28652784 2.012165978 24.99990537 0.980659066 1.120951784 0.214380963 0.122657852 359.7149226 739176.5779 0.053433733 0.035997422 102.8409258 -2.012165978 0.140292719 HSWDGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSWDGLR 7 0 Q86TI2;Q86TI2-4;Q86TI2-2;M0R2A8;M0R145;M0QXG6;M0R0I1;M0R3C4;M0R2G6 Q86TI2 DPP9 Dipeptidyl peptidase 9 0 126.28 0.011451 0 62012 82373 57635 65069 74736 73484 87952 89934 102500 FALSE TRUE 53816.95708 81831.88634 85507.47878 79843.91097 73248.89982 76310.97703 79422.42858 70702.31397 90382.56677 0.595435149 0.905394583 0.946061634 0.883399463 0.810431729 0.844310798 0.878736148 0.782256098 1 16.46375691 4.742794362 24.74326216 0.872178735 0.595435022 0.668191455 0.063020769 235.0939398 1373900.052 0.015369841 0.115366699 55308.81604 -4.742794362 -0.276743713 HSYPPALGS(ph)PGALAGAGVGAAGPLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSYPPALGSPGALAGAGVGAAGPLER 26 0 Q96IF1;H0YJL9 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 HS(0.258)Y(0.217)PPALGS(0.525)PGALAGAGVGAAGPLER 149.74 9.60E-08 191780000 113490 80051 58632 71682 91310 71938 90983 89131 95045 TRUE FALSE 98492.00895 79525.13971 86986.63131 87958.49369 89493.10964 74705.50141 82159.48266 70071.02927 83808.88838 1.175197653 0.948886702 1.037916538 1.049512712 1.067823609 0.891379218 0.980319442 0.83608112 1 16.35481564 2.740457365 24.95538453 0.917751329 1.048573759 0.449465003 0.070317741 143.4243044 1887030.02 0.021776267 0.020746095 550.119912 -2.740457365 0.13082243 HSYTPTTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HSYTPTTSR 9 0 O14639-3;F8W8M4;O14639-5;O14639-2;O14639;J3QSX6;A0A0A0MRL6;A0A3B3IS55;O14639-4;O14639-6;A0A494C1P1;A0A494C1G0;H0Y7N6;F6XFR5 O14639-3 ABLIM1 Actin-binding LIM protein 1 0 64.654 0.068779 76276000 66279 74516 35717 51364 70745 69774 70922 70523 67935 FALSE TRUE 57520.06222 74026.49949 52989.86067 63026.98125 69337.31291 72458.25093 64043.99536 55442.20526 59903.80169 0.960207209 1.235756286 0.8845826 1.052136583 1.157477672 1.209576836 1.069114039 0.925520646 1 15.87035994 1.816865817 6.388038196 0.961845136 1.087118746 0.173970929 0.107150411 0.350990319 22.33899445 0.05396689 0.027963037 65.59425693 -1.816865817 0.12527361 HT(ph)GEKHFK ddPTM_MDA-MB-175_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 371760000 1230100 1243700 568560 538740 805920 760860 1553000 1212200 385110 TRUE FALSE 1067539.168 1235530.053 843517.5177 661069.1511 789883.7688 790130.7765 1402390.299 952980.4634 339582.7345 3.143679168 3.638377124 2.483982346 1.946710135 2.326042194 2.32676958 4.129745586 2.806327785 1 18.37340358 4.230257196 24.81901295 2.531024628 3.391028171 0.197874209 0.783544282 272.9314638 815804.2524 0.208254019 0.445480536 16992.49678 -4.230257196 0.860003543 HT(ph)PYGNQTDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HTPYGNQTDYR 11 0 Q86U70-2;Q86U70;A0A6E1WJ75;Q86U70-3 Q86U70-2 LDB1 LIM domain-binding protein 1 1 HT(0.996)PY(0.004)GNQTDYR;HT(0.999)PY(0.001)GNQTDYR 97.45 0.023024 346150000 676570 725290 369260 439580 791570 807840 671920 786830 898920 TRUE FALSE 587159.5603 720525.5222 547835.3711 539393.3576 775819.3057 838918.1275 606757.3018 618572.5276 792650.7017 0.740754482 0.909007613 0.691143488 0.680493131 0.978765683 1.05837051 0.765478792 0.78038476 1 19.59632573 3.239130825 24.9999963 0.895327489 0.761739094 0.338271227 0.109689903 23.36903161 1024553.948 0.035129835 0.042658234 1734.32636 -3.239130825 -0.133588395 HT(ph)RISELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HTRISELK 8 1 P24593;C9JXX4 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 1 HT(0.5)RIS(0.5)ELK 72.547 0.074159 280730000 213870 242030 116450 161050 218100 272610 169660 194030 204730 TRUE FALSE 185606.5376 240440.089 172765.6095 197618.864 213760.2367 283097.4831 153206.3993 152538.1944 180527.0526 1.028136974 1.331878439 0.957006759 1.094677286 1.184089773 1.568172077 0.848661722 0.84496031 1 17.46185552 HTADRWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HTADRWR 7 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;; 134.08 0.0029266 399250000 315958 389128 126155 133098 262062 349947 370891 364023 79006 FALSE TRUE 274203.3498 386571.7925 187163.98 163319.9352 256847.4789 363409.6875 334922.0479 286179.5143 69666.00068 3.935970876 5.54893045 2.686589988 2.3443277 3.686841162 5.216456865 4.807539469 4.107879187 1 16.08816712 4.241207029 24.99955091 3.581340599 4.742450414 0.147865992 1.280645002 149.8926764 1415897.172 0.33536739 0.807752386 17426.37396 -4.241207029 1.161109815 HTAFIGDRN ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HTAFIGDRN 9 1 Q9HAB8;Q9HAB8-2 Q9HAB8 PPCS Phosphopantothenate--cysteine ligase 0 ; 109.83 0.0038252 308260000 430950 353930 163836 228730 343400 397860 372180 403220 300790 FALSE TRUE 373998.8656 351605.0105 243067.6376 280666.6424 336567.0119 413165.9316 336086.0409 316994.5409 265230.9489 1.410087575 1.325656044 0.916437688 1.058197181 1.268958292 1.557759128 1.267144888 1.195164223 1 18.0168896 -1.999886797 0.01042414 8.61E-05 2.309185507 0.025304325 0.189990784 244605.0413 253.8607181 31698.23583 24929.43548 0.010002607 1.999886797 2.309099389 HTDNVIQWLNAMDEIGLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HTDNVIQWLNAMDEIGLPK 19 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 126.69 2.49E-05 1731200000 1888100 1938510 1222710 1567320 1946140 1484090 2212050 2579000 2213150 FALSE TRUE 1638582.801 1925775.8 1814016.646 1923203.961 1907415.622 1541183.903 1997525.731 2027500.92 1951513.928 0.839646993 0.986811199 0.929543274 0.985493331 0.977403027 0.789737588 1.023577492 1.038937458 1 20.89616233 2.072732497 24.9999962 1.024970103 0.925769311 0.360611076 0.063869345 43.90599814 15090.49635 0.025170268 0.016969792 118.2313087 -2.072732497 -0.099200792 HTDVQFYTEVGEITTDLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HTDVQFYTEVGEITTDLGK 19 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 112.74 0.00019079 83045000 128620 91928 53787 80752 81915 88744 103600 110420 109560 FALSE TRUE 111622.5411 91324.11892 79798.57311 99087.97582 80285.05176 92158.03911 93552.88795 86807.54229 96607.94161 1.15541786 0.945306539 0.826004278 1.025671121 0.831039875 0.953938543 0.968376785 0.898554931 1 16.55985417 4.731242182 5.061889841 0.92675608 1.165193474 0.542805653 0.064793684 0.109299009 9.003971823 0.014368491 0.090447102 53857.00293 -4.731242182 0.238437394 HTGCCGDNDPIDVCEIGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HTGCCGDNDPIDVCEIGSK 19 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;; 316.44 1.03E-61 9093500000 8298100 7959000 5075870 5788280 7020500 6142990 8864100 9939500 8315000 FALSE TRUE 7201485.06 7906716.805 7530577.71 7102597.442 6880805.785 6379314.8 8004460.946 7814015.274 7332010.172 0.982197909 1.078383229 1.027082278 0.9687108 0.938461025 0.87006355 1.091714381 1.06573983 1 22.80577736 HTGMASIDSSAPETTSDSS(ph)PTLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HTGMASIDSSAPETTSDSSPTLSR 24 0 S4R3H3;S4R393;S4R410;A7E2V4-5;A7E2V4;A7E2V4-3;A7E2V4-4;A7E2V4-2;H7BZ52;H0YCW2;S4R3B3;H7C453;S4R3U7 S4R3H3 ZSWIM8 Zinc finger SWIM domain-containing protein 8 1 HTGMASIDSSAPETTSDS(0.004)S(0.972)PT(0.024)LSR;HTGMASIDSSAPETTSDS(0.044)S(0.94)PT(0.015)LSR 259.7 3.56E-44 820380000 579880 588540 250970 347530 596520 679360 537500 609480 562630 TRUE FALSE 503247.3888 584673.842 372339.9314 426441.9982 584650.4191 705495.4188 485373.3327 479147.445 496116.5224 1.01437337 1.178501049 0.750509033 0.859560162 1.178453836 1.422035726 0.978345431 0.965796186 1 18.92031948 3.235761768 24.98824581 1.096896888 0.952702927 0.175745636 0.169096844 159.1133594 1420574.178 0.055181429 0.065387911 1720.924303 -3.235761768 -0.144193961 HTGPGILSMANAGPNTNGSQFFICTAK ddPTM_MDA-MB-175_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 ;;;; 343.56 3.57E-96 5372730000 4981630 4111980 2297091 2708677 3622393 3293277 4847340 5049260 5478340 FALSE TRUE 4323294.974 4084968.133 3407971.891 3323723.512 3550314.466 3419971.497 4377245.713 3969515.042 4830696.886 0.894962999 0.845627086 0.705482453 0.688042241 0.734948714 0.707966486 0.906131313 0.821727203 1 22.2037999 0.793836128 0.964609085 1.341638689 0.766000137 0.453421638 0.076269307 4.251031439 1.729641256 3.152406905 0.02740474 6.220655169 -0.793836128 -0.575638552 HTGPNS(ph)PDTANDGFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 HTGPNSPDTANDGFVR 16 0 P31943;G8JLB6;E9PCY7;D6RBM0;D6RIT2;D6RIU0;D6R9T0;D6RFM3;E5RGV0;D6RDU3;D6RJ04;D6RIH9;D6RAM1;E5RGH4;H0YAQ2;P55795;E7EQJ0 P31943;P55795;E7EQJ0 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 1 HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR 327.77 3.49E-47 21796420000 4807740 4126130 2132531 2865030 4367460 4090550 3810360 4246340 3774770 TRUE FALSE 4172384.978 4099025.18 3163830.124 3515578.851 4280556.091 4247916.105 3440831.874 3338293.236 3328520.991 1.253525211 1.231485453 0.950521308 1.056198492 1.286023463 1.27621731 1.033741978 1.002935912 1 21.66644984 2.087930978 7.957860198 1.00665603 1.167324851 0.356144917 0.103780276 0.296696236 23.35970224 0.046271981 0.031122443 122.4421587 -2.087930978 0.160668821 HTGPNSPDTANDGFVR ddPTM_MDA-MB-175_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 11266940000 6855420 5652190 2501180 3959400 5715090 5923910 5385060 6180190 5541480 FALSE TRUE 5949458.878 5615060.392 3710759.014 4858442.286 5601370.89 6151806.651 4862817.71 4858604.463 4886372.547 1.217561457 1.149126543 0.759409762 0.99428405 1.146324975 1.258972088 0.995179484 0.99431724 1 22.22033243 6.352818928 0.012341178 8.66E-06 2.209673884 0.028607345 0.141890178 75901.16099 138.8838542 11300.60684 13671.56222 2253299.539 -6.352818928 2.209665227 HTGYVIELQHVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HTGYVIELQHVVK 13 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A0U1RQX5;A0A0U1RRC8;A0A0U1RQX9 P47897 QARS Glutamine--tRNA ligase 0 ; 173.06 1.29E-05 632290000 723830 666950 472280 495580 648930 612240 719390 798410 735800 FALSE TRUE 628174.0315 662568.7615 700676.1877 608109.0135 636017.5626 635793.269 649623.6685 627676.2347 648814.5622 0.968187319 1.021198968 1.079932894 0.93726166 0.980276337 0.97993064 1.001247053 0.967420079 1 19.30744667 3.725536302 24.99972324 0.97829313 1.022915657 0.312862341 0.031720299 910.657778 1747976.075 0.008524669 0.012718006 5315.404285 -3.725536302 0.044622527 HTIAVVWGGVNIPHSPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HTIAVVWGGVNIPHSPYR 18 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ; 152.32 2.39E-08 1367550000 333380 460870 249074 258126 318890 333040 376000 412790 442140 FALSE TRUE 289322.9883 457842.5146 369527.0195 316737.4535 312544.7129 345852.2643 339535.5779 324518.0708 389870.7129 0.742099826 1.174344467 0.947819385 0.812416637 0.801662455 0.887094754 0.870892751 0.832373554 1 18.57263626 3.985069435 24.6792818 0.86344563 0.983937049 0.102841373 0.11613625 909.2876549 1503004.682 0.028136214 0.051071739 9662.053432 -3.985069435 0.120491418 HTKEDSAS(ph)VK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 HTKEDSAS(1)VK;HTKEDSAS(1)VK 112.42 0.00098001 146365000 466820 364870 245190 241382 348680 370780 406370 449560 179294 TRUE FALSE 405128.5542 362473.1449 363764.7041 296191.4724 341741.9502 385044.1465 366960.2999 353425.0925 158098.0676 2.56251427 2.292710787 2.300880142 1.873466747 2.161582083 2.435476615 2.321092886 2.235480154 1 17.27046021 1.238496422 6.73092833 0.968576246 2.266277454 0.834114891 0.178433979 0.046520582 10.85150359 0.276087406 0.045538906 17.31794764 -1.238496422 1.297701209 HTLADNFNPVSEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HTLADNFNPVSEER 14 0 P20645;H0YGT2 P20645 M6PR Cation-dependent mannose-6-phosphate receptor 0 ;;;; 216 6.29E-12 2512970000 1633660 1623370 909012 1195810 1781550 1941760 1322340 1799260 1670690 FALSE TRUE 1417767.692 1612705.976 1348613.244 1467336.937 1746100.641 2016460.764 1194099.67 1414502.251 1473182.931 0.962384006 1.094708567 0.915441806 0.996031726 1.185257176 1.368778256 0.810557633 0.960167418 1 20.49050516 HTLDQYVESDYTLLYLHHGLTSDNKPSLSWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HTLDQYVESDYTLLYLHHGLTSDNKPSLSWLR 32 1 Q07960;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 274.79 6.58E-74 9091600000 3061220 3336470 1333940 2434550 2820300 2725760 3495370 4431730 4008290 FALSE TRUE 2656672.021 3314552.509 1979037.846 2987351.787 2764181.548 2830621.751 3156389.555 3484039.027 3534434.522 0.751654049 0.93778863 0.559930544 0.845213504 0.782071794 0.800869767 0.893039476 0.985741568 1 21.75304798 2.001436798 1.554177948 1.00898285 0.774414319 0.479341491 0.093269559 0.352911134 1.573593238 0.083360434 0.028273666 100.3313828 -2.001436798 -0.234568532 HTLGDS(ph)DNES ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 HTLGDSDNES 10 0 G3V192;P02794;G3V1D1 G3V192 FTH1 "Ferritin;Ferritin heavy chain;Ferritin heavy chain, N-terminally processed" 1 HTLGDS(1)DNES;HTLGDS(0.999)DNES(0.001);HTLGDS(1)DNES;HTLGDS(1)DNES;HTLGDS(1)DNES;HTLGDS(1)DNES;HTLGDS(0.999)DNES;HTLGDS(1)DNES 179.95 2.15E-06 3350660000 3075587 2517709 1616611 1949574 2289589 2798026 2459515 2748980 2984937 TRUE FALSE 2669140.385 2501170.004 2398409.487 2392254.574 2244030.658 2905667.871 2220991.614 2161132.02 2632061.148 1.014087529 0.950270477 0.911228635 0.908890196 0.852575427 1.103951507 0.843822194 0.821079716 1 21.32776158 4.644055749 2.039936592 0.910740741 1.032241052 0.10706513 0.082487523 1.238588958 6.609256559 0.021988263 0.259732439 44061.14193 -4.644055749 0.121500312 HTLTQIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HTLTQIK 7 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ; 143 0.002451 1080580000 1306180 1595420 1053330 1252200 1526280 1369550 1674130 1848750 2484500 FALSE TRUE 1133565.004 1584939.581 1562723.911 1536531.149 1495910.014 1422237.475 1511773.13 1453409.199 2190785.24 0.517424065 0.723457303 0.713316797 0.701360919 0.682819104 0.649190732 0.690059939 0.663419295 1 21.06301664 1.237584843 24.99523058 1.000000386 0.672609611 0.764463407 0.057920841 11.14655036 285377.5038 0.07818654 0.013216158 17.28163557 -1.237584843 -0.327390775 HTNFVEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HTNFVEFR 8 0 M0R0N4;M0QYZ2;P53680;M0QZ21 M0R0N4 AP2S1 AP-2 complex subunit sigma 0 ;;;; 162.31 0.00034244 1817360000 497567 533870 372602 436971 556957 607152 575440 666547 679598 FALSE TRUE 431812.2603 530362.9728 552793.5735 536191.9442 545874.6454 630509.5303 519633.9174 524011.1111 599256.6986 0.72057978 0.885034701 0.922465405 0.894761703 0.910919555 1.052152661 0.867130761 0.874435133 1 19.19281461 4.850989224 1.925418666 0.926257676 0.612648487 0.576466524 0.056513642 0.876631776 2.687526645 0.015078222 0.539019107 70956.01624 -4.850989224 -0.313609189 HTNPIVENGQTHPCQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HTNPIVENGQTHPCQK 16 0 E9PFH4;C9J7E5;Q9Y5L0-5;Q9Y5L0-3;Q9Y5L0;Q9Y5L0-1 E9PFH4 TNPO3 Transportin-3 0 74.428 0.018683 71653000 1152200 349910 489310 365520 352730 338900 769940 786840 654200 FALSE TRUE 999933.8507 347611.4182 725941.9526 448516.9026 345711.3631 351937.7023 695271.3373 618580.3892 576861.2213 1.733404524 0.602591066 1.258434309 0.77751266 0.599297284 0.610090762 1.205266209 1.072320978 1 19.13786476 4.752485956 24.43359168 0.909705524 1.733405289 0.537135983 0.245284728 1526.262612 2677937.549 0.061816797 1.214112322 56556.94678 -4.752485956 0.823699765 HTNYTMEHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 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 ;;;;;;;;;; 198.81 1.68E-07 6850210000 1726905 1733675 1322845.3 1769111 1552998 1928628 1306635.4 1659142 4223675 FALSE TRUE 1498690.129 1722286.375 1962577.712 2170814.692 1522096.378 2002823.567 1179918.1 1304347.395 3724356.953 0.402402387 0.462438589 0.526957468 0.582869666 0.408687029 0.53776359 0.316811228 0.350220833 1 21.82855992 1.232464856 24.99892637 1.000000907 0.44636614 0.81068789 0.083746307 93.59458258 383796.197 0.199953117 0.022320672 17.07909507 -1.232464856 -0.553634767 HTPLYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HTPLYER 7 0 Q9NZB2;Q9NZB2-4;Q9NZB2-6;Q9NZB2-2;Q9NZB2-5;A0A0C4DH52;Q5T035 Q9NZB2 FAM120A;C9orf129 Constitutive coactivator of PPAR-gamma-like protein 1;Putative uncharacterized protein C9orf129 0 ; 105.25 0.0079692 1159030000 566400 608100 360500 350530 601120 738040 493790 526500 534540 FALSE TRUE 491548.8049 604105.3511 534839.0058 430123.194 589158.8881 766432.8764 445902.3218 413912.0722 471347.2901 1.042859088 1.28165657 1.134702622 0.912539868 1.249946484 1.626047062 0.946016517 0.87814671 1 18.84643091 2.043443823 24.99999181 0.924880513 1.203923628 0.313759844 0.185536316 155.1909511 89304.86225 0.077635727 0.052341963 110.5207498 -2.043443823 0.279043114 HTPS(ph)PGLPAEGAPEAPRPS(ph)SPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HT(0.051)PS(0.949)PGLPAEGAPEAPRPS(0.536)S(0.464)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 166.8 1.63E-24 106530000 0 0 0 0 0 0 0 0 0 TRUE FALSE 0 0 0 0 0 0 0 0 0 0 HTPS(ph)PGLPAEGAPEAPRPSS(ph)PPPEVLEPHSLDQPPATSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPR 40 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HT(0.425)PS(0.575)PGLPAEGAPEAPRPS(0.462)S(0.538)PPPEVLEPHSLDQPPATSPR 147.26 3.34E-13 284620000 45661 30934 28530 30619 37119 28750 36955 45325 37128 TRUE FALSE 39626.78316 30730.79252 42327.20343 37571.51193 36380.40452 29856.0311 33371.10979 35632.60147 32738.77014 1.210393151 0.938666675 1.292877016 1.147615252 1.111233085 0.911947241 1.019314704 1.088391571 1 14.99871251 2.976969507 21.31568522 1.018449453 1.141190607 0.323247333 0.097428452 155.3658563 143797.6669 0.030403965 0.030705723 948.3518747 -2.976969507 0.122741153 HTPSPGLPAEGAPEAPRPS(ph)SPPPEVLEPHSLDQPPATSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPR 40 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 HTPSPGLPAEGAPEAPRPS(0.495)S(0.495)PPPEVLEPHS(0.006)LDQPPAT(0.002)S(0.002)PR;HTPSPGLPAEGAPEAPRPS(0.5)S(0.5)PPPEVLEPHSLDQPPATSPR;HTPSPGLPAEGAPEAPRPS(0.49)S(0.49)PPPEVLEPHS(0.003)LDQPPAT(0.008)S(0.01)PR 151.13 8.08E-14 1032300000 650640 451390 277034 349346 453640 427710 412450 449280 528470 TRUE FALSE 564656.2755 448424.7894 411008.569 428670.3487 444613.4515 444164.2805 372450.6625 353204.9683 465994.8786 1.211722063 0.962295531 0.882002331 0.919903562 0.954116605 0.953152708 0.799259133 0.757958906 1 18.82995457 7.998574355 0.923799246 0.87432138 199.9998244 0.634607736 0.074025905 707.7647653 1.394299362 0.026277482 297465.7135 99672271.24 -7.998574355 199.125503 HTPSPGLPAEGAPEAPRPS(ph)SPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 HTPSPGLPAEGAPEAPRPS(0.5)S(0.5)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR;HTPSPGLPAEGAPEAPRPS(0.5)S(0.5)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 152.24 6.05E-19 314660000 126184 91864 32716 50461 78480 69269 76659 81508 27324.6 TRUE FALSE 109508.4647 91260.53934 48537.56703 61918.9413 76918.40154 71933.82325 69224.62198 64078.1485 24094.31692 4.544991463 3.787637543 2.014481971 2.569856681 3.192387724 2.985509965 2.873068459 2.659471473 1 14.55640528 4.4122707 4.566994953 2.56069905 4.394037258 0.572661768 0.621067607 0.138326764 5.566072563 0.156975916 0.469915224 25838.70239 -4.4122707 1.833338208 HTPSPGLPAEGAPEAPRPSS(ph)PPPEVLEPHSLDQPPAT(ph)SPRPLIEVGELLDLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HTPSPGLPAEGAPEAPRPS(0.481)S(0.518)PPPEVLEPHS(0.047)LDQPPAT(0.493)S(0.458)PRPLIEVGELLDLT(0.003)R;HTPSPGLPAEGAPEAPRPS(0.482)S(0.518)PPPEVLEPHS(0.171)LDQPPAT(0.429)S(0.4)PRPLIEVGELLDLTR 105.28 4.77E-10 493160000 90601 89316 39875.8 59060 117498 107786 87767 124107 56562 TRUE FALSE 78627.8483 88729.27732 59159.87026 72470.47568 115160.0197 111932.5972 79255.36985 97567.68385 49875.3048 1.576488577 1.779022257 1.186155563 1.453033239 2.308958715 2.244248885 1.589070386 1.956232333 1 15.60603804 HTQENCETWGVNGETGTLVDMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HTQENCETWGVNGETGTLVDMK 22 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 190.8 1.65E-17 663580000 445950 344270 269830 325520 347750 302980 406150 481600 502350 FALSE TRUE 387016.5776 342008.4677 400320.6905 399434.2913 340830.4554 314635.8367 366761.6355 378613.5878 442962.7553 0.873700041 0.772093057 0.903734424 0.901733355 0.769433663 0.710298626 0.82797398 0.854730072 1 18.75682588 1.210272519 2.550864492 1.051930506 0.821163543 0.450809577 0.061042279 0.569291206 3.848754564 0.297848274 0.016926093 16.228281 -1.210272519 -0.230766963 HTQFWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HTQFWR 6 0 P12236 P12236 SLC25A6 "ADP/ATP translocase 3;ADP/ATP translocase 3, N-terminally processed" 0 ;;; 97.068 0.041493 1218560000 1172769 1067893 771377 1016493 1103746 1243849 1209361 1542768 1329978 FALSE TRUE 1017784.605 1060877.941 1144417.497 1247303.272 1081783.614 1291700.676 1092077.356 1212859.069 1172749.516 0.867861885 0.904607443 0.975841373 1.063571764 0.922433648 1.101429298 0.931211091 1.034201296 1 20.16146347 4.245188983 2.785413009 1.007663896 0.874973927 0.46804473 0.053815362 0.20977163 3.231586444 0.012699585 0.039294429 17586.88738 -4.245188983 -0.13268997 HTQLEQMFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HTQLEQMFR 9 0 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ;;;; 147.78 9.16E-05 1795150000 1269492 1161037 691063 849320 1121488 1153044 1124371 1245493 1132488 FALSE TRUE 1101725.416 1153410.071 1025263.378 1042171.087 1099172.583 1197402.349 1015329.673 979154.0144 998606.5588 1.103262748 1.155019523 1.026694016 1.043625318 1.100706353 1.199073187 1.01674645 0.980520312 1 19.92955686 2.021360823 24.7735814 0.991798116 1.101125377 0.513122326 0.048926067 166.765678 193408.4959 0.020738715 0.013980714 105.0414778 -2.021360823 0.109327261 HTQSMS(ph)SARER ddPTM_MDA-MB-175_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(0.029)QS(0.029)MS(0.471)S(0.471)ARER;HT(0.007)QS(0.011)MS(0.491)S(0.491)ARER 72.705 0.027594 2062400000 1326070 1218530 649600 775260 1086120 1287320 922630 1040150 881240 TRUE FALSE 1150826.49 1210525.396 963748.7328 951294.6321 1064508.337 1336844.033 833153.4846 817722.017 777060.8111 1.480999264 1.557825821 1.240248793 1.224221603 1.369916385 1.720385347 1.072185693 1.052326929 1 19.56766798 2.105301462 9.839113721 1.039703595 1.416713469 0.618068694 0.144695595 0.210467173 18.05638798 0.061624874 0.041528848 127.4387379 -2.105301462 0.377009873 HTSALCNSCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HTSALCNSCR 10 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;; 163.9 6.32E-06 229201000 83904 153989 43601.4 66844 202380 227733 126920 139587 156688 FALSE TRUE 72815.87381 152977.4361 64687.18288 82021.95185 198353.0339 236494.0359 114611.3179 109737.4063 138164.5231 0.527022945 1.107212131 0.468189528 0.593654217 1.435629273 1.711684233 0.829527836 0.794251692 1 17.07602769 3.259335386 24.99998546 1.112744288 0.690259759 0.354247825 0.319111245 343.4906132 413347.8315 0.10138742 0.130746075 1816.918246 -3.259335386 -0.42248453 HTSKLS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.003)KLS(0.997)R;HTSKLS(1)R 67.207 0.039842 1304510000 679870 956330 211117 548770 1160160 1464650 1205290 1358720 1246160 TRUE FALSE 590023.4569 950047.8053 313213.8873 673376.6159 1137075.086 1520996.033 1088401.161 1068168.302 1098840.384 0.536951012 0.864591272 0.285040386 0.612806578 1.034795501 1.384182867 0.990499782 0.972086862 1 20.06755041 3.239450408 5.256790625 1.075065442 0.570667758 0.66061674 0.179053385 0.109658386 8.917924247 0.054264734 0.066200824 1735.603065 -3.239450408 -0.504397683 HTTDLDASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HTTDLDASK 9 0 P12532;P12532-2;F8WCN3;C9JSQ1;P17540;C9J8F6;C9J6W7;C9JT96;D6RHV3;D6R998 P12532 CKMT1A;CKMT1B;CKMT2 "Creatine kinase U-type, mitochondrial;Creatine kinase S-type, mitochondrial" 0 ;;; 171.56 5.69E-05 2353895000 4443179 4238455 1416579 3400625 4119513 4286321 3895713 5651050 5169466 FALSE TRUE 3856001.638 4210612.31 2101641.343 4172788.882 4037542.751 4451218.542 3517907.353 4442616.934 4558337.619 0.845922782 0.92371664 0.46105434 0.915419004 0.885748948 0.976500408 0.771752259 0.974613402 1 22.12007635 3.548471495 24.99998905 0.918082133 0.749355806 0.282976009 0.132757718 204.3906104 71614.08306 0.035419913 0.052536205 3535.668138 -3.548471495 -0.168726327 HTTEAAAGALQNITAGDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HTTEAAAGALQNITAGDRR 19 1 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ;;; 188.58 1.03E-14 1424020000 1127885 1097136 509512 760824 1144315 986698 1069980 1321210 854902 FALSE TRUE 978832.1396 1089928.841 755913.7074 933580.7177 1121545.37 1024656.911 966213.5043 1038679.523 753836.4595 1.298467496 1.445842567 1.002755568 1.238439327 1.487783399 1.359256239 1.281728274 1.377857903 1 19.52389205 1.231183082 24.9948622 0.999999448 1.312495275 0.353804683 0.132301286 313.5773804 1062298.533 0.328719399 0.032561607 17.02876226 -1.231183082 0.312495827 HTTENKPHS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HTTENKPHSPK 11 1 A0A2R8Y6S3;C9J167;Q68D20;P54278-3;P54278 A0A2R8Y6S3 PMS2;PMS2CL Protein PMS2CL;Mismatch repair endonuclease PMS2 1 HTTENKPHS(1)PK;HTTENKPHS(1)PK 94.532 0.0050933 118280000 153367 104405 48007 69653 86817 80330 133456 139874 130729 TRUE FALSE 133099.1624 103719.1567 71223.34577 85468.77823 85089.51155 83420.34708 120513.4577 109963.0336 115274.3665 1.154629311 0.899759069 0.617859355 0.741437848 0.738147726 0.723667799 1.045448882 0.953924423 1 16.81471221 2.234154884 24.99995685 0.99213797 0.801077602 0.2707504 0.143828335 152.7084165 866517.809 0.059833576 0.041910886 171.4568671 -2.234154884 -0.191060368 HTTSIFDDFAHYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HTTSIFDDFAHYEK 14 0 A0A024R7W5;A0A087X0Q1;A0A087WY31;Q7Z739 A0A024R7W5 YTHDF3 YTH domain-containing family protein 3 0 102.28 0.0006842 172780000 170610 168410 45643 119400 182940 162530 163300 217640 240600 FALSE TRUE 148063.4562 167303.7036 67716.10747 146511.5949 179299.8519 168782.6343 147463.1911 171099.3797 212156.5421 0.697897198 0.788586117 0.319179917 0.690582499 0.845129969 0.795557057 0.695067848 0.806477038 1 17.69476964 3.44215808 6.559053461 0.811113313 0.601986816 0.357120779 0.139335091 0.211908106 26.74119586 0.040268325 0.052758016 2767.948974 -3.44215808 -0.209126498 HTVDDGLDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HTVDDGLDIR 10 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;;; 175.65 2.74E-06 3308210000 3175490 2925340 1855320 2413810 3114920 2992870 3073970 3602600 4011280 FALSE TRUE 2755840.951 2906123.249 2752558.958 2961902.453 3052939.186 3108007.646 2775856.863 2832212.025 3537071.048 0.779130787 0.821618568 0.778202903 0.837388453 0.863126339 0.878695283 0.784789682 0.800722402 1 21.75412377 1.23516783 24.97729566 1.000000256 0.818385084 0.735240498 0.034329803 53.28979277 392248.2937 0.062478309 0.008854167 17.18572388 -1.23516783 -0.181615172 HTVDDGLDIRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HTVDDGLDIRK 11 1 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 138.25 3.99E-05 430420000 554030 405140 208188 225830 432000 381850 511270 561960 154393 FALSE TRUE 480813.5318 402478.6087 308868.4131 277108.1531 423404.0452 396540.0166 461687.1141 441789.2272 136140.8354 3.53173631 2.956340083 2.268741867 2.035452127 3.110044417 2.912719136 3.391246371 3.245089732 1 17.05474034 HTWMEDADSCVAHNALECAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HTWMEDADSCVAHNALECAR 20 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 221.41 4.55E-25 120130000 35719 33724 22928 25169 37656 43188 32331 41292 40168 FALSE TRUE 30998.64365 33502.46482 34016.05749 30884.00613 36906.71927 44849.47031 29195.5446 32462.02713 35419.3848 0.875188652 0.945879354 0.960379681 0.871952077 1.041992104 1.266240805 0.824281527 0.916504545 1 15.11225153 4.656050579 0.950194017 0.983730415 0.839416858 0.086500085 0.117977312 6.028639126 4.781456114 0.042520229 0.874728701 45295.03287 -4.656050579 -0.144313558 HVAEVLEYTKDEQLESLFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HVAEVLEYTKDEQLESLFQR 20 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ; 306.27 9.69E-56 2158300000 1244280 1026350 709640 814460 1149610 896580 1124990 1495900 1001510 FALSE TRUE 1079845.245 1019607.839 1052824.278 999395.5912 1126735.01 931072.0128 1015888.643 1176013.426 883112.6287 1.22277183 1.154561498 1.192174411 1.131673989 1.275867849 1.054307211 1.150350035 1.331668677 1 19.75223792 4.755761955 21.96570429 1.174391605 1.222772024 0.023424415 0.096019936 3261.101767 4163969.292 0.02250091 0.530340645 56985.18399 -4.755761955 0.048380419 HVAVTNMNEHSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 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 ;;;;;;;; 170.56 1.54E-05 2296064000 772010 860169 252715 522581 963926 1085095 848664 929748 839475 FALSE TRUE 669986.9225 854518.4932 374928.8193 641241.0032 944745.7585 1126839.307 766360.6959 730928.6255 740233.2218 0.905102477 1.154390897 0.506500935 0.866268879 1.276281219 1.522276052 1.035296273 0.987430183 1 19.49762036 3.258416589 22.08622633 1.150382229 0.854119396 0.325132584 0.218661846 85.20592143 94773.90476 0.067413552 0.086830292 1813.078419 -3.258416589 -0.296262833 HVCQPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 82.263 0.024965 75651000 56606 60442 40902 42536 45751 55998 58863 66047 66846 FALSE TRUE 49125.37368 60044.95252 60682.34401 52194.44892 44840.64461 58152.2793 53154.47532 51923.36303 58943.54203 0.833430975 1.018685855 1.029499448 0.885499024 0.760738888 0.986575921 0.901786243 0.880899947 1 15.84704614 3.704758174 24.50413995 0.897864329 0.966353511 0.094722359 0.082969466 981.9709216 711852.19 0.022392913 0.033216458 5067.084821 -3.704758174 0.068489182 HVDAHATLNDGVVVQVMGLLSNNNQALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HVDAHATLNDGVVVQVMGLLSNNNQALR 28 0 Q13283;E5RH42;E5RIZ6;E5RJU8;Q13283-2;E5RIF8 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ; 147.18 4.75E-08 47584000 122079 97849 90330 87433 92663 83105 116808 139686 104101 FALSE TRUE 105945.9508 97206.22348 134013.8901 107285.999 90819.18759 86302.10313 105479.9781 109815.2359 91794.29837 1.154167009 1.058957094 1.459936973 1.16876539 0.989377218 0.940168449 1.149090739 1.196318703 1 16.48611693 3.467871222 23.81096557 1.07443673 1.225570207 0.280260182 0.124283941 167.1789339 430340.285 0.037537966 0.048543501 2936.778704 -3.467871222 0.151133476 HVDNIMFENHTVADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HVDNIMFENHTVADR 15 0 Q8TAT6;Q8TAT6-2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 ;;; 191.37 1.03E-07 1289940000 1129620 947380 685430 808510 997000 1063800 956140 1121300 1070480 FALSE TRUE 980337.8549 941156.5984 1016906.241 992094.5528 977161.6506 1104725.074 863413.69 881518.721 943929.0739 1.038571522 0.997062835 1.077312129 1.051026587 1.035206646 1.170347545 0.914701871 0.93388237 1 19.84831894 2.206200388 24.99998201 0.944817409 1.057690565 0.53445173 0.049147721 144.0285481 111268.7105 0.019709392 0.013289205 160.7682884 -2.206200388 0.112873156 HVDNPNGDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 174.77 3.43E-05 147120000 323730 316000 180948 259030 288970 347350 310780 349450 366330 FALSE TRUE 280948.2603 313924.1752 268455.058 317846.7205 283220.0624 360712.7793 280640.6034 274722.8369 323022.8847 0.869747233 0.971832616 0.831071329 0.983975859 0.876780178 1.116678713 0.868794803 0.850474842 1 18.30127685 3.71642543 24.97375745 0.938039635 0.898978586 0.083163315 0.084885469 2904.274495 3276711.814 0.023491824 0.034874388 5205.056281 -3.71642543 -0.03906105 HVDSLSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HVDSLSQR 8 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 0 ;;; 156.51 0.00039182 3081658000 1025736 1042582 474211 778599 980616 1125899 945332 1136463 1164524 FALSE TRUE 890182.3887 1035733.21 703541.0257 955391.8031 961103.6601 1169213.063 853653.8481 893439.2314 1026855.299 0.86690149 1.008645727 0.68514135 0.930405485 0.93596796 1.138634688 0.831328278 0.870073156 1 19.96980147 3.506886999 24.86825133 0.943418034 0.858854864 0.143407857 0.111548985 1513.304288 1264309.786 0.030934994 0.045801913 3212.824471 -3.506886999 -0.08456317 HVDSLSQRS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.025)QRS(0.975)PK;HVDSLSQRS(1)PK 194.48 3.01E-07 3646840000 3360360 3514820 398335 456400 2781750 2392070 3620180 3581710 3856.5 TRUE FALSE 2916279.912 3491730.916 590971.1384 560032.5956 2726398.617 2484094.481 3269095.501 2815789.189 3400.588963 857.5808318 1026.801814 173.7849369 164.6869415 801.7430647 730.4894851 961.3321504 828.0298559 1 11.73156892 HVDWVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HVDWVK 6 0 P40123;E9PDI2;F8WDB9;Q01518-2;Q01518;Q5T0R1;Q5T0R9;Q5T0R4;Q5T0R3;Q5T0R2 P40123;Q01518-2 CAP2;CAP1 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein;Adenylyl cyclase-associated protein 1 0 ; 123.34 0.018832 1640710000 2949600 2272640 1604700 1967570 1977040 1893960 2260840 2693400 3988300 FALSE TRUE 2559802.887 2257710.878 2380738.287 2414336.841 1937700.772 1966821.867 2041584.085 2117437.37 3516807.717 0.72787684 0.641977344 0.676960038 0.686513746 0.550982859 0.559263407 0.580521953 0.602090743 1 21.74583503 1.236533176 24.99909531 1.000000478 0.62400552 0.804996036 0.057463651 24.43781655 301248.5868 0.095675613 0.015045348 17.23983783 -1.236533176 -0.375994958 HVEAVAYYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HVEAVAYYK 9 0 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 0 75.378 0.03843 172140000 295610 312540 170100 250800 278080 260450 304350 340920 334920 FALSE TRUE 256544.3895 310486.9042 252360.929 307747.9732 272546.7521 270469.68 274834.1838 268016.911 295326.1391 0.868681622 1.051335669 0.85451606 1.042061411 0.922867014 0.915833867 0.930612457 0.907528578 1 18.17194953 HVEAVYIDIADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HVEAVYIDIADR 12 0 F5GWE5;Q00169;I3L4H1;I3L2X8;I3L4C0;I3L459;I3NI10 F5GWE5 PITPNA Phosphatidylinositol transfer protein alpha isoform 0 122.45 0.00035835 205650000 348200 320740 212080 273860 318010 388920 302520 360140 362940 FALSE TRUE 302184.4878 318633.0378 314642.5974 336044.0987 311682.2232 403882.0041 273181.657 283126.8636 320033.6467 0.944227243 0.995623558 0.983154742 1.050027402 0.973904545 1.261998569 0.853602925 0.884678429 1 18.28786406 HVEDGNVTVQHAALSALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HVEDGNVTVQHAALSALR 18 0 P52306-4;P52306;P52306-5;P52306-6;P52306-2;P52306-3;H0Y8M2 P52306-4 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 0 115.26 0.00011239 531770000 689470 571200 312770 506820 618040 440250 746950 763730 547850 FALSE TRUE 598354.7926 567447.7496 464026.6182 621901.2273 605742.2132 457186.7024 674510.904 600412.2829 483083.7971 1.238614907 1.17463627 0.960550987 1.287356833 1.253907121 0.946392127 1.396260665 1.242873983 1 18.88191394 HVEEFSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HVEEFSPR 8 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ;; 172.21 0.00037464 0 592580 602940 341280 449710 594360 600060 541550 626710 537970 FALSE TRUE 514269.0516 598979.2474 506324.1495 551823.5289 582533.3988 623144.6965 489030.5644 492692.9436 474371.7995 1.084105447 1.262678869 1.067357187 1.163272204 1.22801018 1.313620871 1.030901426 1.038621908 1 18.85565872 2.142832338 11.20144265 1.026054868 1.185333259 0.517357143 0.074355395 0.332299913 36.52235411 0.029983465 0.020212808 138.9416134 -2.142832338 0.159278391 HVENDGYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HVENDGYK 8 0 O15305;H3BRM0;H3BV55 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 85.731 0.016535 168640000 216190 201150 133900 138550 148960 175230 202650 241200 192600 FALSE TRUE 187619.9437 199828.6324 198654.4879 170009.8951 145995.9874 181971.2115 182997.0342 189621.257 169831.0474 1.104744666 1.176631926 1.169718322 1.001053092 0.859654284 1.071483773 1.077524027 1.116528809 1 17.3737407 3.742013535 24.83468448 1.029894919 1.152991673 0.420732507 0.071006609 313.031654 2251431.86 0.021192603 0.034904565 5520.946448 -3.742013535 0.123096755 HVFAIFNTEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HVFAIFNTEQR 11 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 ; 220.1 9.40E-12 1500660000 1306540 1189890 744510 799740 1125420 1243730 1272600 1238260 1134330 FALSE TRUE 1133877.429 1182073.534 1104557.526 981333.1903 1103026.344 1291577.098 1149183.448 973467.7352 1000230.8 1.133615791 1.181800775 1.104302654 0.981106751 1.102771825 1.291279071 1.148918278 0.973243111 1 19.9319015 1.731341066 6.901419639 0.988395421 1.134367694 0.390974088 0.076727945 0.135456528 18.43757869 0.04831444 0.021410005 53.86926693 -1.731341066 0.145972273 HVFGQPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HVFGQPVK 8 0 Q9BR76;A0A087WW53;F5H390;F5H0D2 Q9BR76 CORO1B Coronin-1B;Coronin 0 78.496 0.030474 721560000 2824900 2917900 1716700 2289700 2836900 2588800 3063100 3618300 3437300 FALSE TRUE 2451582.308 2898732.123 2546901.862 2809611.381 2780451.24 2688392.811 2766041.033 2844554.703 3030946.31 0.808850457 0.956378578 0.840299234 0.926974975 0.917354171 0.886981337 0.912599812 0.938503824 1 21.53133687 -2 0.595754911 7.678781923 0.887434501 0.431968115 0.041304575 158.4086685 1.299697292 1395.948931 0.018994812 0.01 2 -6.791347422 HVGDLGNVTADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HVGDLGNVTADK 12 0 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ; 124.48 0.00032217 620360000 2715200 2139100 1853870 2343700 1877130 1635260 2297600 2719800 6226800 FALSE TRUE 2356379.441 2125048.111 2750407.733 2875872.906 1839778.786 1698169.51 2074779.106 2138191.936 5490674.798 0.429160263 0.387028587 0.500923445 0.523774037 0.335073348 0.309282479 0.377873245 0.389422432 1 22.38855204 1.237642059 24.99978859 1.000000697 0.405144931 0.888599233 0.066031915 7.644939577 207951.5266 0.103255979 0.017502469 17.28391251 -1.237642059 -0.594855766 HVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGR 36 1 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;; 397.38 6.83E-180 2031305000 884031 772543 348765 600490 763945 634799 874946 1052316 799475 FALSE TRUE 767204.0635 767468.1142 517428.9205 736840.4324 748743.9891 659220.1283 790093.8716 827286.4125 704961.9763 1.088291411 1.088665971 0.733981318 1.045220107 1.062105496 0.935114447 1.120760975 1.173519197 1 19.42718592 2.223920483 24.91793685 1.114751633 0.990459509 0.160423687 0.111976826 360.1294373 612945.6636 0.045664499 0.030937788 167.4636232 -2.223920483 -0.124292124 HVGMAVAGLLADAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HVGMAVAGLLADAR 14 0 P25788-2;P25788 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ; 170.07 3.23E-06 2530600000 2731200 2678200 1352690 1843810 2511500 2648900 2531300 2678000 2743600 FALSE TRUE 2370265 2660606.728 2006855.408 2262475.241 2461526.064 2750804.897 2285814.916 2105330.54 2419254.734 0.979750072 1.099762952 0.829534559 0.935195128 1.017472873 1.137046405 0.944842593 0.870239298 1 21.20613125 2.01357824 24.99726712 0.920357957 0.998339181 0.090967368 0.08917837 465.1222482 856277.519 0.037388995 0.025193956 103.1758938 -2.01357824 0.077981224 HVGNQQYNVTYVVK ddPTM_MDA-MB-175_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 ; 152.99 6.51E-06 1349710000 1530600 1437870 844460 1110170 1396140 1316390 1560030 1669650 1606800 FALSE TRUE 1328327.332 1428424.537 1252843.681 1362251.066 1368359.546 1367032.375 1408738.531 1312608.341 1416845.934 0.937524186 1.008172097 0.884248351 0.961467322 0.965778644 0.964841936 0.994277851 0.926429832 1 20.43425146 3.499110342 24.79537242 0.966071103 0.945310146 0.100885599 0.035372001 1984.48324 2237740.693 0.009320055 0.013672327 3155.806325 -3.499110342 -0.020760957 HVGSSETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HVGSSETK 8 0 A0A0A0MQS1;Q53H96-2;Q53H96;A0A087WTU2;B5MD87 A0A0A0MQS1 PYCRL Pyrroline-5-carboxylate reductase;Pyrroline-5-carboxylate reductase 3 0 114.99 0.0025505 70642000 107130 117000 63888 100140 83522 125020 107170 128790 131010 FALSE TRUE 92972.49907 116231.4193 94784.45049 122878.3175 81860.07561 129829.6003 96776.6699 101249.2607 115522.147 0.804802382 1.006139708 0.820487265 1.063677578 0.708609368 1.123850306 0.837732611 0.876448918 1 16.81780994 4.774976454 22.21307911 0.921099458 0.804801222 0.087068337 0.124325793 10519.02793 6415904.967 0.026882804 4.507046946 59562.98496 -4.774976454 -0.116298236 HVIADQEVMETNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HVIADQEVMETNR 13 0 Q9H307 Q9H307 PNN Pinin 0 166.38 3.37E-05 304790000 92918 85924 42947 69298 82723 98061 79261 98492 108100 FALSE TRUE 80638.65088 85359.55959 63716.31285 85033.17005 81076.97414 101833.4701 71574.28042 77430.25227 95320.54115 0.84597349 0.895500157 0.668442626 0.892076031 0.850571904 1.068326605 0.750879921 0.812314443 1 16.54049952 HVIDFFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HVIDFFK 7 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 91.041 0.016695 225170000 598650 504040 311730 420920 507240 439760 538180 581440 537870 FALSE TRUE 519536.8857 500728.9281 462483.6707 516496.3194 497146.9164 456677.8518 485987.3864 457103.5808 474283.6213 1.09541393 1.055758423 0.975120476 1.089003069 1.048205955 0.962879238 1.024676722 0.963776863 1 18.85539052 2.756438444 22.25776107 0.987528489 1.050577115 0.438989862 0.03639341 189.299391 235675.4591 0.011451564 0.011416295 570.7401754 -2.756438444 0.063048626 HVINFDLPSDIEEYVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 HVINFDLPSDIEEYVHR 17 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8Y7T2;A0A087WVZ1;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;;;;;; 326.37 1.19E-60 3866333000 1971951 1828339 1064227 1409462 1934940 1967450 1867109 2114435 1943685 FALSE TRUE 1711352.679 1816328.521 1578890.737 1729501.889 1896438.48 2043139.075 1686037.057 1662279.53 1713904.774 0.998510947 1.059760466 0.921224307 1.00910034 1.106501662 1.192096029 0.983740219 0.969878581 1 20.70885552 5.079455319 12.29335399 1.026895308 0.729550367 0.015245923 0.076032316 2032776.285 8863611.324 0.019996151 15040571.15 120075.7531 -5.079455319 -0.297344941 HVLEGHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HVLEGHDR 8 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1;A0A3B3IU78 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 135.79 0.00081866 109857000 214074 212036 117319 140963 190802 216760 197435 201141 198226 FALSE TRUE 185783.5785 210643.1216 174054.8608 172970.8036 187005.4135 225098.8975 178287.7841 158128.5624 174791.9481 1.062884077 1.205107694 0.995783059 0.989581073 1.069874302 1.287810451 1.019999983 0.904667315 1 17.4152792 2.00247292 24.99435595 0.950566995 1.100053271 0.316324396 0.0920195 84.42295301 853276.3965 0.038624463 0.025864797 100.5710351 -2.00247292 0.149486276 HVLEISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HVLEISR 7 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ;;; 124.08 0.0041813 1700030000 1697500 2129860 1195440 1303800 2147220 2315320 1996280 2210300 2152260 FALSE TRUE 1473171.074 2115868.809 1773558.783 1599847.717 2104494.523 2404391.859 1802681.073 1737644.546 1897822.275 0.776242904 1.114893021 0.934523114 0.842991327 1.108899685 1.266921508 0.949868224 0.915599194 1 20.85591346 3.233150358 24.99890102 1.035229373 0.932526233 0.197763694 0.12808427 298.4932158 1379230.001 0.040935128 0.047744758 1710.607444 -3.233150358 -0.10270314 HVLPTTSLGHPSLS(ph)APALSSSSSSSSTSSPVLGAPSYPASTPGASPHHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HVLPTTSLGHPSLSAPALSSSSSSSSTSSPVLGAPSYPASTPGASPHHR 49 0 Q53ET0;H0YDQ8;Q5T4K5 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 HVLPT(0.047)T(0.047)S(0.047)LGHPS(0.183)LS(0.674)APALSSSSSSSSTSSPVLGAPSYPASTPGASPHHR;HVLPT(0.053)T(0.053)S(0.053)LGHPS(0.183)LS(0.659)APALS(0.001)SSSSSSSTSSPVLGAPSYPASTPGASPHHR 90.937 5.05E-06 765450000 187830 204872 61723 80996 204890 187171 155851 188852 149037 TRUE FALSE 163007.7896 203526.1823 91572.44925 99387.37975 200813.0899 194371.5895 140736.594 148467.4694 131418.0156 1.240376282 1.548693163 0.696802861 0.756269064 1.52804841 1.479033057 1.070907922 1.129734525 1 17.00380354 -1.999705336 0.01604573 3.15E-05 2.129022593 0.010678438 0.29779974 110868.0427 177.0814084 14122.71677 9762.288536 0.010006787 1.999705336 2.128991051 HVLSVLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HVLSVLSK 8 0 A0A2R8Y430;P48637;A0A2R8Y5T7;A0A2R8Y7I7 A0A2R8Y430 GSS Glutathione synthetase 0 134.15 0.00088892 403600000 1451900 1397700 653030 967620 1280100 1267000 1337300 1378900 1698500 FALSE TRUE 1260027.736 1388518.417 968837.4923 1187332.91 1254628.514 1315742.31 1207608.852 1084032.966 1497705.265 0.84130554 0.927097239 0.646881276 0.792768069 0.837700544 0.878505498 0.806306074 0.723795924 1 20.51432231 3.23723403 24.93422424 0.831818928 0.799866776 0.03905582 0.096711883 180.7277322 3396935.051 0.029157213 0.034883084 1726.768151 -3.23723403 -0.031952152 HVLTGSADNSCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HVLTGSADNSCR 12 0 Q13347;Q5TFK1 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ;;; 238.2 3.96E-16 1871170000 1277080 1152830 686610 858703 1189360 1319050 1110420 1326320 1274570 FALSE TRUE 1108310.642 1145256.984 1018656.893 1053684.641 1165694.063 1369794.707 1002731.639 1042696.789 1123891.787 0.986136437 1.019010013 0.906365635 0.937532112 1.037194218 1.218795905 0.892195896 0.927755503 1 20.1000717 HVLVILTDMSSYAEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HVLVILTDMSSYAEALR 17 0 P21281;P15313;C9JL73;C9JNS9 P21281;P15313 ATP6V1B2;ATP6V1B1 "V-type proton ATPase subunit B, brain isoform;V-type proton ATPase subunit B, kidney isoform" 0 ; 182.1 7.67E-10 212308000 156458 135052 84114 126347 98853 102905 126400 158476 135022 FALSE TRUE 135781.6789 134164.8345 124791.8117 155036.0174 96886.0187 106863.8219 114141.7475 124587.1407 119059.853 1.140448904 1.126868807 1.048143506 1.302168729 0.813758931 0.897563866 0.958692159 1.046424446 1 16.86132749 3.235619634 24.99999998 0.955049086 1.144850144 0.590000979 0.086983335 62.40642571 530490.0074 0.02696918 0.031934219 1720.361179 -3.235619634 0.189801058 HVLVTLGEK ddPTM_MDA-MB-175_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 ; 145.17 9.78E-05 6626200000 7873400 7738100 4586800 6119100 7184600 6375800 8720000 10054500 8495700 FALSE TRUE 6832910.241 7687267.912 6804991.822 7508535.18 7041640.516 6621081.152 7874335.742 7904423.419 7491348.024 0.912106902 1.026152821 0.908380147 1.002294267 0.939969748 0.883830404 1.051124006 1.055140329 1 22.83679392 2.214019198 24.99791522 1.040183869 0.94977271 0.46895665 0.044878993 188.4414741 191945.1947 0.017418001 0.011749288 163.6888878 -2.214019198 -0.090411159 HVMSDSSLDLPTVSGQHPPAAAGSGS(ph)PSATSILQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HVMSDSSLDLPTVSGQHPPAAAGSGSPSATSILQK 35 0 Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-9 SYNRG Synergin gamma 1 HVMSDSSLDLPTVSGQHPPAAAGS(0.073)GS(0.672)PS(0.091)AT(0.139)S(0.025)ILQK 94.569 0.00064753 84075000 22163 18047 6721.5 11272 21640 21559 20334 27866 27090 TRUE FALSE 19234.1034 17928.44807 9972.039882 13831.47988 21209.40634 22388.38868 18362.01181 21907.07275 23887.45106 0.805196978 0.750538348 0.417459354 0.579027032 0.887889055 0.937244774 0.768688621 0.917095453 1 14.5439653 3.230615682 24.79947906 0.89578856 0.630333056 0.558458126 0.116535002 125.29693 391103.6899 0.036770632 0.042445642 1700.652894 -3.230615682 -0.265455504 HVNIDHLHVGWYQSTYYGSFVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HVNIDHLHVGWYQSTYYGSFVTR 23 0 A0A087WZK9;B3KS98;O15372;E5RJT0;E5RGU4;E5RFH0 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 146.99 4.24E-08 34220000 27160 39746 13597 21789 22365 18404 20031 25743 21529 FALSE TRUE 23570.73719 39484.90591 20172.55468 26736.52547 21919.98026 19112.01379 18088.3967 20238.05978 18983.86615 1.241619436 2.079919106 1.062615725 1.408381479 1.154663654 1.006750345 0.952829975 1.066066292 1 14.21248621 3.600756186 1.010583964 1.007271664 1.618282032 0.41171409 0.254820854 0.517349305 1.0638761 0.096022065 0.229617825 3988.009518 -3.600756186 0.611010368 HVPVVYVDYPGPASLTQIYGTFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HVPVVYVDYPGPASLTQIYGTFNR 24 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 210.74 3.83E-25 431360000 221620 179680 144770 161900 231110 217790 216810 268820 213890 FALSE TRUE 192332.3555 178499.6702 214781.2562 198661.8695 226511.3632 226168.5222 195783.7996 211334.935 188604.1679 1.01976726 0.946424845 1.138793796 1.053327038 1.20098811 1.19917033 1.038067195 1.120521022 1 17.52500203 4.236544544 24.99979777 1.109446124 0.983096035 0.372616631 0.066938311 50.23137865 622917.3557 0.016800904 0.038012087 17240.28909 -4.236544544 -0.126350088 HVQELRPIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HVQELRPIAR 10 1 Q8TE77;Q8TE77-2;Q8TE77-3;E9PIT5;Q8TE77-5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ;;;; 157.24 5.72E-06 1482142000 361552 344670 242021 303338 346057 370256 318369 363549 455520 FALSE TRUE 313771.9871 342405.8401 359063.1651 372215.5291 339171.1427 384499.9879 287493.6234 285806.8755 401668.9445 0.781170642 0.852457838 0.893928122 0.926672411 0.844404695 0.957255952 0.7157477 0.711548352 1 18.6156474 1.205580871 24.47366292 1.000001555 0.833288145 0.287455342 0.081383507 5733.697145 4254543.425 3.626316939 0.022209643 16.05391174 -1.205580871 -0.16671341 HVSDDMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 HVSDDMK 7 0 Q01518-2;Q01518;Q5T0S3 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 0 ;;;;;; 196.98 0.00043275 4586190000 6246770 6728380 1626790 4478680 5672840 5803350 7269160 8430670 7611460 FALSE TRUE 5421243.517 6684180.829 2413511.085 5495632.746 5559961.583 6026608.63 6564197.982 6627836.828 6711641.87 0.807737305 0.995908447 0.359600696 0.818820916 0.828405581 0.897933583 0.978031622 0.987513481 1 22.67823431 2.73321339 1.544703144 0.990161188 0.739196704 0.318887431 0.156840224 0.471853175 2.286029326 0.071689117 0.061524616 541.0200875 -2.73321339 -0.250964484 HVTAQQPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HVTAQQPSR 9 0 A0A087WUK2;O14979 A0A087WUK2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 113.1 0.0018559 19748000 17517 21488 14630 15008 21051 21533 18368 22588 19514 FALSE TRUE 15202.08407 21346.84391 21705.11693 18415.79578 20632.12629 22361.38844 16586.67419 17757.73198 17207.07715 0.883478579 1.240585122 1.261406382 1.070245436 1.199048863 1.299546009 0.963944896 1.032001648 1 14.07071444 2.215301603 24.99976908 1.0041513 1.165191723 0.290464596 0.117815956 288.2168089 309785.3424 0.046460402 0.031345655 164.1729503 -2.215301603 0.161040423 HVTENRDDVFLDGTGWEGGDEWIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HVTENRDDVFLDGTGWEGGDEWIR 24 1 H7C0I1;B8ZZW5;Q8NBF6-2;Q8NBF6 H7C0I1 AVL9 Late secretory pathway protein AVL9 homolog 0 67.992 0.020791 80499000 20070 15410 13252 13019 20080 18569 14293 22553 17792 FALSE TRUE 17417.69865 15308.7707 19660.71153 15975.16293 19680.44729 19283.36145 12906.86706 17730.21646 15688.65003 1.110210159 0.975786359 1.253180579 1.018262432 1.254438543 1.229128154 0.822688188 1.130130153 1 13.9374336 2.270265048 24.99991055 1.007926442 1.137485712 0.271384361 0.118263541 289.2772039 228102.978 0.042615318 0.033006613 186.3223905 -2.270265048 0.129559271 HVTLPS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 HVTLPSSPR 9 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 HVTLPS(0.5)S(0.5)PR;HVTLPS(0.5)S(0.5)PR;HVTLPS(0.686)S(0.314)PR;HVTLPS(0.5)S(0.5)PR;HVTLPS(0.666)S(0.334)PR;HVTLPS(0.603)S(0.397)PR;HVTLPS(0.678)S(0.322)PR 140.39 7.03E-05 8700370000 4716270 4401930 2414500 2899550 4622630 5337520 4273300 4873590 5383980 TRUE FALSE 4093002.97 4373013.432 3582160.276 3557937.144 4530648.707 5542857.848 3858876.024 3831410.705 4747492.018 0.862140042 0.921120755 0.754537398 0.749435098 0.95432466 1.167533895 0.81282412 0.807038893 1 22.17873414 3.220210063 24.90995041 0.931476619 0.824096986 0.233953198 0.111443822 443.3722556 601853.5956 0.036986708 0.042017568 1660.389824 -3.220210063 -0.107379633 HVTSNAS(ph)DSESSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HVTSNASDSESSYR 14 0 Q12959;Q12959-3;Q12959-5;A0A590UK48;C9JUA9;Q12959-8;A0A590UJ64 Q12959 DLG1 Disks large homolog 1 1 HVTSNAS(0.972)DS(0.028)ESSYR;HVTSNAS(1)DSESSYR;HVT(0.001)S(0.022)NAS(0.889)DS(0.085)ES(0.001)S(0.001)YR 316.72 6.66E-56 773036000 543143 538091 264199 462094 602690 654995 489520 579538 566382 TRUE FALSE 471365.2764 534556.2448 391966.5201 567019.5054 590697.6481 680193.0815 442046.4257 455608.3087 499424.9652 0.943816007 1.070343459 0.784835656 1.135344736 1.182755548 1.361952503 0.885110791 0.912265787 1 18.92990841 3.702577444 24.99426647 1.066055277 0.946732631 0.165529395 0.152107191 1391.200831 966341.7192 0.046474571 0.06893541 5041.705156 -3.702577444 -0.119322646 HVVFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 112.58 0.026876 1641180000 6080280 5016690 3043430 4015570 4334720 4301250 4886450 5882660 6780100 FALSE TRUE 5276755.593 4983735.033 4515242.928 4927366.543 4248467.553 4466721.871 4412562.831 4624698.938 5978564.302 0.882612501 0.833600641 0.755238666 0.824172208 0.710616686 0.747122828 0.738063958 0.773546742 1 22.51136765 1.237677186 24.99239117 1.000000259 0.779159042 0.637434472 0.051326358 14.51249009 410322.2874 0.075821006 0.012918423 17.28531055 -1.237677186 -0.220841217 HVVFIAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HVVFIAQR 8 0 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ;; 124.34 0.0013089 4542274000 1908994 2791120 1422261 1724311 2745040 2855800 2545670 2816180 2138097 FALSE TRUE 1656715.606 2772784.949 2110071.177 2115842.167 2690419.075 2965664.474 2298791.315 2213961.823 1885333.608 0.878738701 1.47071316 1.119203078 1.122264069 1.427025468 1.573018409 1.219302146 1.174307726 1 20.8463884 1.377972131 2.204018019 0.971288716 1.27371559 0.142679371 0.199304187 0.925659295 6.070111467 0.502278818 0.053087016 23.87658059 -1.377972131 0.302426874 HVVLPVDDDSDLNVVASFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HVVLPVDDDSDLNVVASFDR 20 0 Q15291;Q15291-2 Q15291 RBBP5 Retinoblastoma-binding protein 5 0 ; 221.85 7.56E-25 278730000 274100 242090 137259 176581 221770 241570 218280 250960 282970 FALSE TRUE 237876.9905 240499.6948 203637.9115 216676.4149 217357.2109 250863.3542 197111.2392 197294.157 249517.609 0.953347507 0.963858606 0.816126414 0.868381257 0.871109706 1.005393388 0.789969253 0.790702339 1 17.92878211 4.259171123 24.94172672 0.868987184 0.958603153 0.160748787 0.075275599 395.866729 479048.1082 0.018957087 0.050033147 18162.31161 -4.259171123 0.089615969 HVVQDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HVVQDYR 7 0 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 0 71.342 0.054575 41981000 65770 68230 39894 55778 56701 71056 62792 78915 76578 FALSE TRUE 57078.32786 67781.79264 59186.87184 68443.24741 55572.76103 73789.5703 56702.4415 62039.64137 67525.03608 0.845291335 1.003802391 0.876517441 1.013598087 0.822994911 1.092773504 0.839724712 0.918765024 1 16.04313489 4.770396034 22.66515874 0.939590987 0.845290751 0.118398565 0.084783516 8055.704394 5734890.466 0.018504021 2.036286814 58938.08674 -4.770396034 -0.094300235 HVVRPPPRS(ph)PEPDTLPLAAGSDHPLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HVVRPPPRSPEPDTLPLAAGSDHPLPR 27 2 H3BVB1;H3BME1;H7C112;H3BPZ0;Q6PCT2-2;Q6PCT2-3;Q6PCT2 H3BVB1 FBXL19 F-box/LRR-repeat protein 19 1 HVVRPPPRS(1)PEPDTLPLAAGSDHPLPR;HVVRPPPRS(1)PEPDTLPLAAGSDHPLPR;HVVRPPPRS(0.984)PEPDT(0.016)LPLAAGSDHPLPR 188.77 3.83E-18 992790000 297118 244491 113698 154289 259317 258944 255371 283443 182193 TRUE FALSE 257853.1035 242884.9225 168682.7331 189322.6756 254157.099 268905.7432 230605.1597 222830.9202 160654.3511 1.605017864 1.51184777 1.049973013 1.178447234 1.582011924 1.673815501 1.435411853 1.38702076 1 17.29360053 4.462662414 24.99891036 1.351226856 1.581725565 0.166614732 0.21349031 398.7918826 689499.7823 0.056303151 0.149094562 29017.66178 -4.462662414 0.230498709 HWDHLTQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HWDHLTQVK 9 0 P30084 P30084 ECHS1 "Enoyl-CoA hydratase, mitochondrial" 0 126.07 0.00027983 414250000 402350 400310 216230 470550 486050 515990 462760 603930 601340 FALSE TRUE 349178.4281 397680.3373 320799.5512 577395.5694 476378.5559 535840.4692 417881.6064 474784.2693 530250.2702 0.658516266 0.74998611 0.604996488 1.08891141 0.898403231 1.010542567 0.788083722 0.895396563 1 19.01631393 3.750329845 24.99961699 0.932232305 0.67904826 0.684221687 0.087870379 461.7107652 980740.7511 0.022955769 0.039349134 5627.685833 -3.750329845 -0.253184045 HWDQDDDFEFTGSHLTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HWDQDDDFEFTGSHLTVR 18 0 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 ; 282.5 1.26E-39 1039260000 347440 300800 138562 212558 284890 302210 252890 346750 301280 FALSE TRUE 301524.9237 298824.025 205571.0467 260822.5426 279221.2464 313836.2143 228364.7667 272600.2109 265663.0216 1.134990191 1.124823557 0.773803766 0.981779628 1.051035423 1.181331946 0.859603137 1.02611274 1 18.0192379 4.426797901 24.99999049 0.986281935 1.132455139 0.244009579 0.10813232 131.8177151 65484.97321 0.026719756 0.07069387 26717.62812 -4.426797901 0.146173204 HWDQNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HWDQNER 7 0 F5GZS6;J3KPF3;P08195-2;P08195-3;P08195;P08195-4;F5GZI0 F5GZS6 SLC3A2 4F2 cell-surface antigen heavy chain 0 108.7 0.0071947 295070000 115380 102100 75133 88880 72871 117780 78051 96855 77659 FALSE TRUE 100132.2407 101429.2984 111467.5701 109061.5624 71421.00967 122311.0728 70481.62603 76143.31198 68478.24149 1.462249008 1.481190173 1.62778085 1.59264549 1.04297377 1.786130458 1.029255783 1.111934394 1 16.06335803 2.212970684 24.99921869 1.059835914 1.487431821 0.555628899 0.190156267 165.73091 161903.9628 0.07370434 0.049711488 163.2941716 -2.212970684 0.427595907 HWELTAEGEEIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HWELTAEGEEIAR 13 0 K7ER00;Q9Y285;Q9Y285-2;K7ER16;K7EK06 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ; 147.73 4.07E-05 218510000 870670 726060 673380 696610 879420 901810 835690 998980 983190 FALSE TRUE 755608.7535 721290.4641 999028.8203 854785.9475 861921.2626 936503.2142 754644.9124 785355.9011 866958.3983 0.871562874 0.831978173 1.15233767 0.985959591 0.994189876 1.080217016 0.870451124 0.905874956 1 19.72560324 HWGGNVLGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HWGGNVLGPK 10 0 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 ; 113.22 0.0015171 5842900000 7278500 9798800 5517000 6695600 9613500 8024000 11007600 12127200 11516000 FALSE TRUE 6316627.784 9734431.038 8185039.653 8215938.316 9422210.158 8332688.472 9940084.646 9533892.654 10154591.6 0.622046463 0.958623588 0.806043214 0.809086041 0.92787682 0.820583318 0.978875866 0.938875046 1 23.27562888 7.541982177 0.121471958 1.130700268 2.02E-14 0.47260976 0.082557487 175.9698069 2.15250494 2.822482004 33.55355509 34832302.01 -7.541982177 -1.130700268 HWMLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HWMLDK 6 0 P62701;C9JEH7;P22090;Q8TD47 P62701 RPS4X;RPS4Y1;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1;40S ribosomal protein S4, Y isoform 2" 0 ;;;; 118.06 0.022193 7424940000 15062950 13060970 9675970 10450770 12441790 11034820 15072690 16287480 15557860 FALSE TRUE 13072342.99 12975171.63 14355301.46 12823777.06 12194222.72 11459336.67 13610942.84 12804529.15 13718627.51 0.952890002 0.945806832 1.046409449 0.934771138 0.888880663 0.835312181 0.992150478 0.933368089 1 23.70963282 3.512084686 24.84218842 0.928624718 0.980192199 0.167915648 0.053491183 1043.71397 741576.1349 0.015075544 0.022348921 3251.506946 -3.512084686 0.051567482 HWNSFNTEYFLESQAVIEMVQEAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HWNSFNTEYFLESQAVIEMVQEAGR 25 0 C9J8U3;A0A0A0MRW7;Q7Z2E3-4;Q7Z2E3-5;Q7Z2E3-10;Q7Z2E3-8;Q7Z2E3-7;Q7Z2E3;A0A5K1VW64;Q7Z2E3-2;Q7Z2E3-3 C9J8U3 APTX Aprataxin 0 134.31 5.15E-05 27206000 22717 19017 10939 15648 18474 23399 21271 23279 20879 FALSE TRUE 19714.89089 18892.07607 16229.13699 19201.11756 18106.40354 24299.17467 19208.14169 18300.96701 18410.70841 1.070838257 1.02614607 0.881505297 1.042932034 0.983471312 1.319839201 1.043313558 0.994039263 1 14.16825752 HWPFMVVNDAGR ddPTM_MDA-MB-175_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 ; 172.11 3.66E-05 1728120000 1205900 1205400 818440 1208010 1331740 1306300 1165240 1285990 2728500 FALSE TRUE 1046537.26 1197481.648 1214240.322 1482307.134 1305240.98 1356554.206 1052235.204 1010991.046 2405939.838 0.434980644 0.497718866 0.504684407 0.616103159 0.542507738 0.563835464 0.437348926 0.420206287 1 21.19816914 1.232802714 24.99583318 1.000000801 0.501979331 0.866735471 0.061347152 71.91529809 312161.2343 0.144894365 0.016694601 17.09238686 -1.232802714 -0.498021471 HWPFMVVNDAGRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HWPFMVVNDAGRPK 14 1 P11142;E9PKE3;E9PNE6;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;; 212.59 1.34E-09 14365140000 4772680 4113060 2217680 3090820 3951370 3496210 4601480 5372230 3638760 FALSE TRUE 4141958.246 4086041.038 3290157.466 3792637.921 3872745.468 3630711.461 4155229.178 4223420.421 3208589.938 1.290896726 1.27346938 1.025421612 1.182026371 1.20699296 1.131559823 1.295032789 1.316285503 1 21.61350799 2.248060646 24.99642657 1.231015427 1.182682328 0 0.111865929 775.7779851 2041226.381 0.04227826 0.032319775 177.0356158 -2.248060646 -0.048333099 HWVAPGGPYSAETPGVPS(ph)PIAALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HWVAPGGPYSAETPGVPSPIAALK 24 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 HWVAPGGPYSAETPGVPS(1)PIAALK;HWVAPGGPYSAETPGVPS(1)PIAALK 171.73 4.07E-12 1456520000 1299010 1022970 600550 770190 924220 883570 1064920 1272970 1110900 TRUE FALSE 1127342.537 1016250.043 890977.9887 945073.4111 905829.8302 917561.5096 961644.2223 1000755.272 979570.6675 1.15085371 1.037444338 0.909559686 0.96478329 0.924721268 0.936697617 0.981699692 1.021626417 1 19.90179005 4.592277393 3.235485549 0.966827257 1.153299325 0.751205314 0.034664995 0.154078071 2.665308299 0.009894117 0.057552308 39109.06141 -4.592277393 0.186472068 HWWQDLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HWWQDLFR 8 0 Q9Y6D6;E5RIF2;E5RHL7;Q9Y6D5 Q9Y6D6;Q9Y6D5 ARFGEF1;ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 1;Brefeldin A-inhibited guanine nucleotide-exchange protein 2 0 144.12 0.0012204 0 43394 67762 52449 46990 71520 72046 77458 61563 95991 FALSE TRUE 37659.37295 67316.86696 77813.51183 57659.7977 70096.89193 74817.65624 69946.13508 48398.23153 84643.05333 0.444919831 0.795302914 0.919313621 0.681211221 0.828147015 0.883919628 0.826365925 0.571792127 1 16.36910405 4.738408345 9.669653371 0.79693399 0.443880611 0.47736953 0.120046536 0.069899021 185.7650236 0.029116288 0.163381138 54753.05359 -4.738408345 -0.35305338 HYAMQEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HYAMQEAK 8 0 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 ; 168.27 0.00030783 517420000 449320 513850 399830 472450 568580 596500 619680 590520 569870 FALSE TRUE 389941.2236 510474.4855 593189.1254 579726.9934 557266.3704 619447.741 559583.529 464241.8934 502500.6178 0.776001481 1.015868374 1.18047442 1.153684141 1.108986438 1.232730307 1.113597694 0.923863329 1 18.93876584 4.686115998 3.30012702 1.093663122 0.749787683 0.574034863 0.08783348 0.239547768 4.321374115 0.025386706 0.192985932 48541.81363 -4.686115998 -0.343875439 HYCDSEKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HYCDSEKPR 9 1 Q9UGI8-2;Q9UGI8;H7BYK1 Q9UGI8-2 TES Testin 0 ;;;; 222.42 2.31E-07 1409648000 1812360 1578210 1002328 1339323 1314355 1383698 1602800 1941940 2223150 FALSE TRUE 1572852.034 1567842.635 1487057.173 1643436.757 1288201.907 1436929.757 1447360.703 1526671.243 1960331.74 0.802339728 0.799784344 0.758574247 0.838346247 0.657134648 0.733003363 0.738324373 0.778782087 1 20.90266639 1.237959599 4.599562463 1.019277995 0.760325707 0.701618071 0.048643089 0.111508387 5.146505451 0.094237911 0.012369375 17.29655447 -1.237959599 -0.258952288 HYCESLRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HYCESLRPR 9 1 Q9NZU5;B4DEY6;Q9NZU5-2 Q9NZU5 LMCD1 LIM and cysteine-rich domains protein 1 0 ; 169.09 3.53E-05 982700000 85141 86201 55876 61005 89481 122330 93439 85932 97043 FALSE TRUE 73889.40113 85634.73996 82897.82049 74857.11765 87700.50317 127036.1143 84377.30016 67556.11052 85570.68709 0.863489632 1.000748537 0.968764227 0.874798604 1.024889552 1.484575134 0.986053788 0.789477248 1 16.38482905 5.947373884 0.831216145 1.015748753 1.15E-07 0.069628458 0.180517462 59.00651368 6.679585093 0.06909654 87.0949153 885877.9347 -5.947373884 -1.015748639 HYCTVANPVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HYCTVANPVSR 11 0 Q14764;H3BQK6;H3BP76;H3BRL2;H3BNF6;H3BUK7 Q14764 MVP Major vault protein 0 136.38 0.00010048 109190000 207870 212850 134040 165400 187150 213820 207990 226200 246800 FALSE TRUE 180399.4528 211451.7743 198862.1923 202956.598 183426.0812 222045.7938 187819.1618 177828.8903 217623.5852 0.828951755 0.971639973 0.913789708 0.932603871 0.842859385 1.020320447 0.863045987 0.817139788 1 17.73147539 HYEDGYPGGSDNYGS(ph)LSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HYEDGYPGGSDNYGSLSR 18 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 HYEDGYPGGSDNYGS(0.995)LS(0.005)R;HYEDGYPGGSDNYGS(0.974)LS(0.026)R;HYEDGYPGGSDNYGS(0.99)LS(0.01)R;HYEDGYPGGSDNYGS(0.826)LS(0.174)R;HYEDGYPGGS(0.001)DNYGS(0.977)LS(0.021)R;HYEDGYPGGS(0.002)DNY(0.021)GS(0.755)LS(0.223)R 263.47 7.05E-31 3905350000 3189310 3260000 2214910 2062070 3079290 4147090 2622870 2862680 4331120 TRUE FALSE 2767834.603 3238584.845 3286047.884 2530294.51 3018018.154 4306631.236 2368504.471 2250518.159 3819099.928 0.724734795 0.847996886 0.860424693 0.662536869 0.790243306 1.127656075 0.620173474 0.589279726 1 21.86480124 HYEDGYPGGSDNYGSLSR ddPTM_MDA-MB-175_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 ;;; 262.59 7.59E-31 2186490000 1681570 1378860 753270 1177390 1481680 1649050 1194370 1592780 1368820 FALSE TRUE 1459346.264 1369802.178 1117553.892 1444734.395 1452197.467 1712490.021 1078540.181 1252176.392 1206999.659 1.209069326 1.134881992 0.925894124 1.196963383 1.203146543 1.418799092 0.893571239 1.037428953 1 20.20299384 2.194227367 24.9999936 0.986113235 1.169417362 0.374884121 0.123624374 161.7001019 91183.29286 0.052268924 0.035239899 156.3966215 -2.194227367 0.183304127 HYEMLANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 HYEMLANR 8 0 A0A2R8YFH5;Q15437 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;;; 182.68 0.00022728 3221442000 1320852 1505880 1442407 1523016 1234153 1385086 1485842 1445212 2893047 FALSE TRUE 1146298.062 1495987.775 2139959.85 1868840.061 1209595.77 1438371.155 1341745.272 1136164.66 2551034.279 0.449346397 0.586424019 0.8388597 0.73258132 0.474158964 0.563838427 0.525961287 0.445374125 1 21.28265085 1.22722831 24.98636186 1.000000925 0.578203074 0.532017478 0.124655287 455.7668274 1004844.438 0.506047387 0.033180792 16.87439885 -1.22722831 -0.421797851 HYEMQQQQFQHLYQEWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HYEMQQQQFQHLYQEWER 18 0 P49750;F8VU51 P49750 YLPM1 YLP motif-containing protein 1 0 ; 162.77 2.01E-11 363900000 150401 127778 71722 102341 118233 122579 118217 132586 114981 FALSE TRUE 130525.1268 126938.6179 106406.9991 125579.0882 115880.3946 127294.6934 106752.3335 104233.5157 101388.0772 1.28738142 1.252007351 1.049502092 1.238598184 1.14293907 1.255519357 1.052908158 1.028064824 1 16.62952848 2.135092874 5.642721007 1.02355539 1.197860119 0.602080675 0.068135628 0.143127971 6.67585842 0.028001012 0.018692775 136.4874983 -2.135092874 0.17430473 HYEVEILDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 HYEVEILDAK 10 0 Q9NZ01;M0R3C3;Q9NZ01-2 Q9NZ01 TECR Very-long-chain enoyl-CoA reductase 0 ;; 115.78 0.0011773 660610000 1412680 1241630 973400 1594330 1662920 1421840 1128930 2346540 2440000 FALSE TRUE 1225990.759 1233473.651 1444139.496 1956346.994 1629831.145 1476539.105 1019446.542 1844750.682 2151545.98 0.569818526 0.57329644 0.671210148 0.909275011 0.757516298 0.686268906 0.473820477 0.857407046 1 21.03694224 1.518183225 5.500939427 0.969714683 0.672939994 0.486515909 0.117666709 0.12476433 8.040249044 0.092782038 0.032103973 32.97488011 -1.518183225 -0.296774689 HYFQNTQGLIFVVDSNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 310.97 3.73E-61 12614410000 5298320 5602010 3412970 5386080 5763430 5556730 4964550 6634520 11117070 FALSE TRUE 4598133.588 5565210.027 5063493.708 6609071.785 5648749.019 5770500.999 4483088.705 5215779.528 9802822.649 0.469062203 0.567715058 0.516534256 0.674200893 0.57623699 0.588657084 0.45732631 0.532069151 1 23.22476579 1.237293538 24.99999443 1.000000543 0.548526328 0.84064175 0.0618843 12.42232048 244997.5131 0.092625541 0.015342924 17.27004775 -1.237293538 -0.451474215 HYFQNTQGLIFVVDSNDRER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 275.49 9.79E-45 8348580000 1738880 1877610 801971 1071681 1674570 1771150 1632440 1969510 748885 FALSE TRUE 1509082.602 1865275.856 1189806.858 1315022.551 1641249.333 1839287.287 1474126.22 1548345.613 660352.6684 2.285267667 2.82466619 1.801774892 1.991394316 2.485413343 2.785310599 2.232331738 2.344725307 1 19.33287719 1.238540212 24.02667768 0.999999762 2.343962422 0.645904459 0.312703506 0.200518505 225844.4968 0.430386096 0.077240273 17.3196939 -1.238540212 1.343962661 HYGFQLYQSDPSGNYGGWK ddPTM_MDA-MB-175_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 ; 256.96 5.61E-31 1201690000 1102530 879850 709280 1076750 1042940 886370 1065760 1289950 2046990 FALSE TRUE 956827.867 874070.2074 1052290.18 1321242.545 1022187.534 920469.2275 962402.7592 1014104.231 1804997.174 0.530099371 0.484250181 0.582987162 0.731991475 0.56630977 0.509956049 0.533187959 0.561831478 1 20.78356515 1.238458027 24.99146565 1.000000479 0.563120725 0.809758246 0.066631045 1.096825087 265882.1358 0.096944123 0.017312198 17.31641666 -1.238458027 -0.436879754 HYGGLTGLNK ddPTM_MDA-MB-175_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 ; 179.37 2.11E-06 9011300000 9562400 9132300 4725800 6673000 8869200 8656500 9983700 11828300 10628000 FALSE TRUE 8298704.612 9072309.32 7011212.687 8188206.64 8692720.272 8989521.157 9015482.311 9298910.093 9371569.947 0.885519146 0.968067183 0.748136409 0.873728381 0.927562865 0.959233214 0.962003417 0.992246779 1 23.15985932 2.907111991 1.925850776 0.982693072 0.867946947 0.482117202 0.053644142 0.299683323 2.221349794 0.020566604 0.020985663 807.4432176 -2.907111991 -0.114746125 HYGPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HYGPAK 6 0 Q9Y5Z4-2;Q9Y5Z4;Q5THN1;C9IZA0 Q9Y5Z4-2 HEBP2 Heme-binding protein 2 0 70.49 0.090731 163300000 668580 731000 448000 531760 618570 657950 819050 897290 860500 FALSE TRUE 580225.459 726198.0129 664654.2985 652504.2354 606261.6672 683261.7623 739618.6571 705411.5162 758772.6703 0.764689454 0.95706928 0.875959724 0.859946939 0.799003036 0.900482831 0.974756585 0.929674386 1 19.53330819 2.423423988 4.645044768 0.959447625 0.858092501 0.49866815 0.052908534 0.182953416 8.352111131 0.019483157 0.015074133 265.1087048 -2.423423988 -0.101355124 HYGPGWVSMANAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HYGPGWVSMANAGK 14 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 213.06 8.45E-08 0 1027400 1020400 537090 824310 916030 949620 877870 985310 1297400 FALSE TRUE 891626.4869 1013696.925 796828.5205 1011482.184 897802.7952 986152.4959 792734.3025 774609.1242 1144022.85 0.779378215 0.886081012 0.696514515 0.884145089 0.784776978 0.862004195 0.692935725 0.677092354 1 20.12568444 2.254463205 24.99717565 0.762440213 0.815009877 0 0.10371641 768.056929 1207302.586 0.037431902 0.028898117 179.6648854 -2.254463205 0.052569663 HYGYNSYSVSNSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HYGYNSYSVSNSEK 14 0 P07858 P07858 CTSB Cathepsin B;Cathepsin B light chain;Cathepsin B heavy chain 0 ;;; 216.15 6.24E-12 1398320000 1442150 1464240 680864 1318010 1555760 1515940 1491520 1854160 2244690 FALSE TRUE 1251566.224 1454621.311 1010132.108 1617284.315 1524803.42 1574259.193 1346872.62 1457662.313 1979325.305 0.632319619 0.734907651 0.510341633 0.817088687 0.770365243 0.79535142 0.680470571 0.736444034 1 20.91657731 1.237559866 4.254471745 1.028332195 0.709627974 0.520151093 0.08805146 0.184283537 6.387643768 0.180699833 0.022017654 17.28064173 -1.237559866 -0.318704222 HYIFNPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HYIFNPR 7 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 83.801 0.022013 253830000 257420 187070 132930 164740 207010 273250 239870 266560 201920 FALSE TRUE 223401.2948 185841.1249 197215.3926 202146.7349 202890.906 283762.1043 216607.4443 209558.2184 178049.2476 1.254716309 1.043762483 1.107645189 1.135341697 1.139521277 1.593728185 1.216559167 1.176967728 1 17.44191681 2.960813898 24.99886258 1.247904001 1.128166327 0.113572696 0.152998447 1181.378925 753663.2429 0.05040305 0.050412368 913.7216143 -2.960813898 -0.119737675 HYLDFINHYANLFHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HYLDFINHYANLFHEK 16 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 248.2 7.71E-21 1652260000 1500780 1470020 964340 1074870 1343440 1268720 1561830 1845220 1674690 FALSE TRUE 1302448.121 1460363.342 1430698.05 1318935.662 1316708.172 1317528.479 1410363.967 1450634.063 1476710.056 0.881993127 0.988930316 0.968841543 0.893158177 0.891649764 0.89220526 0.955071689 0.982341833 1 20.49395516 1.853586677 2.69562782 0.993121879 0.922553468 0.408614608 0.035355485 0.294811034 3.869495647 0.026669683 0.010566449 71.3816655 -1.853586677 -0.070568411 HYLFYDGESVSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HYLFYDGESVSGK 13 0 O75436;S4R3Q6;O75436-2;S4R2Y3 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 149.26 4.37E-05 601400000 908110 712460 370920 537430 755650 604530 749940 903760 874310 FALSE TRUE 788100.9626 707779.8033 550298.1527 659461.6956 740614.0434 627786.6603 677210.9342 710497.9571 770950.0678 1.022246441 0.918061795 0.71379221 0.855388336 0.960651116 0.81430262 0.878410889 0.921587515 1 19.5562779 1.336578188 2.167889811 1.020598331 0.875175514 0.174372787 0.082315308 0.967451201 5.601580058 0.256949529 0.022632721 21.70591952 -1.336578188 -0.145422817 HYLGHNDDIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HYLGHNDDIK 10 0 O95834;O95834-2;O95834-3;K7EIK7;A0A0C4DGQ7;C9JRL6;K7ERY9;K7EKU5;K7ERR2;K7EIM1;K7EQR0 O95834 EML2 Echinoderm microtubule-associated protein-like 2 0 ;;; 162.38 3.92E-06 2033840000 1493140 1352810 1029750 1084570 1338490 1115210 1567860 1812040 1618500 FALSE TRUE 1295817.766 1343923.302 1527740.544 1330838.195 1311856.668 1158112.85 1415809.179 1424549.347 1427162.774 0.907967745 0.941674858 1.070473931 0.932506242 0.919206058 0.811479161 0.992044639 0.998168796 1 20.44471846 2.040116375 24.99986191 0.997800249 0.93405454 0.201238309 0.06200485 262.2085925 163403.0194 0.026796276 0.018066024 109.6772052 -2.040116375 -0.063745709 HYLHSQACSVFNYHLS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HYLHSQACSVFNYHLSPR 18 0 P41162 P41162 ETV3 ETS translocation variant 3 1 HYLHSQACSVFNYHLS(1)PR;HYLHSQACSVFNYHLS(1)PR 275.15 7.76E-39 2209810000 481840 834670 403660 787920 1152690 1118140 984960 1287660 1012290 TRUE FALSE 418163.6232 829186.9978 598871.3262 966829.2786 1129753.724 1161155.569 889438.7308 1012303.93 892618.2294 0.468468612 0.928938006 0.670915411 1.083138622 1.265662841 1.300842321 0.996438008 1.134083863 1 19.76768374 3.68924673 5.017267733 1.138236359 0.712290132 0.669335622 0.145890501 0.121564679 7.046194375 0.039349783 0.060558791 4889.300501 -3.68924673 -0.425946227 HYLPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HYLPVK 6 0 P07686 P07686 HEXB Beta-hexosaminidase subunit beta;Beta-hexosaminidase subunit beta chain B;Beta-hexosaminidase subunit beta chain A 0 87.758 0.052076 282760000 675540 677940 409810 535830 710420 723970 702690 789290 757000 FALSE TRUE 586265.6774 673486.5675 607995.4867 657498.3911 696284.0319 751821.5944 634543.232 620506.4758 667508.3224 0.87828969 1.008956061 0.910843305 0.985004035 1.04310914 1.126310443 0.950614712 0.929586126 1 19.3484263 3.546434102 6.579080703 1.002375927 0.940980529 0.236878328 0.061885626 0.476742792 37.21715838 0.018691194 0.027668191 3519.120209 -3.546434102 -0.061395398 HYNGEAYEDDEHHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HYNGEAYEDDEHHPR 15 0 P31689 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 81.632 0.0046667 188670000 85391 71174 36333 53884 68602 83494 73184 74451 64254 FALSE TRUE 74106.363 70706.45331 53903.76033 66119.18577 67236.95442 86706.06821 66086.62694 58530.23303 56657.96532 1.307960188 1.247952568 0.951388918 1.166988355 1.186716714 1.530342075 1.1664137 1.033045093 1 15.78999117 1.766739624 3.950233773 1.013128599 1.223551264 0.27253235 0.142236423 0.284831737 9.031522212 0.095682463 0.040178556 58.44395852 -1.766739624 0.210422666 HYPVFENPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HYPVFENPK 9 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISU1;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 114.84 0.0015728 324890000 799970 707350 434520 526080 691200 618870 780760 865600 790320 FALSE TRUE 694251.9376 702703.3713 644655.3254 645534.5046 677446.4723 642678.3294 705042.0154 680498.1761 696889.2699 0.996215565 1.008342934 0.925046996 0.926308572 0.972100593 0.922210109 1.011698767 0.976479629 1 19.41056992 2.219680225 24.99987813 0.992631966 0.958294234 0.253937008 0.030263243 388.6140192 514567.2275 0.012854791 0.008682728 165.836539 -2.219680225 -0.034337732 HYQEEGQGTEVVQGVLLGLVVEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 HYQEEGQGTEVVQGVLLGLVVEDR 24 0 A0A087WZK9;B3KS98;O15372;E5RGU4;E5RFH0;E5RFW7 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 ;;;;; 206.32 8.76E-25 751377000 608037 607632 394652 501575 594528 608977 653699 715337 681405 FALSE TRUE 527683.3699 603640.4254 585507.0272 615465.2698 582698.056 632404.7393 590303.3716 562367.7493 600850.0772 0.878228014 1.004644001 0.974464429 1.024324192 0.969789434 1.052516698 0.982447026 0.935953528 1 19.19664553 4.743338217 24.71694937 0.989595846 0.87822796 0.562153379 0.031709872 356.3296335 1843400.129 0.008047635 0.064119456 55378.1211 -4.743338217 -0.111367885 HYQGEEKS(ph)D ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HYQGEEKSD 9 1 P13984 P13984 GTF2F2 General transcription factor IIF subunit 2 1 HYQGEEKS(1)D;HYQGEEKS(1)D;HYQGEEKS(1)D;HYQGEEKS(1)D 164.48 3.77E-05 1817040000 3740570 3163650 1994220 2394360 2437660 2723720 3467730 4335960 3731190 TRUE FALSE 3246244.197 3142867.775 2958631.462 2938036.034 2389155.335 2828503.271 3131430.078 3408748.696 3290092.969 0.986672482 0.955251965 0.899254669 0.892994837 0.726166512 0.859703144 0.95177556 1.036064552 1 21.64969692 2.001031717 3.900707771 1.01625838 0.88385787 0.38646485 0.068508935 0.233075192 7.893017848 0.03804476 0.020949893 100.2378441 -2.001031717 -0.13240051 HYSNWETVLILEELRGDEGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HYSNWETVLILEELRGDEGTR 21 1 Q5TFE4;Q5TFE4-2 Q5TFE4 NT5DC1 5-nucleotidase domain-containing protein 1 0 162.85 1.09E-11 84099000 55054 62180 18310 26655 71253 67145 58370 59367 33250 FALSE TRUE 47778.47441 61771.53549 27164.77724 32707.42515 69835.2047 69728.1116 52709.28638 46671.82904 29319.22288 1.629595525 2.106861281 0.926517642 1.115562485 2.381891396 2.378238737 1.797772288 1.591850822 1 14.83955924 3.261943411 24.99895038 1.825189663 1.45492807 0.130131664 0.494618841 573.3563524 612981.166 0.152914887 0.197292132 1827.862026 -3.261943411 -0.370261593 HYTEAIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HYTEAIKR 8 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 194.2 0.00010818 1059160000 2138900 1574290 649690 1041560 1500350 1506230 1736470 1874180 1308710 FALSE TRUE 1856238.946 1563948.385 963882.2571 1278062.117 1470495.97 1564175.643 1568067.407 1473401.192 1153995.795 1.608531811 1.355246174 0.835256299 1.107510203 1.274264583 1.355443105 1.358815529 1.276782115 1 20.13820654 4.479833178 24.99955097 1.192737148 1.545210532 0.416351902 0.164647407 98.16551796 904910.3793 0.043796809 0.120697263 30187.91914 -4.479833178 0.352473384 HYVGELYNYGVDHLGEEAILQVHDKEVLASQLLVLTGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HYVGELYNYGVDHLGEEAILQVHDKEVLASQLLVLTGQR 39 1 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 ; 69.334 0.0012133 809870000 589890 548300 264996 327460 542640 459130 589820 657840 219337 FALSE TRUE 511934.5419 544698.1812 393148.952 401814.7979 531842.5257 476793.0282 532619.3472 517166.0353 193407.2297 2.646925571 2.816327921 2.032752098 2.077558313 2.749858557 2.465228569 2.753875064 2.67397468 1 17.5612822 4.259979794 24.89213303 2.334576252 2.731627 0.113208064 0.519949885 583.408548 677991.4676 0.127590163 0.336868414 18196.16197 -4.259979794 0.397050749 HYYEVSCHDQGLCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HYYEVSCHDQGLCR 14 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ;;; 208.27 4.78E-09 2833270000 911950 998750 308360 623490 984870 1035520 780450 946000 1146080 FALSE TRUE 791433.4969 992189.1455 457483.9274 765062.9339 965273.0139 1075357.124 704762.0791 743705.2618 1010591.728 0.783138705 0.98179029 0.452689167 0.757044524 0.955156259 1.064086609 0.697375666 0.735910696 1 19.94676885 3.391214373 9.12849581 0.865012732 0.737261128 0.150354473 0.167874708 0.68904976 66.36451051 0.050433497 0.065130769 2461.58237 -3.391214373 -0.127751604 HYYFCMMTEAEQDKWQAVLQDCIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HYYFCMMTEAEQDKWQAVLQDCIR 24 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 303.13 1.37E-62 971090000 922730 989850 557010 704170 772450 727770 991180 1403880 706790 FALSE TRUE 800788.8926 983347.6102 826381.8991 864062.5611 757079.7563 755767.7828 895055.5162 1103671.187 623234.0914 1.284892633 1.577814217 1.32595747 1.386417356 1.214759858 1.212654753 1.436146592 1.770877432 1 19.24941463 2.010434427 24.56143452 1.489404577 1.340051607 0 0.214111546 413.5940846 973548.3035 0.085801852 0.05777838 102.4317109 -2.010434427 -0.14935297 HYYTGTQGLIFVVDCADRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HYYTGTQGLIFVVDCADRDR 20 1 P62330 P62330 ARF6 ADP-ribosylation factor 6 0 ;;; 245.03 3.74E-30 1167046000 297807 277028 154138 185207 287451 258560 288050 307533 170110 FALSE TRUE 258451.0504 275208.1848 228679.6524 227261.0801 281731.2875 268506.9705 260114.9553 241769.4612 149999.7896 1.72300942 1.834723806 1.524533154 1.515075992 1.878211218 1.790048981 1.734102135 1.611798669 1 17.19460095 1.221181185 3.11882084 0.853718072 1.711719718 0.782714563 0.117289096 0.189968981 2.323671573 0.415793918 0.031776988 16.6410676 -1.221181185 0.858001646 IAAASSDLYLRPGSEQPGRPGS(ph)HGYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IAAASSDLYLRPGSEQPGRPGSHGYVR 27 2 O75376;O75376-2;A0A088AWL3;E7EVK1 O75376 NCOR1 Nuclear receptor corepressor 1 1 IAAASSDLYLRPGS(0.007)EQPGRPGS(0.992)HGYVR 47.195 0.066711 159400000 186710 131330 121530 107820 135190 132390 147230 180720 159160 TRUE FALSE 162035.8004 130467.2846 180302.3145 132302.1789 132499.9835 137483.129 132951.6573 142074.4344 140344.2861 1.154559298 0.929623059 1.284714323 0.942697295 0.944106719 0.979613298 0.947325046 1.012327885 1 17.0986108 IAAHLADFTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IAAHLADFTPR 11 0 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 99.283 0.0030409 0 72680 64860 48114 45262 65787 62871 49148 70212 80482 FALSE TRUE 63075.15385 64433.93039 71382.09133 55539.42889 64477.96741 65289.68805 44381.63452 55197.71019 70967.50965 0.888789168 0.907935627 1.005841852 0.782603605 0.908556151 0.91999407 0.625379624 0.777788462 1 16.11487106 IAALQAFADQLIAAGHYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IAALQAFADQLIAAGHYAK 19 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 257.81 5.25E-31 534210000 1497730 1341640 910570 1147200 1347090 1233400 1431310 1674290 1592630 FALSE TRUE 1299801.186 1332826.679 1350924.698 1407689.294 1320285.545 1280849.696 1292501.777 1316256.113 1404351.096 0.925552869 0.949069419 0.961956523 1.00237704 0.940139221 0.912058032 0.920355159 0.937269972 1 20.42147223 3.039692863 24.99950738 0.938052899 0.96065061 0.073180412 0.029694323 354.6407853 223358.8035 0.009236026 0.010472646 1095.703031 -3.039692863 0.022597711 IAAPELHKGDS(ph)DS(ph)EEDEPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IAAPELHKGDSDSEEDEPTK 20 1 Q92733 Q92733 PRCC Proline-rich protein PRCC 2 IAAPELHKGDS(1)DS(0.991)EEDEPT(0.009)K;IAAPELHKGDS(1)DS(1)EEDEPTK;IAAPELHKGDS(1)DS(0.967)EEDEPT(0.033)K;IAAPELHKGDS(1)DS(1)EEDEPTK 172.32 3.72E-12 1438640000 2588200 1934100 1793320 1644350 1938560 1419220 2702190 3098460 2822230 TRUE FALSE 2246162.812 1921394.77 2660575.55 2017724.8 1899986.449 1473818.312 2440132.03 2435878.441 2488589.184 0.902584816 0.772081942 1.069109987 0.810790633 0.763479348 0.592230458 0.980528263 0.978819026 1 21.24689666 2.060251935 24.9999997 0.985437589 0.821626906 0.308338043 0.11861887 89.4435411 37111.62389 0.049837761 0.033600607 114.8819861 -2.060251935 -0.163810683 IAAPELHKGDS(ph)DS(ph)EEDEPTKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IAAPELHKGDSDSEEDEPTKK 21 2 Q92733 Q92733 PRCC Proline-rich protein PRCC 2 IAAPELHKGDS(1)DS(1)EEDEPTKK 93.966 0.00088105 105590000 97695 61059 70776 55985 56364 38932 98501 107920 93943 TRUE FALSE 84784.35822 60657.89941 105003.5103 68697.24993 55242.46667 40429.73923 88948.38818 84842.14783 82837.16556 1.023506269 0.732254647 1.267589368 0.82930469 0.666880214 0.488062803 1.073773922 1.024203898 1 16.33799057 IAASSS(ph)FR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IAASSSFR 8 0 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 1 IAASS(0.004)S(0.996)FR;IAAS(0.002)S(0.157)S(0.841)FR;IAAS(0.043)S(0.248)S(0.709)FR;IAASS(0.005)S(0.995)FR 143.39 0.00063163 16814000000 16689700 19770600 12179600 13866400 17753600 20343800 18870500 19517900 22098000 TRUE FALSE 14484113.86 19640725.63 18069695.3 17014978.05 17400338.09 21126439.15 17040441.81 15344148.97 19485599.61 0.743324001 1.007961059 0.927335861 0.873207825 0.892984483 1.084207803 0.874514624 0.78746096 1 24.21590499 4.758902501 23.923194 0.918786813 0.743323698 0.320165466 0.084284264 3769.659538 4433201.892 0.021472201 0.803777834 57398.75882 -4.758902501 -0.175463115 IAAYGHEVGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IAAYGHEVGK 10 0 A0A087WYM2;A0A087X297;Q16719-2;Q16719;B8ZZA3 A0A087WYM2 KYNU Kynureninase 0 79.974 0.025398 137270000 348300 321830 206460 277840 292690 266030 346480 402670 365500 FALSE TRUE 302271.2725 319715.8775 306304.7466 340927.8185 286866.0416 276264.3462 312878.4229 316562.1541 322291.0064 0.937883051 0.992009926 0.950398058 1.057826038 0.890083918 0.857189127 0.970794769 0.982224598 1 18.2980044 1.77436164 3.511499547 0.992298545 0.949979572 0.095314039 0.053846654 0.581988421 14.05393023 0.037568867 0.015289982 59.47872365 -1.77436164 -0.042318973 IAAYLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IAAYLFK 7 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5;J3KRF5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 142.42 0.020052 0 346260 392600 278850 323040 408270 357650 408160 440490 574230 FALSE TRUE 300500.8637 390020.9847 413702.7927 396391.1694 400146.2258 371409.0269 368576.706 346294.6414 506345.1836 0.59347037 0.770266998 0.817037085 0.782847714 0.790263715 0.733509548 0.727915892 0.683910211 1 18.9497617 -1.999986754 0.021891116 1.735411839 1.84E-06 0.174717376 0.094437986 16488.04824 35.86308715 1826.807779 1104.035402 0.010000305 1.999986754 -1.735409997 IACDEEFS(ph)DS(ph)EDEGEGGR ddPTM_MDA-MB-175_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 282.47 1.18E-33 0 457440 405900 308830 357010 352620 378270 379630 384410 780210 TRUE FALSE 396988.145 403233.6162 458181.221 438074.5771 345603.5519 392822.2917 342813.541 302206.913 687974.4626 0.577039071 0.586117128 0.665985797 0.636759939 0.50234939 0.570983827 0.498293992 0.439270539 1 19.39199549 1.229183446 24.99954014 1.000000871 0.556216935 0.811537951 0.066679439 182.2162558 485752.8983 0.232520415 0.018734128 16.95053638 -1.229183446 -0.443783935 IACDEEFS(ph)DS(ph)EDEGEGGRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IACDEEFSDSEDEGEGGRR 19 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 2 IACDEEFS(1)DS(1)EDEGEGGRR;IACDEEFS(1)DS(1)EDEGEGGRR;IACDEEFS(1)DS(1)EDEGEGGRR;IACDEEFS(1)DS(1)EDEGEGGRR;IACDEEFS(1)DS(1)EDEGEGGRR;IACDEEFS(1)DS(1)EDEGEGGRR 140.81 1.15E-07 9601750000 3033930 2932990 1775080 1925511 2571660 2661980 2596060 2900090 2256260 TRUE FALSE 2632988.464 2913722.996 2633514.625 2362727.702 2520488.997 2764388.093 2344294.501 2279928.322 1989527.513 1.323424002 1.464530134 1.323688468 1.187582321 1.266878181 1.389469648 1.178317206 1.145964711 1 20.92399442 -0.005775419 0.470869394 7.63E-12 1.354028939 0.673036255 0.075964021 9.821750611 0.710186532 9.464584146 0.061998102 0.98678964 0.005775419 1.354028939 IACDEEFS(ph)DSEDEGEGGRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IACDEEFSDSEDEGEGGRR 19 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 1 IACDEEFS(0.999)DS(0.001)EDEGEGGRR;IACDEEFS(0.995)DS(0.005)EDEGEGGRR 289.45 1.03E-49 752690000 674750 458020 343160 417560 449270 463360 506230 588850 392600 TRUE FALSE 585580.0779 455011.2365 509113.3238 512373.38 440330.406 481185.759 457135.8925 462929.0099 346187.2753 1.691512426 1.314349975 1.470629801 1.480046832 1.271942782 1.38995796 1.320487277 1.337221334 1 18.40119317 0.426621633 0.770264308 6.16E-50 1.439985032 0.574158594 0.114859125 6.402027222 1.168590329 10.66619033 0.043512085 2.670678641 -0.426621633 1.439985032 IACEEEFS(ph)DS(ph)EEEGEGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IACEEEFSDSEEEGEGGR 18 0 Q13547 Q13547 HDAC1 Histone deacetylase 1 2 IACEEEFS(1)DS(1)EEEGEGGR;IACEEEFS(1)DS(1)EEEGEGGR 196.66 2.82E-15 374090000 571860 580710 372320 425260 486010 491670 489800 589920 698100 TRUE FALSE 496287.2521 576895.2778 552375.1973 521821.7827 476339.3519 510584.8631 442299.2714 463770.1988 615571.4133 0.806222059 0.937170352 0.897337312 0.84770308 0.773816557 0.829448626 0.718518212 0.753397882 1 19.23156671 3.461735463 4.489388811 0.800995215 0.884703603 0.1046763 0.081199408 0.338908369 16.99703615 0.023287333 0.031954401 2895.579295 -3.461735463 0.083708388 IACEEEFS(ph)DS(ph)EEEGEGGRK ddPTM_MDA-MB-175_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 146.99 3.85E-07 4215390000 6723680 6136120 4301800 4357580 5269440 4368270 6542880 7814390 5843500 TRUE FALSE 5835128.652 6095811.424 6382164.869 5347035.14 5164588.453 4536320.174 5908352.505 6143343.51 5152688.087 1.132443601 1.183035208 1.238608812 1.037717605 1.002309545 0.880379347 1.146654407 1.192259925 1 22.29689383 3.728693435 24.79113669 1.056720113 1.184529808 0.358303369 0.088023867 820.630832 2061821.138 0.02750553 0.041375897 5354.185762 -3.728693435 0.127809695 IADDKYNDTFWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IADDKYNDTFWK 12 1 P14625 P14625 HSP90B1 Endoplasmin 0 ; 208.82 5.69E-08 7392300000 6977000 5086500 5334900 6292600 5371800 4950900 6704400 7330300 6530100 FALSE TRUE 6054971.773 5053086.447 7914875.484 7721431.006 5264911.69 5141364.327 6054208.32 5762772.389 5758119.017 1.051553772 0.877558528 1.374559203 1.340964121 0.914345757 0.892889555 1.051421185 1.000808141 1 22.45716618 3.209690951 24.99999483 0.977521756 1.156144852 0.29670386 0.144558806 304.2012876 263425.3882 0.046799907 0.053074836 1620.656407 -3.209690951 0.178623096 IADGVNEINTENMVSSIEPEKQDS(ph)PPPKPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IADGVNEINTENMVSSIEPEKQDSPPPKPPR 31 2 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 IADGVNEINTENMVSS(0.001)IEPEKQDS(0.999)PPPKPPR;IADGVNEINTENMVSSIEPEKQDS(1)PPPKPPR;IADGVNEINTENMVSSIEPEKQDS(1)PPPKPPR;IADGVNEINTENMVSSIEPEKQDS(1)PPPKPPR 391.22 1.17E-155 2279080000 1676200 1367178 1208506 1286924 1488769 1011362 2032260 2430310 2029080 TRUE FALSE 1454685.923 1358196.918 1792943.544 1579139.764 1459145.41 1050269.751 1835171.738 1910607.119 1789204.474 0.813035036 0.759106596 1.002089795 0.882593234 0.815527477 0.587003758 1.025691454 1.067852863 1 20.77088684 2.045037447 24.99997705 1.041173275 0.818753095 0.500007904 0.104031784 103.3151143 57349.06555 0.043554699 0.029364556 110.9270457 -2.045037447 -0.222420179 IADGYEQAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IADGYEQAAR 10 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;; 176.38 5.85E-06 1488360000 1717900 1632520 1044460 1230220 1567060 1698220 1523020 1747720 1602580 FALSE TRUE 1490875.162 1621795.869 1549564.35 1509560.254 1535878.572 1763551.622 1375317.755 1373983.679 1413124.818 1.055020153 1.147666397 1.096551649 1.068242688 1.086866887 1.247980079 0.973245772 0.972301711 1 20.43045747 2.174713636 24.99999837 0.979500765 1.113924185 0.581937851 0.053966192 42.09147528 16480.79482 0.021298302 0.014359317 149.5249398 -2.174713636 0.13442342 IADMGHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IADMGHLK 8 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ;;;;; 105.57 0.0043629 5198050000 6292320 6139250 4160580 4888070 5788470 5034090 6310420 7669950 6693790 FALSE TRUE 5460773.969 6098920.863 6172650.404 5997981.003 5673290.772 5227754.7 5698436.44 6029790.88 5902457.772 0.925169511 1.033284963 1.045776292 1.016183637 0.961174309 0.885691165 0.965434512 1.021572896 1 22.49288438 3.240391026 24.98842797 0.969469689 1.010021752 0.136514691 0.046913891 102.6229526 1400974.177 0.014920039 0.018307539 1739.366197 -3.240391026 0.040552063 GQYISPFHDIPIYADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GQYISPFHDIPIYADK 16 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 163.35 7.76E-09 1205330000 2258070 2262500 763940 2197800 2637800 2332340 2366140 3013500 7334900 FALSE TRUE 1959660.328 2247637.489 1133383.939 2696844.081 2585312.941 2422066.629 2136672.107 2369086.476 6467776.478 0.302988258 0.347513167 0.175235484 0.416966185 0.399722061 0.374482117 0.330356517 0.366290716 1 22.62483839 1.23692986 5.415187066 1.034592463 0.338044274 0.908285379 0.066055695 0.04366899 3.839385394 0.113805436 0.016608597 17.25559186 -1.23692986 -0.69654819 IADPEHDHTGFLTEYVATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IADPEHDHTGFLTEYVATR 19 0 P27361;E9PQW4;P27361-3;P27361-2;E9PJF0;B3KR49 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 ;;; 209.31 1.33E-16 2173690000 1888490 1770150 1068477 1226380 1399100 1522400 1430990 1665560 1593870 FALSE TRUE 1638921.262 1758521.768 1585196.051 1504848.323 1371260.647 1580967.713 1292212.81 1309392.955 1405444.504 1.166123071 1.251221064 1.127896581 1.070727673 0.975677548 1.12488804 0.919433536 0.93165753 1 20.42259506 3.614315431 0.665694922 0.951627379 1.247758393 0.679314312 0.060762949 0.575098282 0.525110875 0.041705124 0.113760059 4114.4845 -3.614315431 0.296131014 IADREDEYKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IADREDEYKK 10 2 O75533;B4DGZ4;A0A494C1M2;O75533-2 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 121.83 0.00028383 1526560000 1033600 663800 592010 628390 654230 495540 915940 1096040 760350 FALSE TRUE 897007.1412 659439.4541 878308.0162 771075.5538 641212.103 514603.7445 827112.2798 861660.3754 670462.2892 1.337893504 0.983559351 1.310003605 1.150065509 0.956373108 0.767535703 1.233644745 1.285173513 1 19.35479666 4.759652737 23.20491706 1.103326427 1.337894133 0.175230696 0.168101303 4036.665155 4440826.378 0.043536736 1.668129707 57497.99979 -4.759652737 0.234567705 IAEAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IAEAFR 6 0 O14908 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 98.807 0.091929 158030000 275870 300630 189510 235120 268290 279810 283070 332100 298030 FALSE TRUE 239413.0805 298655.1417 281157.6699 288507.5896 262951.5539 290574.4718 255617.915 261082.9994 262797.2329 0.91101827 1.136447056 1.069865412 1.097833438 1.000587225 1.105698369 0.972681151 0.993476973 1 18.00359056 2.221230283 24.99489786 0.989042266 1.057685572 0.189923823 0.062758578 359.3665342 518297.0645 0.023728348 0.016039199 166.4294904 -2.221230283 0.068643306 IAEFTTNLTEEEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IAEFTTNLTEEEEK 14 0 P35579 P35579 MYH9 Myosin-9 0 ;; 257.54 1.13E-12 136470000 234588 192086 177398 173150 196341 165896 239606 261960 274302 FALSE TRUE 203586.6014 190824.1744 263188.2662 212466.3539 192434.1982 172278.1265 216369.047 205941.8926 241874.33 0.841704043 0.78893934 1.088119877 0.878416299 0.795595788 0.712262961 0.894551509 0.851441708 1 17.88389814 1.23710434 24.73846804 1.000000194 0.857356825 0.17753392 0.09712886 63.18045642 1072833.551 0.148020425 0.024246819 17.26252577 -1.23710434 -0.142643369 IAELLS(ph)PGSVDPLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IAELLSPGSVDPLTR 15 0 A0A2R8YD12;A0A024QZX5;A0A087X1N8;P35237;A0A2R8Y6A7 A0A2R8YD12 SERPINB6 Serpin B6 1 IAELLS(0.933)PGS(0.067)VDPLTR 60.657 0.079461 0 56022 47316 34037 34809 51780 48113 51644 56223 55149 TRUE FALSE 48618.55076 47005.17808 50497.40705 42712.91547 50749.67931 49963.93824 46635.57283 44200.14898 48629.34805 0.999777968 0.966601034 1.038414231 0.878336173 1.043601885 1.027444131 0.959000577 0.908919218 1 15.56953963 2.013400611 23.68539472 0.943755651 0.990663528 0.091130207 0.051738581 224.038571 395982.2447 0.020345345 0.013705863 103.1337028 -2.013400611 0.046907877 IAESHLQSISNLNENQAS(ph)EEEDELGELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 31 IAESHLQSISNLNENQASEEEDELGELR 28 0 Q9UD71;J3KSJ8;Q9UD71-2;J3KT77 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 1 IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQS(0.001)IS(0.001)NLNENQAS(0.998)EEEDELGELR;IAESHLQSISNLNENQAS(0.999)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSIS(0.001)NLNENQAS(0.999)EEEDELGELR;IAESHLQSIS(0.001)NLNENQAS(0.999)EEEDELGELR;IAES(0.001)HLQS(0.001)IS(0.001)NLNENQAS(0.998)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR 500.32 4.75E-293 1.10769E+11 4770095.7 5382182.5 2644017.1 3579854.1 5182115.8 4986811.2 4818834.7 6211454.2 5207746.7 TRUE FALSE 4139715.467 5346826.589 3922672.613 4392714.688 5079001.834 5178657.054 4351504.852 4883183.057 4592092.818 0.90148776 1.164355078 0.854223285 0.956582295 1.10603205 1.127733532 0.947608209 1.06338945 1 22.13072037 3.260686983 24.99415717 1.047095478 0.974894527 0.151281424 0.093415418 508.4561385 574352.8274 0.026059039 0.033615181 1822.581605 -3.260686983 -0.072200951 IAESNHIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IAESNHIK 8 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ; 111.82 0.0031598 1202350000 1754790 1502190 612150 1630410 1311530 1497870 1279960 1875770 4723200 FALSE TRUE 1522890.055 1492322.015 908187.7875 2000619.51 1285433.119 1555494.028 1155829.676 1474651.183 4164828.677 0.36565491 0.358315343 0.21806126 0.480360578 0.308640095 0.373483317 0.277521542 0.354072471 1 21.98982572 1.238942258 7.208215604 1.012501508 0.339558127 0.902529661 0.067969551 0.027574841 9.049327009 0.090953751 0.015434499 17.33573495 -1.238942258 -0.672943381 IAETDFEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IAETDFEKR 9 1 Q99615;A0A6I8PUD4;A0A6I8PU73;A0A6I8PS32;A0A6I8PIK4;A0A6I8PR89;A0A6I8PLE7;A0A6I8PU89;A0A6I8PRZ0;K7EIH8;K7EK03;Q99615-2;K7ESP1;K7ER44;K7EPP7;A0A6I8PUC2;K7EJV7;K7EN19;K7EJL5 Q99615 DNAJC7 DnaJ homolog subfamily C member 7 0 79.986 0.040715 1155500000 521190 497300 348050 591240 656050 631330 462610 779820 927800 FALSE TRUE 452313.421 494033.2036 516368.1442 725490.0785 642995.8885 655617.6736 417746.1534 613061.5616 818116.541 0.552871624 0.603866538 0.631166977 0.886780846 0.785946569 0.801374426 0.510619371 0.74935725 1 19.64194684 3.92997679 6.713480005 0.767856786 0.587382018 0.348343417 0.123603988 0.304712621 24.41008359 0.033962362 0.059889454 8510.925516 -3.92997679 -0.180474767 IAFQY(ph)GVT(ph)DLRGMLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IAFQYGVTDLRGMLK 15 1 F5GZR4;A8MXZ9;A0A0A0MQU5;Q14896-2;Q14896 F5GZR4 MYBPC3 "Myosin-binding protein C, cardiac-type" 2 IAFQY(1)GVT(1)DLRGMLK 55.401 0.058772 0 28374 23730 17620 23917 23490 24167 28558 29895 31617 TRUE FALSE 24624.30401 23574.11607 26141.09094 29347.7204 23022.59496 25096.72013 25788.44956 23502.18689 27879.27428 0.883247669 0.845578541 0.937653207 1.052671605 0.825796064 0.900192734 0.925004335 0.842998518 1 14.76690539 4.239095824 0.004363099 1.546262182 0.261636424 0.012213958 0.070997694 524747.4522 888.8628161 129233.9916 132483.8176 17341.8659 -4.239095824 -1.284625758 IAGDYVSEEVWYR ddPTM_MDA-MB-175_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 ;;; 238.51 2.06E-16 1253440000 583180 469176 385505 543210 494650 528070 523190 603960 723250 FALSE TRUE 506111.2854 466093.952 571936.5074 666554.1329 484807.4328 548385.1946 472451.1143 474807.854 637748.2089 0.793591073 0.730843216 0.896806137 1.045168177 0.760186271 0.859877279 0.740811354 0.744506762 1 19.28262742 4.24508365 24.99673697 0.849277987 0.762217136 0.131780908 0.103338375 370.0035049 1417842.125 0.027042622 0.068055514 17582.62244 -4.24508365 -0.087060851 IAGEASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 IAGEASR 7 0 Q16778;P33778;P23527;P06899;Q6DRA6;Q6DN03;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;P57053 Q16778;P58876 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST2H2BD;HIST2H2BC;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;H2BFS Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type F-S 0 ;;;;;; 187.72 0.0013498 32674700000 11467700 10247790 6049323 7905840 6830510 10293160 8705770 10986900 9469750 FALSE TRUE 9952214.39 10180471.59 8974795.837 9700981.805 6694596.215 10689144.53 7861485.765 8637436.935 8350246.943 1.191846715 1.219182099 1.074794063 1.16175987 0.801724339 1.280099211 0.941467458 1.034392994 1 22.99338743 3.950798105 1.524118822 1.025696083 1.210474461 0.235584442 0.124916135 0.599840628 2.625302274 0.035388626 0.10608353 8928.90299 -3.950798105 0.184778378 IAGHPLAQNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IAGHPLAQNER 11 0 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 0 ; 129.89 0.0002356 1176180000 1105620 1319610 759010 916860 1243180 1229650 1171510 1378380 1242540 FALSE TRUE 959509.5157 1310941.395 1126069.775 1125047.076 1218443.15 1276955.431 1057897.141 1083624.164 1095648.337 0.875745879 1.196498321 1.027765695 1.026832277 1.112075024 1.165479277 0.965544422 0.989025518 1 20.06335339 2.193851665 24.9999814 0.984920375 1.07165308 0.163902181 0.087532842 216.0797343 120824.1195 0.033485534 0.022576063 156.2613833 -2.193851665 0.086732705 IAGYVTHLMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IAGYVTHLMK 10 0 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 ; 147.95 2.60E-05 5105600000 6430000 8051900 4843000 6077300 8038100 6766600 8575000 9290700 9026600 FALSE TRUE 5580259.208 7999006.539 7185090.999 7457243.851 7878157.536 7026915.481 7743397.82 7303956.105 7959485.631 0.701082892 1.004965259 0.902707955 0.936900221 0.989782242 0.882835375 0.972851536 0.917641723 1 22.92424377 4.747015556 24.94173005 0.946520636 0.701082765 0.778541608 0.041823189 451.8743694 1332980.907 0.00916156 0.102625696 55849.01984 -4.747015556 -0.245437871 IAHFLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IAHFLDR 7 0 P60228;H0YBR5;E5RHS5;E5RIP5;E5RJ25;E5RII3 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 ;;; 120.49 0.0045458 2637360000 3500180 3674030 2321700 2495790 3740990 3729640 3508430 3933470 3532960 FALSE TRUE 3037622.345 3649895.055 3444481.886 3062497.265 3666551.618 3873121.664 3168182.999 3092328.051 3115297.494 0.975066539 1.171604016 1.105667081 0.983051305 1.176950717 1.243259006 1.016976069 0.992626886 1 21.57093851 2.028261899 24.99661864 0.998491085 1.111012706 0.273564493 0.081940991 257.9865239 228178.6554 0.033433713 0.022540607 106.7239522 -2.028261899 0.112521621 IAHIMGPPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 IAHIMGPPDR 10 0 A0A087WTP3;Q92945 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;;;;;;; 152.97 1.30E-05 3458250000 3097510 3102360 1770660 2070228 2834170 2966070 2724510 3006550 2366130 FALSE TRUE 2688166.205 3081980.393 2626957.099 2540304.909 2777775.562 3080176.632 2460287.44 2363622.679 2086408.807 1.288417781 1.47716995 1.259080718 1.217548977 1.33136687 1.476305421 1.179197208 1.132866518 1 20.99259043 1.767973214 1.978062839 1.027752531 1.336222716 0.613327791 0.090798738 0.223043491 1.675243363 0.092540736 0.02646745 58.61020145 -1.767973214 0.308470185 IAIWTTECENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IAIWTTECENR 11 0 D6RBW1;P06730;P06730-3;P06730-2 D6RBW1 EIF4E Eukaryotic translation initiation factor 4E 0 174.92 2.43E-05 244240000 162770 141980 93207 105980 164710 133550 141860 160200 154410 FALSE TRUE 141259.5321 141047.324 138282.217 130044.3788 161432.5932 138687.7549 128102.439 125942.4767 136155.8257 1.037484304 1.035925737 1.015617336 0.955114319 1.185645876 1.01859582 0.940851692 0.924987793 1 17.05489919 2.326508213 5.052654796 0.948564022 1.044195916 0.31885001 0.059920252 0.22799884 9.8219633 0.022887107 0.017349854 212.0841501 -2.326508213 0.095631895 IAIYELLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IAIYELLFK 9 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3 P46783 RPS10 40S ribosomal protein S10 0 ; 152.59 0.00018634 327310000 682760 628140 480340 535770 608610 499480 794820 826910 776010 FALSE TRUE 592531.5361 624013.707 712634.0306 657424.7672 596499.8517 518695.3188 717738.4787 650081.7315 684270.9818 0.865931118 0.911939456 1.041450024 0.960766691 0.871730451 0.758026181 1.048909712 0.95003551 1 19.38420824 IALDFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IALDFQR 7 0 P17931;G3V3R6 P17931 LGALS3 Galectin-3;Galectin 0 ;; 119.07 0.011315 910727000 1110430 1438550 821550 1007400 1240190 1324110 1029500 1424430 1893000 FALSE TRUE 963683.862 1429100.07 1218854.328 1236145.567 1215512.645 1375049.369 929659.2485 1119826.729 1669211.697 0.577328726 0.856152682 0.730197572 0.740556497 0.728195619 0.823771707 0.556945084 0.670871605 1 20.6707355 1.233597407 24.91329189 1.000000464 0.711645542 0.486741154 0.09341918 131.5512589 660252.1817 0.180313703 0.022389351 17.12369196 -1.233597407 -0.288354922 IALEFDKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IALEFDKDR 9 1 P83111 P83111 LACTB "Serine beta-lactamase-like protein LACTB, mitochondrial" 0 119.53 0.000741 356090000 379390 395180 298200 373650 388140 405360 311710 458940 529740 FALSE TRUE 329252.6502 392584.0366 442410.5174 458492.9434 380416.7734 420954.4615 281480.4122 360799.2525 467114.7407 0.704864612 0.840444547 0.947113158 0.981542442 0.81439685 0.901179999 0.602593726 0.772399629 1 18.83341745 IALESEGRPEEQMESDNCS(ph)GGDDDWTHLSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IALESEGRPEEQMESDNCSGGDDDWTHLSSK 31 1 Q13501;Q13501-2 Q13501 SQSTM1 Sequestosome-1 1 IALESEGRPEEQMES(0.003)DNCS(0.997)GGDDDWTHLSSK;IALESEGRPEEQMESDNCS(1)GGDDDWTHLSSK;IALESEGRPEEQMES(0.001)DNCS(0.999)GGDDDWTHLSSK 295.06 1.54E-81 800630000 492020 479490 201917 380170 478080 457800 537610 597280 736730 TRUE FALSE 426998.3104 476340.1986 299564.7366 466493.409 468567.1433 475411.8622 485472.6649 469556.32 649634.6187 0.657289957 0.733243249 0.461128037 0.718085822 0.721277977 0.731814236 0.7473011 0.722800643 1 19.30926899 -0.71425485 0.852330433 10 0.664493987 0.597981102 0.081965088 43.25098606 1.36529604 720.292246 0.029561239 0.193083495 0.71425485 -9.335506013 IALLEEARR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IALLEEARR 9 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 140.75 0.00017373 264500000 224109 227554 72536 78791 220574 221050 206035 257970 12190 FALSE TRUE 194492.4278 226059.1828 107614.6522 96681.7008 216185.0089 229553.9365 186053.7574 202805.123 10748.91209 18.09415002 21.03088954 10.01167852 8.994556846 20.11226878 21.35601582 17.30907797 18.86750225 1 13.39190303 1.234417356 24.99987655 0.999976877 16.97183487 0.58238147 4.250581196 97.55071937 588526.979 8.306591716 1.104741699 17.15605208 -1.234417356 15.97185799 IALLPLLQAETDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IALLPLLQAETDRR 14 1 U3KQP3;B4DEZ3;K7EJE1;E7ENQ6;Q9P0J0;Q9P0J0-2 U3KQP3 NDUFA13 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 0 179.83 2.92E-06 77494000 97800 118710 70790 117970 147690 157790 90396 149210 105710 FALSE TRUE 84875.48221 117930.1862 105024.2808 144756.8916 144751.258 163860.2834 81629.40983 117302.6027 93213.08423 0.910553308 1.26516773 1.126711788 1.552967513 1.552907075 1.757910756 0.875729094 1.258434946 1 16.50824486 2.210504784 24.99968684 1.082203827 1.363473588 0.252872591 0.253569631 350.636124 312438.4912 0.107775119 0.072678724 162.3696238 -2.210504784 0.281269762 IANDNSLNHEYLPILGLAEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IANDNSLNHEYLPILGLAEFR 21 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ;;; 237.5 7.33E-30 2140600000 1921299 1941074 1061673 1339446 1863368 1943781 1841466 2167850 1988266 FALSE TRUE 1667394.469 1928322.957 1575101.614 1643587.686 1826290.622 2018559.513 1662880.911 1704272.148 1753215.459 0.951049377 1.099877912 0.898407327 0.937470451 1.041680652 1.151347088 0.948474931 0.972083687 1 20.74157187 4.26689056 24.99992249 0.993993152 1.0254634 0.030199215 0.076759968 1052.767709 929003.4483 0.019490359 0.051544368 18488.0267 -4.26689056 0.031470248 IANFVEHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IANFVEHK 8 0 Q9Y6Y8;Q9Y6Y8-2 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 ; 109.71 0.0035651 728930000 1159160 1151240 802640 943780 1160200 1067810 1260810 1554770 1428550 FALSE TRUE 1005974.069 1143677.429 1190799.389 1158079.674 1137114.29 1108889.342 1138536.84 1222294.535 1259668.446 0.798602261 0.907919407 0.945327631 0.919352769 0.902709196 0.880302547 0.903838501 0.970330358 1 20.26461263 IANPVEGSTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IANPVEGSTDR 11 0 F8VZX2;Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3;Q15366-5;Q15366-4;Q15366-8;Q15366-7;F8VRH0 F8VZX2;Q15366;Q15366-2;Q15366-5 PCBP2 Poly(rC)-binding protein 2 0 ;; 160.18 6.47E-05 403180000 463570 380810 240367 313362 419880 390890 372930 385840 401760 FALSE TRUE 402308.05 378308.434 356609.2852 384515.6315 411525.2095 405927.7912 336763.306 303331.1186 354264.3905 1.135615266 1.067870337 1.006619053 1.085391707 1.161633008 1.145832892 0.950598804 0.856228079 1 18.43446693 2.134444129 5.486786126 0.914344122 1.096404353 0.656142054 0.056033341 0.1195919 5.386125113 0.024476967 0.0163151 136.2837667 -2.134444129 0.182060231 IANS(ph)MVST(ph)WT(ph)GPPAMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IANSMVSTWTGPPAMK 16 0 Q6P1X5 Q6P1X5 TAF2 Transcription initiation factor TFIID subunit 2 3 IANS(1)MVS(0.052)T(0.976)WT(0.972)GPPAMK 43.164 0.072288 598380000 98187 72234 33667 82865 60615 33988 61986 45736 53798 TRUE FALSE 85211.33918 71759.4901 49948.47381 101680.7648 59408.88009 35295.54035 55974.60726 35955.71232 47438.06173 1.796265195 1.512698611 1.052919786 2.14344265 1.252346279 0.744034201 1.179951398 0.757950705 1 15.53375744 3.000827179 24.99930857 0.92816625 1.592336676 0.561699395 0.293267271 20.82392518 629309.0352 0.084835134 0.09538378 1001.906465 -3.000827179 0.664170425 IAPELYHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IAPELYHK 8 0 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 0 ; 83.005 0.018804 459840000 747970 743010 465720 588130 746720 692650 758780 944020 848430 FALSE TRUE 649123.8694 738129.1184 690943.7497 721673.9055 731861.7329 719296.6937 685193.6324 742148.6694 748129.5719 0.867662359 0.986632725 0.923561607 0.964637588 0.978255319 0.961460047 0.915875616 0.992005526 1 19.51292863 IAQLEEELEEEQGNTELINDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IAQLEEELEEEQGNTELINDR 21 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 310.11 1.66E-66 258939000 207541 216527 130335 151398 188549 208042 207685 228224 227032 FALSE TRUE 180113.931 215104.6199 193365.4419 185775.2299 184797.2438 216045.5104 187543.7407 179420.0736 200192.5356 0.89970353 1.074488713 0.965897362 0.927982801 0.923097573 1.079188641 0.93681685 0.89623758 1 17.61102866 2.044278372 24.99991669 0.933452195 0.979939478 0.050048386 0.064264193 296.656847 167493.4968 0.025455938 0.017162383 110.7333329 -2.044278372 0.046487282 IAQLEEQLDNETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IAQLEEQLDNETK 13 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 243.4 1.29E-16 239550000 348310 314200 251670 261920 278450 267670 384570 401070 391550 FALSE TRUE 302279.951 312135.9995 373378.4538 321392.9392 272909.3898 277967.4381 347274.4606 315304.3016 345261.4051 0.8755104 0.904057027 1.081436988 0.930868422 0.790442794 0.805092704 1.005830526 0.913233559 1 18.39732955 0.910037736 1.273086251 1.105278822 0.910485461 0.092828372 0.085271275 8.947551362 6.924380947 2.82539033 0.027317962 8.129011471 -0.910037736 -0.194793361 IAQLEEQLDNETKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IAQLEEQLDNETKER 15 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 165.02 1.32E-06 179213000 201861 168540 37463 35900 136693 126493 221257 218235 9449.1 FALSE TRUE 175184.5574 167432.8496 55580.23211 44051.6437 133973.0767 131359.2676 199799.5302 171567.1436 8332.038162 21.02541467 20.09506514 6.670664611 5.287018955 16.07926826 15.7655624 23.97967056 20.59125753 1 13.02445373 7.983430224 0.01239243 9.999404893 20.94814533 0 7.702523923 1217407.387 1508.14718 577774.0079 767748.4089 96256534.87 -7.983430224 10.94874043 IAQVS(ph)PGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IAQVSPGPR 9 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 IAQVS(1)PGPR;IAQVS(1)PGPR 110.08 0.0024592 526360000 1048500 955690 603660 751630 1064950 1055410 814380 1016890 916580 TRUE FALSE 909938.0684 949412.0095 895591.9951 922299.0794 1043759.579 1096012.306 735401.5529 799435.9869 808222.9566 1.125850313 1.174690723 1.108100169 1.141144374 1.291425305 1.356076682 0.909899363 0.989128038 1 19.6243938 2.2218575 24.99995278 0.968737619 1.195782896 0.661101305 0.078673584 157.7761036 236145.4682 0.034499396 0.023330294 166.6700247 -2.2218575 0.227045277 IAS(ph)DEEIQGTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IASDEEIQGTK 11 0 Q8WX93-8;Q8WX93-3;Q8WX93-2;Q8WX93-9;Q8WX93-5;Q8WX93;Q8WX93-4;A0A3B3ISX8 Q8WX93-8 PALLD Palladin 1 IAS(1)DEEIQGTK;IAS(1)DEEIQGTK;IAS(1)DEEIQGTK;IAS(1)DEEIQGTK 225.72 6.32E-08 292260000 1063840 1140460 1038800 1298830 1685190 1183130 1932070 2370410 1972210 TRUE FALSE 923250.8486 1132968.243 1541167.155 1593749.203 1651658.016 1228645.777 1744698.149 1863516.268 1739057.581 0.530891478 0.651484031 0.886208238 0.916444183 0.949743145 0.706500918 1.003243463 1.071566743 1 20.72987427 5.127716868 0.564945903 0.988966931 1.34E-27 0.695688223 0.095917721 3.695727896 0.674447077 0.060407778 2.628546209 134188.985 -5.127716868 -0.988966931 IASHYYITNDTVQTYNQLLKPTLSEIELFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IASHYYITNDTVQTYNQLLKPTLSEIELFR 30 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 155.8 4.21E-09 209660000 261390 201280 150660 176740 187870 193910 236540 220970 237090 FALSE TRUE 226846.6492 199957.7784 223519.6799 216871.5183 184131.7546 201369.8432 213600.3872 173717.2851 209061.4903 1.085071425 0.956454382 1.069157594 1.037357564 0.880754051 0.963208685 1.021710823 0.83093871 1 17.67356781 3.25692157 24.98247743 0.933147928 1.033552533 0.366211028 0.06349856 254.7689397 346644.3085 0.017792277 0.022925544 1806.847794 -3.25692157 0.100404605 IASLEVENQSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IASLEVENQSLR 12 0 P29692;P29692-2;E9PRY8;E9PK01;E9PQ49;A0A087X1X7;E9PI39;E9PPR1;E9PL12;E9PMW7;H0YCK7;E9PIZ1;P29692-3;E9PL71;E9PN91 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 ;;; 247.22 3.01E-16 1049020000 987930 869980 774283 739880 843987 690550 1066398 1271890 1029250 FALSE TRUE 857372.5474 864265.0441 1148728.849 907881.0624 827193.3099 717115.9053 962978.8861 999906.2214 907573.2375 0.944686899 0.952281324 1.265714767 1.000339174 0.911434225 0.790146597 1.06104813 1.101736124 1 19.79165454 2.051362869 24.99991067 1.065116662 0.982282275 0.079870118 0.120411438 264.8804701 128924.2971 0.052478716 0.035381132 112.5545016 -2.051362869 -0.082834387 IATEKDFLEAVNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IATEKDFLEAVNK 13 1 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 96.059 0.004023 516630000 325650 243750 215240 244710 248240 182280 363120 390570 219870 FALSE TRUE 282614.5274 242148.7902 319330.7839 300275.1457 243300.5097 189292.4296 327904.6783 307049.6449 193877.2191 1.457698479 1.248980109 1.64707739 1.548790245 1.254920567 0.976352098 1.69130071 1.583732459 1 17.56478377 3.243592132 24.99564756 1.349577592 1.471692571 0.095543843 0.242341704 453.9848567 2255299.895 0.075091334 0.093950844 1752.234116 -3.243592132 0.122114979 IAVAHNGELVNAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IAVAHNGELVNAAR 14 0 Q06203;D6RCC8 Q06203 PPAT Amidophosphoribosyltransferase 0 152.4 3.39E-07 0 200870 221000 101580 140690 210230 247460 197150 240190 196900 FALSE TRUE 174324.5206 219548.2364 150704.4278 172635.8148 206046.8343 256979.9463 178030.4233 188827.2377 173622.7063 1.00404218 1.264513387 0.867999532 0.994315885 1.186750505 1.480105637 1.025386755 1.087572252 1 17.40559611 3.235483513 24.98822214 1.153828098 1.037508987 0.125063185 0.161706579 196.6132373 1596638.371 0.05014028 0.05928825 1719.822052 -3.235483513 -0.11631911 IAVDEVHCCSQWGHDFRPDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IAVDEVHCCSQWGHDFRPDYK 21 1 P46063 P46063 RECQL ATP-dependent DNA helicase Q1 0 ; 243.18 2.82E-30 573180000 856430 674880 325700 588130 688960 523790 751050 891670 886840 FALSE TRUE 743250.6056 670446.6688 483209.6094 721673.9055 675251.0439 543940.5402 678213.2866 700993.3095 781998.7855 0.950449821 0.857350013 0.617916061 0.92285809 0.863493725 0.695577219 0.867281765 0.896412274 1 19.57680684 1.437419012 1.845419813 1.019143302 0.817305037 0.246696439 0.099484894 0.79591795 3.839731572 0.25550319 0.027697236 27.37909017 -1.437419012 -0.201838266 IAVHCTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IAVHCTVR 8 0 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ;;;;; 164.53 0.00032954 4625400000 2461070 3165900 1239310 2232420 3427340 3382630 3036290 3252900 3523670 FALSE TRUE 2135833.364 3145102.994 1838644.461 2739325.081 3359142.639 3512761.965 2741831.063 2557292.649 3107105.747 0.687402856 1.012229145 0.59175471 0.881632395 1.081116291 1.130557584 0.882438928 0.823046545 1 21.56713991 3.480609875 24.95090311 0.964820879 0.77998136 0.345709331 0.136241893 185.356541 1325691.871 0.040052597 0.052841403 3024.195583 -3.480609875 -0.184839519 IAWALSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IAWALSR 7 0 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 ; 139.27 0.0062933 793990000 425760 448090 256500 295140 427160 406820 372610 459970 498160 FALSE TRUE 369494.7373 445146.4673 380544.2579 362156.0479 418660.3517 422470.6286 336474.3396 361608.995 439268.0923 0.841159974 1.013382203 0.866314364 0.824453345 0.953086188 0.961760337 0.765988574 0.823207971 1 18.74474218 2.260650052 24.99999583 0.850716891 0.910804769 0.062330409 0.081249808 531.877068 601957.2472 0.030110576 0.023304343 182.2426628 -2.260650052 0.060087878 IAWTHITIPESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IAWTHITIPESLR 13 0 E9PP67;E9PQ25;F2Z2Y8;E7EN89;Q9H0E2-2;Q9H0E2 E9PP67 TOLLIP Toll-interacting protein 0 ; 138.89 4.38E-05 1260870000 2314600 2223900 1151900 1641160 2291400 2367600 2251700 2514600 2477600 FALSE TRUE 2008719.746 2209291.054 1708962.693 2013810.462 2245805.623 2458683.104 2033330.481 1976872.359 2184700.95 0.919448378 1.011255593 0.782241017 0.921778544 1.027969353 1.125409454 0.930713414 0.90487092 1 21.05900438 3.377124316 7.000405621 0.987181594 0.904886389 0.231146296 0.079925992 0.399019446 24.26340776 0.024833585 0.032111156 2383.001501 -3.377124316 -0.082295205 IAYVYPDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IAYVYPDER 9 0 Q8WTS6;D6RJA0 Q8WTS6 SETD7 Histone-lysine N-methyltransferase SETD7 0 86.833 0.032269 64381000 136680 151150 85432 99903 143120 140760 139300 145030 151970 FALSE TRUE 118617.3917 150157.0857 126747.201 122587.5031 140272.192 146175.1283 125790.7074 114016.4631 134004.2797 0.885176145 1.120539478 0.945844425 0.914802895 1.046773971 1.090824327 0.938706642 0.850841953 1 17.03191955 2.013440885 24.64147092 0.908769054 1.002890659 0.137359022 0.081682575 279.7829225 512929.7713 0.032301847 0.021764711 103.1432675 -2.013440885 0.094121605 ICANHYITPMMELKPNAGSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ICANHYITPMMELKPNAGSDR 21 1 P43487;F6WQW2;P43487-2;C9JXG8;C9JJ34;C9JGV6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ; 188.19 1.57E-17 7305500000 8310300 7518200 4604900 5760000 6940000 6323800 8215900 9374000 6498600 FALSE TRUE 7212072.799 7468812.449 6831845.042 7067896.036 6801907.578 6567080.678 7419123.283 7369443.049 5730342.911 1.258576129 1.303379669 1.192222725 1.233415896 1.18699835 1.146018795 1.294708432 1.286038752 1 22.45019004 ICDECNYGSYQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ICDECNYGSYQGR 13 0 Q7RTV0 Q7RTV0 PHF5A PHD finger-like domain-containing protein 5A 0 ; 288.32 4.08E-33 546910000 236820 231230 138210 151193 203337 182850 193095 247860 206217 FALSE TRUE 205523.637 229711.0349 205048.8183 185523.6815 199290.9915 189884.3578 174368.6766 194857.0678 181838.2612 1.130255182 1.263271181 1.127643968 1.020267573 1.095979417 1.044248645 0.958921821 1.07159553 1 17.47229627 3.935183217 3.825576589 1.035124482 1.19782566 0.665325009 0.049015924 0.122905717 3.523683034 0.01249437 0.024177849 8613.57059 -3.935183217 0.162701178 ICDLLSDFDEFSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ICDLLSDFDEFSSR 14 0 Q8N142;Q8N142-2 Q8N142 ADSSL1 Adenylosuccinate synthetase isozyme 1 0 124.42 0.00022602 11921000 22968 22486 12087 8428 13427 16513 18625 16518 14982 FALSE TRUE 19932.72061 22338.28799 17932.31363 10341.70621 13159.82897 17148.2658 16818.75037 12985.75424 13210.84503 1.50881496 1.690905308 1.357393383 0.782819433 0.99613832 1.298044581 1.273101784 0.982961666 1 13.68943513 3.987551473 5.911163226 1.068159939 1.586467736 0.689053975 0.153038021 0.090794667 12.28330514 0.042484486 0.081564155 9717.431169 -3.987551473 0.518307797 ICDQISDAVLDAHLQQDPDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ICDQISDAVLDAHLQQDPDAK 21 0 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ;;; 304.66 1.85E-55 889670000 1259650 880900 770239 974260 892110 763530 1075020 1337830 1480950 FALSE TRUE 1093184.061 875113.3099 1142729.157 1195480.624 874358.7564 792903.4932 970764.7259 1051745.466 1305873.778 0.837128426 0.670136214 0.875068614 0.915464146 0.669558399 0.607182338 0.743383275 0.80539596 1 20.31658403 1.240415662 2.894146353 1.04815064 0.758081267 0.377937924 0.096233022 0.478330468 4.863815423 0.329008175 0.026358962 17.39464869 -1.240415662 -0.290069373 ICDQWDALGSLTHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ICDQWDALGSLTHSR 15 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ;;; 243.9 5.30E-18 6460110000 3704650 3510450 1937560 3601940 3109260 3588500 2479120 3617830 9005050 FALSE TRUE 3215071.116 3487389.623 2874570.497 4419815.529 3047391.809 3726551.917 2238695.324 2844185.208 7940483.248 0.404896153 0.439191106 0.362014553 0.556617953 0.383779137 0.469310469 0.281934393 0.358187924 1 22.92079538 1.235863181 24.99995383 1.000000793 0.404340341 0.866977906 0.072993167 25.5767885 236999.1627 0.120593274 0.018036641 17.21326206 -1.235863181 -0.595660451 ICGDIHGQYTDLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ICGDIHGQYTDLLR 14 0 P62140;E7ETD8;C9JP48;C9J9S3 P62140 PPP1CB Serine/threonine-protein phosphatase PP1-beta catalytic subunit;Serine/threonine-protein phosphatase 0 ;;; 153.7 6.32E-06 1619010000 3062260 2808330 1868260 2228850 2935250 2816910 2583500 3128000 3066950 FALSE TRUE 2657574.582 2789881.895 2771756.785 2734944.458 2876844.268 2925278.35 2332952.568 2459101.542 2704378.665 0.982693221 1.03161659 1.024914455 1.011302335 1.063772727 1.081682232 0.862657511 0.909303706 1 21.36686574 2.240611046 24.99999999 0.918372638 1.032706855 0.591697473 0.042471659 35.01528372 426935.0959 0.016583488 0.012198116 174.0247609 -2.240611046 0.114334218 ICGDIHGQYYDLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 167.37 3.66E-06 3699410000 5996020 6073720 3817070 4472710 5916170 5901090 5456660 6259940 6507450 FALSE TRUE 5203630.765 6033821.333 5663017.819 5488307.167 5798449.792 6128108.751 4927473.953 4921300.546 5738146.674 0.906848685 1.051527902 0.986907122 0.956459895 1.010509163 1.067959587 0.858722203 0.857646349 1 22.45215342 2.226172762 24.99999781 0.893548543 0.99754733 0.337092127 0.059536367 219.9899138 443959.1254 0.023508464 0.015977269 168.334356 -2.226172762 0.103998787 ICHQIEYYFGDFNLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ICHQIEYYFGDFNLPR 16 0 P05455;E7ERC4;E9PFL9 P05455 SSB Lupus La protein 0 ; 209.13 1.31E-11 4987900000 1135440 1002260 604750 726060 856620 845710 893960 1042000 1019020 FALSE TRUE 985388.7272 995676.0881 897209.1228 890923.0201 839574.9379 878245.0109 807263.8968 819176.4089 898552.6165 1.096639984 1.108088797 0.998504825 0.991509015 0.93436369 0.977399648 0.898404703 0.911662148 1 19.77724346 4.036848783 1.118442308 0.93678578 1.125576875 0.770200176 0.033237987 0.290363104 0.60599896 0.011149446 0.04938121 10885.51004 -4.036848783 0.188791095 ICLTDHFKPLWAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ICLTDHFKPLWAR 13 1 Q9Y3C8 Q9Y3C8 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1 0 ; 222.25 1.07E-11 2502400000 1892470 1783130 957910 1198820 1593990 1411600 1791760 1868370 1639120 FALSE TRUE 1642375.295 1771416.502 1421158.48 1471030.404 1562272.718 1465905.165 1617995.391 1468833.615 1445345.101 1.136320519 1.22560107 0.983265851 1.017771052 1.080899445 1.014225021 1.119452641 1.016251146 1 20.46298257 4.240687551 24.99999977 1.036724919 1.180960816 0.649821017 0.045058068 31.67598424 372295.7993 0.010920389 0.026150259 17405.54197 -4.240687551 0.144235897 ICQGCPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ICQGCPHR 8 0 Q93008;Q93008-3;O00507;O00507-2 Q93008 USP9X;USP9Y Probable ubiquitin carboxyl-terminal hydrolase FAF-X;Probable ubiquitin carboxyl-terminal hydrolase FAF-Y 0 ;;; 114.6 0.0026246 274085000 286625 254367 175860 199098 236267 277418 264846 291951 300094 FALSE TRUE 248746.78 252696.0464 260906.4842 244306.2439 231565.7489 288090.45 239161.2757 229519.5506 264617.2292 0.940024883 0.954949333 0.985976934 0.923243905 0.875097021 1.088706321 0.903800846 0.867364349 1 18.01354747 ICRDPQT(ph)PVLQTK ddPTM_MDA-MB-175_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 253.36 1.43E-23 2484030000 3477840 3584240 2091520 2170710 2882360 2893560 3325800 3931240 2779950 TRUE FALSE 3018234.632 3560694.891 3102986.068 2663602.883 2825006.675 3004877.126 3003264.428 3090574.919 2451307.478 1.231275415 1.452569669 1.265849387 1.086604968 1.152448928 1.22582628 1.225168387 1.260786314 1 21.22512003 3.998042559 24.95632429 1.175882785 1.346244319 0.405849285 0.091959768 74.04690734 944112.3833 0.022917091 0.046565433 9955.029667 -3.998042559 0.170361534 ICSWNVDGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ICSWNVDGLR 10 0 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;H7C4A8;G3V5M0;G3V359;G3V5D9 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ;;; 156.18 2.65E-05 2150190000 1841870 1620590 945650 1056760 1491940 1586070 1445370 1624540 1590730 FALSE TRUE 1598462.213 1609944.238 1402969.503 1296713.51 1462253.313 1647087.139 1305198.24 1277144.763 1402675.712 1.139580731 1.147766532 1.000209451 0.924457092 1.042474252 1.174246567 0.930506053 0.91050608 1 20.41975008 8 0.36502716 0.96510173 3.526386381 0.301063147 0.080740798 103.3863348 1.544747269 0.104817219 182.9468147 100000000 -8 2.561284651 ICTEQSNS(ph)PPPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ICTEQSNSPPPIR 13 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 ICTEQS(0.001)NS(0.999)PPPIR;ICTEQSNS(1)PPPIR 221.63 1.97E-11 370270000 1008590 940490 617200 808280 904980 938300 827440 1005040 1218090 TRUE FALSE 875302.2761 934311.8593 915679.9844 991812.3278 886972.6686 974397.0082 747194.9962 790120.0172 1074088.788 0.814925438 0.869864642 0.852517962 0.923398828 0.825790827 0.907184787 0.695654777 0.735618904 1 20.03468183 2.268750866 24.99975843 0.790057753 0.866028161 0.069023834 0.085221499 376.6093258 311859.1829 0.031291873 0.024235278 185.6739028 -2.268750866 0.075970409 ICYIFHETFGR ddPTM_MDA-MB-175_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 ; 182.28 5.85E-06 779020000 1149050 1218490 457050 816000 1106330 1145700 1129940 1221870 1082500 FALSE TRUE 997200.1312 1210485.659 678080.9087 1001285.272 1084316.197 1189775.82 1020358.593 960582.6091 954528.0832 1.044704864 1.268150912 0.710383404 1.048984613 1.135970975 1.246454495 1.068966551 1.006342952 1 19.86442812 1.730738711 4.977197973 1.002595635 1.076377028 0.037605709 0.150919041 0.655370267 39.43974491 0.095621951 0.040139166 53.7946035 -1.730738711 0.073781393 IDAHLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDAHLNK 7 0 A0AVT1;A0AVT1-2;H0Y8S8 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 86.866 0.019762 178580000 670740 574010 441200 481830 531030 554700 642730 677900 685340 FALSE TRUE 582100.0096 570239.2905 654565.7957 591236.8658 520463.5419 576039.6679 580398.1435 532936.3604 604319.8859 0.963231598 0.943605041 1.083144558 0.978350836 0.861238483 0.953203231 0.960415431 0.881877914 1 19.20495289 3.460530982 24.91979195 0.927650698 0.997920344 0.251835825 0.052581407 285.9036722 429446.4687 0.014737494 0.019030474 2887.559765 -3.460530982 0.070269646 IDASKNEEDEGHS(ph)NS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 2 IDASKNEEDEGHS(0.996)NS(0.692)S(0.312)PR 61.807 0.014329 0 243490 164220 108770 100480 156060 148090 194460 214330 87480 TRUE FALSE 211312.1796 163141.228 161371.5358 123295.5197 152954.7113 153787.1181 175601.2991 168497.1974 77138.21406 2.739396837 2.11492099 2.091979154 1.598371459 1.982865603 1.993656711 2.276450152 2.184354402 1 16.23515812 4.8715886 1.610689133 1.918303971 3.24731123 0.360353871 0.361662493 1.768168169 3.409996034 0.097382279 4.052829981 74402.68365 -4.8715886 1.329007259 IDASKNEEDEGHSNS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 IDASKNEEDEGHS(0.004)NS(0.723)S(0.273)PR;IDASKNEEDEGHS(0.017)NS(0.599)S(0.385)PR;IDASKNEEDEGHSNS(0.743)S(0.257)PR;IDASKNEEDEGHS(0.001)NS(0.79)S(0.209)PR;IDASKNEEDEGHS(0.003)NS(0.499)S(0.499)PR;IDASKNEEDEGHSNS(0.653)S(0.347)PR;IDASKNEEDEGHS(0.001)NS(0.768)S(0.231)PR 214.67 6.01E-19 37339295000 21099280 15686420 7538775 8076617 13831150 10605600 17969590 19339930 3619392 TRUE FALSE 18310956.69 15583374.87 11184551.81 9910536.333 13555937.18 11013604.29 16226901.93 15204236.47 3191511.601 5.737393116 4.882756769 3.504468479 3.105279746 4.247497384 3.450905299 5.084393841 4.763960898 1 21.60580846 4.43759709 3.497080378 3.781640443 5.627141104 0.291288752 1.121084828 0.315060999 7.727327947 0.284580919 1.040543576 27390.31901 -4.43759709 1.845500662 IDASKNEEDEGHSNSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 IDASKNEEDEGHSNS(0.367)S(0.633)PR;IDASKNEEDEGHSNS(0.022)S(0.978)PR;IDASKNEEDEGHSNS(0.026)S(0.974)PR;IDASKNEEDEGHS(0.014)NS(0.226)S(0.761)PR;IDASKNEEDEGHSNS(0.347)S(0.653)PR 288.58 9.05E-41 17001370000 12243520 9401720 4836750 4998440 8088220 6400440 11132740 11988580 2374697 TRUE FALSE 10625507.81 9339959.482 7175818.478 6133412.198 7927280.246 6646669.068 10053088.59 9424915.462 2093963.026 5.074353119 4.460422351 3.42690792 2.929092884 3.785778521 3.174205555 4.800986676 4.500994213 1 20.99780454 4.407221151 3.369664651 3.54333204 4.989084758 0.237200187 1.031807112 0.379903543 8.326333479 0.264792946 0.934571241 25540.01519 -4.407221151 1.445752718 IDASKNEEDEGHSNSSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;;; 214.19 6.12E-19 2129790000 6123460 4771920 2196690 2507760 4296650 3394170 5391780 6373900 1119050 FALSE TRUE 5314229.246 4740572.943 3259016.631 3077185.237 4211155.071 3524745.916 4868886.005 5010891.087 986757.1838 5.385549083 4.804194001 3.302754401 3.11848273 4.267671055 3.572049917 4.934229094 5.078139961 1 19.91233559 4.411973904 5.04719023 3.820291898 5.260786541 0.21606597 1.146380892 0.306792474 14.83704153 0.288142707 0.830913713 25821.05032 -4.411973904 1.440494644 IDASQFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IDASQFR 7 0 Q66K14-2;Q66K14;G3V133 Q66K14-2 TBC1D9B TBC1 domain family member 9B 0 ; 102.98 0.019726 263180000 519120 378130 573410 346000 287010 422790 326010 377430 366910 FALSE TRUE 450516.9767 375646.0391 850712.9939 424564.5883 281299.0625 439055.0049 294393.6004 296719.5317 323534.3178 1.392485903 1.161070151 2.629436654 1.312270646 0.869456645 1.357058527 0.909930057 0.917119191 1 18.30355922 3.482821162 24.57274288 1.016234991 1.720979617 0.406899105 0.395220577 195.6833881 843608.0118 0.110587692 0.147565256 3039.633078 -3.482821162 0.704744626 IDDDDDERENFEITDWDLQNEFNPNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDDDDDERENFEITDWDLQNEFNPNR 26 1 Q9UBB9;F6XM96;F6UKU9;F6SQZ1;F6UQ07 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 0 103.29 0.0033212 49684000 22366 18827 12045 16530 19896 14719 20561 23815 19720 FALSE TRUE 19410.27643 18703.3242 17870.00229 20283.38915 19500.10853 15285.24945 18566.99738 18722.34758 17388.72407 1.11625651 1.075600724 1.027677604 1.16646794 1.121422622 0.879032262 1.067760769 1.076694731 1 14.08586446 IDDIFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IDDIFER 7 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;;;; 150.17 0.0045767 1001442000 1767470 1626927 1128128 1281020 1756249 1708381 1600893 1898570 1809989 FALSE TRUE 1533894.361 1616239.609 1673694.474 1571895.17 1721303.081 1774103.523 1445638.643 1492575.58 1596014.162 0.961078164 1.012672473 1.048671443 0.984887984 1.078501132 1.111583822 0.905780586 0.935189433 1 20.60604202 2.220953678 24.99999966 0.942814492 1.032587203 0.41083018 0.048410825 234.6794639 333217.7879 0.020207891 0.013658022 166.3235239 -2.220953678 0.089772712 IDDIVSGHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IDDIVSGHK 9 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;;; 173.37 5.55E-05 1839380000 4290730 3547040 2236550 3489010 3646450 2799330 4310970 4924220 6024060 FALSE TRUE 3723699.159 3523739.261 3318153.061 4281243.047 3573892.779 2907022.037 3892892.793 3871213.873 5311902.489 0.701010451 0.663366707 0.624663775 0.805971694 0.672808431 0.5472657 0.732862247 0.72878105 1 22.34079723 1.041368716 1.841278032 1.274887841 0.674888351 0.692393503 0.066850294 0.916007908 1.873384764 1.152437966 0.018259963 10.99939291 -1.041368716 -0.59999949 IDDLQMVLNQTEDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDDLQMVLNQTEDHR 15 0 B7Z641;B7Z2A9;Q93050-1;Q93050;Q93050-3 B7Z641 ATP6V0A1 V-type proton ATPase subunit a;V-type proton ATPase 116 kDa subunit a isoform 1 0 78.597 0.010627 0 139790 129220 93446 111750 129500 147110 114780 170690 156490 FALSE TRUE 121316.3973 128371.1453 138636.7982 137124.5455 126923.2034 152769.4169 103648.6533 134189.2718 137989.9305 0.879168479 0.930293572 1.004687789 0.993728637 0.919800473 1.107105543 0.751132006 0.972456985 1 17.07420347 4.608748023 3.781883453 0.958480115 0.879651775 0.082118548 0.089446175 0.669772039 15.26255134 0.021215221 0.110814014 40620.75794 -4.608748023 -0.07882834 IDDPTDSKPEDWDKPEHIPDPDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IDDPTDSKPEDWDKPEHIPDPDAK 24 2 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ;; 213.47 4.73E-26 5395460000 6859490 3632730 7369480 5153800 3212600 2344210 5739120 6237540 7459410 FALSE TRUE 5952991.017 3608866.357 10933385.18 6324049.061 3148675.545 2434393.276 5182541.026 4903690.612 6577567.048 0.905044521 0.548662801 1.662223296 0.961457179 0.478699118 0.370105429 0.787911547 0.745517389 1 22.64912262 3.398068153 7.74106822 0.679897015 1.042246517 0.227379762 0.316567435 0.367775023 31.04447666 0.093048219 0.120290528 2500.737768 -3.398068153 0.362349502 IDDRDS(ph)DEEGASDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IDDRDSDEEGASDR 14 1 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 IDDRDS(1)DEEGASDR;IDDRDS(1)DEEGASDR;IDDRDS(1)DEEGASDR;IDDRDS(1)DEEGASDR 255.49 7.28E-24 2764142000 2077450 1626760 1248477 1409509 1576071 1608350 1493582 1792636 2053970 TRUE FALSE 1802909.719 1616073.706 1852244.653 1729559.561 1544710.271 1670224.265 1348734.648 1409294.742 1811152.006 0.995449146 0.892290487 1.022688679 0.954949974 0.852888253 0.922188894 0.744683297 0.778120631 1 20.7884762 3.088514614 1.743462439 0.834505346 0.967432695 0.284794001 0.078975682 0.401103035 2.512550461 0.029018652 0.034005004 1226.068158 -3.088514614 0.132927349 IDDVVNTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IDDVVNTR 8 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;; 141.2 0.0014829 975730000 742207 618903 460850 527735 670483 687132 663750 754460 763401 FALSE TRUE 644122.4644 614837.3854 683718.6015 647565.2977 657141.7001 713566.4127 599379.6272 593124.6002 673152.6034 0.956874357 0.913369988 1.015696289 0.961988848 0.976215046 1.060036623 0.890406758 0.88111462 1 19.36057407 2.185837442 24.99998397 0.913546107 0.978174328 0.216642502 0.049542358 129.5414841 61424.18092 0.020117495 0.013563223 153.4042676 -2.185837442 0.064628221 IDEDGENTQIEDTEPMS(ph)PVLNSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDEDGENTQIEDTEPMSPVLNSK 23 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 IDEDGENTQIEDTEPMS(1)PVLNSK 259.7 6.93E-44 250460000 332480 290400 231890 283770 277600 205330 376140 441710 348520 TRUE FALSE 288541.9256 288492.3433 344032.7796 348204.3157 272076.3031 213229.178 339662.0007 347253.7539 307318.3626 0.938902326 0.938740988 1.119467046 1.133041035 0.885323938 0.693838065 1.10524473 1.12994795 1 18.22937445 IDEDGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IDEDGKK 7 1 O75821;K7ENA8;K7ER90;K7EL20;K7EL60 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 ;; 100.15 0.016044 701220000 2344620 1863960 1819800 2081830 959300 1225290 2780110 3451390 3985640 FALSE TRUE 2034772.526 1851715.524 2699861.367 2554541.32 940211.8068 1272427.699 2510495.36 2713337.107 3514462.18 0.57897124 0.526884465 0.76821466 0.726865503 0.267526512 0.362054742 0.714332729 0.772049027 1 21.7448725 1.568201607 1.824563326 1.004773954 0.549270998 0.478305703 0.153946173 0.418105048 2.427478724 0.288774264 0.047767932 36.99999001 -1.568201607 -0.455502956 IDEPLEGSEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 IDEPLEGSEDR 11 0 P61978;P61978-2;S4R359;P61978-3 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;; 222.18 1.83E-11 15904240000 4813960 3914270 2644901 3284673 3892750 3464470 3887830 4455860 4280730 FALSE TRUE 4177782.989 3888556.903 3923983.97 4030508.208 3815291.891 3597750.403 3510788.845 3503009.015 3774666.976 1.10679512 1.030172179 1.03955766 1.067778491 1.010762516 0.953130548 0.930092341 0.928031277 1 21.84791794 2.91458083 2.5167919 0.945850543 1.057424286 0.761636503 0.028358509 0.132347609 1.650804335 0.009789105 0.010100019 821.4494252 -2.91458083 0.111573742 IDESIHLQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDESIHLQLR 10 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 143.5 3.39E-05 80863000 76160 75809 35836 53520 77450 70405 62888 75895 87464 FALSE TRUE 66095.26304 75311.00569 53166.40946 65672.534 75908.89653 73113.52591 56789.13144 59665.44487 77124.10556 0.856998763 0.976491139 0.689361764 0.85151761 0.98424346 0.947998364 0.736334393 0.773629003 1 16.23489423 1.832786883 0.005090944 7.46E-05 1.707893476 0 0.110302516 383445.8853 802.0527322 136372.3631 132697.0804 68.04353732 -1.832786883 1.707818892 IDFDSVSSIMAS(ph)SQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDFDSVSSIMASSQ 14 0 Q9UBQ5;A0A087WVB9;K7ERF1;K7EK53 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 1 IDFDSVSSIMAS(0.564)S(0.436)Q 81.619 0.013636 15646000 66601 64518 35807 44842 63913 61929 62576 69459 64618 TRUE FALSE 57799.5091 64094.17701 53123.38497 55024.06147 62641.25634 64311.4487 56507.38915 54605.73338 56978.93365 1.014401383 1.124874983 0.932333787 0.965691317 1.099375722 1.128688176 0.991724231 0.958349514 1 15.798141 2.020488163 24.97091351 0.975850825 1.043282688 0.167739404 0.064249095 393.8476517 480018.4919 0.027375629 0.018454694 104.8306222 -2.020488163 0.067431863 IDFIPVSPAPS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDFIPVSPAPSPTR 14 0 Q96E09 Q96E09 FAM122A Protein FAM122A 1 IDFIPVS(0.061)PAPS(0.913)PT(0.026)R 76.391 0.028944 19300000 36589 36015 25262 34052 49523 45699 46172 58453 78495 TRUE FALSE 31753.67095 35778.41509 37478.7877 41784.02705 48537.58919 47457.0701 41694.24655 45953.28083 69215.41052 0.458765912 0.516914005 0.541480393 0.603680983 0.701254082 0.685643121 0.602383866 0.663916901 1 16.07880566 -0.234184408 1.084835446 10 0.580788564 0.765490944 0.071540697 20.6624005 1.314636312 433.1285825 0.025224359 0.583197418 0.234184408 -9.419211436 IDFSSIAVPGTS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IDFSSIAVPGTSSPR 15 0 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 1 IDFSSIAVPGT(0.047)S(0.476)S(0.476)PR;IDFSSIAVPGTS(0.5)S(0.5)PR 220.34 1.77E-12 847430000 1406230 1306690 867670 1073410 1324340 1394420 1388010 1792690 1540900 TRUE FALSE 1220393.143 1298106.267 1287278.114 1317144.147 1297988.225 1448064.24 1253401.004 1409337.194 1358736.557 0.898182312 0.95537745 0.947408169 0.969388907 0.955290573 1.065743195 0.922475367 1.037240948 1 20.37383433 8 0.267511285 1.018140856 0.215776059 0.401945455 0.039005715 79.50253834 1.272858617 0.098330584 28.63458133 100000000 -8 -0.802364796 IDFSSIAVPGTSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IDFSSIAVPGTSSPR 15 0 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 1 IDFSSIAVPGT(0.201)S(0.16)S(0.639)PR;IDFSSIAVPGT(0.008)S(0.215)S(0.776)PR;IDFSSIAVPGTS(0.13)S(0.87)PR 263.45 4.86E-25 1241100000 2568640 2449040 1638960 1998070 2648060 2489910 2651970 3276140 2902280 TRUE FALSE 2229187.716 2432952.095 2431566.538 2451762.332 2595368.787 2585698.449 2394782.358 2575562.956 2559175.765 0.871056903 0.950677999 0.950136591 0.958028114 1.014142453 1.01036376 0.935763143 1.006403308 1 21.2872478 6.386004952 0.635171852 0.990975914 1.18E-16 0.689702936 0.024599727 13.98489136 0.809211634 0.011001958 15.86638064 2432231.744 -6.386004952 -0.990975914 IDFVGELNDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IDFVGELNDK 10 0 E9PLK3;P55786;P55786-2;A6NEC2;E9PP11;E9PJY4;E9PPD4;A6NEC2-3 E9PLK3 NPEPPS;NPEPPSL1 Puromycin-sensitive aminopeptidase;Puromycin-sensitive aminopeptidase-like protein 0 ; 114.83 0.0030314 105022000 233222 206569 165605 157858 185317 175655 259711 273400 255920 FALSE TRUE 202401.1218 205212.0346 245692.1319 193702.0716 181629.5543 182412.5615 234524.2672 214935.5376 225665.4291 0.896907969 0.909364077 1.088745108 0.85835953 0.804862114 0.808331884 1.039256514 0.952452214 1 17.7838259 2.22212113 24.99972436 0.989657071 0.898229201 0.262172182 0.080802838 401.2909629 610243.1889 0.035368313 0.023922467 166.7712294 -2.22212113 -0.09142787 IDFYFDENPYFENK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IDFYFDENPYFENK 14 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;; 294.69 3.25E-43 3785980000 5488900 3757060 2936860 3344680 3476960 2828060 4483170 5328630 4590070 FALSE TRUE 4763527.958 3732379.625 4357135.319 4104140.714 3407775.299 2936857.298 4048392.863 4189143.942 4047437.154 1.176924502 0.92215876 1.076517103 1.014009745 0.841958792 0.725609117 1.000236127 1.035011486 1 21.94857725 7.835241631 1.046676637 0.947634421 199.998583 0.303686906 0.104118692 2332.70411 3.67460877 0.034464363 1113317.473 68429226.44 -7.835241631 199.0509486 IDGATQSS(ph)PAEPK ddPTM_MDA-MB-175_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(0.011)S(0.989)PAEPK;IDGATQS(0.017)S(0.983)PAEPK;IDGATQS(0.063)S(0.937)PAEPK;IDGATQS(0.016)S(0.984)PAEPK;IDGATQS(0.007)S(0.993)PAEPK 260.08 5.59E-24 2459410000 6233010 5296590 4253980 4809140 5291490 4305070 6837960 7829020 6962820 TRUE FALSE 5409301.936 5261796.352 6311218.957 5901128.74 5186199.702 4470688.829 6174815.692 6154844.999 6139683.352 0.881039237 0.857014287 1.027938836 0.961145454 0.844701494 0.728162769 1.005722175 1.002469451 1 22.54973282 2.101387503 22.16046647 1.002901633 0.888523387 0.346685204 0.077039648 6.4403949 1391.161092 0.033605217 0.02265664 126.2953912 -2.101387503 -0.114378246 IDGDKDGFVTVDELKDWIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDGDKDGFVTVDELKDWIK 19 2 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-13;O43852-14;O43852-11 O43852 CALU Calumenin 0 140.95 9.56E-08 207060000 515130 233170 270550 271630 248190 173700 372660 404280 171360 FALSE TRUE 447054.2653 231638.2909 401388.8849 333307.7431 243251.5046 180382.3514 336519.4906 317827.8681 151102.016 2.958625418 1.532992723 2.656409858 2.205845772 1.609849498 1.193778589 2.227101262 2.103399256 1 17.20516338 3.314467344 5.433974448 1.710469311 2.315436724 0.318134131 0.510933177 0.299192305 15.42830044 0.14694022 0.189254808 2062.84855 -3.314467344 0.604967413 IDGLNVADIGLHDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IDGLNVADIGLHDLR 15 0 O15438;O15438-4 O15438 ABCC3 Canalicular multispecific organic anion transporter 2 0 ; 161.14 1.67E-06 177712000 241240 237710 170244 272420 329740 341890 180228 435500 352520 FALSE TRUE 209359.5228 236148.4674 252574.5678 334277.1247 323178.8191 355042.7295 162749.5163 342371.7141 310845.4872 0.673516366 0.759697268 0.812540565 1.075380337 1.039676728 1.14218396 0.523570465 1.101420893 1 18.24583811 3.978975696 3.564880956 0.973404933 0.722222597 0.295140538 0.17245222 0.300706123 8.107313717 0.045878551 0.094709722 9527.428446 -3.978975696 -0.251182337 IDGVEQLNNILVIGMTNRPDLIDEALLRPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDGVEQLNNILVIGMTNRPDLIDEALLRPGR 31 2 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 235.44 5.55E-46 572710000 147130 135870 79225 100370 128150 147900 142230 172500 124210 FALSE TRUE 127686.3977 134977.461 117538.475 123160.5426 125600.0657 153589.8087 128436.5565 135612.2174 109526.0353 1.165808635 1.23237786 1.073155571 1.124486449 1.146759904 1.402313233 1.172657772 1.238173344 1 16.74091433 IDHILDAL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IDHILDAL 8 0 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ;; 124.37 0.0030419 143019000 437506 509349 329325 502458 667700 670030 379220 773450 659730 FALSE TRUE 379688.4736 506003.0529 488587.6715 616548.7685 654414.0763 695806.4877 342443.3028 608053.7365 581737.471 0.652680105 0.869813409 0.83987657 1.059840219 1.124930246 1.196083323 0.588656086 1.045237357 1 19.15000871 4.623391826 1.330348801 0.988269643 0.569377115 0.300613403 0.164682869 1.472977931 2.717951619 0.048608567 0.790447354 42013.78671 -4.623391826 -0.418892528 IDHYLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IDHYLGK 7 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;; 108.09 0.0074279 4940920000 6421190 6034140 4581360 5433140 5849980 5475510 7399010 7630960 8002690 FALSE TRUE 5572613.472 5994501.337 6796921.02 6666817.477 5733576.843 5686156.413 6681455.149 5999138.588 7056621.105 0.78969997 0.849486071 0.963197672 0.944760584 0.812510231 0.80579024 0.946834902 0.85014322 1 22.75054612 -1.999775663 0.014509522 1.887074943 0.031897684 0.13385531 0.069243898 38912.52151 56.22205717 4245.633492 3040.265562 0.010005167 1.999775663 -1.855177259 IDIIPNPQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IDIIPNPQER 10 0 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ;;;; 125.48 0.00094909 1685660000 1100310 942040 585823 763062 918660 1020880 921860 1043920 921430 FALSE TRUE 954901.2457 935851.6772 869128.9623 936326.8898 900380.4633 1060153.914 832458.1591 820685.8318 812499.5951 1.175263657 1.151818023 1.069697717 1.1524029 1.108161122 1.304805468 1.024564399 1.010075373 1 19.63200757 2.037064736 24.99692313 1.009225948 1.154079106 0.576747957 0.060082964 112.9858213 76198.58296 0.023855389 0.01608327 108.9092422 -2.037064736 0.144853158 IDILDSALLRPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IDILDSALLRPGR 13 1 P62195-2;P62195 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ;; 232.6 4.33E-13 3563532000 2045227 1996107 1262318 1587734 1908326 1845936 1934737 2209095 2007261 FALSE TRUE 1774945.07 1982994.442 1872779.207 1948253.272 1870354.046 1916950.352 1747106.504 1736697.225 1769964.891 1.002813716 1.120358066 1.058088336 1.100729897 1.056718162 1.083044281 0.9870854 0.981204336 1 20.75528931 2.234572703 24.99829006 0.987618542 1.072779633 0.599251871 0.03111636 58.57880039 367196.1891 0.011196169 0.00786397 171.6218988 -2.234572703 0.085161091 IDILTELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDILTELR 8 0 O00139-1;O00139-5;O00139;O00139-4;O00139-2 O00139-1 KIF2A Kinesin-like protein KIF2A 0 108.46 0.008855 8812100 32614 27500 17712 27195 27081 32514 23844 32276 26986 FALSE TRUE 28303.97727 27319.35069 26277.58244 33370.0404 26542.14108 33764.83462 21531.61255 25374.02857 23795.74582 1.189455354 1.148077093 1.104297492 1.402353204 1.115415389 1.418944162 0.904851342 1.066326257 1 14.53841605 2.221917185 24.99999811 1.002647843 1.222989643 0.494083654 0.113818672 206.3299098 309924.5282 0.04380246 0.029623685 166.6929316 -2.221917185 0.220341799 IDIS(ph)PSTFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IDISPSTFR 9 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 IDIS(0.958)PS(0.042)TFR;IDIS(0.961)PS(0.038)TFR;IDIS(0.972)PS(0.026)T(0.002)FR;IDIS(0.499)PS(0.499)T(0.002)FR;IDIS(0.999)PS(0.001)TFR 178.54 5.33E-05 33345020000 7488120 6050152 4807333 5932245 6551333 6440636 6335008 7880040 9760780 TRUE FALSE 6498545.97 6010408.153 7132175.318 7279251.896 6420974.291 6688411.435 5720639.899 6194954.769 8606871.708 0.755041575 0.698326681 0.828660582 0.845748855 0.746028814 0.777101328 0.664659599 0.719768457 1 23.03705753 1.233946145 24.9997481 1.000000372 0.752453618 0.665975851 0.054643121 94.03323016 509378.404 0.11290026 0.014408255 17.13744779 -1.233946145 -0.247546753 IDIS(ph)PSTFRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IDISPSTFRK 10 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 IDIS(0.998)PS(0.002)TFRK;IDIS(0.879)PS(0.121)TFRK 125.82 0.00024439 903290000 2935900 2248500 599690 621340 1716090 1666610 2428100 2693100 156133 TRUE FALSE 2547913.376 2233729.455 889702.0898 762424.7436 1681943.166 1730725.565 2192623.236 2117201.523 137675.1346 18.50670699 16.22463971 6.462329544 5.537853627 12.21675338 12.57108315 15.92606568 15.37824189 1 17.07090849 4.378977153 5.960755586 10 17.94586828 0.320019702 4.590173067 0.246268491 12.16200181 1.23828251 3.387389213 23931.89856 -4.378977153 7.945868275 IDIS(ph)PSTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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(0.752)PS(0.248)TLR;IDIS(0.938)PS(0.062)TLR;IDIS(0.912)PS(0.086)T(0.003)LR;IDIS(0.949)PS(0.047)T(0.004)LR;IDIS(0.714)PS(0.283)T(0.003)LR;IDIS(0.983)PS(0.016)T(0.001)LR;IDIS(0.984)PS(0.015)T(0.001)LR;IDIS(0.989)PS(0.01)T(0.001)LR 193.3 3.54E-05 36826551000 3844402 3037357 2224835 2680835 3015573 2958305 2984758 3369097 4556222 TRUE FALSE 3336354.535 3017404.402 3300772.648 3289559.561 2955568.997 3072112.908 2695296.629 2648641.825 4017590.626 0.830436659 0.751048248 0.821580135 0.818789137 0.735657082 0.764665491 0.670873884 0.659261252 1 21.93789914 4.746422175 22.64227663 0.764399421 0.830436783 0.012517899 0.095766508 1020.029306 2937530.457 0.023222392 0.230524433 55772.76495 -4.746422175 0.066037362 IDIS(ph)PSTLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IDISPSTLRK 10 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 IDIS(0.996)PS(0.004)TLRK;IDIS(0.976)PS(0.023)T(0.001)LRK;IDIS(0.904)PS(0.095)T(0.001)LRK 143.76 2.05E-05 2844210000 6819100 4804900 1946320 2148400 4048310 3474500 5468300 5936300 568830 TRUE FALSE 5917938.658 4773336.296 2887566.862 2636227.056 3967756.551 3608166.263 4937985.108 4666868.441 501583.5654 11.79850989 9.516532488 5.756900866 5.25580828 7.910459642 7.193549614 9.844790476 9.304269045 1 18.93613055 4.466696581 4.02838428 7.049340732 11.46083067 0.322738454 2.482304668 0.261325294 9.532289455 0.632887143 2.274108817 29288.463 -4.466696581 4.41148994 IDISPS(ph)TFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 IDISPSTFR 9 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 IDIS(0.086)PS(0.913)T(0.001)FR;IDIS(0.257)PS(0.731)T(0.012)FR;IDIS(0.362)PS(0.552)T(0.086)FR;IDIS(0.439)PS(0.531)T(0.03)FR;IDIS(0.049)PS(0.949)T(0.003)FR;IDIS(0.081)PS(0.91)T(0.009)FR;IDIS(0.116)PS(0.874)T(0.01)FR 178.54 5.33E-05 32218940000 11444810 9851390 6401776 8204830 9517960 9142190 9774320 10590630 13903870 TRUE FALSE 9932349.361 9786675.57 9497696.286 10067862.05 9328571.218 9493895.965 8826407.951 8325906.191 12260170.33 0.810131433 0.79824956 0.774678983 0.821184517 0.760884308 0.77436901 0.719925394 0.679102 1 23.54747569 1.225507923 24.99783339 1.000000565 0.76385885 0.750583902 0.042111472 374.3400432 716872.6654 0.219646383 0.011953682 16.80768588 -1.225507923 -0.236141715 IDISPS(ph)TLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IDISPSTLR 9 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 IDIS(0.245)PS(0.749)T(0.005)LR;IDIS(0.016)PS(0.984)TLR 196.44 3.11E-05 28686000000 1503000 1266080 891960 1062050 1116820 1120070 1147320 1283110 1776260 TRUE FALSE 1304374.742 1257763.037 1323314.839 1303204.685 1094597.467 1163159.818 1036053.083 1008726.912 1566272.566 0.832789113 0.803029475 0.844881579 0.832042081 0.698855034 0.742629248 0.661476875 0.644030249 1 20.57890386 3.248089164 24.67798551 0.729294721 0.8275813 0.118938366 0.098434491 289.0986757 748731.7412 0.028099534 0.035786856 1770.472414 -3.248089164 0.09828658 IDISPS(ph)TLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.269)PS(0.365)T(0.365)LRK 75.849 0.011588 0 378670 282500 101550 134880 241910 223700 313130 326980 50830 TRUE FALSE 328627.8001 280644.2389 150659.9197 165506.5655 237096.4643 232305.8838 282762.7008 257057.8716 44820.93531 7.332015671 6.261454318 3.361373845 3.692617398 5.289859809 5.182977155 6.308719327 5.735218817 1 15.45188513 4.431984125 6.271290382 4.633823241 7.085644411 0.309035822 1.510461473 0.216649083 20.57003995 0.38311603 1.064286278 27038.59528 -4.431984125 2.45182117 IDKDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDKDKR 6 2 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 69.383 0.052671 590650000 3233200 2314400 1927900 1899700 1109300 1529800 2996700 3445400 3259400 FALSE TRUE 2805924.428 2299196.554 2860238.888 2331055.92 1087227.1 1588652.396 2706080.495 2708628.022 2874077.445 0.976286994 0.799977244 0.995185044 0.81106232 0.378287336 0.552752118 0.941547522 0.942433902 1 21.45466751 2.04207786 24.34802163 0.95957092 0.750810759 0.228290705 0.181516767 174.7465024 101114.7667 0.081649319 0.055047886 110.1736811 -2.04207786 -0.208760161 IDKEACR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IDKEACR 7 1 Q14019 Q14019 COTL1 Coactosin-like protein 0 ; 83.005 0.020932 455930000 1010660 946870 561800 671120 757860 766650 1078880 1152080 610430 FALSE TRUE 877098.7203 940649.9486 833488.3591 823508.0534 742780.0687 796143.5216 974250.3837 905716.6575 538265.6608 1.629490388 1.747557047 1.548470244 1.529928646 1.379950688 1.479090307 1.809980563 1.682657326 1 19.03795886 4.128387467 5.718823002 1.51942553 1.687122739 0.120119142 0.213241617 0.496698738 22.81387741 0.05576138 0.119914331 13439.63478 -4.128387467 0.167697209 IDKELINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IDKELINR 8 1 P23381;P23381-2;G3V277;G3V5U1;G3V3Y5;G3V3H8;G3V456;G3V423;G3V3P2;G3V227;G3V3X0;G3V2Y7 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ;;; 118.18 0.0017663 2820500000 4567000 4304640 2666750 3112880 3949170 3441860 4570610 5145780 3239360 FALSE TRUE 3963459.379 4276362.536 3956399.22 3819706.981 3870589.243 3574270.581 4127352.946 4045394.992 2856406.551 1.387568369 1.497112704 1.385096676 1.33724206 1.355055443 1.251317177 1.444945904 1.416253226 1 21.4457699 1.235799491 24.99981201 0.999999484 1.385668686 0.774577571 0.065154148 37.52572273 339699.1918 0.112109039 0.016663221 17.21073792 -1.235799491 0.385669202 IDKLMIEMDGTENK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDKLMIEMDGTENK 14 1 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879 P06733 ENO1 Alpha-enolase;Enolase 0 177.58 1.90E-06 373370000 776170 732170 526010 466370 615140 423650 846820 885330 529460 FALSE TRUE 673597.1679 727360.3271 780390.1954 572266.4365 602899.9175 439948.0896 764695.5267 696009.0691 466867.842 1.442800526 1.557957652 1.671544119 1.22575681 1.291371697 0.942339673 1.637927178 1.490805334 1 18.83265469 3.733034492 24.89129182 1.299259061 1.557486457 0.29107754 0.210808117 632.4175825 2848597.237 0.06016514 0.092190757 5407.972722 -3.733034492 0.258227396 IDKPILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IDKPILK 7 1 P62917;E9PKZ0;E9PKU4;E9PP36 P62917 RPL8 60S ribosomal protein L8 0 ; 100.15 0.021446 0 5374900 4740800 3545500 4031000 4836600 3662200 6163200 6698700 6079600 FALSE TRUE 4664593.347 4709657.373 5260115.659 4946300.16 4740361.123 3803087.204 5565493.813 5266235.134 5360876.614 0.870117647 0.87852374 0.981204388 0.922666294 0.884251115 0.709415172 1.038168608 0.982345895 1 22.3540375 IDKTDYMVGSYGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IDKTDYMVGSYGPR 14 1 P52565;J3KTF8;J3QQX2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;;; 164.15 3.80E-06 9587390000 5679040 4631110 2768666 3591940 4621840 3657787 4793330 5478370 4265080 FALSE TRUE 4928540.475 4600687.933 4107602.138 4407544.876 4529874.426 3798504.433 4328473.594 4306863.208 3760867.101 1.310479829 1.223305107 1.092195504 1.171949116 1.20447607 1.010007621 1.150924369 1.145178251 1 21.8426339 8 0.534242094 1.101490832 9.617333484 0.520902535 0.065196645 112.0673344 1.103963641 0.035775779 1086.357748 99999999.95 -8 8.515842652 IDKVNEIVETNRPDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDKVNEIVETNRPDSK 16 2 Q15008;Q15008-4;Q15008-3;Q15008-2 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 111.06 0.00047572 1214600000 1125200 914220 747470 656200 732940 584720 1129400 1366800 938210 FALSE TRUE 976501.9691 908214.4286 1108948.992 805200.2394 718355.928 607214.5568 1019870.962 1074520.456 827295.8826 1.180353958 1.097810889 1.340450274 0.973291728 0.868318026 0.733975074 1.232776547 1.298834527 1 19.65804388 3.719275159 24.51967192 1.0425055 1.19536566 0.201786242 0.171538484 1399.373351 1779172.936 0.054861731 0.081519229 5239.322828 -3.719275159 0.152860161 IDLENTLEQEQEALVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IDLENTLEQEQEALVNR 17 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 196.93 3.62E-11 28927000 26499 20414.3 17112.5 17710.2 22074.8 22234.5 20532.3 26559 34769 FALSE TRUE 22997.09001 20280.19712 25388.16224 21731.57159 21635.55467 23089.8756 18541.08071 20879.56453 30658.64843 0.750101234 0.66148373 0.828091372 0.708823536 0.705691731 0.753127642 0.604758581 0.681033431 1 14.90400648 1.235304569 24.997474 1.000000404 0.708288732 0.699124473 0.059414348 52.51948503 403136.5819 0.101805359 0.014550345 17.19113574 -1.235304569 -0.291711671 IDLFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDLFER 6 0 Q9UHG3;F8W8W4 Q9UHG3 PCYOX1 Prenylcysteine oxidase 1 0 103.02 0.081529 105020000 91532 67695 52993 74452 84633 116800 55658 75468 78776 FALSE TRUE 79435.81429 67250.30709 78620.59205 91357.46453 82948.96888 121293.3716 50260.29573 59329.75549 69463.19102 1.143567019 0.968143071 1.131830987 1.315192452 1.194142792 1.746153175 0.723552935 0.854117909 1 16.08396107 IDLGERPVVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IDLGERPVVQR 11 1 Q8TC07-2;Q8TC07-3;Q8TC07;C9JA93 Q8TC07-2 TBC1D15 TBC1 domain family member 15 0 ; 152.85 2.99E-05 561710000 203472 176042 109102 133386 198912 210824 175954 206445 153202 FALSE TRUE 176582.6597 174885.5685 161864.0921 163673.33 194954.0404 218934.5357 158890.0082 162298.3433 135090.6341 1.307142134 1.294579522 1.198188855 1.211581625 1.443135134 1.620649257 1.176173383 1.201403372 1 17.04356813 1.487146315 1.816171008 0.98579269 1.331258805 0.397805127 0.129292624 0.577104101 2.93056863 0.309329758 0.039291316 30.70056127 -1.487146315 0.345466115 IDLGVHVDGFIANVAHTFVVDVAQGTQVTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IDLGVHVDGFIANVAHTFVVDVAQGTQVTGR 31 0 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;; 136.02 9.11E-07 957035000 350739 342436 191188.9 264585 303782 280524 332993 420418 267045 FALSE TRUE 304387.9525 340186.5154 283648.4915 324663.0682 297737.3325 291315.9398 300699.3901 330514.8824 235475.2443 1.292653728 1.444680592 1.204578818 1.378756689 1.264410335 1.237140408 1.276989396 1.403607769 1 17.84521587 1.228415173 24.99997297 0.999999358 1.314341118 0.628239028 0.075625247 275.909926 679838.1345 0.238695471 0.017783085 16.92057717 -1.228415173 0.31434176 IDLMPHDLITQLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IDLMPHDLITQLLR 14 0 F2Z2B9;Q9BSJ2-3;Q9BSJ2;Q9BSJ2-4;B3KTU7 F2Z2B9 TUBGCP2 Gamma-tubulin complex component 2 0 ; 146.96 8.16E-06 149554000 379980 384550 298360 328830 417790 448120 383630 445810 580100 FALSE TRUE 329764.6803 382023.8657 442647.894 403495.8774 409476.7964 465359.4664 346425.6216 350477.0008 511521.2389 0.644674464 0.746838717 0.865355845 0.788815491 0.800507907 0.909755903 0.677245822 0.685166078 1 18.96443462 4.621357047 3.420145473 0.800602024 0.64124266 0.234093493 0.097152094 0.4313617 8.160094015 0.024599602 0.144925224 41817.40193 -4.621357047 -0.159359364 IDNSQVESGSLEDDWDFLPPKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IDNSQVESGSLEDDWDFLPPKK 22 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;;; 267.77 1.21E-37 1598840000 3487320 2645490 2342260 2781530 2583730 2444100 3397370 3648550 2719960 FALSE TRUE 3026461.826 2628111.602 3474984.77 3413118.9 2532318.828 2538126.109 3067893.58 2868335.976 2398409.427 1.261862046 1.095772712 1.448870543 1.423076002 1.055832586 1.058253891 1.279136725 1.19593258 1 21.19364653 3.230044829 24.99831064 1.136712893 1.302384805 0.365195807 0.122716718 246.691908 724169.0566 0.03910661 0.045042224 1698.41896 -3.230044829 0.165671912 IDPAYFDENWLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDPAYFDENWLNR 13 0 Q86VS8 Q86VS8 HOOK3 Protein Hook homolog 3 0 78.653 0.052682 50782000 24100 22749 21440 21449 25171 27443 23400 25754 29346 FALSE TRUE 20915.12394 22599.56032 31808.45571 26319.32328 24670.14635 28498.74997 21130.6716 20246.70752 25876.74931 0.808259325 0.873353915 1.229229195 1.017103152 0.953371154 1.101326508 0.816589107 0.782428553 1 14.65936877 2.221489891 24.99447874 0.846784868 1.000953972 0.183528986 0.127649947 357.5170439 523462.5048 0.053096169 0.03589763 166.5290063 -2.221489891 0.154169104 IDPWSFVSAGPRPS(ph)PLPS(ph)PQPAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IDPWSFVSAGPRPSPLPSPQPAPR 24 1 Q16584;Q16584-2;E9PID4 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 2 IDPWS(0.003)FVS(0.004)AGPRPS(0.992)PLPS(1)PQPAPR;IDPWS(0.002)FVS(0.002)AGPRPS(0.997)PLPS(1)PQPAPR;IDPWS(0.001)FVS(0.001)AGPRPS(0.998)PLPS(1)PQPAPR 92.991 3.96E-05 184446000 355327 329981 219215 253233 329661 324556 294923 360401 356711 TRUE FALSE 308369.6367 327813.3331 325228.1072 310733.4231 323101.3911 337041.8793 266321.4129 283332.0508 314541.0319 0.980379681 1.04219577 1.033976729 0.987894715 1.027215397 1.071535492 0.846698477 0.900779301 1 18.2628887 2.243242906 24.99991862 0.9098109 1.023676181 0.562052242 0.044852679 77.93560979 416120.8203 0.016933818 0.01268142 175.0825671 -2.243242906 0.113865281 IDPWSFVSAGPRPSPLPS(ph)PQPAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDPWSFVSAGPRPSPLPSPQPAPR 24 1 Q16584;Q16584-2;E9PID4 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 IDPWSFVSAGPRPS(0.007)PLPS(0.993)PQPAPR 76.835 0.013545 248450000 124170 117950 115260 105660 176470 156830 129790 164170 148170 TRUE FALSE 107760.6199 117175.1787 171000.1215 129651.7179 172958.5923 162863.3516 117202.9858 129063.5231 130653.5114 0.824781659 0.896839109 1.308806168 0.992332441 1.323795973 1.246528699 0.897051939 0.987830497 1 16.99538637 4.453529876 23.92588866 1.095083235 0.842795886 0.33425717 0.145893927 146.3755159 148450.8118 0.03820482 0.101095684 28413.8364 -4.453529876 -0.252287349 IDQLEGDHQLIQEALIFDNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IDQLEGDHQLIQEALIFDNK 20 0 P12814-3;P12814;P12814-2;P12814-4;H9KV75;H7C5W8;H0YJ11;H0YJW3 P12814-3 ACTN1 Alpha-actinin-1 0 ; 303.06 5.13E-55 447680000 1088640 748120 801920 1154190 693280 629920 808750 1157510 2534900 FALSE TRUE 944773.4657 743205.5505 1189731.194 1416266.48 679485.0844 654153.43 730317.5495 909985.4943 2235227.01 0.422674503 0.332496676 0.532264145 0.633611921 0.303989296 0.292656373 0.326730818 0.407110996 1 21.09198993 1.238707386 11.00972129 1.001400628 0.404607781 0.752509863 0.106972827 0.03445402 144.3685715 0.155883764 0.027923592 17.3263621 -1.238707386 -0.596792847 IDRDSYS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDRDSYSPR 9 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 IDRDS(0.052)YS(0.948)PR 130.4 0.00095297 477980000 1070300 894690 560610 679650 785580 899790 832400 917320 820930 TRUE FALSE 928857.1432 888812.7225 831722.8711 833974.9203 769948.495 934405.5035 751673.9761 721158.2566 723880.5906 1.283163488 1.22784439 1.148977997 1.152089075 1.063640198 1.290828233 1.038394987 0.99623925 1 19.46539221 -1.66184657 0.168855331 5.81E-15 1.331485727 0.562482684 0.072198015 84.22633118 1.278118166 26.96472838 0.846684245 0.021784793 1.66184657 1.331485727 IDRLDGAHAPELTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDRLDGAHAPELTK 14 1 O76003 O76003 GLRX3 Glutaredoxin-3 0 113.4 0.00032326 368500000 442610 364320 277810 304820 359130 317700 479620 582650 373410 FALSE TRUE 384117.9671 361926.7579 412159.8452 374034.0399 351984.0156 329922.1246 433106.5262 458054.8317 329265.8952 1.166588987 1.099192972 1.251753829 1.135963503 1.068996276 1.001993007 1.315370139 1.391139618 1 18.32889356 2.218076256 24.99999785 1.271255311 1.124062347 0.150440132 0.118652066 339.8184743 414726.0768 0.048548245 0.03277305 165.2251887 -2.218076256 -0.147192964 IDRPEAISEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IDRPEAISEER 11 1 Q9Y6B6;D6RD69;Q9H029;D6R9R5 Q9Y6B6 SAR1B;DKFZp434B2017 GTP-binding protein SAR1b 0 ;;; 212.68 4.66E-09 5117400000 5872390 5812830 3624980 4407000 5632270 5357430 5525010 6518640 6336250 FALSE TRUE 5096338.783 5774645.137 5378032.453 5407676.707 5520198.846 5563533.799 4989195.381 5124679.564 5587185.743 0.912147728 1.033551667 0.962565538 0.967871296 0.988010619 0.995766752 0.892971097 0.917220189 1 22.41369035 2.254751719 24.99465817 0.930842479 0.978715453 0.173212429 0.04027187 324.3373464 500688.1901 0.014332586 0.011067844 179.7842815 -2.254751719 0.047872974 IDRTDAISEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IDRTDAISEEK 11 1 Q9NR31;Q9NR31-2;H0Y5E8 Q9NR31 SAR1A GTP-binding protein SAR1a 0 ; 147.42 3.22E-05 900140000 1467030 1232050 844820 993150 1188400 949970 1508730 1736780 1096350 FALSE TRUE 1273158.269 1223956.582 1253377.778 1218659.887 1164753.165 986515.9606 1362413.597 1365383.113 966740.752 1.316959346 1.266064951 1.296498338 1.26058603 1.20482473 1.020455545 1.409285368 1.412357046 1 19.88276953 3.536959631 4.858992186 1.239671545 1.289568686 0.050458325 0.136088601 1.119923048 53.99929623 0.040791854 0.060099529 3443.179236 -3.536959631 0.049897141 IDRVETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDRVETR 7 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 116.25 0.0050141 372960000 457040 438600 281000 280130 390860 477680 454860 490950 357180 FALSE TRUE 396641.006 435718.8077 416892.5399 343737.798 383082.6507 496056.6587 410747.7472 385964.1631 314954.5873 1.259359355 1.383433756 1.323659209 1.091388447 1.216310751 1.575010108 1.304149118 1.225459729 1 18.2647843 1.268637242 2.461208952 0.936046088 1.308184404 0.384045496 0.122547641 0.572903648 3.961541792 0.443541815 0.033825297 18.56253314 -1.268637242 0.372138317 IDS(ph)LSAQLSQLQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IDSLSAQLSQLQK 13 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 IDS(1)LSAQLSQLQK;IDS(0.564)LS(0.436)AQLSQLQK;IDS(1)LSAQLSQLQK;IDS(0.817)LS(0.183)AQLSQLQK 261.61 6.50E-24 197506000 1205180 827400 757920 830490 839790 647900 935690 1237340 1736250 TRUE FALSE 1045912.409 821964.7549 1124452.647 1019065.448 823079.822 672825.1322 844946.9278 972744.47 1530992.503 0.68315972 0.536883592 0.73445993 0.665624061 0.537611922 0.439469907 0.551894883 0.635368539 1 20.54603579 1.237134623 3.947943584 1.047329222 0.591093125 0.690839705 0.08495155 0.152087513 4.0559517 0.202393889 0.022797066 17.2637295 -1.237134623 -0.456236097 IDS(ph)PGFKPASQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IDSPGFKPASQQK 13 1 G3V1L9;Q07157 G3V1L9 TJP1 Tight junction protein ZO-1 1 IDS(1)PGFKPASQQK;IDS(1)PGFKPASQQK;IDS(1)PGFKPASQQK 191.37 2.19E-06 3197700000 13451590 9292280 8961320 9013480 10314240 6927450 13762910 15616900 13600910 TRUE FALSE 11673928.3 9231238.401 13295044.33 11060128.4 10109006.8 7193953.484 12428185.11 12277347.47 11993025.91 0.973393069 0.769717206 1.108564629 0.922213333 0.842907109 0.599844738 1.036284354 1.023707241 1 23.51569237 IDS(ph)PGFKPASQQVYR ddPTM_MDA-MB-175_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 208.37 1.77E-09 3885690000 4932928 4266337 3014709 3519059 4808948 3387054 4741192 6150463 4767669 TRUE FALSE 4281029.066 4238311.151 4472632.356 4318115.131 4713259.343 3517356.159 4281391.93 4835234.35 4204040.602 1.018312969 1.008151812 1.063888953 1.027134498 1.121126028 0.836660844 1.018399282 1.150139784 1 22.00334517 1.952108306 22.10220857 1.085337059 1.012549515 0.091302286 0.079657954 208.068886 96022.68422 0.035876847 0.020705634 89.55880823 -1.952108306 -0.072787544 IDS(ph)TEVIYQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IDSTEVIYQPR 11 0 K7EMR0;K7EQN8;K7EP59;Q15831-2;Q15831 K7EMR0 STK11 Serine/threonine-protein kinase STK11 1 IDS(0.5)T(0.5)EVIYQPR;IDS(0.651)T(0.349)EVIYQPR;IDS(0.938)T(0.062)EVIYQPR;IDS(0.538)T(0.462)EVIYQPR 232.17 5.55E-13 1752010000 959270 831970 620030 642420 924380 799470 915810 990970 949930 TRUE FALSE 832500.039 826504.7343 919878.5819 788291.2798 905986.6465 830226.1282 826994.8872 779058.7772 837630.3576 0.9938752 0.986717741 1.098191551 0.941096837 1.081606747 0.991160505 0.987302907 0.930074669 1 19.6759542 2.237256564 2.746294421 0.961067491 1.019060102 0.161789483 0.048351919 0.389426232 6.061496282 0.021099635 0.013464639 172.685775 -2.237256564 0.05799261 IDSIEDRYPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDSIEDRYPR 10 1 Q13158 Q13158 FADD FAS-associated death domain protein 0 183.03 1.56E-06 263670000 290040 278890 91788 111490 262150 241240 264770 271940 36097 FALSE TRUE 251710.4791 277057.9532 136176.9838 136805.5085 256933.7279 250520.6589 239092.6462 213787.7472 31829.65378 7.908049546 8.704397325 4.278305531 4.298052045 8.072149627 7.870668673 7.511632008 6.716621824 1 14.95808384 4.260774519 24.9046162 5.983648389 8.306225388 0.19483825 2.152464802 424.6860209 476118.5577 0.5448303 1.439000589 18229.48999 -4.260774519 2.322576999 IDSRPPS(ph)PEPPKQEYWGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IDSRPPSPEPPKQEYWGSK 19 2 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 IDS(0.073)RPPS(0.927)PEPPKQEYWGSK;IDS(0.024)RPPS(0.976)PEPPKQEYWGSK 134.03 5.50E-06 888780000 1536470 1002400 875350 1150020 1090350 766670 1441970 1738350 1659690 TRUE FALSE 1333421.597 995815.1684 1298672.188 1411149.618 1068654.168 796164.291 1302127.971 1366617.38 1463483.339 0.911128648 0.680441753 0.887384334 0.964240303 0.730212733 0.544020058 0.889745675 0.933811369 1 20.48097489 2.010417842 24.99923404 0.947058164 0.785347017 0.277187097 0.121790969 283.994754 681486.9639 0.051599885 0.034748364 102.4277994 -2.010417842 -0.161711147 IDTGWLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IDTGWLDR 8 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 133.86 0.0020967 498810000 796290 676990 522190 467480 746790 733490 698190 776120 773450 FALSE TRUE 691058.259 672542.8081 774722.8306 573628.479 731930.3401 761707.8349 630479.6413 610152.7778 682013.6221 1.013261666 0.986113453 1.135934541 0.841080677 1.073190207 1.116851351 0.924438487 0.894634298 1 19.37944103 2.182938357 24.99165511 0.929668238 1.024346428 0.189412991 0.084831245 131.4076931 59041.57167 0.033593051 0.022648445 152.3836449 -2.182938357 0.09467819 IDTHPS(ph)PSHSSTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IDTHPSPSHSSTVK 14 0 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477;H0Y594;B7ZBA0 Q8NI27 THOC2 THO complex subunit 2 1 IDT(0.001)HPS(0.899)PS(0.1)HSSTVK;IDTHPS(0.988)PS(0.012)HSSTVK;IDTHPS(0.993)PS(0.007)HSSTVK 196.22 1.62E-08 806850000 1039730 788680 241031 588670 931320 810320 995200 1092780 1789140 TRUE FALSE 902327.0462 783499.1091 357594.3978 722336.5208 912788.5541 841493.5347 898685.6572 859097.501 1577629.907 0.571951027 0.496630487 0.22666558 0.457861833 0.578582182 0.533390962 0.569642888 0.544549452 1 20.58932738 -0.053617373 1.176407668 10 0.473503023 0.706126842 0.102263858 16.99933555 1.54395367 382.9594785 0.032919346 0.883858264 0.053617373 -9.526496977 IDTIEIITDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 IDTIEIITDR 10 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;; 249.69 1.12E-12 5879464000 3829490 2975359 2200951 2802504 2998695 2751652 2871658 3414299 4713157 FALSE TRUE 3323413.194 2955813.671 3265338.265 3438855.367 2939026.836 2857509.833 2593165.049 2684177.729 4155972.949 0.799671517 0.711220623 0.785697671 0.827448929 0.707181416 0.687566995 0.623961003 0.64586025 1 21.98675483 3.206555351 24.66726273 0.711593364 0.776359632 0.026226958 0.107113257 464.2632571 357817.6829 0.032372484 0.036710121 1608.997434 -3.206555351 0.064766269 IDVDAPDIDIHGPDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IDVDAPDIDIHGPDAK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 134.85 2.60E-05 836470000 1073270 687410 534730 717240 732060 664080 689290 1089480 914230 FALSE TRUE 931434.6502 682894.3584 793327.2166 880100.3043 717493.4383 689627.5873 622442.7619 856503.1803 806150.7709 1.155409985 0.847105012 0.984092859 1.091731641 0.890023882 0.855457332 0.772117058 1.062460288 1 19.62069016 3.210324349 24.99945975 0.920497956 1.004729846 0.1730803 0.110148911 480.8882957 425761.0229 0.034386413 0.038997471 1623.021786 -3.210324349 0.08423189 IDYANLTGISVSSLSDSLFVLHVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IDYANLTGISVSSLSDSLFVLHVQR 25 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 ;; 238.63 1.66E-38 180332000 152126 147803 88689 135687 141523 146363 155118 183227 171312 FALSE TRUE 132022.1637 146832.0724 131579.297 166496.8072 138706.9692 151993.6793 140074.6802 144045.3319 151059.6905 0.873973482 0.972013592 0.871041749 1.102192164 0.918226224 1.006182912 0.927280334 0.95356565 1 17.20475921 IDYIAGLDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IDYIAGLDSR 10 0 H3BQB1;P07741-2;P07741;H3BQF1 H3BQB1 APRT Adenine phosphoribosyltransferase 0 173.37 7.98E-06 641670000 655300 565790 373300 420660 542150 539260 538230 620350 562960 FALSE TRUE 568700.4447 562073.2882 553829.1286 516177.2824 531362.2757 560005.6811 486032.5374 487692.9801 496407.5101 1.145632234 1.132282 1.115674355 1.039825691 1.070415465 1.128116859 0.979099888 0.982444806 1 18.92116542 -1.999671608 0.08859851 0.279438881 1.351917567 0.668991733 0.036716447 215.5399335 1.791316959 29.17109261 3.90775871 0.010007564 1.999671608 1.072478686 IEADSESQEDIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IEADSESQEDIIR 13 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 0 200.67 1.06E-06 0 142020 142000 89512 103200 134970 132340 149460 157160 128400 FALSE TRUE 123251.6972 141067.1927 132800.3026 126633.1373 132284.3611 137431.2054 134965.3922 123552.557 113220.6983 1.088596865 1.245948796 1.172933082 1.118462783 1.168376128 1.213834639 1.192055819 1.091254151 1 16.7887782 1.449864329 2.65383176 0.996100257 1.173626742 0.614772675 0.044492481 0.205783747 2.413859618 0.068446887 0.011485454 28.17502624 -1.449864329 0.177526485 IECDDKGDGSCDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IECDDKGDGSCDVR 14 1 Q60FE5;P21333-2;P21333;A0A087WWY3;Q14315-2;Q14315 Q60FE5;Q14315-2 FLNA;FLNC Filamin-A;Filamin-C 0 85.909 0.0068851 288150000 507080 717730 329910 221180 394960 401950 561680 551890 639070 FALSE TRUE 440068.0932 713015.1844 489455.5795 271402.2995 387101.0687 417413.2766 507208.3601 433872.6183 563519.8726 0.780927372 1.265288447 0.868568445 0.481619749 0.686934193 0.740725034 0.900071825 0.769933128 1 19.10410696 6.07674957 9.27643278 0.827785893 0.750346727 0 0.205682364 0 0 0.047796762 0 1193299.807 -6.07674957 -0.077439166 IECSHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IECSHIR 7 0 D6RIC3;A0A0C4DGU5;A0A087X2G6;Q9Y3C1;Q9Y3C1-3;Q9Y3C1-2;D6RC60 D6RIC3 NOP16 Nucleolar protein 16 0 ; 106.14 0.0077688 198170000 254520 247670 162647 178699 233278 273260 241757 248154 252720 FALSE TRUE 220884.5371 246043.0395 241303.6332 219275.3392 228636.2242 283772.489 218311.4434 195088.1982 222843.7295 0.991208223 1.104105734 1.082837887 0.983987028 1.025993528 1.273414736 0.979661594 0.875448453 1 17.76567284 2.011055451 24.99982128 0.928445845 1.076443417 0.329358125 0.085564094 212.0464135 479501.1725 0.034388029 0.02316175 102.578289 -2.011055451 0.147997572 IEDFGVHCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IEDFGVHCK 9 0 Q92905;E5RHH5 Q92905 COPS5 COP9 signalosome complex subunit 5 0 99.815 0.0051861 0 595020 526920 358950 467310 528800 440980 602370 733510 685510 FALSE TRUE 516386.5994 523458.6278 532539.4206 573419.8779 518277.9146 457944.786 543952.2501 576654.5947 604469.7887 0.854280245 0.865979802 0.881002542 0.948632816 0.857409128 0.757597475 0.89988327 0.953984145 1 19.20531071 1.692082734 2.771094931 0.989794561 0.86412486 0.509146284 0.046851481 0.200647812 3.391476174 0.042304653 0.013527698 49.21332794 -1.692082734 -0.125669702 IEDFLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 IEDFLER 7 0 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 ;;;;;;; 187.63 0.0013526 9999920000 6168800 6446430 4398750 4847550 6307310 5980930 6544390 7616820 7123170 FALSE TRUE 5353577.45 6404082.977 6526000.213 5948260.318 6181806.871 6211020.247 5909716.065 5988022.317 6281076.957 0.852334319 1.019583587 1.038993831 0.947012807 0.984195372 0.988846386 0.940876239 0.95334325 1 22.58258052 4.74958501 24.91849616 0.980383603 0.852334242 0.633942186 0.031355264 1141.275121 2579579.358 0.008143581 0.118617996 56180.42369 -4.74958501 -0.128049361 IEDFLERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IEDFLERR 8 1 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 97.431 0.015182 0 96781 97348 31577 30136 97056 101900 104350 107800 22805 FALSE TRUE 83991.14564 96708.51458 46847.74282 36978.8394 95124.77549 105820.1589 94230.15306 84747.8089 20109.01888 4.176789835 4.809210989 2.329688141 1.83891813 4.730453338 5.262323317 4.685964722 4.214417889 1 14.29555507 IEDHLDEAIHVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IEDHLDEAIHVLR 13 0 K7ENH8;A0A0A0MRB7;P15923-2;X6REB3;P15923;P15923-3 K7ENH8 TCF3 Transcription factor E2-alpha 0 160.69 2.51E-05 18297000 14034 13171 9116.2 11546 15628 13231 13482 17317 12224 FALSE TRUE 12179.37134 13084.47883 13524.82481 14167.69577 15317.03338 13740.00513 12174.51772 13613.89431 10778.89265 1.129927882 1.213898242 1.25475086 1.314392511 1.421021053 1.274713979 1.129477592 1.263014185 1 13.39592135 0.576887824 1.42183306 2.28E-17 1.261291237 0.44252502 0.086238364 7.109316945 3.10251155 20.68642713 0.026189465 3.774746785 -0.576887824 1.261291237 IEDS(ph)EPHIPLIDDTDAEDDAPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IEDSEPHIPLIDDTDAEDDAPTK 23 0 P20020-6;P20020;P20020-4;P20020-1;H0YHH6;A0A0U1RQU3;E7ERY9 P20020-6 ATP2B1 Plasma membrane calcium-transporting ATPase 1;Calcium-transporting ATPase 1 IEDS(1)EPHIPLIDDTDAEDDAPTK 233.22 3.14E-37 40729000 44374 38120 44338 62175 51878 65059 33223 82091 84457 TRUE FALSE 38509.86347 37869.58721 65780.0051 76292.78404 50845.7293 67561.86183 30001.03857 64536.47848 74472.58967 0.517101173 0.508503697 0.883278068 1.024441132 0.682744209 0.907204411 0.402846721 0.866580292 1 16.18442191 4.246758572 24.94145833 0.810228397 0.512802253 0.345986025 0.177032808 204.7371801 622877.6732 0.044233663 0.112804146 17650.56338 -4.246758572 -0.297426143 IEDS(ph)EPHIPLIDDTDAEDDAPTKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IEDSEPHIPLIDDTDAEDDAPTKR 24 1 P20020-6;P20020;P20020-4;P20020-1;H0YHH6;A0A0U1RQU3;E7ERY9 P20020-6 ATP2B1 Plasma membrane calcium-transporting ATPase 1;Calcium-transporting ATPase 1 IEDS(1)EPHIPLIDDTDAEDDAPTKR;IEDS(1)EPHIPLIDDTDAEDDAPTKR;IEDS(0.995)EPHIPLIDDT(0.005)DAEDDAPTKR 128.27 3.70E-05 348296000 409580 301184 303327 484225 391441 413502 260912 549003 468249 TRUE FALSE 355452.9653 299205.5025 450016.9518 594175.6872 383652.0899 429409.6895 235608.7944 431602.9808 412893.1367 0.860883686 0.724656033 1.089911437 1.439054405 0.92918011 1.040002004 0.570628992 1.045314011 1 18.65540891 IEDTVFHVFDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IEDTVFHVFDK 11 0 Q9Y2L1;G3V1J5;Q9Y2L1-2 Q9Y2L1 DIS3 Exosome complex exonuclease RRP44 0 ;; 131.37 0.00020478 361220000 1584850 1312892 966684 1218592 1298500 1114739 1535450 1721570 1586680 FALSE TRUE 1375408.057 1304267.526 1434175.616 1495291.939 1272662.39 1157623.731 1386542.295 1353425.653 1399104.498 0.983063137 0.932215948 1.025066832 1.06874929 0.909626402 0.827403337 0.991021255 0.96735137 1 20.41607229 5.109746571 18.22287514 0.965157008 2.775263037 0.007172259 0.066125464 2109.080851 359011.4411 0.016356428 3989.337026 128749.8023 -5.109746571 1.810106029 IEDVGS(ph)DEEDDSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 IEDVGSDEEDDSGK 14 0 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 1 IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK 363.44 2.27E-83 87292290000 27273150 16584350 17536900 19980810 15991390 12562760 20571880 23783450 48341610 TRUE FALSE 23668934.13 16475406.31 26017803.5 24517758.3 15673192.63 13046057.51 18576822.24 18697544.3 42626719.94 0.555260507 0.386504201 0.610363723 0.575173467 0.367684698 0.306053516 0.435802292 0.438634367 1 25.34525471 1.237467688 24.99542647 1.000000648 0.455745747 0.756169381 0.09644823 14.06197191 321447.8749 0.146416565 0.024572143 17.27697434 -1.237467688 -0.544254901 IEDVGS(ph)DEEDDSGKDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 IEDVGSDEEDDSGKDK 16 1 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 1 IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(0.999)DEEDDS(0.001)GKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK 320.78 1.13E-57 73736210000 28779660 15372060 18195460 16043470 13688850 10215710 23435780 27593100 28042760 TRUE FALSE 24976355.01 15271079.93 26994845.32 19686385.07 13416468.67 10608714.97 21162981.66 21692530.29 24727576.86 1.010060757 0.617572842 1.091689876 0.796130781 0.542571104 0.429023638 0.85584535 0.877260656 1 24.55961754 3.486956296 24.95957257 0.743579432 0.888613665 0.121344013 0.201391818 1201.858497 3050101.212 0.060111346 0.082548691 3068.713159 -3.486956296 0.145034233 IEDVGS(ph)DEEDDSGKDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 IEDVGSDEEDDSGKDKK 17 2 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 1 IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(0.999)DEEDDS(0.001)GKDKK;IEDVGS(1)DEEDDSGKDKK 273.44 6.06E-36 82090975000 19968280 9495332 13436833 9598537 7560110 5162274 16380043 18236367 13327616 TRUE FALSE 17329421.2 9432956.539 19934930.38 11778031.53 7409678.602 5360870.021 14791508.95 14336661.83 11752040.42 1.474588292 0.802665427 1.696295254 1.002211625 0.630501457 0.456165043 1.258633261 1.219929588 1 23.48640793 4.759616686 23.0604547 1.028817274 1.474589569 0.150232232 0.34546832 3924.535919 4297922.759 0.08801843 3.318916709 57493.22705 -4.759616686 0.445772294 IEDVGS(ph)DEEDDSGKDKKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IEDVGSDEEDDSGKDKKK 18 3 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 1 IEDVGS(1)DEEDDSGKDKKK 124.37 2.28E-05 200460000 326830 130770 89471 61599 96788 56215 311700 291250 34807 TRUE FALSE 283638.5874 129910.9633 132739.4749 75585.99443 94862.10816 58377.62743 281471.382 228968.454 30692.15611 9.241403125 4.23270893 4.324866405 2.462713736 3.090760643 1.902037355 9.170792073 7.460161911 1 14.90558238 2.248740759 24.99988491 6.344055651 4.085205976 0.062025422 2.845040145 441.0533453 1083117.694 1.074105279 0.822327834 177.3130739 -2.248740759 -2.258849675 IEDVTPIPSDS(ph)TRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IEDVTPIPSDSTRR 14 1 P62263;A0A2R8Y811 P62263 RPS14 40S ribosomal protein S14 1 IEDVTPIPS(0.001)DS(0.735)T(0.264)RR 129.43 4.16E-05 144950000 138470 138900 46954 147070 108330 49307 150820 161490 144460 TRUE FALSE 120170.8387 137987.5568 69661.11145 180464.4913 106174.4449 51203.8722 136193.4996 126956.6202 127382.1034 0.943388714 1.083257013 0.546867335 1.416717785 0.833511476 0.401970692 1.069172953 0.996659789 1 16.95880307 IEDVTPIPSDST(ph)RR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IEDVTPIPSDSTRR 14 1 P62263;A0A2R8Y811 P62263 RPS14 40S ribosomal protein S14 1 IEDVTPIPSDS(0.364)T(0.636)RR 110.77 0.00040461 113500000 111060 117210 41351 126890 100880 49141 129820 150230 120040 TRUE FALSE 96383.13961 116440.0398 61348.48191 155702.3139 98872.68537 51031.48607 117230.0764 118104.4836 105849.008 0.910571969 1.100057923 0.579584855 1.470985103 0.934091753 0.482115865 1.10752173 1.115782622 1 16.69164822 IEDVTPIPSDSTRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IEDVTPIPSDSTRR 14 1 P62263;A0A2R8Y811 P62263 RPS14 40S ribosomal protein S14 0 ;;;;; 228.17 2.82E-12 8245200000 3394370 3333860 1514560 1807750 3284590 3076950 3227990 3816940 1042080 FALSE TRUE 2945795.404 3311959.654 2247006.282 2218227.267 3219233.085 3195322.258 2914940.027 3000717.084 918886.4895 3.205831665 3.604318588 2.445357841 2.414038396 3.503406701 3.477385176 3.172252569 3.265601485 1 19.80952713 4.253377986 24.95395844 2.862547789 3.405075188 0.103991929 0.743175139 626.4665837 1055014.24 0.183522032 0.481151456 17921.64978 -4.253377986 0.5425274 IEEACEIYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IEEACEIYAR 10 0 P54920;M0R0Y2;M0R2M1 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;;; 183.47 3.87E-06 1146500000 842840 757090 543960 609070 744660 765740 752690 872720 847090 FALSE TRUE 731456.5585 752116.6259 807020.8754 747368.6526 729842.7229 795198.5133 679694.2397 686095.6195 746947.9852 0.979260368 1.00691968 1.080424463 1.000563182 0.977099795 1.064596905 0.909961943 0.91853199 1 19.51064826 2.2296825 24.99995101 0.936399389 1.017800015 0.432313807 0.040458903 164.8273485 464133.774 0.016218547 0.011112138 169.7002569 -2.2296825 0.081400626 IEEDFPHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IEEDFPHIR 9 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 0 ; 214.93 6.58E-07 332570000 498790 424920 283930 342880 438050 359120 429570 475610 402840 FALSE TRUE 432873.6377 422128.6725 421239.4977 420736.1446 429333.662 372935.5788 387910.3675 373904.5027 355216.7141 1.218618439 1.188369398 1.185866208 1.184449177 1.20865276 1.049881844 1.092038612 1.052609542 1 18.43833994 2.736142033 24.93751056 1.053323229 1.195364043 0.901781858 0.024336134 62.48331635 644248.8327 0.00828619 0.007654455 544.680758 -2.736142033 0.142040814 IEEEEQEPEPPEPFEYIDD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 IEEEEQEPEPPEPFEYIDD 19 0 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;;;;;;; 203.7 1.15E-15 2794441000 8246700 7644600 5371742 6082262 7312415 7122079 7774420 8931880 8004126 FALSE TRUE 7156877.701 7594382.119 7969534.399 7463332.549 7166912.248 7396069.988 7020457.945 7021866.97 7057887.343 1.014025494 1.076013508 1.129167131 1.05744569 1.015447244 1.047915563 0.994696799 0.994896437 1 22.75080497 2.804288765 1.15155641 0.996151461 1.073406613 0.46582619 0.031271633 0.409025965 1.168544319 0.017882402 0.015315378 637.2190704 -2.804288765 0.077255152 IEEELGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IEEELGSK 8 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;; 155.75 0.00093967 2078140000 2247040 2147870 1455560 1480250 1834390 1597120 2093280 2328380 2721530 FALSE TRUE 1950087.971 2133760.501 2159473.685 1816363.387 1797889.228 1658562.24 1890274.028 1830474.056 2399793.824 0.812606463 0.889143259 0.899858006 0.756883099 0.749184872 0.691126972 0.787681845 0.76276305 1 21.19447903 5.705995772 14.0102587 0.808954703 0.781053338 0 0.090651174 0 0 0.020629109 0 508154.4949 -5.705995772 -0.027901365 IEEGERPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IEEGERPDR 9 1 Q5JR04;Q9HCE1;Q9HCE1-2 Q5JR04 MOV10 Putative helicase MOV-10 0 90.15 0.010147 0 326350 241120 194560 221610 245230 299340 259940 299330 284420 FALSE TRUE 283222.0206 239536.0668 288649.8668 271929.9376 240350.4028 310855.8035 234731.0588 235320.6089 250796.1916 1.129291553 0.955102489 1.150934011 1.084266614 0.958349492 1.239475773 0.935943474 0.938294188 1 17.93615592 IEEIKDFLLTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IEEIKDFLLTAR 12 1 J3KT73;J3QL01;P63173;J3KSP2 J3KT73 RPL38 60S ribosomal protein L38 0 ; 182.89 1.49E-05 704930000 2008360 2291920 1127080 1377130 1516940 1451330 1416110 2001420 2696360 FALSE TRUE 1742950.137 2276864.227 1672139.658 1689828.415 1486755.862 1507163.604 1278775.87 1573431.908 2377599.393 0.733071409 0.957631565 0.703289067 0.710728822 0.625318069 0.633901409 0.537843286 0.661773347 1 21.18107422 4.095936246 7.924840754 0.678564561 0.844566248 0.17623543 0.131030198 0.347496216 25.19023647 0.033046791 0.06932129 12472.00414 -4.095936246 0.166001687 IEEPVSMEMDNHMSDKDESCYDNAEAAFS(ph)DDEEDLNSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IEEPVSMEMDNHMSDKDESCYDNAEAAFSDDEEDLNSK 38 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 IEEPVSMEMDNHMSDKDESCYDNAEAAFS(1)DDEEDLNSK 274.11 1.34E-76 98957000 57434 48774 23014 30830 52417 35359 70029 77216 65580 TRUE FALSE 49843.95138 48453.60038 34143.64738 37830.42271 51374.00425 36719.28361 63237.59836 60703.9593 57827.20711 0.861946372 0.837903174 0.590442615 0.654197645 0.888405421 0.63498283 1.093561345 1.049747382 1 15.81946081 2.230960267 24.99930487 1.050089671 0.744299223 0.667555214 0.100834486 100.3216781 329977.6265 0.040968534 0.028217759 170.2002786 -2.230960267 -0.305790447 IEEVLSGVLDTELR ddPTM_MDA-MB-175_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 ; 191.52 1.12E-06 26763000 45621 47361 25011 36216 47936 40562 40791 53017 43299 FALSE TRUE 39592.06926 47049.88247 37106.40326 44439.39633 46982.16739 42122.44639 36835.0951 41679.72713 38180.24155 1.036977967 1.232309712 0.971874502 1.163937014 1.230536149 1.103252486 0.964768519 1.091656979 1 15.22053861 2.455551896 19.38271898 1.032057948 1.130440732 0.251439461 0.084659149 26.28587681 23618.1182 0.030074251 0.023305748 285.4643606 -2.455551896 0.098382784 IEGDMIVCAAYAHELPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IEGDMIVCAAYAHELPK 17 0 P46777;A0A2R8Y6J3;A0A2R8Y4A2;Q5T7N0 P46777 RPL5 60S ribosomal protein L5 0 ; 245.76 1.33E-20 758980000 955780 800490 576160 672190 724810 592440 949350 1088840 1005890 FALSE TRUE 829471.2514 795231.5285 854792.9031 824821.0133 710387.6991 615231.5502 857282.1831 856000.0394 886974.8301 0.935168872 0.89656606 0.963717204 0.929926065 0.800910776 0.693629097 0.966523687 0.965078163 1 19.75853364 2.040496436 24.99965618 0.975772495 0.871292779 0.299555353 0.077401107 202.2962392 124882.6609 0.034317903 0.023137096 109.7732282 -2.040496436 -0.104479716 IEGVYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IEGVYAR 7 0 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ;; 138.48 0.0064712 2377950000 1689630 1663880 973670 1200770 1631560 1439200 1577210 1655770 1687370 FALSE TRUE 1466341.115 1652949.863 1444540.069 1473423.181 1599095.148 1494566.955 1424252.417 1301696.471 1487891.041 0.985516462 1.110934751 0.970864149 0.990276264 1.074739416 1.00448683 0.957228976 0.874860077 1 20.50483745 2.206543916 3.297051038 0.92604379 1.026688339 0.341472777 0.051641783 0.218865248 4.944826431 0.022184441 0.014471602 160.8955069 -2.206543916 0.100644548 IEGYEDQVLITEHGDLGNGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IEGYEDQVLITEHGDLGNGK 20 0 P47755;F8W9N7;C9JUG7;A0A0D9SET8;P47755-2 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 286.46 3.08E-45 349660000 649900 561000 495870 696200 571200 517640 660420 737070 1123100 FALSE TRUE 564014.0684 557314.7541 735674.3906 854282.8508 559834.2375 537553.9458 596372.57 579453.3164 990328.3974 0.569522261 0.562757521 0.742859028 0.862625825 0.56530161 0.542803728 0.602196778 0.58511229 1 19.91754748 1.234335061 24.9992512 1.000000543 0.629901502 0.577032311 0.099781317 101.8428307 602441.5901 0.197787178 0.0261109 17.15280149 -1.234335061 -0.370099041 IEGYEDQVLITEHGDLGNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IEGYEDQVLITEHGDLGNSR 20 0 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 ;;; 247.74 3.65E-30 1175530000 1461100 1190890 910980 1237650 1170390 1222540 1150620 1466390 2033570 FALSE TRUE 1268011.933 1183066.965 1351532.975 1518677.349 1147101.529 1269571.905 1039033.049 1152813.91 1793163.671 0.707136751 0.659765187 0.75371423 0.846926231 0.639708214 0.708006706 0.579441278 0.642893858 1 20.77407575 1.233341543 24.98212476 1.000000489 0.689200012 0.640526413 0.072435544 114.0056994 545648.1459 0.156307984 0.018910391 17.11360653 -1.233341543 -0.310800477 IEHAPS(ph)PSSGGTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IEHAPSPSSGGTLK 14 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YD28;A0A2R8YCQ1;A0A2R8Y7Y0 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 IEHAPS(0.829)PS(0.17)S(0.001)GGTLK 173.51 1.73E-06 432260000 465520 295900 268550 348780 301770 268800 329040 445380 710390 TRUE FALSE 404000.3525 293956.2134 398421.6782 427975.8298 295765.3674 279140.9099 297129.7514 350138.953 626408.5035 0.644947108 0.469272387 0.636041299 0.683221616 0.472160524 0.445621201 0.47433863 0.558962643 1 19.25674427 1.239592763 6.518443513 1.012495688 0.543114662 0.741316701 0.083909192 0.062019376 12.45725786 0.129377183 0.0214488 17.36172062 -1.239592763 -0.469381026 IEHFMPLLVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IEHFMPLLVQR 11 0 Q9Y6Q5;K7EPR4;K7EMG5;Q9Y6Q5-2 Q9Y6Q5;Q9Y6Q5-2 AP1M2 AP-1 complex subunit mu-2 0 ; 163.34 2.41E-05 970410000 1231040 1413260 931650 1056680 1413970 1496840 1431010 1551930 1565310 FALSE TRUE 1068354.945 1403976.202 1382199.056 1296615.344 1385834.763 1554424.403 1292230.87 1220061.847 1380260.835 0.774023951 1.017181801 1.001404243 0.93939878 1.004038315 1.126181635 0.936222225 0.883935714 1 20.3965095 4.74466147 24.67190858 0.981571368 0.774023841 0.524134391 0.063932038 539.1790102 2180370.867 0.017050157 0.151951392 55547.11023 -4.74466147 -0.207547527 IEHSFWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IEHSFWR 7 0 Q16531;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 ;;; 169.37 0.0010144 4399490000 2812690 2652530 1787210 2038150 2546190 2687150 2601520 3016430 2875110 FALSE TRUE 2440985.89 2635105.356 2651510.734 2500943.109 2495525.801 2790526.399 2349224.991 2371389.918 2535217.771 0.962830853 1.039400002 1.045870995 0.986480584 0.984343763 1.100704812 0.926636369 0.935379179 1 21.27367825 2.194759861 24.99997883 0.948984346 1.018863442 0.342716633 0.04283852 139.7628761 79770.82643 0.016905039 0.011397455 156.5884988 -2.194759861 0.069879096 IEHTYTGGVDSDLGEAMSDCDPDGPLMCHTTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IEHTYTGGVDSDLGEAMSDCDPDGPLMCHTTK 32 0 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ; 157.64 8.73E-12 231106000 182860 178107 79445 118774 147034 147381 152787 210084 163765 FALSE TRUE 158694.5877 176937.0034 117864.8677 145743.452 144108.3111 153050.8424 137969.7403 165159.1715 144404.8883 1.098955787 1.22528403 0.816211066 1.009269519 0.997946211 1.059873002 0.955436772 1.143722858 1 17.13976005 4.284919115 24.99999586 1.010960758 1.162120015 0.371074702 0.087750044 141.4588378 76282.97953 0.021651045 0.05728293 19271.65956 -4.284919115 0.151159257 IEIESFYEGEDFSETLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IEIESFYEGEDFSETLTR 18 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;; 279.77 7.21E-39 533960000 420850 355682 253057 330879 357722 415461 299396 363774 347302 FALSE TRUE 365233.6062 353345.5015 375436.2116 406010.1341 350604.0321 431444.0535 270360.622 285983.761 306244.3532 1.192621521 1.153802504 1.225936765 1.325771822 1.144850602 1.408822886 0.882826472 0.933841744 1 18.22432372 2.223968973 24.99997121 0.935501775 1.236626372 0.747859291 0.082911883 109.0990588 186918.7487 0.032231789 0.021836855 167.482322 -2.223968973 0.301124597 IEINFPAEYPFKPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IEINFPAEYPFKPPK 15 1 P68036-2;P68036;P68036-3 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 ; 146.78 3.49E-06 1732270000 1325810 1058700 830150 939820 961910 779920 1269950 1544290 1648550 FALSE TRUE 1150600.849 1051745.33 1231613.317 1153220.495 942769.8729 809924.0271 1146790.444 1214055.601 1453660.297 0.79151976 0.723515207 0.847249745 0.793321863 0.648548959 0.557161827 0.788898511 0.835171466 1 20.47125874 1.376898406 1.944270149 1.039000002 0.731083918 0.518149185 0.082247305 0.522243393 2.534607793 0.27006528 0.024646447 23.81762242 -1.376898406 -0.307916084 IEIPIHIVPHVTIGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IEIPIHIVPHVTIGK 15 0 X6RJS7;P46736-2;P46736-3;P46736;A0A087WZR3;H9KVA9;A0A0D9SF50;P46736-4 X6RJS7 BRCC3 Lys-63-specific deubiquitinase BRCC36 0 80.507 0.0096952 97482000 151750 132510 79978 105350 133270 118480 157610 188200 186840 FALSE TRUE 131695.853 131639.5331 118655.6283 129271.3277 130618.1877 123038.0023 142325.0065 147954.8946 164751.988 0.799358202 0.799016356 0.720207566 0.784641989 0.792817066 0.74680739 0.863874289 0.898046186 1 17.32993635 1.499482026 1.143050824 1.049579439 0.772471233 0.862609854 0.029888605 0.341242423 0.532718379 0.106817035 0.00967254 31.58508325 -1.499482026 -0.277108206 IEKEQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 107.57 0.0067915 792780000 1606340 1119620 791760 939420 712920 1110630 1404890 1850070 827710 FALSE TRUE 1394058.099 1112265.142 1174657.784 1152729.669 698734.2868 1153356.655 1268643.984 1454446.928 729859.0667 1.910037379 1.523945092 1.609430968 1.579386654 0.957355082 1.580245704 1.738204048 1.992777776 1 19.47725839 2.475478282 24.35966526 1.668745899 1.49954149 0 0.33969948 139.0780072 2061939.528 0.125849354 0.098257565 298.8672186 -2.475478282 -0.169204409 IELGDVTPHNIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IELGDVTPHNIK 12 0 E7EQ69;Q9GZZ1;A0A087WWJ2;C9J5D1;Q9GZZ1-2;F8WCK0;C9JZU6;C9J5J3;A0A0D9SF32 E7EQ69 NAA50 N-alpha-acetyltransferase 50 0 ; 181.66 1.79E-05 268279000 689270 606160 339280 386670 543930 496300 660970 763160 362680 FALSE TRUE 598181.2231 602178.095 503356.9428 474469.3334 533106.8572 515392.9821 596869.2311 599964.1729 319804.3836 1.870459737 1.882957602 1.573952606 1.483623608 1.666977955 1.611588235 1.866357254 1.876034863 1 18.28683019 4.244781756 24.81365845 1.62455058 1.876708814 0.185614436 0.244095845 252.8386011 1008441.778 0.061143338 0.153347045 17570.40437 -4.244781756 0.252158233 IENFDVSFGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IENFDVSFGDR 11 0 Q9NUQ8-2;Q9NUQ8 Q9NUQ8-2 ABCF3 ATP-binding cassette sub-family F member 3 0 ;; 174.77 2.47E-05 361530000 414490 393550 233243 288643 418040 402680 373980 454910 408170 FALSE TRUE 359714.0963 390964.7441 346040.095 354183.8048 409721.8219 418171.3602 337711.4772 357631.0366 359916.6076 0.999437338 1.086264807 0.961445201 0.984071858 1.138379873 1.16185625 0.938304791 0.993649721 1 18.45730315 2.18292034 24.99998257 0.979095062 1.052935508 0.238876348 0.065458133 142.1650435 63875.4662 0.028268789 0.019058827 152.3773233 -2.18292034 0.073840446 IENHEGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 IENHEGVR 8 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;; 166.07 0.00032063 59657691000 22767708 19003390 12294355 14605941 15682293 18317952 18863382 19439660 20061739 FALSE TRUE 19758897.7 18878555.48 18239946.2 17922443.14 15370246.05 19022655.47 17034014.12 15282639.99 17690063.07 1.116948969 1.067184182 1.031084295 1.013136192 0.86886327 1.075329997 0.962914267 0.863910995 1 24.07643586 5.371943591 0.42375165 0.930992553 1.390459195 0.431599491 0.062623839 9.60719431 0.96880129 0.064536132 2.469795536 235474.3412 -5.371943591 0.459466642 IEPEPFENCLLRPGS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IEPEPFENCLLRPGSPAR 18 1 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2 A0A2R8Y430 GSS Glutathione synthetase 1 IEPEPFENCLLRPGS(1)PAR;IEPEPFENCLLRPGS(1)PAR;IEPEPFENCLLRPGS(1)PAR;IEPEPFENCLLRPGS(1)PAR;IEPEPFENCLLRPGS(1)PAR;IEPEPFENCLLRPGS(1)PAR 270.51 3.75E-39 2357800000 2101260 2006060 1283364 1447280 1890160 1792950 1721360 1915910 2292210 TRUE FALSE 1823573.167 1992882.06 1904003.123 1775907.044 1852549.514 1861925.947 1554422.772 1506207.556 2021227.545 0.902210724 0.985976104 0.942003352 0.878627965 0.916546738 0.921185718 0.769048876 0.745194454 1 20.94680032 2.25733983 23.39149412 0.815853416 0.92558217 0.218990692 0.072924842 127.1957132 158435.1276 0.027122088 0.020960592 180.858877 -2.25733983 0.109728754 IEPEPFENCLLRPGSPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IEPEPFENCLLRPGSPAR 18 1 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2 A0A2R8Y430 GSS Glutathione synthetase 0 ;;; 202.79 1.14E-15 2476550000 1292600 1285310 789010 925300 1157080 1093990 1125110 1108800 1351550 FALSE TRUE 1121779.635 1276866.714 1170577.875 1135403.507 1134056.372 1136076.503 1015997.005 871691.7487 1191771.299 0.941270893 1.071402471 0.98221687 0.95270251 0.951572146 0.953267212 0.852510047 0.731425358 1 20.18467598 2.271452452 3.492865633 0.831347982 0.980834581 0.327415254 0.074474173 0.207880496 5.308432866 0.030925246 0.021636848 186.8325114 -2.271452452 0.149486599 IEPGTST(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IEPGTSTPR 9 0 Q86X27;Q86X27-3;H7C2H2;A0A0A0MR31 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 IEPGT(0.002)S(0.023)T(0.975)PR;IEPGTST(1)PR 141.91 0.0040119 492640000 2037630 1492600 1257120 1018520 1050530 1189060 1266530 1245060 1219040 TRUE FALSE 1768352.033 1482795.012 1865067.437 1249790.533 1029626.508 1234803.908 1143702.116 978813.6081 1074926.48 1.645091144 1.379438538 1.735065115 1.162675361 0.957857609 1.148733361 1.063981711 0.910586562 1 20.03580656 3.57756955 4.534341324 1.016039884 1.562517402 0.850409033 0.109160533 0.079459333 2.704143137 0.029737189 0.044545321 3780.676781 -3.57756955 0.546477519 IEPPDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IEPPDRR 7 1 Q15428 Q15428 SF3A2 Splicing factor 3A subunit 2 0 ; 106.43 0.012353 1953250000 1220990 985450 630270 778080 924420 1026110 988060 1141470 1079360 FALSE TRUE 1059633.078 978976.5141 935070.6801 954754.9562 906025.8506 1065585.116 892238.0933 897375.5234 951759.2904 1.11334146 1.028596751 0.982465514 1.003147504 0.951948523 1.119595182 0.937461922 0.942859747 1 19.86023722 4.703561774 2.049977487 0.987186531 1.144039875 0.360019574 0.051341115 0.72617642 3.557423622 0.013592752 0.206770078 50531.45153 -4.703561774 0.156853344 IEQLQNHENEDIYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IEQLQNHENEDIYK 14 0 O00629;H7C4F6 O00629 KPNA4 Importin subunit alpha-3 0 ; 276.59 4.16E-33 1953140000 2461200 1980340 1536710 1750570 1750020 1685470 2351900 2698700 2476600 FALSE TRUE 2135946.184 1967331.016 2279868.096 2148063.674 1715198.026 1750311.122 2123813.1 2121604.006 2183819.169 0.97807832 0.90086718 1.043982088 0.983627081 0.785412112 0.801490868 0.972522418 0.971510845 1 21.05842197 2.034852682 24.99991443 0.98020967 0.915344776 0.135239051 0.078646654 396.3292271 284286.4296 0.035047584 0.023628969 108.3559295 -2.034852682 -0.064864894 IERDS(ph)REHEEPTTSEMAEETYSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IERDSREHEEPTTSEMAEETYSPK 24 2 P24593 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 1 IERDS(0.982)REHEEPT(0.006)T(0.006)S(0.006)EMAEETYSPK;IERDS(0.942)REHEEPT(0.019)T(0.019)S(0.019)EMAEETYSPK;IERDS(0.449)REHEEPT(0.184)T(0.184)S(0.184)EMAEETYSPK 219.67 5.58E-33 2471970000 1976070 1351840 1062790 1089410 1425420 1351620 2123600 1920960 1059120 TRUE FALSE 1714927.343 1342959.674 1576758.799 1336777.191 1397056.931 1403617.696 1917653.599 1510177.653 933912.0402 1.836283578 1.437993747 1.688337585 1.431373763 1.495919177 1.502944213 2.053355687 1.617044848 1 19.83292715 4.756323915 23.20887965 1.560066489 1.836284204 0.110205333 0.261523345 3505.249371 4579628.628 0.063344907 1.702307805 57058.96838 -4.756323915 0.276217715 IERPGEGS(ph)PMVDNPMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IERPGEGSPMVDNPMR 16 1 A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2 A0A087WVR3 UHRF1 E3 ubiquitin-protein ligase UHRF1 1 IERPGEGS(1)PMVDNPMR;IERPGEGS(1)PMVDNPMR;IERPGEGS(1)PMVDNPMR;IERPGEGS(1)PMVDNPMR 143.04 8.78E-07 1851840000 1226370 1217310 785520 1095670 1270910 1210140 1147700 1476830 1476950 TRUE FALSE 1064302.097 1209313.41 1165400.099 1344458.62 1245621.377 1256694.869 1036396.231 1161021.397 1302346.654 0.817218745 0.928564916 0.894846312 1.032335451 0.956443796 0.964946518 0.795791372 0.891484148 1 20.31268208 4.73909224 23.14983071 0.927006474 0.817218671 0.233249634 0.065187077 26.83879023 1167760.752 0.016690793 0.095594716 54839.34265 -4.73909224 -0.109787803 IES(ph)DEEEDFENVGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 IESDEEEDFENVGK 14 0 Q96T23-2;Q96T23;Q96T23-3 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 IES(1)DEEEDFENVGK;IES(1)DEEEDFENVGK;IES(1)DEEEDFENVGK;IES(1)DEEEDFENVGK;IES(1)DEEEDFENVGK;IES(1)DEEEDFENVGK;IES(1)DEEEDFENVGK;IES(1)DEEEDFENVGK 350.86 6.85E-82 7233990000 9133460 6816810 5825930 5953830 7856350 5890390 9448480 10386800 9321910 TRUE FALSE 7926450.12 6772029.926 8643369.235 7305738.1 7700024.006 6116997.115 8532167.864 8165663.65 8219884.419 0.964301895 0.823859507 1.051519558 0.888788422 0.936755751 0.744170697 1.037991221 0.993403707 1 22.97068668 IES(ph)DVQEPTEPEDDLDIMLGNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IESDVQEPTEPEDDLDIMLGNK 22 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 IES(1)DVQEPTEPEDDLDIMLGNK 167.16 7.01E-12 21694000 141550 111010 121390 108030 124350 106530 154860 162430 196760 TRUE FALSE 122843.8089 110280.768 180094.61 132559.8626 121875.6783 110628.278 139841.701 127695.6085 173499.2569 0.708036513 0.635626745 1.038013725 0.764037063 0.702456486 0.637629694 0.806007492 0.736000896 1 17.40456996 1.235776686 24.85634964 1.000000354 0.755443806 0.317336434 0.113600531 91.99800948 821231.9956 0.185798126 0.027616667 17.20983419 -1.235776686 -0.244556548 IES(ph)PKLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 IESPKLER 8 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;Q5TBM3 Q92598-2 HSPH1 Heat shock protein 105 kDa 1 IES(1)PKLER;IES(1)PKLER;IES(1)PKLER;IES(1)PKLER;IES(1)PKLER;IES(1)PKLER;IES(1)PKLER;IES(1)PKLER;IES(1)PKLER;IES(1)PKLER;IES(1)PKLER 138.76 0.00041873 34557346200 40246146 33003384 24177141 22083179 34260031 27068329 43791041 45315171 18320808 TRUE FALSE 34927515.84 32786582.6 35869287.26 27097502.31 33578323.41 28109665.13 39544192.58 35624874.32 16154942.95 2.162032756 2.029507792 2.220328934 1.677350542 2.078516991 1.740003986 2.447807628 2.205199637 1 23.94547232 3.783443491 24.98460768 1.93541076 2.126511619 0.081149939 0.388023693 1589.735725 884940.8854 0.102295999 0.177180905 6073.562307 -3.783443491 0.191100858 IES(ph)S(ph)IQS(ph)LQDLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IESSIQSLQDLSK 13 0 A0A087X043;O43424-2;O43424 A0A087X043 GRID2 "Glutamate receptor ionotropic, delta-2" 3 IES(0.995)S(0.902)IQS(0.902)LQDLS(0.201)K 49.463 0.082598 597610000 498960 372020 351340 447020 397960 344050 365400 450050 983290 TRUE FALSE 433021.1718 369576.1761 521249.1992 548522.7233 390041.3746 357285.8261 329963.5642 353810.3098 867046.5764 0.499420889 0.426247201 0.601177853 0.632633515 0.449850545 0.412072241 0.380560368 0.408063787 1 19.72574997 1.234259948 24.99974358 1.000000777 0.472968633 0.797718043 0.082870645 63.52647299 369229.4567 0.172787033 0.022672267 17.14983508 -1.234259948 -0.527032144 IES(ph)S(ph)IQSLQDLS(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IESSIQSLQDLSK 13 0 A0A087X043;O43424-2;O43424 A0A087X043 GRID2 "Glutamate receptor ionotropic, delta-2" 3 IES(0.917)S(0.583)IQS(0.583)LQDLS(0.917)K;IES(0.977)S(0.519)IQS(0.519)LQDLS(0.985)K 75.316 0.02122 4198030000 1999970 1560480 1431610 2010540 1555270 1384340 1539360 1809270 4051000 TRUE FALSE 1735668.897 1550229.104 2123941.384 2467063.836 1524323.17 1437596.456 1390073.104 1422371.69 3572095.395 0.485896569 0.43398312 0.594592571 0.690648923 0.426730812 0.402451866 0.389147811 0.398189727 1 21.76833918 1.23345419 24.99920174 1.000000813 0.474823043 0.743845144 0.096309396 91.33867511 447109.2386 0.213626923 0.026108098 17.11804605 -1.23345419 -0.52517777 IESDVQEPT(ph)EPEDDLDIMLGNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IESDVQEPTEPEDDLDIMLGNK 22 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 IES(0.001)DVQEPT(0.999)EPEDDLDIMLGNK;IESDVQEPT(1)EPEDDLDIMLGNK;IESDVQEPT(1)EPEDDLDIMLGNK 220.99 2.76E-25 155727000 345909 282699 274513 261880 300507 284969 378379 395849 442804 TRUE FALSE 300196.2492 280841.9317 407268.405 321343.8566 294527.4986 295931.9418 341683.8628 311199.7719 390456.2156 0.768834602 0.719266131 1.04305781 0.82299588 0.754316328 0.757913256 0.875088804 0.797015797 1 18.57480125 1.234225231 24.97524749 1.000000271 0.819411624 0.285275138 0.090822533 179.3977146 1033333.994 0.168276192 0.022026534 17.14846419 -1.234225231 -0.180588647 IESGAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IESGAFR 7 0 O94933 O94933 SLITRK3 SLIT and NTRK-like protein 3 0 ;; 97.602 0.02763 1657380000 1429700 1469970 1020400 1163100 1603590 1764020 1550400 1618920 1646700 FALSE TRUE 1240761.523 1460313.67 1513868.853 1427199.632 1571681.696 1831882.991 1400042.447 1272726.556 1452029.002 0.854501887 1.00570558 1.042588578 0.982900224 1.082403791 1.261602205 0.964197302 0.876515934 1 20.46963884 4.73473812 4.162094866 1.021461955 0.841447007 0.230893377 0.098923817 0.394636965 15.34022396 0.027315962 0.211588963 54292.28493 -4.73473812 -0.180014948 IET(ph)DEEES(ph)CDNAHGDANQPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IETDEEESCDNAHGDANQPAR 21 0 Q96T23-2;Q96T23;Q96T23-3 Q96T23-2 RSF1 Remodeling and spacing factor 1 2 IET(1)DEEES(1)CDNAHGDANQPAR 193.57 1.20E-17 491120000 201170 168300 150340 137030 200630 220180 236430 219720 246440 TRUE FALSE 174584.8748 167194.4262 223044.9269 168144.7559 196637.8555 228650.4671 213501.055 172734.5879 217306.1439 0.803405148 0.769395762 1.026408747 0.773768992 0.904888615 1.052204337 0.982489731 0.794890493 1 17.72936944 3.008349391 24.72133849 0.939267084 0.849587364 0.225028047 0.09703025 324.4127688 960529.2824 0.030258226 0.034251255 1019.411176 -3.008349391 -0.08967972 IET(ph)DEEESCDNAHGDANQPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IETDEEESCDNAHGDANQPAR 21 0 Q96T23-2;Q96T23;Q96T23-3 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 IET(1)DEEESCDNAHGDANQPAR;IET(1)DEEESCDNAHGDANQPAR;IET(1)DEEESCDNAHGDANQPAR 373.04 6.37E-112 4705340000 867360 930700 529862 602350 1043240 870430 1003420 1141240 980900 TRUE FALSE 752736.1784 924586.1704 786105.0355 739122.7738 1022481.565 903916.0053 906108.4828 897194.7071 864939.1194 0.870276487 1.068960982 0.908855916 0.854537339 1.182142815 1.045063155 1.04759799 1.037292321 1 19.72223906 3.251833903 24.99997681 1.05729901 0.934693526 0.457296933 0.07362307 235.3196984 443217.7289 0.02093789 0.026871447 1785.80446 -3.251833903 -0.122605484 IETELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IETELR 6 0 P63104;E7EX29;B0AZS6;E7ESK7;E9PD24;E7EVZ2 P63104;REV__P53355-4 YWHAZ 14-3-3 protein zeta/delta 0 ;;;; 159.14 0.021423 5135240000 8810600 7563770 5170070 6288700 7129790 7391210 7687220 8480100 8998400 FALSE TRUE 7646256.887 7514083.097 7670333.145 7716645.452 6987921.128 7675554.631 6941714.588 6666696.607 7934619.403 0.963657675 0.946999814 0.966692006 0.972528745 0.880687626 0.96735007 0.874864217 0.840203703 1 22.91972959 3.245781731 24.99973919 0.903473624 0.96166619 0.210769329 0.046068368 230.6482387 798507.2816 0.01357386 0.01715808 1761.090729 -3.245781731 0.058192566 IETIAASST(ph)PTPIRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IETIAASSTPTPIRK 15 1 Q96P47;Q96P47-2;Q96P47-4;Q96P47-5;H7C5G0;H7C4U6;Q96P47-3;Q96P47-6;E7ESL9 Q96P47;E7ESL9 AGAP3 "Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3" 1 IET(0.001)IAAS(0.055)S(0.186)T(0.64)PT(0.117)PIRK;IETIAAS(0.037)S(0.203)T(0.756)PT(0.004)PIRK 84.653 0.0048317 416010000 312370 308170 188700 213114 272210 325800 235100 293520 227460 TRUE FALSE 271089.5131 306145.611 279955.9512 261504.7909 266793.5536 338333.7368 212300.0382 230753.0322 200569.9379 1.351595936 1.52637835 1.395802153 1.303808505 1.330177176 1.686861652 1.058483841 1.150486631 1 17.61374586 2.208865482 24.9999651 1.086030546 1.424547213 0.683884127 0.116010039 120.2469888 101233.6088 0.046139679 0.031112229 161.7578933 -2.208865482 0.338516667 IETIEVMEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 IETIEVMEDR 10 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;;;;;;;; 297.85 5.64E-32 8600450000 5217430 4833590 3074453 3645054 4453248 4357798 4512860 5174688 5105910 FALSE TRUE 4527933.406 4801837.829 4561268.754 4472719.222 4364637.077 4525445.309 4075203.532 4068121.241 4502295.136 1.005694489 1.06653111 1.013098568 0.993430925 0.969424914 1.00514186 0.905139136 0.903566096 1 22.1022292 3.083137241 0.867288388 0.931575909 1.036286671 0.46197696 0.036114694 0.469353775 0.847358383 0.023293551 0.027627783 1210.980755 -3.083137241 0.104710762 IETLDPALIRPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IETLDPALIRPGR 13 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ;;; 180.09 1.20E-05 3256650000 4357980 4138730 2605140 3178790 4112740 3915410 4098960 4807890 4117160 FALSE TRUE 3782061.901 4111542.41 3864994.418 3900582.854 4030904.52 4066038.356 3701443.49 3779760.139 3630434.035 1.041765768 1.132520897 1.06460946 1.074412265 1.110309258 1.119986844 1.019559495 1.04113175 1 21.79171061 2.225809104 24.98548664 1.024556883 1.091484789 0.576217844 0.028361103 160.0955864 313690.5698 0.010986295 0.007460966 168.1934596 -2.225809104 0.066927906 IETSIGQSTVIIDLTEDS(ph)NEQPDSLVDHNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IETSIGQSTVIIDLTEDSNEQPDSLVDHNK 30 0 Q13111;Q13111-2;Q13111-3;K7EJF1 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 IETSIGQSTVIIDLTEDS(0.989)NEQPDS(0.011)LVDHNK 192.69 8.49E-19 57870000 50584 38181 36623 50491 36487 36512 48193 52912 77721 TRUE FALSE 43899.19624 37930.1865 54334.0053 61955.75326 35760.98009 37916.64027 43519.25028 41597.18056 68532.91192 0.640556413 0.553459432 0.792816236 0.904029196 0.521807393 0.553261772 0.63501242 0.606966484 1 16.06450937 1.234218945 24.96883838 1.000000526 0.65037719 0.469782939 0.116523679 125.5172234 721749.2286 0.228347404 0.029823631 17.148216 -1.234218945 -0.349623336 IETWHKPDLGTLENVHGLDPNTWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IETWHKPDLGTLENVHGLDPNTWK 24 1 A0A0A0MSW4;P48739;P48739-3;P48739-2;B3KYB7;B3KYB6 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 155.17 3.10E-08 267440000 453650 346870 294520 370560 359830 274770 479670 581020 528510 FALSE TRUE 393699.0031 344591.3881 436950.8571 454701.3117 352670.087 285340.5797 433151.6772 456773.3945 466030.1499 0.844792989 0.739418658 0.937602121 0.975690761 0.7567538 0.612279227 0.929449902 0.980137003 1 18.83006377 2.014779513 24.99964468 0.978492896 0.814616952 0.362453651 0.101318781 265.3218402 448791.8894 0.044084855 0.029709925 103.4616768 -2.014779513 -0.163875944 IEVEKPFAIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IEVEKPFAIAK 11 1 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 138.94 0.0014129 0 605670 565200 451140 642100 462480 436280 499370 637600 1130700 FALSE TRUE 525629.1749 561487.164 669312.813 787898.6189 453277.5528 453063.9739 450941.1743 501254.2018 997029.9341 0.527194979 0.563159786 0.671306638 0.790245701 0.454627827 0.454413612 0.452284489 0.502747395 1 19.92727729 1.234855094 24.96457547 1.000000651 0.550445067 0.633667485 0.107044997 77.10734377 519401.6014 0.208180465 0.028696659 17.17335288 -1.234855094 -0.449555584 IEVEKPFAIAKE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IEVEKPFAIAKE 12 2 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 132.47 0.00071651 261450000 833420 649540 350120 562670 566540 556270 707930 829320 363850 FALSE TRUE 723281.4354 645273.129 519439.2031 690432.8234 555266.9624 577670.0669 639275.0576 651976.3718 320836.0675 2.254364483 2.011223782 1.619017485 2.151980071 1.730687471 1.800514734 1.992528653 2.032116828 1 18.29147681 1.23520289 24.97825652 0.999998676 1.941490421 0.710410531 0.19037327 51.6879483 384444.4474 0.317458645 0.045063183 17.18711134 -1.23520289 0.941491744 IEVIEIMTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 IEVIEIMTDR 10 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;A0A2R8Y4L2;H0YH80;F8VYN5 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ;;;;;;;; 208.25 2.73E-07 3002622000 3730568 3502070 2191816 2652453 3197422 3150272 3165650 3773916 3453893 FALSE TRUE 3237563.987 3479064.672 3251785.549 3254732.994 3133799.558 3271465.002 2858645.75 2966893.432 3045577.704 1.063037723 1.142333248 1.0677073 1.068675079 1.028967198 1.074168949 0.938621841 0.974164418 1 21.53828448 2.71932365 0.897359123 0.966764561 1.096141921 0.623112631 0.03549926 0.358127319 0.658222806 0.027945613 0.019783459 523.9907854 -2.71932365 0.129377359 IEVLPVDTGAGGYSGNSGS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IEVLPVDTGAGGYSGNSGSPK 21 0 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 IEVLPVDTGAGGYSGNS(0.003)GS(0.997)PK;IEVLPVDTGAGGYSGNS(0.001)GS(0.999)PK;IEVLPVDTGAGGYSGNS(0.058)GS(0.942)PK;IEVLPVDTGAGGYSGNS(0.001)GS(0.999)PK 356.25 1.40E-95 884530000 1184230 952270 790150 1070390 1281620 1018110 1061310 1568000 1456910 TRUE FALSE 1027731.005 946014.4757 1172269.183 1313438.409 1256118.269 1057277.351 958384.3196 1232695.402 1284675.76 0.799992525 0.736383845 0.912501987 1.022389034 0.977770663 0.822991594 0.746012612 0.95953815 1 20.29297285 4.229773708 24.39213876 0.916593876 0.768188185 0.360305661 0.08408669 148.0033821 410857.5642 0.023256199 0.049654858 16973.59002 -4.229773708 -0.148405691 IEVLQQHENEDIYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IEVLQQHENEDIYK 14 0 O00505;H0Y4S9 O00505 KPNA3 Importin subunit alpha-4 0 ;; 228.19 1.75E-12 1243950000 1463020 1083255 918556 1050380 1101748 862487 1419650 1630090 1528350 FALSE TRUE 1269678.2 1076139.027 1362772.754 1288884.833 1079825.37 895667.433 1281972.562 1281507.939 1347670.204 0.942128272 0.798518082 1.011206414 0.956380002 0.801253428 0.664604315 0.95125095 0.95090619 1 20.36203606 2.031500604 24.99995517 0.965686497 0.862728539 0.206274516 0.097565845 326.955127 259481.4875 0.041883813 0.02823781 107.5228096 -2.031500604 -0.102957958 IEVLYEDEGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IEVLYEDEGFR 11 0 A0A087WW66;Q99460-2;Q99460;C9J9M4 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ; 169.41 3.94E-05 58791000 98794 80363 84101 112628 89564 88962 86517 105285 280070 FALSE TRUE 85738.12259 79835.09016 124772.5249 138201.9088 87781.85163 92384.42571 78126.59466 82770.62208 246960.4437 0.347173504 0.323270759 0.505232834 0.559611518 0.355449036 0.374085924 0.316352666 0.335157408 1 17.91392045 1.235498869 24.99988892 1.000000833 0.388872354 0.850527111 0.0804254 34.41797408 280980.4183 0.147803029 0.021486009 17.19882861 -1.235498869 -0.611128479 IEVPLYSLLEQTHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IEVPLYSLLEQTHLK 15 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 311.69 3.54E-56 620840000 1120970 933780 664060 833860 845040 809680 1091650 1259320 1193330 FALSE TRUE 972830.9743 927645.9377 985201.6371 1023200.658 828225.3573 840828.9135 985781.951 990024.218 1052255.887 0.924519394 0.881578283 0.936275719 0.972387677 0.78709501 0.799072663 0.936827214 0.940858807 1 20.00505415 1.621522296 2.086005365 0.992848262 0.886353532 0.278393406 0.058559201 0.47463937 4.108903313 0.080505116 0.017606197 41.83331644 -1.621522296 -0.10649473 IEWLESHQDADIEDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IEWLESHQDADIEDFK 16 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;; 245.96 3.68E-20 1601320000 2992300 2112610 2162430 2875140 2109920 2051650 2319940 2654270 3963560 FALSE TRUE 2596859.973 2098732.126 3208188.381 3527984.481 2067936.72 2130578.303 2094952.576 2086675.016 3494992.452 0.743023056 0.600496898 0.917938572 1.0094398 0.591685604 0.609608842 0.599415479 0.597047074 1 21.73685791 3.190448542 24.99999931 0.659731021 0.809369115 0.148537525 0.15997847 211.577687 109939.1306 0.049525101 0.056156308 1550.417071 -3.190448542 0.149638094 IEYAKPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IEYAKPTR 8 1 A0A3B3ITJ4;M0R1W6;B4DVF8;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;; 120.99 0.0015137 5129270000 2002440 1704970 1056980 1312180 1638150 1508270 1747200 2022900 1532740 FALSE TRUE 1737812.48 1693769.94 1568139.063 1610130.524 1605554.02 1566294.123 1577756.813 1590318.577 1351541.223 1.285800574 1.253213672 1.160259884 1.1913292 1.187943063 1.15889482 1.167376019 1.176670419 1 20.36617409 0.4304336 1.23839357 3.93E-27 1.20308583 0.706137562 0.040399486 5.732580162 1.604884854 14.48173369 0.012869335 2.694223379 -0.4304336 1.20308583 IEYDCELVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IEYDCELVPR 10 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 107.57 0.0052712 200723000 140635 131372 82658 104729 134227 150488 122385 142524 133697 FALSE TRUE 122049.7284 130509.0087 122631.6853 128509.3201 131556.1453 156277.3707 110516.1215 112046.3517 117891.493 1.035271718 1.107026516 1.040208095 1.090064405 1.115908722 1.325603458 0.937439325 0.950419313 1 16.84710009 IEYEPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IEYEPFR 7 0 A0A0C4DG89;Q7L014;D6RJA6 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ;;; 143 0.005702 592877000 1084980 1176340 826907 1015630 1119720 1210260 1015190 1249170 1778290 FALSE TRUE 941597.144 1168612.545 1226801.991 1246244.314 1097439.763 1256819.485 916737.0301 982044.7166 1568062.582 0.600484416 0.745258868 0.782368003 0.794766949 0.699869875 0.801511049 0.584630384 0.626279032 1 20.58055171 4.740457884 23.17171122 0.738287865 0.600484283 0.141341226 0.113188386 137.7465142 1681933.526 0.027516088 0.172073269 55012.05692 -4.740457884 -0.137803582 IEYEPFRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IEYEPFRK 8 1 A0A0C4DG89;Q7L014;D6RJA6 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 89.698 0.022001 437750000 829710 701770 391650 557140 752080 643480 905100 1099600 651480 FALSE TRUE 720061.7213 697160.0267 581053.25 683647.1524 737115.0794 668235.092 817323.5413 864459.0971 574462.7766 1.253452357 1.213586076 1.011472412 1.190063448 1.283138107 1.163234798 1.422761534 1.504813075 1 19.13185389 2.248504699 24.95480953 1.354678108 1.183777324 0.10857632 0.148600389 291.592401 731755.996 0.055746575 0.042653888 177.2167219 -2.248504699 -0.170900784 IEYQFFEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IEYQFFEDR 9 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ;;;; 161.63 0.00014979 917028000 959490 850651 623833 730867 873097 1054440 781269 797688 743114 FALSE TRUE 832690.9655 845063.0176 925520.7254 896821.523 855724.0779 1095004.989 705501.6526 627108.6288 655263.9095 1.270771903 1.289652925 1.412439648 1.368641718 1.305922798 1.671090035 1.076667954 0.957032151 1 19.32171655 2.051156417 10.36930622 0.987798469 1.378698753 0.718311608 0.111907798 0.219914085 43.33058888 0.044468169 0.029950956 112.5010087 -2.051156417 0.390900283 IEYVHTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IEYVHTK 7 0 P48729-2;A0A5F9W493;U3KPX3;A0A590UJ43;P48729;E7ETM0;P48729-3;D6REM4;A0A590UK94;Q8N752 P48729-2 CSNK1A1;CSNK1A1L Casein kinase I isoform alpha;Casein kinase I isoform alpha-like 0 ; 86.794 0.019815 795480000 1036300 866160 590750 769030 838080 752170 966290 1084750 1043230 FALSE TRUE 899350.3294 860470.1379 876438.6759 943650.0154 821403.8477 781106.4666 872579.3445 852784.654 919900.5379 0.977660402 0.935394755 0.952753738 1.025817441 0.892926804 0.849120567 0.948558359 0.927040065 1 19.81111836 3.214671886 24.99949461 0.922124791 0.968787738 0.232055019 0.044313135 378.0263985 395602.4104 0.013819577 0.015678018 1639.35076 -3.214671886 0.046662948 IFAPNHVVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IFAPNHVVAK 10 0 Q02543;M0R3D6;M0R1A7;M0R117 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 131.44 0.00025009 3385500000 11027300 10141100 6706100 8241200 10162200 9302400 11057100 12744000 12293000 FALSE TRUE 9570014.365 10074482.45 9949192.391 10112490.42 9959992.102 9660269.347 9984784.144 10018794.77 10839735.54 0.882864192 0.929402973 0.917844568 0.93290933 0.918840876 0.891190501 0.92112802 0.924265609 1 23.36982622 1.186492353 2.82843159 1.025709947 0.914558367 0.748119861 0.015626691 0.269367391 2.286211004 0.074852828 0.003941428 15.36357742 -1.186492353 -0.111151581 IFAQDGEGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 216.42 1.80E-08 1899910000 2477460 2665440 1545370 1607790 2353730 2504170 2306080 2325230 2472230 FALSE TRUE 2150057.384 2647930.549 2292716.101 1972863.293 2306895.378 2600507.04 2082436.717 1827997.659 2179965.786 0.986280334 1.214666105 1.05172114 0.904997366 1.058225497 1.19291186 0.955261193 0.838544197 1 21.05587406 2.013963541 24.48831903 0.904488472 1.06684129 0.310282639 0.096726096 186.5753496 327201.7673 0.039650731 0.026717441 103.267471 -2.013963541 0.162352819 IFASIAPSIYGHEDIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IFASIAPSIYGHEDIKR 17 1 P49736 P49736 MCM2 DNA replication licensing factor MCM2 0 ; 90.754 0.0024177 933880000 1613480 1754580 950160 1141770 1553040 1317910 1967830 1971920 1515320 FALSE TRUE 1400254.53 1743054.048 1409660.554 1401026.329 1522137.542 1368610.851 1776990.149 1550240.253 1336180.596 1.047953049 1.304504836 1.054992535 1.048530665 1.139170519 1.024270862 1.329902676 1.160202639 1 20.34968358 IFCCHGGLSPDLQSMEQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IFCCHGGLSPDLQSMEQIR 19 0 F8W0W8;P36873;P36873-2;F8VYE8;F8VR82;F8W1A0;P62140;E7ETD8;P62136;P62136-2;P62136-3 F8W0W8;P62140;P62136 PPP1CC;PPP1CB;PPP1CA Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-gamma catalytic subunit;Serine/threonine-protein phosphatase PP1-beta catalytic subunit;Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 ; 308.42 1.86E-61 3061300000 1259550 1229460 675480 990950 1200410 1340690 1113700 1299420 1481920 FALSE TRUE 1093097.276 1221383.596 1002144.387 1215960.343 1176524.19 1392267.212 1005693.545 1021549.145 1306729.106 0.836514065 0.93468768 0.766910588 0.93053743 0.900358142 1.065459708 0.769626651 0.781760459 1 20.31752866 EGPDLDRPGS(ph)DRQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 173.98 7.39E-07 1395500000 1660560 1442670 808380 825120 1289650 1378470 1521200 1556060 562800 TRUE FALSE 1441112.789 1433193.006 1199315.272 1012476.107 1263988.488 1431500.633 1373674.258 1223308.678 496266.4251 2.903909504 2.887950772 2.416676227 2.040186593 2.546995775 2.884540562 2.768017719 2.46502406 1 18.92075533 1.237101538 4.168953724 0.833674598 2.619369791 0.788431589 0.264092695 0.112945143 3.640926937 0.6117729 0.072777915 17.26241439 -1.237101538 1.785695193 IFCGDLGNEVNDDILAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFCGDLGNEVNDDILAR 17 0 K7EP90;Q9BTD8-4;Q9BTD8-2;Q9BTD8-3;Q9BTD8;K7EQ03 K7EP90 RBM42 RNA-binding protein 42 0 151.44 2.73E-08 0 34455 23513 11091 17422 26636 27624 23774 25783 25165 FALSE TRUE 29901.68445 23358.54155 16454.6447 21377.93138 26105.99571 28686.71316 21468.40114 20269.50609 22190.02237 1.34752836 1.052659667 0.741533489 0.963402876 1.176474511 1.292775315 0.967479923 0.913451359 1 14.4376235 2.030023929 24.99995174 0.947519889 1.079893696 0.119290111 0.169636543 468.2608937 389903.7759 0.074229649 0.050045023 107.1578346 -2.030023929 0.132373808 IFDEVMGCFSDS(ph)PPQS(ph)PTFPEAGHTSLYDEDKVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 IFDEVMGCFSDSPPQSPTFPEAGHTSLYDEDKVPR 35 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 2 IFDEVMGCFS(0.121)DS(0.809)PPQS(0.7)PT(0.289)FPEAGHT(0.028)S(0.027)LY(0.026)DEDKVPR;IFDEVMGCFSDS(1)PPQS(0.988)PT(0.012)FPEAGHTSLYDEDKVPR;IFDEVMGCFS(0.001)DS(0.999)PPQS(0.996)PT(0.004)FPEAGHTSLYDEDKVPR;IFDEVMGCFSDS(1)PPQS(0.927)PT(0.073)FPEAGHTSLYDEDKVPR;IFDEVMGCFSDS(1)PPQS(0.999)PT(0.001)FPEAGHTSLYDEDKVPR;IFDEVMGCFSDS(1)PPQS(0.974)PT(0.026)FPEAGHTSLYDEDKVPR;IFDEVMGCFSDS(1)PPQS(1)PTFPEAGHTSLYDEDKVPR 270.72 7.38E-74 2736440000 984115 899994 643725 690284 741367 776811 960024 1046431 881762 TRUE FALSE 854061.7093 894081.8802 955032.5631 847023.5325 726615.2472 806695.4218 866921.0202 822659.874 777521.1009 1.098441841 1.149913332 1.228304366 1.089389769 0.93452801 1.037522224 1.114980699 1.058054724 1 19.5685223 3.481845462 24.99765776 1.037013853 1.158132184 0.538319746 0.054721315 168.0878969 889422.1728 0.016242424 0.021554995 3032.811806 -3.481845462 0.121118331 IFDEVMGCFSDS(ph)PPQSPTFPEAGHTSLYDEDKVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFDEVMGCFSDSPPQSPTFPEAGHTSLYDEDKVPR 35 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 1 IFDEVMGCFSDS(0.996)PPQS(0.004)PTFPEAGHTSLYDEDKVPR 222.29 1.55E-36 100480000 185540 131660 23300 51427 92722 83741 100380 97381 103840 TRUE FALSE 161020.4189 130795.1168 34567.95793 63104.28636 90877.01361 86962.57046 90645.16305 76556.83097 91564.15349 1.758553023 1.428453295 0.377527194 0.689181126 0.992495536 0.949744711 0.989963426 0.836100461 1 16.48249529 4.424766276 6.802175816 0.847679211 1.680353023 0.742027093 0.190986556 0.087578782 8.747205805 0.049335331 0.134470328 26592.93524 -4.424766276 0.832673812 IFDFDDDGTLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IFDFDDDGTLNR 12 0 Q99828;Q99828-2 Q99828 CIB1 Calcium and integrin-binding protein 1 0 ;;;; 271.62 2.37E-27 271298000 736679 678320 508382 707206 738281 768001 523076 822018 1220349 FALSE TRUE 639325.0036 673864.0713 754237.2356 867787.9313 723590.6525 797546.4954 472348.17 646235.8477 1076080.731 0.594123642 0.626220739 0.700911385 0.806433854 0.672431567 0.741158607 0.438952354 0.600545878 1 20.03735489 2.172856167 0.016027635 1.365803471 8.28E-06 0.040085545 0.144914267 14790.47214 131.5350433 5775.167584 5433.082999 148.8867903 -2.172856167 -1.365795193 IFDFDDDGTLNREDLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IFDFDDDGTLNREDLSR 17 1 Q99828;Q99828-2 Q99828 CIB1 Calcium and integrin-binding protein 1 0 ;;; 157.74 1.31E-08 638160000 782790 732700 382550 459694 716730 796970 597530 853210 246210 FALSE TRUE 679342.3182 727886.8455 567552.4596 564074.5487 702468.4753 827629.9516 539581.6326 670757.6812 217103.3343 3.12911969 3.352720712 2.614204252 2.598184641 3.235641118 3.812147586 2.485367783 3.089577981 1 17.72802236 1.2375212 24.98092999 0.999997575 3.028944126 0.721401504 0.398289758 14.07591984 338126.1444 0.578620395 0.097396405 17.27910326 -1.2375212 2.02894655 IFDLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 9295800000 10234030 10523110 6301840 7562670 9962640 10985880 9794350 11085390 10477030 FALSE TRUE 8881577.006 10453983 9349430.902 9279889.812 9764402.956 11408513.91 8844495.445 8714865.615 9238447.449 0.961371167 1.131573574 1.012013215 1.004485858 1.056931157 1.234895146 0.957357337 0.943325777 1 23.13921899 IFDLQDWTQEDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFDLQDWTQEDER 13 0 A0A2R8YDQ9;A0A2R8Y6Y7;Q9P2R7-2;Q9P2R7;Q5T9Q5;Q5T9Q8 A0A2R8YDQ9 SUCLA2 "Succinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial" 0 116.01 0.00144 17292000 14655 13671 12607 16047 12144 14249 11268 13825 25164 FALSE TRUE 12718.30462 13581.1943 18703.78737 19690.71661 11902.35816 14797.16825 10175.23109 10868.63134 22189.14059 0.573176981 0.612064908 0.842925272 0.887403301 0.536404649 0.666865316 0.458568057 0.489817589 1 14.43756617 3.205880378 24.99987693 0.60171142 0.728693379 0.059562398 0.17517594 448.1493289 342825.9527 0.053889868 0.061109563 1606.498697 -3.205880378 0.126981959 IFDLQDWTQEDERDKDAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFDLQDWTQEDERDKDAAK 19 2 A0A2R8YDQ9;A0A2R8Y6Y7;Q9P2R7-2;Q9P2R7;Q5T9Q5 A0A2R8YDQ9 SUCLA2 "Succinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial" 0 130.85 9.42E-06 37556000 56734 47197 48749 67188 52725 37989 61287 80309 54975 FALSE TRUE 49236.45815 46886.9598 72324.17946 82444.0623 51675.87565 39450.46141 55343.39617 63135.54532 48475.91813 1.015689028 0.967221697 1.491961004 1.700722039 1.066011283 0.813815662 1.141667828 1.302410511 1 15.5649806 IFDSEEILAGYKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFDSEEILAGYKR 13 1 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 133.07 0.00017867 588820000 872550 661930 330440 417030 610330 515680 727900 811800 313420 FALSE TRUE 757240.3067 657581.7382 490241.8893 511723.0354 598185.6271 535518.5433 657308.37 638202.8874 276367.8446 2.739972545 2.379371374 1.773874562 1.851601209 2.164454508 1.937702065 2.378382228 2.3092516 1 18.07623024 4.465162137 4.049784589 1.984599101 2.6859873 0.333618727 0.385069418 0.247366017 9.143871078 0.096055477 0.342517245 29185.16393 -4.465162137 0.701388199 IFEDHENLVENLLNWTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFEDHENLVENLLNWTR 17 0 C9K0J5;Q70E73;C9J164;Q70E73-5;Q70E73-2;Q70E73-8;Q70E73-7;Q70E73-4;Q70E73-3;Q70E73-9;Q70E73-6 C9K0J5 RAPH1 Ras-associated and pleckstrin homology domains-containing protein 1 0 227 1.89E-15 217330000 223170 212130 138020 205730 187160 237260 225690 205340 265050 FALSE TRUE 193677.5191 210736.5041 204766.9336 252444.1409 183435.8822 246387.5457 203802.6185 161429.639 233716.0909 0.82868714 0.901677344 0.876135369 1.080131624 0.784866294 1.054217297 0.872009359 0.690708279 1 17.83439754 1.996710979 24.98243144 0.810690949 0.922757603 0.053597022 0.116791964 228.2337859 1733597.992 0.045426801 0.029941817 99.24553536 -1.996710979 0.112066654 IFEQKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFEQKDR 7 1 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 59.205 0.095701 296750000 347940 244120 223690 255110 249400 197540 215640 266700 498460 FALSE TRUE 301958.8474 242516.3596 331867.2322 313036.6246 244437.4279 205139.4916 194727.266 209668.2805 439532.6266 0.686999847 0.55175963 0.755045728 0.712203385 0.556130337 0.466721875 0.443032563 0.477025522 1 18.74561074 3.226375113 23.99621696 0.557628228 0.673202217 0.047641388 0.165578479 332.4951921 654761.54 0.049971274 0.057122233 1684.128063 -3.226375113 0.11557399 IFFDT(ph)DDDDDMPHSTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IFFDTDDDDDMPHSTSR 17 0 Q8NG27-3;Q8NG27 Q8NG27-3 PJA1 E3 ubiquitin-protein ligase Praja-1 1 IFFDT(1)DDDDDMPHSTSR;IFFDT(1)DDDDDMPHSTSR 211.49 8.92E-12 84890000 23919.4 28091 16337.3 19497.7 26499 28334.5 22487 30179 27619 TRUE FALSE 20758.39069 27906.46837 24238.07292 23924.95079 25971.72174 29424.54655 20306.2142 23725.4557 24353.91328 0.852363661 1.145872043 0.99524346 0.982386301 1.066429097 1.208206098 0.833796769 0.974194801 1 14.57186599 2.215688576 24.99899928 0.939696766 1.042792527 0.18743452 0.103687675 394.4626243 431141.9841 0.040538225 0.027352261 164.3193001 -2.215688576 0.103095761 IFGPIWNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IFGPIWNR 8 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 182.31 0.00053332 18891200000 1991870 1956950 1537630 1634720 2010080 2298100 2271400 2127980 2430500 FALSE TRUE 1728639.333 1944094.667 2281233.011 2005908.161 1970083.341 2386509.394 2051119.978 1672928.037 2143169.059 0.806580949 0.907112138 1.064420467 0.935954237 0.919238421 1.113542296 0.957050014 0.780586128 1 21.03131423 7.862605798 19.8192009 0.93835448 0.036006981 0 0.102380273 0 0 0.023797702 0 72879569.33 -7.862605798 -0.902347499 IFHDLDMLTTVQEENEPVIYNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IFHDLDMLTTVQEENEPVIYNR 22 0 P83111;P83111-2 P83111 LACTB "Serine beta-lactamase-like protein LACTB, mitochondrial" 0 ;;; 309.41 3.75E-67 506860000 299841 278913 214433 275134 265169 314684 181617 292747 392078 FALSE TRUE 260216.2521 277080.8021 318133.516 337607.3799 259892.6557 326790.0971 164003.8113 230145.3322 345726.9855 0.752663989 0.801443954 0.920187111 0.9765144 0.751728001 0.945225889 0.474373764 0.665685185 1 18.39927369 2.276948602 24.99997501 0.693463467 0.858780144 0.173282575 0.146761388 238.9310714 155601.7386 0.054453625 0.042178772 189.2119677 -2.276948602 0.165316677 IFHELTQTDK ddPTM_MDA-MB-175_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 ;;; 177.57 2.31E-06 3370170000 5817100 5059860 3619920 4628480 5092030 4511340 5945200 6964800 6451200 FALSE TRUE 5048355.496 5026621.446 5370525.42 5679447.126 4990708.565 4684894.169 5368635.419 5475431.72 5688546.485 0.887459654 0.883638986 0.944094495 0.998400407 0.877325795 0.823566122 0.943762248 0.962536165 1 22.43962864 1.724357981 2.565740303 0.989878497 0.906190502 0.325027055 0.046489311 0.329627792 4.536457098 0.042812852 0.013798896 53.01002164 -1.724357981 -0.083687995 IFHLEVCSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFHLEVCSR 9 0 O75886;O75886-2;Q92783;Q92783-2 O75886;Q92783 STAM2;STAM Signal transducing adapter molecule 2;Signal transducing adapter molecule 1 0 132.01 0.00031705 408690000 274520 336280 169450 202210 244160 298010 262180 306170 346250 FALSE TRUE 238241.4865 334070.9545 251396.5868 248124.8711 239301.6937 309474.6375 236753.824 240697.9281 305316.7194 0.780309335 1.094178383 0.82339607 0.81268026 0.783781819 1.013618377 0.775436813 0.788354888 1 18.21994707 IFHLWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IFHLWR 6 0 E9PDF6;O43795;O43795-2 E9PDF6 MYO1B Unconventional myosin-Ib 0 ; 123.07 0.018947 745880000 885370 875340 525290 630050 845060 905180 729130 837180 875240 FALSE TRUE 768366.1113 869589.8339 779322.001 773112.4822 828244.9593 940002.8603 658419.0848 658155.5719 771770.1243 0.995589343 1.126747209 1.009785137 1.001739324 1.073175721 1.21798296 0.853128495 0.852787056 1 19.55781167 2.212214962 24.99894438 0.889689797 1.067568534 0.511936913 0.077372422 166.9494907 158414.3389 0.0313405 0.02113672 163.0102682 -2.212214962 0.177878736 IFHTVTTTDDPVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IFHTVTTTDDPVIR 14 0 O15371-2;O15371;O15371-3;B0QYA5;B0QYA4 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ;; 153.39 6.40E-06 1011370000 1075190 952750 550210 713570 897580 995620 875120 961240 703570 FALSE TRUE 933100.9173 946491.3225 816293.3963 875596.9747 879719.9141 1033922.146 790250.9971 755686.3064 620394.7561 1.50404385 1.525627535 1.3157645 1.411354571 1.418000242 1.666555263 1.273787358 1.21807333 1 19.24282697 1.610247053 1.714088042 0.99633339 1.460564312 0.691792002 0.10242183 0.256037613 1.316058182 0.170367456 0.029908338 40.76120861 -1.610247053 0.464230922 IFHVNWFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IFHVNWFR 8 0 Q16822;Q16822-3;H0YML5;P35558-2;P35558 Q16822 PCK2;PCK1 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial;Phosphoenolpyruvate carboxykinase, cytosolic [GTP]" 0 ; 155.51 0.00040783 371990000 358090 462170 308630 498280 519080 566500 416590 453180 487190 FALSE TRUE 310767.4992 459133.9748 457884.5003 611422.0897 508751.3236 588293.6216 376189.1659 356270.9837 429594.9532 0.723396532 1.068760169 1.065851675 1.423252497 1.184258148 1.369414648 0.875683392 0.829318364 1 18.71261752 2.199491499 24.98627996 0.885511489 1.147587495 0.249462186 0.193142902 208.0672675 133065.976 0.08105148 0.054645864 158.3038579 -2.199491499 0.262076006 IFLGADAEEEIGT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFLGADAEEEIGTPR 15 0 P28749;P28749-2;H0YE05 P28749 RBL1 Retinoblastoma-like protein 1 1 IFLGADAEEEIGT(1)PR 215.23 2.65E-11 23835000 32007 36375 24540 24591 33393 32666 31638 36339 35582 TRUE FALSE 27777.19385 36136.05023 36407.62608 30174.7624 32728.54463 33922.68216 28569.75163 28568.18764 31375.5365 0.885313749 1.151726927 1.160382583 0.96172897 1.043123028 1.081182537 0.910574123 0.910524276 1 14.93735251 2.236885574 24.99971765 0.93290773 1.053060683 0.259531522 0.08440927 53.29948688 795458.203 0.032611547 0.023292271 172.5383236 -2.236885574 0.120152952 IFLLGLADNEAAIVQAESEETKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFLLGLADNEAAIVQAESEETKER 24 1 Q9UHB9;Q9UHB9-4;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 82.267 0.013544 34467000 15894 11072 12758 10395 12727 14077 18753 21787 10571 FALSE TRUE 13793.56763 10999.2673 18927.81147 12755.34363 12473.7576 14618.5513 16934.33695 17128.0196 9321.308423 1.479788781 1.180013235 2.030595987 1.368406993 1.338198141 1.568293917 1.816733894 1.837512377 1 13.18631676 2.482017343 24.83141183 1.632136744 1.483825877 0 0.316518746 728.320241 3693846.098 0.114254877 0.090999564 303.4012339 -2.482017343 -0.148310867 IFPGLS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IFPGLSPVR 9 0 Q5VZK9;Q5VZK9-2;Q5VZK9-3;A0A0U1RR91 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 IFPGLS(1)PVR;IFPGLS(1)PVR;IFPGLS(1)PVR;IFPGLS(1)PVR 123.96 0.00056976 227241000 229260 354690 238274 252550 352746 385547 317542 339454 396457 TRUE FALSE 198962.7101 352360.018 353504.1034 309895.3375 345727.0447 400379.2426 286746.8257 266864.4037 349588.3051 0.569134342 1.007928506 1.011201171 0.886457965 0.988954835 1.145287862 0.820241471 0.763367652 1 18.4152974 7.340238719 8.827367663 0.909896561 0.004505446 0 0.161873684 0 0 0.035915319 0 21889645.02 -7.340238719 -0.905391114 IFPHLYLGSEWNAANLEELQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IFPHLYLGSEWNAANLEELQR 21 0 Q8TE77;Q8TE77-2;Q8TE77-3;A0A087WWG1;E9PIT5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ;; 322.09 4.42E-67 865400000 476318 442075 292975 336169 422621 486102 450509 533269 446849 FALSE TRUE 413371.3695 439170.9802 434658.6899 412501.3095 414211.6689 504802.6585 406818.7065 419233.5743 394023.0203 1.049104616 1.114582036 1.103130192 1.046896471 1.051237231 1.281150168 1.032474464 1.063982439 1 18.58792039 IFPLLGLHEEGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFPLLGLHEEGLR 13 0 A0A6I8PIQ6;A0A0A0MS45;J3KNI1;Q9H9E3;Q9H9E3-2;Q9H9E3-3 A0A6I8PIQ6 COG4 Conserved oligomeric Golgi complex subunit 4 0 131.13 0.00013401 177160000 245180 262490 150610 159700 267010 331360 178630 210050 182960 FALSE TRUE 212778.8418 260765.6859 223445.4998 195962.3259 261697.0234 344107.6336 161306.4901 165132.4421 161330.6772 1.318898832 1.616342846 1.385015569 1.214662513 1.622115694 2.132933671 0.999850077 1.023565046 1 17.29966127 IFPMGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IFPMGDR 7 0 P49720;A0A087WXQ8;A0A087WY10;A0A087WUL2 P49720 PSMB3 Proteasome subunit beta type-3 0 ;;; 91.14 0.038672 909360000 1284810 1370630 1005480 1058150 1332570 1439310 1300380 1390880 1318740 FALSE TRUE 1115019.103 1361626.241 1491733.491 1298419.13 1306054.464 1494681.187 1174269.348 1093451.136 1162840.06 0.958875723 1.170948859 1.282836344 1.116593051 1.12315916 1.285371255 1.009828771 0.940328059 1 20.14922125 2.070526051 7.982016721 0.968593425 1.159133797 0.443013319 0.092133916 0.204380931 20.229646 0.037088064 0.0249283 117.6321544 -2.070526051 0.190540372 IFQGNVHNFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFQGNVHNFEK 11 0 Q96DI7;Q96DI7-2;Q9NSS8 Q96DI7 SNRNP40;DKFZp434D199 U5 small nuclear ribonucleoprotein 40 kDa protein 0 109.24 0.0019558 434580000 451250 368730 267340 315090 363310 315450 357200 466340 401980 FALSE TRUE 391616.1692 366307.7884 396626.5182 386636.0003 356080.8418 327585.5656 322558.799 366616.8201 354458.3823 1.104829759 1.033429611 1.118964984 1.090779679 1.004577292 0.924186257 0.910004714 1.034301454 1 18.43525672 3.132898338 4.10891023 0.971605039 1.085504091 0.65635644 0.041041506 0.151121332 4.652866009 0.013610372 0.01574057 1357.995522 -3.132898338 0.113899052 IFQIHTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IFQIHTSR 8 0 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 177.36 0.00025528 1024330000 846890 1097350 323980 569900 1328560 1271620 1024260 1152730 1158260 FALSE TRUE 734971.3408 1090141.436 480657.8116 699304.5054 1302124.255 1320540.044 924927.4228 906227.6601 1021331.822 0.719620524 1.067372436 0.470618658 0.684698636 1.274927724 1.292958875 0.90560913 0.887299936 1 19.96202023 3.260484128 24.99968702 1.047600516 0.740351459 0.420096096 0.195285463 278.2403816 317279.3827 0.060402191 0.077912723 1821.730494 -3.260484128 -0.307249057 IFQVAQELSGEDMHQFHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFQVAQELSGEDMHQFHR 18 0 C4P0D6;C4P0D8;Q99598;C4P0D4;Q5VVQ1 C4P0D6 DISC1;TSNAX Translin-associated protein X 0 60.564 0.046646 33668000 84479 79119 41042 60722 71355 76757 76797 86906 68628 FALSE TRUE 73314.88611 78599.26208 60890.04848 74509.85818 69935.1751 79709.89146 69349.23876 68321.8282 60514.87602 1.211518406 1.298841991 1.006199673 1.231265155 1.155669146 1.317194989 1.145986629 1.129008811 1 15.88500221 1.284317377 1.690809355 0.940727792 1.197376596 0.347775382 0.085894163 1.030969317 2.973649823 0.428243637 0.023418072 19.24497612 -1.284317377 0.256648804 IFSHAYFHHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFSHAYFHHR 10 0 S4R3N1;Q9Y3A3-2;Q9Y3A3-3;Q9Y3A3;B4DM50 S4R3N1 HSPE1-MOB4;MOB4 MOB-like protein phocein 0 170.99 2.40E-06 360890000 232520 383650 201980 247370 372860 370520 356020 356350 385320 FALSE TRUE 201791.8929 381129.7779 299658.2036 303539.1393 365440.8155 384774.1442 321493.2352 280147.3256 339767.9086 0.593910984 1.121735656 0.881949696 0.89337201 1.075560129 1.132461702 0.946214245 0.824525562 1 18.37419007 4.753342246 24.71843855 0.971607366 0.593910673 0.581926456 0.103527824 1890.687893 3161622.225 0.026839462 0.584074667 56668.56899 -4.753342246 -0.377696694 IFSNALPDDLRS(ph)PIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFSNALPDDLRSPIR 15 1 Q9NSY0;E9PR11 Q9NSY0 NRBP2 Nuclear receptor-binding protein 2 1 IFSNALPDDLRS(1)PIR 93.684 0.0028839 50137000 16579 21722 18740 21118 26579 26574 25861 30397 34906 TRUE FALSE 14388.04314 21579.30675 27802.72668 25913.16467 26050.1299 27596.31898 23353.0042 23896.8381 30779.45245 0.467456111 0.701094563 0.903288541 0.841898169 0.846348061 0.896582518 0.758720586 0.776389318 1 14.90967995 4.606133094 2.664837254 0.847307548 0.442016843 0.767319091 0.069442304 0.1716522 1.899290198 0.017845353 0.133121974 40376.91133 -4.606133094 -0.405290705 IFTPLLHQIELEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFTPLLHQIELEK 13 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 102.87 0.0012101 0 570670 602700 302860 582910 730910 472630 545110 761680 690820 FALSE TRUE 495254.5136 598740.824 449324.109 715268.6247 716366.321 490812.3819 492245.3161 598800.6594 609152.0466 0.813022818 0.982908664 0.73762226 1.174203762 1.176005769 0.805730498 0.808082841 0.983006891 1 19.21644285 3.763710671 24.99564058 0.978852841 0.858357026 0.197473509 0.136940652 1663.098114 1652881.389 0.03836809 0.066422764 5803.776383 -3.763710671 -0.120495814 IFTSIGEDYDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 IFTSIGEDYDER 12 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 ;;;;;;; 318.75 3.17E-46 4698660000 6053680 5002900 3756724 5100380 5711620 7596740 3630114 5920350 5886270 FALSE TRUE 5253670.85 4970035.62 5573488.292 6258499.233 5597969.937 7888991.504 3278066.103 4654329.225 5190401.866 1.012189612 0.95754351 1.073806698 1.205783173 1.078523413 1.51991921 0.631563063 0.896718471 1 22.30741481 2.213416818 24.99999958 0.845202004 1.12995277 0.388364604 0.176217394 244.0729192 242675.1977 0.071685007 0.0483514 163.4620036 -2.213416818 0.284750766 IFTTPLT(ph)PSQYYSGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFTTPLTPSQYYSGSK 16 0 P49454 P49454 CENPF Centromere protein F 1 IFTTPLT(0.918)PS(0.082)QYYSGSK 168.41 6.69E-08 165810000 385320 340970 246790 311710 360010 342630 342430 454600 544000 TRUE FALSE 334398.9857 338730.1456 366138.4695 382488.5197 352846.5053 355811.1978 309221.1913 357387.3277 479688.9397 0.697116314 0.706145415 0.763283118 0.797367811 0.735573569 0.741754017 0.644628562 0.74503975 1 18.87173965 1.242558492 5.828120478 1.010386687 0.727892734 0.816779014 0.040436068 0.057306954 6.899365454 0.064392024 0.010530527 17.48068683 -1.242558492 -0.282493953 IFVGGIKEDTEEYNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IFVGGIKEDTEEYNLR 16 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;; 296.13 9.99E-46 6419060000 5649320 4816960 2784410 3368010 4550860 3650920 5274790 6216610 2794280 FALSE TRUE 4902748.048 4785317.073 4130959.989 4132768.147 4460306.79 3791373.255 4763241.678 4887236.329 2463943.402 1.989797349 1.942137579 1.676564481 1.677298328 1.810231025 1.538742023 1.933178203 1.983501864 1 21.23253769 1.23142993 24.99994882 0.99999858 1.817948326 0.745571928 0.150343562 137.6854522 482677.7388 0.386091494 0.039109988 17.03844397 -1.23142993 0.817949746 IFVGGLSPDT(ph)PEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFVGGLSPDTPEEK 14 0 Q14103-3;Q14103;H0Y8G5;H0YA96;D6RAF8;D6RF44;Q14103-2;Q14103-4 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 IFVGGLS(0.278)PDT(0.722)PEEK 166.79 4.19E-05 68223000 201700 145250 105720 119460 132300 115650 175080 181590 169430 TRUE FALSE 175044.834 144295.8432 156846.5456 146585.2188 129667.4888 120099.1303 158100.7685 142758.3916 149400.1784 1.171650769 0.965834477 1.049841756 0.981158258 0.867920576 0.803875414 1.058236812 0.955543649 1 17.18882235 7.999999028 0.911913828 0.949229891 117.9699377 0.435571805 0.076116044 1030.441992 2.123696255 0.025638249 251108.6044 99999776.11 -7.999999028 117.0207078 IFVNDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 IFVNDDR 7 0 Q12906;Q12906-5;Q12906-2;Q12906-3;K7EKJ9;K7ER69;K7EM82;K7EJ09;K7ERM6;K7ENK6;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;;;;;;; 172.03 0.0021301 8293500000 15752770 13671870 8820380 10630580 13136360 14381620 12569120 14332470 13540110 FALSE TRUE 13671001.53 13582058.59 13085945.27 13044415.67 12874972.14 14934890.23 11350168.68 11267582.83 11939413.62 1.145031236 1.137581712 1.096029142 1.09255078 1.078358833 1.250889759 0.950647078 0.943730001 1 23.50922865 2.209703606 24.99994364 0.95981484 1.127538414 0.718062479 0.049683067 105.8676716 91716.4716 0.019739892 0.013311193 162.0703633 -2.209703606 0.167723574 IFWEVFHELPLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFWEVFHELPLEK 13 0 Q5GLZ8-6;Q5GLZ8-3;Q5GLZ8-2;Q5GLZ8 Q5GLZ8-6 HERC4 Probable E3 ubiquitin-protein ligase HERC4 0 77.185 0.026638 77207000 122230 117490 68485 97064 90099 86370 111870 126750 115030 FALSE TRUE 106076.9958 116718.2005 101604.5751 119103.8647 88306.20618 89692.70979 101020.8646 99645.49887 101431.2844 1.045801563 1.150712042 1.001708453 1.174232047 0.870601281 0.884270669 0.995953716 0.982394134 1 16.63014317 3.237950149 24.99999905 0.951692302 1.090698769 0.563108656 0.064006272 12.830108 525432.7174 0.018853531 0.022695529 1729.617812 -3.237950149 0.139006467 IFYDMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IFYDMK 6 0 P60981;F6RFD5 P60981 DSTN Destrin 0 ; 100.82 0.086601 7163900000 8200600 7438100 5244400 6176200 6925700 6240900 8746800 9302000 8510900 FALSE TRUE 7116869.932 7389238.631 7780609.381 7578600.607 6787892.12 6480991.461 7898536.682 7312839.688 7504751.098 0.948315253 0.984608088 1.036757819 1.009840368 0.904479313 0.863585131 1.052471505 0.974428011 1 22.83937279 IFYPEIEEVQALDDTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IFYPEIEEVQALDDTER 17 0 P33316-2;H0YNW5;P33316;A0A0C4DGL3;H0YKC5 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 ;;;;; 255.45 1.06E-26 764719000 126632.9 118263.1 89483.1 88150.5 109509.5 123627.9 123947 121137.7 121860 FALSE TRUE 109898.0414 117486.2219 132757.4265 108166.4183 107330.4752 128383.9453 111926.639 95233.34555 107453.8496 1.022746433 1.093364475 1.235483204 1.006631393 0.998851838 1.194782186 1.041625213 0.886272068 1 16.71335764 1.947752574 6.535602205 0.941977518 1.092709852 0.363296684 0.080572179 0.228972821 22.55002832 0.038761447 0.021353718 88.66507254 -1.947752574 0.150732334 IFYPEIEEVQALDDTERGS(ph)GGFGSTGKN ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFYPEIEEVQALDDTERGSGGFGSTGKN 28 2 P33316-2;H0YNW5;P33316;A0A0C4DGL3 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 1 IFYPEIEEVQALDDT(0.006)ERGS(0.993)GGFGST(0.001)GKN 139.54 1.10E-07 30490000 38536 37191 22074 25434 33752 32199 39429 52025 25448 TRUE FALSE 33443.36996 36946.68987 32749.06023 31209.17843 33080.40123 33437.71637 35605.18165 40899.85861 22439.56643 1.490375051 1.646497493 1.459433734 1.390810225 1.474199661 1.490123103 1.586714332 1.822667062 1 14.45375718 4.216464841 24.66089774 1.49870417 1.568436458 0.020027936 0.207484432 1016.23375 1134212.447 0.0534108 0.111335518 16461.32695 -4.216464841 0.069732287 IFYPETTDIYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IFYPETTDIYDR 12 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;;;; 275.63 1.82E-27 3017553000 1593296 1741224 1315971 1427253 1686816 1740439 1557620 1812828 2880470 FALSE TRUE 1382737.897 1729785.785 1952378.977 1751332.608 1653251.662 1807394.815 1406562.252 1425168.84 2539944.118 0.544396976 0.681033009 0.768670052 0.689516197 0.650900801 0.711588417 0.55377685 0.561102439 1 21.27636533 1.230119131 24.98797215 1.000000665 0.645530674 0.697599827 0.073428626 201.4628244 596310.7751 0.219866289 0.019533531 16.98709559 -1.230119131 -0.354469991 IFYPETTDIYDRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IFYPETTDIYDRK 13 1 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;;;; 266.85 2.89E-24 4545460000 2986890 2601020 1572435 1874552 2432890 1924774 3033720 3350540 1403506 FALSE TRUE 2592164.919 2583933.728 2332869.825 2300197.682 2384480.249 1998821.301 2739510.301 2634053.095 1237585.12 2.094534653 2.087883643 1.885017676 1.85861776 1.9267202 1.61509804 2.213593439 2.128381356 1 20.23909632 1.233201524 24.99998213 0.999998466 1.978620018 0.764445742 0.170300291 87.89285405 409971.781 0.367891785 0.043974788 17.10808992 -1.233201524 0.978621552 IFYVNYLSELSEHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IFYVNYLSELSEHVK 15 0 Q07960;H0YE29 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 244.36 4.98E-18 934770000 1143590 908720 664700 931060 945810 847270 1221570 1365310 1438830 FALSE TRUE 992461.684 902750.5585 986151.1433 1142471.403 926990.2314 879865.0252 1103102.329 1073349.081 1268733.157 0.782246195 0.71153698 0.777272304 0.900482026 0.730642394 0.693498882 0.869451802 0.846000655 1 20.27495724 0.984644201 1.09503434 1.226379594 0.771721985 0.565990342 0.062295603 2.184782148 1.47517163 1.326630556 0.020444798 9.652597588 -0.984644201 -0.454657608 IFYYFSNS(ph)PSKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IFYYFSNSPSKR 12 1 Q08999;Q08999-2 Q08999 RBL2 Retinoblastoma-like protein 2 1 IFYYFS(0.008)NS(0.942)PS(0.05)KR 66.66 0.035195 252530000 381510 417670 259350 303890 414250 390950 490690 509260 469710 TRUE FALSE 331092.4869 414926.2983 384772.5275 372892.8692 406007.2355 405990.0995 443102.9593 400358.7121 414181.4189 0.799390006 1.001798437 0.928995145 0.900312887 0.980264244 0.980222871 1.069828194 0.966626444 1 18.65990331 3.075492024 2.917979008 1.003692732 0.915646269 0.401181958 0.055667463 0.284086208 4.903755181 0.017270058 0.019657051 1189.849476 -3.075492024 -0.088046463 IGADFLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IGADFLAR 8 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ; 129.68 0.002513 224670000 870320 855160 564400 659290 877090 868960 841370 957300 922930 FALSE TRUE 755305.0069 849542.3977 837345.7278 808991.8711 859637.625 902389.4535 759774.0669 752588.8447 813822.2668 0.928095774 1.043891808 1.028904912 0.994064557 1.056296516 1.10882866 0.933587219 0.924758237 1 19.63435423 2.19529954 24.99923556 0.946143677 1.027427649 0.326716074 0.049697124 145.4457074 84047.54714 0.020086856 0.013542652 156.7832057 -2.19529954 0.081283972 IGAEVYHNLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IGAEVYHNLK 10 0 P06733;A0A2R8Y6G6;P06733-2;K7EM90 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;;; 155.06 1.34E-05 28206690000 17432280 18134610 11464620 10842460 15995640 14252890 17181190 19252040 20883600 FALSE TRUE 15128560.03 18015482.55 17008948.58 13304406.26 15677358.06 14801207.9 15514960.84 15135141.07 18414764.6 0.821545122 0.978317288 0.923658214 0.722485818 0.851347188 0.80376851 0.842528329 0.8219025 1 24.13435962 IGALEGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IGALEGYR 8 0 O43776;K7EIU7;O43776-2;K7EPK2;K7EMQ6;K7EQ35 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 102.72 0.011425 421090000 519550 478630 321750 369620 529730 510770 529340 595540 613630 FALSE TRUE 450890.1511 475485.848 477349.3762 453547.8703 519189.4094 530419.6524 478004.6883 468188.4055 541087.3604 0.833303795 0.878759851 0.882203894 0.838215607 0.959529731 0.980284684 0.883414996 0.865273225 1 19.04550202 3.243766594 24.99959364 0.926704908 0.861315224 0.440907204 0.043496094 158.2881742 760110.338 0.013629005 0.017065567 1752.938154 -3.243766594 -0.065389684 IGDEDVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IGDEDVGR 8 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 130.22 0.0044219 0 2108800 1816700 1346400 1823900 1674400 2052700 1515900 1810500 2520000 FALSE TRUE 1830116.737 1804765.978 1997523.543 2238044.372 1641082.716 2131668.697 1368888.251 1423338.664 2222088.471 0.823602103 0.812193575 0.8989397 1.007180588 0.738531673 0.959308653 0.616036791 0.640540952 1 21.08348483 2.243166061 24.99999526 0.723258669 0.871641558 0.155748405 0.127054761 166.2307778 902366.5405 0.047640172 0.035650094 175.0515904 -2.243166061 0.148382889 IGDEYAEDS(ph)S(ph)DEEDIR ddPTM_MDA-MB-175_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 183.74 2.83E-09 858590000 464890 355560 306030 339240 355750 342950 388450 417660 531090 TRUE FALSE 403453.6086 353224.3029 454027.1316 416269.627 348671.271 356143.5084 350778.1788 328346.6592 468305.1452 0.861518633 0.754260991 0.969511303 0.888885444 0.74453863 0.760494545 0.749037636 0.70113827 1 18.83708936 3.242067177 24.98393955 0.775126193 0.867592967 0.128937122 0.095215837 157.0219985 1118758.834 0.027456789 0.03404117 1746.09222 -3.242067177 0.092466773 IGDEYFTFITDCKDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IGDEYFTFITDCKDPK 16 1 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 133.71 2.94E-05 764430000 1484400 1028960 1134960 1080860 922290 622080 1570260 1725050 1959220 FALSE TRUE 1288232.779 1022200.694 1683830.452 1326285.783 903938.2334 646011.8201 1417976.427 1356161.482 1727603.244 0.745676291 0.591687182 0.974662706 0.767702763 0.52323254 0.37393529 0.820776664 0.784995911 1 20.7203405 1.378464358 1.767775228 1.048359465 0.676316074 0.274603652 0.164157327 0.994597038 3.847787882 0.587164595 0.048973457 23.90365754 -1.378464358 -0.372043391 IGDKDVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IGDKDVGR 8 1 P45877 P45877 PPIC Peptidyl-prolyl cis-trans isomerase C 0 66.435 0.056263 167490000 308460 251540 140190 187370 195850 234240 238850 287740 132200 FALSE TRUE 267696.2295 249887.6172 207986.3529 229915.2223 191952.9682 243251.3644 215686.3638 226209.0402 116571.4666 2.296412984 2.143643075 1.784196073 1.972311312 1.646654827 2.086714455 1.850250066 1.940518094 1 16.83085518 1.237056685 6.726572642 0.975639827 1.95420956 0.730408598 0.184169104 0.063151275 14.55760296 0.28058675 0.045207183 17.26063167 -1.237056685 0.978569733 IGDPLLEDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IGDPLLEDTR 10 0 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ; 138.06 0.00017366 228690000 604180 569660 398690 490070 583750 541280 525560 646630 777170 FALSE TRUE 524336.0822 565917.866 591497.8175 601347.8838 572134.5171 562103.3919 474591.2721 508353.2066 685293.848 0.765125915 0.82580322 0.863130202 0.877503695 0.834874731 0.820237032 0.692536893 0.741803254 1 19.38636321 2.464148165 24.98217324 0.786897936 0.836043126 0 0.084286671 691.7908638 1332166.133 0.031508824 0.024421775 291.1710314 -2.464148165 0.04914519 IGDQEFDSLPALLEFYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IGDQEFDSLPALLEFYK 17 0 P46108-2;P46108;I3L297 P46108-2 CRK Adapter molecule crk 0 134.24 4.45E-05 0 45892 42290 31281 33903 38861 37079 51230 51278 44569 FALSE TRUE 39827.25592 42012.19421 46408.59623 41601.19432 38087.74213 38505.45312 46261.72249 40312.59875 39300.10359 1.01341351 1.069009757 1.180877198 1.058551773 0.969151189 0.97977994 1.177139963 1.025763168 1 15.26224549 3.483852024 24.660794 1.036050161 1.091528344 0.121333215 0.069558777 588.790564 2157267.297 0.020381548 0.027369237 3046.856666 -3.483852024 0.055478183 IGDYYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IGDYYLR 7 0 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 104.8 0.018775 70662000 133590 136310 84049 100600 121530 143080 118770 134480 149380 FALSE TRUE 115935.743 135414.5706 124695.3775 123442.7676 119111.7908 148584.3802 107251.7037 105722.4985 131720.4666 0.880164989 1.028045027 0.946666686 0.937157078 0.904277018 1.128028043 0.814237198 0.802627726 1 17.00712 IGEEFLTDLSQLKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IGEEFLTDLSQLKK 14 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 198.23 3.58E-08 396290000 944010 597250 542130 530520 543170 386150 840780 968490 518720 FALSE TRUE 819256.6867 593326.6254 804305.8813 650982.6745 532361.9797 401005.4404 759241.285 761385.9503 457397.5125 1.79112624 1.297179388 1.758439561 1.423231777 1.163893474 0.876711021 1.659915641 1.664604484 1 18.80308899 7.999998148 0.691464506 1.354887316 47.0189373 0.183202709 0.288889213 620.5095697 3.430371892 0.12274928 43729.34101 99999573.64 -7.999998148 45.66404999 IGEEQSAEDAEDGPPELLFIHGGHTAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IGEEQSAEDAEDGPPELLFIHGGHTAK 27 0 Q16576;E9PC52;Q16576-2;Q5JNZ6 Q16576 RBBP7 Histone-binding protein RBBP7 0 ; 243.35 1.56E-45 438111000 368280 235054 197162 242880 217978 182176 294086 346800 294393 FALSE TRUE 319610.8649 233509.9148 292510.2027 298029.6162 213640.6643 189184.4286 265565.585 272639.5188 259590.1949 1.231213163 0.899532877 1.126815297 1.148077324 0.822992041 0.728781103 1.023018551 1.05026894 1 17.98587637 4.750714927 24.05836591 0.980791387 1.231213426 0.277481432 0.129657487 1745.73369 3455415.521 0.033729484 0.539100824 56326.7803 -4.750714927 0.250422039 IGEEQSPEDAEDGPPELLFIHGGHTAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IGEEQSPEDAEDGPPELLFIHGGHTAK 27 0 Q09028-3;Q09028;Q09028-2;Q09028-4;H0YF10;H0YCT5;H0YDK2;H0YEU5 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 215.07 2.30E-34 572350000 366040 292600 223900 240430 257800 207310 308830 381740 304770 FALSE TRUE 317666.8866 290677.8913 332178.7889 295023.3062 252670.2844 215285.3498 278879.7141 300107.8717 268740.4378 1.18205838 1.081630639 1.236058078 1.0978002 0.940201953 0.80109027 1.037728882 1.116720186 1 18.0358539 3.426520315 5.432766852 0.992738081 1.159773368 0.490042464 0.087863969 0.200115472 13.03911747 0.028692984 0.037706856 2670.055661 -3.426520315 0.167035286 IGEGT(ph)YGVVYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IGEGTYGVVYK 11 0 P06493;A0A024QZP7;A0A087WZZ9;E5RIU6;P06493-2;G3V317;K7ELV5;G3V5T9;P24941;P24941-2;E7ESI2;Q00526 P06493;G3V5T9 CDK1;CDC2;CDK2;CDK3 Cyclin-dependent kinase 1;Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 1 IGEGT(0.92)Y(0.08)GVVYK;IGEGT(0.889)Y(0.111)GVVYK 196.27 6.83E-07 8150000000 2094880 1684970 1311760 1478280 1705000 1316960 2291000 2440500 2117420 TRUE FALSE 1818036.3 1673901.321 1946131.524 1813946.068 1671073.836 1367624.303 2068819.173 1918618.067 1867101.02 0.973721444 0.896524239 1.042327921 0.971530758 0.895009867 0.732485435 1.108038157 1.027591998 1 20.83236856 IGEGTY(ph)GVVYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IGEGTYGVVYK 11 0 P06493;A0A024QZP7;A0A087WZZ9;E5RIU6;P06493-2;G3V317;K7ELV5;G3V5T9;P24941;P24941-2;E7ESI2;Q00526 P06493;G3V5T9 CDK1;CDC2;CDK2;CDK3 Cyclin-dependent kinase 1;Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 1 IGEGT(0.427)Y(0.573)GVVYK;IGEGT(0.31)Y(0.69)GVVYK;IGEGT(0.002)Y(0.998)GVVYK;IGEGT(0.029)Y(0.971)GVVYK 204.07 3.55E-07 13256920000 4290780 3409050 3094500 3295940 3431880 2712440 4482720 5347700 5356640 TRUE FALSE 3723742.552 3386655.726 4591010.55 4044333.552 3363592.302 2816789.322 4047986.504 4204135.971 4723384.122 0.78836327 0.716997737 0.971974845 0.856236429 0.712114919 0.596349831 0.857009805 0.890068617 1 22.17138943 1.584556003 2.175843026 0.991892537 0.7806551 0.341906553 0.099849908 0.409469757 3.823585952 0.143670364 0.02957868 38.41987988 -1.584556003 -0.211237438 IGEHTPS(ph)ALAIMENANVLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IGEHTPSALAIMENANVLAR 20 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BR04;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 IGEHT(0.131)PS(0.869)ALAIMENANVLAR 121.47 2.08E-05 58698000 20158 31769 22667 18303 31737 21996 26760 30618 28797 TRUE FALSE 17494.06923 31560.30735 33628.83702 22458.97589 31105.49579 22842.20035 24164.81932 24070.57897 25392.65147 0.688942202 1.242891369 1.324353113 0.884467537 1.224980221 0.89955948 0.951646162 0.947934839 1 14.63212343 2.711419339 24.89163291 0.949670483 1.086034221 0.097833457 0.18380798 1548.398444 1420055.558 0.060603546 0.053461036 514.5402337 -2.711419339 0.136363738 IGEHTPSALAIMENANVLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 IGEHTPSALAIMENANVLAR 20 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BR04;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;; 286.69 2.81E-45 14643960000 5374430 5109691 3022171 3583940 4785058 4415482 4620746 5587679 5259350 FALSE TRUE 4664185.458 5076125.103 4483703.004 4397728.354 4689844.708 4585348.45 4172626.764 4392797.329 4637595.634 1.005733537 1.094559661 0.96681629 0.948277664 1.011266414 0.988733993 0.899739238 0.947214392 1 22.1449456 4.187143684 10.83736309 0.962509775 1.050069065 0.460352283 0.03772701 0.397878548 82.25788266 0.009738293 0.020337183 15386.63614 -4.187143684 0.08755929 IGELGAPEVWGLS(ph)PK ddPTM_MDA-MB-175_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 301.04 2.75E-44 3484621000 3727932 2894703 2352253 2449810 3361190 2187234 3592981 4245471 3613336 TRUE FALSE 3235276.341 2875687.505 3489810.419 3006076.804 3294308.895 2271378.307 3244534.256 3337610.065 3186171.534 1.015411853 0.902552632 1.095298976 0.943476135 1.033939592 0.712886385 1.018317508 1.047529936 1 21.60339251 2.032221976 24.99999238 1.028889847 0.950715392 0.099236209 0.101178107 407.2884012 316000.3381 0.040369254 0.027216742 107.7015556 -2.032221976 -0.078174455 IGELVGVLVNHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IGELVGVLVNHFK 13 0 J3QRN6;O94832;K7EIG7 J3QRN6 MYO1D Unconventional myosin-Id 0 141.38 4.16E-06 0 119020 103370 78959 99239 100700 80362 101100 129590 124770 FALSE TRUE 103291.2054 102690.9557 117143.8365 121772.7317 98696.26702 83453.57814 91295.33756 101878.187 110019.8327 0.938841688 0.933385855 1.064751996 1.106825276 0.89707705 0.758532131 0.829808002 0.925998381 1 16.74740409 3.07949404 9.21593146 0.875517091 1.008913675 0.393032025 0.079683096 0.34257516 36.42539318 0.026111598 0.02962955 1200.864593 -3.07949404 0.133396584 IGEMPLTDSILCDGLTDAFHNCHMGITAENVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IGEMPLTDSILCDGLTDAFHNCHMGITAENVAK 33 0 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 165.31 2.25E-14 175720000 52530 53072 48715 56195 54373 37115 56398 84268 53626 FALSE TRUE 45588.02741 52723.36654 72273.73694 68954.93364 53291.08368 38542.83807 50928.53064 66247.94397 47286.39537 0.96408337 1.114979607 1.528425594 1.458240432 1.126985537 0.815093596 1.077022899 1.400993742 1 15.52913755 3.035732463 24.92907228 1.10774591 1.276613783 0.149501245 0.211972494 397.5250198 277334.3877 0.070461816 0.07989598 1085.756564 -3.035732463 0.168867873 IGEWELIQESGVPLKPLFGPGYTGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IGEWELIQESGVPLKPLFGPGYTGIR 26 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 200.09 5.00E-25 699220000 669370 580890 368540 466780 513360 418220 600820 694550 610220 FALSE TRUE 580911.0585 577074.0953 546767.1767 572769.5333 503145.1404 434309.194 542552.5689 546025.8875 538080.4868 1.07959882 1.072467985 1.016143849 1.064468137 0.935074125 0.807145408 1.008311177 1.014766194 1 19.03746246 3.243632415 24.96529524 0.957620915 1.056189175 0.423432993 0.06079793 144.8419431 712961.5161 0.019628137 0.024553638 1752.396655 -3.243632415 0.098568261 IGFPWSEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IGFPWSEIR 9 0 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 ;; 138.54 0.00031079 4778463000 463080 545693 363405 486099 536162 576565 434360 622353 534532 FALSE TRUE 401882.8047 542108.3068 539148.8735 596475.2075 525493.4252 598745.8286 392235.8341 489267.6541 471340.2359 0.852638443 1.150142223 1.143863461 1.265487565 1.11489193 1.270304937 0.832171336 1.038034984 1 18.84640932 2.239656128 24.99999938 0.968482689 1.139380483 0.30421691 0.124905544 35.88146902 818863.9468 0.047251868 0.034502003 173.642539 -2.239656128 0.170897794 IGGAQNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IGGAQNR 7 0 P14174 P14174 MIF Macrophage migration inhibitory factor 0 ;;;;; 114.67 0.013618 988410000 1116650 1008115 788652 1067776 854568 1251870 1071451 1400900 1594360 FALSE TRUE 969081.8733 1001492.626 1170046.745 1310230.861 837563.7687 1300030.249 967541.8469 1101328.437 1405876.577 0.68930793 0.712361698 0.832254242 0.931967203 0.595759103 0.924711507 0.688212509 0.78337491 1 20.42303851 1.242343445 6.26393769 1.006882804 0.7706128 0.318809416 0.105921678 0.143417152 23.90383085 0.144631109 0.024492822 17.47203317 -1.242343445 -0.236270004 IGGELEEQAVMLEDFSHELESTQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IGGELEEQAVMLEDFSHELESTQSR 25 0 O43752;O43752-2 O43752 STX6 Syntaxin-6 0 ;;; 271.11 6.33E-53 140574000 136472 122108 81357.2 94405 111356 123049 101843 152944 125433 FALSE TRUE 118436.8794 121305.8645 120701.814 115841.0981 109140.2335 127782.7747 91966.28154 120238.1158 110604.4536 1.070814741 1.096753888 1.09129253 1.047345693 0.986761653 1.155313104 0.831488051 1.087100129 1 16.75504995 3.360513702 0.976913845 1.006565175 1.092042641 0.140118261 0.081941815 1.126278906 2.364733613 0.036297145 0.06283282 2293.578992 -3.360513702 0.085477466 IGGIFAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IGGIFAFK 8 0 H0YF61;P22307-6;P22307-2;P22307-4;P22307-7;P22307-8;P22307 H0YF61 SCP2 Non-specific lipid-transfer protein 0 117.7 0.0047199 79296000 248830 311700 193800 178110 290240 352350 221680 254500 247700 FALSE TRUE 215946.485 309652.4222 287522.3282 218552.5977 284464.7918 365905.1325 200181.5077 200077.1555 218417.1882 0.988688147 1.417710871 1.316390576 1.000619958 1.302391969 1.675257957 0.916509865 0.9160321 1 17.73672687 IGGIGTVPVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IGGIGTVPVGR 11 0 A0A2U3TZH3;Q05639;P68104;A0A087WVQ9;Q5VTE0 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3 0 ; 122.28 0.00091672 296710000 444880 423020 236270 258920 383490 392950 443480 474790 353970 FALSE TRUE 386087.9808 420241.1538 350530.9623 317711.7433 375859.2993 408067.0408 400471.3779 373259.8533 312124.0698 1.236969584 1.346391369 1.123050082 1.017902091 1.20419838 1.307387287 1.28305189 1.195870134 1 18.25176009 4.237107094 24.99956837 1.172790017 1.291680481 0.21278635 0.102252734 64.00009773 1100844.348 0.027624842 0.062932179 17262.63526 -4.237107094 0.118890464 IGGILANELSVDEAALHAAVIAINEAIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IGGILANELSVDEAALHAAVIAINEAIDR 29 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 163.76 5.44E-12 2058700000 102470 110610 80564 68796 99814 91885 113420 127690 74972 FALSE TRUE 88928.32987 109883.3956 119525.0199 84417.18328 97827.89668 95419.87541 102420.5459 100384.4872 66108.89557 1.345179482 1.662157485 1.808002068 1.276941364 1.479799289 1.443374217 1.54927026 1.518471702 1 16.01255679 1.238414183 24.99979551 0.999999432 1.516296127 0.535423006 0.149324834 2.770263425 471332.293 0.202223466 0.036008257 17.31466858 -1.238414183 0.516296695 IGGVQQDTILAEGLHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IGGVQQDTILAEGLHFR 17 0 Q99623-2;Q99623;F5GY37;J3KPX7;F5H0C5;F5H3X6;F5H2D2 Q99623-2 PHB2 Prohibitin-2 0 ; 119.68 0.00010824 393480000 280382 278864 174077 258516 302960 320880 256142 357930 370110 FALSE TRUE 243328.8083 277032.124 258261.2195 317216.009 296931.6887 333224.4612 231301.3883 281389.4549 326356.0174 0.745593142 0.848864765 0.791348116 0.971993749 0.909839785 1.021045862 0.708739462 0.86221623 1 18.31608711 3.766157841 24.46290011 0.898793366 0.800628254 0.26270811 0.090411958 951.4089462 843350.017 0.024500683 0.042422715 5836.571912 -3.766157841 -0.098165112 IGHPAPNFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IGHPAPNFK 9 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 ;; 133.55 0.00027388 14928940000 15139650 12494380 8145620 10883430 11719230 10597820 13646620 14950280 13750210 FALSE TRUE 13138906.89 12412303.6 12084869.08 13354679.12 11486040.25 11005524.99 12323172.89 11753278.97 12124675.84 1.083650158 1.023722511 0.99671688 1.101446282 0.947327616 0.907696432 1.016371329 0.969368511 1 23.53144284 3.221777367 24.99981519 0.96889831 1.045503361 0.506334566 0.040649609 214.3675582 319314.7402 0.01224516 0.013920346 1666.392747 -3.221777367 0.076605051 IGIARPEEEFHVPLDSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IGIARPEEEFHVPLDSYR 18 1 Q709C8-3;Q709C8;Q709C8-4;Q709C8-2;A0A3B3IU50 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 0 ; 69.148 0.016413 188298000 314010 289110 177703 212680 261750 265120 266590 311260 286590 FALSE TRUE 272512.7829 287210.8174 263640.7652 260972.2446 256541.6871 275319.338 240736.1428 244699.4712 252709.6567 1.078363156 1.1365249 1.043255603 1.032695972 1.015163767 1.089469004 0.952619484 0.968302812 1 17.94712127 3.473711835 0.334701096 0.94576994 1.153311811 0.528439913 0.038358012 2.203073108 0.76590957 0.145209078 0.263995415 2976.540764 -3.473711835 0.207541871 IGIEIIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IGIEIIKR 8 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 126.62 0.0019423 486090000 1541570 1362670 796270 1461600 1501510 1386090 1391060 1836960 552450 FALSE TRUE 1337847.619 1353718.531 1181348.835 1793478.619 1471632.889 1439413.779 1256155.215 1444140.399 487139.9904 2.746330922 2.778910699 2.425070532 3.68164933 3.020965057 2.954825733 2.578632919 2.964528529 1 18.8939769 1.237278647 25 0.999997719 2.894653377 0.761307333 0.333265607 15.81960103 308377.1406 0.489135508 0.080991447 17.26945558 -1.237278647 1.894655659 IGITNHDEYSLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IGITNHDEYSLVR 13 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;; 197.38 1.34E-07 1081390000 1152400 1099543 761499 893278 1271220 1239568 1301390 1336220 1206070 FALSE TRUE 1000107.42 1092320.03 1129762.463 1096110.423 1245925.209 1287254.983 1175181.398 1050479.751 1063489.779 0.940401535 1.0271091 1.062316241 1.030673209 1.171544132 1.21040654 1.105023689 0.987766665 1 20.02037474 4.788191038 1.259248189 1.083241066 0.86578145 0.306528914 0.069205366 2.411038548 3.060198801 0.023258544 0.700254778 61403.20464 -4.788191038 -0.217459616 IGKPAPDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IGKPAPDFK 9 1 P32119;A6NIW5;P32119-2 P32119 PRDX2 Peroxiredoxin-2 0 ; 84.658 0.013993 10137600000 17759500 13269100 9691100 11463200 11866700 9245800 16837700 19378500 14792900 FALSE TRUE 15412537.08 13181934.41 14377748.37 14066094.76 11630575.89 9601491.909 15204782.45 15234558.58 13044100.21 1.181571502 1.010566784 1.102241484 1.07834918 0.891634969 0.736079281 1.165644406 1.167927134 1 23.63689409 7.323251582 1.259560327 1.025303535 129.372806 0.127840402 0.129968542 3598.504931 9.152267208 0.041441972 1331889.783 21049974.9 -7.323251582 128.3475025 IGKPHTVPCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IGKPHTVPCK 10 1 P15880;H0YEN5;E9PPT0;E9PMM9;I3L404;E9PM36 P15880 RPS2 40S ribosomal protein S2 0 ; 119.16 0.00043854 2548400000 6444000 5509600 4091900 4811300 5229400 4248400 6843400 7380500 6447400 FALSE TRUE 5592409.073 5473407.075 6070756.527 5903779.201 5125345.171 4411838.697 6179728.121 5802237.51 5685195.717 0.983679252 0.962747344 1.067818388 1.038447838 0.901524842 0.776022307 1.086985995 1.020587118 1 22.43877859 IGLDDEEKLDLFR ddPTM_MDA-MB-175_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 ; 141.32 3.63E-05 276830000 625320 454910 391650 439410 459030 359230 570110 658310 596700 FALSE TRUE 542682.3776 451921.6663 581053.25 539184.7565 449896.2011 373049.8106 514820.8199 517535.5295 526158.8058 1.031404153 0.858907351 1.104330563 1.02475669 0.855057819 0.709006115 0.9784514 0.983610887 1 19.00513878 4.812009686 20.70721627 0.942569346 1.031413879 0.064379152 0.109747712 64658.53444 18220368.69 0.028101528 124.752416 64864.88998 -4.812009686 0.088844533 IGLEVDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IGLEVDRR 8 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 0 ;;; 190.26 0.00030041 758140000 624620 554590 335866 396483 541210 553750 537960 602810 406209 FALSE TRUE 542074.8844 550946.8618 498291.921 486510.525 530440.9799 575053.1208 485788.722 473903.7726 358187.4348 1.513383307 1.538152398 1.391148523 1.358256817 1.480903372 1.605453081 1.356241662 1.323060852 1 18.4503552 1.052359714 1.343941208 0.606024465 1.470987826 0.789407711 0.07651899 0.973389261 1.087140087 1.312343964 0.023732342 11.28131469 -1.052359714 0.864963361 IGLIHGHQVIPWGDMASLALLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IGLIHGHQVIPWGDMASLALLQR 23 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ; 228.63 3.82E-33 1170420000 462240 406840 316780 377190 383930 402250 491070 498360 457020 FALSE TRUE 401153.8128 404167.4413 469975.8676 462836.7545 376290.5441 417724.8178 443446.107 391789.5922 402991.6162 0.995439599 1.002917741 1.166217481 1.148502192 0.93374286 1.036559573 1.10038544 0.972202836 1 18.6203903 3.243393328 24.99999787 1.01231585 1.079169 0.205331316 0.067895245 223.0819085 1154011.585 0.020868483 0.026057454 1751.432192 -3.243393328 0.06685315 IGQQVDREPGDVAT(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IGQQVDREPGDVATPPR 17 1 H3BT22;Q9Y5N6 H3BT22 ORC6 Origin recognition complex subunit 6 1 IGQQVDREPGDVAT(1)PPR 65.784 0.068725 197280000 119740 109610 61520 69078 96345 86942 102120 104430 87611 TRUE FALSE 103916.0556 108889.9647 91271.27777 84763.21569 94427.923 90286.715 92216.41812 82098.45718 77253.72739 1.345126755 1.409510821 1.181448208 1.097205514 1.222308958 1.168703674 1.193682444 1.062711923 1 16.23731692 8 0.194912785 0.991210219 2.846726947 0.66594981 0.070695134 68.70501418 1.006229156 0.530937063 37.37544023 100000000 -8 1.855516729 IGRPSETGIIGIIDPECR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IGRPSETGIIGIIDPECR 18 1 Q16531;F5GY55;F5H2L3;F5GWI0;F5GZY8 Q16531 DDB1 DNA damage-binding protein 1 0 ;;; 159.7 3.87E-11 731232000 1053330 973836 589128 658966 882164 918971 900284 1042560 954689 FALSE TRUE 914129.7717 967438.8072 874032.2713 808594.302 864610.6623 954324.409 812974.5962 819616.6572 841826.754 1.085888239 1.149213663 1.038256704 0.960523407 1.027064842 1.133635162 0.965726727 0.973616784 1 19.68316383 8 0.236341541 0.970540431 1.859002202 0.296486282 0.056428891 110.2326203 1.730578379 0.231968508 37.08518943 99999999.98 -8 0.88846177 IGSIS(ph)R ddPTM_MDA-MB-175_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 101.41 0.038343 535420000 590910 483570 229740 341120 360180 258560 533430 520890 442600 TRUE FALSE 512819.7463 480393.3968 340843.0324 418576.5097 353013.1227 268506.9705 481698.0407 409501.7271 390276.3322 1.313991406 1.23090579 0.873337695 1.072513179 0.90452096 0.687991939 1.234248662 1.049260981 1 18.57413645 4.362655166 5.60456701 0.986530218 1.293060554 0.432808798 0.142458959 0.191986211 8.436659667 0.036561574 0.100615662 23049.16337 -4.362655166 0.306530337 IGSLEWYYEHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IGSLEWYYEHVK 12 0 Q9BV36-2;Q9BV36-5;C9JKV5;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 0 ; 149.26 5.94E-05 739770000 1159280 1113000 652080 824940 1011970 764070 1045530 1317690 1103260 FALSE TRUE 1006078.211 1105688.63 967428.0691 1012255.235 991833.7769 793464.2673 944134.6615 1035912.248 972833.8596 1.034172691 1.136564706 0.994443254 1.040522208 1.019530485 0.815621557 0.970499384 1.064839836 1 19.89183392 3.77120411 1.464023296 0.980148141 1.079331184 0.230548255 0.071798757 0.710652314 2.934311062 0.024670125 0.05964852 5904.785287 -3.77120411 0.099183043 IGSLGLGTGEDDDYVDDFNSTSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IGSLGLGTGEDDDYVDDFNSTSHR 24 0 O95684;O95684-2;A0A087WV25;O95684-3 O95684 FGFR1OP FGFR1 oncogene partner 0 ;; 269.85 2.43E-45 275894000 169435 162066 81507 138760 177215 162037 175451 205977 161105 FALSE TRUE 147043.7355 161001.3778 120924.0578 170267.5788 173688.7682 168270.6682 158435.789 161930.4215 142059.3504 1.035086638 1.133338828 0.851222095 1.198566503 1.22264932 1.184509627 1.11527885 1.139878656 1 17.11613427 3.685343804 24.99998707 1.146350958 1.019226768 0.333359346 0.09063278 379.3999922 178232.7229 0.024527354 0.036379972 4845.55808 -3.685343804 -0.12712419 IGSS(ph)LPQDDDAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IGSSLPQDDDAPK 13 0 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 IGS(0.035)S(0.965)LPQDDDAPK 63.473 0.072159 92298000 65981 64280 46621 57421 65171 66641 53882 72373 84393 TRUE FALSE 57261.44368 63857.74045 69167.07154 70459.31568 63874.2246 69204.72239 48656.53193 56896.59716 74416.15568 0.769475971 0.858116626 0.929463111 0.946828213 0.858338139 0.929969061 0.653843665 0.764573185 1 16.18332824 IGTEPSTAPAPS(ph)PPAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IGTEPSTAPAPSPPAPK 17 0 Q6NV74 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 IGTEPST(0.001)APAPS(0.999)PPAPK 212.72 1.38E-12 200930000 376100 334440 237400 270310 307500 242780 383020 436760 341780 TRUE FALSE 326397.4321 332243.0416 352207.4341 331688.0169 301381.3516 252119.9037 345874.7794 343362.2729 301375.1578 1.083026997 1.102423452 1.168667772 1.100581811 1.000020552 0.836564983 1.147655241 1.139318434 1 18.20120098 3.390833601 6.602384271 1.039168533 1.119365536 0.193102609 0.088174665 0.451816171 28.38293881 0.028233032 0.036559306 2459.425099 -3.390833601 0.080197003 IGTYTGPLQHGIVYSGGSSDTICDLLGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IGTYTGPLQHGIVYSGGSSDTICDLLGAK 29 0 P49902-2;P49902;Q5JUV6 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ; 224.44 1.36E-34 537990000 346140 375240 197016 303100 380690 280330 390140 567420 391990 FALSE TRUE 300396.722 372775.0237 292293.5966 371923.4876 373115.0138 291114.4765 352304.2828 446081.6487 345649.3888 0.86907928 1.078477312 0.845636087 1.076013729 1.079460939 0.842224769 1.019253308 1.290561081 1 18.39894985 1.979553698 23.32068429 1.162696694 0.971405944 0.285506519 0.115411844 329.5276065 375851.6886 0.048878402 0.028727119 95.40116932 -1.979553698 -0.19129075 IGVDHVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IGVDHVAR 8 0 Q7L5N1;E7EM64;H7C3T0 Q7L5N1 COPS6 COP9 signalosome complex subunit 6 0 159.04 0.00036148 386140000 211740 194020 139270 148810 179450 208690 197010 210540 212930 FALSE TRUE 183758.0225 192745.4698 206621.4378 182599.5849 175879.2961 216718.4393 177904.0005 165517.6594 187757.658 0.978697884 1.026565158 1.100468764 0.972528028 0.936735673 1.15424554 0.947519278 0.881549446 1 17.51851223 2.023501765 24.98348334 0.926980008 1.026907749 0.25009805 0.068665418 256.5638599 272738.2988 0.027199547 0.018336862 105.5605792 -2.023501765 0.099927741 IHAESLLLDS(ph)PAVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IHAESLLLDSPAVAK 15 0 Q9H4L5-5;Q9H4L5;Q9H4L5-6;Q9H4L5-2 Q9H4L5-5;Q9H4L5-6 OSBPL3 Oxysterol-binding protein-related protein 3 1 IHAESLLLDS(1)PAVAK 130.39 5.67E-05 0 61955 58290 40848 55953 57339 62628 67280 68350 87109 TRUE FALSE 53767.48978 57907.08915 60602.22943 68657.98384 56198.06608 65037.33969 60755.19596 53733.8844 76811.07325 0.699996596 0.753889859 0.788977772 0.893855286 0.731640162 0.846718278 0.790969236 0.699559089 1 16.22902669 4.443665633 2.287548404 0.809918719 0.700389791 0.187027614 0.083981652 0.676365398 6.145526031 0.02143502 0.115551346 27775.73967 -4.443665633 -0.109528928 IHAYSQLLESYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHAYSQLLESYR 12 0 Q15008;Q15008-4;Q15008-3;Q15008-2 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 234.79 4.97E-16 1538990000 744450 944910 514570 673400 834390 817150 756150 787210 974890 FALSE TRUE 646069.0463 938702.824 763417.7731 826305.7623 817787.2715 848586.2893 682818.6894 618871.2676 859639.6148 0.751558019 1.091972505 0.888067232 0.961223457 0.951314083 0.987141908 0.794308077 0.719919437 1 19.71337244 2.231965805 24.9926561 0.811636238 0.94483677 0.141277022 0.109808795 208.3905125 789737.8622 0.041222156 0.028517942 170.5948061 -2.231965805 0.133200532 IHCTQTLLEGDGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHCTQTLLEGDGPK 14 0 P29762 P29762 CRABP1 Cellular retinoic acid-binding protein 1 0 ; 166.09 3.86E-06 1163320000 1431900 1491640 626110 1105140 1538910 1262390 1740650 1969160 1744150 FALSE TRUE 1242670.787 1481841.319 928898.8902 1356078.928 1508288.702 1310954.96 1571842.031 1548070.458 1537958.574 0.808000169 0.963511855 0.603981737 0.881739568 0.980708276 0.852399396 1.02203145 1.006574874 1 20.55258521 2.865862042 1.03466181 1.007945626 0.808809011 0.380445168 0.100062631 0.541864157 1.295472544 0.058908674 0.053050356 734.2805789 -2.865862042 -0.199136615 IHDENLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IHDENLR 7 0 O95232;J3KPP4;D6RDI2 O95232 LUC7L3 Luc7-like protein 3 0 ;; 181.81 0.0006665 1697700000 952050 782440 572190 828510 600170 738120 631850 802060 1384960 FALSE TRUE 826234.1803 777300.1001 848902.9979 1016635.858 588227.7912 766515.954 570573.2843 630545.7106 1221231.607 0.676558137 0.636488686 0.695120396 0.832467693 0.481667677 0.627658136 0.467211364 0.516319515 1 20.2199054 3.233607334 24.99126642 0.594892225 0.703822408 0.065850413 0.15719215 296.4367998 1495638.667 0.046508077 0.054396625 1712.408337 -3.233607334 0.108930184 IHDPQLLTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IHDPQLLTER 10 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ;;;; 169.65 4.57E-06 2964430000 2458370 2313400 1321710 1630710 2165650 2336570 2159930 2401730 2297260 FALSE TRUE 2133490.176 2298203.123 1960893.377 2000987.629 2122557.802 2426459.36 1950460.321 1888138.73 2025680.54 1.05322144 1.134533841 0.968017088 0.987810067 1.047824551 1.197848976 0.962866692 0.932100937 1 20.94997524 2.049186634 24.99999694 0.957084315 1.061111311 0.325620313 0.067356743 122.7672558 62398.08998 0.028145316 0.018975564 111.9919054 -2.049186634 0.104026997 IHDVLCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IHDVLCK 7 0 P42704 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 81.784 0.044147 0 261970 279940 190230 280260 287280 271000 275150 329320 331810 FALSE TRUE 227350.0008 278101.0557 282225.8643 343897.3165 281563.6901 281425.5454 248465.9953 258897.4808 292583.7998 0.777042341 0.950500526 0.964598397 1.175380581 0.962335202 0.961863048 0.849213099 0.884866083 1 18.15849036 0.931747029 16.03520341 1.702661702 0.943471841 0.031236149 0.102734601 1577338.571 7718992.941 40069824.74 0.026124334 8.545687922 -0.931747029 -0.759189861 IHEDIFDIIDR ddPTM_MDA-MB-175_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 ;;;;;;; 207.88 2.15E-08 1625940000 1388249 1328756 895970 1074755 1275517 1327535 1273297 1493541 1390333 FALSE TRUE 1204788.377 1320027.314 1329264.089 1318794.549 1250136.707 1378606.13 1149812.853 1174158.88 1225969.417 0.982723028 1.076721243 1.084255505 1.0757157 1.019712801 1.124502872 0.937880535 0.957739128 1 20.22549156 2.22420093 24.99994492 0.962512238 1.061240855 0.549454077 0.040695895 161.8528287 281780.3979 0.015760519 0.010680696 167.5717983 -2.22420093 0.098728617 IHEGCEEPATHNALAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IHEGCEEPATHNALAK 16 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 291.46 8.88E-46 7962470000 9869910 7683940 5603740 6059390 7049880 6136020 8753760 9242280 8595130 FALSE TRUE 8565576.386 7633463.692 8313727.407 7435267.111 6909601.181 6372076.66 7904821.703 7265890.346 7579023.523 1.130168862 1.007183006 1.096939122 0.981032331 0.911674328 0.840751667 1.042986828 0.958684232 1 22.85358055 3.613800123 4.593012646 0.952735604 1.070469309 0.478177457 0.060612831 0.212818046 7.003352933 0.017086745 0.025788865 4109.605393 -3.613800123 0.117733704 IHFFLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHFFLSK 7 0 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;H0Y8X0;A0A494C198;D6RDA2;D6R9L5 H0Y993 DEK Protein DEK 0 ; 127.84 0.0038154 876570000 2152300 3141900 1753280 2284000 2836800 2451600 3066900 3371900 3457800 FALSE TRUE 1867868.102 3121260.652 2601172.072 2802617.109 2780353.23 2545914.638 2769472.51 2650845.425 3049022.823 0.612612043 1.023692125 0.853116629 0.919185349 0.911883378 0.834993631 0.908314785 0.869408194 1 21.53991552 4.753252187 24.86645832 0.906779808 0.612611821 0.716419845 0.059600926 1329.371706 2250008.825 0.013395675 0.296018151 56656.81896 -4.753252187 -0.294167988 IHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGR 39 0 Q99436;Q5TBG5;Q99436-2 Q99436 PSMB7 Proteasome subunit beta type-7;Proteasome subunit beta type 0 ; 232.47 2.88E-41 467979000 28349.8 32307.9 18550.7 31950.5 38445.2 22017.8 28265.2 34644.1 22602.9 FALSE TRUE 24603.3021 32095.66728 27521.88057 39205.34936 37680.21574 22864.83901 25524.04525 27235.72882 19930.81091 1.234435579 1.610354311 1.380871089 1.967072465 1.890551062 1.147210674 1.280632553 1.366513833 1 14.28271279 2.720915865 24.97845704 1.232519017 1.622675088 0.443513741 0.23125988 848.3155213 1200899.866 0.081831358 0.072324369 525.915372 -2.720915865 0.390156071 IHFPLATYAPVISAEK ddPTM_MDA-MB-175_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 ; 197.14 4.41E-11 11681400000 2221200 1760520 1173960 1545910 1641190 1463480 1835520 2048910 1890590 FALSE TRUE 1927662.792 1748955.028 1741690.983 1896932.493 1608533.53 1519781.023 1657511.553 1610766.541 1667086.604 1.15630633 1.049108681 1.044751352 1.137872795 0.964877005 0.911638915 0.994256417 0.966216474 1 20.66889762 3.224812658 24.99704647 0.966476528 1.089855532 0.707852972 0.041259882 128.1326372 232974.8832 0.012197949 0.013904359 1678.079987 -3.224812658 0.123379003 IHFVPGWDCHGLPIEIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IHFVPGWDCHGLPIEIK 17 0 Q9NSE4 Q9NSE4 IARS2 "Isoleucine--tRNA ligase, mitochondrial" 0 87.148 0.0026684 222830000 256480 266750 196290 314420 295870 257440 247560 331760 302110 FALSE TRUE 222585.5182 264997.7017 291216.5006 385813.8666 289982.7659 267343.8834 223551.6693 260815.7058 266394.9 0.83554722 0.994755161 1.09317596 1.448277976 1.088544735 1.003562318 0.839173983 0.979056678 1 18.02320694 2.616595666 3.838149726 0.941741233 1.106090905 0.163753596 0.156032306 0.431827127 11.20948139 0.059901216 0.052021315 413.6144148 -2.616595666 0.164349671 IHGS(ph)GHVEEPASPLAAYQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IHGSGHVEEPASPLAAYQK 19 0 Q12955;A0A087WY90;H0Y951;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;H0Y3A4;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 IHGS(0.542)GHVEEPAS(0.458)PLAAYQK 89.483 0.0039936 563380000 295490 374120 81313 269860 484600 419260 405310 458400 401870 TRUE FALSE 256440.2478 371662.3811 120636.2388 331135.8376 474957.4081 435389.2035 366003.0986 360374.7273 354361.3864 0.723668711 1.048823025 0.340432799 0.934458014 1.340319308 1.228658709 1.032852654 1.016969515 1 18.43486188 3.480307136 24.99033211 1.111433636 0.721873942 0.487462133 0.1960846 112.8651131 885327.937 0.055584952 0.073242657 3022.088206 -3.480307136 -0.389559694 IHGSGHVEEPAS(ph)PLAAYQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHGSGHVEEPASPLAAYQK 19 0 Q12955;A0A087WY90;H0Y951;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;H0Y3A4;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 IHGS(0.356)GHVEEPAS(0.644)PLAAYQK;IHGS(0.002)GHVEEPAS(0.998)PLAAYQK 114.02 0.00027693 1035730000 455150 594150 130616 444510 782990 622750 611530 779660 629660 TRUE FALSE 395000.7743 590246.9895 193782.3345 545442.7894 767410.0309 646707.5955 552223.9147 612935.7763 555222.3121 0.711428136 1.063082258 0.349017556 0.982386294 1.382167132 1.164772347 0.994599645 1.103946587 1 19.08270602 3.487218555 24.92628312 1.123524962 0.730422473 0.480975639 0.199263537 404.1187666 997610.8887 0.054117487 0.074459711 3070.566837 -3.487218555 -0.393102489 IHGTEEGQQILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHGTEEGQQILK 12 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5;F5H763;F5H0Z7;F5H3L6;F5H2F3;F5GZW1;F5H4Y4;F5H7R5;F5GWK2;F5H073;F5H1L0;F8W6T3;F5H068;F5GWA2 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 130.1 0.00022251 863880000 1790960 1877630 936960 1376440 1696040 1551030 1899690 2132890 1967840 FALSE TRUE 1554280.098 1865295.725 1390076.99 1688981.74 1662292.122 1610699.128 1715458.356 1676788.072 1735204.197 0.895733252 1.074971884 0.801102828 0.973361949 0.957980695 0.928247598 0.988620451 0.966334726 1 20.72667402 2.233886268 24.90102014 0.981251053 0.940982362 0.092157171 0.068064384 305.6743956 1628350.191 0.02538424 0.017762122 171.3508518 -2.233886268 -0.040268691 IHGVGFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHGVGFK 7 0 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2;B8ZZK4 H7C2W9 RPL31 60S ribosomal protein L31 0 ; 106.76 0.0076295 3189600000 5845000 5544000 4005800 4679400 5153200 4806700 5887200 6598400 7222500 FALSE TRUE 5072568.441 5507581.099 5943018.279 5741929.29 5050661.402 4991616.859 5316260.25 5187383.509 6368664.278 0.796488592 0.864793756 0.933165577 0.901590827 0.793048775 0.783777672 0.834752786 0.814516715 1 22.60255939 1.232678413 24.98995003 1.000000259 0.841146402 0.518813152 0.048338106 178.246724 757184.9933 0.112994214 0.012889474 17.08749551 -1.232678413 -0.158853857 IHIDLPNEQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IHIDLPNEQAR 11 0 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 191.53 1.79E-06 311350000 263990 251700 157550 213170 245980 257080 238150 265380 352740 FALSE TRUE 229103.0526 250046.5661 233741.707 261573.5066 241085.4793 266970.034 215054.2497 208630.5522 311039.479 0.736572262 0.803906202 0.751485656 0.840965614 0.775096075 0.85831559 0.691404996 0.670752642 1 18.24673818 4.755323742 21.59851689 0.784863508 0.736572007 0.023325521 0.093186944 2435.53365 3137719.338 0.022379612 0.480942787 56927.71367 -4.755323742 -0.048291501 IHIPEPDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IHIPEPDLR 9 0 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 0 99.802 0.0050904 129840000 111060 100970 57528 66704 94691 96829 86134 98647 88533 FALSE TRUE 96383.13961 100306.7214 85348.73322 81850.16271 92806.83436 100554.0743 77780.73794 77552.10672 78066.7296 1.234625046 1.28488438 1.09327922 1.048464091 1.18881417 1.288052859 0.996336574 0.99340791 1 16.25242021 -1.055139484 0.260632943 2.47E-12 1.245460405 0.424198438 0.089283376 51.01998711 1.285286884 24.90307944 0.299854952 0.088076595 1.055139484 1.245460405 IHIVMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHIVMK 6 0 B8ZZF8;Q9Y4Y9 B8ZZF8 LSM5 U6 snRNA-associated Sm-like protein LSm5 0 ; 87.758 0.052076 878410000 2924300 2560400 1548920 2119970 2390900 2165300 2666800 3098800 2951600 FALSE TRUE 2537846.346 2543580.564 2297982.893 2601341.59 2343325.768 2248600.492 2408174.146 2436145.735 2602665.21 0.975095197 0.977298407 0.882934495 0.999491437 0.900356203 0.863960713 0.925272347 0.936019633 1 21.31155831 4.305435377 24.99794987 0.929138039 0.976197563 0.162965374 0.043775939 100.0549021 37397.90094 0.010774724 0.028507283 20203.90776 -4.305435377 0.047059524 IHLAQSLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IHLAQSLHK 9 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 128.28 0.0002439 721460000 526690 622470 185850 384050 631140 584870 603360 670020 681210 FALSE TRUE 457086.582 618380.9536 275727.6816 471254.4223 618581.5488 607370.3274 544846.2401 526741.4371 600678.1298 0.760950931 1.029471397 0.459027336 0.78453734 1.029805345 1.011141071 0.907051902 0.876911296 1 19.19623261 3.335397814 6.718933863 0.951431861 0.753291772 0.340499917 0.142525271 0.271233775 16.06697721 0.041105719 0.053083317 2164.700481 -3.335397814 -0.198140088 IHLDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 IHLDEK 6 0 P37837 P37837 TALDO1 Transaldolase 0 ;;;;;;;; 166.13 0.0070625 15486680000 25089140 23481470 16621680 19265550 19804200 18295540 26046340 29550350 26259950 FALSE TRUE 21773546.58 23327218.68 24659980.04 23640087.58 19410135.17 18999381.26 23520369.96 23231237.61 23155528.63 0.940317405 1.007414646 1.064971586 1.020926275 0.838250574 0.820511661 1.015756122 1.003269586 1 24.46485336 6.505327501 13.60811631 0.969948254 0.516928321 0 0.080067516 0 0 0.019456947 0 3201308.3 -6.505327501 -0.453019933 IHLGSS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHLGSSPK 8 0 Q5JW53;Q9H410-4;Q9H410 Q5JW53 DSN1 Kinetochore-associated protein DSN1 homolog 1 IHLGS(0.002)S(0.998)PK;IHLGS(0.006)S(0.994)PK 133.75 0.00058354 860240000 1820870 1641620 949130 1213520 1759370 1323620 1765130 2213700 1819470 TRUE FALSE 1580237.416 1630836.09 1408132.443 1489068.263 1724361.979 1374540.518 1593947.964 1740317.482 1604374.329 0.98495556 1.016493508 0.877683229 0.928130198 1.074787815 0.856745519 0.993501289 1.084732815 1 20.61357936 1.99388652 24.96788825 1.045628254 0.956822046 0.224144367 0.065811761 343.1789032 1401567.493 0.026757437 0.017352051 98.60218072 -1.99388652 -0.088806209 IHLPETVEQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHLPETVEQLR 11 0 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8YEK3;O14936-6;O14936-2;A0A2U3TZN6;A0A2R8Y3B3;A0A2R8YEJ7;A0A2R8Y6F8;O14936-3;A0A2U3TZM4;A0A2R8YFN5;O14936-4 A0A2U3TZM1;A0A2R8Y6F8 CASK Peripheral plasma membrane protein CASK 0 ; 169.52 3.41E-05 97054000 270060 261237 157972 245635 258455 278557 207088 261660 282041 FALSE TRUE 234370.8868 259520.9169 234367.7876 301410.181 253312.2512 289273.268 187004.6376 205706.0452 248698.4343 0.942389876 1.043516489 0.942377415 1.211950457 1.018551853 1.16314873 0.751933313 0.827130439 1 17.9240379 2.236369731 24.99995956 0.848415334 1.053736395 0.43845341 0.103217056 49.29082732 562437.1503 0.039724707 0.028262012 172.3335091 -2.236369731 0.20532106 IHLPLNYPPGS(ph)PDLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IHLPLNYPPGSPDLGR 16 0 Q08174-2;Q08174 Q08174-2 PCDH1 Protocadherin-1 1 IHLPLNY(0.001)PPGS(0.999)PDLGR;IHLPLNY(0.001)PPGS(0.999)PDLGR;IHLPLNYPPGS(1)PDLGR 137.89 6.18E-06 517060000 409707 408895 237450 444460 483940 498750 276135 535380 408164 TRUE FALSE 355563.1819 406208.9418 352281.6142 545381.4361 474310.5408 517937.2352 249355.4702 420893.1533 359911.3169 0.987918871 1.128636202 0.978801159 1.515321721 1.317853923 1.439069045 0.692824756 1.169435729 1 18.45728194 1.234222209 23.12165812 0.9999994 1.151958042 0.039476901 0.2381718 218.6578705 1164921.526 0.437467924 0.058803354 17.14834486 -1.234222209 0.151958641 IHMS(ph)GPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IHMSGPK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 IHMS(1)GPK;IHMS(1)GPK;IHMS(1)GPK 111.46 0.0042351 474051000 1849950 1690590 1264610 1524820 1716490 1688170 1760300 2166770 2168160 TRUE FALSE 1605474.42 1679484.403 1876179.626 1871053.686 1682335.207 1753114.992 1589586.377 1703423.097 1911842.595 0.839752407 0.878463744 0.981346284 0.978665133 0.879954873 0.916976637 0.831442076 0.890985012 1 20.86653232 4.396533797 0.003261616 1.80674878 3.73E-06 0.026854213 0.058186949 889557.8218 1018.75895 279246.846 285104.4574 24919.18287 -4.396533797 -1.806745047 IHMVYSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHMVYSK 7 0 P08621;P08621-2;M0QYR1;P08621-3 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ; 80.462 0.029846 859240000 2613400 3045000 1572680 1875950 2543200 2659100 2753600 2990500 1972050 FALSE TRUE 2268032.568 3024997.195 2333233.308 2301913.12 2492595.296 2761397.298 2486556.296 2351004.847 1738916.496 1.304279173 1.739587382 1.341774211 1.323762887 1.433418627 1.587998794 1.429945775 1.351994103 1 20.72975722 1.174406144 2.068184301 0.800260828 1.457907401 0.540093615 0.130349563 0.680581753 2.490513068 0.908940686 0.034098123 14.94191095 -1.174406144 0.657646573 IHNADVTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHNADVTLR 9 0 Q9Y295 Q9Y295 DRG1 Developmentally-regulated GTP-binding protein 1 0 ; 125.48 0.0005004 363160000 268270 252170 167581 190942 254370 287650 218312 239380 259070 FALSE TRUE 232817.4398 250513.4787 248623.7321 234298.2995 249308.5347 298716.0816 197140.1358 188190.4499 228443.0397 1.019148756 1.096612438 1.08834015 1.025631158 1.091337845 1.307617347 0.862972827 0.823795945 1 17.80147496 2.192050725 24.9999836 0.879273058 1.099454167 0.541296297 0.090275319 86.94100269 46731.85057 0.036459255 0.02458092 155.6147377 -2.192050725 0.220181109 IHNAENIQPGEQKYEYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IHNAENIQPGEQKYEYK 17 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 137.45 4.16E-06 120990000 291950 225890 134500 134770 190940 152380 272260 303440 62537 FALSE TRUE 253368.0678 224406.1137 199544.6499 165371.5883 187140.6676 158242.1572 245856.2671 238551.7174 55143.9471 4.594666887 4.069460485 3.618613835 2.998907351 3.393675596 2.869619705 4.458445215 4.325981906 1 15.75091492 4.391589888 2.061503211 3.368827965 4.600145809 0.191020795 0.950171498 0.762564423 5.622079159 0.257398903 1.351970508 24637.11712 -4.391589888 1.231317844 IHNLALNCCTQLADLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IHNLALNCCTQLADLYR 17 0 P53992;G5EA31;P53992-2 P53992 SEC24C Protein transport protein Sec24C 0 200.75 1.21E-11 997140000 719200 626720 538920 452300 694520 618970 770800 802500 842310 FALSE TRUE 624155.8978 622603.0351 799543.5146 555001.628 680700.4108 642782.1764 696047.9346 630891.6201 742733.0714 0.840350217 0.838259476 1.076488372 0.74724238 0.916480546 0.865428242 0.937144125 0.84941905 1 19.50248429 1.227165357 24.87060638 1.000000268 0.885505658 0.15512074 0.085110172 913.5773726 1993779.625 0.290579967 0.019099404 16.87195299 -1.227165357 -0.11449461 IHPFFK ddPTM_MDA-MB-175_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 746710000 2390600 2599100 1712890 1940950 2480400 2685600 2550500 3208200 2875500 FALSE TRUE 2074676.153 2582026.341 2541249.333 2381672.363 2431044.893 2788916.77 2303152.903 2522151.396 2535561.666 0.818231393 1.0183252 1.002243159 0.939307608 0.958779637 1.099920703 0.908340323 0.994711125 1 21.27387393 4.744912713 24.73800958 0.987950709 0.818231305 0.528573387 0.051001057 497.3030159 1936667.827 0.01181775 0.107115997 55579.25399 -4.744912713 -0.169719405 IHPMAYQLQLQAASNFKS(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IHPMAYQLQLQAASNFKSPVK 21 1 P67870;Q5SRQ6 P67870 CSNK2B Casein kinase II subunit beta 1 IHPMAYQLQLQAASNFKS(1)PVK;IHPMAYQLQLQAASNFKS(1)PVK;IHPMAYQLQLQAASNFKS(1)PVK;IHPMAYQLQLQAASNFKS(1)PVK;IHPMAYQLQLQAASNFKS(1)PVK 347.76 1.71E-95 7795376000 6035600 4687728 2980320 3345195 4279852 2875159 4984219 6876300 3087067 TRUE FALSE 5237980.168 4656934.006 4421612.721 4104772.653 4194691.319 2985768.227 4500850.209 5405856.756 2722117.456 1.924230035 1.710776291 1.62432841 1.507933702 1.54096632 1.096855031 1.653437179 1.985901359 1 21.37629789 4.584419939 1.324036565 1.518873485 2.024843585 0.220246146 0.276251106 1.912804492 3.678872024 0.084480833 1.212945437 38407.84488 -4.584419939 0.5059701 IHPQTIIAGWR ddPTM_MDA-MB-175_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 2941700000 679340 670540 440940 484570 678680 694220 604180 635690 944000 FALSE TRUE 589563.4978 666135.1786 654180.0589 594599.0247 665175.5958 720927.0926 545586.7166 499752.6404 832401.3954 0.708268272 0.800257162 0.785894957 0.714317669 0.799104374 0.866081072 0.655437052 0.600374583 1 19.66691986 2.222363906 24.99882447 0.716340861 0.778242966 0 0.113184606 760.1890158 1173305.412 0.045510163 0.030786863 166.8644825 -2.222363906 0.061902105 IHPTSVISGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHPTSVISGYR 11 0 P17987;E7ERF2;F5H136;F5H676 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 181.4 6.24E-06 3809400000 928180 855440 319040 650460 1038550 1048930 833550 925550 1003350 FALSE TRUE 805518.6613 849820.5583 473328.8111 798156.8847 1017884.887 1089283.016 752712.4493 727628.3351 884735.106 0.910463093 0.960536722 0.534994947 0.902142211 1.150496776 1.231196782 0.850777192 0.822425074 1 19.75488604 3.479509918 24.98013822 0.990034177 0.801304846 0.251458549 0.163191626 153.4265114 1604513.145 0.050927859 0.066911527 3016.54576 -3.479509918 -0.188729331 IHPVSTMVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHPVSTMVK 9 0 A0A5F9ZHM4;P07195;A0A3B3IS95 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 ; 96.034 0.0057965 1272010000 624370 845110 643800 793450 802520 749510 987920 1010420 1618170 FALSE TRUE 541857.9225 839558.4168 955143.8334 973614.9496 786551.4221 778344.1347 892111.6705 794349.5461 1426871.786 0.379752356 0.58839093 0.669397098 0.682342281 0.551241835 0.545489891 0.625222027 0.556707024 1 20.44442427 1.236507044 24.99965839 1.000000533 0.58141829 0.71672261 0.083914369 30.02453631 365416.2647 0.129432843 0.020299401 17.23880051 -1.236507044 -0.418582243 IHQESELHSYLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IHQESELHSYLSR 13 0 Q9UNE7;Q9UNE7-2;H3BTA3;H3BS86;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ;; 245.4 2.43E-17 1476590000 570174 550465 280198 451633 520010 636272 515214 595713 598447 FALSE TRUE 494824.0613 546848.9592 415702.69 554183.1754 509662.8184 660749.7956 465248.6256 468324.4108 527699.2774 0.937700851 1.036289005 0.787764372 1.050187482 0.965820573 1.25213322 0.881654847 0.887483517 1 19.00935648 5.067957861 13.91312659 0.975149951 0.607563301 0.009631127 0.12397715 2083089.119 11002685.63 0.030091448 21464315.19 116938.5923 -5.067957861 -0.36758665 IHQETFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IHQETFGK 8 0 Q15393;Q15393-2;J3QL37 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ;; 124.23 0.0013137 1118880000 2353390 1999600 1296520 1489860 1871450 1730100 1972040 2365620 2161860 FALSE TRUE 2042383.549 1986464.496 1923521.409 1828155.484 1834211.806 1796658.067 1780791.864 1859750.572 1906287.374 1.071393315 1.042059305 1.009040628 0.959013583 0.962190608 0.942490671 0.934167581 0.97558773 1 20.86233419 4.122863102 1.66070207 0.960362454 1.069429859 0.823493759 0.018308209 0.173582643 0.887738427 0.005667567 0.020913401 13269.76105 -4.122863102 0.109067405 IHQMEENQHSTSEELQATLQELADLQQITQELNSENER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IHQMEENQHSTSEELQATLQELADLQQITQELNSENER 38 0 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1;C9J8U1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 0 76.976 0.0013234 17234000 2875.5 1739.7 940.84 1910.9 3854.7 1978.8 2298.9 3377.6 2658.7 FALSE TRUE 2495.495389 1728.271796 1395.833371 2344.799051 3777.999012 2054.925716 2075.953032 2655.326525 2344.391515 1.064453345 0.737194187 0.595392605 1.000173835 1.611505155 0.876528388 0.885497588 1.132629302 1 11.19499781 3.490022379 24.98920648 1.098477624 0.793656712 0.26116411 0.232022718 829.6095772 1606934.838 0.065388098 0.091956888 3090.45468 -3.490022379 -0.304820912 IHRAS(ph)DPGLPAEEPK ddPTM_MDA-MB-175_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 120.3 8.71E-05 2336000000 3739790 2929340 2969200 2886310 3314660 3362610 4291760 4511780 4129170 TRUE FALSE 3245567.276 2910096.973 4405115.051 3541690.8 3248704.751 3491971.783 3875545.776 3546970.958 3641024.227 0.891388542 0.799252296 1.209856012 0.972718274 0.892250243 0.959063045 1.064410873 0.974168458 1 21.79591291 IHSEIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IHSEIVK 7 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;; 117.93 0.0051196 863610000 1968850 1626990 1463510 1322380 1371200 1562370 1579560 1674720 1710160 FALSE TRUE 1708661.484 1616302.196 2171268.331 1622646.59 1343915.803 1622475.385 1426374.514 1316594.161 1507986.833 1.133074538 1.071827791 1.439845683 1.076034986 0.891198632 1.075921453 0.945879953 0.873080674 1 20.5241924 3.479973866 15.10829132 0.95467051 1.210164204 0.54235685 0.108193641 0.530048611 2796.91165 0.030419534 0.040707255 3019.77 -3.479973866 0.255493694 IHSEVVEDTEAVSAVQQLLDDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IHSEVVEDTEAVSAVQQLLDDER 23 0 Q96GA7;H0YID3 Q96GA7 SDSL Serine dehydratase-like 0 ;; 225.3 1.18E-32 521220000 453356 409561 264920 328327 383310 430252 390723 472476 435118 FALSE TRUE 393443.8559 406870.5668 393036.1981 402878.6635 375682.8809 446804.0729 352830.7436 371440.6842 383678.8457 1.025451 1.06044566 1.024388502 1.050041377 0.979159745 1.164526212 0.919599158 0.968103111 1 18.5495397 2.188898339 24.99999914 0.961930355 1.046640931 0.402726307 0.050416527 105.3419295 53028.32113 0.019090044 0.012870529 154.4892765 -2.188898339 0.084710576 IHSQEEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IHSQEEALR 9 0 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;;; 231.38 5.56E-08 1907330000 921890 1088190 715201 803880 870420 1020070 848892 880470 1750660 FALSE TRUE 800059.9007 1081041.608 1061074.596 986413.2405 853100.3449 1059312.753 766566.5845 692188.3423 1543698.969 0.518274558 0.700293017 0.687358492 0.638993262 0.552633876 0.68621718 0.496577765 0.448395935 1 20.55796001 1.226088931 24.99761218 1.000000952 0.58966215 0.684087438 0.0873234 392.5083753 786674.8654 0.405756513 0.023565683 16.83018658 -1.226088931 -0.410338802 IHTADKPYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IHTADKPYK 9 1 A0A0G2JMG9;Q6ZN08 A0A0G2JMG9 ZNF66 Putative zinc finger protein 66 0 118.18 0.00061987 288520000 686960 515710 389780 506340 491220 318040 612710 713480 620690 FALSE TRUE 596176.4955 512322.2671 578278.9117 621312.2359 481445.6831 330275.2046 553289.4785 560907.8543 547312.7353 1.089279414 0.936068602 1.056578578 1.13520515 0.879653719 0.603448784 1.010920161 1.024839764 1 19.0620059 3.222810399 24.99811788 0.911925769 1.046003044 0.250843978 0.128466763 422.2218109 670132.0491 0.042476279 0.048323505 1670.361222 -3.222810399 0.134077274 IHTDFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IHTDFEK 7 0 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 ;;;;; 166.78 0.0011106 2852260000 6406820 5157510 3408570 4227790 4752650 3989540 5633630 6321120 5633960 FALSE TRUE 5560142.504 5123629.977 5056965.853 5187774.337 4658081.563 4143020.185 5087281.43 4969397.679 4967919.667 1.119209423 1.031343162 1.01792424 1.044254876 0.937632223 0.833954746 1.024026508 1.000297511 1 22.24421041 4.766642733 0.858907803 0.969937276 1.198323022 0.409838765 0.056974342 2.794044827 1.566061239 0.022151259 0.613217054 58430.92115 -4.766642733 0.228385745 IHTEPQLSAALEYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHTEPQLSAALEYVR 15 0 P47897;A0A1B0GVU9;A0A0U1RQT0;A0A0U1RQE9;A0A0U1RQL2;A0A0U1RRI9;A0A0U1RQM8;A0A0U1RQU2 P47897 QARS Glutamine--tRNA ligase 0 ; 204.52 4.86E-09 458190000 564270 611610 454450 548510 598150 631690 563970 620670 859580 FALSE TRUE 489700.2898 607592.2936 674223.54 673057.579 586247.9853 655991.5231 509276.2762 487944.5506 757961.4316 0.646075472 0.801613734 0.889522226 0.887983941 0.773453583 0.865468209 0.671902626 0.643759076 1 19.53176491 2.247771441 24.99364069 0.741027835 0.815678401 3.40E-05 0.117951044 518.8508812 1407908.121 0.044312992 0.033832972 176.9177635 -2.247771441 0.074650565 IHVFYIDYGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHVFYIDYGNR 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 163.66 2.37E-05 5657200000 2392600 2534900 1529110 1909600 2142200 2156500 2375500 2663700 2314900 FALSE TRUE 2076411.848 2518248.075 2268592.711 2343203.866 2099574.411 2239461.95 2145124.376 2094088.484 2041235.159 1.017233041 1.233688369 1.111382341 1.147934306 1.028580368 1.097111198 1.050895271 1.025892815 1 20.96101097 2.353085598 0.637709633 0.992824679 1.135618805 0.331432809 0.058624462 1.20636909 0.992603235 0.114060384 0.042101366 225.4683558 -2.353085598 0.142794126 IHVSDQELQSANASVDDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IHVSDQELQSANASVDDSR 19 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;; 228.01 1.14E-19 1088000000 518450 536530 219241 359056 585420 586830 462120 580880 782950 FALSE TRUE 449935.5189 533005.4991 325266.6809 440585.1526 573771.2874 609405.7298 417303.6735 456663.3324 690390.5429 0.651711591 0.772034763 0.471134323 0.638168001 0.831082194 0.8826971 0.604445814 0.661456529 1 19.39705318 3.262692572 19.69965099 0.769102303 0.631592606 0.262993017 0.131096775 35.94945697 29343.9978 0.039005906 0.050273065 1831.017824 -3.262692572 -0.137509697 IHVSDQELQSANASVDDSRLEELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHVSDQELQSANASVDDSRLEELK 24 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 178.11 2.46E-17 517100000 755790 679300 160219 337550 781410 579210 780560 945130 258808 FALSE TRUE 655910.4366 674837.6336 237701.4443 414195.8866 765861.4698 601492.5835 704861.4113 743021.3045 228212.0131 2.874127561 2.957064462 1.041581646 1.814960926 3.355920924 2.6356745 3.088625361 3.255837826 1 17.80001521 3.253506075 24.99547957 2.770819263 2.147275051 0.071505407 0.839954899 555.243719 928610.2118 0.244050888 0.313780016 1792.693627 -3.253506075 -0.623544212 IHVYGYSMAYGPAQHAISTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IHVYGYSMAYGPAQHAISTEK 21 0 Q9NRX4 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 240.21 4.15E-30 583220000 163290 124390 51249 104140 117630 97252 125410 158780 145490 FALSE TRUE 141710.8128 123572.8739 76033.18782 127786.5787 115289.3931 100993.3474 113247.7575 124826.1326 128290.3379 1.104610176 0.96322822 0.592664959 0.996073288 0.898659985 0.787224892 0.882745804 0.972997146 1 16.96905299 1.67235581 3.946586923 0.993028773 0.881091087 0.081950351 0.134301522 0.431107448 15.62592115 0.096176295 0.035221343 47.02792423 -1.67235581 -0.111937686 IHWWENVYGFDMSCIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHWWENVYGFDMSCIK 16 0 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;H0YDE4 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ; 241.93 6.32E-20 481393000 968300 862050 592090 695620 803470 705970 986200 1085800 1073150 FALSE TRUE 840336.7016 856387.1368 878426.7044 853571.1529 787482.519 733129.1227 890558.4758 853610.1197 946283.4295 0.888039117 0.905000669 0.928291331 0.902024833 0.832184623 0.774745811 0.941111773 0.902066012 1 19.85191284 1.050681216 1.483583755 1.097658149 0.878703394 0.379819168 0.047596988 2.23575261 3.02133561 0.836302023 0.014562932 11.23779787 -1.050681216 -0.218954755 IHYFDPQYFEFEFEA ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHYFDPQYFEFEFEA 15 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ; 87.363 0.01675 172763000 262250 258090 160205 193800 236890 229350 252690 272660 245120 FALSE TRUE 227592.998 256394.5898 237680.6739 237805.252 232176.3525 238173.2429 228184.1627 214353.7808 216142.1928 1.052978112 1.186231094 1.099649591 1.100225962 1.074183386 1.101928503 1.055713184 0.991725762 1 17.7216212 1.973465626 1.725299845 0.988853463 1.107139055 0.619368002 0.034252931 0.232854922 1.280652304 0.028999719 0.010198051 94.07313696 -1.973465626 0.118285591 IHYLDTTTLIEPAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IHYLDTTTLIEPAPR 15 0 P46109 P46109 CRKL Crk-like protein 0 79.652 0.019309 375220000 197600 187240 108320 134260 181580 215740 212120 206000 186050 FALSE TRUE 171486.6593 186010.0081 160703.9143 164745.785 177966.9133 224039.6574 191548.635 161948.5031 164055.3809 1.045297377 1.133824487 0.979571126 1.00420836 1.084797781 1.365634313 1.167585202 0.987157521 1 17.32382339 3.001062405 24.97765835 1.123935257 1.043194096 0.127426777 0.109634701 93.55028894 2199295.712 0.037012193 0.041654196 1002.449272 -3.001062405 -0.080741161 IHYLDTTTLIEPVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IHYLDTTTLIEPVSR 15 0 P46108-2;P46108;I3L297 P46108-2 CRK Adapter molecule crk 0 ; 124.81 9.43E-05 1711700000 570790 567240 321670 418320 487790 524940 462140 568610 542000 FALSE TRUE 495358.6553 563513.7631 477230.6879 513305.9496 478083.9333 545134.7815 417321.7339 447017.1764 477925.3774 1.036476987 1.179083157 0.998546448 1.07402949 1.000331759 1.140627402 0.873194339 0.935328395 1 18.86642585 2.235889535 24.99999999 0.933373862 1.069967118 0.503750984 0.063290994 53.61785741 501825.6454 0.02379243 0.016870626 172.1430667 -2.235889535 0.136593257 IIAEGANGPTTPEADKIFLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IIAEGANGPTTPEADKIFLER 21 1 P00367;P00367-2;P00367-3;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 ;;; 239.57 5.70E-30 1611460000 874550 864796 621486 989120 1014070 916860 874620 1180840 793617 FALSE TRUE 758976.0017 859115.0981 922038.7083 1213714.814 993891.991 952132.1975 789799.487 928326.5553 699796.5024 1.084566726 1.227664178 1.31758119 1.734382509 1.420258586 1.36058439 1.128613082 1.326566441 1 19.41657593 0.484416978 0.968733981 9.67E-15 1.355281062 0.242336662 0.178327068 12.20351343 3.088953378 24.74533949 0.063694189 3.050822762 -0.484416978 1.355281062 IIALDGDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IIALDGDTK 9 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 152.89 0.00018472 348100000 1341770 1324580 877620 912410 1101770 886400 1196540 1263770 1629260 FALSE TRUE 1164451.695 1315878.747 1302039.967 1119586.636 1079846.933 920500.3816 1080499.735 993522.6202 1436650.739 0.810532208 0.915935036 0.906302369 0.779303282 0.751641929 0.640726627 0.752096321 0.691554734 1 20.45427794 3.620093584 4.267150184 0.751428939 0.880969297 0.20752881 0.0969674 0.304814333 9.180921922 0.026596005 0.040431555 4169.592223 -3.620093584 0.129540358 IIALPHDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IIALPHDNR 9 0 A0A3B3IT47;Q9Y2I8;Q9Y2I8-2 A0A3B3IT47 WDR37 WD repeat-containing protein 37 0 93.649 0.0092562 181500000 160060 168510 111990 141890 174810 180280 147690 190690 230610 FALSE TRUE 138907.6655 167403.0467 166148.7386 174108.2932 171331.623 187215.4883 133367.0465 149912.4275 203347.5485 0.683104697 0.823236119 0.817067822 0.856210436 0.842555636 0.920667545 0.655857656 0.737222694 1 17.63358807 4.739623141 22.77214739 0.819431204 0.68310458 0.190462857 0.093259463 49.82844002 1067370.826 0.023129544 0.136573652 54906.42172 -4.739623141 -0.136326624 IIANALSSEPACLAEIEEDKAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IIANALSSEPACLAEIEEDKAR 22 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 138.66 1.04E-06 276950000 244100 235494 139332 164035 243769 213459 280230 343280 272615 FALSE TRUE 211841.5665 233947.0244 206713.4212 201281.6539 238918.4738 221670.9059 253053.3377 269872.2434 240386.7653 0.881253035 0.973210918 0.859920142 0.837324191 0.993891962 0.922142721 1.05269247 1.122658492 1 17.87499794 2.228162895 3.59091387 1.075709241 0.910148222 0.609197923 0.055396078 0.138762222 3.831676424 0.023763659 0.016077247 169.1075102 -2.228162895 -0.165561018 IIAPPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 IIAPPER 7 0 P60709;P63267-2;Q562R1;A0A2R8YFE2;P63261;P68133;P68032;P63267;P62736;A6NL76 P60709;P63261;P68133 ACTB;ACTG2;ACTBL2;ACTG1;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Beta-actin-like protein 2;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 ;;;;;;;; 145.88 0.0052498 15552370000 5815520 5408920 4105750 5097960 5564530 5929040 5037980 5769030 7317440 FALSE TRUE 5046984.297 5373388.448 6091304.433 6255529.735 5453806.74 6157134.005 4549397.475 4535367.829 6452380.579 0.782189494 0.832776118 0.944039856 0.969491749 0.84523947 0.954242226 0.705072712 0.702898376 1 22.6214001 2.241137262 24.99313101 0.777807967 0.889794721 0.122968655 0.100296231 104.2798549 1011515.918 0.038819497 0.028658233 174.2357472 -2.241137262 0.111986754 IIAPPERK ddPTM_MDA-MB-175_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 ;;;;; 114.28 0.0043074 37874110000 21364200 17087100 11382330 13277020 16539610 14557610 20410020 22305170 10632140 FALSE TRUE 18540866.84 16974853.72 16886862.86 16291770.32 16210504.12 15117650.68 18430659.4 17535382.97 9375220.521 1.977645944 1.810608473 1.801223003 1.737747958 1.729079768 1.612511476 1.965890761 1.870396855 1 23.16042119 1.23602429 24.99998456 0.999998932 1.811278624 0.846157617 0.108960445 26.76542027 263764.4614 0.182348937 0.027612505 17.21964881 -1.23602429 0.811279693 IIAPS(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IIAPSPVK 8 0 Q9HCS5 Q9HCS5 EPB41L4A Band 4.1-like protein 4A 1 IIAPS(1)PVK;IIAPS(1)PVK;IIAPS(1)PVK;IIAPS(1)PVK 112.75 0.0049201 432223000 1093210 1205780 823452 1247970 1515800 1247270 962050 1877550 1536000 TRUE FALSE 948739.5287 1197859.152 1221676.141 1531340.663 1485638.546 1295253.284 868750.5391 1476050.544 1354415.83 0.700478766 0.884410183 0.901994878 1.130628149 1.096885102 0.956318773 0.64142084 1.089806034 1 20.36923931 4.667351751 1.772436184 0.977037536 0.636909788 0.292527322 0.136762649 1.056958488 3.770481492 0.038263548 0.576704321 46489.16558 -4.667351751 -0.340127748 IIAPSRGS(ph)PLPVLSWANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IIAPSRGSPLPVLSWANR 18 1 I3L413;C9J2U0;P24864-2;P24864-3;P24864;I3L1Q9 I3L413 CCNE1 G1/S-specific cyclin-E1 1 IIAPS(0.04)RGS(0.96)PLPVLSWANR 85.932 0.0021448 143170000 98961 102420 52798 48926 79809 75746 98142 105980 46779 TRUE FALSE 85883.05311 101747.1963 78331.2894 60035.39609 78220.95704 78659.99763 88624.20395 83317.00174 41248.83991 2.082071964 2.466668069 1.898993755 1.455444474 1.896318956 1.906962664 2.148525974 2.019862908 1 15.33206592 1.237307567 24.96536257 0.999998798 1.984422478 0.601271784 0.251917168 23.68066767 471607.6656 0.396029177 0.065734725 17.27060563 -1.237307567 0.98442368 IIDDSEITKEDDALWPPPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IIDDSEITKEDDALWPPPDR 20 1 P61326;Q96A72;F5H6N1;F5H6P7;F5H3U9 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ;;;;; 197 1.55E-21 1474830000 1877530 1398270 1056814 1223486 1373750 1155330 1627610 1998360 1546180 FALSE TRUE 1629409.653 1389084.672 1567892.785 1501297.196 1346415.063 1199776.293 1469764.633 1571026.265 1363392.362 1.19511426 1.0188444 1.149993816 1.101148311 0.987547753 0.879993409 1.078020293 1.152292113 1 20.37876938 4.747592951 24.24493668 1.053748884 1.195114373 0.241759497 0.081982712 1349.656497 3622677.361 0.021528237 0.249535186 55923.32066 -4.747592951 0.141365489 IIDKNGIHDLDNISFPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IIDKNGIHDLDNISFPK 17 1 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 ; 160.25 1.87E-09 1119780000 3724300 2860900 1352810 1553000 2642800 2176420 3687500 4369500 540840 FALSE TRUE 3232124.319 2842106.56 2007033.441 1905632.386 2590213.451 2260148.286 3329886.818 3435116.428 476902.5113 6.77732711 5.959512672 4.2084774 3.995853116 5.431326925 4.739224961 6.982321834 7.202974081 1 18.86333485 4.461649692 7.712383437 5.114989392 6.581483327 0.112213009 1.736359485 0.333965277 110.8193027 0.439972754 1.238691725 28950.0749 -4.461649692 1.466493936 IIDKPR ddPTM_MDA-MB-175_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 97.071 0.037838 301340000 609220 449880 276300 363440 391030 437000 502290 568750 526380 FALSE TRUE 528710.0334 446924.7087 409919.6042 445964.6068 383249.268 453811.6728 453577.9931 447127.2385 464151.9561 1.139088237 0.962884467 0.883158196 0.960815959 0.825697841 0.977722203 0.977218747 0.963320811 1 18.82423767 4.728720519 4.39178357 0.941841234 1.15151751 0.590727434 0.051342834 0.136995191 6.454772555 0.012674449 0.088127864 53545.1968 -4.728720519 0.209676276 IIDSLFNTVTDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IIDSLFNTVTDKK 13 1 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ; 133.66 0.00016775 755050000 979700 828480 509120 788980 862170 750100 808130 1143830 679470 FALSE TRUE 850230.1628 823037.6603 755332.1349 968129.9678 845014.5038 778956.8324 729757.677 899230.8558 599143.8307 1.419075219 1.373689619 1.260685826 1.61585569 1.410370032 1.300116587 1.21800082 1.500859743 1 19.19254285 1.227829409 24.9955442 0.999999186 1.385467785 0.528009955 0.115076206 384.2750992 895007.8314 0.397594082 0.027826964 16.89777057 -1.227829409 0.3854686 IIECTHCGCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IIECTHCGCR 10 0 P41223;C9JCD9 P41223 BUD31 Protein BUD31 homolog 0 ;;;; 174.98 2.94E-06 1131700000 1234270 1201780 686569 863023 1127936 1150110 1030983 1235840 981617 FALSE TRUE 1071158.092 1193885.428 1018596.065 1058985.563 1105492.28 1194355.476 930998.4273 971565.2333 865571.3565 1.237515641 1.3793033 1.176790402 1.223452642 1.277182143 1.379846349 1.075588304 1.122455389 1 19.72329323 2.219022294 24.98325663 1.078171865 1.27631817 0.674217703 0.069609632 146.2465995 187001.1058 0.028162994 0.019017664 165.5854961 -2.219022294 0.198146305 IIEEDDAYDFSTDYV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IIEEDDAYDFSTDYV 15 0 Q9BVP2-2;Q9BVP2 Q9BVP2-2 GNL3 Guanine nucleotide-binding protein-like 3 0 ;; 187.97 7.41E-07 36373000 157378 140041 90112 101241 128414 141962 128959 141966 132551 FALSE TRUE 136580.0986 139121.0615 133690.4646 124229.3164 125858.8126 147423.37 116452.576 111607.6757 116880.9718 1.168540067 1.190279815 1.143817189 1.062870325 1.076811826 1.26131198 0.996334769 0.954883194 1 16.83468055 2.10497283 8.192999092 0.974749489 1.144516338 0.660296831 0.056403142 0.14395744 10.11368991 0.023493254 0.015812969 127.342341 -2.10497283 0.169766849 IIEGLQDLDDDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IIEGLQDLDDDVR 13 0 A0A0A0MTH9;O14981 A0A0A0MTH9 BTAF1 TATA-binding protein-associated factor 172 0 ;;; 173.11 5.17E-05 135229000 263358 240154 163960 205646 265305 245469 271652 288932 279852 FALSE TRUE 228554.573 238576.4126 243251.6044 252341.0674 260025.9496 254912.3513 245307.2309 227146.1403 246768.2154 0.926191295 0.966803655 0.985749336 1.022583346 1.053725453 1.03300318 0.994079527 0.920483782 1 17.91279706 6.379156252 12.14685056 0.98783479 0.568801084 0 0.042893862 0 0 0.010734092 0 2394176.988 -6.379156252 -0.419033706 IIELKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IIELKR 6 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 92.191 0.075421 267090000 758190 660180 294560 388180 606900 558200 694140 772890 261480 FALSE TRUE 657993.2705 655843.2341 437010.2012 476322.202 594823.8774 579674.3152 626822.4096 607613.4881 230568.1323 2.853791042 2.844466092 1.895362542 2.065863124 2.579818258 2.514112898 2.718599502 2.635288243 1 17.8148336 4.271240095 23.41152273 2.287608973 2.849131454 0.206779076 0.506000983 171.757803 123041.7778 0.125431852 0.331778943 18674.11782 -4.271240095 0.56152248 IIENELEGFGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IIENELEGFGIR 12 0 Q9Y295 Q9Y295 DRG1 Developmentally-regulated GTP-binding protein 1 0 96.103 0.013197 25079000 25552 22160 14100 15481 21248 20783 23654 20757 22587 FALSE TRUE 22175.23846 22014.4295 20918.80716 18996.19766 20825.20637 21582.53546 21360.03872 16318.27708 19916.79059 1.113394166 1.105320127 1.050310142 0.953778048 1.04561055 1.083635205 1.07246389 0.819322622 1 14.28169757 -1.999999991 0.170356918 0.151095455 1.154434004 0.294088054 0.073556905 143.9144067 1.967346183 35.74132409 0.84290961 0.01 1.999999991 1.003338549 IIEPNEVTHSGDTGVETDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IIEPNEVTHSGDTGVETDGR 20 0 Q9NQW7-4;Q9NQW7-3 Q9NQW7-4 XPNPEP1 Xaa-Pro aminopeptidase 1 0 223.93 6.13E-25 200650000 112670 126120 70047 93825 110000 118930 118630 141800 120110 FALSE TRUE 97780.37403 125291.5094 103921.9635 115129.4003 107811.2152 123505.3141 107125.2809 111477.1735 105910.7326 0.923233856 1.182991622 0.981222213 1.087041865 1.017944193 1.16612652 1.01146766 1.052557854 1 16.69248927 4.796562754 22.74038489 1.059343324 0.923230647 0.29417347 0.06760614 35674.47812 13984998.94 0.01486503 27.09888838 62598.33093 -4.796562754 -0.136112677 IIEVVDAIMTTAQSHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IIEVVDAIMTTAQSHQR 17 0 Q01813;Q01813-2;Q5VSR5 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ; 196.64 1.58E-11 638850000 273390 253720 167191 205467 253840 259870 237680 312010 279280 FALSE TRUE 237260.8188 252053.2966 248045.1268 252121.4227 248789.0806 269867.3671 214629.8302 245289.0896 246263.8366 0.963441576 1.023509177 1.00723326 1.023785815 1.010254222 1.095846515 0.871544248 0.996041859 1 17.90984526 2.246442416 24.9999994 0.960719587 1.019863353 0.294178032 0.047117192 229.830079 728991.9281 0.01710866 0.01300378 176.3771885 -2.246442416 0.059143766 IIFDDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IIFDDFR 7 0 P46977;P46977-2 P46977 STT3A Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A 0 ; 107.66 0.017281 228880000 785380 800790 587820 894580 1087900 1098690 628280 1219550 1113620 FALSE TRUE 681590.0431 795529.5578 872091.7181 1097708.062 1066252.918 1140957.315 567349.5023 958758.723 981969.1122 0.694105379 0.810137048 0.88810504 1.117864145 1.085831423 1.16190754 0.577767157 0.976363422 1 19.90531812 4.310055894 2.328602816 0.971846781 0.711134043 0.270743828 0.15998291 0.4757931 4.876208495 0.044628806 0.175003679 20420.00735 -4.310055894 -0.260712738 IIFEDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 IIFEDDR 7 0 P49773;D6REP8;D6RE99;D6RD60;D6RC06 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ;;;;;;;;; 179.16 0.0016406 32133360000 37106310 36225920 24441340 28482080 33046520 34301980 32183860 35387810 38842390 FALSE TRUE 32202617.12 35987949.55 36261253.78 34949371.59 32388958.91 35621599.37 29062674.21 27820402.22 34250486.9 0.940209031 1.050728115 1.058707687 1.020405102 0.94564959 1.040031912 0.84853317 0.81226297 1 25.02962116 2.236650493 24.99938502 0.869776016 1.011031135 0.45499819 0.062169703 38.23199809 500359.3397 0.024213913 0.017266066 172.4449547 -2.236650493 0.141255119 IIFSEHLPLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IIFSEHLPLSK 11 0 Q9Y2L1;G3V1J5;Q9Y2L1-2;F2Z2C0 Q9Y2L1 DIS3 Exosome complex exonuclease RRP44 0 67.153 0.060752 174880000 310180 285180 117100 229880 307600 265180 295240 328780 342960 FALSE TRUE 269188.9271 283306.6338 173729.9517 282077.7675 301479.3618 275381.6462 266607.6702 258472.9556 302415.6595 0.890128929 0.93681205 0.57447406 0.932748549 0.996903938 0.910606437 0.881593469 0.85469435 1 18.20617332 IIGEDS(ph)PSRLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IIGEDSPSRLDR 12 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 IIGEDS(0.995)PS(0.005)RLDR;IIGEDS(0.999)PS(0.001)RLDR 139.6 3.57E-05 806410000 1129040 962290 598730 648850 839640 854970 1071220 1153800 549140 TRUE FALSE 979834.5034 955968.6536 888277.8306 796181.3096 822932.8067 887861.2491 967333.2493 907068.8489 484221.2948 2.023526255 1.974239183 1.834446027 1.64425092 1.699497349 1.833585715 1.997709022 1.873252702 1 18.885307 1.237914449 24.99824623 0.999999016 1.857312031 0.832110753 0.121404228 6.836535125 264276.72 0.188899608 0.032599619 17.29475641 -1.237914449 0.857313015 IIGNLLYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IIGNLLYYR 9 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 170.73 0.00013375 1139460000 264900 622490 332810 349000 559330 536580 498090 518550 519320 FALSE TRUE 229892.7938 618400.8222 493758.0292 428245.7841 548200.4273 557222.5798 449785.3085 407662.1179 457926.5812 0.502029808 1.350436615 1.078247146 0.935184376 1.197136069 1.21683825 0.982221445 0.890234668 1 18.80475679 2.011113133 24.36457171 0.936962238 1.06665337 0.029955423 0.226688643 451.0533141 988890.1659 0.087005247 0.058594165 102.5919142 -2.011113133 0.129691132 IIGS(ph)PETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IIGSPETK 8 0 E9PMS6;H0YDG6 E9PMS6 LMO7 1 IIGS(0.991)PET(0.009)K;IIGS(0.992)PET(0.008)K;IIGS(0.996)PET(0.004)K 115.82 0.002507 661730000 1417400 1618450 1258020 1418300 1788140 1492590 2091580 2449400 2193940 TRUE FALSE 1230086.999 1607818.295 1866402.68 1740346.692 1752559.512 1550010.903 1888738.894 1925614.871 1934574.913 0.63584356 0.831096426 0.964761131 0.899601603 0.905914525 0.80121524 0.97630693 0.99536847 1 20.88358516 4.655164832 2.35575023 0.935494755 0.592776229 0.722996261 0.058852287 0.267662891 2.045764026 0.016690492 0.173839768 45202.74738 -4.655164832 -0.342718526 IIGVDINKDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IIGVDINKDK 10 1 P11766;H0YAG8 P11766 ADH5 Alcohol dehydrogenase class-3 0 65.879 0.074098 0 944470 642180 419920 490330 566160 405400 836130 1009300 264560 FALSE TRUE 819655.8965 637961.4773 622994.7165 601666.9207 554894.5237 420996.0003 755042.2413 793469.0494 233284.0182 3.513553577 2.734698597 2.670541777 2.579117616 2.37862211 1.804649987 3.236579373 3.401300507 1 17.83172795 5.11038885 1.391789082 2.537479203 4.916011706 0.188908757 0.681022929 6.208831762 5.444384728 0.193613403 26.54301807 128940.3517 -5.11038885 2.378532503 IIGVHQEDELLECLS(ph)PATSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IIGVHQEDELLECLSPATSR 20 0 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 1 IIGVHQEDELLECLS(1)PATSR;IIGVHQEDELLECLS(1)PATSR;IIGVHQEDELLECLS(1)PATSR;IIGVHQEDELLECLS(1)PATSR 258.48 1.90E-36 538171000 439009 481249 302362 314057 424846 436163 421614 474772 496699 TRUE FALSE 380992.8483 478087.6436 448585.2745 385368.4419 416392.3958 452942.4728 380725.9392 373245.7025 437979.8101 0.869886784 1.091574617 1.024214505 0.879877184 0.950711394 1.034162905 0.869277374 0.852198421 1 18.74050484 2.224366551 24.99057388 0.894130166 0.977166363 0.139022452 0.077323066 378.2023471 665871.3723 0.031198548 0.021145615 167.6357151 -2.224366551 0.083036197 IIGVHQEDELLECLSPATSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IIGVHQEDELLECLSPATSR 20 0 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 221.86 7.55E-25 209900000 221373 172249 105172 113207 158780 158185 131286 162496 162694 FALSE TRUE 192117.9972 171117.485 156033.531 138912.3796 155620.5886 164270.4793 118553.9039 127747.4949 143460.5007 1.339169989 1.192784663 1.08764106 0.96829705 1.084762621 1.145057201 0.826387078 0.890471554 1 17.13029405 7.999999985 0.321248434 0.904430712 5.165761908 0.667529583 0.085847449 48.43421689 0.762258619 0.150687993 119.5063843 99999996.61 -7.999999985 4.261331196 IIHDFPQFYPLGIVQHD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IIHDFPQFYPLGIVQHD 17 0 P35244;B5MC59 P35244 RPA3 Replication protein A 14 kDa subunit 0 ; 185.02 6.02E-10 1555860000 2451770 1864020 1770720 1490900 1680210 1576430 2435550 2645720 1966490 FALSE TRUE 2127762.383 1851775.13 2627046.115 1829431.632 1646777.108 1637076.282 2199350.736 2079953.367 1734013.792 1.227073505 1.067912573 1.515008777 1.055027151 0.949690894 0.94409646 1.268358271 1.199502205 1 20.72568394 IIIEELSLVAAS(ph)PTLSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IIIEELSLVAASPTLSPR 18 0 Q16513-3;Q16513-2;Q16513;Q16513-4;B1AL79;H0Y5V5 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 IIIEELSLVAAS(0.899)PT(0.1)LSPR;IIIEELSLVAAS(0.986)PT(0.014)LSPR;IIIEELSLVAAS(0.985)PT(0.015)LSPR;IIIEELSLVAAS(0.998)PT(0.002)LSPR;IIIEELSLVAAS(0.997)PT(0.003)LSPR 277.44 4.07E-39 515829000 563127 579447 361249 444064 577324 671407 547655 646597 609047 TRUE FALSE 488708.3402 575640.5745 535950.2247 544895.5183 565836.3819 697236.4617 494543.5024 508327.2634 537046.1575 0.909993179 1.071864246 0.997959332 1.014615803 1.053608473 1.298280328 0.920858469 0.946524347 1 19.03468656 IIILYDDDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IIILYDDDER 10 0 Q9BYV8-5;Q9BYV8-2;Q9BYV8 Q9BYV8-5 CEP41 Centrosomal protein of 41 kDa 0 ; 154.84 3.20E-05 98023000 152548 157138 108727 120658 168742 189964 166301 170251 176252 FALSE TRUE 132388.3953 156105.7501 161307.7409 148055.243 165384.3643 197272.038 150173.1546 133844.1485 155415.6893 0.851834174 1.004440097 1.037911562 0.952640262 1.064142012 1.269318682 0.966267661 0.861201009 1 17.24577263 4.736727339 5.229845883 1.012791473 0.845106299 0.201255308 0.104351384 0.305960937 29.06694491 0.028297087 0.184973426 54541.53283 -4.736727339 -0.167685173 IIKPCNHVLSLSFPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IIKPCNHVLSLSFPIR 16 1 P00367;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 ; 164.65 4.39E-09 590170000 698560 734110 474260 983120 920360 835010 685070 969430 1297370 FALSE TRUE 606243.5261 729287.5831 703613.7223 1206352.422 902046.6367 867133.375 618632.0168 762124.9386 1143996.397 0.529934821 0.637491154 0.615048897 1.054507187 0.788504788 0.757986107 0.540763956 0.666195227 1 20.12565108 3.964615457 24.99792553 0.773713576 0.594351964 0.287598793 0.149945549 887.1162959 626717.4086 0.041992564 0.07277411 9217.549034 -3.964615457 -0.179361612 S(ph)KDAS(ph)PINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKDASPINR 9 1 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(1)KDAS(1)PINR 71.344 0.015825 0 435840 314790 296520 346170 332950 298240 407210 483110 888820 TRUE FALSE 378242.6397 312722.1238 439918.0638 424773.1894 326324.9464 309713.4858 367718.8369 379800.6861 783744.7121 0.482609495 0.399010187 0.561302752 0.541979018 0.416366377 0.395171388 0.469181905 0.484597446 1 19.58002428 1.237313066 5.852064723 1.021827038 0.467015382 0.902524 0.054895152 0.041756776 5.110751837 0.09281676 0.014200041 17.27082431 -1.237313066 -0.554811656 IILDLISES(ph)PIKGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IILDLISESPIKGR 14 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 IILDLISES(1)PIKGR;IILDLIS(0.005)ES(0.995)PIKGR 203.06 9.43E-09 1100090000 1056320 857270 478540 705580 918520 763550 1096720 1260040 667720 TRUE FALSE 916724.6356 851638.5369 709963.5446 865792.7231 900243.2491 792924.2626 990360.2632 990590.2516 588782.9023 1.556982433 1.446438974 1.205815491 1.470478711 1.528990135 1.346717541 1.682046573 1.68243719 1 19.16737625 3.50025677 24.47742014 1.490723834 1.395870341 0 0.211083328 2297.562429 2430819.507 0.058262707 0.085715576 3164.14786 -3.50025677 -0.094853494 IILHNTMESLLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IILHNTMESLLER 13 0 O15498 O15498 YKT6 Synaptobrevin homolog YKT6 0 ; 246.53 3.43E-17 860540000 711250 786510 366640 496960 751310 784140 720380 829850 767140 FALSE TRUE 617256.5104 781343.364 543948.3303 609802.3636 736360.4009 814306.3732 650517.6585 652393.0354 676449.5831 0.91249448 1.155065187 0.804122501 0.901474964 1.088566568 1.203794626 0.96166466 0.964437043 1 19.36762289 IILLAEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IILLAEGR 8 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 101.64 0.012212 554110000 1181500 1132830 734420 1008960 1096960 1119430 1375020 1467740 1448340 FALSE TRUE 1025361.781 1125388.365 1089587.968 1238059.789 1075132.642 1162495.196 1241670.772 1153875.223 1277118.895 0.802871045 0.881193105 0.853160949 0.969416233 0.841842248 0.910248216 0.972243678 0.90349867 1 20.28446141 8 0.177731295 0.991361875 0.274507742 0.501461456 0.044274082 107.8738126 1.507707443 0.405926022 20.165913 100000000 -8 -0.716854133 IILLFDAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IILLFDAHK 9 0 A0A024R571;Q9H4M9;C9JC03;C9J2Z4;C9JDQ8;Q9NZN3;Q9H223 A0A024R571;Q9NZN3;Q9H223 EHD1;EHD3;EHD4 EH domain-containing protein 1;EH domain-containing protein 3;EH domain-containing protein 4 0 ; 133.13 0.0002855 294010000 500540 591360 521830 647700 595090 531340 697420 805560 1220540 FALSE TRUE 434392.3708 587475.3172 774188.7334 794770.1845 583248.8733 551780.9936 629784.3157 633297.2629 1076249.152 0.403616923 0.545854384 0.719339692 0.738463007 0.541927371 0.5126889 0.585165911 0.588429976 1 20.03758067 1.238477902 8.518676678 1.003861517 0.584899754 0.653873576 0.096093115 0.058820516 47.22427296 0.141851642 0.024707838 17.31720914 -1.238477902 -0.418961763 IILLFDAHKLDISDEFSEVIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IILLFDAHKLDISDEFSEVIK 21 1 A0A024R571;Q9H4M9;C9JC03;C9J2Z4;C9JDQ8;Q9NZN3 A0A024R571;Q9NZN3 EHD1;EHD3 EH domain-containing protein 1;EH domain-containing protein 3 0 163.91 1.00E-11 49022000 121620 84584 42655 50100 75159 56834 105550 132030 16289 FALSE TRUE 105547.6089 84028.36213 63283.10067 61475.97073 73663.48295 59020.44076 95313.77725 103796.412 14363.33298 7.348406462 5.850199412 4.40587855 4.280063049 5.128578657 4.109104819 6.635909465 7.226485115 1 13.81010294 4.610475578 3.100695093 4.998862798 7.428228145 0.192791303 1.679376357 0.551904708 8.587087458 0.426922386 2.717505743 40782.66275 -4.610475578 2.429365347 IILTARPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IILTARPFR 9 1 Q14697;F5H6X6;Q14697-2;E9PKU7;E9PNH1 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 144.5 9.07E-05 167480000 240970 228820 127466 121255 230940 274360 211800 220795 62163 FALSE TRUE 209125.204 227316.8664 189108.9839 148787.801 226344.7458 284914.8067 191259.6686 173579.7075 54814.16096 3.815167473 4.147046354 3.450002347 2.714404424 4.129311511 5.197832125 3.489238278 3.1666946 1 15.74226103 4.176573405 6.874931765 3.376938031 3.979026006 0.062726352 1.058596288 0.685578828 60.40473907 0.282491072 0.602161953 15016.66199 -4.176573405 0.602087975 IILWDHDLNPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IILWDHDLNPER 12 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 ;;; 225.97 1.64E-11 947991000 636254 653214 467594 499643 638096 656172 560662 685918 848580 FALSE TRUE 552171.4218 648922.9942 693724.0224 613094.5797 625399.138 681415.3614 506289.0855 539239.7735 748261.8391 0.737938771 0.86724053 0.927113994 0.819358342 0.83580253 0.910664323 0.676620214 0.720656521 1 19.51318367 2.261042996 24.99994784 0.777648351 0.85199411 0.041083162 0.098063796 515.6426934 573382.8851 0.036244442 0.028053453 182.4076283 -2.261042996 0.074345759 IINDLLQSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IINDLLQSLR 10 0 A0A087WTP3;Q92945 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ; 167.67 1.20E-05 439940000 378790 396990 249300 267440 341290 373370 354790 402270 354740 FALSE TRUE 328731.9418 394382.1466 369862.3139 328166.3396 334498.9967 387733.7855 320382.5204 316247.691 312803.0413 1.0509231 1.26080023 1.182412781 1.049114926 1.069359797 1.239546086 1.024230836 1.0110122 1 18.25489501 2.10440334 8.836492764 1.009737916 1.141600874 0.417726871 0.072703359 0.253851045 19.46178056 0.029810707 0.020078303 127.1754666 -2.10440334 0.131862958 IINEPTAAAIAYGLDKK ddPTM_MDA-MB-175_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 ; 193.8 1.76E-10 2276700000 3915500 2799200 2128300 2603700 2626500 2087120 3746100 4634200 2169290 FALSE TRUE 3398056.754 2780811.871 3157552.999 3194909.88 2574237.789 2167412.857 3382803.799 3643212.393 1912839.007 1.776446811 1.453761587 1.6507155 1.670245048 1.345768138 1.133086919 1.768472823 1.904610048 1 20.86728402 3.285546574 24.99954522 1.500155674 1.625570355 0.091777228 0.278730926 491.7185853 261622.3589 0.085732151 0.110679414 1929.952293 -3.285546574 0.125414681 IINEPTAAAIAYGLDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IINEPTAAAIAYGLDKR 17 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 273.33 1.88E-35 4815000000 3057500 2375800 1814530 2203710 2638300 2644800 2463800 3124000 1501310 FALSE TRUE 2653443.628 2360193.213 2692042.777 2704096.037 2585802.992 2746547.167 2224861.055 2455956.911 1323826.842 2.004373642 1.782856442 2.033530891 2.042635752 1.953278865 2.074702733 1.680628451 1.855194979 1 20.336283 0.976983148 1.712978386 5.37E-14 1.952695263 0.846192195 0.124431141 0.749101688 1.134612355 3.042399609 0.033025762 9.483816634 -0.976983148 1.952695263 IINEPTAAAIAYGLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IINEPTAAAIAYGLDR 16 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;P17066 A0A0G2JIW1;P17066 HSPA1B;HSPA1A;HSPA6 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 6 0 ;;; 225.32 1.62E-14 663565000 290018 306634 176195 217220 247877 327568 287309 298196 291599 FALSE TRUE 251691.3865 304619.7011 261403.4913 266543.121 242944.7327 340169.7529 259445.8174 234429.106 257126.4984 0.978862109 1.184707539 1.016633808 1.036622529 0.94484518 1.322966536 1.009020148 0.911726747 1 17.97211877 2.004540062 24.99967124 0.952802694 1.082029522 0.186527768 0.10970146 181.070242 997051.5913 0.043261674 0.029039068 101.0508711 -2.004540062 0.129226828 IINLGPVHPGPLS(ph)PEPQPMGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IINLGPVHPGPLSPEPQPMGVR 22 0 Q86T03-2;Q86T03 Q86T03-2 TMEM55B "Type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase" 1 IINLGPVHPGPLS(1)PEPQPMGVR;IINLGPVHPGPLS(1)PEPQPMGVR;IINLGPVHPGPLS(1)PEPQPMGVR 214.11 5.89E-25 386450000 226280 263368 223695 368440 383230 505340 220094 429510 513820 TRUE FALSE 196376.5247 261637.9183 331874.6502 452099.9333 375604.4728 524780.7568 198749.3178 337662.629 453076.7849 0.433428794 0.577469266 0.732490962 0.99784396 0.829008427 1.158260088 0.438665861 0.745265792 1 18.78939605 4.292059459 2.390441193 0.835126776 0.453552553 0.371441576 0.190781096 0.36160821 3.955085425 0.052112236 0.193425577 19591.12875 -4.292059459 -0.381574223 IIPAIWFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IIPAIWFR 8 0 Q969X5;Q969X5-2 Q969X5 ERGIC1 Endoplasmic reticulum-Golgi intermediate compartment protein 1 0 ; 140.01 0.001527 294860000 259555 554630 350054 365273 571060 557120 406460 533400 617670 FALSE TRUE 225254.1491 550986.599 519341.2853 448213.8175 559697.0233 578552.7669 367041.5718 419336.5609 544649.7563 0.41357615 1.011634711 0.953532576 0.822939536 1.027627419 1.062247362 0.673903858 0.769919671 1 19.05496926 4.746902529 24.61348887 0.89898179 0.413575848 0.609144434 0.125687464 666.7492387 1967242.87 0.032893076 0.362077589 55834.48678 -4.746902529 -0.485405943 IIPELVGS(ph)PTQSTSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IIPELVGSPTQSTSSR 16 0 Q9NSI6-3;Q9NSI6-2;Q9NSI6;H7C409 Q9NSI6-3 BRWD1 Bromodomain and WD repeat-containing protein 1 1 IIPELVGS(0.776)PT(0.222)QSTSSR;IIPELVGS(0.984)PT(0.014)QS(0.001)T(0.001)S(0.001)S(0.001)R;IIPELVGS(0.996)PT(0.004)QSTSSR;IIPELVGS(0.838)PT(0.162)QSTSSR;IIPELVGS(0.986)PT(0.014)QSTSSR;IIPELVGS(0.682)PT(0.318)QSTSSR 289.1 1.84E-45 791868000 735246 695782 454068 478776 681903 759331 635016 746714 654783 TRUE FALSE 638081.3782 691211.3622 673656.8036 587489.4084 668334.4644 788542.9549 573432.2461 587035.022 577375.2997 1.105141454 1.197161296 1.166757227 1.017517391 1.157539065 1.365737252 0.993170727 1.016730405 1 19.13914986 IIPGFMCQGGDFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 230.61 3.01E-12 15415373000 685978 616900 307840.2 417229.9 595238 530022 493380 619692.4 615043 FALSE TRUE 595324.2693 612847.5433 456712.7504 511968.3258 583393.9284 550412.2893 445532.0835 487176.0027 542333.3172 1.097709195 1.130020089 0.842125564 0.944010463 1.075711025 1.014896691 0.821509705 0.898296282 1 19.04882028 4.25604648 24.99910758 0.939366878 1.113864782 0.460409239 0.077134388 227.7966636 325669.6861 0.020519624 0.054019907 18032.10717 -4.25604648 0.174497903 IIPTLEEGLQLPS(ph)PTATSQLPLESDAVECLNYQHYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 IIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYK 36 0 P61978;P61978-2 P61978 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 IIPTLEEGLQLPS(0.991)PT(0.009)ATSQLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.991)PT(0.009)ATSQLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.886)PT(0.111)AT(0.003)SQLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.977)PT(0.023)AT(0.001)SQLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.905)PT(0.084)AT(0.01)S(0.001)QLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.495)PT(0.495)AT(0.009)S(0.001)QLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.901)PT(0.088)AT(0.009)S(0.001)QLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.988)PT(0.011)AT(0.001)SQLPLESDAVECLNYQHYK 195.81 9.24E-30 6976163000 6118181 5158594 3604802 4806802 5603270 5109116 5923238 7378143 7104179 TRUE FALSE 5309647.879 5124706.856 5348096.305 5898259.861 5491775.89 5305666.999 5348803.29 5800384.536 6264331.052 0.84760014 0.818077272 0.853737815 0.941562605 0.876673957 0.846964657 0.853850674 0.925938378 1 22.57872903 1.420297771 2.376056481 1.009465567 0.86353899 0.663890531 0.032012612 0.262542543 2.243627256 0.069600159 0.009361012 26.32072032 -1.420297771 -0.145926577 IIPTLEEYQHYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IIPTLEEYQHYK 12 0 P61978-3;Q5T6W2 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ; 202.18 1.40E-07 1514880000 1174880 1047700 697890 782330 974250 857710 1095680 1325770 1172230 FALSE TRUE 1019616.631 1040817.59 1035391.938 959969.9837 954864.3311 890706.6587 989421.1222 1042264.403 1033650.305 0.98642319 1.006933955 1.001684935 0.928718329 0.92377889 0.861709859 0.957210691 1.008333667 1 19.97931676 3.752255987 23.95232813 0.94922472 0.99920603 0.260182897 0.040949689 774.2227337 1354059.311 0.012639716 0.021727251 5652.700655 -3.752255987 0.049981311 IIQLLDDYPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 115.78 0.002739 108380000 245030 191360 159170 186130 207170 181410 242760 256960 211170 FALSE TRUE 212648.6647 190102.9436 236145.1444 228393.6613 203047.7223 188388.9601 219217.1726 202011.1037 186205.7232 1.142009284 1.020929649 1.268194878 1.226566281 1.090448343 1.011724865 1.177284827 1.084881282 1 17.50653789 3.075465754 10.09965754 1.077904768 1.161438622 0.249104918 0.078975241 0.636322584 80.46800757 0.024605864 0.027913548 1189.777507 -3.075465754 0.083533854 IIQQVLQGLDYLHTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IIQQVLQGLDYLHTK 15 0 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3 H3BLV9 SRPK1 SRSF protein kinase 1 0 78.069 0.024011 26208000 22373 20493 20388 16976 19001 25777 18304 26885 33530 FALSE TRUE 19416.35136 20358.38013 30247.70499 20830.66026 18622.91727 26768.65787 16528.8809 21135.85197 29566.1216 0.656709447 0.68857121 1.023052851 0.704544903 0.629873526 0.905382797 0.559047992 0.714867248 1 14.85165739 1.235957361 24.90487666 1.000000369 0.73463899 0.27573719 0.134839758 93.57286883 894999.4073 0.213425259 0.032180739 17.2169953 -1.235957361 -0.265361379 DREEDEEDAYERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DREEDEEDAYERR 13 2 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 144.68 2.33E-05 232780000 284480 250320 139017 155526 242440 205699 259930 272870 116982 FALSE TRUE 246885.2472 248675.6314 206246.0862 190840.5554 237615.9183 213612.3736 234722.0286 214518.874 103152.5212 2.393400028 2.410756698 1.999428455 1.850081347 2.303539608 2.070840064 2.275485134 2.079628025 1 16.65441956 1.237357129 4.466958137 0.897696252 2.174602069 0.816217042 0.175542022 0.087842039 3.634854547 0.358171189 0.045550006 17.27257668 -1.237357129 1.276905817 IISLETYNLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IISLETYNLLR 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 0 160.36 6.41E-05 109120000 69486 60199 59152 52393 65734 74669 70091 73624 59220 FALSE TRUE 60303.24904 59803.54881 87758.10505 64289.63143 64426.02201 77541.56475 63293.58561 57880.08054 52219.07906 1.154812573 1.145243269 1.680575503 1.231152149 1.233764041 1.484927849 1.212077784 1.108408681 1 15.67228939 1.725999643 2.308624666 1.020071112 1.322260605 0.315737472 0.162009999 0.334149765 3.637948202 0.150984418 0.045308622 53.2107822 -1.725999643 0.302189493 IISNASCT(ph)TNCLAPLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IISNASCTTNCLAPLAK 17 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 IIS(0.001)NASCT(0.978)T(0.021)NCLAPLAK;IIS(0.003)NAS(0.001)CT(0.966)T(0.031)NCLAPLAK 179.46 1.91E-13 0 174293 223850 137003 169432 189901 143448 243180 248410 266550 TRUE FALSE 151259.7384 222379.5146 203258.109 207904.1252 186122.3416 148966.5374 219596.441 195289.4546 235038.7627 0.643552309 0.946139744 0.864785479 0.8845525 0.791879346 0.633795616 0.93429883 0.830881904 1 17.84253918 0.557460801 1.297401043 1.684292022 0.815315775 0.231307335 0.106086121 11.18225198 4.303247853 20.19131285 0.030522877 3.609614319 -0.557460801 -0.868976247 IISPGS(ph)STPSSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IISPGSSTPSSTR 13 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 IISPGS(0.5)S(0.459)T(0.041)PSSTR 190.37 4.69E-06 257220000 256970 219400 163480 214220 218770 230260 193100 228000 378470 TRUE FALSE 223010.7634 217958.747 242539.4748 262861.9251 214416.905 239118.2512 174373.1917 179243.9743 333727.7078 0.668241678 0.653103539 0.726758579 0.787653884 0.64249057 0.716507037 0.522501392 0.537096472 1 18.34831195 IISPGSST(ph)PSSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IISPGSSTPSSTR 13 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 IISPGS(0.033)S(0.164)T(0.802)PS(0.001)STR;IISPGS(0.094)S(0.125)T(0.781)PSSTR 195.71 1.65E-06 258630000 539440 497250 357810 473460 488520 504730 428410 476520 831960 TRUE FALSE 468151.6372 493983.532 530848.1128 580966.3294 478799.4078 524147.2897 386862.8641 374619.9063 733606.6366 0.638150766 0.673362954 0.723614109 0.791931671 0.652665044 0.714480027 0.527343736 0.510655013 1 19.48464716 IISPGSSTPSSTRS(ph)PPPGRDESYPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IISPGSSTPSSTRSPPPGRDESYPR 25 2 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 IISPGSSTPS(0.127)S(0.127)T(0.127)RS(0.62)PPPGRDESYPR;IISPGSSTPS(0.013)S(0.009)T(0.052)RS(0.926)PPPGRDESYPR 130.32 4.81E-05 827050000 350110 332900 117339 131926 289553 331661 334247 342760 38614 TRUE FALSE 303842.0764 330713.158 174084.5329 161881.8147 283791.4618 344420.2133 301831.7774 269463.4414 34049.09691 8.923645677 9.712831999 5.112750372 4.754364414 8.334772066 10.11539937 8.864604491 7.913967354 1 15.05532891 4.263126179 24.98333273 6.949068755 9.318241091 0.150324883 2.591390861 508.0229858 516653.3294 0.662645998 1.751435708 18328.46857 -4.263126179 2.369172336 IISSDRDLLAVVFYGTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IISSDRDLLAVVFYGTEK 18 1 P12956;B1AHC9 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;; 238.19 6.50E-24 2591290000 5414110 4462560 2902320 3539740 3897980 3422670 5018550 5978130 3128260 FALSE TRUE 4698621.646 4433245.15 4305891.66 4343492.069 3820417.824 3554342.33 4531851.793 4699753.421 2758440.667 1.703361505 1.607156247 1.560987594 1.574618632 1.384991844 1.288533182 1.642903488 1.703771801 1 21.39542152 4.106865789 1.104354297 1.45897594 1.702186005 0.192185925 0.196888631 1.561880634 3.02843418 0.068705146 0.350176631 12789.85997 -4.106865789 0.243210065 IISVT(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IISVTPVK 8 0 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 1 IISVT(1)PVK;IISVT(1)PVK;IISVT(1)PVK 157.75 0.004158 706040000 2246560 1859030 1484280 1754330 1802950 1504540 2015270 2437210 3403490 TRUE FALSE 1949671.404 1846817.91 2202082.773 2152677.44 1767074.822 1562420.627 1819829.426 1916031.608 3001133.289 0.649645056 0.615373504 0.733750407 0.717288182 0.588802513 0.520610208 0.60638074 0.638436025 1 21.51707596 1.238772098 7.74620464 1.005191367 0.632571528 0.782514383 0.060680216 0.048451618 23.10585897 0.094989044 0.01635881 17.32894399 -1.238772098 -0.372619839 IITDVIGNPEEERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IITDVIGNPEEERR 14 1 J3KMX2;B9EGA3;Q92925-3;Q92925-2;Q92925;J3QWB6 J3KMX2 SMARCD2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 0 ; 171.08 4.93E-06 233840000 443150 384060 215005 271600 372360 374090 349180 398740 284430 FALSE TRUE 384586.6047 381537.0846 318982.1371 333270.9311 364950.7645 388481.4844 315316.5773 313472.554 250805.0094 1.533408785 1.521249856 1.271833198 1.328804923 1.455117525 1.548938298 1.25721802 1.249865602 1 17.93620664 1.265502061 1.160601123 0.809772985 1.431313425 0.669121094 0.098004609 0.992718376 1.168242547 0.761542874 0.032946097 18.42901235 -1.265502061 0.62154044 IIVDELKQEVISTSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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" 0 152.71 4.75E-07 268660000 1084100 873140 534010 646790 773150 656690 1125200 1443800 608450 FALSE TRUE 940833.4382 867404.2858 792259.0222 793653.5551 757765.8276 681953.2892 1016078.277 1135054.606 536519.7341 1.753585895 1.616723916 1.476663339 1.479262559 1.412372704 1.271068417 1.893832067 2.115587803 1 19.03327171 2.223963417 24.99993946 1.772012093 1.500638739 0.028254829 0.31053189 472.4619646 809157.147 0.125876278 0.085277012 167.4801791 -2.223963417 -0.271373354 IIVEKPFGR ddPTM_MDA-MB-175_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 25386000000 23288600 18481300 16816700 17408300 17585200 18600700 18533500 18646400 23469800 FALSE TRUE 20210952.5 18359895.12 24949312.37 21361120.58 17235288.92 19316280.97 16736124.02 14659012.47 20695226.98 0.976599702 0.887156016 1.205558769 1.032176192 0.832814684 0.933368887 0.808694876 0.70832818 1 24.30279474 3.238875596 24.99277293 0.838342558 1.028370516 0.365182169 0.109040425 8.526054735 676484.0875 0.033114656 0.040129017 1733.307419 -3.238875596 0.190027959 IIWELIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IIWELIK 7 0 O75874;C9J4N6;C9JLU6;C9JJE5 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 123.96 0.009755 600810000 1545330 1189550 861600 1072090 1172710 1016650 1317510 1503400 1378390 FALSE TRUE 1341110.725 1181735.768 1278272.642 1315524.42 1149375.365 1055761.183 1189738.083 1181909.609 1215438.304 1.103396791 0.97227129 1.051696855 1.082345698 0.945646818 0.868625894 0.978855182 0.972414318 1 20.21304523 3.227770971 24.99991036 0.953228539 1.046650004 0.515467857 0.047702236 185.8359905 430586.2011 0.014637057 0.016756308 1689.549699 -3.227770971 0.093421465 IIWQFIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IIWQFIK 7 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 129.16 0.0085786 110026000 251830 342770 214494 304490 323570 342340 282940 340570 310160 FALSE TRUE 218550.0274 340518.3213 318224.0158 373629.1083 317131.5901 355510.0413 255500.5223 267741.7558 273493.2381 0.79910578 1.245070348 1.163553505 1.366136548 1.159559162 1.299886036 0.934211478 0.978970294 1 18.06114564 2.224867406 24.9973997 0.971173014 1.183375174 0.284489176 0.149690003 277.2766219 506173.4072 0.058795083 0.039874352 167.8291543 -2.224867406 0.21220216 IIYIVHDEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IIYIVHDEVK 10 0 P25788-2;P25788;G3V4X5 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;; 187.64 1.21E-06 2047220000 6690600 5685600 4450180 5330020 5487720 4365770 6213630 7336400 7912410 FALSE TRUE 5806420.258 5648250.919 6602301.933 6540282.505 5378525.109 4533723.997 5611033.119 5767567.952 6977013.904 0.832221397 0.809551335 0.94629336 0.937404253 0.77089213 0.649808652 0.80421699 0.826652782 1 22.73417828 IKAEYEGDGIPTVFVAVAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IKAEYEGDGIPTVFVAVAGR 20 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 172.83 5.27E-12 1627970000 3055970 2717100 1506380 1798110 2468470 2055950 2884320 3338700 1554000 FALSE TRUE 2652115.822 2699251.191 2234870.407 2206398.358 2419352.276 2135043.727 2604599.09 2624744.987 1370287.89 1.935444253 1.969842403 1.630949542 1.610171391 1.76557955 1.558098661 1.900767794 1.915469738 1 20.3860476 1.232728227 24.9983836 0.999998733 1.784936511 0.739458272 0.146584702 106.6101323 456897.6596 0.334235616 0.038282257 17.08945555 -1.232728227 0.784937778 IKDAFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IKDAFDR 7 1 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ; 86.011 0.018596 893140000 1102840 1062290 836030 1018660 988120 854950 1153520 1258420 2525200 FALSE TRUE 957096.8998 1055311.747 1240336.904 1249962.322 968458.3452 887840.4797 1041651.808 989316.676 2226673.733 0.429832573 0.473940897 0.557035764 0.561358543 0.434935002 0.398729489 0.467806214 0.444302486 1 21.08645875 1.236749388 24.99998106 1.000000661 0.471812025 0.910263958 0.052198651 14.15729411 195353.0316 0.086968021 0.013867426 17.24842274 -1.236749388 -0.528188637 IKDAFDRNPELQNLLLDDFFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKDAFDRNPELQNLLLDDFFK 21 2 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 167.16 7.01E-12 747070000 1086500 810870 613940 639710 678950 561280 1189900 1223700 469900 FALSE TRUE 942916.2722 805543.3416 910843.4375 784965.9329 665440.2233 582872.8048 1074503.681 962021.2778 414348.9573 2.275657403 1.944118182 2.198252032 1.894456156 1.605989859 1.406719613 2.593233704 2.321765895 1 18.66048677 3.720752841 19.60323475 1.882227548 2.119819908 0.092289288 0.452268578 169.4759337 186563.5146 0.131076364 0.195513612 5257.179921 -3.720752841 0.23759236 IKDCPWYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKDCPWYDR 9 1 O95639;C9K0K2;B7Z7B0;H7C016;O95639-3;O95639-2;H7C419 O95639 CPSF4 Cleavage and polyadenylation specificity factor subunit 4 0 76.143 0.033075 153140000 159630 137410 85531 91406 133090 120600 134690 159810 146560 FALSE TRUE 138534.491 136507.3447 126894.0777 112161.1294 130441.7694 125239.56 121627.7845 125635.8751 129233.8438 1.071967582 1.056281704 0.981895098 0.867892853 1.009346821 0.969092587 0.94114499 0.972159239 1 16.97962441 4.213048103 4.078630604 0.960085435 1.067244115 0.551679265 0.038349974 0.142266236 5.180398228 0.009662085 0.024128583 16332.32838 -4.213048103 0.10715868 IKDHIQNGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKDHIQNGK 9 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 113.22 0.0011031 274140000 922600 755430 608480 698410 737160 579860 1003000 1145300 992130 FALSE TRUE 800676.0724 750467.5306 902742.9632 856994.665 722491.9582 602167.5894 905729.2144 900386.5077 874841.5216 0.915224132 0.857832547 1.031893138 0.979599898 0.825854672 0.688316197 1.035306615 1.029199558 1 19.73866217 IKDIAWTEDSKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IKDIAWTEDSKR 12 2 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ; 164.81 3.17E-05 2561900000 4214100 3032100 2012810 2255800 3001500 2202350 3787800 3907800 1959820 FALSE TRUE 3657196.008 3012181.935 2986211.648 2768013.868 2941776.022 2287075.83 3420459.739 3072147.381 1728132.312 2.116270833 1.743027379 1.727999429 1.601737233 1.702286336 1.323437918 1.979281167 1.777726948 1 20.72078225 7.99999991 0.781885219 1.601740758 114.5993872 0.29372253 0.264195871 657.7053238 2.474386905 0.093788099 131388.8409 99999979.36 -7.99999991 112.9976465 IKDMDLWEQQEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IKDMDLWEQQEEER 14 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 232.26 2.14E-13 2208920000 1941930 1778104 1210625 1445100 1812661 1542223 1896899 2313509 1857034 FALSE TRUE 1685299.03 1766423.518 1796087.299 1773232.042 1776592.593 1601553.317 1712938.027 1818783.104 1637497.556 1.029191784 1.078733529 1.096848843 1.082891413 1.08494366 0.978049287 1.046070585 1.110708897 1 20.64306132 IKDPDASKPEDWDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 IKDPDASKPEDWDER 15 2 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;;;;;; 130.29 3.41E-05 27589820000 24075120 17210110 18589990 19741900 17228370 15574990 23101110 23989660 20194880 FALSE TRUE 20893531.89 17097055.65 27580171.34 24224600.13 16885559.14 16174169.94 20860767.91 18859657.9 17807464.29 1.173301912 0.960106132 1.548798352 1.360362134 0.948229286 0.908280352 1.17146201 1.059087222 1 24.08597876 3.235528056 24.99996071 1.028718394 1.259757868 0.358561782 0.161258273 98.50135997 812029.4537 0.050378069 0.059603273 1719.998453 -3.235528056 0.231039474 IKDQYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKDQYK 6 1 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 0 79.597 0.060858 606350000 1683500 1260200 996710 1052900 980880 975430 1544000 1616500 1599500 FALSE TRUE 1461021.21 1251921.663 1478722.29 1291977.038 961362.4071 1012955.423 1394263.118 1270824.055 1410408.932 1.035884825 0.887630271 1.048435143 0.916030102 0.681619625 0.718199807 0.988552388 0.901032336 1 20.42768209 3.47959518 24.99752996 0.859975981 0.980662201 0.236214848 0.10854255 163.7807146 1654918.524 0.033121389 0.043521435 3017.138039 -3.47959518 0.12068622 IKDWVSFMSSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKDWVSFMSSFR 12 1 Q5SXH7-4;Q5SXH7-3;Q5SXH7-2;Q5SXH7-1;Q5SXH7;A0A494C040 Q5SXH7-4 PLEKHS1 Pleckstrin homology domain-containing family S member 1 0 128.95 0.00022151 82635000 135490 164260 97788 130630 169590 164150 175680 174100 176370 FALSE TRUE 117584.6532 163180.9652 145078.6039 160291.5381 166215.4908 170464.9567 158642.5806 136870.0698 155519.7395 0.756075425 1.049262079 0.932862956 1.030682912 1.068774236 1.096098523 1.020080031 0.880081656 1 17.24673818 4.74521829 24.81097173 1.002883438 0.7560753 0.610549664 0.063457445 556.1209612 2072421.399 0.017299101 0.161438119 55618.3742 -4.74521829 -0.246808138 IKEDEDDKTVLDLAVVLFETATLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKEDEDDKTVLDLAVVLFETATLR 24 2 P14625;H0YIV0 P14625 HSP90B1 Endoplasmin 0 105.16 0.0016428 122820000 177260 121120 136020 141280 106220 83733 172630 171310 123350 FALSE TRUE 153834.6419 120324.3547 201799.727 173359.7833 104106.4298 86954.26269 155888.3692 134676.6896 108767.7035 1.414341178 1.106250761 1.855327643 1.593853485 0.95714469 0.799449284 1.433222952 1.238204773 1 16.73089071 3.243818769 24.99963643 1.11644303 1.490778433 0.396832928 0.247615384 156.1459031 742383.8864 0.076279805 0.095528821 1753.148759 -3.243818769 0.374335403 IKEEVLS(ph)ESEAENQQAGAAALAPEIVIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKEEVLSESEAENQQAGAAALAPEIVIK 28 1 Q9UJX5;Q9UJX5-3 Q9UJX5 ANAPC4 Anaphase-promoting complex subunit 4 1 IKEEVLS(0.5)ES(0.5)EAENQQAGAAALAPEIVIK 65.375 0.0088613 331080000 122320 76276 79640 83817 95416 73981 119640 158160 109000 TRUE FALSE 106155.1021 75774.93793 118154.1704 102848.9309 93517.40828 76827.09694 108037.3312 124338.7148 96114.14417 1.104469098 0.788384879 1.229310955 1.070070714 0.972982791 0.799331853 1.124052367 1.293656786 1 16.55246113 2.014505491 24.98112906 1.180119129 0.994907663 0.168045611 0.148815342 312.4193547 538041.6643 0.059355016 0.039999645 103.3964173 -2.014505491 -0.185211466 IKEGSVIDHIHLISVGDMIEAINGQSLLGCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IKEGSVIDHIHLISVGDMIEAINGQSLLGCR 31 1 O14908;O14908-2;K7ESN1;K7EIT0 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 ; 214.78 5.93E-35 826230000 986300 951700 418500 637700 803710 760100 1108900 1298500 377930 FALSE TRUE 855957.956 945448.22 620887.9998 782499.5316 787717.7434 789341.5389 1001359.049 1020825.88 333251.5459 2.568504082 2.837040763 1.863121139 2.348074724 2.363733201 2.368605783 3.004814414 3.06322924 1 18.34625204 IKETVDQVEELRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKETVDQVEELRR 13 2 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 123.02 0.0001284 171560000 151250 136250 68858 90680 135560 122570 151410 167130 71446 FALSE TRUE 131261.9293 135354.9648 102157.9591 111270.28 132862.6212 127285.3472 136726.2815 131390.5501 62999.73527 2.083531442 2.148500533 1.62156172 1.766202342 2.108939357 2.020410827 2.170267556 2.085573051 1 15.94305815 1.235656368 24.99985465 0.999998651 2.002010548 0.763605687 0.174965838 42.14884439 362750.2969 0.311735382 0.04582019 17.20506697 -1.235656368 1.002011897 IKFPLPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IKFPLPHR 8 1 Q02543;M0R3D6;M0R1A7;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 101.99 0.0030352 3346000000 7996100 8339500 5528300 6478300 8271100 8026000 9063600 9841400 9414800 FALSE TRUE 6939395.125 8284717.275 8201804.371 7949297.03 8106521.292 8334765.414 8184613.467 7736893.196 8301793.069 0.835891122 0.99794312 0.987955771 0.95753977 0.976478361 1.003971714 0.985885025 0.931954474 1 22.98499154 4.743799999 24.96749653 0.976870127 0.835891062 0.810467744 0.021880867 251.6084984 1198965.069 0.005612524 0.046308659 55437.0356 -4.743799999 -0.140979065 IKGEHPGLSIGDVAK ddPTM_MDA-MB-175_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 ; 160.48 1.03E-06 8877200000 26508000 20523300 13176400 16489000 18482900 14253200 24503000 28726000 20496400 FALSE TRUE 23004900.64 20388481.09 19548551.11 20233079.47 18115126.45 14801529.83 22126702.83 22583168.45 18073338.94 1.272863897 1.128097091 1.081623665 1.119498701 1.002312108 0.818970411 1.224273108 1.249529405 1 24.10735972 4.76281895 2.226723182 1.085048169 1.328875703 0.209607586 0.12136177 1.3391263 7.28682115 0.034590718 0.659359254 57918.71926 -4.76281895 0.243827534 IKGS(ph)SPGIQDTLEAEDGAFETDEAPEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IKGSSPGIQDTLEAEDGAFETDEAPEDR 28 1 Q9UNX4 Q9UNX4 WDR3 WD repeat-containing protein 3 1 IKGS(0.5)S(0.5)PGIQDTLEAEDGAFETDEAPEDR;IKGS(0.5)S(0.5)PGIQDT(0.001)LEAEDGAFETDEAPEDR 123.54 2.61E-05 114684000 101928 85974 65555 81621 104142 90492 97275 121072 166246 TRUE FALSE 88457.95655 85409.23113 97257.61727 100154.2955 102069.778 93973.2858 87841.28547 95181.69498 146592.5873 0.603427214 0.582629946 0.66345522 0.68321528 0.696281987 0.641050735 0.599220514 0.649294052 1 17.16145263 1.239122171 6.946140057 1.007847022 0.639899464 0.906674338 0.03632928 0.033372985 9.105314362 0.058054514 0.009772361 17.34291803 -1.239122171 -0.367947558 IKGSEADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IKGSEADR 8 1 P56192 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ; 86.898 0.014325 388560000 1041800 834880 551560 579200 632290 774190 967470 1033800 586540 FALSE TRUE 904123.4904 829395.6183 818296.2609 710716.2125 619708.6661 803973.5903 873644.9083 812729.915 517199.9094 1.748112237 1.603626766 1.582166288 1.374161518 1.198199487 1.554473571 1.689182253 1.571403823 1 18.9803625 4.1808153 1.965668195 1.43496427 1.71267976 0.250824711 0.199113302 0.610638347 4.501119177 0.057946619 0.206048736 15164.05322 -4.1808153 0.277715491 IKIGDPLLEDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IKIGDPLLEDTR 12 1 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ; 114.21 0.00098729 533780000 2913900 2528400 1150010 1468490 2518780 2125270 2929100 3422700 500300 FALSE TRUE 2528820.732 2511790.774 1706158.683 1801933.099 2468661.206 2207030.512 2645036.333 2690782.24 441155.1039 5.732271279 5.693668171 3.86748032 4.084579512 5.595903082 5.002844787 5.995706066 6.099401812 1 18.75092645 4.405827198 21.00093887 4.780791603 5.722623923 0.081688483 1.473536614 30.04002515 8845.349825 0.362598279 0.959346821 25458.17091 -4.405827198 0.94183232 IKIIAPPER ddPTM_MDA-MB-175_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 ; 106.62 0.0026507 7628500000 7975100 6058400 2349700 3241400 6005800 5574400 7057300 7529800 211280 FALSE TRUE 6921170.329 6018601.971 3486022.779 3977409.412 5886296.33 5788850.775 6372884.132 5919610.867 186302.7191 37.15013051 32.30549721 18.71160441 21.34917532 31.59533236 31.07228281 34.20714503 31.77415175 1 17.50728921 1.235967665 24.99981589 0.999962017 29.64068239 0.722206916 5.607152253 41.68225343 401793.5562 9.818521488 1.478337025 17.21740379 -1.235967665 28.64072037 IKKPEGKPDQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKKPEGKPDQK 11 3 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;D6RBK5;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 76.326 0.015621 1200600000 848070 379210 477920 445670 417230 267700 750320 761410 586880 FALSE TRUE 735995.4008 376718.9445 709043.7105 546866.1851 408927.9393 277998.5922 677554.0819 598588.3968 517499.715 1.422214118 0.727959714 1.370133529 1.056746834 0.790199352 0.537195643 1.309283971 1.156693191 1 18.98119854 4.771157107 23.19202498 1.014205363 1.422216129 0.211647433 0.257277232 9696.348433 6898516.124 0.064016546 8.353831289 59041.46256 -4.771157107 0.408010766 IKLDVPEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IKLDVPEDLR 10 1 Q06787;Q06787-2;R9WNI0;G3V0J0;Q06787-9;Q06787-7;Q06787-6;Q06787-5;Q06787-8;Q06787-3;Q06787-4;A8MQB8;Q06787-10;Q06787-11;A0A087WXI3;Q8IXW7;A0A087WY29 Q06787 FMR1 Fragile X mental retardation protein 1 0 ; 94.616 0.00728 433100000 1525140 1303910 842120 988790 1258100 1101180 1400750 1691590 1189750 FALSE TRUE 1323588.885 1295344.529 1249372.049 1213309.882 1233066.271 1143543.107 1264905.481 1329856.642 1049099.11 1.26164332 1.234720835 1.190899922 1.156525509 1.175357275 1.090023903 1.20570637 1.267617739 1 20.00071955 4.244184561 1.923257605 1.16352015 1.261626702 0.237400375 0.070722555 0.65192463 4.468248665 0.019864802 0.080827915 17546.26001 -4.244184561 0.098106552 IKLEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IKLEAER 7 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 87.308 0.017727 282430000 867040 673800 425840 534870 684690 621570 804060 892550 847210 FALSE TRUE 752458.4672 669373.7634 631777.6483 656320.4085 671066.0086 645482.2001 726082.385 701685.1283 747053.7989 1.007234644 0.896018151 0.845692304 0.878545038 0.898283376 0.864037103 0.97192784 0.939269875 1 19.51085262 2.226573439 24.99126229 0.963977665 0.894907759 0.35867099 0.045023633 253.4302326 528354.8523 0.018309884 0.012451046 168.4897318 -2.226573439 -0.069069906 IKLEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKLEER 6 1 Q02040;X6RAJ1;Q02040-2;Q02040-3 Q02040 AKAP17A A-kinase anchor protein 17A 0 74.439 0.073256 176830000 957620 914750 558850 755320 842780 863920 869360 1031500 921990 FALSE TRUE 831068.0907 908740.947 829111.7292 926826.9503 826010.3269 897155.5614 785049.601 810921.7521 812993.3925 1.022232282 1.117771627 1.019825914 1.140017814 1.016011119 1.103521344 0.965628513 0.997451836 1 19.6328841 2.234370967 24.99999564 0.988807067 1.070534855 0.446261641 0.043155976 87.1209557 519849.476 0.015281228 0.010713336 171.5421967 -2.234370967 0.081727788 IKLEGIITR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKLEGIITR 9 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 65.5 0.076233 0 173010 161290 108450 127980 171500 162220 161120 202750 152820 FALSE TRUE 150146.2901 160230.4754 160896.7827 157039.8151 168087.4855 168460.7084 145494.6072 159393.4903 134753.7937 1.114226813 1.189060961 1.194005589 1.165383257 1.247367372 1.250137037 1.079706947 1.182849743 1 17.03996636 0.41481552 1.278650675 4.30E-12 1.186167894 0.518414227 0.052961358 8.138555128 2.239418124 21.30552486 0.01537436 2.599055299 -0.41481552 1.186167894 IKLNGLENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IKLNGLENR 9 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ; 171.85 5.17E-05 1473490000 2223500 2469500 1445100 1803020 2389700 2257600 2633000 2956900 1820380 FALSE TRUE 1929658.841 2453277.692 2143955.194 2212423.248 2342149.645 2344451.333 2377652.065 2324589.946 1605176.75 1.202147266 1.528353617 1.33565054 1.378305067 1.459122583 1.460556498 1.481240035 1.448183164 1 20.61430073 1.236216415 24.99585001 0.999999453 1.419900001 0.664601527 0.091748734 35.45465625 377960.7232 0.13514188 0.020750968 17.22726819 -1.236216415 0.419900548 IKLQLWDTAGQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKLQLWDTAGQER 13 1 Q14964 Q14964 RAB39A Ras-related protein Rab-39A 0 73.386 0.024304 0 278500 271730 136780 127000 258150 233110 293620 341480 81879 FALSE TRUE 241695.5194 269944.9877 202927.2655 155837.2911 253013.3201 242077.8925 265144.7776 268457.1594 72199.3579 3.347613142 3.738883497 2.810651942 2.158430429 3.504370779 3.352909217 3.672398001 3.718276273 1 16.13969839 1.232138808 24.96029034 0.999996081 3.298808075 0.68944378 0.4825296 135.5328171 526737.3805 1.17726361 0.12769352 17.06627771 -1.232138808 2.298811994 IKNENTEGS(ph)PQEDGVELEGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IKNENTEGSPQEDGVELEGLK 21 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 IKNENT(0.003)EGS(0.997)PQEDGVELEGLK;IKNENT(0.002)EGS(0.998)PQEDGVELEGLK;IKNENT(0.001)EGS(0.999)PQEDGVELEGLK;IKNENT(0.001)EGS(0.999)PQEDGVELEGLK;IKNENT(0.004)EGS(0.996)PQEDGVELEGLK 291.08 6.08E-55 2059180000 3267510 2365800 1972180 2410550 2036040 1481760 3030860 3583900 2785430 TRUE FALSE 2835700.275 2350258.904 2925932.845 2957902.22 1995526.787 1538764.266 2736927.664 2817510.875 2456139.639 1.154535447 0.956891403 1.191273004 1.20428911 0.812464713 0.626497061 1.114320872 1.14712976 1 21.22796115 4.756503229 22.44813579 1.016638363 1.154535913 0.06040836 0.179512796 3370.019611 4215967.992 0.047162385 1.212600095 57082.53205 -4.756503229 0.13789755 IKNYILMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKNYILMR 8 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 133.55 0.00083421 341500000 533130 707010 357910 391360 687630 543570 616430 670900 386260 FALSE TRUE 462675.5197 702365.6048 530996.4731 480224.2696 673947.5083 564481.4896 556648.7135 527433.2559 340596.7828 1.358425984 2.062161594 1.559017877 1.409949517 1.978725409 1.657330656 1.634333445 1.548556189 1 18.37770528 1.064848327 1.859245695 0.477607965 1.68116182 0.473836822 0.218445293 1.226683863 2.712397706 3.05344805 0.056118043 11.61043061 -1.064848327 1.203553856 IKPHLMSQELPEDWDKQPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IKPHLMSQELPEDWDKQPVK 20 2 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ; 154.84 2.21E-08 1824950000 4743800 3325100 3265400 3772900 3065500 2633300 3929200 4312500 4033500 FALSE TRUE 4116894.811 3303257.199 4844558.362 4629594.61 3004502.548 2734604.755 3548146.789 3390305.435 3556664.225 1.157515737 0.92875149 1.362107316 1.301667607 0.844752936 0.768867844 0.997605218 0.953226175 1 21.76209335 3.232204934 24.99960834 0.917084864 1.181498954 0.521789633 0.130546417 133.2766997 524233.1697 0.041303762 0.047973925 1706.887643 -3.232204934 0.26441409 IKPMVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKPMVR 6 1 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 76.805 0.067569 731540000 2696500 2411300 1600600 2070300 2483300 2352300 2584800 3017800 2542200 FALSE TRUE 2340150.693 2395460.012 2374655.514 2540393.258 2433887.188 2442794.503 2334126.494 2372466.955 2241664.012 1.043934631 1.068607962 1.059327134 1.133262275 1.085750217 1.089723745 1.041247253 1.058350824 1 21.09613863 0.710582461 0.966155623 0.855855181 1.079636435 0.467893763 0.025526762 4.692039863 1.689261382 1.409233899 0.008914837 5.135496783 -0.710582461 0.223781255 IKPNLSS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKPNLSSSPR 10 1 A0A1P0AZG4;Q96JN0-3 A0A1P0AZG4 1 IKPNLS(0.086)S(0.457)S(0.457)PR 80.69 0.014081 805860000 1611800 1508000 895090 1028000 1456500 1276200 1530700 1846900 1605100 TRUE FALSE 1398796.546 1498093.849 1327958.518 1261423.112 1427518.5 1325296.24 1382252.95 1451954.808 1415346.907 0.988306499 1.058464071 0.938256559 0.891246596 1.008599724 0.936375551 0.976617777 1.025864967 1 20.43272428 1.826401857 6.074232122 1.013237752 0.969931681 0.129741043 0.045147778 0.447222074 23.91610676 0.024007735 0.012415882 67.05047475 -1.826401857 -0.043306071 IKPNLSSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKPNLSSSPR 10 1 A0A1P0AZG4;Q96JN0-3 A0A1P0AZG4 1 IKPNLS(0.019)S(0.099)S(0.882)PR 80.69 0.014081 823130000 1854400 1803000 1063300 1345600 1893400 1529900 1708200 2064400 1862100 TRUE FALSE 1609336.342 1791155.974 1577515.437 1651139.046 1855725.044 1588756.243 1542539.027 1622944.125 1641964.659 0.98012849 1.090861465 0.960748715 1.005587445 1.130185741 0.967594664 0.939447154 0.988415991 1 20.64699165 IKPVLMMNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IKPVLMMNK 9 1 P13639 P13639 EEF2 Elongation factor 2 0 ; 145.17 0.0015723 183040000 1728370 3210440 1925140 2376540 3171190 2463140 3526230 3988650 3910140 FALSE TRUE 1499961.525 3189350.408 2856144.143 2916169.73 3108089.523 2557898.59 3184256.757 3135708.237 3447887.704 0.435037813 0.925015744 0.828375048 0.845784428 0.901447434 0.741874101 0.923538419 0.909457763 1 21.71728136 4.741972216 24.99496018 0.881341 0.435037646 0.808568977 0.068705144 140.9013339 1032262.603 0.016629528 0.117703726 55204.21215 -4.741972216 -0.446303354 IKQEILPEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IKQEILPEER 10 1 O75534-2;O75534;O75534-3;O75534-4 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;; 149.38 2.14E-05 940100000 2021480 1708340 1150350 1401790 1822640 1765910 1979510 2211490 1955240 FALSE TRUE 1754336.296 1697117.802 1706663.108 1720087.845 1786373.03 1833845.7 1787537.425 1738580.073 1724093.755 1.017541124 0.984353547 0.989889966 0.997676513 1.036122905 1.06365776 1.036798272 1.00840228 1 20.7174068 3.249362982 23.03180225 1.028740224 0.995901894 0.407545558 0.018912712 89.24420008 190274.7366 0.006037322 0.007702047 1775.672962 -3.249362982 -0.03283833 IKS(ph)VPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKSVPK 6 1 Q9Y2C9 Q9Y2C9 TLR6 Toll-like receptor 6 1 IKS(1)VPK 72.547 0.051664 270260000 543130 413350 393580 473740 369940 285130 558210 686190 933740 TRUE FALSE 471353.9944 410634.6766 583916.6044 581309.9077 362578.9178 296099.1356 504074.8801 539453.6084 823354.3209 0.572480137 0.498733858 0.709192373 0.706026425 0.440368027 0.35962541 0.61222109 0.65519011 1 19.65115389 1.159197252 1.975267917 1.215047311 0.554577884 0.623968814 0.107774703 0.721075101 2.285322343 0.947539583 0.031508543 14.42770495 -1.159197252 -0.660469427 IKSDYAQLLEDMQNAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKSDYAQLLEDMQNAFR 17 1 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 195.46 1.57E-11 293200000 709850 646740 274280 359860 576230 583840 697250 836270 91775 FALSE TRUE 616041.524 642491.5224 406922.7254 441571.7131 564764.1504 606300.7026 629630.8023 657440.1684 80925.46405 7.612455872 7.939299822 5.028364436 5.456523707 6.978818806 7.492088055 7.780379263 8.124020987 1 16.30430611 4.276570203 24.99357882 6.338879 7.775881364 0.097584084 2.056348321 460.7136635 302939.7508 0.507139461 1.341700707 18904.71797 -4.276570203 1.437002364 IKSEHPGLSIGDTAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKSEHPGLSIGDTAK 15 1 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 148.03 2.17E-06 531830000 696070 525740 189100 331890 539810 411900 621330 756440 331730 FALSE TRUE 604082.5859 522286.3793 280549.3925 407250.6971 529068.8371 427746.0595 561073.5122 594681.1926 292513.2573 2.065146009 1.785513532 0.959099752 1.392246973 1.808700371 1.462313413 1.918113105 2.03300595 1 18.15814249 2.254744761 24.71438809 1.741244135 1.562028237 0 0.398896032 802.2669167 1225119.3 0.151949193 0.117317181 179.7814012 -2.254744761 -0.179215898 IKSESTNHEQQS(ph)PQSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKSESTNHEQQSPQSGK 17 1 P40818;P40818-2;A0A075B720 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 IKSESTNHEQQS(0.999)PQS(0.001)GK 72.015 0.017688 52247000 64938 56694 24807 39444 56505 47559 80356 91453 50487 TRUE FALSE 56356.27877 56321.57338 36803.74817 48400.36306 55380.66105 49388.6255 72563.08749 71896.48764 44518.48437 1.265907399 1.265127827 0.826707124 1.087197009 1.243992508 1.109395933 1.62995413 1.614980578 1 15.44211686 2.254610832 24.99184612 1.465602712 1.128091191 0.269243632 0.213481919 257.1844934 400462.3427 0.080500044 0.062152914 179.7259682 -2.254610832 -0.337511521 IKTEPSS(ph)PLSDPSDIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IKTEPSSPLSDPSDIIR 17 1 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 IKTEPS(0.033)S(0.967)PLS(0.001)DPSDIIR;IKTEPS(0.419)S(0.581)PLSDPSDIIR 138.09 2.90E-06 1208600000 1452050 1146180 548770 674380 1176300 938920 1398000 1533050 378060 TRUE FALSE 1260157.913 1138650.668 814157.0075 827508.2863 1152893.931 975040.86 1262422.175 1205219.188 333366.1775 3.780101278 3.415615455 2.442230384 2.482280274 3.458341035 2.924834389 3.786893394 3.615301339 1 18.34674821 1.232604278 24.99994479 0.999996371 3.235730866 0.67745233 0.485351592 128.4289787 538987.2821 1.127196542 0.1277287 17.08457887 -1.232604278 2.235734496 IKVNGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKVNGK 6 1 P35268;K7ERI7;K7EMH1;K7EP65;K7EKS7;K7ELC4;K7EJT5 P35268 RPL22 60S ribosomal protein L22 0 91.26 0.043863 1155300000 1251400 1103200 770750 922000 807050 647860 1257700 1441000 976790 FALSE TRUE 1086024.319 1095953.007 1143487.278 1131354.192 790991.284 672783.5934 1135728.448 1132853.364 861314.999 1.260890987 1.272418346 1.327606369 1.313519668 0.918353082 0.78111213 1.318598247 1.31526023 1 19.71618143 3.283321951 24.99497305 1.102356216 1.294523942 0.308116429 0.164213842 217.765623 121600.0049 0.053821027 0.069482296 1920.091616 -3.283321951 0.192167726 IKVPVDWNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IKVPVDWNR 9 1 P13796 P13796 LCP1 Plastin-2 0 ; 107.83 0.0024713 1851520000 2066710 2105960 1492410 1922510 2021190 2054410 2357730 2620100 3368800 FALSE TRUE 1793589.037 2092125.81 2214144.468 2359045.279 1980972.273 2133444.482 2129077.707 2059812.005 2970544.302 0.603791378 0.704290392 0.745366587 0.794145799 0.666871816 0.718199853 0.716729828 0.693412316 1 21.50229587 1.236756649 24.97196378 1.00000037 0.708515972 0.779563022 0.049215107 21.61720368 299153.8874 0.074564223 0.0118924 17.24871115 -1.236756649 -0.291484399 IKWDEQTSNTKGDDDEES(ph)DEEAVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IKWDEQTSNTKGDDDEESDEEAVKK 25 3 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 IKWDEQT(0.008)S(0.008)NT(0.008)KGDDDEES(0.976)DEEAVKK 52.669 0.087775 267600000 169150 93270 104810 66343 67815 37487 133740 150240 62965 TRUE FALSE 146796.3989 92657.30323 155496.4666 81407.19214 66465.61418 38929.14915 120769.9154 118112.3452 55521.34943 2.643963096 1.668858992 2.800660794 1.466232233 1.197118133 0.701156394 2.175197769 2.127332033 1 15.76075501 3.715399934 24.34235503 1.520021202 2.300930778 0.389669857 0.538838285 693.1375609 728501.6293 0.156853015 0.232835065 5192.780126 -3.715399934 0.780909576 IKWGDAGAEYVVESTGVFTTMEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 23 IKWGDAGAEYVVESTGVFTTMEK 23 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;;;;;; 308.79 3.72E-73 34603327000 31521034 25331997 15525940 18124891 22174334 16691801 35831644 38929520 9951316 FALSE TRUE 27355449.49 25165589.44 23034336.52 22240424.52 21733108.14 17333945.39 32356696.68 30604745.1 8774882.759 3.117471794 2.867911758 2.625030687 2.534555177 2.476740571 1.975404784 3.687422108 3.487766838 1 23.06494842 4.541517878 2.717619338 2.664758707 3.126186472 0.045415386 0.747282445 1.407571866 17.62994976 0.196249933 1.175063435 34795.08308 -4.541517878 0.461427765 IKYPENFFLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 205.46 2.71E-08 4305300000 5616400 5018100 9483900 4557300 3898590 3615430 5395400 5346500 5048250 FALSE TRUE 4874178.51 4985135.771 14070345.76 5592104.619 3821015.686 3754517.932 4872154.938 4203192.582 4451451.636 1.094963825 1.11988991 3.160844352 1.256242924 0.8583752 0.843436757 1.094509238 0.944229641 1 22.08584445 3.488144377 24.68848568 0.962820117 1.805339252 0.318271952 0.563333257 529.6043751 1186154.092 0.157600901 0.218433679 3077.119606 -3.488144377 0.842519135 ILAAALTECHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILAAALTECHR 11 0 P46060 P46060 RANGAP1 Ran GTPase-activating protein 1 0 185.08 4.62E-06 392790000 342010 347520 227100 301940 335770 332740 321990 352900 383940 FALSE TRUE 296812.512 345237.1182 336926.3196 370500.0919 329088.8339 345540.7231 290763.4594 277435.0813 338551.0506 0.876714196 1.019749068 0.995200928 1.094369937 0.972050842 1.020645845 0.85884672 0.819477833 1 18.36901387 2.237835244 24.99998052 0.87609095 1.000798336 0.315343076 0.070410852 18.5274527 638500.6573 0.026917425 0.019365604 172.9160251 -2.237835244 0.124707387 ILACAPLYHWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILACAPLYHWR 11 0 P06756-3;P06756-2;P06756 P06756-3 ITGAV Integrin alpha-V;Integrin alpha-V heavy chain;Integrin alpha-V light chain 0 97.565 0.0061715 239990000 55274 116380 62343 84352 130550 137540 74931 97965 125920 FALSE TRUE 47969.40085 115615.4921 92492.28332 103505.4108 127952.3104 142831.2528 67664.20315 77015.94711 111033.881 0.432024895 1.04126318 0.83300955 0.93219664 1.152371773 1.286375397 0.609401405 0.693625643 1 16.76064044 4.747482817 24.23953481 0.921776573 0.432024503 0.385866192 0.201141655 960.6327098 2609726.87 0.053914654 0.618884261 55909.14067 -4.747482817 -0.48975207 ILAGDKNYITMDELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILAGDKNYITMDELR 15 1 P12814-3;P12814;P12814-2;H9KV75;H0YJW3 P12814-3 ACTN1 Alpha-actinin-1 0 ; 201.3 5.91E-09 1862160000 1169590 1168230 737550 948960 1222690 1135760 1289500 1458570 594750 FALSE TRUE 1015025.718 1160555.82 1094231.647 1164435.872 1198360.861 1179453.422 1164444.488 1146666.156 524439.3325 1.93544926 2.212945804 2.086478986 2.220344279 2.285032389 2.248979718 2.220360709 2.186461016 1 19.00041637 1.238455418 24.99998854 0.999998703 2.1828804 0.93226873 0.09946782 0.57128262 135114.6727 0.132810377 0.023706982 17.31631264 -1.238455418 1.182881696 ILAT(ph)PPQEDAPSVDIANIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILATPPQEDAPSVDIANIR 19 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 1 ILAT(0.997)PPQEDAPS(0.003)VDIANIR 106.67 0.0034603 73545000 57115 57519 39028 31002 63366 56901 47643 49090 63028 TRUE FALSE 49567.10804 57141.1539 57902.07134 38041.47794 62105.14057 59090.01829 43022.58919 38592.48552 55576.90164 0.891865264 1.028145726 1.04183698 0.684483604 1.117463168 1.063211812 0.77410917 0.694397931 1 15.76219779 2.223351577 24.99565065 0.794047501 0.970588599 0.187981275 0.141160989 329.6002137 541684.8614 0.056804913 0.038460915 167.244397 -2.223351577 0.176541098 ILATPPQEDAPSVDIANIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILATPPQEDAPSVDIANIR 19 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 140.31 4.10E-07 129724000 77421 80980 53850 53735 77070 71992 69169 74260 83958 FALSE TRUE 67189.61869 80448.03705 79892.04012 65936.35304 75536.45778 74761.57883 62461.00103 58380.07689 74032.58089 0.907568234 1.0866572 1.079147034 0.890639665 1.020313717 1.009846988 0.843696117 0.788572763 1 16.1758727 2.24015885 24.94174893 0.857507199 1.002694385 0.320146636 0.08172346 39.33630317 613893.0915 0.031097873 0.022790595 173.8436574 -2.24015885 0.145187186 ILCDLS(ph)DLEYLDEEFHQSLQWMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILCDLSDLEYLDEEFHQSLQWMK 23 0 A0A2R8YE75;A0A2R8Y6F3;Q9P2P5 A0A2R8YE75 HECW2 E3 ubiquitin-protein ligase HECW2 1 ILCDLS(0.98)DLEY(0.02)LDEEFHQSLQWMK 42.03 0.071244 1038600000 932210 501660 659790 444220 568630 368280 818420 985730 783350 TRUE FALSE 809016.0866 498364.5624 978866.6509 545086.9405 557315.3755 382447.9699 739049.7544 774939.3105 690743.2554 1.171225459 0.721490306 1.417120823 0.789131036 0.806834336 0.55367601 1.069934087 1.121891968 1 19.39779004 ILCLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILCLFR 6 0 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 110.43 0.066786 28215000 60280 57308 158210 73373 45202 47301 54697 48008 98862 FALSE TRUE 52313.84527 56931.53997 234720.8852 90033.46109 44302.56864 49120.70008 49392.49336 37741.8628 87174.64698 0.600103896 0.653074511 2.692536113 1.0327941 0.508204738 0.563474608 0.56659241 0.432945404 1 16.411621 3.464176902 10.96579632 0.601891956 1.351007688 0.235305691 0.582067243 0.476751202 391.2474273 0.168777091 0.220689784 2911.902985 -3.464176902 0.749115732 ILCLFRPQSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILCLFRPQSGR 11 1 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ; 234.39 1.55E-15 2932000000 1055560 1485280 774390 877490 1326510 1471030 1253940 1317130 928800 FALSE TRUE 916065.0716 1475523.098 1148887.594 1076737.516 1300115.046 1527621.476 1132333.092 1035471.999 818998.3221 1.118518862 1.801619195 1.402796029 1.314700515 1.587445311 1.865231509 1.38258292 1.264315166 1 19.64350097 1.527874585 2.083754903 0.993573931 1.518722679 0.357891127 0.21961404 0.40945546 3.162919547 0.355839861 0.059302701 33.71899211 -1.527874585 0.525148749 ILDAVVAQEPLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ILDAVVAQEPLHR 13 0 Q15029;Q15029-3;Q15029-2;K7EP67;K7EJ74 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;; 157.52 4.34E-05 938760000 1186530 1031260 612730 770650 996370 1120810 874970 1079750 1000290 FALSE TRUE 1029727.054 1024485.585 909048.2775 945637.8611 976544.1864 1163928.286 790115.5441 848853.8651 882036.8557 1.167442208 1.161499747 1.030623915 1.07210697 1.107146691 1.319591442 0.895785181 0.962379134 1 19.75047941 2.20767709 24.99999755 0.95236105 1.133937004 0.557430036 0.079676392 155.4400942 125826.5748 0.032949783 0.02221743 161.3158682 -2.20767709 0.181575954 ILDDDTIITTLENLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILDDDTIITTLENLKR 16 1 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 255.91 2.03E-26 2545400000 1194400 1172800 648340 690530 1048610 895410 1210050 1311570 768170 FALSE TRUE 1036557.014 1165095.8 961879.3926 847325.3906 1027744.713 929857.0021 1092699.537 1031100.962 677357.8177 1.530294605 1.720059574 1.420046196 1.250927307 1.517284788 1.372770754 1.613179192 1.522239701 1 19.36955862 1.236610956 24.99965509 0.999999374 1.494519503 0.595057672 0.127898044 38.11293185 488572.9825 0.203939139 0.032207262 17.24292568 -1.236610956 0.494520129 ILDEIEEHNIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ILDEIEEHNIK 11 0 Q15019-2;Q15019-3;Q15019;B5MCX3;H7C2Y0;C9J2Q4 Q15019-2 2-Sep Septin-2 0 ;;;;; 221.32 8.50E-12 3742750000 4376550 3752030 2550870 2995160 3451020 2895410 4261020 4944780 4353540 FALSE TRUE 3798177.829 3727382.668 3784479.264 3675256.856 3382351.454 3006798.296 3847786.936 3887377.277 3838869.461 0.9894001 0.970958431 0.985831715 0.957380003 0.881080091 0.783250988 1.002322943 1.012635964 1 21.87225007 2.04680776 24.99999688 1.007299923 0.928522 0.26411822 0.060608347 169.2346889 90387.43308 0.026920244 0.018149638 111.3801402 -2.04680776 -0.078777923 ILDILEYIHEHEYVHGDIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILDILEYIHEHEYVHGDIK 19 0 Q99986;H0YJ50 Q99986 VRK1 Serine/threonine-protein kinase VRK1 0 208.13 9.89E-17 40921000 149060 137330 93504 129280 132280 111270 148810 185660 169840 FALSE TRUE 129361.3433 136427.8702 138722.8472 158634.9999 129647.8868 115550.6289 134378.4291 145958.0538 149761.7087 0.863781166 0.910966304 0.926290494 1.059249399 0.865694495 0.771563238 0.897281623 0.974601953 1 17.19230927 1.652566193 4.157568601 0.993255125 0.900739694 0.213037266 0.070931623 0.284349811 11.2721596 0.054882393 0.019990628 44.93308041 -1.652566193 -0.092515431 ILDLGITGPEGHVLSRPEEVEAEAVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ILDLGITGPEGHVLSRPEEVEAEAVNR 27 1 A0A1C7CYX9;Q16555-2;Q16555 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 0 ;;; 271.54 5.51E-61 1382750000 211401 221862 117279 165201 181723.8 239975 207157 238448 190581 FALSE TRUE 183463.8222 220404.5739 173995.5167 202712.412 178107.8519 249206.9935 187066.946 187457.7508 168050.7313 1.091716893 1.31153594 1.035374945 1.206257244 1.059845742 1.482927159 1.113157584 1.115483101 1 17.3585373 1.493463727 2.150035986 0.999581464 1.192511438 0.171012074 0.132054987 0.684010187 5.367906099 0.223778046 0.034476805 31.15040709 -1.493463727 0.192929974 ILDLIDDAWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILDLIDDAWR 10 0 Q9BS18 Q9BS18 ANAPC13 Anaphase-promoting complex subunit 13 0 ; 155.84 2.79E-05 148049000 382210 374020 280730 317760 364720 382360 344560 424790 436760 FALSE TRUE 331699.9801 371563.038 416491.967 389912.2647 357462.7856 397069.6366 311144.6242 333951.9642 385126.7304 0.861274884 0.964781223 1.081441339 1.012425869 0.928169242 1.031010328 0.807901918 0.867122269 1 18.55497373 2.248222306 24.99989594 0.883069092 0.982914831 0.231868084 0.074974814 257.6863215 666771.5917 0.028480397 0.021775221 177.1015271 -2.248222306 0.09984574 ILDPNTGEPAPVLSSPPPADVS(ph)TFLAFPSPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILDPNTGEPAPVLSSPPPADVSTFLAFPSPEK 32 0 P46060 P46060 RANGAP1 Ran GTPase-activating protein 1 1 ILDPNTGEPAPVLS(0.008)S(0.221)PPPADVS(0.385)T(0.385)FLAFPSPEK 131.99 4.61E-08 161400000 284380 264640 209690 278170 298540 262580 340880 437450 466330 TRUE FALSE 246798.4625 262901.5624 311096.7854 341332.7501 292599.6381 272681.6225 307821.5101 343904.7217 411200.9986 0.600189356 0.639350496 0.756556493 0.830087357 0.711573267 0.663134631 0.748591348 0.836342137 1 18.64948424 1.29711635 1.476727252 1.102490026 0.705652352 0.698339449 0.063415081 0.663364008 1.430311658 0.384761474 0.020271384 19.8205796 -1.29711635 -0.396837674 ILDQMPATPS(ph)SPMYVD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILDQMPATPSSPMYVD 16 0 P45985;P45985-2 P45985 MAP2K4 Dual specificity mitogen-activated protein kinase kinase 4 1 ILDQMPAT(0.007)PS(0.645)S(0.349)PMYVD 132.05 4.32E-05 91932000 249690 197070 145980 167930 187150 209760 204610 201260 210060 TRUE FALSE 216692.8339 195775.4342 216576.4163 206061.0731 183426.0812 217829.6029 184766.9537 158222.1152 185226.9461 1.169877485 1.056948993 1.169248972 1.112478921 0.990277522 1.176014654 0.997516601 0.854206791 1 17.49893447 2.026358848 5.885889019 0.918681262 1.106241797 0.582326194 0.066373243 0.100563732 10.84568338 0.026858372 0.017249851 106.2573175 -2.026358848 0.187560535 ILDQMPATPSS(ph)PMYVD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ILDQMPATPSSPMYVD 16 0 P45985;P45985-2 P45985 MAP2K4 Dual specificity mitogen-activated protein kinase kinase 4 1 ILDQMPATPS(0.04)S(0.946)PMY(0.013)VD;ILDQMPAT(0.001)PS(0.111)S(0.877)PMY(0.012)VD;ILDQMPAT(0.001)PS(0.111)S(0.884)PMY(0.004)VD 146.16 1.21E-06 160147000 735220 549920 442040 512080 605670 675950 627230 702440 678050 TRUE FALSE 638058.8142 546307.5393 655812.0225 628355.5907 593618.352 701954.2339 566401.3311 552228.6724 597891.7014 1.067181251 0.913723234 1.096874268 1.050952186 0.992852636 1.174049133 0.947330979 0.923626588 1 19.18952466 2.101640887 22.33808703 0.949554316 1.044282836 0.27950655 0.069193211 6.514881601 1414.976264 0.027108309 0.01827641 126.3690983 -2.101640887 0.09472852 ILDSVGIEADDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ILDSVGIEADDDR 13 0 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ;;;;;; 301.7 1.30E-40 1907787000 1609027 1512847 1185878 1605883 1435438 1551184 1360789 1572605 4602330 FALSE TRUE 1396390.005 1502909.008 1759372.567 1970523.28 1406875.592 1610859.052 1228819.892 1236315.659 4058247.79 0.344086926 0.370334461 0.433530099 0.485560119 0.346670698 0.396934622 0.302795678 0.304642723 1 21.95242553 1.234831575 24.99994046 1.000000894 0.371807902 0.925660113 0.055834053 30.00158688 201103.9476 0.110407748 0.015202724 17.1724229 -1.234831575 -0.628192992 ILDSVGIEADDDRLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ILDSVGIEADDDRLNK 16 1 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ;;;;;; 314.84 7.99E-58 24589020000 25155160 20176410 14154200 17350310 17440260 15878720 22836240 26103720 22456070 FALSE TRUE 21830841.87 20043869.83 20999218.46 21289963.07 17093232.95 16489584.63 20621584.96 20521642.62 19801338.99 1.102493215 1.012248204 1.060494872 1.07517795 0.863236216 0.832750989 1.041423763 1.036376511 1 24.23909465 3.293202381 24.99988264 0.965358567 1.058856345 0.362383384 0.070228902 131.5320259 60177.866 0.022830879 0.029474517 1964.275416 -3.293202381 0.093497778 ILDVASLEVLNEVNRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILDVASLEVLNEVNRR 16 1 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 207.85 2.62E-11 690090000 396920 309350 188896 200561 301200 349890 337180 411070 204940 FALSE TRUE 344466.0163 307317.8595 280246.7374 246101.4404 295206.7093 363350.4947 304480.3355 323165.8795 180712.2267 1.906157777 1.700592512 1.55079013 1.361841669 1.633573526 2.010658058 1.684890619 1.788290064 1 17.46333459 1.234114848 24.9983051 0.999998959 1.699300333 0.604881801 0.178921418 101.5686649 571041.038 0.356042517 0.046113284 17.1441062 -1.234114848 0.699301375 ILDWHVANTDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILDWHVANTDKK 12 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ; 140.31 3.87E-05 5782500000 9924400 8504300 6241000 7135400 6892200 5857200 10650500 12414500 9007700 FALSE TRUE 8612865.395 8448434.693 9259168.475 8755601.628 6755058.704 6082530.274 9617616.149 9759755.785 7942819.968 1.084358632 1.063656828 1.165728106 1.102329105 0.850461012 0.76578977 1.210856621 1.228751983 1 22.92121987 0.935678876 18.32737959 0.000405445 1.066233129 0.013479321 0.147456017 10710785.63 49042433.84 444560923.4 0.039900781 8.623406846 -0.935678876 1.065827683 ILEFFGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILEFFGLK 8 0 P07237;H7BZ94;H0Y3Z3;I3L398;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ; 138.9 0.0015953 204781000 589840 515460 419150 561100 513710 526620 511910 561260 783250 FALSE TRUE 511891.1495 512073.9093 621852.342 688506.3309 503488.1761 546879.4122 462265.047 441238.9167 690655.0773 0.741167576 0.741432194 0.900380468 0.996888828 0.729000905 0.791827108 0.669313905 0.638870156 1 19.39760586 KQPPVS(ph)PGTALVGSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KQPPVSPGTALVGSQK 16 1 P17096;P17096-3 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KQPPVS(0.999)PGT(0.001)ALVGSQK;KQPPVS(0.999)PGT(0.001)ALVGSQK;KQPPVS(0.919)PGT(0.081)ALVGSQK 199.29 2.36E-11 3442270000 4000090 3781470 3512060 3884580 3607910 2642760 4204300 5216340 9103800 TRUE FALSE 3471467.972 3756629.275 5210503.963 4766633.261 3536119.65 2744428.687 3796567.633 4100866.285 8027559.135 0.432443774 0.467966565 0.649076995 0.593783637 0.44049749 0.341875861 0.472941721 0.510848468 1 22.93652996 1.237470262 5.481823329 1.025570282 0.488618991 0.783131427 0.084650687 0.076579631 7.090348194 0.155457744 0.023011386 17.27707671 -1.237470262 -0.53695129 ILEFVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 117.62 0.012074 48804000 89209 94294 62240 68765 135650 112300 95685 97430 85451 FALSE TRUE 77419.80462 93674.57651 92339.47218 84379.14426 132950.8304 116620.2537 86405.48343 76595.3527 75349.08013 1.027481749 1.243207964 1.225489044 1.119843057 1.764465209 1.547732945 1.146735744 1.016539984 1 16.20130228 2.007899386 24.208598 1.031107304 1.32633896 0.282615897 0.208483262 163.763821 501870.6933 0.091633862 0.061636433 101.8355437 -2.007899386 0.295231657 ILEGPQQSLSGS(ph)PLQPIPASPPPQIPPGLRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILEGPQQSLSGSPLQPIPASPPPQIPPGLRPR 32 1 O15446;O15446-2 O15446 CD3EAP DNA-directed RNA polymerase I subunit RPA34 1 ILEGPQQSLS(0.002)GS(0.998)PLQPIPASPPPQIPPGLRPR 163.4 3.75E-14 243570000 97285 87005 59233 81786 90590 88861 88314 105110 95950 TRUE FALSE 84428.54076 86433.45843 87878.27692 100356.7613 88787.43624 92279.54017 79749.32187 82633.04447 84606.90031 0.997891903 1.021588761 1.038665601 1.186153387 1.049411288 1.090685746 0.942586498 0.976670274 1 16.36848771 2.240481588 24.9999249 0.972561599 1.065864054 0.404473166 0.052009475 50.63947653 659048.7738 0.020870046 0.015341481 173.9728939 -2.240481588 0.093302456 ILELEEENDRLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILELEEENDRLR 12 1 Q14789;Q14789-2;Q14789-4;Q14789-3 Q14789 GOLGB1 Golgin subfamily B member 1 0 ; 210.79 3.60E-08 152146000 218240 217670 119847 118379 222650 227760 170765 236380 115802 FALSE TRUE 189399.0311 216240.1114 177805.4101 145258.7613 218219.7006 236522.0746 154204.2366 185831.9765 102112.0195 1.85481623 2.117675397 1.741277971 1.422543223 2.137061844 2.316300038 1.510147751 1.819883472 1 16.63979317 0.956247231 1.659302903 4.13E-15 1.890204934 0.490105726 0.276116976 2.056688166 2.793833154 7.98040221 0.077917609 9.041640417 -0.956247231 1.890204934 ILELT(ph)PEPDRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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;ILELT(1)PEPDRPR 211.45 5.14E-08 5989670000 3176536 2714907 1781495 2187069 2551237 2717065 2502231 2901914 2746899 TRUE FALSE 2756748.719 2697072.597 2643031.941 2683676.444 2500472.375 2821592.249 2259565.023 2281362.274 2422163.729 1.138134754 1.113497227 1.091186326 1.107966572 1.032330038 1.164905664 0.932870472 0.941869555 1 21.20786496 2.229096207 24.99999973 0.9537774 1.104047361 0.774770836 0.037997913 84.02470017 221946.9732 0.014711286 0.010066231 169.4713181 -2.229096207 0.150269961 ILENEKDLEEAEEYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ILENEKDLEEAEEYK 15 1 E5RJD8;O75347;E5RIW3;E5RHG6 E5RJD8 TBCA Tubulin-specific chaperone A 0 ;;; 215.8 2.09E-12 1599030000 2385270 1582210 2105310 2107460 1565540 1087410 2275040 2744250 4220010 FALSE TRUE 2070050.526 1571816.358 3123444.958 2585991.004 1534388.817 1129243.366 2054406.971 2157413.493 3721125.225 0.556296927 0.422403511 0.839381845 0.694948664 0.412345386 0.303468252 0.552092941 0.579774494 1 21.82730751 1.225537077 3.799773659 1.064407134 0.540715696 0.480374715 0.149178566 0.274223124 6.32759397 0.415092923 0.040407158 16.80881422 -1.225537077 -0.523691438 ILENEKDLEEAEEYKEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ILENEKDLEEAEEYKEAR 18 2 E5RJD8;O75347;E5RIW3;E5RHG6 E5RJD8 TBCA Tubulin-specific chaperone A 0 ;;;;; 211.33 1.76E-16 3824900000 3490340 2581330 2052560 1792600 2348040 1532596 3689270 4178530 1329948 FALSE TRUE 3029082.726 2564373.073 3045184.881 2199637.228 2301318.598 1591555.96 3331485.163 3284983.877 1172723.063 2.582948031 2.186682564 2.596678601 1.875666386 1.962371741 1.357145613 2.840811501 2.801159099 1 20.16143093 3.743048789 24.80262275 2.087295643 2.428561003 0.114974872 0.573848134 1077.03866 5951931.01 0.161689547 0.267866864 5534.122766 -3.743048789 0.34126536 ILENLR ddPTM_MDA-MB-175_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 ;;;;; 160.17 0.020687 2331740000 1728279 1781654 1096448 1441336 1782350 1958332 1471323 1836996 1759057 FALSE TRUE 1499882.551 1769950.198 1626693.92 1768613.368 1746884.722 2033670.299 1328634.322 1444168.701 1551103.285 0.96697787 1.141091128 1.048733463 1.140229271 1.126220761 1.311112109 0.856573727 0.931059017 1 20.56486333 2.213440538 24.99941319 0.926569356 1.120880485 0.494702736 0.092015936 183.3164066 182434.4422 0.036741511 0.024781856 163.4709318 -2.213440538 0.194311129 ILEPDDFLDDLDDEDYEEDTPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILEPDDFLDDLDDEDYEEDTPKR 23 1 Q92785;J3KMZ8 Q92785 DPF2 Zinc finger protein ubi-d4 0 72.443 0.033378 10196000 21621 13863 8731.7 11845 10075 10264 13050 15786 11829 FALSE TRUE 18763.73007 13771.93304 12954.37933 14534.58829 9874.527211 10658.86272 11784.41301 12410.28675 10430.5891 1.798913743 1.320340866 1.241960469 1.393458045 0.946689312 1.021885018 1.12979362 1.1897973 1 13.34853302 8 0.640415083 1.092678614 58.63388425 0.780666299 0.115430659 102.2324114 0.69134761 0.051185889 8317.352986 99999999.9 -8 57.54120564 ILEQQNSSRT(ph)LEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILEQQNSSRTLEK 13 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 1 ILEQQNS(0.035)S(0.199)RT(0.766)LEK;ILEQQNSSRT(1)LEK 220.78 3.27E-11 1019270000 302656 348860 168095 162174 361233 321443 369673 396794 82287 TRUE FALSE 262659.2428 346568.3157 249386.3042 198998.0854 354045.17 333809.1202 333822.1694 311942.691 72559.1246 3.619934008 4.776357455 3.437008172 2.742564584 4.879402446 4.600511956 4.600691797 4.299151797 1 16.14686943 5.046636197 16.08767593 3.903286809 2.026551664 0 1.194339705 45966599.48 412900854.5 0.283814147 2642736481 111336.1493 -5.046636197 -1.876735145 ILEVCVWDAELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILEVCVWDAELR 12 0 Q13217 Q13217 DNAJC3 DnaJ homolog subfamily C member 3 0 87.568 0.02437 42184000 42110 43554 37134 38899 46181 53337 42807 46971 53702 FALSE TRUE 36545.05681 43267.89091 55092.12661 47731.61248 45262.08845 55388.9089 38655.58373 36926.61718 47353.41074 0.771751311 0.913722797 1.163424677 1.00798679 0.955835868 1.169692067 0.816321003 0.779809028 1 15.53118072 2.184265306 24.9999156 0.845505709 0.999465603 0.186396475 0.127400476 132.9512278 61215.31963 0.052282907 0.035249156 152.8499517 -2.184265306 0.153959894 ILEVHIDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILEVHIDK 8 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 90.629 0.013061 141250000 489230 370070 267670 324750 378600 335620 424560 523290 515120 FALSE TRUE 424577.0159 367638.9858 397116.1073 398489.451 371066.6007 348531.5186 383386.2365 411388.5057 454223.1004 0.934732328 0.809379764 0.874275454 0.877298954 0.816925868 0.767313504 0.844048302 0.905697014 1 18.79304155 1.377690814 2.318301217 1.016247245 0.843264838 0.546171282 0.04499297 0.340321194 2.511518229 0.108255643 0.012149999 23.86111938 -1.377690814 -0.172982407 ILEVHVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILEVHVDK 8 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ; 95.502 0.0096049 746350000 2191800 1746760 1070400 1469800 1551250 1427950 1901390 2270360 2080810 FALSE TRUE 1902148.077 1735285.419 1588049.02 1803540.554 1520383.16 1482884.161 1716993.49 1784861.182 1834819.012 1.036695208 0.945752909 0.865507175 0.982952838 0.82862841 0.808190972 0.935783573 0.972772339 1 20.80720633 1.734614524 3.187900206 0.991250851 0.908280988 0.164418044 0.068450917 0.384822274 8.302398443 0.051982143 0.019193195 54.27683606 -1.734614524 -0.082969863 ILFIFIDSDHTDNQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ILFIFIDSDHTDNQR 15 0 P07237;H7BZ94;H0Y3Z3;I3L398;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ;;; 304.19 1.38E-44 3664423000 1163889 1118743 632143 1155836 906891 1100122 880915 1048173 1225794 FALSE TRUE 1010078.12 1111393.904 937849.4692 1418286.23 888845.6434 1142444.405 795483.9989 824029.3608 1080882.03 0.934494322 1.028228681 0.867670517 1.31215636 0.82233363 1.056955684 0.735958205 0.762367528 1 20.04377764 2.243248175 24.99983729 0.81407292 1.004359409 0.224450568 0.148368059 148.0318857 789493.7412 0.053493209 0.040038017 175.0846914 -2.243248175 0.190286489 ILFRPVASQLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILFRPVASQLPR 12 1 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 ; 109.16 0.0014848 1425000000 734160 1002110 684410 798820 1088630 1412890 825790 1074520 906010 FALSE TRUE 637138.8959 995527.0734 1015392.965 980204.2902 1066968.393 1467244.793 745705.0129 844742.2599 798902.5299 0.797517685 1.246118314 1.270984791 1.226938523 1.335542639 1.836575474 0.933411755 1.057378376 1 19.60765997 ILGGSVLHLVLALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILGGSVLHLVLALR 14 0 Q15843 Q15843 NEDD8 NEDD8 0 123.95 0.00055569 0 9707.7 18927 6505.3 8509.6 15571 16179 14409 17624 16054 FALSE TRUE 8424.802849 18802.66729 9651.284839 10441.83474 15261.16756 16801.4166 13011.6174 13855.24475 14156.11441 0.595135261 1.32823646 0.681774996 0.737620115 1.078061898 1.186866404 0.919151755 0.978746311 1 13.78913771 3.223036759 24.99692511 1.025046957 0.8598794 0.180517928 0.205236282 482.7025173 777258.4273 0.060094533 0.068375413 1671.232064 -3.223036759 -0.165167557 ILGSAS(ph)PEEEQEKPILDRPTR ddPTM_MDA-MB-175_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(0.004)AS(0.996)PEEEQEKPILDRPTR;ILGS(0.045)AS(0.955)PEEEQEKPILDRPTR;ILGSAS(0.999)PEEEQEKPILDRPT(0.001)R;ILGS(0.001)AS(0.999)PEEEQEKPILDRPTR 209.41 1.35E-22 2139210000 1232508 977510 770420 861591 1005254 857008 1160149 1320952 1302046 TRUE FALSE 1069628.945 971088.6724 1142997.689 1057228.405 985251.4121 889977.6523 1047637.929 1038476.694 1148119.605 0.931635467 0.845807935 0.995538865 0.920834729 0.858143531 0.775161097 0.912481525 0.904502188 1 20.13084151 1.148091262 2.324578019 1.050216484 0.88955563 0.251766878 0.058237922 1.275171734 5.822494637 0.466338421 0.015964229 14.0634302 -1.148091262 -0.160660854 ILGSASPEEEQEKPILDRPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILGSASPEEEQEKPILDRPTR 21 2 Q7Z422-5;Q7Z422;Q7Z422-4;Q7Z422-2;Q7Z422-3 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 0 202.97 3.43E-22 95446000 43532 37852 24177 36551 39930 30886 52336 49827 49513 FALSE TRUE 37779.1359 37603.34772 35869.07807 44850.4632 39135.47112 32074.20441 47260.46278 39171.8838 43659.62955 0.865310501 0.861284168 0.821561668 1.027275395 0.896376619 0.734642157 1.082475121 0.897210632 1 15.41401227 -1.999999999 0.252287275 1.726064337 0.852237441 0.141551385 0.095136665 173.4824851 2.779114203 62.73338088 0.296440913 0.01 1.999999999 -0.873826896 ILGVGGEDDDGEVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILGVGGEDDDGEVHR 15 0 E9PN66;E9PNB3;E9PKN9;E9PS55;E9PMY0;E9PMW4;E9PQ46;E9PIN5;E9PIK4;U3KQ32;E9PKZ4;E9PPM1;O14683 E9PN66 TP53I11 Tumor protein p53-inducible protein 11 0 230.36 3.39E-13 132390000 105140 108500 76906 98659 148250 139150 77326 140160 158970 FALSE TRUE 91245.48261 107787.2564 114097.9988 121061.0339 145300.115 144503.1905 69826.93642 110187.8747 140176.7477 0.650931657 0.768938202 0.813958097 0.86363135 1.036549338 1.030864198 0.498134944 0.786063855 1 17.09688753 6.265430197 12.40911139 0.821486082 0.482949548 0 0.170441354 0 0 0.039277001 0 1842596.31 -6.265430197 -0.338536534 ILHCLGLAEEIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILHCLGLAEEIQK 13 0 P53004 P53004 BLVRA Biliverdin reductase A 0 ; 148.13 4.31E-05 884390000 1313440 1041130 667100 862130 966360 895180 1203410 1280490 1178120 FALSE TRUE 1139865.576 1034290.748 989711.7913 1057889.793 947131.3267 929618.1539 1086703.483 1006667.178 1038843.996 1.097244226 0.995617006 0.952704925 1.018333646 0.911716611 0.894858283 1.046069947 0.969026324 1 19.98654759 4.71951661 3.092785412 0.971208268 1.114013243 0.434022285 0.045225365 0.330359938 4.927867399 0.011329817 0.112548643 52422.36498 -4.71951661 0.142804975 ILHDFYIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILHDFYIEK 9 0 Q9H6T3;Q9H6T3-3;Q9H6T3-2 Q9H6T3 RPAP3 RNA polymerase II-associated protein 3 0 98.249 0.0055436 0 289300 263320 186330 249450 303250 226860 281910 332360 388990 FALSE TRUE 251068.272 261590.2336 276439.8112 306091.4351 297215.9183 235587.451 254570.4116 261287.4004 343004.0453 0.731968837 0.762644748 0.805937466 0.89238433 0.866508493 0.68683578 0.742179036 0.761761863 1 18.38786607 2.270269056 0.014679334 1.616567531 5.28E-06 0.088107852 0.087953003 9008.6774 81.39142494 4591.538166 4370.57612 186.3241101 -2.270269056 -1.616562255 ILHDVELLSSLALAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILHDVELLSSLALAR 15 0 Q9NTJ4-3;Q9NTJ4-2;Q9NTJ4;Q9NTJ4-4 Q9NTJ4-3 MAN2C1 Alpha-mannosidase 2C1 0 102.28 0.0032252 0 29919 32844 19589 21646 30268 26584 27955 30689 27411 FALSE TRUE 25965.12834 32628.2456 29062.30592 26561.05514 29665.72602 27606.70368 25243.9284 24126.39617 24170.50281 1.074248581 1.349920019 1.202387313 1.098903707 1.227352457 1.142165056 1.044410561 0.998175188 1 14.56095986 2.249228224 2.068534723 0.998935592 1.196042028 0.547072908 0.073993076 0.228823726 2.004478968 0.039312821 0.022556582 177.512207 -2.249228224 0.197106436 ILHGFK ddPTM_MDA-MB-175_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 ; 89.775 0.049783 1411120000 4634400 4256100 2867800 3682600 3909800 3828500 4899100 5263800 5624800 FALSE TRUE 4021952.298 4228141.399 4254677.672 4518790.615 3832002.629 3975784.872 4423986.036 4138177.333 4959842.552 0.81090322 0.852474923 0.857825148 0.911075416 0.772605701 0.801594976 0.891960983 0.834336431 1 22.24186289 1.236587454 24.99937043 1.000000199 0.843229763 0.595720707 0.040989939 37.60425245 476306.8829 0.062921102 0.009925474 17.2419926 -1.236587454 -0.156770435 ILHLLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILHLLGK 7 0 Q9UBF2;Q9UBF2-2;H3BS45;F5H1S1;Q92521 Q9UBF2 COPG2;PIGB Coatomer subunit gamma-2;GPI mannosyltransferase 3 0 88.591 0.018495 266880000 315910 288720 177640 205060 286560 273480 303640 338730 339500 FALSE TRUE 274161.6931 286823.3793 263547.2982 251622.0071 280858.0166 284000.9526 274193.0395 266295.2255 299364.6968 0.915811704 0.958106892 0.880355302 0.840519974 0.938180152 0.948678838 0.915916414 0.889534499 1 18.19154457 ILHLLGQEGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILHLLGQEGPK 11 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 177.57 7.92E-06 526240000 1090800 1021400 744540 898970 951240 812790 1112400 1359500 1308800 FALSE TRUE 946648.0163 1014690.356 1104602.034 1103094.878 932312.1851 844058.5572 1004519.619 1068781.505 1154075.155 0.820265485 0.879223811 0.957131803 0.955825861 0.807843563 0.731372263 0.870410922 0.926093504 1 20.13830575 1.474936061 2.575386897 1.000485274 0.861781979 0.322108173 0.066715451 0.44185366 5.119951802 0.112799547 0.019822397 29.84943128 -1.474936061 -0.138703296 ILHTLLASGEDALDFTQES(ph)EPSYISDVGPPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILHTLLASGEDALDFTQESEPSYISDVGPPGR 32 0 H3BVG0;Q8N1F7;Q8N1F7-2;H3BM93;H3BMX0;H3BP95 H3BVG0 NUP93 Nuclear pore complex protein Nup93 1 ILHTLLASGEDALDFT(0.021)QES(0.888)EPS(0.075)Y(0.015)IS(0.001)DVGPPGR;ILHTLLASGEDALDFT(0.003)QES(0.963)EPS(0.032)Y(0.002)ISDVGPPGR 145.43 3.06E-10 77955000 41503 38527 24819 28342 42985 44597 41744 40376 42293 TRUE FALSE 36018.27339 38273.9136 36821.55141 34777.48428 42129.6826 46312.67545 37695.67331 31741.90661 37293.16972 0.965814214 1.026298217 0.987353762 0.932542998 1.129688973 1.241854093 1.010792957 0.851145313 1 15.1866238 1.984634771 24.44447108 0.919748831 1.049132809 0.217618914 0.094074866 727.5844779 1157508.647 0.044613801 0.026858033 96.52387991 -1.984634771 0.129383979 ILHTYYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILHTYYK 7 0 Q99613-2;Q99613;B5ME19 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 83.801 0.022013 686050000 765370 767450 577560 596330 812290 646930 932530 969710 968830 FALSE TRUE 664224.4153 762408.5704 856869.9478 731735.8408 796127.0182 671817.8157 842093.3841 762345.0628 854296.0211 0.777510838 0.892440737 1.003012921 0.856536637 0.931910015 0.786399327 0.985716149 0.892366398 1 19.70437654 -0.714630035 0.017878375 1.954281797 4.03E-06 0.161935131 0.074005636 14723.93187 35.23216076 2242.155885 1651.649078 0.192916762 0.714630035 -1.954277766 ILHVDNHIGISIAGLTADAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ILHVDNHIGISIAGLTADAR 20 0 P25786;P25786-2;F5GX11;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ;; 200.6 7.76E-22 311855000 208404 199760 119203 156628 187746 185448 182207 192071 209847 FALSE TRUE 180862.8834 198447.7634 176849.9695 192192.7813 184010.2219 192582.3046 164536.5932 150998.1113 185039.1267 0.977430485 1.072463791 0.955743645 1.038660227 0.994439528 1.040765313 0.889198928 0.81603342 1 17.49747084 2.229291361 24.24486607 0.883364935 1.013628007 0.459790828 0.055802292 95.70312759 250319.8218 0.021296103 0.014594326 169.5474887 -2.229291361 0.130263072 ILHVNGFNGEGGEEDPQAAR ddPTM_MDA-MB-175_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 0 109.66 0.00028708 0 25372 21814 31765 28790 27533 31973 23214 33610 25525 FALSE TRUE 22019.02592 21670.7024 47126.66025 35327.20953 26985.14717 33203.022 20962.70985 26422.76305 22507.46358 0.978298858 0.962822946 2.093823681 1.569577549 1.198942168 1.475200521 0.931367045 1.173955606 1 14.45811586 2.243465232 24.99836669 1.059711697 1.393689271 0.196893219 0.326084522 212.3591649 1082382.19 0.129768536 0.097283205 175.1722191 -2.243465232 0.333977574 ILIEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ILIEELR 7 0 C9JEV6;Q9UJ70;Q9UJ70-2;H7C3G9;H0YEB7;H0YE82;H7C1L7 C9JEV6 NAGK N-acetyl-D-glucosamine kinase 0 ;;; 163.84 0.0028378 206606000 536785 514782 322978 369793 470132 508597 449630 513214 520463 FALSE TRUE 465847.5022 511400.3631 479171.2411 453760.1526 460777.293 528163.0557 406024.9518 403467.1799 458934.4571 1.015063252 1.114321131 1.044095151 0.988725396 1.004015467 1.150846374 0.884712284 0.879139001 1 18.8079286 2.217801161 24.99998987 0.910979743 1.050107173 0.524470094 0.058743001 175.154248 210931.3831 0.023728957 0.016017561 165.1205633 -2.217801161 0.13912743 ILIPS(ph)DIESSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILIPSDIESSK 11 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 ILIPS(1)DIESSK;ILIPS(1)DIESSK 170.18 1.68E-05 152447000 1202710 705860 446490 625450 694360 565300 789500 1024680 909850 TRUE FALSE 1043768.826 701223.1592 662414.0574 767467.9819 680543.5945 587047.4568 712934.4115 805560.1561 802288.5695 1.300989277 0.874028605 0.825655609 0.956598425 0.848252886 0.731716092 0.888625912 1.004077818 1 19.61376172 4.740225874 24.95247117 0.893506946 1.300989417 0.71066171 0.082177634 88.39323669 1324383.418 0.022004332 0.136527522 54982.67611 -4.740225874 0.40748247 ILIQHQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILIQHQK 7 0 J3QRS9;O43670-2;O43670;O43670-4;X6R4W8;O43670-3 J3QRS9 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 99.919 0.010175 487700000 414320 378820 276120 369650 407100 414130 571400 658540 754990 FALSE TRUE 359566.5622 376331.5065 409652.5556 453584.6822 398999.5065 430061.8491 515985.7159 517716.3458 665735.9423 0.540103875 0.565286449 0.615337898 0.681328217 0.599335985 0.645994638 0.775060626 0.7776602 1 19.34459053 -2 0.426826187 8.60284825 0.573133748 0.909884016 0.040626292 24.77566902 0.33648459 169.483328 0.03598398 0.01 2 -8.029714502 ILIVTQT(ph)PPYVK ddPTM_MDA-MB-175_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(0.008)QT(0.992)PPYVK 160.69 0.00063833 0 295150 313720 177780 229410 295240 232610 298680 357910 318060 TRUE FALSE 256145.1797 311659.1527 263755.0026 281501.0468 289365.3016 241558.6572 269714.0596 281373.7318 280459.3091 0.913306035 1.111245527 0.940439465 1.003714399 1.031755025 0.861296628 0.961686957 1.003260447 1 18.09743194 ILKEQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ILKEQER 7 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;; 79.906 0.028595 789260000 2324230 1741810 835305 1104908 1760400 1728300 2301650 2578560 386370 FALSE TRUE 2017077.117 1730367.935 1239261.292 1355794.249 1725371.484 1794788.819 2078436.337 2027155.01 340693.7788 5.920498825 5.078953721 3.637463814 3.979509851 5.064288202 5.268041072 6.10059962 5.950079329 1 18.37811608 4.634796749 4.039479443 4.674811159 5.922916528 0.080080554 1.463028053 0.675124439 17.43056723 0.362092938 1.866282193 43131.7172 -4.634796749 1.24810537 ILKS(ph)PEIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ILKSPEIQR 9 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 1 ILKS(1)PEIQR;ILKS(1)PEIQR;ILKS(1)PEIQR 126.83 0.00028006 898880000 1656640 1418030 998790 1201840 1498460 1311970 1471080 1725070 1589460 TRUE FALSE 1437710.827 1408714.868 1481808.185 1474736.141 1468643.578 1362442.335 1328414.888 1356177.205 1401555.85 1.025796316 1.005107908 1.057259463 1.052213611 1.047866611 0.972092789 0.947814451 0.967622664 1 20.4185978 2.731297923 23.34708603 0.968960491 1.037739596 0.742424722 0.019214448 115.2687943 370548.098 0.00689828 0.006221513 538.6391585 -2.731297923 0.068779105 ILLENY(ph)VRSIENER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILLENYVRSIENER 14 1 H0Y9S3;A0A494C037;E7EUS2;Q8TBZ0-2;Q8TBZ0 H0Y9S3 CCDC110 Coiled-coil domain-containing protein 110 1 ILLENY(0.995)VRS(0.005)IENER 68.83 0.058313 145620000 187350 81528 533060 147850 36576 44103 86853 81206 88712 TRUE FALSE 162591.2228 80992.4372 790849.599 181421.6022 35848.20916 45799.67095 78430.00943 63840.72885 78224.56842 2.07851863 1.035383625 10.10998993 2.319240693 0.458273019 0.585489596 1.002626298 0.816121203 1 16.25533417 3.483384237 24.61828951 0.84067103 4.428024028 0.333309328 2.347066366 263.5509581 1035957.398 0.661641399 0.885918901 3043.576603 -3.483384237 3.587352998 ILLVDS(ph)PGMGNADDEQQEEGTSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ILLVDSPGMGNADDEQQEEGTSSK 24 0 Q9UKN8 Q9UKN8 GTF3C4 General transcription factor 3C polypeptide 4 1 ILLVDS(1)PGMGNADDEQQEEGTSSK;ILLVDS(1)PGMGNADDEQQEEGTSSK;ILLVDS(1)PGMGNADDEQQEEGTSSK;ILLVDS(1)PGMGNADDEQQEEGTSSK 280.74 2.01E-52 201557000 375729 260952 182333 219773 250378 214461 308801 341982 304847 TRUE FALSE 326075.4607 259237.7891 270509.8487 269675.8187 245395.9677 222711.4534 278853.5265 268851.8106 268808.3349 1.213040737 0.964396395 1.00632984 1.003227146 0.91290312 0.828513943 1.037369346 1.000161735 1 18.03621835 4.739492443 24.70474952 0.970816776 1.213040824 0.622211496 0.059720601 48.29643391 1280214.898 0.015388893 0.090570658 54889.90037 -4.739492443 0.242224048 ILLWDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILLWDTR 7 0 Q9BQA1;Q9BQA1-2;H0Y711 Q9BQA1 WDR77 Methylosome protein 50 0 ; 85.357 0.048554 805440000 1499820 1496740 1069440 1215360 1451210 1589440 1451920 1568400 1478740 FALSE TRUE 1301614.987 1486907.816 1586624.761 1491326.064 1422333.76 1650586.785 1311113.022 1233009.865 1303925.042 0.998228384 1.14033228 1.216806726 1.143720702 1.090809452 1.265860178 1.005512572 0.94561407 1 20.31442951 2.069366757 8.687861358 0.970883259 1.143411008 0.528192374 0.071284829 0.196220884 22.29431738 0.028343508 0.019074793 117.3185691 -2.069366757 0.172527749 ILMEHIHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILMEHIHK 8 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ; 117.04 0.001247 5026900000 5906600 4982200 3268700 4048900 4792000 4391500 5466300 6210800 5373400 FALSE TRUE 5126027.845 4949471.6 4849454.253 4968264.629 4696648.575 4560443.847 4936179.067 4882668.752 4738162.773 1.081859803 1.044597207 1.023488319 1.048563518 0.991238334 0.962492017 1.041791788 1.030498315 1 22.17589633 4.993676148 0.867022021 1.012078511 1.148576084 0.469765727 0.024464457 3.4332251 1.505428677 0.009175941 0.493674726 98554.42947 -4.993676148 0.136497573 ILNDVQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ILNDVQDR 8 0 O00148;Q13838-2;Q13838;A0A0G2JJZ9;H0Y400 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ;;; 136.39 0.0018447 1349050000 2065020 1728530 1367660 1674450 1751620 1987640 1539950 1956140 2907580 FALSE TRUE 1792122.375 1717175.173 2029064.951 2054659.465 1716766.189 2064105.797 1390605.886 1537834.684 2563849.205 0.698996794 0.669764497 0.79141353 0.801396377 0.669604977 0.805080811 0.542389889 0.599814794 1 21.28987998 ILNDVQDRFEVNISELPDEIDISSYIEQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILNDVQDRFEVNISELPDEIDISSYIEQTR 30 1 Q13838-2;Q13838;A0A0G2JJZ9 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ; 247.36 4.78E-46 56221000 57304 53808 28820 22493.4 44743 56687 50685 58806 14111.3 FALSE TRUE 49731.13121 53454.53171 42757.4484 27600.87026 43852.70184 58867.78557 45769.5765 46230.79453 12443.07819 3.996690405 4.295925083 3.436243649 2.218170604 3.524264749 4.73096646 3.678316234 3.715382466 1 13.60305581 4.169121374 5.811247806 3.285635408 4.143543058 0.134038102 0.99457428 0.426449166 25.64229023 0.258580076 0.561220841 14761.19014 -4.169121374 0.857907651 ILNEDGSPNLDFKPEDQPHFDIKDEF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILNEDGSPNLDFKPEDQPHFDIKDEF 26 2 Q9UMX5 Q9UMX5 NENF Neudesin 0 ; 244.93 1.50E-45 160073000 296030 244890 256300 241800 233970 188160 329340 337290 234615 FALSE TRUE 256908.8855 243281.3015 380247.5373 296704.3857 229314.4548 195398.637 297400.6575 265163.1583 206879.082 1.241831136 1.175958918 1.838018294 1.434192297 1.108446792 0.944506497 1.437557894 1.281730157 1 17.65842825 3.249005856 24.6529925 1.181094642 1.43457003 0.262606666 0.220289329 275.3158672 649799.7441 0.066364722 0.084706776 1774.213403 -3.249005856 0.253475387 ILNFLMHPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILNFLMHPK 9 0 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;H0Y8X0;D6RDA2 H0Y993 DEK Protein DEK 0 92.062 0.01033 109460000 278040 385590 295250 374650 384820 334590 385320 428680 677120 FALSE TRUE 241296.3095 383057.0339 438033.8876 459720.0087 377162.8349 347461.8938 347951.7257 337010.118 597071.645 0.404132924 0.64155958 0.733637062 0.769957864 0.631687735 0.581943384 0.582763775 0.564438323 1 19.18754453 -2 0.035890146 1.622708343 6.73E-10 0.167227914 0.142940396 6397.500233 22.66716757 771.831733 338.4707128 0.01 2 -1.622708342 ILNHVLQHAEPGNAQSVLEAIDTYCEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILNHVLQHAEPGNAQSVLEAIDTYCEQK 28 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ; 319.63 2.89E-83 8387400000 2584900 2221800 1705320 1787200 2181670 1959510 2646600 3021100 2975800 FALSE TRUE 2243298.916 2207204.85 2530018.456 2193011.076 2138259.035 2034893.618 2389933.139 2375061.275 2624004.314 0.85491434 0.841159002 0.964182278 0.835749798 0.814883963 0.77549172 0.910796193 0.905128571 1 21.32333866 1.324883016 1.532887624 1.038779224 0.853011719 0.459117364 0.050413638 0.922321758 2.285316768 0.253779631 0.015274128 21.12919817 -1.324883016 -0.185767506 ILNHVLQHAEPGNAQSVLEAIDTYCEQKEWAMNVGDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILNHVLQHAEPGNAQSVLEAIDTYCEQKEWAMNVGDKK 38 2 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 73.765 0.00098344 382900000 193070 150260 67974 43862 107870 95155 238970 252540 19864 FALSE TRUE 167555.3103 149272.9322 100846.4538 53821.53749 105723.598 98815.67442 215794.7262 198536.2863 17515.70055 9.566006786 8.522235908 5.75748903 3.072759627 6.035933176 5.641548515 12.32007396 11.33476139 1 14.09636107 4.439339695 6.802700561 7.038307451 9.320923346 0.076290067 3.386344105 0.550411557 71.95711389 0.922408898 2.54402452 27500.44335 -4.439339695 2.282615895 ILPALCHDITDWVVGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILPALCHDITDWVVGTR 17 0 Q86Y56;H0Y650;Q86Y56-2;H7C3B1 Q86Y56 DNAAF5 "Dynein assembly factor 5, axonemal" 0 198.15 1.45E-11 100540000 101010 94518 71457 79957 113180 110880 92766 118080 110780 FALSE TRUE 87661.27257 93897.10503 106013.8442 98112.45892 110927.9394 115145.6253 83769.5676 92829.5109 97683.7146 0.897399049 0.96123602 1.085276544 1.004389107 1.135582731 1.178759692 0.857559194 0.95030693 1 16.57583044 2.218594557 24.9999158 0.935678814 1.044291597 0.253064085 0.087316349 356.9831473 446982.7429 0.037444287 0.025280965 165.4224914 -2.218594557 0.108612783 ILPEAHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ILPEAHQR 8 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ;;; 141.93 0.00062562 1199650000 1571430 1528390 1025300 1138330 1429820 1589610 1473080 1608510 1322760 FALSE TRUE 1363761.544 1518349.905 1521138.509 1396805.225 1401369.379 1650763.325 1330220.928 1264542.654 1166384.82 1.16922093 1.301757259 1.304148068 1.197550929 1.201464007 1.415281901 1.140464884 1.084155617 1 20.15361242 1.841067278 2.58971661 1.032637554 1.262382439 0.600674819 0.074605318 0.177679515 2.182283195 0.05291449 0.020232259 69.35332351 -1.841067278 0.229744886 ILPKPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILPKPTR 7 1 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ; 77.923 0.033501 3173100000 3133500 2856700 2025010 2676100 2832100 2632400 2968300 3206700 3965100 FALSE TRUE 2719400.036 2837934.15 3004311.609 3283749.407 2775746.751 2733670.131 2680434.723 2520972.16 3496350.395 0.777782467 0.811684708 0.859270745 0.939193455 0.793898333 0.781863893 0.7666379 0.721029609 1 21.73741834 ILPPGLLAYLESSDLVPEKDADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILPPGLLAYLESSDLVPEKDADR 23 1 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 ; 135.21 1.47E-05 131027000 290481 242000 176294 190555 235594 213451 294772 352291 180504 FALSE TRUE 252093.1999 240410.2861 261550.3681 233823.4252 230906.1403 221662.5981 266185.0568 276956.3112 159165.0228 1.583847981 1.510446717 1.643265358 1.46906287 1.45073419 1.392658979 1.672384122 1.740057623 1 17.28016381 3.714577351 24.1531269 1.494866946 1.572312718 0.05577066 0.199604854 2222.251706 2237990.575 0.055796653 0.082810782 5182.953961 -3.714577351 0.077445772 ILQEHEQIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILQEHEQIK 9 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 185.14 4.32E-05 632090000 1267840 1137160 794250 971040 1134490 1008780 1353690 1474900 1484900 FALSE TRUE 1100291.732 1129689.921 1178351.957 1191529.473 1111915.869 1047588.419 1222409.352 1159504.113 1309356.814 0.840329939 0.862782329 0.899947168 0.910011283 0.849207685 0.800078641 0.933595289 0.885552434 1 20.32042687 -0.706108714 1.075689864 9.993498919 0.86774629 0.542877476 0.037296628 90.43613645 1.947356844 1949.468645 0.011865949 0.196739374 0.706108714 -9.125752629 ILQGGVGIPHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILQGGVGIPHIR 12 0 P48729-2;A0A5F9W493;U3KPX3;A0A590UJ43;P48729;P48729-3;A0A590UK94;A0A590UJQ7;E5RG27;D6RGE5 P48729-2 CSNK1A1 Casein kinase I isoform alpha 0 95.018 0.0020803 0 85486 87559 55646 55330 77973 70101 70403 79469 68929 FALSE TRUE 74188.80851 86983.81916 82556.59172 67893.52217 76421.48985 72797.83083 63575.3279 62475.17278 60780.29214 1.220606316 1.431118807 1.358278955 1.11703185 1.257339956 1.197720976 1.045985889 1.027885365 1 15.89131599 2.436207192 0.549596914 0.932389685 1.349510235 0.690446945 0.078706964 0.746588294 0.503654341 0.197427213 0.083504561 273.0280024 -2.436207192 0.41712055 ILQHSHGIEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ILQHSHGIEEER 12 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 0 ;;; 172.92 1.99E-05 905963000 457589 380353 292628 327388 357464 402370 361600 447489 508621 FALSE TRUE 397117.4543 377854.4361 434143.8796 401726.4492 350351.1658 417849.4343 326532.0877 351796.9597 448492.4048 0.885449675 0.842499075 0.968007206 0.895726315 0.781175248 0.931675609 0.728066037 0.784398924 1 18.77472403 3.34823829 10.07118875 0.833082827 0.899429812 0.081610817 0.082876585 0.667317974 57.30366494 0.02363268 0.030509459 2229.658191 -3.34823829 0.066346985 ILQINKDDVTALHCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILQINKDDVTALHCK 15 1 O76094-2;O76094;R4GNC1;D6RDY6 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 ; 214.53 1.48E-12 1553270000 2769500 2363530 1734710 1884180 2322860 1860350 2992800 3283900 2059820 FALSE TRUE 2403503.558 2348003.816 2573621.558 2312011.867 2276639.631 1931918.868 2702558.717 2581663.54 1816310.426 1.323288973 1.292732664 1.416950275 1.272916696 1.253441921 1.063650156 1.487938778 1.421377923 1 20.79257936 3.598515101 16.76899474 1.274971898 1.340166944 0.066709078 0.14755683 7.23112651 968.9260568 0.042176194 0.062557372 3967.483242 -3.598515101 0.065195046 ILQLCMGNHELYMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ILQLCMGNHELYMR 14 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 240.59 2.10E-17 4978050000 2400570 2566500 1619387 2215378 2576270 2655410 2135653 2828440 2306026 FALSE TRUE 2083328.592 2549640.493 2402527.97 2718413.435 2525007.267 2757565.341 1928537.701 2223600.117 2033410.233 1.024549084 1.253874133 1.181526448 1.33687408 1.24175989 1.356128388 0.948425295 1.093532471 1 20.95546987 2.231732711 24.99984007 1.027826418 1.236280486 0.530042658 0.096635952 125.6027069 459879.286 0.037650339 0.026015015 170.5032695 -2.231732711 0.208454068 ILRPWQSSETR ddPTM_MDA-MB-175_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 ; 185.3 4.13E-06 4255900000 4326800 2986300 3241190 2790500 2772500 2798200 3168100 3439700 3110400 FALSE TRUE 3755002.417 2966682.799 4808640.325 3424125.675 2717332.674 2905848.565 2860858.15 2704146.923 2742692.055 1.369093701 1.081668207 1.753255644 1.248454295 0.990753836 1.059487724 1.043083982 0.985946241 1 21.38716122 3.382818137 4.590483566 1.017881665 1.388333223 0.546616091 0.16138403 0.1581863 5.842564532 0.045635466 0.059755012 2414.449557 -3.382818137 0.370451559 ILS(ph)DVTHSAVFGVPASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ILSDVTHSAVFGVPASK 17 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 ILS(0.687)DVT(0.312)HS(0.001)AVFGVPASK;ILS(0.991)DVT(0.009)HSAVFGVPASK;ILS(0.985)DVT(0.012)HS(0.002)AVFGVPASK 211.43 1.60E-12 531670000 1480280 1570360 1184110 1426080 1869640 1353500 1791030 2257890 2268860 TRUE FALSE 1284657.247 1560044.202 1756749.557 1749893.26 1832437.822 1405570.021 1617336.186 1775057.794 2000637.955 0.642123801 0.779773371 0.878094686 0.874667631 0.915926751 0.702560909 0.808410228 0.887245886 1 20.93202868 4.625658131 2.415847512 0.861530426 0.618457398 0.474241418 0.075800755 0.399940767 3.392933169 0.02018836 0.181471672 42233.60274 -4.625658131 -0.243073028 ILSDDVPIRDYR ddPTM_MDA-MB-175_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 69.451 0.045546 342580000 1132700 1044500 488080 511030 988070 1036200 958290 1102900 366680 FALSE TRUE 983010.8251 1037638.611 724117.1205 627067.1721 968409.3401 1076063.285 865355.1833 867053.4178 323331.5081 3.040256827 3.209209695 2.239550128 1.939393954 2.995097341 3.328049564 2.676371345 2.681623646 1 18.30265458 4.247451039 24.98790004 2.484336242 3.124733547 0.172952171 0.63446725 373.3384307 1049301.836 0.160598942 0.411509991 17678.72902 -4.247451039 0.640397305 ILSDVT(ph)HSAVFGVPASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILSDVTHSAVFGVPASK 17 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 ILS(0.431)DVT(0.551)HS(0.018)AVFGVPASK 123.55 0.00019575 869490000 1829700 1886600 1423800 1575700 2279000 1786900 2204200 2736400 2503600 TRUE FALSE 1587900.509 1874206.8 2112354.442 1933486.768 2233652.359 1855643.199 1990437.023 2151242.155 2207627.26 0.719279263 0.848968861 0.956843794 0.875821205 1.01178872 0.840560013 0.901618248 0.974458956 1 21.07406517 4.626443054 2.181412048 0.93626001 0.688432802 0.629132006 0.05392257 0.321987376 2.100036592 0.013851052 0.141185796 42310.00283 -4.626443054 -0.247827208 ILSGRPPLGFLNPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILSGRPPLGFLNPR 14 1 A0A2R8Y7U1;A0A2R8YGD1;A0A2R8YD45;O14773-2;O14773 A0A2R8Y7U1 TPP1 Tripeptidyl-peptidase 1 0 103.76 0.0010005 125720000 117590 106440 79025 83341 109690 115580 103220 107910 104510 FALSE TRUE 102050.1836 105740.7886 117241.7543 102264.8478 107507.3836 120026.4374 93209.74029 84834.28626 92154.94686 1.107376077 1.147423901 1.272224208 1.109705462 1.166593734 1.30244161 1.011445869 0.920561393 1 16.49177399 2.077790497 6.641341157 0.957873903 1.181862998 0.695638275 0.065123081 0.105233325 7.244395163 0.026255644 0.017560366 119.6163363 -2.077790497 0.223989096 ILSHGGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ILSHGGFR 8 0 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ;; 84.568 0.01736 4867110000 3248470 2746890 1735535 2260770 2703210 2801570 2350740 2669910 3282320 FALSE TRUE 2819176.459 2728845.499 2574845.531 2774112.382 2649421.41 2909348.211 2122765.597 2098970.524 2894287.869 0.974048397 0.942838315 0.889630074 0.958478392 0.915396647 1.005203471 0.73343278 0.725211388 1 21.46477699 2.238901965 24.99999994 0.796306443 0.943778608 0.344525526 0.081064138 8.569706164 627716.783 0.031105591 0.022580472 173.3412664 -2.238901965 0.147472165 ILSQS(ph)TDS(ph)LNMR ddPTM_MDA-MB-175_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 2 ILSQS(0.796)T(0.208)DS(0.996)LNMR;ILSQS(0.888)T(0.138)DS(0.974)LNMR 184.02 2.17E-05 192517000 602970 528580 432130 492740 498260 651640 553480 506160 664120 TRUE FALSE 523285.9868 525107.7232 641109.5134 604624.1481 488345.6008 676709.0125 499803.5948 397921.6229 585608.4902 0.893576503 0.896687347 1.094774963 1.032471623 0.833911408 1.155565576 0.853477371 0.679501117 1 19.15957694 2.015977538 24.91076216 0.801747187 0.982827136 0.210881126 0.123218583 254.5475609 396866.4209 0.04826611 0.032530714 103.7474756 -2.015977538 0.181079949 ILSQS(ph)TDSLNMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 19 ILSQSTDSLNMR 12 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 ILS(0.001)QS(0.702)T(0.297)DSLNMR;ILSQS(0.949)T(0.051)DSLNMR;ILSQS(0.642)T(0.358)DSLNMR;ILSQS(0.98)T(0.02)DSLNMR;ILSQS(0.994)T(0.006)DSLNMR;ILSQS(0.864)T(0.136)DSLNMR;ILSQS(0.993)T(0.007)DSLNMR;ILSQS(0.774)T(0.226)DSLNMR;ILSQS(0.869)T(0.13)DSLNMR;ILSQS(0.881)T(0.119)DSLNMR;ILSQS(0.595)T(0.405)DSLNMR;ILSQS(0.639)T(0.36)DSLNMR;ILSQS(0.921)T(0.079)DSLNMR;ILSQS(0.531)T(0.468)DS(0.001)LNMR;ILSQS(0.866)T(0.132)DS(0.003)LNMR;ILSQS(0.869)T(0.13)DSLNMR;ILSQS(0.644)T(0.354)DS(0.002)LNMR;ILSQS(0.933)T(0.065)DS(0.002)LNMR;ILS(0.002)QS(0.819)T(0.179)DSLNMR 333.15 3.27E-58 20782760000 15134820 15623450 10853250 12907750 14707280 17126620 14728230 15497750 14560070 TRUE FALSE 13134715.19 15520818.53 16101918 15838651.92 14414633.9 17785492.15 13299888.52 12183676.77 12838795.11 1.023048898 1.208899931 1.254161147 1.233655634 1.122740396 1.385292934 1.035914072 0.948973534 1 23.61400648 2.01880212 24.50276467 0.977322533 1.205169279 0.540242356 0.092466457 124.7685632 162596.5522 0.035966672 0.024243982 104.4244315 -2.01880212 0.227846747 ILSQST(ph)DSLNMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILSQSTDSLNMR 12 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 ILSQS(0.431)T(0.569)DSLNMR 248.99 8.02E-16 450070000 829000 889910 557810 628690 789830 870070 780310 851820 815870 TRUE FALSE 719445.5496 884064.1226 827568.7818 771443.6734 774113.9283 903542.1559 704635.6563 669664.9219 719418.778 1.000037213 1.228858837 1.150329693 1.072315176 1.076026859 1.255933517 0.979451298 0.930841594 1 19.45647229 2.10194923 8.696060374 0.95897245 1.130618697 0.499332293 0.075772504 0.190252588 14.58686749 0.029490504 0.019859813 126.4588507 -2.10194923 0.171646247 ILTDYGFEGHPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILTDYGFEGHPFR 13 0 O75489 O75489 NDUFS3 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial" 0 ; 133.71 0.00010402 770720000 766230 939420 680510 987240 1036290 1133810 850060 1029040 1147980 FALSE TRUE 664970.7641 933248.8882 1009606.912 1211407.931 1015669.856 1177428.404 767621.312 808987.804 1012267.112 0.656912347 0.921939355 0.997372037 1.19672754 1.003361508 1.163159793 0.758318929 0.799184123 1 19.9491586 2.217386666 24.99898183 0.837469088 0.997173622 0.141547796 0.15740829 422.6350559 498979.4307 0.065983896 0.044535349 164.9630457 -2.217386666 0.159704534 ILTEAEIDAHLVALAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ILTEAEIDAHLVALAER 17 0 G3V5Z7;P60900;P60900-2;P60900-3;H0YJC4 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ;;; 186.83 5.01E-10 148631000 256257 216065 185983 241239 244259 241951 215478 266313 595995 FALSE TRUE 222391.9882 214645.6548 275925.0009 296016.0021 239398.7238 251259.0115 194580.9767 209364.0374 525537.1501 0.423170823 0.408430983 0.525034245 0.563263705 0.455531495 0.478099429 0.370251612 0.398381042 1 19.00343323 1.235181331 24.99999208 1.000000763 0.451556193 0.89658484 0.058406179 31.95973915 236399.6519 0.112468274 0.015925708 17.18625815 -1.235181331 -0.54844457 ILTEAEIDAHLVALAERD ddPTM_MDA-MB-175_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 ;;;;;;;;;;; 263.08 1.14E-30 1983924100 1843828.3 1735415 1093333.1 1284692.6 1646207 1775865.8 1676536.8 1964482.8 1518388.8 FALSE TRUE 1600161.718 1724014.945 1622072.644 1576401.69 1613450.701 1844184.506 1513946.519 1544393.441 1338886.606 1.19514357 1.287648212 1.211508605 1.177397461 1.205068969 1.377401565 1.130750366 1.153490844 1 20.35260235 1.274448434 1.381229542 0.914737433 1.234997346 0.561721974 0.06485872 0.902645217 1.60101865 0.406602432 0.018973586 18.81258323 -1.274448434 0.320259913 ILTGDWFQEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILTGDWFQEAR 11 0 A0A087X1N4;Q8IYJ3-2;Q8IYJ3 A0A087X1N4 SYTL1 Synaptotagmin-like protein 1 0 79.659 0.061744 27423000 18736 18695 13302 10869 21839 19971 20037 21478 22783 FALSE TRUE 16259.99013 18572.19131 19734.89169 13336.97257 21404.44663 20739.29729 18093.81482 16885.09684 20089.61969 0.80937272 0.924467043 0.982342722 0.66387382 1.065448075 1.032338969 0.90065492 0.840488625 1 14.29416263 3.186349079 24.99999998 0.950066412 0.860491206 0.241545288 0.103942561 199.1000878 95332.40966 0.032549206 0.036907372 1535.850978 -3.186349079 -0.089575206 ILTQDTPEFFIDQGHAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILTQDTPEFFIDQGHAK 17 0 Q8TDL5 Q8TDL5 BPIFB1 BPI fold-containing family B member 1 0 ; 276.18 9.58E-36 916750000 1103030 1164300 778340 1035600 1215680 1096790 1049530 1595060 1284790 FALSE TRUE 957261.7908 1156651.637 1154747.827 1270748.808 1191490.346 1138984.221 947746.7421 1253968.832 1132903.59 0.844963154 1.020962107 1.019281639 1.121674271 1.051713806 1.005367298 0.836564338 1.106862793 1 20.11159366 4.738589313 8.205874983 1.022183793 0.843694327 0.339230668 0.076868452 0.108667259 99.70607531 0.01877075 0.107503205 54775.87369 -4.738589313 -0.178489466 ILTTEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILTTEGR 7 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 128.75 0.0086702 137980000 158840 155070 86137 106580 141280 157980 132120 150160 138640 FALSE TRUE 137848.8916 154051.335 127793.1413 130780.618 138468.8044 164057.5928 119307.0227 118049.4525 122250.1371 1.12759703 1.260132206 1.045341497 1.069778906 1.132667886 1.341982894 0.975925472 0.96563861 1 16.89947656 2.114672431 24.32806538 0.977181701 1.156611132 0.496969393 0.086327206 4.949078665 1025.773866 0.035461761 0.023908315 130.218423 -2.114672431 0.179429432 ILTVEDHYYEGGIGEAVSSAVVGEPGITVTHLAVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILTVEDHYYEGGIGEAVSSAVVGEPGITVTHLAVNR 36 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 136.48 2.45E-09 29388000 30041 36399 17698 13503 28511 25808 23637 21956 28767 FALSE TRUE 26071.00574 36159.89257 26256.812 16569.06253 27943.68688 26800.85046 21344.68738 17260.88026 25366.19803 1.027785311 1.425514873 1.035110266 0.653194559 1.101611162 1.056557645 0.841461829 0.680467772 1 14.63061968 4.00355762 24.22229731 0.877296712 1.227565885 0.394302342 0.172192133 67.2747032 458018.4679 0.044147335 0.09113396 10082.25366 -4.00355762 0.350269173 ILVATNLFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ILVATNLFGR 10 0 O00148;Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;H0Y400 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 77.662 0.075205 80589000 191650 231910 113080 122840 225210 291460 155430 195400 131180 FALSE TRUE 166322.9669 230386.5679 167765.8662 150732.6995 220728.7616 302672.6548 140356.4225 153615.2306 115672.0498 1.437883803 1.991722013 1.450357856 1.303103902 1.908229014 2.616644688 1.21339963 1.32802376 1 16.81968078 2.086753591 21.57666196 1.211364133 1.775316085 0.363376244 0.376103973 9.041266571 2244.228203 0.157559381 0.106226557 122.1106634 -2.086753591 0.563951951 ILVEDELSS(ph)PVVVFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ILVEDELSSPVVVFR 15 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q86XE2;Q6P996-2;Q6P474;Q6XYB5;Q6P996-4 H3BND4;Q6P996-4 PDXDC1;PDXDC2P Pyridoxal-dependent decarboxylase domain-containing protein 1;Putative pyridoxal-dependent decarboxylase domain-containing protein 2 1 ILVEDELS(0.004)S(0.996)PVVVFR;ILVEDELS(0.031)S(0.969)PVVVFR;ILVEDELS(0.2)S(0.8)PVVVFR;ILVEDELS(0.439)S(0.561)PVVVFR 220.85 1.69E-12 53734800 175864 179687 108671 160276 207132 194070 167426 222531 209810 TRUE FALSE 152623.1268 178506.6243 161224.6591 196669.1155 203010.4784 201535.9985 151189.0523 174944.4774 185006.5008 0.824960886 0.964866767 0.871454021 1.063038945 1.097315378 1.089345496 0.817209404 0.945612595 1 17.49721644 5.041864309 1.186658326 0.984863933 0.658933575 0.246124828 0.088909706 4.955774538 3.687810933 0.028374368 2.36139187 110119.5199 -5.041864309 -0.325930358 ILVLDDTNHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ILVLDDTNHER 11 0 K7EN66;C9K0L8;K7ERZ0;K7ERC4;P09543-2;P09543 K7EN66 CNP "2,3-cyclic-nucleotide 3-phosphodiesterase" 0 ;;;; 215.08 1.31E-11 1034674000 1223392 1209302 818224 1068102 1272620 1356940 1093402 1386920 1332590 FALSE TRUE 1061717.648 1201358.016 1213919.863 1310630.884 1247297.352 1409142.36 987364.0423 1090337.951 1175052.728 0.90354894 1.022386474 1.033076928 1.115380487 1.061482027 1.199216278 0.840272116 0.927905552 1 20.16429407 2.221166044 24.99886583 0.920369436 1.056254554 0.364447069 0.082850596 260.9198587 374982.0905 0.034081133 0.023035779 166.4048745 -2.221166044 0.135885118 ILVTLLHTLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILVTLLHTLER 11 0 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 ; 240.37 1.11E-15 2313700000 948390 957590 596180 726110 862140 922060 931520 1073220 988470 FALSE TRUE 823057.8586 951299.5282 884494.6421 890984.3734 844985.1007 957532.2449 841181.3338 843720.2548 871614.2027 0.944291472 1.091422702 1.014777684 1.022223331 0.969448522 1.098573477 0.965084473 0.967997369 1 19.73333018 ILWGNNHFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ILWGNNHFFR 10 0 Q9NQT8;E7ERX9;A0A1B0GUA8;Q9H1H9-3;Q9H1H9-4;Q9H1H9-2;Q9H1H9 Q9NQT8;A0A1B0GUA8 KIF13B;KIF13A Kinesin-like protein KIF13B;Kinesin-like protein;Kinesin-like protein KIF13A 0 ; 196.88 3.25E-07 878540000 661300 957340 547940 592200 898700 858510 763060 752370 861000 FALSE TRUE 573907.5295 951051.1705 812925.6167 726668.0612 880817.6283 891537.4352 689058.5586 591481.5304 759213.5609 0.755923707 1.252679377 1.070746966 0.957132615 1.160171095 1.174290715 0.907595167 0.779071346 1 19.53414624 2.095071241 6.666075271 0.86498608 1.06999101 0.220995989 0.145109766 0.251643314 14.89729107 0.056590519 0.037914139 124.4718776 -2.095071241 0.205004929 ILYSQCGDVMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ILYSQCGDVMR 11 0 F8VPF3;P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;P60660-2;G8JLA2;P14649;F8W1I5 F8VPF3;P60660;P60660-2;P14649 MYL6;MYL6B Myosin light polypeptide 6;Myosin light chain 6B 0 ;;; 223.87 1.54E-11 1512130000 563690 609290 393292 415447 530870 595780 517805 615830 568970 FALSE TRUE 489196.9383 605287.5339 583489.3267 509780.5911 520306.7256 618700.0421 467588.3508 484139.5469 501707.0148 0.975064976 1.206456191 1.163008109 1.016092213 1.037072854 1.233189937 0.931994844 0.964984608 1 18.93648558 2.209817068 24.999626 0.964116374 1.105240173 0.386284769 0.082874016 210.9283304 183452.8357 0.033012209 0.022261067 162.1127106 -2.209817068 0.141123799 IMADIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IMADIR 6 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 113.97 0.059748 11438500000 17439200 18691600 12001900 14161300 17413300 19621700 18263700 19330000 17638300 FALSE TRUE 15134565.53 18568813.65 17806058.98 17376839.61 17066809.4 20376559.5 16492489.19 15196429.93 15553120.27 0.973088697 1.193896358 1.144854452 1.117257458 1.097323823 1.310126788 1.060397457 0.977066316 1 23.89070071 2.004458759 24.99990254 0.996446067 1.143062464 0.361882504 0.083356658 118.4572829 664176.5344 0.032669864 0.021929406 101.0319555 -2.004458759 0.146616397 IMAT(ph)PEQVGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IMATPEQVGK 10 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 1 IMAT(1)PEQVGK;IMAT(1)PEQVGK 155.86 0.00013383 470160000 2036120 1886850 1216810 1541220 1855560 1550790 2021400 2317500 2018170 TRUE FALSE 1767041.583 1874455.158 1805263.386 1891177.557 1818637.986 1610449.895 1825364.939 1821920.66 1779584.242 0.992951916 1.05331072 1.014429856 1.062707521 1.021945432 0.904958505 1.025725502 1.023790061 1 20.7631088 2.983186249 24.94077239 0.993799422 1.032662106 0.214734022 0.038134666 1223.138475 1814349.158 0.012283125 0.012575559 962.0247587 -2.983186249 0.038862683 IMDPNIVGSEHYDVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 IMDPNIVGSEHYDVAR 16 0 P06576;H0YH81 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ;;;;;;;;;; 205.31 2.29E-11 9442000000 5226671 5607172 3202145 6367696 7045366 7657760 4917403 6145297 6120958 FALSE TRUE 4535953.185 5570338.118 4750713.033 7813578.701 6905177.001 7952358.982 4440514.014 4831173.059 5397345.318 0.84040448 1.03205146 0.880194383 1.447670705 1.279365428 1.473383397 0.822721866 0.895101717 1 22.36381856 2.184483863 24.99997924 0.90021509 1.159026183 0.238553349 0.212915361 140.3433661 64880.23844 0.091991565 0.062020755 152.9268922 -2.184483863 0.258811094 IMDYSLLLGIHDIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IMDYSLLLGIHDIIR 15 0 Q8TBX8;Q8TBX8-3;Q8TBX8-2;H0YIJ6 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 ; 209.41 2.40E-09 877173000 1489808 1497106 956207 1148694 1542644 1467734 1387510 1584037 1644770 FALSE TRUE 1292926.098 1487271.412 1418631.904 1409522.529 1511948.403 1524198.677 1252949.494 1245303.015 1450327.164 0.891472028 1.025473044 0.97814613 0.971865221 1.042487819 1.050934378 0.863908175 0.858635931 1 20.46794695 2.230078929 24.99908314 0.895514677 0.995414005 0.314659285 0.058816924 188.3554004 555156.7834 0.023431735 0.016082267 169.8552322 -2.230078929 0.099899328 IMEIVDAITTTAQSHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IMEIVDAITTTAQSHQR 17 0 A0A2R8Y891;P08237;P08237-3;P08237-2;F8VZI0 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 85.619 0.0049917 421830000 53825 50937 40526 36781 44900 64840 49742 66221 51650 FALSE TRUE 46711.88987 50602.39149 60124.50915 45132.68821 44006.57785 67334.43676 44918.0285 52060.15448 45543.99584 1.025643205 1.111066136 1.320141284 0.990969004 0.966243234 1.478448158 0.986255766 1.143073934 1 15.47497325 0.393229137 1.451999936 9.75E-09 1.133356857 0.054557628 0.162140316 40.49755303 11.07474219 121.0701652 0.044599952 2.473028588 -0.393229137 1.133356847 IMEVIDAITTTAQSHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IMEVIDAITTTAQSHQR 17 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 221.78 3.57E-15 471290000 267790 242990 140210 173810 231150 239740 235090 283500 216930 FALSE TRUE 232400.873 241393.7827 208016.025 213276.217 226550.5672 248962.9529 212291.008 222875.7312 191284.7825 1.214947002 1.261960201 1.087467713 1.114966984 1.18436273 1.301530366 1.109816501 1.165151395 1 17.54536258 0.557663933 1.388601444 0.239325441 1.184617109 0.418464163 0.06700016 7.603050921 3.103519593 16.28317253 0.019838338 3.611303035 -0.557663933 0.945291668 IMGIPEEEQMGLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IMGIPEEEQMGLLR 14 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 124.12 0.00023008 32915000 58579 59863 38049 53228 58334 53794 57788 64513 54761 FALSE TRUE 50837.63673 59469.75601 56449.62367 65314.23094 57173.26753 55863.48999 52183.72865 50717.39699 48287.21696 1.052817701 1.231583838 1.169038665 1.352619493 1.184024906 1.15690018 1.080694476 1.050327606 1 15.5593537 2.161709495 1.567488742 1.021532783 1.206122827 0.491682464 0.073398245 0.336759034 1.617247607 0.055563505 0.023994797 145.1140607 -2.161709495 0.184590044 IMGPNYT(ph)PGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IMGPNYTPGKK 11 1 P13639 P13639 EEF2 Elongation factor 2 1 IMGPNYT(1)PGKK 100.11 0.0025036 395600000 463920 350140 314960 391100 371960 271650 467620 514150 645460 TRUE FALSE 402611.7966 347839.9073 467275.7095 479905.2326 364558.7237 282100.5513 422270.2844 404203.0236 569154.4541 0.707385831 0.611152043 0.820999829 0.843189804 0.640526875 0.4956485 0.741925643 0.710181605 1 19.11846069 1.212907305 3.756801512 1.049239679 0.694094301 0.476011751 0.100096165 0.304907516 6.580309661 0.315708423 0.026781563 16.32703428 -1.212907305 -0.355145378 IMGPNYTPGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IMGPNYTPGKK 11 1 P13639 P13639 EEF2 Elongation factor 2 0 ; 128.28 0.00043141 1336080000 2204300 1843420 1257120 1568940 1850240 1470910 2290900 2538100 1468870 FALSE TRUE 1912996.17 1831310.453 1865067.437 1925191.807 1813423.844 1527496.86 2068728.871 1995347.067 1295221.862 1.476964083 1.413897114 1.439959818 1.48637995 1.400087427 1.179332209 1.597200396 1.540544616 1 20.30476781 3.015848005 20.30644476 1.376545359 1.449495805 0.079049075 0.169881326 109.0058137 139661.8807 0.052592799 0.059579342 1037.165363 -3.015848005 0.072950446 IMHFPTWVDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IMHFPTWVDLK 11 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ; 151.15 3.36E-05 207044000 582130 506880 426520 562120 474150 421170 516030 654150 1158580 FALSE TRUE 505200.0456 503550.2719 632786.4986 689757.9375 464715.3427 437372.6824 465985.49 514265.1131 1021613.992 0.494511674 0.492896804 0.619398817 0.675164928 0.454883494 0.428119315 0.45612677 0.503384955 1 19.96241876 1.237720028 24.96923775 1.000000574 0.515099696 0.799780143 0.076174253 9.774760732 290174.8666 0.119358797 0.020340831 17.28701578 -1.237720028 -0.484900877 IMKDILEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IMKDILEK 8 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 108.67 0.0034351 7185900000 19641600 16338300 8066400 8994500 14804000 11371500 24264800 26864600 2274900 FALSE TRUE 17045912.79 16230972.63 11967338.02 11036838.7 14509429.36 11808968.96 21911603.43 21119814.35 2005963.914 8.497616871 8.091358235 5.965879017 5.502012585 7.233145754 5.886929911 10.92322912 10.52851161 1 20.93586422 4.458164727 24.15416299 7.216818847 8.396053837 0.030631907 2.781650585 676.9316742 862537.3776 0.716056568 1.895258088 28718.69671 -4.458164727 1.17923499 IMKKVS(ph)MEPSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IMKKVSMEPSER 12 2 Q5VZK9;Q5VZK9-2;Q5VZK9-3;A0A0U1RR91 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 IMKKVS(0.999)MEPS(0.001)ER 50.207 0.078098 86416000 172130 144320 58924 80991 107820 123100 139670 149620 58775 TRUE FALSE 149382.5844 143371.9524 87419.84349 99381.24442 105674.5929 127835.7367 126124.8249 117624.9273 51826.68646 2.882348739 2.766373122 1.68677277 1.917568944 2.0389996 2.466600614 2.433588437 2.269582244 1 15.66140754 4.317458446 7.443819392 2.043220147 2.842108283 0.403344232 0.424116414 0.246869108 19.63859741 0.106895662 0.285235167 20771.04977 -4.317458446 0.798888136 IMLFTNEDNPHGNDSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IMLFTNEDNPHGNDSAK 17 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;;; 218.43 4.65E-15 1374080000 1769215 1385709 953379 1177802 1322081 1088792 1610085 2006890 1480807 FALSE TRUE 1535408.755 1376606.186 1414436.273 1445239.946 1295774.175 1130678.533 1453939.205 1577732.191 1305747.683 1.175884725 1.054266612 1.083238585 1.106829416 0.992361841 0.865924211 1.113491698 1.208297906 1 20.31644471 2.023418517 24.99916742 1.131587777 1.043817868 0.068407615 0.094615562 428.9938418 457947.3849 0.039539013 0.026655806 105.5403467 -2.023418517 -0.087769909 IMMEFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IMMEFER 7 0 O43633;M0R1L7;M0R1T5 O43633 CHMP2A Charged multivesicular body protein 2a 0 ;; 107.59 0.017314 354310000 590550 760710 461685 529240 725030 765820 643550 796180 756520 FALSE TRUE 512507.3212 755712.8459 684957.4102 649412.0309 710603.3215 795281.591 581138.6201 625923.1029 667085.0674 0.768278809 1.132858286 1.0267917 0.973507072 1.065236439 1.192174177 0.871161188 0.938295779 1 19.34751122 IMNVIGEPIDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IMNVIGEPIDER 12 0 P06576;H0YH81;F8W079 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ;;; 196.88 4.69E-07 451674000 694400 695910 494954 855170 848950 953910 629760 810820 811520 FALSE TRUE 602633.2806 691338.5214 734315.4099 1049349.419 832057.5559 990607.535 568685.9721 637432.4528 715583.0301 0.842157032 0.966119224 1.026177787 1.466425802 1.162768709 1.384336259 0.794716963 0.890787548 1 19.44875965 2.215975876 24.99786831 0.890070047 1.143884005 0.274574795 0.18852613 321.8128631 356195.0861 0.08115335 0.05475735 164.4280384 -2.215975876 0.253813958 IMQIHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IMQIHSR 7 0 P17980;E9PM69;R4GNH3 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ;; 143.94 0.0023875 898064000 1261110 1304000 777419 850012 1235320 1378550 1261665 1309680 1034364 FALSE TRUE 1094451.118 1295433.938 1153381.429 1043020.216 1210739.549 1431583.711 1139308.922 1029615.124 912082.6663 1.199947284 1.420303209 1.264557996 1.143558862 1.327444971 1.56957671 1.249129015 1.128861628 1 19.79880506 1.628468886 2.589500656 1.018367229 1.31949154 0.452545024 0.117775359 0.232911743 3.441790281 0.123329643 0.033070707 42.50782518 -1.628468886 0.301124312 IMRPTDVPDQGLLCDLLWSDPDKDVLGWGENDR ddPTM_MDA-MB-175_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 0 225.57 1.59E-36 187930000 139010 96133 74707 87809 87489 87948 110810 127440 114330 FALSE TRUE 120639.4763 95501.49599 110835.5551 107747.3755 85748.14007 91331.41647 100063.6633 100187.9477 100814.0376 1.196653553 0.947303552 1.099405972 1.068773536 0.850557542 0.905939476 0.992556846 0.993789655 1 16.62133701 7.999999999 0.79929472 0.970696599 50.93214376 0.432458057 0.074068899 547.0177136 1.907405222 0.027184316 49480.2728 99999999.81 -7.999999999 49.96144716 IMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDR ddPTM_MDA-MB-175_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 ; 257.08 1.38E-59 1676890000 1552730 1357260 1023140 1122540 1241290 1100760 1445910 1639750 1533380 FALSE TRUE 1347532.796 1348344.07 1517933.926 1377429.864 1216590.758 1143106.949 1305685.871 1289102.223 1352105.563 0.99661804 0.997218047 1.122644539 1.018729529 0.899774981 0.845427295 0.965668588 0.953403535 1 20.36677636 3.347915105 5.885189135 0.933850002 1.040057576 0.473533106 0.05311676 0.193565966 9.321926844 0.016249816 0.021017845 2227.999583 -3.347915105 0.106207573 IMRPTDVPDTGLLCDLLWSDPDKDVQGWGENDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IMRPTDVPDTGLLCDLLWSDPDKDVQGWGENDR 33 2 P62140 P62140 PPP1CB Serine/threonine-protein phosphatase PP1-beta catalytic subunit 0 145.16 2.00E-10 486180000 272870 226560 141720 169450 187460 159900 220790 282440 232980 FALSE TRUE 236809.5381 225071.7124 210256.266 207926.2124 183729.9128 166051.4565 199377.8198 222042.404 205437.3698 1.152709161 1.095573374 1.023456766 1.012114848 0.894335402 0.808282625 0.970504149 1.08082772 1 17.64833911 4.215128282 1.522835217 0.964155135 1.155784197 0.480066534 0.071428727 0.541300197 2.161669634 0.024718262 0.117542249 16410.74442 -4.215128282 0.191629061 IMSS(ph)IGEGIDFSQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IMSSIGEGIDFSQER 15 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 IMS(0.011)S(0.989)IGEGIDFSQER;IMS(0.028)S(0.972)IGEGIDFSQER;IMS(0.003)S(0.997)IGEGIDFSQER;IMS(0.006)S(0.994)IGEGIDFSQER;IMSS(1)IGEGIDFSQER;IMS(0.004)S(0.996)IGEGIDFSQER 382.56 4.10E-100 734799000 1154291 1044522 729123 688252 987654 1200204 1013507 1013907 1151621 TRUE FALSE 1001748.52 1037660.466 1081729.322 844530.1359 968001.6177 1246376.625 915217.2471 797090.8783 1015477.677 0.986480099 1.021844684 1.065241852 0.831658002 0.95324756 1.227379639 0.901267716 0.784941802 1 19.9537271 2.020142316 24.98768772 0.866908029 1.010758129 0.196159601 0.110765992 308.3577244 382533.689 0.045143991 0.03043258 104.7471743 -2.020142316 0.1438501 IMT(ph)IIEPVS(ph)KK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IMTIIEPVSKK 11 1 A0A1B0GUF7;A0A1B0GVH7 A0A1B0GUF7 2 IMT(1)IIEPVS(1)KK 58.752 0.093268 171700000 110100 111290 47188 79544 109960 97651 121980 138680 126100 TRUE FALSE 95550.00604 110558.9287 70008.27463 97605.68095 107772.0111 101407.6972 110150.3984 109024.3612 111192.6017 0.859319816 0.994301123 0.629612704 0.877807332 0.969237247 0.9120004 0.990627045 0.980500137 1 16.76270127 3.3326888 4.467978312 0.970393825 0.831556589 0.347340069 0.090263489 0.244194549 8.639484155 0.026238168 0.03397595 2151.23968 -3.3326888 -0.138837237 IMTYLFDFPHGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IMTYLFDFPHGPK 13 0 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ; 161.1 4.27E-05 504190000 559470 529200 572410 842960 618810 512590 601410 750440 1619990 FALSE TRUE 485534.622 525723.6504 849229.3906 1034366.952 606496.8917 532309.669 543085.3508 589964.2459 1428476.628 0.339896791 0.368030978 0.594500025 0.724104918 0.424575999 0.372641497 0.380184975 0.413002379 1 20.446046 1.235953335 24.98874281 1.000000728 0.453888949 0.676265621 0.119125692 46.7849464 448303.3936 0.209956354 0.031616889 17.2168357 -1.235953335 -0.546111779 IMVGS(ph)TDDPSVFSLPDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IMVGSTDDPSVFSLPDSK 18 0 O43741 O43741 PRKAB2 5-AMP-activated protein kinase subunit beta-2 1 IMVGS(0.961)T(0.039)DDPSVFSLPDSK 157.74 8.49E-09 57968000 270490 203800 140890 153160 153290 134310 214680 248070 223080 TRUE FALSE 234744.0612 202461.2244 209024.8752 187937.3189 150239.8289 139476.9926 193860.3666 195022.161 196707.7365 1.19336466 1.029248915 1.062616443 0.955413967 0.763771835 0.709056975 0.985524871 0.991431066 1 17.58569417 3.756915219 2.594824632 0.898647642 1.10101852 0.45405888 0.102807805 0.31403416 4.178084715 0.033175891 0.061329382 5713.670865 -3.756915219 0.202370879 IMVQSAS(ph)PDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IMVQSASPDIR 11 0 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 IMVQSAS(1)PDIR;IMVQS(0.008)AS(0.992)PDIR;IMVQS(0.027)AS(0.973)PDIR 157.2 3.22E-05 785451000 827630 894590 449290 555470 762170 757730 633620 762400 681920 TRUE FALSE 718256.5986 888713.3794 666568.1468 681597.9533 747004.3082 786880.3634 572171.6299 599366.693 601304.1944 1.194497902 1.477976351 1.108537331 1.133532677 1.242306831 1.308622775 0.951551037 0.996777835 1 19.1977355 2.234221624 24.99924158 0.984392181 1.243580681 0.594114182 0.101874333 76.07464908 438299.6576 0.041051495 0.028767787 171.4832178 -2.234221624 0.2591885 IMYTVFEHTFHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IMYTVFEHTFHVR 13 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 210.79 1.57E-08 1314380000 740360 654060 402410 478270 557820 559370 577080 603460 552280 FALSE TRUE 642519.5502 649763.4368 597016.822 586868.5134 546720.4734 580889.3259 521114.8704 474414.7751 486990.0876 1.319368847 1.33424366 1.225932185 1.205093345 1.122652159 1.192815502 1.070072849 0.974177478 1 18.89353288 0.225988743 0.101396646 1.49E-07 1.774193033 0.899645725 0.038484748 40.9203382 0.739430782 11.96282503 3.360690305 1.682630446 -0.225988743 1.774192884 INAGMLAQFIDKPVCFVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 INAGMLAQFIDKPVCFVGR 19 1 P35244 P35244 RPA3 Replication protein A 14 kDa subunit 0 85.937 0.0026966 243630000 78120 62798 43620 57561 54076 64803 84824 102110 81301 FALSE TRUE 67796.24407 62385.4758 64714.7779 70631.10481 52999.9934 67296.01334 76597.78154 80274.57112 71689.6884 0.945690316 0.870215469 0.902706921 0.98523381 0.739297305 0.938712594 1.068463028 1.119750593 1 16.129478 2.305313016 4.199231046 1.075994041 0.889450401 0.562898336 0.069581549 0.138135395 4.795594834 0.026648514 0.0196649 201.9821618 -2.305313016 -0.18654364 INEGLEHLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 INEGLEHLAK 10 0 Q99747;J3QS28;J3QKW4 Q99747 NAPG Gamma-soluble NSF attachment protein 0 126.19 0.00038905 147260000 832490 812430 522980 675360 720860 655090 769290 1024200 1668300 FALSE TRUE 722474.3372 807093.0938 775894.8773 828710.8102 706516.2963 680291.7362 694684.3742 805182.8003 1471075.475 0.49111983 0.548641526 0.527433766 0.563336705 0.480271957 0.462445162 0.472228914 0.547342957 1 20.48843984 1.23685183 4.472692255 1.04290846 0.508684354 0.95720965 0.03255948 0.040919944 1.70084028 0.069930202 0.008857298 17.25249182 -1.23685183 -0.534224107 INEKPQVIADYESGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 INEKPQVIADYESGR 15 1 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 ;;; 173.58 8.77E-07 3743000000 2740290 2354980 1552380 2023850 2373020 1994680 2747330 3385680 2726980 FALSE TRUE 2378153.733 2339509.981 2303116.16 2483396.075 2325801.545 2071416.63 2480894.359 2661678.679 2404599.531 0.989001995 0.972931231 0.957796145 1.032769092 0.967230308 0.861439339 1.031728705 1.106911419 1 21.19736521 2.012777506 24.9998055 1.063560606 0.965308288 0.385539088 0.04937227 194.8766418 381284.1558 0.020000905 0.01347508 102.9858377 -2.012777506 -0.098252318 INETDTFGPGDDDEIQFDDIGDDDEDIDDI ddPTM_MDA-MB-175_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 ; 173.07 9.93E-13 43401000 140896 128717 95882 108185 131805 114283 129263 149566 141047 FALSE TRUE 122276.2366 127871.4496 142250.8559 132750.0578 129182.3384 118679.541 116727.0942 117582.4748 124372.5843 0.983144616 1.028132126 1.143747689 1.067357878 1.03867214 0.954225898 0.938527528 0.945405094 1 16.92430898 2.806601868 3.726236533 0.954834862 1.05916411 0.537783162 0.042718404 0.180867906 4.958837629 0.015131293 0.014846643 640.622028 -2.806601868 0.104329248 INFDKYHPGYFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 INFDKYHPGYFGK 13 1 P46776;E9PLL6 P46776 RPL27A 60S ribosomal protein L27a 0 ; 118.52 0.00025291 3281800000 13457100 11689100 4167200 4652000 10233100 9297000 13355000 15255000 710160 FALSE TRUE 11678710.14 11612313.53 6182471.858 5708307.701 10029481.33 9654661.606 12059834.16 11992836.96 626205.6938 18.6499584 18.54392837 9.872909045 9.115707119 16.01627298 15.4177161 19.25858272 19.15159361 1 19.2562771 1.230464421 24.99965148 0.999973081 15.77068146 0.619496174 3.633708346 231.3771366 714394.8191 10.7366354 0.987580192 17.00060674 -1.230464421 14.77070838 INFS(ph)DLDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 126.21 0.00050333 147307000 417603 448600 410746 338652 423870 397584 377496 468000 414050 TRUE FALSE 362415.7055 445653.1171 609384.1395 415548.1126 415435.8163 412879.3138 340886.496 367921.842 365101.4807 0.992643757 1.220628074 1.669081534 1.138171535 1.137863959 1.130861789 0.933676016 1.00772487 1 18.47793799 2.856584103 1.44691602 0.989384553 1.281894043 0.312229631 0.172149843 0.475425289 2.049318067 0.078281339 0.074529284 718.7603354 -2.856584103 0.29250949 INGDWQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 INGDWQR 7 0 P42704 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 98.457 0.026169 220040000 372690 380630 284020 428580 438020 404250 356070 441000 437010 FALSE TRUE 323438.0722 378129.6165 421373.022 525895.6394 429304.259 419801.7591 321538.3862 346695.5819 385347.1756 0.839342008 0.981269983 1.093489322 1.364732046 1.114071378 1.089411797 0.834412204 0.899696699 1 18.55579929 2.25353141 24.11812829 0.905731234 1.090932451 0.254822941 0.135336422 205.9142111 331729.7892 0.054236113 0.041818011 179.2798212 -2.25353141 0.185201217 INGEAQPWLSTSTEGLKIPMTPTSSFVSPPPPTAS(ph)PHSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 INGEAQPWLSTSTEGLKIPMTPTSSFVSPPPPTASPHSNR 40 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 INGEAQPWLSTSTEGLKIPMTPTSSFVSPPPPT(0.126)AS(0.834)PHS(0.039)NR 105.6 6.81E-06 454150000 404580 382910 176830 226030 373470 343110 428670 536910 79679 TRUE FALSE 351113.7279 380394.639 262345.5795 277353.5662 366038.6777 356309.6637 387097.6494 422095.9747 70259.43939 4.997388692 5.414142815 3.733954921 3.94756304 5.20981495 5.071342254 5.509546514 6.007676383 1 16.10040444 INHEGEVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 INHEGEVNR 9 0 Q09028-3;Q09028;Q09028-2;Q09028-4;Q16576;E9PC52;Q16576-2;Q5JP01 Q09028-3;Q16576 RBBP4;RBBP7 Histone-binding protein RBBP4;Histone-binding protein RBBP7 0 ;;;; 148.94 8.88E-05 4582521000 3127265 2644450 1800696 1748759 2466182 2615880 2510494 2761698 2589679 FALSE TRUE 2713989.007 2627078.434 2671518.609 2145841.459 2417109.803 2716514.596 2267026.678 2171130.374 2283530.099 1.188505905 1.15044616 1.169907333 0.939703602 1.058497019 1.189611907 0.992772847 0.950778085 1 21.12283438 8 0.140279041 0.872359235 2.003505743 0.414573692 0.075218255 171.1258061 2.059023971 1.672310463 38.15565995 99999999.99 -8 1.131146509 INHTVILDDPFDDPPDLLIPDRS(ph)PEPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 INHTVILDDPFDDPPDLLIPDRSPEPTR 28 1 Q8WUA2 Q8WUA2 PPIL4 Peptidyl-prolyl cis-trans isomerase-like 4 1 INHTVILDDPFDDPPDLLIPDRS(1)PEPTR;INHTVILDDPFDDPPDLLIPDRS(0.99)PEPT(0.01)R;INHTVILDDPFDDPPDLLIPDRS(0.974)PEPT(0.026)R;INHTVILDDPFDDPPDLLIPDRS(0.999)PEPT(0.001)R;INHTVILDDPFDDPPDLLIPDRS(0.919)PEPT(0.081)R;INHTVILDDPFDDPPDLLIPDRS(0.958)PEPT(0.042)R;INHTVILDDPFDDPPDLLIPDRS(0.974)PEPT(0.026)R;INHTVILDDPFDDPPDLLIPDRS(1)PEPTR;INHTVILDDPFDDPPDLLIPDRS(0.995)PEPT(0.005)R 302.55 6.87E-72 4222437000 822721 747507 454729 567639 677906 728115 607379 795752 738454 TRUE FALSE 713996.3353 742596.5773 674637.4654 696530.1108 664416.9969 756126.0552 548475.4781 625586.6273 651154.8094 1.096507812 1.140430151 1.036063092 1.069684353 1.02036718 1.161207818 0.842311951 0.960734096 1 19.31264105 2.242364854 24.99999515 0.936010781 1.083605724 0.614230367 0.057112143 63.03702083 414259.4974 0.021341786 0.015889948 174.7289448 -2.242364854 0.147594943 INHTVILDDPFDDPPDLLIPDRS(ph)PEPTREQLDSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 INHTVILDDPFDDPPDLLIPDRSPEPTREQLDSGR 35 2 Q8WUA2 Q8WUA2 PPIL4 Peptidyl-prolyl cis-trans isomerase-like 4 1 INHTVILDDPFDDPPDLLIPDRS(0.785)PEPT(0.155)REQLDS(0.06)GR;INHTVILDDPFDDPPDLLIPDRS(0.986)PEPT(0.014)REQLDS(0.001)GR 234.86 1.65E-47 127348000 29459.4 41556 7624.9 13363.3 29524.4 26940.2 33755.2 31386.1 1076.1 TRUE FALSE 25566.26565 41283.0159 11312.32714 16397.64151 28936.9222 27976.60693 30481.6259 24674.42676 948.8846839 26.94349069 43.50688403 11.92170907 17.28096342 30.4957206 29.48367426 32.12363569 26.00360948 1 9.89008896 1.240849133 5.835210183 7.97E-09 27.37044103 0.489911653 8.419137512 0.120827057 14.65211465 13.20368869 2.114893101 17.41201901 -1.240849133 27.37044102 INISEGNCPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 INISEGNCPER 11 0 F8VZX2;F8W1G6;F8W0G4;P57721;P57721-4;E9PFP8;P57721-5;P57721-3;P57721-2;F8VTZ0;J3QT27;F8VXH9;Q15366;Q15366-6;Q15366-2;Q15366-3;Q15366-5;Q15366-4;Q15366-8;Q15366-7;Q15365 F8VZX2;Q15366;Q15366-2;Q15366-5;Q15365 PCBP2;PCBP3;PCBP1 Poly(rC)-binding protein 3;Poly(rC)-binding protein 2;Poly(rC)-binding protein 1 0 ; 194.12 1.52E-06 1114530000 569690 505940 299560 333750 505530 439320 437400 503350 561720 FALSE TRUE 494404.0231 502616.4468 444428.218 409533.0385 495470.9421 456220.9247 394981.0153 395712.5196 495314.1015 0.998162624 1.014742858 0.897265425 0.826814818 1.000316649 0.921073968 0.797435434 0.798912283 1 18.91798417 4.826549315 0.625450426 0.868038941 1.135624271 0.219878265 0.076065797 5.41354346 1.529989444 0.041054813 1.071402439 67073.24455 -4.826549315 0.26758533 INLAEDVLAWEHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 INLAEDVLAWEHER 14 0 K7EQ66;K7ELZ9;K7ENM2;A0A0C4DGP7;K7EMW4;Q969V3-2;Q969V3 K7EQ66 NCLN Nicalin 0 ; 146.16 8.38E-06 77272000 41118 33504 22971.7 39058 44574 44398 29465.8 49335 48333 FALSE TRUE 35684.15212 33283.91002 34080.89096 47926.71586 43687.06461 46106.01979 26608.21125 38785.09418 42619.1278 0.837280206 0.780961783 0.799661859 1.124535352 1.025057688 1.081815189 0.62432557 0.910039604 1 15.37921345 INLWHLEITDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 INLWHLEITDR 11 0 P63151;P63151-2;A0A590UJY3;A0A590UJJ1;Q66LE6 P63151 PPP2R2A;PPP2R2D Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform;Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform 0 122.39 0.00039173 401630000 445940 440070 278290 343640 428090 567490 348740 430330 450920 FALSE TRUE 387007.8991 437179.1512 412871.9748 421668.7142 419571.8465 589321.7075 314919.2485 338307.2783 397612.7513 0.973328692 1.099509887 1.038377098 1.060500985 1.055227342 1.48214992 0.792025023 0.850846149 1 18.6010045 INMAHLCVIGSHAVNGVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 INMAHLCVIGSHAVNGVAR 19 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 144.01 8.07E-08 862680000 489830 395590 308060 328780 391700 385580 373670 428440 417580 FALSE TRUE 425097.7244 392991.3432 457038.8464 403434.5241 383905.9363 400413.5121 337431.5409 336821.4401 368214.1681 1.154484974 1.067290119 1.241231017 1.095651822 1.042615873 1.087447325 0.91640021 0.914743292 1 18.49018561 2.62320902 1.184110001 0.932595923 1.141478339 0.649032658 0.059053678 0.274640876 0.812454903 0.036283617 0.02511211 419.9610569 -2.62320902 0.208882416 INPPSSGGTSS(ph)SPIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 INPPSSGGTSSSPIK 15 0 A0A0C4DG88;P14859-4;P14859-5;P14859-3;P14859;P14859-2;P14859-6;A0A0A0MT46 A0A0C4DG88 POU2F1 "POU domain protein;POU domain, class 2, transcription factor 1" 1 INPPSSGGTS(0.002)S(0.499)S(0.499)PIK 131.61 5.51E-05 979140000 452470 381050 276530 328520 368280 320220 436260 554090 521990 TRUE FALSE 392674.9431 378546.8575 410260.8329 403115.4871 360951.9485 332539.0706 393951.5723 435602.1654 460280.9369 0.853120153 0.822425669 0.891327014 0.875803134 0.784199213 0.722469787 0.85589374 0.946383242 1 18.81215517 1.67521143 2.905527866 0.989622752 0.826003358 0.622855675 0.047751821 0.154550238 2.943511273 0.044300084 0.014139606 47.33816618 -1.67521143 -0.163619394 INPPSSGGTSSS(ph)PIK ddPTM_MDA-MB-175_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 INPPSS(0.003)GGT(0.043)S(0.039)S(0.17)S(0.744)PIK;INPPSSGGTS(0.001)S(0.05)S(0.949)PIK;INPPSSGGTSS(0.068)S(0.932)PIK 240.41 8.08E-18 1695140000 1369270 1124860 836680 966420 1205020 898330 1322230 1569550 1499910 TRUE FALSE 1188317.5 1117470.721 1241301.247 1185860.432 1181042.46 932889.3364 1194000.338 1233913.947 1322592.349 0.898476013 0.84490941 0.93853654 0.896618246 0.892975421 0.70534911 0.902772755 0.93295107 1 20.33493703 1.566552108 2.448135842 0.993869225 0.865633712 0.327183226 0.062777041 0.352057809 4.304154439 0.079938298 0.017487594 36.85972643 -1.566552108 -0.128235513 INPVCPADLVIDHSIQVDFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 INPVCPADLVIDHSIQVDFNR 21 0 P21399 P21399 ACO1 Cytoplasmic aconitate hydratase 0 148.91 1.75E-09 0 68466 62551 49290 60448 76627 73104 76235 81150 76191 FALSE TRUE 59418.04463 62140.09836 73126.80887 74173.64229 75102.27262 75916.35818 68841.74143 63796.70401 67183.78678 0.884410473 0.924927 1.088459171 1.104040809 1.117863047 1.129980339 1.024677898 0.949584819 1 16.03582549 4.333134856 5.136536034 1.053614159 0.895407197 0.566447725 0.056390883 0.179879064 7.540033914 0.017314146 0.047971933 21534.50315 -4.333134856 -0.158206962 INPYMS(ph)SPCHIEMILTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.5)S(0.5)PCHIEMILTEK 196.81 1.23E-15 416402000 758080 694510 434099 477872 647250 581700 791640 817890 633580 TRUE FALSE 657897.8073 689947.7181 644030.7284 586380.1414 634370.9913 604078.3754 714866.8746 642990.5883 558678.8942 1.177595599 1.234962919 1.152774402 1.049583486 1.135484082 1.081262209 1.279566639 1.150912617 1 19.09165979 4.054869026 6.70284159 1.127234346 1.204477245 0.18890699 0.074410018 0.384370809 36.12472779 0.019505553 0.041010908 11346.68572 -4.054869026 0.077242899 INPYMSSPCHIEMILTEK ddPTM_MDA-MB-175_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 0 145.91 8.76E-08 430210000 480900 481410 149380 321590 490820 465160 598790 652630 477910 FALSE TRUE 417347.8466 478247.586 221620.6676 394611.9247 481053.6423 483055.0062 540719.438 513070.1533 421412.0242 0.99035581 1.13486934 0.5259002 0.936404046 1.141528041 1.146277226 1.283113454 1.217502406 1 18.68487195 3.248936649 4.211938395 1.176934178 0.882676015 0.379132503 0.16617314 0.208759484 8.520670632 0.050686231 0.062730471 1773.930699 -3.248936649 -0.294258163 INS(ph)SPNVNTTASGVEDLNIIQVTIPDDDNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 INSSPNVNTTASGVEDLNIIQVTIPDDDNER 31 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 INS(0.54)S(0.405)PNVNT(0.022)T(0.029)AS(0.004)GVEDLNIIQVTIPDDDNER;INS(0.42)S(0.42)PNVNT(0.073)T(0.073)AS(0.013)GVEDLNIIQVTIPDDDNER;INS(0.347)S(0.347)PNVNT(0.093)T(0.093)AS(0.121)GVEDLNIIQVTIPDDDNER;INS(0.565)S(0.424)PNVNT(0.004)T(0.006)ASGVEDLNIIQVTIPDDDNER 174.32 1.96E-13 264455000 369282 312438 215393 241727 299636 327140 303270 353971 388855 TRUE FALSE 320480.4481 310385.5742 319557.7752 296614.8099 293673.8298 339725.2875 273858.9221 278277.0563 342885.0049 0.934658686 0.905217696 0.931967775 0.865056231 0.856479069 0.990784906 0.798690284 0.811575462 1 18.38736529 3.739970314 24.4665704 0.87674983 0.922075017 0.049486292 0.066352278 247.3845681 4293509.158 0.018129128 0.029380814 5495.033113 -3.739970314 0.045325188 INSTATPDQDRDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 INSTATPDQDRDK 13 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 113.65 0.00073402 289290000 177000 146730 116870 130500 134180 141910 150580 199630 155930 FALSE TRUE 153609.0015 145766.121 173388.7229 160132.0196 131510.0805 147369.3695 135976.7748 156940.678 137496.133 1.117187794 1.060147058 1.261044359 1.164629259 0.956463848 1.071807376 0.988949811 1.14141885 1 17.06903152 3.268539664 24.99878752 1.044234912 1.152158416 0.407514129 0.070413551 230.4647297 192177.4132 0.020378518 0.026305268 1855.836295 -3.268539664 0.107923504 INVNEIFYDLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 INVNEIFYDLVR 12 0 F5H823;B7ZB78;F5GZG1;P61224-2;P61224-4;P61224-3;P62834;P61224;A6NIZ1 F5H823 RAP1B;RAP1A Ras-related protein Rap-1b;Ras-related protein Rap-1A;Ras-related protein Rap-1b-like protein 0 112.13 0.0030419 87771000 131540 153040 126940 131540 144560 141170 162790 182150 167910 FALSE TRUE 114156.6557 152034.6702 188328.6086 161408.1675 141683.5388 146600.9012 147002.6509 143198.64 148059.8711 0.771016852 1.02684589 1.271976041 1.090154721 0.956934096 0.990146082 0.992859509 0.967167126 1 17.17582115 3.233630699 24.99517743 0.980933677 1.055628748 0.048222046 0.12073235 347.4571052 1761640.668 0.037397822 0.043755334 1712.500468 -3.233630699 0.074695071 INVYYNEATGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 INVYYNEATGGK 12 0 P68371 P68371 TUBB4B Tubulin beta-4B chain 0 ; 208.42 0.00011613 285570000 800430 776250 506670 657040 721060 646450 852970 957470 906800 FALSE TRUE 694651.1475 771150.7626 751697.3067 806230.9742 706712.3167 671319.3498 770249.1007 752722.4915 799599.137 0.868749246 0.964421704 0.940092694 1.008293952 0.883833266 0.839569878 0.963294062 0.941374817 1 19.60891739 1.183716542 1.657283958 1.034318716 0.9247036 0.189089898 0.049723586 2.246362937 5.042375362 0.419396959 0.014329299 15.26569364 -1.183716542 -0.109615116 INYTEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 148.04 0.0049102 4801280000 5752700 5060130 3278960 3898280 4854640 5118630 4827120 5114900 4898080 FALSE TRUE 4992466.12 5026889.673 4864676.023 4783444.055 4758042.162 5315547.008 4358986.645 4021118.439 4319034.562 1.15592178 1.163891976 1.126334127 1.107526228 1.101644845 1.23072574 1.009250235 0.931022519 1 22.04227743 2.077247054 6.230713671 0.963259858 1.143017282 0.802919927 0.039496026 0.077671917 4.898075697 0.015991468 0.010659143 119.4667514 -2.077247054 0.179757424 IPASSNSTS(ph)S(ph)KLTHINNSRVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IPASSNSTSSKLTHINNSRVPK 22 2 Q4FZB7 Q4FZB7 SUV420H1 Histone-lysine N-methyltransferase SUV420H1 2 IPASSNS(0.001)T(0.002)S(0.537)S(0.563)KLT(0.537)HINNS(0.36)RVPK 54.259 0.055199 6844800000 3124600 3190400 2019000 2998200 3350400 3389800 2877400 3642800 8909000 TRUE FALSE 2711676.193 3169442.052 2995395.153 3678987.135 3283733.595 3520207.799 2598350.191 2863815.568 7855788.169 0.345181939 0.403453095 0.381297852 0.468315471 0.4180018 0.448103707 0.330756142 0.364548471 1 22.9053246 1.236808246 24.99983397 1.000000754 0.395034477 0.951685007 0.042843288 9.447860216 134745.4211 0.06868525 0.010997688 17.25076049 -1.236808246 -0.604966277 IPCES(ph)PPLEVVDTTASTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IPCESPPLEVVDTTASTK 18 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 IPCES(1)PPLEVVDTTASTK 108.56 0.00046904 0 73093 80241 56834 83991 72254 57188 73018 79290 103980 TRUE FALSE 63433.57486 79713.89159 84319.1125 103062.4403 70816.28676 59388.05937 65936.7256 62334.45054 91687.60285 0.691844621 0.869407522 0.919634824 1.124060801 0.772364906 0.647721802 0.719145485 0.679856912 1 16.48443906 3.025232294 24.99993861 0.741034342 0.906269501 0.187040856 0.139419734 324.2223739 321234.4093 0.042202352 0.047851384 1059.820447 -3.025232294 0.16523516 IPDEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IPDEELR 7 0 Q99961-3;Q99961-2;Q99961;Q99962 Q99961-3 SH3GL1;SH3GL2 Endophilin-A2;Endophilin-A1 0 ; 124.59 0.0096111 815880000 565830 604810 466100 452430 585930 502100 557540 619010 582890 FALSE TRUE 491054.1319 600836.9633 691507.519 555161.1465 574271.1394 521416.1119 503469.8566 486639.5286 513981.4082 0.95539279 1.168985791 1.345394032 1.08011912 1.11729944 1.014464927 0.979548771 0.946803758 1 18.97135665 2.744857014 1.686115405 0.96770359 1.154777718 0.375560773 0.095845961 0.365332342 2.085959091 0.041873106 0.037007743 555.7212626 -2.744857014 0.187074128 IPDEINDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IPDEINDR 8 0 C9J363;Q9BUL8;C9J6F3;C9J5C3;H7C5M9;C9JSA3;C9JND6 C9J363 PDCD10 Programmed cell death protein 10 0 ; 112.41 0.0070868 620810000 313270 350480 211475 269760 284830 313690 315050 317460 367420 FALSE TRUE 271870.5758 348177.6738 313745.0173 331013.131 279162.4403 325757.8573 284496.4995 249573.6495 323984.0262 0.839148087 1.074675434 0.968396563 1.021695838 0.861654951 1.005475057 0.878118909 0.77032702 1 18.30556316 2.121864285 6.122830211 0.856111535 0.965102451 0.129859577 0.089174615 0.28800785 14.30752655 0.034897744 0.023349983 132.3927749 -2.121864285 0.108990916 IPDWFLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IPDWFLNR 8 0 P62269;J3JS69 P62269 RPS18 40S ribosomal protein S18 0 ; 133.79 0.0021038 5710000000 1834460 2127200 1308540 1389620 1939180 1989740 1892850 2007280 1884130 FALSE TRUE 1592031.463 2113226.283 1941354.321 1705154.46 1900594.112 2066286.585 1709281.698 1578038.793 1661390.298 0.958252534 1.271962576 1.168511892 1.026341891 1.143978097 1.243709313 1.028826099 0.949830269 1 20.6639596 2.035980829 8.906679555 0.976624401 1.13860581 0.358311026 0.091986099 0.26851744 61.70504958 0.036324735 0.024345852 108.6377667 -2.035980829 0.161981409 IPEFNWSQMHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IPEFNWSQMHQR 12 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 135.02 0.00013516 2350880000 2559550 2621500 1295820 1511890 2569400 2835200 2992400 3120200 1121500 FALSE TRUE 2221298.982 2604279.194 1922482.886 1855187.732 2518273.967 2944271.979 2702197.509 2452969.511 988917.5476 2.246192302 2.633464438 1.944027478 1.875978171 2.546495381 2.977267403 2.732480089 2.480459081 1 19.91549071 3.197526226 24.99970527 2.424362027 2.191174982 0.012437834 0.558429362 608.4191465 370669.7591 0.173012939 0.196179955 1575.891185 -3.197526226 -0.233187045 IPEINSSDMSAHVT(ph)SPSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IPEINSSDMSAHVTSPSGR 19 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 1 IPEINSSDMS(0.001)AHVT(0.537)S(0.37)PS(0.092)GR 109.03 0.0029443 141240000 87627 91315 40145 68567 92030 102930 88256 88311 122970 TRUE FALSE 76046.86993 90715.14575 59559.25628 84136.18533 90198.78305 106889.7837 79696.9467 69426.37989 108432.6267 0.701328302 0.836603784 0.549274311 0.775930528 0.831841723 0.985771414 0.734990465 0.640272047 1 16.72643939 3.489688768 24.33180444 0.81251531 0.701952318 0.196179048 0.125901867 880.0575756 1703866.218 0.036605154 0.051334937 3088.081602 -3.489688768 -0.110562992 IPEINSSDMSAHVTS(ph)PSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IPEINSSDMSAHVTSPSGR 19 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 1 IPEINSSDMSAHVT(0.147)S(0.839)PS(0.014)GR;IPEINSSDMSAHVT(0.386)S(0.61)PS(0.004)GR 111.27 0.00014139 759110000 246140 297980 146206 214951 265440 305530 239550 300720 336170 TRUE FALSE 213611.9754 296022.5498 216911.7106 263758.9099 260158.2633 317283.9368 216318.4779 236413.3682 296428.3656 0.720619213 0.998630982 0.731750857 0.889789711 0.877642944 1.070356193 0.729749589 0.797539627 1 18.17732398 IPEISIQDMTAQVTS(ph)PSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IPEISIQDMTAQVTSPSGK 19 0 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 1 IPEISIQDMTAQVT(0.021)S(0.977)PS(0.002)GK 149.47 1.88E-08 0 88876 79074 58240 79813 73394 61812 85970 103420 173420 TRUE FALSE 77130.81142 78554.55769 86405.0588 97935.76152 71933.60299 64189.94764 77632.64263 81304.43782 152918.4852 0.504391679 0.51370217 0.565039987 0.64044423 0.470404889 0.419765783 0.50767337 0.531684824 1 17.22240329 1.238151394 6.387965605 1.014508112 0.518568649 0.874800029 0.057193617 0.043859107 7.979153349 0.094553356 0.015219197 17.30419474 -1.238151394 -0.495939462 IPGEETDTIQHMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IPGEETDTIQHMR 13 0 P50416;P50416-2 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 ;;;; 238.2 9.08E-17 1274620000 459713 494836 374252 488858 645869 660570 463673 702166 765395 FALSE TRUE 398960.7623 491585.3897 555241.519 599860.6806 633017.4705 685982.5553 418706.0638 552013.2652 674910.875 0.591131032 0.728370823 0.822688653 0.888799844 0.937927501 1.016404655 0.620387194 0.817905424 1 19.36433747 4.513210628 1.763148934 0.865148056 0.561518055 0.423528634 0.110328398 0.628849785 2.765056121 0.031658481 0.276595334 32599.47669 -4.513210628 -0.303630001 IPGGNIYIS(ph)PLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IPGGNIYISPLK 12 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 IPGGNIYIS(1)PLK;IPGGNIYIS(1)PLK 119.01 0.00059083 537430000 526250 434470 335350 516590 449160 323970 433850 568070 1084990 TRUE FALSE 456704.7292 431615.938 497526.3817 633889.6551 440222.5948 336433.3355 391775.2938 446592.6512 956723.7182 0.477363235 0.451139582 0.520031407 0.662562914 0.460135551 0.351651505 0.409496792 0.466793749 1 19.86774284 1.238106562 24.9996995 1.000000594 0.473671247 0.809733904 0.079991898 5.038394318 277099.1013 0.121334398 0.021193782 17.30240854 -1.238106562 -0.526329347 IPGGNIYIS(ph)PLKSPYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IPGGNIYISPLKSPYK 16 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 IPGGNIYIS(1)PLKSPYK;IPGGNIYIS(1)PLKSPYK 103.27 0.00087946 1464920000 2449800 2102070 1413080 1849720 2262490 1337340 2853400 3373800 2195580 TRUE FALSE 2126052.723 2088261.364 2096450.214 2269727.197 2217470.875 1388788.335 2576677.707 2652339.125 1936021.034 1.098155798 1.07863568 1.082865412 1.172367013 1.145375405 0.717341553 1.330914108 1.369994994 1 20.8846632 IPGLLS(ph)PHPLLQLSYTATDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IPGLLSPHPLLQLSYTATDR 20 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 IPGLLS(1)PHPLLQLSYTATDR 109.41 0.00012742 226280000 105220 118910 49668 97437 126730 149810 120840 139150 118950 TRUE FALSE 91314.91041 118128.8724 73687.61093 119561.5601 124208.3209 155573.2876 109120.9554 109393.8554 104887.8665 0.870595555 1.126239634 0.702537037 1.139898866 1.184201043 1.483234361 1.040358232 1.042960058 1 16.67848827 3.540011455 23.91894598 1.146706104 0.922232052 0.327560465 0.166934535 187.1506043 71177.65036 0.047176189 0.069973492 3467.459965 -3.540011455 -0.224474052 IPGLLSPHPLLQLSYTATDR ddPTM_MDA-MB-175_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 ;; 251.7 4.64E-36 38965120000 3059323 3054388 1862185 2490681 3657340 3898100 3460407 3887656 3467761 FALSE TRUE 2655025.714 3034323.524 2762743.895 3056228.189 3584566.089 4048062.429 3124817.262 3056311.018 3057806.245 0.868277942 0.992320403 0.903505217 0.999483925 1.172267241 1.323845301 1.021914736 0.999511013 1 21.54406556 3.455193914 5.794237201 1.095299268 0.931449518 0.409399711 0.100191707 0.2024774 21.77791218 0.032219344 0.042991969 2852.29154 -3.455193914 -0.16384975 IPGTPGAGGRLS(ph)PENNQVLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IPGTPGAGGRLSPENNQVLTK 21 1 Q16514-2;Q16514 Q16514-2 TAF12 Transcription initiation factor TFIID subunit 12 1 IPGT(0.003)PGAGGRLS(0.997)PENNQVLTK;IPGTPGAGGRLS(1)PENNQVLTK;IPGT(0.001)PGAGGRLS(0.999)PENNQVLTK;IPGTPGAGGRLS(1)PENNQVLTK 190.35 1.11E-17 4344380000 3490140 2996950 1513760 1935430 2789190 2378100 3209740 3865250 1352390 TRUE FALSE 3028909.156 2977262.838 2245819.399 2374898.963 2733690.576 2469587.046 2898459.909 3038696.367 1192511.995 2.539940201 2.496631355 1.883267765 1.991509497 2.292379941 2.070911703 2.430549899 2.548147423 1 20.18557235 4.312825802 8.738383981 2.108176345 2.523560017 0.167815065 0.425027024 0.573950671 60.84297192 0.103857913 0.275747069 20550.66133 -4.312825802 0.415383672 IPIFSAAGLPHNEIAAQICR ddPTM_MDA-MB-175_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 ; 164.59 1.79E-11 809940000 321670 287070 127753 174180 275854 268846 242876 265180 261947 FALSE TRUE 279160.4945 285184.2183 189534.7781 213730.2312 270365.0451 279188.6796 219321.9229 208473.3206 230979.9241 1.208592026 1.234671019 0.82056819 0.925319514 1.170513179 1.20871405 0.949528076 0.902560348 1 17.81740794 4.270651837 24.99911327 0.997030324 1.221631976 0.390643136 0.116770238 220.0154241 171388.9517 0.031825473 0.084187621 18648.84061 -4.270651837 0.224601651 IPIHNEDITYDELVLMMQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IPIHNEDITYDELVLMMQR 19 0 Q92734-2;Q92734;Q92734-4;Q92734-3;C9JTY3;C9JUE0;C9JJP5 Q92734-2 TFG Protein TFG 0 ;; 174.02 5.30E-12 542340000 287753 275961 216907 259164 249303 325366 234766 270880 479153 FALSE TRUE 249725.712 274148.194 321803.9507 318011.1473 244342.3581 337883.0406 211998.4295 212954.42 422508.0782 0.591055473 0.648859059 0.761651593 0.752674715 0.57831405 0.799707883 0.501761837 0.504024493 1 18.6886194 2.246709567 24.99959416 0.627358421 0.688103956 0 0.154522205 772.9620917 2371320.874 0.057540966 0.043791947 176.4857184 -2.246709567 0.060745535 IPLNLDGPHPS(ph)PPTPDSVGQLHIMDYNETHHEHS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IPLNLDGPHPSPPTPDSVGQLHIMDYNETHHEHS 34 0 A0A2R8YFV7;A0A2R8Y5N2;A0A2R8Y5S3;Q92574-2;Q92574;A0A2R8Y6S1 A0A2R8YFV7 TSC1 Hamartin 1 IPLNLDGPHPS(0.842)PPT(0.158)PDSVGQLHIMDYNETHHEHS 207.61 8.05E-28 269320000 109440 86606 66500 64216 78844 114160 83853 109340 101840 TRUE FALSE 94977.22671 86037.07948 98659.62243 78797.22428 77275.15866 118551.8091 75720.94897 85958.49188 89800.59122 1.057645896 0.958090346 1.098652259 0.877468881 0.860519487 1.320167356 0.843212143 0.957215211 1 16.45443732 6.359912945 0.015193729 0.358905442 1.705027106 0.006803624 0.140201246 60087.67739 135.0452969 5316.764371 6724.998996 2290408.489 -6.359912945 1.346121664 IPMPPS(ph)SPQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IPMPPSSPQPR 11 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 IPMPPS(0.591)S(0.409)PQPR;IPMPPS(0.562)S(0.438)PQPR 105.03 0.0026436 698880000 327380 455040 268510 432580 567950 538270 466980 543410 493770 TRUE FALSE 284115.9035 452050.8123 398362.3341 530803.9006 556648.9062 558977.5952 421692.3515 427206.0003 435397.0731 0.652544358 1.038249543 0.914940312 1.219126019 1.278485641 1.283834067 0.968523625 0.98118712 1 18.73197218 5.135751853 1.304950811 1.099428261 3.50E-13 0.532479452 0.129791375 3.15402181 2.352147361 0.041363159 5.927417098 136694.7555 -5.135751853 -1.099428261 IPMPPSS(ph)PQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IPMPPSSPQPR 11 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 IPMPPS(0.218)S(0.782)PQPR;IPMPPS(0.261)S(0.739)PQPR;IPMPPS(0.4)S(0.6)PQPR;IPMPPS(0.104)S(0.896)PQPR 143.24 3.91E-05 2595800000 955980 1213990 741760 1097440 1441130 1506490 1310260 1411920 1312790 TRUE FALSE 829644.8209 1206015.22 1100477.617 1346630.525 1412454.333 1564445.645 1183191.187 1109991.896 1157593.462 0.716697915 1.041829675 0.950659842 1.163301772 1.220164401 1.351463788 1.02211288 0.958878857 1 20.14269725 5.232534788 1.206272927 1.101280409 3.58E-12 0.485671864 0.123110385 4.474628643 2.444040402 0.04051898 8.227726742 170818.4543 -5.232534788 -1.101280409 IPMTPTSSFVSPPPPT(ph)ASPHSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IPMTPTSSFVSPPPPTASPHSNR 23 0 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 IPMTPTSSFVSPPPPT(0.734)AS(0.253)PHS(0.013)NR 153.82 1.32E-07 913630000 71630 70716 72920 81993 87878 80327 49507 89793 176170 TRUE FALSE 62163.91401 70251.46194 108184.3559 100610.7638 86129.39973 83417.23167 44705.81876 70591.46572 155343.3833 0.400170981 0.452233371 0.696420753 0.647666876 0.554445242 0.536986062 0.287787081 0.454422095 1 17.24510127 1.23516461 24.99895725 1.000000693 0.502858214 0.638411263 0.117365134 70.17020202 516458.1 0.222862901 0.031528783 17.18559646 -1.23516461 -0.497142479 IPMTPTSSFVSPPPPTAS(ph)PHSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 IPMTPTSSFVSPPPPTASPHSNR 23 0 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 IPMTPTSSFVSPPPPT(0.017)AS(0.966)PHS(0.017)NR;IPMTPTSSFVSPPPPT(0.114)AS(0.883)PHS(0.003)NR;IPMTPTSSFVSPPPPT(0.086)AS(0.899)PHS(0.014)NR;IPMTPTSSFVS(0.001)PPPPT(0.213)AS(0.532)PHS(0.254)NR;IPMTPTSSFVSPPPPT(0.157)AS(0.698)PHS(0.145)NR;IPMTPTSSFVSPPPPT(0.364)AS(0.594)PHS(0.043)NR;IPMTPTSSFVSPPPPT(0.288)AS(0.695)PHS(0.017)NR;IPMTPTSSFVSPPPPT(0.273)AS(0.68)PHS(0.047)NR;IPMTPTSSFVSPPPPTAS(0.993)PHS(0.006)NR 189.12 1.24E-17 7023580000 1014764 990305 764281 1105719 1077925 1098094 917624 1136567 2299189 TRUE FALSE 880660.3663 983799.6212 1133889.848 1356789.399 1056476.401 1140338.387 828632.9657 893520.9918 2027381.496 0.434383153 0.485256289 0.559287855 0.669232407 0.521103899 0.562468578 0.40872079 0.440726619 1 20.95118616 1.233628325 24.99998224 1.00000075 0.509845578 0.803846238 0.07604644 73.26374991 371303.1204 0.164668716 0.020436219 17.12491107 -1.233628325 -0.490155173 IPNFWVTTFVNHPQVSALLGEEDEEALHYLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IPNFWVTTFVNHPQVSALLGEEDEEALHYLTR 32 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 0 ;;; 388.08 2.09E-166 12488306000 2408360 1766064.5 1170126.3 1425109.6 1552185.9 1644708.6 1682910 2074510.2 1726823.4 FALSE TRUE 2090089.124 1754463.106 1736003.293 1748702.516 1521300.437 1707981.604 1519701.647 1630892.338 1522680.305 1.372638181 1.152220266 1.14009703 1.148437075 0.99909379 1.121694159 0.998043806 1.071066811 1 20.53818164 8 0.534388035 1.03858556 13.89540726 0.811890562 0.04832076 51.26060105 0.50472072 0.024648995 750.4644536 99999999.97 -8 12.8568217 IPNPDFFEDLEPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IPNPDFFEDLEPFR 14 0 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 ; 95.401 0.0088007 40161000 15530.6 13174.6 12381.6 16949 17454.9 17632.9 10756.8 21399.4 28204.3 FALSE TRUE 13478.19186 13088.05519 18369.38317 20797.5295 17107.58164 18311.24907 9713.607192 16823.30484 24870.01978 0.541945361 0.526258334 0.738615543 0.836249013 0.687879696 0.736278026 0.390574968 0.676449194 1 14.60212003 -1.999991168 0.03479037 1.668001712 1.23E-06 0.119762284 0.159443947 7780.407381 26.7391451 953.5653357 428.8162452 0.010000203 1.999991168 -1.668000478 IPNSYEVLFPES(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IPNSYEVLFPESPAR 15 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 IPNSYEVLFPES(1)PAR;IPNSYEVLFPES(1)PAR;IPNSYEVLFPES(1)PAR 175.39 9.01E-07 183436000 131002 127414 85297 93235 114100.3 116716 105079 118448 139267 TRUE FALSE 113689.7538 126577.009 126546.9145 114405.4318 111829.9273 121206.14 94888.45475 93118.81696 122803.0139 0.925789605 1.030732105 1.030487042 0.931617459 0.91064481 0.98699646 0.772688322 0.758277944 1 16.90598644 2.246654121 24.99983192 0.822911481 0.970558376 0.365366235 0.076487492 159.4863273 492634.6904 0.029126793 0.022158541 176.4631879 -2.246654121 0.147646894 IPNYQLS(ph)PTKLPSINK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IPNYQLSPTKLPSINK 16 1 O60934;A0A0C4DG07 O60934 NBN Nibrin 1 IPNYQLS(0.997)PT(0.003)KLPSINK 200.99 2.07E-11 1433500000 3603800 2429800 1828900 2182900 2519600 1694200 2938800 3807700 2891100 TRUE FALSE 3127548.699 2413838.484 2713362.157 2678560.809 2469464.89 1759376.97 2653795.628 2993452.987 2549317.452 1.226818063 0.946856768 1.064348481 1.050697239 0.968676886 0.690136479 1.040982804 1.17421743 1 21.2816796 4.747797804 23.79693701 1.002457035 1.226818299 0.257344937 0.124242684 1044.513576 2690770.583 0.032957245 0.385026289 55949.70538 -4.747797804 0.224361263 IPPNATLVFEVELFEFKGEDLTEEEDGGIIRR ddPTM_MDA-MB-175_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 ;; 263.4 9.82E-60 530502000 239153 168901 128051.9 101631.3 149544 127920.1 280808 274779 12265.2 FALSE TRUE 207548.3251 167791.4782 189978.2271 124708.24 146568.367 132841.269 253575.2834 216019.6492 10815.22203 19.19038967 15.51438128 17.5658185 11.5308072 13.5520442 12.28280554 23.4461468 19.97366754 1 13.40077566 1.23123637 24.9936714 0.999972285 16.71074269 0.642675652 3.662713629 185.8144046 634028.1468 9.852140743 0.978478136 17.03085179 -1.23123637 15.71077041 IPPYHYIHVLDQNSNVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IPPYHYIHVLDQNSNVSR 18 0 Q14764;H3BQK6;H3BP76;H3BRL2;H3BNF6;H3BUK7;H3BQE7;H3BUP3;H3BNF2;H3BPZ2 Q14764 MVP Major vault protein 0 183.23 3.72E-14 351130000 379150 259590 362910 261260 198060 212100 314540 300960 248260 FALSE TRUE 329044.3669 257884.7362 538414.4899 320583.0761 194118.9935 220259.6242 284035.9592 236602.0461 218910.9856 1.50309664 1.178034695 2.459513342 1.464444898 0.886748525 1.006160671 1.297495228 1.080813945 1 17.73998483 3.44396504 7.378094902 1.080384304 1.709325191 0.458780542 0.330768102 0.177025984 30.75541803 0.09438904 0.123144569 2779.489517 -3.44396504 0.628940888 IPRPLS(ph)LIGSTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IPRPLSLIGSTLR 13 1 H7C0I3;A0A2R8YD85;Q96BY6-3;Q96BY6 H7C0I3 DOCK10 Dedicator of cytokinesis protein 10 1 IPRPLS(1)LIGSTLR;IPRPLS(1)LIGSTLR;IPRPLS(0.999)LIGSTLR 118.23 0.00026871 1055468000 205699 247189 251510 189574 248975 285858 230798 245886 253291 TRUE FALSE 178515.356 245565.1992 373141.0773 232619.6742 244020.8846 296855.1422 208415.2455 193305.1924 223347.2265 0.799272768 1.099477271 1.670677013 1.04151584 1.09256286 1.329119447 0.933144542 0.865491797 1 17.76892881 2.166039775 9.076570313 0.917424139 1.181727857 0.200668725 0.223888641 0.4644037 53.44198425 0.092179268 0.062140023 146.5682071 -2.166039775 0.264303718 IPRPLS(ph)PTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IPRPLSPTK 9 1 Q13625-2;Q13625;Q13625-3 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 IPRPLS(0.806)PT(0.194)K;IPRPLS(0.985)PT(0.015)K;IPRPLS(0.814)PT(0.186)K 112.64 0.0011683 1085470000 2726740 2769650 1895180 2216270 2862370 2535100 3178530 3708180 3114360 TRUE FALSE 2366394.4 2751455.987 2811695.387 2719507.977 2805414.437 2632626.937 2870276.65 2915214.564 2746183.909 0.861702813 1.001919783 1.023855459 0.990286182 1.021568304 0.958649175 1.045187338 1.061551105 1 21.38899681 4.739875991 3.75334058 1.017572451 0.84522258 0.736765729 0.028443278 0.143204716 3.865557487 0.007589801 0.068733851 54938.39791 -4.739875991 -0.172349871 IPRPSVSQGCS(ph)R ddPTM_MDA-MB-175_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 88.536 0.0060141 627930000 396960 309330 183250 232580 324310 312660 327910 401900 261390 TRUE FALSE 344500.7302 307297.9909 271870.3129 285390.8438 317856.8655 324688.2325 296109.3387 315956.8126 230488.772 1.494652981 1.333244948 1.179538207 1.238198465 1.379055747 1.408694357 1.284701793 1.370812165 1 17.81433695 1.234347316 24.98977715 0.999999512 1.330896843 0.587263263 0.088457764 95.75805194 567879.0464 0.167352233 0.022127584 17.1532855 -1.234347316 0.330897332 IPS(ph)PIGFTPGPQQLLGDPFQGMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IPSPIGFTPGPQQLLGDPFQGMR 23 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B0QYZ7;H7C0J7 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 IPS(0.999)PIGFT(0.001)PGPQQLLGDPFQGMR;IPS(0.998)PIGFT(0.002)PGPQQLLGDPFQGMR 142.04 1.14E-07 537450000 374164 333552 215099 270335 349501 329420 333730 371250 354970 TRUE FALSE 324717.2794 331360.8749 319121.5959 331718.6936 342546.6139 342093.0006 301364.916 291861.0766 313005.851 1.037416005 1.058641153 1.019538756 1.059784322 1.09437767 1.092928453 0.96280921 0.932446073 1 18.2558301 2.225037932 24.84180222 0.95819042 1.060018222 0.724918637 0.027582604 107.0004251 196563.0651 0.01176824 0.007984419 167.8950653 -2.225037932 0.101827802 IPS(ph)PNILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IPSPNILK 8 0 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 IPS(1)PNILK;IPS(1)PNILK;IPS(1)PNILK;IPS(1)PNILK;IPS(1)PNILK;IPS(1)PNILK 117.02 0.0022646 2776060000 7048530 5430070 3526556 4256300 5193190 4419900 5738490 6933480 5479780 TRUE FALSE 6117048.902 5394399.513 5232010.277 5222757.968 5089855.679 4589936.413 5181972.123 5450809.258 4831966.651 1.265954288 1.116398333 1.082791057 1.080876245 1.053371442 0.949910615 1.072435407 1.128072616 1 22.20417907 5.496272496 1.001972825 1.052769479 1.940000787 0.675931688 0.04733057 4.964381916 1.334143201 0.015964332 6.813752371 313525.231 -5.496272496 0.887231308 IPSIVS(ph)SPLNSPLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IPSIVSSPLNSPLDR 15 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 IPSIVS(0.743)S(0.257)PLNSPLDR 173.03 1.04E-06 38318000 45387 46007 35058 46118 44414 41029 38370 52797 86604 TRUE FALSE 39388.99295 45704.77699 52012.16606 56589.79677 43530.24829 42607.41218 34648.88331 41506.77242 76365.77378 0.515793804 0.598498185 0.681092635 0.741036121 0.570023011 0.55793859 0.453722677 0.543525854 1 16.22063856 1.23533818 24.99949015 1.000000575 0.582167295 0.725980243 0.080569769 54.61615626 423636.654 0.153021483 0.021956295 17.19246625 -1.23533818 -0.41783328 IPSIVSS(ph)PLNSPLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IPSIVSSPLNSPLDR 15 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 IPSIVS(0.127)S(0.873)PLNSPLDR;IPSIVS(0.038)S(0.962)PLNSPLDR;IPSIVS(0.007)S(0.993)PLNSPLDR 252.17 1.28E-24 268372000 312715 293320 211477 279857 288100 311551 274674 322843 543868 TRUE FALSE 271388.9204 291393.1616 313747.9845 343402.8092 282367.3737 323536.5686 248036.1578 253805.5368 479572.5446 0.565897534 0.607610183 0.654224242 0.716060194 0.588789698 0.674635302 0.517202581 0.529232834 1 18.87138954 1.231769302 24.99019268 1.000000676 0.60537282 0.797793077 0.062222794 112.9117628 415446.1459 0.159004516 0.016650199 17.05176357 -1.231769302 -0.394627855 IPSKEEEADMS(ph)SPTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IPSKEEEADMSSPTQR 16 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 IPSKEEEADMS(0.493)S(0.493)PT(0.014)QR;IPSKEEEADMS(0.573)S(0.426)PT(0.001)QR;IPSKEEEADMS(0.5)S(0.5)PTQR;IPSKEEEADMS(0.561)S(0.43)PT(0.009)QR;IPSKEEEADMS(0.635)S(0.361)PT(0.004)QR 166.48 1.75E-08 3461930000 1655330 1851910 1375230 1872380 2223770 1889680 2725840 3185060 2270680 TRUE FALSE 1436573.946 1839744.681 2040295.828 2297532.497 2179521.328 1962377.212 2461488.456 2503959.705 2002242.797 0.717482389 0.918841953 1.019005203 1.147479466 1.088539977 0.980089535 1.229365619 1.250577457 1 20.9331855 5.32807263 0.69230421 1.14623984 1.77E-14 0.686518474 0.087224746 3.673145157 0.755126766 0.038842835 3.966034826 212849.4978 -5.32807263 -1.14623984 IPSKEEEADMSS(ph)PTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 IPSKEEEADMSSPTQR 16 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 IPSKEEEADMS(0.02)S(0.979)PT(0.001)QR;IPSKEEEADMS(0.006)S(0.994)PT(0.001)QR;IPSKEEEADMS(0.017)S(0.983)PTQR;IPSKEEEADMS(0.16)S(0.839)PTQR;IPSKEEEADMS(0.064)S(0.934)PT(0.002)QR;IPSKEEEADMS(0.18)S(0.819)PT(0.002)QR;IPSKEEEADMS(0.299)S(0.7)PT(0.001)QR;IPSKEEEADMS(0.288)S(0.657)PT(0.056)QR;IPSKEEEADMS(0.203)S(0.795)PT(0.002)QR;IPSKEEEADMS(0.067)S(0.93)PT(0.003)QR;IPSKEEEADMS(0.034)S(0.966)PT(0.001)QR;IPSKEEEADMS(0.119)S(0.877)PT(0.004)QR;IPSKEEEADMS(0.173)S(0.821)PT(0.005)QR 193.36 2.34E-10 29555020000 10265460 11652940 8784710 11535160 14325420 11735760 16874090 19559890 13951740 TRUE FALSE 8908853.452 11576391.07 13033025.14 14154394.38 14040372.17 12187242.28 15237643.35 15377159.74 12302381.19 0.724156837 0.940987837 1.059390449 1.150541034 1.14127273 0.990640925 1.23859301 1.24993361 1 23.55243425 4.968925405 0.941787353 1.149435148 0.322365977 0.698107619 0.085497272 1.670990328 0.885978509 0.029351642 1.558999832 93094.79603 -4.968925405 -0.827069171 IPTPVIHTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IPTPVIHTK 9 0 P12532;P12532-2 P12532 CKMT1A "Creatine kinase U-type, mitochondrial" 0 ; 135.43 0.00022108 1099130000 1196710 1097250 783090 964030 1069520 1261930 861210 1086470 1133350 FALSE TRUE 1038561.741 1090042.093 1161794.943 1182927.746 1048238.644 1310477.264 777689.9868 854136.8454 999366.6541 1.039219927 1.090732904 1.162531228 1.183677423 1.048902963 1.311307775 0.778182846 0.854678152 1 19.93065455 2.227171329 24.99999996 0.868697461 1.13613461 0.635791954 0.093295121 128.427428 281901.5357 0.036509521 0.024855523 168.72185 -2.227171329 0.26743715 IPTRPFEEGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IPTRPFEEGKK 11 2 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 0 88.187 0.0074051 665470000 442520 385620 310960 301080 324110 272360 402680 506240 455090 FALSE TRUE 384039.8608 383086.8368 461341.2961 369444.8157 317660.8451 282837.8654 363628.1556 397984.5156 401289.7786 0.957013812 0.95463891 1.149646267 0.920643474 0.791599642 0.704822003 0.906148561 0.991763401 1 18.61428488 3.494377456 24.14739005 0.883577144 1.017402154 0.291535841 0.100695228 698.9570121 978080.3524 0.031113198 0.044929675 3121.601464 -3.494377456 0.133825011 IPVAIKVLRENT(ph)S(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IPVAIKVLRENTSPK 15 2 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2;J3QLU9;P04626-6;J3KTI5 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 2 IPVAIKVLRENT(1)S(1)PK 46.746 0.083023 0 414910 484660 471590 419310 349510 425300 365470 369910 353230 TRUE FALSE 360078.5923 481476.2365 699652.5014 514520.7443 342555.4348 441661.5662 330026.7757 290807.6251 311471.5518 1.156056115 1.545811275 2.246280591 1.65190285 1.09979686 1.417983645 1.059572772 0.933657098 1 18.24874088 2.786347714 1.217890574 0.986756711 1.666360095 0.43329986 0.298773577 0.428427833 1.348929588 0.166777103 0.142043428 611.4313666 -2.786347714 0.679603384 IPVEGPLS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IPVEGPLSPSR 11 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 IPVEGPLS(0.531)PS(0.469)R;IPVEGPLS(0.92)PS(0.08)R;IPVEGPLS(0.864)PS(0.136)R;IPVEGPLS(0.974)PS(0.026)R 190.26 2.46E-06 1330200000 869790 908010 635230 786990 940400 891700 804330 965030 1249700 TRUE FALSE 754845.0477 902045.2225 942429.3527 965688.1079 921687.8799 926004.276 726326.2004 758665.8444 1101961.89 0.685001047 0.818581142 0.855228626 0.876335304 0.836406312 0.840323322 0.65912098 0.688468314 1 20.0716429 IPVEGPLS(ph)PSRGDFPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IPVEGPLSPSRGDFPK 16 1 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 IPVEGPLS(0.978)PS(0.022)RGDFPK;IPVEGPLS(0.995)PS(0.005)RGDFPK;IPVEGPLS(0.978)PS(0.022)RGDFPK 155.49 1.54E-07 863320000 987010 893250 510280 581700 938070 719720 1023850 1248280 280785 TRUE FALSE 856574.1277 887382.1819 757053.1148 713783.8757 919404.2423 747408.0941 924557.1846 981345.0361 247590.9172 3.459634697 3.584065975 3.05767725 2.882916239 3.713400527 3.01872178 3.734212851 3.963574461 1 17.91759886 1.230968341 24.99999038 0.999995651 3.43893984 0.827585979 0.34806682 117.80812 387887.9632 0.942668889 0.091196969 17.02034429 -1.230968341 2.43894419 IPVEGPLSPS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IPVEGPLSPSR 11 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 IPVEGPLS(0.121)PS(0.879)R 198.97 5.44E-08 627520000 320250 318500 255110 269860 288420 292950 279200 349070 532710 TRUE FALSE 277928.1511 316407.7525 378482.0493 331135.8376 282681.0063 304219.9761 252123.227 274424.097 469733.6307 0.591671818 0.673589737 0.805737602 0.704943857 0.60179001 0.647643592 0.53673659 0.584212156 1 18.84148336 1.232864447 24.99219258 1.000000575 0.642315742 0.691881106 0.0748076 120.4350745 528358.2383 0.17588338 0.020383121 17.09481666 -1.232864447 -0.357684833 IPVHPNDHVNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IPVHPNDHVNK 11 0 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 ;;;;; 148.28 2.02E-05 2887800000 4377860 3926730 2698950 3897580 4017130 3788460 4307050 5031000 4587250 FALSE TRUE 3799314.709 3900935.052 4004171.247 4782585.11 3937196.972 3934204.508 3889352.954 3955159.801 4044950.531 0.939273467 0.964396232 0.989918472 1.182359357 0.97336097 0.972621167 0.961532885 0.977801773 1 21.94769063 IPVQALLHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IPVQALLHLR 10 0 P36915;A0A140T8Y2;P36915-2 P36915 GNL1 Guanine nucleotide-binding protein-like 1 0 174.41 0.0028808 0 57068 62508 40615 47628 59076 67530 65017 68802 63757 FALSE TRUE 49526.31921 62097.38083 60256.54985 58442.66535 57900.50318 70127.9228 58711.66135 54089.22772 56219.72009 0.880942117 1.104548026 1.071804515 1.039540312 1.029896682 1.247390109 1.044325038 0.96210418 1 15.77878865 4.748124357 24.38098108 1.058100194 0.880941982 0.358654446 0.07608213 1198.581068 3055468.864 0.01980648 0.247688196 55991.79072 -4.748124357 -0.177158212 IQALGLHLPDPPLES(ph)EDEDEEGATALNNHSSIPMDPEHVELVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IQALGLHLPDPPLESEDEDEEGATALNNHSSIPMDPEHVELVK 43 0 A0A2R8Y7W8;A0A2R8Y6W5;Q16626 A0A2R8Y7W8 MEA1 Male-enhanced antigen 1 1 IQALGLHLPDPPLES(0.992)EDEDEEGAT(0.008)ALNNHSSIPMDPEHVELVK;IQALGLHLPDPPLES(0.991)EDEDEEGAT(0.007)ALNNHS(0.001)S(0.001)IPMDPEHVELVK;IQALGLHLPDPPLES(0.25)EDEDEEGAT(0.25)ALNNHS(0.25)S(0.25)IPMDPEHVELVK;IQALGLHLPDPPLES(0.989)EDEDEEGAT(0.011)ALNNHSSIPMDPEHVELVK;IQALGLHLPDPPLES(1)EDEDEEGATALNNHSSIPMDPEHVELVK 286.42 5.88E-82 1829993000 526497.5 488978.7 129847.5 386661 577051 513000 551094 691876 726583 TRUE FALSE 456919.5214 485766.5667 192642.1853 474458.2898 565568.8141 532735.442 497648.9887 543923.7016 640687.1855 0.713171001 0.758196165 0.300680566 0.740545933 0.882753436 0.831506317 0.776742535 0.848969222 1 19.28926061 3.482414769 22.42517911 0.852830006 0.592963823 0.479166259 0.131653722 52.88411583 224036.8752 0.03710075 0.049549562 3036.790058 -3.482414769 -0.259866183 IQALQQQADEAEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IQALQQQADEAEDR 14 0 P67936;A0A2R8Y5V9;A0A2R8YGX3;A0A590UJB9;A0A590UK79 P67936 TPM4 Tropomyosin alpha-4 chain 0 300.7 1.75E-43 798640000 371800 398930 296780 327410 358730 362270 369620 408650 459390 FALSE TRUE 322665.688 396309.4026 440303.8007 401753.4446 351591.9748 376206.7613 333774.3093 321263.3776 405081.4375 0.796545233 0.978345009 1.086951314 0.991784386 0.867953804 0.928718836 0.823968413 0.793083434 1 18.62785245 3.232770596 24.79049479 0.869427657 0.973298157 0.152960665 0.09005405 190.5067033 815670.8228 0.02764522 0.032197318 1709.112284 -3.232770596 0.1038705 IQCRS(ph)ENSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IQCRSENSK 9 1 Q9UKB1-2;Q9UKB1-3;Q9UKB1 Q9UKB1-2 FBXW11 F-box/WD repeat-containing protein 11 1 IQCRS(1)ENSK;IQCRS(1)ENSK 82.171 0.011633 1154220000 4562900 3115700 1896950 2820400 2593200 2917100 3055700 3381400 4129100 TRUE FALSE 3959901.204 3095232.762 2814321.365 3460814.927 2541600.394 3029322.725 2759358.684 2658313.924 3640962.502 1.08759736 0.850113881 0.772960821 0.950521991 0.698057284 0.832011514 0.757865175 0.730112964 1 21.79588845 4.730395953 3.434100427 0.809389988 1.1202953 0.436812246 0.093988605 0.256416249 5.219797085 0.022129128 0.206320471 53752.16396 -4.730395953 0.310905312 IQDFNDTFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IQDFNDTFYR 10 0 Q8TBC4;F8W8D4;Q8TBC4-2 Q8TBC4 UBA3 NEDD8-activating enzyme E1 catalytic subunit 0 ;;; 169.77 1.05E-05 788850000 1032740 928680 613580 729280 992430 977810 909660 1052080 1055640 FALSE TRUE 896260.7924 922579.4399 910309.3403 894874.1703 972682.5847 1015426.983 821441.3132 827100.8793 930843.4418 0.96284805 0.991122028 0.977940327 0.961358409 1.044947562 1.090867634 0.882469894 0.888549935 1 19.82817902 2.212617832 24.99984689 0.914639092 1.002846432 0.36353971 0.05011227 229.4626879 221120.7117 0.021184585 0.014287923 163.1615538 -2.212617832 0.088207341 IQEHFNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IQEHFNK 7 0 Q9NUU7;I3L0H8;F6QDS0;H3BQK0;Q9UMR2;Q9UMR2-2;Q9UMR2-4;I3L352;Q9UMR2-3;Q9NUU7-2 Q9NUU7 DDX19A;DDX19B ATP-dependent RNA helicase DDX19A;ATP-dependent RNA helicase DDX19B 0 71.342 0.054575 199390000 413810 378550 222240 282290 360540 389270 404230 413770 406360 FALSE TRUE 359123.96 376063.2801 329716.0073 346388.259 353365.9594 404245.4688 365027.8368 325288.5055 358320.5837 1.00224206 1.049516263 0.920170435 0.966699304 0.986172649 1.12816703 1.018718582 0.907814176 1 18.4508914 1.759664957 25 0.94931591 1.01022254 0.138421991 0.058179887 18.47325271 21906.57936 0.032144833 0.015436523 57.49961768 -1.759664957 0.06090663 IQELFHVEPGLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IQELFHVEPGLQR 13 0 A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2 A0A087WVR3 UHRF1 E3 ubiquitin-protein ligase UHRF1 0 91.207 0.0066378 70038000 64463 71151 48345 66552 69661 70846 63439 83165 100390 FALSE TRUE 55944.05122 70683.6044 71724.8037 81663.64878 68274.88239 73571.49146 57286.69554 65380.81194 88522.00856 0.631979009 0.798486224 0.810248263 0.922523676 0.771275793 0.831109604 0.647146359 0.738582563 1 16.43374857 4.738435714 5.816058751 0.803790582 0.626807541 0.256980727 0.096165687 0.213123103 32.29041822 0.023795389 0.149838067 54756.50425 -4.738435714 -0.176983042 IQEQES(ph)S(ph)GEEDSDLSPEER ddPTM_MDA-MB-175_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 157.28 1.11E-08 2202600000 620680 559280 386180 470730 589800 557040 555160 615670 631960 TRUE FALSE 538655.5654 555606.0529 572937.9397 577616.4412 578064.1339 578469.6893 501320.6686 484013.7616 557250.4087 0.966631082 0.997049162 1.028151672 1.036547362 1.037350758 1.038078537 0.899632662 0.868574978 1 19.08796624 2.235805013 24.99979088 0.910489706 1.018660218 0.551024596 0.039717521 46.57752378 422558.3009 0.015920058 0.011281756 172.1095674 -2.235805013 0.108170512 IQEQES(ph)SGEEDSDLSPEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IQEQESSGEEDSDLSPEER 19 0 P41236;E7EMN6;Q6NXS1 P41236 PPP1R2;PPP1R2P3 Protein phosphatase inhibitor 2;Protein phosphatase inhibitor 2-like protein 3 1 IQEQES(0.5)S(0.5)GEEDSDLSPEER;IQEQES(0.539)S(0.461)GEEDSDLSPEER 289.37 1.77E-49 828630000 766640 656235 492829 530402 566100 573033 616504 679250 718530 TRUE FALSE 665326.5816 651924.1491 731162.7528 650837.8808 554835.7176 595077.9503 556715.537 533997.6734 633586.202 1.050096387 1.028943097 1.154006749 1.027228621 0.875706756 0.939221764 0.878673707 0.842817713 1 19.27318139 3.351906684 4.468817602 0.898896528 1.075290082 0.690827917 0.053004349 0.113646764 3.908714956 0.015413542 0.020056449 2248.57141 -3.351906684 0.176393554 IQEQST(ph)SPDTSLGSTTPSSHTLELVALDSEVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IQEQSTSPDTSLGSTTPSSHTLELVALDSEVLR 33 0 A0A494C0H4;H0Y9M2;Q17R98-2;Q17R98;A0A5F9ZGW8 A0A494C0H4 ZNF827 Zinc finger protein 827 1 IQEQS(0.061)T(0.469)S(0.469)PDTSLGSTTPSSHTLELVALDSEVLR 224 1.26E-35 150650000 80953 89189 34027 65835 101720 93575 84091 108520 87114 TRUE FALSE 70254.85594 88603.11159 50482.57101 80783.84297 99695.97101 97174.8908 75935.86776 85313.8425 76815.48216 0.914592397 1.153453823 0.65719266 1.05166095 1.297862986 1.265043036 0.988548996 1.110633431 1 16.22910949 3.486180789 24.94167456 1.130010889 0.919835333 0.311250294 0.151761528 531.1554059 1462316.427 0.042677295 0.058224821 3063.238339 -3.486180789 -0.210175555 IQEQSTS(ph)PDTSLGSTTPSSHTLELVALDSEVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IQEQSTSPDTSLGSTTPSSHTLELVALDSEVLR 33 0 A0A494C0H4;H0Y9M2;Q17R98-2;Q17R98;A0A5F9ZGW8 A0A494C0H4 ZNF827 Zinc finger protein 827 1 IQEQS(0.021)T(0.132)S(0.841)PDT(0.003)S(0.003)LGSTTPSSHTLELVALDSEVLR 168.84 1.73E-14 166410000 63105 78410 28757 51854 77177 72363 70726 76601 68449 TRUE FALSE 54765.51436 77894.91955 42663.98139 63628.24324 75641.32869 75146.85144 63867.00341 60220.47226 60357.0372 0.907359223 1.290568974 0.706860101 1.054197591 1.253231308 1.245038771 1.058153388 0.997737382 1 15.88123437 5.021245057 17.079356 1.069300122 0.533936828 0.088752932 0.16842852 20792202.42 400114740.5 0.040994061 298035544.5 105013.4816 -5.021245057 -0.535363294 IQESEVFRVTS(ph)TEFISLRIDSSDEDR ddPTM_MDA-MB-175_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(0.015)EVFRVT(0.015)S(0.194)T(0.194)EFIS(0.194)LRIDS(0.194)S(0.194)DEDR 58.776 0.038007 153020000 37088 52821 34825 42506 64875 56639 50777 61469 54321 TRUE FALSE 32186.72683 52474.01537 51666.48648 52157.63696 63584.11443 58817.93898 45852.65436 48324.3327 47899.23326 0.671967475 1.095508462 1.078649552 1.088903379 1.327455788 1.227951576 0.957273243 1.008874869 1 15.54771494 4.73861666 24.16558061 1.09484085 0.671967848 0.600234465 0.10925801 2.26081853 970898.0955 0.02962842 0.165431704 54779.32292 -4.73861666 -0.422873002 IQEY(ph)IIAFAKEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IQEYIIAFAKEK 12 1 V9GZ60;P31513 V9GZ60 FMO3 Dimethylaniline monooxygenase [N-oxide-forming] 3 1 IQEY(1)IIAFAKEK 63.727 0.082184 1953600000 5385400 6424300 5280700 5478100 3560100 4568900 5556600 5153200 4330300 TRUE FALSE 4673705.745 6382098.35 7834464.183 6721986.333 3489260.975 4744668.539 5017721.787 4051228.282 3818376.867 1.224003263 1.671416566 2.051778663 1.7604303 0.913807384 1.242587807 1.3140981 1.060981779 1 21.86452807 3.247884495 24.99970096 1.123030725 1.703291669 0.605338877 0.2282794 137.2016232 367870.5499 0.067986398 0.086564607 1769.638241 -3.247884495 0.580260944 IQFKPDDGISPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IQFKPDDGISPER 13 1 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ; 131.66 0.00011657 870650000 1828510 1505880 1095670 1284290 1590080 1263170 1649340 2162020 1827870 FALSE TRUE 1586867.771 1495987.775 1625539.677 1575907.674 1558440.519 1311764.967 1489387.261 1699688.848 1611781.291 0.984542865 0.928158047 1.008536137 0.977742875 0.966905701 0.813860401 0.924062879 1.054540624 1 20.62022456 1.746318741 12.37856052 1.026376844 0.942563315 0.291619136 0.054316407 0.119212295 129.7600331 0.030949823 0.014646598 55.75948335 -1.746318741 -0.083813529 IQFKPDDGTTPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IQFKPDDGTTPER 13 1 Q96AE4;E9PEB5;Q96AE4-2 Q96AE4 FUBP1 Far upstream element-binding protein 1 0 ;; 116.19 0.00055176 1180940000 1470680 937440 558440 792390 869960 824910 1054840 1230450 1117180 FALSE TRUE 1276325.912 931281.8949 828503.4519 972314.2604 852649.498 856644.8215 952541.7792 967327.8429 985108.2531 1.295619956 0.945359956 0.841027825 0.987012602 0.865538884 0.869594604 0.966941223 0.981950806 1 19.90992274 4.736916575 5.984500461 0.931856384 1.305263131 0.807863469 0.055742028 0.056369425 9.790197848 0.014150257 0.086129268 54565.30349 -4.736916575 0.373406747 IQFTSLYHKEEAPAS(ph)PLRPLYPQISPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IQFTSLYHKEEAPASPLRPLYPQISPLK 28 2 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 1 IQFTSLYHKEEAPAS(1)PLRPLYPQISPLK 218.98 1.50E-34 1016200000 1212200 991020 340290 634920 1146900 942790 1455600 1610400 441450 TRUE FALSE 1052004.699 984509.9244 504855.3822 779088.2901 1124078.934 979059.7414 1314436.136 1266028.492 389262.2839 2.702560053 2.529168545 1.296954272 2.001448181 2.887716022 2.515167233 3.376736433 3.252379037 1 18.57038304 3.241154242 24.99851569 2.740360813 2.101179632 0.075407583 0.743114774 137.2693276 1323051.707 0.220154711 0.271220297 1742.425596 -3.241154242 -0.63918118 IQHEELNNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IQHEELNNR 9 0 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ; 126.39 0.00047492 567960000 668480 707820 401930 463060 695330 813240 553630 662750 669520 FALSE TRUE 580138.6743 703170.2838 596304.6924 568204.8504 681494.2934 844525.869 499939.0478 521026.07 590370.1083 0.982669458 1.191066881 1.010052311 0.962455318 1.154350947 1.430502421 0.846823104 0.882541414 1 19.17126015 IQHPSNVLHFFNAPLEVTEENFFEICDELGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IQHPSNVLHFFNAPLEVTEENFFEICDELGVK 32 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;; 277.04 9.53E-74 2167860000 745770 711666 174115 407368 635802 565045 786510 852140 715710 FALSE TRUE 647214.605 706991.0192 258317.5964 499867.1306 623150.7841 586782.6468 710234.3813 669916.4924 631099.5791 1.025534838 1.120252719 0.40931353 0.792057462 0.987404848 0.929778225 1.125391942 1.061506796 1 19.26750814 2.821601971 1.945904235 1.054961162 0.834555971 0.18150847 0.190346678 0.568055834 4.26871959 0.077344513 0.074138949 663.135031 -2.821601971 -0.22040519 IQHSITAQDHQPTPDSCIISMVVGQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IQHSITAQDHQPTPDSCIISMVVGQLK 27 0 P61970;H3BRV9 P61970 NUTF2 Nuclear transport factor 2 0 ; 141.53 1.21E-07 778510000 740290 641780 271800 327440 473720 488420 608800 715610 676840 FALSE TRUE 642458.8008 637564.1049 403243.3891 401790.2566 464293.8988 507209.8334 549758.6697 562582.3704 596824.7463 1.076461398 1.06826017 0.675647904 0.673213132 0.777940093 0.84984719 0.921139201 0.942625744 1 19.18694783 1.906470272 1.848296079 0.980530853 0.844013793 0.114069065 0.136552849 0.871913424 5.473659384 0.135135431 0.045402248 80.62510103 -1.906470272 -0.13651706 IQHYAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IQHYAGK 7 0 E9PDF6;O43795;O43795-2;A0A0U1RRI3 E9PDF6 MYO1B Unconventional myosin-Ib 0 81.958 0.043885 0 527090 491870 317330 414690 399500 456990 533290 554270 570740 FALSE TRUE 457433.721 488638.8736 470791.8494 508851.7026 391550.7316 474570.701 481571.6179 435743.6738 503267.7674 0.908927117 0.970932186 0.935469903 1.011095356 0.778016708 0.942978533 0.956889451 0.865828694 1 18.94096668 5.129121483 13.10836418 0.927381244 8.56E-05 0.006663806 0.067869268 830513.7796 820620.0251 0.015771992 22560838.41 134623.6878 -5.129121483 -0.927295653 IQILEGWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IQILEGWK 8 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ; 146.81 0.0012734 2627800000 1465120 1511090 1551210 1541700 1447570 1305460 1925030 2015200 2498140 FALSE TRUE 1271500.68 1501163.55 2301380.344 1891766.548 1418766.189 1355681.891 1738340.887 1584265.162 2202812.735 0.577216874 0.681475791 1.04474625 0.858795901 0.644070268 0.615432201 0.789146013 0.719201018 1 21.07091542 1.23472843 24.79473137 1.000000406 0.746790425 0.264603954 0.135279829 156.7897511 1014283.277 0.252054083 0.03449657 17.16834492 -1.23472843 -0.253209981 IQLLCLMEMTFTRPANHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IQLLCLMEMTFTRPANHR 18 1 Q9UNM6;A0A087WUL9;Q9UNM6-2;E9PL38 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ; 146.58 4.97E-08 192085000 50984 66452 44358 46205 40237 49383 55482 70187 58616 FALSE TRUE 44246.33522 66015.47244 65809.67717 56696.55145 39436.36242 51282.79597 50101.36418 55178.05625 51686.48326 0.856052346 1.277228944 1.273247337 1.096931884 0.762991791 0.992189693 0.969332039 1.067552922 1 15.65749942 3.463763945 24.97108226 0.970508757 1.155582873 0.263136475 0.138316574 288.1277479 538643.8761 0.039383441 0.050870894 2909.135468 -3.463763945 0.185074116 IQLVEEELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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 ;;;;;;;;; 293.77 7.96E-32 23038896000 10148251 9988140 6467926 8448118 9705725 10039117 8869674 10482426 12504792 FALSE TRUE 8807133.918 9922527.251 9595836.648 10366392.31 9512600.061 10425328.33 8009494.381 8240840.774 11026489.74 0.798725082 0.899880877 0.870253079 0.940135307 0.862704296 0.945480255 0.726386599 0.747367564 1 23.39447025 2.247100244 24.99998853 0.804406219 0.88747773 0.092134338 0.083450463 310.2806233 908356.686 0.030845033 0.023507378 176.6445507 -2.247100244 0.083071511 IQLVEEELDRAQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 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 ;;;;;;;; 269.26 1.80E-25 14938390000 6544897 6658859 2373859 2438403 5798750 5814664 5940318 6806940 347879.5 FALSE TRUE 5679972.279 6615116.517 3521865.152 2992079.67 5683366.22 6038357.887 5364226.875 5351328.853 306753.5818 18.51640084 21.56492021 11.48108893 9.754017059 18.5274649 19.68471843 17.48708798 17.44504113 1 18.22672066 1.237083121 24.99474995 0.999980619 16.77477028 0.657322928 3.586847405 25.31738114 428141.9328 5.681792682 0.928451473 17.26168238 -1.237083121 15.77478966 IQNGAQGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IQNGAQGIR 9 0 P31943;G8JLB6;E9PCY7;D6RBM0;D6RIT2;D6RIU0;E7EN40;D6R9T0;D6RFM3;D6RDU3;D6RJ04;D6RIH9;D6RAM1;D6RDL0;D6RF17;E7EQJ0 P31943;E7EQJ0 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 104.21 0.0076709 46843000 59434 51377 32761 40634 50685 60154 45956 51988 52541 FALSE TRUE 51579.64631 51039.5011 48604.32918 49860.57075 49676.46766 62468.1633 41499.19419 40870.77077 46329.66283 1.113317973 1.101659239 1.049097408 1.076212683 1.07223892 1.348340555 0.895737021 0.882172851 1 15.49964856 IQNS(ph)DDEER ddPTM_MDA-MB-175_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 186.76 4.33E-05 1347220000 1222180 922080 919920 1257610 922940 1105610 964300 1212100 2454400 TRUE FALSE 1060665.816 916022.7958 1364796.389 1543169.572 904575.2997 1148143.532 870782.3344 952901.8476 2164243.628 0.490086145 0.423253087 0.630611254 0.713029509 0.417963712 0.530505677 0.402349497 0.440293244 1 21.04543148 1.234084202 24.99940965 1.000000739 0.503862601 0.70917359 0.099408361 80.20572177 447866.6892 0.198337161 0.025647361 17.14289645 -1.234084202 -0.496138138 IQNTGDY(ph)YDLYGGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IQNTGDYYDLYGGEK 15 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 1 IQNTGDY(0.774)Y(0.226)DLYGGEK 217.46 2.13E-11 63093000 110430 77065 53513 74800 76335 68000 88926 103190 103470 TRUE FALSE 95836.39571 76558.75494 79392.06579 91784.48325 74816.08285 70616.004 80301.97021 81123.62153 91237.89447 1.05040122 0.839111373 0.870165475 1.005990809 0.820011063 0.773976695 0.880138353 0.889143946 1 16.47734553 4.748000275 24.5341863 0.882775768 1.050401337 0.342062648 0.072121214 1192.27237 3098696.375 0.017711861 0.216201259 55975.79556 -4.748000275 0.167625568 IQPAGNTS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IQPAGNTSPR 10 0 P49674;H0Y5S9;H0Y682 P49674 CSNK1E Casein kinase I isoform epsilon 1 IQPAGNT(0.062)S(0.938)PR;IQPAGNTS(1)PR;IQPAGNT(0.03)S(0.97)PR 138 8.01E-05 1836130000 2517300 2529970 1516440 1720200 2187230 2279140 2234640 2589890 2254920 TRUE FALSE 2184632.427 2513350.46 2249795.456 2110797.702 2143708.402 2366819.991 2017924.957 2036062.178 1988345.926 1.098718487 1.264040843 1.131490968 1.061584744 1.078136542 1.190346186 1.014876199 1.023997963 1 20.92313734 -1.999999955 0.183407775 0.175506246 1.221843896 0.425523478 0.0623434 102.6726485 1.462723723 29.14765324 0.527645558 0.010000001 1.999999955 1.04633765 IQPFDDDEDEDIWEDSDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IQPFDDDEDEDIWEDSDTR 19 0 O75170-6;O75170-2;O75170-4;O75170-3;O75170-5;O75170;T1ECW5;A0A0A0MSJ8 O75170-6 PPP6R2 Serine/threonine-protein phosphatase 6 regulatory subunit 2 0 ;; 264.87 5.32E-31 218419000 379185 354274 250270 255873 350657 323322 359973 401916 362505 FALSE TRUE 329074.7415 351946.7508 371301.4091 313972.8754 343679.6117 335760.4066 325062.8739 315969.3911 319650.0719 1.029484335 1.101037609 1.161587128 0.982239339 1.075174517 1.050399909 1.016933523 0.988485281 1 18.28613389 2.374900274 0.679041115 0.978476907 1.085723839 0.32752056 0.045624556 1.140932457 1.074233078 0.082288244 0.031673009 237.0829237 -2.374900274 0.107246931 IQPQPPDEDGDHS(ph)DKEDEQPQVVVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IQPQPPDEDGDHSDKEDEQPQVVVLK 26 1 Q96AT1 Q96AT1 KIAA1143 Uncharacterized protein KIAA1143 1 IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK 223.27 1.40E-34 1798950000 906185 642633 680363 670427 687481 439992 861407 1063485 1048470 TRUE FALSE 786430.3563 638411.5015 1009388.822 822657.6972 673801.4731 456918.777 777867.8817 836067.0088 924521.071 0.850635406 0.690532127 1.091796449 0.889820387 0.728811375 0.494222134 0.841373881 0.90432445 1 19.81834668 1.59149033 2.78390492 0.985283829 0.79425637 0.16554204 0.152089648 0.469117575 7.993325557 0.166326433 0.043388978 39.038249 -1.59149033 -0.191027459 IQQFDDGGS(ph)DEEDIWEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IQQFDDGGSDEEDIWEEK 18 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 IQQFDDGGS(1)DEEDIWEEK;IQQFDDGGS(1)DEEDIWEEK;IQQFDDGGS(1)DEEDIWEEK 248.18 1.17E-24 460400000 1155710 995330 794890 883270 1025510 775430 1226850 1445360 1244640 TRUE FALSE 1002979.995 988791.6117 1179301.463 1083829.953 1005104.357 805261.2939 1107870.276 1136281.012 1097500.077 0.913876925 0.900949013 1.074534287 0.987544307 0.915812562 0.733723223 1.009448928 1.035335701 1 20.06578961 2.034763407 24.99998036 1.020852616 0.925055566 0.21440695 0.084520154 280.6564979 201832.0031 0.036541419 0.024636072 108.3336578 -2.034763407 -0.09579705 IQRPNTTQEGEEMETDMDVADVAMES(ph)SPGSSISMEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IQRPNTTQEGEEMETDMDVADVAMESSPGSSISMEHR 37 1 A0A087X1S3 A0A087X1S3 HUWE1 1 IQRPNTTQEGEEMETDMDVADVAMES(0.481)S(0.401)PGS(0.099)S(0.018)IS(0.001)MEHR;IQRPNTTQEGEEMETDMDVADVAMES(0.605)S(0.378)PGS(0.015)S(0.003)ISMEHR 117.25 6.09E-06 182278000 79269 59068.5 38179.7 40285.7 55502 54312 56384 71490 59128 TRUE FALSE 68793.40081 58680.47513 56643.53062 49433.18391 54397.61879 56401.41778 50915.88836 56202.41984 52137.9552 1.319449536 1.125484782 1.08641642 0.948122797 1.043340088 1.081772723 0.976560898 1.077955966 1 15.67004638 4.776239619 1.5120833 1.028562255 1.449710321 0.81714381 0.043904911 0.487571496 0.969939326 0.011695648 0.315146505 59736.47875 -4.776239619 0.421148066 IQRPNTTQEGEEMETDMDVADVAMESS(ph)PGSSISMEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IQRPNTTQEGEEMETDMDVADVAMESSPGSSISMEHR 37 1 A0A087X1S3 A0A087X1S3 HUWE1 1 IQRPNTTQEGEEMETDMDVADVAMES(0.123)S(0.877)PGSSISMEHR 260.69 1.70E-62 217640000 143790 104650 62389 92452 105350 117280 128400 138200 132840 TRUE FALSE 124787.7872 103962.5473 92560.52908 113444.6396 103253.7411 121791.8375 115947.7878 108647.0055 117135.8065 1.065325718 0.887538579 0.790198419 0.968488142 0.88148743 1.039748998 0.989857766 0.927530263 1 16.83782263 2.754740801 24.83028014 0.979688967 0.91251889 0.174551032 0.074442695 1401.228638 2150338.82 0.023926051 0.023856622 568.5135246 -2.754740801 -0.067170077 IQRPPEDSIQPYEK ddPTM_MDA-MB-175_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 ;; 234.22 3.03E-17 2156300000 2617620 2349350 1486340 1912230 2204940 1893730 2571630 3006380 2582500 FALSE TRUE 2271694.885 2333916.965 2205138.996 2346431.048 2161066.008 1966583.019 2322233.718 2363489.033 2277199.792 0.997582598 1.024906542 0.968355523 1.030401924 0.949001495 0.863597048 1.01977601 1.037892697 1 21.11882944 2.042467247 24.99994721 1.023808298 0.973232264 0.179183264 0.047054978 230.170271 135497.3889 0.020174338 0.013601531 110.2725068 -2.042467247 -0.050576035 IQS(ph)TPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IQSTPVK 7 0 P62820;E7END7;P62820-2;P62820-3 P62820 RAB1A Ras-related protein Rab-1A 1 IQS(0.5)T(0.5)PVK 78.098 0.038033 128950000 634530 524900 403940 494230 456270 456260 524440 750120 787900 TRUE FALSE 550675.2528 521451.8973 599286.7351 606452.4753 447191.1197 473812.6174 473579.8895 589712.6754 694755.3596 0.792617495 0.750554695 0.862586703 0.872900751 0.643667031 0.681984832 0.681649854 0.848806227 1 19.40614553 1.372201099 3.14233463 1.008663364 0.756837099 0.522275821 0.075015335 0.254836592 3.689589289 0.133337241 0.021209535 23.56140034 -1.372201099 -0.251826265 IQSSLSSAS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IQSSLSSASPSK 12 0 Q5W0B1 Q5W0B1 RNF219 RING finger protein 219 1 IQSSLSSAS(0.99)PS(0.01)K;IQSSLSSAS(0.999)PS(0.001)K 153.05 6.44E-05 324190000 602450 543200 329520 403640 526470 387460 526940 688980 555300 TRUE FALSE 522834.7061 539631.6834 488876.9742 495292.6313 515994.277 402365.8369 475837.4399 541646.9886 489653.0666 1.067765612 1.102069445 0.998415016 1.01151747 1.053795661 0.821736581 0.971784866 1.106185227 1 18.90140039 4.232083659 24.83857459 1.000017652 1.084917534 0.207747406 0.072623881 225.7480309 865737.5205 0.019886585 0.043021524 17064.11067 -4.232083659 0.084899882 IQVLQQQADDAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 2390750000 1829467 1799286 1112196 1345644 1645499 1711639 1642776 1902062 1977169 FALSE TRUE 1587698.301 1787466.372 1650057.706 1651193.037 1612756.789 1777486.86 1483459.836 1495320.843 1743430.333 0.910674932 1.025258273 0.946443155 0.947094361 0.925048027 1.019534206 0.850885641 0.857688899 1 20.73349729 2.230029188 24.99998313 0.891282397 0.962091033 0.202070027 0.054114414 241.3540483 707242.3216 0.021140301 0.014509833 169.8357793 -2.230029188 0.070808636 IQVLQQQADDAEERAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IQVLQQQADDAEERAER 17 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;Q5VU61;P06753-3;P06753-4 P06753-2;P06753-3 TPM3 Tropomyosin alpha-3 chain 0 ;;;;; 243.09 1.77E-20 1283620000 861580 839533 229298 210786 741809 713587 814797 848698 135620 FALSE TRUE 747720.02 834018.0524 340187.2798 258648.183 727048.4522 741039.1536 735778.1124 667210.5373 119587.1581 6.252510988 6.974143927 2.844680693 2.162842458 6.079653232 6.196644903 6.152651539 5.579282491 1 16.86770295 4.266060543 24.99513278 4.559413412 6.613329682 0.207344767 1.831328227 400.5985405 364103.8317 0.47586586 1.258384033 18452.72641 -4.266060543 2.05391627 IQVTPPGFQLVFLPFADDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IQVTPPGFQLVFLPFADDKR 20 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 155.16 5.30E-08 1155950000 1468790 1084930 1076790 1290840 1186880 954210 1295330 1738940 2376300 FALSE TRUE 1274685.68 1077803.023 1597529.246 1583944.951 1163263.41 990919.0762 1169709.096 1367081.213 2095376.521 0.60833252 0.514372005 0.76240677 0.755923785 0.555157223 0.472907406 0.55823337 0.652427475 1 20.99877808 1.239211202 3.874942137 1.046514343 0.605567145 0.637687378 0.093070737 0.17940878 4.496283321 0.226966588 0.025520915 17.34647369 -1.239211202 -0.440947198 IQWIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IQWIDR 6 0 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 ; 135.87 0.031211 673950000 672400 609910 374660 399690 602780 643180 567210 590380 656560 FALSE TRUE 583540.6364 605903.4611 555846.8292 490445.7234 590785.8573 667923.5508 512202.0615 464131.8313 578942.2248 1.007942782 1.046569822 0.960107599 0.847141049 1.020457365 1.153696383 0.884720512 0.801689377 1 19.14305986 2.040806052 24.99999474 0.873636798 1.000851656 0.240997503 0.089639679 180.2989238 110460.1666 0.03761246 0.02535828 109.8515153 -2.040806052 0.127214859 IQYQLVDISQDNALRDEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 IQYQLVDISQDNALRDEMR 19 1 Q5T123;Q9H299 Q5T123 SH3BGRL3 SH3 domain-binding glutamic acid-rich-like protein 3 0 ;;;;;;; 283.49 7.23E-40 6983930000 3013964 2945678 1727567 2031892 2727336 2932838 2759744 3240877 2026936 FALSE TRUE 2615661.021 2926327.647 2563024.18 2493264.134 2673067.35 3045666.176 2492104.452 2547840.674 1787313.935 1.4634592 1.637276804 1.43400895 1.394978288 1.495577971 1.704046567 1.394329447 1.425513797 1 20.76936163 0.904388883 1.579215634 0.271978972 1.511288907 0.71584254 0.098968187 1.470912548 1.620298784 3.718297135 0.027745918 8.023962364 -0.904388883 1.239309935 IRCEEEDVEMSEDAYTVLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IRCEEEDVEMSEDAYTVLTR 20 1 Q9Y230;Q9Y230-2 Q9Y230 RUVBL2 RuvB-like 2 0 67.995 0.019719 26087000 17285 21757 7408.5 8021.9 16406 14834 20268 18983 6752.5 FALSE TRUE 15000.74346 21614.07683 10991.27538 9843.395002 16079.5527 15404.67358 18302.41248 14923.63318 5954.227142 2.519343501 3.630039016 1.84596172 1.653177611 2.700527258 2.587182721 3.073851911 2.506392991 1 12.53969854 4.23332253 24.9997734 2.282818968 3.074691257 0.232569475 0.649151322 188.0005592 897285.4894 0.167793523 0.366776093 17112.85735 -4.23332253 0.791872289 IRDEMVATEQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IRDEMVATEQER 12 1 P16615-5;P16615-2;P16615-3;P16615;H7C5W9;P16615-4 P16615-5 ATP2A2 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 0 ;; 197.19 1.80E-07 578440000 272200 270689 187122 238894 289963 313828 225302 367503 295954 FALSE TRUE 236228.0803 268910.8261 277614.8251 293138.534 284193.3036 325901.1662 203452.2467 288915.3434 260966.6553 0.905204077 1.030441325 1.063794241 1.123279653 1.089002361 1.248823019 0.779610125 1.107096779 1 17.99350595 6.868953051 8.389679123 1.042619165 0.224877321 0 0.127281248 0 0 0.027100598 0 7395253.252 -6.868953051 -0.817741845 IRDIDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IRDIDLK 7 1 Q13243;Q13243-3;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ;;; 133.86 0.0029461 2448320000 5737380 4518810 2974670 3621600 4089370 3454640 4785290 5453040 4361690 FALSE TRUE 4979170.696 4489125.64 4413230.362 4443939.633 4007999.538 3587542.236 4321213.312 4286949.832 3846055.977 1.294617324 1.167202367 1.147469092 1.155453706 1.042106397 0.932784717 1.123544051 1.114635319 1 21.87494833 4.852847139 0.699756094 1.055535296 1.458627999 0.621206461 0.061247619 2.676905145 0.909310126 0.028914858 0.888889004 71260.21674 -4.852847139 0.403092703 IRDPNQGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IRDPNQGGK 9 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JHW9;F8WCF2;B1AN92;B1AN91;A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-4;O43432-2 Q04637-9;A0A0A0MSA7 EIF4G1;EIF4G3 Eukaryotic translation initiation factor 4 gamma 1;Eukaryotic translation initiation factor 4 gamma 3 0 ;;;; 141.25 9.77E-05 1478690000 2356490 2064248 1464583 1725805 1766549 1859260 2301270 2528430 2434070 FALSE TRUE 2045073.876 2050687.819 2172860.238 2117675.403 1731398.131 1930786.935 2078093.19 1987744.921 2146317.018 0.952829363 0.95544498 1.012366868 0.986655459 0.806683317 0.899581432 0.968213536 0.926118977 1 21.03343175 IRDTQLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IRDTQLER 8 1 A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;Q7Z4S6-3;H0YHT2;O75037-3;O75037-4;O75037-2;O75037 A0A1B0GV47 KIF21A;KIF21B Kinesin-like protein KIF21A;Kinesin-like protein KIF21B 0 81.525 0.020643 120270000 62134 78571 27338 39069 64446 69247 56890 65702 47462 FALSE TRUE 53922.83447 78054.86193 40558.74824 47940.21358 63163.65069 71910.9769 51372.81656 51652.13859 41851.09643 1.288444965 1.865061339 0.969120327 1.145494806 1.509247214 1.718257896 1.227514234 1.23418842 1 15.3529778 1.506683401 1.811024354 0.985398818 1.404030696 0.192494784 0.261771376 0.867287738 4.518756806 0.559184623 0.07562689 32.11318649 -1.506683401 0.418631878 IRDVTK ddPTM_MDA-MB-175_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 ; 82.386 0.054155 543450000 1137890 970360 726130 745260 835010 820460 1193870 1189270 1026970 FALSE TRUE 987514.9535 963985.6413 1077288.897 914482.6736 818394.9347 852023.6271 1078088.671 934953.8654 905562.7765 1.090498615 1.064515532 1.189634694 1.009850115 0.903741801 0.940877484 1.190517874 1.032456158 1 19.78845513 3.701326187 24.31347649 1.018494428 1.109846249 0.260835976 0.080409871 646.02712 421844.9459 0.02367696 0.03511955 5027.200272 -3.701326187 0.091351821 IREDLPNLESSEETEQINK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IREDLPNLESSEETEQINK 19 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;; 314.55 1.12E-61 871520000 846944 620035 427515 557693 645879 526423 771720 841432 755778 FALSE TRUE 735018.2045 615961.9493 634262.684 684325.7195 633027.2715 546674.8335 696878.7132 661498.3148 666430.7858 1.102917542 0.92426995 0.951730769 1.026851901 0.949876994 0.820302491 1.045688056 0.992598675 1 19.34609552 IREESGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IREESGAR 8 1 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ;;;;; 149.27 0.00046321 4648700000 3649420 3255680 1740139 2056080 2600390 3370570 3089180 3442870 1637270 FALSE TRUE 3167139.901 3234293.224 2581676.041 2522944.389 2548647.327 3500238.009 2789591.799 2706639.043 1443713.806 2.193744971 2.240259261 1.788218711 1.747537759 1.765341106 2.424468059 1.932233236 1.874775341 1 20.46135335 1.183566045 2.685097496 0.672660979 2.006637872 0.668106944 0.222353275 0.380022626 2.771733017 1.227706206 0.060537925 15.26040449 -1.183566045 1.333976893 IREESNTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IREESNTK 8 1 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7BZC3 Q00341 HDLBP Vigilin 0 ; 161.27 0.00031786 341470000 333372 284987 182164 228394 192016 246156 288121 354824 327283 FALSE TRUE 289316.0455 283114.9016 270259.1197 280254.3485 188195.2573 255625.7806 260179.0698 278947.6488 288591.9766 1.002508971 0.981021389 0.936474821 0.971109287 0.652115348 0.885768841 0.901546442 0.966581442 1 18.13867167 3.396203657 22.33715455 0.886174614 0.970953639 0.194241521 0.092333744 24.35773682 6719.421037 0.028386244 0.036646497 2490.024712 -3.396203657 0.084779025 IREEYPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 15 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 1.82753E+11 30272254 27226838 17733509 20485790 26626521 27455763 26504295 29478235 26937490 FALSE TRUE 26271698.93 27047983.11 26309493.27 25137401.73 26096705.33 28512003.97 23933912.55 23174543.85 23752970.62 1.106038455 1.138720017 1.107629597 1.058284546 1.098671225 1.200355291 1.007617655 0.975648234 1 24.50160462 2.094169225 7.93399503 0.987780013 1.114913402 0.723602008 0.036188156 0.120011072 8.834593192 0.014948058 0.01005524 124.2136217 -2.094169225 0.12713339 IREHLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IREHLEK 7 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;; 160.88 0.0012129 5246250000 6060630 5320550 3774520 4340700 4896750 4726000 6856960 9078750 5458690 FALSE TRUE 5259702.39 5285598.957 5599890.497 5326322.278 4799314.255 4907812.278 6191973.075 7137329.963 4813369.887 1.092727655 1.098107787 1.163403318 1.106568247 0.997079877 1.019620846 1.28641123 1.482813524 1 22.19861586 2.195653673 8.32439244 1.305838631 1.081796627 0.277335141 0.126442739 0.256296459 44.26890947 0.051033508 0.03457145 156.9111023 -2.195653673 -0.224042004 IREIADGLCLEVEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IREIADGLCLEVEGK 15 1 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;E9PJF7 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 ;; 111.92 0.00073337 1023037000 2229180 1852810 1140726 1292190 1790730 1631630 2410680 2655210 1051450 FALSE TRUE 1934588.215 1840638.769 1692384.909 1585601.489 1755097.977 1694399.862 2176892.625 2087414.004 927148.7788 2.08659954 1.985267965 1.825364977 1.710190992 1.893005758 1.827538256 2.34794315 2.251433699 1 19.82244134 1.229519902 24.99807065 0.999998077 1.997577072 0.715229656 0.196461062 226.4811781 626185.8072 0.663375105 0.055381683 16.96367338 -1.229519902 0.997578995 IRELEEAMAGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IRELEEAMAGER 12 1 Q03252 Q03252 LMNB2 Lamin-B2 0 101.45 0.0024283 164400000 64086 63433 35190 38821 52050 51307 59870 74033 51223 FALSE TRUE 55616.87273 63016.30445 52208.0017 47635.90139 51014.30683 53280.81349 54063.81661 58201.61908 45167.47529 1.231347831 1.395169954 1.155876023 1.054650522 1.129447827 1.179627888 1.19696344 1.288573663 1 15.46299665 4.218418719 24.67704078 1.157000799 1.313258858 0.387731403 0.087384549 199.860241 244861.2358 0.022952811 0.047877917 16535.55282 -4.218418719 0.156258059 IRELESQISELQEDLESER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 IRELESQISELQEDLESER 19 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;; 331.07 2.60E-75 2448442000 1176550 1038025 709646 1126345 887934 945265 941143 1193176 1452364 FALSE TRUE 1021065.937 1031206.145 1052833.179 1382098.847 870265.8506 981629.9562 849871.0967 938024.5977 1280667.182 0.797292185 0.805210096 0.822097414 1.079202205 0.679540994 0.766498876 0.663615894 0.732449937 1 20.28846417 IREPLTAQQLETTTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IREPLTAQQLETTTER 16 1 Q6P1N0-2;Q6P1N0;K7EMP1 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 0 ; 271.26 4.47E-22 596490000 113842 123402 104908 105268 121935 140646 129741 128888 118078 FALSE TRUE 98797.49126 122591.3641 155641.8597 129170.7083 119508.7321 146056.7426 117158.7378 101326.3042 104118.9534 0.948890553 1.177416409 1.494846564 1.240607057 1.147809579 1.402787273 1.125239296 0.973178283 1 16.66787319 1.967258954 4.869538642 0.997943012 1.242922042 0.330196917 0.145315364 0.223585857 13.15268366 0.073378689 0.040001229 92.73826221 -1.967258954 0.24497903 IRETTDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IRETTDFK 8 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ; 122.96 0.0012476 797680000 1493640 1456830 937350 1130870 1168720 1019580 1385020 1382690 1707610 FALSE TRUE 1296251.69 1447259.988 1390655.595 1387651.318 1145464.759 1058803.902 1250700.974 1087012.504 1505738.291 0.860874494 0.961163036 0.923570586 0.921575367 0.760732968 0.703179237 0.830623078 0.721913303 1 20.52203961 3.246248019 24.94223074 0.790162142 0.920448896 0.302264709 0.084312112 180.2270084 584753.4447 0.023399671 0.029624544 1762.982573 -3.246248019 0.130286754 IREYFGEFGEIEAIELPMDPK ddPTM_MDA-MB-175_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 87.772 0.0023304 31829000 96347 76457 45391 48180 64141 58990 86912 104750 34096 FALSE TRUE 83614.49984 75954.74893 67342.23942 59120.00539 62864.71959 61259.38347 78483.28762 82350.02767 30065.20972 2.781104825 2.526333581 2.239872598 1.966392582 2.090945653 2.037550512 2.610435395 2.739047172 1 14.8758074 4.398757442 2.434526451 2.171493516 2.769721372 0.196121698 0.466225087 0.612609181 6.641021059 0.124112579 0.563130735 25047.09956 -4.398757442 0.598227856 IREYFGGFGEVESIELPMDNK ddPTM_MDA-MB-175_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 ;; 188.69 2.21E-17 697329000 1827410 1290948 816824 989250 1138009 960058 1559763 1853940 887035 FALSE TRUE 1585913.138 1282467.678 1211842.819 1213874.332 1115364.847 996992.0525 1408497.424 1457489.358 782170.7328 2.027579238 1.639626265 1.54933286 1.551930137 1.425986425 1.274647607 1.800754446 1.863390302 1 19.57712403 4.792969287 2.110735027 1.535118888 2.209330552 0.30773848 0.246065186 1.167991321 5.161176769 0.065860004 1.572695394 62082.51282 -4.792969287 0.674211664 IRFQESEERPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IRFQESEERPK 11 2 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 63.073 0.043278 67734000 42970 34987 22435 24819 38304 37481 44463 52112 27338 FALSE TRUE 37291.40563 34757.16809 33284.64104 30454.53328 37541.82534 38922.91832 40150.9851 40968.25434 24106.13278 1.546967569 1.441839237 1.380754074 1.263352092 1.557355785 1.614647968 1.665592132 1.699495091 1 14.55711261 3.162713481 24.99994236 1.548653388 1.408658228 0.033624126 0.206559817 90.63467633 29870.68567 0.062130273 0.070449134 1454.499181 -3.162713481 -0.139995161 IRGDGSGFS(ph)L ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IRGDGSGFSL 10 1 R4GMM2;Q9NPB6-2;Q9NPB6 R4GMM2 PARD6A Partitioning defective 6 homolog alpha 1 IRGDGSGFS(1)L;IRGDGSGFS(1)L 108.35 0.0056905 195433000 514300 504960 314610 399120 564750 512060 547590 621880 527140 TRUE FALSE 446333.9519 501642.8845 466756.4483 489746.2962 553512.5799 531759.2795 494484.8061 488895.8015 464822.1097 0.960225305 1.079214766 1.00416146 1.053620914 1.190805188 1.144005994 1.063815158 1.051791193 1 18.82631917 4.740140724 23.30669035 1.074376201 0.960225205 0.275461632 0.057678957 80.58258079 1188293.341 0.015103238 0.092649253 54971.89703 -4.740140724 -0.114150996 IRIEDPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IRIEDPPR 8 1 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ;;; 131.41 0.00091777 1357360000 2932560 2639110 1525310 1783390 2766180 2899750 2924100 3060960 1797700 FALSE TRUE 2545014.766 2621773.513 2262955.018 2188335.957 2711138.43 3011305.259 2640521.232 2406397.524 1585177.954 1.605507293 1.653930088 1.427571594 1.380498607 1.71030541 1.899663852 1.665756974 1.518061438 1 20.59621338 1.235374512 3.176965795 0.889950108 1.618019739 0.64609261 0.143217649 0.254611906 3.373079236 0.469289352 0.040746593 17.19390459 -1.235374512 0.728069632 IRLDETDDPDDYGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IRLDETDDPDDYGDR 15 1 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;;; 167.92 1.17E-06 2918670000 3281680 1878680 1503890 1862410 1940900 1933630 1915860 2176560 2859230 FALSE TRUE 2847997.673 1866338.827 2231176.234 2285298.656 1902279.887 2008017.997 1730060.192 1711119.582 2521215.087 1.129613133 0.740253712 0.884960687 0.906427487 0.754509164 0.796448509 0.686200952 0.678688459 1 21.26568777 3.239372973 24.99541482 0.763500605 0.90064141 0.194952945 0.12853808 33.55194607 1032343.328 0.03651432 0.044412249 1735.293632 -3.239372973 0.137140806 IRLEETLEQLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IRLEETLEQLAK 12 1 P22059 P22059 OSBP Oxysterol-binding protein 1 0 120.47 0.00037019 150560000 388290 352790 209500 281600 349330 270210 368140 438530 314530 FALSE TRUE 336976.4927 350472.4993 310814.9007 345541.584 342379.0165 280605.1535 332437.8395 344753.7721 277346.6217 1.215001252 1.263662406 1.120673109 1.245883515 1.234480573 1.011748951 1.1986367 1.243042984 1 18.08133063 IRPDNELFEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IRPDNELFEVR 11 1 Q92805 Q92805 GOLGA1 Golgin subfamily A member 1 0 68.034 0.057305 0 47919 51325 28276 37880 44819 48812 46551 50114 49323 FALSE TRUE 41586.38274 50987.8427 41950.36818 46481.23296 43927.18959 50689.82923 42036.49118 39397.51109 43492.09113 0.956182645 1.172347463 0.964551648 1.0687284 1.010004082 1.165495333 0.966531847 0.905854606 1 15.40846546 2.023493404 24.97938589 0.943199779 1.056649511 0.276941176 0.075093763 232.1454918 246827.8728 0.027914 0.018818551 105.5585472 -2.023493404 0.113449733 IRPLS(ph)DGNSPWSTILIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IRPLSDGNSPWSTILIK 17 1 Q5TCX8;Q5TCX8-3 Q5TCX8;Q5TCX8-3 MLK4 Mitogen-activated protein kinase kinase kinase MLK4 1 IRPLS(1)DGNSPWSTILIK;IRPLS(0.999)DGNS(0.001)PWSTILIK 183.54 4.15E-10 874130000 825040 868360 572260 723060 819810 702490 905770 1140920 867490 TRUE FALSE 716008.8736 862655.686 849006.8501 887241.8243 803497.3849 729515.2449 817928.5648 896943.1366 764936.3204 0.936037229 1.127748367 1.109905266 1.159889785 1.050410816 0.953694086 1.069276674 1.172572295 1 19.54498013 1.972379733 24.79219538 1.105306265 1.061832564 0.007813798 0.08133202 2224.247836 1996501.189 0.037551794 0.021751847 93.83821396 -1.972379733 -0.043473701 IRS(ph)EDEEDLGNARPSAPSTLFDFLESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IRSEDEEDLGNARPSAPSTLFDFLESK 27 2 Q9H7E2-2;Q9H7E2;Q9H7E2-3 Q9H7E2-2 TDRD3 Tudor domain-containing protein 3 1 IRS(0.851)EDEEDLGNARPS(0.119)APS(0.015)T(0.015)LFDFLESK 72.584 0.0099302 58499000 106940 95463 84961 95700 108270 93426 149170 164330 127630 TRUE FALSE 92807.60805 94835.89727 126048.4238 117430.1477 106115.6388 97020.15867 134703.5164 129189.3083 112541.7268 0.824650649 0.842673202 1.120015015 1.043436519 0.942900397 0.86208166 1.196920646 1.147923637 1 16.78010048 6.035718784 0.478847467 1.078438378 1.05E-32 0.331874375 0.107161057 19.78831113 1.385236055 0.083040736 15.62949203 1085722.366 -6.035718784 -1.078438378 IRS(ph)IEALLEAGQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IRSIEALLEAGQAR 14 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 IRS(1)IEALLEAGQAR 124.76 5.77E-05 15194000 29102 20300 13784 16994 25111 22024 21996 26146 14573 TRUE FALSE 25256.09696 20166.64796 20449.9885 20852.74744 24611.34023 22871.27753 19862.83131 20554.88137 12850.19654 1.965424955 1.569364943 1.591414453 1.622757082 1.915250101 1.779838733 1.545721985 1.599577197 1 13.6495028 0.896741642 1.497205032 5.19E-17 1.716141658 0.714620045 0.140861348 1.590729679 1.574184975 5.295284299 0.040114001 7.883909715 -0.896741642 1.716141658 IRS(ph)SVEKENQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IRSSVEKENQK 11 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 IRS(0.5)S(0.5)VEKENQK;IRS(0.901)S(0.099)VEKENQK 174.59 8.53E-06 1098480000 1032800 651840 442020 501010 566930 432410 900820 992270 317800 TRUE FALSE 896312.8632 647558.0201 655782.3505 614771.978 555649.2022 449045.0925 813458.6151 780080.7824 280230.046 3.198489512 2.31080867 2.340157166 2.193811787 1.982832355 1.60241594 2.902824399 2.783715713 1 18.09625212 5.09627335 1.597011935 2.189261442 4.652669111 0.269307784 0.546483062 4.562482247 5.243465972 0.151060939 23.07545348 124816.888 -5.09627335 2.463407669 IRSS(ph)VEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 IRSSVEK 7 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 IRS(0.005)S(0.995)VEK;IRS(0.017)S(0.983)VEK;IRS(0.185)S(0.815)VEK;IRS(0.098)S(0.902)VEK;IRS(0.068)S(0.932)VEK;IRS(0.169)S(0.831)VEK;IRS(0.002)S(0.998)VEK;IRS(0.085)S(0.915)VEK 109.15 0.004296 10545000000 9386020 6795740 5917740 7116210 5669120 5626930 7525040 9018730 14866570 TRUE FALSE 8145633.676 6751098.336 8779578.858 8732054.245 5556315.603 5843401.638 6795262.779 7090144.773 13109061.03 0.621374304 0.514994806 0.669733617 0.666108291 0.423853058 0.445752875 0.518363807 0.540858324 1 23.64406102 1.238068998 24.99232391 1.000000511 0.547262256 0.743414321 0.083044513 6.397000611 324867.563 0.12290676 0.021431844 17.30091203 -1.238068998 -0.452738256 IRSS(ph)VEKENQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IRSSVEKENQK 11 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 IRS(0.25)S(0.75)VEKENQK;IRS(0.009)S(0.991)VEKENQK;IRS(0.154)S(0.846)VEKENQK;IRS(0.13)S(0.87)VEKENQK 194.77 2.88E-07 4231190000 4599310 2975292 2157075 2005467 2617956 1941984 3813130 4431090 1424702 TRUE FALSE 3991499.53 2955747.111 3200243.685 2460838.934 2565863.798 2016693.381 3443333.24 3483535.886 1256275.353 3.177248938 2.352786039 2.54740625 1.958837232 2.042437426 1.605295668 2.740906468 2.772907929 1 20.26072128 5.564722227 1.009273672 2.14330181 6.977211207 0.297287056 0.528620679 12.57144186 3.031147845 0.167959314 97.9168957 367047.4632 -5.564722227 4.833909397 IRTPS(ph)GEFLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IRTPSGEFLER 11 1 Q9UNN5;B3KT28;B1ANM7;Q9UNN5-2 Q9UNN5 FAF1 FAS-associated factor 1 1 IRT(0.006)PS(0.994)GEFLER 155.1 0.0015271 0 79702 68216 39508 50145 64782 83671 72166 85650 46965 TRUE FALSE 69169.17876 67767.8846 58614.20095 61531.18867 63492.96494 86889.87751 65167.35243 67334.41403 41412.8512 1.670234643 1.636397462 1.415362605 1.485799381 1.533170576 2.098138017 1.573602168 1.625930407 1 15.33779091 1.238323348 9.442758344 0.996469571 1.627858387 0.540054955 0.182658993 0.065482738 96.28642484 0.261164875 0.045881912 17.31104752 -1.238323348 0.631388816 IRTS(ph)PTFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IRTSPTFR 8 1 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3 P62750 RPL23A 60S ribosomal protein L23a 1 IRT(0.309)S(0.69)PT(0.001)FR;IRT(0.009)S(0.988)PT(0.003)FR;IRT(0.351)S(0.648)PT(0.001)FR;IRT(0.392)S(0.607)PT(0.001)FR;IRT(0.102)S(0.896)PT(0.003)FR 115.15 0.0015254 9422310000 596693 556766 318352 353166 524792 560421 507496 612054 476923 TRUE FALSE 517838.5082 553108.5675 472308.092 433357.7381 514349.6659 581980.7585 458279.116 481171.0151 420541.7063 1.231360649 1.315228809 1.123094535 1.030475056 1.223064581 1.383883572 1.089735237 1.144169551 1 18.68188936 1.290121906 1.448555132 0.936621495 1.205099499 0.284216757 0.102103624 1.599824049 3.256568364 0.621155382 0.031503377 19.50391994 -1.290121906 0.268478004 IRVDFSITK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IRVDFSITK 9 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 ; 96.957 0.0063995 821250000 936520 1008440 655350 706930 985550 880690 993280 1207460 946580 FALSE TRUE 812756.5092 1001815.491 972279.452 867449.2612 965939.4832 914570.7142 896951.8585 949254.0755 834676.3907 0.973738467 1.200244193 1.164857977 1.039264164 1.157262256 1.095718921 1.074610314 1.137271985 1 19.67085744 1.229530591 24.93704245 0.999999782 1.109502368 0.199214725 0.065931923 541.56082 1495441.316 0.179405055 0.014845344 16.96409092 -1.229530591 0.109502586 IRVDVADQAQDKDRDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IRVDVADQAQDKDRDDR 17 3 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;; 244.32 7.27E-21 6547140000 6370690 5234190 3154290 3494100 5164040 4302030 6377440 7456840 2027060 FALSE TRUE 5528787.175 5199806.261 4679715.194 4287488.809 5061285.707 4467531.878 5758956.85 5862252.795 1787423.276 3.093160557 2.90910739 2.618134863 2.398698096 2.831610047 2.499425815 3.221932336 3.279722757 1 20.76944989 1.230616856 24.99999926 0.999996622 2.861401092 0.799934774 0.291766903 144.1776543 453707.6613 0.853891973 0.079690094 17.00657489 -1.230616856 1.86140447 IRYESLTDPSK ddPTM_MDA-MB-175_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 ;;;; 129.71 0.00021833 3737190000 6665730 5087220 4075310 5001800 4729520 4273970 5826210 6631750 8176820 FALSE TRUE 5784836.892 5053801.717 6046143.547 6137535.138 4635411.805 4438392.392 5261185.051 5213601.871 7210165.655 0.80231678 0.700927268 0.838558202 0.851233582 0.642899488 0.615574261 0.729689899 0.723090442 1 22.78160098 1.236904196 24.96034732 1.000000334 0.73566352 0.535781377 0.076603879 35.71367343 537989.779 0.122252391 0.019735883 17.25457221 -1.236904196 -0.264336814 IRYESLTDPSKLDSGK ddPTM_MDA-MB-175_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 ; 167.05 3.63E-09 2408100000 7209900 5131390 3429780 3611650 4352850 3330430 6893230 7971500 1885080 FALSE TRUE 6257093.447 5097681.561 5088433.08 4431730.333 4266236.801 3458553.797 6224725.616 6266856.759 1662227.99 3.764281125 3.066776394 3.061212488 2.666138677 2.566577405 2.080673541 3.744808566 3.770154755 1 20.66468684 4.927620001 1.355002164 2.810646648 4.51290844 0.145756749 0.797624295 4.753362944 5.630187076 0.231578545 12.48988592 84648.64309 -4.927620001 1.702261792 IS(ph)APNVDFNLEGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ISAPNVDFNLEGPK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 IS(1)APNVDFNLEGPK;IS(1)APNVDFNLEGPK;IS(1)APNVDFNLEGPK;IS(1)APNVDFNLEGPK;IS(1)APNVDFNLEGPK 258.8 2.25E-24 1586571000 1898832 1470795 1495698 2044480 1959787 1640697 1988472 2785270 2651850 TRUE FALSE 1647896.54 1461133.251 2219022.556 2508710.432 1920791.073 1703815.675 1795630.291 2189661.685 2338351.314 0.704725817 0.624856172 0.948968849 1.072854373 0.821429638 0.728639732 0.767904412 0.936412622 1 21.15706027 4.241357739 24.99874726 0.890872892 0.664790933 0.454802776 0.105371212 69.93114103 624964.0895 0.028917818 0.069797724 17432.42233 -4.241357739 -0.22608196 IS(ph)ASSATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ISASSATR 8 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;A0A1B0GV30;P49023-3;P49023-4 F5GZ78;P49023-3;P49023-4 PXN Paxillin 1 IS(1)ASSATR;IS(1)ASSATR;IS(0.997)AS(0.003)SATR;IS(1)ASSATR;IS(0.997)AS(0.003)SATR;IS(0.805)AS(0.013)S(0.182)ATR 185.33 0.00022379 7769590000 2787390 3220370 2334080 2722290 3356790 3458880 3714690 4078220 3837650 TRUE FALSE 2419029.349 3199215.177 3462848.895 3340427.552 3289996.446 3591945.352 3354439.936 3206124.39 3383967.389 0.714850077 0.945403667 1.023310362 0.987133494 0.972230541 1.061459801 0.991274309 0.947445416 1 21.69028423 4.726576473 3.165185705 0.993632582 0.677345769 0.894250397 0.030319123 0.103909869 1.649359213 0.007967792 0.080310529 53281.50377 -4.726576473 -0.316286813 IS(ph)DAELEAELEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ISDAELEAELEK 12 0 Q8WUX9 Q8WUX9 CHMP7 Charged multivesicular body protein 7 1 IS(1)DAELEAELEK;IS(1)DAELEAELEK;IS(1)DAELEAELEK;IS(1)DAELEAELEK;IS(1)DAELEAELEK;IS(1)DAELEAELEK;IS(1)DAELEAELEK 281.48 4.63E-28 1152577000 1315698 1228078 1265180 1413530 1512869 1127963 1887610 2129560 2485960 TRUE FALSE 1141825.176 1220010.675 1877025.28 1734493.591 1482765.867 1171356.466 1704549.873 1674170.166 2192072.641 0.520888384 0.556555769 0.856278777 0.791257351 0.676421866 0.534360242 0.777597348 0.763738452 1 21.06386418 0.93998351 1.254299011 1.385017074 0.671024833 0.467024526 0.111517162 2.82283461 2.251415334 3.157111447 0.035623447 8.709305212 -0.93998351 -0.713992242 IS(ph)DAELEAELEKLSLSEGGLVPSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ISDAELEAELEKLSLSEGGLVPSSK 25 1 Q8WUX9 Q8WUX9 CHMP7 Charged multivesicular body protein 7 1 IS(1)DAELEAELEKLSLSEGGLVPSSK;IS(0.999)DAELEAELEKLS(0.001)LSEGGLVPSSK;IS(1)DAELEAELEKLSLSEGGLVPSSK;IS(1)DAELEAELEKLSLSEGGLVPSSK 317.84 5.81E-75 276770000 416533 377476 240763 212276 399000 294243 660236 714962 50869.8 TRUE FALSE 361487.1087 374996.3353 357196.7921 260476.5102 391060.6806 305562.7186 596206.4143 562072.9401 44856.0302 8.058829707 8.359998281 7.963183335 5.806945222 8.718129512 6.81207671 13.29155549 12.53059929 1 15.45301433 IS(ph)DS(ph)ESEDPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISDSESEDPPR 11 0 Q96ST2;Q96ST2-3;B8ZZB6 Q96ST2 IWS1 Protein IWS1 homolog 2 IS(1)DS(0.998)ES(0.002)EDPPR;IS(1)DS(1)ESEDPPR 208.51 2.82E-08 567340000 916390 717250 535840 682710 772270 661280 774960 857120 1456320 TRUE FALSE 795286.7397 712538.3375 794974.0163 837729.7401 756903.3379 686719.8695 699804.4985 673831.5581 1284155.509 0.61930719 0.554869198 0.619063666 0.652358483 0.589417195 0.534763792 0.544953079 0.524727382 1 20.29238849 1.234217474 24.99953203 1.000000625 0.577292892 0.910500638 0.041382257 39.83633225 229271.3474 0.086169778 0.011257228 17.14815792 -1.234217474 -0.422707732 IS(ph)EDETER ddPTM_MDA-MB-175_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(0.999)EDET(0.001)ER;IS(1)EDETER 191.4 0.00019025 2807100000 2758700 2048270 2135500 2646100 2293100 2096400 2128200 2600600 8094100 TRUE FALSE 2394130.805 2034814.78 3168234.943 3246937.448 2247471.796 2177049.865 1921807.492 2044481.928 7137224.719 0.335442823 0.285098881 0.443902927 0.454929973 0.314894358 0.305027507 0.269265375 0.28645335 1 22.76693177 1.236015317 24.99999031 1.000000876 0.335077386 0.914136809 0.063867531 20.55112749 201810.8497 0.114405483 0.017287426 17.21929302 -1.236015317 -0.66492349 IS(ph)LTSSPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISLTSSPVR 9 0 E9PKJ6;Q3T1D4;A0A3B3IU27;Q8TD07-4;Q8TD07-3;Q8TD07-5;Q8TD07-2;Q8TD07;Q8TD07-6 E9PKJ6 RAET1E NKG2D ligand 4 1 IS(0.572)LT(0.214)S(0.214)SPVR 72.928 0.047584 239620000 224720 260050 219600 280250 228800 286350 220280 240930 697060 TRUE FALSE 195022.6826 258341.7144 325799.2945 343885.0459 224247.3276 297366.0698 198917.2795 189408.9944 614654.3609 0.317288374 0.420304045 0.530052848 0.559477111 0.364834844 0.483793964 0.323624613 0.308155293 1 19.22941584 1.232258933 24.99976721 1.000000972 0.413397675 0.812269034 0.088620018 97.39954758 386361.5853 0.214708895 0.023515891 17.07099883 -1.232258933 -0.586603297 IS(ph)MSEVDLNVAAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 ISMSEVDLNVAAPK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 IS(1)MSEVDLNVAAPK;IS(1)MSEVDLNVAAPK;IS(1)MSEVDLNVAAPK;IS(0.972)MS(0.028)EVDLNVAAPK;IS(0.974)MS(0.026)EVDLNVAAPK;IS(0.998)MS(0.002)EVDLNVAAPK;IS(0.999)MS(0.001)EVDLNVAAPK 319.82 4.54E-56 977205000 1452923 1164000 1031195 1500663 1394418 1215429 1569450 1864921 2053560 TRUE FALSE 1260915.544 1156353.607 1529884.351 1841411.47 1366671.81 1262187.34 1417244.981 1466122.157 1810790.476 0.696334314 0.638590506 0.844870995 1.016910291 0.754737684 0.697036657 0.782666465 0.809658641 1 20.78818819 4.234570228 24.97887816 0.83515977 0.667462385 0.34459819 0.100509043 111.0375466 695086.4493 0.026623913 0.058889887 17162.09209 -4.234570228 -0.167697385 IS(ph)PGATLPESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISPGATLPESR 11 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 IS(1)PGATLPESR 185.9 4.47E-06 541980000 923970 943220 419380 513540 787640 711120 999380 1042000 531920 TRUE FALSE 801865.0235 937023.9257 622193.5707 630147.106 771967.505 738477.2466 902460.2814 819176.4089 469037.0236 1.709598567 1.997761112 1.326534025 1.343491184 1.645856225 1.574454061 1.924070459 1.746506923 1 18.83934228 4.248414575 24.99998373 1.5535326 1.853679821 0.214325753 0.263957471 359.7579086 912704.6756 0.067637723 0.174288459 17717.99502 -4.248414575 0.300147221 IS(ph)PPIKEEETKGDSVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISPPIKEEETKGDSVEK 17 2 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;A0A087WTC9;Q6PJT7-9;Q6PJT7-2;H0YJA2;Q6PJT7-3;Q6PJT7-11;G3V5I6 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 1 IS(1)PPIKEEETKGDSVEK;IS(1)PPIKEEETKGDSVEK 88.222 0.0022694 1625660000 1699220 983310 1201110 882410 773540 572550 1623770 1663630 1449950 TRUE FALSE 1474663.772 976850.5719 1781970.813 1082774.677 758148.0674 594576.369 1466297.035 1307875.671 1278538.563 1.153397961 0.764036847 1.393756016 0.846884645 0.592980212 0.465043751 1.146853977 1.022945814 1 20.28606424 IS(ph)PTAGNQNGLLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ISPTAGNQNGLLNK 14 0 A0A2R8Y8C6;Q8WXX7-2;Q8WXX7;A0A087WVB5;Q75MD7;A0A2R8Y568;A0A024RDL5;A0A2R8Y522;Q8WXX7-5 A0A2R8Y8C6 AUTS2 Autism susceptibility gene 2 protein 1 IS(0.974)PT(0.026)AGNQNGLLNK;IS(0.979)PT(0.021)AGNQNGLLNK;IS(1)PTAGNQNGLLNK;IS(1)PTAGNQNGLLNK 292.26 1.74E-43 287581000 621113 540767 344850 428922 540876 395376 528551 747109 578824 TRUE FALSE 539031.3434 537214.666 511620.6135 526315.2958 530113.6258 410586.3706 477292.2054 587345.5544 510396.0861 1.056103991 1.052544642 1.002399171 1.031189913 1.03863184 0.80444655 0.935140802 1.150764221 1 18.96125774 4.209981902 1.319049935 0.998225885 1.064028283 0.074242145 0.08665031 2.299240231 6.454363529 0.029714952 0.159784096 16217.42515 -4.209981902 0.065802398 HISQISVAEDDDESLLGHLMIVGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HISQISVAEDDDESLLGHLMIVGK 24 0 P49773 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 199.89 9.21E-25 103530000 31034 43089 13867 37719 39721 39881 35772 51973 156540 FALSE TRUE 26932.77827 42805.94552 20573.12758 46283.67545 38930.62981 41415.24788 32302.83695 40858.9784 138034.0195 0.19511696 0.310111563 0.149043893 0.335306293 0.282036486 0.300036527 0.234020838 0.296006583 1 17.07466435 1.237493374 5.394917772 1.03868388 0.261969474 0.946148268 0.055344159 0.029997522 2.598523126 0.086864977 0.012739817 17.27799618 -1.237493374 -0.776714406 IS(ph)WYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ISWYLR 6 0 M0QYT0;M0R076;Q13011;M0R248;M0QZW4 M0QYT0;Q13011 ECH1 "Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial" 1 IS(1)WYLR;IS(1)WYLR;IS(1)WYLR;IS(1)WYLR;IS(1)WYLR 128.61 0.017364 324495000 590862 501454 414962 526590 561498 560551 488295 530727 596235 TRUE FALSE 512778.0896 498159.9157 615639.0112 646160.3079 550325.2884 582115.7597 440940.2261 417235.1612 525748.7775 0.975329115 0.94752463 1.17097564 1.229028645 1.046745731 1.107212769 0.838689969 0.793601771 1 19.00401406 2.237847551 24.99930216 0.858352018 1.082942027 0.484709757 0.09749771 15.17897633 532118.3039 0.040330766 0.029020232 172.9209255 -2.237847551 0.224590009 IS(ph)YTPPES(ph)PVPSYASSTPLHVPVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISYTPPESPVPSYASSTPLHVPVPR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 2 IS(0.447)Y(0.214)T(0.342)PPES(0.996)PVPS(0.001)YASSTPLHVPVPR 81.532 0.011444 260670000 223660 218370 112400 152650 212760 202880 223200 239690 189110 TRUE FALSE 194102.7643 216935.5131 166757.016 187311.5156 208526.4923 210684.9249 201554.0984 188434.1588 166753.6312 1.164009221 1.300934267 1.000020298 1.123282979 1.250506455 1.263450297 1.208693909 1.130015325 1 17.34735865 1.301511347 2.652311933 0.972907236 1.186785908 0.333346975 0.08370217 0.512385086 4.528572642 0.229581759 0.022639713 20.02217932 -1.301511347 0.213878672 ISAHQGAQVDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISAHQGAQVDSR 12 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 0 115.12 0.0009841 79029000 88331 101840 38083 65500 94976 113840 104140 104170 106560 FALSE TRUE 76657.83455 101171.0063 56500.06618 80372.7761 93086.16342 118219.4985 94040.51883 81894.05615 93962.59819 0.815833491 1.076715718 0.601303788 0.855369877 0.990672514 1.258154848 1.000829273 0.87156015 1 16.51979899 3.230320944 5.192904519 1.016364464 0.836183271 0.287117826 0.1467138 0.261938771 20.20163082 0.045892964 0.055400617 1699.499118 -3.230320944 -0.180181193 ISAPELLLHS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISAPELLLHSPAR 13 0 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 ISAPELLLHS(1)PAR;ISAPELLLHS(1)PAR 152.71 2.62E-05 300840000 458830 433700 264230 300670 402990 405950 346180 425520 378530 TRUE FALSE 398194.453 430850.9961 392012.5118 368941.719 394971.2874 421567.1592 312607.5169 334525.8594 333780.6146 1.192982563 1.290820908 1.174461591 1.105341961 1.183326024 1.26300672 0.936565826 1.002232738 1 18.34854064 2.235702683 24.99999998 0.982521678 1.19926227 0.797784161 0.052685487 33.01985179 288837.691 0.021846273 0.015467462 172.0690192 -2.235702683 0.216740593 ISDDKYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ISDDKYGR 8 1 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 ;;;;; 148.52 0.00047414 4747790000 5746240 4939050 3257350 3918420 4427820 4192430 5390480 5974880 4311470 FALSE TRUE 4986859.825 4906605.055 4832615.355 4808157.15 4339715.045 4353715.495 4867712.079 4697198.409 3801772.928 1.311719537 1.29060971 1.271147816 1.264714448 1.141497698 1.145180309 1.280379489 1.235528396 1 21.85824093 -2 0.044789902 0.15524331 1.863932118 0.44276639 0.071205454 1639.700539 7.209221504 228.922525 81.94838299 0.01 2 1.708688807 ISDEDWDIIHR ddPTM_MDA-MB-175_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 ;;;;; 244.27 7.24E-16 4885580000 6085380 4648060 3336510 4528660 4835780 5656040 4555050 5685760 5233000 FALSE TRUE 5281181.615 4617526.588 4950057.396 5556961.469 4739557.439 5873631.519 4113301.952 4469904.471 4614360.701 1.144509924 1.000686094 1.072750423 1.204275484 1.027131979 1.272902553 0.891413181 0.968694205 1 22.13769935 2.213442565 24.99972305 0.95398034 1.112346154 0.46863223 0.08353986 198.6866087 197749.0759 0.032447786 0.021885909 163.4716948 -2.213442565 0.158365814 ISDYFEYQGGNGSS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ISDYFEYQGGNGSSPVR 17 0 B3KRP1;Q9UKI8;Q9UKI8-4;Q9UKI8-5;Q9UKI8-2;C9JWT6 B3KRP1 TLK1 Serine/threonine-protein kinase tousled-like 1 1 ISDYFEYQGGNGS(0.014)S(0.986)PVR;ISDYFEYQGGNGS(0.087)S(0.913)PVR;ISDYFEYQGGNGS(0.08)S(0.92)PVR;ISDYFEYQGGNGSS(1)PVR 355.79 7.39E-88 1284090000 1602420 1383350 927370 990270 1305620 1401030 1372620 1548230 1504410 TRUE FALSE 1390656.137 1374262.683 1375849.234 1215125.939 1279640.716 1454928.531 1239503.524 1217153.063 1326560.364 1.048317269 1.035959403 1.037155392 0.915997471 0.964630598 1.096767679 0.934374008 0.917525577 1 20.33925889 8 0.29183296 0.951225918 1.837557635 0.189371916 0.054945556 125.5703757 2.009254519 0.122430583 56.37892711 99999999.99 -8 0.886331717 ISEDKNPDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISEDKNPDYR 10 1 P14923 P14923 JUP Junction plakoglobin 0 ; 83.045 0.014768 903170000 3691000 2635900 2238060 3377400 3092900 2967100 2739500 4084400 3920700 FALSE TRUE 3203224.998 2618584.599 3320393.302 4144290.29 3031357.341 3081246.257 2473823.712 3210982.845 3457199.312 0.926537555 0.757429457 0.96042866 1.198742079 0.876824582 0.891255024 0.715557157 0.928781524 1 21.72117235 1.287784751 5.573833053 1.001267215 0.902964779 0.050495344 0.128577187 0.540420656 34.55744995 0.155082968 0.033354754 19.39924158 -1.287784751 -0.098302436 ISEEQQQLQQALAPAQASSNSST(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISEEQQQLQQALAPAQASSNSSTPTR 26 0 Q13439-5;Q13439-3;Q13439-4;Q13439;E7EVX2;Q86W71;C9JHJ5;C9J0Y3 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 ISEEQQQLQQALAPAQAS(0.009)S(0.009)NS(0.139)S(0.139)T(0.564)PT(0.139)R 99.954 5.87E-08 0 28592 28735 19802 18334 27414 27971 26521 33433 33288 TRUE FALSE 24813.49476 28546.23789 29378.31343 22497.01492 26868.51503 29047.06247 23948.9975 26283.61313 29352.73056 0.845355586 0.972524101 1.000871567 0.766436869 0.9153668 0.989586383 0.815903565 0.895440139 1 14.8412071 ISEGLPT(ph)PTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISEGLPTPTK 10 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 ISEGLPT(0.997)PT(0.003)K;ISEGLPT(0.999)PT(0.001)K 146.17 0.00032574 340350000 1416050 1167320 897720 1345460 1312890 993440 1497030 1801410 1876710 TRUE FALSE 1228915.405 1159651.798 1331860.395 1650967.257 1286766.058 1031658.28 1351848.261 1416192.49 1654847.482 0.742615509 0.70076053 0.804823653 0.997655237 0.777573808 0.623415929 0.816902026 0.855784298 1 20.65826683 1.313286541 1.995892277 1.046232796 0.780848704 0.352556492 0.095103031 0.813995469 3.687670239 0.382223337 0.027734191 20.57247489 -1.313286541 -0.265384092 ISEGLPT(ph)PTKMT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISEGLPTPTKMTPR 14 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 2 IS(0.003)EGLPT(0.997)PTKMT(1)PR;ISEGLPT(0.995)PT(0.005)KMT(1)PR 167.53 1.79E-05 731010000 1504080 1413430 1002810 1194300 1434710 1193640 1618240 1831930 1758600 TRUE FALSE 1305312.017 1404145.085 1487772.27 1465484.069 1406162.078 1239560.103 1461303.334 1440186.026 1550700.311 0.841756468 0.905490942 0.959419599 0.945046608 0.90679164 0.799355036 0.942350577 0.92873266 1 20.56448847 1.257251699 1.689463264 1.032444578 0.900493792 0.305731549 0.048049976 1.331726161 3.630318844 0.288949978 0.014035214 18.08221795 -1.257251699 -0.131950785 ISEGLPTPTKMT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ISEGLPTPTKMTPR 14 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 ISEGLPT(0.041)PT(0.141)KMT(0.818)PR;ISEGLPT(0.001)PT(0.04)KMT(0.958)PR;ISEGLPT(0.001)PT(0.014)KMT(0.985)PR 88.19 0.018357 1648130000 2867020 2944120 1452350 1899690 2857580 2607810 2755690 3187660 1993950 TRUE FALSE 2488136.043 2924779.882 2154711.318 2331043.649 2800719.749 2708134.138 2488443.608 2506003.715 1758227.503 1.415138848 1.663482045 1.225501998 1.325791825 1.592922272 1.540263779 1.415313777 1.425301169 1 20.74569033 1.22119583 3.892768798 0.936588863 1.454765984 0.559115206 0.125861861 0.220000785 5.458375595 0.336943421 0.03210859 16.64162876 -1.22119583 0.518177121 ISEQFTAMFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 227.99 5.36E-09 8861813000 1168472 1109436 734995 892131 1110168 1304836 1107813 1271614 1285026 FALSE TRUE 1014055.465 1102148.042 1090441.04 1094702.979 1088077.829 1355033.885 1000377.466 999689.2418 1133111.69 0.894929841 0.97267379 0.962342062 0.966103332 0.960256467 1.195852004 0.882858658 0.882251282 1 20.11185864 4.739289005 21.44729337 0.971296344 0.894929719 0.078986416 0.086429364 27.05022116 795147.044 0.021830206 0.126152073 54864.19422 -4.739289005 -0.076366625 ISESVLRDS(ph)PPPHEDYEDEVFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ISESVLRDSPPPHEDYEDEVFVR 23 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 IS(0.011)ES(0.108)VLRDS(0.881)PPPHEDYEDEVFVR;ISES(0.001)VLRDS(0.999)PPPHEDYEDEVFVR;IS(0.009)ES(0.047)VLRDS(0.945)PPPHEDYEDEVFVR;IS(0.004)ES(0.03)VLRDS(0.967)PPPHEDYEDEVFVR 230.45 2.28E-33 705960000 833270 645468 553958 697140 625480 677560 639981 701130 1156010 TRUE FALSE 723151.2583 641227.8782 821853.9417 855436.2921 613034.1717 703626.1716 577915.7411 551198.8057 1019347.815 0.709425427 0.629057 0.806254676 0.839199613 0.601398426 0.690270937 0.566946564 0.540736732 1 19.95921497 3.219246726 24.99649455 0.654529541 0.74193733 0.036182697 0.13802797 638.5001386 826359.512 0.041731589 0.047387933 1656.710888 -3.219246726 0.087407788 ISESVLRDS(ph)PPPHEDYEDEVFVRDPHPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISESVLRDSPPPHEDYEDEVFVRDPHPK 28 2 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 IS(0.039)ES(0.033)VLRDS(0.927)PPPHEDYEDEVFVRDPHPK;IS(0.054)ES(0.045)VLRDS(0.902)PPPHEDYEDEVFVRDPHPK 186.07 4.42E-18 780660000 563910 388790 281460 323950 353800 342430 461700 482720 279390 TRUE FALSE 489387.8647 386236.0129 417574.9974 397507.7988 346760.0722 355603.5037 416924.4051 379494.0845 246360.8325 1.986467816 1.567765497 1.694973155 1.613518654 1.407529227 1.443425483 1.692332344 1.540399424 1 17.91041338 7.999997782 0.048948279 3.61E-09 4.304898794 0.491149863 0.179578629 1237.226423 5.927412003 148.0549959 454.5274027 99999489.26 -7.999997782 4.30489879 ISEVFDCWFESGSMPYAQVHYPFENKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISEVFDCWFESGSMPYAQVHYPFENKR 27 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 147.11 8.97E-08 152920000 398320 363410 222960 250000 369240 328650 403110 490820 264960 FALSE TRUE 345681.0028 361022.7358 330784.2018 306766.321 361892.8464 341293.3782 364016.4542 385861.9626 233636.7306 1.47956617 1.545231072 1.415805643 1.313005537 1.548955275 1.460786483 1.558044633 1.651546662 1 17.83390758 1.227741285 24.99984862 0.999998938 1.500531103 0.745443815 0.091177474 264.6619523 611504.03 0.353532971 0.024493836 16.89434213 -1.227741285 0.500532164 ISFPGSSES(ph)PLSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISFPGSSESPLSSK 14 0 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 ISFPGS(0.006)S(0.033)ES(0.962)PLSSK 118.51 0.00085444 0 181180 127920 98253 132650 130850 125150 158430 191960 176430 TRUE FALSE 157236.6039 127079.6851 145768.4794 162770.2099 128246.341 129964.6015 143065.483 150910.8478 155572.6464 1.010695695 0.816851086 0.936980136 1.046264968 0.824350193 0.835394939 0.91960564 0.970034587 1 17.24722889 1.65218774 3.147985393 0.993842831 0.908494989 0.141037415 0.07541589 0.395409205 9.054321478 0.06289149 0.020182661 44.89394193 -1.65218774 -0.085347842 ISGETIFVTAPHEATAGIIGVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISGETIFVTAPHEATAGIIGVNR 23 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 342.81 2.55E-87 1922790000 957120 809330 456320 650710 865710 810590 717060 830140 951350 FALSE TRUE 830634.167 804013.4579 676997.8783 798463.651 848484.0647 841773.9218 647519.6316 652621.0212 838882.4868 0.990167491 0.958433953 0.807023497 0.951818239 1.011445677 1.00344677 0.771883597 0.77796477 1 19.6781092 2.240378896 24.99999749 0.831699901 0.94980583 0.243387465 0.084038074 60.76336474 835470.2981 0.033468965 0.024569803 173.9317616 -2.240378896 0.118105929 ISGLIYEETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ISGLIYEETR 10 0 P62805 P62805 HIST1H4A Histone H4 0 ;;; 192.91 1.47E-06 1305100000 674780 565260 508950 1537610 477220 1827410 636920 1063410 1035680 FALSE TRUE 585606.1133 561546.7698 755079.9223 1886747.851 467724.2557 1897711.645 575151.5964 836008.047 913243.0903 0.641237935 0.614892985 0.826811536 2.065986452 0.512157454 2.077991792 0.629790253 0.915427728 1 19.80063941 3.988445704 24.77401825 1.166163948 0.651261944 0.177997964 0.52158243 858.0919729 1839884.059 0.129398547 0.242187324 9737.460387 -3.988445704 -0.514902004 ISHLPLVEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISHLPLVEELR 11 0 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 ; 118.48 0.0009544 177310000 228650 216300 119935 168874 219038 193705 198842 238790 219110 FALSE TRUE 198433.3232 214879.1111 177935.9672 207219.4228 214679.5723 201156.9567 179558.3334 187726.6168 193207.0654 1.027050034 1.112170047 0.920959939 1.072525077 1.111137276 1.041147001 0.929356973 0.971634326 1 17.55978833 2.316409273 7.635321456 0.966590325 1.049179039 0.317820512 0.055622571 0.272230658 22.89002711 0.020637689 0.015909362 207.2093142 -2.316409273 0.082588713 ISHQQNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISHQQNER 8 0 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 0 ; 114.99 0.0025505 697300000 115235 123845 77131 87423 96642 143392 103061 130838 107665 FALSE TRUE 100006.4028 123031.454 114431.8096 107273.7283 94719.01328 148908.383 93066.16008 102859.3119 94936.96635 1.053397919 1.295927801 1.205345125 1.129946874 0.997704234 1.56849738 0.980294227 1.08344848 1 16.53468233 HEDPCAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HEDPCAK 7 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 91.041 0.016695 372240000 441200 389650 343990 399230 278230 390580 454390 538690 952060 FALSE TRUE 382894.3021 387090.3635 510344.7146 489881.2733 272693.7673 405605.8653 410323.3277 423495.3356 839508.5514 0.456093391 0.461091627 0.607908894 0.583533393 0.324825479 0.483146794 0.488766109 0.50445625 1 19.6791855 1.237542797 5.99778342 1.019271957 0.488599511 0.817514868 0.075953485 0.057159966 7.799619653 0.124279071 0.019299937 17.27996255 -1.237542797 -0.530672446 ISHSLYSGIEGLDES(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISHSLYSGIEGLDESPSR 18 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3;B1AP52 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 ISHSLYSGIEGLDES(1)PSR 240.71 3.73E-24 188160000 151410 152780 78646 118820 157160 160240 140810 154990 133620 TRUE FALSE 131400.7849 151776.3781 116679.4687 145799.897 154032.8235 166404.5365 127154.2679 121846.5946 117823.5958 1.115233192 1.288166238 0.99028949 1.237442263 1.307317286 1.412319284 1.07919188 1.034144254 1 16.84626896 2.019047789 24.86482741 1.030658068 1.223626278 0.388142427 0.11260191 229.1734695 299159.8629 0.047252408 0.031852422 104.4835184 -2.019047789 0.19296821 ISICS(ph)SDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISICSSDKR 9 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 1 IS(0.006)ICS(0.966)S(0.028)DKR;IS(0.002)ICS(0.893)S(0.104)DKR 71.153 0.030862 737000000 2173390 1740690 1567330 1705460 1652680 1915020 2339040 2436900 2485200 TRUE FALSE 1886171.005 1729255.293 2325296.03 2092710.759 1619794.901 1988692.059 2112200.261 1915787.899 2191402.487 0.860714093 0.78910894 1.061099476 0.954964125 0.739159014 0.9074974 0.963857746 0.874229134 1 21.06342305 0.034093661 1.999328625 9.991262505 0.894628023 0.114646235 0.090467423 270.3553724 14.90649527 10903.71418 0.024636868 1.081667201 -0.034093661 -9.096634482 ISICSSDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISICSSDKR 9 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 0 85.154 0.024063 585540000 334020 313940 180540 212740 292360 279860 315700 395970 278610 FALSE TRUE 289878.4107 311877.7075 267849.7479 261045.8685 286542.608 290626.3953 285083.4626 311294.8969 245673.0432 1.179935767 1.269482819 1.090269182 1.062574327 1.166357547 1.182980402 1.160418168 1.267110518 1 17.90638004 4.243827019 24.99582334 1.146765938 1.224709281 0.184053746 0.076153519 247.5457917 1174887.241 0.019516926 0.048528397 17531.82064 -4.243827019 0.077943343 ISIEMNGTLEDQLSHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ISIEMNGTLEDQLSHLK 17 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;; 320.92 1.46E-58 1332396000 1515168 1103023 988308 1285118 1036376 922536 1087718 1516918 2844647 FALSE TRUE 1314934.71 1095777.169 1466257.054 1576923.684 1015754.145 958026.5569 982231.2758 1192536.89 2508356.072 0.52422171 0.436850725 0.584549008 0.628668195 0.404948148 0.381934035 0.39158367 0.47542568 1 21.25831073 1.238543227 24.99999987 1.00000057 0.475687704 0.801139529 0.081639497 0.197128853 274978.6572 0.119773871 0.021489818 17.31981412 -1.238543227 -0.524312866 ISINQT(ph)PGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ISINQTPGK 9 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDG6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 ISINQT(1)PGK;ISINQT(1)PGK;ISINQT(1)PGK;ISINQT(1)PGK;ISINQT(1)PGK 212.2 4.37E-05 1250085000 3315450 3479250 2324400 2738730 3470840 2451820 3309800 4347140 4504850 TRUE FALSE 2877304.882 3456394.578 3448487.615 3360600.505 3401777.075 2546143.102 2988816.105 3417537.94 3972291.765 0.724343793 0.870126059 0.868135529 0.846010491 0.856376439 0.640975853 0.752416057 0.86034414 1 21.92154016 1.317399191 3.039133371 1.018264428 0.798818446 0.441307315 0.073260062 0.328999803 4.14981662 0.158404223 0.020083647 20.76821595 -1.317399191 -0.219445982 ISKEEAMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ISKEEAMR 8 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ;;;; 85.355 0.015323 3921970000 2735930 2423780 1365210 1735370 2207690 2102630 2726770 3020170 1487600 FALSE TRUE 2374369.919 2407858.03 2025430.122 2129412.282 2163761.288 2183519.537 2462328.265 2374330.148 1311737.623 1.810095157 1.835624738 1.544081749 1.623352296 1.649538178 1.664600831 1.87714999 1.810064839 1 20.32304775 1.234619681 24.99905478 0.999998951 1.727860755 0.821174917 0.106590311 52.06778157 330241.0031 0.211408265 0.028611678 17.16404643 -1.234619681 0.727861804 ISKPGAVST(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISKPGAVSTPVK 12 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 ISKPGAVS(0.245)T(0.755)PVK;ISKPGAVS(0.086)T(0.914)PVK 151.8 0.00011198 1907380000 3329500 2934400 2665200 3184700 2805200 2105300 3243000 4262100 5942300 TRUE FALSE 2889498.139 2915123.733 3954099.635 3907834.81 2749382.008 2186292.253 2928494.359 3350683.083 5239808.063 0.551451142 0.556341701 0.754626808 0.74579732 0.524710443 0.417246629 0.558893441 0.639466759 1 22.32108254 1.234565266 3.661408397 1.056772567 0.590064235 0.625858825 0.0995199 0.212014014 4.382197541 0.275161088 0.02796484 17.161896 -1.234565266 -0.466708332 ISKSDMSRLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISKSDMSRLR 10 2 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 0 52.725 0.083379 113190000 262780 294470 98215 123770 293070 442130 212000 215140 68568 FALSE TRUE 228052.9572 292535.6072 145712.1025 151873.8702 287238.4804 459139.0272 191440.2726 169133.9852 60461.96915 3.771841381 4.838340717 2.409979439 2.511890902 4.750729829 7.593848391 3.166292387 2.797361508 1 15.88374035 4.276165153 24.99933095 3.546054743 4.305089846 0.036438144 1.762318911 816.3449606 542690.0298 0.467632511 1.237179203 18887.09448 -4.276165153 0.759035103 ISLEVQLEQLRPFSHL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISLEVQLEQLRPFSHL 16 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 0 94.882 0.0035947 237780000 147410 150700 104250 93968 114650 140050 137790 163250 109420 FALSE TRUE 127929.395 149710.0418 154665.6487 115304.8706 112368.6893 145437.8141 124427.147 128340.2579 96484.49225 1.325906288 1.55164875 1.603010443 1.195061174 1.164629535 1.507369845 1.28960773 1.330164619 1 16.55800946 0.695555628 1.376382468 6.04E-13 1.386411366 0.398198567 0.144259211 5.551571088 3.098884562 15.75297528 0.04387266 4.960844664 -0.695555628 1.386411366 ISLPGQMAGT(ph)PITPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISLPGQMAGTPITPLK 16 0 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 1 ISLPGQMAGT(0.999)PIT(0.001)PLK;ISLPGQMAGT(0.955)PIT(0.045)PLK 225.69 7.43E-14 344550000 564910 534940 579350 629800 616910 607410 735260 729690 1712710 TRUE FALSE 490255.7122 531425.9439 859525.5978 772805.7159 604634.698 630777.4557 663954.5984 573651.472 1510235.375 0.324622056 0.351882861 0.569133535 0.5117121 0.400357923 0.417668309 0.439636503 0.379842428 1 20.52634198 1.235693471 24.9989418 1.000000772 0.427016859 0.863168912 0.072020887 29.09670405 253648.9958 0.124601361 0.018394545 17.20653695 -1.235693471 -0.572983913 ISLSKS(ph)PTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISLSKSPTK 9 1 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 ISLS(0.027)KS(0.97)PT(0.003)K;ISLS(0.002)KS(0.995)PT(0.004)K 100.04 0.0029865 2183910000 2175250 1686300 1395750 1626190 1759960 1279100 2083540 2452900 1657630 TRUE FALSE 1887785.201 1675222.584 2070739.369 1995441.294 1724940.239 1328307.805 1881478.611 1928366.423 1461666.87 1.291529035 1.146104231 1.416697205 1.365181996 1.180118586 0.90876234 1.287214379 1.319292695 1 20.47918311 3.13952866 7.127660056 1.159770169 1.301026551 0.2560496 0.138216546 0.398964543 24.96030077 0.044510545 0.050653565 1378.886947 -3.13952866 0.141256382 ISLSKS(ph)PTKTDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISLSKSPTKTDPK 13 2 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 IS(0.001)LS(0.001)KS(0.946)PT(0.04)KT(0.011)DPK;IS(0.036)LS(0.061)KS(0.86)PT(0.017)KT(0.027)DPK 103.01 0.00085802 3837100000 20092300 11586700 10549600 8823000 10093700 6045400 18895900 21322200 4238800 TRUE FALSE 17437051.65 11510586.2 15651421.85 10826397 9892855.118 6277970.45 17063378.53 16762613.46 3737693.893 4.66518986 3.079595744 4.187454162 2.896544584 2.646780448 1.679637399 4.565215616 4.484747532 1 21.83371699 7.090233746 1.02127555 3.161465685 200 0.152727781 1.155476233 549.7316508 5.521305646 0.366980608 247692.4896 12309311.04 -7.090233746 196.8385343 ISMPDFDLHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISMPDFDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 147.28 3.54E-05 1956620000 2850670 1906670 1324610 2168310 2059020 1926400 1766580 2795980 2676820 FALSE TRUE 2473946.737 1894144.959 1965195.827 2660657.926 2018049.53 2000509.855 1595257.344 2198081.435 2360369.389 1.048118463 0.802478192 0.83257978 1.127220993 0.854971912 0.847541009 0.675850717 0.93124468 1 21.17058122 ISMPDLDLHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISMPDLDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 123.01 0.00037892 417750000 387390 303390 188410 292940 332800 291690 284930 402010 364700 FALSE TRUE 336195.43 301397.0111 279525.7062 359456.5043 326177.9311 302911.503 257297.5325 316043.2899 321585.5815 1.04543067 0.93722178 0.869210942 1.117763124 1.014280334 0.941931232 0.800090387 0.982765734 1 18.2948432 2.610474882 5.964888144 0.925602205 0.992745604 0.133791151 0.082889507 0.518665304 23.02788953 0.029636636 0.026001641 407.8259739 -2.610474882 0.0671434 ISMPDLDLHLKS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISMPDLDLHLKSPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ISMPDLDLHLKS(1)PK 188.96 4.67E-07 415470000 1771700 642490 554130 587000 658810 531650 881070 1090800 895020 TRUE FALSE 1537565.356 638269.4409 822109.1215 720287.3217 645700.9699 552102.9195 795623.967 857540.9086 789211.7552 1.948229161 0.808742947 1.041683827 0.912666742 0.818159341 0.699562463 1.008124831 1.086578986 1 19.59005292 4.74279957 24.99937343 0.932102007 1.948229561 0.878877726 0.119681863 154.9511256 913796.3227 0.032027548 0.241854926 55309.47934 -4.74279957 1.016127554 ISMPDVDLHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ISMPDVDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 169.82 1.64E-05 1335878000 3815150 2353294 1817276 3036850 2900755 2399436 2331387 3681580 3895130 FALSE TRUE 3310968.261 2337835.057 2696116.752 3726413.208 2843035.651 2491743.856 2105289.448 2894302.767 3434652.169 0.963989394 0.680661372 0.784975194 1.084946313 0.827750675 0.725471964 0.612955649 0.842677111 1 21.71173257 2.999682525 24.99996095 0.78459238 0.870128125 0.068167895 0.141748656 34.60629272 2725485.41 0.044684593 0.050125754 999.269255 -2.999682525 0.085535745 ISMQDVDLSLGS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 313.04 9.18E-56 1422700000 2501520 1939780 1305466 1869540 2545560 1797824 2287310 3348180 2661800 TRUE FALSE 2170937.794 1927037.457 1936793.724 2294047.631 2494908.336 1866987.453 2065487.028 2632197.763 2347125.036 0.924934872 0.821020366 0.825177055 0.977386205 1.06296354 0.795435873 0.880007241 1.121456131 1 21.16246327 1.747907996 24.99977015 1.060832272 0.897798394 0.392355272 0.084122459 2.227816723 5975.181458 0.046170178 0.022171786 55.96390313 -1.747907996 -0.163033878 ISNCVQQHAWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISNCVQQHAWDR 12 0 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 0 124.3 0.00032541 171730000 106510 102590 59274 81993 106490 106610 99997 106770 106990 FALSE TRUE 92434.43364 101916.0795 87939.10466 100610.7638 104371.0573 110711.3557 90299.30633 83938.06639 94341.76408 0.979782756 1.080285921 0.932133351 1.066449889 1.106308095 1.173513732 0.95715092 0.889723308 1 16.52560896 2.024344304 24.98597482 0.93292042 1.055469335 0.339482656 0.070365221 222.2388213 228095.6367 0.029253706 0.019721886 105.7655675 -2.024344304 0.122548914 ISNDNPEEHVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISNDNPEEHVLK 12 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 107.17 0.0018433 160030000 229950 180430 121600 149980 174490 163510 202390 234500 228990 FALSE TRUE 199561.5249 179244.7434 180406.1667 184035.2513 171017.9904 169800.3355 182762.249 184353.9999 201919.0631 0.988324341 0.887705899 0.893457824 0.911430791 0.846963074 0.840932663 0.905126273 0.913009386 1 17.6234176 1.160748055 2.166254445 1.048266592 0.892614886 0.391970596 0.040084429 0.913950657 3.621317272 0.303076648 0.010810542 14.47931629 -1.160748055 -0.155651706 ISNLLSDYGYHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISNLLSDYGYHLR 13 0 P30876;C9J2Y9;C9J4M6 P30876 POLR2B DNA-directed RNA polymerase II subunit RPB2;DNA-directed RNA polymerase 0 ; 136.83 5.52E-06 391300000 754440 665680 345170 516100 694590 690400 586930 749530 636350 FALSE TRUE 654738.8425 661307.1042 512095.3665 633288.3931 680769.0179 716960.1347 530009.6189 589248.8423 561121.4279 1.166839849 1.178545447 0.912628428 1.128612029 1.213229408 1.277727242 0.944554231 1.050127144 1 19.09795348 2.215840133 24.99851088 1.006803264 1.139352909 0.33968544 0.096732391 315.0460813 346631.0806 0.041586912 0.028060347 164.3766529 -2.215840133 0.132549646 ISNLS(ph)PEEEQGLWK ddPTM_MDA-MB-175_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 384.56 7.68E-114 1655859000 2881860 1896350 1490720 1709640 1882050 1612480 2277770 2687090 2395320 TRUE FALSE 2501014.899 1883892.752 2211637.178 2097839.892 1844600.887 1674513.149 2056872.216 2112476.714 2112147.998 1.184109684 0.891932172 1.047103318 0.993225803 0.873329373 0.792801049 0.973829588 1.000155631 1 21.0102795 4.747478557 24.40941598 0.949522619 1.184109854 0.496414168 0.075142964 807.0098331 2208811.295 0.019556788 0.2266358 55908.59228 -4.747478557 0.234587235 ISNYGWDQSDKFVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISNYGWDQSDKFVK 14 1 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 144.33 8.10E-06 2959400000 2386200 1666960 1119780 1506310 1543880 1182730 2228000 2532300 1263730 FALSE TRUE 2070857.624 1656009.63 1661309.353 1848340.708 1513159.809 1228230.388 2011928.903 1990787.351 1114333.279 1.858382643 1.486099052 1.490855011 1.658696498 1.357905967 1.102210992 1.80550015 1.786527773 1 20.08774935 4.739503553 23.12354754 1.495238257 1.858382847 0.172924036 0.263844417 56.97230422 1396467.043 0.065232201 0.383871883 54891.30466 -4.739503553 0.36314459 ISPFEHQTYCQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ISPFEHQTYCQR 12 0 P28482;P28482-2;P27361;E9PBK7;E9PQW4;P27361-3;P27361-2;E9PJF0 P28482;P27361 MAPK1;MAPK3 Mitogen-activated protein kinase 1;Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 ;;; 177.83 2.28E-05 3941330000 2876430 3066290 1311160 2215290 3176420 2959330 2946950 3436100 3984260 FALSE TRUE 2496302.488 3046147.339 1945241.362 2718305.453 3113215.457 3073177.34 2661155.243 2701316.755 3513245.322 0.710540329 0.867046579 0.553687882 0.773730612 0.886136655 0.874740321 0.757463541 0.768894998 1 21.74437289 3.475080087 24.49367295 0.838852158 0.715690794 0.304266785 0.100105814 70.50599101 846045.2711 0.028433809 0.036972346 2985.933196 -3.475080087 -0.123161363 ISQEHLADHFDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISQEHLADHFDSR 13 0 P19174-2;P19174;V9GY71;V9GYH5 P19174-2 PLCG1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1" 0 ; 164.15 2.17E-05 543000000 402410 394680 193198 267650 392090 457230 357850 384810 428870 FALSE TRUE 349230.4989 392087.3211 286629.199 328424.0233 384288.1761 474819.934 323145.7621 302521.3761 378169.4772 0.923476166 1.036803192 0.757938481 0.868457248 1.01617978 1.255574452 0.854499851 0.799962436 1 18.5286734 ISQHEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISQHEAK 7 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 71.223 0.054899 365940000 1208700 1164130 366360 791220 816260 1055480 1356000 1515690 1559990 FALSE TRUE 1048967.233 1156482.753 543532.9214 970878.594 800018.023 1096084.999 1224495.329 1191571.489 1375569.759 0.762569274 0.840729992 0.395132939 0.70580106 0.581590296 0.796822547 0.890173196 0.866238503 1 20.39159787 2.461148257 2.937646823 0.907896713 0.65568032 0.490663114 0.121676283 0.229908661 4.081013202 0.049006364 0.037988886 289.1666857 -2.461148257 -0.252216394 ISQRDPS(ph)PESNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ISQRDPSPESNK 12 1 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 ISQRDPS(0.979)PES(0.02)NK;ISQRDPS(0.998)PES(0.002)NK;IS(0.009)QRDPS(0.99)PESNK 100.04 0.0014549 452240000 2079820 1617150 982590 1035610 1590630 1322580 1939950 2163130 501113 TRUE FALSE 1804966.517 1606526.835 1457773.811 1270761.079 1558979.575 1373460.508 1751813.948 1700561.483 441871.992 4.084817662 3.635729044 3.299086244 2.875857945 3.528124894 3.108276907 3.964528142 3.848538748 1 18.75326896 1.234281031 24.9999966 0.999996262 3.537548647 0.819375408 0.375238054 56.32480074 328987.8428 0.740586801 0.097378108 17.15066764 -1.234281031 2.537552385 ISQRDPS(ph)PESNKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISQRDPSPESNKK 13 2 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 ISQRDPS(0.975)PES(0.025)NKK;ISQRDPS(0.793)PES(0.207)NKK 88.427 0.0041292 228364000 865000 621750 415600 402940 576610 421300 877000 984550 200253 TRUE FALSE 750688.0584 617665.6833 616585.5501 494433.6856 565136.5891 437507.6836 791948.675 774011.6443 176579.3185 4.251279623 3.497950319 3.491833333 2.800065658 3.200468741 2.477683612 4.484945813 4.383365226 1 17.42995685 4.824129047 1.755450956 3.271572168 4.727463565 0.104101291 0.986851186 3.266657813 8.503377842 0.267764243 8.482172713 66700.49347 -4.824129047 1.455891397 ISQSALPPLPGS(ph)PAIQINGEWETHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISQSALPPLPGSPAIQINGEWETHK 25 0 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 ISQSALPPLPGS(1)PAIQINGEWETHK 111.31 6.56E-07 0 259720 231450 191050 235160 297090 245960 316000 382580 397830 TRUE FALSE 225397.344 229929.5897 283442.419 288556.6722 291178.4902 255422.2404 285354.3686 300768.2442 350798.9906 0.642525634 0.655445414 0.807990977 0.822569847 0.830043695 0.728115665 0.813441248 0.857380586 1 18.42028507 -2 0.050672989 2.205851799 1.87E-11 0.654541183 0.06057992 773.6596565 3.831339044 148.2555733 46.43174638 0.01 2 -2.205851798 ISRPGDSDDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ISRPGDSDDSR 11 1 A0A3B3ITJ4;M0R1W6;B4DVF8;M0QYL7;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;;;;; 125.82 0.00029219 21535570000 11773120 9665130 6160924 7908890 8947250 8978120 8895010 10247920 11152950 FALSE TRUE 10217272.36 9601639.125 9140367.453 9704724.354 8769217.23 9323514.086 8032373.299 8056482.057 9834460.956 1.03892551 0.976325918 0.929422313 0.98680796 0.891682551 0.948045259 0.816757861 0.819209318 1 23.22941455 4.09279912 0.516472833 0.867423149 1.070026051 0.347191894 0.05954204 2.635183438 0.984491633 0.05552887 0.315677432 12382.23721 -4.09279912 0.202602902 ISS(ph)KSPGHMVILDQTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISSKSPGHMVILDQTK 16 1 Q9NWH9;Q9NWH9-3 Q9NWH9 SLTM SAFB-like transcription modulator 1 IS(0.086)S(0.872)KS(0.042)PGHMVILDQTK;IS(0.094)S(0.861)KS(0.045)PGHMVILDQTK 247.55 1.60E-20 1736280000 3014600 2250500 921990 1109550 1988400 1550420 2864100 3016600 442970 TRUE FALSE 2616212.972 2235716.317 1367867.448 1361490.286 1948834.73 1610065.661 2586340.023 2371523.565 390602.5912 6.697889442 5.723762124 3.50194156 3.485615089 4.989303128 4.122004556 6.621410305 6.071448624 1 18.57534199 4.449215176 6.329379568 4.538200454 6.476103714 0.210126872 1.557194267 0.256754945 33.54045632 0.397674557 1.129999449 28132.94364 -4.449215176 1.937903259 ISS(ph)LLEEQFQQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ISSLLEEQFQQGK 13 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 1 IS(0.015)S(0.985)LLEEQFQQGK;IS(0.113)S(0.887)LLEEQFQQGK;IS(0.004)S(0.996)LLEEQFQQGK 244.56 5.01E-17 280647000 426200 390910 326303 345832 431490 349339 469220 541230 486860 TRUE FALSE 369876.5901 388342.0865 484104.2222 424358.4413 422904.1932 362778.2974 423715.1166 425492.1764 429303.9654 0.861572732 0.90458537 1.127649081 0.988480134 0.985092678 0.84503831 0.986981604 0.991121002 1 18.71163997 4.461023662 24.99927717 0.986073638 0.872325777 0.311910278 0.066897264 246.6833717 383095.0373 0.016984459 0.044963561 28908.37385 -4.461023662 -0.113747861 ISS(ph)PTETER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ISSPTETER 9 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 1 IS(0.471)S(0.524)PT(0.005)ETER;IS(0.08)S(0.915)PT(0.005)ETER;IS(0.022)S(0.977)PT(0.001)ETER;ISS(0.999)PT(0.001)ETER;IS(0.028)S(0.971)PT(0.001)ETER 160.77 6.82E-05 8399450000 6834380 7020170 4696090 5462690 7073190 6943310 7421280 8006370 8077560 TRUE FALSE 5931199.367 6974054.041 6967134.831 6703077.256 6932447.357 7210423.629 6701565.408 6294270.081 7122640.059 0.832724849 0.979138912 0.978167474 0.941094482 0.973297443 1.012324583 0.940882222 0.883699026 1 22.76398066 4.744578718 24.79437681 0.957852104 0.832724787 0.556596474 0.036386157 535.4498563 2205967.431 0.009719988 0.085425342 55536.52704 -4.744578718 -0.125127317 ISSDLDGHPVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ISSDLDGHPVPK 12 0 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 ;;;;; 153.34 7.06E-05 8039890000 17593600 17093100 8252890 12165500 15634600 12522000 16981500 18350300 24492700 FALSE TRUE 15268561.18 16980814.3 12244015.21 14927862.71 15323502.05 13003729.44 15334636.74 14426231.15 21597200.91 0.706969447 0.786250699 0.566926023 0.691194325 0.709513335 0.602102536 0.710028897 0.667967632 1 24.36434101 1.237303302 24.99772927 1.000000386 0.679557494 0.734267868 0.060475506 15.89955779 315982.03 0.084941427 0.014076167 17.27043602 -1.237303302 -0.320442891 ISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMR 34 0 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 ;;; 326.47 2.00E-117 3158021000 605117 682663 219616.6 410830 674715 682473 644909 673542 694554 FALSE TRUE 525149.2553 678178.5418 325823.9223 504115.2306 661289.4916 708728.1779 582365.8244 529510.2848 612444.6174 0.857464072 1.107330398 0.532005528 0.823119702 1.079753945 1.157211865 0.950887326 0.864584764 1 19.22421986 3.256793805 24.6455802 0.995115916 0.828506705 0.245407772 0.155984424 345.451275 466938.9068 0.046922021 0.060449309 1806.316315 -3.256793805 -0.166609211 ISSIQSIVPALEIANAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISSIQSIVPALEIANAHR 18 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 163.18 3.38E-11 582480000 818080 752410 481470 872300 895280 935850 687940 908660 1045720 FALSE TRUE 709968.6552 747467.3692 714310.5024 1070369.047 877465.6796 971852.7551 621223.6847 714350.1302 922096.1729 0.769950767 0.810617581 0.774659437 1.160799794 0.951598874 1.053960296 0.673708126 0.774702413 1 19.8145577 7.463773664 13.39528147 0.87802628 0.004400406 0 0.152946917 0 0 0.035710501 0 29092005.71 -7.463773664 -0.873625873 ISSLPVSRPIS(ph)PSPSAILER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ISSLPVSRPISPSPSAILER 20 1 Q5T5P2;Q5T5P2-3;Q5T5P2-7;Q5T5P2-9;Q5T5P2-2;Q5T5P2-10;Q5T5P2-8;Q5T5P2-6;Q5T5P1;Q5T5P2-4;Q5T5P0 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 ISSLPVSRPIS(0.996)PS(0.003)PS(0.001)AILER;ISSLPVSRPIS(0.959)PS(0.038)PS(0.003)AILER;ISSLPVS(0.001)RPIS(0.938)PS(0.031)PS(0.031)AILER;ISSLPVSRPIS(0.995)PS(0.005)PSAILER;ISSLPVSRPIS(0.972)PS(0.023)PS(0.005)AILER 286.23 2.04E-45 6542361000 2688692 2291269 1600872 1980238 2437560 2412879 2262727 2651915 1903001 TRUE FALSE 2333374.54 2276217.503 2375059.054 2429881.304 2389057.325 2505704.016 2043288.084 2084823.614 1678030.39 1.390543672 1.356481693 1.415385006 1.448055601 1.423727091 1.493241143 1.217670488 1.242423038 1 20.67833741 1.289492368 1.0562733 0.825467647 1.41672482 0.8272596 0.060416934 0.645450407 0.635326655 0.433054622 0.020151938 19.47566823 -1.289492368 0.591257173 ISSPTETER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ISSPTETER 9 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;;;;;; 209.87 1.79E-05 10756740000 4206890 4086742 2795375 3170235 4059364 4027143 4075937 4410612 4283339 FALSE TRUE 3650938.828 4059895.923 4147227.7 3890085.311 3978590.598 4182069.797 3680653.257 3467436.947 3776967.543 0.966632301 1.074908872 1.098031067 1.029949362 1.053382258 1.107255953 0.974499573 0.918047854 1 21.84879696 2.092283411 6.398996951 0.951207516 1.056346345 0.49315074 0.043396666 0.147753158 8.486004614 0.017337125 0.011594157 123.675425 -2.092283411 0.105138829 ISSVSSQFSDGPIPS(ph)PSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISSVSSQFSDGPIPSPSAR 19 0 E7EM83;Q92932-2;Q92932-4;Q92932;Q92932-3 E7EM83 PTPRN2 Protein-tyrosine-phosphatase;Receptor-type tyrosine-protein phosphatase N2 1 ISSVSSQFSDGPIPS(0.992)PS(0.008)AR 129.11 2.11E-05 66433000 67114 60369 52916 70939 91120 122700 72547 141220 103460 TRUE FALSE 58244.71485 59972.43206 78506.35459 87046.78418 89306.89027 127420.3484 65511.40311 111021.202 91229.07666 0.638444638 0.657382868 0.860540931 0.954156146 0.978930112 1.39670764 0.718097842 1.216949749 1 16.4772061 3.954307045 1.266010123 1.0719112 0.60671152 0.482549214 0.172374128 0.433911536 1.255165036 0.052645209 0.183254171 9001.337497 -3.954307045 -0.46519968 ISTAS(ph)GDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISTASGDGR 9 0 P63092-4;P63092;P63092-3;A0A590UJ58;B0AZR9;A0A590UJF0;A0A590UJY2;A0A0A0MR13;P63092-2;Q5JWF2 P63092-4;P63092-2;Q5JWF2 GNAS Guanine nucleotide-binding protein G(s) subunit alpha isoforms short;Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas 1 IS(0.003)T(0.052)AS(0.945)GDGR 84.687 0.016074 235350000 576810 493660 328080 475970 488440 586700 369360 634300 594010 TRUE FALSE 500583.097 490417.115 486740.5854 584046.2632 478720.9996 609270.7286 333539.5241 498659.8811 523786.8145 0.955700073 0.936291448 0.929272314 1.115045754 0.913961532 1.163203639 0.63678488 0.95202832 1 18.99862022 1.249377018 9.907528469 1.000168283 0.94522332 0.011408229 0.138625356 0.861510746 791.9940571 0.151636672 0.032736506 17.75730351 -1.249377018 -0.054944963 ISTCAPSTLHITQNTEQELHS(ph)PTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ISTCAPSTLHITQNTEQELHSPTVK 25 0 Q8WVV4-1;Q8WVV4;Q8WVV4-3 Q8WVV4-1 POF1B Protein POF1B 1 ISTCAPSTLHITQNTEQELHS(1)PTVK;ISTCAPSTLHITQNT(0.05)EQELHS(0.949)PT(0.001)VK;ISTCAPSTLHITQNTEQELHS(0.807)PT(0.193)VK 268.45 1.52E-45 2528730000 783930 559080 256514 480121 770590 634680 786850 928610 807480 TRUE FALSE 680331.6643 555407.3667 380565.0284 589139.8112 755256.7666 659096.5503 710541.4081 730033.978 712020.6343 0.955494309 0.78004392 0.534485955 0.827419576 1.060723145 0.925670575 0.997922495 1.025298907 1 19.44155953 3.389226246 5.276741975 0.99943184 0.747139584 0.540729416 0.105499976 0.152469878 7.008322692 0.030900454 0.040251172 2450.339417 -3.389226246 -0.252292256 ISVPPS(ph)PTYPPAGPPAFPAGDSKPELPLTVAIRPFLADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISVPPSPTYPPAGPPAFPAGDSKPELPLTVAIRPFLADK 39 2 Q96KQ4;A0A3B3ISJ2;H0YJL1 Q96KQ4 PPP1R13B Apoptosis-stimulating of p53 protein 1 1 ISVPPS(0.993)PT(0.007)YPPAGPPAFPAGDSKPELPLTVAIRPFLADK 149.37 1.16E-13 465120000 44727 53093 44968 53755 69378 51480 91926 115090 45512 TRUE FALSE 38816.21363 52744.22859 66714.67521 65960.89434 67997.51354 53460.46891 83011.03067 90478.89913 40131.62321 0.967222617 1.314280968 1.662396631 1.643613915 1.694362403 1.332128248 2.068469303 2.254553689 1 15.29245189 5.115519121 0.749337348 1.774687348 2.20E-14 0.279962541 0.352439102 5.510892235 1.615447754 0.143145175 9.330217639 130472.541 -5.115519121 -1.774687348 ISVSS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ISVSSPGR 8 0 O75864;O75864-2 O75864 PPP1R37 Protein phosphatase 1 regulatory subunit 37 1 IS(0.002)VS(0.122)S(0.876)PGR;ISVS(0.012)S(0.988)PGR;ISVS(0.036)S(0.964)PGR;ISVS(0.003)S(0.997)PGR;ISVS(0.046)S(0.954)PGR 142.92 0.00063962 9081630000 11587200 11046300 6983800 7972100 10238100 10898500 10430500 11344300 10675000 TRUE FALSE 10055922.16 10973736.13 10361189.04 9782287.151 10034381.84 11317772.35 9418951.715 8918409.726 9413013.661 1.068299965 1.16580476 1.100730267 1.039230102 1.066011609 1.202353758 1.000630835 0.947455305 1 23.16622526 2.055839272 9.804224943 0.971175342 1.104430695 0.589981801 0.04921316 0.241500303 40.57471248 0.019919462 0.013413956 113.720634 -2.055839272 0.133255354 ISVYDYDTFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISVYDYDTFTR 11 0 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-2;H0YD14 Q9NZM1-6 MYOF Myoferlin 0 ; 134.25 0.0027406 105670000 149805 153057 117741 105392 153159 180740 143473 166608 133136 FALSE TRUE 130007.8897 152051.5585 174680.9414 129322.8644 150111.4356 187693.1848 129559.0105 130980.1757 117396.8137 1.107422642 1.295193231 1.487953002 1.101587516 1.278667033 1.598792836 1.103599037 1.11570469 1 16.84103373 2.037195148 24.99990098 1.079176804 1.311443507 0.354177624 0.15214427 180.319005 121196.738 0.061198293 0.041259781 108.9419509 -2.037195148 0.232266703 ISVYYNEATGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ISVYYNEATGGK 12 0 Q5JP53;P07437 Q5JP53 TUBB Tubulin beta chain 0 212.09 5.65E-08 529680000 230170 187070 129900 143670 167500 165430 194420 223320 205860 FALSE TRUE 199752.4513 185841.1249 192720.0745 176292.4694 164167.0777 171794.1991 175565.1783 175564.7559 181523.4653 1.100422201 1.023785683 1.061681332 0.971182811 0.904384882 0.946402157 0.967176216 0.967173889 1 17.46979653 3.700203356 4.75325183 0.957038703 1.058732091 0.725636046 0.029776328 0.107222176 5.941263823 0.008356684 0.013068407 5014.219665 -3.700203356 0.101693388 ISWYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISWYLR 6 0 M0QYT0;M0R076;Q13011;M0R248;M0QZW4 M0QYT0;Q13011 ECH1 "Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial" 0 ; 166.22 0.016361 3671000000 1925300 2596700 1636910 2537400 2878900 3132800 2229400 2605400 2711300 FALSE TRUE 1670866.727 2579642.107 2428525.151 3113555.452 2821615.522 3253320.843 2013193.131 2048255.485 2390773.203 0.698881318 1.078999089 1.015790686 1.302321545 1.180210452 1.360781876 0.8420678 0.856733496 1 21.18904585 2.188139165 24.99968151 0.888272202 1.113104987 0.220395312 0.182415119 153.0910954 75903.544 0.075754414 0.051073694 154.2194554 -2.188139165 0.224832785 ISYT(ph)PPES(ph)PVPSYASSTPLHVPVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ISYTPPESPVPSYASSTPLHVPVPR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 2 IS(0.137)Y(0.239)T(0.624)PPES(0.973)PVPS(0.027)YASSTPLHVPVPR;IS(0.017)Y(0.033)T(0.95)PPES(0.986)PVPS(0.01)YAS(0.002)S(0.002)TPLHVPVPR;IS(0.039)Y(0.063)T(0.898)PPES(0.997)PVPS(0.002)YASSTPLHVPVPR 139.81 7.21E-07 1930640000 485127 445624 271301 418306 466937 423422 452410 469883 550178 TRUE FALSE 421016.2378 442696.6666 402503.071 513288.7707 457645.8672 439711.3183 408535.3478 369402.1771 485136.5836 0.867830322 0.912519652 0.829669591 1.058029405 0.943334069 0.906366028 0.842103774 0.76143954 1 18.88803145 0.953148231 20.71915955 2.050042959 0.887663169 0.162887381 0.078071338 110.5036292 103967.7867 17313.16126 0.020189294 8.977351515 -0.953148231 -1.16237979 ISYT(ph)PPESPVPSYASSTPLHVPVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ISYTPPESPVPSYASSTPLHVPVPR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 1 IS(0.019)Y(0.002)T(0.975)PPES(0.004)PVPSYASSTPLHVPVPR;IS(0.02)Y(0.062)T(0.917)PPES(0.001)PVPSYASSTPLHVPVPR 145.67 1.01E-06 608980000 503830 414420 186773 305230 453320 384130 360720 492630 429260 TRUE FALSE 437247.589 411697.6477 277097.0475 374537.1366 444299.8189 398907.7297 325737.4299 387284.9082 378513.3718 1.155170785 1.087670023 0.732066733 0.989495126 1.173802174 1.053880152 0.860570469 1.02317365 1 18.52998474 2.652124877 0.010938522 4.98E-07 1.999732895 0.022987085 0.130180655 15867.5423 173.982172 16039.51049 15760.79055 448.8744412 -2.652124877 1.999732398 ITADGAHFELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITADGAHFELR 11 0 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 ; 160.52 2.74E-05 563430000 997290 979380 580170 690750 934310 958560 925590 975430 997110 FALSE TRUE 865495.5997 972946.3883 860742.1526 847595.345 915719.0589 995436.4235 835826.4243 766841.8853 879232.7917 0.984375933 1.106585648 0.978969575 0.964016985 1.041497846 1.132164806 0.950631542 0.872171617 1 19.74588567 2.018595219 24.97156366 0.922289104 1.033195807 0.337767387 0.061382385 219.9060136 295311.0528 0.02480808 0.016722781 104.3746949 -2.018595219 0.110906703 ITADLLSNGIDVYPQKEFDEDSEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ITADLLSNGIDVYPQKEFDEDSEDR 25 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4 Q9UHD8 9-Sep Septin-9 0 ;;;; 324.18 2.30E-75 1944644000 1363316 1174590 1058020 1241283 1243417 1080249 1468042 1700465 1706312 FALSE TRUE 1183150.336 1166874.041 1569682.011 1523135.277 1218675.434 1121806.878 1325671.513 1336833.793 1504593.739 0.786358673 0.775540939 1.043259699 1.012323285 0.809969763 0.745587894 0.881082699 0.888501499 1 20.52094256 -1.999988887 0.012321803 1.896190789 1.03E-11 0.052244971 0.103248452 96974.76512 119.0285594 10550.99656 7945.166796 0.010000256 1.999988887 -1.896190789 ITADLLSNGIDVYPQKEFDEDSEDRLVNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITADLLSNGIDVYPQKEFDEDSEDRLVNEK 30 2 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4 Q9UHD8 9-Sep Septin-9 0 ; 315.84 1.18E-92 620180000 619520 541730 352980 343180 438390 348040 710930 759000 200272 FALSE TRUE 537648.8623 538171.34 523682.3086 421104.2642 429666.8967 361429.324 641984.118 596693.7565 176596.0723 3.044512006 3.047470609 2.965424439 2.384561891 2.433048997 2.046644182 3.635325008 3.378861991 1 17.43009373 3.892926164 6.449336356 2.626394948 3.036544102 0.089202683 0.719713217 0.77846495 40.20880647 0.198050343 0.347989333 7814.949284 -3.892926164 0.410149154 ITAHS(ph)SPPLTK ddPTM_MDA-MB-175_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(0.674)S(0.326)PPLTK 89.629 0.0077874 308100000 412590 345600 215460 253430 317520 286120 329460 414380 379090 TRUE FALSE 358065.1861 343329.7308 319657.1767 310975.1549 311201.9732 297127.2215 297509.0199 325768.0617 334274.4121 1.071171389 1.027089476 0.956271749 0.930299011 0.93097755 0.888872169 0.890014339 0.974552792 1 18.3506734 4.330252753 2.082247575 0.934627726 1.072172242 0.668541818 0.033389965 0.235624544 1.8547966 0.0099204 0.044788958 21392.06713 -4.330252753 0.137544516 ITDFENRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITDFENRR 8 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 80.219 0.041715 599230000 787390 705760 357170 381950 582800 607910 551120 640630 351140 FALSE TRUE 683334.4165 701123.8161 529898.6067 468677.5852 571203.4202 631296.6911 497672.4672 503636.2599 309628.6292 2.206948428 2.264402416 1.711400551 1.513676518 1.844801696 2.038883461 1.607320578 1.626581693 1 18.24017935 0.900124725 0.959244545 8.79E-27 1.917597141 0.603869925 0.23180589 2.859775886 1.345462258 6.688963627 0.086479824 7.945563902 -0.900124725 1.917597141 ITDKEAAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITDKEAAER 9 1 Q9NQG5;A2A2M0 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ; 93.258 0.0086833 524060000 1371380 1232030 781080 882290 1165990 1009000 1377740 1658970 826590 FALSE TRUE 1190148.658 1223936.714 1158812.901 1082627.429 1142789.08 1047816.883 1244126.987 1304212.176 728871.4719 1.632864921 1.679221593 1.589872763 1.485347515 1.567888337 1.437588002 1.706922324 1.789358242 1 19.47530491 1.228405283 24.98323784 0.999998731 1.614735315 0.778524343 0.102422906 221.4612834 544780.8065 0.377820921 0.028128529 16.92019185 -1.228405283 0.614736585 ITDLYTDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITDLYTDLR 9 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 129.29 0.00091533 253080000 454210 449960 309470 393410 466050 509610 441760 463450 544000 FALSE TRUE 394184.9977 447004.1831 459130.7271 482739.7534 456776.5168 529215.0265 398918.1832 364344.8241 479688.9397 0.821751275 0.931862601 0.957142617 1.006359983 0.952234832 1.103246255 0.831618472 0.759543933 1 18.87173965 ITDLYTDLRDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITDLYTDLRDGR 12 1 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 86.772 0.0099619 124302000 174783 178061 59861 52161 157624 177807 198427 190515 19358.6 FALSE TRUE 151684.9837 176891.3056 88809.97982 64004.95228 154487.5908 184647.3503 179183.5801 149774.8498 17070.04836 8.886031281 10.36267161 5.202678864 3.749547214 9.050214007 10.81703733 10.49695796 8.774131547 1 14.05917953 4.26829923 24.94098129 7.448900714 9.624352581 0.09700319 3.097754434 594.8843923 498903.8163 0.805626783 2.130835576 18548.09152 -4.26829923 2.175451867 ITDSAGHILYSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITDSAGHILYSK 12 0 P49755;G3V2K7 P49755 TMED10 Transmembrane emp24 domain-containing protein 10 0 ; 138.75 6.88E-05 3096500000 5110100 5616200 2626500 3920600 6097400 5871100 4918200 6466700 6330900 FALSE TRUE 4434787.338 5579306.812 3896684.185 4810832.153 5976073.669 6096965.016 4441233.721 5083846.529 5582468.214 0.794413361 0.999433691 0.698021742 0.861775109 1.070507424 1.092162961 0.795568116 0.910680784 1 22.4124717 3.453598967 24.70990508 0.959148115 0.836236391 0.271028558 0.109724926 312.8591716 328653.8596 0.032491536 0.041948901 2841.835707 -3.453598967 -0.122911723 ITEAEKNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ITEAEKNER 9 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;; 211.78 4.19E-06 6788530000 9396620 8194990 5289300 6572850 7636410 7563710 9572790 11703300 4191910 FALSE TRUE 8154832.859 8141156.571 7847223.172 8065316.052 7484460.381 7854690.818 8644422.299 9200640.37 3696347.175 2.206186939 2.202486992 2.122967027 2.181969298 2.02482614 2.124987304 2.338639173 2.48911694 1 21.81766884 1.230691114 24.99999926 0.999997798 2.217887835 0.900108763 0.126808734 99.42758663 315837.5277 0.387732383 0.036446966 17.00948302 -1.230691114 1.217890037 ITEDYYVHLIADNLPVATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITEDYYVHLIADNLPVATR 19 0 A0A0C4DFM1;Q92544 A0A0C4DFM1 TM9SF4 Transmembrane 9 superfamily member 4 0 ; 180.05 3.45E-14 499710000 857990 769140 620090 696090 817570 995070 673170 998780 935210 FALSE TRUE 744604.4476 764087.4687 919967.5981 854147.8736 801301.9565 1033350.987 607886.077 785198.6695 824650.5392 0.902933318 0.926559109 1.115584789 1.035769496 0.971686695 1.25307744 0.737143854 0.952159287 1 19.65342335 2.221544372 24.99999886 0.901406751 1.030292474 0.230009539 0.118618162 383.1793397 562956.8873 0.047481732 0.032103363 166.5498985 -2.221544372 0.128885722 ITEFCHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 ITEFCHR 7 0 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 ;;;;;;; 190.88 0.00053407 11728890000 12402570 11875160 8809810 10978310 11388420 14311710 9791920 9815960 13814530 FALSE TRUE 10763538.95 11797151.29 13070263.58 13471103.08 11161812.72 14862290.74 8842301.106 7716893.342 12181392 0.883605006 0.968456749 1.072969623 1.105875509 0.916300265 1.220081477 0.725885934 0.633498482 1 23.53817567 2.213667599 24.99685846 0.752070036 1.025703116 0.416804365 0.132537989 186.4291302 187205.3609 0.052448204 0.035377571 163.556421 -2.213667599 0.273633079 ITESEEVVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ITESEEVVSR 10 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;; 182.4 4.15E-06 1651360000 1024210 921780 685159 790457 830670 799770 826560 950560 1024120 FALSE TRUE 888858.0535 915724.7665 1016504.184 969942.3432 814141.2922 830537.6694 746400.3384 747290.1413 903049.7003 0.984284756 1.014035846 1.125634817 1.074074154 0.901546495 0.919703167 0.826532956 0.827518287 1 19.78444586 3.189112377 5.59745289 0.881094668 1.052506978 0.607866148 0.061156059 0.124534512 8.63127874 0.019402891 0.022485738 1545.654337 -3.189112377 0.17141231 ITEYLCEPLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITEYLCEPLRK 11 1 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;K7ERB2;K7EN71;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 ; 117.98 0.0012547 1776690000 1983770 1707420 1206510 1347640 1696750 1527400 1867270 2080400 1742700 FALSE TRUE 1721609.768 1696203.846 1789982.272 1653642.259 1662987.995 1586160.066 1686182.443 1635522.65 1536679.991 1.120343714 1.103810719 1.164837365 1.076113614 1.082195385 1.032199336 1.097289255 1.064322213 1 20.55138533 3.55264609 5.02653301 1.059825314 1.127079082 0.552772985 0.030395224 0.175213129 8.017898644 0.008343323 0.012376376 3569.818121 -3.55264609 0.067253768 ITEYMEHVYLIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITEYMEHVYLIHR 13 0 A0A2R8YDU7;A0A2R8YEX0;A0A2R8YD49;Q9H1P3-2;Q9H1P3;A0A2R8YG95;A0A2R8YFT0;A0A2R8Y690;A0A2R8YG59;E7ET92;A0A2R8Y5R1;A0A2R8Y362;A0A2R8YG53;A0A087WTV1 A0A2R8YDU7 OSBPL2 Oxysterol-binding protein-related protein 2;Oxysterol-binding protein 0 ; 249.2 9.42E-18 567320000 383400 425200 258390 354370 399600 405390 413240 443070 452000 FALSE TRUE 332732.7186 422406.8332 383348.2683 434835.1247 391648.7418 420985.6156 373164.0484 348322.9285 398565.0749 0.83482658 1.059818985 0.961821023 1.091001576 0.982646916 1.056253149 0.93626881 0.873942426 1 18.60445577 2.081036803 8.20630158 0.921181958 1.002299773 0.11462032 0.076455339 0.387516354 34.49826985 0.029226551 0.019662462 120.5138062 -2.081036803 0.081117815 ITFHGEGDQEPGLEPGDIIIVLDQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITFHGEGDQEPGLEPGDIIIVLDQK 25 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ; 184.29 1.91E-17 377990000 349400 267550 195250 259090 265710 221670 332600 404050 338560 FALSE TRUE 303225.9047 265792.4464 289673.5531 317920.3444 260422.8909 230197.7883 300344.5032 317647.0518 298535.8225 1.015710283 0.89032011 0.970314218 1.06493198 0.872333808 0.771089333 1.006058505 1.064016536 1 18.18754453 2.016039584 24.99899899 1.036117932 0.93038113 0.228083095 0.081247726 324.1256503 505174.3024 0.034390674 0.023179076 103.7622986 -2.016039584 -0.105736801 ITGCDPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ITGCDPFR 8 0 A0A087WT90 A0A087WT90 MRPL46 0 ;;; 105.2 0.010314 2653360000 4001020 5131460 4161830 4544670 4675050 5371540 4674410 5162690 8078400 FALSE TRUE 3472275.07 5097751.101 6174504.908 5576606.784 4582025.652 5578186.62 4221086.438 4058688.92 7123380.755 0.48744763 0.715636476 0.86679417 0.782859569 0.643237503 0.78308135 0.592567853 0.569770037 1 22.76413068 4.734935122 6.122236389 0.727017328 0.481807902 0.272837421 0.129172144 0.182960877 35.46035139 0.032030649 0.187914301 54316.91835 -4.734935122 -0.245209426 ITGEAFVQFASQELAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ITGEAFVQFASQELAEK 17 0 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 147.68 9.08E-07 9831500 23581 19204 12704 14589 18736 16228 16581 24161 22116 FALSE TRUE 20464.7111 19077.84766 18847.69689 17901.65543 18363.19026 16852.30166 14972.97717 18994.35817 19501.47167 1.049393166 0.978277331 0.966475618 0.917964333 0.941630999 0.86415538 0.767787038 0.973996142 1 14.25129538 4.489418023 0.938634629 0.904848233 1.086130164 0.340930554 0.063340529 1.830616535 1.694799418 0.023564625 0.313096312 30861.57051 -4.489418023 0.181281932 ITGMLLEIDNSELLHMLESPESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 164.66 1.16E-11 200900000 73232.5 75619.5 47653.2 52586.7 65131.2 72801.8 65462.1 80197.2 74695.5 FALSE TRUE 63554.63958 75122.75053 70698.44691 64527.31397 63835.21655 75602.53236 59113.59562 63047.65288 65865.08308 0.964921573 1.14055501 1.073382794 0.979689252 0.969181447 1.147839323 0.897495195 0.957224221 1 16.00722623 2.218167692 24.99982041 0.950497215 1.044978073 0.296411942 0.068511193 299.8877323 367631.7146 0.02750354 0.018567702 165.2599786 -2.218167692 0.094480858 ITHEVDELTQIIADVSQDPTLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ITHEVDELTQIIADVSQDPTLPR 23 0 P36954;K7EKS1 P36954 POLR2I DNA-directed RNA polymerase II subunit RPB9 0 ;; 203.64 1.87E-24 306727000 311922 289597 176181 220965 269956 299078 251859 308810 289773 FALSE TRUE 270700.7174 287694.6182 261382.7209 271138.4805 264584.4038 310583.7242 227433.7529 242773.3847 255516.3661 1.05942614 1.125934212 1.022958822 1.061139389 1.035489068 1.215514016 0.89009466 0.950128512 1 17.96305617 2.215961125 24.99999978 0.945086501 1.082132167 0.546575462 0.060007174 173.1750689 191568.2165 0.023540912 0.015883981 164.4224538 -2.215961125 0.137045666 ITHQEVDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ITHQEVDSR 9 0 Q8WTS6;D6RJA0 Q8WTS6 SETD7 Histone-lysine N-methyltransferase SETD7 0 117.67 0.0011135 278590000 371020 312690 231480 317530 272770 347870 328550 410410 448100 FALSE TRUE 321988.767 310635.9188 343424.5023 389630.0396 267342.4107 361252.784 296687.2716 322647.0153 395126.1285 0.814901227 0.786169014 0.869151589 0.986090293 0.676600183 0.914272072 0.750867255 0.816567147 1 18.59195372 1.23670371 24.96576941 1.000000223 0.825852837 0.290617822 0.085015651 60.9101877 818689.2839 0.122453504 0.019455298 17.24660869 -1.23670371 -0.174147385 ITITNDK ddPTM_MDA-MB-175_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 ; 88.954 0.046031 408870000 2310110 1746330 1100230 1307860 1532140 1517440 1865810 2081400 2342570 FALSE TRUE 2004823.11 1734858.243 1632304.908 1604829.602 1501653.412 1575816.899 1684864.033 1636308.807 2065634.043 0.970560646 0.839867182 0.790219794 0.776918645 0.726969725 0.762873222 0.815664342 0.792158133 1 20.97815325 4.716365522 2.774315406 0.802520798 0.997406199 0.321576727 0.072593916 0.470767373 5.148095027 0.018109053 0.20407877 52043.38335 -4.716365522 0.194885401 ITITNDKGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 163.38 5.75E-05 2892220000 1854090 1651200 886923 1104670 1556350 1541640 1955070 2224200 751170 FALSE TRUE 1609067.309 1640353.158 1315841.929 1355502.207 1525381.68 1600947.888 1765467.612 1748572.139 662367.5383 2.429266556 2.476499924 1.986573697 2.046450239 2.302923365 2.417008376 2.665389697 2.639881995 1 19.33727244 3.064278944 24.9991826 2.304707881 2.2268013 0 0.488863139 651.135476 253229.4755 0.148555196 0.168445755 1159.521869 -3.064278944 -0.077906581 ITITNDQNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ITITNDQNR 9 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 104.01 0.0077446 49547000 73702 67360 40547 46315 67269 85440 66146 72938 70332 FALSE TRUE 63962.09396 66917.50772 60155.66482 56831.52863 65930.47851 88726.93209 59731.1711 57340.7763 62017.43108 1.031356714 1.07901128 0.969979952 0.916379922 1.063095929 1.43067732 0.963135203 0.924591285 1 15.92038615 2.042260834 24.99992372 0.952992151 1.078907498 0.143991814 0.136442854 270.0788002 159767.3822 0.058567417 0.039486105 110.2201084 -2.042260834 0.125915347 ITKPGSIDSNNQLFAPGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ITKPGSIDSNNQLFAPGGR 19 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 200.99 5.66E-16 523930000 275160 275460 170730 223880 250080 240420 276030 323760 312300 FALSE TRUE 238796.9088 273650.4851 253295.5991 274715.3758 245103.8973 249669.113 249260.6531 254526.4435 275380.2498 0.86715336 0.993718632 0.91980307 0.997585615 0.890056195 0.906634057 0.905150799 0.924272687 1 18.07106557 3.201397336 24.99986948 0.922669202 0.946307769 0.038861435 0.046494197 524.4747801 352814.4738 0.013355292 0.015143797 1590.000775 -3.201397336 0.023638567 ITKPGSIDSNNQLFAPGGRLS(ph)WGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITKPGSIDSNNQLFAPGGRLSWGK 24 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 ITKPGSIDSNNQLFAPGGRLS(1)WGK;ITKPGSIDSNNQLFAPGGRLS(1)WGK 202.62 1.01E-24 4702200000 6508700 3476900 1426380 1627340 1781920 1322580 2352000 2570600 944380 TRUE FALSE 5648558.804 3454060.015 2116182.139 1996852.419 1746463.278 1373460.508 2123903.402 2020897.194 832736.4722 6.783128868 4.147842841 2.541238687 2.397940388 2.09725806 1.649333918 2.550510843 2.426814799 1 19.66750049 4.80703087 1.231342259 2.049219337 9.543275254 0.925185668 0.438704772 0.420208315 0.492395748 0.128512301 4.170486133 64125.51555 -4.80703087 7.494055917 ITLDNAYMEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ITLDNAYMEK 10 0 P14618;P14618-3;B4DNK4;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 141.1 8.87E-05 1312690000 1811970 1398830 942410 1300970 1353650 1208150 1695450 1754020 1925290 FALSE TRUE 1572513.574 1389640.994 1398162.628 1596375.123 1326715.013 1254628.312 1531025.52 1378936.473 1697684.409 0.926269668 0.818550837 0.8235704 0.940325018 0.781485066 0.739023287 0.901831643 0.812245471 1 20.69513686 1.232273966 24.99906864 1.000000264 0.840749198 0.375478062 0.063614207 227.5847188 904909.9131 0.136483306 0.014977676 17.07158978 -1.232273966 -0.159251065 ITLPVDFVTADKFDENAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITLPVDFVTADKFDENAK 18 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 237.3 6.93E-24 4668700000 7369400 5402700 3801500 3656400 3781900 2964400 5914000 7293100 6368900 FALSE TRUE 6395515.118 5367209.308 5639918.115 4486641.505 3706647.589 3078442.386 5340461.19 5733527.32 5615975.897 1.138807437 0.955703765 1.004263234 0.798906831 0.660018429 0.548158048 0.950940903 1.020931611 1 22.42110531 4.303098107 1.564969967 0.843597364 1.117921441 0.283937196 0.151838396 0.859081965 3.455204776 0.050639843 0.284359953 20095.46716 -4.303098107 0.274324078 ITLQDVVSHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITLQDVVSHSK 11 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 176.05 9.11E-06 2627200000 5873200 5360000 4045800 5205100 5663100 4714400 6566700 7313300 6445500 FALSE TRUE 5097041.739 5324789.807 6002362.412 6386997.51 5550415.39 4895766.019 5929862.445 5749407.707 5683520.333 0.896810681 0.936882336 1.0560994 1.123774903 0.976580546 0.861396763 1.043343227 1.011592705 1 22.43835337 4.412938786 5.740833966 1.009573859 0.905947464 0.265060431 0.066343484 0.251177934 15.48422839 0.017573856 0.048994947 25878.48128 -4.412938786 -0.103626394 ITNDFYPEEDGKTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ITNDFYPEEDGKTK 14 1 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 157.03 4.93E-06 223890000 170590 126670 78636 84148 119090 90115 156250 187900 51327 FALSE TRUE 148046.0993 125837.8964 116664.6326 103255.0895 116720.342 93581.78236 141096.899 147719.0472 45259.18053 3.27107335 2.78038389 2.577700949 2.281417567 2.578931846 2.067686186 3.117531016 3.263847147 1 15.46592284 4.668853946 1.9670013 2.513460042 3.430113949 0.154534798 0.621634028 1.421480281 6.628996513 0.164419824 2.240727185 46650.24688 -4.668853946 0.916653907 ITNFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITNFFR 6 0 P42574;A8MVM1 P42574 CASP3 Caspase-3;Caspase-3 subunit p17;Caspase-3 subunit p12 0 ; 170.31 0.013437 713700000 815480 745480 495220 594840 730740 749590 709690 839140 841330 FALSE TRUE 707712.2518 740582.8928 734710.0484 729907.5136 716199.7037 778427.2123 640864.373 659696.4412 741868.9258 0.953958613 0.998266496 0.990350213 0.98387665 0.965399249 1.049278633 0.863851215 0.889235845 1 19.50080479 2.232181651 24.99998004 0.90952304 0.98914919 0.388555324 0.042444655 137.7430097 539826.0166 0.016613192 0.011504844 170.6796137 -2.232181651 0.07962615 ITNQVHGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITNQVHGLK 9 0 P51665 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ; 84.213 0.015645 1272030000 3336600 3187700 1745270 2423800 3198800 3288300 3282400 3490500 3385400 FALSE TRUE 2895659.856 3166759.789 2589288.41 2974160.835 3135150.138 3414803.029 2964073.353 2744083.738 2985181.869 0.970011203 1.060826418 0.867380456 0.996308087 1.050237566 1.143917918 0.992928901 0.919235028 1 21.5093874 6.06401754 14.8854692 0.997463651 0.991312932 0 0.076064376 0 0 0.017835124 0 1158824.158 -6.06401754 -0.006150719 ITPAHDQNDYEVGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ITPAHDQNDYEVGQR 15 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ;;; 252.36 1.21E-24 3602340000 1050613 926968 622792 803380 924267 907496 909921 1007092 1051395 FALSE TRUE 911771.8301 920878.6862 923976.2943 985799.7079 905875.895 942407.9583 821677.0015 791733.213 927100.2809 0.983466243 0.993289189 0.996630368 1.063315078 0.977106699 1.01651135 0.886287081 0.853988753 1 19.82236587 2.239425116 24.99999957 0.899911897 1.00551356 0.48429639 0.043837518 16.24204649 469721.6847 0.016724458 0.01218931 173.5501992 -2.239425116 0.105601662 ITPFNLQEEMEEGHFDADGNYFLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITPFNLQEEMEEGHFDADGNYFLNR 25 0 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 0 ; 222.72 1.01E-33 136178000 49720 47843 27167.3 33937 43457 47796 40268 44754 33017 FALSE TRUE 43149.37603 47528.71618 40305.49715 41642.91454 42592.29072 49634.74305 36362.81556 35183.70538 29113.76787 1.482095214 1.632516835 1.384413633 1.430351259 1.462960442 1.704854668 1.248990365 1.208490276 1 14.82941394 1.790113238 1.883860454 1.046221316 1.506423262 0.705011442 0.111325858 0.188131347 1.257341839 0.111733497 0.031872676 61.67557945 -1.790113238 0.460201947 ITPHTS(ph)PAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ITPHTSPAPR 10 0 A0A0C4DFZ9;Q58A45-2;Q58A45-4;Q58A45-3;Q58A45 A0A0C4DFZ9 PAN3 PAB-dependent poly(A)-specific ribonuclease subunit PAN3 1 ITPHT(0.039)S(0.961)PAPR;ITPHT(0.196)S(0.803)PAPR;ITPHT(0.037)S(0.963)PAPR 142.97 2.24E-05 1456340000 333876 393370 277181 325582 456300 460530 425330 466170 422670 TRUE FALSE 289753.4407 390785.9266 411226.6587 399510.3693 447220.5227 478246.8871 384081.5621 366483.1732 372702.4341 0.777439089 1.04851992 1.103364564 1.071928522 1.199939903 1.283186916 1.030531402 0.983313066 1 18.50766472 4.741733908 3.204571645 1.091715018 0.730621707 0.549066251 0.089967045 0.311021745 5.022496874 0.025521879 0.282085401 55173.92854 -4.741733908 -0.361093311 ITPLEIEVLEETVQTMDTS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ITPLEIEVLEETVQTMDTS 19 0 Q99436 Q99436 PSMB7 Proteasome subunit beta type-7 0 ;;; 159.08 1.21E-10 43999000 88617 83499 53893.6 62978.9 82476 76802 81266 93959 86243 FALSE TRUE 76906.03892 82950.48957 79956.72522 77279.22182 80834.88896 79756.62264 73384.83583 73866.59904 76047.45079 1.011290163 1.090772783 1.051405726 1.016197401 1.062953302 1.04877444 0.964987453 0.971322487 1 16.21461227 2.244084323 24.9923833 0.976644143 1.048432313 0.642904495 0.023899925 73.63208777 333155.1501 0.008770507 0.006598345 175.4221071 -2.244084323 0.07178817 ITPPAAKPGS(ph)PQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITPPAAKPGSPQAK 14 1 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 ITPPAAKPGS(1)PQAK;ITPPAAKPGS(1)PQAK 117.65 0.00017615 2538550000 2546150 1844560 1410790 1409240 1822710 1207550 2379600 2655470 1987730 TRUE FALSE 2209669.826 1832442.964 2093052.763 1729229.481 1786441.637 1254005.23 2148826.758 2087618.405 1752742.824 1.260692554 1.045471668 1.194158512 0.98658483 1.019226331 0.715453068 1.225979493 1.191058025 1 20.7411829 7.730346545 1.051697288 1.050256817 153.1942173 0.174454245 0.145720825 2555.956718 5.010887 0.046138081 935917.676 53746049.11 -7.730346545 152.1439604 ITPSYVAFTPEGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ITPSYVAFTPEGER 14 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;; 212.89 4.19E-09 746970000 451816 420639 304413 393032 455476 525548 378343 403863 374575 FALSE TRUE 392107.3708 417875.7947 451628.145 482275.9227 446412.9187 545766.1716 341651.3541 317500.0403 330293.1702 1.187149497 1.26516632 1.367355385 1.460145005 1.351565697 1.652368928 1.034388189 0.96126735 1 18.33338761 2.102080329 8.319422987 0.984025583 1.376553913 0.688243109 0.121560208 0.136182934 9.921236146 0.050531734 0.034016188 126.4970301 -2.102080329 0.39252833 ITQAVLGAHDGGVFGLCALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ITQAVLGAHDGGVFGLCALR 20 0 O95834;O95834-2;O95834-3;K7EIK7;A0A0C4DGQ7;C9JRL6;K7EKG3;K7EII6 O95834 EML2 Echinoderm microtubule-associated protein-like 2 0 ;; 195.56 6.82E-22 539612000 445920 551522 322813 393343 566464 534085 451918 534549 434573 FALSE TRUE 386990.5422 547899.0157 478926.4465 482657.54 555192.4747 554631.5955 408091.0619 420239.8562 383198.275 1.009896358 1.429805538 1.249813681 1.259550399 1.448838658 1.44737498 1.064960592 1.096664269 1 18.54773154 2.217584343 24.6862795 1.063251112 1.314720304 0.453945364 0.130862065 182.8477188 215185.5217 0.051769372 0.034945185 165.0381487 -2.217584343 0.251469192 ITS(ph)PLMEPSSIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ITSPLMEPSSIEK 13 0 P28066 P28066 PSMA5 Proteasome subunit alpha type-5 1 IT(0.076)S(0.921)PLMEPS(0.002)S(0.001)IEK;IT(0.022)S(0.978)PLMEPSSIEK;IT(0.097)S(0.903)PLMEPSSIEK;IT(0.023)S(0.977)PLMEPSSIEK;IT(0.023)S(0.977)PLMEPSSIEK 152.55 4.40E-05 955222000 3443270 2621770 2063270 2433590 2617620 2336290 3161750 3606730 3888740 TRUE FALSE 2988233.145 2604547.42 3061074.273 2986173.805 2565534.483 2426168.588 2855123.972 2835458.857 3429017.587 0.871454599 0.759560823 0.892697163 0.870854036 0.74818353 0.707540433 0.832636141 0.826901229 1 21.70936387 1.187554989 2.973504542 1.053506341 0.809504699 0.492562658 0.059462187 0.456289216 4.47625439 0.287468426 0.015887895 15.40121518 -1.187554989 -0.244001643 ITSEIPQTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITSEIPQTER 10 0 F8VZQ9;H0YHG0;P82979 F8VZQ9 SARNP SAP domain-containing ribonucleoprotein 0 ; 154.04 3.54E-05 446840000 192461 202240 128963 146311 192186 196755 168236 197843 190140 FALSE TRUE 167026.7912 200911.4721 191329.9382 179533.1488 188361.8746 204324.2922 151920.4986 155535.8141 167661.8658 0.99621217 1.19831347 1.141165507 1.070804908 1.123462832 1.218668844 0.906112418 0.927675553 1 17.35519506 2.227210576 24.99994396 0.939467377 1.126346817 0.625200197 0.065715076 128.344864 282693.9718 0.025548437 0.017396101 168.7370981 -2.227210576 0.18687944 ITSENPDEGFKPSSGTVQELNFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ITSENPDEGFKPSSGTVQELNFR 23 1 Q13085;Q13085-4;Q13085-3;Q13085-2;O00763-3;O00763-2;O00763 Q13085 ACACA;ACACB Acetyl-CoA carboxylase 1;Biotin carboxylase;Acetyl-CoA carboxylase 2;Biotin carboxylase 0 203.4 1.74E-24 251170000 120340 74337 60830 77336 77730 77718 119430 131200 109860 FALSE TRUE 104436.7641 73848.67535 90247.59146 94896.32081 76183.32508 80707.86175 107847.697 103143.901 96872.47595 1.078085009 0.762328769 0.931612314 0.979600448 0.786429007 0.833135119 1.113295556 1.064738978 1 16.5637992 2.23735677 24.99999929 1.062716582 0.889706473 0.395865534 0.095400247 29.367901 609847.0322 0.035842774 0.025692035 172.7256238 -2.23735677 -0.173010109 ITSLSSS(ph)LDTSLDFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITSLSSSLDTSLDFSK 16 0 E9PR71;Q9P2Y5-2;Q9P2Y5 E9PR71 UVRAG UV radiation resistance-associated gene protein 1 ITSLS(0.013)S(0.104)S(0.882)LDT(0.001)SLDFSK;ITSLSS(0.007)S(0.993)LDTSLDFSK 276.14 2.89E-35 95029000 201195 272200 265740 344670 384720 340830 421750 496200 768980 TRUE FALSE 174606.571 270411.9003 394252.7528 422932.5915 377064.8247 353941.9506 380848.7499 390091.4914 678072.0604 0.257504447 0.398795226 0.581431939 0.62372809 0.556083707 0.521982797 0.561664124 0.575295038 1 19.37107907 0.003083538 1.257272558 9.999999999 0.499658562 0.6904013 0.104452277 17.89719165 1.788649476 431.312055 0.033179746 1.007125374 -0.003083538 -9.500341437 ITVGNDHFCVST(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ITVGNDHFCVSTPER 15 0 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 ITVGNDHFCVS(0.104)T(0.896)PER;ITVGNDHFCVS(0.111)T(0.889)PER;ITVGNDHFCVS(0.175)T(0.825)PER 154.55 9.04E-06 470160000 498240 429950 273811 291698 388299 416030 354303 383112 480040 TRUE FALSE 432396.3216 427125.6301 406226.9154 357932.4892 380572.6096 432034.9433 319942.7496 301186.4802 423290.2181 1.021512672 1.009060951 0.95968888 0.845595939 0.899081985 1.020658935 0.755847255 0.711536594 1 18.69128762 4.181818647 0.423241377 0.808003706 1.128580237 0.246616798 0.096982121 4.969183815 1.219765928 0.146476605 0.826666477 15199.12712 -4.181818647 0.320576531 ITVNGDS(ph)SAEAEELANEI ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ITVNGDSSAEAEELANEI 18 0 A0A0B4J1W3;Q9BXJ9 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 1 ITVNGDS(0.5)S(0.5)AEAEELANEI 159.22 1.21E-09 0 150520 156890 85681 119870 162660 156700 148660 176520 176630 TRUE FALSE 130628.4006 155859.3793 127116.6182 147088.3156 159423.3842 162728.3504 134242.9761 138772.5717 155749.0026 0.838710993 1.000708683 0.816163289 0.944393307 1.023591686 1.044811509 0.861918689 0.891001351 1 17.2488634 3.505690577 24.54986895 0.954415809 0.894001172 0.187319412 0.073116305 1256.128001 1079398.219 0.020965696 0.031019829 3203.985759 -3.505690577 -0.060414638 ITVQAS(ph)PGLDR ddPTM_MDA-MB-175_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 169.8 1.73E-05 688840000 861970 791560 478920 576570 783310 882630 669950 743900 751580 TRUE FALSE 748058.4805 786360.1902 710527.3139 707489.0308 767723.6635 916585.3472 604978.3521 584822.774 662729.0686 1.128754594 1.186548512 1.072123357 1.067538855 1.158427629 1.383046845 0.912859237 0.882446239 1 19.33805967 2.184229709 24.99997853 0.920704224 1.157907552 0.590223299 0.091710132 62.57516912 28792.95136 0.037968289 0.025598235 152.8374241 -2.184229709 0.237203329 ITVQAS(ph)PNLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ITVQASPNLDK 11 0 Q5TCX8;Q5TCX8-2 Q5TCX8 MLK4 Mitogen-activated protein kinase kinase kinase MLK4 1 ITVQAS(1)PNLDK 86.214 0.010481 0 67447 67250 44174 56532 62435 54212 69066 82287 77464 TRUE FALSE 58533.70806 66808.23032 65536.69415 69368.45464 61192.66565 56297.57072 62367.98995 64690.56541 68306.29417 0.856929933 0.978068436 0.959453224 1.015549965 0.89585691 0.824193018 0.913063587 0.94706595 1 16.0597309 1.320840689 2.904142507 1.007417629 0.923537104 0.169097039 0.055720635 0.708990058 8.041810328 0.127317084 0.015404199 20.93344421 -1.320840689 -0.083880526 ITVYEALNHPWLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ITVYEALNHPWLK 13 0 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8YEK3;O14936-6;O14936-2;A0A2U3TZN6;A0A2R8Y3B3;A0A2R8YEJ7;A0A2R8Y6D8;A0A2R8Y6F8;O14936-3;A0A2U3TZM4;A0A2R8YFN5;O14936-4 A0A2U3TZM1;A0A2R8Y6F8 CASK Peripheral plasma membrane protein CASK 0 70.438 0.044989 467600000 243050 178710 168230 193550 207120 166540 186810 234230 223900 FALSE TRUE 210930.3267 177536.0422 249586.5907 237498.4857 202998.7172 172946.9016 168693.195 184141.7373 197430.7971 1.068376007 0.899231756 1.264172532 1.202945484 1.028201883 0.875987456 0.854442151 0.932690036 1 17.59098753 2.945293772 4.764394577 0.914442938 1.106426366 0.447897916 0.100890755 0.206684838 9.935326985 0.034420962 0.035362262 881.6450478 -2.945293772 0.191983427 ITWSIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ITWSIIR 7 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 140.98 0.0060199 278350000 392250 429040 275420 326020 399690 398780 370650 436950 436810 FALSE TRUE 340413.1687 426221.608 408614.0332 400047.8239 391736.951 414121.3246 334704.42 343511.6428 385170.8194 0.883797919 1.106578138 1.06086446 1.038624433 1.017047324 1.075162769 0.868976577 0.891842335 1 18.55513888 2.239422107 24.99997503 0.912212565 1.034969981 0.370673561 0.067158382 20.68247328 600223.662 0.024848738 0.018109228 173.5489967 -2.239422107 0.122757415 IVAFENAFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IVAFENAFER 10 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 118.04 0.002042 196800000 158260 148280 95320 81631 131540 146980 125200 116670 123490 FALSE TRUE 137345.54 147305.9389 141417.0708 100166.5662 128922.6114 152634.4157 113058.1233 91721.02843 108891.1529 1.261310367 1.352781516 1.298701199 0.919877911 1.183958549 1.40171549 1.0382673 0.842318462 1 16.73252722 2.025322714 7.728152832 0.918518767 1.227659082 0.499920355 0.133854427 0.147219794 35.21693976 0.05813074 0.038429641 106.0041124 -2.025322714 0.309140315 IVAHAVEVPAVQS(ph)PR ddPTM_MDA-MB-175_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 114.69 0.00037762 1188780000 1192910 818310 496956 635880 730480 821170 781670 846860 803900 TRUE FALSE 1035263.921 812934.4677 737285.5838 780266.2728 715944.8772 852760.9413 705863.7637 665765.5793 708863.8578 1.46045522 1.146813254 1.04009476 1.100727967 1.009989251 1.202996784 0.995767743 0.939200909 1 19.43514905 7.907845862 0.91377545 1.025711251 199.9999999 0.77272198 0.071269609 406.1389302 1.008904989 0.024849768 168388.008 80880878.98 -7.907845862 198.9742886 IVALNAHTFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IVALNAHTFLR 11 0 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;A6NHQ2 P22087;A6NHQ2 FBL;FBLL1 rRNA 2-O-methyltransferase fibrillarin;rRNA/tRNA 2-O-methyltransferase fibrillarin-like protein 1 0 135.99 0.0001086 599860000 338620 352050 244690 305770 391530 379840 345990 431990 326520 FALSE TRUE 293870.509 349737.3604 363022.9024 375199.7519 383739.319 394452.6906 312435.9431 339612.3002 287919.1776 1.020670146 1.214706722 1.260850026 1.303142622 1.33280222 1.370011869 1.085151554 1.179540394 1 18.13530436 1.294921357 1.261592812 0.922272925 1.246806865 0.319434036 0.105340147 1.62230756 2.417837377 0.685323761 0.033511464 19.720656 -1.294921357 0.32453394 IVATKPLYVALAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IVATKPLYVALAQR 14 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YB86 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ; 144.68 8.01E-06 2057300000 1424940 1635940 996020 1273840 1544510 1503380 1647010 1906080 1635740 FALSE TRUE 1236630.569 1625193.402 1477698.603 1563084.841 1513777.273 1561216.001 1487283.224 1498479.625 1442364.681 0.857363318 1.126756239 1.024497219 1.083696004 1.049510774 1.082400327 1.031142293 1.038904824 1 20.46000454 4.752465205 24.79180851 1.052962588 0.85736317 0.749403346 0.035835433 1040.230654 1854689.803 0.008206455 0.162661417 56554.24449 -4.752465205 -0.195599418 IVDAVIQEHQPSVLLELGAYCGYSAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IVDAVIQEHQPSVLLELGAYCGYSAVR 27 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ;;; 294.68 1.33E-70 6482484000 1085689 1069944 703343.3 905511 1051442 1127299 1135520 1247854 1133772 FALSE TRUE 942212.4479 1062915.467 1043482.472 1111121.112 1030520.361 1170666.922 1025397.445 981010.1329 999738.7658 0.94245865 1.06319321 1.043755137 1.111411451 1.030789639 1.17097282 1.025665384 0.981266473 1 19.93119164 2.003026276 24.99988527 0.993546352 1.063897095 0.198802031 0.057893449 128.6990932 1063168.739 0.023065088 0.015456519 100.6992592 -2.003026276 0.070350743 IVDDLKDEAEQYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IVDDLKDEAEQYR 13 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 106.3 0.001263 240260000 262620 232950 168470 197910 187570 173880 248040 311110 387900 FALSE TRUE 227914.1016 231419.7361 249942.6555 242848.4904 183837.724 180569.2761 223985.119 244581.5476 342042.9039 0.66633191 0.676581018 0.730734807 0.709994236 0.537469779 0.527914113 0.654845098 0.715061019 1 18.38381777 1.196541112 2.359036517 1.123041832 0.64276546 0.743382291 0.065462043 0.385538051 2.058129745 0.404144822 0.019425884 15.72320629 -1.196541112 -0.480276371 IVDDLKDEAEQYRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IVDDLKDEAEQYRK 14 2 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 163.8 2.37E-06 243160000 850530 551900 455410 476730 552450 380180 736850 883160 521170 FALSE TRUE 738130.3055 548274.5326 675647.7993 584978.8329 541457.3259 394805.7706 665390.4004 694303.1068 459557.8763 1.606174855 1.193047842 1.470212641 1.272916564 1.17821357 0.859099128 1.447892496 1.510806674 1 18.80988704 6.724602062 1.604641757 1.26207906 199.9608937 0.219068403 0.207774069 1577.293185 8.867263942 0.05835054 1149271.773 5303982.25 -6.724602062 198.6988147 IVDDWANDGWGLKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IVDDWANDGWGLKK 14 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 115.12 0.00070226 380220000 463890 361080 254740 327950 418670 331570 394950 644340 363140 FALSE TRUE 402585.7612 358708.0417 377933.1161 402416.0599 410339.2861 344325.7125 356647.8098 506552.9053 320210.0029 1.257255418 1.120227471 1.180266427 1.25672545 1.281469293 1.075312168 1.113793469 1.581939667 1 18.28865885 IVDNVRPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IVDNVRPDR 9 1 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ;;;;; 101.38 0.0036678 3981410000 3909010 3672590 2245180 2704060 3804990 3990490 3326330 3801850 3594340 FALSE TRUE 3392424.424 3648464.514 3330956.558 3318058.152 3729278.143 4144006.732 3003743.029 2988853.964 3169421.22 1.070360861 1.151145355 1.050966825 1.046897185 1.176643268 1.307496368 0.947726042 0.943028318 1 21.59578798 2.156249542 25 0.958638341 1.128931455 0.521828736 0.07671587 22.62035321 6868.283373 0.032540124 0.021938551 143.301106 -2.156249542 0.170293113 IVDQIRPDR ddPTM_MDA-MB-175_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 ;;;;;;; 132.88 0.00026701 9419220000 5502280 4735020 2982701 3653940 4543610 4864260 4360730 5204120 5876310 FALSE TRUE 4775139.757 4703915.342 4425145.18 4483622.924 4453201.05 5051391.23 3937827.076 4091259.437 5181619.326 0.921553564 0.907807974 0.854008159 0.86529377 0.859422657 0.974867298 0.759960705 0.789571595 1 22.3049716 5.943935115 0.618634114 0.857656854 1.189214668 0.023298058 0.073503279 41.30112528 3.880100122 0.035134552 13.57135799 878891.1972 -5.943935115 0.331557813 IVEDEPNKICEADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IVEDEPNKICEADR 14 1 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 ;;; 186.77 9.34E-07 1945640000 2330270 1578770 1103310 1083850 1619820 1259460 1910740 1996810 1117990 FALSE TRUE 2022318.915 1568398.956 1636874.406 1329954.708 1587588.751 1307912.241 1725436.729 1569807.721 985822.4958 2.051402685 1.590954723 1.660414946 1.349081314 1.610420494 1.326721846 1.750250919 1.592383748 1 19.91096838 7.808647976 0.904487945 1.476969587 199.9811042 0.437456348 0.20969612 643.9430681 2.049843078 0.066592466 262967.9944 64364733.57 -7.808647976 198.5041346 IVEIDAHIGCAMSGLIADAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IVEIDAHIGCAMSGLIADAK 20 0 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ; 167.22 1.40E-11 49435000 96298 68522 67431 55628 60634 56605 85211 95171 70840 FALSE TRUE 83571.97531 68071.87447 100040.8571 68259.18762 59427.50203 58782.63098 76947.25034 74819.42227 62465.3759 1.337892778 1.089753699 1.601540945 1.092752371 0.951367076 0.94104342 1.231838426 1.197774306 1 15.93076912 3.529556403 24.99979226 1.081519095 1.322634296 0.411523965 0.153363987 376.085337 179307.1499 0.042652437 0.063263205 3384.982309 -3.529556403 0.241115201 IVELFR ddPTM_MDA-MB-175_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 ; 121.68 0.045473 251740000 398960 439330 262420 334010 388170 384770 375390 458150 389450 FALSE TRUE 346236.4252 436444.0123 389327.1897 409852.0755 380446.1764 399572.3509 338984.7356 360178.1878 343409.6647 1.008231453 1.270913597 1.133710637 1.19347857 1.107849358 1.16354428 0.987114722 1.048829503 1 18.38957112 2.243750043 24.99971857 1.018621975 1.151778917 0.464773622 0.067646542 101.3428181 488215.6817 0.023520437 0.017659758 175.287135 -2.243750043 0.133156942 IVEPEVVGES(ph)DS(ph)EVEGDAWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IVEPEVVGESDSEVEGDAWR 20 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 IVEPEVVGES(1)DS(1)EVEGDAWR;IVEPEVVGES(1)DS(1)EVEGDAWR 104.45 0.00039544 59253000 131420 113143 76248 81451 118166 108830 107808 123704 143962 TRUE FALSE 114052.514 112399.7562 113121.7878 99945.69445 115814.7278 113016.7605 97352.79675 97250.86227 126942.9764 0.898454702 0.885435015 0.891122857 0.787327486 0.912336634 0.890295499 0.766901798 0.766098803 1 16.95382105 4.24942183 0.85355187 0.840682283 0.914559912 0.014176087 0.073069873 3.880920786 3.6087635 0.029631931 0.237474787 17759.13588 -4.24942183 0.073877629 IVEPEVVGES(ph)DSEVEGDAWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IVEPEVVGESDSEVEGDAWR 20 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 IVEPEVVGES(1)DSEVEGDAWR;IVEPEVVGES(0.957)DS(0.043)EVEGDAWR;IVEPEVVGES(0.5)DS(0.5)EVEGDAWR;IVEPEVVGES(0.999)DS(0.001)EVEGDAWR;IVEPEVVGES(1)DSEVEGDAWR;IVEPEVVGES(0.999)DS(0.001)EVEGDAWR 330.27 8.66E-80 1609959000 951505 870318 608384 754794 801221 823128 807236 944370 935630 TRUE FALSE 825761.2034 864600.8238 902600.5373 926181.514 785278.2697 854794.2668 728950.377 742423.8246 825020.8873 1.00089733 1.047974466 1.094033559 1.122615837 0.95182835 1.036088031 0.883553845 0.899884883 1 19.65407112 2.689137474 1.545699496 0.924326337 1.0613333 0.453541002 0.056852728 0.312632383 1.517875604 0.026556016 0.021847712 488.807065 -2.689137474 0.137006963 IVETHQPIVETYYGPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IVETHQPIVETYYGPGR 17 0 A0A6I8PIQ6;A0A0A0MS45;J3KNI1;Q9H9E3;Q9H9E3-2;Q9H9E3-3 A0A6I8PIQ6 COG4 Conserved oligomeric Golgi complex subunit 4 0 142.58 5.81E-07 192690000 152360 134850 100090 97207 135010 126130 137890 164840 143270 FALSE TRUE 132225.24 133964.1615 148493.8588 119279.3351 132323.5651 130982.3027 124517.449 129590.2488 126332.7838 1.046642336 1.060406946 1.175418243 0.944167709 1.047420639 1.03680374 0.985630533 1.025784795 1 16.94686955 3.730417219 24.99994843 1.010273104 1.090780954 0.465769724 0.044021988 556.5090673 1708465.135 0.011577788 0.017509636 5375.479613 -3.730417219 0.08050785 IVEYS(ph)PPSAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IVEYSPPSAPR 11 0 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 1 IVEYS(0.999)PPS(0.001)APR;IVEYS(0.998)PPS(0.002)APR;IVEYS(0.996)PPS(0.004)APR;IVEYS(0.992)PPS(0.008)APR;IVEYS(1)PPSAPR 186.58 4.16E-06 1672930000 1845740 1948110 1224150 1483870 1934040 2008540 1668150 2122790 1801090 TRUE FALSE 1601820.782 1935312.737 1816153.035 1820805.363 1895556.388 2085809.833 1506373.07 1668847.878 1588167.192 1.008597074 1.218582494 1.143552797 1.146482166 1.193549645 1.313343988 0.948497789 1.050801129 1 20.59893137 2.21937427 24.99999317 1.008262357 1.171567836 0.508685051 0.079033998 197.8597203 257811.1842 0.03107413 0.020985877 165.7197504 -2.21937427 0.163305479 IVFAAGNFWGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IVFAAGNFWGR 11 0 P04181;P04181-2 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 92.439 0.010982 0 92374 120210 103130 129580 119180 131210 123860 143610 101410 FALSE TRUE 80166.54185 119420.3326 153004.0129 159003.1195 116808.5512 136257.7336 111848.0763 112900.1191 89421.42533 0.896502617 1.335477847 1.71104422 1.778132242 1.30627029 1.523770541 1.250797288 1.262562285 1 16.44833292 1.271434467 1.107844383 0.810414501 1.441866693 0.219461992 0.244767323 2.530043724 2.704536081 1.895716779 0.083368626 18.68247745 -1.271434467 0.631452192 IVFDSIDNLEAAPHDIGYVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IVFDSIDNLEAAPHDIGYVK 20 0 C9JEV6;Q9UJ70;Q9UJ70-2;H7C3G9;H7C286;H0YEB7;E9PPU6;H0YC94 C9JEV6 NAGK N-acetyl-D-glucosamine kinase 0 170.06 9.85E-12 42921000 84942 55385 110000 84922 53535 49939 71710 79051 105110 FALSE TRUE 73716.69948 55021.17229 163196.3679 104204.8381 52469.75824 51860.18564 64755.57524 62146.55883 92684.01554 0.795355046 0.593642517 1.760782234 1.124302151 0.566114426 0.559537536 0.698670368 0.670520785 1 16.50003293 3.245874074 24.99360914 0.688418712 1.084047976 0.248638538 0.318417602 238.8920687 816404.6524 0.095057745 0.120187897 1761.465228 -3.245874074 0.395629264 IVFSGNLFQHQEDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IVFSGNLFQHQEDSK 15 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 240.2 7.85E-18 1466990000 1423900 1181670 769540 1082190 1149370 959190 1352090 1604070 1806560 FALSE TRUE 1235728.007 1173907.532 1141692.118 1327917.78 1126499.786 996090.66 1220964.52 1261052.113 1592990.535 0.775728405 0.736920594 0.716697364 0.833600546 0.707160376 0.625296032 0.766460624 0.791625616 1 20.60330626 1.149004932 2.00285797 1.133362228 0.734990084 0.704007308 0.05325051 0.578722636 1.849963681 0.468058028 0.014777904 14.09304802 -1.149004932 -0.398372144 IVFSGNLFQHQEDSKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IVFSGNLFQHQEDSKK 16 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 189.42 6.63E-10 369550000 505150 430170 288010 367570 373870 271780 551000 576810 325910 FALSE TRUE 438393.1476 427344.1849 427292.5993 451032.3865 366430.7185 282235.5525 497564.1048 453463.6702 287381.2911 1.525475601 1.487028551 1.486849049 1.56945633 1.275068106 0.982094385 1.731372641 1.577916463 1 18.13260662 3.245411692 24.98639331 1.361164962 1.512879018 0.146720639 0.228591766 436.9291903 1593503.731 0.070468056 0.088943677 1759.590839 -3.245411692 0.151714056 IVGAPMHDLLLWNNATVTTCHSK ddPTM_MDA-MB-175_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 ; 255.37 8.76E-44 1443430000 1130830 1061730 690490 932560 998230 925580 1157640 1299820 1136740 FALSE TRUE 981387.9503 1054755.426 1024413.274 1144312.001 978367.176 961187.6615 1045372.251 1021863.608 1002355.892 0.97908134 1.052276376 1.022005539 1.141622462 0.976067666 0.958928529 1.042915255 1.019461866 1 19.93496341 IVGCICEEDNTSVVWFWLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IVGCICEEDNTSVVWFWLHK 20 0 P10606 P10606 COX5B "Cytochrome c oxidase subunit 5B, mitochondrial" 0 ; 258.2 3.02E-36 84831000 76163 93886 65920 121524 78466 81099 82995 116026 82655 FALSE TRUE 66097.86658 93269.25668 97799.13249 149117.8816 76904.68012 84218.93101 74946.15767 91214.74282 72883.62006 0.906896042 1.279701209 1.341853388 2.045972489 1.055170971 1.155526179 1.028299056 1.251512243 1 16.153307 IVGCSVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 114.89 0.0025684 3333860000 3055900 3450420 890914 2214870 3737760 4054640 3177670 4138060 3806770 FALSE TRUE 2652055.072 3427753.964 1321762.99 2717790.086 3663385.889 4210624.625 2869500.052 3253168.071 3356737.987 0.790069133 1.021156247 0.393764123 0.809652137 1.091352945 1.254379889 0.854847791 0.969145666 1 21.6786285 3.353572959 5.587634684 1.022362179 0.739119999 0.377179783 0.180237871 0.236373234 10.64727283 0.053075014 0.068726827 2257.215162 -3.353572959 -0.28324218 IVGCTHITAQTAVLIETLCALGAQCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IVGCTHITAQTAVLIETLCALGAQCR 26 0 O43865-2;O43865 O43865-2 AHCYL1 Putative adenosylhomocysteinase 2 0 132.26 5.69E-05 56121000 30529 27285 15782 26118 31067 32870 32725 33617 36667 FALSE TRUE 26494.5153 27105.76304 23414.22799 32048.49109 30448.82748 34134.53017 29551.33454 26428.26616 32332.26903 0.819444972 0.838350164 0.724175218 0.991223074 0.941747313 1.05574187 0.913988885 0.817395962 1 14.98068714 3.732750203 24.9950724 0.940510573 0.798426122 0.537510709 0.06896059 434.2430688 1868014.889 0.020612422 0.031521267 5404.433816 -3.732750203 -0.142084451 IVGELEQMVSEDVPLDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 IVGELEQMVSEDVPLDHR 18 0 Q00341;A0A024R4E5;Q00341-2 Q00341 HDLBP Vigilin 0 ;;;;;;;;;;;; 277.44 3.88E-39 2356568000 1518613 1414403 928029 1105934 1406007 1514445 1434639 1707055 1535403 FALSE TRUE 1317924.444 1405111.694 1376826.928 1357053.218 1378030.212 1572706.679 1295507.931 1342014.573 1353889.406 0.97343582 1.037833435 1.016941947 1.002336831 1.017830707 1.161621231 0.956878697 0.991229096 1 20.36867847 IVGWYHTGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IVGWYHTGPK 10 0 P51665;H3BNT7;H3BTM8 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ; 142.92 3.49E-05 1660680000 1666230 1709490 1183650 1430850 1618210 1467960 1794770 2085900 2093200 FALSE TRUE 1446033.484 1698260.248 1756067.099 1755746.362 1586010.787 1524433.371 1620713.482 1639846.517 1845744.281 0.783441942 0.920095089 0.951414081 0.95124031 0.859279806 0.825917971 0.87808127 0.888447297 1 20.81577126 IVILLDY(ph)MFQDLY(ph)NLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IVILLDYMFQDLYNLK 16 0 H3BQ49;H0YMX3;Q96FE5-2;Q96FE5 H3BQ49 LINGO1 Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 1 2 IVILLDY(1)MFQDLY(1)NLK 55.656 0.043514 323560000 317380 357230 106130 197520 377530 458120 233650 280240 282770 TRUE FALSE 275437.4289 354883.3326 157454.823 242369.9349 370017.8916 475744.1728 210990.659 220312.8568 249341.2527 1.104660484 1.423283667 0.631483243 0.972041057 1.483981842 1.908004262 0.846192343 0.88357965 1 17.92776207 IVILPDYLEIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IVILPDYLEIAR 12 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 118.71 0.0013866 95589000 197450 144700 127340 125150 168740 157600 181940 208760 170400 FALSE TRUE 171356.4822 143749.4562 188922.0499 153567.2203 165382.4041 163662.974 164295.4868 164118.2986 150255.5061 1.140433962 0.95670009 1.257338615 1.022040551 1.1006745 1.089231125 1.093440707 1.092261461 1 17.19705833 1.238562943 10.54335334 0.999717447 1.092546596 0.128956522 0.076704947 0.141914855 432.8211685 0.093997701 0.016738597 17.32060045 -1.238562943 0.092829149 IVKPNGEKPDEFESGISQALLELEMNSDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IVKPNGEKPDEFESGISQALLELEMNSDLK 30 2 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 259.93 1.60E-58 506640000 919210 576770 649760 573500 460500 360470 853120 1048600 935570 FALSE TRUE 797734.0695 572981.1599 963986.1093 703721.9404 451336.951 374337.5142 770384.5537 824365.0502 824967.9804 0.966987918 0.694549575 1.168513363 0.853029399 0.547096326 0.453760053 0.933835703 0.999269147 1 19.6539786 2.017689123 24.99593183 0.989673538 0.779274762 0.182669881 0.199840599 412.9282311 583493.3173 0.087099127 0.058709587 104.1571584 -2.017689123 -0.210398776 IVLDKLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IVLDKLER 8 1 P30047;H0YNX7;P30047-2 P30047 GCHFR GTP cyclohydrolase 1 feedback regulatory protein 0 ; 104.01 0.0042517 1637430000 4083600 3145400 2920800 4547900 3215400 3266100 3427900 4894900 5706600 FALSE TRUE 3543941.913 3124737.66 4333308.649 5580570.205 3151419.831 3391748.98 3095462.786 3848163.727 5031972.249 0.704284868 0.620976728 0.861155117 1.109022453 0.626279255 0.674039683 0.615158954 0.764742637 1 22.26269254 0.711013999 0.012030615 1.584563382 4.35E-06 0.020363952 0.167029018 90383.27872 234.7828844 16468.2451 14508.32208 5.140602219 -0.711013999 -1.584559032 IVLDNSVFSEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 IVLDNSVFSEHR 12 0 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ;;;;;;; 232.6 6.75E-13 15691390000 12189780 10616440 4847040 7619360 11559250 12400310 10538690 12169950 11952740 FALSE TRUE 10578869.69 10546699.91 7191084.756 9349452.143 11329243.54 12877357.95 9516649.466 9567500.899 10539700.69 1.003716329 1.000664081 0.682285481 0.887069986 1.074911316 1.221795412 0.90293356 0.907758311 1 23.32933056 3.261178503 23.87001354 1.008389348 0.886011101 0.201873383 0.124628476 266.588972 281344.2628 0.038929887 0.050211758 1824.64551 -3.261178503 -0.122378246 IVLDSDAAEYGGHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IVLDSDAAEYGGHQR 15 0 Q04446;E9PGM4 Q04446 GBE1 "1,4-alpha-glucan-branching enzyme" 0 125.97 8.72E-05 244130000 110320 109070 71546 62720 98381 125090 99618 96778 96349 FALSE TRUE 95740.93248 108353.512 106145.8849 76961.53462 96423.41058 129902.2932 89957.06169 76082.77783 84958.73098 1.126911047 1.275366413 1.249381714 0.905869635 1.134944101 1.529004633 1.058832455 0.895526298 1 16.3744746 2.004830008 24.99574792 0.95136428 1.20074298 0.322848254 0.155600752 147.0826564 761163.0082 0.065246379 0.043810987 101.1183578 -2.004830008 0.2493787 IVLEDGTLHVTEGSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IVLEDGTLHVTEGSGR 16 0 A0A1C7CYX9;Q16555-2;Q16555 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 0 ;;; 230.38 2.31E-15 1227130000 1410990 1321410 690550 1087500 1407670 1425550 1285190 1416470 1355970 FALSE TRUE 1224524.097 1312729.571 1024502.29 1334433.496 1379660.121 1480391.831 1160552.472 1113568.913 1195668.771 1.02413321 1.097904037 0.856844566 1.116056159 1.153881538 1.238128708 0.970630412 0.931335618 1 20.18938635 2.03709049 24.99999516 0.957828755 1.078928804 0.227573755 0.098604309 239.1546844 161195.7654 0.042185561 0.028441419 108.9157009 -2.03709049 0.121100049 IVNGWQVEEADDWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IVNGWQVEEADDWLR 15 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;;; 372.77 2.76E-97 1368923000 783076 624642 433924 490298 628439 654843 598517 691580 728986 FALSE TRUE 679590.5225 620538.6856 643771.0978 601627.6546 615934.2934 680035.2339 540472.9135 543690.9989 642806.1055 1.057224747 0.965359041 1.001501218 0.935939546 0.958196084 1.057916576 0.840802396 0.845808704 1 19.29402411 2.230197615 24.99981806 0.882896351 0.990427617 0.389276623 0.058343981 171.7571597 513434.6072 0.023157075 0.015903583 169.9016573 -2.230197615 0.107531267 IVNHPTMLQDPDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IVNHPTMLQDPDVR 14 0 Q13596-2;Q13596;H0YK42;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 0 ;;; 157.35 5.32E-06 1606510000 1506050 1538450 684370 1105050 1481050 1687000 1520290 1556160 1549140 FALSE TRUE 1307021.677 1528343.821 1015333.621 1355968.492 1451580.003 1751899.982 1372852.51 1223387.294 1366002.434 0.956822363 1.118844142 0.743288296 0.992654521 1.062648182 1.282501362 1.005014688 0.895596716 1 20.38152862 IVNHWAS(ph)PELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IVNHWASPELR 11 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 IVNHWAS(1)PELR;IVNHWAS(1)PELR;IVNHWAS(1)PELR;IVNHWAS(1)PELR;IVNHWAS(1)PELR;IVNHWAS(1)PELR 259.27 1.42E-20 1657050000 2133410 2415280 1379930 1538110 2202600 2169970 1961870 2517640 2096960 TRUE FALSE 1851474.463 2399413.867 2047268.764 1887361.384 2158772.569 2253450.15 1771608.149 1979262.278 1849059.778 1.001305899 1.297639966 1.107194472 1.020714099 1.167497447 1.21870054 0.958112967 1.070415517 1 20.81836044 2.232927403 24.99955166 1.020056733 1.137827421 0.300588552 0.090079102 176.7068073 784194.184 0.034881777 0.024245441 170.9729492 -2.232927403 0.117770688 IVNTQEQLNHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IVNTQEQLNHR 11 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 71.153 0.049809 198090000 156060 175540 108610 125230 139420 154050 119780 135780 196900 FALSE TRUE 135436.2756 174386.8662 161134.1593 153665.3855 136645.8148 159976.4032 108163.754 106744.5036 173622.7063 0.780060848 1.004401267 0.928070773 0.885053509 0.787027329 0.921402543 0.622981615 0.614807279 1 17.40559611 2.250272596 24.99925472 0.713489634 0.887391005 0.202631376 0.123881334 262.0521611 559351.2485 0.045985591 0.035318409 177.9395942 -2.250272596 0.173901371 IVPEGEWGQFMDALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IVPEGEWGQFMDALR 15 0 Q08J23;Q08J23-2;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 79.82 0.020734 0 53518 52021 39815 38789 42449 43423 57329 72155 46105 FALSE TRUE 46445.4607 51679.27063 59069.66717 47596.6353 41604.34795 45093.51091 51769.2424 56725.21476 40654.51942 1.142442743 1.271181442 1.452966804 1.170758774 1.023363418 1.109188143 1.273394524 1.39529911 1 15.31112812 IVQMTEAEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IVQMTEAEVR 10 0 P62140;C9JP48;C9J9S3 P62140 PPP1CB Serine/threonine-protein phosphatase PP1-beta catalytic subunit;Serine/threonine-protein phosphatase 0 111.61 0.004027 38579000 36307 30997 24874 24583 33486 37128 28650 39063 33490 FALSE TRUE 31508.93796 30793.37867 36903.1496 30164.94588 32819.69411 38556.33819 25871.52741 30709.68144 29530.85035 1.066983767 1.04275286 1.249647374 1.021472308 1.111369762 1.305629121 0.876084742 1.03991863 1 14.84993528 2.219966563 24.99992022 0.982154139 1.128127695 0.379886041 0.096530638 271.9387318 365622.0985 0.038157917 0.025777055 165.9459139 -2.219966563 0.145973556 IVRGDQPAASGDS(ph)DDDEPPPLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IVRGDQPAASGDSDDDEPPPLPR 23 1 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 1 IVRGDQPAASGDS(1)DDDEPPPLPR;IVRGDQPAASGDS(1)DDDEPPPLPR;IVRGDQPAASGDS(1)DDDEPPPLPR 239.69 1.91E-37 1027030000 716010 562430 420540 497480 772280 616060 569370 877260 282730 TRUE FALSE 621387.4644 558735.3603 623914.5506 610440.4375 756913.1389 639760.2268 514152.585 689664.7758 249305.9815 2.492469136 2.241163076 2.502605621 2.448559131 3.036080941 2.566164771 2.062335536 2.766338664 1 17.92755797 1.232660685 24.99965266 0.999997551 2.512023015 0.766133444 0.26295917 93.85365274 397643.2179 0.56162648 0.06383695 17.08679798 -1.232660685 1.512025464 IVS(ph)PGLTIHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IVSPGLTIHER 11 0 A0A0U1RR07;Q9HCH5-13;Q9HCH5;Q9HCH5-14;Q9HCH5-15;Q9HCH5-6 A0A0U1RR07 SYTL2 Synaptotagmin-like protein 2 1 IVS(1)PGLTIHER;IVS(1)PGLTIHER 190.57 1.42E-06 238900000 134350 152982 99903 121938 172384 181863 162948 178466 175321 TRUE FALSE 116595.3071 151977.0512 148216.425 149625.8866 168953.8957 188859.3873 147145.328 140302.4347 154594.7511 0.75419965 0.983067343 0.958741638 0.967858776 1.092882484 1.221641653 0.951813221 0.907549795 1 17.23813181 5.367593622 1.273174541 1.01403649 8.69E-14 0.460944827 0.087946654 6.55853706 2.947974883 0.028179167 12.8616455 233127.5619 -5.367593622 -1.01403649 IVSGIITPIHEQWEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IVSGIITPIHEQWEK 15 0 Q5QPM7;Q5QPM9;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 0 ; 255.91 9.72E-25 797470000 1079020 992250 635480 800630 929510 854200 958360 1165580 1077380 FALSE TRUE 936424.7731 985731.8444 942800.2536 982425.2784 911014.5696 887061.6267 865418.3947 916329.7876 950013.3638 0.985696422 1.037597872 0.992407359 1.034117325 0.958949215 0.933735946 0.910953917 0.964544103 1 19.85758828 3.150289762 6.242000931 0.950083926 1.01264156 0.532025612 0.027384254 0.160310855 9.197829437 0.008376013 0.009564771 1413.480305 -3.150289762 0.062557634 IVSRPEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IVSRPEELR 9 1 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;; 142.43 9.52E-05 1577990000 1391380 1399960 1078320 1480290 1467450 1491290 1519390 1522860 3206090 FALSE TRUE 1207505.608 1390763.571 1599799.159 1816412.469 1438250.616 1548660.891 1372039.792 1197208.24 2827069.693 0.427122689 0.491945273 0.565886 0.642507142 0.50874254 0.54779721 0.485322239 0.423480271 1 21.43087602 1.23214834 24.9999522 1.000000812 0.512452867 0.850101631 0.064451759 87.59296663 341471.443 0.158516675 0.017169496 17.06665229 -1.23214834 -0.487547945 IVSRPEELREDDVGTGAGLLEIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IVSRPEELREDDVGTGAGLLEIK 23 2 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;; 226.24 5.79E-33 1914530000 887660 740631 524830 615122 706041 644081 922241 1041160 798188 FALSE TRUE 770353.482 735765.7462 778639.5435 754794.8517 691992.1654 668859.2128 832802.2098 818516.0363 703827.1239 1.094520878 1.045378504 1.106293743 1.072415123 0.98318485 0.950317472 1.183248246 1.162950401 1 19.42486159 2.221504693 24.99999952 1.128132986 1.043800153 0.202668349 0.066983095 347.4607582 509292.1493 0.028272094 0.019114648 166.5346825 -2.221504693 -0.084332833 IVTDRETGSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IVTDRETGSSK 11 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;; 149.23 3.14E-05 1169870000 2358150 1888780 486816 599338 1472470 1361130 2062760 2316800 136356 FALSE TRUE 2046514.503 1876372.48 722241.8459 735426.8532 1443170.728 1413493.552 1862713.853 1821370.349 120236.149 17.02079216 15.60572669 6.006861096 6.116520358 12.00280232 11.75597824 15.49212835 15.14827582 1 16.87551118 4.373543895 7.257353703 10 16.65791443 0.281698158 4.422508725 0.296040819 17.88026059 1.174221877 3.14784665 23634.36267 -4.373543895 6.657914431 IVYGHLDDPASQEIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IVYGHLDDPASQEIER 16 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ;;; 220.61 1.13E-14 2480550000 963720 1062010 721484 1221720 1233640 1403220 913570 1199190 1109470 FALSE TRUE 836361.9602 1055033.586 1070396.076 1499130.199 1209092.978 1457202.781 824972.122 942752.5506 978309.7205 0.854905091 1.078424924 1.094128018 1.532367682 1.235899994 1.489510684 0.843262726 0.963654486 1 19.89993175 2.212704986 24.99989469 0.937626542 1.218024232 0.305252596 0.198046772 286.7422587 277249.8877 0.084010294 0.056660912 163.1943 -2.212704986 0.28039769 IVYLQYPSLIPHHQCSQLCLYDWYTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IVYLQYPSLIPHHQCSQLCLYDWYTK 26 0 C9JIF9;P13798;H7C1U0 C9JIF9 APEH Acylamino-acid-releasing enzyme 0 182.39 1.08E-17 258370000 323910 353640 112400 276930 284690 238270 404910 361060 336850 FALSE TRUE 281104.4728 351316.9156 166757.016 339811.1891 279025.226 247436.4011 365641.8905 283850.1288 297027.9767 0.946390559 1.182773823 0.56141855 1.144037652 0.939390387 0.833040725 1.231001519 0.955634321 1 18.1802393 2.270307187 24.99950835 1.04704188 0.938580779 0.095997961 0.182484111 521.6047449 410746.8802 0.064386904 0.049869314 186.34047 -2.270307187 -0.108461101 IVYLYTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IVYLYTK 7 0 P49207 P49207 RPL34 60S ribosomal protein L34 0 119.89 0.01089 236220000 448810 523470 318400 376030 440620 415380 570900 594460 582650 FALSE TRUE 389498.6214 520031.2911 472379.305 461413.3588 431852.5241 431359.9374 515534.2059 467339.3551 513769.7808 0.758118978 1.012187385 0.919437699 0.898093613 0.840556491 0.839597722 1.003434272 0.909627955 1 18.97076251 2.237746698 24.99995571 0.959581139 0.885193222 0.275153418 0.069712098 34.5812846 1062113.627 0.026607864 0.019131899 172.880774 -2.237746698 -0.074387917 IWAHEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IWAHEALR 8 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 163.9 0.00033324 1400600000 441441 926840 560220 556320 950110 1014110 803910 842069 942130 FALSE TRUE 383103.4534 920751.527 831144.2658 682640.9588 931204.6699 1053123.468 725946.9319 661999.0973 830752.4647 0.461152352 1.108334391 1.000471622 0.821714034 1.120917132 1.267674202 0.873842646 0.796866847 1 19.66405914 4.747143516 24.57306448 0.983849085 0.461152015 0.574776243 0.144810097 735.5486363 2105835.311 0.038327016 0.431666577 55865.47766 -4.747143516 -0.52269707 IWDDGDDFCIFSESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IWDDGDDFCIFSESR 15 0 Q6P158-2;Q6P158 Q6P158-2 DHX57 Putative ATP-dependent RNA helicase DHX57 0 ; 168.02 2.97E-06 62664000 68758 69536 43616 51853 63266 66350 71803 75472 74587 FALSE TRUE 59671.45609 69079.21344 64708.84349 63627.01617 62007.13038 68902.52743 64839.55611 59332.90012 65769.40983 0.907282827 1.050324362 0.983874474 0.967425682 0.942795907 1.047637916 0.985861912 0.902135207 1 16.0051291 1.924034559 23.90896298 0.944053374 0.986497672 0.065494675 0.048596515 159.2926276 50133.08131 0.021064971 0.012158169 83.95267887 -1.924034559 0.042444298 IWDILGDRPSLVHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IWDILGDRPSLVHSR 15 1 Q13610;B4DJV5 Q13610 PWP1 Periodic tryptophan protein 1 homolog 0 ; 163.8 9.12E-07 434620000 636330 643980 238810 431700 706310 692500 600880 711230 487550 FALSE TRUE 552237.3782 639749.653 354299.3148 529724.0831 692255.8129 719140.9231 542606.7501 559138.9993 429912.3944 1.284534676 1.488093066 0.824119796 1.232167507 1.610225297 1.67276155 1.262133302 1.300588228 1 18.71368318 1.128270494 2.270030008 0.823748174 1.34262447 0.168891694 0.234056622 1.89357726 7.741075358 2.245394141 0.06585179 13.43601544 -1.128270494 0.518876296 IWDLEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IWDLEGK 7 0 P63244;J3KPE3;H0YAF8;H0Y8W2;D6RAC2;D6REE5;H0YAM7;D6RF23;H0Y9P0 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 ;;; 143 0.005702 2459640000 4746560 4064430 2799350 3358190 3757500 3227900 4373300 5183560 4550380 FALSE TRUE 4119290.07 4037730.492 4153125.023 4120718.366 3682733.101 3352079.402 3949178.039 4075096.033 4012439.26 1.026629888 1.006303206 1.035062403 1.026985855 0.917828997 0.835421843 0.984233725 1.015615631 1 21.93604812 3.257972863 24.6638303 0.955505606 1.023307867 0.341221617 0.050232574 302.4095678 384217.4791 0.016609819 0.021409979 1811.226915 -3.257972863 0.067802261 IWDPTPSHTPAGAAT(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IWDPTPSHTPAGAATPGR 18 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 IWDPTPSHT(0.036)PAGAAT(0.963)PGR;IWDPTPSHT(0.015)PAGAAT(0.985)PGR;IWDPTPSHT(0.001)PAGAAT(0.999)PGR 167.51 8.47E-11 802200000 2008460 1743150 1374580 1839290 1900130 1900580 1618830 1998010 4559840 TRUE FALSE 1743036.922 1731699.133 2039331.486 2256928.906 1862321.131 1973696.542 1461836.116 1570751.11 4020780.91 0.433507063 0.430687265 0.507197863 0.561316062 0.463173988 0.490873934 0.363570199 0.390658219 1 21.9390443 1.234557656 24.99999591 1.000000791 0.453360779 0.901110107 0.056724076 38.73626111 241888.2657 0.116350801 0.015668646 17.16159529 -1.234557656 -0.546640012 IWDPTPSHTPAGAAT(ph)PGRGDT(ph)PGHAT(ph)PGHGGATSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSAR 37 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 3 IWDPT(0.001)PS(0.009)HT(0.034)PAGAAT(0.954)PGRGDT(0.947)PGHAT(0.876)PGHGGAT(0.062)S(0.06)S(0.057)AR 65.641 0.0024259 192540000 85241 79960 49408 67203 88172 84486 77625 84665 77021 TRUE FALSE 73976.18588 79434.7375 73301.87406 82462.46828 86417.54971 87736.23109 70096.93945 66560.04861 67915.66512 1.089235977 1.169608475 1.079307313 1.214189217 1.272424404 1.291840858 1.032117396 0.980039708 1 16.05145676 2.091131697 6.774471357 0.993777023 1.185258955 0.622603652 0.06734133 0.144051916 8.962845976 0.030098511 0.020170913 123.3478821 -2.091131697 0.191481932 IWDPTPSHTPAGAAT(ph)PGRGDT(ph)PGHATPGHGGATSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 IWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSAR 37 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 IWDPTPS(0.001)HT(0.097)PAGAAT(0.902)PGRGDT(0.998)PGHAT(0.002)PGHGGATSSAR;IWDPTPS(0.001)HT(0.018)PAGAAT(0.981)PGRGDT(0.999)PGHAT(0.001)PGHGGATSSAR;IWDPTPS(0.001)HT(0.3)PAGAAT(0.698)PGRGDT(0.968)PGHAT(0.032)PGHGGATSSAR;IWDPTPS(0.002)HT(0.323)PAGAAT(0.676)PGRGDT(0.98)PGHAT(0.02)PGHGGATSSAR;IWDPTPSHT(0.003)PAGAAT(0.997)PGRGDT(0.871)PGHAT(0.127)PGHGGAT(0.001)S(0.001)S(0.001)AR;IWDPT(0.005)PS(0.022)HT(0.117)PAGAAT(0.857)PGRGDT(0.821)PGHAT(0.11)PGHGGAT(0.023)S(0.023)S(0.022)AR 157.85 6.38E-15 2381740000 870347 869830 352625 633995 954101 898859 750237 917082 691723 TRUE FALSE 755328.4388 864116.0295 523155.6295 777953.2548 935116.2568 933438.6874 677479.1312 720971.151 609948.295 1.238348308 1.416703738 0.857704881 1.275441314 1.53310742 1.530357073 1.110715673 1.182020111 1 19.21832743 2.107801634 20.88950864 1.115554619 1.303315969 0.206142809 0.193958974 5.742101565 1084.584594 0.083614905 0.056373167 128.1745006 -2.107801634 0.18776135 IWDPTPSHTPAGAAT(ph)PGRGDTPGHATPGHGGATSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSAR 37 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 IWDPTPSHT(0.002)PAGAAT(0.998)PGRGDTPGHATPGHGGATSSAR;IWDPTPS(0.003)HT(0.075)PAGAAT(0.909)PGRGDT(0.012)PGHATPGHGGATSSAR 131.17 6.07E-09 1726710000 751210 740990 195171 414982 790740 788360 697370 791090 603950 TRUE FALSE 651935.6952 736122.3879 289556.3484 509210.0057 775005.8211 818688.7193 629739.1647 621921.5598 532551.719 1.224173488 1.382255209 0.543714982 0.956170054 1.45526865 1.537294295 1.18249391 1.167814388 1 19.02256211 3.259313177 24.91118096 1.262959292 1.017493613 0.177465913 0.258395027 441.2752068 529699.2842 0.078827828 0.101651284 1816.825332 -3.259313177 -0.245465679 IWDPVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IWDPVHR 7 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8;A0A494C1S4;A0A494C159 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ;;; 107.59 0.0074425 287220000 1152080 1167400 781150 883060 1172280 1319090 1149470 1275860 1340640 FALSE TRUE 999829.709 1159731.273 1158916.753 1083572.27 1148953.922 1369836.246 1037994.576 1003027.268 1182151.066 0.845771524 0.981034747 0.980345732 0.91661066 0.971918018 1.158765817 0.87805578 0.848476389 1 20.17298298 IWDSVSLSTLHVLGLGVFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IWDSVSLSTLHVLGLGVFDR 20 0 O95834;O95834-2;O95834-3;K7EIK7;A0A0C4DGQ7;C9JRL6;K7EKG3;K7ERY9;K7EKU5;K7ERR9 O95834 EML2 Echinoderm microtubule-associated protein-like 2 0 ; 216.96 1.09E-24 400440000 187468 217689 110404 135787 191966 186011 212899 198347 186082 FALSE TRUE 162693.6288 216258.9866 163795.7437 166619.5137 188146.2522 193166.9635 192252.0877 155932.0376 164083.5979 0.991528897 1.317980525 0.998245685 1.015455023 1.146648748 1.177247244 1.171671576 0.950320687 1 17.32407151 1.712506374 8.149838256 0.977366321 1.119580478 0.257640111 0.099722601 0.145529433 23.25371553 0.05501194 0.02480439 51.58297357 -1.712506374 0.142214157 IWDYQNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IWDYQNK 7 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ; 127.31 0.0089977 829890000 2855100 2321700 1598820 1977560 2317700 1764290 2944100 3267900 2856200 FALSE TRUE 2477791.301 2306448.6 2372014.7 2426595.223 2271582.305 1832163.378 2658581.635 2569085.016 2518543.29 0.983819222 0.91578676 0.941820103 0.963491568 0.901942926 0.72746948 1.055602914 1.020067841 1 21.2641581 IWEDLDDDDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IWEDLDDDDPK 11 0 O75717;C9JYB3 O75717 WDHD1 WD repeat and HMG-box DNA-binding protein 1 0 ; 125.48 0.00076173 19868000 135295 117378 91835 107169 120003 90358 118355 158381 165718 FALSE TRUE 117415.423 116606.9362 136246.7132 131503.3594 117615.1751 93834.13073 106876.9503 124512.4557 146127.0068 0.803516239 0.797983472 0.932385574 0.899925088 0.804883215 0.642140921 0.731397656 0.852083803 1 17.15686331 IWEQIQPDLHTNDECVATYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IWEQIQPDLHTNDECVATYK 20 0 Q12904;Q12904-2 Q12904 AIMP1 Aminoacyl tRNA synthase complex-interacting multifunctional protein 1;Endothelial monocyte-activating polypeptide 2 0 ; 230.99 1.30E-25 512490000 464410 386550 261850 274420 353540 317160 413630 488740 443090 FALSE TRUE 403037.0418 384010.7276 388481.5358 336731.2552 346505.2457 329361.3504 373516.2263 384226.7544 390708.405 1.031554573 0.982857606 0.994300432 0.861847994 0.886864069 0.842985066 0.955997418 0.983410517 1 18.57573277 3.902195857 9.304582884 0.925667164 1.002595135 0.359009527 0.051016117 0.499516304 43.95752704 0.015350474 0.026660797 7983.546469 -3.902195857 0.076927971 IWEVIGDHFNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IWEVIGDHFNK 11 0 Q9Y6D6;E5RIF2;E5RHL7 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 0 166.14 2.08E-05 237950000 506790 422850 311930 344640 432710 371570 477440 556320 616630 FALSE TRUE 439816.4175 420072.2705 462780.3913 422895.7795 424099.9176 385864.5383 431137.9423 437355.2973 543732.7039 0.808883509 0.772571279 0.851117448 0.777764104 0.779978682 0.709658506 0.792922587 0.804357167 1 19.05253808 1.218117647 3.493935127 1.037726467 0.78422931 0.787058027 0.034913572 0.155534425 2.687610245 0.108811623 0.009114 16.52409362 -1.218117647 -0.253497157 IWFDKFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IWFDKFK 7 1 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;E9PPR1;E9PL12;E9PMW7;E9PK06;H0YCK7;E9PIZ1;E9PK72;E9PKK3;E9PJD0;E9PNW6;P29692-3;E9PL71;E9PN91 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 83.265 0.020435 210210000 452120 914020 277160 236010 752130 680920 999460 1025400 29999 FALSE TRUE 392371.1965 908015.7424 411195.503 289599.6777 737164.0845 707115.433 902532.523 806126.1897 26452.55239 14.8330184 34.32620523 15.54464374 10.94789166 27.86740854 26.73146328 34.11892015 30.47441992 1 14.69111931 -1.991520679 2.00E-18 9.229656746 36.89889634 0 11.04738437 0 0.124132737 9.997055418 9.997055418 0.010197162 1.991520679 27.66923959 IWGEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IWGEDLR 7 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;;; 139.92 0.0061873 2565150000 6339930 5437720 3801490 4466250 5499210 5879180 5581430 6432150 5946340 FALSE TRUE 5502092.187 5401999.259 5639903.279 5480380.325 5389786.48 6105355.859 5040143.778 5056684.778 5243370.459 1.049342638 1.030253212 1.075625559 1.045201816 1.027924027 1.164395289 0.961241212 0.964395863 1 22.32206305 IWGLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IWGLGR 6 0 P41743 P41743 PRKCI Protein kinase C iota type 0 123.07 0.044078 155340000 159500 148360 95449 133970 143120 153690 157580 149170 147980 FALSE TRUE 138421.6709 147385.4134 141608.4557 164389.9361 140272.192 159602.5538 142297.9159 117271.1563 130485.973 1.060816483 1.129511548 1.085238914 1.259828412 1.074998245 1.223139546 1.090522702 0.898726152 1 16.9935352 1.884295903 4.987019764 0.949339725 1.139909971 0.570721715 0.066922507 0.139483364 4.979738657 0.033030874 0.016792871 76.61184183 -1.884295903 0.190570247 IWHHTFYNELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 18 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 ;;;;;;;;;;;;;;;;; 214.44 1.36E-11 1.19514E+11 14177786.5 23771015 21798211.5 15266745.9 20652029 22024013 17768086.9 21729003 21032936 FALSE TRUE 12304156.09 23614861.64 32339899.49 18733293.89 20241094.03 22871291.03 16044940.57 17082424.8 18546446.27 0.66342392 1.273282293 1.743724864 1.010074578 1.091373179 1.233189944 0.865122101 0.921061887 1 24.14463944 2.240587934 24.98913641 0.924480623 1.189257349 0.149481771 0.267467842 93.61637494 1153960.393 0.104345852 0.076716635 174.0155 -2.240587934 0.264776726 IWHVIGDHFNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IWHVIGDHFNK 11 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 0 117.14 0.0005177 105440000 208930 171180 139460 156110 173000 140510 222260 238380 265350 FALSE TRUE 181319.3711 170055.5073 206903.3225 191557.1615 169557.6385 145915.5106 200705.2594 187404.2921 233980.6253 0.77493327 0.726793114 0.884275449 0.818688134 0.724665293 0.623622193 0.857785807 0.800939359 1 17.83602955 0.830907462 1.488372745 1.411715658 0.768871731 0.483509422 0.073270366 3.15869721 2.668231096 4.121629295 0.021510173 6.774971335 -0.830907462 -0.642843926 IWHYTGSILHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IWHYTGSILHK 11 0 F8WAE5;Q9BY44-4;Q9BY44-3;Q9BY44;Q9BY44-2;H7C5R5 F8WAE5 EIF2A "Eukaryotic translation initiation factor 2A;Eukaryotic translation initiation factor 2A, N-terminally processed" 0 185.77 2.50E-06 344870000 360020 361500 117650 287370 389250 320170 408960 418950 487730 FALSE TRUE 312442.4448 359125.2827 174545.9335 352621.7507 381504.6866 332487.1471 369299.1221 329360.8028 430071.115 0.726490187 0.835036974 0.405853654 0.819914982 0.887073494 0.773098066 0.858693154 0.7658287 1 18.71421571 3.510671335 24.99737087 0.842580896 0.663578982 0.355822732 0.123610833 727.7683664 542241.2304 0.032450548 0.048096781 3240.94257 -3.510671335 -0.179001914 IWLS(ph)TETLANED ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IWLSTETLANED 12 0 Q9NXD2 Q9NXD2 MTMR10 Myotubularin-related protein 10 1 IWLS(0.5)T(0.5)ETLANED 190.85 6.41E-06 104320000 255440 243160 163630 184480 232430 280530 238330 259850 246720 TRUE FALSE 221682.9568 241562.6659 242762.0153 226369.0036 227805.0977 291322.1706 215216.7933 204283.0997 217553.0427 1.018983481 1.110362158 1.115875064 1.040523271 1.047124393 1.33908571 0.989261242 0.939003643 1 17.73100767 2.027870176 24.99998979 0.964840901 1.110753932 0.342007749 0.089111906 214.5196682 192426.6446 0.035651782 0.024035935 106.6277331 -2.027870176 0.145913031 IWNVHSVLNVLHSLVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IWNVHSVLNVLHSLVDK 17 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ; 259.14 1.98E-27 172716000 420485 420204 228940 348341 325173 294876 448640 495650 427150 FALSE TRUE 364916.8419 417443.6523 339656.1498 427437.1481 318702.6935 306220.0705 405130.9619 389659.1047 376652.8136 0.968841407 1.108298245 0.901775156 1.134830626 0.846144465 0.813003539 1.075608484 1.034531246 1 18.52287578 IWPLYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IWPLYLR 7 0 Q9HCS7 Q9HCS7 XAB2 Pre-mRNA-splicing factor SYF1 0 97.306 0.049931 0 91575 128190 63897 71927 106690 120340 97935 100160 89624 FALSE TRUE 79473.13173 127347.9114 94797.80292 88259.12469 104567.0777 124969.5577 88437.27877 78741.56345 79028.75282 1.005623003 1.61141239 1.199535606 1.116797641 1.323152321 1.581317599 1.119051935 0.996366014 1 16.27009002 2.010852936 24.84153887 1.015859049 1.311032667 0.331453958 0.184840532 207.28846 474465.5155 0.072931127 0.049118417 102.5304672 -2.010852936 0.295173618 IWQYVYSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IWQYVYSK 8 0 P61163;R4GMT0;A0A1B0GVS3;P42025 P61163;P42025 ACTR1A;ACTR1B Alpha-centractin;Beta-centractin 0 139.19 0.0030815 0 340020 385710 216980 258990 345340 359690 397330 425830 319140 FALSE TRUE 295085.4955 383176.2456 321912.2538 317797.6379 338468.4096 373527.5071 358796.9978 334769.5683 281411.6328 1.048590254 1.361621913 1.143919498 1.129298156 1.20275202 1.327334991 1.274989929 1.189608137 1 18.10232244 1.248683113 4.261566461 0.981406554 1.217529386 0.335036623 0.093171578 0.235471108 8.180202276 0.167592273 0.02258853 17.72895399 -1.248683113 0.236122832 IWS(ph)PTIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IWSPTIGR 8 0 Q92545 Q92545 TMEM131 Transmembrane protein 131 1 IWS(0.995)PT(0.005)IGR 104.42 0.0048074 47314000 31611 30306 20126 31311 40017 34132 29226 42247 30533 TRUE FALSE 27433.52626 30106.91789 29859.00092 38420.64111 39220.73999 35445.08013 26391.66702 33212.80782 26923.42352 1.018946429 1.118242554 1.109034328 1.427034013 1.456751589 1.316514599 0.980249298 1.233602695 1 14.71657425 3.973657893 24.09158943 1.234852773 1.079855351 0.180537412 0.155636742 850.9670244 778268.3067 0.0441591 0.076872787 9411.479326 -3.973657893 -0.154997421 IWTAHYDPGHCFAESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IWTAHYDPGHCFAESR 16 0 Q9H553;A0A0A0MTE0 Q9H553 ALG2 "Alpha-1,3/1,6-mannosyltransferase ALG2" 0 89.484 0.0033393 180600000 399010 443030 241430 312370 480720 553440 347840 434400 343820 FALSE TRUE 346279.8175 440119.7068 358186.3555 383298.3828 471154.6125 574731.1949 314106.5303 341506.9405 303173.9913 1.142181808 1.451706675 1.181454761 1.264285176 1.554073324 1.89571405 1.03606028 1.126438779 1 18.20978647 IWTVDDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IWTVDDYR 8 0 Q676U5-3;Q676U5;E7EVC7;Q676U5-2;Q676U5-4;Q676U5-5 Q676U5-3 ATG16L1 Autophagy-related protein 16-1 0 ; 89.142 0.032838 195507000 502300 475960 308100 375470 474580 497290 462640 503730 512850 FALSE TRUE 435919.7823 472833.3874 457098.1905 460726.2022 465136.7865 516421.0681 417773.244 396011.2595 452221.4572 0.963952009 1.045579284 1.010783949 1.018806593 1.028559744 1.141964982 0.923824461 0.875702055 1 18.78666992 2.089150531 16.62071092 0.920210435 1.033299985 0.438669081 0.05359818 1.335281712 246.0695848 0.021252101 0.014328163 122.7864747 -2.089150531 0.11308955 IWYEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 IWYEHR 6 0 O75874;P48735;P48735-2;H0YL11 O75874;P48735 IDH1;IDH2 "Isocitrate dehydrogenase [NADP] cytoplasmic;Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;;;;;;;;; 149.11 0.010679 16574940000 7401621 6796355 4492001 6076137 6849361 7539095 6281411 7091535 7141717 FALSE TRUE 6423478.032 6751709.297 6664347.708 7455816.774 6713072.117 7829128.863 5672240.728 5575065.427 6297431.352 1.02001557 1.072137022 1.058264447 1.183945701 1.066001635 1.243225758 0.900722916 0.885291973 1 22.58633206 2.211894785 24.99808519 0.918469547 1.105050895 0.58286864 0.071030341 142.2556064 133357.5262 0.028197123 0.019016505 162.8901355 -2.211894785 0.186581349 IYAMHWGTDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IYAMHWGTDSR 11 0 P62879;E7EP32;C9JZN1;C9JIS1;C9JXA5;P62873-2;P62873;F6X3N5;F6UT28;B1AKQ8 P62879;P62873-2 GNB2;GNB1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2;Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 0 ;; 160.77 2.71E-05 2847630000 1750487 2272983 1491377 2460139 2952240 3847050 2035569 3080520 3144390 FALSE TRUE 1519155.708 2258051.625 2212611.906 3018751.161 2893496.2 3995048.503 1838159.832 2421774.771 2772663.796 0.547904766 0.814397919 0.798009448 1.088754852 1.043579897 1.440870151 0.662958067 0.873446962 1 21.40284126 4.519082437 1.360559753 0.994133308 0.483086733 0.355663862 0.199185068 1.104495402 2.477422773 0.061002636 0.699160337 33043.22571 -4.519082437 -0.511046575 IYDALDVSLIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IYDALDVSLIER 12 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;; 212.28 5.15E-08 107884000 270355 242877 154744 178037 229683 237789 239663 249013 253111 FALSE TRUE 234626.9018 241281.525 229578.716 218463.022 225112.7577 246936.8967 216420.5191 195763.5078 223188.5059 1.051249932 1.081066088 1.028631448 0.978827387 1.008621644 1.10640508 0.969675917 0.877121817 1 17.76790321 2.015119333 14.5602888 0.927866778 1.03907332 0.48578379 0.045812897 1.312235332 1262.538758 0.018747801 0.012576988 103.5426635 -2.015119333 0.111206542 IYDDDFFQNLDGVANALDNVDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IYDDDFFQNLDGVANALDNVDAR 23 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 229.15 5.79E-33 274361000 255281 224904 141112 173366 215384 225722 215238 257140 232727 FALSE TRUE 221544.9691 223426.5908 209354.2352 212731.4 211098.2798 234405.6714 194364.2519 202152.6121 205214.2792 1.079578721 1.08874778 1.02017382 1.036630594 1.028672472 1.142248348 0.947128302 0.985080633 1 17.64677159 2.214991501 24.99980846 0.977741034 1.061926393 0.556014285 0.03720526 177.9606778 188761.8155 0.015066167 0.010164165 164.0557668 -2.214991501 0.08418536 IYDLNKPEAEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IYDLNKPEAEPK 12 1 Q9Y3F4;Q9Y3F4-2 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 67.997 0.049118 177140000 288450 206240 186980 205810 257790 216480 316740 353910 247360 FALSE TRUE 250330.6017 204885.1959 277404.1534 252542.3061 252660.4834 224808.1257 286022.6036 278229.1006 218117.3826 1.147687537 0.939334561 1.271811307 1.157827511 1.158369316 1.030674965 1.311324206 1.275593432 1 17.73474522 4.234752902 24.99992015 1.182844419 1.043511057 0.181665993 0.111824557 137.0447807 899805.3714 0.02815849 0.062416605 17169.31236 -4.234752902 -0.139333362 IYEDGDDDMKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IYEDGDDDMKR 11 1 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;;; 191.52 2.88E-06 4004550000 4882530 3915000 2913280 3375660 3696170 3229250 4540190 5436350 4753120 FALSE TRUE 4237291.29 3889282.107 4322151.952 4142155.197 3622623.448 3353481.337 4099883.073 4273828.858 4191211.568 1.010994368 0.927961293 1.031241655 0.98829542 0.864338006 0.80012218 0.978209524 1.01971203 1 21.99893592 2.006388865 24.99988167 1.007573071 0.935792792 0.168524873 0.067741853 286.4047872 1120709.534 0.030048574 0.020193327 101.4819644 -2.006388865 -0.071780278 IYEFPETDDEEENKLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IYEFPETDDEEENKLVK 17 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4 E7EPK1 7-Sep Septin-7 0 ;;; 247.46 8.60E-21 1826890000 2034360 1444510 1453260 1368910 1316790 927010 1984590 2272290 1777040 FALSE TRUE 1765514.172 1435020.919 2156061.397 1679741.938 1290588.455 962672.6746 1792124.767 1786378.466 1566960.356 1.126712725 0.915799123 1.375951465 1.071974752 0.823625467 0.614356752 1.143695028 1.140027864 1 20.57953725 3.467873748 24.68741558 0.965485634 1.134926278 0.186464116 0.186490373 354.6425797 946758.7582 0.058243723 0.075298226 2936.795786 -3.467873748 0.169440644 IYEKDEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IYEKDEEK 8 1 Q9HC38-2;F6TLX2;Q9HC38;I3L3Q4;Q9HC38-3;I3L1I0 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 71.451 0.044423 398550000 796470 611990 661850 641480 469890 385310 727750 878380 1081000 FALSE TRUE 691214.4715 607969.7974 981922.8738 787137.8384 460540.1083 400133.125 657172.917 690545.2726 953205.4115 0.725147448 0.637816141 1.030127255 0.825779868 0.48314886 0.419776388 0.689434732 0.724445397 1 19.86242762 1.222432019 3.316749306 1.057598283 0.686887862 0.251812403 0.167970999 0.579210822 8.56903614 0.569195515 0.046956326 16.68906548 -1.222432019 -0.370710421 IYEYVESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IYEYVESR 8 0 Q8WWY3-4;Q8WWY3;E7EVX8;Q8WWY3-3;Q8WWY3-2;E7EU94;E7ESX0;E7EN72 Q8WWY3-4 PRPF31 U4/U6 small nuclear ribonucleoprotein Prp31 0 ; 95.815 0.021828 282900000 535960 461290 343330 355620 453440 499830 411600 468150 412260 FALSE TRUE 465131.5281 458259.7556 509365.5364 436368.9563 444417.4311 519058.7835 371683.0954 368039.7656 363523.0924 1.279510264 1.260607002 1.40119169 1.200388546 1.222528748 1.427856426 1.022447 1.012424722 1 18.47168749 2.218527683 24.57598904 1.012241485 1.293680153 0.785821171 0.070613594 84.25178586 103357.3884 0.027925602 0.01885654 165.397021 -2.218527683 0.281438668 IYFMAGSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IYFMAGSSR 9 0 P14625 P14625 HSP90B1 Endoplasmin 0 138.54 0.00031079 413460000 184400 311710 169160 222390 333620 377500 273450 254770 219830 FALSE TRUE 160031.0728 309662.3565 250966.3418 272887.0485 326981.6147 392022.6693 246930.8611 200289.4181 193841.9478 0.825575035 1.597499199 1.294695728 1.407781193 1.686846518 2.022383048 1.27387732 1.033261481 1 17.56452128 2.000222231 24.99979707 1.059375333 1.491142707 0.274700856 0.302683596 9.624594842 1082646.311 0.126201869 0.084129329 100.0511836 -2.000222231 0.431767374 IYGADDIELLPEAQHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IYGADDIELLPEAQHK 16 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ;;;; 216.39 1.52E-14 3079420000 4706800 4347790 2904420 3618010 4290500 3643080 4794170 5846090 5152340 FALSE TRUE 4084784.454 4319229.081 4309007.227 4439534.468 4205127.444 3783231.645 4329232.131 4595949.148 4543236.235 0.899091362 0.950694364 0.948444458 0.977174472 0.925579747 0.832717352 0.952896109 1.011602503 1 22.11528889 1.872074687 4.554851986 1.004195555 0.92509654 0.435582797 0.038544193 0.220408741 6.79996593 0.022216008 0.010943562 74.48600596 -1.872074687 -0.079099015 IYGFYDECK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IYGFYDECK 9 0 F8W0W8;P36873;P36873-2;F8VYE8;F8VR82;H0Y3Y6;P62140;E7ETD8;P62136;P62136-2;P62136-3 F8W0W8;P62140;P62136 PPP1CC;PPP1CB;PPP1CA Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-gamma catalytic subunit;Serine/threonine-protein phosphatase PP1-beta catalytic subunit;Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 ;;; 160.75 0.00015136 939490000 1444400 1611210 1025220 1169330 1353640 1114460 1641520 1781480 1773530 FALSE TRUE 1253518.88 1600625.855 1521019.821 1434844.249 1326705.212 1157333.997 1482325.643 1400524.365 1563865.304 0.801551692 1.023506213 0.972602831 0.917498614 0.848350052 0.740047109 0.947860177 0.895553065 1 20.57668483 5.027564467 12.5324141 0.911783865 0.557357613 0.166050868 0.081019809 207361.9635 2991901.899 0.020499457 1414867.904 106552.7019 -5.027564467 -0.354426253 IYHDGALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IYHDGALR 8 0 Q7Z6K5;A0A0A6YYH1;Q7Z6K5-2 Q7Z6K5 ARPIN;C15orf38-AP3S2 Arpin 0 ;; 155 0.00041606 827210000 916530 960790 633480 690350 891010 1044530 895660 989570 983390 FALSE TRUE 795408.2383 954478.5072 939833.0469 847104.5188 873280.6442 1084713.745 808799.0311 777958.1563 867134.7545 0.917283311 1.10072685 1.083837364 0.976900666 1.007087583 1.250917161 0.932725885 0.89715947 1 19.72589668 2.089096895 23.4472807 0.933080231 1.056770328 0.2525109 0.090940975 15.06175998 3957.462098 0.035979468 0.024257344 122.7713115 -2.089096895 0.123690097 IYHLPDAES(ph)DEDEDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IYHLPDAESDEDEDFK 16 0 Q15019-2;Q15019-3;Q15019;B5MCX3;H7C2Y0 Q15019-2 2-Sep Septin-2 1 IYHLPDAES(1)DEDEDFK;IYHLPDAES(1)DEDEDFK;IYHLPDAES(1)DEDEDFK;IYHLPDAES(1)DEDEDFK;IYHLPDAES(1)DEDEDFK 355.3 1.38E-87 1943930000 2677590 1972102 2118380 2481350 1984331 1732135 2217020 2732930 7415820 TRUE FALSE 2323739.697 1959147.132 3142835.654 3044778.443 1944846.695 1798771.354 2002013.742 2148514.187 6539130.208 0.355359142 0.299603628 0.480619831 0.465624379 0.297416726 0.275078076 0.306159027 0.328562686 1 22.64066732 1.237421732 24.99986683 1.000000775 0.349865453 0.895330218 0.069730733 9.253057004 203023.7111 0.110367562 0.018441934 17.27514624 -1.237421732 -0.650135321 IYHLPDAES(ph)DEDEDFKEQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 18 IYHLPDAESDEDEDFKEQTR 20 1 Q15019-2;Q15019-3;Q15019;B5MCX3;H7C2Y0 Q15019-2 2-Sep Septin-2 1 IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(0.999)DEDEDFKEQT(0.001)R;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR 302.71 3.33E-55 1.51696E+11 21927276 16308627 13830015 14578147 16570689 13869126 19455208 22546799 19949903 TRUE FALSE 19029530.92 16201494.56 20518256.51 17888338.09 16240964.71 14402680.25 17568444.92 17725341.49 17591448.19 1.081748967 0.920986969 1.166376769 1.016876945 0.923230682 0.818731925 0.998692361 1.007611272 1 24.06837092 3.426014386 6.666873085 0.9548901 1.05068553 0.274554391 0.079911068 0.29992199 29.71561125 0.023746551 0.030889932 2666.947003 -3.426014386 0.09579543 IYHLQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IYHLQSK 7 0 F5GWE5;Q00169;I3L4H1;I3L471;I3L4U7 F5GWE5 PITPNA Phosphatidylinositol transfer protein alpha isoform 0 ; 84.244 0.021688 929160000 1691550 1874330 1216340 1413210 1650900 1613050 1924650 2082290 2036740 FALSE TRUE 1468007.382 1862017.403 1804566.092 1734100.93 1618050.32 1675105.077 1737997.739 1637008.488 1795958.917 0.817394745 1.036781735 1.004792523 0.965557126 0.900939495 0.932707904 0.967726891 0.911495509 1 20.77632292 IYHPNIDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IYHPNIDEK 9 0 P68036-2;P68036;P68036-3;A0A1B0GUS4 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 ; 127.4 0.00044656 921390000 3061600 2819700 1822790 2209300 2419000 2267000 2862600 3481300 3574900 FALSE TRUE 2657001.803 2801177.205 2704297.341 2710955.332 2370866.633 2354212.957 2584985.493 2736851.087 3152279.395 0.842882711 0.888619584 0.857886311 0.859998431 0.752111833 0.746828774 0.820036922 0.868213361 1 21.58796398 1.24902125 2.468600414 1.041720608 0.82400311 0.601488636 0.04495446 0.420527694 2.823113671 0.194764975 0.013444829 17.74276294 -1.24902125 -0.217717498 IYHPNINSNGSICLDILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IYHPNINSNGSICLDILR 18 0 P61077-3;P61077-2;P61077;A0A087WY85;H9KV45;D6RAH7;P62837-2;D6RA11;P51668;Q9Y2X8;C9J9H9;A0A087WW00;D6RFM0;D6RAW0;A0A0A0MQU3;P62837 P61077-3;A0A0A0MQU3 UBE2D3;UBE2D2;UBE2D1;UBE2D4 Ubiquitin-conjugating enzyme E2 D3;Ubiquitin-conjugating enzyme E2 D2;Ubiquitin-conjugating enzyme E2 D1;Ubiquitin-conjugating enzyme E2 D4 0 ;; 264.01 6.19E-31 2856571000 1875167 1578591 882673 1266472 1672524 1719879 1579432 1767023 1727114 FALSE TRUE 1627358.93 1568221.132 1309536.615 1554043.824 1639244.045 1786043.858 1426258.928 1389158.882 1522936.55 1.068566467 1.029735041 0.859876017 1.02042585 1.076370545 1.172763145 0.936518943 0.912158082 1 20.53842441 IYHPNVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IYHPNVDK 8 0 P61088;F8VSD4;F8VV71;F8VQQ8;Q5JXB2 P61088 UBE2N;UBE2NL Ubiquitin-conjugating enzyme E2 N;Putative ubiquitin-conjugating enzyme E2 N-like 0 ;;; 103.87 0.0046892 6218500000 10750100 10111100 7049100 8085700 9372600 8213200 11107000 12295800 11642500 FALSE TRUE 9329447.048 10044679.52 10458068.34 9921681.767 9186103.597 8529167.119 10029844.85 9666438.856 10266136.91 0.908759266 0.978428361 1.018695584 0.966447443 0.894796521 0.8308059 0.976983352 0.941584837 1 23.29139007 4.777997661 21.46312684 0.948544009 0.908758661 0.055021417 0.054150871 12158.47489 6616239.882 0.013991763 2.72417675 59978.78455 -4.777997661 -0.039785349 IYHTIAYLTPLPQPNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IYHTIAYLTPLPQPNR 16 0 P10620;F5H760 P10620 MGST1 Microsomal glutathione S-transferase 1 0 ; 171.26 4.99E-09 1110260000 691130 523140 478580 702160 691080 764040 382320 762070 1095740 FALSE TRUE 599795.4194 519703.4589 710022.8888 861596.1598 677328.8601 793433.1132 345242.6652 599107.2609 966202.8655 0.620775865 0.537882341 0.734859018 0.891734221 0.701021374 0.821186877 0.357319024 0.620063635 1 19.88196661 4.234136167 24.98640161 0.709951169 0.579329095 0.110046353 0.171953421 268.1776238 1514527.703 0.045630585 0.100512291 17144.9478 -4.234136167 -0.130622074 IYIDSNNNPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IYIDSNNNPER 11 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;; 218.94 2.38E-11 4156650000 1996580 1623210 1199940 1177520 1652200 1822540 1650340 1857680 1652550 FALSE TRUE 1732726.894 1612547.027 1780234.998 1444893.913 1619324.452 1892654.293 1490290.281 1460429.588 1457187.422 1.189089934 1.106616076 1.221692537 0.991563537 1.111267108 1.298840674 1.022716954 1.002224948 1 20.47475502 2.033376554 24.99970939 1.004631115 1.146246172 0.421674993 0.079972813 173.4657827 129928.7005 0.032115439 0.021652091 107.9882625 -2.033376554 0.141615057 IYITLTGVHQVPTENVQVHFTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 IYITLTGVHQVPTENVQVHFTER 23 0 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;; 296.62 6.18E-62 5443518000 2002050 1504737 726474 1258272 1727645 1829577 1657331 1926339 1844308 FALSE TRUE 1737474.02 1494852.284 1077799.256 1543981.889 1693268.245 1899962.011 1496603.295 1514406.396 1626276.009 1.068375854 0.919187318 0.662740673 0.9493972 1.041193644 1.168290008 0.920264018 0.931211176 1 20.6331407 3.483431194 24.84777559 1.002280986 0.873519732 0.195641512 0.118010519 441.503176 1738588.609 0.035056753 0.046940493 3043.905702 -3.483431194 -0.128761254 IYKPSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IYKPSSR 7 1 O15042-2;O15042;E7ET15;E7EW00;H0Y8D9 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 77.058 0.035639 382010000 1001200 680500 573180 641710 549780 497630 839040 1057300 972640 FALSE TRUE 868888.8833 676029.7507 850371.7652 787420.0634 538840.4536 516774.1481 757670.0299 831204.6229 857655.6072 1.013097654 0.78822985 0.991507265 0.918107521 0.628271359 0.602542727 0.883419899 0.969158968 1 19.71003892 1.809017394 3.716679583 0.985474924 0.820368125 0.188086723 0.134650803 0.382904696 9.405394732 0.08978486 0.039015697 64.41950663 -1.809017394 -0.165106799 IYNDDKNTYIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IYNDDKNTYIR 11 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 122.33 0.00035853 324160000 423880 371310 196930 296990 392710 320620 396470 420270 351700 FALSE TRUE 367863.184 368870.8402 292166.0067 364426.1187 384895.8393 332954.4589 358020.4004 330398.531 310122.4267 1.186186978 1.189436198 0.942098931 1.175104047 1.241109337 1.073622641 1.154448597 1.065380968 1 18.24247833 1.446494379 2.291491243 0.99030932 1.13537245 0.239131909 0.081706982 0.61189058 5.082747033 0.157100259 0.022169076 27.9572454 -1.446494379 0.14506313 IYNEIPDINLDVPHSYSVLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IYNEIPDINLDVPHSYSVLER 21 0 Q53EL6;Q53EL6-2 Q53EL6 PDCD4 Programmed cell death protein 4 0 194.75 2.54E-18 279690000 186980 205110 124770 147260 184320 194700 160720 221560 208320 FALSE TRUE 162270.1193 203762.6189 185109.1893 180697.6337 180652.3926 202190.235 145133.3991 174181.1182 183692.6469 0.883378415 1.10925844 1.007711481 0.983695519 0.983449232 1.100698577 0.790088235 0.948220417 1 17.48693435 2.252504633 24.99997511 0.915043382 1.013122234 0.246104939 0.081276704 310.2227257 556192.4773 0.028854744 0.022235468 178.8564609 -2.252504633 0.098078852 IYNISGNGS(ph)PLADSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 IYNISGNGSPLADSK 15 0 Q53HL2 Q53HL2 CDCA8 Borealin 1 IYNIS(0.003)GNGS(0.997)PLADSK;IYNIS(0.001)GNGS(0.999)PLADSK;IYNIS(0.004)GNGS(0.996)PLADSK;IYNIS(0.001)GNGS(0.999)PLADSK 259.87 7.40E-25 667268000 945730 856630 584050 744480 831550 645770 936650 1139590 956920 TRUE FALSE 820749.3843 851002.7411 866498.5335 913525.5627 815003.7819 670613.1898 845813.8272 895897.5468 843794.0077 0.972689278 1.008543238 1.026907664 1.082640496 0.96588003 0.794759365 1.002393735 1.061749122 1 19.68653132 1.996377937 24.99874131 1.034321094 0.976474379 0.087158456 0.074476186 367.285311 2534932.061 0.033514025 0.022032978 99.16945731 -1.996377937 -0.057846714 IYNYYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IYNYYK 6 0 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ; 124.12 0.043019 2391600000 1914670 2248800 1585600 2012870 2089100 1775670 2309100 2336100 3175300 FALSE TRUE 1661641.508 2234027.485 2352401.464 2469922.898 2047530.997 1843981.174 2085163.837 1836543.195 2799919.651 0.593460426 0.797889855 0.840167489 0.882140635 0.731282055 0.658583604 0.744722741 0.655927106 1 21.416954 -0.668551749 0.008595561 1.576934182 7.15E-08 0.036355022 0.117904445 268827.0711 312.8722508 30859.59061 26683.05812 0.21451035 0.668551749 -1.57693411 IYNYYKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IYNYYKK 7 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ; 88.254 0.030053 1804570000 2682520 3234110 1134630 1474980 3148130 2614390 4186100 4400700 627150 FALSE TRUE 2328018.185 3212864.918 1683340.863 1809896.753 3085488.372 2714967.275 3780132.666 3459644.551 553009.0415 4.209728975 5.809787323 3.043966259 3.272815844 5.579453754 4.909444641 6.835571181 6.256036144 1 19.07694354 3.221061535 24.95352852 5.227220524 4.133046085 0.037954227 1.715392149 627.5821577 894923.9091 0.521907643 0.593110259 1663.648354 -3.221061535 -1.094174438 IYPSREEYEAHQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IYPSREEYEAHQDR 14 1 Q06587;Q06587-2 Q06587 RING1 E3 ubiquitin-protein ligase RING1 0 69.331 0.02842 294650000 197200 228530 215010 94027 170790 309410 128450 136310 46217 FALSE TRUE 171139.5204 227028.7714 318989.5552 115377.2675 167391.6131 321313.2029 115992.9388 107161.1673 40753.27891 4.19940493 5.570809943 7.827334725 2.831116184 4.107439146 7.884352168 2.846223466 2.629510315 1 15.31462852 3.717318145 24.91416987 3.6137844 5.836346302 0.238338889 1.949300549 1204.333252 1412498.679 0.566668496 0.841442734 5215.766552 -3.717318145 2.222561902 IYPTFLHLHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IYPTFLHLHGK 11 0 Q08945;E9PMD4 Q08945 SSRP1 FACT complex subunit SSRP1 0 ; 219.03 5.88E-12 898930000 1601100 1137830 646260 903290 1065550 1034100 1167090 1341940 1335290 FALSE TRUE 1389510.578 1130355.52 958793.4976 1108395.8 1044347.64 1073882.496 1053905.791 1054976.574 1177433.537 1.180118057 0.960016412 0.814307956 0.941365916 0.886969503 0.9120536 0.895087288 0.895996709 1 20.1672142 4.703587656 3.601597436 0.904848347 1.202024273 0.769955301 0.046592367 0.105048179 2.460634225 0.010737018 0.079224171 50534.46312 -4.703587656 0.297175926 IYQY(ph)IQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 IYQYIQSR 8 0 A0A2R8Y6L5;A0A2R8Y6I6;Q13627-2;Q13627;Q13627-5;A0A2R8Y443;A0A2R8YDF3;Q13627-4;Q13627-3;Q9Y463-2;Q9Y463-3;Q9Y463 A0A2R8Y6L5 DYRK1A;DYRK1B Dual specificity tyrosine-phosphorylation-regulated kinase 1A;Dual specificity tyrosine-phosphorylation-regulated kinase 1B 1 IYQY(1)IQSR;IYQY(1)IQSR;IYQY(1)IQSR;IYQY(1)IQSR;IYQY(1)IQSR;IY(0.004)QY(0.996)IQSR;IYQY(1)IQSR;IYQY(1)IQSR 236.1 1.36E-07 23511290000 4296320 4100370 2460210 2849540 3805290 3821850 3684600 4386970 4039530 TRUE FALSE 3728550.427 4073434.399 3649975.785 3496571.609 3729572.174 3968879.043 3327268.059 3448850.605 3561981.365 1.046763036 1.143586668 1.024703784 0.981636693 1.047049884 1.114233522 0.93410597 0.968239373 1 21.76424854 2.464404701 0.23202589 0.894871746 1.130726735 0.256026819 0.055181216 8.34845502 1.68001564 1.001259725 0.597630785 291.3430757 -2.464404701 0.235854989 IYSHSLLPVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IYSHSLLPVLR 11 0 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 222.3 7.78E-12 331800000 433560 477390 344030 389670 493260 575880 456870 552750 666200 FALSE TRUE 376263.9475 474253.9937 510404.0587 478150.5292 483445.091 598034.4762 412562.8177 434548.714 587442.5949 0.640511857 0.807319724 0.868857763 0.813952773 0.822965674 1.018030496 0.702303206 0.739729665 1 19.16408835 4.725222505 3.492660279 0.837818062 0.619250354 0.300311181 0.099206431 0.384592295 8.285022832 0.024813135 0.218194406 53115.65049 -4.725222505 -0.218567708 IYSPVRS(ph)PSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IYSPVRSPSAR 11 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 IYS(0.002)PVRS(0.986)PS(0.011)AR 100.73 0.0023094 300640000 107150 129850 53207 66098 146900 138270 125410 128660 64947 TRUE FALSE 92989.85602 128997.0068 78938.08317 81106.56114 143976.9774 143589.3364 113247.7575 101147.0602 57269.03965 1.623736954 2.25247372 1.378372741 1.416237493 2.514045605 2.507276833 1.977469121 1.766173501 1 15.80546779 1.231133035 2.677153678 0.770800296 1.961332418 0.355976598 0.400130991 0.592777214 4.770774266 1.611803838 0.110648009 17.02680003 -1.231133035 1.190532123 IYVASVHQDLSDDDIK ddPTM_MDA-MB-175_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 ;; 222.57 9.52E-15 747940000 853170 841210 395848 622980 675770 617550 865320 895720 1143700 FALSE TRUE 740421.4228 835684.0361 587281.4168 764437.1307 662323.4991 641307.5481 781401.3996 704177.2485 1008493.089 0.734185917 0.82864627 0.582335589 0.757999375 0.6567457 0.635906736 0.774820778 0.698246975 1 19.94376977 1.237314946 24.99304258 1.000000351 0.708684275 0.621754577 0.071425447 20.30134662 407154.9755 0.099687221 0.016542114 17.27089907 -1.237314946 -0.291316076 IYVDDGLISLQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IYVDDGLISLQVK 13 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 234.72 2.66E-16 467660000 1296630 900250 715970 938740 928830 856750 1174190 1172550 1355330 FALSE TRUE 1125277.06 894336.1985 1062215.487 1151895.265 910348.1002 889709.7269 1060317.235 921809.3073 1195104.431 0.941572159 0.748333095 0.88880558 0.963844861 0.761731006 0.744461909 0.887217223 0.771321136 1 20.18870526 4.803273353 21.60403481 0.841097409 0.9415774 0.097731243 0.090573157 48733.11897 16265463.03 0.021184673 55.31341806 63573.09469 -4.803273353 0.100479991 IYVEIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 IYVEIER 7 0 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 ;;;; 113.7 0.014125 1062350000 1460210 1352710 940605 1132013 1374970 1496720 1302770 1495520 1497660 FALSE TRUE 1267239.549 1343823.959 1395484.724 1389053.853 1347610.787 1554299.787 1176427.566 1175714.686 1320608.341 0.959587721 1.017579488 1.056698402 1.051828775 1.020446975 1.176957421 0.890822456 0.890282645 1 20.33277123 2.198225039 24.99999874 0.917869298 1.045266172 0.453382232 0.061893975 126.3998105 78341.75766 0.024790328 0.016713878 157.8428956 -2.198225039 0.127396874 IYVLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 IYVLLR 6 0 P84090 P84090 ERH Enhancer of rudimentary homolog 0 159.55 0.021132 638210000 743150 854520 464270 548330 704940 768180 659970 762870 801510 FALSE TRUE 644940.8446 848906.6019 688792.5249 672836.7072 690913.0732 797732.3817 595966.211 599736.1872 706756.4009 0.912536263 1.201130405 0.974582648 0.952006528 0.977583043 1.12872325 0.843241335 0.84857553 1 19.43085352 2.221917302 24.99824324 0.884875819 1.024772244 0.282766109 0.094780657 277.6379857 417008.7773 0.037446462 0.025322755 166.6929765 -2.221917302 0.139896425 KAAALEFLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KAAALEFLNR 10 1 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 165.63 9.29E-06 2529800000 5060600 3861900 2464300 3056500 3939000 3830400 4035900 4860400 3490300 FALSE TRUE 4391828.888 3836530.925 3656043.723 3750525.041 3860621.607 3977757.967 3644499.039 3821041.284 3077680.71 1.426993019 1.246565608 1.187921707 1.218620576 1.254393152 1.292453097 1.184170608 1.241532714 1 21.55341214 0.611429207 1.521316976 4.45E-14 1.257623312 0.578923737 0.068597204 4.88028327 2.466258305 15.0822085 0.019072432 4.087231216 -0.611429207 1.257623312 KAAGGAT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KAAGGATPK 9 1 P16403 P16403 HIST1H1C Histone H1.2 1 KAAGGAT(1)PK;KAAGGAT(1)PK;KAAGGAT(1)PK;KAAGGAT(1)PK 73.466 0.02569 842520000 517200 567494 428943 482081 434462 535632 745439 808590 931900 TRUE FALSE 448850.7096 563766.0945 636381.2695 591544.8592 425817.0562 556238.1096 673146.4405 635679.321 821731.8436 0.546225284 0.686070643 0.7744391 0.719875789 0.518194664 0.676909522 0.819180181 0.773584869 1 19.64830815 -0.112613873 0.710477651 3.045566731 0.657744816 0.621031359 0.084075164 12.44587212 1.068102139 36.78676521 0.036817398 0.771589177 0.112613873 -2.387821916 KAALLAQYADVT(ph)DEEDEADEKDDSGATTMNIGSDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAALLAQYADVTDEEDEADEKDDSGATTMNIGSDK 35 2 Q96MW1 Q96MW1 CCDC43 Coiled-coil domain-containing protein 43 1 KAALLAQYADVT(1)DEEDEADEKDDSGATTMNIGSDK 365.84 6.87E-147 304730000 156760 88333 130210 93613 91521 63934 157040 191580 143270 TRUE FALSE 136043.7688 87752.73471 193179.9915 114869.2624 89699.91116 66393.58235 141810.285 150612.1079 126332.7838 1.07686829 0.694615697 1.529135872 0.909259331 0.71002877 0.525545154 1.122513735 1.192185459 1 16.94686955 -1.480233391 8.184196684 2.225707334 0.980924333 0 0.287256553 0 0 0 0.065870712 0.033095322 1.480233391 -1.244783001 KAALS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 66.435 0.037787 179150000 467980 407260 239420 341940 335880 338060 419270 491160 419680 TRUE FALSE 406135.2573 404584.6822 355204.3128 419582.7032 329196.6451 351065.387 378609.2599 386129.2562 370065.9085 1.097467364 1.093277367 0.959840679 1.13380534 0.889562204 0.948656385 1.023086027 1.043406721 1 18.49742271 4.258812631 23.85671621 1.003937218 1.095372568 0.276446723 0.064028335 195.425111 230202.1841 0.015768471 0.041584484 18147.3256 -4.258812631 0.09143535 KAALSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAALSSPR 8 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 KAALS(0.147)S(0.853)PR 77.662 0.019987 151720000 583950 530400 313550 401190 425210 432950 536040 656620 520990 TRUE FALSE 506779.528 526915.7675 465183.8288 492286.3213 416749.1529 449605.8667 484054.9233 516206.9228 459399.1557 1.103135523 1.146967209 1.012591823 1.071587344 0.907161338 0.978682396 1.053669597 1.123656664 1 18.80938868 4.236288946 24.99972272 1.028183017 1.125051382 0.348831504 0.058445854 72.14542465 793999.2292 0.016519768 0.037204468 17230.14555 -4.236288946 0.096868365 FS(ph)PGAPGGSGSQPNQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FSPGAPGGSGSQPNQK 16 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK 362.4 3.86E-88 1744520000 1483950 1409860 1275962 1732290 1650830 1283785 1787860 2156550 4250440 TRUE FALSE 1287842.248 1400598.537 1893021.491 2125632.921 1617981.713 1333173.04 1614473.612 1695388.565 3747957.825 0.343611723 0.373696451 0.505080788 0.567144301 0.431696884 0.355706521 0.43076088 0.452349958 1 21.83767329 1.237572382 5.938862209 1.022018113 0.433965477 0.875535696 0.067279935 0.048556069 6.343123978 0.115947439 0.017930573 17.28113973 -1.237572382 -0.588052637 KAAS(ph)PS(ph)PQSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KAASPSPQSVR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KAAS(0.897)PS(0.776)PQS(0.327)VR;KAAS(0.804)PS(0.804)PQS(0.392)VR;KAAS(1)PS(0.999)PQS(0.001)VR;KAAS(0.784)PS(0.784)PQS(0.432)VR 133.48 0.00010744 2110819000 4270420 3089150 2156453 2604610 3362750 2764170 3617080 4356850 3133540 TRUE FALSE 3706073.177 3068857.17 3199320.884 3196026.509 3295837.854 2870509.409 3266296.138 3425171.533 2763096.471 1.341275347 1.110658713 1.157875202 1.156682926 1.192805929 1.038874118 1.182114404 1.239613444 1 21.3978545 4.744979612 24.29646445 1.145447424 1.341275479 0.443219717 0.071847294 493.2290039 1866840.748 0.017041034 0.15449559 55587.81609 -4.744979612 0.195828055 KAAS(ph)PSPQSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KAASPSPQSVR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KAAS(0.854)PS(0.146)PQSVR;KAAS(0.617)PS(0.382)PQSVR;KAAS(0.876)PS(0.124)PQSVR;KAAS(0.821)PS(0.179)PQSVR;KAAS(0.5)PS(0.5)PQSVR 172.57 8.09E-06 8956850000 4681590 3599340 2107414 2629600 3495080 2981240 4139850 4568930 2423260 TRUE FALSE 4062906.02 3575695.699 3126566.459 3226690.871 3425534.746 3095930.232 3738367.984 3591899.875 2136784.963 1.901410806 1.673399879 1.463210624 1.510068129 1.603125633 1.44887309 1.749529339 1.680983317 1 21.0270103 7.99602881 0.032014156 6.62E-06 3.858616279 0.262226135 0.206391388 5396.700752 17.1082435 712.4834559 1485.873782 99089767.63 -7.99602881 3.858609659 ELNSNHDGADETSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ELNSNHDGADETSEK 15 0 Q01105-2 Q01105-2 SET Protein SET 0 ;;; 239.58 8.27E-18 3234440000 3535600 2447120 1214590 2875250 2661890 2238030 2781760 3523330 8447000 FALSE TRUE 3068361.502 2431044.708 1801969.787 3528119.458 2608923.597 2324128.462 2511985.343 2769893.298 7448405.283 0.411948784 0.32638459 0.241926925 0.473674474 0.350266063 0.312030344 0.337251431 0.371877361 1 22.82850014 1.237731279 5.893044259 1.025881343 0.349478424 0.918600288 0.060543116 0.034621176 4.37287152 0.094438074 0.014582431 17.28746361 -1.237731279 -0.67640292 KAASLTEDRDR ddPTM_MDA-MB-175_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 0 ;; 112.7 0.00083825 822640000 1646330 1769810 1017550 1235620 1874840 1773230 2117190 2295170 873990 FALSE TRUE 1428763.319 1758184.002 1509640.584 1516186.406 1837534.352 1841447.306 1911865.24 1804365.757 770667.8979 1.853928681 2.28137698 1.95887306 1.967366761 2.384340073 2.389417427 2.480790033 2.341301307 1 19.55574977 3.282310333 24.99519988 2.187571171 2.030348991 0 0.434947056 637.3945063 364153.3319 0.124507771 0.160738043 1915.624278 -3.282310333 -0.15722218 KAASPS(ph)PQS(ph)VR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KAASPSPQSVR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KAAS(0.412)PS(0.716)PQS(0.872)VR;KAAS(0.375)PS(0.695)PQS(0.93)VR 122.12 0.00026567 1309570000 1796360 1370460 876380 1187630 1425160 1237290 1529090 1782390 1360110 TRUE FALSE 1558966.475 1361457.358 1300200.299 1457299.543 1396802.104 1284889.347 1380799.087 1401239.769 1199319.345 1.299876035 1.135191693 1.084115173 1.215105509 1.164662364 1.071348805 1.151318948 1.168362517 1 20.19378443 KAASPS(ph)PQSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAASPSPQSVR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KAAS(0.102)PS(0.898)PQSVR 123.76 0.00022251 950470000 546440 451390 282910 334870 415320 376480 485230 578930 313990 TRUE FALSE 474226.5695 448424.7894 419726.2223 410907.3517 407055.9446 390963.4292 438172.4693 455130.3247 276870.4599 1.712810278 1.619619477 1.515966067 1.484114094 1.470203592 1.412080687 1.582590174 1.643838512 1 18.07885161 1.23272892 24.99995077 0.999999109 1.552040499 0.791887438 0.089427479 94.05345134 403156.7488 0.207259603 0.023750081 17.08948283 -1.23272892 0.552041389 KAAWEAYLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAAWEAYLSR 10 1 P11172-2;P11172-3;P11172;P11172-4 P11172-2 UMPS Uridine 5-monophosphate synthase;Orotate phosphoribosyltransferase;Orotidine 5-phosphate decarboxylase 0 81.92 0.031373 388960000 229830 227090 189130 240490 291760 200130 270700 327650 258800 FALSE TRUE 199457.3832 225598.2308 280593.9006 295096.9302 285954.5468 207829.1306 244447.5557 257584.5973 228204.9588 0.874027384 0.988577251 1.229569691 1.293122339 1.25306018 0.910712597 1.071175477 1.128742331 1 17.79997062 4.448989237 5.416934309 1.126433242 0.898189702 0.350224827 0.11586459 0.183498103 14.93414772 0.031007333 0.092161877 28118.31147 -4.448989237 -0.22824354 KACQIFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KACQIFVR 8 1 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 144.38 0.00094027 2462100000 3346200 4758700 2379600 3036000 4170100 3799500 3889600 4570800 3747600 FALSE TRUE 2903991.192 4727439.786 3530382.519 3725370.202 4087123.169 3945669.224 3512387.191 3593369.99 3304562.997 0.878782215 1.430579411 1.068335669 1.127341257 1.236812 1.194006356 1.062890069 1.087396425 1 21.65602807 2.226996779 22.57447437 1.058399474 1.16684722 0.110165252 0.138926657 139.0848022 271508.0748 0.051580587 0.03519307 168.6540516 -2.226996779 0.108447746 KADGPPGPHDGGDRPSAEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KADGPPGPHDGGDRPSAEAR 20 2 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 0 ; 192.27 6.98E-18 220703000 267050 224728 154762 213327 234830 223559 254350 299870 264950 FALSE TRUE 231758.6659 223251.747 229605.4208 261766.1558 230157.3424 232159.4594 229683.1761 235745.1341 233627.9128 0.991999043 0.955586789 0.982782485 1.120440416 0.985144881 0.993714563 0.983115302 1.009062364 1 17.83385313 3.980680374 24.99065873 1.013609373 0.972640818 0.171880361 0.040028132 1286.175092 1663722.305 0.010631804 0.018807952 9564.898686 -3.980680374 -0.040968555 KADGYNQPDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KADGYNQPDSK 11 1 O60506-2;O60506;O43390;O43390-3;B4DT28;O43390-2;O43390-4 O60506-2;O43390;O43390-2 SYNCRIP;HNRNPR Heterogeneous nuclear ribonucleoprotein Q;Heterogeneous nuclear ribonucleoprotein R 0 ;;; 168.31 2.92E-05 909090000 2121070 1478770 1186277 1395480 1241980 1063302 1862830 2098770 1898680 FALSE TRUE 1840765.225 1469055.863 1759964.525 1712345.063 1217267.028 1104207.916 1682173.033 1649964.368 1674220.213 1.099476168 0.877456771 1.051214476 1.022771705 0.727065065 0.65953565 1.004750164 0.985512154 1 20.67505787 7.999975387 0.847719848 0.909038053 60.39289506 0.153086206 0.130981112 1588.923019 4.438829985 0.048638202 182244.7415 99994332.91 -7.999975387 59.48385701 KADIDLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KADIDLTK 8 1 P62269 P62269 RPS18 40S ribosomal protein S18 0 ; 85.958 0.026254 2935300000 5021500 4152800 3111100 3626900 3825400 2871000 5219100 5800700 6496300 FALSE TRUE 4357896.052 4125519.983 4615638.366 4450443.079 3749282.024 2981449.228 4712952.485 4560265.446 5728314.815 0.760764063 0.720197845 0.805758502 0.776920128 0.654517453 0.520475799 0.822746765 0.796091974 1 22.44967935 1.198486165 1.581224678 1.128016664 0.716514099 0.514760509 0.085399687 1.068741475 2.2273089 0.715050493 0.025605467 15.79378295 -1.198486165 -0.411502564 KADKVEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KADKVEQR 8 2 Q99832-3;Q99832;Q99832-4 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;; 75.378 0.021679 1015450000 2733980 2103320 1378950 1700760 1276430 1482430 2621540 2918720 1710930 FALSE TRUE 2372677.616 2089503.152 2045814.832 2086943.552 1251031.54 1539460.041 2367303.454 2294574.442 1508665.804 1.572699274 1.385000672 1.356042423 1.383304073 0.829230395 1.020411569 1.569137079 1.520929575 1 20.52484183 4.54726231 1.333120799 1.255369526 1.628817523 0.185571222 0.233452669 2.088079905 4.290522133 0.075974601 0.965171414 35258.37642 -4.54726231 0.373447996 KADLVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KADLVNR 7 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;; 86.833 0.031726 2463274000 2878500 3371480 1977250 2514460 3188490 3246300 3717910 4421430 4123870 FALSE TRUE 2498098.932 3349332.526 2933454.714 3085406.574 3125045.287 3371187.262 3357347.66 3475941.602 3636350.787 0.686979634 0.921069699 0.806702897 0.848489806 0.859390491 0.927079773 0.923273869 0.955887318 1 21.79405995 3.181559425 0.051256754 1.745960009 6.91E-11 0.662399924 0.051232451 49.62818023 3.181468933 52.76908878 55.06236544 1519.005776 -3.181559425 -1.745960008 KADPQEAINCLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KADPQEAINCLMR 13 1 P54920;M0R2M1;M0R058;M0R0I4 P54920 NAPA Alpha-soluble NSF attachment protein 0 ; 76.01 0.047836 1018520000 271200 235672 115672 163183 188860 160835 211190 233050 201864 FALSE TRUE 235360.2329 234123.8551 171611.3661 200236.1942 185102.0555 167022.4265 190708.8263 183214.0711 177999.8679 1.322249481 1.315303533 0.964109514 1.124923275 1.03989996 0.938328935 1.071398696 1.029293298 1 17.44151664 4.246777923 24.99735287 1.028119444 1.31877669 0.847197362 0.052024234 61.17324891 186087.1057 0.012547116 0.032009222 17651.34985 -4.246777923 0.290657246 KADRDQS(ph)PFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KADRDQSPFSK 11 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 KADRDQS(1)PFSK 73.887 0.022088 229490000 528410 352330 141490 155550 294440 224070 428010 446850 94252 TRUE FALSE 458579.2797 350015.521 209915.0373 190870.0049 288581.2201 232690.1179 386501.6561 351294.6049 83109.63593 5.517763067 4.211491449 2.52576052 2.296604994 3.472295563 2.799797103 4.65050354 4.226881768 1 16.34272814 4.536037136 3.449426374 3.181884401 5.447756658 0.384539242 1.029445409 0.295333625 6.479974271 0.268038701 1.294986477 34358.73267 -4.536037136 2.265872257 KADS(ph)DSEDKGEESKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KADSDSEDKGEESKPK 16 3 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 1 KADS(0.998)DS(0.002)EDKGEESKPK;KADS(0.994)DS(0.006)EDKGEESKPK;KADS(1)DSEDKGEESKPK;KADS(0.997)DS(0.003)EDKGEESKPK;KADS(1)DSEDKGEESKPK;KADS(0.796)DS(0.204)EDKGEESKPK;KADS(0.998)DS(0.002)EDKGEESKPK 202.53 2.15E-11 14082710000 11685148 5977930 10591473 6155738 4498158 2570496 11738402 12603442 10464529 TRUE FALSE 10140926.09 5938660.584 15713544.77 7553492.397 4408653.456 2669384.644 10600013.58 9908294.008 9227424.303 1.098998567 0.643588112 1.702917765 0.81859164 0.477777255 0.289288165 1.148751074 1.073787623 1 23.13749657 KADVSEQVSNGPVESVTLENS(ph)PLVWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KADVSEQVSNGPVESVTLENSPLVWK 26 1 F5GYK2;Q9NRL3;Q9NRL3-3;Q9NRL3-2;M0R0P4;M0R2A7;M0QYS2;M0QXN2;M0R0W8 F5GYK2 STRN4 Striatin-4 1 KADVSEQVSNGPVES(0.001)VT(0.001)LENS(0.998)PLVWK 116.36 0.00061723 58536000 81089 69429 52960 54330 59915 54980 79389 95029 62984 TRUE FALSE 70372.8832 68972.91633 78571.63314 66666.45688 58722.80872 57095.11618 71689.867 74707.78787 55538.10327 1.267109949 1.241902627 1.414733823 1.20037331 1.057342712 1.028035039 1.290823107 1.345162753 1 15.76119029 3.499462472 23.8076495 1.170408341 1.302354121 0.272644321 0.117689586 719.0996112 766297.3321 0.035589556 0.052247469 3158.366115 -3.499462472 0.13194578 KADYQAVDDEIEANLEEFDISEDDIDDGFRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KADYQAVDDEIEANLEEFDISEDDIDDGFRR 31 2 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ; 375.46 1.61E-137 176355000 107504 100121 61579 62582 93319 78530 95079 128746 54959 FALSE TRUE 93297.07402 99463.29856 91358.81037 76792.19961 91462.13448 81551.09992 85858.25321 101214.6698 48461.80963 1.925166946 2.052405788 1.885171253 1.584592078 1.887303326 1.682791058 1.771668328 2.088544992 1 15.56456066 1.229091271 24.99636779 0.9999983 1.859859837 0.757835775 0.152728283 198.3871039 523647.0945 0.488190413 0.039032443 16.94693919 -1.229091271 0.859861537 KAEAAASALADADADLEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KAEAAASALADADADLEER 19 1 O43633;M0R1T5 O43633 CHMP2A Charged multivesicular body protein 2a 0 ;;; 222.72 3.80E-19 1243770000 1793490 1720170 1129909 1383713 1735850 1518350 1852230 2292940 1915850 FALSE TRUE 1556475.752 1708870.09 1676336.772 1697906.185 1701309.981 1576761.907 1672601.02 1802612.625 1689360.396 0.921340264 1.011548569 0.992290796 1.005058595 1.007073438 0.93334845 0.990079455 1.067038525 1 20.6880457 KAEAGAGSATEFQFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KAEAGAGSATEFQFR 15 1 P46783;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 0 ;;; 163.44 2.47E-06 1965930000 2594660 2471440 1387480 1759970 2528300 2498240 2474610 2706320 2036710 FALSE TRUE 2251769.107 2455204.948 2058469.969 2159598.088 2477991.777 2594348.909 2234622.703 2127594.529 1795932.464 1.253816138 1.367092024 1.146184509 1.202494042 1.379780045 1.444569304 1.244268784 1.184674018 1 20.77630167 1.338300322 1.900642881 0.94178157 1.294957244 0.532932073 0.087692208 0.565047322 2.399108711 0.337591306 0.025799684 21.79216215 -1.338300322 0.353175673 KAEDLFQDAYYQSPETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAEDLFQDAYYQSPETR 17 1 O95671;O95671-2;O95671-3 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 0 78.088 0.026304 1697800000 52512 42791 28435 38941 30710 39252 38337 49620 78966 FALSE TRUE 45572.40615 42509.9031 42186.26111 47783.14923 30098.93108 40762.04984 34619.08364 39009.14914 69630.72944 0.654486985 0.610504923 0.605856946 0.686236517 0.432265055 0.585403171 0.497181114 0.560228931 1 16.08743652 1.237344229 24.98494019 1.000000514 0.575089745 0.767611515 0.07276618 14.47502199 297193.6708 0.106488436 0.017723118 17.27206361 -1.237344229 -0.424910769 KAEDS(ph)DS(ph)EPEPEDNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KAEDSDSEPEPEDNVR 16 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 2 KAEDS(1)DS(1)EPEPEDNVR;KAEDS(1)DS(1)EPEPEDNVR;KAEDS(1)DS(1)EPEPEDNVR;KAEDS(1)DS(1)EPEPEDNVR;KAEDS(1)DS(1)EPEPEDNVR 204.78 1.63E-11 5602140000 6073960 4517070 3517820 3540710 4740440 3939800 5365690 6227870 6006640 TRUE FALSE 5271270.797 4487397.07 5219049.518 4344682.322 4646114.519 4091366.655 4845326.21 4896088.466 5296541.862 0.995228761 0.847231493 0.985369257 0.820286601 0.877197734 0.772459987 0.914809386 0.924393424 1 22.33661929 1.365011226 1.969332618 1.017317518 0.882357854 0.216770809 0.067878396 0.888661005 4.339838031 0.204119576 0.018032888 23.17454552 -1.365011226 -0.134959664 KAEDS(ph)DSEPEPEDNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAEDSDSEPEPEDNVR 16 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 1 KAEDS(0.996)DS(0.004)EPEPEDNVR 175.85 2.07E-09 321440000 196280 162740 115050 140240 184170 130550 176610 217330 217420 TRUE FALSE 170341.1007 161670.9502 170688.5648 172083.6354 180505.3773 135572.343 159482.3894 170855.6708 191716.8553 0.88850352 0.843279794 0.890315901 0.897592625 0.941520645 0.707148794 0.831864205 0.89118753 1 17.54861766 1.275837713 3.124443404 1.018425464 0.857283419 0.34479827 0.061675239 0.393276413 5.170443659 0.149652248 0.016322213 18.87285976 -1.275837713 -0.161142045 KAEEELGELEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAEEELGELEAK 12 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 76.548 0.049416 124220000 196040 187310 176010 143080 135810 136960 203620 205020 195050 FALSE TRUE 170132.8173 186079.5483 261129.0247 175568.5008 133107.6467 142228.9398 183872.9637 161178.0685 171991.4112 0.989193682 1.081911864 1.518267819 1.020798071 0.773920313 0.826953735 1.069082243 0.937128589 1 17.391977 3.488247798 24.9823478 0.926789603 1.199091497 0.393138513 0.155888763 543.8797281 1221168.621 0.044246439 0.061385439 3077.852462 -3.488247798 0.272301894 KAEFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAEFER 6 1 Q9NWB6;Q9NWB6-2;Q9NWB6-3 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 0 92.187 0.075427 306300000 672410 618690 415540 557700 524560 535770 655530 723950 769180 FALSE TRUE 583549.3148 614625.7847 616496.5339 684334.3089 514122.2823 556381.4186 591956.8015 569138.9263 678248.4167 0.860376966 0.906195679 0.908953886 1.008972955 0.758014718 0.820320999 0.872772847 0.83913049 1 19.37145425 3.242414719 24.99999825 0.854901189 0.919189118 0.166310339 0.069919141 183.0995345 1187683.107 0.020266865 0.025171653 1747.490081 -3.242414719 0.064287928 KAEGAPNQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KAEGAPNQGR 10 1 Q9P2E9;A0A087WVV2;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;; 127.87 0.00055271 491320000 655830 646700 386820 610610 562510 639380 637850 908140 647290 FALSE TRUE 569160.4038 642451.7851 573887.4458 749258.3331 551317.1515 663977.3623 575991.4052 713941.3282 570768.1136 0.997183252 1.125591584 1.005465148 1.312719325 0.965921428 1.163304933 1.009151337 1.25084305 1 19.12254521 5.722144919 1.298839228 1.115267011 3.93E-10 0.069278334 0.114990092 39.78336315 8.013901836 0.029596902 106.428269 527405.8216 -5.722144919 -1.115267011 KAEGAQNQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KAEGAQNQGK 10 1 Q9P2E9;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;; 150.09 3.56E-05 1767010000 2490100 2181020 1594680 2465510 1863080 1789900 2542820 3738390 3168210 FALSE TRUE 2161026.976 2166692.736 2365872.582 3025341.728 1826008.353 1858758.611 2296217.708 2938964.391 2793667.823 0.773544714 0.775572786 0.846869682 1.082928222 0.653624006 0.665347038 0.821936556 1.05200925 1 21.41372906 1.770705825 5.900991144 1.024725342 0.802408005 0.383046504 0.117776738 0.184000365 15.42962176 0.069829289 0.032472402 58.98014347 -1.770705825 -0.222317337 KAEGEPQEES(ph)PLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 KAEGEPQEESPLK 13 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK 212.35 1.55E-08 17045240000 24910730 15218940 16615540 16678780 15620190 12275720 21409960 25416880 39217840 TRUE FALSE 21618713.91 15118965.78 24650870.72 20465951.92 15309378.78 12747974.89 19333625.37 19981678.01 34581551.63 0.625151646 0.437197438 0.712832986 0.591817051 0.44270364 0.368635133 0.559073392 0.577813229 1 25.04349927 1.208327972 3.230188224 1.10081633 0.53109189 0.678979014 0.099860895 0.244456049 3.23419274 0.36979108 0.026329869 16.15578156 -1.208327972 -0.56972444 KAEGEPQEES(ph)PLKSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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(0.999)PLKS(0.001)K;KAEGEPQEES(1)PLKSK;KAEGEPQEES(1)PLKSK;KAEGEPQEES(0.991)PLKS(0.009)K;KAEGEPQEES(1)PLKSK;KAEGEPQEES(0.99)PLKS(0.01)K 211.33 7.47E-10 6100920000 10159880 5451820 4962370 4258784 5229220 3397530 9130490 10248490 2969738 TRUE FALSE 8817226.116 5416006.635 7362188.73 5225805.999 5125168.753 3528235.178 8245016.485 8056930.167 2618658.957 3.367076913 2.068236729 2.811434727 1.995603889 1.957173056 1.347344284 3.148564445 3.07673901 1 21.32039675 4.745498355 23.73213977 2.273173074 3.367077965 0.212320083 0.699109136 719.6721853 2461671.769 0.173926046 1.623093996 55654.25266 -4.745498355 1.093904891 KAEGS(ph)PNQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAEGSPNQGK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGS(1)PNQGK 111.72 0.0010513 99991000 254820 221930 180190 235160 208220 162060 281330 415600 382550 TRUE FALSE 221144.8914 220472.1272 267330.4867 288556.6722 204076.8294 168294.5531 254046.6599 326727.1742 337325.3748 0.655583327 0.653588919 0.792500377 0.855425336 0.604985111 0.498908667 0.753120515 0.968581668 1 18.36378132 1.772483135 3.55583639 0.991749663 0.682390468 0.624807719 0.096930182 0.146964601 3.659966278 0.069841431 0.028489729 59.22200889 -1.772483135 -0.309359195 KAEGS(ph)PSEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAEGSPSEGK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGS(0.993)PS(0.007)EGK 100.11 0.0025932 241220000 596360 479970 406490 481580 323340 362590 617140 763180 772270 TRUE FALSE 517549.515 476817.0455 603069.9236 590930.0995 316906.1666 376539.0719 557289.8578 599979.8961 680973.1204 0.760014602 0.70019951 0.885600188 0.867773017 0.465372505 0.552942636 0.818372768 0.881062524 1 19.37723833 1.693639146 2.276143742 0.977599222 0.710935814 0.361815356 0.129192651 0.340490767 3.668781102 0.140928445 0.039307908 49.3900136 -1.693639146 -0.266663408 KAEGS(ph)PSEGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KAEGSPSEGKK 11 2 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGS(0.621)PS(0.379)EGKK;KAEGS(0.5)PS(0.5)EGKK 100.11 0.0022293 1148010000 2071810 1411910 1513680 1539800 867410 872490 2155500 2760500 2078070 TRUE FALSE 1798015.059 1402635.07 2245700.711 1889435.124 850150.2381 906055.2549 1946459.942 2170188.557 1832402.932 0.981233455 0.76546214 1.225549617 1.031124264 0.463953764 0.494462893 1.062244503 1.184340256 1 20.80530535 2.027191706 24.99767341 1.110724081 0.830339745 0.21044326 0.2329078 326.2553944 299929.2645 0.10291356 0.069382645 106.4612855 -2.027191706 -0.280384336 KAEGT(ph)PNQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KAEGTPNQGK 10 1 Q9P2E9;A0A087WVV2;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGT(1)PNQGK;KAEGT(1)PNQGK;KAEGT(1)PNQGK 100.02 0.0065249 238109000 686220 585923 401417 549236 350801 411083 592514 938780 836030 TRUE FALSE 595534.2883 582074.0332 595543.6039 673948.4283 343820.7464 426897.629 535052.0835 738029.2026 737195.4858 0.807837676 0.789578944 0.807850313 0.914205854 0.466390195 0.579083347 0.725794031 1.00113093 1 19.49168771 1.727588995 5.162973535 1.002234135 0.723585786 0.449071988 0.125679895 0.148616075 9.767283386 0.084467044 0.035540243 53.40587011 -1.727588995 -0.27864835 KAEGVALTNATGAVESTSQAGDRGS(ph)VS(ph)SYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAEGVALTNATGAVESTSQAGDRGSVSSYDR 31 2 F6U236;Q9BY11 F6U236 PACSIN1 Protein kinase C and casein kinase substrate in neurons protein 1 2 KAEGVALTNATGAVES(0.001)T(0.005)S(0.005)QAGDRGS(0.989)VS(0.591)S(0.408)Y(0.001)DR 113.76 3.90E-05 295620000 162540 160860 114730 141700 202180 197560 201600 253450 229010 TRUE FALSE 141059.9272 159803.3001 170213.8117 173875.1507 198157.0136 205160.261 182048.863 199251.6899 201936.6987 0.698535373 0.791353435 0.842906776 0.861037899 0.981282822 1.015963232 0.901514505 0.98670371 1 17.6235436 4.194297473 0.742028577 0.981206625 0.644725551 0.870152536 0.036962561 0.521998988 0.370266503 0.017607192 0.131416751 15642.18698 -4.194297473 -0.336481074 KAEGVALTNATGAVESTSQAGDRGS(ph)VSS(ph)YDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAEGVALTNATGAVESTSQAGDRGSVSSYDR 31 2 F6U236;Q9BY11 F6U236 PACSIN1 Protein kinase C and casein kinase substrate in neurons protein 1 2 KAEGVALTNATGAVESTS(0.001)QAGDRGS(0.999)VS(0.051)S(0.949)Y(0.001)DR 138.69 1.73E-07 428110000 305110 327590 235650 289780 390610 346230 427460 503870 438730 TRUE FALSE 264788.9404 325438.0397 349611.1282 355578.978 382837.6252 359549.6921 386004.995 396121.3216 386863.8392 0.684449963 0.84122114 0.903705885 0.919132113 0.989592685 0.929395968 0.997779983 1.023929562 1 18.56146636 5.688272617 0.531174712 1.003973462 7.95E-16 0.9369943 0.025118956 2.567224149 0.265967743 0.015600226 1.981490243 487834.6191 -5.688272617 -1.003973462 KAEGVALTNATGAVESTSQAGDRGS(ph)VSSYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAEGVALTNATGAVESTSQAGDRGSVSSYDR 31 2 F6U236;Q9BY11 F6U236 PACSIN1 Protein kinase C and casein kinase substrate in neurons protein 1 1 KAEGVALTNATGAVES(0.006)T(0.01)S(0.006)QAGDRGS(0.971)VS(0.006)SYDR 269.47 6.08E-60 252150000 300930 275280 191410 256880 313850 311640 375260 412100 279520 TRUE FALSE 261161.338 273471.6676 283976.5162 315208.5302 307604.999 323628.9925 338867.343 323975.622 246475.464 1.059583513 1.109528969 1.152149231 1.278863725 1.248014687 1.313027216 1.374852236 1.314433561 1 17.91108451 3.981091945 1.870743258 1.272514206 1.07330529 0.331813498 0.100068324 0.385986826 2.618150499 0.029165591 0.079204779 9573.967411 -3.981091945 -0.199208915 KAEPSEVDMNS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KAEPSEVDMNSPK 13 1 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 KAEPSEVDMNS(1)PK;KAEPSEVDMNS(1)PK 118.72 0.00024828 543190000 1023880 879030 790120 814510 942930 620720 1203030 1406670 1227480 TRUE FALSE 888571.6638 873255.5941 1172224.675 999456.9445 924167.5378 644599.5001 1086360.336 1105864.567 1082368.713 0.820950988 0.806800477 1.083017886 0.923397852 0.853838001 0.595545208 1.003687859 1.02170781 1 20.04576061 2.049071522 24.99955513 1.012495899 0.854872372 0.288008794 0.119117281 146.8443285 74809.35145 0.050801497 0.034250349 111.9622255 -2.049071522 -0.157623527 KAEQGS(ph)EEEGEGEEEEEEGGESK ddPTM_MDA-MB-175_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 321.94 6.38E-74 6736340000 5514090 3832497 4346377 4001518 3568812 2836869 5419379 5985604 7217537 TRUE FALSE 4785389.036 3807321.075 6448299.455 4910123.821 3497799.623 2946005.186 4893808.459 4705629.165 6364287.998 0.75191271 0.598232053 1.013200449 0.771511884 0.549597948 0.462896272 0.768948303 0.739380299 1 22.60156769 1.10438508 2.112733163 1.182202598 0.698813594 0.278439903 0.14911693 1.623217839 5.25934794 1.738207705 0.042049806 12.71701196 -1.10438508 -0.483389004 KAERS(ph)PNQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KAERSPNQGK 10 2 Q9P2E9;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAERS(1)PNQGK;KAERS(1)PNQGK;KAERS(1)PNQGK 117.03 0.00052796 451013000 536847 429887 204141 236302 264587 314844 555222 706410 38071.5 TRUE FALSE 465901.3088 427063.044 302864.2704 289957.9807 259322.2364 326956.2524 501376.6559 555349.7188 33570.73064 13.87819984 12.72129131 9.021676461 8.637225798 7.724652738 9.739324887 14.93493428 16.54267596 1 15.03491632 4.369698217 4.902320363 10 13.60750509 0.114863493 4.168779201 0.509835979 19.29062784 1.121846628 3.17990445 23426.00419 -4.369698217 3.607505086 KAEVEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 99.802 0.016452 3492400000 5004200 3445710 2645270 2907340 1827390 2440350 4756100 5197500 5454700 FALSE TRUE 4342882.291 3423074.904 3924531.42 3567495.983 1791028.514 2534231.844 4294854.154 4086055.072 4809851.58 0.902913992 0.711679944 0.815936075 0.741706043 0.37236669 0.526883585 0.892928624 0.849517912 1 22.19756095 2.171191463 11.19466019 0.900271477 0.675339942 0.351398065 0.15043743 0.68703253 111.0222783 0.066319421 0.044715863 148.3171811 -2.171191463 -0.224931535 KAFDMISQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KAFDMISQR 9 1 O14908;O14908-2;K7ESN1 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 ; 140.07 0.00017632 1322220000 2628050 3056900 1905290 2320450 3183800 3058100 3035400 3495300 2926330 FALSE TRUE 2280746.534 3036819.023 2826694.617 2847343.638 3120448.609 3175747.086 2741027.375 2747857.295 2580382.601 0.88387921 1.17688711 1.095455618 1.103457928 1.209296872 1.230727213 1.062256184 1.064903047 1 21.29915356 4.748069632 24.34143005 1.116360357 0.883879029 0.518945648 0.070788259 814.0877123 2083859.749 0.018461392 0.226691725 55984.73567 -4.748069632 -0.232481329 KAFEEAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KAFEEAEK 8 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 114.5 0.0042411 3359740000 8734700 4721680 3822340 4249400 3972490 3341890 6267200 7164300 5796300 FALSE TRUE 7580387.264 4690662.973 5670836.409 5214291.218 3893445.221 3470454.671 5659407.909 5632270.198 5111068.017 1.483131752 0.917746146 1.109520826 1.020196014 0.761767444 0.679007726 1.107284796 1.101975199 1 22.28519336 4.742262939 24.59367548 0.971214108 1.483132 0.55862637 0.145327833 252.9506048 1680203.341 0.038895894 0.281252747 55241.17906 -4.742262939 0.511917892 KAGEQQETASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 KAGEQQETASR 11 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;;;;;; 221.56 1.33E-11 1287731000 1645123 1555451 969634.3 1189650 1207783 1339559 1608020 1981517 1504370 FALSE TRUE 1427715.827 1545233.14 1438552.691 1459778.215 1183750.481 1391092.702 1452074.468 1557785.01 1326525.092 1.076282564 1.164872907 1.084451926 1.100452772 0.892369461 1.048674246 1.094645308 1.174335125 1 20.33922053 3.761293242 3.05819869 1.059568127 1.11800537 0.11506916 0.075889619 0.69407438 13.19857913 0.023312525 0.04166119 5771.560366 -3.761293242 0.058437243 KAGIAHLYGIAGSTNVTGDQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAGIAHLYGIAGSTNVTGDQVK 22 1 P09467 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 80.277 0.0043339 958430000 584590 403560 885160 443280 296420 225180 507680 469200 353530 FALSE TRUE 507334.9503 400908.9878 1313226.337 543933.4991 290521.8219 233842.8203 458445.2717 368865.2313 311736.0861 1.627450183 1.286052548 4.212622135 1.744852532 0.931948 0.750130738 1.470619836 1.183261251 1 18.24996564 3.477553235 21.50458044 1.118130005 2.385157763 0.372548903 0.777053705 2.776458697 138231.4959 0.22199886 0.291219222 3002.985496 -3.477553235 1.267027758 KAGNFYVPAEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KAGNFYVPAEPK 12 1 P18124;A8MUD9;C9JZ88;C9JIJ5 P18124 RPL7 60S ribosomal protein L7 0 ; 125.28 0.00049383 2088910000 3949900 3289800 2420140 2858800 3139200 2477800 4228600 4748100 3746800 FALSE TRUE 3427910.707 3268189.087 3590527.799 3507934.234 3076736.062 2573122.569 3818511.023 3732755.765 3303857.572 1.037547967 0.989203988 1.086768337 1.061769207 0.931255659 0.778823697 1.155773498 1.129817398 1 21.65572006 KDPELWGSVLLESNPYRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDPELWGSVLLESNPYRR 18 2 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 142.78 6.20E-08 2259200000 369550 286930 199036 208877 336970 336160 363490 368150 123369 FALSE TRUE 320713.0312 285045.1379 295290.4753 256305.7153 330264.9563 349092.2927 328238.7957 289423.9874 108784.4574 2.948151224 2.620274485 2.714454643 2.356087639 3.035957197 3.209027293 3.017331738 2.660527013 1 16.73111292 1.23789412 4.247072574 0.821221526 2.832171536 0.851819567 0.239714062 0.086470995 2.979105897 0.534011097 0.065168047 17.29394684 -1.23789412 2.01095001 KAGSALPGFANS(ph)PAGSTSVVLVPPAHGTLVPDGNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAGSALPGFANSPAGSTSVVLVPPAHGTLVPDGNK 35 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 KAGSALPGFANS(1)PAGSTSVVLVPPAHGTLVPDGNK 199.1 8.93E-28 824360000 189110 181440 56576 132480 164600 117270 186750 239870 188780 TRUE FALSE 164118.6344 180248.1087 83936.34284 162561.6088 161324.782 121781.4528 168639.0137 188575.6672 166462.6435 0.985918708 1.082814167 0.504235311 0.976565105 0.969135048 0.731584278 1.013074226 1.132840758 1 17.34483893 2.015158076 22.71586622 1.075023589 0.876173452 0.204195728 0.163869909 111.2760161 166756.2752 0.065808456 0.044338827 103.5519009 -2.015158076 -0.198850136 KAGTQIENIDEDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KAGTQIENIDEDFR 14 1 O43707;F5GXS2;O43707-3;K7EP19 O43707 ACTN4 Alpha-actinin-4 0 ;;; 146.16 1.34E-05 1908300000 1737730 1534940 1255170 1889000 1603250 1635560 1550270 1724780 3437780 FALSE TRUE 1508084.578 1524856.878 1862174.41 2317926.322 1571348.462 1698481.052 1399925.054 1355949.219 3031369.565 0.497492815 0.503025727 0.614301348 0.764646564 0.518362551 0.560301545 0.46181273 0.44730581 1 21.53153832 1.231023748 24.99571778 1.00000081 0.544564458 0.711038713 0.090971256 166.7282737 552900.2292 0.250945328 0.024403107 17.02251588 -1.231023748 -0.455436352 KAGTQIENIDEDFRDGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KAGTQIENIDEDFRDGLK 18 2 O43707;F5GXS2;O43707-3;K7EP19 O43707 ACTN4 Alpha-actinin-4 0 ;; 195.78 1.14E-15 1512790000 2076650 1726800 1344050 1514540 1586960 1299280 2100640 2409720 1425560 FALSE TRUE 1802215.441 1715456.537 1994037.076 1858439.455 1555382.601 1349264.142 1896920.256 1894420.13 1257031.921 1.433706982 1.364688127 1.586305839 1.478434576 1.237345349 1.073373015 1.509047006 1.507058094 1 20.26158986 3.251032294 24.78267269 1.304252958 1.467171517 0.239527357 0.169759683 387.3508503 769706.4131 0.051994319 0.066637612 1782.511309 -3.251032294 0.162918559 KAGTQIENIEEDFRDGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KAGTQIENIEEDFRDGLK 18 2 P12814-3;P12814;P12814-2;P12814-4;G3V2N5;G3V5M4;G3V380 P12814-3 ACTN1 Alpha-actinin-1 0 ; 226.44 1.98E-19 373860000 673770 497050 387190 418530 479360 396770 688280 781720 272960 FALSE TRUE 584729.5874 493784.8458 574436.3791 513563.6333 469821.6739 412033.9986 621530.7115 614555.2614 240690.9798 2.429378899 2.051530333 2.386613656 2.133705359 1.951970424 1.711879685 2.582276711 2.553295774 1 17.87682255 3.490640648 21.15055439 2.066021702 2.264535033 0.07320808 0.4553667 343.1580638 536853.2873 0.130073588 0.183344368 3094.857436 -3.490640648 0.198513331 KAIVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KAIVER 6 1 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ;; 91.906 0.075939 1532980000 3043700 2787900 1888070 2052760 2366570 2732850 2968740 3301140 2701010 FALSE TRUE 2641467.333 2769586.101 2801146.967 2518870.532 2319479.887 2837984.508 2680832.052 2595216.901 2381699.675 1.109068184 1.162861183 1.176112588 1.057593684 0.973875889 1.1915795 1.125596178 1.089649097 1 21.18356007 1.191378406 0.014918044 2.78E-05 2.138667818 0.131921593 0.067086401 11073.90208 44.82945593 3417.646687 3018.607303 15.53740212 -1.191378406 2.138639986 KALELDQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KALELDQER 9 1 A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P35241-2 A0A2R8Y5S7 RDX Radixin 0 ; 94.82 0.013571 751230000 1379850 1397840 994820 1322030 1432660 1333960 1480170 1843620 1469230 FALSE TRUE 1197499.326 1388657.497 1475918.279 1622217.117 1404152.869 1385278.304 1336623.341 1449376.21 1295539.303 0.924324969 1.071876008 1.139230802 1.25215585 1.083836566 1.06926768 1.031711919 1.118743528 1 20.30512135 4.716862969 3.631522471 1.101436456 0.908361895 0.394205162 0.067513385 0.27075477 6.590390326 0.017335856 0.137042537 52103.02864 -4.716862969 -0.193074561 KALERPYTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KALERPYTSK 10 2 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 69.01 0.032768 804410000 609880 519840 308320 384860 429280 351540 590310 579120 433020 FALSE TRUE 529282.8128 516425.1368 457424.5833 472248.3452 420738.1679 365063.9713 533061.8271 455279.6947 381828.8689 1.386178091 1.352504168 1.197983234 1.236806286 1.101902455 0.956093164 1.396075233 1.192365826 1 18.54256666 4.230023728 1.510204785 1.154619115 1.407559759 0.360594911 0.12122624 0.625543518 2.425299671 0.036442332 0.180178678 16983.36438 -4.230023728 0.252940644 KALVVPEPEPDSDS(ph)NQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KALVVPEPEPDSDSNQER 18 1 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 1 KALVVPEPEPDS(0.01)DS(0.99)NQER;KALVVPEPEPDS(0.021)DS(0.979)NQER;KALVVPEPEPDS(0.034)DS(0.966)NQER;KALVVPEPEPDS(0.008)DS(0.992)NQER;KALVVPEPEPDS(0.085)DS(0.915)NQER 184.34 3.60E-14 2971510000 4260860 3108580 1911570 2178710 2965270 3186850 3639870 3518340 2147240 TRUE FALSE 3697776.555 3088159.533 2836011.646 2673419.405 2906266.928 3309450.182 3286875.968 2765970.371 1893395.733 1.952986631 1.631016421 1.497844109 1.411970756 1.53494955 1.747891433 1.735968826 1.460851697 1 20.85254455 1.280555236 2.849796229 0.905644001 1.628233325 0.642663124 0.151107646 0.260052566 2.681480776 0.419242514 0.041314423 19.07898366 -1.280555236 0.722589324 KALWFQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KALWFQGR 8 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 141.39 0.0010171 326170000 154540 232670 420490 143230 218780 240220 200980 211290 126000 FALSE TRUE 134117.1474 231141.5754 623840.3705 175752.5606 214426.706 249461.4188 181488.9905 166107.2778 111104.4235 1.207126982 2.080399394 5.614901285 1.581868255 1.929956515 2.245287909 1.633499232 1.495055484 1 16.76155673 KAMAMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAMAMK 6 1 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 91.584 0.076526 406450000 452240 406950 279900 333420 286300 352000 461620 575780 474620 FALSE TRUE 392475.3382 404276.7187 415260.5762 409128.107 280603.1901 365541.6678 416852.1635 452653.9277 418510.9643 0.937789859 0.965988357 0.992233446 0.977580379 0.670479902 0.87343391 0.996036422 1.081582005 1 18.67490589 2.072907214 4.689788877 1.044830174 0.903297527 0.289183262 0.092588161 0.261575466 10.91439355 0.043351967 0.02788069 118.2788829 -2.072907214 -0.141532647 KAMEAVAAQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAMEAVAAQGK 11 1 P18669;P15259 P18669 PGAM1;PGAM2 Phosphoglycerate mutase 1;Phosphoglycerate mutase 2 0 122.45 0.00062628 525200000 1829500 1536700 1097700 1214200 1473300 1197500 1822600 2272000 1698100 FALSE TRUE 1587726.94 1526605.317 1628551.392 1489902.668 1443984.212 1243568.6 1645844.533 1786150.481 1497352.552 1.060356118 1.019536324 1.08762054 0.995024629 0.9643582 0.830511557 1.099169684 1.192872365 1 20.51398251 2.027265449 24.99666494 1.120955404 0.994518434 0.251758717 0.082488321 241.6911657 221578.8351 0.034453148 0.023227693 106.4793642 -2.027265449 -0.12643697 KAMLS(ph)QMNVT(ph)APTSPPVQQNMMNSASAMNQRISQS(ph)APVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAMLSQMNVTAPTSPPVQQNMMNSASAMNQRISQSAPVK 39 2 P46937-6;P46937-7;P46937-5;P46937-3 P46937-6 YAP1 Transcriptional coactivator YAP1 3 KAMLS(0.867)QMNVT(0.294)APT(0.295)S(0.295)PPVQQNMMNS(0.084)AS(0.084)AMNQRIS(0.085)QS(0.998)APVK 46.608 0.032296 601680000 0 0 0 0 0 0 0 0 0 TRUE FALSE 0 0 0 0 0 0 0 0 0 0 KANLDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KANLDKR 7 2 E7ETZ4;Q9Y6E2;Q75MG1;B5MCH7;B5MCE7;E9PFD4 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 80.18 0.017218 263260000 1083100 1167000 830140 905980 829710 982660 1408000 1578300 1140800 FALSE TRUE 939965.5908 1159333.9 1231598.481 1111696.606 813200.3943 1020463.566 1271452.377 1240792.827 1005935.924 0.934418951 1.152492791 1.224330946 1.1051366 0.808401783 1.014441916 1.263949668 1.233471037 1 19.94010698 2.251327248 24.98548351 1.183992887 1.045819581 0.1608309 0.133008123 388.6379238 760600.1206 0.052755325 0.040593907 178.3722324 -2.251327248 -0.138173306 KANLQIDQINTDLNLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KANLQIDQINTDLNLER 17 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 250.08 5.57E-21 683860000 1012610 966900 426800 482110 938740 848280 1036310 1150500 203013 FALSE TRUE 878791.0229 960548.3702 633201.9076 591580.4441 920060.9106 880913.8805 935808.8157 904474.5282 179013.0344 4.909089585 5.365801286 3.537183254 3.304678042 5.13963083 4.920948262 5.227601547 5.052562408 1 17.44970511 4.258254222 24.73656718 4.22806697 5.137445927 0.099253136 1.28428856 598.9323988 752286.8861 0.318713797 0.840551817 18124.00704 -4.258254222 0.909378958 KAPAGPSLEETSVS(ph)SPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAPAGPSLEETSVSSPK 17 1 K7EIX2;Q6AI08;A0A087WXZ7 K7EIX2 HEATR6 HEAT repeat-containing protein 6 1 KAPAGPSLEETSVS(0.647)S(0.353)PK 175.73 7.31E-10 291370000 527580 173020 134680 128030 176970 129400 231980 215150 214750 TRUE FALSE 457858.9663 171883.4202 199811.6985 157101.1683 173448.6432 134378.1017 209482.6153 169141.8468 189362.4996 2.417896717 0.907695138 1.05518093 0.829631889 0.915960888 0.709634178 1.106251849 0.893217227 1 17.53079113 4.739004315 24.9992927 0.926735756 2.417897168 0.946225376 0.111682211 7.144127023 402399.7572 0.025621059 0.146399028 54828.24127 -4.739004315 1.491161412 KAPAGPSLEETSVSS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAPAGPSLEETSVSSPK 17 1 K7EIX2;Q6AI08;A0A087WXZ7 K7EIX2 HEATR6 HEAT repeat-containing protein 6 1 KAPAGPSLEETSVS(0.203)S(0.796)PK 167.73 1.34E-09 321830000 976240 309400 264420 223240 315690 253550 401930 402950 408850 TRUE FALSE 847227.4105 307367.531 392294.3964 273930.054 309408.3866 263304.2326 362950.8905 316782.2783 360516.2188 2.350039655 0.852576153 1.088146319 0.759827269 0.858237079 0.730353362 1.006753293 0.878690782 1 18.45970464 4.739594915 24.99775111 0.895849156 2.350040117 0.944836468 0.110351862 17.65572672 426661.3675 0.025713324 0.152441549 54902.85323 -4.739594915 1.454190961 KAPAGQEEPGT(ph)PPS(ph)SPLSAEQLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KAPAGQEEPGTPPSSPLSAEQLDR 24 1 P13051;Q68DM5;F5GYA2;P13051-2 P13051 UNG;DKFZp781L1143 Uracil-DNA glycosylase 2 KAPAGQEEPGT(1)PPS(0.593)S(0.407)PLSAEQLDR;KAPAGQEEPGT(1)PPS(0.619)S(0.38)PLS(0.001)AEQLDR 137.44 1.18E-05 699580000 854030 749340 467700 595760 694340 565030 770320 967330 784360 TRUE FALSE 741167.7717 744417.5362 693881.2844 731036.4136 680523.9925 586767.0697 695614.485 760474.0073 691633.8543 1.0716187 1.076317377 1.003249451 1.056970258 0.983936787 0.848378179 1.005755402 1.099532654 1 19.39964896 4.171438185 1.439766053 1.001166915 1.082520795 0.181739672 0.063989007 1.133559523 4.046442428 0.021689058 0.099440342 14840.14638 -4.171438185 0.08135388 KAPAGQEEPGT(ph)PPSSPLSAEQLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KAPAGQEEPGTPPSSPLSAEQLDR 24 1 P13051;Q68DM5;F5GYA2;P13051-2 P13051 UNG;DKFZp781L1143 Uracil-DNA glycosylase 1 KAPAGQEEPGT(0.992)PPS(0.008)SPLSAEQLDR;KAPAGQEEPGT(0.999)PPS(0.001)SPLSAEQLDR;KAPAGQEEPGT(0.971)PPS(0.025)S(0.004)PLSAEQLDR;KAPAGQEEPGT(0.959)PPS(0.035)S(0.006)PLSAEQLDR 191.22 5.85E-18 1696940000 2399230 2184170 1307470 1629850 2089310 1765080 2056020 2696040 2030790 TRUE FALSE 2082165.677 2169822.043 1939766.865 1999932.353 2047736.819 1832983.77 1856627.497 2119512.827 1790712.32 1.162758336 1.211708893 1.083237572 1.116836206 1.143531988 1.023605941 1.036809473 1.183614366 1 20.77210215 4.232608669 24.99516218 1.091468952 1.187233623 0.357830644 0.056833373 146.4518986 615033.8495 0.014347594 0.031171527 17084.75162 -4.232608669 0.095764672 KAPAQKVPAQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAPAQKVPAQK 11 2 P50914 P50914 RPL14 60S ribosomal protein L14 0 82.171 0.011062 250030000 303110 289080 163770 167390 245920 219920 399800 373410 107020 FALSE TRUE 263053.2455 287181.0144 242969.7198 205398.4579 241026.6731 228380.4647 361027.4575 293559.1774 94368.21752 2.787519489 3.043196343 2.574698624 2.176563925 2.55410857 2.42009938 3.825731449 3.110784384 1 16.52601343 7.364772963 15.81405105 2.687842541 2.706574984 0 0.732004385 0 0 0.162946977 0 23161834.96 -7.364772963 0.018732443 KAPDFVFYAPR ddPTM_MDA-MB-175_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 ; 178.1 1.23E-05 7857900000 9801000 10065600 6379600 8167200 9539400 9207800 9020300 11070700 10295200 FALSE TRUE 8505773.017 9999478.411 9464795.898 10021687.59 9349584.604 9562030.024 8145512.694 8703316.957 9078113.184 0.936953841 1.101493031 1.042595053 1.103939484 1.029903947 1.053305883 0.897269348 0.958714303 1 23.11396104 2.257977412 24.99948986 0.951114285 1.049204811 0.414433607 0.051758103 201.8921545 259939.427 0.018235429 0.014103473 181.1245886 -2.257977412 0.098090525 KAPEINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAPEINR 7 1 H3BUP7;I3L2Q8;Q9UIC8-3;Q9UIC8;Q9UIC8-2 H3BUP7 LCMT1 Leucine carboxyl methyltransferase 1 0 73.931 0.076253 1283200000 241670 210290 124170 186200 180240 180740 237650 271080 235780 FALSE TRUE 209732.6972 208908.5911 184219.0273 228479.5559 176653.5766 187693.1848 214602.7396 213111.6515 207906.357 1.008784436 1.004820604 0.886067314 1.09895416 0.849678573 0.902777517 1.032208648 1.025036726 1 17.66557435 2.207095392 24.98787646 1.020869396 0.958762166 0.139551483 0.070849561 382.4288662 303700.5525 0.028287417 0.019073528 161.0999451 -2.207095392 -0.06210723 KAPETCSTAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KAPETCSTAGR 11 1 Q86VY4 Q86VY4 TSPYL5 Testis-specific Y-encoded-like protein 5 0 ; 153.75 5.18E-05 97885000 99955 107375 68418 82678 96205 91643 100157 116974 108875 FALSE TRUE 86745.6935 106669.6466 101505.1736 101451.3036 94290.70872 95168.56551 90443.78956 91960.02039 96003.92153 0.903564064 1.111096764 1.057302369 1.056741245 0.982154762 0.99129873 0.942084324 0.95787775 1 16.55080572 3.134935038 4.876141176 0.969565569 1.039433924 0.211212704 0.054320697 0.274642058 10.72381206 0.015909863 0.01827733 1364.379038 -3.134935038 0.069868355 KAPKPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAPKPER 7 2 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 0 50.607 0.088157 147170000 219580 198510 134910 135600 137230 183950 207240 222990 212270 FALSE TRUE 190561.9467 197205.9747 200152.9272 166390.0525 134499.3915 191026.6755 187141.8967 175305.3238 187175.6824 1.018091368 1.053587582 1.069331895 0.888951227 0.718572999 1.020574217 0.999819497 0.936581727 1 17.51403349 3.743688298 24.90162717 0.92807624 1.047662018 0.303113786 0.085472438 545.5455352 2649330.676 0.024128942 0.040195221 5542.277894 -3.743688298 0.119585778 KAPKS(ph)PAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KAPKSPAK 8 2 P10412 P10412 HIST1H1E Histone H1.4 1 KAPKS(1)PAK;KAPKS(1)PAK 70.488 0.040322 7032100000 6339980 6369110 5126670 5127690 3635240 4950280 9551600 10114300 5148920 TRUE FALSE 5502135.58 6327270.897 7605944.76 6292010.386 3562905.836 5140720.475 8625287.302 7951435.655 4540220.543 1.211865267 1.393604306 1.67523685 1.38583805 0.7847429 1.132262282 1.899750732 1.751332469 1 22.11433095 2.255717398 24.99901712 1.606788125 1.272275953 0.142708247 0.320736738 410.1179119 597578.9103 0.12604016 0.097387634 180.1844872 -2.255717398 -0.334512172 KAPPLVENEEAEPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAPPLVENEEAEPGR 15 1 O14908;K7ELJ2 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 149 5.51E-06 264420000 120390 104870 75130 97455 116720 102240 126150 129130 156730 FALSE TRUE 104480.1565 104181.1021 111463.1193 119583.6473 114397.5004 106173.239 113915.9924 101516.5544 138201.5579 0.755998398 0.753834498 0.80652578 0.865284365 0.827758399 0.768249219 0.8242743 0.734554341 1 17.07641435 KAPPQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAPPQGR 7 1 I3L0N3;P46459;P46459-2;K7EQD6;I3L2G1 I3L0N3 NSF Vesicle-fusing ATPase 0 88.029 0.030318 41376000 39219 45987 29611 33235 28192 37770 42213 43369 47308 FALSE TRUE 34036.10978 45684.90837 43930.97864 40781.51472 27631.03436 39223.03634 38119.18976 34094.87685 41715.30213 0.815914258 1.095159475 1.053114239 0.977615231 0.66237167 0.940255358 0.913793927 0.817323023 1 15.34828907 3.449969825 24.99915631 0.863430555 1.001537919 0.210460424 0.11329488 284.6994368 262130.5789 0.03110136 0.040152496 2818.187118 -3.449969825 0.138107364 KAPS(ph)SPPPPPPPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KAPSSPPPPPPPLR 14 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 KAPS(0.58)S(0.42)PPPPPPPLR;KAPS(0.585)S(0.415)PPPPPPPLR 72.446 0.023645 677400000 1344490 1141170 844450 1014030 1125310 1066980 1283600 1510580 1373970 TRUE FALSE 1166812.24 1133673.579 1252828.845 1244281.01 1102918.533 1108027.411 1159116.67 1187554.222 1211540.832 0.963081235 0.935728743 1.034078928 1.027023586 0.910343674 0.914560518 0.956729348 0.980201567 1 20.2084116 3.244754405 24.99998011 0.954283189 0.989253213 0.190603376 0.038387119 308.8359217 1246547.15 0.012252273 0.015417936 1756.929782 -3.244754405 0.034970023 KAPSS(ph)PPPPPPPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAPSSPPPPPPPLR 14 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 KAPS(0.203)S(0.797)PPPPPPPLR 84.375 0.0049969 410520000 479100 449150 268500 333740 450190 406100 515870 561010 516800 TRUE FALSE 415785.7211 446199.5041 398347.4981 409520.7679 441232.0998 421722.9298 465841.0068 441042.3773 455704.4927 0.912402067 0.97914221 0.874135551 0.898654225 0.968241715 0.925430705 1.022243612 0.967825388 1 18.79773907 2.521273961 1.638325474 0.991608256 0.921620454 0.443952944 0.034823119 0.354532112 1.946010599 0.017195933 0.012149753 332.1038888 -2.521273961 -0.069987803 KAPT(ph)PQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KAPTPQEK 8 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 KAPT(1)PQEK;KAPT(1)PQEK;KAPT(1)PQEK 107.09 0.0023852 2235380000 14179200 8911700 7802200 8114400 6491600 6222500 11623400 13677500 12990200 TRUE FALSE 12305382.79 8853158.456 11575370.02 9956898.541 6362429.861 6461883.601 10496164.46 10752673.06 11454513.35 1.074282461 0.772896952 1.010551008 0.869255483 0.555451783 0.564134276 0.916334386 0.938728057 1 23.44941283 3.476740312 24.99998776 0.801550412 0.935491248 0.160187147 0.163176842 30.78942567 2020480.14 0.051470654 0.067113751 2997.369694 -3.476740312 0.133940836 KAPTTDEDKK ddPTM_MDA-MB-175_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 0 134.98 8.80E-05 282320000 575930 426830 447290 448070 269880 239980 673140 761110 671710 FALSE TRUE 499819.3913 424026.1256 663600.9401 549811.1418 264509.916 249212.1859 607858.9864 598352.5495 592301.209 0.843860157 0.7158961 1.120377487 0.928262738 0.446580071 0.420752452 1.026266665 1.010216661 1 19.17597151 KAQCPIVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KAQCPIVER 9 1 M0R0F0;M0R0R2;P46782 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;;; 163.88 0.00010051 3207970000 2761720 2560870 1536100 2014650 2509080 2281860 2616220 3045440 2538450 FALSE TRUE 2396751.705 2544047.476 2278963.098 2472107.074 2459154.217 2369644.631 2362499.387 2394196.356 2238357.333 1.070763667 1.136568965 1.018140877 1.104429145 1.098642375 1.058653413 1.055461232 1.069622049 1 21.09400894 -0.313978663 0.852452673 1.33E-13 1.082507971 0.371917529 0.03162629 31.40565399 2.000826537 56.36390915 0.010826639 0.485312343 0.313978663 1.082507971 KAQLNIGNVLPVGTMPEGTIVCCLEEKPGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KAQLNIGNVLPVGTMPEGTIVCCLEEKPGDR 31 2 P62917;E9PKZ0;G3V1A1;E9PKU4 P62917 RPL8 60S ribosomal protein L8 0 ; 143.35 1.19E-08 1109110000 904220 771650 579800 660270 756130 539210 1062340 1165090 700530 FALSE TRUE 784725.036 766580.9803 860193.2193 810194.3951 741084.4923 559953.7576 959314.4303 915944.5702 617714.1414 1.270369226 1.240996326 1.39254254 1.311600853 1.199720781 0.906493344 1.553007072 1.482796829 1 19.23657983 KAQLVVIAHDVDPIELVVFLPALCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KAQLVVIAHDVDPIELVVFLPALCR 25 1 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 ; 90.534 0.0088233 265390000 553540 551010 236923 237510 367960 292570 728880 722880 87990 FALSE TRUE 480388.2865 547390.379 351499.7553 291440.2756 360638.3159 303825.3572 658193.3298 568297.7375 77587.92244 6.191534345 7.055097776 4.530341118 3.756258274 4.648124406 3.915884685 8.483193119 7.324564437 1 16.24354448 4.243146417 24.98010961 5.154698777 6.6233163 0.102394286 2.042828215 319.691203 1741385.517 0.540886371 1.334101814 17504.36729 -4.243146417 1.468617523 KAQPQDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KAQPQDSR 8 1 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ;;;; 111.65 0.0051186 874098000 1985590 1711660 1010235 1378450 961412 1476630 1775670 2101220 1901080 FALSE TRUE 1723189.251 1700415.993 1498788.025 1691448.141 942281.7822 1533436.912 1603465.797 1651890.455 1676336.488 1.027949498 1.014364362 0.894085427 1.009014689 0.56210778 0.914754837 0.956529795 0.985416989 1 20.67688034 4.256918119 8.265357748 0.905322823 1.021838271 0.128417993 0.127739045 0.402787303 136.5125601 0.033080478 0.083429925 18068.33437 -4.256918119 0.116515448 KAQVS(ph)PQS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KAQVSPQS 8 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KAQVS(0.989)PQS(0.011);KAQVS(0.928)PQS(0.072);KAQVS(0.5)PQS(0.5);KAQVS(0.885)PQS(0.115) 80.706 0.026222 19632600000 24268400 18713500 12377590 15470800 13368270 16736000 20713300 24678000 20885500 TRUE FALSE 21061269.45 18590569.79 18363433.92 18983681.6 13102267.58 17379844.75 18704527.35 19400801.74 18416439.98 1.143612418 1.009455128 0.997121808 1.030800829 0.711444101 0.943713593 1.015642946 1.053450165 1 24.13449087 4.986274565 1.358430881 0.965465682 1.312989934 0.263454212 0.094969507 3.685038611 3.940347237 0.028946801 2.059618621 96889.02044 -4.986274565 0.347524252 KAQVSPQS(ph) ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KAQVSPQS 8 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KAQVS(0.096)PQS(0.904);KAQVS(0.075)PQS(0.925) 72.2 0.049541 10327900000 15080100 12318700 7529900 9878400 8238000 10082800 13078400 15009700 12460500 TRUE FALSE 13087226.58 12237777.65 11171384.83 12121441.7 8074079.917 10470691.84 11810058.78 11799992.46 10987433.89 1.191108562 1.113797614 1.016741938 1.103209524 0.734846735 0.952969724 1.074869611 1.073953444 1 23.38935115 4.421731423 1.513278901 0.99295614 1.212489272 0.317105113 0.10173312 0.878957729 2.90510603 0.031098976 0.243607232 26407.75143 -4.421731423 0.219533132 KAS(ph)GS(ph)ENEGDYNPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KASGSENEGDYNPGR 15 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 KAS(1)GS(1)ENEGDYNPGR;KAS(1)GS(1)ENEGDY(0.001)NPGR;KAS(1)GS(1)ENEGDYNPGR;KAS(1)GS(1)ENEGDYNPGR;KAS(1)GS(1)ENEGDYNPGR 172.55 6.82E-07 2474810000 4971730 3930530 2796570 3390000 4465130 3789350 4139470 5149000 5496030 TRUE FALSE 4314703.284 3904710.09 4149000.606 4159751.313 4376282.649 3935128.747 3738024.837 4047926.42 4846295.594 0.890309557 0.805710261 0.856117941 0.858336276 0.903016038 0.811986943 0.771315898 0.835261973 1 22.20845097 1.237799694 24.96698446 1.000000189 0.838787457 0.616732167 0.039213871 12.79842783 419649.0307 0.057407971 0.009830505 17.29018715 -1.237799694 -0.161212733 KAS(ph)GSENEGDYNPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KASGSENEGDYNPGR 15 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KAS(0.973)GS(0.027)ENEGDYNPGR;KAS(0.536)GS(0.464)ENEGDYNPGR;KAS(0.802)GS(0.198)ENEGDYNPGR 243.16 3.56E-18 1471280000 818750 636529 482248 693420 710284 622436 705260 902080 931000 TRUE FALSE 710550.1131 632347.5991 715464.7458 850871.6093 696150.738 646381.5157 636863.9938 709177.212 820938.2406 0.865534187 0.770274264 0.871520792 1.036462388 0.847994043 0.787369236 0.775775768 0.863861831 1 19.64691417 4.098774713 10.46743221 0.876934234 0.818150796 0.090340482 0.084587839 0.979968718 96.24846297 0.022820829 0.047594482 12553.78577 -4.098774713 -0.058783438 KAS(ph)GSENEGDYNPGRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KASGSENEGDYNPGRK 16 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KAS(0.994)GS(0.006)ENEGDYNPGRK;KAS(0.745)GS(0.255)ENEGDYNPGRK;KAS(0.965)GS(0.035)ENEGDYNPGRK;KAS(0.878)GS(0.122)ENEGDYNPGRK 197.72 2.22E-11 674820000 1625130 1004720 669330 825060 1078490 765470 1314870 1603580 618550 TRUE FALSE 1410364.953 998119.9282 993020.2268 1012402.483 1057030.159 794918.1262 1187354.11 1260666.896 545425.7237 2.585805714 1.829983231 1.820633285 1.856169299 1.937991028 1.457426908 2.176930897 2.311344774 1 19.05702322 4.739676467 24.16202638 1.852731765 2.585806097 0.303916811 0.36631455 81.02439121 1754089.561 0.087520382 0.522498223 54913.16395 -4.739676467 0.733074332 KAS(ph)LLSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KASLLSAK 8 1 O94885;A0A087WW74 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 KAS(1)LLSAK 109.24 0.0027762 0 388060 286060 221790 254610 287030 203760 488260 402350 356210 TRUE FALSE 336776.8878 284180.853 329048.3858 312423.092 281318.6646 211598.7791 440908.6204 316310.5836 314099.2596 1.072198923 0.904748561 1.047593637 0.994663573 0.895636191 0.673668506 1.403723845 1.007040208 1 18.26086102 2.24228537 24.99999619 1.120979516 0.936735056 0.281243148 0.154011127 134.9990645 906102.0145 0.058167661 0.043287217 174.6969692 -2.24228537 -0.18424446 KAS(ph)LTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KASLTSK 7 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 KAS(0.999)LT(0.001)SK 86.879 0.012099 561770000 554550 364700 352920 411730 193860 287210 613440 542960 710560 TRUE FALSE 481264.8124 362304.2617 523593.2924 505219.5894 190002.5653 298259.1545 553948.6832 426852.2293 626558.4063 0.76810846 0.578244994 0.835665578 0.806340773 0.303247971 0.476027696 0.884113401 0.681264867 1 19.25708947 0.376028361 1.137753372 2.766011048 0.647431071 0.261765569 0.176754288 14.94888506 3.541230599 61.16301046 0.056579274 2.376995507 -0.376028361 -2.118579978 KAS(ph)PEAASTPR ddPTM_MDA-MB-175_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(0.998)PEAAS(0.001)T(0.001)PR 124.09 0.00021822 180000000 126720 101430 97702 92994 100220 80684 104390 116770 232120 TRUE FALSE 109973.6309 100763.6997 144951.014 114109.709 98225.81808 83787.96569 94266.27387 91799.64421 204679.038 0.537297967 0.492301022 0.708186903 0.557505596 0.479901699 0.40936271 0.460556561 0.448505353 1 17.64300383 1.234248692 24.99996328 1.000000724 0.509115742 0.779654807 0.081570466 65.8107333 381511.1005 0.166317972 0.02177733 17.14939061 -1.234248692 -0.490884982 KAS(ph)PEAASTPRDPIDVDLPEEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KASPEAASTPRDPIDVDLPEEAER 24 2 P29590-2;P29590-5;P29590-9;P29590-3;P29590-8;P29590;P29590-4;H3BVD2;H3BT29 P29590-2 PML Protein PML 1 KAS(1)PEAASTPRDPIDVDLPEEAER 141.64 1.44E-07 267530000 86331 68919 40505 45495 68822 50411 76899 81910 33486 TRUE FALSE 74922.13962 68466.26655 60093.35348 55825.3351 67452.57685 52350.34379 69441.34682 64394.18392 29527.32323 2.537383394 2.318742746 2.035177826 1.890633115 2.284412181 1.772945803 2.351765728 2.18083378 1 14.84976296 1.238028056 24.99054095 0.999998674 2.163015531 0.727043986 0.225529656 6.840908214 320704.6165 0.311899572 0.05418743 17.2992811 -1.238028056 1.163016857 KAS(ph)PEPEGEAAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 195.89 1.84E-07 2184200000 4166750 2595660 2295920 2525490 2595660 1943010 3649000 4228810 4184710 TRUE FALSE 3616103.43 2578608.939 3406234.591 3098941.104 2544011.444 2017758.852 3295120.542 3324511.89 3689998.351 0.979974267 0.698810323 0.923099218 0.839821813 0.689434304 0.546818361 0.892986996 0.900952134 1 21.81518874 1.816284531 2.846586272 0.957457991 0.779701985 0.232805984 0.12602582 0.374123474 5.588825325 0.090547592 0.035323453 65.5065204 -1.816284531 -0.177756006 KAS(ph)PEPPDSAEGALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 198.49 4.84E-09 7852860000 9527650 5930110 5508990 5727910 5867200 4569660 8825160 10251850 9649320 TRUE FALSE 8268546.913 5891154.717 8173155.99 7028519.511 5750454.199 4745457.777 7969297.342 8059571.657 8508588.382 0.971788332 0.692377449 0.960577198 0.826050009 0.675841155 0.557725625 0.936618036 0.947227824 1 23.02048837 2.032061045 24.99969661 0.961468293 0.779261135 0.317980924 0.125229287 225.542878 175866.8415 0.051853722 0.034959495 107.6616533 -2.032061045 -0.182207158 KAS(ph)PPSGLWSPAYASH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KASPPSGLWSPAYASH 16 1 Q8TEM1 Q8TEM1 NUP210 Nuclear pore membrane glycoprotein 210 1 KAS(0.907)PPS(0.076)GLWS(0.017)PAYASH 60.325 0.057818 483440000 116160 118270 86840 122570 170090 151630 116680 159880 140570 TRUE FALSE 100809.1617 117493.0766 128836.1145 150401.3919 166705.5418 157463.3042 105364.3916 125690.9062 123951.9747 0.813292099 0.94789193 1.039403485 1.213384395 1.344920419 1.270357367 0.850042057 1.014029074 1 16.91942173 7.394145114 9.649644073 1.058501551 0.005206281 0 0.174001866 0 0 0.042242013 0 24782499.95 -7.394145114 -1.05329527 KAS(ph)SPNLHR ddPTM_MDA-MB-175_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 74.962 0.018625 69214000 126920 128820 86791 90916 123030 127150 151590 157480 132780 TRUE FALSE 110147.2004 127973.7729 128763.4179 111559.8674 120581.9437 132041.5428 136888.8251 123804.1275 117082.8997 0.940762492 1.093018479 1.099762803 0.952828019 1.029885184 1.127761126 1.169161556 1.057405717 1 16.83717086 2.791236829 11.77882389 1.091256899 1.027438863 0.191738182 0.06624224 2.216242079 492.9836417 0.021839375 0.021832826 618.3535083 -2.791236829 -0.063818036 KAS(ph)VHSSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KASVHSSGR 9 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 1 KAS(0.961)VHS(0.019)S(0.019)GR;KAS(0.605)VHS(0.319)S(0.075)GR;KAS(0.774)VHS(0.183)S(0.043)GR;KAS(0.978)VHS(0.018)S(0.004)GR;KAS(0.992)VHS(0.005)S(0.003)GR;KAS(0.992)VHS(0.007)S(0.001)GR 134.56 0.00015032 1229900000 1807620 1062507 209550 817692 871980 1376980 1557380 1556030 2152350 TRUE FALSE 1568738.437 1055527.322 310889.0809 1003361.466 854629.304 1429953.312 1406345.527 1223285.094 1897901.635 0.826564669 0.556154915 0.163806741 0.528668846 0.450302212 0.753439106 0.741000219 0.644546098 1 20.85597379 2.732265245 23.49718574 0.758738903 0.490284585 0.362699504 0.18216982 261.2468513 975087.1813 0.062541504 0.056597664 539.8402283 -2.732265245 -0.268454318 KAS(ph)VVDPSTESSPAPQEGSEQPASPAS(ph)PLSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KASVVDPSTESSPAPQEGSEQPASPASPLSSR 32 1 Q66K14-2;Q66K14 Q66K14-2 TBC1D9B TBC1 domain family member 9B 2 KAS(1)VVDPSTESSPAPQEGSEQPAS(0.002)PAS(0.996)PLS(0.001)S(0.001)R 183.94 4.67E-19 215860000 181290 116320 70445 103440 121260 103740 182000 162490 168190 TRUE FALSE 157332.0672 115555.8863 104512.4376 126927.633 118847.1632 107730.9449 164349.668 127742.778 148306.7698 1.060855599 0.77916798 0.70470443 0.855845172 0.801360338 0.726406118 1.108173742 0.861341516 1 17.17822493 2.250780383 24.99999254 0.967998898 0.814822593 0.322516503 0.113362739 269.9091667 552197.7176 0.040995734 0.031514683 178.147767 -2.250780383 -0.153176305 KASALLFS(ph)SDEEDQWNIPASQTHLASDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KASALLFSSDEEDQWNIPASQTHLASDSR 29 1 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 KAS(0.003)ALLFS(0.568)S(0.428)DEEDQWNIPASQTHLASDSR 128.39 8.20E-06 70964000 57566 49432 17281 31759 52180 53496 57270 67258 16794 TRUE FALSE 49958.50725 49107.27794 25638.1494 38970.36636 51141.72009 55554.02574 51715.96421 52875.4001 14808.63245 3.373607077 3.316125111 1.731297572 2.63159792 3.453507287 3.751462258 3.492284948 3.570579544 1 13.8541508 3.252266952 24.78434685 3.185992052 2.728950321 0.013071664 0.892981929 710.1935262 1284192.144 0.258722157 0.332132888 1787.58603 -3.252266952 -0.457041731 KASATEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KASATEAR 8 1 O75146;O75146-2 O75146 HIP1R Huntingtin-interacting protein 1-related protein 0 ; 75.387 0.061765 65087000 267630 257470 161721 196596 154741 260000 285130 328470 307130 FALSE TRUE 232262.0174 255778.6626 239929.8165 241236.1266 151661.9568 270002.3682 257478.1365 258229.2467 270821.4413 0.857620491 0.944454994 0.885933608 0.890757118 0.560007199 0.996975598 0.95073025 0.953503701 1 18.04698244 KASDSELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 73.951 0.068095 430970000 1021900 922270 526130 695780 821190 785920 937360 1036400 714680 FALSE TRUE 886853.3258 916211.5476 780568.2278 853767.4833 804849.9256 816154.851 846454.9715 814773.9253 630191.3446 1.407276272 1.453862475 1.238620991 1.354775007 1.277151666 1.295090544 1.34317137 1.292899264 1 19.26543041 1.219358601 3.222042735 0.93358142 1.335136743 0.745717195 0.061589251 0.197397301 2.655152964 0.207048686 0.016150582 16.57137714 -1.219358601 0.401555323 KASDVHEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 KASDVHEVR 9 1 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;; 133.44 0.00017973 28482470000 74453900 57811300 34150180 50340420 50604790 56634500 70175600 69409600 66831000 FALSE TRUE 64614628.47 57431533.76 50665321.27 61770981.77 49597853.69 58813265.86 63369981.11 54566897.19 58930315.31 1.096458217 0.974566884 0.859749706 1.048203822 0.841635641 0.998013765 1.075337554 0.925956308 1 25.81250665 0.933803031 21.18215463 1.661505741 0.9738186 0.005303909 0.08448573 143.3719713 582426.9014 63349.49479 0.018933644 8.58624015 -0.933803031 -0.687687142 KASFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KASFLR 6 1 P46777;A0A2R8Y4A2 P46777 RPL5 60S ribosomal protein L5 0 122.79 0.030574 1176100000 2046000 1973100 1156600 1334900 1815900 1714700 1980400 2200700 1754500 FALSE TRUE 1775615.916 1960138.576 1715935.629 1638009.448 1779767.143 1780665.619 1788341.113 1730097.431 1547085.009 1.147717098 1.266988281 1.109141139 1.058771456 1.150400355 1.150981109 1.155942371 1.118295001 1 20.56112104 1.220599896 2.620820068 0.960804718 1.148142051 0.449563606 0.051365187 0.526212105 3.912677589 0.224837674 0.014078321 16.61880899 -1.220599896 0.187337333 KASGS(ph)ENEGDYNPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KASGSENEGDYNPGR 15 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KAS(0.045)GS(0.955)ENEGDYNPGR;KAS(0.038)GS(0.962)ENEGDYNPGR;KAS(0.109)GS(0.891)ENEGDYNPGR 214.26 1.53E-12 1595220000 792170 630890 444715 654460 688620 562177 643830 876510 725190 TRUE FALSE 687482.7274 626745.642 659780.6615 803065.1458 674917.8093 583804.313 581391.4657 689075.1575 639458.8643 1.075100786 0.98011878 1.031779679 1.255851143 1.055451487 0.912966174 0.90919291 1.077591063 1 19.28649203 2.984467083 24.88560211 0.984746386 1.084484501 0.282265531 0.08355844 1026.141884 1644005.744 0.028247273 0.029121678 964.866178 -2.984467083 0.099738115 KASS(ph)PNLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KASSPNLHR 9 1 A0A087X030;P51956-2;P51956 A0A087X030 NEK3 Serine/threonine-protein kinase Nek3 1 KAS(0.232)S(0.768)PNLHR;KAS(0.14)S(0.86)PNLHR 132.32 0.00014496 131561000 452660 420210 264970 331580 403070 418090 476100 531860 467800 TRUE FALSE 392839.8341 417449.6128 393110.3783 406870.3069 395049.6956 434174.1928 429927.8953 418125.8779 412497.2169 0.952345417 1.012005889 0.953001286 0.986358914 0.957702693 1.052550599 1.042256475 1.013645331 1 18.65402486 2.745037275 24.99892078 1.026428454 0.974200482 0.593017154 0.022536559 376.0219123 1451392.762 0.007157754 0.006988286 555.9519723 -2.745037275 -0.052227972 KASSPS(ph)PLTIGT(ph)PESQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KASSPSPLTIGTPESQR 17 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 2 KAS(0.001)S(0.001)PS(0.998)PLT(0.292)IGT(0.708)PESQR 127.92 3.35E-05 206430000 221470 205180 118930 137180 197720 162050 197630 238610 120580 TRUE FALSE 192202.1784 203832.1591 176444.9458 168328.8157 193785.7588 168284.1684 178463.873 187585.1084 106325.1698 1.807682779 1.917064036 1.659484261 1.583151158 1.822576529 1.582731245 1.678472495 1.764258724 1 16.69812363 1.236638289 24.99954639 0.999999086 1.724230278 0.822095168 0.106267279 20.93866517 272228.8738 0.166265998 0.026317882 17.24401093 -1.236638289 0.724231192 KASSPS(ph)PLTIGTPESQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KASSPSPLTIGTPESQR 17 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 KASSPS(1)PLTIGTPESQR;KASSPS(1)PLTIGTPESQR;KASS(0.001)PS(0.999)PLTIGTPESQR;KAS(0.004)S(0.015)PS(0.982)PLTIGTPESQR 240.87 1.50E-20 2751400000 2397000 1997120 1229030 1387150 2194330 1958630 2426350 2725090 1037210 TRUE FALSE 2080230.377 1984000.787 1823393.019 1702123.609 2150667.126 2033979.764 2191042.95 2142350.71 914592.2154 2.274489485 2.169273643 1.993667766 1.861073799 2.351503861 2.223919829 2.39565012 2.34241083 1 19.80276911 1.234563484 24.9999251 0.999998258 2.204453113 0.839083339 0.16535292 49.8605452 311806.7853 0.330677695 0.044509142 17.16182557 -1.234563484 1.204454855 KASTAPGAEER ddPTM_MDA-MB-175_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 77.912 0.05022 80882000 117850 103730 64481 79701 86412 90567 105180 129740 103790 FALSE TRUE 102275.8239 103048.5908 95664.22728 97798.3302 84692.57026 94051.17109 94979.65979 101996.1106 91520.06444 1.117523513 1.125967201 1.045281468 1.068599884 0.925398936 1.027656303 1.037801496 1.114467207 1 16.48180045 4.199604423 4.483941335 1.035696631 1.122882829 0.376839741 0.048168974 0.226214358 9.982223663 0.013378097 0.031763538 15834.50251 -4.199604423 0.087186198 KASVVDPSTESSPAPQEGSEQPASPAS(ph)PLSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KASVVDPSTESSPAPQEGSEQPASPASPLSSR 32 1 Q66K14-2;Q66K14 Q66K14-2 TBC1D9B TBC1 domain family member 9B 1 KASVVDPSTESSPAPQEGSEQPASPAS(1)PLSSR;KASVVDPSTESSPAPQEGSEQPAS(0.004)PAS(0.993)PLS(0.002)S(0.002)R;KASVVDPSTESSPAPQEGSEQPAS(0.003)PAS(0.529)PLS(0.234)S(0.234)R 323.79 5.40E-105 1693910000 1196890 1046690 617518 681715 1057592 973296 1003505 1336780 640026 TRUE FALSE 1038717.954 1039814.224 916151.7703 836508.8101 1036547.988 1010739.327 906185.2396 1050920 564362.8554 1.840514385 1.842456878 1.62333818 1.482218048 1.836669402 1.790938786 1.605678387 1.862135308 1 19.10626351 1.232326837 25 0.999998792 1.7321622 0.767682215 0.127142793 102.5251731 411127.3812 0.284470607 0.03140455 17.07366818 -1.232326837 0.732163407 KASWTWGPEGQGAILLVNCDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KASWTWGPEGQGAILLVNCDR 21 1 Q9Y2J8;Q9Y2J8-2 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 246.39 4.34E-30 787390000 312200 345810 144160 137760 322880 293350 355980 384070 93697 FALSE TRUE 270941.979 343538.3513 213876.2582 169040.5135 316455.3197 304635.3643 321457.1144 301939.6193 82620.2474 3.27936538 4.1580407 2.588666397 2.045993795 3.830239314 3.687175649 3.890778889 3.654547509 1 16.33420776 4.24223712 24.99319305 3.093862534 3.718702858 0.088285083 0.940878037 272.5367306 1852652.994 0.239762932 0.585141944 17467.75614 -4.24223712 0.624840325 KATDHPHPST(ph)PATAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KATDHPHPSTPATAR 15 1 O14578-4;H7BYJ3;O14578;O14578-3 O14578-4 CIT Citron Rho-interacting kinase 1 KATDHPHPS(0.05)T(0.899)PAT(0.05)AR 86.213 0.0058259 21261000 56345 65814 19002 34960 60620 62299 68847 84758 48830 TRUE FALSE 48898.86549 65381.6635 28191.43076 42898.20233 59413.7806 64695.68284 62170.22854 66633.16129 43057.37303 1.135667646 1.518477764 0.654741076 0.996303288 1.379874721 1.502545982 1.443892745 1.547543582 1 15.39397268 3.197547947 8.024865194 1.4089335 1.07793584 0.248822854 0.253931435 0.312582867 53.19853691 0.077129854 0.088265663 1575.970005 -3.197547947 -0.33099766 KATGAAT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KATGAATPK 9 1 P10412 P10412 HIST1H1E Histone H1.4 1 KAT(0.004)GAAT(0.996)PK;KAT(0.008)GAAT(0.992)PK;KATGAAT(1)PK;KAT(0.001)GAAT(0.999)PK 103.14 0.0020341 3272480000 5858700 6501900 4856470 5090320 3394810 5046740 8051700 8266600 9999600 TRUE FALSE 5084457.951 6459188.591 7205075.136 6246154.957 3327259.923 5240891.353 7270847.373 6498851.921 8817458.68 0.576635302 0.732545377 0.817137386 0.708384942 0.37734908 0.594376628 0.824596705 0.737043649 1 23.07193148 0.914637367 1.117090514 1.410182407 0.650353953 0.424205062 0.126900673 3.523116463 2.199796748 3.784311826 0.043087556 8.2155637 -0.914637367 -0.759828454 KATLELTHNWGTEDDETQSYHNGNSDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KATLELTHNWGTEDDETQSYHNGNSDPR 28 1 Q04760 Q04760 GLO1 Lactoylglutathione lyase 0 ; 153.82 1.30E-08 413190000 388010 463420 140298 335940 400670 407620 371990 541130 357450 FALSE TRUE 336733.4954 460375.7635 208146.5821 412220.3115 392697.4509 423301.4052 335914.4671 425413.5606 315192.6682 1.068341777 1.460616981 0.660378883 1.307835978 1.245896528 1.34299255 1.065743277 1.349693706 1 18.26587445 KAVAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KAVAVR 6 1 P62277;J3KMX5 P62277 RPS13 40S ribosomal protein S13 0 ; 126.04 0.028323 1267920000 3385500 3197600 2075320 2594400 2266100 3186100 3345800 3837100 3457300 FALSE TRUE 2938097.597 3176594.755 3078951.694 3183498.173 2221009.044 3308671.329 3021324.831 3016566.025 3048581.933 0.963758778 1.04199094 1.00996193 1.044255409 0.728538413 1.085314878 0.991059088 0.989498098 1 21.53970689 KAVIFCLSADKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAVIFCLSADKK 12 2 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 60.161 0.052815 852520000 404450 371210 242420 307980 314460 309780 375720 365760 382250 FALSE TRUE 351000.9078 368771.4971 359655.1228 377911.5662 308202.8612 321697.4371 339282.7322 287545.0703 337060.8405 1.041357718 1.094079919 1.067033246 1.12119689 0.914383471 0.954419495 1.006591961 0.853095453 1 18.3626495 3.23472387 24.99993215 0.939125848 1.080865471 0.66831595 0.047208881 54.49300488 355071.393 0.013788678 0.016233122 1716.816466 -3.23472387 0.141739623 KAVLFCLSEDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KAVLFCLSEDKK 12 2 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 164.81 3.17E-05 4373800000 7801460 5379080 4747900 4548710 4430690 3158920 7776060 9075980 4161010 FALSE TRUE 6770477.295 5343744.469 7044000.321 5581564.128 4342527.937 3280445.696 7021938.898 7135152.306 3669100.138 1.84526915 1.456418268 1.919816864 1.521235158 1.183540316 0.894073635 1.913804103 1.944660009 1 21.80699485 3.498624739 23.39198978 1.460883642 1.71349869 0.14827925 0.361448343 930.6189514 1012345.269 0.10921252 0.159963618 3152.279652 -3.498624739 0.252615048 KAVPMAPAPAS(ph)PGSSNDSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KAVPMAPAPASPGSSNDSSAR 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 KAVPMAPAPAS(0.987)PGS(0.011)S(0.002)NDSSAR;KAVPMAPAPAS(0.997)PGS(0.003)S(0.001)NDSSAR 189.64 1.28E-17 954110000 1174810 1099210 469180 599840 1038430 1019930 1144480 1261740 225379 TRUE FALSE 1019555.882 1091989.217 696077.0173 736042.84 1017767.275 1059167.367 1033488.506 991926.7199 198734.9514 5.130229358 5.494701408 3.502539501 3.703640627 5.121229394 5.329547519 5.200335918 4.991204179 1 17.6004861 4.26500609 24.96389534 4.320657734 5.31246634 0.113775956 1.292089493 562.8145995 531273.7785 0.320577439 0.847623932 18407.97816 -4.26500609 0.991808605 KAVVLPGGTATS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KAVVLPGGTATSPK 14 1 Q8N1G0;F8WCX2;Q8N1G0-2;H0Y5I5 Q8N1G0 ZNF687 Zinc finger protein 687 1 KAVVLPGGTAT(0.152)S(0.848)PK;KAVVLPGGT(0.001)AT(0.268)S(0.73)PK 132.59 3.03E-05 1453270000 2036990 1737590 1436570 1435480 1859800 1283470 2233670 2548690 1900400 TRUE FALSE 1767796.61 1726175.657 2131300.057 1761427.674 1822793.619 1332845.921 2017049.027 2003672.477 1675736.877 1.054936867 1.030099463 1.27185842 1.051136189 1.087756463 0.795379 1.203678844 1.195696356 1 20.67636421 0.931184333 15.10895608 9.98E-05 1.091254668 0.040990052 0.129266332 378947.8425 1956499.257 12872248.76 0.032048336 8.534622833 -0.931184333 1.091154843 KAVVVCPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAVVVCPK 8 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 103.74 0.0075598 831540000 2232900 1815700 1261400 1541500 1570400 1364000 2061400 2328600 2362000 FALSE TRUE 1937816.608 1803772.547 1871417.259 1891521.135 1539152.112 1416473.963 1861485.745 1830647.011 2082767.051 0.93040487 0.866046228 0.898524517 0.908177002 0.738993884 0.680092362 0.893756095 0.878949478 1 20.99007006 1.20827765 1.87352221 1.061322807 0.840545908 0.276782987 0.078441342 1.375559222 4.299330244 0.556847113 0.02325025 16.15390966 -1.20827765 -0.220776899 KAYAQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAYAQIR 7 1 P49419;P49419-2;A0A1B0GW77;A0A1B0GW82;A0A1B0GTG2;A0A1B0GUA1;A0A1B0GV49;A0A1B0GTJ4;A0A1B0GUY0 P49419 ALDH7A1 Alpha-aminoadipic semialdehyde dehydrogenase 0 121.29 0.02067 0 501500 609570 425320 489110 626690 615490 674670 718260 712430 FALSE TRUE 435225.5044 605565.6945 631006.1746 600169.9011 614220.0951 639168.2986 609240.6072 564665.6885 628207.337 0.69280551 0.963958329 1.004455277 0.955369136 0.977734673 1.017448 0.969808169 0.898852425 1 19.26088127 4.738134173 6.70420084 0.969683623 0.687952041 0.87821686 0.032824868 0.040283088 12.16628492 0.008719348 0.051753378 54718.49865 -4.738134173 -0.281731582 KAYQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KAYQDR 6 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;; 83.377 0.091487 1856640000 3700580 3722690 2345380 2790510 2137870 3148860 3892870 4324220 3777630 FALSE TRUE 3211538.977 3698235.404 3479613.613 3424137.946 2095330.57 3269998.682 3515340.067 3399519.204 3331042.885 0.964124176 1.110233501 1.044601866 1.027947722 0.6290314 0.981674147 1.055327172 1.020557021 1 21.6675425 3.450029468 24.99970804 0.946945796 1.044972298 0.139194345 0.121587228 478.7399827 441769.4511 0.037081295 0.04787294 2818.574174 -3.450029468 0.098026503 LKAEGSEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LKAEGSEIR 9 1 P07237;H7BZ94;I3L3U6;I3L0S0;I3NI03;I3L514 P07237 P4HB Protein disulfide-isomerase 0 ;;; 123.79 0.00049957 5894800000 6811330 5962970 3897450 4721040 5724830 6278000 6432910 6154570 2880320 FALSE TRUE 5911195.483 5923798.857 5782269.856 5793024.289 5610917.083 6519518.722 5809047.378 4838463.1 2539811.851 2.327414718 2.332377044 2.276652837 2.280887179 2.209186118 2.566929798 2.28719595 1.905047848 1 21.2762902 1.237936855 1.934547878 0.548321939 2.329189538 0.951830077 0.094642973 0.16435635 0.590258288 0.536276268 0.026684217 17.29564868 -1.237936855 1.780867599 KAYWQVHLDQVEVASGLTLCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KAYWQVHLDQVEVASGLTLCK 21 1 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GU92;A0A1B0GU03;C9JH19;H7C469 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ;; 154.75 2.01E-08 3088355000 2508971 2448830 1260816 1533019 1958516 1912650 2830808 3298345 508887 FALSE TRUE 2177404.125 2432743.474 1870550.835 1881114.395 1919545.363 1986230.883 2556276.676 2593019.589 448726.9586 4.85240319 5.421433743 4.168572445 4.19211362 4.277758059 4.426368519 5.696730778 5.778613341 1 18.77547834 4.238240421 24.99930799 4.446726426 5.136918476 0.057462923 1.31442499 29.68329041 2318394.69 0.331244594 0.766353805 17307.74231 -4.238240421 0.690192051 KCAADLGLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KCAADLGLNK 10 1 P49773 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 100.69 0.0061633 550170000 1153300 1039800 831130 813210 985590 820390 1262300 1345000 1174300 FALSE TRUE 1000888.483 1032969.485 1233067.248 997861.7596 965978.6873 851950.9342 1139882.34 1057382.217 1035475.592 0.966597852 0.997579753 1.190822128 0.963674825 0.932884073 0.822762932 1.100829753 1.0211561 1 19.98186212 4.703258023 6.077971922 1.00648637 0.966208264 0.013920334 0.096721717 0.911931072 106.6237269 0.024325874 0.110631011 50496.12154 -4.703258023 -0.040278106 KCEAEEAEPPAATQPQTSETQTSHLPESER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KCEAEEAEPPAATQPQTSETQTSHLPESER 30 1 S4R3H4;Q9UKV3;E7EQT4;A0A087WYN3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 116.57 6.53E-05 276970000 132380 105240 59287 77010 92824 80663 125880 108960 102440 FALSE TRUE 114885.6476 104548.6715 87958.3915 94496.29752 90976.98401 83766.15781 113672.177 85659.75193 90329.6599 1.271848557 1.157412434 0.973748729 1.046127016 1.007166241 0.92733835 1.258414757 0.948301499 1 16.46291216 4.462475332 3.57451371 1.026094359 1.258452367 0.455949153 0.091187609 0.196387173 5.183632345 0.022156241 0.084911453 29005.16447 -4.462475332 0.232358008 KCEEEIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KCEEEIAK 8 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 83.31 0.029266 647960000 571690 476920 351560 411140 438490 379140 621110 596350 547150 FALSE TRUE 496139.718 473787.0811 521575.5919 504495.6209 429764.9069 393725.7611 560874.8478 468825.1933 482466.5503 1.028340136 0.982010216 1.081060628 1.04565927 0.890766223 0.816068515 1.16251551 0.971725797 1 18.8800694 KCEPIVMTVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KCEPIVMTVPR 11 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ; 160.69 4.36E-05 1423010000 2020290 1728300 1101000 1299530 1638590 1428550 1909620 2209300 1808690 FALSE TRUE 1753303.558 1716946.684 1633447.283 1594608.149 1605985.265 1483507.243 1724425.346 1736858.388 1594868.729 1.099340357 1.076544202 1.024189172 0.999836613 1.006970189 0.93017514 1.081233405 1.089029057 1 20.60500625 4.331479335 3.526427677 1.0239364 1.094872939 0.295555425 0.044472071 0.3503446 8.239907636 0.012822813 0.039720331 21452.57036 -4.331479335 0.07093654 KCHS(ph)LGYNFIHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KCHSLGYNFIHK 12 1 Q86X27;Q86X27-3 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 KCHS(1)LGYNFIHK 145.1 2.99E-05 525950000 701720 720520 490060 522190 606920 512230 822950 866020 503510 TRUE FALSE 608985.9241 715786.8567 727054.6552 640761.2207 594843.4794 531935.8196 743140.4357 680828.3624 443985.6214 1.371634338 1.612184769 1.637563516 1.443202639 1.339780954 1.198092447 1.673793924 1.533446872 1 18.76015343 3.516444641 7.235890612 1.388989042 1.54708529 0.153961347 0.193039014 0.535207037 82.189403 0.054941899 0.080186292 3284.313768 -3.516444641 0.158096248 KCLEELQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KCLEELQK 8 1 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 147.2 0.00086764 316940000 629200 459350 412300 547400 447100 402820 597290 676950 720440 FALSE TRUE 546049.6258 456332.4996 611689.6591 671695.5365 438203.5847 418316.7461 539364.9077 532189.5105 635270.4039 0.859554644 0.71832797 0.962880775 1.057337997 0.68979065 0.658486124 0.84903201 0.837736981 1 19.27701128 1.215444292 3.727152027 1.027611538 0.826937815 0.164202825 0.121179314 0.645537912 13.66591023 0.374528295 0.032410532 16.4226899 -1.215444292 -0.200673723 KCLELFSELAEDKENYKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KCLELFSELAEDKENYKK 18 3 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 146.64 3.61E-08 424940000 642330 335220 258720 251160 308690 180130 516710 605410 171650 FALSE TRUE 557444.463 333017.9177 383837.8574 308189.7167 302547.6729 187059.7177 466599.5437 475947.7828 151357.7325 3.682959923 2.200204193 2.535964638 2.036167638 1.99889142 1.235878171 3.082759869 3.144522416 1 17.20760286 4.739839474 23.53513751 2.249859726 3.682960988 0.31904736 0.689397732 66.43654446 1222315.536 0.173282065 1.040258513 54933.77875 -4.739839474 1.433101262 KCLELFTELAEDKENYKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KCLELFTELAEDKENYKK 18 3 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 165.74 1.20E-11 971310000 1791700 1142100 1095800 962360 999930 582450 1993700 2212300 591940 FALSE TRUE 1554922.305 1134597.47 1625732.545 1180878.547 980033.3493 604857.2284 1800351.281 1739216.861 521961.5275 2.978997921 2.173718579 3.11465972 2.262386181 1.877596906 1.15881573 3.449203027 3.332078648 1 18.99358395 3.674423805 24.98342734 2.324193736 2.697590917 0.079396559 0.824885232 817.1538847 318307.2803 0.24300803 0.360439233 4725.23927 -3.674423805 0.373397181 KCLWDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KCLWDFK 7 1 H0YAF9;H0YA75;P19883-2;P19883 H0YAF9 FST Follistatin 0 57.103 0.07634 1178900000 1064800 1055600 500410 763390 917580 942640 1014600 1263500 856530 FALSE TRUE 924083.9821 1048665.694 742409.9498 936729.3672 899321.9532 978903.9708 916204.2482 993310.3576 755271.9992 1.223511507 1.388460972 0.982970308 1.24025433 1.190725929 1.296094615 1.213078532 1.31516905 1 19.52663678 KCS(ph)LPAEEDSVLEK ddPTM_MDA-MB-175_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(1)LPAEEDSVLEK;KCS(1)LPAEEDSVLEK;KCS(0.998)LPAEEDS(0.002)VLEK 259.77 1.21E-24 2342440000 2709600 1912818 1796868 1798365 1787270 1506352 2830720 2877840 2684000 TRUE FALSE 2351519.495 1900252.573 2665839.375 2206711.26 1751706.824 1564302.336 2556197.21 2262436.311 2366700.578 0.99358555 0.802912118 1.126394864 0.932399848 0.740147208 0.660963347 1.080067852 0.955945307 1 21.17444576 KCSASNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KCSASNR 7 1 Q8WVC2;P63220;Q9BYK1;Q9BYK2 Q8WVC2 RPS21 40S ribosomal protein S21 0 72.485 0.082541 31695000 31821 36725 22085 28015 64094 35652 37210 47085 40413 FALSE TRUE 27615.77423 36483.75106 32765.37987 34376.23393 62818.6548 37023.55551 33601.37993 37016.23917 35635.42118 0.774952935 1.023805805 0.919460997 0.96466473 1.762814995 1.038953779 0.942920802 1.038748468 1 15.12102436 3.452405654 24.9999163 1.142181703 0.921881858 0.19986624 0.235335015 423.6182735 428489.9315 0.070453712 0.090958854 2834.037903 -3.452405654 -0.220299845 KCSTPEEIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KCSTPEEIK 9 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;; 99.752 0.0082166 1844430000 2187410 1761150 1468620 1731180 1649930 1382820 2351010 2582810 2074480 FALSE TRUE 1898338.226 1749580.89 2178849.544 2124270.878 1617099.621 1436017.98 2123009.412 2030496.181 1829237.338 1.037775792 0.956453738 1.191124574 1.161287732 0.884029419 0.785036447 1.160598118 1.110023363 1 20.80281084 KCSTPEEIKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KCSTPEEIKK 10 2 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 117.79 0.00051217 908780000 3052200 2205000 2163400 2471200 1784100 1332400 3239400 3387000 2628000 FALSE TRUE 2648844.037 2190515.21 3209627.476 3032323.73 1748599.901 1383658.29 2925243.487 2662716.408 2317320.834 1.143063143 0.945279211 1.385059604 1.308547218 0.75457825 0.597093967 1.262338578 1.149049527 1 21.14402637 5.075212994 17.72095651 1.061929095 2.889723146 0.011991586 0.245168061 773.5222753 211212.2207 0.061044404 8760.56637 118908.5257 -5.075212994 1.827794051 KCYEMASHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KCYEMASHLR 10 1 P07737;K7EJ44;CON__P02584 P07737 PFN1 Profilin-1 0 ; 127.87 0.00022377 1663880000 4585600 4570200 2513800 2913000 4384300 4129300 4340900 5086200 2010300 FALSE TRUE 3979601.342 4540178.055 3729482.088 3574441.172 4297061.008 4288156.843 3919920.186 3998555.711 1772644.624 2.245007988 2.561245494 2.103908498 2.016445442 2.424096149 2.419073053 2.211340126 2.255700695 1 20.75747191 1.237345227 6.479838202 0.962751021 2.281838182 0.865816258 0.158342208 0.042890838 8.308839482 0.248641379 0.039741085 17.27210332 -1.237345227 1.319087161 KDAAEQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDAAEQVR 8 1 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB05;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 0 ; 85.533 0.026737 239190000 263814 234301 161462 200088 198832 228509 254568 292360 307640 FALSE TRUE 228950.3115 232761.8613 239545.5633 245521.0386 194875.6322 237299.8891 229880.0345 229841.0891 271271.1497 0.843990641 0.858041342 0.883048432 0.905076116 0.718379498 0.874770094 0.847417924 0.847274358 1 18.0493761 1.238539575 21.71033947 1.000000418 0.847354634 0.483929077 0.049573226 0.097394916 84664.05364 0.065375769 0.011729923 17.31966847 -1.238539575 -0.152645784 KDAENHEAQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KDAENHEAQLK 11 1 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 ;; 159.99 1.82E-05 548650000 994660 785850 581780 691410 698040 612610 992320 1122840 1050870 FALSE TRUE 863213.1609 780687.6996 863130.7539 848405.208 684150.3697 636177.5031 896084.9591 882729.404 926637.3458 0.931554469 0.842495398 0.931465538 0.915574158 0.738315127 0.686544209 0.967028755 0.95261583 1 19.8216453 2.071400749 24.99999997 0.969005685 0.842469055 0.377359633 0.079993624 50.75434795 17769.83974 0.035015339 0.023607333 117.869312 -2.071400749 -0.12653663 KDCEVVMMIGLPGAGK ddPTM_MDA-MB-175_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 ; 145.1 2.01E-06 1268630000 3766500 2588900 1870880 2237400 2441500 1877370 3110600 3807800 3280600 FALSE TRUE 3268747.482 2571893.345 2775643.826 2745435.867 2392918.927 1949593.639 2808934.491 2993531.602 2892771.205 1.129970969 0.889075963 0.95951032 0.949067753 0.827206425 0.673953625 0.971018546 1.034831789 1 21.46402079 4.743414321 24.30244749 0.917729332 1.129971098 0.305886811 0.1024646 514.2647356 2574789.165 0.027704513 0.219443348 55387.82629 -4.743414321 0.212241766 KDDDS(ph)DDESQSSHTGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KDDDSDDESQSSHTGK 16 1 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 KDDDS(0.997)DDES(0.003)QSSHTGK;KDDDS(0.985)DDES(0.015)QSSHTGK;KDDDS(0.693)DDES(0.307)QSSHTGK;KDDDS(1)DDESQSSHTGK;KDDDS(1)DDESQSSHTGK;KDDDS(0.797)DDES(0.203)QS(0.001)SHTGK;KDDDS(0.968)DDES(0.032)QSSHTGK 290.66 7.57E-46 4138216000 5519533 3852686 2567807 3354809 3082367 2845545 4059310 6137167 5480140 TRUE FALSE 4790112.729 3827377.452 3809607.054 4116569.658 3021033.927 2955014.957 3665638.741 4824781.597 4832284.092 0.991272996 0.792043137 0.788365705 0.851888999 0.625177218 0.611515155 0.75857269 0.998447422 1 22.20427384 1.718004972 5.347441332 1.000634843 0.766077726 0.430621328 0.107132036 0.140498006 9.888804098 0.070399864 0.029459105 52.24021699 -1.718004972 -0.234557117 KDDDS(ph)DDESQSSHTGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 215.08 2.99E-15 270864000 247083 153153 110529 122303 112464 102136 193145 269403 118387 TRUE FALSE 214430.3555 152146.9279 163981.1941 150073.7654 110226.1864 106065.238 174413.8276 211793.2649 104391.4237 2.054099349 1.45746578 1.570830134 1.437606271 1.055893123 1.016034021 1.670767783 2.028837786 1 16.67164367 4.73985482 6.226192156 1.448194197 2.068697395 0.276092682 0.323762104 0.208434489 43.13325527 0.087108947 0.544246754 54935.71994 -4.73985482 0.620503198 KDDDSDDES(ph)QSSHTGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KDDDSDDESQSSHTGK 16 1 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 KDDDS(0.096)DDES(0.902)QS(0.002)SHTGK 245.66 1.82E-20 1359500000 1352200 931840 539520 769960 742590 603750 975980 1380400 1220300 TRUE FALSE 1173503.344 925718.6817 800433.6766 944791.1861 727813.9119 626976.6532 881329.6098 1085212.202 1076037.524 1.090578458 0.860303345 0.743871527 0.878028103 0.676383393 0.582671737 0.819051 1.008526355 1 20.03729696 1.75687693 4.952906602 1.004609764 0.794894942 0.270548104 0.133599298 0.226381312 12.77353184 0.084112829 0.036862682 57.13167146 -1.75687693 -0.209714822 KDDEDSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KDDEDSFR 8 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 91.584 0.019856 264970000 398600 302720 237130 303840 269990 287860 376650 411620 457970 FALSE TRUE 345924.0001 300731.4124 351806.8612 372831.5159 264617.7272 298934.1605 340122.541 323598.2662 403829.3083 0.856609446 0.744699323 0.871177138 0.92324036 0.655271229 0.740248799 0.842243329 0.80132437 1 18.62338609 1.238214588 24.71684663 1.000000223 0.803263437 0.392365853 0.07650564 7.795228117 555865.9696 0.106330955 0.018697559 17.30671284 -1.238214588 -0.196736786 KDDEENYLDLFSHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KDDEENYLDLFSHK 14 1 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ;;;; 236.17 1.91E-17 6347410000 13653680 8995540 7770110 8256620 8297190 6167540 11670280 13665470 12316990 FALSE TRUE 11849311.59 8936447.705 11527761.19 10131411.77 8132092.152 6404809.255 10538498.04 10743215.59 10860889.47 1.091007474 0.82280993 1.061401206 0.932834441 0.748750107 0.589713142 0.970316296 0.989165354 1 23.37263892 4.752551774 23.46313568 0.89393932 1.091007793 0.170992848 0.139203886 2122.067946 3558554.478 0.036472167 0.676260889 56565.51876 -4.752551774 0.197068473 KDDESNLVEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KDDESNLVEEK 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;G5E9S8;G3V2P7 Q07866-6 KLC1 Kinesin light chain 1 0 130.07 0.00037177 209780000 445770 322180 323970 275560 252780 220000 427410 464590 374080 FALSE TRUE 386860.3651 320063.5784 480642.9756 338130.1097 247750.1726 228463.5424 385959.844 365241.0439 329856.6886 1.172813463 0.970311015 1.457126662 1.025081866 0.751084277 0.692614551 1.170083425 1.107271905 1 18.33147983 3.493610096 24.78787644 0.961602179 1.187772762 0.285436217 0.183453154 997.4826302 1499525.338 0.054627381 0.07864624 3116.090744 -3.493610096 0.226170583 KDDEVQVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDDEVQVVR 9 1 P61254;E5RIT6;J3QRI7;J3QQQ9;J3QQV1;J3QRC4;Q9UNX3 P61254;Q9UNX3 RPL26;RPL26L1 60S ribosomal protein L26;60S ribosomal protein L26-like 1 0 ; 132.32 0.00049448 973260000 1776490 1850650 1173370 1132850 1538470 1333640 2304380 2079230 1436310 FALSE TRUE 1541722.345 1838492.958 1740815.657 1390080.907 1507857.457 1384945.994 2080901.582 1634602.845 1266511.068 1.217298754 1.451620128 1.374496995 1.097567121 1.190560031 1.093512744 1.643018869 1.290634473 1 20.27242825 KDDPTLLSSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDDPTLLSSGR 11 1 F6S8N6;A0A0A0MRJ6;P22061;P22061-2;A0A3F2YNX8 F6S8N6 PCMT1 Protein-L-isoaspartate O-methyltransferase;Protein-L-isoaspartate(D-aspartate) O-methyltransferase 0 ; 146.79 5.71E-05 1266240000 1863970 2123210 997240 1303180 1654830 1635540 1703810 2100780 2492400 FALSE TRUE 1617641.642 2109262.494 1479508.6 1599086.937 1621902.121 1698460.282 1538574.768 1651544.545 2197751.311 0.736043989 0.959736656 0.673191999 0.727601403 0.737982552 0.772817322 0.700067729 0.751470167 1 21.06759672 1.237763064 24.97929881 1.000000279 0.757042868 0.495348509 0.076965249 16.73983998 523951.237 0.107431243 0.018340489 17.28872889 -1.237763064 -0.242957411 KDDPVTNLNNAFEVAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KDDPVTNLNNAFEVAEK 17 1 O43707;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ;; 267.36 1.45E-27 1098470000 2634860 2129890 1614230 2090040 1931500 1714860 2363090 3020010 3308280 FALSE TRUE 2286656.575 2115898.612 2394877.027 2564615.526 1893066.929 1780831.774 2133917.896 2374204.363 2917178.907 0.783858875 0.725323568 0.820956514 0.879142352 0.648937549 0.610463681 0.731500523 0.813869988 1 21.47614244 1.273497084 2.505611612 1.050637283 0.742612838 0.525040699 0.076992408 0.429243847 3.134410794 0.276578322 0.022124076 18.77141814 -1.273497084 -0.308024445 KDDRVEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDDRVEER 8 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 94.297 0.0058829 148176000 215668 218110 121892 149843 245640 304150 364280 376880 182974 FALSE TRUE 187166.9274 216677.221 180839.3789 183867.1434 240752.2446 315850.8473 328952.1817 296287.1449 161343.0222 1.160055916 1.342959975 1.12083793 1.139603938 1.492176367 1.957635621 2.038837362 1.836380284 1 17.29977166 3.026242921 4.111374598 1.758635846 1.20069062 0.416216411 0.285662297 0.195888201 7.52290206 0.092140841 0.101803625 1062.289578 -3.026242921 -0.557945226 KDDS(ph)DDDGGGWITPSNIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KDDSDDDGGGWITPSNIK 18 1 Q9ULX3 Q9ULX3 NOB1 RNA-binding protein NOB1 1 KDDS(1)DDDGGGWITPSNIK;KDDS(1)DDDGGGWITPSNIK;KDDS(1)DDDGGGWITPSNIK;KDDS(1)DDDGGGWITPSNIK 246.2 1.76E-24 3696790000 5482440 3754860 3823920 3884120 3955690 2637820 5349700 6491400 6179300 TRUE FALSE 4757921.663 3730194.077 5673180.502 4766068.811 3876979.508 2739298.642 4830886.917 5103264.626 5448790.193 0.873206986 0.684591248 1.041181675 0.874702208 0.711530334 0.502735203 0.886598079 0.936586737 1 22.37750451 2.009242506 24.99594095 0.948112484 0.781882582 0.233590465 0.141167792 308.5630219 834491.3638 0.060718705 0.04087704 102.1509725 -2.009242506 -0.166229902 KDDS(ph)HSAEDS(ph)EDEKEDHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KDDSHSAEDSEDEKEDHK 18 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 KDDS(0.5)HS(0.5)AEDS(1)EDEKEDHK 151.01 2.72E-08 1274100000 870320 487230 896170 535840 447830 332840 746400 868170 1384100 TRUE FALSE 755305.0069 484029.354 1329560.81 657510.6618 438919.0592 345644.5702 674014.2429 682518.6016 1220473.275 0.618862389 0.396591522 1.089381338 0.538734174 0.359630209 0.283205358 0.552256454 0.559224537 1 20.21900927 -0.553209299 7.716347655 5.633892947 0.585767729 0 0.260089686 0 0 0 0.058002275 0.279763274 0.553209299 -5.048125218 KDDSHS(ph)AEDS(ph)EDEKEDHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 KDDSHSAEDSEDEKEDHK 18 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 KDDS(0.051)HS(0.949)AEDS(1)EDEKEDHK;KDDS(0.038)HS(0.962)AEDS(1)EDEKEDHK;KDDS(0.08)HS(0.92)AEDS(1)EDEKEDHK;KDDS(0.078)HS(0.922)AEDS(1)EDEKEDHK;KDDS(0.249)HS(0.751)AEDS(1)EDEKEDHK;KDDS(0.136)HS(0.865)AEDS(0.999)EDEKEDHK;KDDS(0.148)HS(0.852)AEDS(1)EDEKEDHK;KDDS(0.014)HS(0.986)AEDS(1)EDEKEDHK;KDDS(0.141)HS(0.859)AEDS(1)EDEKEDHK 198.55 9.23E-16 7450890000 5203809 2766754 5158339 3113356 2755287 1779126 4833562 5035395 8086713 TRUE FALSE 4516112.456 2748579.011 7652928.994 3820291.064 2700462.179 1847570.128 4364803.901 3958614.965 7130711.002 0.633332701 0.385456515 1.073235052 0.535751773 0.378708684 0.259100408 0.61211342 0.555150105 1 22.7656145 -0.197212029 11.06629619 3.890314962 0.589912328 0 0.259087809 0 0 0 0.057274266 0.635020829 0.197212029 -3.300402634 KDDSHS(ph)AEDS(ph)EDEKEDHKNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 KDDSHSAEDSEDEKEDHKNVR 21 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 KDDS(0.176)HS(0.824)AEDS(1)EDEKEDHKNVR;KDDSHS(1)AEDS(1)EDEKEDHKNVR;KDDS(0.037)HS(0.963)AEDS(1)EDEKEDHKNVR;KDDS(0.126)HS(0.874)AEDS(1)EDEKEDHKNVR;KDDS(0.194)HS(0.806)AEDS(1)EDEKEDHKNVR;KDDS(0.038)HS(0.962)AEDS(1)EDEKEDHKNVR;KDDS(0.004)HS(0.996)AEDS(1)EDEKEDHKNVR;KDDS(0.013)HS(0.987)AEDS(1)EDEKEDHKNVR;KDDS(0.033)HS(0.967)AEDS(1)EDEKEDHKNVR 216.71 2.92E-25 8028030000 3260840 1946639 2278922 1338445 1751409 1133347 3143653 3459987 1312705 TRUE FALSE 2829911.732 1933851.4 3381016.302 1642359.394 1716559.387 1176947.592 2838782.016 2720095.706 1157518.51 2.444809052 1.670687236 2.920917697 1.418862316 1.482964957 1.016785116 2.452472242 2.349937112 1 20.14260383 3.713675101 24.98663138 1.717348614 2.277993186 0.252925188 0.567644589 1364.672127 1370217.265 0.163967248 0.243321179 5172.197517 -3.713675101 0.560644572 KDDSHSAEDS(ph)EDEKEDHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KDDSHSAEDSEDEKEDHK 18 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KDDSHSAEDS(1)EDEKEDHK;KDDSHSAEDS(1)EDEKEDHK;KDDSHSAEDS(1)EDEKEDHK;KDDSHSAEDS(1)EDEKEDHK;KDDSHSAEDS(1)EDEKEDHK;KDDSHSAEDS(1)EDEKEDHK 349.92 1.12E-90 3986400000 3847530 1848620 3412920 2098120 1605350 1417430 3044650 3240980 5246760 TRUE FALSE 3339069.162 1836476.293 5063419.528 2574530.214 1573406.676 1471959.449 2749380.312 2547921.648 4626494.01 0.721727761 0.39694773 1.094439875 0.556475424 0.34008618 0.318158728 0.594268642 0.550724078 1 22.14148789 -0.732305035 8.640010364 5.993378082 0.602577954 0 0.26056188 0 0 0 0.057580354 0.185223022 0.732305035 -5.390800128 KDDSHSAEDS(ph)EDEKEDHKNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KDDSHSAEDSEDEKEDHKNVR 21 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KDDSHSAEDS(1)EDEKEDHKNVR;KDDSHSAEDS(1)EDEKEDHKNVR;KDDSHSAEDS(1)EDEKEDHKNVR;KDDSHSAEDS(1)EDEKEDHKNVR 205.07 2.02E-22 976390000 823114 388677 474202 315123 371367 270479 667519 746971 327200 TRUE FALSE 714337.3994 386123.7552 703527.6733 386676.4935 363977.5233 280884.5022 602783.1101 587237.0646 288518.7887 2.475878269 1.338296743 2.438411988 1.340212522 1.261538373 0.973539725 2.08923347 2.035351206 1 18.13830575 3.719172767 24.93058049 1.523205505 2.009605849 0.26345319 0.484476151 1364.27896 1754308.252 0.137610513 0.204445383 5238.087718 -3.719172767 0.486400343 KDDTDDEIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDDTDDEIAK 10 1 P27824;P27824-2;H0Y9Q7;D6RDP7;D6RAU8;D6RB85;D6RAQ8 P27824 CANX Calnexin 0 ; 138.24 0.00011233 566450000 1143750 673300 950080 1185180 830200 646110 869090 1552710 2504700 FALSE TRUE 992600.5396 668877.048 1409541.866 1454293.233 813680.6443 670966.2698 784805.7856 1220675.05 2208597.219 0.449425785 0.30285153 0.638206846 0.658469195 0.368415136 0.30379748 0.35534129 0.552692469 1 21.07469891 1.252700015 3.169962456 1.08631322 0.442907064 0.667612535 0.123546966 0.221750733 2.981052313 0.351742875 0.034235588 17.89369438 -1.252700015 -0.643406156 KDDVS(ph)PVMQFSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KDDVSPVMQFSSK 13 1 Q8IZE3;Q8IZE3-2 Q8IZE3 SCYL3 Protein-associating with the carboxyl-terminal domain of ezrin 1 KDDVS(1)PVMQFSSK;KDDVS(1)PVMQFSSK;KDDVS(1)PVMQFSSK;KDDVS(1)PVMQFSSK;KDDVS(1)PVMQFSSK 210.39 1.85E-08 4480450000 5065960 3766340 3455490 3349110 3760930 2865910 5466850 5803270 5527490 TRUE FALSE 4396480.55 3741598.665 5126576.522 4109576.613 3686094.851 2976163.412 4936675.728 4562285.872 4874036.429 0.902020454 0.76765915 1.051813337 0.843156729 0.756271502 0.610615751 1.012851627 0.936038525 1 22.2166856 KDEDLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDEDLFR 7 1 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 0 ; 133.86 0.0051797 1166160000 2380100 1745600 1213050 1554880 1629120 1263850 1960790 2261900 2081130 FALSE TRUE 2065563.755 1734133.039 1799685.037 1907939.269 1596703.699 1312471.127 1770632.888 1778210.287 1835101.182 1.125585758 0.944979522 0.980700713 1.039691592 0.870090279 0.715203685 0.964869351 0.968998497 1 20.80742818 7.99999307 0.819505984 0.923563811 56.06021803 0.31308576 0.089109909 796.5392406 2.535449576 0.03321786 81678.31234 99998404.24 -7.99999307 55.13665422 KDEEGQKEEDKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDEEGQKEEDKPR 13 3 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 0 ; 117.92 0.00020534 332480000 384590 266932 289420 254474 210283 140881 422500 465450 361210 FALSE TRUE 333765.4571 265178.5061 429384.4801 312256.2111 206098.7797 146300.7832 381526.015 365917.1396 318508.1653 1.047902357 0.832564232 1.348111373 0.980371134 0.647075341 0.459331343 1.197853169 1.148846967 1 18.28097083 KDEESGGGSNPFQHLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KDEESGGGSNPFQHLEK 17 1 Q9Y678;D6RG17 Q9Y678 COPG1 Coatomer subunit gamma-1 0 225.11 1.62E-15 365840000 645350 485540 360760 464780 475760 354470 616850 753720 703300 FALSE TRUE 560065.3624 482350.4558 535224.7427 570315.4027 466293.3068 368106.6903 557027.9819 592542.8435 620156.6752 0.903103014 0.777788058 0.86304762 0.91963116 0.751895973 0.593570472 0.898205251 0.955472814 1 19.24227322 2.007748626 24.99692395 0.960240876 0.801301975 0.38947358 0.091849835 190.7495767 615352.2047 0.039433086 0.026530101 101.8001988 -2.007748626 -0.158938901 KDEEVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KDEEVLK 7 1 O00148;O00148-2;O00148-3;K7EQN7;A0A0G2JJL7;F6QYI9;A0A0D9SEM9;A0A140T9N3;A0A140T9K2;Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;F6S4E6;A0A0A0MT12;F6TRA5;A0A140T9K1;A0A140T973;A0A140T9L4;F6R6M7 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ;; 92.062 0.025567 991700000 1252410 898590 858560 999690 791510 683970 1068800 1406000 1839670 FALSE TRUE 1086900.845 892687.1031 1273762.488 1226684.894 775760.4996 710282.7685 965147.9405 1105337.842 1622186.308 0.670022204 0.550298753 0.785213438 0.756192361 0.478219114 0.437855236 0.594967382 0.681387727 1 20.62950809 1.228613747 2.832434811 1.087576525 0.609741005 0.555030552 0.108867652 0.37378232 3.502121276 0.424133943 0.03063203 16.92831558 -1.228613747 -0.47783552 KDELSDWSLAGEDDRDSR ddPTM_MDA-MB-175_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 0 126.04 1.60E-05 2209700000 3463600 2938500 2262500 2750300 3108800 2656600 3225500 3882800 3464800 FALSE TRUE 3005876.484 2919196.8 3356652.568 3374797.651 3046940.962 2758801.121 2912691.506 3052493.436 3055195.291 0.983857396 0.955486155 1.098670379 1.10460947 0.997298265 0.902986833 0.953356898 0.999115652 1 21.54283317 3.00412188 24.93186775 0.966360426 1.036495909 0.298011865 0.051884856 160.6807241 971888.5068 0.017080017 0.019289324 1009.536163 -3.00412188 0.070135483 KDENEIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KDENEIEK 8 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 92.538 0.019145 0 207760 182470 121430 119270 129400 134200 188620 218220 156490 FALSE TRUE 180303.9896 181271.3426 180153.9542 146352.0764 126825.1932 139362.7608 170327.6614 171555.3512 137989.9305 1.306645992 1.313656308 1.305558699 1.060599682 0.919090203 1.009948772 1.234348484 1.243245435 1 17.07420347 3.745350673 23.23686015 1.095432206 1.309123988 0.537852087 0.099950217 200.1737718 685025.5954 0.031289752 0.052518172 5563.533062 -3.745350673 0.213691782 KDEQEHEFYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KDEQEHEFYK 10 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 134.3 0.00011308 496960000 1444800 1098000 948080 1069600 1062600 819980 1449300 1710400 1623100 FALSE TRUE 1253866.019 1090787.166 1406574.659 1312469.028 1041456.339 851525.1612 1308747.109 1344644.27 1431218.967 0.87608259 0.762138562 0.982780896 0.917028811 0.727670862 0.594964978 0.914428288 0.939509817 1 20.44881298 2.016617221 24.99885219 0.953894734 0.811708853 0.286036272 0.107151006 328.695434 494485.5568 0.046846568 0.031575431 103.9004004 -2.016617221 -0.142185881 KDEQER ddPTM_MDA-MB-175_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 423880000 464410 526550 356770 449710 1045290 487750 656210 791030 712980 FALSE TRUE 403037.0418 523091.0584 529305.1653 551823.5289 1024490.774 506514.0581 592570.8552 621874.3903 628692.3166 0.641072002 0.832030302 0.841914481 0.877732262 1.629558286 0.805662873 0.942545088 0.989155385 1 19.26199461 3.46422664 24.99991923 1.059110155 0.791393781 0.284757198 0.220711475 322.9071186 626046.0338 0.063510167 0.082039909 2912.236496 -3.46422664 -0.267716374 KDETNVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KDETNVK 7 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ;;;; 111.17 0.010646 3959670000 5406450 3677350 3000820 3491350 2024560 3163530 4224660 6399120 6562200 FALSE TRUE 4691973.934 3653193.246 4452026.589 4284114.379 1984275.217 3285233.046 3814953.123 5030717.986 5786424.192 0.810858966 0.631338651 0.769391673 0.74037337 0.342919073 0.567748395 0.659293719 0.869400137 1 22.46424066 1.606660849 2.659222946 0.98874053 0.637148631 0.477037569 0.129334591 0.223365616 3.471707398 0.141849428 0.0369449 40.42600723 -1.606660849 -0.351591899 KDGADFAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KDGADFAK 8 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78;P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;K7EKH5 H3BPS8;P04075;P09972 ALDOA;ALDOC Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase C 0 ;;;;; 111.06 0.0053021 9623490000 15994880 12983360 9607990 11749600 11009880 9473850 16784980 18239850 18359610 FALSE TRUE 13881116.08 12898071.45 14254446.1 14417526.26 10790804.93 9838315.14 15157175.22 14339400.02 16189157.82 0.857432872 0.796710465 0.880493368 0.890566787 0.666545169 0.607710126 0.936254708 0.88574095 1 23.9485246 KDGNASGTTLLEALDCILPPTRPTDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KDGNASGTTLLEALDCILPPTRPTDK 26 2 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 161.39 9.67E-12 356000000 258670 176920 248330 265470 179720 147840 266570 313350 651700 FALSE TRUE 224486.1041 175757.8009 368423.2186 325749.021 176143.9236 153527.5005 240718.0824 246342.541 574656.7684 0.390643801 0.305848309 0.641118732 0.566858408 0.306520228 0.267163825 0.418890189 0.428677699 1 19.13234099 1.237977565 6.624013571 1.015520744 0.415651753 0.716128667 0.115640576 0.069043906 14.88019902 0.186192134 0.030292976 17.29727002 -1.237977565 -0.599868992 KDGNASGTTLLEALDCILPPTRPTDKPLR ddPTM_MDA-MB-175_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 ; 139.4 3.98E-08 10803600000 305200 226380 227053 223334 235080 185047 278870 341300 434520 FALSE TRUE 264867.0467 224892.8949 336856.5902 274045.3981 230402.3679 192165.8778 251825.2303 268315.651 383151.5406 0.69128535 0.586955476 0.879173263 0.715240236 0.601334834 0.501540141 0.657247078 0.700285977 1 18.54755558 1.225284532 3.460985154 1.056518505 0.661804904 0.537566868 0.097764365 0.277810073 4.722915139 0.297753555 0.026321252 16.79904264 -1.225284532 -0.3947136 KDIDHETVVEEQIIGENS(ph)PPDYSEYMTGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KDIDHETVVEEQIIGENSPPDYSEYMTGK 29 1 P25490;A0A494C032;H0YJV7;H0YJU4 P25490 YY1 Transcriptional repressor protein YY1 1 KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK;KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK;KDIDHETVVEEQIIGENS(0.999)PPDYS(0.001)EYMTGK;KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK 355.53 1.78E-120 970070000 1263000 934355 641440 795836 894587 680328 1151250 1379600 1197060 TRUE FALSE 1096091.35 928217.1605 951642.5295 976542.7274 876786.4689 706500.6584 1039601.952 1084583.276 1055544.93 1.038412784 0.879372477 0.901565156 0.925155054 0.830648174 0.669323151 0.984895974 1.027510289 1 20.00955656 2.024264532 24.99742388 1.012865219 0.871849585 0.315245939 0.091054859 252.9571865 260596.4579 0.038026738 0.025636467 105.746142 -2.024264532 -0.141015634 KDIHFMPCSGLTGANLK ddPTM_MDA-MB-175_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 0 165.75 1.58E-09 486460000 1563800 1299200 825760 1103800 1254200 1109700 1654000 1831800 1364100 FALSE TRUE 1357139.868 1290665.47 1225100.298 1354434.661 1229243.874 1152390.877 1493595.335 1440083.825 1202837.652 1.128281831 1.073017184 1.018508438 1.126032809 1.021953272 0.958060196 1.241726456 1.197238732 1 20.1980105 2.233106642 24.99942999 1.160904615 1.055321496 0.22437211 0.079097347 175.0285538 802268.8576 0.031628392 0.022017477 171.0435267 -2.233106642 -0.105583119 KDIPSFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KDIPSFER 8 1 K7EJR3;R4GMR5;P48556 K7EJR3 PSMD8 26S proteasome non-ATPase regulatory subunit 8 0 86.882 0.025204 192290000 240510 254710 175980 204470 264950 228630 219390 280600 292710 FALSE TRUE 208725.9941 253036.7932 261084.5166 250898.0386 259678.0134 237425.544 198113.5916 220595.8736 258106.1573 0.808682739 0.980359384 1.011539281 0.972073047 1.00608996 0.919875553 0.767566313 0.854671101 1 17.97760503 2.47144094 24.92476482 0.862472492 0.961308529 0.17539819 0.079080695 204.4145092 896942.3495 0.029168728 0.022664443 296.1017271 -2.47144094 0.098836037 KDISENKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDISENKR 8 2 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 145.17 0.00032263 883870000 1071160 911590 664170 818570 646730 661880 984430 1147720 977100 FALSE TRUE 929603.492 905601.7053 985364.8335 1004438.83 633861.3383 687342.9519 888960.1301 902289.0096 861588.3511 1.078941574 1.051083971 1.143660812 1.16579899 0.735689309 0.797762587 1.031768975 1.0472391 1 19.71663922 3.285231456 24.99997565 0.940043355 1.108085884 0.448064026 0.102306191 144.831611 77580.31348 0.033442617 0.043174103 1928.552457 -3.285231456 0.168042528 KDISQNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDISQNKR 8 2 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 0 ; 119.75 0.00091944 1463450000 1653910 1749260 1054090 1301720 1296120 1581710 2475450 2539000 2091970 FALSE TRUE 1435341.603 1737768.996 1563851.45 1597295.422 1270329.748 1642559.407 2235381.24 1996054.609 1844659.69 0.77810645 0.942053976 0.847772334 0.865902492 0.688652631 0.890440343 1.211812267 1.082072005 1 20.81492326 2.377239214 6.12711898 1.097747458 0.830466763 0.701164115 0.081674393 0.112297858 5.868360244 0.030592329 0.023537694 238.363204 -2.377239214 -0.267280694 KDKS(ph)PVREPIDNLTPEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KDKSPVREPIDNLTPEER 18 3 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23;H0Y4X3;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 1 KDKS(1)PVREPIDNLTPEER;KDKS(1)PVREPIDNLTPEER;KDKS(1)PVREPIDNLTPEER;KDKS(1)PVREPIDNLTPEER;KDKS(1)PVREPIDNLTPEER;KDKS(1)PVREPIDNLTPEER;KDKS(1)PVREPIDNLTPEER 213.05 8.89E-17 8415510000 5882860 4064660 3350646 3539060 4195520 3073700 5564950 6526270 5676320 TRUE FALSE 5105425.146 4037958.981 4971029.613 4342657.664 4112037.36 3191947.228 5025262.006 5130677.948 5005271.916 1.020009548 0.806741182 0.993158753 0.867616732 0.821541253 0.637717047 1.003993807 1.025054789 1 22.25501702 2.046000901 24.99998358 1.01438078 0.857129992 0.321593479 0.104036274 137.2979818 74616.37498 0.042348637 0.028551437 111.1734033 -2.046000901 -0.157250789 KDLQHPNEFIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KDLQHPNEFIR 11 1 P53618;E9PP73;E9PP63;E9PKQ1 P53618 COPB1 Coatomer subunit beta 0 100.22 0.0027198 94696000 127570 131780 80607 81103 121720 114160 128020 141350 134550 FALSE TRUE 110711.3013 130914.3285 119588.8148 99518.67573 119298.0101 118551.8091 115604.6401 111123.4025 118643.6523 0.933141379 1.103424633 1.007966398 0.838803205 1.005515321 0.99922589 0.974385379 0.936614815 1 16.85627539 3.983890184 24.91831554 0.958394607 1.027636144 0.14746303 0.062648834 1034.354878 1599926.058 0.015643501 0.028171517 9635.853406 -3.983890184 0.069241538 KDLYANTVLSGGTTMYPGIADR ddPTM_MDA-MB-175_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 ;;;; 267.71 1.24E-37 35081830000 19579000 17132900 10143170 13909010 16636100 15598900 17088900 20588400 16696200 FALSE TRUE 16991585.54 17020352.85 15048440.94 17067263.31 16305074.16 16198999.78 15431621.11 16185730.88 14722394.26 1.154131947 1.15608593 1.022146308 1.159272263 1.10750153 1.100296561 1.048173336 1.099395288 1 23.81150898 -1.733153854 0.368357727 9.39E-14 1.128145128 0.392325983 0.043543166 74.31930632 1.362165015 56.8096011 0.051112954 0.018486136 1.733153854 1.128145128 KDLYLASVFHATAFELDTDGNPFDQDIYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KDLYLASVFHATAFELDTDGNPFDQDIYGR 30 1 P50454;E9PKH2 P50454 SERPINH1 Serpin H1 0 171.22 9.68E-13 41655000 40103 26105 16159 26910 30227 37036 35047 39789 27368 FALSE TRUE 34803.28694 25933.51454 23973.54645 33020.32679 29625.54184 38460.79889 31648.14733 31280.43199 24132.58622 1.442169796 1.074626412 0.99340975 1.368287945 1.227615705 1.59372885 1.311427919 1.296190624 1 14.55869491 4.800613371 21.23072558 1.249578873 1.442179788 0.109735923 0.181821646 33386.19882 11419801.11 0.045460827 77.4038401 63184.91001 -4.800613371 0.192600915 KDNDFIYHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KDNDFIYHDR 10 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;; 143.17 2.24E-05 6662360000 10376000 9708100 6946400 8589400 9747300 8750100 10609200 12581500 12542600 FALSE TRUE 9004785.311 9644326.852 10305702.27 10539754.55 9553347.8 9086722.009 9580321.417 9891044.134 11059828.12 0.81418854 0.872014171 0.931813964 0.952976343 0.86378809 0.821597037 0.866226972 0.894321687 1 23.39882563 1.23659551 3.502479921 1.018134742 0.877481116 0.459171976 0.042338328 0.313679201 5.629964667 0.118743045 0.011672118 17.24231241 -1.23659551 -0.140653625 KDPEDTGAEKS(ph)PTTSADLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KDPEDTGAEKSPTTSADLK 19 2 O75363;G3XAF7;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 KDPEDT(0.115)GAEKS(0.633)PT(0.183)T(0.031)S(0.039)ADLK 65.425 0.014932 175440000 76925 67478 76046 69977 61202 38076 103560 127430 112270 TRUE FALSE 66759.16635 67034.73257 112822.1 85866.34738 59984.19994 39540.80836 93516.76714 100180.0862 98997.5685 0.674351576 0.677135142 1.139645162 0.867358145 0.605915891 0.399411914 0.94463701 1.011944916 1 16.59510547 2.023384993 24.99920247 0.998265477 0.738564827 0.297888786 0.188019111 304.1498457 325143.2385 0.082956913 0.055926363 105.5322002 -2.023384993 -0.259700649 KDPELWGSVLLESNPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDPELWGSVLLESNPYR 17 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 197.09 2.47E-11 5423600000 943930 822220 619660 757860 930550 783040 898630 1056270 1642620 FALSE TRUE 819187.2589 816818.7827 919329.6486 929943.6962 912033.8756 813164.0555 811481.0009 830394.8804 1448431.335 0.565568584 0.563933383 0.634707098 0.642035058 0.629670081 0.561410152 0.560248167 0.573306349 1 20.46605986 1.237021248 24.99972883 1.000000502 0.591397608 0.939711455 0.032528468 9.779391921 158765.8901 0.054465453 0.008861981 17.2592233 -1.237021248 -0.408602894 GIAPAS(ph)PMLGNASNPNKADIPER ddPTM_MDA-MB-175_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(0.932)PMLGNAS(0.068)NPNKADIPER 271.6 7.74E-52 2038990000 3109490 2766660 1376410 1839350 2498300 2059960 2761180 2935890 965680 TRUE FALSE 2698563.018 2748485.628 2042046.48 2257002.53 2448588.718 2139207.994 2493401.189 2308072.771 851518.4105 3.169118817 3.227746569 2.398123698 2.650562222 2.875555816 2.512227531 2.92818236 2.71053772 1 19.6996782 1.238036221 5.262059901 0.898990168 2.80592428 0.827934956 0.259572456 0.06524649 5.10293192 0.453746425 0.065953134 17.29960635 -1.238036221 1.906934112 KDPLEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KDPLEGR 7 1 Q14165;F5GX14 Q14165 MLEC Malectin 0 ;; 75.38 0.069955 497260000 638410 569890 360740 509730 671770 662520 528330 841390 683780 FALSE TRUE 554042.501 566146.3551 535195.0706 625471.9872 658403.0913 688007.5731 477092.6379 661465.2962 602944.3074 0.918894986 0.938969567 0.887635996 1.037362787 1.091979945 1.141079806 0.791271486 1.097058697 1 19.20166522 3.732213675 24.29887848 1.026619666 0.91754712 0.236529771 0.0942237 506.6565261 1939704.741 0.025366909 0.038714188 5397.761291 -3.732213675 -0.109072546 KDPQEGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KDPQEGYR 8 1 Q14562;F5H658;K7END7 Q14562 DHX8 ATP-dependent RNA helicase DHX8 0 69.954 0.084315 56361000 55393 48422 35375 33559 39796 44835 57595 54204 49673 FALSE TRUE 48072.6747 48103.91269 52482.46832 41179.08387 39004.13746 46559.83146 52009.44576 42612.89642 43800.71453 1.097531746 1.098244931 1.198210323 0.940146395 0.890490895 1.06299251 1.187410898 0.972881307 1 15.41866678 3.739580234 24.99993527 1.013690377 1.128020591 0.325131856 0.082859938 124.7139155 3057823.281 0.023885449 0.038555412 5490.099733 -3.739580234 0.114330214 KDPSGASNPSADS(ph)PLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KDPSGASNPSADSPLHR 17 1 P55317-2;P55317 P55317-2 FOXA1 Hepatocyte nuclear factor 3-alpha 1 KDPSGASNPS(0.017)ADS(0.983)PLHR;KDPSGASNPSADS(1)PLHR;KDPSGASNPSADS(1)PLHR;KDPSGASNPSADS(1)PLHR;KDPSGASNPSADS(1)PLHR;KDPSGASNPSADS(1)PLHR;KDPSGASNPSADS(1)PLHR 231.29 2.41E-16 13775150000 5794420 5128755 2798891 3582795 4662422 4097612 4941423 5912012 4814998 TRUE FALSE 5028672.716 5095063.871 4152444.049 4396323.364 4569648.924 4255249.785 4462204.558 4647774.241 4245774.422 1.184394698 1.200031694 0.978018057 1.035458535 1.076281609 1.002231716 1.05097542 1.094682331 1 22.01759629 4.251745301 24.99996837 1.040717281 1.192213303 0.770613574 0.035749799 109.5446568 207707.8241 0.009061217 0.023664114 17854.40166 -4.251745301 0.151496023 KDQGELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KDQGELER 8 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 129.85 0.0017205 4179410000 4804600 4278210 3046800 3816980 3681250 3762060 4974200 5597310 5101710 FALSE TRUE 4169659.937 4250106.157 4520242.671 4683683.648 3608000.327 3906788.883 4491802.85 4400368.815 4498591.656 0.926881179 0.944763713 1.004812843 1.041144431 0.802028858 0.868447101 0.998490904 0.978165869 1 22.10104199 KDREDS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KDREDSPER 9 2 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 1 KDREDS(1)PER 69.258 0.043906 457270000 481320 382570 340190 356460 285620 330940 450090 495480 573780 TRUE FALSE 417712.3425 380056.8725 504707.0219 437399.6911 279936.7208 343671.4759 406440.3411 389525.4578 505948.3821 0.825602685 0.751177167 0.997546469 0.864514458 0.553291068 0.679261933 0.803323729 0.769891696 1 18.94863068 5.133956665 17.04013044 0.795827256 6.537845102 0.000840543 0.134258805 1662.719985 211827.5648 0.032586034 561.3390278 136130.884 -5.133956665 5.742017846 KDS(ph)DDEKSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.995)DDEKS(0.005)DR;KDS(0.998)DDEKS(0.002)DR 96.464 0.0052944 843220000 1257950 925320 939850 734510 634770 605550 1380650 1469410 1479190 TRUE FALSE 1091708.72 919241.512 1394364.604 901291.7218 622139.3189 628845.9003 1246754.776 1155188.106 1304321.843 0.836993359 0.704765865 1.069034158 0.691004085 0.476982979 0.482124794 0.955864369 0.885661857 1 20.31486847 2.170585245 24.99999946 0.934723732 0.714744919 0.301543638 0.169603168 75.93492898 27925.96281 0.074895687 0.050494673 148.1102942 -2.170585245 -0.219978813 KDS(ph)DTESSDLFTNLNLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KDSDTESSDLFTNLNLGR 18 1 Q9Y3S2 Q9Y3S2 ZNF330 Zinc finger protein 330 1 KDS(0.996)DT(0.004)ESSDLFTNLNLGR;KDS(0.985)DT(0.015)ESSDLFTNLNLGR;KDS(0.991)DT(0.009)ESSDLFTNLNLGR;KDS(1)DTESSDLFTNLNLGR 257.51 7.70E-31 724500000 840520 494946 554194 758547 629934 479046 512307 820600 2015190 TRUE FALSE 729443.1524 491694.6671 822204.0721 930786.69 617399.5458 497475.2096 462623.546 645121.0759 1776956.534 0.410501404 0.276706075 0.462703536 0.523809487 0.347447748 0.279959132 0.260346011 0.363048315 1 20.76097696 1.238598946 15.15043366 1.000154606 0.36246778 0.849842377 0.083800668 0.017776256 1026.466646 0.121613491 0.021865045 17.32203638 -1.238598946 -0.637686826 KDS(ph)EEEVSLLGSQDIEEGNHQVEDGCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KDSEEEVSLLGSQDIEEGNHQVEDGCR 27 1 Q9Y487 Q9Y487 ATP6V0A2 V-type proton ATPase 116 kDa subunit a isoform 2 1 KDS(1)EEEVSLLGSQDIEEGNHQVEDGCR 260.65 2.25E-53 225520000 164320 125790 108250 102290 165260 126920 140760 197320 151450 TRUE FALSE 142604.6957 124963.6772 160600.0621 125516.5079 161971.6493 131802.6945 127109.1169 155124.6535 133545.7535 1.067833996 0.935736809 1.202584566 0.939876444 1.212855108 0.986947852 0.951802012 1.161584322 1 17.02697458 RPLS(ph)GPDVGTPQPAGLASGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPLSGPDVGTPQPAGLASGAK 21 1 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 RPLS(1)GPDVGTPQPAGLASGAK;RPLS(1)GPDVGTPQPAGLASGAK 285.26 1.52E-45 585700000 651186 716378 544914 728538 798443 729520 761760 1022275 1715490 TRUE FALSE 565130.1202 711672.0657 808436.233 893963.6879 782555.5464 757585.1065 687884.6324 803669.4466 1512686.726 0.373593627 0.470468904 0.534437315 0.590977413 0.51732823 0.500820886 0.454743616 0.53128611 1 20.52868181 1.238059088 4.852654227 1.035144879 0.497603845 0.888356888 0.05621093 0.058362583 3.305487652 0.106870936 0.014666526 17.30051724 -1.238059088 -0.537541034 KDS(ph)GSSSVFAES(ph)PGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KDSGSSSVFAESPGGK 16 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 2 KDS(0.527)GS(0.181)S(0.237)S(0.055)VFAES(1)PGGK 106.5 0.0042035 341630000 338990 250830 201580 249540 278620 199930 432740 450450 362240 TRUE FALSE 294191.6126 249182.2812 299064.7622 306201.871 273076.0071 207621.4365 390772.9414 354124.7729 319416.3999 0.921028516 0.780117368 0.936284932 0.958629147 0.854921686 0.650002431 1.223396612 1.108661838 1 18.28507886 2.224784571 24.99999707 1.114960692 0.856041128 0.589305857 0.102425321 161.917986 293837.3597 0.041748133 0.028311136 167.7971463 -2.224784571 -0.258919564 KDS(ph)GSSSVFAESPGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDSGSSSVFAESPGGK 16 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 KDS(0.935)GS(0.018)S(0.018)S(0.029)VFAESPGGK;KDS(0.527)GS(0.077)S(0.139)S(0.258)VFAESPGGK 190.57 5.12E-10 966910000 2458000 891390 815560 1105450 1206550 826750 1640390 2002330 1577010 TRUE FALSE 2133169.072 885534.4004 1209967.544 1356459.318 1182542.016 858555.6075 1481305.23 1574147.312 1390577.674 1.534016482 0.636810454 0.870118632 0.975464617 0.850396233 0.617409314 1.065244508 1.132009625 1 20.4072529 2.03991676 24.99988056 1.08239312 0.894503722 0.0704058 0.251773464 324.1157551 202992.4464 0.096970197 0.065377212 109.6268057 -2.03991676 -0.187889399 KDS(ph)ISEDEMVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDSISEDEMVLR 12 1 Q8N5D0-5;Q8N5D0-3;Q8N5D0-6;Q8N5D0-2;Q8N5D0-4;Q8N5D0 Q8N5D0-5 WDTC1 WD and tetratricopeptide repeats protein 1 1 KDS(0.992)IS(0.008)EDEMVLR;KDS(0.998)IS(0.002)EDEMVLR 92.264 0.0015366 0 252480 186982 161670 170272 222010 215792 230702 244300 255220 TRUE FALSE 219114.1283 185753.7029 239854.1528 208934.86 217592.4354 224093.6579 208328.5555 192058.3461 225048.1823 0.973632073 0.82539526 1.065790224 0.928400567 0.966870441 0.995758577 0.925706457 0.853409897 1 17.77987439 0.947081688 22.27655806 1.928279309 0.938505573 0.065121731 0.068165543 91.79608438 368399.5951 46040.3814 0.015847942 8.85282111 -0.947081688 -0.989773736 KDS(ph)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 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;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR 292.2 1.37E-96 3071767000 143202.7 111710.1 99280.5 131719.1 135664.8 126127.5 127787.4 168317.2 189199 TRUE FALSE 124278.1004 110976.269 147292.8819 161627.9349 132965.3359 130979.7065 115394.5976 132323.8766 166832.1098 0.744929142 0.6651973 0.882880892 0.968805916 0.797000866 0.785098904 0.691680983 0.793155927 1 17.34803746 4.24125244 24.9999761 0.833113839 0.705063202 0.277408683 0.092573194 101.5057318 942671.9334 0.024668449 0.059458054 17428.19618 -4.24125244 -0.128050637 KDS(ph)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHRGDEQGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KDSLDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHRGDEQGKR 48 3 Q96TC7;H0YLG5;H0YMB1;Q96TC7-2 Q96TC7 RMDN3 Regulator of microtubule dynamics protein 3 1 KDS(0.997)LDLEEEAAS(0.002)GAS(0.001)SALEAGGSSGLEDVLPLLQQADELHRGDEQGKR 68.722 0.00022339 179330000 13295 13196 7328.9 7512.6 12976 9514.7 11299 22224 4305.4 TRUE FALSE 11538.03206 13109.31461 10873.18055 9218.450653 12717.80299 9880.736666 10203.22472 17471.57055 3796.420517 3.039187048 3.453072322 2.864061161 2.428195352 3.349945806 2.602645472 2.687590765 4.602116776 1 11.89042409 4.222729838 24.17509595 2.947183215 3.246129822 0.020455246 0.896942228 810.061628 1237047.347 0.226109113 0.473432939 16700.514 -4.222729838 0.298946607 KDS(ph)LSQLEEYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KDSLSQLEEYLR 12 1 O60303 O60303 KIAA0556 Uncharacterized protein KIAA0556 1 KDS(0.998)LS(0.002)QLEEYLR 147.49 4.02E-05 68955000 85401 80907 48761 48826 72539 66787 75772 86814 64762 TRUE FALSE 74115.04147 80375.51659 72341.9827 59912.68956 71095.61582 69356.33911 68423.6431 68249.50169 57105.91014 1.297852382 1.407481579 1.266803778 1.049150419 1.244978246 1.214521211 1.19818847 1.195139024 1 15.80135244 8 0.21884334 1.089847783 2.552151244 0.416103421 0.088781294 102.4232257 1.572001599 0.450694135 51.12748837 100000000 -8 1.462303462 KDS(ph)LTQAQEQGNLLN ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KDSLTQAQEQGNLLN 15 1 Q5JTD0-4;Q5JTD0-2;Q5JTD0 Q5JTD0-4 TJAP1 Tight junction-associated protein 1 1 KDS(0.999)LT(0.001)QAQEQGNLLN;KDS(0.955)LT(0.045)QAQEQGNLLN;KDS(1)LTQAQEQGNLLN;KDS(0.939)LT(0.061)QAQEQGNLLN;KDS(1)LTQAQEQGNLLN;KDS(0.999)LT(0.001)QAQEQGNLLN 255.23 1.08E-24 3530801000 7758490 5568930 4586290 4844550 6219820 4848650 7822510 8241550 7369040 TRUE FALSE 6733185.889 5532347.332 6804235.184 5944579.122 6096057.751 5035180.703 7063884.184 6479158.668 6497880.486 1.036212639 0.851407985 1.047146866 0.914848947 0.938160953 0.774895862 1.087105895 0.997118781 1 22.63153778 2.172585084 25 1.024085065 0.929059639 0.250495178 0.082183306 81.03712325 30705.98151 0.031707284 0.021377052 148.7938853 -2.172585084 -0.095025425 KDS(ph)PHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.775)PHS(0.225)R;KDS(0.982)PHS(0.018)R;KDS(0.936)PHS(0.064)R;KDS(0.82)PHS(0.18)R 92.866 0.0094051 343044000 328623 263132 205478 219751 271245 246051 339387 377259 395610 TRUE FALSE 285194.6379 261403.4686 304847.8481 269648.8232 265847.7552 255516.7412 306473.301 296585.0987 348841.4365 0.817548055 0.749347529 0.873886575 0.772983926 0.762087663 0.732472449 0.87854615 0.850200314 1 18.41221189 0.834567044 1.063976328 1.305208505 0.789220579 0.65984091 0.046619936 2.334927428 1.179955827 1.689777651 0.014754304 6.832301839 -0.834567044 -0.515987926 KDS(ph)QNSSQHSVSSHR ddPTM_MDA-MB-175_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(0.735)QNS(0.132)S(0.132)QHSVSSHR;KDS(0.698)QNS(0.151)S(0.151)QHSVSSHR;KDS(0.449)QNS(0.449)S(0.101)QHSVSSHR;KDS(1)QNSSQHSVSSHR;KDS(0.755)QNS(0.123)S(0.123)QHSVSSHR 236.96 4.74E-18 285166200 146567.3 134304.2 31152.4 91886.8 155437.7 143824.2 169162.6 181365.4 182039.5 TRUE FALSE 127198.06 133421.9469 46217.80484 112751.1023 152344.7939 149357.21 152757.2371 142581.8206 160518.9977 0.792417482 0.831191004 0.28792732 0.702415938 0.949076409 0.930464382 0.951645844 0.888255114 1 17.29238453 3.304255352 4.862690016 0.937192458 0.633360849 0.496218157 0.146003226 0.175589689 8.017515713 0.043385589 0.055670406 2014.908607 -3.304255352 -0.303831609 KDS(ph)SSVVEWTQAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDSSSVVEWTQAPK 14 1 Q8TC07-2;Q8TC07-3;Q8TC07;F8WCB5 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 KDS(0.97)S(0.025)S(0.006)VVEWTQAPK;KDS(0.933)S(0.034)S(0.034)VVEWTQAPK 171.79 1.81E-06 1147890000 1479670 995250 699330 873210 900650 558280 1652150 1395530 1178620 TRUE FALSE 1284127.86 988712.1372 1037528.327 1071485.677 882728.8271 579757.3929 1491924.747 1097106.77 1039284.886 1.235587929 0.951338897 0.998309839 1.030983603 0.849361747 0.557842609 1.43553011 1.055636221 1 19.98715975 0.914963607 14.18747392 0.7525835 1.015411676 0.000369186 0.228078301 2829445.518 9627855.83 22405421.76 0.055659064 8.221737506 -0.914963607 0.262828176 KDSETGENIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KDSETGENIR 10 1 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;; 166.14 9.04E-06 2654790000 2271070 2230270 1667280 2698760 2383400 2283540 2270630 2866550 2461940 FALSE TRUE 1970942.345 2215619.21 2473582.185 3311554.706 2335975.003 2371389.261 2050424.652 2253560.59 2170892.258 0.907895055 1.020603027 1.139431114 1.52543485 1.07604373 1.092356957 0.944507792 1.038080348 1 21.0498567 2.548879689 2.818680705 1.002559516 1.149250907 0.131778243 0.158892874 0.568631115 8.914257597 0.065716357 0.053947806 353.8992882 -2.548879689 0.146691391 KDSLSVNEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDSLSVNEFK 10 1 Q99584 Q99584 S100A13 Protein S100-A13 0 ; 161.93 1.11E-05 8896200000 11712500 10833700 8441500 9484200 10075800 8292100 12825000 14897300 13838500 FALSE TRUE 10164663.45 10762532.71 12523837.64 11637732.57 9875311.293 8611102.453 11581233.47 11711628.33 12202528.29 0.832996507 0.881992031 1.026331374 0.95371486 0.809284032 0.705681826 0.949084747 0.959770635 1 23.54067676 2.022197893 24.99991447 0.970236693 0.873170451 0.243290172 0.084831037 379.7143173 427643.5279 0.038042146 0.025645878 105.2441325 -2.022197893 -0.097066242 KDTDDIES(ph)PKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KDTDDIESPKR 11 2 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;Q9UPQ0-8;Q9UPQ0;Q9UPQ0-3;G5EA03;D6RD46;D6RJ93;D6R8Y0;Q9UPQ0-7;D6RGH8 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 KDT(0.001)DDIES(0.999)PKR;KDTDDIES(1)PKR;KDT(0.001)DDIES(0.999)PKR 117 0.00071991 1018430000 906320 681090 696100 693950 674440 465790 1012820 1060720 1012010 TRUE FALSE 786547.5157 676615.8749 1032736.288 851521.9539 661019.9635 483709.2427 914596.8723 833893.2825 892371.3307 0.881412803 0.758222336 1.157294338 0.954223791 0.740745406 0.542049286 1.024906158 0.93446893 1 19.76728464 KDTDFEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KDTDFEHR 8 1 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 87.913 0.0097288 110490000 166390 161290 115070 124390 134980 173070 138230 164230 175420 FALSE TRUE 144401.1399 160230.4754 170718.2369 152634.6507 132294.1621 179728.1149 124824.4759 129110.6925 154682.0474 0.933535225 1.035869889 1.10367195 0.986763837 0.855265134 1.161919679 0.806974552 0.834684404 1 17.23894624 2.211975752 24.99999403 0.867931256 1.009665926 0.28815569 0.097255849 257.5859356 242227.9106 0.038678328 0.026085163 162.9205068 -2.211975752 0.141734671 KDVFFYQADDEHYIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDVFFYQADDEHYIPR 16 1 P23258;K7EIS0;Q9NRH3;K7EKE5 P23258 TUBG1;TUBG2 Tubulin gamma-1 chain;Tubulin gamma chain;Tubulin gamma-2 chain 0 ; 211.29 4.85E-12 186904000 454920 423520 282390 327640 449410 413380 432210 536830 434110 FALSE TRUE 394801.1694 420737.8692 418954.7485 402035.6697 440467.6203 429282.9961 390294.3407 422033.0821 382790.0103 1.031377932 1.099134925 1.094476703 1.050277329 1.150676894 1.1214582 1.0196043 1.102518537 1 18.54619365 0.469536987 2.016077143 1.21E-10 1.085551619 0.281949404 0.040745621 21.88058072 7.693255884 92.59680755 0.010671443 2.948064538 -0.469536987 1.085551619 KDVGRPQPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KDVGRPQPGR 10 2 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ;;;;; 180.66 1.11E-06 3714390000 2953320 2841834 1463987 1638736 2240286 2420750 2331663 2876762 3723230 FALSE TRUE 2563031.279 2823165.805 2171976.01 2010836.055 2195708.692 2513877.819 2105538.681 2261588.833 3283073.991 0.780680328 0.859915376 0.661567792 0.612485756 0.668796591 0.765708548 0.641331474 0.688863193 1 21.64661583 1.236494398 24.99751853 1.000000375 0.706306649 0.6019475 0.07408153 40.70999406 492390.6576 0.122471952 0.01916929 17.23829854 -1.236494398 -0.293693726 KDVHMPK ddPTM_MDA-MB-175_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 ; 85.064 0.013688 1262350000 9488100 7752600 5624400 7201700 7220200 5889200 9856200 11166200 9850500 FALSE TRUE 8234223.545 7701672.66 8344378.652 8836956.056 7076532.146 6115761.335 8900347.241 8778395.025 8685985.112 0.947989599 0.886678087 0.960671535 1.017380981 0.814706916 0.704095305 1.024679081 1.010638968 1 23.05025805 KDVLETFTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDVLETFTVK 10 1 A6NNI4;A0A2R8Y478;G8JLH6;P21926 A6NNI4 CD9 Tetraspanin;CD9 antigen 0 ; 162.6 1.08E-05 1280000000 2622600 2572400 1749840 2392200 2437100 1930830 2486700 3715100 2979400 FALSE TRUE 2276016.765 2555501.735 2596068.477 2935385.572 2388606.478 2005110.28 2245540.217 2920654.776 2627178.726 0.866334956 0.972717124 0.988158305 1.117314762 0.909190705 0.763218071 0.85473447 1.111707684 1 21.32508292 1.728769726 13.11669891 1.054615439 0.929456057 0.239774536 0.096882752 0.144287468 120.96662 0.056938629 0.026998544 53.551264 -1.728769726 -0.125159382 KDWDDDQND ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KDWDDDQND 9 1 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;; 125.18 0.010431 9315320000 14446100 11561000 8667000 10056400 10301600 9341000 13704100 15461800 13367700 FALSE TRUE 12537011.28 11485055.03 12858390.19 12339859.32 10096618.31 9700354.314 12375078.49 12155414.39 11787385.73 1.063595573 0.974351335 1.090860219 1.0468699 0.856561289 0.822943656 1.049857769 1.031222246 1 23.49074045 KDWYDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDWYDVK 7 1 P61247;E9PFI5;D6RG13;H0Y8L7;H0Y9Y4;D6RI02 P61247 RPS3A 40S ribosomal protein S3a 0 ; 103.78 0.013306 3458100000 6421400 5529200 4266300 4531200 5438800 3830900 6738800 7577500 6641300 FALSE TRUE 5572795.72 5492878.321 6329496.95 5560078.215 5330578.521 3978277.202 6085272.213 5957110.593 5856173.08 0.951610488 0.937963794 1.080824775 0.949438847 0.910249483 0.679330537 1.039120964 1.017236088 1 22.48152676 KDYEEIGPSICR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KDYEEIGPSICR 12 1 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ; 150.12 0.00010879 753380000 530210 479580 317480 397010 469960 463700 441660 490500 423270 FALSE TRUE 460141.4051 476429.6074 471014.3899 487157.1884 460608.7155 481538.8391 398827.8812 385610.3921 373231.5028 1.232857896 1.276498912 1.261989908 1.305241344 1.234109961 1.290188088 1.068580434 1.033166786 1 18.50971124 2.169211114 4.470312317 1.028154628 1.267631956 0.950252013 0.025234238 0.038992493 1.504288275 0.010433286 0.006925969 147.6424062 -2.169211114 0.239477328 KEAEDSLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEAEDSLRR 9 2 O43776;K7EIU7;O43776-2;K7EJ19;K7EPK2;K7EMQ6 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 112.83 0.0010677 166039000 699240 461510 305270 322680 390870 396120 543390 554360 291360 FALSE TRUE 606833.6624 458478.3104 452899.5931 395949.4259 383092.4517 411358.9927 490692.1214 435814.428 256915.7527 2.361994763 1.784547291 1.762833101 1.541164454 1.491120913 1.60114352 1.909933962 1.69633206 1 17.97093583 5.794996107 0.963482515 1.580414235 6.939154937 0.541898537 0.232227749 10.83219747 1.690933537 0.074377613 97.01001887 623729.2445 -5.794996107 5.358740702 KEAESCDCLQGFQLTHSLGGGTGSGMGTLLLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEAESCDCLQGFQLTHSLGGGTGSGMGTLLLSK 33 1 Q3ZCM7;A0A075B736;Q5SQY0 Q3ZCM7 TUBB8 Tubulin beta-8 chain 0 ; 280.65 5.47E-74 3143700000 2079060 1557000 919690 1169940 1482750 1220260 2109360 2337020 1143170 FALSE TRUE 1804306.953 1546771.964 1364455.16 1435592.758 1453246.176 1267204.192 1904794.592 1837266.46 1008025.745 1.789941341 1.534456806 1.353591579 1.424162791 1.441675655 1.257114908 1.889628912 1.822638429 1 19.94310105 2.248469282 24.99915948 1.636517749 1.461668967 0.012442905 0.27330316 537.0682306 1355002.292 0.102730135 0.078596675 177.2022704 -2.248469282 -0.174848782 KEAESSPFVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KEAESSPFVER 11 1 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;; 178.22 1.22E-05 3653520000 3383660 2854010 2201030 2767420 3015570 3291330 3061090 3093080 2534710 FALSE TRUE 2936500.758 2835261.82 3265455.47 3395805.008 2955566.057 3417949.595 2764225.963 2431648.912 2235059.471 1.313835625 1.268539767 1.461015025 1.519335415 1.322365733 1.529243243 1.236757231 1.087957141 1 21.09188179 1.841694621 2.422964915 1.025735991 1.400301037 0.729457048 0.089598631 0.145077638 1.572977154 0.069682536 0.025678175 69.45357758 -1.841694621 0.374565046 KECSEAMEVETSVISIDS(ph)PQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KECSEAMEVETSVISIDSPQK 21 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 KECSEAMEVETSVISIDS(1)PQK 157.68 2.06E-09 165160000 114480 92827 69349 71297 80458 63050 111310 134610 108260 TRUE FALSE 99351.17794 92217.21332 102886.4084 87486.07356 78857.04321 65475.5743 100515.1733 105824.699 95461.62613 1.040744663 0.966013435 1.077777663 0.916452789 0.826060129 0.68588371 1.052937996 1.108557473 1 16.54263329 2.038321717 24.99968516 1.067648211 0.919330086 0.244598146 0.111295948 218.0627182 142255.2312 0.048943781 0.032997837 109.2249154 -2.038321717 -0.148318125 KEDAENLAAAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEDAENLAAAQR 12 1 Q9Y6D6;E5RIF2;E5RHL7;E5RHZ1 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 0 ; 208.51 1.06E-07 903320000 1160260 1023810 756370 771210 1074060 950050 1198280 1336010 1342750 FALSE TRUE 1006928.701 1017084.525 1122153.062 946325.0177 1052688.307 986599.0383 1082070.99 1050314.658 1184011.625 0.850438189 0.859015658 0.947755105 0.799253148 0.889086125 0.833268034 0.913902336 0.887081374 1 20.17525181 -0.680208977 1.09160942 9.999999991 0.867212738 0.498107355 0.040829469 89.88906104 1.993719927 1967.803873 0.011901954 0.208829103 0.680208977 -9.132787254 KEDEVEEWQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KEDEVEEWQHR 11 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 195.25 1.02E-07 1885480000 3394560 2870400 2651990 3504140 2950720 2631150 3133790 4007840 6790500 FALSE TRUE 2945960.295 2851544.153 3934501.234 4299808.544 2892006.445 2732372.043 2829875.528 3150794.605 5987734.826 0.491999125 0.476230868 0.657093433 0.7181027 0.482988397 0.456328165 0.472612033 0.526208107 1 22.5135789 1.237870846 24.99175155 1.000000536 0.535426917 0.742496063 0.08602354 9.399275075 340302.5279 0.132174334 0.022760742 17.29302009 -1.237870846 -0.464573619 KEDGTFYEFGEDIPEAPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KEDGTFYEFGEDIPEAPER 19 1 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;; 226.29 2.46E-19 3609500000 4002140 2639010 1850171 2313590 2581440 2330373 3041740 3527900 3134330 FALSE TRUE 3473247.059 2621674.17 2744919.884 2838925.971 2530074.395 2420023.957 2746752.523 2773486.039 2763793.078 1.256695766 0.948578311 0.993171271 1.027184702 0.915435535 0.875616911 0.993834359 1.003507123 1 21.39821818 4.741346193 24.92673945 0.971341009 1.256695873 0.795987611 0.045660212 120.2796325 1076262.721 0.011935854 0.080321454 55124.69411 -4.741346193 0.285354864 KEDIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEDIQK 6 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 91.065 0.077472 1246020000 2293380 1655260 1270150 1413800 997640 1192170 2054670 2402710 2336580 FALSE TRUE 1990304.022 1644386.488 1884398.788 1734824.899 977788.9158 1238033.551 1855408.42 1888909.164 2060352.174 0.966001855 0.798109425 0.914600335 0.842004061 0.474573681 0.600884435 0.900529746 0.916789463 1 20.97445953 2.02243328 24.46159222 0.939313726 0.763300899 0.248779171 0.143495141 273.6771193 298420.1829 0.063854823 0.043047255 105.3011903 -2.02243328 -0.176012827 KEDKPEGQS(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEDKPEGQSPVK 12 2 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 KEDKPEGQS(1)PVK;KEDKPEGQS(1)PVK 91.932 0.0041845 325880000 251910 177418 216410 180194 181212 113042 290380 311820 531730 TRUE FALSE 218619.4552 176252.5295 321066.5998 221109.8018 177606.2357 117390.7989 262218.9923 245139.7196 468869.4851 0.466269318 0.375909576 0.684767531 0.471580704 0.378796747 0.250369885 0.559257961 0.522831465 1 18.83882686 1.007124794 1.868820091 1.538497116 0.450030318 0.685089757 0.114949233 1.067336919 2.062679135 2.554080323 0.032097419 10.16540753 -1.007124794 -1.088466799 KEDLELIMTEMEISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KEDLELIMTEMEISR 15 1 Q9NX55 Q9NX55 HYPK Huntingtin-interacting protein K 0 ;; 249.54 2.27E-18 301973000 977309 853651 570124 725375 788549 686693 931124 1170744 1000672 FALSE TRUE 848155.1395 848043.3104 845837.8734 890082.4804 772858.4177 713110.5241 840823.7378 920389.5063 882373.6961 0.961219881 0.961093145 0.958593708 1.008736417 0.875885604 0.808172917 0.952911155 1.043083571 1 19.75103026 1.864267953 5.442692087 1.021027203 0.929167783 0.31413835 0.055562409 0.277356839 10.77812149 0.031363915 0.016157109 73.15903247 -1.864267953 -0.09185942 KEDLRPSAPQQEGEASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KEDLRPSAPQQEGEASK 17 2 O76070 O76070 SNCG Gamma-synuclein 0 ;;;;; 244.1 9.62E-21 10234680000 8591030 7566900 6892950 8518560 7549270 5344715 9991830 12074210 14161860 FALSE TRUE 7455703.619 7517192.536 10226403.68 10452829.25 7399054.297 5550329.645 9022823.864 9492234.153 12487661.04 0.597045643 0.601969617 0.818920664 0.837052608 0.592509219 0.44446511 0.722539139 0.760129068 1 23.57399995 1.242505071 1.896796946 1.112155849 0.659432951 0.47035911 0.114683406 0.836661623 2.89616713 0.682214664 0.034077635 17.47853673 -1.242505071 -0.452722898 KEDLVFIFWAPESAPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEDLVFIFWAPESAPLK 17 1 G3V1A4;E9PQB7;P23528;E9PP50;E9PK25;Q9Y281;Q9Y281-3 G3V1A4;P23528;Q9Y281 CFL1;CFL2 Cofilin-1;Cofilin-2 0 ; 199.76 2.08E-11 15637900000 42118200 31767900 24351700 30608100 22798300 18226100 38629500 45170500 40361500 FALSE TRUE 36552173.16 31559214.57 36128263.57 37558136.92 22344658.43 18927269.86 34883217.04 35511140.09 35590009.45 1.027034657 0.886743641 1.015123742 1.055299999 0.627835136 0.531814129 0.980140707 0.997783947 1 25.08496898 KEDLYLKPIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEDLYLKPIQR 11 2 P13639 P13639 EEF2 Elongation factor 2 0 ; 188.59 1.73E-06 15199700000 4068500 3531400 2378800 3360500 3185600 2926700 4389000 5242000 4636900 FALSE TRUE 3530837.417 3508202.001 3529195.637 4123552.887 3122212.793 3039292.043 3963355.456 4121039.093 4088730.964 0.863553373 0.858017324 0.863151835 1.00851656 0.763614143 0.743333829 0.969336327 1.00790175 1 21.96322171 2.055498504 10.39202242 0.999769596 0.854288805 0.480374978 0.070368016 0.394302181 71.60893989 0.029947078 0.020174599 113.6314384 -2.055498504 -0.145480791 KEDMEYALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KEDMEYALR 9 1 Q13242;H0YIB4 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 ;;; 136.02 0.00032775 6540790000 7486710 6348310 4496480 5432850 5943580 5090970 6914350 7780470 7439110 FALSE TRUE 6497322.305 6306607.534 6670992.768 6666461.628 5825314.386 5286822.91 6243797.401 6116677.038 6559666.89 0.99049577 0.96142192 1.01697127 1.016280512 0.888050336 0.805959052 0.951846718 0.93246763 1 22.64519112 3.241136502 24.99941288 0.914993468 0.995278693 0.379749554 0.051191216 78.92830809 766007.17 0.015954649 0.019651061 1742.354422 -3.241136502 0.080285224 KEDMMFHKIY(ph)IQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KEDMMFHKIYIQK 13 2 O43306-2;O43306 O43306-2 ADCY6 Adenylate cyclase type 6 1 KEDMMFHKIY(1)IQK;KEDMMFHKIY(1)IQK;KEDMMFHKIY(1)IQK;KEDMMFHKIY(1)IQK 74.326 0.012537 1281889000 1926443 2342839 401004 731270 2498731 2787986 1867216 2311736 114590.2 TRUE FALSE 1671858.677 2327448.736 594930.8757 897316.0303 2449011.142 2895241.625 1686133.68 1817389.246 101043.4771 16.54593374 23.03413148 5.88787018 8.880494378 24.23720177 28.65342433 16.68720959 17.98621048 1 16.62461667 1.238099493 24.99711723 0.999981083 17.76377232 0.377380473 6.756953446 13.16277785 712760.2593 9.957620404 1.738675422 17.30212688 -1.238099493 16.76379123 KEDMTYAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KEDMTYAVR 9 1 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;;;; 164.33 1.00E-04 7203800000 9722560 8517500 5073410 6284920 8347940 7278950 8783630 9643360 9402160 FALSE TRUE 8437699.062 8461547.982 7526928.046 7712007.145 8181832.326 7558975.917 7931794.915 7581202.509 8290647.356 1.01773706 1.020613665 0.907881824 0.930205666 0.986874966 0.911747369 0.956715993 0.914428293 1 22.98305332 4.254274111 24.86977147 0.941911968 1.019175435 0.505372893 0.030875258 167.0744573 264423.9956 0.007171691 0.018834402 17958.66754 -4.254274111 0.077263467 KEDQDRS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEDQDRSPR 9 2 O60318 O60318 MCM3AP Germinal-center associated nuclear protein 1 KEDQDRS(1)PR;KEDQDRS(1)PR 94.122 0.0070376 225850000 494200 404100 276020 335470 281050 369170 421570 544610 428810 TRUE FALSE 428890.2179 401445.4405 409504.1952 411643.5908 275457.6549 383372.2088 380686.2063 428149.3897 378116.5703 1.134280409 1.061697561 1.083010445 1.088668477 0.728499295 1.013899519 1.006795883 1.13232115 1 18.52847155 3.401095895 24.99989577 0.991664712 1.089290976 0.235195719 0.1014661 68.43496842 22501.31075 0.031436518 0.040584378 2518.232907 -3.401095895 0.097626264 KEDQYMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KEDQYMK 7 1 P53004 P53004 BLVRA Biliverdin reductase A 0 ;; 128.69 0.0059864 1117490000 2005610 1455670 1162450 1464890 1324580 1134220 1890620 2314360 2241950 FALSE TRUE 1740563.557 1446107.608 1724614.708 1797515.664 1298223.449 1177854.177 1707267.963 1819452.124 1976909.225 0.880446879 0.731499246 0.872379311 0.909255539 0.656693506 0.595805899 0.863604632 0.920351881 1 20.9148152 1.752047908 2.696922797 0.975564724 0.776495972 0.361400874 0.100808656 0.282508351 4.164944328 0.084522197 0.029378909 56.49992972 -1.752047908 -0.199068752 KEDYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEDYLR 6 1 A0A2R8Y7M0;P82094;P82094-2;F8WF45 A0A2R8Y7M0 TMF1 TATA element modulatory factor 0 ; 100.37 0.060508 393360000 519240 555330 319660 411090 468870 534320 532310 584750 446000 FALSE TRUE 450621.1184 551682.0007 474248.6452 504434.2676 459540.4043 554875.6362 480686.6581 459705.763 393274.3881 1.145818625 1.402791581 1.205897611 1.282652222 1.168498174 1.41091221 1.222267894 1.16891864 1 18.58517671 1.314749371 1.797208394 0.933646036 1.269634052 0.479858989 0.087695446 0.616212917 2.182288195 0.342845005 0.022484285 20.64188578 -1.314749371 0.335988015 KEECPAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KEECPAVR 8 1 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 ;;;;; 172.23 0.0004566 4722260000 7299070 6188630 5105460 7036270 5667840 6867000 6234280 6167630 9413710 FALSE TRUE 6334479.406 6147976.482 7574477.533 8633962.646 5555061.073 7131177.934 5629680.485 4848730.321 8300831.928 0.763113801 0.740645821 0.912496193 1.040132209 0.669217389 0.859091956 0.678206779 0.584125828 1 22.9848245 3.180166089 24.9999999 0.735432163 0.858744662 0.113019213 0.139333498 149.8328444 64145.79947 0.043033605 0.048795547 1514.140196 -3.180166089 0.123312499 KEEEDDDMKELENWAGSM ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KEEEDDDMKELENWAGSM 18 2 Q9H444 Q9H444 CHMP4B Charged multivesicular body protein 4b 0 118.24 0.00043077 45091000 183900 122880 141780 122250 118430 102970 176400 201490 167920 FALSE TRUE 159597.1491 122072.7932 210345.2822 150008.731 116073.4747 106931.3225 159292.7552 158402.9315 148068.6889 1.077858866 0.824433539 1.42059259 1.013102311 0.783916408 0.722173765 1.075803104 1.069793571 1 17.17590707 5.087269925 19.31855564 0.995873862 5.056103436 0.019094367 0.194873788 1967.100512 433793.4306 0.047230947 1322.894079 122255.9276 -5.087269925 4.060229573 KEEELQAALAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KEEELQAALAR 11 1 P35579;P35749;P35749-2;P35749-4;P35749-3;Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 P35579;P35749;Q7Z406 MYH9;MYH11;MYH14 Myosin-9;Myosin-11;Myosin-14 0 ;;;; 213.38 4.38E-09 5046210000 5576060 4462050 3538880 4973440 4168940 3783080 4549800 5481260 9692680 FALSE TRUE 4839169.543 4432738.5 5250294.205 6102735.566 4085986.25 3928617.536 4108561.096 4309135.204 8546822.412 0.566195167 0.518641699 0.6142978 0.714035611 0.478070803 0.459658262 0.480712117 0.504179799 1 23.02695672 1.235876662 24.99995505 1.000000612 0.539669224 0.781746418 0.076048547 36.75216757 342262.1275 0.134839879 0.020148388 17.2137964 -1.235876662 -0.460331388 KEEENADS(ph)DDEGELQDLLSQDWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KEEENADSDDEGELQDLLSQDWR 23 1 Q96NB3;J3QQQ3 Q96NB3 ZNF830 Zinc finger protein 830 1 KEEENADS(1)DDEGELQDLLSQDWR;KEEENADS(1)DDEGELQDLLSQDWR;KEEENADS(1)DDEGELQDLLSQDWR;KEEENADS(1)DDEGELQDLLSQDWR;KEEENADS(1)DDEGELQDLLSQDWR;KEEENADS(1)DDEGELQDLLSQDWR 287.72 5.88E-53 1930120000 779708 555174 436781 478422 550744 464929 623976 746223 678262 TRUE FALSE 676667.6123 551527.0254 648009.7525 587055.0273 539785.2719 482815.1195 563462.9036 586649.0186 598078.639 1.131402408 0.922164728 1.083485867 0.981568291 0.90253227 0.807276983 0.942121766 0.980889435 1 19.18997567 8 0.676858509 0.938458246 19.15052295 0.364628952 0.072340451 324.4214279 1.901812364 0.031247866 8900.917541 99999999.97 -8 18.2120647 KEEEVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEEEVER 7 1 D6RCC6;E7EUJ7;Q8TC20-2;Q8TC20-4;Q8TC20;Q8TC20-3;Q8TC20-5 D6RCC6 CAGE1 Cancer-associated gene 1 protein 0 ; 84.476 0.034502 2002740000 2695910 2227710 1484740 1812390 1719640 1601900 2624450 2983020 2503800 FALSE TRUE 2339638.663 2213076.026 2202765.23 2223920.85 1685422.528 1663526.13 2369931.243 2345124.387 2207803.616 1.059713213 1.002388079 0.997717919 1.007300121 0.763393318 0.753475589 1.073433898 1.06219791 1 21.07418042 KEELLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KEELLK 6 1 P42766;F2Z388 P42766 RPL35 60S ribosomal protein L35 0 ;;; 102.72 0.056601 4395600000 7306700 5509900 3942640 4795670 5017070 4508230 7470600 8456900 7368100 FALSE TRUE 6341101.082 5473705.104 5849313.891 5884600.171 4917240.123 4681664.525 6746102.362 6648457.747 6497051.612 0.975996723 0.84249063 0.900302821 0.905733942 0.756841782 0.720582936 1.038332888 1.023303822 1 22.63135374 2.210880808 24.99628319 1.021861465 0.850509779 0.548246294 0.072836472 166.800172 150627.8878 0.031041034 0.020933051 162.5102687 -2.210880808 -0.171351687 KEELMFFLWAPELAPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEELMFFLWAPELAPLK 17 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ; 128.69 5.79E-05 627620000 895170 762770 617927 742040 591518 525230 975320 1063110 1048020 FALSE TRUE 776871.0164 757759.3136 916758.564 910531.5234 579747.9491 545435.938 880733.6165 835772.1996 924124.2695 0.840656438 0.819975558 0.992029529 0.985291214 0.627348473 0.590219255 0.953046734 0.904393735 1 19.81772734 KEELTLEGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEELTLEGIR 10 1 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3KTB5;J3KTN0 P60842;J3KTN0 EIF4A1 Eukaryotic initiation factor 4A-I 0 ; 136.53 0.00018476 2274100000 3337000 3149700 1712380 2471800 3077200 2381500 4296300 3954300 3850700 FALSE TRUE 2896006.995 3129009.413 2540492.696 3033059.969 3015969.74 2473117.846 3879645.487 3108703.717 3395474.633 0.852901968 0.921523425 0.74819958 0.893265389 0.888232152 0.728357038 1.142592982 0.915543202 1 21.69518182 2.244031023 24.99999328 1.002880252 0.843120886 0.516856655 0.08173719 110.232372 503769.3345 0.029413858 0.022113786 175.4005793 -2.244031023 -0.159759365 KEENLADWYSQVITK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEENLADWYSQVITK 15 1 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 209.67 3.64E-09 1672260000 3475400 2887900 2068180 2678100 2786600 2168050 3419200 4258800 3808200 FALSE TRUE 3016117.084 2868929.195 3068358.766 3286203.537 2731152.112 2251456.286 3087606.51 3348088.762 3357998.934 0.898188815 0.854356791 0.9137462 0.978619589 0.813327272 0.670475581 0.919478109 0.997048786 1 21.67917034 1.999197748 24.9999843 0.986298574 0.855672767 0.356610187 0.079367098 33.75334022 1051845.195 0.035284168 0.023463931 99.81544525 -1.999197748 -0.130625806 KEEPSNNVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEEPSNNVK 9 1 Q14974;Q14974-2;J3KTM9;J3QRG4 Q14974 KPNB1 Importin subunit beta-1 0 ; 131.82 0.000517 412080000 364310 300256 199826 190074 212609 226078 336540 379710 345840 FALSE TRUE 316165.5105 298283.5986 296462.522 233233.2068 208378.4969 234775.367 303902.4026 298511.9714 304955.1892 1.036760553 0.978122718 0.972151098 0.764811405 0.683308579 0.769868411 0.996547734 0.978871592 1 18.21823774 2.208621962 24.98035219 0.989309347 0.864248265 0.224961826 0.108618069 350.0669423 292088.0031 0.050371221 0.033965339 161.6672168 -2.208621962 -0.125061083 KEEQEVQATLESEEVDLNAGLHGNWTLENAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KEEQEVQATLESEEVDLNAGLHGNWTLENAK 31 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 196.45 8.86E-26 100920000 79261 62207 42422 57915 56235 41723 73187 91981 77124 FALSE TRUE 68786.45803 61798.35812 62937.42109 71065.48593 55116.03352 43328.11081 66089.336 72311.57895 68006.48858 1.011469045 0.908712675 0.925462002 1.044980963 0.810452571 0.637117306 0.97180927 1.063304112 1 16.05338478 2.006152868 24.9993982 1.030588697 0.888046614 0.221926287 0.111893205 227.5813818 924669.6104 0.048505929 0.032605828 101.4268337 -2.006152868 -0.142542083 KEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK 41 1 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ;; 158.01 1.83E-16 2430015000 249912 193723.1 123337 183955.5 188628.8 125074.5 240319.1 281030 237078.1 FALSE TRUE 216885.496 192450.5202 182983.1857 225725.4079 184875.4559 129886.1969 217012.9907 220933.9215 209050.9971 1.037476496 0.920591257 0.875304056 1.079762407 0.884355772 0.621313453 1.03808637 1.056842228 1 17.6734954 KEES(ph)DEEETASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KEESDEEETASK 12 1 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 KEES(0.712)DEEET(0.287)AS(0.001)K;KEES(0.994)DEEET(0.006)ASK;KEES(0.479)DEEET(0.384)AS(0.137)K 226.7 1.56E-11 388274000 851800 620550 618510 583630 556360 450180 897710 999720 977130 TRUE FALSE 739232.4718 616473.5662 917623.5048 716152.1117 545289.5245 467498.7159 810650.2224 785937.6578 861614.8046 0.857961664 0.715486274 1.065004338 0.831174334 0.632869261 0.542584358 0.940849923 0.912168238 1 19.71668351 2.074587869 24.99998231 0.942861689 0.777633099 0.261145029 0.139910765 58.64849169 19655.5852 0.060760186 0.040964657 118.7374913 -2.074587869 -0.16522859 KEES(ph)EES(ph)DDDMGFGLFD ddPTM_MDA-MB-175_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 184.6 4.19E-10 16048554000 39653710 32178929 23816665 26842654 36598135 28257817 42465303 48540239 43514554 TRUE FALSE 34413371.75 31967543.5 35334483.86 32937688.85 35869903.72 29344913.51 38347024.45 38160286.63 38370313 0.896874929 0.833132206 0.920880782 0.858415954 0.934834796 0.764781708 0.999393058 0.994526332 1 25.1934872 2.197013661 24.99995319 0.997314451 0.871546571 0.625402581 0.047313279 87.24262502 52495.69459 0.017586943 0.011857237 157.4032377 -2.197013661 -0.12576788 KEES(ph)EESDDDMGFGLFD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KEESEESDDDMGFGLFD 17 1 P05387;H0YDD8;P05386-2;P05386 P05387;P05386 RPLP2;RPLP1 60S acidic ribosomal protein P2;60S acidic ribosomal protein P1 1 KEES(0.579)EES(0.421)DDDMGFGLFD;KEES(0.642)EES(0.358)DDDMGFGLFD;KEES(0.938)EES(0.062)DDDMGFGLFD;KEES(0.816)EES(0.184)DDDMGFGLFD;KEES(0.621)EES(0.379)DDDMGFGLFD;KEES(0.704)EES(0.296)DDDMGFGLFD 195.78 1.76E-11 1721316000 1685579 1356407 1116907 1275525 1496163 1226749 1735380 2138730 1809720 TRUE FALSE 1462825.464 1347496.673 1657046.961 1565152.446 1466392.283 1273942.828 1567083.115 1681379.233 1595776.963 0.916685413 0.844414166 1.038395089 0.980809024 0.918920574 0.798321355 0.982018885 1.053643004 1 20.60582759 2.005939014 24.99517917 1.026806504 0.918979828 0.330644222 0.06637052 170.3753153 717045.3334 0.028204282 0.018956322 101.3769018 -2.005939014 -0.107826675 KEES(ph)PPPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KEESPPPPK 9 1 P78332;E9PGM9;P78332-2 P78332 RBM6 RNA-binding protein 6 1 KEES(1)PPPPK;KEES(1)PPPPK;KEES(1)PPPPK 83.769 0.0097665 958030000 3445560 2291260 2003700 2041860 2132040 1837280 3230000 3743020 3120360 TRUE FALSE 2990220.516 2276208.562 2972696.022 2505495.521 2089616.575 1907961.35 2916755.097 2942604.301 2751474.596 1.086770171 0.827268609 1.080401043 0.910601001 0.759453341 0.693432298 1.06006979 1.069464463 1 21.39177358 KEESEES(ph)DDDMGFGLFD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 KEESEESDDDMGFGLFD 17 1 P05387;H0YDD8;P05386-2;P05386 P05387;P05386 RPLP2;RPLP1 60S acidic ribosomal protein P2;60S acidic ribosomal protein P1 1 KEES(0.019)EES(0.981)DDDMGFGLFD;KEES(0.029)EES(0.971)DDDMGFGLFD;KEES(0.001)EES(0.999)DDDMGFGLFD;KEES(0.001)EES(0.999)DDDMGFGLFD;KEES(0.237)EES(0.763)DDDMGFGLFD;KEES(0.008)EES(0.992)DDDMGFGLFD;KEES(0.015)EES(0.985)DDDMGFGLFD;KEES(0.047)EES(0.953)DDDMGFGLFD;KEES(0.051)EES(0.949)DDDMGFGLFD;KEES(0.264)EES(0.736)DDDMGFGLFD;KEES(0.037)EES(0.963)DDDMGFGLFD;KEES(0.02)EES(0.98)DDDMGFGLFD;KEES(0.069)EES(0.931)DDDMGFGLFD;KEES(0.156)EES(0.844)DDDMGFGLFD 219.68 3.04E-14 7133085000 10429220 8871204 7414109 8479027 10195678 8485149 12166170 14558020 12797270 TRUE FALSE 9050972.153 8812928.477 10999596.91 10404319.67 9992803.955 8811578.173 10986296.71 11444900.71 11284391.32 0.802078898 0.780983947 0.974762094 0.922009826 0.885542133 0.780864286 0.973583457 1.014224019 1 23.42782527 -2 0.250136241 2.216551867 0.814778771 0.415473044 0.068649392 85.19159269 1.362602835 48.84214851 0.240387533 0.01 2 -1.401773096 KEESEKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KEESEKPR 8 2 P83916;J3KS05;K7ELA4 P83916 CBX1 Chromobox protein homolog 1 0 ;;; 99.802 0.0036867 503364000 516713 378738 282749 342826 201645 255914 467867 568269 533850 FALSE TRUE 448428.0679 376250.0451 419487.3621 420669.8831 197632.659 265759.1772 422493.3304 446749.0966 470738.8612 0.952604735 0.799275514 0.891125413 0.893637466 0.41983502 0.564557548 0.897511052 0.949038062 1 18.84456743 2.015838209 24.86103147 0.95659763 0.751210341 0.257665578 0.159625067 321.8660894 505226.9562 0.070921655 0.047799155 103.714197 -2.015838209 -0.205387289 KEESETANKNDSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KEESETANKNDSSK 14 2 Q02880;Q02880-2;E9PCY5 Q02880 TOP2B DNA topoisomerase 2-beta;DNA topoisomerase 2 0 78.95 0.011502 77941000 68669 35533 34713 39843 26481 23752 56434 65156 28568 FALSE TRUE 59594.21766 35299.58138 51500.32291 48889.96211 25954.07991 24665.75481 50961.03937 51222.89644 25190.72358 2.365720757 1.401292871 2.044416181 1.94079229 1.030303073 0.979160234 2.02300816 2.03340314 1 14.62060494 4.748847122 23.69989125 1.608431868 2.365721647 0.237811004 0.446757648 1194.612253 2752244.523 0.113622465 1.468861346 56085.05138 -4.748847122 0.75728978 KEETPGT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KEETPGTPK 9 1 Q99442 Q99442 SEC62 Translocation protein SEC62 1 KEET(0.128)PGT(0.872)PK;KEET(0.022)PGT(0.978)PK;KEET(0.001)PGT(0.999)PK;KEET(0.064)PGT(0.936)PK;KEET(0.057)PGT(0.943)PK;KEET(0.001)PGT(0.999)PK 91.62 0.0074461 3260533000 6669530 5329978 6234091 8858570 7079630 5816250 6171830 13053220 17138800 TRUE FALSE 5788134.712 5294965.024 9248918.259 10870043.71 6938759.214 6040004.901 5573286.877 10261890.48 15112670.59 0.382998801 0.350365939 0.611997609 0.719266899 0.459135212 0.399664961 0.368782396 0.679025618 1 23.84925529 1.369179386 2.810322826 1.033640719 0.478641487 0.679986552 0.116702637 0.21710537 2.44922623 0.241778842 0.033407604 23.39803499 -1.369179386 -0.554999232 KEFSPFGTITSAK ddPTM_MDA-MB-175_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 ; 200.55 1.75E-07 2009800000 4001700 3278400 2205800 2827900 3023600 2736800 3865100 4584900 3587500 FALSE TRUE 3472865.206 3256863.975 3272532.258 3470017.917 2963436.276 2842086.467 3490263.197 3604454.815 3163389.837 1.097830298 1.029548725 1.03450173 1.096930222 0.936791363 0.898430675 1.103330091 1.139427956 1 21.59303993 KEGGLGPLNIPLLADVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEGGLGPLNIPLLADVTR 18 1 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ; 166.06 4.27E-11 4101000000 7406700 5614800 3496600 4379600 5961300 5387200 6091200 7304800 4562400 FALSE TRUE 6427885.829 5577916.009 5187567.455 5374055.118 5842681.793 5594449.07 5500476.362 5742725.366 4023038.27 1.597768999 1.3864934 1.289465103 1.335820034 1.452305795 1.390602996 1.367244354 1.427459791 1 21.93985403 1.236137136 24.99790246 0.999999477 1.399632048 0.707827965 0.081866435 36.86525648 380175.8711 0.129266945 0.019685498 17.2241237 -1.236137136 0.399632571 KEGVFAK ddPTM_MDA-MB-175_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 ; 91.069 0.026738 3144000000 4784400 3805900 4242000 3552000 3593800 3228800 4772500 4955900 5284400 FALSE TRUE 4152129.418 3780898.792 6293445.389 4358535.889 3522290.411 3353014.025 4309663.685 3896119.352 4659684.252 0.891075273 0.811406651 1.350616275 0.935371509 0.755907529 0.719579663 0.924883201 0.836133768 1 22.15180077 3.476334051 24.99952333 0.845364997 1.021390744 0.197125128 0.157624668 41.90788306 1330841.891 0.045359696 0.059096146 2994.567115 -3.476334051 0.176025746 KEIHTVPDMGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEIHTVPDMGK 11 1 Q15257;Q15257-2;A6PVN5;Q15257-3;Q15257-4;Q5T948;Q5T949;A6PVN6;Q68CR8 Q15257 PPP2R4;DKFZp781M17165 Serine/threonine-protein phosphatase 2A activator 0 ; 105.65 0.0015822 2105020000 3202290 2582810 1805080 2260600 2398720 1910110 3146800 3735500 3299100 FALSE TRUE 2779099.263 2565843.351 2678022.726 2773903.781 2350990.165 1983593.168 2841623.82 2936692.395 2909084.156 0.955317589 0.882010699 0.920572449 0.953531638 0.808154745 0.681861734 0.976810456 1.009490354 1 21.4721336 2.025634681 24.99301867 1.001741427 0.86780366 0.373753588 0.079014647 233.0465112 227212.1026 0.034123566 0.023005297 106.0802858 -2.025634681 -0.133937767 KEIMDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KEIMDLK 7 1 A0A087X0P0;Q02224-3;Q02224 A0A087X0P0 CENPE Kinesin-like protein;Centromere-associated protein E 0 93.178 0.024253 1971300000 3487800 3160000 2384400 2626200 2833900 2139500 3881900 4264100 4781600 FALSE TRUE 3026878.393 3139241.752 3537503.815 3222518.849 2777510.934 2221807.949 3505433.935 3352255.398 4216324.695 0.717894994 0.744544592 0.839001754 0.764295703 0.65875167 0.526953712 0.831395632 0.79506576 1 22.00755454 1.1657374 1.543961116 1.145400191 0.721071688 0.498070488 0.087282327 1.254680516 2.324128813 0.868092493 0.026476801 14.64661952 -1.1657374 -0.424328503 KEKPELSEPSHLNGPSS(ph)DPEAAFLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KEKPELSEPSHLNGPSSDPEAAFLSR 26 2 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 KEKPELSEPSHLNGPS(0.071)S(0.929)DPEAAFLSR;KEKPELSEPSHLNGPS(0.145)S(0.855)DPEAAFLSR;KEKPELSEPSHLNGPS(0.249)S(0.751)DPEAAFLSR;KEKPELSEPSHLNGPS(0.268)S(0.732)DPEAAFLSR;KEKPELSEPSHLNGPS(0.06)S(0.94)DPEAAFLSR 286.82 1.09E-61 1909750000 2310950 1834340 936453 1138100 1773890 1471990 2516980 2649080 722382 TRUE FALSE 2005552.102 1822290.1 1389324.803 1396523 1738593.06 1528618.408 2272883.667 2082594.857 636982.8229 3.148518343 2.860815134 2.181102462 2.192402918 2.729419063 2.399779637 3.568202446 3.269467845 1 19.28089494 KEKT(ph)PELPEPSVK ddPTM_MDA-MB-175_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 152.68 0.0021121 720310000 2056270 1228840 1302760 1109970 1336340 787920 1991550 2388150 1802650 TRUE FALSE 1784528.71 1220767.669 1932779.093 1362005.653 1309749.449 818231.7923 1798409.788 1877462.707 1589542.771 1.122667941 0.767999258 1.215933996 0.856853731 0.82397874 0.514759217 1.13140069 1.181133809 1 20.60018041 KELNYFAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KELNYFAK 8 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 102.55 0.0079279 1734850000 4370900 3955900 2362800 2600200 3564000 3276700 3611200 4374700 4337300 FALSE TRUE 3793274.491 3929913.432 3505457.983 3190615.152 3493083.373 3402756.769 3260986.38 3439204.449 3824549.335 0.991822607 1.027549415 0.916567594 0.834246044 0.913332021 0.88971444 0.852645918 0.899244368 1 21.86685833 4.158195412 5.16128141 0.894499402 1.009372815 0.510941475 0.044348168 0.142996962 6.525077062 0.011229829 0.024756522 14394.46116 -4.158195412 0.114873414 KELQAAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KELQAAGK 8 1 P06744;A0A2U3TZU2;P06744-2 P06744 GPI Glucose-6-phosphate isomerase 0 113.22 0.004635 570620000 1458300 1252400 754950 1082700 897450 954910 1502300 1930700 1636400 FALSE TRUE 1265581.96 1244172.902 1120046.345 1328543.583 879592.5008 991646.0056 1356607.177 1517834.83 1442946.656 0.877081599 0.862244558 0.776221588 0.92071566 0.609580747 0.687236774 0.940164469 1.051899475 1 20.46058654 2.045908931 5.684121531 1.020790715 0.789971079 0.550636968 0.091145675 0.137415446 10.48079366 0.04061125 0.026493091 111.1498627 -2.045908931 -0.230819636 KELQAEATVSGS(ph)PEAPGTNVVSEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KELQAEATVSGSPEAPGTNVVSEPR 25 1 Q9BZV1-2;Q9BZV1;K7EJ02 Q9BZV1-2 UBXN6 UBX domain-containing protein 6 1 KELQAEATVS(0.092)GS(0.908)PEAPGTNVVSEPR;KELQAEATVS(0.013)GS(0.987)PEAPGTNVVSEPR 190.82 4.86E-18 595250000 258070 277690 230050 253080 326100 354710 369200 425890 420180 TRUE FALSE 223965.3956 275865.8361 341302.9495 310545.6821 319611.248 368355.9232 333395.0408 334816.7378 370506.7991 0.604483902 0.744563492 0.921178641 0.838164597 0.862632612 0.994194774 0.899835149 0.903672318 1 18.49914049 5.350012987 0.752331987 0.929446165 8.31E-12 0.814804131 0.050482938 2.549180502 0.577423444 0.019193463 2.465831332 223878.8084 -5.350012987 -0.929446165 KELS(ph)PAGSISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KELSPAGSISK 11 1 A0A494C0Q6;A0A494C0K5;A0A494C0W0;O95453-2;O95453-3;O95453;O95453-4 A0A494C0Q6 PARN Poly(A)-specific ribonuclease PARN 1 KELS(1)PAGSISK 119.46 0.00035737 235170000 450730 367190 237140 290710 310230 286170 389860 486720 424410 TRUE FALSE 391164.8885 364777.9047 351821.6972 356720.1487 304057.03 297179.1451 352051.4372 382638.7157 374236.7333 1.045233815 0.974725013 0.940104661 0.95319384 0.812472435 0.794094002 0.94071855 1.022450983 1 18.51359165 4.643884457 1.557317524 0.923916556 1.076468554 0.239178604 0.07142394 1.622491066 4.314992519 0.023135457 0.358240563 44043.767 -4.643884457 0.152551998 KELSDIAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KELSDIAHR 9 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;; 166.55 3.94E-05 9403400000 18695870 17449280 9936500 13666780 17345400 15888870 18692360 21057200 20067000 FALSE TRUE 16225163.41 17334654.53 14741824.64 16770031.28 17000260.48 16500125.11 16879577.8 16554281.65 17694702.12 0.916950356 0.979652238 0.833120814 0.947743068 0.960754262 0.932489567 0.95393399 0.935550174 1 24.07681414 3.511280457 24.99873129 0.952679454 0.912473865 0.226459742 0.039210165 1014.529034 742459.8407 0.010265402 0.01521594 3245.491357 -3.511280457 -0.040205589 KEMGIQEVLMFET(ph)EDLVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KEMGIQEVLMFETEDLVLR 19 1 A0A0C4DGV2;A0A075B7B7;Q8NHY3-2;Q8NHY3 A0A0C4DGV2 GAS2L2 GAS2-like protein 2 1 KEMGIQEVLMFET(1)EDLVLR 46.578 0.079415 192610000 188390 185470 100150 85580 160330 280380 89986 93306 50871 TRUE FALSE 163493.7842 184251.6354 148582.875 105012.247 157139.7467 291166.4 81259.17157 73353.23801 44857.08833 3.64477032 4.107525526 3.312361112 2.341040199 3.50311963 6.490978591 1.811512396 1.635265255 1 15.45304836 4.011178573 5.04828961 2.797113567 3.856372586 0.082303731 1.491254607 0.514328862 38.22810093 0.42630745 0.869193151 10260.73739 -4.011178573 1.05925902 KEMQPTHPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KEMQPTHPIR 10 1 B7Z2E6;H0YB80;P63104-2;P27348;P31946-2;P31946;P63104;E7EX29;B0AZS6 B7Z2E6;P27348;P31946-2;P63104 YWHAZ;YWHAQ;YWHAB "14-3-3 protein zeta/delta;14-3-3 protein theta;14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 ;;;;;; 115.14 0.0008198 2788830000 3861750 3427304 2122691 2645104 3126442 3066779 3549480 3993240 3980340 FALSE TRUE 3351409.953 3404789.814 3149231.468 3245715.291 3064231.921 3184759.973 3205251.976 3139316.701 3509788.74 0.954875123 0.970083976 0.897270947 0.924760871 0.873053095 0.907393638 0.913232167 0.894446058 1 21.74295276 4.243659562 24.99958456 0.912201475 0.962479566 0.247325917 0.033461296 153.178587 750994.7569 0.007983852 0.019797839 17525.06195 -4.243659562 0.050278092 KENPLQFK ddPTM_MDA-MB-175_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 ; 172.23 0.0004566 6259700000 5113200 4423200 3307300 4487700 4135000 3383400 4770000 6240000 5457500 FALSE TRUE 4437477.665 4394143.708 4906721.342 5506700.875 4052721.59 3513561.587 4307406.134 4905624.56 4812320.567 0.922107662 0.913102867 1.019616477 1.144292197 0.842155366 0.730117942 0.895078803 1.019388566 1 22.19830132 KENQWCEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KENQWCEEK 9 1 E5RJR5;P63208 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ;; 175.49 8.64E-05 2599510000 2007900 1481050 1218340 1377270 1478600 1170450 1984240 2109050 2025940 FALSE TRUE 1742550.928 1471320.885 1807533.299 1690000.204 1449178.753 1215477.969 1791808.71 1658046.07 1786435.681 0.975434462 0.823606974 1.011809895 0.94601794 0.811212387 0.680392797 1.003007681 0.928130852 1 20.76865254 KENS(ph)ESEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KENSESEKR 9 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 KENS(0.975)ES(0.025)EKR 101.39 0.0020952 80325000 114210 51554 50537 45299 36191 40236 78793 90949 101900 TRUE FALSE 99116.85913 51215.33838 74976.86224 55584.8303 35470.86991 41783.90496 71151.66699 71500.26412 89853.49808 1.10309405 0.56998714 0.834434539 0.618616208 0.394763372 0.465022574 0.791863072 0.795742688 1 16.45528705 1.454700778 1.764707434 1.029116909 0.658504381 0.20517792 0.199741305 0.90943267 4.051812105 0.51924998 0.057313989 28.49054638 -1.454700778 -0.370612527 KENSESEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KENSESEKR 9 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 0 55.721 0.071225 18244000 48612 37093 23420 25952 15171 22981 38101 48149 31028 FALSE TRUE 42187.80103 36849.33364 34745.99034 31844.79825 14869.12678 23865.09394 34405.97088 37852.71105 27359.90519 1.541957136 1.346837037 1.269960188 1.163922098 0.543464119 0.872265228 1.257532533 1.383510315 1 14.73977561 4.112464499 1.815107032 1.06221489 1.489970772 0.364733796 0.228618864 0.529926938 3.324734796 0.075774077 0.255621273 12955.80788 -4.112464499 0.427755883 KENSETTLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KENSETTLTR 10 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 0 ;;; 161.1 1.15E-05 785393000 740820 792976 403226 634176 801243 820351 963592 1194120 967934 FALSE TRUE 642918.76 787766.8884 598227.4423 778175.3536 785299.8319 851910.4338 870142.9962 938766.7307 853505.9452 0.753268051 0.922977623 0.700906005 0.911739816 0.920087126 0.998130638 1.019492601 1.099894776 1 19.70304168 2.991047742 1.121803373 1.055746998 0.803653683 0.704004884 0.065488695 0.241686134 0.668905146 0.030859793 0.032862801 979.5976657 -2.991047742 -0.252093315 KEPAITSQNS(ph)PEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KEPAITSQNSPEAR 14 1 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;E5RIS7 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 1 KEPAITS(0.001)QNS(0.999)PEAR;KEPAITS(0.012)QNS(0.988)PEAR;KEPAITSQNS(1)PEAR;KEPAITSQNS(1)PEAR;KEPAITS(0.001)QNS(0.999)PEAR;KEPAITSQNS(1)PEAR 212.41 1.52E-09 3004290000 2266780 1884280 1347963 1751060 1870550 1721950 1959190 2335270 3611260 TRUE FALSE 1967219.28 1871902.041 1999842.415 2148664.936 1833329.715 1788194.531 1769188.055 1835890.684 3184340.957 0.617779097 0.587845983 0.628023959 0.674759696 0.575732856 0.561558751 0.55559002 0.576537095 1 21.60256339 1.236920476 24.99990828 1.0000005 0.5956123 0.926802747 0.035569973 11.41302586 173907.9459 0.059124763 0.009548593 17.25521902 -1.236920476 -0.4043882 KEPAVLELEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KEPAVLELEGK 11 1 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 0 ;; 155.98 5.02E-05 1754850000 4549200 4053420 3141160 3774530 3781570 2875830 4933500 5870000 6042700 FALSE TRUE 3948011.694 4026792.817 4660235.483 4631594.727 3706324.156 2986465.041 4455049.929 4614746.18 5328338.89 0.740946058 0.755731364 0.874613192 0.869238016 0.695587167 0.560487068 0.836104839 0.866075953 1 22.34525441 1.50041218 2.022471108 1.006252963 0.758274005 0.428549762 0.090764283 0.454126665 3.101626397 0.184803084 0.027345707 31.65280336 -1.50041218 -0.247978958 KEPEKPIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KEPEKPIDR 9 2 O00422;O00422-2;U3KQ12 O00422 SAP18 Histone deacetylase complex subunit SAP18 0 ;;; 110.38 0.0012914 1785950000 3700810 2526910 1997100 2309120 2259730 1749620 3007980 3710860 3330850 FALSE TRUE 3211738.582 2510310.562 2962904.24 2833440.989 2214765.794 1816929.014 2716266.563 2917321.467 2937080.708 1.093513901 0.854695806 1.008792245 0.964713357 0.754070458 0.618617326 0.924818496 0.99327249 1 21.48595148 7.642558945 1.139020696 0.88651817 199.9999999 0.198016207 0.124485131 3203.694626 5.421159036 0.040150006 1665123.459 43909545.82 -7.642558945 199.1134817 KEPFFHGHDNYDQLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEPFFHGHDNYDQLVR 16 1 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2 P68400 CSNK2A1 Casein kinase II subunit alpha 0 ; 186.85 5.83E-10 405120000 307560 245780 173048 273917 283220 240072 238523 309470 297120 FALSE TRUE 266915.1667 244165.455 256734.5916 336114.0414 277584.4761 249307.7252 215391.0762 243292.2488 261994.8121 1.018780351 0.931947671 0.979922425 1.282903424 1.059503713 0.951575045 0.822119623 0.928614757 1 17.99917872 2.64464079 4.37471196 0.912684117 1.056127611 0.292771661 0.100282282 0.301336916 10.05465293 0.037767575 0.033157104 441.2053707 -2.64464079 0.143443494 KEPVDEDLYPEHYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KEPVDEDLYPEHYR 14 1 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 86.378 0.0047801 174370000 614880 510030 384290 513840 517690 434850 592820 690400 697080 FALSE TRUE 533622.0501 506679.5793 570133.9294 630515.2256 507388.9818 451578.9609 535328.4076 542763.3327 614671.9965 0.868141144 0.824308871 0.927541734 1.025775095 0.825462986 0.734666559 0.870917189 0.88301295 1 19.22945723 1.222797285 3.422497448 1.022864517 0.868508058 0.233334859 0.0745051 0.572141894 9.345637068 0.238872168 0.020429667 16.70310784 -1.222797285 -0.154356458 KEQLADAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KEQLADAR 8 1 P11387 P11387 TOP1 DNA topoisomerase 1 0 73.985 0.067585 258350000 1411200 1332100 974990 1553700 1430600 1413900 1284300 1750300 1751800 FALSE TRUE 1224706.344 1323349.347 1446498.425 1906491.332 1402133.859 1468293.648 1159748.784 1376011.966 1544704.2 0.792841985 0.856700815 0.93642422 1.23421127 0.907703792 0.950533862 0.750790206 0.89079318 1 20.55889917 1.227292488 23.69988392 1.000000362 0.915873346 0.041138206 0.128905233 1128.561528 2373358.389 0.467307507 0.032954559 16.87689263 -1.227292488 -0.084127016 KEQQLQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KEQQLQER 8 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 142.43 0.00099036 120730000 245470 274280 133770 215690 245620 256370 297310 323890 329380 FALSE TRUE 213030.5176 272478.2366 198461.6194 264665.7111 240732.6425 266232.7198 268476.922 254628.644 290441.0716 0.733472426 0.938153255 0.683311139 0.911254423 0.828851929 0.916649695 0.924376571 0.876696407 1 18.14788596 -1.999999917 0.125454812 1.586643996 0.689108754 0.373358493 0.076283836 228.1691104 2.529533671 35.78760875 2.153677815 0.010000002 1.999999917 -0.897535243 KEQSEVSVS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KEQSEVSVSPR 11 1 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 KEQSEVS(0.001)VS(0.999)PR;KEQSEVS(0.001)VS(0.999)PR;KEQSEVSVS(1)PR;KEQSEVS(0.001)VS(0.999)PR 160.79 1.66E-05 3595720000 7554400 5773800 3987530 4922350 5831900 5330000 6461800 7521600 7131600 TRUE FALSE 6556066.9 5735871.528 5915912.845 6040044.801 5715856.6 5535048.549 5835135.631 5913164.373 6288510.372 1.042546885 0.912119276 0.940749477 0.960488962 0.908936499 0.880184371 0.927904271 0.940312415 1 22.58428688 4.745199772 24.74456675 0.93265883 1.042546943 0.53300199 0.031962101 547.8022701 2041632.929 0.007945909 0.073603879 55616.00276 -4.745199772 0.109888113 KEQTPEHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KEQTPEHGK 9 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 65.5 0.043092 88164000 258820 209670 164670 185400 150100 152810 224990 290550 347910 FALSE TRUE 224616.2812 208292.664 244304.9628 227497.9037 147113.3037 158688.6996 203170.5044 228418.1436 306780.4761 0.732172673 0.678963233 0.796351078 0.741565782 0.479539329 0.517271182 0.662266735 0.744565451 1 18.22684715 1.238793743 2.305051595 1.094803817 0.65618858 0.552277906 0.096600568 0.524974528 2.896631651 0.47389191 0.028495119 17.32980766 -1.238793743 -0.438615237 KES(ph)APQVLLPEEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KESAPQVLLPEEEK 14 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 1 KES(1)APQVLLPEEEK;KES(1)APQVLLPEEEK 102.07 0.00073214 262020000 1135030 804200 973220 1085590 911360 714950 1407320 1543460 1784490 TRUE FALSE 985032.9097 798917.1572 1443872.447 1332089.802 893225.719 742454.5891 1270838.323 1213403.09 1573529.625 0.626002138 0.507722984 0.917601057 0.846561628 0.567657389 0.471840236 0.80763546 0.77113457 1 20.58557291 1.217956252 1.476937761 1.141858273 0.671886684 0.340549683 0.143822519 1.625439938 3.02406249 1.16432826 0.044187367 16.517954 -1.217956252 -0.469971589 KES(ph)YSVYVYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 1 KES(0.994)YS(0.006)VYVYK 116.51 0.0012041 0 521190 454600 317730 429240 394300 241880 511920 576380 571760 TRUE FALSE 452313.421 451613.7027 471385.2907 526705.5025 386454.2014 251185.2801 462274.0772 453125.6224 504167.1842 0.897149666 0.895761797 0.934978129 1.044704057 0.766519943 0.498218226 0.916906319 0.898760643 1 18.94354269 3.221911977 24.99945419 0.818084735 0.939180095 0.174668971 0.137091088 496.2304779 745133.4306 0.044797437 0.050931012 1666.909326 -3.221911977 0.121095361 KESYSALMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KESYSALMR 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 ; 117.02 0.0019546 1023870000 1181980 1270350 770660 891860 1284830 1172170 1283390 1352940 953100 FALSE TRUE 1025778.348 1262004.987 1143353.754 1094370.444 1259264.397 1217264.138 1158927.035 1063624.31 840425.6038 1.220546285 1.501626059 1.360446122 1.302162189 1.498365103 1.448390117 1.378976355 1.265578184 1 19.68076059 1.244754684 1.911600765 0.868858621 1.394667565 0.673871027 0.085332084 0.462413197 1.638078035 0.43951905 0.02235287 17.56930913 -1.244754684 0.525808944 KESYSIYVYK ddPTM_MDA-MB-175_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 ; 127.37 0.00057371 18495100000 10706700 8818300 4785490 8004000 8173200 6944200 7410500 10946000 8727900 FALSE TRUE 9291782.468 8760372.007 7099768.971 9821430.533 8010569.311 7211347.867 6691830.851 8605283.082 7696097.605 1.20733688 1.13828754 0.922515453 1.276157221 1.04086119 0.937013567 0.869509613 1.118135908 1 22.87569567 3.009508412 24.9495853 0.991747552 1.125669554 0.311551186 0.107871804 279.9451743 734555.9397 0.032667692 0.036995529 1022.135358 -3.009508412 0.133922002 KESYSVYVYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KESYSVYVYK 10 1 P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;P57053;Q99880 P58876;Q99880 HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;H2BFS;HIST1H2BL Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type F-S;Histone H2B type 1-L 0 ;;; 140.24 6.36E-05 67364020000 84311070 63491680 36979280 61614250 58362900 49618240 65009600 88096740 71689540 FALSE TRUE 73169148.48 63074598.97 54862583.5 75604707.18 57201592.48 51527085.8 58704979 69257937.72 63214484.25 1.15747442 0.997787133 0.867879951 1.196002911 0.904881107 0.815115181 0.928663418 1.095602354 1 25.91375182 KET(ph)ES(ph)EAEDNLDDLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KETESEAEDNLDDLEK 16 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KET(1)ES(1)EAEDNLDDLEK;KET(1)ES(1)EAEDNLDDLEK;KET(1)ES(1)EAEDNLDDLEK;KET(1)ES(1)EAEDNLDDLEK 288.91 2.12E-37 1857410000 3736380 2251620 2173870 1905690 2304180 2048650 3139640 3708330 3992570 TRUE FALSE 3242607.916 2236828.96 3225160.803 2338406.041 2258331.326 2127462.891 2835158.196 2915332.488 3520572.923 0.921045519 0.63535936 0.91608976 0.664211789 0.641466993 0.60429451 0.805311595 0.828084676 1 21.7473788 1.318334511 1.673626978 1.068900536 0.729933263 0.354605895 0.111753588 0.924129764 2.784465845 0.494117909 0.030904793 20.81299171 -1.318334511 -0.338967272 KET(ph)PPPLVPPAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KETPPPLVPPAAR 13 1 Q9BQA1;Q9BQA1-2 Q9BQA1 WDR77 Methylosome protein 50 1 KET(1)PPPLVPPAAR;KET(1)PPPLVPPAAR;KET(1)PPPLVPPAAR 67.646 0.030814 2343430000 3215710 2504590 1875980 2036050 3039970 2377900 3030960 3563580 3508100 TRUE FALSE 2790745.776 2488137.183 2783210.203 2498366.272 2979480.545 2469379.352 2737017.966 2801536.149 3093376.414 0.902168182 0.804343491 0.899732147 0.807650262 0.963180727 0.798279621 0.88479952 0.9056564 1 21.56075097 1.17915917 1.661911595 1.067720766 0.863088629 0.404534667 0.051626918 1.116084541 2.49708241 0.391117232 0.013089947 15.10633705 -1.17915917 -0.204632137 KETEFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KETEFLR 7 1 Q9Y2H1;F5H7Z3;F5GY51;I3L0D0;Q15208 Q9Y2H1;Q15208 STK38L;STK38 Serine/threonine-protein kinase 38-like;Serine/threonine-protein kinase 38 0 ; 87.308 0.031167 280150000 592640 544290 369920 430790 530320 521210 612130 636670 595720 FALSE TRUE 514321.1224 540714.5232 548814.5493 528607.4537 519767.6696 541261.286 552765.7268 500523.0751 525294.6602 0.979109748 1.029354692 1.044774659 1.006306543 0.989478304 1.030395561 1.052296489 0.952842496 1 19.00276739 1.726305857 16.17720141 0.976611042 1.019055284 0.327240392 0.025268333 0.150505256 174.8219879 0.01330725 0.006359687 53.24831347 -1.726305857 0.042444243 KETES(ph)EAEDNLDDLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 KETESEAEDNLDDLEK 16 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KET(0.205)ES(0.795)EAEDNLDDLEK;KET(0.029)ES(0.971)EAEDNLDDLEK;KETES(1)EAEDNLDDLEK;KET(0.233)ES(0.767)EAEDNLDDLEK;KET(0.112)ES(0.888)EAEDNLDDLEK;KET(0.001)ES(0.999)EAEDNLDDLEK;KET(0.124)ES(0.876)EAEDNLDDLEK;KET(0.311)ES(0.689)EAEDNLDDLEK;KET(0.066)ES(0.934)EAEDNLDDLEK;KET(0.007)ES(0.993)EAEDNLDDLEK 301.54 3.58E-46 18830450000 17380080 11853130 12089000 10439270 11804000 8538670 17086480 19763310 18557740 TRUE FALSE 15083258.39 11775266.01 17935280.84 12809665.81 11569123.49 8867158.16 15429435.8 15537079.95 16363865.12 0.921741794 0.71958953 1.096029618 0.782801967 0.706992108 0.541874312 0.942896784 0.949474946 1 23.96401021 2.034029651 24.99999572 0.963646324 0.795719645 0.237026743 0.143706015 270.003878 198358.1674 0.060373187 0.040703379 108.1507789 -2.034029651 -0.167926679 KETQS(ph)PEQVK ddPTM_MDA-MB-175_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 KETQS(1)PEQVK;KETQS(1)PEQVK;KETQS(1)PEQVK;KET(0.016)QS(0.984)PEQVK;KETQS(1)PEQVK;KET(0.009)QS(0.991)PEQVK;KET(0.011)QS(0.989)PEQVK;KETQS(1)PEQVK;KETQS(1)PEQVK 215.09 5.12E-09 17437700000 10166580 6918370 6439340 6962140 6170620 4828160 9130310 10383390 11342940 TRUE FALSE 8823040.694 6872922.772 9553426.362 8543000.297 6047836.735 5013902.439 8244853.941 8162982.852 10001990.56 0.882128477 0.687155495 0.955152508 0.85413001 0.604663312 0.501290459 0.824321308 0.816135829 1 23.25378381 1.235710893 1.94412255 1.080687754 0.752075897 0.241975781 0.134282728 1.297563334 4.692420008 0.785279443 0.038828812 17.20722718 -1.235710893 -0.328611857 KETQS(ph)PEQVKSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KETQSPEQVKSEK 13 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 KETQS(1)PEQVKSEK;KET(0.009)QS(0.991)PEQVKSEK;KET(0.018)QS(0.982)PEQVKSEK 172.97 1.17E-05 1185870000 5866680 3592340 2303930 1969630 3062280 2109990 5959720 6070930 697500 TRUE FALSE 5091383.374 3568741.682 3418118.254 2416864.595 3001346.619 2191162.681 5381747.272 4772708.864 615042.3446 8.27810218 5.802432488 5.557533208 3.929590567 4.879902409 3.56262085 8.750206094 7.75996792 1 19.23032622 4.755600807 2.903154989 5.406745005 8.841977782 0.165259574 2.160740119 0.94356434 10.9874063 0.563335753 7.756824359 56964.04314 -4.755600807 3.435232777 KETTSGTSTEPVKNSS(ph)PAPPQPAPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KETTSGTSTEPVKNSSPAPPQPAPGK 26 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 KETTSGTSTEPVKNS(0.168)S(0.832)PAPPQPAPGK;KETTSGTSTEPVKNS(0.177)S(0.823)PAPPQPAPGK 121.26 7.57E-05 501690000 534750 272224 204947 209788 256891 166913 376275 440490 133449 TRUE FALSE 464081.4326 270435.7426 304060.0547 257423.5718 251779.3717 173334.2511 339783.9084 346294.6414 117672.8112 3.94382889 2.298200746 2.583944851 2.1876215 2.139656298 1.473018697 2.887531154 2.942860273 1 16.84442149 5.445295722 1.504429243 2.23832874 11.99143819 0.456198289 0.59655769 8.545217206 3.745076289 0.16509958 208.9195821 278801.8951 -5.445295722 9.753109452 KETVESHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KETVESHFR 9 1 O94886 O94886 TMEM63A CSC1-like protein 1 0 ; 136.96 0.00011563 156237000 373432 344770 258419 319264 371025 390953 389798 502060 458160 FALSE TRUE 324082.015 342505.1832 383391.2928 391757.7708 363642.3284 405993.2149 351995.45 394698.376 403996.8467 0.802189467 0.847791724 0.948995755 0.969705021 0.900111799 1.004941544 0.871282667 0.976983804 1 18.62398451 4.334053365 3.16880529 0.952109431 0.809194778 0.632016369 0.041360703 0.14833482 2.856946844 0.0100795 0.033103795 21580.09562 -4.334053365 -0.142914653 KEVEVVEIIQATIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEVEVVEIIQATIIR 15 1 Q14764;H3BQK6;I3L155 Q14764 MVP Major vault protein 0 ; 162.4 2.56E-06 705370000 1054410 926760 669840 869880 818590 765710 1132390 1325020 1086540 FALSE TRUE 915067.047 920672.0525 993776.8645 1067399.549 802301.6605 795167.3592 1022570.992 1041674.784 958090.479 0.955094604 0.960944788 1.037247406 1.114090551 0.837396549 0.829950173 1.067301069 1.087240513 1 19.86980238 KEVLAS(ph)PDRLWGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEVLASPDRLWGSR 14 2 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 KEVLAS(0.984)PDRLWGS(0.016)R;KEVLAS(1)PDRLWGSR 149.12 5.96E-06 2374200000 1190410 1146680 586560 872850 1157130 917000 1149010 1556310 806790 TRUE FALSE 1033094.302 1139147.384 870222.3779 1071043.933 1134105.377 952277.5834 1037579.187 1223505.218 711412.2053 1.452173992 1.601248018 1.223232286 1.505518074 1.594160697 1.338573581 1.458478192 1.719826015 1 19.4403262 1.220946727 24.91595861 0.999998433 1.490931907 0.548933533 0.138589223 867.9916592 1227759.286 1.04379477 0.034181758 16.6320862 -1.220946727 0.490933474 KEVLASPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KEVLASPDR 9 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 78.342 0.048174 158070000 320990 288940 180140 216140 273090 238890 265760 302270 307630 FALSE TRUE 278570.3582 287041.9341 267256.3065 265217.8905 267656.0433 248080.2529 239986.6361 237631.9128 271262.3319 1.026940808 1.058171004 0.985231914 0.977717358 0.986705531 0.91454 0.884703138 0.876022525 1 18.0493292 3.3138011 0.942955942 0.907400286 1.038642894 0.568601607 0.038934908 0.385829278 0.770516474 0.019742478 0.032277765 2059.686392 -3.3138011 0.131242608 KEVQDEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 KEVQDEEK 8 1 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ;;;;;;; 150.35 0.00078659 18917310000 18873160 15824170 13736410 14385610 10505340 11105690 22480160 24218100 21242720 FALSE TRUE 16379024.09 15720219.99 20379383.82 17652082.62 10296304.29 11532933.08 20300037.54 19039247.78 18731429.84 0.874413978 0.839242926 1.087978013 0.942377745 0.549680637 0.615699558 1.083742016 1.016433232 1 24.15895769 2.203941805 24.99999255 1.031956782 0.824884198 0.306250989 0.152432785 257.423897 185897.0675 0.068800747 0.046387817 159.9343704 -2.203941805 -0.207072584 KEVS(ph)PEVVR ddPTM_MDA-MB-175_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 142.91 6.32E-05 3652900000 7362500 5822700 3883740 4536640 6108900 4977670 6513700 7636500 6565400 TRUE FALSE 6389526.971 5784450.3 5761929.654 5566753.45 5987344.842 5169164.186 5882002.377 6003493.902 5789245.891 1.103688993 0.999171638 0.995281555 0.961567975 1.034218438 0.892890764 1.016022205 1.037007931 1 22.464944 4.739735745 4.802919303 0.993625448 1.109890909 0.421127353 0.041163797 0.186560105 12.44633746 0.010133139 0.072792841 54920.65961 -4.739735745 0.11626546 KEVVEEAENGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 KEVVEEAENGR 11 1 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;;;;; 210.4 2.06E-08 17490480000 19986590 16321310 10259410 12950820 15743460 13455070 17092750 20223200 18061430 FALSE TRUE 17345311.49 16214094.24 15220894.99 15891501.62 15430195.95 13972695.25 15435097.74 15898626.06 15926228.32 1.08910353 1.018074959 0.955712469 0.997819528 0.968854373 0.877338625 0.969162153 0.998266867 1 23.92490131 4.613613777 2.186138388 0.967355314 1.10501891 0.553373369 0.03553636 0.399058374 2.665378883 0.009941203 0.096270392 41078.42438 -4.613613777 0.137663597 KEWDLKPIADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEWDLKPIADR 11 2 P30038-2;P30038;P30038-3;Q5TF55 P30038-2 ALDH4A1 "Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial" 0 ; 147.26 1.99E-05 1563170000 2128700 2017970 1550860 2497900 2364700 2042010 2377500 3043200 2725600 FALSE TRUE 1847386.902 2004713.822 2300861.083 3065086.373 2317647.096 2120567.446 2146930.416 2392435.362 2403382.673 0.768661155 0.834121775 0.957342794 1.275321823 0.964327122 0.882326177 0.893295288 0.99544504 1 21.19663495 4.266568609 3.708645921 0.996213251 0.788028107 0.37058481 0.107328929 0.249818095 7.173220153 0.029329702 0.082240163 18474.32626 -4.266568609 -0.208185144 KEYEEDGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KEYEEDGAR 9 1 P61163 P61163 ACTR1A Alpha-centractin 0 ;;; 157.97 0.00010786 2404610000 4035210 3550380 2403880 2942770 3139760 3137230 4109320 4518370 4071290 FALSE TRUE 3501946.775 3527057.32 3566404.408 3610970.906 3077284.919 3257921.268 3710798.779 3552151.737 3589986.734 0.975476244 0.98247085 0.993431083 1.005845195 0.857185596 0.907502314 1.033652504 0.989460965 1 21.77554708 2.225062858 24.99988749 1.004984916 0.954757565 0.242670456 0.044899773 395.3459074 732233.8792 0.01984992 0.013466919 167.9047017 -2.225062858 -0.050227352 KEYEEDGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KEYEEDGSR 9 1 P42025 P42025 ACTR1B Beta-centractin 0 ; 89.805 0.019015 493480000 696030 677260 431430 544070 553580 637950 696990 745180 780610 FALSE TRUE 604047.872 672811.0345 640070.991 667609.4091 542564.8411 662492.3493 629396.0171 585829.056 688327.1751 0.877559239 0.97745819 0.929893536 0.969901281 0.788236845 0.96246723 0.914384961 0.851090989 1 19.39273494 5.126112762 10.66661141 0.917212243 0.000140104 0.040592853 0.063668439 548691.9588 945688.7452 0.014812505 11583709.37 133694.2601 -5.126112762 -0.917072138 KFAADAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFAADAVK 8 1 P37837 P37837 TALDO1 Transaldolase 0 ; 111.65 0.0051186 2343100000 2916000 4230000 2755900 3185800 3662200 3329100 4895900 5334600 4904800 FALSE TRUE 2530643.212 4202212.851 4088662.458 3909184.582 3589329.385 3457172.631 4421096.372 4193837.304 4324960.132 0.585125212 0.971618864 0.945364196 0.903866039 0.829910398 0.799353642 1.022228237 0.969682304 1 22.0442554 4.742800891 24.79649938 0.930066048 0.585125058 0.703059628 0.070488833 237.5848539 1389303.486 0.018691523 0.140944275 55309.64751 -4.742800891 -0.34494099 EVSSRPS(ph)TPGLSVVSGISATSEDIPNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVSSRPSTPGLSVVSGISATSEDIPNK 27 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 EVS(0.029)S(0.024)RPS(0.473)T(0.473)PGLS(0.001)VVSGISATSEDIPNK 180.96 1.06E-17 148480000 110060 75233 70657 85239 99203 66140 91946 120420 224250 TRUE FALSE 95515.29214 74738.78947 104826.9615 104593.8177 97229.05439 68684.4486 83029.09107 94669.12011 197739.4205 0.483036169 0.377966059 0.530126776 0.528947731 0.49170294 0.347348285 0.419891445 0.478756941 1 17.59324098 1.238239713 5.574115699 1.025655615 0.454211372 0.891307187 0.059627676 0.046696331 4.64283771 0.102349308 0.015450257 17.3077141 -1.238239713 -0.571444242 KFAYLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFAYLGR 7 1 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ; 135.35 0.0049478 3391700000 2879500 2995800 1903280 2116290 3028400 3001000 3137300 3383600 2762700 FALSE TRUE 2498966.779 2976120.393 2823712.574 2596825.99 2968140.765 3116450.412 2833045.129 2660043.471 2436096.753 1.025807688 1.221675776 1.159113475 1.065978183 1.218400197 1.279280229 1.162944421 1.091928499 1 21.21614 1.443660226 2.479194882 0.994306272 1.166738193 0.337871866 0.073486422 0.40957211 4.060246941 0.129288175 0.019734649 27.77539388 -1.443660226 0.172431921 KFDEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KFDEGR 6 1 P07237;H7BZ94;I3L398;I3L312;I3L3U6;H0Y4J5;Q13087-2;Q13087 P07237 P4HB;PDIA2 Protein disulfide-isomerase;Protein disulfide-isomerase A2 0 ;; 91.041 0.077516 5296090000 17068190 14450110 11873710 15299380 11351390 16071260 13745250 13911660 19324000 FALSE TRUE 14812585.45 14355186.28 17615875.87 18773338.07 11125519.55 16689531.77 12412237.77 10936759.77 17039538.73 0.869306715 0.842463314 1.033823518 1.101751541 0.652923751 0.979459129 0.728437428 0.641845999 1 24.02238295 3.236166272 24.99989063 0.784236473 0.958451568 0.246100847 0.138609521 86.6968003 905222.174 0.04172442 0.049577112 1722.52793 -3.236166272 0.174215094 KFDEVLVNHFCEEFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFDEVLVNHFCEEFGK 16 1 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 208.43 9.65E-12 1257350000 3761800 2870600 2555500 2821400 2699200 2116190 3834700 4539200 4163700 FALSE TRUE 3264668.599 2851742.84 3791348.348 3462041.992 2645491.201 2197601.199 3462811.384 3568527.404 3671472.129 0.889198797 0.77673008 1.032650723 0.942957449 0.720553257 0.598561319 0.943167008 0.971960913 1 21.80792722 2.021616481 24.99977716 0.976053711 0.829023942 0.254060706 0.118448046 345.3775881 399432.6558 0.052088277 0.035114862 105.1033313 -2.021616481 -0.147029769 KFDGVEGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFDGVEGPR 9 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YAN4 Q6PKG0 LARP1 La-related protein 1 0 ; 93.556 0.010566 419010000 932720 878410 522580 683440 821980 754270 829420 1051930 967950 FALSE TRUE 809458.6888 872639.6669 775301.4359 838625.4977 805624.2062 783287.255 748982.9761 826982.9556 853520.0537 0.948376884 1.022400895 0.90835761 0.982549261 0.943884333 0.917713944 0.877522412 0.968908641 1 19.70306552 3.077850596 8.043148961 0.938493533 0.965312955 0.072172642 0.042091053 0.690713509 62.5839066 0.012902934 0.014647498 1196.328905 -3.077850596 0.026819422 KFDGVEGPRT(ph)PK ddPTM_MDA-MB-175_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 118.31 0.0033201 848400000 1633700 1618770 1437960 1587050 2205670 1649470 3118360 3358020 1644260 TRUE FALSE 1417802.406 1608136.193 2133362.266 1947413.959 2161781.482 1712926.178 2815941.927 2639933.555 1449877.456 0.977877406 1.109153182 1.471408675 1.343157624 1.491009791 1.181428245 1.942193056 1.820797712 1 20.46749954 5.380703939 0.497813841 1.587853119 2.84E-18 0.259088083 0.279733227 10.92247935 1.348026156 0.203919229 11.55031902 240272.4292 -5.380703939 -1.587853119 KFDHES(ph)SPGTDEDKSG ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFDHESSPGTDEDKSG 16 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 KFDHES(0.5)S(0.5)PGTDEDKSG 100.39 0.0010807 98970000 138330 106470 44902 67481 106410 84825 107620 140290 91186 TRUE FALSE 120049.34 105770.5916 66616.75739 82803.59243 104292.6492 88088.27264 97183.02896 110290.0752 80406.09496 1.493037811 1.315454899 0.828503827 1.02981736 1.297073925 1.095542231 1.208652516 1.371663122 1 16.29501724 3.211294399 24.9986203 1.212823641 1.153171173 0 0.198288444 1267.571627 1162150.609 0.062880543 0.071317254 1626.651052 -3.211294399 -0.059652468 KFDLGQDVIDFTGHALALYR ddPTM_MDA-MB-175_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 ;; 256.92 2.17E-36 4425887000 5956656 5367843 2472815 3273622 4989063 4542639 5638657 6903649 1726042 FALSE TRUE 5169468.817 5332581.286 3668676.605 4016947.909 4889790.407 4717397.262 5091820.912 5427357.386 1521991.281 3.396516709 3.503687145 2.410445218 2.639271302 3.212758488 3.099490332 3.345499396 3.565958263 1 20.53752866 4.271371326 24.96946213 2.882318924 3.450103027 0.120343648 0.720251297 466.2611023 354824.6418 0.176019383 0.465632487 18679.76146 -4.271371326 0.567784103 KFDQLLAEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KFDQLLAEEK 10 1 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4;P35749;P35749-2;P35749-4;P35749-3;Q7Z406;Q7Z406-6;Q7Z406-2;A0A0C4DFM8;A1L2Z2 P35579;P35580;P35749;Q7Z406 MYH9;MYH10;MYH11;MYH14 Myosin-9;Myosin-10;Myosin-11;Myosin-14 0 ;; 185.25 2.36E-06 9221590000 25359100 22598700 17616100 19961000 19934400 16295600 29967700 33608100 29901900 FALSE TRUE 22007830.68 22450247.65 26135304.88 24493450.13 19537744.44 16922502.28 27061437.07 26421269.35 26366931.45 0.834675462 0.851454698 0.991215263 0.928945797 0.740994244 0.6418078 1.026340024 1.002060835 1 24.65222635 KFDSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 130.77 0.025046 1230260000 2523600 1897520 1370410 1593140 1252930 1873620 1945430 2387030 3855200 FALSE TRUE 2190099.866 1885055.066 2033144.86 1954886.787 1227999.144 1945699.374 1756762.498 1876582.21 3399442.648 0.64425263 0.554518861 0.598081824 0.57506097 0.361235435 0.572358347 0.516779567 0.552026436 1 21.6968668 1.23867273 7.167496001 1.008898599 0.542724021 0.78820614 0.07382184 0.047253365 15.04020063 0.107189603 0.018078689 17.32497954 -1.23867273 -0.466174577 KFDVNTSAVQVLIEHIGNLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KFDVNTSAVQVLIEHIGNLDR 21 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 276.11 5.55E-45 6651350000 6605680 5396940 3586420 4233140 5259620 4997820 5929650 6957250 5146330 FALSE TRUE 5732722.651 5361487.146 5320824.708 5194339.136 5154963.852 5190089.369 5354593.456 5469496.229 4537936.73 1.26328836 1.181481247 1.17252069 1.144647765 1.135970852 1.143711267 1.179962122 1.205282611 1 22.11360506 KFEDATVQSDMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFEDATVQSDMK 12 1 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 152.99 0.00011268 264300000 438440 372610 343710 348620 332410 288190 521380 577420 512830 FALSE TRUE 380499.0431 370162.3004 509929.3056 427779.4993 325795.6913 299276.8558 470816.6478 453943.2265 452203.8216 0.841432613 0.818574021 1.127653685 0.945988244 0.720462048 0.661818502 1.041160259 1.003846506 1 18.78661366 KFEEEGNPYYSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFEEEGNPYYSSAR 14 1 Q9HCC0-2;Q9HCC0 Q9HCC0-2 MCCC2 "Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial" 0 101.3 0.0023104 149710000 216500 149800 134840 166620 182030 167400 169330 213400 186580 FALSE TRUE 187888.9765 148815.9539 200049.075 204453.6176 178407.9591 173839.9863 152908.4027 167766.0707 164522.725 1.142024462 0.904531298 1.215935823 1.24270746 1.084397059 1.056632063 0.929405969 1.019713664 1 17.32792735 2.578134961 2.919012396 0.988811758 1.118926086 0.302185714 0.092829251 0.359321062 5.934986698 0.036704156 0.030791591 378.5602073 -2.578134961 0.130114328 KFEQMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFEQMK 6 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;H0YAP2;H0YAW6 P11940-2 PABPC1 Polyadenylate-binding protein 1;Polyadenylate-binding protein 0 95.62 0.069169 1073300000 2019600 1959500 1506900 1729900 1737300 1708600 2304200 2809500 2740200 FALSE TRUE 1752704.743 1946627.915 2235641.88 2122700.235 1702731.129 1774330.948 2080739.039 2208710.289 2416256.678 0.725380196 0.805637883 0.925250161 0.878507757 0.704697951 0.734330489 0.861141557 0.914104163 1 21.20434229 1.613208869 1.97936494 0.997820109 0.802555837 0.489426327 0.069058928 0.34391371 2.586342631 0.104500392 0.021273943 41.04014333 -1.613208869 -0.195264271 KFESEILEAISQNSVVIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KFESEILEAISQNSVVIIR 19 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;; 240.07 4.20E-24 1693115100 5144000 4209048 2742152 3569764 3949248 3791766 4972204 5478281 3581533 FALSE TRUE 4464207.367 4181398.487 4068265.879 4380333.477 3870665.691 3937637.692 4490000.421 4306793.24 3158128.249 1.41356114 1.324011616 1.288188939 1.387003038 1.225620173 1.246826405 1.421728336 1.363717019 1 21.59063833 1.235367331 24.99991088 0.999999542 1.333180895 0.716131445 0.066051906 50.74914352 397241.4337 0.114364675 0.016472761 17.19362028 -1.235367331 0.333181353 KFFDANYDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFFDANYDGK 10 1 Q15691;C9JB30;Q9UPY8;Q9UPY8-2 Q15691;C9JB30;Q9UPY8-2 MAPRE1;MAPRE3 Microtubule-associated protein RP/EB family member 1;Microtubule-associated protein RP/EB family member 3 0 ; 128.85 0.00051112 1989440000 4996400 4444600 3552500 4406100 4058200 3374500 5173600 5758400 6091300 FALSE TRUE 4336113.081 4415403.13 5270500.882 5406572.348 3977449.76 3504319.199 4671865.068 4527010.972 5371193.453 0.807290432 0.822052523 0.981253222 1.006586785 0.740515082 0.652428409 0.869800187 0.842831488 1 22.35681125 4.454157238 24.80648834 0.863162006 0.810980612 0.038783665 0.112132248 829.7565397 896330.2437 0.029768244 0.078769766 28454.91143 -4.454157238 -0.052181394 KFFVGGNWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFFVGGNWK 9 1 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 0 100.25 0.0076809 601800000 1386800 1695400 1001600 1031700 1427000 1269100 1491500 1660500 1508800 FALSE TRUE 1203530.866 1684262.806 1485977.11 1265963.254 1398605.492 1317923.098 1346854.56 1305414.997 1330431.383 0.904617015 1.265952403 1.116913754 0.951543439 1.051242108 0.990598324 1.012344249 0.981196786 1 20.34346267 3.752996075 24.08156632 0.998921813 1.112840216 0.202154113 0.089668368 645.6823837 1077136.654 0.021862106 0.037618911 5662.341718 -3.752996075 0.113918403 KFGDPVVQSDMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KFGDPVVQSDMK 12 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ;;;; 159.75 0.00011209 9985040000 15140570 12347340 10036870 10479540 11006660 9135960 16442610 18788690 14041890 FALSE TRUE 13139705.31 12266229.51 14890733.9 12859079.73 10787649 9487426.293 14848008.21 14770874.86 12381873.76 1.061204917 0.990660198 1.202623625 1.038540691 0.871245274 0.766235101 1.19917296 1.192943422 1 23.56172632 0.940880864 22.35631354 0.00029215 1.047597096 0.005592132 0.142168743 1604.886712 1184799.438 78639.55524 0.036675454 8.727319263 -0.940880864 1.047304946 KFGEEIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFGEEIAR 8 1 Q8WUM4;Q8WUM4-2;F8WDK9 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 118.18 0.0031054 902790000 1612340 1502540 910710 1175310 1515120 1270170 1548910 1764710 1675560 FALSE TRUE 1399265.184 1492669.716 1351132.402 1442182.099 1484972.076 1319034.262 1398696.947 1387340.499 1477477.206 0.947063805 1.010282737 0.914486123 0.976111234 1.005072749 0.892761159 0.946679205 0.938992828 1 20.49470444 2.763612719 24.97016122 0.943925008 0.969996106 0.108624536 0.03695656 1741.026775 1735329.358 0.011462568 0.011458246 580.2467533 -2.763612719 0.026071099 KFGGPGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFGGPGAR 8 1 P62249;M0R210 P62249 RPS16 40S ribosomal protein S16 0 ; 103.56 0.0076141 4933600000 6609500 6372100 4042000 4887600 5583100 5143000 6408600 7022600 5935400 FALSE TRUE 5736037.829 6330241.256 5996724.72 5997404.282 5472007.233 5340854.538 5787094.958 5520871.64 5233723.774 1.095976417 1.209510003 1.145785483 1.145915326 1.045528475 1.02046932 1.105731829 1.054864926 1 22.31940635 3.258314209 6.283229318 1.049625468 1.154045572 0.646288296 0.038097202 0.101386796 14.01132579 0.010919595 0.013654081 1812.651058 -3.258314209 0.104420104 KFGNPGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KFGNPGER 8 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;; 115.71 0.0038652 2115290000 3161340 2550700 1769520 1989240 2478390 2429020 2874900 3091160 2762510 FALSE TRUE 2743560.909 2533944.284 2625265.791 2440927.346 2429074.888 2522465.971 2596092.64 2430139.489 2435929.215 1.126289259 1.04023724 1.077726633 1.002051837 0.997186155 1.035525152 1.065750443 0.997623196 1 21.21604078 8 0.701367255 1.018112597 14.35998809 0.598418054 0.026874806 213.5286102 1.133100378 0.010783344 4467.582208 100000000 -8 13.34187549 KFGQGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KFGQGSR 7 1 A0A2R8Y851;P62273;P62273-2;A0A2R8Y6P7 A0A2R8Y851 RPS29 40S ribosomal protein S29 0 ;;; 128.61 0.0059987 10479170000 9355000 9688290 5737055 6890576 7609002 8646420 10511600 10936100 9271280 FALSE TRUE 8118713.047 9624646.985 8511513.987 8455186.597 7457597.747 8979053.372 9492186.65 8597500.12 8175239.84 0.99308561 1.177292309 1.041133245 1.034243247 0.91221761 1.09832293 1.161089685 1.051651118 1 22.96282963 KFGYVDFESAEDLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KFGYVDFESAEDLEK 15 1 P19338 P19338 NCL Nucleolin 0 ;;;;;; 273.88 2.95E-33 6276588000 13757750 9653130 6781980 7927730 8697810 6592990 11953170 14627740 8756610 FALSE TRUE 11939628.48 9589717.953 10061768.21 9727842.264 8524740.598 6846626.592 10793953.41 11499711.63 7721413.541 1.54630087 1.24196404 1.303099252 1.259852514 1.104038859 0.886706372 1.397924532 1.489327255 1 22.88043355 6.900699511 1.246734706 1.223936634 77.34971336 0.255870301 0.178571835 617.4273641 5.341188487 0.055606335 132665.7741 7956086.777 -6.900699511 76.12577673 KFHTVSGSK ddPTM_MDA-MB-175_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 ; 136.33 0.00012718 2746100000 5204000 4015500 2098360 3125100 3784000 3338500 4926800 5389700 4578700 FALSE TRUE 4516278.215 3989121.916 3113133.915 3834701.719 3708705.803 3466934.255 4448999.694 4237154.598 4037411.302 1.118607414 0.988039518 0.771071779 0.949792189 0.918585085 0.858702271 1.101943637 1.049473111 1 21.94499913 2.232599222 24.9995613 1.052408739 0.929176514 0.263910856 0.091322908 189.7968359 795917.6629 0.03724441 0.025852158 170.8437999 -2.232599222 -0.123232225 KFIEDR ddPTM_MDA-MB-175_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 ;;; 97.071 0.066524 5017470000 12744540 11181770 7266920 9691310 11157730 10927520 12477020 14193610 12369350 FALSE TRUE 11060316.75 11108316.22 10781226.82 11891870.06 10935713 11347908.77 11267000.52 11158416.96 10907059.53 1.014051194 1.018451965 0.988463186 1.090291111 1.002627057 1.040418706 1.033000735 1.023045388 1 23.37875888 KFLALLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFLALLR 7 1 I3L0N3;P46459;P46459-2;K7EQD6 I3L0N3 NSF Vesicle-fusing ATPase 0 ; 148.07 0.0033815 553250000 446550 809300 420170 457330 783720 740620 742840 745090 716050 FALSE TRUE 387537.2861 803983.655 623365.6174 561173.7664 768125.5053 769112.1306 670799.4911 585758.3018 631399.3847 0.613775204 1.273336139 0.987276251 0.888777816 1.21654459 1.218107191 1.062401243 0.927714401 1 19.26819333 4.756818667 24.59625645 1.060814576 0.613774724 0.551942654 0.129348522 2723.365573 3668696.55 0.032730418 1.037694684 57124.0075 -4.756818667 -0.447039853 KFLDAGHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFLDAGHK 8 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 52.255 0.093523 2325000000 6179700 5177000 4319700 5089200 5772900 5463000 6329000 6586700 5117200 FALSE TRUE 5363036.988 5142991.946 6408721.369 6244780.644 5658030.584 5673165.145 5715214.554 5178185.463 4512250.446 1.188550381 1.13978424 1.420293808 1.383961444 1.253926539 1.257280644 1.266599588 1.147583789 1 22.10541571 1.29373554 1.471999108 0.897742487 1.280419596 0.547320955 0.08151439 0.884263365 1.88072603 0.494244419 0.025645136 19.66688324 -1.29373554 0.38267711 KFLDGIYVSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFLDGIYVSEK 11 1 A0A2R8Y5Y7;P32969;D6RAN4;H0Y9R4;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 172.33 2.16E-05 3961000000 11317400 9636000 6329200 8257300 9222900 7228300 11296700 13611000 10612100 FALSE TRUE 9821776.915 9572700.482 9390022.29 10132246.17 9039382.334 7506377.378 10201147.77 10700393.57 9357549.627 1.04960992 1.022992222 1.00347021 1.082788398 0.965998867 0.802173398 1.090151608 1.143503801 1 23.15769936 2.064874824 25 1.092466354 0.989528015 0.204832885 0.081942935 81.01654146 31219.46533 0.034374589 0.02317534 116.11139 -2.064874824 -0.102938339 KFLDGNELTLADCNLLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFLDGNELTLADCNLLPK 18 1 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ; 201.96 2.16E-15 1124160000 2664800 1861260 1281840 1504490 1680170 1471460 2588800 2852600 1561510 FALSE TRUE 2312639.928 1849033.261 1901742.111 1846107.449 1646737.904 1528068.018 2337738.574 2242593.689 1376910.067 1.679586768 1.342886006 1.381166539 1.340761095 1.195966203 1.109780555 1.697815007 1.628714717 1 20.3930029 4.741420583 23.25532621 1.36679543 1.67958708 0.191871204 0.213283801 201.3235451 1636780.525 0.054984005 0.366253082 55134.13722 -4.741420583 0.31279165 KFLETVELQISLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFLETVELQISLK 13 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 126.71 0.00029734 215890000 657470 524390 396110 488390 454630 418220 760450 844840 499310 FALSE TRUE 570583.6737 520945.2476 587670.1209 599286.4141 445583.7525 434309.194 686701.676 664177.5406 440282.1406 1.295950076 1.183207765 1.334758026 1.361141774 1.012041397 0.98643382 1.559685512 1.5085271 1 18.7480688 2.229348133 24.99998669 1.396316472 1.200533967 0.123208102 0.19175543 343.2036887 931345.1517 0.079676243 0.054555156 169.5696536 -2.229348133 -0.195782505 KFLPLFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFLPLFDR 8 1 P61604;B8ZZL8;S4R3N1 P61604;S4R3N1 HSPE1;HSPE1-MOB4 "10 kDa heat shock protein, mitochondrial" 0 ; 149.72 0.0008028 4433300000 5014800 5335800 3492700 5712200 6188700 6566200 5230900 6666900 5721100 FALSE TRUE 4352081.474 5300748.778 5181781.402 7009242.316 6065556.978 6818805.963 4723608.123 5241235.317 5044758.075 0.862693792 1.050743901 1.027161526 1.389410991 1.202348435 1.351661638 0.936339871 1.038946811 1 22.26635365 4.646624046 1.795766405 1.136088228 0.810483566 0.264785017 0.146281048 1.117891451 4.264877489 0.042417961 0.580792715 44322.47931 -4.646624046 -0.325604662 KFMTNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFMTNR 6 1 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4 E7ETK0 RPS24 40S ribosomal protein S24 0 ; 134.44 0.022501 3822500000 2939100 3074800 1937710 2303000 2731300 2788600 3025000 3278100 2659700 FALSE TRUE 2550690.488 3054601.436 2874793.037 2825931.349 2676952.474 2895879.246 2731635.966 2577103.825 2345273.296 1.087587742 1.302450099 1.225781679 1.204947566 1.141424532 1.234772618 1.164741001 1.098850113 1 21.16132462 1.341640476 1.296278772 0.929044685 1.204618698 0.566997446 0.056832262 0.790776089 1.353495232 0.284236424 0.016622583 21.96041164 -1.341640476 0.275574013 KFNALFAQGNYSEAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFNALFAQGNYSEAAK 16 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 217.37 2.30E-14 1991010000 3082100 2285500 1542390 1899730 2265910 1815340 2859900 3340300 2270650 FALSE TRUE 2674792.676 2270486.4 2288294.963 2331092.732 2220822.824 1885177.304 2582547.338 2626002.839 2002216.344 1.335915914 1.133986548 1.142880973 1.16425617 1.109182248 0.941545258 1.2898443 1.311547999 1 20.93316644 4.742057797 23.80304358 1.151600984 1.335916052 0.226925692 0.112618501 311.1223005 2117414.44 0.029105203 0.204495942 55215.09162 -4.742057797 0.184315068 KFPPDNSAPYGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFPPDNSAPYGAR 13 1 P09467;A0A3B3IUC7 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 82.651 0.01887 332470000 155130 144100 118060 156960 163400 141730 162300 184950 220940 FALSE TRUE 134629.1775 143153.3976 175154.2109 192600.167 160148.6597 147182.4448 146560.171 145399.8818 194820.7249 0.691041354 0.734795529 0.899053276 0.988602045 0.82203092 0.755476323 0.752282238 0.746326562 1 17.57178763 4.392533637 5.931113728 0.837250692 0.701476537 0.27895018 0.091778056 0.281848548 15.08948614 0.024719445 0.067894012 24690.71335 -4.392533637 -0.135774155 KFPSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFPSLR 6 1 Q14137;Q14137-2 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 ; 94.163 0.071825 430300000 803260 660230 442870 579150 681090 663390 670690 743390 773450 FALSE TRUE 697107.1558 655892.9057 657043.4133 710654.8593 667537.6415 688911.0426 605646.587 584421.8336 682013.6221 1.022130839 0.961700594 0.963387522 1.04199511 0.978774646 1.010113318 0.888027112 0.856906394 1 19.37944103 2.23787505 24.99996341 0.901756659 0.994552913 0.421844622 0.043975684 14.72789204 537023.3907 0.016880916 0.012153832 172.9318747 -2.23787505 0.092796254 KFPVFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFPVFK 6 1 P04080;A0A1W2PS52 P04080 CSTB Cystatin-B 0 104.04 0.054791 684250000 310440 274490 192010 198560 212270 227210 226210 307330 767590 FALSE TRUE 269414.5674 272686.8571 284866.6782 243646.0828 208046.2423 235950.9157 204272.189 241609.8711 676846.3846 0.398043889 0.402878501 0.420873458 0.359972496 0.307375864 0.348603348 0.301799926 0.356964116 1 19.36846891 1.238400221 24.99733132 1.000000706 0.359918224 0.964560052 0.03842726 0.706137186 109705.6046 0.058471953 0.010395154 17.31411194 -1.238400221 -0.640082482 KFQAPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFQAPAR 7 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;Q9UHB6-3 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 105.39 0.012727 250520000 272160 345760 187390 273440 351300 337730 321460 360960 369990 FALSE TRUE 236193.3664 343488.6798 278012.4308 335528.7313 344309.8173 350722.6916 290284.8587 283771.513 326250.2037 0.72396389 1.052838208 0.85214485 1.028439914 1.055355103 1.07501141 0.889761463 0.869797198 1 18.31561928 6.385286361 11.56153179 0.950415342 0.518540248 0 0.113865894 0 0 0.02473302 0 2428210.658 -6.385286361 -0.431875094 KFQEQECPPS(ph)PEPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFQEQECPPSPEPTR 15 1 P62070-2;P62070-3;P62070;P62070-4 P62070-2 RRAS2 Ras-related protein R-Ras2 1 KFQEQECPPS(1)PEPTR 89.668 0.0026189 0 84701 88315 60498 93343 100570 94430 81883 123700 146680 TRUE FALSE 73507.54825 87734.85295 89755.03515 114537.9548 98568.85376 98062.7832 73941.99926 97247.71763 129339.6575 0.568329542 0.678329096 0.693948298 0.885559441 0.762093048 0.758180322 0.571688535 0.751878577 1 16.98080517 4.464696661 1.764216697 0.767663788 0.558778907 0.282373155 0.110617864 0.798286419 3.724821093 0.031108364 0.23459589 29153.90007 -4.464696661 -0.208884881 KFQEQECPPS(ph)PEPTRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFQEQECPPSPEPTRK 16 2 P62070-2;P62070-3;P62070;P62070-4 P62070-2 RRAS2 Ras-related protein R-Ras2 1 KFQEQECPPS(0.999)PEPT(0.001)RK 160.13 4.64E-09 214810000 279620 232660 168400 261880 284670 241220 202750 401430 231130 TRUE FALSE 242667.5085 231131.6411 249838.8033 321343.8566 279005.6239 250499.8895 183087.3362 315587.3184 203806.0747 1.190678486 1.13407631 1.225865341 1.57671383 1.368975995 1.229109043 0.898340918 1.548468655 1 17.63683753 0.988197645 16.73350146 0.570365454 1.272652921 0.158485481 0.196616773 5321697.111 142126738.4 86436136.79 0.048052886 9.731900173 -0.988197645 0.702287467 KFRY(ph)GY(ph)NNVVT(ph)IPAGAT(ph)HILVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFRYGYNNVVTIPAGATHILVR 22 2 O75173 O75173 ADAMTS4 A disintegrin and metalloproteinase with thrombospondin motifs 4 4 KFRY(1)GY(1)NNVVT(1)IPAGAT(1)HILVR 41.188 0.083005 196140000 35079 60553 8746.8 18901 80777 96753 39284 39335 35375 TRUE FALSE 30443.22127 60155.22336 12976.78174 23192.76093 79169.69574 100475.1505 35474.24373 30923.51636 31193.0078 0.975962994 1.928484221 0.416015724 0.743524353 2.53805905 3.221079261 1.137249859 0.991360518 1 14.92893505 4.813804906 19.0527335 1.46969555 0.975840354 0.034345344 0.857433958 30927.6836 7823269.289 0.224688318 659.2570916 65133.57349 -4.813804906 -0.493855195 KFS(ph)APGQLCISMTSNLGGSAPISAASATSLGHFTK ddPTM_MDA-MB-175_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(0.989)APGQLCIS(0.01)MT(0.001)SNLGGSAPISAASATSLGHFTK 102.29 1.21E-05 50696000 27381 26799 9942.5 15335 25727 24099 39357 35312 34023 TRUE FALSE 23762.53148 26622.9556 14750.72626 18817.04613 25215.08303 25026.10412 35540.1642 27760.8036 30000.8397 0.792062213 0.887407015 0.491677113 0.627217315 0.840479243 0.834180122 1.184638982 0.92533422 1 14.87271526 2.665716821 2.121108569 1.01646503 0.70645667 0.534973969 0.129143757 0.25299968 2.254887816 0.053116141 0.045702864 463.1448307 -2.665716821 -0.31000836 KFS(ph)FKKPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFSFKKPFK 9 3 P49006 P49006 MARCKSL1 MARCKS-related protein 1 KFS(1)FKKPFK;KFS(1)FKKPFK 90.653 0.0080528 2787900000 2542650 1878270 1009160 1117250 1367780 693340 2817650 2694400 754970 TRUE FALSE 2206632.36 1865931.521 1497193.151 1370938.689 1340563.854 720013.2385 2544394.737 2118223.528 665718.3067 3.314663782 2.802884496 2.248989004 2.059337523 2.013710365 1.081558418 3.822029094 3.181861617 1 19.34455232 4.509389061 2.757361407 2.324430852 3.315556971 0.152017671 0.847220755 0.706947057 9.517689796 0.230290496 1.238533547 32313.87652 -4.509389061 0.991126119 KFS(ph)GSGLAMGLGSASASAWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFSGSGLAMGLGSASASAWR 20 1 Q92796-2 Q92796-2 DLG3 Disks large homolog 3 1 KFS(0.748)GS(0.252)GLAMGLGSASASAWR 120.27 2.37E-05 47419000 56762 51767 41456 52897 66605 50720 68961 69644 52761 TRUE FALSE 49260.75788 51426.93917 61504.26026 64908.07233 65279.69081 52671.23122 62273.17283 54751.17257 46523.65469 1.058832506 1.105393364 1.321999759 1.3951628 1.403150532 1.132138728 1.338527105 1.176845906 1 15.50567681 1.312939575 3.10975257 0.976615387 1.254985652 0.301885933 0.119958557 0.410335869 5.454554754 0.254732196 0.032710354 20.55604574 -1.312939575 0.278370266 KFS(ph)NSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFSNSLK 7 1 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;Q9BV36-3;Q9BV36 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 KFS(0.997)NS(0.003)LK 112.85 0.0066339 524080000 774210 577570 404400 447310 550290 372550 834110 762260 806530 TRUE FALSE 671896.1869 573775.9046 599969.1926 548878.5722 539340.3056 386882.2396 753218.1406 599256.6309 711182.9422 0.94475858 0.80679087 0.843621461 0.771782533 0.7583707 0.543998199 1.059106027 0.842619522 1 19.4398612 2.20454947 24.99999963 0.945106437 0.781296399 0.37877419 0.112888283 220.0391253 161738.9861 0.045726761 0.030830771 160.1583074 -2.20454947 -0.163810038 KFS(ph)PSQVPVQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFSPSQVPVQTR 12 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 KFS(0.973)PS(0.027)QVPVQTR 97.235 0.0007914 0 230280 260550 171090 209830 275240 249040 300340 314450 319250 TRUE FALSE 199847.9145 258838.4299 253829.6963 257475.1086 269763.2625 258620.73 271213.073 247207.3146 281508.6287 0.709917545 0.919468903 0.901676433 0.914625991 0.958277065 0.918695569 0.963427211 0.87815182 1 18.10281962 4.743228751 4.618456944 0.928890425 0.69553826 0.802924387 0.034550303 0.080119709 4.554502708 0.007903319 0.060890519 55364.16455 -4.743228751 -0.233352165 KFSAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFSAPR 6 1 P39023;H7C422;H7C3M2;F8WCR1;Q92901 P39023;Q92901 RPL3;RPL3L 60S ribosomal protein L3;60S ribosomal protein L3-like 0 ; 143.02 0.018363 3958200000 3992000 5223300 3064300 3409900 4797300 4906600 4882100 5232300 4870800 FALSE TRUE 3464447.086 5188987.798 4546205.729 4184169.912 4701843.116 5095360.077 4408634.693 4113413.363 4294979.573 0.806627139 1.208151916 1.058492981 0.974200189 1.09473003 1.186352575 1.026462319 0.957725943 1 22.03421984 1.996519152 24.93565087 0.9807186 1.063918931 0.068321207 0.111515255 311.6737296 2232734.596 0.04402439 0.028978173 99.20170849 -1.996519152 0.083200331 KFSGFSAKPNNSGEAPSS(ph)PTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFSGFSAKPNNSGEAPSSPTPK 22 2 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 KFSGFSAKPNNSGEAPS(0.062)S(0.918)PT(0.02)PK;KFSGFSAKPNNSGEAPS(0.39)S(0.575)PT(0.034)PK 119.85 2.76E-05 2831200000 3167400 2026090 1603380 1703740 2019440 1399210 2887120 3135600 1630980 TRUE FALSE 2748820.065 2012780.481 2378779.931 2090600.207 1979257.095 1453038.514 2607127.547 2465076.341 1438167.402 1.911335259 1.399545337 1.654035495 1.453655676 1.376235542 1.01034032 1.812812293 1.714039921 1 20.45580018 6.712913924 1.540619686 1.455018296 199.4329087 0.227985951 0.27014617 1122.975538 7.80375588 0.074923916 781014.1774 5163140.271 -6.712913924 197.9778904 KFSIEEALQSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFSIEEALQSGR 12 1 O60437;K7EKI8 O60437 PPL Periplakin 0 112.42 0.00036171 0 262490 270870 176850 198920 233070 273010 278520 277530 188090 FALSE TRUE 227801.2814 269090.6371 262375.2515 244087.8263 228432.363 283512.8714 251509.1733 218182.3692 165854.2145 1.373503122 1.622452815 1.581963126 1.471701078 1.37730816 1.709410112 1.516447285 1.315506934 1 17.33955615 1.361587777 2.128104825 0.922897829 1.527858029 0.726795746 0.103122342 0.269560838 1.572503141 0.290152554 0.027623003 22.99258377 -1.361587777 0.6049602 KFSNS(ph)LK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFSNSLK 7 1 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;Q9BV36-3;Q9BV36 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 KFS(0.142)NS(0.858)LK 92.538 0.01652 660050000 907120 695990 444980 469630 604890 378090 943820 878540 910830 TRUE FALSE 787241.7937 691417.9959 660173.8164 576266.6693 592853.8724 392635.367 852288.4817 690671.0578 803152.715 0.98018942 0.860879859 0.821977943 0.717505723 0.738158337 0.488867633 1.06117861 0.859949851 1 19.61531481 2.173788232 24.99999586 0.953653847 0.770947956 0.342064946 0.133527398 77.86305799 30051.40224 0.055670947 0.037533354 149.2066679 -2.173788232 -0.182705891 KFTDFDEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KFTDFDEVR 9 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4;E5RHK8;Q9UQ16-5;Q9UQ16-2;Q9UQ16-3;Q9UQ16;Q9UQ16-4 P50570-2 DNM2;DNM3 Dynamin-2;Dynamin-3 0 ;; 138.76 0.0002044 838950000 2806550 2254290 1656940 2120460 2358020 2246050 2535040 2815640 2883950 FALSE TRUE 2435657.307 2239481.421 2458241.726 2601942.852 2311100.015 2332456.997 2289192.211 2213537.297 2543012.716 0.957784163 0.880641063 0.966665133 1.023173355 0.908803955 0.917202255 0.900189054 0.870438942 1 21.27810725 KFTFGLDWVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFTFGLDWVPK 11 1 P45974-2;P45974;H7C5J3;Q92995-2;Q92995 P45974-2;Q92995-2 USP5;USP13 Ubiquitin carboxyl-terminal hydrolase 5;Ubiquitin carboxyl-terminal hydrolase 13 0 ; 101.6 0.0050768 230170000 1291900 1050560 706690 844410 916710 738260 1178470 1391230 1073830 FALSE TRUE 1121172.142 1043658.802 1048447.648 1036146.196 898469.2645 766661.3399 1064182.161 1093726.291 946883.0407 1.184066134 1.102204557 1.10726204 1.094270519 0.948870374 0.809668467 1.123879207 1.155080664 1 19.85282671 3.460166553 22.11699396 1.024491986 1.12369465 0.253965831 0.096479948 117.6039776 153408.9265 0.031683625 0.040923043 2885.137752 -3.460166553 0.099202664 KFTNFQSPNIDPTEENDLDDSLS(ph)VK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFTNFQSPNIDPTEENDLDDSLSVK 25 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9 Q6ULP2-7 AFTPH Aftiphilin 1 KFTNFQSPNIDPTEENDLDDS(0.001)LS(0.999)VK 193.49 2.07E-18 58839000 96659 80054 72274 64267 82863 75719 87465 123190 95006 TRUE FALSE 83885.26825 79528.12 107225.9481 78859.80461 81214.18842 78631.95893 78982.65776 96846.77717 83774.49891 1.001322232 0.949311796 1.279935416 0.941334244 0.969438069 0.938614494 0.942800718 1.156041259 1 16.35422353 1.742584252 24.99999792 1.084200179 1.005649707 0.075827469 0.107789729 1.814374831 11346.6338 0.05737776 0.027553811 55.28206432 -1.742584252 -0.078550472 KFVADGIFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFVADGIFK 9 1 P23396;P23396-2;E9PPU1;E9PL09;F2Z2S8;H0YCJ7;E9PQ96;E9PJH4;E9PK82;E9PQX2 P23396 RPS3 40S ribosomal protein S3 0 ; 96.113 0.012166 2452900000 7656900 8803600 4901900 6156900 8392000 8271900 9157500 10188100 6925700 FALSE TRUE 6645021.265 8745768.572 7272475.236 7554918.247 8225015.619 8590125.346 8269407.059 8009454.099 6106951.636 1.088107727 1.432100513 1.190851945 1.237101372 1.346828354 1.406614275 1.354097355 1.311530626 1 22.54202099 1.237644997 24.94169624 0.999999635 1.30355111 0.448391364 0.102832661 19.61541047 534020.6855 0.139567352 0.023677913 17.28402944 -1.237644997 0.303551475 KFVEEQHTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFVEEQHTK 9 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 ; 99.568 0.0034073 725640000 1598930 1285460 956380 1089090 1215980 1034410 1539390 1741560 1679220 FALSE TRUE 1387627.349 1277015.729 1418888.567 1336384.53 1191784.377 1074204.422 1390100.195 1369140.947 1480704.525 0.93713994 0.862437919 0.958252334 0.902532888 0.804876569 0.725468454 0.938809987 0.924655071 1 20.49785235 1.610742832 2.08769957 0.989804148 0.869069569 0.257729283 0.068912443 0.498115964 4.289182083 0.096460478 0.020519328 40.80776715 -1.610742832 -0.12073458 KFVEWLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFVEWLK 7 1 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;H0Y503 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 103.56 0.013385 304160000 679550 670460 441970 602540 744720 684950 966290 1132300 960300 FALSE TRUE 589745.7457 666055.7041 655708.1703 739355.9162 729901.529 711300.4697 872579.3445 890166.4566 846774.428 0.69646145 0.786579852 0.774359911 0.873143888 0.86197871 0.840011751 1.030474369 1.051243905 1 19.69161818 2.656455494 0.385540388 1.138838375 0.680548576 0.844059707 0.045959314 0.739452659 0.357016224 0.210578089 0.132307888 453.3728338 -2.656455494 -0.458289799 KFVHLLDQSDQDFQEELDLMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFVHLLDQSDQDFQEELDLMK 21 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 124.2 1.63E-05 506610000 972960 845240 487020 566920 745740 620850 1109710 1219290 355080 FALSE TRUE 844380.8708 839687.5628 722544.501 695647.8508 730901.233 644734.5012 1002090.495 958554.322 313102.8469 2.696816331 2.681826662 2.307690614 2.221787051 2.334380668 2.059178023 3.200515437 3.061467922 1 18.2562771 6.482363801 6.659660751 2.465285949 2.530259895 0 0.615516251 0 0 0.136063308 0 3036433.69 -6.482363801 0.064973946 KFYEQFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KFYEQFSK 8 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 129.85 0.0017205 1096610000 1831180 1803960 1220840 1375260 1724090 1424220 2002330 2179550 1835620 FALSE TRUE 1589184.923 1792109.668 1811242.307 1687533.803 1689783.982 1479010.665 1808144.345 1713470.194 1618615.095 0.981817684 1.107187048 1.119007424 1.042578812 1.043969 0.913750693 1.117093465 1.058602628 1 20.62632852 3.499672238 22.81986861 1.032849648 1.074400826 0.082901679 0.062168106 664.5083416 672428.1716 0.017206 0.025235293 3159.891987 -3.499672238 0.041551179 KGAAPT(ph)PPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 56.122 0.073927 583870000 1050800 828540 551190 740710 767960 610190 1054200 1233800 1046500 TRUE FALSE 911934.1176 823097.2662 817747.3276 908899.5265 752679.0985 633664.4041 951963.8463 969961.4714 922783.9622 0.98824227 0.891971794 0.886174187 0.984953753 0.815661227 0.686687708 1.031621577 1.051125194 1 19.8156334 2.080488175 25 1.032904187 0.877421522 0.412113008 0.085466821 28.31218248 8791.738568 0.035914009 0.024213218 120.3616616 -2.080488175 -0.155482664 KGADSLEDFLYHEGYACTSIHGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KGADSLEDFLYHEGYACTSIHGDR 24 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;;; 201.35 5.82E-25 1344820000 1165820 1094799 322179 728417 1146187 979854 1212830 1357659 912493 FALSE TRUE 1011753.933 1087607.193 477985.842 893815.213 1123380.121 1017549.617 1095209.933 1067334.188 804619.1171 1.257432134 1.351704391 0.594052306 1.110855054 1.396163846 1.26463515 1.361153259 1.326508612 1 19.61794649 3.399978558 7.591695788 1.282023304 1.056425129 0.155273804 0.22176223 0.401549963 33.79076074 0.064422116 0.083305746 2511.762419 -3.399978558 -0.225598175 KGAEPSGGAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGAEPSGGAAR 11 1 O00762;K4DI81;A0A0A0MSE8;A0A087WVK1;O00762-3;O00762-4 O00762 UBE2C Ubiquitin-conjugating enzyme E2 C 0 96.604 0.011045 39573000 79912 84906 51432 64415 71023 73564 88031 108180 73986 FALSE TRUE 69351.42673 84348.2469 76304.68723 79041.41027 69609.78125 76394.05468 79493.76717 85046.54886 65239.45937 1.063028839 1.292902297 1.169609435 1.211558327 1.066988935 1.170979273 1.21849212 1.303605972 1 15.99345721 2.320632185 7.587671529 1.202770631 1.166421764 0 0.100090178 1.08589692 85.96212529 0.036502765 0.028143191 209.2339651 -2.320632185 -0.036348866 KGAGDGS(ph)DEEVDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 20 KGAGDGSDEEVDGK 14 1 P35579;P35579-2 P35579 MYH9 Myosin-9 1 KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK 197.94 2.41E-08 66734754300 19566242 13237618 17230557 16450508 13185830 9487979 20664261 22862766 38770981 TRUE FALSE 16980513.55 13150659.22 25563312 20185847.27 12923457.78 9852987.692 18660244.15 17973741.41 34187519.79 0.496687494 0.38466257 0.747738126 0.590444917 0.378016828 0.288204226 0.545820354 0.525739847 1 25.02696643 1.21237094 3.582341085 1.089657917 0.490415862 0.611461231 0.126748656 0.247216478 4.565839234 0.418829356 0.033975438 16.30688243 -1.21237094 -0.599242056 KGAGDGS(ph)DEEVDGKADGAEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KGAGDGSDEEVDGKADGAEAK 21 2 P35579;P35579-2 P35579 MYH9 Myosin-9 1 KGAGDGS(1)DEEVDGKADGAEAK;KGAGDGS(1)DEEVDGKADGAEAK;KGAGDGS(1)DEEVDGKADGAEAK;KGAGDGS(1)DEEVDGKADGAEAK 238.12 3.66E-30 1708540000 2304500 1455500 2291550 1670590 1204080 773320 2506500 2667200 2879840 TRUE FALSE 1999954.486 1445938.725 3399751.245 2049922.993 1180121.164 803070.1208 2263420.016 2096840.036 2539388.596 0.787573233 0.569404276 1.338807007 0.80725061 0.464726496 0.316245462 0.891324793 0.825726334 1 21.27604975 3.475267433 24.98550606 0.703799765 0.900234618 0.102239468 0.270720789 149.7537806 2018326.797 0.081802506 0.106371544 2987.221542 -3.475267433 0.196434853 KGAGDGS(ph)DEEVDGKADGAEAKPAE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 15 KGAGDGSDEEVDGKADGAEAKPAE 24 3 P35579;P35579-2 P35579 MYH9 Myosin-9 1 KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE 210.58 2.21E-24 1.16191E+11 14913119 9680254 10656644 7477657 8074767 4825867 16737062 17373002 6365691 TRUE FALSE 12942312.54 9616663.774 15810232.68 9175573.311 7914094.935 5011521.226 15113904.3 13657920.72 5613146.262 2.305714467 1.713239478 2.816643634 1.634657798 1.409921382 0.892818571 2.692590501 2.433202358 1 22.42037822 KGAGSVFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGAGSVFR 8 1 P62917;E9PKZ0;G3V1A1;E9PKU4;E9PP36 P62917 RPL8 60S ribosomal protein L8 0 ; 92.838 0.01843 1367230000 2295000 2699600 1197670 1306160 2172440 2205900 2811400 2906500 763800 FALSE TRUE 1991709.935 2681866.15 1776867.218 1602743.591 2129212.694 2290762.4 2538750.861 2284967.593 673504.4341 2.957233589 3.981957674 2.638241306 2.379707557 3.161393729 3.401258083 3.769464212 3.39265412 1 19.36132792 1.23601712 24.99705544 0.999997055 3.229733433 0.677619712 0.478939635 43.49598901 427380.4378 0.813777244 0.123015573 17.21936451 -1.23601712 2.229736378 KGAVAEDGDELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KGAVAEDGDELR 12 1 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;G3V5D9;G3V2D9 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ;;;; 173.68 5.20E-05 2222220000 5830700 3864400 3063750 4061670 3989810 3386900 4094810 4923160 7456700 FALSE TRUE 5060158.222 3839014.502 4545389.748 4983934.252 3910420.587 3517196.235 3697695.956 3870380.546 6575177.421 0.769585047 0.583864778 0.691295376 0.75799236 0.594724726 0.534920354 0.562372043 0.58863515 1 22.64859839 1.234727667 24.99979379 1.000000531 0.629358671 0.668735534 0.080539609 70.79256883 461665.1584 0.149879515 0.020446796 17.16831476 -1.234727667 -0.37064186 KGAVAEDGDELRTEPEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGAVAEDGDELRTEPEAK 18 2 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;G3V5D9 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 143.71 5.82E-08 412430000 267800 153070 92212 87151 139830 84986 220010 195710 61288 FALSE TRUE 232409.5515 152064.4731 136806.0316 106939.9666 137047.6566 88255.46641 198673.4641 153858.9395 54042.60246 4.30048778 2.813788866 2.531447884 1.978808601 2.535918892 1.633072102 3.676237913 2.846993529 1 15.72180953 4.782404213 2.127470487 2.405148791 4.955921421 0.429182875 0.714339006 0.815480883 3.76724136 0.185829548 4.139309184 60590.45484 -4.782404213 2.55077263 KGAVECCPNCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGAVECCPNCR 11 1 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 125.36 0.00052905 85012000 128880 113360 53595 53472 97918 97442 108360 117360 55192 FALSE TRUE 111848.1815 112615.3307 79513.72126 65613.63487 95969.62337 101190.6568 97851.26388 92263.4773 48667.26463 2.298222066 2.313985212 1.633823513 1.348208809 1.971954333 2.079234524 2.010617704 1.895801582 1 15.57066407 4.245348598 24.97342731 1.749062476 2.306103949 0.357592544 0.330625751 184.8161982 679933.1607 0.084802268 0.213921279 17593.35224 -4.245348598 0.557041473 KGDECELLGHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGDECELLGHSK 12 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 145.71 4.16E-05 396990000 557800 439100 326240 647460 492400 388490 547890 703190 505180 FALSE TRUE 484085.3167 436215.5232 484010.7552 794475.6888 482602.2034 403435.4617 494755.7121 552818.2907 445458.1959 1.086713234 0.979251313 1.086545852 1.783502237 1.083383823 0.905664023 1.110666987 1.241010483 1 18.76493052 1.21926698 23.79289037 0.999998999 1.162377403 0.042249909 0.238468635 2955.087613 3643848.902 1.984990345 0.059657111 16.56788153 -1.21926698 0.162378405 KGDEVDGVDEVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGDEVDGVDEVAK 13 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 140.84 6.34E-05 830070000 2058720 1487170 1304860 1416880 1316690 968960 1870080 2231580 2548900 FALSE TRUE 1786654.936 1477400.682 1935894.66 1738604.26 1290490.445 1006236.518 1688719.929 1754373.983 2247571.946 0.794926694 0.657331875 0.861327115 0.773547767 0.574170917 0.447699358 0.751353002 0.780564105 1 21.09993587 1.263284866 1.97864684 1.087197922 0.689021869 0.403760524 0.117378608 0.822377245 3.287853007 0.597288816 0.034316361 18.33516681 -1.263284866 -0.398176053 KGDGGGAGGGGGGGGSGGGGS(ph)GGGGGGGSSRPPAPQENTTSEAGLPQGEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGDGGGAGGGGGGGGSGGGGSGGGGGGGSSRPPAPQENTTSEAGLPQGEAR 51 2 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 KGDGGGAGGGGGGGGS(0.448)GGGGS(0.545)GGGGGGGS(0.003)S(0.003)RPPAPQENTTSEAGLPQGEAR 120.92 7.50E-12 53849000 27599 19908 15172 11790 22483 18606 16596 21040 18256 TRUE FALSE 23951.72222 19777.22304 22509.22995 14467.0997 22035.63229 19321.78486 14986.52247 16540.75973 16097.79648 1.48788825 1.228567094 1.398280192 0.898700621 1.368860162 1.200275136 0.930967322 1.027517012 1 13.9745756 7.99999998 0.168700025 0.841866247 3.254898647 0.468644785 0.149187708 114.9079206 1.559145506 1.642649893 67.80247573 99999995.49 -7.99999998 2.413032399 KGDIFLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGDIFLVR 8 1 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 123.86 0.0021318 5451100000 8171300 5408500 2662100 3563000 4512300 4393500 4569300 5965500 5966500 FALSE TRUE 7091442.002 5372971.207 3949500.464 4372033.607 4422514.058 4562520.788 4126169.989 4689824.249 5261147.167 1.347888925 1.021254688 0.750691881 0.831003861 0.840598812 0.867210257 0.78427192 0.891407159 1 22.32694598 4.632803435 2.892087741 0.851912703 1.381202076 0.841985054 0.068124147 0.117604106 1.540418786 0.017184825 0.126929062 42934.2059 -4.632803435 0.529289373 KGDIIQLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGDIIQLQR 9 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 123.79 0.00087832 2256500000 1727770 1573630 998920 1224400 1661350 1520030 1674860 1879330 1795380 FALSE TRUE 1499440.817 1563292.721 1482001.053 1502418.734 1628292.385 1578506.538 1512432.335 1477449.904 1583132.222 0.947135556 0.987468197 0.936119569 0.949016584 1.028525832 0.997078144 0.955341768 0.933244794 1 20.59435032 KGDILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGDILR 6 1 P46108-2;P46108 P46108-2 CRK Adapter molecule crk 0 95.62 0.069169 498520000 763100 709000 510130 600540 618550 671810 747760 809570 768080 FALSE TRUE 662254.4016 704342.5323 756830.5743 736901.7857 606242.0652 697654.9654 675242.3503 636449.7556 677278.4574 0.977817018 1.039960041 1.117458508 1.0880337 0.895114939 1.030085865 0.996993693 0.939716521 1 19.36938958 3.26100753 24.99953382 0.973030007 1.059087608 0.401917592 0.050501254 239.1430339 266336.1305 0.014620651 0.018860795 1823.927326 -3.26100753 0.086057602 KGDIVDIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KGDIVDIK 8 1 P46778;M0R181;G3V1B3 P46778 RPL21 60S ribosomal protein L21 0 ;;; 96.89 0.013822 5366050000 10746820 8617360 6534830 8011960 7458540 5996310 10590960 11958810 10303920 FALSE TRUE 9326600.508 8560751.995 9695095.646 9831197.973 7310129.646 6226991.926 9563850.329 9401511.545 9085802.316 1.026502689 0.942212003 1.067059937 1.082039608 0.804566222 0.685354106 1.052614838 1.034747534 1 23.11518249 3.269202709 24.9998947 0.929149472 1.025908166 0.190885519 0.114611078 462.0648275 376980.84 0.037162513 0.047970882 1858.671797 -3.269202709 0.096758694 KGDLLLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGDLLLNR 8 1 Q15008;Q15008-4;Q15008-3;Q15008-2 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 113.74 0.0044744 3060900000 2906600 3068500 1705630 2093800 2522800 2351100 2615400 2974100 3010400 FALSE TRUE 2522485.446 3048342.821 2530478.373 2569229.292 2472601.216 2441548.338 2361758.911 2338111.859 2654513.941 0.950262647 1.148361956 0.953273717 0.96787184 0.93147042 0.919772279 0.889714261 0.88080602 1 21.34001629 4.041879424 13.10750561 0.926068613 1.049767733 0.40551632 0.057998713 1.05510194 328.0805389 0.014105963 0.029364716 11012.33525 -4.041879424 0.123699119 KGDRS(ph)PEPGQTWTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 KGDRSPEPGQTWTR 14 2 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 KGDRS(0.978)PEPGQT(0.007)WT(0.015)R;KGDRS(0.995)PEPGQT(0.002)WT(0.003)R;KGDRS(1)PEPGQTWTR;KGDRS(0.673)PEPGQT(0.325)WT(0.003)R;KGDRS(1)PEPGQTWTR;KGDRS(0.994)PEPGQT(0.006)WTR;KGDRS(1)PEPGQTWTR;KGDRS(0.996)PEPGQT(0.003)WT(0.001)R 177.12 1.11E-06 16199230000 6432490 4547261 3045581 4492810 5357424 4509221 4469668 6631334 4285884 TRUE FALSE 5582420.149 4517389.743 4518434.158 5512971.179 5250821.744 4682693.65 4036200.285 5213274.829 3779211.676 1.477138786 1.195325938 1.195602296 1.458762211 1.389396042 1.239066253 1.068000586 1.379460924 1 21.8496539 1.227863521 24.92176176 0.999999358 1.292425126 0.345745403 0.129435629 545.579846 1270985.57 0.444829004 0.031272943 16.89909786 -1.227863521 0.292425768 KGDSNANSDVCAAALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGDSNANSDVCAAALR 16 1 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 0 108.56 0.0036088 0 64504 48585 38730 44975 60224 57044 53794 64438 47597 FALSE TRUE 55979.63297 48265.84194 57459.95754 55187.26115 59025.66023 59238.51959 48577.06616 50658.43516 41970.13688 1.333796769 1.150004396 1.369067671 1.31491735 1.406372831 1.411444517 1.15741977 1.207011435 1 15.35707555 1.291075399 1.198835348 0.883015563 1.320653411 0.582627243 0.085527698 1.056843548 1.39196802 0.579738268 0.027594346 19.54678785 -1.291075399 0.437637848 KGDSSAEELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KGDSSAEELK 10 1 P26373;P26373-2 P26373 RPL13 60S ribosomal protein L13 0 ;;;; 148.78 3.93E-05 7737000000 7990680 6179700 5181100 5983750 5113960 4175260 8434910 9264870 8937780 FALSE TRUE 6934691.392 6139105.144 7686697.29 7342451.893 5012202.201 4335884.954 7616893.726 7283649.65 7881165.83 0.879906798 0.778959011 0.975324902 0.9316454 0.635972178 0.550157813 0.966467892 0.92418429 1 22.90997763 KGDSVGLR ddPTM_MDA-MB-175_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 89.886 0.021787 216410000 424740 417070 217990 368570 333490 362190 453650 493420 490490 FALSE TRUE 368609.5328 414330.2397 323410.6931 452259.4517 326854.2015 376123.6837 409655.0928 387905.9728 432504.831 0.852266857 0.957978293 0.747762036 1.045674914 0.755723816 0.869640422 0.947168826 0.896882405 1 18.72235672 -1.206975485 0.851174469 9.999999981 0.876611576 0.152325064 0.08890978 280.6088449 3.57337896 4797.714019 0.029250577 0.062090408 1.206975485 -9.123388405 KGDTWYLVDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGDTWYLVDSR 11 1 Q9Y4E8;F8W0H4;H0YI31;Q9Y4E8-4;Q9Y4E8-2;Q9Y4E8-3 Q9Y4E8;Q9Y4E8-2 USP15 Ubiquitin carboxyl-terminal hydrolase 15 0 ; 88.075 0.021244 808620000 1252180 1180300 725590 919590 1093170 985540 1085010 1344840 1382170 FALSE TRUE 1086701.24 1172546.532 1076487.751 1128396.965 1071418.056 1023454.362 979785.8972 1057256.432 1218771.437 0.891636616 0.962072539 0.883256465 0.925847891 0.879096788 0.839742654 0.80391275 0.867477198 1 20.21699616 3.139343798 5.065109354 0.868329248 0.916582998 0.095397292 0.053975018 0.415201743 17.21037206 0.016745368 0.019224975 1378.300132 -3.139343798 0.04825375 KGDVEGSQS(ph)QDEGEGSGESER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KGDVEGSQSQDEGEGSGESER 21 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 1 KGDVEGSQS(1)QDEGEGSGESER;KGDVEGSQS(1)QDEGEGSGESER;KGDVEGS(0.006)QS(0.994)QDEGEGSGESER;KGDVEGSQS(1)QDEGEGSGESER;KGDVEGS(0.001)QS(0.999)QDEGEGSGESER 348.33 1.67E-95 4068580000 2445161 2254383 1624830 1810819 2278413 1811597 2484816 3000410 2587620 TRUE FALSE 2122026.779 2239573.81 2410603.223 2221993.131 2233077.039 1881290.309 2243838.927 2358795.671 2281714.511 0.930014149 0.981531124 1.056487659 0.973826094 0.978683805 0.824507317 0.983400384 1.033782123 1 21.12168686 1.994385857 24.9842551 1.016090238 0.959732793 0.151171449 0.057865226 471.8473839 2099829.603 0.025637069 0.016666248 98.71561524 -1.994385857 -0.056357444 KGDVEGSQSQDEGEGSGESER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGDVEGSQSQDEGEGSGESER 21 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 168.86 1.65E-11 256130000 129000 107680 64539 78662 102860 91441 107040 123660 106730 FALSE TRUE 111952.3232 106972.643 95750.27627 96523.40937 100813.2872 94958.79444 96659.27728 97216.27132 94112.50099 1.189558475 1.13664648 1.017402314 1.025617302 1.071199747 1.00899236 1.027060978 1.032979363 1 16.52209875 4.360687329 3.496502152 1.027580231 1.180692774 0.897101214 0.019627709 0.063966191 1.462338209 0.00496365 0.015973376 22944.96126 -4.360687329 0.153112543 KGDVVHCWYTGTLQDGTVFDTNIQTSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGDVVHCWYTGTLQDGTVFDTNIQTSAK 28 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 123.79 2.75E-05 95982000 126660 91032 64818 75243 88897 75278 109730 128520 116030 FALSE TRUE 109921.5601 90434.0048 96164.2016 92328.07317 87128.12362 78173.99337 99088.40149 101036.9981 102313.0656 1.074364838 0.883894977 0.939901478 0.902407455 0.85158355 0.764066573 0.968482382 0.987527815 1 16.64263087 2.021869854 24.99999639 0.988412745 0.898291371 0.206977038 0.076949067 341.5308932 390411.1733 0.031706922 0.021375132 105.1646677 -2.021869854 -0.090121374 KGDVVIVLTGWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGDVVIVLTGWR 12 1 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 79.022 0.038732 600850000 762170 626310 687310 801280 592880 589100 806140 790100 1855370 FALSE TRUE 661447.3034 622195.7284 1019695.415 983222.8708 581082.848 611763.0582 727960.6669 621143.2636 1636030.272 0.404300162 0.3803082 0.623274173 0.600980854 0.355178543 0.37393138 0.444955499 0.379664896 1 20.64176801 1.234410646 24.99999905 1.000000809 0.445574509 0.775125332 0.093891342 62.32819077 375422.1578 0.183860601 0.024454894 17.15578701 -1.234410646 -0.5544263 KGDVVIVLTGWRPGSGFTNTMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KGDVVIVLTGWRPGSGFTNTMR 22 2 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;; 170.18 4.19E-12 4587300000 2522300 2091630 1542040 1877740 1920350 1716870 2756470 2790170 2167910 FALSE TRUE 2188971.664 2077889.945 2287775.702 2304109.566 1882138.792 1782919.1 2489147.964 2193513.859 1911622.149 1.14508595 1.086977333 1.196771916 1.20531642 0.984576786 0.932673384 1.302112954 1.147462044 1 20.86636596 5.238305282 9.699078403 1.115903768 7.124952951 0.005641421 0.113183554 1199972.589 213232.565 0.027574679 159553723 173103.2742 -5.238305282 6.009049182 KGDYIEAESSYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KGDYIEAESSYSR 13 1 Q99614 Q99614 TTC1 Tetratricopeptide repeat protein 1 0 ;; 120.3 0.00044972 487100000 419768 339376 235490 306117 378393 316591 357928 484050 392696 FALSE TRUE 364294.5952 337146.6167 349373.7517 375625.5436 370863.7196 328770.4606 323216.1977 380539.6744 346271.9262 1.052047734 0.973646984 1.008957773 1.084770422 1.071018733 0.949457452 0.933417275 1.098961959 1 18.4015459 3.957777898 24.97797542 1.025946635 1.007460902 0.005379087 0.056803601 2585.751944 1529692.513 0.0157174 0.027226799 9073.563814 -3.957777898 -0.018485733 KGEDFVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KGEDFVK 7 1 P40926;G3XAL0;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 ;; 84.476 0.034502 2698450000 5024000 4638500 3730130 6527400 4990900 4572000 5602800 7501200 7172500 FALSE TRUE 4360065.671 4608029.388 5534033.345 8009545.935 4891590.855 4747887.798 5059441.318 5897126.754 6324575.221 0.689384744 0.728591127 0.875004748 1.266416424 0.77342599 0.750704614 0.799965396 0.932414676 1 22.59253716 4.228746485 4.587999558 0.912652115 0.703321197 0.257714983 0.146162342 0.267788266 13.92005917 0.039057874 0.096759297 16933.49038 -4.228746485 -0.209330918 KGEDVLGSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KGEDVLGSVR 10 1 P56192;P56192-2;F5H2V6 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ;;; 135.6 0.00022432 1050870000 2596930 2036500 1503770 1668360 2027820 1946630 2236080 2503950 2544220 FALSE TRUE 2253739.121 2023122.097 2230998.202 2047186.637 1987470.349 2021518.116 2019225.306 1968499.778 2243445.21 1.004588439 0.901792515 0.994451833 0.912519115 0.885900998 0.901077551 0.900055547 0.877444998 1 21.09728452 7.999999892 0.6045499 0.908634771 6.404380764 0.235453711 0.043379592 250.7375011 1.939269606 0.019609344 1821.369674 99999975.21 -7.999999892 5.495745994 KGEFETGFEK ddPTM_MDA-MB-175_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 ; 170.04 7.13E-06 2530200000 3251100 2446300 1885920 2160510 2079230 1692640 3171400 3605700 3151600 FALSE TRUE 2821458.898 2430230.094 2797957.22 2651086.817 2037857.391 1757756.956 2863838.116 2834649.115 2779021.438 1.015270648 0.874491309 1.006813831 0.953964147 0.733300349 0.632509319 1.03052034 1.020017001 1 21.40614553 KGEIFELK ddPTM_MDA-MB-175_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 ; 98.943 0.011488 3255100000 8238900 6084700 5171400 5609900 6002800 4977300 8256800 9649200 8664400 FALSE TRUE 7150108.49 6044729.205 7672306.337 6883713.537 5883356.024 5168779.952 7456056.807 7585793.67 7640104.503 0.935865274 0.7911841 1.004214842 0.900997301 0.770062245 0.676532625 0.975910317 0.99289135 1 22.86516094 2.035489435 24.996797 0.992477078 0.84814454 0.358600296 0.09048943 191.7581226 135063.0789 0.038474903 0.025939687 108.5149151 -2.035489435 -0.144332538 KGEILVIIEKPEEQWWSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGEILVIIEKPEEQWWSAR 19 2 P46109 P46109 CRKL Crk-like protein 0 ; 114.72 8.55E-05 349680000 579500 471650 369170 493560 417110 289070 468510 551100 552110 FALSE TRUE 502917.6067 468551.7001 547701.8468 605630.3416 408810.3271 300190.71 423073.9723 433251.5537 486840.1848 1.033024024 0.962434316 1.125013637 1.244002366 0.839721822 0.616610377 0.869020236 0.889925621 1 18.89308873 3.211062638 24.64917618 0.839539293 1.084347892 0.525013267 0.117138672 157.5705642 141245.6216 0.037707486 0.042766617 1625.783225 -3.211062638 0.244808599 KGENYVYINEATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGENYVYINEATR 13 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 113.52 0.0013075 299740000 293500 247330 156580 254870 277970 220500 296700 308290 292710 FALSE TRUE 254713.2314 245705.2729 232302.6117 312742.1289 272438.9408 228982.7777 267926.0797 242364.5826 258106.1573 0.986854533 0.951954326 0.900027393 1.211680234 1.055530576 0.887165111 1.03804606 0.939011239 1 17.97760503 KGEPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGEPER 6 1 Q9Y2A7;Q9Y2A7-2;P55160-2;P55160 Q9Y2A7 NCKAP1;NCKAP1L Nck-associated protein 1;Nck-associated protein 1-like 0 83.614 0.091054 52709000 163940 132240 93431 112720 83419 118810 147100 159350 165140 FALSE TRUE 142274.9136 131371.3067 138614.5441 138314.7988 81759.12511 123380.6976 132834.2646 125274.2426 145617.3373 0.977046526 0.902168033 0.951909619 0.949851174 0.561465596 0.847294009 0.912214624 0.860297578 1 17.15182261 KGESGQSWPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KGESGQSWPR 10 1 A0A087WYT3;Q15185-4;Q15185;Q15185-3;B4DDC6 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ;;;; 174.42 4.99E-06 13420600000 9376160 8884210 5298990 7032370 8820930 7820420 9733500 11341020 10624460 FALSE TRUE 8137076.7 8825849.04 7861599.288 8629177.092 8645410.751 8121276.618 8789546.668 8915831.129 9368448.442 0.868561828 0.942082256 0.839157021 0.921089244 0.922822045 0.866875307 0.938207295 0.951687057 1 23.1593787 1.477587184 1.18461481 1.023656297 0.895282412 0.549379728 0.031754531 0.739451479 1.230544405 0.110816984 0.009627629 30.03220249 -1.477587184 -0.128373886 KGESQTDIEITR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KGESQTDIEITR 12 1 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;;; 180.3 3.15E-05 5480150000 4258090 3555200 2702510 3400220 3685260 2997040 4054020 4722220 4986420 FALSE TRUE 3695372.618 3531845.657 4009452.875 4172291.92 3611930.536 3112338.068 3660861.764 3712410.001 4396931.108 0.840443602 0.803252444 0.9118753 0.948910005 0.821466256 0.707843264 0.832594752 0.844318437 1 22.0680655 1.237943706 5.818810447 1.006678397 0.838279998 0.389654673 0.063435002 0.164068793 19.61364002 0.110156079 0.016952136 17.29592151 -1.237943706 -0.168398399 KGESVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGESVKR 7 2 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ; 71.223 0.030877 1900670000 3171700 2417700 1465440 1737340 1297460 1710010 2931000 3380100 1005130 FALSE TRUE 2752551.809 2401817.97 2174131.686 2131829.601 1271643.084 1775795.191 2646752.071 2657291.919 886304.6764 3.105649651 2.709923611 2.45302969 2.405301086 1.434769688 2.003594518 2.986277904 2.998169805 1 19.7574432 4.434301335 1.588219573 2.253313843 3.173151622 0.20731017 0.616770095 1.186591967 4.378787464 0.184574952 1.425439339 27183.24722 -4.434301335 0.919837779 KGETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGETLR 6 1 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 87.582 0.083822 196070000 471240 403540 255120 325240 290290 306580 432070 476300 517470 FALSE TRUE 408964.44 400889.1192 378496.8853 399090.713 284513.7969 318374.331 390167.9179 374446.9516 456295.2861 0.896271455 0.878573878 0.829499881 0.874632557 0.623529994 0.697737497 0.855077687 0.820624194 1 18.79960822 4.049411333 1.838518279 0.80303114 0.891649598 0.08738228 0.099930174 0.957742302 6.239103093 0.030275565 0.091645831 11204.98638 -4.049411333 0.088618458 KGFLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGFLFR 6 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 104.04 0.054791 1813190000 3148200 3177700 1752480 2833200 3417500 3522600 2852900 3822700 3628500 FALSE TRUE 2732157.393 3156825.479 2599985.19 3476521.363 3349498.436 3658116.701 2576226.197 3005245.353 3199542.864 0.853921172 0.98664891 0.812611457 1.086568148 1.046867812 1.143324799 0.805185712 0.939273353 1 21.60943436 4.743291814 22.73160682 0.972086713 0.853920995 0.114357347 0.107174273 349.8619189 1680727.078 0.026511628 0.202455253 55372.20453 -4.743291814 -0.118165719 KGFNGCDS(ph)PEPDGEDSLEQSPLLEDKYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGFNGCDSPEPDGEDSLEQSPLLEDKYR 28 2 Q14814-4;Q14814;Q05BX2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 KGFNGCDS(1)PEPDGEDSLEQSPLLEDKYR 176.98 9.55E-18 138940000 111210 100870 62314 82877 112240 76246 136570 174950 42955 TRUE FALSE 96513.31673 100207.3783 92449.25883 101695.4895 110006.6436 79179.23296 123325.4624 137538.304 37876.90883 2.548077964 2.645606028 2.440781512 2.684894113 2.904319465 2.09043545 3.255953725 3.631191356 1 15.20903098 3.494836567 20.61625824 2.7403298 2.556222858 0 0.711718408 518.5404904 603445.6657 0.198464671 0.285948814 3124.90319 -3.494836567 -0.184106941 KGFSEGLWEIENNPTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGFSEGLWEIENNPTVK 17 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ; 197.14 2.46E-11 2178150000 3876000 3236900 2021580 2357200 2841200 2403900 4000300 4461500 1861970 FALSE TRUE 3363776.779 3215636.591 2999222.85 2892438.288 2784665.679 2496379.589 3612351.522 3507442.944 1641850.028 2.048772252 1.958544652 1.826733745 1.761694575 1.696053617 1.520467489 2.200171429 2.136274864 1 20.64689092 4.329046472 2.247417126 1.783458324 2.045038993 0.09303059 0.33159072 1.028125281 9.646165517 0.09071079 0.380881953 21332.73176 -4.329046472 0.261580668 KGGEFDEFVNDDT(ph)DDDLPISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KGGEFDEFVNDDTDDDLPISK 21 1 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 KGGEFDEFVNDDT(1)DDDLPISK;KGGEFDEFVNDDT(1)DDDLPISK;KGGEFDEFVNDDT(1)DDDLPISK;KGGEFDEFVNDDT(1)DDDLPISK;KGGEFDEFVNDDT(1)DDDLPISK;KGGEFDEFVNDDT(1)DDDLPISK 202.14 3.84E-22 3803700000 2407760 1730761 1493132 1582956 1658768 1300495 2323034 2701650 2302590 TRUE FALSE 2089568.416 1719391.517 2215215.629 1942390.354 1625761.762 1350525.884 2097746.52 2123923.172 2030380.433 1.029151178 0.846832194 1.09103476 0.956663255 0.800717804 0.665159032 1.033179047 1.046071533 1 20.95331864 KGGHERPPS(ph)PGLR ddPTM_MDA-MB-175_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 88.992 0.0039938 438370000 178439 143336 83296 111808 144536 108699 146329 178769 123339 TRUE FALSE 154857.834 142394.4164 123578.2242 137195.7153 141660.0164 112880.7209 132138.0361 140540.6405 108758.0039 1.423875287 1.309277582 1.136267858 1.261476952 1.302524975 1.037907251 1.21497298 1.292232622 1 16.73076205 7.999999984 0.740778144 1.184017172 42.80159889 0.383440986 0.102003049 411.4668395 1.851067257 0.037806524 28537.2514 99999996.24 -7.999999984 41.61758172 KGGSWIQEINVAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGGSWIQEINVAEK 14 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 155.57 9.31E-06 275690000 583940 387730 261880 339680 372520 285660 527470 581350 473950 FALSE TRUE 506770.8495 385182.9761 388526.0439 416809.5357 365107.5808 296649.525 476316.0406 457032.8266 417920.1709 1.212602034 0.921666392 0.92966569 0.99734247 0.873629957 0.70982342 1.139729723 1.09358882 1 18.67286787 -0.724307895 9.889963798 2.638280905 0.986384447 0 0.142631004 0 0 0 0.032903236 0.188665333 0.724307895 -1.651896459 CNEIINWLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 CNEIINWLDK 10 0 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 159.09 1.81E-05 424410000 395660 380130 209860 333880 316470 296420 338720 458550 877580 FALSE TRUE 343372.5285 377632.901 311348.9979 409692.557 310172.8662 307823.4692 305870.9865 360492.6509 773833.4921 0.443729216 0.488002787 0.402346243 0.529432444 0.400826366 0.397790316 0.395267186 0.465852996 1 19.56166365 1.238385089 5.417255663 1.028740544 0.437766022 0.942616987 0.043447784 0.032472828 2.863963515 0.071759316 0.01067022 17.31350866 -1.238385089 -0.590974522 KGHYAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGHYAER 7 1 P16104 P16104 H2AFX Histone H2AX 0 84.476 0.034502 78447000 100680 91960 45548 66322 62737 79693 72353 95400 73734 FALSE TRUE 87374.88291 91355.9087 67575.16515 81381.42377 61488.65644 82758.84128 65336.2172 74999.4524 65017.25052 1.343872314 1.405102615 1.039342092 1.251689715 0.945728341 1.272875131 1.004905878 1.153531591 1 15.98853493 4.242715386 24.99998444 1.102346393 1.374487564 0.536527974 0.107675554 70.30606349 423028.3713 0.023895155 0.058659153 17487.00305 -4.242715386 0.272141172 KGIAFPTSISVNNCVCHFSPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGIAFPTSISVNNCVCHFSPLK 22 1 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7;F8VZ69 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 81.884 0.0031873 259240000 331140 302400 85105 155360 337350 314450 347830 406510 206760 FALSE TRUE 287379.01 300413.5145 126262.0627 190636.8625 330637.395 326547.095 314097.5001 319581 182317.0683 1.576259495 1.6477531 0.692541098 1.045633655 1.813529573 1.791094481 1.722809076 1.752885799 1 17.47609011 3.236798851 24.9998732 1.649923979 1.230489722 0.217973125 0.349958207 68.72436326 975217.3174 0.107265589 0.128016142 1725.038735 -3.236798851 -0.419434256 KGLEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGLEAR 6 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 92.692 0.074506 259270000 1011300 1048600 630440 865960 841390 1136700 1194100 1563500 1387800 FALSE TRUE 877654.1427 1041711.678 935322.8927 1062589.453 824647.9852 1180429.585 1078296.366 1229157.692 1223735.865 0.717192466 0.85125533 0.764317627 0.868316018 0.673877434 0.964611415 0.881151233 1.004430553 1 20.22286077 2.714202324 24.78221692 0.961461456 0.783820314 0.66955654 0.065307213 412.4742124 419652.1652 0.021141417 0.018654002 517.8480244 -2.714202324 -0.177641142 KGLIAAICAGPTALLAHEIGFGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGLIAAICAGPTALLAHEIGFGSK 24 1 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 260.57 3.30E-44 332080000 604390 535890 263660 371790 402320 393110 532980 710040 301440 FALSE TRUE 524518.3302 532369.7033 391166.8579 456210.602 394314.6191 408233.1961 481291.6816 558203.4715 265804.1066 1.973326661 2.002864855 1.471635871 1.716341436 1.483478281 1.535842321 1.810700699 2.100055859 1 18.02000387 4.256077597 24.76255223 1.644857726 1.988096111 0.238084558 0.283633268 361.0323322 510356.619 0.071487019 0.188169781 18033.39923 -4.256077597 0.343238385 KGLPLGSAVSSPVLFS(ph)PVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGLPLGSAVSSPVLFSPVGR 20 1 Q8WUM0 Q8WUM0 NUP133 Nuclear pore complex protein Nup133 1 KGLPLGSAVSSPVLFS(1)PVGR 77.693 0.0059481 270550000 358510 428870 183960 220620 441330 392410 422700 552030 159490 TRUE FALSE 311131.9952 426052.7247 272923.6713 270715.143 432548.3964 407506.2666 381706.6191 433982.6804 140635.2739 2.212332557 3.029486934 1.94064877 1.924944827 3.075675003 2.897610645 2.714159887 3.08587361 1 17.10159897 3.243018938 24.99879063 2.650174576 2.306598319 0.029896634 0.664188074 368.1530981 2064303.908 0.190407011 0.237430946 1749.922995 -3.243018938 -0.343576257 KGLTPSQIGVILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGLTPSQIGVILR 13 1 P62277;J3KMX5 P62277 RPS13 40S ribosomal protein S13 0 ; 183.96 6.54E-07 0 2409700 2215100 1018940 1311150 2094780 1935320 2246000 2661300 763300 FALSE TRUE 2091252.04 2200548.862 1511702.792 1608866.647 2053097.976 2009773.013 2028183.266 2092201.705 673063.5436 3.107064793 3.269451872 2.24600308 2.390363678 3.050377629 2.986007832 3.013360752 3.108475753 1 19.36038319 4.262186626 24.87695246 2.646490858 3.188258866 0.138130027 0.630390435 500.032744 526498.5492 0.154349122 0.407852496 18288.85959 -4.262186626 0.541768008 KGLVGPELHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KGLVGPELHDR 11 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;; 153.34 2.11E-05 1282220000 2064190 1855240 1158640 1401770 1940110 2018500 1891400 2142550 1633430 FALSE TRUE 1791402.062 1843052.806 1718962.179 1720063.303 1901505.607 2096153.001 1707972.319 1684382.356 1440327.766 1.243746114 1.279606524 1.193452088 1.194216583 1.320189509 1.455330551 1.185821977 1.169443786 1 20.45796572 1.376204286 1.755438132 0.953709188 1.273166208 0.551305781 0.078182045 0.563528951 2.133850553 0.28471757 0.023386508 23.77958582 -1.376204286 0.31945702 KGNAEGS(ph)S(ph)DEEGKLVIDEPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 159.56 1.20E-11 502170000 1462630 796360 1272300 959590 813400 530050 1216340 1542220 2278760 TRUE FALSE 1269339.74 791128.6587 1887588.536 1177479.576 797214.9314 550441.3665 1098379.534 1212428.255 2009367.589 0.631711065 0.393720225 0.939394338 0.585995107 0.396749174 0.273937616 0.546629467 0.603387982 1 20.93831008 1.210976169 2.893044167 1.114515451 0.535889987 0.39681342 0.177356818 0.513950915 4.935759127 0.732006993 0.047744566 16.2545956 -1.210976169 -0.578625464 KGNAEGS(ph)S(ph)DEEGKLVIDEPAKEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGNAEGSSDEEGKLVIDEPAKEK 23 3 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 2 KGNAEGS(1)S(1)DEEGKLVIDEPAKEK 106.81 0.0020209 574480000 313830 173590 239820 127190 151700 87542 319370 327840 119860 TRUE FALSE 272356.5704 172449.6759 355797.7541 156070.4335 148681.4668 90909.79739 288397.5466 257733.9673 105690.2873 2.576930929 1.631651121 3.366418647 1.476677161 1.40676566 0.860152808 2.728704347 2.4385776 1 16.68948328 3.671943491 24.99999181 1.757877033 2.435700351 0.240733203 0.708768949 341.6882572 128227.7188 0.203491377 0.301826539 4698.329713 -3.671943491 0.677823318 KGNCSQHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGNCSQHDR 9 1 Q9BRX2 Q9BRX2 PELO Protein pelota homolog 0 ; 111.91 0.00133 22740400 53721 54674 22089.7 36778 40230 50515 58716 66618 57905 FALSE TRUE 46621.63374 54314.84289 32772.35281 45129.00702 39429.50171 52458.34474 53021.73136 52372.25912 51059.53687 0.913083757 1.063755103 0.641845869 0.883850692 0.772225996 1.027395624 1.03842954 1.025709639 1 15.63989283 2.71949262 24.04007155 1.024782707 0.856318666 0.38307165 0.105876465 530.7116777 669095.728 0.036130133 0.031923104 524.1946931 -2.71949262 -0.168464041 KGNEAVAS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KGNEAVASR 9 1 Q8NBJ4-2;Q8NBJ4 Q8NBJ4-2 GOLM1 Golgi membrane protein 1 1 KGNEAVAS(1)R;KGNEAVAS(1)R;KGNEAVAS(1)R;KGNEAVAS(1)R 89.629 0.0073363 1416618000 1619370 1596430 1081658 1328966 1089483 1580640 1440200 1969320 2001890 TRUE FALSE 1405366.152 1585942.946 1604751.427 1630728.042 1067804.42 1641448.244 1300529.626 1548196.243 1765228.845 0.796138221 0.898434756 0.909089737 0.923805458 0.604909909 0.92987844 0.736748456 0.877051294 1 20.7514238 1.300870935 3.825450933 1.009500636 0.831719252 0.223453911 0.100310139 0.347516049 7.769681361 0.153792837 0.024464861 19.99267633 -1.300870935 -0.177781384 KGNEAVASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGNEAVASR 9 1 Q8NBJ4-2;Q8NBJ4 Q8NBJ4-2 GOLM1 Golgi membrane protein 1 0 ; 90.685 0.018059 212740000 224050 249860 175564 188169 179702 249460 217430 295290 303190 FALSE TRUE 194441.2248 248218.6532 260467.3376 230895.6474 176126.2818 259056.8876 196343.6721 232144.5314 267347.2236 0.727298463 0.928450462 0.974266103 0.863654555 0.658792261 0.968990379 0.73441448 0.868325948 1 18.02835517 1.263784578 4.751193845 1.00814828 0.841531678 0.18806804 0.105400256 0.292255067 14.20352161 0.151538379 0.025527567 18.35627595 -1.263784578 -0.166616602 KGNEQHAFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGNEQHAFTR 10 1 Q13045-3;Q13045;Q13045-2;K7EQZ7 Q13045-3 FLII Protein flightless-1 homolog 0 91.855 0.0064039 49853000 194770 190000 104000 123950 174000 158030 197990 197140 141480 FALSE TRUE 169030.651 188751.8775 154294.7479 152094.742 170537.7404 164109.5164 178788.9603 154983.1451 124754.3956 1.354907378 1.512987792 1.236788068 1.219153371 1.366987829 1.315460795 1.433127542 1.242306088 1 16.92873112 1.304596528 2.975454158 0.961663477 1.344790409 0.623549521 0.085470972 0.228983962 2.709467114 0.193925502 0.022671101 20.16492114 -1.304596528 0.383126932 KGNFNYIEFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGNFNYIEFTR 11 1 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ; 96.82 0.010787 898420000 1553290 1325640 925780 1140140 1450920 1374220 1387460 1712150 1150080 FALSE TRUE 1348018.791 1316931.784 1373490.305 1399026.213 1422049.531 1427087.133 1252904.343 1346020.046 1014118.853 1.329251288 1.298597083 1.35436818 1.37954857 1.402251351 1.407218818 1.23546105 1.327280371 1 19.95179531 0.693040632 1.499167539 7.34E-15 1.351987196 0.810349125 0.051706167 2.167744114 1.330160041 6.667901532 0.014833726 4.932199468 -0.693040632 1.351987196 KGNNESYHYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGNNESYHYAR 11 1 Q04446;E9PGM4 Q04446 GBE1 "1,4-alpha-glucan-branching enzyme" 0 111.63 0.001061 56082000 124260 116800 49632 86635 134660 123440 130750 151960 133750 FALSE TRUE 107838.7262 116032.7331 73634.20121 106306.8009 131980.5295 128188.8167 118069.8851 119464.5366 117938.2274 0.914366178 0.983843286 0.624345497 0.90137696 1.11906489 1.086914901 1.001116328 1.012941598 1 16.84767189 3.415161239 6.733922126 1.037738016 0.840281622 0.487270695 0.097320989 0.180918174 15.51258873 0.028399196 0.036849839 2601.125097 -3.415161239 -0.197456394 KGNS(ph)PNSEPPTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KGNSPNSEPPTPK 13 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 KGNS(0.999)PNS(0.001)EPPTPK;KGNS(0.987)PNS(0.013)EPPTPK;KGNS(0.959)PNS(0.041)EPPTPK;KGNS(0.976)PNS(0.024)EPPTPK 114.54 0.00045024 1898980000 2851640 1826290 1597480 1688090 1701340 1283140 2558520 2772340 2500770 TRUE FALSE 2474788.549 1814292.981 2370026.671 2071396.635 1667486.663 1332503.226 2310395.124 2179496.665 2205131.819 1.122285991 0.822759422 1.074777775 0.939352748 0.756184573 0.604273728 1.047735606 0.988374775 1 21.07243347 4.754841718 23.26651229 0.909922038 1.122286422 0.184316275 0.143743005 2356.042801 3366755.763 0.037037003 0.862823383 56864.56456 -4.754841718 0.212364384 KGNYAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 KGNYAER 7 1 Q99878;Q96KK5;Q6FI13;P0C0S8;Q16777;Q9BTM1;Q9BTM1-2;Q96QV6;Q8IUE6 Q99878 HIST1H2AJ;HIST1H2AH;HIST2H2AA3;HIST1H2AG;HIST2H2AC;H2AFJ;HIST1H2AA;HIST2H2AB Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-A;Histone H2A type 1;Histone H2A type 2-C;Histone H2A.J;Histone H2A type 1-A;Histone H2A type 2-B 0 ;;;;;;;;; 141.52 0.004091 1.79359E+11 57609590 55205100 29598910 43277980 34728900 45847420 50389300 62435680 50263830 FALSE TRUE 49996336.72 54842454.06 43913041.88 53104906.82 34037862.84 47611199.91 45502553.44 49084295.71 44321697.28 1.12803299 1.237372606 0.990779789 1.198169522 0.76797291 1.074218788 1.026642846 1.107455236 1 25.40150979 4.235067761 24.99829531 1.030167167 1.182702812 0.256367768 0.112218072 112.3345754 804000.1168 0.027216061 0.060493404 17181.76447 -4.235067761 0.152535645 KGNYSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KGNYSER 7 1 A0A0U1RR32;A0A0U1RRH7;P20671;A0A3B3IS11;Q7L7L0;P04908 A0A0U1RR32;Q7L7L0 HIST1H2AD;HIST3H2A;HIST1H2AB Histone H2A type 1-D;Histone H2A type 3;Histone H2A type 1-B/E 0 ;;;;;; 127.46 0.0061773 21920560000 26129450 24076890 12699240 17970330 14564240 20170490 22429430 27462380 23009470 FALSE TRUE 22676376.98 23918727.32 18840634.94 22050768.09 14274440.12 20946461.8 20254227.33 21589763.75 20289316.67 1.117651094 1.178882843 0.928598792 1.086816695 0.703544646 1.032388727 0.998270551 1.064095164 1 24.27421694 4.242720424 24.99572541 0.979340622 1.148267017 0.315139818 0.106898986 125.7938616 755851.4107 0.026552981 0.065148816 17487.20591 -4.242720424 0.168926395 KGPEADSEWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KGPEADSEWR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 108.56 0.0034226 2054050000 3255720 3051830 2048710 2462580 3019910 2787580 3311570 3872600 3732780 FALSE TRUE 2825468.353 3031782.328 3039473.009 3021746.427 2959819.699 2894820.006 2990414.451 3044474.627 3291495.001 0.8584149 0.921095832 0.923432364 0.918046792 0.899232628 0.879484856 0.908527721 0.924951922 1 21.65031158 1.166030301 2.03846691 1.044822185 0.902522197 0.708574739 0.019871555 0.528481551 1.832428829 0.152278362 0.005380821 14.65650096 -1.166030301 -0.142299988 KGPEFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGPEFTR 7 1 Q9NQG5;E9PIQ9 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 71.223 0.088026 293380000 308370 295160 152500 201660 309380 282900 303810 378910 322890 FALSE TRUE 267618.1232 293221.0745 226249.5101 247449.9852 303223.9433 293783.3461 274346.553 297883.0452 284718.312 0.939939975 1.029863771 0.794643339 0.869104567 1.06499628 1.031838606 0.963571858 1.046237747 1 18.11917576 3.239968757 24.99994514 1.020636214 0.908940142 0.435985569 0.063827117 37.87555299 672431.0808 0.019340042 0.023621553 1737.675818 -3.239968757 -0.111696072 KGPGAGSALDDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGPGAGSALDDGR 13 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 ; 113.65 0.0012905 534860000 1744910 1645610 1064520 1348140 1658550 1591600 1716500 1969440 1861180 FALSE TRUE 1514315.722 1634799.88 1579325.433 1654255.792 1625548.1 1652829.882 1550034.094 1548290.582 1641153.421 0.922714296 0.996128612 0.962326503 1.007983636 0.990491248 1.00711479 0.944478484 0.943416114 1 20.64627868 4.750870486 23.84706003 0.97809351 0.922714229 0.360856224 0.024211128 1342.037798 2599744.753 0.006398994 0.102740917 56346.95941 -4.750870486 -0.055379281 KGPGQPS(ph)SPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KGPGQPSSPQR 11 1 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 KGPGQPS(0.943)S(0.057)PQR;KGPGQPS(0.957)S(0.043)PQR;KGPGQPS(0.5)S(0.5)PQR;KGPGQPS(0.868)S(0.132)PQR 98.654 0.003283 1978520000 2577020 2114240 1718940 2113620 2119480 1986340 2258220 2695640 3903740 TRUE FALSE 2236460.278 2100351.418 2550225.134 2593549.726 2077306.495 2062755.785 2039218.172 2119198.363 3442244.304 0.649709922 0.61016919 0.740861167 0.753447314 0.603474452 0.599247352 0.592409484 0.615644381 1 21.71491806 1.235766875 24.99989538 1.000000477 0.644192799 0.790143965 0.057391431 37.98196421 339816.6889 0.103467561 0.015365675 17.2094454 -1.235766875 -0.355807678 KGPGQPS(ph)SPQRLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGPGQPSSPQRLDR 14 2 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 KGPGQPS(0.5)S(0.5)PQRLDR;KGPGQPS(0.5)S(0.5)PQRLDR 106.94 0.00047602 226000000 529750 402650 218600 236200 405740 356550 480620 555900 135783 TRUE FALSE 459742.1953 400004.9656 324315.6912 289832.8201 397666.5678 370266.7092 434009.5464 437025.111 119730.8884 3.839796074 3.34086693 2.708705293 2.420702159 3.321336483 3.09249112 3.624875352 3.65006154 1 16.86943586 4.541005371 3.479211334 2.959932945 3.813544705 0.144824888 0.765480869 0.558253731 12.34423999 0.190561395 0.926825073 34754.04595 -4.541005371 0.85361176 KGPGQPSS(ph)PQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KGPGQPSSPQR 11 1 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 KGPGQPS(0.377)S(0.623)PQR;KGPGQPS(0.027)S(0.973)PQR;KGPGQPS(0.051)S(0.949)PQR 95.195 0.0048627 3598910000 3213880 2473360 2089200 2476790 2496380 2195980 2784530 3281690 4926460 TRUE FALSE 2789157.615 2457112.335 3099544.108 3039183.025 2446706.922 2280460.772 2514486.709 2579926.132 4344059.511 0.642062478 0.565625846 0.71351327 0.699618184 0.563230526 0.524960758 0.578833394 0.593897511 1 22.05061244 1.237266145 24.99923485 1.000000472 0.608477192 0.806398158 0.060015791 14.98705582 289318.7415 0.094859274 0.015694245 17.26895846 -1.237266145 -0.39152328 KGPGQPSS(ph)PQRLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KGPGQPSSPQRLDR 14 2 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 KGPGQPS(0.014)S(0.986)PQRLDR;KGPGQPS(0.026)S(0.974)PQRLDR;KGPGQPS(0.012)S(0.988)PQRLDR 175.51 1.24E-06 3140250000 3592920 2750030 1289710 1549520 2691680 2203090 2975020 3284320 729400 TRUE FALSE 3118106.519 2731964.872 1913418.07 1901362.199 2638120.834 2287844.298 2686503.018 2581993.727 643171.1629 4.848019778 4.247648261 2.974974906 2.956230485 4.10173992 3.557131336 4.17696435 4.014473713 1 19.2948432 4.429969917 4.611867786 3.404939271 4.731726471 0.252900286 0.923321395 0.271050997 12.35292784 0.228691078 0.69895987 26913.4837 -4.429969917 1.3267872 KGPGRPTGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGPGRPTGSK 10 2 P26583 P26583 HMGB2 High mobility group protein B2 0 ; 63.212 0.045027 4661300000 7179900 4740700 3166000 4043800 4379600 3396300 5718600 6998500 6100000 FALSE TRUE 6231058.023 4709558.03 4697088.19 4962006.596 4292454.529 3526957.859 5164011.052 5501925.237 5378864.949 1.158433625 0.875567257 0.873248954 0.922500684 0.798022365 0.655706714 0.960055904 1.022878486 1 22.35887034 2.011061775 24.897443 1.006591614 0.872314201 0.165371905 0.12344196 331.851937 746917.4852 0.051368492 0.034598572 102.5797827 -2.011061775 -0.134277413 KGPQASS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGPQASSPR 9 1 Q8N1G1 Q8N1G1 REXO1 RNA exonuclease 1 homolog 1 KGPQAS(0.127)S(0.873)PR 68.893 0.027027 0 340930 308520 208320 229210 197810 276920 311010 374700 385060 TRUE FALSE 295875.2367 306493.3118 309064.2488 281255.6338 193873.968 287573.2916 280848.2981 294573.3209 339538.6455 0.871403714 0.902675781 0.910247634 0.828346456 0.570992347 0.846953051 0.827146782 0.867569347 1 18.37321626 1.164143618 1.888050654 1.088205222 0.819996154 0.257967077 0.094559235 1.617272884 4.66965197 0.829891851 0.027595796 14.5929676 -1.164143618 -0.268209067 KGPQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KGPQVR 6 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;; 105.42 0.052902 8326200000 7201900 6320840 4961620 6288860 4348450 5722180 6639270 7868190 11779900 FALSE TRUE 6250150.668 6279317.986 7361076.028 7716841.782 4261924.353 5942315.967 5995394.617 6185638.799 10387293.64 0.601711176 0.604519156 0.70866159 0.742911681 0.410301711 0.572075477 0.577185437 0.595500523 1 23.30831648 1.238069941 24.97709929 1.000000456 0.601128062 0.669825314 0.08790245 7.395313051 376056.0474 0.12625198 0.022025331 17.30094961 -1.238069941 -0.398872393 KGPSGYGFNLHSDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGPSGYGFNLHSDK 14 1 O14745;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 115.82 0.00025807 2289400000 2063100 1651800 1075600 1551000 1730400 1244600 1992500 2476100 2129600 FALSE TRUE 1790456.108 1640949.217 1595763.758 1903178.256 1695968.425 1292480.567 1799267.657 1946605.284 1877841.114 0.953465176 0.873848807 0.849786356 1.013492697 0.903147989 0.688280045 0.958157558 1.036618737 1 20.84064357 2.005765454 24.99233924 1.013863972 0.880532364 0.326826064 0.08311307 165.2296786 716241.2509 0.034531915 0.02320483 101.3363958 -2.005765454 -0.133331607 KGPSS(ph)TGASGQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KGPSSTGASGQAK 13 1 Q9NWH9;H7BXE3 Q9NWH9 SLTM SAFB-like transcription modulator 1 KGPS(0.03)S(0.941)T(0.03)GASGQAK;KGPS(0.001)S(0.965)T(0.033)GASGQAK;KGPS(0.041)S(0.938)T(0.021)GASGQAK;KGPS(0.183)S(0.772)T(0.044)GAS(0.001)GQAK;KGPS(0.007)S(0.964)T(0.029)GASGQAK;KGPS(0.276)S(0.709)T(0.015)GASGQAK 188.96 3.47E-06 1390203000 1814869 1287096 1003491 1149096 1042606 951485 1689115 1858300 1574272 TRUE FALSE 1575029.463 1278640.982 1488782.604 1410015.81 1021860.18 988089.2436 1525304.887 1460917.006 1388163.358 1.134613916 0.921102675 1.072483722 1.015741989 0.736123868 0.711796085 1.098793509 1.052410005 1 20.40474592 7.450857081 1.247918701 0.952829176 199.3912253 0.149928099 0.133153307 4174.581474 7.369724586 0.041506234 2370396.411 28239505.05 -7.450857081 198.4383961 KGPST(ph)PYTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGPSTPYTK 9 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 KGPS(0.098)T(0.902)PYTK 92.856 0.0057385 487880000 1894900 1570500 1069300 1344400 1299700 1180000 1784800 2083300 1887500 TRUE FALSE 1644484.164 1560183.282 1586417.057 1649666.568 1273838.513 1225395.364 1611710.371 1637802.507 1664361.9 0.988056842 0.937406271 0.953168332 0.991170591 0.765361495 0.736255356 0.968365336 0.984042297 1 20.66653774 2.024436991 24.9994446 0.986478219 0.894416003 0.197952021 0.085172169 387.1111311 396019.3643 0.038065762 0.025662682 105.7881424 -2.024436991 -0.092062216 KGQAVDYEGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KGQAVDYEGSR 11 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;; 190.68 3.47E-06 5171940000 4424710 3860900 2617050 3222390 3676690 4126400 3611900 3632510 3326020 FALSE TRUE 3839973.363 3835537.494 3882664.134 3954082.901 3603531.062 4285145.278 3261618.494 2855726.005 2932821.705 1.309310197 1.307797705 1.323866407 1.348217962 1.228690805 1.461099825 1.112109369 0.97371279 1 21.48385794 2.048146406 5.250476745 0.999806465 1.324176526 0.863614704 0.057872805 0.056592274 3.521375539 0.023195216 0.014969371 111.7239818 -2.048146406 0.324370061 KGQGGAGAGDDEEED ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KGQGGAGAGDDEEED 15 1 P46781 P46781 RPS9 40S ribosomal protein S9 0 ;;;;; 122.18 0.0022652 7688498000 10466440 7656330 6459720 6201630 6656600 5913010 9689180 10521940 9611790 FALSE TRUE 9083273.435 7606035.064 9583662.198 7609804.877 6524146.683 6140487.321 8749524.815 8271905.013 8475495.136 1.071710064 0.897414834 1.130749537 0.897859624 0.769765846 0.724498949 1.032331996 0.97597897 1 23.01486622 3.685833069 24.88439093 0.903500627 1.019703968 0.238866703 0.111111339 539.5182385 254621.2625 0.032938182 0.04885526 4851.020045 -3.685833069 0.116203341 KGQSEEIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KGQSEEIQK 9 1 C9JXB8;C9JNW5;P83731 C9JXB8 RPL24 60S ribosomal protein L24 0 ;;; 152.54 0.00012864 1826070000 2318950 2114870 1622130 1766700 1663540 1506320 2686450 2869210 2892460 FALSE TRUE 2012494.882 2100977.28 2406597.494 2167856.237 1630438.809 1564269.105 2425918.492 2255651.77 2550516.674 0.789053803 0.823745754 0.943572539 0.849967483 0.639258243 0.613314597 0.951147866 0.884390129 1 21.2823581 KGS(ph)FSALVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KGSFSALVGR 10 1 Q13619;A0A087WWN2 Q13619 CUL4A Cullin-4A 1 KGS(0.981)FS(0.019)ALVGR;KGS(0.795)FS(0.205)ALVGR;KGS(0.996)FS(0.004)ALVGR;KGS(0.99)FS(0.01)ALVGR 194.86 2.55E-07 4279790000 8107150 6167010 4460280 5304250 6692490 5011480 9162160 8199970 7557820 TRUE FALSE 7035769.587 6126498.505 6617286.327 6508661.033 6559322.543 5204274.878 8273615.133 6446470.228 6664343.129 1.055733393 0.919295178 0.992939019 0.976639544 0.98424142 0.780913404 1.241474962 0.96730767 1 22.66803125 2.242817195 24.99981588 1.055446192 0.95465463 0.232075247 0.099959488 173.9562416 1021691.181 0.036382968 0.027152921 174.9110293 -2.242817195 -0.100791562 KGS(ph)GS(ph)EQEGEDEEGGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KGSGSEQEGEDEEGGER 17 1 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 2 KGS(1)GS(1)EQEGEDEEGGER;KGS(1)GS(1)EQEGEDEEGGER;KGS(1)GS(1)EQEGEDEEGGER 191.2 8.96E-10 609176000 1067843 785431 629172 583534 833029 680626 911734 1047714 1127481 TRUE FALSE 926724.842 780271.452 933441.6837 716034.3135 816453.3527 706810.1226 823314.177 823668.5144 994191.4806 0.932139191 0.784830153 0.938895275 0.720217712 0.821223445 0.710939629 0.828124353 0.828480761 1 19.92316422 1.223874314 3.932173958 1.024545213 0.815688689 0.363374067 0.074536836 0.292134727 7.543819343 0.180967038 0.017884187 16.74458213 -1.223874314 -0.208856524 KGS(ph)ITEYTAAEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KGSITEYTAAEEK 13 1 J3KN59;Q12982;Q12982-2 J3KN59 BNIP2 BCL2/adenovirus E1B 19 kDa protein-interacting protein 2 1 KGS(0.999)IT(0.001)EYTAAEEK;KGS(0.969)IT(0.031)EYTAAEEK;KGS(0.98)IT(0.02)EYTAAEEK;KGS(0.982)IT(0.018)EYTAAEEK 273.33 2.37E-32 3232020000 4158570 2966394 3728320 3404580 3327120 2266202 4739240 5061400 6974940 TRUE FALSE 3609004.438 2946907.562 5531348.022 4177641.925 3260916.821 2353384.257 4279629.234 3979058.998 6150370.539 0.586794635 0.479143093 0.899351996 0.679250445 0.530198433 0.382641053 0.695832748 0.646962483 1 22.5522419 1.052885909 2.066347967 1.309965341 0.605379664 0.437544251 0.138374101 1.41931391 3.812789777 2.297926084 0.038451602 11.29499152 -1.052885909 -0.704585678 KGS(ph)ITEYTAAEEKEDGRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KGSITEYTAAEEKEDGRR 18 3 J3KN59;Q12982;Q12982-2 J3KN59 BNIP2 BCL2/adenovirus E1B 19 kDa protein-interacting protein 2 1 KGS(0.983)IT(0.016)EYT(0.001)AAEEKEDGRR;KGS(0.993)IT(0.007)EYTAAEEKEDGRR;KGS(1)ITEYTAAEEKEDGRR 166.89 1.36E-10 1231080000 1363300 1043790 790650 667190 1038980 726070 1576880 1528230 317358 TRUE FALSE 1183136.451 1036933.275 1173010.985 818685.6869 1018306.331 754002.3827 1423954.42 1201429.907 279840.2988 4.227898755 3.705446568 4.191715738 2.925546072 3.638883803 2.694402436 5.088453759 4.293269813 1 18.09424421 3.770133962 24.7319937 3.484200193 4.008063015 0.079565716 1.081814778 2189.010147 1714685.066 0.288881099 0.500299222 5890.253174 -3.770133962 0.523862822 KGS(ph)PTPGFSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KGSPTPGFSTR 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 KGS(0.749)PT(0.25)PGFS(0.001)TR;KGS(0.5)PT(0.5)PGFSTR;KGS(0.639)PT(0.361)PGFSTR;KGS(0.857)PT(0.143)PGFSTR;KGS(0.804)PT(0.196)PGFSTR 149.35 2.11E-05 12323150000 4983700 3824230 2602350 2976870 4337100 3540690 4146090 5180490 4264460 TRUE FALSE 4325091.418 3799108.381 3860855.164 3652813.832 4250800.195 3676902.635 3744002.83 4072682.528 3760320.397 1.150192261 1.010315074 1.026735692 0.971410265 1.13043564 0.977816315 0.995660591 1.083067957 1 21.84242416 4.743684251 24.60173431 1.027933852 1.150192325 0.394953284 0.048747411 464.6631312 2231046.333 0.011263759 0.091094887 55422.26253 -4.743684251 0.122258473 KGS(ph)QITQQSTNQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGSQITQQSTNQSR 14 1 P50750;P50750-2 P50750 CDK9 Cyclin-dependent kinase 9 1 KGS(1)QITQQSTNQSR 109.89 0.00045405 70135000 26652 18703 15096 18479 22329 18201 24988 25955 29718 TRUE FALSE 23129.87067 18580.13876 22396.47609 22674.93938 21884.69659 18901.20425 22564.66761 20404.72523 26204.77189 0.88265873 0.709036462 0.854671668 0.865298102 0.835141656 0.721288639 0.861090022 0.778664486 1 14.67754193 1.232440486 24.99475666 1.00000031 0.811519296 0.486909174 0.060142543 168.8206763 689398.5132 0.122926538 0.013674561 17.07813671 -1.232440486 -0.188481014 KGS(ph)SGNASEVSVACLTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KGSSGNASEVSVACLTER 18 1 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1;C9J8U1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 KGS(0.973)S(0.027)GNASEVSVACLTER;KGS(0.941)S(0.059)GNASEVSVACLTER;KGS(0.954)S(0.046)GNASEVSVACLTER;KGS(0.999)S(0.001)GNASEVSVACLTER 346.25 1.82E-90 9692700000 4495870 3937530 3618160 3589510 5007180 3979650 5687800 6119100 5428600 TRUE FALSE 3901729.388 3911664.106 5367914.278 4404563.108 4907546.914 4132749.711 5136198.031 4810578.084 4786837.092 0.815095503 0.817170927 1.121390633 0.92014059 1.025217032 0.863357083 1.07298367 1.004959641 1 22.19064128 4.267687595 24.76000606 0.998383387 0.816132812 0.537251539 0.071350535 135.6904257 115344.0752 0.016451345 0.043509938 18521.98786 -4.267687595 -0.182250575 KGS(ph)SPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGSSPSR 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KGS(0.458)S(0.458)PS(0.083)R 74.533 0.048645 75235000 249810 234510 149490 181400 946480 268650 262500 305210 227800 TRUE FALSE 216796.9756 232969.4884 221783.864 222589.6425 927646.8998 278985.1393 237042.7904 239943.2166 200869.7435 1.079291345 1.159803783 1.104117824 1.108129271 4.618151462 1.388885825 1.180082108 1.194521447 1 17.61590075 KGS(ph)VSHDTVQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGSVSHDTVQPR 12 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;F2Z3L2;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 KGS(0.983)VS(0.017)HDTVQPR 136.26 6.93E-05 229660000 172920 148860 78353 137770 176770 114630 205110 206320 206190 TRUE FALSE 150068.1839 147882.1289 116244.7729 169052.7842 173252.6228 119039.8903 185218.4638 162200.0736 181814.4531 0.825391938 0.813368389 0.639359363 0.929809382 0.952908968 0.654732824 1.018722443 0.8921187 1 17.47210736 -1.999999054 0.27134531 2.437585634 0.765434952 0.244650093 0.11350235 113.2978111 1.831311489 86.67391189 0.286462357 0.010000022 1.999999054 -1.672150682 KGSFSALVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGSFSALVGR 10 1 Q13619;A0A087WWN2 Q13619 CUL4A Cullin-4A 0 85.845 0.02538 0 374570 414770 231130 243980 389480 396990 371740 483180 406700 FALSE TRUE 325069.6255 412045.3486 342905.2411 299379.388 381730.11 412262.4622 335688.712 379855.7171 358620.3893 0.906444907 1.148973569 0.956178877 0.834808608 1.064440621 1.149578982 0.936055846 1.059213944 1 18.45209799 KGSPT(ph)PGFSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGSPTPGFSTR 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 KGS(0.34)PT(0.66)PGFSTR 92.528 0.0058181 6010800000 2497200 1942400 1272300 1492400 2022400 1431200 2071300 2613500 2292800 TRUE FALSE 2167188.693 1929640.247 1887588.536 1831272.23 1982158.197 1486259.19 1870425.645 2054623.363 2021747.796 1.0719382 0.954441622 0.933641941 0.905786683 0.980418132 0.735135803 0.925152805 1.016260964 1 20.94717161 4.763000018 2.560366397 0.93004641 1.107269353 0.253312535 0.077088763 0.874153927 6.969757186 0.020701907 0.343971567 57942.87208 -4.763000018 0.177222943 KGTENGVNGTLTSNVADS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KGTENGVNGTLTSNVADSPR 20 1 G3XAN4;Q15629-2;Q15629 G3XAN4 TRAM1 Translocating chain-associated membrane protein 1 1 KGTENGVNGTLTSNVADS(1)PR;KGTENGVNGTLTSNVADS(1)PR;KGTENGVNGTLTS(0.001)NVADS(0.999)PR;KGTENGVNGTLTSNVADS(1)PR;KGTENGVNGTLTSNVADS(1)PR 292.68 1.75E-54 1828777000 1439754 1136154 720138 1349898 1645303 1357409 1085265 2034840 1697410 TRUE FALSE 1249486.861 1128690.53 1068399.146 1656412.973 1612564.689 1409629.403 980016.1673 1599705.301 1496744.123 0.834803252 0.754097185 0.713815494 1.106677452 1.077381674 0.941797185 0.654765335 1.0687901 1 20.51339618 3.754641307 24.88284689 0.96756406 0.766224485 0.365280412 0.128588519 922.1716006 1426940.28 0.035588728 0.061385154 5683.832972 -3.754641307 -0.201339575 KGTVEGFEPADNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KGTVEGFEPADNK 13 1 P37108;H0YLA2 P37108 SRP14 Signal recognition particle 14 kDa protein 0 ;;; 184.02 1.58E-05 2073050000 4684270 3947540 2661530 2601090 3154790 2497320 4594600 5184510 3417980 FALSE TRUE 4065231.851 3921608.35 3948654.81 3191707.24 3092015.851 2593393.516 4149016.399 4075842.882 3013910.298 1.348823106 1.301169564 1.310143441 1.058992115 1.025915022 0.860474686 1.37662239 1.352343792 1 21.52320505 3.762901858 19.50707148 1.139801227 1.318158745 0.271193572 0.156211991 88.22828839 70701.96483 0.04683296 0.080949 5792.977719 -3.762901858 0.178357518 KGTVLLADNVICPGAPDFLAHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGTVLLADNVICPGAPDFLAHVR 23 1 P21964-2;P21964 P21964-2 COMT Catechol O-methyltransferase 0 110.26 0.00069731 2293300000 2265600 1893700 942900 1116500 1816200 1765500 2314400 2346800 611330 FALSE TRUE 1966195.22 1881260.16 1398889.594 1370018.39 1780061.173 1833419.927 2089949.844 1844955.083 539059.2638 3.647456507 3.489894871 2.595057144 2.541498647 3.30216229 3.40114724 3.877031682 3.422545918 1 19.04008437 1.236461332 24.99988945 0.999997079 3.284672283 0.745314377 0.419705785 31.49311955 374949.0963 0.725092357 0.113317493 17.23698612 -1.236461332 2.284675204 KGVAINFVTEEDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KGVAINFVTEEDKR 14 2 Q14240;Q14240-2 Q14240 EIF4A2 "Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 177.84 1.15E-06 571090000 704860 505150 443570 470200 487720 441910 700340 753160 724890 FALSE TRUE 611710.9651 501831.6364 658081.9357 576966.0966 478015.3262 458910.5637 632421.1346 592102.5951 639194.33 0.957003115 0.785100263 1.029549082 0.90264583 0.747840373 0.717951556 0.989403543 0.92632642 1 19.28589509 KGVAINMVTEEDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGVAINMVTEEDKR 14 2 P60842 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 ; 192.4 2.12E-07 5095300000 3364050 2425300 1732020 2033390 2163210 1840650 3199360 3690020 2793420 FALSE TRUE 2919482.269 2409368.045 2569630.665 2495102.278 2120166.353 1911460.997 2889086.56 2900937.939 2463185.07 1.185246819 0.978151449 1.043214615 1.012957698 0.860741801 0.776011929 1.172906817 1.177718221 1 21.2320936 0.93223913 22.62326381 0.000838492 1.029281794 0.003075375 0.134417622 5405.783684 2135141.69 51493.99528 0.03460814 8.555376562 -0.93223913 1.028443302 KGVEGLIDIENPNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KGVEGLIDIENPNR 14 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ;;; 199.68 3.26E-08 1713250000 3016810 2714670 1507960 1920750 2595920 2314590 2840210 3393280 2064570 FALSE TRUE 2618130.915 2696837.154 2237214.5 2356885.644 2544266.271 2403633.775 2564766.871 2667653.479 1820498.887 1.438139256 1.481372592 1.228901878 1.294637235 1.397565409 1.320315982 1.408826388 1.465342 1 20.79590243 1.230546071 24.99990041 0.999999309 1.379354625 0.69648023 0.078709039 182.3677251 568816.1677 0.218852316 0.020338821 17.00380324 -1.230546071 0.379355316 KGVNLPGAAVDLPAVSEK ddPTM_MDA-MB-175_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 ; 193.22 2.16E-14 3666300000 7421200 5120800 4059000 5199600 5323300 4337400 6908400 7820700 7433900 FALSE TRUE 6440469.617 5087161.128 6021945.977 6380248.651 5217376.745 4504262.585 6238424.431 6148304.166 6555072.811 0.982516869 0.776064778 0.918669579 0.973329944 0.79592964 0.687141503 0.951694148 0.937945976 1 22.64418037 2.045880284 24.99993403 0.958625907 0.854324399 0.237274882 0.090896793 184.5246763 100545.7282 0.037585998 0.025340464 111.1425314 -2.045880284 -0.104301509 KGWEVVESDLYAMNFNPIISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KGWEVVESDLYAMNFNPIISR 21 1 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ;;; 249.51 1.74E-30 10839030000 14226330 14746830 8644380 9928580 12388230 12443420 14331000 16210970 9106170 FALSE TRUE 12346284.45 14649957.1 12824831.08 12183015.84 12141728.46 12922126.42 12941181.83 12744380.22 8029648.956 1.537587074 1.824482886 1.597184528 1.517253856 1.51211199 1.609301539 1.611674669 1.587165303 1 22.93690549 1.238089684 6.44243412 0.982349877 1.602795018 0.822298507 0.087619252 0.05033485 9.523701204 0.136823054 0.022074671 17.30173613 -1.238089684 0.620445141 KGWLYYEAGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KGWLYYEAGQR 11 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 130.56 0.00035519 1147940000 1238340 1199820 794090 1038770 1276280 1227050 1293040 1357270 1241110 FALSE TRUE 1074690.231 1191938.303 1178114.58 1274638.605 1250884.525 1274255.408 1167641.18 1067028.373 1094387.39 0.982001658 1.089137461 1.07650599 1.164705128 1.142999761 1.16435498 1.066935887 0.97500061 1 20.06169208 1.886919791 4.095476838 0.988854099 1.106680494 0.439800878 0.053027945 0.207747548 5.599767898 0.031120443 0.014993338 77.0761106 -1.886919791 0.117826395 KGWS(ph)MSEQSEESVGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KGWSMSEQSEESVGGR 16 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KGWS(1)MSEQSEESVGGR;KGWS(1)MSEQSEESVGGR;KGWS(0.98)MS(0.02)EQSEESVGGR 219.87 7.36E-15 1124710000 783300 454540 262403 421540 411560 254554 681090 544370 407580 TRUE FALSE 679784.9204 451554.0968 389301.9685 517257.0998 403370.7612 264346.8571 615037.9966 427960.7118 359396.3567 1.891463026 1.25642369 1.08321067 1.439238574 1.122356289 0.735530153 1.711308379 1.190776433 1 18.45521626 4.734598529 4.549695197 1.201177465 1.933934332 0.423454194 0.257034901 0.186161342 10.07343937 0.06126518 0.435373241 54274.83715 -4.734598529 0.732756867 KGYFEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KGYFEDR 7 1 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ;; 84.743 0.034187 2129240000 5625820 5106510 3727920 4521390 4752500 5116380 6054180 6005130 5906130 FALSE TRUE 4882353.633 5072965 5530754.581 5548040.705 4657934.548 5313210.449 5467046.555 4720979.681 5207914.04 0.937487369 0.974087698 1.061990374 1.065309577 0.894395436 1.020218538 1.049757449 0.906501076 1 22.31227421 1.735307579 24.99999999 0.950512278 1.000990532 0.099837935 0.05879418 0.836396096 6325.662667 0.031239139 0.015001301 54.36352128 -1.735307579 0.050478254 KHDNEGSGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KHDNEGSGSK 10 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 138.25 4.52E-05 99721000 89177 75263 50230 63945 127840 57814 99963 121130 117800 FALSE TRUE 77392.0335 74768.5924 74521.39601 78464.68959 125296.2341 60038.14199 90268.60365 95227.29213 103873.8182 0.745058137 0.719802099 0.717422324 0.755384667 1.206234991 0.577991096 0.869021715 0.916759332 1 16.66447254 -1.99993416 0.046637818 2.249541198 1.72E-05 0.175705208 0.160269287 2302.784001 10.5284739 431.5316842 148.122138 0.010001516 1.99993416 -2.249524005 KHDSGAADLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KHDSGAADLER 11 1 Q9NX55;Q9NX55-3;J3QT56 Q9NX55;J3QT56 HYPK Huntingtin-interacting protein K 0 ;; 162.93 1.59E-05 462637000 681885 799755 237661 515282 943979.4 889277 813105 972937 908230 FALSE TRUE 591772.1696 794501.3567 352594.6545 632284.6537 925196.0568 923488.0616 734250.2022 764881.994 800860.0841 0.738920794 0.992060127 0.440269982 0.789507014 1.155253053 1.153120351 0.916827067 0.955075686 1 19.61119069 3.371836671 6.559782902 1.021726567 0.729138819 0.490190616 0.150589486 0.194436439 10.69421883 0.044131053 0.057091611 2354.163765 -3.371836671 -0.292587748 KHEAFESDLAAHQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KHEAFESDLAAHQDR 15 1 O43707;O43707-2;F6THM6;A0A494C060;P12814-3;P12814;P12814-2;P12814-4;H9KV75;P35609-2;P35609;A0A494C1A0;H7C5W8 O43707;P12814-3 ACTN4;ACTN2;ACTN1 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2 0 ;;;; 193.54 3.61E-08 4695000000 3360942 2411076 2040576 4013080 2499344 2385323 2014067 2823459 11395350 FALSE TRUE 2916784.999 2395237.483 3027405.379 4924311.15 2449611.944 2477087.919 1818743.092 2219684.265 10048204.7 0.290279218 0.23837467 0.301288187 0.490068753 0.243786031 0.246520447 0.181001795 0.220903567 1 23.26043442 1.236028638 24.99999728 1.000000956 0.273736347 0.882208974 0.083074081 23.5340469 232318.644 0.143741646 0.021760251 17.21982119 -1.236028638 -0.726264609 KHEDFDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KHEDFDK 7 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 109.21 0.0045949 791760000 1586730 1283850 1086870 1152210 947830 1024380 1535940 1734030 1633110 FALSE TRUE 1377039.61 1275416.305 1612483.967 1413836.891 928970.0374 1063788.561 1386984.775 1363221.179 1440045.596 0.956247228 0.885677723 1.119745077 0.981800086 0.645097655 0.738718666 0.963153374 0.946651399 1 20.45768306 3.429778698 24.99980535 0.866265354 0.989354978 0.218144174 0.119147035 209.7287839 110749.0072 0.037443103 0.04833885 2690.163634 -3.429778698 0.123089623 KHEDSAIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KHEDSAIPR 9 1 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 0 126.2 0.00031166 45954000 142030 126370 77243 113620 114370 120620 135020 168760 147240 FALSE TRUE 123260.3756 125539.8671 114597.9732 139419.1576 112094.2608 125260.3295 121925.7812 132671.9873 129833.4549 0.949372993 0.966930035 0.882653652 1.07383076 0.863369621 0.964776987 0.939093712 1.021862873 1 16.98630265 1.738454173 8.362701007 1.009910995 0.948908318 0.175889564 0.056019712 0.169552861 42.81015452 0.028873913 0.013190509 54.75883156 -1.738454173 -0.061002678 KHEEEEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KHEEEEAK 8 1 P25789;H0YN18;P25789-2 P25789 PSMA4 Proteasome subunit alpha type-4 0 122.13 0.00091102 216520000 560980 415190 397390 455580 188600 263370 465280 556470 925850 FALSE TRUE 486845.0717 412462.5896 589569.1332 559026.4021 184847.229 273502.0143 420157.2172 437473.221 816397.0677 0.596333685 0.505223017 0.722159788 0.684748175 0.226418291 0.33501102 0.514648121 0.535858393 1 19.63891148 1.234910832 4.884434567 1.035050826 0.510234277 0.51901495 0.146865013 0.164740925 9.54552349 0.297241433 0.0395394 17.17555706 -1.234910832 -0.524816549 KHEIDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KHEIDGK 7 1 A0A087WW29;Q96GD3-6;Q96GD3-5;Q96GD3-4;Q96GD3-3;Q96GD3-2;Q96GD3 A0A087WW29 SCMH1 Polycomb protein SCMH1 0 76.899 0.025647 95791000 357050 277020 156220 142630 178500 203040 334230 376590 58179 FALSE TRUE 309864.9379 275200.2374 231768.5145 175016.3215 174948.1992 210851.0802 301816.426 296059.1591 51301.1449 6.040117398 5.364407323 4.51780394 3.411548062 3.410220173 4.110065781 5.883229831 5.771004911 1 15.6467034 4.335293378 2.633752877 4.216460082 5.951590859 0.20730285 1.370120504 0.540136714 7.153543799 0.375058131 1.397367673 21641.79993 -4.335293378 1.735130777 KHELLNSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KHELLNSTR 9 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 86.882 0.0089828 571640000 736790 711170 439050 624070 695740 701120 698480 738830 782000 FALSE TRUE 639421.3347 706498.2774 651376.0485 765774.6318 681896.1352 728092.5401 630741.5171 580836.9541 689552.8509 0.927298515 1.024574515 0.944635422 1.110537982 0.988896115 1.055890842 0.914710912 0.842338558 1 19.39530161 2.149776391 6.936365724 0.901187966 1.009994591 0.289738007 0.064363558 0.219284074 14.38779754 0.025192678 0.016940449 141.1810447 -2.149776391 0.108806625 KHEPEPLPHWDDWERPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KHEPEPLPHWDDWERPR 17 2 Q13882 Q13882 PTK6 Protein-tyrosine kinase 6 0 ; 119.23 4.18E-05 367030000 64354 69215 47316 63077 73579 84217 68485 86151 80326 FALSE TRUE 55849.45585 68760.32211 70198.17586 77399.59692 72114.92185 87456.88249 61843.33524 67728.27908 70829.95179 0.788500549 0.970780304 0.991080385 1.092752359 1.01814162 1.234744346 0.873124062 0.956209589 1 16.11207194 4.810495915 1.968442442 1.019768044 0.690264175 0.385276901 0.09317254 1.107165402 3.935065449 0.025330091 0.702617206 64639.19132 -4.810495915 -0.32950387 KHGGPKDEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KHGGPKDEER 10 2 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;;;; 167.18 3.20E-06 10698270000 11713570 8384600 6011480 6419060 6264630 5694280 10492250 11101540 5108230 FALSE TRUE 10165592.05 8329521.011 8918651.835 7876605.682 6139976.12 5913342.636 9474713.21 8727562.063 4504340.869 2.256843419 1.849220841 1.980012636 1.748669986 1.363124217 1.312809756 2.103462745 1.937589165 1 22.10288458 4.414193971 1.033894729 1.629317793 2.318040099 0.3039818 0.326531656 1.776578649 2.247940535 0.114837272 1.207675433 25953.38274 -4.414193971 0.688722307 KHGLAHDEMKS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KHGLAHDEMKSPR 13 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 KHGLAHDEMKS(1)PR;KHGLAHDEMKS(1)PR 157.37 1.89E-05 1036970000 2540100 2045200 1431380 1611130 1523290 1251620 1712200 1893990 1280410 TRUE FALSE 2204419.349 2031764.947 2123600.156 1976961.691 1492979.509 1299770.631 1546151.108 1488974.978 1129041.388 1.95246992 1.799548686 1.880887784 1.751009052 1.322342586 1.151216107 1.369437049 1.318795744 1 20.10666694 3.261096522 3.069527669 1.239498396 1.865294162 0.894263744 0.105945776 0.077199948 1.497051314 0.032960654 0.04165246 1824.301107 -3.261096522 0.625795765 KHHYLRPSLFVYPEESLVIGSSTLFSALLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KHHYLRPSLFVYPEESLVIGSSTLFSALLIK 31 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 87.339 0.00020663 16491000 123510 125370 53126 94994 49312 40945 109840 125330 40898 FALSE TRUE 107187.8406 124546.4362 78817.9113 116563.8396 48330.78768 42520.18064 99187.73371 98529.15482 36063.08503 2.97223159 3.453571321 2.185556539 3.232220413 1.340173411 1.179050007 2.750395137 2.732133281 1 15.1382352 3.250514871 24.96780818 1.957011526 2.940704918 0.414561861 0.670912638 273.6553396 571556.7877 0.20620076 0.264082586 1780.38887 -3.250514871 0.983693392 KHLEINPDHPIVETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KHLEINPDHPIVETLR 16 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;; 233.14 4.91E-20 5880050000 3702820 2750160 1245400 1630400 2656030 2569740 2616290 3196700 1024760 FALSE TRUE 3213482.955 2732094.018 1847679.606 2000607.239 2603180.199 2668599.561 2362562.598 2513110.582 903614.0402 3.556256114 3.023518777 2.044766375 2.214006368 2.880854085 2.953251545 2.614570484 2.781176996 1 19.78534716 4.461577798 4.693238823 2.443212143 3.458544417 0.32972845 0.56823304 0.212754032 12.09010581 0.140877268 0.459796197 28945.28283 -4.461577798 1.015332274 KHLEINPDHSIIETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KHLEINPDHSIIETLR 16 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;; 248.97 6.99E-21 3904190000 4138720 3975670 2291340 2438470 3868050 3470190 3807950 4546900 1921100 FALSE TRUE 3591777.666 3949553.562 3399439.688 2992161.883 3791083.373 3603690.455 3438655.595 3574580.819 1693989.747 2.120306615 2.331509721 2.006765209 1.76634002 2.237961228 2.127339001 2.029915235 2.110154932 1 20.69199371 1.237908483 24.98616489 0.999998742 2.089715577 0.842267234 0.148413433 6.053662574 231761.1373 0.211937706 0.036596644 17.29451882 -1.237908483 1.089716835 KHNMCGETEEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 KHNMCGETEEEK 12 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;;;;;;; 206.51 5.80E-08 1985630000 3666400 2801310 2871350 3032090 2573560 2064670 4223670 4179480 3977580 FALSE TRUE 3181875.951 2782908.01 4259944.464 3720572.377 2522351.191 2144099.191 3814059.133 3285730.727 3507355.024 0.90720099 0.793449192 1.21457464 1.060791494 0.7191605 0.61131513 1.087445984 0.936811559 1 21.74195204 KHPDASVNFSEFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KHPDASVNFSEFSK 14 1 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ; 184.99 1.97E-06 1054820000 1918160 1582300 1060620 1339190 1574380 1255360 1899050 2182790 2007610 FALSE TRUE 1664670.296 1571905.767 1573539.38 1643273.558 1543052.918 1303654.512 1714880.423 1716017.345 1770272.633 0.940346851 0.887945584 0.888868387 0.92826016 0.87164705 0.736414543 0.968709786 0.969352016 1 20.75554013 2.038992249 24.99999669 0.978450546 0.876762175 0.442533766 0.055012592 145.1039367 93033.23359 0.022806234 0.015375935 109.3936843 -2.038992249 -0.101688372 KHPDSSVNFAEFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KHPDSSVNFAEFSK 14 1 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 ; 117.92 0.00017898 4058300000 2445700 1668970 1016710 1489180 1628130 1201820 1849390 2544800 2063340 FALSE TRUE 2122494.548 1658006.426 1508394.357 1827321.08 1595733.398 1248054.793 1670036.442 2000614.324 1819414.296 1.16658122 0.911285808 0.829054911 1.004345785 0.877058844 0.685965146 0.917897835 1.099592505 1 20.79504266 1.754500925 24.99999992 1.050896543 0.903241473 0.170183322 0.12392173 8.812573734 13842.09097 0.066282368 0.031830136 56.81996016 -1.754500925 -0.14765507 KHPEVDVLINFASLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KHPEVDVLINFASLR 15 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 201.24 4.23E-09 1623390000 3906400 3660700 2509400 3274300 3534700 3257400 4139400 4779900 4417100 FALSE TRUE 3390159.342 3636652.621 3722954.233 4017779.86 3464366.386 3382714.286 3737961.625 3757755.582 3894915.47 0.870406397 0.93369231 0.955849816 1.031544815 0.889458683 0.868494916 0.959702888 0.964784887 1 21.89316059 KHPS(ph)SPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KHPSSPAR 8 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 KHPS(0.897)S(0.103)PAR;KHPS(0.647)S(0.353)PAR 86.344 0.0098612 423400000 339187 378570 169999 272582 232644 353869 366378 393755 401322 TRUE FALSE 294362.5786 376083.1487 252211.085 334475.9093 228014.8396 367482.5694 330846.718 309553.5575 353878.1703 0.83181898 1.062747522 0.712705971 0.945172484 0.644331464 1.038443736 0.934917002 0.874746123 1 18.43289324 KHPSS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KHPSSPAR 8 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 KHPS(0.119)S(0.881)PAR;KHPS(0.143)S(0.857)PAR;KHPS(0.149)S(0.851)PAR;KHPS(0.143)S(0.857)PAR;KHPS(0.172)S(0.828)PAR 109.24 0.00224 3664320000 1987649 2256850 660886 1498323 1499774 1987929 2220992 2478300 2342200 TRUE FALSE 1724976.149 2242024.604 980492.6801 1838540.138 1469931.432 2064405.915 2005600.538 1948334.831 2065307.784 0.835215052 1.085564399 0.474744098 0.890201524 0.711725121 0.999563325 0.971090388 0.943362944 1 20.97792537 2.724765002 24.68518615 0.972318318 0.802381143 0.255540817 0.151619512 987.3201796 1766657.924 0.050129962 0.044451126 530.5972587 -2.724765002 -0.169937174 KHQALQAEIAGHEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KHQALQAEIAGHEPR 15 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 143.14 1.82E-06 80724000 57136 57653 38173 41038 58093 52036 58814 61333 42473 FALSE TRUE 49585.33284 57274.27365 56633.59048 50356.30513 56937.06296 54037.85859 53110.22733 48217.41524 37451.89033 1.323974101 1.52927591 1.512169078 1.344559772 1.520272073 1.442860644 1.418092034 1.28744944 1 15.19275092 1.137714499 1.463298372 0.716237146 1.451729745 0.808502636 0.068728656 0.608669366 0.951238148 0.711507675 0.018849421 13.73138989 -1.137714499 0.735492599 KHS(ph)PS(ph)PPPPTPTESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KHSPSPPPPTPTESR 15 1 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 2 KHS(1)PS(1)PPPPTPTESR;KHS(0.999)PS(0.993)PPPPT(0.007)PT(0.001)ESR;KHS(1)PS(1)PPPPTPTESR;KHS(1)PS(1)PPPPTPTESR 113.54 0.0023683 2170150000 2487620 1561800 1086910 1244310 1664020 1424650 1640070 1966370 1870180 TRUE FALSE 2158874.714 1551540.433 1612543.311 1526849.604 1630909.258 1479457.207 1481016.264 1545877.078 1649089.451 1.309131359 0.940846739 0.977838595 0.925874338 0.988975617 0.897135814 0.898081219 0.937412508 1 20.65323823 4.738773984 24.98182485 0.943092867 1.309131468 0.914103362 0.034996513 4.535975951 530754.2734 0.008501266 0.047945692 54799.17045 -4.738773984 0.366038601 KHS(ph)QTDLVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KHSQTDLVSR 10 1 E9PN66;E9PNB3;E9PKN9;E9PS55;E9PMY0;E9PMW4;E9PQ46;E9PIN5;E9PIK4;U3KQ32;E9PKZ4;E9PPM1;O14683 E9PN66 TP53I11 Tumor protein p53-inducible protein 11 1 KHS(1)QTDLVSR;KHS(1)QTDLVSR;KHS(0.998)QT(0.002)DLVSR;KHS(0.999)QT(0.001)DLVSR;KHS(0.992)QT(0.008)DLVSR;KHS(0.906)QT(0.094)DLVSR;KHS(0.914)QT(0.086)DLVSR 184.21 9.70E-07 22077060000 11960310 11041240 6820750 9579900 14611730 10872900 11392320 19478150 16008660 TRUE FALSE 10379724.73 10968709.37 10119287.51 11755162.71 14320985.16 11291187.5 10287494.56 15312899.2 14116134.45 0.735309285 0.777033501 0.716859672 0.832746582 1.014511813 0.799878149 0.728775615 1.08477992 1 23.75084174 -2 0.240079377 2.70824195 0.714256052 0.422161303 0.100788449 84.09651068 1.333200156 64.84654972 0.386444057 0.01 2 -1.993985899 KHSQTDLVS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KHSQTDLVSR 10 1 E9PN66;E9PNB3;E9PKN9;E9PS55;E9PMY0;E9PMW4;E9PQ46;E9PIN5;E9PIK4;U3KQ32;E9PKZ4;E9PPM1;O14683 E9PN66 TP53I11 Tumor protein p53-inducible protein 11 1 KHS(0.002)QT(0.001)DLVS(0.996)R 88.338 0.01299 80626000 194280 187830 129990 181070 245470 207680 202260 316480 260240 TRUE FALSE 168605.4058 186596.1324 192853.5988 222184.711 240585.6273 215669.584 182644.8563 248803.2149 229474.7237 0.734745 0.8131446 0.840413252 0.96823174 1.048418856 0.93984026 0.795925814 1.084229282 1 17.80797573 3.960404295 1.999028032 0.97619243 0.76486098 0.547791869 0.077556181 0.270117232 2.104604927 0.023156828 0.058827362 9128.602463 -3.960404295 -0.211331449 KHT(ph)GERPYSCPHCPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KHTGERPYSCPHCPAR 16 2 O15156;O15156-2 O15156 ZBTB7B Zinc finger and BTB domain-containing protein 7B 1 KHT(1)GERPYSCPHCPAR 97.457 0.0030818 48890000 36863 40873 27418 33057 34566 24869 36867 40064 52548 TRUE FALSE 31991.46115 40604.50257 40677.43651 40563.09709 33878.20423 25825.72652 33291.64401 31496.62538 46335.8353 0.690425908 0.876308851 0.877882879 0.875415255 0.731144783 0.557359684 0.718485893 0.679746576 1 15.49984076 5.031262291 16.9149208 0.774549164 0.406168686 0.046179655 0.1261484 24431252.01 351607146.2 0.032212886 263290531.5 107463.8241 -5.031262291 -0.368380479 KICTLPSPPS(ph)PLASLAPVADSSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KICTLPSPPSPLASLAPVADSSTR 24 1 Q9UER7-3;Q9UER7;Q9UER7-2 Q9UER7-3 DAXX Death domain-associated protein 6 1 KICTLPSPPS(1)PLASLAPVADSSTR;KICTLPSPPS(1)PLASLAPVADSSTR 159.1 1.36E-11 686250000 1177480 948220 527100 690360 912140 916820 992110 1126160 547540 TRUE FALSE 1021873.035 941991.0804 782007.323 847116.7895 893990.1986 952090.6587 895895.3249 885339.4478 482810.445 2.116509792 1.951057791 1.619698437 1.754553569 1.851638066 1.971976101 1.855583976 1.833720577 1 18.88109736 1.237042178 5.725168787 0.961942199 1.863609021 0.812673013 0.131227596 0.06354267 7.06874782 0.225071405 0.033928197 17.26005509 -1.237042178 0.901666822 KIDKYTEVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KIDKYTEVLK 10 2 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ; 138.75 3.17E-05 946450000 2956000 2400730 1202170 1173640 2248550 2116880 3395290 3516390 535110 FALSE TRUE 2565357.11 2384959.447 1783543.433 1440132.9 2203808.254 2198317.743 3066015.298 2764437.363 471849.9054 5.436807513 5.054487495 3.77989571 3.052099584 4.670570512 4.658934374 6.497861424 5.858721876 1 18.84796849 4.463492915 22.56094113 4.472127488 5.341228581 0.057230911 1.515145286 226.5263842 375002.9006 0.389958204 1.033669621 29073.20531 -4.463492915 0.869101093 KIDTHPS(ph)PSHSSTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KIDTHPSPSHSSTVK 15 1 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477;H0Y594 Q8NI27 THOC2 THO complex subunit 2 1 KIDTHPS(0.991)PS(0.009)HSSTVK;KIDT(0.002)HPS(0.958)PS(0.04)HSSTVK;KIDT(0.001)HPS(0.97)PS(0.03)HSSTVK;KIDTHPS(0.947)PS(0.053)HSSTVK;KIDTHPS(0.923)PS(0.077)HSSTVK 202.07 2.87E-09 2531930000 3319520 2393940 701123 1675645 2731640 2105932 3480410 3596440 2991890 TRUE FALSE 2880837.021 2378214.051 1040188.428 2056125.808 2677285.708 2186948.567 3142880.374 2827369.294 2638192.173 1.09197391 0.901455957 0.394280765 0.779369232 1.014818305 0.828957265 1.191300773 1.071707104 1 21.33111823 2.710564118 1.488689715 1.079095105 0.786292518 0.247552888 0.193181116 0.533654703 2.414357578 0.095194467 0.079155392 513.5279879 -2.710564118 -0.292802587 KIDYFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KIDYFER 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 106.42 0.012355 3455210000 5362760 5134900 3469050 4078810 5175090 4853690 5308360 6409400 5530180 FALSE TRUE 4654057.678 5101168.504 5146694.183 5004966.151 5072115.834 5040414.595 4793556.064 5038799.688 4876408.42 0.954402765 1.046091316 1.05542722 1.0263632 1.040133516 1.033632576 0.983009554 1.033301408 1 22.21738753 4.748008905 24.58554521 1.027100023 0.954402716 0.535373035 0.02132559 813.9854411 2118027.979 0.005272541 0.062682279 55976.90798 -4.748008905 -0.072697307 KIEEIKDFLLTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KIEEIKDFLLTAR 13 2 J3KT73;J3QL01;P63173;J3KSP2 J3KT73 RPL38 60S ribosomal protein L38 0 ; 204.43 4.39E-08 3204300000 8536400 7293200 5361780 6658190 6544620 4851100 9179100 10966800 7523900 FALSE TRUE 7408293.112 7245290.489 7954754.742 8170033.804 6414394.866 5037724.956 8288912.295 8621635.164 6634433.113 1.116642972 1.092073786 1.199010466 1.231459216 0.966833904 0.75933013 1.249377626 1.299528538 1 22.66154177 KIEFPLPDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KIEFPLPDEK 10 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 85.258 0.026482 0 1032200 892300 564390 750950 763840 624830 1020700 1125800 1032900 FALSE TRUE 895792.1547 886438.4225 837330.8918 921464.6751 748641.0784 648867.6144 921712.6711 885056.431 910791.7387 0.983531269 0.973261378 0.919343969 1.011718306 0.821967357 0.712421498 1.011990592 0.971744026 1 19.79676168 KIEFPLPDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KIEFPLPDRR 10 2 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ; 128.28 0.0001877 2190100000 2493500 2297600 1553900 1783000 2149200 2047340 2372400 2715700 1979510 FALSE TRUE 2163977.657 2282506.914 2305371.237 2187857.401 2106435.125 2126102.495 2142325.013 2134968.689 1745494.583 1.239750429 1.307656258 1.320755309 1.253431218 1.206784109 1.218051614 1.227345552 1.223131088 1 20.73520445 0.575044491 1.387340401 1.23E-15 1.258703765 0.82326398 0.036529775 3.105075521 1.320700509 8.748778233 0.011852071 3.75875909 -0.575044491 1.258703765 KIEFPMPNEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KIEFPMPNEEAR 12 1 P17980;E9PM69;R4GNH3 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ; 91.207 0.013513 600450000 834450 890950 727480 504410 851780 1303300 643440 735330 658350 FALSE TRUE 724175.3183 885097.2908 1079291.761 618943.9999 834831.2445 1353438.794 581039.2878 578085.4018 580520.613 1.247458406 1.524661263 1.859179049 1.066187808 1.438073388 2.331422458 1.000893465 0.995805125 1 19.14698777 2.082658968 25 0.997533866 1.567560772 0.391477985 0.34009556 26.66806286 8062.881377 0.136812329 0.092238845 120.9647877 -2.082658968 0.570026906 KIEFSLPDLEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KIEFSLPDLEGR 12 1 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ; 160.27 0.00010985 1989470000 2818300 2529900 1629960 1850850 2375600 2062880 2544700 3017000 2161270 FALSE TRUE 2445854.514 2513280.92 2418214.108 2271113.781 2328330.208 2142240.328 2297915.386 2371838.028 1905767.123 1.283396321 1.318776513 1.268892762 1.191705825 1.221728605 1.12408295 1.205769246 1.244558162 1 20.86194041 -1.12024701 0.038209183 3.73E-08 2.062404774 0.521292864 0.062630267 1475.179624 6.769918634 261.5093393 126.9155136 0.075814625 1.12024701 2.062404737 KIEISQHAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KIEISQHAK 9 1 Q6P4E4;E9PEL3;P61513;G5E9R3;M0R0A1;C9J4Z3;M0R2L6 Q6P4E4 RPL37A 60S ribosomal protein L37a 0 ; 111.65 0.0013568 2400800000 4150300 3924000 1402210 3145500 4320700 3542800 4891400 5197500 4756300 FALSE TRUE 3601827.339 3898222.986 2080323.446 3859733.851 4234726.523 3679093.808 4417032.781 4086055.072 4194015.632 0.858801601 0.929472689 0.496021863 0.920295533 1.0097069 0.877224629 1.053175088 0.974258427 1 21.99990081 3.493616585 24.78721649 0.98026052 0.766556537 0.423590929 0.118070377 612.2298831 919984.6011 0.031683176 0.045606424 3116.137303 -3.493616585 -0.213703983 KIEITVEPSQRPGTAINRS(ph)PS(ph)PISNQPSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KIEITVEPSQRPGTAINRSPSPISNQPSPR 30 3 F6SS63;Q8N5C8-2;Q8N5C8 F6SS63 TAB3 TGF-beta-activated kinase 1 and MAP3K7-binding protein 3 2 KIEITVEPS(0.004)QRPGT(0.129)AINRS(0.868)PS(0.999)PISNQPSPR;KIEITVEPS(0.016)QRPGT(0.113)AINRS(0.871)PS(0.998)PIS(0.001)NQPSPR 90.672 0.00050216 185714000 255521 225757 142682 165019 206201 221234 290024 305423 155786 TRUE FALSE 221753.2524 224273.9874 211683.4924 202489.0861 202098.0035 229745.0151 261897.5171 240110.6683 137369.1566 1.614287064 1.632637144 1.54098269 1.474050589 1.471203643 1.672464336 1.906523442 1.747922709 1 17.06769859 1.232590511 24.99990399 0.999998961 1.639163215 0.702855955 0.129182307 129.6461734 542840.0333 0.324785313 0.036694957 17.08403731 -1.232590511 0.639164254 KIEMVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KIEMVR 6 1 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;; 105.39 0.05294 3749370000 4683900 3851850 2801830 3660720 3674450 3335960 3980160 4523790 5350550 FALSE TRUE 4064910.748 3826546.944 4156804.36 4491942.427 3601335.634 3464296.54 3594164.696 3556412.713 4718014.074 0.861572408 0.811050345 0.881049589 0.952083304 0.763316001 0.734270073 0.761796095 0.753794426 1 22.16974829 3.211642604 24.96235252 0.790048991 0.872097712 0.157004941 0.081876198 359.7808617 333640.6661 0.024797452 0.028124722 1627.955779 -3.211642604 0.082048721 KIENLCAMGFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KIENLCAMGFDR 12 1 D6RDM7;P61086;P61086-2 D6RDM7 UBE2K Ubiquitin-conjugating enzyme E2 K 0 ; 126.48 0.00045965 2691800000 3134200 2701200 1746680 2217480 2684700 2496700 3144900 3385700 3007400 FALSE TRUE 2720007.529 2683455.639 2591380.29 2720992.726 2631279.723 2592749.665 2839908.082 2661694.403 2651868.598 1.025694686 1.011911239 0.977190307 1.026066197 0.992236088 0.977706688 1.070908296 1.003705238 1 21.33857786 KIEQELTAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KIEQELTAAK 10 1 Q9H444 Q9H444 CHMP4B Charged multivesicular body protein 4b 0 ; 99.732 0.0072071 324350000 1262560 1128230 923490 1105050 1094030 830900 1489030 1616920 1638220 FALSE TRUE 1095709.497 1120818.583 1370092.853 1355968.492 1072260.943 862865.2607 1344624.1 1271154.241 1444551.498 0.758511897 0.775893822 0.948455527 0.938677849 0.742279486 0.597323987 0.93082462 0.879964641 1 20.46219021 1.641276975 1.964633368 0.979452113 0.80681736 0.247899123 0.106654638 0.565210476 4.24029136 0.148512517 0.032298827 43.78012276 -1.641276975 -0.172634753 KIFPGLS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KIFPGLSPVR 10 1 Q5VZK9;Q5VZK9-2;Q5VZK9-3;A0A0U1RR91 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 KIFPGLS(1)PVR;KIFPGLS(1)PVR 87.498 0.0078615 519550000 521460 790530 494350 555650 815020 776600 786070 844850 704880 TRUE FALSE 452547.7398 785336.9564 733419.3135 681818.8251 798802.6966 806476.3045 709837.0524 664185.4021 621549.8894 0.7280956 1.263513951 1.179984626 1.096965564 1.285178728 1.297524653 1.142043566 1.06859548 1 19.24551067 4.746675379 24.89807869 1.163925855 0.728095373 0.671457107 0.096406932 652.0489461 2000598.176 0.025250804 0.276167051 55805.29126 -4.746675379 -0.435830482 KIFQAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KIFQAHK 7 1 Q9Y490 Q9Y490 TLN1 Talin-1 0 58.604 0.070468 297620000 419780 471000 319500 381970 455630 417060 501980 588630 487720 FALSE TRUE 364305.0094 467905.97 474011.2687 468702.1265 446563.8544 433104.5681 453298.0569 462756.0552 430062.2972 0.847098227 1.087995793 1.102192105 1.089847051 1.038370155 1.007074024 1.054028823 1.076020982 1 18.71418613 4.743425593 24.97732219 1.058598934 0.847098139 0.787385343 0.034259234 236.9790423 1216635.843 0.008730618 0.069433208 55389.26377 -4.743425593 -0.211500794 KIFVGGIKEDTEEYNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KIFVGGIKEDTEEYNLR 17 2 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 143.39 3.10E-07 547270000 257700 182670 104970 133400 177730 198320 263420 295660 77121 FALSE TRUE 223644.2921 181470.0287 155733.8431 163690.5089 174193.5207 205949.4987 237873.5689 232435.4098 68003.84324 3.288700777 2.668526073 2.290074144 2.407077322 2.56152465 3.028497934 3.497943022 3.417974614 1 16.05332866 2.746534813 23.43897701 2.914068607 2.611854787 0 0.736427202 1077.796518 3168021.536 0.23984131 0.235340319 557.8723194 -2.746534813 -0.30221382 KIGDEYFTFITDCKDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KIGDEYFTFITDCKDPK 17 2 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 201.96 6.20E-12 1534290000 3057700 2122950 1952030 2032710 1677700 1289840 3035490 3438800 1888360 FALSE TRUE 2653617.198 2109004.202 2896038.237 2494267.874 1644317.052 1339460.979 2741108.647 2703439.381 1665120.232 1.593649003 1.266577729 1.739236712 1.497950614 0.9875065 0.80442298 1.646192626 1.623570075 1 20.66719492 3.440409653 24.98491416 1.272871246 1.525180004 0.208378081 0.289650646 356.2971161 242484.9207 0.091734059 0.118428446 2756.827884 -3.440409653 0.252308758 KIGELVR ddPTM_MDA-MB-175_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 0 103.56 0.032784 0 1523600 1320600 827780 1055200 1296400 1208200 1340100 1497200 1299300 FALSE TRUE 1322252.4 1311924.892 1228097.177 1294799.288 1270604.176 1254680.236 1210137.308 1177035.431 1145698.234 1.154101805 1.145087644 1.071920284 1.1301399 1.109021676 1.09512278 1.056244369 1.027352051 1 20.12779567 -2 0.261048407 0.037672341 1.153787576 0.834417238 0.020384329 30.88559149 0.49734476 14.95076931 0.059900043 0.01 2 1.116115236 KIGGIFAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KIGGIFAFK 9 1 H0YF61;P22307-6;P22307-2;P22307-4;P22307-7;P22307-8;P22307 H0YF61 SCP2 Non-specific lipid-transfer protein 0 ; 126.07 0.0024083 0 1263780 1189540 691970 780680 1069390 989300 1273180 1385890 522220 FALSE TRUE 1096768.271 1181725.833 1026609.007 957945.3259 1048111.231 1027359.011 1149707.2 1089528.209 460483.7465 2.381774122 2.566270454 2.229414207 2.080302146 2.276109068 2.231042939 2.496737851 2.36605139 1 18.81279071 1.237618941 24.99997884 0.999998439 2.330013491 0.900791339 0.138551709 7.24312885 192188.8769 0.21318225 0.036113629 17.28299248 -1.237618941 1.330015053 KIHAQWQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KIHAQWQK 8 1 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 92.47 0.0076307 321130000 695890 902560 650890 725290 858000 702790 1045500 1066800 937360 FALSE TRUE 603926.3733 896631.0239 965662.5811 889978.1799 840927.4786 729826.7861 944107.5709 838673.1218 826546.3686 0.730662424 1.084792164 1.168310234 1.076743198 1.017399036 0.882983476 1.14223183 1.014671595 1 19.65673623 4.742546681 24.87196315 1.048651793 0.730662291 0.61106391 0.079662484 265.4139429 1656042.112 0.019788933 0.146994994 55277.28211 -4.742546681 -0.317989501 KIHIDLPNEQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KIHIDLPNEQAR 12 1 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 98.942 0.0026454 747350000 1181000 1176700 569760 727820 1199200 1086000 1194100 1237700 743480 FALSE TRUE 1024927.858 1168970.18 845297.8417 893082.655 1175338.266 1127779.123 1078296.366 973027.4868 655586.6414 1.563375141 1.783090299 1.289376245 1.362264876 1.792803868 1.720259462 1.644780869 1.484208837 1 19.32242693 1.2372908 3.010525123 0.886396168 1.591876327 0.561152857 0.1638774 0.313172009 3.548470344 0.539178999 0.044440548 17.26993887 -1.2372908 0.705480159 KIHLTENGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KIHLTENGIR 10 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 127.42 0.0002314 216720000 150720 136350 70270 84444 166680 133260 133760 139950 102980 FALSE TRUE 130801.9701 135454.3079 104252.807 103618.3008 163363.3941 138386.5984 120787.9758 110022.7816 90805.82172 1.440457976 1.491691891 1.148085057 1.141097552 1.799040976 1.523983769 1.330178765 1.211626959 1 16.47049717 1.492969558 1.91340688 0.974166367 1.416594863 0.348951878 0.187532649 0.581400224 3.40650254 0.410468262 0.056005962 31.11498225 -1.492969558 0.442428496 KIHPQTIIAGWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KIHPQTIIAGWR 12 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 142.91 4.01E-05 1538580000 4536800 4263200 2162640 2735180 3808600 3635300 4283800 4834600 1802380 FALSE TRUE 3937250.385 4235194.758 3208499.938 3356244.424 3732816.311 3775152.343 3868357.735 3800758.413 1589304.69 2.47734145 2.664809829 2.018807318 2.11176903 2.348710311 2.375348395 2.433993784 2.391459887 1 20.5999643 1.237513421 24.9999504 0.999998402 2.350760872 0.848183946 0.179861874 10.16324647 242510.7431 0.273590209 0.046053413 17.27879377 -1.237513421 1.35076247 KIHSQEEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KIHSQEEALR 10 1 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;;;;; 206.11 1.01E-07 6201750000 1877060 2063160 1228200 1445800 1724420 1771010 2103070 2200090 1624980 FALSE TRUE 1629001.765 2049606.966 1822161.628 1774090.988 1690107.416 1839141.901 1899114.595 1729617.875 1432876.716 1.136875034 1.430414036 1.271680674 1.238132331 1.179520469 1.283531151 1.3253859 1.20709469 1 20.45048306 1.268188274 3.111285869 0.962148233 1.269114304 0.526937581 0.078947659 0.257034656 3.320720211 0.188013976 0.019565519 18.54335335 -1.268188274 0.306966071 KIIPTLEEGLQLPS(ph)PTATSQLPLESDAVECLNYQHYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYK 37 1 P61978;P61978-2 P61978 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 KIIPTLEEGLQLPS(0.88)PT(0.12)ATSQLPLESDAVECLNYQHYK;KIIPTLEEGLQLPS(0.956)PT(0.044)ATSQLPLESDAVECLNYQHYK 223.35 1.33E-39 3629100000 2650400 2373600 1142110 1373300 2137100 1824730 2923100 3319700 689980 TRUE FALSE 2300142.925 2358007.665 1694438.216 1685128.755 2094575.891 1894928.544 2639618.212 2609807.989 608411.3504 3.780572015 3.875679939 2.785020718 2.769719456 3.442696935 3.114551598 4.338542024 4.289545202 1 19.21468754 KILDSVGIEADDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KILDSVGIEADDDR 14 1 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ; 178.14 3.23E-06 1782800000 1665480 1575120 1141590 1599190 1425080 1359210 1437700 1779080 3604700 FALSE TRUE 1445382.598 1564772.933 1693666.742 1962310.532 1396723.696 1411499.688 1298272.075 1398637.587 3178556.472 0.454729249 0.49229043 0.532841482 0.617359027 0.439420759 0.444069407 0.408447069 0.440022884 1 21.59994029 1.236050299 24.99998185 1.000000686 0.477694569 0.882725682 0.059719467 23.94545138 238418.8883 0.106075854 0.016075612 17.22068009 -1.236050299 -0.522306118 KILDSVGIEADDDRLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KILDSVGIEADDDRLNK 17 2 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ; 228.49 7.96E-16 2306890000 3434610 2750530 1796380 2162010 2414650 1836220 3381270 3625280 2157590 FALSE TRUE 2980717.586 2732461.587 2665115.377 2652927.415 2366603.189 1906860.572 3053354.956 2850042.084 1902522.168 1.566718978 1.436231143 1.400832758 1.394426546 1.243929363 1.002280343 1.604898491 1.498033574 1 20.85948183 4.507977624 1.114870704 1.317569041 1.619110084 0.183638673 0.190600917 2.506535287 3.452366958 0.063301277 0.81261466 32209.02841 -4.507977624 0.301541042 KILGVGGEDDDGEVHR ddPTM_MDA-MB-175_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 ; 160.47 5.69E-09 475850000 383100 379660 228031 349930 469980 436870 302560 596890 346160 FALSE TRUE 332472.3643 377165.9885 338307.5543 429386.9548 460628.3175 453676.6716 273217.7778 469249.7185 305237.3591 1.089225661 1.235648184 1.108342554 1.406731326 1.50908237 1.486307813 0.895099402 1.537327278 1 18.21957202 3.747528683 24.52430426 1.320208419 1.153529734 0.108832705 0.214491815 1109.789729 3034848.053 0.054789655 0.093094676 5591.504555 -3.747528683 -0.166678686 KINS(ph)SPNVNTTASGVEDLNIIQVTIPDDDNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KINSSPNVNTTASGVEDLNIIQVTIPDDDNER 32 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 KINS(0.493)S(0.493)PNVNT(0.012)T(0.002)ASGVEDLNIIQVTIPDDDNER 127.83 5.25E-08 48741000 268180 211080 122300 164110 214410 182420 235730 268110 210860 TRUE FALSE 232739.3335 209693.4016 181444.6891 201373.6838 210143.6605 189437.8154 212868.9409 210776.7629 185932.371 1.251741869 1.127793942 0.975863902 1.083048006 1.130215569 1.01885333 1.144872943 1.133620584 1 17.50441844 4.661397129 3.75815833 1.078835126 1.257810655 0.4847851 0.058611056 0.205128689 4.898105667 0.014542072 0.085582495 45856.10135 -4.661397129 0.178975529 KIPDPDS(ph)DDVSEVDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 111.13 0.00051479 158540000 233080 133240 90571 119140 130510 102400 150600 157810 174580 TRUE FALSE 202277.8875 132364.7377 134371.4385 146192.5579 127913.1063 106339.3943 135994.8352 124063.5596 153941.3513 1.313993191 0.859838741 0.87287423 0.94966399 0.830921031 0.69077862 0.883419783 0.805914451 1 17.23202129 4.738676689 7.358244944 0.854789897 1.31947992 0.748173786 0.082389402 0.050244727 24.68529979 0.019851659 0.116065197 54786.89514 -4.738676689 0.464690023 KIPDPDSDDVSEVDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 73.918 0.054086 201920000 318550 232450 175360 228110 242140 244940 219390 308920 298190 FALSE TRUE 276452.8104 230923.0206 260164.6825 279905.8619 237321.8877 254363.0003 198113.5916 242859.862 262938.3179 1.051397958 0.878240275 0.989451384 1.064530511 0.902576276 0.967386581 0.753460329 0.923638152 1 18.00436488 3.166857997 19.06897545 0.902387374 0.987038658 0.215795728 0.080535728 9.450724216 2511.264664 0.024263409 0.027512314 1468.446054 -3.166857997 0.084651284 KIPEPS(ph)PVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 KIPEPSPVTR 10 1 A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;Q7Z4S6-3;H0YHT2;H0YI78 A0A1B0GV47 KIF21A Kinesin-like protein KIF21A 1 KIPEPS(0.996)PVT(0.004)R;KIPEPS(1)PVTR;KIPEPS(1)PVTR;KIPEPS(1)PVTR;KIPEPS(1)PVTR;KIPEPS(1)PVTR;KIPEPS(1)PVTR;KIPEPS(1)PVTR 192.65 4.04E-07 13311510000 6190480 6004410 3845530 4697850 5796580 4843490 5696120 6892440 6430360 TRUE FALSE 5372392.383 5964966.635 5705241.171 5764568.645 5681239.399 5029822.194 5143711.159 5418545.343 5670170.166 0.947483449 1.051990762 1.006185177 1.016648262 1.001952187 0.887067239 0.907152873 0.955623056 1 22.4349606 2.872398831 7.845242252 0.937575056 1.008940798 0.428565028 0.038589655 0.259727761 15.37031732 0.01243395 0.012448517 745.4162063 -2.872398831 0.071365742 KIPNPDFFEDLEPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KIPNPDFFEDLEPFR 15 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 92.575 0.008321 486620000 412640 323840 247100 373790 458080 378370 347310 542500 358630 FALSE TRUE 358108.5785 321712.6737 366598.3865 458664.7325 448965.1042 392926.1387 313627.9297 426490.5967 316233.17 1.132419406 1.017327416 1.159266077 1.450400452 1.419728058 1.242520318 0.991761648 1.348658639 1 18.27062918 7.149296015 6.482091125 1.206521595 0.213517271 0 0.169549862 0 0 0.038862753 0 14102496.95 -7.149296015 -0.993004324 KIPVVFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KIPVVFR 7 1 P10768;X6RA14;U3KQT1;H7BZT7 P10768 ESD S-formylglutathione hydrolase 0 107.66 0.029728 0 1566200 1660800 935120 1401300 1694600 1528900 1638300 2000500 1766500 FALSE TRUE 1359222.702 1649890.095 1387347.16 1719486.583 1660880.775 1587717.772 1479417.918 1572708.643 1557666.382 0.872601937 1.059206332 0.890657445 1.103886302 1.066262195 1.019292571 0.949765582 1.009656921 1 20.57095484 4.751913698 24.25868169 1.010158475 0.8726018 0.347970163 0.060048965 1785.878555 3244337.358 0.014207311 0.263102696 56482.47224 -4.751913698 -0.137556675 KIQALQQQADEAEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KIQALQQQADEAEDR 15 1 P67936;A0A2R8Y5V9;A0A2R8YGX3;A0A590UJB9;A0A590UK79 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;;;; 319.28 2.76E-56 15980400000 6732750 6984820 4237540 5338390 6458010 6058390 7169780 8016890 5925260 FALSE TRUE 5843000.029 6938936.258 6286828.518 6550553.042 6329508.236 6291460.184 6474455.839 6302540.461 5224782.513 1.118324067 1.328081358 1.203270854 1.253746548 1.211439561 1.204157334 1.239181884 1.20627805 1 22.31693955 1.234976037 4.210367233 0.976799159 1.225702195 0.64238348 0.051811385 0.129929008 4.331295024 0.099147878 0.011664938 17.17813601 -1.234976037 0.248903036 KIQEESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KIQEESLR 8 1 Q99613-2;Q99613;B5ME19 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 ;;; 195.7 0.00025347 2018940000 1867400 1877560 1317020 1491910 2191430 2027240 2273300 2526170 1868550 FALSE TRUE 1620618.359 1865226.185 1953935.277 1830670.968 2147824.83 2105229.235 2052835.716 1985968.204 1647652.148 0.983592539 1.132050953 1.18589065 1.111078555 1.303566917 1.277714618 1.245915722 1.20533221 1 20.65198026 5.248652145 1.05382515 1.203978889 0.579090294 0.360846261 0.086132927 5.045413513 2.177427954 0.026754158 4.569456675 177276.8987 -5.248652145 -0.624888595 KIQNDAGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KIQNDAGVR 9 1 A0A087WTP3;Q92945;M0R0I5;Q96AE4;E9PEB5;Q96AE4-2;Q96I24;Q96I24-2 A0A087WTP3;Q96AE4;Q96I24 KHSRP;FUBP1;FUBP3 Far upstream element-binding protein 2;Far upstream element-binding protein 1;Far upstream element-binding protein 3 0 ;;; 199.67 3.91E-05 1919920000 3883420 3375530 1994670 2528470 3173810 3219480 3521940 4046940 2549020 FALSE TRUE 3370216.208 3353355.921 2959299.084 3102597.759 3110657.39 3343335.479 3180382.801 3181533.374 2247677.759 1.499421433 1.491920231 1.316602912 1.380357013 1.383942773 1.487462099 1.414963861 1.415475755 1 21.10000379 1.238209639 7.37439141 0.992608518 1.421647576 0.843906726 0.057276563 0.040388397 14.79553486 0.08637857 0.014561193 17.30651565 -1.238209639 0.429039058 KIQSLGDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KIQSLGDSK 9 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 103.91 0.0053649 379270000 924450 631350 459720 527120 480540 430850 723870 807860 611190 FALSE TRUE 802281.5902 627202.6203 682042.1297 646810.6525 470978.1942 447425.0783 653669.1988 635105.4258 538935.8145 1.488640333 1.163779811 1.265534988 1.200162682 0.873904056 0.830201049 1.212888773 1.178443534 1 19.03975394 5.483188228 0.758293887 1.059260109 2.409944119 0.493775514 0.137151753 7.530488195 1.472578807 0.057380837 11.20749592 304220.3266 -5.483188228 1.35068401 KIQVLQQQADDAEER ddPTM_MDA-MB-175_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 ;;;;;;; 291.13 1.04E-43 20252240000 7056800 6429690 3745390 4946490 6181420 5544510 6558380 7844690 4592510 FALSE TRUE 6124226 6387452.943 5556673.132 6069666.157 6058421.836 5757810.887 5922349.317 6167164.091 4049588.7 1.512308151 1.577309059 1.372157408 1.498835217 1.496058559 1.421826095 1.462456994 1.522911226 1 21.94934396 1.235633572 24.99999373 0.999999348 1.482369608 0.880202819 0.055996762 25.68839997 219364.6118 0.090907808 0.013369195 17.20416392 -1.235633572 0.48237026 KIS(ph)ENSYSLDDLEIGPGQLSSSTFDSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KISENSYSLDDLEIGPGQLSSSTFDSEK 28 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KIS(0.911)ENS(0.088)YS(0.001)LDDLEIGPGQLSSSTFDSEK;KIS(0.999)ENS(0.001)YSLDDLEIGPGQLSSSTFDSEK;KIS(0.983)ENS(0.009)YS(0.008)LDDLEIGPGQLSSSTFDSEK;KIS(0.93)ENS(0.057)YS(0.013)LDDLEIGPGQLSSSTFDSEK 332.76 3.66E-96 6153200000 1021480 887547 1497780 1869050 1573660 1431240 2524190 2824780 5019030 TRUE FALSE 886488.8299 881716.6453 2222111.418 2293446.369 1542347.245 1486300.729 2279394.442 2220722.779 4425685.991 0.200305406 0.199227114 0.502094234 0.518212628 0.348499023 0.335835107 0.515037544 0.501780466 1 22.07746966 -0.172370473 0.985282528 10 0.358956848 0.758473767 0.111683377 14.51771768 1.125893675 271.1450645 0.039122743 0.672402821 0.172370473 -9.641043152 KIS(ph)ENSYSLDDLEIGPGQLSSSTFDSEKNESR ddPTM_MDA-MB-175_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(0.658)ENS(0.31)YS(0.032)LDDLEIGPGQLSSSTFDSEKNESR;KIS(0.996)ENS(0.003)YS(0.001)LDDLEIGPGQLSSSTFDSEKNESR;KIS(0.999)ENS(0.001)YSLDDLEIGPGQLSSSTFDSEKNESR 252.12 2.40E-59 4414630000 635270 578160 602590 677530 848640 803890 1303750 1368460 766540 TRUE FALSE 551317.4599 574362.0289 894004.5395 831373.5419 831753.7243 834816.1685 1177312.526 1075825.478 675920.5144 0.815654279 0.849747887 1.322647442 1.229987142 1.230549608 1.235080384 1.74179138 1.591644957 1 19.36649408 4.738024093 0.578388885 1.45247365 0.292877733 0.459246238 0.215118392 3.388322859 0.898426669 0.132953788 2.664049629 54704.63105 -4.738024093 -1.159595916 KIS(ph)GTTALQEALK ddPTM_MDA-MB-175_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(0.944)GT(0.039)T(0.017)ALQEALK 207.53 3.25E-08 513500000 602200 393580 543680 492530 402260 386400 620790 547900 762280 TRUE FALSE 522617.7442 390994.5471 806605.4665 604366.4643 394255.813 401265.058 560585.8813 430735.8488 672164.1268 0.777515079 0.581695053 1.200012667 0.899135256 0.586546942 0.596974819 0.834001487 0.640819454 1 19.35845402 3.269166333 24.97484164 0.721252586 0.868341633 0.104352954 0.192019157 447.4647827 365136.7539 0.055342258 0.071438166 1858.516121 -3.269166333 0.147089047 KIS(ph)PPSYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KISPPSYAR 9 1 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 KIS(0.862)PPS(0.138)YAR;KIS(0.861)PPS(0.139)YAR;KIS(0.783)PPS(0.217)YAR;KIS(0.793)PPS(0.207)YAR 100.73 0.0027343 3212520000 713140 597190 385088 463308 577280 536543 619800 719880 701070 TRUE FALSE 618896.7421 593267.0196 571317.8448 568509.1626 565793.2574 557184.1564 559691.8914 565939.2641 618190.3033 1.001142753 0.959683477 0.924177946 0.919634552 0.915241236 0.90131494 0.905371515 0.91547742 1 19.2376915 4.550341449 2.013414446 0.92194723 1.009270773 0.436601588 0.027709146 0.445056978 2.622691801 0.007285959 0.062041089 35509.24589 -4.550341449 0.087323543 KIS(ph)PVKFSNTDSVLPPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KISPVKFSNTDSVLPPKR 18 3 G3V2F4;E7EPD8;Q9NUW8;G3V3Q0;G3V5F9;G3V5B8;G3V554;G3V4W8;G3V5H9;G3V2U6;Q9BRS7 G3V2F4 TDP1 Tyrosyl-DNA phosphodiesterase 1 1 KIS(1)PVKFSNTDSVLPPKR 103.58 0.0029368 402610000 296440 212540 130980 135570 185840 123660 320010 376390 35873 TRUE FALSE 257264.7029 211143.8107 194322.3661 166353.2406 182142.1476 128417.2802 288975.4795 295901.9276 31632.13481 8.133017404 6.674978216 6.143194801 5.258995056 5.758136424 4.059709564 9.135503538 9.35447226 1 14.9491033 4.708761274 2.740783962 6.228939797 8.425791487 0.06851689 2.390771398 1.421688313 15.17876304 0.622466187 6.835162709 51140.06482 -4.708761274 2.19685169 KISELDAFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KISELDAFLK 10 1 Q06323;Q06323-3;Q06323-2 Q06323 PSME1 Proteasome activator complex subunit 1 0 82.543 0.031581 0 452440 374180 305070 375150 399860 397600 404340 503770 448130 FALSE TRUE 392648.9077 371721.9869 452602.8724 460333.5413 391903.5683 412895.9293 365127.169 396042.7058 395152.5819 0.993664032 0.940704943 1.145387613 1.164951369 0.991777825 1.044902522 0.924015648 1.002252608 1 18.59205031 2.619978946 2.248437696 0.980916778 1.055575672 0.159250158 0.071662212 0.584042934 5.844391464 0.030720152 0.025747914 416.8491747 -2.619978946 0.074658894 KISGTT(ph)ALQEALK ddPTM_MDA-MB-175_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(0.205)GT(0.312)T(0.483)ALQEALK 105.39 0.00085361 646250000 268360 175410 299070 235950 190960 180280 293450 267150 275010 TRUE FALSE 232895.5461 174257.7202 443701.2523 289526.0538 187160.2696 187215.4883 264991.2642 210022.0515 242498.6311 0.960399426 0.718592593 1.829706215 1.193928611 0.771799283 0.77202699 1.09275365 0.866075204 1 17.88761708 3.255821983 24.33108927 0.90421556 1.189727262 0.179427881 0.291611184 316.8379005 446601.2018 0.085625535 0.110240072 1802.278838 -3.255821983 0.285511702 KISSDLDGHPVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KISSDLDGHPVPK 13 1 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 ;;; 115.8 0.00041236 5639880000 7585660 6224930 3207210 4966420 5793360 4523820 7249250 7937640 6240340 FALSE TRUE 6583195.811 6184038.025 4758227.483 6094121.568 5678083.471 4697854.283 6546218.851 6240237.457 5502614.114 1.196376063 1.123836398 0.864721273 1.107495718 1.031888363 0.853749543 1.189656173 1.134049622 1 22.39168573 0.92370389 15.8314892 7.93E-05 1.061959963 0.026431549 0.119551062 1748670.996 6677674.588 62567082.83 0.029428918 8.38887823 -0.92370389 1.061880687 KISSIQSIVPALEIANAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KISSIQSIVPALEIANAHR 19 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 124.08 1.95E-05 222150000 357200 322880 189800 294740 375280 375140 327920 449090 147920 FALSE TRUE 309995.115 320758.98 281587.9148 361665.2218 367812.6622 389571.8785 296118.3689 353055.5983 130433.0661 2.376660491 2.459184543 2.158869091 2.77280319 2.819934187 2.986757041 2.270270704 2.706795208 1 16.99295013 1.235583849 24.9999986 0.99999787 2.572405387 0.783486996 0.259189066 39.0304488 327731.8466 0.442598144 0.064729433 17.2021943 -1.235583849 1.572407517 KIVDQIRPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KIVDQIRPDR 10 2 P17844;P17844-2;J3KTA4;J3QSF1;J3KRZ1;A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 P17844;A0A1X7SBZ2 DDX5;DDX17 Probable ATP-dependent RNA helicase DDX5;Probable ATP-dependent RNA helicase DDX17 0 ;; 169.65 2.57E-06 6699880000 7562560 6392420 3596950 4873000 6316700 5725650 6597180 7826510 4847230 FALSE TRUE 6563148.535 6350427.772 5336447.051 5979489.129 6191010.028 5945919.46 5957386.499 6152871.742 4274195.991 1.535528214 1.485759611 1.248526521 1.398974016 1.448461896 1.391119984 1.393802837 1.439538981 1 22.02722163 1.236414512 24.99958989 0.999999469 1.413999737 0.754988231 0.074756731 28.85314214 336021.7741 0.117845527 0.018361632 17.23512795 -1.236414512 0.414000267 KIVEPEVVGES(ph)DS(ph)EVEGDAWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KIVEPEVVGESDSEVEGDAWR 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 KIVEPEVVGES(1)DS(1)EVEGDAWR;KIVEPEVVGES(1)DS(1)EVEGDAWR 94.192 0.0056328 129538000 244100 215490 121466 119195 207820 196337 235450 267550 91042 TRUE FALSE 211841.5665 214074.432 180207.3639 146260.0465 203684.7886 203890.2114 212616.0952 210336.5146 80279.11848 2.638812814 2.666626591 2.244760123 1.821894028 2.537207588 2.539766446 2.648460761 2.620065075 1 16.29273715 4.239928347 24.850263 2.27350655 2.652719842 0.111751599 0.497562061 81.97609393 1489262.919 0.124775326 0.29546195 17375.14136 -4.239928347 0.379213292 KIVEPEVVGES(ph)DSEVEGDAWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KIVEPEVVGESDSEVEGDAWR 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 KIVEPEVVGES(0.957)DS(0.043)EVEGDAWR;KIVEPEVVGES(0.998)DS(0.002)EVEGDAWR 180.65 3.25E-17 207476000 241560 212321 74129 98697 188975 154148 213883 237491 58314 TRUE FALSE 209637.234 210926.2494 109978.0323 121107.6623 185214.7672 160078.1733 193140.6596 186705.3978 51420.18535 4.076944347 4.102012623 2.1388105 2.355255266 3.601985601 3.113138784 3.756125309 3.630974811 1 15.65004719 1.234131053 24.9974201 0.999996529 3.334924905 0.555607989 0.659547461 111.6014838 629720.5079 1.310853227 0.170265324 17.14474592 -1.234131053 2.334928376 KIVSWLEYESSFSNEEAQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KIVSWLEYESSFSNEEAQK 19 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 267.38 1.98E-31 520665000 505365 409912 325193 356671 411955 313097 585326 665153 316995 FALSE TRUE 438579.7348 407219.2611 482457.4225 437658.6019 403757.9015 325142.0442 528561.1746 522915.2072 279520.2122 1.569044798 1.456850858 1.726019806 1.565749391 1.444467641 1.163214787 1.890958691 1.87075991 1 18.09259308 3.468103094 24.08417465 1.536135146 1.583697226 0.00786217 0.28074253 1364.731372 3644667.383 0.085216762 0.110184724 2938.347085 -3.468103094 0.04756208 KIWCFGPDGTGPNILTDITK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KIWCFGPDGTGPNILTDITK 20 1 P13639 P13639 EEF2 Elongation factor 2 0 208.92 8.34E-22 450130000 1053100 967400 594690 644220 916560 684360 1144400 1294900 440070 FALSE TRUE 913930.1668 961045.0857 882284.0731 790499.9973 898322.2492 710687.772 1033416.264 1017995.712 388045.4259 2.355214379 2.476630367 2.27366183 2.037132625 2.314992496 1.831455094 2.663132188 2.623393149 1 18.56586602 4.03045369 5.536694353 2.169834511 2.410675788 0.062278069 0.468849936 0.652763771 55.65314425 0.12060559 0.251324905 10726.39263 -4.03045369 0.240841277 KIYEDGDDDMKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KIYEDGDDDMKR 12 2 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;; 186.16 6.82E-06 1672930000 3765120 2781500 1867650 2014680 2517510 1866880 3663790 4279590 1157490 FALSE TRUE 3267549.852 2763228.143 2770851.787 2472143.886 2467416.476 1938700.082 3308476.21 3364432.982 1020652.851 3.201431172 2.707314383 2.714783763 2.422120199 2.417488448 1.899470599 3.241529387 3.296353877 1 19.96106082 4.967931275 1.26084263 2.5186417 3.811654869 0.11670814 0.654958527 6.312385009 5.998494973 0.192448207 12.09790904 92881.93934 -4.967931275 1.293013169 KIYPTIWWLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KIYPTIWWLFR 11 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 156.69 4.96E-05 182090000 127600 129670 70446 110200 110900 108480 208870 158760 118170 FALSE TRUE 110737.3367 128818.1892 104513.9212 135222.5943 108693.307 112653.2958 188613.8195 124810.4095 104200.0772 1.062737569 1.236258098 1.003011936 1.297720673 1.043121175 1.081124878 1.81011209 1.197795748 1 16.66899682 KKAEPSEVDMNS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KKAEPSEVDMNSPK 14 2 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 KKAEPSEVDMNS(1)PK 121.27 6.03E-05 139240000 315700 260510 251750 229380 257570 142490 353990 426200 286330 TRUE FALSE 273979.4451 258798.6927 373497.1421 281464.2349 252444.8609 147971.6825 319660.1043 335060.4467 252480.3936 1.08515137 1.02502491 1.479311469 1.114796404 0.999859266 0.586071973 1.266078921 1.327075112 1 17.94581183 KKAS(ph)LTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KKASLTSK 8 2 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 KKAS(0.945)LT(0.055)SK 74.76 0.042516 0 2770900 1680400 1721800 1879000 1010500 1107500 3183500 2900900 2754100 TRUE FALSE 2404718.544 1669361.342 2554468.239 2305655.669 990393.027 1150106.242 2874764.66 2280565.11 2428513.435 0.99020187 0.687400497 1.051864981 0.9494103 0.407818632 0.473584467 1.183754892 0.939078646 1 21.21164204 2.21958092 24.99996669 1.025672838 0.762606111 0.272854993 0.215658626 368.1829682 484965.2709 0.093109916 0.062889417 165.7986234 -2.21958092 -0.263066727 KKDEEFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KKDEEFQR 8 2 V9GY93;Q9HC07-2;Q9HC07 V9GY93 TMEM165 Transmembrane protein 165 0 122.28 0.00078581 809890000 431030 345600 284950 300770 364830 350080 373600 538610 496530 FALSE TRUE 374068.2934 343329.7308 422752.7731 369064.4255 357570.5968 363547.8041 337368.3295 423432.443 437830.789 0.854367264 0.784160775 0.965562002 0.842938493 0.816686733 0.830338599 0.770545009 0.967114359 1 18.74001389 1.611734931 5.828163971 0.991371645 0.840043988 0.57395195 0.052450658 0.091909863 6.527536783 0.034795227 0.013414248 40.90109466 -1.611734931 -0.151327657 KKDELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KKDELER 7 2 M0R0F0;M0R0R2;P46782;M0QZN2 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;;;;; 107.69 0.0041733 9266320000 9861110 7784900 6497170 7558660 6145780 5484710 10344220 12389910 10215320 FALSE TRUE 8557939.329 7733760.479 9639223.144 9274969.28 6023491.002 5695710.343 9341039.137 9740424.165 9007676.507 0.950071788 0.858574403 1.070112047 1.029673887 0.668706408 0.632317373 1.037008726 1.081347022 1 23.10272359 2.043770444 24.99980149 1.050293424 0.87186491 0.252664712 0.138503393 190.3055761 108693.5423 0.061576254 0.041514674 110.6039009 -2.043770444 -0.178428514 KKDELS(ph)DYAEK ddPTM_MDA-MB-175_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 160.48 1.43E-05 226390000 553060 334150 387020 333240 296090 273560 508290 550310 615190 TRUE FALSE 479971.7197 331954.9466 574184.1665 408907.2353 290198.3883 284084.0302 458996.114 432630.489 542462.939 0.884800943 0.611940324 1.058476304 0.753797552 0.534964451 0.523692975 0.84613359 0.797530039 1 19.04916505 1.168611795 1.653923827 1.130874272 0.735327715 0.194851448 0.162802661 2.184500134 4.730598756 1.485460117 0.047119731 14.74388026 -1.168611795 -0.395546557 KKDQEDDEQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KKDQEDDEQQR 11 2 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 ;; 145.31 2.04E-05 108639000 91897 74613 48654.3 48732.1 56037 52513.7 88163 97651 72358 FALSE TRUE 79752.57861 74122.86229 72183.68222 59797.46813 54921.97333 54533.93602 79612.96583 76769.09357 63803.91967 1.249963623 1.161728976 1.131336172 0.937206812 0.860793093 0.854711377 1.24777547 1.203203408 1 15.96135744 4.164319511 2.541137519 1.038349575 1.22038836 0.261045635 0.130220493 0.50979821 6.526904868 0.041188588 0.119520183 14598.87905 -4.164319511 0.182038785 KKDQVTAQEIFQDNHEDGPTAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KKDQVTAQEIFQDNHEDGPTAK 22 2 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 209.75 3.19E-23 474440000 544910 418500 356450 339570 416820 278040 534680 699550 317750 FALSE TRUE 472898.7629 415750.8459 528830.4123 416674.5585 408526.0975 288736.3787 482826.8159 549956.6764 280185.957 1.687803229 1.483838985 1.887426543 1.487135769 1.458053437 1.030516953 1.723237028 1.962827411 1 18.09602512 KKEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KKEEER 6 2 Q13442;F8WFC5;Q8NFW9-5;Q8NFW9-2;Q8NFW9 Q13442;Q8NFW9-5 PDAP1;MYRIP 28 kDa heat- and acid-stable phosphoprotein;Rab effector MyRIP 0 ;; 77.741 0.040283 284049000 430980 397810 301173 356170 479610 348014 499660 579310 557190 FALSE TRUE 374024.901 395196.7599 446821.2702 437043.8422 470066.6993 361402.3238 451203.0501 455429.0647 491319.633 0.761265938 0.804357761 0.909430929 0.889530588 0.956743162 0.735574765 0.918349319 0.926950674 1 18.90630236 0.16200156 0.032036475 1.95854795 4.84E-06 0.350309722 0.068796516 1922.72129 10.76016907 404.5130196 266.3488925 1.452116833 -0.16200156 -1.95854311 KKEEPSQNDIS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KKEEPSQNDISPK 13 2 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 KKEEPSQNDIS(1)PK;KKEEPSQNDIS(1)PK;KKEEPSQNDIS(1)PK;KKEEPSQNDIS(1)PK;KKEEPSQNDIS(1)PK 190.82 2.13E-06 4539860000 3912940 2780450 2866510 2638530 2791770 1556860 4114510 4751620 3419010 TRUE FALSE 3395835.065 2762185.041 4252763.824 3237648.564 2736219.239 1616753.412 3715485.453 3735523.04 3014818.533 1.126381249 0.916202753 1.410620168 1.07391159 0.907590029 0.536268898 1.23240766 1.239054026 1 21.52363974 3.4792652 24.88804494 1.009544486 1.146695576 0.098121964 0.226081111 246.2658671 2858813.799 0.070295188 0.092265781 3014.846466 -3.4792652 0.13715109 KKEIQNGNLHES(ph)DSESVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KKEIQNGNLHESDSESVPR 19 2 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 1 KKEIQNGNLHES(1)DSESVPR;KKEIQNGNLHES(0.988)DS(0.012)ESVPR 285.82 2.39E-40 626360000 348580 297200 139951 227570 406640 308110 344730 679120 73163 TRUE FALSE 302514.2698 295247.6736 207631.7717 279243.2467 398548.6596 319963.1911 311298.1377 533895.4729 64513.75349 4.689143841 4.576507453 3.218410966 4.328429701 6.177731693 4.959612079 4.825298806 8.275684549 1 15.97731914 3.365615088 7.38159854 5.426869833 4.134246962 0.028316351 1.831931736 0.540934566 33.07126729 0.514558656 0.664866748 2320.679086 -3.365615088 -1.292622871 KKEPAITSQNS(ph)PEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 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(0.999)PEAR;KKEPAIT(0.009)S(0.027)QNS(0.964)PEAR;KKEPAIT(0.004)S(0.036)QNS(0.96)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITSQNS(1)PEAR;KKEPAIT(0.001)S(0.125)QNS(0.875)PEAR;KKEPAITSQNS(1)PEAR 306.69 2.14E-45 60900144700 22374096.4 16679534.8 12189262.5 14786656.4 16169630.8 13258773.4 21146909.2 24124928.7 18500783.8 TRUE FALSE 19417302.87 16569965.84 18084030.62 18144192.74 15847886.78 13768846.99 19096085.2 18966000.44 16313642.22 1.190249401 1.015712225 1.108521958 1.112209799 0.971449942 0.84400815 1.170559275 1.162585288 1 23.95957558 4.750914243 23.24043392 1.057925998 1.190249626 0.164130712 0.098614224 1569.071565 2951689.277 0.025764323 0.396103235 56352.63698 -4.750914243 0.132323627 KKEPEPNFQLLDNPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KKEPEPNFQLLDNPAR 16 2 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 81.594 0.0069424 699650000 215100 203460 130180 156450 174670 175910 204890 259120 197710 FALSE TRUE 186673.99 202123.4579 193135.4834 191974.3637 171194.4087 182677.3715 185019.7993 203709.2045 174336.949 1.070765498 1.159383934 1.107828745 1.10116854 0.98197433 1.047840819 1.061277029 1.168479807 1 17.41151884 3.460506845 24.9984061 1.064673397 1.11519301 0.204640523 0.053824096 466.7818465 702327.857 0.016575468 0.021406134 2887.399286 -3.460506845 0.050519613 KKEPPR ddPTM_MDA-MB-175_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 ; 94.401 0.025042 882160000 1476790 1385710 758810 1234380 911380 1199170 1818800 2199480 2263470 FALSE TRUE 1281628.46 1376607.18 1125773.054 1514664.845 893245.3211 1245302.846 1642413.056 1729138.318 1995885.155 0.642135374 0.689722641 0.56404701 0.758893788 0.447543446 0.623935121 0.82289958 0.86635161 1 20.92859728 1.943301378 1.811651884 0.953444238 0.619672207 0.701364121 0.086639359 0.201880969 1.220104331 0.073569442 0.025668948 87.76096257 -1.943301378 -0.333772031 KKEPPRAS(ph)PPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KKEPPRASPPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGR 47 3 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 1 KKEPPRAS(1)PPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGR;KKEPPRAS(0.998)PPGGLAEPPGS(0.002)AGPQAGPTVVPGSATPMETGIAETPEGR;KKEPPRAS(0.959)PPGGLAEPPGS(0.041)AGPQAGPTVVPGSATPMETGIAETPEGR;KKEPPRAS(1)PPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGR;KKEPPRAS(0.989)PPGGLAEPPGS(0.011)AGPQAGPTVVPGSATPMETGIAETPEGR;KKEPPRAS(0.976)PPGGLAEPPGS(0.022)AGPQAGPT(0.002)VVPGSATPMETGIAETPEGR 206.82 7.39E-39 1241910000 737516 549176 432374 482576 566487 452254 688444 827922 688249 TRUE FALSE 640051.392 545568.4267 641471.5126 592152.2565 555215.017 469652.504 621678.8068 650877.3232 606884.9873 1.054650231 0.898965106 1.056990247 0.975724015 0.914860358 0.773873986 1.024376644 1.072488753 1 19.21106361 2.02479166 24.99997899 1.043525484 0.944582592 0.197708539 0.082029322 318.7859456 321463.2083 0.033878491 0.022840088 105.8745702 -2.02479166 -0.098942891 KKEQSEVSVS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KKEQSEVSVSPR 12 2 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 KKEQSEVS(0.002)VS(0.998)PR 119.56 0.00026331 421250000 955540 726290 496810 572150 661910 540690 861900 968130 649320 TRUE FALSE 829262.968 721518.9532 737068.9777 702065.4023 648739.286 561490.6942 778313.0707 761102.9335 572558.1293 1.448347208 1.260167162 1.28732602 1.226190611 1.133054013 0.980670198 1.359360789 1.329302466 1 19.12706265 5.451579394 0.896962527 1.192756098 2.07913766 0.320014476 0.123757364 9.902412201 2.500657378 0.043714362 11.64364022 282865.1174 -5.451579394 0.886381562 KKFS(ph)FK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KKFSFK 6 2 P49006 P49006 MARCKSL1 MARCKS-related protein 1 KKFS(1)FK 81.594 0.048407 1701100000 3323300 2492900 1874800 2283000 2101800 824600 3728100 3565900 4714200 TRUE FALSE 2884117.485 2476523.976 2781459.551 2801390.043 2059978.292 856322.8956 3366549.436 2803360.035 4156892.646 0.693815725 0.595763275 0.66911989 0.673914455 0.495557251 0.206000724 0.809871633 0.674388365 1 21.98707406 1.138498772 1.442337923 1.245033388 0.576824399 0.399432764 0.158258157 1.691172835 2.567812056 1.773579104 0.047090599 13.75620921 -1.138498772 -0.668208989 KKGDGGGAGGGGGGGGSGGGGS(ph)GGGGGGGSSRPPAPQENTTSEAGLPQGEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KKGDGGGAGGGGGGGGSGGGGSGGGGGGGSSRPPAPQENTTSEAGLPQGEAR 52 3 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 KKGDGGGAGGGGGGGGS(0.055)GGGGS(0.943)GGGGGGGS(0.001)S(0.001)RPPAPQENTTSEAGLPQGEAR 85.214 3.96E-07 148680000 10038 9161.1 7757.6 9196.3 11244 11094 9182.1 14178 16189 TRUE FALSE 8711.452867 9100.920131 11509.20131 11284.46047 11020.2664 11520.79336 8291.621355 11146.14503 14275.15486 0.610252775 0.63753565 0.806240032 0.790496536 0.771989271 0.807052075 0.58084283 0.780807294 1 13.80121878 -2 0.038179223 1.903109959 4.05E-14 0.284109001 0.102717998 3338.930147 12.56789796 484.1356532 201.492618 0.01 2 -1.903109959 KKGFNGCDS(ph)PEPDGEDSLEQSPLLEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KKGFNGCDSPEPDGEDSLEQSPLLEDK 27 2 Q14814-4;Q14814;Q05BX2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 KKGFNGCDS(1)PEPDGEDSLEQSPLLEDK;KKGFNGCDS(1)PEPDGEDSLEQSPLLEDK 184.04 7.20E-18 240050000 196878 164988 167830 147565 161286 92405 243630 345090 172482 TRUE FALSE 170860.0735 163904.183 248993.1494 181071.8886 158076.7242 95959.88014 220002.8001 271295.189 152091.3745 1.123404099 1.077669155 1.637128669 1.190546731 1.039353643 0.630935715 1.446517272 1.783764464 1 17.21457881 2.031544705 24.99035943 1.49804881 1.129969292 0.150545767 0.307424864 278.0620478 220285.3561 0.127883664 0.086218362 107.5337286 -2.031544705 -0.368079519 KKGWEVVESDLYAMNFNPIISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KKGWEVVESDLYAMNFNPIISR 22 2 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 176.54 1.35E-13 438700000 2031000 1919800 730600 875030 1474800 1342800 2255800 2362400 263790 FALSE TRUE 1762598.204 1907188.707 1083920.604 1073718.935 1445454.365 1394458.385 2037032.863 1857219.144 232605.0467 7.57764386 8.199257645 4.659918686 4.616060359 6.214200362 5.994961866 8.757474922 7.984431853 1 17.82752287 4.259279397 24.94672304 5.985844805 7.88845219 0.14938423 2.119086777 531.9288665 640464.7001 0.54059519 1.426857241 18166.84022 -4.259279397 1.902607385 KKKEEEEDEEDEEDEEEEEDEEDEDEEEDDDDE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KKKEEEEDEEDEEDEEEEEDEEDEDEEEDDDDE 33 3 P09429 P09429 HMGB1 High mobility group protein B1 0 87.25 0.00045156 256720000 107150 62035 89734 45528 43960 29553 106000 96371 45822 FALSE TRUE 92989.85602 61627.488 133129.6625 55865.82825 43085.28201 30689.92303 95720.13632 75762.81161 40404.97536 2.301445681 1.525245034 3.294882904 1.382647255 1.066336054 0.759558019 2.369018554 1.875086198 1 15.30224533 KKLEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 96.948 0.0069502 415040000 957060 695280 464040 601140 581000 514020 867120 1013170 757290 FALSE TRUE 830582.0961 690712.6599 688451.2961 737638.0248 569439.2367 533794.682 783026.8359 796511.48 667764.0389 1.243825734 1.034366362 1.030979891 1.104638737 0.85275517 0.799376203 1.172610069 1.192803795 1 19.34897888 -1.937533699 18.66712125 0.005331997 1.051591337 0 0.141769012 0 0 0 0.033769911 0.011546924 1.937533699 1.04625934 KKNDIYGED ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KKNDIYGED 9 2 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ; 107.79 0.010794 2236200000 2312510 1702150 1385660 1501700 1448790 1203530 2251600 2441640 1923090 FALSE TRUE 2006905.944 1690968.465 2055769.811 1842683.937 1419961.914 1249830.578 2033240.179 1919514.287 1695744.491 1.183495482 0.997183522 1.212311066 1.086651879 0.837367847 0.737039445 1.199025083 1.131959618 1 20.69348738 3.462007227 24.93450047 1.000257804 1.122926434 0.190061693 0.141476504 500.6826582 826002.7522 0.045018824 0.058138349 2897.391804 -3.462007227 0.122668629 KKNEGVNWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KKNEGVNWLR 10 2 F8VUA2;F8VVT7;Q9HD42 F8VUA2 CHMP1A Charged multivesicular body protein 1a 0 ; 157.97 4.63E-06 752290000 1765590 1654940 971840 1175950 1521240 1319560 1738800 2149350 1028700 FALSE TRUE 1532262.808 1644068.59 1441825.075 1442967.421 1490970.3 1370324.327 1570171.444 1689728.229 907088.2579 1.689210278 1.812468165 1.589509138 1.590768493 1.643688238 1.510684672 1.73100184 1.862804654 1 19.7908834 1.229132044 24.99621139 0.999998657 1.68213234 0.803916657 0.105339164 179.4499541 475707.296 0.35137995 0.028236943 16.94853031 -1.229132044 0.682133684 KKPALSDGSNPDGDLLQEHWLVEDMFIFENVGFTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KKPALSDGSNPDGDLLQEHWLVEDMFIFENVGFTK 35 2 P47224 P47224 RABIF Guanine nucleotide exchange factor MSS4 0 44.021 0.066261 298690000 273680 269290 184510 262000 171320 121280 364400 400220 267140 FALSE TRUE 237512.4946 267521.0163 273739.6531 321491.1044 167911.0672 125945.7201 329060.5441 314636.0675 235559.0135 1.008292958 1.135685756 1.162085242 1.364800691 0.712819538 0.534667378 1.396934633 1.335699546 1 17.84572901 0.948145736 19.54102755 1.76E-05 1.096990216 0.005621044 0.278102148 195.1345263 222676.9293 35366.78091 0.070512585 8.874537643 -0.948145736 1.096972615 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTTGS(ph)PTEFLEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTTGSPTEFLEEK 44 3 P27816-6;P27816;P27816-2;P27816-5;H7C456 P27816-6 MAP4 Microtubule-associated protein 4 1 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDT(0.005)T(0.03)GS(0.962)PT(0.003)EFLEEK;KKPCS(0.001)ET(0.001)S(0.001)QIEDT(0.001)PS(0.001)S(0.001)KPT(0.001)LLANGGHGVEGS(0.083)DT(0.083)T(0.083)GS(0.625)PT(0.12)EFLEEK 240.01 3.72E-55 1505821000 1145578 757275 733513 801067 742225 509587 1295565 1484285 1228313 TRUE FALSE 994186.9648 752300.4107 1088242.34 982961.5059 727456.1746 529191.1416 1169921.306 1166882.203 1083103.236 0.917906005 0.694578675 1.004744796 0.907541842 0.671640662 0.488587905 1.080156781 1.07735086 1 20.04673933 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTTGSPT(ph)EFLEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTTGSPTEFLEEK 44 3 P27816-6;P27816;P27816-2;P27816-5;H7C456 P27816-6 MAP4 Microtubule-associated protein 4 1 KKPCS(0.001)ET(0.001)S(0.001)QIEDT(0.008)PS(0.027)S(0.027)KPT(0.027)LLANGGHGVEGS(0.1)DT(0.01)T(0.059)GS(0.327)PT(0.411)EFLEEK 63.257 0.0024403 1403100000 1198800 898750 700370 796370 719650 516640 1237600 1603000 1318700 TRUE FALSE 1040375.543 892846.0521 1039071.275 977197.9803 705330.373 536515.4751 1117577.742 1260210.925 1162804.788 0.894712125 0.7678383 0.893590468 0.840380079 0.60657677 0.461397717 0.961105212 1.083768262 1 20.14917749 2.017304059 24.9982266 1.040238391 0.746848904 0.489925091 0.132185847 196.6935135 284151.2566 0.057760864 0.038933278 104.0648491 -2.017304059 -0.293389487 KKPFVYTQGQAVLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KKPFVYTQGQAVLNR 15 2 Q9H4A4;A6NKB8;C9JMZ3;A0A087WU27;A0A087WUS4 Q9H4A4 RNPEP Aminopeptidase B 0 216.88 1.21E-12 1243600000 876690 730280 430720 604590 697150 626010 823640 928410 780000 FALSE TRUE 760833.1953 725482.7426 639017.6327 741871.4001 683278.079 650093.0098 743763.5196 729876.7464 687789.2886 1.106200995 1.054803782 0.929089248 1.078631802 0.993441 0.945192111 1.081382819 1.061192372 1 19.39160712 0.905827011 14.95402783 0.22748806 1.030177417 0.026856748 0.058792172 847388.095 2015170.679 22202915.73 0.014277828 8.050577051 -0.905827011 0.802689357 KKPLKQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KKPLKQPK 8 3 Q9Y2S6 Q9Y2S6 TMA7 Translation machinery-associated protein 7 0 ; 81.296 0.010175 3588200000 5920290 5162300 4093110 4132100 4267520 3380730 7611930 8868400 5559100 FALSE TRUE 5137908.676 5128388.511 6072551.687 5070356.46 4182604.701 3510788.871 6873726.2 6971961.674 4901909.531 1.048144329 1.046202195 1.238813497 1.034363533 0.85326028 0.716208418 1.402254806 1.422295053 1 22.22491243 2.213649139 24.99999902 1.310876302 0.99925516 0.359608322 0.177029025 237.4073246 238249.0909 0.075982699 0.05125176 163.5494691 -2.213649139 -0.311621142 KKPNATRPVT(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KKPNATRPVTPPR 13 3 F8W0W8;P36873;P36873-2 F8W0W8 PPP1CC Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-gamma catalytic subunit 1 KKPNAT(0.001)RPVT(0.999)PPR;KKPNAT(0.001)RPVT(0.999)PPR 93.424 0.0057807 6133700000 3496200 2583200 2062000 2405000 2529500 2198400 2992900 3692200 3719100 TRUE FALSE 3034168.312 2566230.789 3059190.097 2951092.008 2479167.899 2282973.871 2702649.019 2902651.763 3279432.235 0.925211468 0.78252289 0.932841382 0.899878941 0.75597473 0.696149122 0.824121014 0.885108017 1 21.64501463 1.325096375 2.497453328 1.022871701 0.828352233 0.338647737 0.074817408 0.538743355 4.277818333 0.207956073 0.020926677 21.13958102 -1.325096375 -0.194519468 KKPS(ph)SEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KKPSSEER 8 2 O75475 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 KKPS(0.643)S(0.357)EER 112.15 0.002439 100100000 185720 122030 129270 172560 94964 107650 181000 221990 301310 TRUE FALSE 161176.6314 121228.3769 191785.4044 211742.3854 93074.40219 111791.3652 163446.6479 174519.166 265689.4751 0.606635364 0.456278431 0.721840428 0.796954359 0.350312718 0.420759479 0.615179234 0.656853893 1 18.01938155 1.14244912 1.977205899 1.228415291 0.563547311 0.505942843 0.133909484 0.939443599 2.869860041 1.263176825 0.038073246 13.88190665 -1.14244912 -0.66486798 KKPSS(ph)EER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KKPSSEER 8 2 O75475 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 KKPS(0.2)S(0.8)EER 88.187 0.01165 160790000 168980 129510 123320 161990 90747 91455 173590 210130 267370 TRUE FALSE 146648.8649 128659.2403 182957.9645 198772.3054 88941.31224 94973.33303 156755.2685 165195.3347 235761.8232 0.622021254 0.545717023 0.776028799 0.843106414 0.377250698 0.402835929 0.664888261 0.700687382 1 17.8469706 1.184154475 1.936230891 1.172163179 0.601999626 0.428034585 0.143682301 1.0186197 3.260699847 1.113141334 0.042004961 15.28109496 -1.184154475 -0.570163553 KKQDPPVTHDLR ddPTM_MDA-MB-175_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 ; 192.86 2.13E-06 2939400000 2301500 2148940 1272720 1615470 1776030 1651880 2406600 2814500 1902770 FALSE TRUE 1997350.944 2134823.472 1888211.649 1982287.154 1740690.478 1715428.893 2173208.302 2212641.077 1677826.698 1.190439362 1.272374241 1.125391348 1.181461206 1.037467385 1.02241125 1.29525195 1.318754243 1 20.67816228 4.23456265 24.91086325 1.157975555 1.231406801 0.090751835 0.10930119 282.0612364 1757542.537 0.030540497 0.067554621 17161.79262 -4.23456265 0.073431246 KKS(ph)EPDDELLFDFLNSSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KKSEPDDELLFDFLNSSQK 19 2 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 1 KKS(1)EPDDELLFDFLNSSQK;KKS(1)EPDDELLFDFLNSSQK;KKS(1)EPDDELLFDFLNSSQK 254.34 5.28E-31 2127340000 1951220 1262080 1907280 1775570 1540040 934790 1845140 2683190 4370160 TRUE FALSE 1693361.333 1253789.313 2829646.987 2178740.306 1509396.217 970751.9762 1666198.607 2109410.699 3853524.663 0.439431814 0.325361694 0.734300993 0.565388961 0.391692372 0.251912745 0.432383014 0.547397742 1 21.87774719 1.22431307 2.845876445 1.12625797 0.450955524 0.634946606 0.130445897 0.3163588 2.979546264 0.511615728 0.036082969 16.7615073 -1.22431307 -0.675302446 KKS(ph)PIINESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KKSPIINESR 10 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 KKS(0.997)PIINES(0.003)R;KKS(0.627)PIINES(0.373)R;KKS(1)PIINESR;KKS(1)PIINESR;KKS(0.966)PIINES(0.034)R;KKS(1)PIINESR 143.56 1.76E-05 17767530000 31346520 23074460 16883510 19908290 22719720 17961200 28295510 34254470 29894580 TRUE FALSE 27203997.96 22922882.35 25048431.91 24428771.52 22267642.02 18652178.99 25551415.8 26929418.16 26360476.81 1.031999465 0.869592858 0.950226815 0.926719638 0.844735935 0.707581245 0.969307801 1.021583121 1 24.65187313 2.013683025 24.99953017 1.007266941 0.885863839 0.286998034 0.082439273 276.0794946 504408.3616 0.034482278 0.023235646 103.2007909 -2.013683025 -0.121403102 KKS(ph)PNELVDDLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KKSPNELVDDLFK 13 2 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 KKS(1)PNELVDDLFK;KKS(1)PNELVDDLFK 197.69 6.88E-08 13228800000 6721600 4833400 5414700 4655700 4663100 2858000 7743400 8973100 6717900 TRUE FALSE 5833323.53 4801649.077 8033267.031 5712847.843 4570313.433 2967949.109 6992446.26 7054272.394 5923717.515 0.984740328 0.81058036 1.356119196 0.964402477 0.771527917 0.50102813 1.180415211 1.190852261 1 22.49807141 KKS(ph)SSDPGIPGGPQAIPATNSPDHSDHTLSVSSDSGHSTASAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KKSSSDPGIPGGPQAIPATNSPDHSDHTLSVSSDSGHSTASAR 43 2 Q68CZ2;E9PCX8;C9JHU5 Q68CZ2 TNS3 Tensin-3 1 KKS(0.681)S(0.159)S(0.159)DPGIPGGPQAIPATNSPDHSDHTLSVSSDSGHSTASAR 158.24 6.36E-20 744990000 302950 370060 46865 253440 678870 535610 664380 740850 473940 TRUE FALSE 262914.3899 367629.0515 69529.07075 310987.4256 665361.8152 556215.2633 599948.5299 582424.9928 417911.3531 0.629115213 0.879681896 0.166372773 0.744146871 1.592112323 1.330940782 1.435588015 1.393656785 1 18.67283743 3.355039275 5.500969809 1.358819544 0.570969352 0.732223939 0.225822393 0.102031503 4.511320398 0.06373002 0.082556644 2264.849118 -3.355039275 -0.787850192 KKSEAPSGESR ddPTM_MDA-MB-175_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 50.207 0.089133 19441000 59028 50353 30688 39900 42701 42755 60414 70003 30786 FALSE TRUE 51227.30024 50022.22783 45528.81945 48959.90483 41851.33364 44399.81252 54555.05958 55033.40321 27146.51415 1.88706734 1.842675916 1.677151593 1.803542973 1.541683526 1.635562204 2.009652483 2.027273296 1 14.72847933 4.354873155 5.026947139 1.719826615 1.876225897 0.053857073 0.287650956 0.759905027 29.41476427 0.072281344 0.20254595 22639.82965 -4.354873155 0.156399282 KKT(ph)GGSK ddPTM_MDA-MB-175_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 88.942 0.029322 581930000 1137600 1316300 568560 766380 1166100 1462400 1029200 1107000 734930 TRUE FALSE 987263.2777 1307653.139 843517.5177 940398.2924 1142896.891 1518659.474 929388.3424 870276.6647 648047.4126 1.523442974 2.017835598 1.301629327 1.451125757 1.763600732 2.343438836 1.434136337 1.342921286 1 19.30573984 1.635521166 2.222942153 1.04764394 1.716421816 0.372722239 0.303228138 0.330443012 3.380905082 0.359927424 0.086399151 43.20372232 -1.635521166 0.668777876 KKTDELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KKTDELR 7 2 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;H0Y8X0;A0A494C198;D6RDA2;D6R9L5 H0Y993 DEK Protein DEK 0 ;; 97.431 0.0067507 738320000 2274530 1947940 1253650 1773250 1621630 1534800 2549480 3000100 2136980 FALSE TRUE 1973945.098 1935143.854 1859919.333 2175893.515 1589362.736 1593844.749 2302231.822 2358551.962 1884348.659 1.047547697 1.026956368 0.987035666 1.154719168 0.843454702 0.845833249 1.221765309 1.251653695 1 20.8456345 2.218510543 24.99053542 1.180022883 0.987672996 0.34136551 0.112166612 250.8954819 312715.4009 0.046838301 0.0316233 165.3904934 -2.218510543 -0.192349887 KKTEFLDLDNSPLSPPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KKTEFLDLDNSPLSPPSPR 19 2 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 KKTEFLDLDNSPLSPPS(1)PR 159.51 1.74E-11 1281600000 842380 741770 461810 565180 708630 568190 917650 1026500 597920 TRUE FALSE 731057.3487 736897.264 685142.8607 693512.7572 694529.6494 590048.637 828656.4442 806990.9632 527234.5788 1.386588396 1.397664899 1.299502894 1.315377984 1.317306712 1.11913873 1.571703522 1.530610843 1 19.00808547 2.227768561 24.99730777 1.409943397 1.31075413 0.007688513 0.169637631 635.6704013 1472370.093 0.068552853 0.046742681 168.9540321 -2.227768561 -0.099189268 KKVEAQLQELQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KKVEAQLQELQVK 13 2 P35579 P35579 MYH9 Myosin-9 0 ; 145.71 2.36E-05 4069300000 7270200 5561400 4384700 4935800 4975900 3784500 8032600 9261000 5726400 FALSE TRUE 6309424.65 5524866.797 6505155.586 6056548.829 4876889.325 3930092.164 7253599.688 7280607.219 5049431.516 1.249531681 1.0941562 1.288294646 1.199451623 0.965829383 0.778323689 1.436518084 1.441866712 1 22.26768954 0.960656887 18.35306602 8.61E-05 1.189630303 0.073030742 0.201762059 42081644.74 505741125.8 1732392278 0.054111465 9.133913347 -0.960656887 1.189544205 KKVEEEDEEEEEEEEEEEEEEDE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KKVEEEDEEEEEEEEEEEEEEDE 23 2 O15347 O15347 HMGB3 High mobility group protein B3 0 ; 120.32 0.00040109 599700000 564820 404930 427650 385490 415150 281000 603400 700370 527810 FALSE TRUE 490177.6059 402269.9882 634462.9704 473021.3963 406889.3272 291810.2518 544882.3609 550601.3258 465412.9031 1.053210177 0.864329256 1.363226 1.016347835 0.874254505 0.626992182 1.17075044 1.183038378 1 18.82815168 KKVENTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KKVENTR 7 2 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 89.698 0.009945 3970600000 4516200 3886600 2494700 3429000 2369700 3346600 4805900 5470300 4918800 FALSE TRUE 3919372.727 3861068.669 3701145.264 4207606.859 2322547.606 3475345.868 4339824.558 4300518.915 4337305.068 0.903642392 0.89019993 0.853328324 0.970097052 0.535481727 0.801268487 1.000580888 0.991518661 1 22.04836749 2.234996139 24.96562823 0.996282185 0.823234571 0.335378328 0.113902106 106.9517232 749077.3852 0.046692492 0.032886595 171.7893116 -2.234996139 -0.173047613 KKYDVDTLDMVFLDHWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KKYDVDTLDMVFLDHWK 17 2 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ; 233.65 2.46E-20 3200000000 5299300 4228100 2261040 2275100 3432300 2682500 6123500 6412300 665650 FALSE TRUE 4598984.078 4200325.333 3354486.507 2791696.228 3364003.945 2785697.511 5529643.913 5041079.546 586957.6153 7.835291609 7.156096493 5.715040438 4.756214341 5.731255303 4.745994324 9.420857262 8.588489891 1 19.1628968 4.412291325 4.318625176 6.100660578 7.704699594 0.079623899 2.290005032 0.625204918 22.62013683 0.597912042 1.835478523 25839.92951 -4.412291325 1.604039016 KKYELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KKYELR 6 2 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 105.39 0.01857 5746100000 13259400 10536800 7160900 8650900 8764900 7703400 10096800 11520700 17535400 FALSE TRUE 11507136.69 10467583.07 10623935.19 10615219.07 8590495.638 7999754.783 9117613.89 9057087.959 15462384.99 0.744201926 0.676970796 0.687082568 0.68651887 0.555573778 0.517368749 0.589664136 0.585749738 1 23.88225953 1.23485636 24.98369479 1.000000537 0.625500838 0.735049342 0.069682935 61.04481966 411659.2375 0.136019015 0.018767928 17.17340294 -1.23485636 -0.374499699 KLADSDQASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLADSDQASK 10 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 106.01 0.0061009 0 178100 160430 115020 129220 115150 119210 176900 219320 160780 FALSE TRUE 154563.6338 159376.1248 170644.0567 158561.376 112858.7403 123796.0858 159744.2652 172420.1248 141772.7716 1.090220866 1.124165967 1.203644782 1.118419103 0.796053707 0.873200717 1.12676266 1.21617235 1 17.11322095 3.453021647 24.99987272 1.025218955 1.141693923 0.218249691 0.120106984 465.4553102 482841.2489 0.04054513 0.052346257 2838.060482 -3.453021647 0.116474967 KLAEQFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLAEQFPR 8 1 Q96K17;Q96K17-2;E9PL10 Q96K17 BTF3L4 Transcription factor BTF3 homolog 4;Transcription factor BTF3 0 ; 136.57 0.0012594 892670000 1131010 1216730 622600 843560 1226690 1095900 1127310 1348190 1026410 FALSE TRUE 981544.1629 1208737.221 923691.4425 1035103.191 1202281.269 1138059.982 1017983.65 1059890.06 905068.9791 1.084496525 1.335519445 1.020575739 1.143673261 1.32838634 1.257429001 1.124758083 1.17105998 1 19.78766822 0.662122248 1.448720248 0.405133441 1.192238473 0.245523365 0.100694103 7.994781277 4.377189984 14.03481926 0.028233603 4.593272892 -0.662122248 0.787105031 KLALDIEIATYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KLALDIEIATYR 12 1 K7EPI4 K7EPI4 GFAP 0 ;; 138.87 0.00010705 1247749000 1418740 1315790 826946 1037640 1228460 1161310 1366270 1580390 636322 FALSE TRUE 1231249.914 1307146.489 1226859.852 1273252.021 1204016.049 1205986.347 1233769.346 1242435.897 561096.7381 2.194362987 2.329627674 2.186538913 2.269220145 2.145826143 2.149337655 2.198853178 2.214298913 1 19.09789 1.238477157 24.99999573 0.999998674 2.21138994 0.98004212 0.05431055 0.248395273 73957.53593 0.074410083 0.013286116 17.31717944 -1.238477157 1.211391266 KLAPEYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLAPEYEK 8 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 95.573 0.015319 1534890000 1312910 1122340 921980 1161100 1146290 1060040 1346080 1337790 1184400 FALSE TRUE 1139405.617 1114967.275 1367852.612 1424745.501 1123481.072 1100820.425 1215537.369 1051714.019 1044381.581 1.090985936 1.067586115 1.309724948 1.364200142 1.075738113 1.054040443 1.163882426 1.007020842 1 19.99421749 3.03618379 24.9746217 1.059332422 1.207171429 0.364322454 0.09739605 204.6512877 141252.2881 0.031565633 0.035791974 1086.885487 -3.03618379 0.147839007 KLAT(ph)PPAAQESSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLATPPAAQESSR 13 1 H0Y760;Q9Y4B4 H0Y760 RAD54L2 Helicase ARIP4 1 KLAT(0.999)PPAAQES(0.001)SR;KLAT(1)PPAAQESSR 63.691 0.039343 376740000 384780 322710 279921 296630 360100 306950 381320 398570 359530 TRUE FALSE 333930.3481 320590.0968 415291.7319 363984.3752 352934.7145 318758.5651 344339.6451 313338.9072 317026.773 1.053319078 1.01123982 1.309957919 1.148118728 1.113264698 1.005462605 1.086153204 0.988367336 1 18.27424516 2.826780417 4.235026868 1.021149446 1.134417271 0.302760578 0.080887935 0.300031091 9.71463963 0.027795302 0.02763958 671.0894586 -2.826780417 0.113267826 KLAVNMVPFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 201.48 6.94E-08 11172140000 7705370 8253560 4617860 5345850 7733090 7815870 7850450 8190170 6138310 FALSE TRUE 6687085.832 8199341.821 6851072.542 6559706.949 7579216.639 8116551.576 7089114.567 6438765.881 5412645.985 1.235455977 1.514849086 1.265752935 1.211922407 1.400279394 1.499553379 1.3097318 1.18957824 1 22.3679026 1.447795892 2.038634535 0.971167203 1.355489261 0.559701603 0.101559418 0.352401287 2.217478084 0.226597825 0.028259885 28.04115463 -1.447795892 0.384322058 KLCDNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KLCDNLR 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 96.711 0.020093 880070000 1516190 1792400 1088840 1354090 1727910 1695210 1815360 1968450 1959880 FALSE TRUE 1315821.65 1780625.606 1615406.666 1661556.83 1693527.972 1760425.826 1639306.667 1547512.286 1728185.219 0.761389251 1.030344194 0.934741628 0.961446037 0.979945872 1.018655759 0.948571165 0.89545511 1 20.72082642 4.750378517 24.7220397 0.964492597 0.761389108 0.72522209 0.040392152 906.5720406 1896430.275 0.01025595 0.161209064 56283.16577 -4.750378517 -0.203103488 KLCLNICVGESGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLCLNICVGESGDR 14 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ; 207.31 1.54E-08 2015950000 1366790 1175150 738020 919930 1180330 1168920 1404430 1581980 898610 FALSE TRUE 1186165.238 1167430.362 1094928.941 1128814.167 1156843.742 1213889.109 1268228.595 1243685.888 792377.3495 1.496970148 1.473326267 1.381827662 1.424591664 1.459965688 1.531958365 1.600536153 1.569562644 1 19.59582812 1.233294765 24.99997688 0.999999228 1.495094813 0.851609922 0.064578891 72.19860035 342729.1011 0.155156495 0.018687625 17.11176335 -1.233294765 0.495095585 KLCQPQSTGSLLGDPAASS(ph)PPGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KLCQPQSTGSLLGDPAASSPPGER 24 1 U3KQ90;P55199 U3KQ90 ELL RNA polymerase II elongation factor ELL 1 KLCQPQSTGSLLGDPAAS(0.204)S(0.796)PPGER;KLCQPQSTGSLLGDPAAS(0.058)S(0.942)PPGER;KLCQPQSTGSLLGDPAAS(0.06)S(0.94)PPGER;KLCQPQSTGSLLGDPAAS(0.021)S(0.979)PPGER 166.32 8.05E-12 1540470000 1156630 1122130 616275 698208 1076590 1050500 1176570 1329930 581766 TRUE FALSE 1003778.415 1114758.654 914307.6513 856746.7978 1055167.965 1090913.415 1062466.422 1045534.819 512990.2862 1.956720121 2.173059966 1.782309872 1.670103354 2.05689658 2.126577138 2.071123861 2.038118161 1 18.96857198 1.236775018 24.9968809 0.999998764 1.987423086 0.802515935 0.153454044 21.3714521 299094.0769 0.249098935 0.039818481 17.24944069 -1.236775018 0.987424322 KLDALCNIHENIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLDALCNIHENIR 13 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 169.4 1.86E-05 1509190000 1906820 1673030 1007870 1307860 1745000 1518860 1792150 2015970 1449130 FALSE TRUE 1654828.906 1662039.756 1495279.303 1604829.602 1710277.914 1577291.527 1618347.569 1584870.504 1277815.502 1.295045257 1.300688365 1.170184037 1.255916523 1.338438852 1.234365622 1.266495489 1.24029682 1 20.28524812 1.228060169 3.835764757 0.964493649 1.264053184 0.778068691 0.044271752 0.128960567 3.084819449 0.11198846 0.011269616 16.9067515 -1.228060169 0.299559534 KLDDFVETGDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLDDFVETGDIR 12 1 A0A1W2PPX5;A0A1W2PQR6;A0A1W2PQB7;A0A1W2PS43;Q14108;A0A1W2PRS1;A0A1W2PPU6;A0A1W2PRF6;Q14108-2 A0A1W2PPX5 SCARB2 Lysosome membrane protein 2 0 ; 100.45 0.0051704 1246570000 3170400 1996930 1558730 2583900 2208290 2531400 1825060 3510800 2394650 FALSE TRUE 2751423.607 1983812.035 2312537.042 3170613.987 2164349.349 2628784.596 1648065.962 2760042.741 2111557.205 1.303030579 0.939501914 1.095180863 1.501552494 1.025001522 1.244950688 0.780497899 1.307112464 1 21.0098759 KLDDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLDDTK 6 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 ; 89.298 0.080693 527710000 1283450 907470 725250 797200 361910 582140 1120360 1259140 1328750 FALSE TRUE 1113838.831 901508.7698 1075983.326 978216.4444 354708.6991 604535.3025 1011707.66 989882.7096 1171666.689 0.950644788 0.769424256 0.91833568 0.834893109 0.302738571 0.515961842 0.86347736 0.844850092 1 20.16013079 3.455113604 24.98218839 0.711000896 0.869822601 0.147005339 0.196742667 537.099284 609691.2584 0.062404293 0.080569545 2851.764144 -3.455113604 0.158821705 KLDEAVAEAHLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KLDEAVAEAHLGK 13 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;;;;; 136.33 4.78E-05 8611120000 25215900 22387460 16854760 20306570 21330640 17075430 29284840 34075900 27729120 FALSE TRUE 21883554.93 22240395.3 25005778.31 24917487.08 20906202 17732332.84 26444800.72 26789033.96 24451015.02 0.894995766 0.909589859 1.022688763 1.01907782 0.855023891 0.72521868 1.081542042 1.095620527 1 24.54339102 KLDELYGTWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KLDELYGTWR 10 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;; 170.04 7.13E-06 12668420000 14424550 13025650 8554550 9645040 13000590 11570840 13521350 14616200 9409050 FALSE TRUE 12518309.17 12940083.65 12691558.99 11835093.75 12741903.69 12015977.7 12210051.56 11490639.37 8296722.828 1.508825765 1.55966204 1.529707483 1.42647814 1.535775505 1.448279996 1.471671624 1.38496122 1 22.98411016 0.786478606 1.376893541 4.33E-12 1.503507424 0.938666926 0.039861879 0.880661306 0.60088483 2.54379884 0.011750909 6.116156726 -0.786478606 1.503507424 KLDGFPLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLDGFPLLR 9 1 P09661;H0YKK0 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 0 ; 121.6 0.00097687 1007210000 1690340 1479870 952580 1188120 1430790 1389670 1501110 1827920 1578230 FALSE TRUE 1466957.286 1470148.637 1413250.874 1457900.805 1402320.078 1443131.504 1355532.583 1437033.533 1391653.447 1.054111057 1.056404265 1.015519257 1.047603344 1.007664718 1.036990572 0.974044642 1.032608754 1 20.40836856 4.634809283 0.427557506 1.006002923 1.092766329 0.408425563 0.020119027 5.671819484 0.985401406 0.022150149 0.255581953 43132.96201 -4.634809283 0.086763406 KLDLEAWFPGSGAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLDLEAWFPGSGAFR 15 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 83.966 0.013646 189260000 258520 178660 101780 129040 173990 154450 188790 235110 175020 FALSE TRUE 224355.927 177486.3707 151001.1484 158340.5043 170527.9394 160391.7914 170481.1749 184833.5561 154329.335 1.453747773 1.150049475 0.978434518 1.025990971 1.104961279 1.039282593 1.104658261 1.197656662 1 17.23565279 4.707734052 3.509305773 1.076990723 1.48732174 0.784186711 0.063566047 0.129065091 2.810938587 0.017094732 0.133590314 51019.24789 -4.707734052 0.410331016 KLDPAQS(ph)ASRENLLEEQGSIALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLDPAQSASRENLLEEQGSIALR 23 2 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 KLDPAQS(0.862)AS(0.138)RENLLEEQGSIALR 140.55 1.01E-07 2457200000 60524 56158 24870 32015 44840 34570 42416 50346 16291 TRUE FALSE 52525.60005 55789.0944 36897.21519 39284.49507 43947.77173 35899.93027 38302.50285 39579.89969 14365.09654 3.656473864 3.883656072 2.568532351 2.734718487 3.059343988 2.49910818 2.666358889 2.755282541 1 13.81028007 2.501986939 0.136660311 7.34E-28 5.238542911 0.589380858 0.494866876 14.58167529 1.688867409 36.31276394 26.84212543 317.6778533 -2.501986939 5.238542911 KLDPAQSAS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KLDPAQSASR 10 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 KLDPAQS(0.005)AS(0.995)R;KLDPAQS(0.004)AS(0.996)R;KLDPAQS(0.007)AS(0.993)R;KLDPAQS(0.004)AS(0.996)R 82.925 0.010139 2539160000 5249500 3815520 3105960 4024540 3291440 3501060 3163590 3943040 7321700 TRUE FALSE 4555765.274 3790455.598 4608012.645 4938373.318 3225946.784 3635748.044 2856785.529 3099851.581 6456136.967 0.705648796 0.587108919 0.713741463 0.764911486 0.499671367 0.563146052 0.442491469 0.480140306 1 22.62223976 3.236011984 24.99976916 0.569179084 0.686791595 0.065898439 0.160406885 154.6321954 1516803.852 0.04743103 0.0563 1721.916089 -3.236011984 0.117612511 KLDPAQSAS(ph)RENLLEEQGSIALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLDPAQSASRENLLEEQGSIALR 23 2 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 KLDPAQS(0.03)AS(0.97)RENLLEEQGSIALR;KLDPAQS(0.156)AS(0.844)RENLLEEQGSIALR 185.47 1.58E-17 677010000 137036 111776 69309 81651 95309 98292 99612 132145 75164 TRUE FALSE 118926.3454 111041.7361 102827.0642 100191.1075 93412.53737 102073.3568 89951.64357 103886.8201 66278.19755 1.79435093 1.675388592 1.551446298 1.5116752 1.40940069 1.540074423 1.357183009 1.567435808 1 16.01624675 7.999999999 0.048810265 1.05E-08 4.13966374 0.586836824 0.136182469 947.0960504 4.525111786 109.1710256 334.1058543 99999999.71 -7.999999999 4.13966373 KLDPAQSASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLDPAQSASR 10 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 92.247 0.015389 289590000 497360 536650 338620 423040 544550 552840 585870 647790 595570 FALSE TRUE 431632.6159 533124.7108 502377.7646 519097.6978 533714.5204 574108.1125 529052.4176 509265.1496 525162.3931 0.821903132 1.01516163 0.956614128 0.988451772 1.016284729 1.093201113 1.007407279 0.9697289 1 19.00240408 4.740685283 24.90005547 1.004079176 0.821903066 0.716023595 0.036391881 109.9250201 1288174.531 0.009557655 0.061692211 55040.86907 -4.740685283 -0.18217611 KLDPDSIPS(ph)PIQVIENDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLDPDSIPSPIQVIENDR 18 1 O94855;O94855-2 O94855 SEC24D Protein transport protein Sec24D 1 KLDPDS(0.002)IPS(0.998)PIQVIENDR;KLDPDS(0.076)IPS(0.924)PIQVIENDR 116.94 8.94E-05 129860000 148309 141756 101694 120230 149686 126374 167508 211115 181157 TRUE FALSE 128709.5899 140824.7955 150873.5585 147530.0591 146707.5415 131235.6896 151263.0999 165969.7001 159740.8258 0.805740106 0.881582994 0.944489662 0.923558886 0.91840981 0.821553844 0.946928245 1.038993628 1 17.28537355 1.970361523 5.029635771 1.016108399 0.888203882 0.620586819 0.044095068 0.128222064 8.495283246 0.022319199 0.012308569 93.40314993 -1.970361523 -0.127904518 KLDPDSIPSPIQVIENDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLDPDSIPSPIQVIENDR 18 1 O94855;O94855-2 O94855 SEC24D Protein transport protein Sec24D 0 82.482 0.0083618 83358000 71300 80371 34111 50758 71781 56011 74503 94259 69974 FALSE TRUE 61877.52435 79843.03761 50607.19369 62283.37969 70352.69854 58165.77941 67277.71053 74102.44637 61701.75343 1.002848718 1.294015699 0.820190527 1.009426414 1.140205823 0.942692487 1.090369508 1.200977967 1 15.91302387 2.007484045 24.93432703 1.12409332 1.038543307 0.040713686 0.131613502 444.3089763 1480281.345 0.052027816 0.0350033 101.738199 -2.007484045 -0.085550013 KLDPELHLDIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLDPELHLDIK 11 1 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ; 122.35 0.0002549 1531310000 5934430 3928630 3127660 3946770 3968260 3046610 4873800 6054820 5446520 FALSE TRUE 5150180.04 3902822.571 4640206.837 4842944.451 3889299.39 3163815.058 4401139.626 4760043.862 4802638.61 1.072364685 0.812641318 0.966178639 1.008392437 0.809825537 0.658766007 0.916400334 0.991130969 1 22.19539582 1.789756514 4.433082619 0.995355854 0.883055926 0.12254916 0.11528538 0.415462595 15.4735585 0.070533896 0.031788377 61.62494058 -1.789756514 -0.112299928 KLDPGSEETQTLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KLDPGSEETQTLVR 14 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;; 180.74 2.76E-06 3639520000 2776640 2627310 1231280 1074010 1648450 1532680 1726490 2171010 2012250 FALSE TRUE 2409699.989 2610051.028 1826731.126 1317880.386 1615649.07 1591643.191 1559055.266 1706756.406 1774364.097 1.358063992 1.470978268 1.029513125 0.742733911 0.910551038 0.897021752 0.878655777 0.96189751 1 20.75887065 4.137904882 4.373934062 0.903294723 1.414157224 0.890912292 0.073438823 0.058633181 1.960237377 0.01902703 0.043083306 13737.41068 -4.137904882 0.510862501 KLDTNSDGQLDFSEFLNLIGGLAMACHDSFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KLDTNSDGQLDFSEFLNLIGGLAMACHDSFLK 32 1 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;; 229.48 1.16E-36 675954000 407284 376315 251616.6 356011 246202 238192 342753 380997 208556 FALSE TRUE 353460.3875 373842.962 373299.2294 436848.7388 241303.0619 247355.4004 309512.8668 299523.7565 183900.7473 1.922017135 2.032851783 2.02989512 2.375459292 1.312137473 1.34504837 1.683043008 1.628725065 1 17.48856782 3.22947214 24.9999872 1.442414298 2.081672652 0.711621558 0.219003266 114.664046 315409.7515 0.067471264 0.077584209 1696.18079 -3.22947214 0.639258354 KLDVEEPDS(ph)ANSSFYSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLDVEEPDSANSSFYSTR 18 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 KLDVEEPDS(1)ANSSFYSTR 214.95 5.99E-19 323980000 314320 275060 156110 185730 219000 181630 264210 315220 274510 TRUE FALSE 272781.8156 273253.1127 231605.3182 227902.8352 214642.3285 188617.4236 238586.9549 247812.656 242057.7405 1.126928703 1.128875747 0.956818475 0.941522608 0.886740197 0.779224921 0.985661332 1.02377497 1 17.8849917 4.221873757 5.222354056 0.940675641 1.13043041 0.572690528 0.067904048 0.134260084 10.26955601 0.019881102 0.047068456 16667.6264 -4.221873757 0.189754769 KLDVEEPDSANSSFYSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KLDVEEPDSANSSFYSTR 18 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;; 302.49 1.80E-49 3059210000 2594550 2435750 1472310 1849890 2271430 2060700 2328410 2852290 2358500 FALSE TRUE 2251673.644 2419749.398 2184324.041 2269935.798 2226232.987 2139976.462 2102601.157 2242349.98 2079680.817 1.08270155 1.163519603 1.050316964 1.091482779 1.070468588 1.02899274 1.011021085 1.078218331 1 20.98793069 3.485175528 0.878047788 1.034332451 1.118534736 0.458813977 0.034303026 0.605217744 1.000733916 0.016314545 0.034749768 3056.156062 -3.485175528 0.084202286 KLDVLSNDLVMNMLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLDVLSNDLVMNMLK 15 1 P09467;A0A3B3IUC7 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ; 242.19 1.04E-17 1866050000 4511800 3947000 3027300 3558900 3621700 3342600 5271900 6072200 4023800 FALSE TRUE 3915554.199 3921071.897 4491312.406 4367002.639 3549635.256 3471191.985 4760631.949 4773707.284 3548110.948 1.103560248 1.105115357 1.265832008 1.230796529 1.000429611 0.978321151 1.341737059 1.345422213 1 21.75861969 2.222727245 24.99781462 1.257991797 1.120651705 0.136666271 0.128957887 409.9409894 647212.1967 0.054616997 0.036958897 167.0041429 -2.222727245 -0.137340091 KLDVSIEMPEELDISQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLDVSIEMPEELDISQLR 18 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 188.04 6.39E-14 385230000 333670 247710 166190 219900 245360 228650 275810 302800 243540 FALSE TRUE 289574.6641 246082.7767 246560.0399 269831.656 240477.816 237446.3135 249061.9887 238048.5764 214748.9786 1.348433254 1.14590895 1.148131374 1.256497971 1.119808893 1.105692399 1.159781947 1.108496897 1 17.71229174 7.999981051 0.030184315 6.25E-06 2.791140497 0.561512045 0.061538253 2507.598287 7.495849784 244.5512482 489.3679781 99995637.02 -7.999981051 2.791134251 KLDYGQHVVAGTPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLDYGQHVVAGTPGR 15 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ; 128.9 4.49E-05 1155120000 2247600 1823210 1249610 1498150 1792950 1714870 1912080 2383400 1711640 FALSE TRUE 1950573.965 1811233.213 1853925.576 1838327.855 1757273.803 1780842.159 1726646.776 1873728.458 1509291.869 1.292376912 1.200054973 1.228341326 1.218006863 1.164303498 1.179919004 1.144011182 1.24146197 1 20.52544039 KLEAAEDIAYQLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KLEAAEDIAYQLSR 14 1 P35232 P35232 PHB Prohibitin 0 ;;; 177.04 3.44E-06 2640990000 5147878 3903040 2907287 4275208 4804459 5231450 3558350 5409218 5150808 FALSE TRUE 4467572.879 3877400.673 4313260.717 5245959.319 4708859.666 5432707.267 3213261.765 4252498.825 4541885.346 0.98363841 0.853698493 0.949663056 1.155017998 1.036763218 1.196134832 0.707473113 0.936284935 1 22.11485986 2.239944565 24.99999896 0.885476952 1.023631375 0.250020218 0.120426427 57.4083386 1037072.188 0.048371632 0.035393409 173.7579024 -2.239944565 0.138154423 KLEAAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KLEAAEER 8 1 P16949;P16949-2;A2A2D0;E5RIR6;E7EVN3;Q9H169-3;Q9H169;Q9H169-4;Q9H169-2;E5RGX5;Q93045;Q93045-2 P16949;E5RGX5 STMN1;STMN4;STMN2 Stathmin;Stathmin-4;Stathmin-2 0 ;;;;; 138.66 0.0011157 5709370000 17120400 11550800 7117690 9330130 10196820 9487640 12193500 13929800 12526800 FALSE TRUE 14857895.76 11474922.03 10559828.69 11448678.62 9993923.232 9852635.65 11010976.25 10951020.67 11045895.97 1.34510553 1.038840313 0.955995667 1.036464461 0.904763475 0.891972518 0.99683867 0.99141081 1 23.39700711 4.750128586 2.633820343 0.969222544 1.428108632 0.878977168 0.043667023 0.167159685 1.485152235 0.011582999 0.171291078 56250.78478 -4.750128586 0.458886088 KLEAELLQIEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLEAELLQIEER 12 1 Q969G3;Q969G3-4;Q969G3-2;B4DGM3;Q969G3-5;A0A2R8Y855;A0A2R8Y7I9;A0A2U3TZQ7;J3QKS7;A0A2R8YES3;A0A2R8Y4T4;A0A2R8Y765;A0A2R8Y7U4;Q969G3-6;Q969G3-3;J3QR61 Q969G3 SMARCE1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 0 68.481 0.084267 173180000 185350 176070 78971 108600 148520 165400 151790 161940 147240 FALSE TRUE 160855.5279 174913.3846 117161.6397 133259.2898 145564.7426 171763.045 137069.4292 127310.3912 129833.4549 1.238937437 1.34721351 0.902399461 1.02638638 1.121165131 1.322949044 1.05573274 0.980566922 1 16.98630265 KLEDGPK ddPTM_MDA-MB-175_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 ;;;;;;; 101.54 0.014404 61464300000 54910700 40857000 33624850 36620350 26933720 25630130 55412800 59527700 52403900 FALSE TRUE 47654111.87 40588607.68 49885939.93 44935560.17 26397791.67 26616137.69 50038875.18 46798164.6 46208770.64 1.031278504 0.87837454 1.079577302 0.972446563 0.571272321 0.575997529 1.08288696 1.012755024 1 25.46166337 KLEDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLEDIR 6 1 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 93.262 0.073467 1361600000 2610900 2374800 1463200 1827200 2053500 2007300 2353500 2836900 2370500 FALSE TRUE 2265862.95 2359199.782 2170808.414 2242093.687 2012639.368 2084522.13 2125257.932 2230251.012 2090262.19 1.084008963 1.128662133 1.038534029 1.072637537 0.962864552 0.997253904 1.016742274 1.066971896 1 20.99525249 3.927943947 1.743844557 1.01856087 1.105577949 0.509338549 0.03423972 0.327651465 1.918193006 0.010496761 0.027771694 8471.180718 -3.927943947 0.087017079 KLEDNPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KLEDNPK 7 1 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ;;; 117.4 0.0084017 6902000000 10110550 6778000 5425890 6103270 4377110 4411200 8775860 9270010 8666000 FALSE TRUE 8774415.201 6733474.872 8049868.553 7489110.736 4290014.075 4580901.718 7924778.448 7287690.501 7641515.352 1.148255915 0.881170103 1.053438772 0.980055708 0.561408814 0.599475563 1.037068969 0.953697031 1 22.86542733 5.968102558 0.867162508 0.86829576 2.969011618 0.198176437 0.170712304 31.88349587 3.554696474 0.062987177 103.5533419 929185.786 -5.968102558 2.100715859 KLEDQLQGGQLEEVILQAEHELNLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLEDQLQGGQLEEVILQAEHELNLAR 26 1 A0A087X1G1;H7BYD0;Q16718-2;Q16718;A0A087WXR5 A0A087X1G1 NDUFA5 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 0 ; 252.44 1.04E-52 105620000 116992 117002 96411 160210 141366 134971 121242 177548 146688 FALSE TRUE 101531.2108 116233.4062 143035.6821 196588.1292 138553.0932 140163.4217 109483.9695 139580.7419 129346.7117 0.784953938 0.898618949 1.105831607 1.519854092 1.071175999 1.083625705 0.846437981 1.079120915 1 16.98088385 4.367214595 3.755134763 1.098315337 0.808152625 0.302243532 0.167759496 0.294975258 7.616375169 0.045611814 0.142477608 23292.41907 -4.367214595 -0.290162713 KLEDSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLEDSTR 7 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 118.5 0.0080068 346860000 907840 745370 469740 597330 571830 673100 768760 864870 930310 FALSE TRUE 787866.6438 740473.6154 696907.8352 732962.9061 560451.7018 698994.5926 694205.7735 679924.2809 820329.8116 0.960426688 0.902653548 0.849545909 0.893497829 0.683202895 0.852089712 0.846252036 0.828842584 1 19.64584453 4.546518447 1.636595381 0.842134147 0.979684044 0.178071021 0.076788421 1.127324674 3.918092028 0.020857219 0.219252127 35198.03731 -4.546518447 0.137549897 KLEDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLEDVK 6 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 0 94.662 0.070915 595180000 811020 793150 429520 604520 747080 614980 868870 944280 723990 FALSE TRUE 703841.6521 787939.7454 637237.3087 741785.5055 732214.5696 638638.6785 784607.1211 742353.0704 638400.727 1.102507598 1.23424005 0.998177605 1.161943391 1.146951341 1.000372731 1.22901978 1.162832433 1 19.28410277 4.285732135 24.99999912 1.112776345 1.168373384 0.084126878 0.086130563 355.7756295 188548.349 0.020632861 0.054589175 19307.7708 -4.285732135 0.055597039 KLEEAASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLEEAASR 8 1 Q9UH65;E7EMB1;E9PJM7 Q9UH65 SWAP70 Switch-associated protein 70 0 68.657 0.089696 64230000 164550 122260 137560 124160 100980 105360 115510 121740 139230 FALSE TRUE 142804.3006 121456.866 204084.4761 152352.4257 98970.69556 109413.2674 104307.858 95706.84838 122770.388 1.16318196 0.989300987 1.662326555 1.240954176 0.806144683 0.891202424 0.849617401 0.779559713 1 16.9056031 3.261645786 8.055612764 0.854583391 1.274069503 0.561056783 0.174991223 0.139845135 38.48421619 0.051027145 0.06451434 1826.609812 -3.261645786 0.419486112 KLEEEEDGKLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLEEEEDGKLK 11 2 P11387 P11387 TOP1 DNA topoisomerase 1 0 65.563 0.036617 39743000 154610 164610 122680 133860 146840 168710 162690 173610 156330 FALSE TRUE 134177.8968 163528.6661 182008.4583 164254.9589 143918.1713 175200.3829 146912.3488 136484.8525 137848.8455 0.973369754 1.186289704 1.320348079 1.191558466 1.044028847 1.270960103 1.065749577 0.990105155 1 17.07272766 2.027254323 7.694340604 1.004064259 1.168563915 0.340675136 0.098995268 0.200481885 44.87853296 0.041146192 0.027243238 106.4766362 -2.027254323 0.164499655 KLEEEGEQFVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KLEEEGEQFVK 11 1 H0YF61;P22307-6;P22307-2;P22307-4;P22307-7;P22307-8;P22307 H0YF61 SCP2 Non-specific lipid-transfer protein 0 ;; 173.19 4.36E-05 2346990000 2775570 2071120 1882240 2106720 2071660 1689460 2645570 2949540 3466140 FALSE TRUE 2408771.392 2057514.676 2792497.56 2585082.975 2030438.019 1754454.619 2389003.029 2318803.824 3056376.878 0.788113341 0.673187489 0.913662703 0.845799808 0.664328419 0.574030851 0.781645433 0.758677322 1 21.54339102 1.225924092 4.380559644 1.026153286 0.747684305 0.401957814 0.095858394 0.258286352 9.782077375 0.229623039 0.025360394 16.8237998 -1.225924092 -0.278468981 KLEEEQIILEDQNCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KLEEEQIILEDQNCK 15 1 P35579 P35579 MYH9 Myosin-9 0 ;;; 266.45 4.18E-25 4527550000 9952800 8595000 7192500 7120100 7211900 5676390 11469100 12762000 10589600 FALSE TRUE 8637512.263 8538538.879 10670817.06 8736827.529 7068397.3 5894764.396 10356828.45 10032945.61 9337709.552 0.925014021 0.9144147 1.142766007 0.935649956 0.756973352 0.631285902 1.109140137 1.074454668 1 23.15463728 KLEEIIHQITNVEALIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLEEIIHQITNVEALIAR 18 1 Q15042-4;Q15042;Q15042-3 Q15042-4 RAB3GAP1 Rab3 GTPase-activating protein catalytic subunit 0 ; 193.19 8.85E-15 260360000 756800 648750 532050 559180 575100 533900 791450 929550 753520 FALSE TRUE 656786.9625 644488.3185 789351.1596 686150.3655 563656.6352 554439.4785 714695.3008 730772.9663 664439.724 0.988482384 0.969972588 1.187995135 1.032675111 0.848318688 0.834446615 1.075636021 1.099833348 1 19.3417788 KLEELELDEQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLEELELDEQQR 12 1 Q02750;Q02750-2 Q02750 MAP2K1 Dual specificity mitogen-activated protein kinase kinase 1 0 154.1 0.00011418 329640000 619120 531360 379220 488590 570220 554150 641940 662780 759030 FALSE TRUE 537301.7233 527869.4612 562612.0604 599531.8271 558873.7376 575468.5091 579684.7576 521049.6548 669298.3381 0.802783591 0.788690829 0.840599817 0.895761715 0.835014381 0.859808663 0.866108168 0.778501343 1 19.35228991 1.748509165 0.017843649 1.734043909 1.44E-06 0.23403686 0.055605103 4526.5588 31.04039858 1586.795702 1431.776754 56.04142438 -1.748509165 -1.734042464 KLEELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLEELK 6 1 Q15172;Q15172-2;Q9Y2C4-3;Q9Y2C4-4;Q9Y2C4;Q9Y2S6 Q15172;Q9Y2S6 PPP2R5A;EXOG;TMA7 "Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform;Nuclease EXOG, mitochondrial;Translation machinery-associated protein 7" 0 ; 102.71 0.056608 4851100000 3740000 3145000 2607300 2623800 2459200 2100420 4027700 4488900 3656800 FALSE TRUE 3245749.524 3124340.288 3868199.001 3219573.892 2410266.731 2181224.517 3637094.274 3528983.668 3224497.27 1.006590874 0.96893873 1.199628555 0.998473133 0.747486051 0.676454137 1.127957002 1.094429107 1 21.62064282 KLEEQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KLEEQAR 7 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ;;;;;; 150.4 0.003129 7573190000 6063150 6179020 4363450 4907760 4572220 5108200 6412550 6855590 7452800 FALSE TRUE 5261889.365 6138429.611 6473629.015 6022141.918 4481241.767 5304715.759 5790661.888 5389575.429 6571738.474 0.800684535 0.934064804 0.985071004 0.916369685 0.681895937 0.807201288 0.881146125 0.820114107 1 22.64784364 4.8068401 20.56027481 0.870004078 0.800677344 0.057781058 0.093294577 45652.65984 13741060.26 0.02365221 61.24912715 64097.35367 -4.8068401 -0.069326734 KLEEQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KLEEQQR 7 1 Q02818;H7BZI1;C9JKZ2 Q02818 NUCB1 Nucleobindin-1 0 ;; 123.72 0.0067604 1317480000 1557380 1532730 1049720 1243680 1333900 1476370 1571360 1894570 1683700 FALSE TRUE 1351568.287 1522661.396 1557368.103 1526076.552 1307358 1533166.909 1418969.749 1489430.949 1484654.904 0.910358551 1.025599546 1.048976499 1.027899849 0.880580394 1.03267561 0.955757291 1.003216939 1 20.5016962 1.595053561 25 1.001612942 0.98643745 0.016414201 0.055017288 5.911338878 11488.54571 0.034905402 0.013381725 39.35986144 -1.595053561 -0.015175492 KLEEVVQILGDKFPCTLVAQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLEEVVQILGDKFPCTLVAQK 21 2 Q9BY32 Q9BY32 ITPA Inosine triphosphate pyrophosphatase 0 231.6 2.72E-26 189360000 505430 357240 307070 312260 310310 220870 504880 601290 335860 FALSE TRUE 438636.1449 354893.2669 455570.0791 383163.4056 304135.4381 229367.0118 455916.8153 472708.8127 296155.0134 1.481103223 1.198336178 1.538282516 1.293793413 1.026946782 0.774482961 1.539453309 1.596153336 1 18.17599298 3.486396515 24.51866027 1.23663163 1.39029817 0.113750275 0.258520322 1137.621507 3007244.096 0.081407679 0.11127779 3064.760312 -3.486396515 0.15366654 KLEGDSTDLSDQIAELQAQIAELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLEGDSTDLSDQIAELQAQIAELK 24 1 P35579 P35579 MYH9 Myosin-9 0 ; 234.39 3.76E-37 516210000 932100 623130 682730 900640 584940 499600 771180 947120 1919270 FALSE TRUE 808920.6234 619036.618 1012900.512 1105144.077 573300.8384 518819.9353 696391.0823 744585.7585 1692376.087 0.477979233 0.365779582 0.598507932 0.653013291 0.338754986 0.306563027 0.411487191 0.439964712 1 20.69061878 1.238094375 24.97811975 1.000000631 0.447373294 0.71855417 0.108367646 6.462965374 345863.0382 0.161003473 0.02809635 17.301923 -1.238094375 -0.552627338 KLEHLITELVHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLEHLITELVHQR 13 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 198.23 5.19E-08 1195980000 1425900 1294220 875870 935540 1349940 1274860 1439720 1589530 1564160 FALSE TRUE 1237463.702 1285718.184 1299443.662 1147968.656 1323078.835 1323904.689 1300096.176 1249621.379 1379246.787 0.897202527 0.932188638 0.942140068 0.832315628 0.959276359 0.95987513 0.942613163 0.906017249 1 20.39544919 KLEKEEEEGISQES(ph)S(ph)EEEQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLEKEEEEGISQESSEEEQ 19 2 P17096;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 2 KLEKEEEEGIS(0.008)QES(0.994)S(0.998)EEEQ 105.73 0.0016123 360280000 901380 680310 311680 296140 585380 426510 818580 919940 62659 TRUE FALSE 782260.3492 675840.9988 462409.4905 363383.1132 573732.0833 442918.1157 739194.2376 723217.99 55251.5244 14.15816772 12.23207877 8.36917163 6.57688846 10.3840046 8.016396298 13.37871209 13.08955722 1 15.75372665 4.4131127 4.079397276 9.30302398 13.81046258 0.214993769 3.517156668 0.349772064 11.36312432 0.90052812 2.848994387 25888.84649 -4.4131127 4.507438602 KLELSDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KLELSDNR 8 1 P39687;H0YN26 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;;;; 109.88 0.005666 13492300000 29863800 28731200 17646600 22049500 25990300 24189100 29228100 33245400 29848400 FALSE TRUE 25917223.16 28542462.86 26180554.78 27056175.98 25473143.88 25119670.33 26393563.36 26136129.93 26319756.16 0.984706052 1.084450125 0.994711145 1.027979736 0.967833582 0.954403612 1.002804251 0.993023255 1 24.64964279 3.251413958 24.87033778 0.984768112 1.025335901 0.300947817 0.029673004 258.9970437 501138.1373 0.008231469 0.010556095 1784.078493 -3.251413958 0.04056779 KLELSENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KLELSENR 8 1 Q92688;Q92688-2 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 0 ;;; 125.97 0.001987 8928150000 10690780 11384310 7141530 8358130 10106730 9471580 10624830 12293140 11688680 FALSE TRUE 9277966.336 11309525.72 10595197.79 10255971.16 9905625.846 9835957.812 9594435.622 9664347.676 10306857.57 0.90017411 1.097281654 1.027975571 0.99506286 0.961071382 0.954311996 0.930878841 0.937661903 1 23.2971012 3.310253652 2.690437748 0.951210331 1.016822183 0.177357518 0.050817254 0.366262854 5.392877619 0.015052872 0.019803459 2042.930781 -3.310253652 0.065611853 KLEMDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLEMDLK 7 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 87.308 0.031167 1800000000 3340800 2607900 2437800 2543500 2596200 1946000 3474600 3925900 4111500 FALSE TRUE 2899304.815 2590768.533 3616728.234 3121040.55 2544540.699 2020863.879 3137633.827 3086376.836 3625443.154 0.799710461 0.714607407 0.997596178 0.860871462 0.70185646 0.557411548 0.865448359 0.851310228 1 21.78972592 1.334243107 1.84331176 1.042186491 0.781645028 0.25952562 0.115797445 1.080984936 4.230911609 0.468688234 0.03414804 21.58952596 -1.334243107 -0.260541463 KLENDTISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLENDTISK 9 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 133.89 0.00042362 211570000 383610 310990 246250 290240 271090 211470 366290 451300 372290 FALSE TRUE 332914.9666 308947.0862 365337.3237 356143.428 265695.8394 219605.3877 330767.2522 354793.007 328278.3003 1.014124194 0.941113336 1.112889044 1.084882637 0.809361566 0.668961023 1.007581835 1.08076899 1 18.32455986 3.266428808 24.98940238 0.929113709 1.036645001 0.199653207 0.122008654 480.1187782 430519.1396 0.040462305 0.052225532 1846.838026 -3.266428808 0.107531292 KLENLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLENLK 6 1 P39687;H0YN26 P39687;REV__Q9Y2X3 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 89.369 0.080564 1364400000 1338400 1047300 723860 835170 990780 1013800 1139200 1203300 1117000 FALSE TRUE 1161527.049 1040420.217 1073921.117 1024808.113 971065.4164 1052801.542 1028720.559 945983.6591 984949.5325 1.1792757 1.056318302 1.09033111 1.040467638 0.985903728 1.068888818 1.044439868 0.960438711 1 19.90969028 8 0.389577904 0.996643111 3.522675353 0.679626976 0.034492976 51.07681278 0.732269858 0.036218822 97.41606419 100000000 -8 2.526032241 KLENS(ph)PLGEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KLENSPLGEALR 12 1 D6RDK6;D6RBN5;Q9NX40;D6RI08;D6RDK1;D6RIV2;D6R9T5;D6RG39;D6RIT9;Q9NX40-3;Q9NX40-2;Q9NX40-4 D6RDK6 OCIAD1 OCIA domain-containing protein 1 1 KLENS(1)PLGEALR;KLENS(1)PLGEALR;KLENS(1)PLGEALR 168.66 2.81E-05 1026990000 1550790 1537100 1090940 1763420 1848470 1862610 1325510 2322820 1934120 TRUE FALSE 1345849.172 1527002.689 1618522.233 2163831.463 1811689.063 1934265.812 1196962.244 1826103.019 1705470.537 0.789136571 0.895355655 0.949017997 1.268759217 1.062281068 1.134153754 0.701836952 1.070732669 1 20.7017384 4.300760495 2.609954667 1.029747314 0.81170719 0.24712144 0.142922188 0.429211789 5.653217481 0.038365563 0.135412858 19987.59287 -4.300760495 -0.218040124 KLEQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLEQLR 6 1 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;A0A0A0MRE9;A0A087WX84;Q99996-4 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 0 92.692 0.074506 1152800000 1828400 2046800 1183700 1479700 2163400 2435800 1895100 1976700 2067400 FALSE TRUE 1586772.307 2033354.436 1756141.279 1815688.501 2120352.573 2529506.802 1711313.494 1553998.088 1822994.327 0.87042087 1.115392629 0.96332789 0.995992403 1.163115288 1.387556047 0.938737696 0.852442635 1 20.79787864 2.028113925 24.99999241 0.909653673 1.085480725 0.204147125 0.140944089 293.3817623 260885.2092 0.059105721 0.039848268 106.6875948 -2.028113925 0.175827052 KLES(ph)TESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.831)T(0.164)ES(0.005)R;KLES(0.808)T(0.187)ES(0.005)R;KLES(0.881)T(0.114)ES(0.005)R 113.67 0.0017174 1558650000 2079150 1204700 1060960 1285530 1343510 1510620 1844050 1947570 2337870 TRUE FALSE 1804385.06 1196786.246 1574043.805 1577429.235 1316776.78 1568734.529 1665214.315 1531097.312 2061489.672 0.875282124 0.580544381 0.763546782 0.765189007 0.638750122 0.760971326 0.80777233 0.742714035 1 20.9752558 -0.144590119 1.333844925 10 0.729674028 0.482373259 0.082875169 40.1776277 2.526308068 1053.986295 0.022423945 0.716819616 0.144590119 -9.270325972 KLEST(ph)ESR ddPTM_MDA-MB-175_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(0.482)T(0.489)ES(0.028)R 119.45 0.00099159 338910000 1311700 749290 661690 762420 883160 936400 1242000 1204800 1411500 TRUE FALSE 1138355.522 744367.8647 981685.4972 935539.1139 865586.8439 972423.9139 1121551.031 947162.8958 1244634.078 0.914610601 0.598061613 0.788734227 0.751657961 0.69545488 0.781293017 0.90110905 0.760997077 1 20.24729022 -1.119891966 0.76128342 10 0.750638839 0.360017988 0.092141673 97.8034668 1.813507285 1473.080916 0.033675713 0.07587663 1.119891966 -9.249361161 KLESTESR ddPTM_MDA-MB-175_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 ;;;;;;;;; 166.33 0.00051168 15777150000 20319870 17555060 11524080 13879310 12837480 14384080 18038370 20161030 19330590 FALSE TRUE 17634547.7 17439739.65 17097163.63 17030819.47 12582039.26 14937444.87 16289011.65 15849750.63 17045349.67 1.034566497 1.023137688 1.003039771 0.999147556 0.738150845 0.876335491 0.955627897 0.929857758 1 24.02287486 3.448205898 24.99999637 0.903256166 1.017296584 0.417580004 0.067765877 218.6363089 189030.5905 0.020489705 0.026452483 2806.764005 -3.448205898 0.114040418 KLEVEANNAFDQYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KLEVEANNAFDQYR 14 1 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;; 280.62 4.51E-33 7081750000 4083750 3392360 2311210 2794260 3507640 3063500 3846420 4384520 3460800 FALSE TRUE 3544072.091 3370075.364 3428918.887 3428739.441 3437844.827 3181354.827 3473394.78 3446924.518 3051668.167 1.161355658 1.104338735 1.123621147 1.123562345 1.126546085 1.042496973 1.138195436 1.129521406 1 21.54116666 KLFAPQQILQCS(ph)PAN ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLFAPQQILQCSPAN 15 1 P04183;K7ERV3 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 1 KLFAPQQILQCS(1)PAN;KLFAPQQILQCS(1)PAN 246.34 3.83E-18 795370000 1721300 2056970 1149660 1403580 1757550 1586990 1725960 2251980 1719340 TRUE FALSE 1493825.844 2043457.629 1705639.421 1722284.291 1722578.194 1648042.532 1558576.665 1770411.602 1516081.584 0.985320223 1.347854661 1.125031423 1.136010298 1.136204154 1.087040796 1.028029548 1.167754836 1 20.53191596 3.079602641 1.483585245 1.081494076 1.167415186 0.11682589 0.097226506 0.814381229 3.749185923 0.035979346 0.042193682 1201.164923 -3.079602641 0.08592111 KLFDQHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLFDQHK 7 1 Q6ZPD8;Q6E213 Q6ZPD8 DGAT2L6;AWAT2 Diacylglycerol O-acyltransferase 2-like protein 6;Acyl-CoA wax alcohol acyltransferase 2 0 87.616 0.012471 1532800000 5821600 5191000 3603400 4889600 5082500 4874300 5591700 6297100 4914600 FALSE TRUE 5052260.81 5156899.979 5346016.293 5999858.413 4981368.194 5061817.475 5049417.795 4950514.169 4333601.587 1.16583417 1.189980176 1.233619701 1.384497004 1.149475348 1.168039418 1.16517813 1.14235563 1 22.04713509 0.017050083 0.684512333 5.38E-18 1.226496558 0.524377304 0.065044314 12.28336902 1.217599464 17.13407868 0.029824588 1.040040096 -0.017050083 1.226496558 KLFIGGLSFETTDDSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KLFIGGLSFETTDDSLR 17 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;; 286.68 2.80E-36 3066189000 2544824 2395903 1196593 1508897 2322520 2016544 2349833 2874994 1285039 FALSE TRUE 2208519.061 2380164.155 1775269.377 1851515.126 2276306.396 2094121.753 2121946.557 2260198.906 1133123.153 1.949054747 2.100534393 1.566704706 1.633992846 2.008878196 1.848097223 1.872653075 1.994663069 1 20.11187324 1.233609981 24.99979098 0.999998663 1.871341159 0.735974584 0.16410479 83.73881895 422815.5502 0.333362281 0.04135537 17.12418776 -1.233609981 0.871342496 KLFIGGLSFETTDESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KLFIGGLSFETTDESLR 17 1 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;F8W646 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ;; 290.16 9.27E-46 3733270000 3774440 3626980 1710210 1944660 3233880 2950650 3562950 4110180 1883660 FALSE TRUE 3275638.191 3603154.13 2537273.276 2386224.775 3169532.115 3064163.415 3217415.657 3231249.992 1660975.861 1.972116675 2.169299515 1.527579862 1.43664025 1.908234906 1.844797078 1.937063466 1.945392506 1 20.66359968 1.234255283 24.9880184 0.999998751 1.841675287 0.605411823 0.213790695 96.81632033 561843.6656 0.422394747 0.055454762 17.14965086 -1.234255283 0.841676536 KLFIGGLSFETTEESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLFIGGLSFETTEESLR 17 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ; 230.89 1.03E-15 3154400000 1337410 1128870 601190 665650 989690 896150 1138250 1283690 657580 FALSE TRUE 1160667.88 1121454.379 891927.4949 816796.0063 969997.1053 930625.4704 1027862.69 1009182.883 579841.6415 2.001698044 1.934070095 1.53822601 1.408653584 1.672865548 1.60496488 1.772661045 1.740445685 1 19.14529942 4.271479486 5.913611695 1.567861162 1.977120765 0.396484892 0.219721914 0.188493441 18.05692381 0.05487358 0.143284962 18684.4142 -4.271479486 0.409259603 KLFNLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLFNLSK 7 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 94.302 0.039694 0 1239900 1452700 1014700 1120800 1376700 1222100 1659000 1704200 1678700 FALSE TRUE 1076044.073 1443157.118 1505412.314 1375294.77 1349306.363 1269114.978 1498110.435 1339770.092 1480245.998 0.726935979 0.97494411 1.017001441 0.929098793 0.911541977 0.857367613 1.01206856 0.905099621 1 20.49740552 4.742940481 24.89282727 0.947413379 0.726935885 0.648928777 0.051711769 269.6660694 1532580.693 0.012408685 0.094335457 55327.4279 -4.742940481 -0.220477494 KLFVGGIKEDTEEHHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLFVGGIKEDTEEHHLR 17 2 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ; 151.48 7.99E-08 1220280000 1817240 1425700 425580 467090 1213670 1001580 1729520 1862820 46081 FALSE TRUE 1577087.13 1416334.483 631391.9115 573149.9235 1189520.342 1040111.431 1561791.417 1464470.439 40633.35668 38.81262241 34.85644797 15.53875838 14.10540429 29.27447887 25.59747744 38.43618998 36.04108937 1 15.31037693 7.999999998 0.050445772 9.999999974 57.30414888 0.057521951 12.04257371 7202.20529 35.51885088 9297.303129 29529.42059 99999999.49 -7.999999998 47.3041489 KLFVQDLATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLFVQDLATR 10 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 188.96 1.71E-06 1521480000 2588700 2582600 1588190 1993460 2491300 2485700 2664500 3088000 2490000 FALSE TRUE 2246596.736 2565634.731 2356243.996 2446105.561 2441728.004 2581326.487 2406097.2 2427655.231 2195635.037 1.02321046 1.168516027 1.073149206 1.114076575 1.11208282 1.175662824 1.095854803 1.105673388 1 21.06620684 1.212201286 3.695361978 0.981303534 1.11204758 0.37994493 0.04338307 0.322577809 6.583862726 0.121734203 0.010116196 16.30051351 -1.212201286 0.130744045 KLFYSTFATDDRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLFYSTFATDDRK 13 2 P30084 P30084 ECHS1 "Enoyl-CoA hydratase, mitochondrial" 0 50.286 0.094949 689000000 198610 194050 125430 188230 215050 201730 233360 270800 171690 FALSE TRUE 172363.1853 192775.2728 186088.3675 230970.4984 210770.9257 209490.6836 210728.7831 212891.5274 151393.0038 1.138514865 1.273343338 1.229174155 1.525635218 1.392210475 1.38375406 1.391932109 1.406217738 1 17.20793901 3.957327677 24.60415471 1.362825622 1.217261318 0.174485221 0.138052778 611.1557953 352382.7677 0.035516335 0.06152357 9064.162382 -3.957327677 -0.145564303 KLGAGEGGEASVS(ph)PEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLGAGEGGEASVSPEK 16 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 KLGAGEGGEASVS(1)PEK;KLGAGEGGEAS(0.002)VS(0.998)PEK 204.12 1.59E-11 814780000 1555880 1030660 920920 1067740 1102060 791840 1332470 1680610 1821880 TRUE FALSE 1350266.516 1023889.527 1366279.992 1310186.686 1080131.162 822302.5972 1203247.264 1321224.63 1606499.422 0.840502335 0.637341983 0.850470267 0.815553786 0.672350794 0.511859877 0.748987051 0.822424591 1 20.61548903 1.351410687 2.194357 1.039042256 0.720693595 0.424607145 0.102170174 0.520655544 3.19857106 0.301645499 0.028622537 22.46004838 -1.351410687 -0.31834866 KLGCEVLGVSVDSQFTHLAWINTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KLGCEVLGVSVDSQFTHLAWINTPR 25 1 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ;;; 269.28 3.26E-46 3785960000 2944611 2736250 1122576 1867331 2483892 2230552 2712260 3311440 1893687 FALSE TRUE 2555473.196 2718275.394 1665457.508 2291337.044 2434467.409 2316362.779 2449225.443 2603314.326 1669817.48 1.530390732 1.627887734 0.997388953 1.372208083 1.457924257 1.387195191 1.466762369 1.559041246 1 20.67125899 KLGEMWNNLNDSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLGEMWNNLNDSEK 14 1 O15347;E7ES08;E7EQU1;E9PES6 O15347 HMGB3 High mobility group protein B3 0 188.59 1.24E-07 0 820400 694500 537490 588100 602220 442930 828950 934310 740360 FALSE TRUE 711982.0614 689937.7838 797421.9618 721637.0935 590237.0002 459969.8037 748558.5566 734515.0773 652835.4842 1.090599513 1.056832541 1.2214746 1.105388894 0.904112927 0.704572308 1.146626638 1.125115125 1 19.31635995 3.380951547 8.407732183 0.994179137 1.124061015 0.228470529 0.128039668 0.482798312 37.48187768 0.041139821 0.05313736 2404.094565 -3.380951547 0.129881878 KLGEMWNNTAADDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLGEMWNNTAADDK 14 1 P09429;Q5T7C4;B2RPK0 P09429 HMGB1;HMGB1P1 High mobility group protein B1;Putative high mobility group protein B1-like 1 0 119.56 0.0013437 0 149570 124420 99215 102700 94526 79470 143040 147350 243090 FALSE TRUE 129803.9455 123602.6768 147195.7059 126019.6047 92645.11754 82527.26232 129168.0028 115840.3492 214352.1771 0.605563924 0.576633643 0.686700307 0.587909143 0.432209828 0.38500781 0.602597112 0.540420679 1 17.70962354 1.237735719 24.97390597 1.000000529 0.551066059 0.72434847 0.08682595 11.62315699 351672.345 0.133555419 0.022792887 17.28764037 -1.237735719 -0.44893447 KLGEMWNNTAADDKQPYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KLGEMWNNTAADDKQPYEK 19 2 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ;; 269.41 2.14E-32 5481800000 5696730 3802020 2993260 3056820 3194380 2135260 5031590 5687600 2536340 FALSE TRUE 4943892.697 3777044.28 4440810.548 3750917.702 3130818.088 2217404.834 4543627.176 4471351.001 2236496.775 2.210552125 1.688821698 1.985610084 1.677139777 1.399875968 0.991463462 2.031582262 1.999265571 1 21.09280925 5.479059302 0.753967792 1.582760315 3.504111398 0.242439955 0.368519484 13.5068497 2.635005854 0.149140268 28.36201008 301341.7475 -5.479059302 1.921351083 KLGEMWSEQSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLGEMWSEQSAK 12 1 P26583 P26583 HMGB2 High mobility group protein B2 0 ; 232.37 1.96E-12 1991550000 4034200 2650400 1676220 2010700 2491200 1724840 3088800 3610500 2039450 FALSE TRUE 3501070.249 2632989.348 2486845.599 2467260.167 2441629.994 1791195.711 2789248.651 2838422.672 1798348.544 1.946825191 1.46411515 1.382849619 1.371958831 1.35770677 0.996022554 1.551005594 1.578349581 1 20.77824123 4.913492327 1.728242054 1.343367073 2.380436606 0.503883626 0.194112301 1.424714186 2.942470484 0.053148625 2.796330619 81939.31467 -4.913492327 1.037069534 KLGEWVGLCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLGEWVGLCK 10 1 P25398 P25398 RPS12 40S ribosomal protein S12 0 ; 120.96 0.00084614 1239090000 3895500 3996500 2266300 2790100 3354100 2829800 4352100 4797200 2997200 FALSE TRUE 3380699.805 3970246.728 3362290.26 3423634.849 3287359.972 2938664.237 3930034.012 3771356.112 2642874.43 1.279175343 1.502245692 1.272209615 1.295420929 1.243857799 1.111919735 1.487030169 1.426990276 1 21.33367645 4.179823569 24.99918885 1.284339278 1.390714332 0.100584364 0.148623007 181.4525396 77227.49041 0.038535529 0.080218166 15129.46493 -4.179823569 0.106375055 KLGGSLADSYLDEGFLLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLGGSLADSYLDEGFLLDK 19 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 117.55 0.00015507 156200000 226000 174800 154790 196290 155700 152110 220500 261800 320710 FALSE TRUE 196133.5274 173651.7273 229646.9617 240860.6446 152601.8746 157961.7701 199115.9439 205816.1073 282796.0292 0.693551207 0.614052919 0.81205865 0.851711551 0.539618166 0.558571387 0.704097383 0.727789948 1 18.10940234 1.180655568 2.56946479 1.110489862 0.681431972 0.504794985 0.098129166 0.581542917 3.738475353 0.588220358 0.0273694 15.15847697 -1.180655568 -0.42905789 KLGGSQEDQIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLGGSQEDQIK 11 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 96.306 0.011402 154750000 121640 108230 83610 94993 110050 88490 143310 158600 97430 FALSE TRUE 105564.9658 107519.03 124044.0757 116562.6125 107860.2203 91894.26756 129411.8183 124684.6242 85911.93639 1.228757845 1.251502812 1.44385147 1.35676854 1.255474208 1.069633295 1.506331061 1.451307344 1 16.39057097 4.453455825 24.73331282 1.317169769 1.234443765 0.011234052 0.162310005 687.020184 718020.6883 0.040797523 0.107952569 28408.99204 -4.453455825 -0.082726004 KLGQSESQGPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLGQSESQGPPR 12 1 F5H169;F5H5V4;F5GX23;J3KN29;O00233-2;O00233 F5H169 PSMD9 26S proteasome non-ATPase regulatory subunit 9 0 ; 208.51 1.06E-07 240570000 373590 365010 217672 283440 364600 341810 374250 448430 399380 FALSE TRUE 324219.1349 362612.2253 322938.9073 347799.3841 357345.1733 354959.6519 337955.2926 352536.7342 352165.7514 0.920643571 1.029663515 0.917008272 0.987601386 1.014707341 1.007933482 0.959648379 1.001053432 1 18.42589509 3.498024455 24.78716706 0.995562561 0.961351602 0.232320895 0.033581118 1102.819029 1307728.461 0.008594763 0.012578161 3147.92557 -3.498024455 -0.034210959 KLGSSLDWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLGSSLDWDR 10 1 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 ; 153.34 2.63E-05 952270000 2622300 2424200 1466510 1888830 2458000 2394900 2764500 2976700 2026650 FALSE TRUE 2275756.411 2408275.271 2175719.141 2317717.72 2409090.609 2487033.353 2496399.215 2340155.87 1787061.746 1.273462664 1.34761727 1.217484033 1.296943279 1.348073515 1.39168854 1.396929469 1.309499168 1 20.76915805 1.240862557 5.963699845 0.988131597 1.326169359 0.782996498 0.053438969 0.063167576 8.435408096 0.08703443 0.014105584 17.41255722 -1.240862557 0.338037762 KLHELTVMQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLHELTVMQDR 11 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 204.64 2.11E-08 1398190000 1526810 1519040 1036320 1168000 1548190 1505510 1570140 1689450 1621390 FALSE TRUE 1325038.19 1509061.326 1537487.818 1433212.252 1517384.048 1563427.944 1417868.064 1328174.265 1429711.121 0.926787356 1.055500866 1.075383548 1.002448838 1.061322127 1.093527161 0.991716469 0.928980858 1 20.44729224 2.00673466 24.4982407 0.959696935 1.038533707 0.274626901 0.048929163 136.0626967 494943.6995 0.019438856 0.013068794 101.5627988 -2.00673466 0.078836772 KLIEFLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLIEFLLK 8 1 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PNN8;E9PKG4 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 93.111 0.018101 0 489490 534130 350610 444910 493870 406590 622510 699110 517110 FALSE TRUE 424802.6563 530621.2649 520166.1687 545933.6155 484042.9532 422231.7804 562139.076 549610.767 455977.8449 0.931630037 1.163699664 1.140770707 1.197281012 1.061549281 0.925991877 1.232821029 1.205345332 1 18.7986042 4.746046881 24.23066322 1.12408014 0.931629893 0.260554275 0.096712757 848.8338121 2747300.563 0.024226049 0.242399518 55724.5899 -4.746046881 -0.192450247 KLIHLEIKPAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLIHLEIKPAIR 12 2 P36507;G5E9C7;A0A1B0GUL7;Q02750;Q02750-2 P36507;Q02750 MAP2K2;MAP2K1 Dual specificity mitogen-activated protein kinase kinase 2;Dual specificity mitogen-activated protein kinase kinase 1 0 123.64 0.0002025 693690000 232130 200860 134950 173610 204660 188810 242500 257330 183490 FALSE TRUE 201453.4324 199540.5374 200212.2714 213030.804 200587.6664 196073.6429 218982.3873 202301.982 161798.0212 1.245092065 1.233269331 1.237421013 1.316646535 1.239741159 1.211842032 1.353430565 1.250336565 1 17.30383444 1.241747278 6.479775782 0.992922576 1.263330521 0.790160181 0.042299151 0.050375569 9.848159737 0.06020279 0.010269526 17.44806532 -1.241747278 0.270407945 KLILDSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLILDSAR 8 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 130.66 0.0016652 7543200000 5849400 10658800 6252300 5898800 8532300 7218100 9470500 7881400 9475300 FALSE TRUE 5076386.97 10588781.64 9275933.193 7238212.698 8362523.923 7495784.978 8552052.368 6196023.943 8355140.828 0.60757647 1.267337303 1.110206684 0.866318455 1.000883659 0.897146455 1.02356771 0.741582227 1 22.99423271 2.393539444 1.077529577 0.87090249 0.994979377 0.006833017 0.184125596 1.732994104 4.095616829 0.156376495 0.074843822 247.4796219 -2.393539444 0.124076887 KLISEVDS(ph)DGDGEISFQEFLTAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLISEVDSDGDGEISFQEFLTAAK 24 1 Q9NZT1 Q9NZT1 CALML5 Calmodulin-like protein 5 1 KLIS(0.21)EVDS(0.79)DGDGEISFQEFLTAAK 195.74 1.26E-24 150190000 340590 290190 194260 172220 278170 197640 384890 487350 108640 TRUE FALSE 295580.1686 288283.7228 288204.7858 211325.1832 272634.9612 205243.3387 347563.427 383133.9951 95796.70296 3.085494171 3.009328232 3.008504227 2.205975537 2.845974369 2.142488544 3.628135586 3.999448658 1 16.54768838 1.219878006 24.90565146 0.99999316 3.013427905 0.557382138 0.557164846 1061.645817 1415192.477 5.262496829 0.153094972 16.59120791 -1.219878006 2.013434745 KLIYFQLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLIYFQLHR 9 1 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 168.27 3.85E-05 1599940000 1691690 3341300 1638540 2140340 2660200 2371700 3178800 3216700 2937600 FALSE TRUE 1468128.88 3319350.78 2430943.425 2626336.91 2607267.225 2462940.834 2870520.465 2528833.737 2590320.275 0.566775041 1.281444157 0.938472145 1.013904318 1.006542415 0.95082483 1.108172025 0.97626296 1 21.30469906 4.760387495 24.92073345 1.026235235 0.566774541 0.685476331 0.099420384 3273.939172 3737941.711 0.022146513 1.108022746 57595.35973 -4.760387495 -0.459460694 KLKDVLLQVDDERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLKDVLLQVDDERR 14 3 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 163.8 1.85E-06 1220870000 2027100 1874770 533400 524450 1607160 1388870 2266200 2756900 57032 FALSE TRUE 1759213.599 1862454.512 791354.0241 643534.3882 1575180.66 1442300.728 2046424.273 2167358.389 50289.74193 34.98155949 37.03448141 15.73589352 12.79653392 31.32210665 28.67981963 40.69267795 43.09742516 1 15.61797653 -1.600346121 3.26E-12 8.446651616 48.79623558 0 13.55320923 0 0.108159645 11.75192176 11.75192182 0.025098853 1.600346121 40.34958396 KLLASLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLLASLVK 8 1 Q13263;Q13263-2;M0R3C0 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 111.65 0.0088686 0 530490 733510 402130 448430 658360 622040 767720 819410 443560 FALSE TRUE 460384.4024 728691.5245 596601.413 550252.8853 645259.9241 645970.2813 693266.6326 644185.5482 391122.8421 1.177083905 1.863075858 1.525355589 1.406854385 1.649762823 1.651579023 1.772503566 1.647015921 1 18.57726227 1.236038637 24.9999999 0.999999206 1.60330003 0.480132009 0.191148724 56.52814311 560234.9842 0.28810018 0.043617278 17.22021768 -1.236038637 0.603300825 KLLDLVQQSCNYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLLDLVQQSCNYK 13 1 A0A3B3IUA2;B1AHD1;P55769 A0A3B3IUA2 NHP2L1 "NHP2-like protein 1;NHP2-like protein 1, N-terminally processed" 0 73.022 0.060865 225150000 314360 254980 196120 200640 264700 227000 283700 339020 251840 FALSE TRUE 272816.5295 253305.0196 290964.288 246198.3786 259432.9879 235732.8369 256186.8177 266523.2113 222067.7621 1.228528297 1.140665431 1.310250012 1.108663303 1.168260469 1.061535608 1.153642542 1.200188666 1 17.76064044 3.698871334 24.99296552 1.126566793 1.217899765 0.355106677 0.069175355 639.0342552 402409.7912 0.018366524 0.027242337 4998.864141 -3.698871334 0.091332972 KLLEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KLLEDR 6 1 P35579;Q9Y6N9-5;Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 P35579;Q7Z406 MYH9;MYH14 Myosin-9;Myosin-14 0 ;;; 104.45 0.054232 7392300000 14915300 13920700 9144500 11370900 11929500 12263100 15280900 16336700 13724800 FALSE TRUE 12944205.31 13829254.01 13566810.79 13952836.64 11692126.29 12734869.39 13798960.67 12843223.84 12102269.78 1.069568399 1.142699201 1.121013747 1.152910726 0.966110201 1.052271154 1.140196089 1.061224388 1 23.52877431 3.280244639 24.99998968 1.053751203 1.123020666 0.366883074 0.049713376 183.1677721 109853.7085 0.014656126 0.018920823 1906.534372 -3.280244639 0.069269463 KLLEGEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 KLLEGEEER 9 1 P20700;E9PBF6;P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8;Q03252 P20700;P02545;P02545-2;Q03252 LMNB1;LMNA;LMNB2 Lamin-B1;Prelamin-A/C;Lamin-A/C;Lamin-B2 0 ;;;;;;; 173.71 8.86E-05 13018310000 21042500 17070780 11261900 14211180 16153620 14291860 18715700 21371800 17555300 FALSE TRUE 18261680.31 16958640.92 16708192.51 17438045.62 15832194.57 14841677.1 16900654.29 16801606.89 15479932.43 1.17970026 1.095524221 1.079345312 1.126493652 1.022756051 0.958768856 1.091778299 1.085379859 1 23.88389584 7.999993068 0.538414078 1.043651829 6.582945267 0.471115262 0.04610291 137.3031521 1.334466669 0.026905795 874.1163233 99998403.86 -7.999993068 5.539293437 KLLVLDVDYTLFDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLLVLDVDYTLFDHR 15 1 Q8WVY7 Q8WVY7 UBLCP1 Ubiquitin-like domain-containing CTD phosphatase 1 0 179.25 4.40E-07 118710000 502040 491880 306040 360900 440490 432910 534740 598340 283940 FALSE TRUE 435694.142 488648.8079 454041.9676 442847.861 431725.1108 449564.3278 482880.9971 470389.6473 250372.9367 1.740180659 1.951683814 1.813462644 1.768752913 1.724328182 1.795578763 1.928646936 1.878755961 1 17.9337191 1.236529922 24.99997741 0.999998944 1.8302838 0.921725524 0.075558298 14.22290346 175053.0035 0.122784131 0.019269031 17.23970864 -1.236529922 0.830284856 KLLYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLLYEK 6 1 H7C4X7;P05408-2;P05408 REV__J3KTF2 SCG5 Neuroendocrine protein 7B2;N-terminal peptide;C-terminal peptide 0 ; 91.906 0.075939 2567300000 4021500 3750300 2717900 3132900 3092700 2808380 4206200 4938000 4039800 FALSE TRUE 3490048.586 3725664.032 4032285.531 3844272.828 3031161.321 2916420.196 3798283.371 3882047.128 3562219.446 0.979739917 1.045882795 1.131958767 1.079179115 0.850919312 0.81870874 1.066268777 1.089783262 1 21.76434496 4.814120113 18.43380638 1.014147754 0.979727732 0.007673999 0.101430353 35849.5855 8734282.916 0.027267615 67.7880387 65180.86397 -4.814120113 -0.034420022 KLMTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLMTVR 6 1 M0R0F0;M0R0R2;P46782 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ; 92.925 0.074083 1537390000 1730850 2039780 1353870 1594810 1931980 1931310 1917560 2167180 2241920 FALSE TRUE 1502113.787 2026380.551 2008606.06 1956935.986 1893537.378 2005608.745 1731595.326 1703745.422 1976882.772 0.759839586 1.025038298 1.016047127 0.98990998 0.957839992 1.014530944 0.875922109 0.861834321 1 20.91479589 0.948464627 21.14301278 1.732175569 0.940432983 0.05033023 0.084373785 789.1129714 249481.9025 49803.67132 0.020131838 8.881056379 -0.948464627 -0.791742585 KLNCQVIGASVDSHFCHLAWVNTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLNCQVIGASVDSHFCHLAWVNTPK 25 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ; 180.66 1.03E-17 1531820000 1440190 1110930 532645 1036160 1046920 901280 1345290 1549110 1191640 FALSE TRUE 1249865.243 1103632.228 790233.9036 1271435.965 1026088.34 935952.8248 1214823.983 1217844.882 1050765.677 1.189480462 1.050312408 0.752055307 1.210009037 0.976514901 0.890734105 1.156132152 1.159007102 1 20.00300955 2.205929373 24.99959536 1.118416833 1.008918504 0.089156184 0.138581044 414.3771631 317461.8363 0.055412941 0.037362354 160.6679946 -2.205929373 -0.109498329 KLNCYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLNCYK 6 1 Q96EK6;G3V5E4;G3V4W4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 0 91.26 0.077118 524090000 587700 531830 390660 489620 523450 422230 621600 680080 732670 FALSE TRUE 510033.956 528336.3737 579584.4827 600795.7044 513034.3691 438473.4613 561317.3277 534650.1844 646054.5873 0.789459538 0.81778906 0.897113795 0.929945729 0.794103748 0.678694138 0.868838855 0.827561935 1 19.30129654 1.236799951 7.43595187 1.003014015 0.827079005 0.392720872 0.068184999 0.123152235 46.21211501 0.1071029 0.017633767 17.25043104 -1.236799951 -0.17593501 KLNEILQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLNEILQAR 9 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 ; 114.89 0.0025081 1136930000 1393180 1334610 887130 974440 1269520 1269670 1429490 1502740 1514570 FALSE TRUE 1209067.733 1325842.859 1316149.035 1195701.495 1244259.036 1318515.026 1290858.28 1181390.745 1335519.26 0.905316583 0.992754578 0.98549611 0.895308313 0.93166686 0.987267699 0.966559089 0.884592818 1 20.34896935 KLNEQSPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLNEQSPTR 9 1 O75396 O75396 SEC22B Vesicle-trafficking protein SEC22b 0 ; 152.04 0.00013055 195962000 390250 345020 190843 267330 365270 373050 292020 451440 428530 FALSE TRUE 338677.4737 342753.5409 283135.3131 328031.3624 358001.8416 387401.4749 263699.9453 354903.0691 377869.6716 0.896281176 0.907068142 0.749293564 0.868107147 0.947421475 1.025225108 0.697859514 0.939220837 1 18.5275292 3.451928132 13.98412871 0.912042275 0.848536126 0.102786091 0.096589744 4.619416176 2560.084265 0.028025053 0.03623221 2830.923491 -3.451928132 -0.063506148 KLNS(ph)GGGLSEELGSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLNSGGGLSEELGSAR 16 1 A0A0G2JIS2;A2ABF8;A0A0G2JIR1;A2ABF9;A0A0G2JK64;Q96KQ7-2;Q96KQ7 A0A0G2JIS2 EHMT2 Histone-lysine N-methyltransferase EHMT2 1 KLNS(1)GGGLSEELGSAR;KLNS(1)GGGLSEELGSAR 95.666 0.002251 250530000 150900 77460 56344 65912 92807 108875 115969 106598 98049 TRUE FALSE 130958.1827 76951.16016 83592.14686 80878.327 90960.32227 113063.4917 104722.3442 83802.84725 86457.75892 1.514707116 0.890043428 0.966855351 0.935466383 1.052078187 1.307731002 1.211254438 0.969292384 1 16.39970782 KLNSSSSSSSNSSNEREDFDSTSS(ph)SSSTPPLQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLNSSSSSSSNSSNEREDFDSTSSSSSTPPLQPR 34 2 A0A669KAX4;Q13620-1;K4DI93;Q13620;A0A669KAU9 A0A669KAX4 CUL4B Cullin-4B 1 KLNSSSSSSSNSSNEREDFDS(0.002)T(0.01)S(0.058)S(0.536)S(0.344)S(0.024)S(0.016)T(0.011)PPLQPR 274.5 4.93E-74 203800000 121830 116190 62382 72785 111970 104660 123340 150120 54798 TRUE FALSE 105729.8568 115426.7402 92550.14386 89311.9467 109742.0161 108686.3379 111378.5058 118018.0062 48319.84287 2.188125013 2.3888062 1.915365166 1.848349279 2.27115838 2.249310666 2.305026241 2.442433568 1 15.56032814 1.231690916 24.99960655 0.999997939 2.206871985 0.801240228 0.187978716 113.8758125 414368.9422 0.484394874 0.050296758 17.04868614 -1.231690916 1.206874046 KLNTTTMSNATANSSIRPIFGGTVYHS(ph)PVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLNTTTMSNATANSSIRPIFGGTVYHSPVSR 31 2 O43663-2;O43663-4;O43663;O43663-3;G3V3N7 O43663-2 PRC1 Protein regulator of cytokinesis 1 1 KLNTTTMSNATANSSIRPIFGGTVYHS(0.999)PVS(0.001)R 259.19 8.08E-59 312270000 174080 152010 79053 99333 135150 153010 162470 197250 93548 TRUE FALSE 151074.8869 151011.4363 117283.2952 121888.0759 132460.7794 158896.3937 146713.6844 155069.6225 82488.86201 1.831458008 1.830688806 1.421807652 1.477630711 1.605801998 1.926276952 1.77858781 1.879885584 1 16.33191171 4.38333476 24.99999825 1.629989371 1.83137471 0.111825613 0.265903162 36.63474202 9738.097342 0.066658108 0.1763605 24173.23424 -4.38333476 0.20138534 KLNVTEQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KLNVTEQEK 9 1 P06733;K7EM90;A0A2R8YEM5;A0A2R8Y879;A0A2R8Y6I8 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;;; 218.49 8.46E-07 10758940000 13413790 11849800 10361340 9659780 10619560 8824310 13189570 15271470 21669540 FALSE TRUE 11641123.67 11771957.88 15372118.68 11853180.69 10408251.53 9163786.916 11910447.53 12005784.98 19107791.67 0.609234383 0.616081549 0.804494781 0.620332318 0.544712425 0.479583778 0.623329359 0.628318813 1 24.18765772 1.236698994 5.654665159 1.017720946 0.615000063 0.688922779 0.08119294 0.092864615 9.790039098 0.145303089 0.021660425 17.2464214 -1.236698994 -0.402720883 KLNVTEQEKIDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLNVTEQEKIDK 12 2 P06733;K7EM90;A0A2R8YEM5;A0A2R8Y879 P06733 ENO1 Alpha-enolase;Enolase 0 ; 173.68 1.82E-05 3345200000 7351400 5677400 3816800 3007500 4350700 3405800 7540300 8236600 1581410 FALSE TRUE 6379893.864 5640104.786 5662617.246 3690398.842 4264129.582 3536823.33 6809042.867 6475267.187 1394457.511 4.575179819 4.044658758 4.060803001 2.646476362 3.057912878 2.536343561 4.882933192 4.64357439 1 20.41127255 3.944727133 10.25731841 3.366309299 4.246269181 0.161024951 1.104633551 1.49846977 274.4498052 0.306319049 0.532729808 8804.954844 -3.944727133 0.879959882 KLPDFLTAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLPDFLTAK 9 1 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7;Q9BZZ5-3 Q9BZZ5-2 API5 Apoptosis inhibitor 5 0 110.39 0.0042587 0 815240 663830 494450 610060 624680 511830 774620 885870 892250 FALSE TRUE 707503.9684 659469.257 733567.6738 748583.4472 612250.0902 531520.4313 699497.4716 696433.5943 786769.2215 0.899252219 0.838199105 0.932379729 0.951465089 0.778182564 0.675573493 0.889075796 0.885181544 1 19.58558099 1.221192417 2.054416674 1.050370903 0.849621948 0.254643206 0.079377169 1.226576675 4.904917984 0.476857516 0.023084181 16.64149801 -1.221192417 -0.200748954 KLPEEEAECYFHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLPEEEAECYFHSR 14 1 J3QQZ9;Q9NVS9-3;Q9NVS9;J3QQV6 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 97.291 0.0019688 170510000 214140 199830 141150 191090 185690 168110 238630 252280 376000 FALSE TRUE 185840.8564 198517.3036 209410.6121 234479.9051 181995.1323 174577.3005 215487.6993 198331.8852 331549.7083 0.560521852 0.598755778 0.631611511 0.707223982 0.548922613 0.526549401 0.64994085 0.598196531 1 18.33886566 1.237988832 24.99999999 1.000000451 0.604701129 0.851148862 0.052207005 5.190456676 226740.2338 0.074616096 0.012943164 17.29771877 -1.237988832 -0.395299322 KLPEEHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLPEEHAR 8 1 P41743;E9PBE1;Q05513-2;Q05513-3;Q05513 P41743;Q05513 PRKCI;PRKCZ Protein kinase C iota type;Protein kinase C zeta type 0 ; 113.62 0.0018262 61868000 289460 262650 198151 242710 243530 273030 300240 342930 333790 FALSE TRUE 251207.1276 260924.6349 293977.4864 297821.0151 238684.2295 283533.6408 271122.771 269597.0882 294329.7265 0.853488809 0.886504527 0.998803247 1.011861828 0.810941635 0.963319758 0.921153206 0.915969622 1 18.16707373 4.76856928 0.010209041 1.817479736 6.84E-05 0.083951682 0.063514552 36807.1392 104.1691824 8892.837175 9663.499767 58690.69878 -4.76856928 -1.817411334 KLPEELGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLPEELGR 8 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 105.4 0.0070485 731110000 685280 802060 445020 624700 775060 829520 885930 1110580 1101420 FALSE TRUE 594718.5117 796791.215 660233.1605 766547.6829 759637.8224 861432.1712 800012.645 873091.1095 971211.3823 0.612347139 0.820409676 0.679803771 0.789269666 0.782154983 0.886966717 0.823726595 0.898971249 1 19.8894258 -1.999999999 0.140788898 2.033757984 0.553557268 0.733994061 0.056356435 84.57159805 1.020951082 24.78185276 1.077929226 0.01 1.999999999 -1.480200717 KLPEYNPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KLPEYNPR 8 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;;; 115.71 0.0038652 1569800000 1750300 1459040 845250 1052960 1448460 1219130 1498040 1669020 1488090 FALSE TRUE 1518993.42 1449455.47 1254015.727 1292050.661 1419638.48 1266030.72 1352760.311 1312113.061 1312169.695 1.157619648 1.104625016 0.955681061 0.984667354 1.08190159 0.964837646 1.030933968 0.999956839 1 20.32352288 4.400900842 5.056278389 1.005027266 1.146002671 0.702193099 0.035537199 0.095048961 4.264377752 0.008572873 0.024493481 25171.02156 -4.400900842 0.140975405 KLPFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLPFQR 6 1 K7EK07;Q71DI3;Q16695;P84243;P68431;Q6NXT2;K7EMV3;A0A590UJJ6;B4DEB1;K7ES00;K7EP01;P0DPK2;P0DPK5;Q5TEC6;A0A590UJL8 K7EK07;Q5TEC6 H3F3B;HIST2H3A;HIST3H3;H3F3A;HIST1H3A;H3F3C;HIST2H3PS2 Histone H3;Histone H3.2;Histone H3.1t;Histone H3.3;Histone H3.1;Histone H3.3C 0 83.087 0.092247 2360700000 3862300 3407300 2791000 4981300 3244500 7319200 3972500 5145700 4200900 FALSE TRUE 3351887.269 3384917.222 4140736.935 6112380.299 3179940.798 7600774.36 3587247.561 4045332.099 3704274.388 0.904870136 0.913786849 1.117826733 1.650088428 0.858451741 2.051892912 0.968407625 1.092071395 1 21.82075954 4.101026706 4.391430803 1.256806542 0.912975215 0.147629221 0.353503054 0.408039141 13.8174513 0.088710702 0.197299254 12619.0513 -4.101026706 -0.343831328 KLPGDDR ddPTM_MDA-MB-175_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 ; 75.38 0.069955 211880000 1073240 984350 665480 835270 870980 833440 1034370 1220530 1081970 FALSE TRUE 931408.6148 977883.74 987308.3539 1024930.82 853649.202 865502.9761 934056.9566 959529.1577 954060.7392 0.976257146 1.024970109 1.03484853 1.074282567 0.894753517 0.907178066 0.979033009 1.00573173 1 19.86372159 3.250355712 24.99988272 0.962507285 1.027920965 0.402602195 0.042261509 274.94024 582736.8912 0.013560147 0.017359386 1779.736518 -3.250355712 0.06541368 KLPIDVTEGEVISLGLPFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLPIDVTEGEVISLGLPFGK 20 1 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;K7ES59;K7EKJ7;K7ELW5 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ; 157.97 1.16E-09 1208720000 4120900 3440700 2335700 2949900 3001300 2428200 3982600 4788000 3436700 FALSE TRUE 3576312.624 3418097.815 3465252.332 3619719.881 2941580.002 2521614.425 3596368.065 3764123.46 3030417.241 1.180138687 1.127929768 1.143490172 1.194462542 0.970684816 0.832101399 1.186756733 1.242113927 1 21.53108501 3.270528101 24.99596075 1.070624448 1.157820252 0.183613042 0.114360029 501.1416984 391848.7893 0.037683806 0.048645299 1864.352808 -3.270528101 0.087195805 KLPIQEFHLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLPIQEFHLSR 11 1 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 ; 150.14 2.21E-05 1026790000 1013300 827120 204076 549790 1001150 911560 886530 994970 916000 FALSE TRUE 879389.8376 821686.5943 302767.8362 674628.2225 981229.0737 946628.3031 800554.4571 782203.4084 807711.5235 1.088742468 1.017302057 0.374846498 0.835234119 1.214826142 1.171988111 0.991139081 0.968419275 1 19.6234806 3.355707784 8.233127476 1.055446489 0.806664396 0.25696867 0.201190903 0.358949149 24.34314142 0.060806104 0.078521982 2268.338084 -3.355707784 -0.248782093 KLPPPPPQAPPEEENES(ph)EPEEPSGVEGAAFQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLPPPPPQAPPEEENESEPEEPSGVEGAAFQSR 33 1 R4GMQ1;O60341 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 1 KLPPPPPQAPPEEENES(1)EPEEPSGVEGAAFQSR 88.635 0.00015781 40585000 34862 30652 21723 20881 25077 26246 25414 27461 28546 TRUE FALSE 30254.89837 30450.64499 32228.31546 25622.3502 24578.01676 27255.7006 22949.35419 21588.67885 25171.3244 1.201958939 1.209735511 1.280358353 1.017918239 0.976429224 1.08280757 0.91172613 0.857669565 1 14.61949351 3.608777007 3.839661626 0.956461131 1.228143138 0.792377372 0.062055656 0.11189422 2.883993856 0.019843024 0.030355203 4062.346905 -3.608777007 0.271682007 KLPVDSVFNKFEDEDSDDVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLPVDSVFNKFEDEDSDDVPR 21 2 P49756 P49756 RBM25 RNA-binding protein 25 0 138.35 1.00E-06 239390000 330840 208510 172220 217600 188300 159990 299050 338200 208960 FALSE TRUE 287118.6558 207140.2841 255506.168 267009.4058 184553.1984 166144.9188 270048.177 265878.5619 184256.9868 1.558251118 1.12419229 1.386683742 1.449114144 1.0016076 0.901702137 1.465606171 1.442976825 1 17.4913598 4.753640771 23.61247648 1.245643996 1.558251601 0.193170951 0.211228468 2476.211265 3877102.871 0.053777802 1.130674154 56707.53513 -4.753640771 0.312607605 KLPVESIQIVLEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLPVESIQIVLEELR 15 1 K7ENE3;Q9BRG1;K7EKV4 K7ENE3 VPS25 Vacuolar protein-sorting-associated protein 25 0 ; 189.42 4.15E-07 389980000 406340 385110 260570 291080 370090 349450 392070 456860 429270 FALSE TRUE 352641.1395 382580.1871 386582.5236 357174.1629 362725.9331 362893.5676 354047.1117 359164.0443 378522.1896 0.931626069 1.010720633 1.021294218 0.94360165 0.958268611 0.958711477 0.935340441 0.948858625 1 18.53001835 3.71659245 24.89026343 0.955269988 0.990164346 0.195856536 0.028702328 1028.042229 1164786.528 0.007717284 0.01145847 5207.058415 -3.71659245 0.034894358 KLPVESIQIVLEELRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLPVESIQIVLEELRK 16 2 K7ENE3;Q9BRG1;K7EKV4 K7ENE3 VPS25 Vacuolar protein-sorting-associated protein 25 0 ; 145.62 6.76E-07 130115000 137316 123991 79660 91021 105891 90056 152524 174756 106100 FALSE TRUE 119169.3427 123176.495 118183.8424 111688.7092 103783.9763 93520.51259 137732.246 137385.7894 93556.97887 1.273762194 1.316593336 1.263228504 1.193804146 1.109313036 0.999610224 1.472175006 1.468471845 1 16.51355765 1.203749447 24.06764151 0.999996654 1.268262297 0.245232111 0.144159858 5906.506264 4083226.643 7.508738767 0.039729672 15.98635479 -1.203749447 0.268265644 KLQAQMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLQAQMK 7 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 ; 102.72 0.013689 1325220000 1542530 2033400 1255770 1587100 1837570 1687600 2321600 2481100 2225000 FALSE TRUE 1338680.752 2020042.462 1863064.572 1947475.312 1801005.952 1752523.064 2096451.589 1950536.073 1961963.035 0.68231701 1.029602712 0.949592087 0.992615701 0.917961205 0.893249788 1.068547955 0.994175751 1 20.90386643 4.744322799 24.99586934 0.980591117 0.682316882 0.772146059 0.050942603 307.9413256 1335785.78 0.012663377 0.109326273 55503.81041 -4.744322799 -0.298274235 KLQELSSK ddPTM_MDA-MB-175_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 ; 157.99 0.00059004 10409000000 11221800 9682800 8292400 7998800 9516800 8001700 13073900 14063000 15866900 FALSE TRUE 9738810.698 9619193.049 12302632.38 9815049.794 9327434.299 8309530.577 11805995.19 11055736.89 13991133.16 0.696070189 0.687520656 0.879316367 0.70151929 0.666667538 0.593914051 0.843819801 0.790195959 1 23.73800948 0.965874296 1.20853044 1.299138819 0.715987773 0.544192196 0.080762518 2.229930038 1.744439108 1.932108503 0.025304805 9.244305648 -0.965874296 -0.583151046 KLS(ph)CSLEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLSCSLEDLR 10 1 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 KLS(0.696)CS(0.304)LEDLR 60.157 0.061202 256970000 644120 564440 369290 443700 583550 500770 570740 648000 497290 TRUE FALSE 558997.91 560732.1565 547879.8792 544448.8665 571938.4967 520034.9459 515389.7226 509430.2427 438500.9427 1.274792949 1.278747893 1.249438315 1.241613902 1.304303916 1.185938034 1.175344617 1.161754042 1 18.74222042 -0.039199275 0.587052726 3.18E-12 1.269935809 0.888239165 0.02917479 4.716446033 0.39609656 5.673102683 0.015522025 0.913693899 0.039199275 1.269935809 KLS(ph)DASDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KLSDASDER 9 1 Q658Y4;E7ER68 Q658Y4 FAM91A1 Protein FAM91A1 1 KLS(1)DASDER;KLS(0.916)DAS(0.084)DER;KLS(0.983)DAS(0.017)DER;KLS(0.981)DAS(0.019)DER;KLS(1)DASDER 119.32 0.00051882 4107920000 15974510 13663070 12235760 15104980 13945890 12943770 16398000 19995430 27785200 TRUE FALSE 13863438.03 13573316.39 18153014.46 18534796.57 13668394.07 13441725.21 14807724.48 15719562.9 24500465.31 0.565843867 0.554002392 0.740925294 0.756507941 0.55788304 0.548631425 0.604385439 0.641602627 1 24.54630581 1.237207981 5.112464401 1.023251451 0.62122079 0.719866618 0.074376926 0.098596475 6.857381415 0.141164631 0.019926478 17.26664582 -1.237207981 -0.40203066 KLS(ph)FDFQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLSFDFQ 7 1 P23381;P23381-2 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 1 KLS(1)FDFQ 67.334 0.069324 253360000 1284900 1154100 867090 977830 1189200 1173900 1403300 1466000 1434100 TRUE FALSE 1115097.209 1146518.641 1286417.624 1199861.247 1165537.247 1219060.693 1267208.182 1152507.308 1264562.332 0.88180486 0.906652533 1.017282891 0.948835195 0.921692207 0.964017876 1.002092305 0.911388296 1 20.27020672 4.455806723 21.88207729 0.961200624 0.888016722 0.43682772 0.034261013 43.9309253 45100.61378 0.008254263 0.021848977 28563.19094 -4.455806723 -0.073183902 KLS(ph)FLSWGTNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLSFLSWGTNK 11 1 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 KLS(0.999)FLS(0.001)WGTNK 153.2 2.00E-05 911360000 1121000 1223800 768760 802930 1077800 809210 1386000 1373000 1487000 TRUE FALSE 972857.0097 1215760.777 1140534.907 985247.5285 1056353.889 840340.8323 1251585.933 1079394.635 1311208.554 0.741954441 0.927206258 0.869834859 0.751404134 0.805633769 0.640890291 0.954528499 0.823205913 1 20.32246574 0.180453817 1.095089571 2.48090282 0.807938705 0.296607167 0.090826723 19.96482992 3.115984672 66.64234604 0.027915469 1.515143676 -0.180453817 -1.672964115 KLS(ph)FTESLTSGASLLTLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KLSFTESLTSGASLLTLNK 19 1 P19838;P19838-2;P19838-3 P19838 NFKB1 Nuclear factor NF-kappa-B p105 subunit;Nuclear factor NF-kappa-B p50 subunit 1 KLS(0.711)FT(0.157)ES(0.079)LT(0.053)SGASLLTLNK;KLS(0.404)FT(0.346)ES(0.247)LT(0.003)SGASLLTLNK;KLS(0.506)FT(0.484)ES(0.01)LTSGASLLTLNK 285.6 3.00E-40 1041900000 2219620 1704970 1352220 1632790 1866110 1420260 2336610 2649390 2346280 TRUE FALSE 1926291.593 1693769.94 2006158.115 2003539.925 1828978.062 1474898.321 2110005.922 2082838.566 2068905.451 0.931067967 0.818679239 0.96967124 0.968405745 0.884031728 0.712888218 1.019865804 1.006734534 1 20.98043629 KLS(ph)GDQITLPTTVDYSSVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KLSGDQITLPTTVDYSSVPK 20 1 O00559-2;E9PND3;E9PN10;O00559;E9PJ38 O00559-2 EBAG9 Receptor-binding cancer antigen expressed on SiSo cells 1 KLS(1)GDQITLPTTVDYSSVPK;KLS(1)GDQITLPTTVDYSSVPK;KLS(1)GDQITLPTTVDYSSVPK 293.88 9.31E-55 17694680000 5290140 3882100 3578540 3536060 4164020 3470510 5208920 6694760 5188270 TRUE FALSE 4591034.595 3856598.229 5309133.913 4338976.468 4081164.149 3604022.765 4703759.74 5263137.673 4574918.631 1.003522678 0.842987284 1.160487069 0.948427025 0.892073603 0.78777855 1.028162492 1.150433067 1 22.12531465 2.006990542 24.99398143 1.086962582 0.940239353 0.233082538 0.104983632 211.7666932 757146.7258 0.043016149 0.028928638 101.6226562 -2.006990542 -0.14672323 KLS(ph)GDQPAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 KLSGDQPAAR 10 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 KLS(1)GDQPAAR;KLS(1)GDQPAAR;KLS(1)GDQPAAR;KLS(1)GDQPAAR;KLS(1)GDQPAAR;KLS(1)GDQPAAR;KLS(1)GDQPAAR;KLS(1)GDQPAAR;KLS(1)GDQPAAR 153 1.04E-05 4801422800 7702497 6189927 4357205 5487019 6366950 5588760 7374455 8258123 7635302 TRUE FALSE 6684592.506 6149264.962 6464363.912 6732930.528 6240260.152 5803763.214 6659281.489 6492187.661 6732665.296 0.992859768 0.913347789 0.960149306 1.000039395 0.926863267 0.862030557 0.989100333 0.964281956 1 22.68274631 KLS(ph)LPTDLKPDLDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLSLPTDLKPDLDVK 15 2 H0Y332;Q5T5C0-2;Q5T5C0;Q5JRH0 H0Y332 STXBP5 Syntaxin-binding protein 5 1 KLS(0.996)LPT(0.004)DLKPDLDVK;KLS(0.998)LPT(0.002)DLKPDLDVK 182.34 2.87E-07 1568920000 3558000 2505000 2782600 2498000 2306100 1363100 4175900 4147800 3570500 TRUE FALSE 3087801.285 2488544.49 4128274.667 3065209.08 2260213.122 1415539.339 3770921.861 3260825.248 3148399.558 0.980752674 0.790415716 1.311229592 0.973576899 0.71789272 0.449606002 1.197726588 1.035708838 1 21.58618721 KLS(ph)MGSDDAAYTQALLVHQK ddPTM_MDA-MB-175_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(0.974)MGS(0.026)DDAAYTQALLVHQK 244.71 3.07E-30 616270000 624170 460860 353070 479700 481990 361200 725480 628490 543460 TRUE FALSE 541684.3531 457832.5803 523815.8329 588623.2168 472399.342 375095.5977 655123.0613 494092.3044 479212.7779 1.130362916 0.955384751 1.09307568 1.228312858 0.985782024 0.78273288 1.367081788 1.031049937 1 18.87030685 2.235555922 24.99990267 1.121296642 1.035886782 0.091662545 0.151132702 241.5547216 2009766.821 0.059861782 0.042346299 172.0108816 -2.235555922 -0.08540986 KLS(ph)PIIEDSR ddPTM_MDA-MB-175_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 111.83 0.001042 519640000 1163440 939690 648840 710600 967680 921720 1053480 1177390 1144220 TRUE FALSE 1009688.456 933517.1145 962621.1942 871952.5908 948425.0612 957179.1648 951313.6717 925614.311 1008951.615 1.000730304 0.925234769 0.954080632 0.864216458 0.94001045 0.948686885 0.942873432 0.917402081 1 19.94442556 3.005213681 24.98162111 0.945744445 0.932270564 0.022423059 0.038883207 698.1787819 3345319.312 0.011615144 0.013128761 1012.077293 -3.005213681 -0.013473881 KLS(ph)PPPLPPR ddPTM_MDA-MB-175_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 70.089 0.033704 1004510000 1095874 1125710 676490 784250 1088891 1098178 1070239 1258168 876477 TRUE FALSE 951051.4743 1118315.137 1003642.827 962325.949 1067224.199 1140425.618 966447.3865 989118.5643 772860.8875 1.230559716 1.446981151 1.298607347 1.24514769 1.380874898 1.475589769 1.250480393 1.279814492 1 19.55984923 0.878986091 1.491480808 0.481594674 1.341461223 0.611192451 0.082808363 1.990527729 1.881253512 3.353083071 0.023057005 7.568086562 -0.878986091 0.85986655 KLS(ph)PQDPSEDVSSVDPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLSPQDPSEDVSSVDPLK 18 1 Q53T59;H7BZZ1;H7C0Y9;F8WDN8 Q53T59 HS1BP3 HCLS1-binding protein 3 1 KLS(1)PQDPSEDVSSVDPLK;KLS(1)PQDPSEDVSSVDPLK 205.13 6.10E-16 1688520000 1620970 1347330 1417680 1527810 1401670 987140 1854280 2298900 2860400 TRUE FALSE 1406754.707 1338479.301 2103274.79 1874722.612 1373779.509 1025115.915 1674452.211 1807298.125 2522246.771 0.557738729 0.530669448 0.833889378 0.743274859 0.544664989 0.406429667 0.66387327 0.716542943 1 21.266278 1.211974218 1.967354181 1.144921146 0.612030871 0.518843725 0.117990599 0.773957105 2.735027397 0.780942702 0.034613527 16.2919931 -1.211974218 -0.532890276 KLS(ph)PTEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KLSPTEPK 8 1 O14828;O14828-2 O14828 SCAMP3 Secretory carrier-associated membrane protein 3 1 KLS(0.75)PT(0.25)EPK;KLS(0.652)PT(0.348)EPK;KLS(0.974)PT(0.026)EPK;KLS(0.99)PT(0.01)EPK;KLS(0.883)PT(0.117)EPK;KLS(0.987)PT(0.013)EPK 132.32 0.0005924 10071510000 10881100 8547260 7907250 8189060 8364000 7010120 11824600 13781200 12234900 TRUE FALSE 9443135.066 8491112.486 11731222.55 10048511.23 8197572.764 7279803.853 10677852.11 10834197.63 10788504.06 0.875296057 0.787051888 1.087381761 0.931409135 0.759843322 0.674774168 0.989743532 1.004235394 1 23.3629915 2.043129278 24.99997501 1.000791782 0.857394601 0.283876561 0.108791219 186.2583463 107964.2659 0.047372988 0.031938839 110.4407324 -2.043129278 -0.14339718 KLS(ph)SIGIQVDCIQPVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLSSIGIQVDCIQPVPK 17 1 Q9Y2H0-3;Q9Y2H0 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 KLS(0.796)S(0.204)IGIQVDCIQPVPK 187.62 2.80E-10 336510000 1091200 722700 705580 761000 783440 601670 940190 1200600 1553300 TRUE FALSE 946995.1553 717952.5361 1046800.848 933796.6812 767851.0768 624816.6342 849010.5185 943861.0331 1369670.644 0.691403557 0.524178962 0.764271946 0.681767318 0.560610013 0.456180204 0.619864726 0.689115327 1 20.38539759 1.207628369 2.466699777 1.11936106 0.611790035 0.653575122 0.087742293 0.393505849 2.419277229 0.444078627 0.023950279 16.12977722 -1.207628369 -0.507571025 KLS(ph)SSDAPAQDTGSSAAAVETDASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.625)S(0.188)S(0.188)DAPAQDTGSSAAAVETDASR;KLS(0.602)S(0.199)S(0.199)DAPAQDTGSSAAAVETDASR;KLS(0.572)S(0.154)S(0.274)DAPAQDTGSSAAAVETDASR 235.65 1.25E-38 3259400000 900350 738810 590920 792730 898090 727660 1180090 1332610 1093890 TRUE FALSE 781366.4663 733956.7085 876690.8885 972731.4626 880219.7661 755653.5511 1065645.053 1047641.722 964571.5704 0.810065826 0.760914722 0.908891487 1.008459603 0.912549979 0.783408483 1.104785882 1.086121294 1 19.87952876 6.06232671 0.096033344 1.415455477 4.77E-14 0.454784777 0.089148325 163.5976003 2.524357866 9.39366374 35.52579934 1154321.302 -6.06232671 -1.415455477 KLSAS(ph)SPR ddPTM_MDA-MB-175_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(0.05)AS(0.475)S(0.475)PR 73.067 0.027273 276780000 859730 894920 585950 668020 786690 715690 900260 1051600 853290 TRUE FALSE 746114.5022 889041.2116 869317.3799 819704.151 771036.4081 743223.0574 812952.9238 826723.5236 752415.0283 0.991626262 1.181583539 1.155369506 1.08943086 1.024748814 0.987783377 1.080458116 1.098759983 1 19.52116914 3.438511845 5.693272847 1.046962213 1.117758462 0.230979495 0.059085559 0.270162764 22.4906406 0.017203876 0.02267907 2744.807206 -3.438511845 0.070796248 KLSCS(ph)LEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KLSCSLEDLR 10 1 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 KLS(0.356)CS(0.644)LEDLR;KLS(0.024)CS(0.976)LEDLR;KLS(0.034)CS(0.966)LEDLR;KLS(0.273)CS(0.727)LEDLR;KLS(0.011)CS(0.989)LEDLR 176.86 2.53E-06 9199820000 27100600 22941800 14803970 17331100 23733900 19930500 25108300 30002400 19491400 TRUE FALSE 23519187.05 22791093.81 21963219.41 21266391.14 23261641.82 20697239.23 22673300.93 23586620.24 17187148.9 1.368417018 1.326054364 1.277886143 1.237342579 1.353432263 1.20422761 1.319200821 1.372340484 1 24.03482691 1.23100139 24.99996863 0.999999455 1.306654965 0.756868719 0.054746114 137.8264977 455782.5276 0.139108154 0.013495064 17.02163955 -1.23100139 0.30665551 KLSCS(ph)LEDLRSESVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KLSCSLEDLRSESVDK 16 2 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 KLS(0.022)CS(0.978)LEDLRSESVDK;KLS(0.005)CS(0.995)LEDLRSESVDK;KLS(0.008)CS(0.992)LEDLRSESVDK 117.38 0.00018496 314820000 1352220 1119670 360406 287858 895030 663710 1390130 1494810 58166 TRUE FALSE 1173520.701 1112314.814 534699.5471 353220.5585 877220.6541 689243.3532 1255315.407 1175156.514 51289.68174 22.88024922 21.68691199 10.42508998 6.886776181 17.10325789 13.43824586 24.47500869 22.91214284 1 15.646381 7.999999899 0.059647606 9.999999882 28.83186774 0.035010845 7.644730803 7306.97551 42.27073326 3350.277819 13103.86543 99999976.74 -7.999999899 18.83186785 KLSEEEILENPDLFLTSEATDYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLSEEEILENPDLFLTSEATDYGR 24 1 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 229.99 3.76E-33 53561000 85192 69811 52842 60932 66816 73072 70483 86623 53518 FALSE TRUE 73933.66135 69352.40694 78396.56795 74767.54189 65486.49232 75883.12712 63647.56951 68099.34555 47191.16301 1.566684452 1.469605802 1.661255264 1.584354721 1.387685493 1.607994427 1.348717969 1.443052919 1 15.52622911 0.726900889 1.12957657 8.89E-13 1.53644375 0.747546503 0.094488882 2.308507343 1.061858561 5.638931993 0.028017257 5.332131967 -0.726900889 1.53644375 KLSELLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLSELLR 7 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 167.24 0.0017534 13529600000 13498400 14230900 8371900 11264200 13366900 12775400 14400600 16597100 14041000 FALSE TRUE 11714552.24 14137416.28 12420578.84 13821908.77 13100924.84 13266877.9 13004032.03 13047939.32 12381088.98 0.946164934 1.14185564 1.003189531 1.116372623 1.058139948 1.071543701 1.050314076 1.053860395 1 23.56163488 4.770226051 24.18452655 1.060787361 0.946164616 0.412373184 0.04340351 9109.121659 6956913.672 0.009535304 1.331988679 58915.02298 -4.770226051 -0.114622745 KLSFLS(ph)WGTNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLSFLSWGTNK 11 1 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 KLSFLS(1)WGTNK 137.39 4.86E-05 859300000 559740 586380 443100 414780 570320 487630 670640 735070 604810 TRUE FALSE 485768.9408 582528.0312 657384.6421 508962.1385 558971.7478 506389.4416 605601.436 577881.0008 533310.0508 0.910856527 1.092287742 1.232650015 0.954345671 1.048117782 0.949521654 1.135552265 1.08357418 1 19.02461499 1.219490641 22.89982846 0.999999456 1.057072806 0.023563959 0.095747531 1940.202342 2329489.645 0.692705595 0.02278908 16.57641615 -1.219490641 0.05707335 KLSFTES(ph)LTSGASLLTLNK ddPTM_MDA-MB-175_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(0.222)FT(0.12)ES(0.658)LTSGASLLTLNK 292.36 8.64E-50 52902000 188340 143180 130190 146950 157580 122870 216430 249280 203720 TRUE FALSE 163450.3918 142239.4412 193150.3195 180317.2435 154444.4663 127596.8884 195440.6519 195973.4119 179636.4537 0.90989545 0.791818354 1.075228972 1.00378982 0.859761274 0.710306209 1.087978792 1.09094456 1 17.45472062 KLSLS(ph)EGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLSLSEGK 8 1 K7EMM8;Q49A26-4;Q49A26-2;Q49A26-3;Q49A26;K7EPU6 K7EMM8 GLYR1 Putative oxidoreductase GLYR1 1 KLS(0.144)LS(0.856)EGK 119.27 0.0022792 183220000 404410 279840 249900 307940 295790 251730 448370 445540 523580 TRUE FALSE 350966.1939 278001.7126 370752.4759 377862.4836 289904.3577 261414.216 404887.1464 350264.7382 461682.9689 0.760188739 0.602148512 0.803045598 0.818445793 0.627929504 0.566220185 0.876980902 0.758669394 1 18.81654299 0.196281018 1.004827363 2.831174014 0.70885221 0.445535711 0.09815616 12.83348937 2.019147288 48.21881024 0.032097715 1.571379264 -0.196281018 -2.122321804 KLSS(ph)IGIQVDCIQPVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLSSIGIQVDCIQPVPK 17 1 Q9Y2H0-3;Q9Y2H0 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 KLS(0.409)S(0.591)IGIQVDCIQPVPK 121.35 3.71E-05 428070000 925860 656590 593260 666080 718960 599350 831000 953070 1213800 TRUE FALSE 803505.2552 652276.8171 880162.5203 817323.6444 704654.1026 622407.3823 750409.7479 749263.3973 1070305.947 0.750724835 0.609430247 0.82234666 0.763635526 0.658366988 0.581522867 0.70111705 0.700046 1 20.02959182 1.23832709 7.835942087 1.004119853 0.69655042 0.639557229 0.071149612 0.063682112 32.10583085 0.103648781 0.017746323 17.31119665 -1.23832709 -0.307569434 KLSSS(ph)DAPAQDTGSSAAAVETDASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.249)S(0.249)S(0.502)DAPAQDTGSSAAAVETDASR 316.73 6.63E-75 1256700000 435870 382200 285770 386050 477080 303920 588900 644090 569180 TRUE FALSE 378268.6751 379689.303 423969.3278 473708.5529 467587.0414 315611.9991 531788.5686 506356.3658 501892.1888 0.753685121 0.756515665 0.844741834 0.943845239 0.931648374 0.628844214 1.059567334 1.008894693 1 18.93701797 -1.999999999 0.160064922 2.11797649 0.673122153 0.342928628 0.109929011 154.8529273 2.037846856 51.36513381 1.495970489 0.01 1.999999999 -1.444854337 KLSSWDQAETPGHT(ph)PSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLSSWDQAETPGHTPSLR 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 KLSSWDQAETPGHT(1)PSLR;KLSSWDQAETPGHT(1)PSLR 149.85 4.51E-08 431620000 488620 466970 238770 292980 504890 488960 468250 546090 222324 TRUE FALSE 424047.629 463902.4433 354239.9706 359505.5869 494843.6768 507770.6076 422839.1871 429312.9032 196041.11 2.163054622 2.36635287 1.806967787 1.833827542 2.524183202 2.5901231 2.156890395 2.189912632 1 17.58079669 1.238065959 7.418696963 0.979312676 2.205654854 0.690888192 0.253096456 0.064028144 24.14906779 0.3931129 0.066195848 17.30079095 -1.238065959 1.226342177 KLSVEEFFMDLHNFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLSVEEFFMDLHNFR 15 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 205.68 2.78E-09 185310000 561380 511800 223430 276760 445220 453730 508400 599500 106760 FALSE TRUE 487192.2106 508437.9521 331481.4953 339602.588 436360.9931 471185.2867 459095.4463 471301.5903 94138.95442 5.17524561 5.40093052 3.521193722 3.607460802 4.635286165 5.005210538 4.876785057 5.006445984 1 16.52250421 4.255251247 24.95915605 4.144157024 5.288088931 0.163997868 1.194907006 486.4315232 727396.4365 0.294016266 0.773232182 17999.11896 -4.255251247 1.143931907 KLSVPT(ph)S(ph)DEEDEVPAPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLSVPTSDEEDEVPAPKPR 19 2 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 2 KLS(0.037)VPT(0.969)S(0.994)DEEDEVPAPKPR 95.666 0.0026461 223530000 151160 101790 85612 93887 97751 99050 146960 152050 118140 TRUE FALSE 131183.823 101121.3348 127014.2496 115205.4783 95805.94635 102860.5176 132707.8418 119535.2908 104173.6238 1.259280596 0.970699983 1.219255364 1.105898731 0.919675661 0.987395022 1.273910199 1.147462154 1 16.66863052 4.771666669 23.07691629 1.090144908 1.259281508 0.194615377 0.113520995 10197.15816 7107679.839 0.028472895 3.895481897 59110.77709 -4.771666669 0.1691366 KLSVPTS(ph)DEEDEVPAPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KLSVPTSDEEDEVPAPKPR 19 2 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 KLSVPT(0.043)S(0.956)DEEDEVPAPKPR;KLSVPT(0.011)S(0.989)DEEDEVPAPKPR;KLSVPT(0.037)S(0.963)DEEDEVPAPKPR;KLS(0.002)VPT(0.106)S(0.892)DEEDEVPAPKPR 189.09 7.70E-15 4944080000 1875990 1806580 1205860 1397580 1777770 1073700 2164550 2658500 1529670 TRUE FALSE 1628073.168 1794712.457 1789017.929 1714921.9 1742395.855 1115005.934 1954632.274 2090000.463 1348834.155 1.207022496 1.330565696 1.326343882 1.271410494 1.291779162 0.826644202 1.449127209 1.549486611 1 20.36328154 KLT(ph)ATPTPLGGMTGFHMQTEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLTATPTPLGGMTGFHMQTEDR 22 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 KLT(0.697)AT(0.297)PT(0.006)PLGGMTGFHMQTEDR 195.21 6.84E-19 365200000 531880 394190 302720 335780 473490 386450 517530 627890 381070 TRUE FALSE 461590.7104 391600.5399 449116.4045 412023.9811 464068.4754 401316.9816 467340.0203 493620.6097 336020.3387 1.373698724 1.165407253 1.33657506 1.226187625 1.381072578 1.194323484 1.390808729 1.469020035 1 18.35818903 3.259833559 24.98887745 1.312938107 1.271970629 0 0.139459905 1355.187814 1591900.821 0.039213909 0.050576702 1819.003602 -3.259833559 -0.040967478 KLT(ph)SDEEGEPSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KLTSDEEGEPSGK 13 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 KLT(0.634)S(0.366)DEEGEPSGK;KLT(0.5)S(0.5)DEEGEPSGK;KLT(0.5)S(0.5)DEEGEPSGK 140.46 2.31E-05 999250000 1368532 1057228 988383 1115418 1121316 893142 1457572 1715351 1979672 TRUE FALSE 1187677.029 1050283 1466368.325 1368690.705 1099004.005 927501.7507 1316216.892 1348536.538 1745637.431 0.680368676 0.601661594 0.840018837 0.784063563 0.629571746 0.53132554 0.754003591 0.772518115 1 20.73532251 1.1698449 1.708122726 1.156880014 0.685880932 0.549464449 0.089143076 0.979008427 2.282919259 0.812359971 0.026319973 14.78580246 -1.1698449 -0.470999082 KLTATEGPGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KLTATEGPGSPR 12 1 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 KLTATEGPGS(1)PR;KLTATEGPGS(1)PR;KLTATEGPGS(1)PR;KLT(0.001)ATEGPGS(0.999)PR;KLTATEGPGS(1)PR 145.69 3.93E-05 2382120000 4188090 3714880 2082211 2816326 3559390 3269051 3736300 4242580 3627890 TRUE FALSE 3634623.295 3690476.709 3089175.204 3455815.863 3488565.103 3394813.507 3373954.201 3335337.283 3199004.977 1.136173067 1.153632687 0.96566752 1.080278364 1.090515685 1.061209198 1.054688638 1.042617097 1 21.60919181 4.271197481 24.99999989 1.04662528 1.144903066 0.571058487 0.036867904 140.4098569 107552.4875 0.009014119 0.023845451 18672.28559 -4.271197481 0.098277786 KLTATPTPLGGMTGFHMQTEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLTATPTPLGGMTGFHMQTEDR 22 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 233.28 1.34E-30 388710000 447770 371700 189990 241660 358230 308040 415000 407540 242190 FALSE TRUE 388596.06 369258.2782 281869.7995 296532.5965 351101.9239 319890.4981 374753.3639 320390.7425 213558.5741 1.819622844 1.729072596 1.319871144 1.388530513 1.644054449 1.497905198 1.754803643 1.50024762 1 17.7042723 1.251410852 4.190636647 0.949820858 1.581571677 0.576485935 0.158303921 0.163021426 5.323757709 0.304836847 0.041246848 17.84065736 -1.251410852 0.63175082 KLTELGTVDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLTELGTVDPK 11 1 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 107.14 0.0026574 0 1797200 1688200 1266400 1502200 1524000 1131600 2163800 2356000 2008500 FALSE TRUE 1559695.466 1677110.103 1878835.276 1843297.47 1493675.382 1175133.384 1953955.009 1852187.734 1771057.418 0.880657764 0.946954111 1.06085509 1.040789221 0.843380551 0.663520771 1.103270277 1.04580897 1 20.75617955 KLTFEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLTFEYR 7 1 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-4;A6PVN9;Q5T948;Q5T949;A6PVN6;A6PVN8;A6PVN7 Q15257 PPP2R4 Serine/threonine-protein phosphatase 2A activator 0 ; 117.04 0.0085324 1651240000 2948800 3724700 2040300 2489300 3543200 3233900 3583200 4085800 3068000 FALSE TRUE 2559108.609 3700232.2 3026995.904 3054533.612 3472697.252 3358310.226 3235701.816 3212083.466 2705304.535 0.945959531 1.367769193 1.118911333 1.129090486 1.28366223 1.241379735 1.196058253 1.187327868 1 21.36735958 1.238286287 6.699800701 0.995139948 1.191796011 0.209258545 0.111336599 0.169620756 38.65458309 0.151755366 0.024908554 17.3095703 -1.238286287 0.196656062 KLTGMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLTGMER 7 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 80.219 0.048916 425980000 508110 476250 333620 388060 460690 458320 521560 520780 508150 FALSE TRUE 440961.9761 473121.4824 494959.7479 476174.9541 451523.1703 475951.867 470979.1915 409415.2497 448077.0859 0.984120791 1.055893053 1.104630796 1.062707666 1.007690829 1.062209789 1.051111977 0.913716105 1 18.77338743 1.753809196 25 0.954656144 1.049162623 0.488478693 0.038241944 3.805451134 6248.975807 0.019930398 0.009570954 56.72953133 -1.753809196 0.094506479 KLTPQGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KLTPQGQR 8 1 P39019;A0A075B6E2 P39019 RPS19 40S ribosomal protein S19 0 ;;; 128.38 0.0018213 4166550000 3436720 4557640 2717780 3161430 3928380 3960700 4794750 4909450 4546780 FALSE TRUE 2982548.744 4527700.563 4032107.498 3879281.001 3850212.924 4113070.692 4329755.883 3859602.323 4009264.848 0.743914123 1.129309421 1.005697466 0.967579132 0.960328906 1.025891491 1.079937606 0.962670831 1 21.93490629 4.755027157 24.79186043 1.011885155 0.74391389 0.718182866 0.053581137 1646.440696 2478818.936 0.012968913 0.341589039 56888.85034 -4.755027157 -0.267971266 KLTS(ph)DEEGEPSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KLTSDEEGEPSGK 13 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 KLT(0.25)S(0.75)DEEGEPSGK;KLT(0.153)S(0.847)DEEGEPSGK;KLT(0.013)S(0.987)DEEGEPSGK;KLT(0.288)S(0.712)DEEGEPSGK 208.49 2.78E-08 1652470000 2601140 1964040 1698990 1942530 2026540 1401290 2529220 3076980 3419970 TRUE FALSE 2257392.759 1951138.092 2520627.247 2383611.126 1986215.819 1455198.533 2283936.634 2418991.772 3015665.043 0.748555535 0.647000932 0.835844569 0.790409774 0.658632769 0.482546474 0.757357532 0.802142061 1 21.52404476 1.31654632 1.960633352 1.063363791 0.699268703 0.491935482 0.096418498 0.610494256 2.66866976 0.388238569 0.0280128 20.72747116 -1.31654632 -0.364095089 KLTS(ph)DEEGEPSGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KLTSDEEGEPSGKR 14 2 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 KLT(0.027)S(0.973)DEEGEPSGKR;KLT(0.022)S(0.978)DEEGEPSGKR;KLT(0.025)S(0.975)DEEGEPSGKR 147.09 4.24E-06 1261560000 1197700 912330 666270 670210 910560 692760 1242130 1431540 461985 TRUE FALSE 1039420.91 906336.8442 988480.4005 822391.424 892441.6375 719410.9255 1121668.424 1125416.311 407369.6596 2.551542281 2.224851122 2.426494898 2.01878418 2.190741545 1.765990443 2.753441248 2.76264146 1 18.63597901 6.677154118 0.988857252 2.198910633 18.37090714 0.052018231 0.50886933 341.1120702 9.241261966 0.159081657 11758.47572 4755039.379 -6.677154118 16.17199651 KLTSDLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLTSDLGR 8 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 91.867 0.019535 466830000 660200 686410 391720 536570 728060 678010 736980 925320 600090 FALSE TRUE 572952.8973 681900.9275 581157.1022 658406.4195 713573.0304 704093.4834 665507.793 727447.5188 529148.0438 1.082783739 1.288677026 1.098288294 1.244276393 1.348531926 1.33061719 1.257696784 1.374752354 1 19.01331189 6.266243791 0.657216506 1.272006602 7.73E-12 0.12338048 0.117291667 39.89621937 2.68628208 0.048772358 59.12738665 1846051.409 -6.266243791 -1.272006602 KLVEESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLVEESR 7 1 Q15404 Q15404 RSU1 Ras suppressor protein 1 0 ; 122.52 0.006948 203410000 539890 497830 305490 361830 404460 458810 505930 571530 495000 FALSE TRUE 468542.1686 494559.722 453225.9858 443989.0317 396412.0373 476460.7176 456864.9865 449312.7572 436481.6639 1.073452123 1.13305956 1.038362028 1.017199732 0.908198603 1.09159389 1.04669915 1.029396637 1 18.73556152 4.098192861 5.295372555 1.018309939 1.102427662 0.357350258 0.047830211 0.222623822 9.734769757 0.012372034 0.02670776 12536.97791 -4.098192861 0.084117723 IILDLISES(ph)PIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 IILDLISESPIK 12 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 IILDLIS(0.001)ES(0.999)PIK;IILDLISES(1)PIK 166.38 5.46E-05 244783000 746210 656960 545860 704430 674510 486410 692480 917000 1661510 TRUE FALSE 647596.4578 652644.3865 809839.7218 864381.598 661088.5707 505122.5074 625323.3962 720906.6861 1465088.181 0.442018758 0.445464236 0.552758348 0.589986056 0.451227837 0.344772768 0.426816218 0.492056857 1 20.48255607 1.238443784 5.516095492 1.025801011 0.46669261 0.861970328 0.066969915 0.057440697 5.464969121 0.122022661 0.018356488 17.31584875 -1.238443784 -0.559108401 KLVIIEGDLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 ;;;;;; 158.58 4.76E-05 13404513000 12314149 11264261 6430879 8569399 10525949 9917608 11402755 13902601 8966033 FALSE TRUE 10686803.01 11190265.33 9540873.594 10515212.02 10316503.21 10299144.8 10296917.58 10929637.97 7906078.793 1.35171977 1.415400178 1.206776943 1.330016092 1.304882418 1.30268684 1.30240513 1.382434738 1 22.9145309 1.232257249 24.99810169 0.999999462 1.324249649 0.772327122 0.055376364 99.58487699 394898.5527 0.121255781 0.013301468 17.07093264 -1.232257249 0.324250187 KLVIIESDLER ddPTM_MDA-MB-175_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 ;;; 168.59 2.87E-05 2753360000 5664730 5731540 3556840 4318820 5133690 4912550 5517850 6452400 5228260 FALSE TRUE 4916121.578 5693889.136 5276939.721 5299474.09 5031539.613 5101538.977 4982729.756 5072604.473 4610181.059 1.066361931 1.235068442 1.144627435 1.149515393 1.091397398 1.106581046 1.080809993 1.100304827 1 22.13639198 -1.635635307 0.337544903 5.92E-10 1.159114641 0.449813846 0.045378407 54.25235388 1.078195614 37.33371998 0.064378452 0.023140071 1.635635307 1.159114641 KLVILEGELER ddPTM_MDA-MB-175_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 ;;; 170.18 2.57E-05 12924200000 7784100 8109800 4912290 6164500 7542710 7529280 8138000 9763700 6339760 FALSE TRUE 6755411.463 8056526.19 7287889.875 7564243.943 7392624.828 7818936.274 7348778.013 7675808.736 5590280.795 1.208420777 1.44116664 1.303671522 1.353106261 1.322406709 1.398666106 1.314563308 1.373063182 1 22.41448932 1.235575577 24.99998678 0.999999534 1.343614092 0.746762402 0.06206711 36.54246708 305990.4806 0.090455918 0.013240102 17.20186666 -1.235575577 0.343614558 KLVILEGELERAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLVILEGELERAEER 15 2 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ; 203.99 2.88E-09 132185000 274610 306600 60097 57282 237890 215393 318770 330490 10082.7 FALSE TRUE 238319.5927 304585.9244 89160.11021 70288.7536 233156.4544 223679.3081 287855.7345 259817.2854 8890.734692 26.80538797 34.25880256 10.02842997 7.905843109 26.2246555 25.15869788 32.37704694 29.22337629 1 13.11808693 7.999951428 0.020804842 6.87E-05 50.83372879 0.017577859 11.16124903 80350.59659 166.1576905 159648.4028 257657.4574 99988816.55 -7.999951428 50.83366012 KLVPLLLEDGGEAPAALEAALEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLVPLLLEDGGEAPAALEAALEEK 24 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 179.47 6.04E-17 69391000 194330 140680 104760 101980 144650 124530 181330 208720 126400 FALSE TRUE 168648.7981 139755.8638 155422.2864 125136.1177 141771.748 129320.7497 163744.6445 164086.8523 111457.136 1.513126967 1.253897856 1.394457923 1.122728631 1.271984487 1.160273396 1.469126611 1.472196919 1 16.76612946 4.744501442 23.56127675 1.289613252 1.513127193 0.193810499 0.151509343 557.9992879 2212873.383 0.037288627 0.318225431 55526.64609 -4.744501442 0.223513941 KLVWVPSDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLVWVPSDK 9 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ; 115.18 0.0032888 0 14357100 13040400 8862300 10971400 11965000 10427200 14996700 17246100 13026300 FALSE TRUE 12459772.86 12954736.75 13148137.92 13462624.06 11726919.91 10828341.13 13542322.34 13558155.72 11486345.65 1.084746466 1.127837969 1.144675454 1.172054582 1.020944368 0.942714198 1.178993106 1.180371559 1 23.45341655 5.114004056 15.46902031 1.103387294 0.001138386 0 0.082974008 14566332.55 18328644.53 0.021221654 556979794.4 130018.1722 -5.114004056 -1.102248907 KLWGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLWGDR 6 1 P13639 P13639 EEF2 Elongation factor 2 0 ; 110.36 0.046126 25055000000 36962000 35906000 21187700 28599000 32620000 33518000 36138000 42731000 35325000 FALSE TRUE 32077378.05 35670131.12 31434142.59 35092840.06 31970925.82 34807459.15 32633342.32 33593308.18 31148918.74 1.029807112 1.145148293 1.009156782 1.126615031 1.026389586 1.117453207 1.047655702 1.078474295 1 24.89267875 1.236267037 24.96997622 0.999999903 1.073626813 0.198722436 0.045764773 90.3076702 982939.3314 0.062315353 0.009586091 17.22927637 -1.236267037 0.07362691 KLYANMFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KLYANMFER 9 1 Q02790;H0YFG2 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 172.88 8.96E-05 2763500000 3379200 4335600 3082200 3586400 5094300 4607000 5226000 5543600 4440400 FALSE TRUE 2932630.158 4307119.158 4572762.229 4400746.935 4992933.397 4784234.271 4719183.324 4358144.28 3915460.971 0.748987202 1.100028628 1.167873276 1.123940953 1.275184055 1.221882764 1.205268897 1.11306033 1 21.90075074 4.74987244 2.92385902 1.161603319 0.671942329 0.751345872 0.073368694 0.216126503 2.60233113 0.019313424 0.252855093 56217.61793 -4.74987244 -0.48966099 KLYELIITR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KLYELIITR 9 1 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 126.19 0.00077022 206420000 543140 365760 265200 296200 338550 299660 400060 402220 398150 FALSE TRUE 471362.6729 363357.2985 393451.607 363456.7371 331813.5174 311188.1141 361262.2428 316208.3831 351081.1606 1.342603152 1.034966667 1.120685617 1.035249902 0.94511912 0.886370871 1.028999227 0.900670325 1 18.42144506 8 0.578112849 0.948649054 20.98788243 0.773491685 0.061726284 71.55967024 0.60837434 0.029350666 1797.08628 99999999.99 -8 20.03923338 KLYGDADYLEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KLYGDADYLEER 12 1 P17812;B4E1E0;P17812-2;A0A3B3IRI2 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ;;; 146.59 0.00010401 1260480000 1983460 1851260 1209700 1502780 1826830 1577260 1984900 2359140 1594420 FALSE TRUE 1721340.736 1839098.951 1794714.966 1844009.168 1790479.657 1637938.213 1792404.704 1854656.27 1405929.484 1.224343579 1.308101844 1.276532704 1.31159435 1.273520242 1.165021597 1.274889476 1.319167349 1 20.42309281 2.928890746 10.70970189 1.218045724 1.283212763 0.173391994 0.087399203 1.603789479 237.1878727 0.027893657 0.027912693 848.9668759 -2.928890746 0.065167038 KMAVDALEYDESAEDANPAGALEEILENPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KMAVDALEYDESAEDANPAGALEEILENPER 31 1 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 86.57 0.0010687 17315000 21889 20529 10463 13449 18179 16810 18502 22736 7774.2 FALSE TRUE 18996.31319 20394.14365 15522.9418 16502.80101 17817.27347 17456.69158 16707.67889 17874.08333 6855.142932 2.771103882 2.975013628 2.264422777 2.4073606 2.599110426 2.546510226 2.437247342 2.607397615 1 12.74297103 1.23769303 24.99996665 0.999998171 2.568246487 0.864858062 0.195767012 7.669499815 220870.356 0.28884914 0.049123813 17.28594113 -1.23769303 1.568248316 KMCLFAGFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KMCLFAGFQR 10 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 133.23 0.00032508 766670000 1385280 1562650 784710 963370 1431170 1379540 1504590 1579500 708010 FALSE TRUE 1202211.738 1552384.849 1164198.381 1182117.883 1402692.517 1432611.796 1358675.093 1241736.217 624309.8644 1.925665133 2.486561462 1.864776527 1.893479424 2.24678897 2.294712735 2.176283238 1.988974206 1 19.25190274 1.226762844 3.383845116 0.805808529 2.130453691 0.766085254 0.194074812 0.15861575 2.517453811 0.56092174 0.049005209 16.85632296 -1.226762844 1.324645162 KMDLIDLEDETIDAEVMNSLAVTMDDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KMDLIDLEDETIDAEVMNSLAVTMDDFR 28 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;; 146.89 8.85E-08 443257000 333049 211511 127385 176247 186522 183462 193208 272388 233966 FALSE TRUE 289035.7308 210121.5703 188988.8121 216266.5751 182810.5771 190519.9019 174470.7179 214139.9459 206306.806 1.400999494 1.018490734 0.916057089 1.048276493 0.886110258 0.92347851 0.845685711 1.037968403 1 17.65443189 4.73485552 3.299536356 0.953493308 1.460450451 0.827556809 0.06402481 0.126230219 2.255229632 0.016032887 0.162382468 54306.96344 -4.73485552 0.506957144 KMEEEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KMEEEQR 7 1 Q9BQ61;K7EN60;K7ELS0;K7ERU7 Q9BQ61 C19orf43 Uncharacterized protein C19orf43 0 ;; 101.54 0.014404 544910000 789690 629060 435700 534560 509100 557220 691030 767100 766470 FALSE TRUE 685330.4657 624927.6634 646405.9773 655940.0182 498969.906 578656.614 624014.017 603061.6346 675858.7898 1.014014282 0.924642356 0.956421648 0.970528205 0.738275382 0.856179756 0.923290525 0.892289401 1 19.36636232 KMEENEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KMEENEK 7 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 93.551 0.040698 0 149180 119810 110700 113810 73195 79151 148670 187680 193120 FALSE TRUE 129465.485 119022.9602 164234.8903 139652.3 71738.5627 82195.99019 134252.0063 147546.0925 170289.5736 0.760266658 0.698944496 0.96444478 0.820087202 0.421273958 0.482683634 0.788374787 0.866442316 1 17.37763058 -0.454857593 7.175078502 6.210191393 0.753990431 0 0.185707449 25738260.27 3587175.038 0 0.04607741 0.350866906 0.454857593 -5.456200961 KMEIYRPHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KMEIYRPHK 9 2 Q92769;Q92769-3;H3BM24;E5RFI6;E5RJ04;E5RGV4;E5RHE7;E5RH52;E5RG37;E5RFP9;E5RK19;Q13547;Q5TEE2 Q92769;Q13547 HDAC2;HDAC1 Histone deacetylase 2;Histone deacetylase 1 0 ; 145.89 5.77E-05 1024860000 2597300 1980260 1396530 1913510 2022800 1625110 2447300 2676700 2503000 FALSE TRUE 2254060.224 1967251.542 2071896.579 2348001.692 1982550.238 1687629.033 2209961.223 2104308.535 2207098.191 1.021277727 0.891329416 0.938742366 1.063841066 0.898261004 0.764637042 1.001297193 0.953427692 1 21.07371938 KMENCLGESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KMENCLGESR 10 1 Q9UHB6;Q9UHB6-4;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 66.262 0.069783 89259000 167010 148260 97751 117080 141160 132390 160320 185600 133320 FALSE TRUE 144939.2054 147286.0703 145023.7106 143664.8035 138351.1922 137483.129 144772.1911 145910.8843 117559.0615 1.232905431 1.252868715 1.233624263 1.222064906 1.176865402 1.169481342 1.231484747 1.241170885 1 16.84302622 1.235235586 24.99988276 0.999999695 1.220165169 0.870040472 0.026728457 35.67923955 268216.7452 0.051213581 0.007292653 17.1884053 -1.235235586 0.220165475 KMIDQVFGVLES(ph)PELSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KMIDQVFGVLESPELSR 17 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 KMIDQVFGVLES(0.999)PELS(0.001)R 86.856 0.0028705 194730000 389590 343290 184250 188330 311320 265780 298420 390910 79098 TRUE FALSE 338104.6944 341034.9054 273353.9163 231093.2049 305125.3411 276004.7286 269479.2743 307316.9386 69747.12455 4.847578973 4.889590898 3.919214133 3.31330082 4.37473721 3.957220177 3.863661421 4.406159258 1 16.08984612 1.236016113 24.99472848 0.999995806 4.17416211 0.818800885 0.47245672 29.91008264 293744.9588 0.797105636 0.120424967 17.21932458 -1.236016113 3.174166304 KMLGEDS(ph)DEEEEMDTSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KMLGEDSDEEEEMDTSER 18 1 A0A087X0M4;A0A087WWF4;Q9BWU0;H7C256 A0A087X0M4 SLC4A1AP Kanadaptin 1 KMLGEDS(1)DEEEEMDTSER;KMLGEDS(1)DEEEEMDTSER;KMLGEDS(1)DEEEEMDTSER 213.81 2.54E-17 527180000 701566 672130 449520 444740 634739 541579 726261 835760 533279 TRUE FALSE 608852.2756 667714.7338 666909.3756 545725.0144 622108.9357 562413.8946 655828.32 657039.2279 470235.3641 1.294781979 1.419958567 1.418245896 1.160535885 1.322973522 1.196026368 1.394680983 1.397256093 1 18.84302352 3.767505815 24.74042841 1.271607481 1.3818918 0.185147067 0.122815125 1249.433466 1067928.113 0.032346939 0.056013773 5854.715748 -3.767505815 0.110284318 KMPFTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KMPFTEK 7 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 114.89 0.0093038 3589200000 3832700 2966300 1923870 2443100 2625500 2126600 3404500 3932100 3181400 FALSE TRUE 3326198.984 2946814.18 2854259.967 2997843.195 2573257.687 2208411.678 3074332.114 3091251.015 2805298.516 1.185684506 1.050445848 1.017453205 1.068636075 0.917284799 0.787228762 1.09590195 1.101933002 1 21.41972287 5.118598929 1.256857081 1.002045409 1.446154015 0.293085483 0.092161266 5.110555236 3.689947767 0.029432579 3.68745271 131401.0784 -5.118598929 0.444108606 KMPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KMPKPR 6 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 94.95 0.024691 2167000000 670390 549400 329370 397380 563710 530770 702370 856140 497870 FALSE TRUE 581796.2629 545790.9552 488654.4337 487611.2026 552493.2739 551189.0654 634254.2655 673061.1235 439012.3758 1.325238866 1.243224532 1.113076671 1.110700357 1.258491342 1.255520563 1.444729808 1.533125626 1 18.74390208 2.424346827 4.44850059 1.373636985 1.205124992 0.079319113 0.151515358 0.334672492 14.01856127 0.058325021 0.045126939 265.6726371 -2.424346827 -0.168511994 KMPLDLS(ph)PLATPIIR ddPTM_MDA-MB-175_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(0.999)PLAT(0.001)PIIR;KMPLDLS(1)PLATPIIR 96.391 0.002277 730110000 2626420 1612480 1657960 1112710 1208930 1204450 2319370 2373300 999540 TRUE FALSE 2279331.942 1601887.513 2459755.002 1365367.812 1184874.658 1250785.971 2094437.854 1865788.264 881375.5199 2.586107614 1.817485824 2.790813843 1.549132897 1.344347139 1.419129466 2.376328599 2.116905022 1 19.7493973 3.721243992 24.95387979 1.709906708 2.340070805 0.37204228 0.45881071 1018.873642 1468233.776 0.131356419 0.195367909 5263.128729 -3.721243992 0.630164097 KMQQNIQELEEQLEEEESAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 KMQQNIQELEEQLEEEESAR 20 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;; 293.44 2.52E-54 2066314000 3100939 3058290 1728811 1878184 2715803 2590561 3175895 3532559 1393499 FALSE TRUE 2691142.054 3038199.892 2564869.782 2304654.383 2661763.834 2690221.558 2867897.192 2777148.748 1228761.136 2.190126279 2.472571604 2.087362391 1.87559186 2.166217466 2.189377154 2.333974528 2.26012092 1 20.22877306 1.236826201 24.99806626 0.999998504 2.200259132 0.855456797 0.154614899 17.18645262 247632.4962 0.250521129 0.040153613 17.25147373 -1.236826201 1.200260629 KMS(ph)DDEDDDEEEYGKEEHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KMSDDEDDDEEEYGKEEHEK 20 2 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 1 KMS(1)DDEDDDEEEYGKEEHEK;KMS(1)DDEDDDEEEYGKEEHEK 209.16 2.59E-22 892580000 506280 288905 396670 293744 269905 231703 442180 473940 559820 TRUE FALSE 439373.8152 287007.164 588500.9388 360443.0648 264534.4186 240616.7643 399297.4517 372591.6192 493638.7173 0.890071625 0.581411372 1.19216933 0.730175839 0.535886691 0.487434952 0.808886008 0.754786053 1 18.91309603 5.067213326 19.43664942 0.758520378 3.554211955 0.035018442 0.211906306 939.0354611 300210.5521 0.050258938 11817.4524 116738.2896 -5.067213326 2.795691577 KMS(ph)GGSTMSSGGGNTNNSNSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 KMSGGSTMSSGGGNTNNSNSK 21 1 Q86U70-2;Q86U70;A0A6E1WJ75;Q86U70-3 Q86U70-2 LDB1 LIM domain-binding protein 1 1 KMS(0.736)GGS(0.12)T(0.12)MS(0.02)S(0.004)GGGNTNNSNSK;KMS(0.431)GGS(0.248)T(0.248)MS(0.059)S(0.014)GGGNTNNSNSK;KMS(0.941)GGS(0.025)T(0.03)MS(0.004)S(0.001)GGGNTNNSNSK;KMS(0.691)GGS(0.051)T(0.051)MS(0.08)S(0.127)GGGNTNNSNSK;KMS(0.998)GGS(0.002)TMSSGGGNTNNSNSK;KMS(0.997)GGS(0.002)T(0.001)MSSGGGNTNNSNSK;KMS(0.955)GGS(0.035)T(0.01)MSSGGGNTNNSNSK;KMS(0.82)GGS(0.047)T(0.133)MSSGGGNTNNSNSK 261.5 7.39E-37 2309140000 2028011 1631935 1227449 1469154 1661218 1266901 2098599 2517003 2107542 TRUE FALSE 1760004.208 1621214.712 1821047.442 1802747.87 1628163.012 1315639.501 1895077.192 1978761.496 1858390.786 0.947058187 0.872375565 0.979905548 0.97005855 0.876114445 0.707945558 1.019740954 1.064771474 1 20.82562248 2.03279406 24.99898324 1.038585756 0.895271379 0.407938382 0.077168401 175.9884468 134155.643 0.032471032 0.021891826 107.8435212 -2.03279406 -0.143314377 KMS(ph)QPGS(ph)PSPK ddPTM_MDA-MB-175_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(0.973)QPGS(0.966)PS(0.061)PK 76.759 0.022673 35576000 153600 85754 64124 58100 59154 36640 73094 77872 96944 TRUE FALSE 133301.3708 85190.67633 95134.58088 71292.493 57976.95113 38049.56451 66005.35513 61219.6788 85483.39076 1.559383287 0.996575774 1.112901349 0.833992339 0.678224748 0.445110614 0.772142454 0.716158756 1 16.38335651 5.263259802 0.739774221 0.717389473 2.772300328 0.717339298 0.159500255 3.057811928 0.745516779 0.064357131 6.225168187 183341.087 -5.263259802 2.054910854 KMSGGST(ph)MSSGGGNTNNSNSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KMSGGSTMSSGGGNTNNSNSK 21 1 Q86U70-2;Q86U70;A0A6E1WJ75;Q86U70-3 Q86U70-2 LDB1 LIM domain-binding protein 1 1 KMS(0.29)GGS(0.167)T(0.401)MS(0.109)S(0.033)GGGNTNNSNSK 50.539 0.065519 180300000 156840 136560 100120 109870 118570 105440 167520 183210 161150 TRUE FALSE 136113.1966 135662.9284 148538.3669 134817.6628 116210.689 109496.345 151273.9362 144031.9672 142099.0306 0.957875617 0.954706924 1.045315836 0.948758498 0.817814791 0.770563631 1.064566982 1.013602743 1 17.11653719 KMTPSYEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KMTPSYEIR 9 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 152.54 0.00012864 1271460000 1804250 2208300 1255230 1465440 2196800 2057840 2258300 2385700 1689050 FALSE TRUE 1565813.791 2193793.532 1862263.426 1798190.55 2153087.978 2137006.436 2039290.414 1875536.621 1489372.433 1.051324542 1.472965044 1.250367863 1.207347813 1.445634369 1.434836841 1.369227984 1.259279801 1 20.50627313 1.251962148 3.02653258 0.944690617 1.326606881 0.379212883 0.126988377 0.375672207 4.412859204 0.344307306 0.031408221 17.86331874 -1.251962148 0.381916263 KMVDQLFCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KMVDQLFCK 9 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 85.377 0.025338 0 514930 452340 313950 362140 467870 431490 541750 554610 404290 FALSE TRUE 446880.6958 449368.5488 465777.2701 444369.422 458560.3024 448089.6995 489211.1684 436010.9675 356495.2968 1.253538826 1.260517468 1.306545344 1.246494487 1.286301128 1.256930186 1.372279446 1.223048302 1 18.44352352 1.269256593 3.588401824 0.971171716 1.281800619 0.852365383 0.036822842 0.087789032 1.712496204 0.070372114 0.008897892 18.58902419 -1.269256593 0.310628902 KNDDGWYEGVCNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KNDDGWYEGVCNR 13 1 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7;Q8IZP0-11 A0A0A0MRT6 ABI1 Abl interactor 1 0 102.5 0.0027004 255950000 198700 169980 99918 133090 156130 137120 170950 195080 164770 FALSE TRUE 172441.2916 168863.3902 148238.679 163310.1187 153023.3185 142395.0951 154371.2953 153363.6601 145291.0783 1.186867725 1.162241978 1.020287555 1.124020281 1.05321896 0.980067715 1.062496728 1.055561442 1 17.14858659 5.28014476 0.62664592 1.03309624 1.442316397 0.620077718 0.041635912 4.281049067 0.797041053 0.019648059 1.459565451 190609.5954 -5.28014476 0.409220156 KNDFEQGELYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KNDFEQGELYLR 12 1 P83111;P83111-2 P83111 LACTB "Serine beta-lactamase-like protein LACTB, mitochondrial" 0 103.11 0.0036584 126080000 95751 100820 77326 76017 100630 123500 93217 123670 116030 FALSE TRUE 83097.26275 100157.7068 114721.1122 93277.8217 98627.65988 128251.1249 84176.82969 97224.1329 102313.0656 0.812186227 0.97893369 1.12127529 0.911690224 0.963979129 1.253516588 0.822737831 0.950261165 1 16.64263087 6.037010932 14.13147724 0.980081011 0.656917114 0 0.130755178 0 0 0.02828025 0 1088957.505 -6.037010932 -0.323163897 KNDIYGED ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KNDIYGED 8 1 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 72.547 0.044009 0 673590 586230 388250 440110 518780 483230 587220 681880 690050 FALSE TRUE 584573.3748 582379.0165 576008.9986 540043.7022 508457.293 501820.1708 530271.4948 536065.2684 608473.0751 0.960721844 0.957115508 0.946646651 0.887539193 0.835628253 0.824720421 0.87147898 0.881000804 1 19.2148339 3.745744691 3.781670895 0.877313993 0.957049019 0.340774617 0.046718819 0.252340601 8.178745442 0.013372235 0.022748381 5568.582921 -3.745744691 0.079735026 KNEGSCGPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KNEGSCGPAR 10 1 Q9NQZ5 Q9NQZ5 STARD7 "StAR-related lipid transfer protein 7, mitochondrial" 0 72.152 0.078316 23271000 25253 23375 18373 20893 22169 20601 27648 28314 25902 FALSE TRUE 21915.75207 23221.44809 27258.24425 25637.07498 21727.88027 21393.5338 24966.70122 22259.27144 22839.89507 0.959538212 1.01670555 1.193448752 1.122469035 0.951312614 0.936673909 1.093118035 0.974578533 1 14.4792684 3.237657927 24.99999938 0.993992329 1.077617067 0.233864944 0.073354069 38.10833284 1055421.69 0.022778986 0.02733439 1728.454404 -3.237657927 0.083624738 KNEGYMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KNEGYMR 7 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 ; 93.429 0.023958 388650000 493950 538570 332610 368960 471620 475520 554730 608230 543770 FALSE TRUE 428673.256 535032.0982 493461.3085 452738.0072 462235.6847 493813.5621 500932.37 478164.7478 479486.1301 0.894026394 1.115844786 1.029146158 0.944215023 0.964023057 1.029880806 1.04472755 0.99724417 1 18.87112956 2.682150796 24.98577741 1.017234952 0.996164831 0.048190114 0.058866738 1343.402878 595035.9183 0.020146885 0.017767902 481.0063345 -2.682150796 -0.02107012 KNELEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KNELEQK 7 1 O00487 O00487 PSMD14 26S proteasome non-ATPase regulatory subunit 14 0 90.709 0.027161 340470000 702870 613420 440930 557430 582630 521250 851720 939480 865540 FALSE TRUE 609983.9487 609390.4036 654165.2228 684003.0013 571036.8029 541302.8248 769120.3255 738579.513 763216.8472 0.799227573 0.798449885 0.857115806 0.896210564 0.748197324 0.709238569 1.007734995 0.96771909 1 19.54173349 2.223042328 24.99861001 0.987460685 0.805695123 0.747025064 0.052174244 128.7339334 207377.5603 0.022739508 0.015392062 167.1253493 -2.223042328 -0.181765562 KNFEWVAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KNFEWVAER 9 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 167.12 9.66E-05 2171700000 3489700 3225200 2081740 2689300 3060200 2806400 3468200 3627400 3537800 FALSE TRUE 3028527.303 3204013.449 3088476.427 3299946.668 2999308.007 2914364.024 3131854.498 2851708.738 3119565.314 0.970817084 1.027070481 0.990034225 1.057822593 0.961450621 0.934221191 1.00393939 0.914136571 1 21.57291358 3.098870312 11.76237997 0.957994148 1.0109989 0.322144204 0.0347517 0.463190381 51.90212533 0.009709664 0.011012446 1255.654946 -3.098870312 0.053004752 KNGFVVLK ddPTM_MDA-MB-175_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 ; 125.96 0.0045589 0 1850190 1489180 970300 1259250 1567780 1367330 1711940 2112400 1836160 FALSE TRUE 1605682.704 1479397.479 1439540.325 1545181.959 1536584.245 1419932.07 1545916.322 1660679.699 1619091.257 0.99171847 0.913720874 0.889103884 0.95435137 0.949041161 0.876993229 0.954804935 1.025686287 1 20.62675287 1.888699698 4.489692254 1.011840143 0.927806489 0.511375029 0.033249697 0.166482661 5.18420139 0.017658995 0.008749621 77.39264652 -1.888699698 -0.084033655 KNGIPLELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KNGIPLELR 9 1 Q6ICJ4;A0A087WY67;P0CG30;P0CG29 Q6ICJ4 Em:AP000351.3;GSTT2;GSTT2B Glutathione S-transferase theta-2B;Glutathione S-transferase theta-2 0 74.841 0.064057 474060000 1428700 1784300 881850 1227100 1775400 1716100 1529500 1666000 1565400 FALSE TRUE 1239893.675 1772578.816 1308315.61 1505731.81 1740073.014 1782119.477 1381169.325 1309738.865 1380340.195 0.898252242 1.284160834 0.947821134 1.090841095 1.26061171 1.291072653 1.000600671 0.948852224 1 20.39659244 2.026870296 24.75083175 0.971958752 1.133057859 0.214460613 0.131917301 261.9843552 241318.5228 0.052656961 0.035500308 106.3825255 -2.026870296 0.161099107 KNGSTAVAESVAS(ph)PQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KNGSTAVAESVASPQK 16 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 KNGSTAVAESVAS(1)PQK;KNGSTAVAES(0.001)VAS(0.999)PQK;KNGSTAVAESVAS(1)PQK;KNGSTAVAESVAS(1)PQK 190.37 5.31E-10 2537150000 3210650 2499760 1993900 2370870 2833440 2033840 3531930 4242590 3605490 TRUE FALSE 2786354.468 2483338.912 2958156.709 2909212.27 2777060.088 2112083.141 3189403.972 3335345.144 3179253.08 0.87641795 0.781107653 0.930456505 0.915061556 0.873494503 0.664333127 1.003192855 1.049097087 1 21.60025643 2.032524105 24.98383467 1.027482436 0.84542741 0.547831532 0.075998307 131.9502429 101358.8459 0.030900174 0.020832755 107.7765071 -2.032524105 -0.182055026 KNHLEGK ddPTM_MDA-MB-175_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 1729600000 3956200 3037010 2254010 2717580 2242530 2632810 3786500 4511000 4276400 FALSE TRUE 3433378.146 3017059.681 3344056.775 3334648.075 2197908.04 2734095.904 3419285.813 3546357.755 3770848.864 0.910505372 0.80010093 0.886818034 0.884322919 0.58286824 0.725061121 0.906768194 0.940466691 1 21.8464579 2.058839703 5.229830481 0.954743976 0.796753594 0.366761833 0.095469911 0.225945707 12.64643006 0.043657282 0.028381426 114.5090212 -2.058839703 -0.157990382 KNHTVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KNHTVIR 7 1 Q9NZP2 Q9NZP2 OR6C2 Olfactory receptor 6C2 0 70.912 0.089376 358820000 204750 299520 182620 156310 297530 481310 135670 172520 184920 FALSE TRUE 177691.7687 297552.4334 270935.6428 191802.5745 291609.7351 499826.3071 122512.7443 135627.9406 163058.9683 1.089739317 1.824814891 1.66158075 1.176277371 1.788369804 3.06531013 0.751340117 0.831772346 1 17.31503427 KNIIEATHMYDNAAEACSTTEEVFNS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KNIIEATHMYDNAAEACSTTEEVFNSPR 28 1 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 KNIIEATHMYDNAAEACSTTEEVFNS(1)PR;KNIIEATHMYDNAAEACSTTEEVFNS(1)PR;KNIIEATHMYDNAAEACSTT(0.001)EEVFNS(0.998)PR 171.5 1.48E-12 605431000 433952 339150 234739 230221 300718 306721 326103 331014 305477 TRUE FALSE 376604.1437 336922.1013 348259.5656 282496.1968 294734.3001 318520.7553 294477.5813 260229.2321 269363.8571 1.398124261 1.250806641 1.292896417 1.048753162 1.094186515 1.182492554 1.093233459 0.966088156 1 18.03919676 8 0.22090717 0.936359292 3.398006582 0.779668431 0.063759025 44.42792965 0.684035082 0.319961868 37.80525126 100000000 -8 2.461647289 KNITEYCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KNITEYCR 8 1 P46063 P46063 RECQL ATP-dependent DNA helicase Q1 0 76.064 0.058957 262810000 217890 269800 135230 212580 266980 280330 249010 328680 258620 FALSE TRUE 189095.2844 268027.666 200627.6803 260849.5381 261667.6203 291114.4765 224861.0485 258394.3398 228046.2382 0.829197122 1.175321584 0.87976755 1.143844951 1.147432303 1.276558994 0.986032702 1.13307872 1 17.79896685 4.750048977 24.28426904 1.093295626 0.829196887 0.352956959 0.1121438 1340.196807 2832847.255 0.026212203 0.396832227 56240.47461 -4.750048977 -0.264098739 KNLEELFQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KNLEELFQVK 10 1 Q0VF96 Q0VF96 CGNL1 Cingulin-like protein 1 0 91.03 0.015644 0 1071500 910410 642460 756130 847450 685440 1191600 1237500 1043900 FALSE TRUE 929898.5602 904429.4568 953155.8049 927820.8732 830587.403 711809.3203 1076038.815 972870.2552 920491.3312 1.010219791 0.98255076 1.035485911 1.007962641 0.9023305 0.773292802 1.168983106 1.056903224 1 19.81204461 2.203308053 24.99989291 1.07536727 0.957447531 0.321564179 0.084190894 231.3182575 164041.2761 0.035880327 0.024191523 159.7011533 -2.203308053 -0.11791974 KNLTQDEMQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KNLTQDEMQR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 158.02 1.31E-05 258740000 411350 382150 236764 273991 385870 367030 408950 440710 363080 FALSE TRUE 356989.0553 379639.6315 351263.8623 336204.8442 378191.9419 381149.8816 369290.0919 346467.5961 320157.096 1.115043395 1.185791714 1.097160946 1.050124606 1.181269904 1.190508929 1.153465272 1.082179969 1 18.28842046 1.391140529 2.59264801 0.990925996 1.139067161 0.512870328 0.043752008 0.320449391 3.144192805 0.090815947 0.012257061 24.61163859 -1.391140529 0.148141165 KNNIDTHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KNNIDTHAR 9 1 O43847;O43847-2;F5H7V1;G3V1R5 O43847 NRD1 Nardilysin 0 ; 113.22 0.0011917 119747000 424030 393740 236962 295300 358450 381520 427460 472550 348650 FALSE TRUE 367993.3611 391153.496 351557.6158 362352.3784 351317.5463 396197.3213 386004.995 371498.8599 307432.9942 1.196987207 1.272321135 1.143525979 1.17863855 1.142745095 1.288727394 1.255574393 1.208389688 1 18.22991248 1.239308729 8.24276475 0.997746629 1.212116934 0.639795465 0.049722698 0.058542156 39.58883922 0.070906844 0.012486661 17.35036953 -1.239308729 0.214370305 KNPDDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KNPDDFK 7 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 90.709 0.027161 300680000 506080 451850 360100 377540 358990 335410 601010 631200 576040 FALSE TRUE 439200.2458 448881.7676 534245.5645 463266.2273 351846.8014 348313.4397 542724.1427 496222.792 507941.2074 0.864667484 0.883727804 1.051786224 0.912046947 0.692691981 0.68573574 1.06847827 0.976929583 1 18.95430199 2.207403672 24.9998949 1.009398917 0.855100785 0.349992581 0.106736065 265.8712888 213329.5635 0.048204215 0.032502887 161.214341 -2.207403672 -0.154298132 KNPDSQYGELIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KNPDSQYGELIEK 13 1 P30085;P30085-3;Q5T0D2 P30085 CMPK1 UMP-CMP kinase 0 ; 158.89 7.45E-05 1100860000 2314600 1562140 1158720 1351220 1407100 1190280 1947300 2295100 1944870 FALSE TRUE 2008719.746 1551878.199 1719080.868 1658035.153 1379101.463 1236070.842 1758451.146 1804310.725 1714949.684 1.171299522 0.904911796 1.002408924 0.966812711 0.804164388 0.720762162 1.025366028 1.052107092 1 20.70973482 4.744162176 23.99932964 0.940377006 1.171299698 0.340761452 0.103199266 481.3513795 2062191.136 0.028050162 0.234694556 55483.28621 -4.744162176 0.230922691 KNPEVPVNFAEFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KNPEVPVNFAEFSK 14 1 O15347;E7ES08;E7EQU1;E9PES6 O15347 HMGB3 High mobility group protein B3 0 ; 143.02 1.48E-05 2110860000 2382100 2187600 1493200 1808480 2057000 1434610 2590500 2729200 2694000 FALSE TRUE 2067299.45 2173229.512 2215316.514 2219123.025 2016069.724 1489800.375 2339273.709 2145581.819 2375518.389 0.870251924 0.914844323 0.932561299 0.93416369 0.848686221 0.627147482 0.984742412 0.903205729 1 21.17981094 KNPFGLVPVLENSQGQLIYESAITCEYLDEAYPGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KNPFGLVPVLENSQGQLIYESAITCEYLDEAYPGKK 36 2 Q5TA02;P78417-3;P78417;Q5TA01;P78417-2 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 ; 317.58 4.87E-110 619240000 674870 542560 434080 451660 463640 355810 759190 893050 454060 FALSE TRUE 585684.2196 538995.8876 644002.5399 554216.3062 454414.4711 369498.2409 685563.8707 702078.2072 400381.5441 1.462815228 1.346205627 1.608472092 1.384220413 1.134953591 0.922865318 1.712276404 1.753522902 1 18.61101595 3.500585742 24.13747805 1.362050723 1.465948086 0.05046088 0.276105317 2568.735397 2642402.087 0.084664822 0.124593451 3166.54557 -3.500585742 0.103897363 KNPGVGNGDDEAAELMQQVNVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KNPGVGNGDDEAAELMQQVNVLK 23 1 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 221.48 2.83E-32 225580000 312720 274690 232530 242910 249170 208290 335230 430950 341460 FALSE TRUE 271393.2597 272885.5433 344982.2858 298066.4281 244212.0045 216303.0511 302719.4462 338794.6962 301092.9878 0.90136028 0.906316501 1.14576659 0.98994809 0.811084995 0.718392855 1.005401848 1.125216162 1 18.19984958 2.005637997 24.9994135 1.069679196 0.91647995 0.238414796 0.113816602 208.3264106 923734.0925 0.050651597 0.03402978 101.3066599 -2.005637997 -0.153199246 KNQDDDDDDDDGFFGPALPPGFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KNQDDDDDDDDGFFGPALPPGFK 23 1 A0A0A0MRI1;Q8IXQ4;Q8IXQ4-4 A0A0A0MRI1 GPALPP1 GPALPP motifs-containing protein 1 0 112.45 0.0013818 64491000 98060 61242 54694 61596 62036 38980 86294 108310 88020 FALSE TRUE 85101.12255 60839.69727 81144.20134 75582.31324 60801.60497 40479.58582 77925.22116 85148.74937 77614.37587 1.096460824 0.7838715 1.045479016 0.973818476 0.783380711 0.521547527 1.004004996 1.097074458 1 16.24403628 2.01794354 24.99997551 1.053991879 0.863574029 0.194378253 0.161250786 354.5883753 494030.8849 0.067539765 0.045526389 104.2181933 -2.01794354 -0.19041785 KNQELEVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KNQELEVVR 9 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 ; 124.67 0.00083888 311470000 532550 571350 364720 423980 602960 589970 622410 706040 698630 FALSE TRUE 462172.1682 567596.7642 541099.8119 520251.1391 590962.2757 612666.5277 562048.774 555058.8404 616038.7573 0.750232291 0.921365348 0.878353522 0.844510403 0.959293987 0.994525946 0.912359437 0.901012856 1 19.23266159 6.069554104 0.642969105 0.939063329 6.85E-20 0.566732959 0.04837824 13.70428877 1.151732459 0.021991761 13.86188004 1173691.892 -6.069554104 -0.939063329 KNREELDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KNREELDK 8 2 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;; 172.59 0.00015898 9566400000 13971500 10261300 9689100 10904200 8424600 7685220 14699600 16861600 10818800 FALSE TRUE 12125130.88 10193892.84 14374781.17 13380165.27 8256966.942 7980875.386 13274035.05 13255878.06 9539813.789 1.271002888 1.068563084 1.50681989 1.402560424 0.865527056 0.836586076 1.391435446 1.38953216 1 23.18552968 KNREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KNREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR 39 3 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 284.48 1.72E-77 1965702000 1085116 834672 591782 571898 712276 679467 1164319 1284780 246389.3 FALSE TRUE 941715.1713 829188.9847 877969.7546 701756.1818 698103.1011 705606.5352 1051403.523 1010039.795 217261.4376 4.334479149 3.816549286 4.041074956 3.230008001 3.213193785 3.247730213 4.839347166 4.648960286 1 17.7290726 4.5568512 1.408106219 3.597309945 4.435340063 0.059946075 1.05161375 3.563687542 8.308288594 0.30788641 3.853463068 36045.51207 -4.5568512 0.838030118 KNS(ph)FGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KNSFGYR 7 1 Q92615;H0Y4V9 Q92615 LARP4B La-related protein 4B 1 KNS(1)FGYR;KNS(1)FGYR;KNS(1)FGYR;KNS(1)FGYR;KNS(1)FGYR 123.11 0.0026187 5833070000 9203560 7333790 5724570 7287400 7342630 6502930 10438230 9730500 10598520 TRUE FALSE 7987286.227 7285613.851 8492991.2 8942115.551 7196526.029 6753101.925 9425932.061 7649708.298 9345575.039 0.854659686 0.779578979 0.908771388 0.956828821 0.770046359 0.722598866 1.008598403 0.818538 1 23.15585201 -0.29556492 1.39010719 9.999999989 0.849563105 0.202269811 0.088276341 153.627749 5.748248299 4282.508182 0.025193444 0.506331655 0.29556492 -9.150436885 KNS(ph)LISSLEEEVSILNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 KNSLISSLEEEVSILNR 17 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 KNS(0.996)LIS(0.003)SLEEEVSILNR;KNS(0.964)LIS(0.026)S(0.005)LEEEVS(0.004)ILNR;KNS(1)LISSLEEEVSILNR;KNS(1)LISSLEEEVSILNR;KNS(0.999)LIS(0.001)SLEEEVSILNR;KNS(1)LISSLEEEVSILNR;KNS(1)LISSLEEEVSILNR;KNS(0.984)LIS(0.016)SLEEEVSILNR;KNS(0.996)LIS(0.004)S(0.001)LEEEVSILNR 323.79 4.29E-59 2719358200 1780999 1420291 1202753.2 1310715.5 1436012 1269224 1909993 2076150 1722636 TRUE FALSE 1545635.47 1410961.015 1784408.67 1608333.487 1407438.171 1318051.869 1724762.173 1632181.479 1518987.935 1.017542954 0.928882306 1.17473525 1.058819133 0.926563101 0.867717142 1.135467987 1.074519054 1 20.53467898 2.168703767 25 1.073665553 1.000516781 0.13179012 0.089147163 107.1717938 38351.80013 0.038122282 0.025702044 147.4700293 -2.168703767 -0.073148772 KNS(ph)STDQGS(ph)DEEGSLQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KNSSTDQGSDEEGSLQK 17 1 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 2 KNS(0.99)S(0.007)T(0.003)DQGS(1)DEEGSLQK;KNS(0.751)S(0.087)T(0.162)DQGS(1)DEEGSLQK 144.58 1.77E-06 652000000 860480 468320 580810 562640 641860 569510 898170 959430 1259460 TRUE FALSE 746765.3878 465243.5751 861691.6587 690396.0114 629088.2418 591419.4182 811065.6116 754263.3608 1110568.074 0.672417482 0.41892396 0.775901702 0.621660237 0.566456264 0.532537746 0.730315981 0.679168958 1 20.0828664 -0.304718365 1.040673378 9.999999998 0.602741878 0.596908642 0.098974366 27.08044959 1.533676949 545.0913791 0.030098326 0.495771589 0.304718365 -9.39725812 KNS(ph)TGSGHSAQELPTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KNSTGSGHSAQELPTIR 17 1 O94763-3;O94763;O94763-2;O94763-4;I3L280 O94763-3 URI1 Unconventional prefoldin RPB5 interactor 1 1 KNS(0.594)T(0.34)GS(0.065)GHSAQELPTIR;KNS(0.986)T(0.012)GS(0.002)GHSAQELPTIR;KNS(0.913)T(0.043)GS(0.043)GHSAQELPTIR 207.43 2.86E-12 2306290000 942130 716120 445840 685360 1000390 878530 1324080 1116930 1179400 TRUE FALSE 817625.1334 711415.7606 661449.7152 840981.4631 980484.1962 912327.6176 1195670.925 878083.2115 1039972.676 0.786198669 0.684071589 0.636026052 0.808657268 0.942798036 0.877261143 1.149713789 0.844332964 1 19.98811419 3.375638562 2.678411249 0.960722049 0.700402935 0.647864939 0.088486285 0.164491604 2.38855001 0.026182501 0.035906925 2374.863005 -3.375638562 -0.260319114 KNS(ph)WEPKPITVPQFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KNSWEPKPITVPQFK 15 2 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 KNS(1)WEPKPITVPQFK;KNS(1)WEPKPITVPQFK 140.2 2.60E-06 2488800000 1516220 1002960 966890 1074360 1070400 675620 1912700 1837040 1527530 TRUE FALSE 1315847.685 996371.4897 1434481.238 1318309.859 1049101.134 701611.5386 1727206.648 1444203.292 1346947.144 0.976911152 0.739725753 1.06498703 0.978739117 0.778873276 0.520890179 1.282312121 1.072204874 1 20.36126181 2.213199754 24.99982659 1.115434852 0.851940858 0.378128079 0.165882225 251.7311265 248145.5602 0.06873184 0.046358671 163.3803246 -2.213199754 -0.263493995 KNSLISSLEEEVSILNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KNSLISSLEEEVSILNR 17 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 142.3 9.49E-07 250510000 102350 101790 62954 69592 91456 100740 95960 123410 65646 FALSE TRUE 88824.18818 101121.3348 93398.76497 85393.92725 89636.20453 104615.533 86653.81397 97019.73188 57885.40466 1.534483324 1.746922828 1.61351148 1.475223811 1.548511323 1.80728689 1.496988999 1.676065537 1 15.82091201 1.235036544 24.99996751 0.999999137 1.61400067 0.764908323 0.106688971 46.73260923 331471.1579 0.17707315 0.024824306 17.18052947 -1.235036544 0.614001533 KNST(ph)DLDSAPEDPTS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KNSTDLDSAPEDPTSPK 17 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 2 KNS(0.348)T(0.652)DLDSAPEDPT(0.246)S(0.754)PK 114.57 0.00035139 0 195180 131180 164160 159150 207190 140960 239290 275260 291150 TRUE FALSE 169386.4685 130318.2699 243548.3251 195287.44 203067.3244 146382.8224 216083.6926 216397.7911 256730.5787 0.659782989 0.507607121 0.948653356 0.760670743 0.790974435 0.570180705 0.841674933 0.842898389 1 17.96989562 1.448938579 1.401794877 1.047937139 0.71675485 0.353980852 0.124722727 0.971563247 2.386134992 0.427654282 0.038037059 28.1150318 -1.448938579 -0.331182289 KNTFTAWS(ph)DEES(ph)DYEIDDRDVNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KNTFTAWSDEESDYEIDDRDVNK 23 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 2 KNT(0.002)FT(0.009)AWS(0.988)DEES(0.999)DY(0.001)EIDDRDVNK;KNT(0.002)FT(0.004)AWS(0.994)DEES(1)DYEIDDRDVNK 95.741 0.0020575 248325000 168204 151553 114747 104984 131711 107318 182547 200715 151196 TRUE FALSE 145975.4152 150557.4384 170239.033 128822.2218 129090.2088 111446.5929 164843.62 157793.6592 133321.7811 1.094910479 1.12927863 1.27690338 0.966250381 0.968260458 0.835921872 1.236434277 1.183554989 1 17.02455297 3.729047955 24.98017727 1.049541135 1.163255614 0.20642558 0.121683329 1358.969732 3568646.667 0.037259206 0.056071959 5358.558239 -3.729047955 0.113714479 KNTFTAWS(ph)DEESDYEIDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KNTFTAWSDEESDYEIDDR 19 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 KNTFT(0.002)AWS(0.997)DEES(0.002)DYEIDDR;KNTFTAWS(1)DEESDYEIDDR;KNTFTAWS(1)DEESDYEIDDR;KNTFTAWS(1)DEESDYEIDDR;KNTFTAWS(0.999)DEESDYEIDDR 195.27 7.89E-16 1147630000 411186 315532 276877 396935 366783 312349 364895 466618 667796 TRUE FALSE 356846.7283 313459.2495 410775.6433 487065.1585 359484.7359 324365.2681 329507.5391 366835.3719 588849.9176 0.606006246 0.53232452 0.69758971 0.827146517 0.610486178 0.5508454 0.559578136 0.622969217 1 19.16754045 1.238333332 24.86658639 1.000000414 0.625407823 0.656600137 0.085030292 3.439963436 375463.4148 0.125727152 0.022281309 17.31144548 -1.238333332 -0.37459259 KNTLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KNTLAR 6 1 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ; 114.72 0.040155 2237400000 7286600 7046000 4049700 5036600 4873100 7467100 8963900 9760000 9421800 FALSE TRUE 6323657.348 6999714.362 6008148.465 6180237.01 4776134.844 7754364.169 8094582.358 7672899.952 8307965.537 0.761155944 0.8425305 0.723179272 0.743892952 0.574886213 0.93336499 0.974315832 0.923559434 1 22.9860638 2.595509285 7.973519943 0.956889679 0.736216349 0.737297623 0.067903161 0.152700657 9.454436168 0.023657628 0.020823394 394.0118514 -2.595509285 -0.22067333 KNVFIIGATNRPDIIDPAILRPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KNVFIIGATNRPDIIDPAILRPGR 24 3 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 148.87 6.74E-08 3289300000 5985500 3785500 2239800 2628800 3578300 3700100 3776700 4499000 3240000 FALSE TRUE 5194501.01 3760632.801 3322974.772 3225709.219 3507098.831 3842445.241 3410436.215 3536923.861 2856970.891 1.818184787 1.316300706 1.163111176 1.129066183 1.227558475 1.344936784 1.193724523 1.237997864 1 21.44605491 4.731411812 2.820757442 1.196181249 1.92602619 0.835094804 0.087838887 0.159443146 1.787536062 0.02205302 0.266141717 53878.04296 -4.731411812 0.729844941 KNWQNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KNWQNVR 7 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ; 198.39 0.00064228 1647220000 1688310 1975660 1336810 1881380 2441100 2278600 2523040 2734900 3596300 FALSE TRUE 1465195.556 1962681.759 1983295.787 2308576.084 2392526.886 2366259.216 2278355.969 2150062.918 3171149.511 0.462039254 0.618918078 0.625418568 0.727993454 0.754466757 0.746183429 0.71846375 0.678007426 1 21.59657447 5.476873228 0.451681078 0.788471887 1.07E-17 0.613019133 0.084321464 8.1585528 0.826276532 0.073034416 3.925884554 299828.7183 -5.476873228 -0.788471887 KNWVVTGADDMQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KNWVVTGADDMQIR 14 1 P35606;P35606-2;D6R997;D6RBT6;D6RBZ7;D6RCL6;D6RBG7 P35606 COPB2 Coatomer subunit beta 0 85.734 0.013671 0 244390 214030 122460 121290 192390 183480 223100 255370 74268 FALSE TRUE 212093.2423 212624.0228 181682.0656 148830.7483 188561.8154 190538.5943 201463.7963 200761.1128 65488.12165 3.238652094 3.246757083 2.774275106 2.272637305 2.879328505 2.90951381 3.076341041 3.065611102 1 15.99894563 4.18193652 4.346640553 2.645290364 3.250148806 0.169216557 0.608836184 0.392116491 14.92287146 0.155226892 0.364170271 15203.25291 -4.18193652 0.604858442 KPAFNLSAFGTLS(ph)PSLGNSSILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPAFNLSAFGTLSPSLGNSSILK 23 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 KPAFNLSAFGTLS(0.985)PS(0.015)LGNSSILK;KPAFNLSAFGTLS(0.996)PS(0.004)LGNSSILK 291.06 9.83E-62 1540670000 2117370 2068320 1509750 1789640 1890860 1652250 2650600 2864700 2499800 TRUE FALSE 1837554.19 2054733.07 2239870.15 2196005.115 1853235.585 1715813.127 2393545.22 2252106.198 2204276.492 0.833631442 0.932157593 1.016147547 0.996247577 0.84074552 0.778401953 1.085864332 1.021698597 1 21.07187377 2.213333564 24.99867426 1.034988965 0.908058703 0.419017193 0.075212159 251.9739929 249691.0023 0.033005302 0.02226195 163.4306709 -2.213333564 -0.126930262 KPALGFYDTSEENYQALDADFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPALGFYDTSEENYQALDADFR 22 1 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 0 204.31 1.90E-22 102430000 108450 94474 62746 74999 84925 73600 85176 94749 126400 FALSE TRUE 94118.05772 93853.39407 93090.17547 92028.66924 83235.15865 76431.43963 76915.64463 74487.66369 111457.136 0.844432767 0.842058189 0.835210547 0.82568665 0.746790754 0.685747386 0.690091702 0.668307713 1 16.76612946 3.253802787 4.112180561 0.73736832 0.838970009 0.130534571 0.093518089 0.340471689 12.96649437 0.027998335 0.034805993 1793.918822 -3.253802787 0.10160169 KPALPVS(ph)PAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KPALPVSPAAR 11 1 A0A087X0M4;A0A087WWF4;Q9BWU0 A0A087X0M4 SLC4A1AP Kanadaptin 1 KPALPVS(1)PAAR;KPALPVS(1)PAAR;KPALPVS(1)PAAR;KPALPVS(1)PAAR 110.97 0.0010552 1875080000 3044260 2805290 2265220 2533160 2621180 2341600 2828770 3368700 3437630 TRUE FALSE 2641953.328 2786861.865 3360687.969 3108352.695 2569023.646 2431682.867 2554436.321 2648329.72 3031237.298 0.871575884 0.919380963 1.108685213 1.025440238 0.847516507 0.802208019 0.842704173 0.873679445 1 21.53147537 3.232770569 24.9962147 0.867439354 0.985950938 0.310624391 0.079590253 168.006016 725297.5676 0.02514523 0.029282928 1709.11218 -3.232770569 0.118511583 KPALVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPALVAK 7 1 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;H0YE72;H0YE58;P29692-3;E9PL71;P24534 P29692;P29692-3;P24534 EEF1D;EEF1B2 Elongation factor 1-delta;Elongation factor 1-beta 0 ; 79.116 0.07394 0 2881600 2765500 2071430 2479900 2398600 2188900 3395400 3765700 3585200 FALSE TRUE 2500789.259 2747333.248 3073180.477 3042999.198 2350872.553 2273108.399 3066114.631 2960434.36 3161361.74 0.791048119 0.869034762 0.972106557 0.962559633 0.743626559 0.71902825 0.969871493 0.936442775 1 21.5921147 KPANDITSQLEINFGDLGR ddPTM_MDA-MB-175_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 ; 153.36 7.28E-10 1403200000 2601600 2075600 1465320 1939670 2082700 2093550 1890140 2456200 2783900 FALSE TRUE 2257791.968 2061965.247 2173953.653 2380101.719 2041258.345 2174090.223 1706834.514 1930960.744 2454790.513 0.919749346 0.839976053 0.885596405 0.96957427 0.83154075 0.885652039 0.695307605 0.786609176 1 21.22716848 2.753581112 2.352570459 0.815501255 0.89523443 0.073976809 0.084625274 0.592504143 6.481076222 0.032019627 0.029673579 566.9974581 -2.753581112 0.079733175 KPAPAPPKPGNPPPGHPGGQSSS(ph)GTSQHPPSLSPKPPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPAPAPPKPGNPPPGHPGGQSSSGTSQHPPSLSPKPPTR 39 3 Q68EM7;Q68EM7-3;Q68EM7-6;Q68EM7-5;Q68EM7-7;I3L460;Q68EM7-2 Q68EM7;Q68EM7-2 ARHGAP17 Rho GTPase-activating protein 17 1 KPAPAPPKPGNPPPGHPGGQS(0.168)S(0.127)S(0.205)GT(0.205)S(0.205)QHPPS(0.044)LS(0.044)PKPPTR 70.515 0.0013656 266880000 235940 216840 76066 151830 241580 209820 230110 290650 271870 TRUE FALSE 204759.9312 215415.5638 112851.772 186305.3221 236773.0306 217891.9112 207793.9676 228496.7593 239729.8383 0.854127849 0.898576353 0.470745623 0.777146989 0.987666084 0.908906095 0.866783914 0.953142758 1 17.87104996 3.332865189 5.856174087 0.936572587 0.736654336 0.401744373 0.117262824 0.217875852 11.07083934 0.034592309 0.044682779 2152.113583 -3.332865189 -0.199918251 KPASFMTSICDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KPASFMTSICDER 13 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;; 192.32 4.52E-06 5945490000 4626900 4615800 2894500 3735940 4371800 4335800 4676990 5463390 4721470 FALSE TRUE 4015443.442 4585478.506 4294289.882 4584242.277 4284809.733 4502601.032 4223416.23 4295086.565 4163303.195 0.96448499 1.101403931 1.031462202 1.101106997 1.029185128 1.081497268 1.014438784 1.03165356 1 21.9892972 2.211452175 24.98378939 1.018719171 1.054117271 0.145695868 0.040686561 393.4730577 362630.8988 0.015054515 0.01015313 162.7242113 -2.211452175 0.035398099 KPAT(ph)PAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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;KPAT(1)PAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR 341.87 2.45E-117 9258090000 2395855 1578160 1669204 1445432 1502603 1104957 1911415 2492057 2372256 TRUE FALSE 2079236.691 1567792.963 2476436.638 1773639.428 1472704.14 1147465.411 1726046.267 1959150.004 2091810.598 0.993988984 0.749490879 1.183872306 0.847896759 0.704033215 0.548551294 0.825144623 0.936580972 1 20.9963208 3.494775451 24.74072949 0.805571848 0.963609709 0.197689544 0.158816398 1223.838621 1715094.347 0.046572196 0.067421044 3124.463468 -3.494775451 0.158037861 KPATPAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 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 452.08 1.10E-231 2.20825E+11 4252848.4 3111174.3 2908440.2 3500450.1 2871311.6 2236215.7 3868049.1 4729819 4497052 TRUE FALSE 3690823.709 3090736.791 4314971.609 4295280.796 2814178.117 2322244.365 3492926.294 3718384.014 3965415.636 0.930753305 0.779423161 1.088151156 1.08318552 0.709680491 0.585624454 0.880847461 0.937703473 1 21.91904066 3.239053175 24.99999833 0.829636109 0.965150965 0.208949094 0.14220304 26.23936732 1331749.841 0.046443794 0.056350341 1734.016299 -3.239053175 0.135514856 KPATPAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLREER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 301.15 1.45E-90 2818921000 1028204 1113201 363508 260280 768514 506377 1395029 1289174 61847.9 TRUE FALSE 892324.2363 1105888.309 539301.6847 319380.5521 753222.075 525857.6509 1259739.302 1013494.172 54536.31172 16.36202024 20.27801797 9.888855107 5.856291745 13.81138642 9.642339833 23.09909238 18.58384149 1 15.73492951 7.999999994 0.070048075 10 22.29960778 0.02108847 6.709059499 6392.792792 42.97467596 1680.763504 8305.942441 99999998.67 -7.999999994 12.29960778 KPATSYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPATSYVR 8 1 P46779;H0YKD8;P46779-2;P46779-3 P46779 RPL28 60S ribosomal protein L28 0 ; 130.66 0.0016652 4900500000 2369000 4220900 2420600 2959000 4212600 3733000 4126900 4160500 4691700 FALSE TRUE 2055930.648 4193172.63 3591210.256 3630886.175 4128777.502 3876610.926 3726673.873 3270809.452 4137052.571 0.496955408 1.013565227 0.868060097 0.87765048 0.997999767 0.937046571 0.900804089 0.790613461 1 21.98017186 4.747374525 24.79490672 0.911428619 0.496955169 0.784125962 0.070046501 501.1804045 1409864.968 0.017414738 0.203119748 55895.2014 -4.747374525 -0.414473449 KPCNSQPSELSSETSGIARPEEGRPVVS(ph)GTGNDITTPPNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPCNSQPSELSSETSGIARPEEGRPVVSGTGNDITTPPNK 40 3 P27816-6;P27816 P27816-6 MAP4 Microtubule-associated protein 4 1 KPCNSQPSELS(0.001)S(0.004)ET(0.011)S(0.011)GIARPEEGRPVVS(0.395)GT(0.395)GNDIT(0.101)T(0.082)PPNK 46.77 0.031076 394470000 84703 70271 70081 96129 68878 56823 88373 113830 160270 TRUE FALSE 73509.28394 69809.38517 103972.406 117956.5587 67507.46256 59009.01758 79802.60006 89488.34033 141323.0632 0.520150655 0.493970224 0.735707277 0.834658944 0.477681852 0.417546975 0.564682071 0.633218233 1 17.1086374 1.228503314 3.437940237 1.068854204 0.58143893 0.531475006 0.123532433 0.288928168 4.834639579 0.378959414 0.034173123 16.92401157 -1.228503314 -0.487415274 KPCNSQPSELSSETSGIARPEEGRPVVSGTGNDIT(ph)TPPNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPCNSQPSELSSETSGIARPEEGRPVVSGTGNDITTPPNK 40 3 P27816-6;P27816 P27816-6 MAP4 Microtubule-associated protein 4 1 KPCNSQPSELSSETSGIARPEEGRPVVS(0.006)GT(0.028)GNDIT(0.525)T(0.44)PPNK;KPCNSQPSELSSETSGIARPEEGRPVVS(0.004)GT(0.021)GNDIT(0.536)T(0.439)PPNK 130.13 4.48E-09 1344730000 698290 635720 569620 709780 589430 450320 725570 932790 1209840 TRUE FALSE 606009.2073 631543.9135 845090.1373 870946.3973 577701.4962 467644.1018 655204.3331 733320.1175 1066814.093 0.568055119 0.591990598 0.792162517 0.816399411 0.541520308 0.438355759 0.614169176 0.687392604 1 20.02487736 1.226417253 2.989780175 1.078547276 0.626721606 0.528026888 0.111077456 0.374260001 4.079512014 0.416854773 0.031588572 16.84291487 -1.226417253 -0.451825671 KPDGVKES(ph)TESSNTTIEDEDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPDGVKESTESSNTTIEDEDVK 22 2 Q13557;D6R938;Q13557-8;Q13557-12;H0Y9J2 Q13557 CAMK2D Calcium/calmodulin-dependent protein kinase type II subunit delta 1 KPDGVKES(0.95)T(0.05)ES(0.001)SNTTIEDEDVK;KPDGVKES(0.742)T(0.154)ES(0.051)S(0.051)NT(0.002)TIEDEDVK 225.68 3.07E-26 311460000 642890 265394 261013 299693 221297 127780 583460 471254 441043 TRUE FALSE 557930.4576 263650.6093 387239.7598 367742.8762 216893.6227 132695.7793 526876.139 370479.9994 388903.399 1.434624791 0.677933415 0.99572223 0.945589257 0.557705649 0.341204987 1.354773809 0.952627312 1 18.56905232 4.751049752 24.00707134 0.866581913 1.434625417 0.301314658 0.277582556 1596.321186 3068408.604 0.069762405 1.140493662 56370.22284 -4.751049752 0.568043504 KPDHVPISSEDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPDHVPISSEDER 13 1 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ; 126.48 0.00012204 1197800000 1526910 1337570 884600 1057540 1344970 1177590 1396500 1556400 1455210 FALSE TRUE 1325124.975 1328783.415 1312395.519 1297670.62 1318207.728 1222892.649 1261067.645 1223575.972 1283176.732 1.032690932 1.035542012 1.022770665 1.011295318 1.027300212 0.953019658 0.982770038 0.953552182 1 20.29128846 2.748638081 24.96768654 0.970378821 1.02546697 0.762657882 0.014834614 302.6475023 749832.5855 0.004580822 0.004529763 560.5806219 -2.748638081 0.055088149 KPDIYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KPDIYER 7 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31;A0A3B3IRR8 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ;; 111.82 0.010411 1026900000 1972650 1890920 1100020 1457570 1872160 1747820 1834760 2334840 1896300 FALSE TRUE 1711959.304 1878498.422 1631993.351 1788533.546 1834907.679 1815059.766 1656825.258 1835552.636 1672121.574 1.023824661 1.123422155 0.976001612 1.069619323 1.097353032 1.085483134 0.99085215 1.097738743 1 20.67324831 1.20924862 23.79490297 0.999999383 1.058676557 0.12623047 0.04796064 4005.218174 3251027.6 1.100966389 0.010858265 16.19006603 -1.20924862 0.058677174 KPDQPYEWLSYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPDQPYEWLSYK 12 1 E7EPM6;P33121-2;P33121;P33121-3;D6RER0 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 136.51 0.00017411 554620000 1372000 882620 711380 737200 949610 878070 1345100 1615400 820330 FALSE TRUE 1190686.724 876822.0111 1055405.747 904592.5274 930714.6189 911849.9211 1214652.409 1269959.281 723351.5219 1.646069287 1.212165848 1.459049598 1.250557302 1.286669884 1.260590313 1.679200737 1.755659928 1 19.46433739 2.247752653 24.99945055 1.54444436 1.34335224 0.034745497 0.235725297 376.1406441 1022985.924 0.086261878 0.065849088 176.9101102 -2.247752653 -0.20109212 KPDS(ph)PPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPDSPPK 7 1 Q96T23-2;Q96T23;Q96T23-3;H0YCN2 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 KPDS(1)PPK;KPDS(1)PPK 64.297 0.045482 212262000 578990 428950 547950 502550 326910 298370 553420 664180 1644930 TRUE FALSE 502475.0045 426132.1992 812940.4528 616661.6585 320405.1306 309848.487 499749.4136 522150.2757 1450468.249 0.346422615 0.293789402 0.560467596 0.42514661 0.220897721 0.213619627 0.344543504 0.359987387 1 20.46808728 1.237985511 6.541305305 1.018214761 0.344496018 0.812082869 0.098957917 0.053939188 10.95526973 0.161454359 0.026154515 17.29758649 -1.237985511 -0.673718743 KPEDRPNTSEILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPEDRPNTSEILR 13 2 P19525-2;P19525 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 0 ; 152.88 2.44E-05 521110000 380690 332460 202781 276980 303240 257820 324440 391850 366080 FALSE TRUE 330380.852 330276.0484 300846.5699 339872.5424 297206.1173 267738.5022 292975.8587 308055.9269 322802.4394 1.023476937 1.023152269 0.93198357 1.05288096 0.920705921 0.82941908 0.90760113 0.954317221 1 18.30029196 3.21398009 24.26882108 0.92063714 1.003544061 0.399515757 0.051919089 179.9263655 177643.9257 0.016430562 0.018640441 1636.741482 -3.21398009 0.082906921 KPEDWDEEMDGEWEPPVIQNPEYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 KPEDWDEEMDGEWEPPVIQNPEYK 24 1 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ;;;;;;; 269.57 6.24E-45 6010730000 6110830 4279550 4784170 4933960 4443740 4047610 5560440 6147410 5440080 FALSE TRUE 5303268.333 4251437.354 7097810.614 6054291.029 4355318.268 4203324.176 5021189.385 4832834.211 4796959.94 1.105547763 0.886277436 1.479647673 1.262109983 0.907933008 0.876247504 1.046744073 1.007478543 1 22.19368896 3.23645078 24.99999655 0.974013459 1.183333842 0.33024181 0.152501577 72.38005221 857650.6812 0.047248144 0.056244028 1723.656731 -3.23645078 0.209320383 KPEDWDERPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPEDWDERPK 10 2 P27824;P27824-2;P27824-3;D6RGY2 P27824 CANX Calnexin 0 ; 132.76 0.00012091 719690000 1319020 894860 1141800 1496950 1174630 958760 994750 1930200 2702150 FALSE TRUE 1144708.165 888981.6057 1693978.299 1836855.377 1151257.161 995644.1176 898279.2981 1517441.751 2382704.905 0.480423808 0.373097652 0.710947585 0.770911821 0.483172364 0.417862957 0.376999811 0.63685677 1 21.18416886 1.281148007 3.378072201 1.049549702 0.52231128 0.570004076 0.131643127 0.227850702 3.723146907 0.293328108 0.036519506 19.10504244 -1.281148007 -0.527238422 KPEEES(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 79.82 0.016567 1735009000 4110430 2616420 2364630 2945770 2060540 2307980 2887440 3348290 7430590 TRUE FALSE 3567226.261 2599232.565 3508172.977 3614652.102 2019539.285 2396769.484 2607416.513 2632284.24 6552154.115 0.544435646 0.396698936 0.535422842 0.551673852 0.308225242 0.365798704 0.397947983 0.401743334 1 22.64353786 1.236628731 24.99972164 1.000000716 0.433224852 0.822558276 0.082045614 21.072984 272621.8982 0.130500819 0.020622397 17.24363141 -1.236628731 -0.566775864 KPEEES(ph)PRKDDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 139.88 2.79E-05 2400580000 2499700 1222400 1530500 1206250 1056390 771875 1882690 2135890 2037900 TRUE FALSE 2169358.312 1214369.974 2270654.919 1480147.499 1035369.906 801569.5307 1700107.014 1679146.545 1796981.784 1.207223318 0.67578313 1.263593733 0.823685311 0.57617162 0.446064361 0.946090288 0.934426025 1 20.77714435 4.756415725 23.27284314 0.839442476 1.207224123 0.206294801 0.230258123 2561.847044 3339040.082 0.058542529 1.599543753 57071.03191 -4.756415725 0.367781647 KPEENPASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPEENPASK 9 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 138.76 0.0002044 406410000 1127510 850340 660040 841780 667610 618640 1139010 1399170 1229750 FALSE TRUE 978506.6968 844754.0605 979237.5517 1032919.015 654325.8672 642439.4811 1028548.986 1099968.384 1084370.356 0.902373153 0.779027254 0.903047143 0.952551874 0.603415488 0.592453932 0.948521859 1.01438441 1 20.04842615 2.019460396 24.9141791 1.000189756 0.79073429 0.391990697 0.118323641 236.121296 302293.1407 0.051825222 0.034935344 104.5828316 -2.019460396 -0.209455465 KPESPYGNLCDAPDS(ph)PRPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KPESPYGNLCDAPDSPRPVK 20 2 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 KPES(0.002)PYGNLCDAPDS(0.998)PRPVK;KPESPYGNLCDAPDS(1)PRPVK;KPESPYGNLCDAPDS(1)PRPVK 195.39 1.28E-19 719420000 886650 743540 580300 760280 884530 729560 1044690 1264880 1144940 TRUE FALSE 769476.956 738655.6368 860935.021 932913.1942 866929.5836 757626.6453 943376.1246 994395.2553 1009586.498 0.762170411 0.731641755 0.852760039 0.924054746 0.85869768 0.750432625 0.934418326 0.984953006 1 19.94533309 -2 0.211392483 2.214803089 0.730296663 0.593085803 0.06110056 71.62659324 1.089991754 34.6625032 0.359864619 0.01 2 -1.484506426 KPETEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPETEAAR 8 1 P61964;V9GYQ5;V9GZ59 P61964 WDR5 WD repeat-containing protein 5 0 ; 81.338 0.037071 233660000 276370 296820 216540 256770 204590 237070 259680 320160 566940 FALSE TRUE 239847.0043 294870.1699 321259.4683 315073.553 200519.0593 246190.2363 234496.2736 251696.2755 499916.9991 0.479773652 0.589838254 0.642625614 0.630251729 0.401104703 0.492462222 0.469070414 0.503476129 1 18.93132906 1.236886897 24.99966173 1.000000587 0.526278428 0.796037236 0.075391114 20.67616164 308734.6547 0.122929793 0.019827413 17.25388494 -1.236886897 -0.473722159 KPFPDFVYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPFPDFVYK 9 1 A0A1C7CYX9;Q16555-2;Q16555 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 0 ; 103.22 0.005544 1090190000 1732800 1591890 1332640 1795060 1627690 1375380 1947710 2373800 2823600 FALSE TRUE 1503806.09 1581432.77 1977109.161 2202655.809 1595302.154 1428291.759 1758821.384 1866181.343 2489797.225 0.603987375 0.635165287 0.794084411 0.884672771 0.640735775 0.573657864 0.706411497 0.749531458 1 21.24759682 1.195817318 2.492665372 1.099660094 0.694744964 0.52497336 0.091641775 0.562148107 3.458513823 0.516435358 0.026038263 15.69702383 -1.195817318 -0.40491513 KPFSQHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPFSQHVR 8 1 Q02878;F8VZ45;U3KQR5;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ; 182.29 0.00014886 4201400000 4620400 7298500 2348800 4721600 7971400 7713600 7018300 7958500 8657900 FALSE TRUE 4009802.433 7250555.673 3484687.536 5793711.445 7812784.736 8010347.183 6337666.346 6256636.708 7634372.925 0.525230097 0.949725111 0.45644712 0.758898144 1.023369544 1.049247563 0.830148908 0.819535117 1 22.86407823 3.435248795 6.701322933 0.923708541 0.66347407 0.466700716 0.147250838 0.185184269 21.6810757 0.04148577 0.054117785 2724.261514 -3.435248795 -0.260234471 KPFSVSST(ph)PTMSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPFSVSSTPTMSR 13 1 A0A2R8Y7M0;P82094;P82094-2 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 KPFSVS(0.011)S(0.136)T(0.852)PT(0.001)MSR;KPFSVS(0.019)S(0.219)T(0.753)PT(0.009)MSR 97.291 0.0022536 965350000 665330 542260 333630 426500 511940 461520 656120 652540 478020 TRUE FALSE 577404.9548 538697.8584 494974.5839 523343.3436 501753.3956 479274.973 592489.5834 512999.3991 421509.0202 1.369851954 1.278022136 1.174291795 1.241594648 1.190374041 1.137045591 1.405639156 1.21705438 1 18.68520398 4.560308534 2.906709929 1.207894186 1.372762287 0.239657877 0.100216122 0.483610684 6.917800337 0.02534092 0.15011769 36333.60867 -4.560308534 0.1648681 KPGDLSDELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KPGDLSDELR 10 1 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ;;; 139.76 6.49E-05 2926470000 8501900 7374600 4705910 5872160 6905300 6303800 7443000 8539500 8018800 FALSE TRUE 7378352.374 7326155.767 6981703.816 7205523.678 6767898.04 6546311.265 6721179.006 6713394.379 7070826.599 1.043492196 1.036110229 0.987395705 1.019049693 0.957157971 0.9258198 0.950550676 0.949449726 1 22.75344745 3.662730173 1.127427595 0.953542943 1.039519985 0.637171779 0.023883994 0.337406689 0.842264246 0.008960308 0.022060711 4599.707055 -3.662730173 0.085977042 KPGGAVT(ph)PQQQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KPGGAVTPQQQQR 13 1 O95622 O95622 ADCY5 Adenylate cyclase type 5 1 KPGGAVT(1)PQQQQR;KPGGAVT(1)PQQQQR;KPGGAVT(1)PQQQQR;KPGGAVT(1)PQQQQR 144.94 2.44E-05 1232590000 1816510 1605600 1502140 2015440 2059200 2485710 1303960 2568700 3104720 TRUE FALSE 1576453.601 1595052.708 2228579.928 2473076.456 2018225.949 2581336.872 1177502.16 2019403.495 2737683.539 0.575834854 0.582628593 0.814038546 0.903346359 0.737202062 0.942890891 0.430108938 0.737632187 1 21.38452426 4.24583479 24.42603623 0.777440721 0.57923156 0.243808741 0.155622173 193.3253018 649147.631 0.039312853 0.099431823 17613.05901 -4.24583479 -0.198209161 KPGGFDISLFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPGGFDISLFYR 12 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 147.73 0.00010017 5757500000 2408510 2432750 1455970 1944570 2254370 1948370 2402250 2708900 2375290 FALSE TRUE 2090219.301 2416769.105 2160081.962 2386114.339 2209512.448 2023325.055 2169280.165 2129622.816 2094485.922 0.997962927 1.153872213 1.031318444 1.139236275 1.054918739 0.966024662 1.035710072 1.016775903 1 20.99816476 2.992256344 24.63283552 1.009554449 1.084157205 0.356212835 0.04811753 303.2093554 964523.4628 0.013389437 0.014533287 982.3275952 -2.992256344 0.074602756 KPGINVASDWSIHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPGINVASDWSIHLR 15 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 95.347 0.0026747 507320000 605990 463100 242080 353510 498060 618330 438680 496680 416060 FALSE TRUE 525906.8861 460057.8656 359150.6977 433779.8486 488149.5804 642117.5552 396136.8811 390468.8472 366873.8608 1.433481483 1.253994669 0.978948724 1.182367824 1.330565169 1.750240679 1.079763165 1.064313621 1 18.48492459 2.033807617 24.99988625 1.047335806 1.306861512 0.304367061 0.194801571 246.1669821 182033.365 0.084545885 0.05700048 108.0955006 -2.033807617 0.259525706 KPGMFFNPEESELDLTYGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 KPGMFFNPEESELDLTYGNR 20 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;;; 306.69 1.84E-55 22682750000 8875440 8876630 6328455 7262305 8707550 9217790 10019760 11190390 11011140 FALSE TRUE 7702528.117 8818318.833 9388917.005 8911322.348 8534286.791 9572404.346 9048045.217 8797412.182 9709415.573 0.79330502 0.908223442 0.966990952 0.917802136 0.878970184 0.985888829 0.931883608 0.906070207 1 23.21095303 4.710450016 3.350855607 0.936155632 0.778640369 0.61152487 0.03667057 0.190925584 3.627737245 0.008790399 0.074225678 51339.30867 -4.710450016 -0.157515263 KPGMTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPGMTR 6 1 P40926;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial" 0 ; 92.467 0.074917 2865600000 4526600 3962500 2910600 5063200 3400900 4876900 4149300 5178700 5107800 FALSE TRUE 3928398.341 3936470.077 4318175.895 6212876.946 3333228.744 5064517.499 3746901.525 4071275.306 4503961.703 0.872209535 0.874001676 0.95875058 1.379424905 0.740065961 1.124458384 0.831912386 0.903932043 1 22.10276313 0.930407533 18.63668885 1.793407164 0.959960714 0.00479197 0.178260007 112308893.5 416698914.7 3770803772 0.041647005 8.519371025 -0.930407533 -0.83344645 KPGPPLS(ph)PEIR ddPTM_MDA-MB-175_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 128.06 0.0001676 8740620000 9356290 8015420 6086950 7715690 8823940 8010130 9010780 10763700 12735890 TRUE FALSE 8119832.571 7962766.178 9030619.38 9467655.341 8648360.858 8318284.884 8136915.943 8461966.518 11230267.59 0.723031086 0.709045097 0.804132164 0.843048063 0.770093926 0.740702287 0.724552276 0.753496428 1 23.42088897 1.237765182 24.99974736 1.00000028 0.759012441 0.780644239 0.040228737 9.924450712 311716.5303 0.062549802 0.01071743 17.28881321 -1.237765182 -0.240987839 KPGPPLS(ph)PEIRS(ph)PAGS(ph)PELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPGPPLSPEIRSPAGSPELR 20 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 3 KPGPPLS(1)PEIRS(1)PAGS(1)PELR 79.04 0.0053208 191430000 334180 282230 176630 204910 286750 245360 298190 353970 219200 TRUE FALSE 290017.2663 280376.0125 262048.8588 251437.9474 281044.236 254799.158 269271.5797 278276.2701 193286.4257 1.500453357 1.450572701 1.355754072 1.300856728 1.454029868 1.31824652 1.39312204 1.439709328 1 17.5603808 1.23500013 24.99991366 0.999999438 1.398966914 0.800572391 0.062979238 45.4644375 319177.692 0.110853417 0.015464184 17.17908901 -1.23500013 0.398967476 KPGPSGPSES(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPGPSGPSESPK 12 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPGPSGPS(0.006)ES(0.994)PK;KPGPS(0.001)GPS(0.028)ES(0.971)PK 79.97 0.013232 749440000 1198820 1026870 765360 805910 1042530 740930 1264980 1422720 1210840 TRUE FALSE 1040392.9 1020124.423 1135490.656 988904.1831 1021785.693 769434.0565 1142302.434 1118482.4 1067695.875 0.974428135 0.955444755 1.063496341 0.926203994 0.957000694 0.720649086 1.069876227 1.047566471 1 20.02606933 KPGQSFQEQVEHYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPGQSFQEQVEHYR 14 1 O15042-2;O15042;E7ET15;O15042-3;H7C4V2 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 ; 241.27 1.28E-17 420960000 948930 827460 503200 648530 824130 787110 821020 1053130 910920 FALSE TRUE 823526.4962 822024.3608 746549.2031 795788.6487 807731.4254 817390.631 741397.6068 827926.345 803232.0753 1.025265949 1.023395835 0.929431513 0.990733156 1.005601557 1.01762698 0.923017929 1.03074363 1 19.61545736 KPGTPLPPPATSPSS(ph)PRPLS(ph)PVPHVNNVVNAPLSINIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KPGTPLPPPATSPSSPRPLSPVPHVNNVVNAPLSINIPR 39 2 Q06190;Q06190-2 Q06190 PPP2R3A Serine/threonine-protein phosphatase 2A regulatory subunit B subunit alpha 2 KPGTPLPPPAT(0.131)S(0.144)PS(0.499)S(0.532)PRPLS(0.693)PVPHVNNVVNAPLSINIPR;KPGT(0.001)PLPPPAT(0.093)S(0.086)PS(0.394)S(0.429)PRPLS(0.998)PVPHVNNVVNAPLSINIPR;KPGTPLPPPAT(0.002)S(0.008)PS(0.457)S(0.535)PRPLS(0.998)PVPHVNNVVNAPLSINIPR 153.04 1.68E-13 877270000 495250 464570 299616 369753 458490 446730 446320 563940 497330 TRUE FALSE 429801.4577 461518.2091 444511.2998 453711.07 449366.946 463915.9922 403035.9551 443345.8196 438536.214 0.980082018 1.052406151 1.013625068 1.034603427 1.024697463 1.057873848 0.919048284 1.010967408 1 18.74233646 2.268505457 24.99999964 0.981415655 1.027963446 0.355013982 0.031891213 220.2005646 183837.7276 0.011129726 0.008619837 185.5690128 -2.268505457 0.046547791 KPHTLLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPHTLLQR 8 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 138.1 0.00046732 441860000 298450 305140 210350 267810 280640 295410 316270 354760 362830 FALSE TRUE 259009.0763 303135.5152 312075.9636 328620.3537 275055.8131 306774.6139 285598.1841 278897.3347 319936.6507 0.80956363 0.947486056 0.975430489 1.027141945 0.859719611 0.958860491 0.892671044 0.871726744 1 18.28742675 4.741919601 24.49833122 0.935580786 0.809563567 0.364860892 0.054240681 302.0216571 2202620.618 0.01355768 0.095189582 55197.52457 -4.741919601 -0.126017218 KPIDSLRDS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 KPIDSLRDSR 10 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 KPIDS(0.024)LRDS(0.976)R;KPIDSLRDS(1)R;KPIDSLRDS(1)R;KPIDSLRDS(1)R;KPIDS(0.001)LRDS(0.999)R;KPIDSLRDS(1)R;KPIDSLRDS(1)R;KPIDSLRDS(1)R 138.21 5.56E-05 10964410000 12021960 8182800 6918240 9245300 8649640 7960800 9514180 11038980 15757220 TRUE FALSE 10433227.53 8129046.648 10263924 11344586.67 8477529.087 8267057.127 8591496.288 8678380.032 13894419.4 0.750893378 0.58505839 0.738708377 0.816485118 0.610139139 0.594991189 0.618341511 0.624594651 1 23.72800221 1.234542049 24.99883065 1.000000488 0.663356917 0.645396468 0.077426888 78.63088804 489080.3637 0.145133392 0.019495326 17.16097857 -1.234542049 -0.336643571 KPIETGS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KPIETGSPK 9 1 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 KPIET(0.005)GS(0.995)PK;KPIET(0.019)GS(0.981)PK;KPIET(0.301)GS(0.699)PK;KPIET(0.088)GS(0.912)PK;KPIET(0.005)GS(0.995)PK;KPIET(0.002)GS(0.998)PK 97.508 0.0040693 18240500000 22282800 14262200 12201900 12108900 13715700 10653500 19174500 21607600 18343400 TRUE FALSE 19338071.52 14168510.67 18102779.65 14858410.82 13442784.4 11063347.04 17314959.94 16986982.89 16174864.15 1.195563149 0.875958558 1.119192068 0.918611166 0.831091024 0.683983923 1.070485649 1.05020869 1 23.94725026 4.750086703 23.9021542 0.951022552 1.195563422 0.275494205 0.127874683 1457.718011 3022826.321 0.033161546 0.490255383 56245.36024 -4.750086703 0.24454087 LKGDDLQAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKGDDLQAIK 10 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;G3V576;P07910-2;G3V4C1;B2R5W2;G3V2D6;A0A0G2JNQ3;O60812;B2RXH8;A0A0G2JPF8;P0DMR1;B7ZW38 B4DY08;P07910;P07910-2 HNRNPC;HNRNPCL1;HNRNPCL2;HNRNPCL4;HNRNPCL3 Heterogeneous nuclear ribonucleoproteins C1/C2;Heterogeneous nuclear ribonucleoprotein C-like 1;Heterogeneous nuclear ribonucleoprotein C-like 2;Heterogeneous nuclear ribonucleoprotein C-like 4;Heterogeneous nuclear ribonucleoprotein C-like 3 0 110.93 0.0026538 0 2713400 1967700 1950900 2434400 1939600 1775100 2217200 3129100 6535600 FALSE TRUE 2354817.315 1954774.049 2894361.765 2987167.727 1901005.755 1843389.246 2002176.285 2459966.316 5762968.813 0.408611844 0.339195667 0.502234501 0.518338347 0.329865702 0.319867989 0.347420982 0.426857475 1 22.45838078 1.238475446 5.389657485 1.03130869 0.395938712 0.884161703 0.068452902 0.051998867 4.489946887 0.1229771 0.018248799 17.31711121 -1.238475446 -0.635369979 KPIKS(ph)PSKDASSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPIKSPSKDASSGK 14 3 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 KPIKS(0.481)PS(0.481)KDAS(0.017)S(0.021)GK 61.648 0.059457 1016100000 3657400 2052300 2384600 2109200 1882900 1206100 3158000 3703900 2320600 TRUE FALSE 3174065.323 2038818.306 3537800.536 2588126.097 1845433.974 1252499.447 2851737.646 2911849.809 2046261.312 1.551153465 0.996362632 1.728909458 1.264807228 0.901856456 0.612091643 1.393633174 1.423009756 1 20.96455896 3.474957392 24.89852877 1.109931908 1.401613004 0.2321604 0.293530744 121.4614865 1397581.22 0.089728517 0.116623804 2985.089739 -3.474957392 0.291681097 KPITDDDVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KPITDDDVDR 10 1 P53618 P53618 COPB1 Coatomer subunit beta 0 ;;;;; 142.47 5.72E-05 5853790000 9273180 8195260 5719480 7042860 8243690 7250460 9158990 10650200 10344530 FALSE TRUE 8047705.768 8141424.797 8485439.659 8642049.006 8079656.698 7529389.888 8270752.56 8372737.61 9121611.448 0.882267987 0.892542381 0.930256645 0.947425689 0.885770759 0.825445145 0.906720551 0.917901147 1 23.12085729 1.195534121 2.256788911 1.037328889 0.896226622 0.509082038 0.032018153 0.673516024 3.20535326 0.2013246 0.009224305 15.68679138 -1.195534121 -0.141102267 KPLAAPGDGEGLGQTAQPS(ph)PPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KPLAAPGDGEGLGQTAQPSPPAR 23 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 KPLAAPGDGEGLGQTAQPS(1)PPAR;KPLAAPGDGEGLGQT(0.005)AQPS(0.995)PPAR;KPLAAPGDGEGLGQTAQPS(1)PPAR;KPLAAPGDGEGLGQTAQPS(1)PPAR 219.67 1.25E-32 3369760000 1839330 1882580 1324270 1620220 2007810 1935390 2162630 2479670 2448360 TRUE FALSE 1596257.88 1870213.208 1964691.401 1988115.715 1967858.509 2009845.706 1952898.475 1949411.867 2158917.67 0.739378765 0.866273519 0.910035352 0.920885378 0.911502341 0.930950603 0.904572927 0.902957947 1 21.0418768 4.951762385 1.35792028 0.924364922 0.578370336 0.823656039 0.027491785 0.837178355 0.953444829 0.007538558 0.455104229 89487.50192 -4.951762385 -0.345994585 KPLFFGEGTVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPLFFGEGTVLR 12 1 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ; 201.09 2.44E-07 9259200000 3869500 4608900 2604800 3599700 4539900 3940300 4316200 5511400 4841900 FALSE TRUE 3358135.771 4578623.832 3864489.993 4417066.903 4449564.872 4091885.891 3897615.588 4332830 4269496.098 0.786541478 1.072403798 0.905139601 1.034563986 1.04217565 0.958400195 0.912898267 1.014834046 1 22.02563438 4.753823866 24.62669131 0.989623704 0.786541297 0.588078256 0.05413602 1650.481937 2662937.297 0.01256437 0.285692597 56731.44765 -4.753823866 -0.203082407 KPLFHGDSEIDQLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPLFHGDSEIDQLFR 15 1 P06493;A0A024QZP7;A0A087WZZ9;P06493-2 P06493 CDK1;CDC2 Cyclin-dependent kinase 1 0 ; 212.7 4.82E-10 5639600000 5800500 5907600 3597100 4663100 5761300 5888200 5826600 6515400 6400400 FALSE TRUE 5033949.228 5868792.587 5336669.592 5721928.126 5646661.402 6114722.864 5261537.229 5122132.413 5643752.003 0.89195082 1.039874286 0.945588961 1.0138518 1.000515508 1.083449957 0.932276476 0.907575742 1 22.42822316 KPLHYAADCGQLEILEFLLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KPLHYAADCGQLEILEFLLLK 21 1 P58546 P58546 MTPN Myotrophin 0 ;; 195.34 7.08E-19 6570530000 3878390 3419220 2339870 2451210 1988000 1833130 3553500 4027460 3654390 FALSE TRUE 3365850.935 3396758.919 3471438.958 3007794.695 1948442.689 1903651.697 3208882.117 3166219.021 3222372.177 1.044525818 1.054117505 1.07729299 0.933410087 0.604660971 0.590760965 0.995813624 0.982573969 1 21.6196917 3.481964085 24.82033189 0.84547346 1.049385826 0.330635639 0.144902686 274.1945729 1405297.396 0.047591768 0.063172376 3033.640303 -3.481964085 0.203912366 KPLPDHVSIVEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPLPDHVSIVEPK 13 1 P23396;P23396-2;E9PPU1;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 0 ; 151.44 2.90E-05 2934300000 6336200 6064600 1512310 4654200 6742800 5073300 7080800 8632000 7924100 FALSE TRUE 5498855.116 6024761.243 2243668.174 5711007.245 6608631.472 5268473.134 6394105.106 6786113.974 6987321.925 0.786976065 0.86224183 0.321105596 0.817338503 0.945803205 0.754004637 0.915100975 0.971203853 1 22.73630818 2.608179408 0.804336371 0.996341374 0.686989525 0.315950681 0.159867927 0.875567364 1.285810911 0.173911412 0.100758851 405.6760862 -2.608179408 -0.309351849 KPLPDHVSIVEPKDEILPTT(ph)PISEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPLPDHVSIVEPKDEILPTTPISEQK 26 2 P23396;P23396-2;E9PPU1;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 1 KPLPDHVSIVEPKDEILPT(0.189)T(0.805)PIS(0.006)EQK;KPLPDHVSIVEPKDEILPT(0.177)T(0.823)PISEQK 109.14 0.0024729 886620000 1016390 1084940 88175 170825 850840 579580 1545630 1401910 8546.62 TRUE FALSE 882071.4863 1077812.958 130816.7249 209613.4271 833909.9486 601876.8176 1395735.04 1102122.456 7536.24832 117.0438458 143.0171767 17.35833526 27.81402871 110.6531942 79.8642497 185.2028995 146.2428531 1 12.87963079 1.223897414 24.92775987 0.999697132 104.9207899 0.279120105 51.66598294 1174.170364 1995995.163 303.6447127 13.88497686 16.74547278 -1.223897414 103.9210927 KPLRPDS(ph)LIIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPLRPDSLIIYR 12 2 Q1W6H9 Q1W6H9 FAM110C Protein FAM110C 1 KPLRPDS(1)LIIYR;KPLRPDS(1)LIIYR 136.81 8.13E-05 1609200000 1288920 1454090 853360 955920 1291670 1648890 1181100 1525940 2068230 TRUE FALSE 1118585.956 1444537.987 1266047.75 1172976.246 1265968.294 1712323.865 1066557.104 1199629.606 1823726.206 0.613351913 0.792080512 0.694209332 0.643175627 0.694165764 0.938914986 0.58482304 0.657790409 1 20.79845772 2.948333445 24.99991015 0.761076452 0.690754439 0.124373588 0.12865893 1071.219951 518330.3551 0.041706827 0.041707279 887.8374201 -2.948333445 -0.070322013 KPLSTHSTEYNLDSVPS(ph)PAEEFADFATFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPLSTHSTEYNLDSVPSPAEEFADFATFSK 30 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9 Q6ULP2-7 AFTPH Aftiphilin 1 KPLSTHSTEYNLDS(0.001)VPS(0.999)PAEEFADFATFSK;KPLS(0.005)T(0.005)HS(0.005)T(0.005)EY(0.004)NLDS(0.015)VPS(0.956)PAEEFADFAT(0.006)FS(0.001)K 182.92 2.81E-18 295480000 391663 390272 159963.3 320693 461768 407288 522243 617421 678429 TRUE FALSE 339903.7422 387708.2775 237322.0869 393511.2471 452579.7202 422956.6329 471595.9542 485390.3239 598225.8965 0.568186272 0.648096781 0.396709819 0.657797079 0.75653649 0.707018261 0.788324205 0.811383002 1 19.19033084 -2 0.239008249 3.406958494 0.48724689 0.739143399 0.081141792 45.20023741 0.715778952 50.7255026 0.308543902 0.01 2 -2.919711604 KPLTSSSAAPQRPISTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPLTSSSAAPQRPISTQR 18 2 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ; 261.76 4.72E-31 2555000000 1060270 938380 559580 704090 942000 910500 1017440 1114240 1094330 FALSE TRUE 920152.6331 932215.72 830194.7597 863964.3958 923256.043 945527.5242 918768.8254 875968.447 964959.5541 0.953566011 0.966067144 0.86034151 0.895337418 0.956782115 0.979862337 0.952131954 0.907777371 1 19.88010895 3.217108689 24.75944919 0.953358263 0.918024633 0.218511545 0.037091611 398.2252843 459623.0345 0.011910722 0.013518683 1648.574921 -3.217108689 -0.03533363 KPLVIIAEDVDGEALSTLVLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KPLVIIAEDVDGEALSTLVLNR 22 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;;; 182.17 7.55E-17 977729000 996499 896667 641755 1164674 1016907 1022561 901335 1253535 1094275 FALSE TRUE 864809.1323 890776.7354 952109.8645 1429131.033 996672.5402 1061899.583 813923.6704 985476.2953 964911.0561 0.896257875 0.923169788 0.986733294 1.481101314 1.032916489 1.10051551 0.843521965 1.021313093 1 19.88003644 2.283449031 24.99982926 0.964128335 1.076636614 0.094493153 0.166448977 335.9273295 187087.5038 0.0648003 0.050193865 192.065354 -2.283449031 0.112508278 KPLVLCGDLNVAHEEIDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPLVLCGDLNVAHEEIDLR 19 1 P27695;G3V3M6;G3V5Q1;H7C4A8 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 175.73 1.30E-12 1927605000 2865340 1923020 1433960 1501070 1967830 1377260 1836350 2134860 2028730 FALSE TRUE 2486678.059 1910387.555 2127427.852 1841910.886 1928674.033 1430244.083 1658261.06 1678336.802 1788895.851 1.390063071 1.067914353 1.189240755 1.029635619 1.078136568 0.799512215 0.926974625 0.938197046 1 20.77063797 8 0.394427115 0.913566126 7.912467114 0.715274233 0.085178023 45.43836821 0.645539166 0.083418153 244.1717683 100000000 -8 6.998900988 KPMS(ph)PITAQMSQLELQQAALEGLALPHDLAVQAANFYQPGFGKPQVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KPMSPITAQMSQLELQQAALEGLALPHDLAVQAANFYQPGFGKPQVDR 48 2 B1AKL4;Q9NRA8;B0QYZ7;H7C0J7 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 KPMS(0.733)PIT(0.248)AQMS(0.019)QLELQQAALEGLALPHDLAVQAANFYQPGFGKPQVDR;KPMS(0.688)PIT(0.302)AQMS(0.01)QLELQQAALEGLALPHDLAVQAANFYQPGFGKPQVDR;KPMS(0.923)PIT(0.077)AQMSQLELQQAALEGLALPHDLAVQAANFYQPGFGKPQVDR 219.35 3.82E-50 1138760000 386659 352028 243755 280642 340245 261174 421894 495470 383153 TRUE FALSE 335561.0335 349715.5049 361635.7333 344366.0554 333474.7902 271221.5328 380978.7848 389517.5963 337857.0888 0.993204063 1.035098911 1.070380777 1.019265443 0.987029135 0.802769993 1.127632947 1.152906389 1 18.3660536 KPMVLGHEASGTVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPMVLGHEASGTVEK 15 1 Q00796;A0A6I8PIS1;H0YKB3;Q00796-2 Q00796 SORD Sorbitol dehydrogenase 0 160.47 1.11E-06 300690000 610990 481900 340760 451480 487790 410900 573640 678530 691310 FALSE TRUE 530246.1234 478734.3672 505552.6758 553995.4344 478083.9333 426707.5889 518008.4811 533431.6398 609584.1193 0.869848978 0.785345864 0.829340299 0.908808837 0.784278852 0.699997876 0.849773583 0.875074699 1 19.21746579 1.279385383 1.890817346 1.050572016 0.814998307 0.516905334 0.055872268 0.654263965 2.42902924 0.269719056 0.015937219 19.02766002 -1.279385383 -0.235573709 KPNAGGS(ph)PAPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPNAGGSPAPVR 12 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 KPNAGGS(1)PAPVR 95.197 0.0037868 121620000 183290 163880 128530 160620 154810 134520 157360 168800 393570 TRUE FALSE 159067.7621 162803.4615 190687.5379 197091.2259 151729.5839 139695.0714 142099.2514 132703.4336 347042.603 0.458352262 0.469116645 0.549464349 0.567916516 0.43720737 0.402530036 0.409457658 0.382383697 1 18.40475325 1.233711112 24.99998645 1.000000826 0.457602565 0.889754317 0.059782677 53.4221371 275366.6414 0.134669983 0.016860382 17.1281758 -1.233711112 -0.542398261 KPNEGADGQWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KPNEGADGQWK 11 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;; 163.51 3.83E-05 906500000 2316880 1725610 1478238 1747050 1802900 1289920 2243710 2582590 2671350 FALSE TRUE 2010698.438 1714274.354 2193118.841 2143744.404 1767025.817 1339544.057 2026115.35 2030323.226 2355546.046 0.853601839 0.727760919 0.931044776 0.910083846 0.750155498 0.56867666 0.860146781 0.861933151 1 21.1676301 1.33181311 1.970039675 1.036878528 0.796341293 0.273310118 0.103676035 0.927887986 4.234420558 0.387219226 0.029939014 21.46906397 -1.33181311 -0.240537235 KPNFEVGSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPNFEVGSSR 10 1 Q6FI81-3;Q6FI81;H3BV90;H3BT65;H3BPG7;H3BUG4 Q6FI81-3 CIAPIN1 Anamorsin 0 73.848 0.070167 468400000 263810 288620 160350 202550 285910 363220 252680 285110 205810 FALSE TRUE 228946.8401 286724.0362 237895.7963 248542.0733 280220.9504 377193.3084 228175.1325 224141.4452 181479.3763 1.261558447 1.579926282 1.310869594 1.369533434 1.544092536 2.078436218 1.257306131 1.235079434 1 17.46944608 1.761425699 2.621209181 1.080946436 1.513816043 0.330500486 0.236022957 0.302014095 4.143366282 0.191978288 0.066540086 57.73320918 -1.761425699 0.432869607 KPNIFYSGPAS(ph)PARPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPNIFYSGPASPARPR 16 2 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 KPNIFYSGPAS(1)PARPR;KPNIFYSGPAS(1)PARPR 190.57 6.58E-10 6413800000 2051230 1786720 981110 1577790 1734920 1778040 1769230 2225290 1593280 TRUE FALSE 1780154.758 1774982.919 1455578.078 1936051.335 1700398.486 1846442.349 1597650.347 1749429.051 1404924.253 1.267082374 1.263401151 1.036054488 1.378046774 1.210313284 1.314264698 1.137178992 1.245212364 1 20.42206092 1.236107547 24.98886883 0.999999698 1.229072817 0.377666649 0.093325607 69.4652606 707471.5185 0.138700696 0.021087346 17.22295026 -1.236107547 0.229073118 KPNVS(ph)PEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KPNVSPEK 8 1 A0A0U1RR07;Q9HCH5-13;Q9HCH5;Q9HCH5-14;Q9HCH5-15;Q9HCH5-6 A0A0U1RR07 SYTL2 Synaptotagmin-like protein 2 1 KPNVS(1)PEK;KPNVS(1)PEK;KPNVS(1)PEK 128.97 0.00068025 1311310000 2548540 2045560 1953450 2163560 2101420 1792180 2686180 3148030 4391780 TRUE FALSE 2211743.982 2032122.582 2898144.954 2654829.366 2059605.853 1861126.324 2425674.677 2474848.282 3872588.772 0.571128026 0.524745255 0.748374053 0.685543837 0.531842128 0.480589712 0.626370322 0.639068186 1 21.88486688 1.196025115 2.996483272 1.105757748 0.596510799 0.719582441 0.078641332 0.276485706 2.836827734 0.361498986 0.021630836 15.70453621 -1.196025115 -0.509246949 KPPAPPS(ph)PVQS(ph)QSPSTNWS(ph)PAVPVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVKK 26 2 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 3 KPPAPPS(0.998)PVQS(0.49)QS(0.48)PS(0.029)T(0.004)NWS(0.999)PAVPVKK 95.042 0.0058181 2475900000 1306600 791500 685110 641220 668500 601200 1063200 1312600 784250 TRUE FALSE 1133929.499 786300.5844 1016431.488 786818.8014 655198.1579 624328.553 960091.0276 1031910.705 691536.8584 1.639723878 1.137033514 1.469815347 1.137782884 0.947452258 0.902813126 1.38834397 1.492199139 1 19.39944662 6.868116874 1.426102396 1.20130213 199.9991536 0.301536289 0.211411351 1042.765982 5.938873017 0.063612147 674382.7296 7381028.358 -6.868116874 198.7978514 KPPAPPS(ph)PVQS(ph)QSPSTNWSPAVPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVK 25 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KPPAPPS(1)PVQS(0.621)QS(0.37)PS(0.004)T(0.005)NWSPAVPVK 92.991 0.041116 1496800000 1141100 847250 622760 864000 866030 577080 939230 1264600 1581800 TRUE FALSE 990300.7438 841684.359 923928.819 1060184.405 848797.6974 599280.641 848143.6192 994175.1311 1394801.406 0.709994082 0.60344387 0.662408867 0.760097029 0.608543764 0.429653023 0.608074824 0.712771816 1 20.41162829 1.248262041 2.617271902 1.082284807 0.624671897 0.650370632 0.085877568 0.321762201 2.515464631 0.325020149 0.024043171 17.71177315 -1.248262041 -0.45761291 KPPAPPS(ph)PVQSQS(ph)PSTNWS(ph)PAVPVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVKK 26 2 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 3 KPPAPPS(0.994)PVQS(0.342)QS(0.662)PS(0.001)TNWS(1)PAVPVKK 133.47 3.49E-05 2213700000 2675700 1735200 1446800 1459300 1719500 1179800 2550000 2832900 1794300 TRUE FALSE 2322099.466 1723801.357 2146477.319 1790656.369 1685285.314 1225187.669 2302701.392 2227106.381 1582179.898 1.467658304 1.089510339 1.356658192 1.131765339 1.065166683 0.774366854 1.455397958 1.407618933 1 20.59348222 4.751146737 23.71306119 1.183486072 1.467658676 0.173129939 0.205672835 2077.670573 3914317.412 0.052784873 0.864423163 56382.81274 -4.751146737 0.284172604 KPPAPPS(ph)PVQSQSPSTNWS(ph)PAVPVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 162.95 8.28E-12 721450000 653850 468050 326740 372620 441480 300640 613310 742220 469690 TRUE FALSE 567442.0659 464975.3487 484752.5569 457229.0661 432695.4117 312205.8153 553831.2906 583502.029 414163.7833 1.370090985 1.122684714 1.170436857 1.103981286 1.044744686 0.753822106 1.337227718 1.408867826 1 18.65984188 -1.416058841 10.60068472 0.130990443 1.157196814 0 0.1958852 0 0 0 0.04642477 0.038365526 1.416058841 1.026206371 KPPAPPS(ph)PVQSQSPSTNWSPAVPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVK 25 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KPPAPPS(0.998)PVQS(0.002)QSPSTNWSPAVPVK 196.06 5.38E-25 728560000 781040 610530 404460 559200 606330 441180 612640 884940 1035100 TRUE FALSE 677823.5851 606519.3882 600058.2088 686174.9068 594265.2193 458152.4801 553226.2671 695702.4676 912731.6572 0.742631835 0.664510082 0.657431134 0.751781645 0.651084264 0.501957477 0.606121485 0.762220158 1 19.79983125 1.311538502 2.691531621 1.044958891 0.653075615 0.712359128 0.069632441 0.228386577 2.125725384 0.186847426 0.019637749 20.48983694 -1.311538502 -0.391883276 KPPAPPS(ph)PVQSQSPSTNWSPAVPVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVKK 26 2 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KPPAPPS(1)PVQSQSPSTNWSPAVPVKK 167.56 5.36E-12 790560000 326870 197870 161180 193640 240320 150410 235210 361640 198400 TRUE FALSE 283673.3013 196570.1789 239127.1871 237608.9216 235538.1022 156196.37 212399.3704 284306.1003 174945.378 1.621496404 1.123608872 1.366867704 1.358189192 1.346352243 0.892829361 1.214089636 1.625113527 1 17.41654502 2.943101208 24.99875254 1.239955533 1.350347151 0.114410483 0.224191771 1000.726046 439672.2037 0.075036436 0.075036661 877.2052219 -2.943101208 0.110391618 KPPCGSTPYSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPPCGSTPYSER 12 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 0 85.42 0.018734 66425000 36966 32104 22898 27182 30162 28708 37178 39111 38658 FALSE TRUE 32080.84944 31893.10671 33971.54939 33354.08855 29561.83521 29812.41534 33572.48328 30747.41701 34087.89528 0.94112145 0.935613843 0.996586885 0.9784731 0.867223833 0.874574833 0.984879911 0.902003974 1 15.0569719 5.04290789 12.26656527 0.939529183 0.946455083 0 0.048712559 32799513.5 340034456.6 0.011928639 4765313.913 110384.4479 -5.04290789 0.0069259 KPPLS(ph)PAQTNPVVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KPPLSPAQTNPVVQR 15 1 Q8IY33;Q8IY33-4;Q8IY33-2 Q8IY33 MICALL2 MICAL-like protein 2 1 KPPLS(1)PAQTNPVVQR;KPPLS(1)PAQTNPVVQR;KPPLS(1)PAQTNPVVQR;KPPLS(1)PAQTNPVVQR;KPPLS(1)PAQTNPVVQR;KPPLS(1)PAQTNPVVQR 235.56 6.77E-18 3713840000 3073790 3159390 2001710 2709250 3494300 3061130 3548230 4463940 3785480 TRUE FALSE 2667580.864 3138635.759 2969743.651 3324426.621 3424770.266 3178893.652 3204123.201 3509361.169 3337964.867 0.799163853 0.94028424 0.889686911 0.995944162 1.026005486 0.95234485 0.959903213 1.051347545 1 21.67053734 6.193882562 0.523809278 1.008912427 3.69E-13 0.721737398 0.038031427 9.972707783 0.650748019 0.022987733 8.555295884 1562725.007 -6.193882562 -1.008912427 KPPPGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPPPGER 7 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ; 77.058 0.062659 205535000 194834 159026 96969 123094 96190 134452 155645 189081 167022 FALSE TRUE 169086.1933 157981.3477 143863.5327 151044.3741 94276.00719 139624.4554 140550.5719 148647.4996 147276.8494 1.148083992 1.072682831 0.976823807 1.025581241 0.640127811 0.948040754 0.954329023 1.009306623 1 17.16817114 4.30341529 1.624141466 0.929484472 1.154713232 0.334323778 0.107814562 0.628265183 2.770730284 0.032079191 0.17378391 20110.14907 -4.30341529 0.22522876 KPPPNLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPPPNLFK 8 1 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 72.485 0.073513 0 300280 235100 205110 225900 221640 201760 273800 298170 312820 FALSE TRUE 260597.2372 233555.6126 304301.8821 277194.0477 217229.7976 209521.8378 247246.9181 234408.6659 275838.776 0.944744756 0.84671059 1.103187472 1.004913275 0.787524513 0.759580799 0.896345763 0.849803169 1 18.07346575 3.249972252 24.99122871 0.855418501 0.974897611 0.296531913 0.088885195 285.6323897 625525.1157 0.026324773 0.03368389 1778.165794 -3.249972252 0.11947911 KPPS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPPSPK 6 1 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 1 KPPS(1)PK;KPPS(1)PK 67.993 0.059605 3740600000 2465700 1938420 1572500 1622700 1345000 1605310 3175100 3527200 3350100 TRUE FALSE 2139851.498 1925686.391 2332966.26 1991158.836 1318237.131 1667067.314 2867179.291 2772935.729 2954054.994 0.724377678 0.651878992 0.789750449 0.674042575 0.446246645 0.564331848 0.970591034 0.938687917 1 21.49426525 2.230883472 24.98766457 0.963321105 0.641536506 0.738609544 0.091952502 94.54951069 307737.6754 0.040566663 0.02793254 170.1701856 -2.230883472 -0.321784599 KPQSSSTEPAR ddPTM_MDA-MB-175_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 ;; 129.37 0.00039515 360731000 651320 557120 401857 473643 479226 545590 563010 729950 660310 FALSE TRUE 565246.4118 553460.242 596196.3893 581190.8823 469690.3402 566579.2003 508409.3769 573855.873 582248.904 0.970798584 0.950556091 1.023954507 0.99818287 0.806683082 0.97308762 0.873182196 0.985585149 1 19.15127649 KPRGWS(ph)FGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPRGWSFGIR 10 2 B5MC17;A8MYP8 B5MC17 ODF3B Outer dense fiber protein 3B 1 KPRGWS(1)FGIR 58.674 0.086286 294390000 916050 655060 397100 679360 695430 605640 914660 895870 1130500 TRUE FALSE 794991.6715 650756.8677 589138.8882 833619.0714 681592.3036 628939.3627 825956.414 704295.1722 996853.5779 0.797500946 0.652810886 0.590998419 0.836250268 0.68374365 0.630924518 0.828563424 0.706518177 1 19.92702209 -0.041203948 1.431209165 10 0.706548498 0.520022001 0.084377282 34.58653163 2.683230861 971.0233867 0.023148572 0.90948607 0.041203948 -9.293451502 KPRPLS(ph)MDLTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPRPLSMDLTAR 12 2 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 KPRPLS(1)MDLTAR;KPRPLS(0.997)MDLT(0.003)AR 138.91 5.21E-05 762700000 855610 922420 501720 635660 895160 876300 1014420 1121200 757140 TRUE FALSE 742538.9707 916360.5623 744353.4702 779996.3185 877348.0674 910011.828 916041.7045 881440.1052 667631.7717 1.112198374 1.372553855 1.114916188 1.168303175 1.314119706 1.36304452 1.37207626 1.320248889 1 19.34869309 3.235350556 24.95708247 1.291512468 1.199384627 0.083812187 0.126321352 189.965492 1476918.951 0.037276776 0.044054983 1719.295617 -3.235350556 -0.092127841 KPRS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPRSPPR 7 2 A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7;B4DSP0;A0A087WZG9;Q86TG7-2 A0A087WXK2;B4DSP0 PEG10 Retrotransposon-derived protein PEG10 1 KPRS(1)PPR 64.711 0.05714 3159800000 520690 368730 210710 243060 317380 318700 407000 451520 226580 TRUE FALSE 451879.4972 366307.7884 312610.0608 298250.4879 311064.7589 330960.5952 367529.2026 354965.9617 199793.9705 2.261727399 1.833427642 1.564662137 1.492790234 1.55692766 1.656509425 1.839541012 1.77666003 1 17.60815352 4.639757506 2.320986004 1.591793172 2.349667371 0.49592736 0.227130193 0.41863613 3.145422819 0.058974185 0.587766378 43627.21658 -4.639757506 0.757874199 KPS(ph)ASERLPDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPSASERLPDEK 12 2 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;E7EV93;E9PGW9;E5RGQ4;Q15154-3 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 KPS(0.832)AS(0.168)ERLPDEK;KPS(0.993)AS(0.007)ERLPDEK 88.385 0.0052259 170488000 177746 154892 118859 146105 164008 138257 219855 215298 143475 TRUE FALSE 154256.4157 153874.5043 176339.61 179280.3733 160744.5617 143575.8363 198533.4959 169258.1982 126513.5489 1.219287713 1.216268973 1.393839723 1.417084374 1.270571911 1.134865297 1.569266672 1.337866178 1 16.94893237 1.237423251 24.89394463 0.999999593 1.327202584 0.400723051 0.122646981 28.48169254 623092.2309 0.180447523 0.030160051 17.27520663 -1.237423251 0.327202991 KPS(ph)FSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPSFSK 6 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 KPS(0.971)FS(0.029)K;KPS(0.999)FS(0.001)K 90.15 0.030231 2967020000 5440600 4262000 3601880 3580980 4197200 3496800 6106000 6469400 6087100 TRUE FALSE 4721610.925 4234002.641 5343761.216 4394096.241 4113683.932 3631324.159 5513841.06 5085969.155 5367489.972 0.879668327 0.788823577 0.995579171 0.818650107 0.766407381 0.676540464 1.027266206 0.947550751 1 22.35581616 2.211033073 24.99998071 0.983913461 0.824839339 0.481803914 0.083240727 203.8733372 185152.325 0.035018832 0.023615785 162.5672553 -2.211033073 -0.159074122 KPS(ph)GSPDLWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPSGSPDLWK 10 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPS(0.767)GS(0.233)PDLWK 102.87 0.0030607 335220000 661280 544860 424420 483180 609380 388110 638830 758260 790230 TRUE FALSE 573890.1725 541280.7788 629670.9316 592893.4039 597254.5302 403040.8428 576876.3649 596111.9998 696809.9096 0.823596457 0.776798337 0.903648072 0.850868215 0.857126918 0.578408598 0.827881976 0.855487259 1 19.41040562 1.265234471 2.261992636 1.046719326 0.801959598 0.339926291 0.086626338 0.725954608 4.033728999 0.35239097 0.023766666 18.41766082 -1.265234471 -0.244759727 KPS(ph)LIGLDPEQGHLNPMSYTQHCITTMAAPSWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPSLIGLDPEQGHLNPMSYTQHCITTMAAPSWK 33 1 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 1 KPS(0.999)LIGLDPEQGHLNPMSYTQHCITTMAAPSWK;KPS(1)LIGLDPEQGHLNPMSYTQHCITTMAAPSWK 197.7 3.25E-27 789110000 564800 380520 236430 292800 410420 340030 581770 549530 243490 TRUE FALSE 490160.249 378020.3391 350768.3388 359284.7152 402253.445 353111.1741 525350.0349 432017.2859 214704.8896 2.282948702 1.760650816 1.633723105 1.673388603 1.873517859 1.644634991 2.446847093 2.012144608 1 17.71199552 1.234827729 24.9938624 0.999998695 1.914311603 0.529065448 0.271586666 92.98553638 622498.5192 0.499298014 0.068789631 17.17227083 -1.234827729 0.914312908 KPS(ph)LVASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPSLVASK 8 1 P56211;H3BMD8;P56211-2;H3BQ52 P56211 ARPP19 cAMP-regulated phosphoprotein 19 1 KPS(0.975)LVAS(0.025)K;KPS(0.983)LVAS(0.017)K 115 0.0026982 1630100000 2497100 1964590 1467900 1700180 1641050 1033510 2727600 2326100 3427400 TRUE FALSE 2167101.908 1951684.479 2177781.35 2086231.855 1608396.316 1073269.798 2463077.772 1828681.617 3022216.677 0.717057094 0.645779138 0.720590739 0.690298572 0.532190934 0.355126688 0.814990464 0.605079586 1 21.52717567 1.235713587 24.99263414 1.000000493 0.634919697 0.459084216 0.124465116 74.64556051 655149.4197 0.205916013 0.030446787 17.20733393 -1.235713587 -0.365080796 KPS(ph)PAASPATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPSPAASPATK 11 1 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 1 KPS(1)PAASPATK 115.38 0.00069238 545670000 611930 511830 395520 464450 490070 415520 674380 746760 732560 TRUE FALSE 531061.9001 508467.755 586794.7949 569910.4712 480318.5658 431505.3233 608978.7314 587071.1853 645957.5913 0.822131216 0.787153463 0.908410711 0.882272271 0.743576006 0.66800875 0.942753425 0.908838588 1 19.30107993 2.117395149 24.37588468 0.941550943 0.806939176 0.496456653 0.070236655 5.557205649 1138.095267 0.030509384 0.020569423 131.0373644 -2.117395149 -0.134611767 KPS(ph)PAQAAETPALELPLPSVPAPAPL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPSPAQAAETPALELPLPSVPAPAPL 26 1 A0A5H1ZRP4;Q8WX92;Q8WX92-2 A0A5H1ZRP4 NELFB Negative elongation factor B 1 KPS(0.981)PAQAAET(0.019)PALELPLPSVPAPAPL 78.413 0.012669 19345000 57866 43923 26936 30393 39430 40655 44672 55303 48696 TRUE FALSE 50218.86149 43634.46692 39962.3397 37294.19518 38645.42014 42219.02416 40339.71632 43476.88382 42939.21435 1.169533776 1.016191553 0.930672354 0.868534642 0.900002963 0.983227681 0.939460978 1.012521642 1 15.39000817 4.667044663 2.677119029 0.950267431 1.19500793 0.717388652 0.043981462 0.234760735 2.466517189 0.012714246 0.118093263 46456.30488 -4.667044663 0.244740498 KPS(ph)PEPEGEVGPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KPSPEPEGEVGPPK 14 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK 170.53 1.94E-06 11269380000 9440550 7076500 6443210 6586440 6740220 4651601 9250040 11029980 10960300 TRUE FALSE 8192957.398 7030014.006 9559167.907 8081991.869 6606102.809 4830551.1 8352972.545 8671304.612 9664585.82 0.847729799 0.727399408 0.989092351 0.836248135 0.683537084 0.499819774 0.864286654 0.897224648 1 23.20427648 1.691771639 2.611917717 0.973675993 0.76947073 0.257761667 0.128278374 0.363770563 5.386543302 0.121957712 0.037515546 49.17808795 -1.691771639 -0.204205263 KPS(ph)PQPS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPSPQPSSPR 10 1 O75909;G3V5E1;O75909-1;O75909-4 O75909 CCNK Cyclin-K 2 KPS(1)PQPS(0.562)S(0.438)PR 101.62 0.011216 666800000 1672500 1118400 737650 903910 1152700 959710 1225100 1282600 1275200 TRUE FALSE 1451474.887 1111053.157 1094380.007 1109156.581 1129763.525 996630.6647 1106289.991 1008325.971 1124447.309 1.290834062 0.988088235 0.973260373 0.986401561 1.004727848 0.886329361 0.983852229 0.896730299 1 20.10078463 4.751396377 3.455964807 0.957416604 1.337413583 0.866563811 0.040289298 0.106831265 2.150303314 0.009868708 0.10835323 56415.23181 -4.751396377 0.379996979 KPS(ph)PQPSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KPSPQPSSPR 10 1 O75909;G3V5E1;O75909-1;O75909-4 O75909 CCNK Cyclin-K 2 KPS(1)PQPS(0.231)S(0.769)PR;KPS(0.999)PQPS(0.343)S(0.657)PR;KPS(0.993)PQPS(0.289)S(0.717)PR;KPS(1)PQPS(0.259)S(0.742)PR;KPS(1)PQPS(0.311)S(0.689)PR;KPS(0.998)PQPS(0.186)S(0.816)PR;KPS(0.993)PQPS(0.203)S(0.804)PR 114.79 0.00087512 3779406000 6537020 4333860 2951360 3467680 4049840 3940240 4943860 5690790 4819410 TRUE FALSE 5673136.244 4305390.588 4378647.568 4255069.744 3969256.107 4091823.582 4464405.218 4473858.844 4249664.84 1.334960863 1.013112975 1.030351271 1.001271842 0.934016271 0.962857951 1.050531133 1.052755691 1 22.01891763 4.738883143 6.708863269 1.008098334 1.340755539 0.889806323 0.036419462 0.040437994 12.17894228 0.010164985 0.061043042 54812.9458 -4.738883143 0.332657204 KPS(ph)PSESPEPWKPFPAVSPEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPSPSESPEPWKPFPAVSPEPR 22 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPS(0.838)PS(0.131)ES(0.031)PEPWKPFPAVSPEPR 76.162 0.008818 662700000 135690 90948 65412 87071 109130 77344 113420 138130 124240 TRUE FALSE 117758.2227 90350.5566 97045.46199 106841.8013 106958.5265 80319.47373 102420.5459 108591.9744 109552.4887 1.074902305 0.824723908 0.885835302 0.975256725 0.976322197 0.733159736 0.934899308 0.991232383 1 16.74126273 1.792784938 4.332198301 0.995493355 0.907110899 0.118108432 0.091566908 0.402256384 14.07599314 0.053146776 0.02388333 62.05616573 -1.792784938 -0.088382455 KPS(ph)VPDSASPADDSFVDPGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPSVPDSASPADDSFVDPGER 21 1 P16333-2;P16333;C9JAB9;C9K098;C9JVV5;H7C5C7;C9J869 P16333-2 NCK1 Cytoplasmic protein NCK1 1 KPS(1)VPDSASPADDSFVDPGER 82.6 0.0023948 119620000 119480 136610 130150 101800 138820 164620 136200 143320 178000 TRUE FALSE 103690.4153 135712.5999 193090.9753 124915.2459 136057.7536 170953.0379 122991.345 112672.1333 156957.0428 0.660629262 0.864648043 1.230215427 0.795856266 0.866847076 1.089170864 0.783598766 0.717853314 1 17.26001024 0.951941724 20.64757372 2.201077703 0.877741869 0.050248223 0.169148319 21.02105398 187388.517 26105.8737 0.040672824 8.952446294 -0.951941724 -1.323335834 KPS(ph)VSEEVQATPNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KPSVSEEVQATPNK 14 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 KPS(0.908)VS(0.092)EEVQATPNK;KPS(0.94)VS(0.06)EEVQATPNK;KPS(0.997)VS(0.003)EEVQATPNK 205.92 7.09E-09 3313830000 3389220 2473050 2670900 3255700 3691190 2950080 5503630 5904660 5497830 TRUE FALSE 2941325.99 2456804.372 3962556.174 3994956.445 3617742.541 3063571.487 4969888.81 4641994.409 4847882.801 0.606723824 0.50677883 0.817378707 0.824062093 0.746252063 0.631940089 1.025166864 0.957530246 1 22.20892339 -2 0.082777768 2.816883259 2.88E-09 0.607811453 0.108485093 283.6409934 2.219236339 95.44936279 14.54193058 0.01 2 -2.816883256 KPSDEEFASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPSDEEFASR 10 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E9PDQ5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 0 92.856 0.014723 373900000 476820 382890 274640 356710 347340 322500 361980 358760 387710 FALSE TRUE 413807.0289 380374.7704 407456.8226 437706.4575 340428.6136 334906.7837 326875.2353 282041.9659 341875.3655 1.210403178 1.112612399 1.191828554 1.280310024 0.995768189 0.979616602 0.956123981 0.824984759 1 18.38311094 3.089059225 4.723959096 0.929491818 1.191244046 0.800078608 0.061721882 0.093515898 3.670228643 0.020354548 0.023197727 1227.606629 -3.089059225 0.261752228 KPSDGS(ph)PDTKPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KPSDGSPDTKPSR 13 2 Q92733 Q92733 PRCC Proline-rich protein PRCC 1 KPSDGS(0.994)PDT(0.006)KPSR;KPSDGS(1)PDTKPSR;KPSDGS(1)PDTKPSR 183.36 5.44E-06 973870000 2149490 1766750 1454170 1521590 1557070 1204160 2118390 2676840 2248070 TRUE FALSE 1865429.45 1755144.103 2157411.476 1867090.266 1526087.353 1250484.814 1912948.864 2104418.597 1982305.726 0.941040237 0.885405354 1.088334382 0.941878057 0.769854687 0.630823388 0.965012026 1.061601432 1 20.91874805 2.005593774 24.99990885 1.028632633 0.877221517 0.2305394 0.118806733 220.7512447 986585.8521 0.05328191 0.035800623 101.2963446 -2.005593774 -0.151411116 KPSETQELVQQVLSLATQDSDNPDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPSETQELVQQVLSLATQDSDNPDLR 26 1 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1 P63010 AP2B1 AP-2 complex subunit beta 0 225.14 2.99E-34 331920000 282650 187670 178220 250050 213660 205300 195240 296460 342350 FALSE TRUE 245297.0864 186437.1834 264407.7881 306827.6743 209408.584 213198.0238 176305.6549 233064.3361 301877.773 0.812570876 0.617591622 0.875876967 1.016397038 0.69368666 0.706239554 0.584029931 0.77204868 1 18.20360501 1.244985254 6.680128618 1.005526587 0.75508479 0.267284264 0.124989871 0.157859774 35.27370438 0.178514785 0.032226891 17.57863928 -1.244985254 -0.250441798 KPSGS(ph)PDLWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KPSGSPDLWK 10 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPS(0.057)GS(0.943)PDLWK;KPS(0.274)GS(0.726)PDLWK;KPS(0.007)GS(0.993)PDLWK 131.86 0.00014636 3011860000 5291590 4062270 3605400 3916290 4132720 3174470 5182180 6204900 6401110 TRUE FALSE 4592292.974 4035584.681 5348983.499 4805543.501 4050486.958 3296593.915 4679612.981 4878030.422 5644378.068 0.81360478 0.714974198 0.947665701 0.851385829 0.717614396 0.584049097 0.829075042 0.864228151 1 22.42838319 1.405389875 2.053812692 1.022188257 0.776528138 0.354740711 0.096014656 0.618674641 3.632655889 0.259463836 0.028002166 25.43254812 -1.405389875 -0.245660118 KPSKYPLCSADAAVSTT(ph)PPGS(ph)PPPPPPLPEPPVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPSKYPLCSADAAVSTTPPGSPPPPPPLPEPPVLK 35 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 2 KPS(0.001)KYPLCS(0.001)ADAAVS(0.084)T(0.426)T(0.488)PPGS(1)PPPPPPLPEPPVLK 143.39 2.29E-10 569260000 291260 199580 144990 167060 205600 163980 282660 339360 194930 TRUE FALSE 252769.253 198268.9458 215107.649 204993.5264 201508.9622 170288.4167 255247.6767 266790.5049 171885.5975 1.4705668 1.153493654 1.25145825 1.192616074 1.172343496 0.990707885 1.484985831 1.552139963 1 17.39108914 2.212506464 24.99999216 1.394518344 1.202884844 0.094055417 0.185946119 370.2322326 355249.6269 0.074419683 0.050192232 163.1197186 -2.212506464 -0.1916335 KPSLLGGACHPWLFIEEAAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPSLLGGACHPWLFIEEAAGR 21 1 Q96HU1;Q96HU1-2;B0QY81 Q96HU1 SGSM3 Small G protein signaling modulator 3 0 91.729 0.0012804 137180000 201060 213610 134810 130640 190280 173610 198200 211250 220220 FALSE TRUE 174489.4116 212206.7818 200004.5669 160303.8087 186493.8003 180288.889 178978.5945 166075.8314 194185.8425 0.898569171 1.09280254 1.02996472 0.825517487 0.960388244 0.928434775 0.921687144 0.855241707 1 17.5670785 3.768332795 24.91333148 0.911802744 1.015681207 0.288087569 0.067515334 734.0422119 614243.4191 0.016815539 0.029120103 5865.874883 -3.768332795 0.103878463 KPSPAQAAET(ph)PALELPLPSVPAPAPL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPSPAQAAETPALELPLPSVPAPAPL 26 1 A0A5H1ZRP4;Q8WX92;Q8WX92-2 A0A5H1ZRP4 NELFB Negative elongation factor B 1 KPS(0.442)PAQAAET(0.558)PALELPLPSVPAPAPL 100.19 0.0028739 21895000 72488 49777 37152 37638 52420 48240 55257 65836 62752 TRUE FALSE 62908.52714 49450.01161 55118.83147 46184.28316 51376.94456 50095.82402 49898.18464 51757.48374 55333.53005 1.136897051 0.893671732 0.996119919 0.834652753 0.928495697 0.905342999 0.901771215 0.935372887 1 15.75586634 4.743403195 24.93132048 0.923186936 1.136897142 0.657646808 0.048169421 292.3397686 1505018.062 0.011038208 0.088069979 55386.40735 -4.743403195 0.213710206 KPSPQPS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KPSPQPSSPR 10 1 O75909;G3V5E1;O75909-1;O75909-4 O75909 CCNK Cyclin-K 1 KPS(0.02)PQPS(0.49)S(0.49)PR;KPSPQPS(0.846)S(0.154)PR;KPSPQPS(0.655)S(0.345)PR 97.463 0.0037005 824040000 1143310 942530 581087 760884 852267 865383 899971 1096320 997290 TRUE FALSE 992218.6867 936338.4584 862102.6168 933654.3416 835308.5541 898674.844 812691.9509 861880.4996 879391.5123 1.128301414 1.064757216 0.980339934 1.061704973 0.949871067 1.021928039 0.924152598 0.980087353 1 19.74614608 8 0.507470149 0.972579312 6.343116622 0.622547763 0.03698685 71.2770403 0.763211282 0.020781109 408.6893311 100000000 -8 5.37053731 KPSPQPSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KPSPQPSSPR 10 1 O75909;G3V5E1;O75909-1;O75909-4 O75909 CCNK Cyclin-K 1 KPSPQPS(0.002)S(0.998)PR;KPS(0.006)PQPS(0.107)S(0.888)PR;KPS(0.002)PQPS(0.093)S(0.905)PR;KPSPQPS(0.151)S(0.848)PR 108.35 0.0022914 815070000 1355650 1175970 691602 881310 1045670 1078710 1149690 1366800 1176070 TRUE FALSE 1176497.418 1168244.976 1026063.04 1081424.905 1024863.213 1120208.672 1038193.241 1074520.456 1037036.344 1.134480411 1.126522693 0.989418593 1.042803284 0.988261615 1.080201941 1.001115579 1.036145418 1 19.98403503 4.250800559 24.92422865 1.022040825 1.130501645 0.726527037 0.028231795 100.153888 203939.5932 0.00632814 0.016474083 17815.60434 -4.250800559 0.10846082 KPSPSES(ph)PEPWKPFPAVSPEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPSPSESPEPWKPFPAVSPEPR 22 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPSPS(0.001)ES(0.999)PEPWKPFPAVSPEPR;KPSPS(0.001)ES(0.999)PEPWKPFPAVSPEPR 221.29 4.94E-26 1968010000 1332720 990070 771650 952940 1117690 865190 1227240 1516800 1354800 TRUE FALSE 1156597.675 983566.165 1144822.521 1169319.592 1095450.156 898474.4192 1108222.454 1192444.124 1194637.087 0.968158186 0.823317956 0.958301507 0.978807375 0.916973169 0.752089843 0.927664531 0.998164327 1 20.18814099 1.802474894 4.333722438 0.998798447 0.898997733 0.254299202 0.068814779 0.284838137 9.558841599 0.041289328 0.018801407 63.45632162 -1.802474894 -0.099800714 KPSQTAS(ph)YER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KPSQTASYER 10 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 KPSQT(0.03)AS(0.97)YER;KPS(0.001)QT(0.161)AS(0.838)YER;KPSQT(0.136)AS(0.864)YER;KPSQT(0.007)AS(0.993)YER 118.58 0.00049395 2521610000 5283700 3796320 2124610 2830280 2811590 2954210 3111400 3464380 3402500 TRUE FALSE 4585445.658 3771381.724 3152078.502 3472938.332 2755644.86 3067860.37 2809656.907 2723549.297 3000260.326 1.528349263 1.257018163 1.050601668 1.157545664 0.918468586 1.022531393 0.93647104 0.907770993 1 21.51665626 8 0.511379095 0.939104475 21.64501143 0.897389609 0.060862889 32.11085623 0.339765379 0.034187543 716.7382567 100000000 -8 20.70590695 KPSQTASYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPSQTASYER 10 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 0 ; 100.04 0.0068735 199303000 250200 270090 170367 203994 262390 254220 278130 311270 300820 FALSE TRUE 217135.4361 268315.761 252757.051 250313.9556 257168.9524 264000.0079 251156.9954 244707.3328 265257.4023 0.818583889 1.011529777 0.952874637 0.943664355 0.969507166 0.99525972 0.946842551 0.922527819 1 18.01703349 4.750726318 24.9967228 0.962953354 0.818583801 0.731710181 0.028257165 1084.889177 2229068.349 0.006982167 0.117413222 56328.25767 -4.750726318 -0.144369552 KPSVGVPPPAS(ph)PSYPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KPSVGVPPPASPSYPR 16 1 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 KPSVGVPPPAS(0.975)PS(0.025)YPR;KPSVGVPPPAS(0.987)PS(0.013)YPR;KPSVGVPPPAS(0.978)PS(0.022)YPR;KPSVGVPPPAS(0.967)PS(0.033)YPR 115.46 0.00030846 3322030000 3984150 4128550 2203700 2972520 3874250 3581390 3996520 5245360 3066940 TRUE FALSE 3457634.483 4101429.283 3269416.691 3647476.098 3797160.005 3719168.391 3608938.106 4123680.583 2704369.847 1.278536102 1.516593334 1.20893845 1.348734198 1.404083102 1.375243994 1.334483931 1.52482124 1 21.36686104 1.224414748 24.99846195 0.999999038 1.378651677 0.600045694 0.095872263 508.492647 898551.3136 0.467108187 0.022499616 16.76543197 -1.224414748 0.378652638 KPTAEAS(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPTAEASPVK 10 1 Q6ZRI6;H3BMJ2;Q6ZRI6-2 Q6ZRI6 C15orf39 Uncharacterized protein C15orf39 1 KPT(0.001)AEAS(0.999)PVK;KPTAEAS(1)PVK 60.55 0.059637 258490000 584650 457430 319550 364270 461460 348140 586650 678060 453220 TRUE FALSE 507387.0212 454425.1122 474085.4488 446983.071 452277.8488 361533.1711 529756.7733 533062.1457 399640.8479 1.269607508 1.137083746 1.186278758 1.118461922 1.131710763 0.904645191 1.325582147 1.333853004 1 18.60834453 1.18741447 23.2047224 0.999992106 1.177781285 0.167448156 0.123202022 15311.34682 6945136.903 30.37483528 0.032156328 15.39623282 -1.18741447 0.177789179 KPTDGASSSNCVTDISHLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KPTDGASSSNCVTDISHLVR 20 1 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 ;;; 206.71 4.79E-22 1201935000 1203377 797125 537082 638078 818221 760190 815318 1060325 869406 FALSE TRUE 1044347.68 791888.6334 796816.6516 782963.3623 801940.0029 789435.0012 736248.5859 833582.7502 766625.8131 1.362265218 1.032953261 1.039381453 1.021310982 1.046064441 1.0297527 0.960375418 1.087339789 1 19.54816305 4.738650731 7.410206396 1.029348396 1.366118512 0.913697815 0.032363365 0.025848798 13.20467867 0.007469895 0.043588995 54783.62066 -4.738650731 0.336770116 KPTETQELVQQVLSLATQDSDNPDLR ddPTM_MDA-MB-175_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 ; 179.2 3.74E-17 853830000 837360 691580 520680 714760 752220 710050 704520 914610 1079810 FALSE TRUE 726700.7544 687036.9654 772482.5896 877057.1824 737252.2937 737366.083 636195.7588 719027.769 952156.0919 0.76321599 0.721559176 0.811298269 0.921127523 0.774297723 0.77441723 0.668163302 0.755157453 1 19.86083858 3.770152726 0.010930912 1.564261954 3.92E-07 0.046489736 0.093773314 24992.57677 160.9940833 11295.87875 11741.92031 5890.507668 -3.770152726 -1.564261562 KPTGSLPS(ph)PSGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPTGSLPSPSGVR 13 1 G3V497;G3V4H6;G3V538;G3V500;G3V3N9;F8W717;A0A3B3IU69;O00423;O00423-3 G3V497 EML1 Echinoderm microtubule-associated protein-like 1 1 KPTGSLPS(0.997)PS(0.002)GVR 110.74 0.00063397 169990000 258900 272620 201260 268680 320810 284440 298090 394630 525200 TRUE FALSE 224685.709 270829.1413 298590.0092 329687.9005 314426.5087 295382.5909 269181.2777 310241.4455 463111.4543 0.485165519 0.584803375 0.644747623 0.71189753 0.678943493 0.63782182 0.58124513 0.669906656 1 18.82099991 1.238016939 3.791578532 1.046935231 0.624407005 0.789003109 0.061545315 0.126929677 2.954649228 0.151881648 0.016510989 17.29883831 -1.238016939 -0.422528225 KPTMYPEWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPTMYPEWK 9 1 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 70.488 0.083807 475850000 762510 1050000 745710 758270 1027300 990530 1122100 1311500 1163000 FALSE TRUE 661742.3715 1043102.481 1106337.85 930446.7929 1006858.74 1028636.33 1013278.915 1031045.931 1025511.465 0.645280325 1.017153407 1.078815682 0.907300235 0.981811295 1.003047128 0.988071757 1.005396786 1 19.96791219 4.740529763 24.9967663 0.997230093 0.645280205 0.876394367 0.041593735 57.28320655 727112.5782 0.010002155 0.063429242 55021.16256 -4.740529763 -0.351949887 KPTSAKPSSTTPR ddPTM_MDA-MB-175_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 50.843 0.092574 298580000 286740 235640 150350 229890 225230 225020 253970 270540 507050 FALSE TRUE 248846.5825 234092.0653 223059.7629 282090.0381 220748.3637 233676.665 229340.0285 212687.1263 447107.1266 0.556570378 0.523570418 0.498895566 0.630922706 0.493725889 0.522641334 0.512942011 0.475696122 1 18.77026102 1.234947327 24.99999998 1.000000671 0.524925182 0.923578481 0.042768134 26.1069866 180603.7079 0.074844441 0.010405488 17.17700045 -1.234947327 -0.475075489 KPTTEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPTTEEK 7 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ; 88.819 0.029387 789820000 1158450 902990 648340 762730 409660 634660 1105420 1264860 1288390 FALSE TRUE 1005357.897 897058.1992 961879.3926 935919.5041 401508.5675 659075.7809 998216.5385 994379.5322 1136078.002 0.884937386 0.78960969 0.846666682 0.823816237 0.353416374 0.580132508 0.87865141 0.875273996 1 20.11563046 -0.617914437 12.37780873 6.069712958 0.777703235 0 0.184602656 0 0 0 0.044323794 0.241038027 0.617914437 -5.292009723 KPVGEVHSQFSTGHANS(ph)PCTIIIGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPVGEVHSQFSTGHANSPCTIIIGK 25 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 KPVGEVHSQFS(0.001)T(0.001)GHANS(0.865)PCT(0.132)IIIGK 76.002 0.01422 476400000 226690 218250 94244 184100 220620 199180 253630 317820 297820 TRUE FALSE 196732.3421 216816.3014 139820.7136 225902.7188 216230.0936 206842.5835 229033.0016 249856.6663 262612.0589 0.749136742 0.825614415 0.532423051 0.860214568 0.823382196 0.787635512 0.872134367 0.951428763 1 18.00257364 1.518698389 0.529518674 1.151810708 0.724243859 0.535605362 0.085829622 2.650790351 0.758339733 0.698442306 0.066442411 33.01401839 -1.518698389 -0.427566849 KPVTDCVISVPSFFTDAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPVTDCVISVPSFFTDAER 19 1 Q92598-2;Q92598;Q92598-4 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 116.21 0.00019682 1263830000 2816100 2483900 1929040 2486100 2569900 2582400 2716700 3120000 3905000 FALSE TRUE 2443945.25 2467583.097 2861930.196 3050607.003 2518764.018 2681746.599 2453234.852 2452812.28 3443355.349 0.709756909 0.716621681 0.831145759 0.885940222 0.731485357 0.778817847 0.712454744 0.712332023 1 21.71538364 SFS(ph)LEGLTGGAGVGNKPSSSLEVSSANAEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFSLEGLTGGAGVGNKPSSSLEVSSANAEELR 32 1 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36;H0YLH1 Q12802-2 AKAP13 A-kinase anchor protein 13 1 SFS(1)LEGLTGGAGVGNKPSSSLEVSSANAEELR 326.37 1.62E-106 120320000 53219 53545 41067 59260 56854 48753 55748 76514 135600 TRUE FALSE 46185.97431 53193.25937 60927.13856 72715.88873 55722.71663 50628.55946 50341.56754 60152.07653 119569.5225 0.386268786 0.44487306 0.509554085 0.608147354 0.466027759 0.423423615 0.421023405 0.503071981 1 16.86749018 1.238509865 5.034084113 1.033371085 0.469987244 0.883960601 0.060445351 0.05755694 3.766246717 0.113808422 0.016135706 17.3184837 -1.238509865 -0.563383841 FQEHLQLQNLGINPANIGFSTLTMESDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 FQEHLQLQNLGINPANIGFSTLTMESDK 28 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;J3KSQ2;J3QL20 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 254.85 1.65E-53 345390000 251010 195840 167600 228470 188910 164400 209810 288710 582770 FALSE TRUE 217838.3925 194553.5141 248651.9206 280347.6054 185151.0606 170724.5744 189462.6585 226971.6132 513875.5945 0.423912703 0.378600417 0.483875715 0.5455554 0.360303277 0.332229388 0.36869363 0.441685917 1 18.97105961 1.238521754 5.551909606 1.027760386 0.414131951 0.895994524 0.062510458 0.047286479 4.623851943 0.110880095 0.016760346 17.31895778 -1.238521754 -0.613628435 KPVTVSPT(ph)TPTS(ph)PTEGEAS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 2 KPVTVS(0.065)PT(0.913)T(0.022)PT(0.044)S(0.953)PT(0.003)EGEAS 167.41 4.00E-11 326440000 368500 478980 347630 473370 606230 585080 702460 789520 717220 TRUE FALSE 319801.7913 475833.5488 515745.0308 580855.8935 594167.2091 607588.4062 634335.5373 620687.2921 632431.0687 0.50567059 0.752388003 0.815496038 0.918449334 0.939497186 0.960718782 1.003011346 0.981430741 1 19.27054872 5.089855159 0.662138611 0.990981787 3.82E-17 0.983693256 0.019585574 0.521310216 0.127271007 0.008412355 0.43159093 122985.8533 -5.089855159 -0.990981787 KPVTVSPT(ph)TPTSPTEGEAS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 KPVTVSPT(0.633)T(0.134)PT(0.078)S(0.148)PT(0.006)EGEAS(0.001) 179.9 6.73E-14 1194300000 448140 589010 397140 557790 750580 644430 759470 835090 798810 TRUE FALSE 388917.1636 585140.7545 589198.2324 684444.7448 735644.9265 669221.6391 685816.7163 656512.5022 704375.5918 0.552144578 0.830722645 0.836483034 0.971704234 1.044392984 0.950092035 0.973652018 0.932048909 1 19.42598539 5.140325307 0.939630873 0.974717739 2.27E-18 0.911351026 0.041491773 1.117924489 0.469519258 0.01395499 1.323820888 138141.8624 -5.140325307 -0.974717739 KPVTVSPTT(ph)PT(ph)SPTEGEAS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 2 KPVTVS(0.025)PT(0.078)T(0.897)PT(0.816)S(0.171)PT(0.01)EGEAS(0.002) 156.98 8.42E-09 303060000 183970 235470 173340 260050 312870 273800 333670 388540 358470 TRUE FALSE 159657.8984 233923.1821 257167.8038 319098.3271 306644.4991 284333.2632 301310.7348 305453.7446 316092.085 0.505099324 0.740047579 0.813585079 1.009510653 0.970111286 0.899526678 0.953237202 0.966344174 1 18.26998538 4.620009898 1.142066588 0.964548537 0.350389791 0.934003139 0.039854426 0.310300376 0.395762537 0.012409037 0.217893704 41687.88844 -4.620009898 -0.614158746 ETDEFFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ETDEFFK 7 0 O14745;O14745-2;J3QRA3 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 101.64 0.020725 72476000 159030 109960 112320 153780 114510 91552 133810 178370 321820 FALSE TRUE 138013.7826 109237.6655 166638.3277 188698.0994 112231.475 95074.06468 120833.1268 140226.9636 283774.8062 0.486349667 0.384944904 0.587220303 0.664957196 0.395494852 0.335033493 0.425806393 0.494148742 1 18.11438699 1.238603357 5.554267996 1.025098289 0.468980861 0.745306518 0.097159656 0.080413698 7.877816607 0.170942579 0.025872673 17.32221228 -1.238603357 -0.556117428 RKS(ph)LPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RKSLPAR 7 2 Q8NCE2;Q8NCE2-2;C9JSR1;Q8NCE2-3 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 RKS(1)LPAR 79.489 0.025584 302160000 571110 554230 339550 346140 469290 441200 568260 602390 203020 TRUE FALSE 495636.3665 550589.2266 503757.5157 424736.3774 459952.0472 458173.2495 513150.2327 473573.5863 179019.2069 2.768621173 3.075587454 2.813985854 2.372574344 2.569288822 2.559352471 2.866453503 2.645378642 1 17.44975486 1.238879824 5.95713405 0.935374945 2.713417098 0.88785212 0.191036786 0.044647619 5.92707125 0.323482564 0.051020441 17.33324292 -1.238879824 1.778042154 KPVVDCVVSVPCFYTDAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPVVDCVVSVPCFYTDAER 19 1 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 144.88 2.10E-07 4221400000 3012300 2809700 1950530 2326600 2691300 2651500 2775500 3142800 3471700 FALSE TRUE 2614216.923 2791242.896 2893812.832 2854890.09 2637748.395 2753504.921 2506332.437 2470736.677 3061279.581 0.85396216 0.911789604 0.94529518 0.932580646 0.861648969 0.899462087 0.818720529 0.80709279 1 21.54570338 3.226845602 24.76290282 0.865302389 0.913426253 0.055217935 0.057545233 401.2808424 848214.9963 0.017572048 0.020093067 1685.953538 -3.226845602 0.048123864 KPVVGQCTIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPVVGQCTIER 11 1 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-2;H0YD14 Q9NZM1-6 MYOF Myoferlin 0 110.29 0.0018497 0 187490 165180 115440 140640 153490 153870 186750 217010 172270 FALSE TRUE 162712.7215 164094.9217 171267.1701 172574.4615 150435.8493 159789.4785 168639.0137 170604.1003 151904.4369 1.071151869 1.080251012 1.127466542 1.136072554 0.990332162 1.051907909 1.110165162 1.123101496 1 17.21280448 KPYCNAHYPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPYCNAHYPK 10 1 Q14847;Q14847-2;C9J9W2;F6S2S5;O76041-2 Q14847;O76041-2 LASP1;NEBL LIM and SH3 domain protein 1;Nebulette 0 67.113 0.041512 1859600000 5898200 1777000 1270500 1557400 1751100 1692500 1893600 2302900 2418800 FALSE TRUE 5118737.926 1765326.77 1884918.05 1911031.473 1716256.536 1757611.57 1709958.963 1810442.756 2132852.22 2.399949644 0.827683584 0.883754642 0.895998071 0.804676724 0.824066269 0.801724071 0.848836473 1 21.02435258 4.739198915 24.99994267 0.85604349 2.399950118 0.985695013 0.058267286 5.501448539 215427.1467 0.014026041 0.081307802 54852.8143 -4.739198915 1.543906629 KPYIWEYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KPYIWEYSR 9 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 105.4 0.004978 2553100000 2932900 2977600 1730900 1959140 2706400 2605800 3166800 3562500 2515000 FALSE TRUE 2545309.834 2958039.95 2567969.03 2403992.681 2652547.935 2706046.812 2859684.223 2800687.098 2217679.565 1.147735622 1.333844617 1.157953146 1.08401264 1.196091616 1.220215425 1.289493878 1.26289079 1 21.08061949 1.23079997 24.99261129 0.999999611 1.215543991 0.455864389 0.072511111 277.9995166 895202.8425 0.194339435 0.018479624 17.01374699 -1.23079997 0.21554438 KQAEEIGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQAEEIGEK 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 125.74 0.00079063 670910000 1072530 870600 710370 823800 746610 677360 1134030 1277760 1063340 FALSE TRUE 930792.4431 864880.9713 1053907.308 1010856.381 731753.9217 703418.4775 1024051.945 1004520.968 937633.1566 0.992704275 0.92240869 1.124008148 1.078093681 0.78042667 0.750206488 1.09216695 1.071336866 1 19.83866406 KQAEILQESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KQAEILQESR 10 1 E5RJD8;O75347;E5RIW3;O75347-2 E5RJD8 TBCA Tubulin-specific chaperone A 0 ;;; 138.45 0.00010327 1615780000 2190970 2171680 1342651 1702300 2066270 1914090 2216440 2482840 2094440 FALSE TRUE 1901427.763 2157414.091 1991961.514 2088833.233 2025155.27 1987726.281 2001489.99 1951903.987 1846837.689 1.029558674 1.168166593 1.078579632 1.131032383 1.096552925 1.076286396 1.083738978 1.056889839 1 20.81662565 -0.477583057 0.667586232 6.03E-13 1.104124178 0.431409064 0.035687945 23.33361378 1.237996634 32.04961333 0.014453339 0.332979075 0.477583057 1.104124178 KQAESASEAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQAESASEAAK 11 1 P51572;P51572-2;C9JSP1;C9JQ75;C9J0M4;A0A2R8Y5M6;C9JMD7 P51572 BCAP31 B-cell receptor-associated protein 31 0 75.479 0.03462 0 76455 48774 82635 59897 28860 31412 48396 57475 61749 FALSE TRUE 66351.27804 48453.60038 122597.5624 73497.52932 28285.74246 32620.43997 43702.56337 45184.41852 54449.10356 1.218592662 0.889887936 2.25159928 1.349839107 0.51948959 0.59909967 0.802631458 0.829846876 1 15.73262068 3.326936332 6.461066076 0.758089519 1.458891439 0.468073297 0.359335952 0.193459309 11.61273684 0.105441239 0.136097569 2122.933215 -3.326936332 0.70080192 KQALYLMFDTSQESPVKS(ph)SPVR ddPTM_MDA-MB-175_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 KQALYLMFDTSQES(0.128)PVKS(0.491)S(0.381)PVR 92.275 0.0010948 222920000 232990 196050 136840 168480 194990 232960 292310 301000 152740 TRUE FALSE 202199.7812 194762.1346 203016.2817 206735.9591 191110.0805 241922.1219 263961.8212 236633.4924 134683.2512 1.501298635 1.446075387 1.507361011 1.534978976 1.418959513 1.79623019 1.959871171 1.756963025 1 17.03921093 2.748116921 24.58291731 1.679462969 1.48413533 0.061361874 0.251452467 1196.699554 3078423.997 0.082381936 0.081316898 559.9083206 -2.748116921 -0.195327639 KQALYLMFDTSQESPVKSS(ph)PVR ddPTM_MDA-MB-175_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 KQALYLMFDTSQES(0.024)PVKS(0.407)S(0.569)PVR 95.646 0.00082705 268320000 243690 181050 163490 189780 219670 213140 303780 285700 141130 TRUE FALSE 211485.7491 179860.6706 242554.3108 232872.4496 215298.9968 221339.6337 274319.4624 224605.2783 124445.7722 1.699420923 1.44529354 1.949076345 1.871276505 1.730062766 1.77860308 2.204329304 1.804844587 1 16.92515769 1.239763396 9.183323283 0.994872146 1.820266163 0.637272973 0.192029859 0.050851136 65.94637574 0.26972176 0.048740067 17.36854333 -1.239763396 0.825394018 KQAS(ph)VDSGIVQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KQASVDSGIVQ 11 1 A0A096LNH6;Q14185 A0A096LNH6 DOCK1 Dedicator of cytokinesis protein 1 1 KQAS(0.998)VDS(0.002)GIVQ;KQAS(0.997)VDS(0.003)GIVQ;KQAS(0.992)VDS(0.008)GIVQ 130.27 0.00024119 1089370000 4250100 3477930 2027120 2610360 3420810 2116300 6539890 4923420 3672800 TRUE FALSE 3688438.517 3455083.249 3007442.012 3203082.135 3352742.574 2197715.43 5905652.474 3870584.947 3238605.768 1.138897038 1.066842801 0.928622447 0.989031196 1.035242575 0.678599245 1.823516938 1.195139274 1 21.62694143 2.260153413 24.99999668 1.329631805 0.978702153 0.34931594 0.235695946 261.5439232 302813.0998 0.085880578 0.066461202 182.0343774 -2.260153413 -0.350929652 KQDADSLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KQDADSLQR 9 1 P14324-2;P14324;A0A087WVN4;A0A087X1D8 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 ;;;;; 185.08 6.94E-05 9231620000 12294300 12559000 7908170 9966330 10966400 11199000 14054800 15783600 14213800 FALSE TRUE 10669577.11 12476499.1 11732587.46 12229337.55 10748190.1 11629832.78 12691767.66 12408399.97 12533460.76 0.851287391 0.995455233 0.936101185 0.975735097 0.85755964 0.927902756 1.012630741 0.990021847 1 23.57928149 2.245617 24.76287048 0.999110649 0.927135217 0.395393824 0.044684568 147.5934482 517949.7473 0.016294923 0.012342915 176.0422863 -2.245617 -0.071975432 KQDAETPPPPDPPAPETLLAPPPLPS(ph)TPDPPRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQDAETPPPPDPPAPETLLAPPPLPSTPDPPRR 33 2 Q86WR7;Q86WR7-2 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 KQDAETPPPPDPPAPETLLAPPPLPS(0.5)T(0.5)PDPPRR 94.73 9.79E-05 453110000 242660 228540 154210 180020 232430 234350 232680 306430 260660 TRUE FALSE 210591.8662 227038.7057 228786.4718 220896.2924 227805.0977 243365.5961 210114.7294 240902.3291 229845.0717 0.916233986 0.987790184 0.995394289 0.961066038 0.991124569 1.058824513 0.91415808 1.048107437 1 17.81030221 5.996392787 1.059585461 0.998939335 5.22E-18 0.268595458 0.040440871 29.0989133 3.151896323 0.01157383 58.98217471 991728.4843 -5.996392787 -0.998939335 KQDDS(ph)PPRPIIGPALPPGFIK ddPTM_MDA-MB-175_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 102.69 0.00023774 2393300000 2893320 2138670 1473270 1852110 2116520 1409790 2656670 3233460 2737760 TRUE FALSE 2510960.431 2124620.936 2185748.3 2272659.883 2074405.393 1464025.534 2399026.552 2542009.742 2414105.132 1.040120581 0.880086334 0.905407255 0.941408828 0.859285441 0.606446469 0.993753967 1.052982204 1 21.20305707 2.022186834 24.99990725 1.028203507 0.870193877 0.282309342 0.108717579 276.6144714 311685.2249 0.045138762 0.030429889 105.2414526 -2.022186834 -0.15800963 KQDPPVTHDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQDPPVTHDLR 11 1 P25685;P25685-2;M0R080;M0QZD0;M0QYT3;M0QXK0;M0R128;A0A1B0GX60;M0R1D6 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 120.84 0.00027531 644080000 715670 738070 409930 701240 644160 650130 770130 894260 1338760 FALSE TRUE 621092.3962 733221.5696 608173.5191 860467.2598 631342.4763 675140.9218 695442.9111 703029.4581 1180493.318 0.526129531 0.621114545 0.515185906 0.728904812 0.53481241 0.571914226 0.589112112 0.595538702 1 20.17095844 1.238012476 6.694671796 1.010555322 0.586661939 0.822013035 0.060651185 0.043570243 9.87863078 0.083872994 0.013703187 17.29866052 -1.238012476 -0.423893383 KQEAEWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KQEAEWK 7 1 P09496-2;F8WF69;P09496-4;P09496-3;P09496;P09496-5;C9J8P9 P09496-2 CLTA Clathrin light chain A 0 ;;; 135.83 0.004873 4965180000 8824400 7291400 5530100 6514900 6087600 5125890 9280000 10872600 9486700 FALSE TRUE 7658233.182 7243502.313 8204474.857 7994207.619 5966468.67 5323086.305 8380027.028 8547579.101 8365193.133 0.91548791 0.865909752 0.980787261 0.955651291 0.713249363 0.636337526 1.001773288 1.02180296 1 22.99596742 2.046619424 24.99967148 1.012258988 0.848165604 0.353910672 0.103978481 140.777158 75491.16789 0.046336421 0.031239995 111.3318495 -2.046619424 -0.164093384 KQEALVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQEALVAR 8 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 106.68 0.0066515 409640000 508250 484220 331180 391780 444140 498940 459830 544400 543950 FALSE TRUE 441083.4748 481039.1269 491339.7557 480739.637 435302.4829 518134.5447 415235.7574 427984.2965 479644.8507 0.919604316 1.002906893 1.024382426 1.002282494 0.907551665 1.080246236 0.865715032 0.892294155 1 18.87160704 2.214691722 24.9999198 0.91146839 0.988547585 0.233438427 0.059348341 298.1582723 312284.0856 0.023220602 0.015664642 163.9425638 -2.214691722 0.077079195 KQEEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQEEEAR 7 1 Q9NQS7-2;Q9NQS7;Q7Z3H0 Q9NQS7-2 INCENP;ANKRD33 Inner centromere protein;Ankyrin repeat domain-containing protein 33 0 111.04 0.010693 643960000 1171500 843790 611370 757420 526110 800640 1035000 1058400 1307700 FALSE TRUE 1016683.307 838247.0879 907030.5769 929403.7874 515641.4403 831441.1389 934625.8593 832069.3965 1153105.196 0.881691723 0.726947629 0.786598292 0.806000867 0.447176409 0.72104535 0.810529571 0.721590189 1 20.1370927 1.236924015 24.95312866 1.000000336 0.734083994 0.340494275 0.114627297 49.52890661 754915.2882 0.172834446 0.027927374 17.25535962 -1.236924015 -0.265916342 KQEELNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQEELNR 7 1 O14828;O14828-2 O14828 SCAMP3 Secretory carrier-associated membrane protein 3 0 ; 129.47 0.0058649 544960000 824350 772550 554830 622420 704480 754880 836540 1030000 978260 FALSE TRUE 715410.0589 767475.0682 823147.6438 763749.9741 690462.2263 783920.7221 755412.4796 809742.5155 862611.2172 0.829353995 0.88971144 0.954251031 0.885393047 0.800432701 0.908776406 0.875727633 0.938710858 1 19.71835095 1.397638323 1.840100773 1.020717952 0.878608008 0.489928416 0.041437565 0.556619756 2.46605044 0.12750775 0.011899014 24.98263961 -1.397638323 -0.142109944 KQEELQQLEQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 215.51 6.62E-11 2213810000 1788510 1595960 1217358 1518690 1533090 1451480 1693530 1887330 2618440 FALSE TRUE 1552153.872 1585476.034 1806076.401 1863531.776 1502584.508 1507319.375 1529291.721 1483739.167 2308891.006 0.67225082 0.686682927 0.78222679 0.807111194 0.650781914 0.652832624 0.662349031 0.642619839 1 21.13876864 1.232672481 24.99996666 1.000000495 0.693989187 0.745440765 0.056084327 109.886858 466511.9535 0.133171687 0.015196961 17.08726208 -1.232672481 -0.306011308 KQEELVQQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQEELVQQVR 10 1 O95983-2;O95983;K7EIE8 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 0 ; 139.32 6.62E-05 384770000 451270 413520 247940 357180 428540 330230 427030 508220 465010 FALSE TRUE 391633.5261 410803.5599 367844.6133 438283.1782 420012.8924 342934.1618 385616.6963 399541.108 410037.0475 0.955117418 1.001869373 0.897100922 1.068886777 1.024329131 0.836349212 0.940443549 0.97440246 1 18.64539474 KQEFLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQEFLEK 7 1 Q9H444;P59074 Q9H444 CHMP4B;CHMP4BP1 Charged multivesicular body protein 4b;Putative charged multivesicular body protein 4B-like protein CHMP4BP1 0 ; 107.57 0.01194 3231400000 5226500 4634300 3402300 3898900 4363400 3646400 5209600 6390200 5650200 FALSE TRUE 4535804.783 4603856.978 5047663.66 4784204.836 4276576.877 3786679.368 4704373.794 5023705.459 4982239.793 0.910394716 0.924053673 1.013131417 0.960251821 0.858364321 0.760035551 0.944228698 1.008322696 1 22.24836303 1.897921951 4.927537127 1.000483499 0.906552116 0.276585813 0.065572743 0.328313084 12.12626661 0.038237884 0.019509636 79.05365437 -1.897921951 -0.093931383 KQELDLNS(ph)SMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KQELDLNSSMR 11 1 Q8N3R9-2;Q8N3R9;G3V2B0;G3V2H1 Q8N3R9-2 MPP5 MAGUK p55 subfamily member 5 1 KQELDLNS(0.513)S(0.487)MR;KQELDLNS(0.5)S(0.5)MR;KQELDLNS(0.5)S(0.5)MR 75.669 0.022942 576800000 748470 768460 554460 644730 802270 853210 637280 887070 1191260 TRUE FALSE 649557.7931 763411.9357 822598.7106 791125.8006 786306.3966 886033.5408 575476.6837 697376.9837 1050430.6 0.618372878 0.726760945 0.783106195 0.753144283 0.748556256 0.843495554 0.547848362 0.663896295 1 20.00254942 4.720888933 3.971121729 0.745061238 0.608847733 0.118083303 0.116298811 0.547914261 17.8983172 0.028703065 0.209095827 52588.27598 -4.720888933 -0.136213504 KQELEEICHDLEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 KQELEEICHDLEAR 14 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;;;; 262.83 9.06E-25 12837070000 13271200 12564860 8133890 9909410 11414050 10742380 13882190 15922700 14084780 FALSE TRUE 11517377.3 12482320.61 12067466.41 12159493 11186932.74 11155646.31 12535897.35 12517754.52 12419693.35 0.92734796 1.005042576 0.971639642 0.979049373 0.900741461 0.898222363 1.00935643 1.007895619 1 23.56612622 2.192327071 24.99813354 1.006347914 0.95011827 0.405819697 0.033363898 138.2396527 74744.11778 0.014666408 0.009888132 155.7137885 -2.192327071 -0.056229643 KQELEEILHDLESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KQELEEILHDLESR 14 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ;;; 247.38 5.23E-18 236456000 995582 791952 514160 647468 738866 678374 853159 1038922 898367 FALSE TRUE 864013.3162 786749.6152 762809.4958 794485.5053 724164.0122 704471.4867 770419.7715 816756.6152 792163.0767 1.090701324 0.993166228 0.962945028 1.002931756 0.91416027 0.889301089 0.972551984 1.031046055 1 19.59543793 4.741955519 2.692957211 0.970042729 1.115099782 0.463079172 0.041390547 0.500821823 4.819770315 0.01194186 0.163188194 55202.08982 -4.741955519 0.145057053 KQELELVVSELEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQELELVVSELEAR 14 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 ; 153.74 1.01E-05 184821000 286264 252936 179514 203602 261044 240252 311893 350470 308020 FALSE TRUE 248433.4871 251274.4468 266327.5708 249832.946 255849.7351 249494.6499 281645.6649 275524.7179 271606.2265 0.914682591 0.925142439 0.980565042 0.91983512 0.941987739 0.918589581 1.036963211 1.014427104 1 18.05115703 2.239894695 25 1.017393367 0.934997171 0.785075301 0.020624976 15.1966682 284787.7978 0.007874423 0.005763205 173.737951 -2.239894695 -0.082396196 KQELLEALTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQELLEALTK 10 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 169.89 0.0040326 0 7067500 5641500 3782700 4876000 5147300 3838100 6452600 7832600 6663000 FALSE TRUE 6133511.968 5604440.615 5612026.372 5983170.325 5044878.801 3985754.191 5826827.845 6157659.443 5875307.731 1.043947356 0.953897374 0.955188499 1.018358629 0.858657798 0.678390711 0.991748537 1.048057349 1 22.48623299 2.014227074 24.99460505 1.025193919 0.915898463 0.171556562 0.100402592 390.0532657 685256.0311 0.043605487 0.029384871 103.3301535 -2.014227074 -0.109295456 KQESTVMVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQESTVMVLR 10 1 A0A0J9YVP6;A0A0J9YXX5;Q9UHX1-2;Q9UHX1;A0A0J9YYL3;A0A0J9YXJ8;Q9UHX1-4;Q9UHX1-6;Q9UHX1-3;Q9UHX1-5 A0A0J9YVP6 PUF60 Poly(U)-binding-splicing factor PUF60 0 100.93 0.0058961 422070000 516470 517680 335270 426140 497140 422620 548840 604510 711470 FALSE TRUE 448217.1809 514279.326 497407.6934 522901.6001 487247.8866 438878.4649 495613.5813 475240.2408 627360.8271 0.714448785 0.819750459 0.792857431 0.833494183 0.776662912 0.699563068 0.789997653 0.757522976 1 19.25893592 1.235871604 24.97132685 1.000000304 0.774890659 0.745402045 0.041673402 37.12994846 344733.9281 0.06742121 0.01009494 17.21359593 -1.235871604 -0.225109646 KQEVQAWDGEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KQEVQAWDGEVR 12 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;;; 161.76 0.00010344 3986570000 5111620 4544620 2907050 3733710 4290900 4173280 4772800 5672050 4849300 FALSE TRUE 4436106.466 4514766.092 4312909.103 4581505.922 4205519.485 4333828.782 4309934.591 4459126.247 4276021.278 1.037437884 1.055833402 1.00862667 1.071441329 0.983512291 1.013518993 1.007931044 1.042821342 1 22.0278376 3.239288702 24.99998931 1.013790999 1.041748418 0.368182391 0.021550602 24.7860702 851039.4957 0.006213881 0.007566451 1734.956945 -3.239288702 0.027957418 KQFS(ph)LENVQEGEILHDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQFSLENVQEGEILHDAK 18 1 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 KQFS(1)LENVQEGEILHDAK;KQFS(1)LENVQEGEILHDAK 223.85 2.32E-19 331850000 672430 533950 383060 458500 508280 425780 655560 751240 547620 TRUE FALSE 583566.6718 530442.4473 568309.0973 562609.4327 498166.2224 442160.0321 591983.8921 590593.1722 482880.9875 1.208510351 1.098495201 1.176913385 1.165109928 1.031654249 0.915670825 1.225941604 1.223061557 1 18.88130814 7.999961663 0.891679302 1.110646256 43.37112038 0.090458883 0.100144878 2928.091442 6.688155174 0.035311237 251688.1551 99991173.06 -7.999961663 42.26047413 KQGGLGPMNIPLVSDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQGGLGPMNIPLVSDPK 17 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ; 161.14 4.82E-09 1694460000 3497700 2599400 2253400 2585600 2530500 2035010 3327300 3974800 4174300 FALSE TRUE 3035470.083 2582324.37 3343151.777 3172699.998 2480148.001 2113298.152 3004618.958 3124819.952 3680819.009 0.824672464 0.701562441 0.908263017 0.861954905 0.673803302 0.574138024 0.816290872 0.848946918 1 21.81159538 1.36295305 1.98633887 1.035887341 0.761634023 0.375460627 0.096949397 0.68344585 3.392553013 0.320914073 0.028388987 23.0649783 -1.36295305 -0.274253317 KQGGLGPMNIPLVSDPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQGGLGPMNIPLVSDPKR 18 2 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ; 241.74 2.95E-24 5038900000 6208200 4538300 2576600 3248000 4653300 3405200 5995300 6351500 1096490 FALSE TRUE 5387770.64 4508487.608 3822652.378 3985508.043 4560708.434 3536200.247 5413876.729 4993281.152 966864.2013 5.572417133 4.662999832 3.953660062 4.12209702 4.717010339 3.657390813 5.599417913 5.164407934 1 19.88295375 1.233907514 24.99498286 0.999994478 4.675221981 0.761963235 0.646604629 72.72138723 390587.2219 1.290839965 0.164218449 17.13592346 -1.233907514 3.675227503 KQGGS(ph)PDEPDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQGGSPDEPDSK 12 1 Q9ULX6;Q9ULX6-2;V9GZ50 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 1 KQGGS(1)PDEPDSK;KQGGS(1)PDEPDSK 125.53 0.00032161 122694000 338870 206340 173238 164231 153766 139826 289540 308530 272510 TRUE FALSE 294087.4709 204984.539 257016.4762 201522.1587 150706.3574 145205.1967 261460.4554 242553.2605 240294.1782 1.223864319 0.853056618 1.069590941 0.838647695 0.627174402 0.60428096 1.088084852 1.009401319 1 17.87444217 6.978123549 1.402705415 0.886341839 199.9363354 0.275560825 0.16874428 1411.294101 6.041140074 0.051710773 900560.3114 9508752.618 -6.978123549 199.0499936 KQIS(ph)VR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 107.9 0.018912 31507300000 25544000 21009600 12109400 16130600 17185200 15981000 25922200 23199600 21166200 TRUE FALSE 22168295.68 20871586.55 17965546.34 19793299.27 16843248.14 16595799.41 23408269.03 18238546.08 18663955.95 1.187759752 1.118283102 0.962579766 1.060509322 0.902447916 0.889189808 1.254196543 0.977206876 1 24.15375147 4.418835859 4.473717916 1.011555461 1.174405183 0.276089362 0.101251609 0.253856614 10.16116259 0.025417205 0.077434731 26232.26909 -4.418835859 0.162849723 KQISVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQISVR 6 1 P11216;P11217;P11217-2 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form" 0 95.793 0.068854 453740000 883310 787950 509730 579970 749330 763670 776280 864400 910420 FALSE TRUE 766578.3455 782773.9046 756237.1329 711661.0528 734419.799 793048.8791 700996.4851 679554.7868 802791.1848 0.954891334 0.975065396 0.942009762 0.886483392 0.914832914 0.987864459 0.873199032 0.846490096 1 19.61466525 3.974267253 5.350896317 0.910702399 0.963982848 0.131831737 0.047463612 0.305002727 25.78345228 0.013009967 0.024624461 9424.693879 -3.974267253 0.05328045 KQIT(ph)MEELVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 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 184.76 8.93E-07 12650260000 22516680 16550380 8062750 13071510 15680400 10035590 21887320 20757660 15146140 TRUE FALSE 19541043.69 16441659.46 11961922.87 16039596.13 15368390.72 10421665.64 19764691.08 16318795.95 13355580.58 1.463136969 1.231070365 0.895649784 1.200965846 1.150709295 0.78032292 1.479882582 1.221870951 1 23.67093936 4.643003284 3.832929672 1.125397029 1.468935139 0.254828353 0.191834325 0.33775379 8.063611819 0.047278452 0.260064912 43954.4939 -4.643003284 0.343538111 KQITTS(ph)PITVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQITTSPITVR 11 1 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 KQIT(0.008)T(0.038)S(0.954)PITVR;KQIT(0.027)T(0.079)S(0.894)PITVR 151.56 0.00078808 312990000 492660 488740 302460 334970 464650 470600 454960 519520 391320 TRUE FALSE 427553.7328 485529.4348 448730.6677 411030.0582 455404.3741 488704.2865 410838.0492 408424.6909 345058.5954 1.239075735 1.407092712 1.300447732 1.191189159 1.319788523 1.416293618 1.190632706 1.183638653 1 18.39648185 1.292212702 1.28547947 0.885247828 1.308053234 0.633886293 0.073763011 0.831291017 1.288126348 0.464603056 0.022623284 19.59804282 -1.292212702 0.422805405 KQLELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQLELR 6 1 Q15233;Q15233-2;H7C367 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 83.843 0.090636 469070000 1441800 1155000 610110 908510 1064200 1080600 1123600 1318200 1145100 FALSE TRUE 1251262.477 1147412.729 905161.2367 1114801.081 1043024.502 1122171.381 1014633.445 1036313.188 1009727.583 1.239207979 1.136358706 0.896441033 1.104061234 1.032976141 1.11136053 1.0048586 1.026329484 1 19.94553469 4.471440454 24.97868516 1.029412996 1.213495704 0.586960697 0.0597408 79.6804858 350359.4103 0.014011199 0.037310109 29610.13956 -4.471440454 0.184082708 KQLQDEMLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KQLQDEMLR 9 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;; 176.6 6.37E-05 6165010000 10518170 10149730 6322120 7818400 8616690 8812440 10330650 12043400 11094080 FALSE TRUE 9128167.185 10083055.76 9379518.378 9593687.217 8445234.727 9151460.269 9328785.153 9468012.632 9782550.501 0.933107085 1.030718498 0.958800916 0.980693861 0.863295797 0.93548817 0.953614822 0.967847049 1 23.22177922 7.884106809 21.17624274 0.958048213 0.004813141 0 0.044446 0 0 0.010053702 0 76578491.92 -7.884106809 -0.953235072 KQMVIDVLHPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQMVIDVLHPGK 12 1 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4 E7ETK0 RPS24 40S ribosomal protein S24 0 89.959 0.0059267 2293700000 4053900 3675300 2468600 2949200 3673800 3062800 4428200 4992400 4340900 FALSE TRUE 3518166.844 3651156.712 3662423.217 3618860.936 3600698.568 3180627.898 3998753.846 3924814.111 3827723.747 0.919127679 0.953871531 0.956814927 0.945434199 0.940689247 0.830944997 1.044681934 1.025365039 1 21.86805528 2.198870887 24.99997282 1.024657969 0.928975167 0.608070345 0.037296716 105.2091909 66268.97499 0.015167693 0.010226223 158.0778013 -2.198870887 -0.095682802 KQNGAIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQNGAIGR 8 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 121.62 0.0022857 129860000 276880 247900 125140 124800 154270 225270 226600 292430 57943 FALSE TRUE 240289.6065 246271.5286 185658.1226 153137.7474 151200.3288 233936.2827 204624.3669 229896.1202 51093.04455 4.702980779 4.82005977 3.633725964 2.99723277 2.95931335 4.578632664 4.004935871 4.499558056 1 15.64083929 4.216892921 6.260168111 3.524659305 4.768308814 0.233284646 1.015306308 0.237326532 32.09699735 0.257701088 0.582170404 16477.56075 -4.216892921 1.243649509 KQNLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KQNLER 6 1 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2;CON__Q3MHN2;P02748 F1T0B3 DDX1;C9 ATP-dependent RNA helicase DDX1;Complement component C9;Complement component C9a;Complement component C9b 0 ;; 89.427 0.080459 867790000 1196430 1042630 616580 832790 725480 924740 1158950 1280560 1188650 FALSE TRUE 1038318.744 1035780.895 914760.1503 1021887.698 711044.3674 960315.3462 1046555.207 1006722.209 1048129.151 0.990640078 0.988218765 0.872755184 0.974963531 0.678393847 0.916218526 0.99849833 0.960494428 1 19.99938507 2.3229777 6.061370564 0.98115011 0.898051545 0.158099475 0.089886389 0.401109049 22.75941789 0.034801231 0.026644308 210.367042 -2.3229777 -0.083098565 KQNS(ph)PVAPTAQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KQNSPVAPTAQPK 13 1 Q6P1N0-2;Q6P1N0 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 KQNS(1)PVAPTAQPK;KQNS(0.997)PVAPT(0.003)AQPK;KQNS(1)PVAPTAQPK;KQNS(1)PVAPTAQPK 110.37 0.00065182 3094100000 1683329 1430719 1218539 1352707 1426607 1101288 1813670 2215950 2125020 TRUE FALSE 1460872.808 1421320.513 1807828.536 1659859.799 1398220.312 1143655.262 1637780.563 1742086.337 1873802.556 0.779630064 0.758522027 0.96479137 0.885824279 0.746194046 0.610339258 0.874041161 0.929706458 1 20.83753751 1.749154281 2.813001607 0.97782472 0.797598981 0.363448662 0.093759986 0.284288115 4.593807224 0.078253143 0.027737782 56.12473212 -1.749154281 -0.180225739 KQPAS(ph)PDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQPASPDGR 9 1 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 KQPAS(1)PDGR 74.611 0.024869 79286000 220850 155310 147960 191110 136640 145090 176600 210950 513800 TRUE FALSE 191664.1129 154289.7584 219513.9509 234504.4464 133921.1313 150671.7062 159473.3592 165839.9841 453059.1493 0.423044349 0.340551027 0.484514994 0.517602275 0.29559304 0.332565199 0.35199236 0.366044885 1 18.78933989 1.237373143 24.99993782 1.000000733 0.386987677 0.885263832 0.06912652 9.847842783 207236.9684 0.106254447 0.017699212 17.2732136 -1.237373143 -0.613013056 KQPPKEPSEVPT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQPPKEPSEVPTPK 14 2 P17096-2 P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KQPPKEPSEVPT(1)PK 125.18 0.0044209 811360000 1567700 1326200 1210200 1023500 1155800 775150 1766900 1927900 1661200 TRUE FALSE 1360524.473 1317488.105 1795456.768 1255901.318 1132801.841 804970.5221 1595546.31 1515633.588 1464814.828 0.928803045 0.899422971 1.225722687 0.857378894 0.773341326 0.549537393 1.089247787 1.034692958 1 20.48228687 KQPPKEPSEVPTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQPPKEPSEVPTPK 14 2 P17096-2 P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 0 97.45 0.0016704 393640000 676470 508770 423330 485240 486290 309050 790210 825290 693910 FALSE TRUE 587072.7755 505427.8564 628053.804 595421.1584 476613.7804 320939.3535 713575.5558 648808.1559 611876.7503 0.959462466 0.826028863 1.026438419 0.973106362 0.778937556 0.52451634 1.166207991 1.060357589 1 19.22288156 AKHDELTYF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AKHDELTYF 9 1 P04080;A0A1W2PQG6 P04080 CSTB Cystatin-B 0 ;;;;; 113.22 0.0016743 2837230000 7159630 6645550 4210320 5454280 5721010 5450020 5715850 8103770 14929600 FALSE TRUE 6213466.755 6601894.944 6246444.835 6692757.637 5607173.094 5659685.796 5161527.747 6370841.849 13164639.7 0.471981528 0.501486945 0.474486578 0.508388972 0.425926818 0.429915738 0.392075124 0.483935907 1 23.6501647 1.239419263 5.730074679 1.022962013 0.45816262 0.958981123 0.03507148 0.027094942 3.034911577 0.060144859 0.009363415 17.35478601 -1.239419263 -0.564799393 KQPPVS(ph)PGTALVGSQKEPSEVPTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQPPVSPGTALVGSQKEPSEVPTPK 25 2 P17096;P17096-3 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KQPPVS(0.999)PGT(0.001)ALVGSQKEPSEVPTPK;KQPPVS(0.984)PGT(0.016)ALVGSQKEPSEVPTPK 174.98 1.25E-12 955050000 584400 515400 379210 386490 448820 295410 661540 762110 297300 TRUE FALSE 507170.0593 512014.3035 562597.2244 474248.4616 439889.3601 306774.6139 597383.9526 599138.7072 262153.5327 1.934629887 1.95310854 2.146060054 1.809048525 1.67798372 1.170209727 2.278756065 2.285449679 1 18.00005246 3.592546469 6.974191018 1.774116351 2.004342341 0.095654464 0.41055568 0.842205781 45.69972979 0.119630254 0.177816583 3913.329971 -3.592546469 0.23022599 KQQDTPGS(ph)PDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQQDTPGSPDHR 12 1 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;H0Y954 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 KQQDT(0.188)PGS(0.812)PDHR 58.885 0.063058 78082000 70893 87520 55385 84479 84940 89049 100810 144890 98198 TRUE FALSE 61524.31043 86945.07536 82169.37125 103661.2481 83249.86018 92474.77265 91033.46172 113906.401 86589.14431 0.710531452 1.004110574 0.948956961 1.197162173 0.961435303 1.067971896 1.051326496 1.315481311 1 16.40189854 5.432283748 0.699208961 1.123210629 9.91E-15 0.529633642 0.108733278 5.686459005 1.059442568 0.04535478 6.295401525 270572.5585 -5.432283748 -1.123210629 KQQLAEEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQQLAEEEAR 10 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 83.137 0.025521 154190000 218410 179270 142950 175660 173980 158000 208430 243730 234140 FALSE TRUE 189546.5651 178092.3636 212081.0981 215546.2878 170518.1384 164078.3622 188216.4907 191610.2362 206460.2359 0.918077829 0.862598857 1.027224914 1.044008726 0.825912736 0.794721373 0.91163555 0.928073318 1 17.65550442 3.229935154 24.99908266 0.893169363 0.960396774 0.182215905 0.07453548 382.3907378 1108276.429 0.02440906 0.028107091 1697.9901 -3.229935154 0.067227411 KQQLEVELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQQLEVELR 9 1 P15924 P15924 DSP Desmoplakin 0 88.596 0.020327 352210000 331290 259590 185470 202680 278670 273940 263110 345120 311700 FALSE TRUE 287509.1871 257884.7362 275163.9124 248701.5918 273125.0122 284478.6491 237593.6327 271318.7737 274851.1811 1.046054035 0.938270431 1.00113782 0.904859098 0.993719624 1.03502793 0.864444649 0.987147927 1 18.06829115 4.750726578 24.17588653 0.964784491 1.046054115 0.198707796 0.050766717 1947.765215 3870437.315 0.01169088 0.183347112 56328.29136 -4.750726578 0.081269624 KQQMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KQQMAR 6 1 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;;;;; 166.39 0.011194 4890210000 9167970 8452080 5008410 6270060 4557820 7248960 8664750 9902040 9694220 FALSE TRUE 7956399.536 8396557.73 7430493.828 7693772.955 4467128.299 7527832.182 7824443.879 7784565.804 8548180.355 0.930771136 0.982262585 0.869248603 0.900048038 0.522582364 0.880635629 0.91533444 0.910669345 1 23.02718592 1.55298488 1.522669187 1.004041732 0.847303636 0.127065494 0.123747278 1.38133671 4.869075516 0.294451876 0.039110161 35.72603995 -1.55298488 -0.156738096 KQQMGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQQMGK 6 1 P31946-2;P31946;Q4VY19;A0A0J9YWE8;A0A0J9YWZ2 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 ; 110.54 0.04589 1427940000 1527120 1009530 726080 905270 726740 875080 1427640 1559260 1571650 FALSE TRUE 1325307.223 1002898.331 1077214.717 1110825.39 712279.2958 908744.8939 1289187.693 1225824.383 1385851.327 0.956312699 0.723669495 0.777294574 0.8015473 0.513965158 0.655730435 0.930249636 0.884528058 1 20.40234106 2.224840497 24.80767893 0.926731589 0.73191071 0.402974675 0.114406008 225.13171 407062.4606 0.047897868 0.032489477 167.8187557 -2.224840497 -0.194820878 KQQNQELQEQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQQNQELQEQLR 12 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 222.48 3.96E-11 1650020000 1715300 1773930 1012020 1321690 1750720 1573020 1900140 2261130 1514990 FALSE TRUE 1488618.759 1762276.937 1501436.257 1621799.915 1715884.097 1633535.097 1715864.715 1777604.946 1335889.608 1.114327673 1.319178566 1.123922402 1.214022405 1.284450517 1.22280695 1.284436008 1.330652574 1 20.34936936 4.774164841 22.91460507 1.232402993 1.114326886 0.097490768 0.09933584 13226.65116 8512085.921 0.023072909 4.050142877 59451.77707 -4.774164841 -0.118076106 KQQNVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KQQNVDR 7 1 Q13268;C9JZP6;Q13268-2 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ;;; 131.06 0.0056162 2235260000 2740660 2071980 1356400 2873770 1314580 2240850 2026070 2604540 2656070 FALSE TRUE 2378474.837 2058369.027 2012359.577 3526303.401 1288422.43 2327056.95 1829582.043 2047579.39 2342072.43 1.015542818 0.878866512 0.859221752 1.505633795 0.550120659 0.993588806 0.781180812 0.874259636 1 21.15935426 3.186734251 24.99997841 0.847423845 1.036866693 0.208176769 0.214699448 182.6771787 88118.87556 0.062234182 0.070567015 1537.213718 -3.186734251 0.189442849 KQS(ph)LGELIGTLNAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KQSLGELIGTLNAAK 15 1 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 1 KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(0.999)LGELIGT(0.001)LNAAK;KQS(1)LGELIGTLNAAK 276.14 9.59E-34 70811800000 25507770 18649870 14553490 15521180 16171810 12977110 24254390 25983250 24075180 TRUE FALSE 22136853.57 18527357.78 21591606.44 19045501.15 15850022.62 13476347.82 21902202.99 20426934.19 21229039.65 1.042762835 0.872736501 1.017078813 0.897143793 0.746619861 0.634807228 1.031709552 0.962216592 1 24.33953577 KQS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KQSPPR 6 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 KQS(1)PPR;KQS(1)PPR;KQS(1)PPR 75.854 0.046914 543083000 401010 342700 196413 238570 213777 270216 333740 380110 374880 TRUE FALSE 348015.5125 340448.7811 291398.9838 292740.9648 209523.2559 280611.3844 301373.9462 298826.4345 330562.1135 1.052799151 1.029908653 0.881525656 0.88558535 0.633839292 0.848891548 0.911701414 0.903994809 1 18.33456186 4.238048583 3.564243545 0.86211743 1.049958424 0.387032352 0.091943229 0.240708731 6.417270682 0.02539113 0.069150368 17300.09877 -4.238048583 0.187840993 KQS(ph)SEGIPVAQPSVMDDIEVWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQSSEGIPVAQPSVMDDIEVWLR 23 1 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-4;Q6ZVM7-3 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 1 KQS(0.77)S(0.23)EGIPVAQPSVMDDIEVWLR;KQS(0.773)S(0.227)EGIPVAQPSVMDDIEVWLR 140.42 1.19E-07 246520000 218730 152979 123800 161970 149737 144443 211130 207330 200296 TRUE FALSE 189824.2763 151974.0709 183670.0941 198747.7641 146757.5267 149999.8157 190654.6451 162994.0929 176617.2351 1.07477776 0.860471351 1.039933017 1.125302205 0.830935478 0.849293194 1.079479276 0.922866293 1 17.43026661 3.238252664 25 0.941170045 1.014418361 0.167649064 0.096498502 18.85106786 1530391.292 0.028840865 0.034784152 1730.823026 -3.238252664 0.073248317 KQS(ph)SSEISLAVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQSSSEISLAVER 13 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 KQS(0.957)S(0.021)S(0.021)EISLAVER;KQS(0.939)S(0.059)S(0.001)EISLAVER 225.01 8.06E-12 675140000 562480 445950 290780 395961 472320 433140 563340 452810 494970 TRUE FALSE 488146.8429 443020.5251 431402.1806 485869.9969 462921.7561 449803.1761 508707.3735 355980.1053 436455.2105 1.118435136 1.015042356 0.988422569 1.113218459 1.060639775 1.03058267 1.165543133 0.815616578 1 18.73547408 1.736408962 25 0.906608232 1.064752427 0.493760201 0.068209564 0.205672333 2329.29694 0.033826988 0.016244137 54.50156358 -1.736408962 0.158144195 KQSAGPNS(ph)PTGGGGGGGSGGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KQSAGPNSPTGGGGGGGSGGTR 22 1 S4R3H3;S4R393;S4R410;A7E2V4-5;A7E2V4;A7E2V4-3;A7E2V4-4;A7E2V4-2;H7BZ52 S4R3H3 ZSWIM8 Zinc finger SWIM domain-containing protein 8 1 KQSAGPNS(0.988)PT(0.012)GGGGGGGSGGTR;KQSAGPNS(0.928)PT(0.072)GGGGGGGSGGTR;KQSAGPNS(0.932)PT(0.068)GGGGGGGSGGTR;KQSAGPNS(0.998)PT(0.002)GGGGGGGSGGTR 137.7 1.60E-06 1841620000 938130 991690 575959 619118 1048000 978440 1163830 1297210 645383 TRUE FALSE 814153.7436 985175.5231 854494.6989 759698.2045 1027146.85 1016081.22 1050961.946 1019811.736 569086.557 1.430632535 1.731152337 1.50151974 1.334943156 1.804904435 1.785459887 1.846752366 1.792015158 1 19.11828857 3.225141152 24.99994543 1.686151069 1.516243912 0.058320219 0.262121623 599.2498946 1116376.964 0.078875791 0.089934505 1679.349741 -3.225141152 -0.169907158 KQSDS(ph)VKGK ddPTM_MDA-MB-175_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 KQS(0.001)DS(0.999)VKGK;KQS(0.11)DS(0.89)VKGK 134.56 0.00012805 1176640000 1555520 1182280 530600 706150 558470 425330 2179060 1788330 638690 TRUE FALSE 1349954.091 1174513.525 787199.9348 866492.1503 547357.5396 441692.7203 1967735.097 1405909.546 563184.7958 2.39700024 2.085485144 1.397764891 1.538557427 0.971896869 0.784276713 3.493942151 2.496355649 1 19.10324886 2.252613242 24.9986548 2.413229848 1.523575105 0.197825612 0.754074101 344.9020937 613556.802 0.290997251 0.224259639 178.901195 -2.252613242 -0.889654742 KQSEPFFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQSEPFFK 8 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 147.2 0.00086764 3887400000 8110100 7442600 5530200 6286600 7760200 7483600 11086100 12848600 10960000 FALSE TRUE 7038329.737 7393709.071 8204623.217 7714068.615 7605787.203 7771498.935 10010971.73 10101026.88 9664321.286 0.728279776 0.765052077 0.848960105 0.798200762 0.786996518 0.804143271 1.035869093 1.045187404 1 23.20423699 2.250334663 6.577352547 1.031933257 0.78987119 0.924343332 0.032154567 0.035838959 6.54870706 0.012981505 0.00952681 177.9650261 -2.250334663 -0.242062067 KQSFDDNDS(ph)EELEDKDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KQSFDDNDSEELEDKDSK 18 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 KQS(0.002)FDDNDS(0.998)EELEDKDSK;KQSFDDNDS(1)EELEDKDSK;KQSFDDNDS(1)EELEDKDSK;KQS(0.413)FDDNDS(0.587)EELEDKDSK;KQSFDDNDS(1)EELEDKDSK 235.57 4.44E-24 3635770000 4729200 2648330 3597350 2644890 2479070 1620840 4394590 4891740 4020560 TRUE FALSE 4104224.238 2630932.946 5337040.492 3245452.699 2429741.357 1683194.764 3968403.338 3845679.469 3545253.977 1.157667198 0.742099991 1.505404275 0.915435881 0.685350436 0.474774099 1.119356572 1.084740189 1 21.75745755 5.061153456 16.69443423 0.954502441 3.290203089 0.054500872 0.278672388 15862635.35 87190882.31 0.070054686 1274130798 115120.709 -5.061153456 2.335700648 KQSSS(ph)EISLAVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQSSSEISLAVER 13 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 KQS(0.221)S(0.221)S(0.558)EISLAVER 235.4 6.73E-17 471240000 481340 350010 262940 356180 354060 288600 525690 422130 509220 TRUE FALSE 417729.6994 347710.7613 390098.6635 437056.1129 347014.8987 299702.6287 474708.6647 331860.7845 449020.5917 0.930313013 0.774375981 0.868776779 0.973354276 0.772826247 0.66745854 1.05720912 0.739076984 1 18.77642208 1.207225866 24.28526689 1.000001422 0.84691857 0.143925636 0.116537231 5819.739483 4510083.21 3.521704997 0.026620006 16.11483512 -1.207225866 -0.153082852 KQTDFEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQTDFEHR 8 1 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ; 168.8 0.00019783 263100000 1170270 1006280 653850 801940 903670 946810 1085550 1186370 1133600 FALSE TRUE 1015615.854 999669.6804 970054.047 984032.7339 885688.735 983234.3934 980273.5281 932674.0078 999587.0994 1.016035376 1.000082615 0.970454748 0.984439209 0.886054587 0.983640539 0.980678451 0.933059269 1 19.93097276 4.248919621 1.609077047 0.957446441 1.017953797 0.265156756 0.032300457 0.609022107 2.725883972 0.009004581 0.043633963 17738.61147 -4.248919621 0.060507356 KQTIDNSQGAYQEAFDISKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQTIDNSQGAYQEAFDISKK 20 2 P27348 P27348 YWHAQ 14-3-3 protein theta 0 207.67 3.62E-22 467390000 299220 167930 153400 165700 165790 115960 254010 254220 111080 FALSE TRUE 259677.3189 166826.8568 227584.7531 203324.7176 162491.1034 120421.0562 229376.1493 199857.0313 97948.24894 2.651168568 1.703214285 2.323520385 2.075838208 1.658948528 1.229435519 2.341809596 2.040434959 1 16.57973208 8 0.472325903 1.73832414 21.38599741 0.275570074 0.434487474 174.6554718 2.068658836 0.303460017 3343.723978 100000000 -8 19.64767327 KQTIGNSCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQTIGNSCK 9 1 P55010;H0YLZ1;H0YN40 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 127.83 0.00069652 1202110000 1476170 1389010 875250 1076460 964010 1038430 1650860 1954480 1503880 FALSE TRUE 1281090.394 1379885.502 1298523.828 1320886.696 944828.0871 1078379.074 1490759.851 1536529.662 1326093.02 0.966063749 1.040564637 0.979210212 0.996073938 0.712490054 0.813200174 1.12417442 1.158689201 1 20.33875055 2.21995385 24.94083755 1.108950175 0.920506687 0.393017897 0.102744235 245.9067721 329615.2456 0.045803628 0.030942481 165.9410564 -2.21995385 -0.188443488 KQVCDDISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQVCDDISR 9 1 Q9HD15 Q9HD15 SRA1 Steroid receptor RNA activator 1 0 ; 193.52 5.37E-05 244060000 422230 479860 302500 386970 461530 414140 459560 525140 477690 FALSE TRUE 366431.2357 476707.7681 448790.0118 474837.453 452346.456 430072.2338 414991.9419 412842.8976 421218.0324 0.869932452 1.131736373 1.065457738 1.127296119 1.073900976 1.021020471 0.985218842 0.980116866 1 18.68420767 2.489793538 3.31461399 0.986979054 1.062390347 0.14042035 0.071862928 0.402265301 9.235403429 0.026589888 0.021316259 308.8826668 -2.489793538 0.075411293 KQVEEIFNLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQVEEIFNLK 10 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 88.441 0.020506 0 680620 552930 365690 496780 605330 426300 668580 779260 685410 FALSE TRUE 590674.3425 549297.7664 542538.9072 609581.4918 593285.1173 442700.0369 603741.2145 612621.3132 604381.6106 0.977320177 0.908859166 0.897676067 1.008603639 0.981639922 0.732484293 0.998940411 1.013633278 1 19.20510024 2.039197557 24.99999894 1.007340415 0.91866474 0.227713044 0.075121127 221.2681531 141122.7717 0.030534283 0.020586153 109.4454111 -2.039197557 -0.088675674 KQVEELFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQVEELFER 9 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 ; 167.12 9.66E-05 399590000 692890 564610 347990 415090 514950 495970 553460 647530 538660 FALSE TRUE 601322.8309 560901.0397 516279.128 509342.5288 504703.5025 515050.2868 499785.5344 509060.7486 474980.2284 1.265995498 1.180893448 1.086948671 1.072344696 1.062577919 1.084361529 1.052223871 1.07175145 1 18.85750794 4.541069382 1.315970027 1.057594874 1.318012542 0.9101125 0.022279702 0.248924895 0.498948217 0.006297889 0.079305349 34759.16872 -4.541069382 0.260417668 KQVENER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KQVENER 7 1 Q9H307 Q9H307 PNN Pinin 0 ;;; 135.83 0.004873 1286490000 1801730 1572400 1059210 1456740 1014150 1441200 1616580 1986890 2489420 FALSE TRUE 1563626.815 1562070.801 1571447.499 1787515.082 993970.3992 1496643.897 1459804.32 1562009.035 2195123.604 0.712318346 0.711609496 0.715881099 0.814311813 0.452808397 0.681803929 0.665021468 0.711581358 1 21.06587075 1.230962836 3.790606213 1.042981733 0.678963868 0.551601705 0.090216281 0.213277107 4.923607844 0.222282488 0.0227097 17.02012855 -1.230962836 -0.364017865 KQVENERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KQVENERR 8 2 Q9H307 Q9H307 PNN Pinin 0 ;;; 101.25 0.0031081 289146000 605620 510035 193732 231686 357948 430551 542376 596200 49866.4 FALSE TRUE 525585.7826 506684.5465 287421.4432 284293.8474 350825.5351 447114.5756 489776.459 468707.2696 43971.251 11.95294131 11.5230869 6.536576437 6.46544824 7.978520673 10.16833875 11.13856094 10.65940265 1 15.42427296 4.306012507 8.377399 8.209850164 11.78464584 0.235467501 2.913010323 0.450577065 49.75258524 0.738679939 1.96154942 20230.77439 -4.306012507 3.574795676 KQVEVFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KQVEVFR 7 1 A0A087X1Z3;Q9UL46;H0YLG1;H0YLD2 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;; 198.87 0.00062496 7618930000 7847470 7967020 4559080 5782040 7595790 6966590 7904970 9095860 7992050 FALSE TRUE 6810406.957 7914684.121 6763866.337 7094940.555 7444648.64 7234599.225 7138347.226 7150781.123 7047238.954 0.966393647 1.123090074 0.959789555 1.006768836 1.056392254 1.026586337 1.012928222 1.014692587 1 22.7486267 1.498064179 1.389315362 0.997441262 1.024988499 0.021270414 0.045608039 3.53237222 9.100451995 0.126567888 0.013112347 31.48213514 -1.498064179 0.027547237 KQVNYEVDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQVNYEVDRR 10 2 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 74.533 0.023457 64632000 86067 96429 61327 74010 84375 77320 89759 101070 78957 FALSE TRUE 74693.02788 95795.55155 90984.94233 90815.10167 82696.10258 80294.55043 81054.186 79456.96703 69622.79341 1.072824347 1.375922264 1.306826944 1.304387503 1.187773408 1.153279645 1.164190375 1.14124934 1 16.08727208 -0.389456253 0.439645641 3.64E-14 1.271954405 0.458186122 0.08339533 19.79311232 1.007075594 17.69480508 0.071076677 0.407890647 0.389456253 1.271954405 KQVNYNDGSQEDR ddPTM_MDA-MB-175_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 0 101.3 0.0032137 118820000 70882 71715 47927 65676 71181 63767 63532 82905 103890 FALSE TRUE 61514.76411 71243.89944 71104.65751 80588.73959 69764.63736 66220.15775 57370.67642 65176.41092 91608.24255 0.671498136 0.777701847 0.776181875 0.879710574 0.761554151 0.72286244 0.626261075 0.711468849 1 16.48318979 KQVS(ph)AR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQVSAR 6 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 KQVS(1)AR;KQVS(1)AR 89.698 0.030546 288640000 948220 752430 381790 558640 479920 404890 1195540 1090810 903170 TRUE FALSE 822910.3245 747487.2378 566424.921 685487.7503 470370.5309 420466.3803 1079596.715 857548.7702 796398.2715 1.033289943 0.938584706 0.711233238 0.860734854 0.59062224 0.527959936 1.355599018 1.076783816 1 19.60313056 2.235473311 24.99999961 1.138908939 0.776747723 0.499424646 0.173204871 69.81176773 565301.7722 0.071713735 0.050677867 171.978165 -2.235473311 -0.362161216 KQVVES(ph)FVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KQVVESFVPR 10 1 A2A341;Q9BX26 A2A341 SYCP2 Synaptonemal complex protein 2 1 KQVVES(1)FVPR;KQVVES(1)FVPR;KQVVES(1)FVPR 53.756 0.066556 8170690000 9727460 6761040 13717900 9549670 2553090 3549420 5901540 6158680 5389620 TRUE FALSE 8441951.515 6716626.283 20351922.32 11718068.53 2502288.504 3685968.484 5329209.559 4841694.209 4752465.263 1.77633103 1.413293083 4.282392652 2.4656821 0.526524312 0.775590831 1.121356867 1.018775297 1 22.18024465 3.2489614 24.42644585 0.91656534 2.536342309 0.524220068 0.754534103 129.7172259 304641.1321 0.2236088 0.285314557 1774.031799 -3.2489614 1.619776969 KQVVNIPSFIVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQVVNIPSFIVR 12 1 P46781 P46781 RPS9 40S ribosomal protein S9 0 157.52 0.00044032 0 1402500 1437300 842960 995660 1345300 1348300 1457100 1532800 1064800 FALSE TRUE 1217156.072 1427858.282 1250618.276 1221739.821 1318531.162 1400169.973 1315790.666 1205022.648 938920.557 1.296335523 1.520744509 1.331974538 1.301217458 1.404305351 1.491254998 1.401386578 1.283412786 1 19.84064357 1.249662171 2.245344586 0.893716975 1.395282004 0.740573757 0.07314953 0.312795235 1.65286649 0.31418983 0.019412688 17.7689666 -1.249662171 0.501565029 KQVY(ph)DS(ph)HT(ph)PKSAPCGQNETREDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KQVYDSHTPKSAPCGQNETREDGK 24 3 A2A3F3;Q9HCF6-6 A2A3F3 TRPM3 3 KQVY(0.763)DS(0.739)HT(0.785)PKS(0.713)APCGQNETREDGK 65.155 0.020307 606900000 291590 274860 157940 215550 291420 281220 263640 334160 136970 TRUE FALSE 253055.6427 273054.4266 234320.3123 264493.922 285621.3122 292038.7154 238072.2334 262702.4844 120777.5626 2.095220645 2.260804247 1.940098038 2.189925978 2.364854083 2.417988151 1.971162757 2.175093442 1 16.88199294 1.238028627 9.087035635 0.991898782 2.176728665 0.8567946 0.151207891 0.030387062 34.96558487 0.216782798 0.037697845 17.29930387 -1.238028627 1.184829882 KQYDSFTYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQYDSFTYR 9 1 Q9Y3Q3;G3V1J9;F5H4M7;Q9Y3Q3-2 Q9Y3Q3 TMED3 Transmembrane emp24 domain-containing protein 3 0 ; 131.82 0.0020126 382490000 1008830 1127320 761380 826310 1109630 1292640 1073660 1128020 877480 FALSE TRUE 875510.5595 1119914.561 1129585.915 1013936.315 1087550.534 1342368.697 969536.6185 886801.7013 773745.314 1.131522923 1.447394305 1.459893707 1.310426437 1.405566553 1.734897353 1.253043606 1.146115763 1 19.56149924 1.753005993 2.618745592 1.04278318 1.415180392 0.451870827 0.153719326 0.221783667 3.072259767 0.122987031 0.042064645 56.62471034 -1.753005993 0.372397211 KQYQDS(ph)PNQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KQYQDSPNQK 10 1 H0Y9T5;Q8IU60 H0Y9T5 DCP2 m7GpppN-mRNA hydrolase 1 KQYQDS(1)PNQK;KQYQDS(1)PNQK 134.04 0.0018868 85212000 536450 391640 284270 318220 307230 270710 447110 523080 427500 TRUE FALSE 465556.7733 389067.2911 421743.9228 390476.7147 301116.7241 281124.3889 403749.341 411223.4126 376961.437 1.235024933 1.032114304 1.118798586 1.03585321 0.79879981 0.745764318 1.071062717 1.090889869 1 18.52405742 4.692619722 1.014693897 0.968398127 1.325088263 0.340035637 0.117496368 2.574748533 2.270747055 0.043471695 0.986289023 49274.21593 -4.692619722 0.356690137 KRAPS(ph)PLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRAPSPLPK 9 2 Q9BSL1 Q9BSL1 UBAC1 Ubiquitin-associated domain-containing protein 1 1 KRAPS(1)PLPK 90.146 0.0091576 251250000 959430 744210 483750 535720 743620 613890 994550 1157700 415840 TRUE FALSE 832638.8946 739321.2355 717693.118 657363.414 728823.4169 637506.7455 898098.6941 910134.8642 366679.8689 2.270751588 2.016258045 1.957274393 1.792744761 1.987628661 1.738592161 2.449271886 2.482096623 1 18.48416154 KRDAEDDGEEEDD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 KRDAEDDGEEEDD 13 2 Q9BTT0;Q5TB19;Q9BTT0-3;Q9BTT0-2;Q5TB25;H0YCE2 Q9BTT0 ANP32E Acidic leucine-rich nuclear phosphoprotein 32 family member E 0 ;;;;;;; 198.74 4.90E-07 4844660000 5482408 4681057 3657348 4011664 4180005 3645763 5838087 6569892 4843682 FALSE TRUE 4757893.892 4650306.828 5426053.726 4922573.626 4096831.079 3786017.862 5271910.221 5164971.723 4271067.432 1.113982387 1.08879265 1.270420993 1.152539431 0.959205431 0.886433643 1.234330833 1.209292947 1 22.02616524 5.189338278 14.94329329 1.110269198 3.627796783 0 0.123906559 5769.944305 460249.0737 0.03115692 5325.910658 154645.853 -5.189338278 2.517527585 KRDEDRHDINK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRDEDRHDINK 11 3 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 61.375 0.038422 72150000 99814 94425 55511 59868 45929 46100 107620 122410 46094 FALSE TRUE 86623.327 93804.71596 82356.30527 73461.94443 45015.10276 47873.49683 97183.02896 96233.5741 40644.81983 2.131226743 2.307913194 2.026243581 1.807412229 1.107523737 1.177849897 2.391031117 2.367671317 1 15.31078387 3.863898831 3.073736084 1.721783654 2.210751014 0.197426103 0.481102803 0.548644755 9.830659549 0.148162574 0.287603742 7309.687839 -3.863898831 0.48896736 KRDFTNEAPPAPLPDASASPLS(ph)PHRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRDFTNEAPPAPLPDASASPLSPHRR 26 3 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 KRDFTNEAPPAPLPDAS(0.174)AS(0.174)PLS(0.651)PHRR 55.765 0.065069 134240000 184930 182930 56056 71255 177760 164260 219740 244110 16069 TRUE FALSE 160491.0319 181728.3208 83164.8691 87434.53681 174222.9238 170579.1885 198429.6486 191908.9762 14169.34113 11.32664042 12.82546021 5.8693533 6.170684723 12.29576748 12.03861118 14.00415495 13.54395906 1 13.79048505 6.161225478 14.83768692 10 11.79594717 0 4.222801655 0 0 0.956498129 0 1449524.226 -6.161225478 1.795947165 KRDS(ph)DAGSSTPTTSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRDSDAGSSTPTTSTR 16 2 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YFK5;K7EQF0;A0A2R8Y5K3;K7EP28 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 1 KRDS(0.999)DAGS(0.001)STPTTSTR 69.765 0.035676 50026000 66109 35480 28578 38500 40681 33282 53834 61434 47314 TRUE FALSE 57372.52815 35246.92954 42398.41639 47242.01344 39871.52769 34562.38008 48613.18697 48296.81718 41720.59282 1.375160904 0.844832903 1.016246739 1.132342813 0.955679797 0.828424951 1.165208442 1.157625381 1 15.34847204 0.926504311 17.21539014 0.000141194 1.054293336 0.012151129 0.162648142 13286789.45 51244830.45 517945795.6 0.038408132 8.44314622 -0.926504311 1.054152143 KRDS(ph)QGTYSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KRDSQGTYSSR 11 2 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 KRDS(0.997)QGT(0.002)YS(0.002)SR;KRDS(0.996)QGT(0.004)YSSR;KRDS(1)QGTYSSR;KRDS(1)QGTYSSR;KRDS(1)QGTYSSR;KRDS(1)QGTYSSR;KRDS(1)QGTYSSR 163.64 1.53E-05 5286700000 2293802 2222178 1755641 2129563 2384816 2403398 3058580 3350570 2772700 TRUE FALSE 1990670.254 2207580.366 2604674.86 2613112.827 2337362.827 2495858.276 2761959.382 2634076.68 2444914.565 0.814208514 0.902927406 1.065343917 1.068795149 0.956010022 1.020836602 1.129675213 1.077369622 1 21.22135262 4.393931977 3.226049861 1.049809282 0.825538425 0.736555279 0.047775899 0.126412536 2.515259174 0.013210588 0.04696883 24770.3405 -4.393931977 -0.224270857 KRDS(ph)SLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.634)S(0.366)LR;KRDS(0.647)S(0.353)LR;KRDS(0.665)S(0.335)LR;KRDS(0.786)S(0.214)LR 89.247 0.014186 388388000 643960 524880 294959 391857 362918 455717 608940 746190 324356 TRUE FALSE 558859.0544 521432.0287 437602.159 480834.121 355696.6418 473248.7279 549885.0925 586623.0754 286011.0032 1.953977463 1.823118771 1.530018615 1.681173506 1.243646705 1.654652173 1.922601181 2.051050725 1 18.12571112 4.430907468 4.891948525 1.637669116 1.927506979 0.136990763 0.303487625 0.410555428 21.59348428 0.079038281 0.235900411 26971.64707 -4.430907468 0.289837862 KREDSAPPSSVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KREDSAPPSSVAR 13 2 Q9BZE4-2;Q9BZE4;Q9BZE4-3 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 0 166.86 1.85E-05 66036000 139330 107350 70119 91439 82470 90301 124360 142820 112540 FALSE TRUE 120917.1875 106644.8108 104028.7829 112201.6225 80829.00835 93774.9379 112299.5863 112279.0544 99235.64941 1.218485375 1.074662295 1.048300521 1.130658419 0.81451584 0.94497228 1.131645603 1.131438703 1 16.59857087 5.133754273 1.330118268 1.033927058 1.498495697 0.272044277 0.097514444 5.412278467 4.186295252 0.030059299 4.38002514 136067.4586 -5.133754273 0.464568639 KREEGS(ph)DIEDEDMEELLNDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KREEGSDIEDEDMEELLNDTR 21 2 F5H5U2;Q8NHQ9;Q8NHQ9-2 F5H5U2 DDX55 ATP-dependent RNA helicase DDX55 1 KREEGS(1)DIEDEDMEELLNDTR;KREEGS(1)DIEDEDMEELLNDTR 322.32 2.18E-67 379240000 504330 403790 296360 346040 419730 352740 444380 550690 448800 TRUE FALSE 437681.5127 401137.4769 439680.6873 424613.6709 411378.1942 366310.1361 401284.096 432929.229 395743.3753 1.105973062 1.013630302 1.111024757 1.072952063 1.039507468 0.92562544 1.014000792 1.093964564 1 18.59420567 3.121150664 4.699500314 1.018533524 1.073710847 0.292098642 0.048102267 0.349283603 12.8275572 0.015823471 0.018152835 1321.754094 -3.121150664 0.055177323 KREELSNVLAAMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KREELSNVLAAMR 13 2 Q9Y3U8 Q9Y3U8 RPL36 60S ribosomal protein L36 0 ; 191.06 2.18E-06 3885900000 4676000 5105700 2862800 3749800 4742100 4287600 5491000 6027000 4356600 FALSE TRUE 4058054.753 5072160.321 4247259.655 4601249.402 4647741.488 4452546.746 4958483.665 4738172.952 3841567.711 1.056353827 1.320336046 1.105605829 1.197753039 1.209855413 1.159044193 1.290744831 1.233395663 1 21.87326375 4.796366989 22.36963502 1.195064672 1.056349996 0.173763037 0.090611169 35815.48694 13857853.29 0.020768601 32.22653525 62570.12022 -4.796366989 -0.138714676 KREHS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KREHSPSK 8 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 KREHS(0.999)PS(0.001)K;KREHS(0.999)PS(0.001)K;KREHS(1)PSK;KREHS(0.999)PS(0.001)K;KREHS(1)PSK 77.379 0.01741 543015000 765268 401136 332933 391590 236174 268829 531529 645102 576254 TRUE FALSE 664135.8949 398500.9112 493940.5124 480506.4946 231474.5995 279171.0256 479981.3994 507151.9575 508129.9086 1.307019885 0.78425006 0.972075259 0.945637103 0.455542167 0.549408765 0.944603715 0.998075392 1 18.95483786 4.742559827 24.46471158 0.836985455 1.307020131 0.382005626 0.190070223 365.7708818 2237441.049 0.051009756 0.375800143 55278.95531 -4.742559827 0.470034676 KREPEDEGEDDD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 KREPEDEGEDDD 12 2 P39687 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;;;;;;;; 206.51 3.55E-07 25761620000 20070052 15737789 11435168 12678113 14373869 12231129 17523283 19404931 18233704 FALSE TRUE 17417743.78 15634406.43 16965253.49 15556872.33 14087857.13 12701668.45 15823877.71 15255337.51 16078136.29 1.08331858 0.972401661 1.055175376 0.96757933 0.876212073 0.789996317 0.984186067 0.948824991 1 23.93859685 3.515552627 4.878224917 0.921539693 1.029046064 0.407070259 0.064194304 0.227810083 13.04087126 0.019066745 0.027658154 3277.574911 -3.515552627 0.107506371 KREPLNFGIPDGSTGFSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KREPLNFGIPDGSTGFSSR 19 2 O00559-2;E9PND3;E9PN10;O00559;E9PJ40 O00559-2 EBAG9 Receptor-binding cancer antigen expressed on SiSo cells 0 66.76 0.015029 277700000 294690 279840 170830 190160 309120 271690 273620 311130 241450 FALSE TRUE 255745.9699 278001.7126 253443.9594 233338.7344 302969.1168 282142.0901 247084.3745 244597.2707 212906.0561 1.201215102 1.305748262 1.190402772 1.095970395 1.423017844 1.325195231 1.160532392 1.148850696 1 17.69985746 1.397720487 1.509131998 0.951681025 1.252348295 0.437911345 0.090587961 0.817858148 2.224644633 0.349746573 0.027457463 24.98736653 -1.397720487 0.30066727 KREQSNDIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KREQSNDIAR 10 2 P45973 P45973 CBX5 Chromobox protein homolog 5 0 ;; 114.83 0.00073287 67544000 168094 130033 62967 67166 125285 121498 167490 192536 53692.9 FALSE TRUE 145879.952 129178.8047 93418.05181 82417.06687 122792.0736 126172.1067 151246.8456 151363.6747 47345.38653 3.081186208 2.728434894 1.973118368 1.740762362 2.593538307 2.664929277 3.194542418 3.197010011 1 15.53093623 3.018291664 24.97423156 2.678458607 2.350397512 0 0.710524325 905.7806247 1236684.544 0.219429243 0.248770106 1043.017666 -3.018291664 -0.328061095 KRES(ph)ES(ph)ESDETPPAAPQLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KRESESESDETPPAAPQLIK 20 2 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 2 KRES(0.631)ES(0.779)ES(0.556)DET(0.034)PPAAPQLIK;KRES(0.966)ES(0.508)ES(0.506)DET(0.02)PPAAPQLIK 149.73 4.70E-07 583250000 671150 465920 396920 400650 490010 386270 546730 728560 676970 TRUE FALSE 582455.827 462859.3408 588871.8396 491623.7061 480259.7597 401130.0568 493708.2088 572763.1137 596939.3778 0.975736982 0.775387515 0.986485163 0.823573924 0.804536905 0.671977879 0.827065908 0.959499633 1 19.1872249 1.657071622 4.114385336 0.989494958 0.83290714 0.298847054 0.090918257 0.203911422 7.952014498 0.066008698 0.024079369 45.40164853 -1.657071622 -0.156587818 KRES(ph)ESESDET(ph)PPAAPQLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRESESESDETPPAAPQLIK 20 2 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 2 KRES(0.476)ES(0.476)ES(0.476)DET(0.571)PPAAPQLIK 102.36 0.00056907 227480000 291320 203030 160960 175440 197770 148960 247890 341690 280530 TRUE FALSE 252821.3239 201696.2826 238800.7944 215276.3334 193834.7639 154690.5876 223849.666 268622.2525 247366.063 1.022053393 0.815375723 0.965374116 0.870274325 0.783594813 0.62535089 0.904932808 1.085930096 1 17.91628806 1.897496573 5.328000956 1.040197521 0.84299209 0.354997273 0.107320289 0.238191817 9.829263778 0.057007649 0.0296109 78.97626182 -1.897496573 -0.197205431 KRES(ph)ESESDETPPAAPQLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRESESESDETPPAAPQLIK 20 2 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 KRES(0.843)ES(0.135)ES(0.022)DET(0.001)PPAAPQLIK 132.13 6.84E-06 212450000 261620 166550 155360 161420 184610 136190 226340 290310 231670 TRUE FALSE 227046.2541 165455.9221 230492.6156 198072.8782 180936.6222 141429.3174 204389.5816 228229.4657 204282.2365 1.111434151 0.809937883 1.128304739 0.969604022 0.885718823 0.69232313 1.000525475 1.117226194 1 17.64020423 2.002101391 24.99290199 1.064553261 0.928265942 0.138344416 0.130680828 110.4889339 1314088.882 0.053436581 0.035762544 100.4850356 -2.002101391 -0.136287318 KRESES(ph)ES(ph)DETPPAAPQLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRESESESDETPPAAPQLIK 20 2 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 2 KRES(0.575)ES(0.712)ES(0.712)DET(0.001)PPAAPQLIK 185.7 1.75E-16 482210000 945060 629460 490760 518440 702110 489140 824900 1039200 974600 TRUE FALSE 820167.9265 625325.0358 728093.1775 636159.7259 688139.3847 507957.5323 744901.325 816975.1671 859383.8983 0.954367342 0.727643416 0.847226925 0.740250925 0.80073572 0.591071736 0.866785294 0.950652169 1 19.71294322 1.839510574 3.238009546 0.977089195 0.775102889 0.425683725 0.093514465 0.214552883 3.928610261 0.057757387 0.024523776 69.10517544 -1.839510574 -0.201986306 KRET(ph)DDEGEDD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 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 249.62 3.15E-16 83535830000 15866700 12174250 9026690 9823440 8277840 9021980 14107190 15941320 15114490 TRUE FALSE 13769875.39 12094276.55 13392027.48 12054002.19 8113127.179 9369061.409 12739076.89 12532392.77 13327672.21 1.033179326 0.907456033 1.004828695 0.904434173 0.608743001 0.702978079 0.9558366 0.940328707 1 23.66792149 3.479577272 24.9997457 0.846563245 0.971092611 0.218582639 0.120412777 184.0466213 1873417.772 0.038589963 0.050720126 3017.013627 -3.479577272 0.124529365 KRFDTEEEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KRFDTEEEFK 10 2 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 152.54 1.00E-05 249150000 707010 498530 388910 429930 441460 359560 647020 748220 554090 FALSE TRUE 613576.8372 495255.1236 576988.1768 527552.1776 432675.8097 373392.5059 584272.1 588218.9757 488586.1114 1.255821283 1.013649615 1.180934462 1.079752709 0.885567149 0.7642307 1.195842629 1.203920787 1 18.89825333 4.745703273 23.65412327 1.052679533 1.255821489 0.185306162 0.139833085 835.4150874 2766465.748 0.037316506 0.356701041 55680.51879 -4.745703273 0.203141956 KRFS(ph)FK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRFSFK 6 2 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 KRFS(1)FK 87.616 0.041139 1211500000 1378300 1123500 847810 1292600 1086400 696110 1625900 1897300 2706900 TRUE FALSE 1196154.163 1116119.655 1257813.752 1586104.586 1064782.766 722889.8021 1468220.468 1491577.16 2386893.366 0.501134311 0.467603484 0.526966881 0.664505842 0.446095658 0.302858021 0.615117746 0.62490314 1 21.18670268 1.054343272 1.524837011 1.411967351 0.496568565 0.73007519 0.095271084 0.996295284 1.432423796 1.593203824 0.028096926 11.33295781 -1.054343272 -0.915398786 KRGHT(ph)ASESDEQQWPEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRGHTASESDEQQWPEEK 18 2 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 KRGHT(0.566)AS(0.385)ES(0.049)DEQQWPEEK 148.88 3.15E-06 140890000 176230 109030 64879 81501 219730 152460 352400 324220 124600 TRUE FALSE 152940.759 108313.7748 96254.70141 100007.0477 215357.8029 158325.2349 318224.3022 254888.0761 109869.9299 1.392016533 0.985836387 0.876078664 0.910231287 1.960115957 1.441024263 2.896373033 2.319907514 1 16.74543707 3.221208029 9.403434891 2.02286202 1.025081635 0.410624255 0.517633073 0.210653929 102.8682559 0.159566946 0.185480715 1664.209623 -3.221208029 -0.997780385 KRGS(ph)VR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRGSVR 6 2 A0A0A0MSW4;P48739;P48739-3 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 1 KRGS(1)VR 62.2 0.093957 531220000 300570 276790 120960 238250 155880 139410 423810 374320 319460 TRUE FALSE 260848.913 274971.7483 179456.6606 292348.3039 152778.293 144773.1929 382708.9714 294274.581 281693.8027 0.926001603 0.976137017 0.637062863 1.037822988 0.54235589 0.513938154 1.358599187 1.044661182 1 18.1037683 2.235609806 24.99999997 1.125061104 0.77696975 0.427826539 0.197307027 76.71382653 649924.8221 0.078942315 0.055841542 172.0322247 -2.235609806 -0.348091355 KRKPS(ph)PEPEGEVGPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KRKPSPEPEGEVGPPK 16 3 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 KRKPS(1)PEPEGEVGPPK;KRKPS(1)PEPEGEVGPPK 148.91 4.90E-06 711840000 1131630 770230 350500 318340 726430 467500 1309510 1476100 79794 TRUE FALSE 982082.2283 765170.3084 520002.9724 390623.9625 711975.4642 485485.0275 1182513.922 1160447.502 70360.84422 13.95779484 10.87494496 7.390516389 5.551723645 10.11891588 6.899931814 16.80642032 16.49280242 1 16.10248517 4.691445092 4.064899982 9.999999942 14.13962603 0.072758703 4.782928748 0.695855204 22.31704213 1.254535795 7.51150573 49141.12471 -4.691445092 4.139626087 KRKS(ph)ELEFETLK ddPTM_MDA-MB-175_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 141.86 0.0003364 1102120000 502380 303708 348403 390800 325548 231037 584990 617100 457790 TRUE FALSE 435989.2101 301712.9222 516891.8561 479537.113 319070.2317 239925.1429 528257.7598 485137.9673 403670.5877 1.080061871 0.747423596 1.280479361 1.187941672 0.790422293 0.594358742 1.308635744 1.201816486 1 18.62281895 KRLS(ph)QSDEDVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KRLSQSDEDVIR 12 2 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y917;Q9H7D7-3;Q9H7D7-4 A0A499FIZ0 WDR26 WD repeat-containing protein 26 1 KRLS(0.833)QS(0.167)DEDVIR;KRLS(1)QSDEDVIR;KRLS(0.888)QS(0.112)DEDVIR 270.99 5.50E-28 1641290000 1020890 966020 623580 686880 1002770 906910 1241350 1342450 714070 TRUE FALSE 885976.7999 959674.151 925145.3737 842846.6023 982816.8389 941799.4145 1120964.068 1055377.514 629653.4581 1.407086372 1.524130677 1.469292929 1.338588062 1.560885319 1.495742464 1.780287321 1.676124384 1 19.26419851 3.190902914 24.99425285 1.544780255 1.443622078 0.002596311 0.208612386 406.6487293 213266.7688 0.063412182 0.071902797 1552.040015 -3.190902914 -0.101158177 KRNDS(ph)EEEER ddPTM_MDA-MB-175_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 106.58 0.0018885 150177000 191528 143920 148284 177376 133132 148961 178836 204707 379840 TRUE FALSE 166217.0895 142974.58 219994.6384 217651.9318 130482.9337 154691.6261 161492.5122 160932.0011 334935.7479 0.496265599 0.426871664 0.656826391 0.649831895 0.389576014 0.46185463 0.482159678 0.480486189 1 18.35352484 1.236837307 24.99982818 1.000000616 0.505017024 0.765700588 0.085968068 22.55863051 327155.4294 0.13621243 0.021877065 17.25191489 -1.236837307 -0.494983593 KRNDS(ph)EEEERER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KRNDSEEEERER 12 3 Q9Y5B6-2;Q9Y5B6;Q9Y5B6-3;Q9Y5B6-4 Q9Y5B6-2 PAXBP1 PAX3- and PAX7-binding protein 1 1 KRNDS(1)EEEERER;KRNDS(1)EEEERER;KRNDS(1)EEEERER;KRNDS(1)EEEERER;KRNDS(1)EEEERER 243.04 1.40E-15 1578290000 917933 634438 539354 636723 623712 631847 851966 968468 816765 TRUE FALSE 796625.8283 630270.335 800187.3984 781300.6889 611301.3515 656154.5629 769342.4685 761368.6548 720207.9722 1.106105263 0.875122686 1.11105046 1.084826493 0.848784483 0.911062621 1.06822265 1.057151107 1 19.45805404 2.179746766 24.99999868 1.046092601 0.987754471 0.063756842 0.09383712 216.2721059 91928.488 0.038594133 0.02602017 151.267896 -2.179746766 -0.05833813 KRNEDEDSPNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KRNEDEDSPNK 11 2 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2 H7C2W9 RPL31 60S ribosomal protein L31 0 ;;; 178.67 4.19E-06 4162080000 4416600 3530910 3303800 3486790 2691460 2473680 4855610 5517070 5081010 FALSE TRUE 3832935.12 3507715.22 4901528.731 4278518.962 2637905.212 2568844.07 4384713.69 4337287.514 4480338.786 0.85550118 0.782912942 1.094008503 0.954954339 0.588773603 0.573359336 0.978656726 0.968071327 1 22.0951764 2.083642503 24.99984499 0.979361732 0.813382118 0.223175801 0.152792516 43.79108894 13083.32231 0.068408108 0.046120735 121.239044 -2.083642503 -0.165979614 KRPAS(ph)PSHNGSSGGGYGASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRPASPSHNGSSGGGYGASK 20 2 K7ELX9;K7EQ79;K7ENM4;K7ENP7;Q6PI98;Q6PI98-3;Q6PI98-4 K7ELX9 INO80C INO80 complex subunit C 1 KRPAS(0.794)PS(0.069)HNGS(0.069)S(0.069)GGGYGASK 45.546 0.093151 33559000 40253 32429 13781 27565 32802 25271 40513 44023 30700 TRUE FALSE 34933.46406 32215.97176 20445.53769 33824.05455 32149.30438 26243.19172 36584.0555 34609.02404 27070.68097 1.290453834 1.190068761 0.755264994 1.249471877 1.187606045 0.969432271 1.351427233 1.278468911 1 14.72444356 2.234590425 24.99824162 1.230131159 1.104968416 0.066464954 0.176392669 247.9696305 1561313.312 0.06986922 0.04906458 171.6289025 -2.234590425 -0.125162743 KRPIYEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRPIYEDK 8 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 96.948 0.0048254 302470000 450070 370690 238460 281060 344010 395530 397140 403420 409380 FALSE TRUE 390592.1092 368254.913 353780.0536 344878.9687 337164.874 410746.295 358625.4239 317151.7724 360983.5628 1.082021869 1.020143162 0.980044772 0.955386905 0.934017248 1.137853181 0.993467462 0.878576769 1 18.46157362 4.596894901 2.133107423 0.976650848 1.0943416 0.18663518 0.065606947 0.860263023 5.521605771 0.018428495 0.172696135 39527.0953 -4.596894901 0.117690752 KRPQS(ph)PS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRPQSPSPR 9 2 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 2 KRPQS(1)PS(1)PR 87.001 0.067668 129470000 387900 304210 226840 258340 280290 280770 329440 404940 382870 TRUE FALSE 336638.0322 302211.6245 336540.5827 317000.0455 274712.7774 291571.4036 297490.9595 318346.7322 337607.5448 0.997128285 0.895156608 0.996839638 0.938960193 0.813704497 0.86364007 0.881173908 0.942949105 1 18.36498762 7.999976263 0.756593421 0.909363218 15.59144012 0.150394123 0.057862236 869.4835547 3.65630828 0.022732863 21773.55413 99994534.44 -7.999976263 14.6820769 KRPQS(ph)PSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 KRPQSPSPR 9 2 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 KRPQS(0.95)PS(0.05)PR;KRPQS(0.953)PS(0.047)PR;KRPQS(0.998)PS(0.002)PR;KRPQS(0.996)PS(0.004)PR;KRPQS(0.992)PS(0.008)PR;KRPQS(0.995)PS(0.005)PR;KRPQS(0.969)PS(0.031)PR;KRPQS(0.999)PS(0.001)PR;KRPQS(0.932)PS(0.068)PR 95.477 0.0044346 3945063000 3136365 2524445 1687612 1914250 2030333 1941739 2487938 2957381 2424383 TRUE FALSE 2721886.419 2507861.755 2503746.808 2348909.72 1989933.346 2016438.956 2246658.156 2324968.088 2137775.204 1.273233226 1.173117618 1.171192745 1.098763666 0.930843122 0.943241812 1.050932835 1.087564344 1 21.02767872 3.682369499 2.27672542 1.014217433 1.214071407 0.746174932 0.053876611 0.180774163 1.831714056 0.017904911 0.032116887 4812.486222 -3.682369499 0.199853974 KRPYEENR ddPTM_MDA-MB-175_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 ;;;;; 177.36 0.00014358 3138100000 2844190 2340400 1342598 1743811 2082059 2186117 2281940 2524730 2258380 FALSE TRUE 2468323.085 2325025.758 1991882.884 2139769.94 2040630.099 2270218.336 2060637.81 1984836.137 1991396.889 1.239493292 1.167535096 1.000244047 1.074507022 1.024722952 1.140012997 1.034770026 0.996705452 1 20.92534935 4.39453228 4.105263577 1.039406126 1.225999956 0.721875429 0.043536923 0.108450066 3.369328371 0.01152146 0.035471077 24804.60296 -4.39453228 0.18659383 KRQEEIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KRQEEIER 8 2 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6;H0YFJ7 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ;;;; 161.28 0.00019597 407683000 564705 513669 284439 356068 406847 501385 500168 551524 428792 FALSE TRUE 490077.8035 510294.6745 421994.6518 436918.6816 398751.5407 520673.6054 451661.7843 433584.8846 378100.6982 1.296156833 1.349626374 1.116090644 1.155561689 1.054617308 1.377076551 1.194554219 1.146744469 1 18.52841099 8 0.025950986 1.06E-11 2.798390847 0.23812649 0.106773061 7103.798733 18.29101184 730.8190488 1327.242322 99999999.99 -8 2.798390847 KRQS(ph)APSPT(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRQSAPSPTR 10 2 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 2 KRQS(0.965)APS(0.094)PT(0.941)R 83.729 0.017001 135450000 215170 231590 163020 208070 269680 238170 307400 383970 255660 TRUE FALSE 186734.7393 230068.67 241857.0173 255315.4737 264313.8956 247332.554 277588.3953 301861.0036 225436.166 0.828326451 1.020549072 1.072840359 1.132539992 1.172455601 1.097128994 1.231339231 1.339008771 1 17.78235946 5.66169561 0.559036396 1.204811947 3.50E-19 0.587940676 0.088623234 7.117274084 0.799346587 0.050138624 6.959313276 458876.2814 -5.66169561 -1.204811947 KRQS(ph)LYENQV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KRQSLYENQV 10 2 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 KRQS(1)LYENQV;KRQS(1)LYENQV;KRQS(1)LYENQV 122.66 0.00038008 1350360000 2187500 2158860 1593250 1855410 2591040 2582580 2650250 2727440 2515390 TRUE FALSE 1898416.333 2144678.307 2363751.029 2276709.199 2539483.373 2681933.524 2393229.163 2144198.181 2218023.46 0.855904533 0.966932201 1.065701546 1.026458574 1.1449308 1.209154715 1.078991817 0.966715736 1 21.08084319 4.586424204 1.755516042 1.069621545 0.818132946 0.514546089 0.068880984 0.636585044 2.508168497 0.021615146 0.242091202 38585.50633 -4.586424204 -0.251488599 KRQS(ph)PEPSPVTLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KRQSPEPSPVTLGR 14 2 Q9NRL2;Q9NRL2-2 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 1 KRQS(0.872)PEPS(0.126)PVT(0.002)LGR;KRQS(0.999)PEPS(0.001)PVTLGR;KRQS(0.716)PEPS(0.169)PVT(0.115)LGR;KRQS(0.995)PEPS(0.005)PVTLGR 146.67 6.49E-06 1920280000 2226140 1692080 1020050 1297560 1746060 1639300 1867110 2090790 1381100 TRUE FALSE 1931949.959 1680964.615 1513349.592 1592190.83 1711316.822 1702364.932 1686037.96 1643690.829 1217827.931 1.586389923 1.380297308 1.242662902 1.307402129 1.405220539 1.397869837 1.384463204 1.349690532 1 20.21587888 1.233002392 4.294375612 0.962066479 1.377803035 0.656947505 0.086904744 0.145993376 5.213151903 0.189368 0.022237205 17.10024732 -1.233002392 0.415736556 KRQS(ph)VSGLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KRQSVSGLHR 10 2 Q8N1G4;J3KRP5 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 KRQS(0.996)VS(0.004)GLHR;KRQS(1)VSGLHR;KRQS(1)VSGLHR 136.38 6.23E-05 563690000 293679 325648 111538 239821 281659 192135 325096 325491 168128 TRUE FALSE 254868.5761 323508.7968 165478.1499 294276.0235 276054.537 199526.5578 293568.24 255887.2826 148252.0994 1.719156606 2.182153226 1.116194311 1.984970363 1.86206157 1.345859914 1.980196174 1.726028054 1 17.17769301 1.239944394 7.935381311 0.990761618 1.744443551 0.357709533 0.311472651 0.097568664 53.68843622 0.401305055 0.070962536 17.37578341 -1.239944394 0.753681933 EEDFHPELESLDGDLDPGLPSTEDVILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EEDFHPELESLDGDLDPGLPSTEDVILK 28 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 0 ; 112.86 0.00050732 53401000 117049 85106 84642 113573 87069 78228 93234 135469 250083 FALSE TRUE 101580.6781 84546.93308 125575.1543 139361.4855 85336.49725 81237.48178 84192.18103 106500.0086 220518.4726 0.460644756 0.383400683 0.569454127 0.631971933 0.386981173 0.368393091 0.381791965 0.482952776 1 17.75053999 1.239683627 5.660383165 1.023885297 0.455418414 0.795921451 0.086332483 0.067124708 7.132784702 0.148265112 0.023002379 17.36535342 -1.239683627 -0.568466883 KRS(ph)GNSDSIER ddPTM_MDA-MB-175_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(0.911)GNS(0.089)DSIER;KRS(0.975)GNS(0.024)DS(0.001)IER;KRS(0.991)GNS(0.009)DSIER;KRS(0.978)GNS(0.022)DSIER 153.94 2.54E-05 979680000 1231380 1110990 562310 661840 1023680 977490 1291430 1509280 374368 TRUE FALSE 1068650.013 1103691.834 834244.9968 812120.8876 1003310.771 1015094.673 1166187.317 1186532.217 330110.6415 3.237247997 3.343399742 2.52716784 2.460147555 3.039316655 3.075013481 3.532716522 3.59434707 1 18.33259012 KRS(ph)ISESSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KRSISESSR 9 2 Q9H307 Q9H307 PNN Pinin 1 KRS(0.948)IS(0.051)ESSR;KRS(0.967)IS(0.019)ES(0.007)S(0.007)R 124.21 0.00042224 177744000 341210 274000 113257 129651 259170 215139 363470 394170 37522 TRUE FALSE 296118.234 272200.076 168028.464 159090.2411 254013.0241 223415.5365 328220.7353 309879.8129 33086.19191 8.94990378 8.226999249 5.078507206 4.808357565 7.677312179 6.752531001 9.920172629 9.365834963 1 15.01394163 4.459928635 24.05418172 6.821556233 8.769179219 0.100431415 2.534785279 353.5293474 494622.7164 0.646956312 1.712716553 28835.57627 -4.459928635 1.947622986 KRS(ph)PGGSGGASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KRSPGGSGGASR 12 2 E7ER77;Q7Z2K6 E7ER77 ERMP1 Endoplasmic reticulum metallopeptidase 1 1 KRS(1)PGGSGGASR;KRS(1)PGGSGGASR;KRS(0.996)PGGSGGAS(0.004)R 125.98 0.00015429 1626490000 168401 156000 84189 112732 136613 172397 155046 267819 45809.5 TRUE FALSE 146146.3812 154975.2257 124903.082 138329.5236 133894.6686 179029.2241 140009.6628 210547.991 40393.9531 3.618026214 3.836594684 3.092123262 3.424510675 3.314720603 4.432079814 3.466104505 5.212364101 1 15.30185172 KRS(ph)PS(ph)PSPTPEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KRSPSPSPTPEAK 13 2 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 KRS(0.666)PS(0.666)PS(0.666)PT(0.001)PEAK;KRS(0.777)PS(0.864)PS(0.359)PTPEAK;KRS(0.971)PS(0.675)PS(0.355)PTPEAK;KRS(0.959)PS(0.92)PS(0.121)PTPEAK;KRS(0.949)PS(0.968)PS(0.083)PTPEAK;KRS(0.994)PS(0.982)PS(0.024)PTPEAK;KRS(0.998)PS(0.924)PS(0.078)PTPEAK 159.81 2.28E-05 3169070000 7172400 4357640 3952760 3766390 4230620 3431250 5802770 6760840 5865850 TRUE FALSE 6224549.167 4329014.376 5864327.957 4621606.415 4146438.939 3563252.408 5240018.259 5315086.979 5172395.895 1.203417003 0.836945675 1.133773995 0.893513665 0.801647635 0.688897849 1.013073702 1.027587038 1 22.30240127 4.75161255 23.96698174 0.931022815 1.203417317 0.318133105 0.128037661 1662.845059 3053348.523 0.032997623 0.573806575 56443.31987 -4.75161255 0.272394502 KRS(ph)PSPS(ph)PTPEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KRSPSPSPTPEAK 13 2 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 KRS(0.975)PS(0.033)PS(0.988)PT(0.003)PEAK;KRS(0.883)PS(0.121)PS(0.993)PT(0.003)PEAK 176.68 7.94E-05 2218190000 7050800 4247800 3639400 3875100 4044900 3184800 5615800 6632900 5940500 TRUE FALSE 6119018.916 4219895.922 5399426.013 4755000.682 3964414.404 3307321.317 5071180.58 5214505.952 5238220.857 1.168148324 0.805597174 1.030774792 0.907751088 0.7568246 0.631382564 0.968111257 0.995472718 1 22.32064546 4.75031207 24.0654601 0.892353886 1.168148606 0.331306858 0.125325681 1457.446145 2984567.246 0.032935896 0.500365068 56274.55506 -4.75031207 0.27579472 KRS(ph)PTESVNTPVGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRSPTESVNTPVGK 14 2 A0A0A0MRB5;Q8WXG6-6;Q8WXG6-8;Q8WXG6-5;Q8WXG6-4;Q8WXG6-7;Q8WXG6-3;Q8WXG6-2;Q8WXG6 A0A0A0MRB5 MADD MAP kinase-activating death domain protein 1 KRS(0.947)PT(0.05)ES(0.003)VNTPVGK 106.57 0.0027551 0 181200 161760 139020 147940 153780 131140 203880 216170 199250 TRUE FALSE 157253.9609 160697.3879 206250.537 181532.0381 150720.0789 136185.0407 184107.749 169943.7277 175694.892 0.895040027 0.914638929 1.17391311 1.033223198 0.857851228 0.775122368 1.047883333 0.967266184 1 17.42271272 4.452015198 24.99980372 0.977017229 0.899939085 0.078698937 0.106749169 560.8070367 558433.196 0.02814492 0.074470459 28314.91083 -4.452015198 -0.077078143 KRS(ph)SLS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRSSLSPGR 9 2 Q9BUQ8;F8VVA2;F8W1J5 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 2 KRS(0.936)S(0.064)LS(1)PGR 92.906 0.048002 517380000 2203300 1670800 1148800 1364600 1557600 1453600 1759300 2163500 1798200 TRUE FALSE 1912128.323 1659824.405 1704363.523 1674453.287 1526606.807 1509520.933 1588683.357 1700852.361 1585618.845 1.205919272 1.046799116 1.074888539 1.056025092 0.962782962 0.952007437 1.001932692 1.07267416 1 20.59661458 7.999996307 0.808547723 1.010868866 51.7126549 0.698926606 0.039589605 346.5552496 1.159319618 0.015432745 32208.9881 99999149.59 -7.999996307 50.70178604 KRS(ph)VSHGSNHTQKPDEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRSVSHGSNHTQKPDEQR 18 3 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 KRS(0.559)VS(0.44)HGS(0.001)NHTQKPDEQR 86.557 0.0013941 141420000 97862 95942 6432.5 21433 91774 72159 134130 129650 4301.8 TRUE FALSE 84929.28875 95311.75068 9543.278515 26299.69023 89947.87695 74935.00342 121122.0932 101925.3564 3793.246105 22.38960679 25.12669836 2.515860625 6.933293941 23.71263938 19.75484884 31.93098731 26.87021976 1 11.88921726 7.999993463 3.05E-13 9.523964117 27.91036012 0 10.73373534 0 0.197207306 178642652 178642646.5 99998494.8 -7.999993463 18.38639601 KRS(ph)YS(ph)PDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRSYSPDGK 9 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 2 KRS(0.992)Y(0.033)S(0.975)PDGK 85.457 0.072808 336250000 944890 570880 501470 533830 477550 411430 776690 873170 861940 TRUE FALSE 820020.3925 567129.8517 743982.5693 655044.2606 468047.6893 427257.9783 701366.7233 686449.3905 760042.4351 1.078913959 0.746181825 0.978869777 0.861852221 0.615817838 0.562150162 0.922799427 0.903172453 1 19.53572044 4.750447218 23.89213636 0.826042233 1.078914245 0.232819804 0.145457883 1685.592889 3387932.96 0.037889867 0.581112234 56292.06982 -4.750447218 0.252872013 KRSPS(ph)PS(ph)PTPEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRSPSPSPTPEAK 13 2 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 KRS(0.486)PS(0.818)PS(0.696)PTPEAK 166.9 1.76E-05 1022800000 765770 434800 381750 384810 425640 319840 579650 738270 591830 TRUE FALSE 664571.5543 431943.7702 566365.5769 472186.992 417170.5968 332144.4518 523435.6322 580396.7057 521864.5316 1.273456068 0.827693288 1.085273174 0.904807595 0.799384843 0.636457225 1.003010553 1.112159709 1 18.99331583 4.74979201 24.33380406 0.931787411 1.273456359 0.375359781 0.142256267 1482.249108 3211334.553 0.038178568 0.558306019 56207.20759 -4.74979201 0.341668949 KRSS(ph)ISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.262)S(0.737)IS(0.001)K 63.184 0.063761 561900000 812940 590180 561530 589620 359710 516640 1060400 1062800 973070 TRUE FALSE 705507.9193 586303.0687 833087.7862 723502.2328 352552.4748 536515.4751 957562.5712 835528.4907 858034.7731 0.822236978 0.683309217 0.970925436 0.843208522 0.410883668 0.62528407 1.115995064 0.973769965 1 19.71067659 2.237772312 24.99974259 1.021809813 0.726175924 0.472677933 0.151256621 19.97036798 633283.0568 0.063294183 0.045515895 172.8909703 -2.237772312 -0.29563389 KRSVS(ph)HGSNHTQKPDEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRSVSHGSNHTQKPDEQR 18 3 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 KRS(0.473)VS(0.527)HGSNHTQKPDEQR 184.68 2.32E-14 94927000 110670 103480 9059.3 31466 110010 72461 163260 142610 8307.1 TRUE FALSE 96044.6791 102800.2331 13440.40778 38610.83623 107821.0162 75248.62156 147427.0703 112113.9613 7325.044101 13.11182264 14.03407702 1.834856909 5.271072186 14.71950404 10.27278751 20.12644133 15.30556809 1 12.83862173 KRT(ph)EEPDRDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 185.27 4.67E-06 22468806000 21277649 15014482 11146769 12096164 13998192 13748293 17682988 20353995 19583720 TRUE FALSE 18465753.77 14915850.88 16537383.77 14842782.91 13719655.37 14277198.73 15968094.55 16001451.56 17268554.93 1.069328259 0.863757908 0.95765881 0.859526635 0.794487751 0.826774376 0.924691997 0.926623659 1 24.04164402 4.74466285 24.63454674 0.893831503 1.069328354 0.446334453 0.061301131 578.4820886 2335235.763 0.015874935 0.141331788 55547.28674 -4.74466285 0.175496851 KRTEEPDRDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KRTEEPDRDER 11 3 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 ;;;;; 141.37 1.67E-05 442312000 699085 518509 236970 298991 512345 454236 589246 662836 130333 FALSE TRUE 606699.146 515102.8802 351569.4846 366881.4763 502150.3369 471710.7528 532101.0136 521093.6796 114925.1812 5.279079307 4.482071508 3.059116208 3.192350645 4.369367371 4.104503015 4.629977591 4.534199329 1 16.81033542 4.476579553 5.094988188 3.734308941 5.125871892 0.214140231 1.066788439 0.274899034 21.42251852 0.264325292 0.877652002 29962.60391 -4.476579553 1.391562951 KRVPDHHPC ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KRVPDHHPC 9 2 P78371;P78371-2 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 83.005 0.0094755 288730000 924890 1000150 490080 546920 1019170 953390 1145600 1156960 690420 FALSE TRUE 802663.4431 993579.9488 727084.3272 671106.5451 998890.511 990067.5302 1034499.888 909553.1075 608799.3341 1.318436795 1.632031924 1.194292251 1.102344414 1.640754933 1.626262505 1.69924609 1.494011338 1 19.21560726 3.218588055 24.99974068 1.514549195 1.326259874 0.123467279 0.233050996 514.5454186 644056.9633 0.072646482 0.082478482 1654.200148 -3.218588055 -0.18828932 KRVS(ph)SGSSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRVSSGSSER 10 2 K7EMM8;Q49A26-4;Q49A26-2;Q49A26-3;Q49A26;K7EPU6 K7EMM8 GLYR1 Putative oxidoreductase GLYR1 1 KRVS(0.92)S(0.057)GS(0.021)S(0.002)ER 63.16 0.063313 42691000 77376 76165 34395 44133 51492 59338 67381 88527 29798 TRUE FALSE 67150.56555 75664.6671 51028.53704 54154.07218 50467.40994 61620.77126 60846.40099 69596.18997 26275.31439 2.55565222 2.879686461 1.942071417 2.061024709 1.920715741 2.345196345 2.315724946 2.648729105 1 14.68142041 4.238986973 24.99999815 2.111526186 2.717669445 0.282609206 0.439766326 14.96928367 877477.2427 0.109211502 0.255286795 17337.51993 -4.238986973 0.606143259 KRVS(ph)VELTNSLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRVSVELTNSLFK 13 2 P14923 P14923 JUP Junction plakoglobin 1 KRVS(1)VELTNSLFK 198.3 1.00E-07 2038100000 906450 736010 469020 817610 1011000 752150 876490 1449900 378860 TRUE FALSE 786660.3358 731175.1018 695839.6408 1003260.847 990883.078 781085.6972 791488.1347 1139850.168 334071.6024 2.354765656 2.188677806 2.082905688 3.003131184 2.966079939 2.338078698 2.369217045 3.411993596 1 18.34979783 1.219326731 24.91313448 0.999994384 2.606101132 0.587375632 0.418433131 1011.359804 1309914.008 3.99119824 0.109109681 16.57016109 -1.219326731 1.606106748 KRVSS(ph)GSSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRVSSGSSER 10 2 K7EMM8;Q49A26-4;Q49A26-2;Q49A26-3;Q49A26;K7EPU6 K7EMM8 GLYR1 Putative oxidoreductase GLYR1 1 KRVS(0.292)S(0.478)GS(0.152)S(0.079)ER 58.116 0.089145 35331000 78354 80581 41958 46451 50588 60257 62816 87373 32735 TRUE FALSE 67999.32038 80051.65811 62249.02914 56998.40951 49581.39777 62575.12578 56724.11399 68688.96389 28865.10559 2.355762052 2.773302105 2.156549504 1.974647532 1.717693276 2.167846765 1.965144864 2.379653997 1 14.81703888 4.04544236 4.202857229 1.93937258 2.561169769 0.356693112 0.375839473 0.233728628 8.910164446 0.094555718 0.204722216 11103.05164 -4.04544236 0.621797188 KRY(ph)ALT(ph)GQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRYALTGQK 9 2 E5RJA7;P51512-2;P51512 E5RJA7 MMP16 Matrix metalloproteinase-16 2 KRY(1)ALT(1)GQK 50.607 0.066104 0 186270 147950 72140 99665 84121 97437 127590 145300 112160 TRUE FALSE 161653.9476 146978.1067 107027.1453 122295.4615 82447.15668 101185.4644 115216.3414 114228.7257 98900.57257 1.634509724 1.486119877 1.082169117 1.236549581 0.833636798 1.023102918 1.16497143 1.154985484 1 16.59369125 4.326549863 2.718248939 1.074157552 1.626479025 0.776254574 0.110471043 0.129261399 1.835777791 0.029744184 0.106600546 21210.44902 -4.326549863 0.552321473 KRYEDLLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KRYEDLLTR 9 2 Q99988;A0A0A0MTT8 Q99988 GDF15 Growth/differentiation factor 15 0 113.44 0.001012 304610000 255900 201600 137490 157400 221000 234360 301530 288620 190230 FALSE TRUE 222082.1666 200275.6763 203980.6239 193140.0757 216602.5324 243375.9809 272287.667 226900.859 167741.2261 1.323956977 1.193956197 1.216043477 1.151416859 1.291289788 1.450901406 1.623260264 1.352683919 1 17.35587778 2.985861316 6.812022403 1.380365221 1.2189475 0.1321948 0.158344075 0.275131479 62.66936903 0.05154644 0.05445717 967.9687037 -2.985861316 -0.161417721 KS(ph)ESPFRETEPLVSPHQDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSESPFRETEPLVSPHQDK 19 2 Q9BYW2;C9JG86;H7C3H4;Q9BYW2-3;Q9BYW2-2;H7BZ93;H7BXT4 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 KS(0.586)ES(0.405)PFRET(0.009)EPLVSPHQDK 124.81 1.49E-05 70238000 50973 37470 31513 41369 45323 34249 58115 69968 36117 TRUE FALSE 44236.7889 37223.8571 46752.7922 50762.46374 44421.16097 35566.58119 52479.01624 55005.88769 31847.2894 1.389028383 1.168823401 1.468030501 1.593933571 1.394817638 1.116785191 1.647833057 1.727176432 1 14.95888297 4.216382612 24.29697436 1.455034209 1.278925875 0.046664794 0.230948394 383.1155912 419720.8639 0.060135355 0.125361966 16458.21048 -4.216382612 -0.176108334 KS(ph)GVSSDNEDDDDEEDGNYLHPSLFASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KSGVSSDNEDDDDEEDGNYLHPSLFASK 28 1 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 KS(0.416)GVS(0.292)S(0.292)DNEDDDDEEDGNYLHPSLFASK;KS(0.402)GVS(0.299)S(0.299)DNEDDDDEEDGNYLHPSLFASK;KS(0.333)GVS(0.333)S(0.333)DNEDDDDEEDGNYLHPSLFASK 198.44 2.39E-25 430458000 349476 328857 108171 231748 375911 259377 402540 488430 277140 TRUE FALSE 303291.8611 326696.7167 160482.8574 284369.9254 368431.1066 269355.401 363501.7328 383983.0455 244376.8249 1.241082747 1.336856377 0.656702441 1.163653409 1.507635213 1.102213359 1.487464013 1.571274386 1 17.89874795 3.443094469 10.11886645 1.361119118 1.071896872 0.183209532 0.24726376 0.609010192 175.7245048 0.071075804 0.092003782 2773.923433 -3.443094469 -0.289222247 KS(ph)HHANSPTAGAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSHHANSPTAGAAK 14 1 Q15555-4;Q15555-5;Q15555-3;Q15555;K7EL66;K7ERD8;Q15555-2 Q15555-4 MAPRE2 Microtubule-associated protein RP/EB family member 2 1 KS(0.494)HHANS(0.494)PT(0.012)AGAAK 83.404 0.0040173 39242000 68242 63910 28255 41302 45944 46806 65756 77310 45022 TRUE FALSE 59223.6468 63490.171 41919.21251 50680.25036 45029.80429 48606.65711 59378.99324 60777.85813 39699.55045 1.491796409 1.599266749 1.055911516 1.276595069 1.134264841 1.22436291 1.495709462 1.530945752 1 15.27683505 4.265254029 24.99583392 1.280697073 1.545531824 0.328518372 0.172749656 305.9314969 286470.3825 0.046106383 0.121910422 18418.49027 -4.265254029 0.264834751 KS(ph)HSSPSLHQDEAPTTAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSHSSPSLHQDEAPTTAK 18 1 Q8NDX1-2;Q8NDX1 Q8NDX1-2 PSD4 PH and SEC7 domain-containing protein 4 1 KS(0.477)HS(0.477)S(0.045)PS(0.002)LHQDEAPTTAK;KS(0.413)HS(0.413)S(0.087)PS(0.087)LHQDEAPTTAK 126.02 1.34E-05 97318000 94886 104872 23501.3 65485 110219 94300 112159 112306 70306 TRUE FALSE 82346.57469 104183.0889 34866.60729 80354.37013 108025.8575 97927.78202 101281.8374 88290.23587 61994.50477 1.328288289 1.680521351 0.562414482 1.296153109 1.742506984 1.579620361 1.633722825 1.42416229 1 15.91985272 3.466952196 24.70608617 1.489514038 1.187730112 0.136603605 0.331735343 344.5888843 837186.6455 0.095756634 0.123764877 2930.570648 -3.466952196 -0.301783926 KS(ph)LVGTPYWMAPELISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSLVGTPYWMAPELISR 17 1 O96013;O96013-4;O96013-2;O96013-3;M0R1R1 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 KS(1)LVGTPYWMAPELISR 186.92 3.04E-10 313710000 247840 225100 156640 214580 244980 203480 227060 310580 309740 TRUE FALSE 215087.3161 223621.3033 232391.6279 263303.6686 240105.3773 211308.0073 205039.7561 244164.8839 273122.8901 0.787511131 0.818757092 0.850868369 0.96404834 0.879111148 0.773673738 0.750723442 0.893974445 1 18.0591907 2.06846662 0.016452968 1.739084438 5.90E-06 0.122215466 0.075424024 6480.685651 53.4433724 2924.3423 2725.093307 117.0756614 -2.06846662 -1.739078541 KS(ph)MSEDGGLQESNPCADDFVSASTADVSHTNLGTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSMSEDGGLQESNPCADDFVSASTADVSHTNLGTIR 36 1 H7C0I1;B8ZZW5;Q8NBF6-2;Q8NBF6;A0A1W2PRP5 H7C0I1 AVL9 Late secretory pathway protein AVL9 homolog 1 KS(0.778)MS(0.222)EDGGLQESNPCADDFVSASTADVSHTNLGTIR 162.68 7.49E-18 392880000 122090 113580 66579 81998 129820 95737 131140 154810 119140 TRUE FALSE 105955.4972 112833.8855 98776.82709 100616.8992 127236.836 99420.06434 118422.063 121705.0862 105055.4049 1.008567786 1.074041698 0.940235556 0.95775081 1.211140313 0.946358395 1.127234368 1.158484766 1 16.68079086 3.278648564 24.99999907 1.093154184 0.99686175 0.242245432 0.081926138 218.2487916 136104.7089 0.023011837 0.029707775 1899.540528 -3.278648564 -0.096292435 KS(ph)PEIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KSPEIHR 7 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 KS(1)PEIHR;KS(1)PEIHR;KS(1)PEIHR;KS(1)PEIHR 91.549 0.0099975 1815740000 1614630 1122420 946580 1139470 1068430 1090260 1346830 1525790 2524660 TRUE FALSE 1401252.555 1115046.749 1404349.254 1398204.079 1047170.333 1132203.008 1216214.634 1199511.682 2226197.571 0.629437644 0.500875018 0.630828671 0.62806828 0.470385175 0.508581548 0.546319271 0.538816365 1 21.0861502 1.237381372 24.99941866 1.000000533 0.553949289 0.856555814 0.057006689 10.5235882 222997.3605 0.083239166 0.013871406 17.27354088 -1.237381372 -0.446051244 KS(ph)PEKNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSPEKNER 8 2 P19525-2;P19525 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 1 KS(1)PEKNER 60.255 0.073597 29884000 89740 59077 53606 48651 43744 45631 84277 105790 93082 TRUE FALSE 77880.63163 58688.9193 79530.0409 59697.95313 42873.57998 47386.4541 76103.82951 83167.63176 82077.952 0.94886178 0.715038788 0.968957424 0.727332392 0.522351971 0.577334752 0.927214041 1.013276157 1 16.32470711 2.053701632 7.866132457 0.996658403 0.741684915 0.404576641 0.137814664 0.240232798 30.65860535 0.0604098 0.040516643 113.162265 -2.053701632 -0.254973487 KS(ph)PESEILSLHLLVEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSPESEILSLHLLVEELR 18 1 A0A0A6YYJ5;O94854-2;O94854 A0A0A6YYJ5 MACF1;KIAA0754 Uncharacterized protein KIAA0754 1 KS(1)PESEILSLHLLVEELR;KS(1)PESEILSLHLLVEELR 216.65 4.16E-19 32259000 94635 73389 42953 66045 71642 72216 78687 103245 90577 TRUE FALSE 82128.74498 72906.90283 63725.21447 81041.52668 70216.46437 74994.19625 71055.94685 81166.8602 79869.09025 1.02829198 0.912830015 0.797870794 1.014679477 0.879144412 0.938963947 0.889655142 1.016248713 1 16.28534966 1.69512863 7.188439259 1.007487556 0.920409546 0.222817584 0.065662791 0.16884652 18.24680457 0.036742019 0.016082929 49.55969552 -1.69512863 -0.08707801 KS(ph)PGADVTCSLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSPGADVTCSLPR 13 1 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 1 KS(1)PGADVTCSLPR;KS(1)PGADVTCSLPR 109.54 0.00069151 779210000 242631 253174 180837 226231 271439 269650 271962 323540 313640 TRUE FALSE 210566.6986 251510.8833 268290.3781 277600.2063 266037.895 280023.61 245587.1671 254353.4888 276561.8365 0.76137294 0.909420065 0.97009183 1.003754566 0.961947239 1.012517177 0.888000927 0.919698437 1 18.07724256 4.706808416 2.583951214 0.959661781 0.727750501 0.734414218 0.038468339 0.253706825 2.306447207 0.010561902 0.124015448 50910.62355 -4.706808416 -0.23191128 KS(ph)PPKADEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSPPKADEK 9 2 Q13427;E9PG73;C9JM79;Q13427-2 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 KS(1)PPKADEK;KS(1)PPKADEK 79.633 0.020783 798930000 1441690 768370 1036510 801270 612650 494720 1222640 1377550 1590990 TRUE FALSE 1251167.014 763322.5269 1537769.703 983210.6001 600459.4636 513752.1985 1104068.561 1082971.653 1402904.975 0.891840172 0.544101376 1.096132476 0.700839057 0.428011501 0.366205985 0.786987416 0.771949399 1 20.41998586 1.291234027 1.881519306 1.0794756 0.676616336 0.175782649 0.213358953 1.416646583 5.328129938 0.987605997 0.061206582 19.55392869 -1.291234027 -0.402859264 KS(ph)PPPAKDEAR ddPTM_MDA-MB-175_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 118.52 0.00037001 496873000 614177 504798 406715 425540 454114 337451 674225 765960 593395 TRUE FALSE 533011.9533 501481.9487 603403.7344 522165.361 445078.0199 350432.9583 608838.7633 602165.4147 523244.5191 1.018667055 0.958408412 1.153196474 0.997937564 0.85061191 0.669730777 1.163583642 1.150829856 1 18.99712577 KS(ph)PRPAGPQLFLPDPDPQR ddPTM_MDA-MB-175_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 130.1 9.50E-06 8011000000 15215300 14563200 7778100 9318800 14609600 12275000 15752800 19645600 8125800 TRUE FALSE 13204559.55 14467533.38 11539615.18 11434775.97 14318897.54 12747227.19 14225095.88 15444541.32 7165177.181 1.842879697 2.019145237 1.610513583 1.595881816 1.998401042 1.779052614 1.985309717 2.155500266 1 22.77257095 3.225959541 24.94155458 1.845027856 1.773922782 0 0.33020374 1698.633315 3362132.475 0.098727693 0.112670234 1682.51731 -3.225959541 -0.071105074 KS(ph)PSGPVKSPPLSPVGTTPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSPSGPVKSPPLSPVGTTPVK 21 2 C9J4K0;Q9BVC5-2;Q9BVC5 C9J4K0 C2orf49 Ashwin 1 KS(0.367)PS(0.367)GPVKS(0.264)PPLS(0.002)PVGTTPVK 107.17 0.00018238 555340000 491190 303040 282940 305140 331130 180790 487690 526490 414020 TRUE FALSE 426277.997 301049.3103 419770.7304 374426.7008 324541.1608 187745.1083 440393.8989 413904.2106 365075.0273 1.167644909 0.824623126 1.149820445 1.025615758 0.888971134 0.514264451 1.206310665 1.133751092 1 18.47783346 KS(ph)PTMEQAVQTASAHLPAPAAVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSPTMEQAVQTASAHLPAPAAVGR 24 1 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 KS(0.982)PT(0.018)MEQAVQTASAHLPAPAAVGR;KS(0.963)PT(0.037)MEQAVQTASAHLPAPAAVGR 191.04 4.90E-18 1566980000 399470 395790 217827 395910 498010 413770 492180 573910 828230 TRUE FALSE 346679.0274 393190.0294 323168.8658 485807.4166 488100.5753 429687.9996 444448.4594 451183.8127 730317.5929 0.474696256 0.538382251 0.442504561 0.665200211 0.668340158 0.588357728 0.608568743 0.617791242 1 19.47816446 1.160270842 2.6389794 1.164322715 0.571942203 0.772600591 0.07269163 0.342504977 2.238960881 0.499368856 0.020197051 14.4634148 -1.160270842 -0.592380512 KS(ph)RDSESHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSRDSESHSR 10 2 Q15424;Q15424-3;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 KS(1)RDSESHSR 91.961 0.0051095 49328000 49833 34871 17205 15758 20458 30642 45129 45789 6959.5 TRUE FALSE 43247.44279 34641.9301 25525.39555 19336.09475 20050.92583 31820.81757 40752.39653 35997.37868 6136.755838 7.047280995 5.644990777 4.159428242 3.150865906 3.267349452 5.185283301 6.640706849 5.865864576 1 12.58326047 4.52178118 2.925146705 4.434771335 7.0305947 0.256599813 1.579029333 0.47669328 7.288674042 0.427027998 2.256037839 33249.19842 -4.52178118 2.595823364 KS(ph)SGFLNLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSSGFLNLIK 10 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 KS(0.618)S(0.382)GFLNLIK 116.84 0.0012158 0 404410 375390 216370 280320 335340 220940 452560 395730 343360 TRUE FALSE 350966.1939 372924.0384 321007.2557 343970.9404 328667.3901 229439.7048 408670.8009 311106.2191 302768.372 1.159190412 1.231713986 1.060240387 1.136086105 1.085540699 0.757806052 1.349780356 1.027538699 1 18.20785498 4.065241503 1.624111388 1.058564053 1.198540687 0.115250115 0.146304372 0.97092145 4.791916227 0.042029541 0.14324185 11620.94654 -4.065241503 0.139976634 KS(ph)SGTGTEPVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KSSGTGTEPVAK 12 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9;A0A0U1RR74 Q6ULP2-7 AFTPH Aftiphilin 1 KS(0.634)S(0.362)GT(0.005)GTEPVAK;KS(0.607)S(0.377)GT(0.016)GTEPVAK;KS(0.647)S(0.351)GT(0.002)GTEPVAK;KS(0.722)S(0.278)GTGTEPVAK 157.7 4.30E-05 1519280000 1448680 1008090 928550 912830 832400 811640 1455850 1459760 1393890 TRUE FALSE 1257233.268 1001467.79 1377599.886 1120102.003 815836.8686 842864.316 1314661.891 1147601.684 1229105.912 1.022884403 0.81479373 1.120814628 0.91131447 0.663764498 0.685754017 1.069608305 0.933688198 1 20.22917781 KS(ph)SINEQFVDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSSINEQFVDTR 12 1 E9PGA7;Q9Y2L6-2;Q9Y2L6 E9PGA7 FRMD4B FERM domain-containing protein 4B 1 KS(0.627)S(0.373)INEQFVDTR;KS(0.5)S(0.5)INEQFVDTR 103.39 0.0013791 483090000 591000 522310 380550 447670 589140 508300 676890 708570 652310 TRUE FALSE 512897.8526 518878.9112 564585.2529 549320.3157 577417.2666 527854.6299 611245.312 557047.8196 575194.6549 0.8916944 0.902092721 0.98155511 0.955016378 1.003864104 0.917697384 1.062675577 0.968450967 1 19.13369074 5.276680032 0.55020052 0.995599886 0.724452686 0.467672683 0.037856678 6.042276938 0.932747861 0.020862161 1.18701693 189094.9942 -5.276680032 -0.2711472 KS(ph)SLVTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSSLVTSK 8 1 A6NMQ3;Q5T5H1;O43768-2;O43768;O43768-9;O43768-3;O43768-4;A0A1W2PRU0;O43768-6;O43768-5;O43768-7 A6NMQ3 ENSA Alpha-endosulfine 1 KS(0.587)S(0.413)LVTSK 68.551 0.034431 27099000 71003 57080 40562 46256 48698 36815 79135 77202 68174 TRUE FALSE 61619.77365 56705.03772 60177.91887 56759.13178 47729.00508 38231.29687 71460.49988 60692.95309 60114.54738 1.025039301 0.943283118 1.001054179 0.944182968 0.793967636 0.635974128 1.188738883 1.009621726 1 15.87542654 2.200372834 24.99996693 1.059458619 0.896044077 0.31553255 0.121565986 222.1785043 145449.5956 0.052171037 0.035174485 158.625438 -2.200372834 -0.163414542 KS(ph)SMCSAPSSSSSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KSSMCSAPSSSSSAK 15 1 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 KS(0.499)S(0.499)MCS(0.003)APSSSSSAK;KS(0.482)S(0.482)MCS(0.035)APSSSSSAK;KS(0.456)S(0.456)MCS(0.089)APSSSSSAK 148.44 2.16E-06 106020000 397016 304496 269732 278979 302118 245153 498980 424310 396304 TRUE FALSE 344549.3297 302495.7457 400175.2974 342325.4459 296106.4429 254584.1945 450588.9964 333574.6085 349453.3926 0.985966475 0.865625437 1.145146408 0.979602583 0.847341732 0.72852117 1.289410851 0.954561082 1 18.41474053 2.244617434 24.99967844 1.063585319 0.931560393 0.217806024 0.137630287 260.622418 1075731.03 0.052773224 0.039794854 175.6375756 -2.244617434 -0.132024926 KS(ph)SMCSLAQPATTTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KSSMCSLAQPATTTAR 16 1 H3BPV0 H3BPV0 MTSS1L 1 KS(0.499)S(0.499)MCS(0.003)LAQPATTTAR;KS(0.5)S(0.5)MCSLAQPATTTAR;KS(0.499)S(0.499)MCS(0.002)LAQPATTTAR 89.663 0.0024522 1230710000 722712 644978 468891 511180 667550 590406 899450 833230 741526 TRUE FALSE 627203.7781 640741.097 695648.2559 627251.2319 654267.061 613119.3009 812221.4774 655050.2487 653863.641 0.959227182 0.979930764 1.063904173 0.959299757 1.000616979 0.937686793 1.242187861 1.001814763 1 19.31863028 KS(ph)SMDGAQNQDDGYLALSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KSSMDGAQNQDDGYLALSSR 20 1 Q8IVL1-9;Q8IVL1-13;A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-5;Q8IVL1-4;Q8IVL1-10;Q8IVL1-8;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1;E9PNV5 Q8IVL1-9 NAV2 Neuron navigator 2 1 KS(0.5)S(0.5)MDGAQNQDDGYLALSSR;KS(0.5)S(0.5)MDGAQNQDDGYLALSSR;KS(0.5)S(0.5)MDGAQNQDDGYLALSSR 213.05 6.88E-23 263102000 151343 123668 89421 118420 125303 113250 158314 170516 149335 TRUE FALSE 131342.6391 122855.6168 132665.2947 145309.0709 122809.7155 117606.8008 142960.7326 134052.4804 131680.7864 0.997432068 0.932980582 1.007476476 1.10349486 0.932632002 0.893120431 1.085661291 1.018010934 1 17.00668533 2.210212316 24.9995325 1.033239496 0.980817746 0.164255369 0.06002067 442.1117347 389882.2625 0.025433563 0.017150973 162.2603155 -2.210212316 -0.05242175 KS(ph)SPSKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KSSPSKDR 8 2 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 KS(0.443)S(0.443)PS(0.115)KDR;KS(0.676)S(0.299)PS(0.025)KDR;KS(0.93)S(0.032)PS(0.038)KDR 80.916 0.012633 634726000 1235250 925768 768219 821463 885254 663956 1362630 1540700 1081850 TRUE FALSE 1072008.583 919686.5691 1139732.278 1007988.729 867639.1774 689498.817 1230482.352 1211233.295 953954.9254 1.123751819 0.964077594 1.194744372 1.056641884 0.909518002 0.722779241 1.28987473 1.269696568 1 19.86356157 0.940013059 18.75175115 0.000273532 1.075001979 0.012391503 0.171554392 24.278291 119872.152 15504.81611 0.044017985 8.709897793 -0.940013059 1.074728447 KS(ph)SPSSPAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KSSPSSPAVR 10 1 B3KNS5;Q8WVR3-2;Q8WVR3-3;Q8WVR3 B3KNS5 C7orf43 Uncharacterized protein C7orf43 1 KS(0.844)S(0.104)PS(0.026)S(0.026)PAVR;KS(0.527)S(0.29)PS(0.165)S(0.019)PAVR;KS(0.839)S(0.135)PS(0.022)S(0.004)PAVR 92.247 0.010167 230532000 633200 517170 351108 441440 475790 520950 640530 688680 679660 TRUE FALSE 549521.0157 513772.6762 520905.0032 541675.699 466322.7099 540991.2836 578411.4992 541411.1413 599311.3691 0.916920726 0.8572717 0.869172571 0.903830174 0.778097553 0.902688171 0.965126859 0.903388738 1 19.19294622 2.475093854 15.58727994 0.943888999 0.864347131 0.469656152 0.043557105 0.550082501 4189.305154 0.0152934 0.012080807 298.6027848 -2.475093854 -0.079541867 KS(ph)SPSTGSLDSGNESK ddPTM_MDA-MB-175_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(0.499)S(0.499)PS(0.001)TGSLDSGNESK;KS(0.659)S(0.341)PSTGSLDSGNESK 211.33 4.51E-12 997650000 377860 322714 270998 266498 287481 223782 452320 452860 427900 TRUE FALSE 327924.8436 320594.0705 402053.5392 327010.4441 281760.6905 232391.0383 408454.076 356019.4132 377314.1495 0.869102959 0.849674127 1.065567087 0.866679515 0.746753576 0.615908623 1.082530503 0.943562317 1 18.52540668 KS(ph)SPSVKPAVDPAAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSSPSVKPAVDPAAAK 16 2 Q6FI81-3;Q6FI81;H3BV90;H3BT65;H3BPG7 Q6FI81-3 CIAPIN1 Anamorsin 1 KS(0.5)S(0.5)PSVKPAVDPAAAK 133.09 1.86E-05 810470000 1689100 1118200 950580 925350 983180 646120 1500400 1742100 1370700 TRUE FALSE 1465881.155 1110854.471 1410283.667 1135464.861 963616.6416 670976.6545 1354891.439 1369565.472 1208657.408 1.212817748 0.919081341 1.166818371 0.939443099 0.797262016 0.555142136 1.120988818 1.13312959 1 20.20497394 7.79422135 1.042671847 0.954705754 199.9526521 0.162505457 0.180988831 3040.26985 5.395476218 0.059510664 1444229.792 62261753.76 -7.79422135 198.9979463 KS(ph)SSKDSRPSQAAGDNQGDEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSSSKDSRPSQAAGDNQGDEAK 22 3 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 KS(0.328)S(0.328)S(0.328)KDS(0.015)RPS(0.001)QAAGDNQGDEAK;KS(0.376)S(0.376)S(0.249)KDSRPSQAAGDNQGDEAK 155.73 9.38E-08 169640000 222308 171355 193006 144428 153994 79949 260710 294570 158089 TRUE FALSE 192929.4345 170229.3577 286344.3472 177222.5848 150929.8207 83024.68976 235426.3843 231578.4978 139399.8985 1.383999821 1.221158405 2.054121633 1.271325064 1.082711123 0.595586443 1.68885621 1.661252987 1 17.08886999 3.532416968 24.99985646 1.260055423 1.543703769 0.144229868 0.376459487 744.166605 336444.2736 0.111026075 0.164677497 3407.351743 -3.532416968 0.283648345 KS(ph)SSLESLQTAVAEVTLNGDIPFHRPR ddPTM_MDA-MB-175_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(0.333)S(0.333)S(0.333)LES(0.002)LQTAVAEVTLNGDIPFHRPR 93.295 0.0029497 147320000 33330 26226 21970 31623 30917 30116 32099 44507 27286 TRUE FALSE 28925.35605 26053.71968 32594.76549 38803.48548 30301.81219 31274.58201 28986.04392 34989.5244 24060.28016 1.202203626 1.082851883 1.354712633 1.612761165 1.259412275 1.299842803 1.204725952 1.454244263 1 14.55436582 4.232388665 24.99911952 1.327564768 1.142527739 0.156265215 0.160915941 216.9799706 878877.7732 0.039802353 0.086317368 17076.09904 -4.232388665 -0.185037029 KS(ph)STGSISNVLFSTQDPVEDAVFGEATNLKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSSTGSISNVLFSTQDPVEDAVFGEATNLKK 31 2 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 KS(0.324)S(0.324)T(0.103)GS(0.092)IS(0.157)NVLFSTQDPVEDAVFGEATNLKK 103.89 8.60E-05 469520000 354910 326780 257540 323180 361360 201450 489060 615080 316190 TRUE FALSE 308007.7443 324633.3607 382087.2054 396562.9585 354169.643 209199.9119 441631.0365 483549.9286 278810.3784 1.10472123 1.164351781 1.370419593 1.4223393 1.270288592 0.750330433 1.583983491 1.7343326 1 18.08892474 KS(ph)STSDWPTDNQDGWDGKQENEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSSTSDWPTDNQDGWDGKQENEER 24 2 A0A3B3IS53;A0A3F2YNX6;Q92794;A0A3B3ISZ3;A5PLL3 A0A3B3IS53 KAT6A;MYST3 Histone acetyltransferase KAT6A;Histone acetyltransferase 1 KS(0.482)S(0.482)T(0.018)S(0.018)DWPTDNQDGWDGKQENEER 131.2 3.02E-05 161430000 49797 43135 44023 48259 63837 52796 84367 101100 60641 TRUE FALSE 43216.20028 42851.64334 65312.67005 59216.94354 62566.76859 54827.09628 76185.10133 79480.55176 53472.09006 0.808201068 0.801383363 1.22143477 1.107436486 1.17008272 1.025340439 1.424763858 1.486393213 1 15.70649845 5.335236557 0.425460232 1.322872176 9.94E-10 0.453399374 0.167514935 8.676591898 0.902435415 0.176702498 6.412299713 216389.686 -5.335236557 -1.322872175 KS(ph)STTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSSTTLR 7 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 KS(0.63)S(0.314)T(0.017)T(0.039)LR 83.783 0.013491 738990000 1017600 761600 548110 705790 468160 667400 1008300 1047300 1113600 TRUE FALSE 883121.5817 756596.9995 813177.8293 866050.4068 458844.5319 693075.3099 910515.2212 823343.0451 981951.4766 0.899353586 0.770503449 0.828124249 0.881968638 0.467278214 0.705814214 0.927250728 0.838476304 1 19.90529221 2.232338711 24.98983219 0.904749795 0.754863706 0.269190433 0.125488847 224.4918316 901644.1549 0.052202742 0.036183743 170.7413501 -2.232338711 -0.149886089 KS(ph)STVATLQGTPDHGDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KSSTVATLQGTPDHGDPR 18 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 KS(0.563)S(0.328)T(0.109)VATLQGTPDHGDPR;KS(0.675)S(0.302)T(0.023)VATLQGTPDHGDPR;KS(0.649)S(0.342)T(0.009)VATLQGTPDHGDPR;KS(0.48)S(0.48)T(0.04)VATLQGTPDHGDPR;KS(0.532)S(0.288)T(0.18)VATLQGTPDHGDPR 252.84 1.05E-30 17897800000 7844260 6583510 4682930 5149330 6518660 6729490 8099370 7651980 7790000 TRUE FALSE 6807621.166 6540262.489 6947610.611 6318564.079 6388951.42 6988377.835 7313894.344 6015663.625 6869075.074 0.99105354 0.952131461 1.011433204 0.919856605 0.930103595 1.017368097 1.064756793 0.875760355 1 22.71168442 2.754809997 24.94716292 0.978761993 0.960953143 0.049260735 0.053870875 4215.740684 6472286.651 0.01814172 0.018077483 568.6041134 -2.754809997 -0.01780885 KS(ph)SVNGSSATSSG ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSSVNGSSATSSG 13 1 R4GMX3;P35226 R4GMX3 COMMD3-BMI1;BMI1 Polycomb complex protein BMI-1 1 KS(0.628)S(0.369)VNGS(0.003)SATSSG;KS(0.634)S(0.356)VNGS(0.004)S(0.006)ATSSG 93.237 0.0060443 1011480000 1091690 868460 789900 1107960 1056060 1366800 1756230 1989750 1927010 TRUE FALSE 947420.4005 862755.0291 1171898.282 1359539.252 1035046.472 1419381.68 1585911.085 1564257.447 1699201.073 0.557568151 0.507741575 0.689676049 0.800104987 0.609137134 0.835322966 0.933327497 0.920584074 1 20.69642515 2.173422466 0.124191523 1.71388737 7.54E-10 0.822267568 0.07068553 12.17301656 0.870033208 7.327694972 4.632304118 149.0810581 -2.173422466 -1.713887369 KS(ph)TAALEEDAQILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KSTAALEEDAQILK 14 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E9PDQ5;Q15052-2;Q15052 B1ALK7;Q15052-2 ARHGEF7;ARHGEF6 Rho guanine nucleotide exchange factor 7;Rho guanine nucleotide exchange factor 6 1 KS(0.925)T(0.075)AALEEDAQILK;KS(0.921)T(0.079)AALEEDAQILK;KS(0.747)T(0.253)AALEEDAQILK;KS(0.9)T(0.1)AALEEDAQILK 214.55 4.18E-12 745892000 1085310 1262270 1233030 1142210 1482380 1228500 1800920 2029710 1966870 TRUE FALSE 941883.5337 1253978.065 1829327.432 1401566.238 1452883.538 1275761.19 1626267.056 1595672.312 1734348.869 0.543076166 0.723025273 1.05476324 0.808122439 0.837711238 0.735585102 0.937681619 0.920041141 1 20.7259627 4.473653673 5.4286629 0.892402468 0.579692362 0.616882542 0.092601926 0.099887092 9.796468413 0.023357121 0.074955121 29761.42164 -4.473653673 -0.312710107 KSADTLWDIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSADTLWDIQK 11 1 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 ; 150.06 5.46E-05 2018700000 4102600 4213200 2922600 3432300 3868400 3360400 5346600 5733700 3647400 FALSE TRUE 3560431.015 4185523.212 4335979.136 4211656.174 3791426.408 3489676.762 4828087.555 4507592.875 3216208.527 1.107027416 1.301384278 1.348164803 1.309509672 1.178849685 1.085028142 1.501173669 1.401523824 1 21.61692952 2.246913726 24.99995 1.330207418 1.233081878 0.042376196 0.151969943 492.6676727 1474504.392 0.058145103 0.044261486 176.5687025 -2.246913726 -0.09712554 KSADTLWGIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSADTLWGIQK 11 1 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 102.73 0.0045363 2047680000 6460300 5683900 3489500 3799500 5411200 4411100 6833300 7020900 3221800 FALSE TRUE 5606554.987 5646562.087 5177033.872 4662234.547 5303527.707 4580797.871 6170607.618 5519535.172 2840922.474 1.973498058 1.987580491 1.822307338 1.641098829 1.866832958 1.612433255 2.172043649 1.942867228 1 21.43792803 1.236072047 24.99637689 0.999998842 1.879956434 0.738919668 0.163884457 35.96925043 361214.0309 0.271197777 0.041183412 17.22154247 -1.236072047 0.879957592 KSAEFLLHMLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSAEFLLHMLK 11 1 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2;J3KRB3;A0A087WWH0;J3QS96;A0A087WY81 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 0 ; 108.3 0.0013509 1954730000 4548300 5759800 3306900 3801200 5138200 4471400 6693600 7086600 3563600 FALSE TRUE 3947230.631 5721963.495 4906127.901 4664320.558 5035959.873 4643417.651 6044455.702 5571185.738 3142315.268 1.256153598 1.820938705 1.561309889 1.484357921 1.602627185 1.477705849 1.923567557 1.772955691 1 21.5833965 KSAEPSANTTLVS(ph)ETEEEGSVPAFGAAAK ddPTM_MDA-MB-175_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(0.995)ET(0.005)EEEGSVPAFGAAAK;KSAEPS(0.002)ANT(0.002)T(0.002)LVS(0.975)ET(0.02)EEEGSVPAFGAAAK;KSAEPS(0.001)ANT(0.001)T(0.001)LVS(0.998)ETEEEGSVPAFGAAAK;KSAEPS(0.017)ANT(0.004)T(0.004)LVS(0.972)ET(0.004)EEEGSVPAFGAAAK 333.25 1.99E-105 1803060000 2195140 1562560 1488550 1783580 1546760 1267750 2070870 2566800 2066890 TRUE FALSE 1905046.687 1552295.44 2208417.759 2188569.099 1515982.502 1316521.163 1870037.346 2017909.795 1822544.619 1.045267516 0.851718759 1.211722191 1.200831561 0.831794452 0.722353324 1.026058472 1.107193631 1 20.7975227 7.064441172 12.66392941 1.003227799 1.003969563 0 0.158766041 0 0 0.037449388 0 11599550.83 -7.064441172 0.000741764 KSATQFTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSATQFTGR 9 1 Q8NCW5-2;Q8NCW5 Q8NCW5-2 APOA1BP NAD(P)H-hydrate epimerase 0 ; 152.7 0.00012804 1656740000 1455190 1505040 991780 1175610 1416490 1470000 1558000 1640670 1499210 FALSE TRUE 1262882.955 1495153.293 1471408.125 1442550.219 1388304.62 1526551.851 1406905.4 1289825.488 1321975.102 0.955300106 1.130999586 1.113037699 1.091208311 1.05017456 1.154750834 1.064245006 0.975680621 1 20.33426357 1.829470079 4.640155698 0.988315974 1.086658148 0.334377318 0.054110759 0.215369374 7.297313932 0.028615287 0.013738749 67.52585307 -1.829470079 0.098342174 KSCVEEPEPEPEAAEGDGDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KSCVEEPEPEPEAAEGDGDKK 21 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;; 154.65 1.79E-08 346983000 328047 201736 291024 250337 176574 121760 327559 365120 395480 FALSE TRUE 284694.7578 200410.7829 431764.1798 307179.842 173060.5229 126444.186 295792.3786 287041.9294 348726.8049 0.816383352 0.574692797 1.238115837 0.880861 0.496263896 0.36258809 0.848206603 0.82311404 1 18.41173774 3.393820358 24.99989192 0.711831555 0.881838544 0.113592272 0.237585069 65.33835317 19601.70187 0.072484367 0.093576919 2476.397507 -3.393820358 0.170006989 KSDGIYIINLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSDGIYIINLK 11 1 C9J9K3;A0A0C4DG17;P08865;F8WD59 C9J9K3 RPSA 40S ribosomal protein SA 0 162.68 0.0017943 0 3793100 2969900 2367400 2977500 3025700 2487100 3818600 4351700 4038600 FALSE TRUE 3291832.225 2950390.531 3512282.558 3653586.883 2965494.49 2582780.346 3448272.76 3421122.82 3561161.309 0.924370434 0.828491123 0.986274491 1.025953774 0.832732424 0.725263509 0.968300074 0.960676174 1 21.76391636 2.046895594 24.99980352 0.973618947 0.889011365 0.19886855 0.084307939 213.6725542 113906.8246 0.036633852 0.024698528 111.4026686 -2.046895594 -0.084607582 KSDIDEIVLVGGSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KSDIDEIVLVGGSTR 15 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;; 209.23 3.99E-09 5394240000 5944180 4705690 3360230 4292910 4913840 5127280 4854920 5665940 4035470 FALSE TRUE 5158641.552 4674778.013 4985248.467 5267680.829 4816064.198 5324529.779 4384090.606 4454322.823 3558401.334 1.449707627 1.313729839 1.400979822 1.480350397 1.3534348 1.496326378 1.232039389 1.251776403 1 21.7627978 0.977319338 0.948286341 0.594082723 1.409322847 0.773839309 0.070011674 1.416580454 0.727720426 1.34660715 0.023124676 9.49116095 -0.977319338 0.815240124 KSDIYVCMISFAHNVAAQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSDIYVCMISFAHNVAAQGK 20 1 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 119.31 3.42E-05 509790000 222820 219880 106640 116400 159430 140490 277390 284150 90918 FALSE TRUE 193373.7724 218435.5938 158211.4607 142830.3991 156257.6549 145894.7412 250488.7605 223386.7338 80169.77761 2.412053248 2.724662589 1.973455152 1.781599043 1.9490843 1.819822202 3.124478674 2.786420774 1 16.29077085 1.226412413 24.89124187 0.999996777 2.33842812 0.457617752 0.451783614 571.4696031 1170843.026 2.048652282 0.123720874 16.84272714 -1.226412413 1.338431343 KSDLFQDDLYPDTAGPEAALEAEEWVSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KSDLFQDDLYPDTAGPEAALEAEEWVSGR 29 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;; 194.23 1.46E-18 1780060000 1610190 1406290 909729 1040877 1423960 1134400 1563020 1799160 1178490 FALSE TRUE 1397399.312 1397051.988 1349676.987 1277224.032 1395625.982 1178041.102 1411438.561 1414423.635 1039170.255 1.34472605 1.344391818 1.29880256 1.22908063 1.343019564 1.13363628 1.358236107 1.361108662 1 19.98700061 1.231684685 24.99996125 0.999999483 1.302092286 0.639250836 0.071208589 157.9810124 574345.5255 0.167794576 0.017384477 17.04844154 -1.231684685 0.302092803 KSDPVVSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KSDPVVSYR 9 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;; 117.14 0.0019251 1822240000 518710 501726 326049 433608 581433 584409 621914 781760 699180 FALSE TRUE 450161.1593 498430.1289 483727.387 532065.3237 569863.6209 606891.5924 561600.876 614586.7077 616523.7369 0.730160304 0.808452455 0.784604644 0.863008659 0.924317405 0.984376685 0.910915253 0.996858143 1 19.23379692 3.519337306 0.78408194 0.985316146 0.736475736 0.902915667 0.029019916 0.21784031 0.287273219 0.015989893 0.036842489 3306.262308 -3.519337306 -0.24884041 KSDSDMWINQSSSLDSSTS(ph)SQEHLNHSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSDSDMWINQSSSLDSSTSSQEHLNHSSK 29 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 KSDSDMWINQSSSLDSS(0.001)T(0.003)S(0.498)S(0.498)QEHLNHSSK;KSDSDMWINQSSSLDSS(0.005)T(0.021)S(0.487)S(0.487)QEHLNHSSK 225.51 5.58E-35 383356000 272780 266500 57764 178042 314760 244290 348130 407980 320080 TRUE FALSE 236731.4319 264749.344 85698.86361 218469.1573 308496.8918 253687.9944 314368.4062 320736.6519 282240.507 0.838757818 0.938027453 0.303637718 0.774053163 1.093028407 0.898836234 1.113831638 1.136394826 1 18.10656553 3.315987555 5.014612429 1.05679182 0.691919303 0.478825377 0.174456524 0.176040996 7.912368696 0.051693821 0.066586769 2070.082027 -3.315987555 -0.364872517 KSDSDMWINQSSSLDSSTSS(ph)QEHLNHSSK ddPTM_MDA-MB-175_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 KSDSDMWINQSSSLDSS(0.005)T(0.006)S(0.082)S(0.861)QEHLNHS(0.035)S(0.011)K 109.27 0.00014533 234700000 201370 173720 49665 113900 196160 189690 227790 276100 190720 TRUE FALSE 174758.4443 172578.8219 73683.16012 139762.7359 192256.7998 196987.497 205698.9609 217058.1636 168173.2989 1.039156902 1.026196329 0.438138281 0.83106377 1.143206449 1.171336344 1.223136861 1.290681488 1 17.35958914 3.214638418 4.857784312 1.189617405 0.816910802 0.46064824 0.177822676 0.163785732 9.627322882 0.055637787 0.066320389 1639.224429 -3.214638418 -0.372706603 KSDTPQS(ph)PSLNSSQPTNSADSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSDTPQSPSLNSSQPTNSADSK 22 1 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;A0A590UJF3 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 KSDT(0.025)PQS(0.975)PSLNSSQPTNSADSK 163.94 8.89E-12 106910000 124800 117870 87720 118190 119150 90593 140260 201540 143770 TRUE FALSE 108307.3638 117095.7042 130141.6854 145026.8459 116779.1481 94078.17133 126657.6068 158442.2394 126773.6744 0.854336394 0.923659465 1.026567117 1.14398235 0.921162447 0.742095485 0.99908445 1.249803953 1 16.95189566 1.984596105 24.59338289 1.137254886 0.941331721 0.295593899 0.119173505 642.9140371 1026455.085 0.055172807 0.033201267 96.51528669 -1.984596105 -0.195923165 KSDVEAIFSK ddPTM_MDA-MB-175_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 ; 131.69 0.0003903 4700300000 11506800 8558100 6798600 8556200 9099400 8330900 9905400 14488800 12679100 FALSE TRUE 9986147.225 8501881.278 10086425.7 10499015.98 8918339.743 8651395.114 8944775.833 11390482.87 11180191.24 0.893200036 0.760441489 0.902169335 0.939073023 0.797691162 0.773814591 0.800055709 1.018809305 1 23.41444153 1.704483223 6.575637349 1.008571474 0.837530837 0.593778394 0.058732293 0.088157703 8.813151261 0.036502238 0.015751326 50.63877868 -1.704483223 -0.171040637 KSDVETIFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSDVETIFSK 10 1 Q9UKM9;Q9UKM9-2;Q5QPM1;Q5QPL9;Q5QPM2 Q9UKM9 RALY RNA-binding protein Raly 0 127.17 0.00058218 727570000 1852300 1499400 1207300 1563400 1536500 1587800 1647800 2468200 2161800 FALSE TRUE 1607513.862 1489550.343 1791154.318 1918393.865 1505926.656 1648883.693 1487996.61 1940394.638 1906234.467 0.843292832 0.781409826 0.939629594 1.006378753 0.790000749 0.864995216 0.780594746 1.017920236 1 20.86229415 1.65878877 7.525996114 1.009447721 0.861923724 0.433477922 0.071412317 0.114298468 12.0179131 0.043685289 0.018920253 45.5815165 -1.65878877 -0.147523997 KSDYIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSDYIK 6 1 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ; 111.04 0.045205 3753300000 5210800 4252700 3364900 4423800 3767100 4932000 5309300 5484200 4675600 FALSE TRUE 4522179.578 4224763.734 4992176.895 5428291.404 3692142.08 5121737.231 4794404.903 4311446.508 4122855.894 1.096856086 1.024717779 1.210854083 1.316633795 0.895530228 1.242278984 1.162884424 1.045742713 1 21.97521261 1.590513607 4.141018647 1.009560398 1.13584632 0.144062901 0.116550166 0.319681811 12.09254459 0.087735574 0.029617412 38.95055109 -1.590513607 0.126285922 KSEAPAEVTHFS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSEAPAEVTHFSPK 14 1 Q6PID6 Q6PID6 TTC33 Tetratricopeptide repeat protein 33 1 KSEAPAEVT(0.003)HFS(0.997)PK 93.684 0.0020992 122710000 308050 254300 179910 180540 241350 252070 262960 295260 229910 TRUE FALSE 267340.412 252629.4866 266915.0778 221534.3664 236547.6072 261767.296 237458.1797 232120.9467 202730.3017 1.318699818 1.246135799 1.316601788 1.09275409 1.166809328 1.291209522 1.171300874 1.14497411 1 17.62920222 0.113436695 0.723823785 2.13E-23 1.240413643 0.54149285 0.069309392 10.76197489 1.247328393 15.85931204 0.029676624 1.298484276 -0.113436695 1.240413643 KSEAPSGESR ddPTM_MDA-MB-175_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 ;;; 134.08 0.00028903 636518000 1278190 1211750 780590 957750 903220 1067680 1308940 1497330 1492440 FALSE TRUE 1109273.953 1203789.934 1158085.935 1175221.776 885247.6891 1108754.34 1181999.2 1177137.632 1316005.443 0.842909852 0.914730209 0.88000087 0.893021972 0.672677832 0.842515011 0.898171969 0.894477783 1 20.32773403 1.157486347 1.320499955 1.089156101 0.844790798 0.347563027 0.066684247 2.081045165 2.717706498 0.733026938 0.021074347 14.37097874 -1.157486347 -0.244365303 KSEDS(ph)LLRNSDEEESASESELWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSEDSLLRNSDEEESASESELWK 23 2 Q70Z53 Q70Z53 FRA10AC1 Protein FRA10AC1 1 KS(0.137)EDS(0.447)LLRNS(0.415)DEEESASESELWK 127.44 2.41E-05 152090000 959770 781590 534800 553040 702940 536960 981630 1111700 495760 TRUE FALSE 832933.9628 776455.6838 793431.0688 678616.1847 688952.8693 557617.1987 886431.6737 873971.6063 437151.8176 1.905365434 1.776169405 1.815001189 1.552358145 1.576003671 1.275568753 2.02774331 1.999240472 1 18.73777487 3.793103275 8.604294059 1.632738995 1.827301248 0.119196864 0.304924846 1.153775933 171.8818316 0.084265917 0.146078516 6210.166936 -3.793103275 0.194562253 KSEEEIDFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KSEEEIDFLR 10 1 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ;;;; 171.05 6.64E-06 1904560000 6180910 5713860 3825410 4398600 5554580 4722770 6383940 7395970 5845110 FALSE TRUE 5364087.083 5676325.277 5675391.071 5397369.358 5444054.725 4904458.018 5764826.481 5814399.371 5154107.755 1.04074019 1.101320645 1.10113939 1.047197617 1.056255512 0.951562957 1.118491649 1.128109781 1 22.29729127 KSEEWPDWS(ph)EPEEPENQTVNIQIWPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KSEEWPDWSEPEEPENQTVNIQIWPR 26 1 Q8IZE3;Q8IZE3-2;X6RHX1 Q8IZE3 SCYL3 Protein-associating with the carboxyl-terminal domain of ezrin 1 KSEEWPDWS(1)EPEEPENQTVNIQIWPR;KSEEWPDWS(1)EPEEPENQTVNIQIWPR;KS(0.002)EEWPDWS(0.998)EPEEPENQTVNIQIWPR 241.41 2.50E-45 263771000 202749 168225 114869 132707 167655 143449 185064 212306 204813 TRUE FALSE 175955.2059 167119.9189 170420.0326 162840.1526 164318.9935 148967.5759 167116.5218 166906.0141 180600.2405 0.97428002 0.92535823 0.943631261 0.901660774 0.909849251 0.824847052 0.92533942 0.92417382 1 17.46244029 1.176696688 2.579590835 1.030770959 0.912735523 0.326503777 0.037909523 0.806535332 5.186977874 0.226092052 0.010245504 15.02092536 -1.176696688 -0.118035436 KSEGDGDKEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSEGDGDKEEK 11 2 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 71.548 0.027407 134020000 390560 216522 295520 260101 110418 123274 384320 460730 432210 FALSE TRUE 338946.5064 215099.6527 438434.4605 319160.9074 108220.8978 128016.4305 347048.7056 362206.4749 381114.6262 0.889355808 0.564396216 1.15040051 0.837440721 0.28395892 0.335900072 0.910615027 0.950387233 1 18.53986545 -0.379062843 13.86548325 6.323314732 0.768926405 0 0.285901404 0 0 0 0.068115251 0.41776991 0.379062843 -5.554388327 KSEIEYYAMLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSEIEYYAMLAK 12 1 E5RI99;P62888 E5RI99 RPL30 60S ribosomal protein L30 0 ; 145.71 9.86E-05 5766200000 15146200 11554400 9050800 11821600 11867200 8898600 15916700 17924700 15126500 FALSE TRUE 13144591.29 11478498.39 13427797.15 14505874.96 11631065.94 9240934.9 14373100.88 14091642.4 13338262.4 0.985480035 0.860569244 1.006712625 1.087538581 0.872007581 0.692813998 1.077584205 1.056482619 1 23.6690674 KSGIS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSGISPK 7 1 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9;H0Y5B5;Q86U86-6 Q86U86-8 PBRM1 Protein polybromo-1 1 KS(0.001)GIS(0.999)PK;KS(0.001)GIS(0.999)PK 62.408 0.052456 705160000 1194830 791240 695590 790270 594860 574120 1162160 1281080 1120660 TRUE FALSE 1036930.188 786042.2923 1031979.651 969712.882 583023.4498 596206.7679 1049453.902 1007131.011 988176.8515 1.049336651 0.79544698 1.044326882 0.981315116 0.589999097 0.603340148 1.062010206 1.019180939 1 19.91440973 KSGVS(ph)SDNEDDDDEEDGNYLHPSLFASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSGVSSDNEDDDDEEDGNYLHPSLFASK 28 1 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 KS(0.143)GVS(0.428)S(0.428)DNEDDDDEEDGNYLHPSLFASK 194.99 2.19E-19 106410000 229170 199350 59648 128420 236870 147500 261030 279780 156440 TRUE FALSE 198884.6039 198040.4567 88493.97231 157579.7238 232156.7504 153174.4204 235715.3508 219951.2243 137945.8414 1.441758605 1.435639195 0.641512433 1.142330368 1.682955775 1.110395347 1.708752858 1.594475208 1 17.07374244 3.274442475 24.57981606 1.447472514 1.147204816 0.134996847 0.313561472 262.2766008 179662.9088 0.090473057 0.116795597 1881.232509 -3.274442475 -0.300267698 KSHHANS(ph)PTAGAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KSHHANSPTAGAAK 14 1 Q15555-4;Q15555-5;Q15555-3;Q15555;K7EL66;K7ERD8;Q15555-2 Q15555-4 MAPRE2 Microtubule-associated protein RP/EB family member 2 1 KS(0.094)HHANS(0.904)PT(0.002)AGAAK;KS(0.037)HHANS(0.962)PT(0.001)AGAAK;KS(0.004)HHANS(0.996)PTAGAAK 146.76 3.86E-06 436858000 532485 504292 151311 309413 393279 378263 595127 653240 312684 TRUE FALSE 462115.7581 500979.2726 224485.5057 379669.9507 385453.5173 392815.0224 537411.6751 513549.7095 275718.8537 1.676039748 1.816993165 0.814182645 1.377018458 1.397994777 1.424694094 1.949129223 1.862584668 1 18.0728384 2.433862314 24.93727613 1.674285557 1.403878259 0.044254799 0.358839084 309.9242243 178658.666 0.135239945 0.104756477 271.5578206 -2.433862314 -0.270407298 KSKS(ph)PPKVPIVIQDDSLPAGPPPQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSKSPPKVPIVIQDDSLPAGPPPQIR 26 3 Q7Z422-5;Q7Z422;Q7Z422-4 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 KS(0.294)KS(0.706)PPKVPIVIQDDSLPAGPPPQIR;KS(0.199)KS(0.801)PPKVPIVIQDDSLPAGPPPQIR 220.64 1.63E-33 1793380000 1302410 888840 821220 621220 886990 548650 1430510 1605440 350955 TRUE FALSE 1130293.219 883001.1515 1218364.739 762277.4958 869340.6344 569756.9205 1291779.36 1262129.15 309465.4997 3.652404613 2.853310474 3.936996983 2.463206711 2.809168179 1.841099964 4.174227375 4.078416336 1 18.23941906 3.734506759 24.7950669 2.925250271 3.418144638 0.093245067 0.979897332 1107.825818 6775923.437 0.277228582 0.42898592 5426.336961 -3.734506759 0.492894367 KSLDFYTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSLDFYTR 8 1 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 79.07 0.046482 779060000 501300 497530 310110 350500 462660 390410 499720 558850 427710 FALSE TRUE 435051.9349 494261.6927 460080.2333 430086.3821 453453.9712 405429.3253 451257.2313 439344.2765 377146.611 1.153535315 1.310529323 1.219897567 1.140369208 1.202328108 1.074991299 1.196503477 1.164916411 1 18.52476594 0.512876419 1.476947322 5.18E-11 1.1893587 0.476320086 0.060348006 7.933463863 3.020224199 23.80079465 0.017634949 3.257439954 -0.512876419 1.1893587 KSLDS(ph)DES(ph)EDEEDDYQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KSLDSDESEDEEDDYQQK 18 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 KS(0.179)LDS(0.821)DES(1)EDEEDDYQQK;KS(0.008)LDS(0.992)DES(1)EDEEDDYQQK;KS(0.08)LDS(0.92)DES(1)EDEEDDYQQK;KS(0.067)LDS(0.933)DES(1)EDEEDDYQQK;KS(0.005)LDS(0.995)DES(1)EDEEDDYQQK;KS(0.004)LDS(0.996)DES(1)EDEEDDYQQK;KS(0.181)LDS(0.819)DES(1)EDEEDDYQQK 270.67 2.15E-38 11259940000 8360650 6003040 5907340 5192920 6599160 4460920 9802070 10061650 8390170 TRUE FALSE 7255768.919 5963605.635 8764149.383 6372051.855 6467849.627 4632534.479 8851466.76 7910044.447 7398293.661 0.980735458 0.806078524 1.184617668 0.861286689 0.87423532 0.626162557 1.196420035 1.069171462 1 22.81876114 2.195262654 24.99997771 1.088992694 0.896615151 0.29146686 0.146426275 181.1020624 104565.9399 0.059278538 0.039965869 156.7698901 -2.195262654 -0.192377543 KSLDS(ph)DES(ph)EDEEDDYQQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KSLDSDESEDEEDDYQQKR 19 2 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 KS(0.025)LDS(0.975)DES(1)EDEEDDYQQKR;KSLDS(1)DES(1)EDEEDDYQQKR;KS(0.001)LDS(0.999)DES(1)EDEEDDYQQKR;KS(0.012)LDS(0.988)DES(1)EDEEDDYQQKR;KSLDS(1)DES(1)EDEEDDYQQKR 180.83 1.76E-14 2626130000 2697970 1985770 1378850 1097185 2176590 1355870 2961860 3243610 643445 TRUE FALSE 2341426.429 1972725.346 2045666.472 1346317.624 2133280.117 1408031.196 2674619.273 2549989.243 567377.6651 4.126751144 3.476917523 3.605475855 2.372877373 3.759894421 2.481647204 4.714001692 4.494341953 1 19.11394983 2.25971108 24.99260755 3.684825348 3.303903043 0 1.128992253 1165.320124 1377006.245 0.414856974 0.321016393 181.849068 -2.25971108 -0.380922304 KSLESINSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KSLESINSR 9 1 E5RI99;P62888;E5RJH3;A0A0C4DH44 E5RI99 RPL30 60S ribosomal protein L30 0 ;;; 156.58 0.00011318 2489200000 2769510 2614360 1431420 2001420 2842080 2587240 2876830 3230570 1790570 FALSE TRUE 2403512.236 2597186.097 2123659.5 2455873.001 2785528.168 2686772.797 2597835.469 2539737.746 1578890.854 1.522278902 1.644943404 1.345032492 1.555441907 1.764230986 1.701683678 1.645354688 1.608558146 1 20.59048001 1.238165034 24.9860059 0.99999932 1.601711736 0.735309321 0.112823446 5.188793043 327316.6781 0.165103834 0.02893994 17.30473823 -1.238165034 0.601712417 KSLPAPVAQRPDS(ph)PGGGLQAPGQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSLPAPVAQRPDSPGGGLQAPGQK 24 2 Q5JVS0;Q5JVS0-2 Q5JVS0 HABP4 Intracellular hyaluronan-binding protein 4 1 KSLPAPVAQRPDS(1)PGGGLQAPGQK 239.69 8.48E-38 1258800000 2147900 1761000 1320500 1537600 1643700 1392500 2205400 2535500 1195200 TRUE FALSE 1864049.573 1749431.875 1959098.217 1886735.581 1610993.586 1446070.376 1991520.647 1993303.056 1053904.818 1.768707707 1.659952442 1.85889483 1.790233377 1.528594954 1.372107188 1.889658928 1.89135017 1 20.00731315 3.248836774 24.78838195 1.599005235 1.768015205 0.143065836 0.259406065 510.2938421 1230935.195 0.077319414 0.098671711 1773.522791 -3.248836774 0.16900997 KSLS(ph)DS(ph)ESDDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSLSDSESDDSK 12 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 KS(0.04)LS(0.743)DS(0.583)ES(0.199)DDS(0.435)K 91.657 0.0054635 124160000 455170 310960 282390 273610 283840 238790 427830 511010 475910 TRUE FALSE 395018.1312 308917.2833 418954.7485 335737.3324 278192.1393 247976.4058 386339.1124 401734.4882 419648.462 0.94130723 0.736133481 0.998346918 0.800044234 0.662917095 0.590914607 0.920625589 0.957311952 1 18.67882177 2.01925046 24.99559392 0.964615481 0.787415497 0.323199317 0.118500782 283.1524006 367655.3771 0.050559371 0.034082043 104.5322888 -2.01925046 -0.177199984 KSLS(ph)DSESDDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KSLSDSESDDSK 12 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 KS(0.032)LS(0.964)DS(0.004)ESDDSK;KS(0.095)LS(0.901)DS(0.004)ESDDSK;KS(0.031)LS(0.484)DS(0.484)ESDDSK;KS(0.014)LS(0.889)DS(0.096)ESDDSK;KS(0.103)LS(0.874)DS(0.023)ESDDSK;KS(0.001)LS(0.895)DS(0.104)ESDDSK;KS(0.018)LS(0.491)DS(0.491)ESDDSK 187.56 6.32E-06 11633920000 15706540 10096570 8985000 9313450 8639050 6643790 13617660 16470710 13293970 TRUE FALSE 13630880.94 10030244.97 13330176.05 11428211.17 8467149.807 6899380.9 12297021.43 12948576.84 11722372.01 1.162809108 0.855649774 1.137156886 0.974906031 0.722306867 0.588565257 1.049021599 1.104603815 1 23.48276119 4.753107027 23.44256743 0.939206494 1.162809478 0.154890342 0.170145937 2486.533661 4007057.768 0.045532744 0.896771819 56637.8849 -4.753107027 0.223602984 KSLS(ph)PGVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSLSPGVSR 9 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 KS(0.005)LS(0.974)PGVS(0.021)R;KS(0.007)LS(0.933)PGVS(0.06)R 102.33 0.0022061 844910000 1548980 1480870 672850 828540 1348490 1168650 1446420 1736870 535590 TRUE FALSE 1344278.368 1471142.067 998242.5105 1016672.67 1321657.687 1213608.722 1306146.411 1365453.867 472273.1603 2.846400095 3.115023658 2.113697314 2.152721678 2.798502643 2.569717747 2.765658777 2.89123749 1 18.84926202 4.24961427 24.99218503 2.420433236 2.98071205 0.18125408 0.550305618 407.1324486 920503.7126 0.134648442 0.349012644 17767.00687 -4.24961427 0.560278814 KSLSDS(ph)ESDDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KSLSDSESDDSK 12 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 KS(0.027)LS(0.019)DS(0.953)ESDDSK;KSLS(0.235)DS(0.761)ES(0.003)DDSK;KSLS(0.004)DS(0.986)ES(0.01)DDSK 204.26 7.08E-08 4366420000 3659990 2288000 2159000 2055760 1909300 1711510 3213310 3660680 3019590 TRUE FALSE 3176313.048 2272969.977 3203099.621 2522551.728 1871308.665 1777352.897 2901683.691 2877872.069 2662617.51 1.192928776 0.853659968 1.202989017 0.947395455 0.702807917 0.667520923 1.089786152 1.080843215 1 21.34441377 3.504037096 24.22701555 0.921699378 1.062731517 0.181152646 0.167519643 1135.331587 1021911.447 0.050362303 0.074418743 3191.810479 -3.504037096 0.141032139 KSMS(ph)EDGGLQESNPCADDFVSASTADVSHTNLGTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSMSEDGGLQESNPCADDFVSASTADVSHTNLGTIR 36 1 H7C0I1;B8ZZW5;Q8NBF6-2;Q8NBF6;A0A1W2PRP5 H7C0I1 AVL9 Late secretory pathway protein AVL9 homolog 1 KS(0.445)MS(0.555)EDGGLQESNPCADDFVSASTADVSHTNLGTIR 91.336 0.00028027 105910000 39518 43762 24997 29225 47049 40859 52424 62467 55918 TRUE FALSE 34295.59617 43474.52454 37085.63281 35860.98293 46112.81695 42430.87217 47339.92855 49108.91817 49307.43774 0.695546103 0.881703178 0.752130602 0.72729358 0.935210164 0.860536952 0.960097111 0.995973841 1 15.58951766 2.601994773 0.837836565 1.013864407 0.767490308 0.687128372 0.061840318 0.377853275 0.594702662 0.059908727 0.034834792 399.9399361 -2.601994773 -0.246374098 KSNFAEALAAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSNFAEALAAHK 12 1 P07237;H7BZ94;I3L312;I3L3U6;I3L0S0;I3NI03;I3L514;I3L3P5;I3L1Y5 P07237 P4HB Protein disulfide-isomerase 0 ; 102.73 0.0015076 4999100000 12745900 11361700 8146000 9857600 10909900 10526900 12745300 13148700 9833300 FALSE TRUE 11061497.02 11287064.24 12085432.85 12095918.74 10692814.33 10931876.65 11509262.77 10336952.83 8670818.476 1.275715442 1.301729967 1.393805311 1.395014643 1.233195501 1.260766407 1.327355981 1.192154219 1 23.04773675 0.512749942 0.99804613 2.46E-15 1.321353693 0.784292194 0.052592447 3.441875007 0.941349913 6.968148621 0.018475418 3.256491446 -0.512749942 1.321353693 KSNLDEEVNVIPPHT(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KSNLDEEVNVIPPHTPVR 18 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 KSNLDEEVNVIPPHT(1)PVR;KSNLDEEVNVIPPHT(1)PVR;KSNLDEEVNVIPPHT(1)PVR;KSNLDEEVNVIPPHT(1)PVR;KSNLDEEVNVIPPHT(1)PVR;KSNLDEEVNVIPPHT(1)PVR 157.3 4.10E-09 3796900000 4754430 4770690 2966830 3589550 4642900 4114260 5174500 6198690 4411630 TRUE FALSE 4126120.029 4739351.023 4401598.911 4404612.19 4550515.374 4272538.244 4672677.786 4873148.382 3890092.127 1.060674116 1.218313312 1.131489633 1.132264236 1.169770593 1.098312869 1.201174068 1.252707705 1 21.89137289 2.222007452 24.99715445 1.174500121 1.14019599 0 0.076355772 906.4031893 1368760.899 0.029998776 0.020287102 166.7275821 -2.222007452 -0.034304131 KSPLSWIEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSPLSWIEEK 10 1 P53004 P53004 BLVRA Biliverdin reductase A 0 ; 94.191 0.013263 1165270000 2205800 1733180 1176250 1400410 1659650 1324150 2114760 2284000 1948940 FALSE TRUE 1914297.941 1721794.626 1745088.434 1718394.494 1626626.212 1375090.907 1909670.901 1795584.374 1718538.533 1.113910398 1.001894687 1.015449116 0.999916185 0.94651716 0.800151338 1.11121797 1.044832187 1 20.71275077 5.289612369 1.464326421 0.990971429 1.443001747 0.195304757 0.079264352 10.0788218 6.392995482 0.023155209 9.899415574 194810.5037 -5.289612369 0.452030318 KSPSGPVKS(ph)PPLSPVGTTPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSPSGPVKSPPLSPVGTTPVK 21 2 C9J4K0;Q9BVC5-2;Q9BVC5 C9J4K0 C2orf49 Ashwin 1 KS(0.327)PS(0.327)GPVKS(0.343)PPLS(0.002)PVGTTPVK 79.445 0.0039524 720720000 261020 163380 153080 147370 174730 119990 233210 309500 210670 TRUE FALSE 226525.5457 162306.746 227110 180832.6109 171253.2149 124606.0929 210593.3301 243315.8335 185764.8326 1.219421042 0.873721596 1.222567247 0.97344911 0.921881782 0.670773317 1.133655532 1.309805684 1 17.50311788 0.935839804 20.63096385 0.000450711 1.047447478 0.003326789 0.1914309 742.5953453 601050.5053 53495.283 0.047998575 8.626602834 -0.935839804 1.046996767 KSPSSDSWTCADTSTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSPSSDSWTCADTSTER 17 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7;H0YIQ0 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 0 128.38 5.95E-05 189690000 169400 155130 86532 116250 145380 123430 164620 178280 174050 FALSE TRUE 147013.3608 154110.9408 128379.1646 142646.3393 142487.2224 128178.432 148655.1777 140156.2094 153474.0073 0.95790397 1.004150107 0.836487995 0.9294495 0.928412732 0.835180069 0.968601657 0.913224408 1 17.22763481 -0.211985333 1.682493188 9.821773619 0.91967919 0.1697958 0.053202967 256.6239027 8.082638688 8579.753592 0.014385205 0.613782734 0.211985333 -8.902094429 KSRAWWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSRAWWR 7 2 M0R2U1 M0R2U1 LIN7B 0 50.966 0.08694 30947000 34797 39628 16884 21709 36583 51730 31475 36048 27287 FALSE TRUE 30198.48829 39367.68106 25049.15887 26638.36025 35855.06987 53720.08657 28422.55934 28339.41573 24061.16195 1.255071902 1.636150455 1.041061896 1.107110301 1.49016369 2.23264723 1.181262958 1.177807447 1 14.55441869 3.214161787 24.8262726 1.409735189 1.271099518 0.043867871 0.360686829 994.9075293 1012334.085 0.117706139 0.133532019 1637.426397 -3.214161787 -0.138635671 KSREDLS(ph)AQPVQTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSREDLSAQPVQTK 14 2 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 KS(0.423)REDLS(0.577)AQPVQTK 48.547 0.097843 202250000 542320 441140 267490 392710 384010 457110 320170 456780 533430 TRUE FALSE 470651.0379 438242.1223 396849.0587 481880.8077 376368.9523 474695.3175 289119.9627 359101.1517 470368.5131 1.000600646 0.931699529 0.843698181 1.024475054 0.800157625 1.009198754 0.614666915 0.763446408 1 18.84343196 2.260635401 24.99997627 0.77919064 0.928614523 0.247519475 0.115786853 296.7080866 336024.8862 0.041721395 0.032290537 182.2365147 -2.260635401 0.149423883 KSS(ph)LVTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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(0.017)S(0.981)LVT(0.002)SK;KS(0.002)S(0.996)LVT(0.001)S(0.001)K;KS(0.028)S(0.964)LVT(0.003)S(0.004)K;KS(0.002)S(0.943)LVT(0.052)S(0.004)K;KS(0.009)S(0.99)LVTSK;KS(0.003)S(0.99)LVT(0.007)S(0.001)K;KSS(0.998)LVT(0.001)SK 162.1 0.0002105 40566800000 55055350 45748550 31615620 38835810 35281040 26050960 69781110 62296040 51937950 TRUE FALSE 47779646.01 45448024.76 46905039.58 47654074.23 34579016.33 27053157.29 63013748.69 48974516.63 45797904.72 1.04327144 0.99236035 1.024174356 1.040529573 0.755034898 0.590707314 1.375908987 1.069361512 1 25.44877826 2.223743931 24.99999188 1.141430679 0.915924149 0.306407531 0.170337182 328.7885476 554756.0544 0.072592158 0.049168093 167.3955585 -2.223743931 -0.22550653 KSS(ph)MDGAQNQDDGYLALSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSSMDGAQNQDDGYLALSSR 20 1 Q8IVL1-9;Q8IVL1-13;A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-5;Q8IVL1-4;Q8IVL1-10;Q8IVL1-8;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1;E9PNV5 Q8IVL1-9 NAV2 Neuron navigator 2 1 KS(0.104)S(0.896)MDGAQNQDDGYLALSSR 250.98 3.61E-31 369550000 153400 129670 107560 114730 132140 126840 178950 174580 167230 TRUE FALSE 133127.8013 128818.1892 159576.3758 140781.2 129510.6725 131719.6169 161595.4565 137247.4256 147460.2599 0.902804603 0.873579019 1.082165296 0.954706035 0.878275087 0.893255016 1.095857668 0.930741785 1 17.16996668 KSS(ph)PSSPAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSSPSSPAVR 10 1 B3KNS5;Q8WVR3-2;Q8WVR3-3;Q8WVR3 B3KNS5 C7orf43 Uncharacterized protein C7orf43 1 KS(0.12)S(0.843)PS(0.034)S(0.003)PAVR;KS(0.03)S(0.872)PS(0.058)S(0.039)PAVR 95.183 0.0046524 856050000 474880 402500 293830 363600 363680 376720 450620 553840 475170 TRUE FALSE 412123.4048 399855.951 435927.1708 446160.9373 356443.4795 391212.6622 406918.9418 435405.626 418995.9439 0.9835976 0.954319384 1.040409047 1.064833547 0.850708664 0.93369081 0.971176327 1.039164298 1 18.67657675 1.752910258 24.99999462 1.020230864 0.970775658 0.105812481 0.058395395 10.64980427 18585.97776 0.032665817 0.01568636 56.61222938 -1.752910258 -0.049455205 KSS(ph)PSVKPAVDPAAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSSPSVKPAVDPAAAK 16 2 Q6FI81-3;Q6FI81;H3BV90;H3BT65;H3BPG7 Q6FI81-3 CIAPIN1 Anamorsin 1 KS(0.184)S(0.815)PS(0.001)VKPAVDPAAAK 167.51 3.29E-09 708820000 1780600 1163100 1064100 1131300 1069300 643570 1796500 2091700 1620000 TRUE FALSE 1545289.199 1155459.52 1578702.319 1388178.956 1048023.022 668328.5543 1622275.707 1644406.233 1428485.446 1.081767549 0.808870348 1.105158141 0.971783759 0.733660273 0.467858148 1.135661348 1.151153649 1 20.44605491 KSS(ph)TPEEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KSSTPEEVK 9 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 1 KS(0.108)S(0.557)T(0.335)PEEVK;KS(0.005)S(0.497)T(0.497)PEEVK;KS(0.001)S(0.499)T(0.499)PEEVK 124.3 0.00032675 2276720000 6331600 4979560 4189820 4129620 3677490 3209440 6252800 7753000 6335600 TRUE FALSE 5494863.018 4946848.942 6216030.966 5067313.338 3604315.144 3332909.234 5646404.418 6095081.284 5586612.586 0.983576887 0.885482726 1.112665479 0.907045774 0.645170054 0.596588574 1.010702699 1.091015565 1 22.41354235 2.023060053 24.99955952 1.051664132 0.856218465 0.242897585 0.149663282 329.198291 356884.6341 0.067267485 0.045348758 105.4532703 -2.023060053 -0.195445667 KSS(ph)TTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KSSTTLR 7 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 KS(0.033)S(0.912)T(0.027)T(0.027)LR;KS(0.035)S(0.965)T(0.001)TLR;KS(0.004)S(0.992)T(0.003)T(0.001)LR;KS(0.001)S(0.998)T(0.001)TLR;KS(0.001)S(0.999)TTLR 130.98 0.0021501 2556040000 3099830 2501770 1839570 2278930 1512020 2096430 3042810 3022080 3329660 TRUE FALSE 2690179.612 2485335.708 2729192.205 2796395.888 1481933.76 2177081.019 2747718.755 2375831.71 2936031.388 0.916263914 0.846494938 0.92955144 0.952440733 0.504740435 0.741504681 0.935861505 0.809198335 1 21.48543596 KSS(ph)TVATLQGTPDHGDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSSTVATLQGTPDHGDPR 18 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 KS(0.229)S(0.751)T(0.02)VATLQGTPDHGDPR 253.17 1.03E-30 3752600000 2696000 2211000 1630200 1754800 2262800 2351500 2826100 2760600 2774800 TRUE FALSE 2339716.769 2196475.795 2418570.173 2153254.16 2217774.707 2441963.727 2552025.257 2170267.173 2446766.305 0.956248565 0.897705592 0.988476165 0.880040793 0.906410515 0.998037173 1.043019618 0.886994058 1 21.22244488 2.743255043 24.97305295 0.972885445 0.925159302 0.235053708 0.049193962 696.9103021 3707371.796 0.016257255 0.015761618 553.6751636 -2.743255043 -0.047726143 KSS(ph)VNGSSATSSG ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSSVNGSSATSSG 13 1 R4GMX3;P35226 R4GMX3 COMMD3-BMI1;BMI1 Polycomb complex protein BMI-1 1 KS(0.33)S(0.67)VNGSSATSSG 115.1 0.00073171 408900000 702720 555680 526640 680690 669870 837270 1089000 1221400 1233700 TRUE FALSE 609853.7715 552029.7015 781324.8655 835251.0682 656540.8976 869480.3187 983388.9476 960213.1149 1087853.391 0.560602905 0.507448619 0.718226253 0.767797458 0.60351965 0.799262406 0.903971946 0.882667759 1 20.05305271 -1.999999997 0.098985575 2.707978456 0.105247892 0.808394868 0.0690129 126.5992925 1.158016882 45.74690081 4.877098539 0.01 1.999999997 -2.602730563 KSSEAS(ph)PTAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KSSEASPTAQR 11 1 J3KNN7;Q7Z569 J3KNN7 BRAP BRCA1-associated protein 1 KS(0.008)S(0.079)EAS(0.868)PT(0.046)AQR;KS(0.004)S(0.008)EAS(0.977)PT(0.011)AQR;KSSEAS(0.997)PT(0.003)AQR 150.12 2.08E-05 245723000 658143 636642 372162 399325 506098 522239 685450 780570 284306 TRUE FALSE 571167.735 632459.8568 552140.788 489997.8446 496027.64 542329.8723 618975.1645 613651.1799 250695.6686 2.278331087 2.522819243 2.202434494 1.954552495 1.978604747 2.163299731 2.469030151 2.447793308 1 17.93557754 4.037902837 6.036570507 2.08288839 2.39620675 0.120311913 0.410807536 0.454607626 44.26823775 0.105822545 0.2213814 10911.9618 -4.037902837 0.31331836 KSSEASPT(ph)AQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSSEASPTAQR 11 1 J3KNN7;Q7Z569 J3KNN7 BRAP BRCA1-associated protein 1 KSSEAS(0.158)PT(0.841)AQR 164.93 1.30E-05 162040000 497780 427180 232560 270340 356890 355590 502440 567530 195320 TRUE FALSE 431997.1118 424373.8265 345026.7939 331724.8289 349788.5872 369269.7774 453713.4461 446168.126 172229.4921 2.508264447 2.464002078 2.00329682 1.926062864 2.030944776 2.144056589 2.634353969 2.590544282 1 17.39397268 4.260300159 16.96917467 2.125599123 2.486163161 0.124392977 0.448086201 15.65112481 12204.19518 0.113091248 0.296483314 18209.58965 -4.260300159 0.360564038 KSSGEIVYCGQVFEKS(ph)PLR ddPTM_MDA-MB-175_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 153.27 2.48E-08 954780000 723810 485910 420530 462910 540380 444660 633310 771410 535280 TRUE FALSE 628156.6746 482718.0252 623899.7146 568020.7906 529627.4952 461766.3579 571891.6937 606449.9746 471999.8082 1.330840953 1.022708096 1.321821966 1.203434368 1.122092607 0.978318953 1.211635437 1.284852163 1 18.84842675 3.300391631 6.719317075 1.140014976 1.213684313 0.130537 0.122078642 0.62034773 52.90505471 0.035905693 0.046195462 1997.062382 -3.300391631 0.073669337 KSSSISEEKGDS(ph)DDEKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KSSSISEEKGDSDDEKPR 18 3 S4R3H4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 KSSSISEEKGDS(1)DDEKPR;KSSSISEEKGDS(1)DDEKPR;KSSSISEEKGDS(1)DDEKPR 162.11 2.60E-11 984700000 1294470 764800 800130 625259 773510 472866 1190600 1343170 837610 TRUE FALSE 1123402.51 759775.9784 1187075.544 767233.6124 758118.6643 491057.461 1075135.795 1055943.548 738588.7 1.521012317 1.028686167 1.607221373 1.038783307 1.026442273 0.664859158 1.455662394 1.429677367 1 19.49441166 4.75718946 22.92649136 1.182780924 1.521013253 0.140970322 0.276113098 2898.739822 3567291.293 0.069284644 1.987893587 57172.79979 -4.75718946 0.338232328 KSSSKDS(ph)RPSQAAGDNQGDEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSSSKDSRPSQAAGDNQGDEAK 22 3 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 KS(0.142)S(0.142)S(0.142)KDS(0.569)RPS(0.004)QAAGDNQGDEAK 166.42 6.47E-11 101380000 169800 128720 160750 120580 120170 75685 208600 246440 130730 TRUE FALSE 147360.4998 127874.4298 238489.2377 147959.5319 117778.8521 78596.65092 188370.0041 193740.7238 115275.2483 1.278335999 1.109296503 2.068867698 1.283532537 1.021718485 0.681817234 1.634088903 1.680679301 1 16.81472325 KSST(ph)PEEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSSTPEEVK 9 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 1 KS(0.128)S(0.128)T(0.744)PEEVK;KS(0.01)S(0.091)T(0.899)PEEVK 108.37 0.0015365 427340000 2077460 1544310 1190120 1235070 1077140 999470 1859430 2265060 1820900 TRUE FALSE 1802918.397 1534165.326 1765666.013 1515511.52 1055707.021 1037920.258 1679102.765 1780694.546 1605635.276 1.122869199 0.955488054 1.099668174 0.943870344 0.657501138 0.646423427 1.045756025 1.109028041 1 20.61471279 3.587086699 6.238839413 0.908290285 1.047225372 0.190193594 0.154974786 0.551102044 27.08552278 0.050191457 0.074691451 3864.441156 -3.587086699 0.138935087 KSSTPEEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSSTPEEVK 9 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 149.33 0.00014091 4632900000 9826000 7374900 5306000 6274500 5713100 4996700 9427000 10606600 9201700 FALSE TRUE 8527469.204 7326453.796 7871999.348 7699221.125 5599420.487 5188926.282 8512770.991 8338461.131 8113885.509 1.050972336 0.902952573 0.970188615 0.948894474 0.690103463 0.639511893 1.049160847 1.027677938 1 22.95196151 KSSTPEEVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSSTPEEVKK 10 2 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 97.911 0.0032261 2441820000 1970110 1305570 1139510 1107460 937680 825690 1709880 2041420 1702370 FALSE TRUE 1709754.972 1296993.625 1690580.847 1358925.719 919022.0025 857454.8286 1544056.101 1604878.219 1501117.758 1.138987906 0.864018574 1.126214675 0.905275893 0.612225122 0.571210902 1.028604247 1.069122133 1 20.51760573 3.499338937 23.8534346 0.870359619 1.023597778 0.181775724 0.178508802 996.070718 1069401.972 0.055909655 0.082057415 3157.467849 -3.499338937 0.153238158 KSTDEPSEKDALQPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSTDEPSEKDALQPGR 16 2 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 173.03 2.45E-09 288450000 244540 172920 121250 104220 156130 142180 253210 268900 39152 FALSE TRUE 212223.4194 171784.0771 179886.9056 127884.7439 153023.3185 147649.7566 228653.7332 211397.8276 34523.49516 6.147217088 4.975859956 5.21056471 3.704281484 4.43243993 4.276790514 6.623133958 6.123303176 1 15.07529091 4.888365018 1.640686352 4.701570476 7.08213837 0.094989822 1.523546413 4.481976787 8.706469703 0.416449536 18.92921223 77333.02841 -4.888365018 2.380567895 KSTLT(ph)PTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSTLTPTQR 9 1 O75376;O75376-2;A0A088AWL3;E7EVK1 O75376 NCOR1 Nuclear receptor corepressor 1 1 KS(0.027)T(0.027)LT(0.946)PTQR 90.653 0.021828 43736000 93313 79092 51204 61597 75799 79452 90720 103260 87163 TRUE FALSE 80981.45062 78572.43944 75966.42567 75583.5403 74290.7482 82508.56985 81921.98836 81178.65257 76858.68944 1.053640795 1.022297414 0.988390854 0.983409174 0.966588797 1.073509976 1.065878028 1.056206568 1 16.22992076 2.728724633 24.8506692 1.051632323 1.002059918 0.362266081 0.030242412 689.8214986 1742834.28 0.010792551 0.009623815 535.4570405 -2.728724633 -0.049572405 KSTVLQQQYNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSTVLQQQYNR 11 1 Q9Y490 Q9Y490 TLN1 Talin-1 0 114.72 0.0013429 0 146650 184980 100340 117540 162970 128920 126970 132450 104500 FALSE TRUE 127269.8309 183764.8542 148864.7596 144229.2535 159727.2158 133879.6358 114656.4689 104126.5982 92146.12905 1.381173927 1.99427644 1.615529173 1.56522314 1.733412109 1.452905697 1.244289588 1.130015979 1 16.49163594 2.18135271 1.236696748 1.021658086 1.680267018 0.715487905 0.155885283 0.252917008 0.740563306 0.140869683 0.053263604 151.8282933 -2.18135271 0.658608932 KSVAAEGALLPQT(ph)PPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSVAAEGALLPQTPPSPR 18 1 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 2 KSVAAEGALLPQT(1)PPS(1)PR 68.361 0.0092809 0 175140 189360 130560 156360 191190 173490 197100 228860 189800 TRUE FALSE 151994.8053 188116.0817 193699.2527 191863.9278 187385.6931 180164.2726 177985.2723 179920.07 167362.0602 0.908179578 1.124006728 1.157366565 1.14640037 1.119642605 1.076494113 1.063474434 1.075034986 1 17.35261299 -0.096219329 0.938305878 8.66E-09 1.095690574 0.119386913 0.069849654 45.50299085 4.143568077 88.75536703 0.023542329 0.801273299 0.096219329 1.095690565 KSVAAEGALLPQTPPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KSVAAEGALLPQTPPSPR 18 1 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 KSVAAEGALLPQT(0.44)PPS(0.56)PR;KSVAAEGALLPQT(0.023)PPS(0.977)PR 163.46 2.03E-11 1100780000 1145340 1123290 751560 837510 1186400 992220 1286040 1458840 987180 TRUE FALSE 993980.4171 1115911.034 1115016.93 1027679.446 1162792.961 1030391.345 1161320.039 1146878.419 870476.705 1.141880548 1.281953931 1.280926788 1.180593852 1.335811693 1.18370927 1.334119606 1.317529133 1 19.73144616 1.231219887 24.99977483 0.999999539 1.26281385 0.583476117 0.068104435 181.6118677 618447.99 0.160448946 0.015914875 17.03020543 -1.231219887 0.262814312 KSVQPTSEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KSVQPTSEER 10 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4;K7EL40;K7EK18;K7EIE4;K7EQD7;K7ER52;K7ELJ9;K7EJZ2;K7ENQ5;K7ER14;K7EN52;K7EKN4;K7EIR4 Q9UHD8 9-Sep Septin-9 0 ;; 164.48 9.85E-06 1726530000 1383360 1309320 800830 1076190 1181130 1191440 1420800 1552690 1158110 FALSE TRUE 1200545.471 1300718.991 1188114.067 1320555.388 1157627.824 1237275.468 1283011.035 1220659.327 1021199.555 1.175622791 1.273716762 1.163449456 1.293141366 1.133596091 1.211590293 1.256376414 1.195319094 1 19.96183338 1.242357521 4.550716975 0.983084654 1.215982091 0.647305686 0.049582696 0.110882417 4.914273838 0.082916966 0.011268672 17.47259946 -1.242357521 0.232897437 KSVS(ph)NGALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KSVSNGALR 9 1 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 KS(0.008)VS(0.992)NGALR 76.073 0.022335 362230000 501230 466160 326760 384480 462620 469160 529140 565030 415730 TRUE FALSE 434991.1855 463097.7643 484782.2289 471782.0604 453414.7671 487208.8888 477824.0842 444202.7316 366582.873 1.186610771 1.263282598 1.322435565 1.286972456 1.236868388 1.329055241 1.303454469 1.211738912 1 18.48377986 1.250603669 2.679567548 0.941963354 1.277354948 0.809590186 0.041833354 0.190404761 1.592011586 0.142618194 0.01101829 17.80752935 -1.250603669 0.335391594 KT(ph)ASFGNILDVPEIVISGNGQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KTASFGNILDVPEIVISGNGQPR 23 1 O43318;O43318-3 O43318 MAP3K7 Mitogen-activated protein kinase kinase kinase 7 1 KT(0.596)AS(0.404)FGNILDVPEIVISGNGQPR;KT(0.696)AS(0.304)FGNILDVPEIVISGNGQPR;KT(0.5)AS(0.5)FGNILDVPEIVISGNGQPR 163.49 9.02E-12 1786917000 1836835 1831790 1304229 1413303 1879909 1819746 2065681 2390754 1770655 TRUE FALSE 1594092.601 1819756.851 1934958.507 1734215.047 1842502.489 1889752.806 1865351.575 1879509.862 1561330.183 1.020983657 1.165516987 1.239301288 1.110729214 1.180085102 1.210347963 1.194719474 1.203787567 1 20.57434423 4.736456754 6.458142045 1.170690949 1.018032053 0.300289883 0.067310469 0.135293103 34.06801397 0.015577734 0.091304406 54507.56154 -4.736456754 -0.152658896 KT(ph)GSYGALAEITASK ddPTM_MDA-MB-175_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 170.91 6.52E-07 1139500000 1753200 1225000 713970 901890 1092500 833140 1165600 1373100 877610 TRUE FALSE 1521510.178 1216952.894 1059248.28 1106677.909 1070761.387 865191.4349 1052560.291 1079473.25 773859.9456 1.966131193 1.572575117 1.36878551 1.43007519 1.383663018 1.118020696 1.360143134 1.394920692 1 19.56171296 7.999999975 0.605363535 1.263904735 47.36008436 0.763684254 0.124840576 89.13017196 0.687334342 0.05781061 5439.151971 99999994.33 -7.999999975 46.09617963 KT(ph)MEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTMEVK 6 1 Q68D51-2;Q68D51 Q68D51-2 DENND2C DENN domain-containing protein 2C 1 KT(1)MEVK 53.466 0.081651 255960000 337520 326540 153770 197230 236220 217170 456920 366180 340100 TRUE FALSE 292915.8768 324394.9372 228133.6863 242014.086 231519.6842 225524.6704 412607.9687 287875.2566 299893.7654 0.976732132 1.081699504 0.760715002 0.806999391 0.772005659 0.752015201 1.375847104 0.959924112 1 18.194092 2.273657729 24.99999898 1.091254987 0.857814549 0.387289351 0.149592559 195.7035546 139400.7771 0.05702293 0.044167882 187.7836297 -2.273657729 -0.233440437 KT(ph)PAQPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTPAQPQR 8 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 KT(1)PAQPQR 50.292 0.091702 30211000 18553 24364 17472 15494 22830 29974 22835 25073 27398 TRUE FALSE 16101.17404 24203.95128 25921.51764 19012.14951 22375.72767 31127.11918 20620.46521 19711.33407 24159.03965 0.666465815 1.001858999 1.072953148 0.786957999 0.926184484 1.288425352 0.853530004 0.815898908 1 14.56027549 4.744114887 24.17664748 0.957249688 0.666465616 0.298912791 0.144370019 540.3860966 2352079.033 0.036200202 0.302537093 55477.24509 -4.744114887 -0.290784072 KT(ph)PESFLGPNAALVDLDSLVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KTPESFLGPNAALVDLDSLVSR 22 1 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 KT(0.997)PES(0.003)FLGPNAALVDLDSLVSR;KT(0.998)PES(0.002)FLGPNAALVDLDSLVSR;KT(0.995)PES(0.005)FLGPNAALVDLDSLVSR;KT(1)PESFLGPNAALVDLDSLVSR 227.04 2.80E-26 1402675000 328759 279958 238332 272419 282548 255838 344469 332508 590329 TRUE FALSE 285312.6652 278118.9375 353590.1524 334275.8976 276925.8476 265680.2534 311062.4494 261403.7518 520540.9781 0.548107982 0.534288268 0.679274384 0.642170188 0.531996249 0.510392581 0.597575335 0.502177086 1 18.98965221 1.233196419 24.99998346 1.000000677 0.568303006 0.850015579 0.056996295 66.24498197 308702.318 0.122156281 0.014621817 17.10788882 -1.233196419 -0.431697672 KT(ph)PESFLGPNAALVDLDSLVSRPGPTPPGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTPESFLGPNAALVDLDSLVSRPGPTPPGAK 31 2 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 KT(0.782)PES(0.218)FLGPNAALVDLDSLVSRPGPTPPGAK 166.28 6.25E-11 900530000 311650 276750 206060 188860 247250 144660 324500 355500 225620 TRUE FALSE 270464.6629 274932.011 305711.3052 231743.5495 242330.2087 150225.1638 293030.0399 279479.0915 198947.4606 1.359477834 1.381932748 1.536643415 1.16484799 1.218061331 0.75509968 1.472901635 1.404788433 1 17.60202796 3.724931985 24.56255762 1.197565896 1.421609476 0.253587928 0.2037748 1011.479323 1822964.818 0.058999098 0.088073994 5308.013084 -3.724931985 0.224043579 KT(ph)PVASDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KTPVASDQR 9 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 KT(0.997)PVAS(0.003)DQR;KT(0.973)PVAS(0.027)DQR 72.34 0.027558 236680000 532670 487020 347850 349310 408490 407850 490910 592270 647840 TRUE FALSE 462276.3099 483820.7336 516071.4235 428626.1744 400361.8482 423540.2534 443301.6238 465617.6696 571253.0932 0.809232047 0.84694637 0.903402414 0.75032622 0.700848456 0.741423125 0.776016146 0.815081222 1 19.12377055 1.232549175 3.603127254 1.030593934 0.789856828 0.575063368 0.05634189 0.246579032 4.824772576 0.163809699 0.016083181 17.08241133 -1.232549175 -0.240737105 KT(ph)S(ph)TLQTVRIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KTSTLQTVRIER 12 2 Q8N5I9;J3KN91;A0A087WT30 Q8N5I9 C12orf45 Uncharacterized protein C12orf45 2 KT(0.642)S(0.717)T(0.642)LQTVRIER;KT(0.643)S(0.715)T(0.643)LQTVRIER 65.219 0.067697 4047000000 5459100 4215700 2593200 3171600 4017800 3494400 4578700 5119800 2143500 TRUE FALSE 4737666.103 4188006.789 3847280.194 3891760.255 3937853.641 3628831.829 4134658.379 4024970.612 1890097.872 2.506571842 2.215761867 2.03549258 2.059025785 2.083412557 1.91991742 2.187536656 2.129503806 1 20.85002951 1.238593426 12.27173348 0.998664872 2.131361991 0.845023614 0.153656565 0.022283326 206.4660146 0.2113375 0.037882994 17.32181619 -1.238593426 1.132697119 KT(ph)SDANETEDHLESLICK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KTSDANETEDHLESLICK 18 1 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 KT(0.5)S(0.5)DANETEDHLESLICK;KT(0.5)S(0.5)DANETEDHLESLICK;KT(0.344)S(0.344)DANET(0.312)EDHLESLICK;KT(0.5)S(0.5)DANETEDHLESLICK;KT(0.5)S(0.5)DANET(0.001)EDHLESLICK;KT(0.5)S(0.5)DANETEDHLESLICK 288.58 1.14E-40 2810790000 2566110 2235530 1932250 2425430 2886170 1970430 3650160 4658090 4611320 TRUE FALSE 2226992.062 2220844.656 2866692.563 2976160.952 2828740.864 2046233.717 3296168.045 3661993.703 4066175.003 0.547687215 0.546175375 0.705009637 0.731931348 0.695676124 0.503233067 0.810631132 0.900599138 1 21.95524088 1.890794637 2.396128711 0.961407524 0.630934205 0.735206642 0.081707668 0.156642733 1.638159474 0.062466589 0.024295175 77.76687304 -1.890794637 -0.330473319 KT(ph)SLDVSNSAEPGFLAPGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KTSLDVSNSAEPGFLAPGAR 20 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;H0Y6F6;Q8NEY1-6 Q8NEY1-5 NAV1 Neuron navigator 1 1 KT(0.646)S(0.354)LDVSNSAEPGFLAPGAR;KT(0.667)S(0.332)LDVSNSAEPGFLAPGAR;KT(0.639)S(0.361)LDVSNSAEPGFLAPGAR 236.94 8.14E-30 1257740000 1464260 1122460 888330 1060350 1104830 1053400 1590110 1466840 1463830 TRUE FALSE 1270754.331 1115086.486 1317929.359 1301118.674 1082846.045 1093924.98 1435901.377 1153167.681 1290777.685 0.984487372 0.863887329 1.021035128 1.008011441 0.838909796 0.847492943 1.112431206 0.893389849 1 20.29980911 -0.69725514 0.670763748 1.543730525 0.941435472 0.023445971 0.088333038 218.0058045 8.657962011 171.5449298 0.038928065 0.200791285 0.69725514 -0.602295053 KT(ph)SPASLDFPESQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KTSPASLDFPESQK 14 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KT(0.499)S(0.499)PAS(0.002)LDFPESQK;KT(0.5)S(0.5)PASLDFPESQK;KT(0.5)S(0.5)PASLDFPESQK;KT(0.5)S(0.5)PASLDFPESQK 173.87 1.54E-06 4105050000 2935840 2375230 1913500 2226760 2483200 1835550 3270180 3894210 3254300 TRUE FALSE 2547861.306 2359626.958 2838875 2732379.892 2433789.178 1906164.796 2953038.447 3061463.496 2869580.361 0.887886375 0.822289903 0.989299703 0.952187968 0.848134177 0.664266045 1.029083725 1.066868012 1 21.45240835 2.045181028 24.99941415 1.041140754 0.866560422 0.460370224 0.087196252 110.7601597 61284.97408 0.036845043 0.024840913 110.9637252 -2.045181028 -0.174580332 KTAHNSEADLEESFNEHELEPSS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTAHNSEADLEESFNEHELEPSSPK 25 1 Q8IWS0-5;Q8IWS0 Q8IWS0-5 PHF6 PHD finger protein 6 1 KTAHNSEADLEES(0.008)FNEHELEPS(0.207)S(0.785)PK 48.76 0.069498 146100000 102840 94327 31882 71479 123880 93293 122450 128660 97401 TRUE FALSE 89249.43344 93707.35973 47300.24184 87709.39944 121415.0304 96882.04208 110574.8178 101147.0602 85886.36474 1.03915719 1.091062126 0.550730514 1.021226125 1.413670619 1.128025879 1.287454862 1.17768473 1 16.39014149 3.471200761 24.98496113 1.202673903 0.892155685 0.39576999 0.175348949 146.5096713 618278.9396 0.049361638 0.063910373 2959.380183 -3.471200761 -0.310518218 KTAPTLS(ph)PEHWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KTAPTLSPEHWK 12 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KT(0.001)APT(0.076)LS(0.923)PEHWK;KTAPT(0.022)LS(0.977)PEHWK 134.85 6.49E-05 1035820000 2992050 2666240 1625320 1941680 2497630 1957170 2848040 3439420 2158940 TRUE FALSE 2596643.012 2648725.294 2411330.188 2382568.121 2447932.05 2032463.596 2571837.519 2703926.799 1903712.573 1.363989002 1.391347272 1.266646143 1.251537735 1.285872712 1.067631546 1.35095894 1.420344036 1 20.86038424 4.199407498 5.929413054 1.253331754 1.377994705 0.176146259 0.123663944 0.330170413 29.68953206 0.032174312 0.071283664 15827.32418 -4.199407498 0.12466295 KTATNDEESPLSVS(ph)SPEGTGTWLHYTSGVGTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTATNDEESPLSVSSPEGTGTWLHYTSGVGTGR 33 1 A0A087WZV0;O43314-2;O43314;A0A087WWN8 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 KTATNDEES(0.001)PLS(0.288)VS(0.353)S(0.353)PEGT(0.005)GT(0.001)WLHYTSGVGTGR 82.266 0.00033385 364240000 68738 88023 54003 72637 112960 110230 97092 120410 78399 TRUE FALSE 59654.09914 87444.77112 80119.03143 89130.34104 110712.317 114470.6194 87676.03278 94661.25853 69130.75953 0.862916877 1.26491842 1.158949098 1.289300763 1.601491402 1.655856528 1.268263699 1.36930737 1 16.07704016 5.263230668 0.97600273 1.370397008 9.82E-13 0.386917372 0.188172108 5.357214968 2.008085253 0.062384861 9.844542524 183328.7882 -5.263230668 -1.370397008 KTEAAATTR ddPTM_MDA-MB-175_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 ; 149.31 0.000141 330150000 553890 497570 297410 398210 337640 403860 486790 603700 543530 FALSE TRUE 480692.0331 494301.4299 441238.4708 488629.6668 330921.6246 419396.7555 439581.1807 474603.453 479274.5026 1.002957659 1.031353488 0.920638316 1.019519428 0.690463655 0.875065862 0.917180402 0.990253916 1 18.87049267 4.046218672 1.860784827 0.911497212 1.018540752 0.162553262 0.09258406 0.726523071 4.859557129 0.028132692 0.08404372 11122.91637 -4.046218672 0.10704354 KTEEIAQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KTEEIAQER 9 1 Q9NQT8;E7ERX9;A0A1B0GUA8;Q9H1H9-3;Q9H1H9-4;Q9H1H9-2;Q9H1H9 Q9NQT8;A0A1B0GUA8 KIF13B;KIF13A Kinesin-like protein KIF13B;Kinesin-like protein;Kinesin-like protein KIF13A 0 ;; 150.04 0.00013819 1067693000 1082470 1042700 669689 837599 949100 850761 1058560 1275580 1159000 FALSE TRUE 939418.8469 1035850.435 993552.8404 1027788.655 930214.7669 883490.3262 955901.0141 1002807.144 1021984.34 0.919210608 1.013567815 0.972180102 1.005679455 0.910204521 0.86448519 0.93533822 0.981235332 1 19.96294166 KTEELEEESFPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KTEELEEESFPER 13 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ; 120.92 0.00040509 822640000 767290 637450 440930 491980 588860 537380 734040 780380 639100 FALSE TRUE 665890.6824 633262.549 654165.2228 603691.5784 577142.8381 558053.3563 662852.9138 613501.8099 563546.3261 1.181607708 1.123709835 1.160801149 1.071236827 1.024126698 0.990252851 1.176217257 1.088644858 1 19.10417469 3.714788716 7.055002075 1.064476772 1.152292528 0.415083765 0.053906298 0.212673013 46.38181388 0.015524448 0.023791857 5185.477046 -3.714788716 0.087815755 KTEFLDLDNSPLSPPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTEFLDLDNSPLSPPSPR 18 1 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 KTEFLDLDNSPLSPPS(1)PR 181.37 4.52E-14 106070000 254110 226310 149830 206330 212400 209130 211100 261880 359250 TRUE FALSE 220528.7197 224823.3547 222288.2892 253180.3801 208173.6556 217175.3664 190627.5545 205879 316779.8743 0.696157608 0.709714767 0.701712158 0.799231266 0.65715556 0.685571856 0.601766621 0.649911868 1 18.27312116 1.234617609 24.99933599 1.000000454 0.685455254 0.790444596 0.050530912 56.40946214 357594.1911 0.098930813 0.013367071 17.16396457 -1.234617609 -0.3145452 KTEKEESTEVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTEKEESTEVLK 12 2 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0YA91;P20810-5;E9PCH5;P20810-2;P20810-3;F8W7E0;A0A0C4DGB5;E7EVY3;H0Y9H6 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 115.34 0.00053997 213240000 829420 663830 531850 630300 594720 464450 944710 1188600 663920 FALSE TRUE 719810.0455 659469.257 789054.4389 773419.2485 582886.2355 482317.692 853092.1696 934427.1397 585432.1339 1.229536275 1.126465766 1.347815388 1.321108295 0.995651249 0.823866105 1.457200793 1.596132302 1 19.15914241 KTEPATGFIDGDLIESFLDISRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTEPATGFIDGDLIESFLDISRPK 24 2 Q16531;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 241.48 7.76E-38 860990000 650580 578770 388760 454770 476060 362140 662080 828090 611950 FALSE TRUE 564604.2046 574968.0218 576765.6363 558032.4792 466587.3374 376071.7601 597871.5835 651009.3977 539605.9681 1.046326835 1.065533103 1.06886445 1.034148086 0.864681573 0.696937733 1.107978078 1.206453294 1 19.04154678 -0.560708031 11.97152516 0.609479163 1.018917632 0 0.140067444 0 0 0 0.03502823 0.274974214 0.560708031 0.409438469 KTES(ph)PIKLSPATPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTESPIKLSPATPSR 15 2 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 KT(0.011)ES(0.989)PIKLSPATPSR 98.391 0.0015374 700400000 534970 333090 252660 236890 350940 252850 481730 507720 174060 TRUE FALSE 464272.3591 330901.9099 374847.2211 290679.4951 343956.9806 262577.3031 435011.8987 399148.0291 153482.8251 3.024914083 2.155953995 2.442274703 1.893889398 2.241012833 1.710792742 2.834270861 2.600603871 1 17.2277177 5.910936436 1.441074533 2.162385565 20.85717807 0.230408027 0.512982124 54.93647789 6.368962895 0.139497302 3022.425156 814585.0506 -5.910936436 18.69479251 KTESASVQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KTESASVQGR 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 145.09 4.98E-05 398510000 374430 359130 217800 339940 335440 345870 389760 513320 400870 FALSE TRUE 324948.1268 356770.8514 323128.8085 417128.5727 328765.4003 359175.8427 351961.1352 403550.5127 353479.6053 0.919283947 1.009310993 0.914137064 1.180064045 0.930083081 1.016114756 0.995704222 1.141651475 1 18.43126745 7.536510368 0.343380955 1.059816852 5.89E-11 0.157586913 0.081159991 100.7091061 2.099008539 0.110699795 64.18293624 34396192.29 -7.536510368 -1.059816852 KTESHHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KTESHHK 7 1 A0A0U1RR32;A0A0U1RRH7;P20671;Q7L7L0;P04908;Q99878;Q96KK5;Q6FI13;P0C0S8 A0A0U1RR32;Q7L7L0;Q99878 HIST1H2AD;HIST3H2A;HIST1H2AB;HIST1H2AJ;HIST1H2AH;HIST2H2AA3;HIST1H2AG Histone H2A type 1-D;Histone H2A type 3;Histone H2A type 1-B/E;Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-A;Histone H2A type 1 0 ; 62.2 0.056405 87122000 253794 230918 73330 182704 803110 226740 266278 376020 255004 FALSE TRUE 220254.4799 229401.0845 108792.6333 224189.7357 787129.6823 235462.8345 240454.4005 295611.0492 224857.7176 0.97952822 1.020205519 0.483828771 0.997029313 3.500567784 1.047163678 1.069362453 1.314658231 1 17.77865288 3.456212621 24.99999075 1.555940917 0.829311195 0.193445069 0.732032033 413.2106162 494065.1421 0.215331783 0.278017882 2858.989898 -3.456212621 -0.726629722 KTET(ph)QEKNPLPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KTETQEKNPLPSK 13 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 1 KT(0.204)ET(0.796)QEKNPLPSK;KT(0.026)ET(0.974)QEKNPLPSK;KT(0.203)ET(0.797)QEKNPLPSK;KT(0.078)ET(0.922)QEKNPLPSK 127.22 0.0002886 2043100000 5311260 2185890 1887660 3105530 2226570 899733 5922390 3751090 3856600 TRUE FALSE 4609363.534 2171530.745 2800538.69 3810688.052 2182265.613 934346.3107 5348037.529 2948948.595 3400677.141 1.355425212 0.638558338 0.823523838 1.120567432 0.641715024 0.274753019 1.572639009 0.867165118 1 21.69739061 1.219880175 21.749196 1.000001365 0.90755831 0.005429955 0.37125307 2322.004125 2702679.59 2.291366502 0.087375007 16.59129077 -1.219880175 -0.092443055 KTETQEKNPLPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTETQEKNPLPSK 13 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 58.32 0.060674 2683100000 618180 387160 363150 336840 401420 291410 559090 611240 322930 FALSE TRUE 536485.9467 384616.7205 538770.5547 413324.6703 393432.5274 302620.7313 504869.5379 480531.0827 284753.5833 1.884035806 1.350700195 1.892058911 1.451517012 1.381659619 1.062745999 1.773005038 1.687533049 1 18.11935447 3.555219576 13.32639469 1.431323395 1.673033221 0.210577234 0.279511169 3.193232037 541.3994357 0.077601086 0.115097698 3591.034489 -3.555219576 0.241709826 KTEVLMENFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KTEVLMENFR 10 1 Q9Y265;Q9Y265-2;E7ETR0 Q9Y265 RUVBL1 RuvB-like 1 0 ; 127.37 0.00057371 1436320000 1406060 1362810 929580 1186510 1469640 1291910 1438450 1579340 1678970 FALSE TRUE 1220245.608 1353857.611 1379127.997 1455925.23 1440397.039 1341610.614 1298949.34 1241610.431 1480484.079 0.824220689 0.914469551 0.931538553 0.983411609 0.972923019 0.906197258 0.877381499 0.83865166 1 20.49763755 4.736399688 4.509799689 0.92172133 0.817935286 0.299760797 0.049171208 0.296980262 15.53781496 0.013428845 0.097938907 54500.39979 -4.736399688 -0.103786044 KTFEINPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KTFEINPR 8 1 P14625;H0YIV0;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ; 127.4 0.0018889 2031040000 2083000 1929740 1348010 1701020 1901580 2205220 1899700 1858050 1621310 FALSE TRUE 1807726.272 1917063.411 1999912.145 2087262.589 1863742.278 2290056.24 1715467.386 1460720.467 1429640.579 1.264462061 1.340940821 1.398891564 1.459991148 1.303643941 1.601840543 1.199929137 1.021739652 1 20.44722106 1.976164717 4.291649294 1.03005498 1.393163562 0.743006003 0.093410522 0.098757457 4.201358135 0.046417209 0.025056062 94.65961129 -1.976164717 0.363108581 KTFTAWCNSHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KTFTAWCNSHLR 12 1 O43707;F5GXS2;O43707-3;K7EP19;P12814-3;P12814;P12814-2;P12814-4;P35609-2;P35609;A0A494C1A0;Q08043;A0A494C166;A0A494C033;A0A494C0Q3 O43707;P12814-3 ACTN4;ACTN1;ACTN2;ACTN3 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2;Alpha-actinin-3 0 ; 106.55 0.0012398 2756300000 3375600 3780500 1643790 2188900 3575800 3305000 3390500 3505000 1831790 FALSE TRUE 2929505.907 3755665.647 2438732.342 2685923.2 3504648.576 3432145.489 3061689.832 2755483.026 1615237.873 1.813668412 2.325147094 1.509828604 1.662865418 2.169741457 2.124854516 1.895503989 1.705930174 1 20.62331521 1.189989955 2.08646285 0.625627256 1.934325074 0.597081611 0.239305243 0.600752626 2.327018241 1.583496326 0.065493398 15.48780795 -1.189989955 1.308697818 KTGQIWPNDGEGAFHGDADGSFGT(ph)PPGYGCAADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KTGQIWPNDGEGAFHGDADGSFGTPPGYGCAADR 34 1 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 KTGQIWPNDGEGAFHGDADGS(0.052)FGT(0.946)PPGY(0.002)GCAADR;KTGQIWPNDGEGAFHGDADGS(0.016)FGT(0.984)PPGYGCAADR 143.54 1.97E-10 1068030000 292791 377770 205787 231272 348625 368665 462260 393400 333179 TRUE FALSE 254097.9275 375288.404 305306.2815 283785.8424 341688.0446 382847.7811 417430.0963 309274.4714 293790.9582 0.864893627 1.277399435 1.039195636 0.96594478 1.163031179 1.303129897 1.420840515 1.052702484 1 18.16443047 3.06242886 8.223908154 1.197677527 1.054831886 0.189281226 0.154483352 0.506984794 59.53144315 0.04813218 0.054604438 1154.59284 -3.06242886 -0.14284564 KTKFENLCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 80.102 0.014097 852060000 379160 350710 135670 134560 284660 250930 439280 464200 47516 FALSE TRUE 329053.0453 348406.1629 201280.4658 165113.9046 278995.8229 260583.4395 396678.6932 364934.4424 41898.71261 7.85353594 8.31543838 4.803977336 3.940787063 6.65881612 6.219366258 9.467562808 8.709920178 1 15.3546183 4.266778842 24.88277934 6.257014025 8.084489622 0.113673388 2.396903949 550.7572306 485647.1531 0.621483327 1.643558414 18483.27146 -4.266778842 1.827475597 KTKPPRPDS(ph)PATTPNISVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KTKPPRPDSPATTPNISVK 19 3 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 KTKPPRPDS(1)PATTPNISVK;KTKPPRPDS(1)PATTPNISVK 234.64 2.13E-23 1635650000 2313640 1500980 1030720 1152820 1411860 909910 2039730 2278620 1037880 TRUE FALSE 2007886.612 1491119.964 1529179.64 1414585.401 1383766.748 944914.8265 1841917.299 1791354.845 915183.0088 2.193972782 1.629313426 1.670900383 1.545685822 1.512010969 1.032487292 2.012621826 1.957373365 1 19.80370074 4.924753502 2.031073804 1.576219626 2.634923835 0.273014071 0.329829626 2.254493462 6.46488986 0.088758163 5.241594307 84091.77164 -4.924753502 1.058704209 KTKPYIQVDIGGGQTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTKPYIQVDIGGGQTK 16 2 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 126.63 3.97E-05 479620000 670770 476730 356740 469820 461680 408650 552760 665050 362060 FALSE TRUE 582126.045 473598.3292 529260.6572 576499.8117 452493.4713 424371.0299 499153.4203 522834.2329 319257.6793 1.823373666 1.483435983 1.657785205 1.805750806 1.417329952 1.329242983 1.563481328 1.637655934 1 18.2843618 3.220354409 24.93392704 1.430586701 1.675161291 0.369020939 0.192200978 310.3890964 425085.6378 0.058209726 0.066127735 1660.941776 -3.220354409 0.244574591 KTLDMIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KTLDMIK 7 1 P14625 P14625 HSP90B1 Endoplasmin 0 ; 92.062 0.025567 1016710000 1584470 2023290 1614950 2006890 2171020 2297060 2383570 2526930 2501010 FALSE TRUE 1375078.275 2009998.875 2395945.222 2462585.048 2127820.95 2385429.385 2152411.748 1986565.684 2205343.447 0.623521147 0.911422154 1.086427252 1.116644689 0.96484788 1.081658908 0.975998433 0.900796512 1 21.07257192 4.685543465 3.099550814 1.008998068 0.586241585 0.780972986 0.06548964 0.157779035 2.406883548 0.018331804 0.151398256 48477.86281 -4.685543465 -0.422756484 KTLDSVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KTLDSVAK 8 1 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 98.943 0.011488 1267910000 3025400 2589600 1875230 2062450 1988980 2017420 2846800 3102400 2178100 FALSE TRUE 2625585.725 2572588.747 2782097.5 2530760.795 1949403.189 2095031.453 2570717.774 2438975.903 1920607.499 1.367060019 1.339466157 1.448550785 1.317687657 1.014993011 1.090817074 1.338492001 1.269898146 1 20.87313129 3.46171336 23.83880526 1.170389995 1.380911307 0.519044638 0.107578208 128.0010238 198039.4294 0.033123503 0.042781093 2895.431937 -3.46171336 0.210521311 KTLEEEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KTLEEEAK 8 1 P35579 P35579 MYH9 Myosin-9 0 ;; 160.36 0.00056729 1354140000 1721130 1355320 1227600 1229770 1126620 874690 1832130 2023030 1709770 FALSE TRUE 1493678.31 1346416.814 1821271.466 1509008.074 1104202.466 908339.8903 1654450.315 1590420.778 1507642.938 0.990737443 0.893060803 1.208025733 1.000905477 0.732403169 0.602490064 1.097375428 1.054905467 1 20.52386336 KTPEKLDNTPAS(ph)PPRS(ph)PAEPNDIPIAK ddPTM_MDA-MB-175_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 2 KT(0.004)PEKLDNT(0.115)PAS(0.882)PPRS(0.999)PAEPNDIPIAK 91.942 0.0088249 145620000 78468 74914 66448 70020 97240 62644 146890 161540 59581 TRUE FALSE 68098.25499 74421.885 98582.47506 85919.11119 95305.11425 65053.95522 132644.6304 126995.9281 52537.40205 1.29618619 1.416550535 1.876424627 1.635389415 1.814043149 1.238240809 2.524765695 2.417247963 1 15.68105724 2.245097171 24.99997409 2.094295319 1.57149603 0.153066872 0.453852872 226.7441761 867218.4809 0.171102587 0.129326981 175.8316984 -2.245097171 -0.52279929 KTPSKPPAQLS(ph)PSVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTPSKPPAQLSPSVPK 16 2 F5H8D7;P18887;M0QYS5 F5H8D7 XRCC1 DNA repair protein XRCC1 1 KTPSKPPAQLS(0.824)PS(0.176)VPK 115.42 0.00026458 1728200000 2517700 1871200 1495100 1690100 1704300 1163800 2570200 2766300 2338400 TRUE FALSE 2184979.566 1858907.964 2218135.361 2073863.037 1670387.764 1208572.139 2320942.4 2174748.272 2061957.016 1.059663004 0.90152605 1.075742774 1.005774136 0.810098247 0.586128678 1.125601737 1.054701071 1 20.97558283 KTQMAEVLPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KTQMAEVLPSPR 12 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 KTQMAEVLPS(1)PR;KTQMAEVLPS(1)PR 106.94 0.0011437 455570000 1014410 954850 526340 790670 883110 802250 853770 1098060 891930 TRUE FALSE 880353.1483 948577.5275 780879.7845 970203.7081 865537.8388 833113.0766 770971.5168 863248.4141 786487.0515 1.11934856 1.206094272 0.99287049 1.233591457 1.100511238 1.059283907 0.980272358 1.097600288 1 19.58506349 2.786820355 3.445041783 1.037859609 1.135181783 0.326124298 0.070082875 0.294951063 7.157070616 0.022638844 0.021870563 612.0971471 -2.786820355 0.097322174 KTQTVCNFTDGALVQHQEWDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTQTVCNFTDGALVQHQEWDGK 22 1 Q01469;I6L8B7 Q01469 FABP5 "Fatty acid-binding protein, epidermal" 0 329.09 6.90E-81 746350000 848050 825300 675310 725380 701030 576300 926600 1100300 1024100 FALSE TRUE 735978.0438 819878.55 1001892.175 890088.6157 687080.8745 598470.6339 836738.4746 865009.4075 903032.0647 0.815007653 0.907917428 1.109475747 0.985666678 0.760859887 0.662734644 0.926587778 0.957894455 1 19.78441769 4.732579261 7.022793285 0.91375594 0.81373689 0.058775776 0.124470253 0.373612973 143.3088073 0.033141484 0.178541363 54023.0701 -4.732579261 -0.10001905 KTS(ph)DANETEDHLESLICK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTSDANETEDHLESLICK 18 1 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 KT(0.01)S(0.989)DANETEDHLESLICK 196.82 1.17E-15 306030000 359750 307930 249020 347160 394260 260020 552220 641270 703840 TRUE FALSE 312208.126 305907.1876 369446.9049 425987.984 386414.9974 270023.1377 498665.7894 504139.4009 620632.837 0.50304803 0.492895589 0.595274505 0.686376805 0.62261449 0.435077104 0.803479545 0.812298948 1 19.2433805 1.759618564 1.483098985 0.986800601 0.564473301 0.736098569 0.088779597 0.253434431 0.966519521 0.128419934 0.027818631 57.49347562 -1.759618564 -0.4223273 KTS(ph)QSEEEEAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTSQSEEEEAPR 12 1 Q7RTP6;A0A5F9ZHV5;Q7RTP6-2;Q7RTP6-4;Q7RTP6-3;J3KSK6;Q7RTP6-5 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 KT(0.188)S(0.764)QS(0.048)EEEEAPR 121.13 0.00040445 113420000 97194 104410 92943 127330 136460 123520 172970 191910 181650 TRUE FALSE 84349.56664 103724.1238 137890.5457 156242.2226 133744.713 128271.8943 156195.396 150871.5399 160175.5439 0.526607025 0.647565298 0.860871406 0.975443684 0.834988349 0.800820719 0.975151338 0.941913704 1 17.28929436 4.313458332 2.376000742 0.919452759 0.533634818 0.83274931 0.062446028 0.125186172 1.339260454 0.017706545 0.068731837 20580.61422 -4.313458332 -0.385817941 KTS(ph)TSPPPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTSTSPPPEK 10 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KT(0.062)S(0.455)T(0.242)S(0.242)PPPEK 109.24 0.0013037 0 138490 102660 92026 119580 119510 166640 209590 195940 444240 TRUE FALSE 120188.1956 101985.6197 136530.0814 146732.4667 117131.9848 173050.7486 189263.9941 154039.7558 391722.4533 0.306819777 0.260351733 0.348537798 0.374582732 0.299017796 0.441768776 0.483158401 0.393236983 1 18.5794723 0.169953526 1.374744919 10 0.346418396 0.89359255 0.068758768 6.663474061 0.989296317 173.8163503 0.020816975 1.478950116 -0.169953526 -9.653581604 KTSAVS(ph)SPLLDQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTSAVSSPLLDQQR 14 1 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 KT(0.001)S(0.001)AVS(0.648)S(0.351)PLLDQQR 81.317 0.0084781 149100000 342260 260980 169580 200420 308030 278430 338030 347900 122950 TRUE FALSE 297029.4738 259265.6052 251589.4552 245928.4242 301900.8057 289141.3823 305247.9026 273504.2924 108414.9911 2.739745407 2.391418407 2.320615007 2.268398695 2.784677679 2.666987097 2.815550687 2.522753446 1 16.72620473 1.239442532 7.161299336 0.969921685 2.563772479 0.868279436 0.19148277 0.037882025 12.06260575 0.294771913 0.050345307 17.35571586 -1.239442532 1.593850794 KTSAVSS(ph)PLLDQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTSAVSSPLLDQQR 14 1 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 KTSAVS(0.278)S(0.721)PLLDQQR 104.03 0.00066252 533110000 586470 492800 276960 270860 530440 429350 545800 631950 192030 TRUE FALSE 508966.5036 489562.7644 410898.7824 332362.9028 519885.2818 445867.3723 492868.4 496812.4103 169328.4322 3.005794698 2.89120237 2.426637849 1.96282986 3.070277538 2.633151247 2.910724405 2.934016479 1 17.36946471 4.318142913 5.222983647 2.506849411 2.971794884 0.105783035 0.601413179 0.518413823 24.10176801 0.148077735 0.4068832 20803.81162 -4.318142913 0.464945473 KTSFDQDS(ph)DVDIFPSDFPTEPPSLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KTSFDQDSDVDIFPSDFPTEPPSLPR 26 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KT(0.015)S(0.015)FDQDS(0.97)DVDIFPSDFPTEPPSLPR;KT(0.051)S(0.051)FDQDS(0.899)DVDIFPSDFPTEPPSLPR;KT(0.034)S(0.034)FDQDS(0.931)DVDIFPSDFPTEPPSLPR;KT(0.025)S(0.025)FDQDS(0.951)DVDIFPSDFPTEPPSLPR;KT(0.121)S(0.121)FDQDS(0.758)DVDIFPSDFPTEPPSLPR;KT(0.022)S(0.089)FDQDS(0.889)DVDIFPSDFPTEPPSLPR;KT(0.004)S(0.013)FDQDS(0.983)DVDIFPSDFPTEPPSLPR 188.93 5.73E-18 7566993000 1579888 1189974 794941 1055453 1341846 1014700 1213817 1528966 1024220 TRUE FALSE 1371101.798 1182156.982 1179377.127 1295109.735 1315145.89 1053736.166 1096101.214 1202008.519 903137.8784 1.518153353 1.308944083 1.305866086 1.434011092 1.456196137 1.166750051 1.213658778 1.33092471 1 19.78458673 -0.288475305 0.433543563 5.28E-17 1.400531514 0.529465617 0.103802811 19.66580973 1.070458737 18.66064531 0.095766482 0.514665072 0.288475305 1.400531514 S(ph)EPDDELLFDFLNSSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SEPDDELLFDFLNSSQK 17 0 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 1 S(1)EPDDELLFDFLNSSQK;S(1)EPDDELLFDFLNSSQK;S(1)EPDDELLFDFLNSSQK;S(1)EPDDELLFDFLNSSQK 207.39 6.42E-12 72999000 102077 76214.2 98012 113146 106016 81308 90624 145180 294075 TRUE FALSE 88587.26582 75713.5439 145410.931 138837.5286 103906.489 84435.97137 81835.29843 114134.3868 259309.7885 0.341627157 0.291981048 0.560761442 0.535411831 0.400704075 0.325618141 0.315588929 0.440146851 1 17.98431714 1.239968469 5.077901549 1.036180697 0.399598088 0.816505473 0.089391393 0.073882197 5.00468641 0.165930295 0.024070876 17.37674664 -1.239968469 -0.636582609 WMHPQVTPTDDSNPWWAAFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WMHPQVTPTDDSNPWWAAFSR 21 0 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-3;Q03154-4;C9JMV9 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 ; 128.75 1.76E-05 772250000 1579950 1516610 970890 1132160 1380830 1248730 1709990 1739320 726720 FALSE TRUE 1371155.604 1506647.289 1440415.651 1389234.232 1353354.185 1296769.451 1544155.433 1367379.953 640807.9895 2.139729259 2.351168078 2.24781163 2.167941497 2.111949612 2.023647446 2.409700657 2.133837243 1 19.28953261 1.240491539 5.403428335 0.939690796 2.207338674 0.919334478 0.111744947 0.038344755 3.346962933 0.180912429 0.027557861 17.39768805 -1.240491539 1.267647878 KTSYAQHQQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KTSYAQHQQVR 11 1 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;H0Y9Y4;D6RB09;D6RAS7;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ;; 218.54 6.84E-12 1943734000 1926650 2823420 1188878 1717850 2846801 2681430 2895660 3217310 1554789 FALSE TRUE 1672038.321 2804872.768 1763823.377 2107914.098 2790155.23 2784586.347 2614839.339 2529313.294 1370983.616 1.219590301 2.045883507 1.286538626 1.53751954 2.035148486 2.031086525 1.907272493 1.844889512 1 20.3867799 3.292204945 24.61212695 1.797970816 1.542928891 0.093233389 0.362825077 193.1107439 88597.7217 0.102148848 0.13187347 1959.769278 -3.292204945 -0.255041925 KTSYLTELIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KTSYLTELIDR 11 1 B4DR80;Q9Y6E0-2;H0Y630;Q9Y6E0;Q5JV98;Q9P289-2;Q5JV99;Q8NBY1;B4E0Y9;Q9P289-3;Q9P289 B4DR80;Q8NBY1 STK24;STK26 Serine/threonine-protein kinase 24;Serine/threonine-protein kinase 24 36 kDa subunit;Serine/threonine-protein kinase 24 12 kDa subunit;Serine/threonine-protein kinase 26 0 ; 109.84 0.0030064 2414500000 1445070 1128310 754250 1010460 1349870 1261280 1348540 1449930 1058520 FALSE TRUE 1254100.338 1120898.057 1119007.823 1239900.387 1323010.228 1309802.258 1217758.798 1139873.753 933382.9715 1.343607476 1.200898336 1.198873192 1.328394051 1.417435574 1.40328493 1.304672182 1.221228357 1 19.83210962 1.249788299 2.13884188 0.911180081 1.312722769 0.657722866 0.071554767 0.477222114 2.237516722 0.371868089 0.02175413 17.77412781 -1.249788299 0.401542688 KTTAS(ph)PSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTTASPSVR 9 1 Q9Y3P9;Q9Y3P9-2 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 1 KT(0.012)T(0.128)AS(0.837)PS(0.023)VR 76.165 0.022176 69164000 71352 72516 41667 49164 62789 70965 60436 68965 60179 TRUE FALSE 61922.65242 72039.63762 61817.30057 60327.43762 61539.62174 73695.06947 54574.92602 54217.37144 53064.70718 1.166927242 1.357580988 1.164941896 1.136865552 1.159709061 1.388777464 1.028459949 1.021721862 1 15.69546504 2.125257862 9.966378304 1.016379298 1.224578179 0.58598332 0.084163728 0.212069352 17.69206854 0.033927862 0.022866336 133.4313444 -2.125257862 0.208198881 KTTHFVEGGDAGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTTHFVEGGDAGNR 14 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 60.918 0.057853 51200000 89606 68106 45923 60112 70208 67449 73673 84054 95465 FALSE TRUE 77764.34007 67658.6072 68131.5164 73761.34835 68810.99816 70043.80668 66528.2038 66079.70621 84179.23645 0.92379479 0.803744606 0.80936249 0.876241594 0.817434335 0.832079378 0.790316076 0.784988187 1 16.3611768 1.230347024 24.99976674 1.000000321 0.825490723 0.616196036 0.042108841 206.1543756 627423.0383 0.112102054 0.010167313 16.99601179 -1.230347024 -0.174509599 KTTHFVEGGDAGNREDQINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KTTHFVEGGDAGNREDQINR 20 2 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 120.23 2.36E-05 663300000 588880 572020 267360 349650 536430 543450 631640 627800 235270 FALSE TRUE 511058.016 568262.363 396656.1903 429043.3766 525756.0925 564356.8732 570383.65 493549.8555 207456.6486 2.463444866 2.739186074 1.911995556 2.068110998 2.534293772 2.720360504 2.749411281 2.379050557 1 17.66245037 4.265566475 24.98612029 2.267291809 2.601315512 0.086329708 0.508968956 666.9121041 617023.1044 0.128217226 0.33903406 18431.74593 -4.265566475 0.334023703 KTTPS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KTTPSPGR 8 1 Q14686 Q14686 NCOA6 Nuclear receptor coactivator 6 1 KT(0.02)T(0.014)PS(0.965)PGR;KT(0.006)T(0.145)PS(0.849)PGR;KT(0.001)T(0.032)PS(0.967)PGR;KT(0.067)T(0.226)PS(0.707)PGR 91.549 0.0076001 483750000 978710 830630 545747 600012 646287 730493 903640 960720 865260 TRUE FALSE 849370.9938 825173.5368 809672.0746 736253.8952 633427.1531 758595.5384 816005.1319 755277.5043 762969.9485 1.113243052 1.081528229 1.061210964 0.964984134 0.830212454 0.994266602 1.069511497 0.989917763 1 19.54126671 3.8886882 3.569398691 0.977370694 1.093383866 0.440482586 0.059536501 0.258414373 5.990912192 0.017773698 0.033835997 7739.059753 -3.8886882 0.116013172 KTTTTPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KTTTTPGR 8 1 P17096;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 0 ;;; 117.31 0.0033725 2439970000 1823146 1974924 1130591 1477327 1299184 1573107 1932855 2118144 1824446 FALSE TRUE 1582212.637 1961950.594 1677348.589 1812776.675 1273332.78 1633625.444 1745407.02 1665195.389 1608762.072 0.983496978 1.219540557 1.042633102 1.126814652 0.791498508 1.015454971 1.084937947 1.035078722 1 20.61751954 KTVSLTPS(ph)PTTQVETPDLVDHDNTS(ph)PLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTVSLTPSPTTQVETPDLVDHDNTSPLFR 29 1 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 2 KTVSLT(0.004)PS(0.986)PT(0.006)T(0.003)QVETPDLVDHDNT(0.248)S(0.752)PLFR 101.36 0.00067443 309980000 208090 240470 113350 122960 274500 243670 292960 339390 75532 TRUE FALSE 180590.3793 238890.3367 168166.4391 150879.9473 269037.9871 253044.1426 264548.7843 266814.0896 66602.69301 2.711457617 3.586796959 2.524919512 2.265373073 4.039446078 3.799307973 3.972043357 4.006055575 1 16.02329289 3.237615186 24.99999357 3.511153499 2.812668478 0.075302388 0.949691024 58.25524023 1540454.377 0.278984661 0.334939831 1728.284303 -3.237615186 -0.698485022 KTVSLTPSPTTQVETPDLVDHDNT(ph)SPLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTVSLTPSPTTQVETPDLVDHDNTSPLFR 29 1 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 KTVSLTPSPTTQVETPDLVDHDNT(0.5)S(0.5)PLFR 113.97 0.00018126 1396200000 215750 276130 113880 135980 243400 238410 265790 322420 75377 TRUE FALSE 187238.0909 274316.0838 168952.7489 166856.3373 238556.8162 247581.787 240013.7267 253472.9921 66466.01693 2.817049968 4.12716297 2.541941833 2.510400729 3.589154687 3.724937922 3.611074317 3.813572767 1 16.02032928 5.048276593 17.38173046 3.206350963 0.1296085 0.001540946 0.918311009 202087209.8 1643409889 0.215861776 21245846251 111757.4781 -5.048276593 -3.076742463 KTVSLTPSPTTQVETPDLVDHDNTS(ph)PLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTVSLTPSPTTQVETPDLVDHDNTSPLFR 29 1 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 KTVSLTPSPTTQVETPDLVDHDNT(0.112)S(0.888)PLFR 328.87 2.09E-105 1492300000 578590 717400 273070 307970 681280 578810 723080 917370 138900 TRUE FALSE 502127.8655 712687.3522 405127.5654 377899.2955 667723.8609 601077.1952 652955.8129 721197.5645 122479.4002 4.099692394 5.818834439 3.30772003 3.085411055 5.451723797 4.907577879 5.331148027 5.888317244 1 16.9021796 5.03767204 16.61437018 4.522372348 2.315636139 0 1.533339132 291691426.6 3442255428 0.363925454 19379741301 109061.644 -5.03767204 -2.206736209 KTVT(ph)PAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KTVTPAK 7 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 KT(0.017)VT(0.983)PAK 76.228 0.024218 393070000 1590400 1283400 859470 1127100 654270 850060 1544000 1813000 1594600 TRUE FALSE 1380224.61 1274969.261 1275112.567 1383025.282 641251.3071 882762.3583 1394263.118 1425304.059 1406088.205 0.981605995 0.906749133 0.906851051 0.983597812 0.4560534 0.627814354 0.991590082 1.01366618 1 20.42325567 2.046127889 23.63903735 1.006255014 0.810860854 0.236430039 0.162237494 108.1684947 55432.01998 0.071967098 0.048520161 111.2059152 -2.046127889 -0.19539416 KTWTVVDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KTWTVVDAK 9 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 135.99 0.00032937 742400000 2515800 2073650 1664940 1754850 2126510 1650490 2413480 2932430 2458800 FALSE TRUE 2183330.656 2060028.057 2470110.553 2153315.514 2084196.611 1713985.418 2179421.081 2305352.665 2168123.465 1.007013987 0.950143334 1.139285005 0.993170153 0.961290556 0.79053866 1.005210781 1.063293997 1 21.04801548 5.114416431 17.91246992 0.991655597 2.729233771 0.002993955 0.088365085 2928.199423 464607.5607 0.021947364 2805.184269 130141.6867 -5.114416431 1.737578174 KTYVTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KTYVTPR 7 1 P46781;B5MCT8;C9JM19;F2Z3C0;A8MXK4 P46781 RPS9 40S ribosomal protein S9 0 ; 110.87 0.010753 3696300000 3435500 3537700 2025630 2310600 3019100 2877600 3502900 4051500 3194200 FALSE TRUE 2981489.971 3514460.616 3005231.443 2835257.045 2959025.817 2988303.134 3163189.297 3185118.254 2816585.315 1.058547723 1.247773535 1.066976891 1.006629208 1.050572053 1.060966667 1.123058222 1.130843876 1 21.42551574 KVACIGAWHPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVACIGAWHPAR 12 1 P39023;H7C422;G5E9G0;B5MCW2;Q92901 P39023;Q92901 RPL3;RPL3L 60S ribosomal protein L3;60S ribosomal protein L3-like 0 ; 120.96 0.00024977 2418100000 3542300 4205900 1826990 1829670 3506200 3590500 3828300 4218900 1083800 FALSE TRUE 3074176.08 4178271.166 2710528.475 2245124.538 3436433.48 3728628.858 3457032.055 3316721.067 955674.3987 3.216760943 4.372065603 2.836246821 2.349256757 3.59582038 3.901568216 3.617374348 3.470555527 1 19.86615965 4.220954086 24.96038793 3.080770037 3.794413701 0.122606893 0.880071744 493.4223482 699516.0181 0.225203417 0.470472578 16632.36804 -4.220954086 0.713643664 KVAECQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KVAECQR 7 1 Q16543;K7EKQ2;K7EQA9 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;;; 131.06 0.0056162 961370000 670326 769236 473640 546026 520198 675088 749599 833286 778162 FALSE TRUE 581740.7207 764182.8381 702693.8882 670009.5488 509847.0776 701059.0722 676903.0044 655094.2735 686168.5748 0.847810206 1.113695477 1.02408346 0.976450355 0.743034724 1.021700932 0.986496656 0.954713313 1 19.38820353 3.474442436 24.99972484 0.942070527 1.005916417 0.05677675 0.09910126 219.9842688 2052953.333 0.027940639 0.036280886 2981.552326 -3.474442436 0.06384589 KVAGAAT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVAGAATPK 9 1 P16402 P16402 HIST1H1D Histone H1.3 1 KVAGAAT(1)PK;KVAGAAT(1)PK 85.42 0.0086887 995820000 1670320 1875200 1502210 1511340 1411720 1463480 2317880 2490200 2542700 TRUE FALSE 1449582.98 1862881.688 2228683.781 1854512.846 1383629.534 1519781.023 2093092.354 1957690.109 2242104.903 0.646527724 0.830862858 0.994014053 0.827130276 0.617111863 0.677836715 0.933538994 0.873148311 1 21.09642235 2.21507843 24.70580593 0.922475282 0.774980427 0.333811837 0.112172152 293.1489561 308421.7618 0.049638567 0.033489449 164.0886077 -2.21507843 -0.147494855 KVCGDSDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KVCGDSDK 8 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;; 94.309 0.016757 462950000 1016650 773220 623150 682980 544200 577340 1047820 1183240 1017000 FALSE TRUE 882297.1266 768140.6669 924507.4243 838061.0477 533371.4847 599550.6434 946202.5777 930213.334 896771.4186 0.983859553 0.856562387 1.030928735 0.934531398 0.594768604 0.668565736 1.055121247 1.03729146 1 19.77438077 2.196574569 24.99982771 1.033169235 0.846565216 0.305157016 0.13222967 194.5742882 115854.3652 0.0590537 0.039814367 157.2441761 -2.196574569 -0.186604019 KVCGEEGVR ddPTM_MDA-MB-175_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 70.977 0.08159 47764000 70394 69964 46423 53054 66199 69113 76475 82573 51246 FALSE TRUE 61091.25454 69504.40188 68873.31808 65100.72158 64881.76942 71771.82183 69058.46627 64915.40653 45187.75626 1.351942641 1.538124652 1.524158838 1.440671699 1.435826312 1.588302403 1.528256147 1.436570698 1 15.4636443 1.235044372 3.850392857 0.938962054 1.489798134 0.841307029 0.065911199 0.095933176 2.345547605 0.151979317 0.016369844 17.18083915 -1.235044372 0.55083608 KVDAETVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVDAETVGR 9 1 P11172-2;P11172-3;P11172;P11172-4;E9PFD2 P11172-2 UMPS Uridine 5-monophosphate synthase;Orotate phosphoribosyltransferase;Orotidine 5-phosphate decarboxylase 0 ; 139.86 0.0023604 169930000 751510 702480 470300 544100 636160 713550 699580 810920 748960 FALSE TRUE 652196.0494 697865.3626 697738.6531 667646.221 623501.6606 741000.7302 631734.8393 637511.0686 660418.802 0.987549185 1.056701233 1.056509371 1.010943691 0.944100408 1.122016405 0.956567011 0.965313323 1 19.33302167 KVDEGAGDSAAVASGGAQTLALAGS(ph)PAPSGHPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KVDEGAGDSAAVASGGAQTLALAGSPAPSGHPK 33 1 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 1 KVDEGAGDSAAVASGGAQTLALAGS(0.997)PAPS(0.003)GHPK;KVDEGAGDSAAVASGGAQTLALAGS(1)PAPSGHPK;KVDEGAGDSAAVASGGAQTLALAGS(0.999)PAPS(0.001)GHPK 358.41 1.81E-132 1931390000 1361764 1029469 755275 977999 937151 796147 1384692 1558491 1498078 TRUE FALSE 1181803.437 1022706.35 1120528.516 1200068.621 918503.5286 826775.2903 1250404.783 1225219.828 1320976.925 0.894643513 0.774204553 0.848257448 0.90847054 0.695321403 0.625881705 0.946575795 0.927510393 1 20.33317384 2.057657067 24.99730113 0.952118272 0.793293344 0.45189887 0.086568177 75.76105339 32845.81141 0.036875163 0.024861226 114.1976237 -2.057657067 -0.158824928 KVDIEVLSVLASLGASVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVDIEVLSVLASLGASVHK 19 1 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A1B0GTG9;A0A1B0GWF8;P30566-2;A0A096LNY5;A0A096LNY6;A0A096LP92;A0A096LPA2 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 0 150.98 4.55E-08 11550000 47071 47455 14438 37196 44027 37402 57486 67820 60182 FALSE TRUE 40850.44809 47143.26498 21420.26509 45641.92031 43150.94884 38840.87914 51911.01657 53317.22078 53067.35252 0.769784927 0.888366627 0.403642995 0.860075322 0.813135512 0.731916655 0.978210031 1.004708512 1 15.69553696 2.217816533 6.214684082 0.997870909 0.743506911 0.444558457 0.131681564 0.148738581 19.54767179 0.052420902 0.036375652 165.1264076 -2.217816533 -0.254363998 KVDNDYNALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVDNDYNALR 10 1 O94763-3;O94763;O94763-4 O94763-3 URI1 Unconventional prefoldin RPB5 interactor 1 0 130.1 0.00045799 179510000 243280 233360 148240 174340 226410 196250 216920 268010 235410 FALSE TRUE 211129.9316 231827.0428 219929.3598 213926.5616 221904.884 203799.8645 195883.1318 210698.1472 207580.098 1.017101031 1.116807657 1.05949155 1.030573565 1.069008475 0.981789037 0.94365083 1.015020945 1 17.6633086 2.736414166 24.89602221 0.985900687 1.060323313 0.574650723 0.031391002 131.2347234 1522142.514 0.010422625 0.009663592 545.0221674 -2.736414166 0.074422626 KVDNELNPVWNEILEFDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVDNELNPVWNEILEFDLR 19 1 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-5;Q9NZM1-8;Q9NZM1-7;Q9NZM1-4 Q9NZM1-6 MYOF Myoferlin 0 145.75 1.96E-07 262530000 180230 147170 102910 138010 156640 155690 177720 223990 185340 FALSE TRUE 156412.1489 146203.2306 152677.6202 169347.2799 153523.1705 161679.495 160484.7418 176091.4816 163429.3163 0.957062982 0.89459611 0.934211949 1.03621115 0.939385747 0.9892931 0.98198258 1.077477931 1 17.31830728 2.735441895 0.368339697 1.069800665 0.905555607 0.402847422 0.040488722 1.807272421 0.886601048 0.188245167 0.132777924 543.8033702 -2.735441895 -0.164245058 KVDQPPEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVDQPPEAK 9 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 68.536 0.092667 147010000 384290 275900 252420 267060 256690 259450 366390 456790 428790 FALSE TRUE 333505.1028 274087.5947 374491.1563 327700.0548 251582.3712 269431.2094 330857.5542 359109.0132 378098.9347 0.882057769 0.724909725 0.99045811 0.866704518 0.665387675 0.712594468 0.875055505 0.949775258 1 18.52840426 1.783682537 2.727211602 0.984686191 0.807796831 0.344596103 0.094525298 0.296638117 4.268221157 0.07484778 0.027394517 60.76906263 -1.783682537 -0.17688936 KVDSSVLGSLSSVPLTGFSFS(ph)PGNSSLFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVDSSVLGSLSSVPLTGFSFSPGNSSLFGK 30 1 Q9UKX7-2;Q9UKX7 Q9UKX7-2 NUP50 Nuclear pore complex protein Nup50 1 KVDSSVLGSLSSVPLTGFSFS(0.999)PGNSSLFGK;KVDSSVLGSLSSVPLTGFS(0.003)FS(0.997)PGNSSLFGK 209.11 5.02E-26 1019530000 915110 798680 520950 610940 664300 565290 897710 1088370 779480 TRUE FALSE 794175.8949 793433.4185 772883.1625 749663.2646 651081.7297 587037.0721 810650.2224 855630.5452 687330.7624 1.155449368 1.154369136 1.124470495 1.090687782 0.947261152 0.854082349 1.179417926 1.24485996 1 19.390645 3.811220998 3.022956542 1.067460839 1.15137412 0.130541288 0.110035992 0.766917342 13.72399827 0.035839102 0.067080109 6474.720088 -3.811220998 0.083913281 KVDTT(ph)PNQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVDTTPNQGK 10 1 Q9P2E9;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KVDT(0.074)T(0.926)PNQGK;KVDT(0.113)T(0.887)PNQGK 159.52 4.49E-06 955880000 2338300 1932070 1440990 2003620 1727300 1455510 2109330 3242500 2700000 TRUE FALSE 2029287.731 1919378.105 2137857.584 2458572.544 1692930.109 1511504.412 1904767.501 2549116.608 2380809.076 0.852352148 0.806187327 0.897954231 1.032662623 0.711073444 0.634870064 0.800050504 1.070693418 1 21.1830205 1.745278058 8.120545959 1.031990985 0.818715417 0.415653225 0.106342147 0.117161032 28.33148712 0.064988189 0.029740975 55.62602905 -1.745278058 -0.213275569 KVDVDEYDENKFVDEEDGGDGQAGPDEGEVDSCLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVDVDEYDENKFVDEEDGGDGQAGPDEGEVDSCLR 35 2 B1ALC0;O15511;O15511-2 B1ALC0 ARPC5 Actin-related protein 2/3 complex subunit 5 0 60.876 0.012596 182450000 23334 17885 15867 19472 19154 15814 21534 27590 24143 FALSE TRUE 20250.35278 17767.51226 23540.33427 23893.41521 18772.87287 16422.37481 19445.63599 21690.09321 21288.84204 0.951219082 0.834592705 1.105759262 1.12234452 0.881817472 0.771407612 0.91341915 1.018847956 1 14.37780986 KVEAPETNIDKT(ph)PK ddPTM_MDA-MB-175_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 124.26 0.004675 382710000 1129430 847340 880810 742580 738420 469750 1156820 1416820 1146160 TRUE FALSE 980172.9639 841773.7677 1306772.662 911194.1386 723726.8867 487821.5865 1044631.774 1113844.069 1010662.271 0.969832349 0.832893235 1.29298649 0.901581236 0.716091723 0.482675173 1.033611133 1.102093252 1 19.94686955 2.03106398 24.99971593 1.061193824 0.86866751 0.147740402 0.202849407 374.5725332 301447.5913 0.088675844 0.059784596 107.4147644 -2.03106398 -0.192526314 KVEAQLQELQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVEAQLQELQVK 12 1 P35579 P35579 MYH9 Myosin-9 0 117.79 0.0011156 535950000 700400 629020 483660 506050 534040 482450 710840 757530 1050200 FALSE TRUE 607840.3654 624887.9262 717559.5937 620956.387 523413.6488 501010.1637 641902.8462 595538.1046 926046.5524 0.656382083 0.674791051 0.774863415 0.670545542 0.565213107 0.541020494 0.693164771 0.643097372 1 19.82072519 1.237594328 24.99912419 1.000000408 0.652751865 0.740705276 0.064635819 13.404006 346594.6616 0.100431151 0.016975132 17.28201302 -1.237594328 -0.347248544 KVEDLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVEDLAR 7 1 Q9NVP1;H7C452 Q9NVP1 DDX18 ATP-dependent RNA helicase DDX18 0 89.698 0.028352 327700000 481490 427270 303300 382850 401730 412050 432950 506740 489010 FALSE TRUE 417859.8766 424463.2352 449976.8945 469781.944 393736.359 427901.8301 390962.5756 398377.5945 431199.7949 0.969063254 0.984377173 1.04354617 1.08947627 0.91311815 0.992351655 0.90668544 0.923881688 1 18.71799697 3.219442362 24.99981528 0.943509739 1.020522311 0.411641289 0.044071774 237.2820248 310278.716 0.013616064 0.0154635 1657.457351 -3.219442362 0.077012572 KVEDLFLTFAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVEDLFLTFAK 11 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 101.32 0.004148 0 1057000 1025100 698340 791350 999670 994010 1051100 1215100 1111700 FALSE TRUE 917314.7719 1018366.051 1036059.56 971038.1125 979778.5228 1032250.208 949164.4838 955260.3209 980276.0925 0.935771849 1.038856357 1.056905874 0.990576145 0.999492419 1.053019875 0.968262402 0.974480892 1 19.90282861 2.200025531 24.9998669 0.979046922 1.014077284 0.146340342 0.035649174 278.3391593 180571.9626 0.014174581 0.009556656 158.4986366 -2.200025531 0.035030361 KVEDMMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KVEDMMK 7 1 P13639 P13639 EEF2 Elongation factor 2 0 ;; 93.551 0.023814 2528020000 5837630 5552310 4268990 4660180 5020010 3872550 6321470 7340630 6938980 FALSE TRUE 5066172.405 5515836.51 6333487.843 5718345.095 4920121.622 4021529.504 5708414.812 5770893.399 6118661.689 0.827987011 0.901477609 1.03510999 0.934574485 0.804117285 0.657256392 0.932951535 0.943162687 1 22.5447847 2.017007865 24.99752316 0.958682321 0.864460668 0.189990428 0.09733143 463.8575023 681757.9602 0.043790276 0.029516169 103.9938998 -2.017007865 -0.094221653 KVEEAEPEEFVVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KVEEAEPEEFVVEK 14 1 Q13185;S4R2Y4;C9JMM0;B8ZZ43 Q13185 CBX3 Chromobox protein homolog 3 0 ;;;;; 197.88 3.66E-08 4430910000 8581380 5920550 4900090 5731670 5227150 3911570 7241550 8939050 7881870 FALSE TRUE 7447328.891 5881657.517 7269789.914 7033133.277 5123139.942 4062050.629 6539265.596 7027503.721 6950084.308 1.071545115 0.846271391 1.046000249 1.011949347 0.737133496 0.584460627 0.940890111 1.011139349 1 22.72859905 7.999968122 0.808962426 0.891372223 42.58780682 0.114409914 0.145043079 1541.149701 5.143028356 0.056099701 117860.3414 99992660.17 -7.999968122 41.6964346 KVEEAFNCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVEEAFNCR 9 1 P52888;K7EP46 P52888 THOP1 Thimet oligopeptidase 0 ; 121.9 0.00096357 354640000 305310 269630 197056 222070 258480 246130 272910 301080 326490 FALSE TRUE 264962.5099 267858.7828 292352.9407 272494.3876 253336.7537 255598.7804 246443.2302 236696.385 287892.7241 0.920351533 0.930411783 1.015492634 0.946513631 0.879969282 0.887826468 0.856024517 0.822168694 1 18.1351718 3.262113949 4.946454559 0.877904443 0.957052402 0.260754431 0.051732031 0.216484229 13.42900673 0.015397049 0.019255602 1828.57993 -3.262113949 0.079147959 KVEEDLKADEPSS(ph)EES(ph)DLEIDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVEEDLKADEPSSEESDLEIDK 22 2 P50502;Q3KNR6;F6VDH7 P50502 ST13 Hsc70-interacting protein 2 KVEEDLKADEPS(0.002)S(0.998)EES(1)DLEIDK;KVEEDLKADEPS(0.023)S(0.977)EES(1)DLEIDK 191.22 8.06E-18 265380000 684280 333140 585750 488410 321600 241830 524600 661240 1179620 TRUE FALSE 593850.6643 330951.5814 869020.6592 599310.9554 315200.7892 251133.3566 473724.3727 519838.9718 1040166.667 0.57091876 0.318171685 0.835462899 0.576168199 0.303029119 0.24143569 0.455431218 0.499765074 1 19.98838328 1.236121792 4.886197993 1.037366511 0.469276363 0.487243702 0.169460141 0.167272194 9.71905899 0.326361553 0.044043607 17.22351516 -1.236121792 -0.568090148 KVEEEGS(ph)PGDPDHEASTQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KVEEEGSPGDPDHEASTQGR 20 1 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 1 KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(1)PGDPDHEASTQGR 181.64 3.05E-17 4005950000 4722650 4097591 2796044 3315645 4103935 3436265 4654625 5157410 4455191 TRUE FALSE 4098539.837 4070673.655 4148220.231 4068512.874 4022274.723 3568460.338 4203220.184 4054538.007 3928503.395 1.043282753 1.03618942 1.05592889 1.035639393 1.023869479 0.908351089 1.069929121 1.032082093 1 21.90554838 3.183582827 4.242791049 1.009121386 1.043570611 0.167372634 0.040566556 0.454529963 16.73201503 0.012826451 0.015109042 1526.099419 -3.183582827 0.034449224 KVEEEQEADEEDVS(ph)EEEAESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KVEEEQEADEEDVSEEEAESK 21 1 Q9H3N1 Q9H3N1 TMX1 Thioredoxin-related transmembrane protein 1 1 KVEEEQEADEEDVS(1)EEEAESK;KVEEEQEADEEDVS(1)EEEAESK;KVEEEQEADEEDVS(1)EEEAESK 278.08 4.43E-45 1572170000 1665310 1249270 1253070 1531790 1432170 1340370 1389150 2405660 1988790 TRUE FALSE 1445235.064 1241063.463 1859058.843 1879606.331 1403672.619 1391934.901 1254430.447 1891228.33 1753677.512 0.82411678 0.707691953 1.060091625 1.071808425 0.800416616 0.793723414 0.715314212 1.07843564 1 20.74195204 1.663612727 9.416205144 1.03795455 0.86011102 0.272828739 0.125452013 0.159568412 22.11579013 0.075444926 0.034355211 46.09063874 -1.663612727 -0.17784353 KVEELEGEITTLNHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVEELEGEITTLNHK 15 1 Q10589-2;Q10589 Q10589-2 BST2 Bone marrow stromal antigen 2 0 ; 187.89 2.09E-07 310080000 518530 481800 335020 444890 446970 397570 532220 788170 624490 FALSE TRUE 450004.9467 478635.0241 497036.7926 545909.0742 438076.1715 412864.7752 480605.3863 619625.979 550663.5036 0.81720496 0.869196925 0.902614372 0.991365999 0.795542411 0.749758741 0.872775085 1.125235239 1 19.07081147 1.760058576 16.09579881 1.062671997 0.857837892 0.592609575 0.070900176 0.476767778 361.1634725 0.039476238 0.018888159 57.55175554 -1.760058576 -0.204834105 KVEELQACVETAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVEELQACVETAR 13 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 150.05 7.06E-05 921490000 776820 742140 441760 598310 746470 683700 758140 933300 743340 FALSE TRUE 674161.2688 737264.8335 655396.6136 734165.4301 731616.7074 710002.3814 684615.6995 733721.0579 655463.192 1.028526509 1.124799748 0.999898425 1.120071179 1.116182749 1.083207097 1.044476193 1.119393227 1 19.32215524 4.806338544 21.29149661 1.078395072 1.028522985 0.087256391 0.047703024 49892.28605 15668235.02 0.010730196 35.41379416 64023.37201 -4.806338544 -0.049872087 KVEEVLEEEEEEYVVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVEEVLEEEEEEYVVEK 17 1 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 0 ; 186.05 8.74E-10 201776000 666700 521040 408160 490920 448860 351430 654830 816830 799170 FALSE TRUE 578593.9058 517617.2539 605547.5412 602390.8892 439928.5642 364949.7395 591324.6874 642157.2611 704693.033 0.821058076 0.734528695 0.859306837 0.854827366 0.62428397 0.517884699 0.839123788 0.911258138 1 19.42663543 1.757740894 2.789214838 0.971528708 0.739380401 0.41345869 0.106937161 0.255154108 3.995806476 0.088871495 0.031755952 57.24543949 -1.757740894 -0.232148307 KVEEVVYDLSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVEEVVYDLSIR 12 1 E9PGT1;Q15631 E9PGT1 TSN Translin 0 ; 211.06 5.82E-08 359790000 1970290 1723200 1208570 1449050 1654110 1420310 1905700 2204370 1892800 FALSE TRUE 1709911.184 1711880.186 1793038.494 1778078.95 1621196.447 1474950.245 1720885.507 1732982.63 1669035.34 1.0244907 1.025670424 1.074296302 1.065333314 0.9713374 0.883714209 1.031065949 1.038313922 1 20.67058307 3.239226761 24.99999784 0.989969617 1.047809929 0.324855025 0.044480465 26.48352385 993887.2015 0.014710252 0.01788023 1734.709518 -3.239226761 0.057840312 KVEGAPTQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVEGAPTQGR 10 1 Q9P2E9;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 122.33 0.00078811 231720000 287610 247512 161770 229380 239570 206929 238527 300760 249806 FALSE TRUE 249601.6098 245886.0774 240002.5131 281464.2349 234803.0257 214889.6925 215394.6883 236444.8145 220274.2193 1.133140368 1.116272609 1.089562428 1.277790183 1.065957816 0.975555348 0.977847925 1.073411202 1 17.74894113 3.008732615 24.99996255 1.01512535 1.149992505 0.607615793 0.055763862 140.9645887 403553.7932 0.016850225 0.019078189 1020.31111 -3.008732615 0.134867155 KVEGAQNQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVEGAQNQGK 10 1 Q9P2E9 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 121.02 0.00084352 256970000 315180 268720 214720 278970 182303 232158 335280 434600 355510 FALSE TRUE 273528.1644 266954.7606 318559.3102 342314.4023 178675.527 241089.2685 302764.5972 341664.1721 313482.0128 0.872548195 0.851579197 1.016196455 1.091974622 0.569970587 0.769068906 0.965811705 1.089900403 1 18.25802314 2.013066294 7.314306794 1.044811658 0.86546944 0.233125133 0.139418078 0.210155399 61.11051538 0.062799438 0.040584307 103.0543418 -2.013066294 -0.179342217 KVELS(ph)ES(ph)EEDKGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 90.968 0.0112 829720000 2659340 1650700 1615490 1313200 1478610 1183410 2332770 2608320 2234600 TRUE FALSE 2307901.481 1639856.443 2396746.367 1611382.131 1449188.554 1228936.548 2106538.324 2050551.066 1970428.134 1.171269046 0.832233571 1.216358174 0.817782747 0.73546887 0.623690115 1.069076455 1.040662702 1 20.9100777 3.714995523 24.95604148 0.892686381 1.049181652 0.217125663 0.169027735 1503.600969 1592352.279 0.050165811 0.074453818 5187.946904 -3.714995523 0.156495272 KVELS(ph)ESEEDKGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KVELSESEEDKGGK 14 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KVELS(0.986)ES(0.014)EEDKGGK;KVELS(0.999)ES(0.001)EEDKGGK;KVELS(0.885)ES(0.115)EEDKGGK;KVELS(0.616)ES(0.384)EEDKGGK;KVELS(0.983)ES(0.017)EEDKGGK 139.9 5.27E-06 2025940000 3848140 2210380 2446870 1972480 1986040 1424300 3346110 3710810 3099230 TRUE FALSE 3339598.549 2195859.868 3630184.516 2420361.731 1946521.69 1479093.743 3021604.767 2917282.159 2732842.56 1.222023763 0.803507637 1.328354794 0.885657215 0.71226997 0.541229035 1.105663682 1.06749002 1 21.38197092 4.759605793 22.22026937 0.941476536 1.222025059 0.14755217 0.218789997 2367.230433 2499222.407 0.055846215 1.935053429 57491.78508 -4.759605793 0.280548522 KVELSES(ph)EEDKGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVELSESEEDKGGK 14 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KVELS(0.173)ES(0.827)EEDKGGK 188.96 4.03E-07 1422800000 2449200 1356600 1574500 1247000 1146600 748250 2088900 2185400 1825000 TRUE FALSE 2125532.015 1347688.405 2335933.466 1530150.409 1123784.903 777035.6617 1886318.8 1718069.217 1609250.579 1.320821034 0.837463365 1.451566025 0.95084658 0.698328102 0.482855605 1.172172205 1.067620692 1 20.61795756 3.503635037 24.44081456 0.901012264 1.172452332 0.259701286 0.244757442 921.816479 849742.1109 0.070342875 0.103925629 3188.856946 -3.503635037 0.271440068 KVELSSSSQHGPSYDVYNPFYMYQHIS(ph)PDLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KVELSSSSQHGPSYDVYNPFYMYQHISPDLSR 32 1 Q8N9U0;Q8N9U0-2 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 KVELSSSSQHGPSYDVYNPFYMYQHIS(1)PDLSR;KVELSSSSQHGPSYDVYNPFYMYQHIS(0.988)PDLS(0.012)R;KVELSSSSQHGPSYDVYNPFYMYQHIS(1)PDLSR 301.02 4.39E-90 1691850000 684708 750725 157928 535102 1036347 925325 620314 1147146 833317 TRUE FALSE 594222.103 745793.438 234302.509 656605.0876 1015725.722 960922.8515 560156.0438 901837.755 734803.2136 0.80868196 1.014956691 0.318864296 0.893579499 1.382309853 1.307728156 0.762321168 1.227318741 1 19.48699841 3.471628685 24.60698304 1.128837786 0.721242441 0.398335915 0.238677807 119.9528296 537390.643 0.067505476 0.087444142 2962.297588 -3.471628685 -0.407595345 KVENEDMNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVENEDMNK 9 1 Q15019-2;Q15019-3;Q15019;B5MCX3 Q15019-2 2-Sep Septin-2 0 76.332 0.057293 108700000 142470 109760 91920 102470 101960 97423 126730 139860 255080 FALSE TRUE 123642.2285 109038.9793 136372.8195 125737.3797 99931.19548 101170.9259 114439.7441 109952.0274 224924.733 0.549704903 0.484779855 0.606304241 0.559019802 0.44428727 0.449799026 0.508791286 0.488839204 1 17.77908278 1.237070266 24.99916216 1.0000006 0.50985037 0.904940442 0.049760752 11.33862376 190127.7176 0.078272082 0.012768883 17.26117145 -1.237070266 -0.49015023 KVEQCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVEQCR 6 1 Q9Y3L3;Q6ZT62-2;Q6ZT62;Q9Y3L3-2;O14490-3;O14490-7 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 0 83.843 0.090636 37875000 38785 39861 30273 38905 22466 37214 42560 52597 66862 FALSE TRUE 33659.46398 39599.15047 44913.12406 47738.97488 22018.97055 38645.64666 38432.53775 41349.54086 58957.65053 0.570909181 0.671654147 0.761786192 0.809716372 0.373470964 0.655481457 0.651866847 0.701343091 1 15.84739141 1.182757049 2.535845025 1.123631705 0.644771481 0.480489503 0.115984225 0.591323593 3.689734974 0.659841582 0.030838466 15.23200412 -1.182757049 -0.478860223 KVEQNSRPVS(ph)CSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KVEQNSRPVSCSGR 14 2 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 1 KVEQNSRPVS(0.992)CS(0.008)GR;KVEQNSRPVS(0.999)CS(0.001)GR;KVEQNS(0.001)RPVS(0.973)CS(0.026)GR;KVEQNSRPVS(0.997)CS(0.003)GR;KVEQNSRPVS(0.999)CS(0.001)GR;KVEQNSRPVS(0.999)CS(0.001)GR;KVEQNS(0.001)RPVS(0.993)CS(0.006)GR 202.96 8.19E-09 6489530000 1305796 1779739 1217239 1263578 1884302 1914859 1887464 2299220 1733160 TRUE FALSE 1133231.75 1768047.777 1805899.852 1550492.697 1846808.077 1988524.865 1704418.032 1807549.696 1528267.799 0.741513857 1.156896572 1.181664531 1.014542542 1.208432238 1.301162575 1.115261365 1.182744082 1 20.54346594 4.739103348 24.82100986 1.150552065 0.741513722 0.672185452 0.088498684 23.82872666 1089464.76 0.021049486 0.121279819 54840.74528 -4.739103348 -0.409038343 KVEQNSRPVSCSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KVEQNSRPVSCSGR 14 2 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 0 ;; 107.82 0.00048439 246863000 148941 150661 95520 100365 127137 119328 144553 176597 105992 FALSE TRUE 129258.0695 149671.298 141713.7915 123154.4072 124607.2224 123918.6254 130534.2723 138833.1058 93461.74651 1.383005072 1.60141773 1.516275875 1.317698543 1.333243034 1.325875345 1.396659887 1.485453793 1 16.51208838 3.740941509 24.1089517 1.335188934 1.510351394 0.294593937 0.134846224 171.7177471 1738797.105 0.035417594 0.057774451 5507.335184 -3.740941509 0.17516246 KVESLWPIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVESLWPIFR 10 1 P41223;P41223-2 P41223 BUD31 Protein BUD31 homolog 0 ; 143.17 5.52E-05 635590000 1541770 1412860 971990 1143890 1301450 1201980 1410580 1665530 1528460 FALSE TRUE 1338021.188 1403578.83 1442047.615 1403627.708 1275553.691 1248220.948 1273782.169 1309369.371 1347767.2 0.992768772 1.041410438 1.069953042 1.041446704 0.946419894 0.926139877 0.945105482 0.971510043 1 20.36213989 3.24207853 24.99777668 0.95700495 1.03915004 0.682114726 0.026615991 53.31060946 378814.5744 0.008240825 0.01022072 1746.137866 -3.24207853 0.08214509 KVEWTSDTVDNEHMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVEWTSDTVDNEHMGR 16 1 O60927 O60927 PPP1R11 Protein phosphatase 1 regulatory subunit 11 0 ; 205.31 1.49E-11 355410000 657500 527810 667450 466520 483740 438530 549200 661100 457510 FALSE TRUE 570609.7091 524342.7814 990231.0525 572450.4963 474114.5204 455400.5329 495938.6685 519728.9097 403423.689 1.414417955 1.299732256 2.454568434 1.418980868 1.175227269 1.128839345 1.229324608 1.288295467 1 18.62193628 3.482562843 23.85041257 1.193310439 1.723286399 0.403373143 0.309433688 133.1028531 583389.9818 0.087355944 0.116527719 3037.825636 -3.482562843 0.529975961 KVFAENK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVFAENK 7 1 O95994;B5MC07;C9J3E2;H7C3Z9 O95994 AGR2 Anterior gradient protein 2 homolog 0 ; 109.21 0.01135 7511900000 6959000 7592200 5388300 6329800 6370600 6020300 7798300 8234500 6709400 FALSE TRUE 6039350.518 7542326.338 7994099.903 7767077.835 6243837.524 6251904.837 7042022.066 6473616.256 5916222.375 1.020811953 1.274855112 1.351216941 1.312844133 1.055375733 1.056739325 1.190290293 1.094214491 1 22.49624485 3.232169944 24.99991654 1.088378511 1.250375467 0.391739475 0.098708933 159.876494 625425.9972 0.030138171 0.035010883 1706.750126 -3.232169944 0.161996956 KVFASLPQVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVFASLPQVER 11 1 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 ; 104.59 0.0041355 1249570000 1829580 1600440 1055660 1108540 1540780 1505510 1586640 1779140 1340680 FALSE TRUE 1587796.367 1589926.604 1566180.707 1360250.95 1510121.492 1563427.944 1432767.897 1398684.756 1182186.338 1.343101605 1.344903552 1.324817127 1.150623135 1.277397179 1.322488591 1.21196452 1.18313392 1 20.17302602 0.312394264 0.792734935 1.61E-15 1.295769734 0.721135062 0.057482313 5.62302564 0.909707506 9.097679158 0.023356277 2.053025123 -0.312394264 1.295769734 KVFS(ph)PVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVFSPVIR 8 1 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 KVFS(1)PVIR 125.97 0.0012725 0 188300 181520 113640 137700 188020 160670 172470 204800 194770 TRUE FALSE 163415.6779 180327.5832 168596.6841 168966.8896 184278.7699 166851.0789 155743.8859 161005.1138 171744.5125 0.951504508 1.049975807 0.981671447 0.983827007 1.072981996 0.971507482 0.906834715 0.937468752 1 17.38990448 2.482164322 24.95329557 0.943452981 1.008992303 0.312414411 0.040869943 228.713758 1131694.995 0.014289304 0.011371187 303.5039321 -2.482164322 0.065539322 KVFVGR ddPTM_MDA-MB-175_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 ; 154.38 0.016054 5036500000 7273500 6629400 3837100 4437500 5659000 6221300 6384100 7354100 5665400 FALSE TRUE 6312288.546 6585851.035 5692734.394 5445102.198 5546396.972 6460637.437 5764970.965 5781482.945 4995642.866 1.263558808 1.318319025 1.139539904 1.089970269 1.110246893 1.293254464 1.153999819 1.157305096 1 22.25223891 KVGDDIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KVGDDIAK 8 1 P30050 P30050 RPL12 60S ribosomal protein L12 0 ;;;; 111.61 0.0051325 5090400000 11675000 8903000 6879330 8331350 7455620 6367450 12111100 13617000 11885100 FALSE TRUE 10132119.17 8844515.607 10206197 10223110.35 7307267.749 6612409.922 10936567.39 10705110.52 10480057.02 0.966800004 0.843937737 0.973868461 0.975482322 0.697254579 0.630951712 1.043559913 1.021474454 1 23.32114323 KVGLIAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVGLIAAR 8 1 P62917;E9PKU4;E9PP36 P62917 RPL8 60S ribosomal protein L8 0 ; 141.39 0.0010171 3609600000 3363500 5291900 2949800 3203400 5245900 4882200 5444300 5384300 4682300 FALSE TRUE 2919004.953 5257137.16 4376333.146 3930780.931 5141516.853 5070021.393 4916312.624 4232909.346 4128763.828 0.706992474 1.273295683 1.059962092 0.9520479 1.24529207 1.227975637 1.190746875 1.025224382 1 21.97727847 4.752755096 24.46046156 1.1174404 0.706992094 0.578835536 0.111147198 1452.591315 2503102.053 0.027833868 0.564273216 56592.00697 -4.752755096 -0.410448305 KVGTLWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 103.56 0.013385 948730000 472930 423000 260660 331150 419570 392360 366890 414600 424490 FALSE TRUE 410431.1022 420221.2851 386716.0479 406342.6688 411221.3779 407454.3431 331309.0643 325941.0164 374307.2758 1.096508481 1.122663951 1.033151298 1.085585814 1.098619782 1.088555765 0.8851259 0.870784613 1 18.51386357 2.24256848 24.9999795 0.907271319 1.087058029 0.792625396 0.040581096 39.19768259 244506.8347 0.015428422 0.011501215 174.8108883 -2.24256848 0.179786709 KVGYTPDWIFLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVGYTPDWIFLLR 13 1 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ; 176.89 2.55E-05 2202850000 2391600 2413600 919260 1018460 1879880 1815830 2479600 2510500 363860 FALSE TRUE 2075544 2397744.903 1363817.211 1249716.909 1842474.066 1885686.155 2239128.774 1973649.112 320844.8853 6.46899513 7.473221524 4.250705787 3.895081288 5.742569541 5.877251723 6.978851389 6.151412106 1 18.29151646 4.245287565 24.99770637 5.108904455 6.971108733 0.206528509 1.672410796 277.6327629 1031671.447 0.423796055 1.068339182 17590.87996 -4.245287565 1.862204278 KVIEINPYLLGTMAGGAADCSFWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVIEINPYLLGTMAGGAADCSFWER 25 1 P28074;H0YJM8;P28074-2 P28074 PSMB5 Proteasome subunit beta type-5 0 191.18 1.17E-17 111250000 204550 165500 80632 81919 145230 139880 177510 194370 44106 FALSE TRUE 177518.1992 164412.8196 119625.9049 100519.961 142340.2071 145261.2741 160295.1075 152805.4881 38891.83893 4.564407447 4.227437533 3.075861368 2.584602934 3.659899122 3.735006575 4.12156154 3.928985934 1 15.24717983 4.341224519 4.800132352 3.298006008 4.478414916 0.239176377 0.898077908 0.320494805 11.95720717 0.226603008 0.638158182 21939.38851 -4.341224519 1.180408908 KVIIWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVIIWR 6 1 P55735;P55735-4;P55735-3;P55735-2;A8MXL6 P55735 SEC13 Protein SEC13 homolog 0 ; 121.87 0.03121 1223390000 1555880 1511990 777870 836650 1407340 1260810 1421500 1609320 1377760 FALSE TRUE 1350266.516 1502057.638 1154050.534 1026624.17 1379336.687 1309314.177 1283643.149 1265179.442 1214882.782 1.111437692 1.236380711 0.949927475 0.84503969 1.135366068 1.077728811 1.056598355 1.041400422 1 20.21238569 4.240317912 24.99999967 1.020168413 1.173909211 0.385642558 0.083118179 48.61723139 691595.7159 0.021734084 0.051695447 17390.734 -4.240317912 0.153740798 KVIQYLAYVASSHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVIQYLAYVASSHK 14 1 P35579;P35579-2;Q5BKV1 P35579 MYH9 Myosin-9 0 ; 156.24 3.65E-06 982140000 1136130 1168250 514730 876410 1034340 892370 1500270 1527630 1140910 FALSE TRUE 985987.5419 1160575.689 763655.1497 1075412.286 1013758.658 926700.0513 1354774.046 1200958.213 1006032.92 0.980074829 1.153616016 0.759075707 1.068963316 1.007679409 0.921142871 1.346649816 1.193756376 1 19.94024608 2.255591379 24.99988466 1.189911248 0.984590479 0.340532989 0.129859992 249.0554245 365594.1731 0.046946131 0.03627156 180.1322106 -2.255591379 -0.20532077 KVIS(ph)PPPFAPSPTLPPTFHPEEFLDEDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVISPPPFAPSPTLPPTFHPEEFLDEDLK 29 1 Q5TC82-2;Q5TC82 Q5TC82-2 RC3H1 Roquin-1 1 KVIS(0.998)PPPFAPS(0.001)PT(0.001)LPPTFHPEEFLDEDLK 60.48 0.015238 101710000 119570 85552 64966 89069 72779 89387 104850 130140 115040 TRUE FALSE 103768.5215 84990.00328 96383.7749 109293.4778 71330.84029 92825.77573 94681.66314 102310.5738 101440.1023 1.022953637 0.837834361 0.950154552 1.077418845 0.703181865 0.915079674 0.933375076 1.008581138 1 16.63026858 1.822213142 3.448525652 1.005349043 0.913751279 0.10944375 0.100139604 0.494781497 10.335235 0.062408271 0.026715603 66.40689002 -1.822213142 -0.091597764 KVKS(ph)QS(ph)KMASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVKSQSKMASK 11 3 P49796-1;P49796-4;P49796-6;P49796;P49796-2;H7BXY1;A0A087WUY2;P49796-7;P49796-8;P49796-9 P49796-1 RGS3 Regulator of G-protein signaling 3 2 KVKS(1)QS(1)KMASK;KVKS(1)QS(1)KMASK 65.5 0.081334 1182116000 2429730 2080660 1584439 1901305 2208080 1576405 2695230 3569970 2764580 TRUE FALSE 2108635.024 2066992.007 2350679 2333025.36 2164143.528 1637050.32 2433847.009 2806559.697 2437754.502 0.864990721 0.84790819 0.964280447 0.957038684 0.887761063 0.671540272 0.998397094 1.151288899 1 21.21712141 2.007114742 24.93956395 1.082968487 0.871145146 0.511883275 0.087113821 121.4348064 425668.039 0.036137537 0.024304802 101.6517224 -2.007114742 -0.211823341 KVLGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVLGEK 6 1 P14618;P14618-3;B4DNK4;F2Z349;A0A087WZC3;Q5VXJ5;Q5T6T6;A6XNE0;H0Y4U4;H0Y6A4;P09466-2;P09466;Q15431;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM;PAEP;SYCP1 Pyruvate kinase PKM;Pyruvate kinase;Glycodelin;Synaptonemal complex protein 1 0 91.041 0.077516 5030500000 4056600 2838800 2226200 2483900 2093000 2023400 3905900 4101800 3614300 FALSE TRUE 3520510.032 2820151.736 3302797.766 3047907.459 2051353.395 2101241.507 3527106.419 3224661.99 3187021.571 1.104639537 0.884886303 1.036327396 0.956349805 0.643658459 0.659311981 1.106709302 1.011810532 1 21.60377735 2.167457512 25 1.036536861 0.880736136 0.207464149 0.146128724 79.87093605 28080.84458 0.063858902 0.043053672 147.0474549 -2.167457512 -0.155800725 KVLS(ph)PTAAKPSPFEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVLSPTAAKPSPFEGK 16 2 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 1 KVLS(0.847)PT(0.152)AAKPS(0.001)PFEGK 55.763 0.068971 619810000 176870 126790 114370 112920 127920 96274 173010 201220 123200 TRUE FALSE 153496.1814 125957.1081 169679.7145 138560.2119 125374.6423 99977.72308 156231.5168 158190.6689 108635.4363 1.412947621 1.159447712 1.561918654 1.275460536 1.154086056 0.920304888 1.438126656 1.456160846 1 16.72913525 3.489332236 24.52217934 1.229703574 1.366647404 0.146506776 0.192104904 1191.838458 2393457.685 0.056886045 0.079585412 3085.547496 -3.489332236 0.13694383 KVLVTVEEDDTIMEELVDNHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KVLVTVEEDDTIMEELVDNHGK 22 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;; 306.06 1.43E-56 383185000 338917 297808 253664 292842 276996 237025 369399 428678 366343 FALSE TRUE 294128.2597 295851.6796 376336.7589 359336.2519 271484.3215 246143.5051 333574.7418 337008.5457 323034.3479 0.910516983 0.915852081 1.165005397 1.112377845 0.840419365 0.761973167 1.032629329 1.04325917 1 18.30132805 KVMDDLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KVMDDLDR 8 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;; 111.06 0.0053021 1569380000 2870430 2122400 1260530 1698690 1950370 1791720 2059730 2266630 1996870 FALSE TRUE 2491095.403 2108457.815 1870126.524 2084403.527 1911561.453 1860648.628 1859977.702 1781928.813 1760802.303 1.414750195 1.197441536 1.062087732 1.183780555 1.085619578 1.056705017 1.056323983 1.011998229 1 20.74780151 8 0.547885892 1.034632507 17.27939947 0.861849978 0.045621304 50.19384769 0.472946166 0.025309325 957.4180399 100000000 -8 16.24476696 KVMDS(ph)DEDDDY ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 KVMDSDEDDDY 11 1 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 1 KVMDS(1)DEDDDY;KVMDS(0.938)DEDDDY(0.062);KVMDS(1)DEDDDY;KVMDS(1)DEDDDY;KVMDS(0.999)DEDDDY(0.001);KVMDS(1)DEDDDY;KVMDS(1)DEDDDY 115.35 0.0012027 34918410000 28914270 24657600 17314850 20497200 24513640 20360920 28343640 32907800 28050030 TRUE FALSE 25093175.96 24495622.6 25688369.37 25151402.54 24025866.52 21144217.77 25594878.16 25870723.06 24733987.41 1.014522064 0.990362864 1.038585852 1.016876176 0.971370533 0.854864904 1.034805983 1.045958447 1 24.5599915 KVMDSDEDDDY(ph) ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVMDSDEDDDY 11 1 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 1 KVMDS(0.231)DEDDDY(0.769) 94.692 0.0087255 349380000 922510 761680 583660 661800 805970 682720 855070 1068600 936060 TRUE FALSE 800597.9662 756676.4739 865919.9282 812071.805 789932.7739 708984.6802 772145.443 840088.2059 825400.0532 0.969951435 0.916739066 1.049091195 0.983852378 0.957030195 0.85895885 0.935480244 1.017795192 1 19.65473401 1.715915799 8.027868806 1.008030119 0.953074811 0.186089069 0.048462837 0.200592555 32.67447267 0.029366156 0.013221704 51.98951895 -1.715915799 -0.054955307 KVNELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KVNELR 6 1 P50502;Q3KNR6;Q8IZP2;F8WAQ7 P50502 ST13;ST13P4 Hsc70-interacting protein;Putative protein FAM10A4 0 ;;;;; 126.24 0.028181 5218590000 14839780 13490970 8771790 11112180 11421260 12679550 15095230 17918050 15855440 FALSE TRUE 12878665.47 13402346.93 13013856.98 13635370.31 11193999.27 13167340.49 13631296.92 14086414.45 13981027.95 0.921152974 0.958609552 0.930822614 0.975276665 0.800656383 0.941800599 0.974985314 1.007537822 1 23.7369671 2.180293041 3.095045032 1.000765191 0.919673428 0.369676213 0.046254436 0.268572342 5.246288737 0.021722953 0.013605645 151.458287 -2.180293041 -0.081091763 KVNLGVGAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVNLGVGAYR 10 1 P17174 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 115.78 0.0018878 1186800000 696540 779590 414810 527160 661070 649550 740310 764270 653500 FALSE TRUE 604490.4742 774468.822 615413.5035 646859.7351 647916.0004 674538.6088 668514.8501 600836.8081 576243.9745 1.049018299 1.343994656 1.067973863 1.122544901 1.124377918 1.170578156 1.160124669 1.042677815 1 19.13632023 1.633870133 3.530242031 1.007871082 1.151971992 0.311161807 0.079458571 0.207942816 6.003300484 0.059546461 0.019728225 43.03978891 -1.633870133 0.14410091 KVNNADDFPNLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVNNADDFPNLFR 13 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 105.19 0.0023607 266870000 264810 255000 125230 109190 229830 221160 216960 252250 68601 FALSE TRUE 229814.6876 253324.8882 185791.6469 133983.2584 225256.8327 229668.1683 195919.2526 198308.3005 60491.06793 3.799150774 4.187806512 3.071389764 2.214926318 3.723803205 3.796728611 3.238812924 3.27830715 1 15.88443451 4.208264516 8.614805186 2.990120612 3.993291025 0.231070906 0.81493127 0.340955402 87.90991979 0.207341753 0.442910537 16153.42115 -4.208264516 1.003170413 KVNVTVDYIRPAS(ph)PATETVPAFSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KVNVTVDYIRPASPATETVPAFSER 25 2 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 1 KVNVTVDYIRPAS(0.998)PAT(0.002)ETVPAFSER;KVNVTVDYIRPAS(0.998)PAT(0.001)ETVPAFSER;KVNVTVDYIRPAS(0.996)PAT(0.004)ETVPAFSER;KVNVTVDYIRPAS(0.989)PAT(0.011)ETVPAFSER 215.57 8.94E-34 3638100000 2643300 2320970 1522310 1799470 2307860 2282840 2613020 2865020 2054460 TRUE FALSE 2293981.208 2305723.395 2258504.208 2208067.167 2261938.101 2370662.332 2359609.723 2252357.769 1811584.079 1.266284703 1.272766427 1.24670129 1.218859887 1.248596809 1.30861292 1.302511846 1.243308436 1 20.78882034 1.240111941 4.648089262 0.979754903 1.265416661 0.910551069 0.02604499 0.056699851 2.722976971 0.053108483 0.007192136 17.38248812 -1.240111941 0.285661758 KVNVTVDYIRPASPATETVPAFSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVNVTVDYIRPASPATETVPAFSER 25 2 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 219.34 7.54E-34 1364750000 397630 338920 191579 234640 361430 324930 325680 397630 223420 FALSE TRUE 345082.188 336693.6122 284227.2452 287918.5982 354238.2501 337430.2674 294095.6037 312599.9189 197007.5421 1.751619173 1.7090392 1.44272266 1.461459775 1.798094866 1.712778423 1.492813933 1.58674087 1 17.58789134 0.93501607 1.945253681 0.151213396 1.626510265 0.70493301 0.125506463 1.348976909 2.308688662 4.906696248 0.035342975 8.610256123 -0.93501607 1.475296868 KVPGVTAIELDEDTGTFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVPGVTAIELDEDTGTFR 18 1 B4DXZ6;P51114;P51114-3;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 ; 286.6 1.30E-39 969710000 1418500 1078990 754440 927670 1155220 1008350 1210330 1467760 1322540 FALSE TRUE 1231041.631 1071902.044 1119289.707 1138311.652 1132233.382 1047141.877 1092952.383 1153890.946 1166190.828 1.055609084 0.919148066 0.959782637 0.976093813 0.970881742 0.897916406 0.937198576 0.989452942 1 20.15337245 1.598995744 5.777017803 0.997241979 0.956755114 0.109087415 0.041673535 0.267475832 18.54774321 0.027197562 0.010318582 39.71876569 -1.598995744 -0.040486865 KVPLDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KVPLDER 7 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ;;; 105.57 0.012663 4535010000 12637000 12048000 7457700 9504400 10502800 10502600 12415100 13668700 12618300 FALSE TRUE 10966988.43 11968855.89 11064268.66 11662519.29 10293814.83 10906641.82 11211085.51 10745754.87 11126578.95 0.985656821 1.075699543 0.99439987 1.048167576 0.925155421 0.980233176 1.007595018 0.96577348 1 23.40750674 3.263716035 24.99979065 0.9771165 1.027276492 0.361248624 0.033141508 238.9486751 237468.726 0.008864558 0.011439483 1835.33791 -3.263716035 0.050159991 KVPWFDQQNGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVPWFDQQNGR 11 1 Q92522 Q92522 H1FX Histone H1x 0 ; 132.59 0.00028767 1956270000 1130860 1018120 658810 735630 988230 899570 1142320 1045350 837110 FALSE TRUE 981413.9858 1011431.903 977412.7196 902666.0349 968566.1564 934177.04 1031537.982 821810.0374 738147.8094 1.329562959 1.370229498 1.324142275 1.222879786 1.312157462 1.265569074 1.397468053 1.113340752 1 19.49355021 1.568665871 4.083084934 1.020945512 1.313400289 0.830807644 0.050047421 0.063407439 2.308296566 0.040324443 0.013106005 37.03956443 -1.568665871 0.292454777 KVQIPVSRPDPEPVS(ph)DNEEDS(ph)YDEEIHDPR ddPTM_MDA-MB-175_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(0.99)DNEEDS(0.722)Y(0.288)DEEIHDPR;KVQIPVSRPDPEPVS(1)DNEEDS(0.61)Y(0.39)DEEIHDPR;KVQIPVS(0.001)RPDPEPVS(0.999)DNEEDS(0.698)Y(0.302)DEEIHDPR 185.97 2.42E-18 1296140000 808350 722250 473210 545370 725770 690560 790900 898750 541690 TRUE FALSE 701524.4994 717505.4922 702055.9388 669204.594 711328.5969 717126.2901 714198.6397 706559.3066 477652.0253 1.468693656 1.502151052 1.469806264 1.401029533 1.489219263 1.501357164 1.495227911 1.479234399 1 18.86560046 1.238355283 24.99973742 0.999999473 1.476419233 0.963628224 0.029052796 0.86611552 105194.1128 0.041607612 0.007376701 17.31232047 -1.238355283 0.47641976 KVQIPVSRPDPEPVS(ph)DNEEDSY(ph)DEEIHDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVQIPVSRPDPEPVSDNEEDSYDEEIHDPR 30 2 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 2 KVQIPVS(0.001)RPDPEPVS(0.998)DNEEDS(0.372)Y(0.63)DEEIHDPR 62.605 0.043548 327250000 79209 85218 58574 58282 79604 75794 72491 112130 61183 TRUE FALSE 68741.32996 84658.19735 86900.58232 71515.81888 78020.03614 78709.84423 65460.83398 88151.8721 53950.01544 1.274167012 1.569196907 1.610761028 1.325594039 1.446154102 1.458940161 1.213360802 1.63395453 1 15.71933575 1.22297041 24.99864513 0.999998777 1.446187645 0.495882221 0.139832057 745.6248076 1195530.067 0.791552333 0.03244179 16.70976762 -1.22297041 0.446188868 KVQVAALQAS(ph)PPLDQDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 218.25 4.89E-19 14027890000 4292760 4309340 2861550 3629980 4623830 4469700 4929460 5779190 4509160 TRUE FALSE 3725460.89 4281031.662 4245405.151 4454222.44 4531824.829 4641652.251 4451401.728 4543355.192 3976092.242 0.936965408 1.076693246 1.067733064 1.120251284 1.139768535 1.167390485 1.119541866 1.142668458 1 21.9229198 5.66894119 0.97529784 1.119972693 0.118707725 0.576444217 0.04604571 7.072584412 1.384075577 0.01418806 11.43515473 466596.1917 -5.66894119 -1.001264968 KVQVAALQASPPLDQDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 147.06 1.27E-07 703560000 1121610 1041500 703480 862860 996710 1076570 1050900 1208280 990840 FALSE TRUE 973386.3967 1034658.318 1043685.281 1058785.551 976877.421 1117986.345 948983.8797 949898.7248 873704.024 1.114091695 1.184220617 1.194552448 1.211835498 1.118087355 1.279593906 1.086161736 1.087208824 1 19.73678511 1.703529756 1.73578109 1.010604316 1.181206282 0.555298069 0.05259675 0.278688871 1.551737218 0.064558113 0.014450411 50.52772633 -1.703529756 0.170601965 KVQYAPERPGPQPTAETTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KVQYAPERPGPQPTAETTR 19 2 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 ;; 227.64 6.88E-20 1126310000 707140 645390 428580 526580 575110 640800 677780 689190 539830 FALSE TRUE 613689.6573 641150.3906 635842.7215 646148.0373 563666.4362 665451.9907 612048.9999 541812.0818 476011.9124 1.289231722 1.346920894 1.335770608 1.357419889 1.184143551 1.397973398 1.285785049 1.138232191 1 18.86063815 1.53421373 2.091801218 0.98873681 1.318562825 0.783043817 0.056307292 0.161484402 1.272821504 0.088167502 0.015046391 34.21477826 -1.53421373 0.329826016 KVS(ph)IVSKPVLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVSIVSKPVLYR 12 2 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 KVS(1)IVSKPVLYR;KVS(1)IVSKPVLYR 161.14 3.22E-05 2247700000 2919800 2290300 1779630 1752720 2177600 1757550 3056900 2967600 3165800 TRUE FALSE 2533941.032 2275254.868 2640265.021 2150701.865 2134270.02 1825164.086 2760442.309 2333001.834 2791542.73 0.907720668 0.815052854 0.945808564 0.770434871 0.764548576 0.653819147 0.988859056 0.835739252 1 21.41263121 0.712485768 1.124035981 1.345490774 0.823680944 0.223601836 0.096399727 7.703758889 3.430394468 6.406757672 0.030128379 5.158052613 -0.712485768 -0.52180983 KVS(ph)LVLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVSLVLEK 8 1 Q9P2M7;Q9P2M7-2;H0Y4A8 Q9P2M7 CGN Cingulin 1 KVS(1)LVLEK;KVS(1)LVLEK 120.57 0.0015631 1129120000 3259000 2606090 2273900 2542260 2370400 1966010 3656710 3716340 4295700 TRUE FALSE 2828314.893 2588970.423 3373565.646 3119518.989 2323233.678 2041643.677 3302082.827 2921629.612 3787867.24 0.746677408 0.683490275 0.890624046 0.823555524 0.613335561 0.538995574 0.871752524 0.771312569 1 21.85295434 0.829735826 1.358913428 1.449114553 0.731439062 0.363853438 0.108515539 4.232844961 3.104456547 5.57655422 0.033214784 6.756718503 -0.829735826 -0.717675491 KVS(ph)TSGQIR ddPTM_MDA-MB-175_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(0.441)T(0.279)S(0.279)GQIR 120.59 0.00039235 436480000 515130 497130 344820 427870 444350 488940 512540 589410 596830 TRUE FALSE 447054.2653 493864.3203 511576.1054 525024.4231 435508.3044 507749.8382 462833.9497 463369.2583 526273.4373 0.84947146 0.938417722 0.972072822 0.997626682 0.827532369 0.964802329 0.879455273 0.880472442 1 19.00545305 3.267539136 24.99999781 0.907097519 0.941661114 0.052320746 0.059935901 608.762804 525180.6326 0.01681113 0.021699202 1851.565738 -3.267539136 0.034563595 KVSAQEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KVSAQEVR 8 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 114.5 0.0042411 1459830000 3376000 4103160 2645790 3546340 3880460 4139220 4047280 4922900 4081180 FALSE TRUE 2929853.046 4076206.072 3925302.894 4351590.699 3803246.438 4298458.472 3654775.409 3870176.145 3598707.55 0.814140356 1.132686115 1.090753511 1.209209317 1.056836763 1.194445065 1.015579999 1.075435025 1 21.77904744 4.743045817 24.95414708 1.09650124 0.81414024 0.631191189 0.067918483 293.6998166 1633988.567 0.016067931 0.124395854 55340.84892 -4.743045817 -0.282360999 KVSMDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KVSMDNR 7 1 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;C9IZ80;C9JFN4 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 ;;; 94.114 0.023151 294427000 1176130 1261630 772037 890167 1088870 1222600 1328080 1440970 1319430 FALSE TRUE 1020701.441 1253342.269 1145396.676 1092293.023 1067203.617 1269634.213 1199283.006 1132829.779 1163448.488 0.877306946 1.077264943 0.984484218 0.938840897 0.917276208 1.091268093 1.030800261 0.973682798 1 20.14997591 2.75813186 24.96818511 1.016728816 0.965894989 0.220206898 0.059235223 1618.479653 2064786.36 0.019210195 0.019186634 572.9699687 -2.75813186 -0.050833827 KVSQPIEGHAASFAQFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVSQPIEGHAASFAQFK 17 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 182.49 4.83E-10 522110000 1826200 1513700 641340 821110 1368300 1210300 1809800 2069600 467760 FALSE TRUE 1584863.043 1503756.405 951494.1692 1007555.575 1341073.507 1256861.024 1634285.875 1627032.146 412461.9457 3.842446702 3.645806409 2.306865346 2.442784325 3.25138724 3.047216931 3.962270681 3.944684262 1 18.65390149 KVTAAMGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVTAAMGK 8 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ; 99.815 0.010496 1765250000 2928400 3014300 1996600 2236800 2389100 2065300 3352200 3668700 3101800 FALSE TRUE 2541404.52 2994498.865 2962162.438 2744699.627 2341561.584 2144753.427 3027104.16 2884177.055 2735108.738 0.929178605 1.094837227 1.083014506 1.003506584 0.856112794 0.784156548 1.10675825 1.054501788 1 21.38316676 KVTAEADSSS(ph)PTGILATSESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVTAEADSSSPTGILATSESK 21 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-7 A0MZ66 KIAA1598 Shootin-1 1 KVTAEADS(0.006)S(0.039)S(0.952)PT(0.003)GILATSESK;KVTAEADS(0.012)S(0.076)S(0.9)PT(0.012)GILATSESK 220.95 2.75E-25 1876080000 2127800 1808340 1336400 1661250 1712400 1396430 2251600 2692000 2066610 TRUE FALSE 1846605.839 1796460.895 1982687.51 2038462.203 1678326.59 1450151.566 2033240.179 2116336.749 1822297.72 1.013339269 0.985821842 1.088015141 1.118621936 0.920994726 0.795781913 1.115756309 1.161356197 1 20.79732725 KVTEELLTDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVTEELLTDNR 11 1 Q9UHB9;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ; 134.61 0.00021995 741000000 1694970 1500280 1030560 1176590 1583990 1489880 1653110 1849250 1599000 FALSE TRUE 1470975.42 1490424.562 1528942.263 1443752.743 1552471.698 1547196.648 1492791.647 1453802.278 1409968.042 1.043268625 1.057062655 1.084380793 1.023961324 1.101068714 1.097327459 1.058741477 1.031088816 1 20.42723103 1.545689988 2.299422096 1.000148414 1.068099569 0.477431082 0.023477266 0.285386975 2.90180033 0.033543564 0.006511854 35.13095756 -1.545689988 0.067951155 KVTFFEPGS(ph)GDENGTSNKEDEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 163.76 7.87E-12 274880000 134552 125116 96363 97349 153741 117384 187380 211301 111866 TRUE FALSE 116770.6123 124294.1048 142964.4691 119453.5783 150681.8549 121899.8384 169207.9164 166115.9255 98641.32892 1.183789934 1.260061134 1.449336406 1.210989143 1.527573245 1.235788688 1.715385613 1.684039817 1 16.58990462 4.205185851 0.592338734 1.487244233 1.113286437 0.074361274 0.221155933 4.508633597 1.978929634 0.147449563 1.090015397 16039.31627 -4.205185851 -0.373957796 KVTGTEGSSSTLVDYTSTSSTGGS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVTGTEGSSSTLVDYTSTSSTGGSPVR 27 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 KVTGTEGSSSTLVDYTSTSSTGGS(1)PVR 263.74 1.99E-53 325260000 431840 307840 204350 267040 345420 290540 335220 417850 415470 TRUE FALSE 374771.2499 305817.7788 303174.3435 327675.5135 338546.8178 301717.2618 302710.416 328496.0292 366353.6099 1.022976817 0.834761199 0.82754567 0.894424143 0.92409849 0.823568415 0.826279332 0.896663825 1 18.48287731 1.262220466 4.064655586 1.01022528 0.874745693 0.272740681 0.061136311 0.276207942 7.998368502 0.105737657 0.014927845 18.2902847 -1.262220466 -0.135479586 QRYEILTPNSIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QRYEILTPNSIPK 13 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 124.51 0.00019234 881250000 1489090 1371730 740650 829970 1174120 1016410 1455060 1446330 651130 FALSE TRUE 1292302.984 1362719.015 1098830.817 1018427.374 1150757.309 1055511.95 1313948.505 1137043.585 574154.1532 2.250794454 2.37343753 1.913825427 1.77378735 2.00426541 1.83837728 2.288494297 1.980380319 1 19.13107861 1.241919189 5.325405957 0.946156846 2.053954865 0.742707088 0.195268187 0.081712179 6.707431814 0.331772847 0.050891495 17.4549733 -1.241919189 1.107798019 KVTQLDLDGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVTQLDLDGPK 11 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ; 136.93 0.00014254 1772730000 4696700 3947000 3266900 3532500 3614100 2714800 5193500 6164800 4644500 FALSE TRUE 4076019.195 3921071.897 4846783.767 4334608.116 3542186.481 2819240.113 4689835.169 4846505.495 4095432.501 0.995259767 0.957425595 1.183460786 1.058400575 0.864911454 0.688386419 1.145137948 1.183392839 1 21.96558439 KVTS(ph)PLQS(ph)PTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.006)S(0.994)PLQS(1)PTK;KVT(0.016)S(0.984)PLQS(1)PTK;KVT(0.107)S(0.893)PLQS(0.999)PT(0.001)K 151.38 0.00011704 1352790000 2641090 2203710 1957800 2350220 2661670 1860560 3523240 3975420 3588180 TRUE FALSE 2292063.265 2189233.684 2904598.628 2883873.372 2608707.974 1932136.947 3181556.727 3125307.37 3163989.448 0.724421905 0.69192193 0.918017799 0.911467443 0.824499581 0.610664789 1.005552256 0.987774271 1 21.59331336 2.197527419 24.99990084 0.996016306 0.790403872 0.544677989 0.093474571 123.7158866 75374.3493 0.040073355 0.027017774 157.5895511 -2.197527419 -0.205612434 HFCPNVPIILVGNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 HFCPNVPIILVGNK 14 0 Q5JR08;P08134;E9PQH6;Q5JR07;C9JNR4;C9JX21;Q5JR05;P61586 Q5JR08;P61586 RHOC;RHOA Rho-related GTP-binding protein RhoC;Transforming protein RhoA 0 144.47 8.84E-06 194920000 471350 430190 297670 453380 478760 425500 415180 654300 1044900 FALSE TRUE 409059.9033 427364.0536 441624.2076 556326.8585 469233.6127 441869.2603 374915.9075 514383.0368 921373.1124 0.443967702 0.463833867 0.479310935 0.603801925 0.509276434 0.479576899 0.406909972 0.558278758 1 19.81342597 1.242907038 3.744480117 1.062562666 0.488016062 0.909239391 0.050831356 0.075809825 1.697991116 0.121296702 0.013532589 17.49472171 -1.242907038 -0.574546604 KVTSVVFHPSQDLVFSASPDATIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVTSVVFHPSQDLVFSASPDATIR 24 1 Q9UMS4 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 117.54 0.00044613 220390000 155910 130070 43548 88766 132670 138100 134800 142370 90017 FALSE TRUE 135306.0985 129215.5616 64607.95846 108921.677 130030.1266 143412.7964 121727.1167 111925.2834 79375.29281 1.704637472 1.627906582 0.813955529 1.372236538 1.63816878 1.806768722 1.533564318 1.410077109 1 16.27640239 3.44356016 24.60946604 1.491293268 1.35446631 0.02072209 0.309190788 621.4150166 455664.9033 0.093129745 0.120230829 2776.899488 -3.44356016 -0.136826958 KVVDYSQFQES(ph)DDADEDYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 78 KVVDYSQFQESDDADEDYGR 20 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KVVDYSQFQES(1)DDADEDYGR;KVVDYS(0.001)QFQES(0.999)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYS(0.01)QFQES(0.99)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDY(0.001)S(0.003)QFQES(0.996)DDADEDYGR;KVVDYS(0.002)QFQES(0.998)DDADEDYGR;KVVDYSQFQES(0.998)DDADEDY(0.002)GR;KVVDYS(0.002)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;KVVDYS(0.001)QFQES(0.999)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(0.998)DDADEDY(0.002)GR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(0.999)DDADEDY(0.001)GR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(0.999)DDADEDY(0.001)GR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDY(0.001)S(0.003)QFQES(0.996)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYS(0.001)QFQES(0.999)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;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 327.74 5.92E-80 5.31203E+11 45491277.1 40480813.4 27858706.9 33227266.7 40034317.8 36103126.8 44147879 50181562 39532477.9 TRUE FALSE 39479489.57 40214892.27 41331270.74 40772025.45 39237713.2 37492037.45 39866424.49 39450625.48 34858993.4 1.132548181 1.15364468 1.185670231 1.16962716 1.125612342 1.075534139 1.143648184 1.131720157 1 25.05502757 3.051163371 4.247065117 1.099729203 1.161300733 0.397567245 0.040915427 0.252349349 9.634594976 0.012985794 0.014586959 1125.028103 -3.051163371 0.06157153 KVVDYSQFQES(ph)DDADEDYGRDSGPPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 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;KVVDYS(0.343)QFQES(0.657)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYS(0.007)QFQES(0.993)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK 325.11 2.36E-83 38792680000 11381630 8889322 3470092 3744830 7915515 5932036 9944588 11994890 1119872 TRUE FALSE 9877518.758 8830927.458 5148240.098 4595150.888 7758011.738 6160245.263 8980163.386 9429876.118 987482.0079 10.00273289 8.942874288 5.213502683 4.653402139 7.85635756 6.238336713 9.094002032 9.549415627 1 19.91339494 4.402882709 6.044784365 6.687645837 9.753453057 0.22048914 2.456383145 0.308780692 18.66857411 0.623035119 1.711674892 25286.14996 -4.402882709 3.06580722 KVVDYSQFQES(ph)DDADEDYGRDSGPPTKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KVVDYSQFQESDDADEDYGRDSGPPTKK 28 3 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KVVDYSQFQES(1)DDADEDYGRDSGPPTKK;KVVDYSQFQES(1)DDADEDYGRDSGPPTKK;KVVDYSQFQES(1)DDADEDYGRDSGPPTKK;KVVDYSQFQES(1)DDADEDYGRDSGPPTKK 199.21 3.46E-25 3202350000 932710 723630 199831 158181 568358 391156 951050 1059970 37416.4 TRUE FALSE 809450.0103 718876.4269 296469.94 194098.4137 557048.7878 406204.0244 858817.3174 833303.6642 32993.07582 24.53393599 21.78870594 8.985823014 5.883004506 16.88380892 12.31179617 26.03022895 25.25692569 1 15.00987566 7.999924119 0.019982787 9.99999231 24.84221985 0.003230701 8.699722307 244996.4983 486.8239112 143554.522 227332.9954 99982529.18 -7.999924119 14.84222754 KVVDYSQFQESDDADEDYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KVVDYSQFQESDDADEDYGR 20 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ;;; 326.12 9.78E-68 2824800000 2661570 2324420 1460241 1633686 2066260 1907421 2266820 2587910 1473489 FALSE TRUE 2309836.781 2309150.732 2166418.432 2004639.376 2025145.469 1980800.72 2046984.145 2034505.586 1299294.809 1.777761879 1.777233863 1.667380195 1.542867224 1.558649703 1.524519844 1.575457803 1.565853701 1 20.30929738 0.893639457 1.805835491 5.97E-07 1.633186581 0.824754876 0.090571421 1.229451631 1.650058782 4.773687434 0.028007193 7.827795239 -0.893639457 1.633185984 KVVDYTTAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVVDYTTAK 9 1 P62820;E7END7;P62820-2 P62820 RAB1A Ras-related protein Rab-1A 0 120.06 0.0028938 0 551780 548050 367150 471280 519080 436200 495170 695980 657670 FALSE TRUE 478860.875 544449.8235 544704.968 578291.3271 508751.3236 452980.8963 447148.4896 547150.0931 579921.0018 0.825734666 0.938834465 0.939274429 0.997189833 0.877276943 0.781107935 0.771050692 0.943490737 1 19.14549686 3.034135838 24.8832097 0.870035269 0.928479781 0.091863648 0.078523831 424.8547216 309693.7262 0.025404913 0.028806327 1081.772254 -3.034135838 0.058444512 KVVEAVNS(ph)DS(ph)DSEFGIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVVEAVNSDSDSEFGIPK 18 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 KVVEAVNS(1)DS(0.995)DS(0.005)EFGIPK;KVVEAVNS(1)DS(0.993)DS(0.007)EFGIPK 168.25 7.41E-11 645660000 675760 574530 339640 489810 539440 440730 547110 770450 643430 TRUE FALSE 586456.6038 570755.8746 503891.04 601028.8468 528706.1994 457685.1683 494051.3564 605695.2631 567364.4384 1.033650621 1.005977527 0.888125878 1.059334717 0.931863479 0.806686386 0.870783086 1.067559442 1 19.1139162 4.459265691 23.54168854 0.951337313 1.026732403 0.125982852 0.081223102 242.3526246 319530.2663 0.021772858 0.057642354 28791.59279 -4.459265691 0.07539509 KVVGCSCVVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVVGCSCVVVK 11 1 P25398 P25398 RPS12 40S ribosomal protein S12 0 ; 97.86 0.0095433 792590000 1215180 1037450 642280 824890 1013180 768630 1113370 1240820 909230 FALSE TRUE 1054590.884 1030634.923 952888.7563 1012193.882 993019.7003 798199.6935 1005395.549 975480.2991 801741.8652 1.315374599 1.285494705 1.188523137 1.262493486 1.238577831 0.995581905 1.254014032 1.216701212 1 19.61277829 7.999999966 0.169961802 1.066659853 2.088845062 0.362431407 0.088644154 168.6259997 2.298032592 1.004060462 42.53446136 99999992.23 -7.999999966 1.022185209 KVVGDVAYDEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KVVGDVAYDEAK 12 1 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ;;; 170.52 6.56E-05 1912040000 4086970 3492500 2681550 3080790 3198740 2411670 4290800 5203760 4030830 FALSE TRUE 3546866.559 3469557.538 3978356.549 3780330.456 3135091.332 2504448.505 3874678.876 4090976.42 3554309.869 0.997905835 0.976155053 1.119304927 1.063590569 0.882053464 0.704623006 1.090135362 1.150990367 1 21.76113803 2.05199804 24.99999953 1.096570517 0.961115031 0.195318195 0.116156657 153.4026883 73753.31499 0.050919743 0.034330078 112.719237 -2.05199804 -0.135455486 KVVNPLFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVVNPLFEK 9 1 P62424;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 ; 136.96 0.0020986 0 5265500 5491300 3841100 4168400 5125500 4041000 6991900 7362700 6327500 FALSE TRUE 4569650.834 5455227.289 5698668.808 5114898.93 5023512.578 4196459.885 6313826.614 5788243.902 5579470.158 0.819011609 0.977732138 1.021363794 0.916735601 0.900356563 0.75212516 1.131617597 1.037418202 1 22.4116967 2.217478956 24.99999318 1.055538461 0.908098239 0.455508392 0.08115659 235.3136864 279048.0715 0.033861594 0.022855472 164.9981048 -2.217478956 -0.147440221 KVVVS(ph)PTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KVVVSPTK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 KVVVS(0.591)PT(0.409)K;KVVVS(0.982)PT(0.018)K;KVVVS(0.665)PT(0.335)K 89.561 0.008464 8908120000 10597400 7646800 5660600 7143000 6995400 5349190 8920100 11069900 11514400 TRUE FALSE 9196926.74 7596567.667 8398085.094 8764927.324 6856205.226 5554976.801 8055030.075 8702688.031 10153180.75 0.905817297 0.748195847 0.827138342 0.863269111 0.675276585 0.547116902 0.793350407 0.857139082 1 23.27542842 1.412676369 2.259743409 1.017397361 0.759809164 0.36217916 0.100105044 0.506312753 3.787215965 0.232551352 0.028733321 25.86284929 -1.412676369 -0.257588198 KVVVSPT(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KVVVSPTK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 KVVVS(0.285)PT(0.715)K;KVVVS(0.208)PT(0.792)K;KVVVS(0.395)PT(0.605)K 110.93 0.0019518 11058620000 27135000 19379100 14148100 19110200 18277500 12908600 23173500 29467500 29766500 TRUE FALSE 23549041 19251797.42 20990168.48 23449462.99 17913813.51 13405202.19 20926137.54 23166104.44 26247538.28 0.897190462 0.733470591 0.799700462 0.893396658 0.682494995 0.510722265 0.797260959 0.882601035 1 24.64567878 1.560650296 2.556435353 0.990222044 0.751913641 0.348672892 0.109906681 0.324730336 4.365183562 0.139907776 0.031350406 36.36221208 -1.560650296 -0.238308403 KVVVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVVVVR 6 1 P40429;M0QYS1 P40429 RPL13A 60S ribosomal protein L13a 0 ; 136.58 0.021019 2090200000 4692100 4372100 2818300 3647000 4184800 4421600 4586800 5168400 4483100 FALSE TRUE 4072027.097 4343379.387 4181239.307 4475107.091 4101530.667 4591701.813 4141972.842 4063177.881 3953113.025 1.030081121 1.098723806 1.057708009 1.13204633 1.037544498 1.161540736 1.04777496 1.027842577 1 21.91455777 1.820289111 2.910407219 1.011525709 1.086067321 0.340999931 0.040925109 0.258878744 4.008070726 0.026187551 0.010376937 66.11334203 -1.820289111 0.074541612 KVYASQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KVYASQR 7 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 90.657 0.027223 652630000 1667900 1936600 1162400 1130500 1316000 2000000 1678300 1840200 1402000 FALSE TRUE 1447482.789 1923878.347 1724540.528 1387197.304 1289814.175 2076941.294 1515538.724 1446687.55 1236257.157 1.170858976 1.5562121 1.394969095 1.122094457 1.043321907 1.680023676 1.225908959 1.170215713 1 20.23754744 1.533675061 2.206675725 1.003352014 1.323581877 0.222126402 0.193465641 0.546963289 4.924825281 0.297913725 0.053549456 34.17236691 -1.533675061 0.320229862 KVYEDSGIPLPAES(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KVYEDSGIPLPAESPK 16 1 F8W038;F8W1H0;H0YIS7;Q8IXM2;Q8IXM2-3;Q8IXM2-2 F8W038;Q8IXM2-2 C17orf49;RNASEK-C17orf49;BAP18 Chromatin complexes subunit BAP18 1 KVYEDSGIPLPAES(1)PK;KVYEDSGIPLPAES(1)PK;KVYEDSGIPLPAES(1)PK 131.65 2.66E-05 1129740000 1831280 1069330 892390 990270 1241040 907830 1436910 1734470 1519780 TRUE FALSE 1589271.708 1062305.501 1323952.789 1215125.939 1216345.732 942754.8075 1297558.689 1363567.088 1340113.34 1.185923355 0.792698251 0.987940907 0.906733709 0.907643925 0.703488861 0.968245484 1.017501317 1 20.35392359 2.009494859 24.99467186 1.004862599 0.905001604 0.089890649 0.124368963 412.7513453 1086539.819 0.048324897 0.032538716 102.2103461 -2.009494859 -0.099860995 KVYENYPTYDLTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVYENYPTYDLTER 14 1 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;A0A494C198 H0Y993 DEK Protein DEK 0 ; 247.38 1.29E-17 556780000 704700 641700 380470 467290 632590 557540 600610 792310 403720 FALSE TRUE 611572.1095 637484.6304 564466.5646 573395.3366 620002.6966 578988.9246 542362.9346 622880.6723 355992.6815 1.717934501 1.790723977 1.585612834 1.61069417 1.741616412 1.626406819 1.523522709 1.749700779 1 18.44148806 1.234155073 24.99998981 0.999999013 1.665735209 0.864193255 0.083250262 46.23745595 262347.8575 0.155402136 0.020189446 17.14569417 -1.234155073 0.665736196 KVYFAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KVYFAEK 7 1 P52943;H0YFA4;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 ; 109.21 0.01135 3646800000 4038000 3944100 2643700 3015100 3700300 2725500 3998400 4744400 4397900 FALSE TRUE 3504368.069 3918190.947 3922202.163 3699724.538 3626671.27 2830351.749 3610635.783 3729846.981 3877985.272 0.903656879 1.010367671 1.011402026 0.954032643 0.935194699 0.729851082 0.931059695 0.961800192 1 21.88687589 3.262807043 3.609614575 0.909433103 0.977978152 0.132014839 0.075975301 0.480725118 13.22464801 0.024540201 0.030808874 1831.500504 -3.262807043 0.06854505 KWDGS(ph)EEDEDNSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KWDGSEEDEDNSK 13 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK 214.19 1.91E-11 2945370000 4435270 2779090 2762670 2589530 2741620 1970850 4140690 4647630 4201540 TRUE FALSE 3849137.832 2760833.975 4098706.453 3177522.365 2687067.126 2046669.875 3739126.521 3653770.492 3704838.728 1.038948822 0.745196803 1.106311706 0.857668201 0.725285855 0.55243157 1.009254868 0.986215801 1 21.82097931 KWDGS(ph)EEDEDNSKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KWDGSEEDEDNSKK 14 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 KWDGS(1)EEDEDNSKK;KWDGS(1)EEDEDNSKK 188.09 6.88E-07 673470000 918080 530410 687450 541490 450990 312515 896330 975780 703860 TRUE FALSE 796753.4019 526925.7018 1019903.119 664443.5807 442016.1813 324537.6543 809404.0546 767117.0405 620650.4726 1.283739298 0.848989447 1.643280984 1.070560017 0.712182139 0.52289923 1.304122192 1.235988812 1 19.2434215 3.489254984 24.7872379 0.985335167 1.24090497 0.178425755 0.29258732 1128.740029 2305830.894 0.087663836 0.122563548 3084.998688 -3.489254984 0.255569803 KWDSNVIETFDIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KWDSNVIETFDIAR 14 1 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;F5GWK5;H0YH17 Q9Y365 STARD10 PCTP-like protein 0 ; 222.45 6.24E-12 2068200000 3013400 2208940 1700540 2107820 2184350 2074980 2440370 2900050 2842150 FALSE TRUE 2615171.555 2194429.328 2522926.832 2586432.747 2140885.709 2154805.823 2203703.293 2279896.876 2506154.265 1.043499832 0.875616221 1.006692552 1.032032538 0.854251368 0.85980574 0.879316698 0.909719289 1 21.25704379 3.23625039 24.99953402 0.898117916 0.982559442 0.348037829 0.0600377 74.00921167 800871.7106 0.017880147 0.021262673 1722.861596 -3.23625039 0.084441526 KWENPGLGAESHTDS(ph)LRNSSTEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KWENPGLGAESHTDSLRNSSTEIR 24 2 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KWENPGLGAES(0.001)HT(0.008)DS(0.853)LRNS(0.137)S(0.001)TEIR 168.98 5.11E-12 394230000 127800 136660 76081 96731 137210 131240 163180 168150 129520 TRUE FALSE 110910.9062 135762.2715 112874.0261 118695.252 134479.7894 136288.8877 147354.8287 132192.431 114208.2931 0.971128305 1.188725159 0.988317249 1.039287505 1.177495834 1.193336175 1.290228797 1.157467881 1 16.80130789 3.235704691 24.99597764 1.173896772 1.052815493 0.286459113 0.090628207 94.9180645 830753.7774 0.0268621 0.031816923 1720.698148 -3.235704691 -0.121081279 KWENPGLGAESHTDSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KWENPGLGAESHTDSLR 17 1 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ; 195.27 1.80E-11 691160000 657940 580330 294147 422620 547210 609130 622920 723070 520580 FALSE TRUE 570991.562 576517.774 436397.4731 518582.3303 536321.5916 632563.6253 562509.3143 568447.1074 459037.6254 1.243888366 1.255927057 0.950679092 1.129716393 1.168360853 1.3780213 1.225410039 1.238345347 1 18.80825288 2.988406742 24.68748994 1.222538364 1.140332239 0.055998226 0.122076215 1240.277778 2641139.674 0.038829659 0.041002959 973.6586846 -2.988406742 -0.082206125 KWENPGLGAESHTDSLRNS(ph)STEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KWENPGLGAESHTDSLRNSSTEIR 24 2 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KWENPGLGAESHTDS(0.025)LRNS(0.948)S(0.025)T(0.001)EIR 211.73 1.42E-25 566920000 163370 182950 94639 147840 203230 203420 246230 251370 173410 TRUE FALSE 141780.2406 181748.1894 140406.7369 181409.3316 199186.1206 211245.699 222350.6525 197616.4817 152909.6673 0.927215676 1.188598423 0.918233225 1.186382357 1.30263916 1.381506498 1.454130771 1.292374021 1 17.22232009 3.485040985 3.888633322 1.302552338 1.02915413 0.449066323 0.137366204 0.200047261 6.783309754 0.039862647 0.056627339 3055.209422 -3.485040985 -0.273398208 KWESPAQNTAHLDQFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KWESPAQNTAHLDQFER 17 1 P17612-2;P17612;Q15136 P17612-2 PRKACA;KIN27 cAMP-dependent protein kinase catalytic subunit alpha 0 ; 158.58 2.16E-09 1414030000 781010 732690 422270 524030 736240 821000 790700 904120 689560 FALSE TRUE 677797.5497 727876.9111 626481.1844 643019.0208 721590.2644 852584.4013 714018.0357 710780.9739 608041.0023 1.114723427 1.197085243 1.030327202 1.057525756 1.186746061 1.402182415 1.174292577 1.168968821 1 19.21380909 3.168408159 8.521808096 1.194493071 1.102018608 0.142243511 0.104551752 0.556175523 60.88477086 0.032990396 0.037499791 1473.696863 -3.168408159 -0.092474463 KWGLGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KWGLGPK 7 1 O60832;O60832-2;H7C2Q2 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ; 105.12 0.012826 408140000 619410 626220 454880 515410 607200 539070 695600 830300 568620 FALSE TRUE 537553.3991 622106.3196 674861.4895 632441.718 595117.908 559808.3717 628140.8191 652746.8064 501398.3914 1.072108344 1.240742552 1.345958625 1.261355698 1.186916269 1.116494152 1.252777891 1.301852614 1 18.93559784 3.224219482 23.8987809 1.191220748 1.239085487 0.051648768 0.104349096 522.4775795 870678.5154 0.032337341 0.036853256 1675.789566 -3.224219482 0.047864739 KWQDEDGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KWQDEDGKK 9 2 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ; 121.36 0.00034649 2408200000 9499200 6249500 6399000 6508600 5081300 4261400 9772500 11272300 9240700 FALSE TRUE 8243856.652 6208446.623 9493577.803 7986477.108 4980192.071 4425338.815 8824764.454 8861806.366 8148274.973 1.011730296 0.761933863 1.165102778 0.980143298 0.611195877 0.54310131 1.083022417 1.087568399 1 22.95806324 KWQIFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KWQIFK 6 1 B4DZG7;F8VYN9;P40616-2;P40616;F8W1Z8 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ; 119.7 0.033331 1839050000 3219400 3136000 1759560 2030730 3018100 2443470 3504000 4417300 3989200 FALSE TRUE 2793948.133 3115399.41 2610489.101 2491838.284 2958045.715 2537471.872 3164182.619 3472694.77 3517601.321 0.794276519 0.885660177 0.742121936 0.708391332 0.84092694 0.72136426 0.899528494 0.987233758 1 21.74616055 1.992722591 3.370043954 0.987538849 0.784469653 0.727716941 0.053872647 0.123778707 2.849885521 0.029580161 0.01524319 98.33827607 -1.992722591 -0.203069196 KWQVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KWQVSR 6 1 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 ; 151.17 0.016705 1604680000 2037390 1803950 1059310 1333120 1811920 1726800 1854810 2098000 1839690 FALSE TRUE 1768143.749 1792099.734 1571595.859 1635825.271 1775866.337 1793231.113 1674930.812 1649359.027 1622203.944 1.089963907 1.104731461 0.968802884 1.008396803 1.09472446 1.105428895 1.03250323 1.016739623 1 20.62952378 1.862962739 3.183322634 1.008403774 1.059138445 0.197687741 0.044093773 0.463952251 8.145279797 0.03035961 0.013102191 72.93949274 -1.862962739 0.050734671 KWS(ph)LNTYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KWSLNTYK 8 1 P53367;P53367-2 P53367 ARFIP1 Arfaptin-1 1 KWS(0.967)LNT(0.033)YK;KWS(1)LNTYK 174.57 0.00016609 3662700000 8301400 5032300 2325570 4862300 4600200 1424920 11405400 8331500 7042200 TRUE FALSE 7204348.957 4999242.49 3450223.431 5966359.531 4508665.02 1479737.594 10299306.06 6549873.561 6209679.139 1.16018055 0.805072594 0.555620243 0.960816074 0.72607053 0.238295339 1.658589089 1.054784541 1 22.56608729 2.233740595 24.99998532 1.21719794 0.744806625 0.385717247 0.295127839 128.8509985 668301.3398 0.115629499 0.080784826 171.2933864 -2.233740595 -0.472391315 KY(ph)Y(ph)KYS(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KYYKYSK 7 2 Q5TBB1;A0A2R8YEC1;A0A2R8YEH2;A0A2R8Y6Y1;A0A2R8YGP2;A0A2R8Y6Q6;A0A2R8YCJ4;A0A087WZJ6;A0A2R8Y761;A0A087WXR7;A0A2R8YCX2;A0A2R8Y7Q3;A0A2R8Y883;A0A2R8Y6M7;A0A2R8YCP1;A0A2R8YE60;A0A2R8Y687;A0A2R8Y4S2;A0A2R8Y7R8;Q5TBB1-2;A0A2R8Y459 Q5TBB1 RNASEH2B Ribonuclease H2 subunit B 3 KY(0.999)Y(0.636)KY(0.636)S(0.729)K;KY(0.993)Y(0.644)KY(0.644)S(0.72)K 45.718 0.054988 889170000 344830 253960 209217 230090 253860 211555 272800 332880 334310 TRUE FALSE 299259.8418 252291.72 310395.041 282335.4512 248808.6827 219693.6577 246343.898 261696.2025 294788.2526 1.015168817 0.855840481 1.052942369 0.957756792 0.844025094 0.745259201 0.83566389 0.887742982 1 18.16931951 3.270085091 7.148720692 0.857782208 0.968747739 0.313060808 0.079265828 0.238952294 39.24388125 0.023514062 0.029880108 1862.45201 -3.270085091 0.110965532 KYAEAVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KYAEAVTR 8 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;; 117.7 0.0032532 3148400000 5045520 4885430 2335190 2758590 3961600 4018770 4662150 5343410 3303710 FALSE TRUE 4378741.748 4853337.289 3464495.695 3384970.022 3882771.911 4173374.682 4210015.411 4200763.354 2913149.167 1.503095618 1.666010564 1.189261344 1.161962477 1.332843493 1.432599034 1.445176738 1.442000774 1 21.47414815 4.243733841 24.99998765 1.311132269 1.58455314 0.404367173 0.148135911 137.6266667 665070.718 0.038524379 0.095646337 17528.0596 -4.243733841 0.273420871 KYAVLYQPLFDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KYAVLYQPLFDKR 13 2 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W543;F8W118;H0YHC3;H0YH88;F8W020;F8VRJ2;F8VVB5 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 0 ; 185.95 4.63E-06 1554930000 2121050 2143760 1129140 1549840 2078460 1854100 2473570 2895780 1200500 FALSE TRUE 1840747.868 2129677.499 1675195.881 1901754.86 2037102.712 1925428.427 2233683.562 2276539.982 1058578.258 1.738886903 2.011828114 1.582496021 1.796517968 1.924376113 1.818881517 2.110078821 2.150563707 1 20.0136965 3.383406612 8.475498031 1.868331174 1.782789117 0 0.33202999 1.708343726 137.1546197 0.094587631 0.122172026 2417.723392 -3.383406612 -0.085542057 KYCEDESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KYCEDESR 8 1 Q92797;A0A087WUE9 Q92797 SYMPK Symplekin 0 70.552 0.081833 58611000 262250 208630 124470 147380 183760 183110 219500 256760 235130 FALSE TRUE 227592.998 207259.4958 184664.1083 180844.8816 180103.5355 190154.3602 198212.9238 201853.8721 207333.1993 1.097716134 0.999644517 0.890663478 0.872242758 0.868667132 0.917143809 0.956011505 0.97357236 1 17.66159162 4.557137468 3.125265166 0.927446647 1.097552437 0.628006092 0.04291833 0.212245039 3.589202641 0.012585744 0.069214871 36069.2796 -4.557137468 0.17010579 KYCQVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KYCQVIR 7 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ; 84.244 0.034775 887590000 671560 927220 570700 707250 937650 949170 921150 919030 967120 FALSE TRUE 582811.6445 921129.0308 846692.4289 867841.9221 918992.5995 985685.1841 831817.0148 722502.5864 852788.1753 0.683419003 1.080138137 0.992851981 1.017652387 1.077632906 1.15583824 0.975408711 0.847223973 1 19.70182791 7.448111788 9.683528837 0.983216185 0.016953891 0 0.132539446 0 0 0.029547536 0 28061558.52 -7.448111788 -0.966262294 KYDAFLASESLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KYDAFLASESLIK 13 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ; 191.06 6.23E-06 3616100000 8215400 7007700 4743600 6104300 6335700 4861600 9196500 10011300 7700000 FALSE TRUE 7129714.075 6961665.957 7037620.826 7490374.613 6209631.966 5048628.898 8304624.845 7870461.403 6789714.772 1.050075639 1.025325244 1.036511998 1.103194297 0.914564481 0.743570101 1.223118367 1.159174084 1 22.69491954 QKS(ph)DAEEDGGTVS(ph)QEEEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QKSDAEEDGGTVSQEEEDR 19 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 2 QKS(1)DAEEDGGT(0.14)VS(0.86)QEEEDR;QKS(1)DAEEDGGT(0.067)VS(0.933)QEEEDR;QKS(1)DAEEDGGT(0.001)VS(0.999)QEEEDR;QKS(1)DAEEDGGT(0.001)VS(0.999)QEEEDR 186.67 1.14E-14 3148140000 3103440 2355730 2764860 3748900 3789940 3288620 2432300 4835530 8838520 TRUE FALSE 2693312.541 2340255.055 4101955.544 4600145.043 3714527.609 3415135.339 2196415.92 3801489.54 7793640.234 0.345578248 0.300277532 0.526320875 0.590243443 0.476610095 0.438195148 0.281821569 0.487768158 1 22.89386591 1.245365392 4.616037397 1.041578432 0.427965184 0.777967234 0.096103945 0.092145811 4.29442566 0.182421137 0.025843387 17.5940326 -1.245365392 -0.613613248 KYDEVLHMVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KYDEVLHMVR 10 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 124.92 0.00027439 129310000 207150 211590 126610 143580 209230 182080 205550 222970 222030 FALSE TRUE 179774.6026 210200.0514 187839.0195 176182.0335 205066.7324 189084.7354 185615.7926 175289.6007 195781.8663 0.918239294 1.073644129 0.95943012 0.899889437 1.047424545 0.965792895 0.948074488 0.895331135 1 17.57888762 2.265537835 3.825441582 0.935993676 0.981393927 0.04654141 0.057641267 0.487620476 15.36150055 0.023043002 0.016297318 184.3053045 -2.265537835 0.045400251 KYDVDTLDMVFLDHWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KYDVDTLDMVFLDHWK 16 1 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ;;;; 306.26 9.05E-47 10783110000 19599590 16600490 13250620 16362980 14704890 12804200 20985680 24577070 22521790 FALSE TRUE 17009454.52 16491440.29 19658664.15 20078444.7 14412291.46 13296785.86 18950491.98 19321454.84 19859289.64 0.856498638 0.83041441 0.98989765 1.011035393 0.725720392 0.669549923 0.954238159 0.972917722 1 24.24331068 2.02530369 24.99501493 0.978240635 0.851258533 0.261729963 0.102464646 331.2049969 327163.2219 0.045688076 0.030801636 105.9994691 -2.02530369 -0.126982102 KYEDICPSTHNMDVPNIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KYEDICPSTHNMDVPNIK 18 1 P63241;P63241-2;I3L397;I3L504;Q6IS14;F8WCJ1;C9J7B5;C9J4W5;Q9GZV4 P63241 EIF5A;EIF5AL1;EIF5A2 Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A;Eukaryotic translation initiation factor 5A-1-like;Eukaryotic translation initiation factor 5A-2 0 ;;;;; 233.49 6.24E-24 4819210000 3890250 3219200 1498290 2693430 2992450 2630810 3606930 4598880 4159170 FALSE TRUE 3376143.606 3198052.863 2222868.055 3305014.448 2932906.1 2732018.963 3257130.484 3615445.301 3667477.661 0.920562828 0.872003366 0.606102684 0.901168256 0.799706602 0.744931317 0.888111881 0.985812494 1 21.80635675 1.899561591 2.957841803 0.993502672 0.805248169 0.421413875 0.088928279 0.243546856 3.787741084 0.056412525 0.024521616 79.35267858 -1.899561591 -0.188254503 KYEDICPSTHNMDVPNIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KYEDICPSTHNMDVPNIKR 19 2 P63241;P63241-2;I3L397;I3L504;Q6IS14;F8WCJ1;C9J7B5;C9J4W5;Q9GZV4 P63241 EIF5A;EIF5AL1;EIF5A2 Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A;Eukaryotic translation initiation factor 5A-1-like;Eukaryotic translation initiation factor 5A-2 0 155.49 1.52E-08 585930000 1471600 1127700 329420 642950 1165000 863660 1478500 1667100 296280 FALSE TRUE 1277124.331 1120292.064 488728.6138 788941.6244 1141818.779 896885.5591 1335115.298 1310603.638 261254.1159 4.888437171 4.288131731 1.870702064 3.01982467 4.370529342 3.433000686 5.110408664 5.01658561 1 17.99509424 KYEEIDNAPEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KYEEIDNAPEER 12 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ; 152.16 0.00010067 806550000 840270 740890 581120 928480 931840 836390 812900 957240 949290 FALSE TRUE 729226.1905 736023.0448 862151.5757 1139305.575 913298.2071 868566.4645 734065.0831 752541.6753 837066.0176 0.871169269 0.879289123 1.029968434 1.361070156 1.091070702 1.037631974 0.876950047 0.899023087 1 19.67498188 2.309924143 6.518836965 0.918145294 1.054331067 0.14254166 0.137085869 0.402266864 28.89240652 0.05679611 0.043533897 204.1381352 -2.309924143 0.136185773 KYEEVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 KYEEVAR 7 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;P06753-7;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;H0YL42;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;H7BYY1;P09493-3;P67936;P67936-2 TPM3;TPM1;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain 0 ;;;;;;;;; 143.01 0.0039293 70235083200 55230626 54018012 33022738 41216335 45010143 43489929 52981997 61743445 55389396 FALSE TRUE 47931758.84 53663164.12 48992644.55 50575133.81 44114529.22 45163014.71 47843811.09 48540089.77 48841324.7 0.981377125 1.098724583 1.003098193 1.035498814 0.903221391 0.92468857 0.979576442 0.993832376 1 25.54159899 3.281886624 24.9998563 0.964129488 1.032708612 0.405228107 0.041567273 146.5176874 84542.25087 0.01226056 0.01582822 1913.756258 -3.281886624 0.068579124 KYEFGESDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KYEFGESDLR 10 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 118.48 0.0023413 3334520000 15047200 13632400 8952420 10543700 14077300 13011800 15360000 17318000 14828000 FALSE TRUE 13058674.4 13542847.87 13281840.26 12937808.24 13797189.27 13512372.37 13870389.56 13614680.47 13075050.73 0.998747513 1.035777845 1.015815581 0.989503483 1.055230267 1.033447031 1.060828738 1.041271713 1 23.64031321 3.22894503 24.99943323 1.040010132 1.012223333 0.325894419 0.019933373 237.7327226 618078.2339 0.005938426 0.006810682 1694.123355 -3.22894503 -0.027786799 KYEGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KYEGGR 6 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 124.37 0.029477 11783390000 9479070 8507870 6007190 7147160 4433710 8951290 8627710 8193080 8418300 FALSE TRUE 8226386.883 8451981.242 8912287.177 8770031.916 4345487.845 9295651.919 7790996.012 6441053.601 7423098.164 1.108214751 1.138605614 1.200615562 1.181451696 0.585400833 1.252260406 1.049561226 0.86770422 1 22.82359002 KYELGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 KYELGR 6 1 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ;;;; 119.89 0.033075 4297100000 3747670 3490980 3013440 3839500 3448750 3448510 3650990 4101150 8601970 FALSE TRUE 3252405.914 3468047.523 4470749.663 4711317.158 3380126.622 3581176.411 3296917.552 3224150.988 7585054.906 0.428791348 0.457221149 0.589415597 0.621131583 0.445629816 0.472135859 0.434659682 0.425066269 1 22.85472819 1.234552925 24.99978046 1.000000746 0.484289884 0.851595973 0.067661607 47.65069155 297200.5618 0.134920008 0.018162513 17.16140833 -1.234552925 -0.515710863 KYELGRPAANTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KYELGRPAANTK 12 2 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 64.244 0.03654 3317900000 1489200 1098100 729160 941330 1325800 1245800 1159700 1577500 1252700 FALSE TRUE 1292398.447 1090886.509 1081784.215 1155073.364 1299419.174 1293726.732 1047232.472 1240163.901 1104607.233 1.170007228 0.98757864 0.979338341 1.045686946 1.176363086 1.171209724 0.948058677 1.122719338 1 20.07510205 4.769029803 21.92008473 1.059198408 1.170008187 0.168954487 0.080176946 4112.930431 2958649.963 0.01982706 1.709209687 58752.96692 -4.769029803 0.110809779 KYEMFAQTLQQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KYEMFAQTLQQSR 13 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 271.08 7.11E-32 8971030000 8403850 6442560 3969140 5091814 6464270 6232410 6783490 7818950 6711110 FALSE TRUE 7293259.93 6400238.399 5888629.38 6247988.192 6335643.674 6472174.846 6125628.184 6146928.39 5917730.221 1.232442112 1.081536021 0.995082432 1.055808217 1.070620565 1.093692109 1.035131369 1.038730757 1 22.4966125 4.706334679 3.447800293 1.043861243 1.249761165 0.801989545 0.029631857 0.116857921 2.412899494 0.007549955 0.059921788 50855.1195 -4.706334679 0.205899922 KYEMMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KYEMMK 6 1 P80303-2;P80303;E9PKG6;Q2L696;E9PLR0;E9PLE9;A0A2R8Y6G7 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 81.958 0.097018 314400000 231500 228360 220140 215300 257750 246590 313280 350030 287620 FALSE TRUE 200906.6885 226859.8881 326600.4403 264187.1557 252621.2793 256076.4769 282898.1538 275178.8084 253617.8913 0.792162917 0.894494813 1.287765775 1.04167397 0.996070419 1.009694054 1.115450304 1.085013392 1 17.952297 4.462317233 24.93891553 1.074080428 0.817745813 0.578594665 0.084928835 128.7628429 216914.4961 0.020744133 0.054928546 28994.6074 -4.462317233 -0.256334614 KYEPPVPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KYEPPVPTR 9 1 P62191 P62191 PSMC1 26S protease regulatory subunit 4 0 113.47 0.0028778 166230000 419970 378730 259470 329680 363670 330250 400510 500660 440210 FALSE TRUE 364469.9004 376242.0977 384950.5599 404538.8828 356433.6785 342954.9312 361668.6018 393597.7551 388168.8753 0.938946741 0.969274256 0.991708981 1.042172386 0.91824384 0.883519914 0.93173004 1.013985871 1 18.56632492 1.691641558 7.774274064 1.006483199 0.955139312 0.209474425 0.042866765 0.209519709 24.6731482 0.027419193 0.012180314 49.16336016 -1.691641558 -0.051343887 KYESVLQLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KYESVLQLGR 10 1 A0A087X1E4;P53365;P53365-2;P53365-3;E9PRV8 A0A087X1E4 ARFIP2 Arfaptin-2 0 ; 155.97 1.89E-05 1473370000 1698560 1357830 1011180 1297760 1493820 1502950 1675390 1845950 2125950 FALSE TRUE 1474090.992 1348910.325 1500190.03 1592436.243 1464095.905 1560769.459 1512910.936 1451207.958 1874622.613 0.786340132 0.719563669 0.800262421 0.849470305 0.781008345 0.832577954 0.807048269 0.77413339 1 20.83816876 1.235211849 24.99975406 1.000000286 0.793933387 0.775556191 0.034860715 46.37089088 346117.9017 0.061852468 0.00877368 17.18746588 -1.235211849 -0.206066899 KYGLNMCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KYGLNMCR 8 1 A0A2R8Y851;P62273;P62273-2;A0A2R8Y6P7;A0A087WTT6 A0A2R8Y851 RPS29 40S ribosomal protein S29 0 ; 132.08 0.0015671 3994000000 2293340 3972400 2033220 2298080 3698900 3238400 3929600 4199800 3255300 FALSE TRUE 1990269.308 3946305.043 3016491.993 2819894.188 3625299.127 3362983.344 3548507.997 3301705.453 2870462.142 0.693361978 1.374797802 1.050873289 0.98238334 1.262967058 1.171582545 1.236214874 1.150234802 1 21.4528516 3.246159179 24.99645512 1.168224487 1.052137177 0.124726289 0.176361369 425.660099 1400255.797 0.048248022 0.061057789 1762.621971 -3.246159179 -0.11608731 KYHNPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KYHNPK 6 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 77.906 0.04621 2013680000 4698500 3806800 2534950 3386300 2344960 2933100 4467700 5131200 4663200 FALSE TRUE 4077581.321 3781792.88 3760860.299 4155211.171 2298299.884 3045938.255 4034423.142 4033932.811 4111921.808 0.991648555 0.919714201 0.914623496 1.010527769 0.558935697 0.740757825 0.98115269 0.981033444 1 21.9713814 2.119378762 11.50719502 0.986703544 0.85514782 0.185611598 0.129751702 0.704221685 67.28730688 0.056618819 0.038168451 131.6372383 -2.119378762 -0.131555724 KYHNVGLSK ddPTM_MDA-MB-175_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 ; 116.3 0.00086689 2665500000 9196500 7382700 4178900 5806500 6636100 5763400 7893300 9303600 8199100 FALSE TRUE 7981159.224 7334202.558 6199830.018 7124954.572 6504054.593 5985121.727 7127808.981 7314097.541 7229811.738 1.10392352 1.01443894 0.857536855 0.985496556 0.899616038 0.827839222 0.985891367 1.011658091 1 22.78552665 4.492754931 5.341204894 0.943034657 1.086581762 0.431566497 0.061886178 0.174612224 15.47544055 0.016532271 0.057863877 31099.60912 -4.492754931 0.143547105 KYIEIDS(ph)DEEPRGELLSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KYIEIDSDEEPRGELLSLR 19 2 E7EW05;Q9NVU7-2;Q9NVU7 E7EW05 SDAD1 Protein SDA1 homolog 1 KYIEIDS(1)DEEPRGELLSLR 197.33 4.14E-16 147940000 160670 164560 79227 78523 139250 127230 180500 176850 36242 TRUE FALSE 139437.0524 163478.9945 117541.4422 96352.8473 136479.1974 132124.6204 162995.1378 139032.0037 31957.51205 4.363201122 5.115510691 3.678053599 3.015029679 4.270645263 4.13438381 5.100370065 4.350526522 1 14.96386748 4.229091815 24.92081017 3.806926947 4.739355923 0.13106897 1.110369936 389.3816477 1024817.364 0.284462144 0.604898245 16946.96043 -4.229091815 0.932428976 KYKPLDLRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KYKPLDLRPK 10 3 P42766 P42766 RPL35 60S ribosomal protein L35 0 ; 79.693 0.011495 1359400000 3588200 3164800 2516700 2723200 2724900 1952890 4267300 4432300 3546900 FALSE TRUE 3114010.279 3144010.22 3733784.538 3341544.182 2670679.821 2028018.942 3853457.903 3484487.137 3127589.523 0.99565824 1.005250273 1.193821795 1.068408804 0.853909953 0.648428743 1.232085565 1.114112678 1 21.57661975 KYNDDSDDSYFTSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KYNDDSDDSYFTSSSR 16 1 H0Y6A0 H0Y6A0 ARFGAP3 0 ; 130.77 7.72E-05 192960000 189179 189256 146540 171715 209525 168762 200600 239460 221000 FALSE TRUE 164178.5158 188012.7649 217407.2341 210705.5152 205355.8624 175254.3833 181145.8429 188253.3425 194873.6318 0.842487074 0.964793252 1.11563187 1.081241794 1.053789887 0.899323227 0.929555432 0.966027783 1 17.57217937 2.746327273 24.97330136 0.94963262 1.018638807 0.13590763 0.077625146 1204.333666 3872474.582 0.026841543 0.026362567 557.6057883 -2.746327273 0.069006187 KYNRFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KYNRFEK 7 2 P62280;M0QZC5;M0R1H5 P62280 RPS11 40S ribosomal protein S11 0 ; 72.875 0.028358 2621600000 1465950 1338360 754490 894160 1240140 972130 1519870 1608260 422930 FALSE TRUE 1272220.993 1329568.225 1119363.888 1097192.694 1215463.64 1009528.47 1372473.241 1264346.114 372931.6972 3.41140483 3.565178919 3.001525202 2.942074119 3.259212476 2.707006344 3.680226839 3.390288688 1 18.5085519 1.236365751 24.99135099 0.999997092 3.24848519 0.851415731 0.294682281 21.78333262 247970.5327 0.474465876 0.073692366 17.23319296 -1.236365751 2.248488097 KYNWSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 KYNWSAK 7 1 P61927;D6RG19 P61927 RPL37 60S ribosomal protein L37;Ribosomal protein L37 0 ; 128.61 0.0059987 3460400000 3993900 4388600 2829400 3587000 4506400 3731100 4991600 6074300 5290600 FALSE TRUE 3466095.996 4359770.998 4197707.304 4401483.174 4416731.457 3874637.831 4507515.4 4775358.215 4665151.295 0.742976117 0.934540109 0.899800894 0.943481335 0.946749886 0.830549233 0.966209907 1.02362344 1 22.15349244 7.999885759 0.199040872 1.030860347 1.62E-10 0.499160717 0.058019616 99.09645283 1.465268706 0.402376244 30.77325081 99973698.53 -7.999885759 -1.030860347 KYPS(ph)PQK ddPTM_MDA-MB-175_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 94.309 0.0087559 5527190000 12462600 9127430 7634770 8015970 8598820 6490030 12028800 13829900 12374300 TRUE FALSE 10815635.83 9067471.311 11326970.31 9836118.505 8427720.305 6739705.654 10862248.83 10872483.51 10911424.35 0.991221264 0.831007119 1.038083567 0.901451377 0.772375818 0.617674232 0.995493208 0.996431186 1 23.3793361 2.072107912 25 0.997406788 0.858813368 0.246006666 0.114449459 62.99292604 21838.30569 0.049093064 0.033098534 118.0613953 -2.072107912 -0.138593419 KYQEDS(ph)DPERSDYEEQQLQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KYQEDSDPERSDYEEQQLQK 20 2 Q6P6C2-3;Q6P6C2;Q6P6C2-1 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 KYQEDS(1)DPERSDYEEQQLQK 186.82 1.64E-17 370120000 368690 250800 246300 285640 238450 187600 313450 366840 334570 TRUE FALSE 319966.6824 249152.4783 365411.5038 350498.9277 233705.3115 194817.0934 283051.6672 288394.1208 295017.5157 1.084568425 0.844534528 1.238609521 1.188061417 0.792174359 0.660357718 0.95944021 0.977549147 1 18.17044109 3.23635505 24.998792 0.88559776 1.082176122 0.355426776 0.140877837 76.92816584 871936.7791 0.045236351 0.053816313 1723.276835 -3.23635505 0.196578362 KYS(ph)LNGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KYSLNGR 7 1 O95644-6;O95644;K7ER53;O95644-8;O95644-11;O95644-3;O95644-10;O95644-2;O95644-5;O95644-4 O95644-6 NFATC1 "Nuclear factor of activated T-cells, cytoplasmic 1" 1 KYS(1)LNGR 86.624 0.012213 281500000 293880 256270 180180 243770 255320 244410 307900 329300 292000 TRUE FALSE 255043.0134 254586.5455 267315.6507 299121.7043 250239.6315 253812.6109 278039.9054 258881.7576 257480.0926 0.990534883 0.988762055 1.038199295 1.1617275 0.97187953 0.985756251 1.079850106 1.00544378 1 17.97410137 4.240330749 24.507502 1.035047049 0.989648446 0.106078435 0.054355953 82.66361805 1144349.239 0.013840211 0.032949169 17391.24805 -4.240330749 -0.045398603 KYSCDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 1361870000 2549140 2330500 1445600 1823540 1454360 2195210 2441500 2608860 2454760 FALSE TRUE 2212264.69 2315190.792 2144696.995 2237602.628 1425421.081 2279661.149 2204723.706 2050975.591 2164561.069 1.022038473 1.069589038 0.990823048 1.033744282 0.658526618 1.05317479 1.018554633 0.947524937 1 21.04564307 KYTGEDFDEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 KYTGEDFDEDLR 12 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;;;; 148.91 0.00010715 1806930000 6981790 6624950 4097240 4373720 6452620 6083440 7330050 8061940 5081510 FALSE TRUE 6059128.762 6581430.267 6078678.968 5366839.974 6324225.486 6317473.873 6619182.879 6337956.869 4480779.677 1.35224876 1.468813631 1.356611886 1.197746902 1.41141184 1.409905045 1.477239087 1.414476347 1 22.09531836 1.236280109 24.99940224 0.999999497 1.388981986 0.707580206 0.077975261 35.78292797 392167.8194 0.129484905 0.019970616 17.22979493 -1.236280109 0.388982489 KYTLENKEEGS(ph)LSDTEADAVSGQLPDPTTNPSAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KYTLENKEEGSLSDTEADAVSGQLPDPTTNPSAGK 35 2 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 KYT(0.014)LENKEEGS(0.329)LS(0.329)DT(0.329)EADAVSGQLPDPTTNPSAGK 178.8 2.21E-20 335890000 747510 492760 417620 426310 467490 278220 727550 822780 372270 TRUE FALSE 648724.6596 489523.0271 619582.4289 523110.2012 458187.8636 288923.3034 656992.313 646834.8999 328260.6647 1.976248541 1.491263133 1.887470829 1.59358174 1.395804959 0.880164255 2.001434785 1.970491653 1 18.32448236 7.99996178 0.903016577 1.552732451 198.684731 0.114965774 0.377575168 2674.263606 5.759430144 0.129099293 1086626.643 99991199.89 -7.99996178 197.1319986 KYTMGDAPDYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KYTMGDAPDYDR 12 1 A0A0A0MR85;Q03013-3;Q03013-2;Q03013;E9PLF1;E9PHN7;E9PHN6;P28161-2;P28161;F6XZQ7;H3BQT3;B9ZVX7;E7EWW9;P09488-2;P09488 A0A0A0MR85;F6XZQ7;H3BQT3 GSTM4;GSTM2;GSTM1 Glutathione S-transferase Mu 4;Glutathione S-transferase Mu 2;Glutathione S-transferase Mu 1 0 75.764 0.052804 271060000 282760 270580 172310 209110 274130 261220 286560 326470 269850 FALSE TRUE 245392.5496 268802.5422 255639.6923 256591.6215 268675.3493 271269.3024 258769.4553 256656.9311 237948.6404 1.03128368 1.129666224 1.074348195 1.078348761 1.129131685 1.140033 1.087501298 1.07862323 1 17.86029069 1.157315821 2.099935525 0.95392505 1.098421384 0.463096217 0.03208621 0.813683005 2.966599852 0.245538499 0.00839549 14.36533707 -1.157315821 0.144496333 KYVATLGVEVHPLVFHTNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 KYVATLGVEVHPLVFHTNR 19 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ;; 263.31 1.19E-31 2280480000 4483080 4109248 1958949 2661123 3524626 3610281 4061744 4907383 2171864 FALSE TRUE 3890629.619 4082254.079 2906303.289 3265371.65 3454492.838 3749170.846 3667836.692 3857977.335 1915108.712 2.031545047 2.131604359 1.517565698 1.705058115 1.803810309 1.95768043 1.915210697 2.014495214 1 20.86899486 1.23332299 24.9836973 0.999998612 1.882537128 0.713524999 0.176152051 96.85275916 461939.0524 0.375602005 0.045427944 17.11287546 -1.23332299 0.882538516 KYVIS(ph)DEEEEDDD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 KYVISDEEEEDDD 13 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 KYVIS(1)DEEEEDDD;KYVIS(1)DEEEEDDD;KYVIS(1)DEEEEDDD;KYVIS(1)DEEEEDDD;KYVIS(1)DEEEEDDD;KYVIS(1)DEEEEDDD;KYVIS(1)DEEEEDDD;KYVIS(1)DEEEEDDD 180.85 1.33E-05 4299670000 8140460 6914320 4758470 5865820 6947720 6030920 7662590 8793430 7196820 TRUE FALSE 7064677.586 6868899.377 7059682.008 7197744.084 6809473.965 6262933.395 6919473.201 6913023.425 6346020.138 1.113245378 1.082394828 1.112458179 1.134213874 1.073030627 0.986907268 1.090364205 1.089347855 1 22.59742067 3.014679808 13.84247446 1.051040396 1.108071646 0.450896816 0.035151624 1.474173334 1385.74958 0.011021805 0.012432916 1034.379269 -3.014679808 0.05703125 KYVIYIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KYVIYIER 8 1 P61254;E5RIT6;J3QRI7;J3QQQ9;J3QQV1;J3QRC4;J3KS10;Q9UNX3 P61254;Q9UNX3 RPL26;RPL26L1 60S ribosomal protein L26;60S ribosomal protein L26-like 1 0 71.349 0.078523 671960000 1357700 1573700 974530 1214400 1546500 1595000 1712900 1791300 1797400 FALSE TRUE 1178276.505 1563362.261 1445815.968 1490148.081 1515727.676 1656360.682 1546783.222 1408244.435 1584913.42 0.743432727 0.986402312 0.912236561 0.940207877 0.956347304 1.0450796 0.975941779 0.888530829 1 20.5959726 4.743220228 24.90294975 0.957917185 0.743432635 0.706578135 0.044374431 275.5231159 1472459.893 0.011253813 0.088217254 55363.07805 -4.743220228 -0.21448455 KYYLHDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KYYLHDDR 8 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;;; 131.44 0.00065239 745910000 2377050 2144310 1308550 1524750 2140850 2025160 2093480 2430840 2232900 FALSE TRUE 2062916.82 2130223.886 1941369.157 1870967.792 2098251.274 2103069.216 1890454.632 1911023.783 1968929.106 1.047735449 1.081920055 0.986002569 0.950246399 1.065681475 1.068128461 0.960143576 0.970590448 1 20.90897974 LAAAEETAVS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LAAAEETAVSPR 12 0 Q9BUH6 Q9BUH6 C9orf142 Protein PAXX 1 LAAAEETAVS(1)PR;LAAAEETAVS(1)PR;LAAAEETAVS(1)PR;LAAAEETAVS(1)PR;LAAAEETAVS(1)PR 237.65 4.32E-16 15465600000 2604070 2807280 1935621 2322280 2610870 2554940 2322310 2992050 4102600 TRUE FALSE 2259935.552 2788838.793 2871693.79 2849589.168 2558918.795 2653230.195 2097092.734 2352223.392 3617595.302 0.62470657 0.770909557 0.793812892 0.787702584 0.707353527 0.733423718 0.579692464 0.650217395 1 21.78659959 1.231934553 24.99743479 1.000000497 0.705672595 0.63052637 0.07073286 167.7852911 632925.935 0.178902806 0.019044131 17.05825305 -1.231934553 -0.294327902 LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK 37 2 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;;; 378.28 6.32E-162 19474400000 6908360 3886480 4207707 3538155 3314743 2271431 4890900 6584750 4240960 FALSE TRUE 5995402.722 3860949.457 6242568.179 4341547.17 3248786.099 2358814.42 4416581.271 5176652.455 3739598.54 1.60322095 1.032450252 1.669315065 1.16096611 0.868752639 0.630766751 1.181030858 1.384280264 1 21.83445197 3.490997386 23.60944678 1.049419247 1.398140928 0.354349151 0.255849134 430.1686001 731905.9839 0.076242629 0.107905778 3097.400655 -3.490997386 0.348721681 LAADFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LAADFQR 7 0 O94874;O94874-3 O94874 UFL1 E3 UFM1-protein ligase 1 0 83.801 0.051212 197750000 122700 129000 86657 94192 127850 141400 150810 158690 168990 FALSE TRUE 106484.8841 128152.5905 128564.6151 115579.7332 125306.0351 146839.7495 136184.4694 124755.3784 149012.1947 0.714605166 0.860014113 0.862779152 0.775639426 0.840911278 0.985421024 0.913914929 0.837215898 1 17.18507088 2.9504251 8.277367309 0.916873159 0.811114965 0.49929558 0.06109919 0.340400968 53.19263544 0.019631699 0.019777123 892.1237468 -2.9504251 -0.105758193 LAAELEDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LAAELEDRR 9 1 Q9NQG5;A2A2M0;A0A087X2D2 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ;;; 161.28 0.00010366 1687830000 1225410 1274960 741210 887920 1270710 1249250 1228050 1414180 801690 FALSE TRUE 1063468.964 1266584.704 1099661.635 1089535.807 1245425.357 1297309.456 1108953.9 1111768.612 706915.1215 1.50437999 1.791706904 1.555578034 1.541254068 1.761774956 1.835170046 1.568722844 1.572704528 1 19.43117748 1.089809044 2.127537187 0.569437861 1.660249473 0.7589036 0.114159921 0.560921608 1.776708725 1.384759323 0.03024911 12.29727949 -1.089809044 1.090811613 LAAFADALEFADEEKES(ph)PVEFTGHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LAAFADALEFADEEKESPVEFTGHK 25 1 Q5SY16 Q5SY16 NOL9 Polynucleotide 5-hydroxyl-kinase NOL9 1 LAAFADALEFADEEKES(0.998)PVEFT(0.002)GHK 157.96 9.60E-10 39601000 70822 42371 32832 36751 40443 39477 54189 64302 65199 TRUE FALSE 61462.69326 42092.66211 48709.66502 45095.87625 39638.26343 40995.70574 48933.75912 50551.5177 57491.24849 1.069079118 0.732157732 0.847253561 0.784395494 0.68946604 0.713077326 0.851151443 0.879290658 1 15.81105474 1.378695745 1.769818947 1.034056997 0.799687144 0.240415932 0.106061703 0.937809962 3.639949228 0.348978046 0.029164956 23.91639649 -1.378695745 -0.234369853 LAAFGQLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAAFGQLHK 9 0 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ; 133.86 0.00026505 2066040000 3064600 3169800 1906840 2262100 2905900 2624900 2933000 3300300 3422000 FALSE TRUE 2659605.345 3148977.375 2828994.202 2775744.379 2848078.275 2725881.602 2648558.111 2594556.528 3017455.058 0.88140678 1.043587167 0.937543111 0.919895848 0.94386767 0.903371069 0.87774567 0.85984927 1 21.52490085 3.288080539 1.270261375 0.90072986 0.961571489 0.07116469 0.054589082 0.785688771 2.699718669 0.020887614 0.030915453 1941.245844 -3.288080539 0.060841629 LAAGRPFNT(ph)YPR ddPTM_MDA-MB-175_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 155.56 0.00011711 2430830000 991990 1234440 531130 700260 936650 864380 654030 863990 1007960 TRUE FALSE 860896.0081 1226330.882 787986.2445 859264.7358 918012.4975 897633.2579 590602.2713 679232.4621 888800.1171 0.968604742 1.379760037 0.886573066 0.966769377 1.03286721 1.009938276 0.664493917 0.76421284 1 19.76149948 3.121660132 0.720925102 0.799105392 1.135707615 0.270986807 0.160152693 0.831763843 1.122530715 0.13100013 0.163448658 1323.305545 -3.121660132 0.336602222 LAAPSVSHVS(ph)PR ddPTM_MDA-MB-175_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 178.22 1.44E-05 1050470000 486470 498450 177008 328356 526880 470140 403430 496160 462270 TRUE FALSE 422181.7569 495175.6491 262609.6609 402914.2484 516396.1188 488226.59 364305.4207 390060.0451 407620.9672 1.035721395 1.214794353 0.644249639 0.988453197 1.266853671 1.197746508 0.893735725 0.956918501 1 18.63686874 2.19274137 24.99971154 0.949260597 1.05262866 0.078606921 0.173251053 386.4537226 210852.4403 0.074239068 0.05005218 155.8624038 -2.19274137 0.103368063 LAAQLGAPTS(ph)PIPDSAIVNTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LAAQLGAPTSPIPDSAIVNTR 21 0 Q9H8Y5;B8ZZS4 Q9H8Y5 ANKZF1 Ankyrin repeat and zinc finger domain-containing protein 1 1 LAAQLGAPT(0.018)S(0.982)PIPDSAIVNTR 164.53 1.67E-11 123700000 216650 200320 126610 150470 218990 197070 173440 238950 262250 TRUE FALSE 188019.1536 199004.0847 187839.0195 184636.5133 214632.5274 204651.4104 156619.8155 187852.402 231247.1038 0.813065982 0.860568982 0.812287014 0.798438165 0.928152284 0.884990156 0.67728336 0.812344885 1 17.81907577 5.195181896 7.819399883 0.837262853 0.00038564 0.004345366 0.085577077 80742.29842 67800.04059 0.020929376 1156676.246 156740.7413 -5.195181896 -0.836877212 LAASTEPQGPRPVLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LAASTEPQGPRPVLGR 16 1 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;F5GWK5;F5H3G8;F5H5A8;F5GY07 Q9Y365 STARD10 PCTP-like protein 0 ;;; 188.12 1.12E-09 2261290000 1128580 939120 566495 671730 886440 941800 890140 945390 766560 FALSE TRUE 979435.2935 932950.8589 840453.8768 824256.5633 868801.5783 978031.6554 803814.3598 743225.7055 675938.1501 1.449001352 1.380231104 1.243388728 1.219426013 1.285327035 1.446924775 1.1891833 1.099546912 1 19.36653172 1.802055738 2.188739521 1.024102751 1.326695097 0.68012366 0.081298146 0.18612977 1.698760525 0.074657939 0.024395493 63.39510682 -1.802055738 0.302592346 LADALQELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 LADALQELR 9 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;; 218.2 1.25E-06 4472472000 3635500 3563190 2193838 2587391 3260051 3519460 3251690 3656530 3506280 FALSE TRUE 3155059.464 3539783.17 3254785.395 3174897.672 3195182.363 3654855.904 2936341.604 2874609.515 3091771.573 1.020469782 1.144904495 1.052725054 1.026886236 1.033447099 1.182123523 0.949727862 0.929761286 1 21.5600023 2.193848736 24.9945086 0.953144277 1.074528749 0.505040517 0.054404426 98.7278556 55189.40282 0.021457589 0.014466778 156.2603295 -2.193848736 0.121384472 LADAMAES(ph)PSRDVVGSGTDTALDVAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LADAMAESPSRDVVGSGTDTALDVAVK 27 1 Q9H6U6-7;Q9H6U6-3;Q9H6U6-8 Q9H6U6-7 BCAS3 Breast carcinoma-amplified sequence 3 1 LADAMAES(0.786)PS(0.212)RDVVGSGTDTALDVAVK 72.302 0.0010407 0 20285 18294 14410 14950 18593 20167 20950 20400 19910 TRUE FALSE 17604.28585 18173.82551 21378.7242 18344.626 18223.03568 20942.83754 18918.27222 16037.61875 17556.26248 1.002735398 1.035176224 1.217726394 1.044904974 1.037979222 1.192898407 1.077579709 0.913498461 1 14.09969812 1.753884296 24.99740421 0.956184534 1.090603337 0.362815861 0.071636924 5.088710294 8314.344266 0.037585726 0.018049385 56.73934218 -1.753884296 0.134418803 LADAMAES(ph)PSRDVVGSGTELQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LADAMAESPSRDVVGSGTELQR 22 1 K7ESE9;Q9H6U6-6;Q9H6U6-2;Q9H6U6 K7ESE9 BCAS3 Breast carcinoma-amplified sequence 3 1 LADAMAES(0.996)PS(0.004)RDVVGSGTELQR;LADAMAES(0.934)PS(0.066)RDVVGSGTELQR;LADAMAES(0.983)PS(0.017)RDVVGSGTELQR;LADAMAES(0.884)PS(0.116)RDVVGSGTELQR 211.92 1.65E-23 608880000 362988 319795 244319 298336 405790 417134 448158 463400 382129 TRUE FALSE 315018.2161 317694.2456 362472.4856 366077.7486 397715.5729 433181.4149 404695.7061 364305.5162 336954.1449 0.934899365 0.942841186 1.075732384 1.086431949 1.18032551 1.285579719 1.20104089 1.081172384 1 18.36219275 4.078745087 1.635384972 1.147984659 0.921189261 0.536946919 0.076178884 0.354428251 1.771301967 0.024729243 0.085702922 11987.95454 -4.078745087 -0.226795397 LADDVDLEQVANETHGHVGADLAALCSEAALQAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 LADDVDLEQVANETHGHVGADLAALCSEAALQAIR 35 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;; 315.62 4.55E-105 8339905000 5471276 3740693 2256012 2802414 3770114 3433741 3948502 4400879 3661121 FALSE TRUE 4748233.014 3716120.141 3347026.949 3438744.931 3695096.108 3565839.238 3565576.884 3459785.274 3228307.446 1.470811902 1.151104783 1.036774534 1.065185082 1.144592381 1.104553794 1.104472527 1.071702535 1 21.62234655 4.723598773 3.121911636 1.079919031 1.523524879 0.906194784 0.039704877 0.095777414 1.463175222 0.010184885 0.102519365 52917.43355 -4.723598773 0.443605848 LADELHMPSLPEMMFGDNVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LADELHMPSLPEMMFGDNVLR 21 0 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 ; 176.46 3.74E-13 455850000 684940 649580 390420 546170 586490 599160 649160 749740 691640 FALSE TRUE 594423.4436 645312.8662 579228.4179 670186.2462 574819.9964 622210.0729 586204.5631 589413.9355 609875.1071 0.974664217 1.058106584 0.949749237 1.098890967 0.942520837 1.020225396 0.961187883 0.966450227 1 19.21815431 LADFGVLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LADFGVLHR 9 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ; 133.13 0.0002855 528880000 1120490 983330 578820 974320 867980 1221680 603660 805160 1321910 FALSE TRUE 972414.4075 976870.4405 858739.288 1195554.248 850708.8962 1268678.82 545117.1461 632982.7998 1165635.306 0.834235548 0.838058384 0.736713519 1.025667498 0.729824236 1.088401161 0.467656688 0.543036743 1 20.15268505 2.230481446 24.9995031 0.635291754 0.867680219 0.221820973 0.176841132 230.5343234 713338.5865 0.068713036 0.047234696 170.0127317 -2.230481446 0.232388466 LADHFGGK ddPTM_MDA-MB-175_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 ;;; 98.299 0.0076207 2494500000 9900700 7584950 5018110 6572950 7196050 6491670 8490900 9776600 9171400 FALSE TRUE 8592297.41 7535123.964 7444884.781 8065438.759 7052862.684 6741408.746 7667453.825 7685950.172 8087167.54 1.062460666 0.931738328 0.920580011 0.997313178 0.872105425 0.833593308 0.948101271 0.950388394 1 22.94720307 4.738472743 8.157503382 0.93066265 1.063429688 0.398740322 0.050438356 0.099375448 88.33854017 0.012755851 0.072951177 54761.17305 -4.738472743 0.132767039 LADILS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LADILSPR 8 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 LADILS(1)PR;LADILS(1)PR;LADILS(1)PR;LADILS(1)PR;LADILS(1)PR 111.27 0.0034266 310677000 1867360 1190820 640848 783674 1053513 1088775 877866 1122161 1009685 TRUE FALSE 1620583.645 1182997.425 950764.2363 961619.1594 1032550.152 1130660.879 792730.6904 882195.6028 890321.1895 1.820223604 1.328731068 1.067889035 1.080081178 1.159750172 1.269947174 0.890387312 0.990873421 1 19.76396637 4.746644352 1.684682171 1.055422079 2.10746245 0.848512537 0.101750341 0.387275733 1.058632356 0.030044306 0.665560772 55801.30454 -4.746644352 1.052040371 LADQCTGLQGFLVFHSFGGGTGSGFTSLLMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 LADQCTGLQGFLVFHSFGGGTGSGFTSLLMER 32 0 P68363;F8VQQ4;Q9BQE3;F5H5D3 P68363;Q9BQE3 TUBA1B;TUBA1A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 ;;;;;;;; 416.44 1.23E-186 9009335000 1075939 909273.3 555979.1 989724.7 865003.2 865360 1030108.2 1159574 1371156 FALSE TRUE 933750.9351 903300.2238 824852.4524 1214456.82 847791.3287 898650.9592 930208.4653 911608.1239 1209059.5 0.772295272 0.747109819 0.682226518 1.004464065 0.701199014 0.743264462 0.769365334 0.753981193 1 20.20545381 1.235905643 24.98710638 1.000000306 0.771406262 0.40201742 0.087488982 73.34179552 690109.2187 0.135895506 0.020351124 17.21494514 -1.235905643 -0.228594044 LADS(ph)PPPQVWQLISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LADSPPPQVWQLISK 15 0 Q5HY81;P11441 Q5HY81 UBL4A Ubiquitin-like protein 4A 1 LADS(1)PPPQVWQLISK 76.85 0.028986 151840000 258240 192350 114000 143800 187040 208790 211710 238200 171080 TRUE FALSE 224112.9297 191086.4402 169130.7813 176451.9878 183318.2699 216822.2864 191178.3968 187262.7837 150855.1173 1.485617019 1.266688486 1.121147127 1.169678504 1.215194242 1.437288242 1.267298055 1.241341938 1 17.20280411 -1.999999994 0.027303847 1.24E-07 2.159962489 0.177430538 0.127469014 9668.61159 26.17459306 1414.977154 755.2805422 0.01 1.999999994 2.159962366 LADVAAPPGGPPPPHS(ph)PYSGPPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LADVAAPPGGPPPPHSPYSGPPSR 24 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 LADVAAPPGGPPPPHS(0.993)PYS(0.007)GPPSR;LADVAAPPGGPPPPHS(0.999)PYS(0.001)GPPSR 166.97 7.93E-12 872040000 1026920 747890 528340 836100 1003450 994610 859720 1109510 1487620 TRUE FALSE 891209.9201 742977.0613 783846.9912 1025949.284 983483.3082 1032873.29 776344.4867 872249.9207 1311755.258 0.67940259 0.566399149 0.597555822 0.782119437 0.749746038 0.787397865 0.591836382 0.664948675 1 20.32306714 3.746155518 24.24992654 0.742308974 0.609647168 0.281568741 0.108313787 573.0165934 1829587.98 0.029178628 0.049263186 5573.853095 -3.746155518 -0.132661805 LAEAHQQECCQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LAEAHQQECCQK 12 0 Q9Y5X3;A0A087WUY5 Q9Y5X3 SNX5 Sorting nexin-5 0 ;; 219.43 3.19E-11 718510000 639879 580659 386298 481761 585753 530552 665522 699344 757928 FALSE TRUE 555317.3689 576844.6128 573113.0049 591152.1983 574097.6613 550962.6788 600979.7789 549794.7279 668326.6153 0.830907159 0.863117822 0.857534313 0.884525896 0.859007629 0.824391347 0.899230653 0.822643772 1 19.3501938 1.230329708 24.99996581 1.000000265 0.856108262 0.772540751 0.024692809 137.763383 418399.0837 0.061515987 0.005573921 16.99533418 -1.230329708 -0.143892003 LAEDEAFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 120.15 0.0016539 267247000 467290 400676 279209 341879 380938 417211 367365 435100 504850 FALSE TRUE 405536.4425 398043.933 414235.4063 419507.8522 373358.0791 433261.3771 331737.9988 342057.251 445167.2081 0.910975551 0.894144775 0.930516441 0.942360184 0.838691782 0.973255373 0.745198642 0.768379262 1 18.7639878 2.24367572 24.9999991 0.819523433 0.91252479 0.174327103 0.075575798 172.4563435 842882.9526 0.02819317 0.021160579 175.25714 -2.24367572 0.093001356 LAEDEGDS(ph)EPEAVGQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LAEDEGDSEPEAVGQSR 17 0 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 LAEDEGDS(1)EPEAVGQSR;LAEDEGDS(1)EPEAVGQSR;LAEDEGDS(1)EPEAVGQSR;LAEDEGDS(1)EPEAVGQSR 461.21 4.07E-206 3493620000 2324510 1935950 1311410 1870910 2226430 1941680 1587780 2201780 1771630 TRUE FALSE 2017320.114 1923232.617 1945612.262 2295728.711 2182128.399 2016377.686 1433797.34 1730946.481 1562189.92 1.291341141 1.231113191 1.245439007 1.469558011 1.39683938 1.290737868 0.917812439 1.108025637 1 20.57513843 2.316681174 6.738767425 1.026340467 1.325874236 0.757982254 0.083063639 0.108912789 7.625527291 0.032941856 0.025306414 207.3390831 -2.316681174 0.299533769 LAEEEDLFDSAHPEEGDLDLASESTAHAQSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LAEEEDLFDSAHPEEGDLDLASESTAHAQSSK 32 0 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 ;; 348.19 8.70E-132 468430000 541320 460336 211913 387415 437797 413401 529729 618027 614285 FALSE TRUE 469783.1905 457312.0225 314394.8356 475383.497 429085.6962 429304.804 478355.9631 485866.7355 541664.9271 0.867294829 0.844271061 0.580423099 0.87763389 0.792160752 0.79256526 0.883121537 0.896987623 1 19.04704115 1.184090681 0.76108549 1.142785266 0.782355113 0.402282583 0.083400442 2.927098915 1.260304907 0.936773706 0.035244518 15.27885049 -1.184090681 -0.360430153 LAEIGAPIQGNREELVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LAEIGAPIQGNREELVER 18 1 Q13435;E9PPJ0;H0YCG1;E9PJ04;E9PJT3 Q13435 SF3B2 Splicing factor 3B subunit 2 0 77.08 0.012923 243500000 199100 229060 119950 122150 186300 196550 195160 226270 156490 FALSE TRUE 172788.4305 227555.2898 177958.2212 149886.0244 182592.9945 204111.4057 176233.4132 177883.9213 137989.9305 1.252181445 1.649071704 1.28964643 1.08620987 1.323234194 1.479176089 1.277146909 1.289107986 1 17.07420347 0.99906618 1.776858612 0.652892338 1.342921571 0.337501995 0.146837682 2.317567606 3.974390686 3.376831666 0.041285951 9.978521094 -0.99906618 0.690029233 LAELEEFINGPNNAHIQQVGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LAELEEFINGPNNAHIQQVGDR 22 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;;;; 363.82 1.97E-98 9833192000 8490235 7009823 4685125 5098185 7052581 7303170 7651258 8167786 7174279 FALSE TRUE 7368228.933 6963775.011 6950867.121 6255805.825 6912248.436 7584127.676 6909240.177 6421168.526 6326143.91 1.164726734 1.100793012 1.098752608 0.988881365 1.092647991 1.19885475 1.092172463 1.015020938 1 22.59289494 1.722579414 4.059598976 1.004491834 1.10399063 0.364998217 0.053921793 0.209316359 7.874787338 0.038129816 0.015085207 52.79337351 -1.722579414 0.099498796 LAELSDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAELSDYR 8 0 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ; 112.17 0.0071941 434390000 1480470 1324690 908310 1096510 1306450 1421520 1247520 1432630 2007480 FALSE TRUE 1284822.138 1315988.024 1347571.754 1345489.355 1280454.201 1476206.794 1126535.702 1126273.223 1770158.001 0.725823422 0.743429696 0.761272018 0.760095626 0.723355881 0.833940695 0.636404039 0.636255759 1 20.75544671 1.226973953 24.99799301 1.000000608 0.724775472 0.683686411 0.058207414 344.2350124 742632.0848 0.245391494 0.015673611 16.86451879 -1.226973953 -0.275225136 LAENFCVCHLATGDMLR ddPTM_MDA-MB-175_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 ; 198.42 1.42E-11 1627070000 713600 681530 385000 502480 623970 665680 540920 653300 621300 FALSE TRUE 619295.952 677052.9846 571187.2877 616575.7639 611554.2178 691289.1404 488461.6617 513596.879 547850.6218 1.130410238 1.235835021 1.042596768 1.125445038 1.116279134 1.261820491 0.891596436 0.937476127 1 19.06342305 2.227230063 24.99989071 0.939725483 1.148059825 0.688100445 0.066295576 118.2833585 260979.8238 0.026306113 0.0179128 168.7446698 -2.227230063 0.208334342 LAEQAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 LAEQAER 7 0 P27348;E9PG15;P31946-2;P31946;Q4VY19;A0A0J9YWE8;Q4VY20;P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;E5RGE1;P31947-2;P31947;P61981;P62258;B4DJF2;I3L3T1;I3L0W5;Q04917;F8WEB6;A2IDB1 P27348;P31946-2;P63104;P31947-2;P61981;P62258;Q04917 YWHAQ;YWHAB;YWHAZ;SFN;YWHAG;YWHAE;YWHAH "14-3-3 protein theta;14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed;14-3-3 protein zeta/delta;14-3-3 protein sigma;14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed;14-3-3 protein epsilon;14-3-3 protein eta" 0 ;;;;;;;;; 190.54 0.0012539 37995360000 10212120 9244300 5992200 6897010 7384350 8817030 8628680 9758300 9815240 FALSE TRUE 8862562.468 9183573.585 8890047.963 8463081.535 7237415.882 9156226.849 7791871.942 7671563.484 8654893.509 1.023994398 1.061084527 1.027170115 0.977837743 0.836222407 1.057924842 0.900285132 0.886384503 1 23.04508464 3.62046894 3.536602973 0.931798921 1.040410351 0.354057421 0.061521063 0.246105001 5.616178492 0.016927186 0.026283464 4173.197511 -3.62046894 0.10861143 LAEQAERYDEMVESMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAEQAERYDEMVESMK 16 1 P62258;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 ; 295.43 1.06E-45 1097670000 1724750 1434750 684690 761350 1291530 1107200 1762730 1997440 161677 FALSE TRUE 1496819.918 1425325.033 1015808.374 934226.154 1265831.08 1149794.7 1591780.716 1570303 142563.7292 10.49930389 9.997809684 7.125293225 6.553042341 8.879054207 8.065127831 11.16539757 11.01474413 1 17.12124746 4.363715749 6.474466506 8.189583563 10.36808306 0.10475699 2.845418929 0.53184647 27.44444404 0.712073734 1.924813798 23105.52012 -4.363715749 2.1784995 LAEQAERYDEMVESMKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAEQAERYDEMVESMKK 17 2 P62258;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 ; 220.34 2.27E-15 1004340000 1495490 1143960 535530 467750 982580 794550 1473560 1728440 101177 FALSE TRUE 1297857.207 1136445.251 794514.0992 573959.7866 963028.5804 825116.8526 1330654.378 1358826.557 89215.97032 14.54736414 12.73813699 8.905514297 6.433374928 10.79435192 9.248533078 14.91497961 15.23075467 1 16.44501437 4.417053682 4.402851261 10 14.19808206 0.150937257 4.05381203 0.417974729 16.05350902 1.064837079 3.260098008 26124.84255 -4.417053682 4.198082062 LAEQFVLLNLVYETTDKHLSPDGQYVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LAEQFVLLNLVYETTDKHLSPDGQYVPR 28 1 O95994;B5MC07;C9J3E2;H7C3Z9 O95994 AGR2 Anterior gradient protein 2 homolog 0 ;;; 247.57 6.18E-46 8707225000 3453548 3805029 677477.2 1340716 3328462 3170372 4003896 4230765 151092 FALSE TRUE 2997152.882 3780033.514 1005107.44 1645146.059 3262232.118 3292338.262 3615598.782 3326048.829 133230.0759 22.49606826 28.37222368 7.544148221 12.34815824 24.48570337 24.71167445 27.13800738 24.96469965 1 17.02356027 1.232872038 24.99995452 0.999966824 21.61868852 0.489439823 6.581629011 177.3191735 779193.4808 14.8868897 1.727376651 17.09511546 -1.232872038 20.6187217 LAERLS(ph)PFLAESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAERLSPFLAESK 13 1 H9KVB4;O15417;O15417-2 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 LAERLS(1)PFLAESK;LAERLS(1)PFLAESK 180.32 7.87E-06 506430000 1190400 1034450 652020 851040 969250 859210 1116510 1308190 990180 TRUE FALSE 1033085.624 1027654.63 967339.0529 1044281.639 949963.8213 892264.3647 1008231.032 1028443.749 873122.0484 1.183208723 1.176988523 1.107908172 1.19603169 1.088008055 1.021923987 1.15474238 1.177892313 1 19.73582381 3.226769773 24.99734241 1.10132342 1.162664861 0.292527668 0.057930273 369.1702294 782663.1104 0.018360792 0.020987435 1685.659192 -3.226769773 0.061341441 LAES(ph)PQLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LAESPQLSK 9 0 Q96A19 Q96A19 CCDC102A Coiled-coil domain-containing protein 102A 1 LAES(1)PQLSK 93.623 0.0061086 0 329000 248710 210510 232600 261710 208720 278560 367240 481180 TRUE FALSE 285521.8164 247076.2076 312313.3401 285415.3851 256502.483 216749.5935 251545.2941 288708.5839 424295.4486 0.672931603 0.582321136 0.73607516 0.672680761 0.604537437 0.510845907 0.592854095 0.680442331 1 18.69470968 1.234806981 3.316711872 1.062379436 0.624570344 0.787247369 0.060840875 0.160060154 2.415904057 0.182514007 0.016608255 17.17145045 -1.234806981 -0.437809092 LAETYLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LAETYLHR 8 0 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ;;;;; 183.24 0.00022436 3308280000 2485060 2477050 1662930 1965930 2416720 2502600 2270150 2506050 2682610 FALSE TRUE 2156653.025 2460778.095 2467128.51 2412324.454 2368632 2598876.641 2049991.202 1970150.71 2365474.902 0.91172095 1.040289243 1.042973869 1.019805559 1.001334657 1.09867014 0.866629868 0.832877452 1 21.17369842 2.221961377 24.99919628 0.884502498 1.020399394 0.438508623 0.062831888 189.303514 285097.304 0.024776321 0.016756332 166.7098947 -2.221961377 0.135896896 LAFVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAFVIR 6 0 P18124;A8MUD9;C9JZ88;C9JIJ5 P18124 RPL7 60S ribosomal protein L7 0 ; 143.79 0.026415 653400000 661040 686200 435630 422690 650150 660210 620310 717400 634770 FALSE TRUE 573681.8891 681692.307 646302.1251 518668.2249 637213.287 685608.7059 560152.4317 563989.5928 559728.2137 1.024929377 1.217898777 1.154671337 0.926642989 1.138433388 1.224895742 1.0007579 1.0076133 1 19.09436694 2.154601521 24.99998129 1.003708119 1.113643756 0.267490234 0.087191503 35.88232135 10680.24127 0.035915653 0.024214333 142.7583504 -2.154601521 0.109935636 LAGDKANYWWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LAGDKANYWWLR 12 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 82.202 0.014216 379570000 458070 443500 149670 173280 495280 396460 468800 550990 82621 FALSE TRUE 397534.8889 440586.6193 222050.9126 212625.8724 485424.897 411712.0727 423335.8482 433165.0763 72853.6395 5.456623603 6.047558122 3.047904183 2.918534666 6.663015058 5.651221759 5.810771446 5.945688908 1 16.15271343 6.632494306 7.653389678 4.875948755 5.147232285 0 1.817169321 0 0 0.401401614 0 4290365.642 -6.632494306 0.27128353 LAGEDKDSEPAADGPAASEDPSATESDLPNPHVGEVSVLS(ph)SGSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LAGEDKDSEPAADGPAASEDPSATESDLPNPHVGEVSVLSSGSPR 45 1 O14686;O14686-3;F8VWW4 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 LAGEDKDSEPAADGPAASEDPSATESDLPNPHVGEVS(0.057)VLS(0.314)S(0.314)GS(0.314)PR 73.065 0.00050286 285260000 96727 67853 47548 56597 64821 58206 89714 98594 68660 TRUE FALSE 83944.28188 67407.26918 70542.37184 69448.21388 63531.18892 60445.22248 81013.55009 77510.44036 60543.09302 1.386521198 1.113376701 1.165159696 1.147087313 1.04935486 0.998383457 1.33811383 1.280252404 1 15.88567476 4.744476066 23.90990372 1.151342869 1.386521391 0.328780714 0.110480924 498.6909435 2015569.025 0.02886553 0.248855409 55523.40178 -4.744476066 0.235178522 LAGEDKDSEPAADGPAASEDPSATESDLPNPHVGEVSVLSS(ph)GSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LAGEDKDSEPAADGPAASEDPSATESDLPNPHVGEVSVLSSGSPR 45 1 O14686;O14686-3;F8VWW4 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 LAGEDKDSEPAADGPAASEDPSATESDLPNPHVGEVS(0.002)VLS(0.163)S(0.417)GS(0.417)PR 108.41 5.82E-07 215230000 114950 99962 59469 80315 91397 79623 108090 136320 99715 TRUE FALSE 99759.06625 99305.34304 88228.40731 98551.74829 89578.37852 82686.14833 97607.44844 107169.0288 87926.8063 1.134569427 1.12940919 1.003430137 1.120838484 1.018783489 0.940397494 1.110098871 1.218843642 1 16.42401545 2.011932435 24.99111822 1.136878861 1.056885097 0.061397688 0.080772114 384.6412208 805584.33 0.032997739 0.022230551 102.7856377 -2.011932435 -0.079993764 LAGESESNLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAGESESNLRK 11 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 121.02 0.0006739 864370000 877990 528930 289740 379600 544090 446260 655320 736100 322050 FALSE TRUE 761961.397 525455.424 429859.2331 465793.9818 533263.6735 463427.911 591767.1673 578690.7433 283977.6159 2.683174146 1.850340994 1.513708155 1.640248934 1.877836997 1.631917042 2.083851452 2.037804077 1 18.11541769 4.727689197 4.096139174 1.737083856 2.754227113 0.502751501 0.30646029 0.188023319 6.886840091 0.074987894 0.555734174 53418.19356 -4.727689197 1.017143258 LAGFLDLTEQEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LAGFLDLTEQEFR 13 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ;; 188.6 1.39E-05 225777000 338241 364435 246494 348880 390689 336383 432549 449610 551650 FALSE TRUE 293541.5949 362041.0025 365699.3229 428098.5363 382915.0533 349323.8717 390600.4646 353464.4004 486434.5654 0.603455461 0.744274828 0.751795511 0.880074252 0.787187179 0.718131269 0.802986655 0.726643264 1 18.89188622 4.848116231 1.456631939 0.802055352 0.486200158 0.394024351 0.081605179 1.673172122 2.682826492 0.021927783 0.824515224 70488.16919 -4.848116231 -0.315855194 LAGGDWFTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LAGGDWFTSR 10 0 P30153;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ;;; 219.54 1.46E-08 3681350000 695505 650429 497859 510206 604968 684739 579228 674465 655194 FALSE TRUE 603592.2521 646156.2891 738625.2776 626056.0703 592930.3204 711081.3524 523054.5577 530235.9084 577737.7117 1.044751346 1.118424981 1.27847856 1.083633728 1.026296723 1.230803075 0.905349516 0.917779639 1 19.14005514 2.22515628 24.99994762 0.934709225 1.129727241 0.552742011 0.08022603 166.523463 310574.5611 0.032538454 0.022079303 167.9408239 -2.22515628 0.195018016 LAGIINFQRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAGIINFQRPK 11 1 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 ; 133.23 0.00015146 1214430000 1416900 1473480 854540 1014990 1449100 1500420 1467240 1551740 1118340 FALSE TRUE 1229653.075 1463800.613 1267798.402 1245458.993 1420265.745 1558142.128 1324947.291 1219912.477 986131.1192 1.246946832 1.484387405 1.285628632 1.262975043 1.440240266 1.580055733 1.343581259 1.237069242 1 19.91141996 1.35269047 2.050341959 0.938160044 1.384032166 0.578868291 0.103450727 0.42138775 2.208710609 0.329351715 0.028989197 22.52633143 -1.35269047 0.445872122 LAGLVEELEADEWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LAGLVEELEADEWR 14 0 A0A087WUN5;Q96DE5 A0A087WUN5 ANAPC16 Anaphase-promoting complex subunit 16 0 ;;; 224.42 7.34E-12 88553000 79102 84688 51172.6 62005.8 78787 82516 78084 97854 84893 FALSE TRUE 68648.47028 84131.67895 75919.84052 76085.16459 77219.29284 85690.44391 70511.4257 76928.6836 74857.04625 0.917060901 1.123897925 1.014197652 1.016406182 1.03155677 1.144721148 0.941947742 1.02767458 1 16.1918505 LAGS(ph)PIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAGSPIR 7 0 A0A0A0MRB5;Q8WXG6-6;Q8WXG6-8;Q8WXG6-5;Q8WXG6-4;Q8WXG6-7;Q8WXG6-3;Q8WXG6-2;Q8WXG6;F8W8U2 A0A0A0MRB5 MADD MAP kinase-activating death domain protein 1 LAGS(1)PIR;LAGS(1)PIR 96.668 0.013178 524000000 615630 677960 462800 490190 691750 686910 701140 754900 784610 TRUE FALSE 534272.9357 673506.4361 686611.628 601495.1316 677985.5284 713335.8722 633143.5507 593470.5096 691854.2996 0.77223331 0.973480163 0.992422289 0.869395669 0.979954202 1.031049272 0.91514001 0.857796952 1 19.40010872 4.74434314 24.73608932 0.94524186 0.772233223 0.496070384 0.05666185 530.4311875 2268967.812 0.014543679 0.12521136 55506.41003 -4.74434314 -0.173008637 LAGS(ph)PPGSGQWKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAGSPPGSGQWKPK 14 1 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 1 LAGS(0.998)PPGS(0.002)GQWKPK;LAGS(1)PPGSGQWKPK 147.17 4.91E-06 6768800000 8604700 6625400 5852200 6529000 6654500 5398100 8914600 10193300 8567400 TRUE FALSE 7467567.093 6581877.311 8682343.494 8011509.24 6522088.469 5605768.4 8050063.464 8013542.119 7554571.732 0.988483181 0.871244267 1.149283348 1.060484899 0.863330007 0.742036557 1.065588328 1.060753992 1 22.84891854 LAHCEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAHCEELR 8 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 95.815 0.0093826 345880000 636500 642700 338140 471870 608580 786510 527370 616530 590130 FALSE TRUE 552384.9123 638478.0614 501665.635 579015.2956 596470.4487 816767.5486 476225.7386 484689.8573 520365.5037 1.061532535 1.226979992 0.964063973 1.112708839 1.146252864 1.569603563 0.915175459 0.931441177 1 18.9891658 LAHEIEALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAHEIEALK 9 0 O43847;O43847-2;G3V1R5;H0Y5G9 O43847 NRD1 Nardilysin 0 ; 88.948 0.012439 136157000 195581 168225 123123 135369 159533 150130 181188 189624 203485 FALSE TRUE 169734.4753 167119.9189 182665.6946 166106.6004 156358.6054 155905.5982 163616.4156 149074.3833 179429.2351 0.945968895 0.931397377 1.018037526 0.925749922 0.871422125 0.868897413 0.911871555 0.830825496 1 17.45305545 3.475216055 7.268745048 0.88891135 0.963516429 0.285813643 0.048606859 0.140290744 48.7517029 0.013219209 0.017907429 2986.868173 -3.475216055 0.074605079 LAHEVGWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LAHEVGWK 8 0 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ;;;; 130.22 0.0010572 11202360000 16293600 14307680 9830900 11949500 13601910 12880610 15995320 18166700 16919140 FALSE TRUE 14140359.48 14213691.91 14585156.12 14662816.61 13331258.6 13376135.4 14444096.33 14281892.58 14918978.54 0.947810162 0.952725541 0.977624311 0.982829794 0.893577168 0.896585203 0.968169254 0.957296945 1 23.83064543 1.170734014 1.689762254 1.026766782 0.944688722 0.247029712 0.029912084 1.959480113 4.469219896 0.280761215 0.009088746 14.81610387 -1.170734014 -0.08207806 LAHHLVALYYQSEEQAEEELLDMAVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAHHLVALYYQSEEQAEEELLDMAVLK 27 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ; 161.66 7.45E-12 732330000 298520 262920 207720 311310 269240 187425 303130 415010 392700 FALSE TRUE 259069.8256 261192.8612 308174.0868 381997.6936 263882.6508 194635.361 273732.4993 326263.3411 346275.4534 0.748161104 0.754292164 0.889968041 1.103161341 0.762059939 0.562082467 0.790505064 0.942207534 1 18.4015606 1.629691602 4.036011561 0.98611042 0.804158258 0.219207596 0.134761519 0.286653421 10.61024933 0.109700138 0.038453024 42.62767066 -1.629691602 -0.181952162 LAHYIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LAHYIDR 7 0 Q03252 Q03252 LMNB2 Lamin-B2 0 ;;;; 100.19 0.0099773 2644410000 3219845 3158330 1928916 2484327 3316460 3613280 2837542 3788300 3223020 FALSE TRUE 2794334.325 3137582.722 2861746.229 3048431.416 3250468.935 3752285.22 2562357.614 2978201.526 2841998.247 0.983228729 1.104005861 1.006948626 1.072636628 1.14372658 1.320298217 0.90160422 1.04792518 1 21.43847423 LAHYNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LAHYNK 6 0 Q16778;P33778;P23527;P06899;Q6DRA6;Q6DN03;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;Q99880 Q16778;P58876;Q99880 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST2H2BD;HIST2H2BC;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;HIST1H2BL Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type 1-L 0 ;;;;;;; 118.18 0.022086 54398670000 36061600 33398600 25059910 34818900 25124910 29556110 30667000 39769900 69324500 FALSE TRUE 31295968.19 33179202.4 37178966.3 42725063.42 24624973.45 30693152.68 27692919.06 31265416.37 61129036.58 0.51196567 0.542773193 0.608204683 0.698932386 0.402835949 0.502104309 0.453023974 0.511465878 1 25.86535449 1.237344195 24.99988165 1.000000566 0.527984455 0.771697351 0.080524442 15.19185184 312090.0459 0.123355901 0.020497334 17.27206227 -1.237344195 -0.47201611 LAHYNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAHYNKR 7 1 Q16778;P33778;P23527;P06899;Q6DRA6;Q6DN03;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;Q99880 Q16778;P58876;Q99880 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST2H2BD;HIST2H2BC;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;HIST1H2BL Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type 1-L 0 ; 182.31 0.001057 8724000000 3907300 4493600 2141450 2894900 3776600 3956200 3708600 4909100 2353260 FALSE TRUE 3390940.405 4464081.246 3177062.383 3552231.291 3701453.049 4108397.574 3348940.543 3859327.168 2075060.284 1.634140671 2.151301955 1.53106992 1.711868961 1.783780972 1.979893118 1.613900362 1.859862674 1 20.98472182 1.235304792 24.9806207 0.999998902 1.786438011 0.645294926 0.182478628 54.41580448 417438.7298 0.2870813 0.041086052 17.19114456 -1.235304792 0.78643911 LAILDQELEHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LAILDQELEHK 11 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 0 120.57 0.00043369 59441000 131240 97207 89649 125800 105800 86223 118570 151710 229170 FALSE TRUE 113896.3015 96568.44082 133003.5563 154364.8127 103694.787 89540.0546 107071.0996 119267.9971 202077.7837 0.563626042 0.477877573 0.658180003 0.763888093 0.513142935 0.443096975 0.52985092 0.590208359 1 17.6245512 1.238337768 5.1686571 1.025478714 0.565358769 0.690977155 0.091058568 0.10218294 7.431851689 0.168788367 0.024330209 17.31162229 -1.238337768 -0.460119945 LAILQVGNRDDSNLYINVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LAILQVGNRDDSNLYINVK 19 1 V9GYY3;A0A384N5Y3;F5H2F4;P11586 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 108.49 0.00036078 0 158030 162210 98338 147970 164470 154080 213590 266190 73844 FALSE TRUE 137145.9351 161144.4318 145894.5857 181568.8501 161197.3688 160007.5573 192876.0747 209267.34 65114.24644 2.106235464 2.474795312 2.240593936 2.788465812 2.475608297 2.457335622 2.962117896 3.213848757 1 15.99068561 4.917741855 0.921786773 2.579834224 1.772928554 0.004180508 0.596334056 10.07491876 5.464514689 0.197902591 8.798183346 82745.01806 -4.917741855 -0.80690567 LAIQGPEDS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 LAIQGPEDSPSR 12 0 Q15773 Q15773 MLF2 Myeloid leukemia factor 2 1 LAIQGPEDS(0.976)PS(0.024)R;LAIQGPEDS(0.974)PS(0.026)R;LAIQGPEDS(1)PSR;LAIQGPEDS(1)PSR;LAIQGPEDS(0.999)PS(0.001)R;LAIQGPEDS(1)PSR;LAIQGPEDS(0.936)PS(0.064)R 313.24 2.45E-46 17463090000 6115250 5174190 3570770 3940600 4800030 5413360 5172340 5249700 5353140 TRUE FALSE 5307104.218 5140200.405 5297606.316 4835373.458 4704518.794 5621615.462 4670727.263 4127092.508 4720297.888 1.124315529 1.088956784 1.122303389 1.024378879 0.996657183 1.190945062 0.989498412 0.874328826 1 22.17044648 2.00831751 24.45115045 0.929305604 1.085642119 0.536064487 0.061129212 94.9998491 279271.4639 0.024271132 0.016329912 101.9336345 -2.00831751 0.156336515 LAIRES(ph)IESEIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LAIRESIESEIRR 13 2 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 1 LAIRES(1)IESEIRR;LAIRES(1)IESEIRR;LAIRES(1)IESEIRR;LAIRES(1)IESEIRR 157.83 2.03E-05 475263000 454595 403030 216876 305898 388378 380583 380724 415969 233921 TRUE FALSE 394519.119 400382.4694 321757.959 375356.8163 380650.0376 395224.2743 343801.4451 327017.2664 206267.1259 1.912661154 1.941087159 1.559909063 1.819760733 1.845422706 1.916079805 1.666777697 1.585406618 1 17.65415438 0.930509998 1.297772522 3.89E-11 1.821072136 0.837681131 0.113086417 1.098232122 0.913162063 3.262765168 0.03410555 8.52138129 -0.930509998 1.821072136 LALDGETLGEEEQEDEQPPWASPS(ph)PTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LALDGETLGEEEQEDEQPPWASPSPTSR 28 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 LALDGETLGEEEQEDEQPPWASPS(0.333)PT(0.333)S(0.333)R;LALDGETLGEEEQEDEQPPWAS(0.039)PS(0.648)PT(0.157)S(0.157)R 174.1 1.02E-12 130395000 34528 35556 25392.9 35819 40329 36552 31452 45484 40153 TRUE FALSE 29965.03732 35322.43029 37672.99137 43952.25141 39526.5318 37958.17909 28401.78988 35757.60056 35406.15808 0.846322757 0.99763522 1.064023701 1.241373077 1.116374494 1.07207845 0.802170905 1.009926027 1 15.11171269 LALDMEIHAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LALDMEIHAYR 11 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;; 194.5 4.85E-07 5220093000 8815122 7837276 4114305 5266609 7285914 7255960 8072018 9087564 5608743 FALSE TRUE 7650181.293 7785792.418 6103996.66 6462473.069 7140938.566 7535101.476 7289194.937 7144259.158 4945683.792 1.546839955 1.574260051 1.234206819 1.306689497 1.443872853 1.523571218 1.473849774 1.444544265 1 22.23773857 1.238260027 24.93698569 0.999999502 1.440740491 0.641436092 0.104185643 4.866191651 403003.3359 0.152788824 0.026937421 17.30852371 -1.238260027 0.440740989 LALEAEVSELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LALEAEVSELR 11 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 107.15 0.003538 0 15982 15214 11170 10000 14908 16354 14208 15515 14931 FALSE TRUE 13869.93821 15114.05823 16571.84936 12270.65284 14611.35997 16983.14896 12830.11035 12197.23799 13165.87419 1.053476435 1.147972251 1.258697229 0.932004413 1.109790338 1.289937054 0.974497414 0.926428265 1 13.6845157 2.037316799 24.4978274 0.955710087 1.128688989 0.374502551 0.10043951 129.3730826 84930.5719 0.040591713 0.02736684 108.9724711 -2.037316799 0.172978902 LALFNPDVCWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LALFNPDVCWDR 12 0 O00483 O00483 NDUFA4 Cytochrome c oxidase subunit NDUFA4 0 108.48 0.0013378 0 147980 122200 100710 145190 185510 128870 138780 159600 156610 FALSE TRUE 128424.0681 121397.2602 149413.6929 178157.6086 181818.7139 133827.7123 125321.137 125470.782 138095.7442 0.929963981 0.879080386 1.081957259 1.290102093 1.316613448 0.969093675 0.907494562 0.908578195 1 17.07530933 2.499449494 24.82318397 0.932142769 1.101499926 0.240121359 0.136173492 1082.752185 1203738.187 0.05291427 0.046285274 315.827174 -2.499449494 0.169357157 LALGEPPPYGAAPIGIPRPPPPRPGMHS(ph)PPPRPAPSPGTWESQPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LALGEPPPYGAAPIGIPRPPPPRPGMHSPPPRPAPSPGTWESQPAR 46 3 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;G3V5H0;G3V4K1;G3V4U6 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 LALGEPPPYGAAPIGIPRPPPPRPGMHS(1)PPPRPAPSPGTWESQPAR 91.305 1.78E-05 415880000 101790 100540 56691 60763 70998 80216 75067 77713 86653 TRUE FALSE 88338.1936 99879.54612 84106.95722 74560.16785 69585.27871 83301.96143 67787.01389 61094.67971 76408.98106 1.156123173 1.30717024 1.100747007 0.975803719 0.910695022 1.090211652 0.887160291 0.79957459 1 16.2214546 3.85826083 2.267004507 0.92523074 1.232381532 0.664260823 0.084791935 0.180214055 1.802499216 0.025630986 0.054595741 7215.406945 -3.85826083 0.307150792 LALLEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LALLEEAR 8 0 Q5TZA2-2;Q5TZA2;B1AKD8 Q5TZA2-2 CROCC Rootletin 0 ;;;; 178.08 0.00058505 1657503000 1276036 1630400 1058548 1395923 1599993 1718830 1444131 1781020 1791530 FALSE TRUE 1107404.61 1619689.795 1570465.353 1712888.652 1568156.27 1784954.502 1304079.398 1400162.733 1579737.364 0.701005518 1.025290552 0.994130663 1.084286978 0.992668975 1.129905858 0.825503927 0.886326275 1 20.5912533 4.743909789 24.25274066 0.983418869 0.701005334 0.522917112 0.087066642 351.9223309 1595512.105 0.023057429 0.189055742 55451.05191 -4.743909789 -0.282413535 LALLHEGTGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LALLHEGTGPR 11 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 169.65 1.66E-05 485730000 192490 200640 123950 129960 171250 170200 146860 220960 176050 FALSE TRUE 167051.9588 199321.9826 183892.6346 159469.4043 167842.46 176747.7041 132617.5398 173709.4235 155237.5696 1.076105219 1.28398031 1.184588467 1.027260378 1.081197422 1.138562686 0.854287658 1.118990873 1 17.24411823 3.744730754 18.57483614 1.039981858 1.19180087 0.354120344 0.09179482 15.04053429 45270.04698 0.023202099 0.038529454 5555.597241 -3.744730754 0.151819011 LALLIHNDS(ph)LTSLIYGEQSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LALLIHNDSLTSLIYGEQSEK 21 0 G3V4J5;Q9P1W3 G3V4J5 TMEM63C Calcium permeable stress-gated cation channel 1 1 LALLIHNDS(0.916)LT(0.083)S(0.001)LIYGEQSEK;LALLIHNDS(0.693)LT(0.306)S(0.001)LIYGEQSEK 161.41 1.28E-11 226886000 203376 211548 166229 186291 230108 201598 207948 302057 310205 TRUE FALSE 176499.3463 210158.3273 246617.9004 228591.2188 225529.301 209353.6055 187781.235 237464.4612 273532.9183 0.645258155 0.768310917 0.901602271 0.835699119 0.824505154 0.765368961 0.686503241 0.868138514 1 18.06135494 1.385361148 3.502132312 1.000925226 0.783396227 0.494000437 0.073028972 0.231807 4.290960747 0.106341632 0.019609261 24.28628839 -1.385361148 -0.217528999 LALLNVATQGVHLWDLQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LALLNVATQGVHLWDLQDR 19 0 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y9R3 A0A499FIZ0 WDR26 WD repeat-containing protein 26 0 ; 234.11 3.97E-24 732790000 364160 406310 278660 338650 363570 407960 400460 420170 405190 FALSE TRUE 316035.3333 403640.9229 413420.9081 415545.6584 356335.6683 423654.4852 361623.4508 330319.9153 357288.8998 0.884537229 1.129732614 1.15710538 1.163052249 0.997332043 1.185747683 1.012131782 0.924517709 1 18.44673157 2.007595688 24.41558438 0.960304493 1.09156766 0.248179996 0.090878465 155.4055172 499532.4615 0.035777985 0.024064275 101.7643559 -2.007595688 0.131263167 LALQLHPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LALQLHPDR 9 0 Q9UBS4 Q9UBS4 DNAJB11 DnaJ homolog subfamily B member 11 0 108.57 0.00259 97865000 58303 60068 64410 80276 75616 95916 55514 55913 159220 FALSE TRUE 50598.11083 59673.40935 95558.89144 98503.89274 74111.38954 99605.95059 50130.26082 43956.44007 140397.193 0.36039261 0.425032781 0.680632493 0.701608705 0.527869454 0.709458277 0.357060278 0.313086317 1 17.09915457 4.400759854 6.43726379 0.575569999 0.375884459 0.163699177 0.195579432 0.388977736 25.33091924 0.050264815 0.136744838 25162.85145 -4.400759854 -0.19968554 LALS(ph)PEDKPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LALSPEDKPIR 11 1 H9KVB4;O15417;O15417-2;O15417-3 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 LALS(1)PEDKPIR;LALS(1)PEDKPIR 150.11 2.06E-05 294740000 621950 518430 355140 427550 544640 431820 565180 675860 669880 TRUE FALSE 539757.7317 515024.3992 526886.8919 524631.7622 533802.7296 448432.3948 510368.9306 531332.5985 590687.5495 0.913778752 0.871906644 0.891989161 0.888171357 0.903697276 0.759170216 0.864025204 0.899515487 1 19.17203568 1.253844299 2.716384227 1.025912354 0.869496581 0.47707686 0.042463842 0.405104087 3.533545332 0.1421375 0.011385308 17.94090302 -1.253844299 -0.156415774 LALS(ph)PLSLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LALSPLSLGK 10 0 P49454 P49454 CENPF Centromere protein F 1 LALS(1)PLSLGK;LALS(0.998)PLS(0.002)LGK;LALS(0.999)PLS(0.001)LGK;LALS(1)PLSLGK 145.14 3.25E-05 1662695000 3052060 2986700 1769286 2504748 2648850 2200697 2952700 3751030 3393750 TRUE FALSE 2648722.538 2967080.171 2624918.628 3073489.316 2596143.067 2285359.238 2666347.608 2948901.425 2992544.741 0.88510708 0.991490664 0.877152676 1.027048743 0.867536927 0.763684234 0.89099674 0.985415985 1 21.51294139 1.674295691 4.975579051 0.995611532 0.901456079 0.227520743 0.070752723 0.23548189 13.18354693 0.0487952 0.019213937 47.23845567 -1.674295691 -0.094155453 LALVTGGEIASTFDHPELVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LALVTGGEIASTFDHPELVK 20 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 211.29 2.86E-22 169680000 246730 175780 107840 150170 269590 194380 271350 299270 168330 FALSE TRUE 214124.0054 174625.2896 159991.7847 184268.3937 264225.6864 201857.9244 245034.5188 235273.4394 148430.2192 1.442590374 1.17648071 1.077892262 1.241447966 1.780134045 1.35995167 1.650839837 1.585077761 1 17.17942532 3.437163212 24.9123511 1.49765925 1.215559001 0.21801945 0.223494691 189.3693052 118064.0747 0.062227587 0.080335573 2736.296862 -3.437163212 -0.282100249 LAMDLPGHADEVYAVDWSPDGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LAMDLPGHADEVYAVDWSPDGQR 23 0 A0A0A0MRH0;Q9NVX2;K7EN33;Q9NVX2-2 A0A0A0MRH0 NLE1 Notchless protein homolog 1 0 194.25 3.68E-18 127490000 133550 110940 68592 89115 114800 111480 111010 134630 122540 FALSE TRUE 115901.0291 110211.2278 101763.3206 109349.9228 112515.7046 115768.7077 100244.2673 105840.4222 108053.4608 1.072626719 1.019969439 0.941786777 1.011998338 1.04129663 1.071402127 0.927728428 0.97951904 1 16.72138575 2.141925286 0.01116404 5.52E-08 1.987313557 0.10900256 0.045773323 9855.037018 59.15809265 5381.50739 5149.192238 138.6517278 -2.141925286 1.987313502 LAMQEFMILPVGAANFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAMQEFMILPVGAANFR 17 0 P06733;A0A2R8Y6G6;P06733-2;K7EM90 P06733 ENO1 Alpha-enolase;Enolase 0 ; 165.7 5.67E-09 679520000 741830 770580 491350 488640 689780 757100 611050 781430 883310 FALSE TRUE 643795.2859 765518.0092 728968.5035 599593.1804 676054.7275 786226.1269 551790.4651 614327.2756 778886.0981 0.826558964 0.982836914 0.93591156 0.769808553 0.867976369 1.009423751 0.708435375 0.788725434 1 19.57105284 3.783674867 24.97649855 0.847707236 0.921875957 0.06102491 0.100939167 1062.440588 588192.9819 0.026824879 0.046461791 6076.79893 -3.783674867 0.07416872 LAPEYEAAATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LAPEYEAAATR 11 0 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 128.35 0.00062276 810210000 430838 428853 305077 326681 411491 480240 355623 350518 344452 FALSE TRUE 373901.6667 426035.8364 452613.2576 400858.9141 403303.1342 498715.1436 321134.7362 275562.4534 303731.277 1.231027869 1.402673576 1.490176653 1.319781479 1.327828791 1.641961765 1.057298871 0.907257416 1 18.21243595 2.080846053 6.720801899 0.957259067 1.398115478 0.757690919 0.111431612 0.091261554 6.185257934 0.044393247 0.029716237 120.4608861 -2.080846053 0.440856411 LAPGGHVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LAPGGHVGR 9 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;;;;;;; 172.14 5.64E-05 10736460000 14500500 14230470 8937280 10970540 13465060 14296410 13370100 14881410 14476300 FALSE TRUE 12584222.19 14136989.11 13259378.5 13461568.78 13197131.65 14846402.14 12073469.76 11699136.28 12764928.31 0.985843546 1.107486761 1.038735055 1.05457457 1.033858658 1.163061929 0.94583138 0.916506227 1 23.6056821 2.193301365 24.41243508 0.945932468 1.062969833 0.507093143 0.050818992 71.73246986 38691.17657 0.019400678 0.013080001 156.0635079 -2.193301365 0.117037365 LAPPS(ph)PAR ddPTM_MDA-MB-175_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 10734250000 4964260 5197860 3086680 3788200 4760440 5288290 4474350 4880170 5252370 TRUE FALSE 4308220.463 5163714.915 4579408.772 4648368.709 4665716.558 5491733.938 4040428.226 3836583.623 4631440.802 0.930211709 1.114926248 0.988765477 1.003654998 1.007400668 1.185750649 0.872391206 0.82837799 1 22.14302964 2.187369092 24.99990726 0.884120238 1.036676617 0.381618197 0.082054723 92.3091069 45079.32989 0.031907302 0.021511923 153.9462422 -2.187369092 0.152556379 LAPS(ph)EDELTCFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LAPSEDELTCFSK 13 0 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4;A8MV73 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 LAPS(1)EDELTCFSK;LAPS(1)EDELTCFSK;LAPS(1)EDELTCFSK 260.97 5.11E-24 316456000 443619 361356 249987 300613 329038 289593 415285 469004 389156 TRUE FALSE 384993.6252 358982.2286 370881.5494 368871.7762 322490.7876 300733.8301 375010.7246 368711.1444 343150.421 1.121938373 1.046136641 1.08081333 1.074956502 0.939794235 0.876390678 1.092846465 1.074488393 1 18.3884816 3.423391913 22.63863672 1.007599192 1.079047673 0.293579354 0.06371644 62.9663819 26529.72774 0.020530644 0.026504951 2650.89126 -3.423391913 0.071448481 LAPVPS(ph)PEPQKPAPVS(ph)PESVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAPVPSPEPQKPAPVSPESVK 21 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 LAPVPS(1)PEPQKPAPVS(1)PESVK;LAPVPS(1)PEPQKPAPVS(0.999)PES(0.001)VK 182.09 2.73E-17 430990000 888020 684900 549410 649230 679730 498320 900040 1162640 925200 TRUE FALSE 770665.907 680400.8468 815106.5137 796647.5944 666204.7029 517490.6929 812754.2593 914018.4837 815823.91 0.944647365 0.834004542 0.999120648 0.976494541 0.816603552 0.634316654 0.996237361 1.120362461 1 19.63789826 2.010438457 24.99743112 1.065635005 0.869680791 0.378884578 0.105710903 204.915671 490718.7322 0.045115508 0.030382506 102.4326614 -2.010438457 -0.195954214 LAPVPS(ph)PEPQKPAPVSPESVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LAPVPSPEPQKPAPVSPESVK 21 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 LAPVPS(1)PEPQKPAPVSPESVK;LAPVPS(1)PEPQKPAPVSPESVK;LAPVPS(1)PEPQKPAPVSPESVK;LAPVPS(0.999)PEPQKPAPVS(0.001)PESVK 164.96 9.28E-12 1318170000 1570640 1096650 883450 1041780 1104980 777170 1341300 1680930 1472220 TRUE FALSE 1363075.945 1089446.034 1310689.375 1278332.072 1082993.06 807068.2328 1211220.932 1321476.201 1298175.829 1.049993317 0.839213002 1.009639331 0.984714122 0.8342422 0.621694084 0.933017628 1.017948548 1 20.30805437 1.994246946 24.99638701 0.999824373 0.885042041 0.142503368 0.118804003 492.1961002 2138537.147 0.052416152 0.034083359 98.68404568 -1.994246946 -0.114782333 LAQALHEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LAQALHEMR 9 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ;;;; 170.47 5.77E-05 1452680000 1864050 2186040 1284020 1678650 2167690 2295450 1820920 2439440 2474330 FALSE TRUE 1617711.07 2171679.759 1904976.367 2059813.139 2124557.21 2383757.447 1644327.459 1917784.74 2181817.526 0.74145113 0.995353522 0.87311443 0.944081306 0.973755681 1.092555825 0.753650312 0.878984937 1 21.05709902 5.968070179 11.23949487 0.91571223 0.62750196 0 0.109893449 0 0 0.023747389 0 929116.513 -5.968070179 -0.288210269 LAQANGWGVMVSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LAQANGWGVMVSHR 14 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;; 183.81 1.04E-06 20791640000 7323150 8539800 4734390 4730920 6944350 7363490 6968780 7727170 8858690 FALSE TRUE 6355377.173 8483701.492 7023956.84 5805147.694 6806171.021 7646768.225 6292948.788 6074774.828 7811425.76 0.81360015 1.086063128 0.899190117 0.743161091 0.871309698 0.978920937 0.805608218 0.777678111 1 22.89715447 4.004888951 24.99245084 0.852893211 0.96053039 0.101452235 0.102817987 237.0094013 1211564.004 0.025264505 0.052297083 10113.20826 -4.004888951 0.107637179 LAQFEPSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LAQFEPSQR 9 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 93.098 0.022401 175090000 237930 196100 126310 152760 224830 213520 194450 220950 206330 FALSE TRUE 206486.9477 194811.8062 187393.9385 187446.4928 220356.3229 221734.2526 175592.2689 173701.5619 181937.9025 1.134930902 1.070759878 1.029988452 1.03027731 1.21116227 1.218735896 0.965121982 0.954729936 1 17.4730866 2.205669593 24.98754679 0.969078304 1.11044328 0.515023208 0.065083943 166.8715792 126772.3828 0.029167189 0.019666076 160.5719172 -2.205669593 0.141364976 LAQFVEHWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAQFVEHWK 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 132.91 0.0002917 799880000 2056500 1860800 1365460 1799180 1658650 1644130 1655770 2168600 3706800 FALSE TRUE 1784728.314 1848576.282 2025801.023 2207711.318 1625646.11 1707380.745 1495193.68 1704861.766 3268586.327 0.546024531 0.565558348 0.619778957 0.675433076 0.497354497 0.522360609 0.457443534 0.521589946 1 21.64023537 1.236452326 24.99952231 1.000000577 0.548927047 0.841515138 0.061274311 23.35456716 276862.3255 0.105658345 0.016521755 17.2366287 -1.236452326 -0.45107353 LAQGHTTVDELAR ddPTM_MDA-MB-175_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 ;;;;; 185.87 8.29E-06 4852370000 1911218 1792643 725794 1235471 1826494 1959181 1841860 1985995 1737854 FALSE TRUE 1658645.699 1780867.01 1076790.406 1516003.574 1790150.343 2034551.961 1663236.701 1561305.424 1532406.88 1.082379439 1.16213718 0.702679178 0.989295724 1.168195188 1.327683912 1.085375381 1.018858271 1 20.54736798 3.299504274 8.092287689 1.115032943 0.975935447 0.174748211 0.146137797 0.501518056 58.84414449 0.044883126 0.057840246 1992.98612 -3.299504274 -0.139097496 LAQGLTHLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAQGLTHLGK 10 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 129.89 0.00029116 1862200000 4975300 4566800 3063800 3616700 4279200 3883900 5185400 5619800 5384100 FALSE TRUE 4317801.499 4536800.39 4545463.928 4437927.013 4194052.292 4033316.146 4682520.706 4418049.503 4747597.832 0.909470779 0.955599137 0.957423962 0.934773157 0.883405133 0.849548822 0.98629262 0.930586301 1 22.1787663 0.819056658 1.213400363 1.120718632 0.922619829 0.272576624 0.038575837 5.654845982 3.414695997 1.82762051 0.012240987 6.592598966 -0.819056658 -0.198098802 LAQMCGLHIVVHADELEELINYYQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LAQMCGLHIVVHADELEELINYYQDR 26 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;; 252.71 9.12E-53 2055560000 861677 668684 800062 959230 700396 673234 929870 922994 1663441 FALSE TRUE 747804.2012 664291.3708 1186974.659 1177037.832 686459.4899 699133.7476 839691.3505 725618.9158 1466790.9 0.509823316 0.452887573 0.809232358 0.802457823 0.468000919 0.476641727 0.572468339 0.494698267 1 20.48423179 1.232004461 24.96099441 1.000000731 0.574018783 0.513541903 0.130520295 199.7442674 760405.1859 0.316021557 0.033852562 17.06099913 -1.232004461 -0.425981948 LAQMISDHNDADFEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LAQMISDHNDADFEEK 16 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5;Q5VU81;Q5VU80;Q5VU79;Q5VU78;Q5VU77 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 0 245.96 3.68E-20 313050000 446470 366800 179560 326350 365660 316840 421240 469130 566230 FALSE TRUE 387467.8583 364390.4666 266395.8166 400452.7554 358384.0814 329029.0398 380388.2096 368810.2003 499290.9345 0.776036238 0.729815908 0.533548275 0.802042913 0.717786078 0.658992618 0.761856832 0.738667929 1 18.92952119 0.533132005 1.456906046 2.428584616 0.704482171 0.590290646 0.074714921 5.527435256 2.200015874 23.32236026 0.020697484 3.412966335 -0.533132005 -1.724102445 LAQTLSTQLFQMVHTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LAQTLSTQLFQMVHTQR 17 0 P53367;P53367-2 P53367 ARFIP1 Arfaptin-1 0 105.2 0.00081313 416340000 74213 73900 61011 67859 87850 58504 89888 111060 65533 FALSE TRUE 64405.56402 73414.54603 90516.12367 83267.42311 86101.95688 60754.68674 81170.6756 87310.68327 57785.7634 1.114557639 1.27046078 1.56640872 1.440967779 1.490020237 1.051378111 1.404682933 1.510937611 1 15.81842648 LAQTT(ph)PVDSALGSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LAQTTPVDSALGSSR 15 0 H0YLX2;A0A669KBM4;Q2KHR2-2;Q2KHR2 H0YLX2 RFX7 DNA-binding protein RFX7 1 LAQT(0.077)T(0.92)PVDS(0.003)ALGSSR 70.47 0.092131 0 111570 97049 87155 84433 101750 106230 104670 122500 158400 TRUE FALSE 96825.74182 96411.47873 129303.4495 103604.8031 99725.37407 110316.7368 94519.11951 96304.3283 139674.1324 0.693226012 0.690260086 0.925750869 0.741760849 0.713985992 0.789815085 0.676711699 0.689492941 1 17.09170533 1.231755745 24.99872305 1.000000444 0.739809073 0.551170804 0.073698853 190.9954206 701585.8541 0.176454425 0.018397887 17.05123129 -1.231755745 -0.260191371 LAS(ph)DSDAESDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.892)DS(0.108)DAESDSR 122.39 0.00020835 0 59629 55679 47686 54119 45566 53381 53644 67978 88591 TRUE FALSE 51748.87657 55313.24098 70747.1091 66407.54611 44659.32575 55434.60161 48441.61314 53441.43371 78117.8729 0.662446053 0.70807408 0.905645616 0.850094142 0.571691523 0.709627638 0.620109219 0.684112761 1 16.25336505 1.234963572 24.99947758 1.000000404 0.713652148 0.452678655 0.098839361 106.2416426 738264.9897 0.18446656 0.025631138 17.17764297 -1.234963572 -0.286348256 LAS(ph)LNAEALNNLLLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LASLNAEALNNLLLER 16 0 Q8TBE0-3;Q8TBE0-2;Q8TBE0 Q8TBE0-3 BAHD1 Bromo adjacent homology domain-containing 1 protein 1 LAS(1)LNAEALNNLLLER;LAS(1)LNAEALNNLLLER;LAS(1)LNAEALNNLLLER;LAS(1)LNAEALNNLLLER;LAS(1)LNAEALNNLLLER 194.92 3.20E-11 217123400 175152.8 142164.2 138897.4 162905.9 200740.5 208813.9 238784.8 264894.3 244847.3 TRUE FALSE 152005.9137 141230.314 206068.6472 199896.1745 196746.1568 216847.1059 215627.4868 208248.7154 215901.7311 0.704051389 0.654141647 0.954455743 0.925866474 0.911276421 1.004378727 0.998729773 0.964553245 1 17.72001529 4.234190301 24.99927753 0.965313623 0.679096467 0.929495146 0.032805706 23.63104615 135178.5252 0.008855583 0.019513938 17147.08502 -4.234190301 -0.286217156 LAS(ph)LSSHVTELEEDLDTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LASLSSHVTELEEDLDTAR 19 0 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 1 LAS(0.966)LS(0.025)S(0.009)HVTELEEDLDTAR;LAS(0.997)LS(0.003)SHVTELEEDLDTAR;LAS(0.862)LS(0.124)S(0.014)HVTELEEDLDTAR 244.74 1.00E-24 100704000 64754 68468 36904 41177 73269 68909 71439 70777 101074 TRUE FALSE 56196.59483 68018.2292 54750.89784 50526.8672 71811.09025 71559.97382 64510.85678 55641.88934 89125.14686 0.630535789 0.76317663 0.614314812 0.566920437 0.805733205 0.802915634 0.723823287 0.624311895 1 16.44354493 3.2248395 24.99932939 0.765989125 0.650166733 0.308577253 0.105896486 363.9254446 663056.1026 0.03252891 0.0370742 1678.183707 -3.2248395 -0.115822392 LAS(ph)PELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LASPELER 8 0 P05412;P17535 P05412;P17535 JUN;JUND Transcription factor AP-1;Transcription factor jun-D 1 LAS(1)PELER;LAS(1)PELER 92.428 0.012362 869790000 1460460 998520 801260 1081310 1108480 1247490 1238140 1383720 1365080 TRUE FALSE 1267456.511 991960.6564 1188752.016 1326837.962 1086423.417 1295481.748 1118065.373 1087822.246 1203701.798 1.052965538 0.824091696 0.987580162 1.102297899 0.902568576 1.076248079 0.928855781 0.903730682 1 20.1990466 0.916088223 20.48520804 2.724098759 0.967070929 0.006773859 0.086974131 1285.326159 340952.6153 9050.104483 0.019796059 8.243055488 -0.916088223 -1.75702783 LAS(ph)PSGSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LASPSGSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR 38 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LAS(0.167)PS(0.167)GS(0.167)T(0.167)S(0.167)S(0.167)GLEVVAPEGTSAPGGGPGTLDDSATICR;LAS(0.658)PS(0.134)GS(0.176)T(0.031)S(0.001)SGLEVVAPEGTSAPGGGPGTLDDSATICR;LAS(0.238)PS(0.238)GS(0.238)T(0.238)S(0.039)S(0.008)GLEVVAPEGTSAPGGGPGTLDDSATICR 165.04 4.60E-18 4547100000 1922530 1339020 913500 1068950 1220340 1318080 1377330 1559260 1607350 TRUE FALSE 1668462.789 1330223.889 1355271.655 1311671.435 1196057.622 1368787.391 1243756.749 1225824.383 1417330.914 1.17718648 0.938541505 0.956213995 0.925451793 0.843880289 0.965750042 0.877534481 0.864882273 1 20.4347452 LAS(ph)YLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LASYLDR 7 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 LAS(1)YLDR;LAS(1)YLDR 117.89 0.0053807 106853000 240630 247380 149172 189490 255110 210210 235640 265520 292130 TRUE FALSE 208830.1358 245754.9445 221312.0782 232516.6007 250033.8101 218296.9147 212787.6691 208740.6143 257594.7242 0.810692597 0.954037181 0.859148334 0.902645042 0.970648024 0.847443267 0.826056006 0.810345068 1 17.97474352 1.219758495 24.86889438 1.000000444 0.872861568 0.341258188 0.055614676 1544.414385 2042624.796 0.492005728 0.014181133 16.58664291 -1.219758495 -0.127138877 LASDDRPS(ph)PPR ddPTM_MDA-MB-175_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;LASDDRPS(1)PPR;LAS(0.001)DDRPS(0.999)PPR;LASDDRPS(1)PPR;LASDDRPS(1)PPR;LASDDRPS(1)PPR 92.265 0.0061314 10878280000 6315960 5196810 3349260 4019780 5069940 5105260 5152860 5977340 5726890 TRUE FALSE 5481289.883 5162671.813 4968973.339 4932532.487 4969058.113 5301662.656 4653136.43 4699132.357 5049863.588 1.085433257 1.022338866 0.983981696 0.976765491 0.983998484 1.049862548 0.921438045 0.930546395 1 22.26781299 8 0.525845943 0.963633236 5.521001099 0.483605791 0.035610283 112.9793987 1.14306953 0.021670981 574.7184716 100000000 -8 4.557367863 LASDLLEWIR ddPTM_MDA-MB-175_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 ; 118.71 0.0018349 1795120000 1339170 1121590 1055250 1356230 1129070 1184590 1054200 1267530 2704910 FALSE TRUE 1162195.291 1114222.201 1565572.43 1664182.75 1106603.716 1230161.944 951963.8463 996478.5734 2385138.621 0.487265302 0.467151968 0.656386348 0.697729992 0.46395782 0.515761194 0.399123069 0.41778644 1 21.18564169 1.231883451 24.9996773 1.000000828 0.51068243 0.719932708 0.095419478 139.4627822 522107.7046 0.245632604 0.025959161 17.05624599 -1.231883451 -0.489318399 LASDLLEWIRR ddPTM_MDA-MB-175_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 ; 206.11 4.41E-08 312920000 729730 709750 401120 431200 688630 743910 669290 820920 166724 FALSE TRUE 633294.3316 705087.6055 595102.9737 529110.5505 674927.6103 772528.6991 604382.3588 645372.6464 147014.0787 4.307712142 4.79605499 4.047931866 3.599046808 4.590904602 5.254794004 4.11105089 4.38986968 1 17.16559479 1.238513969 24.6667278 0.999996321 4.385381728 0.851376282 0.444756495 0.352921668 184198.6477 0.622055872 0.111475029 17.31864735 -1.238513969 3.385385407 LASDS(ph)DAESDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LASDSDAESDSR 12 0 A0A0A0MRB5;Q8WXG6-6;Q8WXG6-8;Q8WXG6-5;Q8WXG6-4;Q8WXG6-7;Q8WXG6-3;Q8WXG6-2;Q8WXG6 A0A0A0MRB5 MADD MAP kinase-activating death domain protein 1 LASDS(1)DAESDSR;LAS(0.125)DS(0.875)DAESDSR;LASDS(1)DAESDSR;LASDS(1)DAESDSR 324.41 3.79E-47 2741680000 1509215 1336057 1011882 1107613 1309503 1502090 1464283 1416540 1462972 TRUE FALSE 1309768.414 1327280.354 1501231.52 1359113.46 1283446.452 1559876.374 1322277.06 1113623.945 1290021.117 1.015307732 1.028882657 1.163726314 1.05355908 0.994903444 1.209186698 1.025004198 0.863260244 1 20.29896325 1.989354219 24.4343855 0.928543732 1.077998338 0.402406299 0.072856102 319.7108967 733805.1579 0.030416066 0.019035019 97.57851828 -1.989354219 0.149454606 LASFYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LASFYER 7 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ;;; 162.21 0.0029787 873850000 1200770 1623040 757150 871910 1262910 1211200 1433470 1366680 1546230 FALSE TRUE 1042085.202 1612378.143 1123310.273 1069890.492 1237780.562 1257795.648 1294452.3 1074426.118 1363436.451 0.764307864 1.182584008 0.82388165 0.7847014 0.907838837 0.922518719 0.949404205 0.788028013 1 20.37881603 LASHLNLAMCHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LASHLNLAMCHLK 13 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 181.98 6.70E-06 4840200000 2520200 3042600 2214640 2957400 3275700 2728600 3705800 3874100 3780400 FALSE TRUE 2187149.185 3022612.96 3285647.312 3628922.871 3210519.979 2833571.008 3346412.086 3045653.863 3333485.419 0.65611482 0.906742517 0.985649223 1.088627192 0.963112051 0.850032519 1.003877823 0.913654473 1 21.66859999 4.724071859 2.921381676 0.967604201 0.608240163 0.719263305 0.061671173 0.211053613 2.649117894 0.015950984 0.175761487 52975.10895 -4.724071859 -0.359364038 LASLEELKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LASLEELKR 9 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 130.66 0.00056935 759660000 529010 550270 389880 410040 545000 532040 770590 708790 557160 FALSE TRUE 459099.9882 546655.2401 578427.2721 503145.8491 534155.5663 552507.9231 695858.3004 557220.7743 491293.1795 0.934472546 1.112686402 1.177356609 1.024125451 1.087244009 1.124599213 1.41638095 1.13419196 1 18.90622469 2.470325644 24.99955025 1.195454928 1.076683315 0.164515489 0.117989257 299.4260585 1101509.445 0.044023683 0.034179526 295.3422943 -2.470325644 -0.118771614 LASLGDTAS(ph)PLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LASLGDTASPLVK 13 0 Q6P4F7-3;Q6P4F7 Q6P4F7-3 ARHGAP11A Rho GTPase-activating protein 11A 1 LASLGDT(0.013)AS(0.987)PLVK 167.37 3.36E-05 35401000 149640 142640 109570 114700 133240 138890 171960 180040 182240 TRUE FALSE 129864.6949 141702.9884 162558.4185 140744.3881 130588.7847 144233.1882 155283.3457 141539.8471 160695.7948 0.80813997 0.88180894 1.011590992 0.875843629 0.812645937 0.897554216 0.966318663 0.880793721 1 17.29397265 -0.783987388 1.092594584 9.999999945 0.8901958 0.224743088 0.061616783 250.7597144 4.317609199 5531.458425 0.019728271 0.164441948 0.783987388 -9.109804145 LASLSSHVTELEEDLDTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LASLSSHVTELEEDLDTAR 19 0 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 0 ;;;;; 320.73 5.90E-62 509342000 358275 392820 131347.3 272806 424487 429336 333397 435911 549643 FALSE TRUE 310928.051 390239.5396 194867.2936 334750.7719 416040.5392 445852.8337 301064.2103 342694.8249 484664.8307 0.641532109 0.80517404 0.40206609 0.690685089 0.858408766 0.919919923 0.621180228 0.707075907 1 18.88662787 3.462159625 11.70946143 0.794972116 0.620374287 0.299860311 0.142149883 0.750512124 579.6905854 0.041357321 0.053869404 2898.408706 -3.462159625 -0.174597829 LASPS(ph)GSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LASPSGSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR 38 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LAS(0.435)PS(0.542)GS(0.019)T(0.004)SSGLEVVAPEGTSAPGGGPGTLDDSATICR 257.87 1.64E-62 1131900000 655800 445320 322410 400020 403610 476980 497370 537430 584060 TRUE FALSE 569134.3684 442394.6636 478328.5544 490850.6549 395578.9506 495329.7292 449135.134 422504.7768 515013.0922 1.105087185 0.858996927 0.928769699 0.953083839 0.768094941 0.961780849 0.872084886 0.820376769 1 18.97424958 4.743608434 24.40437005 0.88938632 1.105087312 0.469804504 0.069746807 325.9769639 1575907.536 0.016048196 0.128829032 55412.58806 -4.743608434 0.215700992 LASPSGST(ph)SSGLEVVAPEGTSAPGGGPGTLDDSATICR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LASPSGSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR 38 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LAS(0.212)PS(0.212)GS(0.212)T(0.242)S(0.061)S(0.061)GLEVVAPEGTSAPGGGPGTLDDSATICR 116.94 1.62E-05 184980000 120060 99913 62554 78151 85182 92293 100620 105320 115710 TRUE FALSE 104193.7668 99256.66492 92805.32363 95896.37901 83487.04486 95843.57143 90861.88789 82798.1376 102030.8956 1.021198199 0.972809896 0.909580604 0.939875892 0.818252593 0.939358327 0.890533082 0.811500645 1 16.63864655 4.526720396 1.05915966 0.885977226 1.063688454 0.343326327 0.056170213 1.314768618 1.562847986 0.017533607 0.243780682 33629.49891 -4.526720396 0.177711227 LASQEAELQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LASQEAELQLR 11 0 A0A087WYC6;A0A0C4DFR0;Q96DT5 A0A087WYC6 DNAH11 "Dynein heavy chain 11, axonemal" 0 72.2 0.046945 812150000 358550 404530 231610 281730 355740 450230 208720 240560 450970 FALSE TRUE 311166.7091 401872.6158 343617.3707 345701.1025 348661.47 467550.6394 188478.3665 189118.116 397656.8403 0.782500582 1.010601541 0.864105268 0.869345293 0.876789821 1.175764106 0.473972399 0.475581197 1 18.60116446 2.225057861 24.99998863 0.606216659 0.925371018 0.342941843 0.179271729 223.0389179 412947.184 0.071271138 0.048349015 167.90277 -2.225057861 0.319154359 LASS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LASSPK 6 0 Q9P2E9;Q9P2E9-3;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 LAS(0.035)S(0.965)PK;LAS(0.129)S(0.871)PK;LAS(0.076)S(0.924)PK;LAS(0.02)S(0.98)PK 104.06 0.035829 2343170000 7172600 6499260 5144300 7278200 5427440 6022360 7252900 10883400 10504600 TRUE FALSE 6224722.737 6456565.933 7632100.687 8930826.55 5319444.563 6254044.086 6549514.874 8556069.605 9262758.155 0.672016114 0.697045721 0.823955517 0.964164928 0.574283002 0.675181623 0.707080414 0.923706466 1 23.14301042 1.625178478 3.817194806 0.98435031 0.733694833 0.467913766 0.10373942 0.162574775 5.42130624 0.084100934 0.028596774 42.18698393 -1.625178478 -0.250655477 LASTLVHLGEYQAAVDGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LASTLVHLGEYQAAVDGAR 19 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;; 294.65 1.20E-49 8896609000 5171430 4738370 2668704 3348779 4789350 5082950 4664950 5244020 5015710 FALSE TRUE 4488012.423 4707243.335 3959298.181 4109170.455 4694051.305 5278494.376 4212543.867 4122627.132 4422758.478 1.014754128 1.064322947 0.895210127 0.929096734 1.061340186 1.193484655 0.952469796 0.932139332 1 22.07651503 LASYLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 LASYLDR 7 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;; 236.77 1.30E-07 62739020000 21193050 24014950 14781700 14456620 22101090 24273540 22695450 24276110 24012720 FALSE TRUE 18392334.75 23857194.21 21930179.56 17739216.53 21661321.55 25207358.79 20494448.75 19084852.79 21173963.6 0.868629752 1.126723115 1.035714426 0.837784407 1.02301685 1.190488435 0.967908 0.901335865 1 24.33578802 2.010696765 24.99884235 0.940920878 1.017862745 0.059825595 0.106328352 511.0831086 1194420.794 0.043577656 0.029349915 102.4936041 -2.010696765 0.076941866 LAT(ph)QSNEITIPVTFESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 LAT(0.5)QS(0.5)NEITIPVTFESR;LAT(0.54)QS(0.46)NEITIPVTFESR 221.13 4.23E-14 481020000 424420 477190 319343 355932 465856 492660 469920 456936 559620 TRUE FALSE 368331.8217 474055.3075 473778.3429 436751.8007 456586.377 511612.949 424347.2307 359223.7923 493462.3611 0.746423336 0.960671664 0.960110396 0.885076219 0.925270928 1.036782112 0.859938395 0.727965941 1 18.91258052 2.012816315 24.9594762 0.829372004 0.923785576 0.04197995 0.098772117 386.4293169 752559.2235 0.038830399 0.026161559 102.995041 -2.012816315 0.094413572 RQS(ph)LTSPDSQSARPANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RQSLTSPDSQSARPANR 17 2 Q15751 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 RQS(0.995)LT(0.005)SPDSQSARPANR;RQS(0.999)LT(0.001)SPDSQSARPANR 203.06 5.23E-12 172953000 62058 56615 32639 35414 48218 42462 62021 58562 24988 TRUE FALSE 53856.87807 56243.09234 48423.32957 43455.28997 47258.55614 44095.54062 56006.21297 46038.97203 22033.94711 2.444268283 2.55256546 2.197669321 1.972197254 2.144806644 2.001254719 2.541814805 2.08945641 1 14.42744034 1.247044979 4.11602536 0.881366721 2.251534368 0.791542505 0.202250981 0.103206603 3.180498233 0.417185698 0.053466281 17.66220735 -1.247044979 1.370167647 LATATGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LATATGAK 8 0 Q9BZH6 Q9BZH6 WDR11 WD repeat-containing protein 11 0 79.116 0.067164 92130000 162350 169720 130740 185050 146410 158300 189070 182070 397180 FALSE TRUE 140895.0362 168605.0981 193966.3013 227068.4308 143496.7274 164389.9034 170734.0205 143135.7474 350225.8329 0.402297669 0.481418223 0.553832079 0.648348607 0.409726279 0.469382575 0.487496936 0.408695573 1 18.41792598 1.233447176 24.99955473 1.000000798 0.484080935 0.826371913 0.074523691 67.39748012 329467.5247 0.154679076 0.018901668 17.11776958 -1.233447176 -0.515919863 LATELYHQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LATELYHQK 9 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ;; 89.543 0.0116 244520000 902230 759220 630080 651400 729510 707880 751930 904870 983850 FALSE TRUE 782998.0195 754232.6338 934788.7955 799310.326 714994.1783 735112.6017 679007.9443 711370.5922 867540.3738 0.902549372 0.869391969 1.077516187 0.921352308 0.824162425 0.847352612 0.782681665 0.819985575 1 19.72657137 3.35731922 5.310505789 0.845086172 0.95041012 0.240436884 0.077552521 0.271326863 11.51834062 0.022629659 0.029341347 2276.770314 -3.35731922 0.105323948 LATKSS(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LATKSSPVK 9 1 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 1 LAT(0.005)KS(0.119)S(0.876)PVK 65.842 0.039617 422990000 863290 681020 406890 437640 585340 449180 935920 1017100 147450 TRUE FALSE 749204.0392 676546.3348 603663.365 537012.8509 573692.8792 466460.2453 845154.6225 799601.0801 130018.629 5.76228226 5.203456921 4.642899019 4.130276216 4.412389853 3.587641624 6.500257918 6.14989626 1 16.98835882 4.462611799 2.500808867 4.587585063 5.75978647 0.079835012 1.49876683 1.070020309 11.86588287 0.396404601 2.054602338 29014.28005 -4.462611799 1.172201407 LATLGALETEGTDGHTFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LATLGALETEGTDGHTFR 18 0 G3V4I0;O75356 G3V4I0 ENTPD5 Ectonucleoside triphosphate diphosphohydrolase 5 0 211.17 3.32E-16 196700000 99608 93959 87797 95352 112790 154190 101890 99711 107590 FALSE TRUE 86444.55043 93341.77714 130255.9229 117003.129 110545.6997 160121.7891 92008.72348 78388.5786 94870.83277 0.911181529 0.983882764 1.372981759 1.233288731 1.165223246 1.687787325 0.969831515 0.82626637 1 16.53367699 2.022704964 24.99998571 0.899920927 1.228168008 0.297347874 0.21390697 259.7907946 286049.2791 0.088690378 0.059790975 105.3670847 -2.022704964 0.328247081 LATLS(ph)DQVNRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LATLSDQVNRR 11 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 LAT(0.022)LS(0.978)DQVNRR 78.486 0.018222 257310000 447280 430970 288630 348740 404760 468850 435760 538570 366840 TRUE FALSE 388170.8147 428138.9297 428212.4334 427926.7472 396706.0679 486886.9629 393500.0623 423400.9967 323472.5931 1.200011448 1.323570957 1.32379819 1.322915005 1.226397773 1.505187683 1.216486561 1.308923865 1 18.30328396 1.238156143 24.99002104 0.999999655 1.305370635 0.552865139 0.085735875 6.998608412 431858.9856 0.110334856 0.019344904 17.30438396 -1.238156143 0.30537098 LATNTS(ph)APDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 LATNTS(1)APDLK 235.38 1.68E-15 282640000 1770200 1075500 908080 849170 809850 963240 1262600 970090 1314100 TRUE FALSE 1536263.585 1068434.97 1347230.525 1041987.027 793735.5694 1000296.466 1140153.246 762643.8027 1158748.595 1.325795424 0.922059344 1.1626599 0.899234771 0.684993771 0.863255818 0.983952215 0.658161577 1 20.14413616 3.621130394 4.406939043 0.825239969 1.114540347 0.466771601 0.145252354 0.195166624 6.145238705 0.038311473 0.058099647 4179.558362 -3.621130394 0.289300378 LATQS(ph)NEITIPVTFESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 LAT(0.089)QS(0.911)NEITIPVTFESR;LAT(0.003)QS(0.997)NEITIPVTFESR;LAT(0.209)QS(0.791)NEITIPVTFESR;LAT(0.019)QS(0.981)NEITIPVTFESR;LAT(0.361)QS(0.639)NEITIPVTFESR;LATQS(1)NEITIPVTFESR 276.03 1.02E-35 1862076000 1374723 1519880 1010084 1075629 1383213 1539608 1502173 1667668 1713252 TRUE FALSE 1193049.872 1509895.808 1498564.001 1319867.004 1355689.768 1598837.716 1356492.494 1311050.176 1510713.3 0.789726199 0.99945887 0.991957905 0.8736714 0.897383883 1.058332985 0.897915239 0.867835198 1 20.52679846 LATQSNEITIPVTFES(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 LATQSNEITIPVTFES(1)R;LATQSNEITIPVT(0.084)FES(0.916)R;LATQSNEITIPVT(0.007)FES(0.993)R;LATQSNEITIPVTFES(1)R 311.1 4.24E-58 607411000 579546 954480 554776 485537 754460 717410 699892 743190 975570 TRUE FALSE 502957.5277 948209.958 823067.5292 595785.5968 739447.7221 745009.2269 632016.5816 584264.602 860239.226 0.584671697 1.102263102 0.956789117 0.692581295 0.859583822 0.86604889 0.734698631 0.679188515 1 19.71437839 3.754361181 24.63091482 0.792581469 0.903343482 0.039088381 0.157443047 1639.582433 2555875.533 0.039942708 0.068886776 5680.168008 -3.754361181 0.110762012 LATQSNEITIPVTFESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;; 406.25 6.14E-140 7999996000 3745520 3461720 2306037 2672800 3513580 4003320 3680770 3953090 3893340 FALSE TRUE 3250540.042 3438979.733 3421244.206 3279700.091 3443666.632 4157330.311 3323809.492 3107752.466 3433073.781 0.946830814 1.001720311 0.996554232 0.955324674 1.00308553 1.210964452 0.968173044 0.905239055 1 21.71106943 2.012608051 24.99992322 0.943107371 1.019969244 0.126160783 0.075897919 396.497249 786192.9802 0.031866903 0.021469733 102.945662 -2.012608051 0.076861873 LATTILQHWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LATTILQHWK 10 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 126.39 0.00038392 921870000 1707330 1899310 1060490 1347780 2029800 1375150 2154900 2203300 2040100 FALSE TRUE 1481702.015 1886833.308 1573346.511 1653814.049 1989410.951 1428052.91 1945918.13 1732141.441 1798921.702 0.823661204 1.048869056 0.874605331 0.919336315 1.105890795 0.79383828 1.081713633 0.962877617 1 20.77870096 4.76015742 23.41964396 0.97140088 0.823660842 0.19767269 0.094725858 3717.612563 4031237.586 0.021024127 0.870488349 57564.85561 -4.76015742 -0.147740038 LAVYIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 LAVYIDR 7 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;; 143.02 0.0056997 7672920000 6106750 5537140 3664380 3944890 5210370 5605190 4899370 5751310 5471080 FALSE TRUE 5299727.515 5500766.163 5436486.425 4840637.568 5106693.831 5820825.286 4424229.851 4521437.113 4824295.155 1.0985496 1.140221729 1.126897557 1.003387524 1.058536774 1.206564918 0.917072797 0.937222323 1 22.20188674 2.220080109 24.99994809 0.947039751 1.101432644 0.624913374 0.056239856 157.0092468 212396.4108 0.023316206 0.015752357 165.989306 -2.220080109 0.154392893 LAWVGDVFTATPAEPRPLTS(ph)PLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAWVGDVFTATPAEPRPLTSPLR 23 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 LAWVGDVFTATPAEPRPLT(0.118)S(0.882)PLR;LAWVGDVFTATPAEPRPLT(0.113)S(0.887)PLR 229.27 3.39E-33 2490600000 2063130 1848380 882340 929290 1879810 1878710 1858370 2114600 532910 TRUE FALSE 1790482.143 1836237.87 1309042.575 1140299.498 1842405.459 1950985.189 1678145.563 1662409.246 469909.9869 3.810266207 3.907637465 2.785730484 2.426633887 3.920762508 4.151827464 3.571206423 3.537718483 1 18.8420249 4.258105019 24.20825644 3.174355981 3.858952799 0.111005825 0.89720424 439.0396153 543793.2295 0.224728486 0.592451151 18117.78155 -4.258105019 0.684596818 LAYHPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LAYHPLK 7 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 90.285 0.017251 987850000 1233600 1719300 1102100 1325000 1642400 1293300 1821800 1920800 2042200 FALSE TRUE 1070576.634 1708005.805 1635079.246 1625861.501 1609719.453 1343054.088 1645122.116 1510051.868 1800773.442 0.594509342 0.948484559 0.907987206 0.902868436 0.893904483 0.745820688 0.913564182 0.838557384 1 20.78018525 4.746113204 24.74563755 0.886590043 0.59450918 0.662784626 0.066932665 494.8752368 1621386.952 0.015777456 0.160855314 55733.1005 -4.746113204 -0.292080863 LAYIAHPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LAYIAHPK 8 0 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 0 ; 91.906 0.012155 5414300000 9317300 11330700 6764500 6849500 9875600 9221900 11674700 12004400 7844200 FALSE TRUE 8085995.198 11256267.89 10035834.83 8404783.663 9679094.881 9576672.46 10542489.39 9437352.478 6916867.612 1.169025584 1.627364946 1.450921919 1.215114143 1.399346557 1.384538927 1.524171053 1.364396864 1 22.72168741 1.245511622 4.94807792 0.975814101 1.402827232 0.464490147 0.132421464 0.143418456 8.712025666 0.208962615 0.031498705 17.5999576 -1.245511622 0.427013131 LAYQELQIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LAYQELQIDR 10 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;E9PIY6;Q8N6H7-3;H0YDN9 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 0 172.88 8.33E-06 111810000 99579 100980 59382 52195 97907 87038 95510 109640 94544 FALSE TRUE 86419.38285 100316.6557 88099.33382 64046.6725 95958.84225 90386.40818 86247.4549 86194.33922 83367.11602 1.03661236 1.203312055 1.056763602 0.768248628 1.151039484 1.084197373 1.03455006 1.03391293 1 16.34719081 4.008328255 24.74003549 1.015873154 1.122481158 0.151296423 0.1049282 309.8470847 920415.2636 0.026321394 0.054636221 10193.61566 -4.008328255 0.106608004 LCAAAASILGKPADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LCAAAASILGKPADR 15 1 P30046;J3KQ18;B5MC82;P30046-2;A6NHG4 P30046 DDT;DDTL D-dopachrome decarboxylase;D-dopachrome decarboxylase-like protein 0 139.21 5.31E-06 888460000 1681300 1696700 942810 1219500 1609600 1787000 1704700 1962900 1408500 FALSE TRUE 1459111.945 1685554.266 1398756.07 1496406.114 1577572.109 1855747.046 1539378.456 1543149.11 1241988.735 1.174818985 1.357141348 1.126222832 1.204846769 1.270198405 1.494173816 1.239446392 1.242482373 1 20.24422066 1.19284034 2.95842793 0.926508241 1.270077143 0.400289229 0.101624938 0.525618431 5.154314402 0.461591645 0.026592562 15.58979268 -1.19284034 0.343568902 LCAGIMITAS(ph)HNPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LCAGIMITASHNPK 14 0 Q96G03-2;Q96G03 Q96G03-2;Q96G03 PGM2 Phosphoglucomutase-2 1 LCAGIMITAS(1)HNPK;LCAGIMITAS(1)HNPK;LCAGIMITAS(1)HNPK;LCAGIMITAS(1)HNPK;LCAGIMIT(0.001)AS(0.999)HNPK;LCAGIMITAS(1)HNPK 228.9 9.58E-13 6269590000 8251940 8374430 5740220 6982370 7654690 5976240 8914410 9413920 11481080 TRUE FALSE 7161425.221 8319417.818 8516209.592 8567823.827 7502376.645 6206149.82 8049891.89 7400826.467 10123799.8 0.707385109 0.821768306 0.841206835 0.846305142 0.741063315 0.613025736 0.795145306 0.731032479 1 23.27124755 1.233699509 24.99961929 1.00000036 0.763857265 0.529639541 0.07043479 131.1919024 674610.028 0.143971781 0.017980028 17.1277182 -1.233699509 -0.236143095 LCDDGPQLPTS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LCDDGPQLPTSPR 13 0 O60504-2;O60504;H0YAZ3;H0YB51 O60504-2 SORBS3 Vinexin 1 LCDDGPQLPT(0.004)S(0.996)PR;LCDDGPQLPTS(1)PR;LCDDGPQLPT(0.001)S(0.999)PR;LCDDGPQLPTS(1)PR;LCDDGPQLPT(0.485)S(0.515)PR;LCDDGPQLPT(0.018)S(0.982)PR 249.82 1.26E-17 6879230000 8931400 9443600 5879830 7175440 9170900 9030400 8720910 10152900 9899800 TRUE FALSE 7751092.861 9381564.37 8723335.455 8804733.322 8988417.033 9377805.331 7875157.49 7981781.345 8729456.922 0.887923834 1.074701949 0.999298757 1.008623263 1.029665088 1.074271334 0.902136016 0.914350276 1 23.05746047 2.225923371 24.99957691 0.932200209 1.015260993 0.264870923 0.057306034 259.6966224 513739.4525 0.022035538 0.014966516 168.237719 -2.225923371 0.083060784 LCDEQLSSQSHYDFGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LCDEQLSSQSHYDFGLR 17 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 250.95 1.49E-21 2117520000 1005890 1058930 500810 713900 1133640 1136090 1020000 1107660 1131680 FALSE TRUE 872959.0879 1051973.819 743003.3911 876001.9063 1111082.782 1179796.117 921080.557 870795.5288 997894.0796 0.87480135 1.054193867 0.744571399 0.87785059 1.113427572 1.182285917 0.923024373 0.872633225 1 19.92852716 5.037887714 12.15816342 0.962275369 0.622365656 0.049836029 0.127026995 389147.8643 4484444.936 0.032821667 2651930.599 109115.8182 -5.037887714 -0.339909714 LCDFGLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LCDFGLAR 8 0 A0A1C7CYZ1;Q8TD08-2;Q8TD08-3;Q8TD08 A0A1C7CYZ1 MAPK15 Mitogen-activated protein kinase 15 0 ;; 149.99 0.0011546 391415000 1004890 1075410 671980 774740 1063490 1061080 1008910 1128460 1190900 FALSE TRUE 872091.2404 1068345.561 996951.7756 950656.5582 1042328.63 1101900.434 911066.0635 887147.6107 1050113.159 0.830473586 1.017362321 0.949375567 0.905289635 0.992586962 1.0493159 0.867588465 0.844811441 1 20.00211337 2.160555483 24.99999844 0.890251514 0.959010298 0.097911919 0.072119748 59.8265409 19170.7816 0.028623402 0.019297897 144.728974 -2.160555483 0.068758784 LCDFGSASHVADNDITPY(ph)LVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 LCDFGSASHVADNDITPYLVSR 22 0 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 LCDFGSASHVADNDIT(0.005)PY(0.955)LVS(0.04)R;LCDFGSASHVADNDIT(0.001)PY(0.988)LVS(0.01)R;LCDFGSASHVADNDITPY(0.997)LVS(0.002)R;LCDFGSASHVADNDIT(0.001)PY(0.999)LVSR;LCDFGSASHVADNDIT(0.012)PY(0.976)LVS(0.012)R;LCDFGSASHVADNDITPY(1)LVSR;LCDFGSASHVADNDIT(0.001)PY(0.983)LVS(0.016)R;LCDFGSASHVADNDIT(0.004)PY(0.996)LVS(0.001)R;LCDFGSASHVADNDITPY(1)LVSR;LCDFGSASHVADNDITPY(0.999)LVS(0.001)R;LCDFGSASHVADNDITPY(1)LVSR 309.12 2.21E-66 62573827000 8436757 7280412 3287914 5073232 7393715 7612092 6688577 8021660 7230715 TRUE FALSE 7321818.186 7232586.494 4877960.208 6225186.865 7246594.537 7904934.105 6039919.832 6306290.434 6375908.11 1.148356918 1.134361783 0.765061247 0.976360819 1.13655881 1.239813054 0.947303463 0.989081136 1 22.60419941 2.195588156 0.00943926 2.11E-07 2.048295558 0.01437655 0.133303665 44641.57821 239.0076893 26385.4985 25477.29613 156.8874325 -2.195588156 2.048295347 LCDSYEIRPGK ddPTM_MDA-MB-175_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 3140380000 4170300 3250400 2220110 2632370 3228130 2632250 3415750 3967170 3616860 FALSE TRUE 3619184.289 3229047.908 3293762.622 3230089.842 3163896.529 2733514.361 3084491.091 3118821.568 3189278.931 1.134797039 1.012469583 1.032760913 1.012796281 0.992041335 0.857094792 0.96714372 0.977908059 1 21.60479885 7.999994699 0.541486933 0.958975154 8.141225694 0.594366841 0.043298777 101.3830875 0.975549502 0.024689123 842.7583378 99998779.43 -7.999994699 7.182250541 LCPGGQLPFLLYGTEVHTDTNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LCPGGQLPFLLYGTEVHTDTNK 22 0 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ; 257.75 3.74E-37 426390000 430300 376090 361100 421440 403570 352820 443960 488380 915210 FALSE TRUE 373434.7648 373619.44 535729.1678 517134.3933 395539.7466 366393.2137 400904.8275 383943.7376 807014.9164 0.462735889 0.462964726 0.663840478 0.640799052 0.490126934 0.45401046 0.496774991 0.475757919 1 19.62223581 1.235419783 24.99998303 1.000000659 0.519111617 0.806269646 0.074193253 41.28545295 328560.7504 0.13636842 0.019667449 17.19569696 -1.235419783 -0.480889042 LPGS(ph)PGLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LPGSPGLSK 9 0 Q8N9U0;Q8N9U0-2 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 LPGS(1)PGLSK;LPGS(1)PGLSK;LPGS(1)PGLSK;LPGS(1)PGLSK 180.97 5.04E-05 1274960000 3318720 3215620 2969930 4387750 4212000 3598800 3202270 5614000 9031600 TRUE FALSE 2880142.743 3194496.38 4406198.082 5384055.7 4128189.441 3737248.165 2891714.348 4413489.788 7963894.537 0.361650036 0.401122386 0.553271777 0.676058137 0.518363148 0.46927394 0.363103044 0.554187372 1 22.92504269 1.24806187 4.064356814 1.049728996 0.484766237 0.74910157 0.094183472 0.122148204 3.601902017 0.201359005 0.025663347 17.70361147 -1.24806187 -0.564962759 LCQENQWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LCQENQWLR 9 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;G5E9S8;G3V2P7;C9JZE5;C9J8T5;Q9NSK0-4;Q9NSK0-3;Q9NSK0 Q07866-6;Q9NSK0-3 KLC1;KLC4 Kinesin light chain 1;Kinesin light chain 4 0 ;; 111.06 0.0050855 137410000 243761 220714 134093 165259 207748 215878 217155 243688 315580 FALSE TRUE 211547.3662 219264.1152 198940.8233 202783.5818 203614.2213 224182.9664 196095.3415 191577.2176 278272.4919 0.760216595 0.787947503 0.714913723 0.72872306 0.731708046 0.805623886 0.7046882 0.688451871 1 18.08613878 1.231861591 24.99990318 1.000000443 0.738295151 0.835781302 0.036170229 95.12852484 354974.5274 0.089210462 0.009415126 17.0553875 -1.231861591 -0.261705292 LCQFHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LCQFHR 6 0 O43684;O43684-2;J3QT28 O43684 BUB3 Mitotic checkpoint protein BUB3 0 ;; 84.185 0.056138 962700000 4054710 4281510 2185410 2943740 3871800 4714350 3649600 4317270 3996260 FALSE TRUE 3518869.8 4253384.479 3242281.586 3612161.159 3794758.755 4895714.095 3295662.354 3394055.408 3523826.695 0.99859332 1.207035659 0.920102453 1.025067766 1.07688575 1.3893175 0.935250975 0.963173192 1 21.74871154 TVKEEAEKPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TVKEEAEKPER 11 2 K7ELL7;P14314-2;P14314 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;; 119.25 0.00034362 2292340000 4874560 3117150 2572980 2846530 3155290 2899700 4329180 4021100 1587360 FALSE TRUE 4230374.545 3096673.236 3817281.734 3492878.143 3092505.902 3011253.335 3909336.79 3161219.057 1399704.109 3.022334876 2.212377042 2.727206207 2.495440372 2.209399745 2.151349929 2.792973718 2.258490946 1 20.41669045 1.248238863 3.695001358 0.82259164 2.487984543 0.740095791 0.279853379 0.129361504 2.778792744 0.58908893 0.067393162 17.71082789 -1.248238863 1.665392903 LCS(ph)SSSSDTSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LCSSSSSDTSSR 12 0 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 LCS(0.421)S(0.421)S(0.033)S(0.033)S(0.088)DT(0.003)SSR 123.99 0.00020977 0 99452 86211 57595 65163 78003 80035 81120 94970 94208 TRUE FALSE 86309.16622 85644.67426 85448.13464 79959.2551 76450.89291 83113.99824 73252.99489 74661.40456 83070.83756 1.038982738 1.030983637 1.028617709 0.962543023 0.920309644 1.000519565 0.881813607 0.898767928 1 16.34205448 3.647377341 2.598488506 0.93354378 1.035324963 0.549725328 0.03809249 0.206989063 2.722894429 0.011402861 0.019126713 4439.942452 -3.647377341 0.101781182 LCSDHCFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LCSDHCFNR 9 0 Q9UBW7;Q9UBW7-2 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 0 133.13 0.0013476 0 82823 95809 43066 53062 88390 83079 70926 84752 79546 FALSE TRUE 71877.7307 95179.62437 63892.86165 65110.5381 86631.21193 86275.10289 64047.60744 66628.44434 70142.1625 1.02474358 1.356953093 0.910905216 0.928265337 1.235080426 1.230003465 0.913111389 0.949905762 1 16.09799429 2.220165421 24.99369936 0.951697592 1.113138992 0.22652972 0.139319032 371.7218739 505057.5059 0.057857083 0.039089408 166.0219156 -2.220165421 0.1614414 LCSDLMNCLHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LCSDLMNCLHER 12 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22;B0QYG7;B0QYG8 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 ;;; 204.48 1.13E-07 1395090000 1746030 1760550 1062920 1265430 1750460 1691070 1654170 1795610 1684010 FALSE TRUE 1515287.712 1748984.831 1576951.667 1552765.222 1715629.271 1756126.557 1493748.848 1411632.775 1484928.256 1.020445065 1.177824466 1.061971621 1.045683666 1.155361724 1.182633942 1.005940079 0.950640389 1 20.5019618 2.07417641 6.863391037 0.973656431 1.107533424 0.522793229 0.055390758 0.153189395 11.53939646 0.022511248 0.015070344 118.6250503 -2.07417641 0.133876994 LCSS(ph)SSSDTSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LCSSSSSDTSSR 12 0 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 LCS(0.051)S(0.808)S(0.125)S(0.008)S(0.008)DTSSR;LCS(0.002)S(0.492)S(0.492)S(0.014)SDTSSR;LCS(0.004)S(0.937)S(0.058)S(0.001)S(0.001)DTSSR 272.25 1.03E-27 1397850000 956900 1067200 927640 1026900 1412960 1521880 1591150 1724840 1573670 TRUE FALSE 830443.2405 1060189.493 1376249.807 1260073.34 1384844.86 1580427.708 1436840.518 1355996.389 1387632.525 0.59846049 0.76402756 0.991797022 0.908074232 0.997991064 1.138938213 1.035461833 0.977201358 1 20.40419413 4.736127775 1.015332374 1.022921869 0.35810088 0.858895559 0.057119251 0.686440085 0.574331303 0.019267365 0.498861006 54466.28766 -4.736127775 -0.664820989 LCTSYSHSSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LCTSYSHSSTR 11 0 B4DQA8;E9PCW1;K7EJC8;G5E9T8;O95249;F6RU00 B4DQA8 GOSR1 Golgi SNAP receptor complex member 1 0 107.11 0.0022408 92484000 149600 149030 75806 98080 171490 215780 139070 165580 148020 FALSE TRUE 129829.981 148051.0121 112466.0352 120350.5631 168077.6845 224081.1962 125583.0128 130172.0055 130521.2442 0.994703826 1.13430586 0.861668427 0.922076431 1.287741973 1.716817807 0.962165305 0.997324277 1 16.99392512 3.247901107 24.9988954 1.177276232 0.981016977 0.181902012 0.224794478 427.1908893 1143327.393 0.071564663 0.091125442 1769.705933 -3.247901107 -0.196259256 LCVQNSHQEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LCVQNSHQEAR 11 0 Q9H0L4 Q9H0L4 CSTF2T Cleavage stimulation factor subunit 2 tau variant 0 ;; 151.13 3.36E-05 499650000 583150 416384 380933 399974 381926 350877 505008 577310 575200 FALSE TRUE 506085.25 413648.7461 565153.4729 490794.2099 374326.4198 364375.4652 456032.4019 453856.7491 507200.5113 0.997801143 0.815552699 1.114260456 0.967653224 0.738024532 0.718405162 0.899116605 0.894827073 1 18.95219667 3.412622191 20.20900562 0.85276702 0.973358984 0.249816456 0.106545399 16.74250568 5244.479787 0.031789212 0.041039686 2585.962313 -3.412622191 0.120591965 LCWFLDEAAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LCWFLDEAAAR 11 0 M0R1L2;O95336 M0R1L2 PGLS 6-phosphogluconolactonase 0 ; 156.92 7.17E-05 655350000 987490 873860 588390 635880 721040 685670 878640 993660 997520 FALSE TRUE 856990.6945 868119.5561 872937.372 780266.2728 706692.7147 712048.1686 793429.628 781173.5417 879594.322 0.974302213 0.986954479 0.992431795 0.887075159 0.803430283 0.809518832 0.902040416 0.888106622 1 19.74647877 3.712995953 6.359881483 0.877036147 0.984990036 0.446679873 0.053841053 0.166644836 25.65753946 0.015611458 0.024042892 5164.115572 -3.712995953 0.10795389 LCYSSDHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LCYSSDHEK 9 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;; 229.48 1.25E-07 8576800000 4445340 4752970 1920080 3827880 4911710 4341950 5977400 5787800 6128100 FALSE TRUE 3857877.056 4721747.427 2848637.11 4697058.659 4813976.581 4508987.626 5397712.668 4550124.011 5403642.999 0.713940032 0.873808175 0.527169747 0.869239263 0.890876133 0.834434774 0.998902531 0.842047487 1 22.36550093 3.503068755 24.42769371 0.904400274 0.717914213 0.481499787 0.098735393 481.8122649 453590.0114 0.02523658 0.037266527 3184.701664 -3.503068755 -0.186486061 LCYVALDFEQEMATAASS(ph)SSLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LCYVALDFEQEMATAASSSSLEK 23 0 P60709;A0A2R8Y793;A0A2R8YEA7;P63261;I3L4N8;Q6S8J3 P60709;P63261;Q6S8J3 ACTB;ACTG1;POTEE "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;POTE ankyrin domain family member E" 1 LCYVALDFEQEMATAAS(0.138)S(0.753)S(0.096)S(0.013)LEK;LCYVALDFEQEMATAAS(0.023)S(0.819)S(0.135)S(0.023)LEK;LCYVALDFEQEMATAAS(0.003)S(0.802)S(0.171)S(0.024)LEK;LCYVALDFEQEMATAAS(0.001)S(0.908)S(0.09)S(0.002)LEK 270.18 8.48E-46 188146000 261930 257620 170176 205175 219557 183497 267307 334197 297120 TRUE FALSE 227315.2869 255927.6773 252473.6828 251763.1197 215188.2453 190556.2483 241383.6083 262731.5723 261994.8121 0.867632779 0.976842538 0.963659092 0.960946966 0.821345444 0.727328327 0.921329725 1.002812117 1 17.99917872 1.809563402 4.451724691 1.000759968 0.88968334 0.279929273 0.074574201 0.303071851 10.38163776 0.047919057 0.022211754 64.50054764 -1.809563402 -0.111076628 LCYVALDFEQEMATAASSSSLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LCYVALDFEQEMATAASSSSLEK 23 0 P60709;A0A2R8Y793;A0A2R8YEA7;P63261;I3L4N8;Q6S8J3 P60709;P63261;Q6S8J3 ACTB;ACTG1;POTEE "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;POTE ankyrin domain family member E" 0 ;; 123.14 6.28E-05 364390000 415310 354570 253423 333250 292835 264853 415800 460330 392390 FALSE TRUE 360425.7312 352240.8063 375979.2104 408919.5059 287008.1564 275042.0663 375475.78 361892.0118 346002.1012 1.041686539 1.01803083 1.086638518 1.181841106 0.829498305 0.794914439 1.085183525 1.045924318 1 18.40042127 3.248602359 24.99944121 0.965203103 1.077804272 0.30271134 0.097362545 340.3098655 847214.3297 0.031455619 0.040126307 1772.565773 -3.248602359 0.11260117 LDAAERFLSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDAAERFLSTR 11 1 Q96KP6;Q96KP6-2;Q96KP6-3 Q96KP6 TNIP3 TNFAIP3-interacting protein 3 0 51.092 0.091852 311400000 237570 387140 435830 358020 192050 198550 384480 378780 448530 FALSE TRUE 206174.5226 384596.8518 646598.8458 439313.913 188228.5807 206188.347 347193.1888 297780.8447 395505.2944 0.521293964 0.972418972 1.634867737 1.1107662 0.475919244 0.521328918 0.877847133 0.752912411 1 18.59333748 3.265787079 24.9332884 0.730220179 1.094666492 0.224757854 0.305354355 315.9829595 289366.8356 0.091322207 0.117866289 1844.111086 -3.265787079 0.364446313 LDADIHTNTCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDADIHTNTCR 11 0 C9J8T0;P57772-2;P57772 C9J8T0 EEFSEC Selenocysteine-specific elongation factor 0 88.441 0.0094138 0 325400 288090 200750 217260 320100 299200 290360 306860 294790 FALSE TRUE 282397.5655 286197.5178 297833.3715 266592.2036 313730.6363 310710.4176 262200.9319 241240.377 259940.262 1.086394094 1.101012654 1.145776222 1.02559027 1.2069336 1.195314705 1.008696882 0.928060836 1 17.98782058 2.07060394 5.824386354 0.961423039 1.12502722 0.626987844 0.05451059 0.1195332 7.25342325 0.023084004 0.015286692 117.6532531 -2.07060394 0.163604181 LDADYPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LDADYPLR 8 0 O43583;F8VVL1 O43583 DENR Density-regulated protein 0 ;; 155.82 0.00093732 664370000 2516420 2583110 1612140 1911680 2496360 2410490 2444480 2785520 2576390 FALSE TRUE 2183868.721 2566141.38 2391776.296 2345756.162 2446687.32 2503223.11 2207414.706 2189858.225 2271812.109 0.961289322 1.129557048 1.052805506 1.03254849 1.076976089 1.101861857 0.971653728 0.963925765 1 21.11541209 2.222851826 24.99722063 0.975198277 1.061681911 0.41526321 0.044989328 204.5778897 325540.0938 0.017163539 0.011614731 167.0520563 -2.222851826 0.086483634 LDAENAIVHMGGQWLGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDAENAIVHMGGQWLGGR 18 0 E7ETJ9;Q01085;Q01085-2 E7ETJ9 TIAL1 Nucleolysin TIAR 0 ; 126 2.85E-05 1153640000 887000 810030 503860 729350 826840 767560 803800 861950 921470 FALSE TRUE 769780.7026 804708.8596 747528.3813 894960.0649 810387.5017 797088.5299 725847.5997 677628.7002 812534.8663 0.947381749 0.990368405 0.919995452 1.101442045 0.997357203 0.98098994 0.893312558 0.833968766 1 19.6320702 2.263621667 5.146196203 0.892219261 0.992698527 0.262048877 0.061672028 0.19579277 13.56865535 0.024001396 0.017587567 183.4939151 -2.263621667 0.100479266 LDALQMFVFDLHWPEQEFAHHLEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDALQMFVFDLHWPEQEFAHHLEQR 25 0 C9IYE1;A0A087X1P3;Q86UW7-3;Q86UW7-2;Q86UW7;H0Y8B5;H7BYR4;F8W8P5 C9IYE1 CADPS2 Calcium-dependent secretion activator 2 0 116.47 0.00044105 45646000 10186 7270.9 6624.9 7740.2 8853.6 7838.3 9573.9 10443 9187 FALSE TRUE 8839.894292 7223.136979 9828.723799 9497.730712 8677.430682 8139.844473 8645.424652 8209.845718 8100.923326 1.091220585 0.891643667 1.213284388 1.172425701 1.071165635 1.004804532 1.067214724 1.013445676 1 12.98387064 2.899677644 5.692790095 1.024973791 1.090471596 0.135643754 0.084541769 0.534362267 24.84909169 0.028262295 0.028427613 793.7388616 -2.899677644 0.065497806 LDALVAEEHLTVDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LDALVAEEHLTVDAR 15 0 A6NFX8;Q9UKK9 A6NFX8 NUDT5 ADP-sugar pyrophosphatase 0 ;;; 230.16 3.65E-13 1118427000 1330460 1321420 809744 906003 1276083 1432140 1231270 1429150 1620980 FALSE TRUE 1154636.34 1312739.505 1201338.907 1111724.829 1250691.445 1487235.353 1111861.625 1123537.394 1429349.591 0.807805415 0.918417379 0.840479414 0.777783711 0.875007383 1.040497973 0.777879416 0.786048005 1 20.44692738 3.030071526 24.99571858 0.8811512 0.840321595 0.088429447 0.088376327 787.1131049 654250.3615 0.028112849 0.031876586 1071.695794 -3.030071526 -0.040829605 LDAMFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDAMFR 6 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;K7EIV0;Q96L46;K7EMQ1 A0A0C4DGQ5 CAPNS1;CAPNS2 Calpain small subunit 1;Calpain small subunit 2 0 ; 103.28 0.080999 929440000 797930 724320 476370 521920 636650 620900 626190 762520 731040 FALSE TRUE 692481.5288 719561.8942 706744.1254 640429.913 623981.9106 644786.4248 565462.1902 599461.0319 644617.284 1.07425219 1.116262179 1.096377871 0.993504098 0.967988179 1.000262389 0.877206064 0.929948741 1 19.29808335 3.554439943 1.66726954 0.9444205 1.103417473 0.744516525 0.037305372 0.180291562 0.998618446 0.012431534 0.022138036 3584.593745 -3.554439943 0.158996972 LDDDFKEMEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDDDFKEMEK 10 1 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 0 66.498 0.060003 152820000 130560 119760 100130 102740 122420 115030 139360 149690 135270 FALSE TRUE 113306.1652 118973.2887 148553.2029 126068.6873 119984.0815 119455.2785 125844.8886 117679.9584 119278.5347 0.949929218 0.997440897 1.245431152 1.056926861 1.00591512 1.001481774 1.055050592 0.986597955 1 16.86397491 3.303320899 5.598562078 1.009904618 1.0719299 0.099837131 0.07702626 0.451222244 26.8404674 0.023151403 0.029741523 2010.577876 -3.303320899 0.062025282 LDDDSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDDDSER 7 0 Q86VP6;Q86VP6-2;F5H6I6 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 137.18 0.019715 0 632660 618710 471450 509700 410890 576210 560000 615940 1059200 FALSE TRUE 549052.378 614645.6533 699444.7969 625435.1753 402714.0929 598377.1716 505691.2862 484226.0243 933982.5826 0.587861474 0.65809113 0.748884198 0.669643296 0.431179446 0.640672731 0.541435457 0.518452949 1 19.83303612 1.23162403 24.99998711 1.00000069 0.597717665 0.668131043 0.088692641 158.617812 571618.8322 0.223460622 0.02301049 17.04606068 -1.23162403 -0.402283026 LDDFLDLNHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LDDFLDLNHK 10 0 Q8WVY7 Q8WVY7 UBLCP1 Ubiquitin-like domain-containing CTD phosphatase 1 0 ;;; 182.28 1.79E-06 900136000 1993340 1762000 1286382 1506154 1663330 1310338 1836040 2205700 2158330 FALSE TRUE 1729915.069 1750425.306 1908480.638 1848149.286 1630232.987 1360747.551 1657981.123 1734028.22 1903174.686 0.90896284 0.919739695 1.002787948 0.971087572 0.856586103 0.714988257 0.871166024 0.911124046 1 20.85997656 3.235472502 24.99733251 0.868057027 0.952161563 0.22499376 0.073540276 129.699546 1049878.478 0.023692513 0.028025696 1719.778449 -3.235472502 0.084104537 LDDIEEFENIRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDDIEEFENIRK 12 1 Q8NHZ8 Q8NHZ8 CDC26 Anaphase-promoting complex subunit CDC26 0 ; 137.59 0.00014357 230317000 319910 243090 195790 217200 251420 200131 320680 333840 242070 FALSE TRUE 277633.083 241493.1258 290474.6989 266518.5797 246417.2339 207830.1691 289580.503 262450.9139 213452.7604 1.300676939 1.131365673 1.360838334 1.248606854 1.154434515 0.973658849 1.356649136 1.229550339 1 17.70355729 3.264673563 6.881866095 1.161201964 1.258897284 0.179668941 0.121357474 0.381855657 63.41035196 0.036024212 0.045490146 1839.388907 -3.264673563 0.09769532 LDDIHPFYADLMNILYDKDHYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDDIHPFYADLMNILYDKDHYK 22 1 Q9BZE4-2;Q9BZE4;Q5T3R7 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 0 ; 186.86 1.97E-17 257090000 429480 304380 255250 288360 317620 227309 378810 460100 346400 FALSE TRUE 372723.1298 302380.5077 378689.7538 353836.5453 311299.9834 236053.7243 342073.0645 361711.1955 305448.9866 1.220246739 0.989954202 1.239780685 1.158414533 1.019155398 0.772808995 1.119902437 1.184195107 1 18.22057193 3.239891758 24.9946721 1.035066804 1.146780255 0.214758709 0.124040552 72.50720468 1361445.643 0.039250773 0.047950777 1737.367758 -3.239891758 0.111713451 LDDLSVLDLSHNQLTECPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDDLSVLDLSHNQLTECPR 19 0 Q13045-3;Q13045;Q13045-2;J3KS54;J3QQQ2;K7EP37;K7EP27 Q13045-3 FLII Protein flightless-1 homolog 0 290.16 1.61E-49 79005000 79385 77890 65862 80973 73491 70488 73450 97596 164090 FALSE TRUE 68894.07111 77378.33546 97713.0835 99359.15724 72028.67288 73199.71897 66326.83031 76725.85489 144691.4671 0.476144672 0.534781608 0.67532029 0.686696729 0.497808712 0.505902113 0.458401809 0.530272147 1 17.14262032 1.237337868 24.99971644 1.000000544 0.546234494 0.774643608 0.077012036 15.92428483 325442.6776 0.123458222 0.020553724 17.27181062 -1.237337868 -0.45376605 LDDLVNWAR ddPTM_MDA-MB-175_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 ; 128.38 0.00097451 382670000 529400 488180 411910 506860 558060 536670 457360 594210 496770 FALSE TRUE 459438.4487 484973.1134 611111.0538 621950.3099 546955.6978 557316.0422 413005.2976 467142.8156 438042.4165 1.048844658 1.107137335 1.395095613 1.419840377 1.248636381 1.272287845 0.942843163 1.066432834 1 18.74071105 2.24661375 24.99363484 1.013777633 1.256647141 0.500465073 0.115295754 155.5201099 482671.7915 0.047032923 0.035782292 176.4467853 -2.24661375 0.242869507 LDDLVRPYVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDDLVRPYVHK 11 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 151.13 2.02E-05 1578690000 1962010 1478320 1053770 1319590 1552570 1208260 1735150 1936890 1965550 FALSE TRUE 1702725.407 1468608.819 1563376.697 1619223.078 1521676.895 1254742.544 1566875.42 1522701.146 1733184.918 0.982425701 0.847346872 0.902025329 0.934247155 0.877965691 0.723951917 0.904043996 0.878556656 1 20.72499416 4.750993417 24.1909877 0.881095644 0.982425801 0.164974029 0.069743485 2417.419541 4703533.531 0.01693743 0.278610848 56362.9112 -4.750993417 0.101330157 LDDPLHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDDPLHLR 8 0 O75146 O75146 HIP1R Huntingtin-interacting protein 1-related protein 0 ; 135.83 0.00081697 430620000 995810 952880 686290 757770 1044720 1100070 1017820 1128240 1186630 FALSE TRUE 864211.1854 946620.4685 1018182.14 929833.2603 1023932.116 1142390.405 919111.9731 886974.656 1046347.953 0.825930975 0.904689941 0.97308179 0.888646322 0.978577072 1.091788254 0.878399934 0.847686138 1 19.99693126 4.647862176 2.995061303 0.941836369 0.817584645 0.23859248 0.069971058 0.537036162 7.576339327 0.018923307 0.140800279 44449.0185 -4.647862176 -0.124251724 LDDPSCPRPECYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LDDPSCPRPECYR 13 1 P41091;H7BZU1 P41091 EIF2S3 Eukaryotic translation initiation factor 2 subunit 3 0 ;;;;; 150.21 3.82E-05 6468790000 6796490 6176660 4620100 6206110 6319050 6082890 5686110 6773240 8091560 FALSE TRUE 5898316.626 6136085.114 6854395.813 7615302.13 6193313.268 6316902.714 5134671.927 5324835.335 7134984.995 0.826675407 0.859999722 0.960674174 1.067318591 0.868020504 0.885342116 0.719647194 0.746299444 1 22.76647896 2.428794972 7.289935504 0.801434935 0.919681036 0.149993901 0.09861994 0.328261145 40.43088359 0.037996478 0.029441106 268.4077007 -2.428794972 0.118246101 LDDSFVR ddPTM_MDA-MB-175_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 0 111.04 0.015516 106260000 189710 196670 115080 146770 185160 197400 169850 205360 182880 FALSE TRUE 164639.3428 195378.0618 170733.0729 180096.3717 181475.6783 204994.1057 153377.9731 161445.3621 161260.1347 1.020955012 1.211570746 1.058743211 1.116806531 1.125359833 1.271201379 0.95112145 1.001148625 1 17.29903031 2.208283742 24.99983692 0.986270136 1.133017846 0.498235458 0.070951376 162.0419903 133798.1421 0.027345617 0.018438933 161.5413627 -2.208283742 0.14674771 LDDTVHVVIATPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LDDTVHVVIATPGR 14 0 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ;;; 160.27 4.78E-06 2337620000 1787920 1722460 1037830 1252950 1605930 1655400 1639930 1867200 1783660 FALSE TRUE 1551641.842 1711145.047 1539728.059 1537451.448 1573975.135 1719084.309 1480889.841 1467913.811 1572797.747 0.986548871 1.08796255 0.978973973 0.977526482 1.000748595 1.093010409 0.941564066 0.93331378 1 20.58490173 2.176282442 24.99992537 0.952391377 1.019070669 0.303038854 0.044332118 75.8838909 30460.59199 0.017839857 0.012027634 150.0660469 -2.176282442 0.066679292 LDDYQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDDYQER 7 0 Q14444-2;Q14444;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ; 110.12 0.015994 1280110000 1482330 1277720 818050 957860 1148810 1087390 1380770 1602150 1354370 FALSE TRUE 1286436.335 1269326.573 1213661.716 1175356.753 1125950.929 1129222.597 1246863.138 1259542.69 1194257.922 1.077184678 1.062857989 1.016247575 0.984173294 0.942803818 0.945543317 1.044048455 1.054665552 1 20.18768302 4.219443641 3.058480069 1.00016317 1.074348703 0.420658025 0.03568432 0.302697125 5.709190582 0.011279116 0.031955854 16574.62233 -4.219443641 0.074185533 LDEEEEDNEGGEWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDEEEEDNEGGEWER 15 0 Q99613-2;Q99613 Q99613-2 EIF3C Eukaryotic translation initiation factor 3 subunit C 0 267.21 4.87E-25 169170000 184240 161750 115300 123800 165530 143040 148460 171150 178200 FALSE TRUE 159892.2172 160687.4536 171059.4657 151910.6822 162236.2769 148542.8414 134062.3721 134550.9044 157133.399 1.017557172 1.022618072 1.088625758 0.966762529 1.032474814 0.945329524 0.853175537 0.856284566 1 17.26163034 2.566286165 3.350210831 0.891459014 1.025740836 0.560550757 0.049800996 0.16561446 3.543744197 0.018429374 0.015544876 368.371621 -2.566286165 0.134281822 LDEGT(ph)PPEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LDEGTPPEPK 10 0 Q9Y4G6;H0YMT1;A0A1B0GVU7;H0YN01 Q9Y4G6 TLN2 Talin-2 1 LDEGT(1)PPEPK;LDEGT(1)PPEPK;LDEGT(1)PPEPK;LDEGT(1)PPEPK 186.36 1.51E-05 3217250000 5507670 4557170 3929180 4322880 4097830 3281070 5341870 6172480 5983290 TRUE FALSE 4779817.455 4527233.65 5829344.59 5304455.975 4016291.2 3407294.886 4823816.27 4852543.186 5275952.272 0.905962982 0.858088439 1.104889561 1.00540257 0.761244794 0.645816093 0.914302484 0.919747362 1 22.33100008 3.256326715 24.99961425 0.851998504 0.970429207 0.215048733 0.114116246 438.9729132 617698.1819 0.035872401 0.046208693 1804.374644 -3.256326715 0.118430703 LDEIYVAGLVAHSDLDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LDEIYVAGLVAHSDLDER 18 0 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;;;;; 292.13 3.35E-49 1544743000 1437087 1080798 835202.4 1159409 1108063 1008784 1064143 1235274 2379785 FALSE TRUE 1247172.312 1073698.167 1239109.074 1422670.534 1086014.714 1047592.573 960942.5756 971120.268 2098449.528 0.594330383 0.511662612 0.590487909 0.677962712 0.517531968 0.499222192 0.457929801 0.462779902 1 21.00089233 1.233137839 24.99943607 1.000000733 0.534801689 0.823947885 0.066945864 77.64256179 357899.0405 0.152981504 0.018199618 17.10558136 -1.233137839 -0.465199045 LDELEELLTNNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LDELEELLTNNR 12 0 O75306;O75306-2 O75306 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" 0 ;; 116.77 0.0018756 38179800 55673 58506 37169 56993 63181 61699 51289 69873 67683 FALSE TRUE 48315.67199 58121.67023 55144.05272 69934.13173 61923.82171 64072.60045 46315.00067 54931.2027 59681.59284 0.809557347 0.973862584 0.923970861 1.171787286 1.037569856 1.073573901 0.776034929 0.920404434 1 15.86499842 -1.565378548 13.91989395 9.044918696 0.964058655 0 0.117696816 0 0 0 0.027214968 0.027203291 1.565378548 -8.080860041 LDELYGTWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LDELYGTWR 9 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;;;;; 190.51 8.60E-05 1775315000 1492345 1458765 1277640 1540827 1456949 1391163 1315248 1703830 3604620 FALSE TRUE 1295127.827 1449182.277 1895510.977 1890695.32 1427958.565 1444681.941 1187695.451 1339479.214 3178485.93 0.407466906 0.455934778 0.596356573 0.594841494 0.449257476 0.454518904 0.373667047 0.421420526 1 21.59990827 1.235445635 24.97958122 1.000000735 0.468872844 0.839272051 0.073003041 37.11371058 297568.1841 0.137701404 0.019931397 17.19672057 -1.235445635 -0.531127891 LDETDDPDDYGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LDETDDPDDYGDR 13 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;;; 265.67 5.63E-24 1305410000 3604890 2145730 2209540 2608630 2120980 2033310 2243570 2543010 5892270 FALSE TRUE 3128494.653 2131634.558 3278080.934 3200959.312 2078776.648 2111532.751 2025988.927 1999207.101 5195692.553 0.602132367 0.410269572 0.630922808 0.616079431 0.400096162 0.406400635 0.389936261 0.38478164 1 22.30888463 1.232660321 24.99996835 1.000000853 0.473365679 0.726298509 0.100229655 110.1168882 466525.0336 0.229591377 0.026101465 17.08678365 -1.232660321 -0.526635173 LDETDDPDDYGDRESGCSFVLALMQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDETDDPDDYGDRESGCSFVLALMQK 26 1 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 171.58 5.27E-12 189944000 380450 215992 158563 159246 192379 186679 266888 293709 161284 FALSE TRUE 330172.5686 214573.1343 235244.5972 195405.2382 188551.0343 193860.6619 241005.2428 230901.616 142217.1893 2.32160803 1.508770743 1.65412211 1.373991704 1.325796377 1.363131018 1.694628083 1.623584443 1 17.11773632 LDEYWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LDEYWDR 7 0 Q6PKC6;E9PBK6;E9PDU5;A0A087X295;Q9NNW5 Q6PKC6 WDR6 WD repeat-containing protein 6 0 ;; 101.33 0.021265 252896000 387730 375820 269192 306368 392810 364320 375490 442090 420550 FALSE TRUE 336490.4981 373351.2137 399374.1516 375933.5369 384993.8495 378335.6261 339075.0376 347552.4938 370833.0581 0.907390781 1.006790537 1.076964804 1.01375411 1.038186432 1.020231659 0.914360331 0.937220904 1 18.50041033 2.252711959 24.98287134 0.946248011 1.014802325 0.260141809 0.047176487 272.5191708 481106.8508 0.017820911 0.013735777 178.9418648 -2.252711959 0.068554313 LDFIESDS(ph)PCSSEALSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDFIESDSPCSSEALSK 17 0 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-4 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 LDFIESDS(0.949)PCS(0.05)SEALSK;LDFIESDS(0.99)PCS(0.009)SEALSK 330.85 5.57E-72 252980000 598490 514630 406170 448590 480540 430380 599950 665310 744110 TRUE FALSE 519398.0301 511249.3616 602595.1706 550449.2158 470978.1942 446936.9971 541766.9413 523038.6339 656142.1635 0.791593741 0.779174682 0.918391172 0.83891761 0.717799008 0.681158782 0.825685303 0.79714224 1 19.32364891 1.235637395 6.15783198 1.007341726 0.793861113 0.503645003 0.064351783 0.125340047 19.08563698 0.11179593 0.017068508 17.20431538 -1.235637395 -0.213480613 LDFLPEMMVDHCSLNS(ph)SPVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDFLPEMMVDHCSLNSSPVSK 21 0 Q92879-4;G5EA30;F5H0D8;E9PKU1;F5H3J7 Q92879-4 CELF1 CUGBP Elav-like family member 1 1 LDFLPEMMVDHCS(0.043)LNS(0.614)S(0.343)PVSK 117.36 6.96E-05 108500000 216900 211750 68326 191820 262540 195140 284720 340770 300400 TRUE FALSE 188236.1154 210359.0003 101368.6821 235375.6628 257315.9677 202647.1621 257107.8982 267898.9874 264887.0542 0.710627841 0.794146022 0.382686434 0.888588774 0.97141768 0.765032337 0.970632177 1.011370632 1 18.01501781 3.503927419 24.09958353 0.9438533 0.643983406 0.57993104 0.123122018 333.0759621 299444.7081 0.033503992 0.049500975 3191.004517 -3.503927419 -0.299869893 LDFLRPYTVPNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDFLRPYTVPNK 12 1 Q99436 Q99436 PSMB7 Proteasome subunit beta type-7 0 92.906 0.006814 292420000 497330 457360 334550 418880 494740 431650 510390 620020 663590 FALSE TRUE 431606.5804 454355.572 496339.499 513993.1062 484895.6419 448255.8548 460892.4564 487433.548 585141.1462 0.737611059 0.776488844 0.848238929 0.878408756 0.828681499 0.766064492 0.78766031 0.833018753 1 19.15842514 1.236414874 3.516776132 1.028461839 0.806644013 0.691517943 0.040917095 0.191842071 3.487545625 0.114867726 0.011327968 17.23514233 -1.236414874 -0.221817826 LDFNLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDFNLIR 7 0 P31939-2;P31939;C9JLK0 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 157.9 0.0033611 548620000 793380 795530 482190 618990 808120 796090 785350 911770 842870 FALSE TRUE 688532.8228 790304.111 715378.6968 759541.1402 792039.9931 826716.0974 709186.8779 716795.0809 743226.8688 0.926410026 1.063341685 0.962530725 1.021950594 1.065677287 1.112333437 0.95419973 0.964436447 1 19.50344313 LDGAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDGAIR 6 0 Q99714;Q99714-2 Q99714 HSD17B10 3-hydroxyacyl-CoA dehydrogenase type-2 0 97.64 0.095015 236650000 305110 422240 292430 229520 305470 279920 409240 299040 361060 FALSE TRUE 264788.9404 419466.2776 433850.1261 281636.024 299391.7446 290688.7035 369551.9678 235092.6231 318375.8981 0.831686513 1.317518946 1.362697769 0.884602213 0.940371889 0.913036148 1.16074103 0.738412124 1 18.2803716 3.71870374 24.87381152 0.931334992 1.185322879 0.280612645 0.173576136 851.9995556 1067261.23 0.046324353 0.068809579 5232.433775 -3.71870374 0.253987887 LDGEEQRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDGEEQRPR 9 1 P51687 P51687 SUOX "Sulfite oxidase, mitochondrial" 0 89.08 0.011263 404230000 59838 63922 33783 50866 58134 57776 44077 41084 65704 FALSE TRUE 51930.25669 63502.09217 50120.5718 62415.90274 56977.24714 59998.68011 39802.41932 32298.50632 57936.54797 0.896329839 1.096062751 0.865094203 1.077314837 0.983442216 1.035592941 0.687000188 0.557480683 1 15.82218611 2.235908317 24.9998631 0.705886979 0.994701124 0.424577607 0.130918387 52.30039012 492957.6109 0.049422968 0.035036209 172.1505112 -2.235908317 0.288814144 LDGEIIPHIPANQEVLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDGEIIPHIPANQEVLNK 18 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 136.2 6.78E-06 75235000 192010 145240 153390 190450 182900 156520 171200 219680 410750 FALSE TRUE 166635.392 144285.9089 227569.9171 233694.5833 179260.6478 162541.4257 154597.0504 172703.1416 362191.6029 0.460075249 0.398369006 0.62831362 0.645223637 0.494933197 0.448771933 0.426837754 0.476828121 1 18.46639357 1.237154875 24.99991104 1.000000611 0.497161465 0.794807259 0.080252403 17.29015075 307376.6795 0.129460072 0.021264604 17.26453456 -1.237154875 -0.502839146 LDGLVET(ph)PTGYIESLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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(0.988)PT(0.012)GYIESLPR;LDGLVET(0.909)PT(0.091)GYIESLPR;LDGLVET(0.904)PT(0.096)GYIESLPR;LDGLVET(0.999)PT(0.001)GYIESLPR;LDGLVET(0.99)PT(0.01)GYIESLPR;LDGLVET(0.968)PT(0.032)GYIESLPR 218.83 1.40E-14 1786801000 829841 734070 539577 525473 673775 711806 783270 707985 869107 TRUE FALSE 720175.4093 729247.8458 800518.242 644789.676 660368.1957 739189.6374 707308.596 556587.9173 766362.1605 0.939732474 0.951570789 1.044569113 0.841364187 0.861692069 0.964543496 0.922943006 0.726272702 1 19.5476668 3.725722178 24.9675953 0.874032424 0.975918795 0.224082071 0.078965471 1024.455508 1992313.259 0.022278215 0.033275898 5317.679732 -3.725722178 0.101886371 LDGLVETPT(ph)GYIESLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDGLVETPTGYIESLPR 17 0 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W118;F8VUX1;H0YHC3;F8W020;P55209-3;F8VXI6;F8VRJ2 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 1 LDGLVET(0.419)PT(0.581)GYIESLPR 143.28 6.20E-06 110900000 107460 91994 64702 69369 81076 92143 104410 90297 103270 TRUE FALSE 93258.88873 91389.68536 95992.10362 85120.29169 79462.74622 95687.80083 94284.33427 70987.68924 91061.53825 1.024130391 1.003603575 1.054145421 0.934755697 0.872626882 1.050803695 1.035391408 0.779557326 1 16.47455421 7.510512316 0.065496435 0.6594384 1.568111693 0.10002808 0.083525697 1077.921377 7.609055563 26.65929224 102.7391276 32397560.98 -7.510512316 0.908673293 LDGLVETPTGYIES(ph)LPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDGLVETPTGYIESLPR 17 0 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W118;F8VUX1;H0YHC3;F8W020;P55209-3;F8VXI6;F8VRJ2 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 1 LDGLVETPTGYIES(1)LPR 153.86 1.67E-07 9523300 31482 25598 19748 24707 35571 30238 24786 30315 26204 TRUE FALSE 27321.57393 25429.84505 29298.19885 30317.10197 34863.20669 31401.27543 22382.25753 23832.37316 23106.19297 1.182435115 1.100564039 1.267980359 1.312076897 1.50882522 1.358998233 0.968669203 1.031427946 1 14.49599196 2.23460183 24.99359115 1.005266277 1.290094833 0.61724448 0.10704466 74.67918591 471475.1918 0.048268821 0.033907702 171.6334094 -2.23460183 0.284828556 LDGLVETPTGYIESLPR ddPTM_MDA-MB-175_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 ; 141.38 1.46E-06 107332000 92274 93218 62053 71963 103542 89922 97037 107429 86039 FALSE TRUE 80079.75711 92605.64482 92062.03835 88303.29904 101481.7168 93381.35753 87626.36668 84456.14436 75867.56744 1.055520294 1.220622302 1.2134571 1.163913672 1.337616589 1.230846865 1.15499112 1.113204854 1 16.21119566 1.40842255 1.561128402 0.961420468 1.207082761 0.459933953 0.069961188 0.685654912 2.066930433 0.24409083 0.020455108 25.61076494 -1.40842255 0.245662293 LDGMGCLEFDEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDGMGCLEFDEER 13 0 Q13951-2;A0A494C0A9;Q13951;J3KS23;H3BSC0 Q13951-2 CBFB Core-binding factor subunit beta 0 148.76 0.00010102 59690000 42758 42195 27313 37364 39300 34447 38696 42488 37505 FALSE TRUE 37107.42197 41917.81827 40521.65816 45848.06727 38518.00689 35772.19838 34943.26788 33402.27184 33071.20163 1.122046377 1.267502123 1.225285329 1.386344161 1.164699346 1.081672169 1.056607143 1.010010831 1 15.01328785 2.744016778 2.315676609 1.02489429 1.250706758 0.692653486 0.067057294 0.164786032 1.746378627 0.025160394 0.023133066 554.6471404 -2.744016778 0.225812468 LDGQTPHDER ddPTM_MDA-MB-175_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 1633480000 1551240 1354210 888610 1128420 1472230 1444110 1418610 1617280 1496730 FALSE TRUE 1346239.704 1345314.105 1318344.768 1384645.008 1442935.503 1499665.846 1281033.421 1271437.258 1319788.284 1.020042168 1.019340845 0.998906252 1.049141763 1.093308313 1.13629274 0.970635545 0.963364558 1 20.33187509 LDHFNFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LDHFNFER 8 0 Q9UHL4;R4GNE8;R4GMV4 Q9UHL4 DPP7 Dipeptidyl peptidase 2 0 ;;; 151.44 0.00047308 1828380000 1700760 1701920 1141750 1316180 1575800 1893430 1512850 1813440 1652640 FALSE TRUE 1476000.257 1690739.975 1693904.119 1615038.786 1544444.663 1966271.477 1366134.04 1425649.968 1457266.782 1.012855213 1.160213076 1.162384362 1.108265697 1.05982287 1.349287242 0.937463241 0.978304032 1 20.47483359 LDHKFDLMYAK ddPTM_MDA-MB-175_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 ;; 158.4 1.80E-05 23616500000 34468050 29060440 17774580 19637400 26387210 21814760 37817190 41056700 11358870 FALSE TRUE 29913009.86 28869540.06 26370426.34 24096371.81 25862156.15 22653987.93 34149684.73 32277044.21 10016037.33 2.98651142 2.882331516 2.632820294 2.405778954 2.582074657 2.261771516 3.409500545 3.222536333 1 23.25580851 4.296208943 3.546349242 2.604009823 2.962754016 0.056030097 0.646540238 0.879593238 21.88445944 0.167486213 0.496533582 19779.21007 -4.296208943 0.358744193 LDHKFDLMYAKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDHKFDLMYAKR 12 2 P68363;P68363-2;P68366-2;P68366;Q9BQE3;F5H5D3;A6NHL2-2;A6NHL2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA4A;TUBA1C;TUBAL3 Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain;Tubulin alpha chain-like 3 0 122.42 0.00021547 297230000 402310 639790 213100 229210 351880 346110 382920 502020 243770 FALSE TRUE 349143.7142 635587.1774 316155.8728 281255.6338 344878.2764 359425.0757 345784.4773 394666.9297 214951.7883 1.624288483 2.956882482 1.470822249 1.308459148 1.604444788 1.672119495 1.608660621 1.83607186 1 17.71365359 4.200777889 24.99089801 1.538925601 2.290587147 0.415730577 0.38748339 129.809289 85860.56867 0.090981773 0.189400073 15877.34525 -4.200777889 0.751661545 LDHLAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LDHLAEK 7 0 O43707;O43707-2;P12814-3;P12814;P12814-2;P12814-4;H9KV75 O43707;P12814-3 ACTN4;ACTN1 Alpha-actinin-4;Alpha-actinin-1 0 ;;;; 126.28 0.0039676 5558720000 8525120 6349910 6141980 8740640 5021860 5213510 5738070 7815310 21246100 FALSE TRUE 7398503.792 6308197.023 9112262.072 10725335.9 4921934.811 5414077.103 5181592.855 6144066.775 18734410.26 0.394915222 0.336717139 0.486391722 0.572493917 0.262721631 0.288991061 0.276581583 0.327956241 1 24.15918723 1.23650511 24.99856273 1.000000809 0.365450836 0.806838296 0.097119818 25.06027059 304698.1117 0.163494254 0.025637808 17.23872376 -1.23650511 -0.634549973 LDHVNIVHYNGCWDGFDYDPETS(ph)DDSLESSDYDPENSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDHVNIVHYNGCWDGFDYDPETSDDSLESSDYDPENSK 38 0 P19525-2;P19525 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 1 LDHVNIVHYNGCWDGFDYDPET(0.014)S(0.951)DDS(0.035)LESSDYDPENSK 204.2 2.68E-30 147970000 57230 39306 32472 34502 38273 33605 41648 56918 54953 TRUE FALSE 49666.9105 39047.7963 48175.56781 42336.20643 37511.44218 34897.8061 37608.98337 44746.52864 48456.51894 1.024978921 0.805831644 0.994201995 0.873694755 0.774125814 0.720188054 0.776138777 0.923436714 1 15.56440315 4.750002904 24.16289418 0.857433246 1.024979081 0.238448536 0.093511589 1786.471633 3772411.179 0.024238643 0.358044644 56234.50848 -4.750002904 0.167545835 LDIDPETITWQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LDIDPETITWQR 12 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ;;;; 308.04 7.59E-46 954496000 1706430 1631580 983985 1301590 1600970 1589300 1624520 1892020 1638850 FALSE TRUE 1480920.952 1620862.044 1459843.437 1597135.903 1569113.829 1650441.399 1466974.3 1487426.247 1445107.02 1.024782893 1.121620767 1.010197457 1.105202508 1.085811506 1.142089393 1.015131945 1.029284493 1 20.46274491 2.185358345 24.99799913 1.017835318 1.081452198 0.37842262 0.040302483 99.51926107 46760.0238 0.015509445 0.010456472 153.2351315 -2.185358345 0.06361688 LDIDS(ph)PPITAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LDIDSPPITAR 11 0 P14618;B4DNK4;H3BUW1;H3BTJ2;H3BT25;H3BN34;H3BQZ3;P14618-2;H3BTN5;H3BQ34;H3BU13 P14618;P14618-2;H3BU13 PKM Pyruvate kinase PKM;Pyruvate kinase 1 LDIDS(1)PPITAR;LDIDS(1)PPITAR;LDIDS(1)PPITAR;LDIDS(1)PPITAR;LDIDS(1)PPITAR;LDIDS(1)PPITAR 236.5 1.56E-15 6544380000 4152620 3649610 2514650 2901160 3454130 3550320 3850950 3934820 4048060 TRUE FALSE 3603840.746 3625635.472 3730743.151 3559912.719 3385399.571 3686903.108 3477485.462 3093389.364 3569502.958 1.009619767 1.015725582 1.045171609 0.997313285 0.948423243 1.032889775 0.974221202 0.866616277 1 21.76729177 1.987724892 16.25451484 0.922770779 1.006716297 0.360694428 0.040630636 4.970971924 6580.344281 0.017141685 0.010580355 97.21312227 -1.987724892 0.083945519 LDIDSPPITAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LDIDSPPITAR 11 0 P14618;B4DNK4;H3BUW1;H3BTJ2;H3BT25;H3BN34;H3BQZ3;P14618-2;H3BTN5;H3BQ34;H3BU13 P14618;P14618-2;H3BU13 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;; 251.98 5.24E-20 2568510000 1371210 1118200 788150 910215 1100722 1137310 1182411 1265440 1251590 FALSE TRUE 1190001.124 1110854.471 1169301.976 1116893.228 1078819.786 1181063.052 1067740.963 994835.5037 1103628.456 1.078262451 1.006547507 1.059506911 1.012019237 0.977520813 1.070163645 0.967482269 0.901422483 1 20.07382313 2.064318016 6.362293665 0.940926629 1.029991153 0.469412171 0.038746739 0.146847596 11.07939132 0.015249857 0.010150819 115.9626192 -2.064318016 0.089064523 LDINLLDNVVNCLYHGEGAQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDINLLDNVVNCLYHGEGAQQR 22 0 O14980;C9JKM9;C9J673;C9IYM2;F8WF71;C9IZS4;C9JQ02;C9JV99;C9JF49 O14980 XPO1 Exportin-1 0 ; 266.4 1.16E-37 3286600000 1464170 1157930 730810 847710 1170780 1163940 1235570 1416950 1310920 FALSE TRUE 1270676.225 1150323.482 1084232.16 1040195.512 1147483.769 1208717.525 1115744.612 1113946.269 1155944.531 1.099253633 0.995137267 0.937962101 0.899866286 0.99268065 1.045653569 0.965223314 0.96366758 1 20.14064074 4.710006909 3.603887448 0.971558388 1.110145046 0.517131868 0.038267322 0.216130825 5.109625533 0.010078462 0.07708614 51286.95431 -4.710006909 0.138586659 LDIPTGTT(ph)PQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDIPTGTTPQR 11 0 P52732 P52732 KIF11 Kinesin-like protein KIF11 1 LDIPT(0.033)GT(0.162)T(0.806)PQR;LDIPT(0.004)GT(0.194)T(0.801)PQR 132.79 0.0025284 0 462470 452080 384170 471400 455750 421090 401250 518270 1097990 TRUE FALSE 401353.4178 449110.2567 569955.897 578438.5749 446681.4667 437289.6048 362336.8368 407441.9937 968186.873 0.414541272 0.463867327 0.588683768 0.597445174 0.461358731 0.451658267 0.374242666 0.420829909 1 19.88492601 1.235252039 24.9990849 1.000000733 0.471046963 0.845305289 0.071041476 39.74081733 300225.002 0.137517044 0.019592208 17.18905649 -1.235252039 -0.528953771 LDIPTGTT(ph)PQRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDIPTGTTPQRK 12 1 P52732 P52732 KIF11 Kinesin-like protein KIF11 1 LDIPT(0.008)GT(0.259)T(0.734)PQRK;LDIPT(0.004)GT(0.121)T(0.876)PQRK 102.29 0.0013886 570340000 827630 778830 578490 690380 820560 739430 805640 1010050 1012610 TRUE FALSE 718256.5986 773713.8144 858249.6989 847141.3308 804232.4614 767876.3506 727509.1568 794058.6677 892900.3994 0.804408419 0.866517492 0.961193096 0.948752326 0.90069672 0.859979849 0.814770782 0.889302624 1 19.76813973 4.592090606 3.857758185 0.90335896 0.80647085 0.289684977 0.052582106 0.350135135 8.396487197 0.013926087 0.06974068 39092.2445 -4.592090606 -0.09688811 LDKDEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDKDEIR 7 1 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 ; 104.44 0.0074343 1109210000 3561500 2862900 2631300 3218500 2870000 2783000 3193000 3289400 4399700 FALSE TRUE 3090838.751 2844093.421 3903805.481 3949309.617 2812892.615 2890063.811 2883343.351 2585987.408 3879572.478 0.79669571 0.733094545 1.006246308 1.01797547 0.725052214 0.744943889 0.743211621 0.666565046 1 21.88746625 3.202616388 24.99962696 0.758274564 0.885812945 0.167931712 0.120916014 282.5769576 196534.6367 0.037469308 0.042487579 1594.47013 -3.202616388 0.127538381 LDKDNLSYIEHIFEISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDKDNLSYIEHIFEISR 17 1 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 ; 218.79 2.72E-15 2047700000 2229990 2046530 1584080 2258660 2094280 1750620 2340300 2852500 3971000 FALSE TRUE 1935291.171 2033086.21 2350146.386 2771523.274 2052607.925 1817967.484 2113338.066 2242515.073 3501552.904 0.552695111 0.580624159 0.671172606 0.791512609 0.586199318 0.519188924 0.603543092 0.64043444 1 21.73956345 1.236651563 4.932539673 1.02602824 0.618329858 0.723924149 0.074240117 0.103078611 6.21712649 0.145359904 0.019874744 17.24453798 -1.236651563 -0.407698382 LDKELLAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDKELLAQR 9 1 Q9P2M7 Q9P2M7 CGN Cingulin 0 85.958 0.01319 277820000 326650 354660 215850 278540 301440 313560 334440 386550 240800 FALSE TRUE 283482.3749 352330.2151 320235.782 341786.7642 295441.9338 325622.8561 302006.0603 303889.2906 212332.8983 1.335084564 1.659329373 1.508177887 1.609674087 1.391409132 1.533548775 1.422323449 1.431192684 1 17.69596839 0.802889676 1.501372334 2.06E-13 1.508008032 0.715371213 0.096935716 1.85200376 1.484922967 5.852172685 0.025488028 6.351695585 -0.802889676 1.508008032 LDKENALDR ddPTM_MDA-MB-175_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 ;;; 130.01 0.00034047 4494110000 7216300 6327800 4483930 5349270 5914900 5077110 7063000 7791800 6900300 FALSE TRUE 6262647.671 6286232.265 6652373.546 6563903.512 5797205.062 5272429.707 6378031.347 6125584.206 6084554.395 1.029269732 1.033145874 1.093321403 1.078781302 0.952773973 0.866526842 1.048233105 1.006743273 1 22.53672018 3.241446983 24.99901907 0.978928311 1.059287308 0.408478824 0.049957487 86.90946763 752721.6579 0.015804521 0.019510535 1743.600494 -3.241446983 0.080358997 LDKESYPVFYLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDKESYPVFYLFR 13 1 P30040;F8VY02 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 ; 135.02 8.09E-05 399670000 491020 419700 270010 310060 374670 408780 399450 418540 305660 FALSE TRUE 426130.4629 416942.9631 400587.7391 380463.862 367214.8 424506.0311 360711.4005 329038.4781 269525.223 1.581041129 1.546953411 1.486271803 1.411607633 1.362450593 1.575014117 1.338321499 1.220807739 1 18.04006077 0.567506387 0.679512015 1.51E-11 1.50667141 0.837761739 0.072207231 2.792871835 0.514996376 4.010704548 0.034311676 3.694080771 -0.567506387 1.50667141 LDKGQIQEIVLVGGSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDKGQIQEIVLVGGSTR 17 1 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 123.41 4.90E-05 578050000 239760 197920 122310 152280 204710 195920 248700 293980 127030 FALSE TRUE 208075.1085 196619.8505 181459.5251 186857.5015 200636.6715 203457.1692 224581.1123 231114.6648 112012.6581 1.857603525 1.755335993 1.619991242 1.668182013 1.791196414 1.816376583 2.004961904 2.063290602 1 16.77330225 3.113046234 7.811612724 1.801446549 1.720126217 0 0.295408956 1.467883691 95.04393402 0.089288688 0.101443294 1297.317373 -3.113046234 -0.081320332 LDKSQIHDIVLVGGSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDKSQIHDIVLVGGSTR 17 1 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 152.32 1.30E-07 1923580000 4463200 3727300 1066950 1416500 3536400 3283600 4380800 4969300 119823 FALSE TRUE 3873376.812 3702815.121 1582930.589 1738137.975 3466032.559 3409922.217 3955950.69 3906653.866 105657.6614 36.65968713 35.04540107 14.98169245 16.45065726 32.80436564 32.27330768 37.44121 36.97463878 1 16.68903786 1.23057499 24.99999993 0.999946826 30.34600265 0.562319388 8.131753352 254.3346105 796161.1629 23.66521922 2.202248074 17.00493554 -1.23057499 29.34605583 LDLAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 LDLAGR 6 0 P60709;A0A2R8Y793;P63267-2;A0A2R8YEA7;Q562R1;Q9BYX7;P63261;I3L3I0;I3L1U9;I3L4N8;P68133;P68032;P63267;P62736;Q6S8J3;A5A3E0;P0CG38;P0CG39 P60709;P63261;P68133;Q6S8J3 ACTB;ACTG2;ACTBL2;POTEKP;ACTG1;ACTA1;ACTC1;ACTA2;POTEE;POTEF;POTEI;POTEJ "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Beta-actin-like protein 2;Putative beta-actin-like protein 3;Putative beta-actin-like protein 3, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I;POTE ankyrin domain family member J" 0 ;;;;;;;;;;; 159.65 0.021057 61863960000 24617730 21950770 14033570 17173200 19744300 20262060 19999130 21917450 20621360 FALSE TRUE 21364434.61 21806573.95 20820251.39 21072637.54 19351427.06 21041554.56 18059617.45 17230573.88 18183526.31 1.174933522 1.199248901 1.145006256 1.15888619 1.064228507 1.157176787 0.993185653 0.94759254 1 24.11612867 2.327432726 0.872144664 0.941695481 1.173120295 0.779436194 0.041343954 0.311312794 0.465936584 0.052250623 0.020162275 212.5361095 -2.327432726 0.231424814 LDLFEISQPTEDLEFHGVMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDLFEISQPTEDLEFHGVMR 20 0 P55196-5;P55196;J3KN01;P55196-3;Q5TIG5;P55196-6;P55196-2;E9PFY5;F8W9I4;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 0 125.51 2.50E-05 53838000 27264 27948 20874 28977 33992 32739 28900 36728 36217 FALSE TRUE 23660.99332 27764.40775 30968.73622 35556.67074 33315.6257 33998.49051 26097.28245 28874.00302 31935.46752 0.74090017 0.869390991 0.9697286 1.11339127 1.043217097 1.064599743 0.817188051 0.904135911 1 14.96287195 4.519245714 2.465906093 0.980145929 0.735111116 0.489895037 0.082911948 0.362732027 3.685337932 0.024595062 0.151994493 33055.65095 -4.519245714 -0.245034814 LDLHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDLHLK 6 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 76.592 0.07465 376620000 1097500 912700 674510 946830 1103700 744230 1173000 1280600 1612100 FALSE TRUE 952462.5943 906704.4136 1000705.292 1161822.223 1081738.529 772861.0097 1059242.641 1006753.656 1421519.375 0.670031384 0.637841756 0.703968803 0.817310157 0.760973469 0.543686582 0.745148226 0.708223661 1 20.43900233 1.2298198 4.852997439 1.023359998 0.698648642 0.623755848 0.073615857 0.13574028 7.593060841 0.151312987 0.018827479 16.97539152 -1.2298198 -0.324711355 LDLIHESILHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDLIHESILHK 11 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77;H0YEC5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 145.91 2.08E-05 228630000 366330 433350 74733 227660 543600 471450 483330 544280 522870 FALSE TRUE 317918.5623 430503.2953 110874.1288 279353.6826 532783.4235 489586.9866 436456.731 427889.9576 461056.9043 0.689543003 0.933731371 0.240478188 0.605898491 1.155569776 1.061879742 0.946643954 0.928063225 1 18.8145853 3.252100309 24.88940058 1.003923681 0.613082913 0.557327593 0.177311455 176.0425488 323609.0694 0.052310319 0.067148284 1786.900249 -3.252100309 -0.390840769 LDLLEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LDLLEDR 7 0 Q14697;F5H6X6;Q14697-2;E9PKU7;E9PNH1 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;; 188.89 0.0013099 1564540000 2999140 2478030 1908980 2210820 2565320 3142490 2342800 2400430 2162900 FALSE TRUE 2602796.05 2461751.658 2832169.113 2712820.471 2514275.151 3263383.624 2115595.617 1887116.725 1907204.426 1.364717916 1.290764443 1.484984554 1.422406762 1.318303962 1.711082241 1.109265262 0.989467463 1 20.86302806 2.056629233 8.796684869 1.010386072 1.422243111 0.732143855 0.115160288 0.137178831 19.64952565 0.04544422 0.030565782 113.9276745 -2.056629233 0.411857039 LDLLGNLPGS(ph)KR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDLLGNLPGSKR 12 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 LDLLGNLPGS(1)KR 128.9 0.00014937 183440000 425670 381690 340670 326420 394150 333050 439990 519160 548620 TRUE FALSE 369416.631 379182.6533 505419.1515 400538.65 386307.1861 345862.649 397319.8375 408141.6741 483762.7686 0.763631794 0.783819421 1.044766535 0.827965019 0.798546749 0.714942677 0.821311319 0.84368145 1 18.88394022 1.228434957 3.623473777 1.026171814 0.824900474 0.293042881 0.086027996 0.426407188 8.448504906 0.239196825 0.022803411 16.921348 -1.228434957 -0.20127134 LDLRDDKDTIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 115.78 0.00051334 827720000 6238840 4325410 3553000 3842950 4472750 3478740 5165650 8867700 1993720 FALSE TRUE 5414361.487 4296996.097 5271242.684 4715550.533 4383751.026 3612569.379 4664686.058 6971411.364 1758024.693 3.079798315 2.444218283 2.998389446 2.682300512 2.493566241 2.054902524 2.65336777 3.965479775 1 20.7455239 0.849496858 0.01727308 8.09E-06 5.159887307 0.02739942 0.746432537 38051.07974 150.7784735 24515.80616 20663.12498 7.07126085 -0.849496858 5.159879216 LDLRDPAALFETHGAEEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LDLRDPAALFETHGAEEIR 19 1 A0A087WVI0;E9PBL8;Q8WTW3;J3KRP4 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 0 ;; 158 2.27E-10 121398000 353217 353658 206533 221596 365986 381328 352516 385895 240428 FALSE TRUE 306538.4785 351334.7973 306413.0496 271912.7587 358703.5946 395997.9349 318329.0526 303374.3573 212004.8757 1.445902965 1.657201496 1.445311333 1.282577855 1.691959175 1.867871829 1.501517602 1.430978209 1 17.69373792 1.194906819 2.117412138 0.785250044 1.561082378 0.544565236 0.159284842 0.666994358 2.707542011 1.048481219 0.045176087 15.66414947 -1.194906819 0.775832333 LDMEIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDMEIER 7 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 114.6 0.013652 400640000 542870 553440 402840 427360 581960 587320 584260 622470 725420 FALSE TRUE 471128.354 549804.4162 597654.7714 524398.6198 570380.1346 609914.5804 527598.5551 489359.6346 639661.674 0.736527407 0.859523774 0.934329499 0.819806221 0.891690338 0.953495582 0.824808765 0.76502885 1 19.28694952 4.729116024 4.863648322 0.87228677 0.730153676 0.292908076 0.06965939 0.233102635 16.24668585 0.017367288 0.110479525 53593.98169 -4.729116024 -0.142133095 LDNARQS(ph)AER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LDNARQSAER 10 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 LDNARQS(1)AER;LDNARQS(1)AER;LDNARQS(1)AER;LDNARQS(1)AER;LDNARQS(1)AER;LDNARQS(1)AER 134.61 0.00010052 2153200000 2205170 2035114 972702 1076455 1594616 1812100 1982630 2063400 667746 TRUE FALSE 1913751.197 2021745.202 1443103.941 1320880.56 1562886.261 1881812.66 1790354.848 1622157.967 588805.8286 3.250224615 3.43363653 2.450899551 2.243321136 2.654332185 3.195981711 3.040654085 2.75499645 1 19.16743243 4.239144254 24.99995968 2.555809337 3.3419308 0.256858748 0.600027341 22.20132653 950773.57 0.152930619 0.358285405 17343.79991 -4.239144254 0.786121463 LDNLHSCFCALQALIDSCAGPGSLATEPHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDNLHSCFCALQALIDSCAGPGSLATEPHVR 31 0 E5RIA4;E7ETB3;Q9ULA0-2;Q9ULA0;C9JBE1;E7EMB6 E5RIA4 DNPEP Aspartyl aminopeptidase 0 200.79 5.95E-26 187070000 180240 145460 88420 99392 167700 132820 158960 177530 148770 FALSE TRUE 156420.8273 144504.4637 131180.2077 121960.4727 164363.0981 137929.6713 143544.0837 139566.591 131182.5801 1.192390234 1.10155223 0.999981916 0.929700214 1.252933873 1.051432829 1.094231289 1.063911008 1 17.00121663 1.240847697 2.532605115 0.979337029 1.084702209 0.087250628 0.089817578 1.506458947 10.64310817 0.346148741 0.023554014 17.41196144 -1.240847697 0.10536518 LDNLVAILDINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDNLVAILDINR 12 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 205.46 2.36E-07 1642940000 944860 1062910 844870 776190 943770 830600 866560 946870 1384440 FALSE TRUE 819994.357 1055927.674 1253451.958 952435.8028 924990.8235 862553.7195 782521.1446 744389.2191 1220773.08 0.671700884 0.864966382 1.026769002 0.780190699 0.75770906 0.706563516 0.641004587 0.609768704 1 20.21936362 3.338035408 3.107013624 0.714939569 0.860182036 0.09909524 0.135073401 0.425607358 8.206786853 0.041251154 0.05444414 2177.88733 -3.338035408 0.145242467 LDNNWGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LDNNWGR 7 0 P17931;G3V3R6 P17931 LGALS3 Galectin-3;Galectin 0 ;;;;; 221.53 6.01E-05 5678980000 4226820 3923120 2378340 2818060 3570650 3693920 3360540 3962900 5345430 FALSE TRUE 3668235.028 3897348.766 3528513.179 3457943.594 3499601.051 3836027.493 3034635.348 3115464.674 4713499.355 0.778240274 0.826848266 0.748597361 0.733625558 0.742463462 0.813838553 0.643817919 0.660966395 1 22.1683671 1.227717432 24.97540108 1.00000056 0.739616971 0.659654558 0.057829197 325.0059421 748544.2096 0.228263338 0.015806049 16.89341426 -1.227717432 -0.260383589 LDNS(ph)PNMNITQPSK ddPTM_MDA-MB-175_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 117.18 0.00033425 111870000 187900 150500 107150 128360 141620 150480 143050 186690 176880 TRUE FALSE 163068.5389 149511.3556 158968.0984 157506.0999 138802.0391 156269.063 129177.033 146767.7963 155969.4479 1.045515908 0.958593863 1.019225884 1.009852263 0.889930951 1.001920986 0.828220108 0.9410035 1 17.25090393 3.255589351 24.97946679 0.928999328 1.005527421 0.327927387 0.053948275 278.1352723 407994.3299 0.014896779 0.019182501 1801.313696 -3.255589351 0.076528094 S(ph)PGRPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPGRPPK 7 1 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 S(1)PGRPPK;S(1)PGRPPK;S(1)PGRPPK 55.567 0.076824 690350000 981830 845830 719500 1248360 740910 924370 852040 1505950 2458180 TRUE FALSE 852078.6779 840273.687 1067452.607 1531819.218 726167.3406 959931.112 769409.2919 1183914.312 2167576.761 0.393101962 0.387655793 0.492463578 0.706696642 0.335013437 0.442859109 0.354962881 0.546192565 1 21.04765165 1.248719005 3.381781218 1.07811196 0.450105067 0.73479366 0.104088752 0.161821732 2.631450492 0.262334811 0.02701731 17.73041927 -1.248719005 -0.628006893 LDNTPAS(ph)PPRSPAEPNDIPIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDNTPASPPRSPAEPNDIPIAK 22 1 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;O95359-2;Q4VXL4;H0Y911;H0Y8P9 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 LDNT(0.183)PAS(0.808)PPRS(0.009)PAEPNDIPIAK 79.558 0.0045211 261870000 217600 180730 105280 101970 125630 113230 123380 126570 134100 TRUE FALSE 188843.6087 179542.7727 156193.7601 125123.847 123130.2088 117586.0314 111414.6266 99503.99047 118246.8508 1.597028652 1.518372553 1.320912643 1.058157965 1.041297996 0.994411526 0.942220667 0.841493789 1 16.85144224 3.992942014 0.912886448 0.921381448 1.696632248 0.9637973 0.047879655 0.14973096 0.199864862 0.019819424 0.093630697 9838.797325 -3.992942014 0.7752508 LDNVPHT(ph)PSSYIETLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LDNVPHTPSSYIETLPK 17 0 Q99733;Q99733-2;E9PNJ7;C9J6D1;A8MXH2;E9PS34;E9PNW0;E9PJJ2;E9PP22;E9PKI2 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 LDNVPHT(0.996)PS(0.004)SYIETLPK;LDNVPHT(0.741)PS(0.259)SYIETLPK;LDNVPHT(0.909)PS(0.091)SYIETLPK 214.31 2.20E-14 944150000 1170640 1124320 728730 881460 995700 846530 1334910 1436020 1427030 TRUE FALSE 1015936.958 1116934.268 1081146.265 1081608.965 975887.5181 879096.5569 1205450.634 1128938.298 1258328.139 0.807370452 0.887633546 0.859192632 0.859560342 0.775542951 0.698622664 0.957977968 0.897173212 1 20.26307676 2.192766196 24.99981397 0.940614842 0.820258642 0.550068625 0.058000079 111.321862 60771.34219 0.024879799 0.016774028 155.8713137 -2.192766196 -0.120356201 LDNVPHTPSS(ph)YIETLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDNVPHTPSSYIETLPK 17 0 Q99733;Q99733-2;E9PNJ7;C9J6D1;A8MXH2;E9PS34;E9PNW0;E9PJJ2;E9PP22;E9PKI2 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 LDNVPHT(0.029)PS(0.237)S(0.723)Y(0.007)IET(0.004)LPK 107.74 0.00044415 74664000 119520 107090 79419 88773 111030 94637 127430 126940 116190 TRUE FALSE 103725.1292 106386.5187 117826.294 108930.2665 108820.7202 98277.74663 115071.8582 99794.86885 102454.1506 1.01240534 1.038381736 1.150039246 1.063209893 1.062140671 0.959236362 1.123154675 0.974044178 1 16.64461891 2.967213854 24.65846932 1.017251387 1.069117528 0.172799267 0.055266937 964.4559139 725367.4382 0.017424113 0.017438479 927.2863228 -2.967213854 0.051866141 LDNVPHTPSSYIETLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDNVPHTPSSYIETLPK 17 0 Q99733;Q99733-2;E9PNJ7;C9J6D1;A8MXH2;E9PS34;E9PNW0;E9PJJ2;E9PP22;E9PKI2 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 92.977 0.0031758 388380000 149670 131450 95717 130740 147750 108380 189380 205520 179150 FALSE TRUE 129890.7303 130586.4963 142006.0614 160426.5152 144810.0641 112549.4487 171013.9567 161571.1474 157971.0911 0.822243674 0.826648062 0.898937017 1.015543503 0.916687117 0.712468642 1.082564889 1.022789336 1 17.26930104 -1.999999999 0.160346723 1.845690479 0.768550704 0.265288916 0.096588109 185.5159998 2.444083616 45.97149872 1.331132839 0.01 1.999999999 -1.077139776 LDNWLNELETYCTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDNWLNELETYCTR 14 0 H0Y6T8;Q9NP72;Q9NP72-2;Q5W0J0;A0A087X163 H0Y6T8 RAB18 Ras-related protein Rab-18 0 75.479 0.070117 16034000 10512 13693 8591.5 8517 11364 9528 10143 14445 10392 FALSE TRUE 9122.812566 13603.04978 12746.37814 10450.91502 11137.87863 9894.548325 9159.333421 11356.04916 9163.469599 0.99556314 1.484486813 1.390999119 1.140497593 1.215465225 1.079781869 0.999548623 1.23927395 1 13.16167824 3.634934077 5.921705776 1.119720172 1.308992715 0.246743436 0.145220269 0.300414248 14.35108862 0.038543263 0.057610387 4314.535801 -3.634934077 0.189272544 LDPAQS(ph)ASRENLLEEQGSIALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDPAQSASRENLLEEQGSIALR 22 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 LDPAQS(0.5)AS(0.5)RENLLEEQGSIALR;LDPAQS(0.5)AS(0.5)RENLLEEQGSIALR 169.13 5.23E-12 878230000 62103 47570 36916 33715 56552 50302 48079 57501 64202 TRUE FALSE 53895.9312 47257.50954 54768.70108 41370.50605 55426.72584 52237.15049 43416.30598 45204.85862 56612.1127 0.952021195 0.834759688 0.967437859 0.73077128 0.97906125 0.922720386 0.766908421 0.79850153 1 15.78882314 2.277807662 24.99990908 0.839661031 0.894197497 0.034463361 0.094080219 436.6516027 278140.3552 0.033753702 0.026145101 189.5866105 -2.277807662 0.054536466 LDPAQSAS(ph)RENLLEEQGSIALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LDPAQSASRENLLEEQGSIALR 22 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 LDPAQS(0.063)AS(0.937)RENLLEEQGSIALR;LDPAQS(0.208)AS(0.792)RENLLEEQGSIALR;LDPAQS(0.203)AS(0.797)RENLLEEQGSIALR;LDPAQS(0.3)AS(0.7)RENLLEEQGSIALR 256.78 2.43E-37 1196230000 223363 158669 111138 126070 137827 145628 135414 171188 209196 TRUE FALSE 193845.0136 157626.6929 164884.7085 154696.1204 135084.5124 151230.4034 122281.5711 134580.7784 184465.0872 1.050849332 0.854506917 0.8938532 0.838620048 0.732303952 0.819832119 0.662898183 0.72957317 1 17.49298826 7.999999559 0.607881679 0.775536714 18.71776295 0.401768412 0.092483904 174.4681038 1.332872773 0.042534065 4164.502981 99999898.52 -7.999999559 17.94222623 LDPDSIPS(ph)PIQVIENDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LDPDSIPSPIQVIENDR 17 0 O94855;O94855-2 O94855 SEC24D Protein transport protein Sec24D 1 LDPDSIPS(1)PIQVIENDR;LDPDSIPS(1)PIQVIENDR;LDPDSIPS(1)PIQVIENDR 134.44 1.78E-05 116529000 96263 101715 66410 74188 106864 103143 101224 115995 108833 TRUE FALSE 83541.60065 101046.8275 98526.09813 91033.51929 104737.6155 107110.978 91407.31206 91190.37192 95966.88672 0.870525277 1.052934308 1.026667651 0.948593024 1.091393282 1.116124338 0.952488042 0.950227469 1 16.55024907 4.749073012 24.14071503 1.012573855 0.870525146 0.383387086 0.058225457 1158.02014 2659196.88 0.015381646 0.207950037 56114.23059 -4.749073012 -0.142048709 LDPELHLDIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LDPELHLDIK 10 0 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ;; 141.93 3.66E-05 647109000 2525920 1865420 1502270 1825900 1825380 1619280 2124950 2590400 2873620 FALSE TRUE 2192113.272 1853165.933 2228772.797 2240498.502 1789058.509 1681574.749 1918872.676 2036463.119 2533903.917 0.865113021 0.731348146 0.879580627 0.884208153 0.706048283 0.663630037 0.757279178 0.803686006 1 21.27293039 1.238778954 4.172379881 1.021961251 0.781775301 0.450540306 0.074421977 0.22533825 7.291067635 0.163803963 0.019811317 17.32921754 -1.238778954 -0.24018595 LDPHLVLDQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LDPHLVLDQLR 11 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ;;;;; 127.37 0.00028799 10694970000 5857970 7679110 4895150 5703870 7235130 7564350 7124470 7739660 7436430 FALSE TRUE 5083824.422 7628665.421 7262460.913 6999020.862 7091165.068 7855355.439 6433539.996 6084593.939 6557303.717 0.775291895 1.163384487 1.107537675 1.067362618 1.081414767 1.197955101 0.981125821 0.927910953 1 22.64467129 2.024120365 24.67507178 0.95751983 1.074067538 0.1340441 0.113770221 307.8106877 314887.9599 0.044123563 0.029746459 105.7110446 -2.024120365 0.116547708 LDPHNHVLYSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LDPHNHVLYSNR 12 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;;; 62.287 0.045589 5141530000 8350540 6797180 3616630 4598620 6486040 6827660 6170140 6941180 6472040 FALSE TRUE 7246994.981 6752528.877 5365644.365 5642806.957 6356980.494 7090324.498 5571760.772 5456862.673 5706922.804 1.269860349 1.18321714 0.940199219 0.988765251 1.113906866 1.242407641 0.976316128 0.956183019 1 22.44428162 4.412659907 5.420838097 1.030942321 1.250607922 0.465760963 0.08928868 0.167514682 9.282683445 0.02460202 0.069522739 25861.86897 -4.412659907 0.219665601 LDPITGR ddPTM_MDA-MB-175_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 ;;; 126.2 0.009247 812230000 781670 843140 651930 574150 835720 1256770 576070 655080 635580 FALSE TRUE 678370.329 837601.3578 967205.5286 704519.5328 819090.8071 1305118.755 520202.8201 514996.2398 560442.4565 1.210419234 1.494535876 1.725789182 1.257077376 1.461507417 2.328729275 0.928200236 0.918910111 1 19.09620673 LDPPPS(ph)PHANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 77.597 0.033757 154020000 220750 177240 127380 147640 184890 182860 162790 198420 182970 TRUE FALSE 191577.3282 176075.6988 188981.3941 181163.9185 181211.0507 189894.7425 147002.6509 155989.4271 161339.495 1.187417428 1.091336617 1.171327541 1.122873965 1.123166096 1.176988576 0.911138657 0.966839688 1 17.29974012 2.241017391 24.9999992 0.958883619 1.142183417 0.858038475 0.035684225 20.28174262 206388.8714 0.012896025 0.009511449 174.1876624 -2.241017391 0.183299798 LDPPPS(ph)PHSNRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDPPPSPHSNRK 12 1 Q96P47;Q96P47-2;Q96P47-4;H0Y873 Q96P47 AGAP3 "Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3" 1 LDPPPS(0.988)PHS(0.012)NRK 53.169 0.067461 47707000 126150 100080 67546 82445 98417 95367 111400 117290 110360 TRUE FALSE 109478.9579 99422.56789 100211.4715 101165.3973 96458.69425 99035.8302 100596.4451 92208.44625 97313.36652 1.125014598 1.021674323 1.029781161 1.039583779 0.991217319 1.017700176 1.033737181 0.947541428 1 16.57035036 8 0.512169732 0.992794303 5.052358794 0.647589423 0.026626663 79.13633307 0.83536796 0.016339474 346.9843394 100000000 -8 4.059564491 LDQPGNLPGS(ph)NRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDQPGNLPGSNRR 13 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 LDQPGNLPGS(1)NRR 88.487 0.0048304 479900000 582020 515600 320400 372170 458200 494260 507360 560310 519800 TRUE FALSE 505104.5823 512212.9897 475346.5117 456676.8868 449082.7165 513274.502 458156.3053 440492.0668 458349.8362 1.102006682 1.117515376 1.03708232 0.99635006 0.979781558 1.11983132 0.999577766 0.961038997 1 18.80608963 7.999999998 0.313590703 0.984964711 2.287111405 0.401767634 0.045387634 79.02856875 1.251057006 0.083605909 57.61847369 99999999.51 -7.999999998 1.302146695 LDQPVS(ph)APPS(ph)PR ddPTM_MDA-MB-175_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 182.49 2.46E-05 25016180000 7088720 8370610 5604000 6847770 8861640 8448940 8947650 10019370 10141040 TRUE FALSE 6151927.691 8315622.912 8314113.144 8402660.84 8685310.702 8773976.189 8079908.28 7876805.696 8942177.804 0.687967498 0.929932629 0.929763792 0.939666044 0.971274659 0.981190084 0.90357276 0.880859883 1 23.0921948 4.739164329 5.599581257 0.93768736 0.679307304 0.834468698 0.035533414 0.060882607 7.755877767 0.009304341 0.060284704 54848.44618 -4.739164329 -0.258380056 LDQPVSAPPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 LDQPVSAPPSPR 12 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 LDQPVSAPPS(1)PR;LDQPVS(0.001)APPS(0.999)PR;LDQPVSAPPS(1)PR;LDQPVSAPPS(1)PR;LDQPVSAPPS(1)PR;LDQPVSAPPS(1)PR;LDQPVS(0.008)APPS(0.992)PR 205.33 1.08E-07 30990990000 4634070 4999090 3406430 4463090 5968090 5626850 6085560 7275770 5718650 TRUE FALSE 4021665.908 4966250.649 5053790.942 5476502.799 5849336.685 5843318.561 5495383.328 5719903.206 5042597.712 0.797538518 0.984859577 1.002219735 1.086047928 1.159984797 1.15879134 1.089792135 1.134316781 1 22.2657357 4.89981625 0.939002564 1.112396461 0.559366137 0.794454772 0.04932742 1.153952339 0.664459706 0.01642826 0.697268299 79399.22261 -4.89981625 -0.553030324 LDRAS(ph)PDLWPEQLPGVAEFAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDRASPDLWPEQLPGVAEFAASFK 24 1 Q52LA3 Q52LA3 LIN52 Protein lin-52 homolog 1 LDRAS(1)PDLWPEQLPGVAEFAASFK;LDRAS(1)PDLWPEQLPGVAEFAASFK 192.72 3.90E-18 1413450000 1402750 1185100 808350 970480 1018390 877570 1218380 1578890 1230490 TRUE FALSE 1217373.033 1177315 1199270.764 1190842.317 998126.0314 911330.6858 1100221.695 1241256.66 1085022.874 1.121979142 1.085060074 1.105295374 1.097527384 0.919912433 0.839918409 1.014007835 1.143991238 1 20.04929403 3.336588288 10.26336936 0.998778211 1.101948067 0.361436418 0.077086208 0.520841534 50.38520171 0.02638598 0.034062572 2170.642428 -3.336588288 0.103169856 LDRDEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDRDEER 7 1 P40818;A0A075B720;H0YM17;H0YLH2;H0YM47;H0YNL5;H0YKV1 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 0 ; 93.467 0.02482 0 392190 417030 310390 370980 345610 471710 425000 448810 508840 FALSE TRUE 340361.0978 414290.5025 460495.6422 455216.6791 338733.0372 489856.9889 383783.5654 352835.4741 448685.5149 0.758573849 0.923342717 1.026321615 1.014556218 0.754945337 1.091760203 0.855350914 0.786375897 1 18.77534508 0.951562752 20.6423132 1.972154944 0.902752065 0.065867662 0.116591463 40413355.72 313073223.9 1833443688 0.028249946 8.944637661 -0.951562752 -1.069402879 LDRDPASGTALQEISFWLNLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDRDPASGTALQEISFWLNLER 22 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 158.89 1.85E-11 219150000 360930 353310 221220 246670 357960 316110 341000 377270 364240 FALSE TRUE 313232.186 350989.0833 328202.7319 302680.1936 350837.2963 328270.9563 307929.8725 296593.7464 321179.9621 0.975254446 1.092811273 1.021865529 0.942400614 1.092338681 1.022077947 0.958745591 0.923450344 1 18.29302236 2.233760597 5.43406786 0.952165223 1.027119703 0.268323072 0.048976017 0.19016987 17.35631466 0.019103033 0.013524429 171.3012755 -2.233760597 0.07495448 LDRETEELHHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDRETEELHHDR 12 1 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 ; 92.935 0.0044796 1523530000 993200 942230 557090 620370 878050 854180 896110 1049420 616570 FALSE TRUE 861946.1036 936040.4291 826500.5874 761234.4903 860578.5229 887040.8573 809205.3901 825009.6996 543679.797 1.585392925 1.721675946 1.520197351 1.400152249 1.582877509 1.631550155 1.488385985 1.517455135 1 19.05239769 1.179281962 2.966662807 0.832189937 1.561602223 0.806734747 0.085587193 0.237669064 2.262360358 0.451649096 0.023150125 15.11060881 -1.179281962 0.729412286 LDRLDLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LDRLDLAR 8 1 O14579;M0QXB4;O14579-3;O14579-2 O14579 COPE Coatomer subunit epsilon 0 ;;; 174.02 0.00025021 1830160000 2492540 2581020 1526200 1777900 2757480 2598960 2571160 2957980 1383940 FALSE TRUE 2163144.524 2564065.11 2264275.425 2181599.369 2702611.543 2698943.673 2321809.299 2325438.996 1220332.19 1.77258663 2.101120606 1.855458246 1.787709434 2.214652343 2.21164671 1.902604322 1.905578674 1 20.21884249 1.211208977 3.456392897 0.814122739 1.984633769 0.78661034 0.158826781 0.164268847 2.699395312 0.531734743 0.041340373 16.26331138 -1.211208977 1.17051103 LDRPAGGPS(ph)AESPRPSSAYNGDLNGLLVPDPLCSGDSTSANK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDRPAGGPSAESPRPSSAYNGDLNGLLVPDPLCSGDSTSANK 42 2 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 LDRPAGGPS(0.522)AES(0.43)PRPS(0.017)S(0.017)AY(0.014)NGDLNGLLVPDPLCSGDSTSANK 127.97 3.51E-09 776920000 43650 35158 22562 26191 27840 25868 35146 45236 32407 TRUE FALSE 37881.5419 34927.04478 33473.05867 32138.06685 27286.03847 26863.1587 31737.54633 35562.63343 28575.88138 1.325647367 1.222256081 1.171374497 1.124657064 0.954862533 0.940064047 1.11064103 1.244498217 1 14.80251038 4.23723062 1.446670015 1.0748616 1.323976961 0.505539899 0.08926064 0.575743944 1.997349837 0.030738675 0.160739497 17267.54593 -4.23723062 0.249115361 LDRPAGGPSAES(ph)PRPSSAYNGDLNGLLVPDPLCSGDSTSANK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDRPAGGPSAESPRPSSAYNGDLNGLLVPDPLCSGDSTSANK 42 2 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 LDRPAGGPS(0.009)AES(0.981)PRPS(0.005)S(0.005)AYNGDLNGLLVPDPLCSGDSTSANK 340.77 6.43E-134 1028400000 557620 483650 291090 328580 411820 341320 499060 560970 502290 TRUE FALSE 483929.1042 480472.8713 431862.0976 403189.111 403625.5877 354450.8013 450661.238 441010.931 442909.8484 1.092613104 1.084809636 0.975056435 0.910318686 0.911304161 0.800277534 1.017501055 0.995712632 1 18.75665355 4.186170501 3.598914068 0.942964773 1.092750366 0.494851451 0.061552861 0.204584518 5.337743529 0.017669657 0.044546874 15352.19581 -4.186170501 0.149785592 LDS(ph)PDPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LDSPDPFK 8 0 P42566;B1AUU8;P42566-2 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 LDS(1)PDPFK;LDS(1)PDPFK;LDS(1)PDPFK;LDS(1)PDPFK 112.13 0.0032522 328352000 949770 723950 993790 1118490 989010 722940 1029940 1255690 3880830 TRUE FALSE 824255.4881 719194.3248 1474390.168 1372460.25 969330.636 750751.9696 930056.5773 987170.4653 3422042.698 0.240866512 0.210165211 0.430850898 0.401064619 0.283260824 0.219387084 0.271784036 0.288474035 1 21.70642633 1.238265878 24.99999996 1.000000786 0.29445856 0.90565015 0.071690904 2.131426422 180481.6376 0.105823602 0.01868159 17.30875691 -1.238265878 -0.705542226 LDS(ph)PPPS(ph)PITEASEAAEAAEAGNLAVSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LDSPPPSPITEASEAAEAAEAGNLAVSSR 29 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 LDS(0.997)PPPS(0.876)PIT(0.125)EAS(0.003)EAAEAAEAGNLAVSSR;LDS(0.962)PPPS(0.818)PIT(0.21)EAS(0.011)EAAEAAEAGNLAVSSR;LDS(0.993)PPPS(0.905)PIT(0.102)EASEAAEAAEAGNLAVSSR 189.31 2.39E-18 234682000 69707 65166 48419.6 56156 81787 75919 82849 95683 87277 TRUE FALSE 60495.04333 64737.92026 71835.48051 68907.07809 80159.59871 78839.65306 74814.31673 75221.93506 76959.21249 0.786066299 0.8411978 0.93342276 0.895371403 1.041585486 1.024434249 0.972129448 0.977425998 1 16.23180642 4.271773134 0.951547188 0.99611268 0.747536394 0.826009949 0.033761099 0.444823767 0.52579414 0.012424152 0.098839496 18697.05193 -4.271773134 -0.248576286 S(ph)SPVPPVPERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPVPPVPERR 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 S(0.5)S(0.5)PVPPVPERR 79.639 0.01629 2407300000 101430 99660 52687 64482 105020 97450 77995 88792 44856 TRUE FALSE 88025.76851 99005.3269 78166.60943 79123.62365 102930.3075 101198.9646 70431.0569 69804.52178 39553.17478 2.225504501 2.503094314 1.976241095 2.000436731 2.602327324 2.558554784 1.780667602 1.764827278 1 15.27150588 1.282177277 1.211567792 0.4845776 2.289303147 0.73167312 0.248058297 0.76330214 1.015923854 1.747040901 0.080743968 19.15037477 -1.282177277 1.804725546 LDS(ph)PTMSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LDSPTMSR 8 0 P19634 P19634 SLC9A1 Sodium/hydrogen exchanger 1 1 LDS(0.975)PT(0.025)MSR;LDS(1)PTMSR;LDS(0.878)PT(0.122)MSR 204.34 9.27E-05 948620000 1497220 1289050 1121300 1838980 1791190 1690490 1006400 1992810 2427040 TRUE FALSE 1299358.584 1280582.146 1663564.431 2256548.516 1755548.823 1755524.244 908799.4829 1566663.09 2140118.096 0.607143403 0.598369851 0.77732366 1.054403736 0.820304649 0.820293164 0.424649221 0.732045158 1 21.02925898 4.229061025 7.675858653 0.787724195 0.60210527 0.194659275 0.167775879 0.231890052 85.95451623 0.045831139 0.104137963 16945.75897 -4.229061025 -0.185618925 LDSEDKDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LDSEDKDK 8 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;; 114.84 0.0023517 15294220000 25145900 16904700 20215300 19476400 8637570 9702520 25629600 29096200 33051400 FALSE TRUE 21822805.6 16793651.91 29991486.7 23898814.3 8465699.256 10075782.22 23144045.34 22874204.06 29144101.14 0.748789798 0.576228165 1.029075714 0.82002235 0.290477281 0.345722868 0.79412452 0.784865656 1 24.79670057 -0.553513868 8.893822125 6.185005601 0.705077677 0 0.244722963 0 0 0 0.057664197 0.279567145 0.553513868 -5.479927925 LDSEDKDKEGKPLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDSEDKDKEGKPLLK 15 3 P13639 P13639 EEF2 Elongation factor 2 0 96.993 0.0015269 729120000 2924800 1653100 1440400 909000 1097800 664160 3039100 3326600 158900 FALSE TRUE 2538280.27 1642240.677 2136982.258 1115402.343 1075955.928 689710.665 2744368.55 2615232.478 140115.023 18.11568963 11.72066094 15.25162835 7.960619205 7.679090397 4.922460491 19.58654033 18.66489703 1 17.09625212 3.750505634 23.81716822 10 14.69846056 0.143309972 5.813394979 988.1505816 1970262.586 1.71663513 2.940086966 5629.964215 -3.750505634 4.698460561 LDSHPCLEVTAAALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LDSHPCLEVTAAALR 15 0 Q9H4A4;A6NKB8;A0A087WU27;A0A087WUS4 Q9H4A4 RNPEP Aminopeptidase B 0 ;;; 207.31 3.46E-09 3909310000 2978750 2958700 1942170 2148300 2926640 2920710 2834750 3110390 3296590 FALSE TRUE 2585100.64 2939264.105 2881409.908 2636104.35 2868405.59 3033071.604 2559836.381 2445257.304 2906870.886 0.889307005 1.011143673 0.991241105 0.90685292 0.986767456 1.043414628 0.880615783 0.841199145 1 21.47103556 2.204682177 24.99980408 0.892395809 0.971917573 0.188332025 0.060222637 239.3162902 176596.254 0.024047267 0.016213645 160.2072543 -2.204682177 0.079521764 LDSLHPDLIYNVSWNHNGSLFCSACK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDSLHPDLIYNVSWNHNGSLFCSACK 26 0 Q9BR76;A0A087WW53;F5H390 Q9BR76 CORO1B Coronin-1B;Coronin 0 266.46 2.00E-53 788090000 486260 446530 112530 295320 448880 339820 447750 531030 501430 FALSE TRUE 421999.509 443596.715 166949.8844 362376.9197 439948.1662 352893.0953 404327.2739 417473.367 442151.5166 0.954422846 1.003268559 0.377585235 0.819576335 0.995016753 0.798127072 0.914454115 0.944186215 1 18.75418131 3.462796225 20.53893202 0.922737714 0.76718875 0.143437599 0.173150984 54.9000801 78711.62857 0.050475859 0.065243492 2902.66038 -3.462796225 -0.155548964 LDSPT(ph)MSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDSPTMSR 8 0 P19634 P19634 SLC9A1 Sodium/hydrogen exchanger 1 1 LDS(0.411)PT(0.589)MSR 171.33 0.0032419 378530000 527640 423510 419490 611220 611480 625740 348040 729120 878450 TRUE FALSE 457911.0371 420727.9349 622356.7671 750006.8429 599312.7443 649812.6227 314287.1344 573203.362 774600.6417 0.591157575 0.543154643 0.803455011 0.968249705 0.773705458 0.838900186 0.405740865 0.739998563 1 19.56309317 4.239740159 24.99703782 0.772486168 0.567156048 0.244422611 0.160612374 47.91387204 1015281.504 0.042543291 0.100479702 17367.61403 -4.239740159 -0.20533012 LDSQEPGRQT(ph)PDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDSQEPGRQTPDR 13 1 Q8TB03-2;Q8TB03 Q8TB03-2 CXorf38 Uncharacterized protein CXorf38 1 LDSQEPGRQT(1)PDR 101.05 0.0034249 697980000 647850 470100 269540 328070 474770 441310 476210 504040 412000 TRUE FALSE 562234.9811 467011.8821 399890.4456 402563.3077 465323.0059 458287.4813 430027.2275 396254.9684 363293.8294 1.547603993 1.285493571 1.100735584 1.108092886 1.280844783 1.261478848 1.183689875 1.090728596 1 18.47077734 4.643298416 2.643742389 1.1515013 1.586661849 0.70139768 0.083187665 0.228504268 2.383042206 0.023013046 0.197583443 43984.37402 -4.643298416 0.435160549 LDSQNAQGYEWIFIAWSPDHSHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LDSQNAQGYEWIFIAWSPDHSHVR 24 0 Q12792;Q12792-3;F8VS81;F8W1Q9 Q12792 TWF1 Twinfilin-1 0 ;; 211.92 1.45E-25 1228179000 264179 157500 171307.9 239802 159144 159872 225349.6 296522 296112 FALSE TRUE 229267.0758 156465.3721 254152.9734 294252.7092 155977.3458 166022.3793 203495.2305 233113.0778 261105.9767 0.878061386 0.599240868 0.973370953 1.126947429 0.597371794 0.635842892 0.779358761 0.892791045 1 17.99427596 1.466640348 2.89396225 0.998030558 0.796952186 0.134775657 0.167400968 0.618145705 9.138033181 0.238634992 0.046117587 29.28467094 -1.466640348 -0.201078372 LDSQPQETS(ph)PELPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 LDSQPQETSPELPR 14 0 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 LDSQPQET(0.001)S(0.999)PELPR;LDSQPQET(0.032)S(0.968)PELPR;LDSQPQET(0.024)S(0.976)PELPR;LDSQPQETS(1)PELPR;LDSQPQET(0.03)S(0.97)PELPR;LDSQPQET(0.245)S(0.755)PELPR;LDSQPQET(0.117)S(0.883)PELPR;LDSQPQET(0.003)S(0.997)PELPR;LDSQPQET(0.029)S(0.971)PELPR;LDSQPQET(0.026)S(0.974)PELPR 326.03 2.88E-57 23071764000 9486770 7742310 5107660 6321198 7663070 7749370 7717170 8697260 8163130 TRUE FALSE 8233069.308 7691450.256 7577741.46 7756522.619 7510589.9 8047493.278 6968760.041 6837418.631 7198094.071 1.143784622 1.068539836 1.052742766 1.077580057 1.043413691 1.118003349 0.968139618 0.949892925 1 22.77918353 2.226057673 24.99999176 0.967741602 1.079748603 0.72996444 0.031803668 108.7968399 217540.5428 0.012507389 0.008496626 168.289753 -2.226057673 0.112007001 LDSS(ph)PSVSSTLAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 LDSS(0.973)PS(0.026)VSSTLAAK;LDS(0.125)S(0.875)PSVSSTLAAK;LDS(0.005)S(0.995)PSVSSTLAAK;LDS(0.119)S(0.881)PS(0.001)VSSTLAAK;LDS(0.097)S(0.903)PSVSSTLAAK 375.65 2.46E-97 3267860000 6688120 5410470 4175770 5288090 5141850 4155570 5786880 7136940 8732060 TRUE FALSE 5804267.996 5374928.266 6195186.339 6488831.658 5039537.245 4315437.467 5225669.268 5610760.921 7699765.814 0.753823965 0.698063863 0.804594125 0.842731041 0.654505262 0.56046347 0.678678988 0.728692412 1 22.87638314 1.239353551 5.352055486 1.015024986 0.712421952 0.568031608 0.07816179 0.127519363 10.69934231 0.142618759 0.021297624 17.35216028 -1.239353551 -0.302603034 LDSSEMDHS(ph)ENEDYTMSSPLPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LDSSEMDHSENEDYTMSSPLPGK 23 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 LDSS(0.001)EMDHS(0.999)ENEDYTMSSPLPGK;LDS(0.004)S(0.004)EMDHS(0.993)ENEDYTMSSPLPGK;LDS(0.014)S(0.012)EMDHS(0.974)ENEDYTMSSPLPGK;LDS(0.002)S(0.002)EMDHS(0.996)ENEDYTMSSPLPGK 213.05 1.28E-25 845740000 674570 529280 397651 517560 544190 392105 605850 685820 864960 TRUE FALSE 585423.8654 525803.1248 589956.3537 635079.9084 533361.6837 407189.5331 547094.7602 539162.7301 762705.4142 0.767562226 0.689392149 0.773504872 0.832667366 0.699302344 0.533875236 0.717308085 0.706908224 1 19.54076642 1.237779268 24.91568971 1.000000347 0.713332105 0.572666356 0.077340786 14.50063257 462081.3875 0.115592128 0.019798143 17.28937396 -1.237779268 -0.286668242 LDSSPS(ph)VSSTLAAK ddPTM_MDA-MB-175_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(0.001)S(0.12)PS(0.879)VSSTLAAK 279.55 3.32E-33 457240000 779350 608590 517020 618290 576320 480360 680630 841270 1012200 TRUE FALSE 676356.9229 604592.1322 767052.6013 758682.1945 564852.3596 498839.76 614622.6074 661370.9573 892538.8691 0.75778988 0.677384653 0.859405263 0.850027064 0.632860236 0.55889976 0.688622791 0.740999614 1 19.76755547 1.238411042 4.488387849 1.024024257 0.71737479 0.485000015 0.090733266 0.196038718 8.259909311 0.192338375 0.024829037 17.31454337 -1.238411042 -0.306649466 LDSYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDSYLR 6 0 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 ; 142.74 0.026724 401720000 539680 600790 341570 422120 532990 557410 530600 578660 545430 FALSE TRUE 468359.9206 596843.3709 506754.3945 517968.7977 522384.5418 578853.9234 479142.4937 454918.0621 480949.8868 0.973822707 1.2409679 1.053653215 1.076970412 1.08615171 1.203563904 0.996242034 0.945874143 1 18.87552705 2.073874559 8.468222368 0.969654934 1.107245103 0.384328867 0.075048781 0.234999095 24.08723986 0.028458196 0.01914906 118.5426302 -2.073874559 0.137590169 LDTDDLDEIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 236.92 3.37E-15 338546000 1136154 815337 661210 723929 832228 693298 1003868 1185723 1191140 FALSE TRUE 986008.3703 809980.9976 980973.3676 888308.144 815668.291 719969.6227 906513.0359 932165.3638 1050324.786 0.938765212 0.771171935 0.933971454 0.84574615 0.77658673 0.685473324 0.863078781 0.887502015 1 20.00240408 1.347364904 2.00101751 1.028960279 0.825438873 0.338521434 0.075420919 0.708126621 3.463819004 0.249970348 0.020952371 22.25178749 -1.347364904 -0.203521405 LDTGPQSLS(ph)GK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDTGPQSLSGK 11 0 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 LDTGPQS(0.002)LS(0.998)GK 138.55 0.0013483 0 771830 419870 243250 200570 186810 147550 235580 246200 382650 TRUE FALSE 669830.7099 417111.8463 360886.5136 246112.484 183092.8465 153226.344 212733.4879 193552.0459 337413.5529 1.985192071 1.236203593 1.069567332 0.729409005 0.542636314 0.4541203 0.630482937 0.573634474 1 18.3641584 4.84996582 0.923442669 0.619498338 2.925524865 0.881515762 0.15659035 0.79130519 0.468374076 0.053333741 1.925087757 70789.00704 -4.84996582 2.306026527 LDTGS(ph)PEPETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDTGSPEPETR 11 0 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 LDT(0.001)GS(0.999)PEPETR;LDT(0.011)GS(0.989)PEPETR 113.61 0.0014357 290390000 507620 457380 321280 379690 472040 442750 434720 502310 574870 TRUE FALSE 440536.7309 454375.4407 476652.0826 465904.4177 462647.3275 459782.879 392560.9213 394894.9155 506909.5235 0.869063828 0.896363985 0.940309977 0.919107644 0.912682256 0.907031448 0.774420095 0.779024455 1 18.95136874 2.326055134 11.06282878 0.832972048 0.909336303 0.125509154 0.064201005 0.611611972 73.13827828 0.023860515 0.01847131 211.8630079 -2.326055134 0.076364255 LDTIPDIPPPRPPKPHPAHDRS(ph)PVETCSIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDTIPDIPPPRPPKPHPAHDRSPVETCSIPR 31 3 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 LDTIPDIPPPRPPKPHPAHDRS(0.664)PVET(0.168)CS(0.168)IPR 55.413 0.021676 103300000 80745 76006 46515 60591 70675 63360 72018 98078 73645 TRUE FALSE 70074.34367 75506.71158 69009.80958 74349.11263 69268.70577 65797.5002 65033.70544 77104.78294 64938.772 1.079083289 1.162736979 1.0626904 1.144910973 1.066677174 1.013223659 1.001461892 1.187345873 1 15.98679248 3.153848314 9.828169821 1.064346093 1.112360378 0.176488535 0.060564009 0.744787887 80.06403734 0.018830793 0.021371406 1425.109757 -3.153848314 0.048014284 LDVFARPAS(ph)PSLQLLPWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDVFARPASPSLQLLPWR 18 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 LDVFARPAS(0.954)PS(0.046)LQLLPWR;LDVFARPAS(0.985)PS(0.015)LQLLPWR 194.62 3.85E-15 2453400000 1525440 1468170 473240 594990 1113530 946510 1181010 1349460 141069 TRUE FALSE 1323849.239 1458525.495 702100.4469 730091.5734 1091372.932 982922.8522 1066475.832 1060888.481 124391.9835 10.64256073 11.72523706 5.64425799 5.869281546 8.77365969 7.901818303 8.573509335 8.52859204 1 16.92453399 4.245265057 24.99681828 6.985709235 11.18390057 0.394462036 2.318963994 165.8729963 618424.3936 0.572906335 1.444049215 17589.96831 -4.245265057 4.198191334 LDVFYLHLYCTFQALCGLT(ph)S(ph)VFS(ph)LLVDIT(ph)LK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDVFYLHLYCTFQALCGLTSVFSLLVDITLK 31 0 A0A2R8Y5Y7 A0A2R8Y5Y7 4 LDVFY(0.002)LHLY(0.002)CT(0.022)FQALCGLT(0.993)S(0.993)VFS(0.994)LLVDIT(0.993)LK 44.301 0.038716 68377000 56235 56732 83800 38945 25175 57295 24159 27177 18571 TRUE FALSE 48803.40227 56359.32376 124325.9603 47788.05749 24674.06675 59499.17572 21816.0639 21365.41004 16375.55754 2.980258972 3.441673582 7.592166558 2.918255295 1.506761935 3.633413738 1.332233351 1.304713442 1 13.99925641 3.48570489 22.70002033 1.802268467 4.666199613 0.477241663 1.392666835 103.3756356 273384.1751 0.396245833 0.539840931 3059.883487 -3.48570489 2.863931146 LDVGNFSWGSECCTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LDVGNFSWGSECCTR 15 0 P62241 P62241 RPS8 40S ribosomal protein S8 0 ;;; 278.27 3.04E-33 1340220000 305983 274148 181550 238632 296531 267930 253653 335125 287145 FALSE TRUE 265546.5713 272347.1037 269348.1872 292817.0429 290630.6133 278237.4405 229053.7711 263461.1267 253199.0452 1.048766085 1.075624529 1.063780422 1.156469775 1.147834554 1.09888819 0.904639158 1.040529701 1 17.94991244 2.314747715 12.6658709 0.990791321 1.10089806 0.574566059 0.047151561 0.544788875 88.81990332 0.017983403 0.013926158 206.4180711 -2.314747715 0.110106739 LDVTILS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LDVTILSPSR 10 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 1 LDVT(0.002)ILS(0.571)PS(0.427)R;LDVTILS(0.974)PS(0.026)R;LDVTILS(0.922)PS(0.077)R;LDVTILS(0.992)PS(0.008)R 103.91 0.0028866 542775000 541881 541170 352635 390418 503669 498306 473238 604470 636600 TRUE FALSE 470270.0529 537615.0186 523170.4655 479068.3741 493646.9723 517476.1543 427343.4516 475208.7945 561341.8732 0.837760508 0.9577319 0.931999714 0.853434238 0.879405218 0.921855609 0.761289104 0.846558607 1 19.09852016 3.736409036 24.74453394 0.868634139 0.914020827 0.037038245 0.067079048 435.3272158 5006567.33 0.018199748 0.028558689 5450.157285 -3.736409036 0.045386688 LDWELEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDWELEQR 8 0 Q13769;F8WCP5;C9JXG5;H7C072 Q13769 THOC5 THO complex subunit 5 homolog 0 99.755 0.015327 45792000 127920 109510 61688 78161 95047 100620 96533 115720 112020 FALSE TRUE 111015.0479 108790.6216 91520.52313 95908.64967 93155.75066 104490.9165 87171.24452 90974.17853 98777.12321 1.123894322 1.101374671 0.92653562 0.970960143 0.943090339 1.05784531 0.882504386 0.921004536 1 16.59188933 4.265975453 8.524723935 0.953710246 1.113630824 0.645584937 0.047753597 0.139280817 37.09480754 0.011945201 0.030846008 18449.11137 -4.265975453 0.159920578 LDWES(ph)FKEEEGIGEELAIHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDWESFKEEEGIGEELAIHNR 21 1 Q9UEE9 Q9UEE9 CFDP1 Craniofacial development protein 1 1 LDWES(1)FKEEEGIGEELAIHNR 137.16 2.27E-06 11496000 21600 11655 8789.1 9445.4 9271.9 10109 14863 14410 25405 TRUE FALSE 18745.50527 11578.43754 13039.53816 11590.12243 9087.40733 10497.89977 13421.58855 11328.53364 22401.64984 0.836791281 0.516856465 0.582079367 0.517378073 0.405657949 0.468621724 0.599133932 0.505700862 1 14.45131737 1.235539255 24.98999672 1.000000623 0.545140754 0.599313622 0.114395355 57.16433255 472725.7971 0.186037375 0.027104637 17.20042806 -1.235539255 -0.454859868 LDYEDIIDDLPCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDYEDIIDDLPCR 13 0 A0A494C108;Q8N9T8;H0YH26 A0A494C108 KRI1 Protein KRI1 homolog 0 99.343 0.0067562 34913000 33035 28495 21448 29168 32767 24409 21500 29102 68308 FALSE TRUE 28669.34105 28307.81447 31820.32454 35791.0402 32115.00081 25348.03002 19414.93331 22878.76377 60232.70606 0.475976308 0.469974144 0.528289805 0.594212722 0.533182102 0.420834986 0.322332078 0.379839547 1 15.87825946 1.233237293 24.99932498 1.000000843 0.46167737 0.821404646 0.078295572 81.23109357 381433.8762 0.188035042 0.022559318 17.10949903 -1.233237293 -0.538323473 LDYFLLSHSLLPALCDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDYFLLSHSLLPALCDSK 18 0 P27695 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 235.24 8.69E-24 2205210000 6605300 4468100 2782100 3376800 3988000 3376100 5176600 5889700 3995200 FALSE TRUE 5732392.869 4438748.757 4127532.866 4143554.051 3908646.602 3505980.752 4674574.129 4630233.489 3522892.007 1.627183819 1.259972985 1.171631959 1.176179696 1.10949941 0.99519961 1.326913831 1.314327399 1 21.74832882 4.758215631 2.484467013 1.172785446 1.74177574 0.639324668 0.110217706 0.404113766 2.994278301 0.029981429 0.498034617 57308.05 -4.758215631 0.568990294 LDYGQHVVAGTPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LDYGQHVVAGTPGR 14 0 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ; 130.72 6.04E-05 880000000 1423190 1304450 729100 966710 1225630 1174630 1458420 1508020 1291720 FALSE TRUE 1235111.836 1295880.982 1081695.199 1186216.281 1201242.361 1219818.776 1316982.653 1185541.658 1139014.333 1.084369002 1.1377214 0.949676547 1.041441048 1.054633226 1.070942429 1.156247656 1.040848762 1 20.11935447 2.764728578 5.945655419 1.071309413 1.0516854 0.009644557 0.059827054 1.000340711 122.4372133 0.020374266 0.01983225 581.7395331 -2.764728578 -0.019624013 LDYILGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDYILGLK 8 0 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 114.93 0.0059582 37987000 96969 81044 77739 67709 89923 91232 96083 110290 129170 FALSE TRUE 84154.30096 80511.61663 115333.8404 83083.36332 88133.70823 94741.75407 86764.88545 86705.34178 113899.6698 0.738845873 0.706864355 1.012591526 0.729443408 0.773783703 0.831800077 0.761765909 0.761243136 1 16.79740404 1.23372415 24.99703744 1.00000032 0.790250325 0.372279035 0.085880439 164.6157943 850705.8523 0.161056109 0.020192459 17.12869002 -1.23372415 -0.209749994 LDYNNIPTVVFSHPPIGTVGLTEDEAIHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LDYNNIPTVVFSHPPIGTVGLTEDEAIHK 29 0 P00390-5;P00390-4;P00390-2;P00390-3;P00390 P00390-5 GSR "Glutathione reductase, mitochondrial" 0 126.88 1.15E-05 279840000 210040 201710 182230 212810 209430 187230 207670 275070 392590 FALSE TRUE 182282.6818 200384.9537 270357.0375 261131.7631 205262.7527 194432.8593 187530.1954 216248.4211 346178.4574 0.526556976 0.578848711 0.780975915 0.754327017 0.592939128 0.561654993 0.541715382 0.624673247 1 18.40115642 1.238893194 10.3138363 1.001296377 0.62189466 0.664635568 0.084777806 0.046302837 124.7611176 0.125642633 0.022525333 17.33377656 -1.238893194 -0.379401717 LDYVPSSAS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LDYVPSSASR 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 LDYVPSSAS(1)R;LDYVPSS(0.003)AS(0.997)R;LDYVPSSAS(1)R;LDYVPSSAS(1)R;LDYVPSSAS(1)R;LDYVPSSAS(1)R;LDYVPSSAS(1)R;LDYVPSSAS(1)R 195.29 3.89E-07 7581600000 7838090 7600760 4894000 5609160 7228630 7121280 6908390 7066260 6479000 TRUE FALSE 6802266.547 7550830.107 7260754.769 6882805.509 7084794.406 7395240.25 6238415.401 5555195.289 5713060.001 1.19065204 1.321678769 1.270904694 1.204749383 1.240105023 1.294444702 1.09195692 0.972367748 1 22.44583225 2.052572071 3.472892746 0.99166662 1.25454853 0.887906766 0.040069834 0.066857432 1.643882171 0.019679541 0.011269718 112.8683228 -2.052572071 0.262881911 LDYWEDDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LDYWEDDLR 9 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6;Q5T321;A0A0D9SF28;F5GXV7;Q8NFP9 A0A494C1L5;Q5T321 LRBA;NBEA Lipopolysaccharide-responsive and beige-like anchor protein;Neurobeachin 0 ;;;;; 161.92 0.00014929 2307470000 2805310 2818240 1917370 2070410 2693070 2677180 2756900 3135950 3177490 FALSE TRUE 2434581.176 2799726.796 2844616.545 2540528.235 2639483.176 2780172.847 2489536.262 2465351.496 2801850.752 0.868918937 0.999241945 1.015263409 0.906732178 0.942049884 0.992263005 0.888532789 0.879901078 1 21.41794868 2.22866596 24.99966674 0.912443394 0.956213434 0.057728476 0.053958975 432.8750254 1093684.988 0.02150374 0.014697869 169.3035093 -2.22866596 0.043770039 LDYWEDDLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 180.15 3.25E-06 2552032000 2875080 2688770 1770282 2083881 2734580 2751230 2624940 3022960 2744590 FALSE TRUE 2495130.893 2671107.293 2626396.296 2557058.031 2680167.208 2857071.598 2370373.723 2376523.529 2420127.697 1.030991421 1.103705105 1.085230461 1.056579797 1.107448674 1.180545804 0.979441591 0.981982699 1 21.20665174 2.204184818 24.99998925 0.985745745 1.093021288 0.62912879 0.038695848 114.7049059 83418.97522 0.015774021 0.010635411 160.0238878 -2.204184818 0.107275543 LEAAEER ddPTM_MDA-MB-175_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 80.462 0.069435 93576000 287900 274060 161940 185940 245310 234410 240410 262880 259330 FALSE TRUE 249853.2856 272259.6818 240254.7257 228160.5189 240428.8109 243427.9044 217095.0752 206665.1577 228672.3028 1.092625921 1.190610662 1.050650746 0.997761933 1.051412034 1.064527279 0.949371973 0.903761213 1 17.80292211 3.448577366 0.367123778 0.907406035 1.197504247 0.562550275 0.052202836 1.704723976 0.692519286 0.161788026 0.294622074 2809.165756 -3.448577366 0.290098212 LEAAHTLEDCASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEAAHTLEDCASR 13 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 0 ;;; 214.81 3.02E-11 1501020000 823560 765840 482720 611150 750880 816860 761760 819310 811310 FALSE TRUE 714724.4594 760809.1466 716165.0066 749920.9483 735938.9571 848285.1328 687884.6324 644106.9324 715397.856 0.99905871 1.063476973 1.001072341 1.048257193 1.028712836 1.18575297 0.961541367 0.900347865 1 19.44838627 2.024625057 24.99957534 0.939422452 1.052825306 0.407038463 0.056912388 184.7179245 187526.476 0.022419955 0.01511485 105.8339625 -2.024625057 0.113402854 LEAAYLDLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEAAYLDLQR 10 0 E5RJD8;O75347;E5RIW3;E5RHG6;O75347-2 E5RJD8 TBCA Tubulin-specific chaperone A 0 ; 150.35 5.05E-05 283230000 240410 270880 176262 210820 252240 259510 229600 259470 352800 FALSE TRUE 208639.2094 269100.5714 261502.8928 258689.9032 247220.9175 269493.5176 207333.4273 203984.3597 311092.3859 0.670666396 0.865018186 0.840595606 0.83155331 0.794686494 0.866281304 0.666468987 0.655703479 1 18.24698356 2.252905713 24.99836994 0.744917522 0.815375329 0.001498499 0.108782523 596.7780371 1039969.487 0.039804085 0.03068524 179.0217147 -2.252905713 0.070457808 LEADYDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEADYDKK 8 1 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 88.948 0.022854 245890000 281940 226300 199770 216000 171860 174970 313340 323260 274740 FALSE TRUE 244680.9147 224813.4204 296379.4402 265046.1014 168440.3222 181701.2091 282952.335 254133.3646 242260.5502 1.009990749 0.927981961 1.223391262 1.094053907 0.695285807 0.750023927 1.167967029 1.049008452 1 17.88619997 LEAEIATYRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEAEIATYRR 10 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 112.3 0.0038934 0 61795 63495 33042 34862 69660 68884 65061 64258 24240 FALSE TRUE 53628.63418 63077.89716 49021.22172 42777.94993 68273.90229 71534.01205 58751.39423 50516.92676 21374.37481 2.509015335 2.951099048 2.29345757 2.001366136 3.194194117 3.346718333 2.748683634 2.363434121 1 14.3835946 1.223622481 2.559413998 0.540806192 2.723409061 0.647107263 0.397181495 0.36872995 2.588082358 1.801211662 0.11191511 16.73487534 -1.223622481 2.182602868 LEAFHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEAFHER 7 0 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 138.26 0.0028028 124860000 140380 123410 81570 98176 123060 132210 126270 134690 144200 FALSE TRUE 121828.4273 122599.3116 121017.5248 120468.3613 120611.3468 137296.2043 114024.3548 105887.5917 127152.8403 0.958125883 0.964188541 0.951748499 0.947429574 0.948554091 1.079773004 0.896750356 0.832758367 1 16.95620416 2.050108706 24.99986176 0.892528548 0.972412695 0.209515853 0.056313578 123.0961963 61413.64215 0.022438564 0.015128073 112.2299337 -2.050108706 0.079884147 LEAHSDWVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEAHSDWVR 9 0 P55735;P55735-4;P55735-3;P55735-2;A8MXL6 P55735 SEC13 Protein SEC13 homolog 0 ;;; 186.78 4.13E-05 3454250000 2796520 2938500 2207020 2889100 2844490 3008590 2368010 3087450 5576800 FALSE TRUE 2426952.797 2919196.8 3274342.254 3545114.312 2787890.214 3124332.404 2138360.755 2427222.844 4917517.057 0.493532156 0.593632267 0.66585275 0.720915509 0.566930461 0.635347548 0.43484562 0.493587072 1 22.22949863 1.231855701 24.99989087 1.00000072 0.574664297 0.706507399 0.085966439 144.3227219 538070.3047 0.220432771 0.023200819 17.05515618 -1.231855701 -0.425336423 LEALGTGWEELGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEALGTGWEELGR 13 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 72.652 0.062109 0 25863 19243 21585 12618 12882 11699 21240 31278 20526 FALSE TRUE 22445.13902 19116.59147 32023.5782 15483.10975 12625.6734 12149.0681 19180.14807 24589.44311 18099.43966 1.24010132 1.056197972 1.769313238 0.855446911 0.697572612 0.671240012 1.059709495 1.358574827 1 14.14365741 3.681681648 24.99998099 0.970101819 1.325308196 0.353991205 0.261064624 382.6305935 168177.0934 0.079846178 0.118431074 4804.870063 -3.681681648 0.355206377 LEALQKQMDS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEALQKQMDSR 11 1 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 1 LEALQKQMDS(1)R 63.624 0.036834 122310000 343000 235840 289340 291480 101070 111080 226860 274510 266930 TRUE FALSE 297671.6809 234290.7515 429265.7918 357664.989 99058.90474 115353.3195 204859.1521 215808.1727 235373.8395 1.264676149 0.995398435 1.823761692 1.519561349 0.420857751 0.490085558 0.870356504 0.916874081 1 17.84459446 3.250998935 24.99495167 0.759116345 1.402096767 0.595749707 0.270384709 175.7500007 353169.7762 0.084027451 0.107701078 1782.374398 -3.250998935 0.642980422 LEAMCFDGVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEAMCFDGVKR 11 1 P47813;X6RAC9 P47813 EIF1AX "Eukaryotic translation initiation factor 1A, X-chromosomal" 0 96.604 0.011045 636460000 698090 841660 332810 453170 756870 699880 980690 1224300 398730 FALSE TRUE 605835.6378 836131.08 493758.0292 556069.1748 741809.7678 726804.8365 885582.8347 962492.9725 351592.5936 1.723118316 2.378124839 1.404347071 1.581572493 2.10985607 2.067179029 2.518775568 2.737523457 1 18.42354515 3.079732877 5.68758108 2.210801329 1.789955645 0.059192284 0.516663871 0.442466205 23.92712503 0.158766283 0.180484484 1201.52518 -3.079732877 -0.420845684 LEAPLEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEAPLEELR 9 0 Q16401-2;Q16401;F2Z3J2 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ;;; 173.73 0.00012845 238525000 450842 399942 258841 283791 391162 409647 388657 434308 403105 FALSE TRUE 391262.0874 397314.7547 384017.3734 348230.084 383378.6415 425406.3852 350965.104 341434.614 355450.3861 1.100750211 1.117778374 1.080368424 0.979686892 1.078571459 1.196809461 0.987381411 0.960568978 1 18.43928868 2.038497284 24.96483443 0.976420065 1.087603856 0.483155858 0.053329656 131.2537558 85115.29466 0.022540455 0.015196745 109.2690795 -2.038497284 0.111183791 LEAQHQALVTLWHQLHVDMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEAQHQALVTLWHQLHVDMK 20 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 104.18 9.54E-05 21144000 45191 35130 27386 35075 36793 35643 45242 52055 42413 FALSE TRUE 39218.89485 34899.22872 40629.9612 43039.31484 36060.89128 37014.20927 40854.4378 40923.44334 37398.98346 1.048662055 0.933159821 1.086392127 1.150815099 0.964221162 0.989711641 1.092394339 1.094239457 1 15.19071144 4.222407079 24.99779744 1.057580697 0.990910899 0.146906115 0.062704556 387.5946886 599809.3024 0.016327406 0.034158256 16688.10713 -4.222407079 -0.066669799 LEAS(ph)YSDSPPGEEDLLVHVAEGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEASYSDSPPGEEDLLVHVAEGSK 24 0 Q7Z3C6;C9JS65;C9JFV2;F2Z3I6;C9JX27;C9IYZ9;C9JKV7;C9JDK4;C9JXG2;Q7Z3C6-3 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 LEAS(0.988)YS(0.011)DSPPGEEDLLVHVAEGSK 183.49 1.82E-17 32966000 53741 41097 27623 32622 37718 28461 46263 58344 58006 TRUE FALSE 46638.99069 40827.0311 40981.57519 40029.3237 36967.48559 29555.91309 41776.42138 45867.58963 51148.59676 0.91183324 0.798204324 0.801225797 0.782608443 0.722746819 0.577844065 0.816765738 0.896751671 1 15.64240704 1.599215851 2.48428137 0.988992769 0.764630411 0.456614349 0.083861293 0.253997214 3.3402973 0.100259442 0.024221634 39.73890089 -1.599215851 -0.224362359 LEASYSDS(ph)PPGEEDLLVHVAEGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEASYSDSPPGEEDLLVHVAEGSK 24 0 Q7Z3C6;C9JS65;C9JFV2;F2Z3I6;C9JX27;C9IYZ9;C9JKV7;C9JDK4;C9JXG2;Q7Z3C6-3 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 LEAS(0.13)Y(0.002)S(0.173)DS(0.695)PPGEEDLLVHVAEGSK;LEASYS(0.002)DS(0.998)PPGEEDLLVHVAEGSK;LEASYS(0.001)DS(0.999)PPGEEDLLVHVAEGSK;LEAS(0.012)Y(0.009)S(0.212)DS(0.767)PPGEEDLLVHVAEGSK 202.33 8.50E-25 537080000 478100 405869 283680 326966 393343 351421 491948 518198 499486 TRUE FALSE 414917.8736 403202.8198 420868.5969 401208.6277 385516.2439 364940.3933 444238.9587 407385.3903 440437.3341 0.942058816 0.915460132 0.955569758 0.910932377 0.875303282 0.828586419 1.008631477 0.924956535 1 18.74857724 2.214227795 24.9999792 0.968122572 0.906408939 0.404509233 0.041277469 276.3924249 283968.3824 0.017344707 0.011700245 163.7675284 -2.214227795 -0.061713632 LEAVSHTSDMHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 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 ;;;;;;;;;;; 243.4 1.40E-16 9493820000 6130475 8393122 1916902 4247417 10594120 10158600 7695013 8836470 8462810 FALSE TRUE 5320317.196 8337987.029 2843922.219 5211857.948 10383317.74 10549407.92 6948751.824 6946859.656 7462346.243 0.712955018 1.117341217 0.381102957 0.698420815 1.391428031 1.41368513 0.931175209 0.930921647 1 22.83119787 3.266763073 24.9876047 1.106969162 0.730564343 0.410274756 0.240691887 248.6798838 220330.7413 0.073966769 0.095471727 1848.260034 -3.266763073 -0.376404819 LECVEPNCR ddPTM_MDA-MB-175_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 ;;; 190.73 8.54E-05 1662890000 1416810 1470010 908210 897990 1320220 1469460 1322080 1480850 1354770 FALSE TRUE 1229574.969 1460353.408 1347423.394 1101892.354 1293950.205 1525991.077 1193864.885 1164181.751 1194610.634 1.029268394 1.222451371 1.127918466 0.922386193 1.083156443 1.277396194 0.999375739 0.974528201 1 20.18810904 2.036449594 24.98983835 0.985896442 1.109184028 0.253657867 0.09647183 226.6604718 155397.4949 0.040127923 0.027054163 108.7550906 -2.036449594 0.123287586 LEDAGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEDAGVR 7 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 107.66 0.039632 0 258570 260870 197090 225460 285000 333490 286320 291260 318460 FALSE TRUE 224399.3194 259156.3278 292403.3832 276654.1389 279329.0576 346319.5761 258552.7305 228976.3156 280812.0216 0.799108664 0.922881885 1.041278011 0.98519336 0.994719015 1.233279025 0.920732414 0.81540781 1 18.09924517 7.417391874 10.75509029 0.964857852 0.121180839 0 0.12199604 0 0 0.028909726 0 26145194.35 -7.417391874 -0.843677013 LEDEFDMFALTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEDEFDMFALTR 12 0 O60784;O60784-4;O60784-2;O60784-3 O60784 TOM1 Target of Myb protein 1 0 ; 180.36 4.55E-05 54103900 113945 102727 66770 74852 103073 96787 101608 122803 99997 FALSE TRUE 98886.87955 102052.1796 99060.19533 91848.29064 101022.049 100510.4585 91754.0718 96542.5341 88175.46858 1.121478356 1.157376096 1.123443934 1.041653559 1.145693361 1.139891402 1.040585021 1.094891081 1 16.42808972 -0.670636809 0.579045261 1.47E-12 1.122640309 0.469627872 0.038234338 29.23645702 1.247741763 35.09407753 0.020398303 0.213482948 0.670636809 1.122640309 LEDEHLVFFCQMGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEDEHLVFFCQMGK 14 0 Q8NFU3;Q8NFU3-4;R4GNF9;Q8NFU3-2;Q8NFU3-3 Q8NFU3 TSTD1 Thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1 0 ;;; 190.1 6.42E-07 7661360000 7485900 6724710 4485040 5526010 6149860 5814460 6745680 8997560 7809810 FALSE TRUE 6496619.348 6680534.937 6654020.346 6780775.03 6027489.818 6038146.039 6091484.992 7073501.813 6886543.159 0.943378877 0.970085395 0.966235191 0.984641332 0.875256232 0.87680363 0.884549018 1.027148404 1 22.71534854 1.685738701 8.153283624 1.012749359 0.929970409 0.435494702 0.04002238 0.121059256 14.57678048 0.025742146 0.011517716 48.49966078 -1.685738701 -0.08277895 LEDFFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LEDFFAR 7 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;; 197.62 0.00097263 4260917000 6468270 6589110 5284640 5973010 6577160 7424830 7008570 7689040 13554920 FALSE TRUE 5613471.731 6545825.703 7840309.58 7329273.212 6446287.384 7710468.015 6328879.96 6044798.632 11952472.8 0.469649404 0.547654516 0.655957115 0.613201413 0.539326673 0.64509396 0.529503816 0.505736238 1 23.51080579 1.233819285 24.9999866 1.000000658 0.564764462 0.841924098 0.059469375 57.78021425 304624.8133 0.119185293 0.015066174 17.13244257 -1.233819285 -0.435236197 LEDFLDNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEDFLDNER 9 0 Q16512;Q16512-2;Q16512-3 Q16512 PKN1 Serine/threonine-protein kinase N1 0 ; 116.52 0.0030249 57556000 175615 121200 112927 120548 138579 133327 130547 148246 208942 FALSE TRUE 152407.0328 120403.8292 167538.8749 147920.2659 135821.549 138456.176 117886.572 116544.7466 184241.1148 0.827215103 0.65351227 0.909345751 0.802862412 0.737194568 0.751494454 0.639849429 0.632566443 1 17.49123552 3.184817507 5.33927327 0.728041703 0.795850195 0.01417255 0.118141081 0.591261779 35.47434638 0.035785423 0.041506035 1530.444225 -3.184817507 0.067808491 NS(ph)GSSLVSSSSASSNLSHLEEDTWILWGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSGSSLVSSSSASSNLSHLEEDTWILWGR 29 0 Q96CN4;Q96CN4-2 Q96CN4 EVI5L EVI5-like protein 1 NS(0.976)GS(0.011)S(0.011)LVSSSSASSNLSHLEEDTWILWGR 101.25 0.00043245 46674000 4989.1 4257.8 3250.1 5389 3989.1 4850.9 4554.7 8269.4 11798 TRUE FALSE 4329.777794 4229.830231 4821.859231 6612.654816 3909.724715 5037.517262 4112.985895 6501.053163 10403.25388 0.416194572 0.406587235 0.463495295 0.635633321 0.375817486 0.484225159 0.395355717 0.624905749 1 13.34474722 1.283170561 2.435778611 1.106219566 0.458073572 0.846010494 0.073710917 0.180904086 1.251913717 0.238939066 0.019310679 19.19422408 -1.283170561 -0.648145994 LEDHEYKPLDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEDHEYKPLDPK 12 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 151.78 4.16E-05 156880000 585320 407860 395310 390730 374740 269040 568890 660710 573440 FALSE TRUE 507968.479 405180.7408 586483.2382 479451.2184 367283.4072 279390.1429 513719.1354 519422.3082 505648.5765 1.004587974 0.801308972 1.159863323 0.948190583 0.726361003 0.552538177 1.015960806 1.027239732 1 18.94777554 -0.825869663 18.92662673 9.099828055 0.916345953 0 0.176069393 0 0 0 0.041540766 0.149324248 0.825869663 -8.183482102 LEDIDRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEDIDRK 7 1 Q92783;Q92783-2 Q92783 STAM Signal transducing adapter molecule 1 0 87.323 0.031149 151960000 268790 245360 167640 215980 244330 264600 265100 308870 284720 FALSE TRUE 233268.7205 243748.214 248711.2647 265021.56 239468.311 274779.3332 239390.6428 242820.5541 251060.726 0.929132661 0.970873533 0.990641861 1.0556074 0.953826251 1.094473587 0.953516891 0.967178571 1 17.93767684 4.568914231 2.213586746 0.999938551 0.923629419 0.225908708 0.044037581 0.710478862 5.202142713 0.011315005 0.092149058 37060.75228 -4.568914231 -0.076309132 LEDLDT(ph)CMMTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEDLDTCMMTPK 12 0 Q5VZK9;Q5VZK9-2 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 LEDLDT(0.55)CMMT(0.45)PK 49.448 0.064939 64457000 118100 109550 87924 78839 108560 121180 103460 128810 122880 TRUE FALSE 102492.7858 108830.3588 130444.3405 96740.59993 106399.8684 125841.873 93426.46512 101264.9839 108353.2664 0.945913208 1.00440312 1.203880094 0.892825876 0.981971951 1.161403594 0.86223949 0.934581737 1 16.72538312 2.212144435 24.99885925 0.929836523 1.029739878 0.18693181 0.097679233 371.4970007 351562.0707 0.039196177 0.026434586 162.9837983 -2.212144435 0.099903355 LEDLDTCMMT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 277.24 7.70E-27 1705967000 1820400 1576210 1484950 1390930 1688070 1520900 1800000 2061180 2260840 TRUE FALSE 1579829.528 1565855.773 2203076.787 1706761.916 1654480.71 1579410.007 1625436.277 1620412.697 1993566.071 0.792464093 0.785454666 1.10509344 0.856135114 0.829910146 0.792253656 0.815341062 0.812821165 1 20.92691999 3.494589947 24.96637425 0.840197322 0.8996433 0.032266117 0.103303647 2272.052786 3247228.172 0.028737981 0.041590453 3123.129169 -3.494589947 0.059445978 LEDLLQDAQDEKEQLNEYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 130.27 3.68E-06 0 104700 75654 78713 67000 56844 55456 90457 103730 57941 FALSE TRUE 90863.62972 75157.02389 116778.8701 82213.37403 55712.91561 57589.4282 81684.49406 81548.14673 51091.28099 1.778456675 1.471034244 2.285690784 1.609146853 1.090458382 1.127187009 1.598795186 1.596126485 1 15.64078949 3.47358321 24.29815998 1.338772742 1.830951409 0.458966204 0.277713301 73.77380372 506648.7637 0.081853456 0.10624654 2975.659334 -3.47358321 0.492178667 LEDLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 ;;;;;; 196.32 0.00056999 1224300000 1724364 1485625 1210095 1626434 1538962 1516861 1375280 1784334 3237541 FALSE TRUE 1496484.928 1475865.832 1795300.99 1995740.698 1508339.667 1575215.624 1241905.557 1402768.06 2854802.591 0.524199093 0.516976493 0.62887045 0.699081857 0.528351653 0.551777426 0.43502327 0.4913713 1 21.44495956 1.234441885 24.99907711 1.000000664 0.545050121 0.794140226 0.072484465 60.55253999 367479.2937 0.147628842 0.019702486 17.15702109 -1.234441885 -0.454950542 LEDLVCDVVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LEDLVCDVVDR 11 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;; 207.34 5.42E-08 211569000 544400 378698 314649 399078 415887 382055 413130 473880 630930 FALSE TRUE 472456.1607 376210.3079 466814.3088 489694.7594 407611.6624 396752.9031 373064.7162 372544.4497 556342.1742 0.849218669 0.676221084 0.839077694 0.880204274 0.732663604 0.713145473 0.670567024 0.669631869 1 19.08561295 LEDNDSAAS(ph)DPDAETTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEDNDSAASDPDAETTAR 18 0 Q9BYV8-5;Q9BYV8-2;Q9BYV8;F8WF85;C9J6R3;C9J9X8;C9JCX6;C9JXA0 Q9BYV8-5 CEP41 Centrosomal protein of 41 kDa 1 LEDNDS(0.011)AAS(0.989)DPDAETTAR 184.78 5.92E-14 108370000 245390 195250 148000 157420 190610 196290 206310 222200 235350 TRUE FALSE 212961.0898 193967.3899 219573.295 193164.617 186817.2339 203841.4033 186302.088 174684.2592 207527.1911 1.026184032 0.934660123 1.058045906 0.930791845 0.900206055 0.982239495 0.897723749 0.841741548 1 17.66294085 3.559443081 7.767067364 0.914979955 0.998907647 0.324575408 0.053753691 0.337581577 28.55869826 0.014746303 0.02187404 3626.127586 -3.559443081 0.083927692 LEDS(ph)EVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEDSEVR 7 0 Q8N163-2;Q8N163;H0YB24;G3V119;A0A087X2B6 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 1 LEDS(1)EVR;LEDS(1)EVR 99.815 0.010753 345250000 1259980 1104910 907580 959790 927620 1062100 1034090 1244810 1906200 TRUE FALSE 1093470.451 1097651.773 1346488.724 1177724.989 909162.1769 1102959.674 933804.111 978617.0686 1680851.208 0.650545656 0.653033278 0.801075501 0.700671769 0.540893907 0.656191143 0.555554297 0.582215168 1 20.68076059 1.232938432 24.99989009 1.000000573 0.639970678 0.692302596 0.074879915 115.0028015 511322.8431 0.170107937 0.019875472 17.09772912 -1.232938432 -0.360029896 LEDSENHR ddPTM_MDA-MB-175_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 0 108.98 0.0037068 260550000 204930 182920 110220 140440 145490 227040 183150 242910 217740 FALSE TRUE 177847.9813 181718.3865 163522.7607 172329.0485 142595.0336 235774.3757 165388.1412 190965.5868 191999.0253 0.926296272 0.946454735 0.851685369 0.897551684 0.742686237 1.227997775 0.861400942 0.994617481 1 17.55073946 2.771137077 24.99996528 1.001918555 0.877206406 0.326561511 0.103965882 872.2349015 669372.7084 0.031833196 0.031831246 590.387396 -2.771137077 -0.124712149 LEDTAGDTGHSSLEAPRS(ph)PDTLAPVASER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEDTAGDTGHSSLEAPRSPDTLAPVASER 29 1 O43310;O43310-2 O43310 CTIF CBP80/20-dependent translation initiation factor 1 LEDTAGDTGHS(0.002)S(0.039)LEAPRS(0.959)PDTLAPVASER 126.67 1.22E-05 123750000 60596 70208 31576 58864 80730 77846 69933 78322 81513 TRUE FALSE 52588.08507 69746.79903 46846.25922 72229.97088 79123.63095 80840.78599 63150.90842 61573.4498 71876.626 0.731643762 0.970368295 0.651759297 1.004915991 1.100825614 1.124715926 0.878601458 0.856654704 1 16.13323507 3.706977662 24.92986006 0.982592586 0.803168195 0.422543163 0.114333936 730.6494418 576734.7448 0.033508204 0.049705777 5093.046738 -3.706977662 -0.179424391 LEDTENWLYEDGEDQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEDTENWLYEDGEDQPK 17 0 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;; 249.32 1.21E-20 255444000 340481 261222 232664 234471 261101 219145 338242 389229 342533 FALSE TRUE 295485.5732 259506.0155 345181.0886 287711.2242 255905.6009 227575.65 305439.3429 305995.4073 302039.139 0.978302263 0.859180093 1.142835627 0.952562722 0.847259735 0.753464106 1.011257495 1.013098529 1 18.20437598 2.091307857 20.74191452 1.009455085 0.923640323 0.139319532 0.100515928 10.739214 2428.445519 0.04306617 0.029035222 123.3979251 -2.091307857 -0.085814762 LEDTHFVQCPSVPSHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEDTHFVQCPSVPSHK 16 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3;Q9H1B7 Q7Z5L9;Q9H1B7 IRF2BP2;IRF2BPL Interferon regulatory factor 2-binding protein 2;Interferon regulatory factor 2-binding protein-like 0 ; 180.64 1.41E-09 934240000 1229030 1206760 636010 891280 1138400 1024930 1283810 1573350 1590930 FALSE TRUE 1066610.572 1198832.714 943586.5633 1093658.746 1115748.067 1064359.72 1159306.304 1236901.346 1402852.068 0.760315785 0.854568163 0.672620146 0.779596631 0.79534264 0.758711303 0.826392412 0.88170476 1 20.41993145 1.136848744 1.028381466 1.163658351 0.76887718 0.733852204 0.044986823 1.118094085 0.840065521 0.518793959 0.014583412 13.70404398 -1.136848744 -0.394781171 LEDTYFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LEDTYFDR 8 0 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 ;; 160.78 0.00081746 807290000 887100 818760 762990 935290 847420 950890 828490 959830 2008210 FALSE TRUE 769867.4874 813381.5116 1131974.516 1147661.89 830557.9999 987471.3536 748143.1673 754577.8239 1770801.702 0.434756465 0.459329529 0.639244086 0.648102997 0.469029366 0.557640843 0.422488394 0.426122148 1 20.75597123 1.232828694 24.99952842 1.000000791 0.506762618 0.775330104 0.083387123 96.08934203 419045.3945 0.191981569 0.02216543 17.0934094 -1.232828694 -0.493238173 LEDVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEDVLR 6 0 A0A0B4J1W3;Q9BXJ9 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ; 113.08 0.061517 192153000 417460 383830 257400 310310 395690 375630 378630 406230 442540 FALSE TRUE 362291.6033 381308.5955 381879.501 380770.6283 387816.5432 390080.7292 341910.5209 319360.8758 390223.4253 0.92842095 0.97715455 0.978617572 0.975775936 0.993832041 0.999634322 0.876191686 0.818405188 1 18.57394086 2.231722864 24.8617216 0.88065826 0.976622102 0.34153363 0.048639179 129.5176033 470913.9638 0.019167821 0.013251637 170.4994035 -2.231722864 0.095963843 LEEAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 122.79 0.04436 2700470000 4424530 3859170 3005770 3422320 2528620 2911470 4571460 5337320 4862940 FALSE TRUE 3839817.15 3833818.858 4459370.426 4199410.063 2478305.409 3023476.135 4128120.513 4195975.653 4288048.773 0.89546956 0.894070721 1.039953289 0.979328894 0.577956441 0.705093691 0.962703722 0.978527968 1 22.03188988 2.03008737 24.84812281 0.982596076 0.851446806 0.18724034 0.130033749 349.8711077 288945.001 0.058842273 0.039670979 107.1734891 -2.03008737 -0.131149271 LEEAEKAADESER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEEAEKAADESER 13 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;H0YL80;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5;H0YKP3;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;H7BYY1;P09493-3;P67936;P67936-2 TPM3;TPM1;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain 0 ; 133.66 9.54E-05 1143470000 1502600 1245650 306520 332370 1014200 853320 1724930 1633030 59013 FALSE TRUE 1304027.603 1237467.243 454754.0972 407839.6885 994019.4042 886147.7726 1557646.554 1283819.243 52036.55037 25.05983955 23.7807317 8.73912844 7.837561975 19.1023309 17.02933354 29.93370128 24.67149021 1 15.6672377 7.998241724 0.012325884 8.41247454 29.46678295 0.00142748 9.108602888 758208.5852 931.4693683 690156.8796 916458.1212 99595960.5 -7.998241724 21.05430841 LEEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEEALR 6 0 A0A1B0GUG6;A0A1B0GTG4;Q86WH2;Q8WWW0-2;Q8WWW0;Q155Q3-2;Q155Q3 A0A1B0GUG6 RASSF3;RASSF5;DIXDC1 Ras association domain-containing protein 3;Ras association domain-containing protein 5;Dixin 0 113.25 0.061181 121260000 257930 221650 146760 167850 163410 187020 169660 193740 380240 FALSE TRUE 223843.897 220193.9666 217733.6269 205962.9079 160158.4607 194214.7804 153206.3993 152310.2087 335288.4604 0.667615869 0.656729928 0.649391949 0.614285704 0.477673644 0.579246838 0.456939076 0.454266182 1 18.35504331 1.229741531 24.99971748 1.000000832 0.562893234 0.731116757 0.081956201 205.697105 583051.0379 0.267691739 0.022872764 16.9723325 -1.229741531 -0.437107599 LEECVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEECVR 6 0 P24534 P24534 EEF1B2 Elongation factor 1-beta 0 ;;; 187.21 0.0042292 2637720000 2760240 2696400 1995000 1986810 2331570 2533160 2569490 2793790 2872260 FALSE TRUE 2395467.29 2678687.171 2959788.673 2437945.577 2285176.319 2630612.304 2320301.255 2196359.75 2532704.695 0.945813894 1.057638964 1.168627625 0.962585801 0.902267178 1.038657333 0.916135726 0.867199304 1 21.27224744 3.501468116 23.76158046 0.937204116 1.058757861 0.344370416 0.071204069 420.9469221 410826.1886 0.019798084 0.029165038 3172.985708 -3.501468116 0.121553745 LEEEDEDEEDGESGCTFLVGLIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEEEDEDEEDGESGCTFLVGLIQK 24 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 185.87 2.26E-17 23905000 41186 37667 25152 29924 31754 26409 35815 46558 37050 FALSE TRUE 35743.16575 37419.563 37315.59133 36718.70156 31122.15753 27424.97132 32341.66681 36601.93401 32669.99121 1.094067198 1.145380259 1.142197777 1.123927501 0.952622158 0.839454506 0.989950276 1.120353348 1 14.99567845 3.250424022 24.29728297 0.991620213 1.128878372 0.520423111 0.069126721 160.4274994 328566.5833 0.023443771 0.030001511 1780.016474 -3.250424022 0.137258159 LEEEEQDILQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEEEEQDILQR 11 0 H0Y735;A2AAZ6;A0A140TA46;A0A0G2JKY0;A0A096LP39;Q9HCM9-2;Q9HCM9 H0Y735 TRIM39;TRIM39-RPP21 E3 ubiquitin-protein ligase TRIM39 0 ; 91.853 0.024268 95016000 8798.1 9340.6 6914 7275.2 8662.1 11081.6 7159 11927.7 9868.9 FALSE TRUE 7635.408793 9279.240984 10257.63353 8927.145354 8489.741157 11507.91632 6464.721282 9377.054176 8702.209885 0.877410324 1.066308571 1.178738925 1.025848086 0.975584509 1.322413097 0.742882712 1.077548611 1 13.0871661 2.228071346 24.99999764 0.960550705 1.072063237 0.15741978 0.143776777 451.4515978 1075974.881 0.055682722 0.037992484 169.0718661 -2.228071346 0.111512532 LEEENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEEENR 6 0 Q2M1P5;J3KP89;Q5TCS8-3;Q5TCS8-6;Q5TCS8;P51572;P51572-2;C9JSP1;C9JQ75;C9J0M4 Q2M1P5;P51572 KIF7;AK9;BCAP31 Kinesin-like protein KIF7;Adenylate kinase 9;B-cell receptor-associated protein 31 0 153.26 0.027626 0 313370 288540 255880 334510 307650 433420 227810 447020 501470 FALSE TRUE 271957.3605 286644.5617 379624.4239 410465.6082 301528.3669 450093.9479 205717.0213 351428.2517 442186.7879 0.615028237 0.648243162 0.858515981 0.928262941 0.681902705 1.017881945 0.465226522 0.794750683 1 18.75429639 4.310577752 6.427326997 0.805256435 0.626318813 0.18906113 0.160704184 0.363268461 25.07320595 0.038998698 0.10471411 20444.55923 -4.310577752 -0.178937623 LEEEPSASS(ph)PQYACDFNLFLEDSADNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEEEPSASSPQYACDFNLFLEDSADNR 27 0 Q2NKX8;B5MDQ0 Q2NKX8 ERCC6L DNA excision repair protein ERCC-6-like 1 LEEEPSAS(0.037)S(0.925)PQY(0.037)ACDFNLFLEDSADNR;LEEEPSAS(0.043)S(0.952)PQY(0.005)ACDFNLFLEDSADNR 203.47 2.45E-25 82052000 71291 95419 73504 87593 119581 110907 107624 143636 124664 TRUE FALSE 61869.71372 94792.18631 109050.7803 107482.3294 117201.5721 115173.6641 97186.64105 112920.5592 109926.3639 0.562828711 0.862324404 0.992034816 0.977766621 1.066182559 1.047734683 0.884106756 1.02723819 1 16.74617791 4.751251852 1.821465637 1.001010279 0.408655456 0.88920978 0.048882893 0.271153691 0.894746676 0.013053965 0.278714383 56396.46106 -4.751251852 -0.592354823 LEEHQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEEHQAR 7 0 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 155.51 0.0016062 183220000 302800 257160 171590 180330 196210 260500 246060 289860 278250 FALSE TRUE 262784.2128 255470.699 254571.4979 221276.6827 192305.8049 270521.6036 222197.1391 227875.6947 245355.602 1.071034086 1.041226273 1.037561384 0.901861139 0.78378404 1.102569501 0.905612659 0.928756845 1 17.90451469 3.811983703 5.971784606 0.934898471 1.050973589 0.306285607 0.080122848 0.283901788 17.98910937 0.020951299 0.036682088 6486.100943 -3.811983703 0.116075118 LEELHVIDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEELHVIDVK 10 0 Q16531;F5GY55;F5H2L3;F5GWI0 Q16531 DDB1 DNA damage-binding protein 1 0 ;;; 159.83 7.56E-06 1172690000 4117720 3168280 2353020 2874240 3005440 2432680 3784110 4498450 4101190 FALSE TRUE 3573552.869 3147467.36 3490948.342 3526880.122 2945637.624 2526266.774 3417127.595 3536491.474 3616351.99 0.988165112 0.870343199 0.965323163 0.975259082 0.814532886 0.698567723 0.94491012 0.97791683 1 21.78610368 2.009909137 24.99674465 0.979590823 0.883562913 0.204889581 0.085386057 337.6609557 851778.2331 0.037260259 0.025089412 102.3078922 -2.009909137 -0.096027909 LEELKDGAEWSRDS(ph)MEINEADFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEELKDGAEWSRDSMEINEADFR 23 2 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 LEELKDGAEWS(0.093)RDS(0.907)MEINEADFR 47.919 0.079043 118810000 55850 40701 42849 42950 43644 46442 55786 65386 64979 TRUE FALSE 48469.28099 40433.63245 63570.91972 52702.45395 42775.56979 48228.65379 50375.88231 51403.71273 57297.25664 0.845926731 0.705681822 1.109493254 0.919807632 0.746555285 0.841727102 0.879202343 0.897140906 1 15.80617844 1.143818789 1.854290907 1.073408363 0.86396683 0.137262467 0.107115949 2.520036711 6.670635896 1.013351933 0.029801798 13.92575624 -1.143818789 -0.209441533 LEELTNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEELTNR 7 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ;;; 192.56 0.0011853 1596120000 2315500 2266490 1890920 1845630 2093470 1996180 3066680 2786890 2062680 FALSE TRUE 2009500.808 2251601.278 2805375.237 2264708.5 2051814.043 2072974.336 2769273.846 2190935.261 1818832.32 1.104830163 1.237937798 1.542404545 1.245144192 1.128094118 1.139728117 1.522555881 1.204583422 1 20.79458112 1.297116507 4.413758411 0.990455488 1.277547113 0.242521146 0.150993076 0.274112997 8.909702189 0.208960501 0.038300341 19.82058676 -1.297116507 0.287091625 LEEPPELNRQS(ph)PNPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 LEEPPELNRQSPNPR 15 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR 226.65 5.07E-13 50441750000 15426150 15363020 9130700 9941880 14018170 13477960 13779460 15698330 11377330 TRUE FALSE 13387545.19 15262099.31 13546337.06 12199335.81 13739235.84 13996465.84 12443130.09 12341364.29 10032315.01 1.334442268 1.521293869 1.350270306 1.216004062 1.36949805 1.395138194 1.240304962 1.230161163 1 23.25815122 0.393527743 0.752315859 5.67E-16 1.37116611 0.6802985 0.078133152 5.319281834 0.907696724 8.297073621 0.03265964 2.474729544 -0.393527743 1.37116611 LEEPTPAPSTSYS(ph)PQADSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEEPTPAPSTSYSPQADSLR 20 0 G3V1L9;Q07157 G3V1L9 TJP1 Tight junction protein ZO-1 1 LEEPTPAPSTS(0.001)YS(0.999)PQADSLR;LEEPTPAPST(0.004)S(0.007)YS(0.988)PQADSLR;LEEPTPAPSTSYS(1)PQADSLR;LEEPTPAPSTSYS(1)PQADSLR 338.82 3.69E-80 1857700000 1086070 1080420 719580 908270 1010720 1098300 1108770 1245950 1169240 TRUE FALSE 942543.0977 1073322.65 1067571.295 1114506.586 990608.6494 1140552.312 1001241.656 979513.2885 1031013.779 0.914190593 1.041036184 1.035457834 1.080981271 0.960810291 1.106243519 0.971123448 0.950048688 1 19.97563218 2.050710424 24.99981589 0.968194307 1.025492201 0.14603057 0.055631131 159.654781 78707.63368 0.02135069 0.014394629 112.3855368 -2.050710424 0.057297895 LEEQLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LEEQLGR 7 0 Q9BR76;A9Z1Z3-3;A9Z1Z3 Q9BR76 CORO1B;FER1L4 Coronin-1B;Fer-1-like protein 4 0 ;;;;; 224.44 4.48E-05 2153150000 2696310 2552090 1628560 1795920 2332660 2314450 2444290 2710210 2399890 FALSE TRUE 2339985.802 2535325.153 2416137.063 2203711.085 2286244.63 2403488.389 2207243.132 2130652.682 2116177.738 1.105760523 1.198068152 1.141745809 1.041363892 1.080365126 1.135768677 1.043032961 1.006840136 1 21.01302937 -2 0.182266064 0.269835016 1.195509914 0.582877173 0.04085715 79.55831179 1.129666768 19.82458827 0.367226205 0.01 2 0.925674898 LEEQRPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LEEQRPER 8 1 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;E9PJF7;P13693-2;Q9HAU6 Q5W0H4 TPT1;TPT1P8 Translationally-controlled tumor protein;Putative translationally-controlled tumor protein-like protein TPT1P8 0 ;;;;; 177.91 0.00023016 15616980000 8320150 8170880 5547330 6565410 6986490 7752110 7937580 8587960 9649970 FALSE TRUE 7220621.097 8117204.951 8230037.343 8056186.687 6847472.518 8050338.688 7167794.713 6751491.586 8509161.54 0.848570222 0.953937108 0.967197215 0.946766218 0.804717655 0.946078959 0.842362045 0.793437938 1 23.02058555 3.272745538 24.99189207 0.867650265 0.933610514 0.112478097 0.068896996 321.5302054 235061.9399 0.019451609 0.025110661 1873.896233 -3.272745538 0.065960248 LEESHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEESHNR 7 0 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ; 156.4 0.001546 153309000 198375 179152 120173 141419 134492 186817 174405 198896 195009 FALSE TRUE 172159.2411 177975.1387 178289.0648 173530.3454 131815.8723 194003.9709 157491.2299 156363.6382 171955.2582 1.001186256 1.035008412 1.036834038 1.009159867 0.766570756 1.128223545 0.915884932 0.90932746 1 17.39167371 3.451886873 24.99996109 0.941414574 1.025007548 0.155636509 0.089062329 381.8768772 378328.1776 0.024333426 0.03141568 2830.654561 -3.451886873 0.083592974 LEESVALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEESVALR 8 0 Q08209-3;Q08209-2;Q08209;Q08209-4;E9PPC8;E9PK68 Q08209-3 PPP3CA Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 0 ; 72.485 0.046033 959440000 2679400 3105500 1675920 1892260 2674300 3912100 2119890 2455300 2456800 FALSE TRUE 2325310.501 3085099.766 2486400.518 2321926.554 2621086.662 4062601.018 1914303.394 1930253.202 2166359.903 1.073372203 1.424093828 1.147731969 1.07181016 1.209903608 1.875312137 0.883649753 0.891012246 1 21.04684151 LEETDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEETDRR 7 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RQT0;C9J165;A0A0U1RR66;A0A0U1RQL2;A0A0U1RQJ6;A0A0U1RRJ7 P47897 QARS Glutamine--tRNA ligase 0 ; 169.97 0.0015907 3154400000 3275500 3312300 2229900 2247100 2711000 3269400 3194300 3430400 3516100 FALSE TRUE 2842634.376 3290541.283 3308287.099 2757338.4 2657056.404 3395175.934 2884517.278 2696835.655 3100430.664 0.916851459 1.061317488 1.067041149 0.889340449 0.856995912 1.095065912 0.930360195 0.869826146 1 21.5640372 3.737985152 24.99998237 0.935288889 1.019694777 0.161938873 0.079454962 86.93177106 3776639.583 0.021668521 0.034466452 5469.972615 -3.737985152 0.084405888 LEEVMQELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 LEEVMQELR 9 0 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;;;;; 171.46 0.00013244 687469000 620176 590843 475342 565857 553806 571711 567429 657846 1179824 FALSE TRUE 538218.1703 586961.7134 705218.9811 694343.4804 542786.3441 593705.0921 512399.8229 517170.7523 1040346.551 0.517345081 0.56419826 0.677869293 0.667415564 0.521736092 0.570680118 0.492528016 0.49711392 1 19.98863276 1.233290759 24.99997483 1.000000682 0.562906904 0.819618464 0.064337105 76.71060486 363870.7902 0.145453133 0.017533021 17.11160549 -1.233290759 -0.437093779 LEEWLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEEWLGR 7 0 P56192;P56192-2 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ; 91.041 0.038841 311710000 226890 192782 116737 136376 184804 188636 169945 180591 186764 FALSE TRUE 196905.9116 191515.6023 173191.4037 167342.2552 181126.762 195892.949 153463.7601 141973.02 164684.9727 1.195651968 1.162920935 1.051652745 1.016135549 1.099837824 1.189501056 0.931862559 0.862088494 1 17.32934939 2.178361798 8.069937866 0.915616995 1.112465359 0.642831636 0.065598312 0.158925808 18.78000605 0.02818486 0.019017416 150.7862701 -2.178361798 0.196848364 LEFLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEFLHK 6 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ; 111.69 0.027635 1662030000 3215900 2592400 1812410 2439000 2712800 2285100 2779700 3439500 3661700 FALSE TRUE 2790910.667 2575370.354 2688897.538 2992812.228 2658820.588 2373009.276 2510125.122 2703989.691 3228817.997 0.864375344 0.797620168 0.83278077 0.92690645 0.823465612 0.734946744 0.777413011 0.837454974 1 21.62257469 1.24380935 4.913534448 1.011185115 0.821544546 0.544336375 0.050660842 0.141817779 8.406763153 0.091598594 0.013496349 17.53110738 -1.24380935 -0.18964057 LEFQQQLGEAPSDAS(ph)P ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LEFQQQLGEAPSDASP 16 0 Q9BUW7 Q9BUW7 C9orf16 UPF0184 protein C9orf16 1 LEFQQQLGEAPSDAS(1)P;LEFQQQLGEAPS(0.001)DAS(0.999)P;LEFQQQLGEAPS(0.16)DAS(0.84)P 224.67 7.95E-15 210625000 567002 630745 401877 522890 658830 606040 619960 783120 673990 TRUE FALSE 492071.2491 626601.5946 596226.0614 641620.1664 645720.572 629354.751 559836.3746 615655.8822 594311.67 0.827968344 1.054331635 1.003221191 1.079602166 1.086501586 1.058964147 0.941991219 1.035914173 1 19.18086018 4.742470754 24.84611768 1.031644993 0.827968258 0.693583018 0.042733674 215.874868 1371670.987 0.010739441 0.079054139 55267.61882 -4.742470754 -0.203676735 LEGDSDDLLEDS(ph)DSEEHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEGDSDDLLEDSDSEEHSR 19 0 Q9NR09;A0A3B3IUB9 Q9NR09 BIRC6 Baculoviral IAP repeat-containing protein 6 1 LEGDSDDLLEDS(1)DSEEHSR;LEGDSDDLLEDS(0.967)DS(0.033)EEHSR;LEGDSDDLLEDS(1)DSEEHSR;LEGDSDDLLEDS(1)DSEEHSR 299.25 5.01E-50 4229610000 3179900 3044080 2079800 2228590 3193070 2879890 2966490 3711440 3529090 TRUE FALSE 2759668.158 3024083.238 3085598.237 2734625.421 3129534.154 2990681.232 2678800.256 2917777.438 3111885.001 0.886815598 0.971785023 0.991552784 0.878768149 1.005671531 0.961051334 0.860828808 0.9376238 1 21.56935732 LEGFHTQISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEGFHTQISK 10 0 Q06323;Q06323-3;Q06323-2;H0YKK6;H0YLU2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;;; 180.97 1.94E-06 7441580000 14513350 12559140 8308770 10077180 11932940 10542550 14109970 15569100 15219900 FALSE TRUE 12595374.03 12476638.18 12326918.96 12365357.74 11695497.84 10948128.72 12741587.28 12239769.12 13420620.76 0.938509049 0.92966178 0.918505871 0.921370029 0.871457293 0.815769175 0.94940372 0.912012145 1 23.67794807 0.842438713 1.599228794 1.171967483 0.903546625 0.364223884 0.038450324 3.855267359 3.734590966 2.2551667 0.011272434 6.957267681 -0.842438713 -0.268420858 LEGGRQDS(ph)EDEEER ddPTM_MDA-MB-175_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 212.34 1.56E-09 680980000 1006490 985170 574230 587720 912140 949280 791280 1054480 511270 TRUE FALSE 873479.7964 978698.3534 851929.5487 721170.8087 893990.1986 985799.4159 714541.7874 828987.658 450828.243 1.937500167 2.17088962 1.889698709 1.599657563 1.982995104 2.186640769 1.584953468 1.838810391 1 18.78221837 0.962825427 1.625050691 3.20E-13 1.925815914 0.665417262 0.199944428 1.406519904 1.867891149 5.414082067 0.055887213 9.1796353 -0.962825427 1.925815914 LEGLTQDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEGLTQDLR 9 0 Q01094 Q01094 E2F1 Transcription factor E2F1 0 86.953 0.032079 54515000 134560 127090 88174 97129 130590 135750 126760 137060 130050 FALSE TRUE 116777.5551 126255.1374 130815.2413 119183.624 127991.5145 140972.3903 114466.8347 107750.7856 114675.6372 1.018329246 1.100976115 1.140741352 1.039310763 1.116117753 1.22931421 0.998179191 0.939613577 1 16.8071994 2.021622785 24.7254106 0.966514321 1.106625365 0.522465038 0.05822454 143.8821049 164526.7894 0.02348923 0.01583499 105.1048568 -2.021622785 0.140111044 LEGVDGGQS(ph)PR ddPTM_MDA-MB-175_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 153 3.43E-05 1801800000 1805680 1851230 1165274 1362390 1803780 1708372 1611450 2244620 1810537 TRUE FALSE 1567054.813 1839069.148 1728804.404 1671741.472 1767888.307 1774094.176 1455171.827 1764625.481 1596497.378 0.981558025 1.151939974 1.082873312 1.047130734 1.107354344 1.111241522 0.911477743 1.105310603 1 20.60647875 LEGVEGVAHIIDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEGVEGVAHIIDPK 14 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 92.457 0.0049511 496800000 1708620 1456040 1181870 1184800 1328890 1199080 1915740 2055700 1813260 FALSE TRUE 1482821.538 1446475.177 1753426.285 1453826.949 1302447.689 1245209.384 1729951.83 1616104.552 1598898.468 0.927401938 0.904669812 1.096646422 0.909267835 0.814590616 0.77879203 1.08196478 1.010761211 1 20.6086469 2.211226711 24.99994406 1.028838617 0.909967195 0.324462021 0.085287873 292.7599526 267759.901 0.037481165 0.025276561 162.6397548 -2.211226711 -0.118871422 LEGVLAEVAQHYQDTLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEGVLAEVAQHYQDTLIR 18 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;; 273.33 5.25E-39 2988100000 1435610 1593370 736660 872456.7 1119524 1144045 1068128 1496554 2007859 FALSE TRUE 1245890.501 1582903.048 1092911.24 1070561.328 1097247.663 1188057.151 964541.111 1176527.573 1770492.196 0.703697256 0.894046893 0.617292323 0.604668764 0.619741598 0.671032131 0.544786988 0.664520056 1 20.75571905 1.238997566 10.84222802 1.00086489 0.661820238 0.565864534 0.092187896 0.050583273 194.8641991 0.131060921 0.023633073 17.33794282 -1.238997566 -0.339044652 LEHALEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEHALEK 7 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ;;; 123.69 0.0042192 1717510000 5236900 4928700 3533840 3692510 4528400 4329600 5630800 6169800 6039200 FALSE TRUE 4544830.396 4896323.045 5242816.844 4530950.832 4438293.7 4496162.514 5084725.883 4850436.283 5325252.656 0.853448783 0.91945366 0.984519831 0.850842415 0.83344284 0.844309708 0.954832796 0.910836837 1 22.34441854 0.868076605 1.130752469 1.148164471 0.888289278 0.334092362 0.049010255 4.632158087 2.729693914 1.768395173 0.016306521 7.380344001 -0.868076605 -0.259875193 LEHDVNIQFPDKDDGNQPQDQITITGYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEHDVNIQFPDKDDGNQPQDQITITGYEK 29 1 Q00341;A0A024R4E5;Q00341-2 Q00341 HDLBP Vigilin 0 ; 220.38 1.21E-34 1136190000 879370 649620 558340 605450 604190 454641 870710 1066250 863410 FALSE TRUE 763159.0265 645352.6034 828355.0915 742926.6762 592167.8011 472131.3335 786268.6782 838240.7351 761338.6534 1.002391016 0.847655115 1.088024479 0.975816311 0.777798156 0.620133145 1.032744988 1.101009034 1 19.5381788 2.028881485 24.99887904 1.060467085 0.886567766 0.25078191 0.129785071 276.6202558 239432.4921 0.056113581 0.037831119 106.8763184 -2.028881485 -0.173899319 LEHEVDLCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEHEVDLCR 9 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;A0A087X1S3 Q7Z6Z7-2;A0A087X1S3 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ; 101.65 0.003842 353950000 136284 127750 110276 101648 124990 123641 127858 127705 157574 FALSE TRUE 118273.7241 126910.8018 163605.8425 124728.732 122502.9435 128397.5493 115458.3508 100396.2796 138945.7812 0.851222132 0.913383629 1.177479741 0.897679159 0.881660044 0.924083827 0.830959744 0.722557235 1 17.08416251 2.860199319 1.37614753 0.83129191 0.970674362 0.121844528 0.110719763 0.667609832 2.627469981 0.051835237 0.049122072 724.7685159 -2.860199319 0.139382453 LEHEVFDAGEVFGIMQVEEVEEEEDEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 LEHEVFDAGEVFGIMQVEEVEEEEDEAAR 29 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ;;;;;; 259.2 4.61E-58 898815000 382163 371005 271966 289739 311498 341966 361476 389390 423760 FALSE TRUE 331659.1913 368567.8437 403489.6673 355528.6683 305299.7992 355121.6533 326420.1132 306121.9787 373663.5755 0.887587694 0.986362782 1.07982071 0.951467287 0.81704458 0.950378031 0.873566851 0.8192449 1 18.51138041 3.466994305 23.82576921 0.884457034 0.989913695 0.264274978 0.070850314 134.2666482 315887.9584 0.01999342 0.025847042 2930.854815 -3.466994305 0.105456661 LEHEYIHNFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEHEYIHNFK 10 0 Q15555-4;Q15555-5;Q15555-3;Q15555;K7EL66;K7ERD8;Q15555-2;M0QX52;K7ENB3;C9JB30;Q9UPY8;Q9UPY8-2 Q15555-4;C9JB30;Q9UPY8-2 MAPRE2;MAPRE3 Microtubule-associated protein RP/EB family member 2;Microtubule-associated protein RP/EB family member 3 0 177.78 1.32E-06 312360000 210620 181500 138290 171380 183390 155720 213720 233810 248930 FALSE TRUE 182786.0334 180307.7145 205167.5066 210294.4484 179740.8978 161710.6492 192993.4673 183811.551 219501.779 0.832731444 0.821440789 0.934696327 0.958053504 0.818858501 0.736716804 0.879234183 0.837403468 1 17.74387311 1.234807298 24.98386969 1.000000211 0.853191478 0.357891751 0.062127463 134.7699364 896956.8758 0.116265621 0.01599856 17.17146299 -1.234807298 -0.146808733 LEHEYIQNFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEHEYIQNFK 10 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ;;; 185.29 1.47E-06 6718800000 12570820 11608030 7450010 9337520 10761520 9308740 11969800 14239670 13124640 FALSE TRUE 10909554.29 11531776.09 11052859.75 11457746.63 10547386.81 9666853.251 10808970.64 11194627.38 11573060.01 0.942668082 0.996432756 0.95505076 0.990036051 0.91137407 0.835289305 0.933976894 0.967300556 1 23.46426704 5.12795812 14.07096841 0.947601221 0.631545147 0.001060023 0.048860823 8797519.8 7571296.865 0.012782208 87989300.32 134263.548 -5.12795812 -0.316056074 LEHGQATAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEHGQATAK 9 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 157.34 6.88E-05 219947000 582300 513500 373690 474550 474500 515860 576920 635140 650050 FALSE TRUE 505347.5796 510126.7847 554407.7339 582303.8305 465058.3783 535705.468 520970.3872 499320.2537 573201.8295 0.881622412 0.889960147 0.96721208 1.015879225 0.811334428 0.934584365 0.908877747 0.871107223 1 19.12868369 1.237803697 0.004675237 1.167557438 0.670356995 0.004631274 0.061977833 1370840.441 1849.949609 100182.628 96579.44795 17.29034651 -1.237803697 -0.497200444 LEHQGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEHQGIR 7 0 O75436;S4R3Q6;O75436-2 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ;;; 137.18 0.002908 643409000 735130 635420 451788 545050 628630 673380 620090 717960 923380 FALSE TRUE 637980.7079 631245.8842 670274.1879 668811.9331 616121.4929 699285.3643 559953.7672 564429.8412 814219.0683 0.78354921 0.775277697 0.823211116 0.821415217 0.756702363 0.858841793 0.687718808 0.693216191 1 19.63505748 LEHSSFPEGPGPGS(ph)GDEANGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEHSSFPEGPGPGSGDEANGPR 22 0 O15020;O15020-2;A4QPE4 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 1 LEHSSFPEGPGPGS(1)GDEANGPR;LEHSSFPEGPGPGS(1)GDEANGPR;LEHSSFPEGPGPGS(1)GDEANGPR;LEHSSFPEGPGPGS(1)GDEANGPR 183.58 2.71E-17 1130820000 348844 448480 141626 330760 584820 619870 425060 561550 513000 TRUE FALSE 302743.3815 445533.9054 210116.8073 405864.1134 573183.2262 643716.8 383837.7466 441466.9025 452353.7244 0.669262493 0.984923703 0.464496689 0.897227306 1.26711287 1.423038576 0.848534512 0.975932945 1 18.78709182 3.475678689 24.48441 1.083812305 0.725224689 0.449557726 0.200345838 36.92311323 626674.9978 0.05976773 0.077798669 2990.051642 -3.475678689 -0.358587616 LEHSSSVQEDSES(ph)PSPEDIPDYLLQYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEHSSSVQEDSESPSPEDIPDYLLQYR 27 0 Q9HB65-2;Q9HB65 Q9HB65-2 ELL3 RNA polymerase II elongation factor ELL3 1 LEHS(0.002)S(0.002)S(0.002)VQEDS(0.414)ES(0.527)PS(0.052)PEDIPDYLLQYR;LEHSSSVQEDS(0.023)ES(0.947)PS(0.03)PEDIPDYLLQYR 145.64 1.01E-07 193005000 33473 38815 11830.6 25801.4 48583 56928 39289 44084 47858 TRUE FALSE 29049.45824 38560.02171 17551.91773 31660.00222 47616.29335 59118.057 35478.75883 34656.97966 42200.28176 0.688371192 0.913738489 0.415919444 0.75023201 1.12834065 1.400892471 0.840723269 0.821249959 1 15.36496501 3.357182926 5.936483626 1.013233161 0.6795497 0.428520728 0.198781812 0.236652477 11.37257588 0.062368044 0.080716951 2276.055908 -3.357182926 -0.333683461 LEIEPEWAYGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEIEPEWAYGK 11 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ; 199.67 1.15E-07 172939000 512730 405720 313650 408290 416770 351490 453300 540440 875350 FALSE TRUE 444971.4314 403054.7986 465332.1891 500998.4848 408477.0924 365012.0477 409339.0358 424871.1117 771867.1202 0.576487092 0.522181588 0.602865671 0.649073489 0.529206494 0.47289493 0.530323193 0.550445926 1 19.55799298 1.238357645 24.99999989 1.000000494 0.553056564 0.895019943 0.047982391 1.547316397 190112.6447 0.070611261 0.012539079 17.31241463 -1.238357645 -0.44694393 LEIFHPFFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEIFHPFFK 9 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 0 114.84 0.0015728 77675000 303300 275420 191350 235950 278660 265690 303370 360440 319450 FALSE TRUE 263218.1365 273610.7479 283887.5 289526.0538 273115.2112 275911.2662 273949.2241 283362.7109 281684.9849 0.934441488 0.971335934 1.007819072 1.027836304 0.969576746 0.979502923 0.972537546 1.005956036 1 18.10372314 4.592079705 3.111052525 0.994194385 0.933232614 0.542743424 0.017725737 0.235512928 3.755727566 0.004713715 0.028479438 39091.26323 -4.592079705 -0.060961771 LEILSGDHEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEILSGDHEQR 11 0 Q4G0J3;Q4G0J3-3;H0YA82;Q4G0J3-2 Q4G0J3 LARP7 La-related protein 7 0 ; 138.24 6.18E-05 403890000 216860 189106 113231 141132 182341 206507 189271 213950 196755 FALSE TRUE 188201.4015 187863.7502 167989.8903 173178.1777 178712.7708 214451.4579 170915.5276 168198.4575 173494.848 1.084766514 1.082820339 0.968270195 0.998174756 1.030075376 1.236068162 0.985133158 0.969472347 1 17.4045333 2.050713582 24.99999851 0.980976179 1.062544472 0.225297764 0.071176609 158.0609488 77917.66844 0.030100015 0.020293421 112.3863539 -2.050713582 0.081568293 LEIS(ph)PDSS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEISPDSSPER 11 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 2 LEIS(1)PDSS(1)PER;LEIS(1)PDSS(1)PER 190.37 3.36E-06 723130000 1151250 966140 724130 934190 969600 1027480 871640 1034000 1004260 TRUE FALSE 999109.3956 959793.3627 1074321.69 1146312.118 950306.857 1067007.82 787108.487 812887.1466 885537.5269 1.128251898 1.083853968 1.213185955 1.294481694 1.07314126 1.204926712 0.888848257 0.917959004 1 19.75619392 2.238925994 25 0.929978591 1.166281259 0.708377065 0.069748466 5.064825824 346590.8521 0.0275389 0.019987959 173.3508573 -2.238925994 0.236302667 LEKEEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEKEEAK 7 1 P10644;P10644-2;K7EPB2;K7EIE5;K7EID3;K7EJ40;K7EK41;K7EMU2;K7EMZ6;K7EQK3 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 0 67.897 0.058292 269260000 714330 520320 342080 423330 346180 333630 770610 875220 606580 FALSE TRUE 619929.4806 516901.9837 507511.0322 519453.5467 339291.6953 346464.962 695876.3608 688061.014 534870.8034 1.159026585 0.966405308 0.948847888 0.971175737 0.634343272 0.647754485 1.30101766 1.286406006 1 19.02883093 2.220768171 24.99768566 1.219066312 0.886519604 0.409041717 0.173697014 235.0780706 330272.9362 0.075166637 0.050797703 166.2524947 -2.220768171 -0.332546709 LEKHELIEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LEKHELIEFR 10 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;; 186.74 7.85E-07 4245840000 7267900 5746250 3321917 3811690 5861920 4931410 6894140 7372260 2474532 FALSE TRUE 6307428.6 5708502.505 4928407.172 4677192.473 5745279.261 5121124.534 6225547.364 5795759.57 2181995.646 2.890669655 2.616184187 2.258669572 2.143538866 2.633038829 2.346991179 2.853143807 2.656173756 1 21.05721679 4.493688066 3.23595709 2.347988548 2.872223178 0.133450327 0.505772608 0.586775585 11.85816541 0.126113478 0.567047974 31166.50232 -4.493688066 0.524234631 LEKPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEKPAK 6 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;; 81.381 0.056569 88441300000 28665800 27346200 20099390 24276260 20044060 18476790 30968800 34821700 45807800 FALSE TRUE 24877541.9 27166561.01 29819522.23 29788555.87 19645222.42 19187604.07 27965450.54 27375350.44 40392454.07 0.615895777 0.672565251 0.738244876 0.737478238 0.486358724 0.475029421 0.692343439 0.677734272 1 25.26758246 1.094836294 2.138920992 1.234612847 0.629675432 0.615080676 0.090821216 0.853218887 2.772744893 1.166918472 0.026445106 12.44045583 -1.094836294 -0.604937415 LEKPAKYDDIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LEKPAKYDDIK 11 2 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;; 125.61 0.00018261 32827900000 87117000 66057410 51252520 47940150 50217720 34287190 97393680 108069200 25026960 FALSE TRUE 75604267.72 65623474.52 76038410.1 58825693.78 49218485.62 35606240.39 87948455.9 84959442.58 22068301.3 3.425921492 2.973653188 3.445594161 2.665619477 2.230279755 1.613456328 3.985284355 3.849840612 1 24.39547225 3.728850237 23.08781606 2.728321023 3.250915975 0.104500131 0.910748034 762.804859 1813680.467 0.266687928 0.402145066 5356.119239 -3.728850237 0.522594952 LEKPAKYDDIKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEKPAKYDDIKK 12 3 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 82.908 0.016737 8224100000 9148100 4635840 4565440 3576870 3317710 1930670 7520100 7781700 902290 FALSE TRUE 7939155.407 4605386.862 6773302.054 4389053.003 3251694.062 2004944.124 6790801.859 6117644.012 795622.3041 9.97854807 5.788408442 8.51321289 5.51650322 4.086982033 2.519969732 8.535208006 7.689130861 1 19.60172419 3.687921924 6.885284774 5.269443325 7.860634702 0.2690895 2.425810222 0.404708131 46.06794129 0.692691602 1.03932159 4874.408512 -3.687921924 2.591191378 LELAQYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LELAQYR 7 0 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 124.59 0.0096111 472340000 471870 528580 422480 589930 609910 622190 529370 579930 788160 FALSE TRUE 409511.1839 525107.7232 626792.7411 723882.623 597773.9843 646126.0519 478031.7789 455916.4825 694984.6227 0.589237762 0.755567398 0.901880014 1.041580777 0.860125483 0.929698343 0.687830728 0.656009454 1 19.40662153 4.613912141 3.081585668 0.847145042 0.579716342 0.341982352 0.121952081 0.410744313 6.290129065 0.034504274 0.22323729 41106.65525 -4.613912141 -0.2674287 LELKAS(ph)PNVEAPQPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LELKASPNVEAPQPHR 16 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 LELKAS(1)PNVEAPQPHR;LELKAS(1)PNVEAPQPHR;LELKAS(1)PNVEAPQPHR 172.3 2.79E-09 1361120000 1325480 1221590 920692 1063432 1389730 1147580 1520660 1804480 1233780 TRUE FALSE 1150314.46 1213565.295 1365941.731 1304900.489 1362077.092 1191728.145 1373186.627 1418605.994 1087923.934 1.057348243 1.115487266 1.25554893 1.199440925 1.251996624 1.095414953 1.262208307 1.303956968 1 20.05314626 4.41886592 4.885777544 1.207060442 1.069370624 0.207707166 0.089732954 0.24425091 11.68721875 0.021860999 0.064211943 26234.08493 -4.41886592 -0.137689818 LELQGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LELQGPR 7 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;; 175.75 0.0018083 1160490000 1340500 1357420 806290 914910 1308230 1254140 1194890 1394260 1226540 FALSE TRUE 1163349.529 1348503.019 1196214.541 1122654.299 1282198.783 1302387.577 1079009.752 1096108.349 1081539.838 1.075641865 1.246836197 1.106029106 1.038014744 1.185530793 1.204197507 0.997660662 1.013470156 1 20.04465538 2.224315245 24.99981988 1.005491464 1.142961884 0.536185452 0.060934258 183.2025774 321507.5698 0.024872255 0.01685663 167.6159123 -2.224315245 0.13747042 LELSDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LELSDNR 7 0 P39687;H0YN26 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 94.262 0.033338 143670000 379370 333330 198620 257230 343640 360480 330850 390380 399740 FALSE TRUE 329235.2933 331140.3333 294673.2963 315638.003 336802.2363 374347.8989 298764.2179 306900.2749 352483.1926 0.934045368 0.939449994 0.835992474 0.895469655 0.955512897 1.062030493 0.847598479 0.870680592 1 18.42719494 LELSVHLQPITR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LELSVHLQPITR 12 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 138.02 8.19E-05 296160000 228170 223850 82463 152930 225360 235870 222000 253040 229790 FALSE TRUE 198016.7564 222379.5146 122342.3826 187655.0939 220875.7769 244944.0715 200470.4742 198929.3652 202624.488 0.97725975 1.097495751 0.603788732 0.926122483 1.090074448 1.208857202 0.98936943 0.981763691 1 17.62844901 3.344812282 5.99496741 1.047313572 0.890339401 0.234092926 0.13772803 0.333446107 16.53556805 0.041289043 0.053382244 2212.138338 -3.344812282 -0.156974171 LELTELEAIREDFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LELTELEAIREDFLR 15 1 Q9UPU7 Q9UPU7 TBC1D2B TBC1 domain family member 2B 0 ; 173.36 8.89E-07 38894000 62406 59597 35959 47837 60577 54135 55879 73348 43555 FALSE TRUE 54158.88898 59205.50338 53348.89268 58699.12199 59371.63622 56217.60848 50459.86318 57663.10099 38405.97752 1.410168221 1.541570016 1.38907785 1.528385053 1.545895719 1.463772363 1.313854416 1.501409539 1 15.22904325 1.235562636 24.98923279 0.999999369 1.461687409 0.793635493 0.074000032 36.30595728 302567.553 0.120765327 0.017640029 17.20135408 -1.235562636 0.46168804 LEMDGHLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEMDGHLNR 9 0 A0A5F9UP49;Q9BRK5;A0A5F9UJX7;Q9BRK5-6;G3V1E2;Q9BRK5-4;Q9BRK5-3 A0A5F9UP49 SDF4 45 kDa calcium-binding protein 0 ; 153.05 7.90E-05 389380000 405720 385020 277930 300840 394050 475560 330400 389640 406800 FALSE TRUE 352103.074 382490.7783 412337.8776 369150.3201 386209.1759 493855.1009 298357.8589 306318.5182 358708.5674 0.981585348 1.066299534 1.149506633 1.029109293 1.076665603 1.376758588 0.831755598 0.853948152 1 18.45245268 2.165868511 24.99999604 0.883986881 1.107356541 0.448976365 0.113536031 37.08550768 12753.24982 0.045562663 0.030718347 146.5104192 -2.165868511 0.22336966 LEMEQVWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEMEQVWR 8 0 O00754;O00754-2;M0QYZ1 O00754 MAN2B1 Lysosomal alpha-mannosidase;Lysosomal alpha-mannosidase A peptide;Lysosomal alpha-mannosidase B peptide;Lysosomal alpha-mannosidase C peptide;Lysosomal alpha-mannosidase D peptide;Lysosomal alpha-mannosidase E peptide 0 82.279 0.048121 74919000 133150 113380 56469 96394 123340 119320 115960 134000 122940 FALSE TRUE 115553.8901 112635.1993 83777.59728 118281.731 120885.7753 123910.3176 104714.217 105345.1428 108406.1733 1.065934593 1.039010934 0.772812053 1.091097743 1.115118924 1.143019017 0.965943303 0.97176332 1 16.72608739 4.469274584 24.99700282 1.007288193 1.059203827 0.033617937 0.102806864 666.2959339 2122615.02 0.026782641 0.071143631 29462.83841 -4.469274584 0.051915634 LENEGS(ph)DEDIETDVLYSPQMALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LENEGSDEDIETDVLYSPQMALK 23 0 O60502;O60502-3 O60502 MGEA5 Protein O-GlcNAcase 1 LENEGS(1)DEDIETDVLYSPQMALK;LENEGS(0.997)DEDIET(0.003)DVLYSPQMALK;LENEGS(0.999)DEDIET(0.001)DVLYSPQMALK;LENEGS(0.999)DEDIET(0.001)DVLYSPQMALK;LENEGS(0.999)DEDIET(0.001)DVLYSPQMALK 208.46 6.53E-25 169477000 543079 410602 277138 355396 399995 311793 419677 585489 516987 TRUE FALSE 471309.7342 407904.7284 411162.8638 436094.0937 392035.8821 323787.8785 378976.7891 460286.7336 455869.3858 1.033870115 0.89478421 0.901931291 0.956620706 0.859974138 0.710264581 0.831327571 1.009689942 1 18.798261 4.739064512 23.68158602 0.896680759 1.033870108 0.201242067 0.086563599 38.51155271 1808808.16 0.02328711 0.134078555 54835.84144 -4.739064512 0.137189349 LENGELEHIRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LENGELEHIRPK 12 1 M0R1K3;Q15102;M0R389;M0QZT2;M0QXS6;M0R323 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ;;; 210.15 2.82E-08 6919400000 8120200 6940600 4654120 5762320 6546310 5484070 7678500 9069900 8132000 FALSE TRUE 7047094.996 6895006.742 6904867.999 7070742.828 6416051.239 5695045.722 6933840.252 7130372.467 7170644.224 0.982770136 0.96156029 0.962935516 0.986068003 0.894766361 0.794216746 0.966975914 0.994383802 1 22.77367131 2.00693886 24.99989561 0.991957506 0.929728092 0.201122028 0.055537657 287.2263179 1034838.882 0.024712208 0.016619896 101.6105636 -2.00693886 -0.062229414 LENLGIPEEELLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LENLGIPEEELLR 13 0 Q01658 Q01658 DR1 Protein Dr1 0 101.6 0.0043519 12910000 24376 17673 12753 11458 16688 15287 15002 26970 14042 FALSE TRUE 21154.64984 17556.9049 18920.39346 14059.71402 16355.94145 15875.10078 13547.10835 21202.67538 12381.97076 1.708504264 1.417941073 1.528059937 1.135498888 1.320948157 1.28211422 1.094099527 1.712382931 1 13.59595334 4.86005426 1.098821362 1.305490401 1.962449817 0.309985853 0.202592802 2.96364045 2.498920095 0.061239996 2.403819733 72452.64747 -4.86005426 0.656959416 LENLNEAIEEDIVQSVLRPTNCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LENLNEAIEEDIVQSVLRPTNCR 23 1 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 0 ; 160.57 1.71E-11 39627000 21146.5 24596.9 15439.1 14761.8 23311.9 22100.1 21400 25229 18084.7 FALSE TRUE 18351.93645 24435.32134 22905.5004 18113.69231 22848.0388 22950.30515 19324.63129 19833.97468 15946.74737 1.150826311 1.532307547 1.436374445 1.135886328 1.432771102 1.439184093 1.211822753 1.243763021 1 13.96097457 0.671749373 0.96349308 0.279633953 1.356251063 0.40078159 0.131105581 5.36432948 1.813394376 7.869984015 0.04312327 4.696230158 -0.671749373 1.07661711 LENNDNKPVTNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LENNDNKPVTNSR 13 1 A0A024R7W5;A0A087X0Q1;A0A087WY31;Q7Z739 A0A024R7W5 YTHDF3 YTH domain-containing family protein 3 0 ;; 189.86 4.47E-06 1194850000 1064400 872270 648540 720300 775250 717440 1014270 1061060 976390 FALSE TRUE 923736.8432 866540.0009 962176.1132 883855.1241 759824.0418 745040.381 915906.2515 834160.5762 860962.2865 1.072912086 1.006478465 1.117558955 1.026589826 0.882528833 0.865357743 1.063816924 0.968870053 1 19.71559052 3.466150258 24.852775 0.960640782 1.061789653 0.40661486 0.061224333 217.2176101 492064.3 0.018236935 0.023566064 2925.164259 -3.466150258 0.101148871 LENNENKPVTNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LENNENKPVTNSR 13 1 Q9Y5A9;Q9Y5A9-2 Q9Y5A9 YTHDF2 YTH domain-containing family protein 2 0 94.728 0.0017809 0 28260 20406 15598 15756 21012 17278 22643 29691 26662 FALSE TRUE 24525.3694 20271.95164 23141.24497 19333.64062 20593.90231 17942.69584 20447.08535 23341.81071 23510.04873 1.043186668 0.86226753 0.984312931 0.822356467 0.875961702 0.763192626 0.869716842 0.992843995 1 14.52098991 1.692334414 5.426030552 0.998010262 0.883547941 0.245710118 0.077925731 0.191082906 12.94152866 0.049015453 0.020062785 49.24185603 -1.692334414 -0.114462322 LENS(ph)PLGEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LENSPLGEALR 11 0 D6RDK6;D6RBN5;Q9NX40;D6RI08;D6RDK1;D6RIV2;D6R9T5;D6RG39;D6RIT9;Q9NX40-3;Q9NX40-2;Q9NX40-4 D6RDK6 OCIAD1 OCIA domain-containing protein 1 1 LENS(1)PLGEALR;LENS(1)PLGEALR;LENS(1)PLGEALR;LENS(1)PLGEALR 155.43 3.31E-05 374829000 444562 463893 347989 548565 568108 641980 371734 630140 620543 TRUE FALSE 385812.0053 460845.6563 516277.6444 673125.0675 556803.7623 666677.386 335683.2939 495389.4648 547183.1135 0.705087558 0.84221469 0.943518964 1.230164183 1.017582138 1.218380775 0.613475244 0.905344943 1 19.06166418 7.378604144 9.64576434 0.940631707 0.00465543 0 0.195468486 0 0 0.044799312 0 23911352.64 -7.378604144 -0.935976277 LENVSLSQQLTETQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LENVSLSQQLTETQHR 16 0 Q08378;Q08378-4;Q08378-2 Q08378 GOLGA3 Golgin subfamily A member 3 0 178.22 2.82E-09 518940000 153400 133400 77945 102410 150330 126850 118050 157610 129510 FALSE TRUE 133127.8013 132523.6866 115639.4627 125663.7557 147338.7271 131730.0016 106601.5292 123906.328 114199.4753 1.165747924 1.160457929 1.012609404 1.100388206 1.290187426 1.15350794 0.933467766 1.084999101 1 16.8011965 2.263969701 24.86520313 1.019552678 1.14601548 0.423427815 0.077024411 224.7546313 219943.0102 0.029850791 0.023113198 183.6410219 -2.263969701 0.126462802 LENVSQLSLDKS(ph)PTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LENVSQLSLDKSPTEK 16 1 Q86W56-3;Q86W56-2;Q86W56 Q86W56-3 PARG Poly(ADP-ribose) glycohydrolase 1 LENVSQLSLDKS(0.997)PT(0.003)EK 212.65 2.40E-12 590420000 587030 454430 419410 389880 424770 326940 594120 702190 628050 TRUE FALSE 509452.4982 451444.8194 622238.0788 478408.2129 416317.908 339517.5934 536502.3338 552032.1329 553802.6445 0.919917056 0.815172741 1.123573686 0.86386047 0.751744168 0.613066038 0.968760874 0.996802992 1 19.07901242 2.027249449 24.97426159 0.993556083 0.849924181 0.214217808 0.127792409 339.5112275 311162.3717 0.055512423 0.037425544 106.4754413 -2.027249449 -0.143631902 LEPKPQPPVAEATPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEPKPQPPVAEATPR 15 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;K7EJ51;K7ER14;K7EJL9 Q9UHD8 9-Sep Septin-9 0 129.62 5.91E-05 167530000 144910 139020 87243 115240 127270 106450 152580 160190 135380 FALSE TRUE 125759.7763 138106.7685 129434.0066 141407.0033 124737.576 110545.2004 137782.8151 125934.6151 119375.5306 1.053480355 1.156910195 1.08425911 1.184556019 1.044917458 0.926028976 1.154196462 1.054944966 1 16.86514762 3.128570365 10.8832003 1.041443288 1.119857088 0.283039887 0.06596919 0.499688791 46.45586379 0.019601461 0.022235476 1344.529591 -3.128570365 0.078413801 LEPQELS(ph)PLSATVFPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEPQELSPLSATVFPK 16 0 Q3T8J9-3;Q3T8J9;A0A087WUE6;Q3T8J9-2;Q9H869-7;Q9H869-5;Q9H869-6;Q9H869-4;Q9H869-3;Q9H869-2;Q9H869;Q9H869-8;Q9H869-9 Q3T8J9-3 GON4L;YY1AP1 GON-4-like protein;YY1-associated protein 1 1 LEPQELS(0.996)PLS(0.004)AT(0.001)VFPK 160.43 9.21E-09 112350000 208120 169310 119260 147150 172960 165740 204890 227780 221240 TRUE FALSE 180616.4147 168197.7915 176934.5349 180562.6565 169518.4344 172116.125 185019.7993 179071.0196 195085.2592 0.925833225 0.86217581 0.906960042 0.925557663 0.868945378 0.882261047 0.948404816 0.917911585 1 17.57374525 -1.416675293 0.808206292 9.999999985 0.896178139 0.590494219 0.025796303 125.1473372 1.229141965 2038.777948 0.00927732 0.038311107 1.416675293 -9.103821845 LEPQIASASEYAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LEPQIASASEYAHR 14 0 O60664-4;O60664;O60664-3;K7ER39;K7EL96 O60664-4 PLIN3 Perilipin-3 0 ;;;;; 286.09 9.83E-34 5524110000 6102880 6401720 3084570 4423500 6231790 6193640 5896970 6972870 6343800 FALSE TRUE 5296368.945 6359666.68 4576278.369 5427923.284 6107789.571 6431913.339 5325082.757 5481776.013 5593843.191 0.946821133 1.136904712 0.818092001 0.970338835 1.091877152 1.1498201 0.951954242 0.979965978 1 22.41540838 LEPVS(ph)PPS(ph)PPHTDPELELVPPR ddPTM_MDA-MB-175_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(1)PPS(0.943)PPHT(0.057)DPELELVPPR;LEPVS(1)PPS(1)PPHTDPELELVPPR;LEPVS(1)PPS(1)PPHTDPELELVPPR;LEPVS(1)PPS(0.999)PPHT(0.001)DPELELVPPR;LEPVS(1)PPS(1)PPHTDPELELVPPR 125.82 1.09E-05 2022050000 1182990 1038890 692132 836732 1017530 1062345 990977 1144090 1106740 TRUE FALSE 1026654.874 1032065.463 1026849.35 1026724.789 997283.1438 1103214.1 894872.2031 899435.2568 975902.458 1.052005624 1.057549814 1.052204902 1.052077265 1.02190863 1.130455293 0.9169689 0.921644627 1 19.89637743 2.223172918 24.99933505 0.939869686 1.058288423 0.702093544 0.035149567 118.9076174 193179.5203 0.013693445 0.009269799 167.1756106 -2.223172918 0.118418737 LEQDEYALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEQDEYALR 9 0 P55084-2;P55084;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ; 161.27 0.00015044 331080000 492920 459910 340310 547360 540960 562470 412130 527650 507940 FALSE TRUE 427779.3731 456888.8209 504885.0543 671646.4539 530195.9544 584108.5849 372161.696 414816.1537 447891.9118 0.955095106 1.020087233 1.127247537 1.499572634 1.183758716 1.30412845 0.830918546 0.926152366 1 18.77279109 2.234438432 24.99950364 0.916837724 1.186378874 0.395072364 0.153111693 110.6432267 670998.5615 0.064949736 0.045567617 171.5688468 -2.234438432 0.269541151 LEQEHTNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEQEHTNR 8 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 ; 105.4 0.0043959 163551000 200031 153483 115063 141082 143570 175829 168987 188375 181710 FALSE TRUE 173596.3965 152474.7601 170707.8517 173116.8244 140713.2379 182593.2554 152598.6667 148092.4722 160228.4508 1.083430537 0.951608527 1.065402872 1.080437485 0.878203822 1.139580733 0.95238184 0.924258279 1 17.28977082 2.070924236 24.9999606 0.95118549 1.027650513 0.172741392 0.075333424 70.06123358 24694.3285 0.028610596 0.019289257 117.7400555 -2.070924236 0.076465023 LEQGEEPWIMGGEFPCQHS(ph)PEAWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEQGEEPWIMGGEFPCQHSPEAWR 24 0 I3L0D1;Q9NYW8 I3L0D1 RBAK-RBAKDN;RBAK RB-associated KRAB zinc finger protein 1 LEQGEEPWIMGGEFPCQHS(1)PEAWR 105.21 0.0018748 87815000 59981 51311 38543 47683 52959 49031 55081 55335 42183 TRUE FALSE 52054.35888 50973.93466 57182.52372 58510.15394 51905.21951 50917.2543 49739.2531 43502.04087 37196.1738 1.399454663 1.370408014 1.537322737 1.573015393 1.395445128 1.368884192 1.337214235 1.169529993 1 15.1828666 1.317907442 0.866754592 0.760708589 1.461760571 0.854212079 0.063041411 0.776157177 0.507811205 0.520862046 0.02650225 20.79253505 -1.317907442 0.701051982 LEQLDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEQLDHR 7 0 A0A5H1ZRP4;Q8WX92;Q8WX92-2 A0A5H1ZRP4 NELFB Negative elongation factor B 0 150.88 0.0097612 0 450180 355020 248640 280640 314430 364930 341630 393310 384540 FALSE TRUE 390687.5724 352687.8502 368883.1357 344363.6013 308173.4582 378969.0932 308498.7752 309203.7172 339080.1193 1.152198404 1.040131315 1.08789373 1.01558181 0.90885145 1.117638787 0.909810861 0.911889845 1 18.37126667 8 0.25901506 0.92290896 2.38941751 0.433767525 0.065640091 75.57426641 1.206421619 0.192129986 47.57982408 100000000 -8 1.46650855 LEQMPSKEDAIEHFMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LEQMPSKEDAIEHFMK 16 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 146.58 6.67E-07 925310000 1578590 1077250 907890 1231660 1067100 768870 1270030 1653410 1646550 FALSE TRUE 1369975.332 1070173.474 1346948.641 1511327.228 1045866.798 798448.9264 1146862.686 1299841.138 1451896.735 0.943576288 0.737086494 0.927716558 1.040933003 0.720345168 0.549935066 0.789906512 0.895271067 1 20.46950742 3.212926224 24.99979085 0.791967321 0.900910191 0.161670399 0.136074531 511.2628876 498604.4719 0.044908041 0.050939109 1632.774557 -3.212926224 0.10894287 LEQQLVHVERPILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEQQLVHVERPILR 14 1 E5RIA4;E7ETB3;Q9ULA0-2;Q9ULA0;C9JBE1;E7EMB6;E7EPX3;B9ZVU2;F8WAN0;C9JRG3;C9J1E2 E5RIA4 DNPEP Aspartyl aminopeptidase 0 157.35 3.20E-06 782620000 411430 397170 242680 276530 364750 387910 365270 415830 339410 FALSE TRUE 357058.4831 394560.9641 360040.8597 339320.363 357492.1886 402833.1487 329846.1716 326907.9905 299285.3365 1.19303701 1.318343788 1.203002005 1.133768754 1.194486148 1.34598358 1.102112705 1.092295381 1 18.19116207 2.060303807 8.875363902 1.065961037 1.227988908 0.592816736 0.065815164 0.213970802 29.06151786 0.027455208 0.018473635 114.8957083 -2.060303807 0.162027871 LEQTSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LEQTSVR 7 0 O15234 O15234 CASC3 Protein CASC3 0 ;; 99.919 0.02367 3336900000 2540420 2287800 1349720 1913690 2125560 2449330 2041550 2457920 2273270 FALSE TRUE 2204697.06 2272771.291 2002449.107 2348222.563 2083265.515 2543557.31 1843560.795 1932312.936 2004526.61 1.099859213 1.133819466 0.998963594 1.17145991 1.039280548 1.268906732 0.919698838 0.963974699 1 20.93483014 2.204081519 24.99986923 0.960067144 1.112745281 0.496789153 0.074555665 143.5556292 104087.3955 0.028176755 0.01899775 159.9858301 -2.204081519 0.152678137 LERT(ph)PQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LERTPQK 7 1 P35251-2;P35251 P35251-2 RFC1 Replication factor C subunit 1 1 LERT(1)PQK;LERT(1)PQK 73.327 0.079533 906580000 2381600 2281700 1589450 1989290 1794970 1560100 2297900 2752000 2270000 TRUE FALSE 2066865.526 2266711.362 2358113.336 2440988.699 1759253.609 1620118.057 2075050.012 2163506.216 2001643.186 1.032584399 1.132425289 1.178088759 1.219492423 0.878904702 0.809394036 1.036673282 1.080865077 1 20.93275339 3.242398565 24.99999996 0.974203896 1.142734762 0.497005399 0.089175103 101.6664696 662239.614 0.029604909 0.036770311 1747.425083 -3.242398565 0.168530865 LERYHTAIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LERYHTAIRR 10 2 O00515;E9PDI4 O00515 LAD1 Ladinin-1 0 50.108 0.092953 216590000 398010 364980 201450 195350 364230 442600 245600 285800 258300 FALSE TRUE 345411.9701 362582.4223 298871.8938 239707.2032 356982.5356 459627.1084 221781.7498 224683.8941 227764.0683 1.516534073 1.591921084 1.312199488 1.052436432 1.567334735 2.01799657 0.973734582 0.98647647 1 17.79718064 2.122084951 22.81266399 0.986011272 1.487208621 0.511272283 0.24037083 3.5715193 687.8706908 0.103069081 0.069489168 132.460061 -2.122084951 0.501197348 LES(ph)LNIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LESLNIQR 8 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 LES(1)LNIQR;LES(1)LNIQR;LES(1)LNIQR;LES(1)LNIQR 129.89 0.0011238 345484000 545091 411676 397829 348574 431411 553281 551920 504439 713981 TRUE FALSE 473055.8433 408971.6732 590220.4351 427723.0543 422826.7651 574566.0781 498394.8833 396568.6454 629574.9795 0.751389205 0.649599629 0.937490298 0.67938382 0.671606685 0.912625337 0.791637056 0.629898993 1 19.26401868 2.776793721 24.99711977 0.797793159 0.740826842 0.099083851 0.123817771 2024.945956 1323922.287 0.039898579 0.039897926 598.127432 -2.776793721 -0.056966317 LES(ph)VEEYNELMVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LESVEEYNELMVR 13 0 O15018 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 LES(1)VEEYNELMVR;LES(1)VEEYNELMVR;LES(1)VEEYNELMVR 194.77 7.69E-07 107548000 100041 94742 68704 76980 87434 74765 113187 106544 85932 TRUE FALSE 86820.32838 94119.63356 101929.4842 94459.48557 85694.23446 77641.25793 102210.1422 83760.39473 75773.21685 1.145791772 1.242122711 1.34519146 1.246607832 1.1309304 1.024653052 1.34889538 1.105408985 1 16.20940038 3.245307422 7.78881005 1.131928712 1.252182239 0.253695912 0.103699283 0.195572149 79.48423584 0.03080735 0.037856234 1759.16843 -3.245307422 0.120253527 LESALTELEQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LESALTELEQLR 12 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 114.83 0.0023612 7899800 10471 10562 7486.7 10655 10933 10777 10307 12951 13383 FALSE TRUE 9087.23082 10492.61753 11107.29316 13074.3806 10715.45469 11191.59816 9307.428726 10181.52943 11800.87699 0.770047076 0.889138794 0.941226078 1.107916015 0.908021896 0.948370039 0.788706529 0.862777355 1 13.52660646 4.692173066 2.990684727 0.927237652 0.752552768 0.279655185 0.083259243 0.515406948 7.121277941 0.02263486 0.202630916 49223.56523 -4.692173066 -0.174684884 LESDYEILER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LESDYEILER 10 0 A0A0A0MSX9;P41252;J3KR24;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;; 285.32 4.77E-24 675065000 1010310 883750 630520 726010 895120 852260 958150 1051400 1044210 FALSE TRUE 876794.9737 877944.5881 935441.581 890861.6669 877308.8633 885046.9937 865228.7605 826566.292 920764.6834 0.952246529 0.953495072 1.015939901 0.967523715 0.952804641 0.961208667 0.939684999 0.897695477 1 19.81247297 2.662784472 1.590924613 0.936736203 0.972578237 0.076075736 0.030792164 0.642570841 3.297370467 0.014559248 0.01177007 460.0282178 -2.662784472 0.035842034 LESEMEDAYHEHQANLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LESEMEDAYHEHQANLLR 18 0 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 85.636 0.0020799 57743000 32712 26838 20911 24913 29081 29571 24536 29322 46220 FALSE TRUE 28389.02632 26661.69941 31023.62954 30569.87742 28502.345 30708.6155 22156.5025 23051.71848 40755.92425 0.696561956 0.654179727 0.761205398 0.750071995 0.699342378 0.753476116 0.543638818 0.565604115 1 15.31472216 LESEST(ph)SPSLEMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LESESTSPSLEMK 13 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 LESEST(0.869)S(0.131)PSLEMK 344.55 9.61E-63 192770000 687150 536840 387360 426380 494920 381470 609290 718230 609420 TRUE FALSE 596341.3865 533313.4627 574688.5916 523196.0958 485072.0603 396145.3977 550201.1496 564642.1038 537375.0619 1.109730296 0.99244178 1.069436661 0.973614395 0.902669466 0.737186047 1.023868037 1.050741175 1 19.03556985 3.630790913 4.688683303 0.951191037 1.050403543 0.247368087 0.090119169 0.411313987 14.35917841 0.028099145 0.042506329 4273.570894 -3.630790913 0.099212506 LESESTS(ph)PSLEMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.077)S(0.923)PSLEMK;LESEST(0.034)S(0.966)PS(0.001)LEMK;LESEST(0.009)S(0.991)PSLEMK;LESEST(0.092)S(0.705)PS(0.203)LEMK 309.78 1.55E-50 899200000 3930920 3016510 2223690 2551590 2992680 2406690 3537530 4329480 3892020 TRUE FALSE 3411438.962 2996694.347 3299073.922 3130967.508 2933131.523 2499276.922 3194460.885 3403654.394 3431909.829 0.994035138 0.87318563 0.961293882 0.91231054 0.854664507 0.728246675 0.930811427 0.991766848 1 21.71058022 1.862206848 4.216222356 0.993311506 0.885865938 0.279045004 0.070483309 0.29751158 8.191292648 0.041470078 0.0198123 72.8126517 -1.862206848 -0.107445567 LESESTSPS(ph)LEMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LESESTSPSLEMK 13 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 LESEST(0.004)S(0.403)PS(0.593)LEMK 133.48 0.00041724 159810000 440670 326940 247650 301310 395170 294410 402200 467950 431480 TRUE FALSE 382434.343 324792.3096 367414.3683 369727.0407 387306.8901 305736.1432 363194.7059 367882.5341 380470.9259 1.005160492 0.853658683 0.965683166 0.971761613 1.017967113 0.803572947 0.954592536 0.966913656 1 18.53742669 1.568191996 2.740401109 0.995314335 0.935842787 0.084816825 0.065272946 0.633904464 10.12865712 0.070054891 0.017041935 36.99917126 -1.568191996 -0.059471548 LESLSETPGPSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LESLSETPGPSSPR 14 0 A0A2R8YF49;H0Y895;Q12774-2;C9J591;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 LESLSETPGPS(0.018)S(0.982)PR;LESLSETPGPSS(1)PR;LESLSETPGPSS(1)PR;LESLSETPGPS(0.001)S(0.999)PR;LESLSETPGPS(0.001)S(0.999)PR;LESLSETPGPS(0.001)S(0.999)PR;LESLSETPGPS(0.011)S(0.989)PR;LESLSETPGPS(0.015)S(0.985)PR 352.73 5.86E-82 12351000000 8976050 8805020 5693670 7157450 8870850 8886590 8701180 10014030 9714980 TRUE FALSE 7789842.25 8747179.244 8447147.856 8782658.417 8694337.441 9228462.868 7857340.903 7872607.614 8566486.132 0.909339271 1.021093026 0.986069168 1.025234651 1.014924592 1.077275177 0.917218657 0.919000801 1 23.03027212 2.207038789 24.99998002 0.938730784 1.006778667 0.261432698 0.047271015 233.2609012 184997.7637 0.018835066 0.012700004 161.0789496 -2.207038789 0.068047883 LESPTTPLLDDMDGSQDS(ph)PIFMYAPEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LESPTTPLLDDMDGSQDSPIFMYAPEFK 28 0 Q9H3M7-2;Q9H3M7 Q9H3M7-2 TXNIP Thioredoxin-interacting protein 1 LESPTTPLLDDMDGS(0.034)QDS(0.965)PIFMY(0.001)APEFK 84.073 0.0026002 20729000 21653 17743 17044 23890 22152 22076 25674 29836 32018 TRUE FALSE 18791.50119 17626.44506 25286.53541 29314.58964 21711.21854 22925.27801 23184.13943 23455.80358 28232.86852 0.665589512 0.624323563 0.895641737 1.038314248 0.769005053 0.812006686 0.821175483 0.830797748 1 14.7850881 4.238949747 24.99999949 0.872460958 0.644956468 0.574207605 0.084252396 7.288918335 468128.3212 0.021833763 0.051009144 17336.03386 -4.238949747 -0.22750449 LESTESR ddPTM_MDA-MB-175_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 0 114.72 0.032976 0 191980 185900 123910 147670 129500 191560 183420 178150 232900 FALSE TRUE 166609.3566 184678.8107 183833.2905 181200.7305 126923.2034 198929.4372 165631.9566 140054.0089 205366.8273 0.811276869 0.899263104 0.895145983 0.882327165 0.618031671 0.968654187 0.80651758 0.681969969 1 17.64784364 LESTS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LESTSPK 7 0 Q03111 Q03111 MLLT1 Protein ENL 1 LEST(0.003)S(0.996)PK;LES(0.007)T(0.031)S(0.961)PK;LES(0.002)T(0.012)S(0.986)PK;LES(0.002)T(0.048)S(0.95)PK 111.06 0.0069892 2282850000 15810200 11336400 8916400 9476700 8026400 9428200 14664500 16174800 15019700 TRUE FALSE 13720842.01 11261930.44 13228400.86 11628529.58 7866690.343 9790908.955 13242339.05 12715944.89 13244088.18 1.035997483 0.850336414 0.998815523 0.878016623 0.593977497 0.739266367 0.999867931 0.960122337 1 23.65884519 2.2115161 24.99564211 0.981684301 0.845926143 0.215627822 0.123169718 371.982497 343798.6018 0.054120819 0.036498735 162.7481648 -2.2115161 -0.135758157 LETEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LETEEER 7 0 P25098;E9PRV7 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 0 117.16 0.012315 185420000 267600 276950 182700 228030 250360 262480 280320 310520 337410 FALSE TRUE 232235.982 275130.6972 271054.3311 279807.6967 245378.3258 272577.7754 253134.6095 244117.7145 297521.7742 0.780568019 0.924741384 0.911040316 0.94046124 0.824740732 0.916160762 0.850810366 0.820503693 1 18.18263573 3.787962683 0.003630017 1.757550364 2.97E-06 0.031102995 0.065122348 402763.1026 850.3165597 204502.6074 207193.6544 6137.092703 -3.787962683 -1.757547394 LETELDEEKNTVELLTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LETELDEEKNTVELLTDR 18 1 Q9P2M7 Q9P2M7 CGN Cingulin 0 ;; 178.06 8.27E-14 267368000 435500 408671 272963 281574 358797 306322 473408 553953 207702 FALSE TRUE 377947.5716 405986.4133 404968.8198 345509.6803 351657.6417 318106.4056 427496.965 435494.4618 183147.7062 2.06362165 2.216715796 2.21115966 1.886508368 1.920076691 1.736884464 2.334164997 2.37783192 1 17.48264811 3.742663597 23.90190006 1.952882825 2.169120719 0.090935251 0.380240166 603.1670248 3513719.813 0.103004854 0.170210586 5529.216521 -3.742663597 0.216237895 LETHMTPEMFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 LETHMTPEMFR 11 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;;; 184.24 4.99E-06 3233570000 2925370 3082400 1217387 2104606 3150580 3153160 2849510 3298800 2640120 FALSE TRUE 2538774.943 3062151.511 1806119.425 2582488.959 3087889.622 3274464.106 2573164.959 2593377.291 2328008.021 1.090535307 1.315352646 0.775821822 1.109312741 1.326408498 1.4065519 1.1053076 1.113989844 1 21.1506646 5.096964792 13.43625356 1.144857332 6.53E-05 0.008656345 0.179958261 1236277.982 2962029.567 0.044851656 40988149.12 125015.7677 -5.096964792 -1.144792076 LETLLR ddPTM_MDA-MB-175_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 0 116.09 0.055536 172270000 290110 257140 182330 219530 257100 285350 228310 333150 295410 FALSE TRUE 251771.2285 255450.8304 270505.3979 269377.6418 251984.213 296327.5991 206168.5313 261908.4651 260486.9663 0.966540599 0.980666457 1.038460395 1.03413098 0.967358239 1.137590887 0.791473502 1.005457082 1 17.99085166 LEVGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEVGPR 6 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 96.666 0.097591 87898000 334340 326910 309630 330530 202470 282720 231280 278990 237890 FALSE TRUE 290156.1219 324762.5067 459368.1037 405581.8883 198441.2431 293596.4213 208850.5012 219330.1596 209766.9152 1.383231105 1.548206524 2.189897788 1.933488357 0.946008301 1.399631687 0.995631275 1.04558986 1 17.67842763 3.237693091 24.99966467 1.083381783 1.778755459 0.6604812 0.244390268 14.58291755 420242.362 0.075691243 0.090915023 1728.594358 -3.237693091 0.695373676 LEVSVDGLTLSPDPEERPGAEGAPLLPPPLPPPS(ph)PPGSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LEVSVDGLTLSPDPEERPGAEGAPLLPPPLPPPSPPGSGR 40 1 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 1 LEVSVDGLTLSPDPEERPGAEGAPLLPPPLPPPS(0.99)PPGS(0.01)GR;LEVSVDGLTLSPDPEERPGAEGAPLLPPPLPPPS(0.942)PPGS(0.058)GR;LEVSVDGLTLSPDPEERPGAEGAPLLPPPLPPPS(0.947)PPGS(0.053)GR;LEVSVDGLTLSPDPEERPGAEGAPLLPPPLPPPS(0.975)PPGS(0.025)GR 162.89 9.64E-19 906680000 886370 1008680 654930 885900 1161210 1030890 1088570 1378210 1212800 TRUE FALSE 769233.9587 1002053.915 971656.3386 1087057.135 1138104.193 1070549.005 983000.6489 1083490.517 1069424.166 0.719297341 0.937003246 0.908579 1.016488284 1.064221503 1.001051818 0.919186868 1.013153201 1 20.02840275 5.399755613 1.049650726 0.997579425 6.38E-18 0.799798303 0.042845859 2.787804354 0.931367103 0.013525303 4.340858075 251047.3338 -5.399755613 -0.997579425 LEVTEIVKPS(ph)PK ddPTM_MDA-MB-175_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 109.79 0.00094446 1691310000 2809790 1715120 1706840 1629220 1775050 1302970 2461580 2831230 3099050 TRUE FALSE 2438469.132 1703853.264 2532273.533 1999159.302 1739729.978 1353096.099 2222856.35 2225793.497 2732683.839 0.89233489 0.623509108 0.92666173 0.731573581 0.636637855 0.495152816 0.813433416 0.814508237 1 21.38188712 1.326837361 1.805167388 1.059606679 0.72143653 0.309673893 0.127680134 0.928069427 3.404112754 0.517620758 0.03584547 21.22449478 -1.326837361 -0.338170149 LEWSPVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEWSPVHK 8 0 G3V126;Q9UI12-2;Q9UI12 G3V126 ATP6V1H V-type proton ATPase subunit H 0 82.75 0.019463 226940000 185860 185650 115100 139390 167910 135900 218220 216120 171230 FALSE TRUE 161298.1301 184430.4529 170762.745 171040.6299 164568.9195 141128.1609 197057.058 169904.4198 150987.3845 1.068288789 1.22149578 1.130973595 1.132814046 1.089951456 0.934701674 1.305122668 1.125288847 1 17.20406849 3.441594864 3.93277599 1.10374344 1.146646321 0.042048822 0.101416494 0.935403804 31.42021238 0.030031975 0.041039205 2764.361676 -3.441594864 0.042902881 LEYCEALAMLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LEYCEALAMLR 11 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 99.815 0.010454 142730000 129850 123160 90515 111900 118760 125230 127720 158090 133870 FALSE TRUE 112689.9935 122350.9539 134288.3568 137308.6053 116396.9084 130047.6791 115333.7341 124283.6838 118044.0411 0.954643644 1.036485643 1.137612331 1.163198108 0.986046456 1.101687793 0.977039866 1.052858599 1 16.84896569 2.242318924 24.99997452 1.017530154 1.066471108 0.123407524 0.065595488 225.2499572 1498364.911 0.025597231 0.019056418 174.7104667 -2.242318924 0.048940954 LEYDAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LEYDAYR 7 0 A0A087X1E4;P53365;P53365-2;P53365-3 A0A087X1E4 ARFIP2 Arfaptin-2 0 ;; 164 0.0028812 440950000 1724830 1792690 1223840 1349500 1779010 1861150 1739610 2007380 1949080 FALSE TRUE 1496889.345 1780913.701 1815693.117 1655924.601 1743611.182 1932749.645 1570902.89 1578117.408 1718661.983 0.870962039 1.036221037 1.05645737 0.963496381 1.014516641 1.124566473 0.914026671 0.918224424 1 20.7128544 LFATDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFATDER 7 0 Q9NPF4 Q9NPF4 OSGEP Probable tRNA N6-adenosine threonylcarbamoyltransferase 0 83.614 0.084764 0 251020 244300 147480 178240 231160 263630 236790 229560 270960 FALSE TRUE 217847.071 242695.1772 218801.8213 218712.1162 226560.3683 273772.0167 213826.1422 180470.3804 238927.4175 0.911770919 1.015769474 0.915766904 0.915391455 0.948239305 1.145837592 0.894941838 0.755335584 1 17.86621289 2.00985393 24.99828184 0.849675815 0.974761398 0.173596942 0.09075151 252.0963052 639536.5512 0.036266915 0.024420216 102.2948878 -2.00985393 0.125085583 LFAYPDTHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LFAYPDTHR 9 0 P04040 P04040 CAT Catalase 0 ;; 138.1 0.00014615 583960000 887780 879470 586030 761360 914760 1276690 718450 932260 803920 FALSE TRUE 770457.6237 873692.7037 869436.0682 934238.4247 896558.0657 1325805.09 648774.8296 732903.4539 708881.4934 1.086863786 1.232494728 1.226490007 1.317904944 1.264750278 1.870277476 0.915209151 1.033887132 1 19.43518494 LFCLTLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFCLTLHR 8 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 161.9 0.00034486 250470000 216990 321580 206160 186620 310870 352990 305480 294910 365270 FALSE TRUE 188314.2217 319467.5198 305859.6656 228994.9233 304684.2952 366569.7537 275854.5966 231845.7915 322088.1967 0.584666634 0.99186348 0.949614636 0.710969621 0.945965417 1.138103654 0.856456708 0.719820825 1 18.29709627 LFCVHTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFCVHTK 7 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 62.714 0.083792 250370000 218180 169060 132870 148240 162220 177830 197350 197870 188710 FALSE TRUE 189346.9602 167949.4337 197126.3764 181900.1577 158992.1394 184671.2352 178211.0274 155557.0403 166400.9188 1.137896122 1.009305928 1.184647163 1.09314395 0.955476331 1.109796968 1.070973818 0.934832821 1 17.34430387 1.555700556 0.474583719 0.888724313 1.104531677 0.28437276 0.067823048 5.032130461 1.219268743 0.612689615 0.067834774 35.95013748 -1.555700556 0.215807364 LFDANKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LFDANKDR 8 1 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41;A0A2R8YF08;K7ELR7;K7ENA0;K7ERK8;A0A0J9YXM3;A0A0J9YXH9;K7EIL4;A0A0J9YYI8 P06744 GPI Glucose-6-phosphate isomerase 0 ;;;; 112.84 0.0027025 3756640000 17006280 13621690 7326230 8369170 12477970 11018900 15646440 16601030 4541600 FALSE TRUE 14758857.01 13532208.22 10869219.33 10269517.96 12229682.81 11442804.21 14129050.66 13051028.92 4004697.222 3.685386483 3.379083979 2.71411763 2.564368139 3.053834568 2.857345657 3.528119574 3.258930251 1 21.93326174 1.236298117 24.99615957 0.999997249 3.121027711 0.782740705 0.352660389 29.87247766 329953.7263 0.594441 0.091871929 17.23050939 -1.236298117 2.121030462 LFDDEAS(ph)VDEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 178.22 2.34E-05 608370000 870500 840240 601460 669760 846200 912000 719130 846250 1119290 TRUE FALSE 755461.2194 834720.4081 892328.0678 821839.2446 829362.2756 947085.2301 649388.8833 665286.023 986968.8113 0.765435757 0.845741424 0.904109692 0.832690188 0.840312547 0.959589826 0.657962922 0.674069956 1 19.91264497 2.235580642 24.99887501 0.750854604 0.85756782 0.099420322 0.104731232 131.4773066 1102934.529 0.041027482 0.029018217 172.020673 -2.235580642 0.106713216 LFDDS(ph)DER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LFDDSDER 8 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 LFDDS(1)DER;LFDDS(1)DER;LFDDS(1)DER 135.86 0.0008557 489400000 1112510 891780 851160 1302430 1030350 975810 1001480 1153080 3048010 TRUE FALSE 965488.9848 885921.8385 1262783.823 1598166.638 1009848.051 1013350.042 904356.6237 906502.8153 2687677.73 0.359227959 0.329623537 0.469841979 0.594627332 0.375732566 0.377035547 0.336482538 0.337281068 1 21.35792873 1.23512222 24.99997687 1.000000842 0.396783225 0.846731141 0.080560908 39.92938605 290272.6451 0.15210164 0.021437067 17.18391914 -1.23512222 -0.603217617 LFDEEEDS(ph)SEKLFDDSDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFDEEEDSSEKLFDDSDER 19 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 LFDEEEDS(0.975)S(0.025)EKLFDDSDER 141.53 9.94E-08 43656000 80963 55014 62672 71751 65230 56965 78754 100220 152710 TRUE FALSE 70263.53442 54652.60941 92980.38883 88043.1612 63932.05062 59156.48041 71116.4492 78788.73291 134656.7978 0.521797158 0.405865952 0.690499034 0.653833766 0.474777744 0.43931299 0.528131148 0.585107727 1 17.03892754 1.222532744 3.406047203 1.082327109 0.532238618 0.738931653 0.086953622 0.185939452 2.989890643 0.275880024 0.023423628 16.69293662 -1.222532744 -0.550088491 LFDFPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LFDFPGR 7 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;;; 135.35 0.0071789 607451000 3373640 2500980 1679984 1948661 2436880 2567890 2464670 2820190 2575350 FALSE TRUE 2927804.926 2484550.898 2492429.882 2391134.263 2388390.856 2666678.39 2225646.683 2217114.315 2270895.057 1.289273548 1.094084418 1.097553968 1.052947936 1.051739863 1.174285171 0.980074652 0.976317381 1 21.11482961 8 0.484362041 1.015436159 8.067119884 0.639177117 0.057286228 75.7958671 0.868252155 0.039982761 537.8967493 100000000 -8 7.051683724 LFDFQGLQHQVAHVATQLEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFDFQGLQHQVAHVATQLEAAR 22 0 P45954-2;P45954 P45954-2 ACADSB "Short/branched chain specific acyl-CoA dehydrogenase, mitochondrial" 0 213.2 6.84E-24 78032000 51297 55883 35536 49679 57997 77062 56628 62834 55398 FALSE TRUE 44517.97148 55515.90089 52721.32846 60959.37625 56842.97317 80026.62501 51136.22528 49397.43807 48848.91155 0.911340091 1.13648184 1.079273351 1.247916777 1.163648715 1.638247864 1.046824252 1.011229043 1 15.5760388 5.210774005 1.349332042 1.170682806 0.413247699 0.16395227 0.183184877 8.688720974 5.876420522 0.054741865 12.28514102 162470.3086 -5.210774005 -0.757435107 LFDHPES(ph)PTPNPTEPLFLAQAEVYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LFDHPESPTPNPTEPLFLAQAEVYK 25 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 LFDHPES(0.5)PT(0.5)PNPTEPLFLAQAEVYK;LFDHPES(0.499)PT(0.499)PNPT(0.002)EPLFLAQAEVYK;LFDHPES(0.5)PT(0.5)PNPT(0.001)EPLFLAQAEVYK;LFDHPES(0.5)PT(0.5)PNPTEPLFLAQAEVYK;LFDHPES(0.585)PT(0.415)PNPTEPLFLAQAEVYK;LFDHPES(0.849)PT(0.151)PNPTEPLFLAQAEVYK;LFDHPES(0.587)PT(0.412)PNPTEPLFLAQAEVYK;LFDHPES(0.367)PT(0.341)PNPT(0.292)EPLFLAQAEVYK 375.46 3.50E-120 30824940000 2169559 1812466 1593145.3 1716883.7 1981313 1885400.5 2489221 2693596 2806354 TRUE FALSE 1882846.281 1800559.792 2363595.696 2106728.385 1941888.748 1957933.077 2247816.731 2117591.457 2474590.027 0.760872007 0.727619433 0.955146376 0.851344409 0.784731502 0.791215133 0.908359246 0.855734256 1 21.2387581 -1.30234021 0.744682312 10 0.815931078 0.420486431 0.065979473 123.6230534 1.770723696 1830.528963 0.027020246 0.049849383 1.30234021 -9.184068922 LFDHPESPT(ph)PNPTEPLFLAQAEVYK ddPTM_MDA-MB-175_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(0.432)PT(0.568)PNPTEPLFLAQAEVYK;LFDHPES(0.119)PT(0.881)PNPTEPLFLAQAEVYK;LFDHPES(0.086)PT(0.914)PNPTEPLFLAQAEVYK;LFDHPES(0.151)PT(0.843)PNPT(0.006)EPLFLAQAEVYK;LFDHPES(0.134)PT(0.866)PNPTEPLFLAQAEVYK 340.95 8.10E-88 7376640000 3743620 3296280 2797928 2806250 3525920 3343065 4401750 4638960 4917540 TRUE FALSE 3248891.132 3274626.52 4151015.339 3443451.953 3455761.09 3471674.874 3974868.962 3646954.504 4336194.023 0.749249483 0.755184501 0.95729465 0.794118514 0.79695721 0.800627199 0.916672303 0.841049659 1 22.04799788 -1.342351912 0.735224828 9.999999999 0.813317767 0.431430887 0.064515131 122.7262866 1.689388829 1796.045383 0.025946071 0.045461953 1.342351912 -9.186682232 LFDHPESPTPNPTEPLFLAQAEVYK ddPTM_MDA-MB-175_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 0 ;;;; 310.16 1.81E-74 6291108000 4436729 3932291 2603757 3216317 3975113 3792344 5031734 5232085 5406697 FALSE TRUE 3850404.021 3906459.522 3862942.594 3946630.933 3896016.028 3938237.928 4543757.211 4113244.339 4767523.44 0.807631902 0.819389683 0.810261899 0.827815738 0.817199134 0.826055284 0.953064472 0.862763317 1 22.1848086 -2 0.399357391 3.694978014 0.80428754 0.730089873 0.034254905 42.93953744 0.616923495 96.74176301 0.032746645 0.01 2 -2.890690475 LFDIHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFDIHK 6 0 A0A2R8Y430;P48637;A0A2R8Y5T7;A0A2R8YF34;A0A2R8Y790;A0A2R8Y446;A0A0S2Z4J7 A0A2R8Y430 GSS Glutathione synthetase 0 ; 113.97 0.025682 2425300000 7163100 7745700 4935100 5498500 7504500 6368800 7571600 7544900 9655500 FALSE TRUE 6216478.186 7694817.987 7321730.867 6747018.464 7355175.132 6613811.857 6837307.397 5931481.849 8514037.79 0.730144538 0.903780107 0.859959874 0.79245813 0.863888006 0.776812603 0.803062844 0.696670839 1 23.02141206 2.729776558 24.31241322 0.798494391 0.833716116 0 0.088443863 1837.971292 5087103.773 0.028995457 0.025964631 536.7555674 -2.729776558 0.035221725 LFDQAFGLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LFDQAFGLPR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;; 213.53 4.77E-08 67356134000 21216674 22795742 12061003 15261985 19816041 21035998 22100086 24102828 21326521 FALSE TRUE 18412836.77 22645995.27 17893744.39 18727451.96 19421740.55 21845266.46 19956823.06 18948625.8 18805323.98 0.979128931 1.204233189 0.951525451 0.995859044 1.032778833 1.161653289 1.06123261 1.007620279 1 24.16463783 1.687585628 5.008184651 1.002479198 1.057881871 0.069790907 0.077609492 0.412494992 23.8992585 0.049654871 0.019837393 48.7063548 -1.687585628 0.055402673 LFDSTIADEGTWTLEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFDSTIADEGTWTLEDR 17 0 Q8WVJ2 Q8WVJ2 NUDCD2 NudC domain-containing protein 2 0 150.21 6.88E-07 19876000 16099 12258 7272 10807 12883 14768 11294 14830 14907 FALSE TRUE 13971.47636 12177.47639 10788.76352 13260.89452 12626.65351 15336.13452 10198.70962 11658.71991 13144.71144 1.062897152 0.92641641 0.820768381 1.00883877 0.960588109 1.166715191 0.775879308 0.886951376 1 13.68219485 2.197875511 24.99999523 0.882817752 0.979786746 0.175853691 0.103484974 281.0455587 172693.6573 0.042433008 0.028608696 157.7159119 -2.197875511 0.096968994 LFDSTTLEHQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LFDSTTLEHQK 11 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ;; 185.99 4.22E-06 1380550000 1802410 1580940 981150 1267150 1605830 1488400 1682580 2047250 1892360 FALSE TRUE 1564216.952 1570554.701 1455637.422 1554875.775 1573877.125 1545659.711 1519403.651 1609461.519 1668647.357 0.937416133 0.941214268 0.872345745 0.931818079 0.943205356 0.926295005 0.910560068 0.96453065 1 20.67024766 1.502269174 2.97182209 0.998486013 0.923262502 0.608373364 0.020650968 0.173328816 2.94652876 0.025150936 0.005528579 31.78843696 -1.502269174 -0.075223511 LFDVCGS(ph)QDFESDLDR ddPTM_MDA-MB-175_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(1)QDFESDLDR;LFDVCGS(1)QDFESDLDR 212.95 3.33E-12 66321000 99748 64916 57628 55811 57090 63000 61082 67998 96130 TRUE FALSE 86566.04907 64489.56252 85497.09355 68483.74057 55954.02069 65423.65077 55158.27704 53457.15686 84765.62091 1.021240075 0.760798562 1.008629355 0.807918822 0.660102764 0.771818221 0.650715189 0.630646674 1 16.37119164 3.490984844 6.707831466 0.723818667 0.913111693 0.310312942 0.125035991 0.174864129 37.35570492 0.033706265 0.047255125 3097.311208 -3.490984844 0.189293025 LFDVCGSQDFESDLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LFDVCGSQDFESDLDR 16 0 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494C1B7;E7EN38 Q92878-2 RAD50 DNA repair protein RAD50 0 ;; 198.23 9.60E-11 89337000 71171 61733 46588 54861 59103 60803 58779 69755 95997 FALSE TRUE 61765.57203 61327.47186 69118.11263 67318.02855 57926.96593 63142.13075 53078.62163 54838.43608 84648.34402 0.729672538 0.724497007 0.816532366 0.795266928 0.684324857 0.745934625 0.627048553 0.647838262 1 16.36919422 3.245116407 24.92693275 0.7210771 0.767066844 0 0.105632759 587.5692421 2234085.076 0.030607112 0.038589146 1758.394867 -3.245116407 0.045989744 LFDVSEITSAAMVHSLPTAVPES(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LFDVSEITSAAMVHSLPTAVPESPR 25 0 A0A3B3ISF0;Q659C4;Q659C4-9;Q659C4-2;D6RJB0 A0A3B3ISF0 LARP1B La-related protein 1B 1 LFDVSEITSAAMVHSLPTAVPES(1)PR;LFDVSEITSAAMVHSLPTAVPES(1)PR;LFDVSEITSAAMVHSLPT(0.002)AVPES(0.998)PR 281.19 1.78E-53 646900000 539542 607442 313401 411771 608074 570983 612338 707164 389353 TRUE FALSE 468240.1577 603451.6735 464962.7719 505269.8991 595974.5171 592949.0855 552953.555 555942.4818 343324.1319 1.363842836 1.75767334 1.354296796 1.471699342 1.735894631 1.727082458 1.610587499 1.619293344 1 18.38921174 1.236702407 24.99045669 0.999999257 1.58789311 0.611276887 0.145247395 32.44755999 436251.8418 0.217377254 0.034587606 17.24655694 -1.236702407 0.587893853 LFEAEAQDLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LFEAEAQDLFR 11 0 Q9H223 Q9H223 EHD4 EH domain-containing protein 4 0 ;;;;; 195.27 3.46E-07 438138000 563443 565318 380985 423674 546044 571952 550972 619770 601991 FALSE TRUE 488982.58 561604.3888 565230.6203 519875.6572 535178.7927 593955.3635 497538.8202 487237.0086 530824.3098 0.921175935 1.057985436 1.064816757 0.979374244 1.008203247 1.118930223 0.937294715 0.917887519 1 19.01787492 LFEAEEQDLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LFEAEEQDLFR 11 0 Q9NZN3 Q9NZN3 EHD3 EH domain-containing protein 3 0 ;; 89.548 0.028268 47733000 51172 61662 34149 43935 53258 55120 54536 57216 66879 FALSE TRUE 44409.49055 61256.93826 50663.57062 53911.11325 52198.27 57240.50207 49247.10711 44980.80366 58972.64081 0.753052431 1.038734868 0.859102966 0.914171597 0.885126887 0.970628096 0.835083972 0.762740197 1 15.84775818 2.193182211 24.95685507 0.843155298 0.907254098 0.014619885 0.093731069 298.9953256 164436.9604 0.035686147 0.024059715 156.0206959 -2.193182211 0.0640988 LFEASIETGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFEASIETGDR 11 0 P28838-2;P28838;H0Y9Q1 P28838-2 LAP3 Cytosol aminopeptidase 0 108.67 0.0030213 0 72109 79557 50671 58873 76617 81960 60653 85950 88298 FALSE TRUE 62579.61295 79034.38483 75175.66508 72241.01447 75092.4716 85113.05424 54770.8814 67570.26136 77859.51103 0.803750398 1.015089663 0.965529633 0.927838019 0.964461125 1.093161941 0.703457814 0.867848519 1 16.24858566 2.244678991 24.99999998 0.852939104 0.962836827 0.194169771 0.100250916 221.0943992 903407.067 0.036966767 0.027887066 175.6624723 -2.244678991 0.109897723 LFEAVEEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFEAVEEGR 9 0 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 0 ; 95.741 0.018238 69289000 134823 120649 100659 119227 122024 122779 114815 120300 163550 FALSE TRUE 117005.799 119856.4488 149338.0291 146299.3126 119595.9611 127502.3876 103680.259 94574.78118 144215.3053 0.811327194 0.831093818 1.03552136 1.014450667 0.829287577 0.884111345 0.718926876 0.655788794 1 17.13786476 2.34232456 5.08831317 0.76078054 0.908329821 0.150499587 0.115123762 0.295743737 12.17021927 0.045215231 0.034407427 219.9503008 -2.34232456 0.147549282 LFECDRDQMYYNLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFECDRDQMYYNLLK 15 1 P42704 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 232.17 8.72E-14 497250000 178280 206910 135370 221840 222040 194530 218060 299910 173790 FALSE TRUE 154719.8463 205550.7946 200835.3848 272212.1626 217621.8384 202013.695 196912.5748 235776.5804 153244.7442 1.009625793 1.341323617 1.310553167 1.776322993 1.420093326 1.318242241 1.284954834 1.538562263 1 17.22547807 4.809043136 2.215741012 1.400280931 0.861820628 0.249718909 0.196873261 1.118781727 5.395640968 0.049401715 1.264400935 64423.32504 -4.809043136 -0.538460303 LFEDDDS(ph)NEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFEDDDSNEK 10 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 LFEDDDS(1)NEK;LFEDDDS(1)NEK 132.86 0.00022294 265670000 1154940 712210 859840 1133860 813500 691270 1002850 1050650 3391700 TRUE FALSE 1002311.753 707531.4456 1275661.5 1391320.243 797312.9416 717863.6042 905593.7614 825976.6737 2990737.09 0.335138704 0.236574271 0.426537493 0.465209813 0.266594126 0.24002899 0.302799522 0.276178296 1 21.51206966 1.236470366 24.99983709 1.000000872 0.317206063 0.889832459 0.075343868 18.00438115 215281.3474 0.124394236 0.019438278 17.23734468 -1.236470366 -0.68279481 LFEDDDS(ph)NEKLFDEEEDSSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFEDDDSNEKLFDEEEDSSEK 21 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 LFEDDDS(1)NEKLFDEEEDSSEK;LFEDDDS(1)NEKLFDEEEDSSEK 280.36 3.47E-45 201744000 276530 184746 275650 247838 187910 132230 266398 335700 516650 TRUE FALSE 239985.8599 183532.3914 408955.262 304113.4059 184170.9586 137316.9737 240562.763 263913.1674 455572.2256 0.526778953 0.402861239 0.897673824 0.667541586 0.404262921 0.301416474 0.528045279 0.579300389 1 18.79732027 1.228825453 3.772140382 1.064210322 0.534342267 0.444910681 0.162762478 0.290883687 6.586059609 0.441209038 0.04398476 16.93656966 -1.228825453 -0.529868055 LFEDDDS(ph)NEKLFDEEEDSSEKLFDDSDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFEDDDSNEKLFDEEEDSSEKLFDDSDER 29 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 LFEDDDS(1)NEKLFDEEEDSSEKLFDDSDER 105.48 0.00026278 22951000 48966 34664 31550 24358 37849 20197 45679 58453 20125 TRUE FALSE 42495.01904 34436.2899 46807.68553 29888.85619 37095.87895 20973.99166 41249.05761 45953.28083 17745.84543 2.394646072 1.940526871 2.63767008 1.684273444 2.090397953 1.181909971 2.324434628 2.589523335 1 14.11519369 3.726395223 24.87575213 1.910182767 2.28590562 0.165700402 0.508842262 1656.922375 3388068.713 0.142318949 0.21291247 5325.927164 -3.726395223 0.375722853 LFEELAMDVYDEVDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFEELAMDVYDEVDRR 16 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 0 77.754 0.024181 21421000 12321 11227 9052.8 8486.6 10944 14070 12084 12533 12418 FALSE TRUE 10692.74863 11153.2491 13430.76436 10413.61224 10726.23581 14611.282 10912.09554 9852.915482 10949.95819 0.976510453 1.018565451 1.226558507 0.951018448 0.979568655 1.334368749 0.996542211 0.899813069 1 13.41863774 2.008561724 24.9988727 0.944378465 1.081933021 0.175174282 0.121319877 289.2247053 844486.5471 0.049046777 0.033010654 101.9909705 -2.008561724 0.137554556 LFEELGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFEELGK 7 0 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 121.52 0.010306 101638000 243582 206674 156521 182248 219461 200334 236526 272846 251631 FALSE TRUE 211392.0215 205316.3449 232215.0791 223630.1939 215094.1555 208040.9786 213587.7449 214500.0062 221883.4698 0.952716404 0.925334118 1.046563222 1.007872259 0.969401441 0.937613689 0.962612245 0.966723688 1 17.75944267 LFEES(ph)DDKEDEDADGKEVEDADEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LFEESDDKEDEDADGKEVEDADEK 24 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 LFEES(1)DDKEDEDADGKEVEDADEK;LFEES(1)DDKEDEDADGKEVEDADEK;LFEES(1)DDKEDEDADGKEVEDADEK 148.3 8.53E-08 427038000 516375 230470 530510 350975 217647 192337 414229 479006 863060 TRUE FALSE 448134.7354 228956.0274 787066.4104 430669.2381 213316.2505 199736.3288 374057.1353 376574.2945 761030.03 0.588852894 0.300850188 1.034212028 0.56590308 0.280299387 0.262455253 0.491514291 0.494821859 1 19.53759386 1.238242613 24.8377098 1.00000061 0.499373436 0.332329842 0.221636018 8.804322197 686474.5491 0.312521479 0.055062246 17.30782969 -1.238242613 -0.500627174 LFEFAGYDVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFEFAGYDVLR 11 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 155.06 7.38E-05 196750000 196290 157870 123980 121640 127800 150760 167690 158330 140450 FALSE TRUE 170349.7792 156832.9416 183937.1427 149260.2212 125257.03 156559.8348 151427.4496 124472.3616 123846.161 1.375495032 1.266352871 1.485206656 1.205206685 1.01139211 1.264147661 1.222706044 1.005056278 1 16.91818962 -0.554318042 0.125862683 6.69E-12 1.647853077 0.542022589 0.109269542 104.0176931 1.765284138 30.4722145 4.122976197 0.279049956 0.554318042 1.647853077 LFEGNALLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LFEGNALLR 9 0 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 ;;; 129.29 0.00091533 1589086000 1602294 1924048 1099955 1154191 1779770 1609919 1809255 1975780 1788240 FALSE TRUE 1390546.788 1911408.802 1631896.917 1416267.707 1744356.059 1671853.626 1633793.729 1553274.823 1576836.304 0.881858684 1.212179601 1.034918408 0.898170408 1.106237885 1.060258202 1.03612133 0.98505775 1 20.58860147 1.766946461 6.991968916 0.99290441 1.03858679 0.027959879 0.094042255 0.607187625 84.12715606 0.049782201 0.023386836 58.47179969 -1.766946461 0.04568238 LFENLR ddPTM_MDA-MB-175_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 ;;;;;; 159.42 0.02122 2683069000 3119908 2977477 2011742 2318111 2848214 2748262 2609649 2936541 3644268 FALSE TRUE 2707604.253 2957917.758 2984627.16 2844473.533 2791540.114 2853989.418 2356565.642 2308584.559 3213446.789 0.842585682 0.920481325 0.928793086 0.885178352 0.868705878 0.888139622 0.733345158 0.718413813 1 21.61569015 2.284784637 14.33477642 0.793173508 0.891144428 0.129808652 0.079672769 2.602585578 805.6656327 0.029468424 0.022816669 192.6569309 -2.284784637 0.09797092 LFFAGEHTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFFAGEHTIR 10 0 R4GMQ1;O60341;O60341-2;R4GMP9 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 201.33 2.44E-07 535280000 596770 519060 347660 393150 575980 542500 553660 625990 542120 FALSE TRUE 517905.3325 515650.2607 515789.5389 482420.7164 564519.1249 563370.326 499966.1384 492126.91 478031.1912 1.083413263 1.078695847 1.078987205 1.009182508 1.180925294 1.178522106 1.045886017 1.029487027 1 18.86674523 2.015048741 24.99289093 1.023100749 1.100057412 0.349427007 0.050228697 280.9750639 466640.1165 0.021902927 0.014761267 103.5258346 -2.015048741 0.076956663 LFFDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFFDKR 6 1 O15371-2;O15371;O15371-3;B0QYA4 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ; 106.29 0.051713 1056170000 1827630 1961570 1580700 1391860 1831910 1652710 2003440 2207410 1469180 FALSE TRUE 1586104.065 1948684.318 2345131.807 1707903.086 1795458.575 1716290.823 1809146.697 1735372.55 1295495.214 1.224322597 1.504200321 1.810220356 1.318339943 1.385924514 1.324814484 1.396490452 1.339543775 1 20.30507226 0.654010712 1.098874857 9.41E-18 1.445098853 0.417565425 0.156081693 5.750857345 2.240445854 13.32181361 0.050630274 4.508278246 -0.654010712 1.445098853 LFFHCSQYNGNLQDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFFHCSQYNGNLQDLK 16 0 O75534-2;O75534;O75534-3;O75534-4;E9PLD4 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 149.22 8.57E-07 408390000 330870 231160 185170 217230 272070 253200 316780 317880 372390 FALSE TRUE 287144.6912 229641.4947 274718.8314 266555.3917 266656.3393 262940.7678 286058.7244 249903.8357 328366.4784 0.874464082 0.699345121 0.836622644 0.811761885 0.812069309 0.80075399 0.871156903 0.761051606 1 18.32494733 1.230225259 24.99705537 1.000000359 0.806579447 0.582753697 0.050929247 211.1440976 633153.7594 0.125969185 0.011304687 16.99124724 -1.230225259 -0.193420912 LFFLQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFFLQVK 7 0 P15311;E7EQR4;V9GZ54;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P26038;P35241-3;A0A2R8Y5P0;E9PNV3;E9PQ82 P15311;A0A2R8Y5S7 EZR;MSN;RDX Ezrin;Radixin;Moesin 0 135.36 0.019598 0 117640 151570 98170 119930 148460 118110 157050 165750 163520 FALSE TRUE 102093.5759 150574.3267 145645.3404 147161.9395 145505.9365 122653.7681 141819.3152 130305.6524 144188.8519 0.708054573 1.044285496 1.010101256 1.0206194 1.009134441 0.85064668 0.983566436 0.903715167 1 17.1376001 4.74852263 24.68390854 0.971604561 0.708054401 0.676569145 0.058466167 752.4395988 1864351.997 0.014771397 0.191854816 56043.16187 -4.74852263 -0.263550161 LFGDEAAEQWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFGDEAAEQWR 11 0 Q2T9J0-2;Q2T9J0 Q2T9J0-2 TYSND1 "Peroxisomal leader peptide-processing protease;Peroxisomal leader peptide-processing protease, 15 kDa form;Peroxisomal leader peptide-processing protease, 45 kDa form" 0 136.96 0.00020556 50369000 58390 40906 30367 38440 43058 48014 36808 51752 53391 FALSE TRUE 50673.61356 40637.28579 45052.58277 47168.38952 42201.23004 49861.12965 33238.36583 40685.23753 47079.1768 1.07634876 0.863168996 0.956953495 1.001894951 0.896388444 1.059090941 0.70600992 0.86418753 1 15.52280147 2.256283386 24.9973435 0.852005421 0.967270094 0.255778422 0.094787098 320.5919582 452182.9297 0.033922787 0.026217553 180.419463 -2.256283386 0.115264673 LFGPYVWGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFGPYVWGR 9 0 Q9H4A4;C9JMZ3;H7C2T3 Q9H4A4 RNPEP Aminopeptidase B 0 ; 170.31 0.00013447 1065830000 408720 347960 312920 339440 409630 374710 389680 415110 479620 FALSE TRUE 354706.6164 345674.2278 464249.1587 416515.04 401479.1644 389125.3362 351888.8936 326341.9569 422919.87 0.838708799 0.817351589 1.097723686 0.984855689 0.949303149 0.920092348 0.832046254 0.771640162 1 18.69002482 2.342494278 4.641642443 0.846628863 0.941634569 0.08550124 0.095322986 0.39235824 14.35432704 0.038151232 0.028854051 220.0362718 -2.342494278 0.095005706 LFGT(ph)SPATEAAPPPPEPVPAAEGPATVQSVEDFVPDDRLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFGTSPATEAAPPPPEPVPAAEGPATVQSVEDFVPDDRLDR 41 1 Q3YEC7;Q3YEC7-2;G3V154;F2Z2T0 Q3YEC7 RABL6 Rab-like protein 6 1 LFGT(0.458)S(0.428)PAT(0.115)EAAPPPPEPVPAAEGPATVQSVEDFVPDDRLDR 50.645 0.044629 143670000 111000 121850 105700 124630 200110 216070 203150 233580 160430 TRUE FALSE 96331.06876 121049.5593 156816.8735 152929.1464 196128.2025 224382.3527 183448.5443 183630.7347 141464.1482 0.680957472 0.855690724 1.108527324 1.081045257 1.386416312 1.586142889 1.296784709 1.298072601 1 17.11007695 4.21232361 1.139636578 1.312734731 0.621900426 0.663185196 0.15291623 0.47436825 0.921577251 0.05213231 0.320357329 16305.1054 -4.21232361 -0.690834304 LFHEVVQAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFHEVVQAFR 10 0 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 0 162.64 6.71E-06 212750000 137900 128180 72379 75502 113280 120990 91334 113000 105510 FALSE TRUE 119676.1656 127337.9771 107381.7265 92645.88308 111025.9496 125644.5636 82476.44274 88835.82937 93036.728 1.286332486 1.368685033 1.154186404 0.995799026 1.19335613 1.350483474 0.886493372 0.954846879 1 16.50551274 1.834199357 0.078971867 5.66E-10 2.044432191 0.418278072 0.129500834 101.8106074 3.342462096 52.69180223 34.66209342 68.26519836 -1.834199357 2.044432191 LFHTAPNVPHYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFHTAPNVPHYAK 13 0 P53582;H0Y955 P53582 METAP1 Methionine aminopeptidase 1 0 146.36 2.44E-05 675030000 475870 428010 261530 352370 404530 367740 463910 472060 480870 FALSE TRUE 412982.5738 425198.3741 388006.7828 432380.9941 396480.6444 381887.1958 418920.0796 371113.6426 424022.0964 0.973964747 1.002774095 0.915062649 1.019713354 0.93504713 0.900630413 0.987967569 0.875222413 1 18.69377992 3.053416934 24.96763696 0.933174673 0.975446474 0.140788372 0.045018806 156.1949868 73005.93433 0.012603928 0.01429151 1130.881069 -3.053416934 0.042271801 LFIFETFCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFIFETFCR 9 0 P60228;E5RGA2;E5RHS5 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 ; 151.04 0.00019499 228510000 296840 341350 225240 221740 289810 276730 324950 331090 322650 FALSE TRUE 257611.8419 339107.6494 334166.8174 272089.4561 284043.348 287375.9822 293436.399 260288.98 284506.6846 0.905468503 1.191914524 1.174548211 0.956355231 0.998371439 1.010085168 1.03138666 0.914878258 1 18.11810302 3.723661313 24.94650418 0.982331768 1.100770827 0.264510554 0.082235507 891.3122625 1492359.725 0.021973788 0.032740928 5292.505441 -3.723661313 0.118439059 LFIGGLS(ph)FETTDDSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LFIGGLSFETTDDSLR 16 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 1 LFIGGLS(0.968)FET(0.012)T(0.02)DDSLR;LFIGGLS(1)FETTDDSLR;LFIGGLS(1)FETTDDSLR;LFIGGLS(1)FETTDDSLR;LFIGGLS(1)FETTDDSLR 160.81 9.08E-09 100814000 106419 70318.6 29813.9 92727 62080 43068.6 71703.6 87203.8 83303.3 TRUE FALSE 92355.45952 69856.67249 44232.00176 113782.0826 60844.72946 44725.47691 64749.79591 68555.94599 73455.27877 1.257301872 0.951009562 0.602162329 1.548998037 0.828323444 0.608880364 0.881485946 0.933301828 1 16.16457855 LFIGGLS(ph)FETTDESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LFIGGLSFETTDESLR 16 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;F8W646 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 1 LFIGGLS(0.974)FET(0.021)T(0.005)DESLR;LFIGGLS(0.994)FET(0.003)T(0.003)DESLR;LFIGGLS(1)FETTDESLR 211.57 1.37E-12 43719000 82373 63786 24982.6 59406 55969 43974.3 60647 79502 58867 TRUE FALSE 71487.19934 63366.98557 37064.26892 72895.04026 54855.3264 45666.01978 54765.46327 62501.11599 51907.81032 1.377195434 1.220760136 0.714040309 1.404317381 1.056783672 0.879752382 1.055052466 1.204079224 1 15.66366401 4.47168788 24.99933929 1.06035023 1.338086748 0.269511735 0.181576429 160.7335481 739550.003 0.043479326 0.115837054 29627.0138 -4.47168788 0.277736518 LFIGGLS(ph)FETTEESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LFIGGLSFETTEESLR 16 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 LFIGGLS(0.996)FET(0.003)T(0.001)EESLR;LFIGGLS(1)FETTEESLR;LFIGGLS(1)FETTEESLR;LFIGGLS(1)FETTEESLR;LFIGGLS(0.999)FET(0.001)TEESLR 183.7 2.04E-09 219524600 201111 112340 62979.8 139111 93224.3 78661 107472.4 132123 135165 TRUE FALSE 174533.6718 111602.0311 93437.04193 170698.2787 91369.31882 81687.13957 97049.74319 103869.5246 119185.9477 1.46438129 0.936369038 0.783960221 1.43220138 0.766611506 0.685375593 0.814271691 0.871491368 1 16.86285462 3.185376168 24.99990842 0.824937713 1.112223028 0.353421095 0.216253661 118.1554868 55539.62103 0.064320898 0.072933108 1532.414203 -3.185376168 0.287285315 LFIGGLSFETTDDSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LFIGGLSFETTDDSLR 16 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 283.35 2.82E-35 709190000 348405 311347 207284 255460 335669 294639 289306 327674 363905 FALSE TRUE 302362.3965 309301.7411 307527.2357 313466.0975 328989.8436 305973.953 261249.1486 257603.4651 320884.5655 0.942277782 0.963903454 0.958373412 0.976881194 1.025259171 0.953532784 0.814153053 0.802791698 1 18.29169487 2.34158875 6.068155521 0.855931953 0.973601202 0.38626081 0.057172189 0.178405082 9.065887478 0.021589201 0.016564029 219.5779622 -2.34158875 0.117669249 LFIGGLSFETTDESLR ddPTM_MDA-MB-175_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" 0 ;;; 273.04 7.95E-35 702024000 317182.2 302134.9 190577.7 244193.8 284656.8 288951 317932.2 334905.8 297681.5 FALSE TRUE 275265.7686 300150.1559 282741.7132 299641.7346 278992.6866 300067.1319 287099.1842 263288.8009 262489.9322 1.04867172 1.143473022 1.077152601 1.141536104 1.062870047 1.143156728 1.093753127 1.003043426 1 18.00190256 1.746445914 4.232310154 0.999809865 1.104536465 0.608836586 0.033352574 0.104424252 4.127806123 0.019002286 0.007888465 55.77581356 -1.746445914 0.1047266 LFIGGLSFETTEESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LFIGGLSFETTEESLR 16 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;; 270.02 6.03E-28 1199600000 274164 215038 136065.7 162122 203281 223710 219069 222351 225294 FALSE TRUE 237932.5328 213625.4012 201867.5276 198934.278 199236.1058 232316.2685 197823.7221 174802.969 198660 1.197687168 1.075331729 1.016145815 1.00138064 1.002899959 1.169416433 0.995790406 0.879910244 1 17.59994189 8 0.536042949 0.985722908 9.217412087 0.417689869 0.069860472 143.7903252 1.408289434 0.043269612 1352.97331 100000000 -8 8.231689179 LFIHESIHDEVVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFIHESIHDEVVNR 14 0 P49419;P49419-2;A0A1B0GW77;A0A1B0GW82;A0A1B0GTG2;A0A1B0GUA1;A0A1B0GV49;A0A1B0GTJ4;A0A1B0GUY0 P49419 ALDH7A1 Alpha-aminoadipic semialdehyde dehydrogenase 0 ; 219.89 2.80E-12 159302000 180133 186460 83052 128553 206068 198078 185533 208719 220209 FALSE TRUE 156327.9677 185235.132 123216.225 157742.9235 201967.65 205698.1888 167540.0382 164086.0661 194176.1429 0.805083288 0.953954122 0.634559031 0.812370259 1.040125975 1.059338113 0.86282504 0.84503721 1 17.56700643 3.34829378 8.489051382 0.944186815 0.798850675 0.373321949 0.101737912 0.324565387 23.20900097 0.031049539 0.040090302 2229.943092 -3.34829378 -0.14533614 LFIVDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LFIVDAR 7 0 Q9UNZ2;Q9UNZ2-5;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ;; 104.11 0.019134 669583000 1909970 2007490 1464870 1486990 1811000 2083030 1693600 2050060 2569190 FALSE TRUE 1657562.625 1994302.666 2173286.032 1824633.807 1774964.643 2163165.512 1529354.933 1611670.623 2265463.285 0.731666073 0.88030677 0.959311963 0.8054131 0.783488594 0.954844656 0.675073811 0.711408847 1 21.11137468 2.236997856 24.99942274 0.772958943 0.853346076 0.043569967 0.11013066 97.81901555 1564751.717 0.042861506 0.030637703 172.5829374 -2.236997856 0.080387133 LFKDDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFKDDIR 7 1 Q9UBT2;Q9UBT2-2;K7EPL2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 64.836 0.065862 406740000 2038700 1663900 944020 1144200 1689100 1532400 1895400 2135200 718080 FALSE TRUE 1769280.63 1652969.731 1400551.23 1404008.098 1655490.215 1591352.42 1711584.4 1678604.096 633189.4004 2.794236019 2.610545486 2.21189936 2.217358814 2.614526102 2.513232879 2.703116001 2.65103 1 19.27227758 1.235949626 24.99976964 0.999997969 2.535831807 0.865747998 0.190517018 26.60670392 254701.6069 0.333912058 0.050232492 17.21668865 -1.235949626 1.535833837 LFLEFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LFLEFER 7 0 O43663-2;O43663-4;O43663;O43663-3;H0YL53 O43663-2 PRC1 Protein regulator of cytokinesis 1 0 ;; 167.82 0.0024937 241480000 401472 380112 254760 290271 388631 415952 367123 428377 425394 FALSE TRUE 348416.458 377615.0192 377962.7881 356181.4671 380898.0034 431953.9426 331519.468 336771.9122 375104.4059 0.928851948 1.006693105 1.007620231 0.949552875 1.015445293 1.151556569 0.883805849 0.897808468 1 18.51693268 LFNAIIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFNAIIHR 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8;E9PKG0 Q15149-3;Q15149-4;Q15149-5;Q15149-8;E9PKG0 PLEC Plectin 0 ; 146.54 0.00055165 1790620000 1340170 1688400 1032070 1106060 1674530 1803930 1593310 1627350 1660460 FALSE TRUE 1163063.139 1677308.789 1531182.504 1357207.828 1641210.129 1873328.354 1438791.041 1279353.867 1464162.31 0.794353967 1.145575717 1.045773746 0.926951758 1.120920896 1.27945402 0.982671819 0.873778718 1 20.48164406 2.006021388 24.99465111 0.92797903 1.060018253 0.118173208 0.131568771 264.521109 1098015.986 0.053224831 0.035775597 101.3961319 -2.006021388 0.132039222 LFNHANQEVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LFNHANQEVQR 11 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ;;; 181.68 6.12E-06 1878970000 838890 1029470 601570 717730 1012010 1070230 949590 1055000 969590 FALSE TRUE 728028.561 1022707.344 892491.2641 880701.5663 991872.981 1111402.441 857498.908 829396.46 854966.1748 0.851529081 1.196196264 1.04389073 1.030101064 1.160131255 1.299937323 1.002962378 0.970092718 1 19.70550782 2.028931871 24.99972112 0.983995056 1.103274013 0.153921706 0.117022955 335.3415814 289763.6747 0.046710187 0.031491472 106.8887187 -2.028931871 0.119278957 LFNHLSAVSESIQALGWVAMAPK ddPTM_MDA-MB-175_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 86.546 0.00013746 0 99364 109010 44325 81280 105910 100960 102750 129550 213290 FALSE TRUE 86232.79564 108293.9061 65760.71826 99735.86629 103802.5982 104843.9965 92785.32081 101846.7407 188075.0992 0.458501928 0.575801404 0.349651382 0.530298092 0.551921007 0.557458148 0.493341868 0.541521664 1 17.52094933 1.233793312 4.37243591 1.047209821 0.505515022 0.853942185 0.064215877 0.07626089 2.909361963 0.130483817 0.015695712 17.131418 -1.233793312 -0.541694799 LFNVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LFNVDR 6 0 P25788-2;P25788 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;;;;; 168.82 0.014504 2392840000 5282730 4809040 2938770 3308200 4619530 4825670 4620290 5219230 5034300 FALSE TRUE 4584603.846 4777449.1 4359969.002 4059377.373 4527610.391 5011316.648 4172214.987 4103138.281 4439150.789 1.032765964 1.076207889 0.982162852 0.914449084 1.019927145 1.128890836 0.939867823 0.92430703 1 22.08185228 2.555361861 0.016533065 0.000213582 1.980662755 0.077031032 0.064712769 2693.118081 39.00978823 2375.039727 2295.960611 359.2211186 -2.555361861 1.980449173 LFNYHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFNYHK 6 0 P04181 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 ; 91.26 0.048095 1301490000 1361540 1617250 1117660 1980980 2068220 1833990 1662570 2020790 2115650 FALSE TRUE 1181609.039 1606626.178 1658164.114 2430791.786 2027066.468 1904544.782 1501334.217 1588659.784 1865540.267 0.633387046 0.861212275 0.888838554 1.30299615 1.086584141 1.020907892 0.80477181 0.85158161 1 20.83116207 4.609858611 1.990963257 0.986634522 0.586907008 0.417977779 0.137494392 0.661857128 3.490636309 0.041229093 0.438468506 40724.76726 -4.609858611 -0.399727513 LFPADTS(ph)PSTATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LFPADTSPSTATK 13 0 Q6NZY4;Q6NZY4-2 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 LFPADT(0.052)S(0.946)PS(0.002)TATK;LFPADT(0.006)S(0.993)PS(0.001)TATK;LFPADT(0.017)S(0.978)PS(0.005)TATK 223.03 1.73E-11 515087000 2261490 1606940 1002030 1292200 1474280 1240250 1658000 2031710 1706710 TRUE FALSE 1962628.367 1596383.905 1486615.06 1585613.76 1444944.712 1287963.22 1497207.415 1597244.627 1504944.688 1.304119934 1.060759188 0.987820397 1.053602682 0.960131441 0.855820968 0.994858766 1.061331117 1 20.52127903 4.807731789 2.007289382 0.990166094 1.435019365 0.757715567 0.05606281 0.503705208 1.89236886 0.016193321 0.436878899 64229.09297 -4.807731789 0.444853271 LFPDIPIGYSGHETGIAISVAAVALGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LFPDIPIGYSGHETGIAISVAAVALGAK 28 0 Q9NR45;Q5TBR0;Q5TBR1 Q9NR45 NANS Sialic acid synthase 0 ;; 283.93 5.77E-62 716080000 573610 610360 237242 465713 589950 478790 670010 757610 743830 FALSE TRUE 497805.9852 606350.505 351973.0247 571460.2546 578211.1492 497209.3611 605032.5333 595600.9972 655895.2648 0.758971763 0.924462391 0.536629922 0.871267541 0.881560182 0.758062129 0.922452967 0.90807333 1 19.32310593 1.110707428 0.511155623 1.184098012 0.767733632 0.32383371 0.106927583 6.420827971 1.244431884 1.677836964 0.079218849 12.90349708 -1.110707428 -0.416364379 LFPDT(ph)PLALDANK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LFPDTPLALDANK 13 0 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 LFPDT(1)PLALDANK;LFPDT(1)PLALDANK;LFPDT(1)PLALDANK;LFPDT(1)PLALDANK 217.2 2.93E-10 803436000 2669130 2292480 1709040 2086580 2113040 1761400 2513640 3110040 3008240 TRUE FALSE 2316397.708 2277420.548 2535537.46 2560369.88 2070994.638 1829162.198 2269867.58 2444982.148 2652609.294 0.873252504 0.85855861 0.955865406 0.965226913 0.780738665 0.689570907 0.855711237 0.921727204 1 21.33898076 1.473228879 2.755835977 0.998745543 0.853879894 0.270075744 0.078680171 0.453601388 6.104704033 0.123963825 0.023253269 29.73232551 -1.473228879 -0.144865649 LFPDT(ph)PLALDANKK ddPTM_MDA-MB-175_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 136.35 1.62E-05 674950000 1037800 768920 675080 744380 660450 512380 915540 1368700 985630 TRUE FALSE 900652.1005 763868.9139 1001550.946 913402.8561 647308.3371 532091.5902 826751.0717 1076014.156 869109.9442 1.036292481 0.878909416 1.152386936 1.050963531 0.744794535 0.612225868 0.951261779 1.238064486 1 19.72917917 1.89595669 7.227777786 1.127313874 0.909595489 0.209789382 0.163340818 0.392469056 23.9381417 0.085080704 0.046639235 78.69673048 -1.89595669 -0.217718385 LFPEFDDS(ph)DYDEVPEEGPGAPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFPEFDDSDYDEVPEEGPGAPAR 23 0 Q96P48-3;Q96P48 Q96P48-3 ARAP1 "Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1" 1 LFPEFDDS(0.911)DY(0.089)DEVPEEGPGAPAR;LFPEFDDS(0.537)DY(0.463)DEVPEEGPGAPAR 114.72 0.00041372 105277000 100381 94698 52660 70540 92535 87867 79172 94248 97490 TRUE FALSE 87115.39652 94075.9226 78126.55214 86557.18514 90693.73454 91247.30035 71493.91163 74093.79864 85964.84326 1.013383998 1.094353448 0.908819806 1.006890513 1.055009596 1.06144904 0.831664538 0.861908146 1 16.39145915 2.242855335 24.99992157 0.887610052 1.022036032 0.454360408 0.064476201 89.70561102 522187.9988 0.024761648 0.018491566 174.9263907 -2.242855335 0.13442598 LFPHCGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFPHCGR 7 0 J3QL14;R4GN72;F5GYQ1;P61421 J3QL14 ATP6V0D1 V-type proton ATPase subunit d 1 0 118.06 0.0050921 312200000 459100 432940 297320 311680 439750 541250 376570 516140 453670 FALSE TRUE 398428.7718 430095.9886 441104.9465 382451.7077 430999.8354 562072.2377 340050.2994 405767.4776 400037.6494 0.995978184 1.075138776 1.10265858 0.956039284 1.07739818 1.405048346 0.850045739 1.014323222 1 18.60977626 LFPLIQAMHPTLAGK ddPTM_MDA-MB-175_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 0 128.95 6.89E-05 238990000 335790 304780 118140 229530 289930 262990 314420 361010 452130 FALSE TRUE 291414.5007 302777.8801 175272.8992 281648.2946 284160.9602 273107.3955 283927.5968 283810.8209 398679.7065 0.73094892 0.759451447 0.439633361 0.706452548 0.712755015 0.685029589 0.712169675 0.711876768 1 18.60487065 -0.079553905 1.327176746 10 0.670442132 0.562440643 0.088257141 30.39006362 2.312147166 786.5422805 0.025773357 0.832618574 0.079553905 -9.329557868 LFQCLLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFQCLLHR 8 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 203.57 9.45E-05 4479100000 1876770 2706500 1520950 1496560 2628500 2735200 2337000 2627600 2341700 FALSE TRUE 1628750.089 2688720.823 2256486.507 1836376.821 2576197.993 2840424.914 2110358.1 2065708.188 2064866.894 0.788791808 1.302127915 1.092799983 0.889343922 1.247633928 1.375597101 1.02203106 1.000407433 1 20.97761735 2.02994437 24.99957408 1.003528243 1.125767392 0.077105263 0.176045136 484.9613424 404876.3703 0.070902122 0.047801615 107.1382061 -2.02994437 0.122239149 LFQECCPHSTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LFQECCPHSTDR 12 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;; 225.79 1.68E-11 41911500000 9196150 8784080 3131038 4616884 8052650 8223310 7617960 8685480 4143234 FALSE TRUE 7980855.477 8726376.8 4645218.449 5665218.077 7892418.02 8539666.057 6879171.412 6828157.692 3653425.597 2.184485565 2.388546467 1.27146929 1.550659218 2.160278843 2.337440802 1.882937323 1.868974066 1 21.8008184 1.204276671 3.202135757 0.784420424 1.959281472 0.434088287 0.344188909 0.440517601 5.619600443 1.373572776 0.093603687 16.00577365 -1.204276671 1.174861048 LFQEDPEAFLLYHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFQEDPEAFLLYHR 14 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 0 ; 157.38 5.31E-06 110110000 156890 157381 93999 113151 159297 161543 132635 178543 158915 FALSE TRUE 136156.589 156347.1538 139457.2308 138843.664 156127.3014 167757.6637 119772.0781 140362.9689 140128.2497 0.971656959 1.115743286 0.995211394 0.990832785 1.114174349 1.197172334 0.85473185 1.001675031 1 17.09638831 2.227788376 24.99997981 0.958397892 1.062287974 0.308531542 0.078819698 281.7431044 653857.1039 0.031992659 0.021815542 168.9617411 -2.227788376 0.103890082 LFQLGPPS(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LFQLGPPSPVK 11 0 Q9NZH5-2;Q9NZH5;O95997 Q9NZH5-2 PTTG2;PTTG1 Securin-2;Securin 1 LFQLGPPS(1)PVK;LFQLGPPS(1)PVK;LFQLGPPS(1)PVK 139.3 4.16E-05 1333498000 1918528 1865111 1289193 1733735 1862253 1494977 1961646 2387043 2954349 TRUE FALSE 1664989.664 1852858.963 1912651.047 2127406.03 1825197.809 1552489.733 1771405.873 1876592.43 2605089.227 0.639129611 0.711245874 0.734197903 0.816634612 0.700627752 0.595944936 0.679978964 0.720356298 1 21.31290136 1.237187884 4.731030234 1.022683468 0.699859818 0.729707436 0.05757413 0.107446616 5.516263764 0.115902162 0.015442591 17.26584682 -1.237187884 -0.32282365 LFQLMVEHTPDEESIDWTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFQLMVEHTPDEESIDWTK 19 0 Q12907;D6RBV2;D6RDX1 Q12907 LMAN2 Vesicular integral-membrane protein VIP36 0 232.84 1.10E-21 235370000 362780 344260 263430 302630 335890 298490 317650 487610 462220 FALSE TRUE 314837.7038 341998.5334 390825.6291 371346.7669 329206.4462 309973.1034 286844.3519 383338.3961 407576.8782 0.772462131 0.839101901 0.958900394 0.911108522 0.807716197 0.760526713 0.703779746 0.940530282 1 18.63671268 1.54722099 6.546341436 0.98522786 0.827749462 0.425480416 0.072955124 0.129451063 10.64468998 0.055068537 0.020401875 35.25502202 -1.54722099 -0.157478399 LFQQILSGVDYCHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFQQILSGVDYCHR 14 0 Q13131-2;Q13131;Q96E92 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 0 ; 167.32 3.67E-06 537240000 348210 356120 210787 278420 364860 375760 340620 393910 407510 FALSE TRUE 302193.1662 353780.6243 312724.2982 341639.5164 357599.9998 390215.7303 307586.7248 309675.4119 359334.632 0.840979798 0.984543634 0.870287109 0.950755886 0.995172655 1.085939666 0.855989647 0.861802299 1 18.45496846 4.755178763 23.19062748 0.942316192 0.840979579 0.17508933 0.07282114 2476.996136 3456491.467 0.018794397 0.448321821 56908.71286 -4.755178763 -0.101336613 LFRPPS(ph)PAPAAPGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LFRPPSPAPAAPGAR 15 1 Q86U90 Q86U90 YRDC "YrdC domain-containing protein, mitochondrial" 1 LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR 147.06 2.29E-06 5984100000 4016440 3661020 2306630 2763120 3680860 4059750 3554260 3841400 3573770 TRUE FALSE 3485657.278 3636970.519 3422123.983 3390528.628 3607618.087 4215931.21 3209568.412 3019946.504 3151282.982 1.106107353 1.154123746 1.085946265 1.075920077 1.144809307 1.337845961 1.018495778 0.958322855 1 21.58750788 2.020897108 24.99410527 0.979851857 1.147141664 0.517243808 0.072872011 177.8104526 212670.3361 0.030358162 0.020465375 104.9293804 -2.020897108 0.167289807 RT(ph)SSTLDSEGTFNSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RTSSTLDSEGTFNSYR 16 1 Q92609;Q92609-2;C9J397;C9JWX0;C9JW04;C9JDR8;C9JNM0;C9JED7;F2Z3C3;C9K0P2 Q92609 TBC1D5 TBC1 domain family member 5 1 RT(0.433)S(0.433)S(0.116)T(0.018)LDSEGTFNSYR;RT(0.427)S(0.427)S(0.115)T(0.031)LDSEGTFNSYR 127.49 3.86E-05 683370000 192556 178560 81322 99431 150646 164586 148260 141790 66184 TRUE FALSE 167109.2367 177387.0276 120649.5912 122008.3283 147648.4393 170917.7299 133881.768 111469.3119 58359.80292 2.86343045 3.039541238 2.067340621 2.090622692 2.529968094 2.928689293 2.294075054 1.910035784 1 15.83268739 1.303811638 1.565010173 0.512553323 2.558167046 0.704506798 0.326785511 0.583368322 1.458906145 1.811530329 0.101593026 20.12851048 -1.303811638 2.045613723 LFSASEFEDPLVGEDTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFSASEFEDPLVGEDTER 18 0 E9PNM1;P37268;A0A1W2PQ47;P37268-4;P37268-3;P37268-2;P37268-5 E9PNM1 FDFT1 Squalene synthase 0 77.593 0.030985 33400000 76814 71351 58545 64423 84032 121240 70490 93862 84242 FALSE TRUE 66662.83528 70882.29058 86857.55782 79051.22679 82359.92761 125904.1813 63653.89065 73790.34173 74283.00673 0.89741703 0.95421946 1.169278973 1.064189917 1.108731744 1.694925755 0.85691053 0.99336773 1 16.18074459 4.348046893 5.01604656 1.117509023 0.911651413 0.126434193 0.220292111 0.45669922 17.77346256 0.056998998 0.159426482 22286.75777 -4.348046893 -0.20585761 LFSLELVDESGEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 180.88 3.96E-06 47263000 98424 83716 60623 70964 90772 94314 87916 98325 96063 FALSE TRUE 85417.01903 83166.06408 89940.48557 87077.46082 88965.81479 97942.32061 79389.91985 77298.96392 84706.54158 1.008387516 0.981813949 1.061789136 1.027989801 1.050282695 1.156254509 0.937234815 0.912550111 1 16.37018577 2.126222441 20.72939229 0.941574491 1.044826557 0.455192707 0.050102748 2.304997321 414.4573039 0.020724639 0.01397256 133.728028 -2.126222441 0.103252065 LFSLS(ph)NPSLSTTNLSGPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LFSLSNPSLSTTNLSGPSR 19 0 Q6UUV7;Q6UUV7-3 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 LFSLS(1)NPSLSTTNLSGPSR;LFSLS(1)NPSLSTTNLSGPSR;LFSLS(1)NPSLSTTNLSGPSR;LFSLS(0.998)NPS(0.002)LSTTNLSGPSR 402.91 1.84E-147 1701670000 987840 960100 537186 635643 892060 845587 750173 928860 856007 TRUE FALSE 857294.4411 953793.0399 796970.9464 779975.4583 874309.7513 878117.2791 677421.3379 730230.5174 754810.8276 1.135773905 1.263618651 1.055855212 1.03333899 1.158316388 1.163360735 0.897471675 0.967435138 1 19.52575559 2.244066919 24.99853212 0.955170336 1.133723693 0.618538068 0.066658282 89.39380524 405848.2579 0.026457474 0.019900343 175.415077 -2.244066919 0.178553357 LFSSSS(ph)SPPPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LFSSSSSPPPAK 12 0 E9PFH7;A0A087WYG2;A0A669KB35;Q9UPT6 E9PFH7 MAPK8IP3 C-Jun-amino-terminal kinase-interacting protein 3 1 LFSS(0.002)S(0.046)S(0.559)S(0.393)PPPAK;LFSS(0.001)S(0.016)S(0.609)S(0.374)PPPAK;LFSS(0.006)S(0.058)S(0.58)S(0.355)PPPAK 142.12 6.41E-05 1587440000 4806100 4676700 2984070 3725450 4618400 3899600 5042300 5592000 5479400 TRUE FALSE 4170961.708 4645978.45 4427176.233 4571370.362 4526502.876 4049620.135 4553298.522 4396194.317 4831631.574 0.863261539 0.96157548 0.916290111 0.946133887 0.936847689 0.838147544 0.942393569 0.909877802 1 22.20407902 1.235893631 24.95662618 1.000000114 0.916280766 0.333088985 0.038012476 84.8225533 793573.3374 0.057863731 0.008727657 17.21446901 -1.235893631 -0.083719348 LFSSSSS(ph)PPPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFSSSSSPPPAK 12 0 E9PFH7;A0A087WYG2;A0A669KB35;Q9UPT6 E9PFH7 MAPK8IP3 C-Jun-amino-terminal kinase-interacting protein 3 1 LFSS(0.004)S(0.083)S(0.409)S(0.504)PPPAK;LFSS(0.001)S(0.01)S(0.289)S(0.7)PPPAK 158.59 7.66E-05 317090000 1494910 1410210 940830 1106890 1389590 1183190 1579420 1771680 1606720 TRUE FALSE 1297353.856 1400946.238 1395818.535 1358226.292 1361939.878 1228708.085 1426248.091 1392820.019 1416775.392 0.915708914 0.988827337 0.98520806 0.958674395 0.961295549 0.867256794 1.006686098 0.983091623 1 20.43417963 LFSWLVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFSWLVNR 8 0 E9PDF6;O43795;O43795-2;A0A0U1RRI3 E9PDF6 MYO1B Unconventional myosin-Ib 0 ; 135.84 0.0018994 94211000 132160 164421 108486 109012 137604 140990 128978 141907 162113 FALSE TRUE 114694.7211 163340.9076 160950.1925 133764.8407 134865.9496 146413.9765 116469.7334 111561.2924 142948.1858 0.802351709 1.142658136 1.125933789 0.935757526 0.943460379 1.024245084 0.814768881 0.780431677 1 17.12513279 2.240665506 24.99897862 0.845338761 1.003228636 0.224931799 0.111794717 67.31176885 799451.9414 0.042772981 0.031454909 174.046585 -2.240665506 0.157889875 LFTEEELAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFTEEELAR 9 0 Q9UMX5 Q9UMX5 NENF Neudesin 0 ; 195.81 7.13E-05 471470000 485390 535120 365330 436220 547300 625290 482760 435520 416600 FALSE TRUE 421244.4817 531604.7615 542004.81 535270.4182 536409.8008 649345.3109 435942.0095 342387.4372 367350.0226 1.146711463 1.447134147 1.475445152 1.457112795 1.460214422 1.767647396 1.186721064 0.932046866 1 18.48679584 2.015191084 9.11110002 0.99014003 1.461014133 0.660750551 0.14784384 0.109219251 56.88955203 0.061200273 0.040394472 103.5597715 -2.015191084 0.470874104 LFTLPLLHYLEVSGCGSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFTLPLLHYLEVSGCGSLR 19 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 160.97 3.04E-11 185934000 233650 271500 133474 181970 217022 230560 221320 260050 267250 FALSE TRUE 202772.5605 269716.4986 198022.4728 223289.0697 212703.6868 239429.7924 199856.4205 204440.3312 235656.0095 0.86045996 1.144534779 0.84030309 0.947521221 0.90260243 1.016013947 0.848085398 0.867537101 1 17.84632295 4.20278649 24.99992051 0.913332112 1.00249894 0.134968777 0.089054181 269.7398447 188501.2586 0.021020667 0.043760379 15950.94766 -4.20278649 0.089166828 LFTNFHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LFTNFHR 7 0 F5GWE5;Q00169;I3L4H1 F5GWE5 PITPNA Phosphatidylinositol transfer protein alpha isoform 0 ;; 186.67 0.00059542 1869100000 1470440 1531770 982280 1077080 1522340 1540840 1418880 1513410 1832550 FALSE TRUE 1276117.628 1521707.702 1457313.894 1321647.476 1492048.412 1600117.112 1281277.236 1189779.049 1615908.027 0.789721697 0.941704402 0.90185448 0.817897711 0.923349837 0.990227838 0.792914705 0.736291317 1 20.62391366 2.182875501 24.99998665 0.818733539 0.89450492 0.04714657 0.087841947 172.1576172 77289.02796 0.035193782 0.023727655 152.3615917 -2.182875501 0.075771381 LFTTMELMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFTTMELMR 9 0 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 99.136 0.012892 47355000 38372 67610 37937 38301 51748 63937 50818 60467 52149 FALSE TRUE 33301.04298 67165.86546 56283.46009 46997.82744 50718.31604 66396.69776 45889.67818 47536.6026 45984.00463 0.724187535 1.46063541 1.223979089 1.022047293 1.102955614 1.443908557 0.997948712 1.03376387 1 15.48884449 LFVCDVLPLIINNHDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFVCDVLPLIINNHDVR 17 0 Q9NVR2 Q9NVR2 INTS10 Integrator complex subunit 10 0 94.487 0.002803 37886000 48345 57235 37248 50524 50593 46548 49372 63012 60896 FALSE TRUE 41956.08576 56859.01952 55261.25739 61996.24641 49586.29828 48338.73168 44583.91104 49537.37416 53696.94425 0.781349597 1.058887434 1.029132256 1.154558183 0.923447302 0.900213827 0.830287676 0.922536186 1 15.71255237 3.030305633 24.99888242 0.907474691 1.014863017 0.164462663 0.100544824 317.0417194 261523.1933 0.029952874 0.033963037 1072.273647 -3.030305633 0.107388326 LFVDENLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFVDENLDR 9 0 A0A087WTU5;A0A087X0N3;Q96MY1-2;Q96MY1;O94818-4;O94818-3;O94818 A0A087WTU5 NOL4L;NOL4 Nucleolar protein 4-like;Nucleolar protein 4 0 88.819 0.029141 63205000 121330 133030 90688 117040 151170 180840 114360 154000 158860 FALSE TRUE 105295.9331 132156.1172 134545.0201 143615.7208 148162.0128 187797.0318 103269.3848 121068.2984 140079.7518 0.751685606 0.943434833 0.96048871 1.025242542 1.057697568 1.340643665 0.737218502 0.864281218 1 17.09588891 4.839139938 1.957321102 0.987914065 0.636354604 0.201775478 0.152603333 2.047277857 6.716989352 0.04280787 1.414644822 69046.22488 -4.839139938 -0.351559461 LFVDTDADTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFVDTDADTR 10 0 A0A2R8Y653;Q9BZX2;Q9BZX2-2 A0A2R8Y653 UCK2 Uridine-cytidine kinase 2 0 99.653 0.010582 51838000 265770 217410 184690 207230 199170 203210 234630 255630 315380 FALSE TRUE 230647.8211 215981.8194 274006.7018 254284.7388 195206.9067 211027.6202 211875.6187 200965.5138 278096.1357 0.829381611 0.776644447 0.985294891 0.914377103 0.701940378 0.758829747 0.761879047 0.722647632 1 18.08522417 3.252474491 24.98487808 0.777207881 0.877073826 0.161649395 0.096790175 386.864027 694680.4812 0.027823409 0.035732075 1788.440481 -3.252474491 0.099865945 LFVGGIKEDTEEHHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LFVGGIKEDTEEHHLR 16 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;; 195.2 5.86E-11 2793082000 3319310 2893360 1134803 1304400 2522130 2347750 3121570 3581900 258296 FALSE TRUE 2880654.773 2874353.328 1683597.526 1600583.957 2471944.547 2438069.462 2818840.622 2815938.559 227760.5411 12.64773415 12.62006717 7.391963147 7.027485747 10.85326078 10.70452963 12.37633441 12.36359268 1 17.7971583 4.265373182 23.77033511 9.400366816 12.63391076 0.166292849 3.361210644 263.2860507 233405.1885 0.839766944 2.220026382 18423.54427 -4.265373182 3.233543942 LFVGGLNFNTDEQALEDHFSSFGPISEVVVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFVGGLNFNTDEQALEDHFSSFGPISEVVVVK 32 0 P98179 P98179 RBM3 RNA-binding protein 3 0 ; 179.47 1.07E-19 233786000 189269 163084 268069 148097 55927 75407 81271 106761 72080 FALSE TRUE 164256.6221 162012.6905 397708.065 181724.6874 54814.16212 78307.95608 73389.35093 83930.99097 63558.78451 2.584326043 2.54902122 6.257326475 2.859159261 0.862416777 1.232055595 1.154668886 1.320525426 1 15.95580391 3.381852212 4.727022834 1.160268192 3.801269525 0.597774561 1.018215694 0.14385398 5.51868189 0.297960932 0.389459819 2409.085492 -3.381852212 2.641001334 LFVGNLPADITEDEFKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LFVGNLPADITEDEFKR 17 1 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;; 290.5 9.09E-46 2703670000 941200 738387 432128 539224 616103 534152 743663 818870 586176 FALSE TRUE 816818.0353 733536.4872 641106.5462 661663.0507 603843.7557 554701.1731 671542.6767 643761.023 516878.9411 1.580288865 1.419164971 1.240341781 1.280112224 1.16824987 1.073174256 1.299226228 1.245477368 1 18.9794669 4.802794396 0.900334051 1.176975524 1.85566944 0.713722582 0.087600874 1.393090831 0.82743598 0.030812886 0.958262139 63503.02237 -4.802794396 0.678693916 LFVGNLPPDITEEEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFVGNLPPDITEEEMR 16 0 Q15233;C9JYS8;C9IZL7;C9J4X2 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 122.66 0.00021427 26216000 63339 66562 45639 59283 72298 80480 58543 83351 79034 FALSE TRUE 54968.59067 66124.74984 67710.17305 72744.11123 70859.41125 83576.11768 52865.50887 65527.03729 69690.69056 0.788750839 0.948831893 0.971581319 1.043813896 1.016770112 1.199243644 0.758573469 0.940255245 1 16.08867833 4.769318384 2.443163139 0.983365584 0.735303164 0.253534366 0.107582975 0.954856468 6.586837809 0.028232041 0.512763287 58792.02025 -4.769318384 -0.248062419 LFVGNLPTDITEEDFKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFVGNLPTDITEEDFKR 17 1 Q8WXF1;Q8WXF1-2;X6RDA4 Q8WXF1 PSPC1 Paraspeckle component 1 0 ; 144.68 8.06E-07 1529660000 565090 434640 289860 335010 446380 354100 508120 575820 460760 FALSE TRUE 490411.9247 431784.8212 430037.2655 411079.1408 437497.9113 367722.4561 458842.6006 452685.374 406289.4777 1.207050519 1.062751671 1.058450413 1.011788794 1.076813295 0.905075017 1.129348964 1.114194186 1 18.63214848 4.749636095 3.561113534 1.048976872 1.227525952 0.393910017 0.063309226 0.344223808 7.667447187 0.01595771 0.167031805 56187.03242 -4.749636095 0.17854908 LFVLFGAEILKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFVLFGAEILKK 12 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 146.16 0.00010343 57434000 132750 124640 69120 103100 97173 85952 159520 193310 73658 FALSE TRUE 115206.7512 123821.2316 102546.6632 126510.4308 95239.44742 89258.62906 144049.775 151972.1608 64950.23515 1.773769577 1.906401591 1.57884976 1.947805585 1.466344921 1.374261831 2.217848398 2.339824644 1 15.98704713 2.23103641 24.99857424 1.969291994 1.683713705 0.015239089 0.397219871 414.4790033 1377058.844 0.159274826 0.109752745 170.230122 -2.23103641 -0.285578288 LFVLLPEQS(ph)PVSYSK ddPTM_MDA-MB-175_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 201.3 6.80E-09 872760000 1780350 1584440 1031670 1337050 1522000 1352220 1610300 2045340 1941220 TRUE FALSE 1545072.237 1574031.709 1530589.063 1640647.638 1491715.178 1404240.778 1454133.354 1607959.958 1711731.183 0.902637197 0.919555433 0.89417607 0.958472717 0.871465796 0.820362912 0.849510349 0.939376448 1 20.70702472 1.444019851 3.570038276 0.996302121 0.889062831 0.486997981 0.037564101 0.222379012 4.909776283 0.048765029 0.010686294 27.79840325 -1.444019851 -0.10723929 LFVPALDKPETDLLSHLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFVPALDKPETDLLSHLDR 19 1 V9GYV5;V9GY92;Q9UNI6 V9GYV5 DUSP12 Dual specificity protein phosphatase 12 0 ; 185.27 1.39E-14 336300000 342965 271537 250410 254092 284031 235709 313705 354638 331168 FALSE TRUE 297641.3063 269753.2556 371509.1136 311787.4722 278379.3388 244776.8778 283281.9374 278801.4235 292017.6963 1.019257771 0.923756536 1.272214384 1.067700609 0.953296127 0.838226179 0.97008483 0.954741535 1 18.15569627 3.231147014 5.844017325 0.940806074 1.075287301 0.311179177 0.094290106 0.198926938 23.54250795 0.028708682 0.034536216 1702.734806 -3.231147014 0.134481227 LFVT(ph)PPEGSSR ddPTM_MDA-MB-175_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(0.939)PPEGS(0.031)S(0.031)R;LFVT(0.997)PPEGS(0.001)S(0.001)R;LFVT(0.975)PPEGS(0.016)S(0.009)R;LFVT(0.998)PPEGS(0.002)S(0.001)R 108.59 0.022825 627008000 1465960 1310570 820420 1004030 1149300 1302930 1197320 1302450 1340830 TRUE FALSE 1272229.672 1301960.779 1217177.856 1232010.357 1126431.179 1353054.56 1081204.091 1023931.203 1182318.605 1.076046394 1.101192838 1.029483805 1.042029071 0.952730655 1.144407738 0.914477778 0.866036616 1 20.17318743 2.210577769 24.79979899 0.913655992 1.052868526 0.514539575 0.059317774 141.5792989 125473.5399 0.023501604 0.015848664 162.3969129 -2.210577769 0.139212534 LFVWEILHSTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LFVWEILHSTIR 12 0 Q09161 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 196.24 0.00013176 0 98458 95374 40870 63102 85959 81340 116760 104380 97371 FALSE TRUE 85446.52584 94747.48191 60634.8687 77430.27355 84248.58408 84469.20243 105436.6332 82059.14929 85859.91131 0.995185349 1.10351246 0.70620698 0.901821029 0.981233067 0.983802582 1.228007711 0.955732985 1 16.38969706 2.758174923 2.678163124 1.049394228 0.927162816 0.169271002 0.121119944 0.516881965 7.386869885 0.045065485 0.042214208 573.0267849 -2.758174923 -0.122231412 LFYADHPFIFLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFYADHPFIFLVR 13 0 P50454;E9PKH2;H0YEP8 P50454 SERPINH1 Serpin H1 0 ; 228.12 7.97E-12 3998200000 1844870 2053580 1507830 1852200 2179610 2666600 2059840 1928590 1784150 FALSE TRUE 1601065.755 2040089.898 2237021.631 2272770.319 2136240.025 2769185.828 1860077.034 1516176.037 1573229.82 1.017693496 1.296752625 1.421929335 1.444652454 1.357869015 1.760191546 1.182330141 0.963734617 1 20.58529801 2.002984418 24.99691395 1.007403505 1.390041286 0.460785025 0.179923728 75.2430189 630217.0025 0.074860866 0.050164869 100.6895542 -2.002984418 0.382637781 LFYSTFATDDRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LFYSTFATDDRK 12 1 P30084 P30084 ECHS1 "Enoyl-CoA hydratase, mitochondrial" 0 ; 287.13 1.78E-28 1116420000 603750 730670 506740 868780 835050 812760 769960 1074080 841040 FALSE TRUE 523962.9078 725870.1807 751801.1589 1066049.777 818434.1387 844027.4031 695289.3977 844396.3505 741613.2093 0.706517766 0.978771914 1.013737551 1.437474096 1.103586247 1.138096507 0.937536426 1.138594 1 19.50030742 4.653032023 1.913714313 1.116352115 0.628421796 0.488118924 0.132382835 0.572520603 2.550028627 0.03548717 0.466499899 44981.3021 -4.653032023 -0.487930318 LGADES(ph)EEEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGADESEEEGR 11 0 O43847;O43847-2;F5H7V1 O43847 NRD1 Nardilysin 1 LGADES(1)EEEGR;LGADES(1)EEEGR 197.38 6.01E-08 574100000 391150 341790 249550 302240 336690 308780 370680 377020 455080 TRUE FALSE 339458.5365 339544.759 370233.2147 370868.2114 329990.5277 320658.9664 334731.5107 296397.207 401280.9608 0.84593731 0.846152178 0.92262841 0.924210834 0.822342847 0.799088414 0.834157469 0.738627635 1 18.61425318 3.212630482 24.51203664 0.823977105 0.884683338 0.07361471 0.070696934 342.4983906 323766.1381 0.020975621 0.023792786 1631.663061 -3.212630482 0.060706232 LGADESEEEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGADESEEEGR 11 0 O43847;O43847-2;F5H7V1 O43847 NRD1 Nardilysin 0 175.73 2.21E-05 144410000 150510 149290 92609 106550 139630 152290 128890 150300 143880 FALSE TRUE 130619.7222 148309.3042 137395.0222 130743.806 136851.6362 158148.6948 116390.2676 118159.5146 126870.6703 1.029550186 1.168980221 1.082953387 1.03052822 1.078670396 1.246534715 0.917393022 0.931338302 1 16.95299906 2.206197855 24.99999433 0.944436235 1.10330844 0.546689054 0.067144489 139.1368856 107481.2773 0.026802323 0.018071648 160.7673508 -2.206197855 0.158872205 LGAGEGGEASVS(ph)PEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LGAGEGGEASVSPEK 15 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 LGAGEGGEASVS(1)PEK;LGAGEGGEASVS(1)PEK;LGAGEGGEASVS(1)PEK;LGAGEGGEASVS(1)PEK 311.08 3.87E-56 1439200000 2577760 1926920 1661930 2082410 2036780 1679260 2173560 2709290 4594980 TRUE FALSE 2237102.485 1914261.936 2465644.907 2555253.018 1996252.063 1743862.219 1962768.486 2129929.417 4051766.699 0.552130133 0.472451174 0.608535755 0.630651567 0.492686823 0.430395516 0.484422878 0.525679185 1 21.95011968 1.238689936 9.999382568 1.001956624 0.523018227 0.857821822 0.060820094 0.027457318 59.33744602 0.089734888 0.01597381 17.32566592 -1.238689936 -0.478938397 LGAGEGGEASVS(ph)PEKTSTTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.004)VS(0.996)PEKTSTTSK 169.6 5.63E-12 1491800000 1352800 874890 512280 657590 815560 542110 1128200 1209100 356950 TRUE FALSE 1174024.052 869142.79 760020.3215 806905.8601 799331.9516 562965.3225 1018787.338 950543.3742 314751.7776 3.729999752 2.761359432 2.4146657 2.563626062 2.539562946 1.788600931 3.236796136 3.019977779 1 18.263855 4.739594152 2.378328416 2.463145397 4.033985693 0.31262839 0.625895804 0.76023225 5.190119135 0.158670468 2.468031608 54902.75686 -4.739594152 1.570840296 LGAGGGS(ph)PEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LGAGGGSPEK 10 0 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 1 LGAGGGS(1)PEK;LGAGGGS(1)PEK;LGAGGGS(1)PEK;LGAGGGS(1)PEK;LGAGGGS(1)PEK;LGAGGGS(1)PEK 159.44 8.06E-06 1925060000 4574640 3817320 3822340 4385580 3557530 3252430 4718290 5276200 12609910 TRUE FALSE 3970089.733 3792243.774 5670836.409 5381392.968 3486742.113 3377553.087 4260710.962 4147925.689 11119180.81 0.357048761 0.341054241 0.510004874 0.48397387 0.313579046 0.303759166 0.383185689 0.373042382 1 23.40654717 1.237950231 24.99783262 1.000000705 0.383864255 0.89432048 0.066632977 4.7759903 195433.7591 0.100461895 0.017364684 17.29618139 -1.237950231 -0.61613645 LGAGGGS(ph)PEKS(ph)PSAQELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGAGGGSPEKSPSAQELK 18 1 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 2 LGAGGGS(1)PEKS(0.891)PS(0.109)AQELK;LGAGGGS(1)PEKS(0.856)PS(0.144)AQELK 133.1 7.62E-06 1009020000 1602780 1155170 1169590 1087090 1288990 860730 1731260 1956030 1651890 TRUE FALSE 1390968.562 1147581.612 1735207.636 1333930.4 1263341.621 893842.8401 1563362.672 1537748.206 1456605.446 0.95493846 0.787846575 1.191268123 0.915780181 0.867319029 0.613647877 1.073291794 1.055706753 1 20.47417871 LGAGGGS(ph)PEKSPSAQELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LGAGGGSPEKSPSAQELK 18 1 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 1 LGAGGGS(0.998)PEKS(0.002)PSAQELK;LGAGGGS(0.997)PEKS(0.003)PSAQELK;LGAGGGS(0.999)PEKS(0.001)PSAQELK;LGAGGGS(0.967)PEKS(0.033)PSAQELK 275.2 2.80E-39 9785360000 8631600 6216720 5752390 5451310 6062780 4144410 9072600 10314800 6646100 TRUE FALSE 7490912.19 6175881.957 8534265.045 6689113.254 5942142.54 4303848.134 8192740.648 8109060.29 5860405.629 1.278224182 1.053831825 1.45625842 1.141407895 1.013947313 0.734394239 1.397981841 1.383702904 1 22.48256909 3.537399449 24.99942921 1.138001344 1.251370143 0.091630103 0.212658651 873.4765887 362257.8004 0.063651419 0.094410089 3446.667979 -3.537399449 0.113368798 LGAGGGSPEKS(ph)PSAQELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGAGGGSPEKSPSAQELK 18 1 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 1 LGAGGGSPEKS(0.977)PS(0.023)AQELK 140.59 7.63E-08 676600000 728720 557420 520890 520480 556050 389030 739590 916800 800690 TRUE FALSE 632417.8057 553758.2713 772794.1463 638662.939 544985.6929 403996.2358 667864.6756 720749.4545 706033.3403 0.895733628 0.784323119 1.094557583 0.904579009 0.771897957 0.572205607 0.945939289 1.02084337 1 19.42937679 2.010756457 24.99380727 1.003354817 0.839308061 0.24278178 0.129882319 309.7822279 719810.2271 0.056409917 0.037992065 102.5076924 -2.010756457 -0.164046756 LGANSGLHIIIFDEIDAICK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGANSGLHIIIFDEIDAICK 20 0 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 92.492 0.0016448 13739000 23314 20580 13559 18858 22554 20081 22270 29499 24421 FALSE TRUE 20232.99583 20444.80862 20116.17775 23139.99713 22105.21953 20853.52906 20110.25883 23190.86841 21533.9772 0.939584715 0.949420928 0.934159889 1.074580739 1.026527488 0.968401186 0.933885025 1.076943112 1 14.39432718 3.771846876 24.79143448 1.013713618 0.941891729 0.38655142 0.042950424 645.6563794 480879.1012 0.011848046 0.020519707 5913.530969 -3.771846876 -0.071821889 LGAPENSGIST(ph)LER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LGAPENSGISTLER 14 0 A0A1B0GV68;M0QYB0;Q9Y4F1-3;C9JME2;Q9Y4F1;Q9Y4F1-2 A0A1B0GV68;C9JME2 FARP1 "FERM, RhoGEF and pleckstrin domain-containing protein 1" 1 LGAPENSGIS(0.04)T(0.96)LER;LGAPENSGIST(1)LER;LGAPENSGIST(1)LER;LGAPENSGIS(0.045)T(0.955)LER;LGAPENSGIS(0.165)T(0.834)LER 329.37 2.50E-67 4070130000 3011930 3345420 2298630 4236200 4633360 5341520 2209430 4753500 4132480 TRUE FALSE 2613895.819 3323443.716 3410255.156 5198093.956 4541165.201 5547011.731 1995159.819 3737001.017 3643942.922 0.717326225 0.912046041 0.935869532 1.426502574 1.246222923 1.522255384 0.547527736 1.025537748 1 21.79706893 4.294559193 2.294312276 1.102715436 0.756970141 0.191973388 0.268013647 0.60811688 6.07181558 0.075706632 0.291776862 19704.21753 -4.294559193 -0.345745295 LGASNS(ph)PGQPNSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 350.45 7.07E-82 17177140000 19872270 14439450 10555170 12948790 13562510 11700690 16462390 18409180 20450340 TRUE FALSE 17246099.17 14344596.3 15659685.52 15889010.68 13292642.59 12150823.12 14865869.95 14472520.12 18032724.1 0.95637792 0.795475837 0.868403766 0.881120933 0.737140019 0.673820719 0.824382931 0.802569819 1 24.10411402 LGASNS(ph)PGQPNSVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGASNSPGQPNSVKR 15 1 P49756 P49756 RBM25 RNA-binding protein 25 1 LGAS(0.003)NS(0.997)PGQPNS(0.001)VKR 91.637 0.0034003 1618100000 1063900 687790 377380 456720 711640 637030 855500 929010 372490 TRUE FALSE 923302.9194 683271.8622 559882.2303 560425.2565 697479.7563 661536.9563 772533.7417 730348.4411 328454.6565 2.811051392 2.08026237 1.704595198 1.706248474 2.12351916 2.014089139 2.352025542 2.223589852 1 18.32533469 4.716734401 3.735338189 1.93706974 2.884449773 0.367259923 0.377514567 0.281552315 7.491833128 0.093348895 0.711549152 52087.60645 -4.716734401 0.947380033 LGCDLDMFLDLDETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGCDLDMFLDLDETR 15 0 Q9NVV4-2;Q5T852;Q9NVV4 Q9NVV4-2 MTPAP "Poly(A) RNA polymerase, mitochondrial" 0 119.76 0.00043442 8294800 12939 10296 6263.7 11972 12230 11354 9811.8 12208 14322 FALSE TRUE 11229.07837 10228.3649 9292.846271 14690.42558 11986.64693 11790.79573 8860.253146 9597.414203 12628.86948 0.889159429 0.809919282 0.735841501 1.16324154 0.949146474 0.93363826 0.701587198 0.759958302 1 13.62443788 2.271219781 24.98968541 0.802943686 0.913681328 0.093904768 0.132448461 393.4636668 301063.7599 0.051021339 0.039518029 186.732444 -2.271219781 0.110737643 LGCEVLGVSVDSQFTHLAWINTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LGCEVLGVSVDSQFTHLAWINTPR 24 0 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ;;;;; 365.54 1.39E-118 2634513000 2078414 1829249 1009423 1413441 1721178 1825081 1845581 2090502 2464947 FALSE TRUE 1803746.324 1817232.543 1497583.339 1734384.382 1686929.925 1895293.047 1666596.839 1643464.416 2173543.774 0.829864273 0.836068988 0.689005373 0.797952359 0.7761196 0.87198292 0.766764792 0.756122069 1 21.05161772 1.233229165 24.9994327 1.000000332 0.78834689 0.632901636 0.050122985 111.676673 523598.9621 0.101619107 0.012172959 17.10917879 -1.233229165 -0.211653441 LGDAS(ph)DTEAADGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGDASDTEAADGER 14 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 LGDAS(0.992)DT(0.008)EAADGER;LGDAS(0.99)DT(0.01)EAADGER 375.6 2.47E-97 1228030000 1855960 1369730 1061660 1067940 1328040 1248810 1341660 1440080 1607130 TRUE FALSE 1610690.184 1360732.153 1575082.327 1310432.099 1301614.602 1296852.529 1211546.02 1132130.099 1417136.922 1.136580494 0.960198081 1.111453877 0.924703943 0.918481892 0.915121544 0.854925167 0.798885472 1 20.43454773 3.504367676 1.267009849 0.873009295 1.070033251 0.530348004 0.071387389 0.337327481 1.107890404 0.02515084 0.047701996 3194.240973 -3.504367676 0.197023955 LGDDIDLIVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LGDDIDLIVR 10 0 O15371-2;O15371;O15371-3 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ;;; 146.69 6.56E-05 210234000 533165 493692 394165 478040 478534 448370 507798 582523 772200 FALSE TRUE 462705.8944 490448.9047 584784.5124 586586.2884 469012.1096 465619.084 458551.8281 457954.9896 680911.3957 0.679539067 0.720283003 0.85882615 0.861472274 0.6888005 0.683817435 0.673438323 0.672561794 1 19.37710755 3.348945594 0.005090648 1.497335194 2.07E-07 0.012962138 0.110693653 178919.018 907.5898515 132922.4087 134019.5231 2233.29243 -3.348945594 -1.497334988 LGDLWTLDIDTLTWNKPSLSGVAPLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGDLWTLDIDTLTWNKPSLSGVAPLPR 27 1 P51610-2;P51610;A6NEM2;P51610-4;P51610-3 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 0 ; 266.46 1.74E-53 285840000 196928 185375 122013 147072 168879 134245 195644 200642 205410 FALSE TRUE 170903.4658 184157.2594 181018.8949 180466.9455 165518.6383 139409.492 176670.475 157736.2697 181126.6638 0.943557742 1.016731913 0.999405008 0.996357696 0.913828118 0.769679566 0.975397389 0.870861674 1 17.46663942 3.198022132 5.63525029 0.899166137 0.991912796 0.292862973 0.063832376 0.213627266 16.56395891 0.018556936 0.021608214 1577.691669 -3.198022132 0.092746659 LGDS(ph)SGPALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGDSSGPALK 10 0 Q9UHD8 Q9UHD8 9-Sep Septin-9 1 LGDS(0.977)S(0.023)GPALK;LGDS(0.844)S(0.156)GPALK 99.5 0.0048807 375608000 546790 404560 281040 394440 423760 282650 655840 540550 583140 TRUE FALSE 474530.3161 401902.4187 416951.884 484003.6306 415328.0051 293523.7284 592236.7377 424957.5891 514201.8535 0.922848319 0.781604376 0.810871997 0.941271657 0.80771394 0.570833665 1.151759243 0.826441185 1 18.97197529 2.22596184 24.99998162 0.964715216 0.811222407 0.319467971 0.126227272 316.8692295 628764.2798 0.0497448 0.03379358 168.2526219 -2.22596184 -0.153492809 LGDS(ph)SGPALKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGDSSGPALKR 11 1 Q9UHD8 Q9UHD8 9-Sep Septin-9 1 LGDS(0.932)S(0.068)GPALKR;LGDS(0.949)S(0.051)GPALKR 59.709 0.06019 383590000 650240 479460 280570 388100 469820 257770 902560 649020 376720 TRUE FALSE 564309.1365 476310.3957 416254.5905 476224.0367 460471.5012 267686.5787 815029.8701 510232.1237 332184.5908 1.698781798 1.433872639 1.253082178 1.433612666 1.386191636 0.805836833 2.453545085 1.535989741 1 18.34162563 2.272801983 24.9999553 1.669617464 1.342768418 0.123568957 0.411273382 379.2564561 276897.5159 0.150949866 0.11691938 187.4139796 -2.272801983 -0.326849046 LGDS(ph)SLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGDSSLSR 8 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 LGDS(0.5)S(0.5)LSR 63.184 0.078585 338830000 1311800 1122200 743570 921570 978650 997300 1068700 1240000 1658500 TRUE FALSE 1138442.306 1114828.194 1103162.939 1130826.554 959176.7797 1035666.776 965057.6385 974835.6497 1462434.019 0.77845721 0.76231008 0.754333477 0.773249623 0.655876961 0.708180173 0.659898242 0.666584363 1 20.47994011 1.232414181 24.99909788 1.000000466 0.716260764 0.77655523 0.047190158 106.0685563 431364.4866 0.115280373 0.012847153 17.07710232 -1.232414181 -0.283739703 LGDSHDLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LGDSHDLQR 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 121.64 0.00060824 1907100000 4686190 4603760 3045130 3588250 4565970 4936020 4483010 5187890 5096130 FALSE TRUE 4066898.118 4573517.597 4517765.053 4403017.005 4475116.13 5125911.883 4048248.38 4078500.096 4493671.317 0.905027945 1.017768607 1.005361704 0.979826226 0.995870818 1.140695775 0.900877722 0.907609793 1 22.09946317 LGDSS(ph)LSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGDSSLSR 8 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 LGDS(0.14)S(0.86)LSR 139.38 0.0013419 0 573390 554390 511510 445330 610110 697940 545900 652020 1289200 TRUE FALSE 497615.0587 550748.1756 758877.9469 546448.9829 597970.0047 724790.2034 492958.702 512590.597 1136792.245 0.437736148 0.484475662 0.667560806 0.480693799 0.526015204 0.637574902 0.433640099 0.450909653 1 20.11653719 1.233944513 24.99720336 1.000000729 0.514967605 0.785239814 0.079739904 65.74521432 355979.8501 0.154911735 0.019803198 17.13738339 -1.233944513 -0.485033124 LGDTALHAAAWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGDTALHAAAWK 12 0 Q92882 Q92882 OSTF1 Osteoclast-stimulating factor 1 0 111.63 0.00031958 0 1083500 1005500 615210 827770 1053400 967230 1195500 1306300 1248800 FALSE TRUE 940312.7298 998894.8043 912727.6138 1015727.83 1032439.401 1004439.964 1079560.594 1026957.911 1101168.287 0.853922821 0.90712275 0.828872049 0.922409265 0.937585484 0.912158456 0.980377484 0.932607598 1 20.07060354 3.035798742 0.481126929 0.98437736 0.849195772 0.640580436 0.030578939 0.765810555 0.598558204 0.057838968 0.061526965 1085.922277 -3.035798742 -0.135181588 LGDVGMAELCPGLLHPSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGDVGMAELCPGLLHPSSR 19 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 ; 237.86 3.12E-24 1829640000 922220 990070 311520 619050 1110790 1174640 1021780 1096940 1100240 FALSE TRUE 800346.2904 983566.165 462172.114 759614.7641 1088687.452 1219829.161 922687.9329 862367.9174 970170.8806 0.82495394 1.013807139 0.476382175 0.782970072 1.122160512 1.257334337 0.95105713 0.8888825 1 19.88787935 3.255461537 22.59063584 1.028221421 0.770323103 0.403620442 0.162040334 89.67864701 119866.6639 0.049715676 0.063937361 1800.783641 -3.255461537 -0.257898318 LGDVYVNDAFGTAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 LGDVYVNDAFGTAHR 15 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ;;;;;;;;; 238.17 9.25E-18 37858172000 17665572 16517555 8287756 8824837 13145499 14050619 12978478 15550978 15151021 FALSE TRUE 15331021.9 16409050.09 12295742.52 10828651.12 12883929.29 14591155.4 11719827.2 12225522.37 13359884.56 1.147541495 1.228232925 0.920347962 0.810534782 0.964374298 1.092161788 0.877240155 0.915091917 1 23.67140421 4.235152141 24.99990208 0.936068321 1.187887255 0.645654454 0.076314992 48.69230001 357151.1372 0.019933709 0.044368218 17185.10305 -4.235152141 0.251818934 LGEMWNNTAADDKQPYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LGEMWNNTAADDKQPYEK 18 1 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ;; 277.01 3.67E-39 2888440000 2092000 1330230 1436740 1338780 1200660 769913 1735680 2037830 2835210 FALSE TRUE 1815536.9 1321491.632 2131552.27 1642770.461 1176769.215 799532.0513 1567354.021 1602055.913 2500034.704 0.726204679 0.528589315 0.852609072 0.657099063 0.470701152 0.319808381 0.626932906 0.64081347 1 21.25351669 1.195827711 2.893074387 1.111642862 0.592887807 0.433830523 0.143174474 0.519305441 4.812963532 0.675859031 0.039151491 15.69739949 -1.195827711 -0.518755054 LGEMWNNTAADDKQPYEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGEMWNNTAADDKQPYEKK 19 2 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 153.11 2.76E-08 311330000 124650 87787 51861 70228 82766 58777 113430 126180 63352 FALSE TRUE 108177.1867 87210.32142 76941.15306 86174.34077 81119.11853 61038.18922 102429.5761 99197.38893 55862.59873 1.936486829 1.561157615 1.377328567 1.542612459 1.452118598 1.092648581 1.833598479 1.775738888 1 15.76959507 4.715683774 3.528882862 1.481374195 1.98002257 0.253066737 0.260250635 0.418266349 9.305575819 0.065838097 0.535955855 51961.7506 -4.715683774 0.498648374 LGETYKDHENIVIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LGETYKDHENIVIAK 15 1 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ;; 123.07 6.31E-05 1990506000 7057600 5146250 4130260 4320320 4756780 4095840 6795600 6472750 1772872 FALSE TRUE 6124920.278 5112443.945 6127667.551 5301314.688 4662129.384 4253409.615 6136563.758 5088602.783 1563285.092 3.917980355 3.270320923 3.919737726 3.391137494 2.982264341 2.720815056 3.925428439 3.255070243 1 20.57614947 3.347473189 3.117988762 2.914439626 3.661415356 0.234002421 0.75525452 0.464992229 9.01080462 0.231518655 0.307030311 2225.733637 -3.347473189 0.74697573 LGEVALLQGNHQIVEMCYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGEVALLQGNHQIVEMCYQR 20 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 177.61 6.49E-17 493120000 358850 316350 221024 210856 287100 277810 293750 308620 347510 FALSE TRUE 311427.0633 314271.876 327911.9457 258734.0775 281387.2717 288497.5305 265262.1702 242624.0147 306427.7637 1.016314774 1.025598569 1.070111734 0.844355859 0.918282561 0.941486264 0.865659714 0.791782088 1 18.22518749 3.739926234 24.99823894 0.88426721 1.036167385 0.576470453 0.057711781 85.26423148 1560789.88 0.016040529 0.025952706 5494.475407 -3.739926234 0.151900175 LGEWVGLCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGEWVGLCK 9 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 ; 88.819 0.029141 884500000 1424010 1175590 949270 1063550 1176300 1208850 1188150 1424480 1248640 FALSE TRUE 1235823.471 1167867.472 1408340.147 1305045.283 1152893.931 1255355.242 1072923.396 1119866.037 1101027.202 1.122427737 1.060707192 1.279114762 1.185297948 1.047107582 1.140167327 0.974474921 1.017110236 1 20.07041868 2.245013122 24.99999999 1.000397371 1.1398498 0.517222519 0.064618557 124.5831177 482694.4805 0.025344899 0.019151277 175.7976728 -2.245013122 0.139452429 LGEYEDVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGEYEDVSR 9 0 K7EP07;Q99426-2;Q99426;A0A494C0X0;K7EK42;K7EL99 K7EP07 TBCB Tubulin-folding cofactor B 0 132.76 0.00068877 265370000 311280 259370 187050 194370 261440 259660 323520 370070 231590 FALSE TRUE 270143.5593 257666.1814 277508.0056 238504.6793 256237.8555 269649.2882 292145.0802 290933.4104 204211.694 1.322860381 1.261760168 1.358923185 1.167928607 1.254765829 1.320439995 1.430599171 1.42466577 1 17.63970596 2.675933885 7.061507302 1.327484382 1.271577066 0 0.128555382 1.04361538 101.3823652 0.044216463 0.039022211 474.1697944 -2.675933885 -0.055907316 LGFHLPLEVAYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGFHLPLEVAYQR 13 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 138.94 4.33E-05 1905070000 2047570 2160720 1435050 1602390 1908840 1956130 1847300 2088610 2027990 FALSE TRUE 1776978.437 2146526.088 2129044.98 1966237.14 1870857.819 2031383.587 1668149.13 1641977.005 1788243.332 0.99370058 1.200354588 1.190579012 1.099535564 1.046198683 1.135965978 0.93284236 0.918206698 1 20.77011163 2.236415376 24.99891195 0.942923726 1.115257786 0.580661458 0.064210039 36.6358769 426912.7017 0.025340466 0.01803127 172.3516225 -2.236415376 0.17233406 LGFSEYCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LGFSEYCR 8 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ;; 104.21 0.010758 436490000 481620 582170 351270 418170 541960 571820 511180 582940 532920 FALSE TRUE 417972.6967 578345.6869 521145.3469 513121.8898 531176.0563 593818.2854 461605.8423 458282.8174 469918.8047 0.889457269 1.230735355 1.109011475 1.09193734 1.130357098 1.263661465 0.98230979 0.975238303 1 18.84205198 2.133900005 24.97876587 0.983480914 1.123090304 0.288356145 0.098599062 11.47458859 2711.684746 0.037768518 0.025463538 136.1131251 -2.133900005 0.13960939 LGFSLT(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LGFSLTPSK 9 0 P38432 P38432 COIL Coilin 1 LGFSLT(1)PSK;LGFS(0.008)LT(0.991)PS(0.001)K;LGFS(0.009)LT(0.989)PS(0.002)K 181.4 0.0005313 1953701000 3426810 3515130 2229240 2748290 3323200 2723260 3612630 4529060 3544100 TRUE FALSE 2973948.376 3492038.88 3307307.92 3372331.249 3257074.822 2828025.574 3262277.699 3560555.764 3125120.535 0.951626775 1.117409341 1.058297715 1.079104377 1.042223743 0.904933279 1.043888599 1.139333899 1 21.5754804 0.930256545 18.92938766 4.96E-05 1.047840906 0.028943089 0.069939979 150.1879557 82669.13743 6729.2801 0.016939452 8.516409681 -0.930256545 1.0477913 LGFTQSQIDEIDHDYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGFTQSQIDEIDHDYER 17 0 Q13546-2;Q13546 Q13546-2 RIPK1 Receptor-interacting serine/threonine-protein kinase 1 0 111.33 0.00051504 103870000 42701 42034 25873 37033 50252 46527 41266 41055 51426 FALSE TRUE 37057.95466 41757.87589 38385.26934 45441.90866 49252.08352 48316.9238 37264.02967 32275.70774 45346.47686 0.817217946 0.920862629 0.846488459 1.002104503 1.086128117 1.065505573 0.8217624 0.711757781 1 15.46870285 2.139579786 10.10640543 0.814994223 0.957667298 0.171461037 0.109770555 0.463399657 43.6112903 0.046962065 0.031653602 137.9049279 -2.139579786 0.142673075 LGGAVPFAPPEVS(ph)PEQAK ddPTM_MDA-MB-175_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 269.91 4.09E-32 576270000 1997990 1905550 1326120 1674180 1887250 1562980 2148120 2743530 2388050 TRUE FALSE 1733950.559 1893032.317 1967436.068 2054328.157 1849697.417 1623108.852 1939795.653 2156847.46 2105737.449 0.823441004 0.898987819 0.93432164 0.975586086 0.878408378 0.770803052 0.9211954 1.024271787 1 21.00589414 1.847148351 4.491021607 1.010899278 0.885082209 0.475194588 0.056120573 0.201533116 6.174995652 0.033340659 0.016078358 70.33125241 -1.847148351 -0.125817069 LGGLRPES(ph)PESLTSVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 LGGLRPESPESLTSVSR 17 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 LGGLRPES(0.502)PES(0.02)LT(0.099)S(0.099)VS(0.279)R;LGGLRPES(0.308)PES(0.037)LT(0.299)S(0.178)VS(0.178)R;LGGLRPES(0.999)PES(0.001)LTSVSR;LGGLRPES(1)PESLTSVSR;LGGLRPES(0.991)PES(0.009)LTSVSR;LGGLRPES(0.999)PES(0.001)LTSVSR;LGGLRPES(0.997)PES(0.002)LT(0.001)S(0.001)VSR 196.4 9.71E-12 14163530000 2647531 1991831 1234299 1603784 1966343 2047030 1694736 2195964 2044637 TRUE FALSE 2297653.07 1978746.531 1831210.125 1967947.67 1927216.621 2125780.569 1530380.764 1726374.188 1802922.343 1.274404901 1.097521775 1.015689961 1.091532132 1.06894045 1.179074948 0.848833434 0.957542178 1 20.78190583 8 0.208249876 0.908180424 2.439009182 0.449622131 0.086826466 97.58743507 1.470595974 0.519282758 47.74696136 100000000 -8 1.530828758 LGGPEGPGS(ph)PLLAT ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGGPEGPGSPLLAT 14 0 Q9C086 Q9C086 INO80B INO80 complex subunit B 1 LGGPEGPGS(1)PLLAT;LGGPEGPGS(1)PLLAT 209.19 7.33E-09 135806000 499860 438820 273730 331990 427570 435710 426430 503110 459250 TRUE FALSE 433802.2345 435937.3625 406106.7436 407373.4036 419062.1935 452472.0456 385074.8842 395523.8417 404957.9882 1.07122775 1.076500218 1.002836727 1.005964608 1.034828811 1.117330831 0.950900823 0.976703395 1 18.62741272 -2 0.161812104 0.624163664 1.091344086 0.234047694 0.043951956 193.9966498 2.570453151 21.07822091 0.592193203 0.01 2 0.467180421 LGGS(ph)AVISLEGKPL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LGGSAVISLEGKPL 14 1 G3V1A4;P23528;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 1 LGGS(1)AVISLEGKPL;LGGS(1)AVISLEGKPL;LGGS(1)AVISLEGKPL 151.9 1.79E-05 216995000 1297630 1129120 743860 852270 1065630 790990 1161720 1334460 1227900 TRUE FALSE 1126144.908 1121702.736 1103593.184 1045790.93 1044426.048 821419.8971 1049056.573 1049096.114 1082739.061 1.040088927 1.03598621 1.019260525 0.965875313 0.964614731 0.758649916 0.968891408 0.968927927 1 20.04625417 3.628565566 2.021213517 0.931530775 1.036950156 0.331275699 0.065252079 0.42203804 3.378420621 0.020959249 0.037256273 4251.728907 -3.628565566 0.105419381 LGGSLADSYLDEGFLLDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGGSLADSYLDEGFLLDKK 19 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 243.29 3.03E-24 921990000 960200 737910 586600 640200 599120 618640 1093710 1155740 731110 FALSE TRUE 833307.1372 733062.6206 870281.7221 785567.1948 587198.6842 642439.4811 987642.1725 908593.995 644679.0087 1.292592323 1.137097084 1.349945803 1.218540055 0.910838846 0.996526135 1.531990586 1.409374251 1 19.29822148 1.204429669 23.71487253 0.999996661 1.23642842 0.133060698 0.184708854 6407.555822 4451594.129 8.208195829 0.04958749 16.01141334 -1.204429669 0.236431759 LGGSPTSLGTWGSWIGPDHDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGGSPTSLGTWGSWIGPDHDK 21 0 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 275.69 8.82E-45 1232000000 924240 715360 626140 853350 761940 701590 715720 821240 1261200 FALSE TRUE 802099.3423 710660.7531 928943.3983 1047116.16 746778.8847 728580.6213 646309.5846 645624.2169 1112102.373 0.721245959 0.639024581 0.835303854 0.941564541 0.671501926 0.655138087 0.581160153 0.580543871 1 20.08485817 3.092043872 22.89110213 0.67208114 0.781178977 0.070202614 0.140205581 21.09135975 5231.774263 0.043172116 0.048952577 1236.072295 -3.092043872 0.109097838 LGGSPTSLGTWGSWIGPDHDKFSAMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGGSPTSLGTWGSWIGPDHDKFSAMK 26 1 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 227.2 8.22E-35 1662980000 1106340 744900 470210 581730 734380 746070 959110 963340 331822 FALSE TRUE 960134.3659 740006.7029 697605.1288 713820.6877 719767.2748 774771.7957 866095.6598 757337.2377 292594.3812 3.281451824 2.529121372 2.384205486 2.439625412 2.459949066 2.647938052 2.96005568 2.588351952 1 18.15854254 1.239976272 6.560152464 0.956234391 2.648845446 0.787883305 0.271025437 0.05293151 10.9672891 0.400893014 0.067008355 17.37705886 -1.239976272 1.692611055 LGGSVLGQIPFLQNCEDEDS(ph)DEDDELDSVQHKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGGSVLGQIPFLQNCEDEDSDEDDELDSVQHKK 33 1 F5GYK2;Q9NRL3;Q9NRL3-3;R4GN16;Q9NRL3-2 F5GYK2 STRN4 Striatin-4 1 LGGSVLGQIPFLQNCEDEDS(1)DEDDELDSVQHKK 130.88 2.99E-08 272050000 153950 127260 75115 77770 111430 80967 149260 191260 55225 TRUE FALSE 133605.1174 126424.0207 111440.8652 95428.86714 109212.761 84081.85288 134784.7882 150360.5374 48696.36341 2.743636446 2.596169648 2.288484343 1.959671328 2.2427293 1.726655688 2.767861473 3.087715937 1 15.57152642 4.307990483 3.410672413 2.248429181 2.711889702 0.111411167 0.566699381 0.634806597 14.38550829 0.150549954 0.460321147 20323.12475 -4.307990483 0.463460521 LGHASDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LGHASDR 7 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;; 107.67 0.017273 325473000 477730 654560 167322 234221 453530 596650 443230 469820 620140 FALSE TRUE 414596.7701 650260.1523 248239.4789 287404.4579 444505.6403 619603.5116 400245.6228 369352.6491 546827.7557 0.758185308 1.189149866 0.453962836 0.525584985 0.812880538 1.133087165 0.731940942 0.675446053 1 19.06072695 3.011496297 24.99390351 0.852995398 0.735139213 0.082704728 0.229944348 786.2697244 1709402.265 0.073207128 0.082943189 1026.824677 -3.011496297 -0.117856186 LGHDPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LGHDPYR 7 0 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-6 P18583-7 SON Protein SON 0 ;;; 101.64 0.0089085 2006820000 1542560 1519840 941610 1048090 1443050 1657360 1253350 1467040 1369440 FALSE TRUE 1338706.788 1509856.071 1396975.745 1286074.854 1414336.128 1721119.712 1131800.31 1153324.913 1207546.363 1.108617299 1.250350394 1.156871312 1.065031449 1.171247889 1.425303213 0.937272758 0.955097831 1 20.20364715 2.182109034 24.99984813 0.961123554 1.189809078 0.558883144 0.097085628 61.99374998 27453.62644 0.039433572 0.026586123 152.0929325 -2.182109034 0.228685524 GSTAPVGGGAFPTIVEREPWDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 GSTAPVGGGAFPTIVEREPWDGR 23 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ; 149.71 8.40E-08 402520000 451000 448870 222360 231000 377720 463290 322770 306330 115078 FALSE TRUE 391399.2073 445921.3434 329894.0397 283452.0806 370204.111 481113.0661 291467.8151 240823.7134 101473.6099 3.857152688 4.39445629 3.251032854 2.793357611 3.648279698 4.741262939 2.872350902 2.373264473 1 16.63074505 1.498597337 1.629094657 0.730327539 3.722441836 0.705168683 0.57895403 0.343527467 1.342223206 1.486942897 0.177024546 31.52080765 -1.498597337 2.992114298 up LGHELELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LGHELELR 8 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 ;; 182.39 0.00022882 397652000 209876 209721 154876 188004 222959 256193 188765 221635 259636 FALSE TRUE 182140.3548 208343.3289 229774.5516 230693.1817 218522.5521 266048.9105 170458.5994 174240.08 228942.1279 0.795573783 0.910026175 1.003635957 1.007648456 0.954488168 1.162079312 0.744548856 0.761066046 1 17.80462343 2.203581643 24.99998556 0.815982016 0.971643752 0.23961851 0.113361999 228.2150955 163107.1155 0.04635089 0.031251233 159.8017913 -2.203581643 0.155661736 LGHPEALSAGTGS(ph)PQPPSFTYAQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LGHPEALSAGTGSPQPPSFTYAQQR 25 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 LGHPEALSAGTGS(1)PQPPSFTYAQQR;LGHPEALSAGTGS(1)PQPPSFTYAQQR;LGHPEALSAGT(0.002)GS(0.998)PQPPSFTYAQQR;LGHPEALSAGTGS(1)PQPPSFTYAQQR;LGHPEALSAGT(0.001)GS(0.999)PQPPSFTYAQQR 356.71 2.14E-103 14566590000 1748463 1988752 1030915 1380306 1809277 1968034 1824217 2093703 1963170 TRUE FALSE 1517399.185 1975687.757 1529468.942 1693725.574 1773275.927 2043745.541 1647304.716 1645980.907 1731086.279 0.876558958 1.141299415 0.883531318 0.978417768 1.024371777 1.180614488 0.951601741 0.950837013 1 20.7232462 5.026411162 13.52815206 1.006512217 0.580707328 0.18719589 0.088737475 406115.4466 6218792.185 0.021437477 3630765.792 106270.1179 -5.026411162 -0.425804889 LGHVVMGNNAVSPYQQVIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGHVVMGNNAVSPYQQVIEK 20 0 P60228;E5RGA2;H0YAW4 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 132.79 1.19E-05 272370000 137330 122720 69598 91660 107430 108300 140770 182480 150090 FALSE TRUE 119181.4926 121913.8442 103255.8256 112472.8039 105292.3532 112466.3711 127118.1471 143458.0721 132346.5312 0.900526002 0.921171436 0.780192912 0.849835677 0.795580755 0.849787071 0.96049474 1.083957931 1 17.01396086 2.070299956 3.24493118 1.044213183 0.846980912 0.751871945 0.046388256 0.111838647 2.356151438 0.023866855 0.013591801 117.5709306 -2.070299956 -0.197232271 LGIAVIHGEAQDAESDLVDGRHS(ph)PPMVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 17 LGIAVIHGEAQDAESDLVDGRHSPPMVR 28 1 O60256;O60256-2;O60256-3;O60256-4;E7EPA1;I3L0S1;C9K0K7 O60256 PRPSAP2 Phosphoribosyl pyrophosphate synthase-associated protein 2 1 LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.124)DLVDGRHS(0.876)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.001)DLVDGRHS(0.999)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.001)DLVDGRHS(0.999)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR 262.14 5.27E-54 14006266000 4559046 3593534 2259539 2838605 3657179 3671347 3316272 4070739 3339385 TRUE FALSE 3956556.52 3569927.839 3352259.618 3483153.651 3584408.293 3812586.095 2994660.452 3200243.143 2944606.71 1.343662129 1.212361511 1.138440528 1.182892656 1.21727913 1.294769207 1.016998447 1.086815137 1 21.48964353 2.229953458 24.99824082 1.044748115 1.223599516 0.699103943 0.06064249 113.4083271 329374.875 0.024966405 0.017129868 169.8061668 -2.229953458 0.178851401 LGIDDLVHFDFMDPPAPETLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGIDDLVHFDFMDPPAPETLMR 22 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 119.18 7.48E-05 679770000 543400 500420 233220 290060 397730 462550 447420 482540 440070 FALSE TRUE 471588.3132 497132.7081 346005.9721 355922.5563 389815.9511 480344.5978 404029.2773 379352.5761 388045.4259 1.215291514 1.281119876 0.891663576 0.917218791 1.004562675 1.237856616 1.041190671 0.977598371 1 18.56586602 4.252394852 24.99931076 1.013417573 1.248205827 0.527658562 0.09364868 198.1210714 358010.3552 0.025011921 0.065436881 17881.12552 -4.252394852 0.234788254 LGIHEDSQNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 19 LGIHEDSQNR 10 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;;;;;;;;;;;; 242.12 2.39E-12 73648537900 23692777.2 23133656.4 12463044.2 16835010.7 21725374.1 22061825.7 20838391.2 24127355.3 23057985 FALSE TRUE 20561716.66 22981689.89 18490214.06 20657657.19 21293081.66 22910558.41 18817487.23 18967908.13 20332096.28 1.011293493 1.130315811 0.909410117 1.016012166 1.047264452 1.126817328 0.925506498 0.932904697 1 24.27725563 2.205011486 24.99962832 0.947520661 1.037561123 0.286641874 0.064716172 232.5255021 173268.2211 0.026229453 0.017685049 160.3287793 -2.205011486 0.090040462 LGIHEDSQNRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LGIHEDSQNRK 11 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;; 150.09 2.21E-05 8377560000 12571930 10888530 5669470 8664100 10640370 9202140 12451970 14851430 9064150 FALSE TRUE 10910517.6 10817002.53 8411244.655 10631416.33 10428647.45 9556152.28 11244379.87 11675567.27 7992596.513 1.365077992 1.353377781 1.052379492 1.330158017 1.30478843 1.19562551 1.406849432 1.460797783 1 22.93023283 2.242330053 24.98644629 1.329863393 1.265678439 0 0.151122853 383.2899143 2540743.198 0.057297911 0.042641612 174.7149437 -2.242330053 -0.064184953 LGIHEDSTNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 LGIHEDSTNR 10 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;;;; 209.6 9.25E-08 56127890000 19676570 16168485 8703303 12507193 15733956 15673016 15456728 18442980 16985020 FALSE TRUE 17076261.42 16062273.16 12912249.44 15347142.33 15420881.06 16275967.07 13957736.9 14499092.25 14977070.28 1.140160331 1.07245762 0.862134529 1.024709241 1.029632683 1.086725692 0.931940402 0.968086012 1 23.83625211 4.468020469 24.96323721 0.986782359 1.123234703 0.428457129 0.060202184 151.2809379 414960.9897 0.015070041 0.040001237 29377.88111 -4.468020469 0.136452344 LGIHEDSTNRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LGIHEDSTNRR 11 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;; 171.92 9.06E-06 11317510000 9576090 7672360 3830480 5331870 7313880 7447640 7410460 8494900 5078410 FALSE TRUE 8310585.444 7621959.762 5682912.94 6542552.576 7168348.097 7734155.53 6691794.73 6678331.742 4478046.155 1.855850779 1.702072622 1.269060823 1.461028393 1.60077584 1.727127247 1.494355908 1.491349466 1 22.09443797 1.025013511 1.856796073 0.471662528 1.581766739 0.565543183 0.160406673 1.35419121 2.704452474 3.227348217 0.045856708 10.59286679 -1.025013511 1.110104212 LGIHPSSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPEMGTDNDSENWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGIHPSSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPEMGTDNDSENWK 51 0 A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 115.57 1.32E-09 171320000 61031 72545 13961 45880 95107 79522 85659 99181 97413 FALSE TRUE 52965.59872 72068.44712 20712.5863 56297.75523 93214.55677 82581.2628 77351.80336 77971.91498 85896.94611 0.616617949 0.839010586 0.241132977 0.65541044 1.08519058 0.961399288 0.900518666 0.907737917 1 16.39031922 3.358546687 5.861526107 0.955928259 0.570887131 0.612966683 0.152031486 0.142938451 6.774787829 0.043532794 0.056355778 2283.21436 -3.358546687 -0.385041129 LGILTHLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGILTHLYR 9 0 C9JEV6;Q9UJ70;Q9UJ70-2;H7C3G9;H7C286;E9PPU6;H0YC94 C9JEV6 NAGK N-acetyl-D-glucosamine kinase 0 ; 167.23 6.01E-05 1212830000 861750 1115890 610110 687280 946300 1023230 915870 1046670 1135480 FALSE TRUE 747867.5541 1108559.645 905161.2367 843337.4284 927470.4814 1062594.32 827049.0684 822847.7657 1001244.848 0.74693773 1.107181373 0.90403585 0.842288907 0.926317357 1.061273196 0.826020798 0.821824719 1 19.93336339 LGIYDADGDGDFDVDDAK ddPTM_MDA-MB-175_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 ;; 285.54 2.71E-39 2251080000 2650155 2414035 1969941 2965272 3014732 2493526 2269910 4317125 3632991 FALSE TRUE 2299930.302 2398177.045 2922611.057 3638582.329 2954744.731 2589453.559 2049774.478 3393941.415 3203502.943 0.71794231 0.748610845 0.912317269 1.135813637 0.922348062 0.808319394 0.639854095 1.059446948 1 21.61121889 4.248530704 5.042147534 0.926051956 0.728206284 0.261897098 0.134671834 0.25115902 17.5350896 0.03649507 0.092376145 17722.73339 -4.248530704 -0.197845672 LGLALNYSVFYYEIQNAPEQACHLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LGLALNYSVFYYEIQNAPEQACHLAK 26 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;; 299.4 1.53E-70 1092586000 487345 366275 303544 406767 342737 295711 438625 452533 593789 FALSE TRUE 422941.1235 363868.9154 450338.8937 499129.6644 335917.2043 307087.1935 396087.215 355762.3396 523591.9409 0.807768589 0.69494751 0.860095159 0.953279884 0.641562977 0.586500994 0.756480733 0.679464888 1 18.99808337 5.098126343 17.53407945 0.761603913 3.23431539 0.002354249 0.133149832 970.3217929 176772.4931 0.031630577 1856.610721 125350.5786 -5.098126343 2.472711477 LGLAVIHGEAQCTELDMDDGRHS(ph)PPMVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 29 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;LGLAVIHGEAQCT(0.023)ELDMDDGRHS(0.977)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCT(0.001)ELDMDDGRHS(0.999)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK 272.67 9.30E-62 13932047000 6383827.3 5792223.4 4173053.3 5057041.8 5792296.9 5157373.8 6498999.1 7554189.7 7437719.7 TRUE FALSE 5540188.348 5754173.903 6191155.834 6205320.433 5677041.524 5355781.307 5868727.168 5938785.019 6558440.95 0.844741668 0.877369172 0.943998106 0.946157857 0.865608392 0.816624156 0.894835711 0.9055178 1 22.64492147 1.187392331 2.436297629 1.040101157 0.885661528 0.454770148 0.039550404 0.697105968 3.959255479 0.242703889 0.011317266 15.39544798 -1.187392331 -0.154439629 LGLDPTQEDCVATHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGLDPTQEDCVATHR 15 0 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 ; 151.8 2.94E-06 976430000 369230 417900 228442 264189 427090 443110 335020 393840 384280 FALSE TRUE 320435.32 415154.7874 338917.3153 324177.1503 418591.7446 460156.7284 302529.812 309620.3809 338850.8562 0.945652974 1.225184413 1.000196131 0.95669568 1.235327392 1.357991931 0.892811119 0.913736457 1 18.37029089 LGLDYEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LGLDYEER 8 0 Q99623-2;Q99623;F5GY37;J3KPX7;F5H3X6;F5GWA7 Q99623-2 PHB2 Prohibitin-2 0 ;;; 121.31 0.0033468 2181150000 4049010 3731600 3034840 4609860 4876610 5880200 3015530 4642480 4470150 FALSE TRUE 3513923.07 3707086.874 4502498.775 5656599.17 4779575.002 6106415.099 2723084.365 3649721.78 3941693.959 0.891475367 0.940480644 1.142275078 1.435068077 1.212568771 1.549185493 0.690841144 0.925927233 1 21.91038434 2.217551887 24.99066314 0.875878711 1.192888926 0.345318575 0.209565018 290.190557 345189.7784 0.090074808 0.060798676 165.0258155 -2.217551887 0.317010215 LGLGIDEDDPTADDTSAAVTEEMPPLEGDDDTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 15 LGLGIDEDDPTADDTSAAVTEEMPPLEGDDDTSR 34 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;;;;;;;; 339.92 7.37E-118 12109075000 5016116 4637095 3180948 3709343 4526463 4486324 4608178 5245450 5055960 FALSE TRUE 4353223.561 4606633.618 4719265.092 4551606.022 4436395.242 4658915.787 4161277.607 4123751.338 4458250.169 0.976442191 1.03328289 1.058546496 1.020940021 0.995097869 1.04500995 0.933388089 0.924970825 1 22.08804614 2.234133159 24.99905986 0.946183142 1.022537526 0.528755652 0.030381502 76.93004423 434369.01 0.012015409 0.008411192 171.4482903 -2.234133159 0.076354384 LGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 LGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASR 34 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;; 175.17 3.45E-15 2773810000 1694356 1355719 895007 1116151 1277557 1337931 1381897 1565786 1423176 FALSE TRUE 1470442.562 1346813.193 1327835.379 1369590.144 1252136.115 1389402.071 1247880.842 1230954.849 1254929.755 1.171732965 1.073217993 1.058095383 1.091367974 0.997773868 1.107155254 0.994383022 0.98089542 1 20.25917518 8 0.175900793 0.945443885 1.774245755 0.598354375 0.038625261 83.92532081 1.166314452 0.374204415 17.90689438 100000000 -8 0.82880187 LGLGTLSSS(ph)LSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGLGTLSSSLSR 12 0 O95248;O95248-5;O95248-4 O95248 SBF1 Myotubularin-related protein 5 1 LGLGTLS(0.018)S(0.236)S(0.742)LS(0.004)R 91.712 0.0085425 98901000 176580 202050 144500 152750 214070 239550 194570 192960 197900 TRUE FALSE 153244.5056 200722.7202 214380.6833 187434.2221 209810.4258 248765.6435 175700.6313 151697.0056 174504.4874 0.878169426 1.150243889 1.228511005 1.074093995 1.202321092 1.425554421 1.006854517 0.869301459 1 17.41290461 2.012368379 24.98770069 0.929143924 1.165177536 0.327574575 0.138516537 225.2447186 455057.8402 0.056405977 0.038001149 102.8888656 -2.012368379 0.236033612 LGLHQVLQDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGLHQVLQDLR 11 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 175.91 9.28E-06 1240120000 686470 900130 589750 663260 869500 996650 780330 876330 917430 FALSE TRUE 595751.2502 894216.9868 874955.0726 813863.3203 852198.6511 1034991.77 704653.7167 688933.6491 808972.4705 0.736429572 1.105373816 1.08156347 1.006045755 1.053433438 1.279390595 0.871047832 0.851615691 1 19.62573108 LGLHSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGLHSLR 7 0 P61204;P61204-2;H0YGG7;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 114.02 0.013954 808230000 648800 737060 546210 575710 668210 715710 603440 649400 897730 FALSE TRUE 563059.4362 732218.2043 810358.983 706433.7547 654913.9283 743243.8268 544918.4817 510530.8636 791601.3821 0.711291628 0.924983484 1.023695766 0.892410967 0.827327924 0.938911735 0.688374849 0.644934275 1 19.59441461 2.241213031 25 0.746370868 0.892012853 0.131299568 0.122679396 99.98114048 942373.4936 0.046933756 0.034669137 174.2661477 -2.241213031 0.145641985 LGLPLLTDCAQPS(ph)RPHGSPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGLPLLTDCAQPSRPHGSPSR 21 1 U3KQ90;P55199 U3KQ90 ELL RNA polymerase II elongation factor ELL 1 LGLPLLTDCAQPS(0.5)RPHGS(0.5)PS(0.001)R 110.9 0.00015771 392990000 120420 129640 79213 97728 131110 152740 126740 135640 130680 TRUE FALSE 104506.1919 128788.3863 117520.6718 119918.6361 128501.1675 158616.0066 114448.7743 106634.4416 115231.1593 0.906926499 1.11765244 1.019868866 1.0406789 1.115159895 1.376502741 0.9932103 0.925395893 1 16.81417136 2.019204155 24.99952533 0.957949114 1.0997267 0.195584353 0.11880344 345.7833409 450131.0319 0.049255879 0.033203521 104.5211441 -2.019204155 0.141777586 LGLPLLTDCAQPSRPHGS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LGLPLLTDCAQPSRPHGSPSR 21 1 U3KQ90;P55199 U3KQ90 ELL RNA polymerase II elongation factor ELL 1 LGLPLLTDCAQPS(0.002)RPHGS(0.968)PS(0.03)R;LGLPLLTDCAQPS(0.022)RPHGS(0.6)PS(0.378)R;LGLPLLTDCAQPS(0.004)RPHGS(0.988)PS(0.008)R 165.47 8.88E-12 2083310000 656943 710496 462613 491951 637307 684663 653249 654254 642200 TRUE FALSE 570126.3181 705828.705 686334.1941 603655.9936 624625.8376 711002.4286 589897.0125 514346.8735 566279.8476 1.006792526 1.246430909 1.212005331 1.06600296 1.103033845 1.255567246 1.041705819 0.908290973 1 19.11115566 2.012210354 7.210247311 0.95522072 1.150100158 0.505137962 0.080477362 0.100760861 28.34193114 0.033196423 0.021384327 102.8514347 -2.012210354 0.194879438 LGLQSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGLQSLR 7 0 P18085;C9JAK5;U3KQF2 P18085 ARF4 ADP-ribosylation factor 4 0 ; 125.25 0.0094623 721340000 597190 680810 531730 549010 598170 640100 577620 676380 790180 FALSE TRUE 518269.8284 676337.7143 788876.4065 673671.1116 586267.5873 664725.0612 521602.5013 531741.4006 696765.8206 0.743822118 0.970681532 1.132197337 0.966854418 0.841412667 0.954015024 0.748605178 0.763156551 1 19.41031433 2.840320718 1.633056966 0.829150491 0.961447385 0.084742697 0.121734005 0.674572502 3.634499207 0.051983324 0.049624769 692.3420626 -2.840320718 0.132296894 LGLVLDQAEAEGVCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LGLVLDQAEAEGVCR 15 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ;;;; 270.93 5.12E-33 336622000 413694 464093 269965 314796 415007 444172 400462 488819 450930 FALSE TRUE 359023.2897 461044.3425 400520.977 386275.2432 406749.1726 461259.5843 361625.2569 384288.8608 397621.5691 0.902927099 1.159505365 1.007291878 0.971464511 1.022955504 1.160046688 0.909470927 0.966468851 1 18.60103649 2.183293679 24.99999982 0.95822733 1.037902343 0.17680818 0.08006214 147.1408134 66557.83538 0.031112514 0.020976066 152.5083699 -2.183293679 0.079675013 LGMLS(ph)PEGTCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 17 LGMLSPEGTCK 11 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 LGMLS(1)PEGTCK;LGMLS(0.998)PEGT(0.002)CK;LGMLS(0.996)PEGT(0.004)CK;LGMLS(0.999)PEGT(0.001)CK;LGMLS(0.997)PEGT(0.003)CK;LGMLS(0.98)PEGT(0.02)CK;LGMLS(1)PEGTCK;LGMLS(0.999)PEGT(0.001)CK;LGMLS(1)PEGTCK;LGMLS(0.997)PEGT(0.003)CK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(0.996)PEGT(0.004)CK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK 221.75 3.20E-11 31669209000 45990930 43691400 35450630 34178810 45391690 42253530 55711430 59967020 60305270 TRUE FALSE 39913112.07 43404388.32 52594673.24 41939631.2 44488484.18 43879050.64 50308544.09 47143539.44 53176049.68 0.750584376 0.816239427 0.989066949 0.788693998 0.836626347 0.82516567 0.946075242 0.886555878 1 25.66427327 -2 0.478608093 5.178860332 0.831950639 0.373463992 0.066756013 121.8010862 1.454920572 523.8477212 0.04695334 0.01 2 -4.346909694 LGMLSPEGTCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 122.26 0.0021181 0 258960 250890 206930 182490 278350 290330 269010 311990 301800 FALSE TRUE 224737.7799 249241.8871 307002.0401 223927.1437 272811.3796 301499.183 242921.4516 245273.3664 266121.5478 0.844492983 0.936571612 1.153615867 0.841446871 1.025138257 1.132937883 0.912821429 0.921659176 1 18.0217258 4.583347371 4.634429163 0.990134108 0.852960698 0.206012682 0.095342502 0.369351716 12.03561064 0.023147685 0.102997036 38313.1069 -4.583347371 -0.13717341 LGNDFHTNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LGNDFHTNK 9 0 H3BNC9;P08708;H0YN88;A0A075B716;H0YN73;A0A0J9YYC4 H3BNC9 RPS17 40S ribosomal protein S17 0 ;;; 112.75 0.0019122 2582080000 5697430 5181990 4389620 4852410 5138880 4021010 6032700 6557900 11321800 FALSE TRUE 4944500.19 5147949.166 6512454.914 5954223.855 5036626.342 4175700.857 5447649.683 5155544.119 9983349.702 0.495274666 0.515653495 0.652331643 0.596415435 0.504502646 0.418266512 0.545673531 0.516414257 1 23.25109253 1.237427316 24.99993397 1.000000558 0.531684285 0.850760006 0.061788055 11.12885949 245384.3717 0.096062304 0.016067236 17.27536832 -1.237427316 -0.468316273 LGNDFHTNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LGNDFHTNKR 10 1 H3BNC9;P08708;H0YN88;A0A075B716;H0YN73;A0A0J9YYC4 H3BNC9 RPS17 40S ribosomal protein S17 0 ;; 173.71 2.16E-06 5218240000 6196500 5718400 3798450 4256300 5748400 4889100 6523000 7147600 4087500 FALSE TRUE 5377616.825 5680835.454 5635393.125 5222757.968 5634018.087 5077186.841 5890400.464 5619141.363 3604280.406 1.492008451 1.57613582 1.563527942 1.449043187 1.56314644 1.408654785 1.63427919 1.559018924 1 21.78127982 1.236931362 24.99994064 0.99999934 1.53399689 0.865572699 0.065719049 13.87535593 212840.9535 0.095541026 0.015435343 17.25565155 -1.236931362 0.533997549 LGNSCEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LGNSCEFR 8 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ;;; 164.77 0.00076339 1367960000 1288650 1191710 736040 839050 1196600 1198130 1120100 1270940 1149370 FALSE TRUE 1118351.637 1183881.579 1091991.406 1029569.127 1172790.001 1244222.836 1011472.874 999159.3715 1013492.788 1.103462847 1.168120378 1.077453554 1.015862312 1.157176464 1.227658303 0.998006978 0.985857407 1 19.95090439 2.126334424 10.67959067 0.992005767 1.121208104 0.545366592 0.056035784 0.270224748 24.35645794 0.024017217 0.016189305 133.7625143 -2.126334424 0.129202337 LGNSGAS(ph)PSSAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGNSGASPSSAGK 13 0 Q8IWI9-3;Q8IWI9 Q8IWI9-3 MGA MAX gene-associated protein 1 LGNSGAS(0.958)PS(0.042)SAGK;LGNSGAS(1)PSSAGK 220.24 1.42E-07 0 478220 346460 219360 272270 324410 256600 357410 437160 311570 TRUE FALSE 415022.0153 344184.0814 325443.2297 334093.0649 317954.8757 266471.568 322748.4332 343676.736 274736.5495 1.51061814 1.252778642 1.184564741 1.216048849 1.157308251 0.969916702 1.174756085 1.25093198 1 18.06768933 7.999998305 0.782905017 1.132380576 85.82084601 0.667786278 0.085272709 301.5831434 1.129272842 0.031714271 45217.34094 99999609.75 -7.999998305 84.68846544 LGPGGLDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LGPGGLDDR 9 0 Q9Y446;Q9Y446-2;E9PQ15;E9PK71;E9PKC4;E9PRW6;E9PJR7 Q9Y446 PKP3 Plakophilin-3 0 ;; 131.03 0.00080154 352270000 723460 705070 470450 542760 695870 687540 717000 804430 785660 FALSE TRUE 627852.928 700438.3487 697961.1936 666001.9536 682023.5484 713990.1087 647465.4504 632408.9046 692780.1698 0.906280167 1.01105427 1.007478597 0.961346734 0.984473255 1.030615684 0.934590045 0.912856534 1 19.40203811 2.188357804 24.99945629 0.940981241 0.984913791 0.130645619 0.039909727 164.0160556 81673.57101 0.015732048 0.010606562 154.2971144 -2.188357804 0.04393255 LGPGRPLPTFPTSECT(ph)SDVEPDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGPGRPLPTFPTSECTSDVEPDTR 24 1 Q8TDD1-2;Q8TDD1;H0YHZ9 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 LGPGRPLPTFPT(0.005)S(0.021)ECT(0.487)S(0.487)DVEPDTR;LGPGRPLPT(0.036)FPT(0.016)S(0.016)ECT(0.466)S(0.466)DVEPDTR 109.41 0.003481 525770000 300815 265316 191887 184897 279539 257921 209397 298885 284781 TRUE FALSE 261061.5356 263573.1217 284684.195 226880.6898 273976.7208 267843.3878 189089.7112 234970.7687 251114.5146 1.039611494 1.04961325 1.133682756 0.903494926 1.09104295 1.066618503 0.753001918 0.935711618 1 17.93798589 2.281875189 24.99990356 0.898492886 1.04681947 0.418797898 0.083898924 126.1658083 72818.69022 0.030366194 0.023521398 191.3705869 -2.281875189 0.148326584 LGPGRPLPTFPTSECTS(ph)DVEPDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGPGRPLPTFPTSECTSDVEPDTR 24 1 Q8TDD1-2;Q8TDD1;H0YHZ9 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 LGPGRPLPTFPT(0.002)S(0.008)ECT(0.159)S(0.83)DVEPDTR;LGPGRPLPTFPT(0.001)S(0.004)ECT(0.166)S(0.829)DVEPDTR 137.64 7.42E-06 1158350000 464150 425320 219380 286830 398400 434270 348620 442160 486000 TRUE FALSE 402811.4015 422526.0449 325472.9018 351959.1354 390472.6195 450976.6479 314810.8861 347607.5249 428545.6337 0.939949844 0.985953448 0.759482483 0.821287414 0.91115762 1.052342184 0.734602949 0.811133045 1 18.70908931 2.805819012 0.01051399 1.82E-06 1.75926583 0 0.10755958 13516.0354 174.3907189 14655.62636 14518.38123 639.4682873 -2.805819012 1.759264006 LGPLFSLLNENHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGPLFSLLNENHR 13 0 Q16401-2;Q16401;F2Z3J2 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ; 185.57 8.54E-06 903270000 599060 591780 348800 437160 578800 610390 547960 640910 596050 FALSE TRUE 519892.7032 587892.5582 517480.8467 536423.8596 567283.0124 633872.0983 494818.9235 503856.3841 525585.648 0.989168378 1.118547587 0.984579485 1.020621209 1.079335051 1.206030075 0.941462016 0.958657045 1 19.00356636 LGPNYLHIPVNCPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGPNYLHIPVNCPYR 15 0 P04040 P04040 CAT Catalase 0 ; 94.728 0.0043592 1863210000 1308600 1153680 817000 1059290 1295920 1707660 949600 1415050 1155530 FALSE TRUE 1135665.194 1146101.4 1212103.933 1299817.985 1270133.727 1773354.785 857507.9382 1112452.569 1018924.56 1.114572402 1.124814776 1.189591438 1.275676371 1.246543442 1.740418138 0.841581381 1.091790907 1 19.95861581 LGQELCGMLHRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGQELCGMLHRPR 13 1 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 0 ; 107.18 0.00079058 666840000 272470 266990 175798 187107 246430 266640 242100 277160 238580 FALSE TRUE 236462.3991 265236.1251 260814.5008 229592.5041 241526.5251 276897.8133 218621.1793 217891.4909 210375.3442 1.124002435 1.260775716 1.239757928 1.091347016 1.148074296 1.316208486 1.039195825 1.035727317 1 17.68260611 2.123638664 8.912316972 1.025704668 1.194400716 0.597466169 0.066511222 0.181104315 13.37402849 0.027079422 0.018242405 132.9347931 -2.123638664 0.168696048 LGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQAR 34 0 Q9NR31;Q5SQT8;Q9NR31-2 Q9NR31 SAR1A GTP-binding protein SAR1a 0 ;;;;; 228.53 3.77E-37 3110010000 535909.3 532729.9 237612 370491.9 529549.3 479483 474478.4 617896.5 521729.8 FALSE TRUE 465087.5282 529230.3622 352521.958 454617.7485 519012.305 497929.0213 428463.5578 485764.142 460051.4974 1.010946668 1.150372002 0.766266298 0.988188825 1.128161321 1.082333226 0.931338253 1.055890796 1 18.81143584 LGQHVPTLHPTSEELTIAGMTFTTFDLGGHVQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LGQHVPTLHPTSEELTIAGMTFTTFDLGGHVQAR 34 0 Q9Y6B6;D6RD69;D6RDB2;D6RAA2 Q9Y6B6 SAR1B GTP-binding protein SAR1b 0 ;; 228.53 3.77E-37 404522000 193283 165047 90472.5 142374 191627 199602 176030 207729 209684 FALSE TRUE 167740.1618 163962.7954 134225.3036 174702.1928 187813.9976 207280.8181 158958.6377 163307.7699 184895.3964 0.90721654 0.886786792 0.725952653 0.94487043 1.015785148 1.121070736 0.859721988 0.88324411 1 17.49634978 3.506359182 24.44509402 0.964494804 0.843123116 0.343121063 0.085459386 707.5779846 591586.0412 0.025315397 0.037467028 3208.922158 -3.506359182 -0.121371688 LGQSDPAPLQHQMDIYQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LGQSDPAPLQHQMDIYQK 18 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ;;;; 232.84 2.57E-21 3179920000 6401640 6101490 4285010 4330900 5524930 4243370 5478870 5699410 7941180 FALSE TRUE 5555647.054 6061408.91 6357255.168 5314297.039 5414994.702 4406615.19 4947530.031 4480635.524 7002382.747 0.7933938 0.865620908 0.907870278 0.758926958 0.773307444 0.629302246 0.7065495 0.639872981 1 22.73941449 3.556670293 3.894193155 0.728824259 0.856226979 0.160716908 0.105853693 0.346286142 9.844551229 0.029575772 0.044251624 3603.050033 -3.556670293 0.12740272 LGS(ph)FGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LGSFGK 6 0 Q6GQQ9;Q6GQQ9-2 Q6GQQ9 OTUD7B OTU domain-containing protein 7B 1 LGS(1)FGK;LGS(1)FGK;LGS(1)FGK;LGS(1)FGK 103.83 0.036029 1078043000 1979090 1761490 1435650 1490180 1948820 1277450 2472690 2574370 2180220 TRUE FALSE 1717548.242 1749918.656 2129935.142 1828548.145 1910042.295 1326594.328 2232888.904 2023861.009 1922476.875 0.89340385 0.910241719 1.10791197 0.951141815 0.993532 0.690044362 1.161464636 1.052736205 1 20.87453481 LGS(ph)LSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGSLSAR 7 0 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2;H0Y4T4;Q00G26 Q5SW79;Q00G26 CEP170;PLIN5 Centrosomal protein of 170 kDa;Perilipin-5 1 LGS(0.978)LS(0.022)AR 130.75 0.0086682 0 184700 128710 134040 130410 188300 199830 197850 198020 214010 TRUE FALSE 160291.427 127864.4955 198862.1923 160021.5837 184553.1984 207517.5894 178662.5375 155674.964 188709.9816 0.849406193 0.677571448 1.053797953 0.847976256 0.977972637 1.099664086 0.946757219 0.824942924 1 17.52581121 4.241455379 24.99993198 0.952194263 0.763488819 0.445539354 0.092416987 70.90451008 612319.6702 0.023659675 0.05717037 17436.34203 -4.241455379 -0.188705444 LGS(ph)LVDEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGSLVDEFK 9 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 1 LGS(1)LVDEFK 110.39 0.0024908 0 37505 30997 21086 21108 31685 24251 35610 41949 31282 TRUE FALSE 32548.61922 30793.37867 31283.26013 25900.89402 31054.53049 25183.95166 32156.54768 32978.5328 27583.8776 1.179987082 1.116354238 1.134113941 0.938986693 1.125821791 0.912995338 1.165773288 1.195572765 1 14.75153766 4.301013282 2.226318262 1.07439427 1.165916423 0.13525372 0.09348793 0.826571968 7.69662211 0.026122337 0.104545177 19999.2303 -4.301013282 0.091522152 LGS(ph)PDYGNSALLSLPGYRPTTR ddPTM_MDA-MB-175_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(0.992)PDYGNS(0.008)ALLSLPGYRPTTR 222.69 5.04E-26 1768090000 638510 626170 415270 413280 679510 529060 606890 689900 559410 TRUE FALSE 554129.2857 622056.648 616095.961 507121.5406 665989.0804 549413.2805 548033.9012 542370.2538 493277.1871 1.123362889 1.26106916 1.248985311 1.028066073 1.350131524 1.11380233 1.111005973 1.0995243 1 18.91203904 1.11315875 0.705464473 0.853391729 1.199897763 0.329665603 0.088695167 3.98169388 1.374961736 1.165445533 0.038862117 12.97653522 -1.11315875 0.346506034 LGS(ph)PGAPQQEDAMDDKELIEYFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGSPGAPQQEDAMDDKELIEYFK 23 1 H0YGG4 H0YGG4 EIF2B1 1 LGS(1)PGAPQQEDAMDDKELIEYFK 63.901 0.020974 49540000 56328 32514 44595 39237 34870 24522 47423 62589 46416 TRUE FALSE 48884.11208 32300.41339 66161.29116 48146.36055 34176.15522 25465.37721 42823.92476 49204.82942 40928.75336 1.194370902 0.789186348 1.616499056 1.17634564 0.835015788 0.622187951 1.046304157 1.202206893 1 15.3208271 3.328919873 8.286708532 0.966052398 1.197324718 0.204701075 0.245231731 0.49744572 40.35785722 0.074792934 0.096545952 2132.651403 -3.328919873 0.23127232 LGS(ph)PHRRPLSVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGSPHRRPLSVDK 13 2 M0QXN6;M0QX46;Q6UUV9;Q6UUV9-2;Q6UUV9-3 M0QXN6 CRTC1 CREB-regulated transcription coactivator 1 1 LGS(1)PHRRPLSVDK 58.98 0.053676 105500000 127070 96939 47276 64679 109340 75196 118880 115740 43347 TRUE FALSE 110277.3775 96302.20133 70138.83173 79365.35551 107164.3479 78088.83878 107351.0359 90989.90169 38222.56704 2.885137919 2.519511607 1.83501102 2.076400453 2.803693112 2.043003514 2.808577346 2.380528278 1 15.22213705 1.239696108 8.120713747 0.984106538 2.411053579 0.613398785 0.354053058 0.060895004 38.03075299 0.485289851 0.085838976 17.36585251 -1.239696108 1.42694704 LGS(ph)PKPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 113.63 0.0017029 6689190000 9707900 6101300 6077070 5243080 6647060 4832780 7993500 8921700 8069300 TRUE FALSE 8424976.418 6061220.159 9015961.379 6433601.449 6514796.511 5018700.174 7218291.6 7013863.884 7115356.547 1.184055411 0.851850518 1.267113084 0.904185392 0.915596635 0.705333618 1.014466605 0.98573611 1 22.76250462 7.999999631 0.570002118 0.936383937 11.2597112 0.179545982 0.14399396 306.2151503 2.677654212 0.072344095 3894.739421 99999915.11 -7.999999631 10.32332726 LGS(ph)PLAVDEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LGSPLAVDEALR 12 0 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 LGS(1)PLAVDEALR;LGS(1)PLAVDEALR;LGS(1)PLAVDEALR;LGS(1)PLAVDEALR;LGS(1)PLAVDEALR;LGS(1)PLAVDEALR 204.94 1.13E-07 248484000 313795 302016 274740 324696 451557 396833 445073 497673 647291 TRUE FALSE 272326.1957 300032.037 407605.183 398423.1895 442571.8992 412099.4223 401909.889 391249.5018 570768.9954 0.477121564 0.525662815 0.714133364 0.698046307 0.77539583 0.722007372 0.704155082 0.685477847 1 19.12254744 5.279188423 0.575060203 0.77401696 8.78E-11 0.592709036 0.089415036 5.208356992 0.855234103 0.048958031 3.063157473 190190.3262 -5.279188423 -0.77401696 LGS(ph)PSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LGSPSGK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LGS(0.977)PS(0.023)GK;LGS(0.984)PS(0.016)GK;LGS(0.989)PS(0.011)GK 105.36 0.0083336 2170960000 6527300 4586930 3650760 5049530 3296230 3821210 5122620 7862300 6849000 TRUE FALSE 5664700.767 4556798.155 5416279.747 6196102.964 3230641.472 3968214.421 4625829.101 6181008.329 6039319.022 0.937970116 0.754521849 0.896836171 1.025960533 0.534934727 0.657063223 0.765952102 1.02346114 1 22.52595445 1.719618209 6.368973882 1.010323884 0.791870728 0.291861942 0.139079336 0.168264228 17.4780053 0.086812408 0.037603218 52.43463016 -1.719618209 -0.218453156 LGS(ph)PVDNLEDMDRDDLTDDSVFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LGSPVDNLEDMDRDDLTDDSVFTR 24 1 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 LGS(1)PVDNLEDMDRDDLTDDSVFTR;LGS(1)PVDNLEDMDRDDLTDDSVFTR;LGS(1)PVDNLEDMDRDDLTDDSVFTR;LGS(1)PVDNLEDMDRDDLTDDSVFTR;LGS(1)PVDNLEDMDRDDLTDDSVFTR;LGS(1)PVDNLEDMDRDDLTDDSVFTR 212.78 9.42E-26 590854000 237715 169530 131565.3 127939 214988 182497 163571 206727 197249 TRUE FALSE 206300.3605 168416.3463 195190.7191 156989.5054 210710.1594 189517.7777 147707.9096 162520.0398 173930.4479 1.186108372 0.968297088 1.122234327 0.902599328 1.211462179 1.089618177 0.849235492 0.934396719 1 17.40815098 2.253942699 24.99995839 0.925958846 1.074797816 0.34924137 0.097736359 249.7412376 405895.1795 0.034562281 0.02667128 179.4496846 -2.253942699 0.14883897 LGS(ph)SSNLQFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGSSSNLQFK 10 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 LGS(0.493)S(0.493)S(0.014)NLQFK;LGS(0.669)S(0.115)S(0.216)NLQFK 177.64 2.42E-06 442240000 682560 638230 580620 547100 655500 542730 699170 859110 732540 TRUE FALSE 592357.9666 634037.4251 861409.7741 671327.4169 642456.8325 563609.1743 631364.601 675396.0121 645939.9557 0.917048034 0.981573317 1.333575616 1.039303129 0.994607667 0.872541123 0.977435434 1.045601849 1 19.30104054 3.348247041 4.63639906 0.981415389 1.084756023 0.133873368 0.114402051 0.434441017 15.72910974 0.034860528 0.045274196 2229.703115 -3.348247041 0.103340634 LGS(ph)VDSFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LGSVDSFER 9 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 LGS(1)VDSFER;LGS(0.999)VDS(0.001)FER;LGS(1)VDSFER 146.9 9.83E-05 859030000 1663720 1272780 1949480 1486030 1951460 1668080 1873630 2177640 2301930 TRUE FALSE 1443855.187 1264419.024 2892255.049 1823455.824 1912629.764 1732252.117 1691925.651 1711968.632 2029798.458 0.711329335 0.62292836 1.424897648 0.89834329 0.942275701 0.853410894 0.833543668 0.843418038 1 20.95290506 LGS(ph)VSLDLCDGDTGEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGSVSLDLCDGDTGEPR 17 0 Q8N6R0-3;Q8N6R0-4;Q8N6R0;Q8N6R0-2 Q8N6R0-3 METTL13 Methyltransferase-like protein 13 1 LGS(0.999)VS(0.001)LDLCDGDTGEPR;LGS(0.894)VS(0.106)LDLCDGDTGEPR 120.77 6.55E-05 69362000 115000 106862 71561 72506 116318 107127 101260 121105 104960 TRUE FALSE 99802.45863 106160.0165 106168.139 88969.59548 114003.4994 111248.245 91439.82079 95207.63819 92551.74837 1.078342229 1.147034155 1.147121916 0.961295676 1.231781154 1.202011274 0.987985882 1.028696268 1 16.49797262 2.221420107 24.9999324 1.009648305 1.12681783 0.382946483 0.073155066 266.2561262 388339.2254 0.029990948 0.020275988 166.50225 -2.221420107 0.117169525 LGS(ph)YSGPTSVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGSYSGPTSVSR 12 0 V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23;A0A2R8YFI4 V9GYZ0 PANK2 "Pantothenate kinase 2, mitochondrial" 1 LGS(0.978)YS(0.022)GPTSVSR 187.11 1.14E-05 451360000 461100 503410 433450 452930 633320 681000 599520 649340 702210 TRUE FALSE 400164.4667 500103.0666 643067.8698 555774.6791 620718.1711 707198.5107 541378.6427 510483.6942 619195.5338 0.646265105 0.807665817 1.038553792 0.8975754 1.002459057 1.142124696 0.87432582 0.824430517 1 19.24003554 4.508002832 3.47146461 0.955235532 0.658621274 0.575402971 0.091024906 0.197095386 4.655594931 0.025029701 0.11157106 32210.89794 -4.508002832 -0.296614258 LGSLSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LGSLSER 7 0 O60664-4;O60664;O60664-3;O60664-2 O60664-4 PLIN3 Perilipin-3 0 ;;; 130.04 0.0083798 1041130000 997280 1074600 647800 762040 1072450 1202890 1019730 1118210 1124620 FALSE TRUE 865486.9212 1067540.882 961078.2468 935072.8291 1051110.343 1249165.957 920836.7416 879089.4934 991668.7048 0.872758127 1.076509601 0.969152543 0.942928646 1.059941025 1.259660561 0.928572957 0.886474978 1 19.9194987 2.068957898 25 0.926809607 1.032483945 0.142541377 0.104789988 83.33551856 30211.0955 0.04319645 0.029123038 117.2081734 -2.068957898 0.105674338 LGSPDYGNSALLSLPGYRPTTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGSPDYGNSALLSLPGYRPTTR 22 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 240.46 1.15E-30 1420910000 315850 348890 223290 281650 363370 362830 276330 351800 342350 FALSE TRUE 274109.6222 346598.1186 331273.7909 345602.9373 356139.6479 376788.3049 249531.5591 276570.3077 301877.773 0.908015252 1.148140571 1.097377218 1.144843934 1.179747831 1.248148551 0.826597986 0.916166517 1 18.20360501 2.232190389 24.99999285 0.911000725 1.12495135 0.510138919 0.095456062 117.033905 459294.3685 0.038037177 0.026350246 170.6830476 -2.232190389 0.213950624 LGSQHS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LGSQHSPGR 9 0 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7;Q8IZP0-11 A0A0A0MRT6 ABI1 Abl interactor 1 1 LGSQHS(1)PGR;LGSQHS(1)PGR;LGSQHS(1)PGR;LGSQHS(1)PGR;LGSQHS(1)PGR;LGSQHS(1)PGR;LGSQHS(1)PGR;LGSQHS(1)PGR 138.63 8.46E-05 12555480000 7612520 7038280 3081740 5077280 6282500 6997430 6640540 7755400 6784850 TRUE FALSE 6606506.194 6992045.075 4572079.772 6230154.025 6157490.542 7266625.66 5996541.453 6096968.063 5982752.762 1.104258601 1.168700321 0.764210047 1.041352413 1.02920692 1.21459568 1.00230474 1.019090761 1 22.51237801 1.949575006 0.003755537 0.000180399 2.063474417 0.004440376 0.120278824 696012.8615 1182.770555 327818.5112 322004.8823 89.03792003 -1.949575006 2.063294018 LGSQPIRAS(ph)NPDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGSQPIRASNPDLR 14 1 Q9UKE5-6;Q9UKE5-2;Q9UKE5-4;Q9UKE5;Q9UKE5-8;Q9UKE5-5;Q9UKE5-7;Q9UKE5-3 Q9UKE5-6 TNIK TRAF2 and NCK-interacting protein kinase 1 LGSQPIRAS(1)NPDLR 126.63 0.00022167 78460000 82178 100750 53309 64681 100610 96670 82490 96170 70864 TRUE FALSE 71317.96909 100088.1666 79089.41071 79367.80964 98608.05784 100388.9575 74490.1325 75604.7939 62486.53865 1.141333328 1.601755655 1.265703181 1.270158523 1.578068812 1.606569345 1.192098876 1.209937301 1 15.93125781 1.699232101 1.821580466 1.033976587 1.408362947 0.374323221 0.165986221 0.391254229 2.456330924 0.204535572 0.04747738 50.03018413 -1.699232101 0.37438636 LGSS(ph)SNLQFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGSSSNLQFK 10 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 LGS(0.362)S(0.587)S(0.052)NLQFK;LGS(0.348)S(0.643)S(0.009)NLQFK 176.87 2.50E-06 545770000 754480 661810 635170 551310 661720 615200 779050 879750 784250 TRUE FALSE 654773.5564 657462.5265 942340.3365 676493.3617 648553.0666 638867.1421 703497.8509 691622.3087 691536.8584 0.946838261 0.950726658 1.362675503 0.978246284 0.937843094 0.923836719 1.017296247 1.000123566 1 19.39944662 3.557648465 24.99999999 0.977409597 1.089363916 0.16749566 0.116087079 184.7560152 57356.20296 0.031926604 0.047354796 3611.174417 -3.557648465 0.111954318 LGSSGLGS(ph)ASSIQAAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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;LGSSGLGS(0.935)AS(0.017)S(0.048)IQAAVR;LGSSGLGS(0.983)AS(0.001)S(0.016)IQAAVR;LGSSGLGS(0.955)AS(0.016)S(0.03)IQAAVR 302.66 1.75E-46 319824000 522408 414632 257148 272369 405232 418942 413311 460544 441227 TRUE FALSE 453370.4592 411908.2551 381505.6329 334214.5443 397168.676 435058.9698 373228.1628 362060.2496 389065.6467 1.165280109 1.05871145 0.980568796 0.859018387 1.020826895 1.118214814 0.959293543 0.930589099 1 18.56965407 4.552618529 2.490559811 0.977684918 1.173163925 0.451459526 0.065759882 0.355299341 3.558751554 0.01812105 0.122766127 35695.91587 -4.552618529 0.195479008 LGSSLDWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LGSSLDWDR 9 0 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 ;;; 158.07 0.00015607 1290560000 1566340 1505830 967130 1131120 1467520 1506860 1449450 1592800 1704680 FALSE TRUE 1359344.2 1495938.104 1434837.303 1387958.084 1438319.223 1564829.879 1308882.562 1252192.115 1503154.672 0.904327562 0.995199051 0.954550672 0.92336345 0.956867081 1.041030513 0.870757073 0.833042759 1 20.51956204 2.195102168 24.99997699 0.885781979 0.96163636 0.193439529 0.056080214 172.2500062 99087.59657 0.022347684 0.015066896 156.7119691 -2.195102168 0.075854381 LGSVDS(ph)FER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGSVDSFER 9 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 LGS(0.001)VDS(0.999)FER 64.918 0.071361 63570000 244520 192620 112030 119480 166910 170900 139380 167910 188310 TRUE FALSE 212206.0625 191354.6665 166208.0827 146609.7601 163588.8176 177474.6336 125862.9491 132003.7532 166048.2063 1.277978649 1.152404297 1.000962831 0.882934922 0.985188706 1.068813916 0.757990416 0.794972473 1 17.34124261 7.999999998 0.415659435 0.858643461 8.88643206 0.634621342 0.094307586 56.64573903 0.77080181 0.08863811 374.6444956 99999999.55 -7.999999998 8.027788599 LGTLS(ph)PAFSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGTLSPAFSTR 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 1 LGT(0.002)LS(0.998)PAFSTR;LGT(0.009)LS(0.991)PAFSTR 188.68 3.19E-06 249842000 270390 273690 188210 232087 253478 240742 283340 328790 324740 TRUE FALSE 234657.2764 271892.1124 279228.9855 284785.9006 248434.2837 250003.5005 255861.7304 258480.8171 286349.6071 0.819478255 0.949511037 0.975133119 0.99453917 0.867590796 0.87307087 0.893529183 0.902675648 1 18.1274181 1.850144851 0.00406167 1.462661557 0.380680449 0.020529224 0.058938464 612205.7811 1019.854212 137316.7839 134367.6434 70.81819469 -1.850144851 -1.081981108 LGTQGWT(ph)KQRKPCPQNASS(ph)YSAEMTEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGTQGWTKQRKPCPQNASSYSAEMTEPK 28 3 P45844-3 P45844-3 2 LGT(0.001)QGWT(0.584)KQRKPCPQNAS(0.584)S(0.629)Y(0.063)S(0.066)AEMT(0.073)EPK 47.38 0.059274 191560000 394230 153790 381000 265040 77377 86522 229520 265210 203810 TRUE FALSE 342131.5066 152779.7434 565252.8744 325221.3829 75837.34909 89850.55733 207261.1857 208496.9054 179715.814 1.903736233 0.850118529 3.145259517 1.809642544 0.42198484 0.499959104 1.15327183 1.160147795 1 17.45535784 3.334331727 7.023060809 0.894190761 1.952233893 0.449542661 0.593905684 0.218598589 13.7610487 0.17313985 0.223558163 2159.393187 -3.334331727 1.058043132 LGVADIIDCVVLTS(ph)SPEATETSQQLQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGVADIIDCVVLTSSPEATETSQQLQLR 28 0 Q8NCF5;H3BSZ7;Q8NCF5-3;Q8NCF5-2 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 LGVADIIDCVVLT(0.012)S(0.593)S(0.382)PEAT(0.012)ET(0.002)SQQLQLR;LGVADIIDCVVLT(0.088)S(0.581)S(0.33)PEATETSQQLQLR 179.16 1.04E-17 198217000 160919 152697 94962.2 106390 143638 136989 127769 157995 141637 TRUE FALSE 139653.1464 151693.9234 140886.2375 130547.4756 140779.8848 142259.0555 115377.982 124208.9988 124892.8352 1.118183811 1.214592679 1.128057004 1.045275939 1.127205452 1.139048971 0.923815861 0.994524614 1 16.93033119 2.248108976 24.99807714 0.975270073 1.128737416 0.727766247 0.044953457 102.9800082 269607.1169 0.017672937 0.013507257 177.0553181 -2.248108976 0.153467343 LGVADIIDCVVLTSS(ph)PEATETSQQLQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGVADIIDCVVLTSSPEATETSQQLQLR 28 0 Q8NCF5;H3BSZ7;Q8NCF5-3;Q8NCF5-2 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 LGVADIIDCVVLTS(0.098)S(0.902)PEATETSQQLQLR 255.94 9.90E-54 159610000 69896 74666 47014 50663 58633 66698 63440 75401 74680 TRUE FALSE 60659.06651 74175.51413 69750.12765 62166.80849 57466.31801 69263.91522 57287.59856 59277.08292 65851.41548 0.921150534 1.126407285 1.059204683 0.944046655 0.872666405 1.051821206 0.869952425 0.900164142 1 16.00692683 3.70409124 6.68445431 0.932821257 1.044709346 0.264769971 0.074207904 0.227833567 33.47299408 0.019550772 0.029694509 5059.30941 -3.70409124 0.111888089 LGVDLDAQTWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGVDLDAQTWR 11 0 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ; 152.04 7.71E-05 302770000 636430 612100 370940 534270 635710 662150 590490 676590 648330 FALSE TRUE 552324.163 608079.0748 550327.8247 655584.1693 623060.6147 687623.339 533224.3707 531906.4937 571685.166 0.966133452 1.063660754 0.962641428 1.146757356 1.089866682 1.202800737 0.932723818 0.930418568 1 19.12486133 2.17519955 24.99999993 0.948485663 1.070843527 0.357570065 0.074154288 67.54080096 26648.23706 0.030480107 0.020549677 149.6923306 -2.17519955 0.122357864 LGVEPSDDDCVSVQHVCTIVSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGVEPSDDDCVSVQHVCTIVSFR 23 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 261.82 8.61E-44 401570000 177851 154116 75703 121261 153721 173965 132031 145743 138573 FALSE TRUE 154347.5397 153103.6018 112313.224 148795.1634 150662.2529 180657.5461 119226.6539 114576.9936 122191.0578 1.263165591 1.252985322 0.919160747 1.217725471 1.233005553 1.478484182 0.975739601 0.937687223 1 16.89877918 2.049775082 24.9994771 0.962088125 1.215445426 0.444505519 0.134580305 98.96419063 49704.18285 0.056490932 0.038086169 112.1437519 -2.049775082 0.2533573 LGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLK 35 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 209.83 1.90E-28 6608400000 1194540 1219840 241774 753320 1179590 1122800 1237260 1488170 1251240 FALSE TRUE 1036678.512 1211826.791 358696.7151 924372.8198 1156118.467 1165994.843 1117270.716 1169936.426 1103319.833 0.939599273 1.098345878 0.325106741 0.83781039 1.047854333 1.05680584 1.01264446 1.060378316 1 20.07341963 3.293950219 5.29038118 1.038235444 0.783215467 0.268093988 0.193731532 0.266379075 15.4453578 0.057288467 0.073287475 1967.660735 -3.293950219 -0.255019976 LGVIEDHSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 LGVIEDHSNR 10 0 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ;;;;;;;; 207.83 1.25E-07 24753330000 11546400 11181090 8044290 9916400 11286670 14324350 10515500 10394370 8993230 FALSE TRUE 10020513.99 11107640.68 11934535.55 12168070.18 11062087.35 14875417.01 9495708.429 8171614.865 7930060.595 1.263611276 1.400700606 1.504974068 1.534423355 1.39495622 1.8758264 1.197432014 1.030460583 1 22.91890046 2.011696322 24.92075481 1.046368062 1.492991246 0.627084182 0.156903936 126.7523797 270063.7555 0.063167202 0.042551067 102.7297716 -2.011696322 0.446623185 LGVQVVITDPEKLDQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGVQVVITDPEKLDQIR 17 1 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 149.99 2.78E-07 867380000 1863720 1365210 982050 1324700 1428260 1168710 1677180 1899520 1482370 FALSE TRUE 1617424.68 1356241.846 1456972.665 1625493.382 1399840.42 1213671.03 1514527.342 1493322.43 1307125.907 1.237390117 1.037575522 1.11463835 1.243562975 1.070930055 0.928503538 1.158669822 1.142447274 1 20.31796668 3.09491512 24.72056337 1.07118008 1.147890019 0.229013544 0.087302516 28.33787442 7361.691765 0.027133065 0.030766004 1244.271404 -3.09491512 0.076709938 LGVS(ph)VS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGVSVSPSR 9 0 E7ERS3;Q86VM9;H3BP01 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 2 LGVS(1)VS(1)PSR;LGVS(1)VS(0.991)PS(0.009)R 114.76 0.0023176 333100000 791120 617960 429670 490630 639900 705210 620730 686680 781710 TRUE FALSE 686571.4876 613900.5801 637459.8492 602035.0403 627167.2419 732339.885 560531.7001 539838.8257 689297.1343 0.996045759 0.89061821 0.924796894 0.873404241 0.909864862 1.062444407 0.813193139 0.783172886 1 19.39476649 LGVSVS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 LGVSVSPSR 9 0 E7ERS3;Q86VM9;H3BP01 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 LGVS(0.001)VS(0.985)PS(0.013)R;LGVS(0.001)VS(0.999)PSR;LGVS(0.002)VS(0.998)PSR;LGVS(0.001)VS(0.985)PS(0.014)R;LGVSVS(1)PSR;LGVSVS(0.999)PS(0.001)R;LGVSVS(0.999)PS(0.001)R;LGVS(0.002)VS(0.998)PSR;LGVS(0.05)VS(0.931)PS(0.019)R;LGVS(0.002)VS(0.871)PS(0.127)R 201.33 2.27E-05 28389010000 14338000 11837740 7252330 9093500 11597320 11450420 10719600 12948330 11539210 TRUE FALSE 12443196.97 11759977.11 10759581.05 11158318.16 11366556.02 11890925.07 9680014.842 10179430.39 10175057.74 1.222911682 1.155765147 1.057446682 1.096634382 1.117099904 1.168634653 0.951347411 1.000429742 1 23.27853365 -1.999999332 0.060488873 3.82E-11 1.625584632 0.56752482 0.055966761 580.0421586 3.399703716 90.55510463 22.71448826 0.010000015 1.999999332 1.625584632 LGWDPKPGEGHLDALLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGWDPKPGEGHLDALLR 17 1 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ; 133.32 1.24E-05 2840400000 4694600 4174700 3049100 3350500 4304900 3835900 4759600 5448500 5004100 FALSE TRUE 4074196.715 4147276.121 4523654.959 4111282.234 4219240.912 3983469.555 4298014.725 4283380.675 4412520.999 0.923326306 0.939888132 1.025186047 0.931730917 0.956197356 0.902765008 0.974049693 0.97073321 1 22.07317171 1.532827398 1.864737026 1.000214816 0.949965306 0.202187633 0.032576865 0.782229333 4.581313141 0.06110311 0.009258208 34.10573378 -1.532827398 -0.050249509 LGYFSVDPDSHQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LGYFSVDPDSHQGK 14 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RR79 P47897 QARS Glutamine--tRNA ligase 0 ;;; 187.97 8.87E-07 2368360000 5690830 5240920 2608340 4191710 5223710 4580060 5853270 6974730 5797070 FALSE TRUE 4938772.397 5206492.051 3869741.948 5143501.822 5119768.391 4756257.872 5285620.776 5483238.267 5111746.989 0.966161355 1.018534772 0.757029242 1.006212129 1.00156921 0.930456433 1.034014553 1.072674035 1 22.285385 2.380447668 1.143878469 1.050291093 0.936697368 0.204845908 0.076812745 0.761594103 2.023685156 0.063828662 0.031035855 240.1306898 -2.380447668 -0.113593725 LGYLLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LGYLLFR 7 0 P25098;E9PRV7 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 0 98.513 0.026074 59482000 125520 157730 98705 120090 148940 158690 144200 158340 173010 FALSE TRUE 108932.214 156693.8612 146439.0681 147358.27 145976.3854 164794.907 130215.5062 124480.2232 152556.9549 0.714042923 1.027117127 0.959897687 0.96592299 0.956864835 1.080218906 0.853553391 0.815959019 1 17.21898843 LGYLVS(ph)PPQQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LGYLVSPPQQIR 12 0 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 LGYLVS(1)PPQQIR;LGYLVS(1)PPQQIR 112.44 0.0013362 142814000 293010 278400 174489 204848 264880 269550 304690 321530 281160 TRUE FALSE 254287.9861 276571.1721 258872.464 251361.8693 259609.4062 279919.7629 275141.2107 252773.3116 247921.5851 1.025679091 1.115559067 1.044170736 1.013876501 1.047143217 1.12906572 1.10979127 1.019569601 1 17.91952436 1.576547818 6.190134074 1.005060834 1.069455119 0.29570642 0.038716145 0.163387204 12.60259564 0.027531539 0.010337621 37.71792724 -1.576547818 0.064394285 LHAEFAAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LHAEFAAER 9 0 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 ;; 148.94 8.88E-05 752070000 402864 510258 426343 410874 433650 563250 399199 449535 534240 FALSE TRUE 349624.5017 506906.0816 632523.9008 504169.2215 425021.2134 584918.592 360484.7424 353405.4385 471082.7558 0.74217215 1.076044655 1.342702302 1.070234933 0.902221973 1.241647215 0.765225935 0.750198207 1 18.845621 2.220384998 24.99559831 0.817031672 1.068921546 0.260712094 0.17639114 295.9881639 407047.8412 0.071806538 0.048518588 166.1058769 -2.220384998 0.251889874 LHAEFAAERDWEQFHQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHAEFAAERDWEQFHQPR 18 1 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 167.92 1.42E-11 75052000 18384 37486 11878 30260 15218 16454 23014 25019 15932 FALSE TRUE 15954.50782 37239.752 17622.24053 37130.9955 14915.19157 17086.99603 20782.10582 19668.88155 14048.53711 1.135670404 2.650792158 1.254382602 2.643050675 1.061690015 1.216282941 1.479307465 1.40006617 1 13.77813229 3.20253021 24.9999859 1.270372283 1.925492088 0.313641718 0.504998215 201.2240401 139620.2665 0.137341269 0.155735326 1594.153766 -3.20253021 0.655119805 LHAVDEELAS(ph)SPVCMDSFQPMDDSLIAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHAVDEELASSPVCMDSFQPMDDSLIAFR 29 0 A4PB68;Q3T8J9-3;Q3T8J9;A0A087WUE6;Q3T8J9-2 A4PB68;Q3T8J9-3 GON4L GON-4-like protein 1 LHAVDEELAS(0.498)S(0.498)PVCMDS(0.003)FQPMDDSLIAFR 61.099 0.01869 47455000 15866 18592 10372 14047 16606 16206 13524 15567 14725 TRUE FALSE 13769.2679 18469.86793 15387.93389 17236.58604 16275.57309 16829.45531 12212.44456 12238.11819 12984.22727 1.060461097 1.422484953 1.185125119 1.327501874 1.253488001 1.296146082 0.940559981 0.942537275 1 13.66447254 2.23679685 24.99896221 0.956326188 1.264737354 0.68588705 0.094486791 22.34147915 316649.7612 0.033385069 0.02382659 172.5030785 -2.23679685 0.308411165 LHAVDEELASS(ph)PVCMDSFQPMDDSLIAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHAVDEELASSPVCMDSFQPMDDSLIAFR 29 0 A4PB68;Q3T8J9-3;Q3T8J9;A0A087WUE6;Q3T8J9-2 A4PB68;Q3T8J9-3 GON4L GON-4-like protein 1 LHAVDEELAS(0.15)S(0.85)PVCMDSFQPMDDSLIAFR 106.51 0.00030362 50310000 24212 22683 15073 18302 19281 22455 20612 26944 23455 TRUE FALSE 21012.32285 22533.99388 22362.35322 22457.74883 18897.34582 23318.85838 18613.05141 21182.23528 20682.17662 1.015962838 1.089536865 1.0812379 1.085850355 0.913701985 1.1274857 0.899956119 1.024178241 1 14.3361004 3.292942686 24.99999677 0.996690723 1.070610055 0.247532291 0.064814583 125.7269097 57796.86152 0.017076105 0.022045141 1963.101189 -3.292942686 0.073919332 LHCESESFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LHCESESFK 9 0 C9JLU1;P52434;P52434-2;P52434-4 C9JLU1 POLR2H "DNA-directed RNA polymerases I, II, and III subunit RPABC3" 0 ;;; 179.51 4.97E-05 1569320000 2391260 2074090 1265081 1915880 2088280 1773850 2430020 2524600 2643630 FALSE TRUE 2075248.932 2060465.166 1876878.403 2350909.836 2046727.314 1842091.157 2194357.034 1984733.936 2331103.073 0.890243317 0.883901356 0.805146038 1.008496734 0.878008072 0.790222954 0.941338485 0.851414062 1 21.15258137 1.229507916 24.67549201 1.000000272 0.881288032 0.26492452 0.06224397 417.2674522 1137269.739 0.170030266 0.014391333 16.96320522 -1.229507916 -0.11871224 LHDAFFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHDAFFK 7 0 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ; 85.265 0.020938 1139650000 3869400 3400800 2211300 2661900 3182100 2718600 3444500 4100100 3494100 FALSE TRUE 3358048.986 3378459.921 3280692.076 3266325.08 3118782.436 2823186.301 3110452.92 3223325.522 3081031.478 1.089910639 1.096535347 1.064803167 1.060140119 1.012252701 0.91631206 1.009549218 1.046183898 1 21.55498199 3.338518065 2.738132022 0.999319412 1.083305122 0.606633381 0.032978132 0.217628366 3.303256569 0.011444221 0.015292056 2180.309086 -3.338518065 0.083985709 LHDEKEETAGSYDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHDEKEETAGSYDSR 15 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610;A0A2R8YEF8 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 142.45 2.75E-06 706710000 821440 694080 528860 546970 678960 693070 728950 803820 687260 FALSE TRUE 712884.6227 689520.5428 784618.4649 671167.8984 665450.0244 719732.8514 658256.5412 631929.3483 606012.9057 1.176352213 1.137798447 1.294722369 1.1075142 1.098078965 1.18765268 1.086208784 1.042765496 1 19.20898899 0.6459606 0.441823516 0.714105284 1.19111745 0.5674077 0.053903654 6.988522717 0.767019266 1.949248523 0.051321439 4.425482217 -0.6459606 0.477012166 LHDFGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LHDFGYR 7 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;;;; 179.16 0.0007052 2860470000 1843540 1705830 1035554 1180923 1588130 1674320 1577200 1710180 1643780 FALSE TRUE 1599911.518 1694624.29 1536351.378 1449069.616 1556529.32 1738732.174 1424243.387 1344471.316 1449454.201 1.10380274 1.169146489 1.059951654 0.999734669 1.073872716 1.199577174 0.982606684 0.927570747 1 20.46707832 2.070984199 9.301307261 0.957553851 1.096281137 0.534523894 0.057623963 0.238300339 28.95852592 0.024469828 0.016479807 117.7563129 -2.070984199 0.138727286 LHDFLAHSSEESEETSS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHDFLAHSSEESEETSSPPR 20 0 P46100;P46100-4;A0A096LNL9;P46100-6;A0A096LNW1;A0A087WWG0 P46100 ATRX Transcriptional regulator ATRX 1 LHDFLAHSSEESEETS(0.162)S(0.837)PPR 166.27 2.22E-12 79096000 52169 52639 24064 38750 54900 52037 32881 37159 41434 TRUE FALSE 45274.73447 52293.21094 35701.43089 47548.77976 53807.59741 54038.89706 29692.20568 29212.83702 36535.71972 1.239190984 1.431290018 0.977165118 1.301432683 1.472739495 1.479070276 0.812689771 0.799569223 1 15.15702001 2.228840711 24.99999977 0.853503622 1.312967868 0.652409286 0.153294464 121.5875994 312725.393 0.064131339 0.043842292 169.3716471 -2.228840711 0.459464247 LHDINAQLVEDQGFLDTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LHDINAQLVEDQGFLDTLK 19 0 Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 Q10567-4 AP1B1 AP-1 complex subunit beta-1 0 ;; 169.19 1.46E-11 116984000 268191 229463 197839 262458 276773 213842 281134 329173 466122 FALSE TRUE 232748.8798 227955.6424 293514.6021 322053.1003 271265.7588 222068.6401 253869.668 258781.9156 411017.5882 0.566274745 0.554612866 0.714116891 0.783550655 0.659985769 0.540289872 0.617661325 0.629612754 1 18.64884061 1.238041204 24.94065703 1.000000422 0.635055658 0.707407405 0.074115193 7.461487187 357917.1687 0.112388193 0.019524073 17.29980484 -1.238041204 -0.364944764 LHDINAQMVEDQGFLDSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LHDINAQMVEDQGFLDSLR 19 0 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1 P63010 AP2B1 AP-2 complex subunit beta 0 ;;;; 263.52 2.85E-31 1133390000 747048 625217 471806 566084 679210 738650 588066 739709 705447 FALSE TRUE 648323.714 621109.9084 699972.9597 694622.0243 665695.0499 767066.3435 531035.4498 581527.9868 622049.8593 1.042237538 0.998488946 1.125268255 1.116666154 1.070163492 1.233126786 0.853686311 0.934857517 1 19.2466707 2.224162468 24.99999938 0.927468203 1.094020036 0.562116818 0.069901558 173.8299401 301824.532 0.028529424 0.019334745 167.5569583 -2.224162468 0.166551833 LHDPEGMGIIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LHDPEGMGIIPR 12 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ;;;; 193.28 3.00E-06 1660810000 3095920 3078030 2002520 2321520 3079550 3243570 2947240 3318030 3334080 FALSE TRUE 2686786.328 3057810.218 2970945.37 2848656.598 3018272.98 3368352.237 2661417.118 2608495.105 2939928.861 0.913895014 1.04009667 1.010550088 0.968954262 1.026648304 1.145725763 0.905265823 0.887264702 1 21.48734981 LHDSLAIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHDSLAIER 9 0 E9PL01;A0A087WUC6;E9PI68;Q15005;E9PRB9 E9PL01 SPCS2 Signal peptidase complex subunit 2 0 95.573 0.0079534 240960000 35591 38157 20375 31644 52053 57957 34611 55023 52115 FALSE TRUE 30887.55917 37906.34415 30228.41815 38829.25385 51017.24714 60186.64329 31254.43055 43256.75964 45954.02407 0.672140466 0.824875404 0.657796978 0.844958731 1.110180189 1.309714318 0.68012391 0.941305153 1 15.48790358 3.461255225 6.298031096 0.990087635 0.73175731 0.40421913 0.160875505 0.178785148 27.77659905 0.04830092 0.064520572 2892.379167 -3.461255225 -0.258330325 LHDTFGFVDEDVFFQLSAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHDTFGFVDEDVFFQLSAVK 20 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H2E6;F5H3E1 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ; 112.74 0.00014909 48474000 66454 54013 25119.7 42033.9 43696.3 44027 63259 69546 59608 FALSE TRUE 57671.93553 53658.18505 37267.67094 51578.33944 42826.82912 45720.74718 57124.15192 54674.12911 52561.21015 1.097233785 1.020870427 0.709033731 0.981300455 0.814799146 0.869857202 1.086811962 1.040199207 1 15.68171087 2.239489603 24.99989489 1.0437448 0.909331267 0.229305683 0.109200384 35.08932441 944333.0339 0.042744468 0.031167143 173.5759709 -2.239489603 -0.134413533 LHDVEHVLIDVGTGYYVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHDVEHVLIDVGTGYYVEK 19 0 Q99471;H3BPF6;Q99471-3 Q99471 PFDN5 Prefoldin subunit 5 0 ; 113.69 9.96E-05 68406000 111097 84510 60417 73168 65837 61241 78737 87920 77473 FALSE TRUE 96415.24997 83954.84825 89634.86328 89781.9127 64526.97251 63596.9809 71101.09786 69118.99219 68314.2302 1.411349432 1.228951099 1.312096514 1.314249058 0.944561218 0.930947779 1.040794834 1.011780298 1 16.05989851 3.243101119 24.99902074 0.990292143 1.310070489 0.904851019 0.053311401 32.54423285 179180.2824 0.015438306 0.019258048 1750.254161 -3.243101119 0.319778346 LHDVNSDGFLDEQELEALFTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LHDVNSDGFLDEQELEALFTK 21 0 P80303-2;P80303;E9PKG6;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 ;;; 269.41 1.24E-37 1488130000 1476910 1302810 888440 1084020 1244070 1155690 1331810 1728480 1541200 FALSE TRUE 1281732.601 1294251.755 1318092.556 1330163.309 1219315.441 1200150.142 1202651.271 1358858.003 1359001.092 0.943143173 0.952355199 0.969898084 0.978780162 0.897214468 0.883111978 0.884952395 0.99989471 1 20.37411518 1.629003456 8.003642659 1.001002796 0.931301592 0.432343784 0.03329347 0.114177883 15.86206568 0.022776494 0.009649574 42.56017997 -1.629003456 -0.069701204 LHEADLELQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHEADLELQR 10 0 Q96ED9-2;Q96ED9 Q96ED9-2 HOOK2 Protein Hook homolog 2 0 160.33 7.41E-06 176620000 17297 12492 7872.3 10201 10813 15614 16982 14887 15130 FALSE TRUE 15011.15762 12409.93923 11679.37061 12517.29296 10597.84246 16214.68068 15335.08825 11703.5309 13341.34864 1.125160434 0.930186263 0.875426535 0.938232956 0.794360656 1.215370434 1.149440635 0.877237468 1 13.70361689 2.751695977 24.9609627 1.040212527 0.929663697 0.209898728 0.120337616 1481.558137 2815384.642 0.040818844 0.04059566 564.5416359 -2.751695977 -0.11054883 LHEAVFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHEAVFLR 8 0 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-3;Q03154-4;C9JMV9 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 ; 159.04 0.00036148 956560000 438830 496740 359040 369990 439770 476810 408170 465730 500370 FALSE TRUE 380837.5036 493476.8822 532672.9449 454001.8844 431019.4374 495153.1892 368585.7362 366137.2638 441216.8286 0.863152715 1.118445286 1.207281569 1.028976809 0.976888027 1.122244568 0.835384583 0.829835219 1 18.75112829 2.233754007 24.99994604 0.873994954 1.058298123 0.359780485 0.102626683 116.2333816 604539.8124 0.040849237 0.028543175 171.2986765 -2.233754007 0.18430317 LHEDDKEQDIADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHEDDKEQDIADK 13 1 G3XAL9;P55011-3;P55011 G3XAL9 SLC12A2 Solute carrier family 12 member 2 0 75.088 0.019432 67983000 143490 129380 85204 104910 133320 109440 143090 178360 141500 FALSE TRUE 124527.4329 128530.0943 126408.9394 128731.4189 130667.1928 113650.2276 129213.1538 140219.102 124772.0312 0.998039639 1.030119435 1.013119192 1.031732975 1.047247461 0.910863008 1.035593895 1.123802351 1 16.92893505 1.99528447 24.99940644 1.073430385 1.006751715 0.192450717 0.047199888 245.7682423 1302943.481 0.019124722 0.012520848 98.92008245 -1.99528447 -0.06667867 LHEDLCEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHEDLCEK 8 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 66.692 0.061026 108910000 99687 82356 70500 80425 79584 66510 87363 97825 114630 FALSE TRUE 86513.11038 81814.99801 104594.0358 98686.72547 78000.4341 69068.68274 78890.54971 76905.88503 101078.572 0.85589961 0.809419805 1.034779516 0.97633676 0.771681204 0.683316764 0.780487379 0.760852508 1 16.62511766 3.227356416 24.99019506 0.787259612 0.919536172 0.257959845 0.099850473 280.5158963 625669.9001 0.03085119 0.035296316 1687.937712 -3.227356416 0.13227656 LHEEGIIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LHEEGIIYR 9 0 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 ;;; 191.85 3.54E-05 1861770000 1187760 995880 679070 851320 957690 983030 935000 1042310 1028230 FALSE TRUE 1030794.507 989337.9987 1007470.523 1044625.218 938633.8427 1020847.8 844323.8439 819420.1178 906673.8208 1.136896735 1.091173006 1.111171957 1.152151075 1.035249746 1.12592619 0.931232186 0.903765058 1 19.7902241 2.235580309 24.99975506 0.935835003 1.106702369 0.793568411 0.03927153 29.90428122 250841.3425 0.014967361 0.010586427 172.0205408 -2.235580309 0.170867367 LHELNQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHELNQK 7 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 113.7 0.0060716 308100000 689060 592930 431170 503480 535560 573490 626220 731240 729790 FALSE TRUE 597998.9751 589035.0038 639685.2542 617802.8292 524903.4038 595552.5314 565489.2808 574870.0165 643515.0576 0.929269592 0.915339893 0.994048619 0.960044092 0.815681619 0.925467904 0.878750659 0.893327996 1 19.29561438 LHELTVMQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHELTVMQDR 10 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 99.283 0.0048011 205780000 56146 53150 35633 42644 52588 54935 50009 58893 79743 FALSE TRUE 48726.16384 52800.85415 52865.23799 52326.97197 51541.60169 57048.385 45159.13488 46299.19026 70315.87338 0.692961084 0.750909455 0.751825092 0.744170121 0.733000946 0.811315884 0.642232439 0.658445782 1 16.10156279 1.230510391 24.997644 1.000000508 0.721775662 0.759592702 0.048949882 160.2999473 497724.5809 0.140770091 0.013023361 17.00240635 -1.230510391 -0.278224847 LHEVFHDQLHTFLVMELLNGGELFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHEVFHDQLHTFLVMELLNGGELFER 26 0 O75582-3;O75582;O75582-2 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 0 115.43 0.00041502 39672000 44303 34862 21971 27587 21755 18315 35670 42470 27541 FALSE TRUE 38448.2463 34632.98923 32596.24909 33851.04999 21322.11806 19019.5899 32210.72889 33388.121 24285.13435 1.583200889 1.426098317 1.342230544 1.39390005 0.877990533 0.783178286 1.326355803 1.374837813 1 14.56778585 3.381149036 8.693255367 1.11515449 1.434788368 0.470643368 0.189296677 0.30840513 24.96263077 0.062271274 0.080422103 2405.188041 -3.381149036 0.319633878 LHEVGHERDS(ph)LQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHEVGHERDSLQR 13 1 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;E9PPF6;E9PID5;A0A3B3ITS2 Q13136-2 PPFIA1 Liprin-alpha-1 1 LHEVGHERDS(1)LQR 74.141 0.021087 177210000 46546 46597 29017 47475 31937 42775 29120 42950 36005 TRUE FALSE 40394.82817 46290.90124 43049.71826 58254.92436 31301.51618 44420.58193 26295.94688 33765.47674 31748.52992 1.272336964 1.458048652 1.355959421 1.834885726 0.985920175 1.399138229 0.828257149 1.063528826 1 14.95440217 2.686869835 1.471810803 0.990443061 1.446455275 0.420991292 0.221689732 0.358654557 1.589205189 0.10082291 0.081580591 486.2614437 -2.686869835 0.456012215 LHEWVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHEWVK 6 0 Q9NZB2;Q9NZB2-4;Q9NZB2-6;Q9NZB2-2;Q9NZB2-5 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 0 114.67 0.025089 369750000 667790 584540 478430 524090 662870 571200 717740 780720 723860 FALSE TRUE 579539.8595 580700.1183 709800.3483 643092.6447 649680.1839 593174.4336 648133.6853 613769.1036 638286.0954 0.907962532 0.909780304 1.112041063 1.007530399 1.017851068 0.929323759 1.015428175 0.961589337 1 19.28384369 4.404902872 24.99999998 1.001164792 0.908395355 0.427113668 0.046600955 36.47870779 12626.96743 0.011529885 0.030505216 25404.04491 -4.404902872 -0.092769437 LHFFMPGFAPLT(ph)SR ddPTM_MDA-MB-175_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 1 LHFFMPGFAPLT(0.605)S(0.395)R;LHFFMPGFAPLT(0.631)S(0.369)R 109.42 0.0028281 341230000 617230 709130 333980 455970 656760 673700 485040 586060 609060 TRUE FALSE 535661.4916 704471.6783 495493.8451 559504.9576 643691.7609 699617.6749 438000.8955 460735.6297 537057.6206 0.997400411 1.311724573 0.92260835 1.041796887 1.198552513 1.302686431 0.815556616 0.857888636 1 19.03471736 2.221866073 24.99981276 0.881069591 1.127226833 0.421660802 0.131194772 223.5753899 334798.0001 0.053012989 0.035848293 166.6733149 -2.221866073 0.246157242 LHFFMPGFAPLTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 172.69 6.55E-06 6849170000 4913360 5631150 2802510 3141370 4962790 4818470 4500120 4496540 4558260 FALSE TRUE 4264047.027 5594158.605 4157813.21 3854666.071 4864040.189 5003839.659 4063699.055 3534989.913 4019387.696 1.060869802 1.391793733 1.034439453 0.959018229 1.210144569 1.244925854 1.011024405 0.879484683 1 21.93854431 2.043816321 6.083607152 0.93473007 1.149313999 0.348614418 0.123056395 0.190454811 17.44590914 0.052395473 0.034422726 110.6155851 -2.043816321 0.214583929 LHGDEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHGDEER 7 0 Q9ULW8 Q9ULW8 PADI3 Protein-arginine deiminase type-3 0 ; 130.64 0.0035438 200971000 97733 108825 55439 73059 81606 119655 108151 114765 109690 FALSE TRUE 84817.33643 108110.1214 82249.48583 89648.16259 79982.20026 124258.2053 97662.53267 90223.39785 96722.57316 0.876913565 1.117734133 0.850364947 0.926858743 0.826923826 1.28468672 1.009718099 0.932806013 1 16.56156501 LHGELQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LHGELQDR 8 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;;; 144.09 0.000591 2175470000 1300340 1148210 821731 895621 1112910 993580 1221220 1303030 1110920 FALSE TRUE 1128496.774 1140667.333 1219122.86 1098985.437 1090765.268 1031803.666 1102786.272 1024387.175 979588.3032 1.152011279 1.164435436 1.244525742 1.121885014 1.113493561 1.053303375 1.125765047 1.045732346 1 19.90181602 1.024796508 0.291846684 0.823258532 1.209096955 0.678224508 0.039010203 8.492658544 0.695185934 1.249043484 0.126538281 10.58757521 -1.024796508 0.385838424 LHGGFDS(ph)DCS(ph)EDGEALNGEPELDLTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHGGFDSDCSEDGEALNGEPELDLTSK 27 0 O00178;F8WAZ4 O00178 GTPBP1 GTP-binding protein 1 2 LHGGFDS(1)DCS(1)EDGEALNGEPELDLTSK;LHGGFDS(1)DCS(1)EDGEALNGEPELDLTSK 174.46 1.03E-12 248000000 203937 217538 131266 152260 162660 146183 212549 213801 195834 TRUE FALSE 176986.2087 216108.9786 194746.6767 186832.9601 159423.3842 151806.7546 191936.0307 168081.32 172682.7276 1.024921318 1.251479992 1.127771604 1.081943532 0.923215578 0.879107926 1.111495245 0.973353399 1 17.39776426 3.450660761 4.142607154 0.982308444 1.142304244 0.453090975 0.079906395 0.185532183 7.242702428 0.022996994 0.031479544 2822.674247 -3.450660761 0.159995799 LHGGFDS(ph)DCSEDGEALNGEPELDLTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHGGFDSDCSEDGEALNGEPELDLTSK 27 0 O00178;F8WAZ4 O00178 GTPBP1 GTP-binding protein 1 1 LHGGFDS(0.82)DCS(0.18)EDGEALNGEPELDLTSK 106.69 0.0012201 57312000 41476 33552 20607 28308 32886 29838 35404 38171 25295 TRUE FALSE 35994.84151 33331.5947 30572.61413 34735.76406 32231.63294 30985.88717 31970.52553 30008.4287 22304.65392 1.613781664 1.494378475 1.370683188 1.557332572 1.445063127 1.389211744 1.433356718 1.345388671 1 14.44505714 0.711524601 1.148843176 1.97E-14 1.478597833 0.818369373 0.070487791 2.009799867 0.920014122 4.86021882 0.021763582 5.146649597 -0.711524601 1.478597833 LHGSAFRPSLPAPES(ph)PGLPAHPSNPQLPEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHGSAFRPSLPAPESPGLPAHPSNPQLPEAR 31 1 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 LHGS(0.001)AFRPSLPAPES(0.999)PGLPAHPSNPQLPEAR 107.98 6.35E-05 178710000 66648 109020 34311 71544 161940 182340 124110 125040 155210 TRUE FALSE 57840.29794 108303.8404 50903.91436 87789.15868 158717.7108 189354.7378 112073.8313 98301.16906 136861.2506 0.422619972 0.791340427 0.371938106 0.641446416 1.159697943 1.38355259 0.818886506 0.718254207 1 17.06235451 3.372444552 6.023316896 0.980883271 0.547707256 0.542262781 0.209932315 0.195688791 9.80507296 0.067078026 0.086888563 2357.46119 -3.372444552 -0.433176015 LHHSQS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 LHHSQSPAR 9 0 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 LHHS(0.134)QS(0.866)PAR;LHHS(0.076)QS(0.924)PAR;LHHS(0.005)QS(0.995)PAR;LHHS(0.017)QS(0.983)PAR;LHHS(0.053)QS(0.947)PAR;LHHS(0.079)QS(0.921)PAR;LHHS(0.228)QS(0.772)PAR;LHHS(0.088)QS(0.912)PAR;LHHS(0.228)QS(0.772)PAR 190.36 2.39E-05 1575788900 760547.1 1154280.4 304502.5 559006.1 820278.4 1020385.8 746658.4 877658.1 763758.1 TRUE FALSE 660038.8738 1146697.856 451760.9275 685936.9789 803956.4647 1059640.702 674247.5833 689977.7453 673467.4875 0.980060487 1.702677378 0.670798421 1.018515358 1.193756907 1.57341033 1.001158327 1.0245153 1 19.36124877 KFAMEPEEFDSDTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KFAMEPEEFDSDTLR 15 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 147.64 5.89E-06 94154000 107570 99833 57746 68455 110630 110810 104850 84171 49845 FALSE TRUE 93354.35195 99177.19045 85672.15875 83998.75402 108428.6794 115072.9324 94681.66314 66171.68667 43952.38088 2.123988509 2.256469125 1.949204048 1.911130918 2.466958041 2.618127394 2.154187355 1.505531335 1 15.4236537 1.565701627 2.553440982 1.024086673 2.221563737 0.79118652 0.213249006 0.130555739 1.763137669 0.282129351 0.064015446 36.78761449 -1.565701627 1.197477064 up LHIACFPVQLDTLSDGASVDESHGIS(ph)PPLQGEISQTQENSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHIACFPVQLDTLSDGASVDESHGISPPLQGEISQTQENSK 41 0 E9PG22;Q8IW35;Q8IW35-2 E9PG22 CEP97 Centrosomal protein of 97 kDa 1 LHIACFPVQLDTLSDGASVDES(0.043)HGIS(0.957)PPLQGEISQTQENSK 332.51 7.70E-133 215810000 76071 77435 42827 65058 67690 57236 81510 95133 85707 TRUE FALSE 66018.02461 76926.32439 63538.28045 79830.41325 66343.10143 59437.90596 73605.17275 74789.54828 75574.8161 0.87354529 1.017883051 0.840733511 1.056309726 0.87784668 0.786477679 0.973937835 0.989609398 1 16.20561794 2.022765751 24.99956986 0.990375945 0.912982345 0.185129554 0.078636454 389.4033376 427610.5302 0.031375305 0.021151898 105.3818336 -2.022765751 -0.0773936 LHIIEVGTPPTGNQPFPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHIIEVGTPPTGNQPFPK 18 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 120.63 4.00E-05 621350000 779540 603010 420280 470630 641060 589440 689380 810570 829470 FALSE TRUE 676521.8139 599048.7876 623528.8138 577493.7346 628304.1602 612116.1382 622524.0337 637235.9134 731411.0015 0.924954386 0.819031689 0.852501278 0.789561182 0.859030229 0.836897636 0.851127523 0.871241904 1 19.4803228 1.147230455 2.24271254 1.073672975 0.844394526 0.656860727 0.034265291 0.503887233 2.101337126 0.256227893 0.008542098 14.03558294 -1.147230455 -0.229278449 LHIVDTVCAHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHIVDTVCAHFR 12 0 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 ; 193.96 1.23E-06 491480000 291520 343010 199842 260330 328680 331090 304070 368070 303260 FALSE TRUE 252994.8934 340756.7447 296486.2596 319441.9054 322139.9111 343827.2465 274581.3382 289361.0948 267408.9483 0.946097335 1.274290733 1.108737241 1.194581959 1.204671396 1.285773153 1.026821802 1.082092042 1 18.02868822 2.206547639 24.99995131 1.045448443 1.173851733 0.293503575 0.096529361 238.8116171 186493.9636 0.036856265 0.024850746 160.8968861 -2.206547639 0.128403289 LHIVQVVCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHIVQVVCK 9 0 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ; 123.98 0.00054242 2766700000 7624000 9087000 5906400 7014700 8261400 7457400 9218000 10490800 10747600 FALSE TRUE 6616469.083 9027306.899 8762754.796 8607494.848 8097014.303 7744291.004 8324039.779 8247424.059 9477030.972 0.698158432 0.95254589 0.924630807 0.908248045 0.854383016 0.81716426 0.878338353 0.870253995 1 23.17600372 -0.232746669 0.014694764 1.857671879 2.77E-07 0.141347923 0.075780368 25501.19868 57.57787494 4058.232863 3261.025602 0.585131301 0.232746669 -1.857671603 LHKTEDGGWEWS(ph)DDEFDEESEEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LHKTEDGGWEWSDDEFDEESEEGK 24 1 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 LHKT(0.003)EDGGWEWS(0.997)DDEFDEESEEGK;LHKT(0.001)EDGGWEWS(0.999)DDEFDEESEEGK;LHKT(0.023)EDGGWEWS(0.977)DDEFDEESEEGK 172.32 3.37E-12 342886000 644400 374780 646570 360720 409020 305921 493630 511790 355320 TRUE FALSE 559240.9073 372318.0455 959253.4146 442626.9893 400881.3022 317689.9788 445757.8386 402347.6913 313314.4744 1.784918837 1.188320604 3.061631342 1.412724357 1.279485421 1.013965216 1.42271703 1.284165668 1 18.25725189 3.496898033 24.85479058 1.229621 1.980607404 0.384569366 0.468639404 754.6387695 948402.9329 0.124497011 0.181736551 3139.77143 -3.496898033 0.750986404 LHLDEDYPCSLVGNWNTWYGEQDQAVHLWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHLDEDYPCSLVGNWNTWYGEQDQAVHLWR 30 0 Q9BPW8;H7C2U6 Q9BPW8 NIPSNAP1 Protein NipSnap homolog 1 0 ; 235.68 1.14E-45 974940000 287570 294270 197941 355850 335940 347050 291520 399790 308015 FALSE TRUE 249566.8959 292336.921 293665.9297 436651.1813 329255.4513 360401.2381 263248.4353 314298.0197 271601.8176 0.918870492 1.076343758 1.081236982 1.607688731 1.212272636 1.326947077 0.969244012 1.157201459 1 18.05113361 4.400533798 2.326131986 1.200281521 0.936421667 0.203857274 0.179310696 0.582705192 5.680667713 0.048970138 0.233030023 25149.75731 -4.400533798 -0.263859854 LHLELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHLELK 6 0 Q9Y6Y8;Q9Y6Y8-2 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 118.06 0.064277 0 515460 554710 665450 562020 395860 505470 465100 579570 564220 FALSE TRUE 447340.655 551066.0735 987263.8458 689635.2309 387983.1605 524915.758 419994.6736 455633.4657 497518.5544 0.899143662 1.10762919 1.984375934 1.386149772 0.779836565 1.055067702 0.844178915 0.915812007 1 18.9243908 3.248575762 24.94716985 0.919777584 1.373135898 0.35672531 0.282646171 221.3030269 551250.3538 0.084424531 0.107683237 1772.457222 -3.248575762 0.453358313 LHLETPQPS(ph)PQEGGSVDIWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHLETPQPSPQEGGSVDIWR 20 0 O14613 O14613 CDC42EP2 Cdc42 effector protein 2 1 LHLETPQPS(1)PQEGGSVDIWR 155.56 1.84E-08 97756000 83625 54493 48937 43735 55177 58967 53247 69003 51051 TRUE FALSE 72573.74437 54135.03189 72603.09688 53665.7002 54079.08565 61235.49865 48083.11414 54247.24543 45015.80894 1.612183499 1.202578231 1.612835548 1.192152301 1.201335418 1.360310968 1.0681384 1.20507099 1 15.45814412 7.999999875 0.075018529 0.418873593 3.284568912 0.500764363 0.144400019 428.1221448 3.064933749 24.63327492 136.0458509 99999971.13 -7.999999875 2.86569532 LHLGFIEIR ddPTM_MDA-MB-175_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 ; 168.25 5.94E-05 2927300000 3190500 3080000 1721250 2210300 2703900 2652700 2723200 3034800 2745300 FALSE TRUE 2768867.341 3059767.277 2553652.257 2712182.397 2650097.68 2754751.086 2459104.483 2385831.637 2420753.761 1.143803796 1.263972952 1.054899634 1.120387559 1.094740705 1.137972449 1.015842471 0.985573863 1 21.20702491 -1.999771918 0.124192766 0.151537833 1.324414191 0.579825498 0.053861212 132.1532411 1.453833736 26.80246345 1.657208128 0.010005253 1.999771918 1.172876358 LHLGFIQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHLGFIQIR 9 0 Q9NQ29-3;Q9NQ29;Q9NQ29-2;A8MYV2;B8ZZ10 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 0 131.06 0.00034367 263700000 62113 82660 48726 55807 63535 77851 74320 76448 78451 FALSE TRUE 53904.60968 82117.00102 72290.05658 68478.83231 62270.7778 80845.97835 67112.45784 60100.19012 69176.61215 0.779231709 1.187063062 1.045007183 0.989913067 0.900170966 1.168689472 0.970161096 0.868793487 1 16.07799674 2.00096475 24.99923609 0.923360565 1.019634629 0.062018426 0.121423531 67.01608042 1736538.274 0.047005522 0.031404177 100.2223888 -2.00096475 0.096274064 LHLGIPEAVFVEDVDSFMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHLGIPEAVFVEDVDSFMK 19 0 P61758 P61758 VBP1 Prefoldin subunit 3 0 172.24 8.73E-12 330630000 174630 165600 119210 153640 126940 112230 150960 200340 207200 FALSE TRUE 151552.203 164512.1627 176860.3547 188526.3102 124414.1424 116547.5607 136319.9224 157498.85 182705.052 0.829491037 0.900424815 0.968010204 1.031861506 0.680956224 0.637900044 0.746120159 0.862038834 1 17.479157 3.239627215 24.99999928 0.784661163 0.932699827 0.30610796 0.110005417 39.6203203 928646.1391 0.035331376 0.043055528 1736.309794 -3.239627215 0.148038664 LHLIAQELPFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHLIAQELPFDR 12 0 F8W9B8;A0A0A0MSI8;O00471 F8W9B8 EXOC5 Exocyst complex component 5 0 133.71 0.00015835 303510000 249440 240950 145090 165300 230820 256170 201050 256010 233430 FALSE TRUE 216475.872 239367.1836 215256.0093 202833.8915 226227.1336 266025.0257 181552.2019 201264.2538 205834.1713 1.05170036 1.162912757 1.045773925 0.985423801 1.099074717 1.292424013 0.882031398 0.977798062 1 17.65112298 2.198341702 24.99999994 0.95541662 1.100233173 0.409090299 0.086438201 160.3324789 99661.2437 0.035603309 0.024004096 157.885302 -2.198341702 0.144816553 LHLIYLINDVLHHCQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHLIYLINDVLHHCQR 16 0 Q8IWX8 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 182.57 7.38E-10 117150000 48105 49233 22524 34081 37798 37064 43705 53478 42954 FALSE TRUE 41747.80237 48909.58518 33416.68174 41819.61195 37045.89375 38489.87606 39466.49583 42042.14587 37876.02705 1.102222319 1.291307167 0.882264702 1.10411823 0.978082883 1.016206795 1.041991436 1.109993554 1 15.20899739 4.249982139 24.998617 1.029798266 1.196764706 0.465653346 0.078523419 188.7438916 413101.2746 0.018245453 0.047361985 17782.06276 -4.249982139 0.16696644 LHLNEAVSFLSLPELVNYHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHLNEAVSFLSLPELVNYHR 20 0 Q13882 Q13882 PTK6 Protein-tyrosine kinase 6 0 ; 112.32 8.97E-05 335540000 133285 154269 76682 102948 146094 128011 189704 180009 153651 FALSE TRUE 115671.0495 153255.5968 113765.6717 126323.9169 143187.0152 132935.666 171306.5353 141515.4762 135486.5538 0.853745603 1.131149863 0.839682378 0.932372352 1.056835614 0.981172391 1.264380342 1.044498308 1 17.04779015 2.913008706 1.89123254 1.090884581 0.948350659 0.249671541 0.10923689 0.473719697 3.393269181 0.040050381 0.041011625 818.4811962 -2.913008706 -0.142533922 LHLSGIDANPNALFPPVEFPAPR ddPTM_MDA-MB-175_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 ;; 161.64 1.75E-11 11513370000 3131810 4172340 2202900 2320170 5509369 6517520 4006510 4273020 4452880 FALSE TRUE 2717933.374 4144931.624 3268229.808 2847000.06 5399743.336 6768253.212 3617959.277 3359267.926 3926465.599 0.69220863 1.055639358 0.832359211 0.725079588 1.375217279 1.723752072 0.921429002 0.855544978 1 21.90479983 3.252371629 24.99996146 1.143629431 0.84313277 0.297187541 0.263556933 397.3061147 719178.2019 0.085665927 0.110006175 1788.01694 -3.252371629 -0.30049666 LHLSSPDNFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHLSSPDNFR 10 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 ; 87.298 0.012971 337050000 201839 265720 107486 133511 273610 320160 229068 245111 242625 FALSE TRUE 175165.4648 263974.4678 159466.5891 163826.7131 268165.6963 332476.7624 206853.0206 192695.9201 213942.1489 0.818751544 1.233859102 0.745372475 0.765752396 1.253449578 1.55404984 0.966864275 0.900691711 1 17.70686121 3.238578676 25 1.11406208 0.905031306 0.22191887 0.224520222 0.981663785 1353775.56 0.072756706 0.087973056 1732.12279 -3.238578676 -0.209030774 LHLVDLAGSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHLVDLAGSER 11 0 O95239;O95239-2;Q2VIQ3;Q5JRK0;H0Y718;J3KPF9;A0A087X011;E9PES4;Q9Y496 O95239;J3KPF9 KIF4A;KIF4B;KIF6;KIF3A Chromosome-associated kinesin KIF4A;Chromosome-associated kinesin KIF4B;Kinesin-like protein;Kinesin-like protein KIF3A 0 97.214 0.0064334 273220000 55790 57893 37882 45833 50339 61240 51252 56609 54438 FALSE TRUE 48417.21015 57512.69707 56201.86191 56240.08316 49337.35239 63595.94243 46281.58893 44503.60588 48002.40166 1.008641411 1.198121242 1.170813542 1.171609778 1.027810082 1.324849179 0.964151529 0.927112068 1 15.55081897 2.103162778 12.48900041 0.954550131 1.148777987 0.49252411 0.089152914 0.35872747 40.87801488 0.033608903 0.022657947 126.8127083 -2.103162778 0.194227856 LHNAIEGGTQLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHNAIEGGTQLSR 13 0 O60832;O60832-2;C9IYT0;H7C0M1;H7BZF2 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ; 101.3 0.0020043 401410000 202150 207180 117795 147195 192429 215920 163370 179365 176272 FALSE TRUE 175435.3653 205819.0209 174761.056 180617.8745 188600.0394 224226.5821 147526.4025 141009.1906 155433.325 1.128685662 1.324162762 1.124347408 1.162027992 1.213382262 1.442590141 0.949129812 0.907200503 1 17.24593633 2.159783014 11.63680382 0.941963409 1.227636528 0.648249042 0.097240977 0.315643564 45.10466421 0.038712771 0.026099446 144.4717767 -2.159783014 0.285673119 LHNGNAS(ph)PPRVPS(ph)PPPAPEPPWHCGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LHNGNASPPRVPSPPPAPEPPWHCGDR 27 1 O15037 O15037 KHNYN Protein KHNYN 2 LHNGNAS(1)PPRVPS(1)PPPAPEPPWHCGDR;LHNGNAS(1)PPRVPS(1)PPPAPEPPWHCGDR;LHNGNAS(1)PPRVPS(1)PPPAPEPPWHCGDR;LHNGNAS(1)PPRVPS(1)PPPAPEPPWHCGDR 104.29 0.0029247 1602140000 969112 825967 571545 664262 812831 790988 712529 743299 696775 TRUE FALSE 841041.3938 820541.1684 847946.0737 815092.8397 796657.2534 821417.8202 643428.0472 584350.2932 614403.0533 1.368875674 1.335509588 1.380113704 1.326641909 1.296636221 1.336936423 1.047240966 0.951086246 1 19.22882586 2.183262427 3.680415312 0.978198634 1.341964999 0.974031568 0.026434548 0.031073183 0.859879815 0.011909138 0.007785866 152.4973955 -2.183262427 0.363766365 LHNQVNGTEWSWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHNQVNGTEWSWK 13 0 O14980 O14980 XPO1 Exportin-1 0 ; 158.02 4.24E-05 1906970000 2620200 2185430 1587820 1705320 2222110 1781450 2397500 2800400 2583400 FALSE TRUE 2273933.931 2171073.766 2355695.063 2092538.97 2177894.358 1849983.534 2164990.819 2201556.253 2277993.395 0.998217965 0.953064118 1.034109699 0.918588691 0.956058241 0.812111018 0.950393809 0.966445407 1 21.11933213 3.720011711 24.86518698 0.934194373 0.990923952 0.232058144 0.052292366 1219.788468 1635150.565 0.014843304 0.022058833 5248.216118 -3.720011711 0.056729579 LHPESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHPESK 6 0 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 95.957 0.042755 1279900000 2982700 2541800 1562500 2410800 1537100 2209300 2902800 3177600 3407000 FALSE TRUE 2588528.638 2525102.748 2318130.226 2958208.987 1506514.717 2294293.201 2621286.903 2498094.968 3004228.341 0.86162846 0.840516253 0.771622514 0.984681805 0.501464784 0.763688022 0.872532513 0.83152633 1 21.51856304 0.846913356 1.329206962 1.326741224 0.79218225 0.208342985 0.122747739 5.634181586 4.136272386 5.331776854 0.035846856 7.029320677 -0.846913356 -0.534558974 LHPPS(ph)PVPQGVCPAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHPPSPVPQGVCPAHR 16 0 Q96F44-3;Q96F44;Q96F44-2 Q96F44-3 TRIM11 E3 ubiquitin-protein ligase TRIM11 1 LHPPS(1)PVPQGVCPAHR;LHPPS(1)PVPQGVCPAHR 111.95 0.0012982 439160000 275930 270170 147305 225690 291840 277840 242990 311350 401540 TRUE FALSE 239465.1514 268395.2355 218542.1907 276936.364 286032.955 288528.6846 219424.8672 244770.2254 354070.3986 0.676320733 0.758027885 0.617228075 0.78215057 0.807842045 0.814890727 0.619721016 0.691303838 1 18.43367671 1.23494398 24.97372436 1.000000401 0.720285341 0.60404233 0.071004674 75.32889248 520082.2191 0.128630996 0.017882501 17.17686808 -1.23494398 -0.27971506 LHPTDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LHPTDK 6 0 G8JLM4 G8JLM4 USHBP1 0 ;; 119.7 0.020787 2737960000 5803000 4952600 3056460 4264140 2823410 3961880 5648000 6452600 6609600 FALSE TRUE 5036118.847 4920066.044 4534574.279 5232378.16 2767229.665 4114296.087 5100257.829 5072761.704 5828220.618 0.864092006 0.844179788 0.778037514 0.897765974 0.474798373 0.705926621 0.875096906 0.870379149 1 22.47462406 1.597940863 1.677481485 0.996986489 0.763706563 0.277907758 0.120156746 0.667573591 3.203250326 0.221539158 0.036796843 39.62240772 -1.597940863 -0.233279926 LHPVILASIVDSYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHPVILASIVDSYER 15 0 O00303;E9PQV8;A0A1W2PP79 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 0 ; 230.36 3.39E-13 1656810000 1722890 1640800 1047870 1231950 1564560 1641540 1530850 1771530 1691170 FALSE TRUE 1495205.721 1630021.477 1554623.437 1511683.077 1533428.317 1704691.106 1382388.403 1392702.096 1491241.809 1.002658128 1.093063155 1.042502582 1.013707547 1.028289515 1.143135269 0.927004859 0.933921036 1 20.50808278 2.210365149 24.99901869 0.948423506 1.052165107 0.528121209 0.044560567 154.9311476 137365.8783 0.017620015 0.011882047 162.3174266 -2.210365149 0.103741601 LHQEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LHQEGK 6 0 O43488;H7C5H7;H7C4Q7 O43488 AKR7A2 Aflatoxin B1 aldehyde reductase member 2 0 ;; 97.473 0.041032 406521000 1033520 699823 517163 601827 387618 589303 833540 956540 1000610 FALSE TRUE 896937.7134 695225.8166 767264.7566 738481.0187 379905.1602 611973.8677 752703.4191 751991.3648 882319.0257 1.016568483 0.787952879 0.869600149 0.836977326 0.430575732 0.693597044 0.853096666 0.85228964 1 19.75094087 6.513009155 1.246150815 0.781864408 19.05040302 0.182557207 0.148993236 232.643635 5.960285195 0.045466166 11681.8168 3258435.694 -6.513009155 18.26853861 AAEDDEDDDVDTKKQKTDEDD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 AAEDDEDDDVDTKKQKTDEDD 21 3 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;; 183.24 5.36E-17 6149220000 24863.9 0 32573 61303.7 22150.7 35016.1 28154.7 130555 123085 FALSE TRUE 21578.07262 0 48325.41175 75223.64205 21709.94441 36363.19203 25424.26153 102636.8292 108534.0315 0.198813886 0 0.445255843 0.693088066 0.200028914 0.33503954 0.234251517 0.945664948 1 16.72778795 1.690908472 5.041931876 0.987050054 0.30718351 0.70359696 0.18103492 0.084254448 4.973378072 0.124306329 0.049907002 49.0804428 -1.690908472 -0.679866544 down LHQLSGSDQLESTAHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHQLSGSDQLESTAHSR 17 0 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 0 210.98 1.67E-12 176080000 60944 54341 29798 36752 46552 53766 52190 57537 46893 FALSE TRUE 52890.09599 53984.03039 44208.41247 45097.10332 45625.70628 55834.41281 47128.62183 45233.1603 41349.36296 1.279103043 1.305558938 1.069143738 1.090635988 1.103419811 1.3503089 1.139766576 1.093926413 1 15.33557748 7.999978881 0.026281157 8.48E-12 2.730932887 0.250658211 0.099214397 6714.701599 17.50691897 671.4851917 1228.745484 99995137.18 -7.999978881 2.730932887 LHQMWLSWNQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHQMWLSWNQK 11 0 O60664-4;O60664;O60664-3;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 0 ; 199.43 5.03E-08 2127760000 3305300 3606700 2071850 2629400 3118200 3220700 3408400 3690400 3619500 FALSE TRUE 2868496.23 3583007.35 3073803.59 3226445.458 3056153.921 3344602.413 3077853.893 2901236.679 3191606.833 0.898762404 1.122634315 0.963089676 1.010915701 0.957559649 1.047936851 0.964358724 0.9090207 1 21.60585151 2.011987074 24.21494969 0.944615188 1.002882959 0.088260753 0.062581509 258.0316955 521244.1217 0.023361659 0.015736253 102.7985702 -2.011987074 0.058267771 LHQNICR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHQNICR 7 0 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 ; 113.08 0.0062093 389660000 351220 336340 218780 263820 306900 313750 325270 352540 388900 FALSE TRUE 304805.3871 334130.5604 324582.7398 323724.3632 300793.2904 325820.1655 293725.3655 277152.0645 342924.685 0.888840613 0.974355522 0.946513196 0.944010091 0.877140969 0.950121644 0.856530248 0.808200974 1 18.38753223 2.8051008 1.277543576 0.876591573 0.94015988 0.043045741 0.057176536 0.796136701 2.732402299 0.028766819 0.025339706 638.411645 -2.8051008 0.063568307 LHRQTAEYSAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHRQTAEYSAFK 12 1 Q5BJF6-9;Q5BJF6-3;Q5BJF6-4;Q5BJF6-8;Q5BJF6-5;Q5BJF6-6;Q5BJF6-10;Q5BJF6-7;Q5BJF6-2;Q5BJF6 Q5BJF6-9 ODF2 Outer dense fiber protein 2 0 68.536 0.047794 109460000 188890 193420 92276 133660 217710 222920 159380 204240 227710 FALSE TRUE 163927.7079 192149.4113 136900.9822 164009.5459 213377.9969 231495.8766 143923.3521 160564.8654 200790.3832 0.816412147 0.95696521 0.681810454 0.816819726 1.062690322 1.152923128 0.71678409 0.799664122 1 17.61533065 LHS(ph)PQTHWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHSPQTHWK 9 0 Q9H8Y5;B8ZZS4 Q9H8Y5 ANKZF1 Ankyrin repeat and zinc finger domain-containing protein 1 1 LHS(1)PQTHWK 111.94 0.0034163 157270000 201810 191980 134870 174850 199160 167440 206570 220850 211600 TRUE FALSE 175140.2972 190718.8707 200093.5831 214552.3649 195197.1056 173881.5251 186536.8732 173622.9462 186584.8891 0.938662815 1.022156037 1.072399722 1.14989143 1.046157096 0.931916438 0.999742659 0.930530586 1 17.50947263 2.773158815 11.28256771 0.963288837 1.051823093 0.331562532 0.056265287 1.172552857 380.2843153 0.018827363 0.018765899 593.1421887 -2.773158815 0.088534256 LHS(ph)SNPNLSTLDFGEEK ddPTM_MDA-MB-175_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(0.607)S(0.393)NPNLSTLDFGEEK 250.28 1.94E-21 2281900000 749080 675210 507110 613940 626040 654900 826650 863920 974150 TRUE FALSE 650087.1801 670774.5011 752350.0922 753344.4605 613583.0288 680094.4268 746481.6102 679177.431 858987.0968 0.756806688 0.780890078 0.875857268 0.877014874 0.714309948 0.79173998 0.869025406 0.790672449 1 19.71227693 1.235150607 24.99357227 1.000000267 0.809322149 0.561403049 0.053566398 76.81006466 562885.2115 0.09321952 0.013192944 17.18504235 -1.235150607 -0.190678118 LHSELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHSELK 6 0 D6RBP0;A0A494C0G8;Q96NL6-2;Q96NL6 D6RBP0 SCLT1 Sodium channel and clathrin linker 1 0 116 0.06922 0 361570 363780 240150 265910 321020 353120 387900 435310 413120 FALSE TRUE 313787.6084 361390.3052 356287.3433 326288.9297 314632.3301 366704.7549 350281.5177 342222.3441 364281.4242 0.861387893 0.992063501 0.978055206 0.895705649 0.863706764 1.006652359 0.961568431 0.939444949 1 18.4746939 2.71843542 24.99897856 0.969622635 0.924365624 0.274400884 0.046190681 1471.260055 1827556.946 0.016348614 0.014435849 522.9202014 -2.71843542 -0.045257012 LHSFESHKDEIFQVQWSPHNETILASSGTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHSFESHKDEIFQVQWSPHNETILASSGTDR 31 1 Q09028-3;Q09028;Q09028-2;Q09028-4;H0YF10;H0YCT5;H0YDK2;H0YEU5 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 84.035 0.00025095 483790000 187980 179460 111640 156420 163900 169520 190420 216690 201700 FALSE TRUE 163137.9667 178281.1154 165629.4774 191937.5517 160638.7107 176041.5441 171953.0977 170352.5298 177855.2558 0.917251312 1.002394417 0.931259955 1.079178408 0.903199121 0.989802316 0.966814823 0.957815551 1 17.44034408 4.756332047 23.28712873 0.976237332 0.917251185 0.143330267 0.046922422 2761.182366 3618015.812 0.010309153 0.274908039 57060.03669 -4.756332047 -0.058986147 LHSFLGDDVFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHSFLGDDVFLR 12 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 169.89 4.26E-05 305880000 321680 367730 233820 242040 326480 353460 298650 333390 375880 FALSE TRUE 279169.173 365314.3574 346896.1341 296998.8813 319983.6867 367057.8349 269686.969 262097.1429 331443.8946 0.842281839 1.102190637 1.046620981 0.896075885 0.965423385 1.107450887 0.813673063 0.790773785 1 18.33840515 2.218250573 24.97532577 0.849759257 0.995020102 0.255921324 0.098959916 276.0444491 339450.1707 0.039344356 0.02656216 165.2915197 -2.218250573 0.145260846 LHSLLGDYYQAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHSLLGDYYQAIK 13 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 110.07 0.0010877 441960000 551450 486390 378440 424580 533140 482590 578530 608330 713490 FALSE TRUE 478574.4853 483194.8721 561454.8498 520987.3783 522531.5571 501155.5496 522424.2496 478243.3635 629142.025 0.760677981 0.76802193 0.892413521 0.828091842 0.830546262 0.79656982 0.8303757 0.760151674 1 19.26302621 LHSQEEDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHSQEEDFR 9 0 Q4V328-4;Q4V328;Q4V328-2;A0A087WV84;A0A087WW92;A0A087WZF5 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 0 107.83 0.0033565 0 131250 129380 70867 80973 129170 133440 94549 108210 86756 FALSE TRUE 113904.98 128530.0943 105138.5182 99359.15724 126599.7697 138573.5231 85379.65253 85070.13359 76499.80451 1.488957791 1.680136245 1.374363228 1.298815832 1.654903179 1.811423232 1.116076741 1.112030732 1 16.22316844 2.147958133 8.23836573 1.080582023 1.541919582 0.69061464 0.150011465 0.152740698 12.26682387 0.064622967 0.043526718 140.5911984 -2.147958133 0.46133756 LHSS(ph)NPNLSTLDFGEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.056)S(0.924)NPNLS(0.01)T(0.01)LDFGEEK;LHS(0.162)S(0.838)NPNLSTLDFGEEK;LHS(0.001)S(0.994)NPNLS(0.004)TLDFGEEK 385.29 1.03E-121 2469030000 1464720 1343110 1044470 1084970 1306160 1215080 1557350 1802460 1869820 TRUE FALSE 1271153.541 1334287.022 1549579.186 1331329.021 1280169.971 1261824.914 1406318.437 1417017.956 1648772.01 0.770969869 0.809261083 0.939838362 0.80746702 0.776438443 0.765311945 0.852949 0.859438387 1 20.65296049 1.032992403 1.588936627 1.161896821 0.817064549 0.565794272 0.050302588 1.498880591 2.234022923 0.953464334 0.014871001 10.78927848 -1.032992403 -0.344832273 LHSYS(ph)SPSTK ddPTM_MDA-MB-175_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(0.804)S(0.128)PS(0.067)T(0.001)K;LHSYS(0.723)S(0.277)PSTK;LHSYS(0.987)S(0.012)PSTK 224.09 4.33E-09 617206000 1473740 972160 648210 786690 894220 912740 1091650 1181860 1177720 TRUE FALSE 1278981.525 965773.8169 961686.5241 965319.9883 876426.7715 947853.6984 985781.951 929128.4362 1038491.283 1.231576563 0.929977779 0.92604198 0.929540771 0.843942348 0.912721863 0.949244319 0.894690645 1 19.98605768 4.73921361 5.402123933 0.918939421 1.243791585 0.858653913 0.039304698 0.050872448 5.535650644 0.009278247 0.061330454 54854.6704 -4.73921361 0.324852163 LHSYSS(ph)PSTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHSYSSPSTK 10 0 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 LHSYS(0.302)S(0.697)PSTK 100.38 0.0026123 443740000 1150300 749210 489430 612300 665140 701460 854380 891270 972100 TRUE FALSE 998284.9405 744288.3902 726119.985 751332.0734 651905.0153 728445.6201 771522.3591 700678.8464 857179.4454 1.164616051 0.868299391 0.847103823 0.87651667 0.760523387 0.849816948 0.900070998 0.817423761 1 19.70923773 4.738460957 5.716857448 0.858322594 1.174407151 0.703177026 0.061085093 0.072463081 10.15078585 0.014097765 0.089543072 54759.68702 -4.738460957 0.316084557 LHTDDDLNWLDHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LHTDDDLNWLDHSR 14 0 Q9Y4G6 Q9Y4G6 TLN2 Talin-2 0 ;;; 200.44 1.11E-08 551330000 255581 277168 142916 187810 268801 271653 227940 270044 182675 FALSE TRUE 221805.3233 275347.2652 212030.6556 230455.131 263452.386 282103.6667 205834.4139 212297.1921 161079.3696 1.376993986 1.709388768 1.31631168 1.430693028 1.635543935 1.751333317 1.27784467 1.31796637 1 17.29741221 1.410672878 1.398661932 0.900211356 1.52535968 0.531481379 0.154675312 0.708188544 1.629447676 0.59493257 0.046354093 25.74381334 -1.410672878 0.625148324 LHTDDELNWLDHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LHTDDELNWLDHGR 14 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;;;; 309.49 6.40E-56 2244534000 972144 1049635 675957 867210 991838 1019600 930678 1024320 1131780 FALSE TRUE 843672.7073 1042739.879 1002852.066 1064123.285 972102.3643 1058824.672 840420.9908 805277.1393 997982.2577 0.845378463 1.044848113 1.004879654 1.066274753 0.974067782 1.060965427 0.842120172 0.806905266 1 19.92865464 2.229822704 24.99944482 0.865449937 1.003605133 0.314146859 0.079515145 182.7486592 522844.3716 0.030809206 0.021122991 169.7550504 -2.229822704 0.138155196 LHTLEEEKEELAQYQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHTLEEEKEELAQYQK 16 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ; 126.77 4.20E-05 211702000 265870 222771 166995 191316 252770 259071 255030 308430 266730 FALSE TRUE 230734.6059 221307.6026 247754.3406 234757.2219 247740.3715 269037.629 230297.2299 242474.6447 235197.4833 0.981024978 0.940943753 1.05338857 0.99812812 1.053329177 1.14387971 0.979165366 1.030940643 1 17.8435131 4.237173706 24.99682119 1.036354697 0.960984354 0.320649719 0.045978303 40.66404362 732965.0935 0.011695827 0.026649314 17265.28319 -4.237173706 -0.075370343 LHTLSVEHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHTLSVEHQR 10 0 Q5JRA6-2;Q5JRA6;A0A0A0MRH6 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 0 104.22 0.0015674 53085000 39323 42172 20013 36724 54472 55766 34328 52488 43341 FALSE TRUE 34126.36592 41894.96936 29691.35374 45062.74549 53388.11377 57911.35411 30998.87584 41263.84966 38217.27635 0.892956515 1.096231164 0.776909204 1.179119754 1.39696281 1.515318715 0.811122058 1.079717175 1 15.22193734 3.710984801 24.19922005 1.157290825 0.939452152 0.228789501 0.208128103 842.3427323 739199.4863 0.06131058 0.090965666 5140.256617 -3.710984801 -0.217838673 LHTVQPK ddPTM_MDA-MB-175_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 ; 97.602 0.011877 309630000 1020390 895950 626100 745380 792180 760560 992030 1128730 1052500 FALSE TRUE 885542.8762 890064.4455 928884.0542 914629.9214 776417.1679 789819.2353 895823.0833 887359.8733 928074.649 0.954172035 0.959044023 1.000872134 0.985513312 0.836589135 0.851029856 0.965248953 0.956129848 1 19.82388133 LHVAILER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LHVAILER 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 117.4 0.0020865 1987090000 2196130 2190030 1466040 1591500 2150860 2312410 2162110 2254090 2311020 FALSE TRUE 1905905.856 2175643.549 2175021.848 1952874.4 2108062.094 2401369.909 1952428.905 1772070.395 2037813.848 0.935269852 1.06763606 1.067330978 0.958318347 1.034472357 1.178404942 0.958099733 0.869593852 1 20.95859084 2.014478627 24.99813639 0.921991545 1.041190012 0.288298064 0.072398157 238.2846029 411409.7598 0.028891453 0.019470008 103.3900217 -2.014478627 0.119198467 LHVAVK ddPTM_MDA-MB-175_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 1366750000 8910100 7873100 7959600 6491500 5931100 6819200 7224700 8490700 8276700 FALSE TRUE 7732607.71 7821381.088 11808889.18 7965494.291 5813082.714 7081539.037 6524049.706 6675029.88 7298237.955 1.059517072 1.071680745 1.61804661 1.091427046 0.796504958 0.97030805 0.89392121 0.914608419 1 22.79911676 3.47584661 23.95966979 0.918712226 1.252407281 0.481655731 0.159302897 20.41724872 383772.7013 0.045081875 0.058731194 2991.207975 -3.47584661 0.333695055 LHVENEDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LHVENEDKK 9 1 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 ;;; 159.83 4.27E-05 1487630000 3839800 2807380 2645670 2744920 2511400 2024260 4017000 4424160 4225940 FALSE TRUE 3332360.701 2788938.136 3925124.861 3368196.039 2461428.053 2102134.592 3627431.958 3478087.813 3726354.187 0.894268374 0.748436138 1.053341863 0.903885103 0.66054592 0.564126351 0.973453348 0.93337553 1 21.82933338 LHVGNIS(ph)PTCTNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHVGNISPTCTNK 13 0 Q9BWF3;E9PB51;D6R9K7;J3QRR5;Q9BWF3-3;Q9BWF3-4;Q9BWF3-2 Q9BWF3 RBM4 RNA-binding protein 4 1 LHVGNIS(1)PTCTNK;LHVGNIS(1)PTCTNK 176.17 1.10E-05 1210680000 2147700 1857150 1214990 1466910 1772640 1562590 2086000 2371400 1997440 TRUE FALSE 1863876.003 1844950.259 1802563.228 1799994.336 1737367.932 1622703.848 1883700.041 1864294.564 1761304.919 1.058235848 1.047490551 1.023424853 1.021966337 0.986409516 0.921307737 1.06949116 1.05847349 1 20.74821326 4.244126434 2.047701604 1.01394862 1.058245225 0.15865605 0.040361504 0.830769717 6.568724456 0.012317087 0.047465971 17543.91174 -4.244126434 0.044296604 LHVNWVVSELTLGQIWDVDLQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHVNWVVSELTLGQIWDVDLQK 22 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 183.09 4.38E-17 33613000 81327 64495 57301 67032 55008 51046 79045 94137 119270 FALSE TRUE 70579.43089 64071.3281 85011.95526 82252.64012 53913.44842 53009.77265 71379.22807 74006.53512 105170.0365 0.671098283 0.609216563 0.808328666 0.782091962 0.512631261 0.50403874 0.678703084 0.703684601 1 16.68236421 1.177239255 2.512298012 1.126189623 0.651425221 0.551642257 0.097654018 0.562795155 3.379227649 0.622537053 0.027741523 15.03970283 -1.177239255 -0.474764402 LHYCVSCAIHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LHYCVSCAIHSK 12 0 P62854;Q5JNZ5 P62854 RPS26;RPS26P11 40S ribosomal protein S26;Putative 40S ribosomal protein S26-like 1 0 196.24 1.21E-07 1726500000 1682100 1617100 841890 1132900 1628300 1285200 1659600 1761400 1342000 FALSE TRUE 1459806.223 1606477.164 1249030.82 1390142.26 1595900.016 1334642.476 1498652.247 1384738.317 1183350.289 1.233621386 1.357566883 1.055503879 1.174751275 1.348628577 1.12785072 1.266448542 1.170184628 1 20.17444576 1.262630959 2.997867302 0.964803787 1.221481109 0.368708176 0.091591937 0.396088329 4.587021773 0.239036806 0.022935898 18.30758079 -1.262630959 0.256677322 LHYTPPLQS(ph)PIIDNDPLLGQSPWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LHYTPPLQSPIIDNDPLLGQSPWR 24 0 C9J5J4;H7C4T7;H0Y322;Q5TKA1-3;Q5TKA1;Q5TKA1-2 C9J5J4 LIN9 Protein lin-9 homolog 1 LHYT(0.004)PPLQS(0.996)PIIDNDPLLGQSPWR;LHYTPPLQS(1)PIIDNDPLLGQSPWR 187.48 1.21E-17 198360000 87107 90327 51090 73705 93328 102045 95395 115167 93396 TRUE FALSE 75595.58925 89733.63599 75797.29489 90440.84676 91470.95539 105970.7372 86143.60758 90539.43328 82354.83128 0.917925373 1.089597715 0.9203746 1.098185077 1.110693252 1.28675799 1.046005514 1.099382172 1 16.32956567 3.628380911 6.815681454 1.110850577 0.987759471 0.334275194 0.086544518 0.302491665 16.40612822 0.023550856 0.035056629 4249.921525 -3.628380911 -0.123091107 LIALLEVLSQKR ddPTM_MDA-MB-175_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 0 160.22 0.00039712 0 93881 94114 34039 41307 82082 73041 99198 110650 14654 FALSE TRUE 81474.38799 93495.75894 50500.37425 50686.38569 80448.72879 75850.93453 89577.79323 86988.35858 12921.62081 6.305276185 7.235606143 3.908207413 3.922602777 6.225900756 5.870078965 6.932396061 6.732000562 1 13.65749942 4.261442031 24.9943128 5.250740252 6.77044182 0.137562323 1.777154934 549.018014 599704.5966 0.445973982 1.178210652 18257.53032 -4.261442031 1.519701568 LIALSIDSVEDHLAWSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LIALSIDSVEDHLAWSK 17 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;;; 307.7 1.22E-48 16392182000 10524208 10499521 5573989 7260894 9463604 8763623 10899649 12278987 9759016 FALSE TRUE 9133407.248 10430548.96 8269588.724 8909590.959 9275296.796 9100765.248 9842602.718 9653221.185 8605316.246 1.061367995 1.212105245 0.960986033 1.035358923 1.077856587 1.057574758 1.143781639 1.121774135 1 23.03679678 LIAQACVSIFPDSGHFNVDNIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LIAQACVSIFPDSGHFNVDNIR 22 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 235.25 1.85E-30 2170290000 924530 918270 383755 683490 914690 893080 914120 985030 978990 FALSE TRUE 802351.018 912237.8239 569340.2016 838686.851 896489.4586 927437.3655 825468.7831 774389 863254.9175 0.929448535 1.056742111 0.659527319 0.971540195 1.038499104 1.074349357 0.956228301 0.897057155 1 19.71942712 3.509976689 24.99766641 0.984535343 0.885413644 0.185181184 0.106452216 1226.0961 932857.6372 0.02969147 0.044001568 3235.762886 -3.509976689 -0.099121699 LICCDILDVLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LICCDILDVLDK 12 0 P62258;P62258-2;K7EIT4 P62258 YWHAE 14-3-3 protein epsilon 0 ; 190.56 6.15E-05 287110000 878090 746450 655110 731450 702090 638510 837180 922600 1077920 FALSE TRUE 762048.1817 741546.5208 971923.3872 897536.902 688119.7826 663073.8929 755990.4125 725309.1697 950489.5256 0.801742851 0.78017327 1.02255034 0.944289104 0.723963562 0.697613046 0.795369536 0.763090124 1 19.8583112 3.2412445 24.99999019 0.786925074 0.88921359 0.155067467 0.104527549 127.3574953 1186306.714 0.031516871 0.038854219 1742.787756 -3.2412445 0.102288516 LIDEVIEDTRYTLPLTEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LIDEVIEDTRYTLPLTEGK 19 1 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-2;H0YD14;Q9NZM1-5 Q9NZM1-6 MYOF Myoferlin 0 ; 177.6 3.63E-14 45161000 129455 107129 52803 63526 110420 99314 126952 150437 27742 FALSE TRUE 112347.1938 106425.2625 78338.70742 77950.54923 108222.858 103134.6738 114640.2146 118267.2183 24462.37236 4.592653242 4.350569968 3.202416603 3.186549043 4.424054071 4.216053632 4.686389892 4.834658572 1 14.5782767 4.458266913 23.89024288 3.838207813 4.532133128 0.069477387 1.109869169 389.9614663 494118.0377 0.27419164 0.725758233 28725.45475 -4.458266913 0.693925315 LIDLES(ph)PTPESQK ddPTM_MDA-MB-175_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(0.973)PT(0.027)PESQK;LIDLES(1)PTPESQK;LIDLES(0.756)PT(0.244)PESQK;LIDLES(0.904)PT(0.096)PESQK;LIDLES(0.898)PT(0.102)PESQK;LIDLES(0.974)PT(0.026)PES(0.001)QK 360.81 1.47E-76 2940078000 3546900 3264320 2474128 2965549 3542590 2901492 4186540 4893310 4241680 TRUE FALSE 3078168.178 3242876.467 3670624.576 3638922.226 3472099.39 3013114.275 3780529.995 3846913.736 3740233.423 0.822988255 0.867025156 0.981389171 0.972913135 0.928310883 0.805595249 1.010773812 1.028522368 1 21.83469688 -2 0.029033625 2.248375945 6.81E-11 0.34369747 0.064051302 3972.406184 11.42625624 616.6591708 316.3608841 0.01 2 -2.248375945 LIDLESPT(ph)PESQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LIDLESPTPESQK 13 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 LIDLES(0.403)PT(0.597)PESQK 211.77 2.15E-07 112450000 425780 371180 303530 401200 453660 337110 509120 641650 529560 TRUE FALSE 369512.0942 368741.6941 450318.1232 492298.592 444633.0536 350078.8398 459745.6208 504438.1408 466956.0201 0.791320977 0.789671143 0.964369456 1.05427186 0.952194713 0.749704094 0.984558719 1.08026906 1 18.83292715 4.229934796 6.447166369 0.97509963 0.789068418 0.41673542 0.087819778 0.139535577 24.6796478 0.024717427 0.057475297 16979.88703 -4.229934796 -0.186031213 LIDLHSPSEIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LIDLHSPSEIVK 12 0 P60866;P60866-2;G3XAN0 P60866 RPS20 40S ribosomal protein S20 0 ;;; 151.98 6.11E-05 4573170000 7301200 6956060 4730390 5990740 6637800 5950420 7440700 8619600 8735300 FALSE TRUE 6336327.921 6910365.184 7018022.426 7351029.08 6505720.767 6179336.508 6719102.059 6776365.618 7702622.785 0.822619528 0.897144437 0.911121137 0.954354028 0.844611108 0.802237975 0.872313528 0.879747822 1 22.87691834 1.236937999 5.365278625 1.00675487 0.874184188 0.457288277 0.043503319 0.160637263 13.59237316 0.079042229 0.011472443 17.25591526 -1.236937999 -0.132570682 LIDVNHYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LIDVNHYAK 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 79.974 0.025425 871420000 1272700 1053700 784970 897410 1092700 986180 1067400 1146800 1326700 FALSE TRUE 1104509.47 1046778.175 1164584.118 1101180.657 1070957.408 1024118.983 963883.7123 901565.7444 1169859.037 0.944138939 0.894790006 0.995490978 0.941293456 0.915458507 0.875420841 0.823931501 0.770661862 1 20.15790327 2.743557743 2.29362561 0.84447501 0.942941774 0.225278664 0.062748619 0.358597774 3.727812223 0.023793673 0.021853259 554.0612062 -2.743557743 0.098466764 LIDWGLAEFYHPGQEYNVR ddPTM_MDA-MB-175_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 ; 148.15 9.83E-08 1936580000 755670 696030 427260 514600 649190 638870 613070 798050 674750 FALSE TRUE 655806.2949 691457.7331 633884.3651 631447.7952 636272.3891 663447.7423 553614.5658 627393.2179 594981.8237 1.102229125 1.162149339 1.06538442 1.061289219 1.069398028 1.115072286 0.930473073 1.054474596 1 19.18248607 3.236116211 0.397647174 0.987006565 1.15408907 0.418542645 0.048046279 1.656440838 0.924837638 0.127405544 0.177353072 1722.329385 -3.236116211 0.167082505 LIEDFLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LIEDFLAR 8 0 A6NKE1;A0A087WWM0;O43617;O43617-2 A6NKE1 TRAPPC3 Trafficking protein particle complex subunit 3 0 ;;;;; 187.63 0.00046808 104168000 602770 589636 379707 437945 539579 590943 542423 621876 563302 FALSE TRUE 523112.4173 585762.6423 563334.5752 537387.1058 528842.4336 613676.9596 489818.9009 488892.6568 496709.0793 1.053156544 1.179287166 1.13413384 1.081895073 1.064692504 1.23548569 0.986128342 0.984263581 1 18.92204159 2.19838874 24.90637504 0.988741329 1.122998244 0.581598181 0.053816984 97.98658483 60750.53225 0.020948046 0.014123364 157.9024031 -2.19838874 0.134256915 LIEDKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LIEDKPR 7 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;; 133.12 0.0030123 4192460000 7750400 6943100 4543900 5761500 6605100 6169600 8115200 9489200 8494000 FALSE TRUE 6726165.003 6897490.319 6741345.238 7069736.634 6473671.433 6406948.504 7328189.153 7460008.425 7489848.996 0.898037465 0.9209118 0.900064239 0.943909101 0.864326028 0.85541758 0.978416141 0.996015865 1 22.8365052 2.117682282 6.29793556 0.9944847 0.899198204 0.759617924 0.025134729 0.103409234 5.289940582 0.010900309 0.007298927 131.1240281 -2.117682282 -0.095286495 LIEDNEY(ph)TAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LIEDNEYTAR 10 0 J3QRU1;P07947;Q573B4;P06241-3;P06239;P06241-2;P06241;P06239-3;P12931;P12931-2 J3QRU1;P12931 YES1;LCK;FYN;SRC Non-specific protein-tyrosine kinase;Tyrosine-protein kinase Yes;Tyrosine-protein kinase Fyn;Tyrosine-protein kinase Lck;Proto-oncogene tyrosine-protein kinase Src 1 LIEDNEY(0.888)T(0.112)AR;LIEDNEY(0.711)T(0.289)AR 118.4 0.0040935 0 185441 158209 115649 115460 170229 181765 158742 194452 179188 TRUE FALSE 160934.502 157169.7147 171577.2432 141676.9577 166841.7759 188757.6172 143347.2253 152869.953 158004.5988 1.018543152 0.994716077 1.085900313 0.896663507 1.055929873 1.194633692 0.907234513 0.967503188 1 17.26960702 LIEDTEDWRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 206.11 2.51E-08 644840000 907310 891290 585910 722030 848750 863790 785220 936360 858170 FALSE TRUE 787406.6847 885435.0573 869258.0358 885977.947 831861.5356 897020.5602 709069.4853 736126.7008 756718.1202 1.040554816 1.170098923 1.148721053 1.170816349 1.099301726 1.185409119 0.937032518 0.972788521 1 19.52939647 2.235383604 24.99999986 0.969162533 1.137892915 0.759082457 0.044041227 35.264555 277492.4324 0.016421044 0.011593394 171.9426453 -2.235383604 0.168730382 LIEEVHAVVTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LIEEVHAVVTVR 12 0 M0R0N4;M0QYZ2;P53680;X6R390;P53680-2;M0QZ21 M0R0N4 AP2S1 AP-2 complex subunit sigma 0 ; 111.12 0.0014159 223938000 216650 207940 152873 179927 204485 214880 195252 235060 221540 FALSE TRUE 188019.1536 206574.0284 226802.8941 220782.1754 200416.1486 223146.5726 176316.4911 184794.2482 195349.7936 0.962474288 1.057457111 1.161009131 1.130188936 1.025934785 1.142292339 0.902568095 0.945965925 1 17.57570021 2.234532129 24.99999436 0.946816734 1.082393627 0.492093668 0.062387569 83.23418393 516525.8509 0.025080711 0.017604726 171.6058657 -2.234532129 0.135576893 LIEEVMIGEDKLIHFSGVALGEACTIVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LIEEVMIGEDKLIHFSGVALGEACTIVLR 29 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 136.53 2.92E-06 110330000 155940 113250 137170 84902 34987 82908 86902 101040 18413 FALSE TRUE 135332.1339 112506.0533 203505.8708 104180.2967 34290.82715 86097.52441 78474.25742 79433.38229 16236.23612 8.335191292 6.929318623 12.53405465 6.416530038 2.111993624 5.30280071 4.833278899 4.892352004 1 13.98692961 3.480704133 12.14120948 3.987231309 9.106748828 0.643888044 1.908717127 0.142502066 452.5689526 0.523394551 0.706841188 3024.852018 -3.480704133 5.119517519 LIEGLSHEVIVSAACGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LIEGLSHEVIVSAACGR 17 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;; 209.13 4.55E-12 913270000 1161827 873630 584388.1 658421 814565 899204 758971 978960 850867 FALSE TRUE 1008288.618 867891.067 867000.1398 807925.5514 798356.7502 933796.9597 685366.1092 769617.0223 750278.4726 1.343885844 1.156758589 1.155571127 1.076834243 1.064080577 1.244600497 0.913482306 1.025775163 1 19.51706664 8 0.292464914 0.988056351 3.625250535 0.574558833 0.080795715 58.64538214 0.938215926 0.168642712 78.58091593 100000000 -8 2.637194185 LIELYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LIELYK 6 0 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ; 118.03 0.051687 559220000 993120 936580 683600 813110 970030 810020 1102190 1218380 1294750 FALSE TRUE 861876.6758 930427.5443 1014191.247 997739.0531 950728.3008 841181.9936 995299.7834 957838.9184 1141686.13 0.754915605 0.814959138 0.888327553 0.873917119 0.832740519 0.736789185 0.871780568 0.838968691 1 20.12273465 0.956595842 1.917958457 1.213620485 0.825462376 0.551913658 0.04907027 1.716459597 3.043958495 1.582365584 0.013624324 9.0489011 -0.956595842 -0.38815811 LIESAEELIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LIESAEELIR 10 0 Q13217;X6R9L0 Q13217 DNAJC3 DnaJ homolog subfamily C member 3 0 ;; 124.23 0.0010261 54671000 77290 74765 65520 67092 76540 91980 71764 74631 78459 FALSE TRUE 67075.93067 74273.86379 97205.69115 82326.26404 75017.00375 95518.53012 64804.33833 58671.74143 69183.6664 0.9695342 1.073575132 1.405038157 1.18996677 1.084316684 1.380651461 0.936699971 0.848057706 1 16.07814385 2.112014745 8.545268893 0.90721364 1.184295325 0.436616246 0.136580261 0.216896537 15.42187583 0.05580036 0.037576344 129.4239781 -2.112014745 0.277081685 LIETGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LIETGER 7 0 E5RHX8;Q9NPA8-2;Q9NPA8;J3KNT2;E5RI00;E5RHT9;E5RJ84 E5RHX8 ENY2 Transcription and mRNA export factor ENY2 0 94.539 0.032864 84809000 225470 169520 149590 169390 178580 169260 211490 233380 205090 FALSE TRUE 195673.5682 168406.412 221932.2243 207852.5885 175026.6074 175771.5417 190979.7324 183473.5032 180844.4938 1.081999037 0.931222225 1.227199234 1.149344302 0.967829341 0.97194854 1.056043943 1.014537403 1 17.46439015 3.232154694 24.99957524 1.006171782 1.094836848 0.276248744 0.076494093 229.305963 894882.1383 0.023689999 0.027505132 1706.690195 -3.232154694 0.088665066 LIEVDDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LIEVDDER 8 0 P62753;A2A3R7 P62753 RPS6 40S ribosomal protein S6 0 ;;;;; 173.28 0.00064825 10011970000 11973500 12908400 8385580 9114350 12244100 12845000 12174200 13472900 13236300 FALSE TRUE 10391171.64 12823603.87 12440874.54 11183902.47 12000466.37 13339155.46 10993547.96 10591825.18 11671519.69 0.890301513 1.098709012 1.065917281 0.958221617 1.028183705 1.142880774 0.9419123 0.907493237 1 23.47648908 2.070750363 24.99993211 0.940400992 1.032853156 0.210225402 0.07309348 58.6886678 20736.71427 0.028756701 0.019387762 117.6929269 -2.070750363 0.092452164 LIEVDDERK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LIEVDDERK 9 1 P62753;A2A3R7 P62753 RPS6 40S ribosomal protein S6 0 ;; 159.4 0.00010595 1530720000 1435380 1252650 1015150 1070540 1171380 1056640 1551420 1633590 1288310 FALSE TRUE 1245690.896 1244421.26 1506079.935 1313622.469 1148071.83 1097289.625 1400963.527 1284259.491 1136007.459 1.096551687 1.095434057 1.325765886 1.156350214 1.010619975 0.965917623 1.233234444 1.130502692 1 20.11554088 3.453654767 22.91167329 1.083173553 1.17756707 0.199417256 0.097730551 164.1530868 160270.2568 0.029568215 0.038176208 2842.20086 -3.453654767 0.094393517 LIFIVDVWHPELTPQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LIFIVDVWHPELTPQQR 17 0 Q12797;Q12797-10 Q12797 ASPH Aspartyl/asparaginyl beta-hydroxylase 0 80.534 0.011215 155390000 77028 72793 46436 77163 62272 79215 59857 97412 102940 FALSE TRUE 66848.55464 72314.81799 68892.60492 94684.03851 61032.90903 82262.45231 54052.07735 76581.20186 90770.55047 0.73645642 0.79667709 0.758975291 1.043114072 0.67238668 0.906268078 0.59548033 0.843678941 1 16.46993669 2.366047183 0.015503966 1.640367764 1.21E-06 0.042553991 0.135877024 9620.276286 102.4507169 5541.218708 5295.968382 232.2989161 -2.366047183 -1.640366558 LIFPYVELDLHSYDLGIENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LIFPYVELDLHSYDLGIENR 20 0 O75874;C9J4N6;C9JLU6;C9JJE5 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 273.33 1.89E-44 5813400000 1063100 813880 620560 672070 840940 904000 728810 1046540 864850 FALSE TRUE 922608.6414 808533.5687 920664.8916 824673.7654 824206.9393 938777.465 658130.1184 822745.5652 762608.4182 1.209806526 1.060221143 1.207257709 1.081385605 1.080773461 1.231008526 0.862998759 1.078857177 1 19.54058293 2.24872345 24.99999961 0.99618416 1.138227116 0.487966832 0.078670798 179.265318 440982.951 0.027538189 0.021080608 177.3060071 -2.24872345 0.142042956 LIFYDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LIFYDLR 7 0 Q15046;Q15046-2;H3BVA8 Q15046 KARS Lysine--tRNA ligase 0 ; 97.602 0.02763 1016890000 3243000 3097100 2061550 2419400 3024000 3157500 2992500 3285900 3398300 FALSE TRUE 2814429.333 3076754.946 3058522.475 2968761.748 2963828.316 3278971.068 2702287.811 2583235.856 2996556.845 0.939221072 1.026763417 1.020678944 0.990724322 0.989077955 1.094246242 0.901797613 0.86206803 1 21.51487431 2.202832037 24.99780849 0.908138693 1.009517325 0.38954672 0.051547966 149.8450416 104839.3741 0.020272505 0.01366826 159.5262063 -2.202832037 0.101378632 LIGDAAK ddPTM_MDA-MB-175_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 0 114.72 0.01359 456040000 1332400 1313000 974580 1135100 1092900 1053100 1392000 1540500 1740400 FALSE TRUE 1156319.964 1304374.817 1445890.148 1392841.804 1071153.428 1093613.438 1257004.054 1211076.063 1534651.895 0.75347378 0.849948331 0.942161641 0.90759462 0.69797811 0.712613357 0.819080899 0.789153597 1 20.54948002 4.747484336 22.96450192 0.831795147 0.753473654 0.07045352 0.09465727 1276.561878 3284897.043 0.02396131 0.262981147 55909.33626 -4.747484336 -0.078321493 LIGEYGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LIGEYGLR 8 0 P46781;B5MCT8;C9JM19;F2Z3C0;A8MXK4 P46781 RPS9 40S ribosomal protein S9 0 ;;; 168.45 0.00071364 790110000 1111824 1259867 791594 849853 1185339 1231931 1169285 1209825 1286389 FALSE TRUE 964893.6414 1251590.851 1174411.506 1042825.113 1161753.073 1279324.183 1055887.921 951113.3386 1134313.558 0.85064102 1.103390541 1.035349968 0.919344661 1.024190414 1.127839982 0.930860707 0.838492436 1 20.11338807 2.01762761 24.90452218 0.900799916 1.013468604 0.169715055 0.088729011 294.4910121 416059.285 0.034781606 0.023444632 104.1424068 -2.01762761 0.112668688 LIGWGQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LIGWGQIR 8 0 P41091;Q2VIR3 P41091 EIF2S3;EIF2S3L Eukaryotic translation initiation factor 2 subunit 3;Putative eukaryotic translation initiation factor 2 subunit 3-like protein 0 ; 148.07 0.0012262 524270000 311700 558270 391140 407100 561900 617510 522410 555860 594130 FALSE TRUE 270508.0553 554602.6876 580296.6123 499538.2771 550719.2893 641266.0093 471746.7586 436993.6647 523892.6282 0.516342549 1.058618995 1.107663252 0.953512705 1.051206411 1.22404091 0.900464586 0.834128295 1 18.99891164 4.742434972 24.67694376 1.005042079 0.516342321 0.675278134 0.108690136 223.4491195 1423146.298 0.029637792 0.217284576 55263.06544 -4.742434972 -0.488699758 LIHDGCLLWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LIHDGCLLWK 10 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 0 69.349 0.057245 238480000 493200 495960 401390 448810 433160 438170 541030 540630 607520 FALSE TRUE 428022.3704 492702.0061 595503.5466 550719.1701 424540.9635 455026.6834 488560.9939 425020.4817 535699.6777 0.798996879 0.919735491 1.111636933 1.02803715 0.792498075 0.849406304 0.912005391 0.7933932 1 19.0310649 3.242857119 24.99995015 0.862140315 0.97189941 0.184950833 0.098050209 170.8747407 994258.0901 0.029171994 0.036340615 1749.271093 -3.242857119 0.109759095 LIHEDGIIRPYDR ddPTM_MDA-MB-175_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 ;;; 185.87 4.98E-06 598110000 115992 95914.2 64318.6 70495.5 92893.7 112370 77028.8 104972 94585 FALSE TRUE 100663.3633 95284.1333 95423.29009 86502.58073 91045.29711 116692.9466 69558.55883 82524.55469 83403.26905 1.206947455 1.142450822 1.144119303 1.037160554 1.09162744 1.39914116 0.834002787 0.98946427 1 16.34781631 2.214125031 24.99999986 0.946755298 1.158168261 0.516532174 0.103995046 193.9728961 198451.7568 0.041790909 0.028190049 163.7287819 -2.214125031 0.211412963 LIHELAAVYTEAIADIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LIHELAAVYTEAIADIKR 18 1 Q92797;A0A087WUE9 Q92797 SYMPK Symplekin 0 95.347 0.0011653 28994000 98922 80867 55297 63748 79819 61102 93236 107620 63755 FALSE TRUE 85849.20706 80335.77935 82038.81416 78222.95773 78230.75806 63452.63348 84193.98707 84606.3005 56217.95653 1.527078043 1.429005683 1.459299114 1.391423 1.391561752 1.128689789 1.497635138 1.504969332 1 15.77874339 3.573946664 1.631966035 1.334697122 1.47663938 0.185998141 0.155308766 0.857087425 4.536653297 0.051544186 0.094410139 3749.269546 -3.573946664 0.141942258 LIHEQEQQS(ph)SS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LIHEQEQQSSS 11 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 1 LIHEQEQQS(0.545)S(0.228)S(0.228) 85.958 0.015554 511720000 219810 216830 129290 188030 211570 241210 169080 224420 211040 TRUE FALSE 190761.5516 215405.6295 191815.0764 230725.0854 207360.1709 250489.5048 152682.6476 176429.5294 186091.0916 1.025097708 1.157527894 1.030759048 1.239850244 1.114293914 1.346058549 0.820472631 0.948081544 1 17.50564947 2.223232819 24.99997627 0.923841897 1.149236087 0.526111947 0.102610291 182.4830952 297631.5585 0.040040071 0.027108297 167.19867 -2.223232819 0.22539419 LIHEQEQQSS(ph)S ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LIHEQEQQSSS 11 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 1 LIHEQEQQS(0.202)S(0.779)S(0.02) 156 3.28E-05 364240000 210550 239900 167130 202910 247810 294260 180470 246800 224250 TRUE FALSE 182725.284 238324.0811 247954.627 248983.8168 242879.0658 305580.3726 162968.0472 194023.7406 197739.4205 0.924071101 1.205243145 1.253946362 1.25915114 1.228278435 1.545369011 0.824155582 0.98120921 1 17.59324098 2.211445874 24.99975943 0.940099563 1.236127344 0.458689247 0.154054113 195.9119576 180629.1545 0.062115407 0.041889903 162.7218501 -2.211445874 0.296027781 LIHEQEQQSSS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LIHEQEQQSSS 11 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ; 176.33 2.04E-05 751450000 542650 517380 336810 452700 534430 599990 454370 524440 554040 FALSE TRUE 470937.4276 513981.2967 499692.4426 555492.4541 523795.8886 623072.0035 410305.2673 412292.5872 488542.0224 0.963965035 1.052071824 1.022823871 1.137041296 1.072161379 1.275370337 0.839856652 0.843924511 1 18.89812314 2.205799021 24.99781235 0.88175679 1.08429105 0.49255789 0.091835691 149.8136167 114310.0539 0.037236489 0.02510677 160.6197779 -2.205799021 0.20253426 LIHEQEQQSSS(ph) ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LIHEQEQQSSS 11 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 1 LIHEQEQQS(0.029)S(0.124)S(0.847);LIHEQEQQS(0.002)S(0.115)S(0.883);LIHEQEQQS(0.003)S(0.187)S(0.81);LIHEQEQQS(0.004)S(0.243)S(0.753) 169.98 1.70E-05 3110100000 907760 914960 606088 792970 945050 1124410 709780 993870 877890 TRUE FALSE 787797.216 908949.5675 899194.184 973025.9583 926245.354 1167666.78 640945.6448 781338.6348 774106.8443 1.017685377 1.174191359 1.161589244 1.256965967 1.196534252 1.508405188 0.827980852 1.009342109 1 19.56217318 2.212242239 24.99996922 0.954109562 1.215245448 0.494299156 0.130253229 190.3222623 180786.7419 0.05237192 0.0353212 163.0205069 -2.212242239 0.261135887 LIHGEDS(ph)DS(ph)EGEEEGR ddPTM_MDA-MB-175_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 280.69 1.71E-23 316910000 560920 549120 369260 481450 581470 515930 502020 591180 715270 TRUE FALSE 486793.0008 545512.7946 547835.3711 590770.581 569899.8846 535778.161 453334.1777 464760.7576 630711.5954 0.771815524 0.864916387 0.868598857 0.936673093 0.90358238 0.849482021 0.718766201 0.736883166 1 19.26662093 1.217042448 24.81282077 1.00000071 0.829964998 0.363172915 0.07016805 2110.503765 2433502.008 0.938128608 0.019933135 16.48323491 -1.217042448 -0.170035712 LIHLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LIHLNK 6 0 O43813;E9PHS0 O43813 LANCL1 LanC-like protein 1 0 93.595 0.04544 373320000 808750 740070 514030 609000 693810 638850 717120 876690 798780 FALSE TRUE 701871.6384 735208.4314 762616.6273 747282.758 680004.5384 663426.9729 647573.8128 689216.6659 704349.1384 0.996482568 1.043812495 1.082725293 1.060955025 0.965436743 0.941900737 0.919393206 0.978515666 1 19.42593121 3.216828301 9.021800565 0.959033623 1.048476731 0.666096998 0.029844158 0.14159087 52.63430672 0.0094817 0.010968946 1647.510918 -3.216828301 0.089443108 LIHPDEDISLEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LIHPDEDISLEER 13 0 J3QRS9;O43670-2;O43670;O43670-4;X6R4W8;O43670-3;J3KS31 J3QRS9 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 ;;;; 214.81 3.02E-11 3389660000 3588410 3115780 2159710 2398740 2980100 3089660 2869180 3267600 3323690 FALSE TRUE 3114192.527 3095312.236 3204152.98 2943410.579 2920801.84 3208521.219 2590927.365 2568849.168 2930767.155 1.062586129 1.056144031 1.093281319 1.004314033 0.996599759 1.094771795 0.884044084 0.876510836 1 21.48284692 2.233421378 24.99999999 0.909580303 1.048792292 0.641966754 0.04590027 73.47808079 357431.7052 0.018403402 0.012834266 171.1675276 -2.233421378 0.139211989 LIHPDEDISLEERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LIHPDEDISLEERR 14 1 J3QRS9;O43670-2;O43670;O43670-4;X6R4W8;O43670-3;J3KS31 J3QRS9 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 ;; 136.24 1.83E-05 195794000 157738 115593 38976.8 50087.2 111128 115172 109349 122934 9656.8 FALSE TRUE 136892.5236 114833.662 57826.11085 61460.26429 108916.7702 119602.7414 98744.35081 96645.52077 8515.184105 16.07628466 13.48575211 6.790940764 7.217725834 12.79088847 14.04581978 11.59626728 11.3497864 1 13.05582201 4.437406549 6.36266494 9.796371384 15.47984134 0.277203642 3.743907335 0.225389089 24.21968369 0.948935439 2.643977045 27378.30446 -4.437406549 5.683469958 LIHQTNLILQTFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LIHQTNLILQTFK 13 0 C9J363;Q9BUL8 C9J363 PDCD10 Programmed cell death protein 10 0 182.33 1.13E-05 388050000 605370 669490 272150 463020 637130 585800 643110 769330 860630 FALSE TRUE 525368.8207 665092.0761 403762.6503 568155.7678 624452.3595 608336.1051 580741.2912 604814.7664 758887.3018 0.692288327 0.876404276 0.532045601 0.748669488 0.822852561 0.80161587 0.765253668 0.796975737 1 19.53352613 -0.567708429 0.99135218 10 0.742039318 0.430034159 0.090954766 63.91627675 2.183595865 1247.045476 0.029305282 0.270577432 0.567708429 -9.257960682 LIHTLDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LIHTLDDR 8 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;;;;; 178.83 0.00024754 2926340000 1698810 1415750 916570 1134560 1396970 1439000 1330440 1479700 1385240 FALSE TRUE 1474307.954 1406449.845 1359826.318 1392179.189 1369173.03 1494359.261 1201414.134 1163277.67 1221478.505 1.206986409 1.151432333 1.113262585 1.139749232 1.120914551 1.223402012 0.983573701 0.952352141 1 20.22019705 2.220544475 22.71054483 0.973370051 1.15420905 0.846082899 0.036255377 28.66125591 36128.55007 0.014512848 0.00981683 166.1668836 -2.220544475 0.180838999 LIILDEIHLLHDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LIILDEIHLLHDDR 14 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;;;;; 216.46 3.54E-12 552199000 247290.8 208037.7 192292.8 226941.7 195304.2 210726 201784.7 219375 487853 FALSE TRUE 214610.6942 206671.0867 285286.2413 278472.2816 191418.0285 218832.7656 182215.6509 172463.3634 430179.5741 0.498886296 0.4804298 0.663179422 0.647339619 0.444972379 0.508700968 0.423580434 0.400910164 1 18.7145795 1.231073336 24.99988147 1.000000875 0.505792349 0.762232473 0.086257976 147.10579 491141.2189 0.240714492 0.023559097 17.02445961 -1.231073336 -0.494208526 LIILDEIHLLHDDRGPVLEALVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LIILDEIHLLHDDRGPVLEALVAR 24 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 203.84 7.44E-25 676000000 599840 514130 293040 351360 433210 483560 480110 551480 285700 FALSE TRUE 520569.6242 510752.6462 434755.1242 431141.6582 424589.9686 502162.8661 433549.0061 433550.2936 251924.8715 2.066368522 2.027400642 1.725733238 1.711389811 1.685383289 1.993304048 1.720945628 1.720950739 1 17.94263403 0.960738509 1.744885367 3.83E-17 1.84748207 0.778701476 0.140743425 1.060971027 1.597860433 4.215185894 0.040683165 9.135630145 -0.960738509 1.84748207 LIITPET(ph)PEPEAQPVGPPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LIITPETPEPEAQPVGPPSR 20 0 Q96DU7 Q96DU7 ITPKC Inositol-trisphosphate 3-kinase C 1 LIITPET(1)PEPEAQPVGPPSR 199.15 1.66E-20 43369000 51545 51194 35404 33939 47878 48971 44715 51364 47262 TRUE FALSE 44733.19765 50857.70324 52525.49282 41645.36868 46925.32147 50854.94606 40378.54618 40380.20832 41674.7402 1.073388759 1.220348417 1.260367613 0.99929522 1.125989538 1.220282258 0.96889737 0.968937254 1 15.34688559 2.225512124 24.99416678 0.976691245 1.150228007 0.528794657 0.075932622 177.1703364 339363.9554 0.031220134 0.021193982 168.0784847 -2.225512124 0.173536762 LIKDDFLQQNGYTPYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LIKDDFLQQNGYTPYDR 17 1 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 243.37 1.71E-20 2614600000 1616550 1326960 938240 1124400 1272710 1197460 1328860 1651470 1311660 FALSE TRUE 1402918.822 1318243.112 1391976.002 1379712.205 1247385.561 1243527.061 1199987.362 1298315.992 1156597.049 1.212971123 1.139760052 1.203509903 1.192906559 1.078496233 1.075160154 1.037515497 1.122530957 1 20.1414549 3.212801802 6.259797183 1.068335549 1.185267268 0.742556011 0.036366428 0.087117292 10.95847756 0.010451527 0.012242496 1632.306844 -3.212801802 0.116931718 LIKDDIER ddPTM_MDA-MB-175_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 ;;;;; 108.67 0.0034351 3748470000 7946510 7196990 4786320 5656280 7211950 6468750 7696980 8992410 7313790 FALSE TRUE 6896358.57 7149712.499 7101000.361 6940624.825 7068446.305 6717606.998 6950528.064 7069453.101 6449162.078 1.069341798 1.10862658 1.101073329 1.076205675 1.096025533 1.041624775 1.07774126 1.096181646 1 22.6206803 1.233427345 24.9413998 0.999999866 1.083903191 0.651617285 0.019149972 100.627262 488867.1776 0.038494306 0.004717992 17.11698794 -1.233427345 0.083903325 LILADALCYAHTFNPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LILADALCYAHTFNPK 16 0 P28838-2;P28838 P28838-2 LAP3 Cytosol aminopeptidase 0 163.99 7.53E-09 433070000 228560 169470 178860 172250 165910 166800 247000 290520 182450 FALSE TRUE 198355.2169 168356.7404 265357.2943 211361.9952 162608.7156 173216.9039 223045.978 228394.5588 160880.9688 1.232931517 1.046467718 1.649401394 1.313778732 1.010739286 1.076677404 1.386403747 1.419649325 1 17.29563415 3.414159728 24.99999998 1.214106086 1.31635071 0.080535015 0.202412938 225.6315143 89589.12319 0.061810987 0.07979765 2595.133642 -3.414159728 0.102244624 LILDSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LILDSAR 7 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 83.364 0.051959 401970000 479600 561540 392600 403990 493870 567060 602940 549520 688960 FALSE TRUE 416219.6448 557851.2068 582462.6732 495722.1041 484042.9532 588875.1651 544466.9716 432009.4244 607511.9337 0.685121759 0.918255553 0.958767459 0.815987434 0.796762872 0.969322794 0.896224323 0.711112655 1 19.21255322 4.748015593 24.07960981 0.870695561 0.685121592 0.321353704 0.088846328 1033.16018 2631123.962 0.021998205 0.264958766 55977.76993 -4.748015593 -0.185573969 LILDVFCGSQMHFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 LILDVFCGSQMHFVR 15 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;; 228.03 6.51E-13 9048921000 2364235 2745593 1478943 2066702 2743764 3319545 2982351 3061500 3266296 FALSE TRUE 2051795.355 2727557.019 2194164.782 2535978.277 2689168.464 3447250.044 2693123.059 2406822.05 2880158.208 0.712389809 0.947016387 0.761820922 0.880499644 0.93368776 1.196896071 0.935060807 0.835656195 1 21.45771663 3.332205616 3.190873368 0.970623798 0.821544162 0.350989631 0.107533656 0.339892684 6.894775477 0.034317581 0.045059862 2148.847603 -3.332205616 -0.149079636 LILEVHQFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LILEVHQFSR 10 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 193.96 5.15E-07 1306560000 993960 1031700 561190 721750 933040 1158370 908310 1059310 745520 FALSE TRUE 862605.6676 1024922.695 832583.3611 885634.3688 914474.3295 1202933.243 820222.236 832784.8001 657385.4749 1.312176342 1.559089353 1.266507084 1.347207084 1.391077784 1.829874996 1.247703619 1.266813509 1 19.32638005 1.450607616 1.780489242 0.963459042 1.436701247 0.400279744 0.167974385 0.58688302 2.65409698 0.430715134 0.04725962 28.22328853 -1.450607616 0.473242205 LILFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LILFPR 6 0 P26373 P26373 RPL13 60S ribosomal protein L13 0 ; 161.85 0.019487 944360000 378060 748790 451180 452960 681610 803270 609530 637630 676590 FALSE TRUE 328098.4131 743871.1492 669372.1571 555811.4911 668047.2945 834172.3167 550417.8744 501277.7865 596604.301 0.549943091 1.246841747 1.12197005 0.931625015 1.119749377 1.398200307 0.922584489 0.840218191 1 19.18641485 2.033775625 24.99920279 0.900506776 1.076914986 0.07670431 0.223185592 376.2938502 278514.3727 0.087774916 0.059177548 108.0875381 -2.033775625 0.17640821 LILIESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LILIESR 7 0 P62277 P62277 RPS13 40S ribosomal protein S13 0 ;;; 149.4 0.004697 1353730000 1835380 1859820 1300020 1438920 1870570 2030350 1759820 1911190 1960320 FALSE TRUE 1592829.883 1847602.72 1928714.02 1765648.779 1833349.317 2108458.878 1589152.927 1502496.891 1728573.203 0.921470887 1.068859981 1.115783825 1.021448658 1.060614219 1.219768347 0.919343725 0.869212185 1 20.72115027 2.065723626 24.9985536 0.915967562 1.067902946 0.393574813 0.08045536 49.41103549 18793.33666 0.032090184 0.021635195 116.3385445 -2.065723626 0.151935384 LILPHVDIQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LILPHVDIQLK 11 0 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 171.62 0.00082762 0 1220800 1320200 921440 1631700 1335500 1330000 1246200 1576400 1646300 FALSE TRUE 1059468.187 1311527.519 1367051.466 2002202.424 1308926.163 1381165.961 1125343.716 1239299.128 1451676.289 0.729823994 0.903457285 0.941705445 1.379234777 0.901665318 0.951428339 0.775202932 0.853702121 1 20.46928835 0.98854031 20.1773644 1.115970287 0.931859074 0.015712946 0.174423203 23752186.88 730561224.3 125771811.2 0.044241876 9.739581801 -0.98854031 -0.184111213 LIMGIGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LIMGIGHR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;; 143.02 0.00060815 2860100000 3513050 3865510 2352410 2747380 3469990 3854330 3498170 3828900 3758880 FALSE TRUE 3048791.542 3840117.21 3490043.344 3371214.62 3400943.988 4002608.569 3158918.012 3010119.532 3314509.489 0.919831894 1.15857783 1.052959226 1.017108152 1.026077614 1.207602085 0.953057465 0.908164403 1 21.66036395 2.040942234 24.99932472 0.942448669 1.065077285 0.289646092 0.080697184 153.6334348 93807.93861 0.031040621 0.020927564 109.8859668 -2.040942234 0.122628617 LINANMMVLGHEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LINANMMVLGHEPR 14 0 O00487 O00487 PSMD14 26S proteasome non-ATPase regulatory subunit 14 0 136.51 2.66E-05 521750000 67251 64183 50440 69474 69122 76909 64810 99807 69301 FALSE TRUE 58363.60996 63761.37765 74832.95271 85249.13354 67746.60743 79867.739 58524.73618 78464.04975 61108.31473 0.955084594 1.043415744 1.224595262 1.395049658 1.108631579 1.306986445 0.957721325 1.284015933 1 15.89908107 4.398444974 4.058425416 1.188400677 0.971859383 0.252708783 0.134582355 0.261320409 8.042942861 0.032014142 0.099572936 25029.08505 -4.398444974 -0.216541294 LINQVLELQHTLEDLSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LINQVLELQHTLEDLSAR 18 0 A0A0C4DGB0;Q9UIL1-3;Q9UIL1-2;Q9UIL1 A0A0C4DGB0 SCOC Short coiled-coil protein 0 ; 266.7 3.54E-31 1227660000 1105420 1105920 705480 852380 1029290 1230760 1059850 1227660 1106930 FALSE TRUE 959335.9462 1098655.139 1046652.488 1045925.907 1008809.143 1278108.134 957065.9101 965134.4627 976069.9964 0.982855686 1.125590524 1.07231294 1.071568546 1.033541802 1.309443112 0.980529996 0.988796363 1 19.89662509 LIPDSIGKDIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LIPDSIGKDIEK 12 1 P61247;D6RG13;D6RAT0;H0Y9Y4;D6RB09;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 116.84 0.00072819 437830000 924050 736090 382920 329310 642210 510540 1013500 1103300 86848 FALSE TRUE 801934.4513 731254.5763 568101.3928 404084.8687 629431.2775 530180.8042 915210.926 867367.8809 76580.92838 10.47172538 9.548781816 7.418314257 5.276573127 8.219164886 6.923144122 11.95089881 11.32616043 1 16.22469753 4.400171437 4.465985301 7.970366182 10.28228912 0.092858837 3.064003758 0.570195437 20.80054482 0.794819983 2.370615581 25128.78192 -4.400171437 2.311922934 LIPGPLS(ph)PVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 LIPGPLSPVAR 11 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR 194.8 3.70E-07 12486471000 4155064 3907127 2617117 3058701 4102104 4272447 3921568 4378402 3958030 TRUE FALSE 3605961.765 3881460.825 3882763.535 3753225.811 4020480.156 4436810.801 3541254.939 3442114.805 3490116.202 1.033192466 1.112129396 1.112502653 1.075387063 1.151961689 1.271250166 1.014652445 0.986246476 1 21.73484364 2.029714713 24.98651494 0.994633307 1.125298117 0.488630337 0.060940582 162.5515097 136685.6412 0.025433512 0.017147057 107.0815658 -2.029714713 0.13066481 LIQEQHPEEELIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LIQEQHPEEELIK 13 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 94.551 0.005103 296540000 91620 95261 86242 100200 75489 79776 100710 94883 214600 FALSE TRUE 79512.18486 94635.22422 127948.9197 122951.9415 73986.91659 82845.03434 90943.1597 74593.00883 189230.2325 0.420187535 0.500106262 0.676154745 0.649747875 0.39098888 0.437800204 0.480595297 0.394191815 1 17.52978307 1.231594154 24.99988442 1.000000869 0.494259258 0.724042195 0.098226582 143.9021862 516361.4572 0.253698074 0.026091637 17.04488807 -1.231594154 -0.505741612 LIQNLDANHDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 LIQNLDANHDGR 12 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;;;;;;;;;; 263.7 1.72E-21 63422011300 21230148.5 20741068.4 17175289.7 21913141.6 22147724.4 26646532 17304107.4 22922765.3 28750941.9 FALSE TRUE 18424530.59 20604818.96 25481317.25 26888855.32 21707028.02 27671641.33 15625957.73 18020910.33 25352038.3 0.726747505 0.812748021 1.005099351 1.060619071 0.856224172 1.091495721 0.61635903 0.710826882 1 24.59559841 0.950865556 17.56331899 2.036598081 0.857886204 0.074306154 0.155114699 7024640.078 60856273.62 287342867.2 0.041543861 8.930289881 -0.950865556 -1.178711877 LIQNNHYAMEDVATRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LIQNNHYAMEDVATRR 16 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 191.96 3.97E-10 687930000 276450 262100 157029 179654 226080 289260 235570 260540 145419 FALSE TRUE 239916.4321 260378.2478 232968.7496 220447.1865 221581.4503 300388.0194 212724.4577 204825.5485 128227.7315 1.871018299 2.030592328 1.816835929 1.719184953 1.728030651 2.342613535 1.658958286 1.597357655 1 16.96834878 1.211306107 1.535167833 0.596901965 1.896472381 0.686904461 0.190624227 0.710979718 1.423166194 1.456574473 0.054540485 16.26694908 -1.211306107 1.299570416 LIRPEYAWIVQPVSGAVYDRPGAS(ph)PKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LIRPEYAWIVQPVSGAVYDRPGASPKR 27 3 Q12769;G3V198 Q12769 NUP160 Nuclear pore complex protein Nup160 1 LIRPEYAWIVQPVSGAVYDRPGAS(1)PKR;LIRPEYAWIVQPVSGAVYDRPGAS(1)PKR 183.06 8.28E-17 2397500000 2290010 1801650 1178330 1364470 1749910 1583940 2087200 2390840 1041930 TRUE FALSE 1987379.376 1789814.843 1748174.329 1674293.768 1715090.215 1644875.197 1884783.665 1879577.472 918754.2224 2.163124074 1.948088835 1.902766035 1.822352189 1.86675628 1.790332122 2.051455786 2.045789206 1 19.80931945 1.234851314 24.99999428 0.999998659 1.945254926 0.873445697 0.113497151 38.18872561 257345.7607 0.212705014 0.029340185 17.17320339 -1.234851314 0.945256267 LIS(ph)SVEDFTEFV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LISSVEDFTEFV 12 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7 P49815 TSC2 Tuberin 1 LIS(0.5)S(0.5)VEDFTEFV;LIS(0.5)S(0.5)VEDFTEFV;LIS(0.623)S(0.377)VEDFTEFV 139.19 6.41E-05 151045000 185603 178488 114171 124602 198709 186108 162185 201691 184637 TRUE FALSE 161075.0933 177315.5006 169384.4775 152894.7885 194755.0797 193267.6952 146456.3237 158560.9492 162809.4242 0.989347478 1.089098505 1.040384967 0.939102815 1.196215026 1.187079287 0.899556794 0.973905227 1 17.31282469 2.219896265 24.99608072 0.958743972 1.072203924 0.308893129 0.081574213 315.6352908 422708.7677 0.034477159 0.023290141 165.9190549 -2.219896265 0.113459952 LIS(ph)WYDNEFGYSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LISWYDNEFGYSNR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 LIS(1)WYDNEFGYSNR;LIS(1)WYDNEFGYSNR;LIS(1)WYDNEFGYSNR;LIS(1)WYDNEFGYSNR;LIS(1)WYDNEFGYSNR 209.33 7.12E-09 237449800 100427.7 159241 99836.4 76936.3 139817 150665 114201.2 124164 140124 TRUE FALSE 87155.92499 158194.9354 148117.617 94405.86281 137034.9152 156461.18 103125.9852 97612.49485 123558.7003 0.70538072 1.280322106 1.198763151 0.764056781 1.109067309 1.26629027 0.834631514 0.790009077 1 16.91483708 2.186479962 24.99965013 0.855521099 1.060175827 0.151500394 0.197684646 163.8303908 78640.11493 0.078607412 0.05299717 153.6313909 -2.186479962 0.204654729 LISGGHDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LISGGHDNR 9 0 Q15061;C9JEE7 Q15061 WDR43 WD repeat-containing protein 43 0 ; 134.68 0.00024221 264100000 198491 180838 97578 141099 192411 214872 172916 207467 191620 FALSE TRUE 172259.9114 179650.0633 144767.0472 173137.6845 188582.3975 223138.2649 156146.6329 163101.7966 168966.9019 1.01948908 1.063226355 0.856777544 1.024684021 1.116090758 1.320603399 0.924125561 0.965288437 1 17.36638115 5.032805099 13.97098233 1.029784299 0.990070746 0.000366665 0.12441457 17697108.4 236385197 0.031853378 16245306.29 107846.2625 -5.032805099 -0.039713552 LISKPVASDSTYFAWCPDGEHILTATCAPR ddPTM_MDA-MB-175_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" 0 227.57 3.35E-35 388740000 454120 430730 240930 309760 417840 380450 523700 574110 430380 FALSE TRUE 394106.8914 427900.5063 357444.5539 380095.7424 409525.8015 395086.1577 472911.6546 451341.0442 379500.9667 1.038487187 1.127534694 0.941880483 1.001567257 1.079116623 1.041067592 1.246140843 1.189301435 1 18.53374404 2.312393091 11.68647951 1.158504716 1.038006329 0.292227129 0.077483549 0.631683826 97.32579827 0.029002854 0.022454728 205.3019581 -2.312393091 -0.120498387 LISQIVSSITASLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LISQIVSSITASLR 14 0 P68363;P68363-2;F8VVB9;C9JDS9;P68366-2;P68366;Q9BQE3;F5H5D3 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA4A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 ; 122.42 0.00025316 861000000 142780 160370 96662 112105 141290 132830 175655 189933 110174 FALSE TRUE 123911.2612 159316.5189 143408.0665 137560.1537 138478.6054 137940.0561 158620.0051 149317.306 97149.35523 1.275471782 1.639913292 1.476160765 1.415965689 1.425419707 1.419876187 1.632743776 1.536987103 1 16.5679168 1.235020356 24.99999257 0.999999315 1.487485857 0.657338038 0.108218419 61.21231269 432190.2095 0.183467648 0.025637651 17.17988911 -1.235020356 0.487486542 LISS(ph)TESELQQSYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LISSTESELQQSYAK 15 0 O43149 O43149 ZZEF1 Zinc finger ZZ-type and EF-hand domain-containing protein 1 1 LIS(0.001)S(0.306)T(0.306)ES(0.306)ELQQS(0.043)Y(0.038)AK 57.804 0.076721 697960000 563960 447320 728560 351770 281270 275550 377920 404470 284880 TRUE FALSE 489431.2571 444381.5255 1080894.053 431644.755 275673.2773 286150.5868 341269.3766 317977.2381 251201.8109 1.948358793 1.769021982 4.302891165 1.718318643 1.097417556 1.139126289 1.358546641 1.265823829 1 17.93848734 3.488033637 24.72218653 1.21545368 2.654253999 0.50761032 0.674052397 368.3520501 834507.3559 0.185867917 0.257367649 3076.335075 -3.488033637 1.438800319 LISS(ph)VEDFTEFV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LISSVEDFTEFV 12 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7 P49815 TSC2 Tuberin 1 LIS(0.068)S(0.932)VEDFTEFV 183 1.70E-05 25768000 120500 116670 68700 86241 146630 140660 120550 130920 137330 TRUE FALSE 104575.6197 115903.5871 101923.5498 105823.3372 143712.3499 146071.2812 108859.0796 102923.7768 121095.0038 0.863583272 0.957129389 0.841682535 0.873886897 1.186773569 1.206253574 0.898955994 0.849942389 1 16.88577982 LISSDGHEFIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LISSDGHEFIVK 12 0 E5RHG8;Q15369-2;Q15369;R4GMY8 E5RHG8 TCEB1 Transcription elongation factor B polypeptide 1 0 ;; 136.7 0.00010532 1433680000 5194460 4765630 2017730 3858050 4982940 4369000 5314600 6357400 6616600 FALSE TRUE 4507998.95 4734324.263 2993510.977 4734079.219 4883789.243 4537078.257 4799190.91 4997919.483 5834393.086 0.77265945 0.811451027 0.513080098 0.811409027 0.837068941 0.777643568 0.822569004 0.856630572 1 22.47615116 -2 0.437145536 6.187695629 0.725811336 0.458051399 0.088109014 86.33693327 1.145480816 414.6363083 0.074008143 0.01 2 -5.461884293 LISWYDNEFGYS(ph)NR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LISWYDNEFGYSNR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 LISWYDNEFGYS(1)NR;LISWYDNEFGYS(1)NR;LISWYDNEFGYS(1)NR 248.81 5.59E-18 300372000 149471 247096 133598 105238 175724 160745 138180 158101 270676 TRUE FALSE 129718.0286 245472.8101 198206.4397 129133.8964 172227.4362 166928.9642 124779.3249 124292.3315 238676.9916 0.543487781 1.028472868 0.830437984 0.541040406 0.721592119 0.699392778 0.522795784 0.520755397 1 17.86469997 3.761748139 23.68578889 0.646824857 0.82356695 0.095739427 0.181362522 721.2400862 736733.9191 0.046211303 0.079955517 5777.608886 -3.761748139 0.176742094 LISWYDNEFGYSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 42 LISWYDNEFGYSNR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 419.97 1.34E-134 2.77376E+11 22365347 23807480 15481527 17274381 22905586 23058489 22691041 25707280 23204838 FALSE TRUE 19409709.73 23651087.1 22968445.24 21196793.23 22449809.65 23945563.99 20490467.34 20209978.23 20461588.49 0.948592517 1.155877371 1.122515256 1.035930971 1.097168466 1.170269063 1.001411369 0.987703288 1 24.28641481 2.106362831 10.01431382 0.993478947 1.090965344 0.326563924 0.062284518 0.328827016 28.53962593 0.024321102 0.016390943 127.7505655 -2.106362831 0.097486398 LIT(ph)EMYT(ph)VAWFVRDMRLMFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LITEMYTVAWFVRDMRLMFR 20 2 Q9HB58;Q9HB58-6 Q9HB58 SP110 Sp110 nuclear body protein 2 LIT(0.995)EMY(0.197)T(0.807)VAWFVRDMRLMFR;LIT(0.993)EMY(0.204)T(0.803)VAWFVRDMRLMFR 68.88 0.023788 731930000 182940 175072 90565 128584 208992 239010 157421 150334 147127 TRUE FALSE 158764.0155 173921.9405 134362.5369 157780.9625 204833.4681 248204.8694 142154.3356 118186.244 129733.8137 1.223767428 1.340606089 1.035678619 1.216189966 1.578874946 1.91318564 1.09573851 0.910990286 1 16.98519503 2.01350855 24.99985677 0.965405289 1.379382597 0.379417154 0.235557172 244.4110501 452322.2308 0.104354711 0.070316485 103.1593388 -2.01350855 0.413977308 LITIEINPDCAAITQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LITIEINPDCAAITQR 16 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 149.26 1.98E-06 33534000 45855 50479 24138 26472 39926 41147 40677 43068 49628 FALSE TRUE 39795.14557 50147.40013 35811.21754 32482.8722 39131.55071 42729.95172 36732.1508 33858.24336 43761.03438 0.90937397 1.145937267 0.818335719 0.742278437 0.894209912 0.976438339 0.839380315 0.773707565 1 15.41735922 4.220708369 24.9915055 0.854975585 1.027655671 0.324578737 0.097864189 225.6954004 315953.7691 0.024568185 0.051313787 16622.96034 -4.220708369 0.172680086 LITSEEERS(ph)PAK ddPTM_MDA-MB-175_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 139 3.90E-05 586860000 1412430 1422690 1011520 1075680 1326210 1402260 1331770 1506140 1685590 TRUE FALSE 1225773.797 1413344.256 1500694.455 1319929.585 1299821.016 1456205.85 1202615.15 1184063.682 1486321.47 0.824703014 0.950900787 1.009670172 0.888051213 0.874522128 0.979738151 0.809121832 0.796640367 1 20.50331475 2.231331033 24.99936643 0.85112071 0.922995487 0.082060459 0.075748259 303.4217614 1049198.891 0.030214159 0.020843479 170.3456443 -2.231331033 0.071874778 LITSEEERS(ph)PAKR ddPTM_MDA-MB-175_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 166.62 1.74E-05 1012510000 570422 513939 292137 387490 531931 405899 535707 603453 525698 TRUE FALSE 495039.2874 510562.9009 433415.4303 475475.5269 521346.6138 421514.1972 483754.2176 474409.272 463550.5813 1.067929385 1.101417885 0.934990587 1.025725231 1.124681178 0.909316511 1.043584534 1.02342504 1 18.82236724 4.283383054 24.99995951 1.013172335 1.084673811 0.220053052 0.058929827 203.4990365 113499.5233 0.013959087 0.036931974 19203.61783 -4.283383054 0.071501475 LIVAYVDDLDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LIVAYVDDLDRR 12 1 O14776;O14776-2 O14776 TCERG1 Transcription elongation regulator 1 0 ;; 197.07 3.19E-07 423330000 679320 759480 355220 330860 631420 664670 747570 706070 302068 FALSE TRUE 589546.1408 754490.9259 527005.5801 405986.8199 618855.9774 690240.285 675070.7765 555082.4251 266357.8652 2.213361113 2.832621163 1.978562112 1.524215625 2.323400426 2.591401927 2.53445032 2.083972346 1 18.02300636 4.219551406 24.95134897 2.055665379 2.52299126 0.154605876 0.492531669 431.4726573 566349.2966 0.129623156 0.270530775 16578.73564 -4.219551406 0.46732588 LIVENLSS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LIVENLSSR 9 0 Q08170;A0A0D9SEM4;Q13243;Q13243-3;B4DJK0;B4DUA4;Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q08170;Q13243;Q13247 SRSF4;SRSF5;SRSF6 Serine/arginine-rich splicing factor 4;Serine/arginine-rich splicing factor 5;Serine/arginine-rich splicing factor 6 1 LIVENLS(0.074)S(0.926)R;LIVENLS(0.007)S(0.993)R;LIVENLS(0.008)S(0.992)R;LIVENLS(0.242)S(0.758)R 105.36 0.0032631 424890000 1183820 1173830 948710 882160 1190420 1149010 1266490 1146620 1751710 TRUE FALSE 1027375.188 1166119.033 1407509.329 1082467.911 1166732.971 1193213.158 1143665.995 901424.236 1544624.839 0.665129267 0.75495292 0.911230542 0.700796649 0.755350388 0.77249383 0.74041668 0.583587816 1 20.55882505 LIVENLSSR ddPTM_MDA-MB-175_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 0 155.84 0.0001683 268440000 284390 253040 178000 175310 258230 272590 252530 246290 254950 FALSE TRUE 246807.1409 251377.7636 264081.3954 215116.8149 253091.7282 283076.7137 228039.6795 193622.8001 224810.1014 1.097847202 1.11817824 1.174686518 0.956882336 1.125802295 1.259181469 1.014365805 0.861272687 1 17.77834734 2.002843883 24.99630313 0.925854831 1.118617967 0.495058027 0.081111574 63.05233352 554194.8125 0.032998728 0.022107557 100.6569769 -2.002843883 0.192763135 LIVLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LIVLDR 6 0 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ; 118.06 0.05163 200740000 241500 214360 138700 155092 211659 227100 210247 223450 235710 FALSE TRUE 209585.1631 212951.855 205775.7839 190308.009 207447.4 235836.684 189857.2783 175666.9564 207844.6323 1.008374192 1.02457231 0.990046178 0.915626287 0.998088802 1.13467777 0.913457693 0.845183994 1 17.66514596 2.036451732 24.99990672 0.901869617 1.007942789 0.297711461 0.065082034 176.2979587 120910.7321 0.026732419 0.018022949 108.7556258 -2.036451732 0.106073172 LIYFQLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LIYFQLHR 8 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 182.13 0.0002302 1356640000 1184590 1534450 970060 1269630 1405590 1483480 1417370 1488340 2537500 FALSE TRUE 1028043.43 1524370.097 1439184.261 1557918.897 1377621.509 1540550.436 1279913.676 1170070.073 2237519.641 0.459456718 0.681276745 0.643205197 0.69627049 0.615691359 0.688508117 0.572023437 0.522931755 1 21.09346892 1.23036201 24.99999787 1.000000713 0.612671127 0.723883251 0.075695572 169.8634234 517922.662 0.204972088 0.018652553 16.99659828 -1.23036201 -0.387329585 LKAEATEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 2164650000 4011930 3651900 2341470 2828820 3322050 3221740 4038160 4436740 3736040 FALSE TRUE 3481743.286 3627910.428 3473812.724 3471146.817 3255947.704 3345682.423 3646539.865 3487977.678 3294369.607 1.056876945 1.101245719 1.054469637 1.053660406 0.9883371 1.015575913 1.106900652 1.058769383 1 21.65157099 3.981214172 3.426532823 1.041164578 1.079213435 0.185840062 0.034928659 0.444614852 10.93314222 0.009997555 0.020908773 9576.662282 -3.981214172 0.038048857 HQHMHDRDDLYAEQMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 HQHMHDRDDLYAEQMER 17 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ;;;;;;; 191.07 1.58E-10 1776075000 2154995 1583520 850228 1127548 1422044 1355263 1165467 1305286 902525 FALSE TRUE 1870206.951 1573117.753 1261401.105 1383575.007 1393748.107 1407400.845 1052440.19 1026160.747 795829.5227 2.350009515 1.976701929 1.585014213 1.738531893 1.751314907 1.768470262 1.322444267 1.289422819 1 19.60209989 2.286136521 0.153873466 1.84E-27 2.934872819 0.80574524 0.16701804 8.433301779 0.857896625 9.953287841 6.140988033 193.2575728 -2.286136521 2.934872819 up LKAEMDEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKAEMDEHR 9 1 Q7L7X3-3;Q7L7X3;Q7L7X3-2;F5H5C7;Q9H2K8;G3V1Q8 Q7L7X3-3;Q9H2K8 TAOK1;TAOK3 Serine/threonine-protein kinase TAO1;Serine/threonine-protein kinase TAO3 0 104.22 0.0019799 81836000 231710 210310 155620 195480 212290 236870 235550 280130 231520 FALSE TRUE 201088.9364 208928.4598 230878.3525 239866.7217 208065.8443 245982.5422 212706.3973 220226.3795 204149.9693 0.985005959 1.023406765 1.130925237 1.174953503 1.019181365 1.204910992 1.041912462 1.078748041 1 17.63926983 4.407209873 5.26625867 1.093001411 0.993523927 0.254244199 0.064737317 0.240126704 12.05961856 0.015661176 0.044425216 25539.35195 -4.407209873 -0.099477484 LKAEQEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LKAEQEAR 8 1 Q8N5G2;Q8N5G2-2;Q8N5G2-3 Q8N5G2 TMEM57 Macoilin 0 ;; 116.05 0.0021395 449220000 862180 817420 624340 840190 747990 669270 809760 982720 1374230 FALSE TRUE 748240.7285 812050.3142 926272.9123 1030967.981 733106.4624 695017.25 731229.5998 772572.9755 1211770.095 0.617477467 0.670135629 0.764396577 0.850795036 0.604988079 0.573555374 0.603439219 0.637557387 1 20.20868458 1.2356642 24.99990482 1.000000451 0.665387483 0.611785786 0.083792083 61.48248328 530574.7727 0.152333659 0.022418598 17.20537728 -1.2356642 -0.334612968 LKATVT(ph)PS(ph)PVKGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LKATVTPSPVKGK 13 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 LKAT(0.064)VT(0.965)PS(0.97)PVKGK;LKAT(0.024)VT(0.979)PS(0.997)PVKGK;LKAT(0.217)VT(0.786)PS(0.997)PVKGK 94.01 0.0059058 8160300000 15505500 10936600 8858500 7610100 9956100 6171400 16295100 18665500 4140300 TRUE FALSE 13456408.89 10864756.75 13142500.23 9338089.518 9757993.089 6408817.751 14714803.71 14674028.08 3650838.451 3.685840683 2.97596207 3.599858062 2.557793133 2.672808786 1.755437234 4.030527209 4.019358369 1 21.7997964 3.743956522 24.49726858 2.859591959 3.376094432 0.103465022 0.932468463 1140.614919 5178336.822 0.260511143 0.434656872 5545.701917 -3.743956522 0.516502473 LKATVT(ph)PSPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKATVTPSPVK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 LKAT(0.001)VT(0.782)PS(0.217)PVK 106.6 0.0037335 15729000000 3265200 2774900 2083400 2536800 2642300 1843000 3540900 4114400 1904200 TRUE FALSE 2833695.547 2756671.499 3090939.209 3112819.213 2589723.4 1913901.403 3197504.063 3234567.578 1679087.645 1.687640044 1.641767484 1.840844471 1.85387536 1.542339619 1.13984604 1.904310399 1.926384002 1 20.67924611 3.223392335 24.32764478 1.567545544 1.753928151 0.134549556 0.294837777 484.1232979 776458.3552 0.093681118 0.106666377 1672.600935 -3.223392335 0.186382607 LKATVTPS(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKATVTPSPVK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 LKATVT(0.289)PS(0.71)PVK;LKATVT(0.194)PS(0.806)PVK 145.86 2.18E-05 18814410000 6203300 5537540 4223320 4967250 5212580 3872620 6948500 8241700 3780800 TRUE FALSE 5383518.188 5501163.535 6265731.678 6095140.032 5108859.856 4021602.197 6274635.539 6479276.592 3333838.131 1.61481091 1.650099171 1.879434883 1.828265138 1.532425887 1.206297978 1.882105637 1.943488657 1 21.66875263 3.231026469 24.78046712 1.579056618 1.746240315 0.113099825 0.289072297 473.8673158 1558587.558 0.091348395 0.105592047 1702.262255 -3.231026469 0.167183697 LKATVTPS(ph)PVKGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKATVTPSPVKGK 13 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 LKAT(0.006)VT(0.157)PS(0.837)PVKGK;LKAT(0.003)VT(0.081)PS(0.917)PVKGK 141.13 2.07E-05 33568400000 11098700 8135300 4356500 4966600 6503300 4304200 11142300 12261600 1041140 TRUE FALSE 9631978.674 8081858.679 6463317.972 6094342.44 6373897.053 4469785.359 10061721.46 9639552.26 918057.6153 10.49169302 8.803215119 7.040209529 6.638300623 6.942807235 4.868741662 10.95979304 10.4999426 1 19.80822517 4.526912903 2.718442714 7.323433595 10.53146762 0.145236246 2.791506822 0.732785558 9.347674911 0.732135865 4.198517122 33644.40892 -4.526912903 3.208034025 LKCGSGPVHISGQHLVAVEEDAES(ph)EDEEEEDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKCGSGPVHISGQHLVAVEEDAESEDEEEEDVK 33 1 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 1 LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK 174.55 4.50E-15 630150000 728144 470355 120588 200681 614684 432462 817170 973290 161891 TRUE FALSE 631917.9255 467265.207 178904.7601 246248.6883 602452.991 449099.093 737920.9792 765159.5077 142752.4304 4.426670171 3.273255704 1.253251939 1.725005225 4.220264337 3.145999628 5.169235838 5.360045398 1 17.12315578 3.219426298 24.79440594 4.049330508 2.611503964 0.10795065 1.471177842 387.4182412 502018.191 0.457186899 0.519221334 1657.396044 -3.219426298 -1.437826544 LKDALVR ddPTM_MDA-MB-175_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 63.486 0.072179 234680000 390910 382730 223040 304150 412970 378820 445950 477810 245120 FALSE TRUE 339250.2531 380215.8214 330902.89 373211.9061 404752.705 393393.4505 402701.8376 375634.0498 216142.1928 1.569569775 1.759100416 1.53095 1.726696214 1.872622368 1.820067824 1.863133858 1.737902465 1 17.7216212 1.23879739 10.44298709 0.997621563 1.742380286 0.809818073 0.111890747 0.029686024 86.53019934 0.159311475 0.028518631 17.32995319 -1.23879739 0.744758723 LKDDEVAQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LKDDEVAQLK 10 1 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 ;;;; 196.11 3.09E-07 5169040000 10693820 8950680 9743100 10632240 8307540 6063100 13036890 14744310 23535180 FALSE TRUE 9280604.592 8891882.394 14454895.75 13046452.6 8142236.207 6296351.38 11772574.41 11591354.05 20752877.83 0.447196031 0.428465029 0.69652488 0.628657514 0.392342511 0.303396542 0.567274308 0.558542008 1 24.30680808 1.117032763 2.2565586 1.278583862 0.494419647 0.652491492 0.114738563 0.670063467 2.619845624 1.210320565 0.032618411 13.09280691 -1.117032763 -0.784164214 LKDDEVAQLKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKDDEVAQLKK 11 2 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 162.22 1.43E-05 7095000000 13034000 9935100 8725500 9010800 8020500 5473500 15473000 18146000 8161600 FALSE TRUE 11311523.88 9869835.674 12945180.99 11056839.86 7860907.742 5684069.087 13972430.84 14265619.11 7196744.946 1.571755559 1.371430521 1.798755004 1.53636678 1.092286555 0.789811106 1.941493126 1.982232137 1 22.7789131 1.188188005 23.65609354 0.999981571 1.52270712 0.159932721 0.366761024 20234.03344 9500666.975 96.39366368 0.098643689 15.42367995 -1.188188005 0.522725549 LKDELASTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKDELASTK 9 1 P51572;P51572-2 P51572 BCAP31 B-cell receptor-associated protein 31 0 96.015 0.0069808 703760000 885750 708530 489660 759420 906440 659730 780640 1427200 1105600 FALSE TRUE 768695.8933 703875.6198 726461.2138 931857.918 888403.6174 685110.24 704933.653 1122004.386 974897.2275 0.788489157 0.721999817 0.745166971 0.955852465 0.911279253 0.702751245 0.723085094 1.150895043 1 19.89489061 1.739321188 10.28762634 1.071034746 0.795520832 0.631138268 0.089780558 0.056502349 29.92620024 0.052099741 0.024312917 54.86826006 -1.739321188 -0.275513914 LKDFSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKDFSFR 7 1 A0A5F9ZH82;E9PHY0;B7Z7D2;E9PQY3;A0A5F9ZHR7;P11117 A0A5F9ZH82 ACP2 Lysosomal acid phosphatase 0 80.438 0.02728 397920000 370250 402120 292690 359170 404730 436440 513720 507050 506460 FALSE TRUE 321320.5244 399478.4472 434235.863 440725.0381 396676.6648 453230.1292 463899.5135 398621.3034 446586.8758 0.719502838 0.894514525 0.972343538 0.986874138 0.888240758 1.014875613 1.038766562 0.892595204 1 18.76858133 4.710518463 2.218555117 0.966617901 0.664206477 0.730585353 0.048170579 0.307187147 1.83371585 0.012391875 0.178626139 51347.40065 -4.710518463 -0.302411425 LKDIALGMQTEIEEQDDILDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKDIALGMQTEIEEQDDILDR 21 1 O95721;C9JAF7 O95721 SNAP29 Synaptosomal-associated protein 29;Synaptosomal-associated protein 0 ; 176.54 2.51E-13 62369000 58499 45928 34791 40836 48192 48763 48667 59134 49594 FALSE TRUE 50768.20893 45626.29594 51616.04397 50108.43794 47233.07349 50638.94416 43947.28183 46488.65428 43731.05382 1.160918947 1.043338588 1.180306429 1.145831933 1.080080843 1.157963043 1.004944496 1.063058175 1 15.41637049 2.23586663 24.99985965 1.030343799 1.125221691 0.561398773 0.043695986 53.35526361 495119.0185 0.016322268 0.011563611 172.1339876 -2.23586663 0.094877892 LKDIVSLVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKDIVSLVPR 10 1 O95573;F5GWH2 O95573 ACSL3 Long-chain-fatty-acid--CoA ligase 3 0 118.48 0.0027702 0 301730 282470 185620 283150 364340 341680 234820 452940 313610 FALSE TRUE 261855.616 280614.436 275386.4529 347443.5352 357090.3468 354824.6507 212047.1925 356082.3058 276535.3831 0.946915411 1.014750564 0.995845269 1.2564162 1.291300747 1.283107596 0.766799497 1.287655496 1 18.07710456 3.8323786 8.551989128 1.149877179 0.987518971 0.179066462 0.163205552 0.605075636 50.49077433 0.042662495 0.074141833 6797.959925 -3.8323786 -0.162358208 LKDLDLDAFAEELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LKDLDLDAFAEELER 15 1 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ;; 193.69 7.54E-08 198875000 662107 540796 347338 436120 491119 441786 603266 715659 486426 FALSE TRUE 574607.8824 537243.4755 515311.8186 535147.7117 481346.6928 458781.7933 544761.3562 562620.8921 428921.2724 1.33965816 1.252545654 1.201413527 1.247659527 1.122226207 1.06961772 1.270073067 1.311711329 1 18.71035334 4.888693711 1.079063187 1.184405387 1.456371064 0.25494785 0.093211125 3.900685942 3.038306024 0.030201994 1.306982628 77391.57958 -4.888693711 0.271965677 LKDLFDYS(ph)PPLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LKDLFDYSPPLHK 13 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 LKDLFDYS(1)PPLHK;LKDLFDYS(1)PPLHK;LKDLFDY(0.004)S(0.996)PPLHK 129.32 9.36E-05 35965075000 5696039 3936422 3182539 3551717 4086682 3297475 5321445 6269415 5196303 TRUE FALSE 4943293.014 3910563.385 4721625.505 4358188.629 4005365.024 3424330.997 4805372.083 4928749.391 4582001.979 1.078850039 0.853461741 1.030472166 0.951153808 0.874151745 0.747343849 1.048749456 1.075675963 1 22.12754665 2.086821168 24.99968935 1.049044945 0.921316947 0.265223826 0.092994762 27.00527965 7770.62422 0.037537977 0.025308094 122.1296656 -2.086821168 -0.127727998 LKDLFDYSPPLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKDLFDYSPPLHK 13 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ; 99.481 0.001707 237940000 1048360 788950 545690 640700 797310 765800 876310 983780 851490 FALSE TRUE 909816.5698 783767.3355 809587.5092 786180.7275 781445.0909 795260.8215 791325.5911 773406.3028 750827.8222 1.211751274 1.043870928 1.078259869 1.047085236 1.040778016 1.05917868 1.053937491 1.030071449 1 19.51812259 LKDLFGK ddPTM_MDA-MB-175_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 ; 91.069 0.015208 1367540000 4995400 4058300 2746800 3613200 4012800 3328300 5251600 6344100 4968900 FALSE TRUE 4335245.233 4031640.76 4075161.667 4433632.284 3932953.131 3456341.855 4742300.64 4987463.585 4381482.303 0.989447163 0.920154523 0.930087442 1.01190236 0.897630724 0.788852177 1.082350746 1.138305085 1 22.0629876 2.129034149 11.32150723 1.088319933 0.92614346 0.518959733 0.067806562 0.280069363 27.28458429 0.027802155 0.018742141 134.5966184 -2.129034149 -0.162176473 LKDLGHPVEEEDELES(ph)GDQEDEDDESEDPGKDLDHI ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 LKDLGHPVEEEDELESGDQEDEDDESEDPGKDLDHI 36 2 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 1 LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI 375.28 1.30E-161 8320550000 2641643 1458453 1432779 1244308 1300412 1176473 2015887 2279244 1980918 TRUE FALSE 2292543.184 1448872.326 2125675.717 1526847.149 1274536.345 1221732.678 1820386.589 1791845.408 1746736.131 1.312472528 0.829474069 1.216941517 0.874114368 0.729667362 0.699437457 1.042164616 1.025824895 1 20.73623025 6.415268309 1.921645356 0.932132111 199.9999985 0.360162535 0.157154458 1004.280816 8.654137253 0.043753239 877466.669 2601766.45 -6.415268309 199.0678664 LKDLPFIVSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKDLPFIVSHR 11 1 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ; 141.38 2.29E-05 524770000 1756730 1674740 1031010 1287360 1724480 1661180 1747820 2055700 1556890 FALSE TRUE 1524573.68 1663738.523 1529609.885 1579674.764 1690166.222 1725086.67 1578316.685 1616104.552 1372836.238 1.110528436 1.211898752 1.114196903 1.150665113 1.23114919 1.256585907 1.149675862 1.177201263 1 20.38872811 1.238498593 24.51817363 0.999999811 1.176891131 0.573493845 0.04747382 0.868384122 339616.5052 0.065090686 0.011607256 17.3180342 -1.238498593 0.17689132 LKDLSR ddPTM_MDA-MB-175_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 ;;;;; 127.84 0.015398 29576980000 23071640 23261440 16033230 17124610 22371120 23815080 27681340 29304370 23525060 FALSE TRUE 20022664.32 23108634.07 23786953.66 21013014.43 21925978.48 24731261.54 24996807.91 23037858.52 20743954.21 0.96522891 1.113993689 1.146693317 1.012970537 1.056981628 1.192215394 1.205016539 1.110581825 1 24.30618759 2.776418803 24.47312717 1.131713816 1.064514525 0.170302039 0.073485846 822.0832798 531427.6812 0.024213993 0.024213234 597.6113033 -2.776418803 -0.067199291 LKDPANFQYPAESVLAYK ddPTM_MDA-MB-175_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 ; 220.04 6.38E-19 14939100000 7666900 6870800 5012500 6054500 6822200 5810800 8642200 9792500 8860100 FALSE TRUE 6653699.74 6825665.262 7436561.766 7429266.762 6686451.567 6034345.236 7804080.774 7698450.08 7812669.071 0.851655136 0.873666246 0.951859307 0.950925566 0.855847279 0.772379475 0.998900722 0.985380286 1 22.89738408 2.18037965 24.99999875 0.992979185 0.881876692 0.543884211 0.051050497 67.21045999 28879.22264 0.022259551 0.015007393 151.4884948 -2.18037965 -0.111102493 LKDSEAELQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LKDSEAELQR 10 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 ;;;; 152.69 1.60E-05 5096030000 8044830 7058240 4467440 5506730 6736260 5713690 7550010 8846080 6667480 FALSE TRUE 6981685.332 7011873.957 6627908.927 6757117.212 6602221.605 5933499.352 6817811.192 6954414.632 5879258.11 1.187511282 1.192646049 1.127337634 1.149314605 1.122968491 1.009225865 1.159638013 1.182872822 1 22.48720269 4.068744129 1.185213844 1.108704584 1.200129437 0.260973749 0.059184233 1.051516335 2.475601406 0.020145526 0.090156778 11715.04952 -4.068744129 0.091424853 LKDSGSVQR ddPTM_MDA-MB-175_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 56.916 0.071384 97125000 331320 363430 168120 253010 336260 470470 270460 317850 355600 FALSE TRUE 287535.2225 361042.6044 249423.3943 310459.7875 329569.0839 488569.2853 244230.8308 249880.251 313561.3731 0.916998225 1.151425639 0.795453189 0.990108521 1.051051284 1.558129691 0.77889323 0.796910182 1 18.25838832 LKDVLLQVDDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LKDVLLQVDDER 12 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;; 160.27 6.08E-05 3247038000 7588740 7391180 5185220 6597180 7418170 6653780 8215250 9716740 10917020 FALSE TRUE 6585868.782 7342626.852 7692809.736 8095170.551 7270562.93 6909755.222 7418536.319 7638890.767 9626422.332 0.684145008 0.762757606 0.799134868 0.840932412 0.755271552 0.717790575 0.770643139 0.793533724 1 23.19856829 1.20780272 3.044674888 1.055405733 0.764759058 0.757312876 0.042029661 0.227790806 2.520761563 0.169208864 0.011335674 16.13625396 -1.20780272 -0.290646675 LKDVLLQVDDERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LKDVLLQVDDERR 13 2 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 206.2 3.59E-08 5633354000 6846320 6376279 3979248 4726451 5957188 5797170 7275050 8217260 3977048 FALSE TRUE 5941561.466 6334392.803 5903625.643 5799663.939 5838651.614 6020190.881 6569516.771 6460062.896 3506885.916 1.694255704 1.806272846 1.68343818 1.653793159 1.664910623 1.716677139 1.873319215 1.842108084 1 21.74175907 1.234110455 24.9999705 0.999998889 1.746954952 0.904413842 0.07577709 43.60785919 244947.1022 0.163142707 0.021140951 17.14393276 -1.234110455 0.746956063 LKDYAFIHFDER ddPTM_MDA-MB-175_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 ;; 152.99 4.21E-05 3712972000 8909640 7144690 3659060 5059000 6379760 5986150 7253490 8033090 3956250 FALSE TRUE 7732208.5 7097756.061 5428593.655 6207723.272 6252815.258 6216441.064 6550047.656 6315276.217 3488546.632 2.216455537 2.034588271 1.556118988 1.779458304 1.792384026 1.781957279 1.877586384 1.810288605 1 21.73419469 1.237546317 5.474040574 0.957480508 1.8476624 0.708103665 0.172847831 0.088837906 8.177310144 0.298596975 0.044205895 17.2801026 -1.237546317 0.890181892 LKDYAFVHFEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LKDYAFVHFEDR 12 1 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;; 171.21 2.35E-05 2378146000 4441089 3871470 2529787 3084339 3736432 3279925 4075805 4783498 3867010 FALSE TRUE 3854187.836 3846038.059 3753200.455 3784685.311 3662084.313 3406105.837 3680534.058 3760584.178 3409856.483 1.130307934 1.127917869 1.10069162 1.109925104 1.073970219 0.998900058 1.079380929 1.102857025 1 21.70127959 3.195549206 3.47988539 1.055665347 1.117895335 0.505159012 0.032899006 0.233282192 5.818159664 0.010761521 0.012949072 1568.733626 -3.195549206 0.062229988 LKDYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKDYLR 6 1 I3L4J1;Q9UN37 I3L4J1 VPS4A Vacuolar protein sorting-associated protein 4A 0 ; 79.116 0.062014 898750000 1366880 1453090 978670 1052880 1472880 1591260 1411090 1447980 1500080 FALSE TRUE 1186243.345 1443544.556 1451958.085 1291952.496 1443572.57 1652476.802 1274242.709 1138340.745 1322742.251 0.896806119 1.091327169 1.097687841 0.976722786 1.091348347 1.24928103 0.963334095 0.860591505 1 20.33510054 2.014793644 24.99674871 0.917825395 1.069967561 0.279783919 0.095767637 249.0230907 420771.5361 0.038528726 0.025964986 103.4650434 -2.014793644 0.152142166 LKEAETR ddPTM_MDA-MB-175_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 73.248 0.04506 274680000 492330 442100 278320 351460 424420 413060 473390 598400 453900 FALSE TRUE 427267.3431 439195.816 412916.4829 431264.3647 415974.8724 428950.6855 427480.7107 470436.8168 400240.4591 1.067526617 1.097329883 1.031671021 1.077513167 1.039312401 1.071732444 1.068059715 1.175385462 1 18.61050749 1.959976804 24.99611698 1.106670966 1.064203095 0.005844683 0.046092345 950.9824348 593924.7393 0.01983107 0.011451265 91.19621287 -1.959976804 -0.042467872 LKEDILENEDEQNS(ph)PPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKEDILENEDEQNSPPK 17 1 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 LKEDILENEDEQNS(1)PPK 136.64 5.84E-06 205120000 368240 246870 216470 227960 252660 179560 329200 385780 377420 TRUE FALSE 319576.151 245248.2947 321155.616 279721.8022 247632.5603 186467.7894 297274.2347 303283.9491 332801.8376 0.960259575 0.736919894 0.965005537 0.840505582 0.744084114 0.560296754 0.893246975 0.911304912 1 18.34430387 1.727802281 2.683980353 0.972390139 0.802639386 0.220006764 0.11826003 0.375136376 5.666903024 0.099669034 0.033244387 53.43210463 -1.727802281 -0.169750753 LKEDILENEDEQNS(ph)PPKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 212.39 1.03E-16 846510000 1095150 620680 702800 627700 618520 427780 1019620 1145760 1024140 TRUE FALSE 950423.1527 616602.7122 1042676.431 770228.8788 606212.6621 444236.9734 920737.4093 900748.1403 903067.3359 1.052438855 0.682787083 1.154594336 0.852903043 0.671281795 0.491920099 1.019566729 0.997431869 1 19.78447404 LKEEEEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LKEEEEDK 8 1 P27797 P27797 CALR Calreticulin 0 ;; 123.75 0.0012169 1067200000 888220 663150 914440 910400 501890 539690 865750 876750 1793440 FALSE TRUE 770839.4765 658793.724 1356666.243 1117120.235 491903.3709 560452.2235 781789.6983 689263.8354 1581421.566 0.487434529 0.416583243 0.857877666 0.706402555 0.311051387 0.354397736 0.494358819 0.435850788 1 20.59279057 1.233460757 24.87268592 1.000000816 0.507296773 0.474457703 0.162732185 147.4131319 718864.3259 0.34507341 0.042323864 17.11830489 -1.233460757 -0.492704043 LKEEEEDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKEEEEDKK 9 2 P27797 P27797 CALR Calreticulin 0 ; 112.15 0.0011303 938540000 1383900 881290 1279420 881160 566370 521630 1307110 1243570 993500 FALSE TRUE 1201014.109 875500.748 1898151.791 1081240.846 555100.3451 541697.4436 1180346.673 977642.233 876049.5618 1.370943108 0.999373536 2.166717357 1.234223374 0.633640343 0.618341093 1.34735148 1.115966808 1 19.74065297 3.477595863 24.99967193 0.974683966 1.500951359 0.352837567 0.351899707 20.42669849 1076002.847 0.103013374 0.134565798 3003.280273 -3.477595863 0.526267393 LKEEEEDKKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKEEEEDKKR 10 3 P27797 P27797 CALR Calreticulin 0 ; 215.04 3.67E-09 1928220000 2970100 1770330 2553700 2065630 1547380 1300870 2906900 2817400 1774890 FALSE TRUE 2577593.76 1758700.586 3788677.862 2534662.863 1516590.165 1350915.311 2624989.285 2214920.935 1565064.526 1.646956861 1.12372401 2.420780612 1.619526109 0.969027245 0.863169082 1.677240294 1.415226592 1 20.57779071 3.393233246 7.444202714 1.236715619 1.726734987 0.305259682 0.386630381 0.32123915 24.2702857 0.114159961 0.147611181 2473.051987 -3.393233246 0.490019368 LKEEISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKEEISK 7 1 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 64.654 0.066314 649930000 469470 404650 301490 588980 405130 353950 446440 579030 731680 FALSE TRUE 407428.35 401991.8275 447291.5724 722716.911 397068.7056 367566.6855 403144.3175 455208.9405 645181.6239 0.63149404 0.623067695 0.693280087 1.120175907 0.615437097 0.569710407 0.624853999 0.705551621 1 19.29934582 0.334207313 0.023317833 1.555908676 4.88E-06 0.048291381 0.177538568 15591.7367 67.56548284 2597.921037 1951.70166 2.158774669 -0.334207313 -1.555903798 LKEELEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LKEELEEAR 9 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;; 155.11 6.76E-05 1203940000 3902280 3238740 2329160 2722490 3058820 2831590 3827570 4463700 3976160 FALSE TRUE 3386583.811 3217464.504 3455549.567 3340672.965 2997955.466 2940523.1 3456372.851 3509172.492 3506102.894 0.965911131 0.917675436 0.985581334 0.952816579 0.855067737 0.838687052 0.985816148 1.000875501 1 21.74143691 2.028782987 24.99061099 0.998353998 0.920119225 0.390941952 0.045128505 218.5312615 189737.2274 0.019971525 0.013464563 106.8520817 -2.028782987 -0.078234773 LKEELIDAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKEELIDAIR 10 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 ; 137.16 8.99E-05 584220000 2504100 2148800 1465160 1851250 1922470 1796060 2243600 2605000 2637200 FALSE TRUE 2173176.84 2134684.391 2173716.277 2271604.607 1884216.608 1865155.59 2026016.017 2047941.022 2325433.22 0.934525585 0.917972777 0.934757557 0.976852221 0.810264768 0.802068008 0.871242399 0.880670752 1 21.14906808 3.250070762 24.99960167 0.870167307 0.938932477 0.274874638 0.054881607 313.8989272 681772.7338 0.01652922 0.02114951 1778.56918 -3.250070762 0.06876517 LKEELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKEELK 6 1 Q86YL5;Q86YL5-2 Q86YL5 TDRP Testis development-related protein 0 66.682 0.091899 276700000 466140 472910 349820 342590 381450 287700 486190 517320 482340 FALSE TRUE 404538.418 469803.4231 518994.1221 420380.2957 373859.8913 298768.0052 439039.3686 406695.1438 425318.3147 0.951142718 1.104592506 1.220248704 0.988389827 0.879011974 0.702457418 1.03226067 0.956213569 1 18.69818345 3.494006214 10.97299231 0.918993031 1.095148399 0.359337915 0.108392462 0.647721253 414.6244194 0.031391668 0.044453336 3118.934209 -3.494006214 0.176155368 LKEEYQSLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKEEYQSLIR 10 1 Q9Y3C8 Q9Y3C8 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1 0 ; 140.31 3.60E-05 1194320000 2994800 2510900 2067290 2090250 2372200 2036140 2856000 2960100 2781900 FALSE TRUE 2599029.592 2494405.733 3067038.359 2564873.21 2324997.861 2114471.623 2579025.56 2327105.651 2453026.951 1.059519379 1.016868458 1.250307648 1.045595202 0.947807712 0.861984669 1.051364543 0.948666972 1 21.22613165 3.422213255 5.13880404 0.963300156 1.107088526 0.445621395 0.075246833 0.178886194 9.958826055 0.021595278 0.028432503 2643.706599 -3.422213255 0.14378837 LKEFLEDYDDDRDDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKEFLEDYDDDRDDPK 16 2 P49756 P49756 RBM25 RNA-binding protein 25 0 178.66 1.55E-09 275630000 665150 482350 417650 433920 404930 269770 593500 710170 552670 FALSE TRUE 577248.7422 479181.4111 619626.937 532448.1681 396872.6852 280148.2265 535942.4613 558305.672 487333.9822 1.184503366 0.98327108 1.27146261 1.092573446 0.814375151 0.574858796 1.099743668 1.145632549 1 18.8945513 3.437332733 12.34437762 0.949907217 1.138745403 0.260336574 0.171975142 1.637870328 505.1093356 0.055293584 0.071420722 2737.365143 -3.437332733 0.188838186 LKEINFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKEINFR 7 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 109.21 0.0064555 377550000 251580 237280 135560 178110 229550 227590 235030 269060 200210 FALSE TRUE 218333.0656 235721.2921 201117.2694 218552.5977 224982.4041 236345.5346 212236.8268 211523.6128 176541.4019 1.236724435 1.335218196 1.139207389 1.237967952 1.274388907 1.338754151 1.202192939 1.198153014 1 17.42964703 0.997387641 1.545367969 0.741813755 1.255852902 0.650484188 0.058001343 1.325630054 1.732604773 1.259811875 0.016339236 9.940028753 -0.997387641 0.514039147 LKELGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKELGR 6 1 Q9UK61-3;Q9UK61;Q9UK61-2;A0A087X0F1;Q9UK61-4;Q96NU7 Q9UK61-3 FAM208A;AMDHD1 Protein FAM208A;Probable imidazolonepropionase 0 76.134 0.06918 154060000 254530 257270 177760 280900 307980 306260 234900 295240 352300 FALSE TRUE 220893.2156 255579.9764 263725.3306 344682.6383 301851.8006 318042.0204 212119.4342 232105.2236 310651.4953 0.711064389 0.822722505 0.848942737 1.109547655 0.971673419 1.023790405 0.682821224 0.747156306 1 18.24493747 7.911571955 19.36295394 0.87283209 0.004368121 0 0.143725414 0 0 0.034444016 0 81577793.6 -7.911571955 -0.868463969 LKELIFEETAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKELIFEETAR 11 1 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 ; 157.52 2.79E-05 1022580000 2819800 2639800 1560720 1902680 2646500 2303240 3091200 3450700 1826020 FALSE TRUE 2447156.286 2622458.98 2315489.412 2334712.575 2593839.828 2391847.133 2791415.9 2712794.658 1610149.996 1.519831253 1.628704771 1.438058205 1.449996945 1.610930556 1.485480942 1.733637181 1.684808661 1 20.61876366 1.231831774 24.99993517 0.999999024 1.574849563 0.768019366 0.098217809 120.3627877 447147.0888 0.247366617 0.026051229 17.05421658 -1.231831774 0.574850539 LKEQCGCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKEQCGCR 8 1 Q14376;Q14376-2;Q5QPP4;Q5QPP3;Q5QPP9 Q14376 GALE UDP-glucose 4-epimerase 0 74.376 0.034794 0 53787 47078 33333 30540 42166 46760 54629 48484 30279 FALSE TRUE 46678.91167 46768.74152 49452.95029 37474.57377 41326.9791 48558.88746 49331.08799 38116.0739 26699.45111 1.748309786 1.751674269 1.8522085 1.403570943 1.547858753 1.818722312 1.847644275 1.427597659 1 14.70452246 1.374491379 2.805629694 0.957422357 1.701788488 0.723056175 0.14129628 0.188278529 2.136053671 0.279740964 0.039266766 23.68598114 -1.374491379 0.744366131 LKERPS(ph)SREDTPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKERPSSREDTPSR 14 3 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 LKERPS(0.681)S(0.319)REDTPSR 117.84 0.0015485 128380000 97998 105100 45037 51417 95828 82672 116240 120520 20281 TRUE FALSE 85047.316 104409.5912 66817.04384 63092.01571 93921.21028 85852.44534 104967.0627 94747.73589 17883.40328 4.755656105 5.838351321 3.736259971 3.527964712 5.251864469 4.80067714 5.869523883 5.298081936 1 14.12633369 4.244808391 24.99164548 4.431539761 5.297003483 0.079531203 1.386014772 458.6824334 1834719.12 0.346472119 0.870123927 17571.48198 -4.244808391 0.865463721 LKERPSS(ph)REDTPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LKERPSSREDTPSR 14 3 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 LKERPS(0.129)S(0.87)REDTPSR;LKERPS(0.038)S(0.962)REDTPSR;LKERPS(0.15)S(0.85)REDTPSR 151.31 3.85E-05 562400000 506670 462400 186837 218930 426541 387635 517740 614950 86109 TRUE FALSE 439712.2758 459362.464 277191.9981 268641.4026 418053.6686 402547.5693 467529.6545 483447.728 75929.29212 5.791075664 6.049871547 3.650659586 3.53804698 5.505828607 5.301610987 6.157434653 6.367078035 1 16.21236894 4.287929328 24.99960207 4.787901047 5.920478967 0.102525221 1.577124003 309.8211226 156883.6814 0.396872085 1.050021179 19405.70068 -4.287929328 1.132577921 LKESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKESLR 6 1 P35410 P35410 MAS1L Mas-related G-protein coupled receptor MRG 0 99.171 0.087381 0 1393400 1235400 761180 930660 1102900 1061300 1224400 1350300 1243900 FALSE TRUE 1209258.66 1227284.576 1129289.194 1141980.577 1080954.448 1102128.898 1105657.876 1061548.853 1096847.559 1.102485619 1.118919914 1.029577159 1.041147941 0.985510191 1.004815016 1.008032399 0.967818038 1 20.0649316 4.028897981 1.00592742 0.990087255 1.129009218 0.842153762 0.019252015 0.262886174 0.429051348 0.006598271 0.031222909 10688.03781 -4.028897981 0.138921964 LKFEGKT(ph)FY(ph)LY(ph)VSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKFEGKTFYLYVSQK 15 2 A0A087WVP2;H0Y5N1;B5MC67;Q7Z6J6-2;Q7Z6J6;H0YNI9 A0A087WVP2 FRMD5 FERM domain-containing protein 5 3 LKFEGKT(1)FY(1)LY(1)VS(0.001)QK 52.265 0.065797 420610000 459680 394770 432830 628020 448980 499940 451750 728090 1206200 TRUE FALSE 398932.1233 392176.7299 642148.0357 770621.5397 440046.1764 519173.0153 407939.3545 572393.6195 1063604.41 0.375075657 0.368724242 0.60374706 0.724537744 0.413731057 0.488126046 0.383544249 0.538164015 1 20.02053023 1.243196539 4.465560825 1.041818953 0.485673702 0.677552491 0.111856998 0.124777463 5.154537827 0.219197656 0.029505131 17.50638756 -1.243196539 -0.556145251 LKFNFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKFNFK 6 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 119.7 0.018958 923450000 1294760 930010 555190 788070 1034100 699030 1072150 1256940 844700 FALSE TRUE 1123654.185 923900.7031 823681.741 967013.3384 1013523.433 725922.1364 968173.058 988153.1625 744840.5283 1.508583573 1.240400687 1.105849789 1.298282386 1.36072541 0.974600749 1.29983939 1.326664064 1 19.50657205 4.729677427 4.6600528 1.211899143 1.524557152 0.339772057 0.134611114 0.210917667 12.44971214 0.032038242 0.212543457 53663.30637 -4.729677427 0.312658009 LKFS(ph)DDEEEEEVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LKFSDDEEEEEVVK 14 1 Q5JSZ5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 LKFS(1)DDEEEEEVVK;LKFS(1)DDEEEEEVVK;LKFS(1)DDEEEEEVVK 231.21 3.78E-13 1229460000 2892980 1807750 2215810 2090700 1946130 1701240 2625910 3066250 4536300 TRUE FALSE 2510665.363 1795874.771 3287383.127 2565425.389 1907405.821 1766687.804 2371249.652 2410556.299 4000023.782 0.627662609 0.448966024 0.821840896 0.641352534 0.47684862 0.441669325 0.592808889 0.602635492 1 21.93157715 1.231784332 4.498751941 1.038530082 0.57800529 0.582638428 0.111405893 0.15915695 6.722481915 0.237155983 0.028587286 17.05235369 -1.231784332 -0.460524792 LKFS(ph)DEEDGRDS(ph)DEEGAEGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 206.57 2.22E-22 2885190000 2154480 1497340 1278950 1465650 1585270 1464900 1789590 2071240 2427330 TRUE FALSE 1869760.009 1487503.875 1897454.498 1798448.234 1553726.229 1521255.651 1616035.837 1628321.444 2140373.813 0.873567037 0.694973871 0.886506126 0.840249597 0.725913492 0.710742975 0.755025046 0.760764982 1 21.02943135 1.235966838 24.99629417 1.000000295 0.77735313 0.516823486 0.066475113 57.82199157 557115.6643 0.105910677 0.015975494 17.21737103 -1.235966838 -0.222647165 AQKPWAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AQKPWAK 7 1 F6U236;Q9BY11;Q9UNF0-2;Q9UNF0;A0A0U1RR22;B0QYG7;B0QYG8 F6U236;Q9UNF0-2 PACSIN1;PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 1;Protein kinase C and casein kinase substrate in neurons protein 2 0 69.998 0.053096 401990000 228550 271990 125820 248710 377160 372110 493730 646620 590080 FALSE TRUE 198346.5384 270203.2798 186666.9728 305183.4068 369655.2539 386425.3125 445848.1406 508345.345 520321.4146 0.381200029 0.51930071 0.358753201 0.586528631 0.710436364 0.742666555 0.856870634 0.976983324 1 18.98904356 2.71662993 0.573132456 1.070410605 0.371420946 0.938106554 0.055861694 0.221016042 0.197753028 0.096981847 0.06340186 520.7507816 -2.71662993 -0.698989659 down LKGDDLQAIKK ddPTM_MDA-MB-175_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 ; 153.38 1.83E-05 5173100000 15744700 9755500 9038600 10017900 9628300 8405600 12655000 19293300 9371500 FALSE TRUE 13663998 9691415.478 13409697.19 12292617.31 9436715.667 8728968.871 11427720.05 15167577.94 8263611.946 1.653513995 1.172782016 1.622740429 1.487559845 1.141960166 1.056313986 1.382896501 1.8354659 1 22.97834108 4.775958204 22.06678247 1.377210668 1.653517113 0.10862537 0.263499623 10642.53739 6279150.349 0.066818624 11.88377232 59697.7831 -4.775958204 0.276306445 LKGEATVSFDDPPSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKGEATVSFDDPPSAK 16 1 P35637-2;P35637;H3BPE7 P35637-2 FUS RNA-binding protein FUS 0 104.61 0.0025632 0 1353700 978360 614530 769320 851790 674810 1156600 1356100 1113300 FALSE TRUE 1174805.115 971933.0887 911718.7635 944005.8643 834841.0455 700770.3774 1044433.11 1066108.568 981686.9423 1.196720731 0.990064191 0.928726587 0.961615994 0.85041474 0.713843026 1.063916678 1.085996484 1 19.9049035 4.730908788 3.27022057 0.951896495 1.228711363 0.356790558 0.105674478 0.427446857 7.462343638 0.029828667 0.296934525 53815.67456 -4.730908788 0.276814867 LKGEIDASVPELEGDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKGEIDASVPELEGDLR 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 81.01 0.005599 0 97925 64031 45621 78550 75279 63733 63046 98312 90327 FALSE TRUE 84983.96314 63610.37614 67683.46819 96385.97806 73781.09518 66184.84975 56931.80862 77288.74386 79648.64496 1.066985674 0.798637267 0.849775514 1.210139584 0.926332083 0.830960147 0.714786908 0.970371108 1 16.2813622 2.999234161 24.99909646 0.877986366 0.972593632 0.112486538 0.134557233 72.83384876 2377643.183 0.042373954 0.047482899 998.2381448 -2.999234161 0.094607266 LKGELESSDQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKGELESSDQVR 12 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 141.54 5.53E-05 1137680000 1566600 1405720 898260 1298300 1510600 1213310 1392800 1890540 1496970 FALSE TRUE 1359569.841 1396485.733 1332661.54 1593098.858 1480542.015 1259986.821 1257726.47 1486262.733 1319999.912 1.029977221 1.057943808 1.009592143 1.206893155 1.121622814 0.954535534 0.952823147 1.125956691 1 20.3321064 0.948368807 16.96797547 0.563944526 1.058022296 0.049909084 0.078691397 2661726.238 21557240.92 44231264.42 0.019831407 8.879097128 -0.948368807 0.49407777 LKGEMMDLQHGSLFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 88.133 0.0037454 1255559000 535251 505137 120876 265995 595249 526191 547833 647684 179462 FALSE TRUE 464516.2242 501818.7218 179332.0379 326393.2302 583404.7095 546433.9083 494704.24 509181.8169 158246.2068 2.935401951 3.171126385 1.133246992 2.062565902 3.686690008 3.453061652 3.126168077 3.217655748 1 17.27181139 3.267698369 24.99851713 2.981859643 2.300813948 0.085885007 0.900810255 480.348095 412107.8749 0.262827416 0.339254497 1852.244737 -3.267698369 -0.681045695 LKGIEEEEILPGFILCDPNNLCHSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKGIEEEEILPGFILCDPNNLCHSGR 26 1 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 118.01 0.00040482 161640000 592950 536300 276430 366440 449810 406210 637990 649200 183380 FALSE TRUE 514590.1552 532777.01 410112.4726 449645.8027 440859.661 421837.1616 576117.828 510373.6321 161701.0253 3.182355549 3.294827655 2.53623916 2.780723263 2.726387543 2.608747599 3.562858225 3.156279505 1 17.3029693 1.235585501 24.9990427 0.999997303 2.986590311 0.785973002 0.324872972 40.36543385 339116.6208 0.579081169 0.084649097 17.20225975 -1.235585501 1.986593007 LKGMKDDKEEEEDGT(ph)GSPQLNNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKGMKDDKEEEEDGTGSPQLNNR 23 3 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 LKGMKDDKEEEEDGT(0.687)GS(0.313)PQLNNR;LKGMKDDKEEEEDGT(0.5)GS(0.5)PQLNNR 170.44 7.54E-12 823190000 691207 436778 350797 186356 352866 251668 780041 742151 77009 TRUE FALSE 599862.2437 433908.7766 520443.6025 228670.9781 345844.657 261349.8308 704392.7439 583447.7841 67905.08375 8.833834089 6.389930659 7.664280402 3.367508962 5.093059869 3.848752058 10.37319601 8.592107569 1 16.05123197 4.981419562 1.486653429 6.03001417 11.39343699 0.109080585 2.70702196 6.07860113 7.875119091 0.778634342 56.87237178 95811.92416 -4.981419562 5.363422815 LKGMKDDKEEEEDGTGS(ph)PQLNNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKGMKDDKEEEEDGTGSPQLNNR 23 3 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 LKGMKDDKEEEEDGT(0.007)GS(0.993)PQLNNR;LKGMKDDKEEEEDGT(0.184)GS(0.816)PQLNNR 143.08 1.18E-07 325460000 370880 241236 164747 111282 195494 134386 399530 400840 34457 TRUE FALSE 321867.2683 239651.3048 244419.2002 136550.2789 191604.0519 139555.9164 360783.6421 315123.4853 30383.53271 10.59347744 7.887539184 8.044462853 4.494219952 6.306180841 4.59314319 11.87431513 10.37152224 1 14.891002 4.790688089 1.886035065 7.113738783 11.96679516 0.129516204 3.077953907 2.429375352 8.093941921 0.849411957 21.63652152 61757.2699 -4.790688089 4.853056374 LKGPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKGPQK 6 1 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 72.021 0.079067 435370000 1287900 1512900 705610 1159200 1400500 1556500 1670800 1952000 1807400 FALSE TRUE 1117700.752 1502961.66 1046845.356 1422414.077 1372632.79 1616379.562 1508766.073 1534579.99 1593731.231 0.701310692 0.943045873 0.656851881 0.892505618 0.861269933 1.014210885 0.946687901 0.962885059 1 20.60397692 3.148456011 1.723487658 0.97437674 0.787073607 0.532320402 0.082049634 0.271364768 1.670603039 0.026962231 0.033191087 1407.524656 -3.148456011 -0.187303133 LKGSGNLEAIHIIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKGSGNLEAIHIIK 14 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 91.032 0.0033145 954500000 2831700 2340600 1456610 1869630 2388400 2068800 2909400 3307200 2091680 FALSE TRUE 2457483.67 2325224.444 2161031.468 2294158.067 2340875.513 2148388.075 2627246.836 2599981.017 1844403.973 1.3323999 1.260691518 1.171669276 1.243847932 1.269177223 1.164814274 1.42444219 1.409659193 1 20.81472325 2.259012026 24.99696087 1.311556218 1.23969032 0 0.124539562 690.8352067 844379.5744 0.046080332 0.035651613 181.5565936 -2.259012026 -0.071865899 LKHEDTNLASSTLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LKHEDTNLASSTLLR 15 1 P49407-2;P49407;H0YET9 P49407-2 ARRB1 Beta-arrestin-1 0 ;;; 159.22 1.07E-06 1611020000 2215050 1926850 1205974 1436720 1897460 1823620 2427990 2431850 1436085 FALSE TRUE 1922325.53 1914192.395 1789187.06 1762949.235 1859704.258 1893775.841 2192523.904 1911817.802 1266312.667 1.518049673 1.511626982 1.412910971 1.392191108 1.468598006 1.495504144 1.73142381 1.509751779 1 20.27220224 1.238455057 24.96689938 1.000006107 1.508210986 0.753314762 0.09080392 1.328927903 312797.1207 0.134503015 0.024025538 17.31629823 -1.238455057 0.508204879 LKLEDFFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LKLEDFFAR 9 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;; 182.64 4.20E-05 22487560000 14767230 14406330 10636720 12357570 13370750 13233990 17164650 18617050 16267020 FALSE TRUE 12815703.14 14311693.87 15780673.37 15163545.14 13104698.23 13743110.16 15500024.88 14635938.74 14343951.43 0.893456953 0.997751139 1.100162215 1.057138629 0.913604476 0.958111872 1.080596582 1.020356128 1 23.77393917 4.709869718 4.317952621 1.019153792 0.887057628 0.334078209 0.054898834 0.230986976 9.658943651 0.014193035 0.087417594 51270.75565 -4.709869718 -0.132096164 LKLGEIVTTIPTIGFNVETVEYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LKLGEIVTTIPTIGFNVETVEYK 23 1 P61204;F5H423;F5H0C7;P84077;P84085;C9J1Z8;P18085;C9JPM4 P61204;P84077;P84085;P18085 ARF3;ARF1;ARF5;ARF4 ADP-ribosylation factor 3;ADP-ribosylation factor 1;ADP-ribosylation factor 5;ADP-ribosylation factor 4 0 ;; 201.15 2.11E-24 668880000 1409884 1084304 786681 768109 1039032 757730 1550044 1784340 523224 FALSE TRUE 1223564.257 1077181.136 1167122.563 942519.8883 1018357.296 786880.3634 1399720.971 1402772.777 461369.0548 2.652029313 2.334749426 2.529694072 2.042876258 2.207250975 1.705533467 3.033842337 3.04045701 1 18.81556172 5.213614879 1.346361813 2.311402716 3.301647809 0.032859762 0.602688973 21.30636746 14.27666845 0.173459667 39.36526766 163536.5678 -5.213614879 0.990245092 LKLLLPWLEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKLLLPWLEAR 11 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 77.593 0.019018 0 65032 67423 21517 22310 62418 53131 80158 74871 7625 FALSE TRUE 56437.85643 66980.09387 31922.69317 27375.82649 61176.00392 55174.98395 72384.2895 58860.4193 6723.581186 8.394017245 9.961966996 4.74787056 4.071613881 9.098723169 8.206189889 10.76573443 8.754325658 1 12.71501415 4.274114407 24.9962451 7.119436315 9.177993106 0.100919622 2.880147975 504.9424605 354994.2232 0.738204784 1.952948799 18798.11952 -4.274114407 2.058556791 LKLPAVVTADLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKLPAVVTADLR 12 1 P38117-2;P38117;M0QY67 P38117-2 ETFB Electron transfer flavoprotein subunit beta 0 ; 108.17 0.00063975 0 1862560 1959170 1172260 2017370 2342600 2101480 1914670 2519400 1403950 FALSE TRUE 1616417.977 1946300.083 1739168.857 2475444.692 2295986.843 2182325.295 1728985.598 1980645.916 1237976.63 1.305693449 1.572162217 1.40484789 1.999589194 1.854628583 1.762816229 1.396622162 1.599905739 1 20.23955265 0.871793442 1.631693006 5.16E-11 1.638648274 0.433608014 0.217204863 3.028367616 3.255153272 10.78158447 0.06304989 7.443778503 -0.871793442 1.638648274 LKLS(ph)PS(ph)PSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKLSPSPSSR 10 1 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 2 LKLS(1)PS(0.986)PS(0.012)S(0.002)R 59.185 0.060454 501400000 1485800 1433500 885870 1168200 1560200 1120900 1340100 2015100 1696900 TRUE FALSE 1289447.765 1424083.244 1314279.695 1433457.665 1529155.072 1164021.748 1210137.308 1584186.547 1496294.415 0.861760729 0.951739998 0.878356346 0.958005089 1.021961358 0.777936305 0.808756149 1.058739865 1 20.51296264 1.680722764 8.937795619 1.027964361 0.898801444 0.370390994 0.072928047 0.127024368 16.62389408 0.042644904 0.019366893 47.9427304 -1.680722764 -0.129162918 LKLS(ph)PSPS(ph)SR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LKLSPSPSSR 10 1 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 2 LKLS(0.964)PS(0.045)PS(0.734)S(0.257)R;LKLS(0.981)PS(0.075)PS(0.929)S(0.015)R;LKLS(0.744)PS(0.488)PS(0.686)S(0.081)R 123.02 0.0056572 1081910000 3232730 2919850 1904090 2522990 3247570 2543770 2901170 4378280 3450560 TRUE FALSE 2805516.54 2900669.313 2824914.293 3095873.441 3182949.711 2641630.478 2619814.98 3442018.894 3042638.728 0.922066926 0.953340036 0.928442232 1.017496232 1.046114901 0.868203791 0.861033864 1.13126112 1 21.53689161 1.730727569 18.20221534 1.065323959 0.946296371 0.38248687 0.064954957 0.16239697 345.3861967 0.03558548 0.017047052 53.79322338 -1.730727569 -0.119027588 LKLS(ph)PSPSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LKLSPSPSSR 10 1 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 1 LKLS(0.926)PS(0.074)PSSR;LKLS(0.5)PS(0.5)PSSR;LKLS(0.5)PS(0.5)PSSR 146.79 1.70E-05 8327900000 9721600 9461400 6078100 8665500 9072600 7835000 9716100 13633100 11128500 TRUE FALSE 8436865.929 9399247.44 9017489.49 10633134.22 8892073.01 8136417.52 8773834.117 10717767.66 9812901.408 0.859772821 0.957845906 0.918942229 1.083587186 0.906161454 0.829155128 0.894112124 1.092211897 1 23.22624833 1.746022568 15.46516989 1.045481672 0.924785755 0.347652993 0.070913565 0.150853158 298.2357324 0.039193019 0.018712441 55.72147032 -1.746022568 -0.120695917 LKLSILYPATTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKLSILYPATTGR 13 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 81.448 0.010494 0 603380 647930 246020 310470 577570 540490 711100 796270 129560 FALSE TRUE 523641.8042 643673.7052 364996.0949 380966.9587 566077.487 561283 642137.6314 625993.8571 114243.5644 4.583556255 5.634222887 3.194894144 3.334690761 4.955005474 4.913038236 5.620777283 5.47946714 1 16.80175337 4.272331815 24.99966348 4.315219073 5.108888716 0.066768216 1.397850262 656.3624122 485872.4009 0.350864025 0.928183186 18721.1195 -4.272331815 0.793669642 LKLSPS(ph)PSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKLSPSPSSR 10 1 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 1 LKLS(0.326)PS(0.673)PSSR 119.39 0.0018394 779260000 888590 776980 501250 759850 810650 743010 848370 1163600 949880 TRUE FALSE 771160.5801 771875.9672 743656.1766 932385.5561 794519.651 771594.0755 766095.208 914773.1951 837586.2685 0.920693914 0.92154802 0.887856218 1.113181521 0.94858247 0.921211467 0.914646332 1.092154002 1 19.67587827 LKNEITR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKNEITR 7 1 Q86VP6 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 123.98 0.0038219 1534780000 3021100 2592400 1763760 2077800 2355300 2477600 3002100 3070800 3131500 FALSE TRUE 2621853.981 2575370.354 2616720.235 2549596.247 2308434.138 2572914.875 2710956.804 2414133.317 2761297.637 0.949500679 0.932666699 0.9476415 0.923332644 0.83599613 0.931777451 0.981769139 0.874274937 1 21.39691497 1.214295445 24.84249666 1.000000376 0.921448694 0.26589391 0.040654528 3029.295195 3101190.976 0.636844443 0.009920226 16.37930407 -1.214295445 -0.078551683 LKNGFPHPEPDCNPSEAAS(ph)EESNS(ph)EIEQEIPVEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKNGFPHPEPDCNPSEAASEESNSEIEQEIPVEQK 35 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 2 LKNGFPHPEPDCNPS(0.398)EAAS(0.577)EES(0.484)NS(0.541)EIEQEIPVEQK 81.554 0.0018761 113930000 53925 41572 37794 35707 32874 24273 55834 58256 45861 TRUE FALSE 46798.67462 41298.91079 56071.30481 43814.8201 32219.87172 25206.79802 50419.22727 45798.40775 40439.36483 1.157255432 1.02125518 1.38655256 1.083469542 0.796745247 0.623323292 1.246785836 1.132520452 1 15.30347272 3.476640224 24.99999487 0.981961011 1.182205576 0.229498632 0.189835268 29.93443755 1555669.354 0.059372227 0.077379291 2996.678999 -3.476640224 0.200244565 LKNGFPHPEPDCNPSEAASEES(ph)NSEIEQEIPVEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKNGFPHPEPDCNPSEAASEESNSEIEQEIPVEQK 35 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 LKNGFPHPEPDCNPS(0.1)EAAS(0.1)EES(0.4)NS(0.4)EIEQEIPVEQK 153.04 2.50E-11 124030000 92938 66898 55077 57498 56288 45988 82626 90812 84520 TRUE FALSE 80656.00783 66458.54263 81712.42142 70553.7997 55167.97893 47757.18812 74612.94324 71392.5605 74528.14189 1.082222175 0.891724132 1.096396869 0.946673269 0.740230167 0.640794026 1.001137843 0.957927552 1 16.18549767 3.47548914 24.97954478 0.874749626 1.012151995 0.24624087 0.123792304 89.32481199 1367094.756 0.038406167 0.049947138 2988.746911 -3.47548914 0.137402369 LKNWEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKNWEIR 7 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 87.435 0.017642 1000080000 2882100 2622600 1637020 2058600 2629000 2230900 2861600 3466900 2715400 FALSE TRUE 2501223.183 2605371.968 2428688.348 2526036.594 2576688.044 2316724.167 2584082.472 2725530.414 2394388.505 1.044618773 1.088115802 1.014325095 1.054981925 1.076136157 0.96756402 1.079224389 1.138299156 1 21.19122583 2.025017585 24.99862353 1.087948267 1.042398861 0.062616673 0.047199347 376.8221931 376535.0965 0.018568735 0.012518681 105.9296617 -2.025017585 -0.045549406 LKPEGLHQLLAGFEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKPEGLHQLLAGFEDK 16 1 Q9BY32;Q9BY32-3;Q9BY32-2 Q9BY32 ITPA Inosine triphosphate pyrophosphatase 0 146.78 6.56E-07 562920000 1716800 1258300 1068800 1240800 1170700 938090 1610600 1920100 1866900 FALSE TRUE 1489920.53 1250034.144 1585675.255 1522542.604 1147405.36 974178.9293 1454404.26 1509501.557 1646197.209 0.90506807 0.759346534 0.963235296 0.924884696 0.697003588 0.59177535 0.883493334 0.916962773 1 20.65070575 1.685697901 2.642192394 0.979359158 0.809786489 0.234858477 0.11212043 0.380019541 5.804236046 0.107191281 0.032850809 48.49510472 -1.685697901 -0.16957267 LKPEYDIMCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKPEYDIMCK 10 1 J3KQ32;Q9NTK5;Q9NTK5-3;Q9NTK5-2;C9JCJ9 J3KQ32 OLA1 Obg-like ATPase 1 0 79.741 0.023801 497540000 942800 811570 629640 658420 783380 668260 989020 1211400 1195700 FALSE TRUE 818206.5912 806238.7432 934136.01 807924.3243 767792.2707 693968.3946 893104.9926 952351.5371 1054345.708 0.776032553 0.764681581 0.885986449 0.76628028 0.728216812 0.65819815 0.847070354 0.903263066 1 20.00791656 1.658018704 2.08357345 0.990180034 0.768123921 0.638883765 0.058954426 0.214303389 1.875324456 0.073671849 0.017621815 45.50076561 -1.658018704 -0.222056113 LKPFGVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKPFGVQR 8 1 U3KQ56;Q9UBQ7;Q9UBQ7-2 U3KQ56 GRHPR Glyoxylate reductase/hydroxypyruvate reductase 0 100.15 0.0084826 0 129660 214180 131520 147590 187250 197770 181960 229350 255390 FALSE TRUE 112525.1025 212773.0375 195123.5119 181102.5653 183524.0913 205378.3399 164313.5472 180305.2873 225198.0851 0.499671666 0.94482614 0.866452802 0.804192297 0.814945168 0.911989726 0.729640073 0.800651956 1 17.78083503 4.748725011 24.65394802 0.847242639 0.499671433 0.668767842 0.079103374 748.8584268 1816327.478 0.019017181 0.253646579 56069.28404 -4.748725011 -0.347571206 LKPGGVGAPSSSS(ph)PSPSPSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LKPGGVGAPSSSSPSPSPSAR 21 1 Q92797 Q92797 SYMPK Symplekin 1 LKPGGVGAPSSS(0.004)S(0.994)PS(0.002)PSPSAR;LKPGGVGAPSS(0.005)S(0.088)S(0.892)PS(0.015)PSPSAR;LKPGGVGAPSS(0.008)S(0.14)S(0.84)PS(0.011)PSPSAR;LKPGGVGAPSSS(0.007)S(0.989)PS(0.004)PSPSAR;LKPGGVGAPSSS(0.04)S(0.936)PS(0.023)PSPSAR;LKPGGVGAPSSSS(0.975)PS(0.023)PS(0.001)PSAR 219.94 2.95E-25 4014200000 3072430 2223370 1688920 1970800 2206890 1993660 2551890 2693180 3344660 TRUE FALSE 2666400.591 2208764.536 2505687.361 2418300.262 2162977.207 2070357.39 2304408.101 2117264.415 2949258.105 0.904091977 0.748922087 0.849599212 0.819969014 0.733397054 0.701992608 0.78135179 0.717897295 1 21.49192066 4.750511054 23.03603142 0.785347376 0.904092199 0.131405374 0.086243739 1167.242924 2249883.263 0.020176991 0.29862784 56300.34479 -4.750511054 0.118744823 LKPGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKPGTR 6 1 A0A087X2I1;P62333;H0YJC0;H0YJS8;A6PVL3-2;A6PVL3 A0A087X2I1 PSMC6;KNCN 26S protease regulatory subunit 10B;Kinocilin 0 88.591 0.046631 538020000 599470 601560 381590 479870 475800 566760 636320 697060 705640 FALSE TRUE 520248.5206 597608.3128 566128.2003 588831.8179 466332.5109 588563.6239 574609.7843 547999.1435 622220.0431 0.836116622 0.960445295 0.90985208 0.946340164 0.749465589 0.945909137 0.923483245 0.880715994 1 19.24706534 1.233351364 24.87498349 1.000000173 0.896102982 0.219232315 0.062734651 246.7886701 1178310.908 0.119403202 0.014505863 17.11399354 -1.233351364 -0.103897191 LKPGYLEATVDWFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKPGYLEATVDWFR 14 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 212.39 2.28E-09 8847700000 8797600 8813200 5336100 6721700 7700000 7069100 8096800 9529300 9324300 FALSE TRUE 7634974.87 8755305.509 7916655.808 8247964.72 7546785.065 7341052.851 7311573.582 7491533.352 8221991.876 0.92860404 1.064864286 0.962863492 1.003158948 0.917877952 0.892855766 0.889270349 0.911157961 1 22.97105652 3.233487198 24.43362884 0.916907097 0.993300011 0.349019874 0.045474386 91.34983546 439941.1187 0.013014812 0.01522073 1711.934714 -3.233487198 0.076392914 LKPKPIDVQVITHHMQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKPKPIDVQVITHHMQR 17 2 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ; 111.33 0.0001657 2227140000 4930500 4052100 2694700 3703300 3607800 3174500 4966600 5841600 3980600 FALSE TRUE 4278921.933 4025481.488 3997865.933 4544190.866 3536011.839 3296625.069 4484939.896 4592419.299 3510018.003 1.219059825 1.146854941 1.138987302 1.294634632 1.007405613 0.939204604 1.277754101 1.308374856 1 21.743047 LKPLEVELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKPLEVELR 9 1 P49755 P49755 TMED10 Transmembrane emp24 domain-containing protein 10 0 ; 136.96 0.00016245 6091600000 11187400 12039300 7694400 9295700 12389100 10882300 10040900 14326600 14967100 FALSE TRUE 9708956.745 11960213.05 11415437.58 11406430.76 12142581.15 11300949.12 9067135.063 11262968.08 13197706.49 0.735654847 0.906234205 0.864956164 0.864273711 0.920052371 0.856281289 0.687023542 0.853403437 1 23.6537839 3.044104937 0.006911956 1.700412493 3.67E-08 0.040176226 0.08672522 35069.40513 336.740534 41388.65438 41445.13004 1106.891206 -3.044104937 -1.700412457 LKPNLGNGADLPNYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKPNLGNGADLPNYR 15 1 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 ; 220.21 1.55E-12 2596900000 3393700 2659600 1893890 2416600 3059400 2840800 3341800 4004000 3349400 FALSE TRUE 2945213.946 2642128.912 2809781.539 2965325.965 2998523.926 2950087.414 3017712.75 3147775.759 2953437.748 0.997215516 0.894594414 0.951359662 1.004025214 1.015265661 0.998865616 1.021762776 1.065800612 1 21.49396377 3.650436208 2.591375157 1.024754851 0.940671602 0.53910158 0.030569201 0.19728882 2.582723066 0.008957109 0.015071435 4471.324689 -3.650436208 -0.08408325 LKPPVHYNGPSK ddPTM_MDA-MB-175_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 ; 137.59 5.38E-05 997010000 1528480 1215170 778830 985330 1178100 959870 1451510 1599360 1473630 FALSE TRUE 1326487.495 1207187.468 1155474.793 1209064.236 1154658.115 996796.82 1310742.784 1257349.31 1299419.14 1.020831119 0.929020846 0.889224083 0.930465159 0.888595588 0.767109541 1.008714389 0.967624126 1 20.30943543 LKPQYLEELPGQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKPQYLEELPGQLK 14 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 200.44 1.75E-08 1425360000 2138880 1747120 1560890 1929440 1816090 1484650 2509390 2584420 2779950 FALSE TRUE 1856221.589 1735643.054 2315741.625 2367548.842 1779953.362 1541765.446 2266029.744 2031761.895 2451307.478 0.757237354 0.708047876 0.944696512 0.965831036 0.72612407 0.628956367 0.924416771 0.828848243 1 21.22512003 0.758192611 1.311684947 1.397646856 0.804345262 0.232756899 0.109548669 7.119238835 4.273750027 7.825737858 0.033950025 5.730501236 -0.758192611 -0.593301594 LKPVELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKPVELR 7 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 96.253 0.011735 1558660000 6535100 5413600 3348200 4523700 5414500 4316000 5982000 6949500 5936600 FALSE TRUE 5671469.977 5378037.705 4967400.719 5550875.225 5306762.043 4482039.313 5401866.561 5463403.506 5234781.911 1.083420489 1.027366144 0.948922191 1.060383282 1.013750359 0.856203637 1.031918168 1.043673566 1 22.319698 4.620067198 3.665415881 0.997807335 1.084120835 0.194449818 0.057762346 0.437447314 9.422049847 0.014664117 0.080398839 41693.38903 -4.620067198 0.086313501 LKPWGLFEVLVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKPWGLFEVLVEK 13 1 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3 H3BLV9 SRPK1 SRSF protein kinase 1 0 69.108 0.047462 0 170290 142380 97109 119940 136700 109350 173190 184440 147830 FALSE TRUE 147785.745 141444.6964 144071.2372 147174.2102 133979.9374 113556.7653 156394.0605 144998.9413 130353.7058 1.133728758 1.085083815 1.105233152 1.129037408 1.027818401 0.87114336 1.199766892 1.112349974 1 16.99207207 3.243565378 24.99550757 1.054245225 1.110683315 0.141971234 0.083847044 337.2481341 1684323.881 0.02593288 0.03244608 1752.126175 -3.243565378 0.05643809 LKQDGDSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LKQDGDSFR 9 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 140.07 0.00010029 1596490000 2824580 2640000 1500650 1566700 2541890 2274840 2924870 3311640 1526060 FALSE TRUE 2451304.596 2622657.666 2226369.359 1922443.181 2491311.362 2362354.567 2641216.558 2603471.557 1345650.925 1.821649694 1.948988119 1.654492497 1.428634384 1.851380113 1.755547834 1.962779877 1.934730255 1 20.35987278 1.232587353 24.99954898 0.999998703 1.798747405 0.708531968 0.160182005 119.7776812 501247.5307 0.374854601 0.042336046 17.08391308 -1.232587353 0.798748703 LKQDILDEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKQDILDEMR 10 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 ; 110.86 0.0016694 157925000 310940 284050 219700 277910 267470 271710 301320 326980 426740 FALSE TRUE 269848.4912 282184.0568 325947.6549 341013.7131 262147.8703 282162.8595 272098.0328 257057.8716 376291.2833 0.717126607 0.749908566 0.866211016 0.906249303 0.696662086 0.749852234 0.723104799 0.683135334 1 18.52149034 1.226792335 24.99856011 1.000000533 0.761093541 0.52367657 0.071473772 495.4438008 1052370.137 0.304684183 0.019054859 16.85746767 -1.226792335 -0.238906992 LKQEFHYIEEDLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKQEFHYIEEDLYR 14 1 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 0 ; 182.1 9.38E-07 276570000 440630 408760 240400 300180 422610 393440 371560 566100 344530 FALSE TRUE 382399.6291 406074.8286 356658.2441 368340.457 414200.8878 408575.8914 335526.1684 445043.9204 303800.0559 1.258721391 1.336651593 1.173990054 1.212443677 1.363399643 1.344884188 1.104430898 1.464923761 1 18.21276261 1.212033918 24.90559978 0.999998506 1.283241759 0.425798747 0.103068983 2604.712045 2445394.439 1.994879322 0.024059665 16.29423284 -1.212033918 0.283243253 LKQEYFVVAATLQDIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKQEYFVVAATLQDIIR 17 1 P11216;P11217;P11217-2;E9PK47;P06737-2;P06737 P11216;E9PK47 PYGB;PYGM;PYGL "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form;Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ; 205.62 7.04E-12 833800000 2381400 1826280 1172140 1373020 1614050 1615980 2108530 2369000 1692340 FALSE TRUE 2066691.956 1814283.046 1738990.825 1684785.176 1581933.563 1678147.796 1904045.085 1862407.786 1492273.493 1.38492841 1.215784543 1.165329836 1.129005631 1.060082867 1.1245578 1.275935741 1.248033818 1 20.50908054 4.749163285 2.071123169 1.155297536 1.453902663 0.47115291 0.080305051 0.752615549 3.476236171 0.022557431 0.426514467 56125.89572 -4.749163285 0.298605127 LKQFEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKQFEER 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 95.741 0.012078 545470000 1141550 979130 865330 809630 952790 851750 1019850 1173500 861890 FALSE TRUE 990691.2752 972698.0306 1283806.482 993468.8659 933831.3431 884517.3737 920945.104 922556.1572 759998.3461 1.303543988 1.279868615 1.689222732 1.307198721 1.228728125 1.163841182 1.211772511 1.213892322 1 19.53563675 3.306858276 3.131640638 1.169752478 1.419362012 0.470052223 0.126241212 0.227423057 4.503252727 0.038450636 0.049861299 2027.021131 -3.306858276 0.249609535 LKQSAEEQAQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 106.58 0.0017391 269350000 178990 167320 89513 107360 132420 138690 169440 183830 90060 FALSE TRUE 155336.018 166220.8639 132801.7862 131737.7289 129785.1011 144025.494 153007.7349 144519.3851 79413.2094 1.956047604 2.093113541 1.672288366 1.65888937 1.634301171 1.813621375 1.926729017 1.819840631 1 16.27709138 1.238535825 24.40698483 0.99999953 1.819267576 0.762668807 0.144074513 0.234443889 224187.1356 0.211287064 0.037909753 17.31951895 -1.238535825 0.819268046 LKQVEDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LKQVEDEK 8 1 P35579 P35579 MYH9 Myosin-9 0 ;;;; 140.45 0.00059228 3122210000 5131590 4093220 3594520 4090100 3847500 3293620 6472040 7358120 5546220 FALSE TRUE 4453437.38 4066331.368 5332841.895 5018819.718 3770942.278 3420327.693 5844382.557 5784643.299 4890552.19 0.910620561 0.831466716 1.09043758 1.026227617 0.771066769 0.699374541 1.195035311 1.182820073 1 22.22156594 2.21553208 24.98158279 1.140677918 0.895762675 0.448286552 0.123788627 217.7390173 236203.6227 0.053665385 0.036207649 164.2600991 -2.21553208 -0.244915243 LKS(ph)DERPVHIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKSDERPVHIK 11 2 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 1 LKS(1)DERPVHIK 100.11 0.0022293 500820000 451230 229370 237120 275770 302330 248020 457260 507020 499370 TRUE FALSE 391598.8122 227863.2534 351792.0251 338387.7934 296314.2245 257561.4899 412914.9956 398597.7186 440335.0475 0.889320109 0.517476986 0.798918976 0.768477993 0.672929003 0.584921621 0.937729118 0.905214611 1 18.74824215 2.219276366 24.79856109 0.938394503 0.702451697 0.533567385 0.106657483 164.1187608 211046.5693 0.040977328 0.027675388 165.6823959 -2.219276366 -0.235942806 LKS(ph)EDELRPEVDEHTQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LKSEDELRPEVDEHTQK 17 2 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;H0YCR2;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 LKS(1)EDELRPEVDEHTQK;LKS(0.999)EDELRPEVDEHT(0.001)QK;LKS(1)EDELRPEVDEHTQK 163.42 1.29E-09 1405230000 831660 760230 844959 753133 1048150 741080 1304940 1470520 1710240 TRUE FALSE 721754.0238 755235.9991 1253583.999 924143.3586 1027293.866 769589.8271 1178387.12 1156060.742 1508057.376 0.478598517 0.500800574 0.831257497 0.612803845 0.681203436 0.510318665 0.781394089 0.766589362 1 20.52425989 -1.241481579 0.608405034 9.999999962 0.601671684 0.567275035 0.109380794 50.50966742 1.064580109 591.5477542 0.054269687 0.057348019 1.241481579 -9.398328278 LKS(ph)EDGVEGDLGETQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LKSEDGVEGDLGETQSR 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LKS(1)EDGVEGDLGETQSR;LKS(1)EDGVEGDLGETQSR;LKS(0.847)EDGVEGDLGET(0.077)QS(0.077)R 187.39 4.08E-10 221210000 1358180 696580 560340 754400 979960 813830 881420 1196340 1167080 TRUE FALSE 1178693.072 692004.1201 831322.2982 925698.0503 960460.7133 845138.5667 795940.0241 940512.0009 1029109.132 1.145352845 0.672430259 0.807807717 0.899513979 0.933293354 0.821233182 0.773426257 0.913908906 1 19.97296455 1.396490097 3.90093383 0.996668406 0.856689099 0.106537239 0.122858394 0.476548874 11.15703661 0.142016335 0.02942766 24.91667554 -1.396490097 -0.139979307 HLS(ph)ESSGKPLSTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 HLSESSGKPLSTK 13 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 HLS(0.933)ES(0.028)S(0.04)GKPLSTK;HLS(0.856)ES(0.114)S(0.03)GKPLSTK;HLS(0.994)ES(0.004)S(0.001)GKPLSTK;HLS(0.995)ES(0.004)S(0.001)GKPLSTK 117.18 0.00031922 1624200000 1128380 1786570 1411370 1975000 2915310 2268780 3578860 4610170 4388740 TRUE FALSE 979261.724 1774833.904 2093913.253 2423453.936 2857301.035 2356061.435 3231782.708 3624321.022 3869908.157 0.25304521 0.458624296 0.541075697 0.626230349 0.738338203 0.608815853 0.83510579 0.936539286 1 21.8838679 2.981856852 0.220422489 1.342661734 2.28E-19 0.907485082 0.068206742 1.226276733 0.390504938 1.09590503 1.077458645 959.0844544 -2.981856852 -1.342661734 down LKSDTAAAAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LKSDTAAAAVR 11 1 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;; 145.29 3.31E-05 1545870000 3202280 2909590 1746010 2071710 2834520 2513220 3047480 3420370 2388350 FALSE TRUE 2779090.584 2890476.712 2590386.276 2542123.42 2778118.598 2609905.2 2751935.859 2688950.493 2106001.984 1.319604922 1.372494772 1.230001821 1.207085007 1.319143391 1.239270058 1.306710953 1.2768034 1 21.00607536 1.23886202 7.011700134 0.994012624 1.283450666 0.76768475 0.049093824 0.052968587 15.1204879 0.073077402 0.012285132 17.33253236 -1.23886202 0.289438043 LKSEDEPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKSEDEPTR 9 1 O14787-2;O14787;A0A075B780;K7ENW1;K7ESC1;E7EW37;Q92973-2;Q92973 O14787-2;Q92973-2 TNPO2;TNPO1 Transportin-2;Transportin-1 0 ; 138.25 0.00012947 876670000 1750880 1412500 930870 1095500 1256220 1162050 1567640 1788670 1538530 FALSE TRUE 1519496.772 1403221.194 1381041.846 1344250.019 1231223.68 1206754.815 1415610.514 1406176.84 1356646.736 1.120038645 1.034330572 1.017981917 0.990862236 0.907549215 0.889512932 1.043462883 1.036509212 1 20.37161367 4.718262623 1.357062915 0.983237187 1.172512162 0.451929614 0.049225541 1.417366678 2.389283592 0.016271377 0.366123237 52271.21837 -4.718262623 0.189274975 LKSIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKSIFR 6 1 E9PGK7;O94759-3;O94759-2;O94759 E9PGK7 TRPM2 Transient receptor potential cation channel subfamily M member 2 0 117.7 0.020518 274050000 400550 343090 155920 231230 426780 366910 501690 547160 73522 FALSE TRUE 347616.3026 340836.2192 231323.4335 283734.3056 418287.913 381025.2651 453036.181 430154.092 64830.31292 5.361940842 5.257358848 3.568136927 4.376568504 6.452042172 5.877270184 6.988030146 6.635076597 1 15.98438092 7.749664719 13.67260129 5.254092731 4.74683575 0 1.778217928 0 0 0.396933254 0 56190735.76 -7.749664719 -0.507256981 LKTDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKTDLK 6 1 Q8IZT6;Q8IZT6-2;Q5VYL4 Q8IZT6 ASPM Abnormal spindle-like microcephaly-associated protein 0 ; 77.058 0.066961 1226310000 1090930 836620 593830 631130 745920 685230 1048730 1065330 968660 FALSE TRUE 946760.8364 831124.1881 881008.1742 774437.7127 731077.6514 711591.2415 947024.326 837517.4699 854146.1183 1.108429596 0.973046848 1.031449017 0.906680597 0.855916377 0.833102471 1.108738079 0.980531846 1 19.70412337 5.272894775 1.28854508 0.95766237 1.443538923 0.252499195 0.080725309 7.795762691 4.333689569 0.024593628 6.995307998 187454.0271 -5.272894775 0.485876554 LKTEEGEIDYS(ph)AEEGENRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKTEEGEIDYSAEEGENRR 19 2 C9IYN3;V9GYK2;Q8WVV9-4;Q8WVV9;B7WPG3;Q8WVV9-5;Q8WVV9-3;Q8WVV9-2 C9IYN3 HNRNPLL Heterogeneous nuclear ribonucleoprotein L-like 1 LKTEEGEIDYS(1)AEEGENRR 93.767 0.00088898 99034000 114810 76258 64939 65845 90019 77843 91171 110130 72180 TRUE FALSE 99637.56761 75757.05618 96343.71761 80796.11363 88227.79802 80837.67058 82329.25045 86579.55653 63646.96263 1.565472467 1.19026978 1.513720587 1.269441782 1.386205946 1.270094711 1.29352992 1.360309321 1 15.95780405 1.237400462 24.98936734 0.999999582 1.348675807 0.491081399 0.11371064 23.13746883 498151.3153 0.146008315 0.024387836 17.27430018 -1.237400462 0.348676226 LKTEGSDLCDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKTEGSDLCDR 11 1 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ; 106.58 0.0021092 675490000 1056390 975180 630090 887650 1325610 1090740 819680 1742860 689040 FALSE TRUE 916785.3849 968773.9784 934803.6315 1089204.499 1299232.955 1132701.474 740187.5598 1370162.952 607582.4762 1.508906891 1.594473206 1.53856253 1.792685836 2.138364758 1.864276075 1.218250343 2.255106106 1 19.21272073 1.209199218 24.66946687 0.999994827 1.745946025 0.368722817 0.303685777 3443.558607 2893089.836 8.18951109 0.073169473 16.18822449 -1.209199218 0.745951198 LKTEKEPDATPPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LKTEKEPDATPPSPR 15 2 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;A0A090HNM7 R4GMW8 BIVM-ERCC5;ERCC5;ERCC5-201 DNA repair protein complementing XP-G cells 1 LKTEKEPDATPPS(1)PR;LKTEKEPDATPPS(1)PR;LKTEKEPDATPPS(1)PR;LKTEKEPDATPPS(1)PR 150.69 1.64E-06 2415640000 6026200 4724840 3282010 3704580 4380230 3372740 6112000 7047900 2821190 TRUE FALSE 5229822.402 4693802.215 4869201.014 4545761.51 4293071.993 3502491.49 5519259.181 5540761.432 2487672.132 2.10229569 1.886825098 1.957332299 1.827315365 1.725738668 1.407939352 2.218644133 2.227287656 1 21.24636492 4.979275639 0.9468232 1.807099061 2.354584569 0.079111106 0.361739323 10.84200165 5.730728246 0.12253315 6.760077111 95340.10787 -4.979275639 0.547485507 LKTNILQYASTRPPTLS(ph)PIPHIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKTNILQYASTRPPTLSPIPHIPR 24 2 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 LKTNILQYASTRPPT(0.033)LS(0.967)PIPHIPR 156.92 9.77E-09 281330000 171910 180770 58220 82825 142220 127490 197000 231030 31323 TRUE FALSE 149191.6579 179582.51 86375.38673 101631.6822 139390.1002 132394.6228 177894.9703 181626.0324 27620.03062 5.401574675 6.501893949 3.127273388 3.679636838 5.04670332 4.793427806 6.44079555 6.57588092 1 14.7534273 4.278480657 24.99969244 4.700417916 5.951734637 0.113126202 1.649581672 413.9878189 259251.0648 0.420567609 1.112684174 18988.06272 -4.278480657 1.251316722 LKTS(ph)LGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKTSLGK 7 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 LKT(0.012)S(0.988)LGK 70.977 0.033651 479590000 467410 401260 278950 332570 363790 219450 432360 456460 487600 TRUE FALSE 405640.5842 398624.0966 413851.153 408085.1015 356551.2907 227892.3835 390429.7937 358849.5812 429956.4835 0.943445674 0.927126609 0.962541952 0.949131173 0.829272972 0.530035927 0.908068162 0.834618374 1 18.71383112 3.215371483 6.405304588 0.813607211 0.945739706 0.216836829 0.117992349 0.262554478 36.93389368 0.03639045 0.042691654 1641.993688 -3.215371483 0.132132495 LKVDSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKVDSFR 7 1 K7ESG5;K9J957;P61289;P61289-2;A0A087WTV2;K7ENH2;B7Z8D3 K7ESG5 PSME3 Proteasome activator complex subunit 3 0 ; 62.88 0.075507 2417700000 3851600 3649500 2509300 3317100 3985000 3280100 4106500 4852200 3902600 FALSE TRUE 3342601.301 3625526.194 3722805.873 4070298.254 3905706.297 3406287.57 3708252.262 3814594.79 3441239.074 0.971336553 1.053552548 1.081821342 1.182800197 1.134970925 0.989843337 1.077592164 1.108494559 1 21.71449669 4.681797976 2.495773281 1.086118882 0.954239963 0.271774839 0.056789051 0.610771821 5.237602932 0.014900667 0.161966121 48061.5725 -4.681797976 -0.131878919 LKVPEWVDTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKVPEWVDTVK 11 1 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ; 154.36 2.92E-05 4538400000 6736900 5435200 4072200 4983900 4878000 3826800 6937200 8086100 6435500 FALSE TRUE 5846601.596 5399495.813 6041529.541 6115570.669 4780937.344 3974019.472 6264431.412 6356950.441 5674702.521 1.030292174 0.951502884 1.064642511 1.07769009 0.842500083 0.700304458 1.103922433 1.1202262 1 22.43611333 LKVPPAINQFTQALDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LKVPPAINQFTQALDR 16 1 P62424;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 ; 253.1 1.38E-26 4165300000 1796930 1765910 1103110 1272380 1748030 1501080 1973090 2092040 1557050 FALSE TRUE 1559461.148 1754309.621 1636577.686 1561293.326 1713247.623 1558827.519 1781740.035 1644673.526 1372977.323 1.135824403 1.277741148 1.191991782 1.137158859 1.247833882 1.135362903 1.29771993 1.19788834 1 20.38887637 1.241504526 7.1765245 0.996220959 1.206493009 0.546949992 0.057925548 0.072007771 23.29361643 0.074432348 0.013145928 17.43831532 -1.241504526 0.21027205 LKVTELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKVTELR 7 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 83.206 0.020475 213450000 909650 758180 421840 532750 705440 608720 710990 864180 529610 FALSE TRUE 789437.4477 753199.4657 625843.235 653719.0301 691403.1242 632137.8523 642038.2992 679381.8321 467000.1091 1.690443819 1.612846445 1.340135094 1.39982629 1.480520263 1.353613928 1.374814024 1.454778744 1 18.83306336 7.999999994 0.043321072 2.37E-12 3.766066438 0.539871188 0.12471803 1388.216476 5.910376004 155.729148 420.6640915 99999998.55 -7.999999994 3.766066438 LKWGMEYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LKWGMEYK 8 1 P62306;A0A0B4J254;F8W0W6 P62306 SNRPF Small nuclear ribonucleoprotein F 0 111.65 0.0029114 981510000 1135400 1042500 692190 886370 1103100 970360 1262500 1278100 790130 FALSE TRUE 985354.0133 1035651.749 1026935.399 1087633.856 1081150.468 1007690.377 1140062.944 1004788.261 696721.7315 1.414271966 1.486463967 1.473953449 1.561073534 1.551767972 1.446331199 1.636324651 1.442165811 1 19.41022304 1.248376854 4.100442855 0.951890132 1.510689644 0.864580859 0.062907639 0.07212574 2.19187493 0.118257469 0.015256972 17.71645617 -1.248376854 0.558799512 LKYALTGDEVKK ddPTM_MDA-MB-175_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 69.03 0.028726 730700000 325850 288810 165520 147490 246560 197600 313390 335740 123060 FALSE TRUE 282788.0969 286912.7881 245566.0256 180979.8587 241653.9384 205201.7999 282997.486 263944.6137 108511.987 2.606053992 2.64406538 2.263031324 1.66783287 2.226979204 1.891051906 2.607983633 2.432400521 1 16.7274949 4.107369692 4.148660484 2.059872207 2.622537477 0.253506696 0.444519855 0.333287381 10.30316152 0.11587773 0.261602992 12804.70837 -4.107369692 0.56266527 LLAAGQLADALSQFHAAVDGDPDNYIAYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLAAGQLADALSQFHAAVDGDPDNYIAYYR 30 0 Q13217;X6R9L0 Q13217 DNAJC3 DnaJ homolog subfamily C member 3 0 ; 220.66 1.28E-34 534300000 201497 184110 87213 156748 187227 238590 179102 161583 145580 FALSE TRUE 174868.6609 182900.5693 129389.4985 192340.0291 183501.549 247768.7117 161732.7156 127029.7329 128369.6982 1.362226938 1.424795507 1.007944244 1.498328903 1.429477139 1.930118362 1.259897918 0.989561669 1 16.96994517 1.886783544 4.342288928 1.007118595 1.434717783 0.401371879 0.222054964 0.233696811 6.890285975 0.126660391 0.06208945 77.05193395 -1.886783544 0.427599189 LLAAVEAFYS(ph)PPSHDRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLAAVEAFYSPPSHDRPR 18 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 1 LLAAVEAFY(0.001)S(0.985)PPS(0.014)HDRPR;LLAAVEAFY(0.431)S(0.49)PPS(0.078)HDRPR;LLAAVEAFY(0.247)S(0.714)PPS(0.039)HDRPR 134.07 6.83E-06 386584000 317479 324678 224723 239750 291653 311381 295787 339203 295775 TRUE FALSE 275523.3458 322545.1688 333399.7945 294188.9018 285849.6759 323360.0286 267101.6223 266667.0781 260808.8164 1.056418834 1.23671114 1.278330231 1.127986798 1.09601232 1.239835497 1.024128041 1.0224619 1 17.99263311 2.22083018 24.14258753 1.017332245 1.174769299 0.542408042 0.06795936 122.8732309 167308.0288 0.027753415 0.018763559 166.2762343 -2.22083018 0.157437054 LLAAVEAFYSPPSHDRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLAAVEAFYSPPSHDRPR 18 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 113.69 0.0001441 812010000 1071500 1262700 800440 808020 1120700 1128400 1321800 1204300 1201700 FALSE TRUE 929898.5602 1254405.241 1187535.461 991493.2908 1098400.263 1171810.278 1193612.039 946769.8169 1059636.395 0.877563818 1.183807244 1.1207009 0.935691994 1.036582235 1.105860731 1.126435488 0.893485559 1 20.01513787 1.731410923 14.57843428 0.947527236 1.059326051 0.184383711 0.09454561 0.137285172 188.8278748 0.049110029 0.023395981 53.8779326 -1.731410923 0.111798815 LLACIASRPGQCGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLACIASRPGQCGR 14 1 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ; 210.38 4.86E-09 6214800000 1467200 1622690 601720 846470 1417560 1517040 1574850 1771570 467130 FALSE TRUE 1273305.803 1612030.443 892713.8046 1038673.951 1389353.329 1575401.51 1422121.289 1392733.542 411906.4236 3.091250172 3.913584131 2.167273326 2.521626009 3.372982915 3.824658758 3.452534867 3.381189178 1 18.6519571 4.266295788 24.99984818 2.946850655 3.502416528 0.088463307 0.837549716 649.2078327 585170.3606 0.209210378 0.553251691 18462.72445 -4.266295788 0.555565873 LLADQAEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLADQAEAR 9 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 112.01 0.004728 300030000 720800 670150 489750 528870 662150 578970 702060 834760 654660 FALSE TRUE 625544.4537 665747.7405 726594.7381 648958.0168 648974.5105 601243.3505 633974.3293 656253.0701 577266.8406 1.083631364 1.153275563 1.258680886 1.124190705 1.124219278 1.041534535 1.098234447 1.136827935 1 19.13887883 3.198445471 2.576830445 1.083207139 1.165263963 0.325050296 0.056535048 0.353445029 4.802485677 0.018368165 0.022610671 1579.23031 -3.198445471 0.082056824 LLALLSLGEVGHHIDLSGQLELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLALLSLGEVGHHIDLSGQLELK 23 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;; 250.83 1.18E-38 654382000 631871 565470 301784 496785 514432 444283 659306 738667 699119 FALSE TRUE 548367.6464 561755.3903 447727.7518 609587.6271 504195.8097 461374.8545 595366.6056 580708.8104 616469.9483 0.889528594 0.911245377 0.726276687 0.988835918 0.817875731 0.748414186 0.965767443 0.94199046 1 19.23367104 2.192492976 24.98444852 0.96342808 0.849580109 0.359250614 0.07676564 141.1289855 76539.23153 0.030313862 0.020437677 155.7732842 -2.192492976 -0.113847972 LLANQQVFHISCFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLANQQVFHISCFR 14 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ; 201.95 1.71E-08 1333370000 465450 596370 185903 276760 680600 714410 475910 571010 369290 FALSE TRUE 403939.6032 592452.4062 275806.3126 339602.588 667057.3916 741893.815 429756.3215 448903.9551 325632.9569 1.240475187 1.819387116 0.846985254 1.04289993 2.048494716 2.278313049 1.319756838 1.378558115 1 18.31288719 3.271868919 24.99893791 1.588986589 1.251115465 0.150779165 0.432012166 443.2050875 332636.6233 0.133633361 0.172509439 1870.117606 -3.271868919 -0.337871124 LLASS(ph)PALPSSGAQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLASSPALPSSGAQAR 16 0 Q9NYZ3 Q9NYZ3 GTSE1 G2 and S phase-expressed protein 1 1 LLAS(0.006)S(0.994)PALPSSGAQAR 123.02 9.46E-05 104440000 239400 280680 172270 182770 242120 282380 233220 268560 255850 TRUE FALSE 207762.6834 278836.1946 255580.3482 224270.722 237302.2857 293243.3413 210602.3603 211130.5339 225603.7045 0.920918759 1.235955745 1.132873012 0.994091487 1.051854562 1.299816162 0.933505772 0.935846929 1 17.78343123 LLAVAATAPPDAPNREEVFDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLAVAATAPPDAPNREEVFDER 22 1 P18206;P18206-2 P18206 VCL Vinculin 0 120.92 2.56E-05 123710000 61176 61205 49521 66678 57718 72389 60031 77827 159940 FALSE TRUE 53091.4366 60802.94032 73469.52124 81818.25901 56569.52472 75173.85167 54209.20286 61184.3017 141032.0754 0.376449375 0.431128452 0.520941928 0.580139367 0.401111056 0.533026629 0.384374992 0.433832527 1 17.10566379 1.236966953 24.99996192 1.000000667 0.458645961 0.864081928 0.067601435 14.36163459 225218.507 0.102408372 0.016593733 17.25706574 -1.236966953 -0.541354706 LLCEHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLCEHFR 7 0 Q13155;A8MU58;Q13155-2 Q13155 AIMP2 Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 0 ;; 160.03 0.0013616 1330040000 1113840 1681390 1050990 1101830 1640620 1824220 1428610 1565830 1725550 FALSE TRUE 966643.2219 1670344.838 1559252.279 1352017.342 1607974.872 1894398.924 1290063.622 1230989.44 1521557.445 0.635298539 1.097786248 1.024773849 0.888574629 1.056795376 1.245039371 0.847857323 0.809032511 1 20.53711737 LLCEQNEEEVSPQLFTFHEAVSQMVEMEEQVVEDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLCEQNEEEVSPQLFTFHEAVSQMVEMEEQVVEDHR 36 0 O00139-1;O00139-5;O00139;O00139-4;O00139-2 O00139-1 KIF2A Kinesin-like protein KIF2A 0 110.59 9.69E-06 48994000 4390.4 3297.8 2854.6 4428.7 5036.3 4928.5 4659.6 6041.4 5723.9 FALSE TRUE 3810.197516 3276.136535 4235.094108 5434.304023 4936.087483 5118.102584 4207.712709 4749.493624 5047.227063 0.754909076 0.649096324 0.83909324 1.076691014 0.977980071 1.014042467 0.833668202 0.941010493 1 12.30127528 4.012359987 5.042134115 0.963769386 0.707087377 0.739296441 0.066807835 0.089781141 6.611157035 0.017964791 0.036701981 10288.68775 -4.012359987 -0.256682009 LLCGLLAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLCGLLAER 9 0 P14174 P14174 MIF Macrophage migration inhibitory factor 0 ; 169.06 0.00013668 1406890000 987980 1103430 800260 1068670 1276690 1594560 1062640 1261570 1558620 FALSE TRUE 857415.9398 1096181.496 1187268.413 1311327.857 1251286.367 1655903.755 959585.3364 991793.073 1374361.719 0.62386483 0.797593152 0.863868948 0.954135901 0.910449083 1.204852938 0.698204354 0.721639041 1 20.39033033 4.678989492 1.849716196 0.893245009 0.558836634 0.291872347 0.141587242 1.109884745 4.336524656 0.040722616 0.617642171 47751.77193 -4.678989492 -0.334408374 LLDCLLESHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLDCLLESHR 10 0 Q9Y6D6;E5RIF2;E5RHL7;E5RHZ1 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 0 ;; 158.79 7.88E-06 472688000 663800 787800 490575 485459 766580 796160 732890 748920 766750 FALSE TRUE 576077.1481 782624.8899 727818.7109 595689.8857 751326.5578 826788.7904 661814.4406 588769.2861 676105.6885 0.852051917 1.157548152 1.076486596 0.881060307 1.111256081 1.222869153 0.978862406 0.870824334 1 19.36688926 2.006379672 24.99899703 0.925782719 1.055495805 0.146714144 0.116582888 248.2010895 972581.9256 0.046922487 0.031545561 101.4798163 -2.006379672 0.129713087 LLDDAMAADKSDEWFAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLDDAMAADKSDEWFAK 17 1 Q9HC38-2;F6TLX2;Q9HC38;I3L1I0 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 219.95 3.80E-15 683810000 853460 642370 582370 630790 520180 434910 751660 890520 847290 FALSE TRUE 740673.0986 638150.2292 864006.0799 774020.5105 509829.4357 451641.2691 678764.1289 700089.228 747124.3414 0.991365235 0.854141933 1.15644215 1.035999589 0.682389005 0.604506163 0.908502228 0.937045133 1 19.51098884 3.270479812 24.99973418 0.835359899 1.008888027 0.308081026 0.135912686 287.9047156 225490.7154 0.042985938 0.055489803 1864.145523 -3.270479812 0.173528128 LLDDLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LLDDLFR 7 0 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 ;;;;; 148.54 0.0048322 676210000 1890820 1831600 1150093 1371098 1768390 1851060 1660680 1975170 1776940 FALSE TRUE 1640943.346 1819568.099 1706281.822 1682426.757 1733202.499 1922271.476 1499627.509 1552795.266 1566872.177 1.047273268 1.161274114 1.088973208 1.073748568 1.106154365 1.226820862 0.957083501 0.991015916 1 20.57945606 2.21207119 24.99997819 0.98336492 1.115585651 0.614943856 0.050222638 141.9629048 133979.5221 0.019843281 0.013382698 162.956313 -2.21207119 0.132220731 LLDDVSFHPCIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLDDVSFHPCIR 12 0 Q9Y2T2 Q9Y2T2 AP3M1 AP-3 complex subunit mu-1 0 ; 131.12 0.00020444 632790000 520060 628240 242590 381150 635210 629390 575290 620970 574650 FALSE TRUE 451332.7533 624113.0501 359907.3354 467695.933 622570.5638 653603.0406 519498.4643 488180.3979 506715.5316 0.890702426 1.231683284 0.710274923 0.922995061 1.228639197 1.2898816 1.025227039 0.963421027 1 18.95081652 LLDEDEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLDEDEIR 8 0 O43719;Q5H919;Q5H918 O43719 HTATSF1 HIV Tat-specific factor 1 0 ; 127.56 0.0054546 0 527580 571800 311130 328200 447520 464150 424060 495830 660670 FALSE TRUE 457858.9663 568043.8082 461593.5087 402722.8262 438615.2276 482006.1508 382934.7265 389800.6131 582566.3452 0.785934461 0.975071445 0.792344962 0.691290923 0.752901762 0.827384134 0.657323805 0.669109392 1 19.15206283 4.014129043 23.28685816 0.750642726 0.88130445 0.147076716 0.107929928 157.4558148 259502.3932 0.026649423 0.055418951 10330.68318 -4.014129043 0.130661724 LLDEEEATDNDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LLDEEEATDNDLR 13 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;;;; 353.75 1.07E-75 3822350000 2462630 2441220 1528270 1795620 2304610 2285990 2262360 2558920 2448850 FALSE TRUE 2137187.206 2425183.465 2267346.484 2203342.965 2258752.77 2373933.515 2042956.675 2011714.872 2159349.743 0.989736477 1.123108229 1.050013548 1.020373366 1.046033778 1.099374255 0.946098094 0.93162994 1 21.0421655 2.22553033 24.99954192 0.952942299 1.055702176 0.549003545 0.040677264 152.4383279 292461.6136 0.015850544 0.010759417 168.0855306 -2.22553033 0.102759877 LLDEVFFSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLDEVFFSEK 10 0 P25789;H0YN18;H0YMZ1;H0YL69;H0YLC2;H0YMI6;H0YMA1;H0YKT8;H0YLS6 P25789 PSMA4 Proteasome subunit alpha type-4;Proteasome subunit alpha type;Proteasome subunit beta type 0 ; 175.73 6.31E-06 261138000 1001600 874660 672479 798180 767390 749600 1061650 1155480 1104600 FALSE TRUE 869236.0223 868914.3009 997692.0937 979418.9684 752120.4404 778437.5971 958691.3464 908389.594 974015.4464 0.892425295 0.892094991 1.024308287 1.005547676 0.772185332 0.799204571 0.984267087 0.932623397 1 19.89358513 LLDGNLLDGQAEVFGS(ph)DDDHIQFVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LLDGNLLDGQAEVFGSDDDHIQFVQK 26 0 Q9Y6Y0 Q9Y6Y0 IVNS1ABP Influenza virus NS1A-binding protein 1 LLDGNLLDGQAEVFGS(1)DDDHIQFVQK;LLDGNLLDGQAEVFGS(1)DDDHIQFVQK;LLDGNLLDGQAEVFGS(1)DDDHIQFVQK;LLDGNLLDGQAEVFGS(1)DDDHIQFVQK;LLDGNLLDGQAEVFGS(1)DDDHIQFVQK 277.38 7.14E-61 936944000 1027571 1035799 677924.7 971342 1113118 912449 1067798 1377124 1284849 TRUE FALSE 891774.8888 1028994.768 1005771.352 1191900.047 1090969.13 947551.5035 964243.1143 1082636.749 1132955.615 0.787122529 0.908239259 0.887741178 1.052027133 0.96294075 0.836353597 0.851086399 0.955586199 1 20.11165991 4.862195504 1.802061134 0.934158889 0.704723593 0.338603311 0.06492222 1.652941405 4.218710434 0.018326735 0.712047415 72810.74986 -4.862195504 -0.229435297 LLDHMAPPPVADQAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 LLDHMAPPPVADQASPR 17 0 A0A0C4DFS6;Q9C004 A0A0C4DFS6 SPRY4 Protein sprouty homolog 4 1 LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR 175.65 4.03E-09 8762490000 3369006 3611785 2368282 2933319 3693121 4074257 2871675 4117193 3998656 TRUE FALSE 2923783.321 3588058.947 3513591.097 3599373.912 3619635.118 4230996.303 2593180.4 3236763.317 3525939.443 0.829221082 1.017617859 0.996497856 1.020826923 1.026573251 1.199962839 0.735458008 0.917986077 1 21.74957627 2.228962569 24.99995858 0.885252274 1.015164346 0.243696306 0.108484015 287.6081619 749123.8652 0.043225811 0.029563736 169.4191775 -2.228962569 0.129912072 LLDIACWIHHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 151.15 1.94E-05 37658343000 7620043 8039480 5376457 6952787 7613344 7714088 8554857 9914320 8183503 FALSE TRUE 6613035.011 7986668.127 7976529.588 8531523.555 7461853.35 8010853.957 7725208.285 7794219.821 7216058.598 0.916433108 1.106790919 1.105385922 1.182296878 1.034062189 1.110142587 1.070557865 1.08012147 1 22.78277962 4.742484169 24.79175831 1.087690675 0.916433034 0.548692242 0.048360751 267.0558292 1687372.724 0.011491294 0.084706029 55269.32603 -4.742484169 -0.171257641 LLDILHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLDILHK 7 0 O00443 O00443 PIK3C2A Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha 0 81.958 0.043885 0 89681 92791 53624 75618 90265 83015 93611 108840 99841 FALSE TRUE 77829.42863 92181.44981 79556.74576 92788.22265 88468.9031 86208.64077 84532.61963 85565.41299 88037.91072 0.884044476 1.047065396 0.903664627 1.053957572 1.004895532 0.979221793 0.960184299 0.971915534 1 16.42583729 4.763169161 23.80966858 0.986703718 0.884044238 0.374499746 0.042879402 4239.134883 4101391.109 0.009666524 0.583485876 57965.44328 -4.763169161 -0.10265948 LLDLSDSTSVAS(ph)FPSADETDGNLPESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLDLSDSTSVASFPSADETDGNLPESR 27 0 Q13464 Q13464 ROCK1 Rho-associated protein kinase 1 1 LLDLSDSTS(0.005)VAS(0.995)FPSADETDGNLPESR;LLDLS(0.021)DS(0.019)T(0.019)S(0.079)VAS(0.853)FPS(0.009)ADET(0.001)DGNLPESR 147.3 8.76E-08 135948000 133421 131780 87764 99248 141536 162331 167256 167333 118123 TRUE FALSE 115789.0768 130914.3285 130206.964 121783.7753 138719.7105 168575.9786 151035.5389 131550.1401 104158.6335 1.111660867 1.256874482 1.250083258 1.169214411 1.331811928 1.618454207 1.450052999 1.262978744 1 16.6684229 3.188868333 7.454280463 1.347676836 1.20515387 0.148647454 0.158732613 0.45233093 56.49782101 0.051155835 0.058493846 1544.786029 -3.188868333 -0.142522966 LLDPEDISVDHPDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LLDPEDISVDHPDEK 15 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;;; 258.91 7.70E-25 1219961000 1486080 1294350 877253 1160705 1243020 1070077 1458000 1656370 1565260 FALSE TRUE 1289690.763 1285847.33 1301495.485 1424260.811 1218286.334 1111243.555 1316603.384 1302168.165 1380216.746 0.934411763 0.931627104 0.942964566 1.031910977 0.882677549 0.805122498 0.9539106 0.943451939 1 20.39646341 1.258070102 2.036433098 1.02003192 0.925270066 0.144232349 0.056618205 1.591146757 6.740738885 0.281420706 0.016255831 18.11632495 -1.258070102 -0.094761854 LLDPSS(ph)PLALALSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLDPSSPLALALSAR 15 0 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;A0A590UJF3 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 LLDPS(0.334)S(0.666)PLALALSAR 83.633 0.0090617 53593000 144850 174090 105450 125940 164160 168140 143070 182540 150010 TRUE FALSE 125707.7055 172946.3913 156445.9727 154536.6019 160893.5372 174608.4546 129195.0934 143505.2415 132275.9887 0.950344101 1.307466253 1.182723896 1.168289146 1.216347266 1.32003137 0.976708583 1.084892602 1 17.01319168 2.223027273 24.98957685 1.032115762 1.195928774 0.373509439 0.103492333 246.9471986 397278.0335 0.039493851 0.026732712 167.1195559 -2.223027273 0.163813012 LLDSDQELYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLDSDQELYR 10 0 P25098 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 0 242.83 5.95E-06 0 217300 229330 138540 165380 213350 234780 210760 246140 223290 FALSE TRUE 188583.2544 227823.5161 205538.4074 202932.0567 209104.7524 243812.1385 190320.5276 193504.8765 196892.9106 0.957796062 1.157093546 1.04390964 1.030672237 1.062022761 1.238298209 0.966619504 0.982792503 1 17.58705164 LLDSSTVTHLFK ddPTM_MDA-MB-175_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 ; 237.49 4.17E-16 4873100000 10778400 9395200 5571200 8452900 9569100 8250300 10327800 11892600 11922100 FALSE TRUE 9354007.131 9333482.313 8265450.955 10372260.14 9378693.632 8567694.38 9326211.546 9349460.038 10512682.92 0.889783056 0.887830669 0.786236113 0.986642536 0.892131314 0.814986473 0.887139051 0.889350522 1 23.32562757 1.204554539 3.182610146 1.027716745 0.877479558 0.345168845 0.052434282 0.487385791 6.10806657 0.193486274 0.013145773 16.01601766 -1.204554539 -0.150237187 LLDSVEQDFHLEIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLDSVEQDFHLEIAK 15 0 Q6IBS0;H0Y858;H7C5I2;Q9NR96-4 Q6IBS0 TWF2 Twinfilin-2 0 ; 171.91 1.06E-06 87523000 257070 208146 136012 179075 189943 179554 221071 257220 242850 FALSE TRUE 223097.5482 206778.6752 201787.8581 219736.7157 186163.5059 186461.5586 199631.5684 202215.5047 214140.5497 1.041827662 0.965621297 0.942315028 1.026133145 0.869351957 0.870743812 0.932245522 0.944312065 1 17.70819848 3.24783947 24.99937208 0.923992613 0.988259117 0.36568191 0.045954717 252.4210085 680076.9633 0.013887646 0.017681229 1769.454787 -3.24783947 0.064266503 LLDTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLDTLR 6 0 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;E9PPF6;G3V200;O75334-2;O75334-4;O75334-3;O75334;E9PID5;F8VWR9;A0A3B3ITS2;F8VU88 Q13136-2 PPFIA1;PPFIA2 Liprin-alpha-1;Liprin-alpha-2 0 105.22 0.077156 54398000 117440 118360 82933 90470 123570 125910 116640 126570 121260 FALSE TRUE 101920.0064 117582.4854 123039.6762 111012.5962 121111.1988 130753.8392 105328.2708 99503.99047 106924.7809 0.953193502 1.099674784 1.150712446 1.038230757 1.132676613 1.222858144 0.985068848 0.93059803 1 16.70623673 2.026683957 24.64308132 0.959589224 1.100885914 0.413057365 0.071944624 157.6695054 145609.6949 0.029079343 0.019604668 106.3368905 -2.026683957 0.14129669 LLDTVDDMLANDIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLDTVDDMLANDIAR 15 0 A0A024R571;Q9H4M9;C9J2Z4 A0A024R571 EHD1 EH domain-containing protein 1 0 ;; 150.68 7.30E-06 50244100 87584 74794 51198 57897 70396 76534 67731 80090 85167 FALSE TRUE 76009.55249 74302.67329 75957.52405 71043.39875 68995.25733 79478.3125 61162.45804 62963.37676 75098.65428 1.012129355 0.989400862 1.011436553 0.946000956 0.918728278 1.058318731 0.81442815 0.838408855 1 16.19649944 2.2336953 24.99995864 0.871812272 0.98516413 0.390409946 0.06107849 113.0987758 581139.0478 0.024165899 0.01687881 171.2755222 -2.2336953 0.113351858 LLDVVHPAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLDVVHPAAK 10 0 Q99832-3;Q99832;F8WAM2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 122.26 0.00049332 1790650000 6122200 5546400 3470300 4526500 5079500 4767800 5954000 6787900 6416300 FALSE TRUE 5313135.758 5509965.333 5148548.687 5554311.008 4978427.888 4951220.351 5376581.996 5336360.408 5657772.323 0.939086173 0.973875409 0.909995736 0.981713418 0.879927223 0.875118345 0.950300169 0.943191084 1 22.43180269 1.119047551 1.812310673 1.042496319 0.92900773 0.281971528 0.034958509 1.77367593 4.217123448 0.387653914 0.009821095 13.15368844 -1.119047551 -0.113488589 LLDWLVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLDWLVDR 8 0 J3QQY1;Q96JB5;J3KRI2;J3KRK4;J3KS63;J3QS62;Q96JB5-4;J3QL95 J3QQY1 CDK5RAP3 CDK5 regulatory subunit-associated protein 3 0 ; 122.74 0.0032044 146496000 374670 366260 247250 352170 375330 406170 277376 390790 546760 FALSE TRUE 325156.4102 363854.0139 366820.927 432135.5811 367861.6673 421795.6227 250476.1182 307222.5996 482122.6557 0.674426738 0.754691798 0.760845653 0.89631876 0.763004316 0.874872022 0.519527791 0.637229128 1 18.8790407 LLDWLVDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLDWLVDRR 9 1 J3QQY1;Q96JB5;J3KRI2;J3KRK4;J3KS63;J3QS62;Q96JB5-4;J3QL95 J3QQY1 CDK5RAP3 CDK5 regulatory subunit-associated protein 3 0 ; 166.09 9.78E-05 116400000 516500 529100 264610 326870 517270 548510 352100 521210 158130 FALSE TRUE 448243.2164 525624.3073 392576.2811 401090.8294 506977.339 569611.5346 317953.3962 409753.2976 139436.0515 3.214686671 3.769644231 2.815457529 2.87652171 3.635912904 4.08510947 2.280281123 2.938646735 1 17.0892441 1.158683201 1.490379934 5.13E-16 3.311067453 0.644646037 0.517206156 0.954694362 1.616106755 5.031932521 0.14720441 14.41063775 -1.158683201 3.311067453 LLDYTEKPLYENLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLDYTEKPLYENLR 14 1 Q99986;H0YJ50;H0YJJ9 Q99986 VRK1 Serine/threonine-protein kinase VRK1 0 92.063 0.0046581 635480000 199340 186380 135830 157660 211870 158860 201350 236280 231160 FALSE TRUE 172996.7139 185155.6575 201517.8423 193459.1127 207654.2015 164971.447 181823.108 185753.3607 203832.5281 0.848719856 0.908371491 0.988644178 0.949108145 1.018749085 0.80934799 0.892022042 0.911303816 1 17.63702477 4.656354933 3.841455604 0.932922087 0.846431747 0.176397051 0.060343586 0.430068116 10.62396276 0.015193537 0.086081263 45326.78678 -4.656354933 -0.086490341 LLEAAEQLAQTGECDPEEIYQAAHQLEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLEAAEQLAQTGECDPEEIYQAAHQLEDR 29 0 O75962-5;O75962;E7EPJ7;O75962-4;O75962-2;E7EWP2;F5H228 O75962-5 TRIO Triple functional domain protein 0 152.21 2.84E-08 13868000 7234.7 11241 3947.2 3678.5 9222.7 7988.1 9205.1 10226 5366 FALSE TRUE 6278.616065 11167.15713 5856.079123 4513.759647 9039.186314 8295.407376 8312.390819 8039.249479 4731.637593 1.326943567 2.360104068 1.237643207 0.953952952 1.91037165 1.753178939 1.756768276 1.699041679 1 12.20812386 1.235163121 24.85317502 0.999999039 1.637280611 0.203679366 0.387518103 150.0966674 1097784.481 0.657314854 0.093124431 17.18553754 -1.235163121 0.637281572 LLEAFTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLEAFTER 8 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 0 ; 119.27 0.0040145 63615000 72349 71829 48637 49102 64941 78823 72135 70922 77800 FALSE TRUE 62787.89634 71357.15057 72158.01588 60251.35958 63648.80115 81855.37182 65139.3588 55755.88222 68602.57263 0.915241134 1.040152692 1.051826675 0.878266766 0.927790296 1.193182248 0.949517727 0.812737483 1 16.06597506 1.997815864 24.99644973 0.889433257 1.002504817 0.134911445 0.098289505 128.6332764 1472152.714 0.040358909 0.026727965 99.49834652 -1.997815864 0.113071561 LLEAHEEQNVDSYTESVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLEAHEEQNVDSYTESVK 18 0 P54920;M0R0Y2;M0R213 P54920 NAPA Alpha-soluble NSF attachment protein 0 ; 270.95 6.05E-39 353830000 586020 430750 381000 492590 445880 386780 499270 638480 879040 FALSE TRUE 508575.9722 427920.3749 565252.8744 604440.0883 437007.8603 401659.6769 450850.8722 501946.0207 775120.8926 0.656124712 0.552069205 0.729244792 0.779801053 0.563793164 0.518189718 0.581652329 0.64757127 1 19.56406181 1.239337834 5.276045918 1.020402062 0.625613558 0.679074958 0.080382323 0.100310009 7.934803136 0.144541196 0.021379057 17.35153232 -1.239337834 -0.394788503 LLEAHEEQNVDSYTESVKEYDSISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLEAHEEQNVDSYTESVKEYDSISR 25 1 P54920;M0R0Y2;M0R213 P54920 NAPA Alpha-soluble NSF attachment protein 0 220.49 7.38E-34 153650000 211520 171710 79296 81461 150170 153130 226160 225000 34637 FALSE TRUE 183567.0961 170582.0257 117643.8108 99957.9651 147181.9108 159021.0102 204227.038 176885.501 30542.25332 6.010266962 5.585115935 3.851837964 3.272776375 4.81896045 5.206590638 6.686705001 5.791501338 1 14.89851888 4.413103095 7.331263654 4.633282325 5.907244179 0.113284294 1.549051273 0.507863059 47.91841768 0.398656241 1.072971754 25888.27389 -4.413103095 1.273961854 LLEAQIATGGIIDPEESHR ddPTM_MDA-MB-175_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 0 169.59 1.07E-14 0 149690 136790 104830 128880 132610 155430 135120 159090 265080 FALSE TRUE 129908.0872 135891.4175 155526.1386 158144.1738 129971.3204 161409.4927 122016.0832 125069.8415 233742.5444 0.55577425 0.581372201 0.665373687 0.676574195 0.556044775 0.690543919 0.522010589 0.535075212 1 17.83456082 1.233179059 24.99683497 1.000000634 0.596995114 0.814049558 0.060403088 75.16771792 349108.3538 0.129359412 0.015416475 17.10720496 -1.233179059 -0.40300552 LLEAQIATGGIIDPEESHRLPVEVAYK ddPTM_MDA-MB-175_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 0 169.7 3.62E-12 494870000 148890 135310 128770 126710 128720 129700 147420 169390 165160 FALSE TRUE 129213.8093 134421.1397 191043.6027 155481.4421 126158.7238 134689.6429 133123.2311 133167.2667 145634.973 0.887244366 0.92300041 1.311797564 1.067610609 0.866266675 0.924844082 0.914088343 0.914390713 1 17.15199732 3.25088317 24.68963409 0.922036142 1.057411244 0.216474467 0.11602566 296.4386849 593944.5887 0.034706393 0.044464113 1781.899352 -3.25088317 0.135375102 LLEAQIATGGIIDPVHSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLEAQIATGGIIDPVHSHR 19 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 Q15149-3;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 PLEC;EPPK1 Plectin;Epiplakin 0 ; 155.94 1.21E-08 162469000 222730 212126 138824 152885 191827 236750 212000 238400 218210 FALSE TRUE 193295.6662 210732.5303 205959.7507 187599.876 188010.018 245857.9257 191440.2726 187420.0152 192413.4624 1.004584938 1.095206789 1.070401978 0.97498311 0.977114676 1.277758441 0.994942195 0.974048348 1 17.55385022 2.03416451 24.99997499 0.984967142 1.066273163 0.152666198 0.085643952 321.5131808 235266.9065 0.034904861 0.023532754 108.1843675 -2.03416451 0.081306022 LLEAQIATGGVIDPVHSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 195.96 4.96E-16 1357722000 1054328 985679 726829 847570 971594 1069070 982913 1098536 1067162 FALSE TRUE 914995.8835 979204.0097 1078325.935 1040023.723 952261.1803 1110197.815 887590.2485 863622.6252 941003.3241 0.97236201 1.040595697 1.145932122 1.105228532 1.011963673 1.179802224 0.943238165 0.917767879 1 19.84384029 2.202405084 24.99393891 0.945754561 1.075971496 0.44995211 0.063549474 144.6798456 100014.6355 0.025496441 0.017190324 159.3694536 -2.202405084 0.130216935 LLEAQSHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLEAQSHFR 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3;A0A1B0GUH3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 227.08 2.13E-07 549420000 484820 515330 345540 459740 454450 570490 411310 528280 1001260 FALSE TRUE 420749.8086 511944.7633 512644.2998 564130.9937 445407.3341 592437.1195 371421.2195 415311.4331 882892.1834 0.476558539 0.579849695 0.580642019 0.638957966 0.504486666 0.671018648 0.42068695 0.470398811 1 19.75187774 1.233096989 24.99999171 1.000000723 0.541855662 0.773153879 0.077823168 85.57078751 391504.6004 0.165000887 0.019533581 17.10397246 -1.233096989 -0.458145061 LLEASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 122.98 0.044171 3799810000 3214520 3296470 2319330 2587590 3083040 3560740 3406950 3484820 3651450 FALSE TRUE 2789713.037 3274815.272 3440965.746 3175141.858 3021693.536 3697723.972 3076544.513 2739618.362 3219779.741 0.866429775 1.017092949 1.068696005 0.986136355 0.938478337 1.148440039 0.955513967 0.850871358 1 21.61853057 2.002956682 24.9988129 0.911306325 1.007924082 0.13690789 0.081893588 128.4576531 1086105.248 0.032453206 0.02174881 100.6831239 -2.002956682 0.096617757 LLECPHLNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLECPHLNVR 10 0 Q8TEX9;Q8TEX9-2;H0YN14;H0YMR4 Q8TEX9 IPO4 Importin-4 0 ; 195.36 3.63E-07 671580000 655850 604490 442530 530150 693110 682100 497010 662480 836550 FALSE TRUE 569177.7608 600519.0654 656538.9882 650528.6603 679318.467 708340.8284 448810.0467 520813.8074 737654.012 0.771605321 0.814093133 0.890036491 0.881888595 0.920917471 0.960261609 0.608428937 0.706040771 1 19.49258477 1.214191774 24.37426786 1.000001119 0.815584976 0.226693135 0.104783093 2889.937082 2890369.794 1.763115356 0.02866855 16.37539462 -1.214191774 -0.184416143 LLEDFGDGGAFPEIHVAQYPLDMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LLEDFGDGGAFPEIHVAQYPLDMGR 25 0 Q13573;G3V3A4;G3V5R3 Q13573 SNW1 SNW domain-containing protein 1 0 ;;;; 161.16 2.11E-11 624361000 665458 600477 390994 453222 542554 575646 552102 638145 552115 FALSE TRUE 577516.0392 596532.427 580080.0062 556132.9822 531758.2369 597791.4741 498559.233 501682.6578 486844.5937 1.186243098 1.225303587 1.191509598 1.142321368 1.092254579 1.227889725 1.024062379 1.03047803 1 18.8931018 1.497474262 0.439627054 0.853348626 1.212053816 0.681014713 0.047975112 2.685915463 0.546361435 0.512980382 0.055710064 31.4394009 -1.497474262 0.35870519 LLEDGEDFNLGDALDS(ph)SNSMQTIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLEDGEDFNLGDALDSSNSMQTIQK 25 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 LLEDGEDFNLGDALDS(0.33)S(0.33)NS(0.33)MQT(0.01)IQK 79.762 0.015724 14974000 14831 13101 6742.8 10024 10246 8667.2 12875 15010 16973 TRUE FALSE 12871.04577 13014.93867 10003.64063 12300.10241 10042.12465 9000.632792 11626.38448 11800.22831 14966.47128 0.859992014 0.869606364 0.668403423 0.821843852 0.670974772 0.601386434 0.776828704 0.788444256 1 13.86944649 1.16669253 2.365308547 1.102144819 0.748396658 0.441266648 0.086580439 0.755973196 3.781783611 0.603992675 0.023849101 14.67886681 -1.16669253 -0.353748161 LLEDGEDFNLGDALDSSNS(ph)MQTIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLEDGEDFNLGDALDSSNSMQTIQK 25 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 LLEDGEDFNLGDALDS(0.299)S(0.299)NS(0.4)MQT(0.002)IQK 110.94 0.0017463 22621000 24701 22988 14240 16730 19266 15803 22752 25742 31732 TRUE FALSE 21436.70027 22836.99031 21126.51163 20528.8022 18882.64429 16410.95164 20545.51454 20237.27362 27980.67911 0.766125089 0.81616998 0.755039274 0.733677768 0.674845818 0.586510126 0.73427505 0.723258844 1 14.77214336 1.238471124 10.16547799 1.001045306 0.722502137 0.674292719 0.06033593 0.048055103 113.9132206 0.091434442 0.0162098 17.31693888 -1.238471124 -0.27854317 LLEDGEDFNLGDALDSSNSMQTIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LLEDGEDFNLGDALDSSNSMQTIQK 25 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;; 356.9 3.24E-103 322589000 273323 253026 202640 230395 232173 205218 291095 337482 367284 FALSE TRUE 237202.673 251363.8555 300637.3818 282709.7061 227553.2115 213112.8693 262864.6517 265314.1006 323864.1039 0.732414214 0.776139907 0.928282505 0.872926955 0.702619428 0.658031769 0.811651086 0.819214286 1 18.30502905 1.159259943 2.306108848 1.093019613 0.78461071 0.428732585 0.078026444 0.889679796 4.097865252 0.613316071 0.022598841 14.42978776 -1.159259943 -0.308408903 LLEDS(ph)EES(ph)SEETVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LLEDSEESSEETVSR 15 0 O60231;A0A140T947;A2AB15 O60231 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 2 LLEDS(1)EES(0.986)S(0.014)EETVSR;LLEDS(1)EES(0.994)S(0.006)EETVSR;LLEDS(1)EES(0.961)S(0.039)EETVSR;LLEDS(1)EES(0.989)S(0.011)EETVSR 308.42 6.32E-56 2544830000 3965760 3537780 2406170 2765410 3379850 3708480 3703140 3764870 3771340 TRUE FALSE 3441674.768 3514540.09 3569801.86 3393338.607 3312597.598 3851147.625 3344010.053 2959781.849 3325496.482 1.034935622 1.056846732 1.073464332 1.020400601 0.996121216 1.158066967 1.00556716 0.890027058 1 21.66513831 1.995330277 24.99347114 0.940349942 1.055415561 0.46359682 0.049572544 145.5268425 778895.2086 0.019815748 0.012970236 98.93051652 -1.995330277 0.115065619 LLEEALLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LLEEALLR 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 146.54 0.0012834 213411000 440415 407622 248045 296926 410755 358520 430509 458963 422937 FALSE TRUE 382213.0419 404944.3042 368000.3917 364347.5865 402581.7791 372312.4964 388758.3034 360817.3341 372937.8697 1.024870556 1.085822431 0.986760588 0.976965914 1.079487528 0.998323117 1.042421098 0.967499853 1 18.50857578 -1.999999997 0.261230297 0.64242185 1.040975798 0.119404575 0.038240163 157.8974745 2.542813303 27.31980592 0.109082647 0.01 1.999999997 0.398553948 LLEEGVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLEEGVLR 8 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 107.66 0.0092114 97490000 113400 111640 74108 84137 117580 118020 102280 123060 114390 FALSE TRUE 98413.90268 110906.6295 109946.8767 103241.5918 115240.388 122560.3058 92360.90134 96744.57665 100866.9445 0.975680419 1.099533946 1.090018908 1.023542374 1.142499048 1.215069083 0.915670657 0.959130636 1 16.62209394 2.213234064 24.99999372 0.956672116 1.09066486 0.471415252 0.066276903 197.1820543 194638.1254 0.027327313 0.018432153 163.3932321 -2.213234064 0.133992744 LLEEHAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLEEHAK 7 0 P51572;P51572-2;A0A2R8Y5M6 P51572 BCAP31 B-cell receptor-associated protein 31 0 ;; 112.17 0.0064142 946370000 2060650 1696940 1340380 2051340 2192640 2067600 1521130 3080800 2585130 FALSE TRUE 1788329.881 1685792.689 1988592.251 2517128.1 2149010.754 2147141.91 1373611.047 2421994.895 2279518.876 0.78452076 0.739538815 0.872373671 1.104236568 0.942747514 0.941927673 0.602588143 1.062502671 1 21.12029793 4.074693898 5.052122622 0.937386179 0.765779921 0.232654747 0.133723212 0.306953968 14.24907402 0.035131938 0.075772164 11876.64835 -4.074693898 -0.171606258 LLEEHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLEEHSR 7 0 P30038-2;P30038;P30038-3 P30038-2 ALDH4A1 "Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial" 0 147.16 0.0021705 253610000 365830 389640 268090 462210 456580 486230 326300 434100 404010 FALSE TRUE 317484.6386 387080.4292 397739.2207 567161.8449 447494.9513 504935.5827 294655.4762 341271.0932 356248.398 0.891188958 1.086546441 1.116465991 1.592040408 1.256131827 1.417369413 0.82710681 0.957958253 1 18.442524 2.229041138 24.99866054 0.930303664 1.233200635 0.348863766 0.191945742 231.7241875 608514.2041 0.081566695 0.055793804 169.4498302 -2.229041138 0.302896971 LLEELEEGQK ddPTM_MDA-MB-175_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 ;; 168.8 1.12E-05 205534000 359625 297873 249117 273007 262425 247774 318938 374734 426533 FALSE TRUE 312099.6451 295916.2526 369590.8144 334997.412 257203.2559 257306.0261 288007.4418 294600.0503 376108.7546 0.829812232 0.78678374 0.982670065 0.890692939 0.683853414 0.68412666 0.765755751 0.783284214 1 18.52079036 3.275844589 24.99392742 0.777101425 0.874237992 0.163978401 0.099353706 302.1868986 202574.0298 0.029486104 0.038065469 1887.31586 -3.275844589 0.097136567 LLEELEEGQKGVGDGTVSWGLEDDEDMTLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 185.02 2.13E-18 68755000 61447 51643 16828.5 20104.3 47021 37130 61567 70861 3747.05 FALSE TRUE 53326.62326 51303.75373 24966.81889 24669.28859 46085.3741 38558.41513 55596.24182 55707.92659 3304.078018 16.13963804 15.52740385 7.556364818 7.466315401 13.94802842 11.66994693 16.82655238 16.86035448 1 11.69003204 7.999998852 0.023572648 5.15E-07 28.61922933 0.034964866 5.08966619 44461.42276 104.085032 48128.7062 82765.84265 99999735.66 -7.999998852 28.61922881 LLEENETEAVTVPTPS(ph)PTPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 LLEENETEAVTVPTPSPTPVR 21 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 LLEENETEAVTVPTPS(0.999)PT(0.001)PVR;LLEENETEAVTVPT(0.008)PS(0.991)PT(0.001)PVR;LLEENETEAVTVPTPS(0.998)PT(0.002)PVR;LLEENETEAVTVPTPS(0.998)PT(0.002)PVR;LLEENETEAVTVPTPS(0.998)PT(0.002)PVR;LLEENETEAVTVPT(0.004)PS(0.979)PT(0.018)PVR;LLEENETEAVTVPTPS(0.925)PT(0.075)PVR;LLEENETEAVTVPTPS(0.999)PT(0.001)PVR;LLEENETEAVTVPTPS(0.997)PT(0.003)PVR;LLEENETEAVTVPTPS(1)PTPVR 343.72 4.62E-81 7972380000 4998680 5235020 3451300 4032700 5076090 5373660 4629440 5760580 5035080 TRUE FALSE 4338091.773 5200630.809 5120360.224 4948386.171 4975085.74 5580388.177 4180477.621 4528724.796 4439838.578 0.97708322 1.171355831 1.153276213 1.11454191 1.120555546 1.25688988 0.941583246 1.020020146 1 22.08207579 2.218851108 24.99994134 0.992137665 1.133674456 0.480406583 0.071055682 202.4130217 256742.8508 0.027645862 0.018667147 165.5202404 -2.218851108 0.141536791 LLEFVPHHCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLEFVPHHCR 10 0 Q14746-2;Q14746;B7Z2Y2 Q14746-2 COG2 Conserved oligomeric Golgi complex subunit 2 0 98.249 0.0031839 135370000 83862 99141 57511 67454 84269 89890 79280 87231 83019 FALSE TRUE 72779.42422 98489.73624 85323.51196 82770.46167 82592.21177 93348.12647 71591.4378 68577.32948 73204.5884 0.99419211 1.345403866 1.165548688 1.130673138 1.128238183 1.275167698 0.977963805 0.936790043 1 16.15964646 2.176679241 8.785438684 0.963529231 1.176565854 0.508811567 0.093254555 0.215406366 28.02943667 0.035628481 0.024032576 150.2032194 -2.176679241 0.213036622 LLEFYDATAHFAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLEFYDATAHFAK 13 0 P83436 P83436 COG7 Conserved oligomeric Golgi complex subunit 7 0 187.44 6.96E-06 561550000 620520 567290 402190 397940 582120 462750 593330 661120 661750 FALSE TRUE 538516.7098 563563.4346 596690.4292 488298.3591 570536.9509 480552.2919 535788.9479 519744.6328 583518.6689 0.922878287 0.965801892 1.022572989 0.836817029 0.977752695 0.823542275 0.918203609 0.890707805 1 19.15441929 3.747844979 24.99843464 0.906101671 0.969956134 0.2015629 0.058644625 1017.646823 2740038.536 0.014530013 0.024726864 5595.578318 -3.747844979 0.063854462 LLEGEEER ddPTM_MDA-MB-175_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 ;;;;; 198.92 0.00030729 10052670000 6923540 6305870 3904340 4891620 5873340 6054260 6043880 6953700 6845260 FALSE TRUE 6008576.647 6264446.325 5792491.883 6002337.085 5756472.025 6287171.3 5457745.448 5466705.369 6036021.161 0.995453211 1.037843665 0.959654005 0.99441949 0.953686522 1.041608558 0.904195877 0.905680286 1 22.52516643 2.226695044 24.99963408 0.928827258 0.995163642 0.350671995 0.038251645 217.3414125 457913.7401 0.01509167 0.010266736 168.5369166 -2.226695044 0.066336384 LLEIVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LLEIVER 7 0 Q12792;Q12792-3;Q12792-4 Q12792 TWF1 Twinfilin-1 0 ;;; 130.04 0.0083798 331100000 670530 685050 458505 511259 671315 712210 623230 705400 757630 FALSE TRUE 581917.7616 680549.8614 680239.5516 627348.1701 657957.1449 739609.1796 562789.2505 554555.6994 668063.8445 0.871051122 1.018689856 1.018225365 0.939054216 0.984871656 1.107093559 0.842418363 0.830093866 1 19.34962646 2.20601937 24.99998434 0.876164996 0.989900056 0.272120445 0.075053831 215.5465276 165593.2886 0.029890284 0.02015359 160.7012925 -2.20601937 0.11373506 LLEKPYVR ddPTM_MDA-MB-175_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 78.934 0.026759 397760000 488790 457430 333920 371140 434100 396230 554660 600060 468230 FALSE TRUE 424195.1631 454425.1122 495404.8289 455413.0095 425462.2593 411473.2245 500869.1586 471741.8387 412876.3828 1.027414453 1.100632371 1.199886575 1.103025091 1.030483401 0.996601505 1.213121359 1.142574045 1 18.65535037 4.732681402 6.436910418 1.105277875 1.025968304 0.074917636 0.074888018 0.3019797 74.32042197 0.01884334 0.105037315 54035.77716 -4.732681402 -0.07930957 LLELDPEHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLELDPEHQR 10 0 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ; 135.55 0.00014123 166964000 297212 269370 187716 239804 248973 320079 237035 223093 298290 FALSE TRUE 257934.6812 267600.4907 278496.0855 294255.1634 244018.9244 332392.6462 214047.3822 175386.2981 263026.496 0.980641438 1.017389863 1.058813807 1.118728219 0.927735145 1.263723052 0.813786388 0.666800876 1 18.00484861 2.106126505 9.540872662 0.788995673 1.055388338 0.448414889 0.120296526 0.213550125 17.6062328 0.046233703 0.031153177 127.6810675 -2.106126505 0.266392665 LLELFPVNR ddPTM_MDA-MB-175_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 0.016774 0 85281 81583 57429 61159 81979 101200 83617 85928 84099 FALSE TRUE 74010.89978 81047.0759 85201.85649 75046.08571 80347.77829 105093.2295 75507.83621 67552.96589 74156.91203 0.998031037 1.092913306 1.148940189 1.011990436 1.083483334 1.417173755 1.018217104 0.910946317 1 16.17829355 2.008971319 24.9999772 0.953752977 1.126263086 0.27899222 0.116217458 231.1900125 644244.4795 0.047939942 0.032271413 102.0872062 -2.008971319 0.172510109 LLELLGHYQESGSVIIFVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLELLGHYQESGSVIIFVDK 20 0 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ; 112.56 0.00015168 23279800 75314 64718 47394 68408 54786 47977 65149 85708 119190 FALSE TRUE 65361.06408 64292.8632 70313.89692 83941.08195 53695.86579 49822.70624 58830.86001 67380.01118 105099.494 0.621897039 0.611733328 0.669022221 0.798682075 0.510905084 0.47405277 0.559763494 0.641106904 1 16.6813962 1.239325089 4.515529521 1.032523897 0.607423847 0.659559943 0.088187244 0.133681959 5.760724021 0.182389254 0.023890489 17.35102314 -1.239325089 -0.42510005 LLELLGHYQESGSVIIFVDKQEHADGLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLELLGHYQESGSVIIFVDKQEHADGLLK 29 1 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 176.97 8.80E-18 55739000 118650 81287 42796 50275 64840 41117 112100 118770 24652 FALSE TRUE 102970.1019 80753.02034 63492.28874 61690.70716 63549.81086 42698.7976 101228.5593 93371.95977 21737.66864 4.73694321 3.714888734 2.920841687 2.837963361 2.923487882 1.964276772 4.656826862 4.295398982 1 14.4079096 4.616858283 2.659099645 3.118172696 4.857825829 0.22575294 1.040922264 0.63267486 6.882709794 0.274591425 2.128752182 41386.46023 -4.616858283 1.739653133 LLEMNLMHAPQVADAILGNQMFTHYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LLEMNLMHAPQVADAILGNQMFTHYDR 27 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;; 237.13 2.73E-45 9083940000 2578850 2364640 1421210 1489570 2080870 2260410 2095950 2475080 2162430 FALSE TRUE 2238048.439 2349106.524 2108511.91 1827799.635 2039464.758 2347369.435 1892685.092 1945803.403 1906789.989 1.173725713 1.231969193 1.105791368 0.958574172 1.069580169 1.231058192 0.992602805 1.020460258 1 20.86271453 7.999999999 0.284959763 1.009711119 2.632457112 0.319665148 0.081257733 98.64307194 1.580675283 0.193732998 78.4416515 99999999.83 -7.999999999 1.622745994 LLEPFEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLEPFEVR 8 0 Q8WUY1 Q8WUY1 THEM6 Protein THEM6 0 ;; 94.114 0.024634 214656000 211874 226237 156465 214750 264037 266763 226067 333494 301523 FALSE TRUE 183874.3141 224750.8343 232131.9973 263512.2697 258783.1803 277025.5452 204143.0571 262178.9034 265877.2944 0.691575843 0.845317893 0.873079433 0.991104826 0.97331809 1.04193006 0.767809292 0.986089857 1 18.02040105 4.679951216 1.274902989 0.953363979 0.598176085 0.564958211 0.074659253 0.970246348 1.488803183 0.021737457 0.439771263 47857.63308 -4.679951216 -0.355187894 LLEPVDHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLEPVDHGK 9 0 A0A0C4DG89;Q7L014;D6RJA6 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 140.83 0.00010815 218160000 293820 280810 204850 245050 253170 236950 280180 324380 373590 FALSE TRUE 254990.9426 278965.3406 303916.1452 300692.3479 248132.4123 246065.6198 253008.1867 255013.8613 329424.6158 0.77404945 0.846826033 0.922566592 0.912780446 0.753229724 0.746955777 0.768030604 0.774119022 1 18.32958884 3.238086545 24.99998682 0.798065233 0.867004296 0.093343774 0.082398728 26.3400396 1389047.128 0.024672076 0.02973565 1730.161107 -3.238086545 0.068939063 SHLGNVHDQDN ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SHLGNVHDQDN 11 0 Q8WW12;Q8WW12-3 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 0 ;;; 162.49 2.51E-05 557539000 773346 694440 357872 497482 417400 437925 415031 414236 317600 FALSE TRUE 671146.3667 689878.1779 530940.0962 610442.8916 409094.5566 454772.2581 374781.3575 325654.855 280053.6898 2.396491784 2.463378284 1.895851101 2.179735222 1.460771886 1.623875259 1.33824824 1.162830082 1 18.09534391 3.26959445 0.240280122 0.373562312 3.281757378 0.898052229 0.161528121 1.129750171 0.329531044 1.569020277 2.049246107 1860.349107 -3.26959445 2.908195065 up LLEQGLR ddPTM_MDA-MB-175_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 ;;;;;;; 189.31 0.0012958 15123550000 5783490 6032760 4460440 4464650 6308330 7475980 6323150 6452490 6852480 FALSE TRUE 5019187.143 5993130.402 6617523.703 5478417.02 6182806.575 7763585.788 5709931.886 5072675.227 6042387.621 0.830662887 0.991848054 1.09518358 0.90666428 1.023238985 1.284853981 0.94497941 0.83951503 1 22.52668731 2.01180108 24.99875022 0.9034801 1.026838465 0.111364814 0.124192798 387.7674266 821421.6159 0.051120632 0.034436115 102.7545543 -2.01180108 0.123358364 LLEQYKEESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LLEQYKEESK 10 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;; 135.6 0.00012759 2361560000 2917110 1931700 1760400 1898330 1772290 1428450 2611510 2865470 2762710 FALSE TRUE 2531606.522 1919010.536 2611735.328 2329374.841 1737024.896 1483403.396 2358246.162 2252711.54 2436105.571 1.039202304 0.787737017 1.072094477 0.95618797 0.713033506 0.608924101 0.968039395 0.924718356 1 21.21614522 4.764853137 22.589797 0.881446869 1.039203076 0.114262061 0.140147359 5570.722569 4785919.7 0.035847616 2.219324879 58190.64044 -4.764853137 0.157756207 LLESDYFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLESDYFR 8 0 Q96HE7;G3V3E6;G3V503 Q96HE7 ERO1L ERO1-like protein alpha 0 ; 107.19 0.0094252 285840000 676530 673580 525690 515280 691040 896150 619340 571280 577530 FALSE TRUE 587124.8464 669155.2086 779915.4423 632282.1996 677289.656 930625.4704 559276.5021 449116.2177 509255.0613 1.152909202 1.313988332 1.531482947 1.241582554 1.32996156 1.827425078 1.09822473 0.881908206 1 18.95802889 2.012167757 24.99989619 0.949783148 1.397279811 0.531199739 0.184267927 156.2069708 320941.9293 0.074178111 0.049972845 102.8413471 -2.012167757 0.447496663 LLESIFHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLESIFHR 8 0 Q7Z7E8 Q7Z7E8 UBE2Q1 Ubiquitin-conjugating enzyme E2 Q1 0 ; 160.75 0.00035156 305250000 325400 354560 156718 249958 346490 387050 345740 366510 351650 FALSE TRUE 282397.5655 352230.872 232507.349 306714.7843 339595.5269 401940.064 312210.188 288134.6887 310078.3376 0.910729746 1.135941565 0.749834222 0.989152569 1.095192684 1.296253286 1.006875199 0.929231919 1 18.24227322 3.472067647 22.06845386 1.054393308 0.938703837 0.175144872 0.131824722 66.79259224 291666.2796 0.039989231 0.051903335 2965.293238 -3.472067647 -0.115689472 LLESIQQHS(ph)LDAVLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLESIQQHSLDAVLAR 16 0 P38935 P38935 IGHMBP2 DNA-binding protein SMUBP-2 1 LLESIQQHS(1)LDAVLAR;LLESIQQHS(1)LDAVLAR;LLESIQQHS(1)LDAVLAR 183.65 1.26E-09 172880000 118764 118141 56997.4 92913 100587 87272 102044 110971 87594 TRUE FALSE 103069.0365 117364.924 84561.53328 114010.3167 98585.5155 90629.41031 92147.78859 87240.71523 77238.73711 1.334421566 1.519508583 1.094807301 1.476076914 1.276373996 1.173367325 1.193025573 1.129494325 1 16.23703696 -0.51504697 0.272104762 6.89E-13 1.422085936 0.505979767 0.115131337 29.3137631 0.984586873 16.29655128 0.315629458 0.305459073 0.51504697 1.422085936 LLETELLQEISEIEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLETELLQEISEIEKR 16 1 Q8TDB6 Q8TDB6 DTX3L E3 ubiquitin-protein ligase DTX3L 0 78.244 0.0116 0 7585.6 7197.2 6976.9 5551.5 6791.7 7158 8973.7 7367.6 6839.1 FALSE TRUE 6583.143741 7149.921119 10350.95218 6812.052924 6656.558458 7433.372892 8103.431955 5792.096075 6030.589389 1.091625265 1.185609011 1.71640805 1.129583277 1.103798987 1.232611344 1.34372139 0.960452735 1 12.55808329 1.696958792 6.871180269 0.981726251 1.260381955 0.288561134 0.180422355 0.158515494 16.199972 0.108781849 0.047195961 49.7689859 -1.696958792 0.278655704 LLETLFVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLETLFVHR 9 0 Q9NZ01;M0R2N5 Q9NZ01 TECR Very-long-chain enoyl-CoA reductase 0 ; 149.94 8.64E-05 96900000 132571 129803 127473 155306 146211 137496 147513 165940 310450 FALSE TRUE 115051.4065 128950.3155 189119.3692 190570.601 143301.6872 142785.5601 133207.212 130455.0223 273748.9547 0.420280715 0.47105318 0.690849649 0.696150972 0.523478482 0.521593079 0.486603546 0.476549847 1 18.06249393 1.233934732 24.99999029 1.000000694 0.537735419 0.722352157 0.090433283 84.1971512 454975.4225 0.188579275 0.024042355 17.13699744 -1.233934732 -0.462265275 LLETTDRPDGHQNNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LLETTDRPDGHQNNLR 16 1 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;;;; 259.53 5.71E-27 7009480000 4806670 4415560 3149800 3822380 4667800 5082610 4295880 4959290 5288880 FALSE TRUE 4171456.381 4386553.896 4673053.815 4690309.8 4574919.912 5278141.296 3879266.219 3898784.427 4663634.632 0.894464663 0.940586955 1.002019709 1.005719824 0.980977344 1.13176561 0.831811779 0.835996971 1 22.15302334 2.195606247 24.99990511 0.875776998 0.990723604 0.289253249 0.075326454 159.5287981 92846.36414 0.030820502 0.020779337 156.8939681 -2.195606247 0.114946606 LLEVEHPAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LLEVEHPAAK 10 0 P17987;E7ERF2;F5H136;F5GZI8;F5H676;F5H726 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;; 123.51 0.00046005 2465330000 6486020 5696360 3789160 4824070 5437870 4972850 6319540 7181480 6596130 FALSE TRUE 5628876.024 5658940.236 5621610.45 5919448.825 5329667.026 5164158.757 5706671.983 5645776.388 5816343.026 0.967768923 0.972937843 0.966519757 1.017726912 0.916326118 0.887870391 0.98114433 0.970674591 1 22.47168093 1.427787313 2.001617613 1.002242204 0.957430731 0.122825617 0.035164612 1.210240078 6.993354374 0.090513992 0.010307533 26.77856578 -1.427787313 -0.044811473 LLEVQGSRPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLEVQGSRPGK 11 1 P62136;E9PMD7 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit;Serine/threonine-protein phosphatase 0 119.39 0.00054092 2439100000 1600100 1374900 862450 961890 1333400 1201500 1323800 1595300 1297500 FALSE TRUE 1388642.731 1365868.191 1279533.705 1180301.826 1306867.949 1247722.482 1195418.08 1254157.51 1144111.028 1.213730745 1.193824863 1.118364978 1.031632243 1.142256229 1.090560664 1.044844469 1.096185142 1 20.12579563 8 0.378795436 1.052485803 3.606772636 0.64986372 0.040215432 52.03610876 0.760434382 0.043390219 96.59831375 99999999.99 -8 2.554286833 LLEVSDDPQVLAVAAHDVGEYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLEVSDDPQVLAVAAHDVGEYVR 23 0 G3V126;Q9UI12-2;Q9UI12 G3V126 ATP6V1H V-type proton ATPase subunit H 0 ; 244.01 2.01E-37 365800000 433780 382698 254482 271862 329716 362460 346863 385610 385423 FALSE TRUE 376454.8739 380184.0316 377550.3464 333592.4223 323155.2967 376404.0707 313224.2796 303150.3023 339858.732 1.107680452 1.118653122 1.110903769 0.981562016 0.950851828 1.107530969 0.921630813 0.891989152 1 18.37457566 3.709809553 0.507828621 0.928515745 1.173527663 0.497830552 0.060709384 1.459833821 0.752482578 0.071778628 0.2174441 5126.365328 -3.709809553 0.245011918 LLFAIEETEGFGQE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLFAIEETEGFGQE 14 0 A0A590UJQ1;Q96J02-3;Q96J02-2;Q96J02;A0A590UK44;A0A590UJW8;Q9H0M0-3;Q9H0M0;Q9H0M0-6 A0A590UJQ1;Q9H0M0-3 ITCH;WWP1 E3 ubiquitin-protein ligase Itchy homolog;NEDD4-like E3 ubiquitin-protein ligase WWP1 0 ; 158.05 1.19E-05 18482300 55339 47844 34902 37936 40822 50566 45153 47972 46399 FALSE TRUE 48025.81094 47529.70961 51780.72394 46549.94862 40009.72207 52511.30674 40774.06901 37713.56112 40913.76308 1.173830206 1.161704669 1.265606487 1.137757691 0.977903743 1.283463138 0.996585646 0.921781774 1 15.32029862 2.087008548 7.225563669 0.956484485 1.160655013 0.544409239 0.083911116 0.158318774 11.10770289 0.034014894 0.022833281 122.1823709 -2.087008548 0.204170528 LLFEDWTYDDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLFEDWTYDDFR 12 0 Q9BWS9-3;Q9BWS9;Q9BWS9-2 Q9BWS9-3 CHID1 Chitinase domain-containing protein 1 0 ;; 219.03 7.65E-11 213157000 383279 428162 339335 353990 440322 564094 420230 408939 392285 FALSE TRUE 332627.709 425349.3756 503438.541 434368.8399 431560.4537 585795.0612 379476.1593 321490.5772 345909.5142 0.961603238 1.229655035 1.455405302 1.255729669 1.247610823 1.693492191 1.097038803 0.929406576 1 18.40003517 2.010012203 24.99559078 0.975729365 1.312892545 0.382459193 0.184319408 194.7238951 486128.7869 0.074960595 0.050475524 102.3321747 -2.010012203 0.33716318 LLFEVFDENR ddPTM_MDA-MB-175_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 ; 144.77 7.35E-05 63384000 75485 61356 41094 53910 59962 64968 53200 69113 68868 FALSE TRUE 65509.466 60952.9484 60967.19585 66151.08946 58768.87351 67467.361 48040.67219 54333.72279 60726.50349 1.078762356 1.00372893 1.003963547 1.089328146 0.96776317 1.111003551 0.791098934 0.894728326 1 15.89003868 2.244869644 24.99999038 0.890821002 1.037656038 0.526367504 0.065651188 109.2760264 433016.3034 0.023833822 0.017998101 175.7396043 -2.244869644 0.146835036 LLFGHSTEGDILELVDGHFDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLFGHSTEGDILELVDGHFDTK 22 0 Q9UHY7;A0A0C4DGY8;D6RA00;Q9UHY7-2 Q9UHY7 ENOPH1 Enolase-phosphatase E1 0 ; 312.29 1.80E-67 1013530000 892780 656530 370980 636960 574240 500360 598300 875120 905740 FALSE TRUE 774796.861 652217.2112 550387.1689 781591.5033 562813.7475 519609.173 540276.9581 687982.3982 798664.449 0.970115625 0.816634836 0.689134429 0.978623131 0.704693627 0.650597599 0.676475532 0.861416079 1 19.60722997 4.717134154 4.373056147 0.790217717 0.979935053 0.165652211 0.122331116 0.346544049 15.58949496 0.030542607 0.194678437 52135.57336 -4.717134154 0.189717336 LLGELLLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLGELLLDR 9 0 Q9Y376;A0A087X0K1 Q9Y376 CAB39 Calcium-binding protein 39 0 ;; 105.1 0.0073342 203843000 327447 339499 221567 248412 304589 329924 310674 359864 372220 FALSE TRUE 284174.0493 337268.8087 328717.5423 304817.7413 298528.2748 342616.3898 280544.8833 282909.8841 328216.5756 0.865812608 1.027580061 1.00152633 0.928709163 0.909546613 1.043872903 0.854755378 0.861960989 1 18.32428857 2.215122494 24.99975969 0.894369119 0.963568466 0.135420598 0.06621033 378.4964795 403711.947 0.026256234 0.017713285 164.1052571 -2.215122494 0.069199348 LLGELLQDNAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLGELLQDNAK 11 0 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 81.017 0.053104 72593000 81812 69388 53006 54870 65976 78677 71399 77825 66367 FALSE TRUE 71000.33691 68932.18566 78639.87889 67329.07214 64663.20668 81703.7551 64474.73597 61182.72938 58521.16887 1.213241948 1.177901723 1.343785171 1.150507986 1.104954121 1.396140178 1.101733564 1.045480303 1 15.83667096 2.012295212 24.99380752 1.040274171 1.226442362 0.508778714 0.086455938 174.3075119 354332.4552 0.034341484 0.023135056 102.8715331 -2.012295212 0.186168191 LLGGQLGLEDFIFAHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LLGGQLGLEDFIFAHVK 17 0 Q8TF65 Q8TF65 GIPC2 PDZ domain-containing protein GIPC2 0 ;;; 208.26 5.34E-12 692003000 1506086 1424677 1086399 1318313 1370273 1251867 1544619 1997064 1736655 FALSE TRUE 1307052.919 1415318.203 1611785.19 1617656.116 1343007.248 1300027.134 1394822.087 1570007.405 1531349.624 0.853530049 0.924229308 1.052525932 1.056359756 0.877008899 0.848942079 0.91084496 1.025244255 1 20.54637227 1.71565194 8.079226817 1.011424887 0.935796811 0.174973634 0.072304065 0.224575557 36.92194678 0.045335887 0.020431118 51.95794191 -1.71565194 -0.075628077 LLGHEVEDVIIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLGHEVEDVIIK 12 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 114.82 0.0010165 155670000 209860 157280 132570 147100 179170 147170 196690 220490 211760 FALSE TRUE 182126.4693 156246.8173 196681.2954 180501.3033 175604.8675 152831.7251 177615.0341 173339.9294 186725.974 0.975367622 0.836770664 1.05331514 0.966664141 0.940441567 0.818481338 0.951206895 0.928311823 1 17.5105631 2.997104086 24.92163832 0.922250726 0.955846521 0.050135691 0.06820355 398.0172896 3425304.837 0.020661527 0.023005683 993.3540946 -2.997104086 0.033595795 LLGHWEEAAHDLALACK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LLGHWEEAAHDLALACK 17 0 P50502;Q8IZP2;H7C3I1 P50502 ST13;ST13P4 Hsc70-interacting protein;Putative protein FAM10A4 0 ;;; 210.34 2.00E-12 4977378000 5463839 5107839 3629714 4160488 4938134 4246121 5532195 6457604 6014267 FALSE TRUE 4741778.833 5074285.269 5385055.831 5105190.389 4839874.795 4409472.022 4995683.58 5076695.638 5303267.207 0.894124065 0.956822478 1.015422309 0.96265004 0.912621334 0.831463294 0.942001107 0.957276984 1 22.33845001 1.393763424 2.434565675 1.004427643 0.932118552 0.178438918 0.0477757 0.820541169 7.012182644 0.110437265 0.013941335 24.76072882 -1.393763424 -0.072309091 LLGIFENQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LLGIFENQDR 10 0 Q9NZJ9;F8VRL4;F8VRR0;A0A0C4DGJ4 Q9NZJ9 NUDT4 Diphosphoinositol polyphosphate phosphohydrolase 2 0 ;;;;; 155.84 2.79E-05 1531563000 1015685 936040 738719 761555 899209 935304 950881 1030757 1176171 FALSE TRUE 881459.6538 929891.0916 1095965.979 934477.7024 881316.5002 971285.7501 858664.707 810337.6369 1037125.404 0.84990653 0.896604295 1.056734291 0.901026721 0.849768501 0.936517171 0.827927562 0.781330429 1 19.98415892 3.478786799 24.67728875 0.866780023 0.938675046 0.081732564 0.078385907 103.7687179 1537499.641 0.022807596 0.029894072 3011.52726 -3.478786799 0.071895023 LLGLELALS(ph)SDAESAAGGPAGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLGLELALSSDAESAAGGPAGVR 23 0 O94964-2 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 LLGLELALS(0.833)S(0.167)DAESAAGGPAGVR;LLGLELALS(0.544)S(0.455)DAES(0.001)AAGGPAGVR;LLGLELALS(0.543)S(0.451)DAES(0.006)AAGGPAGVR 152.04 5.63E-14 42405000 120105 125099 77567.9 106218 133974 131172 111084 144397 140185 TRUE FALSE 104232.8199 124277.2164 115079.9959 130336.4203 131308.1795 136218.2717 100311.0908 113518.8252 123612.489 0.843222402 1.00537751 0.930973859 1.054395243 1.062256578 1.101978229 0.811496408 0.918344305 1 16.91546499 2.237194738 24.99999786 0.90759428 1.002164294 0.199259181 0.084677247 57.18861871 1046694.716 0.033733501 0.024175054 172.6611931 -2.237194738 0.094570014 LLGPAPEDDGGHNDHSQPQASQDQDSHTLS(ph)PQV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLGPAPEDDGGHNDHSQPQASQDQDSHTLSPQV 33 0 Q92610 Q92610 ZNF592 Zinc finger protein 592 1 LLGPAPEDDGGHNDHSQPQASQDQDS(0.008)HT(0.005)LS(0.987)PQV 179.43 2.27E-19 171840000 72648 79297 58871 51911 85736 79755 64835 71775 115270 TRUE FALSE 63047.38273 78776.09279 87341.21251 63698.18596 84030.02134 82823.22646 58547.31168 56426.4748 101642.9119 0.620283122 0.775027902 0.859294671 0.626685961 0.826717965 0.814845078 0.576009783 0.555144218 1 16.63315009 2.255712091 24.99417992 0.672443902 0.757104105 0 0.143381753 675.1911221 983928.7832 0.052685312 0.040710091 180.1822852 -2.255712091 0.084660203 LLGPQWLDYDCDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLGPQWLDYDCDR 13 0 Q6P9B6 Q6P9B6 TLDC1 TLD domain-containing protein 1 0 ; 102.4 0.0039372 119502000 177437 190704 113089 141519 165042 161389 172362 215063 190665 FALSE TRUE 153988.2509 189451.2529 167779.2187 173653.0519 161757.9871 167597.7393 155646.3598 169073.4511 168124.8009 0.915916332 1.126848935 0.99794449 1.032881829 0.962130431 0.996865057 0.925778701 1.005642536 1 17.35917303 3.244860137 24.81581844 0.97854448 1.024683449 0.111063151 0.055411788 261.1299616 1028666.049 0.014859478 0.018711906 1757.357572 -3.244860137 0.046138969 LLGWDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LLGWDDR 7 0 Q8WUY1 Q8WUY1 THEM6 Protein THEM6 0 ;;;;; 173.85 0.001973 1047714000 2609550 2424480 1854020 2781090 3441650 3483270 2188120 3810850 3752940 FALSE TRUE 2264691.356 2408553.431 2750630.273 3412578.991 3373167.898 3617273.651 1975916.459 2995929.384 3309271.709 0.68434736 0.727819787 0.831189009 1.031217528 1.019308233 1.093072425 0.597084988 0.905313811 1 21.65808232 4.116835541 3.151077711 0.925785146 0.700873296 0.33685852 0.134761439 0.315320504 6.158881342 0.03769423 0.093178217 13086.86255 -4.116835541 -0.22491185 LLGWIQNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLGWIQNK 8 0 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98;O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;O75369-5;O75369-4;Q14315-2;Q14315 Q60FE5;O75369-8;Q14315-2 FLNA;FLNB;FLNC Filamin-A;Filamin-B;Filamin-C 0 160.77 0.0012683 0 251800 266940 153480 175010 200250 204970 270040 277710 267860 FALSE TRUE 218523.992 265186.4536 227703.4414 214748.6954 196265.4168 212855.3285 243851.5624 218323.8776 236193.8959 0.92518899 1.122748971 0.964053031 0.909205102 0.830950419 0.901188948 1.032421102 0.924341744 1 17.84961216 4.012925091 24.75337565 0.933046356 1.028827023 0.212616555 0.071494332 285.4611799 546688.8759 0.018021416 0.037480186 10302.08411 -4.012925091 0.095780667 LLHDLQIGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLHDLQIGEK 10 0 P49756;P49756-2;P49756-3;E9PQU5 P49756 RBM25 RNA-binding protein 25 0 115 0.0012804 318700000 967700 773490 570900 650090 747610 628560 773670 1024600 1036400 FALSE TRUE 839815.9932 768408.8933 846989.1495 797702.8705 732734.0237 652741.1099 698639.6025 805497.2634 913877.9727 0.918958568 0.840822206 0.926807708 0.872876789 0.801785409 0.714254123 0.764477997 0.88140571 1 19.80164201 3.405705627 6.064394754 0.82782027 0.891628939 0.121489862 0.077949739 0.466413857 29.92925479 0.024241942 0.031504935 2545.104547 -3.405705627 0.063808669 LLHDQIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLHDQIEK 8 0 P12270 P12270 TPR Nucleoprotein TPR 0 63.283 0.07429 152200000 299590 284990 177120 215320 280690 264820 303800 342020 330750 FALSE TRUE 259998.4224 283117.8819 262775.8244 264211.697 275104.8182 275007.7968 274337.5228 268881.6846 291649.1118 0.891476819 0.970748308 0.900999913 0.905923201 0.943273293 0.942940628 0.940642408 0.921935551 1 18.15387415 1.235368846 24.99977113 1.000000098 0.928486642 0.482245538 0.023661144 77.63427247 607971.0708 0.037596233 0.005408818 17.19368024 -1.235368846 -0.071513456 LLHDQVGVIQFGPYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLHDQVGVIQFGPYK 15 0 P53621;P53621-2;A0A3B3IS84;A0A3B3ISC6 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 176.32 8.06E-07 1747720000 2574700 2596900 1588380 1970250 2454800 2158700 2642800 3052500 2883500 FALSE TRUE 2234446.872 2579840.793 2356525.881 2417625.376 2405954.283 2241746.586 2386501.663 2399746.63 2542615.915 0.878798429 1.014640386 0.926811583 0.950841754 0.946251563 0.881669376 0.93860093 0.943810119 1 21.27788212 1.21458423 3.154434663 1.01354182 0.936136262 0.227585971 0.037762273 0.624087396 7.79345231 0.12524556 0.009189911 16.39019912 -1.21458423 -0.077405558 LLHDSGLNVVVLEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLHDSGLNVVVLEAR 15 0 P27338-2;P27338 P27338-2 MAOB Amine oxidase [flavin-containing] B 0 65.421 0.061595 83327000 151950 127800 60287 65656 116660 108370 141540 175710 45997 FALSE TRUE 131869.4225 126960.4734 89441.99485 80564.19829 114338.6942 112539.064 127813.4726 138135.7839 40559.28706 3.251275653 3.130244208 2.20521615 1.986331717 2.819050889 2.774680528 3.15127513 3.405774457 1 15.30774467 LLHEDLDES(ph)DDDMDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLHEDLDESDDDMDEK 16 0 O43150;O43150-2 O43150 ASAP2 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2" 1 LLHEDLDES(1)DDDMDEK;LLHEDLDES(1)DDDMDEK;LLHEDLDES(1)DDDMDEK 271.48 2.27E-22 158690000 559991 380891 347942 374820 400616 348788 462406 516600 558279 TRUE FALSE 485986.7705 378388.9019 516207.915 459928.6098 392644.5254 362206.1001 417561.9373 406129.1102 492279.8926 0.987216374 0.768645861 1.04860654 0.934282746 0.797604231 0.735772688 0.848220583 0.824996341 1 18.90911929 3.251338993 24.71247399 0.834518799 0.930964818 0.188553524 0.095532539 332.330426 642699.2724 0.027022639 0.034645189 1783.770564 -3.251338993 0.096446019 LLHEMILVCDAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLHEMILVCDAYR 13 0 P53618;E9PP73;E9PP63;E9PKQ1 P53618 COPB1 Coatomer subunit beta 0 ; 167.14 3.24E-05 1713420000 1706970 1983220 1313380 1380560 1760840 1871740 1775830 2082400 2222200 FALSE TRUE 1481389.59 1970192.097 1948534.961 1694037.249 1725802.729 1943747.049 1603610.28 1637094.965 1959494.048 0.75600617 1.005459598 0.994407186 0.864527887 0.88073895 0.991963743 0.818379766 0.8354682 1 20.90204976 2.223524853 24.99772649 0.871617056 0.919292938 0.018440269 0.088266783 751.3167144 1249093.166 0.035042287 0.023731123 167.3111378 -2.223524853 0.047675881 LLHEVQELTTEVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LLHEVQELTTEVEK 14 0 Q13561;Q13561-3;Q13561-2;F8W1I6;F8VW18;F8VX93;F8VRV7;H0YHL1 Q13561 DCTN2 Dynactin subunit 2 0 ;;; 202.25 1.67E-08 779300000 1226230 1043610 757360 890430 1002430 896140 1229710 1427000 1285850 FALSE TRUE 1064180.599 1036754.457 1123621.829 1092615.741 982483.6042 930615.0857 1110452.913 1121847.155 1133838.278 0.938564714 0.914375954 0.990989501 0.963643372 0.866511233 0.820765275 0.979375044 0.989424309 1 20.11278345 2.028907849 24.99978437 0.991089734 0.917508755 0.354647757 0.047167792 244.0542462 211059.3969 0.020962766 0.01413287 106.8828064 -2.028907849 -0.073580979 LLHHDDPEVLADTCWAISYLTDGPNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLHHDDPEVLADTCWAISYLTDGPNER 27 0 P52292 P52292 KPNA2 Importin subunit alpha-1 0 ;; 273.6 4.68E-61 436270000 204362 214384 136669 175892 190448 226550 215884 211515 193898 FALSE TRUE 177355.0439 212975.6974 202762.5855 215830.9669 186658.4574 235265.5251 194947.6029 166284.1633 170975.5993 1.037312018 1.245649661 1.185915337 1.262349527 1.091725709 1.376018134 1.140207162 0.972560786 1 17.38343092 1.841189986 4.227347598 0.987865616 1.202917487 0.467426307 0.092360787 0.171395792 4.846271481 0.049211944 0.023146726 69.37292174 -1.841189986 0.21505187 LLHIEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LLHIEELR 8 0 Q9Y224 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ;;;;; 243.56 6.85E-09 3183700000 3535670 3384890 2140250 2490950 3230320 3473810 3088330 3551510 3312340 FALSE TRUE 3068422.251 3362654.435 3175282.059 3056558.269 3166042.952 3607449.719 2788824.232 2792047.224 2920758.939 1.050556487 1.151294751 1.087142803 1.046494536 1.083979547 1.235106969 0.954828622 0.9559321 1 21.47791186 2.195981233 24.9998489 0.966626986 1.106029094 0.582700437 0.055319185 95.53254126 56089.84891 0.022097887 0.014898533 157.0294945 -2.195981233 0.139402109 LLHILEFDSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLHILEFDSDR 11 0 Q9Y2G3;H7C4W6 Q9Y2G3 ATP11B Probable phospholipid-transporting ATPase IF;Phospholipid-transporting ATPase 0 82.171 0.015765 0 24110 25318 14449 19914 26769 27259 19672 25321 25135 FALSE TRUE 20923.80241 25151.68439 21436.58473 24435.77807 26236.34927 28307.67137 17764.21247 19906.3012 22163.56893 0.944062866 1.134821042 0.967199136 1.102520002 1.183760131 1.277216294 0.801505052 0.89815414 1 14.43590259 2.223764998 24.99999766 0.895426291 1.100774515 0.445154415 0.106116227 218.5423372 369265.7362 0.043944518 0.029765204 167.4036789 -2.223764998 0.205348223 LLHMDS(ph)DDEIPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LLHMDSDDEIPIR 13 0 Q1MSJ5-1;Q1MSJ5;Q1MSJ5-2 Q1MSJ5-1 CSPP1 Centrosome and spindle pole-associated protein 1 1 LLHMDS(1)DDEIPIR;LLHMDS(1)DDEIPIR;LLHMDS(1)DDEIPIR;LLHMDS(1)DDEIPIR 231.17 1.85E-12 298129000 419654 465390 266974 329964 429262 435026 385836 468870 412978 TRUE FALSE 364195.6606 462332.8224 396083.5194 404887.3694 420720.526 451761.7317 348417.6841 368605.7993 364156.2113 1.000108331 1.269600265 1.087674759 1.111850785 1.155329809 1.240571265 0.956780836 1.012218899 1 18.47419793 2.224734538 24.99967124 0.99299471 1.146357337 0.47888467 0.075937721 188.6711434 341143.5613 0.028766207 0.019505657 167.7778166 -2.224734538 0.153362627 LLHPS(ph)PDLVSQEATLSEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLHPSPDLVSQEATLSEAR 19 0 A0A087WU05;A0A087WY48;Q8IY22-3;Q8IY22-2;Q8IY22 A0A087WU05 CMIP C-Maf-inducing protein 1 LLHPS(1)PDLVSQEATLSEAR;LLHPS(1)PDLVSQEATLSEAR 174.7 2.57E-12 125010000 93174 103456 75185 92780 130088 138909 121046 140320 139640 TRUE FALSE 80860.81983 102776.3907 111544.7175 113847.1171 127499.5033 144252.9191 109306.9776 110313.66 123131.9183 0.656700724 0.834685207 0.905896043 0.924594684 1.035470779 1.171531485 0.887722526 0.895898168 1 16.90984526 4.747212781 1.105755158 0.980796834 0.495003649 0.636810523 0.080687413 1.287118874 1.287226274 0.027651486 0.7363103 55874.3882 -4.747212781 -0.485793185 LLHQLADLVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLHQLADLVER 11 0 H0Y2X5;P47895;H0YNQ3;H0YKF9 H0Y2X5 ALDH1A3 Aldehyde dehydrogenase family 1 member A3 0 ; 149.23 3.45E-05 471850000 705520 662140 505200 510180 574350 721740 689810 650190 789550 FALSE TRUE 612283.7444 657790.3587 749516.4098 626024.1666 562921.5587 749505.8048 622912.3324 511151.9283 696210.2985 0.879452295 0.944815611 1.076566106 0.899188317 0.808551037 1.076550873 0.894718641 0.734191852 1 19.40916363 1.99896894 24.99758414 0.838013305 0.948156804 0.084857621 0.103608089 61.19333682 1483620.583 0.041714697 0.027716693 99.76287119 -1.99896894 0.110143499 LLHSENYVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLHSENYVTK 10 0 Q9Y376;A0A087X0K1 Q9Y376 CAB39 Calcium-binding protein 39 0 87.363 0.012927 279870000 370520 337300 236640 272090 320930 311380 345510 369490 488640 FALSE TRUE 321554.8432 335084.2541 351079.8955 333872.1931 314544.1209 323358.9901 312002.4934 290477.4389 430873.5359 0.746285897 0.777685855 0.814809605 0.774872823 0.730014946 0.750473081 0.724116167 0.674159387 1 18.71690497 1.228154588 24.99999149 1.000000523 0.747578842 0.818238723 0.037164564 212.6060285 510740.8794 0.145923729 0.010574671 16.91042756 -1.228154588 -0.252421681 LLHTLEGHAMPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLHTLEGHAMPIR 13 0 H3BQA8;H0YL19;H0YN81;Q9GZS3;H0YLA1 H3BQA8 WDR61 "WD repeat-containing protein 61;WD repeat-containing protein 61, N-terminally processed" 0 ; 148.18 2.49E-05 306310000 173396 164173 102001 121676 168926 191902 159186 179214 112702 FALSE TRUE 150481.2793 163094.5368 151329.0248 149304.3955 165564.7031 199284.5941 143748.1662 140890.4807 99378.49795 1.514223724 1.641145118 1.522754196 1.502381285 1.666001263 2.005308978 1.446471512 1.417715941 1 16.60064612 1.273807535 1.669925865 0.801510243 1.627192873 0.622800902 0.152925002 0.646385021 1.773424817 0.861710435 0.044613782 18.7848415 -1.273807535 0.82568263 LLHVAVSDVNDDVRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLHVAVSDVNDDVRR 15 1 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ; 147.35 2.42E-06 959090000 283060 250930 170503 187020 250840 304070 291960 305720 164593 FALSE TRUE 245652.9038 249281.6243 252958.8211 229485.7494 245848.7748 315767.7697 263645.7641 240344.1571 145135.003 1.69258207 1.717584449 1.742920838 1.581188167 1.693931647 2.175683075 1.816555335 1.656004079 1 17.14703598 1.230975146 3.178886065 0.857351512 1.774031979 0.706391209 0.1556472 0.216493881 2.853936873 0.505716074 0.042548378 17.02061098 -1.230975146 0.916680467 LLIDGDGAGDDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLIDGDGAGDDRR 13 1 Q6I9Y2;H7C5E3 Q6I9Y2 THOC7 THO complex subunit 7 homolog 0 ; 130.77 0.00022157 245320000 322010 253790 181745 198497 247940 263140 245290 288920 232100 FALSE TRUE 279455.5626 252122.8368 269637.4899 243568.7777 243006.4791 273263.1661 221501.8136 227136.7064 204661.4024 1.365453179 1.231902224 1.317480906 1.190106072 1.187358614 1.335196392 1.082284256 1.109817013 1 17.64287952 -0.539956177 0.33942878 1.77E-12 1.312056756 0.667275609 0.067344666 17.39083499 0.676962358 11.77346934 0.101346573 0.288432253 0.539956177 1.312056756 LLIDPNCSGHS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLIDPNCSGHSPR 13 0 Q8WYQ5-3;Q8WYQ5;Q8WYQ5-2;C9JSD5 Q8WYQ5-3 DGCR8 Microprocessor complex subunit DGCR8 1 LLIDPNCS(0.002)GHS(0.998)PR 120.9 0.0001629 104650000 277230 271600 136560 170820 231290 265210 231350 277010 270110 TRUE FALSE 240593.3531 269815.8417 202600.8728 209607.2918 226687.7815 275412.8003 208913.7126 217773.5672 238177.9035 1.010141367 1.132833221 0.850628332 0.880045079 0.951758237 1.156332289 0.877133057 0.914331531 1 17.86168005 4.248119306 24.99998826 0.945726767 1.071487285 0.245302704 0.090622472 285.6496287 747078.2732 0.022966746 0.059080757 17705.95295 -4.248119306 0.125760518 LLIHQSLAGGIIGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLIHQSLAGGIIGVK 15 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 145.29 8.95E-06 0 75425 83053 22917 50073 95036 83327 85627 96167 89151 FALSE TRUE 65457.39515 82507.41937 33999.73785 61442.83997 93144.96953 86532.64361 77322.90672 75602.43542 78611.67034 0.832667654 1.049556879 0.432502422 0.781599471 1.184874576 1.100760781 0.98360595 0.961720252 1 16.26245588 3.301935199 10.23129207 1.033549533 0.768711721 0.413275714 0.160671419 0.457470278 70.90900515 0.047247052 0.060966199 2004.172963 -3.301935199 -0.264837812 LLILDEVHLLHEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLILDEVHLLHEDR 14 0 Q8N3C0;Q8N3C0-4 Q8N3C0 ASCC3 Activating signal cointegrator 1 complex subunit 3 0 ; 161.63 2.64E-06 34654000 30488 27254 21073.3 24841 32201 29351 18607.6 30907 50557 FALSE TRUE 26458.93355 27074.96668 31264.41837 30481.52872 31560.2631 30480.15196 16803.03782 24297.77857 44580.20905 0.593512999 0.607331532 0.701307128 0.683745756 0.707943363 0.683714873 0.376916981 0.545035097 1 15.44411576 1.232898699 24.99521743 1.000000627 0.608296678 0.603254424 0.098724641 143.7286972 634440.0863 0.230824312 0.026831978 17.09616494 -1.232898699 -0.39170395 LLIPERDPLEEIAES(ph)SPQTAANSAAELLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLIPERDPLEEIAESSPQTAANSAAELLK 29 1 Q68CZ2;Q68CZ2-2 Q68CZ2 TNS3 Tensin-3 1 LLIPERDPLEEIAES(0.5)S(0.5)PQTAANSAAELLK;LLIPERDPLEEIAES(0.69)S(0.308)PQT(0.002)AANSAAELLK 156.5 4.52E-09 56199000 27289.4 28838.5 20993 32328.4 30575 22632.2 32571.9 43800 35262 TRUE FALSE 23683.03665 28649.05799 31145.28502 39669.05733 29966.61732 23502.87538 29413.08215 34433.71085 31093.36653 0.761674894 0.921388103 1.001669761 1.275804513 0.963762393 0.755880691 0.945960037 1.107429484 1 14.92431921 4.612429496 2.537807311 1.011061863 0.742265041 0.267192102 0.129678101 0.568400658 5.544373397 0.035693096 0.288173599 40966.55989 -4.612429496 -0.268796822 LLIQESVWDEAMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLIQESVWDEAMR 13 0 Q8IZ83;F5H4B6;Q8IZ83-3 Q8IZ83 ALDH16A1 Aldehyde dehydrogenase family 16 member A1 0 ; 191.29 8.58E-06 65718000 65995 59753 43831 54246 62080 63558 55112 65841 70382 FALSE TRUE 57273.59354 59360.47861 65027.81821 66563.3834 60844.72946 66003.11739 49767.24672 51761.41453 62061.52014 0.922851928 0.956477999 1.047796091 1.07253872 0.980393798 1.06351113 0.801901832 0.834033946 1 15.92141141 2.240828757 24.99999993 0.866153589 1.008541622 0.433681264 0.068782016 50.5136896 556783.6445 0.026959964 0.019862315 174.1120211 -2.240828757 0.142388032 LLKEGEEPTVYS(ph)DEEEPKDESAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LLKEGEEPTVYSDEEEPKDESAR 23 2 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 1 LLKEGEEPT(0.003)VYS(0.997)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPT(0.294)VYS(0.706)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR 227.59 6.46E-33 9330890000 4232060 3374790 2538040 2745640 4251060 3046730 3835890 7256650 1464294 TRUE FALSE 3672782.548 3352620.782 3765444.633 3369079.526 4166472.223 3163939.675 3463885.978 5704871.869 1291186.831 2.844501244 2.596541957 2.916266292 2.609288946 3.226854644 2.450411976 2.682714766 4.418316335 1 20.30026634 3.078055262 1.072722143 2.961277532 2.746999522 0 0.849467669 4.122902911 10.58829433 0.422070381 0.498833643 1196.892821 -3.078055262 -0.21427801 LLKPGEEPSEYT(ph)DEEDTKDHNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLKPGEEPSEYTDEEDTKDHNK 22 2 U3KQM0;O15173;O15173-2;U3KPU8 U3KQM0 PGRMC2 Membrane-associated progesterone receptor component 2 1 LLKPGEEPSEYT(1)DEEDTKDHNK 256.24 4.20E-37 280390000 281680 201970 292730 327580 244780 197580 249060 433410 699040 TRUE FALSE 244455.2743 200643.2458 434295.2071 401962.0457 239909.3569 205181.0305 224906.1995 340728.6443 616400.2875 0.39658527 0.325508034 0.704566847 0.652112035 0.389210326 0.332869784 0.364870368 0.552771715 1 19.23350801 1.249589221 3.396302288 1.075714748 0.457854468 0.637873925 0.128764692 0.214500528 3.536344291 0.34255593 0.035680323 17.76598212 -1.249589221 -0.617860279 LLKPGEEPSEYT(ph)DEEDTKDHNKQD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LLKPGEEPSEYTDEEDTKDHNKQD 24 3 U3KQM0;O15173;O15173-2;U3KPU8 U3KQM0 PGRMC2 Membrane-associated progesterone receptor component 2 1 LLKPGEEPSEYT(1)DEEDTKDHNKQD;LLKPGEEPSEYT(1)DEEDTKDHNKQD;LLKPGEEPSEYT(1)DEEDTKDHNKQD;LLKPGEEPSEYT(1)DEEDTKDHNKQD;LLKPGEEPS(0.001)EYT(0.999)DEEDTKDHNKQD 285.04 7.96E-53 3734900000 2602410 1625945 2307620 2042038 2030180 1471146 2136310 4069590 2722180 TRUE FALSE 2258494.925 1615264.06 3423592.751 2505713.938 1989783.39 1527741.939 1929130.985 3199339.848 2400366.982 0.940895681 0.672923796 1.426278889 1.043887855 0.828949659 0.63646182 0.803681687 1.332854465 1 21.19482356 1.745386306 25 1.174976701 0.910297213 0.175154939 0.233304366 2.41247543 8870.997428 0.128646639 0.061777649 55.63989556 -1.745386306 -0.264679488 LLLAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLLAAR 6 0 C9J9K3;A0A0C4DG17;P08865;F8WD59 C9J9K3 RPSA 40S ribosomal protein SA 0 ; 112.88 0.061925 416830000 373980 498660 560420 382740 430730 410700 511290 460410 471500 FALSE TRUE 324557.5955 495384.2696 831440.9865 469646.9668 422159.3157 426499.8948 461705.1745 361954.9044 415759.8071 0.780637257 1.191515536 1.999810882 1.129611277 1.015392321 1.025832434 1.110509401 0.87058657 1 18.66539077 3.487127681 24.8743275 1.003637612 1.353069033 0.190680338 0.298481502 688.4442981 1711358.66 0.085227669 0.117171288 3069.924401 -3.487127681 0.349431421 LLLAEDS(ph)EEEVDFLSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 LLLAEDSEEEVDFLSER 17 0 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(0.999)EEEVDFLS(0.001)ER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER 324.03 2.88E-51 808455000 711785 544835.7 395727.1 449748.1 528907 526995.8 517511.3 587610.2 550133 TRUE FALSE 617720.8088 541256.6384 587102.0492 551870.2801 518382.7855 547269.6694 467323.1338 461954.3315 485096.9035 1.273396726 1.115770137 1.210277874 1.137649563 1.068616975 1.128165662 0.963360373 0.952292889 1 18.88791344 2.730885986 0.583757244 0.929823409 1.219502844 0.75428805 0.051162127 0.457090749 0.423965227 0.082752634 0.055327788 538.1284912 -2.730885986 0.289679435 LLLDT(ph)SPPGGVVLSSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLLDTSPPGGVVLSSFR 17 0 O15211;A2AB89 O15211 RGL2 Ral guanine nucleotide dissociation stimulator-like 2 1 LLLDT(0.526)S(0.474)PPGGVVLSSFR 117.4 0.002451 25524000 43536 41151 20518 27036 38959 38909 32651 39721 34369 TRUE FALSE 37782.60729 40880.67637 30440.57343 33174.93702 38183.79212 40405.85441 29484.51105 31226.97326 30305.93597 1.246706498 1.348932975 1.00444261 1.094667957 1.259944328 1.333265352 0.972895576 1.030391316 1 14.88731278 2.221390894 24.99999664 1.006023833 1.207812147 0.486853287 0.103157112 229.5219116 334193.1492 0.04446907 0.030064259 166.4910506 -2.221390894 0.201788314 LLLDTS(ph)PPGGVVLSSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLLDTSPPGGVVLSSFR 17 0 O15211;A2AB89 O15211 RGL2 Ral guanine nucleotide dissociation stimulator-like 2 1 LLLDT(0.016)S(0.984)PPGGVVLSSFR 159.81 3.32E-09 362310000 607050 614700 365610 399080 586820 572490 553530 626730 482400 TRUE FALSE 526826.8044 610661.9952 542420.2189 489697.2136 575143.4301 594514.0608 499848.7458 492708.6667 425371.2216 1.238510688 1.435597813 1.275169056 1.151223188 1.352097652 1.397635831 1.1750883 1.158302776 1 18.69836291 1.510004669 1.400350775 0.962839868 1.304883004 0.566973529 0.085860498 0.549645148 1.469130876 0.244966057 0.02651178 32.35971357 -1.510004669 0.342043136 LLLEFTDTSYEEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLLEFTDTSYEEKR 14 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;; 257.02 3.98E-24 1659960000 2278800 2036590 1499190 1698720 1853210 1852160 2630510 2635130 1537160 FALSE TRUE 1977650.806 2023211.506 2224203.298 2084440.339 1816334.747 1923413.794 2375403.545 2071627.956 1355438.696 1.459048507 1.492661758 1.640947175 1.537834463 1.340034597 1.419034147 1.752497957 1.52838189 1 20.37032843 1.238465608 24.40390417 0.999999353 1.526973583 0.67467012 0.113704974 1.039347387 265018.6302 0.160962321 0.02875238 17.31671894 -1.238465608 0.52697423 LLLEGISSTHVNHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLLEGISSTHVNHLR 15 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39 B7ZC38 SH3GLB2 Endophilin-B2 0 ; 148.48 2.04E-06 1030180000 453740 534640 182263 365220 573900 615020 473910 554350 570560 FALSE TRUE 393777.1094 531127.9146 270405.9964 448148.783 562480.5128 638680.2174 427950.2811 435806.5665 503109.0468 0.782687395 1.055691441 0.537469954 0.890758745 1.11800914 1.269466772 0.850611381 0.866226853 1 18.94051161 3.473443525 24.73152522 1.001484633 0.800955547 0.272646466 0.17032673 145.4550076 978128.1436 0.051158273 0.06637406 2974.702405 -3.473443525 -0.200529087 LLLEHLECLVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLLEHLECLVSR 12 0 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;E9PPF6;O75335;G3V200;O75334-2;O75334-4;O75334-3;B1APN9;O75334;F8VWR9;O75334-5;O75334-6;O75145-2;O75145;R4GN36;R4GNF1 Q13136-2;O75145-2 PPFIA1;PPFIA4;PPFIA2;PPFIA3 Liprin-alpha-1;Liprin-alpha-4;Liprin-alpha-2;Liprin-alpha-3 0 ; 193.15 3.17E-06 598760000 993210 1134930 717150 830430 1065210 1090370 994050 1127410 1079280 FALSE TRUE 861954.782 1127474.57 1063966.139 1018991.824 1044014.405 1132317.239 897647.184 886322.145 951688.7479 0.905710805 1.184709363 1.117977008 1.07071963 1.09701245 1.189797864 0.943215086 0.931315146 1 19.86013029 2.216432221 24.99909841 0.951957092 1.098554538 0.393040049 0.079513624 211.1529209 238543.8877 0.030571223 0.020629446 164.6009059 -2.216432221 0.146597446 LLLERPS(ph)PIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LLLERPSPIR 10 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 LLLERPS(1)PIR;LLLERPS(1)PIR;LLLERPS(1)PIR;LLLERPS(1)PIR;LLLERPS(1)PIR;LLLERPS(1)PIR 152.4 1.10E-05 3672520000 3351710 2447781 1743489 2018335 2132163 2305865 2071349 2221103 3539360 TRUE FALSE 2908773.031 2431701.365 2586646.112 2476628.81 2089737.128 2394573.119 1870469.893 1746137.408 3120940.893 0.932017982 0.779156494 0.8288033 0.793551975 0.669585615 0.767260003 0.599328842 0.559490701 1 21.5735496 3.856176792 0.875296727 0.688097333 0.895586374 0.162774534 0.124557899 1.284427906 1.712926336 0.053255131 0.203232856 7180.865495 -3.856176792 0.207489041 LLLERPS(ph)PIRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 165.16 2.89E-05 4407380000 3168470 2487760 1566310 1758600 2481510 2495420 2500800 2712750 2012710 TRUE FALSE 2749748.662 2471417.741 2323782.755 2157917.009 2432132.806 2591420.422 2258272.801 2132649.523 1774769.717 1.549355184 1.392528686 1.309343253 1.215885638 1.370393456 1.460144602 1.272431448 1.201648587 1 20.75920041 1.331885777 1.355881949 0.879702531 1.371293912 0.650057505 0.090009721 0.745321528 1.39729483 0.495810476 0.028574032 21.4726565 -1.331885777 0.491591381 LLLIQAFRPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLLIQAFRPDR 11 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 222.34 7.06E-12 1695280000 1524400 1696520 1058210 1067580 1572370 1679650 1584950 1709890 1708540 FALSE TRUE 1322946.678 1685375.448 1569963.896 1309990.356 1541082.913 1744267.222 1431241.793 1344243.33 1506558.348 0.878125085 1.11869245 1.042086354 0.869525139 1.022916182 1.157782721 0.950007542 0.892261048 1 20.52282512 2.024284841 24.9998403 0.933244579 1.017849759 0.1005085 0.093108465 417.0957732 429374.2323 0.037582781 0.025337007 105.7510872 -2.024284841 0.08460518 LLLPGELAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 114.89 0.0036389 2327000000 7099200 6122700 3473400 5181600 5415400 5107000 5527000 7230800 6172300 FALSE TRUE 6161022.733 6082479.581 5153147.858 6358161.476 5307644.135 5303469.595 4990992.391 5684549.69 5442617.726 1.131996227 1.117565092 0.94681422 1.168217537 0.975200612 0.974433602 0.917020567 1.044451398 1 22.37586928 3.202664097 24.99913566 0.984720507 1.082725688 0.406710916 0.064981318 189.4670916 131948.4662 0.019267971 0.021848513 1594.645298 -3.202664097 0.098005181 LLLPHAFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLLPHAFSR 9 0 Q92733 Q92733 PRCC Proline-rich protein PRCC 0 133.57 0.00027316 381360000 102510 116120 61882 71752 117360 129360 111760 134440 52523 FALSE TRUE 88963.04377 115357.2001 91808.34218 88044.38826 115024.7656 134336.5629 100921.5324 105691.0522 46313.79077 1.920875884 2.490774306 1.982311114 1.90104042 2.483596434 2.900573688 2.179081667 2.28206438 1 15.49915423 3.259738696 24.97170827 2.220515501 2.097006657 0.00210973 0.50160707 1665.664105 1964022.547 0.145995107 0.188291773 1818.606321 -3.259738696 -0.123508843 LLLPHWAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLLPHWAK 8 0 P04062-4;P04062-5;P04062-2;P04062;A0A0G2JNZ5;A0A0G2JNZ0;A0A0G2JLB3;P04062-3 P04062-4 GBA Glucosylceramidase 0 97.071 0.0084919 315040000 459980 426880 277620 332650 406770 463230 401530 467320 442500 FALSE TRUE 399192.4776 424075.7972 411877.9606 408183.2667 398676.0728 481050.7578 362589.6824 367387.2547 390188.1541 1.023076876 1.086849492 1.05558807 1.046119064 1.021753399 1.232868689 0.929268812 0.941564347 1 18.57381045 LLLPWLEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLLPWLEAR 9 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 153.78 0.00017977 2892900000 1537330 1664870 1067410 1147950 1525160 1641480 1378100 1560430 1674650 FALSE TRUE 1334167.945 1653933.359 1583613.046 1408609.593 1494812.3 1704628.798 1244452.074 1226744.188 1476674.785 0.90349477 1.120039007 1.072418289 0.953906444 1.012282674 1.154369815 0.842739435 0.830747705 1 20.4939207 2.218380813 24.99998336 0.876558317 1.036735448 0.386188266 0.085467655 218.0974688 270190.5817 0.033867835 0.022865923 165.3410963 -2.218380813 0.160177131 LLLQVQHASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLLQVQHASK 10 0 P05141;P12236;P12235;V9GYG0 P05141;P12236;P12235 SLC25A5;SLC25A6;SLC25A4 "ADP/ATP translocase 2;ADP/ATP translocase 2, N-terminally processed;ADP/ATP translocase 3;ADP/ATP translocase 3, N-terminally processed;ADP/ATP translocase 1" 0 ; 141.93 3.66E-05 2509200000 1543990 2133490 644670 2050920 2947900 3023600 1609920 2840100 3095000 FALSE TRUE 1339947.81 2119474.964 956434.5683 2516612.732 2889242.557 3139919.849 1453790.206 2232766.717 2729112.626 0.490982965 0.776616891 0.350456247 0.922135902 1.058674725 1.150527765 0.532697036 0.818129195 1 21.3800005 3.716059412 24.42421451 0.89583607 0.563078513 0.45095568 0.193459466 600.236004 651533.5903 0.0551311 0.08184788 5200.671376 -3.716059412 -0.332757558 LLLSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLLSDR 6 0 Q7Z6L1-3;Q7Z6L1;Q7Z6L1-2;Q7Z6L1-4;C9JUV4 Q7Z6L1-3 TECPR1 Tectonin beta-propeller repeat-containing protein 1 0 107.74 0.072131 120740000 163100 171080 144160 173190 191690 215830 189810 209010 242950 FALSE TRUE 141545.9218 169956.1642 213876.2582 212515.4365 187875.744 224133.1198 171402.2554 164314.838 214228.7278 0.660723346 0.793339745 0.998354704 0.992002514 0.876986695 1.046232791 0.800089966 0.767006553 1 17.70879243 4.501461129 4.063864801 0.909830647 0.677801984 0.471228128 0.091761472 0.214211425 7.765211293 0.025097661 0.100283525 31729.34662 -4.501461129 -0.232028663 LLLWSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLLWSQR 7 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;E9PQ28;Q15149-4;Q15149-5;Q15149-8;E9PKG0 Q15149-3;Q15149-4;Q15149-5;Q15149-8;E9PKG0 PLEC Plectin 0 ; 180.15 0.0016069 808360000 641460 908970 652220 680390 933110 999560 793520 842930 914360 FALSE TRUE 556689.4357 902998.9162 967635.7735 834882.9486 914542.9366 1038013.72 716564.5525 662675.9792 806265.4024 0.690454327 1.11997726 1.200145474 1.035493953 1.134295151 1.287434283 0.888745257 0.821907994 1 19.62089529 2.070600545 24.99957799 0.885359802 1.086229902 0.203082979 0.161000366 61.02420613 21607.39659 0.064562956 0.043528332 117.6523334 -2.070600545 0.2008701 LLMHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLMHGK 6 0 F8VZX2;F8W1G6;F8W0G4;P57721;P57721-4;E9PFP8;P57721-5;P57721-3;P57721-2;F8VTZ0;J3QT27;F8VXH9;H3BSP4;Q15366;Q15366-6;Q15366-2;Q15366-3;Q15366-5;Q15366-4;Q15366-8;Q15366-7;Q15365 F8VZX2;Q15366;Q15366-2;Q15366-5;Q15365 PCBP2;PCBP3;PCBP1 Poly(rC)-binding protein 3;Poly(rC)-binding protein 2;Poly(rC)-binding protein 1 0 ; 72.338 0.085861 7153800000 18640800 17142100 11069500 12840900 15106500 15788600 17346700 19348100 17914700 FALSE TRUE 16177371.05 17029492.42 16422747.23 15756622.61 14805910.21 16395997.66 15664419.7 15210659.38 15796844.57 1.024088765 1.07803127 1.039622005 0.997453797 0.937270107 1.037928656 0.991617005 0.962892261 1 23.91313307 3.742232897 3.69504512 0.98482278 1.052093503 0.491996804 0.028646896 0.175258498 5.343353254 0.007729692 0.013138477 5523.73579 -3.742232897 0.067270723 LLNEEVLS(ph)YS(ph)SLLETIEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLNEEVLSYSSLLETIEVK 19 0 Q8NF91;Q8NF91-4;A0A0C4DG40;Q8NF91-7 Q8NF91 SYNE1 Nesprin-1 2 LLNEEVLS(0.407)Y(0.373)S(0.407)S(0.407)LLET(0.407)IEVK 48.547 0.07517 26951000 13460 14895 11902 15241 13920 18570 13725 11672 18785 TRUE FALSE 11681.2269 14797.15376 17657.84701 18701.70199 13643.01923 19284.39992 12393.95161 9176.033632 16564.2587 0.705206741 0.8933182 1.066020963 1.129039478 0.823642004 1.164217504 0.748234608 0.553965849 1 14.01578602 2.085288397 10.01992426 0.717014414 0.965965943 0.202890922 0.175155406 0.410919788 44.78095207 0.070123075 0.047254387 121.6993887 -2.085288397 0.24895153 LLNGNHENGDLDPTS(ph)PLENMDYIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLNGNHENGDLDPTSPLENMDYIK 24 0 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4;A8MV73;F8WE35;F5H8I0;F5H2W9;F5H2H9;F5GZ10;F5H502;F5H1K9;F5H6X8;F5H221;F5H592 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 LLNGNHENGDLDPT(0.23)S(0.77)PLENMDYIK;LLNGNHENGDLDPT(0.181)S(0.819)PLENMDYIK;LLNGNHENGDLDPT(0.098)S(0.902)PLENMDYIK 171.31 4.42E-12 352604000 407152 325683 289570 369099 340110 297764 352729 469788 677000 TRUE FALSE 353345.8316 323543.5669 429607.0206 452908.5693 333342.4764 309219.1738 318521.3959 369327.4921 596965.8312 0.591902942 0.541980043 0.719650938 0.758684242 0.558394566 0.517984711 0.533567215 0.618674425 1 19.18728883 1.239915384 6.457453632 1.011144507 0.603754633 0.713482404 0.078700206 0.070962043 13.64215118 0.127341333 0.021132148 17.37462275 -1.239915384 -0.407389874 LLNIWQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLNIWQER 8 0 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ; 110.12 0.0081123 906580000 581580 713410 422270 529680 647470 706050 597110 684550 667080 FALSE TRUE 504722.7295 708723.5627 626481.1844 649951.9397 634586.6138 733212.2004 539202.3641 538164.3097 588218.5623 0.858053047 1.204864328 1.065048308 1.104949727 1.07882793 1.246496196 0.916670093 0.91490535 1 19.16599279 2.199351036 24.99856415 0.936693526 1.096746025 0.312580748 0.10401152 165.9125118 105778.5223 0.039445442 0.026594552 158.2526664 -2.199351036 0.1600525 LLNQADPCVQILIQETGEHVLVTAGEVHLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLNQADPCVQILIQETGEHVLVTAGEVHLQR 31 0 Q7Z2Z2-2;Q7Z2Z2 Q7Z2Z2-2 EFTUD1 Elongation factor Tu GTP-binding domain-containing protein 1 0 159.89 1.22E-12 24960000 7937.5 9822 7516.2 9133.8 7912 10598 9914 11213 11124 FALSE TRUE 6888.539264 9757.478635 11151.05946 11207.76889 7754.56668 11005.71192 8952.541806 8815.18721 9808.933393 0.702271999 0.994754296 1.136826912 1.142608319 0.790561661 1.122009038 0.91269269 0.89868968 1 13.25988055 LLNTFLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLNTFLER 8 0 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 99.755 0.018864 111250000 598200 658050 441440 511150 591700 603680 721400 659990 869510 FALSE TRUE 519146.3544 653727.2262 654921.8605 627214.4199 579926.3276 626903.9602 651438.739 518856.2745 766717.5183 0.677102508 0.852631133 0.854189248 0.818051505 0.756375476 0.817646585 0.849646348 0.676724168 1 19.54833562 -0.490726873 0.010333762 1.677432694 3.33E-06 0.068897907 0.090888612 102796.1491 151.3856018 13347.36928 11305.73972 0.323052515 0.490726873 -1.677429366 LLPEEYHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLPEEYHR 8 0 Q5JTH9-2;Q5JTH9-3;Q5JTH9 Q5JTH9-2 RRP12 RRP12-like protein 0 131.06 0.0020001 0 79255 75390 54039 54289 74296 88463 62933 80599 89328 FALSE TRUE 68781.25094 74894.75813 80172.44115 66616.14721 72817.65496 91866.22885 56829.76735 63363.53107 78767.7456 0.873215939 0.950830287 1.017833385 0.845728752 0.924460316 1.166292474 0.721485259 0.804434995 1 16.26531736 2.202050344 24.99998416 0.829132721 0.957906879 0.207745053 0.110219385 252.1746847 172671.9816 0.044328742 0.029887387 159.2393308 -2.202050344 0.128774158 LLPEGEETLES(ph)DDEKDEHTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLPEGEETLESDDEKDEHTSK 21 1 Q8N6N3 Q8N6N3 C1orf52 UPF0690 protein C1orf52 1 LLPEGEETLES(1)DDEKDEHTSK 144.27 7.81E-08 286560000 162690 126310 66708 110640 118560 113230 180020 192250 191820 TRUE FALSE 141190.1043 125480.2613 98968.21192 135762.503 116200.888 117586.0314 162561.6881 151138.8336 169143.2581 0.834736813 0.741857894 0.585114731 0.802648031 0.686996864 0.695186037 0.961088783 0.893555175 1 17.36788615 2.237874464 24.99993836 0.939863717 0.720738104 0.688077354 0.07191619 10.20661496 371848.0549 0.027517837 0.019807743 172.9316414 -2.237874464 -0.219125613 LLPEKHEIENLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLPEKHEIENLR 12 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 ; 194.98 5.02E-07 258410000 470190 386870 257070 257329 371300 350100 435900 501570 223290 FALSE TRUE 408053.2002 384328.6255 381389.9118 315759.4825 363911.8564 363568.5735 393626.4851 394313.1587 196892.9106 2.072462635 1.95196782 1.937042379 1.603711792 1.84827303 1.84652953 1.999190748 2.002678296 1 17.58705164 1.234817275 24.99966592 0.99999871 1.905496807 0.83276077 0.127837185 45.77817321 305680.608 0.242150382 0.033275972 17.17185746 -1.234817275 0.905498097 LLPET(ph)VSPSAPSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLPETVSPSAPSWR 14 0 B0QXZ6;O95503 B0QXZ6 CBX6 Chromobox protein homolog 6 1 LLPET(0.915)VS(0.083)PS(0.002)APSWR 94.09 0.010439 0 42444 33829 41682 34340 34870 44706 31638 35663 39597 TRUE FALSE 36834.91786 33606.77507 61839.55462 42137.42185 34176.15522 46425.86875 28569.75163 28036.74498 34915.88777 1.054961515 0.962506676 1.771100739 1.206826592 0.97881387 1.329648814 0.81824503 0.802979582 1 15.09159603 2.231609746 24.99103221 0.85668703 1.219582847 0.323182722 0.233929774 184.0717467 661800.7385 0.095495597 0.065961825 170.4550003 -2.231609746 0.362895817 LLPETVS(ph)PSAPSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LLPETVSPSAPSWR 14 0 B0QXZ6;O95503 B0QXZ6 CBX6 Chromobox protein homolog 6 1 LLPET(0.161)VS(0.788)PS(0.051)APSWR;LLPET(0.09)VS(0.785)PS(0.126)APSWR;LLPET(0.002)VS(0.977)PS(0.02)APSWR;LLPET(0.002)VS(0.979)PS(0.019)APSWR 218.6 5.58E-12 520150000 569666 533734 384539 416710 505362 655930 503362 566505 658610 TRUE FALSE 494383.1948 530227.8662 570503.3466 511330.3745 495306.2849 681164.0515 454546.0307 445362.3143 580749.8761 0.851284202 0.913005561 0.982356381 0.880465749 0.852873682 1.172904342 0.782688123 0.766874575 1 19.14755742 LLPGPENHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLPGPENHR 9 0 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 0 169.21 5.86E-05 67995000 159090 143060 91123 109730 133500 134040 136350 158300 138800 FALSE TRUE 138065.8534 142120.2294 135190.3876 134645.8736 130843.6112 139196.6055 123126.798 124448.7769 122391.2221 1.128069898 1.16119626 1.104575845 1.100126882 1.069060419 1.137308731 1.006010038 1.016811294 1 16.90114057 1.696439301 0.391949419 0.906233687 1.150284024 0.721039758 0.030075533 2.519672558 0.497980017 0.302007465 0.049593194 49.70948928 -1.696439301 0.244050337 LLPLEEHYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LLPLEEHYR 9 0 A0A024R571;Q9H4M9;C9JC03;C9JIJ3;C9IZH1;Q9NZN3-2;Q9NZN3;Q9NZN4 A0A024R571;Q9NZN3;Q9NZN4 EHD1;EHD3;EHD2 EH domain-containing protein 1;EH domain-containing protein 3;EH domain-containing protein 2 0 ;;;; 168.8 5.90E-05 1225480000 436174 434118 258758 316144 383933 464417 391539 422870 429107 FALSE TRUE 378532.5008 431266.2503 383894.2343 387929.3272 376293.4845 482283.4225 353567.608 332442.5413 378378.4593 1.00040711 1.139774846 1.014577402 1.025241574 0.994489711 1.274605915 0.934428479 0.878597957 1 18.52947043 2.043832953 24.99817434 0.923392047 1.072100408 0.345966669 0.088274569 127.5195631 72724.58032 0.034475251 0.023243195 110.6198215 -2.043832953 0.148708361 LLPPVGTGRS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLPPVGTGRSPR 12 1 Q9NWZ5;Q9NWZ5-4;Q9NWZ5-3;Q9NWZ5-2 Q9NWZ5 UCKL1 Uridine-cytidine kinase-like 1 1 LLPPVGT(0.108)GRS(0.892)PR 86.539 0.0066945 271150000 286700 244940 157650 126970 223820 287010 228070 225270 97396 TRUE FALSE 248811.8686 243330.973 233890.0673 155800.4791 219366.4199 298051.4604 205951.8065 177097.7636 85881.95583 2.897137893 2.833318951 2.723390089 1.814123556 2.554278344 3.470478257 2.398080068 2.062106782 1 16.39006743 1.305450905 1.80549937 0.569587407 2.676911876 0.630381246 0.411545192 0.539173251 1.894079883 1.897418492 0.12016379 20.20463016 -1.305450905 2.107324469 LLPPYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLPPYLR 7 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 84.609 0.049831 126010000 263370 226570 134040 174140 232140 254160 227730 254130 255890 FALSE TRUE 228564.9872 225081.6468 198862.1923 213681.1486 227520.8682 263937.6997 205644.7797 199786.2771 225638.9757 1.012967669 0.997529997 0.881329086 0.947004603 1.008340281 1.169734523 0.911388553 0.8854245 1 17.78365677 LLPQGTVIFEDISIEHFEGTVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLPQGTVIFEDISIEHFEGTVTK 23 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 182.77 3.84E-17 14712000 27316 24940 14534 24086 23178 21218 29646 36798 29849 FALSE TRUE 23706.12139 24776.1675 21562.69101 29555.09443 22716.80315 22034.27019 26770.93548 28929.03406 26320.28522 0.900678742 0.941333549 0.8192423 1.122901754 0.86309107 0.837159248 1.017121785 1.099115523 1 14.6838875 2.052594761 7.579912007 1.057157402 0.918463192 0.319466017 0.086408253 0.239231236 29.29203315 0.034581498 0.02315989 112.8742197 -2.052594761 -0.13869421 LLPQLTYLDGYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 77.379 0.060741 282930000 119030 94902 77790 90279 102950 84374 87909 121690 223770 FALSE TRUE 103299.8839 94278.58251 115409.5042 110778.2268 100901.4964 87619.92238 79383.59871 95667.54049 197316.1655 0.523524688 0.477804656 0.584896346 0.561424993 0.511369639 0.44405851 0.402316751 0.484843906 1 17.59014963 1.23777148 24.99819076 1.000000585 0.496281644 0.898954562 0.05280461 6.314098946 199888.2754 0.083970802 0.014369774 17.28906394 -1.23777148 -0.50371894 LLPQLTYLDGYDRDDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLPQLTYLDGYDRDDK 16 1 P39687;H0YN26 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;; 176.17 2.98E-09 2514793000 1363596 1137258 929159 1160465 1124589 997597 912127 1310092 2546060 FALSE TRUE 1183393.334 1129787.277 1378503.4 1423966.315 1102211.879 1035975.202 823669.0639 1029939.021 2245067.687 0.527108087 0.503230831 0.614014182 0.634264313 0.490948173 0.461444975 0.36687939 0.458756334 1 21.09832751 1.235420307 24.99997794 1.00000068 0.503509196 0.804486021 0.076349328 43.26038207 344335.1737 0.147500807 0.021295626 17.19571773 -1.235420307 -0.496491484 LLPSAPQTLPDGPLAS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR 293.33 1.39E-49 19367880000 3272675 4826074 3764567 4898777 5955964 5435200 5213606 6273718 7638196 TRUE FALSE 2840182.707 4794371.202 5585124.193 6011119.191 5837451.969 5644295.661 4707991.293 4932132.228 6735217.17 0.421691333 0.711836171 0.829241887 0.892490775 0.866705827 0.83802727 0.69901106 0.732290007 1 22.68329303 4.70814604 2.333489955 0.823033421 0.340142646 0.711873568 0.083183496 0.318885012 2.189894209 0.022726143 0.305148734 51067.66964 -4.70814604 -0.482890774 LLPYPTLAS(ph)PASD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLPYPTLASPASD 13 0 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 LLPYPTLAS(0.995)PAS(0.005)D 97.911 0.0037354 11413000 49832 47510 34382 36562 44516 47508 49880 56793 47368 TRUE FALSE 43246.57494 47197.90368 51009.2502 44863.96092 43630.21869 49335.6635 45042.64528 44648.25891 41768.209 1.035394526 1.12999587 1.221245809 1.074117421 1.044579591 1.181177376 1.07839542 1.068953158 1 15.35011766 1.293416621 1.428758476 0.960197668 1.114873849 0.27420564 0.057536226 1.514796374 3.004349446 0.33493382 0.017092952 19.65244644 -1.293416621 0.154676181 LLPYPTLASPAS(ph)D ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LLPYPTLASPASD 13 0 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 LLPYPTLAS(0.01)PAS(0.99)D;LLPYPTLAS(0.001)PAS(0.999)D;LLPYPTLASPAS(1)D;LLPYPTLASPAS(1)D 178.67 1.51E-05 127747000 244830 241866 134185.7 165833.2 219384.4 224159 192997 242155 178869.9 TRUE FALSE 212475.0952 240277.1663 199078.3533 203488.1627 215019.0797 232782.5418 174280.1806 190372.0377 157724.1042 1.347131412 1.523401686 1.26219359 1.290152597 1.363260744 1.47588438 1.104968588 1.206993938 1 17.26704363 2.226722431 24.99902967 1.125487985 1.373867357 0.660489794 0.091824737 143.1835586 302362.1135 0.037288705 0.025364197 168.547545 -2.226722431 0.248379372 LLQAFLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLQAFLER 8 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ; 125.31 0.0029482 336710000 971000 968350 548080 592010 1057770 1122580 867130 920230 954540 FALSE TRUE 842679.8898 961988.8451 813133.3212 726434.9188 1036722.446 1165766.379 783035.8661 723445.9757 841695.3686 1.001169688 1.142918069 0.966066051 0.863061561 1.231707439 1.385021734 0.930307918 0.859510463 1 19.68293865 2.03845676 24.99998855 0.912275808 1.095371559 0.223432155 0.147115572 228.5099252 148548.9398 0.063592528 0.042873998 109.2588841 -2.03845676 0.183095752 LLQDFFNGK ddPTM_MDA-MB-175_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 ; 191.85 8.24E-05 2295800000 2793500 2557200 1695280 1926750 2271610 2094320 2904000 3132100 2920300 FALSE TRUE 2424331.897 2540401.585 2515123.078 2364248.036 2226409.405 2174889.846 2622370.527 2462324.789 2575065.461 0.941464182 0.986538643 0.976721997 0.918131237 0.864603032 0.844595945 1.018370432 0.956218328 1 21.29617768 2.202736035 24.99999851 0.985291429 0.924643444 0.333084442 0.045991344 258.0012561 180043.0891 0.020909062 0.014097444 159.4909463 -2.202736035 -0.060647985 LLQDFFNGR ddPTM_MDA-MB-175_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 ; 185.58 9.93E-05 9945300000 2275800 2223100 1543500 1727510 2169400 2381700 2261400 2599300 2568600 FALSE TRUE 1975047.264 2208496.31 2289941.763 2119767.549 2126233.184 2473325.54 2042089.776 2043459.923 2264943.034 0.872007478 0.975078082 1.011037244 0.935903251 0.938757908 1.09200342 0.901607566 0.902212502 1 21.11104333 4.742861786 23.8469567 0.964232637 0.872007409 0.220342593 0.056894528 401.728754 2227140.208 0.014204564 0.106562849 55317.40343 -4.742861786 -0.092225228 LLQDFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLQDFNR 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 136.33 0.0069565 249640000 462840 514260 297790 366380 536910 462360 527530 533120 536000 FALSE TRUE 401674.5213 510881.7922 441802.24 449572.1788 526226.5414 480147.2884 476370.2218 419116.4367 472634.6906 0.849862546 1.080923179 0.934764732 0.951204361 1.113389584 1.015895147 1.007903633 0.886766133 1 18.850366 4.766017892 23.74318698 0.991142649 0.84986215 0.32692755 0.06637011 6692.317591 5786872.724 0.016826783 1.371146004 58346.91412 -4.766017892 -0.1412805 LLQDHPWLLSQNLVVKPDQLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLQDHPWLLSQNLVVKPDQLIK 22 1 P53396;P53396-2;P53396-3;K7ESG8 P53396 ACLY ATP-citrate synthase 0 ; 264.72 9.98E-38 2263300000 2676500 2146840 1579150 2101460 2029050 1713360 2829000 3234100 3102200 FALSE TRUE 2322793.744 2132737.267 2342832.222 2578628.612 1988675.875 1779274.068 2554644.015 2542512.883 2735461.45 0.849141465 0.779662702 0.856466912 0.942666771 0.726998319 0.650447502 0.933898745 0.929463979 1 21.38335279 2.034874784 24.99813755 0.951290153 0.804428751 0.453863538 0.079571793 170.5149141 122223.8705 0.034180001 0.023044057 108.3614442 -2.034874784 -0.146861403 LLQDMDINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLQDMDINR 9 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6;H0Y9N9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ;; 192.6 8.04E-05 375564000 574590 753030 436690 490480 740410 778010 671970 696900 682180 FALSE TRUE 498656.4757 748083.2963 647874.7446 601850.9805 725677.2896 807940.5481 606802.4528 547873.3583 601533.4575 0.828975462 1.243627078 1.077038586 1.000527856 1.206378931 1.343134846 1.008759272 0.910794489 1 19.19828546 2.012400012 24.99022539 0.952250805 1.124104792 0.193760978 0.140481393 307.748015 620213.8399 0.056101621 0.037796689 102.89636 -2.012400012 0.171853987 LLQDS(ph)SSPVDLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLQDSSSPVDLAK 13 0 Q15596;E7EWM1 Q15596 NCOA2 Nuclear receptor coactivator 2 1 LLQDS(0.442)S(0.279)S(0.279)PVDLAK 107.14 0.0013832 26102000 95564 76433 45716 59301 73805 59436 84973 94330 85702 TRUE FALSE 82934.97527 75930.90659 67824.41051 72766.19841 72336.4249 61722.54138 76732.33154 74158.26358 75570.40719 1.097453069 1.004770378 0.897499604 0.962892766 0.957205705 0.816755443 1.015375388 0.981313537 1 16.20553378 4.602116844 3.316130799 0.950132586 1.099641692 0.417311204 0.056607081 0.274224427 4.933738205 0.014375761 0.083566925 40005.23664 -4.602116844 0.149509107 LLQDSSS(ph)PVDLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLQDSSSPVDLAK 13 0 Q15596;E7EWM1 Q15596 NCOA2 Nuclear receptor coactivator 2 1 LLQDS(0.001)S(0.187)S(0.812)PVDLAK;LLQDSS(0.113)S(0.887)PVDLAK 224.07 1.54E-11 293000000 1179620 1056120 701670 825480 943020 762780 1118170 1299900 1135450 TRUE FALSE 1023730.228 1049182.278 1040999.959 1012917.851 924255.747 792124.6402 1009730.046 1021926.501 1001218.395 1.022484439 1.047905516 1.039733154 1.011685219 0.923131009 0.791160694 1.008501293 1.020682906 1 19.93332527 3.40823843 5.293266409 0.954584099 1.036127405 0.287739898 0.064471651 0.314153019 16.47800747 0.02107958 0.027568404 2559.990948 -3.40823843 0.081543306 LLQELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLQELR 6 0 Q8N163-2;Q8N163;H0YB24;G3V119;A0A087WXM7;E9PNP6;I3L400;I3L0W2;J3KRA9;Q96Q15-2;Q96Q15;P11532-2;A0A087WTU7;A0A5H1ZRP8;A0A087WV90;P11532-3;P11532-4;A0A075B6G3;P11532-11;P11532;H0Y304 Q8N163-2;J3KRA9;P11532-2 CCAR2;SMG1;DMD Cell cycle and apoptosis regulator protein 2;Serine/threonine-protein kinase SMG1;Dystrophin 0 ; 98.133 0.093712 161093000 449980 444490 276010 341540 424930 424380 444320 459850 450310 FALSE TRUE 390514.0029 441570.1159 409489.3592 419091.8771 416474.7244 440706.1732 401229.9148 361514.6561 397074.8648 0.983477015 1.112057587 1.031264871 1.055448013 1.048856932 1.109881819 1.010464148 0.910444574 1 18.59905151 1.987806144 7.870089558 0.952022813 1.058032701 0.49747944 0.042171702 0.103680175 42.40071679 0.017196341 0.010419401 97.2313115 -1.987806144 0.106009888 LLQHGINADDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLQHGINADDKR 12 1 Q96P70 Q96P70 IPO9 Importin-9 0 ;; 172.76 2.27E-05 963780000 1357050 1054280 1459250 1080440 951170 818580 1185070 1421980 1285380 FALSE TRUE 1177712.404 1047354.365 2164948.181 1325770.415 932243.5779 850071.3023 1070142.094 1117900.643 1133423.841 1.039075024 0.92406241 1.910095856 1.169704014 0.822502178 0.750003019 0.944167623 0.986304154 1 20.11225602 3.391161742 5.733957688 0.909877577 1.298570627 0.319794706 0.264913639 0.250033312 13.02850579 0.078294653 0.101720732 2461.284074 -3.391161742 0.38869305 LLQHLLEACGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLQHLLEACGR 11 0 A0A0A0MQS1;Q53H96-2;Q53H96;A0A087WTU2;B5MD87 A0A0A0MQS1 PYCRL Pyrroline-5-carboxylate reductase;Pyrroline-5-carboxylate reductase 3 0 ; 143 3.74E-05 709440000 445630 591350 390420 399690 528240 619080 572760 622630 562980 FALSE TRUE 386738.8664 587465.3829 579228.4179 490445.7234 517729.0575 642896.4082 517213.8234 489485.4198 496425.1457 0.779047697 1.183391671 1.166799109 0.987955037 1.042914651 1.295052061 1.041876762 0.986020599 1 18.92121667 2.000649808 24.99993977 0.998592817 1.086811234 0.055154749 0.135674437 58.3081993 2243210.253 0.054326622 0.036257198 100.1497359 -2.000649808 0.088218417 LLQLVEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LLQLVEDR 8 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;; 131.06 0.0023757 567350000 1023924 979370 575827 731276 934391 1054130 865726 980759 919381 FALSE TRUE 888609.8491 972936.454 854298.8632 897323.3927 915798.4472 1094683.063 781768.0258 771031.3201 810692.8255 1.096111648 1.200129597 1.053788607 1.106859916 1.129649133 1.350305601 0.964320888 0.951077024 1 19.62879585 2.112011337 21.72339489 0.967062275 1.150674608 0.53702368 0.080537247 2.509499825 473.1921186 0.032357199 0.021815223 129.4229626 -2.112011337 0.183612333 LLQTCFS(ph)SPADDSMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLQTCFSSPADDSMDR 16 0 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 1 LLQT(0.021)CFS(0.49)S(0.49)PADDSMDR;LLQT(0.002)CFS(0.499)S(0.499)PADDSMDR;LLQT(0.001)CFS(0.673)S(0.327)PADDSMDR 140.93 6.46E-06 720560000 1181169 1191994 811858 867833 1065578 1306290 1158240 1189638 1412650 TRUE FALSE 1025074.524 1184163.713 1204475.244 1064887.747 1044375.083 1356543.822 1045914.063 935243.1715 1245648.126 0.82292463 0.950640625 0.966946619 0.854886484 0.838419021 1.089026502 0.839654507 0.750808476 1 20.24846516 LLQTCFSS(ph)PADDSMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 LLQTCFSSPADDSMDR 16 0 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 1 LLQT(0.001)CFS(0.382)S(0.617)PADDSMDR;LLQTCFS(0.471)S(0.529)PADDSMDR;LLQTCFS(0.062)S(0.938)PADDSMDR;LLQTCFS(0.064)S(0.936)PADDSMDR;LLQTCFS(0.01)S(0.99)PADDSMDR;LLQTCFS(0.063)S(0.937)PADDSMDR;LLQTCFS(0.026)S(0.974)PADDSMDR;LLQTCFS(0.183)S(0.817)PADDSMDR;LLQT(0.001)CFS(0.217)S(0.782)PADDSMDR 366.58 3.64E-104 2226000000 2887380 2930380 2034280 2249230 2626860 3213500 2821900 2995990 3156020 TRUE FALSE 2505805.417 2911130.141 3018064.612 2759952.049 2574590.625 3337125.424 2548232.572 2355320.853 2782918.911 0.900423439 1.046070775 1.084496066 0.991747204 0.925140368 1.199145764 0.915668999 0.846349078 1 21.40816744 2.037242062 24.99980361 0.90284183 1.025139209 0.220233314 0.090393957 197.233067 132397.5857 0.035314009 0.023808635 108.9537197 -2.037242062 0.122297379 LLQTDDEEEAGLLELLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLQTDDEEEAGLLELLK 17 0 P55060-3;P55060 P55060-3 CSE1L Exportin-2 0 ; 199.68 3.04E-11 61786000 113690 87478 53169 82488 85845 83146 103989 118706 119720 FALSE TRUE 98665.57845 86903.35126 78881.70624 101218.1612 84136.85245 86344.68042 93904.16279 93321.64567 105566.838 0.934626634 0.823206917 0.747220507 0.958806412 0.797000782 0.817914812 0.889523307 0.884005313 1 16.68779718 0.625285632 1.147176986 1.414020488 0.845633575 0.352847785 0.062767959 6.362762619 2.477134679 6.20155276 0.018636655 4.219739409 -0.625285632 -0.568386913 NGAAGPHS(ph)PDPLLDEQAFGDLTDLPVVPK ddPTM_MDA-MB-175_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 259.26 2.95E-58 1122777000 185055 252407 187507 294019 464991 331271 544884 644940 667730 TRUE FALSE 160599.5129 250748.9218 278186.0124 360780.5077 455738.5888 344015.2097 492041.2335 507024.5999 588791.7201 0.272761161 0.425870326 0.472469301 0.612747251 0.774023434 0.584273178 0.835679608 0.861127259 1 19.16739786 3.429526861 0.256252977 1.164744972 1.50E-16 0.891056722 0.073532806 1.439295416 0.37363929 0.602157883 0.942258957 2688.604128 -3.429526861 -1.164744972 down LLRPNS(ph)LR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLRPNSLR 8 1 A0A0A0MRB5;Q8WXG6-6;Q8WXG6-8;Q8WXG6-5;Q8WXG6-4;Q8WXG6-7;Q8WXG6-3;Q8WXG6-2;Q8WXG6 A0A0A0MRB5 MADD MAP kinase-activating death domain protein 1 LLRPNS(1)LR 81.335 0.060836 296350000 291820 335510 227880 270010 350770 409340 404880 419960 415250 TRUE FALSE 253255.2476 333306.0127 338083.5302 331319.8973 343790.3633 425087.5747 365614.7999 330154.8221 366159.6181 0.691652588 0.910275181 0.923322818 0.904851002 0.93890846 1.16093516 0.998512075 0.901669124 1 18.48211317 5.482389795 0.844518543 0.98586759 1.70E-13 0.612919574 0.072222999 5.56652881 1.248400553 0.026898284 6.864732464 303661.5433 -5.482389795 -0.98586759 LLRPSLAELHDELEKEPFEDGFANGEES(ph)TPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLRPSLAELHDELEKEPFEDGFANGEESTPTR 32 2 G3XAL9;P55011-3;P55011 G3XAL9 SLC12A2 Solute carrier family 12 member 2 1 LLRPSLAELHDELEKEPFEDGFANGEES(0.531)T(0.427)PT(0.042)R 138.8 2.73E-09 138770000 92261 98187 79416 131160 125640 102330 71857 169060 145360 TRUE FALSE 80068.47509 97542.00313 117821.8432 160941.8827 123140.0098 106266.7013 64888.3192 132907.8346 128175.7064 0.624677463 0.761002267 0.919221329 1.255634841 0.960712551 0.829070534 0.506245068 1.036919073 1 16.96776332 4.428602001 3.094295792 0.925396785 0.640186477 0.233770569 0.186771436 0.413868561 7.638700242 0.051070686 0.200858031 26828.84653 -4.428602001 -0.285210307 LLS(ph)AACR ddPTM_MDA-MB-175_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 77.732 0.039073 90555000 81147 99283 60842 75521 102820 86183 90683 102840 120770 TRUE FALSE 70423.21835 98630.80344 90265.3947 92669.19732 100774.0832 89498.51578 81888.57662 80848.4663 106492.7082 0.661296154 0.926174243 0.847620426 0.870192888 0.946300314 0.840419192 0.768959472 0.759192509 1 16.70039512 6.28605502 6.875346372 0.842849809 0.79155471 0 0.099184182 78883084.6 0 0.02203736 0 1932213.091 -6.28605502 -0.0512951 LLS(ph)DSLPPSTGTFQEAQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LLSDSLPPSTGTFQEAQSR 19 0 Q9Y490 Q9Y490 TLN1 Talin-1 1 LLS(1)DSLPPSTGTFQEAQSR;LLS(0.985)DS(0.015)LPPSTGTFQEAQSR;LLS(0.979)DS(0.021)LPPSTGTFQEAQSR;LLS(0.979)DS(0.021)LPPSTGTFQEAQSR;LLS(0.973)DS(0.027)LPPSTGTFQEAQSR 194.37 3.27E-15 530327000 397900 445858 301762 356014 535225 465867 458621 547449 477760 TRUE FALSE 345316.5068 442929.1294 447695.1125 436852.42 524575.0696 483789.2049 414144.006 430381.2916 421279.7571 0.819684547 1.051389539 1.062702646 1.036965135 1.245194104 1.148379899 0.983061728 1.021604491 1 18.68441907 4.74260165 4.09403011 1.069231508 0.797523651 0.51206844 0.07659543 0.216346797 7.870616507 0.020574814 0.174728788 55284.27901 -4.74260165 -0.271707857 LLS(ph)FQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LLSFQR 6 0 Q13946-3;Q13946-2;Q13946;A1E5M1;Q9NP56 Q13946-3;A1E5M1 PDE7A;PDE7B "High affinity cAMP-specific 3,5-cyclic phosphodiesterase 7A;cAMP-specific 3,5-cyclic phosphodiesterase 7B" 1 LLS(1)FQR;LLS(1)FQR;LLS(1)FQR;LLS(1)FQR;LLS(1)FQR;LLS(1)FQR 127.46 0.017883 3244200000 1757540 1741570 1344840 1419030 1823020 1988710 1844180 1939520 2403230 TRUE FALSE 1525276.636 1730129.512 1995209.122 1741242.45 1786745.469 2065216.961 1665331.707 1524768.741 2119122.887 0.719767903 0.816436613 0.941525918 0.821680734 0.843153306 0.974562152 0.78585896 0.719528231 1 21.01503582 4.663695751 3.834204988 0.853920087 0.715276293 0.21604218 0.086743202 0.391105266 9.816370035 0.022058747 0.127799253 46099.45074 -4.663695751 -0.138643794 LLS(ph)PGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLSPGAR 7 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 1 LLS(1)PGAR;LLS(1)PGAR 124.74 0.0043183 523270000 1265540 1302300 886040 1053010 1302490 1305110 1282910 1441530 1442100 TRUE FALSE 1098295.683 1293745.106 1314531.908 1292112.015 1276572.997 1355318.426 1158493.586 1133270.027 1271616.581 0.863700347 1.017401884 1.033748637 1.016117621 1.003897729 1.065823179 0.911040012 0.891204192 1 20.2782323 2.213156582 24.98457258 0.924188552 1.003328838 0.208805337 0.059345682 287.0197754 282278.4234 0.023722501 0.016000778 163.364084 -2.213156582 0.079140286 LLS(ph)PLSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LLSPLSSAR 9 0 A0A087WZ13;Q8IY67-2;E9PAU2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 LLS(1)PLSSAR;LLS(0.995)PLS(0.005)SAR;LLS(1)PLSSAR;LLS(0.947)PLS(0.053)SAR;LLS(1)PLSSAR;LLS(0.991)PLS(0.009)SAR;LLS(0.966)PLS(0.034)SAR;LLS(1)PLSSAR 199.33 2.61E-05 4059619000 2916180 2932584 1896842 2086265 2807111 2809632 2828690 3223123 3055146 TRUE FALSE 2530799.424 2913319.663 2814161.136 2559983.355 2751254.983 2917720.361 2554364.079 2533883.229 2693970.12 0.939431141 1.081422411 1.044614829 0.950264198 1.021264105 1.083055947 0.948178326 0.940575847 1 21.36130242 2.196615236 24.98497152 0.957649187 1.020805723 0.227097117 0.049316764 190.646111 113557.9587 0.019676553 0.01326607 157.2589009 -2.196615236 0.063156535 LLS(ph)PQQPALQR ddPTM_MDA-MB-175_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 197.38 6.01E-08 4471960000 1792000 1810430 1194910 1358420 1780600 1879870 1589530 1818810 1713430 TRUE FALSE 1555182.66 1798537.166 1772772.473 1666870.023 1745169.544 1952189.815 1435377.625 1429871.635 1510870.257 1.029329059 1.190398155 1.173345272 1.103251596 1.155075716 1.292096264 0.950033676 0.946389426 1 20.52694835 2.212562097 24.99996331 0.960854835 1.156934503 0.643662953 0.067235088 129.5023925 124527.4533 0.02660733 0.017945274 163.1406156 -2.212562097 0.196079667 LLS(ph)PRPSLLT(ph)PTGDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLSPRPSLLTPTGDPR 16 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 2 LLS(1)PRPS(0.304)LLT(0.692)PT(0.005)GDPR 81.665 0.027833 57569000 110990 90150 63672 61239 83278 105690 99825 102590 71295 TRUE FALSE 96322.39029 89557.79871 94463.99217 75144.25093 81620.93073 109755.9627 90143.98686 80651.92686 62866.58632 1.532171475 1.424569139 1.502610492 1.195297142 1.298319752 1.745855296 1.433893458 1.282906097 1 15.94000581 1.344966011 2.317462194 0.940643249 1.443421472 0.497576583 0.144018365 0.426745053 2.945006963 0.40341205 0.039927692 22.12921514 -1.344966011 0.502778223 LLS(ph)PRPSLLTPTGDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LLSPRPSLLTPTGDPR 16 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 LLS(1)PRPSLLTPTGDPR;LLS(1)PRPSLLTPTGDPR;LLS(0.98)PRPS(0.019)LLT(0.001)PTGDPR;LLS(0.996)PRPS(0.004)LLTPTGDPR 114.4 0.00035506 2479190000 3890250 3366930 2057300 2258560 3227780 3442700 3374690 3703660 2459240 TRUE FALSE 3376143.606 3344812.415 3052217.161 2771400.568 3163553.493 3575142.897 3047413.083 2911661.131 2168511.449 1.556894527 1.542446279 1.407517199 1.2780198 1.458859484 1.648662219 1.405301819 1.342700373 1 21.04827363 1.16185992 1.774082538 0.759395983 1.47119772 0.690844316 0.099510055 0.713327809 1.779428085 0.92726909 0.029401847 14.51643321 -1.16185992 0.711801737 LLS(ph)WSDNWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LLSWSDNWR 9 0 Q8TCD5;J3KSY6;J3KSX6 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 1 LLS(0.919)WS(0.081)DNWR;LLS(0.944)WS(0.056)DNWR;LLS(0.996)WS(0.004)DNWR;LLS(0.999)WS(0.001)DNWR 192.14 3.68E-05 1036357000 799000 859570 555244 632530 848030 800550 733340 913920 818150 TRUE FALSE 693410.1256 853923.4281 823761.8556 776155.6041 831155.8621 831347.6765 662220.7997 718485.3201 721429.239 0.961161661 1.183655142 1.14184706 1.075858258 1.152096169 1.15236205 0.917928972 0.995919324 1 19.46049837 2.243492322 24.99998033 0.974192302 1.116108992 0.507782191 0.064778923 90.67977481 459679.8753 0.023421478 0.017560903 175.1831465 -2.243492322 0.141916691 LLSAACR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LLSAACR 7 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;; 198.52 0.0009254 2730800000 1398433 2182250 1615122 1417245 2043490 2334360 2236950 2040790 2192630 FALSE TRUE 1213626.536 2167914.656 2396200.401 1739052.138 2002828.547 2424164.34 2020010.933 1604382.94 1933419.779 0.627709796 1.12128503 1.239358585 0.899469508 1.035899482 1.253822044 1.044786525 0.829816141 1 20.88272348 1.760934343 24.99999528 0.907070473 1.046801146 0.0616057 0.181828697 26.91680058 30106.14047 0.094217302 0.045245839 57.66792735 -1.760934343 0.139730673 LLSAEFLEQHYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LLSAEFLEQHYDR 13 0 Q9Y376 Q9Y376 CAB39 Calcium-binding protein 39 0 ;;; 234.04 1.19E-16 1963140000 2507780 2194960 1828140 2127440 2177280 2489980 2104450 2391550 3300360 FALSE TRUE 2176370.519 2180541.163 2712234.619 2610507.768 2133956.388 2585771.142 1900360.763 1880135.644 2910195.201 0.747843484 0.749276599 0.931976872 0.897021536 0.733269159 0.888521547 0.653001133 0.646051386 1 21.47268449 2.246658348 24.9753962 0.736565544 0.825239615 0.031931091 0.118012598 400.8744442 1236398.104 0.044552304 0.033892564 176.4649055 -2.246658348 0.088674071 LLSDATVEKDESHAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLSDATVEKDESHAGK 16 1 Q14320 Q14320 FAM50A Protein FAM50A 0 ;; 178.12 1.71E-09 447170000 960540 703840 584060 638720 640160 507560 873660 1036760 800390 FALSE TRUE 833602.2053 699216.4287 866513.3696 783751.1382 627422.0685 527086.1616 788932.5877 815056.9421 705768.806 1.181126451 0.990715972 1.227758102 1.110492744 0.888990932 0.746825529 1.117834312 1.154849768 1 19.42883614 3.442025865 23.10733539 1.001621907 1.127314072 0.237512937 0.127470031 149.8035623 98631.72094 0.040813545 0.052690516 2767.106439 -3.442025865 0.125692165 LLSDFLDSEVSELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLSDFLDSEVSELR 14 0 Q9BPX3 Q9BPX3 NCAPG Condensin complex subunit 3 0 132.76 0.00011283 7549500 16085 17127 9960.6 13259 17471 17048 16263 17287 16696 FALSE TRUE 13959.3265 17014.49161 14777.57948 16269.6586 17123.36128 17703.84759 14685.81676 13590.30958 14722.2179 0.948180946 1.155701656 1.00376041 1.105109211 1.163096579 1.20252585 0.997527469 0.923115639 1 13.84570741 2.017695903 22.59917116 0.957342697 1.098451996 0.369501346 0.07664576 70.93710647 90591.65558 0.030711351 0.020697227 104.1587845 -2.017695903 0.141109299 LLSGPSQES(ph)PQTLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLSGPSQESPQTLGK 15 0 Q9BWE0;Q9BWE0-4;C9JZE3;C9JYJ8;E7EVL6 Q9BWE0 REPIN1 Replication initiator 1 1 LLSGPS(0.106)QES(0.892)PQT(0.003)LGK;LLSGPS(0.011)QES(0.981)PQT(0.008)LGK 121.03 0.0001233 460850000 237520 218190 125859 147801 208060 192710 211703 242140 220970 TRUE FALSE 206131.1302 216756.6955 186724.8334 181361.476 203920.0131 200123.6784 191172.0756 190360.2453 194847.1783 1.057911805 1.112444621 0.95831428 0.930788311 1.04656385 1.027080197 0.981138538 0.97697204 1 17.57198351 4.239651715 24.99971863 0.988612209 1.085178229 0.570371063 0.034813317 20.07704142 459955.1795 0.009102781 0.021476684 17364.07747 -4.239651715 0.096566021 LLSHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLSHGK 6 0 Q02878;F8VZ45;U3KQR5;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ; 117.56 0.022615 2188000000 4640300 4070500 2771600 3481300 3089800 3530400 4281400 4847000 5686300 FALSE TRUE 4027072.598 4043760.617 4111955.03 4271782.373 3028319.025 3666216.772 3866190.487 3810506.769 5014072.092 0.803154108 0.806482345 0.82008295 0.851958706 0.603963998 0.731185493 0.771067989 0.759962501 1 22.25755131 1.237463538 24.99513628 1.000000277 0.767306033 0.538487197 0.067350446 22.84951891 520343.5059 0.101585489 0.017022061 17.27680922 -1.237463538 -0.232694244 LLSLLEKDEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLSLLEKDEFK 11 1 P35270 P35270 SPR Sepiapterin reductase 0 ; 165.7 1.94E-05 640940000 834000 681370 542500 674310 619030 451220 911640 1070500 740770 FALSE TRUE 723784.7869 676894.0356 804854.8146 827422.3917 606712.5141 468578.7254 823229.2931 841581.9056 653197.0145 1.108065057 1.03627852 1.23217773 1.266727149 0.928835406 0.717362013 1.260307801 1.288404397 1 19.31715867 LLSPGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLSPGAR 7 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ;; 95.62 0.045975 235000000 383824 398150 254936 312782 391862 466330 395448 428240 410454 FALSE TRUE 333100.6859 395534.5264 378223.9023 383803.9337 384064.7129 484270.0169 357097.5138 336664.2086 361930.5957 0.920344093 1.092846339 1.045017765 1.060435172 1.061155695 1.338019009 0.986646385 0.930189966 1 18.46535355 2.02313053 24.99962147 0.959601208 1.089065595 0.213579534 0.103545481 310.5456944 335638.3379 0.042034297 0.028337762 105.4703847 -2.02313053 0.129464387 LLSSNEDDANILSS(ph)PTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLSSNEDDANILSSPTDR 18 0 F5GY88;A0A0B4J1W0;O75448-2;O75448;H0YEG1 F5GY88 MED24 Mediator of RNA polymerase II transcription subunit 24 1 LLSSNEDDANILS(0.002)S(0.997)PT(0.001)DR;LLSSNEDDANILS(0.001)S(0.999)PTDR;LLSSNEDDANILS(0.003)S(0.997)PTDR 446.14 9.88E-191 1034280000 1672820 1601700 912260 1084400 1566050 1475970 1471620 1741320 1534870 TRUE FALSE 1451752.599 1591178.327 1353431.987 1330629.594 1534888.669 1532751.521 1328902.519 1368952.269 1353419.417 1.072655365 1.175672749 1.000009288 0.9831613 1.134082051 1.132502978 0.981885218 1.011476747 1 20.36817756 2.223497711 24.99974996 0.99997668 1.081235303 0.317966625 0.05877352 317.0926118 526271.2501 0.025087217 0.01698705 167.3006819 -2.223497711 0.081258624 LLSSS(ph)LTADCSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLSSSLTADCSLR 13 0 Q147X3;Q147X3-2 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 LLS(0.001)S(0.051)S(0.947)LT(0.002)ADCSLR;LLSSS(0.976)LT(0.024)ADCSLR;LLSS(0.017)S(0.982)LT(0.001)ADCSLR 351.37 5.98E-76 455923000 557909 680808 675077 702432 1020304 1257590 978175 1068937 1346830 TRUE FALSE 484179.9121 676335.7274 1001546.495 861929.9216 1000001.947 1305970.301 883311.7391 840353.141 1187609.292 0.40769293 0.569493462 0.843329959 0.725768927 0.842029406 1.099663256 0.743773011 0.707600679 1 20.17962886 4.469069293 1.706955802 0.844014662 0.353291596 0.613720411 0.122588866 0.409197753 1.746331346 0.035173011 0.278264356 29448.9146 -4.469069293 -0.490723066 LLSSSLTADCSLRS(ph)PSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLSSSLTADCSLRSPSGR 18 1 Q147X3;Q147X3-2 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 LLSSSLTADCSLRS(0.998)PS(0.002)GR;LLSSSLTADCSLRS(1)PSGR 276.79 2.48E-39 788070000 358750 434820 231130 263240 500710 511870 458710 593550 166687 TRUE FALSE 311340.2785 431963.6388 342905.2411 323012.6654 490746.8506 531561.9701 414224.3748 466623.9515 146981.4528 2.118228339 2.938898961 2.332983071 2.197642351 3.338835217 3.616524127 2.818208468 3.174713154 1 17.16527459 3.257555322 24.98599338 2.881273296 2.431081489 0.058112603 0.730228555 663.0925392 872239.2201 0.207725823 0.267717302 1809.486395 -3.257555322 -0.450191807 LLSVHDFDFEGDS(ph)DDSTQPQGHSLHLSSVPEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 LLSVHDFDFEGDSDDSTQPQGHSLHLSSVPEAR 33 0 Q9BV36-2;Q9BV36-5;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 1 LLSVHDFDFEGDS(0.991)DDS(0.004)T(0.004)QPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(1)DDSTQPQGHSLHLSSVPEAR;LLS(0.002)VHDFDFEGDS(0.997)DDSTQPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(1)DDSTQPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(1)DDSTQPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(1)DDSTQPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(1)DDSTQPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(1)DDSTQPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(0.966)DDS(0.028)T(0.006)QPQGHSLHLSSVPEAR 355.87 9.40E-132 4026491000 569583 740521 178240.7 305112.3 846156 873039 626027 696952 317895.9 TRUE FALSE 494311.1634 735656.4688 264438.4987 374392.7111 829319.1511 906625.3753 565314.9979 547914.2385 280314.6089 1.763415633 2.624395752 0.943363244 1.335616123 2.958529898 3.234313684 2.016716147 1.954640326 1 18.09668741 3.26805807 24.99857549 2.231930496 1.683438135 0.13059804 0.725263907 499.7588504 423533.5433 0.222041794 0.286612666 1853.779476 -3.26805807 -0.548492361 LLSWSDNWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLSWSDNWR 9 0 Q8TCD5;J3KSY6;J3KSX6 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 0 106.42 0.0068354 281020000 173860 189410 129090 146880 188950 186120 174040 191180 206590 FALSE TRUE 150883.9605 188165.7532 191518.3558 180231.3489 185190.2647 193280.1568 157161.6276 150297.6448 182167.1655 0.828271989 1.032929028 1.051333017 0.989373405 1.016595192 1.06100436 0.862733013 0.82505343 1 17.47490342 2.225825644 24.99932906 0.879779918 1.001306893 0.259798712 0.078260284 250.7612903 492251.8435 0.031020855 0.021065652 168.1998656 -2.225825644 0.121526975 LLT(ph)GPSDYYTDYVATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLTGPSDYYTDYVATR 16 0 A0A5H1ZRP5 A0A5H1ZRP5 1 LLT(0.858)GPS(0.038)DY(0.032)Y(0.032)T(0.038)DYVATR 85.909 0.013045 153590000 4121.9 6482.3 3966 3221 7155.8 7813.7 1996.5 5260.1 5561.7 TRUE FALSE 3577.180471 6439.717344 5883.970865 3952.37728 7013.41358 8114.298095 1802.879737 4135.268549 4904.202162 0.729411299 1.313101934 1.199781467 0.805916467 1.430082478 1.654560279 0.367619376 0.843209234 1 12.25980274 2.231435697 24.99994951 0.743693334 1.188520194 0.320526534 0.310087569 199.9356135 701527.3986 0.124281784 0.085784056 170.3867019 -2.231435697 0.444826859 LLT(ph)PTHSFLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLTPTHSFLAR 11 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 LLT(0.917)PT(0.083)HSFLAR;LLT(0.989)PT(0.011)HSFLAR 181.98 0.00014003 309730000 358800 365240 233250 252510 354270 408070 349470 364620 384480 TRUE FALSE 311383.6709 362840.7144 346050.4802 309846.2549 347220.7201 423768.717 315578.4532 286648.8505 339027.2124 0.918462175 1.07024068 1.020715941 0.913927389 1.024167699 1.249954875 0.930835171 0.84550396 1 18.37104155 2.023723883 24.99856697 0.904652261 1.033427001 0.202455215 0.099204421 297.9416061 313948.6909 0.040494145 0.027299704 105.6145817 -2.023723883 0.12877474 LLTDDGNKWLYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLTDDGNKWLYK 12 1 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 170.07 3.84E-05 966600000 1551980 1327730 646470 814700 1247470 1058700 1606980 1854670 335510 FALSE TRUE 1346881.911 1319008.054 959105.0543 999690.0869 1222647.788 1099428.874 1451135.327 1458063.254 295846.39 4.55263933 4.458422001 3.241902172 3.37908496 4.132711532 3.716215277 4.905029691 4.928447001 1 18.17448877 1.230163397 24.99442802 0.999994107 4.175684608 0.745370764 0.581197363 183.2796295 545490.8436 1.792351893 0.159902523 16.98882711 -1.230163397 3.175690501 LLTPTHSFLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLTPTHSFLAR 11 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 166.69 2.01E-05 332460000 268460 309650 223210 215510 352440 385730 246020 273350 311440 FALSE TRUE 232982.3308 307615.8888 331155.1026 264444.8394 345427.1335 400569.2827 222161.0183 214896.2297 274621.918 0.848374858 1.120143254 1.20585824 0.962941492 1.257827984 1.458620949 0.808970456 0.782516673 1 18.06708725 2.175222789 24.99999989 0.844601634 1.141281105 0.36681553 0.171845381 64.66584286 25523.30162 0.07069056 0.047659565 149.7003408 -2.175222789 0.296679471 LLVDADNCLHR ddPTM_MDA-MB-175_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 ;;; 237.37 1.40E-15 1361560000 1832010 1847270 1159660 1371450 1834160 1962350 1716010 1888180 1900000 FALSE TRUE 1589905.237 1835135.162 1720475.455 1682858.684 1797663.804 2037842.874 1549591.614 1484407.401 1675384.164 0.948979506 1.095351861 1.026914001 1.004461376 1.072986031 1.216343641 0.92491719 0.886010165 1 20.67606051 2.100521351 23.79087805 0.925767036 1.059841672 0.379885666 0.074133005 7.821975012 1836.482421 0.029809413 0.020097503 126.0437603 -2.100521351 0.134074637 LLVDSQGLSGCS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLVDSQGLSGCSPR 14 0 O94885;A0A087WW74 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 LLVDSQGLS(0.001)GCS(0.999)PR;LLVDSQGLS(0.002)GCS(0.998)PR;LLVDS(0.01)QGLS(0.312)GCS(0.679)PR 115.66 0.00042647 1497390000 1775810 1922410 1211880 1450460 1807560 2004160 1619400 1923310 2022060 TRUE FALSE 1541132.209 1909781.562 1797949.221 1779809.112 1771593.092 2081261.332 1462350.837 1512025.124 1783014.37 0.86434088 1.071097123 1.008376181 0.998202337 0.993594399 1.167271205 0.820156507 0.84801623 1 20.7658869 2.210893372 24.99999821 0.877886408 1.017269048 0.318727585 0.087511928 226.5747682 204730.2973 0.034205949 0.023067515 162.5149701 -2.210893372 0.13938264 LLVDVDESTLSPEEQKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLVDVDESTLSPEEQKER 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;; 277.44 3.54E-39 353727000 817800 677410 400984 394924 626720 504003 748350 853080 202787 FALSE TRUE 709725.658 672960.0491 594901.2036 484597.5302 614249.4982 523392.3215 675775.1322 670655.4807 178813.7519 3.969077605 3.763469208 3.326932058 2.710068578 3.435135674 2.927024997 3.779212309 3.750581114 1 17.44809817 1.234297491 24.99975835 0.999996389 3.451307118 0.792856438 0.394779322 60.81613846 356589.2179 0.775402849 0.102111323 17.15131769 -1.234297491 2.451310729 LLVGNDDVHIIARS(ph)DDELLDDFFHDQSTATSQAGTLSSIPTALTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLVGNDDVHIIARSDDELLDDFFHDQSTATSQAGTLSSIPTALTR 45 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 LLVGNDDVHIIARS(1)DDELLDDFFHDQSTATSQAGTLSSIPTALTR 156.56 2.48E-15 45766000 17091 18780 9353.3 9763.5 16381 19820 16269 19895 9128.2 TRUE FALSE 14832.38105 18656.63294 13876.58716 11980.4519 16055.05015 20582.48823 14691.23488 15640.60907 8049.074595 1.842743644 2.317860609 1.723997834 1.488426 1.994645466 2.557124795 1.825207943 1.943156184 1 12.97460721 1.233726437 5.483934149 0.949081167 1.966344335 0.507952693 0.297429323 0.140164909 12.88735481 0.538980179 0.075887312 17.12878024 -1.233726437 1.017263168 LLVHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLVHLK 6 0 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ; 74.949 0.078979 785980000 1122920 1060590 647690 852380 1008070 951790 1033150 1342610 1190180 FALSE TRUE 974523.2769 1053622.914 960915.0504 1045925.907 988011.3793 988405.9772 932955.272 1055503.3 1049478.276 0.928578799 1.003949237 0.91561214 0.996615109 0.941430996 0.941806991 0.888970542 1.00574097 1 20.00124087 1.609230701 25 1.002878257 0.94803404 0.327098576 0.034162724 0.147380324 2617.411849 0.018744824 0.008214245 40.66592928 -1.609230701 -0.054844217 LLVLDVDYTLFDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLVLDVDYTLFDHR 14 0 Q8WVY7 Q8WVY7 UBLCP1 Ubiquitin-like domain-containing CTD phosphatase 1 0 ;; 173.72 2.66E-06 367206000 469336 470946 326383 384153 402178 445853 455406 508067 560209 FALSE TRUE 407312.0585 467852.3247 484222.9105 471380.8101 394175.4446 463005.2534 411240.7962 399420.8258 493981.7302 0.824548832 0.94710451 0.980244574 0.954247457 0.797955512 0.937292262 0.832502036 0.808574086 1 18.91409816 3.269705367 24.99973985 0.866822532 0.931841816 0.10336579 0.071960838 370.1272293 297096.8652 0.020283669 0.026183296 1860.824291 -3.269705367 0.065019284 LLVSMCQGNRDENQSINHQMAQEDAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLVSMCQGNRDENQSINHQMAQEDAQR 27 1 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 232.06 1.11E-35 258820000 47841 62238 18609 24677 51098 63157 32007 70865 18581 FALSE TRUE 41518.69064 61829.15448 27608.37464 30280.29001 50081.24977 65586.69066 28902.96607 55711.07122 16384.37535 2.534041717 3.773665652 1.685042857 1.848119893 3.056646879 4.003002206 1.764056636 3.400256039 1 14.00003305 4.250159717 24.99972993 2.511638048 3.15385311 0.090569722 0.945552346 617.8557156 1331648.798 0.227900983 0.592169283 17789.33515 -4.250159717 0.642215062 LLVVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLVVDR 6 0 O14745;O14745-2;J3QRA3;P51817 O14745 SLC9A3R1;PRKX Na(+)/H(+) exchange regulatory cofactor NHE-RF1;cAMP-dependent protein kinase catalytic subunit PRKX 0 ; 102.98 0.081604 265070000 314710 290920 191965 251020 285830 307800 272500 326900 353350 FALSE TRUE 273120.2761 289008.9274 284799.9161 308017.9276 280142.5422 319641.2652 246072.9919 256994.9789 311577.3655 0.876572904 0.927567145 0.914058425 0.98857607 0.899110697 1.02588089 0.789765301 0.824819154 1 18.24923091 2.229686679 24.9999643 0.858390349 0.93748231 0.167493035 0.068429973 281.9164059 794216.6379 0.026937576 0.01846214 169.7018901 -2.229686679 0.079091961 LLVVTDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLVVTDPR 8 0 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ; 83.614 0.041959 273810000 1196410 1299390 825660 919890 1247060 1304780 1164530 1321080 1307150 FALSE TRUE 1038301.387 1290854.222 1224951.938 1128765.084 1222245.946 1354975.731 1051594.06 1038577.323 1152620.216 0.900818303 1.119930228 1.062754167 0.979303563 1.06040648 1.17556131 0.912350873 0.901057702 1 20.1364858 2.18970883 24.99999824 0.929086855 1.050851199 0.314037543 0.077660886 121.0765788 61960.21481 0.030592181 0.020625279 154.7778571 -2.18970883 0.121764344 LLWHGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLWHGSR 7 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 127.31 0.0038676 2997400000 3182200 3594600 922940 1912200 4326500 4523700 3160400 3675300 4372500 FALSE TRUE 2761664.207 3570986.836 1369276.871 2346394.236 4240411.115 4697729.666 2853904.894 2889365.696 3855588.031 0.71627575 0.92618475 0.355140866 0.608569748 1.099809181 1.218421063 0.740199646 0.749396894 1 21.87851948 3.255569258 24.87123176 0.931284667 0.649988414 0.370890608 0.198465051 300.4167757 439287.7999 0.062079425 0.079932153 1801.230359 -3.255569258 -0.281296254 LLYDLADQLHAAVGASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LLYDLADQLHAAVGASR 17 0 H0YL12;P13804-2;P13804;H0YK49;H0YNX6 H0YL12 ETFA "Electron transfer flavoprotein subunit alpha, mitochondrial" 0 ;; 242.26 2.13E-20 764734000 621105 680559 408229 662164 803000 868248 599008 785343 713146 FALSE TRUE 539024.4006 676088.3631 605649.9098 812518.4567 787021.871 901650.0624 540916.2964 617403.511 628838.6923 0.857174355 1.075137983 0.963124434 1.292093611 1.251548101 1.433833626 0.86018291 0.981815398 1 19.26233046 3.862301296 19.47909843 1.120955555 0.976095849 0.173987841 0.173319149 7.895598806 1213.368655 0.050627433 0.087690102 7282.848841 -3.862301296 -0.144859706 LLYNNVSNFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LLYNNVSNFGR 11 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 254.5 4.52E-20 1551140000 590560 546170 326400 320740 559370 516050 488790 565430 536910 FALSE TRUE 512515.9997 542582.1733 484248.1317 393568.9192 548239.6314 535902.7774 441387.221 444517.1947 473437.1114 1.082542934 1.146049095 1.022835177 0.83130137 1.157998852 1.131940789 0.932303806 0.938914977 1 18.85281327 LLYPDHFHLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LLYPDHFHLLR 11 0 H0YDU8;P53041;A8MU39 H0YDU8 PPP5C Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5 0 106.29 0.0013597 127270000 130870 113960 117230 153680 111540 125460 109540 112750 321090 FALSE TRUE 113575.1979 113211.3893 173922.8201 188575.3929 109320.5722 130286.5274 98916.82766 88639.28992 283131.106 0.401139951 0.399855003 0.614283688 0.666035589 0.386112899 0.460163241 0.349367574 0.313068003 1 18.11111073 1.22999781 24.96111997 1.000001061 0.446568173 0.707508346 0.11138038 201.2963867 586744.946 0.344614077 0.030263439 16.98235088 -1.22999781 -0.553432888 LMATLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LMATLR 6 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 121.68 0.045473 350510000 530060 503700 340450 313390 410630 346460 606520 519980 450300 FALSE TRUE 460011.228 500391.1615 505092.7587 384549.9894 402459.2664 359788.5404 547699.7838 408786.3235 397066.047 1.15852572 1.26022148 1.272062325 0.968478651 1.013582676 0.906117617 1.379366954 1.029517196 1 18.59901948 3.749727799 24.81220957 1.060572207 1.233265015 0.302920536 0.128507161 895.9507337 1990695.558 0.034457041 0.058971617 5619.889794 -3.749727799 0.172692808 LMDERDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LMDERDLR 8 1 Q9H2K0 Q9H2K0 MTIF3 "Translation initiation factor IF-3, mitochondrial" 0 61.999 0.075163 226190000 202640 180330 148140 150870 171260 212570 134910 195950 490290 FALSE TRUE 175860.6106 179145.4004 219780.9995 185127.3394 167852.2611 220747.7055 121826.449 154047.6174 432328.4747 0.406775452 0.414373355 0.508365774 0.428209915 0.38825169 0.510601819 0.281791406 0.356320775 1 18.72176833 1.235449194 24.99919447 1.000000809 0.409095019 0.884915773 0.066652303 28.82829677 231584.3808 0.117914745 0.017075356 17.19686151 -1.235449194 -0.590905789 LMDLLGEGLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LMDLLGEGLKR 11 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 130.56 0.00035527 1437160000 2427170 2189270 1187400 1510670 2074930 2308630 2130200 2349730 1650250 FALSE TRUE 2106413.335 2174888.541 1761630.612 1853690.713 2033642.953 2397444.49 1923613.532 1847258.525 1455159.325 1.44754825 1.494605095 1.210610125 1.273874744 1.397539718 1.647547763 1.321926403 1.269454481 1 20.47274569 1.275018021 1.84798112 0.884933121 1.400482939 0.530097623 0.119908678 0.694177986 2.419433741 0.618715341 0.035069265 18.83727253 -1.275018021 0.515549818 LMEDLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 29 LMEDLDR 7 0 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;; 246.13 4.80E-08 3.90801E+11 148297000 152588710 103433207 115348070 141148180 152842490 121661290 152516990 171087930 FALSE TRUE 128699175.7 151586344.7 153453851.9 141539612.3 138339607.4 158722439.5 109862596.8 119902418.6 150862109.8 0.853091448 1.004800641 1.017179543 0.938205176 0.916993721 1.052102743 0.728231873 0.794781531 1 27.16865527 2.241355362 24.99999984 0.826675836 0.964740853 0.301991075 0.0870415 77.51602452 693418.442 0.032861592 0.024292984 174.3232691 -2.241355362 0.138065017 LMEDLDRNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 LMEDLDRNK 9 1 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;;;;;;; 172.59 5.11E-05 15313190000 14921110 11978990 5393209 6150333 12384480 9969060 19059300 17842600 1468583 FALSE TRUE 12949247.51 11900299.23 8001382.912 7546860.11 12138053.08 10352576.19 17210932.02 14027098.84 1294968.791 9.999659915 9.18964172 6.178822971 5.827831654 9.373239853 7.994459992 13.2906153 10.83199761 1 20.3044859 4.47047556 24.75171121 8.302360552 9.797156527 0.035070284 3.274845486 582.2350107 2168528.497 0.838980075 2.231760612 29544.42624 -4.47047556 1.494795975 LMEEDELPSWIIKDDAEVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LMEEDELPSWIIKDDAEVER 20 1 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YFK5;K7EQF0;A0A2R8Y5K3;F6VDE0;P51531-2;P51531;A0A0U1RQZ9;A0A0U1RRG6 A0A2R8Y4P4;F6VDE0 SMARCA4;SMARCA2 Transcription activator BRG1;Probable global transcription activator SNF2L2 0 95.5 0.0011101 16717000 41109 33958 28487 31935 32250 36111 34632 38543 48515 FALSE TRUE 35676.34149 33734.92766 42263.40848 39186.32985 31608.2881 37500.21354 31273.39397 30300.87939 42779.61197 0.833956641 0.788574887 0.987933423 0.916004799 0.738863366 0.876590783 0.731035008 0.708301876 1 15.38463578 3.248000882 24.99582431 0.795413551 0.882565542 0.102228455 0.098202728 385.5938823 1020964.831 0.028550145 0.036356918 1770.112552 -3.248000882 0.087151991 LMELHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LMELHFK 7 0 A0A087WUB9;Q8WYA6;Q8WYA6-4;Q8WYA6-3;Q8WYA6-2 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 81.784 0.026263 435630000 330150 319130 201680 246130 306200 287140 320350 406120 355240 FALSE TRUE 286519.841 317033.614 299213.1226 302017.5784 300107.2191 298186.4616 289282.5063 319274.3984 313243.9319 0.914686006 1.012098182 0.955208041 0.964160986 0.958062355 0.951930528 0.923505539 1.019251663 1 18.25692704 1.677998863 8.521860906 1.00915185 0.957029328 0.428953553 0.026339069 0.105209281 12.88915263 0.014203727 0.006390637 47.64297394 -1.677998863 -0.052122522 LMELHGEGSSSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 LMELHGEGSSSGK 13 0 P61247;D6RG13;D6RAT0;H0Y9Y4;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ;;;;;;;; 198.57 1.25E-07 6822530000 12919050 12837280 5342970 9585310 12372930 11135860 14374960 15917910 14689240 FALSE TRUE 11211764.81 12752951.06 7926848.163 11761801.14 12126732.9 11564263.74 12980878.59 12513988.82 12952694.78 0.865593222 0.984578984 0.611984479 0.908058233 0.936232429 0.892807554 1.002175903 0.96613014 1 23.62674894 2.894501246 1.310515287 0.981018178 0.837035697 0.284544882 0.096451881 0.570043228 2.059689088 0.044609787 0.043438637 784.3343699 -2.894501246 -0.143982481 LMELYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LMELYER 7 0 Q9UG63;Q9UG63-2;C9JHK9;C9JZV3 Q9UG63 ABCF2 ATP-binding cassette sub-family F member 2 0 ; 105.04 0.041389 70911000 296160 297460 236590 244711 298880 317720 281573 318030 276410 FALSE TRUE 257021.7056 295505.9657 351005.7153 300276.3727 292932.8727 329942.894 254266.0938 250021.7594 243733.1247 1.05452103 1.212416105 1.44012315 1.231988361 1.201859095 1.353705593 1.043215173 1.025801313 1 17.89494281 2.162621071 7.47955984 1.022006072 1.252908 0.531997128 0.100010872 0.180675995 15.12757645 0.041414164 0.027894311 145.4189724 -2.162621071 0.230901928 LMENMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LMENMR 6 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 125.86 0.041275 535150000 432670 492490 289350 326740 490500 548790 424700 478090 384780 FALSE TRUE 375491.5633 489254.8008 429280.6278 400931.3109 480740.0096 569902.3064 383512.6594 375854.174 339291.7467 1.106692299 1.441988511 1.265225671 1.181671275 1.416892731 1.679682196 1.130333004 1.107761028 1 18.37216681 2.02516716 24.99993536 1.078818291 1.3496772 0.398049174 0.15754799 221.1527726 219682.3257 0.06475413 0.043655641 105.966151 -2.02516716 0.270858909 LMFEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LMFEELR 7 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;;;;;;; 146.94 0.0050827 870771000 1955877 2004902 1332936 1450230 1959242 1988433 1899946 2201900 1976718 FALSE TRUE 1697402.899 1991731.667 1977548.308 1779526.887 1920256.917 2064929.304 1715689.529 1731040.82 1743032.65 0.973821631 1.142681789 1.134544616 1.020937208 1.101675816 1.184676205 0.984312904 0.993120135 1 20.73316816 2.199645047 24.9983399 0.99227118 1.094311479 0.385731714 0.059818062 157.7558113 101337.0817 0.023679545 0.015965012 158.3598372 -2.199645047 0.102040299 LMHNAS(ph)DS(ph)EVDQDDVVEWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LMHNASDSEVDQDDVVEWK 19 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 2 LMHNAS(1)DS(1)EVDQDDVVEWK;LMHNAS(1)DS(1)EVDQDDVVEWK 160.67 2.92E-11 182012000 181612 138316 97429 126547 146844 128780 148445 190973 194751 TRUE FALSE 157611.5141 137407.3931 144545.9903 155281.4305 143922.0917 133734.2499 134048.8267 150134.9101 171727.7586 0.917798702 0.800146663 0.841715931 0.904230229 0.838082863 0.778757325 0.780589159 0.874261164 1 17.38976373 1.280354277 3.513501364 1.015584024 0.836023844 0.54861834 0.046115045 0.204400406 3.728258733 0.09163097 0.011966147 19.07015736 -1.280354277 -0.17956018 LMHNAS(ph)DSEVDQDDVVEWK ddPTM_MDA-MB-175_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(0.999)DS(0.001)EVDQDDVVEWK;LMHNAS(0.994)DS(0.006)EVDQDDVVEWK;LMHNAS(0.996)DS(0.004)EVDQDDVVEWK;LMHNAS(0.599)DS(0.401)EVDQDDVVEWK;LMHNAS(0.984)DS(0.016)EVDQDDVVEWK;LMHNAS(0.918)DS(0.082)EVDQDDVVEWK;LMHNAS(0.958)DS(0.042)EVDQDDVVEWK;LMHNAS(0.962)DS(0.038)EVDQDDVVEWK 271.11 1.65E-39 3540584000 5337890 4206180 2974360 3975100 4090290 3357740 4640890 5797670 5118240 TRUE FALSE 4632474.312 4178549.327 4412770.445 4877707.211 4008901.232 3486914.431 4190817.202 4557883.388 4513167.498 1.026435273 0.925857356 0.977754636 1.080772476 0.888267771 0.772609134 0.928575597 1.009907873 1 22.10570889 4.750663734 22.94779039 0.949633491 1.026435411 0.082938349 0.081833255 1848.313977 3504236.657 0.021479738 0.318820969 56320.14108 -4.750663734 0.076801921 LMIEMDGTENK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LMIEMDGTENK 11 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879 P06733 ENO1 Alpha-enolase;Enolase 0 111.65 0.0037955 143430000 131120 112470 90947 89310 105310 102570 123490 143240 145340 FALSE TRUE 113792.1598 111731.1772 134929.2734 109589.2005 103214.537 106515.9343 111513.9588 112609.2407 128158.0708 0.88790475 0.871823183 1.052834773 0.85510963 0.805368998 0.831129352 0.870128258 0.878674593 1 16.96756481 LMIWDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LMIWDTR 7 0 Q09028-3;Q09028;Q09028-2;Q09028-4;H0YF10;H0YCT5;H0YDK2;Q16576;E9PC52;Q16576-2;Q5JP01;Q5JP02 Q09028-3;Q16576 RBBP4;RBBP7 Histone-binding protein RBBP4;Histone-binding protein RBBP7 0 ;;;; 132.96 0.0077193 4096415000 7103323 7711791 4528015 4706161 7003274 7480851 6426859 7305765 7225769 FALSE TRUE 6164600.868 7661131.737 6717778.199 5774766.784 6863922.549 7768644.179 5803583.203 5743484.008 6371546.82 0.967520296 1.202397464 1.054340239 0.90633671 1.077277268 1.219271301 0.910859383 0.901426949 1 22.60321223 2.177832221 24.99998261 0.928820718 1.069173803 0.298408858 0.096351531 85.04055702 35007.54772 0.03947157 0.026611735 150.6025136 -2.177832221 0.140353085 LMKPPS(ph)PEHQSLDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LMKPPSPEHQSLDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR 43 1 Q9Y6X9;Q9Y6X9-2;H7C1V1 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 LMKPPS(0.998)PEHQS(0.002)LDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.964)PEHQS(0.031)LDT(0.005)QQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.999)PEHQS(0.001)LDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR 269.62 2.09E-68 724290000 500627 377395 122866 279873 433312 382769 449139 534308 476816 TRUE FALSE 434467.8735 374915.8674 182284.4086 343422.4422 424689.939 397494.3711 405581.5689 420050.3922 420447.3557 1.033346667 0.891707041 0.43354871 0.816802479 1.010090641 0.945408184 0.96464293 0.999055854 1 18.68156565 3.314350624 5.484028135 0.982170355 0.770968068 0.283291887 0.149461856 0.261283296 13.68236843 0.044806119 0.057710086 2062.294219 -3.314350624 -0.211202287 LMKPPSPEHQS(ph)LDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LMKPPSPEHQSLDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR 43 1 Q9Y6X9;Q9Y6X9-2;H7C1V1 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 LMKPPS(0.411)PEHQS(0.464)LDT(0.126)QQEGGEEEVGPVAQQAIAVAEPSTSECLR 58.158 0.007975 151640000 38220 21785 9918.2 21757 33147 24473 36886 38270 30859 TRUE FALSE 33169.13016 21641.8929 14714.67469 26697.25938 32487.43955 25414.49215 33308.8014 30086.25832 27210.88417 1.218965542 0.795339569 0.540764299 0.981124289 1.193913411 0.933982593 1.224098459 1.10567 1 14.73189621 3.481919016 24.76480254 1.094651682 0.831869697 0.264581016 0.181788722 218.2553489 1126580.373 0.050920933 0.067616134 3033.325501 -3.481919016 -0.262781985 LMLLESWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LMLLESWR 8 0 Q5JY65;Q9BZJ0-2;Q9BZJ0-3;Q9BZJ0 Q5JY65 CRNKL1 Crooked neck-like protein 1 0 135.84 0.0018994 60469000 61467 144170 80606 65731 130350 134200 120350 137220 143920 FALSE TRUE 53343.98021 143222.9378 119587.3312 80656.22819 127756.29 139362.7608 108678.4755 107876.5708 126905.9416 0.420342653 1.128575511 0.942330436 0.635559117 1.00670062 1.098157889 0.856370271 0.850051381 1 16.95340009 3.175257934 24.99999971 0.947084146 0.817938578 0.158682924 0.197240946 158.8298456 62724.87248 0.058458913 0.066286203 1497.124557 -3.175257934 -0.129145568 LMLLLEVISGERLPKPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LMLLLEVISGERLPKPER 18 2 O43707 O43707 ACTN4 Alpha-actinin-4 0 ; 213.99 1.18E-17 134486000 222228 229596 87538 106004 148326 149235 254026 281060 73862 FALSE TRUE 192860.0067 228087.7688 129871.6696 130073.8284 145374.6028 154976.167 229390.5976 220957.5062 65130.1185 2.96114933 3.502032147 1.994033983 1.997137904 2.232064153 2.379485414 3.522035625 3.392554954 1 15.99103723 SSSQSTFHIPLS(ph)PVEVKPGNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSSQSTFHIPLSPVEVKPGNVR 22 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 SSSQSTFHIPLS(1)PVEVKPGNVR;SSSQSTFHIPLS(1)PVEVKPGNVR;SSSQSTFHIPLS(1)PVEVKPGNVR;SSSQSTFHIPLS(1)PVEVKPGNVR 147.17 4.83E-08 2158250000 873120 1705580 694180 1626170 2894390 2581530 2771970 3495650 2956260 TRUE FALSE 757734.9798 1694375.933 1029887.77 1995416.753 2836797.302 2680843.13 2503144.776 2748132.451 2606774.311 0.290679165 0.649989501 0.395081295 0.765473537 1.08824047 1.028413975 0.960246066 1.054227226 1 21.31383425 3.501042258 3.2115462 1.023904886 0.467358599 0.882925971 0.096273109 0.072934839 1.537750035 0.0260539 0.038115098 3169.875883 -3.501042258 -0.556546287 down LMLPDS(ph)PLVEEGRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LMLPDSPLVEEGRR 14 1 Q9P2F8;Q9P2F8-2 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 LMLPDS(1)PLVEEGRR;LMLPDS(1)PLVEEGRR;LMLPDS(1)PLVEEGRR;LMLPDS(1)PLVEEGRR;LMLPDS(1)PLVEEGRR;LMLPDS(1)PLVEEGRR 272.24 3.44E-33 708538000 313195 455500 308009 383109 560416 642464 533405 600816 381236 TRUE FALSE 271805.4872 452507.7905 456963.1826 470099.7539 549264.818 667180.0058 481675.4652 472336.174 336166.7144 0.808543724 1.346081486 1.359335006 1.398412555 1.633906019 1.984670038 1.432846991 1.405065266 1 18.35881736 5.067510631 1.313253156 1.485940369 9.23E-11 0.411048635 0.243504699 3.067097654 2.636843863 0.072833901 7.490093613 116818.2325 -5.067510631 -1.485940369 LMLSTSEYSQS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LMLSTSEYSQSPK 13 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LMLSTSEYSQS(1)PK;LMLSTSEYSQS(1)PK 221.85 1.93E-11 262610000 403760 316460 234587 250318 333460 294540 363560 439430 367050 TRUE FALSE 350402.093 314381.1534 348034.0578 307156.5278 326824.7984 305871.1444 328302.0072 345461.3141 323657.7671 1.082631497 0.971338201 1.075315018 0.949016396 1.009785124 0.945044969 1.014349231 1.067366055 1 18.3041096 1.98658047 24.45864827 1.039203722 1.002676777 0.048526422 0.048571387 1052.001745 1917396.11 0.020041866 0.01222944 96.95729038 -1.98658047 -0.036526945 LMNESLMLVTALNPHIGYDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LMNESLMLVTALNPHIGYDK 20 0 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 ; 202.53 1.15E-21 714700000 1275070 1206000 884340 1115560 1265630 1122010 1399230 1686310 1162600 FALSE TRUE 1106566.269 1198077.707 1312009.782 1368864.948 1240446.439 1165174.451 1263532.89 1325705.729 1025158.752 1.079409668 1.168675294 1.279811326 1.335271191 1.210004242 1.136579528 1.232524121 1.293171156 1 19.96741591 1.227162068 24.98881186 0.99999951 1.22266325 0.444145776 0.076027785 513.2380839 1125088.064 0.299621089 0.01953166 16.87182524 -1.227162068 0.22266374 LMQLVDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 4994030000 4385065 4374401 2663156 3014815 4328689 4496041 3777456 4676684 4236584 FALSE TRUE 3805567.55 4345665.272 3951067.149 3699374.824 4242556.558 4669006.607 3411118.899 3676611.521 3735739.866 1.018691795 1.163267633 1.057639796 0.990265639 1.135667019 1.249821126 0.913103969 0.984172253 1 21.83296257 2.206695227 24.99994646 0.967400922 1.099677425 0.415959955 0.076355245 198.8987222 156044.3364 0.031477973 0.021224463 160.9515737 -2.206695227 0.132276503 LMQQLLESDKYAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LMQQLLESDKYAER 14 1 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 118.71 0.0002095 582380000 743490 791070 330650 396560 733460 867060 548520 740170 476400 FALSE TRUE 645235.9127 785873.4091 490553.446 486605.009 718865.581 900416.3593 495324.6148 581890.4055 420080.5347 1.535981459 1.870768446 1.167760478 1.15836124 1.711256584 2.143437472 1.179118226 1.385187738 1 18.68030641 1.496832798 1.642395628 0.98448272 1.561867352 0.231313366 0.317085216 0.956702044 3.807563623 0.803673272 0.095836316 31.39299837 -1.496832798 0.577384632 LMS(ph)DVEDVSLENVHTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LMSDVEDVSLENVHTR 16 0 Q9NSI6-3;Q9NSI6-2;Q9NSI6 Q9NSI6-3 BRWD1 Bromodomain and WD repeat-containing protein 1 1 LMS(1)DVEDVSLENVHTR;LMS(1)DVEDVSLENVHTR;LMS(1)DVEDVSLENVHTR 267.39 1.66E-27 150821000 146613 139188 116920 82499 174913 151716 162972 158619 162244 TRUE FALSE 127237.7206 138273.6649 173462.9031 101231.6589 171432.5735 157552.6127 147167.0005 124699.5612 143063.6991 0.889378098 0.966518171 1.212487194 0.7075985 1.198295406 1.101275961 1.028681639 0.871636634 1 17.12629812 1.75961067 25 0.929588646 1.019187772 0.045152827 0.149555462 29.49204869 35063.55822 0.075930747 0.036464759 57.49243061 -1.75961067 0.089599125 LMSELYHPDDHVL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LMSELYHPDDHVL 13 0 P49770 P49770 EIF2B2 Translation initiation factor eIF-2B subunit beta 0 ; 131.43 0.0001305 133253000 251382 227370 125024 174190 214540 247074 203399 221858 209872 FALSE TRUE 218161.2318 225876.3915 185486.0246 213742.5018 210271.0737 256579.0967 183673.3963 174415.3932 185061.1712 1.178860105 1.220549886 1.002295745 1.154982973 1.1362247 1.386455597 0.992500993 0.942474275 1 17.4976427 2.034073445 24.99980285 0.967235807 1.172129979 0.502257404 0.094539089 140.3034269 102940.5497 0.038313597 0.025830878 108.1616852 -2.034073445 0.204894172 LMSLLTSPHQPPPPPPASASPSAVPNGPQS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LMSLLTSPHQPPPPPPASASPSAVPNGPQSPK 32 0 Q96RU3-5;Q96RU3-2;Q96RU3 Q96RU3-5 FNBP1 Formin-binding protein 1 1 LMSLLTSPHQPPPPPPAS(0.001)ASPS(0.002)AVPNGPQS(0.997)PK 66.432 0.0028588 457980000 88806 84294 34702 60002 96986 76491 90241 106870 84479 TRUE FALSE 77070.06209 83740.26716 51484.00327 73626.37117 95056.16835 79433.65827 81489.44171 84016.68216 74491.98886 1.034608731 1.124151314 0.691134766 0.988379721 1.27605894 1.066338266 1.093935643 1.127861982 1 16.18479766 3.458289113 24.91749394 1.112905484 0.946112494 0.266426962 0.127654831 296.7511141 392640.8474 0.036300861 0.046871284 2872.692317 -3.458289113 -0.166792991 LMSNLDSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LMSNLDSNR 9 0 P26447 P26447 S100A4 Protein S100-A4 0 ;; 140.88 0.00025136 1817480000 2248990 2194900 1777810 1886140 2159420 2359260 2252060 2200030 2863520 FALSE TRUE 1951780.273 2180481.557 2637564.862 2314416.915 2116451.767 2450022.259 2033655.568 1729570.705 2524997.928 0.772982921 0.863557761 1.044581001 0.916601511 0.838199407 0.970306641 0.805408807 0.684979059 1 21.26785077 2.147515735 8.870908006 0.797993053 0.903604526 0.064363439 0.105954872 0.48649088 42.64659455 0.043046302 0.029004599 140.4480567 -2.147515735 0.105611473 LMSSLPNFCGIFNHLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LMSSLPNFCGIFNHLER 17 0 Q96PU8-5;Q96PU8-9;Q96PU8-8;Q96PU8-6;Q96PU8-3;Q96PU8;H0YFB7 Q96PU8-5 QKI Protein quaking 0 141.86 6.08E-07 141230000 101030 129950 85032 97769 97265 105190 98484 130410 123370 FALSE TRUE 87678.62952 129096.3499 126153.7596 119968.9458 95329.6168 109236.7274 88933.03684 102522.8364 108785.3391 0.805978363 1.186707243 1.159657732 1.102804355 0.876309414 1.004149348 0.817509395 0.942432474 1 16.73112461 3.244409564 24.99778275 0.925384822 1.079414884 0.250569956 0.115167794 175.4670254 749922.5266 0.032284443 0.040563131 1755.535291 -3.244409564 0.154030062 LMVESHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LMVESHR 7 0 P51570;P51570-2;K7EII7 P51570 GALK1 Galactokinase 0 ;; 141.78 0.0025335 740060000 844180 916030 605480 727330 889880 1006450 858420 964920 939140 FALSE TRUE 732619.4741 910012.5386 898292.1532 892481.393 872173.129 1045168.783 775170.5605 758579.367 828115.9391 0.884682252 1.098895089 1.084742016 1.077725172 1.053201717 1.262104415 0.936065258 0.91603039 1 19.65947324 LMVMEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LMVMEIR 7 0 Q06323;Q06323-3;Q06323-2;H0YKK6 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;; 111.28 0.015389 195511000 433358 580112 393726 402030 583359 648027 532428 576784 662211 FALSE TRUE 376088.6423 576301.2061 584133.2105 493317.0561 571751.2972 672957.018 480793.2145 453443.2301 583925.17 0.644069928 0.986943594 1.000356279 0.844829238 0.979151656 1.152471331 0.823381555 0.776543389 1 19.15542397 7.33580147 11.45288355 0.910101113 0.179299293 0 0.143772517 0 0 0.032113357 0 21667134.06 -7.33580147 -0.73080182 LMYEHELEQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LMYEHELEQLR 11 0 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 0 ;;; 202.65 3.93E-08 780893000 734684 771358 500854 630742 787809 825223 736840 849925 930834 FALSE TRUE 637593.6479 766290.8985 743068.6697 773961.6114 772133.1422 856969.8628 665381.3702 668175.1529 820791.8649 0.776803079 0.933599529 0.905307059 0.942945032 0.940717343 1.044076945 0.810657852 0.814061617 1 19.64665691 7.16834195 9.300313057 0.903397003 0.184282844 0 0.085376983 0 0 0.019418198 0 14734722.12 -7.16834195 -0.719114159 LMYEHNLQRTACNMTYGSFGGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 65.784 0.038834 47594730000 2021479 1705739 841592 1372349 1673786 1613352 1952942 2158756 2132298 FALSE TRUE 1754335.428 1694533.888 1248588.706 1683961.815 1640480.933 1675418.695 1763545.985 1697122.829 1880220.16 0.933047877 0.901242272 0.664065163 0.895619487 0.872494067 0.891075807 0.937946536 0.902619207 1 20.84247017 1.658276301 0.652565936 1.017953035 0.843018282 0.26256104 0.074593532 3.109498044 1.511338892 0.38820559 0.043271676 45.52776183 -1.658276301 -0.174934753 LNAS(ph)PAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LNASPAAR 8 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 LNAS(1)PAAR;LNAS(1)PAAR;LNAS(1)PAAR;LNAS(1)PAAR 140.61 0.0006785 1925100000 2627340 2666200 1705560 2122320 2484090 2565020 2478710 2835760 2696780 TRUE FALSE 2280130.362 2648685.557 2530374.521 2604225.194 2434661.469 2663697.979 2238325.086 2229354.792 2377969.741 0.95885592 1.113843255 1.064090294 1.095146481 1.023840391 1.120156381 0.94127568 0.937503432 1 21.18129893 2.224496751 24.99701061 0.954227779 1.064759937 0.491812092 0.049254857 168.8541376 300117.7456 0.018531133 0.012564325 167.6859793 -2.224496751 0.110532158 LNCQVIGASVDSHFCHLAWVNTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNCQVIGASVDSHFCHLAWVNTPK 24 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ; 152.96 4.93E-08 2635360000 718310 632780 307640 538560 594890 511390 696510 874910 877910 FALSE TRUE 623383.5135 628623.2265 456415.733 660848.2794 583052.8529 531063.5042 628962.5674 687817.3051 774124.4799 0.805275546 0.812044113 0.589589588 0.853671853 0.753177128 0.686018228 0.812482467 0.888509953 1 19.56220605 1.545426425 1.731835509 1.016341634 0.750555333 0.554646357 0.073945637 0.359666104 1.766909279 0.141584032 0.020761963 35.10964397 -1.545426425 -0.265786301 LNDDWAYGNDLDARPWDFQAEECALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNDDWAYGNDLDARPWDFQAEECALR 26 1 Q5VSL9;Q5VSL9-2 Q5VSL9 STRIP1 Striatin-interacting protein 1 0 ; 283.43 4.85E-61 169224000 100116 96345 52429 69598 78398 76571 79126 103448 107592 FALSE TRUE 86885.41694 95712.10335 77783.83976 85401.28964 76838.03318 79516.73592 71452.3727 81326.45023 94872.59633 0.915811523 1.008848783 0.81987679 0.900168151 0.809907562 0.838142298 0.753140269 0.857217504 1 16.53370381 4.233037104 24.99978766 0.848440348 0.962330161 0.302457217 0.067937818 138.7299267 627911.7756 0.017073328 0.037228122 17101.61415 -4.233037104 0.113889813 LNDGHFMPVLGFGTYAPPEVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNDGHFMPVLGFGTYAPPEVPR 22 0 A0A0A0MSS8;P42330 A0A0A0MSS8 AKR1C3 Aldo-keto reductase family 1 member C3 0 ; 179.5 5.65E-17 372480000 330940 325220 172328 208043 308899 328450 331657 377670 314893 FALSE TRUE 287205.4405 323083.6084 255666.3972 255282.3429 302752.5143 341085.684 299492.9552 296908.2095 277666.7083 1.034353172 1.163566243 0.920767199 0.91938405 1.090345026 1.228399638 1.07860592 1.069297113 1 18.08299469 3.043680691 24.99884137 1.09660039 1.013017045 0.185705435 0.087030908 252.256335 144366.8174 0.027783587 0.031503614 1105.810453 -3.043680691 -0.083583345 LNDHFPLVVWQTGSGTQTNMNVNEVISNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LNDHFPLVVWQTGSGTQTNMNVNEVISNR 29 0 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 232.47 6.74E-36 43801000 26066 25259 16940 23858 29603 31968 26482 33664 29741 FALSE TRUE 22621.31206 25093.07197 25132.24066 29275.32355 29013.95822 33197.82965 23913.77972 26465.21557 26225.05286 0.86258404 0.956835897 0.958329457 1.116311326 1.10634508 1.265882278 0.911867741 1.009157759 1 14.67865806 4.10886372 2.12566229 1.061136556 0.894283913 0.335742553 0.094878329 0.428951863 3.800650277 0.028093889 0.084126969 12848.83405 -4.10886372 -0.166852642 LNDS(ph)PTLK ddPTM_MDA-MB-175_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(1)PTLK;LNDS(0.997)PT(0.003)LK;LNDS(0.997)PT(0.003)LK;LNDS(0.891)PT(0.109)LK 178.1 0.00026369 2892600000 4694690 3792650 2814300 3166710 4018560 3024420 4559690 5315520 4673430 TRUE FALSE 4074274.822 3767735.832 4175304.893 3885759.906 3938598.518 3140771.394 4117491.966 4178837.413 4120942.429 0.988675501 0.914289849 1.013191755 0.942929918 0.955751891 0.762148816 0.9991627 1.014048967 1 21.97454288 2.036548378 24.99999734 1.007602057 0.929934942 0.220915804 0.066427773 243.6384369 166653.7626 0.027121406 0.018285202 108.7798305 -2.036548378 -0.077667116 LNDSHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LNDSHK 6 0 P11387 P11387 TOP1 DNA topoisomerase 1 0 73.039 0.084013 63842000 156370 127470 89273 149490 79079 119700 138130 155550 196440 FALSE TRUE 135705.3083 126632.6412 132445.7214 183433.9893 77505.48262 124304.9365 124734.1739 122286.843 173217.087 0.783440656 0.731063219 0.764622727 1.058983224 0.447447096 0.717625141 0.720103172 0.70597448 1 17.40222173 1.23413185 24.91246488 1.000000407 0.7389574 0.23663668 0.146056689 193.0541559 1085810.129 0.264959675 0.034432404 17.14477735 -1.23413185 -0.261043007 LNDYIFSFDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNDYIFSFDK 10 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 160.18 0.0010142 126760000 619850 477200 333270 396730 430220 374020 534870 652770 562310 FALSE TRUE 537935.252 474065.2418 494440.4867 486813.6101 421659.4637 388408.7914 482998.3897 513180.2154 495834.3524 1.084909203 0.956096002 0.997188848 0.981806944 0.850403893 0.783343852 0.974112397 1.034983181 1 18.9194987 LNECIS(ph)PVANEMNHLPAHSHDLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 153.25 3.65E-08 666530000 107677 76689 54983 54184 72989 77726 74010 84262 84501 TRUE FALSE 93447.21163 76185.22491 81572.96271 66487.30535 71536.6617 80716.16952 66832.52159 66243.22703 74511.38804 1.254133282 1.022464175 1.09477175 0.892310653 0.96007689 1.083272928 0.89694372 0.889034935 1 16.18517332 7.999999977 0.650298597 0.945128433 27.61460368 0.624815663 0.069589587 147.2182347 0.958182564 0.029829923 5650.300628 99999994.73 -7.999999977 26.66947524 LNECVDHTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNECVDHTPK 10 0 Q5TA02;P78417-3;P78417;Q5TA01;P78417-2 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 ; 85.288 0.014341 2791800000 5205700 4690700 3271700 3829800 4172600 3551500 5450500 5775700 5459000 FALSE TRUE 4517753.555 4659886.483 4853905.063 4699414.625 4089573.424 3688128.503 4921911.349 4540611.502 4813643.239 0.938531032 0.968058132 1.008364106 0.976269821 0.849579668 0.766182353 1.022491927 0.943279607 1 22.19869779 5.151325733 15.79037512 0.941223451 0.280096462 0.000124369 0.078568909 27728281.71 3495659.801 0.020052294 664602589.9 141685.6062 -5.151325733 -0.661126989 LNEDKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LNEDKPK 7 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ;; 82.543 0.022074 1792140000 3046200 1957570 1749910 1850680 1212910 1240340 2615390 3080250 2639680 FALSE TRUE 2643636.952 1944710.594 2596172.329 2270905.18 1188775.464 1288056.682 2361749.88 2421562.508 2327620.038 1.135768257 0.835493149 1.115376345 0.975633971 0.510725739 0.553379272 1.014662979 1.040359882 1 21.15042414 7.999996793 0.881394542 0.874044508 107.2520971 0.132285465 0.202578078 2160.010284 5.16375881 0.07490889 461695.7036 99999261.55 -7.999996793 106.3780526 LNEELKVDEETQEVLENLKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNEELKVDEETQEVLENLKDR 21 2 A0A5F9UP49;Q9BRK5;A0A5F9UJX7;Q9BRK5-6;Q9BRK5-2 A0A5F9UP49 SDF4 45 kDa calcium-binding protein 0 ; 161.16 1.14E-11 104433000 155512 102402 110120 105231 104128 84757 141728 187479 94432 FALSE TRUE 134960.6952 101729.3145 163374.4003 129125.3069 102056.0565 88017.65664 127983.2404 147388.0748 83268.35654 1.620792109 1.221704363 1.962022635 1.550712807 1.225628327 1.057036073 1.536997314 1.770037034 1 16.34548073 3.422408908 10.85571922 1.378561972 1.595574459 0.168457372 0.283457376 1.242519416 240.9895473 0.085774097 0.110770534 2644.897877 -3.422408908 0.217012487 LNEHFLNTTDFLDTIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNEHFLNTTDFLDTIK 16 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 258.14 1.07E-26 1031580000 1416180 1328380 868510 1560690 1498630 1333830 1294250 1791440 1546410 FALSE TRUE 1229028.225 1319653.784 1288524.341 1915068.518 1468810.195 1385143.303 1168733.834 1408354.497 1363595.171 0.901314591 0.967775343 0.944946395 1.404426004 1.077160015 1.015802441 0.857097369 1.032824497 1 20.37898397 2.477600803 24.99969991 0.968091096 1.06484887 0.084911196 0.142803566 48.11986998 2508861.355 0.055264352 0.043308613 300.3314432 -2.477600803 0.096757774 LNENHSGELWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LNENHSGELWK 11 0 A0A0A0MTH3;Q13418;Q13418-3 A0A0A0MTH3 ILK Integrin-linked protein kinase 0 91.858 0.010428 151950000 260070 180730 165240 201200 216450 174070 225140 292400 292570 FALSE TRUE 225701.0906 179542.7727 245150.6167 246885.5351 212143.0685 180766.5855 203305.9575 229872.5355 257982.7079 0.874869065 0.695948865 0.950259879 0.956984819 0.82231507 0.700692643 0.788060406 0.89103854 1 17.97691484 1.366926295 2.997321984 1.008469655 0.827195701 0.284164421 0.08775724 0.434294892 5.630426715 0.161976714 0.02400691 23.27696184 -1.366926295 -0.181273954 LNEQAS(ph)EEILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNEQASEEILK 11 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 1 LNEQAS(1)EEILK;LNEQAS(1)EEILK 171.21 1.55E-05 161067000 368840 185154 202921 259520 190950 185420 212040 279690 681070 TRUE FALSE 320096.8595 183937.7112 301054.2743 318447.9825 187150.4686 192553.2274 191476.3934 219880.4701 600554.6805 0.533002023 0.306279706 0.501293694 0.530256433 0.311629356 0.320625638 0.318832572 0.366128976 1 19.19593608 1.237048311 24.99989976 1.000000744 0.392552228 0.809099405 0.091779325 16.50388336 272731.4241 0.139002427 0.022655569 17.26029886 -1.237048311 -0.607448516 LNFAVASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNFAVASR 8 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 146.81 0.0012734 826220000 947250 1015650 710340 781110 1029510 1208240 879330 942900 807260 FALSE TRUE 822068.5125 1008978.128 1053862.8 958472.964 1009024.765 1254721.775 794052.7119 741268.1727 711826.6424 1.154871795 1.417449233 1.480504855 1.346497738 1.41751475 1.76267886 1.115514178 1.041360534 1 19.44116641 2.024781045 24.92314858 1.040075369 1.42827978 0.594827375 0.148260771 138.2919237 139084.3128 0.059686858 0.040239079 105.8719825 -2.024781045 0.388204411 LNFDMTAS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LNFDMTASPK 10 0 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 LNFDMT(0.001)AS(0.999)PK;LNFDMT(0.002)AS(0.998)PK;LNFDMT(0.001)AS(0.999)PK 112.08 0.0017494 151429000 750380 608040 530720 557510 676760 557760 710740 820690 1301490 TRUE FALSE 651215.3818 604045.7452 787377.9672 684101.1665 663293.8001 579217.3881 641812.5442 645191.8301 1147629.335 0.567444001 0.526342197 0.686090834 0.596099407 0.57796867 0.504707723 0.559250731 0.56219531 1 20.13022532 1.237739397 24.99998326 1.000000497 0.572302303 0.887826508 0.047753656 6.463830264 196652.8052 0.070104543 0.011973254 17.28778676 -1.237739397 -0.427698194 LNFGDDIPSALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNFGDDIPSALR 12 0 Q9UNE7;Q9UNE7-2;H3BS86;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ; 183.03 3.75E-05 175306000 402060 386590 270040 291710 400370 427590 367550 412670 379980 FALSE TRUE 348926.7523 384050.4648 400632.2472 357947.214 392403.4203 444039.664 331905.0576 324423.7319 335059.1973 1.041388373 1.146216752 1.195705865 1.068310367 1.171146542 1.32525735 0.990586321 0.968257951 1 18.35405648 2.049727536 24.98619875 0.981129683 1.155887728 0.531845498 0.075938264 77.96798596 39175.57967 0.030810535 0.020772453 112.1314752 -2.049727536 0.174758044 LNFSHGTHEYHAETIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LNFSHGTHEYHAETIK 16 0 P14618;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;; 184.92 6.07E-10 10748009100 4431752.8 3329660.5 1340190.5 2753928.9 3712917.2 3311947.5 4317380.8 4613894.6 4864419.4 FALSE TRUE 3846085.439 3307787.741 1988311.108 3379250.548 3639037.412 3439360.263 3898681.875 3627249.145 4289353.28 0.896658584 0.771162347 0.463545663 0.787822855 0.848388364 0.801836556 0.908920674 0.845640102 1 22.03232871 3.36433597 3.887662824 0.874964204 0.704752297 0.300946491 0.117618534 0.281807079 7.948735467 0.035169762 0.046240254 2313.854096 -3.36433597 -0.170211907 LNGLENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LNGLENR 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 75.972 0.097758 198640000 178400 159940 124090 146340 201150 184040 164790 201030 261750 FALSE TRUE 154823.988 158889.3436 184100.3391 179568.7337 197147.5085 191120.1379 148808.6912 158041.2989 230806.2132 0.670796448 0.688410166 0.797640308 0.778006498 0.854168984 0.828054563 0.644734338 0.684735895 1 17.81632254 4.28074679 6.349323408 0.782197433 0.677397855 0.194111863 0.096321092 0.359573987 36.1546098 0.024936979 0.065776881 19087.40069 -4.28074679 -0.104799578 LNGPGENVS(ph)EDEAQSSNQR ddPTM_MDA-MB-175_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 276.79 1.84E-39 429130000 179441 169696 99973 137314 178430 156603 157481 206278 166584 TRUE FALSE 155727.4172 168581.2558 148320.2772 168493.2424 174879.5921 162627.6187 142208.5169 162167.055 146890.6293 1.060158963 1.147665148 1.009732737 1.147065972 1.190542875 1.10713406 0.96812518 1.10399864 1 17.16438284 2.43384629 24.08460852 1.038263356 1.113381907 0.305091905 0.060133352 128.0092704 71242.1312 0.021982783 0.017027808 271.5478007 -2.43384629 0.075118551 LNGTDPEDVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LNGTDPEDVIR 11 0 J3QRS3;P19105;O14950;J3KTJ1;P24844 J3QRS3;P24844 MYL12A;MYL12B;MYL9 Myosin regulatory light chain 12A;Myosin regulatory light chain 12B;Myosin regulatory light polypeptide 9 0 ;; 154.84 7.40E-05 790650000 749210 664730 423691 515760 611590 649470 615010 693510 706930 FALSE TRUE 650200.0002 660363.3449 628589.3848 632871.1909 599420.5556 674455.5312 555366.4249 545208.2834 623357.5407 1.043061097 1.059365295 1.008393007 1.015261948 0.961599911 1.081972202 0.890927579 0.874631729 1 19.24970037 2.226905252 24.99899272 0.910726727 1.025162754 0.541688179 0.045706251 151.6356845 325232.7104 0.018259454 0.012423705 168.6185118 -2.226905252 0.114436026 LNHNDWIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LNHNDWIK 8 0 P21283;E7EV59 P21283 ATP6V1C1 V-type proton ATPase subunit C 1 0 80.239 0.027085 0 505650 418100 315830 381340 417500 381260 462670 474880 470990 FALSE TRUE 438827.0713 415353.4736 468566.4444 467929.0754 409192.5668 395927.3189 417800.3346 373330.6075 415310.0988 1.056625092 1.00010444 1.128232725 1.126698043 0.985269966 0.95332938 1.005996088 0.898920129 1 18.66382943 3.095620705 5.888777815 0.95936332 1.075439167 0.583394978 0.045981271 0.148639993 7.574278345 0.014462704 0.01646541 1246.294575 -3.095620705 0.116075847 LNHQEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNHQEFK 7 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 154.01 0.0017073 655620000 1488290 1203960 960400 1122810 1094820 1087700 1242170 1533970 1886820 FALSE TRUE 1291608.706 1196051.107 1424852.652 1377761.172 1073035.224 1129544.523 1121704.545 1205942.453 1663762.289 0.776318056 0.71888341 0.856403984 0.828099772 0.644945033 0.6789098 0.674197601 0.724828577 1 20.66601789 1.237167527 24.98048171 1.000000325 0.735423109 0.601714566 0.067009239 26.72132859 478978.3673 0.107341796 0.017647124 17.26503755 -1.237167527 -0.264577215 LNHS(ph)PPQSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LNHSPPQSSSR 11 0 A0A087X0H9;Q5T8P6-3;Q5T8P6-2;Q5T8P6 A0A087X0H9 RBM26 RNA-binding protein 26 1 LNHS(1)PPQSSSR;LNHS(1)PPQSSSR;LNHS(1)PPQSSSR 132.23 0.00012037 1631740000 444939 400218 305979 366748 437236 432659 434903 419202 716140 TRUE FALSE 386139.1838 397588.9416 453951.4678 450023.7388 428535.859 449303.6717 392726.174 329558.9145 631478.745 0.611484055 0.629615715 0.718870542 0.712650651 0.678622776 0.711510364 0.621915111 0.521884414 1 19.26837465 1.225289547 24.99999211 1.000000847 0.6495822 0.769946283 0.059980852 366.2846773 689964.144 0.316795661 0.01680034 16.79923661 -1.225289547 -0.350418647 LNHVAAGLVS(ph)PSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNHVAAGLVSPSLK 14 0 Q05519-2;Q05519;Q5T757;Q5T760 Q05519-2;Q5T760 SRSF11 Serine/arginine-rich splicing factor 11 1 LNHVAAGLVS(0.998)PS(0.002)LK;LNHVAAGLVS(0.999)PS(0.001)LK 192.24 4.16E-07 1607890000 2994680 2105010 1763060 1694850 1978060 1617290 2205500 2471660 2572640 TRUE FALSE 2598925.45 2091182.051 2615681.713 2079691.597 1938700.476 1679508.193 1991610.949 1943114.743 2268505.43 1.14565538 0.921832508 1.153041857 0.916767299 0.854615753 0.740358904 0.877939688 0.856561645 1 21.11331068 3.549313141 5.284821185 0.861154637 1.057534694 0.535797007 0.087989729 0.168888311 8.684822249 0.023535774 0.034860427 3542.526771 -3.549313141 0.196380056 LNHYVLYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LNHYVLYK 8 0 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 112.94 0.0029442 295540000 902210 931300 691270 817360 911560 826040 985930 1151000 1819800 FALSE TRUE 782980.6626 925182.229 1025570.484 1002954.081 893421.7394 857818.2933 890314.6604 904867.6071 1604665.317 0.487940167 0.576557753 0.639117998 0.625023841 0.556765158 0.534577699 0.55482888 0.563898027 1 20.613841 1.238102674 25 1.000000486 0.569570641 0.910949754 0.042507824 3.189134146 173909.7828 0.062224478 0.010876196 17.30225364 -1.238102674 -0.430429845 LNIHQKT(ph)HTGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNIHQKTHTGEK 12 1 Q9GZX5 Q9GZX5 ZNF350 Zinc finger protein 350 1 LNIHQKT(0.997)HT(0.003)GEK;LNIHQKT(0.991)HT(0.009)GEK 115.33 0.0014098 762900000 1308570 758180 1725100 939740 262530 300560 917870 1033260 1059600 TRUE FALSE 1135639.159 753199.4657 2559364.13 1153122.33 257306.1666 312122.7377 828855.1087 812305.3898 934335.2951 1.215451418 0.806134018 2.739235201 1.234163299 0.275389539 0.334058597 0.887106709 0.869393883 1 19.83358084 3.469210046 22.31053238 0.702072133 1.588499252 0.386653649 0.531657852 51.78758156 146044.2028 0.154635454 0.200220605 2945.846044 -3.469210046 0.886427119 LNKSELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNKSELK 7 1 P26447 P26447 S100A4 Protein S100-A4 0 ; 79.906 0.028595 1218000000 2280760 2285490 974120 1346200 2126690 2156310 3599700 3491500 479720 FALSE TRUE 1979351.787 2270476.466 1445207.69 1651875.285 2084373.03 2239264.641 3250601.648 2744869.896 423008.0481 4.679229618 5.367454534 3.41650164 3.90506822 4.927502063 5.293669118 7.684491259 6.488930667 1 18.69032559 2.897910917 3.231877578 5.568946598 4.356029792 0.013352742 1.780047892 0.68464683 13.56561358 0.611186903 0.623671316 790.5164602 -2.897910917 -1.212916805 LNLDSIIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNLDSIIGR 9 0 P62136;P62136-2;P62136-3;E9PMD7 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit;Serine/threonine-protein phosphatase 0 ; 131.5 0.00077069 159780000 635340 623550 476940 512610 631380 673350 550990 650070 886760 FALSE TRUE 551378.2093 619453.859 707589.7793 629005.9353 618816.7733 699254.2102 497555.0746 511057.5894 781928.243 0.705151929 0.792213179 0.904929302 0.804429231 0.791398416 0.894269028 0.636318075 0.653586303 1 19.57667669 2.247878087 24.99742073 0.73515315 0.816824682 0.025920827 0.11264602 455.2969101 1221496.838 0.04212189 0.0321775 176.9612134 -2.247878087 0.081671532 LNLGTDSDSS(ph)PQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LNLGTDSDSSPQK 13 0 Q16512;Q16512-2;Q16512-3;K7EN76 Q16512 PKN1 Serine/threonine-protein kinase N1 1 LNLGTDSDS(0.017)S(0.982)PQK;LNLGTDS(0.001)DS(0.137)S(0.862)PQK;LNLGTDSDS(0.005)S(0.995)PQK;LNLGTDSDS(0.315)S(0.685)PQK 319.91 2.46E-62 1106800000 3720790 3033450 2113640 2470960 3066610 2614640 3537620 4109310 3570640 TRUE FALSE 3229078.174 3013523.067 3135803.374 3032029.234 3005590.461 2715226.893 3194542.157 3230566.035 3148523.007 1.025585065 0.957122772 0.995960127 0.963000501 0.954603303 0.86238115 1.014616107 1.026057624 1 21.58624378 2.058265783 24.99999276 1.016527815 0.959318408 0.270517589 0.041546914 95.01862238 40768.76304 0.017051629 0.011496205 114.3577977 -2.058265783 -0.057209407 LNLGTVGFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LNLGTVGFYR 10 0 E9PLK3;P55786;P55786-2;H0YCQ5 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 82.417 0.042053 159860000 208970 164260 130710 132490 168590 162770 176740 230080 165720 FALSE TRUE 181354.085 163180.9652 193921.7932 162573.8795 165235.3888 169031.8672 159599.782 180879.1825 146128.7704 1.241056669 1.116692933 1.327061007 1.112538476 1.130751928 1.15673229 1.092185896 1.237806778 1 17.15688072 LNLHYAVVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LNLHYAVVSK 10 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A1B0GTT3;A0A0U1RQQ5 P47897 QARS Glutamine--tRNA ligase 0 88.441 0.013352 0 941970 903260 545810 757730 849200 797410 987600 1124500 1167300 FALSE TRUE 817486.2779 897326.4256 809765.5416 929784.1777 832302.5814 828086.8787 891822.704 884034.4259 1029303.124 0.794213346 0.871780533 0.78671241 0.903314248 0.808607846 0.804512159 0.866433496 0.858866942 1 19.97323648 0.634998059 1.400407133 1.547925106 0.83247485 0.659284214 0.037348213 3.391528765 1.678841393 5.285845017 0.009922534 4.315171485 -0.634998059 -0.715450256 LNLKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNLKPR 6 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 94.669 0.040328 1711640000 3427700 3435200 2094100 2420600 3752500 3250600 3919800 4577600 4035900 FALSE TRUE 2974720.76 3412633.945 3106813.764 2970234.227 3677832.592 3375652.685 3539658.399 3598715.863 3558780.5 0.835882056 0.958933529 0.872999547 0.834621362 1.033453058 0.948541975 0.994626783 1.011221643 1 21.76295152 3.235567208 24.9999982 0.996603337 0.881374465 0.698054426 0.039774246 44.66069031 372991.7001 0.011539491 0.013655742 1720.153518 -3.235567208 -0.115228872 LNLTS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.079)S(0.921)PK;LNLT(0.009)S(0.991)PK;LNLT(0.025)S(0.975)PK 99.788 0.013666 1376660000 6780800 6045200 4564700 5107200 6770500 5570200 7380600 8634000 7655300 TRUE FALSE 5884700.1 6005488.683 6772204.188 6266867.819 6635780.296 5784489.198 6664830.548 6787686.29 6750299.155 0.871768786 0.889662598 1.003245046 0.928383717 0.983034995 0.856923385 0.987338545 1.005538589 1 22.68652001 -1.996469853 0.020394275 2.148157398 9.94E-06 0.316161394 0.047529766 8193.503275 16.62393708 1105.897876 691.9674847 0.010081616 1.996469853 -2.148147458 LNLVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LNLVQR 6 0 P00338;P00338-3;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2;Q9BYZ2;A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50;C9J7H8 P00338;A0A5F9ZHM4 LDHA;LDHAL6B;LDHB L-lactate dehydrogenase A chain;L-lactate dehydrogenase A-like 6B;L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 ;; 130.01 0.037103 1426190000 1720160 1932480 1183660 1367760 2017720 2216810 1809020 1956080 2111390 FALSE TRUE 1492836.498 1919785.412 1756081.935 1678330.813 1977571.32 2302092.115 1633581.519 1537787.514 1861783.88 0.801831251 1.031153741 0.943225449 0.901463823 1.062191665 1.236498039 0.877428114 0.825975308 1 20.82825418 4.751269552 23.76128393 0.973695868 0.801831031 0.195815512 0.114564182 2059.733302 3850842.877 0.030515436 0.503958546 56398.75948 -4.751269552 -0.171864837 LNLWISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNLWISR 7 0 O00515;E9PDI4 O00515 LAD1 Ladinin-1 0 ; 98.458 0.026167 530300000 288720 391110 228700 269930 378580 397080 335110 392370 395600 FALSE TRUE 250564.9205 388540.7727 339300.085 331221.7321 371046.9987 412355.9245 302611.0838 308464.7289 348832.6187 0.718295558 1.113831539 0.972673044 0.949514794 1.063682061 1.18210254 0.867496523 0.884277193 1 18.41217542 4.755507313 24.14643401 0.993145099 0.718295207 0.456750572 0.097328248 2282.725233 3252446.13 0.0254432 0.67996675 56951.78137 -4.755507313 -0.274849892 LNNDDNVDGLLVQLPLPEHIDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LNNDDNVDGLLVQLPLPEHIDER 23 0 P13995-2;P13995 P13995-2 MTHFD2 "Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial;NAD-dependent methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase" 0 ;;; 213.97 3.58E-26 215800000 169770 161583 126498 194404 207188 197734 141516 202253 194212 FALSE TRUE 147334.4644 160521.5506 187672.8559 238546.3995 203065.3642 205340.9549 127791.8001 159002.7699 171252.4786 0.860334785 0.937338554 1.095884027 1.392951515 1.185765986 1.199053915 0.746218689 0.928469889 1 17.38576534 2.24921958 24.99828579 0.893195801 1.1193603 0.304811598 0.156575857 267.9982443 628532.2238 0.06389499 0.048969813 177.5086741 -2.24921958 0.226164499 LNNMNKYDYVLTGYTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNNMNKYDYVLTGYTR 16 1 O00764;F2Z2Y4 O00764 PDXK Pyridoxal kinase 0 ; 224.86 6.76E-15 2347600000 1126010 1063320 561300 688020 1045410 975850 1169990 1322920 395910 FALSE TRUE 977204.9256 1056334.981 832746.5574 844245.4567 1024608.386 1013391.581 1056524.55 1040023.853 349105.9708 2.799164171 3.02582903 2.385368991 2.418307125 2.934949477 2.902819389 3.026372042 2.97910646 1 18.41330551 1.23541795 24.99999766 0.999997516 2.81535138 0.858245656 0.231034438 34.15860114 271685.0161 0.425283102 0.061374875 17.19562439 -1.23541795 1.815353865 LNPEDIKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNPEDIKK 8 1 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ; 107.15 0.0065062 1256440000 2352010 1929320 1301450 1531430 1748020 1445600 2787300 3299400 1301690 FALSE TRUE 2041185.919 1916646.17 1930835.573 1879164.588 1713237.822 1501213.167 2516988.075 2593848.986 1147805.691 1.778337514 1.669835047 1.682197247 1.637180058 1.49262008 1.307898348 2.192869485 2.259832832 1 20.130447 2.236004192 24.99809043 1.925343592 1.599365349 0.051680573 0.362299749 129.4768925 1266065.2 0.142930336 0.101410049 172.1885194 -2.236004192 -0.325978243 LNQPGT(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LNQPGTPTR 9 0 P36507;G5E9C7;M0R1B6 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 LNQPGT(0.915)PT(0.085)R;LNQPGT(0.612)PT(0.388)R;LNQPGT(0.997)PT(0.003)R;LNQPGT(0.965)PT(0.035)R;LNQPGT(0.951)PT(0.049)R;LNQPGT(0.993)PT(0.007)R;LNQPGT(0.999)PT(0.001)R;LNQPGT(0.79)PT(0.21)R 156.14 0.00080078 91758870000 16892910 18210030 12250900 15416550 20494050 21452520 19800990 22693600 21365920 TRUE FALSE 14660469.14 18090407.11 18175476.22 18917113.3 20086258.5 22277812.33 17880693.04 17840750.24 18840065.28 0.77815384 0.960209365 0.964724694 1.004089584 1.066145908 1.182470018 0.949078083 0.946957984 1 24.16730063 5.246671153 1.150680015 1.017937644 0.31812291 0.555683451 0.067648732 3.959845287 1.961872824 0.022269189 4.425628537 176470.1086 -5.246671153 -0.699814734 LNQS(ph)PSLAPVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNQSPSLAPVKR 12 1 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 LNQS(0.846)PS(0.154)LAPVKR;LNQS(0.75)PS(0.25)LAPVKR 135.47 7.79E-05 521200000 1045210 836860 536980 632630 754200 707200 935940 1009520 700370 TRUE FALSE 907082.8503 831362.6116 796665.3241 776278.3106 739192.8956 734406.4416 845172.6829 793642.0041 617573.0565 1.468786309 1.346176947 1.289993655 1.256982154 1.196931906 1.189181481 1.368538789 1.285098169 1 19.23625029 7.999998532 0.572771971 1.221501574 14.5705794 0.450842439 0.092592752 161.3416485 1.397376104 0.047424508 2669.121811 99999661.93 -7.999998532 13.34907783 LNS(ph)CETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LNSCETK 7 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 LNS(0.99)CET(0.01)K;LNS(0.983)CET(0.017)K;LNS(0.998)CET(0.002)K;LNS(0.848)CET(0.152)K 120.63 0.0047376 584450000 2324490 1619890 1266890 1335480 1208730 1133990 2366500 2279900 1994530 TRUE FALSE 2017302.757 1609248.836 1879562.241 1638721.146 1184678.638 1177615.329 2136997.194 1792361.127 1758738.936 1.147016602 0.915001541 1.068698829 0.931759178 0.673595503 0.669579382 1.215073568 1.019117216 1 20.74610992 2.219068041 24.99998968 1.071491762 0.900272996 0.218813631 0.157596637 413.6863319 530564.981 0.068253386 0.046089975 165.6029392 -2.219068041 -0.171218766 LNS(ph)PTLSVNSDGFIPMLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LNSPTLSVNSDGFIPMLAK 19 0 Q96JB2;Q96JB2-2 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 1 LNS(0.963)PT(0.037)LSVNSDGFIPMLAK 133.93 5.86E-07 0 101210 105770 73236 72336 119780 78611 116470 129050 107850 TRUE FALSE 87834.84207 105075.1899 108653.1746 88760.99439 117396.6123 81635.21604 105174.7573 101453.6618 95100.09586 0.923604138 1.104890473 1.142513828 0.933342849 1.234453144 0.858413604 1.105937448 1.066809248 1 16.53715917 4.752436498 23.29560582 1.057304201 0.923603903 0.132507616 0.106233539 1760.788311 2955974.182 0.023361763 0.416317455 56550.50632 -4.752436498 -0.133700298 LNS(ph)SENGEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LNSSENGEDR 10 0 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 LNS(0.5)S(0.5)ENGEDR 251.14 1.22E-13 517710000 493790 360190 292740 306230 350660 410760 475140 508470 477860 TRUE FALSE 428534.4004 357823.8882 434310.0432 375764.2019 343682.5521 426562.203 429060.9959 399737.6474 421367.9352 1.017007619 0.849195817 1.030714506 0.89177218 0.815635276 1.012327155 1.018257347 0.948666507 1 18.68472101 LNS(ph)VQSSERPLFLVHPIEGSTTVFHSLASR ddPTM_MDA-MB-175_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 1 LNS(0.998)VQS(0.001)S(0.001)ERPLFLVHPIEGSTTVFHSLASR;LNS(0.964)VQS(0.018)S(0.018)ERPLFLVHPIEGSTTVFHSLASR 270.21 1.62E-60 7926600000 1685350 1523700 581000 1291900 1656610 1240280 1671660 1778700 1269250 TRUE FALSE 1462626.727 1513690.714 861973.5433 1585245.64 1623646.702 1287994.374 1509542.67 1398338.847 1119200.711 1.306849355 1.352474761 0.770168867 1.416408715 1.450719863 1.150816258 1.348768506 1.249408469 1 20.09403735 1.24003021 8.149984767 0.997187704 1.255666327 0.14932364 0.191849375 0.177949843 113.76323 0.258686181 0.046072512 17.37921717 -1.24003021 0.258478623 LNSAIIYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LNSAIIYDR 9 0 P23921 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 98.04 0.014618 84729000 131550 149180 83244 113930 142590 135920 121770 131340 156650 FALSE TRUE 114165.3342 148200.0268 123501.0768 139799.5478 139752.738 141148.9304 109960.7641 103253.9631 138131.0155 0.826500361 1.072894645 0.894086505 1.012079346 1.011740466 1.021848206 0.796061361 0.74750745 1 17.07567777 2.235032326 24.99997897 0.824792123 0.977647712 0.269046204 0.094691143 93.19934371 660358.7344 0.035682445 0.025144055 171.8036261 -2.235032326 0.152855589 LNSDDTYQTALLSGS(ph)DEE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNSDDTYQTALLSGSDEE 18 0 Q96B21 Q96B21 TMEM45B Transmembrane protein 45B 1 LNSDDTYQTALLSGS(1)DEE;LNSDDTYQTALLSGS(1)DEE 246.38 2.91E-24 141440000 317750 268320 183562 228930 312330 334380 217668 353200 283240 TRUE FALSE 275758.5324 266557.3883 272333.1972 280912.0555 306115.2441 347243.815 196558.5909 277670.9286 249755.6899 1.104113114 1.067272535 1.09039837 1.124747371 1.22565874 1.390333951 0.787003455 1.111770181 1 17.93015802 2.232719622 24.99999933 0.989104083 1.159802235 0.375177866 0.120739038 177.514916 759770.8243 0.049201787 0.034170938 170.8911694 -2.232719622 0.170698152 LNSGVDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNSGVDYR 8 0 P62312 P62312 LSM6 U6 snRNA-associated Sm-like protein LSm6 0 ; 78.334 0.07187 268230000 1152370 1037430 625070 743330 1010880 1062550 993400 1086650 1023380 FALSE TRUE 1000081.385 1030615.054 927355.9427 912114.4376 990765.4658 1103426.986 897060.2209 854278.3538 902397.1822 1.108249676 1.142085851 1.027658287 1.010768269 1.097926152 1.222773085 0.994085796 0.946676664 1 19.78340304 2.025092197 24.95145317 0.969784986 1.096820098 0.482726237 0.059329791 180.4800895 179466.977 0.025288758 0.017048995 105.947862 -2.025092197 0.127035112 LNSHMNALHLGSQANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LNSHMNALHLGSQANR 16 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;; 267.46 1.45E-27 20795350000 3455588 3739013 1690768 2597050 3760709 4041828 3773517 3962230 3646880 FALSE TRUE 2998923.29 3714451.177 2508429.06 3186749.896 3685878.249 4197319.739 3407561.902 3114937.949 3215750.001 0.932573518 1.155080829 0.780044798 0.990981853 1.146195521 1.305238199 1.059647641 0.968650532 1 21.61672382 3.388216291 6.886744318 1.087141765 0.961312522 0.2109124 0.126812343 0.406072571 26.33335084 0.038998872 0.050460508 2444.647752 -3.388216291 -0.125829243 LNSLCMAWLVDHVYAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LNSLCMAWLVDHVYAIR 17 0 P30153;B3KQV6;P30154-4;P30154;P30154-2;P30154-3;P30154-5 P30153 PPP2R1A;PPP2R1B Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform;Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform 0 137.45 6.93E-06 91545000 218650 181000 123350 175120 172460 188730 192680 221780 234340 FALSE TRUE 189754.8485 179810.9991 183002.4726 214883.6725 169028.3834 195990.5652 173993.9233 174354.0729 206636.5922 0.918302255 0.870179852 0.885624713 1.039911036 0.817998311 0.948479469 0.842028614 0.843771527 1 17.65673623 LNSNDEDIHTANER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LNSNDEDIHTANER 14 0 A0A5F9ZHC6;A0A5F9ZHM8;P04424-3;P04424-2;P04424;F8W943 A0A5F9ZHC6 ASL Argininosuccinate lyase 0 ;; 224.59 3.09E-12 1625810000 1037995 1059342 598053 746921 929738 975998 988618 1044480 1013529 FALSE TRUE 900821.3308 1052383.113 887273.4312 916520.829 911238.0328 1013545.275 892741.9785 821126.0802 893710.7562 1.007956237 1.177543299 0.992797082 1.02552288 1.0196118 1.134086468 0.998916005 0.91878281 1 19.76944846 2.005641788 24.69066526 0.955167936 1.05920963 0.33071421 0.060261939 122.9242138 537961.1869 0.023664114 0.015898297 101.3075442 -2.005641788 0.104041694 LNSS(ph)ENGEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LNSSENGEDR 10 0 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 LNS(0.314)S(0.686)ENGEDR 257.9 3.40E-17 517450000 375310 290340 233240 240520 253730 291860 335840 352740 364040 TRUE FALSE 325711.8326 288432.7374 346035.6441 295133.7421 248681.2694 303088.0431 303270.2885 277309.296 321003.6059 1.014667208 0.89853426 1.077980552 0.919409429 0.774699302 0.944188905 0.944756641 0.863882184 1 18.29222998 3.4995032 24.70646159 0.899896328 0.989122539 0.248045493 0.07281701 913.7664454 1008664.924 0.019234136 0.028267223 3158.662324 -3.4995032 0.089226211 LNSVQSSERPLFLVHPIEGSTTVFHSLASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNSVQSSERPLFLVHPIEGSTTVFHSLASR 30 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 271.47 2.04E-71 44959000000 16641400 18247000 7380500 10778900 18472300 22112900 19105000 20452400 18049700 FALSE TRUE 14442196.83 18127134.26 10949734.49 13226413.99 18104737.37 22963597.57 17252200.04 16078813.42 15915885.03 0.907407713 1.138933476 0.687975219 0.831019699 1.137526273 1.442809968 1.083961087 1.010236842 1 23.92396405 3.230019733 24.94236871 1.130897353 0.89449407 0.356435681 0.162558008 225.5289665 658622.229 0.052330418 0.060277425 1698.320817 -3.230019733 -0.236403283 VLS(ph)PPHIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLSPPHIK 8 0 A0A0D9SG79;Q9NZ09-2;Q9NZ09;Q9NZ09-3;Q9NZ09-4 A0A0D9SG79 UBAP1 Ubiquitin-associated protein 1 1 VLS(1)PPHIK 70.1 0.033626 148970000 132030 159100 121230 171890 231870 197520 247260 313960 349080 TRUE FALSE 114581.901 158054.8616 179857.2335 210920.2517 227256.2406 205118.7222 223280.7633 246822.0972 307812.1601 0.372246181 0.51347829 0.584308409 0.685223909 0.738295201 0.66637628 0.72537993 0.801859476 1 18.2316907 3.539721951 0.16396609 1.226155393 3.45E-27 0.853150715 0.064427698 5.281192925 0.709501609 2.07685387 3.056089348 3465.1493 -3.539721951 -1.226155393 down LNTLLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNTLLQR 7 0 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;A0A1W2PPE9;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 110.31 0.015895 265920000 664350 808050 484790 539030 832290 889830 706980 771690 711790 FALSE TRUE 576554.4643 802741.8663 719236.0655 661425.0001 815729.0573 924062.3359 638417.1884 606670.0988 627642.9971 0.918602561 1.278978448 1.145931794 1.053823596 1.299670451 1.472273793 1.017166114 0.966584669 1 19.25958466 2.029659725 24.99998814 0.98419618 1.198986979 0.293983761 0.146925562 235.2623666 198300.1557 0.05999602 0.040448778 107.0680086 -2.029659725 0.214790799 LNTQEIFDDWAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LNTQEIFDDWAR 12 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;;;; 330.12 9.07E-58 1489418000 1350881 1333897 910510 965860 1390304 1432913 1287977 1559826 1420923 FALSE TRUE 1172358.653 1325134.543 1350835.681 1185173.275 1362639.67 1488038.09 1163069.189 1226269.348 1252943.102 0.935683872 1.057617494 1.078130108 0.945911489 1.087551118 1.18763421 0.928269757 0.978711122 1 20.25688947 LNTVAS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNTVASPK 8 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 LNT(0.034)VAS(0.966)PK;LNT(0.089)VAS(0.911)PK 79.889 0.028184 572680000 1284010 933260 825930 941550 1098640 887430 1224010 1372850 1737390 TRUE FALSE 1114324.825 927129.3536 1225352.511 1155343.318 1076779.213 921570.0063 1105305.699 1079276.711 1531997.733 0.72736715 0.605176714 0.799839637 0.754141663 0.702859534 0.601547892 0.721479983 0.704489757 1 20.54698273 1.23797481 7.606918665 1.004630927 0.701349674 0.706410922 0.060353802 0.056221321 24.10997024 0.087314165 0.014761814 17.29716028 -1.23797481 -0.303281253 LNVDFALIHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNVDFALIHK 10 0 B1ALA9;P60891;A0A2R8Y7H4;P60891-2 B1ALA9 PRPS1 Ribose-phosphate pyrophosphokinase 1 0 ; 120.06 0.00060965 811310000 1457040 1417840 896730 1143310 1324370 1195220 1484080 1694860 1667750 FALSE TRUE 1264488.472 1408526.116 1330391.627 1402916.01 1298017.628 1241200.887 1340154.15 1332427.378 1470590.495 0.85985084 0.957796287 0.904664917 0.953981421 0.882650631 0.844015306 0.911303422 0.906049225 1 20.48796413 1.236536861 6.079907145 1.00352209 0.903820153 0.424253467 0.03566124 0.137758725 19.9021912 0.056877882 0.008756984 17.23998412 -1.236536861 -0.099701937 LNVEAVNTHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 121.02 0.00052607 390150000 281940 259210 173642 201464 250170 286890 275470 301690 296150 FALSE TRUE 244680.9147 257507.2324 257615.852 247209.4804 245192.1064 297926.8439 248754.9618 237175.9413 261139.4844 0.936974028 0.986090759 0.986506704 0.946656845 0.938931572 1.140872452 0.952575067 0.9082347 1 17.99446108 LNVWDIGGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LNVWDIGGQR 10 0 P36405 P36405 ARL3 ADP-ribosylation factor-like protein 3 0 125.48 0.00094909 280700000 294860 290140 192330 239080 302030 304440 284970 319080 299470 FALSE TRUE 255893.5039 288234.0512 285341.4313 293366.7681 296020.1939 316152.0038 257333.6533 250847.2251 264066.9978 0.969047651 1.091518644 1.08056453 1.11095582 1.121004126 1.197241634 0.974501378 0.949937808 1 18.01054448 2.133273239 10.42092901 0.968773451 1.096075713 0.500123987 0.056580345 0.262369054 24.11513301 0.023275169 0.015688675 135.9168306 -2.133273239 0.127302262 LNWLSVDFNNWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LNWLSVDFNNWK 12 0 A0A087WYT3;Q15185-4;Q15185;B4DDC6 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ; 202.16 3.26E-07 2230320000 2490000 2254060 1891260 2319410 2024840 1755610 2337100 2818350 3855400 FALSE TRUE 2160940.191 2239252.931 2805879.662 2846067.49 1984549.646 1823149.453 2110448.402 2215667.785 3399619.004 0.635641873 0.658677613 0.825351211 0.837172485 0.583756487 0.536280522 0.620789682 0.651740028 1 21.69694164 1.236780455 24.99260546 1.000000415 0.668695689 0.545045943 0.095131042 40.67091314 570830.3935 0.159816128 0.025547542 17.24965665 -1.236780455 -0.331304726 LNYSDHDVIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LNYSDHDVIK 10 0 A0A087WY71;Q96CW1-2;Q96CW1;E9PFW3 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 ;;; 137.89 7.91E-05 2174990000 4347560 3944400 1604330 3371960 4248960 3656400 4216080 5124140 4842610 FALSE TRUE 3773018.931 3918488.977 2380189.354 4137615.055 4164414.009 3797064.074 3807205.211 4028382.537 4270122.163 0.883585712 0.917652664 0.557405447 0.968968778 0.9752447 0.889216732 0.891591637 0.943388124 1 22.02584591 LPADVSPINYSLCLKPDLLDFTFEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPADVSPINYSLCLKPDLLDFTFEGK 26 1 E9PLK3;P55786;P55786-2;E9PP11;E9PJY4;E9PPD4;E9PJF9;E9PPZ2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 75.112 2.06E-05 0 40852 34265 27401 29316 37573 30459 45742 49223 46759 FALSE TRUE 35453.30469 34039.91096 40652.21525 35972.64587 36825.37081 31630.77744 41305.94788 38697.0445 41231.20429 0.859865854 0.825586144 0.985957504 0.872461683 0.893143226 0.767156283 1.001812792 0.938537818 1 15.33144898 2.204302754 24.99999851 0.972358613 0.872257163 0.459589863 0.057268811 179.6290195 131084.8049 0.02298336 0.015496232 160.0673498 -2.204302754 -0.100101449 LPAGYTLHETPPAGAS(ph)PVLTPQESQSALEAAAANGGQRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPAGYTLHETPPAGASPVLTPQESQSALEAAAANGGQRPR 40 1 P0C7T5 P0C7T5 ATXN1L Ataxin-1-like 1 LPAGYTLHETPPAGAS(1)PVLTPQESQSALEAAAANGGQRPR 95.854 0.00010084 69458000 78719 70871 51384 52219 66305 70096 59382 76711 58997 TRUE FALSE 68316.0847 70405.44373 76233.47427 64076.12207 64985.66022 72792.63848 53623.14278 60306.94962 52022.44187 1.313204114 1.353366763 1.465395924 1.231701546 1.249185119 1.39925455 1.030769431 1.159248729 1 15.6668465 1.89143961 0.687488192 0.950260714 1.360595456 0.613103282 0.093239415 1.010169697 0.668069482 0.297920172 0.050882825 77.88245088 -1.89143961 0.410334742 LPAHYQFLLDLGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPAHYQFLLDLGVR 14 0 Q9BVJ7 Q9BVJ7 DUSP23 Dual specificity protein phosphatase 23 0 ; 171.87 2.95E-06 183109000 316490 344980 281450 226440 286830 299180 292160 359120 260690 FALSE TRUE 274665.0446 342713.8037 417560.1614 277856.6629 281122.6442 310689.6482 263826.3682 282324.9827 229871.5252 1.19486328 1.490892808 1.816493631 1.208747637 1.222955492 1.351579531 1.147712262 1.228185972 1 17.81046824 3.540709713 24.99715707 1.201209368 1.501907462 0.420248278 0.170137486 207.5474855 81587.86355 0.046062066 0.068321018 3473.03942 -3.540709713 0.300698094 LPALGEAHVS(ph)PEVATADK ddPTM_MDA-MB-175_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 256.06 9.01E-31 269370000 290190 216520 271060 372790 228230 211020 239830 325920 1121060 TRUE FALSE 251840.6563 215097.6659 402145.5226 457437.6672 223688.6695 219138.0759 216571.3235 256224.5443 988529.5639 0.254762898 0.217593559 0.406811832 0.462745561 0.226284249 0.221680852 0.219084316 0.259197654 1 19.91492459 1.237404754 24.99098671 1.00000086 0.283031889 0.876419708 0.084552043 10.27197643 221991.3347 0.133835702 0.022327651 17.27447088 -1.237404754 -0.716968971 LPASFDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPASFDAR 8 0 P07858;E9PKQ7;E9PNL5;E9PHZ5;E9PLY3;E9PSG5;E9PQM1;E9PS78;E9PR54;E9PJ67;E9PCB3 P07858 CTSB Cathepsin B;Cathepsin B light chain;Cathepsin B heavy chain 0 ; 85.813 0.038332 356240000 690110 789680 516350 638180 822870 919440 728190 837810 760870 FALSE TRUE 598910.215 784492.5401 766058.5871 783088.523 806496.4969 954811.4518 657570.2459 658650.8513 670920.8154 0.892669002 1.16927739 1.141801789 1.167184718 1.202074043 1.42313583 0.980101125 0.981711755 1 19.35578298 LPASVFVVGHINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPASVFVVGHINR 13 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 0 96.059 0.0017961 0 199800 239830 127670 119400 194180 157460 246530 192180 165950 FALSE TRUE 173395.9238 238254.5409 189411.639 146511.5949 190316.1979 163517.5881 222621.5585 151083.8025 146331.5801 1.184952173 1.628182658 1.294400286 1.001230185 1.300581856 1.117445653 1.521350063 1.032475714 1 17.15888163 1.602716777 9.304502189 1.009967268 1.288109164 0.289277928 0.180265941 0.11976127 28.55214435 0.111598911 0.045319894 40.06053799 -1.602716777 0.278141896 LPCPAEGEAELELRVS(ph)EDEEKLPASPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPCPAEGEAELELRVSEDEEKLPASPK 27 2 Q7RTP6;J3QR21;J3QLA3 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 LPCPAEGEAELELRVS(1)EDEEKLPASPK 122.77 4.60E-05 98333000 165670 111270 90026 75099 96293 61154 112600 132330 104560 TRUE FALSE 143776.2897 110539.06 133562.8747 92151.37577 94376.95769 63506.63395 101680.0693 104032.2593 92199.03592 1.559412073 1.198917743 1.448636348 0.999483073 1.023621958 0.688799328 1.10283224 1.128344329 1 16.49246404 3.732380457 24.36206689 1.000698865 1.381981632 0.634899684 0.146806813 236.8214928 933546.7245 0.040882113 0.06245211 5399.83459 -3.732380457 0.381282767 LPDAYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LPDAYER 7 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;; 173.59 0.0019951 18848910000 8170410 8410730 6500790 7079940 8212820 9468750 8851190 9091180 10036410 FALSE TRUE 7090669.617 8355479.361 9644593.788 8687548.587 8049400.95 9833018.94 7992802.956 7147101.905 8849917.043 0.801213117 0.944130812 1.089794824 0.98165311 0.909545356 1.111086001 0.903150043 0.807589706 1 23.0772325 0.947490039 22.68071538 1.888278419 0.942776418 0.02971422 0.10134974 485.2301599 782956.0227 106599.3362 0.025156583 8.861148987 -0.947490039 -0.945502 LPDGYEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPDGYEFK 8 0 P09382 P09382 LGALS1 Galectin-1 0 ; 107.01 0.0095055 605620000 1675350 1558440 1149770 1385870 1479470 1348720 1677030 2002720 1843070 FALSE TRUE 1453948.253 1548202.505 1705802.618 1700552.965 1450031.442 1400606.131 1514391.889 1574453.913 1625184.364 0.894635885 0.952631922 1.049605605 1.046375416 0.892225814 0.861813688 0.93182775 0.968784802 1 20.63217196 3.226692094 24.99956305 0.932273682 0.987998869 0.183490693 0.057406203 421.1788558 887158.6564 0.018982769 0.021691237 1685.357718 -3.226692094 0.055725187 LPDLS(ph)PVENK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LPDLSPVENK 10 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;H7C5N8;A0A2R8YET2;A0A2R8Y7F4 E7EPN9 PRRC2C Protein PRRC2C 1 LPDLS(1)PVENK;LPDLS(1)PVENK;LPDLS(1)PVENK;LPDLS(1)PVENK;LPDLS(1)PVENK;LPDLS(1)PVENK 208.63 1.16E-07 2155508000 3931430 3229750 3155680 4142330 3514650 2883290 3986530 4843700 7389890 TRUE FALSE 3411881.565 3208533.56 4681777.403 5082909.338 3444715.341 2994212.032 3599916.934 3807912.449 6516265.623 0.523594611 0.492388393 0.718475531 0.780034092 0.528633352 0.459498155 0.552450919 0.584370354 1 22.63561398 1.23869696 9.234769385 1.002615134 0.581155529 0.640633284 0.098874624 0.05573711 72.69192272 0.147608203 0.0260916 17.32594616 -1.23869696 -0.421459605 LPDLSLDNMIGQSAIAGEEHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPDLSLDNMIGQSAIAGEEHPR 22 0 Q9BZH6;S4R3Z0 Q9BZH6 WDR11 WD repeat-containing protein 11 0 159.14 2.00E-11 70815000 36245 33383 26703 32250 34677 31459 35688 34069 34635 FALSE TRUE 31455.13142 33163.70487 39616.66012 39572.85541 33986.99554 32669.24809 32226.98325 26783.60948 30540.48976 1.029948494 1.085893027 1.297184833 1.295750518 1.112850377 1.069702822 1.05522156 0.876986901 1 14.89843558 2.288360392 1.497776557 0.93420826 1.17480794 0.487118498 0.090738324 0.343248447 1.555989868 0.066909824 0.033656096 194.2497156 -2.288360392 0.24059968 LPDNVTFEEGALIEPLSVGIHACR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPDNVTFEEGALIEPLSVGIHACR 24 0 Q00796;A0A6I8PIS1 Q00796 SORD Sorbitol dehydrogenase 0 ; 219.23 1.11E-32 181430000 140369 130714 65819 92551 123069 124643 119567 150240 130307 FALSE TRUE 121818.881 129855.3311 97649.28855 113566.1191 120620.1677 129438.0969 107971.4107 118112.3452 114902.2549 1.060195739 1.130137361 0.849846582 0.988371544 1.049763277 1.126506151 0.939680521 1.027937574 1 16.81004758 LPDS(ph)DDDEDEETAIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LPDSDDDEDEETAIQR 16 0 H3BRF9;Q96K21-2;Q96K21;Q96K21-4;H3BRM1;Q96K21-3 H3BRF9;Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 LPDS(1)DDDEDEETAIQR;LPDS(1)DDDEDEETAIQR;LPDS(1)DDDEDEETAIQR;LPDS(1)DDDEDEETAIQR;LPDS(1)DDDEDEETAIQR;LPDS(1)DDDEDEETAIQR;LPDS(1)DDDEDEETAIQR;LPDS(1)DDDEDEETAIQR 449.27 3.23E-182 20485380000 580349 470170.7 379735.7 378281.2 460869 497732 527812 596540 517815 TRUE FALSE 503654.4092 467082.1177 563377.1547 464175.7281 451698.6086 516880.0721 476624.8735 468974.5633 456599.5006 1.103055103 1.022958013 1.233854075 1.01659272 0.989266541 1.132020669 1.043857632 1.027102664 1 18.80056976 LPEADDIQYPSMLLLTADHDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LPEADDIQYPSMLLLTADHDDR 22 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ;;;;; 282.86 8.86E-46 1614990000 1202352 1005464 740639 810700 1037677 1087082 993136 1132417 1184218 FALSE TRUE 1043458.137 998859.0408 1098814.498 994781.8258 1017029.258 1128902.748 896821.8236 890258.437 1044221.097 0.99926935 0.956558954 1.052281457 0.952654403 0.973959692 1.081095518 0.85884285 0.852557413 1 19.99399578 2.22135344 24.98256733 0.891251295 0.999223314 0.399774437 0.056292116 213.0766097 309356.9791 0.02231333 0.015084652 166.4766929 -2.22135344 0.107972019 LPEASQS(ph)PLVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LPEASQSPLVLK 12 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;F8W9Y9 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 LPEAS(0.056)QS(0.944)PLVLK;LPEAS(0.008)QS(0.992)PLVLK;LPEAS(0.078)QS(0.922)PLVLK;LPEAS(0.011)QS(0.989)PLVLK 147.12 6.44E-05 402999000 1796600 1803810 1223768 1575680 2055200 1760563 1465920 2242080 2611840 TRUE FALSE 1559174.758 1791960.653 1815586.298 1933462.227 2014305.541 1828292.998 1323755.304 1762628.64 2303071.251 0.676998055 0.778074344 0.788332666 0.839514725 0.874617119 0.79384995 0.574778268 0.765338302 1 21.13512761 4.750667729 3.128951907 0.792361059 0.657742299 0.117461049 0.10551254 0.991815283 14.628285 0.02738618 0.333638154 56320.65915 -4.750667729 -0.134618761 LPEDPLLSGLLDSPALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 146.5 1.01E-06 80293000 150370 145720 107700 127450 133960 127680 162740 189610 196890 FALSE TRUE 130498.2235 144762.7557 159784.0802 156389.4705 131294.4581 132591.9322 146957.4998 149063.377 173613.8885 0.751657743 0.833820134 0.920341579 0.900788939 0.75624398 0.763717312 0.846461658 0.858591316 1 17.40552284 1.140887113 2.114716492 1.08769493 0.826863389 0.47911787 0.057054134 0.954178433 3.399201251 0.531223455 0.016432412 13.83206794 -1.140887113 -0.260831541 LPEEWSQWLGGSSWPGYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPEEWSQWLGGSSWPGYVR 19 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ; 350.97 2.16E-90 4148700000 185437 132928 137889 157575 154888 171225 153326 141162 393860 FALSE TRUE 160931.0306 132054.7872 204572.5816 193354.8121 151806.0318 177812.1365 138456.4681 110975.6048 347298.3195 0.463379814 0.380234455 0.589039941 0.556739844 0.437105576 0.511986746 0.398667256 0.319539712 1 18.4058159 1.229839355 24.99988592 1.000001033 0.45382803 0.815851673 0.081047716 154.0149277 441456.6662 0.252394179 0.021783754 16.97615589 -1.229839355 -0.546173003 LPEEWSQWLGGSSWPGYVRPLPPAAIESPAVAAPAYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPEEWSQWLGGSSWPGYVRPLPPAAIESPAVAAPAYSR 38 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ; 258.36 1.47E-62 766630000 233780 191454 121373 157951 206980 227290 187846 226880 196970 FALSE TRUE 202885.3807 190196.3261 180069.3888 193816.1887 202861.5029 236033.9934 169628.7238 178363.4776 173684.431 1.168126467 1.095068366 1.036761831 1.115909973 1.167988989 1.358981873 0.976648988 1.026939931 1 17.40610891 LPEGPVDS(ph)EDDEEEDEEIDRTDPLQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPEGPVDSEDDEEEDEEIDRTDPLQGR 27 1 E9PCH4;Q8TEU7-2;Q8TEU7-5;Q8TEU7-3;Q8TEU7;Q8TEU7-4;B7Z7Y1;D6RD23;D6RIH0;D6RB02;Q8TEU7-6 E9PCH4 RAPGEF6 Rap guanine nucleotide exchange factor 6 1 LPEGPVDS(1)EDDEEEDEEIDRTDPLQGR;LPEGPVDS(1)EDDEEEDEEIDRTDPLQGR 165.87 5.63E-12 725270000 172743 154206 108838 169379 152801 165289 121664 180465 244220 TRUE FALSE 149914.5749 153193.0106 161472.4208 207839.0907 149760.5591 171647.7748 109865.044 141873.9641 215348.5898 0.696148394 0.711372249 0.749818798 0.965128636 0.695433201 0.797069416 0.510173037 0.658810741 1 17.71631435 LPEHCIEYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LPEHCIEYVR 10 0 Q8TBC4;F8W8D4;Q8TBC4-2 Q8TBC4 UBA3 NEDD8-activating enzyme E1 catalytic subunit 0 ;;; 119.22 0.0007208 2205200000 2074220 1975970 1133560 1331580 1882010 2067700 1720440 1965420 1780580 FALSE TRUE 1800106.572 1962989.723 1681753.408 1633935.591 1844561.683 2147245.757 1553591.994 1545130.228 1570081.861 1.146504916 1.250246737 1.071124665 1.040669045 1.174818797 1.367601149 0.989497447 0.984108069 1 20.58240835 2.096532886 24.99999956 0.989539111 1.168622637 0.480803185 0.089938228 12.44997354 3213.073402 0.037950299 0.025586081 124.8915011 -2.096532886 0.179083526 LPESENLQEFWDNLIGGVDMVTDDDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LPESENLQEFWDNLIGGVDMVTDDDRR 27 1 P49327;A0A0U1RQF0;A0A0U1RRG3 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 137.24 1.82E-05 1337986000 115544.8 87147.8 57921.9 73542.2 97409.4 108665 107594.4 116816.5 74432 FALSE TRUE 100275.2619 86575.32036 85933.12458 90241.08053 95471.14352 112845.4129 97159.91165 91836.20054 65632.73375 1.527823941 1.319087526 1.309302838 1.374940146 1.454626953 1.719346527 1.48035753 1.399243873 1 16.00212791 1.234130957 3.734451377 0.939757474 1.450532438 0.597040306 0.116501035 0.216013982 4.763123215 0.311171462 0.032189239 17.14474213 -1.234130957 0.510774964 LPFPIIDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 LPFPIIDDR 9 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;;;;;; 182.39 0.00010791 6245735000 1481902 1474005 1143194 1274446 1482982 1508456 1425298 1537918 2217956 FALSE TRUE 1286064.896 1464322.164 1696046.442 1563828.443 1453473.56 1566487.278 1287072.819 1209046.204 1955751.768 0.657580843 0.748725982 0.867209464 0.79960477 0.743178957 0.800964265 0.658096206 0.618200235 1 20.89929184 2.279049667 24.99402309 0.725285963 0.773205079 0 0.113834064 596.7857849 368395.611 0.042316746 0.032778002 190.1295704 -2.279049667 0.047919116 LPFTPLSYIQGLSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPFTPLSYIQGLSHR 15 0 J3KS45;Q9UM00-1;Q9UM00;J3QQY2;Q9UM00-2 J3KS45 TMCO1 Transmembrane and coiled-coil domain-containing protein 1 0 ; 230.16 3.65E-13 274120000 162368 172427 109140 173125 232251 229910 134419 263430 220106 FALSE TRUE 140910.6574 171294.3157 161920.4691 212435.6773 227629.6595 238754.7865 121383.0661 207097.5445 194085.3194 0.726024296 0.882572243 0.834274687 1.094547892 1.172832959 1.230153765 0.625410858 1.06704384 1 17.56633147 3.783062227 8.89920712 1.024064956 0.820566935 0.278289764 0.164617355 0.63465617 121.1891998 0.044740283 0.077358993 6068.232714 -3.783062227 -0.203498021 LPFYNQDHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPFYNQDHER 10 0 P31751;P31751-2;M0R0P9;J3QKW1;J3QL45;M0QZW8 P31751 AKT2 RAC-beta serine/threonine-protein kinase 0 110.08 0.0030424 0 90714 75587 73595 71573 71613 85478 79216 79589 126600 FALSE TRUE 78725.91506 75090.46402 109185.7882 87824.74357 70188.04141 88766.39397 71533.64451 62569.51171 111633.4922 0.705217704 0.672651751 0.978073748 0.786723965 0.628736412 0.795159161 0.64079017 0.560490499 1 16.7684104 3.3545791 10.40907817 0.701721459 0.791996231 0.028215776 0.142629277 0.880903961 76.2906715 0.040949224 0.052865075 2262.450571 -3.3545791 0.090274772 LPGAWDPAAHQGGNGVLLEGELIDVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPGAWDPAAHQGGNGVLLEGELIDVSR 27 0 Q7Z6K5;A0A0A6YYH1;Q7Z6K5-2 Q7Z6K5 ARPIN;C15orf38-AP3S2 Arpin 0 249.79 5.91E-46 160710000 36864 43751 26370 27540 38313 33046 35684 46715 38867 FALSE TRUE 31992.329 43463.5968 39122.6202 33793.37792 37550.64626 34317.301 32223.37117 36725.36079 34272.18754 0.933477881 1.268188579 1.141526789 0.986029208 1.095659453 1.001316329 0.940219271 1.071579127 1 15.06475066 3.745647404 24.61450137 1.019610944 1.129776842 0.200260546 0.090959867 617.2503923 2143882.232 0.022741506 0.03831475 5567.335628 -3.745647404 0.110165898 LPGEYFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPGEYFR 7 0 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 131.3 0.0080945 239810000 119100 115030 73372 98961 113780 128990 111300 127680 131210 FALSE TRUE 103360.6332 114274.3604 108854.9446 121431.6076 111516.0006 133952.3288 100506.1431 100376.6256 115698.5033 0.893361887 0.987690913 0.940850067 1.049552104 0.963849985 1.157770628 0.868690089 0.867570649 1 16.82001068 LPGGELNPGEDEVEGLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LPGGELNPGEDEVEGLKR 18 1 O43809;H3BND3;H3BV41 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 ;; 166.6 4.05E-11 876150000 737760 561320 402835 523020 573920 467870 617560 704550 667880 FALSE TRUE 640263.1468 557632.652 597647.3534 641779.6849 562500.1149 485869.2617 557669.1263 553887.4653 588923.9873 1.087174509 0.946866937 1.01481238 1.089749609 0.955131947 0.825011839 0.946928871 0.940507565 1 19.16772191 3.035090343 11.67633961 0.927181696 1.026455183 0.430573487 0.058187141 0.746946395 245.9555586 0.01755103 0.019884405 1084.15242 -3.035090343 0.099273487 LPGMEYVDGDFQCHTFDSS(ph)NVE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPGMEYVDGDFQCHTFDSSNVE 22 0 P24593 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 1 LPGMEYVDGDFQCHTFDS(0.415)S(0.585)NVE 152.41 2.67E-08 64579000 38647 31439 19380 20435 29570 31320 31387 31846 37114 TRUE FALSE 33539.70103 31232.47514 28752.23282 25075.07908 28981.61485 32524.90067 28343.09357 25035.98073 32726.4252 1.024850738 0.954350344 0.878563199 0.766202814 0.885572276 0.993842146 0.866061398 0.765008111 1 14.9981684 4.427758491 2.71956358 0.868425845 1.019936108 0.272907769 0.077923303 0.368414293 5.075534181 0.020803451 0.091173691 26776.7887 -4.427758491 0.151510263 YSSS(ph)GS(ph)PANSFHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YSSSGSPANSFHFK 14 0 O00418;H3BRH4 O00418 EEF2K Eukaryotic elongation factor 2 kinase 2 Y(0.009)S(0.008)S(0.069)S(0.917)GS(0.997)PANSFHFK;Y(0.006)S(0.004)S(0.022)S(0.97)GS(0.997)PANS(0.001)FHFK;YS(0.002)S(0.019)S(0.98)GS(0.999)PANSFHFK 113.25 0.00079863 530930000 538220 864750 500030 1054680 1681720 1434110 1651580 1980760 1704010 TRUE FALSE 467092.8633 859069.4003 741846.1805 1294161.214 1648257.062 1489281.14 1491410.026 1557189.888 1502563.879 0.310863897 0.571735693 0.493720228 0.86130196 1.096963054 0.99115995 0.992576786 1.036355199 1 20.5189949 3.663447821 2.477027768 1.021904057 0.449985574 0.931416306 0.070050844 0.064383288 0.772007342 0.019301854 0.033219322 4607.3141 -3.663447821 -0.571918483 down LPHLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPHLLK 6 0 Q5XPI4;Q5XPI4-2;C9JI97 Q5XPI4 RNF123 E3 ubiquitin-protein ligase RNF123 0 78.002 0.070933 353180000 589300 590070 366470 503260 584100 527050 640850 780610 613090 FALSE TRUE 511422.5119 586193.7913 543696.1178 617532.8748 572477.5528 547325.9545 578700.4656 613682.6262 540611.1986 0.946007987 1.084316775 1.005706354 1.142286502 1.05894505 1.012420675 1.070455934 1.135164473 1 19.04423187 5.519524985 1.699394807 1.069880756 4.68E-14 0.33587709 0.050185581 14.91288795 5.548861976 0.013118674 49.19693624 330769.1409 -5.519524985 -1.069880756 LPHSSS(ph)SENIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPHSSSSENIK 11 0 F5H527;Q76I76;A0A3B3IS79;K7EKN7 F5H527 SSH2 Protein phosphatase Slingshot homolog 2 1 LPHSS(0.017)S(0.98)S(0.003)ENIK 117.93 0.00050775 266570000 97869 87949 32545 71622 114230 94467 98522 119670 114800 TRUE FALSE 84935.36368 87371.25723 48283.87086 87884.86977 111957.0465 98101.20662 88967.3516 94079.50177 101228.4748 0.839046166 0.86310949 0.47697914 0.868183285 1.105983734 0.969106833 0.878876737 0.929377845 1 16.62725564 3.483453354 24.82686706 0.965230425 0.728806351 0.486673554 0.117087292 227.5212476 892065.5178 0.033247029 0.044529181 3044.061021 -3.483453354 -0.236424075 LPIGDVATQYFADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPIGDVATQYFADR 14 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 160.52 1.10E-05 1014280000 315150 281540 211531 225470 291730 316600 251620 328270 343040 FALSE TRUE 273502.129 279690.5452 313828.0991 276666.4096 285925.1438 328779.8069 227217.9311 258072.0151 302486.202 0.904180512 0.924639019 1.037495585 0.914641421 0.945250203 1.086924973 0.75116792 0.853169544 1 18.20650981 2.234774768 24.99999975 0.860126715 0.966428238 0.251276883 0.081517921 128.0662039 845675.9323 0.03195824 0.022479119 171.7017685 -2.234774768 0.106301523 LPIGDVATQYFADRDMFCAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPIGDVATQYFADRDMFCAGR 21 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 199.99 7.03E-22 1079570000 433950 424860 137016 178113 302480 364610 373120 435050 59864 FALSE TRUE 376602.408 422069.0667 203277.3959 218556.2789 296461.2398 378636.7826 336934.8798 342017.9431 52786.94612 7.134385217 7.995709124 3.850902749 4.140347094 5.616184712 7.172924567 6.382920487 6.479214431 1 15.68789358 4.253712891 24.98866877 5.23676262 7.565048372 0.26310304 1.769930579 362.0352034 597046.8266 0.445223874 1.168113345 17935.47532 -4.253712891 2.328285752 LPISSS(ph)TSNLHVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LPISSSTSNLHVDR 14 0 Q86TV6;Q86TV6-2;G3V3H1 Q86TV6 TTC7B Tetratricopeptide repeat protein 7B 1 LPIS(0.03)S(0.181)S(0.713)T(0.073)S(0.003)NLHVDR;LPIS(0.004)S(0.031)S(0.893)T(0.071)S(0.001)NLHVDR;LPISS(0.001)S(0.974)T(0.025)SNLHVDR;LPISS(0.002)S(0.976)T(0.022)SNLHVDR;LPISS(0.033)S(0.849)T(0.056)S(0.061)NLHVDR 187.39 6.14E-07 1424870000 1243432 1464582 855940 967106 1174936 1263033 1167708 1113035 1285594 TRUE FALSE 1079109.311 1454961.064 1269875.447 1186702.199 1151557.072 1311622.697 1054463.858 875021.1269 1133612.542 0.951920759 1.283472977 1.120202362 1.046832277 1.015829509 1.157029098 0.930180127 0.771887302 1 20.11249619 2.10181358 5.04104419 0.864547758 1.098873318 0.440594808 0.103571395 0.159045255 6.516621903 0.042377183 0.027885866 126.4193578 -2.10181358 0.23432556 LPIVNEDDELVAIIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPIVNEDDELVAIIAR 16 0 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 169.62 1.29E-08 139656000 18108.5 11765.8 12313.8 11235.5 15300.9 12679.5 13015.1 17494.2 14437 FALSE TRUE 15715.41584 11688.50969 18268.79487 13786.692 14996.44203 13167.28857 11752.89761 13753.20147 12730.27431 1.234491533 0.918166365 1.435066867 1.082984676 1.178014053 1.034328739 0.923224223 1.080353898 1 13.63597589 2.68628689 4.863655116 1.010405881 1.165958312 0.265770218 0.132661666 0.297961696 15.64365113 0.043525671 0.038774353 485.6091816 -2.68628689 0.155552431 LPLDINPVVHPHGHIFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPLDINPVVHPHGHIFK 17 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 76.548 0.006838 216510000 409470 333970 232540 289130 336620 336250 326810 423740 342680 FALSE TRUE 355357.502 331776.1291 344997.1218 354781.3856 329921.9206 349185.7551 295116.0165 333126.4985 302168.7608 1.176023296 1.097982889 1.141736561 1.174116691 1.091846555 1.155598462 0.976659585 1.102451814 1 18.20499499 2.256033982 24.99998149 1.040149449 1.137163473 0.60475037 0.042621944 166.3202121 237961.8402 0.014806532 0.011440884 180.3158826 -2.256033982 0.097014024 LPLGLLLHPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPLGLLLHPFR 11 0 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 0 ; 154.56 3.19E-05 73882000 42274 94258 51322 64101 84613 90278 81266 82239 124426 FALSE TRUE 36687.38379 93638.81299 76141.49086 78656.11177 82929.36684 93751.05308 73384.83583 64652.82983 109716.5 0.334383468 0.853461539 0.693983957 0.716903217 0.75585137 0.85448454 0.668858702 0.589271712 1 16.74342098 4.747825954 24.82260767 0.746754235 0.334383229 0.572282825 0.116310267 880.4380456 2358711.97 0.027860379 0.339801949 55953.33208 -4.747825954 -0.412371006 LPLLPHEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LPLLPHEVR 9 0 O43681 O43681 ASNA1 ATPase ASNA1 0 ;;; 96.331 0.0074403 2237910000 2287080 2157520 1423019 1680479 2278240 2328660 2130230 2401060 2400270 FALSE TRUE 1984836.583 2143347.109 2111195.748 2062057.441 2232907.481 2418245.057 1923640.622 1887612.004 2116512.815 0.937786235 1.012678541 0.997487817 0.974271182 1.054993603 1.142561028 0.908872655 0.891850024 1 21.01325779 LPLLPPES(ph)PGPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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;LPLLPPES(1)PGPLR 187.45 7.29E-06 1726563000 1087779 1031144 664900 1046206 1190959 1102122 919267 1308512 1145265 TRUE FALSE 944026.2491 1024370.347 986447.864 1283763.063 1167261.246 1144521.347 830116.6278 1028696.892 1009873.076 0.934796928 1.014355537 0.976803805 1.271212287 1.155849456 1.133331874 0.82200095 1.018639783 1 19.94574255 2.266920159 24.99994372 0.956626645 1.085330501 0.25298871 0.108092538 314.3618997 277120.1662 0.042429524 0.032859208 184.8928679 -2.266920159 0.128703856 LPLPS(ph)PALEYTLGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPLPSPALEYTLGSR 15 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 LPLPS(1)PALEYTLGSR;LPLPS(1)PALEYTLGSR 178.03 7.64E-07 214566000 150886 130620 83185 107136 133061 125149 113736 118398 106899 TRUE FALSE 130946.0328 129761.9486 123413.5442 131462.8663 130413.3464 129963.563 102705.9002 93079.50907 94261.522 1.389178002 1.37661631 1.309267468 1.394660976 1.383526848 1.378755194 1.089584573 0.987460282 1 16.52438136 2.152376162 3.526202083 1.002649451 1.372488113 0.975399884 0.02619407 0.032551257 0.797526984 0.012577463 0.007966156 142.0287163 -2.152376162 0.369838662 LPLQES(ph)EEEEREER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPLQESEEEEREER 14 1 P23497;P23497-2;P23497-3;P23497-4;E9PHV6;P23497-7;P23497-6;P23497-5;C9JBL0 P23497 SP100 Nuclear autoantigen Sp-100 1 LPLQES(1)EEEEREER;LPLQES(1)EEEEREER 127.32 4.86E-05 552360000 194411 168238 116540 124497 162466 152655 200034 210410 172254 TRUE FALSE 168719.0938 167132.8335 172899.1338 152765.9467 159233.2445 158527.7366 180634.7335 165415.4589 151890.3284 1.110795504 1.100352046 1.138315623 1.005764806 1.04834354 1.043698689 1.189244473 1.08904537 1 17.21267048 LPLQLDDAVRPEAEGEEEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LPLQLDDAVRPEAEGEEEGR 20 1 P14868;P14868-2;C9J7S3;C9JLC1 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ;;;;;;; 252.91 3.96E-36 6462850000 1857000 1577710 1085445 1243543 1500450 1633240 1511557 1686320 1709190 FALSE TRUE 1611592.745 1567345.919 1610369.833 1525908.445 1470593.981 1696071.8 1364966.435 1325713.591 1507131.505 1.069311297 1.039952993 1.06849988 1.012458726 0.97575691 1.125364173 0.905671755 0.879627017 1 20.52337387 2.217133508 24.99994814 0.917316581 1.044122752 0.56418811 0.049346205 157.325513 183557.2067 0.019543613 0.013189763 164.8669137 -2.217133508 0.126806171 LPLS(ph)PPLVEDSAFEPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LPLSPPLVEDSAFEPSR 17 0 O96007 O96007 MOCS2 Molybdopterin synthase catalytic subunit 1 LPLS(1)PPLVEDSAFEPSR;LPLS(1)PPLVEDSAFEPSR;LPLS(1)PPLVEDSAFEPSR;LPLS(1)PPLVEDSAFEPSR;LPLS(1)PPLVEDSAFEPSR;LPLS(1)PPLVEDSAFEPSR 200.69 1.28E-11 526134000 132856 151784 118499 167009 174019 171572 168073 196309 329484 TRUE FALSE 115298.743 150786.9209 175805.5128 204930.946 170556.3624 178172.4859 151773.3063 154329.848 290532.7769 0.39685279 0.51900141 0.605114213 0.70536257 0.587046887 0.613261222 0.522396502 0.531195997 1 18.14834141 1.235931152 24.97447642 1.000000586 0.564089663 0.749686213 0.079866129 37.92932061 360174.862 0.135997249 0.020432218 17.21595633 -1.235931152 -0.435910923 LPLVPES(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LPLVPESPR 9 0 C9J0I9;Q86WB0;Q86WB0-2;Q86WB0-3 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 LPLVPES(1)PR;LPLVPES(1)PR;LPLVPES(1)PR;LPLVPES(1)PR 137.89 0.00015927 391812000 307877 276476 194640 253274 291871 272303 260549 316441 405127 TRUE FALSE 267190.2744 274659.811 288768.555 310783.7328 286063.3381 282778.6726 235280.9981 248772.5547 357233.3476 0.747943259 0.768852664 0.808347141 0.869974024 0.800774452 0.791579718 0.658619918 0.696386707 1 18.44650724 2.454729902 24.98668277 0.756106891 0.801360178 0 0.094997769 856.5727627 955849.3753 0.03556312 0.027548903 284.9245704 -2.454729902 0.045253288 LPLVPES(ph)PRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LPLVPESPRR 10 1 C9J0I9;Q86WB0;Q86WB0-2;Q86WB0-3 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 LPLVPES(1)PRR;LPLVPES(1)PRR;LPLVPES(1)PRR;LPLVPES(1)PRR;LPLVPES(1)PRR;LPLVPES(1)PRR 96.551 0.0040812 2975880000 2478680 2182050 1352290 1687640 2068470 2236950 1945690 2203820 1966220 TRUE FALSE 2151116.158 2167715.97 2006261.967 2070844.456 2027311.494 2323006.914 1756997.283 1732550.243 1733775.712 1.2407119 1.250286271 1.157163498 1.194413119 1.169304357 1.339854341 1.013393642 0.999293179 1 20.72548585 2.176239402 10.08164166 1.002941727 1.219291922 0.808835495 0.050607655 0.165952009 25.69081317 0.020208546 0.013628544 150.0511754 -2.176239402 0.216350195 LPLVTPHTQCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPLVTPHTQCR 11 0 P62191 P62191 PSMC1 26S protease regulatory subunit 4 0 88.187 0.013166 387150000 438860 520630 301310 411940 550050 558910 494670 550230 684390 FALSE TRUE 380863.5391 517209.9472 447024.5238 505477.2731 539105.0812 580411.6294 446696.9795 432567.5964 603482.1939 0.631109821 0.857042598 0.740741862 0.837600974 0.893323923 0.961770928 0.740199105 0.716786014 1 19.20295168 4.743348492 24.21909671 0.830565551 0.631109694 0.326874022 0.09415838 437.1073353 2210955.321 0.023542308 0.185405182 55379.43131 -4.743348492 -0.199455858 LPNGLGGPNGFPKPTPEEGPPELNRQS(ph)PNSSSAAASVASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LPNGLGGPNGFPKPTPEEGPPELNRQSPNSSSAAASVASR 40 2 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 LPNGLGGPNGFPKPTPEEGPPELNRQS(0.988)PNS(0.009)S(0.002)S(0.001)AAASVASR;LPNGLGGPNGFPKPTPEEGPPELNRQS(0.998)PNS(0.001)SSAAASVASR;LPNGLGGPNGFPKPTPEEGPPELNRQS(0.965)PNS(0.023)S(0.006)S(0.002)AAAS(0.002)VAS(0.002)R 116.33 1.68E-06 1228098000 340749 249276 166858.1 198160 266498 233458 298635 361379 204035 TRUE FALSE 295718.1563 247638.4895 247551.2353 243155.2567 261195.2112 242439.2803 269673.4237 284100.9131 179914.2147 1.64366199 1.37642537 1.375940393 1.351506645 1.451776401 1.347527102 1.49890004 1.579090977 1 17.45694965 -1.999939416 0.020350681 1.28E-05 2.540935295 0.131492293 0.161439612 23683.38265 47.91202085 3776.989055 2364.790647 0.010001395 1.999939416 2.540922533 LPNNS(ph)SRPS(ph)TPTINVLESK ddPTM_MDA-MB-175_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(0.539)S(0.46)RPS(0.595)T(0.373)PT(0.032)INVLESK 105.73 0.00018651 201580000 377370 266300 155610 173750 168750 163590 180410 243510 270570 TRUE FALSE 327499.5984 264550.6578 230863.5165 213202.5931 165392.2052 169883.4132 162913.866 191437.2815 238583.5228 1.37268322 1.108838761 0.967642332 0.893618262 0.693225597 0.712050066 0.682837876 0.802391042 1 17.86413488 4.51145113 1.02372525 0.774210307 1.537226254 0.805770729 0.094574435 0.572805586 0.637710624 0.032618354 0.442497169 32467.67054 -4.51145113 0.763015947 LPNNSSRPST(ph)PTINVLESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPNNSSRPSTPTINVLESK 19 1 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 1 LPNNS(0.004)S(0.003)RPS(0.035)T(0.957)PTINVLESK 110.26 0.00038692 248470000 227800 178970 154770 216960 245910 222470 308060 347870 285430 TRUE FALSE 197695.6528 177794.3343 229617.2897 266224.084 241016.8721 231028.5649 278184.3886 273480.7076 251686.7906 0.785482831 0.706411067 0.912313631 1.057759461 0.957606363 0.917920898 1.105280051 1.086591422 1 17.94126998 4.044590132 3.485294887 1.0250897 0.746954378 0.780373466 0.059636802 0.107221812 2.702511594 0.017385463 0.038928241 11081.28519 -4.044590132 -0.278135323 LPNTYPNSSS(ph)PGPGGLGGSVHYATMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPNTYPNSSSPGPGGLGGSVHYATMAR 27 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A0U1RRC1;A0A0U1RQJ5 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 LPNTYPNS(0.014)S(0.042)S(0.944)PGPGGLGGSVHYATMAR 87.498 4.10E-06 0 76993 75941 38047 56670 91357 76039 81963 88803 78533 TRUE FALSE 66818.17997 75442.13857 56446.65646 69537.78965 89539.17444 78964.26953 74014.24088 69813.16952 69248.91821 0.964898539 1.089434182 0.815126906 1.004171494 1.293004667 1.140296074 1.068814399 1.008148161 1 16.07950391 3.46463944 24.92540187 1.095084279 0.959759247 0.299309968 0.103422605 301.7988407 602670.9242 0.03136047 0.040513498 2915.005911 -3.46463944 -0.135325032 LPPEEASPYVVDHGESGPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPPEEASPYVVDHGESGPLR 20 0 P53992;G5EA31 P53992 SEC24C Protein transport protein Sec24C 0 ; 143.57 1.66E-07 374690000 60794 54101 44691 32848 44652 73148 55606 64290 72285 FALSE TRUE 52759.91887 53745.60697 66303.71708 40306.64045 43763.51256 75962.05089 50213.33868 50542.08381 63739.54965 0.82774226 0.843206569 1.040228829 0.632364688 0.686599024 1.191756944 0.787789355 0.792946986 1 15.95990121 LPPKVESLESLYFTPIPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPPKVESLESLYFTPIPAR 19 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 61.862 0.046609 108480000 196660 178250 97550 116650 183480 139900 180900 239360 103600 FALSE TRUE 170670.8827 177079.064 144725.5063 143137.1654 179829.107 145282.0435 163356.3458 188174.7267 91352.52602 1.868266704 1.938414532 1.584252922 1.566865982 1.968518166 1.590345115 1.78819736 2.059874367 1 16.479157 1.226675486 24.99508169 0.999998205 1.797334671 0.68011914 0.171468755 341.8029726 718784.5343 0.699987961 0.04326757 16.8529327 -1.226675486 0.797336466 LPPQSSGVDTSPCPNS(ph)PVFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPPQSSGVDTSPCPNSPVFR 20 0 O75815;O75815-3;O75815-2 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 LPPQSSGVDT(0.446)S(0.078)PCPNS(0.477)PVFR 145.77 1.48E-07 133490000 21540 23411 18948 24434 31967 27985 29212 38389 32969 TRUE FALSE 18693.43442 23257.2116 28111.31618 29982.11315 31330.91924 29061.60106 26379.02474 30179.81109 29071.44238 0.643017095 0.800001985 0.966973562 1.03132527 1.077721526 0.999661478 0.907386169 1.038125687 1 14.82731503 4.437797341 1.977930905 1.008750598 0.626768029 0.889286862 0.043480202 0.137430139 0.879689717 0.012414494 0.076749938 27402.95145 -4.437797341 -0.381982569 LPPS(ph)SPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPPSSPQK 8 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 LPPS(0.584)S(0.416)PQK 85.533 0.017491 209320000 467440 278180 238700 273310 321750 267760 424910 483910 389670 TRUE FALSE 405666.6197 276352.6173 354136.1184 335369.2128 315347.8045 278060.9005 383702.2936 380429.6123 343603.6565 1.180623698 0.804277289 1.030652939 0.976035052 0.917766149 0.809248956 1.116700263 1.107175681 1 18.39038586 2.200809135 24.99843509 1.083159863 0.949297197 0.208298563 0.111106296 223.9819765 148315.8006 0.042537225 0.028679328 158.7848763 -2.200809135 -0.133862666 LPPVLSHPIFDNR ddPTM_MDA-MB-175_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 ; 182.07 1.15E-05 671480000 1036670 895790 767150 828550 885490 965720 894790 1050440 1060270 FALSE TRUE 899671.4329 889905.4965 1138146.306 1016684.941 867870.4814 1002871.873 808013.4035 825811.5805 934926.0885 0.962291505 0.951845828 1.217365009 1.087449536 0.928277104 1.072675034 0.864253777 0.883290766 1 19.83449279 2.240778134 24.99933178 0.906915612 1.038393167 0.28644741 0.089481865 70.62609118 796222.4307 0.035582617 0.026197234 174.0917271 -2.240778134 0.131477555 LPQT(ph)SDDEKKDF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPQTSDDEKKDF 12 2 Q9GZT3-2;Q9GZT3 Q9GZT3-2 SLIRP "SRA stem-loop-interacting RNA-binding protein, mitochondrial" 1 LPQT(0.5)S(0.5)DDEKKDF;LPQT(0.869)S(0.131)DDEKKDF 120.7 0.00062591 789660000 772810 642040 698920 830290 788030 548300 837200 1034180 823920 TRUE FALSE 670681.2004 637822.397 1036920.05 1018820.035 772349.7448 569393.4558 756008.4729 813028.655 726517.1162 0.923145767 0.877917922 1.427247929 1.402334524 1.063085408 0.78373027 1.04059279 1.119077083 1 19.47063726 3.009188531 24.82329431 1.001977643 1.16640776 0.149363434 0.191177942 406.1714313 1097283.562 0.062976197 0.071310149 1021.382778 -3.009188531 0.164430117 LPQTLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPQTLSR 7 0 O95994;B5MC07;C9J3E2 O95994 AGR2 Anterior gradient protein 2 homolog 0 101.41 0.02112 185700000 122420 108060 80706 87912 114750 127560 106880 129030 121770 FALSE TRUE 106241.8868 107350.1467 119735.6915 107873.7633 112466.6995 132467.3157 96514.79405 101437.9386 107374.4893 0.989451847 0.999773293 1.115122338 1.004649838 1.047424767 1.233694489 0.898861496 0.944711721 1 16.71229174 LPQTS(ph)DDEKKDF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPQTSDDEKKDF 12 2 Q9GZT3-2;Q9GZT3 Q9GZT3-2 SLIRP "SRA stem-loop-interacting RNA-binding protein, mitochondrial" 1 LPQT(0.136)S(0.864)DDEKKDF 122.31 0.00028418 526150000 482190 356480 432190 488190 450940 324730 480570 649000 479750 TRUE FALSE 418467.3698 354138.2594 641198.5296 599041.001 441967.1762 337222.5732 433964.3954 510216.4005 423034.5015 0.989203879 0.837138007 1.51571214 1.41605708 1.044754446 0.797151466 1.025836885 1.206086971 1 18.6904158 3.036708223 24.99862261 1.026838839 1.192999784 0.141898152 0.212831625 401.9737115 273745.1565 0.070056315 0.079436185 1088.198751 -3.036708223 0.166160945 LPS(ph)AESLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LPSAESLSR 9 0 O43281-3;O43281-2;O43281 O43281-3 EFS Embryonal Fyn-associated substrate 1 LPS(1)AESLSR;LPS(0.999)AES(0.001)LSR;LPS(1)AESLSR;LPS(1)AESLSR 157.14 7.26E-05 768250000 2093650 1979200 1654160 1074100 1312110 1801500 1426640 1272600 1594080 TRUE FALSE 1816968.848 1966198.505 2454117.309 1317990.822 1286001.578 1870804.871 1288284.672 1000464.393 1405629.678 1.292636941 1.39880264 1.745920242 0.937651532 0.914893587 1.33093723 0.916517837 0.711755314 1 20.42278513 3.719159176 24.7303415 0.951469222 1.471088199 0.619321243 0.18831623 460.9668398 587578.3651 0.055125537 0.081904797 5237.923801 -3.719159176 0.519618977 LPS(ph)GSGAAS(ph)PTGSAVDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 LPS(0.999)GS(0.001)GAAS(0.918)PT(0.078)GS(0.003)AVDIR;LPS(0.999)GS(0.001)GAAS(0.994)PT(0.006)GSAVDIR 287.91 5.45E-40 519400000 384970 251197 128889 294307 290912 278069 312066 358090 301480 TRUE FALSE 334095.2391 249546.8704 191220.1515 361133.9026 285123.4204 288766.4944 281801.8874 281515.2402 265839.3778 1.256756022 0.938712964 0.719307098 1.35846655 1.072540203 1.086244245 1.060045692 1.05896742 1 18.0201953 4.758546919 22.93840437 1.042403061 1.256756652 0.162571996 0.156436973 2904.638611 3333504.379 0.037722135 1.253585641 57351.7823 -4.758546919 0.214353591 LPS(ph)PTSPFSSLSQDQAATSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPSPTSPFSSLSQDQAATSK 20 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDG6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 LPS(0.935)PT(0.058)S(0.007)PFSSLSQDQAATSK;LPS(0.922)PT(0.064)S(0.014)PFSSLSQDQAATSK 114.99 0.00014506 105807000 166651 147441 120332 167019 163421 127243 174602 207642 411390 TRUE FALSE 144627.6481 146472.4504 178524.9577 204943.2167 160169.2418 132138.1205 157669.1249 163239.3742 362755.9429 0.398691327 0.403776846 0.49213517 0.564961707 0.441534439 0.364261766 0.434642431 0.449997794 1 18.46863972 1.238543385 8.455949769 1.005338191 0.444751756 0.910348826 0.05486076 0.025909274 19.9737801 0.083123703 0.014481886 17.31982044 -1.238543385 -0.560586434 LPS(ph)VEEAEVPKPLPPASKDEDEDIQSILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LPSVEEAEVPKPLPPASKDEDEDIQSILR 29 2 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 LPS(1)VEEAEVPKPLPPASKDEDEDIQSILR;LPS(1)VEEAEVPKPLPPASKDEDEDIQSILR;LPS(1)VEEAEVPKPLPPASKDEDEDIQSILR 197.58 2.16E-25 586040000 481686 443548 469496 531524 533449 357728 730470 897360 916090 TRUE FALSE 418029.9747 440634.304 696545.836 652214.648 522834.4086 371490.0276 659629.1318 705466.5473 807790.8838 0.517497762 0.545480659 0.862284844 0.807405309 0.647239798 0.459883907 0.816584026 0.873328186 1 19.62362234 1.810370008 2.388339912 0.957811226 0.654635734 0.474195619 0.128643737 0.272236914 2.937147768 0.110168925 0.038630954 64.62045445 -1.810370008 -0.303175492 LPSANQGS(ph)PFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPSANQGSPFK 11 0 E5RFP7;E5RIE3;E5RFE4;Q56NI9 E5RFP7 ESCO2 N-acetyltransferase ESCO2 1 LPSANQGS(1)PFK;LPSANQGS(1)PFK 177.41 8.39E-06 385500000 778970 678120 565000 706500 715720 564430 725920 881910 1033530 TRUE FALSE 676027.1408 673665.3851 838235.8898 866921.6232 701478.5723 586143.9873 655520.3901 693320.4095 911347.2608 0.741788745 0.739197246 0.919776605 0.951252789 0.769716004 0.643162066 0.719287168 0.760764244 1 19.79764136 1.235413912 24.97104696 1.000000305 0.780563005 0.363614621 0.091210014 111.7735453 886835.0322 0.170231813 0.024614296 17.19546451 -1.235413912 -0.2194373 LPSEGPRPAHVVVGDVLQAADVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPSEGPRPAHVVVGDVLQAADVDK 24 1 P30043;M0R192;A0A2R8YEP4;A0A2R8Y7Y9;M0QZL1 P30043 BLVRB Flavin reductase (NADPH) 0 ; 118.22 0.00033893 1269160000 1463630 1326310 1082490 1321850 1107420 995490 1169930 1481330 2730100 FALSE TRUE 1270207.587 1317597.382 1605985.785 1621996.246 1085384.509 1033787.144 1056470.369 1164559.107 2407350.688 0.527637121 0.547322577 0.667117505 0.673768161 0.450862649 0.429429393 0.438851877 0.483751334 1 21.19901489 1.235514229 24.99998711 1.000000647 0.525269573 0.748881075 0.086009144 48.66784439 399317.5678 0.163139151 0.023736142 17.19943691 -1.235514229 -0.474731074 LPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTR 39 2 P30043;M0R192;A0A2R8YEP4;A0A2R8Y7Y9;M0QZL1 P30043 BLVRB Flavin reductase (NADPH) 0 ; 296.05 8.87E-93 1408980000 1327040 1159050 773377 757110 1105090 900200 1122350 1492600 629073 FALSE TRUE 1151668.302 1151436.124 1147384.704 929023.3972 1083100.871 934831.2765 1013504.67 1173419.105 554704.7066 2.076182675 2.075764115 2.068460372 1.674807129 1.952571987 1.685277347 1.827106671 2.115394175 1 19.08136044 1.231593206 24.99428905 0.999998394 1.931166439 0.769710095 0.160622437 121.6514668 436362.4484 0.395726885 0.040694853 17.04485087 -1.231593206 0.931168045 LPSFELLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPSFELLHK 9 0 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 141.48 0.00010661 146650000 370850 359800 195920 229330 254880 239170 243240 287320 494320 FALSE TRUE 321841.2329 357436.4501 290667.5673 281402.8816 249808.3867 248371.0247 219650.6222 225878.8539 435882.0527 0.738367709 0.820030207 0.666849129 0.6455941 0.573110054 0.56981246 0.503922152 0.518210953 1 18.73357828 4.013135042 2.628174424 0.609195966 0.779505718 0.126257306 0.141668815 0.461431228 6.385772009 0.038371333 0.09082128 10307.06564 -4.013135042 0.170309752 LPSGSGAAS(ph)PTGSAVDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LPSGSGAAS(1)PTGSAVDIR;LPSGSGAAS(0.8)PT(0.188)GS(0.012)AVDIR;LPSGSGAAS(0.971)PT(0.029)GSAVDIR;LPSGSGAAS(1)PTGSAVDIR;LPSGSGAAS(0.998)PT(0.002)GSAVDIR;LPSGSGAAS(0.974)PT(0.026)GSAVDIR;LPSGSGAAS(0.997)PT(0.003)GSAVDIR;LPSGSGAAS(0.968)PT(0.031)GS(0.001)AVDIR;LPSGSGAAS(0.958)PT(0.04)GS(0.002)AVDIR 378.48 4.62E-108 11845640000 2972978 1691211 1137808 1819520 1927832 2168876 1466799 2167031 1980061 TRUE FALSE 2580091.425 1680101.324 1688055.755 2232669.826 1889471.915 2252314.063 1324549.059 1703628.285 1745980.444 1.477732144 0.962268122 0.966823976 1.278748472 1.082183893 1.289999593 0.75862766 0.97574305 1 20.73560597 2.24254422 24.99999675 0.918481968 1.157422405 0.355246853 0.166815406 116.9452821 733922.6739 0.061503579 0.045842865 174.8011237 -2.24254422 0.238940438 LPSLS(ph)GSDGIPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPSLSGSDGIPYR 13 0 P21709 P21709 EPHA1 Ephrin type-A receptor 1 1 LPSLS(0.648)GS(0.352)DGIPYR 125.61 0.00020785 92050000 73261 80404 50381 96955 106030 123230 79693 138330 113420 TRUE FALSE 63579.37323 79875.82083 74745.42011 118970.1146 103920.2104 127970.7378 71964.38513 108749.206 100011.6168 0.635719882 0.798665429 0.747367381 1.189562957 1.039081396 1.279558735 0.719560261 1.087365743 1 16.60980806 3.76148542 21.36620796 1.04424086 0.734391795 0.513689193 0.148992825 105.2627748 98104.1639 0.038126412 0.065916794 5774.114875 -3.76148542 -0.309849065 LPSLSGS(ph)DGIPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LPSLSGSDGIPYR 13 0 P21709 P21709 EPHA1 Ephrin type-A receptor 1 1 LPS(0.002)LS(0.137)GS(0.861)DGIPYR;LPSLS(0.023)GS(0.977)DGIPYR;LPSLS(0.023)GS(0.977)DGIPYR;LPSLS(0.116)GS(0.883)DGIPYR 214.61 3.20E-11 628152000 450060 512008 377313 705928 726778 801100 490456 855590 740190 TRUE FALSE 390583.4307 508644.5857 559782.8288 866219.7418 712316.5397 831918.8354 442891.6526 672628.7367 652685.5814 0.598425094 0.779310284 0.857660786 1.327162368 1.091362457 1.274608876 0.678568158 1.030555532 1 19.31602864 4.182078056 2.573971621 1.049342934 0.655605212 0.432803155 0.179399532 0.280736915 3.686730723 0.049083505 0.144925783 15208.20844 -4.182078056 -0.393737722 LPSPT(ph)SPFSSLSQDQAATSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPSPTSPFSSLSQDQAATSK 20 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDG6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 LPS(0.343)PT(0.516)S(0.141)PFSSLSQDQAATSK 195.48 2.07E-20 170390000 120820 102660 80759 115010 96920 75408 102470 136120 302890 TRUE FALSE 104853.3309 101985.6197 119814.3225 141124.7783 94991.48162 78308.99456 92532.47517 107011.7973 267082.6893 0.392587521 0.381850355 0.448603849 0.52839358 0.355663191 0.293201311 0.346456281 0.400669162 1 18.02692695 1.238778278 8.084541919 1.007127126 0.39233987 0.903177318 0.062420272 0.0285164 17.1614947 0.096322591 0.016732503 17.32919059 -1.238778278 -0.614787256 LPSPTS(ph)PFSSLSQDQAATSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPSPTSPFSSLSQDQAATSK 20 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDG6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 LPS(0.208)PT(0.314)S(0.477)PFSSLSQDQAATSK 212.47 1.78E-22 157270000 79858 74345 65914 84723 63470 60588 78967 94426 196110 TRUE FALSE 69304.56297 73856.6228 97790.23087 103960.6521 62207.07118 62918.85957 71308.79249 74233.73472 172926.0992 0.40077561 0.42709934 0.565503017 0.601185434 0.359732114 0.363848256 0.412365703 0.429280109 1 17.3997961 1.237537482 24.9988042 1.000000655 0.445600144 0.829300191 0.079136015 10.95660313 267574.0106 0.124000058 0.020873954 17.27975109 -1.237537482 -0.554400512 LPSQDCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LPSQDCK 7 0 P21709 P21709 EPHA1 Ephrin type-A receptor 1 0 ;; 77.674 0.037406 186410000 491550 665930 330918 378960 322589 573410 606110 485530 537640 FALSE TRUE 426590.4221 661555.462 490951.0517 465008.66 316170.11 595469.4537 547329.5455 381703.1879 474080.8117 0.899826383 1.39544872 1.035585157 0.980863702 0.666911848 1.256050528 1.154506852 0.805143719 1 18.85477348 4.012333152 24.96910234 0.972094622 1.164607432 0.106998439 0.199768371 429.0309095 868581.5049 0.049794812 0.103546892 10288.05203 -4.012333152 0.19251281 LPSS(ph)PASPSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.031)S(0.969)PASPSPK;LPS(0.002)S(0.998)PASPSPK;LPS(0.064)S(0.936)PASPSPK 164.9 2.33E-05 365157000 1343370 1164910 934000 1446920 1283280 1085190 1140920 1583130 2649260 TRUE FALSE 1165840.251 1157257.63 1385685.524 1775465.301 1257745.239 1126937.962 1030273.754 1244589.969 2336067.501 0.499061029 0.495387068 0.593170156 0.760023116 0.538402781 0.482408133 0.441029103 0.532771407 1 21.15565053 1.237829261 24.99866849 1.000000529 0.542401547 0.73206555 0.086928886 10.28089218 351169.3669 0.134052507 0.023007498 17.29136433 -1.237829261 -0.457598982 LPSS(ph)PLGCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPSSPLGCR 9 0 C9JWC4;Q8NCD3-3;Q8NCD3-2;Q8NCD3 C9JWC4 HJURP Holliday junction recognition protein 1 LPS(0.09)S(0.91)PLGCR 109.83 0.0025024 331630000 454520 434210 274770 317910 398980 432250 399890 462550 439360 TRUE FALSE 394454.0304 431357.6459 407649.6911 390096.3245 391041.0786 448878.9372 361108.7293 363637.2821 387419.3613 1.018157763 1.113412723 1.052218169 1.00690973 1.009348313 1.15863837 0.932087462 0.938614118 1 18.56353653 2.202666354 24.99998943 0.952056891 1.057179391 0.481274429 0.050217672 142.3693552 99157.85845 0.020041952 0.013512842 159.4653586 -2.202666354 0.1051225 QASES(ph)SSRPH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QASESSSRPH 10 1 A0A2R8Y653;Q9BZX2;Q9BZX2-2 A0A2R8Y653 UCK2 Uridine-cytidine kinase 2 1 QAS(0.477)ES(0.479)S(0.022)S(0.022)RPH 121.71 0.0013358 200560000 153600 184620 140500 212240 264950 408650 326860 367940 383000 TRUE FALSE 133301.3708 183407.2191 208446.2699 260432.3359 259678.0134 424371.0299 295161.1675 289258.8943 337722.1763 0.394707189 0.543071293 0.617212267 0.771143722 0.768910162 1.256568445 0.873976269 0.856499557 1 18.36547739 3.756901454 1.073131518 0.959481479 0.422981042 0.734112734 0.124071301 0.327453695 0.712693156 0.047577895 0.137972448 5713.489767 -3.756901454 -0.536500437 down LPSSPVYEDAAS(ph)FK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LPSSPVYEDAASFK 14 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 LPSSPVYEDAAS(1)FK;LPSSPVYEDAAS(1)FK 185.27 1.26E-06 324950000 134094 158349 286470 285180 308140 332400 295980 324820 1067180 TRUE FALSE 116373.1381 157308.795 425007.8502 349934.4777 302008.6169 345187.6431 267275.9052 255359.7708 941019.1961 0.123667125 0.167168529 0.451646313 0.371867523 0.320937785 0.366823168 0.284028111 0.271365103 1 19.84386463 1.237164298 24.99970217 1.000000851 0.29950134 0.842167239 0.095938325 14.14812688 253213.8435 0.14871937 0.024420738 17.26490917 -1.237164298 -0.700499511 LPSTSDDCPAIGT(ph)PLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 285.19 9.15E-35 523909000 459401 399704 337789 361857 373627 423903 331305 428546 796039 TRUE FALSE 398689.9939 397078.3181 501144.8902 444022.1625 366192.5537 440210.8227 299175.0921 336904.7728 701932.1763 0.567989341 0.565693284 0.713950588 0.632571319 0.521692218 0.627141535 0.426216524 0.479967701 1 19.42097211 1.231846697 24.99816288 1.000000741 0.563312269 0.738297892 0.081010481 132.2763559 492463.2153 0.207147568 0.021842567 17.0548026 -1.231846697 -0.436688473 LPTGYYFGASAGTGDLSDNHDIISMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPTGYYFGASAGTGDLSDNHDIISMK 26 0 Q12907;D6RBV2;D6RDX1 Q12907 LMAN2 Vesicular integral-membrane protein VIP36 0 141.45 1.09E-12 0 45400 49571 13637 25352 45268 47395 44737 47299 50064 FALSE TRUE 39400.27497 49245.36484 20231.89881 31108.55908 44367.25537 49218.31632 40398.41263 37184.47693 44145.49095 0.892509611 1.115524231 0.45830046 0.704682594 1.00502349 1.114911518 0.915119795 0.842316534 1 15.42997847 3.229403108 24.91318887 0.961274841 0.791919665 0.208952108 0.175451658 345.02661 938649.9164 0.05587803 0.064240191 1695.9112 -3.229403108 -0.169355175 LPVGSQCSVDLES(ph)ASGEKDLAPPSEPSESFQEHTVDGENQIVFTHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPVGSQCSVDLESASGEKDLAPPSEPSESFQEHTVDGENQIVFTHR 46 1 F5H7V9;E9PC84;J3QSU6;P24821-6;P24821-5;P24821-2;P24821-3;P24821-4;P24821 F5H7V9 TNC Tenascin 1 LPVGS(0.001)QCS(0.003)VDLES(0.497)AS(0.497)GEKDLAPPSEPSESFQEHTVDGENQIVFTHR 53.656 0.0077018 176960000 46276 52403 30845 31808 55701 42613 56681 74481 47237 TRUE FALSE 40160.50935 52058.76124 45761.74517 39030.49255 54592.65908 44252.34968 51184.08534 58553.81776 41652.69567 0.964175516 1.249829342 1.098650266 0.937046016 1.310663288 1.062412623 1.22883008 1.405762984 1 15.34612225 2.692410452 1.286159713 1.24226708 1.091353369 0.074473293 0.15011933 0.87130045 3.011303827 0.079828551 0.062118169 492.5047824 -2.692410452 -0.150913712 LPVGSQCSVDLESAS(ph)GEKDLAPPSEPSESFQEHTVDGENQIVFTHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPVGSQCSVDLESASGEKDLAPPSEPSESFQEHTVDGENQIVFTHR 46 1 F5H7V9;E9PC84;J3QSU6;P24821-6;P24821-5;P24821-2;P24821-3;P24821-4;P24821 F5H7V9 TNC Tenascin 1 LPVGS(0.005)QCS(0.005)VDLES(0.465)AS(0.524)GEKDLAPPSEPSESFQEHTVDGENQIVFTHR 48.065 0.011395 187860000 54439 65209 36534 39699 60267 57762 80004 92925 54836 TRUE FALSE 47244.74822 64780.63779 54201.9646 48713.26471 59067.80461 59984.14152 72245.22439 73053.71189 48353.35055 0.977072895 1.339734208 1.120955714 1.007443417 1.22158659 1.240537436 1.494109996 1.510830399 1 15.56132824 2.624783292 2.56351823 1.375388407 1.132755346 0.208019057 0.172046868 0.370096519 4.768503802 0.066004694 0.056331324 421.4861345 -2.624783292 -0.24263306 LPVWVVEDHQEVLPFIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LPVWVVEDHQEVLPFIYR 18 0 Q49AR2;E5RFG1;B4DR92;E5RHP8 Q49AR2 C5orf22 UPF0489 protein C5orf22 0 152.68 3.88E-08 97244000 43210 38945 37789 44132 39895 41736 50561 58535 33617 FALSE TRUE 37499.68902 38689.16773 56063.8868 54152.84512 39101.16755 43341.61093 45657.602 46017.74577 29642.83656 1.265050629 1.305177649 1.891313157 1.826844236 1.319076448 1.462127649 1.540257523 1.55240696 1 14.85539589 3.170596931 25 1.413757016 1.575868949 0.125392124 0.247229606 139.6616468 51371.61025 0.078599763 0.089123783 1481.142797 -3.170596931 0.162111933 LPYDVTPEQALAHEEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LPYDVTPEQALAHEEVK 17 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;; 237.59 3.19E-20 1837560000 1628840 1508100 1297600 1594400 1433560 1159990 1597870 1971640 3044830 FALSE TRUE 1413584.667 1498193.192 1925123.7 1956432.889 1405034.961 1204615.566 1442908.813 1550020.129 2684873.666 0.526499509 0.558012547 0.717025804 0.728687131 0.523315111 0.448667504 0.537421493 0.577315852 1 21.35642277 1.238497154 24.83834233 1.000000367 0.578082758 0.705186096 0.085927762 0.863002916 334843.0626 0.128282223 0.022969647 17.31797682 -1.238497154 -0.421917609 LQAALDDEEAGGRPAMEPGNGS(ph)LDLGGDSAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LQAALDDEEAGGRPAMEPGNGSLDLGGDSAGR 32 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR 257.95 1.89E-59 5518437000 3123152 2444868 1426853 1946872 2344203 2164071 2301583 2510841 2514713 TRUE FALSE 2710419.55 2428807.501 2116883.883 2388939.044 2297557.947 2247324.212 2078375.835 1973917.192 2217426.494 1.222326674 1.095327177 0.954657974 1.077347569 1.03613714 1.013483071 0.937291874 0.890183822 1 21.08045485 8 0.380906893 0.941235144 4.729238163 0.670700559 0.053532138 52.04606077 0.757826963 0.062485913 144.3718053 100000000 -8 3.788003019 LQAALDDEEAGGRPAMEPGNGSLDLGGDSAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 LQAALDDEEAGGRPAMEPGNGSLDLGGDSAGR 32 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;;;;;; 311.26 4.58E-104 6707220000 2243520 2015219 1317258 1553534 2043567 1968403 1877664 2262172 1975079 FALSE TRUE 1947033.148 2001980.894 1954288.375 1906287.639 2002904.015 2044128.737 1695568.434 1778424.122 1741587.411 1.117964643 1.149515024 1.122130513 1.094569028 1.15004507 1.173715844 0.973576419 1.021151227 1 20.73197145 2.235474144 24.99999991 1.001987419 1.133640004 0.877055548 0.024060912 25.78858577 208879.8638 0.009655986 0.006823314 171.978495 -2.235474144 0.131652586 LQAEAPHIVVGTPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LQAEAPHIVVGTPGR 15 0 Q14240;Q14240-2;E7EQG2 Q14240 EIF4A2 "Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ;; 190.11 2.30E-07 976700000 1767680 1517450 962650 1191830 1525630 1741440 1532740 1578470 1689790 FALSE TRUE 1534076.609 1507481.771 1428190.76 1462453.217 1495272.948 1808434.324 1384095.111 1240926.474 1490024.951 1.029564376 1.01171579 0.958501238 0.981495791 1.003522086 1.213693987 0.928907338 0.832822614 1 20.50690506 2.020054257 24.9987497 0.897388444 1.028888178 0.301419636 0.079575409 244.649821 304968.4179 0.032560431 0.021949578 104.7259376 -2.020054257 0.131499733 LQAEEAERR ddPTM_MDA-MB-175_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 ; 127.51 0.00071077 452470000 1534210 1340900 807940 947840 1100230 1080520 1510670 1693060 878500 FALSE TRUE 1331460.261 1332091.54 1198662.486 1163061.559 1078337.576 1122088.304 1364165.456 1331012.294 774644.7308 1.718801159 1.719616085 1.547370606 1.501412858 1.392041452 1.448519894 1.761020764 1.718222872 1 19.56317528 4.191891383 3.866878546 1.51096357 1.723817452 0.177502513 0.206794844 0.423967749 13.00080564 0.054839416 0.135466106 15555.76535 -4.191891383 0.212853882 LQAFGFCEYKEPESTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQAFGFCEYKEPESTLR 17 1 P49756;P49756-2;P49756-3;E9PQU5 P49756 RBM25 RNA-binding protein 25 0 85.636 0.0045488 430780000 114260 103280 60209 73780 86456 85901 104460 102310 79331 FALSE TRUE 99160.2515 102601.5469 89326.27379 90532.87666 84735.69475 89205.66706 94329.48528 80431.80268 69952.57955 1.417535309 1.466729998 1.276954679 1.294203548 1.211330523 1.275230558 1.348477581 1.14980467 1 16.09408964 -0.2198478 0.41530703 2.60E-41 1.377046477 0.690819175 0.073689489 13.45039707 0.74564019 11.73466412 0.080077055 0.602770793 0.2198478 1.377046477 LQAKES(ph)PQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LQAKESPQR 9 1 Q15061 Q15061 WDR43 WD repeat-containing protein 43 1 LQAKES(1)PQR;LQAKES(1)PQR;LQAKES(1)PQR;LQAKES(1)PQR;LQAKES(1)PQR;LQAKES(1)PQR 108.01 0.0016237 3523970000 6245550 5491710 2725260 3159510 4955790 4273080 5701720 6733380 1574080 TRUE FALSE 5420184.743 5455634.595 4043204.851 3876925.036 4857179.475 4437468.153 5148768.072 5293499.086 1387994.056 3.90504896 3.930589309 2.91298427 2.793185619 3.499423831 3.197036857 3.70950297 3.813776482 1 20.40456996 4.247374614 24.51968205 3.120216857 3.917819761 0.178393402 0.790465622 284.3535362 791021.0555 0.193159301 0.49426954 17675.61828 -4.247374614 0.797602904 LQALDTGWNELHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQALDTGWNELHK 13 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 137.93 5.49E-05 798010000 815380 704040 477080 663950 636250 601390 621790 775540 1353960 FALSE TRUE 707625.4671 699415.1149 707797.4837 814709.9953 623589.8698 624525.8625 561488.9015 609696.8063 1193896.391 0.592702576 0.585825638 0.592846656 0.682395894 0.522314896 0.523098878 0.470299521 0.510678155 1 20.18724621 1.234929524 24.99996044 1.000000627 0.556826081 0.846706795 0.058820268 43.50235902 299466.2089 0.115824361 0.016065569 17.17629634 -1.234929524 -0.443174545 LQAMHLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQAMHLER 8 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 87.913 0.014987 84665000 99945 99830 64159 78420 95007 93899 93499 109700 131160 FALSE TRUE 86737.01502 99174.21016 95186.507 96226.45957 93116.54658 97511.35529 84431.48137 86241.50869 115654.4142 0.749967181 0.857504755 0.823025283 0.83201718 0.805127476 0.843126965 0.730032502 0.745682811 1 16.81946081 1.229367258 24.99764498 1.000000393 0.797932096 0.679229184 0.043558009 237.7333337 646372.065 0.139922479 0.011501767 16.9577121 -1.229367258 -0.202068297 LQASLS(ph)SSDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LQASLSSSDVR 11 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 LQASLS(0.468)S(0.468)S(0.064)DVR;LQASLS(0.497)S(0.497)S(0.005)DVR;LQAS(0.005)LS(0.472)S(0.472)S(0.051)DVR;LQASLS(0.498)S(0.498)S(0.004)DVR 191.84 1.74E-06 1447570000 2114190 1821670 1368860 1452280 1814590 2180070 1711600 1865730 2895410 TRUE FALSE 1834794.435 1809703.33 2030845.275 1782042.371 1778483.209 2263938.704 1545609.295 1466758.159 2553117.928 0.718648526 0.708820893 0.795437317 0.697986705 0.69659266 0.886734874 0.605381083 0.574496831 1 21.28382875 1.221660842 24.89321081 1.000000913 0.706490196 0.520996119 0.087157964 878.973476 1294644.562 0.640035797 0.022892542 16.65945702 -1.221660842 -0.293510717 LQASLS(ph)SSDVRFPQSPHSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQASLSSSDVRFPQSPHSGR 20 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 LQASLS(0.947)S(0.052)S(0.001)DVRFPQSPHSGR;LQASLS(0.745)S(0.247)S(0.008)DVRFPQSPHSGR 153.82 2.93E-08 203694000 100986 104584 49866 44427 98818 109888 89648 102769 29021 TRUE FALSE 87640.44423 103896.9808 73981.36439 54514.82937 96851.71513 114115.4625 80953.95076 80792.6491 25590.17044 3.424769852 4.060034733 2.891007098 2.130303489 3.784723332 4.459347496 3.163478373 3.157175107 1 14.64330214 4.229555987 24.98226451 3.027522599 3.742402331 0.10830896 0.930653123 435.6020831 1208536.796 0.243044865 0.51784272 16965.08294 -4.229555987 0.714879732 LQASVR ddPTM_MDA-MB-175_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 ; 105.39 0.076811 810300000 832150 928280 724570 722150 874590 1106830 920010 916070 1029030 FALSE TRUE 722179.2691 922182.0676 1074974.476 886125.1949 857187.3701 1149410.466 830787.5718 720175.5594 907379.2457 0.795895732 1.01631382 1.184702516 0.976576442 0.944684788 1.266736562 0.91559023 0.793687494 1 19.79134614 2.018409198 24.96369135 0.873866549 1.035805588 0.15888625 0.136457359 330.1005429 447629.284 0.054462501 0.036711944 104.3299977 -2.018409198 0.161939039 LQAVEVVITHLAPGTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQAVEVVITHLAPGTK 16 0 Q9Y2V2 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 0 124.92 7.98E-05 94864000 197940 195750 125740 143070 164800 151890 187610 221390 229140 FALSE TRUE 171781.7275 194464.1054 186548.2846 175556.2302 161520.8024 157733.3066 169415.6111 174047.4714 202051.3302 0.85018855 0.962449023 0.923271747 0.86886946 0.799404796 0.78065958 0.838478078 0.861402254 1 17.62436232 LQAVTDDHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LQAVTDDHIR 10 0 P30043;A0A2R8YEP4 P30043 BLVRB Flavin reductase (NADPH) 0 ;;;;;;; 243.13 2.14E-12 27503470000 13004330 12894830 7917120 9021080 12050620 12206650 11112590 13120470 12262210 FALSE TRUE 11285774.84 12810123.01 11745865.71 11069454.09 11810836.24 12676247.72 10034892.73 10314759.59 10812585.5 1.04376283 1.184741893 1.08631425 1.023756445 1.092323037 1.172360461 0.928075226 0.953958662 1 23.36620821 2.227786792 24.99987899 0.957919635 1.099859656 0.616543716 0.051980078 135.8575219 315244.6713 0.021023901 0.014330114 168.9611248 -2.227786792 0.141940022 LQAYHTQTTPLIEYYR ddPTM_MDA-MB-175_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 ; 189.81 9.58E-10 1727210000 792860 708020 429120 559600 752420 761340 513980 680780 693350 FALSE TRUE 688081.5421 703368.97 636643.8673 686665.733 737448.3141 790629.2425 464134.2987 535200.4948 611382.9529 1.125450978 1.150455646 1.041317662 1.123135229 1.20619705 1.293181694 0.759154792 0.875393225 1 19.2217168 2.235081855 24.99999035 0.872642035 1.151832746 0.701833296 0.085490192 49.66250175 356891.0517 0.035184482 0.02479614 171.8232208 -2.235081855 0.279190712 LQCPQVDLFYLHAPDHGTPVEETLHACQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQCPQVDLFYLHAPDHGTPVEETLHACQR 29 0 O43488;H3BLU7;H7C5H7 O43488 AKR7A2 Aflatoxin B1 aldehyde reductase member 2 0 ; 254.85 2.23E-58 591080000 223749 206286 97899 148078 215133 206350 186815 258790 219695 FALSE TRUE 194180.0027 204930.8937 145243.2839 181701.3731 210852.2742 214288.418 168697.7101 203449.7724 193722.9074 1.002359532 1.057855761 0.749747595 0.937944694 1.088422 1.106159416 0.870819628 1.050210195 1 17.56363503 3.360991505 9.963763404 1.01914944 0.931408336 0.153946771 0.099849912 0.60269319 49.82946524 0.029133466 0.037612448 2296.103732 -3.360991505 -0.087741105 LQDAEIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 LQDAEIAR 8 0 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;;;;;;;; 221.16 1.31E-05 97247820000 35113180 35404510 24145150 26866750 31951540 34919140 29398830 35307440 38547560 FALSE TRUE 30472884.3 35171935.44 35821825.3 32967256.22 31315766.87 36262501.91 26547735.99 27757218.72 33990511.37 0.896511499 1.034757467 1.05387721 0.969895859 0.921309083 1.066841905 0.781033733 0.816616685 1 25.01862873 2.23744892 24.99999138 0.852084154 0.991337213 0.360778418 0.077487175 28.24748961 635202.6765 0.029957945 0.021486164 172.7622773 -2.23744892 0.139253058 LQDLIEEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LQDLIEEIR 9 0 O75843;G3V2V9;G3V3Z2;G3V532 O75843 AP1G2 AP-1 complex subunit gamma-like 2 0 ;;; 119.68 0.0018329 186661000 359324 389881 244173 276776 388855 404348 388372 412445 397091 FALSE TRUE 311838.423 387319.846 362255.8795 339622.2211 381117.5463 419903.5292 350707.7432 324246.8464 350147.3543 0.890591973 1.106162423 1.034581227 0.969940846 1.088449025 1.199219483 1.001600437 0.926029691 1 18.41760266 2.003416894 24.99647207 0.959556375 1.052782844 0.154406562 0.082882008 155.6474325 1138640.023 0.033736602 0.022618277 100.789872 -2.003416894 0.093226469 LQDSSDPDTGSEEEGSSRLS(ph)PPHS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQDSSDPDTGSEEEGSSRLSPPHSPR 26 1 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GYF0 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 2 LQDSSDPDTGSEEEGS(0.1)S(0.117)RLS(0.784)PPHS(0.998)PR 123.73 7.13E-05 457500000 196680 212810 142760 179030 236780 236280 262570 265290 240450 TRUE FALSE 170688.2397 211412.0371 211799.2135 219681.4978 232068.5413 245369.8445 237106.0018 208559.798 212024.2749 0.805041025 0.997112416 0.998938511 1.036114841 1.094537601 1.157272414 1.118296487 0.983659999 1 17.69386992 5.511963186 0.973149093 1.063717602 8.12E-15 0.691774045 0.053380673 5.021965273 1.273556031 0.019187464 8.031402358 325059.7417 -5.511963186 -1.063717602 LQEAGILSAEELQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQEAGILSAEELQR 14 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 96.734 0.0075703 66676000 58389 56631 31870 35955 53805 52258 57593 54909 50303 FALSE TRUE 50672.74571 56258.98723 47282.4386 44119.13229 52734.38577 54268.39908 52007.63972 43167.13765 44356.23665 1.14240408 1.268344465 1.065970474 0.994654543 1.188883227 1.223467164 1.172498924 0.973192068 1 15.43684935 1.723966985 6.785147577 0.98829186 1.150383539 0.43960262 0.076916464 0.121402703 14.98129414 0.04809375 0.02113419 52.96231809 -1.723966985 0.16209168 LQEALEDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQEALEDER 9 0 Q9UH65;E7EMB1 Q9UH65 SWAP70 Switch-associated protein 70 0 ; 78.939 0.049285 0 761540 781510 452370 528730 724670 779410 711970 735310 799500 FALSE TRUE 660900.5595 776376.2094 671137.6451 648786.2276 710250.4848 809394.407 642923.259 578069.6787 704984.0208 0.93746885 1.101267811 0.951989868 0.920285011 1.007470331 1.148103195 0.911968555 0.819975576 1 19.42723103 2.024393848 24.92139418 0.887781775 1.010035028 0.238491271 0.082511672 246.1073183 251428.6103 0.033209331 0.022388588 105.7776339 -2.024393848 0.122253254 LQEALRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQEALRR 7 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 105.25 0.012778 98334000 201270 223020 121160 135560 214390 270250 172680 185260 149270 FALSE TRUE 174671.6595 221554.9669 179753.3813 166340.9699 210124.0584 280646.6924 155933.5202 145643.5907 131623.4706 1.327055568 1.683248176 1.365663588 1.263763743 1.596402658 2.132193377 1.18469388 1.106516869 1 17.00605724 2.023063782 24.97681239 1.086288023 1.555456195 0.452958409 0.243073052 204.9174602 221913.4655 0.101501258 0.068427935 105.454176 -2.023063782 0.469168173 LQEDGLLSNVSHVIVDEVHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LQEDGLLSNVSHVIVDEVHER 21 0 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 0 ;; 215.48 3.79E-25 114071000 117246 113908 65190 103214 114007 103994 105962 134603 174312 FALSE TRUE 101751.644 113159.7308 96716.10205 126650.3162 111738.4838 107994.7165 95685.82155 105819.1959 153705.0339 0.661992919 0.736213564 0.629231845 0.823982878 0.726966976 0.702610147 0.622528873 0.68845628 1 17.22980489 1.237367113 24.98983548 1.000000362 0.698794783 0.728611098 0.057732345 15.83607599 331435.1384 0.083962528 0.013986584 17.27297376 -1.237367113 -0.30120558 LQEDKEQMAQQLAEETQGFQR ddPTM_MDA-MB-175_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 ;;; 259.2 1.39E-36 1107570000 1351120 1084810 754150 920600 1113990 934850 1222180 1471480 1189060 FALSE TRUE 1172566.069 1077683.812 1118859.462 1129636.3 1091823.778 970814.2844 1103653.172 1156815.453 1048490.681 1.118337139 1.027843004 1.06711436 1.07739279 1.041329025 0.925915987 1.052611331 1.103314959 1 19.99988261 3.124604319 5.98686123 1.030946885 1.068822946 0.184143188 0.049363196 0.513755539 25.02919644 0.016214375 0.018494407 1332.30703 -3.124604319 0.037876061 LQEDPNYS(ph)PQRFPNAQR ddPTM_MDA-MB-175_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;LQEDPNY(0.138)S(0.862)PQRFPNAQR 222.51 2.02E-15 2589200000 2855140 2553650 1516780 1783770 2322430 2485720 2393930 2723250 1797630 TRUE FALSE 2477826.015 2536874.905 2250299.881 2188802.242 2276218.187 2581347.257 2161767.037 2140904.18 1585116.229 1.563182541 1.600434629 1.419643456 1.380846528 1.4359945 1.628490838 1.363790867 1.350629147 1 20.5961572 0.726770986 1.127046952 9.91E-12 1.49468155 0.761410273 0.08654476 2.376466317 1.089495392 5.633039225 0.028095266 5.330537288 -0.726770986 1.49468155 LQEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LQEEER 6 0 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 ;;;; 158.12 0.022155 3463710000 4903130 4978700 3144800 3813220 3718530 4614330 4579300 5079580 4963600 FALSE TRUE 4255168.948 4945994.592 4665635.799 4679069.882 3644538.528 4791846.261 4135200.191 3993351.346 4376808.863 0.972208082 1.130045827 1.065990301 1.06905968 0.832693097 1.094826485 0.944797984 0.912388791 1 22.06144795 LQEEERER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LQEEERER 8 1 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 ;; 116.3 0.0044767 279420000 1057870 1057810 478100 480630 878880 1006050 993570 1115870 319423 FALSE TRUE 918069.7992 1050861.176 709310.7591 589764.3875 861392.0075 1044753.395 897213.7343 877249.8842 281661.1768 3.259482935 3.7309408 2.518312134 2.093878873 3.058256083 3.709255945 3.185436291 3.114557335 1 18.1036012 4.239159953 24.99999126 2.766608148 3.495211962 0.165621591 0.746576334 30.72531558 1281359.584 0.191447545 0.448496818 17344.42683 -4.239159953 0.728603813 LQEEKS(ph)LNLAS(ph)DMVSRAETIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQEEKSLNLASDMVSRAETIQK 22 2 E9PHT3;Q8IYS0-2;Q8IYS0 E9PHT3 GRAMD1C GRAM domain-containing protein 1C 2 LQEEKS(0.661)LNLAS(0.661)DMVS(0.661)RAET(0.018)IQK 46.027 0.092558 404170000 163880 148190 53353 69960 130750 119410 146940 176760 20532 TRUE FALSE 142222.8428 147216.5301 79154.68926 85845.48727 128148.3308 124003.78 132689.7814 138961.2495 18104.73035 7.855562609 8.131384853 4.372044638 4.741605404 7.078168431 6.849247549 7.329011747 7.675411169 1 14.14407907 4.267894296 24.9196695 5.928126019 7.99347732 0.188666537 1.981588558 382.3611329 324818.6088 0.491833684 1.300830194 18530.80544 -4.267894296 2.065351301 LQEELDKYSQALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQEELDKYSQALR 13 1 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 65.038 0.054424 55010000 121060 111900 64833 89585 100580 93769 97871 119230 97574 FALSE TRUE 105061.6143 111164.9215 96186.45565 109926.6435 98578.65478 97376.35411 88379.48548 93733.59235 86038.91288 1.221094163 1.292030755 1.117941318 1.277638685 1.145745006 1.131771089 1.027203652 1.089432551 1 16.39270168 2.663905132 1.191054733 1.039807998 1.228025798 0.685639917 0.05413355 0.261311937 0.783955227 0.030319643 0.022141565 461.2168151 -2.663905132 0.1882178 LQEGYDHSYYFIATFITDHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LQEGYDHSYYFIATFITDHIR 21 0 P10768;X6RA14 P10768 ESD S-formylglutathione hydrolase 0 ;;; 308.19 1.07E-66 6044828000 1745474 1963543 1158336 1602258 1475576 1462046 2074017 2262199 1839039 FALSE TRUE 1514805.188 1950644.357 1718511.164 1966075.168 1446214.925 1518291.856 1872879.151 1778445.348 1621629.904 0.934125095 1.202891209 1.059743138 1.212406828 0.891827982 0.936275195 1.154936244 1.096702363 1 20.62901317 4.832853677 20.83219789 1.069961276 0.934084702 0.13919073 0.105672115 148205.4687 32712856.37 0.025741121 881.9090525 68054.0031 -4.832853677 -0.135876574 LQEKEDLQELNDR ddPTM_MDA-MB-175_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 ;;;;;;; 258.91 5.42E-24 33347410000 16779200 13834300 8820930 10482800 11940590 10387810 15142400 17253900 8814990 FALSE TRUE 14561786.21 13743421.57 13086761.25 12863079.96 11702995.62 10787435.77 13673892.38 13564287.76 7772891.924 1.873406494 1.768122046 1.683641221 1.654864121 1.505616666 1.387827835 1.759176959 1.745076078 1 22.89002003 7.999987276 0.040100644 4.85E-06 4.194180052 0.356179065 0.202508562 2575.886713 10.17325888 334.7264768 840.1981372 99997070.31 -7.999987276 4.194175205 LQEKEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LQEKEELR 8 1 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 0 ;;;;; 134.25 0.00080692 4106910000 11887720 9908720 4901840 6801890 9440540 8358250 10408320 13859500 3923970 FALSE TRUE 10316727.68 9843628.966 7272386.22 8346363.085 9252691.724 8679797.286 9398922.728 10895753.78 3460082.737 2.981641905 2.844911441 2.101795469 2.412185985 2.674124415 2.508551947 2.7163867 3.148986486 1 21.72237511 1.228367198 24.99965927 0.999996566 2.672043184 0.762695522 0.293374801 228.7753201 561039.1567 1.050735293 0.077935826 16.91870813 -1.228367198 1.672046618 LQELESCSGLGS(ph)TSDDTDVR ddPTM_MDA-MB-175_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 LQELESCSGLGS(0.937)T(0.063)SDDTDVR;LQELESCSGLGS(0.992)T(0.008)SDDTDVR;LQELESCSGLGS(0.981)T(0.019)SDDTDVR;LQELESCSGLGS(0.909)T(0.091)SDDTDVR 384.57 1.00E-130 1227530000 862350 1014570 745461 759270 1136440 1161170 1151590 1223730 1182850 TRUE FALSE 748388.2626 1007905.223 1105968.433 931673.8582 1113827.067 1205840.961 1039908.979 962044.8626 1043014.821 0.717524093 0.966338352 1.060357352 0.893250834 1.067891889 1.156111052 0.997022246 0.922369312 1 19.99232823 4.72640873 3.652188143 1.007914427 0.688936103 0.609418949 0.073842279 0.190582155 4.736937573 0.019409704 0.162788461 53260.92813 -4.72640873 -0.318978323 LQELNAHIVVSDPEDITDCPRT(ph)PDTPNNDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQELNAHIVVSDPEDITDCPRTPDTPNNDPR 31 1 Q16513-3;Q16513-2;Q16513;B1AL79 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 LQELNAHIVVSDPEDIT(0.006)DCPRT(0.994)PDTPNNDPR;LQELNAHIVVSDPEDIT(0.042)DCPRT(0.957)PDT(0.001)PNNDPR 165.55 2.06E-12 235544000 98930 122505 69874 73592 149712 146749 139327 175525 81336 TRUE FALSE 85856.14984 121700.2566 103665.3001 90302.18838 146733.0241 152394.529 125815.089 137990.3447 71720.55074 1.197092729 1.69686729 1.445405801 1.259083867 2.045899294 2.124837685 1.754240419 1.924000071 1 16.13009895 3.245500216 24.99984556 1.805656551 1.424115865 0.231980628 0.329805744 237.592844 855920.9843 0.09453612 0.119363352 1759.949539 -3.245500216 -0.381540686 LQELPDAVPHGEMPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQELPDAVPHGEMPR 15 0 P33992;B1AHB1;B1AHB2 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ; 130.29 6.06E-05 892120000 993270 971710 484810 666750 900340 889990 803020 1011150 829670 FALSE TRUE 862006.8529 965326.773 719265.7376 818145.7781 882424.9955 924228.4912 725143.244 794923.4413 731587.3578 1.178269203 1.319496247 0.983157691 1.118315905 1.206178573 1.263319385 0.9911916 1.086573507 1 19.48067062 2.227239032 24.9921141 1.037110397 1.174243616 0.377462299 0.091677553 257.5071859 568435.6083 0.037836374 0.025769448 168.7481546 -2.227239032 0.13713322 LQELSAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LQELSAEER 9 0 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 ;; 129.85 0.00087862 971900000 1099250 921260 603410 670050 875590 875440 910370 1011490 979130 FALSE TRUE 953981.3274 915208.1824 895221.0943 822195.0936 858167.4721 909118.7433 822082.4575 795190.7349 863378.3668 1.10494004 1.060031404 1.036881544 0.952299855 0.993964529 1.052978368 0.952169395 0.921022307 1 19.71963342 7.999999977 0.347447494 0.954437665 2.780663077 0.578420825 0.036861178 57.26450228 0.876774902 0.052940546 67.50465371 99999994.81 -7.999999977 1.826225412 LQEPTPSSGDPGEHDPASTHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQEPTPSSGDPGEHDPASTHK 21 0 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 ; 121.63 1.70E-05 273230000 216960 241340 94142 173675 270000 215120 267830 313710 283630 FALSE TRUE 188288.1863 239754.6216 139669.3861 213110.5632 264627.5282 223395.8056 241855.8878 246625.5578 250099.5845 0.752852855 0.958636625 0.55845509 0.852102828 1.058088636 0.893227416 0.967038343 0.986109426 1 17.93214314 3.463907053 11.34542175 0.974278856 0.764929394 0.50233438 0.10260375 0.333641453 280.3747829 0.027856423 0.036376983 2910.094235 -3.463907053 -0.209349462 LQEVFGHAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQEVFGHAIK 10 0 P54136;P54136-2;E5RH09;E5RJM9 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 112.15 0.0016593 702390000 1648670 1898090 873740 1338180 1443380 1306270 1548730 1712940 1090380 FALSE TRUE 1430794.082 1885621.322 1296283.586 1642034.222 1414659.562 1356523.052 1398534.403 1346641.111 961476.5186 1.488121711 1.961172515 1.348221783 1.70782561 1.471340729 1.410874864 1.454569483 1.400596983 1 19.8748921 0.336884702 0.503435824 1.52E-25 1.632036857 0.517831797 0.170466708 9.112231201 0.930342459 10.66629333 0.113704205 2.172124438 -0.336884702 1.632036857 LQEVPHEGPMCDLLWSDPDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 140.2 1.27E-07 1326170000 907473 901980 608312 738946 859733 846080 791468 900020 989970 FALSE TRUE 787548.1438 896054.834 902493.7179 906734.9834 842625.9953 878629.2451 714711.5552 707557.727 872936.8744 0.902182239 1.026482968 1.033859085 1.038717701 0.965277124 1.006520942 0.818743687 0.810548561 1 19.7355178 2.247317276 24.99133509 0.860301664 0.999248069 0.420792096 0.064845356 147.1263904 419896.6787 0.024152781 0.018417076 176.7328482 -2.247317276 0.138946405 LQFHDVAGDIFHQQCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LQFHDVAGDIFHQQCK 16 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;; 253.02 8.81E-27 22654891000 18304562 17357552 13986985 14524444 16954172 17340045 21394561 23488419 24301857 FALSE TRUE 15885567.75 17243529.1 20751137.73 17822441 16616817.15 18007127.75 19319719.77 18465603.38 21428919.15 0.741314466 0.804684967 0.968370714 0.831700417 0.775438884 0.840318993 0.901572293 0.861714175 1 24.35305575 -1.018199615 0.867262477 9.999998363 0.832579702 0.411637846 0.061860168 120.9135236 2.112566573 2091.505733 0.022545621 0.095895976 1.018199615 -9.16741866 LQFQVPEGLCASSPTLTSPMEY(ph)PSPVNSLHTPPLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQFQVPEGLCASSPTLTSPMEYPSPVNSLHTPPLHR 36 0 Q14289 Q14289 PTK2B Protein-tyrosine kinase 2-beta 1 LQFQVPEGLCASSPTLT(0.008)S(0.053)PMEY(0.318)PS(0.272)PVNS(0.2)LHT(0.148)PPLHR;LQFQVPEGLCASSPT(0.01)LT(0.052)S(0.052)PMEY(0.25)PS(0.225)PVNS(0.225)LHT(0.184)PPLHR 165.52 9.65E-18 521870000 498120 513000 210200 310350 537840 549350 467780 574480 395620 TRUE FALSE 432292.1799 509630.0692 311853.4231 380819.7109 527138.0363 570483.85 422414.7676 451631.9226 348850.2543 1.239191242 1.460884901 0.893946383 1.091642349 1.51107253 1.635325883 1.210877052 1.294629765 1 18.41224836 1.238295747 22.44934186 0.999999256 1.292620121 0.158685527 0.21143824 3.654436627 307374.4178 0.303450348 0.053751942 17.30994735 -1.238295747 0.292620865 LQGDANNLHGFEVDSR ddPTM_MDA-MB-175_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 ;;; 228.9 3.68E-15 3718400000 4143610 3440050 2244800 3126450 3669820 3809050 3522710 4100810 3893150 FALSE TRUE 3596021.44 3417452.085 3330392.788 3836358.257 3596797.762 3955586.618 3181078.126 3223883.694 3432906.242 1.047515192 0.995498229 0.970137998 1.117524915 1.047741333 1.152255943 0.92664288 0.939112072 1 21.71099902 2.203203882 24.99999226 0.950697138 1.051042096 0.41872941 0.055238647 174.3870898 123304.2392 0.023090741 0.015568428 159.6628518 -2.203203882 0.100344959 LQGEGLSVAGIVCHVGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQGEGLSVAGIVCHVGK 17 0 Q13268;C9JZP6;Q13268-2 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ; 178.88 9.47E-10 720170000 723980 532430 496270 769010 639440 628920 590680 737540 727570 FALSE TRUE 628304.2087 528932.4323 736267.8319 943625.4741 626716.395 653114.9594 533395.9445 579822.8105 641557.5035 0.979342 0.824450543 1.147625627 1.47083538 0.976867064 1.018014684 0.83140785 0.903773719 1 19.29121906 2.650165157 2.617142422 0.911033339 1.093989919 0.164746261 0.169804972 0.517871154 6.963910599 0.069508218 0.060408139 446.8534932 -2.650165157 0.182956581 LQGIDLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQGIDLDR 8 0 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494C1B7 Q92878-2 RAD50 DNA repair protein RAD50 0 74.464 0.095172 67985000 137800 129580 81614 87613 133210 145370 124110 148370 128030 FALSE TRUE 119589.3809 128728.7804 121082.8034 107506.8707 130559.3816 150962.478 112073.8313 116642.2301 112894.4393 1.059302669 1.140257937 1.072531156 0.952277822 1.156473095 1.337200299 0.992731192 1.033197303 1 16.7846149 LQGPPT(ph)PAGK ddPTM_MDA-MB-175_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 139.48 0.00045826 1985860000 4906370 4437920 2953380 3522200 4450030 3779830 4672210 5605400 5518220 TRUE FALSE 4257980.773 4408767.011 4381644.446 4321969.343 4361483.109 3925242.506 4219099.793 4406728.831 4865862.318 0.875072186 0.906060781 0.90048673 0.888222695 0.896343304 0.806690007 0.867081622 0.905641907 1 22.21426407 1.255539945 2.820642532 1.022603734 0.877962202 0.65621287 0.027849182 0.274995826 2.664824757 0.091070969 0.00773792 18.01108788 -1.255539945 -0.144641532 LQGQVS(ph)AK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQGQVSAK 8 0 O95235-2;O95235 O95235-2 KIF20A Kinesin-like protein KIF20A 1 LQGQVS(1)AK;LQGQVS(1)AK 87.066 0.016351 322830000 433980 373350 317780 308520 341510 347880 453930 525820 562340 TRUE FALSE 376628.4434 370897.4393 471459.4709 378574.1814 334714.6192 361263.1687 409907.9385 413377.4849 495860.8058 0.759544693 0.747987005 0.95078995 0.763468653 0.675017294 0.72855762 0.826659284 0.8336563 1 18.91957567 1.034025445 1.485774369 1.197352888 0.776208916 0.487374493 0.071664107 1.859079224 2.434889558 1.355860838 0.021690441 10.81497314 -1.034025445 -0.421143972 LQGS(ph)PTPTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQGSPTPTSK 10 0 Q8WXD9 Q8WXD9 CASKIN1 Caskin-1 1 LQGS(0.432)PT(0.432)PT(0.125)S(0.011)K 73.273 0.047709 180970000 182990 153920 115770 129250 165510 156120 183460 207740 194330 TRUE FALSE 158807.4079 152908.8894 171756.7592 158598.188 162216.6748 162126.0374 165668.0774 163316.4176 171356.5288 0.926766018 0.892343528 1.002335659 0.925545056 0.94666177 0.946132829 0.966803416 0.953079633 1 17.38664163 LQHAAELIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQHAAELIK 9 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 87.298 0.013556 1166070000 1483500 1782170 1226520 1288610 1588710 1493070 1748580 1986480 1996860 FALSE TRUE 1287451.716 1770462.808 1819669.174 1581208.596 1557097.779 1550509.369 1579002.981 1561686.711 1760793.486 0.73117701 1.005491457 1.033437021 0.898009113 0.884315959 0.880574231 0.896756487 0.886922131 1 20.74779428 LQHALEDQIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQHALEDQIYR 11 0 Q8ND04;Q8ND04-2;Q8ND04-3 Q8ND04 SMG8 Protein SMG8 0 90.697 0.011294 262040000 483610 396150 278090 370240 421740 381460 425520 496270 504040 FALSE TRUE 419699.7132 393547.6646 412575.2542 454308.6508 413348.1991 396135.013 384253.1359 390146.5225 444452.9654 0.94430625 0.885465269 0.928276525 1.022174867 0.930015618 0.891286691 0.86455298 0.877812846 1 18.76167123 2.876396888 5.439137242 0.899852703 0.943633012 0.097829279 0.049066184 0.462610662 18.6540228 0.016400701 0.016469672 752.3100924 -2.876396888 0.043780309 LQHFQELGEEKDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQHFQELGEEKDNR 14 1 Q13439-5;Q13439-3;Q13439-4;Q13439;H0Y6I0 Q13439-5 GOLGA4 Golgin subfamily A member 4 0 ; 104.41 0.00063637 284000000 584660 528770 379610 419540 456120 376660 572890 596800 466000 FALSE TRUE 507395.6997 525296.4751 563190.6657 514802.9693 447044.1044 391150.3539 517331.216 469178.9643 410910.0109 1.234809779 1.278373515 1.370593684 1.25283628 1.087936756 0.951912447 1.258989079 1.141804658 1 18.64846295 3.315755558 4.632682884 1.100786943 1.295017023 0.552652165 0.087691352 0.173459713 6.865439386 0.02667586 0.034359574 2068.976499 -3.315755558 0.19423008 LQHSSALTASVEEGGVPGEDPS(ph)SRPAT(ph)PELAEPESAPTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQHSSALTASVEEGGVPGEDPSSRPATPELAEPESAPTLR 40 1 Q6NV74 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 2 LQHSSALTASVEEGGVPGEDPS(0.514)S(0.514)RPAT(0.972)PELAEPES(0.001)APTLR 117.8 3.24E-05 91358000 27034 35071 11078 19816 42021 37766 23311 32453 28547 TRUE FALSE 23461.3884 34840.61629 16435.35785 24315.52567 41184.86431 39218.88246 21050.30281 25513.1785 25172.20618 0.932035446 1.384090693 0.652916861 0.965967206 1.636124542 1.558023249 0.836251803 1.013545587 1 14.61954404 LQHSSALTASVEEGGVPGEDPS(ph)SRPATPELAEPESAPTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQHSSALTASVEEGGVPGEDPSSRPATPELAEPESAPTLR 40 1 Q6NV74 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 LQHSSALTASVEEGGVPGEDPS(0.33)S(0.33)RPAT(0.33)PELAEPES(0.007)APT(0.003)LR 49.585 0.022503 76408000 18804 20604 7788.8 16117 23529 23696 16922 25410 21078 TRUE FALSE 16319.00376 20468.65097 11555.48973 19776.61118 23060.81893 24607.60045 15280.90704 19976.26924 18586.18285 0.878018036 1.101283202 0.621724742 1.064049103 1.240750676 1.323972795 0.822164893 1.074791387 1 14.18194289 3.512382749 24.99182355 1.087910857 0.882511204 0.262184325 0.174323314 894.804556 634196.5542 0.048155732 0.071391132 3253.739268 -3.512382749 -0.205399653 LQHYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQHYAK 6 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 90.285 0.049203 1667610000 4818000 4275400 2915600 3487300 3573500 4168800 5001700 5303300 5301900 FALSE TRUE 4181289.093 4247314.616 4325593.912 4279144.765 3502394.341 4329176.434 4516635.904 4169230.565 4675115.422 0.894371308 0.908494065 0.925237886 0.915302485 0.749156764 0.926004182 0.966101475 0.891792007 1 22.15657055 -1.254657011 0.86559955 9.999999489 0.890221278 0.244511548 0.05662121 274.0882019 3.060375713 4786.315203 0.020541554 0.055634346 1.254657011 -9.109778211 LQIDVDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQIDVDGR 8 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ; 139.74 0.0015372 229473000 367750 285080 202440 241510 312870 332930 279040 319050 352630 FALSE TRUE 319150.9057 283207.2907 300340.6611 296348.5367 306644.4991 345738.0325 251978.7437 250823.6403 310942.4831 1.026398524 0.910802821 0.965904234 0.953065447 0.986177559 1.111903491 0.810370912 0.806656067 1 18.24628822 2.213098442 24.9998927 0.856075524 0.98539581 0.357108785 0.074476564 225.7194556 221619.6446 0.030284402 0.02042611 163.3422154 -2.213098442 0.129320286 LQINS(ph)PPFDQPMSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQINSPPFDQPMSR 14 0 Q00537;Q00537-2;F5H6Z0;F8VQZ9 Q00537 CDK17 Cyclin-dependent kinase 17 1 LQINS(1)PPFDQPMSR 107.69 0.00091174 99399000 163600 173760 126120 142190 193930 177060 174790 217840 197000 TRUE FALSE 141979.8455 172618.5591 187112.0538 174476.4127 190071.1724 183871.6128 157838.8927 171256.6112 173710.8844 0.817334193 0.99371182 1.0771464 1.00440691 1.094181133 1.05849218 0.908629838 0.985871506 1 17.40632863 4.728622575 4.453401392 1.014467186 0.805404497 0.588688511 0.052283547 0.146181489 7.251488835 0.01382684 0.09476045 53533.12241 -4.728622575 -0.20906269 LQIVEMPLAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQIVEMPLAHK 11 0 P50454;E9PKH2;E9PR70;E9PPV6 P50454 SERPINH1 Serpin H1 0 ; 138.75 5.09E-05 1507310000 2274040 2269070 1768430 2117100 2489500 2816800 2414790 2578600 2351200 FALSE TRUE 1973519.852 2254164.33 2623648.663 2597819.913 2439963.821 2925164.119 2180604.037 2027186.457 2073243.814 0.951899549 1.087264466 1.265480039 1.253021904 1.176882238 1.410911779 1.051783694 0.977784881 1 20.98345836 2.016253792 24.99114051 0.99554918 1.195071861 0.349949002 0.11847355 248.0529156 381394.2364 0.049793201 0.033561055 103.81349 -2.016253792 0.199522681 LQKEEEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQKEEEKR 8 2 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 85.67 0.0093241 262910000 608430 456790 318420 353920 348580 310930 620380 661880 308180 FALSE TRUE 528024.4339 453789.3164 472408.9771 434282.9453 341643.94 322891.6783 560215.6431 520342.1128 271747.3115 1.943071418 1.66989441 1.738412698 1.598113126 1.257211849 1.188205604 2.061531502 1.914801327 1 18.05190624 4.818518066 1.175772825 1.568119429 2.145279889 0.13906315 0.324509183 4.783113636 4.966710192 0.10414446 3.538518143 65844.28195 -4.818518066 0.57716046 LQLATLEAGPGAAGAGS(ph)E ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LQLATLEAGPGAAGAGSE 18 0 C9JI98 C9JI98 TMEM238 Transmembrane protein 238 1 LQLATLEAGPGAAGAGS(1)E;LQLATLEAGPGAAGAGS(1)E;LQLATLEAGPGAAGAGS(1)E;LQLATLEAGPGAAGAGS(1)E;LQLATLEAGPGAAGAGS(1)E 373.42 1.03E-107 412051000 770535 892279 617924 983682 1233928 1250691 745314 1442061 1272181 TRUE FALSE 668706.8475 886417.5605 916754.1132 1207042.033 1209375.247 1298805.892 673033.563 1133687.477 1121785.211 0.596109523 0.790184744 0.817227847 1.076001021 1.078080933 1.157802651 0.599966514 1.010610111 1 20.09736504 4.369973276 1.641373235 0.972878504 0.593708463 0.40507511 0.152667111 0.568620962 2.434798415 0.043940957 0.276529768 23440.84569 -4.369973276 -0.379170041 LQLEEEQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LQLEEEQHR 9 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 ;; 156.26 0.00050878 535640000 356030 345302 246897 313004 336081 387450 344953 373946 465990 FALSE TRUE 308979.7334 343033.6884 366297.215 384076.3422 329393.6456 402355.4522 311499.5112 293980.558 410901.1931 0.751956282 0.834832544 0.89144841 0.934717028 0.801637112 0.979202443 0.758088602 0.715453162 1 18.64843199 1.207605886 24.51823462 1.000001362 0.832942416 0.284199084 0.083081082 4817.542422 3815541.251 2.847077769 0.02154753 16.12894222 -1.207605886 -0.167058946 LQLEETDHQK ddPTM_MDA-MB-175_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 ;;; 191.52 7.83E-07 2384980000 1790700 1517420 1131850 1289440 1502550 1485920 1779050 2046630 1980920 FALSE TRUE 1554054.458 1507451.968 1679216.446 1582227.06 1472652.195 1543084.304 1606518.005 1608974.101 1746737.894 0.889689554 0.863009827 0.961344259 0.905818248 0.843087105 0.883409187 0.919724711 0.921130816 1 20.73623171 0.846665693 1.252923506 1.165519455 0.892979869 0.529936059 0.031315723 2.960622924 1.979404465 1.339755625 0.00976368 7.025313245 -0.846665693 -0.272539586 LQLEETMPS(ph)PYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQLEETMPSPYGR 13 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 LQLEETMPS(1)PYGR;LQLEETMPS(1)PYGR 172.43 2.45E-05 235053000 315220 301310 198061 218640 254250 261400 265320 292710 361430 TRUE FALSE 273562.8783 299330.6748 293843.9621 268285.5537 249190.9224 271456.2271 239589.3072 230116.2444 318702.1571 0.858365318 0.939217599 0.922001799 0.84180652 0.781892801 0.851755224 0.751765565 0.722041691 1 18.28184926 3.569784293 3.752781201 0.805527081 0.909245422 0.184587331 0.077566356 0.32295757 8.346269014 0.021960158 0.033133748 3713.507392 -3.569784293 0.103718341 LQLELS(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQLELSK 7 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 LQLELS(1)K;LQLELS(1)K 79.148 0.035045 121815000 288140 241619 255331 242440 244043 234939 238849 272240 582700 TRUE FALSE 250061.5689 240031.7889 378809.9256 297489.7075 239187.0218 243977.2554 215685.4607 214023.5946 513813.8698 0.486677343 0.467157083 0.737251265 0.578983412 0.465512972 0.474835869 0.419773528 0.416539154 1 18.97088631 1.232394866 24.99982362 1.000000816 0.503700038 0.73369674 0.093553941 119.4736202 484372.9437 0.22671486 0.025117263 17.07634284 -1.232394866 -0.496300778 LQLERPVS(ph)PETQADLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LQLERPVSPETQADLQR 17 1 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 LQLERPVS(1)PETQADLQR;LQLERPVS(0.882)PET(0.118)QADLQR;LQLERPVS(0.999)PET(0.001)QADLQR;LQLERPVS(1)PETQADLQR 246.69 6.78E-21 2507130000 1700410 1768230 1261610 1844890 1944770 1806740 1626560 2111500 2275510 TRUE FALSE 1475696.51 1756614.381 1871728.816 2263800.472 1906072.882 1876246.457 1468816.462 1659972.157 2006501.8 0.735457357 0.875461154 0.932831865 1.128232465 0.949948254 0.935083366 0.732028479 0.82729662 1 20.93625102 1.213975205 23.58077005 1.000000987 0.890923869 0.084582077 0.114120162 3389.082625 3250239.856 1.757872951 0.030245623 16.36723073 -1.213975205 -0.109077118 LQLGT(ph)PPPLLAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQLGTPPPLLAAR 13 0 Q9P2N5 Q9P2N5 RBM27 RNA-binding protein 27 1 LQLGT(1)PPPLLAAR 86.578 0.097946 71362000 384180 378610 235800 249440 332910 368100 343400 325310 375020 TRUE FALSE 333409.6396 376122.886 349833.6687 306079.1645 326285.7423 382261.0452 310097.1209 255744.9881 330685.5628 1.008237665 1.137403408 1.057904269 0.925589741 0.986694852 1.155965328 0.937740125 0.773378148 1 18.33510054 2.006728197 24.37006629 0.866018989 1.042361843 0.380584803 0.086031294 102.3874671 370853.3925 0.034849998 0.023427583 101.5612873 -2.006728197 0.176342855 LQLHESQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 LQLHESQK 8 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;;; 144.09 0.000591 5556410000 9276910 10629900 3197850 6951820 10841450 9897370 11317210 12991330 12368580 FALSE TRUE 8050942.839 10560071.49 4744340.956 8530336.983 10625726.36 10278128.23 10219668.72 10213235.18 10906380.56 0.738186495 0.968247112 0.435005998 0.782141879 0.974266971 0.942395891 0.937035771 0.936445883 1 23.37866907 3.330636262 4.937164496 0.95270089 0.720272211 0.442295381 0.127996983 0.198578157 8.14344522 0.036554951 0.04725018 2141.096599 -3.330636262 -0.232428679 LQLKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQLKPR 6 1 Q15056;K7EJP0;Q15056-2 Q15056;Q15056-2 EIF4H;TNNI3 Eukaryotic translation initiation factor 4H 0 ; 119.23 0.019322 5141300000 5339100 5587000 3388500 4285300 5147400 4590700 5493400 6128900 5782500 FALSE TRUE 4633524.407 5550298.629 5027189.934 5258342.862 5044976.811 4767307.2 4960650.914 4818282.43 5098899.437 0.908730298 1.08852875 0.985936278 1.031270165 0.989424654 0.93496788 0.972886595 0.944965181 1 22.28175445 2.992417352 21.62135028 0.961366334 1.008659793 0.137397596 0.047121231 94.28379527 268849.9754 0.013254299 0.014364269 982.6918447 -2.992417352 0.047293459 LQLLEDDKENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LQLLEDDKENR 11 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;;;; 170.66 1.41E-05 4987870000 6688836 4607255 3474250 4500997 4676072 3902789 5684192 6545298 5640622 FALSE TRUE 5804889.375 4576989.639 5154408.921 5523017.162 4583027.316 4052931.818 5132939.935 5145636.958 4973794.093 1.167094831 0.920220973 1.03631329 1.110423363 0.92143487 0.814857178 1.03199687 1.034549654 1 22.24591535 3.231017446 24.99926929 0.967887121 1.047049405 0.227261586 0.088058732 337.9734023 1120095.006 0.02771897 0.032035741 1702.226889 -3.231017446 0.079162283 LQLLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQLLHK 6 0 Q9BZZ2-2;Q9BZZ2-3;Q9BZZ2 Q9BZZ2-2 SIGLEC1 Sialoadhesin 0 ; 87.989 0.051813 919610000 820440 933400 775500 1105180 1083460 860730 913760 1311520 2149650 FALSE TRUE 712016.7753 927268.4339 1150534.394 1356128.011 1061901.266 893842.8401 825143.6958 1031061.654 1895520.826 0.375631207 0.489189262 0.606975338 0.715438202 0.56021609 0.471555273 0.435312387 0.54394636 1 20.85416288 1.239958468 6.6953612 1.011642425 0.527456926 0.718089595 0.093620736 0.066800164 15.26564442 0.147709499 0.024874775 17.37634649 -1.239958468 -0.484185499 LQLLSNLFHGMDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LQLLSNLFHGMDK 13 0 Q7L2H7;J3KNJ2;E9PN86 Q7L2H7 EIF3M Eukaryotic translation initiation factor 3 subunit M 0 ;; 189.1 5.55E-06 803860000 1494470 1443620 822979 1157490 1315240 1197100 1608980 1776860 1680620 FALSE TRUE 1296972.003 1434136.765 1220974.397 1420315.796 1289069.297 1243153.212 1452941.367 1396892.317 1481939.018 0.875185812 0.967743441 0.823903266 0.958417167 0.869853133 0.838869344 0.980432629 0.9426112 1 20.49905465 2.217886815 24.99611104 0.967989679 0.891901515 0.416134525 0.047377459 246.1079738 297559.9439 0.018230541 0.012306583 165.1531324 -2.217886815 -0.076088164 LQLNGNLQLELAQVLAQERPK ddPTM_MDA-MB-175_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 ;;; 366.02 2.74E-112 3729045000 1788252 1673590 1370619 1473756 1623437 1602093 2058224 2252862 2359946 FALSE TRUE 1551929.967 1662596.077 2033454.933 1808394.825 1591133.78 1663726.554 1858617.753 1771104.993 2080955.872 0.745777452 0.798957873 0.9771735 0.869021227 0.764616781 0.799501122 0.893155774 0.851101658 1 20.98881494 -0.405668369 1.235208622 9.99475743 0.834711941 0.372195988 0.066782889 97.90384495 3.386636687 2411.052497 0.020816959 0.392944877 0.405668369 -9.160045489 LQLPVWEYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQLPVWEYK 9 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 116.52 0.0030249 84220000 239890 193250 159960 178540 166230 180610 202460 255350 274320 FALSE TRUE 208187.9287 191980.528 237317.191 219080.2358 162922.3482 187558.1836 182825.4604 200745.3896 241890.2021 0.860671192 0.793668062 0.981094682 0.905701157 0.673538435 0.775385617 0.755820032 0.829902939 1 17.88399281 5.109001653 17.32757789 0.833643474 2.952792459 0.001514981 0.100722268 1234.772372 206609.6317 0.024416259 5419.991045 128529.1553 -5.109001653 2.119148985 LQLQGLDLS(ph)SR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LQLQGLDLSSR 11 0 P49454 P49454 CENPF Centromere protein F 1 LQLQGLDLS(0.915)S(0.085)R;LQLQGLDLS(0.903)S(0.097)R;LQLQGLDLS(0.944)S(0.056)R;LQLQGLDLS(0.92)S(0.08)R 186.51 4.19E-06 453888000 772580 929730 493166 573519 810050 820030 700290 927090 901650 TRUE FALSE 670481.5955 923622.5424 731662.7271 703745.2546 793931.5898 851577.0847 632375.9836 728839.0181 795057.9642 0.84331159 1.161704661 0.920263377 0.88514962 0.99858328 1.07108805 0.795383497 0.916711801 1 19.60070052 2.246412794 24.9983584 0.902146424 0.98209101 0.108973698 0.10226294 369.2562103 1175574.848 0.037352764 0.028397003 176.3651588 -2.246412794 0.079944586 LQLQVTVSS(ph)AK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQLQVTVSSAK 11 0 Q9H0M0-3;Q9H0M0;Q9H0M0-2 Q9H0M0-3 WWP1 NEDD4-like E3 ubiquitin-protein ligase WWP1 1 LQLQVTVS(0.154)S(0.846)AK 161.21 0.0011293 0 486930 468720 325020 372370 455710 369050 519240 554040 534820 TRUE FALSE 422580.9668 465640.9475 482200.7591 456922.2998 446642.2626 383247.5923 468884.1847 435562.8575 471594.1889 0.896069071 0.987376347 1.022490884 0.968888741 0.947090259 0.812663941 0.994253525 0.923596744 1 18.84718642 3.167643472 4.758202025 0.931498074 0.973963487 0.071009931 0.059190425 0.499676289 21.32539671 0.017910003 0.020778711 1471.104324 -3.167643472 0.042465413 LQLS(ph)PWESSVVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LQLSPWESSVVNR 13 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 LQLS(0.964)PWES(0.029)S(0.007)VVNR;LQLS(0.842)PWES(0.155)S(0.003)VVNR;LQLS(1)PWESSVVNR 236.31 1.09E-16 720960000 814930 874500 654680 714830 803710 956540 818050 967510 1211630 TRUE FALSE 707234.9357 868755.3519 971285.4378 877143.077 787717.7434 993338.7128 738715.6369 760615.5157 1068392.482 0.66196173 0.813142517 0.909109203 0.820993307 0.737292481 0.929750752 0.691427214 0.711925185 1 20.0270103 4.738217872 9.294514338 0.814255396 0.661401695 0.205713822 0.099087337 0.137096411 281.6177448 0.023994945 0.134491635 54729.04523 -4.738217872 -0.1528537 LQLWDTAGQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 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 5313670000 5221520 4957260 3332120 3854936 5048490 5498950 4052050 5261500 5471820 FALSE TRUE 4531482.902 4924695.433 4943544.377 4730258.138 4948034.926 5710498.165 3659082.815 4136369.17 4824947.673 0.939177626 1.020673335 1.024579894 0.980375013 1.025510588 1.183535771 0.758367357 0.857287882 1 22.20208187 2.22705175 24.99999307 0.864114121 1.02603163 0.43361992 0.084433299 198.2397372 430620.0986 0.033998581 0.023138805 168.6754007 -2.22705175 0.16191751 LQMEAPHIIVGTPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LQMEAPHIIVGTPGR 15 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3KTB5;J3QR64;J3QLN6;J3KS25;J3QKZ9 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;;;;; 197.88 8.20E-09 6820260000 4859500 4313060 2871690 3391270 4339080 4541380 3909900 4756610 4253840 FALSE TRUE 4217304.763 4284727.225 4260448.889 4161309.686 4252740.797 4716089.827 3530718.5 3739445.967 3750955.881 1.12432801 1.142302752 1.135830179 1.109399795 1.133775211 1.257303465 0.941284998 0.996931472 1 21.83882686 2.222789691 24.99990266 0.981468349 1.146823928 0.778583097 0.042974432 107.696856 170718.5973 0.017240619 0.011667067 167.0281578 -2.222789691 0.16535558 LQNAHTGLDLTVPQHQEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQNAHTGLDLTVPQHQEVR 19 0 Q53T59;F6TR53;B5MC96;A0A494C0K6 Q53T59 HS1BP3 HCLS1-binding protein 3 0 125.73 1.55E-05 103880000 77718 67976 35076 49925 63378 67852 61329 69786 70426 FALSE TRUE 67447.36939 67529.46118 52038.87092 61261.23431 62116.9018 70462.31035 55381.32302 54862.80698 62100.31851 1.086103437 1.087425359 0.837980741 0.986488246 1.00026704 1.134652962 0.89180417 0.883454518 1 15.92231305 4.303327974 24.95644465 0.959703268 1.086766324 0.287449123 0.081537648 78.83251049 30374.03393 0.021275277 0.056289078 20106.10628 -4.303327974 0.127063056 LQNALNEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQNALNEQR 9 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 106.68 0.0067373 47830000 56015 65480 40592 42489 60267 70793 55543 69038 55561 FALSE TRUE 48612.47583 65049.85757 60222.42697 52136.77685 59067.80461 73516.45252 50156.44841 54274.76095 48992.64188 0.992240344 1.327747496 1.229213708 1.064175657 1.205646447 1.500561099 1.023754721 1.107814539 1 15.58027747 LQNDPQLEAEYQQLQEDHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LQNDPQLEAEYQQLQEDHQR 20 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 ;; 273.8 1.83E-44 508670000 705190 671210 454820 559420 683100 709000 619020 751960 703930 FALSE TRUE 611997.3548 666800.7773 674772.4733 686444.8612 669507.6465 736275.6888 558987.5357 591159.2058 620712.1973 0.98595993 1.074251127 1.087093948 1.105898779 1.078612035 1.186178864 0.900558323 0.952388576 1 19.24356497 2.224933613 24.99999086 0.949174264 1.086356371 0.588713196 0.053322998 156.3472975 286831.1158 0.021428469 0.01453367 167.8547414 -2.224933613 0.137182107 LQPERGS(ph)PK ddPTM_MDA-MB-175_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 93.091 0.0097045 11178080000 7957940 5858680 3608650 3945130 5470680 4828170 7016750 7606610 2773100 TRUE FALSE 6906278.066 5820193.945 5353805.21 4840932.064 5361824.171 5013912.824 6336266.665 5979995.646 2445267.277 2.82434486 2.380187229 2.18945604 1.9797149 2.192735421 2.050455944 2.591236845 2.445538654 1 21.22156074 4.684611044 1.795577355 2.124038994 3.006998672 0.245419991 0.424008426 1.243670834 4.457669568 0.11246235 1.798228512 48373.89348 -4.684611044 0.882959678 LQPFATEADVEEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LQPFATEADVEEALR 15 0 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ;; 222.29 3.31E-12 59281700 54167 51068.4 29798.5 38580.6 52751.1 50178 47270.1 52499 50975 FALSE TRUE 47008.69371 50732.92832 44209.15427 47340.9149 51701.45632 52108.38013 42685.85298 41272.4974 44948.79357 1.045827707 1.128682758 0.983544846 1.05321881 1.150230122 1.159283175 0.949655143 0.918211461 1 15.45599477 2.216672701 24.58034287 0.947829556 1.085365387 0.547591714 0.055890812 144.3789241 162137.4218 0.02369036 0.015988345 164.6920747 -2.216672701 0.13753583 LQPFHS(ph)TELEDDAIYSVHVPAGLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LQPFHSTELEDDAIYSVHVPAGLYR 25 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QQI0 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 LQPFHS(0.992)T(0.008)ELEDDAIYSVHVPAGLYR;LQPFHS(0.988)T(0.012)ELEDDAIYSVHVPAGLYR;LQPFHS(0.978)T(0.022)ELEDDAIYSVHVPAGLYR 312.13 2.66E-74 1645060000 215592 260135 105726 215341 318661 355454 277664 332292 300935 TRUE FALSE 187100.971 258426.1561 156855.4472 264237.4653 312320.2695 369128.5454 250736.188 261233.9417 265358.8071 0.70508672 0.973874426 0.591106996 0.995774243 1.176973446 1.391054435 0.944894917 0.984455517 1 18.01758491 3.527657059 7.380164841 1.088112215 0.77946986 0.501233791 0.155471231 0.250766615 31.97166127 0.04471442 0.06582342 3370.210747 -3.527657059 -0.308642356 LQPQEIS(ph)PPPTANLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LQPQEISPPPTANLDR 16 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-6;B4DWJ1 E7ESA6 PTK2 Focal adhesion kinase 1 1 LQPQEIS(1)PPPTANLDR;LQPQEIS(1)PPPTANLDR;LQPQEIS(0.995)PPPT(0.005)ANLDR;LQPQEIS(0.998)PPPT(0.002)ANLDR;LQPQEIS(1)PPPTANLDR;LQPQEIS(1)PPPTANLDR;LQPQEIS(1)PPPTANLDR;LQPQEIS(1)PPPTANLDR 251.8 1.71E-26 10722780000 1137794 1279422 882230 1042058 1323199 1371610 1320446 1509330 1425490 TRUE FALSE 987431.6401 1271017.393 1308879.379 1278673.196 1296869.929 1424376.724 1192389.35 1186571.525 1256970.196 0.785564879 1.011175441 1.041297067 1.017266121 1.031742783 1.133182576 0.948621816 0.943993365 1 20.26151901 4.738490077 9.293684628 1.01218568 0.784723976 0.655445072 0.052424644 0.05532185 111.6673227 0.014083801 0.079412388 54763.35883 -4.738490077 -0.227461704 LQPSSS(ph)PENSLDPFPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.023)S(0.154)S(0.823)PENSLDPFPPR;LQPS(0.001)S(0.039)S(0.959)PENSLDPFPPR;LQPS(0.002)S(0.074)S(0.924)PENSLDPFPPR;LQPS(0.001)S(0.096)S(0.903)PENSLDPFPPR 354.81 8.29E-88 1754840000 1556650 1424410 904240 1082200 1283640 1494120 1354000 1526180 1458160 TRUE FALSE 1350934.758 1415052.957 1341533.489 1327930.05 1258098.075 1551599.763 1222689.288 1199818.284 1285777.986 1.050674979 1.100542218 1.043363242 1.032783315 0.978472247 1.206740028 0.950933444 0.933145766 1 20.29421012 LQQELDDLLVDLDHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 21 LQQELDDLLVDLDHQR 16 0 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;;;;;;;;;;;;;;; 361.65 1.29E-87 58012670400 2660510.7 2641273 1761807 2130534.1 2586599.5 2744216.8 2596140.8 3074242 2904231 FALSE TRUE 2308917.47 2623922.304 2613822.758 2614304.431 2535131.231 2849788.596 2344367.465 2416839.272 2560896.12 0.901605283 1.024610988 1.020667234 1.020855321 0.989939112 1.112809135 0.915448091 0.943747485 1 21.2882173 LQQELDDLTVDLDHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LQQELDDLTVDLDHQR 16 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ;;; 314.34 9.14E-58 433841000 494593 407203 262993.4 313408 373281 425425 403500 467498 420223 FALSE TRUE 429231.2819 404528.0567 390177.8879 384572.0765 365853.4384 441791.375 364368.6321 367527.1908 370544.7157 1.158379175 1.091711849 1.052984623 1.037856054 0.987339511 1.19227547 0.98333242 0.991856516 1 18.49928813 8 0.394002095 1.013202169 3.182464529 0.318810254 0.060214022 106.679403 1.516815527 0.061064316 177.4198193 100000000 -8 2.16926236 LQQELEFLEVQEEYIKDEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LQQELEFLEVQEEYIKDEQK 20 1 P43686 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;; 267.78 5.75E-37 490420000 403460 314320 259514 269476 229956 200505 400940 435464 420224 FALSE TRUE 350141.7388 312255.2112 385015.8384 330664.6445 225380.3255 208218.5571 362056.9005 342343.4124 370545.5974 0.944935633 0.842690382 1.039051175 0.892372347 0.608239113 0.56192425 0.977091357 0.923890109 1 18.49929156 3.46917228 24.99783865 0.820515125 0.937845489 0.135981102 0.148584067 449.0323601 1412104.589 0.047398803 0.061303032 2945.589884 -3.46917228 0.117330365 LQQLFNHTMFILEQEEYQR ddPTM_MDA-MB-175_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 ; 288.55 6.83E-41 2735800000 819990 752830 528980 720700 727320 751920 671090 796630 856700 FALSE TRUE 711626.2439 747884.6102 784796.4973 884345.9502 712847.755 780846.849 606007.7951 626276.8739 755421.902 0.942024903 0.990022408 1.038885019 1.170664959 0.943641895 1.033656619 0.802211047 0.829042516 1 19.52692309 2.250088092 24.99259045 0.863956042 1.022722831 0.402495852 0.081405897 190.1582383 412279.966 0.030779196 0.02363384 177.8640153 -2.250088092 0.158766789 LQQLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQQLFR 6 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 102.14 0.083281 419260000 295080 270890 164690 152320 236270 288340 239170 280910 204880 FALSE TRUE 256084.4304 269110.5058 244334.6349 186906.5841 231568.6893 299432.6264 215975.3302 220839.5825 180659.3198 1.41749914 1.48960212 1.352460726 1.03458036 1.281797637 1.657443561 1.195484022 1.222409023 1 17.46291216 1.398438096 1.630576617 0.943981568 1.353794022 0.322425674 0.164110431 0.962037789 3.172826431 0.589895985 0.049382138 25.02868863 -1.398438096 0.409812455 LQQLGEAHQAETEVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQQLGEAHQAETEVLR 16 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 244.97 4.34E-20 1325500000 859380 873500 674930 808310 900990 858790 733560 985850 1548600 FALSE TRUE 745810.7556 867761.921 1001328.406 991849.1397 883062.0618 891828.207 662419.4641 775033.6494 1365526.272 0.546170931 0.635478012 0.733291205 0.726349364 0.646682587 0.653102196 0.485101955 0.567571394 1 20.38102564 1.233349941 24.99843103 1.000000586 0.623598625 0.705284524 0.076339946 104.4983983 501278.4486 0.172265697 0.020871267 17.11393746 -1.233349941 -0.37640196 LQQLGEAHQAETEVLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQQLGEAHQAETEVLRR 17 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 146.88 2.73E-07 148850000 308480 272400 153300 172270 329810 354770 188700 272130 138380 FALSE TRUE 267713.5864 270610.5865 227436.3928 211386.5365 323247.4263 368418.2315 170399.903 213937.1172 122020.874 2.193998269 2.217740109 1.863913814 1.732380121 2.649115807 3.01930497 1.396481581 1.753282944 1 16.89676844 2.18847211 24.99997043 1.46089302 2.24966146 0.517713663 0.404760372 101.7609275 50789.67359 0.174454899 0.117617665 154.3377305 -2.18847211 0.78876844 LQQLKDETGELSSADEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQQLKDETGELSSADEKR 18 2 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 116.82 8.41E-05 70925000 188980 141670 100590 98163 107240 94995 175960 223820 68182 FALSE TRUE 164005.8142 140739.3604 149235.6605 120452.4095 105106.1338 98649.51912 158895.4263 175957.8348 60121.60163 2.727901615 2.340911696 2.482230287 2.003479718 1.748225778 1.640833185 2.642900754 2.926699056 1 15.87559582 3.751739939 20.80998104 2.106523955 2.499404844 0.152303388 0.539369179 221.6414994 349957.9747 0.152813358 0.261442587 5645.987844 -3.751739939 0.392880889 LQQQAALS(ph)PTTAPAVSSVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQQQAALSPTTAPAVSSVSK 20 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR30 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 LQQQAALS(0.982)PT(0.018)TAPAVSSVSK 365.98 5.75E-112 255620000 453570 335370 213860 260340 300310 265100 391820 469890 406790 TRUE FALSE 393629.5753 333166.9324 317283.4113 319454.176 294334.4185 275298.5685 353821.3567 369407.6802 358699.7496 1.097379008 0.928818414 0.884537588 0.890589348 0.820559309 0.767490272 0.986399787 1.029852071 1 18.45241721 2.020886728 24.92899837 1.014378653 0.89360483 0.266020129 0.084683674 283.6258769 338515.4324 0.036004567 0.024271746 104.9268724 -2.020886728 -0.120773823 LQQQHSEQPPLQPS(ph)PVMTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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(0.999)PVMT(0.001)R;LQQQHSEQPPLQPS(0.998)PVMT(0.002)R;LQQQHSEQPPLQPS(1)PVMTR;LQQQHSEQPPLQPS(1)PVMTR;LQQQHSEQPPLQPS(1)PVMTR;LQQQHSEQPPLQPS(1)PVMTR;LQQQHSEQPPLQPS(0.978)PVMT(0.022)R;LQQQHSEQPPLQPS(1)PVMTR 222.03 1.63E-19 10817670000 2954840 3236395 2209897 3332881 4330910 4170350 2476733 4920040 3932570 TRUE FALSE 2564350.407 3215134.908 3278610.581 4089662.571 4244733.364 4330786.063 2236539.815 3867927.734 3467666.055 0.739503276 0.927175471 0.945480484 1.179370362 1.22408943 1.24890517 0.644969781 1.115426824 1 21.72553354 4.528976971 1.675207933 1.057423951 0.706223726 0.26598096 0.171297152 0.942042808 3.558645018 0.048441332 0.469680572 33804.69102 -4.528976971 -0.351200225 LQQVLQMESHIQSTSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LQQVLQMESHIQSTSDR 17 0 Q14974;Q14974-2;J3KTM9;J3QKQ5 Q14974 KPNB1 Importin subunit beta-1 0 ;;; 249.69 4.35E-21 3267300000 957407 936750 577713 690960 907900 986150 835752 1040890 943150 FALSE TRUE 830883.2392 930596.4276 857096.9391 847853.0287 889834.5663 1024087.829 754700.8997 818303.7737 831651.8814 0.999075764 1.118973513 1.030595804 1.019480684 1.069960384 1.231390022 0.907472124 0.983949886 1 19.66562024 2.187470745 24.99999997 0.965656436 1.07488563 0.382602434 0.068426656 111.1889623 54407.61027 0.027417745 0.018485065 153.9822796 -2.187470745 0.109229194 LQQWYR ddPTM_MDA-MB-175_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 ;;; 160.24 0.020638 12885450000 4098500 3888520 2380490 2795620 3739510 3681910 3600330 3821610 3953710 FALSE TRUE 3556872.841 3862976.056 3531702.926 3430408.249 3665101.067 3823555.46 3251170.551 3004388.441 3486306.908 1.020240884 1.108042452 1.013021234 0.983966226 1.051284687 1.096735187 0.932554315 0.861768204 1 21.73326815 2.143754085 6.613906341 0.914576281 1.044108964 0.532855254 0.049730078 0.145282295 8.555034784 0.020363356 0.01367627 139.2368164 -2.143754085 0.129532683 LQS(ph)PLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQSPLR 6 0 Q9H788-2;Q9H788 Q9H788-2 SH2D4A SH2 domain-containing protein 4A 1 LQS(1)PLR 125.47 0.018787 591160000 470740 474220 374560 462160 400070 468980 396960 429070 926720 TRUE FALSE 408530.5163 471104.8176 555698.4688 567100.4917 392109.3897 487021.9641 358462.8803 337316.7195 817164.2173 0.499936864 0.576511805 0.680032798 0.693985957 0.479841605 0.595990321 0.438666883 0.412789391 1 19.64026651 1.228175759 24.99883452 1.000000943 0.544900432 0.69729573 0.093743175 285.4974742 687213.3718 0.353917588 0.025712864 16.91125193 -1.228175759 -0.455100511 LQSEPESIRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LQSEPESIRK 10 1 P09496-2;F8WF69;P09496-4;P09496-3;P09496 P09496-2 CLTA Clathrin light chain A 0 ;;; 142.71 5.66E-05 2786420000 4107450 3762490 2213300 2587420 3586530 3159450 4314870 4990380 2268750 FALSE TRUE 3564640.076 3737773.955 3283659.283 3174933.257 3515165.07 3280996.086 3896414.572 3923226.072 2000540.96 1.781838087 1.868381618 1.64138568 1.587037367 1.757107273 1.640054441 1.947680478 1.961082603 1 20.93195874 1.2302523 24.99072277 0.999998551 1.778462931 0.785354331 0.126985726 160.1611843 481712.9464 0.387141353 0.034905318 16.99230519 -1.2302523 0.77846438 LQSEVAELK ddPTM_MDA-MB-175_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 0 103.83 0.0078128 316670000 896970 743930 526460 647730 746410 604710 828590 934500 1054500 FALSE TRUE 778433.1419 739043.0748 781057.8169 794806.9964 731557.9013 627973.585 748233.4693 734664.4473 929838.2113 0.837170523 0.794808243 0.839993246 0.854779882 0.786758269 0.675357904 0.804692107 0.790099222 1 19.82662019 1.237427167 24.94645716 1.000000249 0.796714448 0.624407946 0.049237429 19.54964059 430073.0384 0.075247066 0.012592205 17.27536242 -1.237427167 -0.203285801 LQSFDS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LQSFDSPER 9 0 P78332;E9PGM9;P78332-2 P78332 RBM6 RNA-binding protein 6 1 LQSFDS(1)PER;LQSFDS(1)PER;LQSFDS(1)PER 193.04 3.57E-05 1476180000 1369300 1196620 777940 859160 1156590 1186930 1143450 1268480 1563320 TRUE FALSE 1188343.536 1188759.324 1154154.386 1054245.409 1133576.122 1232591.965 1032558.395 997225.4233 1378506.091 0.862051712 0.862353335 0.837250117 0.76477385 0.822322172 0.89415054 0.749041591 0.723410241 1 20.39467421 3.994803217 10.38093235 0.811987133 0.859165713 0.015404738 0.079065468 0.473100942 820.423641 0.020550227 0.039653309 9881.052743 -3.994803217 0.04717858 LQSGICHLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LQSGICHLFR 10 0 P14868;P14868-2;C9J7S3;C9JLC1 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ; 217.02 7.45E-09 1647490000 1811760 2262600 1034220 1479320 2181300 2189300 1835370 2037640 2276100 FALSE TRUE 1572331.326 2247736.832 1534372.251 1815222.216 2137896.398 2273523.788 1657376.1 1601906.543 2007022.051 0.783415073 1.119936291 0.76450194 0.904435612 1.065208226 1.132784658 0.825788685 0.798150943 1 20.93662504 LQSIGTENTEENRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 LQSIGTENTEENRR 14 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;;;;;;; 289.18 3.18E-43 1.37786E+11 14436147.8 13429929.3 8384890.2 8946274.8 12550341.5 13183967.4 12101207.3 13533941.1 11568773.1 FALSE TRUE 12528374.29 13341707.21 12439851.15 10977663.23 12300614.26 13691163.16 10927634.08 10639813.12 10201125.92 1.228136422 1.307866142 1.21945864 1.076122706 1.205809472 1.342122748 1.071218428 1.043003801 1 23.28222506 2.085741912 7.21557031 1.034180799 1.224583699 0.626688827 0.070314032 0.152177244 10.79589107 0.030524174 0.020487869 121.8265404 -2.085741912 0.1904029 LQSLHEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LQSLHEGR 8 0 B1AHC3;B1AHC4;H0Y9T8;P85298-4;P85298-3;P85298;P85298-2;P85298-5 B1AHC3 PRR5-ARHGAP8;ARHGAP8 Rho GTPase-activating protein 8 0 ;;; 134.25 0.00088478 934640000 783950 867150 451934 634530 880000 976290 857220 1017610 938390 FALSE TRUE 680349.0212 861453.6346 670490.794 778609.7347 862489.7217 1013848.508 774086.9363 800002.0205 827454.6032 0.822219151 1.041088697 0.810305232 0.94096973 1.042340835 1.22526179 0.935503813 0.966822853 1 19.65832064 3.366127486 4.748732607 1.027285879 0.901871695 0.309717274 0.098070953 0.299300701 11.17314885 0.029297824 0.03815948 2323.418732 -3.366127486 -0.125414184 LQTMKEELDFQK ddPTM_MDA-MB-175_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 ; 194.85 9.10E-07 2752100000 5136000 4656900 2635500 3231600 4257100 3569100 6590600 7493400 1715340 FALSE TRUE 4457264.587 4626308.517 3910036.615 3965384.172 4172392.039 3706405.587 5951444.626 5890994.724 1512554.459 2.946845688 3.058606246 2.585055097 2.621647206 2.758506983 2.45042786 3.934697749 3.89473231 1 20.52855566 LQVEEVHQLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LQVEEVHQLSR 11 0 Q9NR28-2;Q9NR28;Q9NR28-3 Q9NR28-2 DIABLO "Diablo homolog, mitochondrial" 0 ;;;; 183.06 5.51E-06 3263170000 2766460 2551360 1567630 1998670 2575990 2924000 1909410 2480720 2463600 FALSE TRUE 2400865.302 2534599.948 2325741.111 2452498.571 2524732.839 3036488.172 1724235.712 1950237.333 2172356.015 1.105189612 1.166751643 1.070607716 1.12895794 1.162209519 1.3977857 0.793716914 0.897752173 1 21.05082913 2.219816711 24.99985599 0.892970487 1.164683383 0.627680765 0.099634224 155.5781515 207502.2524 0.040653949 0.027460593 165.8886646 -2.219816711 0.271712896 LQVVDQPLPVR ddPTM_MDA-MB-175_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 ;; 148.32 8.12E-05 452603000 1050680 1079170 773740 776088 1147190 1300940 1088780 1200940 1260540 FALSE TRUE 911829.9759 1072080.861 1147923.252 952310.6422 1124363.163 1350988.004 983190.2832 944128.3267 1111520.397 0.820344798 0.964517488 1.032750505 0.856763983 1.011554234 1.215441486 0.884545426 0.84940261 1 20.08410299 4.73673514 6.511251611 0.96931598 0.817486418 0.173640403 0.106230313 0.237603392 62.30226284 0.027392564 0.16072506 54542.51252 -4.73673514 -0.151829562 LQWDGSSDLS(ph)PSDSGSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LQWDGSSDLSPSDSGSSK 18 0 K7EKG9;Q14CW9;K7EJK2;K7ENU1;Q14CW9-2 K7EKG9 ATXN7L3 Ataxin-7-like protein 3 1 LQWDGSSDLS(1)PSDSGSSK;LQWDGSSDLS(0.999)PS(0.001)DSGSSK;LQWDGSS(0.01)DLS(0.989)PS(0.001)DSGSSK 296.81 2.46E-49 420300000 1803520 1608910 1098480 1380960 1647170 1246550 1822940 2349740 1989650 TRUE FALSE 1565180.262 1598340.964 1629708.602 1694528.075 1614394.54 1294505.585 1646151.559 1847266.387 1754435.844 0.892127386 0.911028448 0.928907494 0.965853543 0.920178726 0.737847206 0.938279713 1.052911905 1 20.74257576 1.909861748 5.501040161 1.023787253 0.895139276 0.444586029 0.06091005 0.209239363 9.808059594 0.032275073 0.016960396 81.2571804 -1.909861748 -0.128647977 LQWVTIT(ph)S(ph)PQAIMMS(ph)ICLQS(ph)MVDELMVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LQWVTITSPQAIMMSICLQSMVDELMVK 28 0 Q15036-2;Q15036 Q15036-2 SNX17 Sorting nexin-17 4 LQWVT(0.659)IT(0.702)S(0.702)PQAIMMS(0.973)ICLQS(0.964)MVDELMVK 47.487 0.043752 576120000 90024 78368 24213 63257 106610 108960 98064 108880 129020 TRUE FALSE 78127.10031 77853.19545 35922.48779 77620.46867 104488.6696 113151.7617 88553.76837 85596.85931 113767.4026 0.686726589 0.684319002 0.315753783 0.682273366 0.918441199 0.9945886 0.778375584 0.752384755 1 16.79572772 3.414722044 5.083476557 0.866581674 0.562826573 0.575396014 0.128966289 0.154586376 7.933426988 0.038778031 0.050941461 2598.495949 -3.414722044 -0.303755101 LRAELDEVNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LRAELDEVNK 10 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 174.4 2.84E-06 610330000 1458630 1234070 900240 1086010 1298550 1161240 1340830 1921150 1336310 FALSE TRUE 1265868.35 1225963.313 1335599.075 1332605.169 1272711.396 1205913.654 1210796.513 1510327.023 1178332.954 1.074287488 1.040421817 1.133464926 1.130924128 1.080094884 1.023406542 1.027550412 1.281748947 1 20.16831582 LHQLAMQQSHFPMTHGNTGFSGIESSS(ph)PEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LHQLAMQQSHFPMTHGNTGFSGIESSSPEVK 31 0 F8VZX2;Q15366;Q15366-6;Q15366-2;Q15366-3;Q15366-5;Q15366-4;F8VRH0 F8VZX2;Q15366;Q15366-2;Q15366-5 PCBP2 Poly(rC)-binding protein 2 1 LHQLAMQQSHFPMTHGNTGFSGIES(0.208)S(0.208)S(0.585)PEVK;LHQLAMQQSHFPMTHGNTGFSGIES(0.271)S(0.043)S(0.687)PEVK;LHQLAMQQSHFPMTHGNTGFSGIES(0.011)S(0.047)S(0.942)PEVK 318.6 1.18E-92 6346400000 1406080 1583200 1132850 1827980 2444470 2456510 3093920 3369750 2948110 TRUE FALSE 1220262.965 1572799.855 1680700.049 2243050.798 2395829.83 2551013.529 2793872.115 2649155.186 2599587.794 0.46940633 0.605018941 0.646525596 0.862848642 0.921619125 0.981314628 1.074736587 1.019067404 1 21.30985145 3.8170003 0.845165767 1.035971399 0.440167174 0.975653149 0.031631482 0.113812164 0.144501114 0.013908498 0.050516792 6561.457199 -3.8170003 -0.595804225 down LRDDFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LRDDFEK 7 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;;; 156.51 0.0014034 2122430000 2497320 1853640 1464950 1772420 1833640 1514700 2161390 2488830 3062730 FALSE TRUE 2167292.835 1841463.317 2173404.72 2174875.051 1797154.151 1572971.489 1951778.73 1956613.073 2700657.548 0.80250561 0.681857394 0.804768721 0.805313155 0.665450587 0.582440188 0.722705006 0.724495067 1 21.36487928 1.238348708 7.709223168 1.004059536 0.720947431 0.603306174 0.070388466 0.071726555 33.16437176 0.105806967 0.018062793 17.3120584 -1.238348708 -0.283112104 LRDDQYTLEHMHAFGMYNYLHCDSWYQDSVYYIDTLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LRDDQYTLEHMHAFGMYNYLHCDSWYQDSVYYIDTLGR 38 1 Q96RS6-2;Q96RS6;E5RHQ3;E5RGX7 Q96RS6-2 NUDCD1 NudC domain-containing protein 1 0 ; 95.56 9.64E-05 1597200000 306990 297380 136623 231310 209958 225400 283650 335050 186790 FALSE TRUE 266420.4937 295426.4912 202694.3398 283832.4709 205780.2466 234071.2839 256141.6667 263402.1649 164707.899 1.617533193 1.793638878 1.230629138 1.723247474 1.249364771 1.42112968 1.555126792 1.599207849 1 17.32955022 7.999808078 0.033276388 5.71E-07 3.666284392 0.198740106 0.220005587 5121.682055 16.85256965 632.0833526 1357.574517 99955818.17 -7.999808078 3.666283821 LRDDTELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LRDDTELR 8 1 P16930;H0YLC7;P16930-2 P16930 FAH Fumarylacetoacetase 0 ; 143.91 0.00054162 711330000 835880 904580 584060 648920 883010 944070 722880 859590 1149870 FALSE TRUE 725416.3401 898637.7544 866513.3696 796267.2041 865439.8286 980388.9838 652775.2089 675773.3678 1013933.679 0.715447524 0.886288495 0.85460557 0.785324742 0.853546782 0.966916283 0.643804642 0.666486756 1 19.95153186 2.230277678 24.99997927 0.743249489 0.843916085 0.068020723 0.114877361 358.8569573 1083109.193 0.045679868 0.031380511 169.9329819 -2.230277678 0.100666597 LRDEELAELEDALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LRDEELAELEDALR 14 1 Q15628-2;Q15628 Q15628-2 TRADD Tumor necrosis factor receptor type 1-associated DEATH domain protein 0 ;; 136.01 2.69E-05 225466000 248382 211681 156609 176224 213836 233529 219661 278122 255765 FALSE TRUE 215557.6894 210290.4536 232345.6362 216238.3526 209581.082 242513.0117 198358.31 218647.7746 225528.7531 0.95578806 0.932433008 1.030226226 0.958806137 0.929287637 1.075308618 0.879525592 0.969489574 1 17.78295185 LRDFLLDIEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRDFLLDIEDR 11 1 Q9NRL2;Q9NRL2-2 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 0 122.45 0.00035622 43667000 33309 29271 15335 19708 24775 30340 26379 24822 27765 FALSE TRUE 28907.13126 29078.71687 22751.05729 24183.00262 24282.02597 31507.19943 23820.76864 19514.00847 24482.65333 1.18071889 1.187727346 0.929272534 0.987760693 0.991805326 1.286919314 0.972965157 0.797054478 1 14.5794723 -1.000562551 0.069595068 1.39E-18 1.573128827 0.193537304 0.128735051 728.0506327 6.187789021 130.7230089 36.70632147 0.099870552 1.000562551 1.573128827 LRDLEDSLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 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 ;;;;;;;; 234.39 3.96E-12 12981171000 5968708 5681138 2454428 2636058 5066603 5353414 5587904 5818049 855522 FALSE TRUE 5179928.115 5643818.23 3641397.59 3234615.259 4965787.513 5559363.301 5045989.93 4573904.497 754383.1638 6.866441835 7.481368224 4.826986822 4.287761729 6.582579982 7.369415925 6.688895209 6.063105219 1 19.52493795 4.246166262 24.99720058 5.49596777 7.17390561 0.155891828 1.787156305 360.6993014 1185468.855 0.451281825 1.146093062 17626.50716 -4.246166262 1.67793784 LRDPDSHIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRDPDSHIVK 10 1 A0A1B0GUA3;Q96EK5 A0A1B0GUA3 KIAA1279 KIF1-binding protein 0 69.721 0.033726 57485000 234620 230300 165480 194750 228840 221990 248600 272010 284150 FALSE TRUE 203614.3725 228787.1441 245506.6815 238970.9641 224286.5317 230530.0989 224490.8103 213842.7783 250558.1107 0.81264331 0.91311011 0.979839291 0.953754654 0.895147761 0.9200664 0.895963055 0.8534658 1 17.93478571 4.731960809 5.398323713 0.920950871 0.808850059 0.404636149 0.043012091 0.161939027 17.54487714 0.011031535 0.066898644 53946.19391 -4.731960809 -0.112100812 LRDTEEMLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LRDTEEMLSK 10 1 Q9H444 Q9H444 CHMP4B Charged multivesicular body protein 4b 0 ;; 137.92 7.15E-05 1278810000 3168400 2809860 2084760 2532080 2527630 2637540 3087820 3368270 2553910 FALSE TRUE 2749687.912 2791401.845 3092956.909 3107027.464 2477335.108 2739007.871 2788363.692 2647991.672 2251989.669 1.221003786 1.239526932 1.373432992 1.379681047 1.100065041 1.216261295 1.238177834 1.175845391 1 21.10276878 3.234751099 24.99995339 1.160209509 1.303849587 0.472325896 0.081882654 98.78104025 648249.6294 0.025442139 0.029948164 1716.924108 -3.234751099 0.143640079 LRDVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRDVEK 6 1 A0A0D9SFE4;A0A0D9SFB1;A0A0U1RQP1;Q05193-5;Q05193-3;Q05193-2;Q05193 A0A0D9SFE4 DNM1 Dynamin-1 0 65.313 0.09519 307030000 2090100 1946300 1204900 1438800 1413700 1481600 2145900 2187200 2144600 FALSE TRUE 1813887.989 1933514.627 1787593.67 1765501.531 1385570.136 1538598.111 1937790.948 1719484.301 1891067.831 0.959187164 1.02244594 0.945282681 0.933600319 0.732691928 0.813613391 1.024707267 0.909266327 1 20.85076968 3.866865857 2.899115452 0.899644093 0.989005296 0.156724507 0.084566527 0.523143417 8.425054636 0.025019446 0.049443784 7359.797354 -3.866865857 0.089361204 LRDWAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LRDWAPR 7 1 A0A1W2PR36;Q14353;Q14353-2 A0A1W2PR36 GAMT Guanidinoacetate N-methyltransferase 0 ; 135.77 0.0027774 551370000 400410 476650 264900 300850 463630 512570 422150 482160 402050 FALSE TRUE 347494.804 473518.8548 393006.526 369162.5907 454404.6701 532288.8996 381209.958 379053.8362 354520.107 0.980183626 1.335661491 1.108559199 1.041302266 1.281745834 1.501435008 1.075284449 1.069202645 1 18.43550793 2.028893698 24.99808647 1.049353655 1.212110436 0.205329497 0.149198138 323.2692958 279682.997 0.061410343 0.041402179 106.8793238 -2.028893698 0.162756781 LRDYQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRDYQVR 7 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 130 0.0032884 109300000 165540 151970 104980 106380 171450 183790 160420 172180 151520 FALSE TRUE 143663.4696 150971.6991 155748.6791 130535.2049 168038.4804 190860.5202 144862.4931 135360.6469 133607.4782 1.075265183 1.129964438 1.165718276 0.97700523 1.257702658 1.428516748 1.084239408 1.013121786 1 17.02764123 2.005525496 24.9976014 1.019852847 1.172736004 0.258574074 0.116796269 205.4670624 929538.7689 0.050667459 0.034046077 101.2804205 -2.005525496 0.152883157 LREAAEGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LREAAEGLR 9 1 Q9Y490;Q9Y4G6 Q9Y490;Q9Y4G6 TLN1;TLN2 Talin-1;Talin-2 0 77.379 0.029885 125700000 112160 137950 74182 68984 119360 135660 142190 127510 74135 FALSE TRUE 97337.77182 137043.7974 110056.6633 84647.87155 116984.9695 140878.928 128400.4357 100242.9788 65370.84475 1.489008933 2.096405483 1.683574134 1.294887222 1.789558785 2.155072778 1.964185046 1.53345087 1 15.99635972 1.324266792 2.964585095 0.928866278 1.784360787 0.475075032 0.260007586 0.302523703 3.619199549 0.556741749 0.070158922 21.09923904 -1.324266792 0.855494508 LREAIAELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LREAIAELER 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 162.68 6.10E-06 206179000 151683 149525 67258 70979 142552 147067 138893 159932 37005 FALSE TRUE 131637.7072 148542.7604 99784.19376 87095.8668 139715.4941 152724.7627 125423.1782 125731.7864 32630.31106 4.034215518 4.55229373 3.058021531 2.669170596 4.281770218 4.680456842 3.843762875 3.853220589 1 14.99392512 4.24515948 24.94564165 3.471046469 4.293254749 0.12019948 1.025171526 368.212596 1391914.062 0.258369415 0.650377263 17585.69271 -4.24515948 0.82220828 LREAQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LREAQDR 7 1 Q9Y3Q3 Q9Y3Q3 TMED3 Transmembrane emp24 domain-containing protein 3 0 123.98 0.0038219 184150000 116350 119230 68737 73459 126240 179100 112790 141460 76974 FALSE TRUE 100974.0527 118446.7703 101978.4431 90138.9887 123728.071 185990.0929 101851.6432 111209.8798 67874.22141 1.48766425 1.74509214 1.502462069 1.3280298 1.822902251 2.740216964 1.500593908 1.638470063 1 16.05057612 3.213723677 24.9467913 1.759691666 1.5312355 0.059951759 0.436416841 741.9575391 745236.7159 0.137998467 0.156543072 1635.775418 -3.213723677 -0.228456165 LRECLPLIIFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LRECLPLIIFLR 12 1 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ; 243.11 2.29E-16 1161100000 814820 971310 457160 521180 840400 812540 876530 1036460 378080 FALSE TRUE 707139.4725 964929.4007 678244.1051 639521.8847 823677.6842 843798.9396 791524.2555 814821.0947 333383.8131 2.1210972 2.894349884 2.034424223 1.918275152 2.470658898 2.531013524 2.374213217 2.444093152 1 18.34682453 1.236341785 24.99998371 0.999998251 2.357517471 0.700121035 0.277305052 33.21307689 374127.7353 0.430568177 0.066724905 17.23224199 -1.236341785 1.35751922 LREDGIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LREDGIQK 8 1 O00170;E9PMH2 O00170 AIP AH receptor-interacting protein 0 ; 117.31 0.0019182 840310000 816440 721020 509870 650560 686740 650200 829830 923880 1018170 FALSE TRUE 708545.3854 716283.5721 756444.8374 798279.5912 673075.2176 675213.6147 749353.2143 726315.4516 897803.1025 0.789199083 0.797818107 0.842550928 0.889147731 0.749691347 0.752073158 0.834652066 0.808991916 1 19.77603956 1.238441136 11.84885312 1.00028556 0.809016804 0.679026099 0.04147691 0.039481062 269.9684699 0.058889318 0.010500841 17.31574318 -1.238441136 -0.191268756 LREDLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LREDLER 7 1 P62269;J3JS69 P62269 RPS18 40S ribosomal protein S18 0 ;;;;;;; 199.02 0.00035238 18586770000 7062940 7269150 4381560 5304260 6638460 7307290 6882580 7646720 6883480 FALSE TRUE 6129554.584 7221398.475 6500497.071 6508673.304 6506367.634 7588406.175 6215108.451 6011528.435 6069722.836 1.00985741 1.189741059 1.070970989 1.072318041 1.071938177 1.250206373 1.023952595 0.990412346 1 22.53319921 2.02132456 24.99767045 0.998319611 1.111425991 0.36243316 0.067082119 224.7537763 263466.14 0.026005051 0.017530991 105.0327074 -2.02132456 0.11310638 LREEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LREEGK 6 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 97.068 0.037842 154310000 282020 232810 151970 185150 157830 186970 243800 292070 278130 FALSE TRUE 244750.3425 231280.6558 225463.2003 227191.1373 154689.4918 194162.8569 220156.3135 229613.1034 245249.7882 0.997963522 0.943041205 0.919320673 0.926366294 0.630742611 0.79169429 0.897681972 0.936241801 1 17.90389237 3.901777909 2.172802073 0.860421048 0.968796237 0.174130241 0.099415604 0.654243989 6.021112594 0.031409189 0.071349411 7975.867095 -3.901777909 0.108375189 LREEIEELKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LREEIEELKR 10 2 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;;; 198.81 1.63E-07 1365840000 1534290 1028100 650183 798580 931010 773753 1163260 1322760 1142450 FALSE TRUE 1331529.689 1021346.343 964613.6735 979909.7945 912484.7225 803519.7786 1050447.224 1039898.068 1007390.862 1.321760737 1.013853095 0.957536652 0.972720551 0.905790152 0.797624645 1.042740473 1.032268712 1 19.94219212 4.747560475 3.026270746 0.962737071 1.383890155 0.727224425 0.069364779 0.231219848 3.100823401 0.019192685 0.2372966 55919.13891 -4.747560475 0.421153084 LREETER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LREETER 7 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4;K7EMQ3 P50570-2 DNM2 Dynamin-2 0 ;; 171.73 0.0008451 724140000 1415100 1189840 842836 922690 986720 1254580 1176510 1343610 1258470 FALSE TRUE 1228090.95 1182023.863 1250434.309 1132200.867 967086.2025 1302844.504 1062412.241 1056289.457 1109695.11 1.106692224 1.065178941 1.126826907 1.020281027 0.871488207 1.174056272 0.957391117 0.95187358 1 20.08173192 3.577100425 5.56381513 0.988896813 1.094773247 0.294687793 0.076533312 0.28707205 12.95908005 0.020713515 0.030853479 3776.595101 -3.577100425 0.105876434 LREEWQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LREEWQR 7 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDG6;H0YDQ3;U3KQE6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 0 ;;;;; 169.57 0.00091849 1882190000 1150180 1245820 767464 875470 1240030 1270060 1152720 1312150 1239460 FALSE TRUE 998180.7988 1237636.126 1138612.157 1074258.844 1215355.829 1318920.03 1040929.392 1031556.934 1092932.451 0.913305116 1.132399469 1.041795544 0.982914217 1.112013673 1.206771772 0.95241878 0.943843266 1 20.05977281 LRENELTYYCCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LRENELTYYCCK 12 1 E9PNW4;A0A2U3TZL5;P13987;P13987-2;H0YET2 E9PNW4 CD59 CD59 glycoprotein 0 ; 118.76 0.00053906 509540000 283300 305300 201566 291720 302050 307710 279670 412370 303930 FALSE TRUE 245861.1872 303294.4642 299043.9918 357959.4847 296039.796 319547.8028 252547.6464 324187.8846 267999.7416 0.917393374 1.131696853 1.115836866 1.335671007 1.104627169 1.192343697 0.942342873 1.209657452 1 18.03187208 4.738795004 7.27973615 1.134004533 0.914673617 0.272660566 0.108361949 0.136274077 63.03861263 0.024996084 0.146785984 54801.82285 -4.738795004 -0.219330916 LRENVFQEHQTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LRENVFQEHQTLK 13 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;; 127.27 0.00010749 1896800000 3500260 3546310 1293110 2012100 3363900 2989110 3423860 4144800 1883310 FALSE TRUE 3037691.772 3523014.056 1918462.321 2468978.058 3296964.971 3104102.996 3091814.584 3258466.775 1660667.237 1.829199556 2.121444909 1.155235846 1.486738585 1.985325475 1.869190242 1.861790559 1.962143108 1 20.66333159 3.250815278 24.99625815 1.780129136 1.646752756 0.005802637 0.368819373 1074.46927 2191620.146 0.107217371 0.137371047 1781.620814 -3.250815278 -0.13337638 LREQGTES(ph)R ddPTM_MDA-MB-175_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" 1 LREQGT(0.011)ES(0.989)R;LREQGT(0.038)ES(0.962)R 75.479 0.023102 88822000 388485 359439 145838 173061 224363 222931 162518 228899 224261 TRUE FALSE 337145.723 357077.8215 216365.7446 212357.1451 219898.6153 231507.2998 146757.0294 179950.7301 197749.1201 1.704916426 1.805711304 1.094142642 1.073871505 1.112008059 1.170712162 0.742137458 0.909995099 1 17.59331175 4.193362579 4.811078243 0.995217875 1.761647747 0.867127324 0.12073883 0.064498836 3.25635251 0.034845933 0.080395946 15608.55067 -4.193362579 0.766429872 LREQLQLLEEQHR ddPTM_MDA-MB-175_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 ;;; 182.02 6.95E-06 2065450000 2611750 1848720 1179990 1357890 1931120 2064660 1914250 2136310 1265160 FALSE TRUE 2266600.62 1836575.637 1750637.111 1666219.679 1892694.49 2144088.806 1728606.33 1679476.731 1115594.226 2.031742875 1.646275674 1.569241817 1.493571443 1.696579676 1.921925335 1.549493794 1.505454844 1 20.08938094 1.035686733 1.447159377 0.383264526 1.699722878 0.650884941 0.163037162 1.324153193 1.653330921 2.942202645 0.047881269 10.85642241 -1.035686733 1.316458353 LRETFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRETFER 7 1 Q9Y2W2;F5H5G4 Q9Y2W2 WBP11 WW domain-binding protein 11 0 127.46 0.01023 0 71332 72003 32104 41231 56744 59707 57936 56957 48462 FALSE TRUE 61905.29547 71530.00755 47629.60178 50593.12873 55614.90542 62003.96693 52317.37564 44777.18879 42732.87757 1.44865731 1.673886984 1.114589152 1.183939196 1.301454725 1.450966339 1.224288618 1.047839306 1 15.38305885 -0.397994029 0.158038755 1.34E-31 1.663669091 0.439894337 0.154721684 83.20751955 1.839088474 30.11282976 2.831409182 0.399950249 0.397994029 1.663669091 LREVVETPLLHPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LREVVETPLLHPER 14 1 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ;; 127.3 4.83E-05 698111000 299680 311363 138027 144570 272062 296551 276573 315413 72050.9 FALSE TRUE 260076.5287 309317.636 204777.3189 177396.8281 266648.4985 307959.5089 249750.993 247964.3845 63533.12468 4.093557967 4.868604173 3.223158311 2.792194292 4.196999594 4.847227496 3.931035885 3.902914987 1 15.95522135 1.237477551 6.165721363 0.897303869 3.98377477 0.687981805 0.631357748 0.08105413 12.51168554 1.050990797 0.165066166 17.27736672 -1.237477551 3.086470901 LREYEAALNSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LREYEAALNSK 11 1 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 ;; 179.59 6.42E-06 1264260000 1752830 1390080 776650 1196650 1452120 1241620 1513540 2077200 1093170 FALSE TRUE 1521189.074 1380948.473 1152240.538 1468367.672 1423225.653 1289385.925 1366757.124 1633006.945 963936.6879 1.578100609 1.432613252 1.195348774 1.523303024 1.476472128 1.337625117 1.417890968 1.694101869 1 19.87857887 1.218461157 24.98640184 0.999998386 1.456241195 0.536243818 0.133540556 1263.488432 1570606.47 1.375866733 0.033909452 16.53716869 -1.218461157 0.456242809 LREYQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LREYQQR 7 1 Q08379;B7ZC06;R4GND7 Q08379 GOLGA2 Golgin subfamily A member 2 0 ; 147.34 0.0019685 211317000 240270 238860 163326 171948 239770 274810 240600 265330 215958 FALSE TRUE 208517.7107 237290.9129 242310.9999 210991.4215 234999.0461 285382.1185 217266.649 208591.2443 190427.6913 1.09499679 1.246094575 1.272456743 1.107987079 1.234059209 1.498637707 1.140940415 1.09538294 1 17.53888376 1.736289442 2.729345153 1.029375312 1.240133329 0.332077652 0.112425746 0.279778323 4.328647412 0.091402765 0.031220527 54.4865666 -1.736289442 0.210758018 LRGDVAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRGDVAIK 8 1 A0A087X1E4;P53365;P53365-2;P53365-3 A0A087X1E4 ARFIP2 Arfaptin-2 0 66.299 0.056584 357510000 398990 339460 254430 277850 340420 322400 388090 424630 369030 FALSE TRUE 346262.4606 337230.0649 377473.199 340940.0892 333646.308 334802.9366 350453.0915 333826.179 325403.6938 1.064101199 1.03634369 1.160015102 1.047744988 1.025330426 1.028884868 1.076979451 1.025883189 1 18.3118711 3.495072294 24.85141315 1.03424414 1.08545698 0.330468487 0.035907517 835.4904111 1156651.396 0.009796148 0.014188414 3126.599787 -3.495072294 0.05121284 LRGYDYGPHFQGILEASLEGDSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 250.62 8.03E-39 1379015000 585510 614933 230845 205545.8 643515 735018 697396 734633 127035.8 FALSE TRUE 508133.37 610893.4646 342482.4141 252218.1155 630710.3105 763294.6181 629762.6433 577537.4499 112017.7724 4.536185276 5.453540553 3.057393543 2.251590171 5.630448604 6.814049248 5.621988632 5.155766244 1 16.77336812 7.388165103 14.16514054 4.530540486 4.730333542 0 1.785336258 0 0 0.408014164 0 24443596.35 -7.388165103 0.199793056 LRHDKEENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LRHDKEENR 9 2 F5GWN5;O00750;Q5SW97;Q5SW98 F5GWN5 PIK3C2B Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit beta 0 ; 60.518 0.053543 36629000 58061 59557 32715 36955 49126 71191 52826 62593 40852 FALSE TRUE 50388.09174 59165.76615 48536.08343 45346.19757 48148.48871 73929.76384 47702.94265 49207.97405 36022.5231 1.398794071 1.642465909 1.347381562 1.258829023 1.336621774 2.052320534 1.324253232 1.366033521 1 15.13661161 1.213839548 1.859151723 0.816047884 1.487539349 0.303986415 0.22866754 1.218903168 3.787140961 1.485865566 0.063409037 16.36211903 -1.213839548 0.671491464 LRIDYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRIDYER 7 1 P15924 P15924 DSP Desmoplakin 0 125.53 0.0036848 182490000 189700 161370 107820 98168 163910 166790 182400 175240 127340 FALSE TRUE 164630.6644 160309.9498 159962.1126 120458.5448 160648.5117 173206.5192 164710.8761 137766.2897 112286.0103 1.466172535 1.427692991 1.424595212 1.072783195 1.430708165 1.542547632 1.466886887 1.22692301 1 16.77681867 1.415010287 2.831281226 0.988817072 1.398684657 0.525785909 0.12486659 0.269062713 3.373276606 0.214477426 0.034636396 26.00221155 -1.415010287 0.409867585 LRIEEEIR ddPTM_MDA-MB-175_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 ;;; 186.41 0.00018937 1012270000 1399610 1296840 826410 959210 1251510 1349730 1306980 1386620 1103240 FALSE TRUE 1214647.992 1288320.973 1226064.64 1177013.291 1226607.4 1401654.986 1180229.281 1090102.104 972816.224 1.248589366 1.324321019 1.260325034 1.209903024 1.260882959 1.440821968 1.213208879 1.120563244 1 19.89180776 1.61545277 2.204278609 1.007912799 1.286870562 0.692419953 0.064336478 0.175301184 1.738458937 0.080443821 0.018219461 41.25273721 -1.61545277 0.278957764 LRLEQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRLEQER 7 1 Q99583 Q99583 MNT Max-binding protein MNT 0 110.22 0.0062499 108320000 198690 204370 125960 164760 177070 208890 196340 205960 163210 FALSE TRUE 172432.6131 203027.48 186874.6773 202171.2762 173546.6534 216926.1335 177298.977 161917.0568 143915.4997 1.198151786 1.410740889 1.298502786 1.404791538 1.20589272 1.507315987 1.231965823 1.125084213 1 17.13486245 1.679624402 2.198278099 1.015053025 1.336790175 0.585108417 0.095893957 0.186410771 1.858746492 0.093220211 0.024536286 47.82163299 -1.679624402 0.32173715 LRLEQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRLEQQK 7 1 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 101.33 0.020912 0 297320 365760 228790 247690 304210 298650 345590 426000 383540 FALSE TRUE 258028.4087 363357.2985 339433.6093 303931.8002 298156.8162 310139.2588 312074.735 334903.2151 338198.3381 0.76294996 1.074391141 1.003652505 0.898679165 0.881603434 0.917033657 0.92275656 0.990256833 1 18.36751004 1.67937068 4.661518946 0.997464465 0.929144849 0.119599093 0.080057658 0.361796425 18.13146587 0.05253588 0.020422913 47.79370296 -1.67937068 -0.068319616 LRLEVNLQAMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRLEVNLQAMK 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 80.245 0.022744 197780000 247030 263410 159720 193860 236080 207170 279020 301930 233850 FALSE TRUE 214384.3596 261679.6424 236961.1262 237878.876 231382.4699 215139.964 251960.6833 237364.6191 206204.5194 1.039668579 1.269029617 1.149155833 1.15360651 1.122101836 1.043332923 1.221896999 1.151112594 1 17.65371643 3.290772443 3.916709566 1.118278879 1.162181665 0.06008936 0.080293371 0.70555753 22.18245818 0.023600998 0.030089279 1953.315709 -3.290772443 0.043902787 LRLPLDKEPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LRLPLDKEPAR 11 2 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 123.84 0.0002034 1903200000 2029050 1786590 1118430 1381720 1847590 1672700 2056660 2310620 1632310 FALSE TRUE 1760905.902 1774853.773 1659306.489 1695460.644 1810826.574 1737049.851 1857205.43 1816511.894 1439340.171 1.223411905 1.233102367 1.152824414 1.177942976 1.258094931 1.206837609 1.290317235 1.26204488 1 20.45697617 1.233188135 24.97515653 0.999999638 1.227221081 0.756201302 0.040242059 91.69169392 426201.317 0.089962755 0.010755629 17.1075625 -1.233188135 0.227221443 LRLPLEAALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRLPLEAALR 10 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 150.94 1.89E-05 320960000 89046 164030 87273 80339 142350 168680 138900 156320 123020 FALSE TRUE 77278.34549 162952.4761 129478.5147 98581.19785 139517.5135 175169.2288 125429.4994 122892.1845 108476.7157 0.712395697 1.502188511 1.193606516 0.908777494 1.28615171 1.614809478 1.156280392 1.132889981 1 16.72702588 4.761708219 23.97580674 1.217315707 0.712394706 0.368983252 0.210219286 4419.095466 4577078.83 0.052264687 2.700968485 57770.77838 -4.761708219 -0.504921001 LRLS(ph)PS(ph)PTSQR ddPTM_MDA-MB-175_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(0.579)PS(0.798)PT(0.557)S(0.066)QR 100.31 0.049333 109400000 210690 231760 132440 162610 223650 226740 213950 230890 228800 TRUE FALSE 182846.7827 230237.5533 196488.427 199533.0858 219199.8026 235462.8345 193201.1619 181515.9703 201751.5246 0.906296907 1.141193623 0.973912972 0.989004104 1.086483995 1.16709321 0.95761934 0.899700612 1 17.62222005 2.026606205 24.99562632 0.93847816 1.046135933 0.219857829 0.080704112 265.9094883 249811.7774 0.031868272 0.021484942 106.3178547 -2.026606205 0.107657773 LRLS(ph)PSPT(ph)SQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LRLSPSPTSQR 11 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 LRLS(0.986)PS(0.215)PT(0.472)S(0.326)QR;LRLS(0.81)PS(0.233)PT(0.878)S(0.079)QR 124.16 0.008899 15895100000 1003750 1008880 649870 780870 924520 986820 892650 1036570 927710 TRUE FALSE 871101.8943 1002252.601 964149.3057 958178.4684 906123.8608 1024783.604 806080.9404 814907.5721 818037.1807 1.06486834 1.22519199 1.178613061 1.171314081 1.107680534 1.252734751 0.985384234 0.996174247 1 19.64180689 2.222056406 24.98575316 0.993983523 1.167454903 0.705446042 0.052659879 117.8567466 178422.2115 0.019844476 0.013421344 166.7463767 -2.222056406 0.17347138 LRLS(ph)PSPTS(ph)QR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LRLSPSPTSQR 11 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 LRLS(0.596)PS(0.405)PTS(1)QR;LRLS(0.839)PS(0.46)PT(0.2)S(0.502)QR 180.95 7.70E-05 7167220000 1816420 1872870 1141840 1378220 1775690 1696590 1676200 1770680 1644530 TRUE FALSE 1576375.495 1860566.994 1694037.643 1691165.916 1740357.243 1761858.915 1513642.382 1392033.861 1450115.537 1.087068895 1.283047417 1.168208739 1.166228395 1.200150746 1.214978304 1.043808127 0.959946864 1 20.46773642 2.106189163 3.905815645 0.982592836 1.18973927 0.760884342 0.049757887 0.091952815 2.629423216 0.020782326 0.013083546 127.6994902 -2.106189163 0.207146434 LRLS(ph)PSPTSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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(0.991)PS(0.009)PTSQR;LRLS(0.999)PS(0.001)PTSQR;LRLS(0.853)PS(0.147)PTSQR;LRLS(0.949)PS(0.051)PTSQR;LRLS(0.987)PS(0.013)PTSQR;LRLS(0.82)PS(0.18)PTSQR;LRLS(0.842)PS(0.158)PTSQR;LRLS(0.959)PS(0.041)PTSQR;LRLS(0.712)PS(0.288)PTSQR;LRLS(0.655)PS(0.345)PTSQR 200.42 1.23E-07 98621690000 7376940 7303390 4533376 5234488 6125020 6790590 5645710 7116220 6305150 TRUE FALSE 6402058.688 7255413.55 6725731.797 6423058.505 6003144.085 7051828.391 5098189.913 5594471.731 5559762.35 1.151498623 1.304986273 1.209715699 1.155275729 1.079748325 1.268368673 0.916979826 1.006242961 1 22.40659179 2.236434954 24.99998692 0.978647122 1.19356846 0.711136896 0.066233053 30.24803041 355738.0601 0.026313102 0.018734463 172.3593922 -2.236434954 0.214921338 LRLSPS(ph)PT(ph)SQR ddPTM_MDA-MB-175_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(0.269)PS(0.76)PT(0.947)S(0.023)QR 167.01 0.00049514 576770000 616900 585450 364780 483010 585370 572100 565910 626790 575190 TRUE FALSE 535375.102 581604.1404 541188.8281 592684.8028 573722.2823 594109.0572 511028.1353 492755.8362 507191.6935 1.055567567 1.14671464 1.067030149 1.16856173 1.131174445 1.171369849 1.007564087 0.97153767 1 18.95217159 2.141442197 5.975900831 0.985965491 1.124019221 0.720057699 0.038412606 0.098649357 5.061052091 0.015181632 0.01016616 138.4975839 -2.141442197 0.13805373 LRLSPS(ph)PTS(ph)QR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LRLSPSPTSQR 11 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 LRLS(0.157)PS(0.845)PT(0.155)S(0.844)QR;LRLS(0.115)PS(0.889)PT(0.359)S(0.637)QR 189.07 3.43E-05 11175000000 3692360 3772160 2311590 2582430 3295160 3613940 3270740 3857960 3479230 TRUE FALSE 3204405.271 3747380.433 3429482.656 3168810.201 3229592.763 3752970.61 2953544.138 3032965.277 3067919.393 1.044488091 1.221472911 1.117852921 1.032885743 1.05269805 1.223295051 0.962718951 0.988606573 1 21.54882915 2.209739991 24.99877038 0.983904293 1.113772224 0.467900599 0.066176823 185.4380565 160846.158 0.026772558 0.018053566 162.0839423 -2.209739991 0.129867931 LRLSPS(ph)PTSQR ddPTM_MDA-MB-175_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 1 LRLS(0.244)PS(0.754)PT(0.001)S(0.001)QR 192.35 3.76E-06 6994300000 1728400 1664000 1017900 1124700 1576300 1535900 1536400 1579400 1478700 TRUE FALSE 1499987.561 1653069.074 1510159.845 1380080.325 1544934.714 1594987.067 1387400.164 1241657.601 1303889.771 1.150394454 1.267798177 1.158195945 1.058433279 1.184866044 1.223252995 1.064047127 0.952271909 1 20.31439048 2.019269433 4.172425607 0.979454702 1.172152728 0.695000068 0.054765243 0.113821109 4.595573299 0.02734153 0.015932385 104.5368556 -2.019269433 0.192698027 LRNPSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LRNPSDR 7 1 Q9P0L0-2;Q9P0L0 Q9P0L0-2 VAPA Vesicle-associated membrane protein-associated protein A 0 ; 90.37 0.015676 190125000 417700 408930 256993 342260 383180 585710 323220 432470 539090 FALSE TRUE 362499.8867 406243.7119 381275.6744 419975.3641 375555.4677 608242.6427 291874.1741 339989.656 475359.3943 0.762580673 0.85460331 0.802078762 0.883490195 0.790045326 1.2795427 0.614007376 0.715226542 1 18.85865915 4.739442475 22.48769796 0.852538032 0.76258065 0.02709828 0.178650222 99.23061311 2528544.494 0.043207938 0.252538482 54883.58543 -4.739442475 -0.089957382 LRPENVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LRPENVR 7 1 A0A3B3ISG5;P14735 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 171.38 0.00085693 900090000 713390 685870 474190 533500 718980 772180 688500 805470 753260 FALSE TRUE 619113.704 681364.4748 703509.8701 654639.329 704673.7047 801886.2643 621729.376 633226.5087 664210.4609 0.932104717 1.025826172 1.059167104 0.985590212 1.060919311 1.207277379 0.936042734 0.953352207 1 19.34128092 LRPGFMEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LRPGFMEDR 9 1 Q5BKZ1 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 0 ;; 141.95 9.62E-05 256760000 655780 588740 340366 426200 583900 573240 529660 623180 571980 FALSE TRUE 569117.0115 584872.5282 504968.1361 522975.2241 572281.5324 595292.9137 478293.6547 489917.8066 504361.176 1.128391793 1.159630352 1.001203423 1.036906187 1.134666108 1.180290915 0.948315766 0.971363043 1 18.9440977 2.223209339 24.99998249 0.971800125 1.102530569 0.569275731 0.054700464 186.8508308 304289.4187 0.023776802 0.016097393 167.1896311 -2.223209339 0.130730444 LRPGSIETYEQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LRPGSIETYEQEK 13 1 Q9BVJ7 Q9BVJ7 DUSP23 Dual specificity protein phosphatase 23 0 ; 139.3 3.57E-05 473900000 515770 512520 351120 387010 490610 384040 571510 626840 562970 FALSE TRUE 447609.6877 509153.2224 520922.8064 474886.5356 480847.8209 398814.2673 516085.0482 492795.1441 496416.3279 0.901682041 1.025657686 1.049366786 0.956629564 0.968638205 0.803386683 1.039621421 0.992705349 1 18.92119104 LRPKS(ph)PPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRPKSPPPK 9 2 Q9HCE5 Q9HCE5 METTL14 N6-adenosine-methyltransferase subunit METTL14 1 LRPKS(1)PPPK 69.349 0.028955 1257400000 5797800 4145900 2789600 3351400 3571500 2946600 5068300 5720900 2888800 TRUE FALSE 5031606.04 4118665.31 4138659.891 4112386.593 3500434.138 3059957.609 4576777.046 4497530.055 2547289.355 1.975278557 1.616881609 1.624730965 1.614416747 1.37418002 1.201260313 1.796724442 1.765614121 1 21.28053142 7.999999305 0.804446263 1.498150665 124.3286028 0.298833462 0.242917406 777.8159679 2.649013815 0.088385541 174175.9164 99999839.9 -7.999999305 122.8304521 LRPLFEACGEVVQIRPIFSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LRPLFEACGEVVQIRPIFSNR 21 2 A0A499FI31;Q15020-4;Q15020 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 ; 288.92 4.07E-47 1351490000 374470 340560 190527 227920 325350 332300 300580 351310 310410 FALSE TRUE 324982.8407 338322.8389 282666.4945 279672.7195 318876.1715 345083.796 271429.7979 276185.0904 273713.6834 1.187309442 1.236046495 1.032708672 1.021771057 1.164999015 1.260747332 0.991655932 1.009029169 1 18.06230803 2.204690082 24.99766973 1.001704528 1.143921458 0.464064558 0.075944899 185.0387972 136564.0613 0.033279444 0.022438318 160.2101704 -2.204690082 0.14221693 LRPLSYPQTDVFLICFSLVSPASFENVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRPLSYPQTDVFLICFSLVSPASFENVR 28 1 P63000;J3KSC4;J3QLK0;P60763 P63000 RAC1;RAC3 Ras-related C3 botulinum toxin substrate 1;Ras-related C3 botulinum toxin substrate 3 0 62.858 0.022153 243010000 87572 103510 56402 103210 93080 78955 79910 115320 97781 FALSE TRUE 75999.13832 102830.036 83678.19585 126645.408 91227.89011 81992.44994 72160.3405 90659.71542 86221.44157 0.881441286 1.192627195 0.970503326 1.468838907 1.058065006 0.950951973 0.836918743 1.051475292 1 16.39575906 2.998089141 24.99665186 0.967284496 1.139391631 0.195270377 0.160503218 117.4083484 1535894.888 0.047418043 0.052973538 995.6097497 -2.998089141 0.172107135 LRPLWK ddPTM_MDA-MB-175_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 ; 116.09 0.021771 7792300000 6073700 6265100 3821900 5055300 5973400 5253000 6675900 7787600 6993200 FALSE TRUE 5271045.156 6223944.146 5670183.623 6203183.13 5854541.027 5455086.309 6028472.246 6122282.343 6166471.863 0.854791082 1.009320124 0.919518284 1.005953367 0.949415023 0.884636536 0.977620977 0.992833906 1 22.55601386 -1.988180081 0.014947379 1.904546603 0.158904141 0.174898957 0.048632293 25016.90198 37.32750864 2586.471286 1835.203458 0.010275901 1.988180081 -1.745642461 LRPLYDIPYMFEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LRPLYDIPYMFEAR 14 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 186.42 9.72E-07 3544500000 1906850 2040690 1137390 1230290 1715210 1845320 1607450 1898280 1846640 FALSE TRUE 1654854.941 2027284.573 1687435.608 1509646.148 1681080.677 1916310.654 1451559.746 1492347.594 1628332.323 1.01628821 1.245006652 1.03629682 0.927111823 1.032394096 1.176854766 0.891439497 0.916488344 1 20.63496374 2.921461209 0.313688249 0.884184539 1.160111259 0.1718797 0.101293505 3.573939242 1.6497868 0.640967889 0.58359116 834.5670022 -2.921461209 0.27592672 LRPQTYDLQESNVQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRPQTYDLQESNVQLK 16 1 A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599;Q92599-3;C9J4G8;C9JV02;A0A0A0MRP8 A0A087X142 8-Sep Septin-8 0 176.04 2.45E-12 0 190560 167240 110900 151670 167350 147390 164660 215890 205560 FALSE TRUE 165377.0132 166141.3894 164531.6109 186108.9916 164020.0624 153060.1887 148691.2985 169723.6036 181258.931 0.912379943 0.916596984 0.907715885 1.026757637 0.904893687 0.844428398 0.820325364 0.93635995 1 17.46769256 3.023622407 24.99892897 0.895780573 0.940394714 0.100470776 0.058420439 543.314022 574969.8727 0.018623222 0.021115845 1055.899069 -3.023622407 0.044614142 LRPSGDDVELIGEEEDVSVYDIADHPDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LRPSGDDVELIGEEEDVSVYDIADHPDFR 29 1 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 0 ;; 254.3 3.99E-58 233552000 186423 160446 104987 130971 162377 177590 163474 191954 184061 FALSE TRUE 161786.7282 159392.0197 155759.0644 160709.9673 159146.0154 184422.0022 147620.3166 150906.1309 162301.5183 0.996828187 0.982073497 0.959689509 0.990193863 0.980557774 1.136292526 0.909543658 0.929788781 1 17.30831697 LRPT(ph)RTSSESIYSRPGSSIPGSPGHTIYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRPTRTSSESIYSRPGSSIPGSPGHTIYAK 30 3 O14639-3;F8W8M4;O14639-2;O14639;A0A494C1P1;A0A494C1G0;H0Y7N6;F6XFR5 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 LRPT(0.306)RT(0.306)S(0.306)S(0.052)ES(0.014)IYS(0.014)RPGSSIPGSPGHTIYAK 123.42 8.61E-06 600060000 192770 208150 39770 54466 213640 206930 251530 235820 17343 TRUE FALSE 167294.9561 206782.6489 59002.90502 66833.33776 209388.982 214890.731 227136.6593 185391.7282 15292.7303 10.9395087 13.52163053 3.858232237 4.370268517 13.69206008 14.05182246 14.85259041 12.12286652 1 13.90055838 LRPTRTSSES(ph)IYSRPGSSIPGSPGHTIYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRPTRTSSESIYSRPGSSIPGSPGHTIYAK 30 3 O14639-3;F8W8M4;O14639-2;O14639;A0A494C1P1;A0A494C1G0;H0Y7N6;F6XFR5 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 LRPT(0.15)RT(0.15)S(0.15)S(0.044)ES(0.245)IYS(0.245)RPGS(0.008)S(0.008)IPGSPGHTIYAK 103.01 0.00026656 501680000 257030 269710 28465 94224 241690 254830 291250 323270 19443 TRUE FALSE 223062.8343 267938.2573 42230.76921 115618.9993 236880.8419 264633.475 263004.6198 254141.2262 17144.47069 13.01077405 15.62826069 2.463229689 6.743806876 13.81674863 15.43549986 15.34049225 14.82350962 1 14.06545574 7.971678857 4.09E-11 9.810029907 12.9090825 0 5.569923865 0 0.582473452 455148697.8 455148698.6 93686897.55 -7.971678857 3.099052591 LRPTVTNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LRPTVTNDR 9 1 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 0 ;; 106.4 0.0026831 665430000 868010 785940 465004 554610 616370 816610 703620 775630 810400 FALSE TRUE 753300.2792 780777.1084 689881.4897 680542.6772 604105.4429 848025.5151 635383.0407 609767.5605 714595.4352 1.054163296 1.092614184 0.965415473 0.952346802 0.845381055 1.186721148 0.889150713 0.853304584 1 19.44676717 4.170062402 5.095392932 0.946186857 1.073394453 0.200152484 0.096452773 0.283803214 13.69902633 0.025060121 0.055768522 14793.20929 -4.170062402 0.127207596 LRQDLQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LRQDLQDR 8 1 P12270 P12270 TPR Nucleoprotein TPR 0 ;; 116.52 0.0020575 1396570000 1768960 1642460 1026640 1368570 1666470 1764930 1483410 2103430 1838560 FALSE TRUE 1535187.454 1631670.572 1523126.538 1679324.736 1633310.507 1832827.999 1339549.127 1653627.863 1621207.531 0.946940737 1.006453857 0.939501272 1.035848097 1.007465408 1.130532621 0.826266286 1.019997645 1 20.62863735 4.74936867 22.28693965 0.993779264 0.946940616 0.038196452 0.076414094 1422.469344 2932950.127 0.01765291 0.22539608 56152.44484 -4.74936867 -0.046838648 LRQPFFQK ddPTM_MDA-MB-175_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 ; 161.9 0.00031451 9849300000 6940100 7017100 3966500 4727000 6301900 5847800 7168300 7958700 6100700 FALSE TRUE 6022948.201 6971004.208 5884712.667 5800337.598 6176504.519 6072768.65 6473119.369 6256793.94 5379482.196 1.119614859 1.29585041 1.093918049 1.078233441 1.148159673 1.128876057 1.203297852 1.163084794 1 22.35903588 0.52272914 0.012341239 1.06E-06 2.21112906 0.09557963 0.074262867 27554.03796 67.9012425 6524.508825 5667.543832 3.332185268 -0.52272914 2.211127996 LRRES(ph)PESEGPIYEGLIL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LRRESPESEGPIYEGLIL 18 2 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 1 LRRES(0.921)PES(0.077)EGPIY(0.002)EGLIL;LRRES(0.987)PES(0.013)EGPIYEGLIL 82.635 0.0039076 128485000 205999 151915 97118 127784 158477 158794 165859 179743 119367 TRUE FALSE 178775.7102 150917.0604 144084.5896 156799.3103 155323.6178 164902.9079 149774.0197 141306.3582 105255.5692 1.698491695 1.43381544 1.368902289 1.489700843 1.475680754 1.566690572 1.422955771 1.342507187 1 16.68353705 1.040096637 1.427486437 0.567946585 1.493160217 0.761038158 0.088082836 0.983137294 1.205922992 1.511176692 0.025250426 10.96722207 -1.040096637 0.925213631 LRRPS(ph)PPEPWDEEDGASCSTFFGSEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LRRPSPPEPWDEEDGASCSTFFGSEER 27 2 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 LRRPS(1)PPEPWDEEDGASCSTFFGSEER;LRRPS(0.901)PPEPWDEEDGAS(0.07)CS(0.018)T(0.007)FFGS(0.004)EER;LRRPS(0.996)PPEPWDEEDGAS(0.002)CS(0.001)TFFGS(0.001)EER;LRRPS(1)PPEPWDEEDGASCSTFFGSEER 250.03 2.68E-46 1276110000 466866 553649 255605 206409 502621 533158 507258 562908 145439 TRUE FALSE 405168.4752 550012.0433 379216.4329 253277.3182 492619.8255 553668.9333 458064.1972 442534.5048 128245.3671 3.159322511 4.288747856 2.956960095 1.97494322 3.841229017 4.317262649 3.571779687 3.450686093 1 16.96854718 4.210794894 24.96942616 3.123442846 3.724036535 0.074030805 0.98556787 591.1896801 531651.1101 0.255620579 0.532306587 16247.81232 -4.210794894 0.600593689 LRRY(ph)CVFS(ph)HEELICK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LRRYCVFSHEELICK 15 2 P41229-4;P41229-3;P41229-2;P41229-5;P41229 P41229-4 KDM5C Lysine-specific demethylase 5C 2 LRRY(1)CVFS(1)HEELICK;LRRY(1)CVFS(1)HEELICK;LRRY(1)CVFS(1)HEELICK 89.261 0.015292 1176860000 539620 664180 416499 622460 832240 781200 757770 884440 957660 TRUE FALSE 468307.8498 659816.9578 617919.3095 763799.0567 815680.0522 811253.2695 684281.582 695309.3887 844446.5258 0.554573718 0.781360261 0.731744747 0.904496654 0.965934523 0.960692293 0.810331455 0.823390668 1 19.68764654 4.92310425 0.909039188 0.898081247 0.290801317 0.706247584 0.071785831 1.799186955 0.942810128 0.026096934 1.169980454 83773.03496 -4.92310425 -0.607279931 LRS(ph)DGAAIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRSDGAAIPR 10 1 O43295-2;O43295 O43295-2 SRGAP3 SLIT-ROBO Rho GTPase-activating protein 3 1 LRS(1)DGAAIPR 137.93 0.0046126 0 64827 66377 33741 41142 69894 72781 78845 82427 36273 TRUE FALSE 56259.9477 65940.96512 50058.26046 50483.91992 68503.24615 75580.93217 71198.62404 64800.6275 31984.84726 1.758956272 2.06163139 1.565061732 1.578369892 2.141740606 2.363023076 2.226011069 2.025978957 1 14.96510097 3.233944401 24.99950399 2.001862401 1.751339358 0.058689922 0.389517162 312.6338614 1693093.056 0.119190814 0.139624212 1713.737897 -3.233944401 -0.250523043 LRS(ph)GSASPMDLLS(ph)Y(ph)FK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRSGSASPMDLLSYFK 16 1 P11678 P11678 EPX Eosinophil peroxidase;Eosinophil peroxidase light chain;Eosinophil peroxidase heavy chain 3 LRS(0.985)GS(0.077)AS(0.266)PMDLLS(0.844)Y(0.828)FK 51.606 0.036005 0 20907 18113 15244 18304 16334 17862 16676 25210 18482 TRUE FALSE 18144.08698 17994.01451 22616.04939 22460.20296 16008.98536 18549.1627 15058.76409 19819.03768 16297.07901 1.113333682 1.104125132 1.387736377 1.378173533 0.982322375 1.138189407 0.924016143 1.216109811 1 13.99232579 3.229126508 24.9995037 1.067320071 1.245854845 0.379006014 0.122357094 233.9689291 619994.6735 0.037727223 0.043337599 1694.831424 -3.229126508 0.178534774 LRS(ph)PFLQK ddPTM_MDA-MB-175_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 122.51 0.00084022 5915700000 5923110 6783310 4802500 5910320 7359430 6161840 7989860 9390120 8606060 TRUE FALSE 5140356.006 6738749.99 7125005.063 7252348.49 7212991.741 6398889.972 7215004.607 7382115.912 7588661.391 0.677373221 0.888002461 0.938901434 0.955682184 0.950495927 0.843217221 0.950761173 0.972782357 1 22.85541399 4.775580078 2.216794154 0.944678802 0.591740534 0.813857513 0.039986029 0.313992876 1.641573772 0.010922882 0.225665605 59645.8289 -4.775580078 -0.352938268 LRS(ph)PPEALVQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LRSPPEALVQGR 12 1 Q9UHB6;Q9UHB6-4;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 LRS(1)PPEALVQGR;LRS(1)PPEALVQGR;LRS(1)PPEALVQGR;LRS(1)PPEALVQGR;LRS(1)PPEALVQGR;LRS(1)PPEALVQGR 163.8 3.57E-05 21423200000 2244050 2339930 1489500 1905380 2362950 2288710 2258900 2636610 2468120 TRUE FALSE 1947493.107 2324558.846 2209827.182 2338025.651 2315931.918 2376758.155 2039832.226 2072791.47 2176341.665 0.894847136 1.06810382 1.015386149 1.074291637 1.064139861 1.092088707 0.937275731 0.952420065 1 21.05347363 2.224140035 24.99999467 0.95989794 1.038567887 0.258617019 0.056799726 289.1106009 501207.8176 0.022436132 0.015205537 167.5483036 -2.224140035 0.078669947 LRS(ph)PS(ph)NDSAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LRSPSNDSAHR 11 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 LRS(1)PS(1)NDSAHR;LRS(1)PS(0.968)NDS(0.032)AHR 110.57 0.0010108 927230000 965650 742990 425050 577700 759400 739270 676150 829560 791800 TRUE FALSE 838036.9059 738109.2498 630605.6017 708875.6146 744289.4257 767710.1953 610577.0771 652165.0496 698194.306 1.200291808 1.057168819 0.903194994 1.015298476 1.066020475 1.099565248 0.874508818 0.934073859 1 19.41326907 4.623974167 3.28792866 0.982130078 1.207280586 0.492223632 0.069190628 0.244185495 4.265511321 0.018643184 0.115334753 42070.16033 -4.623974167 0.225150508 LRS(ph)PSNDSAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 LRSPSNDSAHR 11 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 LRS(0.998)PS(0.002)NDSAHR;LRS(0.996)PS(0.004)NDSAHR;LRS(1)PSNDSAHR;LRS(1)PSNDSAHR;LRS(1)PSNDSAHR;LRS(0.999)PS(0.001)NDSAHR;LRS(0.986)PS(0.014)NDSAHR 160.65 1.65E-05 2891563000 2121016 2098886 1099665 1365730 1779364 1904980 1715930 1837242 1493681 TRUE FALSE 1840718.362 2085098.28 1631466.672 1675839.87 1743958.138 1978265.813 1549519.373 1444362.096 1317099.734 1.397554274 1.583098247 1.238681195 1.272371277 1.324089659 1.501986344 1.176463204 1.096623178 1 20.32893316 2.039641613 4.117041532 1.072128382 1.380303693 0.649425688 0.104596373 0.138073161 5.111568124 0.051095891 0.03064344 109.5573738 -2.039641613 0.30817531 LRS(ph)YEDMIGEEVPSDQYYWAPLAQHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 19 LRSYEDMIGEEVPSDQYYWAPLAQHER 27 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 LRS(0.993)Y(0.007)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.783)Y(0.217)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.994)Y(0.006)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.525)Y(0.473)EDMIGEEVPS(0.002)DQYYWAPLAQHER;LRS(0.942)Y(0.014)EDMIGEEVPS(0.044)DQYYWAPLAQHER;LRS(0.995)Y(0.005)EDMIGEEVPSDQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER;LRS(0.996)Y(0.004)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.923)Y(0.077)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.541)Y(0.459)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.976)Y(0.024)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.987)Y(0.013)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.984)YEDMIGEEVPS(0.016)DQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER;LRS(0.999)Y(0.001)EDMIGEEVPSDQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER 268.64 5.00E-54 15240695000 1990984 1764332 1438936.3 1681722 1868959 1996687 1752511 2091490 1907731 TRUE FALSE 1727870.42 1752741.987 2134810.708 2063582.684 1831770.372 2073500.841 1582552.753 1644241.139 1682201.214 1.02714848 1.041933612 1.26905788 1.226715726 1.088912763 1.232611666 0.940763055 0.977434284 1 20.68191885 2.22811768 24.99733909 0.972379902 1.149352746 0.508604646 0.081076249 174.0715265 416672.7524 0.034127059 0.023283336 169.0899051 -2.22811768 0.176972845 LRTACER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRTACER 7 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931;P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89;P54652;P17066;P48741 A0A0G2JIW1;Q53FA3;P11142;P54652;P17066 HSPA1B;HSPA1A;HSPA1L;HSPA8;HSPA2;HSPA6;HSPA7 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like;Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2;Heat shock 70 kDa protein 6;Putative heat shock 70 kDa protein 7 0 78.149 0.032941 43335000 58162 48992 57955 44128 54552 67041 77999 62291 41093 FALSE TRUE 50475.74434 48670.16833 85982.23185 54147.93685 53466.52193 69620.11065 70434.66899 48970.5544 36235.03235 1.393009501 1.343179933 2.37290341 1.494353208 1.475547791 1.921348102 1.943827959 1.351469868 1 15.14509756 1.483719108 3.697379479 1.036780408 1.708285645 0.358773103 0.312979197 0.231974107 6.125274115 0.322191553 0.081242987 30.45924316 -1.483719108 0.671505237 LRVEFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 161.11 0.001205 8923270000 1979609 2447382 1443148 1347943 2358726 2470357 2193398 2519372 2202331 FALSE TRUE 1717998.655 2431304.986 2141059.2 1654014.06 2311791.967 2565393.232 1980682.6 1980623.904 1941973.938 0.884666175 1.251976115 1.102516959 0.851717949 1.190434085 1.321023512 1.019932637 1.019902412 1 20.88909241 2.046223859 24.99991529 1.013933346 1.106025181 0.073780726 0.144746857 325.403477 175991.1378 0.05922665 0.03993057 111.2304922 -2.046223859 0.092091835 LRVQS(ph)PEPPAPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LRVQSPEPPAPER 13 1 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 LRVQS(1)PEPPAPER;LRVQS(1)PEPPAPER 102.39 0.0010255 880960000 457770 414050 265030 331940 400250 458220 386360 467530 295830 TRUE FALSE 397274.5347 411330.0783 393199.3945 407312.0504 392285.8081 475848.0199 348890.8667 367552.3478 260857.3144 1.522957236 1.576839351 1.507335132 1.561436187 1.503832886 1.824169742 1.337477799 1.409016836 1 17.99290136 0.927920788 1.187861224 0.330965127 1.565877292 0.701917208 0.114047776 1.607185235 1.141009723 2.964057112 0.033421907 8.470728998 -0.927920788 1.234912164 LRYFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LRYFLK 6 1 O75436;S4R3Q6;O75436-2 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 123.34 0.017175 1093800000 18590 34577 19780 10726 31761 28435 16139 111580 38542 FALSE TRUE 16133.2844 34349.86141 29345.67416 13161.50224 31129.01824 29528.91285 14573.84226 87719.48532 33985.60867 0.474709297 1.010717853 0.86347355 0.387266927 0.915947057 0.868865205 0.42882393 2.581077366 1 15.05263634 1.752520201 25 1.853677142 0.726755402 0.519238381 0.432143807 2.829698069 5076.654187 0.207932692 0.099851888 56.5614066 -1.752520201 -1.12692174 LS(ph)EGS(ph)QPAEEEEDQETPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSEGSQPAEEEEDQETPSR 19 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 2 LS(1)EGS(1)QPAEEEEDQETPSR;LS(1)EGS(1)QPAEEEEDQETPSR 312.26 3.12E-48 0 345850 242379 251990 302790 285010 338470 347280 339510 739120 TRUE FALSE 300145.0462 240786.7964 373853.2069 371543.0974 279338.8586 351491.1599 313600.8391 266908.4286 651742.0756 0.460527343 0.369451053 0.573621408 0.570076893 0.428603383 0.539310217 0.481173229 0.409530762 1 19.31394161 1.233933687 24.99948833 1.000000784 0.478562541 0.855948838 0.067164896 51.83548188 280034.1597 0.130963162 0.016701716 17.13695623 -1.233933687 -0.521438243 LS(ph)FSDTYQDYEEYWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSFSDTYQDYEEYWR 15 0 Q9UHI6;E9PJ60 Q9UHI6 DDX20 Probable ATP-dependent RNA helicase DDX20 1 LS(1)FSDTYQDYEEYWR;LS(1)FSDTYQDYEEYWR;LS(0.998)FS(0.002)DTYQDYEEYWR;LS(0.976)FS(0.024)DTYQDYEEYWR 208.66 2.91E-09 118744000 155779 127428 130131 157019 149616 158619 177292 192036 339931 TRUE FALSE 135192.4105 126590.9171 193062.7869 192672.5638 146638.9343 164721.1756 160098.2491 150970.5958 299744.7444 0.451025124 0.422329063 0.644090649 0.642788798 0.489212695 0.549538161 0.534115283 0.503663863 1 18.19337493 1.236476744 24.999597 1.000000598 0.531716196 0.809236614 0.071770172 24.54668157 294403.9117 0.116606262 0.018244221 17.23759782 -1.236476744 -0.468284402 LS(ph)GFSFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSGFSFK 7 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 LS(0.994)GFS(0.006)FK 90.906 0.017617 251310000 241990 248630 198760 285430 228230 157430 272670 290790 768280 TRUE FALSE 210010.4084 246996.7332 294881.0008 350241.244 223688.6695 163486.434 246226.5054 228606.8214 677454.8136 0.309999138 0.364595141 0.435277741 0.516995727 0.3301898 0.241324485 0.363458197 0.337449549 1 19.3697652 1.237127818 24.99992808 1.000000775 0.363675398 0.882101915 0.073253678 12.552253 218936.0944 0.11684944 0.019141424 17.26345903 -1.237127818 -0.636325377 LS(ph)GPAELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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;LS(1)GPAELR 104.22 0.0048482 699270000 1210370 1110920 863850 1137490 1302640 1263220 1074830 1578710 1924030 TRUE FALSE 1050416.538 1103622.293 1281610.749 1395774.49 1276720.013 1311816.891 970593.152 1241115.152 1696573.365 0.619140062 0.650500778 0.755411334 0.822702112 0.75252862 0.77321554 0.572090292 0.731542282 1 20.69419239 -1.999999999 0.031722133 1.787358815 5.81E-08 0.213013167 0.105293173 6258.805262 19.64483676 795.2372618 383.6206499 0.01 1.999999999 -1.787358757 LS(ph)LDLSHR ddPTM_MDA-MB-175_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 158.79 0.00032374 217841000 360684 332980 306914 384221 419220 396350 482620 444140 959060 TRUE FALSE 313018.6955 330792.6325 455338.637 471464.2505 410878.3422 411597.841 435815.5867 349164.1173 845681.0194 0.370138017 0.391155323 0.538428351 0.55749655 0.485854989 0.486705781 0.515342755 0.412879217 1 19.68975407 1.234602929 24.99997632 1.000000761 0.47268676 0.87884371 0.061864317 40.2458227 254188.9868 0.117879951 0.015928318 17.16338438 -1.234602929 -0.527314 LS(ph)LQGHPTDLQTSNVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSLQGHPTDLQTSNVK 16 0 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 LS(1)LQGHPTDLQTSNVK;LS(1)LQGHPTDLQTSNVK;LS(1)LQGHPTDLQTSNVK 208.72 9.10E-12 1226630000 1356140 1083750 794460 1106930 1126240 1034340 1430980 1323070 1772630 TRUE FALSE 1176922.663 1076630.775 1178663.513 1358275.375 1103830.027 1074131.729 1292203.78 1040141.777 1563071.701 0.752955007 0.688791675 0.754068743 0.868978291 0.70619283 0.687192871 0.826707936 0.665447258 1 20.57595253 1.227625705 24.99625487 1.000000548 0.743576909 0.615067813 0.063697827 323.0643081 738447.5133 0.220147482 0.015101103 16.88984658 -1.227625705 -0.256423639 LS(ph)NGSFSAPSLTNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSNGSFSAPSLTNSR 15 0 O94806;O94806-2 O94806 PRKD3 Serine/threonine-protein kinase D3 1 LS(0.998)NGS(0.002)FSAPSLTNSR 75.911 0.031914 121820000 169170 165440 85296 91807 128560 150780 149960 162800 113200 TRUE FALSE 146813.7559 164353.2137 126545.4309 112653.1825 126001.9075 156580.6042 135416.9023 127986.4869 99817.62496 1.470819967 1.646535006 1.267766398 1.128590092 1.262321234 1.568666899 1.356643201 1.282203288 1 16.60700696 7.999996894 0.036703587 2.92E-07 3.385201535 0.263691347 0.166260815 3459.991316 12.53314517 378.2083818 878.5216842 99999284.72 -7.999996894 3.385201244 LS(ph)PANQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSPANQR 7 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LS(1)PANQR;LS(1)PANQR 153.05 0.0018595 657080000 1820760 1582000 1162880 1336810 1347220 1519070 1453570 1828030 1949440 TRUE FALSE 1580141.953 1571607.738 1725252.658 1640353.142 1320412.958 1577509.606 1312603.005 1437120.01 1718979.424 0.919232616 0.914267917 1.003649394 0.954259905 0.768137733 0.917701273 0.763594367 0.836030955 1 20.71312085 3.275185139 24.9949113 0.850478134 0.949439171 0.279814408 0.071898572 206.9976542 141267.1026 0.020159778 0.026025451 1884.452256 -3.275185139 0.098961038 LS(ph)PCLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSPCLHR 7 0 Q9C073;D6RJ87;D6RFX7;K7ENS5 Q9C073 FAM117A Protein FAM117A 1 LS(1)PCLHR 120.15 0.0029763 104680000 160030 157020 130010 149010 164700 157490 150510 181190 286950 TRUE FALSE 138881.63 155988.5253 192883.2709 182844.998 161422.7922 163548.7422 135913.5634 142443.9285 253027.0979 0.548880461 0.616489406 0.762302822 0.722630104 0.637966422 0.646368486 0.537150228 0.562959184 1 17.94893237 1.232265946 24.99989827 1.000000614 0.629380078 0.725133354 0.07171768 128.2574808 509337.448 0.178747853 0.019595434 17.0712745 -1.232265946 -0.370620536 DKPSVEPVEEYDYEDLKESSNSVS(ph)NHQLSGFDQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 DKPSVEPVEEYDYEDLKESSNSVSNHQLSGFDQAR 35 2 Q9Y450;E9PN23;G5E991;E9PLR4;E9PMN1;Q9Y450-2 Q9Y450;Q9Y450-2 HBS1L HBS1-like protein 1 DKPSVEPVEEYDYEDLKES(0.07)S(0.07)NS(0.383)VS(0.477)NHQLSGFDQAR 125.07 2.46E-08 94727000 9246.4 12123 9718.7 15008 22546 22678 32591 28826 35128 TRUE FALSE 8024.464813 12043.36321 14418.69583 18415.79578 22097.37871 23550.43733 29430.32984 22661.78422 30975.20786 0.259060887 0.388806534 0.465491495 0.594533405 0.713389199 0.760299574 0.950125338 0.7316104 1 14.91882634 3.885145412 0.511000908 0.91400273 0.09830462 0.906054179 0.071778469 0.589929326 0.260778668 0.071331704 0.286817466 7676.184622 -3.885145412 -0.81569811 down LS(ph)PDFAEELR ddPTM_MDA-MB-175_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 205.46 1.76E-07 126305000 179409 138291 133675 235920 171272 157805 148424 192843 474170 TRUE FALSE 155699.6461 137382.5573 198320.6771 289489.2418 167864.0223 163875.8605 134029.8633 151605.0252 418114.1628 0.372385487 0.328576665 0.474321835 0.692368897 0.401478919 0.391940468 0.320558056 0.362592418 1 18.67353739 1.235304356 24.99938529 1.000000805 0.417065 0.746834196 0.106485316 50.66217473 388884.1507 0.196167631 0.02805595 17.19112729 -1.235304356 -0.582935805 LS(ph)PENNQVLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LSPENNQVLTK 11 0 Q16514-2;Q16514 Q16514-2 TAF12 Transcription initiation factor TFIID subunit 12 1 LS(1)PENNQVLTK;LS(1)PENNQVLTK;LS(1)PENNQVLTK;LS(1)PENNQVLTK;LS(1)PENNQVLTK;LS(1)PENNQVLTK 230.23 2.05E-12 3127840000 2702000 2092530 2025950 2463220 2389930 1768000 2518490 3041450 5445120 TRUE FALSE 2344923.854 2078784.033 3005706.196 3022531.749 2342375.069 1836016.104 2274247.227 2391059.586 4801404.117 0.488382939 0.432953357 0.626005669 0.629509967 0.487852097 0.382391496 0.473662948 0.497991739 1 22.19502494 1.23826237 24.99999997 1.000000555 0.502263882 0.809181419 0.075948508 3.26864427 273526.2081 0.113146447 0.019967116 17.30861708 -1.23826237 -0.497736673 LS(ph)PEVAPPAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSPEVAPPAHR 11 0 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 LS(1)PEVAPPAHR;LS(1)PEVAPPAHR 112.44 0.00098295 439070000 462270 379030 303210 367520 432990 367280 370390 457590 898390 TRUE FALSE 401179.8483 376540.127 449843.3702 450971.0332 424374.3461 381409.4993 334469.6348 359737.9395 792183.3576 0.506422969 0.475319411 0.567852588 0.569276076 0.535702173 0.481466185 0.422212398 0.454109438 1 19.59547487 1.235407692 24.99999913 1.000000686 0.499411946 0.917535706 0.046958471 26.86546055 212982.8541 0.091973053 0.013265244 17.19521821 -1.235407692 -0.500588741 LS(ph)PGESAYQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSPGESAYQK 10 0 A0A0G2JHC2;Q6NYC8-2;Q6NYC8 A0A0G2JHC2 PPP1R18 Phostensin 1 LS(1)PGESAYQK;LS(1)PGESAYQK;LS(1)PGESAYQK;LS(1)PGESAYQK 253.76 4.53E-17 806590000 1568180 1393350 1068260 1426220 1445070 1163070 1614040 1878610 1971210 TRUE FALSE 1360941.04 1384196.992 1584874.109 1750065.049 1416315.934 1207814.056 1457510.649 1476883.871 1738175.799 0.782970883 0.796350399 0.911803115 1.006840073 0.814828934 0.694874509 0.838528905 0.849674625 1 20.72914257 1.231418252 4.198969918 1.017443428 0.83758089 0.284525223 0.081468376 0.35364781 11.62899435 0.195647993 0.022154009 17.03798582 -1.231418252 -0.179862538 LS(ph)PGSYPTVIQQQNATSQR ddPTM_MDA-MB-175_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 301.82 5.70E-50 578260000 202595 242801 149316 208905 274070 233707 250405 313550 279570 TRUE FALSE 175821.5574 241206.0242 221525.717 256340.0732 268616.5432 242697.8595 226120.7616 246499.7725 246519.5531 0.713215464 0.978445812 0.89861317 1.039836678 1.089635852 0.984497402 0.917252846 0.999919761 1 17.91134256 5.293708506 1.39385965 0.99531788 1.56E-10 0.715343961 0.054460087 2.941527441 1.736755748 0.015625188 6.014669509 196656.5906 -5.293708506 -0.995317879 LS(ph)PHKVQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 LSPHKVQGR 9 1 Q9GZP8-2;Q9GZP8 Q9GZP8-2 IMUP Immortalization up-regulated protein 1 LS(1)PHKVQGR;LS(1)PHKVQGR;LS(1)PHKVQGR;LS(1)PHKVQGR;LS(1)PHKVQGR;LS(1)PHKVQGR;LS(1)PHKVQGR;LS(1)PHKVQGR;LS(1)PHKVQGR 98.156 0.0037471 34874420000 11470940 9752350 8344870 9160670 9986660 8425950 11487270 12863460 7994770 TRUE FALSE 9955026.215 9688286.171 12380477.04 11240740.14 9787945.005 8750101.749 10373236.32 10112709.18 7049637.398 1.412133086 1.374295673 1.75618636 1.594513235 1.388432405 1.241213023 1.47145672 1.434500615 1 22.74911762 3.089184696 5.094504855 1.325903449 1.537389574 0.3265454 0.163344284 0.289399824 12.62665541 0.051548646 0.058717657 1227.961345 -3.089184696 0.211486124 LS(ph)PIMTEQDDLGEGDVHSMVYPPSAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSPIMTEQDDLGEGDVHSMVYPPSAAK 27 0 Q12778 Q12778 FOXO1 Forkhead box protein O1 1 LS(0.984)PIMT(0.016)EQDDLGEGDVHSMVYPPSAAK 67.809 0.015069 50801000 51454 35751 31796 36395 34335 29480 40206 46975 74394 TRUE FALSE 44654.22353 35516.14933 47172.65195 44659.04101 33651.80068 30614.11468 36306.82831 36929.76181 65599.22607 0.680712658 0.541411103 0.719103788 0.680786096 0.512990819 0.466684083 0.553464278 0.562960328 1 16.00139117 1.236628073 24.96559036 1.000000533 0.585935987 0.71761598 0.080842518 28.610999 369508.758 0.131444916 0.020810995 17.24360528 -1.236628073 -0.414064546 LS(ph)PIPEEVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LSPIPEEVPK 10 0 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 LS(1)PIPEEVPK;LS(1)PIPEEVPK;LS(1)PIPEEVPK;LS(1)PIPEEVPK;LS(1)PIPEEVPK;LS(1)PIPEEVPK 182.35 1.88E-06 4175180000 6266300 4905130 4860120 5476280 5198950 4095280 6292590 7435760 10370890 TRUE FALSE 5438192.578 4872907.878 7210490.288 6719753.074 5095501.067 4252828.072 5682335.59 5845680.589 9144855.199 0.594672355 0.53285785 0.788475064 0.734812408 0.55719866 0.465051439 0.621369663 0.639231618 1 23.1245289 1.232581062 4.479867843 1.035163105 0.615227404 0.62837764 0.092814483 0.152183388 6.336420457 0.205922401 0.024956978 17.08366559 -1.232581062 -0.419935701 LS(ph)PISHGNTIALFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSPISHGNTIALFFR 15 0 Q9BQ70 Q9BQ70 TCF25 Transcription factor 25 1 LS(0.996)PIS(0.004)HGNTIALFFR;LS(1)PISHGNTIALFFR;LS(0.998)PIS(0.002)HGNTIALFFR 195.25 1.18E-08 1083820000 277863 318057 247111 334849 355392 292687 315192 437985 565192 TRUE FALSE 241142.7005 315967.6626 366614.7061 410881.5833 348320.3945 303946.8583 284624.7284 344325.3162 498375.6456 0.483857313 0.63399499 0.735619225 0.824441537 0.698911348 0.609875023 0.57110481 0.690895149 1 18.92687404 -1.999999349 0.040444858 1.778139175 1.48E-06 0.23448131 0.124542546 3729.972396 14.8521025 517.6408352 204.5846023 0.010000015 1.999999349 -1.778137696 LS(ph)PLPVVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSPLPVVSR 9 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 LS(1)PLPVVSR;LS(1)PLPVVSR;LS(1)PLPVVSR;LS(1)PLPVVSR 172.21 5.91E-05 978270000 1099840 741786 823206 1255750 990020 903587 749557 1061502 2918840 TRUE FALSE 954493.3574 736913.1589 1221311.175 1540887.23 970320.5389 938348.5766 676865.0775 834508.0579 2573778.06 0.370853016 0.286315736 0.474520781 0.598686909 0.377002413 0.364580222 0.262985021 0.324234661 1 21.29545622 1.235426298 24.98536667 1.000000856 0.379983471 0.803951771 0.095840309 41.38475329 329842.1754 0.177734464 0.025678325 17.19595493 -1.235426298 -0.620017386 LS(ph)PPPEELPAS(ph)PLPEALHLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSPPPEELPASPLPEALHLSR 21 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 2 LS(1)PPPEELPAS(1)PLPEALHLSR 90.946 0.0011027 14125000 9114.8 9896.5 6282.8 11273 12203 9796.7 8515.3 11735 27107 TRUE FALSE 7910.256086 9831.48924 9321.183095 13832.70695 11960.18417 10173.58539 7689.487517 9225.561572 23902.44134 0.330939253 0.411317367 0.389967826 0.578715235 0.500375004 0.425629552 0.321703018 0.385967334 1 14.54487036 1.236596246 24.99978104 1.000000736 0.418792292 0.854177418 0.075562011 20.22439659 257318.8036 0.126264459 0.019937648 17.24234164 -1.236596246 -0.581208444 LS(ph)PSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSPSFR 6 0 B4DF95;Q15735 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 LS(0.944)PS(0.056)FR;LS(0.953)PS(0.047)FR 169.57 0.0062989 1190680000 1190140 1200620 904890 1043310 1286690 1329380 1302800 1399070 1385640 TRUE FALSE 1032859.984 1192733.048 1342497.831 1280209.481 1261087.386 1380522.109 1176454.657 1099889.768 1221831.218 0.845337694 0.976184788 1.098758823 1.047779319 1.032128962 1.129879552 0.962861842 0.900197795 1 20.22061358 2.017513627 24.91856227 0.939538027 1.026575039 0.133927429 0.079548899 366.3613305 521260.4889 0.033157653 0.022349775 104.1150775 -2.017513627 0.087037012 LS(ph)PSTSGPHSHDYLPQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSPSTSGPHSHDYLPQER 18 0 Q5JR04;Q9HCE1 Q5JR04 MOV10 Putative helicase MOV-10 1 LS(0.978)PS(0.02)T(0.002)S(0.001)GPHSHDYLPQER 91.337 0.0042439 252230000 102640 110650 58340 71427 109480 96498 94182 114070 128400 TRUE FALSE 89075.86394 109923.1329 86553.41914 87645.59204 107301.5622 100210.3405 85048.24414 89677.01819 113220.6983 0.786745403 0.970874889 0.764466396 0.774112803 0.947720371 0.885088522 0.751172228 0.792054983 1 16.7887782 4.221409359 24.99526932 0.837773721 0.878810291 0.018247353 0.092263436 904.5439728 1318235.652 0.023347526 0.048792693 16649.81297 -4.221409359 0.04103657 LS(ph)PSWNPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSPSWNPK 8 0 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 1 LS(0.994)PS(0.006)WNPK;LS(0.933)PS(0.067)WNPK;LS(1)PSWNPK 182.16 0.0002413 1860890000 1721030 1682380 1577530 1970850 2038920 1661460 2345170 2721810 4010790 TRUE FALSE 1493591.525 1671328.335 2340428.785 2418361.615 1998349.481 1725377.441 2117735.774 2139772.113 3536638.975 0.422319478 0.472575331 0.661766384 0.683802229 0.565041978 0.48785795 0.59879897 0.60502984 1 21.75394752 1.186906617 2.91687697 1.127079142 0.560696249 0.742507862 0.081369476 0.287442054 2.664326383 0.415322174 0.022488582 15.37823937 -1.186906617 -0.566382893 LS(ph)PTPSMQDGLDLPSETDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSPTPSMQDGLDLPSETDLR 20 0 Q9UK58;Q9UK58-6;Q9UK58-5;Q9UK58-4 Q9UK58 CCNL1 Cyclin-L1 1 LS(0.999)PT(0.001)PSMQDGLDLPSETDLR;LS(0.998)PT(0.002)PSMQDGLDLPSETDLR;LS(0.988)PT(0.011)PS(0.001)MQDGLDLPSETDLR 272.13 2.13E-44 242881000 350818 280032 245116 314154 321723 309610 312249 378434 594649 TRUE FALSE 304456.5124 278192.4514 363654.9175 385487.4672 315321.3417 321520.897 281967.14 297508.8341 524350.2726 0.580635747 0.530546976 0.693534335 0.735171673 0.601356304 0.613179613 0.537745768 0.567385676 1 19.00017135 1.235088962 24.99995611 1.000000551 0.606567308 0.787790561 0.064028112 49.21721816 354364.384 0.121158367 0.017045681 17.18260326 -1.235088962 -0.393433242 GYYSPYSVS(ph)GSGSTAGS(ph)R ddPTM_MDA-MB-175_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(0.01)VS(0.99)GSGS(0.177)T(0.022)AGS(0.801)R;GYYSPYS(0.002)VS(0.996)GS(0.002)GS(0.055)T(0.135)AGS(0.809)R 214.94 1.43E-18 400710000 1426190 1107370 613800 417070 526570 691510 508270 492120 526310 TRUE FALSE 1237715.378 1100095.614 910635.733 511772.118 516092.2872 718112.8372 458978.0536 386883.9677 464090.2314 2.666971408 2.370434754 1.962195434 1.102742707 1.112051606 1.547356071 0.988984518 0.833639541 1 18.82404581 3.991450439 1.576533264 1.056399455 2.651585283 0.906915143 0.1929086 0.125605636 0.588257322 0.0640646 0.198937741 9805.064141 -3.991450439 1.595185828 up LS(ph)S(ph)Y(ph)T(ph)LRILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSSYTLRILR 10 1 Q96DU3-2;Q96DU3 Q96DU3-2 SLAMF6 SLAM family member 6 4 LS(1)S(1)Y(1)T(1)LRILR 48.277 0.071715 419340000 9888.2 7613.8 7054.1 6832.7 18128 14716 5763.9 12049 24799 TRUE FALSE 8581.449316 7563.784446 10465.48635 8384.168966 17767.28827 15282.13404 5204.917865 9472.415115 21867.29047 0.392433133 0.345894909 0.478590906 0.383411423 0.812505248 0.698858144 0.23802299 0.433177358 1 14.41648685 LS(ph)SDSFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSSDSFAR 8 0 A0A087WSV0;Q9HB09-3;Q9HB09 A0A087WSV0 BCL2L12 Bcl-2-like protein 12 1 LS(0.996)S(0.004)DSFAR;LS(0.962)S(0.038)DSFAR 160.82 0.00036831 501320000 766020 822090 615850 863790 912220 921580 664140 1033270 1403200 TRUE FALSE 664788.5162 816689.6367 913677.1199 1059926.722 894068.6067 957033.7789 599731.805 812313.2514 1237315.295 0.537283035 0.660049739 0.738435162 0.8566343 0.722587533 0.773476076 0.484704107 0.656512738 1 20.23878175 4.618886604 2.629838518 0.728705045 0.522588175 0.200034613 0.132114319 0.691345148 7.305223184 0.034748441 0.274907301 41580.20285 -4.618886604 -0.20611687 LS(ph)SFTSYENPT ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSSFTSYENPT 11 0 Q13882 Q13882 PTK6 Protein-tyrosine kinase 6 1 LS(0.269)S(0.269)FT(0.205)S(0.159)Y(0.098)ENPT 60.973 0.094677 72431000 118330 137520 102110 116430 165930 170800 174960 162430 194500 TRUE FALSE 102692.3907 136616.6221 151490.7375 142867.211 162628.3176 177370.7865 157992.4061 127695.6085 171506.4316 0.598766995 0.796568507 0.88329479 0.833013723 0.948234513 1.034193207 0.921203973 0.744552886 1 17.38790315 5.050538205 1.167537083 0.904071877 0.245293781 0.606443942 0.080527979 2.323776062 1.652932587 0.025996739 2.213573666 112340.9793 -5.050538205 -0.658778096 LS(ph)SGFDDIDLPSAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LSSGFDDIDLPSAVK 15 0 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 LS(0.973)S(0.027)GFDDIDLPSAVK;LS(0.981)S(0.019)GFDDIDLPSAVK;LS(0.5)S(0.5)GFDDIDLPSAVK;LS(0.73)S(0.27)GFDDIDLPSAVK;LS(0.979)S(0.021)GFDDIDLPSAVK 209.13 1.90E-11 166491000 439770 384207 270009 424924 413480 289793 529613 586080 694637 TRUE FALSE 381653.2803 381683.1189 400586.2555 521409.4888 405252.557 300941.5242 478251.2128 460751.3529 612517.8052 0.623089283 0.623137998 0.653999365 0.851256052 0.661617595 0.491318818 0.780795609 0.75222524 1 19.22439226 1.000896585 1.342683848 1.328114677 0.663616273 0.555169074 0.094058222 1.867705038 1.888692344 1.998767757 0.028452685 10.02066595 -1.000896585 -0.664498404 LS(ph)SLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSSLPR 6 0 Q63ZY3-3;Q63ZY3;Q63ZY3-2;K7ES05 Q63ZY3-3 KANK2 KN motif and ankyrin repeat domain-containing protein 2 1 LS(0.742)S(0.258)LPR 91.906 0.049679 109250000 187170 216810 175060 196830 290460 288400 271200 305520 329200 TRUE FALSE 162435.0103 215385.7608 259719.6015 241523.2599 284680.4143 299494.9346 244899.0657 240186.9256 290282.351 0.559575908 0.741987103 0.894713718 0.832028744 0.980701766 1.03173663 0.843658131 0.827425177 1 18.14709733 4.693543931 1.342513176 0.914197913 0.421344221 0.73892042 0.070445622 0.682071628 1.162933227 0.021742118 0.449109579 49379.18652 -4.693543931 -0.492853692 GYYSPYSVS(ph)GSGS(ph)TAGSR ddPTM_MDA-MB-175_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 GYYSPYS(0.069)VS(0.929)GS(0.007)GS(0.561)T(0.425)AGS(0.009)R 121.77 5.49E-05 76681000 378060 297990 160050 117290 149790 190580 132310 131360 155740 TRUE FALSE 328098.4131 296032.4841 237450.7153 143922.4872 146809.4721 197911.7359 119478.5966 103269.6862 137328.5946 2.389148553 2.155650721 1.729069725 1.048015437 1.069037898 1.441154601 0.870019801 0.751989682 1 17.06727253 4.049075042 1.265024805 0.971622348 2.477989831 0.891734555 0.181923897 0.183199819 0.508920125 0.064472052 0.263518371 11196.31328 -4.049075042 1.506367483 up LS(ph)SPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSSPVK 6 0 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 LS(0.755)S(0.245)PVK 98.997 0.041224 228120000 1216200 1016800 866840 1126500 835240 747740 1211800 1472800 2109800 TRUE FALSE 1055476.089 1010120.574 1286046.723 1382289.042 818620.3581 776506.0417 1094279.823 1157853.181 1860381.847 0.56734379 0.54296411 0.691281053 0.743013615 0.440028137 0.417390679 0.588201731 0.622373941 1 20.82716734 1.205743103 3.022961609 1.10362307 0.570728088 0.651981 0.097860595 0.307376274 3.314537249 0.417775879 0.027329771 16.05990984 -1.205743103 -0.532894982 TVAISDAAQLPHDYCT(ph)TPGGTLFST(ph)TPGGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDYCT(0.903)T(0.097)PGGTLFS(0.2)T(0.625)T(0.175)PGGTR 221.47 9.83E-35 14570000000 190960 252900 225420 332440 505750 580700 503270 536380 517240 TRUE FALSE 165724.1522 251238.6832 334433.866 407925.583 495686.5645 603039.9048 454462.9529 421679.3111 456092.4764 0.36335647 0.550850313 0.733258897 0.894392265 1.086811535 1.322187793 0.996427208 0.924547834 1 18.79896685 4.05883281 1.303560132 1.052620837 0.364188712 0.838102142 0.109371618 0.238170311 0.707211974 0.039295578 0.159291807 11450.72038 -4.05883281 -0.688432125 down LS(ph)SSASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSSSASR 7 0 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 LS(0.44)S(0.428)S(0.132)ASR 71.501 0.056795 108870000 302260 294350 166240 214140 187260 276590 278640 282710 374640 TRUE FALSE 262315.5752 292416.3955 246634.22 262763.7599 183533.8924 287230.5963 251617.5357 222254.6666 330350.486 0.794052336 0.885170169 0.746583494 0.795409031 0.555573248 0.869472298 0.761668429 0.672784439 1 18.33363794 1.225830198 24.96467988 1.00000058 0.757688375 0.390773902 0.094098543 652.1694719 1278841.028 0.4015846 0.022644051 16.8201629 -1.225830198 -0.242312205 LS(ph)STSSEETQLFHIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 1 LS(0.583)S(0.409)T(0.007)S(0.001)S(0.001)EETQLFHIPR 187.39 8.67E-10 92706000 25612 31400 23694 29013 39238 37518 24912 43097 38764 TRUE FALSE 22227.30931 31193.73133 35152.49765 35600.84509 38457.24057 38961.34174 22496.03807 33881.04193 34181.36408 0.650275666 0.912594689 1.0284112 1.041527922 1.125093793 1.13984163 0.658137517 0.991213863 1 15.06092235 4.707152015 2.905967896 0.989797732 0.604117946 0.406284515 0.131427039 0.397729155 5.014976742 0.034469444 0.346797802 50950.91818 -4.707152015 -0.385679786 LS(ph)TGSFPEDLLESDSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LSTGSFPEDLLESDSSR 17 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 LS(0.988)T(0.011)GS(0.001)FPEDLLESDSSR;LS(0.988)T(0.011)GSFPEDLLESDSSR;LS(0.993)T(0.007)GSFPEDLLESDSSR;LS(0.992)T(0.008)GSFPEDLLESDSSR;LS(0.992)T(0.008)GSFPEDLLESDSSR;LS(0.991)T(0.009)GSFPEDLLESDSSR;LS(0.986)T(0.012)GS(0.002)FPEDLLESDSSR;LS(0.959)T(0.018)GS(0.023)FPEDLLESDSSR 271.19 1.39E-35 191341000 314016 310563 233225.9 277009 338532 331944 318654 369580 460229 TRUE FALSE 272517.99 308522.8912 346014.7253 339908.1273 331795.8755 344714.1005 287750.9841 290548.1931 405821.2519 0.671522225 0.760243308 0.852628402 0.837580895 0.817591178 0.849423481 0.709058441 0.715951153 1 18.63048489 4.608808907 3.204774591 0.810831271 0.667897972 0.260300606 0.081256188 0.436337432 7.286385041 0.020800448 0.127239238 40626.45298 -4.608808907 -0.142933299 LS(ph)TPQKK ddPTM_MDA-MB-175_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(0.658)T(0.342)PQKK 79.489 0.019898 421140000 691620 414930 284090 286170 330390 281660 467690 601530 426820 TRUE FALSE 600220.6647 412204.2975 421476.8742 351149.2723 323815.8854 292495.6425 422333.4958 472897.4906 376361.8258 1.594796878 1.095234079 1.119871478 0.933009801 0.860384511 0.777166074 1.122147537 1.256496962 1 18.52176078 4.973739523 1.747218046 1.018799714 2.118474939 0.639932307 0.136766762 1.483468279 2.719973946 0.042822123 3.285457294 94132.48491 -4.973739523 1.099675226 LS(ph)VS(ph)SHILER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSVSSHILER 10 0 A0A0C4DGQ4;Q86W25 A0A0C4DGQ4 NLRP13 "NACHT, LRR and PYD domains-containing protein 13" 2 LS(0.667)VS(0.667)S(0.667)HILER 47.261 0.097071 677310000 715760 662910 446010 542840 581700 680440 578160 665270 658060 TRUE FALSE 621170.5025 658555.3006 661701.9278 666100.1188 570125.3081 706616.9671 522090.1322 523007.1876 580264.8965 1.070494711 1.134921834 1.140344577 1.147924203 0.982525932 1.217748948 0.899744471 0.901324879 1 19.14635213 2.222978798 24.99975494 0.925532648 1.113072602 0.62825619 0.065865778 139.1092267 223187.637 0.025302741 0.017126757 167.1009035 -2.222978798 0.187539954 LS(ph)WGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSWGYR 6 0 Q8N1Q1;Q9BTY2 Q8N1Q1;Q9BTY2 CA13;FUCA2 Carbonic anhydrase 13;Plasma alpha-L-fucosidase 1 LS(1)WGYR;LS(1)WGYR 116.73 0.024472 313460000 509730 593340 421310 453600 608610 587150 599800 686230 1183600 TRUE FALSE 442367.889 589442.3105 625056.9252 556596.8128 596499.8517 609738.0404 541631.4883 539485.0547 1043676.156 0.42385551 0.564775105 0.598899305 0.533304138 0.571537299 0.584221491 0.518965088 0.516908479 1 19.99324269 1.236655196 24.99767669 1.000000578 0.541998319 0.897311571 0.04899571 14.53310082 190610.424 0.073735301 0.011695074 17.24468224 -1.236655196 -0.458002259 LS(ph)YASAESLETMSEAELPLGFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSYASAESLETMSEAELPLGFSR 23 0 A0A087X165;Q9C0H9;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 LS(0.336)Y(0.275)AS(0.331)AES(0.058)LETMSEAELPLGFSR 139.17 5.09E-07 13934000 30166 19162 14432 18788 19157 23526 19897 21045 19888 TRUE FALSE 26179.48667 19036.12356 21411.36347 23054.10256 18775.81318 24431.06044 17967.392 16544.69052 17536.8633 1.492826067 1.085491929 1.220934617 1.314608101 1.070648317 1.393126013 1.024549927 0.94342359 1 14.09810311 2.098024555 6.684684116 0.972612055 1.245923917 0.505635751 0.127486501 0.161936331 9.432108515 0.048428224 0.032454988 125.3212031 -2.098024555 0.273311863 LS(ph)YSDKNLIDSMDQSAFAGFSFVNPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSYSDKNLIDSMDQSAFAGFSFVNPK 26 1 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 1 LS(0.994)YS(0.006)DKNLIDSMDQSAFAGFSFVNPK;LS(0.962)YS(0.038)DKNLIDSMDQSAFAGFSFVNPK 226.1 9.89E-35 953008000 756472 564632 549783 560009 535003 456184 797691 923480 584402 TRUE FALSE 656502.3085 560922.8952 815659.8977 687167.6027 524357.487 473733.6937 720331.0496 726000.9885 515314.6613 1.273983369 1.088505601 1.582838524 1.333491271 1.017548163 0.919309558 1.397846993 1.40884986 1 18.97509411 LSAEEAAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSAEEAAHR 9 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7;H7C408 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 0 124.74 0.00052108 83314000 139210 144600 96788 102480 157020 175700 119160 161370 152910 FALSE TRUE 120813.0458 143650.1131 143595.0005 125749.6503 153895.6092 182459.2927 107603.8815 126862.2813 134833.154 0.896018837 1.065391625 1.064982879 0.932631527 1.141378101 1.353222759 0.798052099 0.940883436 1 17.04081576 LSAEKVEIATLTR ddPTM_MDA-MB-175_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 ; 144.18 3.76E-05 1462220000 1445530 1413080 639190 843400 1338240 1152490 1676590 1934190 456580 FALSE TRUE 1254499.548 1403797.384 948304.422 1034906.861 1311611.642 1196827.036 1513994.56 1520578.52 402603.6325 3.115966789 3.486797612 2.355429374 2.570535328 3.257823666 2.972717927 3.760508941 3.776862396 1 18.61900066 3.203069009 24.98420034 3.117968733 2.887742554 0 0.827874058 1057.759566 744602.9129 0.2514571 0.285135478 1596.132752 -3.203069009 -0.230226178 LSAIYGGTYMLNKPIEEIIVQNGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSAIYGGTYMLNKPIEEIIVQNGK 24 1 P50395;P50395-2;Q5SX87;Q5SX91 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ; 249.34 2.81E-38 614680000 479660 367050 267950 321390 326870 281160 423800 536520 445380 FALSE TRUE 416271.7157 364638.8244 397531.5162 394366.5116 320365.9265 291976.4071 382699.9412 421789.3732 392727.6838 1.059950019 0.928477516 1.012231968 1.004172937 0.815745718 0.743457666 0.974466423 1.073999595 1 18.58316977 1.996387124 24.99339669 1.036869761 0.923777496 0.186649651 0.094149277 233.8497989 1617743.646 0.042056139 0.027692004 99.17155527 -1.996387124 -0.113092265 LSAKPAPPKPEPKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSAKPAPPKPEPKPK 15 3 P05204 P05204 HMGN2 Non-histone chromosomal protein HMG-17 0 94.01 0.0020309 1755100000 4347000 2955500 1963700 1955600 2235000 1219700 4405700 4843800 645800 FALSE TRUE 3772532.936 2936085.126 2913351.888 2399648.869 2190527.873 1266622.648 3978435.892 3807991.064 569454.2597 6.624821699 5.155963057 5.116041962 4.213944893 3.84671435 2.224274604 6.986401145 6.687088558 1 19.11922044 4.829252862 1.405005903 4.534891707 7.784003765 0.139835651 1.803266957 3.802442732 5.804414319 0.5313901 18.4833532 67492.08769 -4.829252862 3.249112059 LSALGNVTTCNDYVALVHPDLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSALGNVTTCNDYVALVHPDLDR 23 0 P56537 P56537 EIF6 Eukaryotic translation initiation factor 6 0 ; 192.58 8.72E-18 215132000 99374 79631 64257 74065 97940 110861 80796 88944 146780 FALSE TRUE 86241.47412 79107.89872 95331.90013 90882.59026 95991.18562 115125.8944 72960.41636 69924.01776 129427.8356 0.666328643 0.611212405 0.736564122 0.70218736 0.741657968 0.889498722 0.563715031 0.540254864 1 16.9817884 4.23535675 24.9841374 0.716113859 0.638770518 0.066608384 0.136458789 265.9534148 2074004.941 0.035713273 0.079614548 17193.2014 -4.23535675 -0.07734334 LSALHLEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSALHLEVR 9 0 A0A0C4DGG1;Q9UKS6;E9PIY1;E9PJ75;E9PNM9 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 0 112.11 0.0020162 232630000 164750 212320 100120 160520 247200 269980 196780 257280 262370 FALSE TRUE 142977.8701 210925.2559 148538.3669 196968.5194 242281.2036 280366.3053 177696.3059 202262.6742 231352.9175 0.618007638 0.911703463 0.642042333 0.851376855 1.047236431 1.211855499 0.768074627 0.874260313 1 17.81973577 3.475229491 6.716939725 0.962025673 0.742774739 0.415606837 0.137729986 0.158269982 37.71664171 0.040587703 0.055179386 2986.960582 -3.475229491 -0.219250934 LSAS(ph)SEDISER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSASSEDISER 11 0 Q13233 Q13233 MAP3K1 Mitogen-activated protein kinase kinase kinase 1 1 LSAS(0.94)S(0.06)EDISER;LSAS(0.698)S(0.302)EDISER;LS(0.001)AS(0.813)S(0.187)EDISER 240.65 1.13E-15 609020000 503886 427149 281098 351921 412605 395032 424808 491907 415528 TRUE FALSE 437296.1884 424343.0301 417037.933 431830.0418 404394.9677 410229.1367 383610.1855 386716.5161 366404.7532 1.193478481 1.158126434 1.1381892 1.178560153 1.103683738 1.119606482 1.046957449 1.055435315 1 18.48307869 0.51577181 0.275529242 0.736900032 1.204449796 0.886951935 0.020654123 6.044519308 0.346171271 1.032551762 0.064372885 3.279229487 -0.51577181 0.467549764 LSASETSLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSASETSLHR 10 0 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ; 142.83 3.51E-05 274019000 137036 154698 57106 81730 156794 144576 162288 156140 137124 FALSE TRUE 118926.3454 153681.7787 84722.65261 100288.0457 153674.1062 150137.9323 146549.3347 122750.6761 120913.3569 0.98356665 1.27100746 0.700688946 0.829420737 1.270944005 1.241698486 1.212019403 1.015195337 1 16.8836141 3.239969542 24.9999939 1.140864376 0.951839139 0.265952599 0.166240985 60.2999414 1069949.052 0.051951874 0.063477586 1737.678957 -3.239969542 -0.189025237 LSASTASELS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSASTASELSPK 12 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;H0YF21 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 LSASTASELS(1)PK;LSASTASELS(1)PK 162.1 6.67E-05 182760000 408620 391520 333120 313160 435890 331100 470690 499800 482020 TRUE FALSE 354619.8317 388948.0793 494217.9462 384267.7644 427216.6418 343837.6313 425042.5562 392921.6594 425036.1447 0.834328647 0.915094126 1.162766867 0.904082557 1.005130145 0.808960921 1.000015085 0.924442931 1 18.69722601 3.154015726 0.002611678 1.756252369 0.146558016 0.005783093 0.100020087 794780.2463 2624.713123 808134.029 809573.3644 1425.659218 -3.154015726 -1.609694353 LSCS(ph)ELSLYQPLQNSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSCSELSLYQPLQNSSK 17 0 Q12923-3;Q12923;Q12923-4 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 LS(0.002)CS(0.998)ELSLYQPLQNSSK 173.58 1.19E-13 0 78751 88540 57497 59248 84375 76932 93078 97777 118810 TRUE FALSE 68343.85582 87958.37491 85302.74152 72701.16395 82696.10258 79891.62382 84051.30989 76868.14945 104764.4171 0.652357524 0.839582535 0.814233915 0.693949014 0.789352958 0.762583576 0.802288718 0.733723831 1 16.67678927 1.233972296 24.99555877 1.000000354 0.764623025 0.638643358 0.056438494 86.59654654 471687.8173 0.099692301 0.012760244 17.13847976 -1.233972296 -0.235377329 LSCS(ph)LEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LSCSLEDLR 9 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 LS(0.001)CS(0.999)LEDLR;LSCS(1)LEDLR;LS(0.001)CS(0.999)LEDLR;LS(0.001)CS(0.999)LEDLR;LSCS(1)LEDLR;LSCS(1)LEDLR 158.08 7.04E-05 6807280000 7952220 7183040 5303130 6640670 7014490 6853840 6450350 7880860 10922100 TRUE FALSE 6901313.979 7135854.137 7867741.406 8148535.62 6874915.373 7117511.66 5824796.05 6195599.418 9630901.78 0.716580247 0.740933123 0.816926762 0.846082309 0.713839216 0.739028579 0.604802767 0.643304185 1 23.19923946 3.143749218 24.99998268 0.717869491 0.779991997 0.009498163 0.110395513 46.8140143 12313.50214 0.03378383 0.038307267 1392.35256 -3.143749218 0.062122506 LSCS(ph)LEDLRSESVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSCSLEDLRSESVDK 15 1 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 LS(0.001)CS(0.999)LEDLRSESVDK;LS(0.028)CS(0.972)LEDLRSESVDK 186.45 2.31E-07 781320000 1844810 1637770 826860 855450 1418270 1142710 1771690 2071280 415490 TRUE FALSE 1601013.684 1627011.381 1226732.262 1049692.997 1390049.202 1186670.793 1599871.776 1628352.891 366371.2455 4.369921777 4.440881758 3.348331171 2.865107483 3.794100161 3.238984521 4.366804972 4.444543371 1 18.48294675 4.241186804 24.72129748 3.454763283 4.405402189 0.172312259 0.963823242 113.1991257 1065518.38 0.240891176 0.579607793 17425.56241 -4.241186804 0.950638906 LSDDFDS(ph)PVKGPLCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSDDFDSPVKGPLCK 15 1 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 LSDDFDS(1)PVKGPLCK;LSDDFDS(1)PVKGPLCK;LSDDFDS(1)PVKGPLCK 191.35 1.08E-07 1472600000 1461900 1277510 937430 1022690 1196350 830010 1477660 1895580 1386480 TRUE FALSE 1268706.211 1269117.953 1390774.284 1254907.395 1172544.976 861941.0218 1334356.761 1490224.968 1222571.914 1.037735447 1.03807223 1.137580757 1.026448736 0.959080576 0.705022757 1.091434169 1.218926226 1 20.2214879 2.015667828 24.99999478 1.134124667 0.986227545 0.169444279 0.122411099 352.417825 562325.134 0.05244581 0.035346551 103.6735162 -2.015667828 -0.147897122 LSDETLIDIMTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSDETLIDIMTR 12 0 P19367-4;P19367-2;P19367;P19367-3;B1AR62 P19367-4 HK1 Hexokinase-1 0 ;;; 276 1.77E-27 217196000 535530 475677 287653 395743 439313 516416 365972 494036 483139 FALSE TRUE 464758.3536 472552.2465 426762.9529 485602.4967 430571.5308 536282.8577 330480.0918 388390.246 426022.8578 1.090923515 1.109218057 1.001737219 1.139850803 1.010677063 1.258812404 0.77573324 0.911665275 1 18.70057131 2.230615531 25 0.894102133 1.095233656 0.546014223 0.08843603 128.9299664 405686.9654 0.033625236 0.023129349 170.06523 -2.230615531 0.201131524 LSDFLITGGGKGS(ph)GFSLDVIDGPISQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSDFLITGGGKGSGFSLDVIDGPISQR 27 1 O43166-3;O43166-2;O43166 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 LSDFLIT(0.002)GGGKGS(0.998)GFSLDVIDGPISQR;LSDFLIT(0.001)GGGKGS(0.523)GFS(0.476)LDVIDGPISQR;LSDFLIT(0.029)GGGKGS(0.787)GFS(0.184)LDVIDGPISQR 193.44 1.48E-18 840175000 1429024 1312122 717788 845741 1155065 1068203 1348022 1547478 760283 TRUE FALSE 1240174.858 1303502.584 1064912.678 1037779.42 1132081.466 1109297.461 1217291.034 1216561.872 670403.2099 1.849893973 1.94435612 1.588465959 1.547992917 1.688657587 1.654672061 1.815759555 1.814671908 1 19.35466953 1.234880612 24.97700424 0.999998942 1.736975092 0.782127972 0.12241961 53.02265119 359820.8315 0.234387708 0.032397484 17.17436197 -1.234880612 0.73697615 LSDGFNGADLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSDGFNGADLR 11 0 A0A087X2I1;P62333;H0YJC0 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ; 152.04 7.71E-05 442490000 944070 914010 585720 805110 1001760 960610 865570 1112780 1244110 FALSE TRUE 819308.7575 908005.8081 868976.1511 987922.5308 981826.9359 997565.2883 781627.1546 874820.6567 1097032.733 0.746840758 0.827692539 0.792115062 0.900540614 0.894984175 0.909330468 0.712492099 0.79744262 1 20.06517514 4.84911414 1.256910405 0.851548094 0.685879236 0.172469514 0.078040422 3.963575294 4.554341204 0.023713285 0.905286458 70650.32112 -4.84911414 -0.165668859 LSDPPTSPSS(ph)PSQMMPHVQTHF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSDPPTSPSSPSQMMPHVQTHF 22 0 Q13496-2;Q13496 Q13496-2 MTM1 Myotubularin 1 LSDPPT(0.001)S(0.003)PS(0.25)S(0.737)PS(0.008)QMMPHVQTHF;LSDPPT(0.001)S(0.004)PS(0.082)S(0.908)PS(0.005)QMMPHVQTHF 183.25 2.79E-17 800520000 234578 244679 133466 170603 268967 263012 245008 309660 209424 TRUE FALSE 203577.923 243071.6875 198010.604 209341.0187 263615.0829 273130.2418 221247.1619 243441.6188 184666.1333 1.102410709 1.316276478 1.072262686 1.133618899 1.427522623 1.479048903 1.198092785 1.318279722 1 17.49455978 4.756555647 22.59054189 1.251268676 1.102410236 0.077405317 0.150375097 2692.229496 3379550.208 0.037030052 0.968366082 57089.42208 -4.756555647 -0.14885844 LSDQFHDILIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LSDQFHDILIR 11 0 O75340-2;O75340;A0A024QZ42;H0Y9X3;A0A087WZ38 O75340-2 PDCD6 Programmed cell death protein 6 0 ;;;;; 190.78 2.12E-06 3948280000 6215540 3582040 1669750 2522980 3322500 3501110 3353390 3878080 3606960 FALSE TRUE 5394140.641 3558509.343 2477246.685 3095861.17 3256388.75 3635799.967 3028178.754 3048782.771 3180549.298 1.695977687 1.118834833 0.778873853 0.973373113 1.023844766 1.143135863 0.95209301 0.958571142 1 21.60084452 4.706922897 3.532270199 0.978969402 1.75829685 0.86167285 0.089998819 0.089003352 1.975208329 0.022736548 0.175338811 50924.04548 -4.706922897 0.779327448 LSDSFSLYPQFMFHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSDSFSLYPQFMFHLR 16 0 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;; 220.21 1.17E-14 1260177000 1520383 1600566 892554 1091863 1560191 1525260 1446767 1635509 1495717 FALSE TRUE 1319460.534 1590051.777 1324196.1 1339787.182 1529146.252 1583937.739 1306459.759 1285768.128 1318895.04 1.000428764 1.205593871 1.004019319 1.01584064 1.159414665 1.200958144 0.99057144 0.974882829 1 20.33089833 2.096385583 13.14933711 0.984774906 1.097423874 0.317037247 0.075558017 0.70105663 91.42511698 0.030737701 0.020722716 124.8491481 -2.096385583 0.112648968 LSEAVWQPEEHYSS(ph)SPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSEAVWQPEEHYSSSPEK 18 0 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 LSEAVWQPEEHYS(0.022)S(0.864)S(0.114)PEK 153.56 2.08E-08 333330000 186120 188190 86225 156140 269110 215220 275490 289480 300030 TRUE FALSE 161523.7704 186953.7675 127923.6984 191593.9735 263755.2375 223499.6527 248773.0222 227576.9547 264560.7952 0.610535549 0.706657112 0.483532333 0.724196392 0.996955113 0.844795059 0.940324594 0.860206648 1 18.01323976 3.422508305 4.967416502 0.915163029 0.609026518 0.81002023 0.073295602 0.078050784 4.060814593 0.019870073 0.026229442 2645.503283 -3.422508305 -0.30613651 LSEAVWQPEEHYSSS(ph)PEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSEAVWQPEEHYSSSPEK 18 0 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 LSEAVWQPEEHYS(0.001)S(0.062)S(0.937)PEK;LSEAVWQPEEHYS(0.002)S(0.185)S(0.813)PEK;LSEAVWQPEEHYS(0.001)S(0.104)S(0.895)PEK 184.96 3.58E-14 949210000 486318 517770 229415 360568 646590 589400 669980 771800 819680 TRUE FALSE 422049.8441 514368.7348 340360.8613 442440.4753 633724.124 612074.5994 605005.4427 606756.5762 722778.3642 0.583927058 0.711654859 0.470906267 0.612138516 0.876789007 0.846835807 0.837055275 0.839478056 1 19.4631938 3.253009705 6.538851213 0.870575311 0.592685473 0.787610116 0.073576276 0.069581487 11.93452679 0.021195342 0.026334215 1790.64587 -3.253009705 -0.277889838 LSEDYGVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSEDYGVLK 9 0 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ; 175.44 0.00012542 291050000 964090 756350 508730 673220 758980 641780 842310 905920 1057680 FALSE TRUE 836683.0638 751381.487 754753.5296 826084.8905 743877.7829 666469.6919 760622.9058 712196.0579 932642.2753 0.897110378 0.805648111 0.80926369 0.885746778 0.797602471 0.714603776 0.815556968 0.763632613 1 19.8309643 4.743478455 22.94690771 0.816118653 0.897110483 0.075302697 0.076172515 406.3874164 1896008.23 0.017824628 0.138836415 55396.00612 -4.743478455 0.080991831 GYYSPYSVS(ph)GS(ph)GSTAGSR ddPTM_MDA-MB-175_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 GYYSPY(0.01)S(0.106)VS(0.873)GS(0.569)GS(0.184)T(0.157)AGS(0.101)R 76.151 0.022967 88641000 451330 347420 198390 148940 192920 225750 190700 183310 185810 TRUE FALSE 391685.597 345137.7751 294332.0676 182759.1034 189081.2694 234434.7486 172205.9434 144110.583 163843.7535 2.390604394 2.106505545 1.796419219 1.115447489 1.154034044 1.430843371 1.051037587 0.879561045 1 17.32196115 4.069789543 1.1602552 1.053842582 2.485711397 0.911985024 0.15065724 0.189399504 0.423435476 0.055213862 0.25201301 11743.28344 -4.069789543 1.431868815 up LSEEFLTAHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSEEFLTAHPR 11 0 Q15813-2;Q15813;A0A2R8Y5Q8;A0A2R8YHI9;A0A2R8Y7E7;A0A2U3TZJ6;A0A2R8Y6Q1 Q15813-2 TBCE Tubulin-specific chaperone E 0 175.15 1.02E-05 252320000 163680 161190 118660 143190 179450 195570 200270 225960 225070 FALSE TRUE 142049.2733 160131.1323 176044.3729 175703.478 175879.2961 203093.7045 180847.8462 177640.2124 198462.481 0.715748753 0.806858462 0.887041077 0.885323398 0.886209299 1.023335511 0.91124451 0.895082091 1 17.59850677 5.846624553 0.560032561 0.944205448 0.026515521 0.758157202 0.042644604 6.489064136 0.615701814 0.023688616 5.076674343 702464.7769 -5.846624553 -0.917689927 LSEELSGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSEELSGGR 9 0 B4DXW1;P61158;Q9P1U1-2;Q9P1U1 B4DXW1 ACTR3;ACTR3B Actin-related protein 3;Actin-related protein 3B 0 ; 141.2 0.0002496 240354000 164322 157031 136873 140001 165868 177008 157493 177202 202303 FALSE TRUE 142606.4314 155999.453 203065.2406 171790.3668 162567.5513 183817.6123 142219.3531 139308.7313 178386.9698 0.799421794 0.874500269 1.138341219 0.963020825 0.911319652 1.030443045 0.797251914 0.780935578 1 17.44465071 2.229046143 24.99783266 0.840460609 0.956287384 0.136904493 0.106910716 325.5681332 855372.6239 0.043892884 0.030021736 169.4517832 -2.229046143 0.115826775 LSEGFSIHTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSEGFSIHTR 10 0 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ;;; 211.64 5.52E-08 3016960000 3298250 3499080 1067620 2170460 3766120 3856290 3156140 3643070 3177750 FALSE TRUE 2862377.906 3476094.313 1583924.603 2663296.116 3691181.58 4004643.972 2850058.029 2864027.831 2802080.015 1.021518975 1.240540703 0.565267442 0.950471115 1.317300563 1.429168314 1.017122285 1.022107797 1 21.41806672 3.368353062 10.82501262 1.143219772 0.936661143 0.198942334 0.210986177 0.652966978 60.75213378 0.064319183 0.083036237 2335.35583 -3.368353062 -0.206558628 LSEGS(ph)QPAEEEEDQETPSR ddPTM_MDA-MB-175_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 373.25 4.49E-108 683460000 525580 439150 387780 383300 494230 528020 524420 532620 588520 TRUE FALSE 456123.2713 436265.1947 575311.705 470334.1234 484395.7899 548333.2711 473561.8291 418723.3579 518945.836 0.878941962 0.840675779 1.108616093 0.906326038 0.933422635 1.056629099 0.912545773 0.80687295 1 18.98522444 2.005179552 24.99311888 0.880661977 0.955502093 0.044935145 0.091475118 291.1763691 1405020.002 0.036831488 0.024736368 101.1997761 -2.005179552 0.074840116 LSEHATAPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LSEHATAPTR 10 0 P33316-2;H0YNJ9;H0YNW5;P33316;A0A0C4DGL3;H0YKC5;H0YMM5;H0YKI0 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 ;;;;; 141.27 3.78E-05 1667440000 1986700 2031240 973530 1423180 1957050 2189210 1902090 2183380 1898950 FALSE TRUE 1724152.561 2017896.651 1444332.364 1746334.771 1918108.534 2273430.325 1717625.605 1716481.178 1674458.294 1.029677817 1.205104157 0.862566938 1.042925212 1.145509888 1.357710928 1.025779866 1.025096405 1 20.67526301 2.040014337 24.99999701 1.017668158 1.107086662 0.101966746 0.126562394 375.7163567 234737.1075 0.053694909 0.036201051 109.6514393 -2.040014337 0.089418504 LSEHS(ph)S(ph)PEEEASPHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSEHSSPEEEASPHQR 16 0 Q9UD71;J3KSJ8;Q9UD71-2 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 2 LSEHS(1)S(1)PEEEASPHQR;LS(0.003)EHS(0.998)S(0.999)PEEEASPHQR;LS(0.089)EHS(0.965)S(0.947)PEEEASPHQR;LS(0.017)EHS(0.985)S(0.998)PEEEASPHQR 180.08 1.33E-09 2473530000 797612 831392 531260 646893 1008240 986920 956730 1066320 990490 TRUE FALSE 692205.5533 825930.5312 788179.113 793779.9428 988177.9966 1024887.451 863946.4719 838295.7661 873395.4006 0.792545453 0.945654775 0.902431032 0.908843741 1.131421113 1.173451853 0.989181385 0.959812435 1 19.73627541 3.358787037 7.478058111 1.040627213 0.890038194 0.544022942 0.074180374 0.216865959 13.29673855 0.023842217 0.030800214 2284.4783 -3.358787037 -0.150589019 LSEHS(ph)SPEEEASPHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSEHSSPEEEASPHQR 16 0 Q9UD71;J3KSJ8;Q9UD71-2 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 1 LS(0.013)EHS(0.724)S(0.263)PEEEASPHQR 145.62 7.74E-07 2069500000 121030 143390 56987 77242 140200 136680 145120 138530 117360 TRUE FALSE 105035.5788 142448.0616 84546.10381 94780.97667 137410.2943 141938.168 131046.2847 108906.4375 103485.8345 1.014975425 1.376498168 0.816982384 0.915883581 1.327817425 1.371570986 1.266320993 1.052380145 1 16.65907377 3.239758548 24.99999966 1.197813565 1.040464248 0.183976399 0.179845628 66.8731381 1395580.265 0.056492769 0.068901515 1736.834944 -3.239758548 -0.157349318 LSEHSS(ph)PEEEASPHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LSEHSSPEEEASPHQR 16 0 Q9UD71;J3KSJ8;Q9UD71-2 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 1 LSEHS(0.009)S(0.991)PEEEASPHQR;LS(0.002)EHS(0.175)S(0.823)PEEEASPHQR;LSEHS(0.248)S(0.752)PEEEASPHQR;LS(0.002)EHS(0.093)S(0.905)PEEEASPHQR;LSEHS(0.001)S(0.999)PEEEASPHQR 259.34 6.23E-27 2860070000 804500 854930 410957 548773 907230 900890 880080 932860 890220 TRUE FALSE 698183.2867 849313.9085 609697.1798 673380.2971 889177.898 935547.8213 794729.9771 733375.1485 784979.2057 0.889429021 1.081957206 0.77670488 0.857832019 1.132740704 1.191812235 1.012421694 0.934260606 1 19.58229491 3.249554718 24.99993138 1.042990106 0.905459382 0.349896659 0.102774002 302.1867327 687150.8842 0.032444679 0.041481522 1776.457075 -3.249554718 -0.137530725 LSEHSSPEEEASPHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSEHSSPEEEASPHQR 16 0 Q9UD71;J3KSJ8;Q9UD71-2 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 0 ; 262.66 3.90E-27 1643670000 728840 896020 133838 484010 984400 851080 716200 851110 865450 FALSE TRUE 632521.9474 890133.9856 198562.5045 593911.8681 964812.3659 883821.5983 646743.0342 669106.7498 763137.4869 0.828844026 1.166413655 0.260192309 0.778250156 1.264270702 1.15814203 0.847479052 0.876784015 1 19.54158347 3.442306829 24.94755892 1.004721478 0.74760034 0.225431243 0.247563875 291.0433906 208556.946 0.073357139 0.094704008 2768.897181 -3.442306829 -0.257121138 LSELLR ddPTM_MDA-MB-175_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 ;;;;;;; 159.75 0.020987 17227670000 8366420 7413030 4414080 5653320 7020040 7221520 6677380 7902000 7874240 FALSE TRUE 7260776.399 7364333.318 6548743.852 6936992.712 6880354.938 7499336.547 6029808.715 6212218.793 6943356.318 1.045715655 1.060630188 0.9431669 0.999083497 0.99092638 1.0800737 0.868428529 0.894699697 1 22.72720178 2.232016273 24.99999945 0.913362348 1.016027089 0.45536015 0.050631571 134.3688614 513295.5117 0.020464911 0.014159674 170.6146315 -2.232016273 0.102664741 LSELSNSQQSVQTLSLWLIHHR ddPTM_MDA-MB-175_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 ; 237.24 9.38E-31 728180000 609340 592220 324740 511740 593920 568950 546350 674930 659540 FALSE TRUE 528814.1751 588329.6678 481785.3502 627938.3885 582102.154 590837.8747 493365.0611 530601.4718 581569.9326 0.909287337 1.011623254 0.82842204 1.079729803 1.000915146 1.015936075 0.848333164 0.912360564 1 19.14959316 1.202152202 23.17346248 1.000000847 0.949921547 0.037008082 0.078711743 10228.16414 6509092.086 3.700774801 0.019074239 15.92766828 -1.202152202 -0.0500793 LSEMEAYLENIEKEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSEMEAYLENIEKEEER 17 1 O00566;U3KQ48 O00566 MPHOSPH10 U3 small nucleolar ribonucleoprotein protein MPP10 0 ; 164.69 2.34E-09 74751000 92985 68164 56063 68816 63880 57590 75886 96525 81857 FALSE TRUE 80696.79666 67716.2262 83175.25432 84441.72459 62608.91298 59805.52457 68526.5874 75883.87991 72179.95871 1.117994497 0.938158284 1.152331697 1.169877707 0.867400233 0.828561357 0.94938524 1.051315092 1 16.1393107 3.238262888 24.99999977 0.948545638 1.087541177 0.436274074 0.087184632 9.475332248 795655.5146 0.028502225 0.034379959 1730.863773 -3.238262888 0.138995539 LSEMTEAEQQQLIDDHFLFDKPVS(ph)PLLTAAGMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSEMTEAEQQQLIDDHFLFDKPVSPLLTAAGMAR 34 1 P12532;P12532-2;F8WCN3 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 1 LSEMTEAEQQQLIDDHFLFDKPVS(1)PLLTAAGMAR;LSEMT(0.001)EAEQQQLIDDHFLFDKPVS(0.892)PLLT(0.107)AAGMAR 326.37 7.63E-107 735280000 283239 248362 217315 262920 276048 237824 244131 353904 319325 TRUE FALSE 245808.2485 246730.4937 322409.2609 322620.0045 270555.1849 246973.2432 220455.2132 278224.3837 281574.7623 0.872976848 0.87625216 1.14502187 1.145770316 0.960864471 0.877114274 0.782936693 0.988101282 1 18.1031585 3.002162522 24.95839282 0.912616308 1.015498272 0.153898596 0.10794036 134.674476 1554284.429 0.03551012 0.040001968 1004.991809 -3.002162522 0.102881963 LSEMTEAEQQQLIDDHFLFDKPVSPLLTAAGMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSEMTEAEQQQLIDDHFLFDKPVSPLLTAAGMAR 34 1 P12532;P12532-2;F8WCN3 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ; 315.15 1.06E-104 2453800000 1403010 1349150 905740 1170400 1248820 1242090 1063480 1618310 1536100 FALSE TRUE 1217598.674 1340287.345 1343758.894 1436157.208 1223970.925 1289874.006 960343.8733 1272247 1354504.008 0.898925855 0.989504156 0.992067122 1.060282731 0.903630346 0.952285116 0.709000393 0.939271492 1 20.36933323 3.091478717 9.513439526 0.892715154 0.985937912 0.195641671 0.084412177 0.482185744 45.81594511 0.025741483 0.029209273 1234.464817 -3.091478717 0.093222758 LSESQLSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSESQLSFR 9 0 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 104.2 0.0076752 106990000 166430 156900 121660 161890 146570 176320 177460 205040 215660 FALSE TRUE 144435.8538 155869.3136 180495.1829 198649.5988 143653.5438 183103.1445 160249.9565 161193.7916 190164.9205 0.759529431 0.819653347 0.949150782 1.044617474 0.75541558 0.962864991 0.842689367 0.847652612 1 17.53689161 4.428229178 4.739493829 0.905162112 0.771539861 0.284060524 0.084066477 0.238875306 11.45498514 0.020663173 0.062222213 26805.82498 -4.428229178 -0.133622251 LSESSAS(ph)PQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSESSASPQPK 11 0 Q8N5Y2;Q8N5Y2-3;Q8N5Y2-2;A0A3B3IT59;Q8N5Y2-6;Q8N5Y2-4;A0A3B3ITL5;A0A3B3ITF3;A0A3F2YNX2;A0A3B3IRN2;A0A3B3IU80;A0A3B3IUB0;A0A3B3IS72;A0A3B3ISB4;A0A3B3IRI6;A0A3B3ITV8;A0A3B3IRT2;A0A3B3ITF8;A0A3B3IT49;Q8N5Y2-5;A0A3B3ITX5 Q8N5Y2 MSL3 Male-specific lethal 3 homolog 1 LSES(0.002)S(0.077)AS(0.921)PQPK;LSESS(0.019)AS(0.981)PQPK;LSESS(0.006)AS(0.994)PQPK 169.6 1.75E-05 391148000 1086930 920890 574090 716780 805720 606760 850220 1099520 833740 TRUE FALSE 943289.4466 914840.613 851721.8442 879535.8543 789687.7484 630102.4498 767765.7953 864396.2045 735176.207 1.2830794 1.244382781 1.158527488 1.196360608 1.074147586 0.857076771 1.044328949 1.175767382 1 19.48773055 3.237408265 3.625595699 1.038404962 1.221944441 0.569706553 0.082861617 0.204324969 5.745310861 0.02832152 0.034939312 1727.461056 -3.237408265 0.183539479 LSETSIKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSETSIKDR 9 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 109.79 0.0021816 279350000 770380 742030 391300 416700 664580 678610 780550 727060 234400 FALSE TRUE 668572.3311 737155.5561 580533.9888 511318.1039 651356.1582 704716.5658 704852.3811 571583.877 206689.499 3.234670045 3.5664877 2.808725124 2.473846549 3.151375185 3.409542183 3.410199282 2.765422915 1 17.65710557 4.227198489 23.85930334 2.79003388 3.4005788 0.139334803 0.687924866 243.7259656 511805.9408 0.178729233 0.377958156 16873.24022 -4.227198489 0.61054492 LSEVLQAVTDHDIPQQLVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSEVLQAVTDHDIPQQLVER 20 0 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ;; 191.22 1.54E-17 575436000 498705 486428 264529 353078 439487 452357 443123 450316 442356 FALSE TRUE 432799.8707 483232.6224 392456.1092 433249.7564 430742.0685 469759.4665 400148.9997 354019.4278 390061.1776 1.109569205 1.238863671 1.006139887 1.110722577 1.104293617 1.204322536 1.025862154 0.907599751 1 18.57334089 2.021018712 6.156662679 0.95223337 1.126152244 0.56010413 0.065431544 0.104973061 14.09734754 0.027258596 0.017485884 104.9587651 -2.021018712 0.173918875 LSFASETPLEKEPHS(ph)PADQPEQQAESTLTSAETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSFASETPLEKEPHSPADQPEQQAESTLTSAETR 34 1 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2 H3BSS6 ZNF106 Zinc finger protein 106 1 LS(0.005)FAS(0.009)ET(0.009)PLEKEPHS(0.977)PADQPEQQAESTLTSAETR 69.551 0.0026895 150110000 24437 21158 13709 13973 14114 18867 28283 24575 13034 TRUE FALSE 21207.58853 21019.0117 20338.71825 17145.78321 13833.15901 19592.8257 25540.11901 19319.82749 11493.13537 1.845239602 1.828831823 1.769640538 1.49182818 1.203601852 1.704741576 2.222206404 1.680988423 1 13.4884848 3.916260841 5.302958877 1.598667118 1.829210053 0.120771267 0.322010342 0.592718901 27.81283865 0.091627382 0.164591456 8246.332472 -3.916260841 0.230542936 LSFDKDAMVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSFDKDAMVAR 11 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ;;; 168.83 1.61E-05 12086870000 12930600 12067120 7463860 8846160 11083450 9943700 13200030 14352320 9272770 FALSE TRUE 11221788.45 11987850.29 11073407.66 10854815.83 10862911.03 10326240.57 11919893.12 11283188.06 8176553.694 1.372434997 1.466125062 1.354287891 1.327553911 1.328543961 1.262908673 1.457813838 1.379944226 1 22.96306146 1.237641325 24.99979681 0.999999567 1.370152968 0.789078398 0.059902869 10.59400297 287940.157 0.088983891 0.015087947 17.28388329 -1.237641325 0.370153401 LSFFFDFR ddPTM_MDA-MB-175_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 ; 141.39 0.0014757 7805000000 1351730 1918330 1567400 1711510 1972810 2101880 2258100 2299500 4639500 FALSE TRUE 1173095.456 1905728.364 2325399.883 2100134.504 1933554.941 2182740.684 2039109.81 1807769.82 4091023.595 0.286748641 0.465831673 0.568415172 0.513351843 0.472633534 0.5335439 0.498435113 0.441886921 1 21.96403043 1.236128936 24.99996839 1.000000682 0.478337462 0.828802474 0.075288741 26.18606829 269157.8782 0.119481943 0.018213752 17.22379852 -1.236128936 -0.521663219 LSFGDTLQVQNIHGAFNALGGADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSFGDTLQVQNIHGAFNALGGADR 24 0 Q969X5;Q969X5-2 Q969X5 ERGIC1 Endoplasmic reticulum-Golgi intermediate compartment protein 1 0 ; 208.97 5.80E-25 1909810000 582730 615480 375860 440570 648810 649190 514570 630190 707490 FALSE TRUE 505720.7541 611436.8714 557627.1532 540608.1522 635899.9504 674164.7594 464667.0806 495428.7726 623851.3382 0.810643054 0.98010028 0.893846208 0.866565669 1.019313275 1.080649697 0.744836233 0.794145564 1 19.25084275 2.220466485 24.99980161 0.831227329 0.94150823 0.16446304 0.099576789 386.3998494 533866.2378 0.040913891 0.027645748 166.1370463 -2.220466485 0.1102809 LSFLS(ph)WGTNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSFLSWGTNK 10 0 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 LSFLS(1)WGTNK;LSFLS(1)WGTNK 147.24 2.86E-05 328720000 1277140 1350090 1017130 1111240 1355770 1127770 1502380 1554570 1807700 TRUE FALSE 1108362.713 1341221.17 1509017.47 1363564.026 1328792.83 1171156.042 1356679.419 1222137.303 1593995.765 0.695336046 0.841420786 0.946688506 0.855437672 0.833623814 0.734729707 0.851118584 0.766713018 1 20.60421637 -1.828566897 0.009939671 1.76101544 3.60E-08 0.068664887 0.087880826 151948.124 155.6088161 15394.61635 12338.19981 0.014839973 1.828566897 -1.761015404 LSFQHDPETSVLVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSFQHDPETSVLVLR 15 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 128.06 7.43E-05 529500000 405040 360240 149022 254740 406340 518070 308320 358580 301820 FALSE TRUE 351512.9378 357873.5597 221089.5376 312582.6105 398254.629 538000.4881 278419.1739 281900.4575 266139.1834 1.320786114 1.344685721 0.830729 1.174508039 1.49641486 2.021500484 1.046141234 1.059221922 1 18.02182141 3.444374247 24.35420679 1.308160329 1.153210142 0.053463628 0.322941302 550.5406722 409439.0894 0.102091163 0.131800248 2782.109681 -3.444374247 -0.154950187 LSFS(ph)PENILIQNQDIVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSFSPENILIQNQDIVR 17 0 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 LS(0.001)FS(0.999)PENILIQNQDIVR;LSFS(1)PENILIQNQDIVR;LSFS(1)PENILIQNQDIVR 218.66 4.80E-15 480807000 291010 280153 154424 201537 275629 250094 240286 299434 250283 TRUE FALSE 252552.2912 278312.6565 229103.9629 247299.0562 270144.5222 259715.278 216983.1007 235402.3693 220694.8289 1.144350742 1.261074661 1.038102995 1.120547579 1.22406367 1.176807265 0.983181626 1.06664198 1 17.7516933 2.245458791 24.9991494 1.025638877 1.160846817 0.538774114 0.062716436 126.6444994 458964.1346 0.023791489 0.018013174 175.9781676 -2.245458791 0.13520794 LSGAEPDDEEYQEFEEMLEHAESAQDFASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSGAEPDDEEYQEFEEMLEHAESAQDFASR 30 0 Q96GC9;K7EPE7;Q96GC9-2 Q96GC9 VMP1 Vacuole membrane protein 1 0 ;;; 262.98 2.01E-58 209417000 57016 45750.2 35923.7 47845.7 64728 56199 35713.4 76812 70380 FALSE TRUE 49481.19114 45449.66392 53296.52148 58709.79746 63440.03944 58361.0119 32249.91996 60386.35155 62059.75658 0.797315263 0.732353242 0.858793595 0.946020428 1.02224119 0.940400271 0.519659144 0.973035585 1 15.92137042 4.106093262 5.146397553 0.891558858 0.766269929 0.129372814 0.141966202 0.459023894 18.89677005 0.037847697 0.082144607 12767.12946 -4.106093262 -0.125288929 LSGAQADLHIEDGDSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSGAQADLHIEDGDSIR 17 0 M0QXB5;O95571 M0QXB5 ETHE1 "Persulfide dioxygenase ETHE1, mitochondrial" 0 ;;; 242.26 2.13E-20 1955590000 1470080 1658210 1052610 1597150 1815010 1935910 1588930 1849930 1789940 FALSE TRUE 1275805.203 1647317.109 1561655.717 1959807.318 1778894.852 2010385.71 1434835.813 1454336.866 1578335.332 0.808323287 1.0437054 0.989432147 1.24169261 1.127070284 1.273738013 0.909081729 0.921437185 1 20.58997232 LSGDWNPLHIDPNFASLAGFDKPILHGLCTFGFSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSGDWNPLHIDPNFASLAGFDKPILHGLCTFGFSAR 36 1 P51659-3;P51659;P51659-2;A0A2R8YD50;A0A2R8Y7L2;E7ET17;E7EPL9 P51659-3 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 ; 197.74 3.19E-30 686260000 247905 213727 116059 213936 210862 281389 242815 297289 170667 FALSE TRUE 215143.7261 212323.0133 172185.5206 262513.4386 206666.2587 292214.2169 219266.8387 233716.0609 150490.9417 1.429612465 1.410869059 1.144158703 1.744380331 1.373280388 1.941739573 1.457010211 1.553024111 1 17.19931713 1.235555531 24.99038982 0.999999304 1.509115773 0.354940122 0.214676461 94.95668891 789518.1186 0.34775059 0.050793137 17.20107269 -1.235555531 0.509116468 LSGEHS(ph)ESSTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSGEHSESSTPR 12 0 Q7Z3K3-5;Q7Z3K3-7;Q7Z3K3-2;Q7Z3K3-3;Q7Z3K3-6;Q7Z3K3 Q7Z3K3-5 POGZ Pogo transposable element with ZNF domain 1 LS(0.003)GEHS(0.985)ES(0.004)S(0.004)T(0.004)PR 61.423 0.086218 0 129550 121900 80920 80950 127740 147380 101100 134060 153980 TRUE FALSE 112429.6393 121099.2309 120053.1827 99330.93474 125198.2239 153049.804 91295.33756 105392.3123 135776.6598 0.828048351 0.891900206 0.884196023 0.731575919 0.922089438 1.12721733 0.672393456 0.776218184 1 17.05087597 LSGEHS(ph)ESSTPRPR ddPTM_MDA-MB-175_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(0.97)ES(0.021)S(0.003)T(0.006)PRPR;LSGEHS(0.903)ES(0.095)S(0.001)TPRPR;LSGEHS(0.984)ES(0.016)STPRPR;LSGEHS(0.995)ES(0.001)S(0.001)T(0.002)PRPR 187.78 5.51E-07 2058820000 879694 903260 385201 551762 755991 758254 703507 834887 738526 TRUE FALSE 763440.209 897326.4256 571485.492 677047.9953 740948.2582 787424.522 635280.9994 656352.9121 651218.2976 1.172326103 1.377919553 0.877563628 1.039663655 1.137787837 1.209156016 0.97552695 1.007884629 1 19.31278171 4.247516029 24.99999961 1.039727053 1.27512283 0.491240342 0.101361495 163.8611675 457426.1773 0.025630492 0.065712133 17681.37475 -4.247516029 0.235395777 LSGEHSES(ph)STPRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSGEHSESSTPRPR 14 1 Q7Z3K3-5;Q7Z3K3-7;Q7Z3K3-2;Q7Z3K3-3;Q7Z3K3-6;Q7Z3K3 Q7Z3K3-5 POGZ Pogo transposable element with ZNF domain 1 LSGEHS(0.376)ES(0.556)S(0.058)T(0.01)PRPR 146.1 5.09E-06 1397200000 493370 520730 244890 374390 465440 504300 485610 496550 481120 TRUE FALSE 428169.9045 517309.2903 363319.6231 459400.9717 456178.6546 523700.7473 438515.6169 390366.6467 424242.5417 1.009257353 1.219371561 0.856396017 1.082873419 1.07527796 1.234437134 1.033643668 0.920149698 1 18.69452977 1.992453617 24.98758589 0.961128865 1.080618332 0.175805519 0.106199278 534.9929337 1771467.247 0.043893888 0.028198932 98.27739071 -1.992453617 0.119489467 LSGEHSESS(ph)TPRPR ddPTM_MDA-MB-175_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 LSGEHSES(0.011)S(0.816)T(0.172)PRPR;LSGEHSES(0.074)S(0.463)T(0.463)PRPR 117.07 0.00019672 708915000 1386200 1149649 725920 928251 928320 1080496 1078154 1387707 1439811 TRUE FALSE 1203010.158 1142096.88 1076977.34 1139024.577 909848.2482 1122063.38 973594.791 1090956.657 1269598.184 0.947551889 0.899573499 0.848282042 0.897153597 0.716642683 0.883794097 0.766852697 0.859292862 1 20.27594054 4.552260609 1.577377724 0.845125997 0.966551002 0.141790191 0.075290884 1.348583291 4.229990593 0.020427584 0.227000093 35666.50951 -4.552260609 0.121425004 LSGFS(ph)FK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSGFSFK 7 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 LSGFS(1)FK;LSGFS(1)FK;LSGFS(1)FK;LSGFS(1)FK 138.08 0.0029586 3219390000 4168950 3896310 2419470 3592580 3491800 1473470 4705130 4407730 9529710 TRUE FALSE 3618012.695 3870714.883 3589533.785 4408330.198 3422320.012 1530155.344 4248827.217 3465171.24 8403118.54 0.430555951 0.46062838 0.427166863 0.524606451 0.407267849 0.182093747 0.505625048 0.412367292 1 23.00249341 1.238122859 24.99792944 1.000000655 0.419677668 0.796106817 0.092437343 4.673932863 266595.2046 0.128687078 0.022534679 17.30305781 -1.238122859 -0.580322987 LSGFS(ph)FKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSGFSFKK 8 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 LSGFS(1)FKK;LSGFS(1)FKK 125.74 0.0013232 10115600000 9000780 8041610 3888770 5770450 5824250 2392610 10550000 9308320 6453830 TRUE FALSE 7811304.118 7988784.134 5769392.179 7080718.868 5708358.82 2484655.255 9526862.624 7317808.205 5690865.57 1.372603872 1.403790695 1.013798711 1.244225291 1.003073917 0.436604103 1.674062145 1.285886675 1 22.44021667 4.251108757 24.65815506 1.120809493 1.388197497 0.131374967 0.308599295 451.1164869 886462.1484 0.079137335 0.206144246 17828.25169 -4.251108757 0.267388003 LSGINEIPRPFS(ph)PPVT(ph)SNTSPPPAAPLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSGINEIPRPFSPPVTSNTSPPPAAPLAR 29 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 2 LS(0.002)GINEIPRPFS(0.998)PPVT(0.357)S(0.326)NT(0.273)S(0.045)PPPAAPLAR 78.22 0.010134 286120000 247950 243700 143980 173380 233220 256480 207540 243890 238880 TRUE FALSE 215182.7793 242099.1187 213609.2096 212748.5789 228579.3783 266346.9516 187412.8027 191736.0215 210639.8785 1.021567145 1.149350827 1.014096718 1.010010927 1.085166683 1.264465938 0.889730872 0.910255089 1 17.68441907 2.189531088 24.99999986 0.926704833 1.086028281 0.459656801 0.080255549 98.20912879 50075.76558 0.032690644 0.022040077 154.7145248 -2.189531088 0.159323447 LSGINEIPRPFS(ph)PPVTSNTS(ph)PPPAAPLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSGINEIPRPFSPPVTSNTSPPPAAPLAR 29 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 2 LS(0.016)GINEIPRPFS(0.86)PPVT(0.296)S(0.115)NT(0.237)S(0.475)PPPAAPLAR 48.096 0.057047 485520000 150860 153580 94311 116020 155450 158440 148500 178140 143100 TRUE FALSE 130923.4688 152571.1229 139920.1151 142364.1143 152356.8491 164535.2893 134098.4929 140046.1473 126182.881 1.037569183 1.209126956 1.108867652 1.128236359 1.207428836 1.303943039 1.062731266 1.109866459 1 16.94515667 1.430757537 1.581777066 0.982665259 1.16137271 0.28595518 0.076277886 0.924608764 2.995100028 0.239640117 0.022005234 26.9623373 -1.430757537 0.178707451 LSGINEIPRPFSPPVT(ph)SNTSPPPAAPLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSGINEIPRPFSPPVTSNTSPPPAAPLAR 29 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 LSGINEIPRPFS(0.159)PPVT(0.36)S(0.36)NT(0.121)S(0.001)PPPAAPLAR 186.59 1.06E-17 873860000 725220 602200 405880 515890 683300 713790 654080 766400 653090 TRUE FALSE 629380.3395 598244.1085 602164.9256 633030.7094 669703.6669 741249.9632 590647.4223 602511.3241 575882.4442 1.09289725 1.038830259 1.045638622 1.099235991 1.162917317 1.287154993 1.025638875 1.046240131 1 19.13541482 LSGINEIPRPFSPPVTSNT(ph)SPPPAAPLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSGINEIPRPFSPPVTSNTSPPPAAPLAR 29 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 LSGINEIPRPFS(0.21)PPVT(0.08)S(0.109)NT(0.541)S(0.061)PPPAAPLAR 148.66 7.38E-08 1416800000 489950 518590 261690 388600 465340 512820 455170 609670 459130 TRUE FALSE 425201.8661 515183.3481 388244.1593 476837.5694 456080.6444 532548.5172 411027.6835 479296.815 404852.1744 1.050264499 1.272522122 0.958977582 1.177806616 1.126536235 1.315414739 1.015253738 1.183881044 1 18.6270357 1.226700363 24.42852945 0.999999579 1.139122785 0.134420018 0.109658073 810.8904497 1670045.194 0.381572001 0.024257613 16.85389806 -1.226700363 0.139123206 LSGLANVVLHELS(ph)GDDDTDQNMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSGLANVVLHELSGDDDTDQNMR 23 0 Q14789;Q14789-2;E7EU81;F8WF12;C9J8Q0 Q14789 GOLGB1 Golgin subfamily B member 1 1 LSGLANVVLHELS(0.996)GDDDT(0.003)DQNMR 53.073 0.073301 9889700 6772.4 7958.7 4664.3 6336.5 6303.9 8288.5 7637.6 8215.4 6854.8 TRUE FALSE 5877.410181 7906.418776 6919.971081 7775.299172 6178.464723 8607.363958 6896.906728 6458.600642 6044.433353 0.972367439 1.308049624 1.144850258 1.286357003 1.022174348 1.424015033 1.141034457 1.068520449 1 12.56139138 1.697500129 2.966717558 1.0180203 1.197231856 0.192913183 0.132496152 0.320897879 6.268984164 0.098077715 0.032937358 49.83106039 -1.697500129 0.179211555 LSGLS(ph)FK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSGLSFK 7 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 LSGLS(1)FK;LSGLS(1)FK;LSGLS(1)FK 114.97 0.0060691 1719676000 4940180 4809910 2704077 3857730 3750010 1835966 4830540 4347250 10361160 TRUE FALSE 4287322.696 4778313.385 4011777.682 4733686.558 3675392.138 1906596.8 4362074.974 3417624.418 9136275.468 0.469263729 0.523004522 0.439104282 0.518119947 0.402285609 0.208684251 0.477445649 0.374071954 1 23.12317472 1.235463721 24.98100171 1.000000794 0.42513794 0.800005119 0.090113496 38.60990297 311389.6013 0.1557647 0.022576508 17.19743677 -1.235463721 -0.574862854 LSGLS(ph)FKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSGLSFKR 8 1 P49006 P49006 MARCKSL1 MARCKS-related protein 1 LSGLS(1)FKR;LSGLS(1)FKR;LSGLS(1)FKR;LSGLS(1)FKR 133.81 0.00055346 9743760000 13764520 14760810 5661790 8532520 10083120 4546110 12895790 11298270 10213380 TRUE FALSE 11945503.81 14663845.27 8399850.582 10469959.08 9882485.639 4721001.793 11645158.27 8882222.884 9005965.852 1.326398968 1.628236828 0.932698471 1.162558159 1.097326572 0.524208272 1.293049348 0.986259889 1 23.10244958 4.232808171 24.9999876 1.006343496 1.477317939 0.470904538 0.210490434 104.1655696 452708.5614 0.0513096 0.111640173 17092.60163 -4.232808171 0.470974443 LSGLTTNVVDIILAHHFGQEELQANLDLIQTYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSGLTTNVVDIILAHHFGQEELQANLDLIQTYR 33 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 0 ; 324.57 2.63E-105 468210000 420020 397520 281550 321660 367710 457940 396450 494620 451190 FALSE TRUE 364513.2928 394908.6649 417708.5217 394697.8193 360393.2904 475557.2481 358002.34 388849.3621 397850.8322 0.916205933 0.992604848 1.049912399 0.992074887 0.905850287 1.195315454 0.899840621 0.977374761 1 18.60186809 4.730192605 5.276620931 0.999492668 0.91314566 0.097340443 0.081747105 0.369064763 36.05956347 0.018937415 0.114440304 53727.00172 -4.730192605 -0.086347007 LSGQNAMGS(ph)QDSLLEITFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSGQNAMGSQDSLLEITFR 19 0 O75052-3;O75052;E9PIP8;H7C2G1;O75052-2 O75052-3 NOS1AP Carboxyl-terminal PDZ ligand of neuronal nitric oxide synthase protein 1 LSGQNAMGS(1)QDSLLEITFR 104.89 0.00036107 45875000 77953 54885 36773 70433 62273 72989 37514 77410 59260 TRUE FALSE 67651.31354 54524.45682 54556.5458 86425.88915 61033.88914 75796.93406 33875.89805 60856.47391 52254.35031 1.294654189 1.043443398 1.044057489 1.653946296 1.168015462 1.450538254 0.64828857 1.164620238 1 15.67326353 2.256707002 24.99916792 0.972868253 1.26697396 0.339615602 0.220231549 299.2329887 412234.3241 0.080697879 0.062382451 180.5955324 -2.256707002 0.294105707 QAS(ph)ESSSRPH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QASESSSRPH 10 1 A0A2R8Y653;Q9BZX2;Q9BZX2-2 A0A2R8Y653 UCK2 Uridine-cytidine kinase 2 1 QAS(0.992)ES(0.008)SSRPH;QAS(0.631)ES(0.367)S(0.002)SRPH;QAS(0.842)ES(0.077)S(0.077)S(0.005)RPH;QAS(0.916)ES(0.066)S(0.018)SRPH 138.35 4.07E-05 1178794000 490879 582197 494590 776955 798557 1316320 1132500 1219450 1232720 TRUE FALSE 426008.0964 578372.5096 733775.3783 953374.5078 782667.2781 1366959.682 1022670.324 958680.1073 1086989.246 0.39191565 0.53208669 0.675053025 0.877078142 0.720032218 1.257565047 0.940828374 0.881959146 1 20.05190624 4.09452519 0.880971952 0.979084039 0.313800749 0.738420819 0.125455252 0.534621795 0.609314274 0.049798768 0.289316369 12431.5474 -4.09452519 -0.66528329 down LSHETVTIELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSHETVTIELK 11 0 P62314;J3QLR7 P62314 SNRPD1 Small nuclear ribonucleoprotein Sm D1 0 123.67 0.0003651 331030000 559230 469580 243960 338800 439160 368300 493770 503000 611140 FALSE TRUE 485326.3386 466495.2981 361939.872 415729.7182 430421.5752 382468.7393 445884.2614 395437.3644 538891.7254 0.900600836 0.865656821 0.671637464 0.771453148 0.798716245 0.709732069 0.827409738 0.733797432 1 19.03963591 1.230914112 24.95687597 1.0000004 0.781125553 0.486563645 0.069353947 238.0585173 776914.6952 0.174029655 0.016743073 17.01821915 -1.230914112 -0.218874847 LSHIAEDVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSHIAEDVGR 10 0 P98171-2;P98171;E7EQN5;E9PCM6;A0A0B4J1X7;S4R352;S4R314;C9JLA8;C9J5M2;F8WAR0 P98171-2 ARHGAP4 Rho GTPase-activating protein 4 0 85.958 0.013885 157440000 148660 151900 108540 130580 160320 175720 155960 176200 167680 FALSE TRUE 129014.2043 150902.1589 161030.307 160230.1848 157129.9457 182480.0621 140835.0232 138521.0012 147857.0614 0.872560317 1.020594874 1.089094464 1.083683006 1.062715194 1.234165351 0.952507928 0.936857529 1 17.17384362 LSIPTYGLQCTR ddPTM_MDA-MB-175_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 0 191.04 1.37E-05 1397700000 302330 297000 241640 168840 315700 315740 248800 306790 320270 FALSE TRUE 262376.3245 295048.9874 358497.9122 207177.7026 309418.1877 327886.7221 224671.4143 241185.3459 282408.0455 0.929068165 1.044761267 1.269432362 0.733611191 1.095642255 1.161038885 0.795555997 0.854031427 1 18.10742166 2.228887698 24.99882335 0.873468242 1.038368618 0.195008793 0.148713643 310.1493149 801546.8358 0.058876821 0.040252663 169.3899728 -2.228887698 0.164900376 LSIQCYLSALDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSIQCYLSALDR 12 0 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 73.067 0.09352 104490000 95539 89528 94063 57580 71619 69538 97108 99948 66514 FALSE TRUE 82913.27909 88939.88467 139552.1814 70654.41906 70193.92202 72213.17186 87690.48111 78574.898 58650.79069 1.41367709 1.516431128 2.379374255 1.204662686 1.19681118 1.231239528 1.495128711 1.339707395 1 15.83986294 TDGFAEAIHS(ph)PQVAGVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TDGFAEAIHSPQVAGVPR 18 0 P12270 P12270 TPR Nucleoprotein TPR 1 TDGFAEAIHS(1)PQVAGVPR;TDGFAEAIHS(1)PQVAGVPR;TDGFAEAIHS(1)PQVAGVPR;TDGFAEAIHS(1)PQVAGVPR;TDGFAEAIHS(1)PQVAGVPR;TDGFAEAIHS(1)PQVAGVPR 255.47 1.53E-30 5638880000 1423132 1942363 1406749 1966019 3152440 3134670 2909060 3808220 3600030 TRUE FALSE 1235061.5 1929603.49 2087057.522 2412433.663 3089712.612 3255262.783 2626939.809 2993861.789 3174438.555 0.389064548 0.60785662 0.657457212 0.759956011 0.973309944 1.025460952 0.827528952 0.943115369 1 21.59807002 4.134129271 0.854724752 0.954208862 0.337328506 0.887698329 0.067927955 0.365632781 0.376222142 0.028612035 0.182025743 13618.49987 -4.134129271 -0.616880356 down LSIYEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSIYEAR 7 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 89.123 0.042118 230200000 387000 408030 273940 328470 435720 479410 367210 457360 450890 FALSE TRUE 335856.9695 405349.6241 406418.3003 403054.1338 427050.0245 497853.2129 331598.0307 359557.1232 397586.2979 0.844739799 1.019526141 1.022214051 1.013752577 1.074106494 1.252189061 0.834027814 0.904349886 1 18.60090851 LSKDDIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 LSKDDIDR 8 1 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 ;;;;;; 112.75 0.002719 6135760000 11611140 10359710 7236560 8296070 9669660 8879410 12756360 13687200 8559400 FALSE TRUE 10076698.43 10291656.38 10736184.62 10179819.49 9477252.684 9221006.648 11519250.17 10760298.79 7547517.483 1.335101039 1.363581655 1.422478934 1.34876395 1.255678136 1.2217271 1.52623034 1.425673914 1 22.84757076 1.232934406 24.99293359 0.999999413 1.366805988 0.636026105 0.086100372 128.2320527 569575.5088 0.193830455 0.022643108 17.0975706 -1.232934406 0.366806575 LSKDPNIVIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSKDPNIVIAK 11 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 106.01 0.0017891 0 3515700 2636000 1827000 2443400 2680400 2609300 3040600 3241800 1951900 FALSE TRUE 3051091.337 2618683.942 2710543.311 2998211.315 2627065.284 2709681.459 2745723.08 2548566.298 1721148.606 1.77270651 1.521474633 1.574845601 1.741982828 1.526344254 1.574344859 1.595285306 1.480735765 1 20.71494024 1.076772093 1.844840277 0.551594974 1.612593492 0.843711264 0.082869448 0.505097777 1.130694929 1.088543089 0.021547451 11.93361692 -1.076772093 1.060998517 LSKEDIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 LSKEDIER 8 1 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;;;; 144.65 0.00053079 37400540000 83280670 67339620 43516060 52870720 63581250 54888820 73258580 88211950 35970190 FALSE TRUE 72274918.45 66897261.6 64560572.17 64875825.05 62316107.52 57000428.42 66153974.19 69348510.96 31717835.12 2.278683844 2.109137063 2.035465912 2.045405206 1.964702423 1.797109677 2.085702695 2.18642006 1 24.91879097 1.23433636 24.99999412 0.999998448 2.058371442 0.873049214 0.127358968 45.10095879 266880.3743 0.250422189 0.033058714 17.15285278 -1.23433636 1.058372994 LSKEEIER ddPTM_MDA-MB-175_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 ;;;;;;;; 127.76 0.0010601 41258270000 49606730 40467090 24887010 32192840 38885300 33489320 49693030 53853430 24212580 FALSE TRUE 43051074.94 40201259.02 36922451.28 39502716.36 38111558.61 34777675.81 44873807.6 42337293.08 21350196.38 2.016425244 1.882945633 1.729372912 1.850227308 1.785068293 1.628915969 2.101798354 1.982993146 1 24.347746 1.234161018 24.99991163 0.999998706 1.873029963 0.795748408 0.138873953 62.39166358 354482.761 0.275492651 0.035839185 17.14592888 -1.234161018 0.873031256 LSLDELHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSLDELHR 8 0 P05023-4;P05023;P05023-3;P05023-2;Q5TC02;Q5TC01 P05023-4 ATP1A1 Sodium/potassium-transporting ATPase subunit alpha-1 0 ;;; 194.9 0.00016297 1080460000 1486980 1506300 1034086 2133180 2107430 2258460 946997 2428420 2400260 FALSE TRUE 1290471.825 1496405.016 1534173.448 2617551.123 2065496.266 2345344.418 855157.3767 1909121.281 2116503.997 0.609718586 0.707017335 0.72486206 1.236733371 0.975900007 1.108121894 0.40404241 0.902016383 1 21.01325178 3.977060309 24.496987 0.914890936 0.672760754 0.239594567 0.215552575 933.4644484 996838.1488 0.059219513 0.103579924 9485.501754 -3.977060309 -0.242130182 LSLDGNPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LSLDGNPK 8 0 B8ZZZ7;Q9NUQ6;Q9NUQ6-4;Q9NUQ6-3;F8VT91 B8ZZZ7 SPATS2L SPATS2-like protein 0 ;;;; 65.038 0.065307 2068810000 5094460 4731580 2355240 3230920 3740160 5472580 3813010 4106520 4186300 FALSE TRUE 4421214.203 4700497.939 3494241.942 3964549.768 3665738.133 5683113.694 3443224.877 3228372.655 3691400.383 1.197706492 1.273364429 0.946589798 1.073996141 0.993048099 1.53955494 0.93276928 0.874565834 1 21.8157368 2.051234947 24.99999993 0.920920542 1.159671074 0.305928064 0.165862722 117.6208003 57392.27046 0.066852177 0.045071718 112.5213533 -2.051234947 0.238750532 LSLEGDHST(ph)PPSAYGSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSLEGDHSTPPSAYGSVK 18 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YKS4;H0YMM1;H0YMW4;H0YKX9;H0YMT9;H0YLV6;H0YKZ7;H0YKL9;H0YKV8;H0YNB8;H0YKN4;H0YMD9 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 1 LSLEGDHS(0.148)T(0.85)PPS(0.002)AYGSVK;LSLEGDHS(0.056)T(0.943)PPSAYGSVK;LSLEGDHS(0.043)T(0.957)PPSAYGSVK;LSLEGDHS(0.324)T(0.676)PPSAYGSVK 134.86 1.44E-05 811730000 1177750 947250 592845 1176290 1075020 1129380 772110 1523480 1394130 TRUE FALSE 1022107.353 941027.4524 879546.8249 1443384.623 1053629.205 1172827.979 697230.891 1197695.658 1229317.54 0.831442911 0.765487697 0.715475698 1.174134897 0.85708466 0.954048032 0.567169074 0.974276881 1 20.22942619 LSLEGDHSTPPSAYGSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSLEGDHSTPPSAYGSVK 18 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YKS4;H0YMM1;H0YMW4;H0YKX9;H0YMT9;H0YLV6;H0YKZ7;H0YKL9;H0YKV8;H0YNB8;H0YKN4;H0YMD9 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 ; 188.27 3.87E-14 570090000 569600 501500 200276 538650 590580 572290 356970 725440 708190 FALSE TRUE 494325.9168 498205.6135 297130.1435 660958.7152 578828.6135 594306.3666 322351.1043 570310.3014 624468.585 0.791594531 0.797807328 0.475812796 1.058433893 0.926913903 0.951699382 0.516200674 0.913273005 1 19.25226947 3.730248878 24.99787477 0.876485798 0.699345125 0.244014339 0.168618939 1021.19088 3071272.184 0.046983685 0.07098709 5373.396376 -3.730248878 -0.177140673 LSLFPAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LSLFPASPR 9 0 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 LSLFPAS(1)PR;LSLFPAS(1)PR;LSLFPAS(1)PR;LSLFPAS(1)PR;LSLFPAS(1)PR 156.01 7.55E-05 617593000 1177987 1268661 744541 902121 1153191 1203338 1099158 1231656 1218224 TRUE FALSE 1022313.033 1260327.082 1104603.518 1106961.361 1130244.755 1249631.192 992561.8263 968275.9492 1074206.947 0.951690954 1.17326283 1.028296756 1.030491717 1.052166679 1.163305819 0.92399498 0.901386788 1 20.03484053 2.211740237 24.99990938 0.932634048 1.067357383 0.420675046 0.06872293 184.0746973 171579.0251 0.026391611 0.017798582 162.83218 -2.211740237 0.134723334 LSLFSDGDS(ph)SESEDTLSSSER ddPTM_MDA-MB-175_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(0.811)S(0.189)ESEDTLSSSER 237 7.96E-30 85577000 141210 142770 88163 99050 147110 145960 143350 163650 147410 TRUE FALSE 122548.7407 141832.1345 130798.9217 121540.8164 144182.7988 151575.1756 129447.9391 128654.721 129983.3577 0.942803316 1.091156106 1.006274372 0.935049059 1.109240455 1.166112172 0.995880868 0.989778409 1 16.9879674 4.767141652 23.01135357 1.033294299 0.942802917 0.157105338 0.067938296 7847.35389 6317804.522 0.017439978 1.508274589 58498.08541 -4.767141652 -0.090491382 LSLFSDGDSS(ph)ESEDTLSSSER ddPTM_MDA-MB-175_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(0.199)S(0.788)ES(0.013)EDTLSSSER 183.56 4.48E-17 89698000 127790 127360 84029 103630 134280 143970 124020 149200 149200 TRUE FALSE 110902.2277 126523.3638 124665.7055 127160.7754 131608.0907 149508.6191 111992.5595 117294.7411 131561.746 0.842967132 0.961703289 0.94758324 0.96654825 1.000352266 1.136414069 0.851254737 0.891556586 1 17.00538053 4.739133998 6.698621465 0.963350895 0.840809732 0.215634607 0.075012673 0.211320192 62.9998073 0.019410939 0.117091231 54844.61576 -4.739133998 -0.122541163 LSLGTYASLHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSLGTYASLHGR 12 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ; 234.63 5.01E-16 1375210000 1122320 1420990 483230 822650 1516600 1544500 1206990 1431370 1522650 FALSE TRUE 974002.5684 1411655.423 716921.6443 1009445.256 1486422.627 1603917.914 1089936.296 1125282.664 1342644.052 0.725436177 1.051399603 0.533962552 0.751833857 1.107086145 1.194596522 0.811783506 0.838109448 1 20.35664545 3.263236052 24.9952087 0.968113629 0.769518377 0.304707888 0.166721457 345.6999059 350177.476 0.050511 0.065180046 1833.310609 -3.263236052 -0.198595252 LSLMPWFHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSLMPWFHGK 10 0 P41240;H3BUM9;K7ENL8;K7ES68;K7EQY5;P42679-3;P42679;P42679-2 P41240 CSK;MATK Tyrosine-protein kinase CSK;Non-specific protein-tyrosine kinase;Megakaryocyte-associated tyrosine-protein kinase 0 107.79 0.0035657 0 86211 82407 53698 63729 89448 86889 95460 105980 97626 FALSE TRUE 74817.99792 81865.66299 79666.53241 78199.64349 87668.1598 90231.67605 86202.30389 83317.00174 86084.7655 0.869120076 0.950988976 0.92544287 0.908402817 1.018393432 1.048172409 1.00136538 0.967848391 1 16.39347032 3.240931433 24.99880119 1.00385902 0.917021135 0.732377622 0.028060119 37.24515164 392723.9934 0.008804627 0.010834323 1741.531896 -3.240931433 -0.086837885 LSLPGLLSQVS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSLPGLLSQVSPR 13 0 Q96Q42;Q96Q42-3 Q96Q42 ALS2 Alsin 1 LSLPGLLS(0.003)QVS(0.997)PR 113.52 0.00085535 102410000 168170 168570 118470 115100 129610 150290 177860 209420 146480 TRUE FALSE 145945.9084 167462.6526 175762.4883 141235.2142 127031.0146 156071.7536 160611.1646 164637.1627 129163.3013 1.129933247 1.296518833 1.360777299 1.093462406 0.983491544 1.208328929 1.243473672 1.274643502 1 16.97883669 3.727034003 24.86468856 1.152243331 1.265820702 0.219746858 0.110546777 1209.099853 2608215.624 0.03245915 0.048589941 5333.766541 -3.727034003 0.113577371 LSLPNTAWGSPSPEAAGYPGAGAEDEQQQLAANRHS(ph)LVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSLPNTAWGSPSPEAAGYPGAGAEDEQQQLAANRHSLVEK 40 1 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 LSLPNTAWGSPSPEAAGY(0.001)PGAGAEDEQQQLAANRHS(0.999)LVEK;LSLPNTAWGSPSPEAAGY(0.001)PGAGAEDEQQQLAANRHS(0.999)LVEK 102.93 8.01E-06 206962000 88997 97109 96541 109763 115918 118388 127099 152691 214559 TRUE FALSE 77235.82096 96471.08458 143228.5505 134686.3668 113611.4586 122942.463 114772.9585 120039.2179 189194.0794 0.40823593 0.50990541 0.757045627 0.711895252 0.600502188 0.649821936 0.606641386 0.634476609 1 17.52950742 -2 0.061927162 1.949608787 1.39E-12 0.401255563 0.121074538 993.9089772 5.955672967 188.8108494 45.84940781 0.01 2 -1.949608787 LSLS(ph)PLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 LSLSPLR 7 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 LSLS(1)PLR;LS(0.006)LS(0.994)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR;LS(0.009)LS(0.991)PLR 184.04 0.00066496 14062946000 5564070 6965000 4479060 5037380 6557910 7391040 6339340 6940980 7997910 TRUE FALSE 4828764.052 6919246.456 6645148.398 6181194.121 6427420.421 7675378.091 5724551.783 5456705.442 7052406.191 0.684697381 0.981118539 0.942252646 0.876465982 0.911379783 1.08833466 0.811716119 0.773736693 1 22.74968414 7.482237103 10.2640803 0.893349244 0.066602296 0 0.117665043 0 0 0.025975738 0 30355479.9 -7.482237103 -0.826746948 LSLSPALQDALHTFPQLQVEQSGEGS(ph)PEEGAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSLSPALQDALHTFPQLQVEQSGEGSPEEGAVR 33 0 Q9ULL5;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 LSLSPALQDALHTFPQLQVEQSGEGS(1)PEEGAVR;LSLSPALQDALHTFPQLQVEQS(0.079)GEGS(0.92)PEEGAVR;LSLSPALQDALHTFPQLQVEQS(0.067)GEGS(0.933)PEEGAVR 284.38 3.01E-74 398972000 221332 183404 114788 154472 164029 183195 176415 201958 195251 TRUE FALSE 192082.4154 182199.207 170299.8607 189547.2286 160765.1438 190242.6302 159306.3005 158770.8533 172168.6492 1.115664299 1.058260072 0.989145594 1.100939279 0.933765494 1.104978352 0.925292155 0.92218214 1 17.39346294 8 0.126399004 0.855107285 1.660418066 0.322102067 0.062352254 216.368751 2.411498809 1.806287787 30.68335514 100000000 -8 0.805310781 LSLTSDPEEGDPLALGPES(ph)PGEPQPPQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSLTSDPEEGDPLALGPESPGEPQPPQLK 29 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 LSLTSDPEEGDPLALGPES(1)PGEPQPPQLK;LSLTSDPEEGDPLALGPES(1)PGEPQPPQLK 108.11 0.00027129 109075000 142149 122449 83597 97792 107324 100320 135171 151362 152334 TRUE FALSE 123363.6495 121644.6245 124024.7888 119997.1683 105188.4624 104179.3753 122062.1372 118994.4142 134325.2481 0.918395099 0.905597616 0.923317028 0.893332936 0.783087795 0.775575529 0.908705839 0.885867817 1 17.03537098 1.035050014 1.900529493 1.112170578 0.869671106 0.360780612 0.052719305 1.989878482 4.275595926 1.047914599 0.015803808 10.84051748 -1.035050014 -0.242499472 LSMEDSKS(ph)PPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LSMEDSKSPPPK 12 1 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 1 LSMEDS(0.001)KS(0.999)PPPK;LSMEDSKS(1)PPPK;LSMEDSKS(1)PPPK;LSMEDS(0.001)KS(0.999)PPPK;LSMEDS(0.002)KS(0.998)PPPK;LSMEDS(0.001)KS(0.999)PPPK 157.37 3.99E-05 4486530000 4503590 3507150 3107230 3432950 3345700 2345220 4776080 5355150 4538510 TRUE FALSE 3908429.171 3484111.301 4609896.821 4212453.767 3279127.116 2435442.131 4312896.497 4209992.846 4001972.518 0.97662569 0.870598507 1.151906166 1.052594376 0.81937772 0.608560434 1.077692682 1.051979449 1 21.93227983 LSMEDSKS(ph)PPPKATEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSMEDSKSPPPKATEEK 17 2 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 1 LS(0.006)MEDS(0.024)KS(0.969)PPPKAT(0.001)EEK 69.398 0.01818 162280000 440590 302420 228300 165630 258370 158020 469280 559490 77871 TRUE FALSE 382364.9152 300433.3831 338706.6436 203238.823 253228.9425 164099.1317 423769.2978 439847.4175 68665.17909 5.56854173 4.375338229 4.932727885 2.959852806 3.687880027 2.389844952 6.17153124 6.405683685 1 16.06729106 4.94371455 1.51150069 4.170804198 6.682542907 0.076990655 1.648523436 6.632992891 9.605199998 0.475944426 28.69246369 87844.49492 -4.94371455 2.511738709 LSMPQSAAVST(ph)TPPHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSMPQSAAVSTTPPHNR 17 0 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 LSMPQSAAVS(0.007)T(0.84)T(0.154)PPHNR 143.4 1.56E-06 380790000 109910 101570 60925 68957 98985 111050 83848 96068 155140 TRUE FALSE 95385.11502 100902.78 90388.53378 84614.74079 97015.39216 115322.1654 75716.43387 75524.6058 136799.5259 0.697262029 0.737595977 0.660737186 0.61853095 0.709179301 0.843001206 0.553484622 0.552082365 1 17.06170371 1.226044894 24.96517691 1.000000787 0.666969255 0.58787436 0.086369767 466.2151142 929903.0749 0.397236527 0.022940849 16.82848014 -1.226044894 -0.333031532 RNGAAGPHS(ph)PDPLLDEQAFGDLTDLPVVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RNGAAGPHSPDPLLDEQAFGDLTDLPVVPK 30 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 RNGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;RNGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;RNGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;RNGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;RNGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK 213.1 1.07E-26 1122434000 426701 553486 401622 682515 957877 692938 1267187 1473460 906302 TRUE FALSE 370311.3817 549850.114 595847.7425 837490.4623 938817.1218 719595.7733 1144295.4 1158372.045 799160.01 0.463375766 0.688035071 0.745592541 1.047963426 1.17475488 0.900440167 1.431872698 1.449487 1 19.60812487 4.156507864 0.541561072 1.321055172 0.192817242 0.710549534 0.168254186 1.318159567 0.508305644 0.139193145 0.905267344 14338.6368 -4.156507864 -1.128237929 down LSMPQSAAVSTT(ph)PPHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LSMPQSAAVSTTPPHNR 17 0 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 LSMPQSAAVS(0.006)T(0.156)T(0.838)PPHNR;LSMPQSAAVS(0.001)T(0.204)T(0.795)PPHNR;LSMPQSAAVS(0.012)T(0.24)T(0.748)PPHNR;LSMPQSAAVST(0.114)T(0.886)PPHNR;LSMPQSAAVST(0.013)T(0.987)PPHNR;LSMPQSAAVS(0.002)T(0.012)T(0.986)PPHNR 161.96 1.07E-08 5700080000 1260062 1259533 895965 981357 1315306 1393673 1175043 1249809 1955230 TRUE FALSE 1093541.614 1251259.045 1329256.671 1204189.106 1289133.984 1447288.502 1061087.511 982547.0714 1724084.937 0.634273632 0.725752553 0.770992567 0.69845115 0.747720693 0.839453133 0.615449673 0.569894818 1 20.71739942 4.736919623 6.746326998 0.72847308 0.632701043 0.063727415 0.118811566 0.380627126 119.5975026 0.028967485 0.168402322 54565.68649 -4.736919623 -0.095772037 LSMPQSAAVSTT(ph)PPHNRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSMPQSAAVSTTPPHNRR 18 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 LSMPQSAAVS(0.003)T(0.189)T(0.808)PPHNRR 118.48 7.73E-05 379180000 206490 231400 127000 121350 212000 242640 199220 188310 113540 TRUE FALSE 179201.8233 229879.9182 188417.6248 148904.3722 207781.6148 251974.5178 179899.6751 148041.3719 100117.4305 1.789916325 2.296102856 1.881966245 1.487297181 2.075379019 2.516789698 1.796886657 1.4786773 1 16.61133365 1.53582329 2.12101947 0.98626727 1.999243038 0.577885978 0.280864052 0.27545884 2.254374753 0.465015825 0.080871315 34.34181858 -1.53582329 1.012975767 LSMWDRPDDLIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSMWDRPDDLIGR 13 1 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 150.12 4.02E-05 321560000 108930 104910 59427 77647 92946 99187 92512 105140 104250 FALSE TRUE 94534.62451 104220.8393 88166.09597 95277.93811 91096.55645 103002.7881 83540.20048 82656.6292 91925.68376 1.028380977 1.133751037 0.959101878 1.036467005 0.990980461 1.120500646 0.908779756 0.899167956 1 16.48818038 2.218482188 24.99845532 0.927179366 1.042174845 0.432955752 0.058397121 206.0310969 256515.1546 0.022934309 0.01548383 165.3796956 -2.218482188 0.11499548 LSNHISSLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSNHISSLFR 10 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 163.9 6.32E-06 14889000000 2392000 3895800 1376460 1991800 5281700 6030900 3571300 3523600 4481500 FALSE TRUE 2075891.139 3870208.233 2042120.66 2444068.633 5176604.503 6262912.626 3224955.876 2770105.561 3951702.175 0.525315686 0.979377509 0.51676988 0.618485029 1.30996828 1.584864534 0.816092846 0.700990469 1 21.91404279 3.262007015 24.99926482 1.039861471 0.672570686 0.362758384 0.274771572 335.9028551 358147.4642 0.088891083 0.114687226 1828.129744 -3.262007015 -0.367290785 LSNRPAFMPSEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSNRPAFMPSEGK 13 1 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ; 158.93 3.81E-05 3729000000 3510500 2985600 2505600 3618900 2911100 2604100 3138600 3851300 6093100 FALSE TRUE 3046578.531 2965987.397 3717316.541 4440626.556 2853174.805 2704281.412 2834219.055 3027729.466 5372780.659 0.567039439 0.552039546 0.691879452 0.826504344 0.531042487 0.503329948 0.527514379 0.563531188 1 22.35723751 1.23588445 24.99918473 1.000000539 0.594687685 0.635018839 0.096406802 52.54965512 490788.6869 0.169977584 0.025458197 17.2141051 -1.23588445 -0.405312854 LSPEDYTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSPEDYTLK 9 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;A0A1B0GU92;A0A1B0GU03;H7C469;H7C1V0;A0A1B0GVF1 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ; 115.71 0.0033294 1030620000 752160 681660 592830 683370 688600 675300 810790 945350 865750 FALSE TRUE 652760.1503 677182.1306 879524.5709 838539.6032 674898.2072 701279.228 732159.7106 743194.2592 763402.0213 0.855067359 0.887058341 1.152111923 1.098424657 0.884066571 0.918623751 0.959074891 0.973529331 1 19.54208348 4.451431135 24.99954051 0.992340498 0.863064812 0.312872006 0.078543157 246.6567384 240026.2117 0.020989698 0.055537218 28276.85695 -4.451431135 -0.129275686 LSPFFTLDLS(ph)PTEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSPFFTLDLSPTEDK 15 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 LSPFFTLDLS(0.999)PT(0.001)EDK 131.4 5.65E-05 80624000 185620 143120 128270 162230 121580 109290 166500 216540 293480 TRUE FALSE 161089.8467 142179.8353 190301.801 199066.801 119160.7959 113494.457 150352.8556 170234.6061 258785.1287 0.622484945 0.549412696 0.735366062 0.76923586 0.460462301 0.43856638 0.58099496 0.657822213 1 17.98139519 1.224117271 3.009330341 1.086072689 0.594182172 0.601042858 0.10318561 0.315570645 3.491099178 0.385424374 0.028938877 16.75395214 -1.224117271 -0.491890516 LSPFHGSSPPQSTPLS(ph)PPPLTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSPFHGSSPPQSTPLSPPPLTPK 23 0 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 LSPFHGSSPPQST(0.002)PLS(0.998)PPPLTPK;LSPFHGSSPPQS(0.001)T(0.005)PLS(0.993)PPPLTPK 105.17 0.0010087 795750000 111263 197541 77027 162339 407840 319810 318530 365200 307890 TRUE FALSE 96559.31265 196243.3402 114277.5148 199200.5511 399724.7819 332113.2976 287639.0096 287104.822 271491.5949 0.355662254 0.722833943 0.420924688 0.733726402 1.472328386 1.223291269 1.059476665 1.057509062 1 18.05054801 3.432184395 6.677083471 1.143696546 0.53016807 0.786822709 0.159707567 0.089667753 9.870788691 0.046686153 0.060840649 2705.106667 -3.432184395 -0.613528476 LSPFVLSAGSGS(ph)PSATSILQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSPFVLSAGSGSPSATSILQK 21 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2 Q9UMZ2-4 SYNRG Synergin gamma 1 LSPFVLSAGS(0.295)GS(0.638)PS(0.064)AT(0.002)SILQK 186.11 3.52E-17 139270000 763400 660770 496100 584030 734540 614430 829250 943170 968710 TRUE FALSE 662514.7558 656429.3584 736015.6194 716642.9378 719924.0911 638067.5197 748829.4626 741480.4353 854190.2074 0.775605656 0.768481484 0.861653076 0.838973488 0.842814732 0.74698529 0.876654235 0.868050733 1 19.70419783 0.184716336 0.916802359 2.057302157 0.810183265 0.686228502 0.040081482 7.560301736 1.120410004 14.86234079 0.013916914 1.530087741 -0.184716336 -1.247118893 LSPS(ph)FR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSPSFR 6 0 B4DF95;Q15735 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 LS(0.14)PS(0.86)FR 139.14 0.012588 241430000 491150 496350 304360 364780 498820 542190 502700 542650 489370 TRUE FALSE 426243.2831 493089.4442 451549.514 447608.8743 488894.4579 563048.4001 453948.2314 426608.5204 431517.2361 0.987778117 1.142687714 1.046422892 1.037290835 1.132966234 1.304810916 1.05198169 0.98862452 1 18.71905866 2.002826112 24.99992888 1.001540711 1.111334591 0.239562155 0.084337579 119.174941 1054220.345 0.0357097 0.023922413 100.6528582 -2.002826112 0.109793881 LSPS(ph)PSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LSPSPSSR 8 0 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 1 LS(0.002)PS(0.982)PS(0.017)SR;LSPS(0.997)PS(0.002)SR;LS(0.002)PS(0.998)PS(0.001)SR;LS(0.002)PS(0.998)PSSR;LS(0.022)PS(0.921)PS(0.057)SR 199.81 0.00013103 10141990000 6140570 6242220 3643560 5005590 5817370 6220550 5262610 7157370 6110590 TRUE FALSE 5329078.116 6201214.446 5405597.803 6142185.715 5701615.718 6459858.584 4752242.892 5626822.124 5388203.011 0.989026973 1.150887306 1.00322831 1.139932126 1.058166462 1.198889235 0.88197176 1.044285472 1 22.36137278 2.236776754 24.99981576 0.985872629 1.089663875 0.336247156 0.075427262 54.84027045 768528.6159 0.027242986 0.019432173 172.4950963 -2.236776754 0.103791246 LSPS(ph)PTSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 LSPSPTSQR 9 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 LSPS(0.999)PT(0.001)SQR;LSPS(0.999)PT(0.001)SQR;LSPS(0.831)PT(0.169)SQR;LSPS(0.874)PT(0.126)SQR;LSPS(0.998)PT(0.002)SQR;LSPS(0.614)PT(0.384)S(0.001)QR;LS(0.026)PS(0.969)PT(0.004)SQR;LS(0.001)PS(0.989)PT(0.009)S(0.001)QR;LS(0.002)PS(0.955)PT(0.043)SQR 242.32 2.03E-10 69270370000 8702980 8320790 5431333 6274074 7328750 7828454 7833680 8841740 7968616 TRUE FALSE 7552859.142 8266130.183 8057943.806 7698698.395 7182922.213 8129619.691 7073970.919 6951002.707 7026575.294 1.074899055 1.176409536 1.146781109 1.095654437 1.0222508 1.156981794 1.006745196 0.989244748 1 22.74439027 2.102577865 0.634857204 0.9506937 1.132612353 0.509428426 0.048413336 1.10635484 0.73695047 0.135285575 0.033130922 126.6420303 -2.102577865 0.181918653 LSPS(ph)PTTEDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSPSPTTEDPR 11 0 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2 Q9BTC8 MTA3 Metastasis-associated protein MTA3 1 LSPS(0.99)PT(0.009)TEDPR;LSPS(0.992)PT(0.005)T(0.003)EDPR;LS(0.001)PS(0.947)PT(0.043)T(0.009)EDPR;LSPS(0.985)PT(0.012)T(0.003)EDPR 165.58 2.25E-05 1687660000 1552310 1132220 828510 1066230 1157060 1244350 1187440 1209430 1959780 TRUE FALSE 1347168.3 1124782.372 1229180.207 1308333.818 1134036.77 1292220.95 1072282.252 950802.8063 1728097.041 0.779567506 0.650879173 0.711291194 0.757095109 0.656234426 0.747771056 0.620498864 0.550202207 1 20.7207528 3.231474054 24.98559257 0.688907235 0.71847638 0 0.122508279 1129.701507 3983065.931 0.036413194 0.04216403 1704.017515 -3.231474054 0.029569145 LSPT(ph)PSMQDGLDLPSETDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSPTPSMQDGLDLPSETDLR 20 0 Q9UK58;Q9UK58-6;Q9UK58-5;Q9UK58-4 Q9UK58 CCNL1 Cyclin-L1 1 LS(0.147)PT(0.85)PS(0.003)MQDGLDLPSETDLR 140.35 2.27E-06 31737000 46295 40538 28998 38828 41629 37466 44055 48494 72783 TRUE FALSE 40176.99845 40271.70321 43021.52979 47644.49085 40800.66435 38907.34126 39782.55288 38123.93548 64178.67665 0.62601787 0.627493512 0.670339933 0.742372597 0.63573552 0.606234707 0.619871817 0.594028071 1 15.96980642 1.234136377 24.99999495 1.000000535 0.639665869 0.881714172 0.041408179 47.53474277 268569.1333 0.086196381 0.01117808 17.14495609 -1.234136377 -0.360334665 LSPWIRPDSK ddPTM_MDA-MB-175_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 ; 130.01 0.00026271 609030000 2214300 1920700 1150560 1420730 1751990 1506350 2111700 2387400 1834280 FALSE TRUE 1921674.645 1908082.795 1706974.664 1743328.461 1717128.827 1564300.259 1906907.659 1876873.089 1617433.508 1.188101171 1.179697827 1.055360023 1.077836246 1.06163797 0.967149655 1.178971284 1.160402007 1 20.62527497 4.249413494 24.37460648 1.081434193 1.18389961 0.341197989 0.063737213 206.0194711 462688.959 0.017015113 0.043989049 17758.79498 -4.249413494 0.102465416 LSQELEYLTEDVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSQELEYLTEDVKR 14 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ;; 169.92 5.22E-06 280070000 314296 251537 168361 215814 256787 219185 318054 372496 275955 FALSE TRUE 272760.9873 249884.6369 249780.9427 264817.8672 251677.4411 227617.1888 287209.172 292840.6292 243331.9143 1.120942101 1.026929154 1.026503011 1.088298952 1.034296886 0.93541856 1.180318549 1.203461659 1 17.89256602 2.211168805 24.99995837 1.145846197 1.039690569 0.245264704 0.071478153 251.1054808 229177.0614 0.028746341 0.019385675 162.6180709 -2.211168805 -0.106155629 LSQMQS(ph)PIPLTETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSQMQSPIPLTETR 14 0 H3BSW6;Q2VPK5-3;Q2VPK5;Q2VPK5-5 H3BSW6 CTU2 Cytoplasmic tRNA 2-thiolation protein 2 1 LSQMQS(1)PIPLTETR;LSQMQS(1)PIPLTETR 149.19 7.92E-06 311750000 326670 397720 249060 293610 441270 435670 392320 473710 462930 TRUE FALSE 283499.7318 395107.3511 369506.2491 360278.638 432489.5903 452430.5068 354272.8668 372410.8029 408202.9428 0.69450683 0.967918919 0.905202316 0.882596866 1.059496503 1.108347 0.867884157 0.912317781 1 18.63892706 4.739913679 24.68010697 0.957798567 0.69450673 0.544261594 0.077075324 84.30240432 1537496.321 0.019855341 0.120556993 54943.16575 -4.739913679 -0.263291837 LSQSSQDSS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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;LSQSSQDSS(1)PVR;LSQSSQDSS(1)PVR;LSQSSQDS(0.054)S(0.946)PVR;LSQSSQDS(0.008)S(0.992)PVR 289.99 4.49E-36 6723103000 10650140 8469840 4330160 5542160 7356530 6867480 6577400 8545430 6610470 TRUE FALSE 9242697.015 8414201.063 6424239.86 6800592.135 7210149.446 7131676.399 5939524.76 6718056.295 5828987.767 1.585643577 1.443509817 1.10211929 1.166684921 1.236947088 1.223484537 1.018963326 1.152525372 1 22.47481394 4.354468943 3.558477368 1.132850479 1.561017952 0.813774372 0.077966645 0.092356198 2.177481561 0.020340945 0.064377955 22618.76784 -4.354468943 0.428167473 LSQTSNVDKEEEAVTIEMNEPVQLTFALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSQTSNVDKEEEAVTIEMNEPVQLTFALR 29 1 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 127.24 1.76E-05 101290000 200320 161720 114850 153660 156720 131940 172910 242830 169270 FALSE TRUE 173847.2045 160657.6507 170391.8442 188550.8515 153601.5786 137015.8172 156141.2148 190902.6942 149259.0934 1.164734426 1.07636759 1.141584343 1.263245322 1.029093606 0.917972996 1.046108557 1.279002102 1 17.1874593 3.200208186 24.99999145 1.075058661 1.153982498 0.198910676 0.101699646 391.5495654 255229.8422 0.034569322 0.039198655 1585.65312 -3.200208186 0.078923837 LSQYLDSSQVKPLFQFFVPDALNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSQYLDSSQVKPLFQFFVPDALNDR 25 1 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 178.15 2.70E-17 691480000 422390 326940 316620 345800 382990 400450 378910 469890 831150 FALSE TRUE 366570.0913 324792.3096 469738.491 424319.1752 375369.2483 415855.5706 342163.3665 369407.6802 732892.3938 0.500169049 0.443165071 0.640937872 0.578965178 0.512175118 0.567416955 0.466867127 0.504040816 1 19.48324187 1.236930056 24.99999573 1.000000585 0.526257277 0.871232112 0.057181854 14.49450487 222160.3815 0.088534821 0.014302728 17.25559966 -1.236930056 -0.473743308 LSRPERPDLVFEEEDLPYEEEIMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSRPERPDLVFEEEDLPYEEEIMR 24 2 Q9HCS7 Q9HCS7 XAB2 Pre-mRNA-splicing factor SYF1 0 67.992 0.019462 40902000 21321 21949 16472 15987 19126 20589 17373 24050 19963 FALSE TRUE 18503.37583 21804.81557 24437.9143 19617.0927 18745.43002 21381.07215 15688.16913 18907.09466 17602.99688 1.051149185 1.238699053 1.388281465 1.114417779 1.064899923 1.214626822 0.891221491 1.07408385 1 14.10353345 2.805990092 1.087419634 1.008160374 1.21641553 0.330915095 0.112905833 0.561318993 1.452056693 0.066100947 0.055841091 639.7202412 -2.805990092 0.208255156 LSS(ph)ATANALYSSNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSSATANALYSSNLR 15 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 LSS(1)ATANALYSSNLR;LSS(1)ATANALYSSNLR;LSS(1)ATANALYSSNLR;LS(0.002)S(0.998)ATANALYSSNLR 417 1.38E-133 903370000 832140 851190 836080 1021090 1400500 1527920 1271800 1351210 1967150 TRUE FALSE 722170.5906 845598.4768 1240411.085 1252944.091 1372632.79 1586700.071 1148461.032 1062264.257 1734595.768 0.416333652 0.487490222 0.715100952 0.72232627 0.791327187 0.914737658 0.662091453 0.612398736 1 20.72616806 4.266123667 2.25452702 0.764204823 0.412331073 0.5910351 0.112770568 0.245740944 2.387492702 0.031493533 0.116779335 18455.4087 -4.266123667 -0.35187375 LSS(ph)GFDDIDLPSAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSSGFDDIDLPSAVK 15 0 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 LS(0.023)S(0.977)GFDDIDLPSAVK;LS(0.018)S(0.982)GFDDIDLPSAVK;LS(0.002)S(0.998)GFDDIDLPSAVK;LS(0.013)S(0.987)GFDDIDLPSAVK 377.85 6.00E-98 2376020000 3464450 2291080 889548 2047250 1801300 542031 4241940 3185370 2831030 TRUE FALSE 3006614.155 2276029.745 1319736.388 2512109.403 1765457.654 562883.2833 3830557.312 2504203.414 2496348.859 1.204404643 0.91174346 0.52866665 1.006313438 0.70721592 0.225482621 1.534463943 1.003146417 1 21.25138813 2.222738086 24.99991876 1.157327206 0.768428016 0.296630821 0.300736726 322.3041769 509243.2039 0.121397123 0.082149631 167.0083117 -2.222738086 -0.38889919 LSS(ph)LPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSSLPR 6 0 Q63ZY3-3;Q63ZY3;Q63ZY3-2;K7ES05 Q63ZY3-3 KANK2 KN motif and ankyrin repeat domain-containing protein 2 1 LS(0.271)S(0.729)LPR 104.75 0.035211 197850000 200190 220530 154810 180180 288530 285120 285830 326000 311530 TRUE FALSE 173734.3843 219081.3239 229676.6338 221092.6229 282788.8175 296088.7509 258110.2506 256287.4369 274701.2783 0.632448401 0.797525681 0.836095978 0.804847448 1.029441214 1.077857201 0.939603384 0.932967762 1 18.0675041 4.332158217 0.770376599 0.985635199 0.566557142 0.765035584 0.063817223 0.881639044 0.601521324 0.029708545 0.290692296 21486.13089 -4.332158217 -0.419078057 S(ph)APAS(ph)PTHPGLMSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 S(1)APAS(0.929)PT(0.071)HPGLMSPR 91.547 0.0029505 1250300000 421830 348130 149870 138910 202990 179880 178350 189990 184160 TRUE FALSE 366084.0967 345843.1111 222347.6333 170451.6386 198950.8961 186800.1 161053.6445 149362.117 162388.8146 2.254367689 2.129722493 1.36922998 1.049651351 1.225151478 1.150326151 0.991777943 0.91978082 1 17.30909274 4.171843834 2.30348085 1.047295556 2.276238795 0.966184301 0.08684692 0.056750746 0.591518673 0.028216529 0.088017261 14854.01418 -4.171843834 1.228943239 up LSS(ph)LRAS(ph)TSKSESSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSSLRASTSKSESSQK 16 2 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 LS(0.464)S(0.536)LRAS(0.814)T(0.1)S(0.068)KS(0.012)ES(0.003)S(0.002)QK 92.336 0.0025776 625550000 115230 276200 185230 198810 416110 291640 589450 653230 53863 TRUE FALSE 100002.0635 274385.624 274807.8476 243952.8491 407830.2251 302859.5795 532285.2297 513541.8479 47495.3775 2.1055115 5.777101656 5.785991438 5.136349303 8.586735101 6.376611693 11.20709546 10.81245955 1 15.53549949 4.599525619 0.633949574 8.261268142 6.87E-14 0.19982209 2.940493049 4.318012321 1.534270919 1.562317837 25.47638708 39767.25548 -4.599525619 -8.261268142 AYSGS(ph)DLPSSSSGGANGTAGGGGGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AYSGSDLPSSSSGGANGTAGGGGGAR 26 0 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 AYS(0.465)GS(0.52)DLPS(0.006)S(0.006)S(0.002)SGGANGTAGGGGGAR 298.96 1.70E-70 171810000 65643 73832 69082 93032 135460 128830 132980 162260 134800 TRUE FALSE 56968.11123 73346.99273 102490.2863 114156.3375 132764.611 133786.1735 120083.6201 127561.9617 118864.0976 0.479270969 0.617065996 0.862247629 0.960393759 1.116944593 1.125538966 1.010259805 1.073174864 1 16.85895349 4.202308873 1.321513477 1.063776482 0.435325219 0.95587939 0.044825998 0.112764208 0.319700519 0.014128933 0.074631401 15933.41518 -4.202308873 -0.628451263 down LSS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSSPER 6 0 O14579;M0QXB4;O14579-3;O14579-2;M0R061;Q8TDZ2-3;Q8TDZ2-2;Q8TDZ2;Q8TDZ2-4 O14579;Q8TDZ2-2 COPE;MICAL1 Coatomer subunit epsilon;Protein-methionine sulfoxide oxidase MICAL1 1 LS(0.055)S(0.945)PER;LS(0.08)S(0.92)PER 75.854 0.080343 921270000 909870 991080 674960 827580 810670 986470 924260 1117720 1065340 TRUE FALSE 789628.3742 984569.5302 1001372.914 1015494.688 794539.253 1024420.139 834625.4075 878704.2761 939396.7188 0.840569653 1.048087044 1.065974464 1.081007276 0.845797348 1.090508535 0.888469579 0.935392107 1 19.84137503 3.265212178 24.99988123 0.952109656 1.015784001 0.084744447 0.091649292 524.5508008 492039.3214 0.025365657 0.032737161 1841.671544 -3.265212178 0.063674345 LSS(ph)PGPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSSPGPSR 8 0 Q86VQ6;H0YBI6;H0YBQ0 Q86VQ6 TXNRD3 Thioredoxin reductase 3 1 LS(0.028)S(0.972)PGPSR;LS(0.1)S(0.9)PGPSR 123.6 0.0014065 685130000 1998890 1774820 1259240 1455080 1483070 1832440 1928180 1969100 2610200 TRUE FALSE 1734731.622 1763161.091 1868212.676 1785478.154 1453559.809 1902935.153 1741185.4 1548023.289 2301625.13 0.753698593 0.766050504 0.811692856 0.775746724 0.631536296 0.826778926 0.756502602 0.672578375 1 21.13422145 1.227814142 24.99999179 1.000000532 0.74809942 0.645169186 0.058417636 303.5619547 706141.7508 0.204652398 0.014297484 16.89717655 -1.227814142 -0.251901111 LSS(ph)PISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSSPISK 7 0 A0A494C142;Q99728-3;Q99728-2;Q99728 A0A494C142 BARD1 BRCA1-associated RING domain protein 1 1 LSS(1)PISK 129.38 0.0038451 367970000 1100200 982000 674520 956890 961680 760160 1085900 1415300 1438300 TRUE FALSE 954805.7824 975549.1773 1000720.128 1174166.5 942544.4495 789403.8471 980589.5851 1112649.109 1268265.813 0.752843586 0.769199302 0.789046049 0.925804739 0.743175792 0.622427759 0.773173554 0.877299615 1 20.27442572 1.463123854 2.505126204 1.004854379 0.768656884 0.523684848 0.072844511 0.296874743 3.14569327 0.12808724 0.021057182 29.04850954 -1.463123854 -0.236197495 LSS(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSSPVK 6 0 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 LS(0.002)S(0.998)PVK;LS(0.011)S(0.989)PVK;LS(0.132)S(0.868)PVK;LS(0.002)S(0.998)PVK 134.15 0.01485 3004490000 11609900 9343800 7933700 10142800 7202000 6677600 10857800 13125300 18810500 TRUE FALSE 10075622.3 9282419.963 11770463.86 12445877.76 7058694.29 6934491.593 9804812.227 10318556.74 16586744.12 0.607450276 0.559628815 0.709630761 0.750350863 0.425562379 0.418074309 0.591123379 0.622096577 1 23.98352739 1.219565898 3.46383465 1.07357959 0.580208115 0.612742061 0.104016178 0.252859671 4.263525202 0.341650475 0.028750461 16.57928886 -1.219565898 -0.493371476 SWS(ph)ASDPFYTNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SWSASDPFYTNDR 13 0 Q9Y2G3 Q9Y2G3 ATP11B Probable phospholipid-transporting ATPase IF 1 S(0.014)WS(0.978)AS(0.008)DPFYTNDR 75.02 0.034118 52940000 116960 130000 119240 158900 216150 260210 196590 264200 251990 TRUE FALSE 101503.4397 129146.0214 176904.8628 194980.6736 211849.0379 270220.4471 177524.7321 207702.886 222200.0293 0.456811099 0.581215141 0.796151393 0.877500666 0.953415887 1.216113463 0.798941083 0.93475634 1 17.76149948 4.214517853 1.278000919 0.969857995 0.412674674 0.766594993 0.102786751 0.31372325 0.81104901 0.032577878 0.182033481 16387.69426 -4.214517853 -0.557183321 down LSS(ph)TDDGYIDLQFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSSTDDGYIDLQFK 14 0 Q96A57;Q96A57-2;Q5JWB9;A0A087WTT2 Q96A57 TMEM230 Transmembrane protein 230 1 LS(0.004)S(0.994)T(0.002)DDGYIDLQFK;LS(0.021)S(0.958)T(0.021)DDGYIDLQFK;LS(0.14)S(0.853)T(0.007)DDGYIDLQFK;LS(0.02)S(0.961)T(0.02)DDGYIDLQFK 287.48 5.41E-34 616440000 1389590 964000 691260 1084380 1118620 773260 1413760 1873310 1574880 TRUE FALSE 1205952.161 957667.4205 1025555.648 1330605.053 1096361.651 803007.8126 1276653.773 1472717.235 1388699.481 0.868403983 0.689614588 0.738500779 0.958166307 0.789488054 0.578244483 0.919316087 1.060501034 1 20.405303 2.006348797 24.99840272 1.021173007 0.772524346 0.539280591 0.100948224 114.0809811 449192.0867 0.04161081 0.027974052 101.472602 -2.006348797 -0.24864866 LSS(ph)TS(ph)SEETQLFHIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 2 LS(0.002)S(0.515)T(0.506)S(0.956)S(0.02)EETQLFHIPR;LS(0.058)S(0.919)T(0.023)S(0.977)S(0.023)EETQLFHIPR;LS(0.117)S(0.882)T(0.056)S(0.861)S(0.083)EETQLFHIPR 224.36 1.15E-14 299594000 499560 511890 382818 568320 680510 769500 487070 768940 767900 TRUE FALSE 433541.8803 508527.3609 567950.0652 697365.7422 666969.1824 799103.1629 439834.0264 604508.1649 677119.7368 0.640273583 0.751015416 0.838773461 1.029900185 0.985009218 1.180150451 0.6495661 0.892764059 1 19.36905145 4.251986398 2.14081432 0.940361761 0.656918408 0.39406922 0.134025491 0.382824111 3.33394172 0.037880318 0.142735466 17864.31623 -4.251986398 -0.283443353 LSS(ph)TSS(ph)EETQLFHIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 2 LS(0.144)S(0.776)T(0.256)S(0.219)S(0.597)EET(0.008)QLFHIPR;LS(0.153)S(0.732)T(0.114)S(0.111)S(0.89)EETQLFHIPR 94.188 0.0022063 398250000 98005 95991 71770 99818 124599 135927 95349 151535 140976 TRUE FALSE 85053.39094 95360.4288 106478.2121 122483.2025 122119.7237 141156.1996 86102.06866 119130.4195 124309.9779 0.684204055 0.767118058 0.856554026 0.985304676 0.982380705 1.135517857 0.692640045 0.958333527 1 16.92358258 4.207236239 1.998848208 0.950226347 0.694625381 0.440886282 0.109181893 0.351114185 2.665046413 0.030415407 0.111780086 16115.22002 -4.207236239 -0.255600965 LSS(ph)TSSEETQLFHIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 1 LS(0.034)S(0.95)T(0.013)S(0.001)S(0.002)EETQLFHIPR;LS(0.224)S(0.763)T(0.012)S(0.001)SEETQLFHIPR;LS(0.031)S(0.955)T(0.012)S(0.002)SEETQLFHIPR 300.86 4.18E-46 519996000 149511 178665 134080 171364 246357 268938 181091 258036 248400 TRUE FALSE 129752.7425 177491.3379 198921.5365 210274.8153 241454.9777 279284.2189 163528.8227 202857.0094 219034.435 0.592385131 0.810335315 0.908174719 0.960008025 1.102360812 1.275069917 0.746589561 0.92614209 1 17.74079817 4.629798944 1.353086192 0.991908954 0.476832286 0.498017895 0.13291719 1.00623618 1.919232749 0.04104857 0.674222641 42638.20797 -4.629798944 -0.515076668 LSSAGPRS(ph)PYCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSSAGPRSPYCK 12 1 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 LSSAGPRS(1)PYCK;LSSAGPRS(0.999)PYCK;LSSAGPRS(0.992)PY(0.008)CK;LS(0.001)S(0.005)AGPRS(0.994)PYCK 144.55 3.58E-05 1517070000 2368840 2319070 1120200 1608250 2098070 1788840 2169780 2731930 822360 TRUE FALSE 2055791.792 2303835.876 1661932.467 1973427.743 2056322.512 1857657.832 1959355.07 2147728.029 725141.5376 2.835021421 3.177084413 2.291873215 2.72143801 2.835753305 2.561786542 2.702031214 2.961805272 1 19.46790309 1.234575953 24.99999998 0.999997456 2.760752259 0.849225213 0.233172597 42.79466326 268457.8682 0.416123604 0.056028431 17.16231832 -1.234575953 1.760754803 LSSAHNGGSAFGAAGYGGAQPTPPMPTRPVS(ph)FHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSSAHNGGSAFGAAGYGGAQPTPPMPTRPVSFHER 35 1 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 LSSAHNGGSAFGAAGYGGAQPT(0.123)PPMPT(0.219)RPVS(0.658)FHER 359.76 5.23E-133 484070000 57003 86439 28433 52441 93616 106590 62525 77034 102220 TRUE FALSE 49469.90912 85871.17652 42183.2939 64348.53056 91753.22476 110690.5863 56461.33512 60560.87858 90135.66805 0.548838326 0.95268808 0.467997795 0.713907512 1.0179458 1.228044221 0.626403913 0.671885835 1 16.45981049 3.421223727 10.22772149 0.873536222 0.670324007 0.233166998 0.210736249 0.818098013 144.642144 0.064204267 0.082927553 2637.689846 -3.421223727 -0.203212215 LSSANGHEER ddPTM_MDA-MB-175_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 ; 117.79 0.00091062 889710000 509810 475780 157597 356490 492280 530630 468110 574640 529910 FALSE TRUE 442437.3168 472654.5699 233811.4363 437436.5031 482484.5911 551043.6795 422712.7642 451757.7079 467264.6435 0.94686667 1.011535061 0.500383326 0.936164354 1.032572436 1.179296759 0.904653862 0.966813377 1 18.83388035 3.485796839 24.73984072 1.007820805 0.81870317 0.268583338 0.1480767 497.7064441 1419291.473 0.042158631 0.057366309 3060.531399 -3.485796839 -0.189117635 LSSCDSFTSTINELNHCLSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSSCDSFTSTINELNHCLSLR 21 0 P07814;V9GYZ6;V9GZ76 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 303.86 2.33E-55 988950000 719140 654950 399080 579340 688150 689350 681710 807640 707670 FALSE TRUE 624103.8269 650647.5903 592076.4228 710888.0017 674457.1613 715869.7406 615597.8691 634932.4711 624010.0588 1.000150267 1.042687664 0.948825126 1.139225228 1.080843412 1.147208656 0.986519144 1.017503584 1 19.25120976 5.96682468 13.15115729 1.040867139 0.74011635 0 0.064878971 0 0 0.014723354 0 926455.7471 -5.96682468 -0.300750789 LSSERPS(ph)SDGEGVVENGITTCNGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSSERPSSDGEGVVENGITTCNGK 24 1 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 LSSERPS(0.692)S(0.308)DGEGVVENGITTCNGK 278.97 2.30E-52 393570000 214290 163900 131350 147860 161640 142420 176130 227740 239120 TRUE FALSE 185971.0336 162823.3301 194871.2993 181433.8729 158423.6802 147898.9896 159048.9397 179039.5733 210851.506 0.882000025 0.772218009 0.924211086 0.86048175 0.751351903 0.701436724 0.754317305 0.849126367 1 17.6858678 1.273363871 3.376996264 1.021836398 0.8055866 0.447725319 0.067151543 0.28840995 4.709835077 0.154345865 0.018442988 18.76566119 -1.273363871 -0.216249798 LSSERPSS(ph)DGEGVVENGITTCNGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSSERPSSDGEGVVENGITTCNGK 24 1 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 LSS(0.001)ERPS(0.329)S(0.671)DGEGVVENGITTCNGK 306.35 4.16E-63 350190000 193110 152790 97017 125210 167660 131550 163260 190310 232760 TRUE FALSE 167590.0242 151786.3124 143934.7457 153640.8442 164323.894 136610.8136 147427.0703 149613.6875 205243.378 0.816542906 0.739543044 0.701288135 0.748578813 0.800629456 0.665604001 0.718303664 0.728957441 1 17.64697615 1.237494051 24.99997884 1.000000312 0.737027406 0.776330932 0.043845694 12.13641802 284336.8682 0.062531912 0.010503137 17.27802312 -1.237494051 -0.262972906 LSSESHHGGS(ph)PIHWVLPAGMSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 LSSESHHGGSPIHWVLPAGMSAK 23 0 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 LS(0.034)S(0.034)ES(0.034)HHGGS(0.897)PIHWVLPAGMSAK;LS(0.002)S(0.002)ES(0.009)HHGGS(0.987)PIHWVLPAGMSAK;LS(0.002)S(0.002)ES(0.002)HHGGS(0.995)PIHWVLPAGMSAK;LS(0.007)S(0.007)ES(0.041)HHGGS(0.946)PIHWVLPAGMSAK;LS(0.001)S(0.001)ES(0.005)HHGGS(0.993)PIHWVLPAGMSAK;LS(0.101)S(0.114)ES(0.101)HHGGS(0.685)PIHWVLPAGMSAK;LSSES(0.001)HHGGS(0.999)PIHWVLPAGMSAK;LS(0.031)S(0.031)ES(0.031)HHGGS(0.908)PIHWVLPAGMSAK;LS(0.002)S(0.002)ES(0.01)HHGGS(0.986)PIHWVLPAGMSAK 241.48 4.49E-37 19714270000 9788670 9132610 1477914 6215330 10565170 9446850 9759170 11164800 10825670 TRUE FALSE 8495072.458 9072617.284 2192638.154 7626615.672 10354943.79 9810276.432 8812727.195 8777294.405 9545871.625 0.889921088 0.95042314 0.229694913 0.798943876 1.084756237 1.027698341 0.923197749 0.919485904 1 23.1864455 3.466194785 16.54191267 0.975475564 0.68243459 0.337989833 0.194645111 4.410860858 6675.2995 0.056489204 0.07330101 2925.464183 -3.466194785 -0.293040974 LSSFTSY(ph)ENPT ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSSFTSYENPT 11 0 Q13882 Q13882 PTK6 Protein-tyrosine kinase 6 1 LSSFTS(0.014)Y(0.986)ENPT;LSSFT(0.059)S(0.32)Y(0.621)ENPT;LSSFT(0.275)S(0.168)Y(0.557)ENPT 194.94 3.03E-06 546775000 675480 753520 551050 675950 906210 1035120 975090 1006060 1042480 TRUE FALSE 586213.6066 748570.0775 817539.6232 829434.7787 888178.194 1074941.736 880525.9219 790921.8982 919239.202 0.637716065 0.814336547 0.88936549 0.902305708 0.966210092 1.169381956 0.957885521 0.860409235 1 19.8100808 4.853558625 0.917236184 0.975246635 0.400299863 0.668545073 0.078437994 1.787364544 1.038708088 0.029654834 1.079196048 71377.0549 -4.853558625 -0.574946772 LSSGLVS(ph)PAPSFYSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSSGLVSPAPSFYSK 15 0 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 LSSGLVS(1)PAPSFYSK 304.03 1.52E-44 380790000 737680 565560 312420 412270 543310 479970 556020 644050 592980 TRUE FALSE 640193.719 561844.7991 463507.357 505882.2047 532499.194 498434.7565 502097.266 506324.9195 522878.5799 1.224364018 1.0745225 0.886453136 0.967494604 1.018399327 0.953251435 0.960255947 0.968341292 1 18.99611644 4.560185126 3.343433486 0.966617418 1.221312235 0.845604392 0.035782249 0.093153315 1.812791408 0.008842497 0.046358396 36323.28563 -4.560185126 0.254694817 LSSGPEQITLEASSTEGHPGAPS(ph)PQHTDQTEAFQK ddPTM_MDA-MB-175_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 LSSGPEQITLEASSTEGHPGAPS(1)PQHTDQTEAFQK;LSSGPEQITLEASSTEGHPGAPS(1)PQHTDQTEAFQK 438.52 6.01E-210 2256800000 339560 394270 184261 307020 462190 378800 404470 562230 479400 TRUE FALSE 294686.2857 391680.0144 273370.2359 376733.5835 452993.3233 393372.6811 365244.5617 442001.4898 422725.8781 0.697109642 0.92655793 0.646684412 0.891200665 1.071600644 0.930562101 0.864022244 1.045598372 1 18.68936291 3.482547369 23.78986033 0.979033791 0.772958221 0.56008137 0.090864466 92.84532103 407065.4093 0.024547534 0.03274526 3037.717404 -3.482547369 -0.20607557 LSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 35 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ;;; 476.85 1.28E-283 631220000 310050 316126 82636 220123 322465 276508 321656 383930 342594 FALSE TRUE 269076.1069 314049.3475 122599.046 270105.2915 316048.5774 287145.4417 290461.8506 301829.5572 302092.9276 0.89070641 1.039578616 0.405832228 0.894113257 1.046196546 0.950520239 0.961498347 0.999128181 1 18.20463288 3.480946866 24.98026688 0.986496752 0.778989669 0.273854097 0.158275039 207.7425558 1356510.57 0.044509307 0.058814625 3026.543122 -3.480946866 -0.207507083 LSSLIILMPHHVEPLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSSLIILMPHHVEPLER 17 0 P50454;E9PKH2;E9PR70;E9PPV6 P50454 SERPINH1 Serpin H1 0 ;; 147.92 2.21E-07 5674110000 3957750 4071050 2721790 3227590 3881720 5081680 3730820 3844370 2870170 FALSE TRUE 3434723.31 4044307.004 4038056.748 3960463.64 3804481.366 5277175.518 3369005.651 3022281.392 2530861.772 1.357135877 1.597996006 1.59552639 1.564867621 1.503235541 2.085129886 1.331169362 1.194170865 1 21.27119728 1.84242451 2.917350876 1.085851639 1.610820297 0.541999423 0.195313925 0.188097777 2.863790215 0.129720053 0.052750063 69.57040156 -1.84242451 0.524968658 LSSLRAS(ph)TSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSSLRASTSK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 1 LS(0.002)S(0.001)LRAS(0.965)T(0.031)S(0.002)K;LSSLRAS(0.912)T(0.087)S(0.001)K;LSSLRAS(0.962)T(0.036)S(0.001)K 131.06 0.00015755 1006590000 473209 823980 666270 768710 1448620 1087150 2117700 2236800 208982 TRUE FALSE 410673.2317 818567.2211 988480.4005 943257.3545 1419795.296 1128973.364 1912325.78 1758477.727 184276.386 2.228572204 4.442062484 5.364118658 5.118709862 7.704705561 6.126522168 10.37748689 9.542610232 1 17.49151168 4.276936827 0.766131794 7.53848902 1.314599464 0.229566406 2.567032326 2.057865953 1.457422892 1.135621478 9.931026773 18920.68378 -4.276936827 -6.223889556 LSSPAAFLPACNS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSSPAAFLPACNSPSK 16 0 Q86YS7;Q86YS7-5;H0YFE9;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 LSSPAAFLPACNS(0.988)PS(0.012)K;LSSPAAFLPACNS(1)PSK;LSSPAAFLPACNS(0.988)PS(0.012)K;LSSPAAFLPACNS(0.998)PS(0.002)K 238.45 9.02E-20 3315670000 1374590 1410310 1123100 1389340 1642830 1233670 1803820 2175100 2239490 TRUE FALSE 1192934.449 1401045.581 1666234.917 1704810.882 1610140.897 1281130.083 1628885.814 1709971.792 1974740.043 0.604096956 0.709483552 0.843774309 0.863309015 0.815368535 0.648758852 0.824860882 0.865922478 1 20.91323132 -2 0.045575696 2.137498334 4.22E-08 0.438619411 0.086697487 1543.485817 6.901405175 271.7990619 95.57335019 0.01 2 -2.137498292 LSSS(ph)LGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSSSLGR 7 0 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 1 LSS(0.002)S(0.998)LGR;LSS(0.002)S(0.998)LGR;LSS(0.009)S(0.991)LGR;LSS(0.008)S(0.992)LGR 139.74 0.0028023 1624330000 3003880 3182770 2275170 2589440 3133330 3510050 3460370 3673220 3705790 TRUE FALSE 2606909.647 3161862.174 3375449.822 3177411.929 3070982.863 3645083.895 3124783.85 2887730.488 3267695.728 0.797782249 0.967612176 1.032975559 0.972370806 0.93980074 1.115490608 0.956265243 0.88372074 1 21.63984222 4.73454898 5.22108849 0.978963318 0.790409514 0.479944843 0.060714446 0.148264455 13.98016842 0.015736286 0.100411882 54268.6453 -4.73454898 -0.188553804 LSSS(ph)PGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSSSPGK 7 0 A0A5F9ZHP4;C9J1X3;A0A5F9ZI29;A0A5F9ZGX5;A0A5F9ZHJ2;A0A499FJ16;Q07912;Q07912-3;A0A5F9ZHD0 A0A5F9ZHP4 TNK2 Activated CDC42 kinase 1 1 LSS(0.027)S(0.973)PGK;LSS(0.009)S(0.991)PGK 128.28 0.0039576 673220000 1894680 1808860 1404420 1710000 1295290 1848640 2520400 2948800 2984600 TRUE FALSE 1644293.237 1796977.48 2083602.21 2098281.636 1269516.263 1919758.377 2275971.996 2318222.068 2631763.988 0.624787498 0.682803431 0.79171317 0.79729096 0.482382261 0.729456891 0.864808549 0.880862447 1 21.32759869 2.164295656 2.595469733 0.923420431 0.6827332 0.591175085 0.092365603 0.212379071 2.898748266 0.049329799 0.028456072 145.980772 -2.164295656 -0.240687231 LSSS(ph)PGLFGAFSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSSSPGLFGAFSVR 14 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 LS(0.008)S(0.308)S(0.684)PGLFGAFSVR 67.846 0.053963 27735000 156280 122830 80290 86462 118930 109320 118480 142290 122260 TRUE FALSE 135627.202 122023.1216 119118.5126 106094.5186 116563.5257 113525.6111 106989.8278 111862.3908 107806.5621 1.258060729 1.131871004 1.104928218 0.984119302 1.081228484 1.053049174 0.992424077 1.037621353 1 16.71808547 5.441360448 0.740496684 1.02236964 1.759493555 0.84400824 0.032288594 2.525831824 0.503190168 0.012088407 1.966077364 276286.998 -5.441360448 0.737123915 LSSS(ph)SATLLNSPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSSSSATLLNSPDR 14 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 LSS(0.006)S(0.968)S(0.026)ATLLNSPDR;LSS(0.005)S(0.849)S(0.147)ATLLNSPDR;LSS(0.062)S(0.931)S(0.007)ATLLNSPDR 327.29 2.65E-68 595440000 1489880 1749950 846860 644650 855500 1432880 950350 903050 1539740 TRUE FALSE 1292988.583 1738454.463 1256404.329 791027.6354 838477.2238 1488003.821 858185.2033 709939.785 1357713.691 0.952327867 1.28042788 0.925382381 0.582617411 0.617565566 1.09596289 0.632081129 0.522893589 1 20.37274785 3.994103257 6.094554429 0.72329536 1.115963228 0.381554816 0.196907308 0.138218485 21.97074499 0.051397252 0.099941963 9865.140099 -3.994103257 0.392667868 LSSSDRYS(ph)DAS(ph)DDS(ph)FSEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSSSDRYSDASDDSFSEPR 19 1 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 3 LSS(0.003)S(0.014)DRY(0.065)S(0.942)DAS(0.976)DDS(0.99)FS(0.01)EPR 160.2 2.60E-11 378720000 248700 194930 125900 147350 187820 205770 199980 212180 203020 TRUE FALSE 215833.6649 193649.492 186785.6611 180808.0696 184082.7495 213686.1051 180585.9704 166806.9582 179019.2069 1.205645297 1.081724667 1.043383357 1.009992574 1.028284912 1.193649043 1.00875193 0.931782467 1 17.44975486 7.999998708 0.029640143 0.076128017 2.421236536 0.336180478 0.069689163 3860.935769 11.33612463 318.4421656 629.3397224 99999702.45 -7.999998708 2.345108519 LSSSDRYS(ph)DAS(ph)DDSFSEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSSSDRYSDASDDSFSEPR 19 1 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 2 LSSSDRY(0.001)S(0.999)DAS(0.999)DDS(0.001)FSEPR;LS(0.005)S(0.006)S(0.008)DRY(0.002)S(0.979)DAS(0.53)DDS(0.404)FS(0.067)EPR;LSSSDRYS(1)DAS(1)DDSFSEPR 168.26 9.33E-12 736750000 977240 764790 532613 611535 755150 809950 773130 873710 792490 TRUE FALSE 848095.258 759766.0441 790186.4283 750393.3685 740123.9924 841109.3006 698151.9716 686873.9157 698802.735 1.213640439 1.087239654 1.130771803 1.073827177 1.059131505 1.203643401 0.999068745 0.982929633 1 19.41452573 -1.999999998 0.209729715 0.068935512 1.184487458 0.473113865 0.05853249 84.34586034 1.279519268 30.35497307 0.325595142 0.01 1.999999998 1.115551946 LSSSDRYS(ph)DASDDS(ph)FSEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSSSDRYSDASDDSFSEPR 19 1 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 2 LSS(0.003)S(0.004)DRYS(0.993)DAS(0.013)DDS(0.987)FSEPR;LSSSDRY(0.001)S(0.998)DAS(0.129)DDS(0.755)FS(0.117)EPR 229.15 1.04E-18 780070000 1192970 944140 632820 787530 923000 962290 984490 1091710 1013620 TRUE FALSE 1035315.992 937937.8822 938853.8687 966350.7231 904634.1058 999309.919 889014.3113 858256.3122 893790.9983 1.15834238 1.049392849 1.050417682 1.081181982 1.012131592 1.118057712 0.9946557 0.960242734 1 19.76957799 -1.999999954 0.09221715 0.444488008 1.25464825 0.479176407 0.043249695 294.9914946 2.5387988 31.18921579 3.857385419 0.010000001 1.999999954 0.810160241 LSSSSATLLNS(ph)PDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 356.74 3.76E-82 2113580000 2769740 2388570 1549430 1903700 2281640 2222930 2291900 2430370 2652300 TRUE FALSE 2403711.841 2372879.326 2298739.531 2335964.181 2236239.828 2308447.556 2069631.891 1910654.289 2338748.116 1.027777137 1.014593795 0.982893162 0.998809648 0.956169591 0.987044111 0.884931505 0.816955993 1 21.15730506 2.245864048 5.756776749 0.881891722 0.993884792 0.438353762 0.048666757 0.122107453 13.68866611 0.019000065 0.013736277 176.1424563 -2.245864048 0.11199307 LSST(ph)PPLSALGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSSTPPLSALGR 12 0 Q8N201 Q8N201 INTS1 Integrator complex subunit 1 1 LSS(0.008)T(0.974)PPLS(0.019)ALGR;LSS(0.036)T(0.956)PPLS(0.007)ALGR;LSS(0.025)T(0.973)PPLS(0.002)ALGR 138.42 0.00083514 918810000 2120550 1667610 1287570 1251420 1614580 1494990 1760180 1853180 1739750 TRUE FALSE 1840313.945 1656655.36 1910243.159 1535574.038 1582453.017 1552503.233 1589478.015 1456891.878 1534078.737 1.199621571 1.079902433 1.24520542 1.000974722 1.031533114 1.012010137 1.036112408 0.949685204 1 20.5489411 3.72018135 24.72049605 1.002619638 1.165409066 0.744409888 0.046793756 327.4717309 440456.2815 0.012275893 0.018247779 5250.266519 -3.72018135 0.162789428 LSST(ph)S(ph)SEETQLFHIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 2 LS(0.001)S(0.067)T(0.903)S(0.993)S(0.035)EETQLFHIPR 169.64 2.95E-08 127710000 282220 273310 214540 308800 385950 417660 247080 455050 437850 TRUE FALSE 244923.9119 271514.6086 318292.2616 378917.7597 378270.3501 433727.6505 223118.2196 357741.0987 386087.8718 0.634373493 0.70324563 0.824403678 0.981428808 0.979751963 1.123391026 0.57789492 0.926579478 1 18.55856971 4.178472612 2.484212116 0.918530907 0.649206707 0.375714652 0.13906692 0.328599373 4.009980923 0.038181776 0.114588794 15082.47492 -4.178472612 -0.2693242 LSSTSS(ph)EETQLFHIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 1 LSST(0.001)S(0.016)S(0.982)EETQLFHIPR;LS(0.001)S(0.005)T(0.027)S(0.315)S(0.652)EETQLFHIPR 296.47 1.11E-45 386950000 220225 190239 132500 187624 225421 234500 144177 223745 214162 TRUE FALSE 191121.7083 188989.3075 196577.4432 230226.8969 220935.5631 243521.3667 130194.7367 175898.8729 188844.0123 1.012061256 1.000769392 1.040951422 1.219137922 1.169936819 1.289537136 0.689430049 0.931450623 1 17.52683552 2.241225645 24.99999907 0.877998647 1.119453503 0.493695672 0.118553939 61.67835828 578599.1384 0.047700491 0.035234 174.2712093 -2.241225645 0.241454857 LSSWDQAET(ph)PGHT(ph)PSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSSWDQAETPGHTPSLR 17 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 LSSWDQAET(1)PGHT(0.973)PS(0.027)LR;LSSWDQAET(1)PGHT(0.985)PS(0.015)LR;LSSWDQAET(1)PGHT(0.832)PS(0.168)LR 202.46 1.79E-11 859510000 653080 565062 484898 535685 558962 570400 440509 590870 1176360 TRUE FALSE 566773.8233 561350.0705 719396.2947 657320.4667 547839.7498 592343.6571 397788.505 464517.0487 1037292.061 0.546397533 0.541168772 0.693533019 0.633688902 0.528144165 0.571048097 0.383487467 0.447817029 1 19.98439073 1.231582409 24.97403472 1.000000804 0.539074826 0.735855101 0.085987342 143.3123179 512848.0481 0.233009908 0.023970724 17.04442714 -1.231582409 -0.460925978 LSSWDQAET(ph)PGHTPSLR ddPTM_MDA-MB-175_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 285.46 9.77E-36 2006870000 1073680 909750 773610 967140 1054470 1077280 867040 1062950 1923130 TRUE FALSE 931790.4676 903773.7923 1147730.384 1186743.919 1033488.11 1118723.659 782954.5943 835646.4144 1695779.762 0.54947611 0.532954699 0.67681571 0.699821961 0.60944713 0.659710467 0.461707712 0.492780037 1 20.69351738 1.230913168 24.99669233 1.000000745 0.583081967 0.733520923 0.078534909 164.5839632 537918.8845 0.224530661 0.021594568 17.01818217 -1.230913168 -0.416918778 LSSWDQAETPGHTPSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSSWDQAETPGHTPSLR 17 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 267.22 9.48E-28 440150000 113940 107600 62326 98490 95196 101250 92315 107160 203890 FALSE TRUE 98882.54031 106893.1685 92467.06207 120853.6598 93301.78585 105145.153 83362.30551 84244.66792 179786.3565 0.550000246 0.59455662 0.514316347 0.67220707 0.518959212 0.584833883 0.463674258 0.468582097 1 17.45592402 1.232827484 24.99981456 1.000000732 0.543270205 0.842057823 0.061798127 74.2241991 323626.9211 0.137226139 0.015846533 17.09336175 -1.232827484 -0.456730527 LST(ph)PQKK ddPTM_MDA-MB-175_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(0.024)T(0.976)PQKK;LS(0.106)T(0.894)PQKK 80.755 0.017025 978750000 1068230 541480 386140 493148 488350 402520 701520 838760 656292 TRUE FALSE 927060.699 537922.9822 572878.5956 605124.7907 478632.7904 418005.2049 633486.6984 659397.7012 578705.9074 1.601954788 0.929527374 0.989930443 1.045651656 0.827074312 0.722310243 1.094660846 1.139434889 1 19.14247085 4.741360194 24.57802233 0.978791067 1.601955075 0.724174036 0.122702804 127.1906646 1116554.258 0.033488124 0.225175028 55126.47138 -4.741360194 0.623164008 LSTDHIPILYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSTDHIPILYR 11 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 79.659 0.02654 1603700000 1238670 1294860 595930 868160 1348460 1291720 1055340 1378990 1265520 FALSE TRUE 1074976.621 1286353.979 884123.7413 1065288.997 1321628.284 1341413.304 952993.2892 1084103.72 1115911.667 0.963316948 1.152738176 0.792288285 0.954635594 1.184348478 1.202078393 0.854004235 0.971495999 1 20.0897914 2.201298983 24.99999813 0.944353719 1.037829185 0.119077613 0.127545096 415.6051225 278839.812 0.054242457 0.036571326 158.9640735 -2.201298983 0.093475466 LSTIQNS(ph)PTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSTIQNSPTK 10 0 Q5VYV7 Q5VYV7 SLX4IP Protein SLX4IP 1 LSTIQNS(0.962)PT(0.038)K;LSTIQNS(0.999)PTK 157.5 0.0017578 131130000 380690 359800 228407 294950 385070 291790 403630 496500 426430 TRUE FALSE 330380.852 357436.4501 338865.3892 361922.9055 377407.8604 303015.3501 364486.0247 390327.3388 376017.9312 0.878630577 0.950583524 0.90119476 0.962515017 1.003696444 0.805853458 0.969331499 1.03805512 1 18.52044194 2.000536614 24.99999562 1.016330056 0.920858169 0.386341002 0.053349603 17.43702219 812336.668 0.021282175 0.014203927 100.1236363 -2.000536614 -0.095471887 LSTTPS(ph)PT(ph)SSLHEDGVEDFRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSTTPSPTSSLHEDGVEDFRR 21 1 O94842-3;O94842-2;O94842;C9J919;C9JNL1 O94842-3 TOX4 TOX high mobility group box family member 4 2 LS(0.002)T(0.002)T(0.009)PS(0.974)PT(0.53)S(0.1)S(0.384)LHEDGVEDFRR 93.633 0.0014644 238900000 189300 148360 84575 118440 164260 151870 146790 158470 131130 TRUE FALSE 164283.5254 147385.4134 125475.7529 145333.6122 160991.5474 157712.5372 132554.3284 124582.4237 115627.9608 1.420794108 1.274652017 1.085167913 1.256907164 1.392323676 1.363965395 1.146386458 1.077442021 1 16.81913078 1.921851491 2.514628822 1.035489252 1.289524899 0.562441529 0.095413736 0.236086037 2.72000662 0.07053689 0.029216709 83.53173279 -1.921851491 0.254035647 LSTTPS(ph)PTS(ph)SLHEDGVEDFRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSTTPSPTSSLHEDGVEDFRR 21 1 O94842-3;O94842-2;O94842;C9J919;C9JNL1 O94842-3 TOX4 TOX high mobility group box family member 4 2 LS(0.013)T(0.015)T(0.091)PS(0.8)PT(0.109)S(0.843)S(0.129)LHEDGVEDFRR 102.95 0.0015736 334260000 353210 280590 185090 219670 311960 306860 276960 340020 273140 TRUE FALSE 306532.4036 278746.7858 274600.1431 269549.4309 305752.6063 318665.1028 250100.4618 267309.369 240849.7004 1.272712414 1.157347447 1.140130723 1.119160333 1.269474722 1.32308698 1.038408856 1.10985967 1 17.8777736 2.21159832 24.99994694 1.061554852 1.205993269 0.552233565 0.069197512 192.4011755 178396.538 0.029683569 0.020018468 162.7789789 -2.21159832 0.144438417 LSTTPS(ph)PTSS(ph)LHEDGVEDFRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSTTPSPTSSLHEDGVEDFRR 21 1 O94842-3;O94842-2;O94842;C9J919;C9JNL1 O94842-3 TOX4 TOX high mobility group box family member 4 2 LS(0.003)T(0.01)T(0.045)PS(0.772)PT(0.228)S(0.25)S(0.692)LHEDGVEDFRR 91.503 0.0070187 464540000 411940 363030 158640 227060 328730 358630 309450 399520 296790 TRUE FALSE 357501.0853 360645.232 235358.8346 278617.4434 322188.9161 372426.7282 279439.5866 314085.7571 261703.8243 1.366052201 1.378066343 0.899332806 1.064628857 1.231120397 1.423084776 1.06777036 1.200157307 1 17.99757548 4.352976773 22.27199193 1.141843627 1.372183775 0.337331138 0.141784069 4.480062913 855.4761443 0.036000607 0.095248622 22541.18653 -4.352976773 0.230340147 LSTTPS(ph)PTSSLHEDGVEDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSTTPSPTSSLHEDGVEDFR 20 0 O94842-3;O94842-2;O94842;C9J919;C9JNL1 O94842-3 TOX4 TOX high mobility group box family member 4 1 LSTT(0.005)PS(0.639)PT(0.257)S(0.08)S(0.019)LHEDGVEDFR 167.1 9.16E-12 70682000 54711 37912 20604 40767 52940 41097 45917 45497 88052 TRUE FALSE 47480.80273 37662.95358 30568.16332 50023.77043 51886.59758 42678.02818 41463.97641 35767.82061 77642.59287 0.61153036 0.48508109 0.393703535 0.644282585 0.66827492 0.549672887 0.534036472 0.460672671 1 16.24456068 1.232523213 24.99998563 1.00000075 0.539838813 0.745296242 0.08386209 107.5030613 445109.1945 0.192224109 0.021573549 17.08139016 -1.232523213 -0.460161938 LSTTPS(ph)PTSSLHEDGVEDFRR ddPTM_MDA-MB-175_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 LS(0.001)T(0.001)T(0.01)PS(0.724)PT(0.248)S(0.013)S(0.003)LHEDGVEDFRR;LST(0.001)T(0.007)PS(0.73)PT(0.197)S(0.052)S(0.012)LHEDGVEDFRR;LSTT(0.001)PS(0.764)PT(0.174)S(0.053)S(0.007)LHEDGVEDFRR 197.28 5.63E-22 704490000 280216 218321 135879 177826 243900 241751 261583 288583 193585 TRUE FALSE 243184.7456 216886.835 201590.5389 218204.1112 239046.8672 251051.3174 236214.7209 226871.7712 170699.6018 1.424635693 1.270576104 1.180966661 1.27829303 1.40039499 1.470719994 1.383803585 1.329070301 1 17.38110017 1.239353025 6.402634889 0.99001827 1.340929646 0.620816805 0.084123398 0.091131071 16.81514826 0.139609852 0.022898323 17.35213927 -1.239353025 0.350911376 LSTTPSPT(ph)SSLHEDGVEDFRR ddPTM_MDA-MB-175_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 1 LST(0.001)T(0.01)PS(0.278)PT(0.622)S(0.086)S(0.003)LHEDGVEDFRR;LSTTPS(0.158)PT(0.722)S(0.093)S(0.026)LHEDGVEDFRR 215.32 3.87E-25 560490000 247296 185144 112847 168390 216951 214100 226279 240782 155460 TRUE FALSE 214615.207 183927.7769 167420.1867 206625.5232 212634.0996 222336.5655 204334.4974 189292.6431 137081.6959 1.565600758 1.341738411 1.221316862 1.507316654 1.551148738 1.62192745 1.490603804 1.380874681 1 17.06467642 1.230115135 2.873324073 0.898630345 1.465945832 0.620011593 0.115180006 0.323775927 3.168365777 0.439353752 0.032603713 16.98693932 -1.230115135 0.567315488 LSVDYGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSVDYGK 7 0 P68363;F8VQQ4;C9JDS9;P68366-2;P68366;C9JEV8;C9JQ00;C9JJQ8;Q9BQE3;F5H5D3 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA1A;TUBA4A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 ;;; 120.49 0.010575 1283080000 2627510 2194930 1892400 2286380 2311050 2132890 2548500 2842720 4260880 FALSE TRUE 2280277.896 2180511.36 2807570.97 2805537.524 2265064.626 2214943.658 2301346.862 2234826.45 3757163.62 0.606914717 0.580361033 0.747258106 0.746716887 0.60286558 0.589525472 0.612522396 0.594817441 1 21.84121251 1.234717807 24.99989954 1.000000523 0.635021291 0.776425404 0.061533339 57.37599802 373212.435 0.119315215 0.016282541 17.167925 -1.234717807 -0.364979232 LSVDYGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSVDYGKK 8 1 P68363;F8VQQ4;C9JDS9;P68366-2;P68366;C9JEV8;C9JQ00;C9JJQ8;Q9BQE3;F5H5D3 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA1A;TUBA4A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 68.371 0.090884 5374500000 14296000 10098000 6160400 7149100 9302300 7460000 13143000 13656000 3744200 FALSE TRUE 12406747.38 10031665.57 9139590.045 8772412.422 9117202.43 7746991.027 11868393.88 10735770.67 3301564.941 3.757838358 3.038457747 2.768259964 2.657046757 2.761479054 2.346460289 3.594778262 3.251721793 1 21.65471859 4.75009815 1.871011097 2.725774282 4.10780939 0.211714684 0.679954668 1.520800938 5.385931344 0.178811703 3.715217927 56246.84275 -4.75009815 1.382035109 LSVEEFFMDLHNFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSVEEFFMDLHNFR 14 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 185.2 1.20E-06 961030000 760000 689650 562610 697330 653360 721770 628000 769640 1200640 FALSE TRUE 659564.0744 685119.6437 834690.0778 855669.4345 640359.4143 749536.9589 567096.6567 605058.4753 1058701.707 0.622993304 0.647131897 0.788409117 0.808225234 0.604853482 0.707977473 0.535652916 0.57150987 1 20.01386473 3.212376535 24.99928988 0.660010669 0.716844419 0 0.137990731 909.2255204 868081.2272 0.042046729 0.047691114 1630.709251 -3.212376535 0.056833749 LSVHDMKPLDS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSVHDMKPLDSPGR 14 1 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 1 LSVHDMKPLDS(1)PGR;LSVHDMKPLDS(1)PGR;LSVHDMKPLDS(1)PGR 182.49 9.19E-07 999620000 1600770 1384390 477999 1050710 1511260 1311960 1620480 1845510 2170620 TRUE FALSE 1389224.189 1375295.851 709160.9152 1289289.765 1481188.883 1362431.95 1463326.099 1450862.048 1914011.776 0.725817994 0.718540956 0.370510215 0.673605973 0.773866128 0.711820046 0.764533488 0.758021485 1 20.86816828 -1.92167782 0.492838707 10 0.631639395 0.484058639 0.10948475 94.27610718 1.173765773 901.0609245 0.076244746 0.011976287 1.92167782 -9.368360605 LSVHDMKPLDS(ph)PGRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 LSVHDMKPLDSPGRR 15 2 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 1 LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR 177.61 3.89E-07 4968950000 5432720 4711640 1639785 3312810 4946820 4296680 5459950 6201580 4465070 TRUE FALSE 4714772.287 4680688.927 2432790.511 4065034.144 4848387.96 4461976.06 4930444.889 4875420.378 3937214.511 1.19748931 1.18883259 0.617896359 1.032464483 1.231425909 1.133282438 1.252267276 1.238291783 1 21.90874389 3.335762053 5.955735626 1.18310681 0.989992317 0.176295291 0.172483948 0.333219581 17.02568194 0.050920647 0.065787949 2166.516761 -3.335762053 -0.193114493 LSVPT(ph)S(ph)DEEDEVPAPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSVPTSDEEDEVPAPKPR 18 1 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 2 LS(0.003)VPT(0.997)S(1)DEEDEVPAPKPR;LS(0.029)VPT(0.978)S(0.993)DEEDEVPAPKPR;LSVPT(1)S(1)DEEDEVPAPKPR 156.05 3.29E-08 568990000 983100 991290 737320 871500 1080860 880310 1179170 1371450 1312590 TRUE FALSE 853180.8441 984778.1507 1093890.418 1069387.395 1059353.001 914176.0953 1064814.275 1078176.09 1157417.106 0.737142073 0.850841193 0.945113402 0.923942967 0.915273323 0.789841528 0.919991825 0.931536336 1 20.14247744 4.622178125 2.780659281 0.914614186 0.725021827 0.549749895 0.052207557 0.27286648 3.286421696 0.013707928 0.102527875 41896.53672 -4.622178125 -0.189592359 LSVPTS(ph)DEEDEVPAPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LSVPTSDEEDEVPAPKPR 18 1 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 LSVPT(0.024)S(0.976)DEEDEVPAPKPR;LSVPT(0.016)S(0.984)DEEDEVPAPKPR;LSVPT(0.131)S(0.869)DEEDEVPAPKPR;LSVPT(0.023)S(0.977)DEEDEVPAPKPR;LSVPT(0.039)S(0.961)DEEDEVPAPKPR;LSVPT(0.175)S(0.825)DEEDEVPAPKPR 296.81 1.42E-49 12651759000 6268410 6406080 3980106 5778161 6450890 4629462 6971230 8703510 7488480 TRUE FALSE 5440023.736 6363998.039 5904898.574 7090180.769 6322529.91 4807560.399 6295161.188 6842332.117 6603200.425 0.823846527 0.96377478 0.89424797 1.073749139 0.957494776 0.728065194 0.953350009 1.036214514 1 22.65473401 1.99354758 24.99668731 1.012920504 0.912259053 0.202213518 0.090404824 476.1541631 1844622.075 0.03902314 0.02525526 98.52525791 -1.99354758 -0.100661451 LSVQSNPS(ph)PQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSVQSNPSPQLR 12 0 O75152;E9PBY7;E9PQ61;A0A1W2PPR9 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 LSVQSNPS(1)PQLR;LSVQSNPS(1)PQLR;LSVQSNPS(1)PQLR;LSVQSNPS(1)PQLR 251.87 5.03E-21 1302520000 2141200 2104540 1240570 1405170 1826310 1942380 1857070 1903850 1905750 TRUE FALSE 1858234.995 2090715.138 1840513.801 1724235.325 1789970.004 2017104.615 1676971.637 1496726.493 1680454.406 1.105793164 1.244136783 1.095247687 1.026053024 1.065170229 1.200332843 0.997927484 0.890667719 1 20.68041997 2.054415001 6.086173999 0.939181699 1.119455262 0.564748896 0.067220992 0.131569507 10.40732492 0.029014255 0.019178096 113.3482974 -2.054415001 0.180273563 LSVVHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LSVVHEK 7 0 P20810-6;P20810-10;P20810;P20810-8;B7Z574;E7ES10;E9PDE4;H0YA91;E7EQK6;D6RBZ8;P20810-5;E9PCH5;P20810-2;F8W7E0;A0A0C4DGB5;H0Y944;E7EN75;E7EVY3 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ;;;;; 86.953 0.019698 2528010000 3788680 4206040 1925030 3136440 3917600 3492640 4502880 5283020 4953660 FALSE TRUE 3287996.339 4178410.246 2855980.947 3848616.639 3839647.425 3627004.121 4066191.391 4153287.286 4368043.958 0.752738839 0.956586126 0.653835212 0.881084686 0.879031315 0.83034973 0.930895254 0.95083459 1 22.05855594 1.657558643 0.589270436 1.075470291 0.806935905 0.410036652 0.079695106 2.474946329 0.975449058 0.439434045 0.050380249 45.45259076 -1.657558643 -0.268534386 LSWLDGSGLGFSLEYPTISLHALSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSWLDGSGLGFSLEYPTISLHALSR 25 0 P54105;E9PMI6;E9PJF4;J3KN38 P54105 CLNS1A Methylosome subunit pICln 0 133.58 5.89E-05 133020000 201860 235180 104410 146410 195370 184980 281710 274430 167910 FALSE TRUE 175183.6896 233635.0871 154903.0252 179654.6282 191482.5192 192096.3003 254389.8076 215745.2801 148059.8711 1.183194935 1.577977107 1.046218831 1.213391765 1.29327763 1.297423123 1.718154998 1.457148912 1 17.17582115 2.450442201 24.99991787 1.431674255 1.268523282 0.058478308 0.217351984 500.1827619 468698.8156 0.080134813 0.062073885 282.1254088 -2.450442201 -0.163150973 LSYAGGRPPSYAGS(ph)PVHHAAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LSYAGGRPPSYAGSPVHHAAER 22 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 LSYAGGRPPSYAGS(1)PVHHAAER;LSYAGGRPPSYAGS(1)PVHHAAER;LSYAGGRPPSYAGS(1)PVHHAAER;LSYAGGRPPSYAGS(1)PVHHAAER;LSYAGGRPPS(0.001)YAGS(0.999)PVHHAAER;LSYAGGRPPS(0.011)YAGS(0.989)PVHHAAER 214.62 9.01E-26 4652016000 2539750 1478769 1034947 1225185 1521894 1694938 1622014 1612544 1858340 TRUE FALSE 2204115.603 1469054.869 1535450.831 1503381.98 1491611.287 1760143.362 1464711.332 1267714.014 1638649.162 1.345080847 0.896503598 0.937022315 0.917452018 0.910268849 1.074142899 0.893852916 0.773633578 1 20.64407557 4.740173745 24.90975087 0.916324303 1.345080996 0.744082528 0.077196107 71.92784053 1110599.358 0.020056278 0.123696447 54976.07688 -4.740173745 0.428756693 LSYLEEAVMHLDHSDPITR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LSYLEEAVMHLDHSDPITR 19 0 Q6P2E9;Q6P2E9-2;I3L0V0;I3L3M2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 ;;;; 269.16 2.80E-32 276553000 245198 197088 119917.6 175589 186674 202313 193183 230657 215550 FALSE TRUE 212794.463 195793.316 177910.1525 215459.1662 182959.5526 210096.112 174448.1424 181332.7955 190067.9246 1.119570614 1.03012287 0.936034593 1.133590355 0.962600886 1.105373842 0.917819999 0.954042067 1 17.53615556 LSYLLMCLESAVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSYLLMCLESAVHR 14 0 Q92896;Q92896-3;Q92896-2;H3BM42 Q92896 GLG1 Golgi apparatus protein 1 0 142.85 9.29E-06 49802000 66263 71654 44473 54104 67636 77477 62585 71542 69025 FALSE TRUE 57506.17666 71183.30016 65980.29155 66389.14013 66290.17593 80457.59032 56515.51633 56243.30004 60864.94313 0.944816075 1.169528738 1.084044249 1.090761557 1.089135593 1.321903647 0.928539705 0.92406724 1 15.89332389 LSYLPATVEPAS(ph)PTPAHSLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LSYLPATVEPASPTPAHSLPR 21 0 M0R344;Q9NRA0-4;Q9NRA0-2;Q9NRA0;Q9NRA0-5;E9PCV4 M0R344 SPHK2 Sphingosine kinase 2 1 LSYLPATVEPAS(0.975)PT(0.025)PAHSLPR;LSYLPATVEPAS(0.947)PT(0.053)PAHSLPR;LSYLPATVEPAS(0.946)PT(0.054)PAHSLPR;LSYLPATVEPAS(0.998)PT(0.002)PAHSLPR 206.32 2.75E-22 1189170000 841640 970930 602240 738440 1028700 1029850 959930 1095480 1052920 TRUE FALSE 730415.1416 964551.8969 893485.2784 906114.0883 1008230.883 1069468.996 866836.1363 861220.127 928444.9971 0.786708037 1.038889649 0.962345945 0.975948054 1.085934962 1.15189268 0.933642961 0.927594128 1 19.82445692 4.744276058 24.71065179 1.003884893 0.786707927 0.504247832 0.069233188 519.7261871 2246953.651 0.018567627 0.15793204 55497.83707 -4.744276058 -0.217176967 LSYLSAPGSEYSMYS(ph)TDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSYLSAPGSEYSMYSTDSR 19 0 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 LSYLSAPGS(0.011)EY(0.001)S(0.031)MY(0.006)S(0.317)T(0.317)DS(0.317)R 62.203 0.050709 71264000 103570 75367 50520 53856 68311 71543 63701 85923 83261 TRUE FALSE 89882.96209 74871.90921 74951.64098 66084.82794 66951.74475 74295.3055 57523.28682 67549.0351 73417.97943 1.224263631 1.019803457 1.020889455 0.90011777 0.911925734 1.011949744 0.783504085 0.920061212 1 16.16384579 7.022477975 0.691181559 0.9116675 8.990409443 0.672877642 0.065344524 35.79068247 0.862159022 0.025605299 413.4815498 10531202.78 -7.022477975 8.078741943 LT(ph)IHMDEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTIHMDEELR 10 0 O94915;A0A669KB90;A0A6E1XQM6;F2Z2S2 O94915 FRYL Protein furry homolog-like 1 LT(1)IHMDEELR;LT(1)IHMDEELR 101.11 0.010089 1204690000 674930 701510 507270 845160 753830 903280 286330 477620 1499380 TRUE FALSE 585736.2904 696901.7346 752587.4687 1037066.495 738830.2578 938029.7661 258561.7607 375484.6798 1322125.004 0.443026407 0.527107295 0.569225653 0.784393678 0.558820274 0.709486443 0.195565291 0.284000891 1 20.33442716 LT(ph)PPPADLPLALPAHGLWSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTPPPADLPLALPAHGLWSR 20 0 Q15742 Q15742 NAB2 NGFI-A-binding protein 2 1 LT(1)PPPADLPLALPAHGLWSR;LT(1)PPPADLPLALPAHGLWSR 118.46 0.00024033 519168000 199278 178723 137303 161762 222470 204299 212273 222358 248770 TRUE FALSE 172942.9074 177548.9568 203703.1901 198492.5345 218043.2823 212158.5147 191686.7971 174808.4721 219360.694 0.788395151 0.809392757 0.928622108 0.904868283 0.993994313 0.967167412 0.873842955 0.796899704 1 17.74294551 4.284930458 5.875364243 0.91307437 0.79572481 0.419093469 0.060130555 0.217057601 17.22505446 0.016840529 0.044775117 19272.16291 -4.284930458 -0.117349561 LT(ph)QTSSTEQLNVLETETEVLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LTQTSSTEQLNVLETETEVLNK 22 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 LT(0.446)QT(0.25)S(0.142)S(0.081)T(0.081)EQLNVLETETEVLNK;LT(0.486)QT(0.221)S(0.133)S(0.08)T(0.08)EQLNVLETETEVLNK;LT(0.33)QT(0.135)S(0.135)S(0.157)T(0.242)EQLNVLETETEVLNK 264.91 5.91E-37 296228000 343913 288630 235095 247787 261340 251888 316024 391650 360770 TRUE FALSE 298464.0257 286733.9705 348787.7283 304050.8255 256139.8453 261578.2944 285376.0411 307898.6953 318120.1816 0.938211541 0.90133851 1.096402393 0.955773456 0.805166915 0.822262495 0.897069905 0.967869105 1 18.27921237 5.131725963 17.67182722 0.930061222 2.676929705 0.000721401 0.084184947 5376.289645 744681.9225 0.02135053 12350.54848 135433.4565 -5.131725963 1.746868484 LTADFREDPDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTADFREDPDPR 12 1 P17174 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 64.878 0.056781 657970000 1444300 1468800 580760 614550 1226700 1379200 1350500 1467600 129500 FALSE TRUE 1253432.096 1459151.356 861617.4785 754092.9703 1202291.07 1432258.716 1219528.718 1153765.161 114190.6575 10.97666064 12.77820259 7.545428822 6.603806184 10.52880416 12.54269611 10.67975914 10.103849 1 16.8010851 4.2433031 24.9937622 8.855985603 11.87743211 0.158538438 3.186824287 240.4999759 1267437.124 0.807183271 1.9945948 17510.68357 -4.2433031 3.021446507 LTAEDLFEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 189.72 2.28E-06 590044000 836455 738271 547815 703704 774071 819709 786638 856418 963496 FALSE TRUE 725915.3524 733421.2492 812740.1663 863490.7486 758668.5015 851243.7357 710349.9678 673279.6754 849592.6005 0.854427583 0.863262284 0.956623405 1.016358603 0.892979177 1.001943443 0.836106585 0.792473563 1 19.69641168 0.952017719 20.64742902 1.976231911 0.900265651 0.156150153 0.071686922 152.0097516 104050.4777 18277.7193 0.018640016 8.954012976 -0.952017719 -1.075966259 LTAEEMDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LTAEEMDER 9 0 P46940;H0YLE8;A0A0J9YXZ5;A0A087X225 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;; 125.82 0.0024001 4860700000 5901910 6359610 3790130 4645490 6390260 6525350 5923850 6908690 5951780 FALSE TRUE 5121957.64 6317833.303 5623049.545 5700319.506 6263106.328 6776384.437 5349355.939 5431320.407 5248167.349 0.975951661 1.203817044 1.071431068 1.086154295 1.193389218 1.291190617 1.019280748 1.034898479 1 22.32338229 LTAIIEEAEEAPGARPQLQDAWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LTAIIEEAEEAPGARPQLQDAWR 23 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;; 263.75 6.06E-44 3777409000 1336532 1359955 858703 941830 1294963 1433126 1283198 1429920 1120623 FALSE TRUE 1159905.91 1351021.366 1273974.643 1155686.896 1269195.77 1488259.285 1158753.655 1124142.736 988144.2256 1.173822484 1.367230948 1.289259817 1.169552851 1.284423606 1.50611545 1.172656405 1.137630223 1 19.9143621 1.651449809 2.09099271 1.017769903 1.293834397 0.474975711 0.100451278 0.277131847 2.443910683 0.119321888 0.028188092 44.81772514 -1.651449809 0.276064494 LTAT(ph)PTPLGGMTGFHMQTEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTATPTPLGGMTGFHMQTEDR 21 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 LT(0.003)AT(0.996)PT(0.002)PLGGMTGFHMQTEDR 216.48 2.27E-24 284820000 297960 256040 170170 194700 282980 317830 243410 328120 303540 TRUE FALSE 258583.8311 254358.0564 252464.7812 238909.6108 277349.2516 330057.1258 219804.1357 257954.0914 267655.847 0.966105669 0.950317578 0.943244035 0.892600007 1.036215927 1.23313998 0.821219256 0.963752873 1 18.03001964 3.231597776 24.9804824 1.001866754 0.939311676 0.110178394 0.100991388 460.2539803 1651244.937 0.031700083 0.036741561 1704.503023 -3.231597776 -0.062555078 LTATEGPGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTATEGPGSPR 11 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 LTATEGPGS(1)PR;LTATEGPGS(1)PR 210.84 1.19E-08 1989440000 1333500 1236460 728750 974290 1193550 1184030 1070300 1251320 1518240 TRUE FALSE 1157274.596 1228337.613 1081175.938 1195517.436 1169800.69 1229580.4 966502.4707 983734.9558 1338755.397 0.864440658 0.917522063 0.807597818 0.893006623 0.87379718 0.918450378 0.721941045 0.734813065 1 20.35246096 2.254696151 24.99911773 0.797355431 0.878016717 0.0898685 0.081134256 400.7660476 620914.2793 0.029898759 0.023086662 179.7612796 -2.254696151 0.080661286 LTDCVVMRDPASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LTDCVVMRDPASK 13 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;; 198.23 1.16E-07 3506820000 3851930 3032580 1605430 2212130 2865990 2486580 3442460 3975110 1658090 FALSE TRUE 3342887.691 3012658.782 2381821.318 2714427.927 2808962.406 2582240.342 3108610.759 3125063.661 1462072.489 2.286403524 2.060539956 1.629071975 1.856561796 1.921219657 1.766150694 2.126167329 2.137420466 1 20.47958341 4.466834317 5.551357673 1.834705316 2.239225257 0.207689149 0.321639309 0.250643439 25.96314268 0.078643594 0.244093739 29297.75322 -4.466834317 0.404519941 LTDDHVQFLIYQILR ddPTM_MDA-MB-175_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 ; 198.59 7.85E-09 1277060000 1005930 1031130 680600 865510 894270 914350 1052610 1082880 1060390 FALSE TRUE 872993.8018 1024356.439 1009740.436 1062037.274 876475.7766 949525.6362 950528.0442 851314.539 935031.9022 0.933651354 1.095531005 1.07989945 1.135829988 0.937375264 1.015500791 1.016572848 0.910465768 1 19.83465606 3.224509318 24.99996459 0.972813422 1.065011859 0.326802212 0.060592603 256.5226892 456401.9299 0.01811581 0.020638025 1676.908314 -3.224509318 0.092198437 LTDEEAQHVLEVVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTDEEAQHVLEVVQR 15 0 Q9BV36-2;Q9BV36-5;C9JKV5;C9JI01;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 0 ; 138.91 7.70E-06 291880000 279070 253452 171257 189253 237940 240264 258430 307560 257890 FALSE TRUE 242190.1924 251787.0571 254077.458 232225.7862 233205.4595 249507.1116 233367.4984 241790.6874 227402.538 1.065028537 1.107230638 1.117302649 1.021210178 1.02551828 1.097204604 1.026230844 1.063271719 1 17.79488883 3.739571597 24.99981641 1.042523138 1.097591612 0.457364824 0.029400342 84.35760789 2086010.559 0.007666659 0.012382463 5489.990552 -3.739571597 0.055068474 LTDEGAVHVNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTDEGAVHVNDR 12 0 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 0 126.95 0.00023647 0 235550 208530 127090 144620 202120 236810 186590 199230 245420 FALSE TRUE 204421.4707 207160.1527 188551.1491 177458.1814 198098.2074 245920.2339 168494.5305 156626.2149 216406.7272 0.944616987 0.957272241 0.871281367 0.820021557 0.91539764 1.136379803 0.778601168 0.723758531 1 17.72338582 LTDIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTDIFR 6 0 O75340-2;O75340;A0A024QZ42;H0Y9X3;A0A087WZ38 O75340-2 PDCD6 Programmed cell death protein 6 0 106.76 0.074087 66443000 264780 153070 81343 105720 150580 159030 136230 162300 161700 FALSE TRUE 229788.6521 152064.4731 120680.7469 129725.3418 147583.7526 165147.987 123018.4356 127593.408 142584.0102 1.611601832 1.066490365 0.846383453 0.909816898 1.035065239 1.158250401 0.86277862 0.894864774 1 17.12145268 4.720606209 3.414946542 0.955282923 1.682738247 0.829800228 0.092236654 0.115195332 2.316129993 0.024262509 0.212829202 52554.0523 -4.720606209 0.727455324 LTDIHGNVLQYHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTDIHGNVLQYHK 13 0 O95861-3;O95861-4;O95861;A6NF51;O95861-2 O95861-3 BPNT1 "3(2),5-bisphosphate nucleotidase 1" 0 ; 119.69 0.00019018 1979560000 3628600 3728000 2212100 2890200 3305600 3185000 3619800 4050500 4150200 FALSE TRUE 3149071.316 3703510.523 3281878.959 3546464.084 3239825.027 3307529.011 3268752.353 3184332.096 3659568.084 0.860503547 1.012007548 0.896794071 0.969093621 0.885302569 0.903803109 0.893207143 0.870138777 1 21.80324196 3.224199652 24.99738498 0.90381578 0.937428435 0.039865118 0.052677371 579.0926477 1007994.126 0.014787176 0.016842001 1675.713049 -3.224199652 0.033612655 LTEDFVSHLETELEQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LTEDFVSHLETELEQSR 17 0 Q96CN4;Q96CN4-2 Q96CN4 EVI5L EVI5-like protein 0 ;;; 209.67 4.06E-12 98750000 175593 175687 120350 130512 171046 188847 170577 191590 188537 FALSE TRUE 152387.9402 174532.9005 178551.6625 160146.7444 167642.5192 196112.0663 154034.4688 150619.9695 166248.3706 0.916628172 1.049832247 1.074005489 0.963298129 1.008385938 1.179633013 0.926532201 0.905993658 1 17.34298068 LTEDKADVQSIIGLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTEDKADVQSIIGLQR 16 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 269.91 3.19E-28 2946200000 4882500 3512600 2382700 2808700 3120000 2904500 3921400 4942300 3168500 FALSE TRUE 4237265.254 3489525.499 3534981.69 3446458.263 3057918.104 3016237.994 3541103.232 3885427.606 2793923.54 1.516600291 1.248969576 1.265239238 1.233554968 1.094488829 1.079570701 1.267430258 1.390670701 1 21.41386111 5.809827663 1.145993136 1.201445751 4.200541846 0.457027523 0.111151638 17.00572936 2.743298003 0.034923031 107.5635183 645398.0708 -5.809827663 2.999096095 LTEDLEYHELLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LTEDLEYHELLDR 13 0 P22059;H0YCV6 P22059 OSBP Oxysterol-binding protein 1 0 ;;;;; 269.14 6.11E-25 4169250000 5641610 5073300 3284710 3772380 4827690 5112460 4919470 5836420 5370610 FALSE TRUE 4896056.944 5039973.158 4873206.743 4628956.536 4731628.414 5309139.644 4442380.557 4588347.002 4735702.604 1.033860729 1.064250351 1.029035636 0.977459297 0.999139686 1.12108806 0.938061557 0.96888411 1 22.17514705 2.192108368 24.99998248 0.967673158 1.033836345 0.384761941 0.040642823 132.6437293 71386.11397 0.016684854 0.011248975 155.6353934 -2.192108368 0.066163186 LTEEETVCLDLDKVEAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTEEETVCLDLDKVEAYR 18 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 198.42 1.58E-15 247430000 157798 122586 82697 87928 90595 73763 122710 143211 130263 FALSE TRUE 136944.5945 121780.7245 122689.5458 107893.3963 88792.33675 76600.71034 110809.6031 112586.4421 114863.4565 1.192238146 1.060221659 1.068133848 0.939318732 0.773025115 0.666884949 0.964707196 0.980176337 1 16.80956036 3.785942548 2.431254527 0.884377632 1.119774043 0.507123944 0.104394295 0.290255813 3.360184669 0.033919232 0.065671655 6108.612101 -3.785942548 0.23539641 LTEGCSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LTEGCSFR 8 0 P42677;C9J1C5;H0YMV8;Q71UM5 P42677;H0YMV8 RPS27;RPS27L 40S ribosomal protein S27;40S ribosomal protein S27-like 0 ;;;;; 175.24 0.00062186 5223640000 1724910 1689490 1096830 1232060 1655990 1706920 1596770 1661100 1620350 FALSE TRUE 1496958.773 1678391.629 1627260.657 1511818.054 1623039.039 1772586.317 1441915.491 1305886.692 1428794.069 1.047707858 1.174691067 1.138904963 1.058107733 1.135950291 1.240617074 1.009183564 0.913978242 1 20.44636657 2.042599062 8.094018936 0.953923357 1.131439408 0.633713772 0.057721447 0.13252923 22.20071227 0.023140423 0.015494787 110.3059811 -2.042599062 0.177516052 LTELLR ddPTM_MDA-MB-175_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 0 141.55 0.027076 156960000 317610 273340 189600 201710 263150 302980 275710 301720 293380 FALSE TRUE 275637.0338 271544.4115 281291.1942 247511.3384 257913.8298 314635.8367 248971.6866 237199.526 258696.9506 1.065482346 1.049662205 1.087338654 0.956761716 0.996972826 1.216233264 0.962406731 0.916901129 1 17.98090352 2.033641908 24.99959338 0.9486563 1.057780377 0.321039085 0.069644437 196.0120506 145657.4471 0.028173673 0.018994568 108.0542637 -2.033641908 0.109124077 LTEYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LTEYSR 6 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;; 153.26 0.023621 2462590000 3714270 3573620 2393680 2760640 3309190 3623790 3546700 4016160 3815740 FALSE TRUE 3223419.809 3550144.655 3551271.654 3387485.506 3243343.593 3763199.546 3202741.58 3157335.438 3364647.564 0.958025989 1.05513121 1.055466163 1.006787618 0.963947496 1.118452817 0.951880255 0.938385188 1 21.68202396 LTFDEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTFDEYR 7 0 P12429;D6RA82 P12429 ANXA3 Annexin A3;Annexin 0 102.72 0.019862 181780000 538510 498700 300900 295610 473400 498580 433300 484210 486570 FALSE TRUE 467344.5391 495424.0069 446416.2465 362732.7686 463980.2662 517760.6952 391278.6327 380665.4596 429048.2489 1.089258703 1.154704647 1.04048029 0.845435844 1.081417457 1.206765665 0.911968837 0.887232288 1 18.71078037 6.421689067 0.031277436 1.42E-06 2.322901761 0.145813566 0.107619488 3448.866796 15.6469997 453.4780917 741.5731497 2640517.603 -6.421689067 2.322900344 LTFDSSFS(ph)PNTGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTFDSSFSPNTGKK 14 1 P21796;C9JI87 P21796 VDAC1 Voltage-dependent anion-selective channel protein 1 1 LTFDSSFS(1)PNTGKK 126.07 5.36E-05 300470000 344050 251250 227670 307030 311000 268770 264030 440090 341410 TRUE FALSE 298582.9208 249599.5222 337771.9735 376745.8542 304811.7085 279109.7558 238424.4112 345980.1783 301048.8987 0.991808713 0.829099602 1.121983754 1.251444054 1.012498998 0.927124321 0.791979018 1.149249108 1 18.19963831 4.239770635 24.99975666 1.03624987 0.910454175 0.138641036 0.130435011 65.24325871 1347820.172 0.034696043 0.081873271 17368.83282 -4.239770635 -0.125795695 LTFSCLGGSDNFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTFSCLGGSDNFK 13 0 A0A087WYT3;Q15185-4;Q15185;Q15185-3;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ; 198.25 2.96E-07 335100000 460210 392720 289960 343460 367490 345200 410610 489020 513670 FALSE TRUE 399392.0825 390140.1965 430185.6259 421447.8425 360177.668 358480.0674 370789.1054 384446.8786 452944.5178 0.881768223 0.861342132 0.949753466 0.930462399 0.795191583 0.791443661 0.818619259 0.848772561 1 18.78897482 3.254007809 24.99886482 0.845169248 0.90579102 0.157402618 0.062511187 438.9023536 710290.803 0.018592654 0.023914766 1794.765898 -3.254007809 0.060621771 LTGFHETSNINDFSAGVANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LTGFHETSNINDFSAGVANR 20 0 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ;;; 329.93 8.45E-80 2735060000 648650 647690 377374 503754 622600 808390 721960 681610 1018230 FALSE TRUE 562929.259 643435.2817 559873.3286 618139.0451 610211.4781 839489.2864 651944.4303 535853.0058 897856.0094 0.626970531 0.716635268 0.623566945 0.688461222 0.67963178 0.934993226 0.726112454 0.596813966 1 19.77612457 2.964334368 24.9472376 0.776088207 0.667199743 0.267659848 0.113745455 1045.783047 731499.4724 0.037320989 0.037335619 921.1585078 -2.964334368 -0.108888464 LTGIKHELQANCYEEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTGIKHELQANCYEEVK 17 1 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 127.83 2.34E-05 526510000 1106200 800860 524960 581970 687510 560530 963810 1155400 236660 FALSE TRUE 960012.8672 795599.0979 778832.4119 714115.1834 673829.8961 582093.9518 870339.8545 908326.7013 208682.3244 4.600355445 3.812489152 3.73214365 3.422020458 3.228974462 2.789378322 4.170644816 4.352676749 1 17.67094888 7.999962338 0.611052702 3.301730058 91.86956876 0.200813399 0.911513295 365.5927614 2.761078381 0.421389713 43341.50903 99991328.49 -7.999962338 88.5678387 LTGIKHELQANCYEEVKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTGIKHELQANCYEEVKDR 19 2 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 213.15 2.93E-17 4056870000 4948170 3566410 1712460 1872730 2892120 2289890 4455620 4849280 383902 FALSE TRUE 4294256.797 3542982.018 2540611.384 2297961.969 2834572.47 2377983.55 4023514.658 3812299.209 338517.5429 12.68547787 10.4661696 7.505109963 6.788309846 8.373487666 7.024698128 11.88569025 11.26174784 1 18.36887107 4.485599914 3.236604889 8.209964308 12.52295009 0.231315926 2.963259171 0.424212305 8.641431546 0.762530053 3.350287269 30591.43952 -4.485599914 4.312985786 LTGMAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 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 ;;;;;;;;;; 167.25 0.0025431 79595480000 15040580 20640520 12692050 12669970 18923960 18698060 16929390 18199120 19542410 FALSE TRUE 13052929.25 20504931.07 18829967.83 15546880.34 18547410.22 19417386.47 15287580.36 14307379.81 17232128.55 0.757476316 1.189924449 1.092724429 0.902203131 1.07632729 1.126813 0.887155659 0.830273507 1 24.03859758 2.211201819 24.7674251 0.889295623 1.031708409 0.154241145 0.128023225 293.2270456 265450.7157 0.049898753 0.033651477 162.6304334 -2.211201819 0.142412786 LTGS(ph)QLSITQVASIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTGSQLSITQVASIK 15 0 Q9UJF2;Q9UJF2-2;H0Y638 Q9UJF2 RASAL2 Ras GTPase-activating protein nGAP 1 LT(0.002)GS(0.998)QLSITQVASIK 191.47 1.14E-11 0 194420 200650 124080 109640 179800 193650 222200 221340 194820 TRUE FALSE 168726.9044 199331.9169 184085.503 134535.4377 176222.3318 201099.8408 200651.0782 174008.1635 171788.6015 0.98217753 1.160332613 1.071581591 0.783145311 1.025809222 1.170623889 1.168011593 1.01292031 1 17.39027479 2.984006553 24.90649065 1.085301042 1.002036263 0.131815774 0.107929075 1615.653059 2516050.49 0.036424356 0.03744783 963.8435671 -2.984006553 -0.08326478 LTGS(ph)T(ph)SSLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 2 LT(0.178)GS(0.815)T(0.448)S(0.129)S(0.43)LNK;LT(0.029)GS(0.964)T(0.611)S(0.187)S(0.209)LNK 112.84 0.0083121 429340000 2385800 1961220 1662250 1603700 2021200 1900950 2220600 2545200 3000700 TRUE FALSE 2070510.485 1948336.617 2466119.66 1967844.596 1980982.074 1974080.777 2005246.554 2000928.787 2645960.664 0.782517485 0.736343757 0.932031868 0.743716497 0.748681604 0.746073365 0.75785199 0.756220156 1 21.33536018 1.2357129 24.97641029 1.000000307 0.774633286 0.604156269 0.057123873 54.38395904 476892.2106 0.093109863 0.013776858 17.20730673 -1.2357129 -0.225367021 LTGS(ph)TSS(ph)LNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 2 LT(0.01)GS(0.765)T(0.394)S(0.309)S(0.523)LNK 77.74 0.046919 534600000 1908400 1537900 1342400 1316500 1740100 1658000 1904200 2263400 2655700 TRUE FALSE 1656200.105 1527797.434 1991589.13 1615431.446 1705475.414 1721784.333 1719530.977 1779389.524 2341746.171 0.707250053 0.652418034 0.850471821 0.689840541 0.728292176 0.735256602 0.734294348 0.759855848 1 21.15915328 1.211941645 3.200533722 1.057399119 0.729494345 0.738861148 0.050331583 0.196799823 2.553055797 0.16949848 0.012343127 16.29077121 -1.211941645 -0.327904774 LTGS(ph)TSSLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 1 LTGS(0.446)T(0.446)S(0.08)S(0.029)LNK;LTGS(0.885)T(0.085)S(0.028)S(0.002)LNK;LTGS(0.498)T(0.498)S(0.003)SLNK;LTGS(0.396)T(0.396)S(0.2)S(0.007)LNK;LTGS(0.925)T(0.072)S(0.004)SLNK;LTGS(0.498)T(0.498)S(0.003)SLNK 238.92 3.36E-12 2380870000 4915700 4003450 3044690 3306270 3913720 3624370 4945830 5484590 4926540 TRUE FALSE 4266077.79 3977151.073 4517112.268 4057009.137 3835844.629 3763801.859 4466184.168 4311753.11 4344130.054 0.982032706 0.915523022 1.03981976 0.933906003 0.882994888 0.866410953 1.028096331 0.992546967 1 22.05063586 2.206965523 24.99998873 1.004778808 0.937922906 0.31132323 0.049096011 263.7760486 208714.1087 0.020963451 0.014134904 161.0517776 -2.206965523 -0.066855903 LTGSTSS(ph)LNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 1 LTGSTS(0.026)S(0.974)LNK;LTGST(0.001)S(0.021)S(0.978)LNK;LTGSTS(0.078)S(0.922)LNK 224.03 4.36E-09 1332090000 5000500 3787370 2721580 3259870 3797780 3094170 4551450 5130500 4928000 TRUE FALSE 4339671.255 3762490.517 4037745.191 4000073.307 3722211.608 3213204.722 4110051.08 4033382.501 4345417.454 0.998677642 0.865852489 0.929196155 0.920526819 0.856583205 0.739446729 0.945835728 0.92819218 1 22.05106335 1.490542498 1.969031542 1.001225004 0.887078242 0.197815228 0.068043924 0.746787005 4.683491378 0.138272857 0.019264611 30.9415808 -1.490542498 -0.114146763 LTGVFAPRPSTGPHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTGVFAPRPSTGPHK 15 1 P62701;C9JEH7;P22090;Q8TD47 P62701 RPS4X;RPS4Y1;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1;40S ribosomal protein S4, Y isoform 2" 0 ; 166.35 8.25E-07 3505500000 2433700 2691700 829900 1512580 2789800 2466600 2985400 3351200 724960 FALSE TRUE 2112080.379 2674018.045 1231242.416 1856034.407 2734288.438 2561491.698 2695876.367 2634571.959 639256.0547 3.30396617 4.183015594 1.926055149 2.903428749 4.277297678 4.00698856 4.217208969 4.121309356 1 19.28603439 3.269923437 24.96035317 3.675225111 3.075604636 0.029549773 1.092995045 606.006139 482290.9218 0.313418865 0.404580742 1861.758893 -3.269923437 -0.599620475 LTHDVELNLDYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LTHDVELNLDYER 13 0 P02786;G3V0E5;H7C3V5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ;;; 228.38 7.53E-12 1694800000 1550820 1432820 963040 1065110 1552340 1549660 1113200 1461800 1592380 FALSE TRUE 1345875.208 1423407.711 1428769.365 1306959.505 1521451.471 1609276.423 1005242.035 1149205.446 1404130.65 0.95851138 1.013728823 1.017547309 0.930796222 1.083554063 1.146101627 0.715917735 0.818446236 1 20.42124575 2.237542211 24.99999207 0.833930542 1.022561117 0.468234665 0.090280218 22.86162446 561181.2043 0.035876193 0.025756196 172.7993922 -2.237542211 0.188630576 LTHVNTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTHVNTGR 8 0 Q99470;K7ELI9 Q99470 SDF2 Stromal cell-derived factor 2 0 ; 96.034 0.0092277 289970000 369280 312720 222570 264360 284890 426520 290060 277580 274800 FALSE TRUE 320478.7124 310665.7217 330205.5965 324386.9785 279221.2464 442928.5004 261930.0258 218221.6771 242313.4571 1.322579093 1.282082 1.362720835 1.338708062 1.152314237 1.827915403 1.080955342 0.900575972 1 17.886515 2.014831933 24.99922227 0.95745997 1.370985659 0.532156727 0.17416615 161.0914254 271518.6072 0.067494731 0.045486018 103.4741656 -2.014831933 0.413525689 LTIAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LTIAEER 7 0 P62701;Q8TD47 P62701 RPS4X;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 2" 0 ;;; 166.86 0.0025772 2092680000 4204820 4312930 2706450 3402150 4263180 4427820 4090930 4610350 4291840 FALSE TRUE 3649142.383 4284598.079 4015298.273 4174660.156 4178351.059 4598161.101 3694192.238 3624462.53 3784463.564 0.964242969 1.132154665 1.060995357 1.103104861 1.104080139 1.215010007 0.976146863 0.957721608 1 21.85165739 2.109776529 14.69428628 0.973173064 1.097224889 0.444314904 0.062476939 0.601230453 76.79914292 0.024460778 0.016491366 128.7586841 -2.109776529 0.124051825 LTIFGNSAVSQPASSSNHS(ph)SR ddPTM_MDA-MB-175_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(0.038)S(0.083)S(0.163)NHS(0.358)S(0.358)R;LTIFGNSAVSQPAS(0.022)S(0.046)S(0.134)NHS(0.399)S(0.399)R 77.873 0.006056 345680000 197325 185903 67509 75667 159690 201576 134115 165748 167276 TRUE FALSE 171248.0013 184681.791 100156.5782 92848.34885 156512.4814 209330.7592 121108.5479 130304.0801 147500.8218 1.16099693 1.252072962 0.679023865 0.629476824 1.061095657 1.41918368 0.821070326 0.88341257 1 17.17036347 LTIQNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTIQNR 6 0 P30050 P30050 RPL12 60S ribosomal protein L12 0 ; 129.2 0.037913 315260000 401510 372120 224672 339610 348060 335620 391330 353210 353790 FALSE TRUE 348449.4362 369675.5192 333324.1307 416723.6411 341134.287 348531.5186 353378.8768 277678.7902 311965.3492 1.116949165 1.184989038 1.068465237 1.33580105 1.093500569 1.117212278 1.132750409 0.890094976 1 18.25102627 1.792769953 6.855455452 0.944349146 1.152588141 0.54731463 0.077496793 0.140995847 13.67303816 0.038599055 0.019423847 62.05402446 -1.792769953 0.208238995 SPPAS(ph)PESWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPPASPESWK 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 SPPAS(0.999)PES(0.001)WK 98.182 0.0058228 423430000 156090 185480 179580 278260 347970 321920 379830 480170 435820 TRUE FALSE 135462.311 184261.5697 266425.4887 341443.1859 341046.0778 334304.4707 342994.1451 377489.3822 384297.8561 0.352493018 0.479475924 0.693278623 0.888485794 0.88745246 0.869909799 0.89252162 0.982283341 1 18.5518654 4.223062568 1.073415827 0.93926221 0.260928109 0.966853813 0.039043083 0.14961241 0.248173132 0.014588006 0.096225423 16713.31383 -4.223062568 -0.678334101 down LTIYDWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LTIYDWDR 8 0 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-2;Q9NZM1-5 Q9NZM1-6 MYOF Myoferlin 0 ;;; 155.88 0.0009351 713970000 959440 964990 678115 779180 999400 1096390 850670 1093250 1545440 FALSE TRUE 832647.5731 958650.9172 1006053.682 956104.728 979513.8953 1138568.833 768172.1543 859466.9952 1362739.844 0.611009927 0.70347317 0.738258066 0.701604736 0.718782752 0.835499775 0.563696848 0.630690443 1 20.37807874 1.232180916 24.99990533 1.00000052 0.6874452 0.632478146 0.074772744 150.0184223 587815.1494 0.174624547 0.01898141 17.06793249 -1.232180916 -0.312555319 LTKEEIVDKYDLFVGSQATDFGEALVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTKEEIVDKYDLFVGSQATDFGEALVR 27 2 O43852;O43852-3;O43852-15;O43852-6;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ; 230.75 2.69E-35 489250000 822160 591690 377540 443890 557210 525150 747610 744320 117584 FALSE TRUE 713509.4729 587803.1494 560119.6068 544682.0089 546122.6112 545352.8603 675106.8973 585152.9603 103683.3535 6.881620328 5.669214293 5.402213451 5.253321683 5.267215931 5.259791876 6.511237095 5.643653882 1 16.66182476 1.239115071 8.421796491 0.954424144 5.714087652 0.88007968 0.549425133 0.028123391 21.43548 0.771598685 0.135875403 17.34263447 -1.239115071 4.759663508 LTLDDIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTLDDIER 8 0 Q5HY81;P11441 Q5HY81 UBL4A Ubiquitin-like protein 4A 0 ; 122.19 0.0032597 131260000 456840 465990 273950 321380 432040 420160 408270 476180 478540 FALSE TRUE 396467.4365 462928.881 406433.1363 394354.241 423443.2493 436323.8271 368676.0382 374352.6126 421967.5464 0.939568552 1.097072239 0.963185771 0.934560595 1.003497195 1.034022239 0.873707093 0.887159726 1 18.68677252 2.238482355 25 0.911446108 0.996092527 0.27123447 0.057358768 2.431896411 776246.6548 0.022122194 0.016003596 173.1738671 -2.238482355 0.084646419 LTLDKLDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTLDKLDVK 9 1 P00558 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 126.67 0.0014322 0 17997600 14819000 8456600 7962800 10195700 8467600 15467200 18455600 9380200 FALSE TRUE 15619171.56 14721653.01 12546240.05 9770875.444 9992825.518 8793354.051 13967193.32 14509013.56 8271283.442 1.888361301 1.77985111 1.5168432 1.181301005 1.208134818 1.063118452 1.688636766 1.754142953 1 22.97967978 4.191348955 2.958244837 1.368695586 1.860783996 0.417991116 0.246243477 0.297760597 5.208970776 0.07266403 0.201340767 15536.34852 -4.191348955 0.49208841 LTLEDLEDSWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LTLEDLEDSWDR 12 0 Q6P2Q9;I3L3Z8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;; 236.92 1.01E-15 523144000 842440 731160 491080 602380 742790 757450 712900 824820 959820 FALSE TRUE 731109.4195 726356.9618 728567.9306 739159.5858 728009.9322 786589.5916 643763.0677 648438.6618 846351.173 0.863836954 0.858221723 0.860834077 0.873348569 0.860174778 0.929389143 0.760633515 0.766157929 1 19.69089687 2.242282354 24.99801474 0.823007166 0.872272484 0.021207201 0.068522526 224.1609417 1505650.541 0.025969934 0.019328926 174.6957557 -2.242282354 0.049265318 LTLEGLEEDDDDRVS(ph)PTVLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LTLEGLEEDDDDRVSPTVLHK 21 1 Q9NPB8 Q9NPB8 GPCPD1 Glycerophosphocholine phosphodiesterase GPCPD1 1 LTLEGLEEDDDDRVS(0.939)PT(0.061)VLHK;LTLEGLEEDDDDRVS(0.917)PT(0.083)VLHK;LTLEGLEEDDDDRVS(0.96)PT(0.04)VLHK;LTLEGLEEDDDDRVS(0.994)PT(0.006)VLHK 311.46 9.18E-67 1179263000 567952 569901 415730 513815 560306 421352 569060 746479 898120 TRUE FALSE 492895.7042 566157.2828 616778.4185 630484.5489 549157.0068 437561.6841 513872.6488 586850.275 791945.2767 0.622386065 0.71489445 0.778814442 0.796121358 0.693427972 0.55251505 0.648873936 0.74102377 1 19.59504122 1.244277966 3.408117167 1.044960368 0.690923807 0.655736 0.070775041 0.213837576 3.548824274 0.197782393 0.019937128 17.55003416 -1.244277966 -0.354036562 LTLEGLEEDDDDRVSPTVLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTLEGLEEDDDDRVSPTVLHK 21 1 Q9NPB8 Q9NPB8 GPCPD1 Glycerophosphocholine phosphodiesterase GPCPD1 0 186.3 1.98E-17 171510000 67323 56847 45369 67028 69738 52578 64018 77108 83720 FALSE TRUE 58426.09498 56473.56831 67309.60015 82247.73186 68350.35024 54600.70968 57809.54421 60619.05426 73822.71697 0.791437885 0.764989025 0.911773542 1.114124964 0.925871507 0.739619346 0.783086109 0.821143636 1 16.17177722 4.241550875 24.89823089 0.889070053 0.778213417 0.176104921 0.107163867 149.4935446 1244687.887 0.029855796 0.072242338 17440.17645 -4.241550875 -0.110856637 LTLENFYSNLILQHEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTLENFYSNLILQHEER 17 0 Q9Y2H1;F5H7Z3;F5GY51;F5H5E6;F5H0V1;F5H277 Q9Y2H1 STK38L Serine/threonine-protein kinase 38-like 0 115.15 0.00095912 0 57017 48687 40881 38374 44036 54937 61775 63925 50178 FALSE TRUE 49482.05899 48367.17189 60651.18834 47087.40321 43159.76975 57050.46194 55784.07001 50255.13621 44246.014 1.11833936 1.093141902 1.370771802 1.06421797 0.975449896 1.289392123 1.260770518 1.135811606 1 15.43325987 1.269570404 4.310624763 0.989434675 1.167856998 0.168727695 0.115729446 0.363680552 12.47361644 0.186344327 0.029419587 18.60246104 -1.269570404 0.178422322 LTLHGLQQYYVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTLHGLQQYYVK 12 0 O00148;O00148-2;Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;H0Y400;H0YCC6 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ; 167.2 4.99E-05 3523300000 2912270 2710340 2306690 2828410 3059920 2903610 2731730 3670400 4796970 FALSE TRUE 2527406.141 2692535.598 3422212.999 3470643.72 2999033.579 3015313.756 2466807.245 2885513.523 4229877.671 0.597512821 0.636551647 0.809057203 0.820506877 0.709011894 0.712860747 0.583186427 0.682174225 1 22.01218451 -1.999067757 0.025072053 1.675742732 2.35E-06 0.136219051 0.115152925 14548.94902 36.2059121 1612.178258 905.8030055 0.010021489 1.999067757 -1.675740379 LTLNS(ph)PIFDKPLSR ddPTM_MDA-MB-175_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 LTLNS(1)PIFDKPLSR;LTLNS(1)PIFDKPLSR 197.84 1.39E-08 4550000000 3671300 3382700 2386610 2960110 3731900 3388420 4119700 4644700 4529700 TRUE FALSE 3186128.403 3360478.821 3540782.579 3632248.218 3657642.491 3518774.71 3720172.128 3651467.05 3994204.026 0.797687945 0.8413388 0.886480149 0.90937974 0.91573752 0.880970198 0.931392614 0.91419142 1 21.9294766 7.610192739 0.281223271 0.954837202 2.01E-14 0.76085383 0.026243108 33.38633745 0.655465124 0.063595951 14.69382629 40756111.21 -7.610192739 -0.954837202 LTLPHSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTLPHSIR 8 0 O76021;J3QSV6;I3L3U9;I3L3C4;I3L234 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 169.12 0.00042016 0 298430 311860 180900 213380 321620 333490 251610 323100 247600 FALSE TRUE 258991.7194 309811.3711 268383.8451 261831.1903 315220.3912 346319.5761 227208.9009 254007.5794 218329.0101 1.186245105 1.419011477 1.229263326 1.199250572 1.443786106 1.586227941 1.040672061 1.16341653 1 17.73614431 2.201388093 24.99979832 1.086761688 1.340121443 0.503766041 0.128615923 151.3664106 101798.0831 0.053409157 0.036009492 158.9966934 -2.201388093 0.253359755 LTNGIWVLAELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTNGIWVLAELR 12 0 Q10567-4;Q10567-3;Q10567-2;Q10567 Q10567-4 AP1B1 AP-1 complex subunit beta-1 0 133.32 0.00038451 94436000 78211 107550 72122 71970 103300 83907 107520 101300 89444 FALSE TRUE 67875.21819 106843.497 107000.4404 88311.88849 101244.5321 87134.95659 97092.72695 79637.78332 78870.03221 0.860595796 1.354677993 1.356667893 1.119714117 1.283688231 1.104791695 1.231047132 1.009734383 1 16.26718961 1.686709299 5.401100513 1.001677033 1.198126415 0.21318139 0.144198413 0.197172129 13.05313661 0.087151285 0.035458146 48.6081731 -1.686709299 0.196449382 LTNSMMMHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTNSMMMHGR 10 0 M0R0F0;M0R0R2;P46782 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ; 188.28 1.14E-06 3330800000 1368680 2052250 943850 1228440 1904510 1996450 1683540 1830430 1574640 FALSE TRUE 1187805.47 2038768.635 1400299.017 1507376.078 1866613.977 2073254.723 1520270.55 1439006.789 1388487.853 0.855466951 1.468337393 1.008506494 1.085624245 1.344350239 1.493174549 1.094910947 1.03638414 1 20.40508313 2.012488453 24.94841017 1.034247836 1.219220143 0.141785301 0.196782432 392.5346196 784170.5576 0.078306249 0.052755419 102.9173162 -2.012488453 0.184972307 LTPAEEENNSFQRLS(ph)P ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LTPAEEENNSFQRLSP 16 1 Q5HYI7-5;Q5HYI7 Q5HYI7-5 MTX3 Metaxin-3 1 LTPAEEENNSFQRLS(1)P;LTPAEEENNSFQRLS(1)P;LTPAEEENNS(0.002)FQRLS(0.998)P 168.05 1.61E-08 411945000 591050 529970 369128 472410 619830 727010 467861 699230 410839 TRUE FALSE 512941.245 526488.5922 547639.5355 579677.9108 607496.5957 754978.5451 422487.9122 549705.1059 362270.0814 1.415908382 1.453304093 1.511688554 1.600126371 1.676916275 2.084021242 1.166223583 1.517390295 1 18.46670614 0.790014181 1.220303346 8.35E-15 1.585683067 0.366804886 0.230150876 4.555541631 2.627145319 12.07559769 0.069844057 6.166151361 -0.790014181 1.585683067 LTPEEEEILNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTPEEEEILNK 11 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ; 191.48 4.21E-06 292260000 374100 302250 230411 258760 295540 242680 350680 429370 327030 FALSE TRUE 324661.7372 300264.4998 341838.5303 317515.4129 289659.3322 252016.0566 316671.1076 337552.5669 288368.886 1.125855642 1.041251378 1.18542099 1.101073758 1.004474984 0.873936367 1.098145892 1.17055821 1 18.13755599 3.388211517 7.392532689 1.044695544 1.115287072 0.191490208 0.082995528 0.519404676 36.89165245 0.026781652 0.034625272 2444.620879 -3.388211517 0.070591528 LTPEELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTPEELER 8 0 Q5H8X8;O95399;O95399-2 Q5H8X8 UTS2 Urotensin-2 0 ; 212.2 5.80E-05 765710000 1210660 991760 765250 1010490 1078040 1226800 845430 1014910 1108270 FALSE TRUE 1050668.214 985245.0633 1135327.46 1239937.199 1056589.113 1273995.79 763440.3287 797879.3945 977251.5831 1.075125619 1.008179552 1.161755559 1.268800399 1.081184345 1.303651805 0.781211657 0.816452394 1 19.89837049 2.228016272 24.99998997 0.852060701 1.146182357 0.624411785 0.103583903 130.6141275 309675.313 0.042273811 0.028835854 169.050427 -2.228016272 0.294121656 LTPGCEAEAETEAICFFVQQFTDMEHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 LTPGCEAEAETEAICFFVQQFTDMEHNR 28 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;; 275.69 1.51E-61 21829603000 7790330 8759047 6319922 6686183 8143514 9288586 8703091 9088918 11013755 FALSE TRUE 6760818.152 8701508.244 9376257.418 8204383.042 7981474.004 9645923.914 7859066.574 7145323.616 9711721.431 0.696150338 0.895980008 0.965457822 0.844791843 0.821839265 0.993224938 0.809235173 0.735742233 1 23.21129561 4.743695749 24.14024787 0.871166753 0.696150218 0.311170736 0.085833735 474.7070251 2231478.07 0.021615102 0.174528809 55423.72983 -4.743695749 -0.175016536 LTPHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LTPHEK 6 0 O00148;O00148-2;O00148-3;K7EQN7 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ;; 103.29 0.034815 587780000 2893250 2227580 1545290 1871390 1550760 2103410 2377820 2891920 2735150 FALSE TRUE 2510899.682 2212946.88 2292597.413 2296317.702 1519902.91 2184329.544 2147219.382 2273505.413 2411803.683 1.041087921 0.917548512 0.950573809 0.952116343 0.630193461 0.905682979 0.890296087 0.942657742 1 21.20168105 5.137178494 1.125509756 0.889003868 1.248720749 0.176742497 0.099553147 6.92548982 3.994402141 0.030825667 3.646840953 137144.531 -5.137178494 0.359716881 LTPIHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LTPIHDR 7 0 P28072;A0A087X2I4;I3L3X7 P28072 PSMB6 Proteasome subunit beta type-6;Proteasome subunit beta type 0 ;;; 157.58 0.0014664 4352510000 5656970 5291380 3774990 4765960 4948020 5499980 5090380 5644270 7997500 FALSE TRUE 4909387.082 5256620.576 5600587.791 5848144.061 4849564.083 5711567.79 4596715.731 4437286.784 7052044.661 0.696165058 0.745403756 0.794179286 0.829283469 0.687681987 0.809916565 0.651827371 0.629219893 1 22.74961018 3.220329529 24.99921781 0.734832264 0.766762741 0 0.108688788 1379.384112 1891463.503 0.032821876 0.03728569 1660.846628 -3.220329529 0.031930478 LTPLSHEVISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LTPLSHEVISR 11 0 P41091;Q2VIR3;Q2VIR3-2;H7BZU1 P41091 EIF2S3;EIF2S3L Eukaryotic translation initiation factor 2 subunit 3;Putative eukaryotic translation initiation factor 2 subunit 3-like protein 0 ;;; 255.52 1.82E-20 2396470000 2455370 2604080 1531750 1944210 2353250 2557360 2047790 2452870 2366620 FALSE TRUE 2130886.633 2586973.627 2272509.423 2385672.596 2306424.929 2655743.294 1849195.641 1928342.839 2086840.88 1.021106427 1.239660221 1.088971107 1.143198132 1.105223188 1.27261418 0.886122013 0.924048813 1 20.99288917 2.224498587 24.99991832 0.931974581 1.144971482 0.624844721 0.076094305 135.788516 241407.1572 0.028644271 0.019416958 167.686688 -2.224498587 0.212996901 LTPPS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTPPSPVR 8 0 Q8TAP8 Q8TAP8 PPP1R35 Protein phosphatase 1 regulatory subunit 35 1 LT(0.001)PPS(0.999)PVR 92.445 0.012349 105410000 207850 205180 161990 198380 224860 218580 197750 234850 297520 TRUE FALSE 180382.0959 203832.1591 240328.9058 243425.211 220385.7259 226988.914 178572.2354 184629.1551 262347.5245 0.68756927 0.776954764 0.916070797 0.927873101 0.840052622 0.865222245 0.680670556 0.703757946 1 18.00111965 1.22030465 24.9194626 1.000000661 0.799916575 0.329992686 0.089663371 1651.323653 2253936.053 0.808280513 0.02456068 16.60751487 -1.22030465 -0.200084085 LTPRPS(ph)PSPMIESTPMSIAGDATPLLDEMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTPRPSPSPMIESTPMSIAGDATPLLDEMDR 31 1 Q7KZ85;Q7KZ85-3;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 1 LT(0.052)PRPS(0.787)PS(0.102)PMIES(0.029)T(0.029)PMS(0.002)IAGDATPLLDEMDR;LT(0.014)PRPS(0.963)PS(0.021)PMIES(0.002)T(0.001)PMSIAGDATPLLDEMDR 109.55 0.00016987 147954000 32954 26048 13415.2 20189.1 29140 30026 26681 27520 27760 TRUE FALSE 28599.04541 25876.88897 19902.83559 24773.34373 28560.17101 31181.11965 24093.48073 21635.06216 24478.24442 1.168345446 1.05713827 0.81308264 1.012055575 1.166757326 1.2738299 0.984281401 0.883848604 1 14.57921247 2.010014275 24.999606 0.9337589 1.074198858 0.191707 0.123151512 340.872862 850950.3323 0.054655146 0.036803258 102.3326628 -2.010014275 0.140439958 LTPS(ph)PDIIVLSDNEAS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 LTPS(1)PDIIVLSDNEAS(0.571)S(0.429)PR 154.6 5.00E-08 20278000 34294 29420 18424 21160 28333 28741 27376 33277 28770 TRUE FALSE 29761.96101 29226.73808 27333.90802 25964.70141 27769.22873 29846.68487 24721.07973 26160.97251 25368.84337 1.173169804 1.152072156 1.077459765 1.023487789 1.094619424 1.176509486 0.974466174 1.031224488 1 14.63077012 LTPS(ph)PDIIVLSDNEASSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 LT(0.003)PS(0.997)PDIIVLSDNEASSPR;LTPS(1)PDIIVLSDNEASSPR;LTPS(1)PDIIVLSDNEASSPR;LTPS(1)PDIIVLSDNEASSPR 254.59 6.92E-31 156692000 67522 68500 35101.7 53092 73593 71588 62507 71253 68391 TRUE FALSE 58598.79662 68050.01899 52076.99953 65147.35006 72128.64328 74342.03668 56445.08076 56016.10044 60305.89389 0.971692696 1.128414067 0.863547427 1.080281642 1.196046334 1.232749104 0.935979506 0.9288661 1 15.88001139 LTPSGYEWGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTPSGYEWGR 10 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 133.13 0.00047738 467170000 267150 214810 128912 169241 226580 216490 203199 249940 239950 FALSE TRUE 231845.4506 213398.899 191254.2744 207669.7557 222071.5013 224818.5104 183492.7923 196492.276 211583.3844 1.095763977 1.008580611 0.903919157 0.981503138 1.049569662 1.062552766 0.867236304 0.928675362 1 17.69086681 LTPSPDIIVLSDNEAS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 LTPSPDIIVLSDNEAS(0.5)S(0.5)PR;LTPSPDIIVLSDNEAS(0.715)S(0.285)PR 212.41 8.75E-17 183455000 477430 419690 242003 322530 405520 395940 374150 451580 403280 TRUE FALSE 414336.4158 416933.0288 359036.4603 395765.3661 397450.9454 411172.068 337864.9906 355013.1312 355604.6978 1.16516013 1.172462094 1.009650498 1.11293627 1.117676307 1.156261631 0.950113968 0.998336449 1 18.43991486 2.237831133 25 0.984687434 1.118871186 0.660270596 0.047134114 12.19617812 417943.689 0.018921721 0.013614776 172.9143886 -2.237831133 0.134183752 LTPTHGEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTPTHGEMR 9 0 Q8NE71;Q8NE71-2;H0YGW7 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 68.893 0.056782 99703000 292400 282320 243780 254810 285290 256660 371650 344440 338320 FALSE TRUE 253758.5992 280465.4213 361672.8234 312668.505 279613.2872 266533.8763 335607.4402 270784.1864 298324.195 0.850613539 0.940136355 1.212348276 1.048082959 0.937279952 0.893437008 1.1249756 0.907684294 1 18.18652146 3.244550601 24.99520203 0.972012085 1.021859142 0.029002797 0.109887349 557.5319128 2326474.098 0.032708287 0.04111114 1756.105493 -3.244550601 0.049847056 LTPVRPAAAS(ph)PIVSGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 178.77 5.77E-10 2484450000 1696270 1398240 931680 1020310 1256530 1539570 1380970 1406730 1461600 TRUE FALSE 1472103.622 1389054.869 1382243.564 1251986.98 1231527.511 1598798.254 1247043.742 1105911.737 1288811.313 1.14221811 1.077779854 1.072494903 0.971427677 0.955552996 1.240521586 0.967592175 0.858086615 1 20.29760963 -1.999999953 0.148374072 0.21244966 1.181523465 0.202370334 0.096141876 230.215989 2.882418572 46.86931593 1.739379212 0.010000001 1.999999953 0.969073805 LTPVS(ph)PESSSTEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LTPVSPESSSTEEK 14 0 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 LTPVS(1)PESSSTEEK;LTPVS(1)PESSSTEEK;LTPVS(1)PESSSTEEK;LTPVS(0.995)PES(0.004)SSTEEK;LTPVS(0.998)PES(0.002)SSTEEK;LTPVS(0.999)PES(0.001)SSTEEK 330.04 2.25E-68 2982540000 5329420 4067840 3382490 4039430 3955582 3432077 4949390 5615440 5896470 TRUE FALSE 4625123.644 4041118.091 5018273.478 4956644.32 3876873.657 3564111.223 4469398.92 4414621.855 5199396.034 0.889550173 0.777228367 0.965164693 0.953311555 0.74563923 0.685485622 0.859599632 0.849064358 1 22.30991262 1.206686385 3.434187548 1.032121258 0.837645505 0.24874928 0.087020519 0.591162797 9.409433348 0.318451758 0.023574778 16.09482965 -1.206686385 -0.194475753 LTPYEVDELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTPYEVDELR 10 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ; 141.52 8.69E-05 231370000 171818 158407 96762 128974 148876 143589 149705 172521 215286 FALSE TRUE 149111.816 157366.414 143556.4268 158259.5179 145913.6589 149112.9617 135186.6321 135628.7267 189835.1343 0.785480604 0.828963587 0.756216321 0.833668217 0.76863358 0.78548664 0.712126512 0.714455347 1 17.5343875 1.229824351 24.99466368 1.000000436 0.770872923 0.757937759 0.040274959 184.1414803 526792.6225 0.126574875 0.010905964 16.97556941 -1.229824351 -0.229127513 LTPYEVDELRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LTPYEVDELRR 11 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;;;; 237.8 2.18E-15 10742511000 4708756 4381934 2656327 3181375 4334764 4388308 3995725 4959391 3535073 FALSE TRUE 4086481.964 4353148.787 3940935.622 3903754.818 4248510.677 4557129.048 3608220.205 3898863.829 3117160.697 1.31096288 1.396510867 1.26427092 1.252343141 1.362942463 1.461948706 1.157534229 1.250774088 1 21.5718011 0.484259588 0.958706068 1.29E-10 1.330322091 0.615758099 0.079850443 5.132796428 1.285165641 10.08629337 0.026752769 3.049717335 -0.484259588 1.330322091 LTQAEISEQPTMATVVPQVPTS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTQAEISEQPTMATVVPQVPTSPK 24 0 C9K0J5;Q70E73 C9K0J5 RAPH1 Ras-associated and pleckstrin homology domains-containing protein 1 1 LTQAEISEQPTMATVVPQVPT(0.166)S(0.834)PK 118.43 0.00033888 58778000 136380 126050 117110 139180 177580 149790 220030 247700 221640 TRUE FALSE 118357.0375 125221.9693 173744.7877 170782.9462 174046.5054 155552.5182 198691.5245 194731.2826 195437.9717 0.605598986 0.640724871 0.889002205 0.873847312 0.890546008 0.795917584 1.016647496 0.996384075 1 17.57635127 5.44880611 0.376126291 1.009354885 2.42E-12 0.784362439 0.065945318 6.095980073 0.504579424 0.094263474 3.068781915 281064.5741 -5.44880611 -1.009354885 LTQDQDVDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTQDQDVDVK 10 0 P30153;B3KQV6;E9PH38 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 203.97 4.55E-07 66069000 230280 209990 152030 165860 194880 177160 230740 275860 265360 FALSE TRUE 199847.9145 208610.5619 225552.2165 203521.048 191002.2693 183975.4598 208362.8703 216869.4857 233989.4431 0.854089449 0.891538349 0.963941849 0.869787309 0.816285841 0.786255386 0.890479791 0.926834488 1 17.83608392 1.457597964 2.111331527 1.007668281 0.866763559 0.464389714 0.046803503 0.446130791 3.118492747 0.106706472 0.014296501 28.68124269 -1.457597964 -0.140904723 LTQEPESIRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LTQEPESIRK 10 1 P09497-2;P09497;H0Y9Q6 P09497-2 CLTB Clathrin light chain B 0 ;;; 132.17 0.00036992 1651760000 2732280 2355690 1295080 1689400 2291880 2092010 2785290 3237150 1491290 FALSE TRUE 2371202.275 2340215.317 1921385.02 2073004.091 2246276.072 2172490.978 2515173.004 2544910.664 1314991.395 1.803207446 1.779643065 1.461138854 1.576439282 1.708205909 1.652095205 1.912691607 1.935305945 1 20.32662193 3.122928348 15.56683375 1.699251766 1.649100968 0 0.273647346 7.784588433 1019.891019 0.08341 0.094581469 1327.175476 -3.122928348 -0.050150798 LTQTSS(ph)TEQLNVLETETEVLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LTQTSSTEQLNVLETETEVLNK 22 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 LTQT(0.002)S(0.01)S(0.494)T(0.494)EQLNVLETETEVLNK;LT(0.024)QT(0.019)S(0.019)S(0.469)T(0.469)EQLNVLETETEVLNK;LTQT(0.008)S(0.008)S(0.492)T(0.492)EQLNVLETETEVLNK 303.78 3.33E-56 919930000 743500 603330 431030 515620 525800 503010 674730 780790 716940 TRUE FALSE 645244.5912 599366.6855 639477.5497 632699.4018 515337.6087 522361.1202 609294.7885 613824.1346 632184.1699 1.020659203 0.948088728 1.011536796 1.000815003 0.815170062 0.826279975 0.963793175 0.970957774 1 19.26998538 LTQYHGGS(ph)LPNVSQLR ddPTM_MDA-MB-175_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 234.73 7.10E-20 2251940000 3069710 2800180 1371710 1893940 2449080 2529870 2083430 2739550 2474520 TRUE FALSE 2664040.046 2781785.433 2035073.544 2323988.024 2400348.1 2627195.736 1881379.279 2153718.552 2181985.065 1.220924968 1.274887477 0.932670703 1.065079712 1.100075403 1.204039284 0.862232886 0.987045506 1 21.0572098 8 0.305553341 0.967786155 3.516784626 0.346212013 0.106939685 88.25817245 1.404178582 0.20444826 121.4906938 100000000 -8 2.548998472 LTRDETNYGIPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 147.66 3.91E-05 768830000 1056130 958370 565720 574850 837460 697690 967100 1192450 670770 FALSE TRUE 916559.7446 952074.4044 839304.0842 705378.4785 820796.1845 724530.5858 873310.7909 937453.8472 591472.3347 1.549624033 1.609668531 1.419008185 1.192580679 1.38771695 1.224961073 1.476503193 1.584949611 1 19.17395116 4.107998705 4.630396261 1.346710108 1.577406911 0.29993882 0.16212444 0.289230515 10.38976445 0.042888205 0.09470584 12823.2676 -4.107998705 0.230696803 LTRPAAS(ph)PAVGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTRPAASPAVGEK 13 1 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 LT(0.007)RPAAS(0.993)PAVGEK;LTRPAAS(1)PAVGEK 149.99 0.00011581 191248000 279200 248770 157420 173294 209397 189710 243300 255470 257040 TRUE FALSE 242303.0126 247135.8135 233548.8385 212643.0513 205230.4094 197008.2665 219704.8034 200839.7286 226653.024 1.069048223 1.090370687 1.030424542 0.938187577 0.905482776 0.869206433 0.969344241 0.886110959 1 17.79012588 3.83525173 2.550652774 0.921161403 1.078955627 0.743837987 0.03814977 0.128900758 1.631638088 0.010210581 0.020393116 6843.081771 -3.83525173 0.157794223 LTS(ph)DEEGEPSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTSDEEGEPSGK 12 0 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 LT(0.005)S(0.995)DEEGEPSGK 187.11 1.14E-05 93094000 397860 301170 310880 359310 341280 287370 386230 472400 747850 TRUE FALSE 345281.793 299191.5944 461222.6078 440896.8272 334489.1957 298425.3099 348773.474 371380.9362 659440.025 0.523598477 0.453705543 0.69941555 0.668592761 0.507232171 0.45254352 0.528893396 0.563176213 1 19.33088193 1.2383635 6.259838394 1.014518573 0.549281773 0.756431915 0.080355095 0.066586511 11.04159161 0.132176279 0.021167249 17.31264802 -1.2383635 -0.4652368 LTS(ph)PGALLFQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LTSPGALLFQ 10 0 O60566-3;O60566;O60566-2 O60566-3 BUB1B Mitotic checkpoint serine/threonine-protein kinase BUB1 beta 1 LT(0.111)S(0.889)PGALLFQ;LT(0.14)S(0.86)PGALLFQ;LT(0.195)S(0.805)PGALLFQ;LT(0.263)S(0.737)PGALLFQ 88.948 0.012427 41131900 150218 153133 88741 106120 143287 141474 126348 164790 145686 TRUE FALSE 130366.3107 152127.0592 131656.4444 130216.1679 140435.869 146916.5963 114094.7904 129550.9409 128463.167 1.014814703 1.184207604 1.024857533 1.013645942 1.093199493 1.143647628 0.888151779 1.008467593 1 16.97099524 2.244585256 24.99999872 0.971258582 1.07904678 0.417058358 0.063148174 141.0416231 585272.5879 0.023413558 0.017659073 175.6245628 -2.244585256 0.107788198 LTSEEFNAIFTFYDKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LTSEEFNAIFTFYDKDR 17 1 P22676;H3BMN5 P22676 CALB2 Calretinin 0 ;; 206.74 6.12E-12 1265615000 1256717 1187896 868068 1041744 1103383 955321 1465801 1671964 1282957 FALSE TRUE 1090638.664 1180092.633 1287868.588 1278287.897 1081427.837 992072.817 1323647.845 1314427.51 1131287.285 0.964068702 1.043141427 1.13840985 1.12994101 0.955926802 0.876941543 1.170036879 1.161886576 1 20.10953391 LTSMHFYGWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTSMHFYGWK 10 0 P23921;E9PL69 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ; 107.24 0.0023096 965960000 1933560 3123500 1019660 2027860 3012800 2428890 2820000 3419600 3364600 FALSE TRUE 1678035.147 3102981.523 1512770.987 2488316.607 2952851.174 2522330.97 2546516.834 2688345.151 2966840.821 0.565596622 1.04588743 0.509892872 0.838709171 0.995284666 0.850174014 0.858326074 0.906130566 1 21.50049609 3.483995539 24.864403 0.912124076 0.729885019 0.300609125 0.147817667 385.6077347 1394751.37 0.038612298 0.051888714 3047.86368 -3.483995539 -0.182239057 LTSNPLASHDYILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTSNPLASHDYILK 14 0 Q969X5;Q969X5-2 Q969X5 ERGIC1 Endoplasmic reticulum-Golgi intermediate compartment protein 1 0 ; 203.2 1.54E-08 817360000 2284660 2341530 1337200 1613590 2310630 2028560 1890870 2884600 2714310 FALSE TRUE 1982736.392 2326148.335 1983874.393 1979980.272 2264652.984 2106600.016 1707493.718 2267750.738 2393427.364 0.828408843 0.97189009 0.828884311 0.827257305 0.946196662 0.880160412 0.713409458 0.947490938 1 21.19064659 1.522255595 8.271629271 0.986823541 0.86113523 0.331712273 0.070810807 0.121854698 15.10961332 0.046466325 0.017450509 33.28553906 -1.522255595 -0.125688311 LTTPTYGDLNHLVSATMSGVTTCLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 333.54 6.07E-88 11955369000 6158120 5366702 3150287 4298840 5602216 6112810 5378220 6333720 5514096 FALSE TRUE 5344308.839 5331447.781 4673776.33 5274957.326 5490742.862 6347973.756 4856641.052 4979303.267 4862225.853 1.099148621 1.096503524 0.961242129 1.084885294 1.129265285 1.305569496 0.99885139 1.024078975 1 22.21318548 LTTTGQVTS(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LTTTGQVTSPVK 12 0 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 LTTTGQVT(0.16)S(0.84)PVK;LTTTGQVT(0.001)S(0.999)PVK;LTTTGQVT(0.248)S(0.752)PVK;LTTTGQVT(0.141)S(0.859)PVK;LTTTGQVT(0.005)S(0.995)PVK;LTTTGQVT(0.21)S(0.79)PVK 271.67 1.06E-27 4590300000 7337000 5826800 4796910 6107440 6017900 4764920 6422730 8100270 11999000 TRUE FALSE 6367396.86 5788523.367 7116711.721 7494227.598 5898155.564 4948229.556 5799854.633 6368090.297 10580491.89 0.601805372 0.547093975 0.67262579 0.708306162 0.557455705 0.467674812 0.548164934 0.601870911 1 23.33490336 1.238938438 6.065666552 1.014689549 0.586176487 0.788623121 0.067061122 0.063996577 9.209958093 0.113652546 0.018096273 17.33558244 -1.238938438 -0.428513063 LTTTGQVTS(ph)PVKGASFVTSTNPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LTTTGQVTSPVKGASFVTSTNPR 23 1 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 LTTTGQVT(0.034)S(0.966)PVKGASFVTSTNPR;LTTTGQVT(0.097)S(0.903)PVKGASFVTSTNPR;LTTTGQVT(0.052)S(0.947)PVKGASFVTSTNPR 257.19 8.06E-44 2822830000 2940650 2374080 1085524 1384655 2428890 1997921 2736090 3226300 722781 TRUE FALSE 2552035.652 2358484.512 1610487.037 1699062.081 2380559.841 2074782.314 2470744.413 2536380.852 637334.6536 4.004231745 3.700543347 2.526909573 2.665886864 3.735180298 3.255404836 3.876682994 3.979668825 1 19.28169158 1.231194995 24.94779281 0.999995544 3.465686844 0.691451889 0.518128402 164.0868668 555722.3279 1.391878735 0.137645205 17.02922936 -1.231194995 2.4656913 LTVADIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTVADIR 7 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 86.113 0.047262 360870000 811210 877740 646430 731540 931020 1091600 998020 1004600 1231100 FALSE TRUE 704006.5432 871974.0681 959045.7102 897647.3379 912494.5235 1133594.558 901232.174 789774.1078 1085560.76 0.648518783 0.803247593 0.8834565 0.82689737 0.840574343 1.044247913 0.83019966 0.727526396 1 20.05000905 4.705694971 2.341690409 0.865703227 0.604863715 0.391757808 0.09002424 0.612804311 4.266223626 0.023980987 0.316723389 50780.26591 -4.705694971 -0.260839511 LTVAS(ph)PK ddPTM_MDA-MB-175_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 136.57 0.0031129 1764510000 4999080 4127920 3199590 3555840 4364410 3724280 4953600 5719900 5505500 TRUE FALSE 4338438.912 4100803.422 4746922.426 4363247.82 4277566.78 3867555.462 4473200.634 4496743.897 4854646.062 0.893667398 0.844717281 0.977810198 0.898777741 0.881128454 0.796670944 0.921426728 0.926276363 1 22.21093469 1.343844395 1.797224724 1.022558216 0.88587543 0.376714568 0.04644837 0.803911369 3.020144645 0.179082795 0.013236461 22.07213759 -1.343844395 -0.136682786 LTVEDLEKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LTVEDLEKER 10 1 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ;;; 143.97 3.01E-05 2072650000 4607520 3907270 1744310 1817230 3499580 2947170 4581500 5027610 403389 FALSE TRUE 3998624.558 3881602.886 2587864.15 2229859.846 3429945.205 3060549.537 4137186.835 3952494.726 355700.812 11.24153902 10.91254997 7.275395679 6.268919753 9.642781488 8.604280435 11.63108628 11.11185185 1 18.44030474 4.300589578 8.455457285 8.442442401 11.10787096 0.144534829 2.986724434 0.625672267 76.27704391 0.746366636 1.979951072 19979.7283 -4.300589578 2.665428562 LTVEDPVTVEYITR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTVEDPVTVEYITR 14 0 O14818;H0Y586;O14818-2;O14818-4;Q8TAA3-2;Q8TAA3-5;Q8TAA3;A0A087WYS6 O14818 PSMA7;PSMA8 Proteasome subunit alpha type-7;Proteasome subunit alpha type-7-like 0 ; 161.93 1.05E-05 152617000 203504 165636 123143 147572 185581 196266 191100 189252 205350 FALSE TRUE 176610.4308 164547.9262 182695.3667 181080.4781 181888.3012 203816.48 172567.1514 148781.9326 181073.7569 0.975350784 0.908734258 1.008955521 1.000037118 1.004498411 1.125599222 0.953021323 0.821664802 1 17.46621795 1.997344446 24.99489571 0.894868827 1.002932158 0.242126514 0.067609741 116.3202229 1094846.322 0.028178783 0.018614501 99.39040171 -1.997344446 0.10806333 LTVENS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTVENSPK 8 0 O43583;F8VVL1 O43583 DENR Density-regulated protein 1 LTVENS(1)PK;LTVENS(1)PK 126.66 0.0012689 966270000 1831560 1711100 1452710 1774320 1994050 1556180 1921010 2439520 3785660 TRUE FALSE 1589514.705 1699859.671 2155245.415 2177206.475 1954372.306 1616047.252 1734710.746 1917847.632 3338123.587 0.476170119 0.509226105 0.645645782 0.652224646 0.585470326 0.48411846 0.519666423 0.574528648 1 21.67060594 1.238786832 5.916389808 1.017120345 0.55679828 0.840824782 0.060780681 0.055909823 7.199084629 0.104204041 0.016358695 17.32953192 -1.238786832 -0.460322065 LTVENS(ph)PKQEAGISEGQGTAGEEEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTVENSPKQEAGISEGQGTAGEEEEK 26 1 O43583;F8VVL1 O43583 DENR Density-regulated protein 1 LTVENS(1)PKQEAGISEGQGTAGEEEEK;LTVENS(1)PKQEAGISEGQGTAGEEEEK 295.3 1.39E-70 298210000 328860 311700 281140 210822 281590 183212 399730 489060 112303 TRUE FALSE 285400.3178 309652.4222 417100.2444 258692.3573 275986.9099 190260.2842 360964.2461 384478.3249 99026.66728 2.882055164 3.126959946 4.21199921 2.612350435 2.786995842 1.921303518 3.645121623 3.882573608 1 16.59552947 LTVIDTPGFGDHINNENCWQPIMK ddPTM_MDA-MB-175_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 ; 352.9 5.44E-102 1283320000 1417860 1417470 655750 1228600 1352120 1271800 1555750 1806790 1711440 FALSE TRUE 1230486.209 1408158.546 972872.8934 1507572.408 1325215.457 1320726.969 1404873.604 1420422.019 1509115.513 0.815369134 0.933101896 0.644664298 0.998977477 0.878140504 0.875166253 0.930925163 0.941228161 1 20.52527181 -1.999997316 0.21177331 1.821361838 0.795186749 0.269393268 0.088392132 130.6059454 1.988932504 43.79464454 0.45129454 0.010000062 1.999997316 -1.026175089 LTVNADVGYYSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LTVNADVGYYSWR 13 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;H0YH17 Q9Y365 STARD10 PCTP-like protein 0 ;; 150.49 0.00010299 1188959000 326759 277156 167269 192210 301775 324309 245341 259062 282765 FALSE TRUE 283576.9702 275335.344 248160.8479 235854.2182 295770.2679 336785.3771 221547.8676 203663.6073 249336.8438 1.137324777 1.104270591 0.995283505 0.94592606 1.186227689 1.350724473 0.888548456 0.816821149 1 17.92773656 2.062557091 24.99984 0.882530958 1.109594521 0.432234572 0.116802177 59.17625323 23648.21822 0.050268992 0.033891343 115.49338 -2.062557091 0.227063563 LTWFVNEGLVDGWDDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTWFVNEGLVDGWDDPR 17 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 139.3 1.85E-06 263690000 218064 191940 173838 206823 186769 210438 202885 200753 454310 FALSE TRUE 189246.2899 190679.1335 257906.6383 253785.3232 183052.6623 218533.686 183209.2439 157823.5332 400601.9894 0.472404768 0.475981494 0.643797697 0.633509893 0.456943967 0.545513232 0.457334833 0.393965925 1 18.61181006 1.230315348 24.99967203 1.000000907 0.508470398 0.792010286 0.078921869 153.5402532 465497.1647 0.234492698 0.02125478 16.99477223 -1.230315348 -0.491530508 LTWFVNEGLVDGWDDPRFPTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTWFVNEGLVDGWDDPRFPTVR 22 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 180.63 4.79E-17 281380000 54096 53430 24595 22546 41974 57447 34234 47569 11217 FALSE TRUE 46947.07654 53079.01481 36489.22427 27665.41389 41138.79952 59657.02326 30913.99195 37396.73953 9890.939038 4.746473146 5.366428264 3.689156725 2.797046245 4.159241035 6.031482252 3.125486046 3.780908909 1 13.27189178 4.227306563 21.58872936 3.602792535 5.056450184 0.205877892 1.251270605 61.29026538 117579.1964 0.321500295 0.682805228 16877.43964 -4.227306563 1.453657649 LTWHAYPEDAENKEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTWHAYPEDAENKEK 15 1 P45973 P45973 CBX5 Chromobox protein homolog 5 0 136.81 1.23E-05 89425000 578350 383920 300570 353780 339680 248720 505630 599440 284850 FALSE TRUE 501919.5821 381398.0042 445926.6573 434111.1562 332921.0326 258288.4193 456594.0804 471254.4208 251175.3575 1.998283538 1.518453116 1.775359899 1.728319054 1.325452608 1.028319107 1.817829922 1.876196875 1 17.9383354 7.999999902 0.705565448 1.511024022 59.3535706 0.202318902 0.310275384 621.2436937 3.239918562 0.128376453 56730.0918 99999977.38 -7.999999902 57.84254658 LTWHS(ph)CPEDEAQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LTWHSCPEDEAQ 12 0 Q13185 Q13185 CBX3 Chromobox protein homolog 3 1 LTWHS(1)CPEDEAQ;LTWHS(1)CPEDEAQ 175.21 2.97E-05 2230590000 2026410 2028930 1002810 1276990 1698740 1784400 1692690 2066230 1768890 TRUE FALSE 1758614.784 2015601.825 1487772.27 1566950.097 1664938.398 1853047.023 1528533.184 1624382.794 1559773.839 1.127480626 1.292239794 0.953838456 1.004600832 1.067422953 1.188022889 0.979971035 1.041422002 1 20.57290543 4.238742277 25 1.037121168 1.209860213 0.491423992 0.074474888 3.804993237 523265.4284 0.01857259 0.043285304 17327.75414 -4.238742277 0.172739044 LTWHSCPEDEAQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LTWHSCPEDEAQ 12 0 Q13185 Q13185 CBX3 Chromobox protein homolog 3 0 ;;;;; 213.03 3.10E-08 3352030000 4716970 4348750 2356650 2765400 4019190 4234200 3802250 4350130 2909030 FALSE TRUE 4093610.463 4320182.775 3496333.823 3393326.336 3939215.982 4397092.414 3433508.38 3419888.552 2565127.787 1.595869993 1.684197877 1.363025203 1.322868339 1.535680211 1.714180648 1.338533073 1.333223463 1 21.29059927 1.163670866 1.268155127 0.696017762 1.520181806 0.610553437 0.1319923 1.256117417 1.522440204 1.437931666 0.042461946 14.57709103 -1.163670866 0.824164044 LTYHQLLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LTYHQLLER 9 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 101.38 0.0040217 147780000 132820 173630 80337 107460 159340 161800 135800 160390 116280 FALSE TRUE 115267.5005 172489.4131 119188.2419 131860.4354 156169.4457 168024.5507 122630.1369 126091.8467 102533.5109 1.124193442 1.682273548 1.162432076 1.286022826 1.523106391 1.638728151 1.196000565 1.229762305 1 16.64573597 1.551822977 1.668733229 0.993443615 1.39822552 0.29251092 0.191018615 0.639764027 2.872966052 0.373933256 0.053959206 35.63058695 -1.551822977 0.404781905 LVAIVDVIDQNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVAIVDVIDQNR 12 0 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ; 141.95 0.00014181 363860000 318200 331340 239614 234890 321790 264300 377980 394630 341300 FALSE TRUE 276149.0638 329163.4057 355492.1319 288225.3646 315387.0086 274467.792 341323.5578 310241.4455 300951.9028 0.917585372 1.093740902 1.181225733 0.957712385 1.047964826 0.911998859 1.134146535 1.0308672 1 18.19917341 4.753335361 23.45446008 1.045320589 0.917585156 0.202884537 0.079179484 1880.09916 2984477.967 0.018832055 0.382843962 56667.67062 -4.753335361 -0.127735434 LVALHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVALHK 6 0 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 ; 118.11 0.022145 1065550000 1509510 1510420 1004870 1201700 1360630 1335100 1559710 1819220 1800820 FALSE TRUE 1310024.429 1500497.952 1490828.493 1474564.352 1333556.125 1386462.161 1408449.564 1430193.96 1587929.111 0.824989239 0.944940137 0.938850785 0.928608426 0.839808349 0.87312598 0.88697257 0.900666126 1 20.59871508 1.237291836 4.829465331 1.007598 0.893793914 0.425347194 0.039413652 0.190968518 10.6131616 0.073825625 0.010008146 17.26998005 -1.237291836 -0.113804085 LVALLNTLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVALLNTLDR 10 0 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;A6PVN9;Q5T948;Q5T949;A6PVN6;A6PVN8;C9IZ76;A6PVN7 Q15257 PPP2R4 Serine/threonine-protein phosphatase 2A activator 0 96.143 0.016149 80190000 309050 292050 111090 149870 275610 252990 260650 286180 154380 FALSE TRUE 268208.2595 290131.5043 164813.4956 183900.2741 270125.9002 262722.689 235372.2031 224982.6341 136129.3723 1.970245326 2.131292457 1.210712228 1.35092281 1.984332225 1.929948582 1.729033192 1.652711904 1 17.05461886 1.205485637 2.960373704 0.813462769 1.749101283 0.406356887 0.285321132 0.518909522 5.260476707 1.221771049 0.078159337 16.05039174 -1.205485637 0.935638515 LVASMEEARR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVASMEEARR 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 187.97 1.88E-06 168780000 129458 133806 63039 69415 125351 143076 117940 127844 48220 FALSE TRUE 112349.7973 132927.0196 93524.87125 85176.73669 122856.7603 148580.2263 106502.197 100505.5555 42519.48653 2.642313124 3.126261167 2.199576685 2.003240012 2.889422483 3.494403118 2.504785585 2.363752803 1 15.37583655 4.2360963 24.9887309 2.407827428 2.884287153 0.101205537 0.643779182 161.1756389 1634432.907 0.169173273 0.380608805 17222.50421 -4.2360963 0.476459726 LVDEPGHCADFHPSGTVVAIGTHSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVDEPGHCADFHPSGTVVAIGTHSGR 26 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 ; 216.87 1.34E-34 692380000 295700 333208 121458 217445 372690 382520 341280 369100 416080 FALSE TRUE 256622.4958 331019.1347 180195.4951 266819.2107 365274.1982 397235.7919 308182.7181 290170.8373 366891.4964 0.69945065 0.902226238 0.491141105 0.727242831 0.99559189 1.082706456 0.839983268 0.790890059 1 18.48499394 3.306461676 7.091245377 0.922083736 0.701736858 0.456788542 0.127435858 0.234601815 20.14578292 0.038613355 0.049754488 2025.17089 -3.306461676 -0.220346878 LVDLDWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LVDLDWR 7 0 Q9P000;Q9P000-2 Q9P000 COMMD9 COMM domain-containing protein 9 0 ;; 105.12 0.018609 357555000 1159010 1218470 773850 900410 1185480 1281170 1152150 1360100 1216060 FALSE TRUE 1005843.892 1210465.79 1148086.448 1104861.852 1161891.267 1330457.439 1040414.67 1069253.199 1072298.772 0.93802578 1.128851232 1.070677761 1.030367544 1.083551802 1.240752553 0.970265655 0.997159772 1 20.03227551 LVDMMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 101.28 0.021339 192822000 294048 278500 185452 215339 284916 318412 254209 311718 264438 FALSE TRUE 255188.8118 276670.5152 275137.2075 264235.0112 279246.729 330661.5157 229555.8503 245059.5315 233176.4409 1.094402208 1.186528597 1.179952857 1.13319772 1.197576942 1.418074289 0.984472743 1.050961798 1 17.83106251 LVDPLGEMLAPSWEEHATCLANAEEQDMQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVDPLGEMLAPSWEEHATCLANAEEQDMQR 30 0 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A494C099;A0A494C163;D6RCQ8;D6RF77 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 207.01 1.16E-25 119080000 65284 58085 32687 44006 58275 60108 49580 67001 68276 FALSE TRUE 56656.55399 57703.43581 48494.54253 53998.23489 57115.44151 62420.39366 44771.73923 52673.35755 60204.48906 0.941068596 0.958457363 0.80549712 0.896913764 0.948690744 1.036806302 0.743661144 0.874907476 1 15.87758344 LVDQNIFSFYLSR ddPTM_MDA-MB-175_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 ; 199.82 2.67E-07 5512800000 1111300 1224570 917280 1049730 1175200 1334540 1111640 1184550 1321130 FALSE TRUE 964438.8893 1216525.719 1360879.676 1288087.241 1151815.819 1385880.617 1003833.324 931243.2007 1164947.516 0.827881836 1.04427513 1.168189688 1.105704096 0.988727649 1.189650691 0.861698325 0.799386399 1 20.15183353 2.210978266 24.88739529 0.867713945 1.058190174 0.327862663 0.11150705 207.5796395 187296.2777 0.044968141 0.030325279 162.5467408 -2.210978266 0.190476229 LVDQNIFSFYLSRDPDAQPGGELMLGGTDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVDQNIFSFYLSRDPDAQPGGELMLGGTDSK 31 1 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;A0A1B0GU92;A0A1B0GU03;C9JH19;H7C469;F8WD96 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 219.85 6.03E-35 227080000 474070 431040 133000 131930 358890 375080 498680 596850 40304 FALSE TRUE 411420.4484 428208.4699 197319.2449 161886.7229 351748.7912 389509.5703 450318.0904 469218.2722 35539.30703 11.57649045 12.04886942 5.552141033 4.555145737 9.897457787 10.95996526 12.6709868 13.20279745 1 15.11712793 LVDTGDKFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVDTGDKFR 9 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 108.43 0.0023825 414740000 743690 635560 441810 597860 702330 605440 737440 821410 594700 FALSE TRUE 645409.4822 631384.9645 655470.7938 733613.2507 688355.0071 628731.6686 665923.1823 645757.8637 524395.2435 1.230769139 1.204024965 1.249955643 1.39897007 1.312664475 1.198965239 1.269887915 1.231433488 1 19.00029507 1.205948207 2.944972915 0.933030089 1.267385015 0.675373672 0.057553909 0.298806693 2.986858311 0.250403039 0.015995935 16.06749626 -1.205948207 0.334354926 LVEAEVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LVEAEVHR 8 0 F8VZX1;H0YIC9;F8VYY9;P54619-2;P54619;P54619-3;H0YHF8 F8VZX1 PRKAG1 5-AMP-activated protein kinase subunit gamma-1 0 ;;; 184.49 0.00021773 366591000 668947 661696 432753 493487 679204 689080 615946 716277 702297 FALSE TRUE 580543.9591 657349.2754 642033.7983 605540.7658 665689.1692 715589.3535 556211.6517 563106.7376 619272.2487 0.93746161 1.061486732 1.03675532 0.97782642 1.074953981 1.155532732 0.898169832 0.909304008 1 19.24021427 2.203832496 24.99999192 0.928730476 1.040139826 0.378745396 0.063079504 178.1749715 128262.8964 0.025701971 0.017329083 159.8941209 -2.203832496 0.11140935 LVEALCAEHQINLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVEALCAEHQINLIK 15 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 ; 147.35 3.72E-06 2551900000 2503300 2295330 1546190 1932930 2137180 1921450 2386900 2815100 2686900 FALSE TRUE 2172482.562 2280251.826 2293932.656 2371831.299 2094654.299 1995369.425 2155418.805 2213112.772 2369257.743 0.916946486 0.962432995 0.968207306 1.001086229 0.884097269 0.842191792 0.909744333 0.934095406 1 21.17600372 3.231557659 24.9999896 0.912621663 0.962618526 0.227271253 0.044064798 259.6214984 926825.7986 0.01413064 0.016368284 1704.345582 -3.231557659 0.049996864 LVEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVEALR 6 0 O75688;O75688-3 O75688 PPM1B Protein phosphatase 1B 0 126.68 0.040453 516850000 344570 334860 241910 244490 332540 332090 321930 341040 344000 FALSE TRUE 299034.2015 332660.2826 358898.4851 300005.1913 325923.1046 344865.7172 290709.2782 268111.25 303332.7119 0.985829058 1.096684497 1.183184243 0.989030129 1.074473975 1.136922276 0.958384199 0.883885053 1 18.21054156 2.120512334 6.02697092 0.930360566 1.078758181 0.466937208 0.065378739 0.160295919 7.823851123 0.026535169 0.017741179 131.9812794 -2.120512334 0.148397615 LVEDEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVEDEER 7 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 167.24 0.0025446 753700000 1028010 1066340 747920 804790 979110 1095970 1033320 1137950 1592430 FALSE TRUE 892155.8739 1059335.142 1109616.614 987529.8699 959627.6266 1138132.675 933108.7854 894608.248 1404174.74 0.635359581 0.754418316 0.790226873 0.703281324 0.683410404 0.810534931 0.664524691 0.637106069 1 20.42129105 1.229581387 24.99942276 1.000000556 0.710340767 0.698989766 0.059836082 210.5980279 586289.9308 0.17974225 0.015113467 16.96607519 -1.229581387 -0.289659789 LVEDEERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LVEDEERR 8 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 144.12 0.00094678 1553140000 1108640 1070210 686935 731859 1054500 1053130 1023320 1043020 703930 FALSE TRUE 962130.4151 1063179.72 1019139.064 898038.7717 1033517.513 1093644.593 924078.5839 819978.2898 620712.1973 1.550042708 1.712838453 1.641886639 1.446787699 1.665051078 1.761918965 1.488739206 1.321028157 1 19.24356497 1.429239803 1.582322668 0.891463035 1.626327586 0.833378292 0.09106184 0.277544737 0.897472736 0.2960192 0.027042944 26.86827616 -1.429239803 0.734864551 LVEDKPGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LVEDKPGSR 9 1 Q08170;A0A0D9SEM4 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 0 ;; 120.09 0.00065789 599890000 1311230 1031830 661120 794090 957260 882150 1092330 1207490 1106860 FALSE TRUE 1137947.633 1025051.841 980839.8433 974400.2714 938212.3988 916086.8813 986396.0047 949277.6602 976008.2717 1.165920071 1.050249133 1.004950339 0.998352473 0.961275049 0.938605653 1.010643079 0.97261231 1 19.89653385 4.998874958 1.108557152 0.978044124 1.353721405 0.893565614 0.020357625 0.818135179 0.572032308 0.006201778 0.410605558 99741.28475 -4.998874958 0.375677281 LVEGILHAPDAGWGNLVYVVNYPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVEGILHAPDAGWGNLVYVVNYPK 24 0 Q13148;A0A087WYY0;A0A087X260;G3V162;B1AKP7;K7EN94;A0A0A0N0M3;K7EJM5;A0A087WX29;A0A1W2PNU8;K7EJ99;A0A0A0MSV7 Q13148 TARDBP;TDP43 TAR DNA-binding protein 43 0 ; 249.28 3.17E-38 627000000 749970 663140 402190 488400 579190 490890 668310 806050 657630 FALSE TRUE 650859.5643 658783.7897 596690.4292 599298.6847 567665.2522 509774.8559 603497.3991 633682.4802 579885.7306 1.122392792 1.136057942 1.028979328 1.033477206 0.978926058 0.879095361 1.040717795 1.092771294 1 19.14540911 4.181631291 4.103726385 1.01084914 1.130769736 0.462830498 0.054592338 0.212465069 7.183169864 0.016077235 0.038416705 15192.57156 -4.181631291 0.119920596 LVEHFCAEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVEHFCAEFK 10 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 121.9 0.00050283 616680000 1409900 1272200 942300 1191100 1215900 1195400 1650500 1820200 1684000 FALSE TRUE 1223578.143 1263842.834 1397999.432 1461557.46 1191705.969 1241387.812 1490434.764 1430964.395 1484919.438 0.824003048 0.851118789 0.941464833 0.984267174 0.80253914 0.835996741 1.003714225 0.963664666 1 20.50195323 2.231371973 24.99692713 0.984429639 0.877161776 0.493395862 0.055195777 158.94747 552698.8987 0.023683773 0.016344599 170.361703 -2.231371973 -0.107267863 LVEHGLNETIHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVEHGLNETIHIR 13 0 Q7Z3B4-2;Q7Z3B4-3;Q7Z3B4 Q7Z3B4-2 NUP54 Nucleoporin p54 0 ; 192.4 1.59E-06 177857000 152078 141216 99928 172526 132716 138003 125713 147894 204628 FALSE TRUE 131980.507 140288.3428 148253.515 211700.6652 130075.2113 143312.0647 113521.3726 116268.019 180437.111 0.731448793 0.777491626 0.821635385 1.173265655 0.720889459 0.794249387 0.629146477 0.644368658 1 17.46113657 LVEIVHPSQEEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 ;;;;;; 222.29 1.77E-11 2593400000 3302530 3567550 1751050 2949410 3898170 3983170 3218800 3838500 5112480 FALSE TRUE 2866092.293 3544114.529 2597863.637 3619118.619 3820604.044 4136405.127 2906641.271 3017666.646 4508088.439 0.635766652 0.786167924 0.57626723 0.802805595 0.847499799 0.917551903 0.644761369 0.669389407 1 22.10408439 3.699246586 24.3942568 0.793820509 0.678077278 0.250007096 0.116582082 697.8274453 432999.8394 0.033209897 0.049259276 5003.185278 -3.699246586 -0.115743231 LVEKPSPLTLAPHDFANIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVEKPSPLTLAPHDFANIK 19 1 P53618 P53618 COPB1 Coatomer subunit beta 0 ; 222.79 1.41E-19 1103220000 2049720 1616320 1219990 1401180 1596770 1352620 2012960 2422900 2148060 FALSE TRUE 1778844.309 1605702.287 1809981.245 1719339.335 1564997.401 1404656.167 1817743.449 1904781.69 1894118.794 0.939140837 0.847730508 0.955579582 0.907725186 0.826240364 0.74158821 0.959677637 1.005629476 1 20.85309538 2.015124666 24.96657662 0.997047888 0.870523131 0.474694499 0.060105483 197.1843815 325494.7109 0.025615418 0.01726306 103.5439351 -2.015124666 -0.126524757 LVELLMHNDYK ddPTM_MDA-MB-175_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 ; 193.73 8.23E-07 1345510000 2596500 2260000 1640890 1928540 2047080 1926470 2470400 2954000 3126200 FALSE TRUE 2253365.946 2245153.911 2434429.892 2366444.483 2006347.113 2000582.547 2230820.988 2322310.088 2756624.197 0.817436758 0.814457739 0.883119975 0.858457415 0.727827578 0.72573641 0.809258291 0.84244711 1 21.39447117 1.207600183 2.514914636 1.058625829 0.805064327 0.607485283 0.048895306 0.455184494 2.945379848 0.259984025 0.014303297 16.1287304 -1.207600183 -0.253561502 LVEPHS(ph)PSPSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LVEPHSPSPSSK 12 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 LVEPHS(0.974)PS(0.025)PS(0.001)SK;LVEPHS(0.989)PS(0.011)PSSK;LVEPHS(0.996)PS(0.004)PSSK;LVEPHS(0.987)PS(0.013)PSSK 167.61 3.14E-05 2302220000 5635000 4615600 2770140 3773940 4637500 3943770 5010300 5675300 5343900 TRUE FALSE 4890320.473 4585279.82 4109788.97 4630870.758 4545222.823 4095489.384 4524401.877 4461681.26 4712150.23 1.037810815 0.973075899 0.872168494 0.982751086 0.964575109 0.869133874 0.960156544 0.946846141 1 22.1679541 4.636541214 3.895273257 0.942274739 1.038717073 0.332630165 0.042521697 0.253380552 6.16107231 0.010128416 0.054123151 43305.31623 -4.636541214 0.096442334 LVEQANS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LVEQANSPK 9 0 O95391 O95391 SLU7 Pre-mRNA-splicing factor SLU7 1 LVEQANS(1)PK;LVEQANS(1)PK;LVEQANS(1)PK 139.76 0.00011614 1569240000 5256500 3746180 2858760 3207650 3960860 3229950 4433760 5190600 4872550 TRUE FALSE 4561840.207 3721571.097 4241265.898 3935995.958 3882046.635 3354208.267 4003774.638 4080630.583 4296522.69 1.061751685 0.866182112 0.987139183 0.916088717 0.903532209 0.780679752 0.931863958 0.949751899 1 22.03473808 4.75193304 24.28036418 0.917666533 1.061751827 0.351130416 0.061873152 1844.891314 3349689.23 0.01539933 0.281562049 56484.98788 -4.75193304 0.144085294 LVEQLKEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LVEQLKEER 9 1 O95232;J3KPP4 O95232 LUC7L3 Luc7-like protein 3 0 ;;; 157.38 7.42E-05 788080000 2879900 2209580 1359690 1688140 2057180 1772820 2379570 2740390 1699810 FALSE TRUE 2499313.918 2195065.123 2017240.632 2071457.989 2016246.143 1841021.533 2148799.668 2154378.924 1498860.398 1.667476118 1.464489372 1.345849576 1.382021962 1.345186079 1.228280856 1.433622284 1.437344616 1 20.51543459 7.9999999 0.692919668 1.313225248 44.42568903 0.473922689 0.124284596 268.876526 1.477145656 0.049242408 17932.40449 99999976.97 -7.9999999 43.11246378 LVES(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVESPK 6 0 Q96S94;Q96S94-3 Q96S94 CCNL2 Cyclin-L2 1 LVES(1)PK 76.478 0.07862 138440000 849700 674300 586850 632110 708770 658870 779690 913730 1343200 TRUE FALSE 737409.9921 669870.4789 870652.6229 775640.2367 694666.8637 684217.1552 704075.7838 718335.9502 1184408.426 0.622597725 0.565573888 0.735094925 0.654875649 0.586509559 0.577686835 0.594453542 0.606493448 1 20.17573523 1.237586743 24.99900884 1.000000451 0.617219292 0.859867746 0.048474593 8.839124012 226777.9342 0.072408208 0.012250967 17.28171119 -1.237586743 -0.382781159 LVEVDSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVEVDSGR 8 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ; 150.88 0.0013652 206480000 518740 486410 312080 396870 482680 535170 421660 525730 501290 FALSE TRUE 450187.1947 483214.7407 463002.9318 486985.3993 473075.6123 555758.3362 380767.4781 413306.7307 442028.0673 1.018458392 1.093176602 1.047451432 1.101706962 1.070238854 1.257291963 0.861410183 0.935023727 1 18.75377845 2.215867291 24.9999999 0.92979717 1.094434002 0.551045554 0.070533596 170.7789761 188136.4868 0.027943935 0.018854532 164.3869324 -2.215867291 0.164636833 LVEYDIDEVVYDEDSPYQNIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVEYDIDEVVYDEDSPYQNIK 21 0 P52788;H7C2R7;P52788-2 P52788 SMS Spermine synthase 0 133.93 2.65E-08 0 24875 15870 10541 14093 16509 13423 18282 21031 19193 FALSE TRUE 21587.70572 15765.74893 15638.66286 17293.03105 16180.5032 13939.3915 16509.01445 16533.68431 16924.0254 1.275565665 0.931560226 0.924051015 1.021803657 0.956067059 0.823645153 0.975478 0.976935683 1 14.04678514 4.740745 24.97785941 0.951867042 1.275565778 0.782217873 0.053788082 92.49071229 1057536.627 0.013373486 0.086047948 55048.4379 -4.740745 0.323698736 LVFGFLNGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVFGFLNGR 9 0 P00491;G3V5M2;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 ; 143.02 0.00023948 639980000 217300 236580 160842 187932 205960 205227 192301 233040 255530 FALSE TRUE 188583.2544 235025.8904 238625.7292 230604.833 201861.799 213122.2155 173651.6786 183206.2095 225321.5345 0.836951758 1.043068923 1.059045376 1.023447819 0.895883296 0.945858175 0.770683898 0.813087883 1 17.78162568 2.858752559 1.833349441 0.854250395 0.996443126 0.232572935 0.088646544 0.409132206 2.747280101 0.034780529 0.034116347 722.3581198 -2.858752559 0.14219273 LVFHTQLAHGSPTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVFHTQLAHGSPTGR 15 0 O14908 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 ; 161.82 9.43E-07 1343480000 444840 449580 222296 306830 533040 570690 482590 565600 570900 FALSE TRUE 386053.2669 446626.6794 329799.0891 376500.4411 522433.5469 592644.8136 435788.4961 444650.8415 503408.8524 0.766878185 0.887204659 0.655131684 0.747901908 1.037791736 1.177263393 0.865675075 0.883279743 1 18.94137106 3.245421912 25 0.978800265 0.765263218 0.554249173 0.101401971 142.499402 519211.6957 0.03205914 0.040459213 1759.632247 -3.245421912 -0.213537047 LVFLGLDNAGK ddPTM_MDA-MB-175_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 0 173.32 2.86E-05 135640000 255360 247280 148830 192390 234540 195950 280580 356290 314420 FALSE TRUE 221613.529 245655.6014 220804.6858 236075.09 229873.1129 203488.3233 253369.3948 280100.1562 277249.6258 0.799328505 0.886044844 0.796411123 0.851489301 0.829119651 0.733953464 0.9138674 1.010281458 1 18.08082599 1.987838097 4.489638189 0.997224993 0.820135788 0.794169529 0.039920574 0.082223268 4.146873643 0.019311059 0.01079067 97.23846557 -1.987838097 -0.177089205 LVFVHSAEGNEFWSALLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LVFVHSAEGNEFWSALLEK 19 0 P07384;E9PRM1;E9PL37 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;; 221.91 2.56E-19 566545000 525045 304070 209202 244117 231117 226983 294734 407676 285215 FALSE TRUE 455658.973 302072.5441 310372.7869 299547.4959 226518.2239 235715.1829 266150.742 320497.6599 251497.2076 1.811785416 1.20109701 1.23410033 1.191056946 0.900678882 0.937247714 1.058265197 1.274358721 1 17.94018286 7.483411277 0.979214073 1.075358317 199.9845054 0.792035903 0.117324399 233.4889717 1.106355868 0.040412139 103143.2278 30437661.08 -7.483411277 198.9091471 LVGATATS(ph)SPPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVGATATSSPPPK 13 0 H9KVD1;Q96QD9-4;Q96QD9 H9KVD1 FYTTD1 UAP56-interacting factor 1 LVGAT(0.002)AT(0.083)S(0.583)S(0.332)PPPK 92.856 0.0061688 118470000 473050 384490 274430 332440 368890 305390 449520 473930 477740 TRUE FALSE 410535.2439 381964.2599 407145.2659 407925.583 361549.8107 317138.5509 405925.6196 372583.7576 421262.1214 0.974536335 0.906713992 0.966489141 0.968341473 0.858253786 0.752829497 0.963593922 0.884446378 1 18.68435867 4.740255508 22.04545806 0.909513286 0.974536442 0.068129892 0.071206349 87.26651325 1134488.453 0.017523326 0.107493447 54986.42798 -4.740255508 0.065023156 LVGATATSS(ph)PPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LVGATATSSPPPK 13 0 H9KVD1;Q96QD9-4;Q96QD9 H9KVD1 FYTTD1 UAP56-interacting factor 1 LVGATAT(0.049)S(0.02)S(0.931)PPPK;LVGATAT(0.027)S(0.064)S(0.909)PPPK;LVGATAT(0.001)S(0.003)S(0.996)PPPK;LVGATAT(0.009)S(0.004)S(0.987)PPPK;LVGAT(0.004)AT(0.204)S(0.154)S(0.638)PPPK 193.45 1.95E-06 1049611000 3845620 3040590 2260410 2510580 2954760 2552630 3632210 3801520 3737710 TRUE FALSE 3337411.573 3020616.164 3353551.837 3080645.561 2895966.057 2650831.328 3279958.833 2988594.531 3295842.182 1.012612677 0.916492962 1.017509836 0.934706637 0.878672551 0.804295589 0.995180792 0.906777196 1 21.65221573 3.491020814 23.05003898 0.915098512 0.975713009 0.188398215 0.061382581 409.3526887 678839.5772 0.016954774 0.02399344 3097.567751 -3.491020814 0.060614496 LVGGPMDASVEEEGVRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVGGPMDASVEEEGVRR 17 1 P01034 P01034 CST3 Cystatin-C 0 123.73 8.44E-05 816700000 330230 338660 212970 235490 337200 353990 283320 333290 235160 FALSE TRUE 286589.2688 336435.3202 315963.0043 288961.6037 330490.3797 367608.2244 255843.67 262018.5272 207359.6527 1.382087909 1.622472433 1.523743892 1.393528587 1.593802726 1.772804977 1.233816062 1.263594551 1 17.66177568 1.78406489 1.822695041 1.063738989 1.540088958 0.62312973 0.13636851 0.233648143 1.453351379 0.142970219 0.03923605 60.82258724 -1.78406489 0.476349969 LVGIISS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 LVGIISSR 8 0 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 1 LVGIIS(0.09)S(0.91)R;LVGIIS(0.002)S(0.998)R;LVGIIS(0.004)S(0.996)R;LVGIIS(0.005)S(0.995)R;LVGIIS(0.003)S(0.997)R;LVGIIS(0.006)S(0.994)R;LVGIIS(0.003)S(0.997)R 132.57 0.0010036 1585777000 4124480 4118860 2855634 3204190 3988830 4212770 3612280 3963760 4676690 TRUE FALSE 3579419.518 4091802.937 4236628.154 3931750.312 3909460.087 4374837.988 3261961.642 3116140.77 4123817.036 0.867986986 0.99223678 1.027355995 0.953425013 0.948019772 1.060871021 0.791005424 0.755644769 1 21.97554889 2.226714496 24.99993986 0.827047076 0.975942016 0.338381729 0.081221815 207.0503352 436953.3345 0.03225546 0.021943007 168.5444655 -2.226714496 0.14889494 LVGILDILDEENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVGILDILDEENR 13 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 125.74 0.0002386 0 7199.1 5048.2 7719.6 5468.4 7145 6954.1 8205.7 6466 11966 FALSE TRUE 6247.720695 5015.038042 11452.82438 6710.083799 7002.828479 7221.628727 7409.912477 5083.296218 10551.39311 0.592122825 0.475296294 1.085432441 0.635942925 0.663687572 0.684424194 0.702268639 0.481765409 1 13.36514587 LVGLNLS(ph)PPMSPVQLPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVGLNLSPPMSPVQLPLR 18 0 Q8N0Z3 Q8N0Z3 SPICE1 Spindle and centriole-associated protein 1 1 LVGLNLS(0.998)PPMS(0.002)PVQLPLR;LVGLNLS(0.991)PPMS(0.009)PVQLPLR 201.61 1.45E-15 681480000 665210 723580 368730 467890 726920 722020 591830 726270 521050 TRUE FALSE 577300.8131 718826.7553 547049.0613 574131.5758 712455.7142 749796.5766 534434.4177 570962.8123 459452.0626 1.256498469 1.564530479 1.190655361 1.249600606 1.550663872 1.631936469 1.163199518 1.242703774 1 18.80955482 1.556192828 1.576204294 0.995616199 1.395370043 0.36761636 0.160995493 0.627755295 2.435600781 0.348763171 0.048304986 35.99091004 -1.556192828 0.399753844 LVGSQEELASWGHEYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVGSQEELASWGHEYVR 17 0 Q13200;Q13200-3;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 272.4 1.24E-35 1153860000 486010 469580 211799 406800 438710 485310 395850 521750 520350 FALSE TRUE 421782.5471 466495.2981 314225.7048 499170.1575 429980.5293 503980.1897 357460.5279 410177.8228 458834.8158 0.919247042 1.016695512 0.684834049 1.087908198 0.937113999 1.098391343 0.779061474 0.893955316 1 18.80761534 LVGYLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LVGYLDR 7 0 P07602;C9JIZ6;P07602-2;P07602-3;Q5BJH1 P07602 PSAP Prosaposin;Saposin-A;Saposin-B-Val;Saposin-B;Saposin-C;Saposin-D 0 ;;;;; 133.47 0.0076042 6265270000 2795790 2946080 1986920 2331130 2849580 3173140 2599150 2897090 3314060 FALSE TRUE 2426319.268 2926727.006 2947801.158 2860448.696 2792878.933 3295212.749 2347084.833 2277569.849 2922275.602 0.830284203 1.001523266 1.008734821 0.97884289 0.95572058 1.127618746 0.803170252 0.779382289 1 21.47866082 2.20583369 24.99988762 0.8414748 0.984227196 0.275683156 0.092167733 208.6977556 159421.455 0.036493712 0.024605934 160.6326003 -2.20583369 0.142752396 LVHDMNHPPSGEYFGQCGGCGEDVVGDGAGVVALDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVHDMNHPPSGEYFGQCGGCGEDVVGDGAGVVALDR 36 0 Q15654;H7BZE2 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 193.58 4.64E-24 106240000 30354 36584 26346 26104 46628 39854 24663 28543 58693 FALSE TRUE 26342.64199 36343.6773 39087.01372 32031.31217 45700.19403 41387.20917 22271.18606 22439.30157 51754.3804 0.508993476 0.70223384 0.755240685 0.618910166 0.883020793 0.799685144 0.430324658 0.433572992 1 15.65939335 2.254409692 24.99775279 0.574232256 0.716529887 0.029395788 0.185804728 525.7094106 829167.5874 0.069285627 0.05348758 179.6427488 -2.254409692 0.142297631 LVHDS(ph)LEDLQMTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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;LVHDS(1)LEDLQMTR 287.78 1.98E-33 768800000 641910 549070 410180 667460 715020 835370 382510 808710 745700 TRUE FALSE 557079.9671 545463.123 608544.42 819016.9945 700792.5009 867507.2245 345414.2391 635773.6599 657544.1955 0.847212964 0.829545948 0.925480636 1.245569499 1.065772469 1.319313942 0.52530954 0.966891145 1 19.32672834 3.999444205 21.86685857 1.00499608 0.848162548 0.11361961 0.208776505 10.61675412 418157.905 0.05549644 0.112795009 9987.210522 -3.999444205 -0.156833532 LVHGDIFRPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVHGDIFRPPR 11 1 Q99805 Q99805 TM9SF2 Transmembrane 9 superfamily member 2 0 180.88 3.89E-06 744250000 206330 180660 136990 144050 169580 223420 138080 185810 312890 FALSE TRUE 179062.9677 179473.2326 203238.8222 176758.7542 166205.6898 232015.112 124689.0229 146075.9775 275900.5006 0.649012841 0.650499844 0.736638106 0.64066123 0.602411701 0.840937626 0.451934747 0.529451658 1 18.07378855 1.228510754 24.98234438 1.000000754 0.632745981 0.540414786 0.104913949 346.6760233 861719.7428 0.355552758 0.026692716 16.92430152 -1.228510754 -0.367254773 LVHLWSSDSHQPLWSR ddPTM_MDA-MB-175_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 ; 226.24 3.55E-15 2934700000 1036690 1167810 441600 694340 1175470 1401440 1144210 1292870 1177590 FALSE TRUE 899688.7899 1160138.579 655159.2371 852000.5093 1152080.447 1455354.304 1033244.69 1016399.812 1038376.652 0.866437808 1.117261812 0.630945655 0.820512006 1.109501494 1.40156686 0.995057707 0.978835387 1 19.98589842 3.235397983 24.99661297 1.089806337 0.860977077 0.337285633 0.16573176 107.2021443 847296.8153 0.052171812 0.06167152 1719.483382 -3.235397983 -0.22882926 LVHSGS(ph)GCRSPSLGSDLTFATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVHSGSGCRSPSLGSDLTFATR 22 1 Q13425 Q13425 SNTB2 Beta-2-syntrophin 1 LVHS(0.217)GS(0.381)GCRS(0.381)PS(0.016)LGS(0.006)DLTFATR 49.141 0.086033 87616000 23061 11613 11537 9659 18529 17389 17864 17339 22595 TRUE FALSE 20013.43042 11536.71344 17116.33179 11852.22358 18160.30915 18057.96608 16131.55203 13631.18978 19923.84484 1.0044964 0.579040518 0.859087788 0.594876324 0.911486176 0.906349464 0.809660593 0.684164622 1 14.28220846 LVHSGSGCRS(ph)PSLGSDLTFATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVHSGSGCRSPSLGSDLTFATR 22 1 Q13425 Q13425 SNTB2 Beta-2-syntrophin 1 LVHSGS(0.338)GCRS(0.661)PSLGSDLTFATR 192.3 6.76E-18 113700000 45230 50590 21978 24531 47876 46612 41550 45340 22444 TRUE FALSE 39252.7409 50257.67096 32606.63431 30101.13848 46923.36127 48405.1938 37520.4874 35644.39384 19790.69589 1.983393668 2.539459514 1.647573915 1.520974232 2.370980866 2.445856077 1.895864987 1.801068241 1 14.27253472 1.130551582 1.754576599 0.373796672 2.068810346 0.507692095 0.327568672 1.124362376 2.554980733 3.539091913 0.094523296 13.50677242 -1.130551582 1.695013674 LVHSYPYDWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LVHSYPYDWR 10 0 Q9NSE4 Q9NSE4 IARS2 "Isoleucine--tRNA ligase, mitochondrial" 0 ;; 159.4 7.69E-06 1875800000 953196 1193010 774573 1252000 1377480 1502990 1038100 1234120 1193370 FALSE TRUE 827228.7335 1185173.039 1149159.094 1536285.736 1350070.843 1560810.998 937425.2218 970213.0419 1052291.158 0.786121528 1.126278625 1.092054309 1.459943594 1.282982217 1.483250131 0.890842059 0.922000565 1 20.00510251 2.197867257 24.99993155 0.932412165 1.211507234 0.289993587 0.197079872 191.7062127 117773.2219 0.083343616 0.056190941 157.7129145 -2.197867257 0.279095069 LVIASTLYEDGTLDDGEYNPTDDRPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LVIASTLYEDGTLDDGEYNPTDDRPSR 27 1 C9JLU1;P52434;P52434-3;P52434-4 C9JLU1 POLR2H "DNA-directed RNA polymerases I, II, and III subunit RPABC3" 0 ;;; 249.85 5.21E-46 570130000 176499 169586.2 110894.1 124153 166124 161823 169012 188059.4 182749 FALSE TRUE 153174.21 168472.1771 164522.8577 152343.8362 162818.4574 168048.4355 152621.2423 147844.3608 161144.6214 0.950538768 1.045471922 1.020964003 0.945385796 1.010387166 1.042842349 0.947107269 0.917463825 1 17.29799651 2.206368227 23.96871741 0.946743765 1.003135394 0.243617969 0.038779386 145.7623344 108525.149 0.015529389 0.010471272 160.8304316 -2.206368227 0.056391629 LVIEEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LVIEEAER 8 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;; 128.61 0.0026201 2136080000 2611210 2497950 1632120 2058190 2540160 2498630 2891680 2823310 2683270 FALSE TRUE 2266131.983 2481540.802 2421418.691 2525533.497 2489615.786 2594753.913 2611245.319 2219567.128 2366056.877 0.957767332 1.0488086 1.023398344 1.067401854 1.052221445 1.096657455 1.10362745 0.93808697 1 21.17405332 1.716565681 10.88732185 0.970235741 1.051438655 0.380501343 0.042857211 0.103446206 32.83321308 0.023572221 0.011027941 52.06737477 -1.716565681 0.081202914 LVIGDHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVIGDHK 7 0 E9PM92;O00193;E9PRZ9 E9PM92 C11orf58;SMAP Small acidic protein 0 ; 158.12 0.0014326 682680000 1306130 1072490 731220 874150 973440 876810 1171410 1394120 1248910 FALSE TRUE 1133521.611 1065444.743 1084840.438 1072639.118 954070.4485 910541.4481 1057806.838 1095998.287 1101265.283 1.029290244 0.967473287 0.985085478 0.974006114 0.866340258 0.826813904 0.960537715 0.995217324 1 20.07073061 3.460327061 24.94784685 0.933760801 0.989342678 0.227501043 0.054728531 448.7770965 666657.8831 0.018027897 0.023279017 2886.204244 -3.460327061 0.055581877 LVIIEGDLER ddPTM_MDA-MB-175_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 ;;;;; 248.96 1.55E-12 1151610000 1390390 1396530 919599 1115360 1259880 1405810 1181850 1454540 2085970 FALSE TRUE 1206646.439 1387356.102 1364320.152 1368619.535 1234810.853 1459892.42 1067234.369 1143497.94 1839369.003 0.656011076 0.754256541 0.741732708 0.744070131 0.671323074 0.793691977 0.580217655 0.621679466 1 20.8107795 1.230241886 24.99786364 1.000000568 0.693652123 0.681735356 0.065402593 200.7182249 603112.122 0.190265364 0.017064947 16.99189775 -1.230241886 -0.306348445 LVIIEGDLERTEER ddPTM_MDA-MB-175_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 0 117.93 0.00025056 52366000 50944 49294 13281 14345 40938 45280 44712 55815 9181.2 FALSE TRUE 44211.62132 48970.18447 19703.73602 17602.2515 40123.41389 47021.9509 40375.83712 43879.3966 8095.808995 5.461050446 6.0488315 2.43381928 2.17424244 4.956072199 5.808184324 4.987251694 5.420013816 1 12.98295954 4.277719943 24.99553565 4.082432402 5.754944585 0.19228647 1.577006516 308.0150364 196602.3683 0.408844111 1.081660871 18954.83217 -4.277719943 1.672512184 LVIIESDLER ddPTM_MDA-MB-175_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 ; 146.79 6.52E-05 105960000 174519 176076 122663 132810 159897 172937 137682 174487 245330 FALSE TRUE 151455.872 174919.3452 181983.2371 162966.5404 156715.3625 179589.9983 124329.6208 137174.3129 216327.3669 0.700123494 0.8085863 0.841240014 0.753332982 0.72443614 0.830176972 0.574729044 0.634105222 1 17.72285666 3.487221542 15.49489097 0.729346196 0.787751294 0 0.118975027 12.06912196 18508.38002 0.033936389 0.046877487 3070.587954 -3.487221542 0.058405098 LVIIESDLERAEER ddPTM_MDA-MB-175_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 ; 127.76 7.09E-05 67403000 90300 88570 25070 24454 72911 81834 80998 83000 4928.2 FALSE TRUE 78366.62621 87988.17784 37193.93585 30006.65446 71460.21375 84982.20693 73142.82643 65251.09591 4345.59381 18.0335829 20.24767654 8.558999639 6.905075754 16.44429205 19.55594808 16.83149176 15.01546135 1 12.08533761 1.238822726 9.318060415 0.915942194 15.13880338 0.513682382 4.341665707 0.071164267 98.58414689 6.450588711 1.144459623 17.33096425 -1.238822726 14.22286119 LVILEGELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 LVILEGELER 10 0 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;;;;;;;;; 267.52 1.69E-17 1340407000 991022 1018733 754386 881002 987234 1049052 897691 1053858 1453619 FALSE TRUE 860055.9318 1012040.876 1119209.593 1081046.969 967589.9749 1089409.709 810633.065 828498.6678 1281773.818 0.670988844 0.789562762 0.873172456 0.843399166 0.754883554 0.849923515 0.632430663 0.646368849 1 20.28971028 2.268638508 24.99935512 0.73071106 0.800309469 0.001913669 0.114416075 559.5072545 465034.8719 0.042494259 0.032911858 185.6258725 -2.268638508 0.06959841 LVILEGELERAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LVILEGELERAEER 14 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;;;;; 216.46 5.58E-12 754031000 1004119 1098024 337935 299772 891398 981739 999568 1049203 17075.36 FALSE TRUE 871422.13 1090811.008 501361.4963 367839.8143 873660.9238 1019507.135 902630.0492 824839.1034 15056.73039 57.87592042 72.44673841 33.29816522 24.43025841 58.02461099 67.71105731 59.9486094 54.78208627 1 13.8781209 1.237744674 24.99040034 0.999938465 53.54872857 0.564223476 14.51786197 16.43922878 503178.6023 22.16481906 3.78427909 17.28799681 -1.237744674 52.5487901 LVINGNPITIFQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LVINGNPITIFQER 14 0 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;; 341.46 1.22E-68 16778903000 1434213 1528459 1198431 1462005 1450713 1451051 1427686 1557596 2189349 FALSE TRUE 1244678.118 1518418.452 1777996.24 1793975.581 1421846.65 1506873.871 1289229.231 1224516.217 1930526.655 0.644735008 0.786530685 0.920990257 0.929267449 0.736507132 0.780550668 0.667812189 0.634291277 1 20.88056304 3.115537568 18.68229313 0.741222737 0.826160702 0.030654206 0.124487115 4.131837693 652.585803 0.038472401 0.043623909 1304.780831 -3.115537568 0.084937965 LVINGNPITIFQERDPS(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LVINGNPITIFQERDPSK 18 1 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 LVINGNPITIFQERDPS(1)K;LVINGNPITIFQERDPS(1)K;LVINGNPITIFQERDPS(1)K;LVINGNPITIFQERDPS(1)K 223.89 2.97E-19 4960507000 3148240 2583850 2261838 2674341 2695040 2136600 3089910 3735400 3969160 TRUE FALSE 2732192.107 2566876.519 3355670.422 3281590.999 2641413.977 2218796.385 2790251.004 2936613.779 3499930.426 0.780641834 0.73340787 0.958782037 0.937616066 0.75470471 0.633954426 0.79723042 0.839049187 1 21.73889481 1.234079699 2.815835764 1.043172921 0.801053647 0.309756158 0.093487324 0.625445119 5.822069454 0.355823571 0.026455018 17.14271871 -1.234079699 -0.242119273 LVINGNPITIFQERDPS(ph)KIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LVINGNPITIFQERDPSKIK 20 2 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 LVINGNPITIFQERDPS(1)KIK;LVINGNPITIFQERDPS(1)KIK;LVINGNPITIFQERDPS(1)KIK 193.88 2.99E-18 12167090000 5700000 4351770 3808490 4091480 3967630 2852140 6496800 7123800 2513170 TRUE FALSE 4946730.558 4323182.936 5650288.503 5020513.068 3888681.926 2961863.671 5866741.336 5600430.807 2216065.906 2.232212745 1.950836807 2.54969335 2.265507111 1.754768175 1.336541329 2.647367716 2.527195059 1 21.07956936 3.270957908 24.33901192 1.971159813 2.249663205 0.10676027 0.509795235 477.573314 358780.9171 0.154386096 0.199293002 1866.198808 -3.270957908 0.278503393 LVINGNPITIFQERDPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVINGNPITIFQERDPSK 18 1 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 289.68 3.53E-49 1.01993E+11 30981100 23636900 14994800 18309100 23233500 19415700 31927000 33423800 9116500 FALSE TRUE 26886869.14 23481627.65 22246335.43 22466460.99 22771198.81 20162634.54 28830724.45 26276380.47 8038757.756 3.344654729 2.92105178 2.767384727 2.794767758 2.832676329 2.5081779 3.586465139 3.268711569 1 22.93854115 1.233975733 24.99998939 0.999996994 3.005577976 0.797186043 0.317501807 66.23447198 361111.1574 0.648015475 0.082993902 17.13861541 -1.233975733 2.005580983 LVKPGNQNTQVTEAWNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVKPGNQNTQVTEAWNK 17 1 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 253.1 4.82E-27 2845000000 2417600 1813390 1385290 1824090 2011590 1489020 2274050 2786900 2724800 FALSE TRUE 2098108.035 1801477.722 2055220.878 2238277.514 1971563.295 1546303.563 2053512.981 2190943.123 2402677.248 0.873237567 0.749779324 0.85538783 0.931576439 0.820569345 0.64357523 0.854676999 0.911875752 1 21.19621143 1.566029822 2.439907398 0.993487179 0.814202018 0.383528176 0.077234219 0.316668488 3.837333433 0.100388588 0.021861219 36.8154253 -1.566029822 -0.179285161 LVLEVAQHLGESTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVLEVAQHLGESTVR 15 0 P06576 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 ; 156.49 2.12E-06 2335700000 1011630 1013030 642970 1292380 1257470 1411410 952010 1284580 1226640 FALSE TRUE 877940.5324 1006375.339 953912.4426 1585834.632 1232448.807 1465707.856 859684.2167 1009882.564 1081628.017 0.811684349 0.930426472 0.881922831 1.466155284 1.139438687 1.355094204 0.794805796 0.933669014 1 20.044773 3.921689424 24.99999604 1.093710922 0.879787189 0.248776427 0.194384741 185.0729729 59081.80729 0.055721963 0.096513329 8350.056697 -3.921689424 -0.213923733 LVLSDCATSHGSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LVLSDCATSHGSLR 14 0 Q8TDL5 Q8TDL5 BPIFB1 BPI fold-containing family B member 1 0 ;; 193.16 2.91E-07 805230000 477849 666550 252933 457945 866100 806540 516968 708840 813550 FALSE TRUE 414700.0439 662171.3892 375252.2448 561928.4115 848866.3045 837568.1157 466832.5229 557260.0822 717373.0458 0.578081441 0.923050278 0.5230922 0.783314086 1.183298299 1.167548907 0.650752807 0.776806552 1 19.45236401 3.469310801 24.99748821 0.926705767 0.691843998 0.31281878 0.18935928 271.8381661 870018.3099 0.058135286 0.075193544 2946.52955 -3.469310801 -0.234861769 LVLTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVLTSR 6 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 126.16 0.040975 1426120000 1051310 1195720 813340 755380 1155900 1290840 1126250 1144350 1202580 FALSE TRUE 912376.7198 1187865.237 1206673.944 926900.5743 1132899.851 1340499.45 1017026.448 899639.6578 1060412.362 0.860398042 1.120191803 1.137928967 0.874094463 1.068357831 1.264130349 0.959085809 0.848386618 1 20.01619396 2.012393051 24.99936374 0.910475459 1.058295569 0.170838257 0.123650482 318.7373488 642957.1376 0.049807409 0.033555649 102.8947107 -2.012393051 0.14782011 LVLVS(ph)PTSEQYDSLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVLVSPTSEQYDSLLR 16 0 O00178 O00178 GTPBP1 GTP-binding protein 1 1 LVLVS(0.995)PT(0.004)S(0.001)EQYDSLLR 80.632 0.01576 22303000 58611 61368 37752 52043 57758 54925 57970 67405 63276 TRUE FALSE 50865.40785 60964.86957 56008.99347 63860.15858 56608.7288 57038.00029 52348.07832 52990.9653 55795.58336 0.911638606 1.092646871 1.003824857 1.144537878 1.014573652 1.022267299 0.938211865 0.949734049 1 15.76786331 2.362915794 4.509451564 0.959190966 1.039343079 0.213370311 0.061790578 0.279590281 9.755253874 0.022639622 0.017174551 230.6299972 -2.362915794 0.080152114 LVLVSPT(ph)SEQYDSLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVLVSPTSEQYDSLLR 16 0 O00178 O00178 GTPBP1 GTP-binding protein 1 1 LVLVS(0.071)PT(0.746)S(0.183)EQYDSLLR 145.69 1.34E-05 25306000 19005 17971 12577 13631 18839 17890 18375 20466 18102 TRUE FALSE 16493.4411 17852.94732 18659.27927 16726.12689 18464.14076 18578.23988 16592.99533 16089.50517 15962.00218 1.033294001 1.11846541 1.168981125 1.047871482 1.156755935 1.163904106 1.039530952 1.007987907 1 13.96235401 2.071130648 5.629900811 1.009844859 1.116103203 0.524823326 0.045222546 0.149099442 8.519814064 0.018772083 0.012392815 117.7960285 -2.071130648 0.106258344 LVNACLAEELPHIHAFEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVNACLAEELPHIHAFEQK 19 0 Q9H3K6;A0A087WZT3 Q9H3K6 BOLA2 BolA-like protein 2 0 ; 207.56 1.80E-16 1770020000 1286790 1133720 913560 1026450 1140500 1029300 1372770 1544490 1502740 FALSE TRUE 1116737.441 1126272.519 1355360.672 1259521.161 1117806.281 1068897.837 1239638.977 1214212.833 1325087.789 0.842764872 0.84996068 1.022845945 0.950519031 0.843571491 0.806661903 0.935514603 0.916326332 1 20.33765651 1.109691071 1.631618664 1.068218775 0.893368381 0.220340298 0.063352877 2.607564179 4.842425457 0.810317805 0.019012759 12.873335 -1.109691071 -0.174850394 LVNHFVEEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LVNHFVEEFK 10 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ;;; 182.28 1.79E-06 12569230000 14735840 12914380 9385460 10978810 11602680 11011970 15461250 18094190 18440150 FALSE TRUE 12788461.41 12829544.59 13924299.85 13471716.61 11371809.37 11435607.61 13961820.35 14224888.28 16260176.47 0.786489706 0.789016319 0.85634371 0.828509865 0.699365679 0.703289268 0.858651219 0.874829883 1 23.95483958 1.419987502 1.568546388 1.03501348 0.7827688 0.639154536 0.052414183 0.518787724 1.614929323 0.189450286 0.016620373 26.30192298 -1.419987502 -0.25224468 LVNHFVEEFKR ddPTM_MDA-MB-175_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 ; 218.75 6.74E-12 11325200000 14861000 12677000 8838800 10693700 11574700 11299700 15215900 18098800 13348900 FALSE TRUE 12897081.2 12593723.95 13113273.24 13121868.03 11344386.12 11734406.77 13740264.36 14228512.47 11770808.25 1.095683569 1.069911572 1.114050367 1.114780544 0.96377291 0.996907478 1.167316982 1.208796555 1 23.48871005 2.220259579 24.99887628 1.144499225 1.060356112 0.142483725 0.071548981 371.3053922 507192.4845 0.030139765 0.020364026 166.0579145 -2.220259579 -0.084143112 LVNLQHLDLLNNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVNLQHLDLLNNK 13 0 Q96AG4 Q96AG4 LRRC59 Leucine-rich repeat-containing protein 59 0 170.18 2.72E-05 277390000 649740 472760 292910 479020 631730 495650 415160 810530 654560 FALSE TRUE 563875.2128 469654.4084 434562.2557 587788.8124 619159.809 514717.9762 374897.8471 637204.4671 577178.6625 0.976950898 0.813707157 0.752907694 1.018382783 1.072735098 0.891782752 0.649535181 1.103998655 1 19.13865844 1.616875917 25 1.05200168 0.886813663 0.235433782 0.126936749 0.961054391 2662.018352 0.071101801 0.03335749 41.3881407 -1.616875917 -0.165188017 LVPDSDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVPDSDVR 8 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 100.45 0.014179 364970000 745480 677600 451960 535940 656810 838110 523870 664130 773310 FALSE TRUE 646962.9292 673148.801 670529.3677 657633.3683 643740.766 870352.634 473065.168 522110.9678 681890.1728 0.948778784 0.987180675 0.983339245 0.96442711 0.944053444 1.276382428 0.693755662 0.765681907 1 19.37917987 2.20312791 24.99999587 0.80328298 1.008704497 0.363238227 0.122291788 179.4020621 126578.2189 0.04871364 0.032844132 159.6349239 -2.20312791 0.205421517 LVPFDHAESTYGLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVPFDHAESTYGLYR 15 0 M0R1L2;O95336;M0R0U3;M0R261 M0R1L2 PGLS 6-phosphogluconolactonase 0 118.51 0.00028569 517430000 853430 768610 346110 418220 645910 598970 794850 878380 352640 FALSE TRUE 740647.0632 763560.9503 513489.9537 513183.2431 633057.6547 622012.7635 717765.5693 690545.2726 310951.3009 2.381874785 2.455564418 1.651351682 1.650365319 2.035873955 2.000354273 2.308289328 2.22075055 1 18.24632913 4.254229591 24.70049219 1.903637833 2.418720059 0.285309558 0.370917138 301.7981143 475743.439 0.093619373 0.245772306 17956.82667 -4.254229591 0.515082226 LVPLLDRPFDETTYEETED ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LVPLLDRPFDETTYEETED 19 1 O15270 O15270 SPTLC2 Serine palmitoyltransferase 2 0 ;;;; 157.52 4.25E-08 495543000 449005 450260 370320 479669 600786 785375 366811 677338 653647 FALSE TRUE 389667.8516 447302.2124 549407.9906 588585.1777 588831.534 815588.8845 331237.7257 532494.5398 576373.5963 0.676068186 0.776062983 0.953215057 1.02118692 1.021614345 1.415035126 0.574692748 0.92387046 1 19.13664472 4.338296347 2.682966464 0.97951026 0.686134643 0.234982849 0.200271776 0.447595723 6.15712437 0.053403037 0.197252377 21791.96271 -4.338296347 -0.293375617 LVPLLDTGDIIIDGGNSEYRDTTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LVPLLDTGDIIIDGGNSEYRDTTR 24 1 P52209-2;P52209;K7EM49;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;; 258.4 5.66E-44 628070000 48943 61844 22816.2 19658.2 49922 72905 55875 57901 2734.9 FALSE TRUE 42475.05854 61437.74269 33850.19064 24121.89477 48928.64987 75709.70253 50456.2511 45519.32174 2411.583238 17.61293489 25.47610289 14.03650105 10.00251386 20.28901558 31.39419007 20.92245887 18.87528534 1 11.23576489 1.240072411 5.145643996 6.43E-15 19.98881845 0.511395086 5.792436215 0.146486977 10.46521093 10.44676379 1.531829689 17.38090602 -1.240072411 19.98881845 LVPTGPTHREPS(ph)PVRYDNLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVPTGPTHREPSPVRYDNLSR 21 2 Q9C0B5;Q9C0B5-2 Q9C0B5 ZDHHC5 Palmitoyltransferase ZDHHC5 1 LVPTGPTHREPS(1)PVRYDNLSR 179.64 2.96E-17 626440000 79593 77718 41790 44057 84597 90083 44587 106890 30489 TRUE FALSE 69074.58339 77207.46534 61999.78378 54060.81522 82913.68521 93548.5513 40262.9596 84032.40532 26884.62515 2.569296875 2.871807396 2.306142765 2.010845043 3.08405584 3.479630115 1.497620271 3.125667732 1 14.71449374 1.227026958 24.99503216 0.999996447 2.610081587 0.436346874 0.577907476 499.1699702 1081700.095 2.089952709 0.134418807 16.8665772 -1.227026958 1.610085141 LVPVS(ph)PLPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LVPVSPLPPK 10 0 O95396 O95396 MOCS3 Adenylyltransferase and sulfurtransferase MOCS3;Molybdopterin-synthase adenylyltransferase;Molybdopterin-synthase sulfurtransferase 1 LVPVS(1)PLPPK;LVPVS(1)PLPPK;LVPVS(1)PLPPK;LVPVS(1)PLPPK;LVPVS(1)PLPPK 129.82 0.00030737 1327750000 2994850 2665430 1847836 2234340 2557320 2292740 3043950 3504560 3172300 TRUE FALSE 2599072.985 2647920.615 2741455.67 2741681.047 2506434.335 2380943.191 2748748.198 2755137.117 2797274.308 0.929144838 0.94660742 0.980045347 0.980125917 0.896027368 0.851165431 0.982652359 0.984936339 1 21.4155903 2.035510127 24.99998539 0.989113047 0.932748851 0.34970527 0.037751948 215.1306315 151456.2999 0.016847827 0.011358759 108.5200854 -2.035510127 -0.056364196 LVQAEYWHDPIKEDVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LVQAEYWHDPIKEDVYR 17 1 A0A2C9F2P4;A0A286YFF7;P50897;Q5T0S4;A0A286YFE3;A0A286YFL8;P50897-2 A0A2C9F2P4 PPT1 Palmitoyl-protein thioesterase 1 0 ;;; 208.13 3.28E-12 2081290000 1390480 1133350 916480 1307440 1121770 1207450 1218320 1538030 1392490 FALSE TRUE 1206724.545 1125904.949 1359692.793 1604314.235 1099448.972 1253901.383 1100167.514 1209134.253 1227871.419 0.982777616 0.916956721 1.107357638 1.306581626 0.895410509 1.021199259 0.895995702 0.984740124 1 20.22772806 LVQAFQFTDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVQAFQFTDK 10 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 ; 218.55 1.57E-08 2536800000 2208100 1878070 1254940 1564580 1657180 1479390 1992890 2299800 2114500 FALSE TRUE 1916293.99 1865732.835 1861833.182 1919841.802 1624205.36 1536303.091 1799619.835 1808005.667 1864526.219 1.027764572 1.000647143 0.998555645 1.029667367 0.871108888 0.823964327 0.965188806 0.969686373 1 20.83037765 3.257200592 24.99898812 0.929290424 1.012079089 0.425073397 0.050846191 285.442458 382818.5439 0.016358267 0.021080826 1808.009016 -3.257200592 0.082788665 LVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSKEYFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSKEYFSK 39 3 P32119 P32119 PRDX2 Peroxiredoxin-2 0 172.47 9.23E-19 920450000 1430000 934840 756930 720910 700920 554760 1290100 1613200 674580 FALSE TRUE 1241021.877 928698.9745 1122983.88 884603.6339 686973.0633 576101.9762 1164986.301 1268229.734 594831.9209 2.086340415 1.561279652 1.887901171 1.487148895 1.154902821 0.968512206 1.958513421 2.132080827 1 19.18212254 7.296880058 1.026218923 1.54734023 122.4180965 0.167707606 0.396406621 892.6581052 5.475005975 0.133032646 250537.2819 19809798.48 -7.296880058 120.8707563 LVQDLPEELVHAGWEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVQDLPEELVHAGWEK 16 0 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 0 ; 92.211 0.0048486 80500000 169602 149598 106208 120268 141244 130414 153961 173163 164179 FALSE TRUE 147188.666 148615.2809 157570.544 147576.6876 138433.5207 135431.111 139029.8859 136133.44 144769.9457 1.016707337 1.026561696 1.088420275 1.019387601 0.956231075 0.935491896 0.960350474 0.940343242 1 17.1434026 3.320833776 3.970819724 0.954932674 1.04365608 0.712869593 0.025280159 0.111287503 3.355446537 0.007398012 0.009564129 2093.3111 -3.320833776 0.088723406 LVQS(ph)PNSYFMDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVQSPNSYFMDVK 13 0 P42677;H0YMV8;Q71UM5;C9JLI6 P42677;H0YMV8 RPS27;RPS27L 40S ribosomal protein S27;40S ribosomal protein S27-like 1 LVQS(0.989)PNS(0.011)YFMDVK 119.54 0.0013303 38825000 89581 79174 63121 79039 75926 74072 106270 114910 115320 TRUE FALSE 77742.64388 78653.90078 93646.52673 96986.01299 74415.22115 76921.59777 95963.95176 90337.39073 101687.001 0.76452883 0.77349022 0.920929183 0.95377002 0.731806627 0.756454582 0.943718969 0.888386813 1 16.63377574 1.594934088 1.363557227 1.000392347 0.826116268 0.331915105 0.07880892 0.883759671 2.432361694 0.19143109 0.02591361 39.34903516 -1.594934088 -0.174276079 LVQSDHSAVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVQSDHSAVQR 11 0 O75843;H0YJ08 O75843 AP1G2 AP-1 complex subunit gamma-like 2 0 ; 148.78 3.47E-05 463050000 144231 176075 79729 102147 182387 210890 176688 198894 179652 FALSE TRUE 125170.5079 174918.3517 118286.2111 125341.0376 178757.8555 219003.0748 159552.825 156362.0659 158413.7452 0.790149287 1.104186707 0.746691589 0.79122577 1.128423896 1.382475204 1.007190536 0.987048603 1 17.27333799 3.23205491 24.99977354 1.093814886 0.867688447 0.401437703 0.147066573 179.6371831 690299.007 0.046736032 0.054244232 1706.298112 -3.23205491 -0.22612644 LVREDENDAS(ph)DDEDDDEKRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVREDENDASDDEDDDEKRR 20 3 Q9Y5B6-2;Q9Y5B6;Q9Y5B6-3;Q9Y5B6-4 Q9Y5B6-2 PAXBP1 PAX3- and PAX7-binding protein 1 1 LVREDENDAS(1)DDEDDDEKRR 105.24 0.0014306 497840000 139300 117740 82439 65148 111410 136980 157440 150820 57649 TRUE FALSE 120891.1521 116966.5582 122306.7761 79940.84912 109193.159 142249.7092 142171.493 118568.3167 50833.80089 2.378164724 2.300960309 2.40601281 1.572592403 2.148042386 2.798329197 2.796790532 2.332470022 1 15.63350049 1.239187722 9.845902807 0.994064353 2.347903791 0.603300958 0.341893013 0.053954099 107.9668205 0.502203548 0.090320503 17.34553589 -1.239187722 1.353839438 LVRLS(ph)SDSFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LVRLSSDSFAR 11 1 A0A087WSV0;Q9HB09-3;Q9HB09 A0A087WSV0 BCL2L12 Bcl-2-like protein 12 1 LVRLS(0.969)S(0.031)DSFAR;LVRLS(0.492)S(0.492)DS(0.015)FAR;LVRLS(0.529)S(0.223)DS(0.248)FAR 195.87 3.78E-08 886582000 584546 633841 363589 481525 663390 769289 466880 777513 373188 TRUE FALSE 507296.765 629677.2567 539421.8565 590862.6109 650189.8369 798884.0456 421602.0495 611247.8956 329070.1398 1.5416068 1.913504693 1.639230642 1.795552192 1.975839672 2.42770142 1.281192058 1.857500337 1 18.32803559 0.93423079 1.763791939 2.30E-19 1.828567939 0.396572525 0.303893371 2.473687101 3.551241776 10.08445442 0.080816636 8.594701344 -0.93423079 1.828567939 LVRLSS(ph)DSFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LVRLSSDSFAR 11 1 A0A087WSV0;Q9HB09-3;Q9HB09 A0A087WSV0 BCL2L12 Bcl-2-like protein 12 1 LVRLS(0.257)S(0.742)DS(0.001)FAR;LVRLS(0.257)S(0.742)DS(0.001)FAR;LVRLS(0.268)S(0.72)DS(0.012)FAR;LVRLS(0.244)S(0.755)DS(0.001)FAR 218.6 6.36E-12 2379490000 852410 900420 538392 707434 973400 1022270 667458 978110 497495 TRUE FALSE 739761.8588 894505.0817 798760.172 868067.7022 954031.2444 1061597.388 602728.0259 768948.7882 438681.7078 1.686329394 2.039075406 1.820819418 1.97880989 2.174768693 2.41997186 1.373952948 1.752862666 1 18.74281502 0.954312396 1.063590362 2.37E-09 1.986183034 0.549441237 0.269499485 2.352678184 1.436967071 6.159546812 0.086646704 9.001448398 -0.954312396 1.986183032 LVS(ph)PEPPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LVSPEPPPK 9 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 LVS(1)PEPPPK;LVS(1)PEPPPK;LVS(1)PEPPPK 125.74 0.001424 153612000 633880 540500 486690 757570 609650 546650 619230 790860 1082770 TRUE FALSE 550111.152 536949.4199 722054.9119 929587.8472 597519.1578 567679.9792 559177.1699 621740.7435 954766.1641 0.576173698 0.562388405 0.756263616 0.973628813 0.625827747 0.594574882 0.585669236 0.651196876 1 19.86478791 -2 0.027120301 1.637548979 6.78E-09 0.088102643 0.154078319 15908.04351 42.77807809 1761.442524 944.1558316 0.01 2 -1.637548972 LVS(ph)PETEASEESLQFNLEKPATGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LVSPETEASEESLQFNLEKPATGER 25 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LVS(0.999)PET(0.001)EASEESLQFNLEKPATGER;LVS(0.976)PET(0.024)EASEESLQFNLEKPATGER;LVS(0.922)PET(0.078)EASEESLQFNLEKPATGER;LVS(0.997)PET(0.003)EASEESLQFNLEKPATGER 261.81 2.51E-45 543397000 425894 348514 298232 339352 347376 340646 421786 478524 560425 TRUE FALSE 369611.0288 346224.5886 442457.9927 416407.0583 340463.8972 353750.872 380881.2586 376195.3665 494172.1949 0.747939752 0.700615276 0.895351858 0.842635548 0.688958021 0.715845359 0.770746033 0.761263726 1 18.91465431 1.23785793 24.93300118 1.000000275 0.765983967 0.578056584 0.062983254 12.96022616 459514.165 0.093001418 0.015984337 17.29250581 -1.23785793 -0.234016308 LVS(ph)PGSANETSSILVESVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LVSPGSANETSSILVESVTR 20 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;A0A0A0MT44 O75369-8 FLNB Filamin-B 1 LVS(0.999)PGS(0.001)ANETSSILVESVTR;LVS(0.951)PGS(0.049)ANETSSILVESVTR;LVS(0.996)PGS(0.004)ANETSSILVESVTR;LVS(0.969)PGS(0.031)ANETSSILVESVTR 321.3 9.97E-67 964820000 216177 216791 165342 200226 201061 229372 193207 221642 249769 TRUE FALSE 187608.6617 215366.8856 245301.9442 245690.3736 197060.2795 238196.0893 174469.8149 174245.5831 220241.5934 0.851831204 0.977866544 1.113785732 1.115549383 0.894745976 1.081521822 0.792174685 0.791156568 1 17.74872743 2.234224345 24.99998304 0.843664364 1.009447713 0.298504757 0.103378816 119.9961818 691805.3877 0.041431685 0.029022154 171.4842922 -2.234224345 0.165783349 LVSDVSATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVSDVSATK 9 0 Q9BVV2 Q9BVV2 C20orf195 Uncharacterized protein C20orf195 0 72.138 0.09227 0 174930 126350 75632 92154 107560 118570 144920 159500 142420 FALSE TRUE 151812.5573 125519.9985 112207.8882 113078.9742 105419.7664 123131.4646 130865.6807 125392.1662 125583.2698 1.208859727 0.99949618 0.893493921 0.900430243 0.839441166 0.980476657 1.042063014 0.998478272 1 16.93828476 4.71409416 3.58026262 0.954660597 1.231925665 0.642368105 0.060040682 0.18757542 4.360275934 0.016995098 0.134421982 51771.90676 -4.71409416 0.277265068 LVSFHDDS(ph)DEDLLHI ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 LVSFHDDSDEDLLHI 15 0 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 1 LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI 343.94 4.01E-70 5601124000 2056749.6 2052659.2 914864.3 1506485.7 2118419 2211343 1706879.2 2322772 2037937 TRUE FALSE 1784944.929 2039175.147 1357295.736 1848556.303 2076266.607 2296414.796 1541346.318 1826065.284 1797014.409 0.993283593 1.134757259 0.755305983 1.028681959 1.155397862 1.277905611 0.857726187 1.016166189 1 20.77717055 5.835860127 13.9981188 1.023242836 1.026100033 0 0.147368364 0 0 0.033001104 0 685267.4879 -5.835860127 0.002857197 LVSFHDDSDEDLLHI ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVSFHDDSDEDLLHI 15 0 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 0 ; 213.73 2.24E-10 50278000 74619 82434 27966 51630 81791 89967 65952 93882 81552 FALSE TRUE 64757.91009 81892.48563 41490.45114 63353.38062 80163.51912 93428.08871 59555.98519 73806.06489 71911.01546 0.900528378 1.138803076 0.57696934 0.880996885 1.114759938 1.299218042 0.828190018 1.0263527 1 16.13392516 3.260317866 19.34605374 1.045646993 0.87197427 0.20383336 0.175733578 31.89119666 28353.91774 0.051230026 0.06595882 1821.033209 -3.260317866 -0.173672723 LVSPGS(ph)ANETSSILVESVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVSPGSANETSSILVESVTR 20 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;A0A0A0MT44 O75369-8 FLNB Filamin-B 1 LVSPGS(0.999)ANETSSILVESVTR;LVS(0.002)PGS(0.993)ANET(0.002)S(0.002)S(0.002)ILVESVTR 130.85 1.62E-05 115462000 42536 49655 32933.7 35786 58329 51078 45357 48759 44588 TRUE FALSE 36914.75983 49328.81304 48860.54748 43911.75825 57168.36702 53043.00371 40958.28512 38332.26729 39316.85743 0.93890413 1.254647911 1.242737865 1.116868466 1.454042127 1.349116058 1.0417487 0.974957557 1 15.26286039 2.098241467 6.2597782 0.992424187 1.232859341 0.376264481 0.134775667 0.210012578 11.31099159 0.056488844 0.037760176 125.3838113 -2.098241467 0.240435154 LVSS(ph)PELGHDEFSTQALAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LVSSPELGHDEFSTQALAR 19 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 1 LVS(0.119)S(0.881)PELGHDEFSTQALAR;LVS(0.027)S(0.973)PELGHDEFSTQALAR;LVS(0.094)S(0.906)PELGHDEFSTQALAR;LVS(0.023)S(0.977)PELGHDEFSTQALAR 275.37 1.26E-39 769090000 381201 363286 258235 347657 419041 514031 372134 444921 439240 TRUE FALSE 330824.322 360899.5503 383118.3097 426597.8355 410702.9039 533806.1052 336044.502 349778.1065 387313.5476 0.854151176 0.931802031 0.989168368 1.101427611 1.060388686 1.378227301 0.867629093 0.903087715 1 18.56314244 4.343686867 2.107494561 1.038579938 0.859035915 0.187447402 0.137406538 0.73563332 5.907135681 0.040275467 0.185129168 22064.133 -4.343686867 -0.179544023 LVTDQNISENWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LVTDQNISENWR 12 0 P24666;F2Z2Q9;G5E9R5;P24666-4 P24666 ACP1 Low molecular weight phosphotyrosine protein phosphatase 0 ;; 328.66 9.95E-58 1106000000 419430 430530 307111 340979 399700 459220 391093 433820 421250 FALSE TRUE 364001.2628 427701.8201 455630.9068 418403.4935 391746.752 476886.4906 353164.8611 341050.969 371450.3049 0.97994606 1.151437526 1.226626821 1.126405034 1.054641083 1.283850045 0.950772839 0.918160423 1 18.50280968 2.173192325 14.14764223 0.94801782 1.137616727 0.500881979 0.084963673 1.037705521 223.2593164 0.03344616 0.022550059 149.0020779 -2.173192325 0.189598906 LVTFYEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVTFYEDR 8 0 Q14894;I3NI53;I3L2W5;I3L325 Q14894 CRYM Ketimine reductase mu-crystallin 0 ; 147.06 0.0012641 672020000 679360 859120 521560 542070 800770 808780 716790 844760 789550 FALSE TRUE 589580.8547 853476.3842 773788.1605 665155.2785 784836.2437 839894.29 647275.8161 664114.6479 696210.2985 0.846843053 1.225888767 1.111428777 0.955394196 1.127297665 1.206380158 0.929713073 0.953899489 1 19.40916363 2.2046549 24.99816232 0.958370165 1.083623186 0.195812803 0.112086873 276.4374083 203811.1812 0.043832404 0.029553485 160.1971923 -2.2046549 0.125253021 LVTSGAESGNLNTS(ph)PSSNQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LVTSGAESGNLNTSPSSNQTR 21 0 Q8NHV4-2;Q8NHV4;Q8NHV4-3 Q8NHV4-2 NEDD1 Protein NEDD1 1 LVTSGAESGNLNT(0.144)S(0.856)PSSNQTR;LVTSGAESGNLNT(0.029)S(0.971)PSSNQTR 400.61 2.26E-132 639180000 461520 520940 325864 396310 481380 534800 523720 516910 495520 TRUE FALSE 400528.9627 517517.9108 483452.9203 486298.2427 471801.4798 555374.1021 472929.715 406372.8191 436940.1901 0.916667708 1.184413617 1.106451023 1.112962949 1.079785038 1.271052914 1.082367165 0.930042208 1 18.73707629 1.852991287 5.306338402 0.965487277 1.11799111 0.30445666 0.089915742 0.233720975 8.932370017 0.044831324 0.02281108 71.2838729 -1.852991287 0.152503834 LVTSIGDVVNHDPVVGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LVTSIGDVVNHDPVVGDR 18 0 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;;;;; 286.16 9.58E-40 4743920000 3373630 2766720 1903700 2157960 2872920 2988730 2686780 3032630 3032010 FALSE TRUE 2927796.248 2748545.234 2824335.687 2647957.8 2815754.513 3103708.377 2426216.489 2384125.674 2673569.232 1.095088997 1.028043412 1.056391454 0.990420509 1.053181821 1.160885733 0.9074822 0.891738896 1 21.35033561 2.211989645 24.99914645 0.923395885 1.058185157 0.579149381 0.052240633 148.6592639 139864.1218 0.021238379 0.014323334 162.9257184 -2.211989645 0.134789272 LVTVWSAPNYCYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVTVWSAPNYCYR 13 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" 0 123.51 0.00051771 180430000 117320 149800 87908 107410 152480 171360 132900 132760 153320 FALSE TRUE 101815.8647 148815.9539 130420.6028 131799.0822 149445.9463 177952.3301 120011.3785 104370.3071 135194.6843 0.753105533 1.100752997 0.964687358 0.974883612 1.105412888 1.316267212 0.887693027 0.772000081 1 17.0446789 2.028428058 24.99553524 0.857753646 1.041459435 0.173257847 0.150623537 286.6099874 252002.3283 0.060908127 0.04106346 106.7647919 -2.028428058 0.183705789 LVVADTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVVADTR 7 0 P22314;P22314-2;Q5JRR9;Q5JRS0 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 103.29 0.019566 159650000 222630 224080 133000 152870 197020 226530 215720 214130 208420 FALSE TRUE 193208.8814 222608.0037 197319.2449 187581.47 193099.6875 235244.7557 194799.5076 168339.9659 183780.825 1.051300545 1.211268932 1.073666117 1.020680313 1.050706391 1.280028837 1.059955562 0.915982208 1 17.48762672 1.990009831 24.7315739 0.962783517 1.114969142 0.385671 0.080879537 397.653901 984428.1173 0.034921898 0.021975323 97.72593425 -1.990009831 0.152185625 LVVEEYYEVLDHCSSILNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVVEEYYEVLDHCSSILNK 19 0 O00170;E9PMH2;V9GYQ3 O00170 AIP AH receptor-interacting protein 0 176.21 1.07E-12 419590000 281360 216990 161010 241440 194060 202230 344700 279020 415190 FALSE TRUE 244177.5631 215564.5784 238874.9745 296262.6422 190198.5857 210009.919 311271.0471 219353.7443 366106.7112 0.666957353 0.588802586 0.652473629 0.809224833 0.519516796 0.573630345 0.850219451 0.599152481 1 18.48190469 1.232359055 24.98898111 1.000000565 0.659301197 0.524525222 0.102469093 166.9428626 672623.819 0.217464906 0.024091555 17.07493482 -1.232359055 -0.340699368 LVVLDEELEGISPDELKDELPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LVVLDEELEGISPDELKDELPER 23 1 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 ;;;;; 288.25 5.20E-53 1113870000 904254 758206 635323 681316 586577 596847 780573 947222 1235674 FALSE TRUE 784754.5428 753225.2949 942567.3278 836019.2111 574905.2653 619808.0903 704873.1506 744665.9466 1089594.027 0.720226546 0.691289853 0.865062862 0.767275875 0.527632541 0.568843142 0.646913559 0.683434314 1 20.05535927 1.238694611 10.77808715 1.000849736 0.682058681 0.525543351 0.094395822 0.059909822 215.5687592 0.14125391 0.025267579 17.32585244 -1.238694611 -0.318791055 LVVLDEELEGISPDELKDELPERQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LVVLDEELEGISPDELKDELPERQPR 26 2 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 57.238 0.046237 47109000 42690 37987 21842 21277 29941 28395 39556 38860 24628 FALSE TRUE 37048.40834 37737.4609 32404.86426 26108.26805 29345.23268 29487.37402 35719.86521 30550.09141 21716.5059 1.706002269 1.737731709 1.492176707 1.202231527 1.351287026 1.35783234 1.644825617 1.406768269 1 14.40650438 4.094256805 3.829712261 1.356586617 1.721100013 0.491464179 0.162879835 0.201407807 5.6023673 0.043880454 0.100176664 12423.86732 -4.094256805 0.364513395 LWACNFCYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LWACNFCYQR 10 0 F5H365;Q15436;G3V4V1;G3V1W4;G3V3G5;G3V2R6 F5H365 SEC23A Protein transport protein Sec23A 0 ; 110.31 0.0061199 348200000 93209 109941 77037 71614 100492 133191 87342 90131 195159 FALSE TRUE 80891.19449 109218.7903 114292.3509 87875.05325 98492.40581 138314.944 78871.58628 70857.18705 172087.5253 0.470058445 0.634670004 0.664152446 0.510641623 0.572339021 0.803747649 0.458322508 0.411750863 1 17.39278299 1.22581971 24.9995114 1.000001024 0.564615896 0.585707189 0.114784412 482.9104159 947482.2635 0.525126227 0.029553131 16.81975674 -1.22581971 -0.435385128 LWAHVYAGAPVSSPEYTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LWAHVYAGAPVSSPEYTK 18 0 D6RDM7;P61086;P61086-2 D6RDM7 UBE2K Ubiquitin-conjugating enzyme E2 K 0 ; 197.88 1.79E-15 1313050000 1435810 1298370 802540 1079830 1276790 1168410 1335940 1659390 1559190 FALSE TRUE 1246064.071 1289840.922 1190651.028 1325021.906 1251384.377 1213359.489 1206380.744 1304542.362 1374864.334 0.906317838 0.938158689 0.866013467 0.963747384 0.910187533 0.88253034 0.877454389 0.948851701 1 20.39085784 1.433624733 3.359428366 0.998454725 0.907574183 0.529625717 0.028798487 0.197533611 3.729091849 0.036286835 0.007338046 27.14093052 -1.433624733 -0.090880543 LWDEESAQLLPHWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LWDEESAQLLPHWK 14 0 Q8TE77;Q8TE77-2;Q8TE77-3;A0A087WWG1;Q8TE77-5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 204.35 1.38E-08 1690800000 1578800 1550700 1025200 1193600 1548000 1567200 1618100 2052800 1561600 FALSE TRUE 1370157.58 1540513.35 1520990.149 1464625.123 1517197.829 1627491.198 1461176.911 1613824.695 1376989.427 0.995038562 1.118754668 1.104576491 1.063642969 1.101822424 1.181919894 1.061138802 1.171994979 1 20.39308605 4.742839484 23.87445065 1.105787755 0.995038478 0.276062826 0.053046723 284.3204826 1586281.931 0.011932547 0.08937681 55314.56282 -4.742839484 -0.110749278 LWDFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LWDFLR 6 0 O15020;O15020-2;A4QPE4 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 121.68 0.045473 285070000 431950 528060 322750 377470 564840 542000 434200 515170 558220 FALSE TRUE 374866.7131 524591.1391 478832.9795 463180.3328 553600.7891 562851.0907 392091.3508 405004.9046 492227.8675 0.761571495 1.065748556 0.972787221 0.940987627 1.124683964 1.143476686 0.796564715 0.822799624 1 18.90896681 2.219056782 24.99996766 0.859447867 1.00599886 0.203185818 0.118641807 339.9480569 435741.279 0.048052636 0.032450123 165.5986463 -2.219056782 0.146550993 LWDFQGFECIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LWDFQGFECIR 11 0 P43034;I3L3N5;P43034-2 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ; 185.18 1.07E-05 270580000 330070 252120 185825 239633 284410 227076 292580 297270 256034 FALSE TRUE 286450.4132 250463.8071 275690.5915 294045.3352 278750.7974 235811.7607 264205.6366 233701.1239 225765.9522 1.26879368 1.109395835 1.221134493 1.302434368 1.234689264 1.044496561 1.170263426 1.035147778 1 17.7844684 1.933971964 0.838559551 0.973847238 1.221618586 0.573687851 0.068242123 0.805121013 0.858131648 0.160822425 0.031318833 85.89580686 -1.933971964 0.247771348 LWDLYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LWDLYLR 7 0 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9;H0Y5B5;Q86U86-6;C9JQF1;C9JPI5 Q86U86-8 PBRM1 Protein polybromo-1 0 ; 115.78 0.013037 188809000 474960 545760 339820 370180 543890 544050 498550 564090 560880 FALSE TRUE 412192.8326 542174.8666 504158.0886 454235.0268 533067.6531 564979.9555 450200.6977 443463.7433 494573.4054 0.83343105 1.096247515 1.019379698 0.918438036 1.077833234 1.14235814 0.910280846 0.896659097 1 18.91582514 LWDVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LWDVDR 6 0 Q9BZK7;A0A0D9SF63 Q9BZK7 TBL1XR1 F-box-like/WD repeat-containing protein TBL1XR1 0 ;;;;; 125.86 0.041275 1189355000 3134420 2647950 1771280 2039420 2600750 2790190 2637140 2836110 2691060 FALSE TRUE 2720198.455 2630555.442 2627876.933 2502501.482 2549000.163 2897530.415 2381390.569 2229629.947 2372925.952 1.146347804 1.108570387 1.107441608 1.054605804 1.074201309 1.221079154 1.003567164 0.939612104 1 21.17823565 2.038577412 12.41443069 0.96731513 1.112798198 0.66215263 0.046677208 0.522227169 167.1706659 0.018751234 0.012632872 109.2892415 -2.038577412 0.145483068 LWDWDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LWDWDKK 7 1 P35606;P35606-2;D6RBT6 P35606 COPB2 Coatomer subunit beta 0 ; 98.392 0.018113 800110000 1776410 1545440 1291090 1573800 1483630 1065260 2366620 2497100 2353750 FALSE TRUE 1541652.918 1535287.903 1915465.442 1931155.344 1454108.666 1106241.242 2137105.557 1963114.597 2075492.356 0.742789012 0.739722263 0.922896891 0.930456495 0.70060902 0.533001838 1.029686065 0.945854891 1 20.98502219 2.183591659 24.99997748 0.98384243 0.772820721 0.47554809 0.11348186 89.19784398 40566.51432 0.049364783 0.033281752 152.6130456 -2.183591659 -0.211021708 LWEAGWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LWEAGWK 7 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 119.89 0.01089 420800000 569430 503430 333990 396940 488370 443160 527090 621770 574020 FALSE TRUE 494178.3827 500122.9352 495508.6811 487071.2938 478652.3925 460208.652 475972.8929 488809.3241 506160.0095 0.976328381 0.988072795 0.978956598 0.962287191 0.945654306 0.909215749 0.940360526 0.965720948 1 18.949234 3.622592169 2.907920191 0.951010517 0.982283483 0.252872298 0.022583977 0.39341071 6.386105958 0.00711548 0.011428174 4193.649882 -3.622592169 0.031272965 LWEEQLAAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LWEEQLAAAK 10 0 K7ELL7;P14314-2;P14314 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 147.12 6.39E-05 80486000 80209 65189 48119 64871 65340 71599 57592 69901 67236 FALSE TRUE 69609.17743 64760.76917 71389.50935 79600.95204 64039.86184 74353.45986 52006.7367 54953.21512 59287.43668 1.174096593 1.092318589 1.204125416 1.342627654 1.080159059 1.25411831 0.87719658 0.926894772 1 15.8554388 2.237016974 24.99999951 0.930675743 1.189162174 0.697100393 0.079695544 21.70349892 351485.37 0.030935671 0.022115494 172.5905345 -2.237016974 0.258486431 LWFTYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LWFTYR 6 0 Q9Y4P1;H0Y2Y0;F2Z2K8;C9JIK8;Q9Y4P1-6;Q9Y4P1-2;G5E979;Q8WYN0-2;Q8WYN0 Q9Y4P1 ATG4B;ATG4A Cysteine protease ATG4B;Cysteine protease ATG4A 0 ; 133.99 0.033099 254380000 760670 1447870 465520 435300 1179560 998030 1583830 1595290 208804 FALSE TRUE 660145.5322 1438358.847 690647.0291 534141.5181 1156089.064 1036424.86 1430230.41 1254149.648 184119.429 3.585420267 7.812097042 3.751081745 2.901060041 6.279017212 5.629090127 7.767949413 6.811609481 1 17.49028235 7.095718187 13.87832433 5.324088538 5.237097898 0 2.247131557 0 0 0.493889429 0 12465743.53 -7.095718187 -0.08699064 LWHLDPDTEYEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LWHLDPDTEYEIR 13 0 Q5TG12;E9PGC5;Q15262;Q15262-2;Q15262-3;Q15262-4;H0YDP9 Q5TG12 PTPRK Protein-tyrosine-phosphatase;Receptor-type tyrosine-protein phosphatase kappa 0 ;; 133.71 0.00010402 91154000 133845 126452 72294 92264 129046 132278 101464 123553 121089 FALSE TRUE 116157.0441 125621.3285 107255.6202 113213.9514 126478.2371 137366.8203 91624.0369 97132.15244 106773.9964 1.087877649 1.176516125 1.004510685 1.060313889 1.184541568 1.286519424 0.8581119 0.909698576 1 16.70420081 2.220916429 24.9971373 0.917227779 1.128487311 0.586457904 0.083328451 173.8731358 246330.2271 0.035325092 0.023874229 166.3092592 -2.220916429 0.211259532 LWKEEEDGQWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LWKEEEDGQWK 11 1 P55735;P55735-4;P55735-3;P55735-2;A8MXL6 P55735 SEC13 Protein SEC13 homolog 0 100.55 0.0035971 227900000 360940 254250 240560 266970 223310 139210 281330 343210 384120 FALSE TRUE 313240.8645 252579.815 356895.6206 327589.6189 218866.5679 144565.4988 254046.6599 269817.2124 338709.7712 0.924806106 0.745711628 1.053691541 0.967169083 0.646177307 0.426812307 0.750042312 0.796602978 1 18.36969008 3.243170599 24.99990657 0.720114392 0.919538466 0.278862207 0.158844521 169.3987892 918642.8966 0.049462693 0.061725868 1750.534198 -3.243170599 0.199424075 LWLFGYDEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LWLFGYDEQR 10 0 Q9NT62;Q9NT62-2 Q9NT62 ATG3 Ubiquitin-like-conjugating enzyme ATG3 0 ; 163.99 1.46E-05 596050000 784110 731890 524550 573090 737460 732280 749890 836350 635850 FALSE TRUE 680487.8768 727082.1664 778224.1345 703218.8436 722785.9888 760451.2854 677165.7832 657503.061 560680.5374 1.213682002 1.296785099 1.387999195 1.254223746 1.289122665 1.356300486 1.207756892 1.172687506 1 19.09681947 1.192704715 1.162022824 0.830380779 1.300365283 0.764224167 0.052470866 0.822929746 0.868306924 0.49261396 0.016387077 15.58492495 -1.192704715 0.469984504 LWPSGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LWPSGDR 7 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;;;; 153.38 0.0040715 5436040000 2997530 2998180 1842840 2271380 3114770 3382750 2544490 3286150 3126620 FALSE TRUE 2601398.816 2978484.758 2734043.588 2787131.545 3052792.171 3512886.581 2297725.751 2583432.395 2756994.545 0.94356328 1.080337559 0.991675371 1.010931106 1.107289884 1.274172481 0.833416865 0.937046611 1 21.39466498 2.19469387 24.99991744 0.922559716 1.06428058 0.334273193 0.096036018 161.3452234 91950.46398 0.03967051 0.026746005 156.5647073 -2.19469387 0.141720865 LWS(ph)LER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LWSLER 6 0 O60437;K7EKI8;K7EQ71;M0QZ12;Q96CP6-2;Q96CP6-3;Q96CP6 O60437;M0QZ12 PPL;GRAMD1A Periplakin;GRAM domain-containing protein 1A 1 LWS(1)LER;LWS(1)LER;LWS(1)LER 93.429 0.047864 57017000 121249 104804 81843 89787 135916 121574 117335 125547 120654 TRUE FALSE 105225.6374 104115.5356 121422.5485 110174.5107 133211.5375 126251.0304 105955.8698 98699.75106 106390.4216 0.989051795 0.978617568 1.141292108 1.035567949 1.252100852 1.186676663 0.995915499 0.927712755 1 16.69900874 2.05534747 8.146147442 0.959568812 1.097874455 0.317192047 0.085739969 0.292391808 38.27057077 0.037603094 0.025250476 113.5919277 -2.05534747 0.138305643 LWSLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LWSLER 6 0 O60437;K7EKI8;K7EQ71;M0QZ12;Q96CP6-2;Q96CP6-3;Q96CP6 O60437;M0QZ12 PPL;GRAMD1A Periplakin;GRAM domain-containing protein 1A 0 118.06 0.05163 38638000 79349 71587 47562 43641 69323 88495 64021 74713 74118 FALSE TRUE 68862.82861 71116.74028 70563.14229 53550.35606 67943.60793 91899.45991 57812.25327 58736.20637 65355.85448 1.053659678 1.088146439 1.07967592 0.819365862 1.039594822 1.406139674 0.884576504 0.89871377 1 15.99602886 LWSLGQDDMAIPSKPPAAS(ph)PEKPSALLGNSLALPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LWSLGQDDMAIPSKPPAASPEKPSALLGNSLALPR 35 2 Q8TEH3;Q8TEH3-7;Q8TEH3-6 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 LWSLGQDDMAIPS(0.056)KPPAAS(0.942)PEKPS(0.001)ALLGNSLALPR 85.416 0.00043747 188640000 279540 178110 133480 150080 193540 158360 271350 309420 262760 TRUE FALSE 242598.0807 176939.9837 198031.3745 184157.9578 189688.9327 164452.2117 245034.5188 243252.9409 231696.8121 1.047049713 0.763670342 0.854700471 0.794823011 0.818694616 0.709773303 1.057565344 1.04987608 1 17.82187867 2.220911351 24.99397097 1.03964985 0.827182854 0.543477509 0.088213378 166.5469826 235853.3923 0.03405186 0.023014382 166.3073146 -2.220911351 -0.212466996 LWSWGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LWSWGR 6 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 172.15 0.012125 1725000000 1424640 991040 709800 646860 951500 1106990 1013170 1198940 1078660 FALSE TRUE 1236370.214 984529.793 1053061.654 793739.4496 932567.0116 1149576.622 914912.9293 942556.0112 951142.0436 1.299879679 1.0351028 1.107154984 0.834512001 0.980470812 1.208627701 0.96190988 0.990972923 1 19.85930128 5.107232104 1.556637181 1.005569171 1.733866406 0.465986436 0.096207891 2.801363995 3.001756814 0.026130246 4.11503834 128006.5238 -5.107232104 0.728297235 LWTFLEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LWTFLEDR 8 0 Q86TU7 Q86TU7 SETD3 Histone-lysine N-methyltransferase setd3 0 ; 201.49 0.00025906 422430000 490340 500340 357170 395970 488960 558310 503080 529690 548630 FALSE TRUE 425540.3266 497053.2336 529898.6067 485881.0405 479230.6526 579788.547 454291.379 416419.9156 483771.5864 0.879630674 1.027454376 1.095348759 1.004360434 0.990613476 1.198475816 0.939061722 0.860777952 1 18.88396651 2.023541439 24.9994335 0.91428702 1.035123565 0.221362226 0.086721355 270.5968513 287354.5543 0.034424131 0.023207587 105.5702231 -2.023541439 0.120836545 LWYTLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LWYTLDR 7 0 P00387-2;P00387;P00387-3 P00387-2 CYB5R3 NADH-cytochrome b5 reductase 3;NADH-cytochrome b5 reductase 3 membrane-bound form;NADH-cytochrome b5 reductase 3 soluble form 0 ; 116.3 0.012765 631730000 430370 507130 397330 449330 594520 663400 387280 578630 727660 FALSE TRUE 373495.5141 503798.6296 589480.117 551357.2441 582690.2152 688921.4273 349721.6452 454894.4774 641636.8638 0.582097967 0.78517719 0.918712983 0.859297954 0.908130826 1.073693652 0.545046061 0.708959387 1 19.29139751 4.700424611 3.530231265 0.838936651 0.561318979 0.249647316 0.147670422 0.417367996 9.186852274 0.038795077 0.288909305 50167.7486 -4.700424611 -0.277617672 LYADS(ph)DS(ph)GDDSDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYADSDSGDDSDKR 14 1 O43896 O43896 KIF1C Kinesin-like protein KIF1C 2 LYADS(1)DS(1)GDDSDKR 143.46 2.81E-06 0 281320 240710 187400 176730 247150 227040 260110 310520 277950 TRUE FALSE 244142.8492 239128.7602 278027.2668 216859.2476 242232.1985 235774.3757 234884.5722 244117.7145 245091.0676 0.996131159 0.975673094 1.134383515 0.884810898 0.988335482 0.961986816 0.958356314 0.996028606 1 17.90295838 3.72591651 24.94972405 0.96860345 1.02942365 0.286151474 0.05197361 1034.558742 2041421.95 0.013760996 0.020552972 5320.059754 -3.72591651 0.0608202 LYAEVHSEEALFLLATCYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYAEVHSEEALFLLATCYYR 20 0 I3L3H6;F6QPS0;G5EA36;P30260;P30260-2 I3L3H6 CDC27 Cell division cycle protein 27 homolog 0 126.88 2.25E-05 8317000 11971 9476.9 9383.6 12909 10696 11062 9471.2 13932 14924 FALSE TRUE 10389.00202 9414.64562 13921.54035 15840.18575 10483.17053 11487.5623 8552.684482 10952.75022 13159.70172 0.789455737 0.715414819 1.057891785 1.203688814 0.796611561 0.872934854 0.649914767 0.832294717 1 13.68383917 LYANMFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LYANMFER 8 0 Q02790;H0YFG2 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;;; 183.74 0.00051576 5392618000 3598350 4339270 2851740 3198959 4247200 4573880 4368400 4267996 4523030 FALSE TRUE 3122818.93 4310765.05 4230851.002 3925331.534 4162689.03 4749840.123 3944753.24 3355318.269 3988322.546 0.782990567 1.080846647 1.06080964 0.984206139 1.043719253 1.190936808 0.989075782 0.841285586 1 21.92735066 1.989795474 24.92489567 0.911068421 1.032505053 0.127459398 0.108388792 734.4108006 1793821.553 0.045314856 0.028454649 97.67771104 -1.989795474 0.121436633 LYASHSQFIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYASHSQFIK 10 0 Q9BW91-2;Q9BW91 Q9BW91-2 NUDT9 "ADP-ribose pyrophosphatase, mitochondrial" 0 113.93 0.0025922 0 426380 473900 228240 319370 523880 497360 410250 506680 397670 FALSE TRUE 370032.8027 470786.9197 338617.6274 391887.8398 513455.813 516493.761 370464.0181 398330.425 350657.9056 1.055252988 1.342581793 0.965663748 1.117578795 1.464264187 1.472927753 1.056482721 1.135951646 1 18.41970473 LYAVHQEGNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LYAVHQEGNK 10 0 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;;; 140.45 3.93E-05 3088620000 8835350 8384130 5725160 6941880 7815620 6884650 8971560 10305300 9923100 FALSE TRUE 7667736.112 8329054.098 8493866.526 8518139.954 7660104.453 7149506.94 8101499.492 8101591.791 8750002.422 0.876312456 0.951891633 0.970727334 0.97350144 0.875440267 0.817086281 0.9258854 0.925895948 1 23.06085199 1.187758292 2.652123108 1.0273565 0.914349286 0.242185841 0.04790751 1.000956083 7.133777497 0.270272542 0.013617285 15.40842654 -1.187758292 -0.113007214 LYAYEPADTALLLDNMKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYAYEPADTALLLDNMKK 18 1 O95994 O95994 AGR2 Anterior gradient protein 2 homolog 0 ; 195.92 3.22E-15 1850450000 2543790 2102350 1327070 1446080 2000010 1717230 2537900 2727300 690101 FALSE TRUE 2207621.706 2088539.524 1968845.491 1774434.566 1960213.714 1783292.949 2291774.849 2144088.119 608518.0459 3.627865634 3.432173521 3.23547593 2.915993335 3.221291015 2.93055064 3.766157576 3.523458562 1 19.21494052 1.2357041 24.99998333 0.999996863 3.332150327 0.87687741 0.274574178 27.77602306 243046.9214 0.486002694 0.071719369 17.20695803 -1.2357041 2.332153464 LYAYHLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYAYHLSR 8 0 G3V1D3;G3V180;Q9NY33-4;Q9NY33;Q9NY33-2;E9PKK8;E9PPK9;E9PQF2 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ; 102.51 0.0049505 812710000 1233790 1698750 650130 920210 1908700 1795350 1554530 1444340 1455960 FALSE TRUE 1070741.525 1687590.799 964535.0426 1129157.745 1870720.604 1864418.276 1403771.92 1135479.131 1283838.067 0.834016028 1.31448883 0.751290266 0.879517264 1.457131278 1.452222304 1.093418209 0.884441083 1 20.29203181 LYDAYELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYDAYELK 8 0 P08758;D6RBL5;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 103.56 0.011047 61744000 302020 291970 148130 156210 185460 163920 197620 243360 358670 FALSE TRUE 262107.2918 290052.0298 219766.1635 191679.868 181769.7088 170226.1085 178454.8428 191319.3578 316268.4412 0.828749434 0.91710709 0.69487225 0.606067008 0.574732364 0.538232989 0.564251185 0.604927122 1 18.27079008 4.111809121 4.366966444 0.631846008 0.871619379 0.318192867 0.132514131 0.225931289 7.471379919 0.03414951 0.076393713 12936.27149 -4.111809121 0.239773371 LYDDIDFDIEEFAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYDDIDFDIEEFAK 14 0 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 210.35 1.25E-08 157488000 508610 392770 303630 372610 362490 322510 454270 549180 526760 FALSE TRUE 441395.8998 390189.868 450466.4836 457216.7955 355277.1582 334917.1684 410214.9653 431742.1307 464487.0329 0.950286808 0.840044695 0.969814982 0.984347814 0.764880681 0.721047402 0.88315698 0.929503087 1 18.8252788 1.476976162 2.591953632 0.999644499 0.870439079 0.19367811 0.084228937 0.572856851 6.766386249 0.136495015 0.024301639 29.98997899 -1.476976162 -0.12920542 LYDEVQEVVYFPAVVHDNLGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYDEVQEVVYFPAVVHDNLGER 22 0 H9KVC8;F8WBX0;C9JNS3;F8W0M9;C9JID8;Q0VDG4-2;Q0VDG4 H9KVC8 SCRN3 Secernin-3 0 ; 129.84 1.45E-05 95007000 131423 118798 82842 90160 110385 126122 115469 129072 115151 FALSE TRUE 114055.1176 118017.6081 122904.6683 110632.206 108188.5545 130973.995 104270.8342 101470.9572 101537.98 1.123275425 1.162300138 1.210430504 1.089564772 1.065498393 1.289901523 1.026914601 0.999339925 1 16.63165994 2.029448253 24.91728265 1.003674109 1.152813495 0.560085397 0.062121702 134.5541613 113850.8059 0.024610438 0.016592074 107.0158864 -2.029448253 0.149139386 LYDLNHNEIGELIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LYDLNHNEIGELIR 14 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;;; 185.95 1.12E-06 1325050000 1367410 1150500 733050 835190 1218040 1285440 1109300 1322190 1261870 FALSE TRUE 1186703.304 1142942.29 1087555.432 1024832.655 1193803.387 1334891.709 1001720.257 1039449.958 1112693.166 1.066514417 1.027185503 0.977408207 0.92103797 1.072895407 1.199694354 0.900266387 0.934174838 1 20.08562438 LYDNLLEQNLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYDNLLEQNLIR 12 0 O00231;O00231-2 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 75.739 0.07677 41788000 70244 64223 53598 49843 68725 83009 64110 71793 85841 FALSE TRUE 60961.07742 63801.11488 79518.17207 61160.61495 67357.50696 86202.40994 57892.62207 56440.62564 75692.97477 0.80537299 0.84289348 1.050535698 0.808009133 0.88987792 1.13884294 0.764834811 0.745652101 1 16.20787179 LYEEGSNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYEEGSNKR 9 1 P25788-2;P25788 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ; 138.66 0.00020906 4627900000 3995800 2982800 2062200 2625400 2712800 2401900 3461000 3700800 3189500 FALSE TRUE 3467744.906 2963205.79 3059486.818 3221537.197 2658820.588 2494302.647 3125352.753 2909412.72 2812440.943 1.233001857 1.053606405 1.087840377 1.1454595 0.945378282 0.886881786 1.111259868 1.034479578 1 21.42339137 8 0.635058508 1.015796462 17.30840058 0.436917377 0.074132471 222.8098834 1.537645425 0.03397831 5082.970742 100000000 -8 16.29260412 LYEIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LYEIAR 6 0 Q7Z5M8-2;Q7Z5M8 Q7Z5M8-2 ABHD12B Abhydrolase domain-containing protein 12B 0 ;; 109.88 0.067884 533133000 1738580 998190 686867 711822 853480 979050 1428030 1490880 894510 FALSE TRUE 1508822.248 991632.8242 1019038.179 873452.0646 836497.4178 1016714.687 1289539.87 1172066.914 788762.0468 1.912899149 1.257201495 1.291946263 1.107370807 1.060519356 1.289000518 1.634890872 1.485957544 1 19.58923061 4.74045808 24.53159478 1.290522729 1.912899427 0.527676337 0.191121974 122.3516702 1581678.954 0.051267832 0.322815162 55012.08183 -4.74045808 0.622376698 LYENFISEFEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LYENFISEFEHR 12 0 Q9UNM6;J3KNQ3;A0A087WUL9;E9PQG3;E9PPD2 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ;;;;;;; 243.88 2.28E-16 2866073000 1692299 1577846 1141258 1593965 1752242 1740251 1655239 1966152 2479137 FALSE TRUE 1468657.399 1567481.026 1693174.186 1955899.115 1717375.812 1807199.582 1494714.177 1545705.695 2186056.248 0.671829648 0.717035999 0.774533678 0.894715823 0.785604585 0.826693999 0.683749184 0.707074988 1 21.05989909 4.311567816 2.922038251 0.797992395 0.680622121 0.224318742 0.089941592 0.453503215 7.525303187 0.024023329 0.080081589 20491.21998 -4.311567816 -0.117370274 LYEQLSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYEQLSGK 8 0 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 99.802 0.018836 0 350100 293540 197110 234520 281490 231110 285640 366590 462850 FALSE TRUE 303833.398 291611.7164 292433.0553 287771.3504 275888.8997 240000.9512 257938.6768 288197.5813 408132.4003 0.74444812 0.714502735 0.716515168 0.705093127 0.675978921 0.588046798 0.631997549 0.706137472 1 18.63867772 1.240595955 4.827250876 1.021893053 0.681092615 0.830435392 0.044804138 0.076747095 4.258857392 0.088350944 0.012411162 17.40187141 -1.240595955 -0.340800438 LYFHSDTCLPLRPQEMEVDS(ph)EDEKDPEWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LYFHSDTCLPLRPQEMEVDSEDEKDPEWLR 30 2 J3QQW9;Q15022 J3QQW9 SUZ12 Polycomb protein SUZ12 1 LYFHS(0.001)DT(0.007)CLPLRPQEMEVDS(0.992)EDEKDPEWLR;LYFHSDTCLPLRPQEMEVDS(1)EDEKDPEWLR;LYFHSDTCLPLRPQEMEVDS(0.999)EDEKDPEWLR;LYFHSDTCLPLRPQEMEVDS(1)EDEKDPEWLR;LYFHSDT(0.001)CLPLRPQEMEVDS(0.999)EDEKDPEWLR 302.3 1.14E-81 1463540000 967714 708128 568659 673771 728971 600610 782370 979709 916520 TRUE FALSE 839828.143 703476.2605 843664.3945 826761.0035 714465.9033 623715.8553 706495.8778 770205.8545 808170.0497 1.039172564 0.870455742 1.043919401 1.023003765 0.884053924 0.77176314 0.874192106 0.953024496 1 19.62429936 3.229987411 24.92970118 0.895735664 0.988859256 0.292418402 0.0751821 260.9938541 758932.9056 0.023954798 0.027594859 1698.194426 -3.229987411 0.093123592 LYFLQCETCHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYFLQCETCHSR 12 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ; 246.51 1.50E-16 3046500000 2538300 2914800 1851460 2193800 2740300 2772700 2516400 2897000 2501300 FALSE TRUE 2202857.224 2895652.487 2746832.249 2691935.82 2685773.391 2879367.563 2272359.915 2277499.094 2205599.163 0.998756828 1.312864339 1.245390502 1.220500925 1.217706932 1.305480892 1.03026876 1.03259882 1 21.07273919 2.221331603 24.37767347 1.023769367 1.222661981 0.535378065 0.085868088 128.2237079 181424.329 0.0328535 0.022215266 166.4683225 -2.221331603 0.198892614 LYGDADYLEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYGDADYLEER 11 0 P17812;B4E1E0;P17812-2;A0A3B3IRI2 P17812 CTPS1 CTP synthase 1;CTP synthase 0 82.749 0.042076 90343000 160200 142200 110950 121930 163970 135700 151730 183270 193140 FALSE TRUE 139029.1641 141265.8788 164605.7911 149616.0701 160707.3178 140920.4668 137015.248 144079.1367 170307.2092 0.816343388 0.829476799 0.966522744 0.878506968 0.943631914 0.827448629 0.804518191 0.845995524 1 17.37777998 4.250390632 0.005305923 1.736004722 7.06E-05 0.036464117 0.067176628 215360.1689 439.1531405 70745.088 72940.97622 17798.79626 -4.250390632 -1.735934171 LYGDVPFIEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYGDVPFIEER 11 0 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 0 117.02 0.0018904 0 63131 54691 42502 52351 57038 61439 51396 68738 74449 FALSE TRUE 54788.0784 54331.73122 63056.10936 64238.09468 55903.05539 63802.59809 46411.62383 54038.91362 65647.72403 0.834576967 0.827625512 0.960522399 0.978527369 0.851561211 0.971893528 0.706979937 0.823165074 1 16.00245737 1.226454881 24.71282925 1.00000035 0.867184488 0.194813735 0.08336576 900.8335355 1838839.84 0.349829343 0.021364999 16.8443742 -1.226454881 -0.132815863 LYGPSSVSFADDFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYGPSSVSFADDFVR 15 0 P50454;E9PR70;E9PPV6;E9PK86;E9PMI5;E9PQ34;E9PIG2;E9PRS3;E9PNX1;E9PJH8 P50454 SERPINH1 Serpin H1 0 210.79 3.97E-09 214390000 60856 66348 71311 65713 86211 109380 66721 76535 71927 FALSE TRUE 52813.72541 65912.15562 105797.2381 80634.14101 84495.56977 113587.9194 60250.40769 60168.58585 63423.872 0.83271052 1.039232603 1.668098064 1.271353175 1.332236067 1.790933221 0.949964198 0.948674118 1 15.95273834 LYGPTNFAPIINHVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYGPTNFAPIINHVAR 16 0 Q99829;B0QZ18;F2Z2V0;A6PVH9;E7ENH5;Q5JX45;H0Y524 Q99829 CPNE1 Copine-1 0 ; 241.89 6.35E-20 2714400000 939130 1027780 616670 664300 950930 1038000 907810 965800 956630 FALSE TRUE 815021.591 1021028.446 914893.6746 815139.4682 932008.3535 1077932.532 819770.7259 759271.1859 843538.2912 0.966193947 1.210411497 1.084590568 0.966333688 1.104879723 1.277870303 0.971823964 0.90010281 1 19.68609403 2.024927716 24.9949687 0.940830048 1.101947913 0.329913882 0.097184279 224.6043664 225209.3501 0.039037017 0.026317666 105.9077437 -2.024927716 0.161117865 LYGS(ph)PTQIGPSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYGSPTQIGPSYR 13 0 E7EWD6;Q76L83;Q76L83-2 E7EWD6 ASXL2 Putative Polycomb group protein ASXL2 1 LYGS(0.976)PT(0.024)QIGPSYR;LYGS(0.937)PT(0.063)QIGPSYR 153.51 4.80E-05 130760000 297730 295620 179864 209960 281730 275670 353870 346090 305060 TRUE FALSE 258384.2261 293678.0528 266846.832 257634.627 276124.1242 286275.2033 319551.7419 272081.3468 268996.1543 0.960549889 1.091755581 0.99200984 0.957763235 1.026498408 1.064235301 1.187941674 1.011469281 1 18.03722602 2.839931782 4.076963888 1.068756155 1.005302456 0.196372119 0.061687482 0.411366146 12.04697459 0.020940403 0.020894175 691.7223084 -2.839931782 -0.063453699 LYGS(ph)VCDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LYGSVCDLR 9 0 Q8N9U0;Q8N9U0-2 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 LYGS(1)VCDLR;LYGS(1)VCDLR;LY(0.001)GS(0.999)VCDLR 149.17 9.26E-05 691690000 1133380 1150840 728480 946210 1229900 1399200 721460 1192170 1421810 TRUE FALSE 983600.9614 1143280.056 1080775.365 1161061.442 1205427.396 1453028.129 651492.9202 937233.723 1253725.242 0.78454268 0.911906388 0.862051213 0.926089229 0.961476531 1.158968553 0.519645692 0.747559108 1 20.25778978 2.237878238 24.99999994 0.744194636 0.930755755 0.244450232 0.147335828 25.05792472 917964.8541 0.057794628 0.041603239 172.9331442 -2.237878238 0.186561119 LYHDIAQQAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYHDIAQQAFK 11 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 126.03 0.00031606 1732000000 2540450 2810000 1965570 2403520 2719900 2445610 3049600 3390300 3578200 FALSE TRUE 2204723.096 2791540.925 2916126.226 2949275.952 2665779.311 2539694.199 2753850.261 2665310.728 3155189.272 0.698760963 0.884745948 0.924231789 0.934738203 0.844887289 0.804926101 0.872800337 0.844738777 1 21.58929512 4.738864695 23.61754871 0.883219887 0.698760848 0.539880729 0.054939062 9.522723466 738842.523 0.013503004 0.076455428 54810.61749 -4.738864695 -0.184459039 LYHEADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYHEADK 7 0 O75663 O75663 TIPRL TIP41-like protein 0 ; 100.45 0.0097841 392459000 672420 579170 460370 612120 462350 463760 692470 763270 1241860 FALSE TRUE 583557.9933 575365.3941 683006.4718 751111.2017 453150.1396 481601.1473 625314.366 600050.6503 1095048.726 0.532905961 0.525424468 0.623722448 0.685915781 0.41381733 0.439798829 0.571037938 0.547967078 1 20.06256364 1.237991558 7.563062996 1.007257505 0.54291208 0.770262255 0.078513504 0.050833227 21.1582621 0.120243829 0.020309813 17.29782734 -1.237991558 -0.464345425 LYKDDQLLDDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LYKDDQLLDDGK 12 1 B8ZZU8;Q15370;Q15370-2 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 ;;; 154.47 6.52E-05 3201780000 4062630 3134070 2955660 3128190 2869720 2215000 4174810 4912890 4559770 FALSE TRUE 3525743.152 3113482.088 4385027.062 3838493.351 2812618.187 2300212.483 3769937.569 3862306.706 4020719.185 0.876893658 0.774359498 1.09060764 0.954678299 0.699531118 0.572089812 0.937627672 0.960600959 1 21.93902215 2.021337855 24.99978246 0.968974875 0.830557266 0.183796834 0.138781777 434.6450674 509235.2165 0.061537282 0.041484843 105.0359227 -2.021337855 -0.138417609 LYKEELEQTYHAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYKEELEQTYHAK 13 1 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 129.77 9.00E-05 1305400000 1102800 813950 469030 693850 711150 585810 934570 1244400 714480 FALSE TRUE 957062.1859 808603.1089 695854.4768 851399.2473 696999.5063 608346.4898 843935.5452 978294.7439 630014.9883 1.519110186 1.283466463 1.104504638 1.351395226 1.106322102 0.965606376 1.339548361 1.552811857 1 19.26502663 4.709374051 3.966541829 1.232807227 1.537826568 0.223207234 0.178375569 0.385492496 12.25009002 0.047301647 0.319770923 51212.27288 -4.709374051 0.305019341 LYLEAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYLEAFR 7 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 0 ; 110.36 0.036942 0 518120 660710 482190 465990 727300 716830 673400 713040 838780 FALSE TRUE 449649.1293 656369.7525 715378.6968 571800.1517 712828.1529 744406.914 608093.7716 560561.9449 739620.3839 0.607945831 0.887441405 0.96722415 0.773099504 0.9637757 1.006471604 0.822170109 0.757904943 1 19.49642546 4.738659016 24.99999887 0.886651589 0.607945759 0.500781389 0.090229968 7.320557288 1857378.535 0.022686727 0.126761965 54784.66567 -4.738659016 -0.27870583 LYLEDDDPVQAEAYINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYLEDDDPVQAEAYINR 17 0 D6RFN0;Q9BT78;D6RAX7;Q9BT78-2;D6RD63 D6RFN0 COPS4 COP9 signalosome complex subunit 4 0 ; 342.43 2.36E-72 169205000 142103 134817 102717 104989 138619 137149 143403 152905 143269 FALSE TRUE 123323.7285 133931.3783 152391.2848 128828.3571 135860.7531 142425.2108 129495.7991 120207.4557 126331.902 0.97618833 1.060154847 1.206277134 1.019761082 1.075427116 1.127389111 1.025044324 0.951520983 1 16.94685948 2.005597442 5.965493814 0.976343544 1.079884979 0.320495406 0.061648065 0.163449604 23.05593115 0.027117691 0.016767594 101.2972003 -2.005597442 0.103541435 LYNDLWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYNDLWK 7 0 Q9UP83-3;Q9UP83;Q9UP83-2 Q9UP83-3 COG5 Conserved oligomeric Golgi complex subunit 5 0 89.298 0.067313 0 246020 187390 136080 131360 179570 163160 229460 245140 138780 FALSE TRUE 213507.8337 186159.0228 201888.7432 161187.2957 175996.9083 169436.8708 207207.0045 192718.7187 122373.5865 1.744721551 1.521235326 1.649773852 1.317173912 1.438193595 1.384586949 1.693233078 1.574839181 1 16.90093267 7.999999214 0.030319185 6.80E-07 3.62204492 0.246363779 0.188165708 6138.237262 18.4293269 775.561113 1556.776336 99999819 -7.999999214 3.62204424 LYNLDVFQYELYNPMALYGSVPVLLAHNPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYNLDVFQYELYNPMALYGSVPVLLAHNPHR 31 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 184.75 1.38E-18 1451010000 157255 141410 73901 107745 125079 143434 134686 136001 98521 FALSE TRUE 136473.3533 140481.0684 109639.7708 132210.149 122590.1726 148951.9988 121624.1725 106918.2445 86873.95962 1.57093511 1.617067635 1.262055641 1.521861667 1.4111268 1.714575915 1.40000724 1.230728345 1 16.40663617 1.549239664 2.004850166 0.987502379 1.506192734 0.658201516 0.122652745 0.237591004 1.719673496 0.198544112 0.034024649 35.41927476 -1.549239664 0.518690355 LYNNHEIR ddPTM_MDA-MB-175_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 ;;;;; 172.94 0.00028066 4756070000 4815520 4024120 2290780 2703290 3527290 3844420 3200800 3812920 4754280 FALSE TRUE 4179136.831 3997685.291 3398608.87 3317113.312 3457103.83 3992317.325 2890386.909 2997556.73 4192234.434 0.996875746 0.953592971 0.810691511 0.791251864 0.824644682 0.952312517 0.689462136 0.715026027 1 21.99928797 4.29872355 3.96130368 0.811581391 0.986760463 0.295527665 0.094513123 0.247510453 7.662947137 0.024619396 0.070543826 19894.0658 -4.29872355 0.175179072 LYPLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYPLRK 6 1 P42766 P42766 RPL35 60S ribosomal protein L35 0 ; 133.45 0.023186 1963440000 1831370 1798730 1153360 1232330 1645320 1604410 1981360 2097600 1113010 FALSE TRUE 1589349.814 1786914.024 1711128.754 1512149.361 1612581.351 1666132.691 1789208.012 1649044.564 981431.2257 1.619420467 1.820722611 1.743503476 1.540759374 1.643091547 1.697656083 1.823060002 1.680244647 1 19.90452765 1.239637365 6.923143077 0.984672719 1.701334537 0.865811418 0.086137337 0.03794271 10.20546515 0.128358462 0.02176151 17.36350373 -1.239637365 0.716661818 LYPPGDEEEAELADSSGLYHEGSPSPGS(ph)PWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LYPPGDEEEAELADSSGLYHEGSPSPGSPWK 31 0 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 LYPPGDEEEAELADSSGLYHEGSPS(0.01)PGS(0.99)PWK;LYPPGDEEEAELADSSGLYHEGSPS(0.008)PGS(0.991)PWK;LYPPGDEEEAELADSSGLYHEGS(0.002)PS(0.002)PGS(0.996)PWK 209.24 2.45E-26 255551000 140356 129272 71633 121745 159134 132228 149478 177116 161583 TRUE FALSE 121807.599 128422.8037 106274.9584 149389.063 155967.5447 137314.8967 134981.6466 139241.1217 142480.8418 0.854905105 0.901333836 0.745889462 1.048485264 1.094656255 0.963742879 0.947366992 0.977262065 1 17.12040842 3.728014332 24.99977087 1.000714384 0.840771901 0.670051736 0.056510251 444.7167009 1054192.636 0.016242864 0.02438494 5345.820002 -3.728014332 -0.159942482 LYQAGEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYQAGEGR 8 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 75.696 0.087759 153710000 290130 248880 197960 172180 238410 277830 197830 284210 250890 FALSE TRUE 251788.5854 247245.0909 293694.1181 211276.1006 233666.1074 288518.2999 178644.477 223433.9032 221230.07 1.138130026 1.117592608 1.327550627 0.955006255 1.056213142 1.304154991 0.807505404 1.009961725 1 17.75518797 2.234990792 24.99999982 0.948421559 1.143286612 0.404513571 0.120117968 96.79336331 677846.2381 0.046733356 0.032912754 171.7871966 -2.234990792 0.194865053 LYQHAVEYFLHAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYQHAVEYFLHAIK 14 0 I3L4J1;Q9UN37 I3L4J1 VPS4A Vacuolar protein sorting-associated protein 4A 0 ; 162.37 2.57E-06 212081000 651830 680740 414310 521300 591080 562470 718640 790280 626080 FALSE TRUE 565689.014 676268.1741 614671.7018 639669.1326 579318.6644 584108.5849 648946.4034 621284.772 552065.5356 1.024677285 1.22497807 1.113403504 1.158683329 1.049365749 1.058042111 1.175487984 1.125382281 1 19.07448001 3.257012319 24.99495352 1.092978194 1.135972005 0.099467679 0.067461226 639.8811811 866786.9114 0.019014071 0.024501353 1807.225387 -3.257012319 0.042993811 LYQQHGAGLFDVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYQQHGAGLFDVTR 14 0 A0A2R8Y7U1;A0A2R8YGD1;A0A2R8YD45;O14773-2;O14773 A0A2R8Y7U1 TPP1 Tripeptidyl-peptidase 1 0 ; 112.24 0.00060531 1171050000 680140 734940 408820 539150 746870 799210 627180 765040 767260 FALSE TRUE 590257.7757 730112.1307 606526.7194 661572.2479 732008.7482 829956.1259 566356.1801 601442.1495 676555.3969 0.872445595 1.0791609 0.896492323 0.977853774 1.081964244 1.226737869 0.837117231 0.888976945 1 19.36784854 LYQTDPSGTYHAWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LYQTDPSGTYHAWK 14 0 O14818;H0Y586;O14818-2;Q8TAA3-2;Q8TAA3-5;Q8TAA3;A0A087WYS6 O14818 PSMA7;PSMA8 Proteasome subunit alpha type-7;Proteasome subunit alpha type-7-like 0 ;; 183.6 1.39E-06 7259790000 5187220 4539850 2576780 3605790 4436720 3898370 4752310 5358450 5184750 FALSE TRUE 4501715.734 4510027.426 3822919.427 4424539.731 4348437.952 4048342.816 4291431.708 4212587.167 4571814.761 0.984667133 0.986485162 0.836192984 0.967786308 0.951140451 0.885500185 0.938671388 0.921425602 1 22.12433552 1.232899785 24.79854581 1.000000121 0.932276818 0.169410586 0.045800106 299.8236467 1313289.038 0.092431529 0.010793414 17.09620768 -1.232899785 -0.067723303 LYQVEYAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYQVEYAFK 9 0 G3V5Z7;P60900;G3V3I1;G3V295;G3V3U4 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ; 141.88 0.00024582 319170000 608580 631340 440310 526920 623760 509780 661170 712380 657960 FALSE TRUE 528154.6111 627192.686 653245.3887 646565.2395 611348.3964 529391.5665 597049.8352 560043.0807 580176.7184 0.910334032 1.081037322 1.125942093 1.114428103 1.053727902 0.912466064 1.02908272 0.965297405 1 19.14613288 2.918597095 9.348341415 0.979997527 1.066876085 0.269130397 0.065015393 0.550431595 60.07262493 0.020715289 0.020736292 829.0812532 -2.918597095 0.086878558 LYRPGSVAYVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYRPGSVAYVSR 12 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 152 6.33E-05 1925240000 711230 851030 508730 507790 867870 909910 753380 764940 850170 FALSE TRUE 617239.1535 845439.5279 754753.5296 623091.4806 850601.085 944914.8265 680317.3236 601363.5338 749663.8711 0.823354542 1.127758133 1.006789254 0.831161144 1.134643295 1.260451334 0.907496479 0.802177558 1 19.51588435 2.024925067 24.99965883 0.877321937 1.034198882 0.150231042 0.140301309 339.4467071 340461.068 0.057349602 0.03866354 105.9070978 -2.024925067 0.156876944 LYSESLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LYSESLAR 8 0 P50395;P50395-2;Q5SX87;Q5SX91;P31150 P50395;P31150 GDI2;GDI1 Rab GDP dissociation inhibitor beta;Rab GDP dissociation inhibitor alpha 0 ;;; 155.51 0.00094878 2682750000 2863940 2824460 1886390 2267060 2823170 2795040 2579480 2932390 3026720 FALSE TRUE 2485463.073 2805905.936 2798654.514 2781830.623 2766994.44 2902566.997 2329322.427 2305321.218 2668904.61 0.931267106 1.051332418 1.048615415 1.042311746 1.036752843 1.087549921 0.872763462 0.863770556 1 21.34781631 2.232101938 24.99998808 0.900450828 1.035113674 0.524512298 0.05380583 104.6161191 404938.9558 0.021114094 0.014615735 170.6482889 -2.232101938 0.134662846 SGGLQT(ph)PECLS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 140.84 0.00031839 382080000 1904660 1451760 623110 527090 710600 647600 568580 620670 696390 TRUE FALSE 1652954.355 1442223.293 924448.0802 646773.8406 696460.4503 672513.5911 513439.1991 487944.5506 614063.5675 2.691829385 2.348654715 1.505459905 1.053268545 1.134182985 1.095185623 0.836133629 0.794615698 1 19.22802848 4.230116779 1.315113852 0.933648919 2.886789707 0.973271036 0.104910236 0.098118732 0.269487681 0.036250771 0.204057145 16987.0036 -4.230116779 1.953140789 up LYSGS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LYSGSPTR 8 0 Q6PJI9-4;Q6PJI9-3;Q6PJI9;H3BMH3 Q6PJI9-4 WDR59 WD repeat-containing protein 59 1 LYSGS(0.999)PT(0.001)R;LYSGS(1)PTR;LYS(0.003)GS(0.996)PT(0.001)R 174.42 0.00028536 887030000 1267940 941830 722530 767480 937750 1078990 1065170 1152820 1145470 TRUE FALSE 1100378.516 935643.0567 1071947.925 941748.0642 919090.6097 1120499.443 961869.9773 906298.4143 1010053.842 1.089425604 0.926329883 1.061278004 0.932374123 0.909942195 1.109346252 0.952295747 0.89727733 1 19.94600077 4.752822461 23.62902733 0.970347131 1.089425781 0.223372673 0.06762786 1782.58465 2953276.449 0.016344407 0.313663874 56600.78589 -4.752822461 0.119078651 LYSILGTTLKDEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYSILGTTLKDEGK 14 1 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 242.43 1.60E-17 454200000 611710 422530 305660 355090 385670 281690 526560 629640 319870 FALSE TRUE 530870.9736 419754.3726 453478.1984 435718.6117 377995.9216 292526.7966 475494.2922 494996.3859 282055.333 1.882151874 1.488198674 1.607763248 1.544798345 1.34014811 1.037125565 1.685819187 1.754961981 1 18.10561869 7.999961562 0.858160021 1.439002765 161.7226403 0.25215852 0.249028239 1213.270195 3.246124061 0.08769421 379858.1064 99991149.69 -7.999961562 160.2836376 LYSILQGDS(ph)PTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYSILQGDSPTK 12 0 O15042-2;O15042;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 LY(0.018)S(0.021)ILQGDS(0.958)PT(0.004)K 54.7 0.085423 15912000 28194 24111 10504 16754 23704 22634 25807 32197 29098 TRUE FALSE 24468.09147 23952.61325 15583.76953 20558.25177 23232.33678 23504.74463 23304.24111 25311.92211 25658.06759 0.953621756 0.933531458 0.607363336 0.801239287 0.905459333 0.916076183 0.90826174 0.986509293 1 14.6471249 2.412698864 1.116666213 0.989389764 0.824561926 0.291199262 0.09573321 0.706810938 1.804458147 0.084056679 0.042253417 258.6418893 -2.412698864 -0.164827839 LYSLALHPNAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYSLALHPNAFK 12 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 103.88 0.001141 749090000 1803200 2093700 1193630 1536950 2191100 1673790 2277500 2406200 2530000 FALSE TRUE 1564902.551 2079946.347 1770873.46 1885937.988 2147501.397 1738181.784 2056628.401 1891652.855 2230906.282 0.701464944 0.932332462 0.793791059 0.845368541 0.9626139 0.77913707 0.921880232 0.84793022 1 21.08919848 LYSLLGIDLTAPSNNS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYSLLGIDLTAPSNNSSPR 19 0 A3KN83-3;A3KN83-2;A3KN83;A3KN83-4 A3KN83-3 SBNO1 Protein strawberry notch homolog 1 1 LYSLLGIDLTAPS(0.026)NNS(0.487)S(0.487)PR 244.1 6.08E-29 0 117890 92766 61814 80709 82519 93038 86888 100180 112870 TRUE FALSE 102310.5378 92156.61404 91707.45716 99035.21201 80877.03335 96617.23206 78461.61513 78757.2866 99526.63718 1.027971412 0.92594924 0.921436308 0.995062375 0.81261696 0.970767573 0.788347897 0.791318674 1 16.60279508 LYSNWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYSNWR 6 0 Q9Y5B9;G3V5A4;G3V401;G3V2X0 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 101.21 0.08557 790030000 1012630 890820 518340 690610 847130 797060 829340 955880 922140 FALSE TRUE 878808.3798 884968.1448 769010.9577 847423.5558 830273.7704 827723.414 748910.7344 751472.5007 813125.6597 1.080778068 1.088353484 0.94574676 1.042180315 1.021089127 1.017952642 0.921027058 0.924177575 1 19.6331188 7.999999992 0.188120422 0.910038863 1.712778997 0.439210387 0.044385482 99.62299242 1.434356884 0.365045396 22.403313 99999998.27 -7.999999992 0.802740134 LYSSGSS(ph)TPTGLAGGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYSSGSSTPTGLAGGSR 17 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 LYSSGS(0.03)S(0.485)T(0.485)PTGLAGGSR 183.31 7.33E-10 62449000 131810 107580 78395 92400 110570 106880 107670 116660 153220 TRUE FALSE 114390.9745 106873.2999 116307.0842 113380.8322 108369.8733 110991.7428 97228.17997 91713.16685 135106.5061 0.846672583 0.791030002 0.860854799 0.839195946 0.802106993 0.821512938 0.719640991 0.678821246 1 17.04373762 2.432546062 22.15410548 0.77095777 0.826714108 0 0.08639797 109.4491485 54394.44329 0.031733542 0.024580746 270.7360337 -2.432546062 0.055756338 LYTDFDEIR ddPTM_MDA-MB-175_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 ;;;; 209.84 1.81E-05 465443000 988217 980818 796668 1033224 1042708 1002082 896340 1091650 1956010 FALSE TRUE 857621.6196 974374.942 1181939.309 1267833.301 1021960.151 1040632.743 809413.0848 858209.1427 1724772.726 0.497237466 0.56492947 0.685272495 0.735072675 0.592518733 0.603344851 0.469286807 0.497578104 1 20.71797484 1.231626127 24.98700822 1.000000725 0.580223663 0.716140289 0.082970663 150.1177581 540869.098 0.221782611 0.022880851 17.04614299 -1.231626127 -0.419777063 LYTDFDEIRQEIENETER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LYTDFDEIRQEIENETER 18 1 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;F8VZ52;B4DDQ3;B4DPZ9;F8VUJ9;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 0 ;;;;; 240.61 5.32E-24 692666000 863684 837036 432171 464336 767603 826164 804486 915515 256171 FALSE TRUE 749545.9711 831537.4554 641170.3411 569770.5857 752329.2021 857947.0637 726467.0715 719739.2418 225886.7562 3.318237792 3.68121385 2.838459199 2.522372694 3.330559147 3.798129107 3.216067572 3.186283489 1 17.78524016 4.233143161 24.85623082 2.932731556 3.499725855 0.109025579 0.747615223 283.9075368 1302642.304 0.19023479 0.41515216 17105.79097 -4.233143161 0.5669943 LYTLQDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LYTLQDK 7 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 147.16 0.0050496 2184640000 2730520 2624510 2111880 2085510 2513590 2518300 3243820 3292600 3872230 FALSE TRUE 2369674.864 2607269.421 3133192.232 2559056.921 2463574.477 2615180.631 2929234.836 2588503.113 3414459.381 0.694011731 0.763596555 0.91762469 0.749476457 0.72151231 0.765913528 0.857891253 0.758100427 1 21.70322574 1.234716315 24.96126594 1.000000319 0.782077865 0.535171547 0.064794603 91.09281391 591382.0331 0.115339457 0.015721186 17.16786601 -1.234716315 -0.217922455 LYTLVLTDPDAPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LYTLVLTDPDAPSR 14 0 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 229.16 6.26E-09 164150000 478010 434040 307470 334630 379860 398060 346510 424990 584500 FALSE TRUE 414839.7674 431188.7627 456163.5204 410612.856 372301.5292 413373.6258 312905.5135 334109.1958 515401.0759 0.804887275 0.836608193 0.88506513 0.796686067 0.722353031 0.802042613 0.607110711 0.64825087 1 18.97533602 3.417810813 3.965487679 0.733904927 0.84203488 0.100519695 0.106661761 0.392166426 12.60431246 0.031702785 0.042607848 2617.042728 -3.417810813 0.108129953 LYTWVEWVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYTWVEWVK 9 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 137 0.0029822 0 249680 219290 127350 168450 210120 191650 242300 252800 234110 FALSE TRUE 216684.1554 217849.4696 188936.886 206699.1471 205939.0231 199022.8995 218801.7833 198740.6873 206433.7825 1.049654532 1.05529951 0.915242087 1.001285471 0.997603302 0.964100435 1.059912678 0.962733352 1 17.65531956 4.356812433 21.36205043 0.987750407 1.052529698 0.362570747 0.036662555 2.885940664 517.3361938 0.008554614 0.022633375 22741.15051 -4.356812433 0.064779291 LYTYEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYTYEPR 7 0 Q8TD06;B5MC62;H7C040 Q8TD06 AGR3 Anterior gradient protein 3 homolog 0 77.282 0.089494 292950000 997600 951920 734370 828180 966620 1022900 1025000 1034200 1008400 FALSE TRUE 865764.6324 945666.7748 1089513.788 1016230.927 947386.1532 1062251.625 925595.6578 813044.3782 889188.1008 0.973657465 1.063517128 1.225290563 1.142875086 1.065450777 1.194630949 1.040944719 0.914367137 1 19.76212912 1.987418467 6.415806524 0.957924565 1.113933683 0.430122147 0.073043155 0.134874486 24.66766837 0.033741741 0.020055627 97.14455584 -1.987418467 0.156009118 LYVELHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LYVELHR 7 0 A0A087WTZ5;Q04323;E9PJ81;E9PRQ7;Q04323-2 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 0 ;; 134.06 0.0032115 475300000 375912 338475 213809 264707 329016 360909 309206 340473 363185 FALSE TRUE 326234.2768 336251.5354 317207.7475 324812.7701 322469.2253 374793.4028 279219.2497 267665.4985 320249.683 1.018687274 1.049966802 0.990501363 1.01424853 1.006930662 1.170316233 0.871879863 0.83580254 1 18.28883762 2.201552132 24.99999973 0.887374279 1.03698191 0.503220373 0.064503221 123.865765 83673.06799 0.025679311 0.017313518 159.0567601 -2.201552132 0.14960763 LYVGSLHFNITEDMLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYVGSLHFNITEDMLR 16 0 Q86U06-3;Q86U06-5;Q86U06-2;Q86U06;Q86U06-4;G3V546;G3V5Z6;H0YJJ3;G3XAP0;Q14498-2;Q14498;G3XAC6;H0Y4X3;A0A0U1RQH7;A0A0U1RQW2;Q14498-3 Q86U06-3;Q14498-2;Q14498-3 RBM23;RBM39 Probable RNA-binding protein 23;RNA-binding protein 39 0 197.88 4.22E-11 499680000 557500 651590 254930 373790 634990 630820 516500 708960 622830 FALSE TRUE 483824.9625 647309.6624 378215.0007 458664.7325 622354.9413 655088.0536 466409.9095 557354.4211 549199.7469 0.880963557 1.178641589 0.68866565 0.835151027 1.133203256 1.192804726 0.849253686 1.014848285 1 19.06697144 3.249361412 24.99959886 1.0287068 0.9012552 0.183055694 0.148318833 435.0462416 1006955.505 0.043778281 0.055938256 1775.666542 -3.249361412 -0.1274516 LYVHEAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LYVHEAVK 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 65.252 0.064752 208910000 236210 301830 203140 224490 268380 271960 336470 358440 386860 FALSE TRUE 204994.25 299847.2589 301379.1835 275463.8856 263039.7631 282422.4772 303839.1912 281790.3954 341125.8515 0.600934374 0.878993068 0.883483858 0.807513955 0.77109302 0.827912854 0.890695296 0.826059925 1 18.37994457 -1.999989803 0.033292845 2.048811478 1.74E-06 0.362490774 0.081720825 3431.471326 11.29415271 508.3084653 236.5425338 0.010000235 1.999989803 -2.048809734 LYVYNTDTDNCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LYVYNTDTDNCR 12 0 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 0 ;;;;; 342.09 1.85E-58 1145690000 1131830 1338010 757080 743358 972388 1035095 933604 1121678 1469810 FALSE TRUE 982255.7978 1329220.524 1123206.42 912148.7954 953039.3812 1074915.774 843063.2278 881815.8886 1296050.736 0.757883754 1.02559297 0.866637693 0.703790963 0.735341106 0.829377851 0.650486284 0.680386858 1 20.30569077 3.877010997 5.390312837 0.752185549 0.90384587 0.175560817 0.116356161 0.3051089 12.10623895 0.02989637 0.053126381 7533.746399 -3.877010997 0.15166032 MAADDVEEYMIERPEPEFQDLNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MAADDVEEYMIERPEPEFQDLNEK 24 1 C9J363;Q9BUL8;C9J6F3;C9J5C3;H7C5M9;C9JSA3;C9JND6 C9J363 PDCD10 Programmed cell death protein 10 0 65.425 0.034798 170270000 32162 29976 21570 28243 34365 28470 35227 39416 41944 FALSE TRUE 27911.71021 29779.08568 32001.32415 34656.00482 33681.20373 29565.25932 31810.69096 30987.19514 36985.4281 0.754667761 0.805157253 0.865241415 0.937017809 0.910661454 0.799375885 0.860087137 0.837821724 1 15.17466935 4.37120036 2.582282447 0.881614158 0.759361575 0.411885174 0.055002013 0.316916514 3.968430523 0.014601331 0.059205032 23507.17063 -4.37120036 -0.122252584 MAEWLLSASWQRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MAEWLLSASWQRR 13 1 G3V4M2;G3V5E8;P54803-3;P54803 G3V4M2 GALC Galactocerebrosidase 0 62.338 0.081222 503640000 1237700 942380 621190 688520 966200 1273700 721660 846660 1031700 FALSE TRUE 1074134.809 936189.4437 921599.5618 844858.9894 946974.5103 1322700.063 651673.5243 665608.3477 909733.6013 1.180713571 1.029080868 1.013043335 0.928688341 1.04093606 1.453942188 0.716334456 0.731651933 1 19.79508461 TAS(ph)EGDGGAAAGAAAAGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TASEGDGGAAAGAAAAGAR 19 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 TAS(1)EGDGGAAAGAAAAGAR;TAS(1)EGDGGAAAGAAAAGAR 353.62 2.92E-70 210810000 320900 354560 358860 460350 657120 662270 692000 719650 855980 TRUE FALSE 278492.2519 352230.872 532405.8963 564879.5035 644044.5976 687747.9554 624889.9465 565758.4478 754787.0195 0.368967993 0.466662599 0.705372353 0.74839589 0.853279907 0.911181483 0.827902349 0.749560383 1 19.52571009 4.2494914 1.171326968 0.851961194 0.298680371 0.874709737 0.067892767 0.257607711 0.520453377 0.022069204 0.143627083 17761.98096 -4.2494914 -0.553280823 down SVT(ph)PDSLGHTPPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVTPDSLGHTPPAR 14 0 P35568 P35568 IRS1 Insulin receptor substrate 1 1 S(0.117)VT(0.883)PDSLGHTPPAR;S(0.112)VT(0.888)PDSLGHTPPAR 213.51 3.46E-09 327530000 435560 348260 146510 168395 231450 214110 183835 243140 181173 TRUE FALSE 377999.6424 345972.2571 217362.726 206631.6585 226844.5978 222346.9502 166006.71 191146.4031 159754.9343 2.36612186 2.165643638 1.360601017 1.29342896 1.419953623 1.391800204 1.039133537 1.196497648 1 17.28550097 4.253794168 2.888082604 1.226370001 2.350309179 0.912977417 0.132659559 0.072045686 1.196626434 0.037882087 0.116346552 17938.83224 -4.253794168 1.123939178 up MAGTAFDFENMKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MAGTAFDFENMKR 13 1 P31150 P31150 GDI1 Rab GDP dissociation inhibitor alpha 0 ; 126.83 0.00029498 997850000 1073900 909900 431720 614720 751580 705300 1016400 1177170 389330 FALSE TRUE 931981.3941 903922.807 640501.236 754301.5714 736625.0284 732433.3474 917829.6844 925441.3562 343303.8509 2.714742033 2.633010974 1.86569779 2.197183543 2.145694045 2.133484216 2.673519921 2.695691743 1 18.38912651 4.363076919 7.894560414 2.192022282 2.693047931 0.183751397 0.473692271 0.418898951 26.73016435 0.117676415 0.313918901 23071.55777 -4.363076919 0.501025649 MALIQLGSVEEAIQALIELHNHDLGENHHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MALIQLGSVEEAIQALIELHNHDLGENHHLR 31 0 O95758-1;O95758-6;O95758;O95758-5;O95758-4;O95758-7 O95758-1 PTBP3 Polypyrimidine tract-binding protein 3 0 ;;; 255.7 6.26E-59 1661670000 1470621 1218712 825824 1229554 1081610 1228641 1287689 1361902 1411030 FALSE TRUE 1276274.709 1210706.201 1225195.249 1508743.028 1060088.077 1275907.614 1162809.119 1070669.856 1244219.641 1.025763191 0.973064691 0.98470978 1.212601842 0.852010403 1.025468151 0.934569011 0.860515154 1 20.24680975 MALIQMGSVEEAVQALIDLHNHDLGENHHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 25 MALIQMGSVEEAVQALIDLHNHDLGENHHLR 31 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ;;;;;;;;;;;;;;;;;;;;;;;; 297.14 7.78E-82 35445719500 5872734.5 5419131.8 3674958.4 4353445.1 5212830.1 5467435.2 5229792.1 5997877.4 5989502 FALSE TRUE 5096637.756 5383533.166 5452180.574 5341961.348 5109104.98 5677770.97 4722607.667 4715277.994 5281429.897 0.965010964 1.019332505 1.032330388 1.011461186 0.967371541 1.075044274 0.894191111 0.892803291 1 22.33249715 2.223005594 24.99991431 0.920007234 1.011006744 0.449880324 0.042752593 190.203675 305691.5767 0.016792822 0.011364857 167.1112138 -2.223005594 0.090999509 MALLMAEMSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MALLMAEMSR 10 0 P18206;P18206-2 P18206 VCL Vinculin 0 113.62 0.0034053 58762000 79865 85754 49348 67703 94035 86758 84214 94637 84254 FALSE TRUE 69310.6379 85190.67633 73212.85786 83076.00093 92163.88748 90095.6364 76046.93924 74399.61402 74293.5881 0.932928933 1.146676026 0.98545325 1.118212258 1.240536227 1.212697336 1.023600302 1.001427121 1 16.18095008 2.026375862 24.67418971 1.004324915 1.109862021 0.203132111 0.091824597 286.6427886 268148.3555 0.038675218 0.026074012 106.2614805 -2.026375862 0.105537106 MALLQEFASRPLGAAPQAEHQGLPVPGS(ph)PGGQK ddPTM_MDA-MB-175_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 187.45 4.10E-20 1476570000 1075030 1118620 859510 1044370 1598950 1302060 1735470 2119130 1309870 TRUE FALSE 932962.0617 1111271.712 1275171.911 1281510.171 1567134.023 1352151.091 1567164.387 1665970.541 1155018.661 0.80774631 0.962124465 1.104027107 1.109514689 1.356804073 1.170674671 1.356830361 1.442375433 1 20.13948473 4.366777719 0.778081235 1.297207635 0.666648021 0.586036844 0.126874331 1.103651592 0.74597675 0.052842863 0.555329727 23268.99997 -4.366777719 -0.630559615 MALPPQEDATAS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 15 MALPPQEDATASPPR 15 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MALPPQEDAT(0.001)AS(0.999)PPR;MALPPQEDAT(0.003)AS(0.997)PPR;MALPPQEDAT(0.01)AS(0.99)PPR;MALPPQEDATAS(1)PPR;MALPPQEDAT(0.002)AS(0.998)PPR;MALPPQEDAT(0.053)AS(0.947)PPR;MALPPQEDAT(0.034)AS(0.966)PPR;MALPPQEDAT(0.052)AS(0.948)PPR;MALPPQEDATAS(1)PPR;MALPPQEDATAS(1)PPR;MALPPQEDATAS(1)PPR;MALPPQEDATAS(1)PPR;MALPPQEDAT(0.002)AS(0.998)PPR;MALPPQEDAT(0.002)AS(0.998)PPR;MALPPQEDAT(0.01)AS(0.99)PPR 204.07 5.34E-09 9760032000 8263284 6665424 4267845 5200458 6724906 6467359 5968373 7327268 7685031 TRUE FALSE 7171270.083 6621638.391 6331789.117 6381301.473 6591093.528 6716162.486 5389561.105 5760388.759 6776515.39 1.058253346 0.977145038 0.934372425 0.941678887 0.97263758 0.991093814 0.79532928 0.850051749 1 22.69211217 2.261677176 24.99902334 0.871578066 0.975062626 0.361870136 0.060302524 229.8957536 248616.2841 0.022672931 0.017551034 182.6741841 -2.261677176 0.10348456 MALPPQEDATAS(ph)PPRQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MALPPQEDATASPPRQK 17 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MALPPQEDAT(0.046)AS(0.954)PPRQK;MALPPQEDAT(0.138)AS(0.862)PPRQK 128.67 2.19E-05 868800000 800660 613800 164440 196735 509450 512820 711270 751910 38738 TRUE FALSE 694850.7524 609767.9074 243963.734 241406.6887 499312.9417 532548.5172 642291.1449 591119.8979 34158.43777 20.34199447 17.85116496 7.142122121 7.06726374 14.6175579 15.59054079 18.80329391 17.30523807 1 15.05995437 8 0.117184388 10 27.72793376 0.072121338 6.021323366 1231.27703 12.93952127 255.178354 3556.473932 100000000 -8 17.72793376 MANSS(ph)PVLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MANSSPVLSK 10 0 Q9NXE8 Q9NXE8 CWC25 Pre-mRNA-splicing factor CWC25 homolog 1 MANS(0.005)S(0.995)PVLSK;MANS(0.209)S(0.791)PVLSK;MANS(0.023)S(0.977)PVLSK;MANS(0.126)S(0.874)PVLSK 203.88 2.07E-07 1882920000 5785640 2836830 1868870 2394040 2785610 2559020 3045960 3608150 3892690 TRUE FALSE 5021053.015 2818194.677 2772661.783 2937643.373 2730181.811 2657467.155 2750563.268 2836575.201 3432500.623 1.462797408 0.821032532 0.807767307 0.855831854 0.795391498 0.774207334 0.801329284 0.826387381 1 21.71082855 4.739031308 24.95162453 0.8295938 1.462797605 0.908283683 0.062648069 10.09228523 534840.1676 0.014905537 0.085241127 54831.64915 -4.739031308 0.633203805 MAPALSGANLTS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 MAPALSGANLTSPR 14 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MAPALSGANLT(0.023)S(0.977)PR;MAPALSGANLT(0.368)S(0.632)PR;MAPALSGANLT(0.005)S(0.995)PR;MAPALSGANLT(0.001)S(0.999)PR;MAPALSGANLTS(1)PR;MAPALSGANLT(0.011)S(0.989)PR 240.87 2.15E-17 3248946000 2806700 2616300 1534760 1841070 2387090 2639510 2318560 2761850 2531040 TRUE FALSE 2435787.484 2599113.353 2276975.069 2259113.082 2339591.579 2741053.658 2093706.408 2171249.87 2231823.335 1.091389021 1.164569486 1.020230873 1.012227557 1.048287086 1.228167846 0.938114758 0.972859203 1 21.0897914 2.184501183 24.99997891 0.969510384 1.088180216 0.436249304 0.066119618 91.18677292 42168.84595 0.027385114 0.018463053 152.9329911 -2.184501183 0.118669832 MAPPVDDLS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MAPPVDDLSPK 11 0 Q92576-2;Q92576;E7EVH3;E7ER40 Q92576-2 PHF3 PHD finger protein 3 1 MAPPVDDLS(1)PK;MAPPVDDLS(1)PK 138.02 6.95E-05 277210000 512240 419730 284130 408270 520000 415570 463430 671240 554320 TRUE FALSE 444546.1861 416972.766 421536.2184 500973.9435 509653.0174 431557.2468 418486.6299 527700.5496 488788.9211 0.909484988 0.853073276 0.862409519 1.024929007 1.042685289 0.882911269 0.856170449 1.079608246 1 18.89885206 7.999992957 0.038160506 1.55755431 2.11E-09 0.199618367 0.076234125 3052.222611 11.48503289 150.8130475 362.1655791 99998378.34 -7.999992957 -1.557554308 MAPTPIPT(ph)RSPSDSSTASTPVAEQIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MAPTPIPTRSPSDSSTASTPVAEQIER 27 1 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 MAPTPIPT(0.587)RS(0.4)PS(0.013)DSSTASTPVAEQIER 186.85 1.68E-17 473680000 259090 100840 59560 70489 103110 101020 102570 120600 61454 TRUE FALSE 224850.6 100177.5754 88363.41522 86494.60481 101058.3127 104906.3048 92622.77719 94810.62851 54188.97813 4.149378856 1.848670687 1.630652916 1.596166006 1.864923758 1.935934361 1.709254915 1.749629386 1 15.72571182 4.739668898 4.309632551 1.673944579 4.336608313 0.905555666 0.252638785 0.058272192 2.564851786 0.060813484 0.477714694 54912.20693 -4.739668898 2.662663734 MAPTPIPTRS(ph)PSDSSTASTPVAEQIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MAPTPIPTRSPSDSSTASTPVAEQIER 27 1 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 MAPTPIPT(0.157)RS(0.839)PS(0.004)DSSTASTPVAEQIER;MAPTPIPT(0.314)RS(0.673)PS(0.013)DSSTASTPVAEQIER;MAPTPIPT(0.143)RS(0.851)PS(0.006)DSSTASTPVAEQIER;MAPTPIPT(0.144)RS(0.831)PS(0.025)DSSTASTPVAEQIER 227.11 7.82E-35 1525500000 1062100 467567 268176 318310 428960 439122 441843 499844 265299 TRUE FALSE 921740.794 464495.5216 397866.8106 390587.1506 420424.5352 456015.3075 398993.1339 392956.2504 233935.6544 3.940146688 1.98556959 1.70075319 1.669634975 1.797180238 1.949319391 1.705567861 1.679762118 1 17.83575224 4.757415445 2.882830285 1.669167771 4.398033104 0.894006068 0.246507109 0.133236254 1.513375574 0.061690087 0.867787566 57202.55731 -4.757415445 2.728865333 MAQALEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MAQALEELR 9 0 Q03252 Q03252 LMNB2 Lamin-B2 0 ;; 115.71 0.0033294 222285000 215610 252942 158799 183163 250825 297915 237230 275249 285329 FALSE TRUE 187116.5922 251280.4073 235594.7276 224752.9586 245834.0732 309375.9828 214223.4711 216389.1433 251597.7307 0.743713354 0.998738767 0.936394485 0.893302805 0.977091775 1.229645363 0.851452319 0.860059996 1 17.94075938 4.745199355 24.05962375 0.959494358 0.743713186 0.30049201 0.106951324 652.9299117 2366191.124 0.027151706 0.250902464 55615.94939 -4.745199355 -0.215781173 MAQYLEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 MAQYLEEER 9 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ;;;; 265.55 4.41E-15 2246830000 1872930 2068750 1189510 1491240 2026200 2102950 1822980 2071010 1966160 FALSE TRUE 1625417.555 2055160.245 1764761.015 1829848.834 1985882.584 2183851.847 1646187.68 1628140.628 1733722.805 0.937530239 1.185403018 1.017902637 1.055444867 1.145444115 1.259631494 0.949510311 0.93910089 1 20.72544182 2.125646809 20.54879674 0.957306405 1.100778597 0.34268167 0.089557611 2.702931206 479.3108628 0.035612701 0.024010091 133.5508968 -2.125646809 0.143472192 MARS(ph)GSATPPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MARSGSATPPAR 12 1 H3BN50;Q15599-3 H3BN50 SLC9A3R2 Na(+)/H(+) exchange regulatory cofactor NHE-RF2 1 MARS(0.5)GS(0.5)ATPPAR 65.179 0.037213 172130000 12789 16096 5491.9 10532 4951.6 0 0 0 5985.9 TRUE FALSE 11098.90125 15990.26432 8147.801209 12923.45157 4853.072848 0 0 0 5278.253721 2.102760086 3.029461098 1.543654708 2.448433185 0.919446678 0 0 0 1 12.36584499 3.088071722 3.180973925 0.196385147 2.291281404 0.807115923 0.469166366 0.097179909 1.97344644 0.14594912 0.166994561 1224.818458 -3.088071722 2.094896257 MASNIFGT(ph)PEENQASWAK ddPTM_MDA-MB-175_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(0.999)PEENQAS(0.001)WAK;MASNIFGT(1)PEENQASWAK;MASNIFGT(1)PEENQASWAK 340.48 2.48E-74 577584000 1932200 2019000 1401165 1840960 2176590 2080840 2424230 2983920 2759960 TRUE FALSE 1676854.874 2005737.056 2078773.081 2258978.105 2133280.117 2160891.261 2189128.548 2345831.929 2433680.673 0.689020089 0.82415786 0.854168381 0.928214671 0.876565336 0.887910762 0.89951347 0.963902929 1 21.21470845 6.03769614 0.464040709 0.948235595 4.49E-34 0.836177649 0.034258485 7.105797376 0.483769976 0.028105336 4.745988664 1090676.964 -6.03769614 -0.948235595 MATEVAADALGEEWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MATEVAADALGEEWK 15 0 P62753;A2A3R5;A2A3R7 P62753 RPS6 40S ribosomal protein S6 0 129.34 0.00015461 34643000 115200 96610 79278 88556 104490 94287 114400 129220 125730 FALSE TRUE 99976.02812 95975.36255 117617.106 108663.9933 102410.8534 97914.2819 103305.5056 101587.3086 110866.3426 0.901770779 0.865685295 1.060891008 0.980135095 0.923732586 0.883174096 0.931802233 0.916304319 1 16.75846193 3.883450553 0.003029597 1.47103821 0.402707054 0.008421743 0.058376425 1174953.728 1917.912594 336127.2551 340188.4878 7646.286254 -3.883450553 -1.068331156 MATGLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MATGLER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 103.75 0.019324 215950000 231820 202250 134660 173270 179710 195500 194870 224920 208420 FALSE TRUE 201184.3996 200921.4064 199782.0264 212613.6018 176134.1226 203021.0115 175971.5374 176822.6083 183780.825 1.094697445 1.09326643 1.087066762 1.156886752 0.958392273 1.104690935 0.957507604 0.962138505 1 17.48762672 2.659783281 0.966201289 0.967141711 1.102223555 0.464879403 0.052687034 0.458271499 0.94406173 0.038443641 0.025648581 456.8601537 -2.659783281 0.135081844 MATHTLITGLEEYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MATHTLITGLEEYVR 15 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 0 ; 265.95 2.95E-25 816860000 656920 622080 426890 473650 599190 634710 574900 718150 669350 FALSE TRUE 570106.3576 617993.5155 633335.4319 581199.4718 587267.2913 659127.7044 519146.2865 564579.2111 590220.2055 0.965921451 1.047055844 1.073049391 0.984716325 0.994996928 1.116748797 0.879580675 0.956556902 1 19.17089379 2.229322975 24.99999411 0.944966297 1.029422036 0.371130819 0.052169205 205.9726644 557422.1447 0.020546785 0.014062552 169.5598312 -2.229322975 0.084455739 MAYLLIEEDIRDLAASDDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MAYLLIEEDIRDLAASDDYR 20 1 H7C1M5;Q9H147 H7C1M5 DNTTIP1 Deoxynucleotidyltransferase terminal-interacting protein 1 0 ; 142.43 1.64E-07 57200000 98679 99472 44569 59903 85865 94677 94817 105880 29097.7 FALSE TRUE 85638.32013 98818.56188 66122.71747 73504.89171 84156.45449 98319.28545 85621.66193 83238.38596 25657.80305 3.337710557 3.851403866 2.577099736 2.864816273 3.279955588 3.831944818 3.337061312 3.244174327 1 14.64711002 1.238318308 6.870466876 0.947123817 3.292798859 0.781795689 0.380390047 0.053799129 13.84835439 0.588179765 0.097390817 17.31084661 -1.238318308 2.345675041 MCDHLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 MCDHLIR 7 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ;;;;;;; 177.65 0.00072716 2392680000 2238769 2358678 1484085 1526553 2298556 2508193 2188060 2360335 2340566 FALSE TRUE 1942910.004 2343183.689 2201793.47 1873180.191 2252819.233 2604684.808 1975862.278 1855595.728 2063866.954 0.941393049 1.135336599 1.06682917 0.907607047 1.091552548 1.262041045 0.957359327 0.899086894 1 20.97691854 2.030390903 24.99896187 0.938101389 1.068125192 0.226890565 0.099917706 260.6643418 214416.3362 0.040958908 0.027614208 107.24842 -2.030390903 0.130023803 MCDLVSDFDGFSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 MCDLVSDFDGFSER 14 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ;;;; 376.77 4.57E-97 2598270000 3012902 2985505 1972828 2202204 2896151 3271524 3041479 3256779 3158752 FALSE TRUE 2614739.367 2965893.021 2926894.22 2702248.077 2838523.261 3397381.645 2746516.835 2560342.155 2785327.937 0.938754583 1.064827226 1.050825714 0.970172324 1.019098406 1.219742063 0.986065877 0.91922467 1 21.40941577 2.010552653 24.99556683 0.953483405 1.045874681 0.184814432 0.075919229 298.7898656 707726.4468 0.030925629 0.020828576 102.4595992 -2.010552653 0.092391276 MCEDLWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MCEDLWR 7 0 Q14376;Q14376-2;Q5QPP9 Q14376 GALE UDP-glucose 4-epimerase 0 ; 94.262 0.033338 436390000 1237320 1151320 769050 889600 1176270 1226820 1171770 1251020 1202370 FALSE TRUE 1073805.027 1143756.903 1140965.152 1091597.277 1152864.528 1274016.559 1058131.926 983499.1084 1060227.188 1.012806537 1.078784732 1.076151569 1.029588081 1.08737499 1.201644868 0.998023761 0.92763053 1 20.01594201 2.013393696 24.99910001 0.959900332 1.080442528 0.485145216 0.052248713 171.2098817 319558.9698 0.021303092 0.014354539 103.1320607 -2.013393696 0.120542196 MCHNVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 MCHNVNR 7 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;;;;; 106.76 0.0076295 791716000 282012 283208 180201 195973 245542 277877 255002 279594 242451 FALSE TRUE 244743.3997 281347.588 267346.8063 240471.6649 240656.1946 288567.108 230271.9453 219804.9989 213788.719 1.144790992 1.316007642 1.250518772 1.124809887 1.125673028 1.349777057 1.077100543 1.028141241 1 17.7058262 2.04780001 9.174725226 1.026933696 1.216046392 0.575468428 0.075546949 0.223292572 40.36438577 0.030955825 0.020815607 111.6349057 -2.04780001 0.189112696 MCINTEWGAFGDDGSLEDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MCINTEWGAFGDDGSLEDIR 20 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 259.53 6.25E-36 198322000 172887 147856 115029 168236 160564 194432 126288 152362 261620 FALSE TRUE 150039.5449 146884.7242 170657.4091 206436.5551 157369.0905 201911.9249 114040.6092 119780.572 230691.5816 0.650390204 0.636714713 0.739764355 0.894859507 0.682162259 0.875246177 0.494342309 0.519223853 1 17.81560583 2.240907576 24.99978111 0.632160793 0.745041457 0.028448128 0.160252695 150.8633425 1607023.159 0.061706484 0.045482773 174.143623 -2.240907576 0.112880664 RRNDS(ph)YTEEEPEWFSAGPTSQSETIELTGFDDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RRNDSYTEEEPEWFSAGPTSQSETIELTGFDDK 33 2 B1AKL4;Q9NRA8;Q9NRA8-3 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 RRNDS(0.493)Y(0.014)T(0.493)EEEPEWFSAGPTSQSETIELTGFDDK;RRNDS(0.256)Y(0.243)T(0.256)EEEPEWFS(0.049)AGPT(0.049)S(0.049)QS(0.049)ET(0.049)IELT(0.002)GFDDK 201.9 2.69E-27 503650000 48915.9 51667.8 58034.2 74494.4 85583.1 81409 101299 131386 100725 TRUE FALSE 42451.53988 51328.39082 86099.73323 91409.4921 83880.16375 84540.85691 91475.03857 103290.1263 88817.40525 0.477964198 0.577909146 0.969401583 1.029184447 0.944411329 0.951850109 1.029922438 1.162949155 1 16.4385548 4.256406477 3.167129455 1.028775294 0.491950331 0.920033143 0.059901132 0.068620314 1.390213579 0.01857032 0.054622599 18047.0606 -4.256406477 -0.536824964 down MCIVLRPS(ph)RVHNSEENTMRALTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MCIVLRPSRVHNSEENTMRALTLK 24 3 F8WF29;C9J131 F8WF29 FAP 1 MCIVLRPS(0.333)RVHNS(0.333)EENT(0.333)MRALT(0.001)LK;MCIVLRPS(0.333)RVHNS(0.333)EENT(0.333)MRALTLK 63.69 0.024181 390790000 303800 283190 165496 287620 275850 252480 240698 318750 341130 TRUE FALSE 263652.0603 281329.7062 245530.4192 352928.517 270361.1247 262193.069 217355.145 250587.793 300802 0.876497032 0.935265411 0.816252615 1.17329179 0.898800954 0.871646694 0.722585438 0.833065581 1 18.19845463 2.792144195 3.861850662 0.839497275 0.948313077 0.117637622 0.112971234 0.423616564 13.07386974 0.038075315 0.037110947 619.6467769 -2.792144195 0.108815802 MCIVLRPSRVHNSEENT(ph)MRALTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MCIVLRPSRVHNSEENTMRALTLK 24 3 F8WF29;C9J131 F8WF29 FAP 1 MCIVLRPS(0.189)RVHNS(0.189)EENT(0.622)MRALTLK;MCIVLRPS(0.218)RVHNS(0.218)EENT(0.565)MRALTLK;MCIVLRPS(0.265)RVHNS(0.265)EENT(0.469)MRALTLK;MCIVLRPS(0.169)RVHNS(0.169)EENT(0.661)MRALTLK 65.155 0.022324 2973185000 506794 485782 323188 486929 439760 450259 398024 519964 514557 TRUE FALSE 439819.8888 482590.8661 479482.7978 597493.6717 431009.6364 467580.7551 359423.6937 408773.745 453726.6576 0.969349897 1.063615853 1.056765764 1.316858204 0.949932364 1.030534017 0.792159085 0.900925123 1 18.7914639 2.703005902 2.192788953 0.900065293 1.091693428 0.326771459 0.110876869 0.332744691 3.163307574 0.04296348 0.038162095 504.6681564 -2.703005902 0.191628135 MCSFLEWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MCSFLEWR 8 0 A0A2R8YGH5;H7C1E4;P61966;P61966-2;F6SFB5;A0A5F9ZI43;H7BZG6;H0Y673;A0A5F9ZHX2;A6NH01;A0A5F9ZHW1;P56377;P56377-2 A0A2R8YGH5 AP1S1;AP1S2 AP-1 complex subunit sigma-1A;AP-1 complex subunit sigma-2 0 ; 130.27 0.0024544 1759950000 1702970 2020430 1242890 1310110 1970250 2073700 1958250 2093570 2206690 FALSE TRUE 1477918.2 2007157.662 1843955.761 1607590.499 1931045.88 2153476.581 1768339.216 1645876.348 1945817.622 0.759535829 1.031524044 0.947650869 0.826177377 0.992408465 1.106720669 0.908789805 0.845853347 1 20.89194506 3.195506929 24.99986966 0.957292752 0.90527347 0.126452857 0.097403943 455.3628933 264412.6936 0.030953679 0.035098442 1568.580922 -3.195506929 -0.052019282 MCTLIDKFDEHDGPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MCTLIDKFDEHDGPVR 16 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1;A0A3B3ITX2;A0A3B3IS23 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 186.68 8.79E-10 1888930000 2448300 2066150 1420860 1666870 2181700 1847420 2307000 2756400 1878680 FALSE TRUE 2124750.952 2052577.325 2107992.648 2045358.31 2138288.438 1918491.443 2083267.495 2166965.31 1656584.591 1.28260939 1.239041662 1.272493213 1.234683892 1.290781316 1.1581005 1.257567834 1.308092157 1 20.65978044 1.231291908 24.99640664 0.999999553 1.255428143 0.792005366 0.04113594 115.2705871 396369.918 0.099784396 0.009974818 17.03302988 -1.231291908 0.25542859 MDADGFLPITLIASFHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MDADGFLPITLIASFHR 17 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 0 ; 128.64 3.63E-05 591550000 448760 459300 185201 398450 527390 508160 429790 510570 747270 FALSE TRUE 389455.229 456282.8281 274764.8231 488924.1624 516895.9708 527709.244 388109.032 401388.5788 658928.5919 0.591043148 0.692461723 0.416987252 0.741998706 0.784449145 0.800859532 0.589000139 0.60915338 1 19.3297626 3.638492267 24.99999997 0.732004141 0.579330797 0.302231185 0.130914376 59.51520582 14856.96913 0.036402238 0.053993242 4350.030147 -3.638492267 -0.152673345 MDAEHPELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MDAEHPELR 9 0 Q12765;Q12765-2;Q12765-3;C9K052 Q12765 SCRN1 Secernin-1 0 ;;; 132.78 0.00029547 3307920000 5815230 4635850 3012980 3820810 4543070 5021090 4617960 5046740 5225670 FALSE TRUE 5046732.622 4605396.796 4470067.206 4688383.308 4452671.795 5214254.581 4170110.95 3967533.925 4607897.246 1.095235495 0.999457356 0.9700883 1.017466983 0.96631317 1.131590898 0.904992175 0.861029166 1 22.13567711 2.18170087 24.99998105 0.90859391 1.022444892 0.395699694 0.061722486 75.42448562 33161.74634 0.024277255 0.016367729 151.9500579 -2.18170087 0.113850982 MDATANDVPSPYEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MDATANDVPSPYEVR 15 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 172.33 2.40E-06 134980000 106060 97594 64510 77529 95320 124970 87191 81706 77352 FALSE TRUE 92043.90228 96952.89859 95707.25177 95133.14441 93423.31849 129777.6768 78735.23024 64233.80774 68207.53468 1.349468247 1.421439714 1.403177116 1.394760049 1.369692057 1.902688279 1.154347985 0.941740645 1 16.0576435 2.011201926 24.99735295 0.991109481 1.46540762 0.644116103 0.158860874 123.1157695 274734.615 0.063796098 0.042970614 102.6128917 -2.011201926 0.474298139 MDDPDYWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MDDPDYWR 8 0 Q14137;Q14137-2;A0A075B729 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 89.298 0.032581 128260000 479410 400890 279000 350750 405890 374540 378090 424920 606860 FALSE TRUE 416054.7538 398256.5272 413925.3332 430393.1484 397813.5831 388948.7962 341422.89 334054.1647 535117.7021 0.777501384 0.744240988 0.773522034 0.804296226 0.743413237 0.726847186 0.638033256 0.624262968 1 19.02949673 2.952737105 3.749765228 0.718409965 0.772859487 0 0.103602866 0.787390851 22.74145079 0.034052335 0.035587212 896.8857105 -2.952737105 0.054449522 MDDPTVNWSNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 MDDPTVNWSNER 12 0 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ;;;;;; 230.95 1.07E-11 1535200000 1296794 1117151 834122 1002636 1233942 1272402 1217138 1288211 1472992 FALSE TRUE 1125419.387 1109812.362 1237506.189 1230299.828 1209388.968 1321352.128 1099100.144 1012737.103 1298856.564 0.866469338 0.854453365 0.952765859 0.947217624 0.931118187 1.017319514 0.846205944 0.779714351 1 20.30881069 MDDSALQLNHTANEFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MDDSALQLNHTANEFAR 17 0 Q96RF0-3;Q96RF0-2;Q96RF0 Q96RF0-3 SNX18 Sorting nexin-18 0 157.47 2.47E-08 128310000 76018 77928 46326 62819 73860 74055 71223 82393 106700 FALSE TRUE 65972.02869 77416.08584 68729.40855 77083.01408 72390.3305 76903.94377 64315.80442 64773.89813 94086.04755 0.701188225 0.82282217 0.730495226 0.819282094 0.769405585 0.817378833 0.683584932 0.688453812 1 16.52169317 2.619759874 0.009979276 1.549860594 1.09E-06 0.052272751 0.09155804 18985.31223 181.4724332 14212.87372 13966.69883 416.6389561 -2.619759874 -1.549859506 MDEFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MDEFSR 6 0 O00422;O00422-2;H7BZW6;U3KQ12;U3KPY7 O00422 SAP18 Histone deacetylase complex subunit SAP18 0 ;;; 189.97 2.29E-05 800680000 1743370 1494420 908770 1173540 1447400 1561840 1353300 1581230 1553800 FALSE TRUE 1512979.237 1484603.057 1348254.212 1440010.193 1418599.572 1621924.995 1222057.174 1243096.27 1370111.534 1.104274506 1.083563651 0.984047049 1.051016766 1.035389847 1.183790484 0.891939922 0.907295675 1 20.38586191 2.215351939 24.99382188 0.925992949 1.067284772 0.562823185 0.058122061 166.5833639 179395.0561 0.023607887 0.015927497 164.1919796 -2.215351939 0.141291823 MDEISDHAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MDEISDHAK 9 0 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ;;; 150.27 8.56E-05 699800000 1021080 1042817 416972 805347 1064710 903710 1094080 1359520 1595440 FALSE TRUE 886141.6909 1035966.666 618621.0539 988213.3453 1043524.354 938476.3085 987976.29 1068797.228 1406828.901 0.629885902 0.736384265 0.439727286 0.702440321 0.741756409 0.667086316 0.702271818 0.759720835 1 20.42401545 -0.749679808 0.808673039 9.999999904 0.645286923 0.629440194 0.083585996 36.8986661 1.166461781 579.2925586 0.030860114 0.177959096 0.749679808 -9.35471298 MDELQLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 MDELQLFR 8 0 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;; 183.74 0.00051576 2196141000 2276440 1559856 820393 1058158 1384146 1499685 1362208 1664348 1578432 FALSE TRUE 1975602.686 1549609.203 1217137.799 1298428.947 1356604.203 1557378.852 1230101.278 1308440.132 1391831.567 1.419426555 1.11335972 0.874486416 0.932892296 0.974689923 1.11894204 0.883800387 0.94008511 1 20.4085532 4.640143646 2.846425498 0.96039832 1.454778298 0.814102658 0.069452056 0.135677275 1.702005893 0.017758425 0.137207222 43666.02368 -4.640143646 0.494379978 MDEQEDLAKDMLEQLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MDEQEDLAKDMLEQLLK 17 1 A0A0J9YYF7;Q86T65-4;Q86T65 A0A0J9YYF7 DAAM2 Disheveled-associated activator of morphogenesis 2 0 71.692 0.031457 148350000 224590 249010 128470 180140 228370 279190 219970 244530 254090 FALSE TRUE 194909.8625 247374.2369 190598.5217 221043.5403 223825.8838 289930.62 198637.3433 192239.1624 224051.7697 0.869932261 1.1040941 0.850689651 0.986573508 0.998991814 1.294034055 0.886568955 0.858012247 1 17.7734726 MDGLEEAHGMS(ph)AAMGPEPVVQS(ph)VR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MDGLEEAHGMSAAMGPEPVVQSVR 24 0 G5E9D8;A0A096LP62;C9J2H1;Q86UX2-4;Q86UX2-2;Q86UX2-3;Q86UX2 G5E9D8 ITIH5 Inter-alpha-trypsin inhibitor heavy chain H5 2 MDGLEEAHGMS(1)AAMGPEPVVQS(1)VR 48.088 0.055892 229780000 3614 3546.1 0 0 0 2991.1 4386.6 0 0 TRUE FALSE 3136.400743 3522.805436 0 0 0 3106.169552 3961.188207 0 0 0 MDHRS(ph)RLRGT(ph)GLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MDHRSRLRGTGLNR 14 3 A6NJJ0 A6NJJ0 PRDX4 2 MDHRS(1)RLRGT(1)GLNR;MDHRS(1)RLRGT(1)GLNR;MDHRS(1)RLRGT(1)GLNR;MDHRS(1)RLRGT(1)GLNR 69.349 0.016515 92557000 142267.4 152059.2 98979.6 120313.1 146279.6 191654.9 106647.2 129379.7 208563 TRUE FALSE 123466.4026 151060.3131 146846.4656 147632.0282 143368.9222 199027.988 96304.57096 101712.858 183906.9197 0.671352676 0.821395483 0.798482547 0.802754069 0.779573288 1.082221312 0.523659311 0.553067052 1 17.48861624 2.202509215 24.99999102 0.6562232 0.821343689 0.116997243 0.163151146 294.161241 203985.3008 0.065380441 0.044081026 159.4076703 -2.202509215 0.165120489 MDIDAPDVDVHGPDWHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MDIDAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 164.53 1.76E-11 568320000 881470 581090 389410 644410 663430 594630 616560 869790 770130 FALSE TRUE 764981.5061 577272.7815 577729.9785 790733.1397 650229.041 617505.8009 556766.1061 683792.1772 679086.1087 1.126486754 0.850073023 0.850746277 1.164407767 0.957506026 0.909318852 0.819875564 1.006930003 1 19.373235 3.004588419 24.9864913 0.934574231 0.98736713 0.065230018 0.111316413 479.2833908 2609929.178 0.034200071 0.038641163 1010.621234 -3.004588419 0.052792898 MDIDAPDVEVQGPDWHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MDIDAPDVEVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 166.57 2.54E-11 436450000 1161420 749760 515500 833690 820930 746200 700330 1103830 1001930 FALSE TRUE 1007935.404 744834.7772 764797.5242 1022992.057 804595.0991 774906.7969 632412.1044 867784.5445 883482.9768 1.140865677 0.84306636 0.865661868 1.157908057 0.910708095 0.877104389 0.715816966 0.9822312 1 19.75284281 3.023848973 24.9996619 0.891254 0.987490636 0.145552425 0.124430939 511.4727266 536146.9052 0.03792469 0.043000519 1056.450062 -3.023848973 0.096236637 MDIDVPDVEVQGPDWHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MDIDVPDVEVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 245.66 3.15E-24 241270000 564430 354790 240980 378170 406320 375090 342180 550110 465710 FALSE TRUE 489839.1454 352459.3611 357518.734 464039.2785 398235.027 389519.955 308995.4363 432473.2575 410654.2943 1.192826064 0.858287289 0.870607562 1.129999819 0.969757366 0.948534961 0.752446621 1.053132193 1 18.64756486 2.885258578 4.795655871 0.939673534 0.997710197 0.064894121 0.126074381 0.870626384 30.75861319 0.041147071 0.041448201 767.8185112 -2.885258578 0.058036663 MDKEETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MDKEETK 7 1 O43852;O43852-3;O43852-15;H0Y875;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 73.985 0.043238 175420000 264530 180610 217630 257130 107220 162100 267660 252910 427510 FALSE TRUE 229571.6903 179423.561 322876.5959 315515.2965 105086.5318 168336.0919 241702.3744 198827.1646 376970.2548 0.608991525 0.475962118 0.856504172 0.836976638 0.278766111 0.446550065 0.641170945 0.527434624 1 18.52409117 1.233874771 24.98801152 1.000000633 0.58327299 0.363676418 0.172911544 171.1984429 912829.0746 0.343579454 0.043575407 17.1346316 -1.233874771 -0.416727644 MDKEETKDWILPSDYDHAEAEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MDKEETKDWILPSDYDHAEAEAR 23 2 O43852;O43852-3;O43852-15;H0Y875;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 205.38 9.36E-25 522660000 543680 427100 260430 317350 377400 328580 497200 528010 187950 FALSE TRUE 471831.3105 424294.352 386374.8191 389409.1679 369890.4784 341220.6852 448981.6205 415099.1705 165730.7651 2.846974792 2.560142359 2.331340345 2.34964925 2.231875766 2.058885597 2.709102442 2.504659712 1 17.33848191 1.237039192 24.99961417 0.99999823 2.441575932 0.800525512 0.227299329 17.82444631 292785.9384 0.354273704 0.057658823 17.25993645 -1.237039192 1.441577701 MDMMSLNSQLLDAIQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 MDMMSLNSQLLDAIQQK 17 0 H0YHW1;H0YHP2;Q6ZP65-2;Q6ZP65 H0YHW1 CCDC64 Bicaudal D-related protein 1 0 ;;;;;; 73.156 0.02038 26522140000 11320940 13213440 10089380 12559590 11408870 13592100 11648290 11581190 24715770 FALSE TRUE 9824849.095 13126640.04 14968637.91 15411436.87 11181855.81 14114996.88 10518640.63 9104642.643 21793899.83 0.450807298 0.602307992 0.686826958 0.707144522 0.513072736 0.647658152 0.482641506 0.417761058 1 24.37742104 1.226495931 24.99803375 1.000000991 0.563508595 0.659443695 0.098574561 389.9563512 807938.5498 0.434156654 0.026302131 16.84596642 -1.226495931 -0.436492396 MDPKELGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 MDPKELGK 8 1 A0A3B3IU97;A0A2R8Y5X9;Q76EJ3 A0A3B3IU97 SLC35D2 UDP-N-acetylglucosamine/UDP-glucose/GDP-mannose transporter 0 ;;;; 72.547 0.041835 25749200000 21827200 22300800 8232200 13679400 27132900 32829100 18152300 18843200 18545000 FALSE TRUE 18942680.22 22154304.58 12213319.46 16785516.85 26593008.37 34092056.72 16391892.74 14813728.32 16352631.23 1.158387293 1.354785311 0.746871821 1.026471925 1.626221983 2.084805573 1.002400929 0.905892643 1 23.96301946 MDPVNNINVDKDKPYLYCFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MDPVNNINVDKDKPYLYCFR 20 2 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 174.82 1.60E-12 1937840000 1902780 1595010 1334140 1288650 1430530 1175320 2058150 2308880 1503450 FALSE TRUE 1651322.802 1584532.274 1979334.566 1581257.678 1402065.252 1220535.321 1858550.93 1815143.98 1325713.854 1.245610278 1.195229476 1.493033026 1.192759413 1.057592668 0.920662719 1.40192465 1.369182327 1 20.33833798 3.514391374 24.92129753 1.179315597 1.306886708 0.151612356 0.166782833 1359.30214 908916.8741 0.049792695 0.073831007 3268.822763 -3.514391374 0.127571111 MDQVNWQQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MDQVNWQQER 10 0 Q9Y450;Q9Y450-4;J3QT46;B7Z524;H0YDX7;H0YES5 Q9Y450 HBS1L HBS1-like protein 0 129.89 0.00067737 107370000 39432 40706 31144 37487 45264 45562 49934 49952 47237 FALSE TRUE 34220.96129 40438.59961 46205.34257 45998.9963 44363.33496 47314.79962 45091.40837 39270.15353 41652.69567 0.821578549 0.970851921 1.109300174 1.104346203 1.065077163 1.135936075 1.082556786 0.942799809 1 15.34612225 4.610115584 2.992715347 1.057063817 0.811766123 0.648846221 0.056672175 0.223177543 3.21558493 0.016595504 0.109743717 40748.87136 -4.610115584 -0.245297694 MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(ph)PTMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFSPTMGR 38 2 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.996)PT(0.004)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.99)PT(0.009)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.997)PT(0.003)MGR;MDRDPLGGLADMFGQMPGS(0.326)GIGT(0.218)GPGVIQDRFS(0.449)PT(0.007)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.999)PT(0.001)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.999)PT(0.001)MGR;MDRDPLGGLADMFGQMPGS(0.044)GIGT(0.088)GPGVIQDRFS(0.851)PT(0.017)MGR 393.61 6.21E-180 8524892000 2630248 2607739 1257918 1285566 2344218 2404573 2127325 2584085 1215001 TRUE FALSE 2282654.063 2590608.591 1866251.352 1577473.409 2297572.648 2497078.479 1921017.349 2031498.532 1071364.966 2.130603609 2.418044899 1.741938006 1.472395924 2.144528449 2.330744946 1.793055971 1.896177864 1 20.03101859 1.003082054 1.899447502 5.61E-18 2.009742619 0.551743274 0.281663549 1.475091739 2.912940819 6.645955748 0.080521749 10.07121932 -1.003082054 2.009742619 MDRT(ph)PEKDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MDRTPEKDK 9 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 MDRT(1)PEKDK 117.79 0.0017591 276860000 944160 604440 601740 571390 485770 410990 855380 965660 924240 TRUE FALSE 819386.8638 600469.3938 892743.4767 701132.8326 476104.1274 426801.0512 772425.3793 759161.1238 814977.4001 1.005410535 0.736792694 1.095421145 0.860309541 0.584193043 0.523696794 0.947787484 0.931511872 1 19.63640053 3.48163603 24.99194375 0.803646731 0.933783051 0.130119179 0.173933294 488.9274443 2706508.301 0.053942003 0.071492249 3031.349633 -3.48163603 0.13013632 MDRT(ph)PPPPTLS(ph)PAAITVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 MDRTPPPPTLSPAAITVGR 19 1 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;H7C4H9 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 2 MDRT(1)PPPPT(0.002)LS(0.998)PAAITVGR;MDRT(1)PPPPT(0.006)LS(0.994)PAAITVGR;MDRT(1)PPPPT(0.021)LS(0.979)PAAITVGR;MDRT(1)PPPPT(0.004)LS(0.996)PAAITVGR;MDRT(1)PPPPT(0.098)LS(0.902)PAAITVGR;MDRT(1)PPPPT(0.003)LS(0.997)PAAIT(0.001)VGR;MDRT(1)PPPPT(0.018)LS(0.982)PAAITVGR;MDRT(1)PPPPTLS(1)PAAITVGR;MDRT(1)PPPPT(0.021)LS(0.979)PAAITVGR;MDRT(1)PPPPT(0.014)LS(0.986)PAAITVGR 173.4 1.49E-11 6895430000 5442360 4963720 3060150 3566640 5062560 5168920 4757500 5660910 4892210 TRUE FALSE 4723138.337 4931112.996 4540048.776 4376500.125 4961824.961 5367771.697 4296118.382 4450368.45 4313858.507 1.09487558 1.143086401 1.0524334 1.014521018 1.150205773 1.244308706 0.995887643 1.031644511 1 22.04054743 MDRT(ph)PPPPTLSPAAITVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 MDRTPPPPTLSPAAITVGR 19 1 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;H7C4H9 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 MDRT(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR 139.47 2.99E-07 6221720000 2007236 1802986 1045192 1335063 1813479 1737878 1668223 2032332 1803074 TRUE FALSE 1741974.677 1791142.066 1550650.347 1638209.459 1777394.316 1804735.291 1506438.99 1597733.617 1589916.646 1.095638996 1.126563503 0.97530292 1.030374431 1.117916666 1.135113149 0.947495577 1.004916592 1 20.6005197 2.231227839 24.99951801 0.986939648 1.076949389 0.450084199 0.049914406 172.292092 587386.6008 0.021274243 0.014669277 170.3051728 -2.231227839 0.090009741 MDS(ph)FDEDLARPSGLLAQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 MDSFDEDLARPSGLLAQER 19 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER 301.9 3.24E-50 1374074000 1234143 629570 424881 524474 724599 592282 866730 822647 638932 TRUE FALSE 1071047.876 625434.3132 630354.8727 643563.8378 710180.8976 615067.4718 782674.658 646730.3409 563398.1868 1.901049561 1.110110625 1.11884434 1.142289508 1.260531031 1.091710066 1.389203367 1.147909873 1 19.1037954 4.741271541 24.95189572 1.167148463 1.90104983 0.83317466 0.104473793 95.14752695 875708.3186 0.024845281 0.166015956 55115.21944 -4.741271541 0.733901367 MDYEDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MDYEDDR 7 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;; 128.57 0.0087129 497140000 1267610 1081450 897540 1126640 1187560 1153050 1051850 1241650 2765220 FALSE TRUE 1100092.127 1074345.884 1331593.346 1382460.832 1163929.879 1197408.58 949841.7489 976132.81 2438318.842 0.451168284 0.44060927 0.546111248 0.566972952 0.477349336 0.491079575 0.389547803 0.400330258 1 21.21745536 1.234069271 24.99999465 1.000000792 0.46863891 0.898169825 0.056039095 45.97424543 255871.7509 0.121192623 0.015661635 17.1423071 -1.234069271 -0.531361882 MDYEDDRLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 MDYEDDRLR 9 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;;; 145.89 8.76E-05 7591620000 5358630 4665366 2685310 3020484 4613265 4520780 4423218 4956420 3299769 FALSE TRUE 4650473.468 4634718.904 3983934.898 3706331.057 4521470.052 4694697.332 3994254.999 3896528.154 2909674.068 1.598279862 1.592865316 1.369203149 1.273795955 1.553943826 1.613478769 1.372749973 1.339163103 1 21.47242613 1.028159189 1.348327513 0.559138949 1.487144577 0.65449937 0.111813374 1.484977958 1.594392749 2.188513043 0.03533853 10.66987149 -1.028159189 0.928005628 MDYYDSEHHEDFEFISGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MDYYDSEHHEDFEFISGTR 19 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ; 178.06 2.24E-14 123210000 147349 126075 59575 92313 137190 124364 111572 144223 144860 FALSE TRUE 127876.4563 125246.805 88385.66927 113274.0776 134460.1874 129148.3636 100751.7646 113382.0338 127734.8158 1.001108864 0.980522062 0.691946582 0.886790941 1.052651045 1.011066268 0.78875727 0.8876361 1 16.96279228 4.448303655 24.99911351 0.899391606 0.995963129 0.107045681 0.106290261 403.9384426 350414.1606 0.027417911 0.072543342 28073.95858 -4.448303655 0.096571523 MEANKENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 MEANKENR 8 1 P16949;P16949-2 P16949 STMN1 Stathmin 0 ;;;;;;;; 116.52 0.0020575 2500379000 6375863 4093675 2149717 2697549 2771054 3244684 4424453 5102369 1715649 FALSE TRUE 5533276.55 4066783.379 3189327.332 3310068.73 2715915.447 3369509.093 3995370.229 4011267.096 1512826.93 3.65757407 2.68820134 2.10819048 2.188002253 1.795258528 2.227293173 2.640996237 2.651504291 1 20.52881552 4.66276777 2.183233856 2.163681811 3.917251103 0.532632396 0.468437357 0.452729442 2.802985601 0.12287963 1.449534317 46001.05268 -4.66276777 1.753569292 MECCDVPAETLYDVLHDIEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 18 MECCDVPAETLYDVLHDIEYR 21 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;F5GWK5;F5GY07 Q9Y365 STARD10 PCTP-like protein 0 ;;;;;;;;;;;;;;;;; 289.14 1.12E-54 5804105300 1976907 1689521 1060284.9 1176291 1534067 1658399 1579903 1744923 1773149 FALSE TRUE 1715653.731 1678422.425 1573042.224 1443385.85 1503542.068 1722198.683 1426684.25 1371784.795 1563529.345 1.097295511 1.073483162 1.006084234 0.923158785 0.961633418 1.101481522 0.912476798 0.877364278 1 20.57637487 7.999999997 0.360678291 0.934039984 3.197243222 0.36519379 0.062302959 85.6035895 1.287334546 0.081500363 131.665663 99999999.31 -7.999999997 2.263203238 MEDGEFWMSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MEDGEFWMSFR 11 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;;; 222.28 1.81E-11 354762000 563660 366643 244487 305748 346711 395325 340952 408699 424241 FALSE TRUE 489170.9029 364234.498 362721.731 375172.7565 339812.1294 410533.4086 307886.5275 321301.8993 374087.7123 1.307636917 0.973660684 0.969616801 1.002900507 0.908375545 1.097425537 0.823032988 0.858894555 1 18.51301705 MEDIS(ph)PVQTDALDSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MEDISPVQTDALDSVR 16 0 Q8IWI9-3;Q8IWI9 Q8IWI9-3 MGA MAX gene-associated protein 1 MEDIS(0.954)PVQT(0.046)DALDSVR 85.636 0.0052035 0 12742 9117.2 5883.1 10573 11166 8769.9 9345.3 12655 15904 TRUE FALSE 11058.11242 9057.308513 8728.186838 12973.76125 10943.81845 9107.283728 8438.994244 9948.826731 14023.84724 0.788522025 0.645850483 0.622381768 0.925121404 0.780372052 0.649414071 0.60176028 0.70942207 1 13.77559457 1.238336659 23.87437326 1.000000518 0.7112014 0.459707096 0.096886357 2.918544638 309835.462 0.138089721 0.024464174 17.31157808 -1.238336659 -0.288799118 MEDQFAALHENPDIIIATPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MEDQFAALHENPDIIIATPGR 21 0 Q8TDD1-2;Q8TDD1;F8VRX4 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 0 72.676 0.015439 82191000 44696 34055 26546 26319 117460 66000 37199 52684 34837 FALSE TRUE 38789.31035 33831.29046 39383.73439 32295.13121 115122.7758 68539.06271 33591.44671 41417.93659 30718.60955 1.262730017 1.101328835 1.282080634 1.051321388 3.747655819 2.231190269 1.093521068 1.34830115 1 14.90682529 MEDSVGCLETAEEVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 MEDSVGCLETAEEVKR 16 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;; 309.88 2.01E-57 2016920000 1260570 1085344 834439 910356 982936 922308 1241583 1408487 1368420 FALSE TRUE 1093982.481 1078214.304 1237976.491 1117066.244 963377.4967 957789.7856 1121174.472 1107293.016 1206646.947 0.906630132 0.893562369 1.025964136 0.925760635 0.798392189 0.793761413 0.9291653 0.917661143 1 20.20257219 1.175900862 1.891741038 1.047086966 0.894919778 0.196816252 0.065770074 1.922287499 5.723796865 0.554840553 0.019696697 14.99342537 -1.175900862 -0.152167188 MEDTLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MEDTLKR 7 1 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 79.469 0.052177 364070000 708030 501300 323410 409970 500710 455540 532480 636030 603010 FALSE TRUE 614462.0416 498006.9273 479812.1577 503059.9545 490746.8506 473064.9186 480840.1716 500019.9341 531722.8448 1.155605872 0.936591181 0.90237266 0.946094304 0.922937307 0.889683269 0.904306024 0.940377001 1 19.02031493 4.737676679 5.553573688 0.927448235 1.16355627 0.84324647 0.030534898 0.053471585 6.588956794 0.00753526 0.048087668 54660.88755 -4.737676679 0.236108034 MEEADALIESLCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MEEADALIESLCR 13 0 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;; 254.53 1.91E-23 111594000 286818 270915 190966 198663 255353 259318 250121 276559 268695 FALSE TRUE 248914.2746 269135.3415 283317.7963 243772.4705 250271.9749 269294.1313 225864.3039 217419.01 236930.1832 1.050580687 1.135926786 1.195786001 1.028878918 1.056311068 1.136596982 0.953294768 0.917650116 1 17.85410247 2.229257805 24.99947648 0.94863389 1.101324732 0.623274567 0.052529514 120.4517802 323687.3998 0.02164301 0.014815218 169.5343887 -2.229257805 0.152690841 MEEDPDDVPHGHITSLAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MEEDPDDVPHGHITSLAVK 19 0 P41227-2;P41227;F8W808;A8MWP7 P41227-2 NAA10 N-alpha-acetyltransferase 10 0 107.98 0.00016418 594840000 661850 534750 257610 440240 618740 520530 611160 756760 696350 FALSE TRUE 574384.8456 531237.192 382191.0577 540203.2206 606428.2845 540555.1259 551889.7973 594932.7631 614028.2963 0.935437095 0.865167282 0.622432321 0.879769261 0.987622701 0.880342371 0.898801897 0.968901216 1 19.22794562 3.48076441 24.85940926 0.942054325 0.803039916 0.356474895 0.085532318 152.7752484 1042480.514 0.024659218 0.032556262 3025.271876 -3.48076441 -0.139014409 MEEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 108.24 0.07115 154700000 312110 274200 182520 203170 195130 288150 279530 299610 307470 FALSE TRUE 270863.8727 272398.7621 270787.2825 249302.8538 191247.2948 299235.317 252421.2236 235540.7331 271121.2469 0.999050705 1.00471197 0.99876821 0.919525329 0.705393978 1.103695562 0.931027083 0.868765306 1 18.04857865 3.736065822 7.001227256 0.915002041 1.00148811 0.121975884 0.099548575 0.267635421 91.14695673 0.026581351 0.042535401 5445.851842 -3.736065822 0.086486069 MEEEGTEDNGLEDDS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MEEEGTEDNGLEDDSR 16 0 Q14151;K7ERX3 Q14151 SAFB2 Scaffold attachment factor B2 1 MEEEGTEDNGLEDDS(1)R;MEEEGTEDNGLEDDS(1)R;MEEEGTEDNGLEDDS(1)R 327.71 1.95E-71 1102150000 1034340 645230 763740 972870 759130 866200 917200 808380 2214840 TRUE FALSE 897649.3483 640991.4416 1133087.219 1193775.003 744024.7982 899523.2745 828250.0852 635514.2278 1953004.138 0.459624908 0.328207928 0.580176558 0.611250626 0.380964271 0.460584418 0.424090287 0.325403421 1 20.89726358 1.231062889 24.99965385 1.000000985 0.443635357 0.775467879 0.093626542 133.7307003 445859.8158 0.246042825 0.024042844 17.0240501 -1.231062889 -0.556365628 MEEETKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MEEETKR 7 1 F5GWE5;Q00169 F5GWE5 PITPNA Phosphatidylinositol transfer protein alpha isoform 0 ; 101.99 0.013952 324420000 452070 365280 288000 335360 286100 367820 439170 482060 473200 FALSE TRUE 392327.8041 362880.4516 427277.7633 411508.6137 280407.1697 381970.2734 396579.361 378975.2204 417258.8351 0.940250442 0.869677095 1.024011303 0.986219054 0.672022127 0.915427647 0.950439698 0.908249721 1 18.67058307 -0.500429053 1.30075317 9.521442277 0.904484053 0.084361322 0.094136624 366.1643148 8.666794354 9102.883193 0.028190492 0.315915509 0.500429053 -8.616958224 MEEIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MEEIGR 6 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144;P12814-3;P12814;P12814-2;P12814-4;H9KV75;H0YJ11;H0YJW3 O43707;P12814-3 ACTN4;ACTN1 Alpha-actinin-4;Alpha-actinin-1 0 ; 138.53 0.028531 1102290000 1847020 1580750 1150740 1639210 1315390 1581380 1400060 1642750 3416800 FALSE TRUE 1602931.627 1570365.949 1707241.713 2011417.684 1289216.313 1642216.712 1264282.397 1291460.696 3012869.796 0.532028178 0.521219321 0.566649682 0.667608566 0.427903096 0.545067269 0.419627293 0.428648028 1 21.5227069 1.232719246 24.99910779 1.00000079 0.51022234 0.803515328 0.075574406 88.12162714 377091.9523 0.172187207 0.019691071 17.08910217 -1.232719246 -0.48977845 MEELHNQEMQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MEELHNQEMQK 11 0 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;; 182.35 5.83E-06 1508420000 2398560 1761740 1226360 1618640 1731370 1572360 1882460 2207290 3169630 FALSE TRUE 2081584.219 1750167.014 1819431.798 1986176.951 1696919.124 1632849.707 1699899.319 1735278.211 2794919.952 0.744774181 0.626195757 0.650978142 0.710638224 0.607144088 0.584220563 0.608210377 0.620868662 1 21.41437553 1.23670632 24.99807615 1.000000453 0.640058898 0.837342215 0.049263531 18.634931 251148.9331 0.076275616 0.012144322 17.24671235 -1.23670632 -0.359941555 MEELHNQEVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 MEELHNQEVQK 11 0 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;;;; 158.31 3.00E-05 2878449000 6298620 4751540 3636529 4603460 4902220 4078090 5343570 6379710 8707640 FALSE TRUE 5466241.408 4720326.821 5395166.588 5648745.952 4804675.413 4234976.761 4825351.404 5015458.663 7678232.719 0.711914005 0.614767355 0.702657341 0.735683087 0.625752773 0.551556187 0.628445579 0.653204826 1 22.87234286 1.238682681 9.28702927 1.002120392 0.650633956 0.805049756 0.053654699 0.035118841 47.39421374 0.077973134 0.01378664 17.32537649 -1.238682681 -0.351486436 MEGMDDDPEDR ddPTM_MDA-MB-175_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 ; 116.3 0.00099855 378440000 590130 569700 394530 437280 552620 597000 587150 630500 608700 FALSE TRUE 512142.8253 565957.6032 585326.0276 536571.1074 541623.9432 619966.9763 530208.2834 495672.4816 536740.1794 0.954172698 1.054434948 1.090520237 0.999685002 1.009098935 1.155059748 0.987830432 0.92348682 1 19.03386436 2.010293746 24.9986338 0.956092294 1.045231004 0.278676062 0.056628186 222.8495684 541194.1718 0.022475695 0.015134543 102.3985356 -2.010293746 0.08913871 MEGMDDDPEDRMS(ph)YLTAMGADYLSCDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.976)Y(0.022)LT(0.002)AMGADYLSCDSR;MEGMDDDPEDRMS(0.8)Y(0.183)LT(0.015)AMGADYLS(0.001)CDS(0.001)R;MEGMDDDPEDRMS(0.982)Y(0.006)LT(0.013)AMGADYLSCDSR 110.31 0.00039842 197571000 152389 173823 108011 112576 154254 153005 151085 158327 175908 TRUE FALSE 132250.4075 172681.1453 160245.4809 138138.1014 151184.6472 158891.2014 136432.8 124470.0032 155112.3566 0.852610394 1.11326492 1.033092942 0.890568001 0.974678294 1.024361984 0.879574026 0.802450597 1 17.24295409 2.222428451 22.73172148 0.874332094 0.985333328 0.171333546 0.086837611 110.1911304 155265.8048 0.034480263 0.023357994 166.8892839 -2.222428451 0.111001234 MEIATKDPLNPIKQDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MEIATKDPLNPIKQDVK 17 2 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 151.95 1.30E-07 1516580000 4576600 3351300 2183600 2170500 2656700 2055790 4820300 5549400 878080 FALSE TRUE 3971790.714 3329285.09 3239596.264 2663345.199 2603836.868 2134877.572 4352828.048 4362703.995 774274.3827 5.129694076 4.29987762 4.184041647 3.439795063 3.36293816 2.757262308 5.621815916 5.634571016 1 19.56248539 4.71342321 1.791222431 3.927109709 5.477691766 0.089471737 1.346842126 2.638648741 8.942084018 0.375823098 6.825322153 51691.98502 -4.71342321 1.550582057 MEISMPPPQIYVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MEISMPPPQIYVEK 14 0 P56597 P56597 NME5 Nucleoside diphosphate kinase homolog 5 0 63.76 0.06652 374850000 788230 804990 343390 557930 760220 840370 577480 637370 704250 FALSE TRUE 684063.4084 799701.9677 509454.5526 684616.5339 745093.1093 872699.5777 521476.0785 501073.3855 620994.3673 1.101561374 1.287776524 0.820385143 1.102452083 1.199838756 1.405326076 0.839743653 0.806888777 1 19.24422066 2.195178388 24.99953096 0.864748755 1.143749082 0.394614886 0.157278271 136.9573167 78922.33611 0.065188164 0.043950149 156.7394749 -2.195178388 0.279000326 AYS(ph)GSDLPSSSSGGANGTAGGGGGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AYSGSDLPSSSSGGANGTAGGGGGAR 26 0 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 AYS(0.836)GS(0.164)DLPSSSSGGANGTAGGGGGAR;AYS(1)GSDLPSSSSGGANGTAGGGGGAR 388.03 7.10E-145 589920000 151897 179883 163169 209359 320150 304050 308220 345080 339660 TRUE FALSE 131823.4266 178701.3367 242078.0742 256897.1608 313779.6414 315747.0002 278328.8718 271287.3274 299505.7817 0.4401365 0.596654047 0.808258434 0.8577369 1.047658044 1.054226728 0.929293819 0.905783273 1 18.19222433 4.286547848 1.221879118 0.973071834 0.378689753 0.923831174 0.054163448 0.207302998 0.45176145 0.018936247 0.129179623 19344.0697 -4.286547848 -0.594382081 down MEITIRNS(ph)PYRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MEITIRNSPYRR 12 2 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;Q9UQ88-9;A0A087X1I0;A0A087WYI9 P21127-2 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 MEITIRNS(1)PYRR;MEITIRNS(1)PYRR 176.25 1.33E-05 463990000 613740 557210 251910 284830 451920 572100 526630 594600 128859 TRUE FALSE 532632.704 553549.6508 373734.5186 349505.0049 442927.6762 594109.0572 475557.5037 467449.4172 113625.4358 4.687618579 4.871705414 3.289180067 3.07593984 3.898138414 5.228662517 4.185308512 4.113950488 1 16.7939263 4.248410192 24.96837872 3.683539971 4.779662595 0.174485162 1.085946101 390.7939372 990630.0328 0.272475146 0.702223681 17717.81618 -4.248410192 1.096122624 MEIVDHALHALTDEVIIPHSGWER ddPTM_MDA-MB-175_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 ; 298.23 1.64E-62 415300000 195359 186575 109068 160731 178254 213078 165655 221975 147387 FALSE TRUE 169541.8132 185349.3765 161813.6496 197227.4302 174707.0941 221275.2485 149589.8036 174507.3737 129963.0768 1.304538315 1.426169503 1.245074014 1.517565104 1.344282534 1.702600877 1.151017715 1.342745786 1 16.98774228 0.643106569 1.149535829 1.35E-09 1.402026704 0.397018487 0.149134629 5.575353594 2.250030388 13.30338396 0.043262238 4.396494854 -0.643106569 1.402026702 MEKGEHSIVYLKPSYAFGSVGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MEKGEHSIVYLKPSYAFGSVGK 22 2 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 124.08 1.40E-05 588560000 1185700 930950 463210 562390 909430 711570 1317200 1472900 141630 FALSE TRUE 1029006.741 924834.5282 687219.9053 690089.2451 891334.1223 738944.5583 1189458.147 1157931.797 124886.6627 8.239524687 7.405390678 5.502748574 5.525724124 7.137144213 5.916921328 9.524300839 9.271861155 1 16.93025989 4.474647275 24.41764901 6.686337772 8.030991915 0.053057545 2.372528521 182.239306 1798697.374 0.597604849 1.603922805 29829.58938 -4.474647275 1.344654143 MELAGSNTTASS(ph)PAR ddPTM_MDA-MB-175_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 MELAGSNTTAS(0.028)S(0.972)PAR;MELAGSNTTAS(0.008)S(0.992)PAR 255.72 9.84E-18 166410000 434430 436070 230580 290080 388660 397230 369000 432830 374960 TRUE FALSE 377018.9748 433205.4275 342089.2592 355947.0976 380926.4264 412511.6951 333214.4368 340272.6728 330632.656 1.140295636 1.310231823 1.03465055 1.076563646 1.152113742 1.247643533 1.007808608 1.029156276 1 18.3348697 2.215238574 24.88371434 1.015640712 1.15718439 0.44751762 0.077402428 215.6833863 230123.9575 0.03224431 0.021753853 164.1491259 -2.215238574 0.141543678 MELGAPEEMGQVPPLDS(ph)RPSSPALYFTHDASLVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MELGAPEEMGQVPPLDSRPSSPALYFTHDASLVHK 35 1 Q9Y3Q8;Q9Y3Q8-2 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 MELGAPEEMGQVPPLDS(0.186)RPS(0.165)S(0.165)PALY(0.155)FT(0.165)HDAS(0.165)LVHK;MELGAPEEMGQVPPLDS(0.269)RPS(0.269)S(0.269)PALY(0.055)FT(0.069)HDAS(0.069)LVHK;MELGAPEEMGQVPPLDS(0.333)RPS(0.333)S(0.333)PALYFTHDASLVHK;MELGAPEEMGQVPPLDS(0.333)RPS(0.333)S(0.333)PALYFTHDASLVHK 204.91 1.47E-27 1686690000 607290 452511 275656 438402 491615 456228 495278 605165 818216 TRUE FALSE 527035.0878 449538.4254 408964.1636 537947.8747 481832.8233 473779.3864 447246.0158 475755.1741 721487.4366 0.730484082 0.62307173 0.566834768 0.745609483 0.66783259 0.656670321 0.619894392 0.659408813 1 19.46061475 1.238833374 8.76153181 1.002779357 0.655697339 0.811275788 0.051714078 0.033780503 32.22813836 0.070051341 0.012339254 17.33138915 -1.238833374 -0.347082018 MELGAPEEMGQVPPLDSRPS(ph)SPALYFTHDASLVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MELGAPEEMGQVPPLDSRPSSPALYFTHDASLVHK 35 1 Q9Y3Q8;Q9Y3Q8-2 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 MELGAPEEMGQVPPLDS(0.12)RPS(0.431)S(0.431)PALY(0.006)FT(0.004)HDAS(0.008)LVHK 132.96 1.06E-08 637430000 1284200 999690 583130 951770 909370 850180 947710 1206800 1644900 TRUE FALSE 1114489.716 993122.9706 865133.6185 1167883.925 891275.3162 882886.9747 855801.2301 948735.2113 1450441.796 0.768379482 0.684703773 0.596462141 0.805191859 0.614485406 0.608702105 0.590027971 0.65410085 1 20.46806097 1.237884338 24.923609 1.000000406 0.660684331 0.678788035 0.072306643 9.340790265 343976.5781 0.101335804 0.017456796 17.29355734 -1.237884338 -0.339316075 MELLAHLLGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MELLAHLLGEK 11 0 Q9Y2Q3-3;Q9Y2Q3;Q9Y2Q3-2;Q9Y2Q3-4 Q9Y2Q3-3 GSTK1 Glutathione S-transferase kappa 1 0 ; 118.9 0.00065773 492420000 1377360 1341410 934830 1175310 1375890 1285030 1538120 1788600 1363360 FALSE TRUE 1195338.386 1332598.189 1386916.915 1442182.099 1348512.481 1334465.936 1388953.359 1406121.809 1202185.134 0.994304748 1.10848001 1.153663338 1.199633948 1.121717814 1.110033636 1.155357291 1.169638327 1 20.19722765 4.714950835 3.156494094 1.136242013 0.976977264 0.384498222 0.053030987 0.315482907 5.016010655 0.012824935 0.120565177 51874.13108 -4.714950835 -0.159264749 MELSLNIPVNHGPQEESCGSSQLHENSGS(ph)PETSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MELSLNIPVNHGPQEESCGSSQLHENSGSPETSR 34 0 O43353-2;O43353 O43353-2 RIPK2 Receptor-interacting serine/threonine-protein kinase 2 1 MELSLNIPVNHGPQEESCGSSQLHENS(0.012)GS(0.988)PETSR 169.15 2.78E-14 113580000 63183 51060 35522 42062 63857 62047 61240 74081 76786 TRUE FALSE 54833.20646 50724.5835 52700.55801 51612.81998 62586.37063 64433.98824 55300.95423 58239.35465 67708.44655 0.809842926 0.749161827 0.778345401 0.762280374 0.924351005 0.95163885 0.816751189 0.86014903 1 16.0470482 3.242445617 24.99757287 0.899290427 0.77331418 0.627271798 0.051554001 72.32131149 465339.6371 0.015590522 0.019372425 1747.614411 -3.242445617 -0.125976247 MEPGEELEEEGS(ph)PGGREDGFTAEHLAAEAMAADMDPWLVFDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MEPGEELEEEGSPGGREDGFTAEHLAAEAMAADMDPWLVFDAR 43 1 Q9H3H3-1;Q9H3H3;Q9H3H3-3 Q9H3H3-1 C11orf68 UPF0696 protein C11orf68 1 MEPGEELEEEGS(0.993)PGGREDGFT(0.007)AEHLAAEAMAADMDPWLVFDAR 134.26 1.30E-09 30531000 14191 9699.9 8100.7 8473.8 9038.7 9042.9 9902.9 11917 9090.7 TRUE FALSE 12315.62339 9636.180718 12018.22562 10397.9058 8858.847554 9390.786215 8942.518282 9368.642288 8016.007802 1.536378669 1.202117183 1.499278183 1.297142675 1.105144577 1.171504126 1.115582532 1.168741663 1 12.9686682 3.37891032 3.821308913 1.122531788 1.393189592 0.657942289 0.099472378 0.137188114 3.811297264 0.027039031 0.035795253 2392.821597 -3.37891032 0.270657804 MEQELKEPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MEQELKEPGR 10 1 C9JVE2;Q96GG9 C9JVE2 DCUN1D1 DCN1-like protein;DCN1-like protein 1 0 ; 144.1 2.99E-05 333320000 1207150 1071070 656430 707350 975840 895150 1198080 1351260 793070 FALSE TRUE 1047622.069 1064034.071 973881.7436 867964.6287 956422.6932 929586.9997 1081890.386 1062303.565 699314.1681 1.498070705 1.521539416 1.392624071 1.241165514 1.36765811 1.329283807 1.547073455 1.51906484 1 19.41558121 4.175816292 5.067628291 1.364541081 1.510151846 0.164226021 0.151691033 0.390777567 19.46343518 0.039833932 0.08912374 14990.50597 -4.175816292 0.145610765 MEREDS(ph)S(ph)EEEEEEIDDEEIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MEREDSSEEEEEEIDDEEIER 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 MEREDS(1)S(1)EEEEEEIDDEEIER;MEREDS(1)S(1)EEEEEEIDDEEIER;MEREDS(1)S(1)EEEEEEIDDEEIER 251.47 4.38E-32 1514240000 814670 733960 506624 545952 673870 698720 703910 795340 620959 TRUE FALSE 707009.2954 729138.5684 751629.061 669918.746 660461.3054 725600.2105 635644.9165 625262.7303 547549.9344 1.291223414 1.331638491 1.37271327 1.223484296 1.206212007 1.325176326 1.160889403 1.141928235 1 19.06263101 -0.152897481 0.454516095 5.97E-12 1.319974042 0.78096276 0.051626582 8.333675206 0.521094052 7.713508215 0.042897291 0.703238306 0.152897481 1.319974042 MES(ph)EGGADDS(ph)AEEGDLLDDDDNEDRGDDQLELIKDDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MESEGGADDSAEEGDLLDDDDNEDRGDDQLELIKDDEK 38 2 P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 2 MES(1)EGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK 79.448 0.00091012 68575000 55269 27730 36672 38524 28706 28605 36482 52261 76459 TRUE FALSE 47965.06162 27547.8398 54406.70186 47271.463 28134.80676 29705.45286 32943.98126 41085.39185 67420.10412 0.711435591 0.408599781 0.806980389 0.701147879 0.417305893 0.440602299 0.488637354 0.609393776 1 16.04089123 1.242278807 4.355241702 1.038087953 0.564370525 0.495818166 0.135889927 0.181081696 6.831705342 0.266324563 0.034702433 17.46943289 -1.242278807 -0.473717428 MES(ph)HS(ph)EDEDLAGAVGGLGWNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 216.48 7.08E-26 127387000 124087 125397 77039 83818 116455 112210 100074 127326 126885 TRUE FALSE 107688.5886 124573.2589 114295.3181 102850.158 114137.7733 116526.7913 90368.83888 100098.3258 111884.7998 0.962495251 1.113406459 1.021544644 0.919250498 1.020136547 1.041489027 0.807695406 0.894655269 1 16.77165453 2.258156108 24.99540135 0.89562813 1.014059355 0.380007684 0.067486129 231.5404656 295345.2596 0.025317688 0.019582065 181.1991298 -2.258156108 0.118431225 MES(ph)HSEDEDLAGAVGGLGWNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MESHSEDEDLAGAVGGLGWNSR 22 0 Q96MH2;K7ESM2;K7ELS4;K7EJA3;K7ERG7;K7EIM4 Q96MH2 HEXIM2 Protein HEXIM2 1 MES(0.5)HS(0.5)EDEDLAGAVGGLGWNSR 143.15 3.67E-07 73380000 58765 57808 28643 36348 51684 40412 40457 48757 48746 TRUE FALSE 50999.05636 57428.25544 42494.85061 44601.36894 50655.58952 41966.67579 36533.48637 38330.69498 42983.30341 1.18648527 1.336059606 0.98863622 1.037644048 1.178494566 0.976348313 0.84994599 0.891757774 1 15.39148874 3.849694602 0.433251169 0.878219626 1.36043306 0.533678661 0.100225601 2.092441301 0.720946963 0.160054844 0.557340861 7074.481278 -3.849694602 0.482213434 MESEGGADDS(ph)AEEGDLLDDDDNEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MESEGGADDSAEEGDLLDDDDNEDR 25 0 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 MESEGGADDS(1)AEEGDLLDDDDNEDR;MESEGGADDS(1)AEEGDLLDDDDNEDR 246.4 2.23E-38 367330000 497090 353600 364210 368880 368760 351760 446330 512690 754890 TRUE FALSE 431398.297 351277.1783 540343.1742 452639.842 361422.3975 365292.4348 403044.9853 403055.2333 665647.7642 0.648087953 0.527722314 0.811755411 0.679999042 0.542963436 0.548777378 0.605492885 0.605508281 1 19.34439943 1.237238904 24.9982817 1.00000046 0.619957461 0.6759767 0.082396595 20.61445518 389739.4397 0.124237114 0.020504719 17.26787531 -1.237238904 -0.380042998 MESEGGADDS(ph)AEEGDLLDDDDNEDRGDDQLELIK ddPTM_MDA-MB-175_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(0.013)EGGADDS(0.987)AEEGDLLDDDDNEDRGDDQLELIK;MES(0.004)EGGADDS(0.996)AEEGDLLDDDDNEDRGDDQLELIK 241.41 2.50E-47 122547000 75871 48211 57424 70976 57885 64215 54546 84664 169865 TRUE FALSE 65844.45512 47894.29877 85194.43847 87092.1856 56733.20175 66685.3926 49256.13732 66559.26246 149783.7532 0.439596777 0.3197563 0.568782906 0.581452819 0.378767393 0.445211121 0.328848331 0.444369039 1 17.19252162 1.239141951 8.649227374 1.004804494 0.436357636 0.806785423 0.086383026 0.036421434 32.43368886 0.122867345 0.021738769 17.34370792 -1.239141951 -0.568446858 MESEGGADDS(ph)AEEGDLLDDDDNEDRGDDQLELIKDDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 15 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;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(0.164)EGGADDS(0.836)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK 335.18 1.19E-129 36142902000 9124667 4513352 6577951 6841299 5162193 5541208 6075013 8979795 14270272 TRUE FALSE 7918819.137 4483703.494 9759070.106 8394720.501 5059475.459 5754381.857 5485859.174 7059535.72 12583256.7 0.629313963 0.356322977 0.775559963 0.667134169 0.402079969 0.457304654 0.435964974 0.561026123 1 23.58500202 1.241343662 5.319948414 1.024316691 0.52942603 0.56240306 0.128961661 0.116932375 9.563328507 0.212125312 0.032301791 17.43185728 -1.241343662 -0.49489066 MESEGGADDS(ph)AEEGDLLDDDDNEDRGDDQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MESEGGADDSAEEGDLLDDDDNEDRGDDQVK 31 1 B4DY08 B4DY08 HNRNPC 1 MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQVK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQVK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQVK 361.46 1.93E-121 1232590000 758300 598220 524880 567300 613630 645630 566010 923160 811250 TRUE FALSE 658088.7337 594290.2534 778713.7236 696114.1356 601419.9635 670467.8039 511118.4373 725749.418 715344.9492 0.919959992 0.830774376 1.088584919 0.973116727 0.84074119 0.937265028 0.71450625 1.014544688 1 19.44827957 1.59657269 25 1.007303394 0.904084958 0.170423824 0.097520849 1.486386689 3276.972679 0.062662013 0.024153356 39.49778035 -1.59657269 -0.103218436 MESMNRPYTSLVPPLS(ph)PQPK ddPTM_MDA-MB-175_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 160.69 1.43E-11 1879740000 1371250 1507520 1153150 1691130 2159700 1822950 2606000 2987500 2636500 TRUE FALSE 1190035.838 1497617.002 1710817.197 2075126.914 2116726.195 1893080.066 2353270.521 2348646.374 2324815.974 0.511883887 0.644187333 0.7358936 0.892598355 0.910491935 0.814292438 1.012239484 1.010250446 1 21.14868509 5.034905855 0.411938712 1.024063932 1.55E-12 0.911240828 0.049594611 2.364995405 0.290764679 0.060964379 1.258271665 108369.197 -5.034905855 -1.024063932 MESSFGS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MESSFGSPSK 10 0 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4;A8MV73 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 MESSFGS(0.998)PS(0.002)K;MESSFGS(0.999)PS(0.001)K 185.3 1.54E-06 352310000 786160 583400 535620 710530 678430 529430 730610 886520 1955530 TRUE FALSE 682266.9641 579567.607 794647.6235 871866.6963 664930.5703 549797.5147 659755.5547 696944.5969 1724349.471 0.395666294 0.336107974 0.46083908 0.505620648 0.385612419 0.318843439 0.382611278 0.404178276 1 20.71762076 1.238570868 8.41673023 1.005907908 0.398212516 0.925103489 0.053772848 0.023354005 17.54501693 0.080896633 0.014091662 17.32091649 -1.238570868 -0.607695392 MESSFGS(ph)PSKQESSESLPK ddPTM_MDA-MB-175_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 MESSFGS(0.785)PS(0.215)KQESSESLPK;MESSFGS(0.953)PS(0.047)KQESSESLPK 191.41 5.88E-15 1645070000 814660 483000 432270 430120 487310 350590 766030 795320 506030 TRUE FALSE 707000.6169 479827.1412 641317.2179 527785.32 477613.4844 364077.4242 691740.5285 625247.0072 446207.7099 1.584465264 1.075344801 1.437261624 1.182824295 1.070383756 0.815937099 1.550265747 1.401246535 1 18.76735592 4.753288486 23.89771333 1.216709795 1.584465748 0.229311459 0.222131594 2481.636636 4026621.598 0.055848171 1.15387095 56661.55465 -4.753288486 0.367755953 MESTAGITTTTS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MESTAGITTTTSPR 14 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 MESTAGITTT(0.004)T(0.104)S(0.892)PR 95.6 0.0038852 259320000 179560 171040 129280 183830 186500 198980 191670 213780 301640 TRUE FALSE 155830.6911 169916.427 191800.2404 225571.4112 182789.0149 206634.8894 173081.8729 168064.8106 265980.4628 0.585872697 0.638830481 0.721106499 0.848075113 0.687227223 0.776879953 0.650731528 0.631869006 1 18.02096075 4.310727902 3.019172651 0.744496165 0.59602028 0.248032627 0.106538756 0.398554804 7.071180747 0.027488333 0.089755606 20451.6288 -4.310727902 -0.148475885 METEADAPS(ph)PAPSLGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 METEADAPSPAPSLGER 17 0 Q12873-3;Q12873;Q12873-2 Q12873-3 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 METEADAPS(1)PAPSLGER;METEADAPS(1)PAPSLGER;METEADAPS(1)PAPSLGER 227.88 1.69E-15 1778700000 3635990 2431670 1596510 1934710 2472620 2569730 2551830 2700800 2384220 TRUE FALSE 3155484.709 2415696.2 2368587.576 2374015.476 2423419.7 2668589.176 2304353.919 2123254.938 2102360.228 1.50092485 1.149040097 1.126632603 1.129214415 1.152713825 1.269330128 1.096079487 1.009938692 1 21.00357846 4.752441664 3.352890275 1.110422023 1.559260603 0.725135459 0.074680803 0.204959586 3.735858842 0.021048841 0.240962309 56551.17899 -4.752441664 0.44883858 GRAS(ph)SHS(ph)SQTQGGGSVTK ddPTM_MDA-MB-175_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(0.736)S(0.265)HS(0.796)S(0.203)QTQGGGSVTK;GRAS(0.799)S(0.267)HS(0.832)S(0.102)QTQGGGSVTK 172.52 6.03E-12 449380000 1422000 1076450 462800 473320 622390 587290 668360 763380 660360 TRUE FALSE 1234079.097 1069378.729 686611.628 580794.5402 610005.6567 609883.4263 603542.5501 600137.1276 582292.9931 2.11934389 1.83649596 1.179151451 0.997426634 1.047592301 1.047382389 1.036492895 1.030644598 1 19.15138573 4.287953756 2.470907897 1.028468449 2.102202218 0.996306895 0.024024408 0.017182992 0.202250234 0.007245001 0.026026147 19406.79221 -4.287953756 1.073733769 up METVSNASSSSNPS(ph)SPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 METVSNASSSSNPSSPGR 18 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 METVSNASSSSNPS(0.5)S(0.5)PGR 77.506 0.052631 31704000 46943 51249 31569 45025 63060 59372 59803 68022 60148 TRUE FALSE 40739.36361 50912.34194 46835.87399 55248.61441 61805.22937 61656.07926 54003.31426 53476.02465 53037.37196 0.768125609 0.959933346 0.883073053 1.041692157 1.165314703 1.162502533 1.018212484 1.008270634 1 15.69472167 3.716744348 4.183549355 1.066804991 0.876741464 0.616215689 0.07298337 0.158769977 6.671554407 0.021781357 0.035310731 5208.879942 -3.716744348 -0.190063526 METVSNASSSSNPSS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 METVSNASSSSNPSSPGR 18 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 METVSNASSSSNPS(0.002)S(0.998)PGR;METVSNASSSSNPS(0.001)S(0.999)PGR;METVSNASSSSNPS(0.014)S(0.986)PGR;METVSNASSSSNPS(0.025)S(0.975)PGR;METVSNASSSSNPS(0.063)S(0.936)PGR;METVSNASSSSNPS(0.195)S(0.805)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPS(0.007)S(0.993)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPS(0.027)S(0.973)PGR;METVSNASSSSNPSS(1)PGR 428.65 7.10E-169 14735600000 7828680 8231170 5280469 7055670 10290190 9549120 9921160 10138190 9076320 TRUE FALSE 6794100.103 8177098.902 7834121.471 8657767.713 10085435.35 9916480.826 8959007.43 7970216.964 8003327.789 0.848909389 1.021712357 0.978858005 1.081770976 1.260155228 1.239044693 1.119410284 0.995862868 1 22.93216857 4.526420596 1.168441633 1.110680172 0.806444135 0.451022762 0.091228317 1.251021623 1.894536714 0.032446929 0.426038853 33606.29196 -4.526420596 -0.304236038 MEVDRS(ph)PGLPMSDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 MEVDRSPGLPMSDLK 15 1 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK 159.26 1.08E-06 1261570000 2119142 2021890 1302227 1596023 2160001 1826980 2874080 3180900 1546699 TRUE FALSE 1839092.015 2008608.071 1931988.333 1958424.416 2117021.206 1897265.103 2595352.164 2500689.289 1363850.006 1.348456214 1.472748515 1.416569508 1.435952932 1.552239027 1.391109795 1.902960114 1.833551547 1 20.37925356 MEVGPFSTGQES(ph)PTAENAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MEVGPFSTGQESPTAENAR 19 0 Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2 Q9Y4W2-3 LAS1L Ribosomal biogenesis protein LAS1L 1 MEVGPFSTGQES(0.666)PT(0.334)AENAR;MEVGPFSTGQES(0.866)PT(0.134)AENAR 322.33 4.46E-62 242000000 198065 137878 108653 177110 154757 167751 113224 182122 329540 TRUE FALSE 171890.2084 136972.2703 161197.9542 217325.5325 151677.6385 174204.4895 102243.5539 143176.6276 290582.1566 0.591537383 0.471371924 0.554741406 0.747897032 0.521978501 0.599501675 0.351857647 0.492723398 1 18.14858659 1.235295976 24.9902193 1.000000645 0.536162138 0.668650741 0.101384429 58.41753987 447099.2283 0.180191751 0.025773595 17.19079557 -1.235295976 -0.463838507 MEVGPTMVGDEQS(ph)DPELMQHLGAS(ph)KR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MEVGPTMVGDEQSDPELMQHLGASKR 26 1 P30047;H0YNM1 P30047 GCHFR GTP cyclohydrolase 1 feedback regulatory protein 2 MEVGPT(0.002)MVGDEQS(0.999)DPELMQHLGAS(0.999)KR 44.616 0.047485 1069500000 566490 368660 327660 362930 379500 316190 539170 585390 601340 TRUE FALSE 491626.9112 366238.2482 486117.472 445338.8035 371948.6925 328354.0339 486881.3764 460208.904 530250.2702 0.927160133 0.690689414 0.916769871 0.839865302 0.701458751 0.619243501 0.91821052 0.867908853 1 19.01631393 1.590353889 1.738123255 0.990867197 0.787798377 0.274983596 0.104484711 0.606512173 3.174494284 0.179705159 0.030245022 38.93622912 -1.590353889 -0.20306882 MEWWSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MEWWSR 6 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 ; 122.79 0.04436 1039357000 1111560 1149280 743059 899424 1108130 1206360 1207630 1282450 1183680 FALSE TRUE 964664.5297 1141730.304 1102404.818 1103651.966 1086080.381 1252769.45 1090514.228 1008208.048 1043746.699 0.924232413 1.093876805 1.056199573 1.057394449 1.040559345 1.200261952 1.044807356 0.965950885 1 19.9933402 1.854512676 5.444028546 0.983618129 1.066475501 0.184255004 0.067049824 0.330680012 13.02284355 0.034102035 0.017484951 71.53402722 -1.854512676 0.082857371 MFADYLAHESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 MFADYLAHESR 11 0 O14579;M0QXB4;O14579-3;O14579-2;M0R061 O14579 COPE Coatomer subunit epsilon 0 ;;;;;;;;; 221.32 8.50E-12 4191100000 4379296 5191170 1579159 3285699 5749980 6149280 4607280 5319310 5736701 FALSE TRUE 3800560.938 5157068.862 2342845.574 4031767.177 5635566.648 6385846.781 4160466.695 4181816.951 5058514.743 0.751319534 1.019482817 0.463148907 0.797025882 1.114075363 1.262395605 0.822468038 0.826688695 1 22.27028242 3.391602421 7.548718864 0.981092923 0.749031808 0.309537314 0.182924438 0.335573645 25.3692059 0.05587351 0.072231825 2463.78281 -3.391602421 -0.232061115 MFDYTDDPEGPVMPGSHSVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MFDYTDDPEGPVMPGSHSVER 21 0 Q09161 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 81.574 0.0051019 141650000 414180 279620 240000 238110 327080 336510 260290 321090 332860 FALSE TRUE 359445.0636 277783.1578 356064.8028 292176.5148 320571.7479 349455.7575 235047.1159 252427.4022 293509.67 1.224644706 0.9464191 1.213128013 0.995457883 1.092201657 1.190610713 0.800815577 0.860030956 1 18.16304851 2.236680229 24.99986102 0.877752053 1.101572408 0.518377057 0.101169723 36.43498948 484390.6301 0.037155024 0.026495779 172.4567626 -2.236680229 0.223820355 MFEELGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MFEELGQR 8 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;; 195.6 0.00036962 899609000 1422670 1427510 900780 1039280 1424940 1538670 1397500 1537630 1533300 FALSE TRUE 1234660.555 1418132.593 1336400.221 1275264.408 1396586.482 1597863.631 1261970.665 1208819.79 1352035.021 0.913186815 1.04888747 0.988436098 0.943218474 1.032951411 1.181821185 0.933386078 0.894074319 1 20.36670109 2.067444826 25 0.931729016 1.018925251 0.176925445 0.075682149 77.42525459 28698.41175 0.031032369 0.020922017 116.8005332 -2.067444826 0.087196235 MFEFYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MFEFYER 7 0 O75306;O75306-2 O75306 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" 0 ;; 104.37 0.019001 333645000 497855 601290 327888 497900 624020 731380 410185 509500 688990 FALSE TRUE 432062.2003 597340.0864 486455.7335 610955.8049 611603.2229 759516.6619 370405.3218 400547.3899 607538.3871 0.711168561 0.983213734 0.800699584 1.005625024 1.006690665 1.250154193 0.609682169 0.659295607 1 19.21261604 2.204268681 24.99994694 0.730001158 0.957677142 0.230611945 0.172781319 241.3491175 175949.8123 0.070266742 0.047376369 160.054792 -2.204268681 0.227675984 MFEIDYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MFEIDYSR 8 0 P16278-3;P16278;E7EQ29;P16278-2;F8WF40;C9JF15;C9JWX1 P16278-3 GLB1 Beta-galactosidase 0 ;;; 119.29 0.0048542 745380000 1383960 1469490 911530 1112640 1451230 1686140 1211240 1502230 1485640 FALSE TRUE 1201066.179 1459836.823 1352348.957 1365281.918 1422353.362 1751006.897 1093774.131 1180989.805 1310009.332 0.916837881 1.114371316 1.032320094 1.042192513 1.085758191 1.336636965 0.834936137 0.901512513 1 20.32114566 MFFDALYDEDVVKEDAFYSWESSKDPAEQQGK ddPTM_MDA-MB-175_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 0 218.16 4.36E-36 248990000 857600 577460 592960 567470 420930 338810 848840 933780 613140 FALSE TRUE 744265.9871 573666.6272 879717.4393 696322.7367 412554.3165 351844.2399 766519.6274 734098.4137 540655.2877 1.376599848 1.061058017 1.627131852 1.28792366 0.763063501 0.650773696 1.417760345 1.35779383 1 19.04434952 3.455506146 24.96227825 1.081411774 1.347540346 0.231613219 0.267504527 433.7422917 500906.9061 0.084790061 0.109472311 2854.342904 -3.455506146 0.266128572 MFGIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 MFGIDR 6 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;;;;; 175.34 0.009844 6893990000 5305680 6569160 3611280 3212100 5716010 5315710 4596770 4464180 5996360 FALSE TRUE 4604520.945 6526006.755 5357707.087 3941456.399 5602272.584 5520208.803 4150975.953 3509549.847 5287477.152 0.870835147 1.234238289 1.013282315 0.745432327 1.059536036 1.044015633 0.785057946 0.66374752 1 22.33414809 2.230527239 24.55461909 0.783192763 0.997932193 0.228633542 0.150251934 175.2261384 535584.9362 0.060387123 0.0415429 170.0306592 -2.230527239 0.21473943 MFGIDRDAIAQAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MFGIDRDAIAQAVR 14 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 254.1 2.76E-24 1450000000 1139480 784920 1022380 2482100 945370 1323260 1538570 2624300 2539900 FALSE TRUE 988894.8309 779763.8088 1516806.388 3045698.742 926558.9866 1374166.668 1389359.718 2063113.867 2239635.915 0.441542674 0.348165433 0.677255788 1.359907975 0.413709648 0.61356699 0.620350705 0.921182703 1 21.09483279 4.113673219 5.043234658 0.80879551 0.400293613 0.314115486 0.256047399 0.248799654 9.863538383 0.066728867 0.145521172 12991.91644 -4.113673219 -0.408501897 MFIGGLSWDTSKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MFIGGLSWDTSKK 13 1 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 104.17 0.0024902 530770000 559860 450600 258720 329890 307860 372540 451150 496300 198530 FALSE TRUE 485873.0825 447639.9789 383837.8574 404796.5666 301734.1883 386871.8549 407397.5424 390170.1072 175060.0096 2.775465874 2.557065889 2.192607314 2.312330312 1.723604318 2.2099385 2.327187937 2.228779195 1 17.41749003 8 0.062644684 7.10E-13 6.659095193 0.45723074 0.358450946 821.5519711 4.977156314 128.3122676 536.9396131 100000000 -8 6.659095193 MFLGDNAHLSIINEYLSQSYQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MFLGDNAHLSIINEYLSQSYQK 22 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;; 298.22 1.24E-55 1573643000 1034310 1283480 325489 788051 1441930 1230110 1319730 1519530 1372780 FALSE TRUE 897623.3129 1275048.735 482896.5691 966990.0242 1413238.414 1277433.128 1191742.788 1194590.334 1210491.512 0.74153623 1.053331413 0.398926026 0.798840813 1.167491387 1.055301185 0.984511478 0.986863867 1 20.20716153 3.3781127 6.767144617 1.027907216 0.737191693 0.442745341 0.163065437 0.207265661 12.19203927 0.046273794 0.059858527 2388.431005 -3.3781127 -0.290715523 MFLQYYLNEQGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MFLQYYLNEQGDR 13 0 Q9NPE3;H0YM60 Q9NPE3 NOP10 H/ACA ribonucleoprotein complex subunit 3 0 181.31 2.83E-05 285510000 289680 233850 170150 222270 235370 287780 280890 288630 296490 FALSE TRUE 251398.054 232313.824 252435.1091 272739.8007 230686.5975 298851.0828 253649.331 226908.7206 261439.29 0.961592476 0.888595681 0.96555919 1.043224225 0.882371573 1.143099352 0.970203565 0.86792127 1 17.99611644 6.561692942 9.467741235 0.964323904 0.433418283 0 0.082493554 0 0 0.018326458 0 3644961.469 -6.561692942 -0.530905621 MFLYADNEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 MFLYADNEDR 10 0 A0A087WY55;Q9NP79;Q5TGM0;Q9NP79-2 A0A087WY55 VTA1 Vacuolar protein sorting-associated protein VTA1 homolog 0 ;;;; 140.83 8.98E-05 950240000 1365000 1273473 877123 1032206 1232053 1258078 1304351 1361065 1688650 FALSE TRUE 1184611.792 1265107.472 1301302.617 1266584.149 1207537.556 1306477.075 1177855.241 1070011.842 1489019.721 0.795564877 0.84962439 0.873932426 0.850616101 0.810961426 0.877407503 0.791027294 0.718601525 1 20.50593143 2.222159468 24.992309 0.810075331 0.843611577 0 0.074775904 914.9534484 1394209.103 0.02981272 0.020164639 166.785952 -2.222159468 0.033536245 MFS(ph)PMEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MFSPMEEK 8 0 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 MFS(1)PMEEK;MFS(1)PMEEK 128.81 0.0011723 371397000 908730 723980 572392 648230 812840 698140 962070 1046680 1040360 TRUE FALSE 788639.0281 719224.1277 849202.6857 795420.5291 796666.0743 724997.8976 868768.5995 822855.6273 917369.826 0.859674044 0.784006741 0.925692847 0.867066374 0.86842411 0.790300571 0.947021119 0.896972632 1 19.80714393 -1.751374353 0.65230142 9.982340611 0.851695707 0.469022753 0.04809182 137.3028262 1.301219009 1783.824148 0.021085401 0.017726608 1.751374353 -9.130644904 MFVGGLSWDTSKK ddPTM_MDA-MB-175_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 ; 132.79 0.00018395 1559820000 2418370 1800940 1246730 1386650 1528920 1185770 2085560 2357540 1185350 FALSE TRUE 2098776.277 1789109.507 1849652.798 1701510.076 1498497.483 1231387.339 1883302.712 1853398.417 1045219.273 2.007977016 1.711707344 1.769631354 1.627897724 1.433668056 1.178113885 1.801825474 1.773214927 1 19.9953742 4.40601157 0.890795049 1.498309024 2.089199024 0.339815036 0.248795682 2.028082221 1.804274385 0.095877918 1.062973462 25468.98103 -4.40601157 0.59089 MFVLDEADEMLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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 ;;;;;;;;; 325.62 1.70E-51 1764075000 1700874 1457185 909225 1079953 1383632 1502110 1378247 1511668 1382592 FALSE TRUE 1476099.191 1447612.656 1348929.251 1325172.835 1356100.43 1559897.144 1244584.818 1188409.562 1219143.549 1.21076734 1.187401317 1.106456457 1.086970305 1.112338602 1.279502439 1.020868149 0.97479051 1 20.21743658 2.069659385 9.083112412 0.989233185 1.156394917 0.657733045 0.056431408 0.183300865 22.02917197 0.023664508 0.015933649 117.3976449 -2.069659385 0.167161732 MFYEEHLHLDDEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MFYEEHLHLDDEIR 14 0 Q9BV57;Q9BV57-2;A0A0G2JQN5 Q9BV57 ADI1 "1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase" 0 ;; 203.85 8.36E-09 102618000 93154 90976 58783 72140 83654 96449 80052 87866 137104 FALSE TRUE 80843.46288 90378.37267 87210.65542 88520.48959 81989.44907 100159.4554 72288.56936 69076.53967 120895.7213 0.668704086 0.747572964 0.721370901 0.732205314 0.678183216 0.828478083 0.597941503 0.571372907 1 16.88340366 MGAGLGHGMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 20 MGAGLGHGMDR 11 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;;;;;;;;;;;;;;;;; 185.77 4.32E-06 11527050000 9241035 7994127 4380406 5643801 7824198 8126666 7349703 8341487 7257728 FALSE TRUE 8019808.811 7941613.053 6498784.993 6925312.277 7668511.768 8439304.1 6636929.934 6557724.919 6399727.664 1.253148451 1.240929844 1.015478366 1.08212609 1.198255952 1.318697379 1.037064432 1.024688122 1 22.60957908 2.036486499 24.3539069 1.019138088 1.175769332 0.448725712 0.085652278 126.9086651 84707.99837 0.037389718 0.025208038 108.7643325 -2.036486499 0.156631243 MGANNLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MGANNLER 8 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 80.684 0.057726 95320000 109120 101440 59308 75803 105040 107190 102380 91388 82791 FALSE TRUE 94699.51553 100773.634 87989.54717 93015.22973 102949.9095 111313.6687 92451.20336 71845.38738 73003.5423 1.297190692 1.380393756 1.205277777 1.274119403 1.410204303 1.524770787 1.266393389 0.984135634 1 16.15567885 1.801967284 3.932219663 0.989865114 1.346088632 0.740159969 0.085883249 0.108848831 3.032554606 0.056173838 0.02471877 63.38219625 -1.801967284 0.356223518 MGANSLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MGANSLER 8 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;; 130.28 0.0024537 974330000 870440 876230 536123 687557 797390 829310 758470 906900 1673450 FALSE TRUE 755409.1486 870473.9874 795393.876 843677.3255 781523.4991 861214.0923 684913.6961 712966.4925 1475616.647 0.511927776 0.589905237 0.539024738 0.5717456 0.529625022 0.583629965 0.464154221 0.483165119 1 20.49288654 1.234842857 24.99999657 1.000000664 0.532951315 0.927764185 0.040850347 28.42463333 191111.9864 0.078007221 0.010753734 17.17286899 -1.234842857 -0.467049349 MGAPESGLAEYLFDKHTLGDS(ph)DNES ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MGAPESGLAEYLFDKHTLGDSDNES 25 1 G3V192;P02794;G3V1D1 G3V192 FTH1 "Ferritin;Ferritin heavy chain;Ferritin heavy chain, N-terminally processed" 1 MGAPESGLAEYLFDKHTLGDS(1)DNES;MGAPESGLAEYLFDKHTLGDS(0.84)DNES(0.159);MGAPESGLAEYLFDKHT(0.003)LGDS(0.499)DNES(0.499) 170.32 5.27E-12 200241000 271271 219215 102165 125899 172972 171994 211966 251792 76949 TRUE FALSE 235421.85 217774.9622 151572.3357 154486.2922 169530.1956 178610.7205 191409.5699 197948.2402 67852.17688 3.469628549 3.209550117 2.233861059 2.276806719 2.498522574 2.632350629 2.820979057 2.917345461 1 16.05010748 4.336788092 4.933522286 2.432252337 3.401936889 0.371704492 0.533318168 0.226046989 8.855766446 0.132245581 0.369629955 21716.41298 -4.336788092 0.969684552 MGAT(ph)PTPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MGATPTPFK 9 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 MGAT(0.835)PT(0.165)PFK 111.86 0.022995 406080000 629580 695830 524340 532140 743850 810900 725880 814430 929020 TRUE FALSE 546379.4078 691259.0469 777912.5778 652970.5203 729048.8403 842095.8477 655484.2693 640270.4824 819192.3139 0.666973308 0.843829996 0.949609224 0.797090633 0.889960548 1.027958678 0.800159203 0.781587512 1 19.64384265 4.714145072 3.797324454 0.879760512 0.650330755 0.40341041 0.084577079 0.253202438 7.07711705 0.02120167 0.155689232 51777.97623 -4.714145072 -0.229429756 MGEIEDGEADHITTDVQGQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MGEIEDGEADHITTDVQGQK 20 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3;E9PG59 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 ; 251.35 2.37E-31 156233000 505900 421280 292510 368920 396220 368850 518320 593820 556890 FALSE TRUE 439044.0332 418512.5839 433968.8144 452688.9246 388335.9972 383039.8982 468053.4062 466836.2141 491055.0986 0.894083036 0.852272149 0.883747701 0.92186992 0.790819601 0.780034459 0.953158632 0.950679904 1 18.90552538 2.111376365 8.154801065 0.96579714 0.855471132 0.592522783 0.044716283 0.181520108 12.3117829 0.01938792 0.013050289 129.2338747 -2.111376365 -0.110326008 MGESDDSILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 MGESDDSILR 10 0 Q8WVC2;P63220 Q8WVC2 RPS21 40S ribosomal protein S21 0 ;;;; 234.03 1.03E-11 4300210000 4528560 4364690 3047690 3676350 4411920 4378670 4377030 5080830 6050700 FALSE TRUE 3930099.322 4336018.064 4521563.078 4511121.457 4324131.424 4547120.268 3952546.304 3994334.044 5335393.139 0.736609134 0.812689515 0.847465774 0.845508726 0.810461631 0.852255898 0.740816319 0.748648495 1 22.34716315 4.726987999 4.237921311 0.822789532 0.730747976 0.14086072 0.071318163 0.451990812 18.66126727 0.017418573 0.123754804 53332.01574 -4.726987999 -0.092041557 MGFCTDREDINSLCMTVVQNLMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MGFCTDREDINSLCMTVVQNLMER 24 1 Q01581;D6RIW1 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 ; 287.32 5.86E-53 453030000 233130 211012 114636 145007 205975 210427 223156 262720 159607 FALSE TRUE 202321.2798 209625.8483 170074.353 177933.0556 201876.5005 218522.2629 201514.3655 206539.3725 140738.4423 1.437569413 1.489471141 1.20844277 1.264281832 1.434409087 1.552683541 1.43183598 1.467540561 1 17.10265692 1.233765774 24.99923691 0.999999376 1.411158016 0.615561933 0.102020306 111.0373272 578853.3345 0.214312784 0.026888248 17.13033177 -1.233765774 0.41115864 MGFTEVT(ph)PVTGASLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MGFTEVTPVTGASLR 15 0 P55265-5;P55265;P55265-4 P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 1 MGFT(0.028)EVT(0.964)PVT(0.007)GAS(0.001)LR 84.046 0.094786 50844000 66133 81714 53603 56085 64585 68298 52618 86679 101000 TRUE FALSE 57393.35649 81177.21535 79525.59009 68819.95646 63299.88486 70925.46825 47515.11446 68143.37039 89059.89506 0.644435483 0.91149013 0.892945024 0.772737902 0.710756338 0.796379428 0.533518644 0.765140924 1 16.44248829 4.811242712 20.41033829 0.782339137 0.644417408 0.116610481 0.12645189 36980.42028 10379299.39 0.031657871 121.0011294 64750.4382 -4.811242712 -0.137921729 MGGAGGEGS(ph)DDDTSLT ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 MGGAGGEGSDDDTSLT 16 0 Q9Y365;F5H8H3;F5GY11 Q9Y365 STARD10 PCTP-like protein 1 MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(1)DDDTSLT 380.02 2.18E-104 12271670000 9857590 7551330 4833320 5542130 7841870 7808550 7739470 8629560 8105960 TRUE FALSE 8554884.506 7501724.816 7170729.718 6800555.323 7685832.129 8108949.971 6988897.391 6784195.749 7147682.643 1.196875258 1.049532442 1.003224412 0.951434984 1.075290064 1.134486571 0.977785072 0.94914619 1 22.76904415 4.726042068 2.71518897 1.010083402 1.23011039 0.512965034 0.055898241 0.393254534 3.98624282 0.015665512 0.192038443 53215.98044 -4.726042068 0.220026988 MGGDIANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MGGDIANR 8 0 Q9UQ80;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 104.37 0.010688 291458000 548360 485250 318720 381260 495820 553070 522860 582430 542260 FALSE TRUE 475892.8366 482062.3608 472854.0581 467830.9102 485954.1521 574346.9608 472153.1177 457881.877 478154.6405 0.995269723 1.008172503 0.988914502 0.978409223 1.016311693 1.201174081 0.987448573 0.957602077 1 18.86711775 3.009687159 23.49277013 1.029518761 0.994006584 0.088069709 0.064764781 346.4319999 840133.4335 0.021545568 0.024391733 1022.556135 -3.009687159 -0.035512177 MGGEEAEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MGGEEAEIR 9 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 122.13 0.0013826 815540000 968600 855240 527850 598640 842370 872050 804920 957590 979330 FALSE TRUE 840597.0559 849621.8721 783120.0256 734570.3616 825608.4851 905598.3278 726858.9823 752816.8305 863554.7231 0.973414925 0.9838657 0.906856282 0.850635567 0.956058097 1.048686671 0.841705757 0.871765055 1 19.71992808 4.242457481 24.84015142 0.918731209 0.978640337 0.099325181 0.064856865 195.9347233 1248910.824 0.016906374 0.041352383 17476.62153 -4.242457481 0.059909128 MGGFHWMQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MGGFHWMQR 9 0 Q969E4;Q5H9L2;Q6IPX3-2;Q6IPX3 Q969E4 TCEAL3;TCEAL5;TCEAL6 Transcription elongation factor A protein-like 3;Transcription elongation factor A protein-like 5;Transcription elongation factor A protein-like 6 0 113.89 0.0017272 404190000 117610 251970 126770 132100 232340 241620 213710 229000 241250 FALSE TRUE 102067.5405 250314.7925 188076.396 162095.324 227716.8886 250915.2777 192984.4371 180030.1321 212729.6998 0.479799203 1.176680044 0.884109723 0.761977872 1.070451793 1.179502805 0.907181448 0.846285837 1 17.69866194 3.236997125 24.9999246 0.983312754 0.85489217 0.162852121 0.18993084 104.5820185 1672252.241 0.055940248 0.066852296 1725.826465 -3.236997125 -0.128420584 MGIGGLDKEFSDIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MGIGGLDKEFSDIFR 15 1 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 ; 171.91 9.64E-07 874150000 1619470 1535440 799750 917280 1468330 1286140 1614570 1830320 544790 FALSE TRUE 1405452.936 1525353.594 1186511.775 1125562.444 1439113.106 1335618.638 1457989.25 1438920.312 480385.5468 2.925676981 3.175269538 2.469915639 2.343039775 2.995746053 2.780305625 3.035039792 2.995344721 1 18.87383322 4.239587585 24.99906048 2.607792408 3.050473332 0.106842017 0.597983168 67.25114157 1636859.987 0.148009488 0.348762951 17361.5136 -4.239587585 0.442680925 TAS(ph)QGPQTDSVIQNSENIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TASQGPQTDSVIQNSENIK 19 0 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 T(0.015)AS(0.985)QGPQTDSVIQNSENIK 389.89 5.84E-127 227540000 88651 76968 99998 112830 168590 144370 179300 210040 219090 TRUE FALSE 76935.54574 76462.39214 148357.3673 138449.776 165235.3888 149924.0073 161911.5136 165124.5805 193189.4298 0.398238899 0.395789729 0.767937291 0.716652956 0.85530243 0.776046637 0.838097166 0.854728857 1 17.55965663 4.307131744 0.928161972 0.865258069 0.237631356 0.84078932 0.077693387 0.420634151 0.453380554 0.026915732 0.234499262 20282.97915 -4.307131744 -0.627626712 down MGLS(ph)MER ddPTM_MDA-MB-175_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 119.62 0.0049738 2949921000 5262390 2582880 1355065 1829770 2446040 1875860 3147630 2655220 2590400 TRUE FALSE 4566951.828 2565912.891 2010378.966 2245247.245 2397368.59 1948025.548 2842373.327 2087421.866 2284165.863 1.999395886 1.123347885 0.880137033 0.982961562 1.049559766 0.85283892 1.244381318 0.913866151 1 21.12323598 4.732091512 3.623795372 0.992974723 2.106071715 0.89392169 0.108469758 0.073513327 1.777622754 0.024885938 0.219999195 53962.43174 -4.732091512 1.113096992 MGLSMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MGLSMER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 129.39 0.0085261 523370000 581000 566370 377750 379650 567700 569990 507570 582830 542780 FALSE TRUE 504219.3779 562649.4782 560431.1635 465855.3351 556403.8807 591917.8841 458345.9395 458196.3401 478613.1667 1.05350085 1.175582949 1.170948069 0.973344169 1.162533585 1.236735479 0.957654263 0.957341695 1 18.86850056 2.213262059 24.99915196 0.96809733 1.127288374 0.507562434 0.072911965 180.887402 178745.244 0.029814629 0.020109567 163.403765 -2.213262059 0.159191044 MGPGAASGGERPNLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MGPGAASGGERPNLK 15 1 Q9H0U4;E9PLD0 Q9H0U4 RAB1B Ras-related protein Rab-1B 0 ;;; 201.76 5.70E-09 1682410000 1817170 1550990 1017750 1432890 1727470 1496370 1552530 2203020 2062280 FALSE TRUE 1577026.38 1540801.445 1509937.304 1758249.575 1693096.727 1553936.322 1401965.88 1731921.317 1818479.608 0.867222472 0.84730202 0.830329522 0.966878907 0.931050708 0.854525019 0.770954963 0.952400736 1 20.79430132 2.523449979 0.017425576 1.793401857 3.44E-06 0.137730415 0.06559475 2682.475579 39.22934808 2056.422519 1979.265862 333.7720597 -2.523449979 -1.793398412 MGPGIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MGPGIDR 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 86.866 0.045975 212170000 398730 400810 216050 267250 399970 370420 403400 439570 375140 FALSE TRUE 346036.8202 398177.0527 320532.5026 327933.1972 392011.3795 384670.2971 364278.3301 345571.3762 330791.3766 1.046087791 1.203710498 0.968986876 0.991359571 1.185071339 1.162878855 1.101232849 1.044680728 1 18.3355621 1.520923043 3.000869511 1.003501047 1.095576632 0.142313698 0.077246559 0.506857359 9.15467545 0.090291701 0.021076888 33.18356511 -1.520923043 0.092075585 MGPLGLDHMASSIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 MGPLGLDHMASSIER 15 0 A0A087X0X3;P52272-2;P52272;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;;;;;; 225.32 1.01E-12 6160750000 5345470 4779420 2466789 3443060 4836850 5107760 4712790 5440610 4692030 FALSE TRUE 4639052.596 4748023.675 3659736.411 4224859.397 4740606.148 5304258.832 4255744.351 4277177.89 4137343.559 1.121263567 1.147601984 0.884561884 1.021152664 1.14580916 1.282044567 1.028617588 1.033798095 1 21.98027333 2.042897676 24.99998874 1.022879804 1.096545336 0.121274771 0.100729779 342.2041857 199428.9671 0.044316638 0.029878225 110.3818519 -2.042897676 0.073665532 MGPLINRPHLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MGPLINRPHLER 12 1 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ;;; 150.68 4.11E-05 4058620000 1233830 1352860 678848 889717 1267700 1525020 1208460 1351480 1183540 FALSE TRUE 1070776.239 1343972.974 1007141.163 1091740.843 1242475.25 1583688.506 1091263.735 1062476.519 1043623.249 1.026018 1.287795164 0.965042858 1.046106288 1.190540026 1.517490634 1.045649123 1.018065207 1 19.99316956 2.025780367 24.99918323 1.016782763 1.172983423 0.178374591 0.153982111 378.2569609 366793.5138 0.064560703 0.043525487 106.1158768 -2.025780367 0.156200659 MGPPVGGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 MGPPVGGHR 9 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;;;;;;;; 121.62 0.0006088 1685051000 1567486 1443818 862259 1073553 1341339 1538746 1326132 1533734 1643805 FALSE TRUE 1360338.754 1434333.464 1279250.336 1317319.617 1314648.978 1597942.554 1197523.923 1205756.92 1449476.246 0.938503655 0.989552929 0.882560401 0.908824564 0.906982079 1.102427556 0.826176991 0.831856971 1 20.46710026 SHSGT(ph)SPDNTAPPPPPPRPQPSHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHSGTSPDNTAPPPPPPRPQPSHSR 25 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.003)HS(0.091)GT(0.453)S(0.453)PDNTAPPPPPPRPQPSHSR 126.18 0.00019688 903830000 316040 225910 87066 83459 110540 124740 104800 114960 95853 TRUE FALSE 274274.5133 224425.9823 129171.4088 102409.6415 108340.4703 129538.8285 94636.51213 90376.69862 84521.36754 3.245031656 2.655257349 1.528269272 1.211642032 1.281811611 1.532616335 1.119675591 1.069276341 1 16.36702849 4.313134682 1.99397148 1.194849305 3.287645107 0.961885667 0.144745211 0.071096041 0.511067253 0.0441243 0.200002036 20565.28263 -4.313134682 2.092795801 up MGPSGGEGMEPERRDS(ph)QDGSSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 18 MGPSGGEGMEPERRDSQDGSSYR 23 2 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 1 MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(0.468)QDGS(0.468)S(0.065)YR;MGPSGGEGMEPERRDS(0.982)QDGS(0.017)S(0.001)YR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(0.957)QDGS(0.038)S(0.005)YR;MGPSGGEGMEPERRDS(0.881)QDGS(0.068)S(0.051)YR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(0.999)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR 321.37 6.12E-74 31332203000 8913477 5047546 2650782.6 3480883 4768143 4899803 5321104 5311186 2817787 TRUE FALSE 7735538.431 5014388.338 3932709.932 4271270.687 4673266.283 5088301.592 4805064.153 4175430.206 2484671.431 3.113304373 2.018129349 1.582788727 1.719048496 1.88083874 2.047877047 1.933883126 1.680475798 1 21.24462365 4.717856375 2.893580531 1.725382481 3.320841058 0.709985466 0.283790665 0.214367161 2.63842475 0.072733111 0.781887475 52222.34566 -4.717856375 1.595458577 MGPSGGEGMEPERRDSQDGS(ph)SYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MGPSGGEGMEPERRDSQDGSSYR 23 2 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 1 MGPSGGEGMEPERRDS(0.361)QDGS(0.594)S(0.045)YR 155.42 2.27E-08 271610000 268700 144210 78668 93826 142440 142450 174770 159950 81775 TRUE FALSE 233190.6142 143262.675 116712.1079 115130.6273 139605.7227 147930.1437 157820.8323 125745.9372 72107.65266 3.233923247 1.986788777 1.618581435 1.59664922 1.9360736 2.051517949 2.188683537 1.743863967 1 16.13786476 4.730131283 3.429551336 1.772992935 3.405463743 0.677728494 0.321846074 0.181063225 3.671186191 0.081967459 0.76401255 53719.41605 -4.730131283 1.632470809 MGPVMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MGPVMDR 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 97.071 0.028538 501720000 722800 657320 444090 467100 669670 869090 612520 662920 650060 FALSE TRUE 627280.1487 653002.0216 658853.4094 573162.1942 656344.8772 902524.4547 553117.9047 521159.7168 573210.6474 1.094327455 1.139200789 1.149408882 0.999915471 1.145032599 1.574507485 0.964947018 0.909194062 1 19.12870588 2.040983357 24.99999299 0.944796561 1.178341302 0.332797846 0.150419872 161.9056501 98762.36476 0.062385493 0.042060249 109.8963725 -2.040983357 0.233544741 MGQAPSQSLLPPAQDQPRS(ph)PVPSAFSDQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 MGQAPSQSLLPPAQDQPRSPVPSAFSDQSR 30 1 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MGQAPS(0.007)QS(0.007)LLPPAQDQPRS(0.979)PVPS(0.003)AFS(0.003)DQSR;MGQAPSQSLLPPAQDQPRS(0.999)PVPS(0.001)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.998)PVPS(0.002)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.999)PVPS(0.001)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.999)PVPS(0.001)AFSDQSR;MGQAPSQSLLPPAQDQPRS(1)PVPSAFSDQSR;MGQAPSQSLLPPAQDQPRS(1)PVPSAFSDQSR;MGQAPSQSLLPPAQDQPRS(0.999)PVPS(0.001)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.994)PVPS(0.002)AFS(0.003)DQS(0.001)R;MGQAPSQSLLPPAQDQPRS(0.968)PVPS(0.031)AFS(0.001)DQSR;MGQAPSQSLLPPAQDQPRS(1)PVPSAFSDQSR;MGQAPSQSLLPPAQDQPRS(0.999)PVPS(0.001)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.999)PVPS(0.001)AFSDQSR 252.38 2.98E-58 17420020000 5432300 4841850 2172733 2461725 4537372 4744475 4416913 4951647 1451759 TRUE FALSE 4714407.791 4810043.569 3223473.946 3020697.286 4447087.174 4926998.023 3988561.457 3892775.823 1280133.705 3.682746399 3.757454046 2.51807599 2.359673271 3.47392398 3.84881517 3.115738178 3.040913467 1 20.28786307 4.251453525 24.71865555 2.858204422 3.720100929 0.204539839 0.765946179 355.6220872 681794.2916 0.193297693 0.504173518 17842.41043 -4.251453525 0.861896507 MGS(ph)PAPLLPGDLLGGGSDSI ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 MGSPAPLLPGDLLGGGSDSI 20 0 Q9UPQ9-1;Q9UPQ9;Q9UPQ9-2 Q9UPQ9-1 TNRC6B Trinucleotide repeat-containing gene 6B protein 1 MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI 215 1.29E-24 291768000 592336 504296 349190 368672 593783 545152 517528 577057 515004 TRUE FALSE 514057.2968 500983.2464 518059.452 452384.6124 581967.88 566124.3502 467338.2142 453657.8512 454120.8138 1.131983563 1.103193756 1.140796537 0.996176785 1.28152655 1.246638192 1.029105471 0.99898053 1 18.79271664 2.080223788 8.327909661 1.003772392 1.146322493 0.430179957 0.076764228 0.252183091 23.14290158 0.032765327 0.022047042 120.288411 -2.080223788 0.142550101 TELESTIFGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TELESTIFGSPR 12 0 Q9UQK1 Q9UQK1 PPP1R3C Protein phosphatase 1 regulatory subunit 3C 1 TELESTIFGS(1)PR 148.62 0.00031986 0 12340 17141 14359 22858 27841 30035 26761 30906 31891 TRUE FALSE 10709.23773 17028.39964 21303.06043 28048.25826 27287.01857 31190.46589 24165.72234 24296.99241 28120.88231 0.380828653 0.605542865 0.757553059 0.997417434 0.97034717 1.109156731 0.859351498 0.864019562 1 14.77935424 4.313547595 1.523620916 0.956106993 0.35911127 0.871437613 0.076840895 0.199971284 0.745730623 0.024200879 0.142983663 20584.8447 -4.313547595 -0.596995723 down MGSGVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MGSGVER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 89.55 0.041389 379390000 553910 528310 300370 350120 412310 517000 443640 505120 441090 FALSE TRUE 480709.3901 524839.4968 445629.9367 429620.0972 404105.8377 536889.3245 400615.8611 397104.0188 388944.8427 1.235932033 1.349393125 1.145740701 1.104578465 1.038979807 1.380373939 1.030006873 1.02097772 1 18.56920605 -1.934026495 0.129609556 3.38E-12 1.419307865 0.350988392 0.110051461 209.7336197 2.426625942 53.77191653 3.078446374 0.01164055 1.934026495 1.419307865 KPVTVSPTTPTSPTEGEAS(ph) ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 KPVTVSPTTPT(0.017)S(0.093)PT(0.093)EGEAS(0.797) 101.01 0.00057729 856170000 380090 473900 381150 608880 669120 647600 739630 915330 827530 TRUE FALSE 329860.1435 470786.9197 565475.4149 747135.5101 655805.8211 672513.5911 667900.7964 719593.8026 729700.3461 0.452048769 0.645178425 0.774941958 1.023893594 0.898733055 0.92162981 0.915308318 0.986149735 1 19.47694461 4.324732916 1.446988035 0.956150825 0.420901264 0.928111463 0.048036286 0.142213128 0.461000962 0.013988011 0.089279726 21121.89679 -4.324732916 -0.535249561 down MGVMSS(ph)PTENSFTLDADF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MGVMSSPTENSFTLDADF 18 0 P31350;P31350-2 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 MGVMS(0.386)S(0.533)PT(0.081)ENSFTLDADF;MGVMS(0.21)S(0.78)PT(0.01)ENSFTLDADF 246.3 2.95E-24 27023000 54813 74416 46487 67316 97185 97986 95259 113178 95996 TRUE FALSE 47569.32317 73927.1564 68968.26869 82601.12666 95251.20864 101755.5848 86020.79684 88975.76545 84647.46224 0.561969868 0.873353488 0.81477066 0.975825199 1.125269513 1.202110283 1.016224167 1.05113329 1 16.3691792 4.729006332 0.788996747 1.075554871 0.310125713 0.80370525 0.079012098 1.174673776 0.573854831 0.032595272 0.794357689 53580.44698 -4.729006332 -0.765429158 MGVMSSPT(ph)ENSFTLDADF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MGVMSSPTENSFTLDADF 18 0 P31350;P31350-2 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 MGVMS(0.032)S(0.292)PT(0.675)ENSFTLDADF 142.08 1.29E-06 14166000 21706 25925 16270 22706 32433 31896 32802 43920 33311 TRUE FALSE 18837.4971 25754.69697 24138.22642 27861.74434 31787.64675 33123.05976 29620.86709 34528.04979 29373.01153 0.64131991 0.876814995 0.821782485 0.948549124 1.082205913 1.127669859 1.008438207 1.175502544 1 14.84220357 4.233414433 0.685810831 1.102923587 0.570623082 0.802704016 0.069595838 0.726500246 0.419833164 0.034258232 0.276377559 17116.47905 -4.233414433 -0.532300506 MHAPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MHAPGK 6 0 P62277;J3KMX5;E9PS50 P62277 RPS13 40S ribosomal protein S13 0 ;;; 78.002 0.070933 3095400000 9746050 9311900 5956030 7199850 7329010 8209670 9995210 11506940 10201240 FALSE TRUE 8458084.799 9250729.516 8836386.03 8834685.985 7183177.04 8525501.317 9025876.073 9046270.428 8995261.028 0.940282308 1.028400342 0.982337922 0.982148929 0.798551261 0.947776978 1.003403464 1.005670697 1 23.10073372 2.239823033 9.368054429 1.003644725 0.946783559 0.169521795 0.058886923 0.195093136 240.8082052 0.024481138 0.017758436 173.709285 -2.239823033 -0.056861166 MHDLNTDQENLVGTHDAPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MHDLNTDQENLVGTHDAPIR 20 0 O43684;O43684-2;J3QT28;J3QSX4 O43684 BUB3 Mitotic checkpoint protein BUB3 0 ;; 318.97 7.98E-67 1263780000 2528852 2711028 824162 1742329 2551731 2197823 2818354 3086217 2702067 FALSE TRUE 2194657.801 2693219.079 1222729.5 2137951.429 2500956.545 2282374.673 2545030.463 2426253.512 2382631.717 0.9211066 1.13035475 0.51318443 0.897306711 1.049661401 0.95792172 1.068159399 1.01830824 1 21.18412454 3.339159664 5.657274615 1.018906061 0.855262624 0.205731536 0.150913367 0.335038659 15.84234121 0.043555417 0.056309442 2183.532518 -3.339159664 -0.163643437 MHEGDEGPGHHHKPGLGEGT(ph)P ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MHEGDEGPGHHHKPGLGEGTP 21 1 P06702 P06702 S100A9 Protein S100-A9 1 MHEGDEGPGHHHKPGLGEGT(1)P 55.063 0.075127 94341000 83022 100550 50201 78318 77434 66819 59229 97178 60496 TRUE FALSE 72050.43235 99889.48043 74478.37151 96101.29892 75893.2149 69389.57017 53484.9807 76397.24094 53344.2318 1.350669602 1.872545111 1.396184161 1.801531219 1.422707055 1.300788629 1.002638503 1.432155612 1 15.70304466 2.844876041 2.688625613 1.199104786 1.609122081 0.491343478 0.201192939 0.229197953 3.228925478 0.065025642 0.064420985 699.6422716 -2.844876041 0.410017296 MHIAQDINQDNLQLFLNSYNGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MHIAQDINQDNLQLFLNSYNGR 22 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 0 246.31 5.98E-31 310690000 187080 174220 109870 137520 135020 184960 178130 182000 172600 FALSE TRUE 162356.904 173075.5373 163003.4995 168746.0179 132333.3662 192075.5309 160854.98 143080.7163 152195.4246 1.066765998 1.137192775 1.071014453 1.108745669 0.86949635 1.262032228 1.056897607 0.940111811 1 17.21556546 1.859667285 5.692790737 0.970302922 1.084704942 0.192325907 0.096379259 0.339476337 14.00597124 0.04723431 0.024552466 72.38811795 -1.859667285 0.11440202 MHLAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MHLAGK 6 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ; 84.566 0.055705 1865730000 7579100 7064400 4390500 5820400 5770500 5871900 7100200 8171300 7125600 FALSE TRUE 6577502.732 7017993.491 6513760.485 7142010.779 5655678.34 6097795.793 6411623.697 6423931.084 6283219.686 1.046836345 1.116942243 1.036691507 1.1366801 0.900124239 0.970489032 1.020436021 1.022394792 1 22.58307259 3.252816629 24.99997276 0.989873099 1.083220299 0.557356036 0.044732265 195.4770052 342795.2165 0.012996279 0.016698098 1789.849969 -3.252816629 0.0933472 MHSLLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MHSLLIK 7 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 124.37 0.0041527 280160000 1264450 1193450 693080 938530 1156480 1007210 1232250 1482330 1377140 FALSE TRUE 1097349.729 1185610.148 1028255.806 1151637.581 1133468.311 1045958.02 1112746.585 1165345.265 1214336.078 0.903662296 0.976344333 0.846763779 0.948368085 0.933405777 0.861341468 0.916341534 0.959656298 1 20.21173632 1.531689452 2.608113751 0.998465811 0.912421962 0.378907671 0.037826827 0.293257411 3.934393777 0.046253252 0.009747807 34.01648635 -1.531689452 -0.086043849 MHTTFEHDIQALGTQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MHTTFEHDIQALGTQVR 17 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 166.92 1.32E-09 109520000 79978 82344 29894 55107 78337 100590 69794 71337 67987 FALSE TRUE 69408.70466 81803.07684 44350.83839 67619.88661 76778.24696 104459.7624 63025.38862 56082.1377 59949.65431 1.157783234 1.364529584 0.739801403 1.127944563 1.280712088 1.742458127 1.051305289 0.935487257 1 15.87146381 2.01426591 24.99902714 0.972213587 1.231101554 0.181024927 0.245235369 396.7376324 695225.0185 0.104912152 0.070699359 103.339394 -2.01426591 0.258887967 MIDLS(ph)AFSRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MIDLSAFSRK 10 1 Q8N1W2 Q8N1W2 ZNF710 Zinc finger protein 710 1 MIDLS(0.5)AFS(0.5)RK;MIDLS(0.5)AFS(0.5)RK;MIDLS(0.5)AFS(0.5)RK 66.071 0.071047 566406000 1161830 1462800 981989 1095409 1356410 1705150 1009397 1085735 1496120 TRUE FALSE 1008291.222 1453190.77 1456882.165 1344138.356 1329420.095 1770748.224 911505.8343 853559.0194 1319250.398 0.764291012 1.101527635 1.104325735 1.018865227 1.007708693 1.342238158 0.690927087 0.647003041 1 20.33128699 2.205573901 24.99999678 0.748063235 1.056786432 0.374183484 0.167363471 173.4770684 131473.7516 0.066061245 0.044541792 160.5365408 -2.205573901 0.308723197 MIDQVFGVLES(ph)PELSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 MIDQVFGVLESPELSR 16 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 MIDQVFGVLES(0.992)PELS(0.008)R;MIDQVFGVLES(1)PELSR;MIDQVFGVLES(1)PELSR;MIDQVFGVLES(0.992)PELS(0.008)R;MIDQVFGVLES(0.999)PELS(0.001)R;MIDQVFGVLES(0.963)PELS(0.037)R;MIDQVFGVLES(0.998)PELS(0.002)R;MIDQVFGVLES(0.995)PELS(0.005)R;MIDQVFGVLES(1)PELSR;MIDQVFGVLES(0.999)PELS(0.001)R 220.34 1.21E-14 431100000 404838.4 400374.9 260959.5 303470.1 389515.8 403345 355900.1 412832.1 516030.3 TRUE FALSE 351337.9797 397744.8109 387160.3871 372377.6245 381765.1977 418861.9431 321384.9631 324551.1681 455025.7858 0.772127626 0.874114882 0.85085373 0.818365983 0.838996843 0.920523531 0.706300551 0.713258849 1 18.79558878 2.239597599 24.99999988 0.782914647 0.845785409 0.019734734 0.088496788 66.54314442 1604325.374 0.033822324 0.024695681 173.6191395 -2.239597599 0.062870762 MIDVDSLTDKECDWLNNYHLTCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MIDVDSLTDKECDWLNNYHLTCR 23 1 Q9NQW7-4;Q9NQW7-3;Q5T6H7;Q9NQW7-2;Q9NQW7 Q9NQW7-4 XPNPEP1 Xaa-Pro aminopeptidase 1 0 157.83 1.40E-09 407720000 316070 345580 250280 401180 358780 304630 313230 504910 420330 FALSE TRUE 274300.5487 343309.8622 371316.2451 492274.0507 351640.9799 316349.3132 282853.0028 396938.9257 370639.0662 0.740074573 0.926264643 1.001827058 1.328176373 0.948742353 0.853523932 0.763149459 1.070958142 1 18.49965543 4.680554858 2.827435349 0.99368637 0.711328104 0.230915242 0.14643362 0.591977444 7.088569954 0.039256451 0.359412313 47924.19846 -4.680554858 -0.282358266 MIEYDPERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MIEYDPERR 9 1 O60832;O60832-2;C9IYT0;H7C0M1;H7BZF2 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ; 87.913 0.021068 539160000 366436 348397 207822 258474 332550 381831 271430 348676 280638 FALSE TRUE 318010.5542 346108.3572 308325.4143 317164.4722 325932.9056 396520.2856 245106.7604 274114.3508 247461.2953 1.285092094 1.398636327 1.245954095 1.281673046 1.317106601 1.602352744 0.990485239 1.107705956 1 17.91684337 2.21084347 24.99999876 1.046589931 1.347082596 0.682816713 0.1033447 126.9161777 114473.5117 0.04135125 0.027885839 162.4962975 -2.21084347 0.300492664 MIFDVESMKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MIFDVESMKK 10 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 121.9 0.00080625 1026960000 1762320 1328570 831680 991500 1159530 980230 1596680 1901360 771790 FALSE TRUE 1529424.947 1319842.536 1233883.23 1216635.229 1136457.622 1017940.082 1441834.219 1494768.96 680549.8654 2.247337079 1.939376676 1.813068068 1.787723855 1.669910875 1.495761199 2.118631261 2.196413571 1 19.37634135 4.749946513 1.65202331 1.777500164 2.42694141 0.195401623 0.331266966 1.994183439 5.160737523 0.091691045 2.089862175 56227.20718 -4.749946513 0.649441246 MIGGLFIYNHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MIGGLFIYNHK 11 0 A0A087WY71;Q96CW1-2;Q96CW1;E9PFW3;C9JJ47;C9JJD3;C9JGT8;C9JPV8;C9JTK4 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 ; 195.7 6.30E-08 497370000 1320040 1252260 746620 1076200 1283940 1172870 1398620 1566340 1543210 FALSE TRUE 1145593.369 1244033.822 1107687.929 1320567.659 1258392.106 1217991.068 1262982.048 1231390.38 1360773.472 0.84186927 0.914210813 0.814013465 0.970453706 0.924762374 0.895072614 0.928135413 0.904919449 1 20.37599549 8 0.133957713 0.994531655 0.521215602 0.349176022 0.043711048 235.6963162 2.743306924 1.04738662 20.90229469 100000000 -8 -0.473316053 MIIEEAKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MIIEEAKR 8 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;; 106.36 0.0085318 1208620000 993350 909300 578135 754693 988580 913890 1188200 1308870 869220 FALSE TRUE 862076.2807 903326.7484 857723.0197 926057.5804 968909.1921 949047.9397 1072968.547 1028978.336 766461.8018 1.124747872 1.178567211 1.119068188 1.208224047 1.264132394 1.238219488 1.399898265 1.342504393 1 19.54785437 3.431117832 2.493466051 1.272687785 1.144245361 0.160011325 0.104921178 0.440380469 5.535843359 0.032599744 0.046952197 2698.47148 -3.431117832 -0.128442424 MIKPFFHSLSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MIKPFFHSLSEK 12 1 P10599 P10599 TXN Thioredoxin 0 ;;; 181.32 1.10E-05 11202010000 20701200 20609500 12306080 15983500 17089500 14641600 21386300 25011300 27715400 FALSE TRUE 17965483.97 20474114.84 18257341.45 19612797.97 16749452.39 15204871.83 19312259.92 19662828.13 24438916.99 0.735117844 0.837766864 0.747060169 0.802523204 0.685359846 0.622158168 0.790225685 0.804570356 1 24.54267702 1.142004342 1.833169703 1.139077 0.744403978 0.638213355 0.060122056 0.800364279 2.056273078 0.601909316 0.017428537 13.86769694 -1.142004342 -0.394673022 MILELFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MILELFSK 8 0 Q5TA02;P78417-3;P78417;Q5TA01;P78417-2 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 103.74 0.010969 47724000 99557 107850 69609 83121 91011 78545 120550 124340 123490 FALSE TRUE 86400.2902 107141.5262 103272.1452 101994.8935 89200.05916 81566.67698 108859.0796 97750.85861 108891.1529 0.793455556 0.983932334 0.948397941 0.936668322 0.819167185 0.749066153 0.999705455 0.897693302 1 16.73252722 1.030425935 1.269592621 1.088662168 0.888257222 0.153078377 0.081886901 4.999054504 4.805460382 1.501670662 0.025240199 10.72570715 -1.030425935 -0.200404946 MILIQDGSQNTNVDKPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MILIQDGSQNTNVDKPLR 18 1 A0A087WTP3;Q92945;M0R0I5;M0QYH3 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 221.79 5.51E-19 861450000 361600 337860 242670 287040 304960 284050 352690 447420 393270 FALSE TRUE 313813.6438 335640.5754 360026.0237 352216.8191 298891.8926 294977.5873 318486.1781 351742.7148 346778.0686 0.904940861 0.967882937 1.038202978 1.015683663 0.861911175 0.850623537 0.918414995 1.014316494 1 18.40365314 1.705768289 7.311812644 1.006421745 0.938806453 0.192276839 0.059660517 0.228711317 27.73160274 0.039112034 0.017257794 50.78883939 -1.705768289 -0.067615292 MIMATNRPDTLDPALLRPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MIMATNRPDTLDPALLRPGR 20 2 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ; 159.7 1.41E-11 2264000000 2633100 2716600 1622310 1905910 2580100 2874000 2367000 2873200 2744200 FALSE TRUE 2285129.164 2698754.476 2406864.542 2338675.996 2528761.058 2984564.64 2137448.704 2258788.539 2419783.802 0.944352616 1.115287437 0.994660986 0.966481383 1.045035947 1.233401363 0.88332218 0.933467088 1 21.20644672 MIMDTAGNDPYCFVEFHEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MIMDTAGNDPYCFVEFHEHR 20 0 C9JTN7;P31483-2;H7BY49;F8W8I6;P31483-3;P31483;E5RGV5;E5RG67 C9JTN7 TIA1 Nucleolysin TIA-1 isoform p40 0 ; 109.42 0.00011431 197843000 55261 51067 21982.7 23062 39331 38142 35143 45172 41295 FALSE TRUE 47958.11884 50731.53751 32613.60725 28298.57958 38548.39005 39609.34742 31734.83727 35512.31933 36413.15214 1.317054856 1.393220156 0.895654601 0.777152702 1.058639194 1.087775847 0.871521288 0.975260785 1 15.15217201 4.240171207 24.99999953 0.952393369 1.355137639 0.769135649 0.091757792 18.75460056 291089.0784 0.023894456 0.056782398 17384.86038 -4.240171207 0.40274427 MINLSEPDTIDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MINLSEPDTIDER 13 0 Q14651;C9JAM8 Q14651 PLS1 Plastin-1 0 ; 144.57 9.63E-05 104523000 138142 153454 92258 113512 142503 162513 138882 152784 168426 FALSE TRUE 119886.1847 152445.9506 136874.2774 139286.6345 139667.4691 168764.9803 125413.245 120112.3306 148514.8702 0.807233542 1.026469271 0.921620019 0.937863221 0.940427507 1.136350724 0.844449077 0.808756257 1 17.18024786 MINTDLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MINTDLSR 8 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;;; 145.65 0.0013167 1038580000 1540490 1704460 1082876 1143980 1771060 1974050 1514420 1699130 1645420 FALSE TRUE 1336910.343 1693263.29 1606558.456 1403738.144 1735819.371 2049992.981 1367551.781 1335784.272 1450900.322 0.921435004 1.167043155 1.107283823 0.967494543 1.196373965 1.41291097 0.942553917 0.920658885 1 20.46851698 MIPCDFLIPVQTQHPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MIPCDFLIPVQTQHPIR 17 0 P06744;A0A2U3TZU2;P06744-2;K7EQ48;K7ESF4 P06744;K7ESF4 GPI Glucose-6-phosphate isomerase 0 ; 123.36 5.38E-05 2534200000 832800 794260 602430 655190 687200 775750 626360 770900 1230370 FALSE TRUE 722743.37 789042.4538 893767.163 803960.9035 673526.0645 805593.6045 565615.7036 606049.0342 1084917.06 0.666173845 0.727283663 0.823811511 0.741034437 0.620808806 0.742539346 0.521344649 0.55861324 1 20.04915333 3.281802355 12.61571016 0.662559395 0.744759407 0.013394136 0.135604233 2.970640693 861.2577883 0.039026368 0.05033512 1913.384958 -3.281802355 0.082200012 MIPCDFLIPVQTQHPIRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MIPCDFLIPVQTQHPIRK 18 1 P06744;A0A2U3TZU2;P06744-2;K7EQ48;K7ESF4 P06744;K7ESF4 GPI Glucose-6-phosphate isomerase 0 ; 144.33 6.43E-08 2215900000 4088000 3504600 1684670 2069020 2964600 2852800 3475900 3866500 1421550 FALSE TRUE 3547760.442 3481578.052 2499382.047 2538822.614 2905610.26 2962549.062 3138807.753 3039679.064 1253495.978 2.83029264 2.777494393 1.993929051 2.025393506 2.318005251 2.363429251 2.504042938 2.424961162 1 20.25752594 4.249583316 23.89056665 2.157663544 2.803894427 0.316181309 0.427571807 160.755524 348408.6326 0.105224844 0.272090322 17765.74057 -4.249583316 0.646230883 MIST(ph)PSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MISTPSPK 8 0 Q53F19;Q53F19-2 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 MIS(0.109)T(0.472)PS(0.419)PK 80.755 0.066589 0 244590 154780 115280 131810 190370 149550 196180 216460 214310 TRUE FALSE 212266.8118 153763.24 171029.7936 161739.4751 186582.0095 155303.2853 177154.4938 170171.7135 188974.5159 1.12325628 0.813671829 0.905041575 0.855879822 0.987339528 0.821821315 0.937451767 0.900500857 1 17.52783217 1.233948626 24.10458601 1.000000215 0.911736619 0.072460518 0.089511111 224.3599482 1172381.94 0.150516943 0.019552775 17.13754572 -1.233948626 -0.088263596 MISTPS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MISTPSPK 8 0 Q53F19;Q53F19-2 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 MIST(0.001)PS(0.999)PK 112.89 0.0030979 247000000 600410 344260 258690 316810 388900 295970 422370 474600 473850 TRUE FALSE 521064.2973 341998.5334 383793.3493 388746.5526 381161.6509 307356.1574 381408.6224 373110.4833 417831.9928 1.247066539 0.818507293 0.918535095 0.930389629 0.912236634 0.735597471 0.912827713 0.892967723 1 18.67256344 4.74557845 24.87200791 0.889425136 1.247066717 0.717779217 0.070336632 416.5646405 1476313.73 0.016798551 0.162643503 55664.51763 -4.74557845 0.357641582 MITHFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MITHFER 7 0 Q8NBN3-3;Q8NBN3 Q8NBN3-3 TMEM87A Transmembrane protein 87A 0 ; 126.04 0.0039912 378300000 368110 408500 246520 271930 407420 450490 337800 443880 388050 FALSE TRUE 319463.3308 405816.5366 365737.8966 333675.8627 399313.1391 467820.6418 305040.208 348959.7163 342175.1711 0.933625107 1.1859906 1.068861588 0.975160944 1.166984553 1.367196341 0.891473823 1.019827696 1 18.38437555 MIVDPVEPHGEMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MIVDPVEPHGEMK 13 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 155.98 4.70E-05 531360000 1136250 805290 594550 800780 852580 790350 900940 1023700 1174470 FALSE TRUE 986091.6836 799999.997 882076.3687 982609.3382 835615.326 820755.2759 813566.9775 804789.7214 1035625.495 0.952170151 0.772480014 0.851732961 0.948807598 0.806870177 0.792521312 0.785580291 0.777104972 1 19.98207096 MKDTDSEEEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MKDTDSEEEIR 11 1 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ; 106.49 0.0021197 649090000 574320 462410 476260 785770 525940 444880 341700 636970 1608920 FALSE TRUE 498422.1569 459372.3983 706580.929 964191.0882 515474.823 461994.8215 308561.9866 500758.9224 1418715.31 0.351319361 0.323794629 0.498042788 0.679622671 0.363339156 0.325643079 0.217493943 0.352966461 1 20.43615369 1.236631856 24.99957933 1.000000774 0.386962444 0.707081821 0.123577649 31.14706065 403601.2175 0.208766523 0.033051677 17.24375551 -1.236631856 -0.61303833 MKDTDSEEEIREAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 MKDTDSEEEIREAFR 15 2 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ;;;;;;;;;; 216.99 1.20E-12 9238516000 13310490 10842470 7307466 9264857 10692530 9503965 8097761 14907270 4744838 FALSE TRUE 11551475.02 10771245.1 10841381 11368584.39 10479769.57 9869588.683 7312441.385 11719466.32 4183908.657 2.760929066 2.574445568 2.591208817 2.717216201 2.504779724 2.358939808 1.747753592 2.801080827 1 21.99641992 1.231252579 24.99948383 0.999997384 2.491840722 0.714226395 0.299448762 146.9940306 502796.2885 0.738652978 0.073421201 17.03148744 -1.231252579 1.491843338 MKEIAEAYLGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MKEIAEAYLGGK 12 1 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 ; 138.87 6.09E-05 720370000 2941600 2508600 1592140 1885520 2472100 2108150 3256400 3569500 1238830 FALSE TRUE 2552860.107 2492120.841 2362104.229 2313656.134 2422910.047 2189251.895 2940594.829 2806190.203 1092376.929 2.33697732 2.281374474 2.162352726 2.118001647 2.218016495 2.00411766 2.691923229 2.568884539 1 20.05903932 1.231499327 24.99999032 0.999997747 2.306875609 0.799776443 0.204011389 122.0801382 432177.3471 0.550301097 0.056040345 17.04116678 -1.231499327 1.306877862 MKEIAEAYLGK ddPTM_MDA-MB-175_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 ;;; 150.21 3.10E-05 8870720000 26415300 21774600 11834300 15848560 20272300 17216200 25885100 31746400 9242610 FALSE TRUE 22924451.18 21631561.22 17557407.06 19447217.78 19868920.89 17878518.35 23374766.99 24957679.41 8149959.175 2.812830185 2.654192586 2.154293867 2.386173643 2.437916616 2.193694222 2.868083936 3.062307292 1 22.9583614 1.227476877 25 0.999996623 2.575947952 0.74195593 0.291185728 286.4168024 645986.4745 1.190852949 0.080209572 16.88405964 -1.227476877 1.575951329 MKEIAEAYLGYPVTNAVITVPAYFNDSQR ddPTM_MDA-MB-175_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 ; 204.53 2.20E-25 2142400000 1736620 1456190 769200 864860 1488970 1495580 1842990 1962170 469030 FALSE TRUE 1507121.267 1446624.192 1141187.693 1061239.682 1459342.41 1553115.93 1664257.113 1542575.215 413581.8077 3.644070505 3.497794548 2.759279232 2.56597283 3.528545944 3.755281063 4.024009476 3.729794653 1 18.6578132 4.458099398 23.90434819 3.1852007 3.607502085 0.042890106 0.868226284 512.7576336 644370.958 0.218048072 0.577140855 28714.377 -4.458099398 0.422301385 MKELEENLNIAIDVIDAYQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MKELEENLNIAIDVIDAYQK 20 1 A0A1W2PQD2;Q9UBB4-2;Q9UBB4 A0A1W2PQD2 ATXN10 Ataxin-10 0 133.47 9.76E-06 67108000 130860 120990 92482 87583 114220 87729 179170 170030 100130 FALSE TRUE 113566.5194 120195.2087 137206.6045 107470.0588 111947.2455 91103.9914 161794.121 133670.4077 88292.74547 1.286249723 1.361325985 1.553996354 1.217201461 1.267909893 1.031840056 1.832473553 1.513945534 1 16.43000728 2.257075095 24.99991134 1.478363466 1.298000311 0.089211156 0.236513883 537.8655249 726273.1363 0.088924718 0.068753152 180.7486636 -2.257075095 -0.180363156 MKETAEAYLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MKETAEAYLGK 11 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 139.78 3.55E-05 2026700000 4248500 3263200 2443600 3306100 3364100 3229200 3710900 4289700 2878900 FALSE TRUE 3687049.961 3241763.824 3625333.133 4056800.536 3297160.992 3353429.414 3351017.489 3372381.037 2538559.722 1.45241805 1.277009084 1.428106301 1.598071734 1.298831366 1.320996857 1.320046742 1.328462359 1 21.27557877 0.652127971 1.224789703 2.65E-19 1.39382014 0.624230482 0.093416871 3.879789763 1.718170276 9.88302356 0.028823534 4.48877639 -0.652127971 1.39382014 MKETIMNQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MKETIMNQEK 10 1 P20290-2;D6RDG3 P20290-2 BTF3 Transcription factor BTF3 0 114.24 0.0012603 420570000 420700 369030 274290 304940 350870 303030 446210 496060 366800 FALSE TRUE 365103.4291 366605.8176 406937.5614 374181.2877 343888.3735 314687.7602 402936.6229 389981.4293 323437.3219 1.128822818 1.133467887 1.258165134 1.156889643 1.063230339 0.9729482 1.245795076 1.205740349 1 18.30312664 3.463172676 24.40857246 1.115420602 1.175824186 0.12202452 0.089618017 481.4325742 842453.0635 0.027721387 0.035807563 2905.177528 -3.463172676 0.060403584 MKFNPFVTSDR ddPTM_MDA-MB-175_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 ; 189.24 2.55E-06 2670400000 3245750 3249130 1151440 1432780 3190430 3005060 3532000 3705100 543660 FALSE TRUE 2816815.914 3227786.251 1708280.235 1758114.598 3126946.685 3120666.603 3189467.184 2912793.198 479389.1341 5.875844305 6.733123513 3.563452139 3.667406023 6.522773384 6.509673208 6.653190397 6.076051772 1 18.87083768 MKGDYFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 MKGDYFR 7 1 P27348;E9PG15;P31946-2;P31946 P27348;P31946-2 YWHAQ;YWHAB "14-3-3 protein theta;14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 ;;;;; 119.29 0.0043911 29851160000 17959050 14632340 9169890 11533250 14551190 13369310 14998790 17189210 13811500 FALSE TRUE 15585716.04 14536219.2 13604479.48 14152050.69 14261649.79 13883636.01 13544209.65 13513431.21 12178720.2 1.279749906 1.193575265 1.117069712 1.162031022 1.171030252 1.139991376 1.112120931 1.1095937 1 23.5378592 MKGDYHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MKGDYHR 7 1 P62258;P62258-2 P62258 YWHAE 14-3-3 protein epsilon 0 ; 72.485 0.046948 1202150000 1050600 1056650 693700 844420 785510 894230 1022250 1243470 1086980 FALSE TRUE 911760.5481 1049708.797 1029175.64 1036158.467 769879.8878 928631.6067 923112.3523 977563.6172 958478.4627 0.951258253 1.095182456 1.073759798 1.081045123 0.803231286 0.96886017 0.963101821 1.019911928 1 19.87038649 5.117519594 11.02077436 0.999503153 0.000213444 0.033349891 0.083347432 563298.072 1118440.004 0.021088341 13307378.38 131074.9179 -5.117519594 -0.999289708 MKGDYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 MKGDYYR 7 1 B7Z2E6;H0YB80;P63104-2;P63104;E7EX29;B0AZS6;E7ESK7;P31947-2;P31947;P61981;Q04917;A2IDB2 B7Z2E6;P63104;P31947-2;P61981;Q04917 YWHAZ;SFN;YWHAG;YWHAH "14-3-3 protein zeta/delta;14-3-3 protein sigma;14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed;14-3-3 protein eta" 0 ;;;;;;; 119.29 0.0043911 49276200000 20839740 20668080 11690510 16171610 18652140 18014910 20550150 22600500 18723910 FALSE TRUE 18085715.56 20532310.02 17344079.74 19843621.22 18280998.91 18707955.24 18557199.62 17767558.95 16510390.69 1.095414148 1.243599283 1.05049481 1.201886835 1.107242054 1.133101911 1.123970956 1.076144065 1 23.97687092 -0.139178064 0.731142762 1.19E-09 1.145477055 0.414886448 0.053382959 16.45789264 1.376250188 24.4103851 0.019658386 0.72580831 0.139178064 1.145477054 MKGYPHWPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MKGYPHWPAR 10 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;M0R0J3;H3BPQ6;P51858;O75475;O75475-3;O75475-2;Q9Y3E1 Q7Z4V5-2;P51858;O75475;Q9Y3E1 HDGFRP2;HDGFRP3;HDGF;PSIP1 Hepatoma-derived growth factor-related protein 2;Hepatoma-derived growth factor;PC4 and SFRS1-interacting protein;Hepatoma-derived growth factor-related protein 3 0 ; 123.63 0.00027464 4386200000 9037100 11172800 5019400 6132400 10933300 10264100 12493400 12947500 2703900 FALSE TRUE 7842824.338 11099405.14 7446798.629 7524855.148 10715748.72 10658966.57 11281791.99 10178777.88 2384248.022 3.289433089 4.655306427 3.123332203 3.156070626 4.494393461 4.470577922 4.731803019 4.269177446 1 21.18510289 5.01812424 18.17447494 3.842993087 2.107595772 0.007719112 1.131470935 90618407.17 1972654667 0.269088524 4384513687 104261.565 -5.01812424 -1.735397315 MKLDYILGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MKLDYILGLK 10 1 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 135.99 0.0043373 0 4062000 3957100 2606000 3123700 3499400 2714800 4678500 5176800 3996600 FALSE TRUE 3525196.408 3931105.55 3866270.317 3832983.828 3429768.786 2819240.113 4224779.79 4069781.606 3524126.501 1.000303595 1.115483666 1.097086133 1.087640817 0.973225219 0.799982666 1.198816157 1.154834143 1 21.74883428 MKLPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MKLPGR 6 1 J3QQ67;Q07020;F8VYV2;G3V203;H0YHA7;Q07020-2;F8VUA6;A0A075B7A0 J3QQ67 RPL18 60S ribosomal protein L18 0 ; 98.03 0.036843 1430050000 2861500 2596600 1525680 1968220 2577500 2468500 2970000 3240500 2906100 FALSE TRUE 2483345.525 2579542.764 2263503.951 2415134.433 2526212.793 2563464.792 2681969.857 2547544.293 2562544.169 0.969093745 1.006633484 0.88330339 0.942475241 0.985822146 1.000359262 1.046604343 0.994146491 1 21.28914544 2.998808344 2.9095292 1.010871877 0.949963026 0.418960039 0.033190535 0.267169214 4.606854058 0.011398439 0.012372019 997.259871 -2.998808344 -0.060908851 MKPILLQGHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MKPILLQGHER 11 1 Q13347;Q5TFK1 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ; 132.76 0.00010557 2320300000 2832000 3340700 1838850 2592400 3295800 3149000 3187200 3762600 3629400 FALSE TRUE 2457744.025 3318754.722 2728124.011 3181044.042 3230220.028 3270144.068 2878105.835 2957997.271 3200336.467 0.767964259 1.037001814 0.852449122 0.993971751 1.009337631 1.021812582 0.899313514 0.924276963 1 21.60979216 4.753405995 24.35514264 0.96099137 0.767964063 0.527405716 0.059026433 1587.161352 2603813.742 0.014133523 0.303117603 56676.8879 -4.753405995 -0.193027307 MKPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MKPKPR 6 2 E7ETZ8;Q49MG5;A0A0C4DG83;A2VCS9;Q49MG5-2;A8MSM7 E7ETZ8 MAP9 Microtubule-associated protein 9 0 57.5 0.081893 1810700000 4707800 4572100 2708000 3659200 4046800 3864300 5648200 6661900 4027500 FALSE TRUE 4085652.302 4542065.574 4017597.858 4490077.287 3966276.597 4012962.122 5100438.433 5237304.528 3551373.538 1.150442852 1.278960246 1.13128 1.264321322 1.116828899 1.129974664 1.436187542 1.474726461 1 21.75994568 2.247107883 24.99861311 1.344804334 1.182127921 0.132512185 0.137770486 263.0523299 769363.5887 0.051093996 0.038935229 176.6476576 -2.247107883 -0.162676413 MKS(ph)LEQDALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MKSLEQDALR 10 1 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 MKS(1)LEQDALR;MKS(1)LEQDALR;MKS(1)LEQDALR;MKS(1)LEQDALR 103.88 0.0016693 1025280000 2891690 2301150 1184930 1819450 2397700 2215750 2255660 2897690 2417560 TRUE FALSE 2509545.84 2286033.594 1757966.111 2232583.931 2349990.461 2300991.336 2036906.44 2278041.543 2131758.811 1.177218467 1.072369718 0.824655258 1.047296683 1.102371642 1.079386338 0.955505112 1.068620677 1 21.02361279 2.189334608 0.006650671 8.00E-07 2.056013852 0.028861387 0.09359624 85238.19307 319.4093121 49983.28867 48759.03225 154.644546 -2.189334608 2.056013053 MKS(ph)SSSVTTSETQPCTPSSSDYSDLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MKSSSSVTTSETQPCTPSSSDYSDLQR 27 1 P50552;K7EM16 P50552 VASP Vasodilator-stimulated phosphoprotein 1 MKS(0.496)S(0.153)S(0.153)S(0.153)VT(0.015)T(0.011)S(0.015)ET(0.004)QPCTPSSSDYSDLQR 144.51 1.04E-07 331600000 72116 59399 33142 55194 59813 43468 89593 79680 51343 TRUE FALSE 62585.68788 59008.80406 49169.58205 67726.64129 58622.83832 45140.24209 80904.28465 62641.05207 45273.28903 1.382397639 1.303391146 1.086061629 1.495951426 1.294865904 0.997061249 1.787020258 1.383620528 1 15.4663725 2.277486831 24.99992662 1.405377895 1.266339358 0.06384799 0.231863196 437.3287652 280867.931 0.085276447 0.066053578 189.4466067 -2.277486831 -0.139038538 MKYNTEGRVS(ph)PSPSQESLSSSK ddPTM_MDA-MB-175_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(0.031)EGRVS(0.958)PS(0.011)PSQESLSSSK 96.793 0.0012503 100490000 126940 88808 46204 42069 86809 60553 110160 135380 34767 TRUE FALSE 110164.5574 88224.6144 68548.40894 51621.40943 85081.67074 62882.51309 99476.70016 106430.0405 30656.88487 3.593468738 2.877807539 2.235987421 1.683843928 2.775287545 2.051170997 3.244840452 3.471652159 1 14.90392349 -0.253239904 16.98888592 2.646308184 2.610357814 0 0.824227435 0 0 0 0.183261073 0.558161782 0.253239904 -0.03595037 MLADLDDLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MLADLDDLNR 10 0 Q9BQS8;Q9BQS8-4 Q9BQS8 FYCO1 FYVE and coiled-coil domain-containing protein 1 0 ; 148.14 7.19E-05 133840000 215760 206800 126737 149249 221120 222370 198291 225900 209350 FALSE TRUE 187246.7693 205441.5172 188027.4371 183138.2666 216720.1446 230924.7178 179060.7693 177593.043 184600.8815 1.014333018 1.112895646 1.018561968 0.99207688 1.173993011 1.250940493 0.969988702 0.962037892 1 17.49404992 MLAEDELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 MLAEDELR 8 0 P61204;F5H423;P61204-2;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 ;;;;;;;;;;;; 195.6 0.00036962 13747070000 15951430 16522720 11424690 14054420 15623000 15792600 14444920 17464060 20333510 FALSE TRUE 13843408.11 16414181.16 16949708.3 17245690.87 15312132.87 16400151.54 13044053.88 13729506.67 17929705.61 0.772093441 0.915474103 0.945342253 0.961850197 0.854009162 0.914691624 0.727510767 0.765740775 1 24.09584846 2.278099446 24.99996474 0.813154901 0.898502688 0.089502097 0.087692691 266.825245 168709.6358 0.03256506 0.025224422 189.7140285 -2.278099446 0.085347787 MLAEDELRDAVLLVFANK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MLAEDELRDAVLLVFANK 18 1 P61204;F5H423;P61204-2;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 ; 229.96 1.46E-19 281308000 363050 357820 151265 163784 286741 267336 404980 409080 69165 FALSE TRUE 315072.0226 355469.4569 224417.26 200973.6605 281035.4151 277620.5889 365705.1019 321601.4255 60988.39249 5.166098167 5.828477229 3.679671668 3.29527722 4.608014798 4.552023386 5.996306625 5.273157929 1 15.89624707 4.246385772 24.97817739 4.280215166 5.497287951 0.149075997 1.350809623 382.6938242 1221543.937 0.343191355 0.87288818 17635.41859 -4.246385772 1.217072785 MLAES(ph)DES(ph)GDEESVSQTDKTELQNTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 MLAESDESGDEESVSQTDKTELQNTLR 27 1 P22059 P22059 OSBP Oxysterol-binding protein 1 2 MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(0.999)DES(0.998)GDEES(0.001)VS(0.001)QT(0.001)DKTELQNTLR;MLAES(0.999)DES(0.828)GDEES(0.12)VS(0.026)QT(0.023)DKT(0.005)ELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(0.999)GDEES(0.001)VSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(0.997)GDEES(0.003)VSQTDKTELQNTLR 218.69 1.80E-34 6633996000 6629720 5303261 3740070 4369009 5211561 4971028 5744850 7024170 5755058 TRUE FALSE 5753585.704 5268423.529 5548780.362 5361059.27 5107861.132 5162266.664 5187715.331 5522105.908 5074701.599 1.133778133 1.038174053 1.093420027 1.056428475 1.006534282 1.017255214 1.022270025 1.088163668 1 22.27489156 7.999999999 0.732485527 1.03692454 14.95650036 0.471795226 0.031370554 355.99032 1.659392027 0.012257612 8155.728691 99999999.78 -7.999999999 13.91957582 MLAESDES(ph)GDEESVSQTDKTELQNTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MLAESDESGDEESVSQTDKTELQNTLR 27 1 P22059 P22059 OSBP Oxysterol-binding protein 1 1 MLAESDES(1)GDEESVSQTDKTELQNTLR;MLAESDES(1)GDEESVSQTDKTELQNTLR 320.45 1.23E-82 425610000 343720 270230 214295 224682 241787 271222 308760 360260 307210 TRUE FALSE 298296.5311 268454.8413 317928.7788 275699.4821 236975.9117 281656.0858 278816.5027 283221.2025 270891.9838 1.101164113 0.991003269 1.173636718 1.01774692 0.874798539 1.039735772 1.029253427 1.045513413 1 18.04735818 3.502454617 24.71192838 1.002629471 1.081649946 0.291476979 0.06440462 930.4703253 907643.0701 0.017717602 0.026149092 3180.201346 -3.502454617 0.079020475 MLAPEGALNIHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MLAPEGALNIHEK 13 0 F5GWE5;Q00169;I3L4H1;I3L2X8;I3L471;I3L4C0;I3L4U7;I3L459;I3L3W1 F5GWE5 PITPNA Phosphatidylinositol transfer protein alpha isoform 0 128.96 0.00015921 399130000 255780 250760 158080 184550 211560 208970 237750 277030 249490 FALSE TRUE 221978.0249 249112.741 234528.0167 226454.8982 207350.3699 217009.2111 214693.0416 217789.2903 219995.5764 1.009011311 1.13235341 1.066057875 1.029361144 0.942520633 0.986425339 0.975897084 0.989971225 1 17.74711499 3.526116341 3.399990511 0.980499576 1.074659398 0.605721751 0.033140234 0.148015629 3.434162226 0.009051801 0.013413594 3358.275654 -3.526116341 0.094159822 MLDAEDIVNTARPDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 MLDAEDIVNTARPDEK 16 1 O43707 O43707 ACTN4 Alpha-actinin-4 0 ;;;;;;;;; 262.36 6.39E-27 8613820000 7991430 6558760 4964700 6648070 6314710 5751520 6414230 8047200 10495930 FALSE TRUE 6935342.278 6515675.074 7365645.526 8157615.903 6189059.626 5972784.696 5792178.962 6326368.903 9255113.112 0.749352514 0.704008151 0.795846084 0.881417202 0.668717881 0.645349724 0.625835567 0.683553926 1 23.14181919 1.234531686 24.99780073 1.000000412 0.716302066 0.576616072 0.075563707 97.8328013 606925.4209 0.151972878 0.020367898 17.1605691 -1.234531686 -0.283698345 MLDEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MLDEQK 6 0 H3BV99 H3BV99 SNAP23 Synaptosomal-associated protein 0 95.445 0.032873 2492600000 1846300 2179400 2578200 1596200 888080 2148000 997200 1025000 1160800 FALSE TRUE 1602306.777 2165083.378 3825026.144 1958641.606 870408.9455 2230634.95 900491.6975 805811.7266 1023571.546 1.565407697 2.115224271 3.736940673 1.91353659 0.850364538 2.179266274 0.879754523 0.787254911 1 19.96518052 3.444229678 6.033599403 1.141682114 2.499645266 0.462909345 0.661137051 0.153967989 16.13788479 0.194546799 0.256442836 2781.183719 -3.444229678 1.357963153 MLDHEYTTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MLDHEYTTK 9 0 P11387;E5RJ33;H0YBR3;H0YC03;E5RGE7;E5RGR4;E5RFE3;E5RGR2;E5RJ95;E5RFS0;E5RIC7;Q969P6-2;Q969P6 P11387;Q969P6-2 TOP1;TOP1MT "DNA topoisomerase 1;DNA topoisomerase I, mitochondrial" 0 155.84 7.23E-05 161840000 685170 656910 468450 797610 733540 637160 650490 824540 768610 FALSE TRUE 594623.0485 652594.715 694993.9869 978719.5412 718943.9891 661671.9575 587405.5799 648218.5376 677745.8014 0.877354087 0.962890089 1.025449343 1.444080567 1.060787079 0.976283374 0.86670486 0.956433129 1 19.37038475 2.703828149 4.27005932 0.940519162 1.086428482 0.145848955 0.149337246 0.413388355 17.5154588 0.055475723 0.050186243 505.6245456 -2.703828149 0.14590932 MLDLLEDFLEHEGYKYER ddPTM_MDA-MB-175_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 ; 224.19 2.85E-19 411300000 924010 810260 506570 530740 710710 640810 924640 1078830 354710 FALSE TRUE 801899.7374 804937.3487 751548.9464 651252.6289 696568.2615 665462.3754 834968.5551 848130.6 312776.5879 2.563809979 2.57352174 2.402829929 2.082165527 2.227047319 2.127596505 2.66953662 2.711617918 1 18.254773 4.020991309 4.017588589 2.232548472 2.562489087 0.110708144 0.468408132 0.576234316 21.14629986 0.123817368 0.262833367 10495.21426 -4.020991309 0.329940615 MLDMGFEPQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MLDMGFEPQIR 11 0 P17844;P17844-2;J3KTA4;J3QSF1;J3KRZ1;A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2;A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;O15523-2;O15523 P17844;A0A1X7SBZ2;A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX5;DDX17;DDX3X;DDX3Y Probable ATP-dependent RNA helicase DDX5;Probable ATP-dependent RNA helicase DDX17;ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ; 123.63 0.00085159 168362000 314170 293030 171226 216252 295020 300740 262930 313430 279720 FALSE TRUE 272651.6385 291105.0666 254031.4663 265355.3218 289149.6792 312309.6624 237431.0891 246405.4336 246651.8203 1.105411013 1.180226711 1.029919285 1.07582957 1.172298988 1.266196463 0.962616407 0.999001075 1 17.91211641 2.206260526 24.99988655 0.988638508 1.133996485 0.551598852 0.06414169 154.9961225 119964.0806 0.027272227 0.018388548 160.7905519 -2.206260526 0.145357977 MLDQTLLDLNEM ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MLDQTLLDLNEM 12 0 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 91.855 0.018759 32172000 82536 96005 58566 73315 95242 103670 89428 106970 97889 FALSE TRUE 71628.65848 95374.33683 86888.71349 89962.2913 93346.87054 107658.252 80755.28632 84095.29794 86316.67394 0.829835711 1.104935263 1.00662722 1.042235378 1.081446565 1.247247456 0.93556995 0.97426481 1 16.39735165 6.526229901 13.93689546 1.027448502 0.514714875 0 0.110029368 0 0 0.024253107 0 3359153.896 -6.526229901 -0.512733627 MLDSGADYLHLDVMDGHFVPNITFGHPVVESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MLDSGADYLHLDVMDGHFVPNITFGHPVVESLR 33 0 Q96AT9-4;Q96AT9;C9J9T0;C9IZU8 Q96AT9-4 RPE Ribulose-phosphate 3-epimerase 0 150.68 7.05E-11 334310000 182610 187960 136800 154510 145780 183870 147040 199900 211120 FALSE TRUE 158477.6258 186725.2784 202956.9376 189593.857 142879.2632 190943.5979 132780.0834 157152.9406 186161.6341 0.851290474 1.003027714 1.09021893 1.01843679 0.767501123 1.02568716 0.7132516 0.844174695 1 17.50619625 3.260422724 24.97816471 0.862892237 0.998726363 0.228111092 0.109370989 317.9983164 363320.9986 0.030785143 0.039709325 1821.472943 -3.260422724 0.135834126 MLEDRDLFVMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MLEDRDLFVMR 11 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 144.65 3.34E-05 310106000 277314 296910 107994 115804 257199 282395 244978 291486 55031 FALSE TRUE 240666.2523 294959.5787 160220.2596 142099.0682 252081.2431 293258.9184 221220.0713 229153.9872 48525.29787 4.959603811 6.078470233 3.301788276 2.92835025 5.194841746 6.043423353 4.558860656 4.722361269 1 15.56644945 4.245840494 24.99991337 4.144988773 5.519037092 0.164643315 1.411027208 338.2811161 1161666.59 0.357644207 0.905910202 17613.29033 -4.245840494 1.37404832 MLEQLDMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MLEQLDMR 8 0 O00148;O00148-2;O00148-3;K7EQN7;K7EPJ3;Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;F6S4E6;A0A0A0MT12;F6TRA5;A0A140T9K1;A0A140T973;A0A140T9L4 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ;;; 133.23 0.0021592 1409470000 2491820 2322410 1662510 1990870 2406770 2735750 2079790 2580180 2996960 FALSE TRUE 2162519.674 2307153.936 2466505.397 2442927.462 2358879.986 2840996.073 1878092.286 2028428.586 2642662.803 0.818310861 0.873041363 0.933340945 0.924418908 0.892614821 1.07505054 0.710681773 0.767569962 1 21.33356092 2.216933179 24.99969824 0.809085155 0.916988658 0.162177419 0.097424744 372.6275284 430726.3104 0.039429222 0.026609733 164.7908824 -2.216933179 0.107903503 MLEVHFVGDDDVLNHILDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MLEVHFVGDDDVLNHILDR 19 0 Q13416;C9JK08;B8ZZ80 Q13416 ORC2 Origin recognition complex subunit 2 0 172.84 5.30E-12 22510000 27747 22151 13857 16131 23604 24901 22079 24258 21129 FALSE TRUE 24080.16365 22005.48862 20558.29155 19793.7901 23134.32658 25858.95758 19937.78198 19070.61548 18631.15369 1.292467662 1.181112506 1.103436314 1.062402813 1.241701237 1.387941832 1.070131368 1.02358747 1 14.18542939 2.01811541 24.96217331 1.023492759 1.202246412 0.471546742 0.090980813 218.1522047 300602.1826 0.03969324 0.026756083 104.2594453 -2.01811541 0.178753653 MLFKDDYPSSPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MLFKDDYPSSPPK 13 1 P63279;H3BQQ9;B0QYN7;H3BPC4 P63279 UBE2I SUMO-conjugating enzyme UBC9 0 115.78 0.00058109 362540000 719740 546750 322360 395500 496370 328060 618100 764630 343920 FALSE TRUE 624624.5354 543158.3632 478254.3742 485304.3198 486493.2081 340680.6805 558156.7571 601119.8249 303262.1694 2.05968498 1.791052159 1.577032754 1.600279787 1.604200119 1.123386676 1.840509017 1.98217874 1 18.21020601 4.599685329 1.943482103 1.576983103 2.133554884 0.25201649 0.293414302 0.934460256 4.69882768 0.08016346 0.843589181 39781.88242 -4.599685329 0.556571781 MLGEDS(ph)DEEEEMDTSER ddPTM_MDA-MB-175_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 333.65 1.67E-71 2678480000 2451770 2356290 1628430 1979950 2441070 2331050 2343730 2673360 3041520 TRUE FALSE 2127762.383 2340811.376 2415944.195 2429527.909 2392497.483 2420727.002 2116435.425 2101682.768 2681954.971 0.793362456 0.872800402 0.9008146 0.905879456 0.892072204 0.902597929 0.78913906 0.78363835 1 21.35485358 2.267630019 24.97159181 0.83933303 0.880643078 0 0.067306132 562.1320254 482888.2878 0.025052897 0.01940253 185.1953247 -2.267630019 0.041310048 MLISAVS(ph)PEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MLISAVSPEIR 11 0 A0AVK6;E9PMT9 A0AVK6 E2F8 Transcription factor E2F8 1 MLISAVS(1)PEIR;MLISAVS(1)PEIR;MLISAVS(1)PEIR;MLISAVS(1)PEIR 239.87 1.21E-15 565690000 618430 724440 422373 616430 790760 817040 699410 925060 709180 TRUE FALSE 536702.9086 719681.1059 626633.9956 756399.853 775025.4231 848472.0575 631581.3259 727243.1178 625341.5483 0.858255637 1.15086085 1.002066786 1.209578758 1.239363393 1.356813824 1.009978191 1.162953461 1 19.25428485 4.739359205 24.02615195 1.144531866 0.858255498 0.376448909 0.114483191 43.15322679 1297883.478 0.02788669 0.163181875 54873.06319 -4.739359205 -0.286276368 MLITILGTVKPNANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MLITILGTVKPNANR 15 1 P17931;G3V3R6 P17931 LGALS3 Galectin-3;Galectin 0 ; 161.04 1.53E-06 282690000 278327 262190 158568 208700 215907 236180 244441 292276 368333 FALSE TRUE 241545.3818 260467.6566 235252.0152 256088.5248 211610.8731 245265.9974 220735.1494 229775.0519 324789.0923 0.74369918 0.801959372 0.724322401 0.788476371 0.651533189 0.755154663 0.679626116 0.707459263 1 18.30914366 1.235658673 24.99999888 1.000000364 0.729961418 0.774445536 0.045526448 37.50765402 323064.5729 0.074756993 0.011010539 17.20515831 -1.235658673 -0.270038946 MLKPAFIFDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MLKPAFIFDGR 11 1 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ; 147.24 3.23E-05 3620500000 5246600 6559800 3536200 4988800 6114500 5730000 6123900 7225900 7614000 FALSE TRUE 4553248.517 6516708.242 5246318.148 6121583.289 5992833.413 5950436.808 5530005.121 5680697.517 6713881.594 0.678184215 0.970631988 0.781413564 0.911780049 0.892603381 0.886288613 0.823667359 0.846112258 1 22.67871566 4.755659507 24.55832176 0.880011215 0.678184008 0.506588618 0.064860476 2365.57861 3397497.194 0.014744147 0.415373482 56971.74307 -4.755659507 -0.201827206 MLLHSEQHPGQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MLLHSEQHPGQLK 13 0 J3QKT4;J3KQ22;E2QRB3;P32322-2;P32322;P32322-3 J3QKT4 PYCR1 "Pyrroline-5-carboxylate reductase;Pyrroline-5-carboxylate reductase 1, mitochondrial" 0 ; 68.676 0.028788 1232080000 1248310 1177440 693850 1048300 1270470 1127210 1085540 1415430 1303250 FALSE TRUE 1083342.671 1169705.319 1029398.181 1286332.537 1245190.133 1170574.498 980264.4979 1112751.309 1149181.27 0.942708256 1.017859715 0.895766584 1.11934694 1.083545447 1.018616061 0.853011204 0.968299205 1 20.13217495 0.905165616 16.21987141 1.474526485 0.986260489 0.002277054 0.079851031 12357592.49 23537328.55 216566589.2 0.020314864 8.038326007 -0.905165616 -0.488265996 MLLS(ph)WDGGESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MLLSWDGGESR 11 0 Q658Y4;E7ER68 Q658Y4 FAM91A1 Protein FAM91A1 1 MLLS(0.998)WDGGES(0.002)R 66.023 0.066971 13162000 56718 51240 37869 37780 38655 35466 42531 44206 46212 TRUE FALSE 49222.57259 50903.40107 56182.57506 46358.52643 37885.84113 36830.39997 38406.35017 34752.89091 40748.87 1.207949388 1.249197857 1.378751731 1.137664098 0.929739674 0.90383856 0.942513256 0.852855328 1 15.31447243 3.372462796 3.16555574 0.915101464 1.275354076 0.89025486 0.057011408 0.069917291 1.395267278 0.016805949 0.022558285 2357.560225 -3.372462796 0.360252612 MLLVDELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MLLVDELR 8 0 P18085;C9JPM4;C9JAK5;U3KQF2 P18085 ARF4 ADP-ribosylation factor 4 0 ; 128.1 0.0026707 390290000 580970 597740 430930 492550 589290 670290 563580 659380 657680 FALSE TRUE 504193.3425 593813.4066 639329.1894 604391.0057 577564.2819 696076.49 508924.0983 518376.7183 579929.8196 0.869404065 1.023940116 1.1024251 1.042179562 0.995920993 1.200277114 0.877561527 0.89386112 1 19.1455188 MLLYTEVTR ddPTM_MDA-MB-175_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 ; 167.24 0.00013989 687320000 529410 486920 347940 414270 547480 504350 473720 519940 473130 FALSE TRUE 459447.1271 483721.3905 516204.9478 508336.3352 536586.2191 523752.6709 427778.7073 408754.8772 417197.1104 1.101271116 1.159455275 1.23731669 1.218456031 1.286169549 1.255408194 1.025363543 0.979764402 1 18.67036964 2.169583664 5.636288832 0.993896578 1.212355207 0.784911423 0.051413157 0.092128671 5.337863159 0.023126332 0.015533505 147.7691121 -2.169583664 0.218458629 MLMRRDQVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 966710000 1473060 1577090 1087080 1057550 1333540 1151150 2201560 1708130 1620100 FALSE TRUE 1278391.389 1566729.992 1612795.524 1297682.891 1307005.163 1195435.485 1988053.05 1342859.692 1428573.624 0.894872597 1.096709309 1.128955132 0.908376628 0.914902208 0.836803554 1.391634997 0.94000034 1 20.44614396 MLNS(ph)SFEDDPFFSESILAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MLNSSFEDDPFFSESILAHR 20 0 A0A494C175;A0A0S2Z4A4;P58340 A0A494C175 MLF1 Myeloid leukemia factor 1 1 MLNS(0.5)S(0.5)FEDDPFFSESILAHR 99.387 0.00042809 30978000 23305 21987 9792.2 15747 20143 19361 21684 23590 22934 TRUE FALSE 20225.1852 21842.56595 14527.74067 19322.59703 19742.19371 20105.8302 19581.08902 18545.46208 20222.76865 1.000119497 1.080097702 0.718385347 0.955487222 0.976235947 0.994217486 0.968269447 0.91705851 1 14.30369291 3.494141605 24.98812229 0.965378895 0.929148184 0.032064054 0.092336964 3306.333862 4854128.652 0.025844762 0.037352443 3119.906685 -3.494141605 -0.036230711 MLPAATELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MLPAATELR 9 0 F5H3Z4 F5H3Z4 FOLR2 0 69.423 0.046981 0 2442700 2117100 1345600 1548400 2272700 2036400 2643200 2834200 1853000 FALSE TRUE 2119891.006 2103192.631 1996336.661 1899987.886 2227477.716 2114741.626 2386862.871 2228128.386 1633940.451 1.297410199 1.287190503 1.221792789 1.162825662 1.363255139 1.294258689 1.460801628 1.36365336 1 20.63992397 3.220410729 24.99297483 1.317025039 1.244045727 0.030674705 0.123741428 693.4693855 954927.1027 0.037673159 0.042801281 1661.157185 -3.220410729 -0.072979312 MLPDKDCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 15 MLPDKDCR 8 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;;;;;;;;;;;;; 151.04 0.00245 87803360000 177729350 173728600 100993590 113161060 148562340 141715150 174160960 188198200 162124490 FALSE TRUE 154241966.1 172587365.4 149834427.9 138856008.2 145606240.1 147167023.5 157270856.9 147953479.5 142958317.5 1.07892964 1.207256552 1.048098709 0.971304158 1.01852234 1.029440092 1.100116871 1.034941388 1 27.09101932 4.10474538 7.249721609 1.029619179 1.142126315 0.538086439 0.044307008 0.160357543 9.835967485 0.011174083 0.023532128 12727.56666 -4.10474538 0.112507136 MLPHAPGVQMQAIPEDAIPEES(ph)GDEDEDDPDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 23 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 301.02 3.22E-90 21388570000 7695295 6501852 5149100 5570089 6461935 5312062 7743838 9401735 7347649 TRUE FALSE 6678342.268 6459140.906 7639221.983 6834862.841 6333355.136 5516420.463 6992841.783 7391247.135 6479018.306 1.030764531 0.996932035 1.179070906 1.054922601 0.97751771 0.851428442 1.079305761 1.140797384 1 22.6273438 2.031690006 24.99901087 1.089334864 1.017128612 0.082430399 0.086860176 414.7872767 327207.7073 0.037458326 0.025254272 107.5697119 -2.031690006 -0.072206252 MLPHAPGVQMQAIPEDAVHEDS(ph)GDEDGEDPDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 33 MLPHAPGVQMQAIPEDAVHEDSGDEDGEDPDKR 33 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 1 MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR 308.81 1.61E-104 43255754000 15393791 10838723 8108963 9470855 10449735 9534452 12602982 14745470 12736793 TRUE FALSE 13359462.52 10767522.71 12030484.63 11621357.38 10241805.72 9901248.538 11380746.75 11592265.99 11231063.84 1.189509979 0.958726873 1.071179436 1.034751253 0.911917683 0.881594894 1.01332758 1.032160991 1 23.42099125 6.777343563 1.643816531 0.988806195 168.1394886 0.522486165 0.059138695 1089.618632 4.448292442 0.016926952 685618.1666 5988851.756 -6.777343563 167.1506824 MLQEDELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MLQEDELR 8 0 P84085 P84085 ARF5 ADP-ribosylation factor 5 0 ; 150.24 0.0011453 716710000 1180650 1094840 745300 890940 980890 1110900 971290 1180270 1303160 FALSE TRUE 1024624.111 1087647.924 1105729.573 1093241.544 961372.2081 1153637.042 877094.4453 927878.4454 1149101.909 0.891673839 0.946519987 0.962255448 0.951387806 0.836629197 1.003946676 0.76328691 0.807481423 1 20.13207532 2.240985159 24.99938152 0.842721009 0.930637778 0.176829299 0.074312251 90.39096815 932035.0809 0.028014662 0.020660383 174.1747354 -2.240985159 0.087916769 MLQEDELRDAVLLVFANK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MLQEDELRDAVLLVFANK 18 1 P84085 P84085 ARF5 ADP-ribosylation factor 5 0 ; 239.58 5.82E-24 558630000 1103510 932350 384930 432310 847950 716050 1099960 1228340 82738 FALSE TRUE 957678.3576 926225.3315 571083.4355 530472.5929 831077.454 743596.9068 993286.0485 965669.05 72956.8079 13.12664829 12.69552984 7.827692192 7.27104993 11.39136262 10.1922895 13.61471365 13.23617463 1 16.15475499 4.351332976 8.102148744 9.859453034 13.00570224 0.135529109 3.610380616 0.533344913 35.38378904 0.905995076 2.413644573 22456.02979 -4.351332976 3.146249201 MLQHAASNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MLQHAASNK 9 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 137.14 0.00017317 2093250000 4463400 5431700 2993600 4107700 4970200 5164000 6000600 6981900 6502300 FALSE TRUE 3873550.381 5396018.805 4441314.973 5040416.067 4871302.744 5362662.422 5418662.736 5488875.018 5733605.501 0.675587182 0.941121395 0.774611189 0.879100605 0.849605496 0.935303697 0.94507073 0.957316477 1 22.45101121 7.391928215 0.096288206 1.226147197 1.73E-12 0.602348606 0.06130611 187.1532203 1.946582969 4.673283288 31.68723808 24656317.55 -7.391928215 -1.226147197 MLQHIDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 MLQHIDYR 8 0 P14678-2;P14678;P14678-3;J3QLE5;P63162;P63162-2;J3KRY3;S4R3P3 P14678-2;S4R3P3 SNRPB;SNRPN Small nuclear ribonucleoprotein-associated proteins B and B;Small nuclear ribonucleoprotein-associated protein N 0 ;;;;;;;;; 146.79 0.00054775 8054800000 5516902 6085230 3756653 4229873 5963030 6169750 5300550 5417010 6265420 FALSE TRUE 4787829.423 6045255.723 5573382.956 5190330.314 5844377.369 6407104.275 4786503.477 4258624.567 5524729.185 0.866617939 1.094217566 1.008806544 0.939472351 1.057857711 1.159713727 0.866377938 0.77082956 1 22.39747232 2.108946961 10.27694971 0.854002617 1.021733718 0.312784238 0.097087127 0.312723645 27.43882083 0.038501186 0.025949528 128.5129702 -2.108946961 0.1677311 MLRPVS(ph)R ddPTM_MDA-MB-175_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 61.691 0.054478 679920000 273520 309140 192637 194394 213620 238950 244010 193566 255440 TRUE FALSE 237373.639 307109.239 285796.8975 238534.1288 209369.3799 248142.5611 220345.9478 152173.4172 225242.1742 1.053859651 1.363462416 1.26884274 1.059011838 0.929530097 1.101670067 0.97826239 0.675599131 1 17.78111746 2.931721194 0.708573787 0.822102837 1.251586784 0.469497052 0.135440475 0.57322161 0.757963789 0.135326825 0.125680966 854.5179578 -2.931721194 0.429483948 MLS(ph)EEEKEELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MLSEEEKEELK 11 1 Q16890-5;E9PNQ9;Q16890-4 Q16890-5 TPD52L1 Tumor protein D53 1 MLS(1)EEEKEELK 69.721 0.067715 292830000 400750 492610 176820 245430 545290 572480 362010 394460 230880 TRUE FALSE 347789.8721 489374.0125 262330.7434 301158.6327 534439.7958 594503.676 326902.3259 310107.7987 203585.6294 1.708322307 2.403774834 1.288552361 1.479272547 2.62513517 2.920165228 1.605723974 1.523230297 1 17.6352762 5.054389259 15.62667798 1.858218628 0.648475244 0.005644098 0.614107563 23035286.49 167312275.6 0.157919064 856361056.4 113341.5791 -5.054389259 -1.209743384 MLS(ph)SSDAITQEFMDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.971)S(0.014)S(0.014)DAITQEFMDLR;MLS(0.984)S(0.016)SDAITQEFMDLR 159.88 1.05E-08 0 48580 27064.9 25857 29828.1 39829 44075 37997 40663 46749 TRUE FALSE 42160.02991 26887.10889 38361.53169 36601.026 39036.48082 45770.59377 34312.05679 31967.53389 41222.38648 1.022745977 0.652245326 0.930599486 0.887891972 0.94697285 1.11033343 0.832364638 0.775489646 1 15.33114041 5.053869753 21.5299097 0.886639757 2.989255366 0.097409905 0.124143464 1048.258824 589873.5443 0.029522002 41691.73642 113206.0801 -5.053869753 2.102615609 MLSCAGADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MLSCAGADR 9 0 P27635;X1WI28;A0A087WV22;H7C123;H7C2C5;Q96L21;A6QRI9;B8A6G2;F8W7C6 P27635;F8W7C6 RPL10;RPL10L 60S ribosomal protein L10;60S ribosomal protein L10-like 0 ;; 129.29 0.00091533 510488000 924910 898530 525300 616910 925890 959750 818930 853960 873450 FALSE TRUE 802680.8001 892627.4973 779336.837 756988.8444 907466.6005 996672.2035 739510.2946 671347.2995 770191.736 1.042183086 1.158967898 1.011873798 0.982857656 1.178234663 1.294057255 0.960163892 0.871662559 1 19.55485812 2.024209922 24.97521723 0.923438919 1.107944978 0.412322136 0.094236867 201.1185429 207475.1787 0.039886582 0.026890221 105.7328459 -2.024209922 0.184506059 MLSGGFGYSPFLSITDGNMPGTRPAS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MLSGGFGYSPFLSITDGNMPGTRPASR 27 1 Q15773;F5H7L5;F5H800;F5H0Y3 Q15773 MLF2 Myeloid leukemia factor 2 1 MLSGGFGYS(0.001)PFLS(0.001)IT(0.002)DGNMPGT(0.062)RPAS(0.935)R 49.57 0.068987 711700000 81443 74109 55893 47355 51301 75052 52679 78188 48918 TRUE FALSE 70680.1012 73622.1731 82923.04175 58107.67653 50280.21047 77939.29901 47570.19869 61468.10466 43134.96977 1.638580057 1.706786245 1.922408714 1.347112954 1.165648446 1.806870375 1.102822117 1.425017914 1 15.39657032 0.401355873 0.14816957 1.31E-13 2.099654944 0.404533626 0.239458378 70.04798726 1.985442452 31.57951363 5.762924545 2.51974083 -0.401355873 2.099654944 MLSLDFLDDVRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MLSLDFLDDVRR 12 1 H0YKT4;H0YNG3;P67812-4;P67812;P67812-3 H0YKT4 SEC11A Signal peptidase complex catalytic subunit SEC11;Signal peptidase complex catalytic subunit SEC11A 0 ; 118.61 0.00097382 109970000 679550 578540 354700 473230 620780 600870 547440 806420 612500 FALSE TRUE 589745.7457 574739.5326 526234.1064 580684.1044 608427.6925 623985.8577 494349.3531 633973.3586 540090.9478 1.091937845 1.064153241 0.974343504 1.075159854 1.126528217 1.155334783 0.915307607 1.17382704 1 19.04284284 4.740642544 19.5930331 1.065401811 1.091938015 0.01157192 0.080811487 72.18775603 678078.2875 0.018674866 0.11541047 55035.45275 -4.740642544 0.026536204 MLTFNPNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MLTFNPNKR 9 1 P27361;E9PBK7;E9PQW4;P27361-3;P27361-2;B3KR49;E9PRH7;H0YEX6 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 138.66 0.00020906 373520000 366070 396770 233050 291440 370270 382650 409990 404020 363000 FALSE TRUE 317692.922 394163.5917 345753.7595 357615.9064 362902.3514 397370.7931 370229.2329 317623.4671 320086.5535 0.992521924 1.231428148 1.080188329 1.117247515 1.133763188 1.241447942 1.156653501 0.992304936 1 18.28810255 1.7137524 6.003131161 0.996348201 1.140930308 0.401092321 0.070759041 0.122822647 10.90798683 0.040832162 0.017404737 51.73118179 -1.7137524 0.144582107 MLVLVLGDLHIPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MLVLVLGDLHIPHR 14 0 Q9UBQ0 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ; 92.856 0.0027715 150332000 102833 110895 59848 75931 83430 86003 99590 113361 101755 FALSE TRUE 89243.3585 110166.5234 88790.69298 93172.29408 81769.90623 89311.59106 89931.77713 89119.63233 89725.63982 0.994624933 1.227815412 0.989579937 1.038413259 0.911332662 0.995385391 1.002297418 0.993245994 1 16.45323269 4.171629709 24.98127129 0.990087287 1.111220548 0.388133173 0.063256314 42.41850404 15831.75305 0.014520191 0.030226209 14846.69236 -4.171629709 0.121133261 MLVQCMQDQEHPSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MLVQCMQDQEHPSIR 15 0 H0Y8C6;O00410-2;O00410;O00410-3;H0Y3V4 H0Y8C6 IPO5 Importin-5 0 ; 188.59 2.93E-07 367870000 384050 458300 151169 237240 412300 469790 385970 453310 244880 FALSE TRUE 333296.8194 455289.3971 224274.834 291108.968 404096.0367 487863.1253 348538.6888 356373.1842 215930.5654 1.543537011 2.108499074 1.038643296 1.348160079 1.871416564 2.259351864 1.614123912 1.650406387 1 17.72020795 3.238776099 24.99999541 1.699622476 1.518832937 0.040550315 0.401392289 22.73847685 2637834.119 0.122536469 0.148368995 1732.910364 -3.238776099 -0.18078954 MLVTFDEELRPLPVSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MLVTFDEELRPLPVSVR 17 1 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 176.49 1.00E-09 1162990000 554290 451610 311730 370340 430010 431500 404760 471810 466140 FALSE TRUE 481039.1721 448643.3442 462483.6707 454431.3573 421453.6423 448100.0842 365506.4375 370917.1031 411033.4602 1.170316333 1.091500784 1.125172803 1.105582395 1.025351177 1.090179091 0.889237673 0.902401237 1 18.64889632 2.247197811 24.66736065 0.922961554 1.098723445 0.754891564 0.045796373 71.29814443 203624.0857 0.01750541 0.01333836 176.6842391 -2.247197811 0.175761891 MLWGSDPYPHAEPQQATT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MLWGSDPYPHAEPQQATTPK 20 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 MLWGSDPYPHAEPQQAT(0.423)T(0.577)PK;MLWGSDPYPHAEPQQAT(0.009)T(0.991)PK;MLWGSDPYPHAEPQQAT(0.197)T(0.803)PK;MLWGSDPYPHAEPQQAT(0.041)T(0.959)PK 178.76 2.23E-16 1326404000 668388 710878 521675 657939 812473 705964 923815 1120220 931689 TRUE FALSE 580058.8323 706208.1956 773958.7749 807334.1059 796306.3769 733122.8919 834223.5635 880669.6706 821545.7878 0.706057825 0.859609052 0.94207625 0.982701291 0.969278145 0.892370094 1.015431612 1.071966631 1 19.64798146 5.611867975 0.635937565 1.009338124 4.80E-21 0.81624605 0.043529071 4.269474641 0.583323453 0.022730664 4.021783542 409136.2642 -5.611867975 -1.009338124 MMLDDIVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MMLDDIVSR 9 0 A0A087WTP3;Q92945;M0R0I5;M0QYH3;M0QXW7 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;; 106.93 0.0072949 109340000 426990 427090 284459 321144 383360 467520 386853 445210 451940 FALSE TRUE 370562.1896 424284.4177 422024.3239 394064.6536 375731.886 485505.7969 349336.0556 350005.3061 398512.1681 0.929864178 1.064671174 1.058999844 0.988839702 0.942836671 1.218296042 0.876600725 0.878280098 1 18.60426425 MMLDQCLELQLFHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MMLDQCLELQLFHR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 158.81 5.01E-06 393120000 319600 332210 209612 246820 302620 321380 293280 305490 324990 FALSE TRUE 277364.0502 330027.6906 310981.0643 302864.2534 296598.4541 333743.6966 264837.7507 240163.3408 286570.0524 0.967875212 1.151647522 1.085183402 1.056859399 1.034994591 1.164614703 0.924164087 0.838061545 1 18.12852833 2.13181105 6.942497183 0.900226335 1.077454031 0.536669576 0.067792005 0.139080947 8.098004056 0.026216054 0.017613486 135.4599932 -2.13181105 0.177227695 MMLEQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MMLEQER 7 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 113.7 0.014125 104250000 73938 73605 56738 62794 96870 98861 75230 88642 88259 FALSE TRUE 64166.90596 73121.48391 84176.68658 77052.33745 94942.47652 102664.2466 67934.20618 69686.59811 77825.12156 0.824501198 0.939561448 1.0816133 0.990070248 1.219946395 1.319165901 0.872908449 0.895425496 1 16.2479483 4.525223909 2.885141767 1.043297292 0.824018515 0.236550721 0.135444722 0.527401267 7.770130066 0.038979747 0.210506772 33513.81815 -4.525223909 -0.219278777 MMNGGHYTYSENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 15 MMNGGHYTYSENR 13 0 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ;;;;;;;;;;;;;; 210.91 2.62E-08 6547958000 3456273 3900992 2196102.6 3502903 4252967 4608767 3695828 4116879 7718139 FALSE TRUE 2999517.766 3875366.127 3258145.163 4298290.665 4168341.277 4786069.249 3337407.169 3236516.463 6805709.4 0.440735505 0.569428681 0.478737038 0.63157129 0.612477118 0.703243258 0.490383437 0.475559016 1 22.69831412 1.232612381 24.99998698 1.000000728 0.551586775 0.748064405 0.082019231 104.7620462 440262.2125 0.184488421 0.020898338 17.08489765 -1.232612381 -0.448413953 MMNGGHYTYSENRVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MMNGGHYTYSENRVEK 16 1 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ;;; 83.966 0.0045956 961590000 1071150 1004180 353719 564588 981420 909230 998120 1199830 344659 FALSE TRUE 929594.8136 997583.4755 524778.6915 692786.3346 961891.6621 944208.6665 901322.476 943255.6916 303913.8057 3.058744934 3.282455278 1.726735284 2.279548746 3.165014699 3.106830453 2.965717448 3.103694778 1 18.21330269 3.259283808 24.99681847 2.76692108 2.575117633 0 0.752056401 1629.666339 1965730.854 0.218213357 0.281410992 1816.702477 -3.259283808 -0.191803446 MMSKETRQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MMSKETRQSK 10 2 A0A0G2JRP8;H0YM25 A0A0G2JRP8 GOLGA6L22 Golgin subfamily A member 6-like protein 22 0 60.91 0.079588 279820000 282280 269670 134290 163420 236480 200880 241390 278010 261410 FALSE TRUE 244975.9828 267898.52 199233.0932 200527.0087 231774.5107 208607.9836 217980.035 218559.725 230506.4076 1.062772985 1.162217236 0.864327787 0.869941147 1.005501379 0.904998632 0.945657161 0.948172015 1 17.81444733 4.242721558 24.99996645 0.935183972 1.112495144 0.668425458 0.052235617 57.94706701 348147.8592 0.012845729 0.03153066 17487.25157 -4.242721558 0.177311172 MMVAGFKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MMVAGFKK 8 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 117.17 0.0071231 0 220200 189680 106390 100800 184070 150200 223770 228840 49303 FALSE TRUE 191100.0121 188433.9796 157840.5599 123688.1806 180407.3671 155978.2912 202068.8198 179904.3468 43474.45551 4.395685003 4.334360888 3.630650643 2.845077165 4.149732642 3.587814715 4.647989664 4.138162163 1 15.40788034 4.233883504 5.444967163 3.564649989 4.377954713 0.121766547 0.99675492 0.380959907 35.27861415 0.251681942 0.607410644 17134.97613 -4.233883504 0.813304724 MMVDKDGDVTVTNDGATILSMMDVDHQIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MMVDKDGDVTVTNDGATILSMMDVDHQIAK 30 1 P48643;B7ZAR1;E9PCA1 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ; 256.75 2.24E-58 811420000 1053050 728560 599440 680550 690840 564100 998000 1231180 680700 FALSE TRUE 913886.7744 723774.0414 889331.189 835079.2791 677093.6356 585801.292 901214.1136 967901.7381 600228.4215 1.52256498 1.205831006 1.481654579 1.391269139 1.128059938 0.975963935 1.501451916 1.61255566 1 19.19515211 4.762406952 22.12869859 1.3172148 1.522566124 0.091169925 0.21575638 3942.062447 3657833.802 0.055330101 2.508110483 57863.80017 -4.762406952 0.205351325 MMYGVSPWGDSPIDFEDSAHVPCPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MMYGVSPWGDSPIDFEDSAHVPCPR 25 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 95.153 0.010127 61083000 59939 47633 30084 31482 40522 48451 46261 54995 49665 FALSE TRUE 52017.90928 47320.09569 44632.72302 38630.46927 39715.69148 50314.94132 41774.61534 43234.74722 43793.66028 1.187795424 1.080523879 1.019159457 0.882101862 0.906882211 1.148909249 0.95389641 0.987237581 1 15.41843441 4.489204071 2.101058682 0.982108634 1.195678524 0.472301295 0.07103959 0.386223841 2.726741244 0.019182705 0.12858216 30846.3705 -4.489204071 0.213569891 MNDFHIS(ph)DDEEKNPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MNDFHISDDEEKNPSK 16 1 E7ETZ8;Q49MG5;A0A0C4DG83;A2VCS9;Q49MG5-2;A8MSM7 E7ETZ8 MAP9 Microtubule-associated protein 9 1 MNDFHIS(1)DDEEKNPSK;MNDFHIS(1)DDEEKNPSK 177.03 1.83E-09 304880000 266470 245290 223620 210153 252950 163141 326350 399550 324980 TRUE FALSE 231255.3144 243678.6738 331763.38 257871.4506 247916.7899 169417.1398 294700.6272 314109.3418 286561.2346 0.807001389 0.850354634 1.157739917 0.899882536 0.865144199 0.591207461 1.028403677 1.096133405 1 18.12848393 2.029532767 24.99956745 1.057134326 0.871113426 0.273045663 0.137716266 265.7477994 224955.1903 0.058548283 0.0394727 107.0367138 -2.029532767 -0.1860209 MNEAFGDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MNEAFGDTK 9 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 135.86 0.0029162 0 780340 617890 350180 447090 564130 492620 649040 745500 669230 FALSE TRUE 677216.0919 613831.0399 519528.2193 548608.6178 552904.9167 511571.4102 586096.2007 586080.6265 590114.3918 1.147601383 1.040189916 0.880385611 0.929664867 0.936945318 0.866902108 0.993190827 0.993164435 1 19.17063512 4.509085865 3.814352387 0.946727686 1.136277343 0.681470551 0.045869452 0.141858437 4.249780495 0.012549426 0.053025928 32291.32498 -4.509085865 0.189549657 MNEEHNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MNEEHNKR 8 1 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9;G3V200;O75334-2;O75334-4;O75334-3;O75334;O75334-5;O75334-6;F8VYK7;F8W1Y8;O75334-7;H0YHK3;F8VWG6 Q13136-2 PPFIA1;PPFIA2 Liprin-alpha-1;Liprin-alpha-2 0 92.439 0.0056207 23689000 15605 16716 13679 15470 11525 16313 23227 23886 24056 FALSE TRUE 13542.75971 16606.1915 20294.21015 18982.69994 11295.67505 16940.57167 20974.44911 18778.16478 21212.12708 0.63844421 0.782863097 0.956726785 0.894898464 0.532510248 0.798626729 0.988795185 0.885256095 1 14.37260168 2.316042928 6.21688396 0.943660429 0.770122301 0.352326127 0.12170676 0.263794646 16.49939357 0.047896252 0.036673353 207.0345982 -2.316042928 -0.173538129 MNGFIDQIDGIVHFETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MNGFIDQIDGIVHFETR 17 0 D6RFN0;Q9BT78;D6RD63 D6RFN0 COPS4 COP9 signalosome complex subunit 4 0 ;;; 197.09 1.54E-11 600675000 707008 678974.7 386628 472263.1 657070.9 651212.4 586505.1 728059.8 672772.2 FALSE TRUE 613575.1015 674514.4705 573602.594 579497.6549 643996.4746 676264.9624 529625.9257 572369.8775 593237.8369 1.034281806 1.137005141 0.966901567 0.976838662 1.085562037 1.139955883 0.892771655 0.96482362 1 19.17825109 2.229401527 24.99983606 0.95260257 1.0539974 0.381297069 0.062520196 216.2576595 590272.0939 0.0260371 0.017829 169.5905025 -2.229401527 0.10139483 MNGVMFPGNS(ph)PSYTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 MNGVMFPGNSPSYTER 16 0 Q9NY27-2;Q9NY27;Q9NY27-3 Q9NY27-2 PPP4R2 Serine/threonine-protein phosphatase 4 regulatory subunit 2 1 MNGVMFPGNS(0.502)PS(0.491)Y(0.002)T(0.005)ER;MNGVMFPGNS(0.939)PS(0.061)YTER;MNGVMFPGNS(0.981)PS(0.019)YTER;MNGVMFPGNS(0.992)PS(0.008)YTER;MNGVMFPGNS(0.945)PS(0.055)YTER;MNGVMFPGNS(0.991)PS(0.009)YTER;MNGVMFPGNS(0.5)PS(0.5)YTER;MNGVMFPGNS(1)PSYTER;MNGVMFPGNS(0.996)PS(0.004)YTER;MNGVMFPGNS(0.999)PS(0.001)YTER;MNGVMFPGNS(0.991)PS(0.009)YTER 401.1 3.64E-123 5523003000 4411389 4206739 2381805 2988531 4294731 4393618 3855257 4893632 4205761 TRUE FALSE 3828412.767 4179104.655 3533653.865 3667122.64 4209274.256 4562643.328 3481374.77 3847166.879 3708560.726 1.03231767 1.12688047 0.952836997 0.98882637 1.135015594 1.230300288 0.938740128 1.037374648 1 21.82242796 MNGVMFPGNSPS(ph)YTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MNGVMFPGNSPSYTER 16 0 Q9NY27-2;Q9NY27;Q9NY27-3 Q9NY27-2 PPP4R2 Serine/threonine-protein phosphatase 4 regulatory subunit 2 1 MNGVMFPGNS(0.336)PS(0.664)YTER 171.04 1.98E-08 273220000 213600 203010 109510 148700 206080 197130 183600 206350 182980 TRUE FALSE 185372.2188 201676.4139 162469.4023 182464.6077 201979.4112 204713.7187 165794.5003 162223.6583 161348.3129 1.148894683 1.249944362 1.006948256 1.130873974 1.25182227 1.268768883 1.027556454 1.005425191 1 17.29981897 2.123701712 7.392024161 1.007394342 1.172942871 0.516180418 0.075554919 0.189890295 11.53510741 0.032493318 0.021849199 132.9540932 -2.123701712 0.165548529 MNLAIS(ph)IALLLT(ph)VLQVS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MNLAISIALLLTVLQVSR 18 0 E9PIM6;E9PNQ8;P04216 E9PIM6 THY1 Thy-1 membrane glycoprotein 3 MNLAIS(1)IALLLT(1)VLQVS(1)R 56.407 0.044433 56371000 17128 16598 9837.4 13917 16127 24885 11599 14234 11038 TRUE FALSE 14864.4914 16488.96665 14594.79954 17077.06756 15806.10425 25842.34205 10474.13077 11190.16987 9733.100215 1.527210352 1.694112491 1.49950162 1.754535264 1.623953715 2.655098734 1.076135099 1.149702523 1 13.24868369 MNLSEEVDLEDYVARPDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MNLSEEVDLEDYVARPDK 18 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;; 258.81 1.03E-30 1691480000 842090 833230 506813 716776 685688 618363 880540 993880 1050230 FALSE TRUE 730805.6729 827756.4573 751909.462 879530.946 672044.1503 642151.8247 795145.3663 781346.4964 926073.0058 0.789144774 0.893834991 0.811933246 0.949742559 0.725692409 0.693413825 0.858620607 0.843720194 1 19.82076641 1.093351986 2.03648085 1.118424255 0.817406242 0.369174888 0.07433056 1.408638999 4.08016882 0.921834509 0.020528204 12.39801012 -1.093351986 -0.301018012 MNS(ph)LTFK ddPTM_MDA-MB-175_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(0.994)LT(0.006)FK;MNS(0.955)LT(0.045)FK 68.657 0.065359 75171000 322950 337700 251320 325180 423450 355090 414090 457630 648170 TRUE FALSE 280271.3392 335481.6265 372859.1926 399017.0891 415024.1735 368750.5421 373931.6155 359769.3858 571544.081 0.490375718 0.586974194 0.652371716 0.698138783 0.726145519 0.64518303 0.654248076 0.629469183 1 19.12450525 1.237534296 24.99977363 1.000000425 0.640097098 0.763758109 0.063684505 13.23580095 322244.4764 0.096897715 0.01630414 17.27962432 -1.237534296 -0.359903328 MNS(ph)TGGQTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MNSTGGQTPR 10 0 Q96ST2;Q96ST2-3;Q96ST2-2;A0A1B0GW95 Q96ST2 IWS1 Protein IWS1 homolog 1 MNS(0.919)T(0.081)GGQTPR;MNS(0.868)T(0.13)GGQT(0.002)PR 119.87 0.00066684 616260000 445500 553480 443200 526190 722740 878680 719280 835890 1243820 TRUE FALSE 386626.0462 549844.1534 657533.0024 645669.4818 708358.888 912483.3882 649524.3363 657141.4284 1096777.017 0.352511076 0.501327202 0.599513841 0.58869713 0.645854971 0.831968007 0.592211841 0.599156819 1 20.06483881 5.074090209 0.452051414 0.742650182 2.57E-14 0.54543858 0.118136745 6.925266993 0.944262424 0.111890811 2.935569888 118601.5073 -5.074090209 -0.742650182 MNSEEEDEVWQVIIGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MNSEEEDEVWQVIIGAR 17 0 Q9NR28-2;Q9NR28;Q9NR28-3;H7BZK7;A0A2U3TZH2;H7BZQ7 Q9NR28-2 DIABLO "Diablo homolog, mitochondrial" 0 ; 252.2 1.29E-26 75799000 62576 54325 33313 39335 46106 57625 40863 51840 52683 FALSE TRUE 54306.42305 53968.1355 49423.27823 48266.61295 45188.5808 59841.87104 36900.11255 40754.41942 46454.87576 1.169014493 1.161732426 1.06389862 1.038999936 0.972741398 1.288172018 0.794321628 0.877290462 1 15.5035424 2.543638981 0.378745147 0.820835727 1.190147717 0.284150205 0.121819966 2.823324992 1.181970302 0.620628821 0.336269306 349.6543863 -2.543638981 0.36931199 MNT(ph)S(ph)RFADHHDLLTET(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MNTSRFADHHDLLTETK 17 1 C9J4A2;C9JYK8;A2RUB1-1;A2RUB1-2 C9J4A2 C17orf104 3 MNT(0.668)S(0.699)RFADHHDLLT(0.633)ET(1)K 53.779 0.053709 678600000 245870 227430 94507 106130 223370 264110 207900 208400 54200 TRUE FALSE 213377.6565 225935.9974 140210.9013 130228.4386 218925.374 274270.4826 187737.89 163835.2818 47792.53774 4.464664707 4.727432524 2.933740452 2.724869713 4.580743864 5.738772108 3.928184166 3.428051522 1 15.54449776 4.258697845 24.92882967 3.58963839 4.596049476 0.119864878 1.232006863 594.1267862 735484.6225 0.320851742 0.846554348 18142.52978 -4.258697845 1.006411085 MNVPETMNEVLDMS(ph)DDEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MNVPETMNEVLDMSDDEVR 19 0 Q12955;Q12955-4;Q12955-5;H0Y8Z4 Q12955;Q12955-4 ANK3 Ankyrin-3 1 MNVPETMNEVLDMS(1)DDEVR;MNVPETMNEVLDMS(1)DDEVR 175.21 3.15E-12 71644000 140033 142945 97383 122269 136366 143063 130367 155266 151710 TRUE FALSE 121527.2843 142005.9849 144477.7445 150032.0452 133652.5834 148566.7262 117724.0284 122063.5742 133775.0166 0.908445294 1.061528441 1.080005431 1.121525147 0.999084783 1.11057154 0.880015053 0.912454188 1 17.02944918 2.234256873 24.99978558 0.92487922 1.050255716 0.399179566 0.066889997 99.15041674 575940.991 0.026031575 0.018250513 171.4971367 -2.234256873 0.125376495 MPEMHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MPEMHFK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 78.496 0.035177 711500000 2154800 1565020 1169070 1757400 1675530 1683780 1356270 2031040 2554200 FALSE TRUE 1870037.72 1554739.281 1734436.162 2156444.53 1642190.231 1748556.106 1224739.144 1596717.902 2252245.386 0.830299279 0.690306345 0.770092004 0.95746429 0.729134686 0.776361278 0.543785838 0.70894491 1 21.10293259 2.456578437 24.92140329 0.72304251 0.792762501 0.008831929 0.130227387 753.6215943 914245.1952 0.048847346 0.037840786 286.1399102 -2.456578437 0.069719991 MPFGELMFESSSSCGWVHGVCFSASGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MPFGELMFESSSSCGWVHGVCFSASGSR 28 0 A0A1W2PNV4;C9JEY1;C9K057;O15143 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 117.08 0.00025874 36813000 14934 15038 6071.6 11274 13669 18178 15685 16360 13736 FALSE TRUE 12960.43406 14939.21439 9007.846068 13833.93401 13397.01364 18877.31942 14163.87111 12861.54131 12112.14573 1.070036173 1.233407748 0.743703574 1.142153861 1.106080949 1.558544609 1.169394047 1.061871414 1 13.56416685 3.498708353 24.70583492 1.177419235 1.02172565 0.136420298 0.188467056 1459.877816 1670786.458 0.05359273 0.078609441 3152.886617 -3.498708353 -0.155693584 MPGGPKPGGGPGLS(ph)TPGGHPKPPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MPGGPKPGGGPGLSTPGGHPKPPHR 25 2 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 1 MPGGPKPGGGPGLS(0.638)T(0.362)PGGHPKPPHR 85.184 0.0083602 837830000 1488700 1167700 608630 889460 993840 981350 1263700 1331100 1399500 TRUE FALSE 1291964.523 1160029.302 902965.5037 1091425.488 974064.5284 1019103.17 1141146.569 1046454.624 1234052.704 1.046928157 0.940016012 0.731707406 0.884423723 0.789321659 0.825818189 0.924714613 0.847982116 1 20.23497258 4.476380791 24.99484755 0.85634057 1.020200169 0.412984054 0.072909784 19.26660126 650390.6211 0.017477268 0.047143802 29948.89415 -4.476380791 0.163859598 MPGGPKPGGGPGLST(ph)PGGHPKPPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MPGGPKPGGGPGLSTPGGHPKPPHR 25 2 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 1 MPGGPKPGGGPGLS(0.347)T(0.653)PGGHPKPPHR 87.265 0.016123 962510000 862950 782740 399960 534170 619250 584750 771780 935110 924140 TRUE FALSE 748908.9711 777598.1294 593381.9938 655461.4628 606928.1365 607245.7109 696932.8944 735144.0035 814889.222 0.919031631 0.954237838 0.728175042 0.804356525 0.744798336 0.745188051 0.855248635 0.902139805 1 19.63624442 1.469398752 1.889987526 1.014729383 0.814978199 0.38972397 0.073584912 0.561461487 3.054820043 0.178956178 0.022250815 29.47126324 -1.469398752 -0.199751184 MPLDLS(ph)PLATPIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 MPLDLSPLATPIIR 14 0 B8ZZU6;E9PBF9;P15336-5;P15336;E9PEK8;H7C2N6;P15336-3;P15336-7;P15336-4;C9JCI8 B8ZZU6 ATF2 Cyclic AMP-dependent transcription factor ATF-2 1 MPLDLS(1)PLATPIIR;MPLDLS(1)PLATPIIR;MPLDLS(0.998)PLAT(0.002)PIIR;MPLDLS(1)PLATPIIR;MPLDLS(1)PLATPIIR;MPLDLS(1)PLATPIIR 127.36 8.40E-05 643060900 782713 791827 586447 701669 747608 797176 762319 784183 1270635 TRUE FALSE 679275.4939 786625.4363 870054.7307 860993.6708 732732.0635 827843.8766 688389.4207 616491.568 1120421.978 0.606267556 0.70207962 0.776542006 0.768454821 0.65397866 0.738867938 0.614401926 0.550231591 1 20.09561076 3.212729894 24.99863304 0.685424526 0.717046774 0 0.12684314 1498.21614 1449949.731 0.038354057 0.043504062 1632.036599 -3.212729894 0.031622248 MPLLELGGET(ph)TPPLSTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MPLLELGGETTPPLSTER 18 0 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 MPLLELGGET(0.643)T(0.357)PPLSTER 103.61 0.0059319 93562000 49677 41580 25470 36862 39999 41916 39988 43728 49779 TRUE FALSE 43112.05858 41306.85824 37787.37719 45232.0805 39203.09816 43528.53564 36109.96991 34377.10749 43894.18333 0.982181586 0.9410554 0.860874365 1.030480056 0.893127407 0.991669792 0.822659568 0.78318139 1 15.42174215 2.231749388 24.99769694 0.8489005 0.946531958 0.198372236 0.07334358 201.1313235 738158.3716 0.028342103 0.019590186 170.5098171 -2.231749388 0.097631458 MPLLELGGET(ph)TPPLSTERS(ph)PEAVGSECPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MPLLELGGETTPPLSTERSPEAVGSECPSR 30 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 2 MPLLELGGET(0.5)T(0.5)PPLS(0.056)T(0.232)ERS(0.712)PEAVGSECPSR 143.22 1.06E-07 43927000 35677 33474 21003 25114 36866 36422 31495 43790 33306 TRUE FALSE 30962.19406 33254.10709 31160.12105 30816.51754 36132.43873 37823.17791 28440.61975 34425.84927 29368.60262 1.054261738 1.132301305 1.061001146 1.049301458 1.230308408 1.287878024 0.968402212 1.17219909 1 14.841987 4.748886502 22.50469816 1.116117654 1.054261609 0.032042234 0.099305134 1511.292326 3293491.794 0.023606263 0.287434363 56090.13721 -4.748886502 -0.061856046 MPLLELGGETT(ph)PPLS(ph)TERSPEAVGSECPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MPLLELGGETTPPLSTERSPEAVGSECPSR 30 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 2 MPLLELGGET(0.48)T(0.52)PPLS(0.377)T(0.348)ERS(0.275)PEAVGSECPSR 64.668 0.019298 34415000 29832 29236 21568 22065 27067 32256 29039 31829 25588 TRUE FALSE 25889.62562 29043.94679 31998.35694 27075.19549 26528.41966 33496.90919 26222.80225 25022.61604 22563.01579 1.1474364 1.287236913 1.418177306 1.199981232 1.175747954 1.484593616 1.162202894 1.109010262 1 14.46167229 1.748607307 2.363285645 1.028243572 1.28302948 0.436476079 0.107768279 0.250865771 2.814787036 0.093188569 0.029582079 56.05409005 -1.748607307 0.254785908 MPLLELGGETT(ph)PPLSTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MPLLELGGETTPPLSTER 18 0 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 MPLLELGGET(0.02)T(0.979)PPLSTER;MPLLELGGET(0.168)T(0.832)PPLSTER 115.31 0.0021564 121891000 117489 98308 63513 82882 93234 102143 86645 109697 126033 TRUE FALSE 101962.531 97662.20827 94228.09924 101701.6249 91378.82581 106072.5073 78242.18124 86239.15021 111133.5223 0.917477723 0.878782623 0.847881875 0.915130041 0.822243585 0.95446005 0.704037626 0.775995833 1 16.76193453 2.257997131 24.99902744 0.811008973 0.885089329 0.103746265 0.082005381 439.5296105 565316.8672 0.029958181 0.023171238 181.1328127 -2.257997131 0.074080356 MPLLELGGETT(ph)PPLSTERS(ph)PEAVGSECPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MPLLELGGETTPPLSTERSPEAVGSECPSR 30 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 2 MPLLELGGET(0.129)T(0.871)PPLS(0.211)T(0.182)ERS(0.607)PEAVGSECPSR 137.47 4.46E-06 61217000 39326 36528 24209 31467 36137 41610 35617 43421 31091 TRUE FALSE 34128.96946 36288.04516 35916.55337 38612.06329 35417.9444 43210.76363 32162.86882 34135.75705 27415.4574 1.244880542 1.323634497 1.310084047 1.408404855 1.291896899 1.576146004 1.173165501 1.245128124 1 14.74270192 1.181682577 1.322875172 0.820520718 1.34735849 0.514219815 0.103662309 1.249634861 1.709978496 0.938002214 0.029818324 15.19436577 -1.181682577 0.526837771 MPLLELGGETTPPLSTERS(ph)PEAVGSECPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MPLLELGGETTPPLSTERSPEAVGSECPSR 30 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 MPLLELGGETTPPLS(0.014)T(0.014)ERS(0.973)PEAVGSECPSR;MPLLELGGETTPPLST(0.002)ERS(0.998)PEAVGSECPSR 262.89 1.24E-58 741730000 146338 143200 101248 115540 153112 174589 141954 169291 150819 TRUE FALSE 126999.0625 142259.3098 150211.8715 141775.1229 150065.3708 181305.5518 128187.3229 133089.4371 132989.3496 0.95495664 1.06970453 1.129503016 1.066063736 1.128401418 1.363308809 0.963891645 1.000752597 1 17.02095119 MPLPS(ph)PTESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MPLPSPTESR 10 0 A6NF31;O75665-3;O75665 A6NF31 OFD1 Oral-facial-digital syndrome 1 protein 1 MPLPS(0.991)PT(0.009)ESR;MPLPS(0.996)PT(0.004)ESR 136.81 0.00011319 366890000 396740 345210 222210 304730 395790 366620 324160 405460 411040 TRUE FALSE 344309.8038 342942.2928 329671.4992 373923.604 387914.5534 380724.1086 292723.0131 318755.5343 362447.3195 0.949958202 0.946185209 0.909570803 1.031663317 1.07026465 1.050426057 0.807629129 0.879453419 1 18.46741179 2.246375793 24.99999851 0.888641309 0.992358572 0.315220814 0.067344734 207.4793428 663708.1968 0.027267114 0.020722075 176.3501336 -2.246375793 0.103717264 MPPSHQLDHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MPPSHQLDHSK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ;;; 138.89 3.36E-05 563155000 826028 823148 519392 624470 818660 837048 875700 984280 939210 FALSE TRUE 716866.3069 817740.6866 770571.7085 766265.4579 802370.2677 869249.7782 790774.7488 773799.3817 828177.6638 0.865594833 0.987397659 0.930442515 0.925242845 0.968838334 1.049593362 0.954837088 0.934339835 1 19.65958077 3.171634838 5.726214212 0.977545626 0.931753021 0.292061306 0.041667853 0.323402026 19.62531998 0.012901934 0.014834723 1484.686769 -3.171634838 -0.045792605 MPQDGS(ph)DDEDEEWPTLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MPQDGSDDEDEEWPTLEK 18 0 Q13895;F8WBL2 Q13895 BYSL Bystin 1 MPQDGS(1)DDEDEEWPTLEK 99.366 0.00067603 38039000 75876 64010 47783 44849 53691 67108 69463 74426 57695 TRUE FALSE 65848.79435 63589.5141 70891.01862 55032.65092 52622.65414 69689.68818 62726.48895 58510.57908 50874.36283 1.294341407 1.249932393 1.393452708 1.081736416 1.034364879 1.369839037 1.232968542 1.150099497 1 15.6346512 1.332026918 2.270659634 0.963612023 1.234037584 0.317299888 0.111078188 0.66084103 4.233950175 0.33572595 0.030735528 21.47963604 -1.332026918 0.270425561 MPS(ph)PFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MPSPFR 6 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7 E9PHV5 SSFA2 Sperm-specific antigen 2 1 MPS(1)PFR;MPS(1)PFR;MPS(1)PFR 89.296 0.052792 704100000 505190 548430 358800 382460 510840 570420 499810 535720 502390 TRUE FALSE 438427.8615 544827.3272 532316.8801 469303.3885 500675.2834 592364.4265 451338.5031 421160.447 442998.0265 0.989683554 1.229864005 1.201623593 1.059380314 1.130197548 1.337171705 1.018827345 0.950705018 1 18.75694075 2.020546019 24.95115431 0.975711813 1.159201153 0.421804321 0.093822113 194.1025937 235717.8783 0.037013377 0.024951575 104.8445884 -2.020546019 0.183489341 MPSGEFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MPSGEFAR 8 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ; 122.74 0.0032044 704390000 827380 811660 606160 746040 779020 716170 791300 908070 1628670 FALSE TRUE 718039.6367 806328.152 899301.0035 915439.7845 763519.0261 743721.5233 714559.8478 713886.2971 1436130.488 0.499982169 0.561458836 0.626197279 0.637434963 0.531650176 0.517864866 0.497559138 0.497090134 1 20.45375541 1.234796871 24.99999792 1.000000647 0.546071631 0.888895325 0.0504256 38.57292938 256175.4099 0.101800434 0.013960878 17.17105073 -1.234796871 -0.453929016 MPVSSQHRYS(ph)TPHAFTFNTSSPSSEGSLSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MPVSSQHRYSTPHAFTFNTSSPSSEGSLSQR 31 1 P04049;P04049-2 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 MPVS(0.11)S(0.11)QHRYS(0.627)T(0.154)PHAFTFNTSSPSSEGSLSQR 157.47 4.94E-10 106730000 44850 39656 24839 30852 44005 42510 38715 47096 35459 TRUE FALSE 38922.95886 39395.49712 36851.22348 37857.41814 43129.38659 44145.38721 34960.42526 37024.8869 31267.07742 1.244854399 1.259967364 1.178595076 1.210775719 1.379386568 1.41188083 1.11812258 1.18414927 1 14.93235675 1.321040059 1.35302635 0.924030625 1.269214869 0.499122291 0.083837229 1.031820135 1.890091026 0.483355316 0.02672888 20.94305626 -1.321040059 0.345184244 MQAHIQDLEEQLDEEEGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MQAHIQDLEEQLDEEEGAR 19 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ; 273.46 2.23E-39 110109000 189274 156261 87287 107705 150221 158028 161351 176499 112680 FALSE TRUE 164260.9613 155234.5112 129499.2852 132161.0664 147231.896 164107.4394 145703.2049 138756.0624 99359.09877 1.653205025 1.562358286 1.303346012 1.330135519 1.481815937 1.651659903 1.466430419 1.396510879 1 16.60036447 1.188258533 2.40276692 0.827336936 1.486637969 0.640264799 0.115275081 0.480536909 2.638185316 0.706668039 0.032736861 15.42618492 -1.188258533 0.659301033 MQAQWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MQAQWER 7 0 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 ;;; 142.64 0.0057586 1441940000 1169940 1175550 744880 757480 1151090 1298390 1135140 1258420 1115470 FALSE TRUE 1015329.465 1167827.735 1105106.459 929477.4114 1128185.561 1348339.903 1025054.298 989316.676 983600.4073 1.032258077 1.187298954 1.123531925 0.94497461 1.146995825 1.370820806 1.042145052 1.005811576 1 19.90771281 2.018116948 24.99976481 1.009517994 1.134725312 0.215445042 0.108212815 363.1214501 501073.2596 0.045560824 0.030711061 104.2598146 -2.018116948 0.125207318 MQAS(ph)IEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MQASIEK 7 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK 130.41 0.0037403 2622900000 3079320 2797340 1866160 2054980 2538600 2145410 2757720 3505030 3169250 TRUE FALSE 2672380.06 2778964.089 2768641.218 2521594.617 2488086.827 2227945.311 2490276.739 2755506.611 2794584.875 0.956270852 0.994410338 0.990716454 0.902314558 0.890324301 0.797236588 0.891107928 0.986016433 1 21.41420256 3.739020959 24.96163056 0.912094303 0.981860329 0.253276065 0.056060431 65.65453307 3560026.819 0.017242119 0.027672705 5483.03425 -3.739020959 0.069766026 MQASIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MQASIEK 7 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 84.498 0.050021 117840000 284710 259890 167060 207970 269330 259550 252730 330150 269710 FALSE TRUE 247084.8521 258182.7655 247850.7748 255192.7671 263970.8599 269535.0565 228220.2835 259549.9917 237825.1911 1.038934736 1.085598899 1.042155264 1.073026646 1.109936499 1.13333266 0.959613582 1.091347769 1 17.85954201 -0.541107624 0.793229324 2.80E-15 1.072180728 0.142582555 0.047930782 80.27216933 3.648087406 136.1252487 0.017687157 0.287668545 0.541107624 1.072180728 MQEHSDQVPVGNIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MQEHSDQVPVGNIPR 15 0 P33993;P33993-3;P33993-2;C9J8M6 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 129.29 6.68E-05 442840000 678010 573620 355790 448060 637650 619630 594500 712010 643970 FALSE TRUE 588409.2606 569851.8525 527851.234 549798.8712 624962.0125 643467.5671 536845.4815 559752.2024 567840.6002 1.036222596 1.003541931 0.929576423 0.968227476 1.100594097 1.133183444 0.945415811 0.985755866 1 19.11512648 4.742878709 21.1846002 1.006655625 1.036222662 0.018092324 0.063676927 327.2379673 1604850.036 0.016656174 0.120817655 55319.55902 -4.742878709 0.029567037 TSS(ph)IADEGTYTLDSILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TSSIADEGTYTLDSILR 17 0 A0A087WY00;G3V394;F8WE88;F8W6H6;Q9Y4I1-2;Q9Y4I1;Q9Y4I1-3;E7ERV5 A0A087WY00 MYO5A Unconventional myosin-Va 1 TS(0.007)S(0.993)IADEGTYTLDSILR;TS(0.02)S(0.98)IADEGTYTLDSILR;T(0.026)S(0.026)S(0.947)IADEGTYTLDSILR;T(0.001)S(0.004)S(0.995)IADEGTYTLDSILR;TS(0.027)S(0.972)IADEGTYTLDSILR 321.81 1.28E-58 573166000 481892 497289 422888 552660 808985 747424 818555 982086 1021114 TRUE FALSE 418208.7512 494022.2758 627398.0513 678149.8999 792887.7813 776177.8849 739171.6621 772074.5515 900399.0662 0.464470441 0.548670356 0.69679998 0.75316593 0.880595961 0.862037639 0.820937837 0.8574804 1 19.78020503 4.32849287 0.707639629 0.892310585 0.310902731 0.913435924 0.04719657 0.520602024 0.295729052 0.023023901 0.224194883 21305.55591 -4.32849287 -0.581407854 down MQFS(ph)FEEYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MQFSFEEYEK 10 0 A0A1W2PR28;Q5JU85-3;Q5JU85;A0A1W2PR18 A0A1W2PR28 IQSEC2 IQ motif and SEC7 domain-containing protein 2 1 MQFS(1)FEEYEK;MQFS(1)FEEYEK;MQFS(1)FEEYEK 150.12 2.32E-05 557380000 1140740 1071240 704100 871860 1000990 868390 1303640 1276210 1131190 TRUE FALSE 989988.3187 1064202.954 1044605.115 1069829.139 981072.2574 901797.5252 1177213.193 1003302.423 997462.0069 0.992507295 1.066910766 1.047263062 1.072551266 0.983568548 0.904092105 1.180208555 1.005855277 1 19.92790236 1.508920861 25 1.001330066 1.036689756 0.034796813 0.070919976 2.402589995 1878.380846 0.045646422 0.01725403 32.27905862 -1.508920861 0.035359689 MQFS(ph)FEGPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 MQFSFEGPEK 10 0 A0A0C4DGT3;A0A3B3IU98;Q6DN90-2;A0A3B3IRZ4;Q6DN90-3;A0A2R8Y7T6;Q6DN90;A0A2R8Y695 A0A0C4DGT3;A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 MQFS(1)FEGPEK;MQFS(1)FEGPEK;MQFS(1)FEGPEK;MQFS(1)FEGPEK;MQFS(1)FEGPEK;MQFS(1)FEGPEK;MQFS(1)FEGPEK 186.51 1.40E-06 1880110000 5354010 5679890 3163680 3717890 4506910 3161330 6898370 6180170 5140130 TRUE FALSE 4646464.013 5642578.429 4693646.23 4562093.749 4417231.309 3282948.411 6229367.139 4858588.74 4532469.687 1.025150599 1.244923589 1.035560424 1.006535965 0.974574926 0.724317786 1.374386939 1.071951734 1 22.11186594 4.104156998 24.93599095 1.036013327 1.136348593 0.067648114 0.164329261 30.73491912 7296.783862 0.042439348 0.088344565 12710.33504 -4.104156998 0.100335266 MQHLIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 15 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 27212610000 17793240 17180140 10640300 12866136 16871490 19624190 18683840 18660430 18527580 FALSE TRUE 15441818.25 17067282.53 15785984.67 15787588.83 16535780.36 20379145.29 16871884.07 14670042.26 16337270.6 0.945189599 1.044683837 0.966255934 0.966354124 1.01215073 1.247402078 1.032723549 0.897949396 1 23.96166364 4.756002234 22.27106081 1.015271266 0.945189339 0.061543002 0.090588911 2908.778494 3713913.14 0.023864166 0.585047877 57016.72057 -4.756002234 -0.070081927 MQMELSHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MQMELSHK 8 0 Q9Y6D9;C9JJ38 Q9Y6D9 MAD1L1 Mitotic spindle assembly checkpoint protein MAD1 0 ;;; 90.629 0.0070471 1891310000 1456010 1395110 1861190 1820270 1233470 958030 2108370 1740120 7044500 FALSE TRUE 1263594.589 1385945.431 2761267.709 2233590.125 1208926.36 994886.034 1903900.602 1368008.88 6211707.235 0.203421466 0.223118279 0.444526377 0.359577495 0.194620628 0.160163059 0.306501986 0.22023074 1 22.5665584 1.236396349 24.99622553 1.000000944 0.265893246 0.878780712 0.085901631 19.69525498 227414.3492 0.141605386 0.022033544 17.23440715 -1.236396349 -0.734107698 MQMLEDEDDLAYAETEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MQMLEDEDDLAYAETEKK 18 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 195.97 3.21E-15 195361000 317870 265840 199637 188535 208248 195039 361040 352900 219500 FALSE TRUE 275862.6741 264093.6795 296182.1209 231344.7533 204104.2722 202542.2765 326026.3964 277435.0813 193550.9601 1.425271536 1.364465872 1.530253949 1.195265336 1.054524721 1.046454518 1.684447322 1.433395532 1 17.56235394 3.733330312 24.72944392 1.268891724 1.432443993 0.165360011 0.20740255 904.2616436 4275453.458 0.062106481 0.09547425 5411.657617 -3.733330312 0.163552268 MQNGFGSPEPSLPGTPHS(ph)PAPPSGGTWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MQNGFGSPEPSLPGTPHSPAPPSGGTWK 28 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 MQNGFGSPEPSLPGTPHS(1)PAPPSGGTWK 218.19 1.96E-34 265240000 295280 257910 145070 224720 237640 219630 282520 317200 291740 TRUE FALSE 256257.9999 256215.7722 215226.3372 275746.1106 232911.4289 228079.3082 255121.2539 249369.2485 257250.8296 0.996140616 0.995976467 0.836640012 1.071895905 0.905386503 0.886602809 0.991721793 0.969362271 1 17.9728162 MQNT(ph)DDEERPQLS(ph)DDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MQNTDDEERPQLSDDER 17 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 2 MQNT(1)DDEERPQLS(1)DDER;MQNT(1)DDEERPQLS(1)DDER;MQNT(1)DDEERPQLS(1)DDER;MQNT(1)DDEERPQLS(1)DDER 191.44 5.55E-10 2918110000 2209480 1787410 1641730 2134930 1997420 1949890 1878530 2153980 4148090 TRUE FALSE 1917491.62 1775668.386 2435676.119 2619698.487 1957675.25 2024903.53 1696350.45 1693368.139 3657707.526 0.524233172 0.485459369 0.665902372 0.716213221 0.535219187 0.553599082 0.463774219 0.462958869 1 21.80250829 1.231848205 24.99967948 1.000000765 0.549017847 0.745603864 0.08243133 132.0898782 491909.4573 0.213207609 0.02249364 17.05486183 -1.231848205 -0.450982917 MQQENMKPQEQLTLEPYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MQQENMKPQEQLTLEPYER 19 1 P22087;M0QXL5;M0R299 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 243.23 1.73E-24 793170000 448210 357510 256770 324680 325380 351660 421760 455270 374470 FALSE TRUE 388977.9129 355161.4933 380944.8308 398403.5564 318905.5746 365188.5878 380857.7801 357914.0534 330200.5832 1.178004924 1.075593174 1.153677038 1.20655013 0.965793493 1.105959851 1.153413408 1.083929198 1 18.33298314 3.266285813 24.99997444 1.0736594 1.147910388 0.342919862 0.061623981 310.9449694 280378.8054 0.017955892 0.023175612 1846.23004 -3.266285813 0.074250988 MQQHEQALADCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MQQHEQALADCR 12 0 Q9UNE7;Q9UNE7-2 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ;;; 120.14 0.00044215 544489000 520113 506946 345844 393481 468093 509135 492538 529826 621355 FALSE TRUE 451378.7493 503615.8383 513095.3152 482826.875 458778.8651 528721.7529 444771.7406 416526.833 547899.1197 0.823835507 0.919176214 0.936477714 0.881233164 0.837341855 0.964998362 0.811776702 0.76022541 1 19.06355076 2.198846881 24.99791274 0.835204836 0.89379192 0.023792706 0.073864212 332.2991491 209164.3275 0.02940412 0.019824569 158.0690637 -2.198846881 0.058587084 MQQMSEQVHTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MQQMSEQVHTLR 12 0 Q08379;Q08379-2;B7ZC06 Q08379 GOLGA2 Golgin subfamily A member 2 0 159.5 7.06E-05 193270000 138160 130660 57797 76408 118510 118020 105640 126670 103480 FALSE TRUE 119901.8059 129801.6859 85747.82252 93757.60422 116151.8829 122560.3058 95395.04906 99582.60625 91246.71228 1.314039738 1.422535482 0.939736023 1.027517615 1.27294321 1.343175033 1.045462863 1.091355554 1 16.47748496 4.255555702 24.98721393 1.110742484 1.368287743 0.439316329 0.124405481 244.4866088 359452.9029 0.032759 0.086195304 18011.74137 -4.255555702 0.25754526 MQQNIQELEEQLEEEESAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 MQQNIQELEEQLEEEESAR 19 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;; 308.84 4.22E-61 1122161000 861756 833646 511157 614673 789516 889025 807068 931148 894965 FALSE TRUE 747872.7612 828169.7245 758354.2349 754243.8993 773806.1763 923226.367 728798.6696 732029.2464 789163.2572 0.947678132 1.049427627 0.960959888 0.955751414 0.980540046 1.169880071 0.923508112 0.927601785 1 19.58996426 MQSLS(ph)LNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MQSLSLNK 8 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 MQS(0.023)LS(0.977)LNK;MQS(0.013)LS(0.987)LNK 90.913 0.037253 186770000 1056370 1003120 753800 866490 950110 611721 1449160 1183320 1278930 TRUE FALSE 916768.028 996530.4387 1118340.201 1063239.798 931204.6699 635254.3027 1308620.686 930276.2266 1127736.352 0.812927619 0.883655507 0.991668131 0.942808836 0.825729053 0.563300368 1.160395941 0.824905772 1 20.1049984 2.200470493 24.99999911 0.966530154 0.850186227 0.21260642 0.138551318 341.3896464 224064.6741 0.056877796 0.038347867 158.6611117 -2.200470493 -0.116343927 MQTEAQHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MQTEAQHER 9 0 Q9H2K8;G3V1Q8;F5GWV8 Q9H2K8 TAOK3 Serine/threonine-protein kinase TAO3 0 138.22 0.00014275 99673000 87728 85136 57674 68629 81246 99104 81095 84341 77729 FALSE TRUE 76134.52253 84576.73601 85565.33931 84212.26338 79629.36356 102916.595 73230.41938 66305.33349 68539.96617 1.110804787 1.233976915 1.248400664 1.228659249 1.161794614 1.501555965 1.068433842 0.967396648 1 16.06465786 2.014696581 24.99877588 0.992333177 1.24576661 0.557389789 0.101002415 153.8160875 261639.0521 0.039558989 0.026659195 103.4419219 -2.014696581 0.253433433 MREDYDS(ph)VEQDGDEPGPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 MREDYDSVEQDGDEPGPQR 19 1 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 1 MREDYDS(1)VEQDGDEPGPQR;MREDYDS(1)VEQDGDEPGPQR;MREDYDS(1)VEQDGDEPGPQR;MREDYDS(1)VEQDGDEPGPQR;MREDYDS(1)VEQDGDEPGPQR;MREDYDS(1)VEQDGDEPGPQR 267.24 7.81E-32 2473780000 1954680 1865870 1269790 1356170 1824750 1903960 1776290 1971380 1761830 TRUE FALSE 1696364.085 1853612.977 1883864.691 1664109.126 1788441.045 1977206.573 1604025.669 1549815.728 1553548.464 1.091928655 1.193147829 1.212620484 1.071166535 1.151197459 1.272703503 1.032491555 0.997597284 1 20.56713582 2.08246838 8.004934266 1.003511727 1.163715326 0.627475252 0.056846094 0.149971649 12.68213776 0.023036379 0.015492966 120.9117147 -2.08246838 0.160203598 MREDYDSVEQDGDEPGPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MREDYDSVEQDGDEPGPQR 19 1 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ; 166.61 2.05E-11 625920000 324100 320880 199612 224137 294614 323960 276365 347050 243266 FALSE TRUE 281269.3638 318772.1182 296145.0309 275030.7316 288751.7578 336422.9508 249563.1648 272836.0582 214507.3706 1.311234029 1.486066037 1.380582075 1.282150496 1.346115786 1.568351474 1.163424661 1.27191927 1 17.71066769 0.690636019 0.900250366 0.302279223 1.386031097 0.560113508 0.104587043 3.898807217 1.233663349 5.285137511 0.035819321 4.904966195 -0.690636019 1.083751874 MREEFDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MREEFDK 7 1 O43809;H3BND3;H3BV41 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 ;; 114.64 0.0053443 1376880000 2923670 2176040 1262130 1647720 2082200 1749190 2286280 2546430 2224690 FALSE TRUE 2537299.602 2161745.45 1872500.29 2021860.01 2040768.294 1816482.471 2064556.917 2001895.761 1961689.683 1.293425573 1.101981353 0.954534403 1.030672704 1.040311478 0.925978501 1.052438077 1.020495636 1 20.90366541 4.644933002 2.791211629 1.007366063 1.318133188 0.843743797 0.039572244 0.121991162 1.45364508 0.009600578 0.077372482 44150.23319 -4.644933002 0.310767125 MREESGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MREESGAR 8 1 F8VZX2;F8W1G6;F8W0G4;P57721;P57721-4;E9PFP8;P57721-5;P57721-3;P57721-2;F8VTZ0;J3QT27;F8VXH9;Q15366;Q15366-6;Q15366-2;Q15366-3;Q15366-5;Q15366-4;Q15366-8;Q15366-7 F8VZX2;Q15366;Q15366-2;Q15366-5 PCBP2;PCBP3 Poly(rC)-binding protein 3;Poly(rC)-binding protein 2 0 ; 100.09 0.0057914 212382000 175833 154341 67512 79563 128776 180349 152651 155839 44897 FALSE TRUE 152596.2235 153327.1238 100161.029 97628.99519 126213.6095 187287.1427 137846.9295 122514.0426 39589.32781 3.85447877 3.872940823 2.530000749 2.466043265 3.188071547 4.730748237 3.481921446 3.094622955 1 15.27282395 4.262654524 24.27181774 3.029233175 3.863711475 0.14181075 0.931782024 379.891201 382686.7774 0.23931777 0.63234525 18308.5742 -4.262654524 0.8344783 MREEVITLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 MREEVITLIR 10 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;;;;;; 202.16 2.09E-07 3006430000 2601997 2681609 1644824 2017074 2722844 3231427 2351790 2732692 2262129 FALSE TRUE 2258136.504 2663993.334 2440266.388 2475081.481 2668664.732 3355742.088 2123713.768 2148327.082 1994702.687 1.132066708 1.335534038 1.22337349 1.240827266 1.33787594 1.68232695 1.064676847 1.077016187 1 20.9277423 2.052374324 24.99996687 1.052055816 1.322526461 0.454138161 0.143749401 87.75882713 41889.68213 0.059013168 0.039786661 112.816942 -2.052374324 0.270470644 MREHLELFWSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MREHLELFWSR 11 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 123.95 0.0002159 961320000 1023250 1017910 404690 450870 899590 997120 1040180 1069110 157518 FALSE TRUE 888024.9199 1011223.282 600399.4376 553246.9246 881689.919 1035479.852 939303.5037 840489.1463 138896.4015 6.393433598 7.280413829 4.322642136 3.983162405 6.347824059 7.455051683 6.762619432 6.05119454 1 17.0836497 4.254466735 24.96848601 5.386622615 6.836924112 0.118456859 1.834088177 606.7170819 952371.6221 0.465287781 1.222346886 17966.63459 -4.254466735 1.450301497 MRHCSDKELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MRHCSDKELK 10 2 Q8NG31-2;Q8NG31;H0YEY7;H0YCZ2 Q8NG31-2 CASC5 Protein CASC5 0 58.699 0.061533 1287100000 1393500 1700300 1839600 961480 874190 1875600 1137900 747950 670660 FALSE TRUE 1209345.444 1689130.617 2729236.713 1179798.729 856795.3293 1947755.546 1027546.633 588006.7131 591375.3388 2.044971045 2.856275036 4.615066835 1.995008334 1.448818158 3.293602925 1.737554081 0.994303743 1 19.17371456 1.729661573 0.652549448 0.083683625 2.935163184 0.381029691 0.877389073 2.041917587 1.054710166 4.118428412 0.524621505 53.66134733 -1.729661573 2.851479558 MRPFEGFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MRPFEGFQR 9 1 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ; 173.37 5.06E-05 1644110000 777790 712870 486270 645800 748000 986580 538510 802170 941350 FALSE TRUE 675003.0808 708187.11 721431.7985 792438.7604 733116.2634 1024534.371 486285.3831 630632.188 830064.6754 0.813193358 0.853171001 0.869127214 0.954671104 0.883203785 1.234282582 0.585840354 0.759738616 1 19.66286422 2.201257279 24.99998856 0.769083993 0.926506758 0.18190333 0.151251493 277.4131697 185915.1401 0.061057151 0.041165873 158.9488092 -2.201257279 0.157422765 MRPGAYSTGYGGYEEYSGLSDGYGFTTDLFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MRPGAYSTGYGGYEEYSGLSDGYGFTTDLFGR 32 1 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 203.75 5.45E-27 483926000 108765 129919 62117 73413 96580 125985 114433 117401 87776 FALSE TRUE 94391.42967 129065.5535 92156.98897 90082.5437 94658.24696 130831.7245 103335.3053 92295.70977 77399.22127 1.219539785 1.667530389 1.190670752 1.163868863 1.222987071 1.690349364 1.335094896 1.192463028 1 16.24003143 1.473918711 2.508712144 0.99626475 1.361091663 0.282727859 0.185787313 0.444483907 4.838161436 0.295550359 0.050352961 29.77958979 -1.473918711 0.364826912 MRPGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 MRPGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVK 41 2 A0A2R8Y5Y7;P32969;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ;;;; 269.6 3.62E-68 375130000 300523 247210 163677 178400 203084 177003 317844 361861 124553 FALSE TRUE 260808.1241 245586.0612 242831.7447 218908.4467 199043.0257 183812.4199 287019.5378 284479.8412 109828.4862 2.374685595 2.2360871 2.211008756 1.993184593 1.812307832 1.673631553 2.613343292 2.590219085 1 16.74489277 4.033506583 2.429713024 2.040254324 2.315717839 0.080005793 0.4609658 1.056516967 12.42258611 0.133081108 0.334138926 10802.05994 -4.033506583 0.275463515 MRQLLRPIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MRQLLRPIDR 10 2 F8WBN2 F8WBN2 KDM2B 0 72.643 0.076196 85451000 109640 143770 52999 62478 116650 179600 88880 87533 31773 FALSE TRUE 95150.79621 142825.5654 78629.49367 76664.58482 114328.8932 186509.3282 80260.43128 68814.74913 28016.83214 3.396201103 5.09784849 2.806509076 2.73637592 4.080721641 6.657045569 2.864721853 2.456193077 1 14.77400622 4.224113157 24.96709707 3.275586107 4.247025302 0.073761517 1.492931632 642.9984023 1111189.966 0.407031792 0.853374379 16753.79344 -4.224113157 0.971439195 MRTPPALGS(ph)QGSEVTGPTFADGELIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MRTPPALGSQGSEVTGPTFADGELIPR 27 1 Q86YS3-2 Q86YS3-2 RAB11FIP4 Rab11 family-interacting protein 4 1 MRT(0.281)PPALGS(0.338)QGS(0.338)EVT(0.042)GPT(0.001)FADGELIPR 48.798 0.07173 140450000 21114 20170 16033 17314 22384 22606 23914 26683 31155 TRUE FALSE 18323.7314 20037.50194 23786.61243 21245.40833 21938.60219 23475.66745 21594.82396 20977.0481 27471.89139 0.666999266 0.729381958 0.86585274 0.773350769 0.79858361 0.85453408 0.786069792 0.76358223 1 14.74566862 4.422236871 4.431758876 0.822606772 0.678778549 0.410193696 0.068717539 0.18890925 7.54770134 0.016641325 0.051177453 26438.5036 -4.422236871 -0.143828223 MS(ph)ADMSEIEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MSADMSEIEAR 11 0 O43318;O43318-3;Q9UG54;O43318-2;O43318-4 O43318 MAP3K7;DKFZp586F0420 Mitogen-activated protein kinase kinase kinase 7 1 MS(1)ADMSEIEAR;MS(0.995)ADMS(0.005)EIEAR;MS(1)ADMSEIEAR;MS(1)ADMSEIEAR 194.06 7.14E-07 1064391000 812930 852100 616100 721910 984600 932580 970130 1110960 1043460 TRUE FALSE 705499.2408 846502.499 914048.0207 885830.6992 965008.3863 968456.9561 876046.9419 873389.8495 920103.3475 0.766760867 0.920008064 0.993418862 0.962751306 1.048804342 1.052552367 0.952117981 0.949230162 1 19.81143639 4.735243185 1.902783316 0.991683176 0.696447759 0.805053056 0.035533732 0.383484977 1.458937961 0.010515397 0.200254761 54355.46118 -4.735243185 -0.295235417 MS(ph)DEFVDSFK ddPTM_MDA-MB-175_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 97.911 0.0060167 26622000 198918 77030 72053 78793 86953 101577 101497 121904 213281 TRUE FALSE 172630.4823 76523.98486 106898.0718 96684.15493 85222.80542 105484.7329 91653.83656 95835.77826 188067.1632 0.917919319 0.406897108 0.568403702 0.514093759 0.453150906 0.560888627 0.487346302 0.509582729 1 17.52088845 1.236325891 24.99614851 1.000000596 0.539177322 0.504192986 0.138988875 45.47060752 508482.1889 0.199062904 0.030781832 17.23161138 -1.236325891 -0.460823274 MS(ph)GFIYQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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 168.3 6.22E-05 6838360000 14070400 14457470 7667930 7566310 11602850 9724550 12072290 14153360 17819040 TRUE FALSE 12210960.99 14362497.93 11376166.6 9284356.329 11371975.99 10098659.73 10901521.17 11126774.11 15712493.39 0.777149793 0.914081398 0.724020454 0.590890071 0.723753748 0.642715289 0.6938123 0.708148212 1 23.9054088 -1.897873406 16.00245476 9.953728783 0.742507326 0 0.122079982 0 0 0 0.027440342 0.012651051 1.897873406 -9.211221457 MS(ph)GFIYQGKLPTTGMTITK ddPTM_MDA-MB-175_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 198.39 4.50E-16 439720000 992680 1061750 582620 426230 1180440 769460 1468720 1491220 448080 TRUE FALSE 861494.8229 1054775.294 864376.9807 523012.036 1156951.553 799061.6241 1326283.76 1172334.208 395108.4929 2.180400671 2.669583958 2.187695269 1.323717524 2.928187003 2.022385341 3.356758421 2.967119738 1 18.59188933 MS(ph)GGSTMSSGGGNTNNSNSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MSGGSTMSSGGGNTNNSNSK 20 0 Q86U70-2;Q86U70;A0A6E1WJ75;Q86U70-3 Q86U70-2 LDB1 LIM domain-binding protein 1 1 MS(0.972)GGS(0.023)T(0.004)MSSGGGNTNNSNSK;MS(0.999)GGS(0.001)TMSSGGGNTNNSNSK 108.49 0.00022166 50470000 140039 103800 75668 107344 115861 87150 123142 133780 222962 TRUE FALSE 121532.4913 103118.131 112261.2979 131718.0959 113555.5928 90502.71689 111199.7078 105172.1881 196603.6864 0.618159779 0.524497444 0.571003016 0.669967579 0.577586285 0.460330722 0.565603371 0.534945148 1 17.58493085 1.236315074 24.99987083 1.000000564 0.563140225 0.858982877 0.055351261 21.62097962 240651.5449 0.089141809 0.013783945 17.23118219 -1.236315074 -0.436860339 MS(ph)PGVAGSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MSPGVAGSPR 10 0 Q15596;E7EWM1 Q15596 NCOA2 Nuclear receptor coactivator 2 1 MS(1)PGVAGSPR 116.6 0.0011208 145890000 314700 275220 219110 248410 302050 314560 295540 355550 505900 TRUE FALSE 273111.5977 273412.0617 325072.3289 304815.2872 296039.796 326661.3267 266878.5763 279518.3994 446093.0783 0.612230072 0.612903618 0.728709645 0.683299746 0.663627862 0.732271677 0.598257604 0.626592101 1 18.76698524 1.235445251 24.99916444 1.000000469 0.657242614 0.840165682 0.046983948 34.77549484 279005.6322 0.082534343 0.011922176 17.19670539 -1.235445251 -0.342757855 MS(ph)PMGTASGSNSPTSDSASVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MSPMGTASGSNSPTSDSASVQR 22 0 Q5QPB1;O76080 Q5QPB1 ZFAND5 AN1-type zinc finger protein 5 1 MS(1)PMGTASGSNSPTSDSASVQR;MS(1)PMGTASGSNSPTSDSASVQR 405.31 3.50E-152 548160000 290856 226694 124451 175250 245211 206359 192302 251366 222125 TRUE FALSE 252418.6427 225204.8322 184635.9199 215043.191 240331.7808 214297.7643 173652.5816 197613.337 195865.6355 1.288733687 1.149792466 0.942666228 1.097911793 1.227023721 1.094105986 0.886590346 1.008922961 1 17.57950477 7.99998117 0.780939032 1.02837637 59.01779987 0.406165712 0.095502352 506.0299469 1.914378748 0.037505646 51808.55134 99995664.33 -7.99998117 57.9894235 MS(ph)PNQLCSVPLQPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 MSPNQLCSVPLQPGR 15 0 Q86TB9-4 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 MS(1)PNQLCSVPLQPGR;MS(1)PNQLCSVPLQPGR;MS(1)PNQLCSVPLQPGR;MS(1)PNQLCSVPLQPGR;MS(1)PNQLCSVPLQPGR;MS(1)PNQLCSVPLQPGR;MS(0.999)PNQLCS(0.001)VPLQPGR;MS(1)PNQLCSVPLQPGR;MS(1)PNQLCSVPLQPGR 264 4.47E-25 2872440000 1441656 1415598 822407 943377 1431812 1445073 1291272 1514595 1329090 TRUE FALSE 1251137.507 1406298.844 1220125.776 1157585.166 1403321.742 1500665.893 1166044.64 1190710.646 1171966.494 1.06755399 1.199947994 1.041092712 0.987728892 1.197407732 1.280468256 0.994947079 1.015993761 1 20.16049989 MS(ph)PSKSPFLPSMK ddPTM_MDA-MB-175_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(0.776)PS(0.204)KS(0.02)PFLPSMK 70.117 0.027774 318190000 440810 328860 226370 273080 322240 227910 424050 519110 253970 TRUE FALSE 382555.8416 326699.697 335843.2892 335086.9878 315828.0545 236677.8452 382925.6963 408102.3662 223945.9559 1.708250725 1.45883276 1.499662219 1.496285059 1.410286929 1.056852508 1.709902261 1.822325233 1 17.77279109 4.739836649 23.20106991 1.46706856 1.708250882 0.091336836 0.253160839 119.5973604 2173816.577 0.063215966 0.379855395 54933.4214 -4.739836649 0.241182322 MS(ph)PSQFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MSPSQFAR 8 0 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 MS(0.991)PS(0.009)QFAR;MS(0.983)PS(0.017)QFAR;MS(0.879)PS(0.121)QFAR;MS(0.77)PS(0.23)QFAR 148.56 0.00054476 913990000 1383610 1346770 849370 898700 1234710 1475490 1318810 1315310 1342990 TRUE FALSE 1200762.433 1337922.979 1260128.173 1102763.571 1210141.687 1532253.055 1190912.009 1034041.192 1184223.252 1.013966269 1.129789486 1.0640968 0.931212564 1.021886443 1.293888675 1.005648223 0.873180957 1 20.17550966 1.998858772 24.99999998 0.931096735 1.075460114 0.258612183 0.097952781 51.2990407 1123772.5 0.041112724 0.027308205 99.73756761 -1.998858772 0.144363379 MS(ph)SPEDDSDTKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MSSPEDDSDTKR 12 1 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 MS(0.593)S(0.407)PEDDSDTKR;MS(0.5)S(0.5)PEDDSDTKR 111.88 0.00081732 533550000 902270 765030 559510 624440 724300 722590 944940 994390 899030 TRUE FALSE 783032.7334 760004.4676 830090.9074 766228.646 709887.8471 750388.5049 853299.8642 781747.4369 792747.6976 0.9877452 0.958696531 1.047106046 0.96654793 0.895477652 0.946566615 1.076382646 0.986123882 1 19.59650226 2.2785581 24.9999867 1.015918743 0.967011271 0.249024145 0.043775319 239.9435892 149973.0557 0.017036277 0.013196041 189.9144891 -2.2785581 -0.048907472 MSCFSRPS(ph)MS(ph)PTPLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 MSCFS(0.003)RPS(0.995)MS(0.629)PT(0.373)PLDR;MSCFS(0.001)RPS(0.995)MS(0.622)PT(0.382)PLDR;MS(0.047)CFS(0.087)RPS(0.871)MS(0.585)PT(0.41)PLDR;MSCFSRPS(0.987)MS(0.986)PT(0.026)PLDR;MSCFS(0.009)RPS(0.992)MS(0.866)PT(0.134)PLDR;MS(0.028)CFS(0.035)RPS(0.938)MS(0.973)PT(0.026)PLDR;MSCFS(0.001)RPS(0.999)MS(0.521)PT(0.479)PLDR;MSCFSRPS(1)MS(0.947)PT(0.053)PLDR;MSCFSRPS(1)MS(0.994)PT(0.006)PLDR;MS(0.004)CFS(0.005)RPS(0.989)MS(0.978)PT(0.024)PLDR;MS(0.003)CFS(0.004)RPS(0.992)MS(0.958)PT(0.043)PLDR;MS(0.011)CFS(0.012)RPS(0.936)MS(0.628)PT(0.413)PLDR 259.55 1.13E-25 6019340000 4785630 4370690 2091119 2530160 4221880 4313960 3859070 4612770 2565550 TRUE FALSE 4153196.87 4341978.65 3102391.143 3104671.499 4137872.848 4479920.833 3484817.985 3626365.032 2262253.602 1.835867061 1.919315609 1.371371954 1.372379956 1.829093274 1.98029117 1.540418803 1.602987848 1 21.10932924 0.984556917 1.814682327 0.253314086 1.694121119 0.509471399 0.211669586 1.779688168 3.064561473 5.603440199 0.061511533 9.650657812 -0.984556917 1.440807033 MSCFSRPS(ph)MSPT(ph)PLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 MSCFS(0.002)RPS(0.998)MS(0.389)PT(0.611)PLDR 204.78 6.10E-10 954390000 372500 337360 148680 174890 301600 318870 277630 314400 167430 TRUE FALSE 323273.1812 335143.8599 220582.1453 214601.4475 295598.7501 331137.1352 250705.4853 247168.0067 147636.6161 2.189654502 2.270059208 1.49408833 1.453578747 2.002204858 2.24292011 1.698125383 1.67416467 1 17.17169105 1.032956117 1.482508619 0.193078727 1.9101534 0.498793321 0.287694865 1.873293065 2.43764732 5.563334526 0.088579123 10.78837707 -1.032956117 1.717074673 MSCFSRPSMS(ph)PTPLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MSCFSRPSMS(0.977)PT(0.023)PLDR;MSCFSRPS(0.001)MS(0.895)PT(0.104)PLDR;MS(0.001)CFS(0.002)RPS(0.144)MS(0.63)PT(0.222)PLDR;MS(0.008)CFS(0.006)RPS(0.184)MS(0.795)PT(0.006)PLDR;MSCFSRPS(0.292)MS(0.688)PT(0.019)PLDR;MS(0.001)CFS(0.001)RPS(0.088)MS(0.784)PT(0.126)PLDR 154.34 2.21E-07 4693770000 2957720 2545430 1088954 1082132 2291060 2433270 2132980 2391230 663501 TRUE FALSE 2566849.808 2528708.903 1615575.797 1327846.61 2245472.388 2526879.471 1926123.928 1879884.073 585062.6676 4.387307463 4.322116318 2.761372219 2.269580138 3.838003196 4.31898942 3.292166864 3.213132844 1 19.15823164 1.16717018 2.433971127 4.38E-10 3.57512837 0.577948683 0.69142096 0.587206074 3.164562076 4.837750269 0.195667756 14.69501995 -1.16717018 3.575128369 MSCFSRPSMSPT(ph)PLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MSCFSRPS(0.014)MS(0.092)PT(0.894)PLDR;MSCFSRPSMS(0.442)PT(0.557)PLDR;MSCFSRPS(0.001)MS(0.064)PT(0.935)PLDR 137.89 2.65E-05 3473160000 2550550 2153760 927610 952000 1884350 2137450 1934370 2125360 631590 TRUE FALSE 2213488.355 2139611.809 1376205.299 1168166.15 1846855.122 2219679.085 1746775.095 1670868.304 556924.1497 3.97448801 3.841837008 2.471082102 2.097531865 3.316169936 3.985603939 3.136468577 3.000172114 1 19.08712133 4.25430712 21.20336631 2.808054879 3.908170779 0.274680158 0.794832039 58.54613859 78825.05254 0.202746418 0.529746302 17960.03257 -4.25430712 1.1001159 MSDT(ph)GSPGMQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MSDTGSPGMQR 11 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4;A0A0U1RQL3 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 MSDT(0.572)GS(0.428)PGMQR;MSDT(0.629)GS(0.371)PGMQR;MS(0.013)DT(0.493)GS(0.493)PGMQR;MS(0.008)DT(0.496)GS(0.496)PGMQR 160.11 0.00031145 796990000 1536290 1609150 958126 1198160 1662670 1696850 1546550 1740810 1513500 TRUE FALSE 1333265.384 1598579.388 1421478.938 1470220.541 1629586.12 1762128.918 1396565.819 1368551.328 1334575.754 0.999018137 1.197818395 1.065116711 1.101638881 1.221051795 1.32036635 1.046449266 1.025457959 1 20.34794977 2.024834051 24.98852505 1.020969147 1.152811366 0.32156238 0.087672528 255.7932391 257383.242 0.036393939 0.024535596 105.8849048 -2.024834051 0.131842219 MSDTGS(ph)PGMQR ddPTM_MDA-MB-175_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 MSDT(0.25)GS(0.75)PGMQR;MS(0.016)DT(0.353)GS(0.631)PGMQR 144.92 3.83E-05 931470000 968330 953970 563210 710730 922260 966250 965060 1025240 980430 TRUE FALSE 840362.7371 947703.3083 835580.2398 872112.1093 903908.8304 1003422.263 871468.6297 806000.4044 864524.6823 0.972051758 1.09621313 0.966519819 1.008776415 1.04555584 1.160663522 1.008032099 0.932304677 1 19.72154763 1.996047674 24.99115189 0.963972374 1.043129257 0.219220762 0.058727295 215.8112031 1364607.274 0.024407654 0.016027299 99.09407177 -1.996047674 0.079156883 MSES(ph)PTPCSGSSFEETEALVNTAAK ddPTM_MDA-MB-175_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(0.08)ES(0.46)PT(0.46)PCSGSSFEETEALVNTAAK;MS(0.076)ES(0.91)PT(0.013)PCSGSSFEETEALVNTAAK;MS(0.115)ES(0.87)PT(0.015)PCSGSSFEETEALVNTAAK;MS(0.016)ES(0.867)PT(0.117)PCSGSSFEETEALVNTAAK;MS(0.112)ES(0.804)PT(0.084)PCS(0.001)GSSFEETEALVNTAAK;MS(0.106)ES(0.733)PT(0.16)PCSGSSFEETEALVNTAAK;MS(0.058)ES(0.469)PT(0.469)PCS(0.001)GS(0.001)S(0.001)FEETEALVNTAAK 327 6.11E-88 1440984000 992641 848397 641646 733766 843047 798418 1059667 1170066 1059049 TRUE FALSE 861460.9768 842823.8242 951948.1518 900378.7852 826272.0141 829133.6571 956900.6574 919856.4914 933849.4337 0.922483803 0.902526461 1.019380767 0.96415841 0.884802179 0.887866531 1.02468409 0.985015847 1 19.83283043 2.227861241 24.99995008 1.000331794 0.932478282 0.420149595 0.04033695 235.516604 550298.5276 0.017469516 0.011913885 168.9900914 -2.227861241 -0.067853512 MSESPT(ph)PCSGSSFEETEALVNTAAK ddPTM_MDA-MB-175_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(0.057)ES(0.411)PT(0.51)PCS(0.01)GS(0.012)SFEETEALVNTAAK 136.14 9.30E-05 182900000 83668 76636 48020 64402 68394 53758 81103 93086 78965 TRUE FALSE 72611.06181 76132.57307 71242.63262 79025.45842 67033.09321 55826.10505 73237.64354 73180.2833 69629.84766 1.042815176 1.093389913 1.023162265 1.134936541 0.962706303 0.801755381 1.051813928 1.050990139 1 16.08741825 3.219289656 24.98263116 0.980437427 1.071390289 0.304162998 0.074804378 356.7217044 462448.3835 0.024415971 0.027726969 1656.874661 -3.219289656 0.090952863 MSGHKCS(ph)YPWDLQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MSGHKCSYPWDLQDR 15 1 F8WET5;Q6LCT9;C9J3Y4;Q6LCR0;E7ENI6;A0A3B3IST8;Q05084;Q05084-2 F8WET5 ICA1;ICAp69 Islet cell autoantigen 1 1 MS(0.159)GHKCS(0.841)YPWDLQDR 77.468 0.032513 89506000 97024 98663 24181 25408 78084 76048 98093 110730 6690.6 TRUE FALSE 84202.03257 98014.87626 35875.01248 31177.27474 76530.28117 78973.61577 88579.95596 87051.2512 5899.64489 14.27238997 16.61369084 6.080876587 5.284601924 12.97201486 13.38616429 15.01445555 14.75533745 1 12.5264124 7.999952858 0.030361835 0.000227616 27.75902735 0.042507776 5.041128423 21860.709 65.72650964 21157.88314 42510.91742 99989145.8 -7.999952858 27.75879973 MSGS(ph)ASSENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MSGSASSENR 10 0 A0A5F9UY30;A0A5H1ZRP2;O43493-4;O43493;O43493-5;O43493-3;O43493-7;O43493-6 A0A5F9UY30 TGOLN2 Trans-Golgi network integral membrane protein 2 1 MS(0.063)GS(0.724)AS(0.205)S(0.008)ENR 88.338 0.047938 364040000 697440 777390 448750 564040 598030 937370 582570 846210 895130 TRUE FALSE 605271.5369 772283.2739 665767.001 692113.9028 586130.373 973431.2305 526072.4511 665254.5767 789308.7511 0.766837484 0.978429889 0.843481084 0.8768608 0.742586944 1.233270541 0.66649768 0.842831878 1 19.59023022 4.780600686 21.30008205 0.886090669 0.76683497 0.061881476 0.154424462 11290.53382 5719626.898 0.035344167 8.715081588 60339.35812 -4.780600686 -0.119255698 MSGSAS(ph)SENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MSGSASSENR 10 0 A0A5F9UY30;A0A5H1ZRP2;O43493-4;O43493;O43493-5;O43493-3;O43493-7;O43493-6 A0A5F9UY30 TGOLN2 Trans-Golgi network integral membrane protein 2 1 MSGS(0.029)AS(0.949)S(0.022)ENR 150.29 8.54E-05 388860000 1015700 1021800 497200 753510 757020 1229800 815790 1245200 1195200 TRUE FALSE 881472.6715 1015087.729 737647.583 924605.9622 741956.7831 1277111.202 736674.8114 978923.6702 1053904.818 0.836387363 0.963168316 0.699918599 0.877314485 0.704007393 1.211789889 0.698995582 0.928853967 1 20.00731315 MSQPGS(ph)PSPK ddPTM_MDA-MB-175_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(0.984)PS(0.016)PK;MSQPGS(0.998)PS(0.002)PK;MSQPGS(0.998)PS(0.002)PK;MSQPGS(0.999)PS(0.001)PK;MSQPGS(0.999)PS(0.001)PK;MSQPGS(1)PSPK;MS(0.001)QPGS(0.965)PS(0.034)PK;MS(0.015)QPGS(0.974)PS(0.011)PK;MSQPGS(0.756)PS(0.244)PK;MSQPGS(0.709)PS(0.291)PK;MSQPGS(0.979)PS(0.021)PK;MSQPGS(0.974)PS(0.026)PK;MSQPGS(0.986)PS(0.014)PK;MSQPGS(0.993)PS(0.007)PK;MSQPGS(0.997)PS(0.003)PK;MSQPGS(0.995)PS(0.005)PK 225.92 3.43E-09 26048180000 19133880 19401070 14413540 18279210 23713440 18744310 27245980 31171150 27721050 TRUE FALSE 16605289.28 19273623.09 21383976.15 22429784.01 23241588.94 19465415.73 24603669.05 24505442.15 24443899.05 0.679322445 0.788483992 0.874818543 0.917602546 0.950813489 0.796330229 1.006536191 1.002517728 1 24.54297109 6.03455358 0.358893448 1.000647991 5.07E-14 0.728088253 0.05672184 11.42627658 0.622789907 0.08398591 5.873380868 1082813.295 -6.03455358 -1.000647991 MSS(ph)PLADAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MSSPLADAK 9 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 MS(0.229)S(0.771)PLADAK 103.08 0.0036503 122420000 269430 256880 179350 223740 266280 228030 285380 340670 326060 TRUE FALSE 233824.1429 255192.5384 266084.2599 274543.5867 260981.549 236802.4617 257703.8915 267820.3716 287513.5582 0.813263014 0.887584363 0.925466825 0.954889183 0.907719102 0.823621895 0.896319092 0.93150519 1 18.13327047 MSSCVPRPPS(ph)HGGPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MSSCVPRPPSHGGPTR 16 1 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 MSSCVPRPPS(0.852)HGGPT(0.148)R;MSSCVPRPPS(0.999)HGGPT(0.001)R;MSSCVPRPPS(0.994)HGGPT(0.006)R;MSSCVPRPPS(0.999)HGGPT(0.001)R 150.98 4.16E-07 1242116000 247520 267673 178431 194261 260832 298888 259589 280755 257425 TRUE FALSE 214809.6049 265914.6384 264720.8284 238370.9291 255641.9535 310386.4148 234414.0987 220717.7281 226992.5098 0.946329044 1.17146878 1.166209531 1.05012685 1.126213168 1.367386153 1.032695303 0.972356878 1 17.79228517 2.016137494 24.99994785 0.989700492 1.141554184 0.278644398 0.105207144 278.2670184 431085.1881 0.042408417 0.028583258 103.7856941 -2.016137494 0.151853693 MSSEGPPRMS(ph)PK ddPTM_MDA-MB-175_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 MS(0.002)S(0.001)EGPPRMS(0.997)PK;MS(0.001)S(0.002)EGPPRMS(0.997)PK 66.387 0.035243 856330000 2968200 2261770 1514320 1478450 2100300 1889920 2567400 2747140 1462760 TRUE FALSE 2575944.85 2246912.284 2246650.217 1814154.669 2058508.139 1962626.445 2318413.943 2159685.489 1289834.179 1.997113188 1.742016393 1.741813214 1.406502245 1.595947892 1.521611442 1.797451161 1.674390029 1 20.29875417 8 0.042988504 3.04E-09 4.295722926 0.37594595 0.211553267 2146.017559 9.068639871 275.7154864 739.1593966 100000000 -8 4.295722923 MSSPEDDSDTKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MSSPEDDSDTKR 12 1 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 85.845 0.014139 0 128470 89882 60687 63331 95766 80790 103870 121130 102470 FALSE TRUE 111492.364 89291.55922 90035.43619 77711.2715 93860.44396 83898.04358 93796.70339 95227.29213 90356.11333 1.233921645 0.988218239 0.996450963 0.860055492 1.038783548 0.928526477 1.03807811 1.053910893 1 16.46333459 4.739040403 24.43968026 0.991493184 1.233921737 0.644089462 0.057398073 19.48697229 992241.1064 0.014341922 0.082212446 54832.7974 -4.739040403 0.242428553 MSSSFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MSSSFDR 7 0 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WUT0;H0YN19;A0A0C4DGV1;H0YKS1;Q9P2K5-3 A0A0A0MQW0 MYEF2 Myelin expression factor 2 0 76.134 0.096736 97138000 186320 166880 109950 130920 163840 186560 188260 180760 171970 FALSE TRUE 161697.3399 165783.7543 163122.1878 160647.387 160579.9045 193737.0839 170002.5742 142105.8807 151639.9025 1.066324478 1.093272625 1.075720737 1.05940049 1.058955472 1.277612823 1.12109393 0.937127223 1 17.21028991 1.751011592 9.597610046 0.970541761 1.108563789 0.436229473 0.065599512 0.105443576 44.42826958 0.037776979 0.017620415 56.36527008 -1.751011592 0.138022028 MSSYAFFVQTCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MSSYAFFVQTCR 12 0 P26583;D6R9A6;P09429;Q5T7C4;B2RPK0 P26583;P09429 HMGB2;HMGB1;HMGB1P1 High mobility group protein B2;High mobility group protein B1;Putative high mobility group protein B1-like 1 0 ; 280.49 1.16E-27 1933510000 956240 1087250 606190 616090 936240 908970 934510 997190 865460 FALSE TRUE 829870.4612 1080107.783 899345.5116 755982.6508 917610.6557 943938.6641 843881.364 783948.6786 763146.3047 1.087432981 1.415335141 1.178470637 0.990613001 1.202404637 1.236903931 1.105792374 1.027258697 1 19.54160014 -0.67594495 0.371653974 2.27E-14 1.2196035 0.271575853 0.109855015 39.37482756 1.486731615 28.43642538 0.138449273 0.210889545 0.67594495 1.2196035 MSTS(ph)QNSIPFEHHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MSTSQNSIPFEHHGK 15 0 P48730-2 P48730-2 CSNK1D Casein kinase I isoform delta 1 MS(0.031)T(0.023)S(0.93)QNS(0.017)IPFEHHGK 151.41 5.03E-06 492670000 282320 228510 119200 163570 210570 164660 226540 255550 231540 TRUE FALSE 245010.6967 227008.9028 176845.5187 200711.0685 206380.069 170994.5767 204570.1857 200902.6212 204167.605 1.200046877 1.11187523 0.866178152 0.983070103 1.010836509 0.837520608 1.001971815 0.984008316 1 17.63939445 4.414524094 5.445231677 0.959201417 1.180487976 0.677744722 0.059086761 0.0972588 5.53173836 0.014469984 0.040900704 25973.1183 -4.414524094 0.221286559 MSTSQNS(ph)IPFEHHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MSTSQNSIPFEHHGK 15 0 P48730-2 P48730-2 CSNK1D Casein kinase I isoform delta 1 MS(0.003)T(0.003)S(0.027)QNS(0.967)IPFEHHGK 122.22 0.00018427 412880000 220030 199420 122270 135580 175210 151670 216330 215720 201820 TRUE FALSE 190952.478 198109.9969 181400.181 166365.5112 171723.6638 157504.843 195350.3499 169589.9567 177961.0695 1.073001407 1.113220984 1.019325077 0.934842163 0.964950729 0.885052239 1.097713957 0.952960989 1 17.44120215 4.061380031 4.355067167 0.97437386 1.091628165 0.44872637 0.054662796 0.181618143 6.970165165 0.013807761 0.030125565 11518.07842 -4.061380031 0.117254306 MSVIEEGDCKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MSVIEEGDCKR 11 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;; 134.98 0.00020785 923000000 747890 658720 374730 443230 670960 618120 647100 643280 495590 FALSE TRUE 649054.4416 654392.8249 555950.6814 543872.1458 657609.2087 641899.4764 584344.3416 505719.578 437001.9148 1.485243931 1.497459857 1.272192781 1.244553233 1.504819971 1.468871084 1.337166547 1.157247968 1 18.73728008 1.595065144 2.020097457 0.99309856 1.406542848 0.705834629 0.090652728 0.212628126 1.659498359 0.139679233 0.027587102 39.36091121 -1.595065144 0.413444289 MSVQPTVSLGGFEITPPVVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MSVQPTVSLGGFEITPPVVLR 21 0 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 0 ; 214.53 1.61E-24 148697000 108205 82867 52574 63281 91941 88039 73381 90813 85843 FALSE TRUE 93905.43509 82322.64122 77998.96225 77649.91824 90111.55398 91425.9173 66264.52191 71393.34666 75694.73833 1.240580748 1.087560946 1.030441005 1.025829799 1.190459944 1.207823943 0.875417808 0.943174496 1 16.2079054 2.234068738 24.99999975 0.937618492 1.121926405 0.578774196 0.076543751 86.03099841 478807.0958 0.032071686 0.022447694 171.4228605 -2.234068738 0.184307913 MSWFVDLAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MSWFVDLAGK 10 0 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 0 ;;; 77.923 0.073392 1969415000 1601350 1457070 933966 1180880 1404020 1172470 1605490 1772210 1662770 FALSE TRUE 1389727.54 1447498.411 1385635.082 1449016.853 1376082.749 1217575.68 1449789.827 1393236.683 1466199.225 0.947843592 0.98724538 0.94505239 0.988281011 0.938537359 0.830429903 0.988808207 0.950236952 1 20.48364972 1.047103823 1.691190324 1.043406439 0.945467728 0.117258025 0.045641438 4.104344863 7.151468512 0.776105025 0.012929098 11.14560951 -1.047103823 -0.097938711 MSYLTAMGADYLS(ph)CDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 MSYLTAMGADYLSCDSR 17 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 MSYLTAMGADYLS(1)CDSR;MSYLTAMGADYLS(1)CDSR;MSYLTAMGADYLS(1)CDSR;MSYLTAMGADYLS(0.826)CDS(0.174)R;MSYLTAMGADYLS(0.997)CDS(0.003)R 323.47 8.24E-59 612470000 849844 1114094 696550 828633 1141433 1232956 1060358 1130334 1218015 TRUE FALSE 737534.9622 1106775.443 1033403.91 1016786.788 1118720.716 1280388.615 957524.6444 888620.8704 1074022.654 0.686703357 1.030495436 0.962180738 0.946708883 1.04161743 1.192143024 0.891531143 0.827376282 1 20.03459299 6.944406835 13.00771299 0.953201016 0.339405658 0 0.134929669 0 0 0.030432979 0 8798463.464 -6.944406835 -0.613795358 MT(ph)S(ph)VGT(ph)NRAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MTSVGTNRAR 10 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5;Q5VU81;Q5VU80;Q5VU79;Q5VU78;Q5VU77 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 3 MT(1)S(1)VGT(1)NRAR;MT(1)S(1)VGT(1)NRAR 53.237 0.062192 396570000 47473 42162 28793 25336.7 49410 45442 23990 39156 40789 TRUE FALSE 41199.32277 41885.03505 42717.39111 31089.78498 48426.83767 47190.18314 21663.45349 30782.79411 35966.97089 1.145476579 1.164541634 1.187683868 0.864398202 1.346425247 1.312042187 0.602315206 0.855862847 1 15.13438504 2.245498535 24.99996388 0.81794573 1.164761462 0.52001233 0.158775552 126.2407844 454895.1396 0.060440844 0.045774757 175.9942727 -2.245498535 0.346815732 MTDFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MTDFDR 6 0 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 103.02 0.081529 1345900000 1538600 1783200 1156200 1116900 1776400 1783500 1946000 1843300 1858600 FALSE TRUE 1335270.112 1771486.042 1715342.187 1370509.216 1741053.115 1852112.399 1757277.22 1449124.64 1638878.425 0.814746287 1.080913639 1.046656153 0.83624825 1.062344277 1.130109696 1.072243793 0.88421729 1 20.64427741 MTDQEAIQDLWQWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 20 MTDQEAIQDLWQWR 14 0 P06748;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;;;;;;;;;;;;;;;;; 303.51 1.05E-43 22409452000 8416903 7137849 4273819 5164788 7313277 6906070 6563411 7968205 7111035 FALSE TRUE 7304587.943 7090960 6340652.163 6337532.054 7167757.096 7171750.982 5926892.411 6264266.369 6270376.543 1.164936092 1.130866695 1.01120756 1.010709965 1.1431143 1.143751246 0.945221132 0.999025549 1 22.58012065 -1.999994094 0.036579446 1.75E-07 1.754284266 0.332282657 0.064023501 2589.053562 9.345904882 340.1886274 146.8525351 0.010000136 1.999994094 1.754284091 MTEEEVEMLVAGHEDS(ph)NGCINYEELVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 MTEEEVEMLVAGHEDSNGCINYEELVR 27 0 P60660-2;G8JLA2;F8VZU9;F8W180;F8VXL3 P60660-2 MYL6 Myosin light polypeptide 6 1 MTEEEVEMLVAGHEDS(1)NGCINYEELVR;MTEEEVEMLVAGHEDS(1)NGCINYEELVR;MTEEEVEMLVAGHEDS(1)NGCINYEELVR;MTEEEVEMLVAGHEDS(1)NGCINYEELVR;MTEEEVEMLVAGHEDS(1)NGCINYEELVR;MTEEEVEMLVAGHEDS(1)NGCINYEELVR;MTEEEVEMLVAGHEDS(1)NGCINYEELVR;MTEEEVEMLVAGHEDS(1)NGCINYEELVR;MTEEEVEMLVAGHEDS(1)NGCINYEELVR 369.81 5.06E-127 920094000 955030 946804 597596 628600 751035 869084 802432 896977 991927 TRUE FALSE 828820.3658 940584.3822 886595.4244 771333.2375 736090.8729 902518.2239 724612.2681 705165.4488 874662.5201 0.947588752 1.07536834 1.013642867 0.881863827 0.841571299 1.031847373 0.828447832 0.80621432 1 19.73836695 3.745664273 10.12519911 0.887544304 1.018595587 0.317410536 0.077468006 0.236840523 301.5063811 0.02084993 0.034211802 5567.551885 -3.745664273 0.131051282 MTEEEVEMLVAGHEDSNGCINYEAFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MTEEEVEMLVAGHEDSNGCINYEAFVR 27 0 P60660;J3KND3;G3V1Y7 P60660 MYL6 Myosin light polypeptide 6 0 ; 316.24 3.45E-82 365150000 239710 251360 150806 184362 219330 254510 229330 278990 251260 FALSE TRUE 208031.7162 249708.7996 223736.286 226224.2099 214965.7621 264301.1644 207089.6119 219330.1596 221556.329 0.938956323 1.127066876 1.00983929 1.021068596 0.970253312 1.192929877 0.934704112 0.989952129 1 17.75731401 MTEEEVEMLVAGHEDSNGCINYEELVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 16 MTEEEVEMLVAGHEDSNGCINYEELVR 27 0 P60660-2;G8JLA2;F8VZU9;F8W180;F8VXL3 P60660-2 MYL6 Myosin light polypeptide 6 0 ;;;;;;;;;;;;;;; 416.25 7.74E-166 5094194000 2368802 2285643.4 1410808.2 1774527.5 2288861.2 2349071 2287606.5 2658097 2557672.5 FALSE TRUE 2055758.814 2270628.858 2093079.764 2177461.091 2243317.34 2439441.281 2065754.774 2089683.642 2255307.371 0.911520461 1.006793525 0.928068516 0.965483073 0.994683638 1.081644708 0.915952655 0.92656268 1 21.10489264 4.762551371 23.13169577 0.972430685 0.911520262 0.144480889 0.049073282 5643.02127 5440712.219 0.012438076 0.642505799 57883.04525 -4.762551371 -0.060910423 MTEELEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MTEELEALR 9 0 Q9Y5S2;H0YLY0;Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;H0Y6V3;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q9Y5S2;Q5VT25-2;Q5VT25-3 CDC42BPB;CDC42BPA Serine/threonine-protein kinase MRCK beta;Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 0 87.639 0.030999 26830000 39154 43271 30790 33615 47872 58329 46818 54757 48539 FALSE TRUE 33979.6997 42986.74995 45680.14699 41247.79952 46919.44086 60572.95437 42277.59757 43047.64167 42800.77472 0.793903847 1.004345137 1.067273835 0.96371619 1.096228776 1.415230326 0.987776456 1.005767815 1 15.38534929 5.410431071 1.079189445 1.08059544 6.73E-16 0.330049218 0.127324432 8.365257758 2.839668158 0.040621652 14.66672798 257294.8365 -5.410431071 -1.08059544 MTELETAMGMIIDVFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MTELETAMGMIIDVFSR 17 0 P25815 P25815 S100P Protein S100-P 0 ; 169.62 3.49E-13 614230000 195442 235150 145048 150467 188199 167976 214250 247800 221051 FALSE TRUE 169613.8445 233605.2842 215193.698 184632.8321 184454.2081 174438.1454 193472.068 194809.8984 194918.6026 0.870177819 1.198476087 1.104018268 0.947230432 0.946314029 0.894928155 0.992578776 0.99944231 1 17.57251226 3.733834873 24.67285815 0.965424882 1.071649263 0.204646679 0.085945429 450.4042778 2351538.825 0.022600618 0.034799342 5417.948507 -3.733834873 0.106224381 MTGSAPPPS(ph)PTPNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 MTGSAPPPSPTPNK 14 0 Q9UBW7 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 1 MTGSAPPPS(0.999)PT(0.001)PNK;MTGSAPPPS(0.999)PT(0.001)PNK;MTGSAPPPS(0.965)PT(0.035)PNK;MTGSAPPPS(0.995)PT(0.005)PNK;MTGSAPPPS(1)PTPNK 252.01 3.58E-24 509750000 2031870 1652520 1247118 1493377 1801260 1571330 1907740 2167720 2478540 TRUE FALSE 1763353.231 1641664.487 1850228.436 1832471.073 1765418.45 1631780.082 1722727.668 1704169.947 2185529.825 0.806831008 0.75115172 0.846581188 0.838456219 0.807775959 0.746629061 0.78824258 0.779751403 1 21.05955164 1.235977651 24.99601556 1.000000271 0.79496382 0.797986729 0.032306295 32.07671055 310349.0779 0.054353644 0.008190527 17.21779967 -1.235977651 -0.205036451 MTGSEFDFEEMKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 MTGSEFDFEEMKR 13 1 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;;;;; 254.18 1.35E-23 5856870000 4385550 3688820 2446250 2963980 3485650 2820390 4101460 4674090 3505530 FALSE TRUE 3805988.456 3664587.899 3629264.682 3636996.961 3416292.385 2928892.228 3703701.04 3674572.227 3091110.237 1.231269079 1.185524817 1.174097461 1.176598918 1.105199143 0.947521118 1.198178246 1.188754831 1 21.55969367 3.284769344 4.374967949 1.101497 1.192208974 0.305986065 0.076662622 0.331929715 13.48794253 0.024322071 0.030890889 1926.501466 -3.284769344 0.090711974 MTHNLLLNYGLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MTHNLLLNYGLYR 13 0 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 ; 165.73 3.48E-05 1022260000 900990 1040160 572600 736760 1036200 1008550 916220 1108650 1073130 FALSE TRUE 781921.8887 1033327.12 849511.2752 904052.6187 1015581.647 1047349.571 827365.1254 871573.825 946265.7939 0.826323739 1.09200515 0.897751225 0.955389727 1.073251991 1.106823873 0.874347494 0.921066608 1 19.85188595 4.772172225 23.01331038 0.981541016 0.826322852 0.280987389 0.081310096 8047.279887 5509550.06 0.020506122 2.942494628 59179.62717 -4.772172225 -0.155218164 MTILQTYFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MTILQTYFR 9 0 O75348 O75348 ATP6V1G1 V-type proton ATPase subunit G 1 0 92.051 0.017709 0 93423 112240 68218 70019 95954 104160 89563 92027 102320 FALSE TRUE 81076.91385 111502.688 101208.453 85917.88412 94044.70313 108167.1026 80877.19405 72347.7422 90223.84616 0.89861957 1.235844988 1.121748377 0.952274679 1.042348638 1.198874878 0.896405967 0.801869409 1 16.46122117 2.131640724 7.922791118 0.876065415 1.077025192 0.350593444 0.111371733 0.224857926 15.11893037 0.044248089 0.029784414 135.4068777 -2.131640724 0.200959777 MTNHCVFSANEDHETIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 123 3.18E-05 455090000 469003 424930 312157 330011 407410 383730 427673 527884 477730 FALSE TRUE 407023.0652 422138.6069 463117.1693 404945.0415 399303.3381 398492.3414 386197.3383 415000.1146 421253.3036 0.966219284 1.002101594 1.099379317 0.961286328 0.947893666 0.945968466 0.916781744 0.985155751 1 18.68432847 3.528966744 24.99992705 0.95820943 1.022155697 0.363184842 0.039355364 372.2874137 179516.2182 0.010948061 0.01623841 3380.389502 -3.528966744 0.063946267 MTNNEDSLS(ph)PTSSTLSNLELDAAEKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MTNNEDSLSPTSSTLSNLELDAAEKDR 27 1 Q9ULH7-4;Q9ULH7;Q9ULH7-5 Q9ULH7-4 MKL2 MKL/myocardin-like protein 2 1 MT(0.004)NNEDS(0.447)LS(0.479)PT(0.036)S(0.011)S(0.01)T(0.01)LS(0.003)NLELDAAEKDR;MTNNEDS(0.021)LS(0.968)PT(0.01)S(0.001)STLSNLELDAAEKDR 146.39 2.24E-07 335460000 409110 337100 223970 316240 356250 324050 419570 545060 354280 TRUE FALSE 355045.0769 334885.5679 332282.6411 388047.1254 349161.322 336516.4132 378880.166 428503.1607 312397.422 1.136517308 1.071985696 1.063653596 1.242158539 1.117683109 1.077206115 1.212814637 1.371660361 1 18.25302302 2.128886281 6.345206218 1.235277092 1.119582602 0.069488106 0.103588311 0.329246241 17.20106519 0.041915409 0.028094323 134.5507988 -2.128886281 -0.11569449 MTPHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MTPHEK 6 0 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;F6S4E6;A0A0A0MT12;F6TRA5;A0A140T9K1;A0A140T973;A0A140T9L4;H0YCC6 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ;;; 122.79 0.019068 1510980000 4134190 3391650 2234970 2771940 1999770 3117050 3515960 4361100 3944200 FALSE TRUE 3587846.317 3369370.028 3315808.968 3401351.343 1959978.489 3236964.93 3174982.74 3428512.703 3477921.169 1.031606567 0.968788499 0.95338819 0.977984025 0.563548854 0.930718315 0.912896695 0.985793679 1 21.7297938 3.413548333 24.99998778 0.885680215 0.980157231 0.152316463 0.12161981 141.9025911 55801.72978 0.03684504 0.047566745 2591.482816 -3.413548333 0.094477016 MTPSYEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MTPSYEIR 8 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 112.37 0.0071052 97733000 145240 134950 91725 108160 140410 147470 136210 157300 155240 FALSE TRUE 126046.166 134063.5046 136083.5168 132719.3811 137616.1157 153143.2663 123000.3752 123662.6191 136887.704 0.920799767 0.979368494 0.994125205 0.969549325 1.005321235 1.118751077 0.898549479 0.903387342 1 17.06263334 MTSACHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MTSACHR 7 0 P62072 P62072 TIMM10 Mitochondrial import inner membrane translocase subunit Tim10 0 ; 112.37 0.0063695 39122000 84757 90901 32611 58429 61580 108818 67245 89955 90329 FALSE TRUE 73556.1477 90303.86535 48381.78868 71696.19748 60354.67848 113004.2989 60723.59025 70718.82328 79650.40852 0.923487388 1.133752695 0.607426749 0.900135967 0.757744745 1.418753538 0.762376382 0.887865167 1 16.28139414 MTSHHFEGAQILSQLQCSGMVSVLDLMQGGYPSR ddPTM_MDA-MB-175_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 ; 163.51 1.68E-14 214119000 124325 110716 42971.2 90421 129844 136746 117923 157512 111053 FALSE TRUE 107895.1363 109988.6993 63752.21605 110952.47 127260.3584 142006.7071 106486.8456 123829.2846 97924.44085 1.101820294 1.123199666 0.651034772 1.13304165 1.299577075 1.450166127 1.087438894 1.264539103 1 16.57938136 3.487948602 24.45900576 1.226384328 0.961286681 0.322343465 0.173098788 445.2824071 1005893.64 0.048049057 0.066477152 3075.732784 -3.487948602 -0.265097647 MTSSDKDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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 ;;;;;;;;; 102.61 0.0032439 4778080000 17562870 15567340 10059580 11701600 15110580 14457650 17774460 19056220 17409520 FALSE TRUE 15241892.23 15465077.12 14924426.54 14358627.13 14809909.02 15013845.15 16050695.6 14981195.65 15351386.38 0.992867475 1.007405894 0.972187538 0.935330971 0.964727788 0.978012329 1.04555349 0.975885518 1 23.87186561 2.445941294 24.99792751 1.00359811 0.973761143 0.265614155 0.024942523 300.75346 241121.2399 0.009752714 0.007554475 279.2166382 -2.445941294 -0.029836967 MTTLTPAYHAENYSPEDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MTTLTPAYHAENYSPEDNR 19 0 Q6IA69;H0YED2;H0YDH3;A0A0B4J216;Q6IA69-2 Q6IA69 NADSYN1 Glutamine-dependent NAD(+) synthetase 0 191.35 9.84E-15 202730000 57800 60024 37179 65420 80399 79397 69530 69553 98755 FALSE TRUE 50161.58355 59629.69839 55158.88876 80274.61088 78799.2172 82451.45397 62786.9913 54679.63221 87080.2964 0.576038273 0.684766828 0.633425597 0.921845862 0.904902951 0.946843975 0.721024088 0.627921981 1 16.4100587 3.757379866 23.7633982 0.82794602 0.636745828 0.449861506 0.113491663 514.9269791 650203.6951 0.033513345 0.057893048 5719.787127 -3.757379866 -0.191200192 MTVNNLHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MTVNNLHPR 9 0 F6VRR5;Q9BY77-2;Q9BY77 F6VRR5 POLDIP3 Polymerase delta-interacting protein 3 0 101.65 0.003842 32274000 40729 36117 28237 34235 52119 41869 45384 53410 44537 FALSE TRUE 35346.55946 35879.74505 41892.50765 42008.58 51081.93387 43479.72752 40982.66667 41988.68714 39271.8866 0.900047401 0.913624176 1.066730205 1.069685814 1.300725234 1.107146391 1.043562462 1.069179272 1 15.26120929 4.204363149 3.108244996 1.099292324 0.897943375 0.499256203 0.078495167 0.212349244 4.132289201 0.021927863 0.060349637 16008.96109 -4.204363149 -0.20134895 MVDPEKPQLGMIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MVDPEKPQLGMIDR 14 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 77.078 0.026943 528770000 1542160 1227360 828150 1055190 1158740 1068530 1306530 1594400 1865440 FALSE TRUE 1338359.649 1219297.391 1228646.11 1294787.017 1135683.341 1109637.041 1179822.922 1253449.968 1644909.808 0.813637101 0.741254861 0.746938284 0.787147727 0.690422864 0.674588379 0.717256907 0.762017444 1 20.64957705 1.235755768 4.093885315 1.028545303 0.736952863 0.799645101 0.040789229 0.106773841 3.225635208 0.093406467 0.010777886 17.2090053 -1.235755768 -0.29159244 MVEDCEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MVEDCEHR 8 0 Q92896;Q92896-3;Q92896-2;H3BM42 Q92896 GLG1 Golgi apparatus protein 1 0 ; 155.1 0.00041434 338260000 629540 527230 474740 434500 405920 644160 482960 539750 579390 FALSE TRUE 546344.6939 523766.5914 704325.8519 533159.8659 397842.9862 668941.252 436122.6135 424328.6628 510895.1742 1.069387071 1.025193852 1.378611284 1.043579765 0.778717448 1.309351283 0.853644026 0.830559152 1 18.96266778 2.507323145 0.746217465 0.87029471 1.128959592 0.150832552 0.178105972 1.392666995 1.702695777 0.239329133 0.116040914 321.605261 -2.507323145 0.258664882 MVEGFFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 MVEGFFDR 8 0 P00367;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 ;;;;; 180.18 0.0005594 2695270000 2177340 2501930 1665000 2539240 2993170 3192640 2013280 2717490 2535290 FALSE TRUE 1889599.002 2485494.657 2470199.569 3115813.252 2933611.773 3315462.927 1818032.415 2136375.911 2235570.904 0.845242259 1.111794152 1.104952459 1.393743874 1.312242778 1.483049775 0.813229592 0.955628787 1 21.09221187 2.216987408 24.99979465 0.925188468 1.212536878 0.358476579 0.180012891 273.7619482 317242.598 0.077139382 0.052060153 164.8114604 -2.216987408 0.28734841 MVEINFLCVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MVEINFLCVHK 11 0 P30419;P30419-2;Q5VUC6;O60551 P30419;O60551 NMT1;NMT2 Glycylpeptide N-tetradecanoyltransferase 1;Glycylpeptide N-tetradecanoyltransferase;Glycylpeptide N-tetradecanoyltransferase 2 0 128.67 0.00026089 144600000 228760 199570 178760 187210 189790 168030 212820 255230 288360 FALSE TRUE 198528.7864 198259.0115 265208.9339 229718.8918 186013.5503 174494.2228 192180.7492 200651.0507 254270.4093 0.780778176 0.7797172 1.043019259 0.903443277 0.731557993 0.68625454 0.755812482 0.789124662 1 17.95600405 3.249893352 24.97598208 0.784051695 0.881686456 0.125188567 0.108964106 429.8521842 947337.2149 0.032686155 0.04181271 1777.842779 -3.249893352 0.097634761 MVEKDQDGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 MVEKDQDGGR 10 1 P39019;A0A075B6E2 P39019 RPS19 40S ribosomal protein S19 0 ;;;; 171.92 3.53E-06 3523380000 5245710 4672620 2209060 2595690 3838780 3721040 5344410 5864220 651927 FALSE TRUE 4552476.133 4641925.252 3277368.805 3185081.087 3762395.788 3864190.817 4826109.941 4610202.188 574856.9327 7.919320223 8.074922624 5.701190363 5.54065004 6.544925484 6.722004375 8.395323542 8.019738349 1 19.13284343 4.250611212 24.70780478 6.329336005 7.997122712 0.129370687 2.020917137 461.252917 945703.934 0.501416693 1.304063328 17807.83865 -4.250611212 1.667786708 MVEPENAVTITPLRPEDDYS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 MVEPENAVTITPLRPEDDYSPR 22 1 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;A0A669KAX5;H0YDF9 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 MVEPENAVTITPLRPEDDYS(1)PR;MVEPENAVTITPLRPEDDYS(1)PR;MVEPENAVTITPLRPEDDYS(1)PR;MVEPENAVTITPLRPEDDYS(1)PR;MVEPENAVTITPLRPEDDYS(1)PR;MVEPENAVTITPLRPEDDYS(1)PR;MVEPENAVTITPLRPEDDYS(1)PR;MVEPENAVTITPLRPEDDYS(1)PR 252.2 3.26E-37 3934680000 2406040 2453300 1422457 2633370 2747430 2882870 2019545 3259850 2820790 TRUE FALSE 2088075.718 2437184.111 2110361.963 3231316.907 2692761.518 2993775.874 1823689.837 2562756.446 2487319.42 0.839488367 0.979843639 0.848448312 1.299116182 1.082595784 1.203615366 0.733194869 1.030328644 1 21.24616036 7.300026668 8.145087827 1.00386463 0.004958321 0 0.169640347 0 0 0.037466736 0 19953848.41 -7.300026668 -0.998906309 MVGFIIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MVGFIIGR 8 0 Q96I24;Q96I24-2 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ; 127.66 0.0027148 184248000 748880 438170 1866760 1123230 236460 239200 551200 642140 1060170 FALSE TRUE 649913.6106 435291.6324 2769531.38 1378276.539 231754.9086 248402.1788 497744.7088 504823.3581 934837.9103 0.695215292 0.465633269 2.962579234 1.474348145 0.247909189 0.265716844 0.532439585 0.540011645 1 19.83435672 3.247364701 24.84191036 0.508631851 1.444395993 0.290925508 0.682723655 228.1837835 643847.3056 0.20419351 0.259526517 1767.521485 -3.247364701 0.935764142 MVINHLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MVINHLEK 8 0 P50990-2;P50990;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;; 95.099 0.0098907 1958980000 3842420 3477930 2129420 2855040 3178750 2973790 3844470 4273650 3989610 FALSE TRUE 3334634.462 3455083.249 3159214.634 3503320.469 3115499.094 3088193.626 3471633.891 3359763.205 3517962.851 0.947887912 0.982126132 0.898023876 0.995837824 0.885597497 0.877835769 0.986830742 0.955030894 1 21.74630882 2.144493142 23.80272848 0.97554933 0.932821063 0.251641627 0.03977697 18.47529155 4662.600401 0.016206365 0.010926329 139.4739633 -2.144493142 -0.042728267 MVIPGGIDVHTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MVIPGGIDVHTR 12 0 A0A1C7CYX9;Q16555-2;Q16555;E5RFU4 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 0 101.89 0.0024174 586980000 493360 449100 370230 401160 478060 477240 457260 578380 597380 FALSE TRUE 428161.226 446149.8325 549274.4663 492249.5093 468547.5413 495599.7316 412914.9956 454697.938 526758.4169 0.812822752 0.846972385 1.042744546 0.934488171 0.889492272 0.940848244 0.783879255 0.863200138 1 19.00678194 MVIQGPS(ph)SPQGEAMVTDVLEDQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MVIQGPSSPQGEAMVTDVLEDQK 23 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MVIQGPS(0.643)S(0.357)PQGEAMVTDVLEDQK;MVIQGPS(0.784)S(0.216)PQGEAMVTDVLEDQK;MVIQGPS(0.641)S(0.359)PQGEAMVTDVLEDQK;MVIQGPS(0.636)S(0.364)PQGEAMVTDVLEDQK 273.36 7.40E-52 666180000 863980 674060 666160 796570 707670 601700 814980 1001840 1581790 TRUE FALSE 749802.854 669632.0555 988317.2042 977443.3933 693588.7515 624847.7884 735943.365 787604.3123 1394792.588 0.537573013 0.48009436 0.708576467 0.700780461 0.497270173 0.447986169 0.527636418 0.564674862 1 20.41161917 1.238755175 7.820614525 1.005997824 0.557923929 0.723809276 0.085802636 0.055233059 27.72151992 0.13144452 0.022675885 17.32826874 -1.238755175 -0.448073895 MVIQGPS(ph)SPQGEAMVTDVLEDQKEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MVIQGPSSPQGEAMVTDVLEDQKEGR 26 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MVIQGPS(0.56)S(0.44)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.582)S(0.418)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.578)S(0.422)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.556)S(0.444)PQGEAMVTDVLEDQKEGR 138.16 1.46E-05 1089336000 973002 806716 490818 525532 723716 684113 1003151 1090166 263552 TRUE FALSE 844417.3204 801416.6295 728179.2265 644862.0729 709315.4675 710431.2698 905865.5704 857042.4846 232395.1828 3.63354055 3.448507924 3.133366267 2.77485129 3.052195226 3.05699654 3.897953303 3.687866823 1 17.82622064 4.311041006 2.993163775 3.058791389 3.600335461 0.081617585 0.776201096 0.807289556 14.0717549 0.201548046 0.661722064 20466.37872 -4.311041006 0.541544073 MVIQGPSS(ph)PQGEAMVTDVLEDQKEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 MVIQGPSSPQGEAMVTDVLEDQKEGR 26 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MVIQGPS(0.21)S(0.776)PQGEAMVT(0.014)DVLEDQKEGR;MVIQGPS(0.041)S(0.959)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.191)S(0.808)PQGEAMVT(0.001)DVLEDQKEGR;MVIQGPS(0.035)S(0.965)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.088)S(0.912)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.062)S(0.938)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.066)S(0.934)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.369)S(0.627)PQGEAMVT(0.004)DVLEDQKEGR;MVIQGPS(0.005)S(0.995)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.002)S(0.998)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.071)S(0.929)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.143)S(0.857)PQGEAMVTDVLEDQKEGR 339.3 1.43E-95 6741960000 5448340 4634010 2629690 2867092 4327678 3717020 5287560 6025510 1685564 TRUE FALSE 4728328.065 4603568.883 3901416.88 3518109.059 4241565.675 3860016.165 4774773.245 4737001.577 1486298.544 3.181277465 3.097337948 2.624921417 2.367027185 2.853777723 2.597066505 3.212526355 3.187113111 1 20.5032925 4.268502271 5.665650059 2.646906153 3.151556767 0.121279069 0.619178538 0.423329014 37.21080647 0.153706885 0.400297605 18556.76513 -4.268502271 0.504650613 MVIQLRPGRS(ph)PEPDGPAPAFLR ddPTM_MDA-MB-175_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 188.39 1.31E-17 5058100000 1046890 1045130 536690 624630 981610 1028470 949640 1040340 588180 TRUE FALSE 908540.834 1038264.472 796235.0791 766461.7884 962077.8815 1068035.906 857544.059 817871.3869 518646.0305 1.75175511 2.001874904 1.535218689 1.477812888 1.854979745 2.059277125 1.653428367 1.576935596 1 18.98439073 1.139272174 1.798919 0.57147954 1.767615836 0.634688848 0.181764564 0.829025132 2.02958342 1.865494444 0.052762492 13.78072842 -1.139272174 1.196136296 MVMISLEGEDGLDEIYSFSESLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MVMISLEGEDGLDEIYSFSESLRK 24 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 248.98 5.73E-38 75492000 175883 146082 73429 92120 117491 112373 163879 184762 54301 FALSE TRUE 152639.6159 145122.3777 108939.51 113037.254 115153.159 116696.062 147986.0398 145252.0841 47881.59764 3.187855532 3.030859137 2.275185361 2.36076613 2.404956489 2.437179789 3.090666291 3.033568036 1 15.54718367 4.335344439 5.62226607 2.473535676 3.14368956 0.210306388 0.570551242 0.348430246 16.28023154 0.143029401 0.391215386 21644.34456 -4.335344439 0.670153884 MVNHFIAEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MVNHFIAEFK 10 0 P11142;E9PKE3;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;; 158.79 7.88E-06 21733100000 28286400 25031700 16526600 21699700 23488300 22443800 26964800 33311800 31409400 FALSE TRUE 24548280.57 24867265.11 24518919.04 26626948.54 23020928.78 23307227.51 24349757.85 26188330.8 27696216.51 0.886340579 0.897857839 0.885280451 0.961392995 0.831193993 0.841531099 0.879172714 0.945556256 1 24.72318557 1.513506701 2.713964055 0.998411949 0.883311835 0.558145944 0.034858131 0.217696966 3.08926147 0.046750705 0.009723555 32.62170835 -1.513506701 -0.115100114 MVNHFIAEFKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MVNHFIAEFKR 11 1 P11142;E9PKE3;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 150.04 2.21E-05 1041310000 2076640 1921880 706380 952690 1729030 1624280 2037130 2439000 194135 FALSE TRUE 1802206.762 1909255.044 1047987.731 1169012.825 1694625.686 1686767.103 1839569.446 1917438.83 171184.5815 10.52785681 11.15319515 6.121975015 6.82896097 9.899406076 9.853499002 10.74611645 11.20100195 1 17.38519324 4.285300843 24.9690275 8.487724247 10.84053518 0.119393768 2.998707604 304.6532847 162743.354 0.745199116 1.971599524 19288.60604 -4.285300843 2.352810931 MVPPVVVGS(ph)PPGS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MVPPVVVGSPPGSPSR 16 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 2 MVPPVVVGS(1)PPGS(0.978)PS(0.022)R;MVPPVVVGS(1)PPGS(0.984)PS(0.016)R;MVPPVVVGS(1)PPGS(0.686)PS(0.314)R 169.06 8.42E-09 554010000 408980 419360 275246 317674 401230 464390 397730 443880 448310 TRUE FALSE 354932.2568 416605.1965 408355.8862 389806.737 393246.308 482255.3838 359158.2058 348959.7163 395311.3025 0.897855069 1.05386614 1.032998256 0.986075365 0.994776283 1.219938263 0.908545249 0.88274662 1 18.59262968 MVPPVVVGS(ph)PPGSPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MVPPVVVGSPPGSPSR 16 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 MVPPVVVGS(0.994)PPGS(0.005)PS(0.001)R;MVPPVVVGS(0.997)PPGS(0.003)PSR 143.88 1.44E-06 637510000 260490 315490 194164 227460 335300 383000 315880 360040 280570 TRUE FALSE 226065.5865 313417.5254 288062.3598 279108.2695 328628.186 397734.2578 285246.0062 283048.2478 247401.3342 0.913760579 1.266838461 1.164352491 1.12815992 1.328320185 1.607647991 1.152968747 1.144085373 1 17.91649376 4.743464453 24.04991298 1.224852086 0.913760357 0.267559487 0.161334618 458.3788532 2247899.598 0.041355584 0.327179219 55394.22013 -4.743464453 -0.311091729 MVPTSDKGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MVPTSDKGR 9 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;; 121.8 0.00055067 1675680000 3010150 2669650 1571290 1865840 1908320 2085920 3257410 3680310 2409179 FALSE TRUE 2612351.051 2652112.893 2331171.1 2289507.49 1870348.166 2166166.692 2941506.88 2893304.347 2124368.603 1.229707051 1.248424068 1.097347747 1.077735515 0.880425442 1.019675535 1.38464995 1.361959663 1 21.01860268 0.978334289 18.71440394 0.573213873 1.167802109 0.098533037 0.15371507 11579240.54 249434716.8 207647908.3 0.043136024 9.513367837 -0.978334289 0.594588236 MVQEAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MVQEAEK 7 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 A0A0G2JIW1;P11142 HSPA1B;HSPA1A;HSPA8 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock cognate 71 kDa protein 0 ;;; 157.34 0.0034487 982960000 2900300 2690040 1925890 2283250 2103280 2234640 2926970 3353970 3730210 FALSE TRUE 2517018.007 2672368.95 2857256.846 2801696.81 2061428.843 2320608.047 2643112.9 2636749.616 3289228.823 0.765230436 0.812460639 0.868670743 0.851779235 0.62672102 0.705517363 0.803566137 0.801631555 1 21.64931795 1.151682882 2.517723311 1.094209629 0.776095267 0.498150365 0.069885732 0.708262804 3.996974255 0.541704583 0.019914864 14.18021716 -1.151682882 -0.318114362 MVQEAEKYKAEDEKQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MVQEAEKYKAEDEKQR 16 3 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 56.121 0.056607 52749000 202260 158260 95154 78449 130700 107810 197540 217700 36232 FALSE TRUE 175530.8285 157220.3796 141170.7927 96262.04447 128099.3257 111957.5205 178382.6012 171146.5491 31948.69424 5.494147186 4.921026771 4.41867175 3.01301968 4.009532432 3.504290962 5.583408195 5.356918436 1 14.96346935 4.297449805 2.579312993 4.015846441 5.388832358 0.165929903 1.278451434 0.618413256 7.953115036 0.345090275 1.221359122 19835.80385 -4.297449805 1.372985917 MVQFEENGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MVQFEENGR 9 0 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8;E9PQ35;Q5SZW8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;; 211.85 1.04E-05 792270000 544410 501960 358414 463169 491192 549190 499565 508580 797530 FALSE TRUE 472464.8391 498662.5917 531744.2092 568338.6005 481418.2402 570317.6947 451117.2632 399824.1248 703246.9119 0.671833507 0.709086074 0.756127329 0.808163663 0.684565025 0.810977887 0.641477773 0.568540178 1 19.42367179 1.221328772 24.99786084 1.000000888 0.704258172 0.611387041 0.073559598 842.2649107 1221788.515 0.587556072 0.019947632 16.64672373 -1.221328772 -0.295742716 MVQFEENGRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MVQFEENGRK 10 1 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8;E9PQ35;Q5SZW8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 112.13 0.0026644 413440000 657510 608410 359540 435620 603800 517680 726080 772170 372660 FALSE TRUE 570618.3876 604413.3146 533414.7466 534534.179 591785.5613 537595.4846 655664.8734 607047.4545 328604.5593 1.736489563 1.839333319 1.623272506 1.626679131 1.800904901 1.635995209 1.995300597 1.847349458 1 18.32599297 1.235005317 24.99898517 0.999998917 1.768941722 0.807252989 0.11716509 45.78785731 321905.3165 0.215597791 0.030107788 17.17929418 -1.235005317 0.768942805 MVS(ph)PLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MVSPLRR 7 1 Q53ET0;H0YDQ8 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 MVS(1)PLRR;MVS(1)PLRR;MVS(1)PLRR 76.17 0.025411 321410000 292523 276360 164979 179336 242443 279878 249007 282460 258037 TRUE FALSE 253865.3444 274544.573 244763.3962 220056.9798 237618.8586 290645.0878 224858.3395 222058.1271 227532.1598 1.115733902 1.206618762 1.075730993 0.96714671 1.044330871 1.277380253 0.988248605 0.975941719 1 17.79571095 2.062624394 24.99997889 0.98499829 1.109178615 0.333080715 0.084085574 76.56290372 30563.61773 0.035665406 0.024045608 115.5112793 -2.062624394 0.124180324 MVSDEYEQLSSEALEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MVSDEYEQLSSEALEAAR 18 0 F8W7C6 F8W7C6 RPL10 0 ; 162.93 8.00E-11 71853000 30562 31032 24693 36413 31289 31895 22645 30101 72635 FALSE TRUE 26523.15427 30828.14875 36634.61739 44681.12819 30666.41012 33122.02129 20448.89139 23664.1354 64048.17305 0.414112581 0.481327527 0.571985361 0.697617529 0.478802262 0.517142328 0.319273609 0.369474011 1 15.9668698 1.231142801 24.9995337 1.000000919 0.479037559 0.705978825 0.105207622 169.4327689 570973.4471 0.294110386 0.028963753 17.0271829 -1.231142801 -0.52096336 MVSDINNGWQHLEQAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 MVSDINNGWQHLEQAEK 17 0 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 ;;;;;; 320.73 1.51E-58 3453080000 4387900 3334010 3035711 4793900 3206041 3159510 3257980 4371900 10290210 FALSE TRUE 3808027.897 3312108.669 4503790.993 5882428.265 3142247.057 3281058.394 2942021.601 3437003.207 9073713.096 0.419676913 0.365022415 0.496355896 0.648293395 0.346302227 0.361600412 0.324235687 0.378786851 1 23.11326161 1.236381491 24.99997547 1.000000751 0.41540402 0.788935323 0.094674671 28.02511619 321438.9145 0.159245733 0.02472905 17.23381757 -1.236381491 -0.584596731 MVSQSQPGS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MVSQSQPGSR 10 0 E3W994;J3KR49;O75122;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 MVSQSQPGS(1)R;MVSQSQPGS(1)R;MVSQSQPGS(1)R 139.19 4.69E-05 837510000 924720 893830 640010 694830 811080 1023990 881750 972600 905190 TRUE FALSE 802515.9091 887958.3719 949520.9767 852601.7713 794941.0949 1063383.558 796238.0207 764617.0588 798179.4694 1.005432913 1.112479594 1.189608369 1.068183039 0.995942799 1.332261225 0.997567654 0.957951298 1 19.60635365 2.030143338 24.99986593 0.976508024 1.116990289 0.299967477 0.095458673 222.4098544 184458.3293 0.037510728 0.025289427 107.1873017 -2.030143338 0.140482265 MVVNEGSDGGQSVYHVHLHVLGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MVVNEGSDGGQSVYHVHLHVLGGR 24 0 P49773 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ;; 188.32 5.85E-18 4647190000 1301237 1363781 455907 871044 1166025 1305701 1029830 1288103 1227697 FALSE TRUE 1129275.234 1354822.233 676385.1501 1068827.853 1142823.384 1355932.162 929957.2451 1012652.197 1082560.059 1.043152501 1.251498447 0.624801501 0.987315063 1.055667419 1.252523729 0.859035244 0.935423572 1 20.04601564 MVVPGLDGAQIPR ddPTM_MDA-MB-175_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 99.568 0.0065159 59103000 125070 124520 87222 99503 145180 157000 105560 124070 153520 FALSE TRUE 108541.6826 123702.0199 129402.8509 122096.677 142291.202 163039.8916 95322.80745 97538.59601 135371.0405 0.801808734 0.913799728 0.955912361 0.901940892 1.051119955 1.20439269 0.704159524 0.720527785 1 17.04655962 2.195770278 24.99999857 0.785621735 0.96862363 0.250631059 0.13109177 179.4046505 104814.8347 0.054873105 0.036995734 156.9532373 -2.195770278 0.183001895 MVVS(ph)AGPWSSEKAEMNILEINETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MVVSAGPWSSEKAEMNILEINETLR 25 1 A0A087WUL8;A0A087WVE3;A0A075B762;A0A087WVU4;A0A087WZJ2;A0A087X002;A0A087WYI5;A0A075B757;A0A075B7F7;A0A087WV19;A0A087X230;A0A087WUR2 A0A087WUL8 NBPF19;NBPF14;NBPF10;NOTCH2NL 1 MVVS(0.333)AGPWS(0.333)S(0.333)EKAEMNILEINETLR;MVVS(0.333)AGPWS(0.333)S(0.333)EKAEMNILEINETLR 50.499 0.068579 3747400000 553990 800190 414950 306440 596960 1270220 359420 326050 249120 TRUE FALSE 480778.8179 794933.4992 615621.2079 376021.8856 585081.6639 1319086.185 324563.5037 256326.7448 219669.3174 2.188648026 3.618773476 2.802490649 1.711763345 2.663465571 6.004872237 1.477509502 1.166875501 1 17.74497385 3.980412496 21.98788686 2.322673018 2.980440998 0.028852803 1.448446636 655.924832 736319.1469 0.411637215 0.729743715 9559.000746 -3.980412496 0.65776798 MWDPHNDPNAQGDAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 MWDPHNDPNAQGDAFK 16 0 P08621;P08621-2;M0QYR1;P08621-3 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;; 132.64 3.80E-05 1207480000 3056340 2166620 1558740 1879690 2136480 1776930 2517880 2912070 2564860 FALSE TRUE 2652436.925 2152387.331 2312551.878 2306502.344 2093968.228 1845289.647 2273696.385 2289346.492 2261645.173 1.172790921 0.951690989 1.022508705 1.019833868 0.925860632 0.815905903 1.005328516 1.012248305 1 21.10894117 4.74200413 24.67777849 0.971339166 1.172791012 0.510979295 0.062569237 258.9891395 1855933.982 0.016314483 0.115371424 55208.26888 -4.74200413 0.201451846 MWFQWSEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MWFQWSEQR 9 0 Q5T8U5;O15260-3;O15260-2;O15260;B7Z1G8 Q5T8U5 SURF4 Surfeit locus protein 4 0 ; 146.23 0.00022166 526850000 259400 319770 241420 410400 436350 417910 263940 490490 699950 FALSE TRUE 225119.6328 317669.4098 358171.5195 503587.5926 427667.4887 433987.2681 238343.1394 385602.5305 617202.7084 0.36474181 0.514692184 0.580314238 0.815919285 0.692912528 0.703151918 0.38616671 0.624758325 1 19.23538487 4.402290855 1.91985995 0.674746271 0.36292217 0.333919882 0.155415536 0.575845401 3.538542663 0.043541321 0.252884225 25251.71358 -4.402290855 -0.311824101 MWGTS(ph)PEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MWGTSPEDK 9 0 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 1 MWGT(0.296)S(0.704)PEDK;MWGT(0.046)S(0.954)PEDK 131.42 0.0011669 0 920620 784580 547870 694650 771600 690860 924460 1026780 1069590 TRUE FALSE 798957.7344 779426.0423 812821.7645 852380.8996 756246.6696 717437.8312 834806.0115 807211.0874 943144.2887 0.847121426 0.826412302 0.861821223 0.903765108 0.801835603 0.760687246 0.88513075 0.855872317 1 19.84711898 0.879422425 1.691734592 1.2598581 0.83865298 0.600261792 0.040377443 2.089115321 2.426675266 1.97526319 0.011536183 7.575694021 -0.879422425 -0.42120512 MWVFEETVNGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MWVFEETVNGR 11 0 Q8N335;C9K0P5;C9JFA7;C9JM46 Q8N335 GPD1L Glycerol-3-phosphate dehydrogenase 1-like protein;Glycerol-3-phosphate dehydrogenase [NAD(+)] 0 ; 193.38 2.28E-06 76620000 133861 119158 74394 95899 130329 136128 111173 132530 132828 FALSE TRUE 116170.9297 118375.2433 110371.1872 117674.3337 127735.7079 141364.9322 100391.4596 104189.4908 117125.2252 0.991852349 1.010672493 0.942334899 1.004688217 1.090590927 1.206955479 0.857129277 0.889556376 1 16.8376923 2.178476918 24.99999992 0.907709232 1.035894555 0.358009507 0.078854676 82.23803404 34217.178 0.033954818 0.022892344 150.8262447 -2.178476918 0.128185323 MY(ph)SLDRIFAGFRT(ph)RS(ph)QMLLGHIEEQDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MYSLDRIFAGFRTRSQMLLGHIEEQDK 27 3 Q86VH2-4 Q86VH2-4 3 MY(0.788)S(0.478)LDRIFAGFRT(0.808)RS(0.926)QMLLGHIEEQDK 64.176 0.0091486 113740000 151600 81677 250880 111500 34164 38919 77742 95211 92845 TRUE FALSE 131565.6759 81140.45841 372206.4071 136817.7792 33484.20324 40416.23911 70202.59281 74850.86858 81868.96987 1.607027377 0.991101495 4.546367296 1.671179928 0.408997491 0.493669814 0.857499403 0.914276419 1 16.32102912 3.469540673 12.87182948 0.780170453 2.386742972 0.407375224 0.913594649 0.522391173 877.8919151 0.26074803 0.341738359 2948.089563 -3.469540673 1.60657252 MYEEHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 MYEEHLK 7 0 P84090;G3V279 P84090 ERH Enhancer of rudimentary homolog 0 ;;;;; 126.54 0.0039421 5801380000 8958740 7178900 5409150 6329400 6765870 6378880 7700600 8717980 12517740 FALSE TRUE 7774819.81 7131741.333 8025033.033 7766587.009 6631242.424 6624279.641 6953796.997 6853707.82 11037907.04 0.70437446 0.646113553 0.727042999 0.703628594 0.600769911 0.600139104 0.62999235 0.620924583 1 23.3959633 1.235487197 24.9989202 1.000000476 0.651657055 0.856200815 0.044536379 33.26546467 270529.9707 0.081175188 0.011781023 17.1983664 -1.235487197 -0.34834342 MYEEHLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MYEEHLKR 8 1 P84090;G3V279 P84090 ERH Enhancer of rudimentary homolog 0 ;;; 144.12 0.00038331 2232580000 1093790 856978 524654 648384 896000 813551 931012 1091070 600163 FALSE TRUE 949242.8802 851348.4551 778378.4293 795609.4971 878171.353 844848.8334 840722.5995 857753.1712 529212.4138 1.793689746 1.608708399 1.470824208 1.503384041 1.659392958 1.596426711 1.588629778 1.620810753 1 19.01348738 1.237314668 24.99989538 0.99999928 1.599328062 0.827589213 0.086778867 12.77666988 256256.8102 0.128537512 0.021348814 17.27088801 -1.237314668 0.599328782 MYPIDFEKDDDSNFHMDFIVAASNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MYPIDFEKDDDSNFHMDFIVAASNLR 26 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;; 203.25 2.55E-25 682449000 2179390 1598715 1100778 1406356 1564301 1368430 1912777 2259680 1673103 FALSE TRUE 1891378.09 1588212.936 1633117.923 1725690.625 1533174.471 1421074.388 1727276.181 1776465.017 1475310.669 1.282020207 1.076527791 1.106965439 1.169713377 1.039221435 0.963237383 1.170788104 1.204129445 1 20.49258736 4.743431906 24.44551068 1.101168508 1.28202031 0.369284035 0.077376795 472.7084393 2372075.192 0.019871145 0.158437636 55390.069 -4.743431906 0.180851801 MYPPRS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 67.334 0.087849 0 65446 59010 48198 51502 72284 57537 67507 81807 70559 TRUE FALSE 56797.14528 58622.35942 71506.71401 63196.31626 70845.68982 59750.48562 60960.18153 64313.20967 62217.5954 0.912879145 0.942215125 1.149300508 1.015730612 1.138676115 0.960347073 0.97979006 1.03368202 1 15.92503502 4.451760975 24.90600325 1.036424655 0.920213035 0.368579067 0.061470772 189.0597269 185673.0265 0.01498944 0.039661475 28298.34095 -4.451760975 -0.11621162 RPPPPPVPLLPPGTS(ph)PPVDPFTTLASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPPPPPVPLLPPGTSPPVDPFTTLASK 27 1 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 RPPPPPVPLLPPGT(0.241)S(0.759)PPVDPFTTLASK 83.639 0.0056225 78279000 55525 65924 57716 83165 96973 93906 106980 127280 122170 TRUE FALSE 48187.23057 65490.9409 85627.65065 102048.8843 95043.42702 97518.62459 96605.09607 100062.1625 107727.2018 0.44730792 0.607933185 0.794856352 0.947289846 0.882260241 0.905236774 0.896756757 0.92884769 1 16.71702306 4.33408742 1.518064683 0.925233352 0.41206364 0.959594526 0.034288909 0.100369212 0.364424879 0.009994562 0.062252865 21581.78789 -4.33408742 -0.513169713 down MYS(ph)FDDVLEEGKRPPTMTVSEASYQSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MYSFDDVLEEGKRPPTMTVSEASYQSER 28 2 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 MY(0.001)S(0.999)FDDVLEEGKRPPTMTVSEASYQSER;MYS(1)FDDVLEEGKRPPTMTVSEASYQSER;MY(0.001)S(0.998)FDDVLEEGKRPPT(0.001)MTVSEASYQSER;MYS(1)FDDVLEEGKRPPTMTVSEASYQSER 262.03 4.62E-54 874343000 188028 213357 156982 174089 281133 201306 294342 351423 189683 TRUE FALSE 163179.6234 211955.4438 232899.0203 213618.5682 275539.0033 209050.3721 265796.7581 276273.9262 167258.8918 0.975611052 1.267229751 1.392446271 1.277173165 1.6473803 1.249861038 1.589133799 1.651774224 1 17.35172338 5.360112987 0.883872911 1.449803543 1.41E-18 0.297842335 0.201851364 6.730694409 1.896558975 0.065987326 12.23242115 229146.373 -5.360112987 -1.449803543 MYSYPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MYSYPAR 7 0 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;G3V576;G3V555;G3V575;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ;;; 114.59 0.01366 1057611000 811770 913430 582420 678860 990770 1266650 778480 1057590 957830 FALSE TRUE 704492.5377 907429.6182 864080.2601 833005.5387 971055.6154 1315378.845 702983.1294 831432.6087 844596.4286 0.834117353 1.074394335 1.023068806 0.986276416 1.149727352 1.557405171 0.832330218 0.984414071 1 19.68790262 4.739190853 23.95171183 1.070276795 0.834117287 0.138471184 0.18910252 66.33524652 2519971.332 0.047310632 0.273847771 54851.79611 -4.739190853 -0.236159508 NAATEDLWESLENASGKPIAAVMNTWTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NAATEDLWESLENASGKPIAAVMNTWTK 28 1 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ; 217.84 2.84E-34 226620000 201962 165375 104101 142206 184304 157222 224694 261880 211465 FALSE TRUE 175272.21 164288.6407 154444.5918 174496.0458 180636.711 163270.4321 202903.2105 205879 186465.8486 0.939969497 0.881065578 0.828272807 0.935806997 0.968738846 0.875605015 1.088152131 1.104111029 1 17.5085519 2.235605789 24.99991974 1.073428624 0.904648194 0.7148562 0.047268609 38.47393669 325509.592 0.019192831 0.013577194 172.0306335 -2.235605789 -0.16878043 NACDHLSGFNVCNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NACDHLSGFNVCNR 14 0 Q9Y3B4 Q9Y3B4 SF3B6 Splicing factor 3B subunit 6 0 193.51 2.51E-07 314050000 236660 262340 60239 130580 372800 337770 253780 303630 280100 FALSE TRUE 205384.7814 260616.6713 89370.78189 160230.1848 365382.0094 350764.2305 229168.4547 238701.0874 246986.8971 0.831561446 1.055184199 0.361844223 0.648739616 1.479357867 1.420173437 0.92785673 0.966452432 1 17.91407498 3.267024646 24.99996813 1.130480718 0.722072434 0.430853138 0.24691831 239.1173205 210015.2462 0.077196537 0.099641335 1849.373566 -3.267024646 -0.408408283 NADDDRGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NADDDRGPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 90.108 0.010628 203394000 359837 331081 156173 191666 278842 382128 344097 383879 153004 FALSE TRUE 312283.6287 328906.1071 231698.7852 235186.6947 273293.5897 396828.7114 310726.5259 301789.4632 134916.0414 2.314651582 2.437857675 1.717355347 1.743207792 2.025656748 2.941301177 2.303110309 2.236868648 1 17.04170237 1.237893956 24.97691119 0.999998598 2.213605544 0.543654191 0.34983419 13.757344 515031.8014 0.527144194 0.090850601 17.29394034 -1.237893956 1.213606945 NADGFIDLEEYIGDMYSHDGNTDEPEWVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NADGFIDLEEYIGDMYSHDGNTDEPEWVK 29 0 O43852;O43852-3;O43852-15;H0Y875;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;; 289.76 1.25E-80 235216000 153574 117943 100429 149756 128878 124191 123311 141950 255955 FALSE TRUE 133278.8068 117168.2247 148996.8003 183760.3887 126313.5799 128968.7081 111352.3182 111595.0972 225696.2915 0.590522804 0.519141116 0.660165036 0.814193213 0.559661743 0.571425907 0.493372388 0.494448076 1 17.78402319 1.230871753 24.998975 1.000000743 0.584847138 0.653610384 0.094266766 195.1243253 634358.8741 0.263454437 0.025276782 17.01655937 -1.230871753 -0.415153605 NADGTICYDSTHYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NADGTICYDSTHYK 14 0 P14550;Q5T621 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ;;; 193.47 2.55E-07 2338010000 1972090 1667400 795330 1259330 2006050 1748230 2002070 2282830 2214290 FALSE TRUE 1711473.31 1656446.74 1179954.248 1545280.124 1966133.53 1815485.539 1807909.56 1794664.57 1952519.159 0.876546231 0.848363885 0.604324031 0.791428917 1.006972721 0.929817017 0.925936912 0.919153372 1 20.89690527 3.307426477 7.022496802 0.947879779 0.770734527 0.563649397 0.076740998 0.170238015 14.20947188 0.02267883 0.029223984 2029.674882 -3.307426477 -0.177145253 NADHSMNYQYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 NADHSMNYQYR 11 0 Q12906;K7ELV3;Q12906-7 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;;;;;;;;;; 207.88 2.15E-08 3878053000 851414 748557 429110 537923 916050 941899 782232 895524 897194 FALSE TRUE 738897.4827 743639.6798 636629.0313 660066.6388 897822.3972 978134.464 706371.261 704023.1616 791128.7474 0.933978806 0.939973022 0.804709769 0.834335297 1.134862562 1.236378361 0.892865116 0.889897079 1 19.59355297 3.261561073 24.99786892 1.013121456 0.877405226 0.315630849 0.109917926 371.3507112 403596.968 0.036119717 0.046598817 1826.253549 -3.261561073 -0.135716229 NADNDWFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NADNDWFR 8 0 Q9Y3C8 Q9Y3C8 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1 0 ;;;; 131.41 0.0023411 3453780000 6318780 5986250 3183180 4248870 6461190 6138340 5906990 6769310 6896460 FALSE TRUE 5483737.213 5946925.93 4722576.495 5213640.873 6332624.96 6374485.912 5334131.019 5321745.735 6081168.355 0.901757178 0.977924896 0.776590323 0.857341973 1.041350048 1.04823375 0.877155623 0.875118961 1 22.5359171 3.286400231 24.99984901 0.95386754 0.878239802 0.245554644 0.076035085 220.9656809 115469.7521 0.023957829 0.030929343 1933.749573 -3.286400231 -0.075627738 NADSGVHLNR ddPTM_MDA-MB-175_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 ; 100.72 0.0038198 494980000 464440 475810 166891 272640 482590 547520 458760 477070 437060 FALSE TRUE 403063.0773 472684.3728 247600.0458 334547.079 472987.4032 568583.4487 414269.5258 375052.2931 385391.2647 1.045854211 1.226505155 0.642464084 0.868071256 1.227291448 1.475340779 1.074932319 0.973172792 1 18.55596435 3.240814292 24.99993026 1.138644165 0.944118091 0.204441457 0.199654188 114.6334351 1271613.942 0.06407283 0.07873627 1741.062222 -3.240814292 -0.194526074 NAEAVLQS(ph)PGLSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NAEAVLQSPGLSGK 14 0 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 1 NAEAVLQS(0.999)PGLS(0.001)GK;NAEAVLQS(1)PGLSGK;NAEAVLQS(1)PGLSGK;NAEAVLQS(1)PGLSGK;NAEAVLQS(1)PGLSGK 350.81 6.88E-82 1964912000 3752960 3571950 2096810 2662000 4155320 3536600 4524530 5212250 4609350 TRUE FALSE 3256996.827 3548485.625 3110834.329 3266447.786 4072637.262 3672655.29 4085741.777 4097650.899 4064437.894 0.801340041 0.873056919 0.765378734 0.803665321 1.002017344 0.903607187 1.005241532 1.008171611 1 21.95462441 3.240412046 24.999925 0.984450589 0.812054165 0.824300226 0.039673791 19.78432606 267145.5947 0.011885054 0.014564682 1739.450385 -3.240412046 -0.172396424 NAEEES(ph)ESEAEEGD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NAEEESESEAEEGD 14 0 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;H0Y503 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 1 NAEEES(0.987)ES(0.013)EAEEGD;NAEEES(0.996)ES(0.004)EAEEGD 257.55 2.50E-24 423310000 934520 890380 472060 674450 895660 803030 931460 1018320 875630 TRUE FALSE 811020.8142 884531.0352 700349.7949 827594.1808 877838.1183 833923.0837 841127.1526 800560.1926 772114.0189 1.050389961 1.145596393 0.907054888 1.071854882 1.136928092 1.080051732 1.08938205 1.036841934 1 19.55845438 1.446781703 3.334744746 1.001472784 1.068561381 0.10803145 0.064684934 0.595574438 11.43568967 0.080284118 0.016742781 27.97574775 -1.446781703 0.067088597 NAEMHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NAEMHK 6 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 68.422 0.096181 87132000 249820 208180 102120 150570 136450 179280 297260 282800 314360 FALSE TRUE 216805.654 206812.4519 151505.5736 184759.2198 133734.912 186177.0176 268431.771 222325.4208 277196.7189 0.782136437 0.746085497 0.546563373 0.666527441 0.482454888 0.671642213 0.968380044 0.802049251 1 18.08055066 2.300955012 6.627577782 0.899620906 0.640444127 0.621304048 0.100331193 0.140667604 11.62474013 0.038187035 0.029237982 199.9654715 -2.300955012 -0.259176779 NAEQYKDQADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NAEQYKDQADK 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 183.79 4.74E-06 5512970000 3921230 2928600 2104500 2173520 2956360 2054890 4495860 4641260 2203150 FALSE TRUE 3403029.52 2909361.834 3122243.239 2667050.936 2897534.22 2133942.948 4059852.189 3648762.667 1942696.117 1.751704495 1.497589772 1.607170165 1.372860589 1.491501525 1.098444028 2.089803008 1.878195275 1 20.88962882 2.237704666 24.99999935 1.720365279 1.473951579 0.057672507 0.320989274 51.26027397 1497079.353 0.124775522 0.089706117 172.8640428 -2.237704666 -0.2464137 NAFACFDEEATGTIQEDYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NAFACFDEEATGTIQEDYLR 20 0 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ; 344.38 1.01E-80 235890000 249080 253310 112286 146051 281820 270290 250850 284780 262770 FALSE TRUE 216163.4469 251645.9899 166587.8852 179214.1118 276212.3334 280688.2312 226522.6056 223882.0132 231705.6299 0.932922722 1.086059022 0.718963476 0.773456009 1.192082961 1.211400134 0.977630995 0.966234671 1 17.82193357 3.244031077 24.99999865 1.056773979 0.881373313 0.361707669 0.125821216 181.5748343 829791.7291 0.040176252 0.050372518 1754.00601 -3.244031077 -0.175400666 NAFMMLIHADQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NAFMMLIHADQDR 13 0 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ; 124.45 0.00021168 2006190000 1999270 2201570 940490 1213430 2511200 2465100 2269930 2518400 2073880 FALSE TRUE 1735061.404 2187107.742 1395314.11 1488957.828 2461232.033 2559933.992 2049792.538 1979859.758 1828708.269 0.948790703 1.195985045 0.763005305 0.814212881 1.345885549 1.399859144 1.120896412 1.082654785 1 20.80239351 3.244420198 24.99999559 1.181786422 0.937498017 0.389324319 0.161126371 174.4555088 744312.5627 0.050782267 0.063790225 1755.578275 -3.244420198 -0.244288404 NAIEHPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NAIEHPVR 8 0 Q99805 Q99805 TM9SF2 Transmembrane 9 superfamily member 2 0 ;;; 120.99 0.0014525 868908000 1596180 1353020 946461 1345630 1943650 2127000 967630 1829040 2970170 FALSE TRUE 1385240.769 1344131.923 1404172.705 1651175.858 1904975.168 2208827.066 873789.3915 1437914.03 2619039.886 0.528911673 0.513215522 0.536140252 0.630450825 0.727356302 0.843372825 0.333629662 0.549023341 1 21.3206066 3.716088888 3.786846669 0.65549364 0.522346559 0.139809083 0.174599797 0.566168326 18.07221083 0.050707027 0.083409607 5201.02436 -3.716088888 -0.133147081 NALESYAFNMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NALESYAFNMK 11 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 0 ; 199.09 1.20E-07 987160000 1166220 1078550 557150 738370 1088020 1028610 1218870 1321820 1331550 FALSE TRUE 1012101.072 1071464.934 826589.6036 906028.1938 1066370.531 1068181.292 1100664.175 1039159.079 1174135.676 0.861996695 0.912556322 0.703998371 0.77165545 0.908217468 0.909759676 0.937425033 0.885041738 1 20.1631677 3.144515988 6.170406462 0.923888544 0.812296301 0.468892594 0.061170661 0.207071677 11.24969186 0.019284293 0.022015631 1394.813005 -3.144515988 -0.111592243 NALFPEVFS(ph)PTPDENSDQNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NALFPEVFSPTPDENSDQNSR 21 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 NALFPEVFS(1)PTPDENSDQNSR;NALFPEVFS(1)PTPDENSDQNSR;NALFPEVFS(1)PTPDENSDQNSR 205 3.21E-22 180576000 200655 230476 150591 161122 309298 376876 273298 325554 356184 TRUE FALSE 174137.9334 228961.988 223417.3113 197707.2127 303143.5749 391374.6636 246793.602 255936.8106 314076.3333 0.55444462 0.729001086 0.711347171 0.629487777 0.96519076 1.246113196 0.785775864 0.814887285 1 18.26075571 3.236639875 24.99824302 0.944894856 0.665227846 0.569607644 0.13171777 44.01907936 572905.2857 0.042069828 0.050144497 1724.40739 -3.236639875 -0.27966701 NALLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NALLHK 6 0 A0A1B0GVP4;A8MVM7 A0A1B0GVP4 Putative uncharacterized protein ENSP00000382790 0 69.39 0.09363 939580000 869090 888180 552180 605810 880940 941570 934330 946130 1079800 FALSE TRUE 754237.5545 882345.4871 819216.0949 743368.4197 863411.0175 977792.8072 843718.8204 743807.4623 952147.2741 0.792143794 0.926690136 0.860388006 0.780728402 0.906804064 1.026934418 0.886122182 0.78118951 1 19.86082522 3.109986904 19.31919326 0.905653323 0.847132859 0.196154293 0.077045464 4.858534304 828.7662342 0.024855612 0.028183763 1288.210706 -3.109986904 -0.058520464 NALPPVLTTVNGQS(ph)PPEHSAPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NALPPVLTTVNGQSPPEHSAPAK 23 0 Q6PKG0;A0A0B4J210;H0YBM7 Q6PKG0 LARP1 La-related protein 1 1 NALPPVLTTVNGQS(0.999)PPEHS(0.001)APAK;NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK 230.94 1.95E-33 8192800000 4384220 3908140 2257980 2888740 4903620 4249490 5218670 6138700 5422800 TRUE FALSE 3804834.219 3882467.171 3349946.68 3544672.569 4806047.556 4412970.63 4712564.187 4825986.776 4781722.762 0.795703642 0.811938994 0.700573172 0.741296128 1.005087036 0.922882996 0.985536892 1.009256918 1 22.18909906 3.238599343 25 0.984631127 0.761503398 0.894705142 0.037872564 0.320393826 206628.1895 0.01186018 0.014342718 1732.205221 -3.238599343 -0.223127729 NALVSHLDGTTPVCEDIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NALVSHLDGTTPVCEDIGR 19 0 P31930 P31930 UQCRC1 "Cytochrome b-c1 complex subunit 1, mitochondrial" 0 148.91 4.37E-08 0 55646 52982 33123 56184 86264 79085 47207 78686 65395 FALSE TRUE 48292.24011 52633.95775 49141.39359 68941.43592 84547.51517 82127.45112 42628.87241 61859.61124 57664.0776 0.83747529 0.912768572 0.852201156 1.195569907 1.46620771 1.424239397 0.739262192 1.072758185 1 15.81538524 3.743251132 24.34402504 1.140639504 0.872010338 0.295614266 0.204987349 414.5820919 2151689.728 0.060503819 0.100489949 5536.701779 -3.743251132 -0.268629166 NAMS(ph)LPQLNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 186.67 4.12E-06 1206788000 4094030 3681260 1953070 2060900 3051540 2932720 3594890 3554320 4077610 TRUE FALSE 3552993.563 3657077.561 2897581.185 2528858.844 2990820.324 3045543.636 3246258.121 2794256.328 3595559.591 0.988161501 1.017109428 0.80587767 0.703328308 0.831809416 0.847029109 0.902851987 0.777140875 1 21.77778489 4.240838108 25 0.831550317 1.002635525 0.434903365 0.077587403 50.04919171 549355.6275 0.019221964 0.046080476 17411.577 -4.240838108 0.171085208 NANKPLLDEIVPVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NANKPLLDEIVPVYR 15 1 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 107.07 0.0010818 296520000 836990 700480 445680 552870 767130 738020 721260 881440 860200 FALSE TRUE 726379.6508 695878.5008 661212.3387 678407.5836 751865.6139 766412.107 651312.3162 692950.9154 758508.1359 0.957642531 0.917430503 0.871727418 0.89439724 0.991242649 1.010420417 0.858675452 0.913570841 1 19.53280513 3.285081395 24.99997638 0.945204748 0.908053623 0.151668836 0.049347078 300.1914099 161318.9712 0.015231934 0.019664282 1927.886201 -3.285081395 -0.037151125 NAPAAVDEGSIS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NAPAAVDEGSISPR 14 0 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;A0A090HNM7 R4GMW8 BIVM-ERCC5;ERCC5;ERCC5-201 DNA repair protein complementing XP-G cells 1 NAPAAVDEGSIS(1)PR;NAPAAVDEGSIS(1)PR;NAPAAVDEGSIS(1)PR;NAPAAVDEGSIS(1)PR;NAPAAVDEGSIS(1)PR;NAPAAVDEGSIS(1)PR 317.75 5.95E-56 4921750000 2842820 2845820 1363513 1855990 3417440 3058120 2809640 3190790 2841230 TRUE FALSE 2467134.134 2827125.621 2022912.447 2277420.897 3349439.63 3175767.855 2537161.545 2508464.389 2505343.026 0.984749038 1.128438538 0.807439311 0.90902558 1.336918576 1.267598018 1.012700265 1.001245883 1 21.25657672 NAPWTLTPEFLAEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NAPWTLTPEFLAEHR 15 0 P49585;C9JEJ2;C9J050;H7C1T3;C9J2E1;H7BZN1 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 0 ; 115.1 0.00055402 705350000 282525 284974 138828 173010 344587 393692 286420 309295 271722 FALSE TRUE 245188.6054 283101.987 205965.6852 212294.5648 337730.3929 408837.586 258643.0325 243154.6712 239599.3347 1.023327572 1.181564162 0.859625447 0.886039876 1.40956315 1.706338569 1.07948143 1.014838674 1 17.87026438 3.250796992 24.99686145 1.224666163 0.992347203 0.241193432 0.222973735 417.0737792 852006.8352 0.072458815 0.092845538 1781.545799 -3.250796992 -0.232318961 NAQAIEDMVGYAQETQHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NAQAIEDMVGYAQETQHEK 19 0 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ; 306.82 8.45E-51 883440000 393518 385921 205230 237803 414484 322009 424246 484780 497810 FALSE TRUE 341513.5993 383385.8595 304479.9145 291799.8057 406236.5793 334396.8946 383102.6882 381113.5696 438959.4689 0.778007136 0.873396946 0.693640156 0.664753414 0.925453506 0.761794467 0.872751849 0.868220409 1 18.74372821 -1.999985418 0.531727866 9.589832203 0.772729494 0.450743945 0.076671895 120.3979441 1.228669968 1199.617191 0.045282269 0.010000336 1.999985418 -8.817102709 S(ph)LPTTVPES(ph)PNYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLPTTVPESPNYR 13 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 2 S(1)LPTTVPES(1)PNYR;S(1)LPTTVPES(1)PNYR;S(1)LPTTVPES(1)PNYR;S(1)LPTTVPES(1)PNYR;S(1)LPTTVPES(1)PNYR;S(1)LPTTVPES(1)PNYR 290.82 2.29E-40 12698640000 1764460 2267990 2507510 3032900 4310860 4713970 4202630 4642940 4763430 TRUE FALSE 1531282.14 2253091.424 3720150.223 3721566.3 4225082.32 4895319.476 3795059.589 3650083.412 4200302.732 0.364564708 0.536411675 0.885686214 0.886023351 1.005899477 1.16546825 0.903520492 0.869004842 1 22.00206188 4.336494022 1.771659472 0.968928929 0.329192375 0.871654299 0.083249145 0.163728873 0.872294152 0.025437585 0.136467808 21701.71331 -4.336494022 -0.639736554 down NASYYGNR ddPTM_MDA-MB-175_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 ; 151.5 0.0010986 133161000 139166 139034 65231 87940 169215 173835 137077 146703 137233 FALSE TRUE 120774.8605 138120.6765 96776.92978 107908.1211 165847.9526 180522.5449 123783.2936 115331.7051 121009.4711 0.998061221 1.141403853 0.799746738 0.891732855 1.37053696 1.49180509 1.022922359 0.953079987 1 16.88476044 3.280808578 24.99993032 1.146197019 0.959570249 0.236709967 0.185091133 275.3177521 162915.518 0.060461304 0.078054517 1909.011647 -3.280808578 -0.18662677 NATDLQNSS(ph)MSEEELTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NATDLQNSSMSEEELTK 17 0 Q5QNY5;P40855;P40855-5;H0YJ60 Q5QNY5 PEX19 Peroxisomal biogenesis factor 19 1 NATDLQNS(0.001)S(0.921)MS(0.079)EEELTK;NATDLQNSS(0.999)MS(0.001)EEELTK 402.19 3.59E-140 483880000 1194820 1053470 573580 646260 911770 708700 1050330 1287390 1176870 TRUE FALSE 1036921.51 1046549.686 850965.2065 793003.2105 893627.5608 735964.1476 948469.1583 1012091.667 1037741.769 0.999209573 1.008487581 0.820016339 0.764162371 0.8611271 0.709197769 0.913974157 0.97528277 1 19.98501606 1.840438005 3.613298795 0.987116045 0.85825314 0.237842723 0.092014274 0.3519755 7.746279538 0.060761503 0.026983897 69.25290646 -1.840438005 -0.128862905 NATTGRIVSPGFPGNYSNNLTCHWLLEAPEGQRLHLHFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NATTGRIVSPGFPGNYSNNLTCHWLLEAPEGQRLHLHFEK 40 2 H0YGK0;H0YFX0;H0YF95;A0A0A0MSU7;C9JFF1;Q53EL9-4;Q53EL9-2;Q53EL9-3;Q53EL9 H0YGK0 SEZ6 Seizure protein 6 homolog 0 ; 22.28 0.090815 5784500000 8133200 3540000 7472300 2194600 1394540 1796230 3970000 4308100 5752100 FALSE TRUE 7058377.013 3516745.507 11085929.27 2692917.472 1366791.382 1865332.13 3584990.011 3386846.341 5072093.291 1.39161025 0.693351897 2.185671406 0.530928222 0.26947284 0.367763766 0.706806797 0.667741334 1 22.27414985 NAVEEYVYDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NAVEEYVYDFR 11 0 O95757;E9PDE8 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 134.98 0.0027971 0 52943 63098 29218 41690 72859 62526 60027 70566 65973 FALSE TRUE 45946.44841 62683.50508 43347.92253 51156.35169 71409.24845 64931.41568 54205.59078 55476.01005 58173.7471 0.789814146 1.077522219 0.745145786 0.879371783 1.227516741 1.116163543 0.931787851 0.953626211 1 15.82808061 3.395752068 24.99999856 1.031459463 0.878245305 0.337943181 0.119183471 38.53538398 11836.43216 0.035295782 0.045566656 2487.436871 -3.395752068 -0.153214158 NAVEEYVYEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 NAVEEYVYEFR 11 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;;;;; 324.1 4.58E-46 3589257000 1335713 1298686 679114 910182 1431742 1469896 1400024 1574854 1447725 FALSE TRUE 1159195.143 1290154.846 1007535.802 1116852.734 1403253.135 1526443.85 1264249.888 1238083.728 1276576.6 0.908049813 1.010636453 0.789248214 0.874881096 1.099231441 1.195732282 0.990343931 0.969846798 1 20.28384868 3.246792593 24.98841114 1.043566428 0.896309359 0.464251336 0.082696296 191.9962808 582806.8723 0.026255094 0.033318094 1765.194611 -3.246792593 -0.147257069 NAVEEYVYEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NAVEEYVYEMR 11 0 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;;;; 194.17 1.72E-05 1871810000 1589750 1484740 809450 1083600 1675960 1672240 1598640 1977960 1677150 FALSE TRUE 1379660.51 1474986.645 1200902.727 1329647.942 1642611.675 1736572.155 1443604.139 1554988.647 1478879.238 0.932909513 0.997367877 0.812035694 0.899091628 1.110713866 1.17424879 0.976147411 1.051464249 1 20.49607282 3.248014596 24.99708536 1.060242674 0.909544086 0.53778002 0.070078612 164.2437752 434271.3119 0.021054165 0.026810241 1770.168451 -3.248014596 -0.150698588 NAYAVLYDIILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NAYAVLYDIILK 12 0 Q06323;H0YKK6 Q06323 PSME1 Proteasome activator complex subunit 1 0 212.38 4.87E-08 40436000 133390 117240 68696 93453 136010 115100 155310 159960 154890 FALSE TRUE 115762.1735 116469.8427 101917.6154 114672.932 133303.6671 119527.9715 140248.0601 125753.7988 136579.0807 0.847583488 0.852764876 0.74621688 0.839608317 0.97601819 0.875155777 1.026863407 0.920739825 1 17.059377 3.307807297 5.242885913 0.955665798 0.815714656 0.65351836 0.050089176 0.121176761 6.182673225 0.01388416 0.017847634 2031.455422 -3.307807297 -0.139951142 NCCFEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NCCFEHR 7 0 Q9BTY7 Q9BTY7 HGH1 Protein HGH1 homolog 0 ; 126.52 0.0039439 134142000 157807 145954 73329 94233 166027 188442 156474 184462 170451 FALSE TRUE 136952.4051 144995.2186 108791.1497 115630.0429 162723.3875 195691.4857 141299.1756 145016.2368 150300.477 0.911190755 0.964702318 0.723824381 0.769325855 1.082653833 1.302001761 0.940111292 0.96484216 1 17.19749006 3.231726185 24.99955349 1.049655084 0.842546896 0.450763344 0.118094497 167.9160348 614216.3039 0.038665978 0.044810594 1705.007075 -3.231726185 -0.207108189 NCES(ph)DTEEDIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NCESDTEEDIAR 12 0 Q9UIK4 Q9UIK4 DAPK2 Death-associated protein kinase 2 1 NCES(1)DTEEDIAR;NCES(0.867)DT(0.133)EEDIAR 346.46 2.23E-71 652450000 913710 1002260 589620 653070 1096330 888980 965660 1151750 1045000 TRUE FALSE 792960.9085 995676.0881 874762.2042 801359.525 1074515.178 923179.6358 872010.4418 905457.2254 921461.2905 0.860547173 1.080540331 0.949320621 0.869661627 1.166099096 1.001864805 0.946334318 0.982631864 1 19.81356404 NCGQTVHDEVANK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NCGQTVHDEVANK 13 0 O14964-2;O14964;I3L1P5;I3L2H4;I3L165 O14964-2 HGS Hepatocyte growth factor-regulated tyrosine kinase substrate 0 67.964 0.051719 88664000 146060 137120 82706 86237 123950 121020 130760 161770 192540 FALSE TRUE 126757.8009 136219.2497 122702.8982 105818.4289 121483.6375 125675.7177 118078.9153 127176.7444 169778.1405 0.746608489 0.802336798 0.722724951 0.623274755 0.715543456 0.740234976 0.695489507 0.749076082 1 17.37329119 1.236535986 4.048921767 1.030772683 0.721014192 0.792163275 0.044585442 0.11334673 3.296664921 0.104368033 0.01199823 17.23994937 -1.236535986 -0.309758491 NCGSFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NCGSFTR 7 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 96.492 0.029528 153740000 184900 171080 105800 118790 173400 184250 174220 193040 184570 FALSE TRUE 160464.9965 169956.1642 156965.2339 145763.0851 169949.6793 191338.2167 157324.1712 151759.8982 162750.3449 0.985957951 1.044275294 0.964454078 0.895623817 1.044235448 1.175654754 0.966659526 0.932470517 1 17.31230107 2.030479976 24.99999197 0.957857324 1.01756276 0.099676735 0.072669012 435.9905371 357602.2636 0.031502131 0.021238548 107.2704187 -2.030479976 0.059705436 NCIVLIDSTPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NCIVLIDSTPYR 12 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ; 147.91 0.00015227 167154000 375710 373360 181953 223400 446610 452790 391290 421050 413750 FALSE TRUE 326058.9716 370907.3736 269946.0794 274126.3845 437723.3348 470209.1243 353342.756 331011.7341 364836.9463 0.893711492 1.01663874 0.739908834 0.751366843 1.199777981 1.288819921 0.968494994 0.907286769 1 18.47689231 3.24586775 24.99990265 1.05514592 0.854387529 0.404477189 0.133134989 217.5547422 744315.8503 0.043889756 0.055497349 1761.439578 -3.24586775 -0.200758391 NCLTNFHGMDLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 NCLTNFHGMDLTR 13 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;D6RB09;D6RAS7;D6RED7 P61247 RPS3A 40S ribosomal protein S3a 0 ;;;;;; 216.54 2.73E-11 7635850000 3728318 4268049 1908374 2336401 5051222 4835300 4062607 4564120 4244675 FALSE TRUE 3235611.33 4240011.905 2831270.05 2866916.557 4950712.565 5021317.12 3668615.998 3588118.456 3742874.357 0.864472334 1.132822398 0.756442717 0.76596655 1.32270338 1.341567106 0.980160072 0.958653194 1 21.83571519 3.256094617 24.99996192 1.10088464 0.889169823 0.340525765 0.16495312 358.824571 511608.7596 0.052439587 0.067538525 1803.410597 -3.256094617 -0.211714817 NCNDFQYESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NCNDFQYESK 10 0 Q04917;A2IDB2 Q04917 YWHAH 14-3-3 protein eta 0 164.97 1.39E-05 241330000 156020 159660 91953 121890 153810 125820 166850 204020 178030 FALSE TRUE 135401.5617 158611.1829 136421.7784 149566.9875 150749.4819 130660.3768 150668.9127 160391.9107 156983.4962 0.862520997 1.010368521 0.869019876 0.952756125 0.960288728 0.832319193 0.959775494 1.021711929 1 17.26025337 1.998025307 24.98896186 1.005907898 0.918597844 0.364840256 0.052342928 75.11787379 950592.2534 0.020317417 0.013469689 99.54634225 -1.998025307 -0.087310054 NCPAVTLTS(ph)PAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NCPAVTLTSPAK 12 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 NCPAVTLT(0.035)S(0.965)PAK;NCPAVTLT(0.002)S(0.998)PAK 169.3 4.64E-05 392820000 1280190 1258630 677230 921650 1599700 1144910 1510570 1909330 1441700 TRUE FALSE 1111009.648 1250361.977 1004740.693 1130924.719 1567869.1 1188955.429 1364075.154 1501034.638 1271263.868 0.873941025 0.98355818 0.790347872 0.889606593 1.233315237 0.935254638 1.073007098 1.180741996 1 20.27783208 3.307881199 12.0013896 1.08813656 0.884454968 0.526907936 0.094182586 0.517361237 87.82396243 0.02628643 0.033931521 2031.801138 -3.307881199 -0.203681592 NCPHIVVGTPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 93.011 0.0074126 1494570000 1225500 1186250 531811 798310 1512800 1544270 1106060 1373030 1250280 FALSE TRUE 1063547.07 1178457.446 788996.5784 979578.4869 1482698.24 1603679.066 998794.4714 1079418.219 1102473.323 0.964691887 1.068921507 0.715660472 0.888528064 1.344883553 1.454619385 0.90595795 0.979087836 1 20.07231232 3.336068786 22.4374503 1.115953389 0.906982477 0.266774605 0.185557336 11.29964845 2584.565315 0.059038518 0.076218338 2168.047463 -3.336068786 -0.208970912 NCPHVVVGTPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NCPHVVVGTPGR 12 0 O00148;O00148-2;O00148-3;K7EQN7;K7EPJ3;A0A0D9SEM9 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 86.772 0.010923 377280000 316120 234520 145080 187640 283810 213540 259830 324760 320860 FALSE TRUE 274343.9411 232979.4227 215241.1733 230246.5299 278162.7363 221755.022 234631.7266 255312.6013 282928.2963 0.969658902 0.823457483 0.760762271 0.81379817 0.983156297 0.783785238 0.829297492 0.902393308 1 18.11007695 1.341124896 2.621647239 1.016101135 0.848764086 0.296572568 0.072303218 0.49395843 4.52778209 0.165389328 0.018911287 21.93435643 -1.341124896 -0.167337048 NCPS(ph)PVLIDCPHPNCNKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NCPSPVLIDCPHPNCNKK 18 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 NCPS(1)PVLIDCPHPNCNKK;NCPS(1)PVLIDCPHPNCNKK;NCPS(1)PVLIDCPHPNCNKK 237.01 3.64E-24 1930880000 1515490 1159970 734870 785710 1246840 913090 1576940 1853630 1083140 TRUE FALSE 1315214.157 1152350.081 1090255.59 964117.4643 1222030.323 948217.1631 1424008.602 1457245.649 955092.4231 1.37705433 1.206532533 1.141518416 1.00944939 1.279489078 0.992801472 1.490964191 1.525764014 1 19.86528082 2.22758114 24.99803787 1.384173051 1.166251126 0.151593809 0.180495648 304.892543 694172.1389 0.071871468 0.048973827 168.8811355 -2.22758114 -0.217921925 NCQHANAERPTVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NCQHANAERPTVAR 14 1 Q9Y5J1;F6VJE8 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 0 ; 97.631 0.0017413 56754000 170326 167811 102368 123443 128889 170328 164022 170045 162874 FALSE TRUE 147816.9875 166708.6385 151873.5072 151472.6199 126324.3611 176880.6284 148115.1717 133682.2 143619.2213 1.029228443 1.160768294 1.057473407 1.054682086 0.879578374 1.231594398 1.031304657 0.930809949 1 17.13188932 1.990585201 24.92558821 0.96664115 1.068974 0.177359888 0.091320686 673.5332067 1783171.393 0.038087655 0.024067447 97.85549117 -1.990585201 0.10233285 NCSASTS(ph)QER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NCSASTSQER 10 0 H7BZV4;A0A0C4DG62;Q66PJ3-4;Q66PJ3-3;F8WEP2 H7BZV4 ARL6IP4 ADP-ribosylation factor-like protein 6-interacting protein 4 1 NCSAS(0.008)T(0.048)S(0.943)QER;NCSAST(0.003)S(0.996)QER;NCSAS(0.002)T(0.005)S(0.993)QER;NCS(0.001)AS(0.012)T(0.049)S(0.938)QER;NCS(0.076)AS(0.021)T(0.04)S(0.863)QER 185.9 1.47E-06 1473779000 2148640 2185300 998174 1406760 2084770 2471950 2192880 2697790 2461400 TRUE FALSE 1864691.78 2170944.62 1480894.285 1726186.359 2043287.156 2567047.516 1980214.835 2120888.603 2170416.096 0.859140228 1.000243513 0.68230893 0.795325082 0.941426466 1.182744415 0.912366453 0.977180646 1 21.04954022 3.047331729 6.029089999 1.008157063 0.837534887 0.417896363 0.101997314 0.203550513 17.32555125 0.031728577 0.035826916 1115.145995 -3.047331729 -0.170622176 NCSETQYESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NCSETQYESK 10 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 163.84 0.0073165 0 129990 118760 64896 103670 115190 121850 117000 134040 153560 FALSE TRUE 112811.4921 117979.8577 96279.92266 127209.858 112897.9444 126537.6483 105653.358 105376.5891 135406.3117 0.833133188 0.871302499 0.71104457 0.939467713 0.833771653 0.934503324 0.780269078 0.77822509 1 17.04693546 3.721237371 24.99126282 0.861789653 0.811774302 0.130782337 0.080954858 2218.33662 3200267.976 0.022292078 0.033157755 5263.048484 -3.721237371 -0.050015351 NCSS(ph)PEFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NCSSPEFSK 9 0 Q99829;B0QZ18;F2Z2V0;A6PVH9;E7ENH5;Q5JX45;Q5JX60;Q5JX52;Q5JX44;Q5JX61;Q5JX59;Q5JX58;Q5JX56;Q5JX54;Q5JX55;E7EV27;Q5JX57;Q5JX53 Q99829 CPNE1 Copine-1 1 NCS(0.002)S(0.998)PEFSK;NCS(0.004)S(0.995)PEFS(0.001)K 220.29 4.84E-07 1617520000 7270700 7084300 4416900 5379200 7647700 6608300 8430000 9552400 9734800 TRUE FALSE 6309858.573 7037762.767 6552927.614 6600629.576 7495525.732 6862525.577 7612459.898 7509693.597 8583963.034 0.735075227 0.819873378 0.763391872 0.768948975 0.873201073 0.799458892 0.886823472 0.874851577 1 23.03321243 -2 0.361324358 3.51027309 0.766499853 0.776215776 0.03661602 35.21064161 0.538310717 65.71183574 0.042930784 0.01 2 -2.743773237 NCTYTQVQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NCTYTQVQTR 10 0 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;B7Z4S1;A0A0A0MT58;Q15560-2;Q15560 A0A1W2PRL9 TCEA1;TCEA2 Transcription elongation factor A protein 1;Transcription elongation factor A protein 2 0 93.561 0.014518 0 21922 17191 11490 14622 19458 19867 19233 20971 19221 FALSE TRUE 19024.95216 17078.07119 17046.60243 17942.14858 19070.82387 20631.29635 17367.78662 16486.51485 16948.71528 1.122501136 1.007632196 1.005775491 1.058614077 1.125207637 1.217277889 1.024725847 0.972729471 1 14.0488883 2.009068381 24.99913012 0.98871006 1.085427435 0.336947482 0.061318654 236.418332 651740.1736 0.027305932 0.018381206 102.1100245 -2.009068381 0.096717375 NCVAIAADRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NCVAIAADRR 10 1 P49720;A0A087WXQ8;A0A087WY10;A0A087WUL2 P49720 PSMB3 Proteasome subunit beta type-3 0 ; 145.46 4.87E-05 309850000 310950 305760 154837 213709 403420 340570 311550 354740 290060 FALSE TRUE 269857.1697 303751.4424 229716.6911 262234.8948 395392.7313 353671.9483 281335.929 278881.6116 255769.4372 1.055079812 1.187598666 0.898139721 1.02527846 1.545895145 1.382776426 1.099959135 1.090363315 1 17.96448436 NCVLLSRPEISTDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NCVLLSRPEISTDER 15 1 O94855;O94855-2;E9PDM8 O94855 SEC24D Protein transport protein Sec24D 0 ; 125.67 8.12E-05 1558050000 2076320 2332560 961820 1162890 3311500 2977900 2550200 2635900 2222710 FALSE TRUE 1801929.051 2317237.26 1426959.369 1426941.948 3245607.629 3092461.74 2302881.997 2072233.298 1959943.756 0.919377939 1.182297835 0.728061387 0.728052498 1.655969779 1.577831879 1.174973511 1.057292227 1 20.90238082 3.261769859 24.99795695 1.269086461 0.898837735 0.413022461 0.238100888 286.4775294 308554.0372 0.076208445 0.098322362 1827.131729 -3.261769859 -0.370248726 NCVVLSDIHIDIMDYIQPATCTDAEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NCVVLSDIHIDIMDYIQPATCTDAEFR 27 0 P53618 P53618 COPB1 Coatomer subunit beta 0 166.23 8.99E-12 51375000 78938 80853 32695 51155 81773 87823 79892 87411 97813 FALSE TRUE 68506.1433 80321.87132 48506.41136 62770.52461 80145.87729 91201.60764 72144.08614 68718.83788 86249.65857 0.794277269 0.93127176 0.562395401 0.727777079 0.929231241 1.05741413 0.836456484 0.796743303 1 16.39623113 3.237646738 24.99953986 0.908174642 0.752916534 0.34585025 0.115065076 32.73523548 895494.6026 0.035967225 0.043191145 1728.40987 -3.237646738 -0.155258108 NCWQNYLDFHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NCWQNYLDFHR 11 0 P14854;A0A494C160 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 0 ;;; 234.61 1.68E-15 5549550000 2356230 2246570 1173475 1728500 3187770 3909400 1780210 2766340 2728010 FALSE TRUE 2044848.236 2231812.134 1740971.435 2120982.343 3124339.614 4059797.148 1607565.508 2174779.719 2405507.766 0.850069272 0.927792529 0.723743843 0.881719184 1.29882749 1.687709018 0.668285312 0.904083433 1 21.19791003 3.449793012 23.6627443 1.082164204 0.836505973 0.193324551 0.267627322 237.4345604 205586.2095 0.083988877 0.108432898 2817.03999 -3.449793012 -0.245658231 NDAPTPGTST(ph)TPGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NDAPTPGTSTTPGLR 15 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 NDAPTPGT(0.002)S(0.008)T(0.71)T(0.28)PGLR;NDAPTPGT(0.092)S(0.271)T(0.544)T(0.093)PGLR 195.45 1.13E-07 892270000 1819770 1455280 750930 925740 1706940 1811740 1474960 1647090 1543310 TRUE FALSE 1579282.784 1445720.17 1114082.26 1135943.416 1672975.234 1881438.81 1331918.606 1294872.621 1360861.65 1.160502086 1.062356464 0.818659457 0.834723659 1.229349974 1.382534962 0.978731825 0.951509377 1 20.37608897 1.807521779 0.007816665 0.886436209 1.189956625 0 0.173981565 1018815.83 3175.260568 62987.11262 60321.80814 64.19804148 -1.807521779 0.303520416 NDAPTPGTSTT(ph)PGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NDAPTPGTSTTPGLR 15 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 NDAPTPGT(0.001)S(0.001)T(0.012)T(0.986)PGLR;NDAPTPGT(0.001)S(0.005)T(0.354)T(0.64)PGLR 182.28 6.18E-06 896950000 1642500 1310320 667010 821650 1603670 1541820 1272390 1423600 1399860 TRUE FALSE 1425439.463 1301712.422 989578.267 1008218.191 1571760.105 1601134.813 1148993.814 1119174.218 1234370.146 1.154790942 1.054555983 0.801686812 0.816787569 1.273329649 1.297126975 0.930834092 0.90667635 1 20.23534364 1.89100072 0.009323709 7.40E-05 2.011974853 0.00423311 0.172883192 83639.90164 334.4400341 36946.8612 35227.69731 77.80378416 -1.89100072 2.011900893 NDEELNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 174.73 0.001897 12678400000 7526300 5934500 3889600 4935400 4610200 4437800 6352500 7952400 6761000 FALSE TRUE 6531680.386 5895515.879 5770623.57 6056058.003 4518466.04 4608525.038 5736435.528 6251841.146 5961722.282 1.095602928 0.988894752 0.967945721 1.015823568 0.757912869 0.773019074 0.962211129 1.048663599 1 22.50729774 4.803636172 1.193231544 0.930781486 1.18464485 0.239930184 0.095312834 3.199182661 3.509920796 0.032540871 1.045994277 63626.22727 -4.803636172 0.253863364 NDEELNKLLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NDEELNKLLGK 11 1 A0A0U1RR32;A0A0U1RRH7;P20671;Q99878;Q96KK5;Q6FI13;P0C0S8;Q16777;Q9BTM1;Q9BTM1-2;H0YFX9 A0A0U1RR32;Q99878 HIST1H2AD;HIST1H2AJ;HIST1H2AH;HIST2H2AA3;HIST1H2AG;HIST2H2AC;H2AFJ Histone H2A type 1-D;Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-A;Histone H2A type 1;Histone H2A type 2-C;Histone H2A.J;Histone H2A 0 ; 158.2 2.75E-05 2010590000 4170200 3177260 921430 1149860 2974260 2054300 4207600 5231900 158727 FALSE TRUE 3619097.504 3156388.37 1367036.63 1410953.288 2915078.045 2133330.25 3799547.6 4113098.9 139962.4749 25.85762725 22.55167589 9.767165314 10.08093983 20.82756859 15.24215867 27.14690207 29.38715469 1 17.09468055 2.24224263 8.13E-10 9.174033464 28.50604413 0 9.05212852 76704040.01 0.163873874 476891873.3 476891873.9 174.6797775 -2.24224263 19.33201066 NDEELNKLLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NDEELNKLLGR 11 1 Q7L7L0;P04908 Q7L7L0 HIST3H2A;HIST1H2AB Histone H2A type 3;Histone H2A type 1-B/E 0 ;;; 158.4 2.73E-05 2300520000 6065900 4698360 853230 1104380 4256340 3585560 5061000 6310400 213373 FALSE TRUE 5264275.946 4667496.164 1265854.882 1355146.358 4171647.161 3723498.813 4570184.999 4960970.068 188148.287 27.97939875 24.80754004 6.727963895 7.202544227 22.17212406 19.79023499 24.29033541 26.36734113 1 17.52151063 7.999999853 0.045428595 9.999999993 32.79400363 0.027099073 9.348508517 15588.04998 69.49254538 10313.79829 29229.10312 99999966.26 -7.999999853 22.79400363 NDEWAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NDEWAR 6 0 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 0 ;;; 122.54 0.04461 1661230000 2323200 1974920 1939740 1579910 1978150 1980320 2174700 2357230 2294320 FALSE TRUE 2016183.234 1961946.62 2877804.752 1938652.713 1938788.685 2056504.192 1963797.929 1853154.708 2023088.103 0.996586965 0.969778141 1.42248118 0.958264106 0.958331316 1.016517367 0.970693232 0.916002969 1 20.94812772 NDFTEEEEAQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NDFTEEEEAQVR 12 0 E5RJR5;P63208 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 296.74 6.17E-36 369180000 133090 126010 92567 101490 149820 140030 133400 132330 164160 FALSE TRUE 115501.8193 125182.232 137332.7108 124534.8557 146838.8751 145417.0447 120462.8885 104032.2593 144753.1918 0.797922435 0.864797732 0.948737013 0.860325455 1.014408548 1.004586102 0.832195042 0.718687153 1 17.14323563 2.035008917 24.1013695 0.820107161 0.916557668 0.06695994 0.094822778 200.9869285 138365.3502 0.038981029 0.026280828 108.394917 -2.035008917 0.096450507 NDHQEDFWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NDHQEDFWK 9 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ;;;;; 185.08 4.33E-05 4210170000 7698610 6470390 4354160 4982030 7958110 6413680 8239930 9292670 8430120 FALSE TRUE 6681219.183 6427885.582 6459846.34 6113276.057 7799759.181 6660418.42 7440822.857 7305504.836 7433520.817 0.898796055 0.864716161 0.869015706 0.822393077 1.049268492 0.895997816 1.000982312 0.982778553 1 22.82561426 3.24616756 24.99999997 0.982074962 0.864178198 0.679711538 0.041595468 98.29531289 323042.899 0.011325419 0.014338826 1762.655984 -3.24616756 -0.117896764 NDHSAYKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NDHSAYKR 8 1 Q7L576;Q96F07;Q96F07-2;E7EVJ5;A0A087WTQ3;A0A087WWZ1;A0A0G2JR96;A0A0G2JQT1 Q7L576;A0A0G2JR96 CYFIP1;CYFIP2 Cytoplasmic FMR1-interacting protein 1;Cytoplasmic FMR1-interacting protein 2 0 ; 114.89 0.0016673 104044000 135024 130012 56891 64192 119806 134264 143412 155336 60539 FALSE TRUE 117180.2363 129157.9426 84403.67789 78767.77471 117422.095 139429.223 129503.9263 122118.6052 53382.14839 2.195120276 2.419496901 1.581121788 1.475545236 2.19965098 2.611907298 2.425978164 2.287630021 1 15.70406975 NDIASHPPVEGSYAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NDIASHPPVEGSYAPR 16 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;; 161.14 1.00E-08 3477530000 1547760 1606420 730378 1014040 1923240 1833320 1645750 1858410 1623870 FALSE TRUE 1343219.594 1595867.321 1083591.244 1244293.281 1884971.287 1903849.007 1486145.418 1461003.484 1431897.939 0.938069368 1.11451192 0.756751731 0.868981823 1.316414554 1.329598259 1.037885018 1.02032655 1 20.44949723 3.266199961 24.99982424 1.12749588 0.921871944 0.375087906 0.141319539 279.0262624 252377.8295 0.044575074 0.057532855 1845.865109 -3.266199961 -0.205623936 NDIHTLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NDIHTLLK 8 0 O43324;H0YAL7;D6RBD7;C9J1V9;O43324-2;H0YAH9 O43324 EEF1E1;EEF1E1-BLOC1S5 Eukaryotic translation elongation factor 1 epsilon-1 0 134.25 0.00179 0 571630 418550 295260 382980 543340 455400 539300 634980 670780 FALSE TRUE 496087.6472 415800.5175 438048.7236 469941.4625 532528.597 472919.5327 486998.769 499194.4684 591481.1526 0.838720972 0.702981854 0.74059625 0.794516377 0.900330627 0.799551314 0.82335467 0.843973584 1 19.17397267 -1.187022737 0.756878967 10 0.78665914 0.591029612 0.052389263 76.27065037 1.279464422 1143.659159 0.021760683 0.065009565 1.187022737 -9.21334086 NDIYVTLIHGEFDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NDIYVTLIHGEFDK 14 0 Q9H7D0;H0Y7N4 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 0 71.697 0.040695 345510000 251420 261470 137440 154640 264220 257600 265880 261720 216850 FALSE TRUE 218194.21 259752.3864 203906.4437 189753.3755 258962.5389 267510.0387 240094.9985 205753.2147 191214.24 1.141098121 1.358436413 1.066376875 0.992360064 1.35430572 1.399006887 1.255633464 1.076035 1 17.54483044 1.598493756 3.891519639 1.015420894 1.225484136 0.267813948 0.130297962 0.246488252 8.372973568 0.109371446 0.036197457 39.67288247 -1.598493756 0.210063242 NDKS(ph)EEEQSSSSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(0.997)EEEQS(0.003)SSSVK;NDKS(1)EEEQSSSSVK;NDKS(0.838)EEEQS(0.139)S(0.02)S(0.002)SVK;NDKS(0.564)EEEQS(0.406)S(0.028)S(0.002)SVK 281.92 3.32E-33 4125210000 5457730 3084320 3127980 2639400 3525850 2906440 4064220 5720600 5093540 TRUE FALSE 4736477.152 3064058.899 4640681.59 3238716.111 3455692.483 3018252.628 3670072.57 4497294.208 4491387.504 1.054568805 0.682207647 1.033240082 0.721094786 0.769404216 0.672008956 0.817135588 1.001315118 1 22.09872977 1.731658102 5.170439446 1.001556286 0.812109317 0.242165694 0.130972025 0.200343183 13.22864047 0.076457163 0.032364999 53.90860602 -1.731658102 -0.189446969 NDKSEEEQS(ph)SSSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NDKSEEEQSSSSVK 14 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 NDKS(0.437)EEEQS(0.442)S(0.054)S(0.054)S(0.013)VK 130.27 0.00016589 614450000 1380400 818180 719110 707310 894040 689280 1039300 1514700 1400300 TRUE FALSE 1197976.643 812805.3217 1066874.001 867915.5461 876250.3532 715797.0476 938508.846 1190793.192 1234758.129 0.970211586 0.658270881 0.864034807 0.702903286 0.709653439 0.579706285 0.760075049 0.964393888 1 20.23579704 1.716243163 4.035731663 0.990523612 0.739144212 0.45011371 0.107143517 0.150392134 5.62765231 0.070129341 0.027442422 52.02872251 -1.716243163 -0.2513794 NDKSEEEQSSSS(ph)VKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NDKSEEEQSSSSVKK 15 2 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 NDKSEEEQSS(0.003)S(0.125)S(0.872)VKK 111.01 0.00045731 81356000 100350 55703 75568 64328 46508 39619 74120 110270 189550 TRUE FALSE 87088.49325 55337.08333 112112.9376 78934.65559 45582.58179 41143.16857 66931.85381 86689.61862 167141.6149 0.52104614 0.331079027 0.67076615 0.472262133 0.272718328 0.246157539 0.400449965 0.518659693 1 17.35071145 1.219059792 2.756847634 1.146071926 0.414262984 0.686186656 0.123123345 0.298110784 2.540151714 0.515162741 0.033799507 16.55997941 -1.219059792 -0.731808942 NDKSEEEQSSSS(ph)VKKDETNVK ddPTM_MDA-MB-175_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 1 NDKSEEEQSS(0.002)S(0.319)S(0.679)VKKDETNVK 121.84 2.07E-05 1075000000 389970 176730 263220 142030 147520 112540 319010 379040 179420 TRUE FALSE 338434.4764 175569.049 390514.0724 174280.0823 144584.6406 116869.4866 288072.4593 297985.2457 158209.172 2.139158382 1.109727374 2.468340283 1.101580143 0.913882797 0.738702347 1.820832861 1.883489067 1 17.27147372 4.757047682 22.91285251 1.430379466 2.139160342 0.160399236 0.535045615 2625.84092 3254296.137 0.133923368 3.802367036 57154.13833 -4.757047682 0.708780876 NDKSEEEQSSSSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NDKSEEEQSSSSVK 14 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ;;;;; 261.74 1.46E-24 3108690000 3130140 1934840 1738400 1692220 2068900 1766750 2537150 3662110 2809000 FALSE TRUE 2716484.068 1922129.909 2579096.055 2076464.415 2027732.938 1834718.016 2291097.584 2878996.275 2476923.22 1.096717107 0.776015136 1.0412499 0.838324094 0.818649897 0.740724622 0.924977232 1.162327622 1 21.24011772 1.888556073 5.930131123 1.084242309 0.878567558 0.318519568 0.116524848 0.233956003 10.62747685 0.056027028 0.02967587 77.3670564 -1.888556073 -0.205674751 NDKSEEEQSSSSVKK ddPTM_MDA-MB-175_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 0 127.75 4.29E-05 82423000 296300 168870 148530 125780 170810 139360 239260 350070 118420 FALSE TRUE 257143.2043 167760.6819 220359.6048 154340.2714 167411.2152 144721.2694 216056.602 275210.2547 104420.5225 2.46257343 1.606587267 2.110309348 1.478064539 1.603240543 1.385946612 2.069100947 2.635595457 1 16.67204576 2.106263486 18.99141403 2.061918282 1.757997362 0 0.510020411 5.644183548 980.3403752 0.202739567 0.136687096 127.7213457 -2.106263486 -0.30392092 NDLAVVDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NDLAVVDVR 9 0 P19338 P19338 NCL Nucleolin 0 ;;;;; 135.86 0.00048624 1828740000 4930420 4452850 2042750 2808950 5358220 4919080 4457700 5324470 4583550 FALSE TRUE 4278852.505 4423598.935 3030630.733 3446765.03 5251601.905 5108320.191 4025392.94 4185873.526 4041687.941 1.058679583 1.094492945 0.749842832 0.852803354 1.29935858 1.263907621 0.995968269 1.035674596 1 21.9465265 3.26498484 24.9844151 1.106588853 0.936556577 0.292526268 0.138351806 335.0364533 316778.6979 0.043448051 0.056073812 1840.707748 -3.26498484 -0.170032276 NDLQDTEIS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NDLQDTEISPR 11 0 Q9NS91 Q9NS91 RAD18 E3 ubiquitin-protein ligase RAD18 1 NDLQDT(0.232)EIS(0.768)PR 66.246 0.066329 185870000 583170 528490 382320 443620 592460 542150 549740 643440 765060 TRUE FALSE 506102.6069 525018.3144 567211.2308 544350.7013 580671.2051 563006.8613 496426.2994 505845.3633 674615.4784 0.750209005 0.778248248 0.840791901 0.806905146 0.86074397 0.834559656 0.735865564 0.749827686 1 19.36370589 -1.999691089 0.013389892 1.735912641 0.014741744 0.119430799 0.072305555 56258.69826 75.01115227 5622.515443 4130.89945 0.010007115 1.999691089 -1.721170897 NDLSICGTLHSVDQYLNIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NDLSICGTLHSVDQYLNIK 19 0 Q9Y333 Q9Y333 LSM2 U6 snRNA-associated Sm-like protein LSm2 0 192.55 2.89E-21 0 225080 158290 84592 122630 206180 142750 202860 220640 170000 FALSE TRUE 195335.1077 157250.1826 125500.9741 150475.0158 202077.4214 148241.6849 183186.6684 173457.853 149902.7937 1.303078501 1.049014356 0.837215712 1.003817288 1.348056407 0.98891876 1.222036387 1.15713556 1 17.19366774 NDNKLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NDNKLTR 7 1 Q86W56-3;Q86W56-2;Q86W56 Q86W56-3 PARG Poly(ADP-ribose) glycohydrolase 0 63.486 0.072179 150610000 207810 212380 119280 140810 185240 270260 280720 330440 233820 FALSE TRUE 180347.382 210984.8618 176964.207 172783.0626 181554.0864 280657.0771 253495.8176 259777.9775 206178.066 0.874716625 1.023313808 0.858307629 0.838028341 0.880569354 1.361236346 1.229499445 1.259969029 1 17.65353134 2.7525723 24.7666884 1.221642885 0.896914256 0.709171169 0.101015567 366.3431075 647538.0021 0.03221444 0.032054512 565.6819216 -2.7525723 -0.324728629 NDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK 41 0 P68104;A0A087WVQ9;A0A087WV01 P68104 EEF1A1 Elongation factor 1-alpha 1;Elongation factor 1-alpha 0 ; 335.71 1.20E-133 4523400000 1732520 1598440 759490 1231060 1699410 1557380 1766120 2101190 2198170 FALSE TRUE 1503563.092 1587939.742 1126781.904 1510590.989 1665595.066 1617293.416 1594841.954 1651866.87 1938304.847 0.77571033 0.819241486 0.581323369 0.779336125 0.85930501 0.834385478 0.822802438 0.852222432 1 20.88636406 -2 0.38977499 4.319504766 0.740246946 0.51360544 0.071817251 73.10320445 1.068797263 197.3481187 0.078732363 0.01 2 -3.579257821 NDQCYDDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NDQCYDDIR 9 0 Q9ULV4;Q9ULV4-2;Q9ULV4-3;F8W1H8;F8VUX3;F8VSA4;F8VRE9;F8VTT6;F8VVB7 Q9ULV4 CORO1C Coronin-1C;Coronin 0 98.048 0.014605 305690000 467190 423820 215380 319220 465240 466620 455540 498830 406460 FALSE TRUE 405449.6578 421035.8985 319538.4884 391703.78 455982.6342 484571.1733 411361.8009 392159.0864 358408.7618 1.131249291 1.174736623 0.891547647 1.092896775 1.272241872 1.352007052 1.147744823 1.09416713 1 18.45124638 3.460296887 24.64323336 1.171484724 1.062648465 0.155180591 0.117961498 402.6545578 589779.4384 0.036582484 0.047240083 2886.003723 -3.460296887 -0.108836259 NDQDTWDYTNPNLSGQGDPGSNPNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NDQDTWDYTNPNLSGQGDPGSNPNKR 26 1 A0A3B3ITJ4;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;; 250.4 7.73E-46 4598340000 1079225 798432 507245 596082 914740 726110 901471 1082038 1033721 FALSE TRUE 936602.6818 793187.0476 752550.3786 731431.5286 896538.4637 754043.9216 814046.4812 850652.5941 911515.681 1.027522292 0.870184753 0.825603327 0.802434389 0.983568887 0.827241854 0.893069092 0.9332287 1 19.79790795 1.386389224 2.06081354 1.015077641 0.884390585 0.201813713 0.069965327 0.82331664 4.684925041 0.185673149 0.018736115 24.3438478 -1.386389224 -0.130687057 NDQWHWDNIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NDQWHWDNIR 10 0 O75116;E9PF63;C9JFJ0;D6REE7 O75116 ROCK2 Rho-associated protein kinase 2 0 ; 124.12 0.00044388 333230000 391020 417830 192193 237270 501260 460400 421960 466270 393400 FALSE TRUE 339345.7163 415085.2472 285138.1776 291145.7799 491285.9067 478111.8859 381038.3841 366561.789 346892.7002 0.97824404 1.196581096 0.821978028 0.839296358 1.416247463 1.378270242 1.098432985 1.056700786 1 18.40412996 3.259623895 24.99847329 1.175831428 0.966204161 0.328257238 0.163301408 350.7745989 416306.2338 0.051507163 0.066428719 1818.125654 -3.259623895 -0.209627267 NDRGPGGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NDRGPGGPR 9 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 90.108 0.010628 50249000 42130 33076 13673 17106 42092 41885 37973 41936 15358 FALSE TRUE 36562.41376 32858.72158 20285.30853 20990.17875 41254.45155 43496.34305 34290.3843 32968.31275 13542.39474 2.699848474 2.426359755 1.497911479 1.549960635 3.04631879 3.211864955 2.532076857 2.434452207 1 13.72519526 3.244388232 24.99694489 2.488512448 2.031893882 0.076967725 0.681015665 379.119903 1626185.319 0.207228498 0.260322919 1755.449062 -3.244388232 -0.456618566 NDS(ph)GEENVPLDLTR ddPTM_MDA-MB-175_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 265.27 9.88E-25 299562000 293290 350580 277070 287498 468520 452350 556490 503250 480740 TRUE FALSE 254530.9834 348277.0169 411061.9787 352778.815 459197.3686 469752.1972 502521.6855 395633.9038 423907.4649 0.600439965 0.821587365 0.969697429 0.832207131 1.083249074 1.108147971 1.185451371 0.933302517 1 18.69338985 5.21245871 0.693171595 1.049290271 4.80E-16 0.716056597 0.08950048 3.15681962 0.734148494 0.040033263 3.010330942 163101.7836 -5.21245871 -1.049290271 NDS(ph)PTQIPVSSDVCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NDSPTQIPVSSDVCR 15 0 Q8TC07-2;Q8TC07-3;Q8TC07 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 NDS(0.997)PT(0.003)QIPVSSDVCR;NDS(1)PTQIPVSSDVCR;NDS(0.999)PT(0.001)QIPVSSDVCR;NDS(0.887)PT(0.113)QIPVSSDVCR 357.45 1.21E-82 2755720000 1802030 1838270 1086597 1147150 1982230 1816870 1774000 2036560 1907730 TRUE FALSE 1563887.17 1826194.283 1612078.944 1407627.941 1942787.501 1886766.165 1601957.753 1601057.493 1682200.333 0.929667614 1.085598575 0.958315673 0.836777828 1.154908523 1.121606106 0.952299035 0.951763866 1 20.6819181 5.106358858 10.40948996 1.002318031 8.66E-05 0.061626849 0.093601972 184909.7254 517326.6285 0.023416713 4002238.731 127749.3969 -5.106358858 -1.002231392 NDS(ph)WGSFDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NDSWGSFDLR 10 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 NDS(0.999)WGS(0.001)FDLR;NDS(0.997)WGS(0.003)FDLR;NDS(0.519)WGS(0.481)FDLR;NDS(1)WGSFDLR;NDS(0.999)WGS(0.001)FDLR;NDS(0.941)WGS(0.059)FDLR 242.48 2.41E-12 1887746000 2583570 2223130 1244979 1694189 2701680 2248930 2481170 2798100 2507650 TRUE FALSE 2242144.679 2208526.113 1847055.009 2078880.507 2647921.854 2335447.792 2240546.515 2199748.09 2211198.474 1.013995218 0.998791442 0.835318507 0.940160068 1.197505283 1.056190939 1.013272459 0.994821639 1 21.07639709 NDSDPTYGQQGHPNTWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NDSDPTYGQQGHPNTWK 17 0 Q93052;A0A087WZF1;C9JUT4;C9JXK9 Q93052 LPP Lipoma-preferred partner 0 ; 237.86 3.13E-20 809570000 1337140 1088650 601920 808570 1329880 1096520 1378150 1422460 1380000 FALSE TRUE 1160433.561 1081498.586 893010.5253 992168.1767 1303417.99 1138703.834 1244497.225 1118277.999 1216857.972 0.953631063 0.888763201 0.733865863 0.815352489 1.071134035 0.935773821 1.022713623 0.918988102 1 20.21472936 3.255744571 24.98956022 0.980657173 0.842676175 0.505762227 0.069256242 211.282177 307252.7351 0.020251807 0.026079315 1801.957612 -3.255744571 -0.137980997 NDSWGSFDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NDSWGSFDLR 10 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 0 ; 128.81 0.00074382 202126000 329670 300010 127414 180139 359210 339550 329890 327630 307040 FALSE TRUE 286103.2742 298039.2146 189031.8366 221042.3132 352062.4238 352612.7082 297897.3186 257568.8741 270742.081 1.056737369 1.100823387 0.69819895 0.816431315 1.300360928 1.302393433 1.100299287 0.951344073 1 18.04655962 3.254745603 24.9999596 1.114719827 0.915399682 0.31000872 0.156728199 366.137876 565547.6411 0.050673143 0.065213671 1797.817498 -3.254745603 -0.199320146 NDSYTLHK ddPTM_MDA-MB-175_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 ; 111.46 0.0032301 1504500000 1579110 1526000 672270 1001370 1758770 1714810 1847530 2035070 1911200 FALSE TRUE 1370426.613 1515975.606 997382.0206 1228746.363 1723773.918 1780779.85 1668356.825 1599886.117 1685260.113 0.813184031 0.899549923 0.591826753 0.729113775 1.02285333 1.056679522 0.989969923 0.94934076 1 20.68453985 3.238099878 24.99999997 0.998575867 0.756599981 0.697292856 0.08028269 7.378842977 400387.6524 0.02500118 0.03012084 1730.214224 -3.238099878 -0.241975886 NDTKEDVFVHQTAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NDTKEDVFVHQTAIK 15 1 P67809;P16989;P16989-3;P16989-2;Q9Y2T7 P67809;P16989;P16989-2;Q9Y2T7 YBX1;YBX3;YBX2 Nuclease-sensitive element-binding protein 1;Y-box-binding protein 3;Y-box-binding protein 2 0 ; 264 2.56E-25 686910000 2026890 1511100 554380 1045650 1755590 1235910 2182690 2465900 1265300 FALSE TRUE 1759031.351 1501173.485 822480.0223 1283080.814 1720657.194 1283456.257 1971013.06 1938586.475 1115717.675 1.576591811 1.345477909 0.737175757 1.150004918 1.542197665 1.150341422 1.766587644 1.737524212 1 20.08954058 2.251599941 24.99099417 1.561620021 1.240010188 0.115983865 0.311463046 379.9878165 728279.3136 0.118978102 0.091580261 178.4842673 -2.251599941 -0.321609833 NECDPALALLSDYVLHNSNTMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NECDPALALLSDYVLHNSNTMR 22 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;;; 146.5 6.45E-08 270195000 321060 346699 103736 171125 456120 459596 391472 441080 368380 FALSE TRUE 278631.1075 344421.5114 153903.0766 209981.5467 447044.1044 477276.9555 353507.1057 346758.4745 324830.5361 0.857773752 1.060311372 0.473794978 0.646434135 1.376237929 1.469310617 1.088281631 1.067505779 1 18.30932774 3.244568978 24.9999888 1.188725278 0.760646321 0.538792323 0.202443606 128.0614212 532843.2145 0.0640377 0.080505146 1756.1798 -3.244568978 -0.428078957 NEDEEEEEEEKDEAEDLLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NEDEEEEEEEKDEAEDLLGR 20 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 303.06 4.68E-55 654350000 1291730 680720 630720 621650 764950 582060 872720 1094510 998750 FALSE TRUE 1121024.608 676248.3055 935738.3016 762805.1338 749728.9916 604452.2248 788083.7487 860457.554 880678.9128 1.27290956 0.767871577 1.062519254 0.866155784 0.851307986 0.686348016 0.894859338 0.977038897 1 19.7482566 4.750564077 24.69843603 0.892797497 1.272909834 0.548644558 0.109573804 1311.034836 2697538.97 0.027231974 0.439296377 56307.21879 -4.750564077 0.380112337 NEDS(ph)PGPPVGSHHAFFSDDQEPYPVTDISDLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NEDSPGPPVGSHHAFFSDDQEPYPVTDISDLIR 33 0 J3KQ40;O95759-2;O95759 J3KQ40 TBC1D8 TBC1 domain family member 8 1 NEDS(0.645)PGPPVGS(0.177)HHAFFS(0.177)DDQEPYPVTDISDLIR 63.433 0.017397 17486000 10330 9089.5 4173.6 8368 10856 12163 8919 15766 17162 TRUE FALSE 8964.864327 9029.790476 6191.96692 10268.0823 10639.98684 12630.91848 8054.036753 12394.56359 15133.12791 0.592399957 0.59669029 0.409166364 0.678516851 0.703092375 0.83465352 0.532212296 0.819035144 1 13.88542259 -2 0.439620229 9.09947417 0.571775615 0.56787942 0.110814208 72.82216918 0.96060899 550.1165431 0.094199633 0.01 2 -8.527698555 NEEDAAELVALAQAVNAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NEEDAAELVALAQAVNAR 18 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 220.6 1.56E-18 104472000 168311 142928 82434 107301 158799 144432 156760 180993 173406 FALSE TRUE 146068.2749 141989.0966 122299.3581 131665.332 155639.2106 149988.3925 141557.4393 142289.0554 152906.1402 0.955280636 0.928602974 0.799832878 0.86108597 1.01787417 0.980918047 0.925779953 0.930564693 1 17.22228682 3.253708299 24.99998987 0.963070521 0.883060219 0.417280999 0.049252838 270.4443511 446343.3934 0.015190351 0.019533929 1793.52857 -3.253708299 -0.080010303 NEEDDMVEMEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NEEDDMVEMEEER 13 0 P80303-2;P80303;E9PKG6;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 ;;;;; 420.87 1.22E-145 1811490000 1344250 1228370 968730 1199430 1439930 1385770 1201760 1569190 1880200 FALSE TRUE 1166603.957 1220300.757 1437211.068 1471778.914 1411278.21 1439081.469 1085213.5 1233630.93 1657924.898 0.703653077 0.736041034 0.866873445 0.887723512 0.851231688 0.868001603 0.654561314 0.74408131 1 20.66094723 4.372235596 5.642982716 0.823543373 0.711645437 0.217214815 0.091220137 0.345159441 15.56050089 0.024235463 0.066762261 23563.272 -4.372235596 -0.111897936 NEEDEGHS(ph)NSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 2 NEEDEGHS(0.96)NS(0.082)S(0.958)PR;NEEDEGHS(1)NS(0.011)S(0.989)PR 209.9 5.00E-08 275788000 524970 425900 296240 333000 382350 419060 395620 433680 662290 TRUE FALSE 455593.8844 423102.2349 439502.6549 408612.7396 374741.9831 435181.5094 357252.8333 340940.9069 583994.8307 0.78013342 0.724496541 0.752579701 0.699685542 0.641687158 0.745180413 0.611739718 0.58380809 1 19.15559607 1.226693057 24.96689194 1.000000715 0.686715092 0.697742835 0.063524014 340.9888462 717323.5056 0.278431903 0.017229866 16.85361454 -1.226693057 -0.313285624 NEEDEGHSNS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 NEEDEGHS(0.052)NS(0.474)S(0.474)PR;NEEDEGHS(0.004)NS(0.498)S(0.498)PR 115.8 0.00040935 229060000 168989 130133 95240 114752 123433 137051 138600 158176 223626 TRUE FALSE 146656.6755 129278.1478 141298.3826 140808.1955 120976.9248 142323.4407 125158.5933 124351.2933 197189.189 0.743735882 0.655604642 0.716562522 0.71407665 0.613506883 0.72176087 0.634713262 0.630619224 1 17.58922093 1.233742689 24.99998392 1.000000493 0.675351557 0.836560248 0.044591227 56.24557373 291820.1641 0.085341563 0.010720115 17.12942123 -1.233742689 -0.324648937 NEEDEGHSNSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 NEEDEGHSNS(0.043)S(0.957)PR;NEEDEGHS(0.007)NS(0.036)S(0.957)PR;NEEDEGHSNS(0.042)S(0.958)PR;NEEDEGHSNS(0.057)S(0.943)PR;NEEDEGHSNS(0.019)S(0.981)PR;NEEDEGHS(0.002)NS(0.322)S(0.677)PR;NEEDEGHSNS(0.041)S(0.959)PR;NEEDEGHSNS(0.252)S(0.748)PR;NEEDEGHSNS(0.094)S(0.906)PR;NEEDEGHSNS(0.031)S(0.969)PR 276.14 3.34E-32 54329340000 26302190 21574554 15059902 19802890 20805827 21786306 21587305 25585210 35107130 TRUE FALSE 22826288.95 21432829.33 22342920.98 24299438.84 20391831.75 22624439.29 19493771.48 20114011.95 30956805.09 0.737359327 0.692346296 0.721745055 0.784946598 0.658718873 0.730838962 0.629708765 0.649744439 1 24.88375325 1.233012184 24.99959454 1.00000048 0.69762501 0.804495651 0.046350788 80.62225384 363220.7861 0.101352182 0.01192828 17.10063288 -1.233012184 -0.30237547 NEEDEGHSNSSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;;;;; 256.52 7.18E-24 3533600100 5749950 4738865 2734187.6 4233675.2 4926263 5042977 4723393.9 5928931 8731977 FALSE TRUE 4990079.539 4707735.084 4056449.869 5194995.862 4828240.004 5236983.588 4265319.887 4661075.245 7699692.627 0.648088149 0.611418574 0.526832702 0.67470172 0.627069188 0.68015489 0.553959761 0.605358612 1 22.87636942 1.237800175 24.99997423 1.000000447 0.613809521 0.863698391 0.047940372 6.334453118 208109.5119 0.067031154 0.01148391 17.2902063 -1.237800175 -0.386190926 NEEPS(ph)EEEIDAPKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NEEPSEEEIDAPKPK 15 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 NEEPS(1)EEEIDAPKPK;NEEPS(1)EEEIDAPKPK;NEEPS(1)EEEIDAPKPK;NEEPS(1)EEEIDAPKPK;NEEPS(1)EEEIDAPKPK 207.07 2.17E-09 5018830000 4590510 3446090 3413450 3368060 3576990 2124020 5100420 5724390 4951710 TRUE FALSE 3983862.473 3423452.408 5064205.837 4132829.501 3505814.897 2205732.424 4605782.053 4500273.746 4366324.485 0.912406416 0.784058175 1.159832682 0.946523676 0.802921292 0.505169149 1.054841909 1.030677807 1 22.05798792 NEEPVRS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NEEPVRSPER 10 1 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 1 NEEPVRS(1)PER;NEEPVRS(1)PER 94.551 0.0048609 851750000 582610 419930 338200 384670 465410 460430 440570 454200 760430 TRUE FALSE 505616.6124 417171.4522 501754.6512 472015.2028 456149.2516 478143.04 397843.5892 357072.8646 670532.8317 0.754051984 0.622149181 0.748292444 0.703940479 0.680278772 0.713079237 0.593324548 0.532521075 1 19.35494845 NEEPVRS(ph)PERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NEEPVRSPERR 11 2 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 1 NEEPVRS(1)PERR;NEEPVRS(1)PERR;NEEPVRS(1)PERR;NEEPVRS(1)PERR 91.076 0.0057453 3554250000 3031600 2305670 1329960 1599830 2516980 2644960 2437640 2640910 2274350 TRUE FALSE 2630966.379 2290523.902 1973133.104 1963095.853 2466897.022 2746713.323 2201238.048 2076171.948 2005478.934 1.311889312 1.142133115 0.983871269 0.978866355 1.230078751 1.369604675 1.097612152 1.035249941 1 20.93551538 1.813939882 3.657267831 1.017014018 1.158313249 0.195146449 0.123925755 0.423870522 9.98988551 0.084109334 0.036525607 65.15381969 -1.813939882 0.141299232 NEFNLESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NEFNLESK 8 0 H3BMH2;H3BSC1;P62491-2;Q15907-2;P62491;Q15907 H3BMH2 RAB11A;RAB11B Ras-related protein Rab-11A;Ras-related protein Rab-11B 0 98.055 0.018133 91339000 109320 88720 58397 79178 106670 93745 99421 125240 134020 FALSE TRUE 94873.08502 88137.19248 86637.98453 97156.57506 104547.4757 97351.43081 89779.16672 98458.40062 118176.3083 0.802809687 0.745811015 0.733124818 0.822132426 0.884673732 0.823781283 0.759705291 0.833148387 1 16.85058131 1.249788297 3.377643594 1.028632728 0.797072512 0.679300882 0.043738001 0.198904431 3.224856129 0.118600256 0.012284564 17.77412776 -1.249788297 -0.231560216 NEFSHDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NEFSHDSR 8 0 P57735 P57735 RAB25 Ras-related protein Rab-25 0 ;;; 154.56 0.00042313 3004400000 6324800 5134700 6396433 4381750 5031240 5773470 5086870 5959640 5592310 FALSE TRUE 5488961.655 5100969.818 9489769.394 5376693.308 4931128.167 5995579.127 4593546.13 4685217.364 4931193.483 1.113110178 1.034429056 1.924436635 1.090343205 0.999986755 1.215847471 0.931528269 0.95011834 1 22.23350543 3.499422802 24.98776975 1.016873032 1.355428039 0.287367466 0.244365315 965.5024151 1081795.084 0.066692515 0.097993024 3158.077636 -3.499422802 0.338555007 NEFWFS(ph)DGSLSDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NEFWFSDGSLSDK 13 0 Q9P2F8;Q9P2F8-2 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 NEFWFS(0.999)DGS(0.001)LSDK 166.92 3.44E-05 35337000 103380 120460 75369 77874 117480 83047 113460 122590 136460 TRUE FALSE 89718.07107 119668.6903 111817.7005 95556.48193 115142.3778 86241.87183 102456.6667 96375.0825 120327.8543 0.745613488 0.994521934 0.92927528 0.794134347 0.956905436 0.71672409 0.851479213 0.800937431 1 16.87661112 3.754854163 24.64260616 0.846405558 0.900275399 0.02186668 0.100602542 2126.75841 3216530.531 0.025037097 0.043178056 5686.619404 -3.754854163 0.053869842 NEGNLENEGKPEDEVEPDDEGKS(ph)DEEEKPDVEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NEGNLENEGKPEDEVEPDDEGKSDEEEKPDVEGK 34 3 Q969E4 Q969E4 TCEAL3 Transcription elongation factor A protein-like 3 1 NEGNLENEGKPEDEVEPDDEGKS(1)DEEEKPDVEGK 187.18 3.23E-20 236860000 293910 147870 319560 150280 113780 70237 256630 266240 311730 TRUE FALSE 255069.0488 146898.6322 474100.2849 184403.3709 111516.0006 72939.06284 231742.0621 209306.6479 274877.6345 0.927936714 0.53441464 1.724768498 0.67085622 0.405693249 0.265351028 0.843073546 0.761453904 1 18.06843 3.528520357 24.99974929 0.651673946 1.04094997 0.226084419 0.352250889 552.8535033 268898.0242 0.097353468 0.144396661 3376.916768 -3.528520357 0.389276024 NEGS(ph)ESAPEGQAQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NEGSESAPEGQAQQR 15 0 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NEGS(1)ESAPEGQAQQR;NEGS(1)ESAPEGQAQQR;NEGS(0.992)ES(0.008)APEGQAQQR;NEGS(0.999)ES(0.001)APEGQAQQR 353 2.05E-82 982770000 1002483 710760 627573 772917 855829 921156 830963 849341 2342430 TRUE FALSE 870002.3316 706090.9708 931069.4019 948419.6181 838799.6773 956593.4674 750376.3362 667716.0367 2065510.594 0.421204488 0.341848148 0.450769609 0.459169573 0.406097979 0.463126875 0.363288544 0.323269238 1 20.97806703 1.234015622 24.99999867 1.000000896 0.401161614 0.937399221 0.048432555 33.95801374 186764.2155 0.099952963 0.01284235 17.1401896 -1.234015622 -0.598839282 NEGSES(ph)APEGQAQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NEGSESAPEGQAQQR 15 0 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NEGSES(1)APEGQAQQR 216.53 9.16E-12 0 157330 131700 92122 122200 152970 123270 133730 165770 373360 TRUE FALSE 136538.4419 130834.854 136672.5073 149947.3777 149926.1963 128012.2767 120760.8852 130321.3755 329221.8061 0.414730857 0.397406404 0.415138076 0.455460042 0.455395704 0.388832921 0.366807067 0.39584673 1 18.32870037 1.237717417 24.99999613 1.000000687 0.410158316 0.978266876 0.02758004 3.048017678 90316.04078 0.044400412 0.007573721 17.28691184 -1.237717417 -0.58984237 NEHFQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NEHFQK 6 0 P15924 P15924 DSP Desmoplakin 0 ; 95.62 0.043138 183458000 708410 598220 302870 373970 595290 609320 638940 733140 651510 FALSE TRUE 614791.8236 594290.2534 449338.945 458885.6043 583444.8937 632760.9347 576975.6971 576363.7163 574489.23 1.070153784 1.03446718 0.782153819 0.798771466 1.015588915 1.101432197 1.004328135 1.003262875 1 19.13192032 3.039804199 24.97085093 1.025485691 0.917976142 0.237252169 0.092342685 239.749494 150403.4231 0.030161313 0.034199665 1095.983963 -3.039804199 -0.107509548 NEKAPVDFGYVGIDSILEQMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NEKAPVDFGYVGIDSILEQMR 21 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4;K7EL40;K7EK18;K7EIE4;K7EQD7;K7ER52;K7ELJ9;K7EJZ2;K7ENQ5;K7ER14;K7EN52;K7EKN4;K7EIR4;K7EJL9;K7EQ08 Q9UHD8 9-Sep Septin-9 0 114.2 0.00016682 116070000 153510 148870 40261 51449 160850 120280 177830 193960 28347 FALSE TRUE 133223.2646 147892.0632 59731.35426 63131.2818 157649.3997 124907.2494 160584.074 152483.1634 24995.84995 5.329815342 5.916664704 2.389650857 2.525670538 6.307022966 4.997119508 6.424429426 6.100339204 1 14.60940096 3.224629056 24.99515294 5.218566911 4.056550948 0.047877076 1.869791822 642.143882 1152092.269 0.574330128 0.654437272 1677.370711 -3.224629056 -1.162015963 NEKDNALLSAIEESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NEKDNALLSAIEESR 15 1 H3BVG0;Q8N1F7;H3BM93;H3BNN5;H3BV11;H3BRI8 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 190.46 1.97E-07 314260000 428780 345260 171280 246430 388010 307680 396180 479150 310260 FALSE TRUE 372115.6366 342991.9643 254111.5809 302385.6979 380289.3601 319516.6487 357758.5246 376687.5012 273581.4162 1.360164158 1.253710756 0.928833487 1.105285959 1.390040908 1.167903336 1.307685769 1.376875324 1 18.06161071 3.268292158 24.99975237 1.264956955 1.151894799 0.064589937 0.154664683 488.2407119 410533.6539 0.044955614 0.058029212 1854.778946 -3.268292158 -0.113062156 NELMYQLEQDHDLQAILQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NELMYQLEQDHDLQAILQER 20 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;; 220.86 8.23E-25 4617355000 358071 334673 183963 223333 391918 388218 348458 405397 384123 FALSE TRUE 310751.0101 332474.511 272928.1221 274044.1711 384119.5986 403152.9977 314664.5968 318706.0064 338712.4165 0.917447944 0.981583476 0.805781273 0.809076248 1.134058215 1.190251606 0.929002249 0.940933933 1 18.36970135 3.247491582 24.99997733 1.025941397 0.880645117 0.418444407 0.093245954 238.0652043 666399.6404 0.030351963 0.038602811 1768.037946 -3.247491582 -0.14529628 NELVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NELVIR 6 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 100.07 0.088599 144500000 193740 232180 143840 143750 198720 225420 251000 223710 266820 FALSE TRUE 168136.7681 230654.7943 213401.5051 176390.6346 194765.8608 234092.0533 226658.0586 175871.3574 235276.8436 0.714633729 0.980354848 0.907022986 0.749715237 0.827815682 0.994964272 0.963367475 0.747508147 1 17.84399981 NENEEILERPAQLANAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NENEEILERPAQLANAR 17 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;; 323.98 5.94E-59 1949440000 1112710 989240 594550 710060 1147420 1085670 1025710 1239490 948620 FALSE TRUE 965662.5543 982741.6173 882076.3687 871289.9756 1124588.587 1127436.427 926236.8021 974434.7092 836475.2243 1.154442506 1.174860401 1.054515834 1.04162078 1.344437413 1.347841986 1.107309308 1.164929553 1 19.67396328 0.981694489 1.914984222 0.806386696 1.177815002 0.21685475 0.10337799 3.400425703 6.442328312 2.917408113 0.030208433 9.58725963 -0.981694489 0.371428306 NENESEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NENESEKR 8 1 P47813;O14602;A6NJH9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 102.07 0.0080756 64571000 146950 136280 75021 90331 72712 101450 154920 185590 180840 FALSE TRUE 127530.1852 135384.7677 111301.4065 110842.0342 71265.17346 105352.8471 139895.8822 145903.0228 159461.3012 0.799756331 0.849013313 0.69798381 0.695103033 0.446912028 0.660679716 0.877303027 0.91497449 1 17.28284682 2.122728736 3.936330024 0.937825779 0.688258689 0.533630074 0.106693205 0.19519329 5.615945889 0.052735376 0.033601143 132.6565614 -2.122728736 -0.24956709 NENLAANFLLQQNFDED ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NENLAANFLLQQNFDED 17 0 P54727;P54727-2 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 ;; 268.44 1.33E-27 598700000 1082500 918683 509829 671705 1100680 1063570 932734 1059580 1235350 FALSE TRUE 939444.8823 912648.1109 756384.0097 824225.8866 1078778.621 1104486.226 842277.6002 832997.0627 1089308.33 0.862423298 0.837823494 0.694370904 0.756650678 0.990333583 1.013933517 0.773222399 0.764702738 1 20.05498094 3.273160118 24.99948358 0.885605186 0.784714205 0.257552589 0.097512669 332.6697553 240364.6864 0.031062105 0.040099085 1875.68592 -3.273160118 -0.100890981 NENLAANFLLSQNFDDE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NENLAANFLLSQNFDDE 17 0 P54725-2;P54725;K7EQ16;P54725-3 P54725-2;P54725-3 RAD23A UV excision repair protein RAD23 homolog A 0 ;;; 225.32 5.66E-15 194586000 540059 500899 301498 434139 623640 605330 532085 625130 918710 FALSE TRUE 468688.8348 497608.5615 447303.4413 532716.8953 611230.7841 628617.4368 480483.4786 491450.8143 810101.1504 0.578555943 0.614254851 0.552157519 0.657593061 0.754511685 0.775974008 0.593115413 0.606653643 1 19.62774253 3.497657843 4.504879772 0.718303986 0.5862352 0.292772743 0.112664773 0.315767187 15.82379347 0.032857284 0.046881057 3145.269354 -3.497657843 -0.132068786 NENQLIIFADDTYPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NENQLIIFADDTYPR 15 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 228.93 1.23E-12 32015000 63972 58021 29778 35282 66381 60696 59911 66563 66146 FALSE TRUE 55517.93812 57639.85623 44178.7404 43293.31735 65060.14797 63031.0144 54100.84044 52329.02044 58326.29523 0.951850926 0.988231054 0.757441223 0.742260711 1.115451405 1.080662061 0.927554891 0.897177169 1 15.83185882 3.240490242 24.99939317 0.988873685 0.861787453 0.343674543 0.097760095 75.20510486 974315.7061 0.031985656 0.039216426 1739.763608 -3.240490242 -0.127086232 NENTFLDLTVQQIEHLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NENTFLDLTVQQIEHLNK 18 0 A0A087WYS1;E7EUC7;Q16851;Q16851-2;C9JVG3;C9JQU9;C9JNZ1;C9JWG0 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 257.81 1.23E-30 559320000 976560 765020 477450 614320 923000 716350 951470 1081700 931170 FALSE TRUE 847505.1217 759994.5332 708346.417 753810.7453 904634.1058 743908.448 859196.5858 850386.8728 821088.1434 1.032173133 0.925594334 0.862692298 0.918063123 1.101750297 0.906003155 1.046412121 1.035682807 1 19.64717758 3.28157656 24.99996852 1.016718831 0.928846686 0.297049756 0.063411181 167.4612475 97323.79506 0.017777348 0.022950288 1912.390424 -3.28157656 -0.087872144 NEQEEQEEKREIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NEQEEQEEKREIK 13 2 Q9C0D0;Q4VY13;Q4VY12 Q9C0D0 PHACTR1 Phosphatase and actin regulator 1;Phosphatase and actin regulator 0 53.252 0.082297 1456100000 639120 656860 267360 420530 730450 572560 593400 772590 439620 FALSE TRUE 554658.6727 652545.0434 396656.1903 516017.7639 715915.4741 594586.7537 535852.1593 607377.6408 387648.6244 1.43082843 1.683341568 1.023236419 1.331148188 1.846815464 1.533829134 1.3823141 1.566825219 1 18.56439002 1.231818344 24.83301412 0.999999115 1.476159236 0.318418542 0.218297921 274.3037168 1010208.294 0.507106884 0.053498865 17.05368921 -1.231818344 0.476160121 NEQEHHAGGDS(ph)QKDIMQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NEQEHHAGGDSQKDIMQR 18 1 Q86SF2;E9PBY3 Q86SF2 GALNT7 N-acetylgalactosaminyltransferase 7 1 NEQEHHAGGDS(1)QKDIMQR 114.88 0.0001241 112390000 70986 75277 45835 51562 83208 63213 64144 90924 101840 TRUE FALSE 61605.02024 74782.50043 68000.95931 63269.94018 81552.32359 65644.84501 57923.32475 71480.61017 89800.59122 0.686020208 0.832761783 0.757244005 0.704560397 0.908149072 0.731006824 0.645021641 0.795992646 1 16.45443732 1.26039091 4.34905618 1.017044966 0.756245397 0.518599217 0.074346726 0.1570745 5.716978767 0.121573257 0.018289133 18.21339516 -1.26039091 -0.260799569 NES(ph)SPIRFDILLDDLDTVPVSTLQR ddPTM_MDA-MB-175_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 105.02 0.0025767 49643000 38829 36335 20630.9 25211 43988 38034 39154 43647 35761 TRUE FALSE 33697.64927 36096.31299 30608.07225 30935.54288 43112.72486 39497.19259 35356.85111 34313.42871 31533.37532 1.068634389 1.144701848 0.97065639 0.98104128 1.367209327 1.252552009 1.121251713 1.088162252 1 14.94459198 4.76567685 20.55861644 1.117202073 1.068633654 0.014120657 0.123013508 4795.630005 3635212.98 0.031688369 1.624368106 58301.1136 -4.76567685 -0.048568419 NESEDNKFS(ph)DDS(ph)DDDFVQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NESEDNKFSDDSDDDFVQPR 20 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 2 NESEDNKFS(1)DDS(1)DDDFVQPR;NESEDNKFS(1)DDS(1)DDDFVQPR 157.43 3.98E-09 184705000 430920 360990 257266 266749 426060 323750 484980 498440 436740 TRUE FALSE 373972.8302 358618.6329 381680.6981 327318.4375 417582.2396 336204.872 437946.7142 391852.4849 385109.0947 0.971082832 0.931213097 0.991097596 0.849936919 1.084321937 0.873012029 1.137201692 1.017510337 1 18.55490767 2.242035872 24.9999996 1.048042724 0.952661954 0.3007197 0.07279901 107.7478529 775115.3616 0.025614628 0.019034038 174.596636 -2.242035872 -0.09538077 NETDEDGWTTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NETDEDGWTTVR 12 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 101.89 0.0027683 0 90437 100770 68155 60093 92329 106420 73601 90049 103440 FALSE TRUE 78485.52131 100108.0352 101114.986 73738.03411 90491.83354 110514.0463 66463.18635 70792.72211 91211.44104 0.860478909 1.097538139 1.10857788 0.808429658 0.992110557 1.211624825 0.728671596 0.776138621 1 16.47692718 2.215766263 24.99900991 0.818259423 1.011042649 0.276226267 0.135046341 284.5541404 312073.7011 0.054620362 0.036853071 164.3486962 -2.215766263 0.192783226 NFAFLEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NFAFLEFR 8 0 P26368-2;P26368;K7ENG2 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ;; 149.65 0.0011673 1250364000 1015020 987769 530344 662243 1050482 1066131 915665 1024973 1714312 FALSE TRUE 880882.5353 981280.2804 786820.1323 812615.3949 1029579.463 1107145.749 826863.9492 805790.5003 1511647.988 0.582729936 0.649146023 0.520504865 0.537569197 0.681097366 0.732409766 0.546995038 0.533054326 1 20.52769079 1.233039699 24.99312866 1.000000642 0.596603766 0.764287802 0.070167523 91.91639727 416059.1183 0.155489371 0.018305135 17.10171636 -1.233039699 -0.403396875 NFDEILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 NFDEILR 7 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;;;;;;; 217.38 8.20E-05 25248120000 30981360 33278070 16615070 21385260 36940650 34861060 33939990 37081500 34764920 FALSE TRUE 26887094.78 33059464.17 24650173.43 26241110.14 36205603.34 36202187.54 30648494.99 29151909.79 30655050.76 0.877085313 1.078434494 0.804114585 0.856012614 1.181064863 1.180953436 0.999786144 0.950965961 1 24.86962146 3.260294272 24.9983465 1.049817991 0.909249281 0.372324749 0.101502414 321.2968434 369557.6117 0.03187649 0.041115817 1820.934283 -3.260294272 -0.14056871 NFDFEGSLS(ph)PVIAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NFDFEGSLSPVIAPK 15 0 Q9H1A4;H0Y564 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 NFDFEGS(0.02)LS(0.98)PVIAPK;NFDFEGS(0.126)LS(0.874)PVIAPK;NFDFEGSLS(1)PVIAPK;NFDFEGS(0.004)LS(0.996)PVIAPK 274.79 1.81E-33 1054640000 1304530 1162920 635915 864960 1409000 1055570 1511210 1813720 1507740 TRUE FALSE 1132133.055 1155280.702 943445.621 1061362.388 1380963.657 1096178.461 1364653.087 1425870.092 1329496.695 0.851550109 0.868960943 0.70962615 0.798318937 1.038711613 0.824506345 1.026443384 1.072488633 1 20.34244876 2.607004058 0.887357295 1.056241359 0.809087148 0.514897804 0.083598593 0.486943116 0.850187279 0.077183122 0.046155872 404.5796722 -2.607004058 -0.247154211 NFDLRPGVIVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NFDLRPGVIVR 11 1 P31153;P31153-2;Q00266 P31153 MAT2A;MAT1A S-adenosylmethionine synthase isoform type-2;S-adenosylmethionine synthase isoform type-1 0 69.554 0.049416 788800000 1439500 1422400 636090 893750 1795200 1627600 1364800 1672300 1654600 FALSE TRUE 1249266.428 1413056.161 943705.2516 1096689.598 1759479.032 1690214.825 1232441.906 1314691.659 1458995.073 0.8562513 0.968513319 0.646818669 0.751674641 1.20595269 1.158478775 0.844719718 0.901093968 1 20.47654358 3.27464307 24.99990948 1.00045179 0.806078887 0.390473955 0.132729406 223.2013814 154644.7458 0.041913682 0.054108548 1882.101626 -3.27464307 -0.194372903 NFEATLGWLQEHACSR ddPTM_MDA-MB-175_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 ; 208.43 1.49E-11 1370090000 782320 758900 339280 472030 838640 874170 774820 817940 724720 FALSE TRUE 678934.4299 753914.7359 503356.9428 579211.626 821952.7048 907799.8856 699678.0757 643029.8962 639044.4272 1.062421329 1.179753244 0.787671281 0.906371453 1.286221536 1.420558332 1.094881742 1.006236607 1 19.28555671 3.251339157 24.99983869 1.150108372 0.984005464 0.234086857 0.158812271 418.7363427 819208.1101 0.051123355 0.065561055 1783.771238 -3.251339157 -0.166102908 NFEDVAFDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NFEDVAFDEK 10 0 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 108.47 0.004995 370640000 939390 740320 606120 692590 859100 835070 851100 867600 1003600 FALSE TRUE 815247.2314 735456.7892 899241.6593 849853.1451 842005.5908 867195.6833 768560.453 682070.4917 884955.5513 0.921229581 0.83106636 1.016143306 0.960334272 0.951466534 0.979931345 0.868473509 0.770739831 1 19.75524547 2.135570872 6.740652685 0.854809929 0.942493022 0.116433352 0.073250849 0.317534901 18.20276549 0.029954176 0.020116234 136.6378034 -2.135570872 0.087683093 NFEDVAFDEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NFEDVAFDEKK 11 1 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ;; 143.98 5.92E-05 3048960000 3496240 2707482 2293883 2315562 2476844 2206760 3579890 3607660 1924502 FALSE TRUE 3034203.026 2689696.372 3403212.491 2841345.743 2427559.65 2291655.485 3232712.819 2836189.984 1696989.566 1.787991563 1.58498109 2.005441023 1.674344852 1.430509473 1.350424028 1.904969178 1.671306672 1 20.69454626 3.458728277 8.343742466 1.525137301 1.783302361 0.245131676 0.251573213 0.317121239 115.3715535 0.073432687 0.096371592 2875.598692 -3.458728277 0.25816506 NFEHLNSDFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NFEHLNSDFDR 11 0 P48163 P48163 ME1 NADP-dependent malic enzyme 0 ; 146.5 3.57E-05 622900000 493580 403550 173752 290830 471580 482270 446760 457730 476520 FALSE TRUE 428352.1524 400899.0535 257779.0484 356867.3966 462196.4806 500823.239 403433.284 359848.0016 420186.3485 1.019433768 0.954098235 0.613487443 0.849307451 1.099979765 1.19190745 0.960129441 0.856400982 1 18.68066977 3.26470238 23.73139659 1.00491782 0.848325961 0.257879525 0.134868286 205.1549564 186236.5477 0.042762245 0.055181223 1839.510959 -3.26470238 -0.156591859 NFETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NFETLR 6 0 Q9BVG4;A6NDF3 Q9BVG4;A6NDF3 PBDC1 Protein PBDC1 0 100.74 0.086812 81112000 183530 164580 90712 98170 170730 158210 146530 181720 148570 FALSE TRUE 159276.0455 163498.8631 134580.6266 120460.9989 167332.807 164296.4411 132319.5432 142860.5921 131006.2239 1.215789913 1.248023631 1.027284221 0.919505924 1.277288988 1.254111723 1.010024862 1.090487062 1 16.99927583 -1.999894142 0.029078905 3.31E-07 1.915769135 0.122183014 0.11863326 8463.219177 24.38114522 1119.993897 573.9880125 0.010002438 1.999894142 1.915768805 NFEWVAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NFEWVAER 8 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;;;; 134.77 0.0020067 2557343000 4426180 4637850 2617670 2998960 5399350 5931440 4057730 4321750 4366790 FALSE TRUE 3841249.098 4607383.658 3883583.968 3679919.704 5291913.499 6159626.335 3664211.969 3397577.394 3850553.061 0.997583733 1.196551141 1.008578224 0.955686013 1.374325562 1.599673148 0.951606668 0.882360882 1 21.87663425 2.039955139 24.99999315 0.928037563 1.186817324 0.262470483 0.192633556 202.8230734 126905.9003 0.083716717 0.056441726 109.636494 -2.039955139 0.258779762 NFGEDMDDER ddPTM_MDA-MB-175_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 ;;;;;;;;; 284.04 6.42E-24 14249130000 8393490 7842950 4997530 6424440 8915960 8731310 8217320 8906200 11920350 FALSE TRUE 7284269.03 7791429.145 7414352.224 7883207.293 8738549.84 9067209.146 7420405.571 7001678.438 10511139.8 0.693004676 0.741254449 0.705380421 0.749985962 0.831360823 0.862628537 0.70595632 0.666119809 1 23.32541578 3.467336083 6.978826182 0.789513924 0.717731633 0.180145902 0.091245019 0.32601455 83.73450437 0.027096216 0.036277889 2933.162221 -3.467336083 -0.071782291 NFGEDMDDERLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NFGEDMDDERLK 12 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YBN4 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ;;;;; 194.24 1.62E-06 1852920000 1955580 1595770 740699 752507 1560940 1377450 1898900 2151510 223453 FALSE TRUE 1697145.148 1585287.282 1098903.514 923375.2157 1529880.348 1430441.393 1714744.97 1691426.33 197036.6409 8.613347956 8.045647117 5.577153107 4.686312208 7.764445947 7.259773544 8.702670541 8.584323818 1 17.58810441 4.397609564 6.677180248 6.608605519 8.475705338 0.114622296 2.267932759 0.479060367 31.82011042 0.56831957 1.538393954 24980.98529 -4.397609564 1.867099819 NFGEEVDDESLKELFSQFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NFGEEVDDESLKELFSQFGK 20 1 B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0YCC8 B1ANR0 PABPC4 Polyadenylate-binding protein;Polyadenylate-binding protein 4 0 220.04 8.02E-25 321720000 632730 421480 288520 331130 432910 309630 537030 660160 379920 FALSE TRUE 549113.1274 418711.2701 428049.237 406318.1275 424295.938 321541.6665 484948.9133 518989.9214 335006.2904 1.639112886 1.249860919 1.277734924 1.212867158 1.266531257 0.959807847 1.447581515 1.549194556 1 18.35382866 4.740565626 24.10779777 1.270376068 1.639113081 0.319743422 0.177167355 152.3622374 1831742.251 0.045224014 0.28585895 55025.70632 -4.740565626 0.368737013 NFGIWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NFGIWLR 7 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 137.83 0.0066179 2820800000 2780600 3928600 1630590 1785110 4871900 4631100 3592600 4018700 4773200 FALSE TRUE 2413136.665 3902792.768 2419148.778 2190446.509 4774958.722 4809261.414 3244190.205 3159332.279 4208917.734 0.573338995 0.927267534 0.574767418 0.52042987 1.134486114 1.142636116 0.770789645 0.750628185 1 22.00501788 3.246957647 24.99999306 0.92855057 0.663531902 0.44939569 0.168635291 219.996079 654977.7342 0.053187074 0.067528176 1765.865604 -3.246957647 -0.265018668 NFGLYNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NFGLYNER 8 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 86.332 0.037475 166290000 229170 226160 148180 183890 274490 253440 251680 301050 346940 FALSE TRUE 198884.6039 224674.3401 219840.3436 225645.0351 269028.186 263190.0008 227272.1123 236672.8003 305925.1484 0.650108711 0.734409516 0.718608276 0.737582498 0.879392189 0.860308484 0.742901045 0.773629764 1 18.22281918 7.212006341 0.208581249 0.898550309 2.94E-16 0.492365097 0.071250814 76.64353421 1.566826012 0.466191974 20.72138862 16293198.22 -7.212006341 -0.898550309 NFGSYVTHETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NFGSYVTHETK 11 0 P63167;Q96FJ2 P63167;Q96FJ2 DYNLL1;DYNLL2 "Dynein light chain 1, cytoplasmic;Dynein light chain 2, cytoplasmic" 0 165.58 2.14E-05 211300000 518180 517620 258210 511030 653440 502580 680630 711150 1532400 FALSE TRUE 449701.2001 514219.7201 383081.2197 627067.1721 640437.8224 521914.5778 614622.6074 559076.1067 1351241.418 0.332805962 0.380553551 0.283503166 0.46406746 0.473962546 0.386248209 0.454857733 0.413749978 1 20.36585402 1.236297616 6.052696092 1.022371726 0.400346276 0.911245105 0.058983215 0.038554547 5.455097327 0.098873742 0.015139581 17.23048952 -1.236297616 -0.62202545 NFHEVMLALTVLETCVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NFHEVMLALTVLETCVK 17 0 O60784;O60784-4;O60784-2;O60784-3;V9GYF4;B0QY02;V9GZ68;Q6UW50;H7BYN7 O60784 TOM1 Target of Myb protein 1 0 105.6 0.00079379 78706000 124830 122340 65404 99818 104730 100290 152820 183240 173440 FALSE TRUE 108333.3992 121536.3405 97033.59316 122483.2025 102646.0779 104148.2212 137999.5399 144055.552 152936.1208 0.70835718 0.794686957 0.63447139 0.800878183 0.671169619 0.68099165 0.902334512 0.941932823 1 17.22256966 2.130440688 4.182015165 0.955338453 0.717048594 0.808542115 0.053932615 0.086714157 2.736572115 0.022586911 0.014619872 135.03324 -2.130440688 -0.238289859 NFHQYSVEGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NFHQYSVEGGK 11 0 Q9HCY8 Q9HCY8 S100A14 Protein S100-A14 0 ;;; 172.11 1.37E-05 2216900000 4362580 4176830 2435210 4710500 5678590 5359320 3656750 6958320 6886590 FALSE TRUE 3786054 4149392.129 3612885.701 5780091.02 5565597.169 5565496.508 3302118.948 5470337.418 6072465.175 0.623478915 0.683312627 0.594961947 0.951852477 0.916530109 0.916513532 0.543785572 0.900842946 1 22.53385088 3.746664194 24.94014572 0.857891804 0.638857297 0.442988438 0.124964626 623.1229376 1917762.371 0.034337787 0.058180915 5580.385407 -3.746664194 -0.219034507 NFIQYFHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NFIQYFHK 8 0 B0QY89;Q9Y262-2;Q9Y262;H7C3A0;C9JHP4;C9K0Q7 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 101.6 0.0052792 782510000 1975500 1978900 1223000 1312600 2205300 1779400 2021100 2376600 2369000 FALSE TRUE 1714432.67 1965900.476 1814446.891 1610645.892 2161418.845 1847854.669 1825094.033 1868382.585 2088939.519 0.820719152 0.941099758 0.86859714 0.771035196 1.034696709 0.884589837 0.873694052 0.894416793 1 20.99433929 3.251039642 24.99999347 0.924668273 0.858146518 0.288978374 0.065727222 383.5544097 768393.7432 0.018910368 0.024241811 1782.54147 -3.251039642 -0.066521756 NFLEGDWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NFLEGDWK 8 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39 B7ZC38 SH3GLB2 Endophilin-B2 0 ; 111.17 0.0076435 537020000 1235449 1089346 638711 715352 1158150 1015550 1302995 1505820 1120552 FALSE TRUE 1072181.284 1082190.014 947593.776 877783.6051 1135105.081 1054618.866 1176630.745 1183812.111 988081.6191 1.085114087 1.095243544 0.959023787 0.888371556 1.14879688 1.067339828 1.190823433 1.198091421 1 19.91427069 3.193898186 24.99851116 1.13319804 1.009822906 0.318723688 0.081752111 151.262167 84664.03721 0.025800035 0.029254621 1562.78123 -3.193898186 -0.123375134 NFLIEPFVPHSQAEEFYVCIYATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NFLIEPFVPHSQAEEFYVCIYATR 24 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ;;; 258.83 5.98E-44 1479892000 1664475 1850165 850546 1065551 1786431 1788468 1859579 2077173 1848318 FALSE TRUE 1444510.412 1838011.144 1261872.891 1307500.64 1750884.518 1857271.521 1679237.315 1632985.719 1629811.952 0.886304957 1.127744304 0.77424447 0.802240184 1.074286218 1.139561849 1.030325807 1.001947321 1 20.63627408 3.217926947 24.97955639 1.046414151 0.905256437 0.357015397 0.100819026 296.3542524 358771.6456 0.031753417 0.036043744 1651.683944 -3.217926947 -0.141157713 NFLYAWCGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NFLYAWCGK 9 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 157.54 0.0001589 1010000000 1110060 1207380 515880 593210 1275560 1077960 1275700 1361900 1287240 FALSE TRUE 963362.7585 1199448.641 765361.2935 727907.3971 1250178.852 1119429.819 1151982.81 1070668.283 1135063.954 0.848729938 1.056723401 0.674289137 0.641291968 1.101417103 0.986226208 1.014905642 0.943266923 1 20.11434216 3.224540243 24.99991383 1.000209969 0.813865378 0.426391124 0.117073451 260.1922369 463951.0682 0.037131156 0.042307108 1677.027728 -3.224540243 -0.186344591 NFPNAIEHTLQWAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NFPNAIEHTLQWAR 14 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 214.65 6.79E-12 6923300000 1269320 1130930 533310 671040 1349950 1342390 1132750 1295820 1149180 FALSE TRUE 1101576.146 1123500.846 791220.4998 823409.8882 1323088.636 1394032.612 1022896.079 1018718.977 1013325.25 1.087090395 1.108726785 0.780815933 0.81258203 1.305689991 1.375701052 1.009444973 1.0053228 1 19.95066588 3.247923685 24.9999826 1.12458261 0.946942046 0.259664908 0.159974738 341.3807123 911502.8122 0.051690397 0.065815668 1769.79794 -3.247923685 -0.177640563 NFQAATESVPNSGNIHNGSLEQTEEPETSSHS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NFQAATESVPNSGNIHNGSLEQTEEPETSSHSPSR 35 0 E7EUR8;A0A1B0GVL4;P78312-4;P78312-6;P78312-2;P78312-5;P78312 E7EUR8 FAM193A Protein FAM193A 1 NFQAATESVPNSGNIHNGSLEQTEEPETS(0.001)S(0.011)HS(0.98)PS(0.008)R 234.54 5.39E-47 179050000 67968 81413 24257 46513 111760 109440 88757 103210 92451 TRUE FALSE 58985.85659 80878.19264 35987.76633 57074.48756 109536.1947 113650.2276 80149.3598 81139.34468 81521.5481 0.723561536 0.992108155 0.441450968 0.700115355 1.343647136 1.394112726 0.983167784 0.995311627 1 16.31489383 3.257497126 24.97183901 1.125293053 0.714661761 0.556431185 0.189926062 204.0790273 269120.2103 0.058700245 0.075654766 1809.243936 -3.257497126 -0.410631293 NFQLLVITHDEDFVELLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NFQLLVITHDEDFVELLGR 19 0 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494BZX8 Q92878-2 RAD50 DNA repair protein RAD50 0 85.636 0.0030049 19108000 24325 18106 8751.4 9232.8 18385 16079 20137 22124 20419 FALSE TRUE 21110.38962 17987.06049 12983.60631 11329.24835 18019.17447 16697.56953 18184.11684 17392.95477 18005.08908 1.172467935 0.998998695 0.721107585 0.629224788 1.0007823 0.927380557 1.009943175 0.96600215 1 14.13611712 NFQTAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NFQTAHR 7 0 O75475;O75475-3;O75475-2;V9GYT7 O75475 PSIP1 PC4 and SFRS1-interacting protein 0 ; 95.909 0.01312 276830000 592370 723810 260190 430580 663840 909120 568870 705060 673910 FALSE TRUE 514086.8036 719055.2445 386018.7543 528349.77 650630.8828 944094.4347 513701.075 554288.4058 594241.1275 0.865114816 1.210039513 0.649599525 0.8891168 1.094893727 1.588739639 0.864465705 0.932766818 1 19.18068893 3.237328705 24.95457889 1.082997663 0.907232196 0.141935573 0.234117614 76.40183201 1547662.792 0.072604889 0.086955655 1727.144622 -3.237328705 -0.175765467 NFRNPLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NFRNPLAK 8 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 155.75 0.00036837 3781000000 2604800 2742800 934950 1185690 2951000 2630900 3388700 3579200 830450 FALSE TRUE 2260569.08 2724782.366 1387094.947 1454919.037 2892280.874 2732112.425 3060064.396 2813815.933 732275.1471 3.087048754 3.720981624 1.894226443 1.986847488 3.949718743 3.730991604 4.17884508 3.842566479 1 19.48202631 3.227688763 24.99872546 3.485601997 2.691608551 0.08597628 1.022542459 469.490842 1079544.124 0.313137785 0.358481441 1689.22991 -3.227688763 -0.793993446 NFRPDDPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NFRPDDPTR 9 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4;K7EMQ3 P50570-2 DNM2 Dynamin-2 0 ; 79.148 0.025319 829330000 1246140 1121840 531640 727500 1310040 1279250 1193100 1305070 1366130 FALSE TRUE 1081459.442 1114470.559 788742.8822 892689.9941 1283972.767 1328463.575 1077393.346 1025990.937 1204627.668 0.897754112 0.925157697 0.654760723 0.741050549 1.065866908 1.102800152 0.894378715 0.851707929 1 20.20015587 3.246895671 24.99934469 0.965894962 0.802577684 0.414262367 0.104229308 225.3134979 675779.6277 0.033710627 0.042790207 1765.613621 -3.246895671 -0.163317278 NFS(ph)AAK ddPTM_MDA-MB-175_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 85.676 0.057109 229300000 565820 337340 293610 575330 329500 244810 497840 511650 1463700 TRUE FALSE 491045.4534 335123.9913 435600.7781 705967.4699 322943.5947 254227.9991 449559.5534 402237.6292 1290663.053 0.380459836 0.25965258 0.337501548 0.546980459 0.250215262 0.196974724 0.348316745 0.311651928 1 20.29968098 1.237747173 24.99300166 1.000000784 0.327391735 0.834496725 0.093912877 7.837898307 240667.3979 0.135489049 0.023130461 17.28809632 -1.237747173 -0.672609049 NFTKPQDGDVIAPLIT(ph)PQKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NFTKPQDGDVIAPLITPQKK 20 2 Q9Y3Z3-4;Q9Y3Z3;Q9Y3Z3-3 Q9Y3Z3-4 SAMHD1 Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 1 NFTKPQDGDVIAPLIT(1)PQKK 160.67 1.13E-09 1402900000 2901600 2580700 1762300 1803000 2539400 1595100 3563100 4064200 3434800 TRUE FALSE 2518146.208 2563747.212 2614554.175 2212398.707 2488870.908 1656464.529 3217551.11 3195102.458 3028741.857 0.831416584 0.846472672 0.863247612 0.730467901 0.821750755 0.546915058 1.06233917 1.054927296 1 21.53028719 2.198357438 24.99991833 1.043357676 0.781033955 0.652511586 0.091275119 91.15118457 56680.77418 0.036659532 0.024716204 157.8910226 -2.198357438 -0.262323721 NFWNGR ddPTM_MDA-MB-175_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 ;; 122.51 0.044642 2821290000 1598410 1599230 836730 1094240 1902520 1760280 1728230 1949420 2062860 FALSE TRUE 1387176.069 1588724.553 1241375.427 1342703.916 1864663.574 1827999.111 1560626.521 1532551.703 1818991.041 0.762607422 0.873409773 0.682452744 0.73815862 1.025108718 1.004952234 0.857962731 0.842528451 1 20.79470701 3.25386979 24.99420519 0.929493699 0.766124833 0.582208633 0.075859952 206.4975111 337131.9789 0.023690502 0.030468977 1794.195611 -3.25386979 -0.163368866 NFWSHETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NFWSHETR 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 139.38 0.00066655 2332350000 2299530 2324280 946390 1309830 2760790 2356300 2475510 2661640 2546130 FALSE TRUE 1995641.284 2309011.652 1404067.369 1607246.921 2705855.68 2446948.386 2235435.421 2092468.999 2245129.412 0.888875837 1.0284537 0.625383714 0.715881638 1.205211453 1.089891911 0.995682213 0.932003736 1 21.09836718 3.251474237 24.99917694 1.029089648 0.816401584 0.448565042 0.126013484 251.5051311 486880.2538 0.039167578 0.050237095 1784.326136 -3.251474237 -0.212688064 NFYELSPHIFALSDEAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NFYELSPHIFALSDEAYR 18 0 E9PDF6;O43795;O43795-2;E7EQD9;C9JUP5;C9JYW1 E9PDF6 MYO1B Unconventional myosin-Ib 0 159.7 4.24E-11 174810000 155620 167730 92673 95845 181730 178610 152070 190670 75965 FALSE TRUE 135054.4227 166628.1706 137489.9728 117608.0721 178113.9285 185481.2423 137322.2748 149896.7043 66984.50424 2.01620396 2.487562944 2.052563863 1.75575043 2.659031825 2.769017169 2.050060329 2.237781797 1 16.03153977 1.234341168 5.760209515 0.943207572 2.261250626 0.61560005 0.311219906 0.104435938 11.82488774 0.54216591 0.078895895 17.15304265 -1.234341168 1.318043054 NFYES(ph)DDDQKEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NFYESDDDQKEK 12 1 O00203;O00203-3 O00203 AP3B1 AP-3 complex subunit beta-1 1 NFYES(1)DDDQKEK;NFYES(1)DDDQKEK;NFYES(1)DDDQKEK;NFYES(1)DDDQKEK 192.85 2.15E-06 4766850000 6494240 4721580 5815000 4650090 5369350 4009260 7010920 8210550 11650830 TRUE FALSE 5636009.73 4690563.63 8627153.45 5705964.007 5262510.44 4163498.827 6331002.057 6454787.777 10273482.15 0.548597802 0.456569989 0.83974969 0.55540701 0.512242136 0.405266565 0.616246952 0.628296004 1 23.29242192 1.118510479 2.15087223 1.246738818 0.560718272 0.585011933 0.114924786 0.765016592 2.680674138 1.161931395 0.031165318 13.13743194 -1.118510479 -0.686020546 NFYNEHEEITNLTPQQLIDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NFYNEHEEITNLTPQQLIDLR 21 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ;;; 219.78 4.93E-25 566240000 511133 527296 259254 355798 572213 570883 491218 620600 550591 FALSE TRUE 443585.479 523832.1579 384630.1016 436587.3739 560827.0808 592845.2384 443579.754 487889.5195 485500.7592 0.913665881 1.078952294 0.79223378 0.899251681 1.15515181 1.221100538 0.913654089 1.004920199 1 18.88911403 3.265390289 24.99993388 1.049418147 0.923106873 0.283663433 0.10831146 341.0028066 317744.6471 0.032900388 0.042462507 1842.426997 -3.265390289 -0.126311274 NFYQEHPDLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NFYQEHPDLAR 11 0 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4;X6RLV5 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;;;; 203.61 3.60E-08 7813360000 4522600 4016580 1830292 2623210 4970920 4699800 4123890 4701620 4288790 FALSE TRUE 3924926.951 3990194.822 2715427.333 3218849.924 4872008.417 4880604.347 3723955.783 3696215.151 3781774.132 1.03785335 1.055111882 0.718030014 0.851148115 1.288286462 1.290559451 0.984711316 0.977375967 1 21.85063177 3.272860078 24.99999038 1.091693612 0.91139794 0.300363574 0.144830886 280.0231975 204099.8713 0.046326082 0.059803892 1874.390517 -3.272860078 -0.180295672 NFYVEHPEVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NFYVEHPEVAR 11 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;; 147.24 3.54E-05 9704750000 4719040 4439240 2056420 2804550 5372260 5057810 4667900 4937550 4638300 FALSE TRUE 4095406.907 4410078.34 3050911.59 3441365.942 5265362.537 5252387.224 4215207.776 3881693.357 4089965.458 1.001330439 1.078267869 0.745950454 0.841416872 1.287385576 1.284213101 1.030621852 0.949077296 1 21.96365723 3.26725388 24.99856288 1.092836826 0.916079648 0.317380641 0.139730546 322.3405833 280832.1862 0.045300346 0.05847198 1850.34998 -3.26725388 -0.176757178 TSS(ph)FAEPGGGGGGGGGGPGGSASGPGGTGGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSSFAEPGGGGGGGGGGPGGSASGPGGTGGGK 32 0 P49840 P49840 GSK3A Glycogen synthase kinase-3 alpha 1 T(0.041)S(0.179)S(0.779)FAEPGGGGGGGGGGPGGSASGPGGTGGGK;T(0.145)S(0.145)S(0.709)FAEPGGGGGGGGGGPGGSASGPGGTGGGK 309.5 3.61E-104 777760000 1172420 1267900 1343610 1567350 2327560 2269370 2325470 2779340 2807230 TRUE FALSE 1017481.726 1259571.081 1993384.29 1923240.773 2281246.11 2356674.132 2099946.277 2184999.77 2475362.467 0.41104353 0.508843088 0.805289858 0.776953193 0.921580633 0.952052139 0.848338902 0.882698917 1 21.23920836 4.342716988 1.116159033 0.909884331 0.302024364 0.911128734 0.056452053 0.241725112 0.397717942 0.01776056 0.148915472 22014.91375 -4.342716988 -0.607859966 down NGDECAYHHPIS(ph)PCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 161.47 2.76E-06 365890000 441250 411970 214940 271310 434560 336810 467020 524480 535580 TRUE FALSE 382937.6945 409263.7419 318885.7029 332915.0822 425913.1062 349767.2986 421728.4723 412324.0335 472264.3425 0.810854558 0.866598862 0.675227143 0.704933767 0.901853195 0.740617631 0.892992408 0.873078902 1 18.84923509 0.533242484 0.661881408 1.426160364 0.777791759 0.47673445 0.072005397 6.708183898 1.151853011 4.066008485 0.03376002 3.413834668 -0.533242484 -0.648368605 NGDGFVSLEEFLGDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NGDGFVSLEEFLGDYR 16 0 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 ;;;; 161.21 1.98E-08 228795500 184874.5 147060.3 123706.3 180368.8 208613.6 254643.8 149883.2 174191.6 286070 FALSE TRUE 160442.8664 146094.2512 183531.0805 221324.2928 204462.5975 264440.1118 135347.5503 136942.0819 252251.1305 0.636044192 0.579161929 0.727572876 0.877396634 0.810551759 1.048320819 0.536558746 0.542879953 1 17.94450121 4.119118554 4.90704835 0.771661132 0.609109805 0.170558297 0.166972339 0.440330054 16.83015372 0.046796059 0.10265767 13155.83912 -4.119118554 -0.162551326 NGDLDEVKDYVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NGDLDEVKDYVAK 13 1 P58546;C9JL85 P58546 MTPN Myotrophin 0 176.23 1.54E-05 842350000 2524600 1841500 1356000 1343000 1852700 1251400 2814200 3037600 1468000 FALSE TRUE 2190967.713 1829403.065 2011766.136 1647948.676 1815834.895 1299542.168 2541279.317 2388032.879 1294454.712 1.692579657 1.413261544 1.554141768 1.2730833 1.402779779 1.003930192 1.963204501 1.844817633 1 20.30391306 2.226047829 24.99991947 1.668142573 1.393754263 0.083903221 0.306720582 438.3552712 875804.2013 0.123533048 0.083921183 168.2859384 -2.226047829 -0.27438831 NGDLDEVKDYVAKGEDVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NGDLDEVKDYVAKGEDVNR 19 2 P58546 P58546 MTPN Myotrophin 0 134.9 4.97E-06 113500000 113780 71868 40740 54003 110790 80032 176750 155740 13633 FALSE TRUE 98743.68472 71395.89438 60442.00027 66265.20653 108585.4958 83110.88283 159608.8122 122436.213 12021.32227 8.214045218 5.939104931 5.027899503 5.512305971 9.032741433 6.913622392 13.27714278 10.18492061 1 13.55330797 7.511035622 8.097791907 7.586362179 6.323825992 0 3.316911736 0 0 0.766690244 0 32436622.19 -7.511035622 -1.262536188 NGEELHGGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NGEELHGGKR 10 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 90.685 0.0069214 77024000 186309 156189 108463 117245 159868 145556 172995 205792 152320 FALSE TRUE 161687.7936 155162.9842 160916.0696 143867.2692 156686.9396 151155.6335 156217.9715 161784.9823 134312.9031 1.203814301 1.155235131 1.198068583 1.071135132 1.166581437 1.125399198 1.163089829 1.2045379 1 17.03523838 1.429172252 0.011028741 1.35E-05 2.253995815 0.169406754 0.058868199 19091.03401 65.33896615 6946.866167 6414.077011 26.86409729 -1.429172252 2.253982326 NGEFELMHVDEFIDELLHSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NGEFELMHVDEFIDELLHSER 21 0 Q8NAV1 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 0 ;;;;; 255.41 1.18E-36 255707000 167748.7 141461 76994.9 103371.2 150480.2 147895.7 149298.1 172841.4 150793 FALSE TRUE 145580.2843 140531.7334 114229.8912 126843.2109 147485.9384 153585.3433 134819.1932 135880.6117 132966.4233 1.094865009 1.056896394 0.859088244 0.953949183 1.109196854 1.155068621 1.013934119 1.021916724 1 17.02070246 3.24882883 24.99974256 1.056555532 0.986455796 0.164537723 0.076510362 423.0113152 1029887.195 0.023913962 0.03052933 1773.490352 -3.24882883 -0.070099736 NGGCNHMQCSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NGGCNHMQCSK 11 0 O95376 O95376 ARIH2 E3 ubiquitin-protein ligase ARIH2 0 78.908 0.028596 15083000 35569 37310 17477 18927 42036 44388 45961 51845 45111 FALSE TRUE 30868.46653 37064.90815 25928.93566 23224.66463 41199.56584 46095.63508 41503.70929 40758.35021 39778.02897 0.776018001 0.931793483 0.651840635 0.583856597 1.035736735 1.158821497 1.043382751 1.024644792 1 15.27968417 3.173462703 9.204365667 1.054498777 0.744164984 0.722254835 0.097520684 0.183368761 24.15884827 0.03123061 0.035478941 1490.948709 -3.173462703 -0.310333794 NGGS(ph)FEDDLSLGAEANHLHESDAQIENCNNILAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NGGSFEDDLSLGAEANHLHESDAQIENCNNILAK 34 0 E9PHV5;P28290-3;P28290 E9PHV5 SSFA2 Sperm-specific antigen 2 1 NGGS(0.848)FEDDLS(0.146)LGAEANHLHES(0.006)DAQIENCNNILAK 140.22 5.30E-10 87129000 51691 48040 11490 26779 56699 33187 59858 62822 44875 TRUE FALSE 44859.90338 47724.42208 17046.60243 32859.58124 55570.80083 34463.72536 54052.98037 49388.00418 39569.92862 1.13368674 1.206078043 0.430796896 0.830418006 1.404369499 0.870957481 1.366011571 1.248119618 1 15.27211684 3.259742008 24.86896776 1.185432466 0.88855805 0.223703205 0.256381741 336.9824629 395646.8092 0.074483547 0.096060199 1818.620189 -3.259742008 -0.296874417 NGHDGDTHQEDDGEKS(ph)D ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NGHDGDTHQEDDGEKSD 17 1 K7EQH5;Q08117;Q08117-2 K7EQH5 AES Amino-terminal enhancer of split 1 NGHDGDTHQEDDGEKS(1)D;NGHDGDTHQEDDGEKS(1)D;NGHDGDTHQEDDGEKS(1)D;NGHDGDTHQEDDGEKS(1)D 222.3 2.06E-15 234831000 730510 542578 508936 523539 529139 474641 609100 653460 1000740 TRUE FALSE 633971.2526 539013.7694 755059.1519 642416.5317 518610.1691 492900.7464 550029.5758 513722.6642 882433.6572 0.718435032 0.610826395 0.855655432 0.728005473 0.58770443 0.558569749 0.623309833 0.582165764 1 19.75112829 1.231181075 24.9987706 1.000000608 0.654468471 0.591371086 0.089276608 203.9034237 690678.928 0.235900106 0.023312287 17.02868356 -1.231181075 -0.345532137 NGHLAVVAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NGHLAVVAPR 10 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 107.79 0.0022375 207171000 165097 163525 113100 117170 183520 194532 153322 165803 163520 FALSE TRUE 143279.0131 162450.7935 167795.5383 143775.2393 179868.3111 202015.7719 138452.856 130347.3187 144188.8519 0.993689951 1.126652937 1.163720607 0.997131453 1.247449499 1.401049868 0.960218867 0.904004138 1 17.1376001 2.040312945 24.99999466 0.941234495 1.153554567 0.388704366 0.118209606 144.4641732 89588.59279 0.049495192 0.033369609 109.7268584 -2.040312945 0.212320073 NGIHDLDNISFPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NGIHDLDNISFPK 13 0 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 136.33 7.36E-05 442090000 645910 497280 338120 432640 608250 506920 600600 721280 926860 FALSE TRUE 560551.357 494013.3349 501635.9629 530877.5245 596147.015 526421.5404 542353.9044 567039.885 817287.6667 0.685867877 0.604454655 0.613781393 0.649560181 0.729421279 0.64410802 0.663602213 0.693806977 1 19.64048444 1.210218856 3.172288676 1.075129735 0.655242766 0.902861193 0.035174631 0.120870454 1.520517605 0.132833692 0.009450355 16.22627589 -1.210218856 -0.419886969 NGLEGSSEET(ph)SFHDESLQDDREEIENNSYHMHPAGIILTK ddPTM_MDA-MB-175_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(0.194)S(0.229)EET(0.284)S(0.284)FHDES(0.008)LQDDREEIENNS(0.001)YHMHPAGIILTK 45.556 0.026718 89977000 16064 18897 6560 14807 21547 19316 18217 22696 18915 TRUE FALSE 13941.1017 18772.86436 9732.437942 18169.15566 21118.25686 20059.09902 16450.31814 17842.63702 16678.89025 0.835853075 1.125546369 0.583518315 1.089350394 1.266166786 1.20266389 0.986295725 1.069773633 1 14.02573568 3.524243254 24.99961458 1.103943776 0.869430575 0.378243396 0.152877404 454.541363 241146.3603 0.041101973 0.060961982 3343.822797 -3.524243254 -0.234513201 NGLHRPVS(ph)TDFAQYNSYGDVSGGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NGLHRPVSTDFAQYNSYGDVSGGVR 25 1 O14639-3;F8W8M4;O14639-5;O14639-2;O14639;J3QSX6;A0A0A0MRL6;A0A3B3IS55;O14639-4;O14639-6 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 NGLHRPVS(0.573)T(0.427)DFAQYNSYGDVSGGVR 265.24 1.50E-45 213100000 44838 63733 36024 41176 80090 86967 74141 82154 73050 TRUE FALSE 38912.54469 63314.33373 53445.32689 50525.64014 78496.36569 90312.67677 66950.81723 64586.00642 64414.11222 0.604099682 0.982926436 0.829714562 0.784387744 1.218620625 1.402063518 1.0393812 1.00266858 1 15.97508918 3.246004843 24.96409833 1.122800432 0.815430387 0.552571667 0.14814524 147.758136 495501.9439 0.04579819 0.05793318 1761.995696 -3.246004843 -0.307370046 NGLS(ph)PPPCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NGLSPPPCK 9 0 Q6NXG1;Q6NXG1-2;Q6NXG1-4;H0YBR2;H0YBB3 Q6NXG1 ESRP1 Epithelial splicing regulatory protein 1 1 NGLS(1)PPPCK;NGLS(1)PPPCK 110.08 0.0024604 825050000 1071970 967190 548370 770670 1154670 881910 1091980 1293120 1254380 TRUE FALSE 930306.4485 960836.4652 813563.5662 945662.4025 1131694.326 915837.6484 986079.9477 1016596.351 1106088.625 0.841077674 0.868679456 0.735531989 0.854960788 1.023149773 0.827996625 0.891501752 0.919091226 1 20.07703556 3.467022739 24.83667191 0.923923014 0.816253288 0.42460348 0.06306143 190.1273006 467604.3087 0.017727423 0.022911731 2931.046706 -3.467022739 -0.107669725 NGLYEIENGRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NGLYEIENGRPR 12 1 Q9BW91-2;Q9BW91;D6RAW2 Q9BW91-2 NUDT9 "ADP-ribose pyrophosphatase, mitochondrial" 0 110.8 0.00037979 0 167820 166820 94321 111250 190300 198800 156180 193270 188860 FALSE TRUE 145642.1618 165724.1484 139934.9511 136511.0128 186513.4023 206447.9646 141033.6876 151940.7145 166533.186 0.874553387 0.995141884 0.840282676 0.81972258 1.119977386 1.239680629 0.846880379 0.912374994 1 17.34545017 4.752026155 21.90304084 0.965409461 0.87455305 0.049543652 0.131207902 1595.920952 2595652.632 0.033797017 0.541989677 56497.09989 -4.752026155 -0.090856411 NGMVLKPHFHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NGMVLKPHFHK 11 1 P26373;P26373-2;J3QSB4;H3BTH3 P26373 RPL13 60S ribosomal protein L13 0 ; 90.108 0.0075695 1546970000 1186290 1206170 598690 820370 1503820 1315010 1440730 1636270 1621650 FALSE TRUE 1029518.771 1198246.59 888218.4865 1006647.547 1473896.924 1365599.286 1301008.226 1286366.394 1429940.384 0.719973212 0.837969613 0.621157704 0.703978682 1.030740121 0.955004349 0.909833893 0.899594422 1 20.44752357 3.248855055 24.99999904 0.947712981 0.722026013 0.770526811 0.064444736 104.5568361 253914.4 0.019070732 0.024341254 1773.597447 -3.248855055 -0.225686967 NGPFKPNYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NGPFKPNYYR 10 1 O43865-2;O43865;H0Y8B3;Q96HN2-4;Q96HN2-3;Q96HN2-2;Q96HN2 O43865-2 AHCYL1;AHCYL2 Putative adenosylhomocysteinase 2;Adenosylhomocysteinase;Putative adenosylhomocysteinase 3 0 ; 109.29 0.0018589 784820000 690310 788700 408200 539220 1061580 1024950 941570 1008470 1025740 FALSE TRUE 599083.7845 783518.9778 605606.8853 661658.1425 1040456.635 1064380.49 850256.6863 792816.5384 904478.1857 0.662352939 0.866266307 0.669564944 0.731535766 1.150339114 1.176789564 0.940052176 0.876545782 1 19.78672618 3.257215132 24.99352326 1.010470599 0.737499245 0.665666565 0.103873876 176.3485491 236272.2753 0.033347189 0.042973924 1808.06955 -3.257215132 -0.272971354 NGPLNES(ph)QEDEEDSEHGTSLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NGPLNESQEDEEDSEHGTSLNR 22 0 Q9H2K8 Q9H2K8 TAOK3 Serine/threonine-protein kinase TAO3 1 NGPLNES(1)QEDEEDSEHGTSLNR;NGPLNES(1)QEDEEDSEHGTSLNR;NGPLNES(1)QEDEEDSEHGTSLNR;NGPLNES(1)QEDEEDSEHGTSLNR 374.61 2.02E-113 1494613000 640325 513932 196732 354624 657685 481056 701906 660347 572747 TRUE FALSE 555704.4289 510555.9469 291872.2532 435146.7993 644598.3552 499562.5356 633835.2642 519136.9329 505037.5021 1.100323098 1.010926802 0.57792194 0.861612845 1.276337604 0.989159287 1.255026135 1.027917592 1 18.946031 3.268190628 24.99378352 1.104340737 0.874371455 0.311621294 0.163309495 253.0501083 213453.5111 0.047379333 0.061157633 1854.345386 -3.268190628 -0.229969282 NGQLDLSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NGQLDLSGK 9 0 Q92734-2;Q92734;Q92734-4;Q92734-3;C9JTY3;C9JUE0;C9JJP5 Q92734-2 TFG Protein TFG 0 ; 65.224 0.067163 512460000 880200 935940 289825 638550 1028480 1671240 718400 814930 662360 FALSE TRUE 763879.3399 929791.7485 429985.3394 783542.5371 1008015.26 1735533.684 648729.6786 640663.5613 584056.5554 1.307885911 1.591954991 0.736204971 1.341552509 1.725886391 2.971516488 1.110730926 1.096920419 1 19.15574855 3.4664579 20.80976211 1.552842281 1.214821164 0.076767595 0.589868816 92.48264978 180475.3158 0.18412868 0.238250624 2927.237096 -3.4664579 -0.338021117 NGRAYVES(ph)PARK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NGRAYVESPARK 12 2 Q96C34;Q96C34-2 Q96C34 RUNDC1 RUN domain-containing protein 1 1 NGRAY(0.001)VES(0.999)PARK 48.405 0.092479 259310000 249800 258580 118270 174200 240060 312380 205500 222620 156020 TRUE FALSE 216788.2971 256881.371 175465.7676 213754.7725 235283.2757 324397.4607 185570.6416 175014.4454 137575.4933 1.575776992 1.867202979 1.275414417 1.553727101 1.710212117 2.35795964 1.348864083 1.272133875 1 17.06986398 2.015818664 24.99919295 1.202003033 1.713927543 0.434607299 0.283049188 230.3949625 364105.7726 0.11858176 0.079921792 103.7095295 -2.015818664 0.51192451 NGS(ph)GTLDLEEFLR ddPTM_MDA-MB-175_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(0.995)GT(0.005)LDLEEFLR;NGS(0.944)GT(0.056)LDLEEFLR 142.1 4.21E-05 42481000 114915 99193 67096 83598 115629 102660 119796 121830 122485 TRUE FALSE 99728.69159 98541.39465 99543.85002 102580.2036 113328.2091 106609.3966 108178.2024 95777.60258 108004.9628 0.92337138 0.912378395 0.921659963 0.949773056 1.049287053 0.987078684 1.001603996 0.886788904 1 16.72073808 3.478293422 24.99926667 0.976354223 0.92133671 0.347125763 0.040465799 62.71543135 1337574.918 0.012876612 0.016847425 3008.107978 -3.478293422 -0.055017513 NGS(ph)PPPGAPSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NGSPPPGAPSSR 12 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 NGS(1)PPPGAPSSR;NGS(1)PPPGAPSSR;NGS(1)PPPGAPSSR;NGS(1)PPPGAPSSR 171.11 4.13E-05 1464260000 1060470 980870 563811 690376 1285630 1062540 1105120 1189280 989910 TRUE FALSE 920326.2026 974426.6004 836471.8854 847136.4225 1260048.478 1103416.601 997945.6325 934961.727 872883.9675 1.054351136 1.116330047 0.958285312 0.970502901 1.443546365 1.264104557 1.1432741 1.071117997 1 19.73543036 NGSEADIDEGLYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NGSEADIDEGLYSR 14 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 338.52 2.19E-68 364160000 558560 499950 255420 315520 542260 491270 679510 761960 393100 FALSE TRUE 484744.8808 496665.7955 378941.9663 387163.6384 531470.0869 510169.4748 613611.2248 599020.7836 346628.1658 1.398457854 1.432848927 1.093223239 1.116942236 1.533257073 1.471806175 1.770228981 1.728136495 1 18.40302936 3.183737006 10.1580889 1.548314121 1.260905394 0.194164614 0.232289125 0.606688128 108.5932177 0.071939417 0.081704126 1526.641295 -3.183737006 -0.287408727 NGSGTLDLEEFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 NGSGTLDLEEFLR 13 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ;;;;;;; 341.74 1.11E-62 934792400 1358041 1472420 709898.9 952380 1811387 1745930 1594618 1814299 1660849 FALSE TRUE 1178572.441 1462747.576 1053208.383 1168632.435 1775343.943 1813097.057 1439972.192 1426325.278 1464505.323 0.804758045 0.998799767 0.719156404 0.797970766 1.2122482 1.238026949 0.983248179 0.973929733 1 20.48198201 3.255781428 24.99832668 1.068504147 0.834286444 0.552784401 0.11196053 217.5371699 315782.6338 0.035217703 0.045354101 1802.110544 -3.255781428 -0.234217703 NGSLDSPGKQDT(ph)EEDEEEDEKDKGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NGSLDSPGKQDTEEDEEEDEKDKGK 25 3 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 1 NGS(0.001)LDS(0.064)PGKQDT(0.936)EEDEEEDEKDKGK 68.733 0.021987 94615000 115240 78784 80653 66563 83496 53375 117110 128440 97023 TRUE FALSE 100010.742 78266.46272 119657.0606 81677.1465 81834.59296 55428.37079 105752.6902 100974.1055 85553.05147 1.16899094 0.914829587 1.398629955 0.954695889 0.956536226 0.647883037 1.236106584 1.180251362 1 16.38453169 NGVAAEVS(ph)PAKEENPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NGVAAEVSPAKEENPR 16 1 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 NGVAAEVS(1)PAKEENPR 173.09 2.63E-09 147430000 153970 104870 72996 112480 161390 133870 165540 186200 231430 TRUE FALSE 133622.4744 104181.1021 108297.1098 138020.3031 158178.6548 139020.0655 149485.9563 146382.579 204070.609 0.654785493 0.510514976 0.530684503 0.676336018 0.775117277 0.681235118 0.732520753 0.717313383 1 17.63870889 -2 0.359303267 4.935686152 0.57889495 0.678224499 0.076684634 52.29210878 0.801651989 153.7734903 0.104078581 0.01 2 -4.356791202 NGVGPAPSLSELDLRPPS(ph)PINLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NGVGPAPSLSELDLRPPSPINLSR 24 1 Q5FWE3-2;Q5FWE3 Q5FWE3-2 PRRT3 Proline-rich transmembrane protein 3 1 NGVGPAPSLSELDLRPPS(1)PINLSR;NGVGPAPSLSELDLRPPS(1)PINLSR 216.21 8.18E-33 342700000 172174 182494 76294 180742 298760 285810 142988 333550 224130 TRUE FALSE 149420.7697 181295.1849 113190.0336 221782.2336 292815.2605 296805.2956 129121.0458 262222.9282 197633.6067 0.756049399 0.917329739 0.57272665 1.122188869 1.481606622 1.501795674 0.653335472 1.326813453 1 17.59246877 3.613191824 6.161074273 1.194033303 0.768080226 0.39035326 0.255317133 0.248578011 11.41425319 0.070300778 0.104795978 4103.853263 -3.613191824 -0.425953077 NGVMPSHFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NGVMPSHFSR 10 0 P39019;A0A075B6E2 P39019 RPS19 40S ribosomal protein S19 0 ;;;;; 145.55 2.29E-05 1228360000 1242617 1431160 452937 731916 2035580 1927920 1384900 1577700 1506930 FALSE TRUE 1078402.015 1421758.616 671978.8482 898108.7144 1995075.941 2002088.33 1250592.611 1240321.133 1328782.452 0.811571536 1.069970945 0.505710206 0.675888452 1.501431583 1.506708887 0.941156778 0.933426785 1 20.3416735 3.268714878 24.99979138 1.145009436 0.768935886 0.408522022 0.243949009 252.1420673 209040.1216 0.077981423 0.100660913 1856.585175 -3.268714878 -0.37607355 NGYDYGQCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NGYDYGQCR 9 0 Q13242;S4R3G0 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 103.87 0.007798 408460000 397830 401850 189470 266650 445160 449040 342470 407840 394810 FALSE TRUE 345255.7575 399210.2209 281098.3257 327196.958 436302.1869 466314.8594 309257.3121 320626.5898 348136.0116 0.991726641 1.14670763 0.807438232 0.939853813 1.253252098 1.339461716 0.888323247 0.920980821 1 18.40929153 NGYGFINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 115.46 0.0057224 1732530000 2147530 2071730 1282600 1424180 2516280 2407790 2227250 2483200 2676180 FALSE TRUE 1863728.469 2058120.669 1902869.65 1747561.836 2466210.951 2500419.239 2011251.638 1952187.004 2359805.049 0.789780694 0.872157075 0.80636731 0.740553478 1.045090971 1.059587206 0.852295675 0.827266221 1 21.17023625 3.24962531 24.99999307 0.937945834 0.807507154 0.46609975 0.080754316 258.8836874 584928.5182 0.026290641 0.033611903 1776.745849 -3.24962531 -0.130438681 NGYGFVEFDDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NGYGFVEFDDLR 12 0 Q08170;A0A0D9SEM4 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 0 110.08 0.0035567 109820000 227200 184720 131150 165340 233790 205550 195210 245990 266840 FALSE TRUE 197174.9443 183506.5622 194574.5787 202882.9741 229138.0364 213457.6415 176278.5642 193386.9528 235294.4792 0.837992226 0.779901691 0.826940689 0.862251315 0.973835158 0.907193582 0.749182747 0.821893287 1 17.84410794 3.780496884 3.718578385 0.875471656 0.808878406 0.169877921 0.072173776 0.50363903 14.73715071 0.021302205 0.037635484 6032.493798 -3.780496884 -0.06659325 NGYGFVEFEDS(ph)RDADDAVYELNGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NGYGFVEFEDSRDADDAVYELNGK 24 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 NGYGFVEFEDS(1)RDADDAVYELNGK;NGYGFVEFEDS(1)RDADDAVYELNGK 278.48 2.41E-52 197660000 231983 200211 120577 157713 196132 185007 214944 258691 302981 TRUE FALSE 201325.8588 198895.8008 178888.4405 193524.1471 192229.3569 192124.339 194098.764 203371.9428 267162.9313 0.753569583 0.744473793 0.669585558 0.724367509 0.719521065 0.719127979 0.72651832 0.761228146 1 18.02736032 1.193459084 2.732709527 1.083454048 0.721481219 0.938239269 0.022182702 0.124269133 0.975207143 0.108936108 0.005884479 15.61201946 -1.193459084 -0.361972828 NGYGFVEFEDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NGYGFVEFEDSR 12 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;; 150.06 0.00015772 878040000 864482 913237 491056 707688 1024771 918970 838943 1002440 1646100 FALSE TRUE 750238.5134 907237.886 728532.3241 868379.3767 1004380.062 954323.3706 757582.437 788076.007 1451499.933 0.516871201 0.625034742 0.501916884 0.598263463 0.691960116 0.657473933 0.521930742 0.542939058 1 20.46911307 1.235255227 24.99992293 1.000000578 0.582535117 0.81308264 0.062977132 41.25514546 311976.2081 0.112660235 0.016071515 17.18918268 -1.235255227 -0.417465461 NGYGFVEFEDSRDADDAVYELNGK ddPTM_MDA-MB-175_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 ;;; 216.8 1.19E-32 1845290000 956653 824344 383250 470345 871538 735202 1001492 1130190 227941 FALSE TRUE 830228.8822 818928.83 568590.9819 577144.021 854196.0989 763485.6967 904367.46 888507.6636 200994.0747 4.130613719 4.074392896 2.828894249 2.871447937 4.249857119 3.798548281 4.499473238 4.420566453 1 17.61679345 4.433487277 24.99831932 3.554337302 4.116567151 0.058307559 1.0383996 422.4038276 241998.378 0.258558783 0.684083097 27132.34168 -4.433487277 0.562229849 NHAAPFSK ddPTM_MDA-MB-175_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 ; 99.802 0.0065549 1081790000 2115370 1946800 1095930 1227550 2093800 1842170 2014890 2190920 1749620 FALSE TRUE 1835818.495 1934011.343 1625925.414 1506283.989 2052137.476 1913039.472 1819486.278 1722408.808 1542781.917 1.189940376 1.253586992 1.053891931 0.976342783 1.33015396 1.23999345 1.179354164 1.116430514 1 20.55710271 1.309934851 2.380787973 0.971126904 1.173505606 0.237800856 0.099435548 0.790092534 5.433916805 0.313751703 0.02780302 20.41431684 -1.309934851 0.202378701 NHAGS(ph)PGCEESDAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NHAGSPGCEESDAGK 15 0 P42575 P42575 CASP2 Caspase-2;Caspase-2 subunit p18;Caspase-2 subunit p13;Caspase-2 subunit p12 1 NHAGS(1)PGCEESDAGK;NHAGS(1)PGCEESDAGK 172.57 6.56E-07 800920000 638550 672260 385480 517500 548050 495580 618240 692830 712880 TRUE FALSE 554163.9996 667843.8798 571899.4174 635006.2845 537144.8772 514645.2833 558283.18 544673.6961 628604.1385 0.881578669 1.062423613 0.909792638 1.010184702 0.854504201 0.818711255 0.888131569 0.866481244 1 19.26179224 3.232318754 24.99999963 0.880029821 0.968868225 0.258868264 0.067183526 180.3157354 722202.6239 0.019032528 0.022119555 1707.335043 -3.232318754 0.088838404 NHAVVCQGCHNAIDPEVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NHAVVCQGCHNAIDPEVQR 19 0 Q9UGI8-2;Q9UGI8 Q9UGI8-2 TES Testin 0 ;;; 205.06 2.48E-16 1185470000 335402 355067 159957 226422 359708 362277 292604 350237 302092 FALSE TRUE 291077.7759 352734.5415 237312.7402 277834.5757 352550.5146 376214.0306 264227.3091 275341.5431 266379.0279 1.092720317 1.324182854 0.890883723 1.043004691 1.323492008 1.412326014 0.991922342 1.033645724 1 18.02312098 NHDEESLECLCR ddPTM_MDA-MB-175_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 ;; 215.51 4.13E-11 2555510000 1687650 1664160 911300 1130330 1625090 1564580 1446920 1557270 1438800 FALSE TRUE 1464622.777 1653228.023 1352007.728 1386988.703 1592753.888 1624770.405 1306597.921 1224259.929 1268706.703 1.154421879 1.303081334 1.065658221 1.093230373 1.255415365 1.280650919 1.029866019 0.964966864 1 20.27492716 2.096830157 5.98774167 0.985094702 1.189181392 0.59377162 0.076180386 0.14205538 7.31328603 0.032801764 0.021873528 124.9770178 -2.096830157 0.20408669 NHEESSETMNDLLAQVATNTDTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NHEESSETMNDLLAQVATNTDTSR 24 0 O75843 O75843 AP1G2 AP-1 complex subunit gamma-like 2 0 ; 211.68 2.78E-25 281570000 217940 224560 124248 168674 242880 267560 215130 246030 253350 FALSE TRUE 189138.6768 223084.8506 184334.7484 206974.0097 238047.1632 277853.2063 194266.7257 193418.3991 223399.2516 0.846639706 0.99859265 0.825135926 0.926475842 1.065568311 1.243751733 0.869594344 0.865796988 1 17.76926483 3.462378611 23.60864272 0.992673404 0.896775765 0.18263988 0.11434175 274.0109183 438793.3765 0.036286274 0.046870301 2899.870546 -3.462378611 -0.095897639 NHEGDEDDSHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NHEGDEDDSHVR 12 0 Q9UNE7;Q9UNE7-2;H3BTA3;H3BS86;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ; 187.63 5.92E-06 594590000 362260 348930 164521 245750 270810 282660 184389 209739 180293 FALSE TRUE 314386.4232 346637.8559 244083.9059 301551.2936 265421.4108 293534.1131 166506.9832 164887.947 158978.9669 1.977534697 2.180400732 1.535322003 1.896799931 1.669537901 1.846370742 1.047352278 1.037168314 1 17.27847638 2.235844349 7.89568708 1.028915705 1.846333169 0.838710495 0.170100037 0.044492228 20.73999664 0.067687484 0.048512829 172.125157 -2.235844349 0.817417464 DSAYISSS(ph)PLGSHQVFDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DSAYISSSPLGSHQVFDFR 19 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 DSAYISS(0.046)S(0.954)PLGSHQVFDFR;DSAYIS(0.016)S(0.142)S(0.841)PLGSHQVFDFR;DSAYIS(0.001)S(0.041)S(0.958)PLGSHQVFDFR;DSAYISS(0.008)S(0.992)PLGSHQVFDFR 261.26 2.45E-31 1620840000 859770 1145950 803760 1222000 1708870 1673750 1479010 2009380 1893780 TRUE FALSE 746149.2161 1138422.179 1192461.024 1499473.777 1674866.83 1738140.246 1335575.838 1579689.724 1669899.486 0.446822831 0.68173096 0.714091497 0.897942535 1.002974637 1.04086519 0.799794149 0.945978927 1 20.67132984 4.349883931 1.046316056 0.951456572 0.381572229 0.841575681 0.073164627 0.408311619 0.567369603 0.025372998 0.226682631 22381.22899 -4.349883931 -0.569884343 down NHFTVAQSEAFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NHFTVAQSEAFDR 13 0 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 ;;; 236.05 1.05E-16 1692640000 2049840 2118500 836481 1346210 2111020 2172980 1982900 2144080 1904800 FALSE TRUE 1778948.45 2104583.434 1241006.009 1651887.556 2069014.832 2256575.947 1790598.663 1685585.177 1679616.714 1.059139526 1.253014105 0.738862622 0.983490782 1.231837487 1.343506485 1.066075759 1.003553467 1 20.67970062 3.276053882 24.99067183 1.119321352 1.006814048 0.121606623 0.159543848 432.2149573 288084.6186 0.049232375 0.063557227 1888.225602 -3.276053882 -0.112507304 NHKPS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NHKPSR 6 1 P84103 P84103 SRSF3 Serine/arginine-rich splicing factor 3 1 NHKPS(1)R;NHKPS(1)R;NHKPS(1)R;NHKPS(1)R;NHKPS(1)R;NHKPS(1)R 79.596 0.040413 33307290000 19127370 14377970 9668420 13869470 9712900 13179640 15601240 17550560 34362470 TRUE FALSE 16599639.59 14283520.17 14344100.25 17018745.15 9519632.293 13686669.28 14088234.15 13797509.32 30300177.94 0.547839674 0.471400537 0.473399868 0.561671459 0.314177439 0.451702604 0.464955492 0.45536067 1 24.85282293 1.237946135 24.99710999 1.000000613 0.464823385 0.864924376 0.066117736 5.002884188 203349.0731 0.090709499 0.015695364 17.29601824 -1.237946135 -0.535177228 NHLEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NHLEGK 6 0 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 88.734 0.050966 40100000 258470 242330 131120 170140 124780 175840 211110 238150 255230 FALSE TRUE 224312.5346 240738.1183 194530.0706 208772.8874 122297.1221 182604.6786 190636.5847 187223.4758 225057.0002 0.996692102 1.069676207 0.86435912 0.927644496 0.543405102 0.811370801 0.847059121 0.83189359 1 17.77993091 4.053679022 2.266306393 0.815972697 1.035763615 0.324926249 0.118695472 0.351461071 3.574731232 0.033127615 0.088428566 11315.63739 -4.053679022 0.219790918 NHLS(ph)PQQGGATPQVPSPCCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NHLSPQQGGATPQVPSPCCR 20 0 A0A087X0R7;Q9H4L4 A0A087X0R7 SENP3-EIF4A1;SENP3 Sentrin-specific protease 3 1 NHLS(1)PQQGGATPQVPSPCCR;NHLS(1)PQQGGATPQVPSPCCR;NHLS(1)PQQGGATPQVPSPCCR 168.06 8.25E-12 645940000 361778 328757 132598 173878 310292 312317 266904 274070 181779 TRUE FALSE 313968.1207 326597.3736 196722.8363 213359.6575 304117.7963 324332.0371 241019.6912 215462.2633 160289.2937 1.95875915 2.037549521 1.227298666 1.331091132 1.897305735 2.023416721 1.503654334 1.344208701 1 17.29031854 1.560495675 1.869353617 0.983464142 1.720661222 0.429141247 0.279668342 0.456257249 2.796153546 0.518839329 0.08587792 36.34926847 -1.560495675 0.73719708 NHQLYCNDCYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NHQLYCNDCYLR 12 0 E9PMS6;E9PMT2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 0 185.25 1.33E-05 302870000 92515 95820 35036 50208 92125 88379 74705 81793 68807 FALSE TRUE 80288.90835 95190.55211 51979.52679 61608.49378 90291.89274 91778.99732 67460.1206 64302.20346 60672.71485 1.323311616 1.568918621 0.856719976 1.01542339 1.488179538 1.512689807 1.111869162 1.059820772 1 15.88876025 2.018036681 24.7082679 1.049681732 1.285397106 0.210325395 0.219551465 352.9244285 483465.6387 0.095430833 0.064325045 104.2405469 -2.018036681 0.235715374 NHSDSSTSESEVSSVS(ph)PLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NHSDSSTSESEVSSVSPLK 19 0 Q9NY27-2;Q9NY27;Q9NY27-3;H7C559;C9IZ04 Q9NY27-2 PPP4R2 Serine/threonine-protein phosphatase 4 regulatory subunit 2 1 NHSDSSTSESEVSS(0.038)VS(0.962)PLK;NHSDSSTSESEVSS(0.002)VS(0.998)PLK;NHSDSSTSESEVSS(0.002)VS(0.998)PLK;NHSDSSTSESEVSS(0.001)VS(0.999)PLK;NHSDSSTSESEVSS(0.058)VS(0.942)PLK 234.39 2.52E-24 3026820000 4149790 3697770 1677870 3023020 4115830 3449960 3902440 4514060 4736790 TRUE FALSE 3601384.737 3673479.105 2489293.544 3709442.895 4033933.035 3582682.194 3523981.969 3548763.397 4176812.082 0.862232886 0.879493507 0.595979301 0.888103851 0.965792321 0.857755179 0.843701344 0.849634441 1 21.99397081 3.529703376 24.99983729 0.893270411 0.781391114 0.286532118 0.08994453 463.7248534 220473.6579 0.024542503 0.03640202 3386.128036 -3.529703376 -0.111879297 NHSGNDERDEEDEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NHSGNDERDEEDEER 15 1 A0A0D9SGE8;Q8IWS0-3;Q8IWS0-5;Q8IWS0 A0A0D9SGE8;Q8IWS0-5 PHF6 PHD finger protein 6 0 ; 79.837 0.011271 236670000 96846 96095 79732 82263 82735 99114 76674 86914 83152 FALSE TRUE 84047.55572 95463.74562 118290.6619 100942.0715 81088.73537 102926.9797 69238.16728 68328.11747 73321.86529 1.146282291 1.301981956 1.613306773 1.376698084 1.10592843 1.403769248 0.944304499 0.931892788 1 16.16195587 2.232360658 24.944432 0.952539572 1.329173446 0.604134339 0.13957412 96.72687013 389158.4537 0.058042861 0.040242164 170.7499785 -2.232360658 0.376633874 NHSGSRT(ph)PPVALNSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NHSGSRTPPVALNSSR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 NHS(0.065)GS(0.251)RT(0.684)PPVALNSSR;NHS(0.113)GS(0.142)RT(0.745)PPVALNSSR;NHS(0.345)GS(0.129)RT(0.526)PPVALNSSR 132.64 5.57E-05 588180000 291907 274635 123719 133601 238559 270383 236830 234047 100494 TRUE FALSE 253330.7504 272830.9046 183549.9222 163937.149 233812.1426 280784.809 213862.2631 183997.8704 88613.7138 2.85882105 3.078879023 2.071348941 1.85002007 2.638554831 3.168638317 2.413421737 2.076404007 1 16.43524237 4.240290546 24.99959146 2.218697096 2.968850252 0.256770585 0.558162049 67.06136923 969042.8788 0.147923706 0.351945893 17389.63817 -4.240290546 0.750153156 NHSVNEEEQEEQGEGS(ph)EDEWEQVGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NHSVNEEEQEEQGEGSEDEWEQVGPR 26 0 Q14694;Q14694-3;Q14694-2;H3BNA1 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 NHSVNEEEQEEQGEGS(1)EDEWEQVGPR 432.09 2.06E-187 1735700000 379880 297830 203940 252010 283300 249630 249600 260260 259150 TRUE FALSE 329677.8955 295873.5351 302566.0661 309232.7222 277662.8843 259233.4276 225393.8304 204605.4243 228513.5822 1.44270591 1.294774395 1.32406163 1.353235634 1.215082629 1.134433346 0.986347631 0.895375331 1 17.80192039 2.605924151 1.192042811 0.925806655 1.35478195 0.923424897 0.049423818 0.110061941 0.329138795 0.030196378 0.020503652 403.5749026 -2.605924151 0.428975295 NHVQPYIPSILEALMVPTSQGFTEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NHVQPYIPSILEALMVPTSQGFTEVR 26 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 98.326 0.0059792 157010000 113750 102260 42048 62713 93658 107990 98281 96842 75399 FALSE TRUE 98717.64929 101588.2473 62382.55344 76952.94516 91794.38904 112144.4452 88749.72375 76133.09193 66485.41611 1.484801556 1.527977912 0.938289283 1.15744098 1.380669542 1.68675255 1.334875059 1.145109655 1 16.02075029 1.585672797 3.022689059 1.020581468 1.354830392 0.268957388 0.203205595 0.330543702 6.717110584 0.212506782 0.058389841 38.51880429 -1.585672797 0.334248924 NHYNEEMSNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NHYNEEMSNLR 11 0 P15924;P15924-3 P15924 DSP Desmoplakin 0 134.75 0.00013427 166590000 96559 85520 46746 57049 92741 89140 73954 83831 76582 FALSE TRUE 83798.4835 84958.21349 69352.52196 70002.84739 90895.63554 92569.27348 66781.95246 65904.39302 67528.5632 1.240933903 1.258107821 1.027010182 1.036640557 1.346032423 1.370816571 0.988943779 0.975948397 1 16.04321024 2.177176707 14.56592302 0.985653247 1.204826411 0.47393516 0.111480007 1.630118294 385.2699925 0.049497543 0.033372611 150.3753694 -2.177176707 0.219173164 NICFTVWDVGGQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NICFTVWDVGGQDR 14 0 P18085;C9JPM4;C9JAK5 P18085 ARF4 ADP-ribosylation factor 4 0 ;;; 201.04 4.28E-08 1027302000 682053 763756 360969 317603 743335 752039 704111 784952 823122 FALSE TRUE 591917.9679 758738.8365 535534.8158 389719.6154 728544.0878 780970.427 635826.4236 617096.1233 725813.4549 0.815523554 1.045363421 0.737840849 0.536941845 1.003762169 1.075993317 0.876019064 0.850213122 1 19.46923928 NIDDGTSDRPYSHALVAGIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 NIDDGTSDRPYSHALVAGIDR 21 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;;;;;; 218.69 3.21E-25 20455650000 5198750 5046970 2656851 3847149 5278190 4921610 5095530 5510310 6125920 FALSE TRUE 4511722.016 5013816.122 3941713.03 4720702.98 5173164.346 5110947.521 4601366.285 4331973.088 5401720.716 0.835237927 0.928188699 0.729714333 0.873925778 0.957688229 0.946170265 0.85183343 0.801961692 1 22.36498762 3.486574219 24.93101853 0.896972706 0.834270975 0.189342775 0.0726786 929.2644489 2450818.767 0.021294459 0.029176532 3066.014606 -3.486574219 -0.062701731 NIDDGTSDRPYSHALVAGIDRYPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NIDDGTSDRPYSHALVAGIDRYPR 24 2 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;; 288.49 1.22E-53 2567430000 1325782 1295379 425709 511433 1299913 1285886 1340208 1457247 192877 FALSE TRUE 1150576.55 1286869.57 631583.2963 627561.6794 1274047.275 1335354.866 1210234.834 1145626.069 170075.3008 6.765100778 7.566469464 3.713550959 3.689904863 7.491077591 7.851550815 7.11587649 6.735993199 1 17.37581412 NIDEHANEDVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NIDEHANEDVER 12 0 P61026 P61026 RAB10 Ras-related protein Rab-10 0 ;;; 192.18 4.42E-06 2808200000 3283100 3420600 1830180 2233100 3648820 3815600 2559420 3081010 3480450 FALSE TRUE 2849230.017 3398129.853 2715261.17 2740159.486 3576215.621 3962388.601 2311207.842 2422159.988 3068995.166 0.928391823 1.107245098 0.884739474 0.89285233 1.165272484 1.291102914 0.75308292 0.789235517 1 21.54933494 2.196526181 24.99996707 0.831382041 1.039042851 0.302169335 0.140587694 176.3063236 104856.8841 0.059627409 0.040201176 157.2266573 -2.196526181 0.20766081 NIDLATPLHHTWTYQALVHDVLDFHLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NIDLATPLHHTWTYQALVHDVLDFHLNR 28 0 Q8WVM8;Q8WVM8-2;Q8WVM8-3 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 ;; 241.94 8.57E-46 1565850000 631588 547983 151006.3 333305 548424 592397 518473 644511 599978 FALSE TRUE 548122.0456 544383.2636 224033.4518 408986.9945 537511.4354 615186.8959 468191.5683 506687.3382 529049.2843 1.03605101 1.028984028 0.423464237 0.773060293 1.015995015 1.162815855 0.884967775 0.957731828 1 19.0130426 3.236586451 24.99015833 0.997456445 0.802651909 0.211548501 0.180211595 86.11070067 1090042.86 0.056050668 0.066798325 1724.195276 -3.236586451 -0.194804536 NIDNPALADIYTEHAHQVVVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NIDNPALADIYTEHAHQVVVAK 22 0 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ; 185.5 2.04E-17 629350000 873840 740650 430890 595440 775310 634580 867810 933410 921930 FALSE TRUE 758359.83 735784.6214 639269.8452 730643.7527 759882.8479 658992.7032 783649.9198 733807.5353 812940.4857 0.932860207 0.90509039 0.786367337 0.898766596 0.934733675 0.810628471 0.963969606 0.902658372 1 19.63279021 -1.523629632 0.752185053 9.999885475 0.880635757 0.296598153 0.053902711 216.7397941 2.111290495 3276.515778 0.020626988 0.029948175 1.523629632 -9.119249718 NIDPKPCTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NIDPKPCTPR 10 1 K7EQ55;K7EK33;Q96EP5;Q96EP5-2 K7EQ55 DAZAP1 DAZ-associated protein 1 0 ; 76.143 0.033636 733560000 1917200 1520750 856960 1128990 1617680 1377830 1835810 2018370 1569270 FALSE TRUE 1663837.162 1510760.093 1271388.722 1385344.435 1585491.333 1430836.012 1657773.429 1586757.282 1383752.688 1.202409344 1.091784757 0.918797653 1.001150312 1.145790969 1.034025822 1.198027251 1.146705835 1 20.40015469 3.231576119 24.99871858 1.113574045 1.046643471 0.067505572 0.090191098 383.497743 1372604.661 0.027984001 0.032411433 1704.418027 -3.231576119 -0.066930574 NIEDYIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NIEDYIHR 8 0 Q9BUQ8 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 ;;; 185.72 0.00021128 1143440000 2035820 1851500 965120 1310730 1947870 1920980 1766960 2027950 1844100 FALSE TRUE 1766781.229 1839337.375 1431855.26 1608351.28 1909111.198 1994881.344 1595600.491 1594288.674 1626092.599 1.086519446 1.13113938 0.880549645 0.989089601 1.174048267 1.22679443 0.981248234 0.980441504 1 20.63297798 NIEVPFKPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NIEVPFKPAR 10 1 P21399 P21399 ACO1 Cytoplasmic aconitate hydratase 0 ; 120.06 0.00055601 637600000 597970 632440 351640 383460 659120 591600 677310 841530 695950 FALSE TRUE 518946.7494 628285.46 521694.2802 470530.4538 646004.8015 614359.2348 611624.5804 661575.3583 613675.5838 0.845636951 1.023807165 0.850114122 0.766741363 1.052681284 1.001114027 0.996657838 1.078053903 1 19.22711666 3.213893443 24.99970577 1.028837878 0.880915678 0.559344877 0.06771971 177.4605027 179852.2595 0.020789418 0.02358319 1636.414966 -3.213893443 -0.1479222 NIGRDT(ph)PTSAGPNSFNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NIGRDTPTSAGPNSFNK 17 1 Q8WW12;Q8WW12-3 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 1 NIGRDT(0.974)PT(0.025)S(0.001)AGPNSFNK;NIGRDT(0.917)PT(0.077)S(0.007)AGPNSFNK;NIGRDT(0.991)PT(0.008)SAGPNSFNK 192.11 3.32E-10 3385220000 1910100 1457680 962950 991150 1492550 1408680 1687910 1940300 1664440 TRUE FALSE 1657675.445 1448104.404 1428635.841 1216205.756 1462851.175 1462872.831 1524216.748 1525381.944 1467671.799 1.12945922 0.986667731 0.973402801 0.8286633 0.996715462 0.996730217 1.038526971 1.039320879 1 20.48509796 2.507113201 2.828710201 1.02881914 0.974535273 0.060864566 0.072261148 0.674424225 10.89169402 0.029631149 0.023649319 321.4498301 -2.507113201 -0.054283867 NIGS(ph)DFIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NIGSDFIPR 9 0 Q5T853;Q5T857;P41279-2;P41279 Q5T853 MAP3K8 Mitogen-activated protein kinase kinase kinase 8 1 NIGS(1)DFIPR 105.65 0.0032137 41316000 138140 150630 87890 90956 155580 149080 148930 151470 171590 TRUE FALSE 119884.449 149640.5016 130393.898 111608.95 152484.2624 154815.2041 134486.7915 119079.3192 151304.8257 0.792337247 0.989000192 0.861796029 0.737643029 1.007795103 1.023200703 0.888846677 0.787016004 1 17.20709848 3.219012194 24.99961356 0.922229266 0.856651737 0.187608543 0.09357356 622.7549655 796411.8481 0.030553737 0.034692634 1655.816455 -3.219012194 -0.065577529 NIHESCMSQIGWNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 NIHESCMSQIGWNR 14 0 P11413;P11413-3;P11413-2;E9PD92 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;; 254.45 2.96E-24 5922100000 4104420 4290880 2008011 2755395 5053830 4967920 4840390 5139760 5260010 FALSE TRUE 3562010.498 4262692.927 2979091.836 3381049.548 4953268.671 5159039.097 4370969.723 4040662.322 4638177.61 0.767976304 0.919044781 0.642297921 0.728960776 1.067934238 1.112298737 0.942389466 0.871174556 1 22.14512664 3.245986752 24.99660519 0.98426052 0.766870113 0.60674532 0.093272708 137.4789889 462755.9546 0.02971597 0.037592735 1761.922298 -3.245986752 -0.217390407 NIHLNLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NIHLNLDR 8 0 Q9Y5S9;Q9Y5S9-2;A0A0J9YW13 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ;;;;; 149.72 0.00050068 4630160000 2867660 3548510 1662870 2018340 4266060 4195910 3304960 3633530 5340230 FALSE TRUE 2488691.465 3525199.604 2467039.494 2476634.945 4181173.752 4357329.373 2984445.488 2856527.886 4708914.093 0.528506449 0.74862262 0.523908367 0.525946088 0.88792738 0.925336349 0.633786353 0.606621363 1 22.16696297 3.247360647 24.99933261 0.777679186 0.589534385 0.393597195 0.137733061 254.9307097 724209.1604 0.042419371 0.053924566 1767.504985 -3.247360647 -0.1881448 NIIEATHMYDNAAEACSTTEEVFNS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NIIEATHMYDNAAEACSTTEEVFNSPR 27 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 NIIEATHMYDNAAEACSTTEEVFNS(1)PR;NIIEATHMYDNAAEACSTTEEVFNS(1)PR;NIIEATHMYDNAAEACSTTEEVFNS(1)PR;NIIEATHMYDNAAEACSTTEEVFNS(1)PR;NIIEATHMYDNAAEACSTTEEVFNS(1)PR;NIIEATHMYDNAAEACSTTEEVFNS(1)PR 302.51 3.42E-71 3568391000 1456941 1320553 644703 762781 1110660 1299483 1158612 1174972 1208394 TRUE FALSE 1264402.555 1311878.2 956483.5272 935982.0844 1088560.039 1349474.952 1046249.987 923713.3814 1065539.038 1.186631846 1.231187365 0.897652262 0.878411819 1.021605028 1.26647162 0.981897377 0.866897738 1 20.02315202 4.248689476 24.99798103 0.983763799 1.208909724 0.398704991 0.112934259 221.781589 547344.9034 0.030806491 0.079502125 17729.21374 -4.248689476 0.225145925 NIIGSS(ph)PVADFSAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NIIGSSPVADFSAIK 15 0 P42566;B1AUU8 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 NIIGS(0.003)S(0.997)PVADFSAIK;NIIGS(0.001)S(0.999)PVADFSAIK;NIIGSS(1)PVADFSAIK;NIIGS(0.001)S(0.999)PVADFSAIK 288 1.31E-34 757900000 2061810 1925620 1367190 1752970 2285550 1827960 2352210 2758960 2701160 TRUE FALSE 1789336.585 1912970.475 2028367.657 2151008.631 2240072.027 1898282.804 2124093.036 2168977.874 2381831.942 0.751243844 0.803150903 0.851599822 0.903090009 0.940482822 0.796984359 0.891789634 0.910634305 1 21.18364019 6.662810494 0.388891208 0.92418489 1.71E-21 0.560583664 0.049056654 24.84465478 0.951605323 0.055234112 14.42446671 4600557.827 -6.662810494 -0.92418489 NIIHGSDSVESAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 NIIHGSDSVESAEK 14 0 P15531;P15531-2 P15531 NME1 Nucleoside diphosphate kinase A 0 ;;;;;;; 230.38 9.34E-13 10757750000 11106360 12473540 2389685 6600260 14398660 11854080 14695470 16466170 17740390 FALSE TRUE 9638626.386 12391600.49 3545344.659 8098949.912 14112154.84 12310114.13 13270305.58 12945007.69 15643141.3 0.616156704 0.79214272 0.226638921 0.517731685 0.902130497 0.78693364 0.848314627 0.827519706 1 23.89902691 3.241185186 24.99908541 0.861145033 0.534056497 0.559043459 0.147529345 53.98925417 514244.637 0.043782411 0.053948027 1742.549749 -3.241185186 -0.327088537 NIIHGSDSVESAEKEIGLWFHPEELVDYTSCAQNWIYE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NIIHGSDSVESAEKEIGLWFHPEELVDYTSCAQNWIYE 38 1 P15531;P15531-2 P15531 NME1 Nucleoside diphosphate kinase A 0 82.317 0.00060714 157970000 138290 164120 18022 33957 153780 138360 169510 190060 14998 FALSE TRUE 120014.6261 163041.8849 26737.49948 41667.45585 150720.0789 143682.7987 153070.9463 149417.148 13224.95353 9.074861842 12.3283522 2.021746196 3.150669359 11.39664337 10.86452202 11.57440334 11.29812273 1 13.69097503 5.881541654 14.80538899 8.430519607 10.44457908 0 4.379237671 0 0 1.001506801 0 761275.1514 -5.881541654 2.014059474 NIIHGSDSVK ddPTM_MDA-MB-175_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 ;;;;;; 183.99 1.61E-06 11882320000 10534010 12296440 1870380 5517420 14537860 12574330 14277810 15893320 14596870 FALSE TRUE 9141913.889 12215663.88 2774902.024 6770234.539 14248585.03 13058072.61 12893150.18 12494657.2 12871244.66 0.71025873 0.949066248 0.215589253 0.525996881 1.107009105 1.014515143 1.001701897 0.970741955 1 23.61764823 3.240582569 24.99999995 1.011291379 0.597670584 0.565983445 0.182060552 41.80873249 516929.9154 0.055205122 0.067748837 1740.133505 -3.240582569 -0.413620795 NIILEEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NIILEEGK 8 0 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 93.551 0.025564 527180000 510930 409430 292090 358850 426880 419800 511700 535470 963130 FALSE TRUE 443409.306 406740.4274 433345.701 440332.3772 418385.9232 435949.9776 462075.4128 420963.9075 849269.8686 0.522106485 0.47892954 0.510256771 0.518483457 0.492641902 0.51332326 0.54408549 0.495677432 1 19.69586354 1.23759081 24.99999814 1.000000577 0.509368481 0.986802744 0.017828834 2.361178944 60835.1213 0.024907177 0.004211767 17.28187305 -1.23759081 -0.490632096 NIILEEGKEILVGDVGQTVDDPYATFVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NIILEEGKEILVGDVGQTVDDPYATFVK 28 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 356.23 3.96E-111 2067900000 4441800 3081300 1819300 2112710 2916300 2152480 4159600 4819500 1225550 FALSE TRUE 3854804.876 3061058.737 2699119.565 2592433.096 2858271.336 2235287.298 3756202.632 3788887.43 1080666.875 3.567061196 2.832564602 2.497642546 2.398919737 2.644914359 2.068433252 3.475819162 3.506064188 1 20.04349044 4.708938021 3.139856444 2.638624932 3.675805027 0.163827321 0.710532307 0.667766336 10.49051163 0.179589691 1.64192787 51160.88172 -4.708938021 1.037180094 NIIQHFENNQQYDAPEPGT(ph)QRLSTGSFPEDLLESDSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NIIQHFENNQQYDAPEPGTQRLSTGSFPEDLLESDSSR 38 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 NIIQHFENNQQYDAPEPGT(0.541)QRLS(0.113)T(0.139)GS(0.172)FPEDLLES(0.033)DS(0.001)S(0.001)R 104.78 2.78E-05 84625000 25136 25217 14316 20412 31362 29816 30674 31514 18075 TRUE FALSE 21814.21391 25051.34787 21239.26548 25046.85658 30737.95756 30963.04081 27699.2402 24774.97634 15938.19409 1.368675384 1.571780826 1.332601759 1.571499031 1.92857217 1.942694426 1.737915854 1.554440622 1 13.96020055 1.242906079 3.734750946 0.921095136 1.642673472 0.493952409 0.200654467 0.253074311 5.62008248 0.507656793 0.056468185 17.49468307 -1.242906079 0.721578336 NIITHAPNLDNIELYWNSYNNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NIITHAPNLDNIELYWNSYNNR 22 0 Q9UN36;Q9UN36-5;G3V578;H0YJT9;A0A0A0MS87;Q9UN36-2;Q9UN36-3;Q9UN36-6;Q9UN36-4;G3V5H8;G3V4S9;G3V5L7;A0A0U1RR50;G3V2I9;H7C0X0 Q9UN36 NDRG2 Protein NDRG2 0 178.41 6.04E-17 257050000 142180 149680 78157 103620 175780 172260 128900 188890 246380 FALSE TRUE 123390.5528 148696.7422 115953.9866 127148.5047 172282.3219 178886.9537 116399.2978 148497.3434 217253.2371 0.567957258 0.684439708 0.533727314 0.585254823 0.793002324 0.823402938 0.535777047 0.683521891 1 17.72901815 3.248519971 24.95233716 0.742149292 0.595164559 0.324011316 0.122149677 292.6242949 733141.824 0.036207616 0.046176717 1772.229541 -3.248519971 -0.146984733 NILFVITKPDVYK ddPTM_MDA-MB-175_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 ; 164.33 3.39E-05 1086370000 3186800 2763500 1438110 1477810 2495770 1937130 3072900 3579300 3798600 FALSE TRUE 2765656.306 2745346.387 2133584.806 1813369.347 2446109.06 2011652.645 2774890.631 2813894.549 3349533.835 0.825683943 0.819620437 0.636979625 0.541379618 0.730283431 0.600576899 0.828440842 0.840085423 1 21.67552889 1.532660718 1.4088195 1.030067764 0.693152892 0.517144118 0.094304135 0.593871035 1.660865269 0.259912954 0.030300219 34.09264673 -1.532660718 -0.336914872 NILPFDHTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NILPFDHTR 9 0 Q06124;Q06124-1;Q06124-3 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 91.549 0.010678 137930000 263440 249370 140940 174930 294860 304140 251300 307790 329770 FALSE TRUE 228625.7365 247731.8721 209099.0554 214650.5301 288992.8629 315840.4626 226928.9647 241971.5037 290784.9663 0.786236439 0.851941815 0.719084821 0.738176161 0.993837015 1.086165033 0.780401296 0.832132097 1 18.14959316 3.247295082 24.99833418 0.92073518 0.77552458 0.432136654 0.092539873 227.4126467 650858.9134 0.029365645 0.037316877 1767.238165 -3.247295082 -0.1452106 NINDAWVCTNDMFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NINDAWVCTNDMFR 14 0 P61970 P61970 NUTF2 Nuclear transport factor 2 0 ;;; 265.26 2.19E-24 2148230000 1667260 1666140 770523 828190 1612370 1545080 1467860 1596250 1611670 FALSE TRUE 1446927.367 1655195.017 1143150.5 1016243.198 1580286.992 1604520.227 1325507.163 1254904.36 1421140.209 1.0181454 1.164695085 0.804389668 0.715090032 1.111985279 1.129037246 0.932706819 0.883026426 1 20.43861747 2.793060338 0.010714961 6.62E-07 1.930991536 0.002939829 0.144257376 16421.33206 212.7017922 19259.73996 19063.94234 620.9552996 -2.793060338 1.930990874 NINMDNDLEVLTS(ph)SPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NINMDNDLEVLTSSPTR 17 0 Q9Y5T5-4;Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5 Q9Y5T5-4 USP16 Ubiquitin carboxyl-terminal hydrolase 16 1 NINMDNDLEVLT(0.001)S(0.499)S(0.499)PT(0.002)R;NINMDNDLEVLT(0.001)S(0.499)S(0.499)PT(0.001)R 236.16 5.04E-19 100290000 358670 371430 189767 253794 395870 410840 349250 417410 368300 TRUE FALSE 311270.8507 368990.0519 281538.9559 311421.8067 387992.9615 426645.2806 315379.7888 328150.1198 324759.9936 0.958464272 1.136193063 0.86691391 0.958929095 1.194706766 1.313724871 0.971116501 1.010438867 1 18.3090144 4.800041204 20.37947154 1.052284833 0.958456768 0.05309618 0.129024655 27001.12308 8946897.16 0.033093898 42.5165933 63101.72094 -4.800041204 -0.093828065 NINMDNDLEVLTSS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NINMDNDLEVLTSSPTR 17 0 Q9Y5T5-4;Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5 Q9Y5T5-4 USP16 Ubiquitin carboxyl-terminal hydrolase 16 1 NINMDNDLEVLTSS(1)PTR;NINMDNDLEVLTS(0.08)S(0.919)PT(0.002)R;NINMDNDLEVLTSS(0.999)PTR;NINMDNDLEVLTS(0.007)S(0.993)PTR 465.34 2.94E-206 1994500000 3104690 3304600 1605810 2196730 3698480 3689140 3234480 3882100 3506210 TRUE FALSE 2694397.35 3282891.865 2382385.087 2695531.121 3624887.484 3831063.603 2920800.627 3051943.126 3091709.848 0.871491014 1.061836985 0.770572015 0.871857727 1.17245397 1.239140732 0.944720162 0.987137628 1 21.5599735 3.260402826 24.99758361 1.057721145 0.897120101 0.37590677 0.111355698 302.5453672 346249.6286 0.034321784 0.044270778 1821.389488 -3.260402826 -0.160601044 NINTFVET(ph)PVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NINTFVETPVQK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 NINTFVET(1)PVQK;NINTFVET(1)PVQK 271.79 1.13E-26 368970000 1045460 959920 624580 651340 1012170 898660 1036660 1230660 1362410 TRUE FALSE 907299.8121 953614.2223 926628.9771 799236.7021 992029.7973 933232.0317 936124.8728 967492.936 1201347.442 0.755235147 0.7937872 0.771324718 0.665283559 0.825764273 0.776821092 0.779229089 0.805339823 1 20.19622202 1.052535479 1.928154406 1.188302138 0.765829073 0.759723661 0.040878375 0.708153326 1.639952643 0.646772739 0.01093586 11.28588132 -1.052535479 -0.422473065 NIQFEAFHVFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NIQFEAFHVFK 11 0 Q9Y376;A0A087X0K1 Q9Y376 CAB39 Calcium-binding protein 39 0 ; 119.76 0.0005424 726700000 1422930 1571130 784530 818440 1592350 1542160 1596840 1827210 1894820 FALSE TRUE 1234886.195 1560809.144 1163931.332 1004279.311 1560665.35 1601487.893 1441978.703 1436475.361 1670816.538 0.739091436 0.934159501 0.696624259 0.601070966 0.934073439 0.958506129 0.863038323 0.859744519 1 20.6721219 3.198529661 24.99999489 0.912425731 0.753115563 0.488060849 0.091139817 152.1954214 95048.02982 0.028623015 0.032455864 1579.53648 -3.198529661 -0.159310168 NIQVSHQEFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NIQVSHQEFSK 11 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;; 227.93 3.64E-12 1374660000 3497090 3528360 1626480 2258570 3882150 3271830 3760930 4476440 4083980 FALSE TRUE 3034940.696 3505181.971 2413051.168 2771412.839 3804902.81 3397699.417 3396195.587 3519188.142 3601176.537 0.842763654 0.973343555 0.670073001 0.769585387 1.056572143 0.943497044 0.94307945 0.977232886 1 21.78003689 3.245687813 24.99987776 0.978117153 0.815050938 0.525264877 0.080257452 142.9203642 501315.1758 0.023816643 0.030091853 1760.709927 -3.245687813 -0.163066215 NIRDDEGFIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NIRDDEGFIIR 11 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;;; 249.2 2.16E-16 1212350000 858220 778730 382912 535982 835220 876410 803080 907850 595571 FALSE TRUE 744804.0525 773614.4714 568089.524 657684.9051 818600.7561 910126.0598 725197.4252 713713.3424 525163.2749 1.418233316 1.473093242 1.081738863 1.252343674 1.558754763 1.733034474 1.38089897 1.359031327 1 19.00240651 1.197340165 2.80730252 0.883577824 1.413471079 0.361655901 0.171330546 0.652539408 5.573578399 0.848634626 0.048410047 15.75216183 -1.197340165 0.529893255 NISFNDKK ddPTM_MDA-MB-175_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 ; 136.63 0.0012547 4389700000 4317200 3357500 2241700 2811400 3398700 2875100 4550700 5982200 4545300 FALSE TRUE 3746671.082 3335444.361 3325793.618 3449771.34 3331072.519 2985706.957 4109373.814 4702953.084 4007959.812 0.934807547 0.832205041 0.829797147 0.860730023 0.831114252 0.744944335 1.025303149 1.173403254 1 21.93443661 2.08051934 5.528541168 1.099353748 0.839809569 0.753424646 0.061837408 0.082347376 4.238209919 0.024926605 0.016472164 120.3702993 -2.08051934 -0.259544179 NISFTVWDVGGQDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NISFTVWDVGGQDK 14 0 P61204;F5H423;F5H0C7;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 ; 232.5 3.34E-13 664730000 1489740 1322100 773870 721140 1279590 1083770 1418360 1649560 1675230 FALSE TRUE 1292867.084 1313415.038 1148116.12 884885.8589 1254128.662 1125463.333 1280807.666 1296814.431 1477186.218 0.875222818 0.889133017 0.777231812 0.599034738 0.848998351 0.761896719 0.867059041 0.877895024 1 20.49442028 1.22331971 1.113889183 1.106983942 0.790339315 0.386783204 0.082196504 1.951478852 1.968344154 0.750287143 0.027961206 16.72321255 -1.22331971 -0.316644628 NISHYEEQLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NISHYEEQLVK 11 0 P13861-2;P13861;H7C330 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 0 127.56 0.00028413 531820000 943380 799640 524380 616240 940920 827010 989670 1122400 1093500 FALSE TRUE 818709.9428 794387.1122 777971.9219 756166.7106 922197.5329 858825.6098 893691.9557 882383.4945 964227.6757 0.849083638 0.823858444 0.806834259 0.784220086 0.956410562 0.890687575 0.926847443 0.915119444 1 19.87901431 3.236437602 24.99999997 0.931797629 0.815905849 0.775373792 0.032489943 26.54252744 312557.8016 0.009540477 0.011355767 1723.604433 -3.236437602 -0.115891781 NIVSLLLSMLGHDEDNTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NIVSLLLSMLGHDEDNTR 18 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 92.897 0.0017064 46125000 71694 67992 34642 40197 58986 59709 65083 73847 61408 FALSE TRUE 62219.45625 67545.35608 51394.98707 49324.34322 57812.294 62006.04387 58771.26068 58055.39373 54148.4162 1.149054037 1.247411482 0.949150329 0.910910174 1.067663619 1.145112789 1.085373586 1.072153127 1 15.72463152 4.247967092 24.99566843 1.04011502 1.19823279 0.476702121 0.071703911 191.0739465 507726.4558 0.019503045 0.050137033 17699.74838 -4.247967092 0.15811777 NIYAFMGT(ph)PVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NIYAFMGTPVQK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 NIYAFMGT(1)PVQK;NIYAFMGT(1)PVQK 198.78 2.00E-06 451840000 2153460 2151070 1162200 1218840 2142040 1879940 2211970 2622460 2504460 TRUE FALSE 1868874.805 2136939.48 1724243.807 1495596.251 2099417.595 1952262.508 1997453.49 2061667.337 2208385.592 0.846262904 0.967647809 0.780771172 0.677235106 0.950657169 0.88402248 0.904485837 0.933563117 1 21.07456066 1.603801787 0.772902552 1.035940137 0.839420893 0.294504156 0.080461785 2.376051142 1.59551875 0.3820967 0.038047281 40.16074744 -1.603801787 -0.196519244 NIYSEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 ;;;;;; 239.76 2.35E-08 9772730000 7045970 6806810 3390115 4328530 7287080 7483560 6799880 7451320 7082820 FALSE TRUE 6114827.212 6762095.617 5029585.953 5311388.894 7142081.365 7771457.396 6140428.684 5857913.204 6245497.088 0.979077746 1.082715358 0.805313954 0.850434932 1.143556912 1.24432968 0.983176935 0.937941868 1 22.57438497 3.242392054 24.99937972 1.049548294 0.93147539 0.251432807 0.11240671 180.5428484 1177998.369 0.036848823 0.045775686 1747.398885 -3.242392054 -0.118072904 NKCPEPNCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NKCPEPNCR 9 1 H0YKX0;Q96EP0-3;Q96EP0;H0YNT1;H0YMN0;A0A0B4J293;Q96EP0-2 H0YKX0 RNF31 E3 ubiquitin-protein ligase RNF31 0 64.297 0.064237 34252000 29845 23065 10963 13942 28290 21584 30861 33409 8557.6 FALSE TRUE 25900.90763 22913.4845 16264.74347 17107.74419 27727.08435 22414.35045 27868.10497 26264.74534 7545.930277 3.432433998 3.036535411 2.155432514 2.267148458 3.67444216 2.970389286 3.693130462 3.480650414 1 12.88148305 3.253500486 24.99668412 3.083377568 2.70475875 0.008719708 0.840969035 906.6618325 1516975.099 0.242265923 0.311455163 1792.67056 -3.253500486 -0.378618818 NKDEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NKDEVK 6 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 71.342 0.080698 98112000 243390 190790 123530 151690 169730 148880 272080 271320 296600 FALSE TRUE 211225.3948 189536.6879 183269.5212 186133.5329 166352.7051 154607.5099 245693.7235 213300.3294 261536.2859 0.807633228 0.724705129 0.700742234 0.711692958 0.636059752 0.591151279 0.939424993 0.815566867 1 17.9966516 2.227554932 24.9993842 0.897800476 0.694961533 0.675925488 0.072325427 135.8743638 308635.5961 0.029752619 0.020273022 168.8709442 -2.227554932 -0.202838943 NKDLPESALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NKDLPESALR 10 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 77.64 0.029542 116960000 333910 261780 120610 175250 309690 276820 312370 368600 153930 FALSE TRUE 289782.9475 260060.3499 178937.3994 215043.191 303527.7749 287469.4445 282076.4055 289777.7584 135732.5708 2.134955124 1.915976014 1.318308483 1.584315318 2.236219157 2.117910557 2.078177728 2.134916895 1 17.05040743 3.260522391 24.9991691 1.963707268 1.721067844 0.035851606 0.402685131 679.654076 773647.6258 0.116579588 0.150372848 1821.891004 -3.260522391 -0.242639424 NKDQEVNFQEYVTFLGALALIYNEALKG ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NKDQEVNFQEYVTFLGALALIYNEALKG 28 2 P06703 P06703 S100A6 Protein S100-A6 0 ;; 163.76 3.09E-11 5667477000 1406781 1398760 968589 1035277 956045 693709 1732280 1920600 1051778 FALSE TRUE 1220871.327 1389571.453 1437001.88 1270352.466 937021.575 720396.4341 1564283.752 1509894.636 927438.003 1.316391309 1.498290397 1.549431741 1.369743812 1.010333383 0.776759667 1.686672044 1.628027568 1 19.82289132 3.476216909 24.99815101 1.275558729 1.459150551 0.112473591 0.282526078 91.7155468 2535165.053 0.090866973 0.118360248 2993.7595 -3.476216909 0.183591822 NKDQGTYEDYVEGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 NKDQGTYEDYVEGLR 15 1 F8VPF3;P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;G3V1Y7;P60660-2;G8JLA2;F8VZU9;F8W180 F8VPF3;P60660;P60660-2 MYL6 Myosin light polypeptide 6 0 ;;;;;;;; 273.54 1.72E-33 32171929000 17473202 17231025 9257676 11873492 19232970 15981727 20064471 23612390 12319959 FALSE TRUE 15164074.08 17117833.26 13734719.08 14569549.83 18850271.53 16596554.38 18118621.69 18563064.15 10863507.48 1.395872752 1.575718827 1.264298764 1.341146021 1.735192023 1.527734427 1.667842704 1.70875421 1 23.37298664 4.772263855 21.09932292 1.503252528 1.395871249 0.001426019 0.227451597 9204.693806 5761607.529 0.054940742 5.838426513 59192.11461 -4.772263855 -0.107381279 NKDSGSDTASAIIPSTTPSVDS(ph)DDESVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NKDSGSDTASAIIPSTTPSVDSDDESVVK 29 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 NKDSGSDTASAIIPSTT(0.001)PS(0.002)VDS(0.997)DDESVVK;NKDSGSDTASAIIPSTTPS(0.001)VDS(0.999)DDESVVK;NKDSGSDTASAIIPSTTPS(0.043)VDS(0.955)DDES(0.001)VVK 204.25 1.50E-25 1674420000 3034750 2061360 1597810 1628410 2616130 1921490 3267110 4065200 1294670 TRUE FALSE 2633700.098 2047818.79 2370516.26 1998165.379 2564074.131 1995410.964 2950266.175 3195888.615 1141615.587 2.306993814 1.793790145 2.07645751 1.75029616 2.246004837 1.747883425 2.584290375 2.799443745 1 20.12264551 2.245772385 24.99661551 2.286829751 1.983219417 0 0.509388108 459.0913257 1591255.135 0.187636933 0.142250218 176.1052831 -2.245772385 -0.303610334 NKDVYPSCSSTTASTVGNSSSHNTASQS(ph)PDFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NKDVYPSCSSTTASTVGNSSSHNTASQSPDFVR 33 1 Q6PIJ6-2;Q6PIJ6 Q6PIJ6-2 FBXO38 F-box only protein 38 1 NKDVYPSCSSTTASTVGNSSSHNTASQS(1)PDFVR 275.38 8.30E-74 168850000 102200 124990 34473 76361 177600 161600 146510 161330 125820 TRUE FALSE 88694.01106 124168.9325 51144.25811 93699.93215 174066.1075 167816.8566 132301.4828 126830.835 110945.7029 0.799436199 1.119186496 0.460984579 0.844556659 1.568930593 1.512603482 1.192488571 1.143179336 1 16.75949427 3.347770261 8.181047209 1.269778321 0.798121965 0.524034139 0.226190692 0.21303312 14.6768696 0.068357028 0.088265683 2227.256633 -3.347770261 -0.471656356 NKEDQYDHLDAADMTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NKEDQYDHLDAADMTK 16 1 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 190.19 1.21E-09 276860000 256880 217410 150110 145010 183720 148020 255800 297610 270420 FALSE TRUE 222932.6571 215981.8194 222703.6981 177936.7368 180064.3314 153714.4252 230992.5554 233968.4175 238451.2557 0.9349192 0.905769268 0.933959008 0.746218494 0.755141049 0.644636677 0.968720231 0.981200191 1 17.86333485 2.038327624 24.97064029 0.984968415 0.821515549 0.418991727 0.090801439 161.245078 105051.3458 0.040390811 0.027231428 109.226401 -2.038327624 -0.163452865 NKEEAAEYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NKEEAAEYAK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ;;;; 129.34 0.00027873 7793550000 8802660 7543290 5270840 5874280 7232090 5536480 10871190 11246360 9808780 FALSE TRUE 7639366.178 7493737.631 7819835.854 7208125.057 7088185.558 5749471.968 9816903.667 8841413.433 8649197.203 0.883245693 0.86640846 0.904111176 0.833386601 0.819519476 0.664740534 1.135007497 1.022223592 1 23.0441348 2.224425317 24.9999994 1.049563009 0.833530049 0.677015052 0.072820456 141.1447346 249629.6861 0.030152777 0.020438891 167.6584001 -2.224425317 -0.21603296 NKEFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 86.953 0.048328 481130000 773360 648590 354820 463490 655670 679210 832780 879120 574640 FALSE TRUE 671158.5166 644329.3696 526412.1388 568732.4885 642623.4498 705339.6482 752017.1238 691127.0293 506706.7138 1.324550274 1.271602195 1.038889212 1.122409617 1.268235514 1.392007702 1.484127017 1.363958697 1 18.95079142 3.016027328 6.382006164 1.334530173 1.185105172 0.123692106 0.145573064 0.276476754 44.94737426 0.04647505 0.051456682 1037.593704 -3.016027328 -0.149425001 NKEGLHNAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NKEGLHNAK 9 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 53.683 0.084113 307520000 531600 476090 311750 313350 338800 487170 486090 608860 391670 FALSE TRUE 461347.7131 472962.5334 462513.3427 384500.9068 332058.5429 505911.7451 438949.0666 478660.0272 345367.2188 1.3358179 1.36944825 1.339192945 1.113310372 0.961465144 1.464851664 1.270963319 1.385945165 1 18.39777163 3.916372877 10.98297525 1.224495704 1.353059112 0.156656076 0.15581614 1.427861705 182.7079519 0.042521269 0.073734931 8248.460088 -3.916372877 0.128563408 NKEIFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NKEIFLR 7 1 P14625;Q96GW1;A0A1W2PRR1;F8W026 P14625 HSP90B1 Endoplasmin 0 ; 131.06 0.0031944 2369740000 3297400 3011800 1240200 1528110 4337800 4221300 3626500 3534200 578720 FALSE TRUE 2861640.235 2992015.287 1839964.868 1875090.731 4251486.267 4383696.143 3274802.588 2778438.833 510304.3809 5.607712461 5.863197338 3.605622325 3.674455485 8.331275266 8.590355691 6.417351508 5.444669764 1 18.9609985 5.089746453 15.58936438 5.520325519 7.823448513 0 2.254899172 194725698.1 436685390.6 0.570094978 15280987953 122955.0734 -5.089746453 2.303122994 NKELYEINPPEISEEIIGS(ph)PIPEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NKELYEINPPEISEEIIGSPIPEPR 25 1 Q86YS7;Q86YS7-5;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 NKELYEINPPEISEEIIGS(1)PIPEPR;NKELYEINPPEIS(0.004)EEIIGS(0.996)PIPEPR;NKELYEINPPEISEEIIGS(1)PIPEPR;NKELYEINPPEISEEIIGS(1)PIPEPR 199.29 4.37E-25 353733000 317739 340791 166268 205768 442119 396071 438233 546760 178228 TRUE FALSE 275748.9861 338552.3215 246675.7609 252490.7694 433321.6969 411308.1077 395733.2311 429839.6289 157158.0889 1.754596204 2.154215058 1.569602702 1.606603715 2.757234451 2.617161551 2.518058306 2.735077984 1 17.261857 3.24854963 24.99679558 2.40572706 1.784204996 0.207565928 0.525018738 291.3671409 729121.288 0.148959151 0.189981887 1772.350573 -3.24854963 -0.621522064 SGT(ph)FDLLEMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGTFDLLEMDR 11 0 H0YA26;E9PHT6;Q9NVE7;H0YA31 H0YA26 PANK4 Pantothenate kinase 4 1 S(0.002)GT(0.998)FDLLEMDR;S(0.008)GT(0.992)FDLLEMDR;S(0.023)GT(0.977)FDLLEMDR;S(0.038)GT(0.962)FDLLEMDR 243.85 8.55E-15 364037000 271950 395613 509751 500113 796790 818100 714420 782670 1001650 TRUE FALSE 236011.1185 393014.1922 756268.2886 613671.3004 780935.4379 849572.8364 645135.6584 615302.1112 883236.0781 0.267211818 0.444970718 0.856247053 0.694798724 0.884175202 0.961886473 0.730422674 0.696645129 1 19.75243958 4.36298538 3.368949897 0.817232842 0.293613967 0.78156066 0.106123773 0.108224032 2.316177041 0.027873007 0.091884272 23066.69534 -4.36298538 -0.523618875 down NKESKDPADETEAD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NKESKDPADETEAD 14 2 P16949 P16949 STMN1 Stathmin 0 ; 91.812 0.020687 686720000 2079310 1165550 771010 789570 1163810 875810 1619460 1906990 716440 FALSE TRUE 1804523.915 1157893.425 1143873.015 968853.9363 1140652.458 909502.9774 1462405.018 1499195.029 631743.2794 2.856419647 1.832854362 1.810661153 1.533619696 1.805563265 1.439671789 2.314872301 2.373107998 1 19.26897889 4.738557974 7.571519141 1.82198776 2.867263143 0.415969556 0.401670446 0.109053787 62.88632121 0.100665198 0.583910656 54771.92114 -4.738557974 1.045275383 NKFEEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NKFEEAER 8 1 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;;; 147.4 0.00049049 7282080000 9941750 8115800 4822060 6437290 9472000 9778480 8997120 8875440 6538090 FALSE TRUE 8627922.548 8062486.775 7154024.345 7898975.082 9283525.732 10154664.45 8124580.687 6977496.225 5765164.448 1.496561395 1.398483399 1.240905513 1.370121382 1.610279432 1.761383312 1.409253935 1.210285723 1 22.45893033 1.564160965 2.492618053 1.012468365 1.472576783 0.564901518 0.13996973 0.234890919 2.988574707 0.193054975 0.042665245 36.65734147 -1.564160965 0.460108418 NKHEAMITDLEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 NKHEAMITDLEER 13 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;;;; 215.87 1.71E-11 12140330000 13562420 13029190 7170880 9077890 14471530 12308160 15242450 16814560 13369700 FALSE TRUE 11770111.83 12943600.39 10638741.55 11139163.67 14183574.87 12781662.88 13764239.55 13218897.2 11789149.3 0.998385171 1.097924886 0.902418087 0.944865774 1.203104186 1.084188736 1.167534586 1.121276596 1 23.49095628 3.250068525 24.99999984 1.118349727 0.98793747 0.445589224 0.071616125 206.4318461 448454.2626 0.020603597 0.026370174 1778.560016 -3.250068525 -0.130412257 NKIFMEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NKIFMEFR 8 1 F5H5U2;Q8NHQ9 F5H5U2 DDX55 ATP-dependent RNA helicase DDX55 0 ;;; 61.962 0.049659 1023260000 1006820 1070190 557029 468973 1154720 1733720 741356 743034 245238 FALSE TRUE 873766.186 1063159.851 826410.0876 575460.4875 1131743.331 1800417.33 669459.4092 584141.9614 216246.243 4.040607475 4.916431549 3.821615932 2.661135192 5.233586098 8.325773919 3.095819839 2.701281434 1 17.72231554 4.209727883 23.07488307 3.861966146 4.478519961 0.018617426 1.936752684 510.2782444 408376.6923 0.535439229 1.115102432 16207.94236 -4.209727883 0.616553816 NKKS(ph)PEIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 NKKSPEIHR 9 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR 130.15 0.00019262 22921693000 12505140 8057033 5457214 5573829 9053669 6877049 12431138 13729770 7003359 TRUE FALSE 10852554.07 8004105.82 8096340.944 6839452.065 8873518.7 7141613.525 11225568.15 10793765.53 6175429.877 1.757376293 1.296121238 1.311057061 1.107526472 1.436907046 1.156456096 1.817779227 1.747856545 1 22.55810814 2.247005438 24.99997227 1.581286542 1.3339975 0.069368633 0.278124585 345.9576639 1024172.245 0.103092502 0.078526613 176.6059935 -2.247005438 -0.247289041 NKKS(ph)PEIHRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NKKSPEIHRR 10 3 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 NKKS(1)PEIHRR;NKKS(1)PEIHRR;NKKS(1)PEIHRR 133.48 0.00013993 3155600000 4385200 3044260 1527630 1394280 3127420 2234880 4143610 4524210 615469 TRUE FALSE 3805684.709 3024262.056 2266396.978 1710872.584 3065190.461 2320857.28 3741763.34 3556742.899 542708.956 7.012386045 5.572530216 4.17608177 3.15246794 5.647945233 4.276430772 6.894604002 6.553683811 1 19.04981919 4.621479778 3.258119688 4.819696476 7.080372099 0.166384522 1.704312118 0.568911974 9.760307471 0.431969174 2.681842757 41829.22117 -4.621479778 2.260675624 NKLDLETLTDILQHQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NKLDLETLTDILQHQIR 17 1 P18440;F5H5R8 P18440 NAT1 Arylamine N-acetyltransferase 1 0 ; 198.07 8.73E-12 290020000 620550 496000 259397 351070 570800 509230 596970 703690 563820 FALSE TRUE 538542.7452 492741.7433 384842.2568 430785.8093 559442.1968 528820.4076 539075.9413 553211.3696 497165.8419 1.083225555 0.991101363 0.7740722 0.866483119 1.125262738 1.063670033 1.084298027 1.112730045 1 18.92336765 3.235966759 24.99978389 1.081491244 0.922130013 0.426229769 0.085365001 65.24987609 628882.8763 0.026621237 0.031589935 1721.736788 -3.235966759 -0.159361232 NKPEWFFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NKPEWFFK 8 1 Q5TA02;P78417-3;P78417;Q5TA01;P78417-2 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 ; 120.99 0.0013247 2671400000 3955400 4049000 2177930 2950200 4580600 3663000 5219900 6064100 5401000 FALSE TRUE 3432683.868 4022401.852 3231184.233 3620088.001 4489455.022 3803917.98 4713674.901 4767339.406 4762499.933 0.720773526 0.844598826 0.67846389 0.760123475 0.942667734 0.798722947 0.989748025 1.001016162 1 22.18328764 2.527410959 0.772738161 1.032566032 0.746881685 0.685702131 0.067238162 0.426359594 0.561437203 0.08063624 0.040737673 336.8301501 -2.527410959 -0.285684347 NKPGPNIES(ph)GNEDDDASFK ddPTM_MDA-MB-175_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 301.97 3.20E-50 37136270000 19625237 13154680 11290600 11412577 14409795 10023881 20523721 22788690 19080750 TRUE FALSE 17031712.21 13068266.04 16750771.92 14003977.04 14123068.27 10409506.19 18533333.7 17915505.99 16825045.47 1.012283279 0.77671505 0.995585537 0.832329224 0.839407436 0.618691118 1.101532458 1.064811742 1 24.00410707 2.189068673 24.99998549 1.059319403 0.848592969 0.439168998 0.11160583 98.35871815 49683.40567 0.044054201 0.029701393 154.5498801 -2.189068673 -0.210726434 NKPLS(ph)PIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NKPLSPIK 8 1 P35251-2;P35251;A0A1W2PP02;D6RAD2 P35251-2 RFC1 Replication factor C subunit 1 1 NKPLS(1)PIK;NKPLS(1)PIK 89.805 0.0082639 1660980000 3648000 3462300 2752000 3210900 4580100 2124200 4633700 5174600 6305300 TRUE FALSE 3165907.557 3439555.923 4082876.405 3939983.921 4488964.971 2205919.349 4184324.487 4068052.059 5559894.617 0.569418627 0.618636892 0.734344207 0.708643633 0.807383103 0.396755604 0.752590611 0.731677907 1 22.40662611 1.085115919 1.660203205 1.246341367 0.654625639 0.475635394 0.113765347 1.386813545 2.532767156 1.509601799 0.031146055 12.1651066 -1.085115919 -0.591715728 NKPQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NKPQER 6 1 A0A0A0MRI1;Q8IXQ4;Q8IXQ4-3;Q8IXQ4-2 A0A0A0MRI1 GPALPP1 GPALPP motifs-containing protein 1 0 83.843 0.051552 22428000 19528 21985 13242 15156 19491 21893 28031 30762 33588 FALSE TRUE 16947.32532 21840.57909 19645.87549 18597.40144 19103.16723 22735.23788 25312.55793 24183.78569 29617.2649 0.572211019 0.73742728 0.66332511 0.627924338 0.645001059 0.76763462 0.854655486 0.816543518 1 14.8541508 0.392061123 0.440063163 1.603601022 0.631932313 0.813245992 0.054458788 5.126493647 0.466332879 3.028812029 0.05140017 2.466386435 -0.392061123 -0.971668709 NKPRPPPLSPLGGPVPSALPNGPPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NKPRPPPLSPLGGPVPSALPNGPPSPR 27 2 Q15642 Q15642 TRIP10 Cdc42-interacting protein 4 1 NKPRPPPLSPLGGPVPSALPNGPPS(1)PR;NKPRPPPLSPLGGPVPSALPNGPPS(1)PR 147.27 7.11E-08 2607110000 1015170 1038980 536970 673190 1328210 1218600 1269600 1262230 1305740 TRUE FALSE 881012.7124 1032154.872 796650.4881 826048.0786 1301781.22 1265480.331 1146474.387 992311.9372 1151376.905 0.765181852 0.896452645 0.691911124 0.717443676 1.130629956 1.099101715 0.99574204 0.861848047 1 20.13492875 3.250562706 24.99999532 1.000465016 0.771523656 0.659344494 0.088706541 167.3385995 348559.4199 0.02883942 0.036937194 1780.584981 -3.250562706 -0.22894136 NKPRS(ph)PVVELSK ddPTM_MDA-MB-175_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 178.01 1.18E-05 1825660000 3549650 3015610 1987373 2112510 4052880 2803420 5174140 5541190 2609390 TRUE FALSE 3080554.759 2995800.259 2948473.23 2592187.683 3972235.617 2911269.381 4672352.699 4356249.64 2300910.887 1.338841403 1.302006208 1.281437385 1.12659195 1.726375254 1.265268202 2.03065348 1.893271776 1 21.13377368 3.233589648 24.99979117 1.639556728 1.266433875 0.210075423 0.298194465 169.8869101 854387.5761 0.090333499 0.105623203 1712.338605 -3.233589648 -0.373122852 NKPYPK ddPTM_MDA-MB-175_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 ; 88.591 0.046631 3480100000 2016780 2107750 1103420 1306860 1848650 1756120 2454850 2469410 2531640 FALSE TRUE 1750257.413 2093904.051 1637037.603 1603602.537 1811865.482 1823679.073 2216779.025 1941345.888 2232352.403 0.784041718 0.937980961 0.733324004 0.718346501 0.811639542 0.816931534 0.993023781 0.869641319 1 21.09013336 2.331750755 6.422210285 0.937748284 0.798931502 0.525282539 0.06848469 0.184269879 10.56705115 0.026069901 0.020024312 214.6598171 -2.331750755 -0.138816782 NKQDDDLNCEPLS(ph)PHNITPEPVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NKQDDDLNCEPLSPHNITPEPVSK 24 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4;A8MV73;F8WE35;F5H8I0;F5H2W9;F5H2H9;F5GZ10;F5H502;F5H1K9 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 NKQDDDLNCEPLS(1)PHNITPEPVSK;NKQDDDLNCEPLS(1)PHNITPEPVSK;NKQDDDLNCEPLS(1)PHNITPEPVSK;NKQDDDLNCEPLS(1)PHNITPEPVSK;NKQDDDLNCEPLS(1)PHNITPEPVSK 267.64 8.41E-45 2997710000 4448914 3556673 2539575 2683773 3393600 2403462 4880513 5580200 4257527 TRUE FALSE 3860978.743 3533308.981 3767721.964 3293164.679 3326073.999 2495924.738 4407201.6 4386917.655 3754207.008 1.028440556 0.94115987 1.00359995 0.877193152 0.885959137 0.664834074 1.173936757 1.168533766 1 21.84007677 2.192041093 24.99999869 1.127976534 0.905065987 0.463327115 0.108126413 105.4094519 56647.18467 0.044763237 0.030179475 155.6112865 -2.192041093 -0.222910547 NKQGLETDNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NKQGLETDNK 10 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ; 52.49 0.089993 3500200000 4244200 3686400 1645420 3088300 2213000 3143800 4206000 4683800 4330800 FALSE TRUE 3683318.217 3662183.796 2441150.616 3789545.717 2168965.63 3264744.02 3798102.767 3682205.819 3818817.758 0.964517935 0.958983651 0.639242501 0.99233479 0.567967829 0.854909615 0.994575549 0.964226641 1 21.86469464 2.302711379 5.310499534 0.982081814 0.820481693 0.227439002 0.136339998 0.286231353 15.54142145 0.050653228 0.03826402 200.7758065 -2.302711379 -0.161600121 NKQPT(ph)PVNIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NKQPTPVNIR 10 1 X6R700;Q9Y3Y2-4;Q9Y3Y2;Q9Y3Y2-3;A0A087X1B7 X6R700 CHTOP Chromatin target of PRMT1 protein 1 NKQPT(1)PVNIR 133.16 0.00033069 198310000 199450 218390 122240 128220 268320 186970 256930 297020 230610 TRUE FALSE 173092.1772 216955.3817 181355.6729 157334.3107 262980.957 194162.8569 232012.9681 233504.5844 203347.5485 0.851213493 1.066919091 0.891850795 0.773721207 1.293258556 0.954832543 1.140967618 1.148302923 1 17.63358807 3.247764307 24.99995474 1.107456321 0.907848861 0.454010289 0.114945405 185.2461613 503180.828 0.031832181 0.040515846 1769.148576 -3.247764307 -0.19960746 NKS(ph)EDEDEDEGDATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NKSEDEDEDEGDATR 15 1 Q9BZI1 Q9BZI1 IRX2 Iroquois-class homeodomain protein IRX-2 1 NKS(1)EDEDEDEGDATR;NKS(1)EDEDEDEGDATR 219.22 1.11E-12 545260000 667740 467900 343990 351980 512720 393880 585130 659690 555170 TRUE FALSE 579496.4672 464826.3341 510344.7146 431902.4387 502517.8751 409032.8185 528384.1827 518620.4272 489538.4351 1.183760918 0.94951959 1.04250183 0.882264614 1.026513628 0.835547914 1.079351783 1.059406964 1 18.90106261 4.746095923 24.43232025 0.989990376 1.183761046 0.393413827 0.077524849 737.5389446 2391301.415 0.018785431 0.188793647 55730.88285 -4.746095923 0.19377067 NKS(ph)NEDQSMGNWQIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NKSNEDQSMGNWQIK 15 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 NKS(1)NEDQSMGNWQIK;NKS(1)NEDQSMGNWQIK;NKS(0.998)NEDQS(0.002)MGNWQIK;NKS(1)NEDQSMGNWQIK 280.64 6.17E-34 1905290000 2213990 1699140 1581690 1614780 1848840 1345950 2423080 2661480 2918390 TRUE FALSE 1921405.612 1687978.237 2346600.574 1981440.479 1812051.701 1397729.567 2188090.075 2092343.214 2573381.259 0.746646306 0.655937876 0.911874432 0.769975484 0.704152055 0.543149043 0.850278235 0.813071598 1 21.29523378 1.235187501 1.505565217 1.105183146 0.733638936 0.41396813 0.098898393 1.244634025 2.497849293 0.708203877 0.02917099 17.18650231 -1.235187501 -0.37154421 NKTEDLEATSEHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NKTEDLEATSEHFK 14 1 C9JXZ5;Q9BV40 C9JXZ5 VAMP8 Vesicle-associated membrane protein 8 0 ; 185.67 6.92E-07 1154290000 2161850 1749290 806220 1412950 2119120 1679560 2409410 3053720 2186780 FALSE TRUE 1876156.045 1737798.799 1196110.689 1733781.893 2076953.658 1744173.76 2175745.789 2400705.742 1928261.36 0.972978085 0.901225755 0.620305273 0.89914258 1.077112108 0.904531822 1.128345895 1.245010553 1 20.87886918 2.72979342 1.094288986 1.149741445 0.839882462 0.418921771 0.126887451 0.443560531 1.15070339 0.081393109 0.062544572 536.7764079 -2.72979342 -0.309858983 NKYNTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NKYNTPK 7 1 P46777;A0A2R8Y4A2;R4GNJ2 P46777 RPL5 60S ribosomal protein L5 0 89.698 0.016126 1121900000 700840 600660 260630 398870 595960 580370 791490 886710 411050 FALSE TRUE 608222.2183 596714.2249 386671.5398 489439.5298 584101.562 602697.2094 714731.4216 697093.9669 362456.1373 1.678057441 1.646307411 1.066809194 1.350341406 1.611509647 1.662814193 1.97191149 1.923250554 1 18.46744689 3.041669306 3.766832982 1.710295509 1.425395204 0.071165871 0.310666807 0.448246156 13.49844825 0.101338241 0.112995421 1100.70086 -3.041669306 -0.284900305 NKYQELINDIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NKYQELINDIAR 12 1 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 203.82 1.10E-07 2324100000 3349500 3464200 1218100 1621090 4314700 3419100 4067500 4633300 631880 FALSE TRUE 2906855.088 3441443.442 1807177.234 1989183.261 4228845.912 3550634.989 3673034.476 3642504.851 557179.8662 5.217085657 6.176539481 3.243435996 3.570091782 7.589732092 6.372511292 6.592188086 6.537394964 1 19.0877836 6.452746357 8.892828137 5.335666466 5.238348323 0 2.005344854 0 0 0.445260317 0 2836262.067 -6.452746357 -0.097318142 NLANTVTEEILEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLANTVTEEILEK 13 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ; 129.71 0.00042297 40295000 152489 114146 77830 76355 103492 85676 136787 149786 81064 FALSE TRUE 132337.1923 113396.1674 115468.8483 93692.56976 101432.7117 88972.01116 123521.4178 117755.4295 71480.70627 1.8513694 1.586388458 1.615384827 1.310739284 1.419022237 1.244699665 1.728038575 1.647373616 1 16.12526627 4.684824636 1.269014332 1.439440144 1.993001472 0.314270823 0.209212639 1.840899422 2.773971261 0.062983974 1.298950569 48397.69024 -4.684824636 0.553561328 NLAPHHAS(ph)PDPPAPPASASDPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NLAPHHASPDPPAPPASASDPHR 23 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 NLAPHHAS(1)PDPPAPPASASDPHR;NLAPHHAS(1)PDPPAPPASASDPHR;NLAPHHAS(1)PDPPAPPASASDPHR;NLAPHHAS(1)PDPPAPPASASDPHR 147.26 1.99E-07 1501980000 649110 592900 326328 399470 648700 657930 579511 641610 715840 TRUE FALSE 563328.4689 589005.2009 484141.3123 490175.769 635792.1392 683240.9928 523310.1124 504406.6945 631214.2107 0.892452133 0.933130451 0.76700002 0.776560098 1.007252575 1.082423338 0.829053123 0.799105416 1 19.26777016 NLCYHAQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLCYHAQTR 9 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ; 76.282 0.035873 167997000 280740 272930 153472 187712 291730 338940 260940 282770 243490 FALSE TRUE 243639.4977 271137.1049 227691.5725 230334.8786 285925.1438 351979.2411 235634.079 222301.836 214704.8896 1.134764551 1.262836191 1.0604862 1.072797546 1.331712307 1.63936295 1.097478867 1.035383202 1 17.71199552 2.015109954 24.99957995 1.034082434 1.248773037 0.269442565 0.163373369 329.2642714 544769.2497 0.071496006 0.048184008 103.5404274 -2.015109954 0.214690604 NLDDGIDDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NLDDGIDDER 10 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YAP2 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ;;;;; 254.57 9.56E-17 9318560000 6092320 5833570 4059250 4897680 6218180 5976070 5696050 6518280 7960720 FALSE TRUE 5287204.476 5795248.895 6022316.877 6009773.1 6094450.384 6205973.28 5143647.948 5124396.547 7019612.75 0.75320458 0.825579573 0.857927224 0.856140262 0.868203219 0.884090548 0.732753804 0.730011288 1 22.74296001 4.729990954 4.569956882 0.833350224 0.748619223 0.107905814 0.077093295 0.495558809 27.15639316 0.019685713 0.133306137 53702.06102 -4.729990954 -0.084731001 NLDDGIDDERLR ddPTM_MDA-MB-175_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 ;; 206.32 8.35E-08 5254200000 7539030 6801810 2733060 3347290 7036670 6682640 6865490 7774140 929260 FALSE TRUE 6542728.084 6757128.462 4054776.958 4107343.355 6896654.034 6939725.485 6199675.837 6111700.659 819403.9414 7.984740802 8.246394874 4.948446978 5.012598972 8.416671785 8.469236154 7.566080077 7.458715233 1 19.64421531 1.23738667 24.95036518 0.999992339 7.248100247 0.701608758 1.283541434 17.61107666 374126.4027 2.008658118 0.335075715 17.2737516 -1.23738667 6.248107908 NLDDTIDDEKLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLDDTIDDEKLR 12 1 B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0YEU6;P0CB38 B1ANR0;P0CB38 PABPC4;PABPC4L Polyadenylate-binding protein;Polyadenylate-binding protein 4;Polyadenylate-binding protein 4-like 0 119.17 0.00021326 0 143170 140430 92317 107910 149660 142520 150260 174780 161440 FALSE TRUE 124249.7218 139507.5061 136961.81 132412.6148 146682.0588 148002.8366 135687.8083 137404.6571 142354.7471 0.872817551 0.979998974 0.962116212 0.930159461 1.030398085 1.039676158 0.953166727 0.965227082 1 17.11913108 4.739003608 7.319428981 0.980939076 0.871486279 0.51147832 0.033682698 0.094169484 44.70668853 0.00861508 0.050716428 54828.15194 -4.739003608 -0.109452796 NLDFGIDMDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLDFGIDMDSR 11 0 Q8NE71;Q8NE71-2;H0YGW7 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 125.23 0.00077404 137590000 209620 225690 123810 137870 225410 276230 196220 209760 227810 FALSE TRUE 181918.1859 224207.4275 183684.9301 169175.4907 220924.782 286856.7468 177190.6146 164904.4564 200878.5613 0.905612748 1.116134176 0.914407834 0.842177929 1.099792733 1.428010759 0.882078274 0.820916156 1 17.61596408 NLDIERPTYTNLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 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 ;;;;;;;;;;;;; 270.97 5.51E-33 1.86696E+11 26229993.2 23107959.7 12097208.3 15155871 26668011 28557196 24299551.6 27623853.3 26860552.7 FALSE TRUE 22763633.14 22956161.99 17947458.7 18597243.15 26137369.76 29655809.81 21942984.83 21716707.24 23685128.76 0.961093916 0.969222596 0.757752211 0.785186492 1.10353505 1.252085649 0.926445663 0.916892091 1 24.49747818 3.237369593 24.99999938 1.026542987 0.867624318 0.354324133 0.114246954 43.95072505 922544.9119 0.03802409 0.045578635 1727.307238 -3.237369593 -0.158918669 NLDKDMYGDDLEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLDKDMYGDDLEAR 14 1 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 0 110.97 0.0015108 0 309850 255150 133620 165900 282630 242570 292840 311270 237790 FALSE TRUE 268902.5374 253473.9028 198239.0789 203570.1306 277006.216 251901.8249 264440.4219 244707.3328 209678.7371 1.282450196 1.208867939 0.945441973 0.970866829 1.321098266 1.201370384 1.261169471 1.167058407 1 17.67782104 2.487413336 0.003389354 0.911881015 1.394651721 0.001778973 0.1340433 2927760.905 7892.591864 564349.9242 559834.4395 307.1944291 -2.487413336 0.482770707 NLDSLEEDLDFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NLDSLEEDLDFLR 13 0 P61758;P61758-2 P61758 VBP1 Prefoldin subunit 3 0 ;;; 312.64 2.85E-50 658674000 366153 329083 221767 295918 365411 342436 340539 405342 641550 FALSE TRUE 317764.9533 326921.2321 329014.263 363110.7047 358140.036 355609.7345 307513.5802 318662.7677 565706.6899 0.561713268 0.577898826 0.581598678 0.641870975 0.633084322 0.628611506 0.54359191 0.563300335 1 19.10969471 1.236185673 24.9999888 1.000000532 0.59120036 0.937415331 0.03317459 16.1477819 169942.3221 0.058985708 0.00903907 17.2260488 -1.236185673 -0.408800172 NLDSLEEDLDFLRDQFTTTEVNMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NLDSLEEDLDFLRDQFTTTEVNMAR 25 1 P61758;P61758-2 P61758 VBP1 Prefoldin subunit 3 0 ;;; 240.43 1.30E-38 1179431000 409177 449448 193638.3 217542 390708 454185 445102 485830 123425.1 FALSE TRUE 355103.2227 446495.5465 287282.4296 266938.236 382933.6752 471657.7908 401936.0765 381939.0352 108833.9253 3.262799001 4.102540135 2.639640432 2.452711646 3.518513866 4.333738672 3.693113848 3.509374804 1 16.73176881 4.244131686 24.99292039 3.144976855 3.682669338 0.069528669 0.923401322 453.72374 2035434.19 0.234942881 0.585744039 17544.12391 -4.244131686 0.537692483 NLDSTTVAVHGEEIYCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLDSTTVAVHGEEIYCK 17 0 P21291;E9PS42;E9PND2 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ; 243.95 1.74E-20 2239800000 2940500 3296100 1739890 2197600 3242800 2742800 3397700 4246400 4399700 FALSE TRUE 2551905.475 3274447.702 2581306.624 2696598.668 3178274.624 2848317.291 3068191.577 3338340.406 3879572.478 0.657780075 0.84402282 0.665358525 0.695076244 0.819233213 0.734183291 0.790858167 0.860491826 1 21.88746625 -1.404833103 0.631711754 9.999999973 0.728864929 0.686262612 0.058383396 48.83959534 0.793437544 602.4455081 0.026053176 0.039370134 1.404833103 -9.271135044 NLEAQHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NLEAQHK 7 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 ;;;;; 116.88 0.0053555 2391670000 4877110 4338820 2296210 3043750 3453420 4114610 5110850 5680880 5314790 FALSE TRUE 4232587.556 4310318.006 3406664.836 3734879.958 3384703.699 4272901.709 4615200.554 4466068.021 4686481.581 0.903148233 0.919734332 0.726913096 0.796947538 0.722227035 0.911750454 0.984790076 0.952968222 1 22.16007378 2.508297313 5.806081615 0.971249386 0.813612311 0.586503547 0.063964642 0.140069773 14.27380298 0.024050323 0.020378916 322.3274655 -2.508297313 -0.157637075 NLEELEEKSTT(ph)PPPAEPVSLPQEPPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLEELEEKSTTPPPAEPVSLPQEPPKPR 28 2 Q9UN86-2 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 NLEELEEKS(0.024)T(0.14)T(0.836)PPPAEPVSLPQEPPKPR;NLEELEEKS(0.021)T(0.131)T(0.848)PPPAEPVSLPQEPPKPR 149.55 3.06E-06 423000000 1250180 875990 185498 186776 698010 507230 1237960 1220670 38001 TRUE FALSE 1084965.545 870235.564 275205.4533 229186.3455 684120.9666 526743.4663 1117902.83 959639.2198 33508.56507 32.37875281 25.97054103 8.212988311 6.839634732 20.41630148 15.71966646 33.36170401 28.63862471 1 15.03224229 7.99999889 0.027127786 9.99998342 33.49663447 0.012255909 11.12385086 80525.00111 216.6317724 68583.36619 127960.7111 99999744.53 -7.99999889 23.49665105 NLEQILNGGES(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NLEQILNGGESPK 13 0 Q13033-2;Q13033;G3V340;G3V3G7 Q13033-2 STRN3 Striatin-3 1 NLEQILNGGES(1)PK;NLEQILNGGES(1)PK;NLEQILNGGES(1)PK;NLEQILNGGES(1)PK;NLEQILNGGES(1)PK 242.48 6.48E-17 1416767000 2915770 2495600 2093640 2491020 3680260 2819750 3556600 4286380 5021440 TRUE FALSE 2530443.607 2479206.239 3106131.307 3056644.164 3607030.026 2928227.607 3211681.479 3369770.994 4427811.084 0.571488611 0.559916896 0.701504931 0.690328496 0.814630516 0.661326229 0.725342933 0.761046696 1 22.07816224 -1.212170225 0.658465569 10 0.654611316 0.689352627 0.069864404 48.22169706 0.963090383 618.9390217 0.033929083 0.061352148 1.212170225 -9.345388684 NLETFCEETRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLETFCEETRR 11 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 198.32 8.67E-08 617880000 708980 659090 269260 387360 715830 729940 636070 695540 415520 FALSE TRUE 615286.4967 654760.3944 399475.0366 475316.0084 701586.3835 758021.2641 574384.0293 546804.1837 366397.699 1.679285919 1.787021033 1.090277144 1.297267995 1.914822024 2.068848321 1.567651846 1.492378869 1 18.48305092 1.206783123 2.289976867 0.79138277 1.627375159 0.330593866 0.280287884 0.920334327 4.66136412 1.62779786 0.08095595 16.09841516 -1.206783123 0.835992389 NLFQQYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLFQQYDR 8 0 Q9UBV8 Q9UBV8 PEF1 Peflin 0 ; 111.95 0.0072944 279995000 358330 306960 206983 272210 369300 339080 292950 371880 457970 FALSE TRUE 310975.7826 304943.5595 307080.6711 334019.441 361951.6525 352124.627 264539.7541 292356.356 403829.3083 0.770067393 0.755129836 0.760421953 0.82713026 0.896298622 0.87196402 0.655078145 0.723960223 1 18.62338609 3.750420735 21.59702277 0.811836424 0.761198697 0.084228027 0.093571184 429.9152497 782849.98 0.026548832 0.045339833 5628.863727 -3.750420735 -0.050637727 NLGFSPGDREENIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLGFSPGDREENIR 14 1 O95340;O95340-2 O95340 PAPSS2 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 2;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ; 178.23 1.83E-06 591390000 338620 352800 192322 226050 398900 378150 346720 411840 374150 FALSE TRUE 293870.509 350482.4336 285329.5625 277378.1075 390962.6704 392697.6752 313095.1478 323771.2209 329918.4132 0.890736913 1.062330623 0.864848857 0.84074758 1.185028343 1.190287233 0.949007801 0.981367538 1 18.33174977 3.254557813 24.99896381 1.049214561 0.921655123 0.352440757 0.097713956 345.1416229 539353.0775 0.030667062 0.039458432 1797.040286 -3.254557813 -0.127559438 NLGLEELGIELDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLGLEELGIELDPR 14 0 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 ; 84.892 0.018502 57123000 127086 117212 72098 124834 164780 172853 114664 150937 137745 FALSE TRUE 110291.2631 116442.0267 106964.834 153179.4677 161501.2004 179502.7668 103543.9029 118660.2971 121460.943 0.908038917 0.958678763 0.880652095 1.261141762 1.329655413 1.477864096 0.85248723 0.976942005 1 16.89013295 3.753980565 24.40988744 1.134286539 0.920078786 0.266088062 0.181872121 1031.394949 1632699.407 0.054770237 0.094390345 5675.192077 -3.753980565 -0.214207753 NLGQNLWGPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLGQNLWGPHR 11 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 180.36 6.70E-06 1225020000 1389010 1195090 582150 701040 1393400 1373820 1171030 1347530 1305400 FALSE TRUE 1205448.809 1187239.375 863679.6872 860221.8467 1365674.066 1426671.744 1057463.691 1059371.196 1151077.099 1.047235507 1.031416033 0.750323056 0.747319052 1.186431445 1.239423272 0.918673208 0.920330356 1 20.13455304 3.239660098 24.99999941 1.035641676 0.893615744 0.235732233 0.140252433 55.51534882 1262292.668 0.046248204 0.056350493 1736.441264 -3.239660098 -0.142025932 NLGS(ph)INTELQDVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NLGSINTELQDVQR 14 0 O75396;A0A087X1A9 O75396 SEC22B Vesicle-trafficking protein SEC22b 1 NLGS(0.853)INT(0.147)ELQDVQR;NLGS(1)INTELQDVQR;NLGS(0.755)INT(0.245)ELQDVQR 271.26 6.24E-33 656040000 626910 492090 345090 416560 645330 627420 554970 687760 729980 TRUE FALSE 544062.2551 488857.4284 511976.6783 511146.3147 632489.1956 651557.2534 501149.0948 540687.8762 643682.596 0.845233751 0.7594697 0.795386859 0.794096839 0.982610373 1.012233758 0.778565551 0.839991448 1 19.29598994 3.267539688 24.86883106 0.906013199 0.795529763 0.39455383 0.074802051 247.6260669 212502.3308 0.023205374 0.029952656 1851.568093 -3.267539688 -0.110483436 NLGSGS(ph)PKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLGSGSPKPR 10 1 A0A1C7CYX9 A0A1C7CYX9 1 NLGS(0.018)GS(0.982)PKPR;NLGS(0.003)GS(0.997)PKPR 160.18 4.52E-06 1382350000 1422780 1248040 806020 803520 1400610 1150320 1553150 1663640 1400680 TRUE FALSE 1234756.018 1239841.543 1195813.968 985971.497 1372740.601 1194573.555 1402525.752 1307883.532 1235093.206 0.999726994 1.003844517 0.968197349 0.79829724 1.11144697 0.967193042 1.135562681 1.058935088 1 20.23618849 3.189807186 24.99999991 1.056864398 0.948729145 0.36110825 0.073860939 126.7746054 65007.51416 0.021959998 0.024900349 1548.129143 -3.189807186 -0.108135254 NLGSINT(ph)ELQDVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLGSINTELQDVQR 14 0 O75396;A0A087X1A9 O75396 SEC22B Vesicle-trafficking protein SEC22b 1 NLGS(0.305)INT(0.695)ELQDVQR 292.76 1.79E-42 188400000 323500 256930 195320 263670 347260 360960 293540 375790 392720 TRUE FALSE 280748.6554 255242.2099 289777.4053 323540.3034 340350.2054 374846.3648 265072.536 295430.2329 346293.089 0.810725551 0.737069893 0.836798118 0.93429616 0.982838573 1.082454073 0.765457193 0.853121943 1 18.40163407 3.930643504 3.536885363 0.924642976 0.774723528 0.38107912 0.086613064 0.283015515 6.870600981 0.025342906 0.049855999 8524.001227 -3.930643504 -0.149919448 NLHDNLSDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLHDNLSDLR 10 0 O14841 O14841 OPLAH 5-oxoprolinase 0 83.182 0.019783 0 111790 115350 84598 105250 139420 145970 123130 140600 278800 FALSE TRUE 97016.66826 114592.2583 125509.8758 129148.6211 136645.8148 151585.5604 111188.8716 110533.7842 245840.5816 0.394632439 0.466124256 0.510533594 0.525334834 0.555830994 0.616601048 0.45228038 0.449615696 1 17.90736356 1.235191553 24.99996042 1.000000698 0.498128998 0.867439817 0.061869666 35.34370213 262222.8926 0.114025258 0.016173036 17.18666267 -1.235191553 -0.5018717 NLHSEISGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLHSEISGK 9 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 88.681 0.01262 161900000 345900 274840 139410 203520 291320 275070 313800 352540 356860 FALSE TRUE 300188.4386 273034.5579 206829.1423 249732.3266 285523.302 285652.1209 283367.7243 277152.0645 314672.4173 0.953971248 0.867678713 0.657283991 0.793626365 0.907366792 0.907776167 0.900516565 0.88076377 1 18.2634912 3.230570174 23.39467736 0.912486565 0.810188827 0.282576947 0.079224922 109.6769095 321114.8559 0.02472112 0.02857741 1700.474698 -3.230570174 -0.102297738 NLHTHHFPSPLSNNQEVSAFGEDGEGDDLDLWTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLHTHHFPSPLSNNQEVSAFGEDGEGDDLDLWTVR 35 0 Q9HCN8 Q9HCN8 SDF2L1 Stromal cell-derived factor 2-like protein 1 0 197.59 7.26E-28 203380000 32311 31996 20226 26309 43597 51389 32625 44332 29219 FALSE TRUE 28041.01948 31785.81617 30007.36125 32282.86056 42729.505 53365.96808 29461.03252 34851.94679 25764.76311 1.088347654 1.233693321 1.164666686 1.252984956 1.658447424 2.071277266 1.143462193 1.352698127 1 14.65311171 3.460249884 23.31134257 1.443513931 1.175955603 0.172976066 0.287981984 211.1014428 291678.4878 0.087936163 0.113566435 2885.691394 -3.460249884 -0.267558328 NLHYFNSDSFASHPNYPYSDEY ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLHYFNSDSFASHPNYPYSDEY 22 0 A0A0A0MSS8;P42330;S4R3Z2;P42330-2 A0A0A0MSS8 AKR1C3 Aldo-keto reductase family 1 member C3 0 ; 279.79 1.33E-45 967970000 257050 290082 111672 148129 337255 366421 300629 371661 406310 FALSE TRUE 223080.1912 288176.4322 165676.9527 181763.9535 330544.2853 380517.453 271474.0459 292184.1874 358276.4947 0.622648135 0.804340883 0.462427637 0.507328714 0.92259551 1.062077637 0.757722178 0.815527091 1 18.45071387 3.23008761 24.99994387 0.895562337 0.604071754 0.615450161 0.12231383 138.6517244 409096.6832 0.03882306 0.044723261 1698.586275 -3.23008761 -0.291490583 NLIDAGVDALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLIDAGVDALR 11 0 P12268;H0Y4R1 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 134.2 0.00033943 43071000 81214 80144 35966 61640 90909 97177 77513 84305 81491 FALSE TRUE 70481.36413 79617.52879 53359.2779 75636.30411 89100.08876 100915.4621 69995.80119 66277.03181 71857.22681 0.980852828 1.107996124 0.742573576 1.052591471 1.239960025 1.404388487 0.974095499 0.922343301 1 16.13284564 4.802737427 19.3369748 1.048073724 0.980842665 0.0156211 0.177737013 30354.79878 9140122.784 0.046648989 56.70907958 63494.69293 -4.802737427 -0.067231059 NLIQHNNS(ph)TQTDIFYTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLIQHNNSTQTDIFYTDR 18 0 Q8TDM6-4;Q8TDM6;Q8TDM6-3 Q8TDM6-4 DLG5 Disks large homolog 5 1 NLIQHNNS(0.996)T(0.004)QTDIFYTDR;NLIQHNNS(0.996)T(0.004)QTDIFYTDR 195.97 1.29E-15 260030000 318610 237910 205590 223350 210150 215360 266770 259480 350040 TRUE FALSE 276504.8812 236347.1535 305014.0117 274065.0312 205968.4262 223645.0386 240898.6865 203992.2213 308658.67 0.895827359 0.765723359 0.988191946 0.887922673 0.667301606 0.724570732 0.780469528 0.660899048 1 18.23565279 3.263815087 24.62785298 0.752362272 0.883350905 0.223544385 0.107233976 258.4574871 252042.5115 0.029690285 0.038313729 1835.756552 -3.263815087 0.130988633 NLKPIKPMQFLGDEETVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLKPIKPMQFLGDEETVR 18 2 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ; 218.14 4.52E-19 10545100000 5866700 5461000 2822900 3524000 6174500 4838800 6623000 7360000 9445300 FALSE TRUE 5091400.731 5425126.331 4188063.882 4324178.061 6051639.53 5024951.767 5980702.479 5786121.276 8328687.394 0.6113089 0.651378311 0.50284801 0.519190823 0.726601833 0.603330577 0.718084639 0.694721869 1 22.98965771 -0.707801801 0.803514078 10 0.597532222 0.760326419 0.0680606 25.35991579 0.866494505 394.4651614 0.025673177 0.195973884 0.707801801 -9.402467778 NLKPIKPMQFLGDEETVRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLKPIKPMQFLGDEETVRK 19 3 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 229.6 3.35E-20 2787400000 2583200 2217100 1175200 1288700 2165000 1633000 2929400 3361400 1512500 FALSE TRUE 2241823.575 2202535.724 1743530.651 1581319.032 2121920.736 1695822.567 2645307.239 2642590.768 1333693.973 1.680913028 1.651455108 1.307294391 1.185668574 1.591010216 1.271523004 1.983443948 1.981407146 1 20.34699624 2.247446865 24.9998946 1.736649447 1.445410075 0.067993249 0.316115387 351.6124918 989201.2376 0.119424913 0.09110866 176.7855911 -2.247446865 -0.291239372 NLLALIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLLALIHR 8 0 O15042-2;O15042;E7ET15;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 ; 105.57 0.0043629 498420000 483150 574420 216511 270480 661080 640510 521120 622280 583560 FALSE TRUE 419300.5034 570646.5972 321216.4438 331896.618 647925.8014 665150.8342 470581.8626 489210.2646 514572.2016 0.814852614 1.108972843 0.624239791 0.644995235 1.259154302 1.292628774 0.914510852 0.950712578 1 18.973014 3.242849217 24.99968458 1.064609797 0.808028171 0.388931864 0.176537465 139.5769004 813635.0074 0.05590547 0.069636435 1749.239264 -3.242849217 -0.256581627 NLLDDVEEFHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLLDDVEEFHER 12 0 P29375;P29375-2;E7EV89 P29375 KDM5A Lysine-specific demethylase 5A 0 140.08 5.94E-05 19173000 42429 43599 25337 29850 38099 43646 40426 43473 39455 FALSE TRUE 36821.90015 43312.5953 37590.05795 36627.89873 37340.90444 45325.08986 36505.49274 34176.63726 34790.67485 1.058384188 1.244948409 1.080463604 1.05280794 1.073302102 1.302794213 1.049289584 0.982350512 1 15.08641304 2.008828518 24.99979494 0.997686188 1.135071139 0.357799795 0.081574846 198.1497301 561100.3568 0.032915569 0.022155917 102.0536444 -2.008828518 0.137384951 NLLDEELQR ddPTM_MDA-MB-175_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 ; 117.53 0.0026459 227540000 594140 573290 340110 393300 588970 648120 594190 618360 666810 FALSE TRUE 515622.8936 569524.0202 504588.3336 482604.7762 577250.6493 673053.5958 536565.5453 486128.5261 587980.4814 0.876938793 0.968610419 0.858171911 0.820783668 0.98175138 1.14468697 0.91255673 0.826776639 1 19.16540874 4.775077856 20.91231265 0.930661979 0.876937809 0.033304583 0.096097571 9304.072192 5327276.729 0.024935375 3.41004798 59576.89378 -4.775077856 -0.053724169 NLLEDDS(ph)DEEEDFFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 NLLEDDSDEEEDFFLR 16 0 O75379 O75379 VAMP4 Vesicle-associated membrane protein 4 1 NLLEDDS(1)DEEEDFFLR;NLLEDDS(1)DEEEDFFLR;NLLEDDS(1)DEEEDFFLR;NLLEDDS(1)DEEEDFFLR;NLLEDDS(1)DEEEDFFLR;NLLEDDS(1)DEEEDFFLR;NLLEDDS(1)DEEEDFFLR 341.19 4.44E-72 1633869000 1734526 1512331 1025553 1259550 1817596 1940071 1370417 2125169 2139495 TRUE FALSE 1505303.994 1502396.398 1521513.861 1545550.079 1781429.396 2014706.787 1237514.17 1670718.147 1886566.338 0.797906739 0.796365528 0.806498998 0.81923972 0.944270742 1.067922578 0.655961121 0.885586747 1 20.8473314 3.373415638 6.486648435 0.896098563 0.802026981 0.192754198 0.105682891 0.428949552 23.45559156 0.031422824 0.040659959 2362.738393 -3.373415638 -0.094071582 NLLHVTDTGVGMTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NLLHVTDTGVGMTR 14 0 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 ;;; 169.37 2.54E-06 2915820000 1873680 1877930 1040160 1282060 2253510 2631810 2108250 2145950 1808810 FALSE TRUE 1626068.441 1865593.754 1543184.855 1573171.318 2208669.56 2733057.434 1903792.239 1687055.292 1594974.542 1.019494918 1.169669925 0.967529458 0.986330049 1.384767908 1.713542982 1.193619201 1.057731799 1 20.60510197 3.250189679 24.98818007 1.259864355 1.040448002 0.252194743 0.199884398 386.1827487 829813.5019 0.065061361 0.083275633 1779.056246 -3.250189679 -0.219416353 NLLQQS(ph)WEDMKR ddPTM_MDA-MB-175_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 199.68 1.03E-07 654760000 309460 270660 202651 264637 306410 297500 342810 379370 359320 TRUE FALSE 268564.0769 268882.0166 300653.7014 324726.8756 300313.0405 308945.0175 309564.339 298244.6778 316841.5989 0.84762884 0.848632306 0.948908547 1.024887125 0.94783337 0.975077195 0.977031867 0.941305304 1 18.27340224 4.190647735 4.188828541 0.973350419 0.84596675 0.829144075 0.023919456 0.073693073 2.680550013 0.006034897 0.014473125 15511.28347 -4.190647735 -0.127383668 NLLSSWDEVIHIADQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLLSSWDEVIHIADQLR 17 0 Q15813-2;Q15813;A0A2R8Y5Q8;A0A2R8YHI9;A0A2R8Y7E7;A0A2R8Y6Q1;A0A2R8YFL4;A0A2R8YER9;A0A2R8Y897;A0A2R8Y6L2;A0A2R8Y809;A0A2R8Y4V6;A0A2R8Y784;A0A2R8Y4E7 Q15813-2 TBCE Tubulin-specific chaperone E 0 ; 156.73 5.23E-08 270790000 272470 265770 144629 154094 242690 244450 257700 266090 246550 FALSE TRUE 236462.3991 264024.1394 214572.0682 189083.3979 237860.9438 253854.1497 232708.2937 209188.7242 217403.1399 1.08766782 1.214444923 0.986977779 0.869736279 1.094100775 1.167665517 1.070399875 0.962215745 1 17.73001325 4.230639734 24.99930607 1.021283195 1.15105638 0.285472992 0.085156159 215.1475068 679040.1273 0.023315936 0.049965295 17007.47081 -4.230639734 0.129773184 NLLSVAYK ddPTM_MDA-MB-175_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 ; 138.1 0.0016748 3107400000 4136800 3758700 1908500 2381200 4341900 3605600 4255500 5064100 4997200 FALSE TRUE 3590111.399 3734008.852 2831456.984 2921887.854 4255504.685 3744309.765 3842802.265 3981181.624 4406436.709 0.814742531 0.847398726 0.642572938 0.663095387 0.965747375 0.849736423 0.872088383 0.903492297 1 22.07118105 3.233741122 24.99998417 0.909489665 0.74238574 0.584159252 0.073692425 95.13135318 493470.878 0.023217023 0.027169849 1712.935941 -3.233741122 -0.167103925 NLNDQVLFIDQGNRPLFEDMTDSDCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLNDQVLFIDQGNRPLFEDMTDSDCR 26 1 Q14116-2;Q14116 Q14116-2 IL18 Interleukin-18 0 ; 188.3 9.35E-18 153104000 111879 128768 77829 97863 134790 148607 127337 150511 182178 FALSE TRUE 97093.90668 127922.1145 115467.3647 120084.2899 132107.9427 154324.0075 114987.8773 118325.3939 160641.1244 0.604415009 0.79632233 0.718790815 0.747531433 0.822379345 0.960675593 0.715805979 0.736582207 1 17.29348175 5.965441679 0.5533396 0.827151341 2.20E-11 0.342634527 0.095163329 20.42579875 1.715114593 0.053798955 14.613536 923510.1633 -5.965441679 -0.827151341 NLNHVSYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NLNHVSYGR 9 0 P00367;P00367-2;P00367-3;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 ;;; 125.16 0.00050936 1106790000 1072980 1379490 383744 891190 1877210 2013230 1107350 1353440 1186650 FALSE TRUE 931182.9744 1370428.039 569323.8819 1093548.31 1839857.194 2090680.261 999959.3674 1064017.388 1046365.589 0.889921252 1.309702894 0.544096526 1.045092004 1.758331135 1.998039962 0.955650088 1.016869629 1 19.99695557 3.462520121 24.88231764 1.316535714 0.927504367 0.220759598 0.376290973 403.6845664 687930.8624 0.118708007 0.153314341 2900.815594 -3.462520121 -0.389031347 NLNIINTHAYNQPEDLVYS(ph)QPEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLNIINTHAYNQPEDLVYSQPEMR 24 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 NLNIINTHAYNQPEDLVYS(1)QPEMR;NLNIINTHAYNQPEDLVYS(1)QPEMR 178.72 2.54E-17 247240000 75963 93580 40497 49263 93837 105145 82224 85299 66590 TRUE FALSE 65924.29708 92965.26682 60081.48465 60448.91709 91969.82729 109189.9962 74249.92914 67058.47265 58717.80606 1.122730931 1.583255116 1.023224277 1.029481875 1.566302174 1.859572139 1.264521516 1.142046632 1 15.84151044 3.246710267 24.99814369 1.355439926 1.205896924 0.089182112 0.277400645 631.7297848 1937750.159 0.08784257 0.111415243 1764.860029 -3.246710267 -0.149543002 NLNNSNLFS(ph)PVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 NLNNSNLFSPVNR 13 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3;H0YEN4 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR 314.56 1.11E-50 8511430000 4866710 5082080 2530210 3142520 6355240 6080060 5397510 6120560 5742300 TRUE FALSE 4223561.943 5048695.482 3753828.019 3856077.196 6228783.158 6313963.843 4874060.311 4811725.874 5063451.836 0.834127011 0.997085713 0.741357505 0.761551077 1.230145632 1.246968283 0.962596361 0.9502857 1 22.2716898 3.253644277 24.99981605 1.061828274 0.838629063 0.504122161 0.11983817 245.78572 407365.4755 0.038534787 0.049552262 1793.264195 -3.253644277 -0.223199212 NLNS(ph)S(ph)VRGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLNSSVRGDR 10 1 Q9NS56-2;Q9NS56 Q9NS56-2 TOPORS E3 ubiquitin-protein ligase Topors 2 NLNS(1)S(1)VRGDR;NLNS(1)S(1)VRGDR 70.412 0.03076 373910000 382430 410530 229838 308170 364240 425620 313410 398920 381760 TRUE FALSE 331890.9065 407833.2014 340988.4256 378144.7086 356992.3366 441993.8768 283015.5464 313614.0624 336628.7677 0.985925561 1.211522129 1.012950937 1.123328559 1.060492658 1.313000906 0.840734879 0.931631793 1 18.36079895 2.214237871 24.99999981 0.922212236 1.114998132 0.450735827 0.100782475 195.4606673 200901.6331 0.03833479 0.025859483 163.7713282 -2.214237871 0.192785896 NLPFDFTWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLPFDFTWK 9 0 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 140.75 0.00025206 1011160000 1184820 1077850 522590 619900 1046100 932010 1053610 1221420 1180620 FALSE TRUE 1028243.035 1070769.532 775316.272 760657.7696 1025284.657 967865.0278 951431.0644 960228.8381 1041048.449 0.987699503 1.028549184 0.74474562 0.730665101 0.984857773 0.929702195 0.913916221 0.9223671 1 19.98960578 NLPIMSTAS(ph)VEIDDALYSR ddPTM_MDA-MB-175_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;NLPIMST(0.001)AS(0.999)VEIDDALYSR 285.91 4.68E-40 137232000 103234.1 93381.7 43803.9 46824.4 84421.7 58613.5 112049.6 88239 80684.8 TRUE FALSE 89591.45212 92768.26946 64987.61256 57456.59569 82741.87334 60868.39927 101183.047 69369.77653 71146.33486 1.259256043 1.303907919 0.913435846 0.807583353 1.16298153 0.855538088 1.422182144 0.975029517 1 16.11850182 4.251989065 24.99045104 1.028828622 1.281582146 0.282515338 0.173121971 306.0781287 569603.4671 0.042133289 0.110107778 17864.42593 -4.251989065 0.252753524 NLPIYSEEIVEMYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLPIYSEEIVEMYK 14 0 P35579;Q5BKV1 P35579 MYH9 Myosin-9 0 ; 182.02 3.66E-06 61306000 93878 75084 54640 58076 86675 77840 87582 109776 122144 FALSE TRUE 81471.78444 74590.76826 81064.08676 71263.04344 84950.33708 80834.55517 79088.31112 86301.25668 107704.2755 0.75643965 0.6925516 0.752654307 0.661654731 0.788736907 0.750523179 0.734309857 0.801279766 1 16.716716 1.073579572 1.703506849 1.204070263 0.731402255 0.848647788 0.035299887 0.536405165 1.007451299 0.481672195 0.009330382 11.84621396 -1.073579572 -0.472668008 NLPLGWDGKPIPYWLYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLPLGWDGKPIPYWLYK 17 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 68.257 0.033984 159630000 222190 194830 115590 106570 183200 168750 215150 276330 149300 FALSE TRUE 192827.0285 193550.1489 171489.7106 130768.3473 179554.6784 175241.9217 194284.7861 217238.9799 131649.9241 1.464695327 1.470188078 1.302619138 0.993303629 1.363879848 1.331120568 1.475768311 1.650126131 1 17.00634716 2.335538465 5.711605219 1.436236456 1.312294283 0 0.208274101 0.624373443 30.30770015 0.080580677 0.061630655 216.5401657 -2.335538465 -0.123942173 NLQEEIDALESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLQEEIDALESR 12 0 Q9NQP4;E9PQY2 Q9NQP4 PFDN4 Prefoldin subunit 4 0 95.401 0.014116 40641000 31561 29658 17361 24118 32440 34537 31430 30352 32325 FALSE TRUE 27390.13388 29463.17465 25756.83767 29594.36052 31794.50747 35865.66074 28381.92344 23861.461 28503.57532 0.96093678 1.033665928 0.903635329 1.038268364 1.115456819 1.258286384 0.995732048 0.837139226 1 14.79885527 1.992994183 24.99607235 0.90978636 1.053158063 0.228339338 0.100464659 424.0622353 1513012.505 0.04504921 0.029046635 98.39979255 -1.992994183 0.143371702 NLQLDYVDLYLIHFPVSVKPGEEVIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLQLDYVDLYLIHFPVSVKPGEEVIPK 27 1 S4R3P0;P52895;H0Y804;Q04828;A6NHU4 S4R3P0 AKR1C2;AKR1C1 Aldo-keto reductase family 1 member C2;Aldo-keto reductase family 1 member C1 0 ; 175.11 8.44E-13 532370000 710560 596460 386870 451730 566660 442340 888040 983310 851760 FALSE TRUE 616657.6957 592541.815 573961.626 554302.2008 555384.5747 459357.106 801918.0175 773036.8086 751065.9031 0.821043391 0.788934516 0.764196089 0.738020723 0.73946184 0.611606923 1.067706594 1.029252966 1 19.51857998 2.225884084 24.99999999 1.033155447 0.74638198 0.854648404 0.056068294 79.7083678 157195.4037 0.023297509 0.015824284 168.2225006 -2.225884084 -0.286773467 NLQLLMDRVDEMSQDIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLQLLMDRVDEMSQDIVK 18 1 A0A087WZK9;B3KS98;O15372;E5RJT0 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 97.32 0.0013034 63166000 77030 75314 38094 44345 63761 68889 83839 104620 33742 FALSE TRUE 66850.29033 74819.25737 56516.38582 54414.21002 62492.28085 71539.20441 75708.30668 82247.82715 29753.0592 2.24683754 2.514674436 1.89951512 1.828861014 2.100364888 2.404431891 2.544555374 2.764348587 1 14.86075039 2.758779933 21.41911744 2.304231994 2.111878185 0 0.504018516 576.8556541 611081.1933 0.162358601 0.161981523 573.825618 -2.758779933 -0.192353809 NLQS(ph)PTQFQTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NLQSPTQFQTPR 12 0 O75385 O75385 ULK1 Serine/threonine-protein kinase ULK1 1 NLQS(0.935)PT(0.065)QFQTPR;NLQS(1)PTQFQTPR;NLQS(0.999)PT(0.001)QFQTPR;NLQS(0.999)PT(0.001)QFQTPR 303.29 1.12E-36 1138690000 925340 856600 593510 726160 1397050 1646390 1330260 1460660 1493610 TRUE FALSE 803053.9745 850972.9382 880533.4212 891045.7267 1369251.438 1709727.689 1201251.59 1148309.226 1317037.127 0.609742852 0.646126765 0.668571449 0.676553233 1.039645284 1.298162104 0.912086353 0.871888273 1 20.32886459 3.25895409 7.434066227 1.010799244 0.649841343 0.729312131 0.113105897 0.102469229 24.4383081 0.037111664 0.046645535 1815.32375 -3.25895409 -0.360957901 NLRPGDSQTAAQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLRPGDSQTAAQAR 14 1 Q8WZA9;M0QZP8 Q8WZA9 IRGQ Immunity-related GTPase family Q protein 0 ; 221.73 3.79E-12 489770000 312470 298870 161197 167019 320920 339430 293490 323180 321770 FALSE TRUE 271176.2978 296906.7033 239152.4084 204943.2167 314534.3199 352488.0917 265027.385 254070.472 283730.7172 0.955752343 1.046438349 0.842885151 0.722315929 1.10856633 1.242333207 0.934080693 0.895463398 1 18.11416282 3.205816673 24.99984199 1.021172134 0.899392215 0.243158632 0.124603406 364.8765038 278580.3521 0.042185749 0.047837366 1606.263064 -3.205816673 -0.121779918 NLS(ph)FEIK ddPTM_MDA-MB-175_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 134.84 0.0032884 5879165000 5523030 4186960 2543527 3268600 4402390 2416588 7374110 6467160 4966990 TRUE FALSE 4793147.592 4159455.584 3773585.165 4010785.587 4314791.052 2509555.704 6658969.947 5084208.161 4379798.101 1.09437638 0.94969117 0.86158884 0.915746684 0.985157524 0.572984335 1.520382857 1.160831628 1 22.06243294 2.234844646 24.9999999 1.225492755 0.90230997 0.422508821 0.182050356 91.07045271 612685.5257 0.070297151 0.049468172 171.7293976 -2.234844646 -0.323182785 NLS(ph)NEELTK ddPTM_MDA-MB-175_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(0.999)NEELT(0.001)K;NLS(1)NEELTK;NLS(1)NEELTK;NLS(1)NEELTK 196.11 3.17E-05 3959690000 7390500 6452040 4904220 5201370 7142820 5668080 8336040 9156340 8349860 TRUE FALSE 6413826.7 6409656.124 7275917.196 6382420.556 7000691.857 5886134.705 7527612.124 7198327.946 7362749.063 0.87111847 0.870552027 0.988206597 0.866852924 0.950825812 0.799447958 1.022391509 0.977668515 1 22.8118131 2.207968581 24.99999936 0.996295639 0.896247593 0.494720521 0.051642913 170.8215573 139595.2484 0.019802553 0.01335259 161.424177 -2.207968581 -0.100048046 NLS(ph)PGAVESDVR ddPTM_MDA-MB-175_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 206.19 9.75E-08 3743350000 1035100 1111140 582591 808383 1275310 1208660 1168660 1309800 1198180 TRUE FALSE 898308.9124 1103840.848 864333.9562 991938.7155 1249933.826 1255157.932 1055323.533 1029709.463 1056532.525 0.850242554 1.044776968 0.818085516 0.93886245 1.18305286 1.187997437 0.998855698 0.974612175 1 20.01090575 3.450164809 23.86374519 1.058103806 0.911753319 0.414231553 0.092252303 148.3417227 131321.654 0.028405071 0.036672078 2819.452673 -3.450164809 -0.146350487 NLS(ph)PTAVINITSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLSPTAVINITSEK 14 0 H0YAJ5;G5E9Y1;Q92870-2;Q92870;Q92870-4;D6RB55 H0YAJ5 APBB2 Amyloid beta A4 precursor protein-binding family B member 2 1 NLS(0.5)PT(0.5)AVINITSEK 83.252 0.0090252 15148000 58741 46328 38052 44719 59613 46479 57750 60853 117460 TRUE FALSE 50978.22802 46023.66832 56454.07448 54873.13244 58426.81793 48267.07721 52149.41389 47840.05951 103574.0126 0.492191301 0.444355366 0.545060224 0.529796336 0.564106927 0.466015326 0.50349902 0.461892499 1 16.66030254 1.235864669 24.99998293 1.000000665 0.500567867 0.945360834 0.037711459 16.0671921 148963.9114 0.063559169 0.009504034 17.21332106 -1.235864669 -0.499432797 NLS(ph)SDEATNPISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLSSDEATNPISR 13 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 NLS(0.816)S(0.184)DEATNPISR;NLS(0.93)S(0.07)DEATNPISR 276.1 3.35E-32 466350000 448340 467430 241480 300590 471940 434330 442810 514270 444290 TRUE FALSE 389090.7331 464359.4216 358260.5357 368843.5537 462549.3173 451038.9561 399866.3544 404297.3626 391766.5423 0.993169888 1.185296271 0.914474558 0.941488141 1.180675906 1.151295242 1.020675099 1.031985427 1 18.57963467 2.08197287 22.75443998 1.02059908 1.062212582 0.045414424 0.093595398 53.23671046 14767.57658 0.039497579 0.026629269 120.7738385 -2.08197287 0.041613501 NLS(ph)STTDDEAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLSSTTDDEAPR 12 0 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 NLS(0.699)S(0.255)T(0.034)T(0.012)DDEAPR 244.37 2.24E-16 470040000 279280 357300 237030 340770 543970 591520 557790 661540 534590 TRUE FALSE 242372.4404 354952.8728 351658.5008 418147.0368 533146.0613 614276.1572 503695.6117 520074.8191 471391.3792 0.514163922 0.752989741 0.746001128 0.887048545 1.131005115 1.303112836 1.068529536 1.103276051 1 18.84656585 3.627205248 1.59955026 1.125330843 0.636805824 0.820737467 0.096921901 0.161867866 0.816234238 0.032152815 0.062781816 4238.432272 -3.627205248 -0.488525019 NLSDIGWPVFEIPS(ph)PR ddPTM_MDA-MB-175_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 197.09 4.64E-11 602785000 408756 437171 299182 341775 485531 484979 451569 477348 805885 TRUE FALSE 354737.8589 434299.1949 443867.4159 419380.2375 475869.883 503636.456 407775.9079 375270.8449 710614.1934 0.49919895 0.611160316 0.624625036 0.590165861 0.669659975 0.708734023 0.573835862 0.528093653 1 19.43870698 1.23200073 24.99999033 1.000000668 0.602301884 0.808638335 0.061043177 101.9347067 388440.486 0.147780324 0.015801527 17.06085255 -1.23200073 -0.397698784 NLSDIGWPVFEIPS(ph)PRPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 150.91 4.29E-08 270690000 514820 443960 268710 331620 523350 416090 540330 713980 296370 TRUE FALSE 446785.2326 441043.5975 398659.0548 406919.3895 512936.3589 432097.2515 487928.8798 561300.9332 261333.4762 1.709636435 1.687665904 1.525480243 1.557088649 1.962765606 1.653432456 1.867073774 2.147834029 1 17.99553242 3.268119135 24.97440985 1.78584747 1.618054246 0.008719879 0.303597313 621.2786236 524923.115 0.085461617 0.110314014 1854.040151 -3.268119135 -0.167793225 NLSEAQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLSEAQLR 8 0 Q9NZT1 Q9NZT1 CALML5 Calmodulin-like protein 5 0 79.059 0.067509 420520000 202920 179120 90388 122940 402390 242320 176140 189230 156860 FALSE TRUE 176103.6079 177943.3489 134099.9391 150855.406 394383.2263 251642.2072 159057.9699 148764.6371 138316.1895 1.273195918 1.286496899 0.969517304 1.090656174 2.851316449 1.819325765 1.149959166 1.075540308 1 17.0776105 NLSFDIPTGSLRDS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLSFDIPTGSLRDSR 15 1 Q5THJ4-2;Q5THJ4 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 NLSFDIPT(0.011)GS(0.011)LRDS(0.977)R 77.391 0.010451 0 230470 263210 137830 129600 269680 335680 212940 253460 253240 TRUE FALSE 200012.8056 261480.9562 204485.049 159027.6608 264313.8956 348593.8268 192289.1116 199259.5514 223302.2557 0.895704367 1.170973197 0.915732125 0.712163253 1.183659766 1.561085112 0.861115849 0.892331118 1 17.7686383 NLSLCFEGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLSLCFEGSPR 11 0 Q96JQ2 Q96JQ2 CLMN Calmin 1 NLSLCFEGS(1)PR 129.77 0.00024969 84139000 73365 79188 59948 75318 110880 133780 94281 138790 211970 TRUE FALSE 63669.62937 78667.80881 88939.05331 92420.10306 108673.7049 138926.6032 85137.64313 109110.8386 186911.1481 0.340641155 0.42088345 0.475836001 0.49446009 0.581419065 0.743276175 0.455497941 0.583757789 1 17.51199309 0.079146506 1.357831577 9.999999921 0.501480349 0.680690892 0.106157689 17.28516277 2.007945312 449.772604 0.033181318 1.199904014 -0.079146506 -9.498519573 NLSS(ph)TTDDEAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NLSSTTDDEAPR 12 0 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 NLS(0.18)S(0.718)T(0.077)T(0.025)DDEAPR;NLS(0.023)S(0.751)T(0.222)T(0.004)DDEAPR;NLS(0.185)S(0.806)T(0.009)TDDEAPR 262.48 2.14E-21 1838180000 1242510 1419140 1069900 1528440 2409490 2506240 2475170 2484430 2479240 TRUE FALSE 1078309.155 1409817.576 1587307.219 1875495.663 2361545.863 2602656.675 2235128.394 1953153.978 2186147.072 0.493246392 0.644886885 0.726075221 0.857900041 1.080231927 1.190522224 1.022405319 0.893422956 1 21.05995903 3.854105094 1.455210298 1.023904873 0.5425583 0.842062619 0.083823962 0.193903464 0.780232683 0.030684659 0.082969112 7146.692456 -3.854105094 -0.481346573 NLSSHVVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLSSHVVER 9 0 Q9BS34 Q9BS34 ZNF670 Zinc finger protein 670 0 67.897 0.0596 175650000 410800 432820 266600 262540 379220 703700 268610 228070 269690 FALSE TRUE 356511.7392 429976.7769 395528.6517 322153.7197 371674.2639 730771.7944 242560.2435 179299.0053 237807.5554 1.499160691 1.808087115 1.663229963 1.354682441 1.562920334 3.072954486 1.019985438 0.753966816 1 17.85943503 2.028526375 24.99997381 0.867678159 1.806873729 0.448823899 0.472900314 176.426265 154615.9191 0.191704074 0.129244505 106.7889644 -2.028526375 0.93919557 NLSYQVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NLSYQVHR 8 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30 O60716-13 CTNND1 Catenin delta-1 0 ;;; 138.4 0.0012841 544500000 644100 639130 263721 407663 747900 777280 571090 702220 617320 FALSE TRUE 558980.5531 634931.5129 391257.3577 500229.1149 733018.2532 807182.4646 515705.7797 552055.7177 544341.1329 1.026893834 1.166422074 0.718772354 0.918962549 1.346615585 1.482861419 0.947394471 1.014172335 1 19.05415153 3.292678321 24.99998207 1.140627771 0.955595819 0.205272187 0.19425639 181.5873287 83883.768 0.061117273 0.078902003 1961.906569 -3.292678321 -0.185031951 NLTANDPSQEYVAS(ph)EGEEDPEVEFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLTANDPSQEYVASEGEEDPEVEFLK 26 0 Q86X95 Q86X95 CIR1 Corepressor interacting with RBPJ 1 1 NLTANDPSQEYVAS(1)EGEEDPEVEFLK;NLTANDPSQEYVAS(1)EGEEDPEVEFLK 258.83 6.63E-53 215230000 412450 300080 189772 251840 356230 287190 347910 409220 394620 TRUE FALSE 357943.6875 298108.7547 281546.3739 309024.1211 349141.72 298238.3851 314169.7417 321711.4876 347968.4732 1.028667006 0.856711966 0.809114606 0.888080803 1.003371704 0.857084501 0.902868409 0.924542056 1 18.40859707 1.219627791 2.378241872 1.029190807 0.902222001 0.161016612 0.066009525 1.142144573 6.554357893 0.310616239 0.017350745 16.58165181 -1.219627791 -0.126968806 NLTELEDEHLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLTELEDEHLAK 12 0 E9PGD8;E7EWK7;E9PH71;O15381-5;O15381 E9PGD8 NVL Nuclear valosin-containing protein-like 0 70.622 0.046786 80754000 98791 105350 65976 71142 107610 92123 96313 140310 123940 FALSE TRUE 85735.51905 104657.9489 97882.21428 87295.87844 105468.7715 95667.03142 86972.58008 110305.7984 109287.9544 0.784491937 0.957634805 0.89563589 0.798769443 0.965053945 0.875366658 0.795811218 1.009313414 1 16.73777487 1.646806914 7.618805287 1.005755194 0.873809296 0.44687908 0.062979311 0.101867685 11.4311679 0.035832984 0.015388314 44.34114607 -1.646806914 -0.131945898 NLTEQNSYSNIPHEGKHTPLY(ph)ER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLTEQNSYSNIPHEGKHTPLYER 23 1 Q9NZB2;Q9NZB2-4;Q9NZB2-6;Q9NZB2-2;Q9NZB2-5;A0A0C4DH52;Q5T035 Q9NZB2 FAM120A;C9orf129 Constitutive coactivator of PPAR-gamma-like protein 1;Putative uncharacterized protein C9orf129 1 NLTEQNSY(0.001)S(0.006)NIPHEGKHT(0.444)PLY(0.549)ER 155.93 8.68E-09 168580000 127180 130580 58978 81783 133590 128800 138970 138560 121410 TRUE FALSE 110372.8408 129722.2114 87499.95807 100353.0801 130931.8204 133755.0193 125492.7108 108930.0223 107057.0481 1.030972203 1.21171108 0.817320855 0.93737948 1.223009813 1.24938079 1.172204101 1.017495104 1 16.70802025 3.247626441 24.99997302 1.126884711 1.001513062 0.221810274 0.123583515 354.2154974 976781.6249 0.038635959 0.049161558 1768.587052 -3.247626441 -0.125371649 NLVDFTFVENVVHGHILAAEQLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLVDFTFVENVVHGHILAAEQLSR 24 0 Q15738 Q15738 NSDHL "Sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating" 0 105.17 0.0016874 254150000 81411 87590 31935 45775 92760 84369 76787 88867 19529 FALSE TRUE 70652.33008 87014.61552 47378.87282 56168.91338 90914.25748 87614.73002 69340.20856 69863.48361 17220.30387 4.102850369 5.053024394 2.751337792 3.261784101 5.279480442 5.087873634 4.026654181 4.057041278 1 14.07182298 4.270226489 24.99687696 3.793007108 4.577936782 0.081306818 1.230635314 617.6588367 487566.907 0.309070561 0.817564686 18630.58486 -4.270226489 0.784929674 NLVLTGFSHIDLIDLDTIDVSNLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NLVLTGFSHIDLIDLDTIDVSNLNR 25 0 Q9UBT2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 ;;;; 232.06 8.22E-35 638643000 518401 492925 214425 244701 458343 464113 453084 539413 485884 FALSE TRUE 449892.9944 489686.9432 318121.6472 300264.1021 449222.871 481967.7274 409143.9834 424063.7277 428443.347 1.050064139 1.142944444 0.742505746 0.700825685 1.048500051 1.124927556 0.954954689 0.989777833 1 18.70874492 NLVS(ph)PAYCTQESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLVSPAYCTQESR 13 0 Q9NUQ3 Q9NUQ3 TXLNG Gamma-taxilin 1 NLVS(1)PAYCTQESR;NLVS(1)PAYCTQESR 157.84 4.46E-05 364690000 283520 276060 183287 219313 340200 324030 300280 376920 372690 TRUE FALSE 246052.1137 274246.5437 271925.2063 269111.3686 333430.6856 336495.6438 271158.8918 296318.5912 328631.0128 0.748718484 0.834512061 0.827448402 0.818886101 1.014605051 1.023931494 0.825116563 0.901675678 1 18.32610911 3.321251682 8.474959063 0.94044637 0.809857273 0.566251867 0.062823773 0.239174712 21.85047224 0.01938299 0.025016241 2095.326387 -3.321251682 -0.130589097 NLVTEDVMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NLVTEDVMR 9 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41;A0A2R8YF08;K7ELR7;K7ENA0;K7ERK8;A0A0J9YXM3;A0A0J9YXH9;K7EIL4;A0A0J9YYI8 P06744 GPI Glucose-6-phosphate isomerase 0 ; 121.64 0.001415 376970000 410390 369170 210713 314050 478000 439450 371220 432560 462180 FALSE TRUE 356155.9217 366744.898 312614.5116 385359.8525 468488.7352 456355.9259 335219.1415 340060.4102 407541.6069 0.873913033 0.899895598 0.767073855 0.945571804 1.149548236 1.11977751 0.822539677 0.834418878 1 18.63658783 3.502170896 23.98317743 0.968800306 0.852932347 0.245886788 0.108476986 854.8109013 818415.2679 0.034488046 0.050860419 3178.124425 -3.502170896 -0.115867959 NLVTGDHIPTPQDLPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 88.283 0.0043343 271040000 136820 141960 83350 106190 184080 172510 155760 164390 211030 FALSE TRUE 118738.8903 141027.4554 123658.3388 130302.0625 180417.1681 179146.5713 140654.4192 129236.4778 186082.2738 0.638098879 0.757876892 0.664535833 0.700238985 0.969555909 0.962727764 0.755872208 0.694512568 1 17.50558111 3.343642178 9.988818812 0.84893691 0.692179844 0.446866052 0.100468629 0.379400035 33.32720549 0.031633819 0.04083833 2206.186272 -3.343642178 -0.156757066 NLVYDQS(ph)PNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLVYDQSPNR 10 0 Q9NXR1;Q9NXR1-1;I3L533;I3L2R9;I3L2T8 Q9NXR1 NDE1 Nuclear distribution protein nudE homolog 1 1 NLVYDQS(1)PNR 164.68 6.38E-06 281020000 323960 348730 166320 209460 350240 375790 336470 355930 353680 TRUE FALSE 281147.8652 346439.1697 246752.9083 257021.0944 343270.9092 390246.8845 303839.1912 279817.1394 311868.3533 0.901495334 1.110850671 0.791208552 0.824133297 1.100691704 1.251319284 0.974254643 0.897228386 1 18.25057764 3.232706567 24.99907655 1.031312707 0.913223056 0.230310459 0.123580757 277.0763886 1183222.629 0.040935264 0.047647094 1708.860325 -3.232706567 -0.118089651 NLYPS(ph)SSPYTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NLYPSSSPYTR 11 0 Q9Y2Z0;Q9Y2Z0-2 Q9Y2Z0 SUGT1 Suppressor of G2 allele of SKP1 homolog 1 NLYPS(0.588)S(0.314)S(0.098)PYTR 77.124 0.018752 0 386290 436150 215340 274870 444740 428270 363340 461930 420360 TRUE FALSE 335240.7978 433284.9019 319479.1443 337283.4346 435890.5441 444745.824 328103.3427 363149.8642 370665.5197 0.904429411 1.168937705 0.861906833 0.909940139 1.175967337 1.199857555 0.885173628 0.979723888 1 18.49975839 NLYSDDIPHALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NLYSDDIPHALR 12 0 P60228;H0YBR5;E5RIT4 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 ;;; 172.76 3.49E-05 3708790000 3145870 3065930 1587710 2089290 3684590 3614560 3093920 3559700 3425130 FALSE TRUE 2730135.309 3045789.704 2355531.867 2563695.227 3611273.868 3753614.462 2793872.115 2798485.857 3020215.033 0.90395395 1.008467831 0.779921906 0.848845264 1.195700911 1.242830203 0.92505735 0.92658497 1 21.52621984 3.273084337 24.99968434 1.040870147 0.886568244 0.349116172 0.115884444 263.2489163 190624.9524 0.037518863 0.048434407 1875.358654 -3.273084337 -0.154301903 NMADAMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NMADAMR 7 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 101.28 0.021339 157220000 243720 297620 165660 191800 284350 336050 308520 295260 278470 FALSE TRUE 211511.7845 295664.9146 245773.7301 235351.1215 278691.9913 348978.061 278599.7779 232120.9467 245549.5938 0.861381121 1.204094497 1.000912794 0.958466751 1.134972316 1.421212129 1.134596778 0.945311874 1 17.90565491 4.757763245 23.59471069 1.093107503 0.861380666 0.217570172 0.141651115 3615.323508 4442075.109 0.037256336 1.201639728 57248.38577 -4.757763245 -0.231726837 NMAPSQQS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NMAPSQQSPVR 11 0 H7C3Q7;B7Z836;E7EW77;E7EP65;A0A0C4DG21;F8WAL6;Q9NYB9-3;Q9NYB9-2;Q9NYB9-4;Q9NYB9;H0Y6B5 H7C3Q7 ABI2 Abl interactor 2 1 NMAPS(0.004)QQS(0.996)PVR 87.989 0.013965 221700000 141890 154760 66467 99781 152430 146010 131080 160700 157840 TRUE FALSE 123138.877 153743.3714 98610.66352 122437.8011 149396.9412 151627.0992 118367.8818 126335.5556 139180.335 0.884743358 1.104634296 0.708510031 0.879706182 1.07340553 1.089429043 0.850464125 0.907711248 1 17.08659586 SQPWDLTPMLSSS(ph)EPWGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SQPWDLTPMLSSSEPWGR 18 0 Q9H201 Q9H201 EPN3 Epsin-3 1 SQPWDLTPMLS(0.001)S(0.268)S(0.732)EPWGR;SQPWDLTPMLS(0.072)S(0.154)S(0.773)EPWGR;SQPWDLTPMLSS(0.002)S(0.997)EPWGR 269.85 1.77E-31 425249000 527920 722670 588950 753490 1132630 1335270 1190180 1306620 1348770 TRUE FALSE 458154.0344 717922.7332 873768.1899 924581.4209 1110092.879 1386638.701 1074756.527 1027209.481 1189319.947 0.385223535 0.603641379 0.734678832 0.777403442 0.933384563 1.165908891 0.90367317 0.863694823 1 20.18170545 4.365131003 0.852606803 0.963771186 0.252010313 0.83189918 0.088437193 0.632815635 0.528186563 0.037347539 0.383284243 23180.93786 -4.365131003 -0.711760873 down NMDPLNDNIATLLHQSSDKFVSELWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NMDPLNDNIATLLHQSSDKFVSELWK 26 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 215.07 2.57E-34 4140000000 1731110 1780090 226383 909870 1939750 1510460 2259530 2534430 825090 FALSE TRUE 1502339.427 1768396.472 335862.576 1116469.89 1901152.77 1568568.374 2040401.128 1992461.867 727548.8001 2.064932864 2.430622484 0.461635805 1.534563578 2.613093128 2.15596311 2.804486968 2.738595496 1 19.47268449 3.247578873 24.97869043 2.357279928 1.597680005 0.160632582 0.707128175 308.5770095 854689.1119 0.206416901 0.262578712 1768.393351 -3.247578873 -0.759599923 NMFHPMDFEDDPLVLNEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NMFHPMDFEDDPLVLNEIR 19 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 ;;;; 221.85 2.57E-19 444509000 460448 458329 239040 311294 502431 529117 451241 542744 528731 FALSE TRUE 399598.6302 455318.2066 354640.5435 381978.0605 492433.6061 549472.4734 407479.7173 426682.4192 466225.0235 0.857093914 0.97660611 0.760663898 0.819299783 1.056214449 1.178556374 0.873997955 0.915185581 1 18.83066691 3.245625467 24.99913449 0.99246902 0.855590067 0.374549861 0.096454916 215.6450279 763060.2626 0.030424049 0.038431964 1760.457184 -3.245625467 -0.136878953 NMGGPYGGGNYGPGGSGGS(ph)GGYGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 NMGGPYGGGNYGPGGSGGSGGYGGR 25 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 NMGGPYGGGNYGPGGS(0.055)GGS(0.945)GGYGGR;NMGGPYGGGNYGPGGS(0.004)GGS(0.996)GGYGGR;NMGGPYGGGNYGPGGS(0.004)GGS(0.996)GGYGGR;NMGGPYGGGNYGPGGSGGS(1)GGYGGR;NMGGPYGGGNYGPGGSGGS(1)GGYGGR;NMGGPYGGGNYGPGGSGGS(1)GGYGGR;NMGGPYGGGNYGPGGSGGS(1)GGYGGR;NMGGPYGGGNYGPGGSGGS(1)GGYGGR;NMGGPYGGGNYGPGGS(0.023)GGS(0.977)GGYGGR;NMGGPYGGGNYGPGGS(0.069)GGS(0.931)GGYGGR 438.36 3.06E-182 4279480000 3229725 2871918 1274290 1623837 3217857 3395769 2726919 3124720 3076735 TRUE FALSE 2802908.658 2853052.182 1890540.906 1992554.01 3153827.941 3526406.431 2462462.815 2456522.945 2713006.893 1.033137315 1.051619953 0.696843385 0.734444875 1.162484308 1.29981477 0.907650777 0.905461372 1 21.37146128 3.234404356 24.99993775 1.037558886 0.878328573 0.228232607 0.15907936 200.5665279 1206409.053 0.053074313 0.062344577 1715.553857 -3.234404356 -0.159230313 NMGGPYGGGNYGPGGSGGSGGYGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NMGGPYGGGNYGPGGSGGSGGYGGR 25 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ; 214.5 4.24E-33 209395000 80028 62334 25845 32919 72301 82623 60902 69566 63330 FALSE TRUE 69452.09703 61924.52385 38343.72845 40393.76209 70862.35155 85801.56027 54995.73341 54689.85226 55843.19955 1.243698384 1.108899998 0.686632012 0.723342545 1.268952211 1.536472856 0.984824184 0.979346683 1 15.76909398 3.224010542 24.99611525 1.138543156 0.934517854 0.173381555 0.229871008 493.7166869 848172.252 0.076733775 0.087383697 1674.983532 -3.224010542 -0.204025301 NMITQYWPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NMITQYWPDR 10 0 O95373 O95373 IPO7 Importin-7 0 ; 130.98 0.0082162 0 260190 285740 202621 194757 324790 320800 347040 374650 401680 FALSE TRUE 225805.2323 283862.9551 300609.1933 238979.5535 318327.3144 333141.3836 313384.1142 294534.013 354193.848 0.637518787 0.801433895 0.848713762 0.674714016 0.898737559 0.940562309 0.884781359 0.831561628 1 18.43417963 3.217259583 24.6209827 0.900678419 0.752663523 0.5724342 0.072593048 162.7914446 188163.2543 0.02172393 0.024657411 1649.147813 -3.217259583 -0.148014896 NMLAFSSPAAGGVCEPLKS(ph)PQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NMLAFSSPAAGGVCEPLKSPQR 22 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 NMLAFSSPAAGGVCEPLKS(1)PQR;NMLAFSSPAAGGVCEPLKS(1)PQR 302.39 4.24E-56 2612500000 2098480 2090970 1133010 1372420 2431800 2004790 2487300 3213700 1839020 TRUE FALSE 1821160.551 2077234.28 1680937.426 1684048.937 2383411.938 2081915.569 2246082.029 2526475.264 1621613.151 1.123054873 1.280967831 1.036583494 1.038502269 1.469778373 1.283854641 1.385091153 1.558001218 1 20.62899826 3.240803356 24.99999999 1.367333533 1.125348327 0.310703198 0.159412573 65.97767367 735452.7844 0.046073893 0.056620566 1741.018379 -3.240803356 -0.241985206 NMMAACDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NMMAACDPR 9 0 Q13509;A0A0B4J269;Q13509-2;Q5JP53;P07437;Q5ST81;A6NNZ2;P68371;Q13885;Q3ZCM7;A0A075B736;Q5SQY0;Q9BVA1;P04350;K7ESM5;Q9BUF5 Q13509;Q5JP53;P68371;Q13885;Q3ZCM7;Q9BVA1;P04350;K7ESM5 TUBB3;TUBB;TUBB4B;TUBB2A;TUBB8;TUBB2B;TUBB4A;TUBB6 Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-8 chain-like protein LOC260334;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-8 chain;Tubulin beta-2B chain;Tubulin beta-4A chain;Tubulin beta-6 chain 0 ;; 105.57 0.0071582 2556250000 2803660 3000740 1399490 1730630 3608280 3725270 3111090 3273650 3230500 FALSE TRUE 2433149.227 2981027.941 2076288.045 2123595.993 3536482.287 3868583.547 2809376.971 2573605.423 2848593.97 0.854157965 1.046490996 0.72888171 0.745489183 1.241483456 1.35806773 0.986232857 0.903465166 1 21.44181857 3.247712838 24.99992339 1.078191386 0.850030879 0.397486277 0.154313684 256.7960726 701452.2647 0.050596485 0.064386477 1768.938924 -3.247712838 -0.228160508 NMPGLSAATLASLGGT(ph)SSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NMPGLSAATLASLGGTSSR 19 0 Q32MZ4-2;Q32MZ4;C9JTC6;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 NMPGLSAATLASLGGT(0.333)S(0.333)S(0.333)R;NMPGLSAATLASLGGT(0.333)S(0.333)S(0.333)R 162.65 3.04E-10 127991000 259230 220669 100886 99488 196279 205755 174921 197947 210820 TRUE FALSE 224972.0987 219219.4108 149674.807 122078.271 192373.4319 213670.528 157957.1883 155617.5745 185897.0998 1.210196926 1.179251377 0.805148694 0.656698093 1.034838264 1.14940216 0.849702274 0.837116742 1 17.50414474 4.253236624 23.36592448 0.900250116 1.194724826 0.441231156 0.135614795 105.3659252 167747.899 0.035862398 0.093796805 17915.81728 -4.253236624 0.29447471 NMPGLSAATLASLGGTSS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NMPGLSAATLASLGGTSSR 19 0 Q32MZ4-2;Q32MZ4;C9JTC6;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 NMPGLSAATLASLGGT(0.002)S(0.079)S(0.919)R;NMPGLSAATLASLGGT(0.002)S(0.092)S(0.906)R;NMPGLSAATLASLGGT(0.001)S(0.042)S(0.957)R;NMPGLSAATLASLGGT(0.007)S(0.225)S(0.768)R 383.27 9.23E-127 5466810000 3718600 3100080 1351550 1292770 2519710 2948380 2221680 2458200 2800450 TRUE FALSE 3227177.588 3079715.37 2005164.101 1586313.187 2469572.701 3061806.086 2006221.816 1932533.06 2469383.991 1.306875561 1.247159365 0.81200984 0.64239227 1.00007642 1.239906834 0.812438172 0.782597225 1 21.23571976 4.274739201 7.796961672 0.890250505 1.281012343 0.488225659 0.160985212 0.193083811 34.12536629 0.042814871 0.111909787 18825.18274 -4.274739201 0.390761838 NMQNVEHVPLSLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NMQNVEHVPLSLDR 14 0 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ;;;;; 128.71 5.47E-05 3673760000 10950000 11032160 5243930 7998560 11912670 11913560 9914150 12327160 11937990 FALSE TRUE 9502929.756 10959689.01 7779912.088 9814755.298 11675631.17 12371882.36 8952677.259 9691092.764 10526694.42 0.902745855 1.041133007 0.739065064 0.932368216 1.109145065 1.175286549 0.850473748 0.920620698 1 23.32754914 3.466366766 24.84883848 0.998210935 0.896783161 0.18040591 0.114143821 410.7472277 949049.8786 0.034970662 0.045192726 2926.622896 -3.466366766 -0.101427775 NMSVHLSPCFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NMSVHLSPCFR 11 0 P62280;M0QZC5;M0R1H5 P62280 RPS11 40S ribosomal protein S11 0 ; 133.05 0.00016976 2179880000 1646130 2566370 782540 1171650 3751300 3359470 2232500 2722700 2258030 FALSE TRUE 1428589.75 2549511.346 1160978.961 1437691.04 3676656.469 3488710.985 2015992.494 2140471.793 1991088.266 0.717491924 1.280461238 0.583087642 0.722062937 1.846556244 1.752162897 1.012507847 1.07502607 1 20.92512575 3.295561474 24.99992085 1.300871554 0.840917682 0.36112127 0.335850095 111.5789122 48936.18796 0.104634276 0.1350822 1974.974417 -3.295561474 -0.459953872 NMSVIAHVDHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 NMSVIAHVDHGK 12 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;; 216.34 2.27E-11 11638780000 14204570 13503550 5157807 8174827 15394850 13506730 15672540 18505600 16566080 FALSE TRUE 12327400.08 13414844.29 7652139.717 10031046.41 15088522.6 14026342.64 14152619.48 14548321.45 14607656.89 0.843899893 0.918343331 0.523844431 0.686697838 1.032918743 0.960204826 0.968849391 0.995938059 1 23.80022145 3.237264857 24.99964717 0.988852875 0.740038855 0.58928446 0.103011356 25.63655247 494618.8025 0.032012688 0.03833254 1726.890726 -3.237264857 -0.24881402 NMTVADSGTNHDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NMTVADSGTNHDSR 14 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 96.773 0.0024564 28364000 22663 25476 9406.9 15789 33737 35923 27473 27953 27298 FALSE TRUE 19668.02713 25308.64648 13956.1083 19374.13377 33065.69971 37304.98106 24808.67269 21975.46848 24070.86154 0.817088624 1.051422544 0.579792638 0.804879117 1.373681605 1.549798332 1.03065163 0.91294898 1 14.55500016 3.2652269 24.91790528 1.148969486 0.813625759 0.407682459 0.214571875 261.7398506 244577.0556 0.069318902 0.089463627 1841.733974 -3.2652269 -0.335343727 NMTVEQLLTGSPTS(ph)PTVEPEKPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NMTVEQLLTGSPTSPTVEPEKPTR 24 1 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 NMTVEQLLTGSPT(0.033)S(0.959)PT(0.008)VEPEKPTR;NMTVEQLLTGSPT(0.001)S(0.994)PT(0.005)VEPEKPTR;NMTVEQLLTGSPT(0.012)S(0.987)PT(0.001)VEPEKPTR;NMTVEQLLTGSPT(0.287)S(0.712)PT(0.001)VEPEKPTR;NMTVEQLLTGSPT(0.284)S(0.707)PT(0.009)VEPEKPTR;NMTVEQLLTGS(0.001)PT(0.084)S(0.913)PT(0.002)VEPEKPTR 273.63 3.52E-52 1734020000 993780 1015660 676178 846809 1413250 1160060 1484110 1855280 1622780 TRUE FALSE 862449.4551 1008988.063 1003179.942 1039089.926 1385129.09 1204688.259 1340181.241 1458542.81 1430936.797 0.602716666 0.705124129 0.701065166 0.726160602 0.96798761 0.841887819 0.936576125 1.019292266 1 20.44852852 3.461544408 0.410825338 1.062973078 0.51748671 0.863234643 0.053708554 0.674631053 0.317562446 0.115741207 0.223150914 2894.305756 -3.461544408 -0.545486368 NMVDLVNTHHLHSS(ph)SDDEDDRLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NMVDLVNTHHLHSSSDDEDDRLK 23 1 Q9UPN7 Q9UPN7 PPP6R1 Serine/threonine-protein phosphatase 6 regulatory subunit 1 1 NMVDLVNTHHLHS(0.008)S(0.639)S(0.353)DDEDDRLK 260.49 4.99E-44 1564000000 428100 468310 217770 345370 590600 512330 578600 712700 648930 TRUE FALSE 371525.5003 465233.6408 323084.3004 423791.5371 578848.2155 532039.6666 522487.4611 560294.6512 572214.2347 0.649276928 0.813041013 0.564621222 0.740616908 1.011593526 0.929791037 0.913097629 0.979169369 1 19.12619586 3.328152645 5.087842494 0.962059189 0.684603197 0.806994096 0.067178495 0.084375038 3.644142196 0.018651333 0.024090928 2128.887172 -3.328152645 -0.277455993 NMVDLVNTHHLHSSS(ph)DDEDDRLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NMVDLVNTHHLHSSSDDEDDRLK 23 1 Q9UPN7 Q9UPN7 PPP6R1 Serine/threonine-protein phosphatase 6 regulatory subunit 1 1 NMVDLVNTHHLHS(0.002)S(0.289)S(0.709)DDEDDRLK;NMVDLVNTHHLHS(0.001)S(0.192)S(0.807)DDEDDRLK 246.53 6.74E-38 2094610000 498610 465450 236440 310440 552270 534840 608020 726420 643450 TRUE FALSE 432717.4252 462392.4283 350783.1748 380930.1468 541280.9075 555415.6409 549054.314 571080.736 567382.074 0.762656145 0.814957767 0.618248603 0.671382062 0.953997196 0.978909392 0.967697675 1.006518821 1 19.11396104 3.186834154 6.058994083 0.985570036 0.716864086 0.861155126 0.052847608 0.070694965 5.665650519 0.017098911 0.019706431 1537.567372 -3.186834154 -0.26870595 NNASTDYDLSDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NNASTDYDLSDK 12 0 P39023;G5E9G0;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 132.99 0.0003983 277600000 458770 374740 208520 293150 413190 376870 492210 474290 482610 FALSE TRUE 398142.3821 372278.3083 309360.9695 359714.188 404968.3274 391368.4328 444475.55 372866.7744 425556.3956 0.935580774 0.874803697 0.726956457 0.845279713 0.951620823 0.919662909 1.044457455 0.876186513 1 18.69899081 3.245530636 6.498600881 0.952903559 0.838726618 0.406508563 0.067311607 0.150424519 27.28784431 0.019878703 0.024409975 1760.07282 -3.245530636 -0.114176941 NNAYLAQS(ph)PQLYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NNAYLAQSPQLYK 13 0 P14868;P14868-2 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 1 NNAYLAQS(1)PQLYK 174.52 5.84E-07 0 267250 236980 135760 189940 322770 255530 316740 309180 348840 TRUE FALSE 231932.2354 235423.2628 201413.9901 233068.7801 316347.5085 265360.4044 286022.6036 243064.263 307600.5326 0.754004661 0.765353885 0.654790772 0.757699533 1.028436153 0.862678625 0.929850807 0.790194545 1 18.23069848 3.400653987 8.621985569 0.903032706 0.725067382 0.622590822 0.07274325 0.190767152 19.33378853 0.020610501 0.026626639 2515.671834 -3.400653987 -0.177965323 NNDLCYWVPELVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NNDLCYWVPELVR 13 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 232.39 1.91E-12 111737000 195255 195772 92488 122617 228470 199679 210584 227302 192710 FALSE TRUE 169451.557 194485.9608 137215.5062 150459.0639 223923.894 207360.7803 190161.5961 178695.2362 169928.0433 0.997195953 1.14451951 0.807491827 0.885428096 1.317757149 1.220285812 1.119071298 1.051593561 1 17.37456444 3.264746197 24.99987757 1.13270015 0.96113696 0.361921957 0.120443121 287.5061803 274485.7442 0.037203351 0.04801412 1839.696562 -3.264746197 -0.171563189 NNFEGEVTKENLLDFIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NNFEGEVTKENLLDFIK 17 1 P07237;H7BZ94;I3L398;I3L312;I3L4M2;I3NI03 P07237 P4HB Protein disulfide-isomerase 0 101.92 0.0008872 427300000 600210 466380 239330 339420 566740 480930 558440 622940 343800 FALSE TRUE 520890.7278 463316.3191 355070.7885 416490.4987 555462.9828 499431.6883 504282.5748 489729.1287 303156.3557 1.718224665 1.528308117 1.171246394 1.373847161 1.832265669 1.64743928 1.663440549 1.615434147 1 18.20970254 1.235538696 24.99382123 0.999999226 1.566313667 0.483772027 0.184632131 82.15539193 679370.059 0.332161563 0.048396228 17.20040592 -1.235538696 0.566314441 NNLAGAEELFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NNLAGAEELFAR 12 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 208.33 1.58E-07 1336490000 645360 610130 278031 354516 775850 774620 612160 718550 693420 FALSE TRUE 560074.0409 606122.0159 412487.7216 435014.2762 760412.1029 804420.1326 552792.8174 564893.6743 611444.6775 0.915984817 0.991294941 0.674611681 0.711453206 1.243631895 1.315605748 0.904076587 0.923867187 1 19.22186245 3.249891648 24.99999145 1.05714666 0.824710048 0.394034944 0.155447687 281.2227418 620466.6111 0.050371215 0.064447103 1777.835802 -3.249891648 -0.232436612 NNQFQALLQYADPVSAQHAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NNQFQALLQYADPVSAQHAK 20 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;K7EK45;A0A087WU68;K7EKJ7 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ; 212.69 1.48E-22 1043730000 1225060 1067990 403060 681480 1401580 1128370 1123270 1426590 1476630 FALSE TRUE 1063165.217 1060974.303 597981.1642 836220.4498 1373691.3 1171779.124 1014335.448 1121524.83 1302064.484 0.816522707 0.814840061 0.459256183 0.642226603 1.055010191 0.899939395 0.779020902 0.861343539 1 20.31236947 3.259418593 24.99997639 0.900388606 0.676616559 0.470069262 0.123465178 238.3086285 285630.3945 0.037290858 0.048089839 1817.266385 -3.259418593 -0.223772046 NNQITNNQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NNQITNNQR 9 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;;; 191.78 0.00013336 291822000 662905 604361 277800 342776 612350 715476 555062 619056 674968 FALSE TRUE 575300.4247 600390.9128 412145.0092 420608.5298 600165.433 743000.8247 501232.1727 486675.6919 595174.052 0.966608713 1.008765269 0.692478121 0.706698366 1.008386423 1.248375702 0.84216066 0.817703141 1 19.1829521 3.201703127 24.99911063 0.965287641 0.844634893 0.169727416 0.150605224 390.8229082 265079.9045 0.050409902 0.057160926 1591.120704 -3.201703127 -0.120652748 NNRPAFFS(ph)PSLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NNRPAFFSPSLKR 13 2 B0QY16;Q6ICG6-3;Q6ICG6;Q6ICG6-2 B0QY16 KIAA0930 Uncharacterized protein KIAA0930 1 NNRPAFFS(0.99)PS(0.01)LKR;NNRPAFFS(0.998)PS(0.002)LKR 168.41 1.58E-05 1033650000 1266620 1205990 637510 796710 1649940 1412300 1598280 1775210 1138050 TRUE FALSE 1099232.958 1198067.772 945811.9683 977615.1824 1617109.422 1466632.095 1443279.052 1395595.156 1003511.025 1.095387026 1.193876043 0.942502817 0.97419476 1.611451575 1.461500729 1.438229392 1.39071233 1 19.93662504 3.254184478 24.99023974 1.390065409 1.053875711 0.491012168 0.166220241 206.1786339 329779.1672 0.048618173 0.062545195 1795.496149 -3.254184478 -0.336189698 NNRPSEGPLQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NNRPSEGPLQTR 12 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;; 208.68 5.84E-08 3106490000 1191630 1031454 542081 668097 1503310 1419320 1128356 1237380 1279040 FALSE TRUE 1034153.076 1024678.311 804233.1848 819798.6351 1473397.072 1473922.159 1018928.209 972775.9163 1127833.348 0.916937842 0.908536986 0.713078032 0.726879229 1.306396086 1.306861657 0.903438624 0.862517426 1 20.10512248 3.270947434 24.9999704 1.047798095 0.81556505 0.38911248 0.159418871 260.7783007 201297.7866 0.052714194 0.06804846 1866.153801 -3.270947434 -0.232233046 NNS(ph)GEAGGAATQELFCSACDQLFLSPHQLQQHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NNSGEAGGAATQELFCSACDQLFLSPHQLQQHLR 34 0 A0A0C4DFM2;Q6ZN55;Q6ZN55-2 A0A0C4DFM2 ZNF574 Zinc finger protein 574 1 NNS(1)GEAGGAATQELFCSACDQLFLSPHQLQQHLR 219.75 5.46E-36 179320000 22329 14858 10725 14825 17719 18266 13045 20497 26353 TRUE FALSE 19378.16608 14760.39682 15911.64587 18191.24284 17366.42657 18968.70484 11779.89791 16113.87606 23237.57836 0.833915039 0.635195139 0.684737696 0.782837289 0.747342356 0.816294389 0.506933112 0.693440418 1 14.50417211 1.23716343 24.99448242 1.000000359 0.705282905 0.472584802 0.095143604 31.61211882 565303.8053 0.139823752 0.022993394 17.26487467 -1.23716343 -0.294717454 NNS(ph)PPTVGAFGHTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NNSPPTVGAFGHTR 14 0 Q86XL3;F5H1D4;Q86XL3-3 Q86XL3 ANKLE2 Ankyrin repeat and LEM domain-containing protein 2 1 NNS(0.966)PPT(0.034)VGAFGHTR 123.83 6.48E-05 183120000 339250 347830 143670 201950 429910 458100 310020 367740 310340 TRUE FALSE 294417.253 345545.0818 213149.2925 247805.8341 421355.6321 475723.4034 279954.3081 289101.6628 273651.9587 1.075882133 1.262717371 0.778906511 0.905551107 1.539750105 1.738424989 1.023030529 1.056457495 1 18.06198266 3.274784532 24.98752083 1.249355891 1.00791392 0.202979752 0.259614281 351.9971946 242807.9931 0.082927438 0.107055388 1882.714782 -3.274784532 -0.241441972 NNSDKDQSLGNWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NNSDKDQSLGNWR 13 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 127.36 0.00016223 575520000 463830 373140 218200 300310 430150 408600 415840 529770 433200 FALSE TRUE 402533.6903 370688.8188 323722.2498 368499.9755 421590.8566 424319.1064 375511.9008 416482.8082 381987.5895 1.053787352 0.970421105 0.847467977 0.964690963 1.103676842 1.11081909 0.983047385 1.090304553 1 18.54316624 3.328846313 6.9311442 1.058508951 0.950465278 0.368284259 0.063825962 0.227440061 14.71937815 0.018503281 0.023885414 2132.29021 -3.328846313 -0.108043673 NNSLWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NNSLWDR 7 0 E7EPM6;P33121-2;P33121;P33121-3;B7Z3Z9;H0Y9U7 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 ;; 115.49 0.013186 1048830000 1115630 888290 461300 582060 1149400 1293150 984940 996420 978940 FALSE TRUE 968196.6689 882454.7645 684386.223 714225.6192 1126529.189 1342898.317 889420.6704 783343.3371 863210.8284 1.121622479 1.022293437 0.792837857 0.827405769 1.305045247 1.555701427 1.030363199 0.907476263 1 19.71935344 3.24880627 24.99997206 1.138284777 0.936257864 0.223804105 0.20007454 404.5939346 987226.3555 0.066200824 0.084488085 1773.398227 -3.24880627 -0.202026913 NNSQIASGQNQPQAAAGS(ph)HQLSMGQPHNAAGPSPHTLR ddPTM_MDA-MB-175_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(0.341)HQLS(0.341)MGQPHNAAGPS(0.27)PHT(0.047)LR 111.61 3.92E-06 168450000 43551 44424 14829 30550 75611 73102 44905 61473 49309 TRUE FALSE 37795.62501 44132.17582 22000.354 37486.84443 74106.48903 75914.28124 40550.12001 48327.47733 43479.74619 0.869269679 1.015005369 0.505990856 0.862167968 1.704391022 1.745968822 0.9326209 1.111494007 1 15.4080559 3.444916327 24.60850593 1.271528451 0.79616339 0.406747419 0.291375505 181.1606415 138428.2084 0.091044957 0.117539502 2785.584432 -3.444916327 -0.475365061 NNSQIASGQNQPQAAAGSHQLS(ph)MGQPHNAAGPSPHTLRR ddPTM_MDA-MB-175_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(0.016)HQLS(0.355)MGQPHNAAGPS(0.289)PHT(0.34)LRR 76.853 0.00080934 60835000 19421 21423 5088.5 6134.3 27370 29626 17169 22870 1119.3 TRUE FALSE 16854.46564 21282.2709 7549.31562 7527.186572 26825.39055 30765.73139 15503.95302 17979.42847 986.9776291 17.07684667 21.56307324 7.648922729 7.626501706 27.17932986 31.17166031 15.70851513 18.21665248 1 9.946873575 1.237906208 8.412435393 0.827356159 18.28170492 0.350836525 7.38436053 0.114671404 84.47566122 11.22313979 1.928763311 17.29442822 -1.237906208 17.45434876 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(ph)PHTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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(0.95)PHT(0.05)LR;NNSQIASGQNQPQAAAGS(0.003)HQLS(0.003)MGQPHNAAGPS(0.817)PHT(0.177)LR;NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(0.901)PHT(0.099)LR;NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(0.997)PHT(0.003)LR;NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(0.999)PHT(0.001)LR;NNSQIASGQNQPQAAAGSHQLS(0.004)MGQPHNAAGPS(0.875)PHT(0.121)LR;NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(0.999)PHT(0.001)LR;NNSQIASGQNQPQAAAGS(0.021)HQLS(0.122)MGQPHNAAGPS(0.736)PHT(0.122)LR 364.23 5.60E-161 2738790000 478382 482767 133249.6 286447 704853 750937 448548 542962 501177 TRUE FALSE 415162.6066 479595.6718 197689.5523 351489.1694 690827.8043 779826.0323 405047.884 426853.8016 441928.426 0.93943404 1.085233815 0.447333868 0.795353158 1.563211968 1.764598035 0.916546346 0.965888991 1 18.75345321 3.282339946 24.92485768 1.209244016 0.80961586 0.318779541 0.306713387 191.264817 108891.3236 0.097741464 0.126182925 1915.754903 -3.282339946 -0.399628156 NNSVWNQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NNSVWNQR 8 0 P49354;P49354-2;E9PQP6;B3KVN2 P49354 FNTA Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha 0 128.61 0.0026201 41525000 70873 74649 34043 43078 84384 80430 77574 81372 79291 FALSE TRUE 61506.95348 74158.6258 50506.30867 52859.51831 82704.92349 83524.19415 70050.88542 63971.23104 69917.30831 0.879709974 1.06066191 0.72237204 0.75602908 1.182896274 1.194613983 1.001910501 0.914955575 1 16.09336202 3.245383982 24.99996416 1.043399886 0.859953795 0.407448458 0.121486645 202.3979052 741556.3175 0.039174926 0.049440482 1759.47857 -3.245383982 -0.183446091 NNTAAET(ph)EDDES(ph)DGEDRGGGTSGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NNTAAETEDDESDGEDRGGGTSGVR 25 1 A0A590UJS4;Q6KC79-2 A0A590UJS4 NIPBL Nipped-B-like protein 2 NNT(0.276)AAET(0.724)EDDES(1)DGEDRGGGTSGVR 84.889 0.040851 179430000 217750 186110 124720 126260 251070 216790 221150 226050 189620 TRUE FALSE 188973.7858 184887.4312 185035.0092 154929.2628 246074.1982 225130.0516 199702.907 177710.9666 167203.3396 1.130203417 1.105763985 1.106646611 0.926591916 1.47170624 1.346444707 1.194371521 1.062843404 1 17.35124414 1.609277006 3.643442459 1.012589028 1.184543655 0.163415239 0.145671302 0.358065175 10.83888773 0.126047185 0.040921456 40.67026538 -1.609277006 0.171954627 NNTAAETEDDES(ph)DGEDRGGGTSGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NNTAAETEDDESDGEDRGGGTSGVR 25 1 A0A590UJS4;Q6KC79-2 A0A590UJS4 NIPBL Nipped-B-like protein 1 NNTAAETEDDES(1)DGEDRGGGTSGVR;NNTAAETEDDES(1)DGEDRGGGTSGVR 264.41 1.74E-45 730310000 281150 246460 105514 159132 249150 277420 218270 246880 166057 TRUE FALSE 243995.3152 244840.988 156540.9233 195265.3528 244192.4025 288092.5269 197102.209 194086.6332 146425.9306 1.666339521 1.672114952 1.069079245 1.333543532 1.667685508 1.967496643 1.346088143 1.325493595 1 17.15981154 1.428605589 1.847775229 0.946494659 1.536838141 0.339108132 0.242192158 0.733987539 3.492052431 0.691798549 0.072725819 26.82906814 -1.428605589 0.590343482 NNWEVSALSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NNWEVSALSR 10 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 217.45 1.69E-08 501160000 352190 307870 156209 204681 421580 350970 372240 388730 356850 FALSE TRUE 305647.1992 305847.5817 231752.1949 251156.9494 413191.3828 364472.043 336140.2221 305603.1146 314663.5995 0.971345906 0.971982721 0.736507798 0.798176051 1.313121007 1.158291088 1.068252644 0.971205805 1 18.26345077 3.270230248 24.99995264 1.086065071 0.867323359 0.495066071 0.116120952 196.3119349 154967.0015 0.036670313 0.04733688 1863.074612 -3.270230248 -0.218741713 NPDDITNEEYGEFYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 NPDDITNEEYGEFYK 15 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;; 402.95 1.74E-132 8646930000 4756020 4017730 2778967 3475562 3873544 3367265 4580920 5470950 4876560 FALSE TRUE 4127499.907 3991337.267 4122884.736 4264741.473 3796468.053 3496805.863 4136663.083 4301029.917 4300058.632 0.959870611 0.928205313 0.95879733 0.991786819 0.882887509 0.813199578 0.962001553 1.000225877 1 22.0359249 2.003409766 24.9998274 0.994424482 0.922546653 0.306573626 0.048451331 128.8264998 944528.2628 0.021477561 0.014400783 100.7882178 -2.003409766 -0.07187783 NPDDITQEEYGEFYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NPDDITQEEYGEFYK 15 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;; 309.49 9.46E-56 4480130000 3936160 2757050 1865520 2263970 2764590 2486960 3079230 3774620 3395830 FALSE TRUE 3415986.483 2738938.757 2767691.712 2778038.991 2709580.068 2582634.96 2780606.749 2967446.887 2994378.846 1.140799698 0.914693463 0.924295774 0.927751341 0.904888863 0.862494391 0.928608867 0.991005828 1 21.51382533 4.741612164 24.90963118 0.932846055 1.140799778 0.734120863 0.039538601 165.3835067 1349947.241 0.010875671 0.07436745 55158.46403 -4.741612164 0.207953724 NPDELAEALDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NPDELAEALDER 12 0 O14908;O14908-2;K7EM11 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 ;; 169.65 0.00010064 971520000 2593280 3292700 1753150 2067550 3032570 3496230 3124780 2668160 2504870 FALSE TRUE 2250571.477 3271070.037 2600979.204 2537018.828 2972227.79 3630732.23 2821739.317 2097594.748 2208747.122 1.018935783 1.480961765 1.177581253 1.14862349 1.345662326 1.643797153 1.277529369 0.949676279 1 21.07479682 1.766129339 5.525998775 0.976403833 1.311996663 0.373672189 0.1740227 0.172126269 12.43798563 0.100731417 0.04587995 58.36188888 -1.766129339 0.33559283 NPDGGPLESSSDLAALS(ph)PLTSSGHQEQDTELGSTHTAGATSSLTPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NPDGGPLESSSDLAALSPLTSSGHQEQDTELGSTHTAGATSSLTPSR 47 0 Q7Z434;Q7Z434-4 Q7Z434 MAVS Mitochondrial antiviral-signaling protein 1 NPDGGPLESSSDLAALS(0.992)PLT(0.007)SSGHQEQDTELGSTHTAGATSSLTPSR 219.14 1.80E-49 63369000 10351 10456 3644.7 9002.5 14104 21227 11355 16141 16536 TRUE FALSE 8983.089124 10387.31385 5407.289111 11046.65522 13823.35799 22043.61643 10253.79385 12689.37276 14581.13292 0.616076211 0.712380438 0.370841494 0.75759924 0.948030449 1.511790377 0.703223399 0.870259727 1 13.8318152 3.384243887 3.566856438 0.991876799 0.578502161 0.456585256 0.21991567 0.231469114 5.757054673 0.067550101 0.090172588 2422.389005 -3.384243887 -0.413374638 NPDTQWITKPVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NPDTQWITKPVHK 13 1 P61313;A0A2R8YEM3;E7EQV9;E7ENU7 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 207.41 3.25E-08 3229700000 3532200 2982900 1784820 2372400 3100200 2618000 3441100 4408700 3828400 FALSE TRUE 3065410.821 2963305.133 2647964.922 2911089.68 3038512.085 2718716.154 3107382.652 3465933.814 3375810.913 0.908051695 0.877805425 0.784393732 0.862337896 0.900083614 0.805352025 0.920484805 1.026696667 1 21.68680267 1.929637721 3.703545734 1.011306507 0.856271297 0.732667401 0.038824581 0.113532808 2.856731597 0.021863199 0.01062077 85.04283343 -1.929637721 -0.15503521 NPDVDTSFLPDRDREEEENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NPDVDTSFLPDRDREEEENR 20 2 Q14320;B0S8I6;Q9Y247 Q14320 FAM50A;FAM50B Protein FAM50A;Protein FAM50B 0 ; 242.34 4.93E-30 708700000 384860 322060 208575 260560 354490 361730 311820 408850 371670 FALSE TRUE 333999.7759 319944.3667 309442.5676 319724.1304 347436.3425 375645.9872 281579.7444 321420.6092 327731.596 1.019125955 0.976239003 0.944195102 0.975567001 1.060124647 1.146200097 0.8591779 0.980743429 1 18.32215524 2.212720449 24.99998487 0.950101069 1.014567485 0.213526218 0.065880112 419.1210761 405490.2845 0.028197172 0.019017577 163.2001107 -2.212720449 0.064466416 NPDVDTSFLPDRDREEEENRLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NPDVDTSFLPDRDREEEENRLR 22 3 Q14320;B0S8I6;Q9Y247 Q14320 FAM50A;FAM50B Protein FAM50A;Protein FAM50B 0 ; 91.166 0.00099314 272780000 202124 155121 115734 137765 139939 144103 142333 171669 243450 FALSE TRUE 175412.8013 154101.9999 171703.3495 169046.6489 137154.4877 149646.7357 128529.5676 134958.9203 214669.6183 0.817129143 0.717856589 0.799849326 0.787473561 0.638909636 0.697102537 0.598731989 0.628681978 1 17.7117585 4.738958598 19.05496985 0.718717295 0.817129925 0.035740619 0.115359258 3.900808318 184302.7158 0.027971754 0.158604871 54822.46995 -4.738958598 0.09841263 NPEAALS(ph)PTFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NPEAALSPTFR 11 0 Q86U44;F5H6D8;B4DTN4;B4E349 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 1 NPEAALS(0.685)PT(0.315)FR;NPEAALS(0.946)PT(0.054)FR;NPEAALS(0.97)PT(0.03)FR 170.26 1.67E-05 499660000 586370 548120 274060 392306 603620 546570 537490 624820 609780 TRUE FALSE 508879.7188 544519.3636 406596.3327 481385.0733 591609.143 567596.9016 485364.3025 491207.1054 537692.5031 0.946414012 1.012696589 0.756187468 0.895279496 1.100274115 1.055616172 0.902680063 0.913546502 1 19.03642183 5.141277517 13.31158664 0.95038759 0.645873761 0 0.096762419 7160067.263 4564026.866 0.024663596 65515250.51 138445.077 -5.141277517 -0.304513829 NPEFFEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NPEFFEHR 8 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ;;; 87.806 0.015063 628759000 716110 580870 313501 441092 669713 667743 577628 665740 655389 FALSE TRUE 621474.2491 577054.2267 465111.1322 541248.6803 656387.0216 693431.5053 521609.7255 523376.6818 577909.659 1.075383045 0.998519782 0.804816332 0.936562786 1.135795208 1.19989603 0.902580044 0.90563754 1 19.14048446 NPEHFVVCNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NPEHFVVCNR 10 0 Q2TAY7;Q2TAY7-2 Q2TAY7 SMU1 "WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed" 0 ; 109.16 0.002056 712630000 421850 407410 200178 273240 442870 418430 391970 432780 407230 FALSE TRUE 366101.4537 404733.6969 296984.7504 335283.3182 434057.7535 434527.2729 353956.8097 340233.3649 359087.7333 1.019532052 1.127116466 0.827053455 0.933708637 1.208779118 1.210086652 0.985711226 0.9474937 1 18.45397684 2.024171832 24.99315899 0.968978057 1.052970189 0.087928025 0.116553951 574.1622231 593669.0405 0.051442296 0.034680572 105.7235731 -2.024171832 0.083992132 NPEISHMLNNPDIMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NPEISHMLNNPDIMR 15 0 Q9UMX0;Q9UMX0-2 Q9UMX0 UBQLN1 Ubiquilin-1 0 ;;;;; 255.21 1.02E-24 1202220000 1164060 1166570 584291 763098 1326450 1304070 1208090 1350040 1149460 FALSE TRUE 1010226.522 1158906.725 866856.0819 936371.0641 1300056.24 1354238.417 1090929.618 1061344.452 1013572.148 0.996699173 1.143388487 0.855248522 0.92383267 1.282647952 1.336104607 1.076321621 1.047132613 1 19.95101736 3.259325839 24.99913133 1.139751998 0.98258167 0.314572318 0.123301517 355.7282568 428256.3591 0.039067025 0.050381233 1816.878305 -3.259325839 -0.157170328 NPEISHMLNNPELMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NPEISHMLNNPELMR 15 0 Q9NRR5 Q9NRR5 UBQLN4 Ubiquilin-4 0 ; 179.46 6.70E-07 251540000 247090 220507 105621 165017 250010 243870 209251 229424 202170 FALSE TRUE 214436.4305 219058.475 156699.6689 202486.632 245035.2901 253251.8367 188957.8702 180363.463 178269.6929 1.202876535 1.228803794 0.879003415 1.135844398 1.374520179 1.420610719 1.0599551 1.011744958 1 17.44370193 2.020038487 24.99837838 1.015452901 1.200988141 0.267973298 0.144258693 343.5606011 428596.5172 0.064406642 0.043417252 104.7221348 -2.020038487 0.18553524 NPEVGLKPVWYSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NPEVGLKPVWYSPK 14 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 156.49 5.07E-06 870660000 1105690 979990 556910 745100 1047550 863780 1238100 1399650 1275630 FALSE TRUE 959570.265 973552.3812 826233.5388 914286.3431 1026705.804 897010.1755 1118029.253 1100345.74 1124826.475 0.85308293 0.865513395 0.734543112 0.812824346 0.912768172 0.797465383 0.993957093 0.97823599 1 20.10127103 2.232675943 24.98283937 0.988262354 0.829738224 0.728723478 0.046403157 73.40781836 311642.2074 0.018936647 0.01315016 170.8739831 -2.232675943 -0.158524129 NPEYDYLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NPEYDYLFK 9 0 Q9H0U4;E9PLD0 Q9H0U4 RAB1B Ras-related protein Rab-1B 0 ; 127.4 0.0010389 321320000 449790 344930 256270 298340 460360 425870 465970 629580 550250 FALSE TRUE 390349.1119 342664.1321 380203.0292 366082.6568 451199.7367 442253.4945 420780.3011 494949.2164 485200.0718 0.804511653 0.706232649 0.783600521 0.754498357 0.929925123 0.911486869 0.8672305 1.02009304 1 18.88822024 2.66473666 0.554141284 1.036228238 0.729512422 0.759198899 0.050774807 0.510197133 0.419173103 0.099106326 0.059795939 462.1007354 -2.66473666 -0.306715815 NPFDTFFGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NPFDTFFGQR 10 0 P25685;P25685-2;M0R080;M0QZD0;M0QYT3;M0QXK0;M0R128;A0A1B0GX60;M0R1D6 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 102.06 0.0069722 469910000 201420 151390 159370 110310 137780 144200 148840 189180 177310 FALSE TRUE 174801.8367 150395.5091 236441.8651 135357.5715 135038.4476 149747.4673 134405.5197 148725.3292 156348.6138 1.118026137 0.961924161 1.512273498 0.865742063 0.863700958 0.957779309 0.859652775 0.951241751 1 17.2544069 NPGFEIIHGLLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NPGFEIIHGLLDR 13 0 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 ; 169.04 2.92E-05 589160000 695980 648220 342930 469420 758880 736300 677680 731110 754330 FALSE TRUE 604004.4796 643961.8001 508772.095 576008.9856 743779.7727 764625.9374 611958.6979 574767.816 665153.9667 0.908067169 0.968139457 0.764893725 0.865978427 1.118206926 1.149547286 0.920025631 0.864112438 1 19.3433288 4.758470759 20.65914433 0.94973929 0.90806678 0.014083966 0.115742968 3066.703263 3181490.436 0.030646752 0.825801127 57341.72573 -4.758470759 -0.04167251 NPHPSSAFLNLIGFVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NPHPSSAFLNLIGFVSR 17 0 P53004;C9J1E1 P53004 BLVRA Biliverdin reductase A 0 ; 202.16 1.08E-11 1082100000 1063290 1214480 364670 665750 1469110 1570150 1101600 1338740 1130190 FALSE TRUE 922773.5325 1206502.001 541025.6317 816918.7129 1439877.585 1630554.687 994767.0016 1052460.869 996580.2257 0.925940038 1.210642124 0.542882166 0.819721977 1.444818539 1.63614995 0.998180554 1.056072398 1 19.92662642 3.259580715 24.99978663 1.208963342 0.875077261 0.321597905 0.253463902 337.0398298 400848.2633 0.078799273 0.101622003 1817.944896 -3.259580715 -0.333886081 NPISGLLEYAQFASQTCEFNMIEQSGPPHEPR ddPTM_MDA-MB-175_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 ; 238.26 1.15E-46 349380000 152186 142353 75216 90741 146309 165324 140129 172209 150249 FALSE TRUE 132074.2345 141417.8738 111590.7092 111345.1309 143397.7371 171684.1213 126539.3111 135383.4455 132486.7344 0.996886482 1.067411575 0.842278359 0.840424752 1.082355436 1.295858956 0.955109293 1.02186416 1 17.01548839 3.211272529 24.99191741 1.067437391 0.939335208 0.265586128 0.110835375 333.1454839 305111.785 0.035686336 0.040474204 1626.569143 -3.211272529 -0.128102183 NPLFDHAALSAPLPAPSS(ph)PPALP ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NPLFDHAALSAPLPAPSSPPALP 23 0 Q5SPY9;Q9NQX5 Q5SPY9 NPDC1 Neural proliferation differentiation and control protein 1 1 NPLFDHAALSAPLPAPS(0.113)S(0.887)PPALP;NPLFDHAALSAPLPAPS(0.021)S(0.979)PPALP;NPLFDHAALSAPLPAPS(0.023)S(0.977)PPALP;NPLFDHAALSAPLPAPS(0.023)S(0.977)PPALP 237.09 4.04E-37 783930000 793160 912400 446811 722268 1312080 1489980 782830 1421770 1182610 TRUE FALSE 688341.8964 906406.3843 662890.2941 886269.9886 1285972.175 1547300.495 706911.2671 1117735.55 1042803.193 0.660088021 0.869201773 0.635681113 0.849891901 1.2331878 1.483789564 0.677895188 1.071856662 1 19.99203547 3.425517753 6.146421546 1.077853749 0.73694108 0.406597266 0.207875879 0.211363883 17.65758301 0.06148426 0.080225746 2663.89899 -3.425517753 -0.34091267 NPLPNIDHELQELLIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NPLPNIDHELQELLIDR 17 0 Q9ULX3 Q9ULX3 NOB1 RNA-binding protein NOB1 0 ;;; 257.02 4.08E-27 174122000 220800 221010 111767 157096 258277 249245 225244 275554 263911 FALSE TRUE 191620.7206 219558.1708 165817.895 192767.0479 253137.793 258833.6164 203399.8715 216628.9215 232711.7422 0.823425233 0.943476976 0.712546318 0.828351187 1.087774044 1.112249919 0.87404215 0.930889518 1 17.82818448 3.264726714 24.34560704 0.98827017 0.827101443 0.492853008 0.087197983 164.2668501 152836.6139 0.026775371 0.034553897 1839.614033 -3.264726714 -0.161168727 NPLPNIDHELQELLIDRGEDVPS(ph)EEEEEEENGFEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NPLPNIDHELQELLIDRGEDVPSEEEEEEENGFEDR 36 1 Q9ULX3 Q9ULX3 NOB1 RNA-binding protein NOB1 1 NPLPNIDHELQELLIDRGEDVPS(1)EEEEEEENGFEDR 135.71 3.26E-09 36982000 11832 7835.7 0 2892.1 12690 10906 13560 10887 0 TRUE FALSE 10268.37122 7784.226771 0 3548.795508 12437.49383 11325.56088 12244.95329 8558.899773 0 0 NPLPSKETIEQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NPLPSKETIEQEK 13 1 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 ; 151.54 4.08E-05 761450000 1252980 754150 402180 381350 692920 536350 1064750 1072270 96514 FALSE TRUE 1087395.518 749195.939 596675.5932 467941.3461 679132.2477 556983.7316 961490.7089 842973.4049 85104.22487 12.77722134 8.803275515 7.011116007 5.498450245 7.980006265 6.544724806 11.29780232 9.905188681 1 16.37694313 4.697925229 2.799361163 7.489220725 13.49592164 0.294211575 2.746236189 0.537486363 6.164380461 0.700019971 7.059808508 49879.8604 -4.697925229 6.006700919 NPPGFAFVEFEDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NPPGFAFVEFEDPR 14 0 P84103;P84103-2;A0A087X2D0;Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2 P84103;Q16629 SRSF3;SRSF7 Serine/arginine-rich splicing factor 3;Serine/arginine-rich splicing factor 7 0 ;;; 117.93 0.00063916 2490190000 1848090 1678830 1019540 1400320 1887010 1907350 1722390 2009280 2579400 FALSE TRUE 1603860.224 1667801.655 1512592.954 1718284.059 1849462.193 1980726.989 1555352.883 1579611.108 2274466.27 0.70515894 0.733271659 0.665032045 0.755466933 0.813141183 0.870853534 0.683832028 0.694497487 1 21.11709661 3.5040242 5.732427179 0.790643782 0.704704775 0.221493709 0.090570824 0.353652004 36.23138563 0.026196562 0.037526393 3191.715703 -3.5040242 -0.085939007 NPPGFAFVEFEDPRDAADAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NPPGFAFVEFEDPRDAADAVR 21 1 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;; 145.02 1.11E-07 3094800000 887360 790940 210555 253601 786450 850570 800010 850930 61475.1 FALSE TRUE 770093.1277 785744.2631 312380.1023 311184.9831 770801.1837 883291.9783 722425.1533 668965.2414 54207.58371 14.20637252 14.49509846 5.762664205 5.74061712 14.21943446 16.29462001 13.32701264 12.34080539 1 15.72620708 4.29916755 24.99180708 10 14.35078359 0.142638195 4.608124899 157.3089569 64864.27006 1.207447923 3.194605611 19914.41487 -4.29916755 4.350783585 NPPGFAFVEFEDPRDAEDAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NPPGFAFVEFEDPRDAEDAVR 21 1 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ;;;;; 195.03 1.42E-18 3581690000 681671 541260 247096 284269 606192 578814 625057 696607 163031 FALSE TRUE 591586.4502 537704.4274 366592.4521 348816.6212 594129.9652 601081.3491 564439.0683 547643.0141 143757.6609 4.115164691 3.740353203 2.550072461 2.426421097 4.132857765 4.181212642 3.926323403 3.809487513 1 17.13327931 4.46854084 24.50931672 3.284108142 4.021462252 0.091563394 0.983982945 359.9147448 1028073.004 0.248933906 0.661125332 29413.10276 -4.46854084 0.737354109 NPPPNSDPNLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NPPPNSDPNLRR 12 1 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ;; 108.56 0.0027135 505254000 134425 120293 65640 72603 128752 137918 111502 121506 49924 FALSE TRUE 116660.3957 119502.7874 97383.72355 89088.62082 126190.0871 143223.7947 100688.5532 95522.88746 44022.04159 2.650045101 2.714612568 2.212158274 2.023727605 2.866520555 3.25345644 2.287230432 2.16988772 1 15.42593843 1.14366362 1.725358611 0.117531035 2.58363322 0.672695324 0.345914714 0.809662983 1.824941851 3.618842632 0.102989965 13.92078161 -1.14366362 2.466102186 NPPS(ph)PRPSQLPVLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NPPSPRPSQLPVLDR 15 1 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 NPPS(1)PRPSQLPVLDR;NPPS(1)PRPSQLPVLDR 110.75 0.00054316 2934000000 766430 632300 354390 509440 754060 723000 670020 736070 486590 TRUE FALSE 665144.3336 628146.3797 525774.1894 625116.1383 739055.6813 750814.2778 605041.5635 578667.1586 429065.8845 1.550214915 1.463985841 1.225392669 1.456923426 1.722475983 1.74988109 1.41013673 1.348667371 1 18.71083967 1.254599674 1.771340846 0.829073321 1.514865883 0.547145814 0.148387544 0.787265012 2.381831114 0.91938467 0.045783298 17.97213508 -1.254599674 0.685792563 NPQNSAQTADGSHCAVSDVEMQEHYDEFFEEVFTEMEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NPQNSAQTADGSHCAVSDVEMQEHYDEFFEEVFTEMEEK 39 0 Q01081-2 Q01081-2 U2AF1 Splicing factor U2AF 35 kDa subunit 0 ;; 286.35 1.34E-77 158902000 68544.3 45831.8 28748.1 38507.4 45313.9 38190.9 62474.6 72130.5 64339 FALSE TRUE 59485.99709 45530.72789 42650.77732 47251.09372 44412.24205 39660.12864 56415.82291 56705.9539 56732.91672 1.048527037 0.802545163 0.751781854 0.832869108 0.782830227 0.69906733 0.994410761 0.999524741 1 15.79189842 2.20975411 23.40357757 0.998152375 0.814676803 0.46339893 0.09038123 88.43638719 71847.99942 0.036482485 0.024603665 162.0892117 -2.20975411 -0.183475573 NPS(ph)PTTRPVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NPSPTTRPVSR 11 1 H0Y5D5;Q9BTG3;Q5SYW2;F5H2X7;Q9ULV3-5;Q9ULV3-2;Q9ULV3;A0A494C0L7;Q9ULV3-3;Q9ULV3-4;A0A0U1RQR2 H0Y5D5 CIZ1 Cip1-interacting zinc finger protein 1 NPS(0.539)PT(0.459)T(0.003)RPVSR;NPS(0.978)PT(0.022)TRPVSR;NPS(0.806)PT(0.192)T(0.002)RPVSR;NPS(0.996)PT(0.004)TRPVSR 128.22 0.00016369 2748790000 493326 497005 235986 305278 458464 462236 378677 516398 385733 TRUE FALSE 428131.7192 493740.1414 350109.6189 374596.0358 449341.4634 480018.518 341952.9628 405970.3063 340132.0842 1.258721947 1.45161296 1.029334295 1.1013252 1.321079323 1.411270916 1.005353446 1.193566633 1 18.37573557 2.222667 24.98892977 1.090279475 1.255608472 0.308043306 0.136617537 356.7447977 560891.9795 0.057415864 0.038850597 166.980978 -2.222667 0.165328997 NPSDSAVHS(ph)PFTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NPSDSAVHSPFTK 13 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 NPSDSAVHS(1)PFTK;NPSDSAVHS(1)PFTK;NPSDSAVHS(1)PFTK;NPSDSAVHS(1)PFTK;NPSDSAVHS(1)PFTK;NPSDSAVHS(1)PFTK 179.9 8.60E-06 6053470000 5576120 5416160 3486510 5362070 6203190 5686570 6584340 7798340 11376000 TRUE FALSE 4839221.614 5380580.888 5172597.898 6579609.948 6079758.655 5905336.028 5945791.72 6130725.678 10031142.24 0.482419798 0.536387658 0.515653928 0.655918318 0.606088371 0.588700258 0.592733268 0.61116925 1 23.25798256 1.213052978 3.401396214 1.081732358 0.572019231 0.882566764 0.049062823 0.122804427 1.927281792 0.170868143 0.013319263 16.33251171 -1.213052978 -0.509713127 NPSDSAVHS(ph)PFTKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NPSDSAVHSPFTKR 14 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 NPSDSAVHS(1)PFTKR;NPSDSAVHS(0.99)PFT(0.01)KR;NPSDSAVHS(1)PFTKR 228.46 7.76E-13 2259840000 1334900 1351780 531870 804230 1402670 1352780 1648580 1764200 516860 TRUE FALSE 1158489.583 1342900.068 789084.111 986842.7134 1374759.611 1404822.322 1488700.965 1386939.559 455757.3996 2.541899668 2.946523895 1.731368732 2.165280727 3.016428504 3.082390595 3.266432902 3.043153134 1 18.79790655 3.242139947 24.99538227 2.790756913 2.345222255 0.041123065 0.702550975 251.5571892 1756676.103 0.206955123 0.256577025 1746.384819 -3.242139947 -0.445534657 NPTDAYQLNYDMHNPFDICAASYRPIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NPTDAYQLNYDMHNPFDICAASYRPIYR 28 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITI7 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 275.6 9.15E-62 1589570000 540470 505540 281490 430770 531640 589330 537380 630880 536050 FALSE TRUE 469045.5201 502219.0745 417619.5055 528582.9124 521061.4041 612001.9064 485264.9703 495971.2215 472678.7797 0.99231347 1.062495496 0.883516509 1.118270875 1.10235836 1.294752235 1.026627366 1.049277528 1 18.85050057 3.703920396 24.9727816 1.097254368 0.987747129 0.279183762 0.089872575 862.0099385 621438.7724 0.025559284 0.037912431 5057.319551 -3.703920396 -0.109507238 NPVWYQALTHGLNEEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NPVWYQALTHGLNEEQR 17 0 O95373 O95373 IPO7 Importin-7 0 ; 180.32 8.67E-10 1033870000 2242040 1733240 1061110 1128930 1487340 1312200 2070030 2349560 651980 FALSE TRUE 1945748.733 1721854.232 1574266.345 1385270.811 1457744.844 1362681.183 1869278.809 1847124.878 574903.6671 3.384477861 2.995030873 2.738313278 2.409570316 2.535633233 2.370277424 3.251464404 3.212929372 1 19.13296071 4.481879695 1.825696629 2.589726666 3.444768932 0.182865245 0.618718212 1.043562692 5.209983358 0.168978262 1.291827174 30330.50873 -4.481879695 0.855042266 NPWGEVEWTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NPWGEVEWTGR 11 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;; 155.53 7.33E-05 1172240000 283525 317247 213574 226359 295057 304780 270520 360247 361480 FALSE TRUE 246056.4529 315162.9836 316859.1008 277757.2706 289185.943 316505.0838 244285.012 283210.9825 318746.2462 0.771950904 0.988758259 0.994079474 0.871405621 0.907260702 0.99296882 0.766393377 0.888515507 1 18.28204883 NQAIYAAVDDDDDDAA ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NQAIYAAVDDDDDDAA 16 0 Q9UK59;Q9UK59-2 Q9UK59 DBR1 Lariat debranching enzyme 0 164.48 1.14E-08 0 217460 182670 90219 125300 216180 204130 190310 212860 192100 FALSE TRUE 188722.11 181470.0287 133849.2102 153751.2801 211878.4409 211983.0132 171853.7655 167341.5455 169390.1568 1.11412678 1.071313895 0.790182928 0.90767541 1.250830892 1.251448237 1.014543989 0.98790596 1 17.36999052 4.472337602 24.9924626 1.029026504 1.103423672 0.039514585 0.138763865 472.3693602 2467930.847 0.037869443 0.100992987 29671.37017 -4.472337602 0.074397168 NQALNTDNYGHDLASVQALQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NQALNTDNYGHDLASVQALQR 21 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 287.84 7.82E-46 1294710000 630380 630040 267110 390070 790740 792710 605370 731850 647430 FALSE TRUE 547073.6858 625901.2258 396285.2894 478641.3553 775005.8211 823206.0667 546661.3106 575349.5728 570891.563 0.958279508 1.096357463 0.694151596 0.83841028 1.357535951 1.441965725 0.957557172 1.007808856 1 19.12285722 3.268159231 24.99981474 1.134621499 0.896578876 0.32617659 0.1818994 298.6281658 252227.7816 0.057697097 0.074475615 1854.211331 -3.268159231 -0.238042624 NQAS(ph)DS(ph)ENEELPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NQASDSENEELPKPR 15 1 Q96ST2;Q96ST2-3 Q96ST2 IWS1 Protein IWS1 homolog 2 NQAS(1)DS(1)ENEELPKPR 130.89 3.24E-05 267320000 540770 393840 390830 386370 445730 376160 508520 577950 1027000 TRUE FALSE 469305.8744 391252.8391 579836.6952 474101.2138 436860.8451 390631.1186 459203.8087 454359.8901 905589.23 0.518232615 0.432042284 0.640286651 0.523527885 0.48240508 0.431355747 0.507077374 0.50172846 1 19.78849727 1.238390926 24.99999977 1.000000547 0.504149801 0.878784743 0.057824269 1.305792945 191811.3056 0.07903922 0.014052399 17.31374139 -1.238390926 -0.495850746 NQDECVIALHDCNGDVNR ddPTM_MDA-MB-175_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 ;;; 258.95 1.12E-30 3052740000 1670400 1586970 886030 1067250 1602290 1628060 1487230 1726610 2195940 FALSE TRUE 1449652.408 1576545.09 1314517.072 1309585.424 1570407.564 1690692.522 1342998.664 1357387.888 1936338.475 0.748656512 0.814188795 0.678867403 0.67632051 0.81101914 0.873138939 0.693576397 0.701007549 1 20.88489973 3.212854399 24.97392975 0.795112437 0.731939664 0.151607437 0.094539767 572.9520406 556628.7691 0.029575989 0.033547202 1632.504545 -3.212854399 -0.063172773 NQDLEFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NQDLEFER 8 0 P21399 P21399 ACO1 Cytoplasmic aconitate hydratase 0 95.311 0.02266 339320000 312050 288990 134420 223140 306700 283460 376780 327030 312520 FALSE TRUE 270811.8019 287091.6057 199425.9616 273807.3475 300597.27 294364.8896 340239.9336 257097.1795 275574.2416 0.982718124 1.041794051 0.723674174 0.993588319 1.09080322 1.068187244 1.234657969 0.932950692 1 18.07208152 3.479787042 23.65123313 1.059851854 0.916967981 0.278231452 0.109816978 71.73685216 636465.9458 0.031779299 0.041867393 3018.471238 -3.479787042 -0.142883873 NQEIPHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NQEIPHK 7 0 O00743;O00743-2;O00743-3 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed" 0 ; 87.616 0.019211 1375920000 2583900 2441500 1375430 1685690 2773100 2671500 2939900 3224500 2985900 FALSE TRUE 2242431.068 2425461.626 2040592.549 2068451.679 2717920.735 2774274.334 2654788.95 2534965.768 2632910.304 0.851692921 0.921209364 0.775033067 0.785614184 1.032287629 1.053691168 1.008309682 0.962799897 1 21.32822694 3.233505486 24.99999638 1.007221046 0.83549221 0.79112965 0.045420772 61.57538712 304518.9448 0.01485102 0.017357116 1712.006801 -3.233505486 -0.171728836 NQEQMKPLEEKQEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NQEQMKPLEEKQEEER 16 2 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 54.004 0.082537 129950000 90723 75795 34545 36060 67175 46953 99781 93579 9391.1 FALSE TRUE 78733.72569 75297.09765 51251.07755 44247.97414 65838.34893 48759.31229 90104.25398 73567.85908 8280.894856 9.50787651 9.092869667 6.189074784 5.343380747 7.950632156 5.888169472 10.88098032 8.884046997 1 13.01557096 4.314488706 6.692585072 7.007082064 9.36699564 0.145185707 2.587447741 0.470166552 33.08560683 0.650412391 1.743754718 20629.50017 -4.314488706 2.359913576 NQESLGS(ph)PHICDLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NQESLGSPHICDLGK 15 0 A4D1E1;A0A087WUA7 A4D1E1 ZNF804B Zinc finger protein 804B 1 NQES(0.005)LGS(0.995)PHICDLGK 78.342 0.024337 51515000 123140 86041 87948 93595 82065 78714 110490 115030 93626 TRUE FALSE 106866.737 85475.79101 130479.947 114847.1753 80432.06706 81742.17851 99774.69681 90431.72966 82557.64094 1.294449984 1.03534682 1.580470874 1.391115031 0.974253457 0.990122508 1.20854588 1.095376862 1 16.33311413 3.241943128 24.99997736 1.067313973 1.322854723 0.456210809 0.146960763 89.32598026 660199.0015 0.044292812 0.054859572 1745.593547 -3.241943128 0.25554075 NQEYETLDHLECDLNLMFENAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NQEYETLDHLECDLNLMFENAK 22 0 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9;H0Y5B5;Q86U86-6 Q86U86-8 PBRM1 Protein polybromo-1 0 172.61 4.69E-12 17467000 29831 23471 11809 17226 22871 19316 25413 25237 36103 FALSE TRUE 25888.75777 23316.81746 17519.8719 21137.42658 22415.91185 20059.09902 22948.45117 19840.26394 31834.94447 0.813218248 0.7324284 0.550334615 0.663969325 0.704129133 0.630096875 0.72085727 0.623222822 1 14.95832363 1.23293002 24.99701892 1.000000518 0.67537026 0.665732354 0.071248232 110.2419973 489366.8368 0.147320783 0.017170955 17.09739794 -1.23293002 -0.324630258 NQGFSLLNSLTGTNHSIGSADPCHPEQPHLPAADS(ph)TESLSDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NQGFSLLNSLTGTNHSIGSADPCHPEQPHLPAADSTESLSDHR 43 0 Q6PD74;Q6PD74-2 Q6PD74 AAGAB Alpha- and gamma-adaptin-binding protein p34 1 NQGFSLLNSLTGTNHSIGSADPCHPEQPHLPAADS(0.705)T(0.243)ES(0.022)LS(0.03)DHR 89.531 6.94E-05 598230000 55531 50983 13728 22081 52748 65774 46579 60398 51711 TRUE FALSE 48192.43765 50648.08932 20366.90672 27094.82854 51698.418 68304.36834 42061.77575 47482.35772 45597.78449 1.056903053 1.11075768 0.446664393 0.594213707 1.133792323 1.497975595 0.922452181 1.041330368 1 15.47667611 3.215205367 24.95550182 1.113581674 0.798788459 0.295197588 0.243266864 315.0454331 336630.6405 0.078580312 0.089154269 1641.365749 -3.215205367 -0.314793215 NQGFSLLNSLTGTNHSIGSADPCHPEQPHLPAADST(ph)ESLSDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NQGFSLLNSLTGTNHSIGSADPCHPEQPHLPAADSTESLSDHR 43 0 Q6PD74;Q6PD74-2 Q6PD74 AAGAB Alpha- and gamma-adaptin-binding protein p34 1 NQGFSLLNSLTGTNHSIGSADPCHPEQPHLPAADS(0.456)T(0.518)ES(0.021)LS(0.005)DHR 69.106 0.0015282 482490000 73236 85707 8320 32722 99269 105080 84491 95777 61419 TRUE FALSE 63557.67704 85143.98507 12343.57983 40152.03022 97293.74112 109122.4956 76297.07582 75295.83389 54158.11579 1.17355776 1.572137136 0.227917453 0.741385287 1.79647574 2.014887224 1.408783794 1.390296409 1 15.72488993 3.243924465 24.99973244 1.521756682 0.924646207 0.325482748 0.424413396 170.7611257 795875.6462 0.130881819 0.164002841 1753.575485 -3.243924465 -0.597110475 NQGGYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NQGGYDR 7 0 P98179 P98179 RBM3 RNA-binding protein 3 0 ;;; 139.27 0.0062933 780608000 953514 1103824 513875 662383 792052 1161376 971171 1194124 986082 FALSE TRUE 827504.709 1096572.907 762386.6688 812787.184 776291.7148 1206054.886 876986.9859 938769.8753 869508.5093 0.951692479 1.261141088 0.876801849 0.934766222 0.892793695 1.387053575 1.008600809 1.079655766 1 19.72984062 NQGGYDRYS(ph)GGNYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NQGGYDRYSGGNYR 14 1 P98179 P98179 RBM3 RNA-binding protein 3 1 NQGGYDRYS(1)GGNYR;NQGGYDRYS(1)GGNYR;NQGGYDRYS(1)GGNYR 214.39 4.17E-12 1878740000 711807 806896 412331 599899 1120012 1005563 834909 1071102 1038494 TRUE FALSE 617739.9015 801595.447 611735.6508 736115.2368 1097725.952 1044247.659 753939.6537 842055.1726 915724.4224 0.674591489 0.875367553 0.668034657 0.803861095 1.198751421 1.140351435 0.823325921 0.919550852 1 19.80455397 3.454114406 24.09175884 0.99648963 0.750103677 0.547602582 0.11815812 132.4163799 138659.8013 0.036282909 0.046844613 2845.210524 -3.454114406 -0.246385953 NQGGYDRYS(ph)GGNYRDNYDN ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NQGGYDRYSGGNYRDNYDN 19 2 P98179 P98179 RBM3 RNA-binding protein 3 1 NQGGYDRYS(1)GGNYRDNYDN 126.1 2.05E-05 461100000 210950 243590 93116 96345 317610 299260 279090 319110 49327 TRUE FALSE 183072.423 241989.8413 138147.2091 118221.6048 311290.1824 310772.7258 252023.8948 250870.8098 43495.61825 4.208985419 5.563545271 3.176117839 2.718011826 7.156817052 7.144920301 5.794236405 5.767726035 1 15.40858245 3.246511018 24.99998023 5.542334522 3.98140349 0.129020701 1.847566378 369.3605248 1161445.145 0.545315571 0.691250906 1764.050517 -3.246511018 -1.560931032 NQGGYGGSSS(ph)SSSYGSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NQGGYGGSSSSSSYGSGR 18 0 F8W6I7;P09651-2;P09651;P09651-3;A0A2R8Y4L2;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 NQGGYGGS(0.064)S(0.14)S(0.265)S(0.265)S(0.265)S(0.002)YGSGR;NQGGYGGS(0.045)S(0.107)S(0.401)S(0.401)S(0.045)SYGSGR 219.96 7.39E-19 93643000 116451 133379 56175 57754 134236 126985 114873 110858 134589 TRUE FALSE 101061.7053 132502.8246 83341.41789 70867.92841 131564.9662 131870.1951 103732.6341 87151.8794 118678.0417 0.851561955 1.116489812 0.702248004 0.597144403 1.108587269 1.111159176 0.874067625 0.734355557 1 16.8566935 1.320051975 0.006321034 0.734847469 1.043203668 0 0.184774205 2616054.169 4800.511207 119985.5664 114247.5833 20.89546185 -1.320051975 0.308356199 NQGGYGGSSSS(ph)SSYGSGR ddPTM_MDA-MB-175_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 NQGGYGGSS(0.002)S(0.054)S(0.471)S(0.471)S(0.002)YGSGR 243.17 4.70E-24 197460000 284030 360270 129850 141270 362420 358350 274610 312110 391260 TRUE FALSE 246494.7159 357903.3626 192645.8943 173347.5127 355208.5511 372135.9564 247978.3645 245367.7053 345005.6885 0.714465657 1.037383946 0.55838469 0.502448274 1.029573027 1.078637161 0.718766017 0.711199014 1 18.39626062 3.224394521 24.99991105 0.877465421 0.716701098 0.223014478 0.184168562 488.6660502 862381.4584 0.060148444 0.068522484 1676.465116 -3.224394521 -0.160764324 NQGGYGGSSSSSS(ph)YGSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NQGGYGGSSSSSSYGSGR 18 0 F8W6I7;P09651-2;P09651;P09651-3;A0A2R8Y4L2;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 NQGGYGGSSSSS(0.066)S(0.934)YGSGR;NQGGYGGSSSS(0.006)S(0.278)S(0.716)YGSGR 239.58 6.70E-24 390970000 648540 684140 313610 366560 810910 766780 669900 687360 738830 TRUE FALSE 562833.7958 679645.8393 465272.845 449793.0505 794774.4775 796278.5228 604933.2011 540373.413 651486.3591 0.86392261 1.043223438 0.714171277 0.690410542 1.21994032 1.222248957 0.928543158 0.829447011 1 19.31337545 3.250808339 24.9997772 1.014461008 0.835184216 0.318015257 0.151631377 369.8719591 754970.0315 0.049508506 0.063430543 1781.59235 -3.250808339 -0.179276792 NQGGYGGSSSSSSYGS(ph)GR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NQGGYGGSSSSSSYGSGR 18 0 F8W6I7;P09651-2;P09651;P09651-3;A0A2R8Y4L2;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 NQGGYGGSSSSSSYGS(1)GR 263.09 7.44E-31 80593000 100230 96607 34568 59301 107390 73441 126790 113990 93328 TRUE FALSE 86984.35155 95972.38226 51285.20042 72766.19841 105253.1491 76266.32279 114493.9253 89614.12557 82294.87016 1.056983885 1.166201272 0.623188302 0.884213053 1.278975821 0.926744555 1.391264426 1.088939388 1 16.32851488 3.255569395 24.95333809 1.139688128 0.927224888 0.225739676 0.188078093 358.5500769 526020.6701 0.053848249 0.069335062 1801.230926 -3.255569395 -0.212463239 NQGGYGGSSSSSSYGSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NQGGYGGSSSSSSYGSGR 18 0 F8W6I7;P09651-2;P09651;P09651-3;A0A2R8Y4L2;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 ;;;; 366.59 3.99E-107 808834000 77025.4 70969.9 31583.7 44010.6 99337.7 87435.1 76337.7 89212.5 77193.9 FALSE TRUE 66846.29823 70503.69405 46857.68296 54003.87939 97361.07412 90798.78488 68934.4816 70135.10113 68068.12508 0.982049941 1.035781344 0.688393913 0.793379858 1.430347523 1.333939855 1.012727786 1.030366284 1 16.05469175 3.274196879 24.99995963 1.142555069 0.873070624 0.421479031 0.166006622 204.5971286 143529.9959 0.052569357 0.06786424 1880.168964 -3.274196879 -0.269484445 NQIGDKEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NQIGDKEK 8 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;; 128.36 0.0010368 1376640000 3934000 2718680 2067550 2499370 2356800 2607330 3539200 3909600 2681430 FALSE TRUE 3414111.933 2700820.812 3067424.096 3066890.159 2309904.291 2707635.672 3195968.929 3073562.465 2364434.4 1.443944451 1.142269294 1.297318333 1.297092513 0.976937356 1.145151531 1.35168433 1.299914459 1 21.17306368 4.748075283 23.97636676 1.20390362 1.443944682 0.273572725 0.128585759 1098.035735 2766877.735 0.031942685 0.386136289 55985.46409 -4.748075283 0.240041062 NQKDPGVLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NQKDPGVLDR 10 1 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;;;; 189.58 9.08E-07 39899500000 43891100 41578400 13267500 17001600 47109000 40145900 50807700 56593500 3904690 FALSE TRUE 38090779.93 41305268.75 19683707.38 20862073.13 46171623.07 41690338.75 45880377.07 44491420.44 3443081.996 11.06298949 11.99659747 5.716886033 6.059127594 13.40996907 12.10843622 13.32538032 12.92197528 1 21.71526911 7.073404783 12.5391494 10 11.47257838 0 4.158810925 0 0 0.93310555 0 11841447.2 -7.073404783 1.472578378 NQKPEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NQKPEVR 7 1 C9JXB8;C9JNW5;P83731 C9JXB8 RPL24 60S ribosomal protein L24 0 ; 111.01 0.0060882 862910000 2242510 2123450 1151120 1437860 2122030 2056940 2697260 2566490 2584400 FALSE TRUE 1946156.622 2109500.917 1707805.482 1764348.089 2079805.755 2136071.813 2435680.14 2017666.086 2278875.176 0.853998781 0.925676377 0.749407208 0.774218837 0.912645755 0.937336031 1.068808053 0.885378062 1 21.11989047 2.984536782 3.312130467 0.967030085 0.827901515 0.523315578 0.06571411 0.210978479 4.811628278 0.022009456 0.023603825 965.0210405 -2.984536782 -0.13912857 NQKPSQVNGAPGS(ph)PTEPAGQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NQKPSQVNGAPGSPTEPAGQK 21 1 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 NQKPSQVNGAPGS(0.988)PT(0.012)EPAGQK;NQKPSQVNGAPGS(0.959)PT(0.041)EPAGQK 238.61 4.09E-30 657210000 1040940 715910 475870 583560 972770 708920 1048730 1178120 1080900 TRUE FALSE 903377.1416 711207.1401 706002.3237 716066.2172 953413.7802 736192.6111 947024.326 926188.2061 953117.2334 0.947813249 0.746190621 0.740729785 0.75128871 1.000311134 0.772405099 0.993607389 0.971746364 1 19.86229415 2.317761091 0.883592055 1.01436577 0.801019234 0.375477745 0.091343396 0.723810861 1.106871447 0.112756456 0.043107942 207.8552945 -2.317761091 -0.213346536 NQLNPIGSLQELAIHHGWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NQLNPIGSLQELAIHHGWR 19 0 O75569;O75569-3;O75569-2 O75569 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 0 ; 174.59 2.43E-12 439290000 492500 429160 179018 243100 530800 515770 434240 472530 435640 FALSE TRUE 427414.8772 426340.8197 265591.7036 298299.5706 520238.1185 535612.0056 392127.4716 371483.1367 384139.1355 1.112656425 1.109860413 0.691394547 0.776540433 1.354296062 1.394317725 1.020795424 0.967053607 1 18.55126943 3.253373858 24.99997765 1.127626716 0.919472217 0.254982594 0.189151683 416.4902115 702897.1913 0.061123568 0.078570184 1792.147944 -3.253373858 -0.2081545 NQLS(ph)QNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NQLSQNR 7 0 O94776;O94776-2 O94776 MTA2 Metastasis-associated protein MTA2 1 NQLS(1)QNR;NQLS(1)QNR 70.268 0.03703 2047500000 0 11634 17367 13740 0 10999 0 8427.6 0 TRUE FALSE 0 11557.57549 25765.73929 16859.877 0 11422.13865 0 6625.423324 0 0 NQLTSNPENTVFDAKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NQLTSNPENTVFDAKR 16 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 105.28 0.0020781 220490000 116950 77612 36000 50059 102290 102230 113440 125430 19641 FALSE TRUE 101494.7612 77102.16166 53409.72041 61425.66105 100254.6291 106162.8543 102438.6063 98607.7706 17319.06336 5.860291582 4.451866714 3.083868874 3.546708029 5.788686551 6.129826543 5.914789048 5.693597198 1 14.08007329 7.423691103 6.021215689 4.736551624 4.535844845 0 1.660158147 0 0 0.37368019 0 26527181.15 -7.423691103 -0.200706779 NQMAEKDEYEHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NQMAEKDEYEHK 12 1 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 ;;;; 194.7 7.18E-07 1812593000 1783866 1494494 1324407 1435708 1730157 1212815 2110380 2337510 2597990 FALSE TRUE 1548123.588 1484676.571 1964894.655 1761707.445 1695730.261 1259472.778 1905715.672 1837651.677 2290858.582 0.675783132 0.648087395 0.857711022 0.769016236 0.740216037 0.549781985 0.831878357 0.802167227 1 21.12745697 1.141044608 1.385558045 1.16843484 0.719457382 0.506867584 0.087031653 1.427120037 2.00127553 0.970735091 0.026014972 13.83708498 -1.141044608 -0.448977459 NQNYLVPS(ph)PVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NQNYLVPSPVLR 12 0 C9J3R1;C9IZP0;J3KR59;J3KR68;Q9UID6 C9J3R1 ZNF639 Zinc finger protein 639 1 NQNYLVPS(1)PVLR;NQNYLVPS(1)PVLR 183.89 1.58E-05 452910000 820860 706440 371840 452390 861970 951150 774760 799400 805900 TRUE FALSE 712381.2712 701799.3491 551663.0677 555112.0638 844818.4834 987741.356 699623.8944 628454.5309 710627.4201 1.002468032 0.987577075 0.776304224 0.781157676 1.188834626 1.389956717 0.98451576 0.884365721 1 19.43873383 3.240967781 24.99999748 1.071033154 0.886171601 0.299084498 0.15270593 103.2711281 1072530.073 0.05146088 0.063310909 1741.677657 -3.240967781 -0.184861553 NQPTVYIAAS(ph)PPNTDELMSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NQPTVYIAASPPNTDELMSR 20 0 A0A1B0GV57;Q9NYJ8;Q9NYJ8-2 A0A1B0GV57 TAB2 TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 1 NQPTVYIAAS(0.947)PPNT(0.053)DELMSR;NQPTVYIAAS(0.999)PPNT(0.001)DELMSR 253.95 4.28E-36 474380000 210166 327140 176272 262140 571740 598800 545130 601730 441000 TRUE FALSE 182392.0306 324990.9958 261517.7288 321662.8936 560363.4926 621836.2235 492263.3765 473054.7222 388865.4824 0.469036309 0.835741434 0.672514637 0.827182941 1.441021428 1.599103679 1.265896303 1.216499647 1 18.56891165 3.354236121 4.762939793 1.303944779 0.688103917 0.745592103 0.176746703 0.113838535 4.246645277 0.054708409 0.071085554 2260.664532 -3.354236121 -0.615840862 NQQFHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NQQFHK 6 0 Q15233;Q15233-2;H7C367 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;; 135.25 0.01368 3508500000 7042340 5739220 2752830 3808900 5262570 6172140 6831240 7670820 7407690 FALSE TRUE 6111676.926 5701518.686 4084107.796 4673768.96 5157855.153 6409586.22 6168747.396 6030474.837 6531961.327 0.935657243 0.872864734 0.625249843 0.715523061 0.789633449 0.981265182 0.944394354 0.923225741 1 22.63908482 2.74743945 20.97396025 0.954456978 0.779467805 0.507830616 0.084959515 64.26207513 151801.6156 0.029482444 0.028925754 559.0355804 -2.74743945 -0.174989173 NQS(ph)PTEAEKPASSSLPS(ph)SPPPQLLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NQSPTEAEKPASSSLPSSPPPQLLTR 26 1 Q99567;I3L2W3 Q99567 NUP88 Nuclear pore complex protein Nup88 2 NQS(0.996)PT(0.003)EAEKPASS(0.001)S(0.001)LPS(0.543)S(0.456)PPPQLLTR 148.12 1.01E-07 148060000 179920 149720 109370 118750 177830 141670 168420 215970 212530 TRUE FALSE 156143.1161 148736.4795 162261.6978 145714.0025 174291.5309 147120.1366 152086.6543 169786.4962 187404.9455 0.833185676 0.793663577 0.865834663 0.777535524 0.930026315 0.785038709 0.811540239 0.905987276 1 17.5157995 1.424332985 2.557621323 1.008001973 0.828791048 0.611722281 0.044734761 0.224398138 2.28938058 0.075106963 0.011146215 26.566417 -1.424332985 -0.179210925 NQS(ph)PTEAEKPASSSLPSSPPPQLLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NQSPTEAEKPASSSLPSSPPPQLLTR 26 1 Q99567;I3L2W3 Q99567 NUP88 Nuclear pore complex protein Nup88 1 NQS(0.99)PT(0.01)EAEKPASSSLPSSPPPQLLTR 212.17 4.73E-26 832120000 365430 267990 201130 217310 297540 241730 341340 392700 334140 TRUE FALSE 317137.4996 266229.556 298397.1407 266653.5569 291619.5361 251029.5095 308236.8993 308724.161 294638.3499 1.076361919 0.903580801 1.012757304 0.905019856 0.989754172 0.851991975 1.046153359 1.047807121 1 18.1685857 NQS(ph)PVLEPVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NQSPVLEPVGR 11 0 B4DG22;B1AXG1;B7ZB17;P51812;A0A2R8Y603 B4DG22 RPS6KA3 Ribosomal protein S6 kinase alpha-3 1 NQS(1)PVLEPVGR;NQS(1)PVLEPVGR;NQS(1)PVLEPVGR;NQS(1)PVLEPVGR 182.72 5.94E-06 1481940000 1153370 1224850 639468 849410 1545420 1331970 1245120 1522040 1256930 TRUE FALSE 1000949.232 1216803.88 948716.8637 1042281.523 1514669.166 1383211.748 1124368.454 1196563.591 1108337.167 0.903108965 1.097864364 0.855982179 0.940401129 1.366614069 1.248006282 1.014464269 1.079602513 1 20.0799654 NQSFCPTVNLDKLWTLVSEQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NQSFCPTVNLDKLWTLVSEQTR 22 1 P46776;E9PLL6;E9PJD9 P46776 RPL27A 60S ribosomal protein L27a 0 ; 339.42 3.46E-81 1053360000 969610 868120 256750 309910 1037160 877940 1036840 1231720 103231 FALSE TRUE 841473.5818 862417.2626 380915.1588 380279.8022 1016522.545 911714.9199 936287.4164 968326.2633 91027.14878 9.244204538 9.474286233 4.18463243 4.177652571 11.1672458 10.01585716 10.28580406 10.63777429 1 16.47400927 NQSLGQS(ph)APSLTAGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NQSLGQSAPSLTAGLK 16 0 Q6P0Q8;Q6P0Q8-2 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 NQSLGQS(0.992)APS(0.008)LT(0.001)AGLK 123.14 0.00078143 0 105280 76466 37295 48391 92431 75640 77925 95410 87496 TRUE FALSE 91366.98125 75963.68981 55330.98674 59378.91616 90591.80394 78549.91975 70367.84549 75007.31398 77152.32256 1.184241488 0.984593688 0.717165536 0.769632257 1.174194126 1.018114778 0.912063865 0.972197745 1 16.23542197 3.252285748 24.99988365 1.002320864 0.904904227 0.109258203 0.140147976 610.2555799 1111554.343 0.042705928 0.054832573 1787.663397 -3.252285748 -0.097416637 NQSPTEAEKPASSSLPS(ph)SPPPQLLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NQSPTEAEKPASSSLPSSPPPQLLTR 26 1 Q99567;I3L2W3 Q99567 NUP88 Nuclear pore complex protein Nup88 1 NQSPTEAEKPAS(0.005)S(0.005)S(0.022)LPS(0.535)S(0.432)PPPQLLTR 132.6 3.28E-05 139540000 198030 156150 83086 118920 200180 154820 184120 235560 215480 TRUE FALSE 171859.8338 155124.2404 123266.6675 145922.6036 196196.8096 160776.0256 166264.0707 185187.3271 190006.1999 0.904495926 0.81641673 0.648750765 0.767988643 1.032581094 0.846161997 0.875045503 0.974638339 1 17.53568697 3.258729194 24.92282339 0.939030344 0.777008761 0.485456984 0.082187471 209.0936154 258380.5984 0.024397607 0.031456575 1814.383943 -3.258729194 -0.162021583 NQTAEKEEFEHQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NQTAEKEEFEHQQK 14 1 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;; 213.99 1.57E-10 10263650000 8755930 6199430 6054330 7292120 6327600 4840130 7544010 9557340 26470500 FALSE TRUE 7598811.666 6158705.536 8982224.239 8947907.299 6201693.14 5026332.933 6812393.071 7513577.216 23341187.65 0.325553771 0.263855706 0.384822931 0.3833527 0.265697412 0.215341782 0.291861459 0.321902096 1 24.47637463 1.23818117 6.54411168 1.019227804 0.304586892 0.946067388 0.052049717 0.026632316 5.42481479 0.084645432 0.013755893 17.3053812 -1.23818117 -0.714640912 NQTYSFS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NQTYSFSPSK 10 0 Q86YS7;H0YFE9;Q86YS7-3 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 NQTYSFS(0.999)PS(0.001)K;NQTYSFS(0.991)PS(0.009)K;NQTYSFS(1)PSK;NQTYSFS(1)PSK;NQTYSFS(1)PSK 271.6 1.01E-23 3846970000 2632060 3061590 2149418 2718680 4420970 3256600 4318310 5041780 6776210 TRUE FALSE 2284226.602 3041478.214 3188883.734 3335997.846 4333001.346 3381883.509 3899520.961 3963634.582 5975134.173 0.382288755 0.50902258 0.533692406 0.558313462 0.725172226 0.565992898 0.652624836 0.663354908 1 22.51053968 -1.59326859 0.517397507 10 0.516901062 0.742463261 0.083110328 43.51614431 0.722740057 434.0855139 0.05386651 0.025511231 1.59326859 -9.483098938 NQVEEDAEDS(ph)GEADDEEKPEIHKPGQNSFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NQVEEDAEDSGEADDEEKPEIHKPGQNSFSK 31 2 O75717;O75717-2 O75717 WDHD1 WD repeat and HMG-box DNA-binding protein 1 1 NQVEEDAEDS(1)GEADDEEKPEIHKPGQNSFSK 389.93 1.20E-155 513250000 379140 250490 203130 232890 278550 181260 403140 501250 344950 TRUE FALSE 329035.6884 248844.5147 301364.3474 285771.234 273007.4 188233.1895 364043.5448 394061.5882 304170.404 1.081747876 0.8181089 0.990774722 0.939510321 0.897547547 0.618841238 1.196840784 1.295529029 1 18.21452026 2.184973295 24.99459374 1.192863851 0.894796807 0.454387822 0.139823032 74.55188663 34772.38662 0.055319672 0.037296548 153.0993317 -2.184973295 -0.298067043 NQVGDENWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NQVGDENWR 9 0 Q92973-2;Q92973;Q92973-3;S4R398 Q92973-2 TNPO1 Transportin-1 0 ;; 121.73 0.0014089 714190000 876840 772050 448520 563730 901310 959350 782030 906960 940540 FALSE TRUE 760963.3724 766978.3527 665425.7722 691733.5126 883375.6944 996256.8153 706188.851 713013.662 829350.4327 0.917541418 0.924794059 0.802345723 0.83406662 1.065141657 1.201249527 0.851496332 0.859725436 1 19.6616223 3.256744345 24.94555374 0.978032343 0.868813076 0.253632755 0.104901005 440.4720534 604262.7116 0.034107659 0.043942599 1806.110615 -3.256744345 -0.109219267 NQVIIPLVLS(ph)PDRDEDLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NQVIIPLVLSPDRDEDLMR 19 1 Q96G25-2;Q96G25 Q96G25-2 MED8 Mediator of RNA polymerase II transcription subunit 8 1 NQVIIPLVLS(1)PDRDEDLMR;NQVIIPLVLS(1)PDRDEDLMR 108.4 0.00016687 100898000 66834 53837 29686 36118 66504 63018 61727 62488 65638 TRUE FALSE 58001.71756 53483.3412 44042.24889 44319.14393 65180.70051 65442.34324 55740.72504 49125.42748 57878.35042 1.00213149 0.924064712 0.76094513 0.765729217 1.126167212 1.130687775 0.963066926 0.848770346 1 15.82073618 3.248193159 24.99992352 0.995164549 0.860258701 0.324786544 0.105940926 308.9422712 801812.3005 0.034897781 0.044471061 1770.896418 -3.248193159 -0.134905849 NQYDNDVTVWSPQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NQYDNDVTVWSPQGR 15 0 P25786;P25786-2;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ;;; 325.68 4.31E-57 1514270000 709343 655812 338921 464759 736735 757746 626089 738384 688254 FALSE TRUE 615601.5253 651503.9278 502824.3292 570289.6343 722075.4149 786896.9789 565370.9851 580486.3277 606889.3962 1.014355382 1.073513447 0.828527129 0.939692863 1.189797382 1.296606901 0.931588175 0.956494431 1 19.21107409 NQYVTLHDMILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NQYVTLHDMILK 12 0 K7ESG5;K9J957;P61289;P61289-2;A0A087WTV2;B3KQ25;P61289-3 K7ESG5 PSME3 Proteasome activator complex subunit 3 0 150.21 6.79E-05 827530000 854300 827620 416950 603840 1021100 798560 990410 1191300 1057600 FALSE TRUE 741402.0905 822183.3097 618588.4146 740951.1011 1000782.108 829281.1199 894360.1906 936549.7657 932571.7328 0.79500811 0.8816301 0.663314566 0.794524512 1.073142229 0.889241107 0.959025627 1.004265659 1 19.83085518 3.298098756 9.064474672 0.980646286 0.78129022 0.678925072 0.068824996 0.187330684 26.52218225 0.019411421 0.02503023 1986.546595 -3.298098756 -0.199356066 NRDEAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NRDEAIK 7 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 136.8 0.002686 7268320000 10854700 10644200 5879450 6966970 8381700 10348100 11158240 12048300 10720100 FALSE TRUE 9420223.893 10574277.55 8722771.686 8548927.022 8214920.569 10746198.1 10076115.6 9471864.805 9452781.99 0.996555713 1.118641852 0.922772967 0.904382121 0.869047924 1.136829149 1.065941816 1.002018751 1 23.17230755 2.736554943 24.99333699 1.044895541 0.965555484 0.250142761 0.076034681 320.6971773 3996283.687 0.027587933 0.025550676 545.1988646 -2.736554943 -0.079340057 NRDHDTFLAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NRDHDTFLAVR 11 1 Q12907;D6RBV2;D6RDX1;D6RIU4 Q12907 LMAN2 Vesicular integral-membrane protein VIP36 0 91.937 0.0062301 123720000 248220 293160 101350 130600 362120 375940 226330 288360 96161 FALSE TRUE 215417.0981 291234.2127 150363.199 160254.7261 354914.5205 390402.6551 204380.5514 226696.458 84792.95613 2.540506994 3.434651013 1.77329823 1.889953286 4.185660421 4.604187339 2.410348227 2.673529363 1 16.3716568 5.067587973 15.07962503 2.783602646 0.000174196 0.002449808 1.098289387 11665773.01 56736035.17 0.276084879 1006574419 116839.0382 -5.067587973 -2.78342845 NRDSDKTDTDWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NRDSDKTDTDWR 12 2 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 71.241 0.025376 332930000 798460 626700 163501 178753 678800 563680 833800 889890 30746 FALSE TRUE 692941.488 622583.1664 242570.6305 219341.6007 665293.208 585365.1343 752938.2043 699593.9486 27111.24291 25.55919293 22.96402155 8.947233859 8.090429549 24.53938428 21.59123196 27.77217581 25.80456938 1 14.72660363 1.5645623 0.003221888 9.084231472 29.20963125 0 9.215382628 13361192.77 13535.45435 42759494.16 41793079.24 36.6912325 -1.5645623 20.12539978 NRDVITLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NRDVITLR 8 1 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;H0YH17 Q9Y365 STARD10 PCTP-like protein 0 ; 168.83 0.00027777 270050000 206458 195137 73135 82592 223060 213845 194394 209112 72587 FALSE TRUE 179174.0522 193855.1322 108503.3306 101345.7759 218621.5424 222071.7555 175541.6998 164395.0261 64005.84755 2.799338796 3.028709713 1.695209653 1.583383079 3.415649519 3.469554174 2.742588475 2.56843761 1 15.96591609 NREEEWDPEYTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NREEEWDPEYTPK 13 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 73.022 0.034619 250920000 404400 304220 187350 252540 323710 276720 331470 438780 323240 FALSE TRUE 350957.5154 302221.5588 277953.0866 309883.0668 317268.8043 287365.5975 299324.0904 344950.3116 285026.9354 1.231313507 1.06032631 0.975181824 1.087206254 1.113118674 1.008205056 1.050160715 1.210237591 1 18.12073874 NREELDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NREELDK 7 1 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;; 150.4 0.0017797 8545000000 4437960 3393310 3439310 4124510 3102710 3142260 4570410 4997590 12313400 FALSE TRUE 3851472.342 3371019.123 5102571.82 5061043.035 3040972.141 3263144.776 4127172.342 3928894.27 10857723.88 0.354721891 0.310471988 0.469948571 0.466123756 0.280074551 0.300536725 0.380113953 0.361852476 1 23.37221836 1.238333892 24.99564642 1.000000702 0.365988614 0.908772858 0.063180138 1.564454388 172092.9963 0.090921451 0.016111066 17.31146777 -1.238333892 -0.634012089 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 26 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR 38 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;;;;;;;;;;;;;;; 284.98 3.39E-77 14506301800 2030663.8 1722413 1265488.9 1522844.1 1697645.9 1635418.8 1990877.1 2328775.7 2047285.3 FALSE TRUE 1762306.434 1711098.356 1877483.565 1868629.128 1663866.068 1698334.419 1797802.145 1830785.139 1805257.564 0.976207755 0.947841676 1.040008696 1.035103891 0.921677937 0.940771252 0.995870163 1.014140683 1 20.78377326 2.008279416 24.81149203 1.007157908 0.977754468 0.104164477 0.037526351 410.6919619 1230740.811 0.01650791 0.011109522 101.9246938 -2.008279416 -0.02940344 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 15 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR 39 3 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;;;; 389.5 1.30E-179 7320341000 2038617 1811129 931401.2 1058163 1700903 1641657 2133993 2403984 564535 FALSE TRUE 1769208.598 1799231.574 1381829.936 1298435.082 1667058.358 1704812.607 1927038.687 1889910.729 497796.3154 3.554081345 3.614393113 2.775894262 2.608366197 3.348876451 3.424719216 3.871138913 3.796554275 1 18.92519603 1.232469293 24.99999718 0.999996092 3.382995682 0.773909717 0.403272593 109.0780379 447633.0258 1.002509711 0.112133524 17.07926957 -1.232469293 2.38299959 NREELGFRPEYSASQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NREELGFRPEYSASQLK 17 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 152.25 1.24E-07 1681110000 689960 586480 305080 420670 624210 570320 729560 742900 553860 FALSE TRUE 598780.0379 582627.3743 452617.7084 516189.553 611789.4422 592260.5794 658807.3835 584036.6163 488383.3018 1.226045272 1.192971529 0.926767371 1.056935303 1.252682964 1.212696211 1.348955587 1.195857054 1 18.89765435 3.239135311 24.99999464 1.212817388 1.094849802 0.153197458 0.116538567 27.01640013 1175215.919 0.035704762 0.043343874 1734.344274 -3.239135311 -0.117967585 NRENS(ph)PSSQSAGLSSINK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NRENSPSSQSAGLSSINK 18 1 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2 H3BSS6 ZNF106 Zinc finger protein 106 1 NRENS(0.979)PS(0.009)S(0.012)QSAGLSSINK 181.83 4.33E-14 1314200000 142610 130480 73248 105040 158490 124290 161750 187510 139140 TRUE FALSE 123763.7272 129622.8683 108670.9778 128890.9374 155336.3591 129071.5167 146063.5099 147412.4457 122691.0277 1.008743096 1.05649835 0.885728809 1.050532707 1.266077577 1.052004528 1.190498707 1.201493283 1 16.90467022 3.469293146 24.69346638 1.149469042 0.987139211 0.421388767 0.085237785 136.3372698 430068.1071 0.023286103 0.030122186 2946.409771 -3.469293146 -0.162329831 NRENSS(ph)PCQGNGEQAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NRENSSPCQGNGEQAGR 17 1 Q5T5X7 Q5T5X7 BEND3 BEN domain-containing protein 3 1 NRENS(0.186)S(0.814)PCQGNGEQAGR 163.68 1.63E-09 85428000 33626 29072 12365 13651 32079 35571 30853 30498 12411 TRUE FALSE 29182.2389 28881.02412 18344.75536 16750.66819 31440.69066 36939.43939 27860.88081 23976.24004 10943.78572 2.666557958 2.639034139 1.676271432 1.53061003 2.872926378 3.375380361 2.545817464 2.190854303 1 13.41782427 4.425378258 24.99951193 2.232188419 2.659692893 0.075049443 0.677995083 286.3195038 138333.7864 0.179161612 0.474017313 26630.43482 -4.425378258 0.427504474 NREPVQLETLSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NREPVQLETLSIR 13 1 P62314;J3QLI9 P62314 SNRPD1 Small nuclear ribonucleoprotein Sm D1 0 ;;;; 235.38 1.00E-16 6010030000 3219250 3193340 1582890 1902340 3432670 3264180 2970660 3292550 3391620 FALSE TRUE 2793817.956 3172362.739 2348380.898 2334295.372 3364366.583 3389755.117 2682565.85 2588463.805 2990666.547 0.934179024 1.060754413 0.785236622 0.780526794 1.124955434 1.13344469 0.896979255 0.865514013 1 21.51203563 NRHS(ph)PDHPGMGSSQASSSSSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 NRHSPDHPGMGSSQASSSSSLR 22 1 J3KR33;A0JLT2 J3KR33 MED19 Mediator of RNA polymerase II transcription subunit 19 1 NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR 306.21 1.20E-56 4035050000 765884.1 641799 235260.5 468560.8 882018.8 747246.1 673355.7 781991 706006.5 TRUE FALSE 664670.5757 637582.9801 349033.2647 574954.6911 864468.3515 775993.141 608053.7679 614768.3101 622543.2159 1.067669776 1.024158587 0.560657085 0.923557878 1.388607778 1.246488792 0.976725394 0.987511059 1 19.24781446 3.455295956 24.99803534 1.10411455 0.872152379 0.273186153 0.18264516 334.6140038 383255.4462 0.056269824 0.072649775 2852.961795 -3.455295956 -0.231962171 NRLENDGATALAEAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NRLENDGATALAEAFR 16 1 P46060 P46060 RANGAP1 Ran GTPase-activating protein 1 0 ; 258.14 9.78E-27 523160000 487780 474770 213885 249330 564210 535910 483990 520110 202769 FALSE TRUE 423318.6371 471651.2046 317320.5014 305944.1873 552983.3249 556526.8045 437052.7243 408888.524 178797.8798 2.367581973 2.637901552 1.774744207 1.711117534 3.092784576 3.112602929 2.444395452 2.286875686 1 17.4479701 1.222416983 3.417381051 0.74654295 2.44765613 0.491549761 0.459235135 0.324490415 5.271613386 1.492359695 0.127020275 16.6884877 -1.222416983 1.70111318 NRNEQESAVHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NRNEQESAVHPR 12 1 Q9UJU6-2;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ;;; 145.83 3.86E-05 2113680000 1613260 1611170 524558 798110 1923080 1980960 1657140 1828040 608120 FALSE TRUE 1400063.604 1600586.118 778236.0033 979333.0738 1884814.47 2057168.813 1496430.818 1437127.872 536228.7464 2.6109447 2.984894281 1.451313471 1.826334527 3.51494485 3.836364289 2.790657584 2.680064957 1 19.03248904 3.259083458 24.99870878 2.809430757 2.218333631 0.093475597 0.838465135 613.7208451 747563.7626 0.253098245 0.326363187 1815.864581 -3.259083458 -0.591097126 NRPCLS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NRPCLSPK 8 1 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9 A0A0G2JQJ7 MAPT Microtubule-associated protein tau 1 NRPCLS(1)PK 59.265 0.060389 324160000 293740 236060 147340 205260 310120 284800 298230 357620 347020 TRUE FALSE 254921.5148 234509.3063 218594.1168 251867.4202 303949.2187 295756.4403 269307.7005 281145.746 305995.6909 0.833088577 0.766381074 0.714369919 0.823107735 0.993312088 0.966537925 0.880102918 0.918789886 1 18.22315181 3.397073374 5.072095443 0.942295922 0.77028441 0.777498952 0.045010358 0.09811878 4.451204361 0.013595684 0.01777019 2495.016225 -3.397073374 -0.172011513 NRPDYVS(ph)EEEEDDEDFETAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NRPDYVSEEEEDDEDFETAVK 21 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 NRPDYVS(1)EEEEDDEDFETAVK 185.35 2.20E-17 180530000 154000 146130 83196 112100 146440 103110 160020 188570 185520 TRUE FALSE 133648.5098 145170.0624 123429.8639 137554.0183 143526.1305 107076.7084 144501.285 148245.773 163588.0369 0.816982172 0.887412461 0.754516444 0.84085622 0.877363242 0.654550971 0.88332428 0.906214022 1 17.31970772 1.595884084 2.063206448 0.993906336 0.811451365 0.446619868 0.06894952 0.316730653 2.612431028 0.092843746 0.018754847 39.43520327 -1.595884084 -0.18245497 NRPEDYQGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 NRPEDYQGGR 10 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;;;;;;; 232.84 2.41E-11 6362171000 1952910 1865166 952891 1286130 2196263 2735253 1855331 1643975 1488821 FALSE TRUE 1694827.995 1852913.602 1413712.275 1578165.474 2152561.663 2840479.953 1675401.285 1292423.74 1312814.277 1.290988394 1.411405736 1.076856261 1.202123942 1.639654367 2.163657116 1.276190634 0.984468071 1 20.3242314 NRPLLDFVSMEELNDMDDYDS(ph)EDDNDWRPTVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NRPLLDFVSMEELNDMDDYDSEDDNDWRPTVVK 33 2 A0A0U1RRH6;O94880 A0A0U1RRH6 PHF14 PHD finger protein 14 1 NRPLLDFVSMEELNDMDDYDS(1)EDDNDWRPTVVK;NRPLLDFVSMEELNDMDDYDS(1)EDDNDWRPTVVK;NRPLLDFVSMEELNDMDDYDS(1)EDDNDWRPTVVK;NRPLLDFVSMEELNDMDDY(0.123)DS(0.877)EDDNDWRPTVVK 227.35 1.89E-36 312696000 175770 131273.8 73684 131419 136464.9 125135 93852.1 164301.2 222159 TRUE FALSE 152541.5492 130411.4538 109317.8289 161259.6926 133749.5155 129949.0244 84750.33779 129166.667 195895.6161 0.778687916 0.665719103 0.558041221 0.823191942 0.682759105 0.663358512 0.432630089 0.659364765 1 17.57972559 1.240364274 8.94047094 1.002461199 0.650515127 0.499608208 0.107364832 0.066291404 73.26702511 0.146198651 0.026639452 17.39259058 -1.240364274 -0.351946071 NRPLSDEELDAMFPEGYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NRPLSDEELDAMFPEGYK 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 192.69 1.47E-14 592070000 1383080 1066850 630100 739860 1194930 926130 1300120 1588420 1355090 FALSE TRUE 1200302.474 1059841.792 934818.4676 907856.5211 1171153.231 961758.8204 1174034.563 1248748.744 1194892.804 1.004527326 0.886976462 0.782345048 0.759780725 0.980132466 0.804891298 0.982543839 1.045071775 1 20.18844977 2.087410845 5.56646916 1.022452292 0.867059814 0.41619405 0.078727312 0.185184075 9.183393637 0.033210443 0.021997101 122.2956036 -2.087410845 -0.155392479 NRPPFGQGYTQPGPGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NRPPFGQGYTQPGPGYR 17 1 Q92734-2;Q92734 Q92734-2 TFG Protein TFG 0 209.66 3.71E-12 589090000 48020 60236 34517 35781 73854 85813 63455 57356 66839 FALSE TRUE 41674.03533 59840.30575 51209.53665 43905.62293 72384.44989 89114.28164 57301.14387 45090.86574 58937.36956 0.707090181 1.015320266 0.868880594 0.744953893 1.228158814 1.512016608 0.972237891 0.765064102 1 15.84689505 3.248084727 24.99883321 1.065773307 0.849495412 0.274063461 0.207654933 377.3509556 990463.2078 0.068885913 0.087757051 1770.454323 -3.248084727 -0.216277895 NRPT(ph)SISWDGLDSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NRPTSISWDGLDSGK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 1 NRPT(0.64)S(0.36)ISWDGLDSGK;NRPT(0.496)S(0.496)IS(0.009)WDGLDSGK;NRPT(0.662)S(0.335)IS(0.003)WDGLDSGK 198.49 1.28E-08 1785010000 1690760 1682210 972510 1107760 1596830 1328500 1718690 1981220 2892170 TRUE FALSE 1467321.782 1671159.452 1442819.089 1359293.839 1565056.207 1379608.255 1552011.708 1557551.521 2550260.957 0.575361426 0.655289588 0.56575351 0.533001862 0.61368473 0.540967484 0.608569764 0.610742017 1 21.28221345 1.229069147 4.306910054 1.043102269 0.585971357 0.929109381 0.035827325 0.054948845 1.971056851 0.078945205 0.008912903 16.9460759 -1.229069147 -0.457130912 NRPTSIS(ph)WDGLDSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NRPTSISWDGLDSGK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 1 NRPT(0.004)S(0.03)IS(0.965)WDGLDS(0.001)GK;NRPT(0.006)S(0.133)IS(0.861)WDGLDSGK 202.63 1.53E-08 1045470000 1156580 1153040 618500 742000 1063830 903470 1168790 1389670 2050500 TRUE FALSE 1003735.023 1145465.604 917608.6688 910482.4408 1042661.864 938227.0755 1055440.926 1092499.885 1808092.226 0.555134859 0.633521669 0.507501031 0.503559734 0.576664093 0.518904435 0.583731798 0.604227964 1 20.78603684 1.184886876 2.82387484 1.13605385 0.553873103 0.924572628 0.039654353 0.137431559 1.156245851 0.200209721 0.010390456 15.30688698 -1.184886876 -0.582180747 NRPTSISWDGLDSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NRPTSISWDGLDSGK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ;;; 215.37 2.14E-12 5588590000 7014600 5755540 2973580 3804190 5839920 5082180 6029740 6857800 10865600 FALSE TRUE 6087602.837 5717731.479 4411613.234 4667989.483 5723717.018 5277694.753 5444976.743 5391312.837 9581081.146 0.635377443 0.596773098 0.460450461 0.487209054 0.597397823 0.550845429 0.568305044 0.562704016 1 23.19175703 1.237852846 6.824156047 1.010629858 0.554457948 0.879975643 0.051371707 0.038211039 9.490109034 0.080536473 0.013206164 17.29230337 -1.237852846 -0.45617191 NRSAEEGELAES(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NRSAEEGELAESK 13 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 NRS(0.173)AEEGELAES(0.827)K 235.35 2.90E-16 530970000 554500 445230 311710 396190 564760 477640 618380 739820 423560 TRUE FALSE 481221.4201 442305.2548 462453.9986 486150.9949 553522.3809 496015.1199 558409.6028 581615.2503 373487.2193 1.288454852 1.184258073 1.238205686 1.30165363 1.482038346 1.328064507 1.495123726 1.557256099 1 18.51069935 3.453026054 4.963024257 1.402662451 1.23631982 0.124122218 0.153504342 0.29922147 19.45543087 0.043715045 0.058937766 2838.089284 -3.453026054 -0.16634263 NRT(ph)PSDVK ddPTM_MDA-MB-175_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(1)PSDVK 77.358 0.054028 274000000 536240 432850 283750 312800 423300 378600 591650 578650 574140 TRUE FALSE 465374.5253 430006.5798 420972.4491 383826.0208 414877.1582 393164.987 534271.8741 454910.2006 506265.8233 0.91922959 0.849369166 0.831524527 0.758151159 0.819484822 0.776597923 1.055318865 0.898559965 1 18.94953557 2.247965619 24.99999882 0.969641327 0.82370914 0.626466285 0.057439558 130.4521871 346763.2205 0.02142609 0.016368798 176.9968831 -2.247965619 -0.145932187 NRT(ph)SVDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NRTSVDFK 8 1 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 1 NRT(0.764)S(0.236)VDFK 74.962 0.064057 211690000 306570 278670 132760 199890 327650 230910 365770 377920 314330 TRUE FALSE 266055.9978 276839.3984 196963.1801 245278.0796 321130.406 239793.2571 330297.6817 297104.749 277170.2655 0.959900938 0.998806268 0.710621609 0.884936482 1.158603379 0.865147842 1.191677906 1.071921436 1 18.08041297 3.261275858 24.68486589 1.059725983 0.883730148 0.349494389 0.11439559 222.8621767 242184.5389 0.032298974 0.041666515 1825.054582 -3.261275858 -0.175995835 NRTPSDVK ddPTM_MDA-MB-175_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 ; 122.28 0.0012742 537630000 855580 732280 264605 391060 711770 685630 929310 1008240 290768 FALSE TRUE 742512.9352 727469.6045 392568.8631 479856.15 697607.1696 712006.6298 839185.6592 792635.7221 256393.7383 2.895987009 2.837314239 1.531117202 1.871559552 2.72084324 2.777004753 3.273034922 3.091478472 1 17.9680015 3.190875405 24.82006187 2.700117579 2.269739603 0.020952745 0.730036235 317.5343997 165274.6784 0.226123728 0.256400937 1551.941709 -3.190875405 -0.430377976 NRTS(ph)VDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NRTSVDFK 8 1 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 1 NRT(0.207)S(0.793)VDFK;NRT(0.001)S(0.999)VDFK;NRT(0.226)S(0.774)VDFK;NRT(0.003)S(0.997)VDFK 147.58 0.0004406 1825650000 5610000 5176130 2710400 4099910 5765330 3587600 7603100 7175200 5934190 TRUE FALSE 4868624.286 5142127.661 4021158.506 5030857.229 5650611.213 3725617.293 6865752.532 5640839.317 5232656.818 0.93043065 0.982699198 0.768473578 0.961434583 1.079874222 0.711993433 1.312096851 1.07800674 1 22.31911221 2.235916492 24.99999997 1.126781298 0.913509038 0.401206826 0.128878136 70.07357529 662525.0186 0.049026407 0.034759498 172.153752 -2.235916492 -0.21327226 NRVPS(ph)AGDVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NRVPSAGDVEK 11 1 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 1 NRVPS(1)AGDVEK;NRVPS(1)AGDVEK;NRVPS(1)AGDVEK;NRVPS(1)AGDVEK 107.73 0.0013066 1565900000 2713120 2151900 1489870 1743210 2425250 2152150 2696840 3220690 3025400 TRUE FALSE 2354574.318 2137764.027 2210376.115 2139032.474 2376992.27 2234944.603 2435300.872 2531970.507 2667740.659 0.882609901 0.801338773 0.828557344 0.801814249 0.891013248 0.837766818 0.912870171 0.94910669 1 21.34718699 1.61746984 0.826022481 1.048801965 0.830131633 0.787288204 0.029607635 0.603199155 0.478123645 0.113183533 0.011755003 41.44478017 -1.61746984 -0.218670332 NRVPSAGDVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NRVPSAGDVEK 11 1 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 75.102 0.035575 129490000 156160 125470 68326 83587 151870 125740 149600 168850 127670 FALSE TRUE 135523.0603 124645.7793 101368.6821 102566.7059 148848.0841 130577.2992 135091.815 132742.7415 112576.998 1.203825495 1.107204682 0.900438668 0.911080484 1.322189139 1.159893241 1.199994825 1.179128453 1 16.78055256 3.246180406 24.99999497 1.174566183 1.026806553 0.269890536 0.11561893 239.6213931 786176.7592 0.034525391 0.043699572 1762.708124 -3.246180406 -0.14775963 NS(ph)EEEEEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSEEEEEEK 9 0 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 NS(1)EEEEEEK;NS(1)EEEEEEK 170.79 6.03E-05 471160000 332460 237548 275940 340200 168080 218622 297430 349910 1818580 TRUE FALSE 288524.5687 235987.5315 409385.507 417447.6096 164735.5368 227032.5298 268585.2844 275084.4695 1603589.544 0.179924202 0.147162054 0.2552932 0.260320736 0.102729241 0.141577706 0.167490045 0.171542943 1 20.61287349 1.238290654 24.99999992 1.000000914 0.177929721 0.966429092 0.048132208 1.102037124 101865.1377 0.069568807 0.012302007 17.30974435 -1.238290654 -0.822071192 NS(ph)FTPLSSSNTIR ddPTM_MDA-MB-175_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(1)FTPLSSSNTIR;NS(0.999)FT(0.001)PLSSSNTIR;NS(0.878)FT(0.122)PLSSSNTIR;NS(0.999)FT(0.001)PLSSSNTIR 116.99 0.00026043 1693810000 666400 908830 501483 638270 1113530 1042600 927720 1102020 1381660 TRUE FALSE 578333.5516 902859.8359 744001.8562 783198.9588 1091372.932 1082709.497 837749.8572 866361.5989 1218321.729 0.474696903 0.741068483 0.610677655 0.642850686 0.895800268 0.88868931 0.687626131 0.711110685 1 20.21646373 3.321416869 7.246855486 0.812075205 0.623651504 0.485270112 0.110657175 0.235977971 17.42193196 0.03248116 0.041912615 2096.12351 -3.321416869 -0.188423701 QFCQEGQPHVLEALS(ph)PPQTSGLS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QFCQEGQPHVLEALSPPQTSGLSPSR 26 0 E9PR76;E9PSH4;Q9H063 E9PR76 MAF1 Repressor of RNA polymerase III transcription MAF1 homolog 2 QFCQEGQPHVLEALS(0.999)PPQT(0.001)SGLS(0.965)PS(0.035)R;QFCQEGQPHVLEALS(1)PPQTSGLS(0.87)PS(0.13)R;QFCQEGQPHVLEALS(0.998)PPQT(0.002)S(0.002)GLS(0.953)PS(0.045)R;QFCQEGQPHVLEALS(1)PPQT(0.001)S(0.005)GLS(0.966)PS(0.028)R 194.29 8.84E-19 1181160000 371413 452811 447095 544190 761210 857960 767060 833540 821150 TRUE FALSE 322329.831 449836.4547 663311.6374 667756.6569 746063.4103 890966.2764 692670.6393 655293.9576 724074.5825 0.445161091 0.621257072 0.916081925 0.922220822 1.030368181 1.230489646 0.956628856 0.905008922 1 19.46577878 4.373484157 1.509686546 1.008191529 0.384367686 0.836022351 0.087912739 0.251576765 0.86843604 0.027936685 0.193050677 23631.11194 -4.373484157 -0.623823843 down NS(ph)LESISSIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSLESISSIDR 11 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 NS(1)LESISSIDR;NS(0.729)LES(0.271)ISSIDR 223.9 6.35E-05 513180000 570710 465870 332960 576610 609080 525290 493700 696280 836200 TRUE FALSE 495289.2275 462809.6693 493980.5697 707538.1134 596960.4996 545498.2462 445821.05 547385.9405 737345.3886 0.671719435 0.627670121 0.669944611 0.959574881 0.809607694 0.739813735 0.604629875 0.742373858 1 19.49198104 3.969328561 24.90799889 0.788839261 0.649472844 0.281416059 0.11236683 921.9656432 748721.9394 0.031225208 0.054174661 9318.125619 -3.969328561 -0.139366417 NS(ph)PATLFEVPDTW ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSPATLFEVPDTW 13 0 A0A494C0Q6;A0A494C0K5;A0A494C0W0;O95453-2;O95453-3;O95453;O95453-4 A0A494C0Q6 PARN Poly(A)-specific ribonuclease PARN 1 NS(0.889)PAT(0.111)LFEVPDTW;NS(0.889)PAT(0.111)LFEVPDTW 111.65 0.0010099 16547300 58747 50202 29326 41703 55208 52941 51053 54557 86994 TRUE FALSE 50983.4351 49872.21976 43508.15169 51172.30354 54109.46881 54977.67453 46101.88792 42890.41011 76709.66842 0.664628542 0.650142554 0.567179504 0.667090663 0.705380038 0.716698112 0.600991881 0.559126522 1 16.2271208 1.230770638 24.99100689 1.000000653 0.638761932 0.820429703 0.052710527 128.8047286 413183.4523 0.150833751 0.014284502 17.01259791 -1.230770638 -0.361238721 NS(ph)PEDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSPEDKR 7 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 NS(1)PEDKR;NS(1)PEDKR 66.92 0.040772 1636770000 2013410 1452660 1096030 1352870 1301590 1374100 1840080 2167000 2986500 TRUE FALSE 1747332.767 1443117.381 1626073.774 1660059.811 1275690.906 1426962.516 1661629.325 1703603.914 2633439.372 0.66351737 0.547997192 0.617471506 0.630377076 0.484420078 0.54186268 0.63097307 0.646912145 1 21.32851682 1.042609705 1.918657 1.350265045 0.582414664 0.854331664 0.052943451 0.543809503 1.215057854 0.907738498 0.014370224 11.03086844 -1.042609705 -0.767850381 NS(ph)PEDLGLSLTGDSCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NSPEDLGLSLTGDSCK 16 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 NS(1)PEDLGLSLTGDSCK;NS(1)PEDLGLSLTGDSCK;NS(1)PEDLGLSLTGDSCK;NS(1)PEDLGLSLTGDSCK;NS(1)PEDLGLSLTGDSCK;NS(1)PEDLGLSLTGDSCK 381.42 2.65E-105 3174070000 5401890 4343200 3112310 3268510 4799240 3484990 5563380 6499100 5677890 TRUE FALSE 4688016.55 4314669.233 4617433.526 4010675.152 4703744.514 3619059.82 5023844.264 5109318.041 5006656.312 0.936356773 0.861786582 0.922258936 0.801068598 0.939498184 0.722849661 1.00343302 1.020505048 1 22.25541599 2.048537823 24.99905568 1.011792943 0.866764429 0.518619781 0.065387809 78.023611 40185.13883 0.024349314 0.016416299 111.824721 -2.048537823 -0.145028513 NS(ph)PFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSPFTR 6 0 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 NS(0.998)PFT(0.002)R 87.639 0.054767 142120000 342990 281670 180780 218950 320280 317870 276490 332030 450790 TRUE FALSE 297663.0025 279819.6912 268205.8127 268665.9439 313907.0546 330098.6646 249676.0424 261027.9684 397498.1197 0.748841284 0.703952239 0.674734796 0.675892364 0.789707018 0.83044082 0.628118801 0.65667724 1 18.60058851 3.24465233 24.98890156 0.756457189 0.699210648 0.104946027 0.103251316 463.6957139 1902121.668 0.030882928 0.038850297 1756.51689 -3.24465233 -0.05724654 NS(ph)PGSQVASNPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NSPGSQVASNPR 12 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 1 NS(1)PGSQVASNPR;NS(1)PGSQVASNPR;NS(0.999)PGS(0.001)QVASNPR;NS(1)PGSQVASNPR;NS(1)PGSQVASNPR 303.02 1.19E-36 4853160000 2672251 2227913 1072240 1386460 2521070 2418866 2335899 2446841 2289181 TRUE FALSE 2319106.26 2213277.693 1590778.85 1701276.934 2470905.639 2511921.34 2109363.875 1923603.093 2018556.63 1.148893336 1.096465494 0.788077395 0.842818531 1.224095278 1.244414599 1.044986226 0.952959687 1 20.94489263 1.754116872 24.04088156 0.976345828 1.052504778 0.047897602 0.146268057 15.85502868 24553.51375 0.085635349 0.04111892 56.76973561 -1.754116872 0.07615895 NS(ph)PGVPTGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSPGVPTGAK 10 0 Q08379;B7ZC06;R4GND7 Q08379 GOLGA2 Golgin subfamily A member 2 1 NS(1)PGVPTGAK;NS(1)PGVPTGAK 136.6 0.00011884 471710000 1365490 1138480 608110 751360 1176000 913610 1304820 1516340 1290470 TRUE FALSE 1185037.037 1131001.25 902194.03 921967.7718 1152599.901 948757.1679 1178278.757 1192082.491 1137912.107 1.041413506 0.993926722 0.792850366 0.810227579 1.01290767 0.833770168 1.035474313 1.047605069 1 20.1179577 2.212982988 24.85376106 1.032165761 0.912054565 0.281351653 0.085374288 268.421233 260822.5032 0.035798837 0.024145481 163.2987979 -2.212982988 -0.120111195 NS(ph)PLDCGSASPNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSPLDCGSASPNK 13 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 NS(1)PLDCGSASPNK;NS(1)PLDCGSASPNK 252.47 9.75E-24 176240000 458710 383513 286352 353862 484150 350589 447890 548680 697980 TRUE FALSE 398090.3113 380993.6779 424832.785 434211.7755 474516.3622 364076.3857 404453.6967 431349.0518 615465.5995 0.646811636 0.619033262 0.690262438 0.705501292 0.770987627 0.59154628 0.657150777 0.700849978 1 19.2313187 1.232756965 4.003522011 1.038695264 0.670678289 0.817949832 0.048730966 0.105876483 2.950680662 0.115584716 0.012682412 17.09058644 -1.232756965 -0.368016975 NS(ph)PPFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSPPFLK 7 0 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 NS(1)PPFLK;NS(1)PPFLK 81.771 0.027586 437400000 1913520 1517280 928810 1116940 1903520 1403420 1826040 2087400 1830700 TRUE FALSE 1660643.484 1507312.888 1377985.623 1370558.298 1865643.676 1457410.476 1648950.922 1641025.754 1614276.732 1.028722927 0.933738843 0.853624162 0.849023139 1.155714903 0.902825672 1.021479706 1.016570283 1 20.62245649 3.275022136 24.9999906 1.013312577 0.913049346 0.301374798 0.077588355 221.4452121 151833.3552 0.02170668 0.028022379 1883.745103 -3.275022136 -0.100263231 NS(ph)PQALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSPQALR 7 0 Q7L7X3-3;Q7L7X3 Q7L7X3-3 TAOK1 Serine/threonine-protein kinase TAO1 1 NS(1)PQALR 123.29 0.0044667 511420000 971350 933090 705820 939210 999030 995490 904590 1049200 1878000 TRUE FALSE 842983.6364 926960.4704 1047156.913 1152471.985 979151.2576 1033787.144 816863.001 824836.7449 1655984.979 0.509052707 0.559763815 0.632346867 0.695943502 0.591280277 0.624273262 0.493279233 0.49809434 1 20.65925816 1.232194741 24.99941144 1.000000707 0.575086558 0.809137723 0.064792196 102.8689426 403937.1949 0.163140568 0.017764644 17.06847582 -1.232194741 -0.424914149 NS(ph)PQALRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSPQALRR 8 1 Q7L7X3-3;Q7L7X3 Q7L7X3-3 TAOK1 Serine/threonine-protein kinase TAO1 1 NS(1)PQALRR 63.944 0.042944 387130000 113410 92332 72630 92667 94370 121250 107590 140580 113500 TRUE FALSE 98422.58116 91725.46501 107754.1109 113708.4587 92492.22163 125914.566 97155.93836 110518.061 100082.1593 0.983417842 0.916501659 1.076656536 1.136151133 0.924162931 1.258112004 0.970761812 1.104273347 1 16.6108253 4.23075815 24.88982111 1.069485923 0.949959744 0.21212915 0.093819 203.6816628 649750.7151 0.021646844 0.046434409 17012.10873 -4.23075815 -0.119526178 NS(ph)PVT(ph)KTPPRDLPTIPGVTSPSSDEPPMEASQSHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NSPVTKTPPRDLPTIPGVTSPSSDEPPMEASQSHLR 36 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 NS(0.714)PVT(0.677)KT(0.599)PPRDLPT(0.01)IPGVTSPSSDEPPMEASQSHLR;NS(0.999)PVT(0.552)KT(0.447)PPRDLPT(0.002)IPGVTSPSSDEPPMEASQSHLR;NS(0.999)PVT(0.676)KT(0.322)PPRDLPT(0.003)IPGVTSPSSDEPPMEASQSHLR;NS(0.845)PVT(0.608)KT(0.546)PPRDLPT(0.001)IPGVTSPSSDEPPMEASQSHLR;NS(0.992)PVT(0.54)KT(0.464)PPRDLPT(0.004)IPGVTSPSSDEPPMEASQSHLR 175.09 3.55E-18 1463890000 339755 248173 136415 174616.8 422233 364830 511279 472918 137138.3 TRUE FALSE 294855.5159 246542.7352 202385.7503 214266.2133 413831.3894 378865.2462 461695.2413 371788.166 120925.9664 2.438314323 2.038790696 1.673633516 1.771879272 3.422187986 3.133034678 3.817999186 3.074510604 1 16.88376454 3.246677921 24.99879554 2.994475384 1.962876817 0.254347868 0.761330171 231.8549728 714037.6361 0.223129091 0.283015947 1764.728587 -3.246677921 -1.031598566 NS(ph)PVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSPVTK 6 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 NS(1)PVTK 86.744 0.055835 305140000 803280 544890 680300 920040 1604500 1091400 1344000 1612900 2617900 TRUE FALSE 697124.5127 541310.5817 1009295.355 1128949.144 1572573.589 1133386.864 1213659.087 1267993.887 2308414.844 0.301992735 0.234494499 0.437224426 0.489058172 0.681235261 0.490980582 0.525754324 0.549292035 1 21.13847108 -2 0.124915784 2.565615183 8.65E-17 0.640741449 0.125549404 151.7997716 1.677337439 67.75382937 4.124548865 0.01 2 -2.565615183 NS(ph)QKHSPTSEPTPPGDALPPVS(ph)SPHTHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSQKHSPTSEPTPPGDALPPVSSPHTHR 28 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 2 NS(0.249)QKHS(0.249)PT(0.249)S(0.249)EPT(0.005)PPGDALPPVS(0.453)S(0.453)PHT(0.093)HR 73.676 0.0049032 263440000 169940 149400 45486 94261 185220 166860 181720 205450 166260 TRUE FALSE 147481.9984 148418.5816 67483.18174 115664.4007 181534.4844 173279.2122 164096.8224 161516.1163 146604.9322 1.005982515 1.012370998 0.460306353 0.788952998 1.238256324 1.181946675 1.119313108 1.101709976 1 17.16157412 3.249127716 24.99508491 1.126943476 0.805393911 0.477991911 0.161471219 188.9439197 446919.5561 0.048600741 0.062070457 1774.711304 -3.249127716 -0.321549565 NS(ph)QKHSPTSEPTPPGDALPPVSS(ph)PHTHR ddPTM_MDA-MB-175_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(0.711)QKHS(0.182)PT(0.047)S(0.055)EPT(0.004)PPGDALPPVS(0.289)S(0.703)PHT(0.008)HR 141.76 1.63E-07 438520000 195340 233070 61537 131310 351130 260620 298990 339080 247700 TRUE FALSE 169525.3241 231538.9478 91296.49903 161125.9424 344143.2 270646.22 269993.9958 266570.3807 218417.1882 0.77615377 1.060076589 0.417991367 0.73769809 1.57562325 1.2391251 1.23613896 1.2204643 1 17.73672687 3.26467039 24.98793899 1.247927436 0.746701617 0.601637729 0.204674851 154.3999464 147764.9213 0.058587375 0.07561112 1839.37547 -3.26467039 -0.501225819 NS(ph)QKHSPTSEPTPPGDALPPVSSPHT(ph)HR ddPTM_MDA-MB-175_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(0.236)QKHS(0.29)PT(0.236)S(0.236)EPT(0.003)PPGDALPPVS(0.299)S(0.288)PHT(0.412)HR 80.359 0.0093233 748510000 218040 252920 87113 159890 436820 329250 361160 419160 312100 TRUE FALSE 189225.4616 251258.5519 129241.1382 196195.4683 428128.1366 341916.4606 326134.7588 329525.8959 275203.8935 0.687582792 0.912990542 0.469619585 0.712909493 1.555676161 1.242411421 1.185065933 1.197388204 1 18.07014136 3.295849797 11.8870278 1.227655075 0.694572113 0.712973168 0.170310791 0.401051372 82.06665312 0.048687017 0.062833833 1976.286011 -3.295849797 -0.533082963 NS(ph)QKHSPTSEPTPPGDALPPVSSPHTHR ddPTM_MDA-MB-175_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(0.394)QKHS(0.394)PT(0.091)S(0.116)EPT(0.004)PPGDALPPVSSPHTHR;NS(0.2)QKHS(0.2)PT(0.2)S(0.2)EPT(0.2)PPGDALPPVSSPHTHR;NS(0.23)QKHS(0.23)PT(0.23)S(0.23)EPT(0.079)PPGDALPPVSSPHTHR 97.243 0.0009558 822512000 468297 446979 180164 322620 507749 512440 540930 567730 469750 TRUE FALSE 406410.3649 444042.7655 267291.913 395875.8019 497645.7883 532153.8984 488470.6919 446325.3576 414216.6901 0.981154006 1.072005972 0.645294889 0.955721513 1.201414139 1.284723458 1.179263664 1.077516595 1 18.66002616 3.338888329 5.473066422 1.148139625 0.899516586 0.451271756 0.129621649 0.198577804 9.029253504 0.039255125 0.050762397 2182.168734 -3.338888329 -0.248623039 NS(ph)RDGDPLPSSLSCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NSRDGDPLPSSLSCK 15 1 P53602;H3BP35 P53602 MVD Diphosphomevalonate decarboxylase 1 NS(1)RDGDPLPSSLSCK;NS(1)RDGDPLPSSLSCK;NS(1)RDGDPLPSSLSCK 200.74 4.10E-09 1496330000 1666040 1055620 812440 934030 1301430 1039330 1675070 1560660 1341670 TRUE FALSE 1445868.593 1048685.563 1205338.701 1146115.787 1275534.089 1079313.698 1512621.969 1226925.004 1183059.301 1.222143803 0.886418425 1.018832023 0.968772898 1.07816581 0.912307352 1.278568173 1.037078195 1 20.17409096 NS(ph)RFAQDFLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSRFAQDFLIR 11 1 A0A087WVD4;Q9HBK9-2;Q9HBK9 A0A087WVD4 AS3MT Arsenite methyltransferase 1 NS(1)RFAQDFLIR 60.255 0.057415 768850000 67368 82442 34381 50934 73676 91351 71627 60972 57592 TRUE FALSE 58465.14811 81900.43307 51007.7666 62499.34318 72209.99174 94865.33208 64680.62456 47933.61228 50783.53937 1.151261784 1.612735821 1.004415353 1.230700813 1.421917272 1.868033092 1.273653341 0.943880889 1 15.63207333 1.824637862 4.595440478 0.975212266 1.383314698 0.324402129 0.239320848 0.246434971 8.374429357 0.137493868 0.065495053 66.77868485 -1.824637862 0.408102431 NS(ph)SEASSGDFLDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NSSEASSGDFLDLK 14 0 Q9UK76;J3KT51;Q9UK76-2;Q9UK76-3;J3KSH8 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 NS(0.942)S(0.058)EASSGDFLDLK;NS(0.987)S(0.013)EASSGDFLDLK;NS(0.986)S(0.014)EASSGDFLDLK 197.69 2.42E-08 389544000 411073 305872 280057 383839 382582 278038 427924 487398 1007450 TRUE FALSE 356748.6615 303862.7067 415493.5019 470995.5116 374969.3667 288734.3018 386423.9963 383171.7306 888350.4087 0.401585521 0.342052757 0.467713526 0.530191135 0.422096239 0.325022985 0.434990509 0.431329492 1 19.76076933 1.237764255 6.629199583 1.015439194 0.419275607 0.908838748 0.057804338 0.034662611 7.489762831 0.092890103 0.015066043 17.28877629 -1.237764255 -0.596163587 NS(ph)TELAPPLPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NSTELAPPLPVR 12 0 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 NS(0.983)T(0.017)ELAPPLPVR;NS(0.774)T(0.226)ELAPPLPVR;NS(0.756)T(0.244)ELAPPLPVR;NS(0.966)T(0.034)ELAPPLPVR 200.19 1.71E-07 1768900000 1444130 1687010 1473270 1914860 2676170 2521960 2246820 2565830 5186240 TRUE FALSE 1253284.562 1675927.92 2185748.3 2349658.23 2622919.453 2618981.433 2028923.742 2017147.222 4573128.615 0.274054081 0.366472947 0.477954697 0.513796665 0.573550336 0.572689214 0.443662078 0.441086921 1 22.12475006 1.237130428 24.99574185 1.000000655 0.463168351 0.781563866 0.090026651 18.3229793 320118.1699 0.144369843 0.023665111 17.26356275 -1.237130428 -0.536832304 NS(ph)TGSGHSAQELPTIR ddPTM_MDA-MB-175_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(0.839)T(0.08)GS(0.08)GHS(0.001)AQELPTIR 63.936 0.041533 109370000 290230 182970 293770 378850 315650 222770 790090 570900 539640 TRUE FALSE 251875.3702 181768.058 435838.1546 464873.6829 309369.1826 231340.1061 713467.1934 448817.4777 475844.374 0.529322997 0.381990558 0.915925833 0.976944792 0.65014782 0.486167576 1.499370871 0.943202237 1 18.86013029 4.449154876 0.273401628 1.195762194 2.86E-13 0.3166359 0.269928572 13.76728049 1.460956764 1.253769087 6.2066903 28129.03773 -4.449154876 -1.195762194 NS(ph)TPSEPGSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSTPSEPGSGR 11 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 NS(0.712)T(0.287)PS(0.001)EPGSGR 122.55 0.00040753 112400000 348190 317240 175750 213300 346110 371130 335080 354400 347910 TRUE FALSE 302175.8093 315156.0296 260743.2878 261733.0251 339223.0882 385407.6113 302583.9932 278614.3179 306780.4761 0.984990352 1.027301455 0.849934426 0.853160633 1.10575188 1.256297715 0.986320893 0.908187905 1 18.22684715 3.235310212 24.99998994 1.038796195 0.930242608 0.249416064 0.104305165 158.508277 1219142.067 0.035608471 0.042061787 1719.135911 -3.235310212 -0.108553587 NS(ph)WDSPAFSNDVIR ddPTM_MDA-MB-175_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(1)WDSPAFSNDVIR;NS(1)WDSPAFSNDVIR;NS(1)WDSPAFSNDVIR;NS(1)WDSPAFSNDVIR;NS(1)WDSPAFSNDVIR;NS(1)WDSPAFSNDVIR 369.41 4.67E-97 2868880000 1633970 1742460 1041490 1355300 2251650 1986760 1942130 2267280 2105160 TRUE FALSE 1418036.725 1731013.666 1545158.048 1663041.579 2206846.57 2063191.943 1753782.532 1782439.816 1856290.383 0.763908889 0.932512327 0.832390267 0.895895165 1.18884771 1.111459695 0.944778116 0.960216048 1 20.82399098 3.457027609 24.89062676 1.028627982 0.853935986 0.562612021 0.081517105 192.6809257 238679.0514 0.025224645 0.032568838 2864.360059 -3.457027609 -0.174691996 NSASATT(ph)PLSGNSSR ddPTM_MDA-MB-175_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 NSASAT(0.003)T(0.513)PLS(0.481)GNS(0.002)S(0.002)R 124.78 0.0010566 152600000 499500 375480 171560 213840 362450 326980 303100 317010 315510 TRUE FALSE 433489.8094 373013.4472 254526.9898 262395.6403 355237.9541 339559.1322 273705.4087 249219.8785 278210.7672 1.558134553 1.340758486 0.914871097 0.943154152 1.276866304 1.220510391 0.983805952 0.895795231 1 18.08581873 4.425315461 4.071745405 1.031682553 1.520775844 0.669195876 0.125959506 0.128126601 4.322441911 0.035843178 0.1158164 26626.58448 -4.425315461 0.489093291 NSASATTPLS(ph)GNSSR ddPTM_MDA-MB-175_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(0.039)PLS(0.958)GNS(0.002)S(0.001)R 214.39 2.60E-12 165760000 389070 296400 138560 164090 267610 289690 225240 230790 222490 TRUE FALSE 337653.4137 294452.9289 205568.0795 201349.1425 262285.0846 300834.5618 203396.2595 181437.3545 196187.4857 1.721075188 1.500875185 1.047814435 1.026309817 1.336910373 1.533403421 1.03674431 0.924816147 1 17.58187349 4.392828279 3.735324547 1.124798317 1.683617848 0.562308289 0.181276454 0.176300309 4.629922054 0.052280524 0.168830505 24707.47015 -4.392828279 0.558819531 NSASATTPLSGNS(ph)SR ddPTM_MDA-MB-175_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 NSASAT(0.002)T(0.019)PLS(0.184)GNS(0.398)S(0.398)R 60.093 0.08214 0 622600 638970 436130 479190 796510 736470 771070 792720 814340 TRUE FALSE 540321.8325 634772.564 647043.9268 587997.4135 780661.0093 764802.4775 696291.7501 623202.997 718069.6529 0.752464375 0.883998595 0.901087971 0.818858465 1.087166135 1.065081186 0.969671601 0.867886555 1 19.45376427 3.260585017 24.9908586 0.982936095 0.846736729 0.54696117 0.070963413 235.9199644 267694.2187 0.022815657 0.02942989 1822.153742 -3.260585017 -0.136199366 NSASATTPLSGNSS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NSASATTPLSGNSSR 15 0 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 NSASATTPLSGNS(0.247)S(0.753)R;NSASATTPLSGNS(0.104)S(0.896)R;NSASATTPLSGNS(0.12)S(0.88)R;NSASATTPLS(0.012)GNS(0.325)S(0.663)R 240.77 7.82E-18 1450770000 2555480 2626680 1190810 1296230 2797820 2892460 2422020 2525970 2597930 TRUE FALSE 2217766.843 2609425.166 1766689.699 1590558.833 2742148.856 3003734.808 2187132.873 1985810.973 2290805.675 0.968116531 1.139086215 0.771208889 0.694322897 1.197023775 1.311213273 0.954743956 0.866861382 1 21.12742365 3.224273128 24.99991305 1.045000439 0.90203555 0.199139974 0.168886936 525.3586923 919258.0342 0.0574628 0.065452102 1675.996578 -3.224273128 -0.142964889 NSATCHS(ph)EDS(ph)DLEID ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSATCHSEDSDLEID 15 0 Q13371-2;Q13371 Q13371-2 PDCL Phosducin-like protein 2 NSATCHS(1)EDS(1)DLEID;NSATCHS(1)EDS(1)DLEID 144.97 6.86E-06 411650000 665660 593660 272180 365250 628940 611550 569800 604020 598720 TRUE FALSE 577691.3444 589760.2084 403807.1584 448185.595 616425.3245 635076.7242 514540.8837 474855.0235 527940.0037 1.094236732 1.117097027 0.764873197 0.848932818 1.16760488 1.202933515 0.974619995 0.899448839 1 19.01001446 0.304978009 0.008589711 1.46E-05 1.950880058 0.003830373 0.141223061 210154.5657 333.3624651 39914.19019 35893.59119 2.018264165 -0.304978009 1.950865416 NSATCHSEDS(ph)DLEID ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSATCHSEDSDLEID 15 0 Q13371-2;Q13371 Q13371-2 PDCL Phosducin-like protein 1 NSATCHS(0.026)EDS(0.974)DLEID;NSATCHS(0.012)EDS(0.988)DLEID 247.9 2.67E-18 817280000 1384170 1285840 538370 805370 1416040 1403350 1324700 1344340 1309610 TRUE FALSE 1201248.427 1277393.232 798727.5327 988241.5678 1387863.574 1457337.783 1196230.798 1056863.353 1154789.398 1.040231604 1.106169865 0.691665107 0.855776447 1.201832626 1.261994426 1.035886544 0.915200083 1 20.13919834 3.256559166 24.9999284 1.06742831 0.919954574 0.225396305 0.145301629 458.6784966 637098.9295 0.046674801 0.060128477 1805.340671 -3.256559166 -0.147473737 NSATFKS(ph)FEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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;NSATFKS(1)FEDR;NSATFKS(1)FEDR;NSATFKS(1)FEDR;NSATFKS(1)FEDR;NSATFKS(1)FEDR;NSATFKS(1)FEDR 191.52 1.09E-06 19871190000 22258190 20416010 4732750 5611870 19517920 9569580 31469720 23690120 790000 TRUE FALSE 19316713.8 20281895.89 7021523.73 6886130.856 19129551.58 9937727.935 28417791.4 18624172.19 696607.1 27.72971134 29.11525864 10.07960403 9.88524357 27.46103446 14.26590102 40.79457617 26.73554748 1 19.40998565 2.195118029 0.009424093 0.007904937 42.99308512 0.002502188 11.84235697 181362.5152 952.1568721 2210007.71 2132895.016 156.7176925 -2.195118029 42.98518018 NSDEINALQDYGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSDEINALQDYGKR 14 1 J3KNC9;O75596 J3KNC9 CLEC3A C-type lectin domain family 3 member A 0 ; 196.95 3.87E-08 767880000 706510 697480 277860 365120 693020 518420 797970 910660 208231 FALSE TRUE 613142.9134 692898.208 412234.0254 448026.0765 679230.2579 538363.9529 720582.9922 715922.4458 183614.1684 3.339300658 3.773664168 2.245110108 2.440040877 3.699225739 2.932039273 3.924441118 3.899058836 1 17.48631786 3.230550285 24.99643802 3.246532008 2.958080099 0 0.932338361 977.8452087 3051384.082 0.281452424 0.324688311 1700.396825 -3.230550285 -0.288451909 NSDGGS(ph)DPETQKEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSDGGSDPETQKEK 14 1 O75554-2;O75554 O75554-2 WBP4 WW domain-binding protein 4 1 NSDGGS(0.999)DPETQKEK 103.1 0.00068748 224630000 1032600 708030 532710 527800 603740 496150 983600 1098600 504090 TRUE FALSE 896139.2937 703378.9043 790330.3378 647645.0569 591726.7552 515237.2116 888210.6234 863672.9393 444497.0545 2.016074763 1.58241522 1.77803279 1.457028906 1.331227618 1.159146515 1.998237366 1.943034112 1 18.76181433 6.450534668 1.140995942 1.55785003 22.64279058 0.182677267 0.319832034 158.8242067 5.700475048 0.099811089 8235.55677 2821854.832 -6.450534668 21.08494055 NSEGWEQNGLYEFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NSEGWEQNGLYEFFR 15 0 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 ;; 234.9 2.67E-17 269571000 122438 138341 71618 78214 148315 136186 142604 158425 144594 FALSE TRUE 106257.5081 137432.2289 106252.7043 95973.68413 145363.8217 141425.1635 128774.286 124547.0466 127500.262 0.833390507 1.077897619 0.833352831 0.75273323 1.140106062 1.109214689 1.009992324 0.976837574 1 16.96014069 3.231209247 24.99959765 1.038737439 0.885955211 0.44559565 0.095173075 185.903571 632195.8667 0.030005531 0.034696608 1702.978823 -3.231209247 -0.152782228 NSESFAAWCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NSESFAAWCR 10 0 Q96KN1 Q96KN1 FAM84B Protein FAM84B 0 ;; 245.27 3.71E-12 650250000 289246 310280 164611 199258 365750 346500 318830 330747 327300 FALSE TRUE 251021.4082 308241.7502 244217.4302 244502.5744 358472.2906 359830.0792 287909.9157 260019.3279 288606.9669 0.869769053 1.06803295 0.846193815 0.847181816 1.242077745 1.246782374 0.997584774 0.900946123 1 18.1387466 3.278182258 24.99979867 1.05788558 0.914839976 0.312639943 0.122934166 259.9763627 164033.7266 0.040113403 0.051785422 1897.50207 -3.278182258 -0.143045604 NSFLQESWGEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSFLQESWGEEER 13 0 E9PN19;F6V2D4;O00214;O00214-2 E9PN19 LGALS8 Galectin;Galectin-8 0 147.18 9.92E-05 69872000 45777 43938 20776 35204 62298 64585 43822 57130 61417 FALSE TRUE 39727.45347 43649.36838 30823.34309 43197.60626 61058.39168 67069.62674 39572.14918 44913.19409 54156.35223 0.733569597 0.80598797 0.569154713 0.797646158 1.127446535 1.238444319 0.730701895 0.82932458 1 15.72484295 3.466171083 23.5525725 0.959575244 0.708243794 0.423972421 0.151464052 122.0015708 262409.159 0.047797095 0.061782389 2925.304524 -3.466171083 -0.25133145 NSGS(ph)SQGLGGSPGSHSHTTMANK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSGSSQGLGGSPGSHSHTTMANK 23 0 Q9Y3L3;Q6ZT62-2;Q6ZT62;Q9Y3L3-2 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 NS(0.095)GS(0.455)S(0.353)QGLGGS(0.086)PGS(0.011)HSHTTMANK 96.887 0.0022368 98754000 65199 65841 19727 46759 100660 87634 91121 92560 110590 TRUE FALSE 56582.78696 65408.48614 29267.04318 57376.34562 98657.06294 91005.33669 82284.09944 72766.7643 97516.17618 0.580240009 0.670744985 0.300125008 0.588377722 1.011699462 0.933233236 0.843799487 0.746201986 1 16.57335394 3.349961711 5.981315794 0.882365885 0.519318904 0.704628774 0.119668386 0.124972317 6.101108656 0.035788415 0.046289231 2238.523772 -3.349961711 -0.363046981 NSGSSQGLGGS(ph)PGSHSHTTMANK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NSGSSQGLGGSPGSHSHTTMANK 23 0 Q9Y3L3;Q6ZT62-2;Q6ZT62;Q9Y3L3-2 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 NSGSSQGLGGS(0.695)PGS(0.231)HS(0.048)HT(0.01)T(0.016)MANK;NSGSSQGLGGS(0.997)PGS(0.002)HS(0.001)HTTMANK;NSGSSQGLGGS(0.868)PGS(0.041)HS(0.041)HT(0.041)T(0.009)MANK 189.45 2.07E-17 391146000 190217 163441 98530 120801 224065 195435 232472 229569 256803 TRUE FALSE 165079.3415 162367.3453 146179.4376 148230.7134 219606.5449 202953.5109 209926.9012 180477.4559 226444.0419 0.72900722 0.717030768 0.645543315 0.654601959 0.969804915 0.896263418 0.927058621 0.797006865 1 17.78879505 3.244407186 24.99965117 0.902488504 0.685794528 0.790456274 0.058920878 67.65013053 289266.9066 0.017508633 0.021995822 1755.525675 -3.244407186 -0.216693976 NSGTQS(ph)DGEEKQPGLVMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSGTQSDGEEKQPGLVMER 19 1 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 1 NS(0.001)GT(0.018)QS(0.981)DGEEKQPGLVMER;NSGT(0.001)QS(0.999)DGEEKQPGLVMER 221.85 1.56E-19 226750000 471450 365600 246378 266816 446390 367550 400590 519100 392550 TRUE FALSE 409146.688 363198.3495 365527.2249 327400.6508 437507.7123 381689.8863 361740.8435 408094.5046 346143.1862 1.182015722 1.049271989 1.056000059 0.94585323 1.263950093 1.10269363 1.045061286 1.178975987 1 18.40100942 4.754732763 23.30744055 1.087779618 1.182015908 0.108745818 0.08928185 3048.420247 4393219.979 0.021163343 0.485974593 56850.30032 -4.754732763 0.09423629 NSHLINVLMWELEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSHLINVLMWELEK 14 0 A0A087WZK9;B3KS98;O15372;E5RJT0 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 ; 136.48 2.69E-05 398120000 921410 845720 513240 644840 882080 703440 964970 1197220 1060140 FALSE TRUE 799643.3339 840164.4096 761444.5807 791260.7778 864528.3338 730501.792 871387.3579 941203.8198 934811.4569 0.855406005 0.898752795 0.814543484 0.846438896 0.924815723 0.781442917 0.932153058 1.006838131 1 19.83431589 1.99798519 4.982012299 0.996047565 0.856288259 0.710571264 0.039739508 0.090048496 6.510942346 0.017769433 0.01041204 99.53714742 -1.99798519 -0.139759307 NSILQGSVHTGFSLLVQGHVEELWGLATHPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSILQGSVHTGFSLLVQGHVEELWGLATHPSR 32 0 O95834;O95834-2;O95834-3;K7EIK7;A0A0C4DGQ7;C9JRL6;K7ELI8 O95834 EML2 Echinoderm microtubule-associated protein-like 2 0 118.68 2.99E-07 24728000 13651 16329 5196.3 7644.7 18430 21592 15746 22760 15837 FALSE TRUE 11846.98576 16221.73372 7709.248061 9380.545977 18063.27906 22422.65821 14218.95534 17892.95112 13964.7679 0.848348204 1.16161857 0.552049853 0.671729458 1.293489386 1.605659211 1.018202053 1.28129241 1 13.76950398 3.230632195 24.99984185 1.246606184 0.815350467 0.475083441 0.225153803 158.9255973 501122.0942 0.068681568 0.079263431 1700.717557 -3.230632195 -0.431255717 NSKYEYDPDIS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSKYEYDPDISPPR 14 1 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 NSKYEYDPDIS(1)PPR 80.238 0.010208 138350000 310890 261000 94276 115580 292870 224450 295400 334170 40826 TRUE FALSE 269805.0988 259285.4738 139868.1889 141824.2055 287042.46 233084.7367 266752.1535 262710.346 35999.59679 7.49467002 7.202454942 3.885270987 3.939605389 7.973490972 6.474648539 7.409865033 7.297591347 1 15.13569313 4.444282002 24.92481997 5.759188209 7.421622 0.111353121 2.107765911 395.6740568 300314.0895 0.527897403 1.396704614 27815.18815 -4.444282002 1.66243379 NSLDASRPAGLS(ph)PTLTPGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSLDASRPAGLSPTLTPGER 20 1 Q14135-4;G5E9M7;Q14135;Q14135-2;A0A0A6YYI5;A0A075B6E4;Q14135-6;E7ERW0;G5E9M9;E7EWF5;F8W708;E7EQU6;Q14135-5 Q14135-4 VGLL4 Transcription cofactor vestigial-like protein 4 1 NSLDASRPAGLS(0.997)PT(0.003)LTPGER 201.21 7.76E-22 442770000 370940 340510 159310 216500 380500 377360 322300 398910 306160 TRUE FALSE 321919.3392 338273.1674 236352.8489 265659.634 372928.7944 391877.2834 291043.3956 313606.2008 269966.1136 1.192443507 1.253020844 0.8754908 0.984048074 1.381391129 1.451579527 1.078073806 1.161650241 1 18.0424188 3.262783563 24.99956209 1.209545134 1.074537279 0.147327023 0.165047355 517.7004709 534294.9099 0.050960445 0.06575649 1831.401489 -3.262783563 -0.135007855 NSLES(ph)ISSIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSLESISSIDR 11 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 NS(0.144)LES(0.817)IS(0.039)SIDR 229.17 2.87E-12 239760000 238360 169810 138060 244740 282630 223000 185760 295240 382030 TRUE FALSE 206860.1221 168694.5069 204826.2778 300311.9576 277006.216 231578.9543 167745.0238 232105.2236 336866.8486 0.61407088 0.500775032 0.608033348 0.891485638 0.8223018 0.687449523 0.497956461 0.68901177 1 18.36181893 3.982368089 23.26548902 0.740128872 0.556668203 0.296311048 0.13648318 409.3353599 540127.9276 0.038002579 0.067877597 9602.141217 -3.982368089 -0.183460669 NSLESYAFNMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSLESYAFNMK 11 0 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 186.72 9.08E-06 725740000 597220 647520 348810 461740 671710 582600 594910 687130 842990 FALSE TRUE 518295.8638 643266.3985 517495.6827 566585.1243 658344.2852 605012.999 537215.7198 540192.5968 743332.6825 0.69725962 0.865381563 0.696183142 0.762222808 0.885665733 0.813919545 0.722712363 0.726717134 1 19.50364852 NSLFTGDTLGAGQFSFQRPLLVLVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSLFTGDTLGAGQFSFQRPLLVLVDR 26 1 Q8WVM8;Q8WVM8-2;Q8WVM8-3;H0YJY1 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 118.85 0.00046066 137320000 114210 72859 25249 26134 78933 96498 92672 125460 44173 FALSE TRUE 99116.85913 72380.38443 37459.50085 32068.12413 77362.38773 100210.3405 83684.6837 98631.35533 38950.91826 2.544660397 1.858245907 0.96171034 0.823295716 1.98615055 2.572733711 2.148464977 2.532195895 1 15.24936972 3.017532005 24.91121331 2.159569841 1.512071075 0.125777349 0.634005455 397.5995354 564944.8832 0.195556014 0.221695974 1041.194835 -3.017532005 -0.647498766 NSLLAGGDDDTMSVIS(ph)GISSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSLLAGGDDDTMSVISGISSR 21 0 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 1 NSLLAGGDDDTMSVIS(0.982)GIS(0.009)S(0.009)R;NSLLAGGDDDTMSVIS(0.701)GIS(0.15)S(0.15)R 251.12 6.05E-38 80986000 75293 72755 40976 46944 72748 77107 63838 69068 76511 TRUE FALSE 65342.83928 72277.06761 60792.13066 57603.35269 71300.45713 80073.35618 57647.00059 54298.34569 67465.95674 0.968530537 1.071311682 0.901078612 0.853813619 1.056836078 1.186870535 0.854460581 0.804825846 1 16.04187208 NSLLAGGDDDTMSVISGIS(ph)SR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NSLLAGGDDDTMSVISGISSR 21 0 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 1 NSLLAGGDDDTMSVISGIS(0.5)S(0.5)R;NSLLAGGDDDTMSVIS(0.002)GIS(0.499)S(0.499)R;NSLLAGGDDDTMSVISGIS(0.5)S(0.5)R 288.82 1.42E-46 144907000 139907 122903 62169 78987 144644 143790 101116 123307 123657 TRUE FALSE 121417.9355 122095.6421 92234.13634 96922.20559 141765.8674 149321.6943 91309.78588 96938.75763 109038.4103 1.113533617 1.119748919 0.845886656 0.888881315 1.300146132 1.369441226 0.837409364 0.889033115 1 16.73447691 NSLS(ph)PVQATQKPLVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSLSPVQATQKPLVSK 16 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 NSLS(1)PVQATQKPLVSK;NSLS(1)PVQATQKPLVSK 208.27 9.25E-12 1796360000 1128180 1065720 749880 935880 1361350 931540 1583670 1716270 1653120 TRUE FALSE 979088.1546 1058719.215 1112524.476 1148385.858 1334261.798 967376.9466 1430085.927 1349259.017 1457690.037 0.67167102 0.726299274 0.763210592 0.787812106 0.915326143 0.663636934 0.981063114 0.925614488 1 20.47525255 -1.999999999 0.148092601 2.184652845 0.563328968 0.598004021 0.07843761 102.0035298 1.275486138 34.66849938 1.294167692 0.01 1.999999999 -1.621323877 NSMDRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSMDRPK 7 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 ; 75.854 0.038615 113224000 256500 227900 139502 170437 200248 228450 269950 300880 273630 FALSE TRUE 222602.8751 226402.9099 206965.6338 209137.3258 196263.4566 237238.6193 243770.2905 236539.1535 241281.7731 0.922584712 0.938334077 0.857775667 0.866776313 0.813420152 0.98324302 1.01031374 0.980344062 1 17.88035941 2.624179212 7.227931282 0.994190401 0.881291801 0.726389659 0.03471793 0.147715174 8.397509618 0.012720768 0.011192422 420.9002773 -2.624179212 -0.1128986 NSMFHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 NSMFHNR 7 0 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;Q99873-5;H0YDE4;E9PNR9;E9PMW9;E9PMZ2 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ;;;;;;;; 152.34 0.0018205 951140000 1080588 1258764 293302.6 657605.1 1680325 1684088 1295543 1381767 1397956 FALSE TRUE 937785.5579 1250495.096 435144.7184 806924.3888 1646889.82 1748875.955 1169901.439 1086286.88 1232691.234 0.760762738 1.014443083 0.353003823 0.654603818 1.336011626 1.41874616 0.949062836 0.881231934 1 20.23338005 3.258685055 24.97325677 1.090028909 0.693991794 0.45658644 0.227329207 257.4754445 319510.0463 0.071751646 0.09251346 1814.19955 -3.258685055 -0.396037115 NSMPTVSFLDQDQS(ph)PPR ddPTM_MDA-MB-175_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 377.42 4.09E-105 540200000 305145 302956 145957 199574 362491 362217 311215 369436 327172 TRUE FALSE 264819.3151 300965.8621 216542.2934 244890.327 355278.1383 376151.7224 281033.4172 290434.9864 288494.0989 0.917936679 1.043230566 0.750595226 0.848857318 1.231491873 1.303845465 0.974139223 1.006727651 1 18.13818228 3.257075931 24.99561681 1.091524323 0.89112032 0.418210433 0.124457848 283.2502584 382384.5697 0.039284758 0.0506217 1807.490117 -3.257075931 -0.200404003 NSNILEDLETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NSNILEDLETLR 12 0 B0YIW6;P48444;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 ;;;; 218.75 7.81E-11 244299000 409793 406141 188140 254958 485098 449246 427735 474906 431465 FALSE TRUE 355637.8168 403473.033 279125.1333 312850.1107 475445.4989 466528.7843 386253.3255 373351.0476 380457.6992 0.934763096 1.060493805 0.733656156 0.822299329 1.249667177 1.226230367 1.0152333 0.981320784 1 18.53737653 3.259105857 24.999967 1.080986912 0.88912763 0.418835078 0.120393301 285.5240047 347430.6238 0.038208182 0.049269005 1815.958238 -3.259105857 -0.191859282 NSNLVGAAHEELQQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 288.72 6.47E-37 14978340000 6992430 6336380 2491400 4003100 8753740 8379870 6517350 7816020 7073080 FALSE TRUE 6068362.659 6294755.903 3696249.373 4912065.039 8579557.7 8702249.021 5885298.4 6144624.947 6236908.54 0.972976054 1.009275006 0.592641266 0.787580098 1.375610632 1.395282449 0.943624291 0.985203632 1 22.57239967 3.271490757 24.99997486 1.118644745 0.834952207 0.38405647 0.187223307 237.6264485 180400.2106 0.059531161 0.076849296 1868.48991 -3.271490757 -0.283692538 NSNS(ph)PPS(ph)PSSMNQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NSNSPPSPSSMNQR 14 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 2 NSNS(1)PPS(0.92)PS(0.079)S(0.001)MNQR;NSNS(1)PPS(1)PSSMNQR;NSNS(1)PPS(1)PSSMNQR;NSNS(1)PPS(1)PSSMNQR;NSNS(1)PPS(0.997)PS(0.002)SMNQR;NSNS(1)PPS(0.998)PS(0.002)SMNQR 408.27 2.10E-132 3707290000 2812490 2819000 1585508 1943132 3495160 3211400 2889740 3377440 3282330 TRUE FALSE 2440812.321 2800481.803 2352264.972 2384349.82 3425613.154 3334944.636 2609493.46 2655200.739 2894296.687 0.84331794 0.967586294 0.812724204 0.823809746 1.183573602 1.152246987 0.901598468 0.917390657 1 21.46478139 3.285114939 24.99997009 1.013128478 0.865901654 0.419530809 0.097543204 155.7771938 83652.22396 0.031378105 0.040508832 1928.035114 -3.285114939 -0.147226824 NSNS(ph)PPSPSSMNQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NSNSPPSPSSMNQR 14 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 NSNS(1)PPSPSSMNQR;NSNS(1)PPSPSSMNQR;NSNS(1)PPSPSSMNQR;NSNS(1)PPSPSSMNQR 168.42 1.37E-05 851360000 893180 889260 460232 549045 1004940 953350 898300 1070810 929410 TRUE FALSE 775144 883418.3925 682801.7346 673714.0589 984943.6601 990025.9914 811183.0043 841825.6146 819536.2086 0.945832523 1.07794919 0.833156275 0.822067472 1.20183056 1.208032032 0.989807401 1.027197585 1 19.64444817 3.243609867 24.99999964 1.07706699 0.924865862 0.397766103 0.100890835 155.1850767 768352.1121 0.031896638 0.03990702 1752.305671 -3.243609867 -0.152201128 NSNSPPS(ph)PSSMNQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 NSNSPPSPSSMNQR 14 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 NSNS(0.002)PPS(0.987)PS(0.009)S(0.002)MNQR;NSNSPPS(0.99)PS(0.01)SMNQR;NSNSPPS(0.984)PS(0.016)SMNQR;NSNSPPS(0.999)PSSMNQR;NSNSPPS(1)PSSMNQR;NSNSPPS(0.998)PS(0.001)SMNQR;NSNSPPS(0.997)PS(0.003)SMNQR;NSNSPPS(0.963)PS(0.034)S(0.002)MNQR 368.02 5.16E-97 3624353000 1982878 1898014 971373 1210294 2350961 2209920 1946179 2214903 1969585 TRUE FALSE 1720835.648 1885545.821 1441132.232 1485109.751 2304181.476 2294937.052 1757438.86 1741263.23 1736742.905 0.990840753 1.0856793 0.829790194 0.85511203 1.326725717 1.321402866 1.011916534 1.00260276 1 20.72795277 3.268934256 24.99999874 1.116686697 0.942838323 0.326280219 0.136143952 305.2250631 251223.2643 0.043877276 0.056638454 1857.523241 -3.268934256 -0.173848374 NSPGLGS(ph)LVSPHGPHMPPAASIPPPPGLGGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSPGLGSLVSPHGPHMPPAASIPPPPGLGGVK 32 0 Q8ND24;E9PN76;Q8ND24-2 Q8ND24 RNF214 RING finger protein 214 1 NS(0.221)PGLGS(0.385)LVS(0.385)PHGPHMPPAAS(0.009)IPPPPGLGGVK 119.36 1.04E-06 366360000 896780 716230 246800 487860 908670 674730 807060 1058200 853880 TRUE FALSE 778268.2508 711525.038 366153.3055 598636.0695 890589.2448 700687.2997 728791.4454 831912.1649 752935.2791 1.033645617 0.945001593 0.486301168 0.795069757 1.182823105 0.930607609 0.96793372 1.104891998 1 19.52216633 3.263091793 24.8474613 1.035175365 0.800811073 0.33391232 0.155386876 249.7838573 253002.5194 0.045924125 0.059258794 1832.701742 -3.263091793 -0.234364291 NSPNNISGISNPPGT(ph)PR ddPTM_MDA-MB-175_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 182.17 2.26E-09 181460000 122230 115830 54349 81278 164420 143870 118530 150100 119490 TRUE FALSE 106076.9958 115069.1051 80632.35819 99733.41216 161148.3637 149404.772 107034.9788 118002.2831 105364.0283 1.006766707 1.092109963 0.765274064 0.946560356 1.529443836 1.417986521 1.015858833 1.119948477 1 16.68502288 NSPNNMSLSNQPGT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSPNNMSLSNQPGTPR 16 0 H0Y9V4;A0A087X159;P81877-4;P81877-5;P81877-3;P81877 H0Y9V4 SSBP2 Single-stranded DNA-binding protein 2 1 NSPNNMSLSNQPGT(1)PR 177.61 3.27E-08 175020000 102370 118690 40064 71690 148690 129390 106990 122240 101800 TRUE FALSE 88841.54513 117910.3176 59439.08441 87968.31021 145731.3599 134367.717 96614.12627 96099.92727 89765.31997 0.989709001 1.313539768 0.662160893 0.979981024 1.623470623 1.496877826 1.076296796 1.070568537 1 16.45387056 NSPQS(ph)SPTSTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSPQSSPTSTPK 12 0 Q9Y6Y0 Q9Y6Y0 IVNS1ABP Influenza virus NS1A-binding protein 1 NSPQS(0.473)S(0.473)PT(0.053)S(0.001)TPK 176.4 2.63E-05 209040000 498440 597710 306120 431180 721240 523710 697470 885520 724520 TRUE FALSE 432569.8911 593783.6037 454160.6559 529086.0092 706888.7351 543857.4626 629829.4668 696158.4391 638868.071 0.677087979 0.929430708 0.710883321 0.828161608 1.106470596 0.851282898 0.985852158 1.089674803 1 19.28515851 3.47571863 0.489204153 1.065192348 0.695039221 0.497126823 0.102802011 1.284275251 0.777736977 0.143139182 0.297428969 2990.326639 -3.47571863 -0.370153127 NSPQSS(ph)PTSTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NSPQSSPTSTPK 12 0 Q9Y6Y0 Q9Y6Y0 IVNS1ABP Influenza virus NS1A-binding protein 1 NSPQS(0.028)S(0.963)PT(0.009)STPK;NSPQSS(0.971)PT(0.02)S(0.008)TPK;NSPQS(0.038)S(0.957)PT(0.005)STPK 227.34 1.38E-11 444230000 1262430 1469160 772610 1017770 1733540 1292460 1720450 2133610 1748490 TRUE FALSE 1095596.677 1459508.991 1146246.78 1248870.234 1699045.946 1342181.773 1553601.024 1677354.105 1541785.504 0.710602528 0.946635565 0.743454117 0.810015551 1.10199891 0.870537289 1.00766353 1.087929612 1 20.55617064 3.254413825 24.91911411 1.015312222 0.808729411 0.595899716 0.086249084 161.1529806 253309.29 0.024085667 0.030989763 1796.444584 -3.254413825 -0.206582812 NSPRPS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NSPRPSPK 8 1 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 NS(0.002)PRPS(0.998)PK;NSPRPS(1)PK;NS(0.001)PRPS(0.999)PK 63.408 0.044512 361776000 348730 286758 225784 254288 358630 350480 468730 470310 571670 TRUE FALSE 302644.4469 284874.2678 334973.8976 312027.9769 351493.9646 363963.1924 423272.6367 369737.8665 504087.8238 0.600380395 0.565128246 0.664514955 0.618995267 0.697287155 0.722023376 0.839680343 0.733479066 1 18.94331558 -2 0.265848186 3.21518368 0.557180055 0.812833362 0.054881956 33.95124009 0.547839552 40.13482161 0.14697273 0.01 2 -2.658003625 NSPTFKS(ph)FEEKVENLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSPTFKSFEEKVENLK 16 2 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 1 NS(0.001)PT(0.062)FKS(0.937)FEEKVENLK;NS(0.001)PT(0.208)FKS(0.791)FEEKVENLK 125.04 4.13E-05 1097240000 2416000 1219950 410390 1145640 1000670 371850 2538800 1917160 140204 TRUE FALSE 2096719.479 1211936.068 608855.9767 1405775.072 980758.6248 386155.3101 2292587.567 1507190.253 123629.2428 16.95973728 9.80298868 4.924854045 11.37089446 7.933063426 3.123494905 18.54405571 12.19121155 1 16.91566051 3.262624573 24.37277577 9.489651601 10.27880286 0.019455377 5.568008711 2160.442854 2188148.845 1.649062613 2.127641441 1830.731156 -3.262624573 0.789151255 NSPTFKS(ph)FEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NSPTFKSFEER 11 1 Q16890-5;E9PPQ1;J3KNE7;Q16890;E9PNK6 Q16890-5 TPD52L1 Tumor protein D53 1 NSPT(0.005)FKS(0.995)FEER;NSPT(0.042)FKS(0.958)FEER;NS(0.084)PT(0.288)FKS(0.628)FEER 132.23 0.00011318 1252170000 4580820 2866980 904320 1064600 3007360 1887700 5225350 3700580 636253 TRUE FALSE 3975453.031 2848146.62 1341652.177 1306333.701 2947519.42 1960321.041 4718596.361 2909239.765 561035.8952 7.085915652 5.076585374 2.391383846 2.32843159 5.253709157 3.494109838 8.410507067 5.185478844 1 19.09773355 NSQAQS(ph)PQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSQAQSPQSK 10 0 A8MXZ4 A8MXZ4 GPRC5C 1 NSQAQS(0.995)PQS(0.005)K 159.66 0.0039968 0 156810 111030 93558 141960 146760 191170 123340 224060 258900 TRUE FALSE 136087.1612 110300.6366 138802.9617 174194.1877 143839.7631 198524.4336 111378.5058 176146.5126 228293.1369 0.596107106 0.483153537 0.608003217 0.763028578 0.630066085 0.869603161 0.487874963 0.771580412 1 17.80052796 1.357882913 3.301577416 1.013609588 0.640358116 0.505736113 0.115548958 0.229895835 3.629492877 0.18394509 0.029634493 22.79727368 -1.357882913 -0.373251471 NSQDDYDEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSQDDYDEER 10 0 O76094-2;O76094;R4GNC1;D6RDY6 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 163.84 0.0073165 0 263360 228600 120980 147780 235320 234500 226940 257290 267250 FALSE TRUE 228556.3087 227098.3115 179486.3327 181335.7077 230637.5924 243521.3667 204931.3937 202270.5357 235656.0095 0.969872609 0.963685637 0.761645472 0.769493246 0.978704481 1.033376434 0.869620911 0.858329631 1 17.84632295 3.204152594 24.99806348 0.935186293 0.865672657 0.174557964 0.085944476 412.7000082 299832.812 0.028535893 0.032358163 1600.12015 -3.204152594 -0.069513636 NSQEDS(ph)EDS(ph)EDKDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK 252.44 6.86E-25 28296820000 28983140 19018250 19312910 14029000 19517490 13896770 30834050 31856290 28385720 TRUE FALSE 25152944.62 18893317.86 28652697.87 17214498.87 19129130.13 14431387.73 27843768.58 25044070.29 25029992.52 1.004912191 0.754827148 1.144734576 0.687754855 0.764248336 0.576563805 1.112416177 1.000562436 1 24.57715452 2.199117605 24.99999776 1.033045907 0.825030549 0.285423803 0.160630221 208.5361673 132174.186 0.064858258 0.043728158 158.1676294 -2.199117605 -0.208015358 NSQEDS(ph)EDSEDKDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 NSQEDS(0.996)EDS(0.004)EDKDVK;NSQEDS(0.999)EDS(0.001)EDKDVK;NSQEDS(0.848)EDS(0.152)EDKDVK;NSQEDS(1)EDSEDKDVK;NSQEDS(0.949)EDS(0.051)EDKDVK;NSQEDS(0.994)EDS(0.006)EDKDVK;NSQEDS(0.999)EDS(0.001)EDKDVK 306.39 3.20E-45 14041590000 9859510 6242410 6749910 5459720 6218540 3821776 10005620 11295390 9061850 TRUE FALSE 8556550.773 6201403.198 10014189.05 6699432.873 6094803.22 3968802.196 9035276.512 8879958.749 7990568.416 1.070831301 0.77609037 1.25325115 0.83841756 0.762749645 0.496685841 1.130742651 1.111305014 1 22.9298667 NSQEDSEDS(ph)EDKDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 NSQEDS(0.447)EDS(0.552)EDKDVK 149.44 2.03E-06 5389900000 1135100 645670 732320 574400 708920 422840 1104900 1122300 886780 TRUE FALSE 985093.659 641428.5513 1086472.401 704826.2992 694813.879 439106.9284 997746.9681 882304.8787 781945.8786 1.259797751 0.820297886 1.389447059 0.901374786 0.888570294 0.561556676 1.275979573 1.1283452 1 19.57670923 NSQEDSEDSEDKDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ;;; 188.27 2.79E-07 2415070000 1537720 931620 1100020 822550 924000 638930 1412360 1626730 1462340 FALSE TRUE 1334506.406 925500.1269 1631993.351 1009322.549 905614.2078 663510.0505 1275389.545 1278866.449 1289463.831 1.034931243 0.717740277 1.265637168 0.782745917 0.702318426 0.514562747 0.989085164 0.991781559 1 20.29833988 NSQGSEMFGDDDKRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSQGSEMFGDDDKRK 15 2 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 110.04 0.00053558 82605000 86954 63952 47422 45909 66980 60071 84744 82983 52744 FALSE TRUE 75462.80859 63531.8951 70355.43782 56333.34013 65647.22904 62381.97024 76525.53992 65237.73122 46508.66441 1.622553766 1.366022781 1.512738298 1.211243987 1.411505359 1.341297821 1.645403946 1.402700595 1 15.50521189 1.245572326 5.813617937 0.983982383 1.43764159 0.535429048 0.128923702 0.101834719 12.02227612 0.181861459 0.030773366 17.60241785 -1.245572326 0.453659207 NSQKHS(ph)PTSEPTPPGDALPPVS(ph)SPHTHR ddPTM_MDA-MB-175_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(0.266)QKHS(0.368)PT(0.164)S(0.194)EPT(0.008)PPGDALPPVS(0.519)S(0.478)PHT(0.003)HR 114.75 0.00052567 534810000 280200 358600 106560 229310 521310 420410 445780 525140 391080 TRUE FALSE 243170.8601 356244.333 158092.7724 281378.3403 510936.9509 436583.4447 402548.3242 412842.8976 344846.9679 0.70515586 1.033050501 0.458443272 0.815951325 1.48163388 1.266020831 1.167324528 1.197177113 1 18.39559676 3.365098736 7.200382479 1.216092172 0.742514294 0.630135901 0.17939058 0.143734532 8.547760666 0.05077132 0.065611406 2317.921564 -3.365098736 -0.473577877 NSQKHS(ph)PTSEPTPPGDALPPVSSPHTHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NSQKHSPTSEPTPPGDALPPVSSPHTHR 28 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 NS(0.294)QKHS(0.646)PT(0.045)S(0.015)EPTPPGDALPPVSSPHTHR;NS(0.102)QKHS(0.638)PT(0.13)S(0.13)EPTPPGDALPPVSSPHTHR;NS(0.121)QKHS(0.803)PT(0.057)S(0.019)EPTPPGDALPPVSSPHTHR;NS(0.049)QKHS(0.714)PT(0.187)S(0.049)EPTPPGDALPPVSSPHTHR 161.61 4.55E-12 8149950000 2448390 2728060 405969 1516660 4116430 3521520 3430510 3827410 2939980 TRUE FALSE 2124829.058 2710139.194 602296.9663 1861040.834 4034521.097 3656995.153 3097819.668 3008948.156 2592418.914 0.81963183 1.045409436 0.232330108 0.717878127 1.556276679 1.410649773 1.194953351 1.160672043 1 21.30586743 3.287355401 12.01931666 1.253535651 0.694079092 0.56113615 0.246224095 0.642343044 156.6081505 0.073316184 0.094585508 1938.007266 -3.287355401 -0.559456559 NSQKHSPT(ph)SEPTPPGDALPPVSSPHTHR ddPTM_MDA-MB-175_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 1 NS(0.218)QKHS(0.218)PT(0.277)S(0.277)EPT(0.008)PPGDALPPVSSPHTHR 89.039 0.0017922 4106500000 1499500 1678800 212010 901630 2497900 2199900 2092400 2133500 1823200 TRUE FALSE 1301337.276 1667771.852 314538.7451 1106358.872 2448196.677 2284531.577 1889479.37 1677267.628 1607663.373 0.809458807 1.037388722 0.195649631 0.688178191 1.522829168 1.421026077 1.175295402 1.043295292 1 20.61653392 3.264640348 23.02329238 1.213977062 0.673217822 0.529893014 0.256937291 79.17536661 69895.08795 0.078120572 0.10080008 1839.248236 -3.264640348 -0.540759239 NSQPNRYT(ph)NR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NSQPNRYTNR 10 1 P50750;P50750-2 P50750 CDK9 Cyclin-dependent kinase 9 1 NSQPNRYT(1)NR;NSQPNRYT(1)NR;NSQPNRYT(1)NR 137.62 0.00013942 662220000 617764 778900 271977 386309 774850 620087 616064 600749 655567 TRUE FALSE 536124.9222 773783.3546 403505.9869 474026.3628 759432.001 643942.1481 556318.2081 472283.5014 578066.6161 0.927444878 1.338571253 0.698026794 0.820020305 1.313744783 1.113958375 0.962377333 0.817005321 1 19.14087623 2.001579472 21.89625326 0.893709495 1.036749974 0.064583439 0.201278495 26.6127179 368916.6694 0.084014417 0.055982715 100.364349 -2.001579472 0.143040479 NSRDGDPLPS(ph)SLSCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSRDGDPLPSSLSCK 15 1 P53602;H3BP35 P53602 MVD Diphosphomevalonate decarboxylase 1 NS(0.126)RDGDPLPS(0.856)S(0.017)LSCK 118.62 0.00072773 118350000 606270 458310 331540 339320 480210 415590 576530 589870 513610 TRUE FALSE 526149.8834 455299.3314 491873.8529 416367.7922 470654.7605 431578.0162 520618.2093 463730.8909 452891.6109 1.161756744 1.005316328 1.086074109 0.919354173 1.039221635 0.952938862 1.149542621 1.023933497 1 18.78880629 4.743824268 24.39788922 1.025340003 1.161756826 0.319152008 0.063968383 509.4949404 2361487.999 0.014840411 0.123158449 55440.13355 -4.743824268 0.136416823 NSRPEANEALER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSRPEANEALER 12 1 Q9Y696 Q9Y696 CLIC4 Chloride intracellular channel protein 4 0 ; 197.25 1.80E-07 1089960000 1242630 1117010 501700 722430 1348220 1252610 1075110 1314130 1098660 FALSE TRUE 1078413.297 1109672.288 744323.7981 886468.7732 1321393.06 1300798.717 970845.9977 1033113.526 968777.6664 1.113169032 1.145435456 0.768312301 0.915038408 1.363979689 1.34272162 1.002134991 1.066409313 1 19.88580608 3.309485749 24.99999991 1.14190945 0.981400705 0.215570514 0.159547439 85.12288328 30002.5138 0.04989449 0.064413508 2039.321738 -3.309485749 -0.160508744 NSS(ph)PAPPQPAPGK ddPTM_MDA-MB-175_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;NSS(1)PAPPQPAPGK;NSS(1)PAPPQPAPGK;NSS(1)PAPPQPAPGK;NSS(1)PAPPQPAPGK;NSS(1)PAPPQPAPGK 267.46 1.56E-24 2888080000 5570070 3245100 2425280 3115960 3834470 2960240 3762270 4518380 7065740 TRUE FALSE 4833971.137 3223782.724 3598153.52 3823486.342 3758171.549 3074122.348 3397405.634 3552159.599 6230436.267 0.775863989 0.517424878 0.577512291 0.61367875 0.603195569 0.493404028 0.545291772 0.570130156 1 22.57090176 1.237722855 24.99013593 1.000000491 0.580245372 0.741427762 0.076543764 9.815328425 292608.5044 0.103025172 0.017560523 17.28712829 -1.237722855 -0.419755119 NSS(ph)VPFGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSSVPFGSK 9 0 Q9BXT8-2 Q9BXT8-2 RNF17 RING finger protein 17 1 NS(0.004)S(0.513)VPFGS(0.483)K;NSS(0.5)VPFGS(0.5)K 70.363 0.0552 1694870000 1221830 1164610 713610 1081500 1036600 1147520 1192540 1387160 2059650 TRUE FALSE 1060362.07 1156959.6 1058714.183 1327071.105 1015973.688 1191665.837 1076887.654 1090526.629 1816160.523 0.58384821 0.637035981 0.582940863 0.730701437 0.559407428 0.656145655 0.592947397 0.600457181 1 20.79246029 1.236931704 24.99964525 1.000000472 0.618337189 0.859078882 0.048630472 13.62514916 209043.8569 0.067146181 0.010828618 17.25566514 -1.236931704 -0.381663283 NSSLGS(ph)PSNLCGS(ph)PPGSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSSLGSPSNLCGSPPGSIR 19 0 Q9C0B0 Q9C0B0 UNK RING finger protein unkempt homolog 2 NSSLGS(0.998)PS(0.002)NLCGS(0.98)PPGS(0.02)IR;NS(0.012)S(0.02)LGS(0.968)PSNLCGS(0.988)PPGS(0.012)IR 166.85 2.79E-11 469370000 365380 413990 214920 287420 578010 584630 510970 573470 519130 TRUE FALSE 317094.1072 411270.4724 318856.0309 352683.1039 566508.7319 607121.0944 461416.208 450837.9032 457759.0428 0.692709652 0.898443141 0.696558672 0.770455788 1.237569723 1.32628968 1.00798928 0.984880387 1 18.80422886 3.254413865 24.92270741 1.098533074 0.769250118 0.67225093 0.120121679 160.7761546 252752.8067 0.038257212 0.04921981 1796.44475 -3.254413865 -0.329282956 NSSLGSPSNLCGS(ph)PPGSIR ddPTM_MDA-MB-175_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(0.999)PPGS(0.001)IR;NSSLGSPSNLCGS(1)PPGSIR;NSSLGSPSNLCGS(1)PPGSIR 364.79 8.56E-108 3535110000 1131490 1344140 618537 855392 2068710 1883630 1564810 1903560 1636040 TRUE FALSE 981960.7297 1335310.256 917663.5621 1049621.827 2027546.718 1956094.465 1413054.967 1496498.508 1442629.215 0.680674368 0.925608772 0.636104934 0.727575607 1.405452418 1.35592323 0.979499758 1.037341052 1 20.46026911 3.264601695 24.99985178 1.137658755 0.747971526 0.629329165 0.157195852 166.9273883 160251.825 0.048916117 0.063129829 1839.084546 -3.264601695 -0.389687229 NSSNTSVGS(ph)PSNTIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NSSNTSVGSPSNTIGR 16 0 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 NSSNTSVGS(1)PSNTIGR;NSSNTS(0.009)VGS(0.99)PSNTIGR;NSSNTS(0.001)VGS(0.999)PSNTIGR 393.03 1.52E-121 297570000 864430 559627 235455 318246 615443 599850 506705 593276 546200 TRUE FALSE 750193.3853 555950.7734 349321.8255 390508.6184 603196.8884 622926.6177 457564.8271 466408.5443 481628.8582 1.557617183 1.154313667 0.725292556 0.810808181 1.252410187 1.293374778 0.950036152 0.968398252 1 18.87756231 4.668121423 3.667073886 1.00436037 1.582495818 0.504921983 0.17281506 0.209107648 4.797874974 0.045994766 0.284426038 46571.62832 -4.668121423 0.578135448 NSSQSGGKPGS(ph)SPITK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSSQSGGKPGSSPITK 16 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 NSSQSGGKPGS(0.657)S(0.343)PITK 95.814 0.0021952 640910000 774290 385100 228020 280950 489980 349290 533340 605690 506540 TRUE FALSE 671965.6147 382570.2527 338291.2347 344743.9916 480230.3566 362727.4123 481616.7689 476167.907 446657.4183 1.50443178 0.8565183 0.757384118 0.771830888 1.075164851 0.812093111 1.078268824 1.066069626 1 18.7688092 NSSQSGGKPGSS(ph)PITK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NSSQSGGKPGSSPITK 16 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 NSSQSGGKPGS(0.5)S(0.5)PITK;NSSQSGGKPGS(0.21)S(0.79)PITK;NSSQSGGKPGS(0.285)S(0.715)PITK 201.85 1.93E-11 1445040000 2632460 1253860 758670 899380 1451430 1128400 1821580 1962890 1735730 TRUE FALSE 2284573.741 1245623.311 1125565.35 1103597.975 1422549.383 1171810.278 1644923.452 1543141.249 1530533.977 1.492664505 0.813848846 0.735406967 0.721054215 0.929446457 0.765621865 1.074738279 1.008237172 1 20.54560364 2.216964783 24.96301167 1.025574051 0.889722004 0.054433121 0.221587457 658.1898271 760807.6021 0.08917262 0.06018178 164.8028746 -2.216964783 -0.135852047 NSSS(ph)PVS(ph)PASVPGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSSSPVSPASVPGQR 15 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 2 NS(0.001)S(0.049)S(0.951)PVS(1)PASVPGQR;NSS(0.181)S(0.819)PVS(1)PASVPGQR 271.82 3.06E-33 692220000 841160 791150 487370 552310 891850 929160 791800 923330 1083630 TRUE FALSE 729998.5748 785952.8836 723063.7622 677720.427 874103.9299 964905.3864 715011.3579 725883.0649 955524.4959 0.763976829 0.822535568 0.756719231 0.709265362 0.914789661 1.00981753 0.748292023 0.75966976 1 19.86593333 3.235300985 24.99998636 0.866456844 0.766910412 0.304308437 0.089825836 140.595053 1078304.167 0.028972974 0.034233136 1719.099384 -3.235300985 -0.099546432 NSSS(ph)PVSLDAALPESSNVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSSSPVSLDAALPESSNVYR 20 0 Q70EL1-7;Q70EL1;H7C296;H7C1E9;Q70EL1-6;R4GN32 Q70EL1-7 USP54 Inactive ubiquitin carboxyl-terminal hydrolase 54 1 NSS(0.001)S(0.999)PVSLDAALPESSNVYR 311.97 2.80E-66 61788000 93102 74807 39538 50296 67137 75081 63780 67860 107410 TRUE FALSE 80798.33481 74315.58789 58658.70905 61716.47553 65801.10505 77969.41465 57594.62542 53348.66709 94712.11216 0.853094002 0.78464714 0.619336933 0.651621784 0.694748576 0.823225381 0.608102006 0.563271855 1 16.53126131 1.223155091 24.91319216 1.000000877 0.691399497 0.491389969 0.095661439 777.9133332 1257935.476 0.595955541 0.025088542 16.71687486 -1.223155091 -0.30860138 NSSS(ph)PVSPASVPGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NSSSPVSPASVPGQR 15 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 NSS(0.011)S(0.989)PVSPASVPGQR;NSS(0.027)S(0.973)PVSPASVPGQR;NSS(0.109)S(0.891)PVSPASVPGQR;NSS(0.016)S(0.984)PVSPASVPGQR 307.89 4.67E-56 4047920000 3592020 3092150 1732700 2268990 3589380 3493480 3222170 3497060 3983160 TRUE FALSE 3117325.456 3071837.463 2570639.516 2784198.859 3517958.361 3627876.436 2909684.449 2749240.933 3512275.362 0.887551554 0.874600407 0.731901474 0.792705176 1.001618039 1.032913443 0.828432896 0.782752105 1 21.74397453 3.272114135 24.99998203 0.90847975 0.819055516 0.249126831 0.088704583 355.7470098 265056.9023 0.028587115 0.036903561 1871.173829 -3.272114135 -0.089424234 NSSSPVS(ph)PASVPGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSSSPVSPASVPGQR 15 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 NSSS(0.01)PVS(0.99)PASVPGQR 144.5 9.39E-06 0 83387 71173 47860 58582 85200 79775 78669 84030 90465 TRUE FALSE 72367.19667 70705.45988 71005.25608 71883.93847 83504.68669 82843.99587 71039.69249 66060.83842 79770.33076 0.907194392 0.886362877 0.890121119 0.901136272 1.046813845 1.038531432 0.890552813 0.828137953 1 16.28356464 3.44517451 24.99253959 0.945671074 0.89405441 0.173396616 0.065746893 481.6871194 376831.4492 0.022096243 0.028526393 2787.240922 -3.44517451 -0.051616664 NSSTETDQQPHS(ph)PDSSSSVHSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSSTETDQQPHSPDSSSSVHSIR 23 0 Q92613 Q92613 JADE3 Protein Jade-3 1 NSSTETDQQPHS(0.992)PDS(0.006)S(0.002)SSVHSIR;NSSTETDQQPHS(0.97)PDS(0.006)S(0.007)S(0.009)S(0.009)VHSIR 190.31 1.01E-17 458520000 215405 163018 46601 94569 227343 210252 184270 205583 155542 TRUE FALSE 186938.6835 161947.124 69137.39947 116042.3368 222819.3191 218340.5305 166399.5238 161620.6753 137154.002 1.362983805 1.180768492 0.504085907 0.846073284 1.62459218 1.591937001 1.213231268 1.17838833 1 17.06543719 3.261765268 24.99980021 1.309110182 0.954756281 0.266857667 0.285578821 348.5277961 375487.9806 0.088653533 0.114379184 1827.112411 -3.261765268 -0.354353902 NSSYFVEWIPNNVK ddPTM_MDA-MB-175_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 ; 296.17 2.88E-43 1449130000 2915000 2575310 1303800 1722850 3052600 2558460 3110300 3522200 3243500 FALSE TRUE 2529775.364 2558392.619 1934322.041 2114049.425 2991859.232 2656885.612 2808663.585 2769004.94 2860057.125 0.884519173 0.894525007 0.676322869 0.739163357 1.046083732 0.928962428 0.98203059 0.968164207 1 21.44761253 3.240192069 24.99999993 0.979907091 0.796745638 0.644025874 0.068801846 29.31175325 449161.6533 0.021182385 0.025919136 1738.569549 -3.240192069 -0.183161452 NST(ph)PSEPGSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NSTPSEPGSGR 11 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 NS(0.03)T(0.967)PS(0.003)EPGSGR;NS(0.019)T(0.978)PS(0.002)EPGSGR;NS(0.009)T(0.96)PS(0.031)EPGSGR 203.97 3.89E-07 3069580000 2490350 2520670 1356970 1528650 2625400 2624530 2603740 2731750 2545670 TRUE FALSE 2161243.938 2504111.553 2013205.231 1875753.346 2573159.677 2725497.367 2351229.696 2147586.521 2244723.793 0.962810634 1.115554422 0.896861002 0.835627685 1.146314609 1.214179391 1.04744722 0.956726404 1 21.09810651 3.223564166 24.99929594 1.063558432 0.960355432 0.261223752 0.099403191 431.1618461 718751.11 0.033563276 0.038207679 1673.26284 -3.223564166 -0.103203 NSTFSEIFKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSTFSEIFKK 10 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 154.66 2.26E-05 4488000000 3433600 3254600 1766100 1675920 3550500 2382800 3644500 3756300 2387600 FALSE TRUE 2979841.06 3233220.318 2620191.867 2056463.251 3479851.996 2474467.858 3291056.951 2953044.477 2105340.648 1.415372407 1.535723125 1.244545328 0.976784091 1.65286886 1.175328971 1.563194514 1.402644498 1 21.00562225 -1.999886513 0.016295258 2.86E-05 2.459415197 0.038545246 0.226067204 65170.2938 105.7078572 9617.020025 6609.764667 0.010002613 1.999886513 2.459386618 NSTGGTSVGWDS(ph)PPASPLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSTGGTSVGWDSPPASPLQR 20 0 Q13424-2;Q13424 Q13424-2 SNTA1 Alpha-1-syntrophin 1 NSTGGTSVGWDS(1)PPASPLQR 222.62 7.37E-25 79127000 134650 130650 78004 81193 150070 159810 142300 138810 130660 TRUE FALSE 116855.6613 129791.7515 115726.9953 99629.11161 147083.9006 165957.9941 128499.7679 109126.5617 115213.5236 1.014252994 1.126532263 1.004456696 0.864734525 1.276620105 1.440438491 1.115318444 0.947167991 1 16.81395054 1.767489802 7.552963706 0.97496854 1.124821954 0.132389386 0.155820371 0.354732329 60.50466049 0.093302979 0.044132628 58.54499887 -1.767489802 0.149853414 NSTMVNSEDIFLLLCLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSTMVNSEDIFLLLCLK 17 0 Q96BQ3;A6NCK2 Q96BQ3 TRIM43;TRIM43B Tripartite motif-containing protein 43;Tripartite motif-containing protein 43B 0 52.823 0.098121 170930000 4903 10195 7032.1 0 9489.7 9144.8 8727.3 7052.6 4639.6 FALSE TRUE 4255.056127 10128.02837 10432.84708 0 9300.873536 9496.606373 7880.927789 5544.456373 4091.111773 1.040073301 2.475617616 2.550125164 0 2.273434228 2.321277662 1.926353575 1.355244413 1 11.99827724 1.540293872 3.329600782 1.043203564 1.820698034 0.108036844 0.771803143 0.478716085 11.23153378 0.748005562 0.200412442 34.6971555 -1.540293872 0.77749447 NSTPS(ph)EPGSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NSTPSEPGSGR 11 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 NSTPS(1)EPGSGR;NST(0.008)PS(0.888)EPGS(0.104)GR 149.02 3.62E-05 369932000 549584 627585 324224 439501 702390 682430 648830 713290 807130 TRUE FALSE 476955.0819 623462.3528 481019.8109 539296.4194 688413.8132 708683.5237 585906.5665 560758.4843 711712.0109 0.670151795 0.876003697 0.675862994 0.757745283 0.967264571 0.995744786 0.823235463 0.78790083 1 19.44093406 3.296117737 9.565764884 0.896064251 0.748944531 0.468956971 0.088552053 0.396573403 62.47491002 0.026565353 0.03425925 1977.505668 -3.296117737 -0.14711972 NSTWSGESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSTWSGESK 9 0 P19338 P19338 NCL Nucleolin 0 106.62 0.0067617 230910000 218030 195790 123920 175700 221970 209960 219380 252930 233140 FALSE TRUE 189216.7831 194503.8426 183848.1265 215595.3704 217553.2313 218037.2971 198104.5614 198842.8878 205578.4548 0.920411544 0.94612951 0.894296665 1.048725513 1.05824918 1.060603833 0.963644569 0.967236027 1 17.64932955 3.741933211 24.99759707 1.011574471 0.922864265 0.609813725 0.036091161 249.8337012 1851757.029 0.011315891 0.018596193 5519.925435 -3.741933211 -0.088710206 NSVLSDPGLDS(ph)PRT(ph)SPVIMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NSVLSDPGLDSPRTSPVIMAR 21 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 2 NSVLSDPGLDS(0.999)PRT(0.736)S(0.265)PVIMAR;NSVLS(0.001)DPGLDS(0.994)PRT(0.59)S(0.415)PVIMAR;NSVLSDPGLDS(1)PRT(0.545)S(0.455)PVIMAR;NSVLSDPGLDS(1)PRT(0.562)S(0.438)PVIMAR;NSVLSDPGLDS(1)PRT(0.535)S(0.465)PVIMAR 137.28 1.81E-06 2158630000 381672 401172 241828 259943 475147 478988 395563 439467 386323 TRUE FALSE 331233.0782 398536.6747 358776.8297 318967.0311 465692.5043 497414.9783 357201.3611 345490.402 340652.335 0.972349355 1.16992204 1.053205256 0.936341831 1.367060949 1.460183674 1.048580398 1.01420236 1 18.37794057 2.021384103 24.95901674 1.015098111 1.163020123 0.14673178 0.159865541 452.1119283 527692.0032 0.069808142 0.047060351 105.0471085 -2.021384103 0.147922012 NSVLSDPGLDS(ph)PRTS(ph)PVIMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NSVLSDPGLDSPRTSPVIMAR 21 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 2 NSVLSDPGLDS(0.999)PRT(0.147)S(0.855)PVIMAR;NSVLSDPGLDS(1)PRT(0.023)S(0.977)PVIMAR;NSVLSDPGLDS(0.998)PRT(0.293)S(0.709)PVIMAR;NSVLSDPGLDS(0.999)PRT(0.16)S(0.841)PVIMAR;NSVLSDPGLDS(1)PRT(0.117)S(0.883)PVIMAR 171.96 3.54E-12 2820380000 339219 372375 170091 208197 372233 414980 340446 393607 304909 TRUE FALSE 294390.3497 369928.8441 252347.5765 255471.3109 364826.2916 430944.5491 307429.5993 309437.2061 268863.0054 1.094945544 1.375900874 0.938573071 0.950191383 1.356922612 1.602840631 1.14344329 1.150910315 1 18.03651173 1.33375532 2.209248592 0.969656954 1.214115358 0.097406739 0.200634236 1.421575222 8.56091177 0.642516937 0.057251767 21.56529088 -1.33375532 0.244458404 NSVSNFLHSLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NSVSNFLHSLER 12 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 187.97 9.80E-06 203720000 295350 284730 96946 138930 374140 395710 293530 321560 316390 FALSE TRUE 256318.7492 282859.5899 143829.4099 170476.1799 366695.346 410933.2198 265063.5058 252796.8964 278986.7346 0.918748877 1.013881862 0.51554211 0.611054788 1.31438273 1.472948957 0.950093581 0.906125149 1 18.089837 3.244331065 24.9999905 1.104702676 0.764793349 0.40653773 0.217403898 173.236174 750526.8682 0.071091647 0.089269995 1755.218005 -3.244331065 -0.339909327 NSWGEPWGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NSWGEPWGER 10 0 Q9UBR2 Q9UBR2 CTSZ Cathepsin Z 0 ;;; 191.24 1.89E-06 1719190000 1462820 1507180 734860 1158450 1749930 1870570 1488440 1759730 1632630 FALSE TRUE 1269504.631 1497279.235 1090240.754 1421493.778 1715109.817 1942532.038 1344091.318 1383425.434 1439622.341 0.88183171 1.040050013 0.757310249 0.987407418 1.191360934 1.349334463 0.933641608 0.960964132 1 20.45725897 4.743123989 22.47809838 1.023390385 0.881831485 0.078672412 0.156106658 371.157344 1827938.237 0.040790047 0.306010481 55350.81107 -4.743123989 -0.141558901 NSYNNSQAPS(ph)PGLGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NSYNNSQAPSPGLGSK 16 0 Q9UHB7 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 NSYNNSQAPS(1)PGLGSK;NSYNNSQAPS(1)PGLGSK;NSYNNSQAPS(1)PGLGSK;NSYNNS(0.002)QAPS(0.996)PGLGS(0.001)K 276.26 2.86E-35 666804000 1682550 1357840 724297 835006 1613290 1390770 1700060 1896340 1751660 TRUE FALSE 1460196.754 1348920.26 1074569.452 1024606.875 1581188.685 1444273.822 1535188.443 1490822.448 1544580.75 0.945367702 0.873324531 0.695702994 0.663355978 1.023700888 0.935058799 0.993919187 0.965195538 1 20.55878387 3.221340076 24.99845189 0.979627509 0.793020056 0.566772599 0.082123532 189.3937485 274935.4776 0.026324847 0.029920439 1664.715703 -3.221340076 -0.186607453 NSYVAGQYDDAASYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NSYVAGQYDDAASYQR 16 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;; 589.95 0 2321470000 825261 852923 430235 544936 1122400 1232640 1016460 986790 1040110 FALSE TRUE 716200.6679 847320.0927 638298.085 668672.0476 1100066.436 1280060.458 917883.8656 775772.6377 917149.3807 0.780898601 0.923862689 0.695958694 0.729076486 1.199440853 1.395694622 1.000800835 0.845852 1 19.80679721 3.248123203 24.99892679 1.066844545 0.786372157 0.490219656 0.154122219 218.8266165 572062.8116 0.051645903 0.065802412 1770.611182 -3.248123203 -0.280472388 NT(ph)PSQHSHSIQHS(ph)PER ddPTM_MDA-MB-175_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(0.998)PS(0.002)QHSHSIQHS(1)PER;NT(0.436)PS(0.436)QHS(0.101)HS(0.027)IQHS(1)PER;NT(1)PSQHSHSIQHS(1)PER;NT(0.999)PS(0.001)QHSHSIQHS(1)PER;NT(0.982)PS(0.018)QHS(0.004)HS(0.011)IQHS(0.985)PER;NT(0.991)PS(0.009)QHS(0.007)HS(0.015)IQHS(0.978)PER 273.46 7.06E-35 1432967000 1086573 977962 346855 654697 1389001.9 1384214 1140424 1042386 998631 TRUE FALSE 942979.625 971537.7032 514595.2382 803355.9603 1361363.48 1437465.608 1029825.856 819479.8658 880573.9808 1.07086928 1.103300489 0.58438615 0.912309446 1.545995577 1.632418899 1.169493851 0.930620122 1 19.74808469 3.407627924 24.74567233 1.227597355 0.906304345 0.301391884 0.253454003 66.62145498 23721.7922 0.082683049 0.10674337 2556.394789 -3.407627924 -0.32129301 NTADHDES(ph)PPRT(ph)PTGNAPSSESDIDISSPNVSHDESIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NTADHDESPPRTPTGNAPSSESDIDISSPNVSHDESIAK 39 1 O95251-4;O95251 O95251-4 KAT7 Histone acetyltransferase KAT7 2 NT(0.182)ADHDES(0.818)PPRT(0.817)PT(0.182)GNAPS(0.001)S(0.001)ESDIDISSPNVSHDESIAK;NTADHDES(0.99)PPRT(0.879)PT(0.103)GNAPS(0.014)S(0.012)ES(0.002)DIDISSPNVSHDESIAK;NT(0.123)ADHDES(0.876)PPRT(0.877)PT(0.124)GNAPSSESDIDISSPNVSHDESIAK 222.36 2.03E-39 633420000 672590 415373 267991 333913 413260 401010 466370 568200 520630 TRUE FALSE 583705.5274 412644.3874 397592.344 409733.0502 405036.9345 416437.1142 421141.5092 446694.8517 459081.7145 1.271463247 0.898847361 0.866060075 0.892505707 0.882276339 0.907108911 0.917356313 0.973018174 1 18.80839144 4.740424342 24.93218277 0.917751544 1.271463371 0.882496717 0.040630931 57.79141693 773049.7216 0.011182 0.070300788 55007.80832 -4.740424342 0.353711827 NTAEWLLSHTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NTAEWLLSHTK 11 0 P00491;G3V5M2;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 127.56 0.00028413 406080000 843500 920980 434750 732240 1156600 1024200 840500 1311900 1628200 FALSE TRUE 732029.3378 914930.0217 644996.5542 898506.2836 1133585.923 1063601.637 758988.4394 1031360.394 1435716.051 0.509870554 0.637263908 0.449250779 0.625824503 0.789561364 0.74081615 0.528648014 0.71835959 1 20.45333902 1.279968264 2.97858966 1.053074019 0.618664068 0.588208501 0.1020973 0.266990056 3.093941234 0.265266063 0.027688377 19.05321483 -1.279968264 -0.434409951 NTCEHIYDFPPLSEELISEMIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NTCEHIYDFPPLSEELISEMIR 22 0 K7EN86;Q13432 K7EN86 UNC119 Protein unc-119 homolog A 0 130.3 1.38E-05 19657000 14613 13251 7006.3 8700.4 12550 12923 11387 12425 12404 FALSE TRUE 12681.85503 13163.95331 10394.57011 10675.9588 12300.27955 13420.15617 10282.69049 9768.010441 10937.61325 1.159471882 1.203548983 0.950350856 0.976077555 1.124585343 1.226973003 0.940121968 0.893065993 1 13.41701033 -2 0.187811586 0.005555018 1.180704266 0.221752647 0.104784287 165.4467274 2.386254875 54.36059388 0.90072918 0.01 2 1.175149248 NTDDDRPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NTDDDRPPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 135.43 0.00020163 868000000 1481060 1469120 840761 1167970 1558830 1626210 1496410 1639360 2586850 FALSE TRUE 1285334.168 1459469.254 1247355.832 1433175.44 1527812.333 1688771.351 1351288.389 1288795.622 2281035.54 0.563487129 0.639827494 0.546837526 0.628300355 0.669788921 0.740352932 0.592401287 0.565004621 1 21.12125749 1.233632444 24.99993869 1.000000583 0.618725517 0.813304799 0.057480206 68.16713505 345761.4655 0.119108988 0.014815932 17.12507351 -1.233632444 -0.381275066 NTDDDRPPRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NTDDDRPPRR 10 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 173.28 1.95E-06 1855030000 2914190 2930530 1318276 1742420 2992610 3348580 3020500 3277890 1562540 FALSE TRUE 2529072.408 2911279.155 1955798.683 2138063.092 2933062.916 3477402.039 2727572.375 2576938.732 1377818.301 1.835563082 2.112963047 1.419489552 1.551774345 2.128773375 2.523846603 1.979631402 1.870303747 1 20.39395422 1.235915047 4.557338996 0.920998356 1.936829748 0.477716985 0.305605156 0.196841396 8.766395502 0.64991204 0.082832949 17.21531791 -1.235915047 1.015831392 NTDEMVELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NTDEMVELR 9 0 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ; 174.42 0.00012722 3985000000 4603900 4200700 2128700 3064500 4682700 4481300 4138500 4723100 4887700 FALSE TRUE 3995482.95 4173105.325 3158146.44 3760341.563 4589523.432 4653698.511 3737148.907 3713101.82 4309881.674 0.927051658 0.968264477 0.732768711 0.872492993 1.06488386 1.079774078 0.867111719 0.861532195 1 22.03921683 NTDKNGEELHGGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NTDKNGEELHGGKR 14 2 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 201.06 1.10E-08 375080000 741250 568870 257940 298760 587780 439220 763050 842270 171058 FALSE TRUE 643291.9344 565133.0555 382680.6468 366598.0243 576084.328 456117.0776 689049.5284 662157.1151 150835.7181 4.264851472 3.746679252 2.537069147 2.430445712 3.819283225 3.023932815 4.56821194 4.389922515 1 17.20261858 NTDVAQS(ph)PEAPKQEAPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NTDVAQSPEAPKQEAPAK 18 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 NTDVAQS(1)PEAPKQEAPAK;NTDVAQS(1)PEAPKQEAPAK;NTDVAQS(1)PEAPKQEAPAK;NTDVAQS(1)PEAPKQEAPAK 302.71 6.53E-50 1566240000 3548240 2945160 2180570 2469000 3358650 2112010 3878890 5115580 2674610 TRUE FALSE 3079331.094 2925813.05 3235100.946 3029624.186 3291819.436 2193260.391 3502715.845 4021653.026 2358420.653 1.305675088 1.240581508 1.371723463 1.284598735 1.395772816 0.929969973 1.485195544 1.705231432 1 21.16938963 NTEDLTEEWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NTEDLTEEWLR 11 0 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 ; 230.95 3.31E-12 1024130000 756080 741670 366150 464160 724880 836450 689430 808740 926140 FALSE TRUE 656162.1123 736797.9209 543221.3647 569554.6222 710456.3062 868628.7728 622569.1847 635797.2446 816652.7843 0.803477469 0.902216872 0.665180325 0.697425679 0.869961286 1.063645149 0.762342573 0.778540473 1 19.63936329 3.133402979 8.659473541 0.879598498 0.769679033 0.247083101 0.10913975 0.467730944 35.01720063 0.034997887 0.039741408 1359.574402 -3.133402979 -0.109919465 NTEEEGLKYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NTEEEGLKYK 10 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ; 111.63 0.0015759 379380000 337630 287170 179846 195524 247762 216014 379540 403550 202156 FALSE TRUE 293011.3401 285283.5614 266820.1271 239920.7126 242832.0209 224324.1984 342732.2692 317253.9729 178257.348 1.643754624 1.600402814 1.496825405 1.345923269 1.362255322 1.2584289 1.92268242 1.779752569 1 17.44360202 4.310587797 3.945026396 1.492480766 1.632716633 0.053749279 0.258964727 0.896671668 26.69773406 0.070440312 0.204580318 20445.03211 -4.310587797 0.140235867 NTEESSS(ph)PVRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NTEESSSPVRK 11 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 NTEESS(0.002)S(0.998)PVRK;NTEES(0.008)S(0.178)S(0.813)PVRK;NTEESS(0.003)S(0.997)PVRK 162 1.57E-05 2216050000 1526960 1311650 750270 871030 1254410 1159860 1496370 1728370 1389800 TRUE FALSE 1325168.367 1303033.685 1113103.082 1068810.674 1229449.695 1204480.565 1351252.268 1358771.526 1225499.427 1.081329242 1.063267478 0.908285273 0.872142941 1.003223394 0.982848737 1.102613545 1.108749213 1 20.22493838 2.247670457 24.41212849 1.07977234 0.980918624 0.25142321 0.068473528 182.2619084 488417.7744 0.027647847 0.021091957 176.8766309 -2.247670457 -0.098853716 NTEISFILGQEFDEVTADDRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NTEISFILGQEFDEVTADDRK 21 1 P15090 P15090 FABP4 "Fatty acid-binding protein, adipocyte" 0 173.55 6.66E-12 28914000 49714 90978 37374 39610 50510 46545 61838 64855 59426 FALSE TRUE 43144.16894 90380.35953 55448.19141 48604.0559 49504.94982 48335.61627 55840.96028 50986.26295 52400.72598 0.823350596 1.724792125 1.058156931 0.927545468 0.944737862 0.922422645 1.065652417 0.973006805 1 15.67729918 4.019064661 24.9991794 0.976305859 1.303422251 0.241916201 0.216757413 266.0242468 348828.3918 0.049051072 0.102085488 10448.75776 -4.019064661 0.327116392 NTENCDFLFS(ph)PPEVTGR ddPTM_MDA-MB-175_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 116.06 0.00029839 79849000 143149 159520 74262 90852 146437 147902 140718 161063 150857 TRUE FALSE 124231.497 158472.1026 110175.3516 111481.3352 143523.1902 153591.8856 127071.19 126620.9308 133022.8573 0.933910904 1.19131483 0.828243761 0.838061499 1.078936305 1.154627774 0.955258311 0.951873485 1 17.02131464 NTETSKS(ph)PEKDVPMVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NTETSKSPEKDVPMVEK 17 2 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3 O14617-5 AP3D1 AP-3 complex subunit delta-1 1 NTET(0.019)S(0.002)KS(0.979)PEKDVPMVEK;NT(0.003)ET(0.097)S(0.097)KS(0.802)PEKDVPMVEK;NT(0.003)ET(0.046)S(0.046)KS(0.905)PEKDVPMVEK;NT(0.002)ET(0.038)S(0.038)KS(0.923)PEKDVPMVEK 218.25 2.46E-15 2149100000 3579570 2653200 3389140 2618300 3082240 1807290 4827140 5323640 5862070 TRUE FALSE 3106520.755 2635770.955 5028139.44 3212825.033 3020909.454 1876817.616 4359004.706 4185221.015 5169062.763 0.600983369 0.50991274 0.972737162 0.621548853 0.584421121 0.363086637 0.843287247 0.809667285 1 22.30147129 2.035867344 24.97596913 0.871810314 0.618877484 0.403226667 0.157877545 183.3071761 127643.9116 0.065761257 0.044336065 108.6093823 -2.035867344 -0.252932831 NTFTAWS(ph)DEES(ph)DYEIDDRDVNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NTFTAWSDEESDYEIDDRDVNK 22 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 2 NTFTAWS(1)DEES(1)DYEIDDRDVNK;NTFT(0.007)AWS(0.993)DEES(1)DYEIDDRDVNK 182.72 2.57E-17 509650000 991470 824590 510170 509730 800750 722640 968250 1089180 774410 TRUE FALSE 860444.7274 819173.214 756889.9184 625471.9872 784816.6416 750440.4284 874349.264 856267.333 682860.132 1.260059985 1.199620794 1.108411347 0.915959152 1.149308043 1.098966528 1.280422188 1.253942488 1 19.38123058 2.275914039 24.9967137 1.198180335 1.11683073 0.039895731 0.11465485 407.0151192 272371.0077 0.044224534 0.03425532 188.7617691 -2.275914039 -0.081349605 NTFTAWS(ph)DEESDYEIDDRDVNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NTFTAWSDEESDYEIDDRDVNK 22 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 NTFTAWS(1)DEESDYEIDDRDVNK;NTFTAWS(1)DEESDYEIDDRDVNK;NTFTAWS(1)DEESDYEIDDRDVNK 312.41 1.87E-67 1448380000 1084300 803810 486880 563580 817430 645290 979890 1223530 591850 TRUE FALSE 941007.0077 798529.7192 722336.7965 691549.4528 801164.7423 670114.7239 884860.4186 961887.631 521882.1672 1.803102437 1.530095813 1.384099404 1.325106501 1.53514489 1.284034531 1.695517636 1.843112663 1 18.99336458 2.209711424 24.99899608 1.589285838 1.470872337 0 0.259202197 795.7572122 689550.1499 0.104848798 0.070702123 162.073281 -2.209711424 -0.118413501 NTGKEEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NTGKEEQR 8 1 P23921;E9PL69 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ; 80.239 0.02368 92440000 277600 307520 112271 146299 214189 258200 332240 397340 130971 FALSE TRUE 240914.4567 305499.8809 166565.6311 179518.424 209927.058 268133.1211 300019.4159 312371.9331 115487.7576 2.086060563 2.645301002 1.442279551 1.554436832 1.817742957 2.321744977 2.597846059 2.704805597 1 16.8173804 2.733680462 22.74674339 2.283248361 1.904415552 0.024211415 0.562767344 307.7464485 1434416.92 0.193677248 0.176618627 541.6022532 -2.733680462 -0.378832808 NTHCSSLPHYQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NTHCSSLPHYQK 12 0 P43243;A0A0R4J2E8;P43243-2;B3KM87;A8MXP9;Q68E03 P43243;A8MXP9 MATR3;DKFZp686L22104 Matrin-3 0 52.576 0.085396 76456000 72484 71349 31525 51465 88145 88765 71027 86272 76081 FALSE TRUE 62905.05575 70880.30372 46770.59544 63150.91484 86391.08695 92179.84699 64138.81247 67823.40417 67086.79085 0.937666789 1.056546346 0.69716549 0.94133158 1.287751074 1.374038701 0.956057246 1.010980005 1 16.03374111 3.452346436 23.74141116 1.111415536 0.897431597 0.33077258 0.15410853 167.9052932 160900.4762 0.047948866 0.061905446 2833.651494 -3.452346436 -0.213983939 NTHTLLLAGVFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NTHTLLLAGVFR 12 0 Q9Y678;H0Y8X7 Q9Y678 COPG1 Coatomer subunit gamma-1 0 153.38 7.06E-05 320910000 164060 176420 117660 135890 233240 230880 187380 185970 208010 FALSE TRUE 142379.0553 175261.0854 174560.7695 166745.9014 228598.9803 239762.103 169207.9164 146201.7627 183419.2948 0.776249061 0.955521531 0.951703417 0.909096841 1.246319154 1.307180378 0.92251972 0.79709042 1 17.48478589 5.088783344 1.150425492 1.014002559 0.483794814 0.207380559 0.152145434 6.691197097 4.347061206 0.0523179 5.167308104 122682.7052 -5.088783344 -0.530207744 NTIQWLENELNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NTIQWLENELNR 12 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 193.73 5.65E-06 201719000 161207 153643 86003 124001 185891 201913 175141 194497 167331 FALSE TRUE 139903.0865 152633.709 127594.3385 152157.3223 182192.1328 209680.7238 158155.8528 152905.3301 147549.3198 0.948178458 1.034458913 0.864757212 1.031230252 1.234788022 1.421089057 1.071884662 1.036299797 1 17.17083774 3.451861672 7.413949306 1.144932813 0.955894495 0.366078046 0.123394472 0.225191002 48.32826347 0.039322864 0.051552297 2830.490305 -3.451861672 -0.189038318 NTKDEFEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NTKDEFEER 9 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 110.84 0.0020266 122400000 563000 474570 261280 341020 516240 470940 543500 614700 510030 FALSE TRUE 488598.1235 471452.5184 387635.8819 418453.8032 505967.834 489057.3665 490791.4537 483251.1886 449734.8344 1.086413785 1.048289975 0.861920964 0.930445612 1.1250359 1.087434926 1.091290725 1.074524701 1 18.77871511 3.238646586 25 1.077277077 0.97795871 0.32256685 0.067487493 2.836159453 824535.7016 0.021065056 0.025484188 1732.393663 -3.238646586 -0.099318367 NTLQLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NTLQLHR 7 0 P61313;E7ERA2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;;;; 142.19 0.002506 5182140000 5914070 6578100 2553270 3610380 7581590 8217010 6050090 6935700 6774880 FALSE TRUE 5132510.665 6534888.028 3788039.912 4430171.96 7430731.192 8533123.692 5463353.203 5452554.529 5973961.404 0.859146941 1.093895254 0.634091795 0.741580278 1.243853231 1.428386144 0.914527703 0.91272008 1 22.51025649 3.248843802 24.99861249 1.079021979 0.836723554 0.32444058 0.19059437 310.4998401 754826.611 0.060889127 0.077718885 1773.551493 -3.248843802 -0.242298425 NTNPNFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NTNPNFVR 8 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ; 145.65 0.0023183 0 248820 277100 136078 190242 318730 347740 268060 285850 316350 FALSE TRUE 215937.8066 275279.7119 201885.776 233439.3538 312387.8966 361117.7828 242063.5825 224723.202 278951.4634 0.774105301 0.98683731 0.723730837 0.836845776 1.119864699 1.29455418 0.867762368 0.805599653 1 18.08965459 3.318388824 12.36503385 0.993646988 0.833686344 0.27579552 0.147884042 1.156487447 174.5747778 0.047690476 0.061564661 2081.559475 -3.318388824 -0.159960644 NTPSQHS(ph)HSIQHS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NTPSQHSHSIQHSPER 16 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 NT(0.168)PS(0.232)QHS(0.538)HS(0.063)IQHS(1)PER 82.635 0.0044669 355160000 123940 74375 145580 87604 29859 56674 59142 48558 38475 TRUE FALSE 107561.015 73886.42573 215982.9749 107495.8271 29264.86432 58854.28545 53406.41794 38174.24958 33926.52933 3.17041021 2.177836259 6.366197168 3.168488769 0.862595287 1.734757036 1.574178644 1.125203501 1 15.05012623 3.353738792 5.034238226 1.297512185 3.883751964 0.573285377 1.067122136 0.151700849 6.057138714 0.309041977 0.400960729 2258.077233 -3.353738792 2.586239779 NTPSQHSHSIQHS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 NTPSQHSHSIQHSPER 16 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 NTPSQHSHSIQHS(1)PER;NTPSQHSHS(0.001)IQHS(0.999)PER;NTPSQHSHS(0.083)IQHS(0.916)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHS(0.002)IQHS(0.998)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER 293.72 2.21E-45 37995290000 3265470 3310123 1004004 1631918 4771476.1 4536282.9 3693006 3566309 1339376.9 TRUE FALSE 2833929.866 3288378.584 1489543.693 2002469.924 4676533.061 4710796.639 3334858.847 2803681.573 1181037.289 2.399526156 2.784313938 1.26121648 1.695517951 3.959682819 3.988694247 2.823669395 2.373914524 1 20.17162308 NTPVFRDDVCFFLSQSGETADTLMGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NTPVFRDDVCFFLSQSGETADTLMGLR 27 1 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 55.153 0.073999 101020000 20775 12992 6676.7 8648.5 18328 18239 12775 19825 6237 FALSE TRUE 18029.53111 12906.6547 9905.574452 10612.27411 17963.30866 18940.66613 11536.08247 15585.57803 5499.668965 3.27829388 2.34680574 1.801121943 1.929620524 3.266252709 3.443964764 2.09759579 2.833912028 1 12.42512907 NTS(ph)LPPLWS(ph)PEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NTSLPPLWSPEAER 14 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 2 NT(0.121)S(0.879)LPPLWS(1)PEAER 103.5 0.0034234 0 50895 48955 26876 30833 53711 49711 51536 54538 45833 TRUE FALSE 44169.0968 48633.41138 39873.32349 37834.1039 52642.25618 51623.41434 46538.04665 42875.47312 40414.67495 1.09289749 1.203360201 0.986605077 0.936147673 1.302553002 1.277343302 1.15151357 1.060888728 1 15.30259162 1.536942165 3.372156458 1.007814715 1.136432979 0.138964325 0.113951223 0.461667071 11.0674791 0.119888219 0.032196606 34.43040769 -1.536942165 0.128618265 NTSLPPLWS(ph)PEAER ddPTM_MDA-MB-175_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 225.13 3.03E-12 1298522000 1155076 1213794 498030 656707 1396055 1278638 1157868 1337305 1239973 TRUE FALSE 1002429.78 1205820.507 738878.9738 805822.3615 1368276.237 1327828.031 1045578.14 1051332.733 1093384.805 0.916813345 1.102832692 0.675772126 0.736997952 1.251413255 1.214419686 0.95627645 0.96153955 1 20.0603698 3.250561051 24.99996935 1.060181526 0.862560969 0.348521635 0.147511739 312.157436 650299.9307 0.046423242 0.059462215 1780.578195 -3.250561051 -0.197620558 NTVDLVTTCHIHS(ph)SS(ph)DDEIDFK ddPTM_MDA-MB-175_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(0.001)VDLVT(0.037)T(0.016)CHIHS(0.71)S(0.327)S(0.909)DDEIDFK 108.88 0.00019291 80901000 73733 69283 40366 63445 97468 68786 88513 110770 107070 TRUE FALSE 63988.99723 68827.87541 59887.13262 77851.15695 95528.57749 71432.24193 79929.02288 87082.69751 94412.30657 0.67776119 0.729013811 0.634314898 0.824586961 1.011823362 0.756598843 0.846595383 0.922365957 1 16.52668731 3.553315598 4.854033849 0.899075004 0.687720348 0.650301703 0.075666809 0.14230578 6.092583832 0.021257769 0.031553487 3575.325593 -3.553315598 -0.211354656 NTVDLVTTCHIHS(ph)SSDDEIDFK ddPTM_MDA-MB-175_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 1 NT(0.008)VDLVT(0.006)T(0.006)CHIHS(0.327)S(0.327)S(0.327)DDEIDFK 60.036 0.097443 110180000 137820 106970 77387 189700 168970 128770 193420 206430 202280 TRUE FALSE 119606.7378 106267.307 114811.612 232774.2844 165607.8276 133723.8652 174662.1582 162286.5509 178366.6888 0.670566565 0.595780006 0.643683037 1.305032268 0.928468363 0.749713223 0.979230816 0.909847865 1 17.44448668 3.945613712 24.99496148 0.961047863 0.629812324 0.575368529 0.137976431 213.8787155 98294.82752 0.036312697 0.062895924 8822.947846 -3.945613712 -0.331235539 NTVDLVTTCHIHSS(ph)SDDEIDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NTVDLVTTCHIHSSSDDEIDFK 22 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;E9PQP7;H0YDW1 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 NTVDLVTTCHIHS(0.069)S(0.552)S(0.379)DDEIDFK;NT(0.007)VDLVT(0.037)T(0.037)CHIHS(0.135)S(0.648)S(0.135)DDEIDFK;NT(0.01)VDLVT(0.057)T(0.044)CHIHS(0.157)S(0.574)S(0.157)DDEIDFK;NT(0.021)VDLVT(0.061)T(0.061)CHIHS(0.061)S(0.398)S(0.398)DDEIDFK;NT(0.005)VDLVT(0.017)T(0.017)CHIHS(0.093)S(0.434)S(0.434)DDEIDFK 160.41 1.19E-11 1257255000 541688 519572 310030.4 403262.1 659354 564990 757216 747419 815031 TRUE FALSE 470102.5583 516158.8973 459962.1384 494828.9233 646234.1454 586725.5309 683781.3089 587589.2633 718678.9637 0.654120382 0.7182051 0.640010577 0.688525682 0.899197247 0.816394469 0.951441942 0.817596302 1 19.45498793 3.254743668 7.289521679 0.887276749 0.674955559 0.780919588 0.0582363 0.068183619 16.93441294 0.015771788 0.019691857 1797.809489 -3.254743668 -0.21232119 NTVDLVTTCHIHSSS(ph)DDEIDFK ddPTM_MDA-MB-175_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 NTVDLVTTCHIHS(0.004)S(0.203)S(0.793)DDEIDFK;NTVDLVTTCHIHS(0.003)S(0.129)S(0.867)DDEIDFK;NTVDLVTTCHIHS(0.001)S(0.208)S(0.79)DDEIDFK;NTVDLVTT(0.002)CHIHS(0.007)S(0.193)S(0.798)DDEIDFK 225.57 3.85E-26 3156690000 1952878 1876394 905044 1465297 2474301 2121330 2584449 3014810 3086190 TRUE FALSE 1694800.224 1864067.844 1342726.306 1798015.08 2425067.251 2202938.938 2333809.534 2370116.343 2721344.134 0.62278056 0.684980566 0.493405552 0.660708455 0.891128476 0.809503991 0.857594416 0.870935915 1 21.37588798 3.305494672 4.387387915 0.878716818 0.604699673 0.803960859 0.06668871 0.090656947 3.404070646 0.01956045 0.025101791 2020.66664 -3.305494672 -0.274017145 NTVELLTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NTVELLTDR 9 0 Q9P2M7 Q9P2M7 CGN Cingulin 0 ; 66.299 0.064123 19822400000 2521480 3276010 1992960 1643920 2915250 4741600 1824450 1764720 1649010 FALSE TRUE 2188260.029 3254489.675 2956762.122 2017197.162 2857242.229 4924012.42 1647515.12 1387348.361 1454065.916 1.504924918 2.238199547 2.03344435 1.387280411 1.965001859 3.386374967 1.133040188 0.954116554 1 20.47166124 2.033238516 24.99988784 0.994718226 2.070376221 0.467491419 0.533387137 154.8814541 116491.3163 0.216938346 0.146258957 107.9539445 -2.033238516 1.075657995 NTVGNVPLEWYDDFPHVGYDLDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NTVGNVPLEWYDDFPHVGYDLDGR 24 0 Q14137;Q14137-2;A0A075B729 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 145.14 2.16E-07 41447000 43770 34754 26352 34548 47956 47429 37203 51709 71237 FALSE TRUE 37985.6836 34525.69869 39095.91534 42392.65143 47001.76942 49253.62432 33595.05879 40651.43275 62815.44301 0.604718868 0.549637112 0.622393371 0.674876263 0.748251818 0.784100564 0.534821649 0.647156667 1 15.93883167 1.238836602 11.72534922 1.00056074 0.64527864 0.672724718 0.077652797 0.038057273 258.722367 0.11215979 0.020215258 17.33151799 -1.238836602 -0.3552821 NTWLYQALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NTWLYQALR 9 0 P56545;P56545-3;P56545-2;A0A087WYL1 P56545 CTBP2 C-terminal-binding protein 2 0 79.986 0.059073 342160000 36139 53138 55968 38061 78516 64980 61669 62893 53943 FALSE TRUE 31363.13959 52788.93298 83034.312 46703.33178 76953.68521 67479.82265 55688.34987 49443.82138 47565.91999 0.659361568 1.109805781 1.745668159 0.981865415 1.617832373 1.418659045 1.170761543 1.039479976 1 15.53764066 1.849274471 3.189461413 1.017795826 1.275825044 0.085059519 0.308210152 0.584918468 10.35774353 0.198144881 0.084427355 70.67640826 -1.849274471 0.258029218 NVADDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NVADDTR 7 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 79.713 0.096743 0 415250 351500 179950 198620 230890 389970 365350 407640 370420 FALSE TRUE 360373.6604 349190.9734 266974.4219 243719.7067 226295.7407 404972.3982 329918.4132 320469.3583 326629.3696 1.103310645 1.069074021 0.817361961 0.746165928 0.692821166 1.239852983 1.010069651 0.981140669 1 18.31729499 2.740105633 24.99999965 1.041321622 0.884377957 0.255880817 0.144550075 240.56234 3892578.035 0.051827858 0.049249105 549.6745545 -2.740105633 -0.156943665 NVAEALGHS(ph)PKDPGGGGGPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NVAEALGHSPKDPGGGGGPVR 21 1 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 NVAEALGHS(1)PKDPGGGGGPVR;NVAEALGHS(1)PKDPGGGGGPVR;NVAEALGHS(1)PKDPGGGGGPVR 157.09 5.38E-09 944760000 1296710 996850 541550 650810 1184470 1055520 1169000 1355930 849550 TRUE FALSE 1125346.488 990301.6267 803445.3914 798586.3575 1160901.364 1096126.537 1055630.56 1065974.921 749117.1668 1.502230276 1.32195826 1.072523 1.066036653 1.549692646 1.463224427 1.409166158 1.422974894 1 19.51483186 3.238040522 24.9999999 1.383479243 1.234480444 0.100376892 0.187737469 30.72608694 1476967.454 0.056891029 0.068491448 1729.97777 -3.238040522 -0.148998799 NVALLSQLYHS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NVALLSQLYHSPAR 14 0 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 1 NVALLSQLYHS(1)PAR;NVALLSQLYHS(1)PAR;NVALLSQLYHS(1)PAR;NVALLSQLYHS(1)PAR;NVALLSQLYHS(1)PAR 287.03 3.32E-33 1162210000 1280240 1250690 522588 573950 1283440 1456310 1135010 1285670 1782470 TRUE FALSE 1111053.04 1242474.135 775313.3048 704274.1198 1257902.055 1512335.188 1024936.905 1010739.476 1571748.427 0.706889869 0.790504456 0.493280789 0.448083235 0.800320225 0.962199269 0.652099844 0.643066955 1 20.58393889 3.190050763 24.99981881 0.786054018 0.614289456 0.306534237 0.14805661 174.9238419 90147.20578 0.047683113 0.05406768 1548.997665 -3.190050763 -0.171764562 NVALLSQLYHS(ph)PARR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NVALLSQLYHSPARR 15 1 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 1 NVALLSQLYHS(1)PARR;NVALLSQLYHS(1)PARR 157.62 1.18E-06 1196530000 726430 623540 244932 233463 602750 629720 530500 584100 199931 TRUE FALSE 630430.435 619443.9247 363381.9344 286474.3424 590756.4543 653945.7359 479052.1917 459194.7605 176295.3849 3.57598944 3.513670678 2.061210704 1.624967905 3.35094679 3.70937524 2.717326899 2.604689627 1 17.42763518 4.257616682 23.47802971 2.517091407 3.544832693 0.253793698 0.779732386 187.2255792 230662.7707 0.201988017 0.531981644 18097.4207 -4.257616682 1.027741286 NVALLSQLYHSPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NVALLSQLYHSPAR 14 0 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 0 ; 275.66 4.47E-33 2871400000 1941690 2035800 681030 901990 2508700 2378800 1775960 2241500 2233500 FALSE TRUE 1685090.747 2022426.696 1010378.386 1106800.616 2458781.778 2470313.975 1603727.673 1762172.668 1969458.174 0.85561134 1.026894971 0.513023531 0.56198229 1.248455951 1.254311469 0.814298924 0.894749983 1 20.90936735 3.244887064 24.99984772 1.017404191 0.74374681 0.367865254 0.19580803 203.4287345 803872.7057 0.06244241 0.078609949 1757.466535 -3.244887064 -0.273657381 NVDLLSDMVQEHDEPILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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 ;;;;;;;;; 306.82 1.98E-50 3670445000 5220960 4840404 2904452 3882283 5200190 4462847 5670130 7044050 6083570 FALSE TRUE 4530996.908 4808607.067 4309054.702 4763814.692 5096716.393 4634535.612 5120241.665 5537734.724 5364377.285 0.844645458 0.896396135 0.803272118 0.888046168 0.950104014 0.863946618 0.954489476 1.032316414 1 22.35497928 2.036630114 0.740010053 1.056668331 0.857221966 0.685703732 0.039594068 0.649932613 0.566197954 0.095265723 0.021277829 108.8003054 -2.036630114 -0.199446365 NVEFIHSLLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NVEFIHSLLQR 11 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 0 161.99 2.57E-05 191730000 240250 283820 134020 138970 332050 371350 301450 331990 295100 FALSE TRUE 208500.3538 281955.5677 198832.5203 170525.2625 325442.8546 385636.0748 272215.4254 260996.522 260213.6142 0.801266123 1.083554251 0.764112673 0.655327981 1.250675741 1.481998073 1.046122918 1.003008712 1 17.98933692 3.229328672 24.99998154 1.145206041 0.840032131 0.465858516 0.175233328 207.6462184 562302.0227 0.057872352 0.066515999 1695.620552 -3.229328672 -0.30517391 NVFEVGPGDS(ph)PTFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NVFEVGPGDSPTFPR 15 0 Q16584;Q16584-2 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 NVFEVGPGDS(0.999)PT(0.001)FPR;NVFEVGPGDS(1)PTFPR;NVFEVGPGDS(0.954)PT(0.046)FPR;NVFEVGPGDS(0.997)PT(0.003)FPR;NVFEVGPGDS(0.997)PT(0.003)FPR;NVFEVGPGDS(0.993)PT(0.007)FPR 283.12 7.53E-34 1074191000 1135040 1163370 605748 706647 1198540 1259830 1077530 1219910 1117740 TRUE FALSE 985041.5882 1155727.746 898689.7589 867102.0018 1174691.399 1308296.475 973031.3064 959041.7399 985602.0505 0.99943135 1.172610939 0.911818069 0.879768869 1.191851618 1.327408435 0.987245619 0.973051689 1 19.91064573 2.054435143 24.99988077 0.983256404 1.07997368 0.10018977 0.132309453 221.5089056 101728.9214 0.057720045 0.03891484 113.3535544 -2.054435143 0.096717275 NVFIIGATNRPDIIDPAILRPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NVFIIGATNRPDIIDPAILRPGR 23 2 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 174.7 1.34E-12 4792400000 4799800 3415900 1442060 2016650 3982100 3979800 3511300 4074300 4214100 FALSE TRUE 4165494.269 3393460.728 2139445.039 2474561.205 3902864.001 4132905.481 3170774.666 3203042.651 3715913.899 1.120987833 0.913223724 0.575752049 0.665936099 1.050310666 1.112217773 0.853296054 0.861979782 1 21.82528564 3.226290287 24.99997946 0.959026193 0.808333895 0.181692401 0.162344671 440.8226558 898144.6779 0.053045331 0.060574208 1683.799153 -3.226290287 -0.150692299 NVHLAPGWLMQLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NVHLAPGWLMQLEK 14 0 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 100.31 0.0018357 577130000 782050 842630 420250 361280 869900 884110 844280 1079680 1006370 FALSE TRUE 678700.111 837094.708 623484.3057 443314.1458 852590.6919 918122.2838 762401.8555 848798.8341 887398.0851 0.764820347 0.943313629 0.702598209 0.499566264 0.960775898 1.034622791 0.859143003 0.956502891 1 19.75922191 3.11068777 21.29789112 0.957477829 0.739775187 0.506328182 0.114787651 2.96913162 556.8233298 0.035986303 0.040804699 1290.291304 -3.11068777 -0.217702642 NVHMNDNVLHSAFEVGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NVHMNDNVLHSAFEVGAR 18 0 Q13630;E9PP14;A0A0J9YX13;E9PKL9;E9PLH9 Q13630 TSTA3 GDP-L-fucose synthase 0 216.17 5.27E-19 121080000 77157 76120 39473 57183 76365 78012 79457 84926 88028 FALSE TRUE 66960.50696 75619.96271 58562.27483 70167.27414 74845.48591 81013.17212 71751.27237 66765.23579 77621.43012 0.862654899 0.974215015 0.754460137 0.903967809 0.964237399 1.043695948 0.924374522 0.860139213 1 16.24416739 3.473385114 17.43646643 0.946644257 0.867219946 0.268288884 0.070504537 4.067831595 18975.15581 0.020934981 0.027372757 2974.302345 -3.473385114 -0.079424311 NVHS(ph)EDFENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NVHSEDFENR 10 0 A0A669KBJ7;Q9H2P0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 NVHS(1)EDFENR;NVHS(1)EDFENR 190.86 5.51E-07 492420000 323250 357510 177646 235597 367700 308600 289650 375150 312430 TRUE FALSE 280531.6935 355161.4933 263556.1998 289092.8997 360383.4894 320472.0417 261559.7876 294927.0919 275494.8813 1.018282779 1.289176378 0.956664598 1.049358516 1.308131344 1.163259514 0.949417958 1.07053565 1 18.07166599 2.25073513 24.99523225 1.017575737 1.134452293 0.208993348 0.113057384 360.7212385 740589.1699 0.0418967 0.032206917 178.1292053 -2.25073513 0.116876556 NVIGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NVIGAR 6 0 P62258;P62258-2;B4DJF2;I3L3T1;K7EIT4 P62258 YWHAE 14-3-3 protein epsilon 0 ; 110.54 0.066582 444640000 599960 610500 296380 406230 629390 674060 604280 727170 722990 FALSE TRUE 520673.7659 606489.5853 439710.3593 498470.7303 616866.3704 699991.5244 545677.0186 571670.3543 637518.9458 0.81671889 0.95132794 0.689721242 0.781891634 0.967604766 1.097993289 0.855938513 0.896711161 1 19.28210869 3.234677441 24.99299061 0.953921124 0.811430584 0.422169182 0.088960558 109.8257067 706862.004 0.027723766 0.032625525 1716.632935 -3.234677441 -0.14249054 NVIIWGNHSSTQYPDVNHAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NVIIWGNHSSTQYPDVNHAK 20 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51;C9JF79 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic;Malate dehydrogenase" 0 263.09 1.04E-36 1237400000 358110 325990 118550 173630 427530 403390 399570 456310 407450 FALSE TRUE 310784.8562 323848.5502 175881.1765 213055.3453 419022.9894 418908.6743 360819.7629 358731.6575 359281.7252 0.865017156 0.901377742 0.489535549 0.593003569 1.166279719 1.165961542 1.004280868 0.99846898 1 18.45475603 3.237641135 25 1.058676446 0.709836793 0.641540127 0.131684383 17.27586423 469720.974 0.042439084 0.050955623 1728.387573 -3.237641135 -0.348839653 NVKDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NVKDLR 6 1 A0A0A0MSQ3 A0A0A0MSQ3 UHRF2 0 ; 73.039 0.07662 1740230000 3559100 3411300 1666120 2100800 2797200 3211900 3813200 4440400 325360 FALSE TRUE 3088755.917 3388890.946 2471861.205 2577818.749 2741541.193 3335463.871 3443396.451 3490855.015 286896.3115 10.76610536 11.81224997 8.615869588 8.985193067 9.555860718 11.62602563 12.00223326 12.16765387 1 18.13016989 1.233400109 24.99999773 0.999984946 10.73261288 0.851522631 1.271702676 67.33466274 326164.3854 2.890723191 0.351656169 17.11591451 -1.233400109 9.73262793 NVKLPDAYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NVKLPDAYER 10 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 68.676 0.054049 499180000 1175910 1194810 291420 269540 1278420 1239290 1567070 1647510 132881 FALSE TRUE 1020510.514 1186961.214 432351.6867 330743.1767 1252981.943 1286966.288 1415095.793 1295202.807 117171.9596 8.709511371 10.13007906 3.689890383 2.8227161 10.69353067 10.98356888 12.07708566 11.05386316 1 16.83826783 NVLFSHLDDNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NVLFSHLDDNER 12 0 P10644;P10644-2;K7EPB2;K7EIE5;K7EID3;K7EJ40;K7EK41 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 0 ;;; 172.57 3.54E-05 2346060000 2210890 1952620 908010 1120480 2146020 2118990 2020550 2160110 2055750 FALSE TRUE 1918715.285 1939793.111 1347126.673 1374902.109 2103318.401 2200508.916 1824597.372 1698187.286 1812721.577 1.058472139 1.070099863 0.743151453 0.758473958 1.160309684 1.213925483 1.006551362 0.936816392 1 20.78972592 3.228728363 24.99995965 1.050930092 0.907417381 0.256296545 0.131050173 348.7930211 886855.8727 0.04418528 0.050697313 1693.27838 -3.228728363 -0.143512712 NVLS(ph)DSRPAMAPGSSHLGAPASTTTAADATPSGSLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NVLSDSRPAMAPGSSHLGAPASTTTAADATPSGSLAR 37 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 1 NVLS(0.978)DS(0.018)RPAMAPGS(0.002)S(0.002)HLGAPASTTTAADATPSGSLAR 166.6 5.31E-18 458790000 40432 43609 18942 35365 74034 62107 60012 60400 54518 TRUE FALSE 35088.80876 43322.52961 28102.41456 43395.16377 72560.86825 64496.29648 54192.04548 47483.93003 48072.94415 0.729907631 0.901183199 0.584578604 0.902694115 1.509390979 1.341634003 1.127287842 0.987747492 1 15.55293754 3.466741845 24.75765475 1.173281911 0.752955317 0.605901346 0.169551777 142.8939712 340838.5312 0.053404264 0.069020354 2929.15157 -3.466741845 -0.420326594 NVLSDSRPAMAPGSSHLGAPASTTTAADATPSGSLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NVLSDSRPAMAPGSSHLGAPASTTTAADATPSGSLAR 37 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;; 275.47 1.73E-76 820870000 610954 634005 181095 366604 815880 790650 630615 735686 614644 FALSE TRUE 530214.8809 629840.1794 268673.1477 449847.0414 799645.5842 821066.8171 569458.0544 578365.274 541981.4865 0.978289654 1.162106447 0.495723847 0.830004442 1.475411253 1.514935173 1.050696506 1.067131052 1 19.04788405 3.268692353 24.99835495 1.204166552 0.861157148 0.361063927 0.234039229 257.435929 213576.2821 0.07260992 0.093726591 1856.488884 -3.268692353 -0.343009405 NVMEEGKDFQPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NVMEEGKDFQPSR 13 1 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 0 ;;;;; 151.3 3.97E-05 2537650000 2956350 2472689 1351256 1611405 2599411 2108350 2875450 3089520 2044881 FALSE TRUE 2565660.857 2456445.743 2004727.921 1977299.134 2547687.807 2189459.589 2596589.302 2428850.191 1803137.498 1.422886974 1.362317486 1.111799807 1.096588106 1.41291932 1.214249935 1.440039545 1.3470133 1 20.78207798 7.999999851 0.008518289 3.76E-08 2.686632206 0.042271349 0.152386678 292213.3228 248.0988643 35464.71555 43149.85248 99999965.68 -7.999999851 2.686632168 NVMNDAWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NVMNDAWR 8 0 A0A3B3ISG5;P14735;Q5T5N3 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 131.06 0.0023757 667800000 847610 915090 522860 586480 1075000 1099080 929440 1021870 1073910 FALSE TRUE 735596.1909 909078.7135 775716.8449 719649.2478 1053609.603 1141362.319 839303.0519 803351.0527 946953.5832 0.776802796 0.960003457 0.819170927 0.759962537 1.112630674 1.205299118 0.886319104 0.848353147 1 19.85293419 3.248909302 24.9980799 0.990673348 0.837642404 0.37710222 0.114124083 301.0456334 727195.7197 0.037194943 0.047485385 1773.819 -3.248909302 -0.153030944 NVMSAFGLTDDQVSGPPS(ph)APAEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NVMSAFGLTDDQVSGPPSAPAEDR 24 0 Q92734-2;Q92734;Q92734-4;Q92734-3 Q92734-2 TFG Protein TFG 1 NVMSAFGLTDDQVSGPPS(1)APAEDR;NVMSAFGLTDDQVSGPPS(1)APAEDR;NVMSAFGLTDDQVSGPPS(1)APAEDR;NVMSAFGLTDDQVSGPPS(1)APAEDR;NVMSAFGLTDDQVSGPPS(1)APAEDR 207.6 4.72E-25 293449000 299866 296869 147025 201096 351777 365724 275706 358638 347830 TRUE FALSE 260237.9483 294918.848 218126.7818 246757.9204 344777.3259 379793.6389 248968.0746 281946.0546 306709.9336 0.848482295 0.961556232 0.711182645 0.804531883 1.12411529 1.238282811 0.811737891 0.919259612 1 18.22651537 3.260498271 24.99967598 1.001711297 0.832142657 0.343341212 0.127474838 332.630202 379055.702 0.039847439 0.051399989 1821.789822 -3.260498271 -0.16956864 NVMVEPHRHEGVFICR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NVMVEPHRHEGVFICR 16 1 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 92.977 0.002757 241670000 104870 87573 46006 57042 110040 91325 75674 93925 34922 FALSE TRUE 91011.16379 86997.7272 68254.65548 69994.25793 107850.4193 94838.33185 68335.14713 73839.86968 30793.56094 2.955525798 2.825192168 2.21652363 2.273016039 3.502369196 3.079810484 2.219137542 2.397899672 1 14.91034109 1.119374376 1.575300759 2.27E-12 2.751351699 0.637888409 0.407404467 1.050710653 1.84892924 4.950944556 0.121339833 13.16359089 -1.119374376 2.751351699 NVNHSWIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NVNHSWIER 9 0 Q4G0J3;Q4G0J3-3;D6RFF0 Q4G0J3 LARP7 La-related protein 7 0 147.95 9.12E-05 233300000 351090 345360 189420 198380 397350 447010 299460 358760 303240 FALSE TRUE 304692.567 343091.3074 281024.1456 243425.211 389443.5124 464206.764 270418.4153 282041.9659 267391.3127 1.139500622 1.283105663 1.050984577 0.91037068 1.456455367 1.736057762 1.011320871 1.054791059 1 18.02859307 NVNIFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NVNIFK 6 0 P00338;P00338-3;P00338-2;P00338-5;F5GXY2;F5GYU2 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 119.7 0.04836 881790000 1755880 1359320 876140 952170 1531230 1282390 1681510 1854810 1693170 FALSE TRUE 1523836.009 1350390.537 1299844.235 1168374.752 1500761.519 1331724.373 1518437.419 1458173.316 1493005.371 1.020650051 0.904478017 0.870622611 0.782565672 1.00519499 0.891975607 1.01703413 0.976669839 1 20.50978793 2.412711728 1.577931439 0.995943907 0.90264494 0.217551305 0.069018024 0.568123296 2.908525124 0.039454014 0.024140299 258.6495505 -2.412711728 -0.093298966 NVNIQNFHISWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NVNIQNFHISWK 12 0 P12814-3;P12814;P12814-2;P12814-4;H9KV75;G3V2N5;G3V2W4;G3V2X9 P12814-3 ACTN1 Alpha-actinin-1 0 147.24 6.54E-05 382990000 351310 451560 60248 177720 541900 477070 367670 503040 638030 FALSE TRUE 304883.4934 448593.6726 89384.13432 218074.0423 531117.2502 495423.1916 332013.42 395468.8107 562602.8202 0.541916042 0.797354113 0.158876086 0.387616333 0.944035883 0.880591376 0.590138208 0.702927174 1 19.10175726 3.245735592 24.99986497 0.793809734 0.472394105 0.444861895 0.193869483 179.4047907 625098.988 0.058696818 0.074175746 1760.903645 -3.245735592 -0.321415629 NVNVQNFHISWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NVNVQNFHISWK 12 0 O43707 O43707 ACTN4 Alpha-actinin-4 0 167.84 4.81E-05 1685100000 1460200 1709700 241390 719100 2097500 1921500 1497500 1796100 2491200 FALSE TRUE 1267230.87 1698468.868 358127.0114 882382.6458 2055763.854 1995421.348 1352272.68 1412017.992 2196693.174 0.576881144 0.773193493 0.163030056 0.401686797 0.935844786 0.908375085 0.615594702 0.642792543 1 21.06690194 3.246896701 24.99999774 0.787328498 0.477185536 0.431899651 0.192721868 207.4780755 622225.2118 0.058944401 0.074819799 1765.61781 -3.246896701 -0.310142963 NVPESSPHS(ph)PCEGLPSEAALTPRPEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NVPESSPHSPCEGLPSEAALTPRPEGK 27 1 S4R3H3;S4R393;S4R410;A7E2V4-5;A7E2V4;A7E2V4-3;A7E2V4-4;A7E2V4-2;H7BZ52;H0YCW2;S4R3B3;H7C453;S4R3U7 S4R3H3 ZSWIM8 Zinc finger SWIM domain-containing protein 8 1 NVPES(0.005)S(0.034)PHS(0.961)PCEGLPSEAALTPRPEGK;NVPES(0.314)S(0.275)PHS(0.41)PCEGLPS(0.001)EAALTPRPEGK 187.77 5.61E-18 685710000 251500 233655 138526 219289 320370 287980 347930 370020 372000 TRUE FALSE 218263.6378 232120.1049 205517.6369 269081.9191 313995.2638 299058.7769 314187.8022 290894.1025 328022.5838 0.665392106 0.707634524 0.626535023 0.820315223 0.957236725 0.91170179 0.957823692 0.886811204 1 18.32343562 3.507208298 3.332778233 0.934625995 0.671715554 0.920204285 0.037004495 0.05977784 1.360894364 0.010250353 0.015010768 3215.202257 -3.507208298 -0.26291044 NVPHEDICEDSDIDGDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NVPHEDICEDSDIDGDYR 18 0 O00629 O00629 KPNA4 Importin subunit alpha-3 0 ;; 189.48 3.25E-14 1752910000 514039 532841 270626 368532 560928 509774 543083 624398 536015 FALSE TRUE 446107.4437 529340.7324 401501.6388 452212.8233 549766.6302 529385.3356 490414.8942 490875.3468 472647.9173 0.943847264 1.119947244 0.849472988 0.956764659 1.163163129 1.120041613 1.0375903 1.038564498 1 18.85040637 3.281533429 24.99956489 1.067546039 0.96996535 0.300500589 0.078928647 195.6630759 113826.3226 0.023029913 0.029731268 1912.200505 -3.281533429 -0.097580689 NVPLPEFPEHPFQEEHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NVPLPEFPEHPFQEEHLK 18 0 A0A3B3ISG5;P14735 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 212.55 1.04E-16 699490000 339970 335470 189724 262680 367420 328730 378930 471990 390800 FALSE TRUE 295042.1031 333266.2755 281475.161 322325.5088 360109.0608 341376.4558 342181.4269 371058.6115 344600.0692 0.856187011 0.967110298 0.816816902 0.935361126 1.045005771 0.990645349 0.992981306 1.076780432 1 18.39456347 3.393640107 4.463230398 1.023928362 0.886714696 0.67356337 0.045165264 0.119426504 4.380505859 0.0127315 0.016752381 2475.369907 -3.393640107 -0.137213666 NVPNLHVMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NVPNLHVMK 9 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;S4R435;Q9NQ39 P46783 RPS10;RPS10-NUDT3;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 0 ; 118.18 0.0010317 2122800000 2025000 2574500 1320330 1803200 2973200 2398400 2712400 3091700 3250400 FALSE TRUE 1757391.119 2557587.94 1958846.004 2212644.12 2914039.137 2490668 2449351.865 2430564.015 2866141.415 0.613155761 0.892345342 0.683443599 0.771994051 1.01671157 0.868996898 0.854581652 0.84802655 1 21.45067836 3.404311968 9.010219972 0.901578878 0.74290722 0.491791661 0.089313488 0.275625748 31.25619585 0.024407773 0.031528111 2536.950349 -3.404311968 -0.158671658 NVPNWHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 NVPNWHR 7 0 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ;;;;;;; 135.35 0.0030858 10825080000 7333260 6682990 3377180 4352640 7790740 7525690 6714210 7770990 7716390 FALSE TRUE 6364151.111 6639088.999 5010395.544 5340973.438 7635719.516 7815208.164 6063066.948 6109224.262 6804167.165 0.935331387 0.975738667 0.736371612 0.784956235 1.122212217 1.14859144 0.891081421 0.897865105 1 22.69798715 3.252933706 24.99997414 0.995456366 0.857807438 0.338957929 0.105371294 348.3888698 605970.0625 0.034015065 0.043706531 1790.332543 -3.252933706 -0.137648929 NVPQEESLEDS(ph)DVDADFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NVPQEESLEDSDVDADFK 18 0 O00505 O00505 KPNA3 Importin subunit alpha-4 1 NVPQEESLEDS(1)DVDADFK;NVPQEESLEDS(1)DVDADFK;NVPQEESLEDS(1)DVDADFK 323.47 7.55E-62 884550000 696950 507200 365360 404850 550620 433710 596800 730560 731290 TRUE FALSE 604846.2917 503868.1698 542049.3181 496777.3802 539663.7393 450395.1043 538922.4279 574335.4292 644837.7293 0.937982169 0.781387544 0.840598019 0.770391306 0.836898517 0.698462704 0.835748908 0.890666602 1 19.29857663 1.414582246 2.057454466 1.019275241 0.808592478 0.492159657 0.061023378 0.399233478 2.39949847 0.143157305 0.01601141 25.97659638 -1.414582246 -0.210682762 NVRS(ph)DIS(ph)DQEEDEESEGCPVSINLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NVRSDISDQEEDEESEGCPVSINLSK 26 1 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;H0YBA1 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 2 NVRS(1)DIS(1)DQEEDEESEGCPVSINLSK 142.71 1.57E-07 297530000 289820 274780 160200 174360 235900 221610 282580 342970 241280 TRUE FALSE 251519.5527 272974.9521 237673.2558 213951.1029 231206.0515 230135.4801 255175.4351 269628.5345 212756.1533 1.182196373 1.283041397 1.117115779 1.005616522 1.086718518 1.0816866 1.199379812 1.267312509 1 17.69884133 4.22331298 24.94401499 1.121959332 1.232618878 0.263697213 0.083999564 330.5537373 540763.5618 0.023853083 0.049960287 16722.95343 -4.22331298 0.110659546 NVS(ph)ES(ph)PNR ddPTM_MDA-MB-175_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 142.97 0.00089029 734490000 1942930 1662380 1152980 1382390 1365500 1684810 1593230 1933670 2458000 TRUE FALSE 1686166.878 1651459.716 1710564.984 1696282.778 1338329.222 1749625.731 1438718.8 1520169.718 2167418.04 0.777961079 0.761947943 0.78921784 0.782628338 0.617476277 0.807239627 0.663793866 0.701373565 1 21.04754601 1.234169253 24.99957519 1.000000393 0.734724266 0.649082551 0.060574907 83.51337205 475370.6307 0.112282557 0.014606683 17.146254 -1.234169253 -0.265276127 NVS(ph)ES(ph)PNRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NVSESPNRK 9 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 NVS(1)ES(1)PNRK 93.348 0.0063225 141190000 877450 621500 492750 551550 526570 626390 747210 884240 1099100 TRUE FALSE 761492.7593 617417.3256 731045.5481 676787.8574 516092.2872 650487.6286 674745.6892 695152.1572 969165.6501 0.785719922 0.637060677 0.754304022 0.698320104 0.532511947 0.671183124 0.696212963 0.71726867 1 19.88638375 1.183490117 2.759430712 1.101725975 0.678205035 0.680780318 0.067730182 0.333514202 2.621643823 0.348554778 0.017560005 15.25773673 -1.183490117 -0.42352094 NVS(ph)ES(ph)PNRKNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NVSESPNRKNEK 12 2 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 NVS(1)ES(1)PNRKNEK;NVS(1)ES(1)PNRKNEK 84.41 0.060267 432150000 2080300 1396040 748740 686770 1253170 1016180 1990640 2173100 502850 TRUE FALSE 1805383.084 1386869.321 1110833.168 842711.6251 1228234.369 1055273.102 1797588.039 1708399.476 443403.6458 4.071646909 3.1277806 2.505241395 1.900551863 2.77001414 2.379937811 4.054066889 3.852921581 1 18.75826111 NVSES(ph)PNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NVSESPNR 8 0 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 NVS(0.004)ES(0.996)PNR;NVS(0.24)ES(0.76)PNR 84.06 0.018587 863300000 537870 477570 296690 328290 354930 433550 421200 473690 468580 TRUE FALSE 466789.1167 474432.8112 440170.2764 402833.2621 347867.5874 450228.949 380352.0888 372395.0798 413185.0062 1.12973392 1.148233368 1.065310381 0.974946467 0.841917258 1.089654615 0.920537007 0.901279268 1 18.65642838 3.878635113 2.516307659 0.946619721 1.137661576 0.590373896 0.064785039 0.190037054 2.33727738 0.017847666 0.037282466 7561.972845 -3.878635113 0.191041855 NVSES(ph)PNRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NVSESPNRK 9 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 NVS(0.005)ES(0.995)PNRK;NVS(0.001)ES(0.999)PNRK;NVS(0.001)ES(0.999)PNRK;NVS(0.007)ES(0.993)PNRK 132.5 0.00018574 2110724000 2850640 1992000 1217393 1469610 1496660 1746510 2099090 2558820 2360240 TRUE FALSE 2473920.701 1978914.421 1806128.327 1803307.412 1466879.394 1813699.37 1895520.575 2011636.256 2081215.116 1.188690531 0.950845689 0.867823952 0.866468535 0.70481873 0.871461751 0.910775902 0.966568155 1 20.98899466 4.724388472 2.714840373 0.885604302 1.242082153 0.60229948 0.077464194 0.335878749 3.412524852 0.021844744 0.265227398 53013.74344 -4.724388472 0.356477851 NVSKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 NVSKPR 6 1 Q9Y3U8;J3QSB5;J3KTD3 Q9Y3U8 RPL36 60S ribosomal protein L36 0 ;;;; 121.68 0.017826 748380000 1949070 1882420 903260 1150980 1286180 1895720 2227080 2375240 2262380 FALSE TRUE 1691495.461 1870054.259 1340079.557 1412327.601 1260587.534 1968649.575 2011098.124 1867313.41 1994924.014 0.847899694 0.93740626 0.671744662 0.707960599 0.631897519 0.986829354 1.008107632 0.936032349 1 20.92790236 2.716293326 24.56108419 0.977821928 0.761546542 0.614877611 0.087790668 476.0784097 525119.1885 0.032409291 0.02860556 520.3473246 -2.716293326 -0.216275387 NVSSFPDDATS(ph)PLQENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NVSSFPDDATSPLQENR 17 0 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 1 NVSSFPDDAT(0.003)S(0.997)PLQENR;NVSSFPDDAT(0.013)S(0.987)PLQENR;NVSSFPDDATS(1)PLQENR;NVSSFPDDAT(0.001)S(0.999)PLQENR;NVSSFPDDAT(0.023)S(0.977)PLQENR;NVSSFPDDAT(0.001)S(0.999)PLQENR 420.54 2.18E-160 3284950000 2452690 2752760 1278930 1589170 2674290 2753600 2455230 2922480 2711570 TRUE FALSE 2128560.802 2734676.938 1897424.826 1950015.337 2621076.861 2859532.774 2217122.172 2297530.395 2391011.284 0.890234528 1.143732343 0.793565818 0.81556091 1.096221034 1.195951183 0.927273822 0.9609032 1 21.18918951 3.227261662 24.99977842 1.026508371 0.919041339 0.213012698 0.118412264 425.0921351 940546.1123 0.037804641 0.043244755 1687.569477 -3.227261662 -0.107467032 NVSTGS(ph)AENEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NVSTGSAENEEK 12 0 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 NVST(0.002)GS(0.998)AENEEK;NVST(0.004)GS(0.996)AENEEK 154.99 7.55E-05 634460000 905120 796640 712960 782140 1028360 911300 972540 1148690 1943710 TRUE FALSE 785506.0987 791406.8194 1057749.841 959736.8413 1007897.648 946358.3007 878223.2205 903051.5826 1713926.818 0.45830784 0.461750648 0.617149945 0.559963723 0.588063409 0.55215794 0.512404154 0.526890398 1 20.70887408 1.237839928 24.99972183 1.000000535 0.536502836 0.896049257 0.049814596 5.527054365 191590.4009 0.074048987 0.012708948 17.29178903 -1.237839928 -0.463497699 NVTELNEPLSNEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NVTELNEPLSNEER 14 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ; 298.82 2.22E-43 593610000 445380 437560 277880 319030 448990 499690 406470 430760 540020 FALSE TRUE 386521.9046 434685.6395 412263.6975 391470.6376 440055.9774 518913.3976 367050.602 338645.3262 476179.4508 0.811714793 0.912860979 0.86577381 0.822107373 0.92413895 1.089743366 0.770824111 0.711171651 1 18.86114584 NVTFHGVLLDAFFNESSADWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 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 ;;;;;;;;;;; 285.46 2.36E-45 13252716400 4872990 4677050 3078485.6 2940778 5235680 5907574 5924060 6165777 7695868 FALSE TRUE 4229012.025 4646326.151 4567251.533 3608526.592 5131500.211 6134842.194 5349545.573 4847273.571 6786071.252 0.623190041 0.68468573 0.673033242 0.531754893 0.756181304 0.90403445 0.788312615 0.714297476 1 22.69414515 3.030296268 8.12090348 0.82497632 0.635980278 0.597888167 0.085153155 0.173882008 39.70211891 0.025978252 0.029285228 1072.250526 -3.030296268 -0.188996042 NVVGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NVVGAR 6 0 P31946-2;P31946;Q4VY19;A0A0J9YWE8;Q4VY20;A0A0J9YWZ2;P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;P61981;Q04917;A2IDB2 P31946-2;P63104;P61981;Q04917 YWHAB;YWHAZ;YWHAG;YWHAH "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed;14-3-3 protein zeta/delta;14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed;14-3-3 protein eta" 0 ;;; 124.94 0.042201 1340780000 1321550 1207370 604618 721820 962440 1374380 1190650 1302370 1305840 FALSE TRUE 1146903.819 1199438.707 897013.2871 885720.2633 943289.327 1427253.288 1075180.946 1023868.311 1151465.083 0.99603873 1.041663117 0.779019095 0.769211569 0.81920793 1.239510697 0.933750369 0.889187459 1 20.13503923 NVVHQLS(ph)VTLEDLYNGATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NVVHQLSVTLEDLYNGATR 19 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 1 NVVHQLS(0.997)VT(0.003)LEDLYNGATR 115.55 8.74E-05 17190000 16902 17647 10071 10738 17694 19880 13896 18118 22613 TRUE FALSE 14668.35788 17531.0757 14941.36929 13176.22702 17341.92402 20644.79646 12548.36806 14243.60669 19939.7169 0.735635212 0.879203841 0.749327052 0.660803114 0.869717665 1.03536056 0.629315257 0.714333446 1 14.28335731 NVWSFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NVWSFLK 7 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 83.206 0.052228 70035000 208580 252950 221110 145320 258580 257520 204220 262080 236170 FALSE TRUE 181015.6245 251288.3548 328039.5356 178317.1271 253434.7639 267426.961 184414.7758 206036.2315 208250.2516 0.869221636 1.206665312 1.575217955 0.856263681 1.216972186 1.284161526 0.885544072 0.989368464 1 17.66795871 2.23341323 24.99896519 0.961744222 1.176392095 0.188039701 0.204968445 208.0520762 1010418.744 0.080355076 0.056022115 171.1643164 -2.23341323 0.214647872 NVYQNYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NVYQNYR 7 0 Q8IYI6 Q8IYI6 EXOC8 Exocyst complex component 8 0 ; 138.62 0.0064404 136629000 104799 137846 90175 63247 145996 143235 123338 124256 134531 FALSE TRUE 90949.54662 136940.4805 133783.9316 77608.19802 143090.9652 148745.3431 111376.6997 97684.82136 118626.8984 0.7666857 1.154379676 1.127770627 0.654220915 1.206226978 1.253892204 0.938882338 0.82346266 1 16.85607165 2.013015291 24.99568543 0.89373675 1.034370874 0.062411295 0.192425868 532.4614441 1022580.769 0.078029713 0.052576605 103.04224 -2.013015291 0.140634124 NVYSS(ph)SR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NVYSSSR 7 0 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 1 NVYS(0.431)S(0.568)S(0.001)R 91.085 0.027125 0 199910 199260 110990 130970 174890 243760 176210 230840 262100 TRUE FALSE 173491.387 197951.0479 164665.1352 160708.7403 171410.0312 253137.6049 159121.1813 181476.6624 231114.8366 0.750671785 0.856505151 0.712481889 0.695363148 0.741666064 1.095289289 0.688494013 0.785222901 1 17.81825035 NWADVQSQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NWADVQSQLR 10 0 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 161.44 1.65E-05 152000000 178190 145710 222640 147090 133500 119510 189310 152720 144690 FALSE TRUE 154641.74 144752.8214 330309.4487 180489.0326 130843.6112 124107.627 170950.7453 120062.0165 127584.913 1.212069173 1.134560647 2.58893815 1.414658115 1.025541407 0.97274532 1.339897808 0.941036159 1 16.96109821 3.39664278 5.153764743 1.063459508 1.655195265 0.312723681 0.40159092 0.246455339 11.42430721 0.117715413 0.153721786 2492.543694 -3.39664278 0.591735757 NWDDMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NWDDMK 6 0 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 105.95 0.075704 566400000 1041500 811110 558050 697260 803620 695660 1022700 1160200 988600 FALSE TRUE 903863.1362 805781.765 827924.8466 855583.54 787629.5343 722422.4904 923518.7114 912100.2587 871728.8342 1.036862727 0.924349102 0.949750443 0.981478995 0.903525848 0.828723867 1.059410536 1.046311907 1 19.7335199 2.191247497 24.99999885 1.038554522 0.93787123 0.413331696 0.054872926 113.946039 60207.63768 0.022497098 0.015167579 155.3271942 -2.191247497 -0.100683292 NWDDVLTVDYTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NWDDVLTVDYTR 12 0 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 0 ; 240.8 7.43E-16 109489000 240528 231168 139065 188323 259202 287701 226727 285142 351699 FALSE TRUE 208741.6154 229649.4422 206317.2991 231084.6155 254044.3873 298769.0436 204739.0504 224166.6023 310121.5449 0.673096142 0.740514311 0.665278832 0.745142088 0.819176841 0.963393381 0.660189702 0.722834663 1 18.24247423 3.415429707 3.861734429 0.81243377 0.69816436 0.277193753 0.10156852 0.368648781 11.16985645 0.031035593 0.041769786 2602.733529 -3.415429707 -0.11426941 NWDEWVPESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NWDEWVPESR 10 0 H0YMJ0;H0YLJ3;Q9UBU8-2;B3KTM8 H0YMJ0 MORF4L1 0 94.692 0.01845 62895000 112800 103650 58411 67019 117450 100790 99554 103670 93639 FALSE TRUE 97893.1942 102969.1163 86658.75497 82236.68827 115112.9748 104667.4565 89899.2684 81500.97726 82569.10409 1.185591091 1.247065927 1.049530038 0.99597409 1.394141017 1.26763464 1.088776115 0.987063844 1 16.33331443 1.98888707 4.400366004 1.001354431 1.186809709 0.354179735 0.110039617 0.237869089 11.29947913 0.057913095 0.032267615 97.47361432 -1.98888707 0.185455278 NWEEGGYFNTDKPHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NWEEGGYFNTDKPHPR 16 1 O95573 O95573 ACSL3 Long-chain-fatty-acid--CoA ligase 3 0 205.78 1.31E-11 241900000 539990 468820 330570 506040 788630 616230 450780 827380 923480 FALSE TRUE 468628.9533 465740.2906 490434.7577 620944.1163 772937.8059 639936.7669 407063.425 650451.2257 814307.2464 0.575494023 0.571946636 0.602272373 0.762542786 0.949196767 0.785866477 0.499889233 0.798778629 1 19.63521372 3.742289105 4.216002153 0.787619874 0.578178461 0.377198374 0.130979223 0.252131916 11.20665696 0.038106908 0.063740634 5524.450738 -3.742289105 -0.209441413 NWGGPDFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NWGGPDFER 9 0 A0A2R8Y4Z8;Q9Y3X0 A0A2R8Y4Z8;Q9Y3X0 CCDC9 Coiled-coil domain-containing protein 9 0 ; 93.178 0.022276 368160000 723110 825850 405920 545910 823780 786840 784910 803270 890380 FALSE TRUE 627549.1814 820424.937 602224.2697 669867.2092 807388.3897 817110.244 708789.549 631496.9616 785120.2907 0.799303226 1.044967181 0.767047135 0.853203283 1.028362659 1.040745289 0.902778284 0.804331475 1 19.58255419 NWQNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NWQNVR 6 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ; 109.8 0.068051 464880000 586540 593290 327930 426760 717420 650970 544220 697940 724290 FALSE TRUE 509027.2529 589392.6389 486518.0449 523662.3806 703144.7456 676013.2371 491441.6282 548690.9624 638665.2613 0.797017285 0.92285063 0.761773145 0.819932463 1.100959749 1.05847817 0.769482322 0.859121351 1 19.28470046 NWQWWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NWQWWR 6 0 P35579;P35579-2;P35749;P35749-2;P35749-4;P35749-3 P35579;P35749 MYH9;MYH11 Myosin-9;Myosin-11 0 ; 116 0.055721 8863800000 3431600 3892000 2141760 2539670 4577800 4322100 3665600 4111700 5276400 FALSE TRUE 2978105.365 3866433.196 3177522.3 3116340.89 4486710.736 4488373.984 3310110.676 3232444.952 4652630.003 0.640090737 0.831020991 0.682951857 0.669802002 0.964338607 0.964696093 0.711449368 0.694756503 1 22.14961503 3.265796218 24.99262591 0.83872425 0.71325495 0.314245081 0.113828179 363.9551995 333979.381 0.035279894 0.045534927 1844.149895 -3.265796218 -0.1254693 NWRDPDQTDGLGLSYLSSHIANVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NWRDPDQTDGLGLSYLSSHIANVER 25 1 P06396-2;A0A0A0MS51;A0A0A0MT01;P06396-4;P06396-3;P06396 P06396-2 GSN Gelsolin 0 ;;; 256.88 3.94E-45 1569610000 737906 582112 200692 275374 623848 698530 574656 662010 280929 FALSE TRUE 640389.8525 578288.0679 297747.3225 337901.8755 611434.6453 725402.9011 518925.9496 520444.3133 247717.8937 2.58515783 2.334462236 1.201961304 1.364059215 2.46827 2.928342763 2.094826264 2.10095567 1 17.91833856 3.214417005 24.99783556 2.15500759 1.856666825 0.035633689 0.620667798 844.7252839 874609.6984 0.19840765 0.225082549 1638.388931 -3.214417005 -0.298340765 NWTEDMEGGIS(ph)SPVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.834)S(0.166)PVKK;NWTEDMEGGIS(0.5)S(0.5)PVKK 149.3 8.99E-07 716092000 1568970 1122080 824030 946160 1309670 832680 1656490 2023650 1517280 TRUE FALSE 1361626.639 1114708.983 1222533.664 1161000.089 1283610.129 864713.7384 1495843.855 1590908.196 1337908.887 1.017727479 0.833172568 0.913764514 0.867772163 0.959415205 0.646317359 1.118046131 1.189100552 1 20.35154844 2.125331037 14.65243502 1.121688256 0.87676987 0.503645064 0.106724568 0.496874437 62.00272071 0.040732318 0.027461605 133.4538284 -2.125331037 -0.244918386 NWTEDMEGGISS(ph)PVKK ddPTM_MDA-MB-175_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(0.019)S(0.981)PVKK;NWTEDMEGGIS(0.166)S(0.834)PVKK;NWTEDMEGGIS(0.093)S(0.907)PVKK 258.37 6.44E-27 2151240000 4296200 3259860 2479340 2620740 3194590 2322990 4294800 5145500 4039670 TRUE FALSE 3728446.285 3238445.765 3678357.117 3215819.073 3131023.909 2412356.928 3878290.957 4045174.867 3562104.815 1.046697523 0.909138258 1.032635845 0.902786201 0.878981409 0.677227946 1.088763851 1.135613655 1 21.76429854 2.093588529 24.9007792 1.088181905 0.909661403 0.357861472 0.104850974 15.86034856 4210.599387 0.043319632 0.02920609 124.0476464 -2.093588529 -0.178520502 NYAGAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NYAGAYR 7 0 Q8NFU3;Q8NFU3-4;R4GNF9;Q8NFU3-2 Q8NFU3 TSTD1 Thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1 0 ;;; 189.97 0.0012733 4206390000 3400080 4203440 1754640 2249820 4894370 4867290 4126010 4412850 4270690 FALSE TRUE 2950750.813 4175827.326 2603189.773 2760676.017 4796981.613 5054537.796 3725870.185 3469196.368 3765813.893 0.78356257 1.108877774 0.691268832 0.733088808 1.273823335 1.342216567 0.989393074 0.921234152 1 21.84453027 3.250612825 24.99976128 1.085469666 0.839324324 0.396875324 0.167955076 288.5783712 598591.5854 0.053320318 0.068303148 1780.79048 -3.250612825 -0.246145341 NYDTTIHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NYDTTIHGK 9 0 J3QRN6;O94832;K7EIG7;J3KRL0 J3QRN6 MYO1D Unconventional myosin-Id 0 95.573 0.0079534 151330000 252780 212400 108790 168200 253530 225730 214780 259140 260260 FALSE TRUE 219374.4825 211004.7304 161401.2079 206392.3808 248485.249 234413.9792 193950.6687 203724.9276 229492.3593 0.955911923 0.919441201 0.703296652 0.899343148 1.082760445 1.021445681 0.84512909 0.887719871 1 17.8080866 3.473355728 24.99873032 0.954623084 0.854835853 0.219655069 0.092353689 189.4370266 1257631.655 0.028440252 0.036888894 2974.101103 -3.473355728 -0.099787231 NYDYYASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NYDYYASR 8 0 O95861-3;O95861-4;O95861 O95861-3 BPNT1 "3(2),5-bisphosphate nucleotidase 1" 0 ;;; 138.98 0.0015873 3198050000 2248480 2102590 1213130 1425640 2007200 2001840 2445890 2531630 1976900 FALSE TRUE 1951337.671 2088777.948 1799803.726 1749353.352 1967260.647 2078852.08 2208687.964 1990260.626 1743193.134 1.119404174 1.19824815 1.032475226 1.00353387 1.128538547 1.192554078 1.267035718 1.141732713 1 20.73330099 3.003987274 24.93580783 1.15999698 1.088986253 0.106491705 0.082871313 240.9649345 1506938.467 0.026466184 0.029889432 1009.223312 -3.003987274 -0.071010726 NYEEIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NYEEIAK 7 0 P49755 P49755 TMED10 Transmembrane emp24 domain-containing protein 10 0 105.57 0.018373 215530000 91677 94602 61114 65273 107820 94805 98669 108930 108740 FALSE TRUE 79561.65217 93980.55323 90668.93481 80094.23229 105674.5929 98452.2097 89100.09557 85636.16719 95884.88108 0.829762224 0.980139436 0.945601995 0.835316594 1.102098597 1.026775114 0.929240299 0.893114391 1 16.54901573 3.277238149 24.99994097 0.975355992 0.907014561 0.275797342 0.071608612 307.562014 198796.4592 0.022006499 0.028409688 1893.381586 -3.277238149 -0.068341432 NYEQWQLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NYEQWQLQR 9 0 A0A590UJQ1;Q96J02-3;Q96J02-2;Q96J02;A0A590UK44;A0A590UJW8;A0A590UK95 A0A590UJQ1 ITCH E3 ubiquitin-protein ligase Itchy homolog 0 81.972 0.045998 85782000 93076 69347 30463 44003 99695 100390 76069 93612 58512 FALSE TRUE 80775.77078 68891.45499 45195.00869 53994.55369 97711.26455 104252.0683 68691.84009 73593.80229 51594.77802 1.565580353 1.335240845 0.87596091 1.046511988 1.893820815 2.020593406 1.331371947 1.42638083 1 15.65493744 3.265286291 24.99654257 1.530005518 1.191505992 0.195241048 0.330877809 394.6819817 369143.6467 0.101993488 0.131634801 1841.985855 -3.265286291 -0.338499527 NYEYCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NYEYCR 6 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 111.73 0.064213 253410000 170770 184710 98937 104190 198020 216010 169540 199030 191130 FALSE TRUE 148202.3118 183496.6278 146783.2641 127847.9319 194079.7894 224320.0445 153098.0369 156468.9834 168534.8291 0.879357178 1.088775708 0.870937271 0.758584636 1.151570808 1.331001109 0.908405922 0.928407405 1 17.36268724 3.225523065 24.99984953 1.048639189 0.91090549 0.240739225 0.143078181 440.8514422 845342.2583 0.047496355 0.054179441 1680.827191 -3.225523065 -0.137733699 NYFESTDGLIWVVDSADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NYFESTDGLIWVVDSADR 18 0 V9GYD0;P36404-2;P36404 V9GYD0 ARL2-SNX15;ARL2 ADP-ribosylation factor-like protein 2 0 190.87 2.89E-18 0 46837 42529 22179 32318 42255 44504 38053 43371 33963 FALSE TRUE 40647.37178 42249.6242 32904.83858 39656.29585 41414.20817 46216.09768 34362.62592 34096.44916 29947.93283 1.357268029 1.410769299 1.098734887 1.324174729 1.382873683 1.54321495 1.147412281 1.138524297 1 14.8701688 2.036482128 16.51330448 1.098298359 1.344104524 0.533539277 0.114333641 4.018426121 1818.258836 0.048364392 0.032603192 108.7632379 -2.036482128 0.245806165 NYGFVHIEDK ddPTM_MDA-MB-175_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 0 113.38 0.001496 366420000 1397100 1041900 640430 751780 1236700 1023300 1318600 1526400 1494700 FALSE TRUE 1212469.695 1035055.69 950144.0901 922483.1392 1212092.09 1062667.013 1190722.375 1199991.238 1317998.269 0.919932692 0.785324014 0.720899346 0.699912254 0.919646192 0.806273451 0.903432427 0.910464958 1 20.32991704 1.574124222 0.728505734 1.057013236 0.790421837 0.449479142 0.071686524 1.788260462 1.023984276 0.374865812 0.034991408 37.50802714 -1.574124222 -0.266591399 NYGYNPS(ph)PVKPEGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 NYGYNPSPVKPEGLR 15 1 E9PRF4;Q15047-3;Q15047 E9PRF4 SETDB1 Histone-lysine N-methyltransferase SETDB1 1 NYGYNPS(1)PVKPEGLR;NYGYNPS(1)PVKPEGLR;NYGYNPS(1)PVKPEGLR 167.97 7.75E-07 1394640000 1323160 1096720 580997 791909 1328660 1038170 1349720 1553890 1312320 TRUE FALSE 1148301.054 1089515.574 861969.0925 971724.042 1302222.265 1078109.072 1218824.362 1221602.716 1157179.025 0.992327919 0.941527241 0.744888279 0.839735271 1.125342093 0.931670078 1.053272083 1.055673055 1 20.14218065 3.251996288 24.99819348 1.032431644 0.874417948 0.477622968 0.07972092 204.3664098 380238.6159 0.023373713 0.030002565 1786.472307 -3.251996288 -0.158013697 NYHIFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NYHIFYR 7 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ; 79.597 0.032193 729180000 542840 657590 257870 326550 737950 845140 527150 547630 529680 FALSE TRUE 471102.3186 653270.248 382576.7945 400698.1685 723266.2388 877653.0827 476027.0741 430523.5862 467061.8338 1.008650856 1.398680433 0.819113802 0.857912464 1.548544939 1.879093985 1.019194975 0.921769999 1 18.83325403 3.264690952 24.99982585 1.240906501 1.033633476 0.128422432 0.320025188 662.7031259 634027.2508 0.103518868 0.133599265 1839.462557 -3.264690952 -0.207273025 NYILDQTNVYGS(ph)AQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NYILDQTNVYGSAQR 15 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 1 NYILDQTNVYGS(1)AQR 111.43 0.0017474 0 55052 47621 28962 32988 43615 59018 45248 50197 59203 TRUE FALSE 47776.73872 47308.17452 42968.12007 40478.42959 42747.14683 61288.46065 40859.85592 39462.76218 52204.08878 0.915191508 0.906215885 0.823079592 0.775388107 0.818846719 1.174016482 0.782694553 0.755932401 1 15.67187519 2.538520304 0.00607733 0.66592288 1.078304017 0 0.127721388 508758.4519 2663.15988 90931.24653 89769.59229 345.5574842 -2.538520304 0.412381137 NYILSAS(ph)ASALWNDEVDKAEQELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NYILSASASALWNDEVDKAEQELR 24 1 B7ZC38;Q9NR46;Q9NR46-2 B7ZC38 SH3GLB2 Endophilin-B2 1 NYILS(0.003)AS(0.87)AS(0.127)ALWNDEVDKAEQELR 135.35 1.73E-05 42747000 19227 16252 10202 11924 17353 14288 20311 21974 19269 TRUE FALSE 16686.10323 16145.23954 15135.72132 14631.52645 17007.70925 14837.66861 18341.24235 17275.0311 16991.04077 0.98205304 0.950220752 0.890806015 0.861131854 1.000981016 0.873264258 1.079465501 1.016714122 1 14.05248661 2.237096063 24.9999832 1.030838078 0.926295929 0.514131407 0.048410841 30.73275325 524588.6654 0.018625529 0.013323154 172.6219679 -2.237096063 -0.104542149 NYIQIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NYIQIER 7 0 H7BZD3;C9J060;C9JIU5;Q8IYM9 H7BZD3 TRIM22 E3 ubiquitin-protein ligase TRIM22 0 ; 107.43 0.0074794 308890000 91395 93899 44317 50522 80216 118881 60002 64213 66087 FALSE TRUE 79316.91918 93282.17129 65748.84943 61993.79228 78619.85854 123454.429 54183.01528 50481.54966 58274.27015 1.361096741 1.600743708 1.128265515 1.063827863 1.349135019 2.118506653 0.929793117 0.866275108 1 15.83057141 2.061669506 24.99999437 0.915892567 1.418959178 0.403246608 0.288827667 66.51280874 26962.8443 0.120651702 0.081343349 115.2575824 -2.061669506 0.503066611 NYISQYSEIAIQMMMHMQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NYISQYSEIAIQMMMHMQPK 20 0 P07602 P07602 PSAP Prosaposin;Saposin-A;Saposin-B-Val;Saposin-B;Saposin-C;Saposin-D 0 ; 202.97 1.11E-21 104660000 115410 127924 72193 73823 96887 88808 149449 150147 77660 FALSE TRUE 100158.2761 127083.6588 107105.7763 90585.64046 94959.13826 92224.50123 134955.459 118039.2325 68479.12327 1.462610374 1.855801487 1.564064654 1.322821265 1.386687412 1.346753533 1.970753312 1.723725814 1 16.06337661 4.010631165 24.79908314 1.505307503 1.671887753 0.069059969 0.272807345 632.0686144 1474384.235 0.072529285 0.150745039 10247.81236 -4.010631165 0.16658025 NYIVEDGDIIFFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NYIVEDGDIIFFK 13 0 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 172.92 5.25E-05 17955000 76490 66625 27721 46751 61442 50419 63753 81763 71249 FALSE TRUE 66381.6527 66187.33599 41126.96832 57366.52909 60219.42441 52358.65156 57570.24387 64278.61873 62826.02439 1.056594832 1.053501899 0.654616757 0.913101372 0.958510824 0.833391132 0.916343895 1.023120902 1 15.93907467 1.772165623 5.753559208 1.011007728 0.906162754 0.115030506 0.113553515 0.371116025 28.77307028 0.065485697 0.030431315 59.17872756 -1.772165623 -0.104844974 NYLLSLPHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NYLLSLPHK 9 0 P28482 P28482 MAPK1 Mitogen-activated protein kinase 1 0 ; 75.294 0.038668 1060980000 1226560 1551380 640380 826660 1847100 1610320 1602900 1786280 1832270 FALSE TRUE 1064466.988 1541188.883 950069.9099 1014365.788 1810346.324 1672270.052 1447451.005 1404297.923 1615661.128 0.658842978 0.953906024 0.588037859 0.627833257 1.120498781 1.035037622 0.895887745 0.869178504 1 20.62369321 3.248035532 24.99984939 0.965681181 0.716271717 0.567867009 0.119337996 170.7678543 450573.6251 0.036020795 0.045879448 1770.253787 -3.248035532 -0.249409464 NYLPAINGIVFLVDCADHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NYLPAINGIVFLVDCADHER 20 0 Q9Y6B6;D6RD69;D6RDB2;Q9H029;D6R9R5 Q9Y6B6 SAR1B;DKFZp434B2017 GTP-binding protein SAR1b 0 ; 181.14 5.21E-17 903120000 431400 498820 228450 270300 587490 508580 532760 628600 558020 FALSE TRUE 374389.397 495543.2186 338929.1841 331675.7463 575800.0984 528145.4017 481093.0172 494178.7818 492051.5113 0.760874397 1.007096223 0.688808339 0.674067122 1.170202886 1.073353886 0.97772897 1.004323268 1 18.90844983 3.240818794 24.99999999 1.036379127 0.79203163 0.611236298 0.103741747 44.88571474 496919.6737 0.031451384 0.038655077 1741.08027 -3.240818794 -0.244347497 NYLPAINGIVFLVDCADHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NYLPAINGIVFLVDCADHSR 20 0 Q9NR31;Q5SQT8;Q9NR31-2 Q9NR31 SAR1A GTP-binding protein SAR1a 0 ; 171.25 8.10E-12 2010520000 483690 525000 210265 285070 550290 541260 572740 603260 538600 FALSE TRUE 419769.141 521551.2404 311949.8573 349799.5005 539340.3056 562082.6224 517195.763 474257.5436 474927.3216 0.883859744 1.098170639 0.656837042 0.736532696 1.135627034 1.183512923 1.08899981 0.998589725 1 18.85734723 3.230305624 24.99999102 1.076683789 0.848657711 0.472192822 0.124668759 180.0828711 545374.4951 0.04004791 0.046170732 1699.43917 -3.230305624 -0.228026078 NYLSIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NYLSIFR 7 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 87.323 0.045195 277440000 858170 827570 524360 663530 955640 941260 1022210 1035830 1187930 FALSE TRUE 744760.6602 822133.6382 777942.2499 814194.6279 936624.6337 977470.8813 923076.2315 814325.8153 1047494.269 0.710992587 0.784857409 0.742669696 0.777278361 0.894157287 0.933151532 0.881223181 0.7774036 1 19.99851092 3.315342233 4.485935596 0.882912311 0.75183471 0.596292094 0.058211004 0.17240755 6.479691684 0.017739761 0.022849172 2067.008359 -3.315342233 -0.131077601 NYQQNYQNS(ph)ESGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NYQQNYQNSESGEK 14 0 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NYQQNYQNS(0.999)ES(0.001)GEK 252.36 1.04E-12 0 139980 105300 96352 108430 120080 113420 121520 153300 396190 TRUE FALSE 121481.2883 104608.2774 142948.1495 133050.6887 117690.6429 117783.3408 109735.0091 120517.988 349352.8695 0.347732333 0.29943443 0.409179835 0.380848994 0.336881856 0.337147197 0.314109368 0.344974948 1 18.41432546 1.238521018 24.9998769 1.000000713 0.345720133 0.97796419 0.030838275 0.127292252 79337.93488 0.043107745 0.007727565 17.31892846 -1.238521018 -0.65428058 NYQQNYQNS(ph)ESGEKNEGSESAPEGQAQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NYQQNYQNS(0.999)ES(0.001)GEKNEGSESAPEGQAQQR;NYQQNYQNS(0.822)ES(0.178)GEKNEGSESAPEGQAQQR;NYQQNYQNS(1)ESGEKNEGSESAPEGQAQQR;NYQQNY(0.003)QNS(0.881)ES(0.116)GEKNEGSESAPEGQAQQR 482.24 1.72E-272 5912960000 2333380 1661284 1064410 1167624 1952080 1824280 2037930 2441210 1989470 TRUE FALSE 2025017.921 1650370.916 1579162.236 1432750.875 1913237.427 1894461.232 1840291.862 1919176.239 1754277.123 1.15433183 0.940769787 0.900178322 0.816718668 1.090612995 1.0799099 1.049031443 1.093998328 1 20.74244524 3.185531444 24.99994949 1.066455702 0.948351474 0.280001303 0.087163016 118.8700972 56039.2263 0.026443133 0.029983725 1532.962192 -3.185531444 -0.118104228 NYQQNYQNSESGEKNEGS(ph)ESAPEGQAQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NYQQNYQNSESGEKNEGS(0.992)ES(0.008)APEGQAQQR;NYQQNYQNSESGEKNEGS(0.999)ES(0.001)APEGQAQQR 476.35 2.52E-272 2251630000 962779 650019 473964 539141 919256 693387 932362 1041544 798224 TRUE FALSE 835545.3158 645748.9824 703174.5757 661561.2043 900964.6041 720062.0466 841941.6767 818817.9209 703858.8681 1.18709212 0.917440998 0.999027799 0.939906044 1.280035878 1.023020494 1.196179682 1.163326852 1 19.42492666 3.263280234 24.99989146 1.135664892 1.003347839 0.243057034 0.106222766 293.7247474 297052.9929 0.028567041 0.036862575 1833.497128 -3.263280234 -0.132317053 NYQQNYQNSESGEKNEGSESAPEGQAQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ; 373.54 1.14E-136 607260000 194246 144037 90315 99674 166348 132669 165059 191212 143586 FALSE TRUE 168575.8989 143090.8115 133991.6361 122306.5051 163038.0003 137772.8623 149051.6036 150322.8018 126611.4267 1.33144301 1.130157169 1.058290232 0.965998949 1.287703682 1.088155042 1.177236585 1.187276739 1 16.95004809 4.735489658 5.453610847 1.118776911 1.339054976 0.35116266 0.093513943 0.171206037 19.49734984 0.022495611 0.141166443 54386.31805 -4.735489658 0.220278065 NYS(ph)SPPPCHLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 NYSSPPPCHLSR 12 0 Q12986;Q12986-2;Q12986-3 Q12986 NFX1 Transcriptional repressor NF-X1 1 NYS(0.618)S(0.382)PPPCHLSR;NY(0.001)S(0.643)S(0.356)PPPCHLSR 111.43 0.00089039 510830000 439070 555420 115199 250410 613240 613150 447420 518450 565940 TRUE FALSE 381045.787 551771.4094 170909.6217 307269.4178 601037.7238 636738.2773 404029.2773 407583.5021 499035.2179 0.763564922 1.105676292 0.342480081 0.61572692 1.204399414 1.27593856 0.80962077 0.816742962 1 18.92878211 3.253996659 24.9997363 0.992616643 0.709321474 0.304295409 0.23403918 365.20424 591470.0507 0.072405632 0.093131149 1794.71982 -3.253996659 -0.283295169 NYS(ph)VGSRPLKPLSPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NYSVGSRPLKPLSPLR 16 2 O60825 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 NYS(0.995)VGS(0.005)RPLKPLSPLR 121.63 5.10E-05 1205600000 453930 955690 573300 648070 1383200 1197900 1320700 1370400 1107700 TRUE FALSE 393942.0004 949412.0095 850549.7976 795224.1986 1355677.026 1243983.988 1192618.717 1077350.624 976748.9679 0.403319597 0.972012299 0.87079672 0.814154122 1.387948256 1.273596419 1.221008423 1.10299643 1 19.8976283 3.309517193 8.306059801 1.190557684 0.784940853 0.59663889 0.176186943 0.200663636 20.93020226 0.050660612 0.065350597 2039.469398 -3.309517193 -0.405616831 NYSEVIEVDES(ph)DVEEDIFPTTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NYSEVIEVDESDVEEDIFPTTSK 23 0 F8W7U8;P49959-2;P49959;P49959-3 F8W7U8 MRE11A Double-strand break repair protein MRE11A 1 NY(0.004)S(0.004)EVIEVDES(0.993)DVEEDIFPTTSK 58.904 0.045843 15308000 145400 115370 82335 89409 121780 106590 135840 145950 145200 TRUE FALSE 126185.0216 114612.1269 122152.4814 109710.68 119356.8163 110690.5863 122666.2577 114739.7283 128034.6214 0.985553909 0.895165117 0.954058207 0.856882918 0.93222298 0.864536366 0.958071 0.896161734 1 16.96617445 1.230188746 24.98294758 1.000000158 0.916005355 0.28096902 0.041217792 387.7309099 1156956.857 0.100641451 0.008998367 16.98981875 -1.230188746 -0.083994803 NYSS(ph)PPPCHLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NYSSPPPCHLSR 12 0 Q12986;Q12986-2;Q12986-3 Q12986 NFX1 Transcriptional repressor NF-X1 1 NYS(0.284)S(0.716)PPPCHLSR 90.561 0.0056626 151320000 192180 222930 67668 153390 251770 245910 192030 229470 241200 TRUE FALSE 166782.9261 221465.5582 100392.4711 188219.5439 246760.2696 255370.3168 173406.9602 180399.6262 212685.6108 0.78417588 1.041281342 0.472022864 0.884966046 1.160211397 1.200693906 0.815320602 0.848198548 1 17.69836291 3.478947349 24.97940305 0.984664646 0.774225875 0.26866235 0.178812491 107.7781693 1474327.68 0.053502912 0.070155788 3012.640767 -3.478947349 -0.210438771 NYSVGSRPLKPLS(ph)PLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NYSVGSRPLKPLSPLR 16 2 O60825 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 NYSVGSRPLKPLS(1)PLR 81.884 0.0060189 913870000 1232400 1271000 585200 655010 1214300 1083100 1279000 1448400 830790 TRUE FALSE 1069535.217 1262650.717 868204.6774 803740.0317 1190137.806 1124767.558 1154962.777 1138670.931 732574.9526 1.459966948 1.723578881 1.185141089 1.097143751 1.624595274 1.535361745 1.57657967 1.554340518 1 19.48261685 1.232514339 24.99459795 0.999999224 1.472885154 0.371615826 0.19186203 236.8027781 978815.8289 0.436091495 0.048945571 17.08104115 -1.232514339 0.47288593 NYTDNELEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 NYTDNELEK 9 0 P00367;P00367-2;P00367-3 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 130.94 0.0026856 0 94275 91311 68531 96132 117880 100150 101970 132450 115420 FALSE TRUE 81816.31989 90711.17203 101672.8208 117960.2399 115534.4186 104002.8353 92080.96509 104126.5982 101775.1791 0.803892664 0.891289731 0.998994271 1.159027584 1.135192487 1.021888011 0.904748741 1.023104053 1 16.63502623 4.339733591 2.710712979 1.035977738 0.816182842 0.568656631 0.070431905 0.229448002 3.223410935 0.020696745 0.076053527 21864.20001 -4.339733591 -0.219794896 NYTEEEDRFLICMLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 148.56 5.53E-07 94510000 81439 86667 47840 54422 91907 81545 87548 103230 88171 FALSE TRUE 70676.62981 86097.67877 70975.58402 66779.34689 90078.23051 84682.08892 79057.60844 81155.06784 77747.52482 0.909053117 1.107400898 0.91289831 0.858925696 1.158599334 1.089193374 1.016850486 1.043828315 1 16.24650913 3.239922142 24.99995538 1.057472712 0.956080965 0.352872593 0.076583661 48.00840066 881511.3708 0.022924778 0.028000678 1737.489311 -3.239922142 -0.101391747 NYYEQWGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 NYYEQWGK 8 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;; 242.87 1.73E-08 24302760000 11456460 8447670 4393650 5834230 9650900 7862750 9569480 10668680 9591880 FALSE TRUE 9942459.784 8392176.7 6518433.836 7158981.092 9458865.972 8165235.08 8641433.302 8387265.806 8457938.874 1.175518047 0.992224799 0.770688218 0.846421474 1.118341728 0.965393012 1.021694934 0.991644174 1 23.0118747 3.245177788 24.99987175 1.013413369 0.936962218 0.093913949 0.110476672 402.8645142 1522025.991 0.033374696 0.042069876 1758.643405 -3.245177788 -0.076451151 NYYGYQGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NYYGYQGYR 9 0 Q1KMD3 Q1KMD3 HNRNPUL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;; 161.9 0.00014932 1100270000 666215 589963 287506 396052 698510 729200 587302 644036 628927 FALSE TRUE 578172.9998 586087.4942 426544.8632 485981.6599 684611.0176 757252.7959 530345.5424 506313.9133 554575.9665 1.042549686 1.05682094 0.769136942 0.876312154 1.234476535 1.365462699 0.956308197 0.912974856 1 19.08102557 3.270836073 24.99978669 1.074501683 0.932886912 0.199977146 0.153934266 409.1074232 316882.158 0.050281695 0.064908301 1865.675347 -3.270836073 -0.14161477 PAAPPRPLDRES(ph)PGVENK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 PAAPPRPLDRESPGVENK 18 2 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 PAAPPRPLDRES(1)PGVENK;PAAPPRPLDRES(1)PGVENK 191.99 1.03E-14 446750000 531210 363940 420240 445790 377360 284390 513270 585200 829900 TRUE FALSE 461009.2526 361549.2542 623469.4696 547013.433 369851.2743 295330.6673 463493.1544 460059.534 731790.1674 0.629974647 0.494061372 0.851978473 0.747500386 0.505406182 0.403572883 0.633368929 0.628676846 1 19.48107051 1.232149213 4.70755323 1.031770852 0.609607406 0.479851316 0.127133737 0.189806061 9.50542254 0.268301809 0.033630275 17.0666866 -1.232149213 -0.422163447 PAAS(ph)PRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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;PAAS(1)PRPR 91.584 0.0074996 280800000 412570 432790 376700 407570 405240 451230 406170 489310 941990 TRUE FALSE 358047.8292 429946.974 558873.38 500114.9978 397176.5168 468589.1101 366779.6959 384674.8643 830629.0153 0.431056251 0.517616127 0.672831516 0.602091895 0.478163548 0.564137661 0.441568605 0.463112722 1 19.66384474 1.234259504 24.99999522 1.000000704 0.521987414 0.799461485 0.07534284 60.94967895 354219.7178 0.150305303 0.019728311 17.14981753 -1.234259504 -0.478013291 PANKQEDEVMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PANKQEDEVMR 11 1 O15145 O15145 ARPC3 Actin-related protein 2/3 complex subunit 3 0 88.441 0.011834 151430000 180160 122390 98711 109650 107190 97630 159580 190590 95256 FALSE TRUE 156351.3995 121586.012 146447.9698 134547.7084 105057.1287 101385.8893 144103.9562 149833.8117 83994.9442 1.861438221 1.447539649 1.743533152 1.601854846 1.250755384 1.207047522 1.715626548 1.783843219 1 16.35801487 7.999999764 0.740274364 1.4772029 58.4306157 0.185707464 0.256415698 793.167813 3.575991003 0.100557936 75224.74008 99999945.65 -7.999999764 56.9534128 PAQPQEHPFASSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 PAQPQEHPFASSR 13 0 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;; 157.5 4.77E-05 1307350000 1187000 1011710 725030 842800 1003350 955330 1153280 1331850 1170430 FALSE TRUE 1030134.943 1005064.01 1075656.933 1034170.621 983385.298 992082.1633 1041435.083 1047044.242 1032063.099 0.998131746 0.973839692 1.042239505 1.002042048 0.952834472 0.961261152 1.009080825 1.014515724 1 19.97709975 2.073790486 25 1.009349684 0.988847565 0.11993888 0.024739271 87.06165368 29493.79483 0.010805456 0.007285031 118.5196842 -2.073790486 -0.020502119 PAS(ph)PSLQLLPWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 PASPSLQLLPWR 12 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 PAS(0.91)PS(0.09)LQLLPWR;PAS(0.918)PS(0.082)LQLLPWR;PAS(0.5)PS(0.5)LQLLPWR;PAS(0.97)PS(0.03)LQLLPWR;PAS(0.998)PS(0.002)LQLLPWR 188.13 1.01E-05 1712125000 1629531 1342982 876231 1390296 1116867 851510 1250406 1535095 1640905 TRUE FALSE 1414184.35 1334159.863 1299979.242 1705983.956 1094643.532 884268.1407 1129141.819 1206826.88 1446919.08 0.977376253 0.922069438 0.898446403 1.179045863 0.756534036 0.611138627 0.780376618 0.834066602 1 20.46455281 3.195030193 24.9999547 0.790660725 0.9822386 0.401330191 0.119537982 146.7564821 84283.16288 0.037331224 0.042329882 1566.859997 -3.195030193 0.191577875 PAT(ph)PGASSVEQLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PATPGASSVEQLRK 14 1 Q9H3U1 Q9H3U1 UNC45A Protein unc-45 homolog A 1 PAT(0.637)PGAS(0.26)S(0.103)VEQLRK 74.338 0.019527 336470000 469290 311320 332660 365180 369090 312560 456150 482580 327110 TRUE FALSE 407272.1375 309274.9184 493535.4887 448099.7004 361745.8311 324584.3855 411912.6432 379384.0224 288439.4284 1.411984969 1.072235235 1.711054176 1.55353137 1.254148343 1.125312123 1.428073289 1.31529876 1 18.13790886 3.157890511 9.931965673 1.245699916 1.430531322 0.226203338 0.193089329 0.643381379 74.00533143 0.059833065 0.067905133 1438.435893 -3.157890511 0.184831407 PCSEETPAIS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 PCSEETPAISPSK 13 0 P33316-2;H0YNJ9 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 1 PCSEETPAIS(1)PSK;PCSEETPAIS(1)PSK;PCSEETPAIS(0.999)PS(0.001)K;PCSEETPAIS(1)PSK 249.32 1.62E-17 926310000 1564170 1143890 1293910 1307200 1207020 864610 1663860 1875040 3014220 TRUE FALSE 1357460.971 1136375.711 1919649.204 1604019.739 1183002.663 897872.1062 1502499.113 1474077.288 2657882.345 0.510730271 0.427549291 0.722247622 0.603495389 0.445092186 0.337814843 0.565299332 0.554605922 1 21.34184581 1.206745537 3.37267393 1.098480139 0.516486857 0.676851645 0.10423973 0.241449489 3.633317258 0.384624808 0.028057055 16.09702197 -1.206745537 -0.581993282 PCSEETPAIS(ph)PSKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 PCSEETPAISPSKR 14 1 P33316-2;H0YNJ9 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 1 PCSEETPAIS(0.81)PS(0.19)KR;PCSEETPAIS(0.999)PS(0.001)KR;PCSEETPAIS(1)PSKR;PCSEETPAIS(1)PSKR;PCSEETPAIS(0.997)PS(0.003)KR;PCSEETPAIS(0.969)PS(0.031)KR;PCSEETPAIS(0.999)PS(0.001)KR;PCSEETPAIS(0.854)PS(0.146)KR;PCSEETPAIS(0.995)PS(0.005)KR 239.55 1.41E-17 29165150000 8026470 5560440 5489250 5475100 5365050 3886690 7553870 8901640 7093660 TRUE FALSE 6965751.653 5523913.104 8143869.66 6718305.137 5258296.002 4036213.479 6821296.85 6998093.559 6255055.596 1.113619463 0.883111752 1.301965991 1.07406002 0.840647365 0.645272199 1.090525375 1.118789985 1 22.57659128 5.055154918 17.0568095 1.004545589 2.065334917 0.039882878 0.177777106 31047518.61 202810935 0.045759646 1135986636 113541.576 -5.055154918 1.060789328 PCSEETPAIS(ph)PSKRARPAEVGGMQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 PCSEETPAISPSKRARPAEVGGMQLR 26 3 P33316-2;H0YNJ9 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 1 PCSEETPAIS(0.5)PS(0.5)KRARPAEVGGMQLR;PCSEETPAIS(0.848)PS(0.152)KRARPAEVGGMQLR;PCSEETPAIS(0.981)PS(0.018)KRARPAEVGGMQLR 177.78 1.40E-16 1344990000 5880.9 4303.6 22705.6 7699.2 17684.3 5543.1 13785.3 16900.4 0 TRUE FALSE 5103.724165 4275.329368 33686.10411 9447.421035 17332.41703 5756.346644 12448.40373 13286.38098 0 0 PCSEETPAISPS(ph)KRARPAEVGGMQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PCSEETPAISPSKRARPAEVGGMQLR 26 3 P33316-2;H0YNJ9 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 1 PCSEETPAIS(0.154)PS(0.846)KRARPAEVGGMQLR 153.06 4.93E-07 258460000 5204.4 8292.4 2768.2 2868.4 6606.4 7946.8 8520.4 16637 6356.6 TRUE FALSE 4516.625354 8237.926678 4106.910779 3519.714061 6474.945565 8252.518538 7694.092919 13079.30702 5605.129989 0.805802071 1.469711977 0.732705715 0.627945127 1.155182052 1.472315281 1.372687687 2.333452934 1 12.45253212 2.586540638 1.787770989 1.729948063 0.93868139 0.339427203 0.401951105 0.340976786 2.200030911 0.182113436 0.141574776 385.958525 -2.586540638 -0.791266673 PEEQLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 PEEQLRK 7 1 A0A590UK20;Q9BXX2 A0A590UK20 ANKRD30B Ankyrin repeat domain-containing protein 30B 0 ; 102.71 0.013691 1902200000 1694530 1387410 1101570 1525180 1197560 1108960 1456650 1775810 1984010 FALSE TRUE 1470593.567 1378296.012 1634292.937 1871495.43 1173730.899 1151622.409 1315384.307 1396066.851 1749462.598 0.840597318 0.787839657 0.934168549 1.069754467 0.670909398 0.658272095 0.751879068 0.797997541 1 20.73848039 3.218325899 24.98845692 0.770912977 0.901363566 0.239851189 0.116560616 377.5251572 466215.7577 0.037136336 0.042159059 1653.201912 -3.218325899 0.130450589 PEINTNHLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PEINTNHLDK 10 0 Q13907 Q13907 IDI1 Isopentenyl-diphosphate Delta-isomerase 1 0 96.64 0.0066024 241470000 702100 592400 491710 514560 551000 514880 699600 672620 713900 FALSE TRUE 609315.7061 588508.4854 729502.6007 631398.7126 540036.178 534687.7668 631752.8997 528785.4473 629503.5553 0.967930524 0.934877143 1.158853821 1.003010559 0.857876296 0.849380059 1.003573204 0.840003909 1 19.263855 3.344679269 6.568455889 0.905701097 1.022746504 0.302597595 0.079995953 0.250814585 13.78455296 0.022663493 0.029283491 2211.460919 -3.344679269 0.117045407 PERTVLGSRELCDSEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PERTVLGSRELCDSEGK 17 2 P0C7T5 P0C7T5 ATXN1L Ataxin-1-like 0 51.888 0.083126 782660000 116010 19250 38701 36038 24616 29200 29608 36948 24324 FALSE TRUE 100678.9846 19123.54548 57416.93305 44220.97871 24126.18976 30323.34289 26736.62072 29046.95773 21448.44443 4.693999367 0.891605242 2.676974232 2.061733607 1.124845666 1.413778188 1.246552905 1.354268736 1 14.3885854 4.745198775 24.98304222 1.495065881 4.694000829 0.783321399 0.532554498 363.0698065 1366395.759 0.13193553 1.24372355 55615.87506 -4.745198775 3.198934947 PFPTPS(ph)PASLDVYVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 PFPTPSPASLDVYVAR 16 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 PFPTPS(0.999)PAS(0.001)LDVYVAR;PFPTPS(0.972)PAS(0.028)LDVYVAR;PFPT(0.488)PS(0.492)PAS(0.021)LDVYVAR 176.56 3.28E-09 89052000 144596 132846 141022 126278 129111 118949 135397 156580 266673 TRUE FALSE 125487.2722 131973.3259 209220.7109 154951.3499 126541.9437 123525.045 122266.2198 123096.5855 235147.2217 0.533654071 0.56123702 0.889743495 0.658954628 0.538139225 0.525309396 0.519956047 0.523487306 1 17.84320476 1.232521577 24.99492838 1.000000666 0.593437253 0.561152222 0.112887654 167.4293899 692901.9339 0.265361276 0.029763017 17.08132583 -1.232521577 -0.406563412 PFPTPSPAS(ph)LDVYVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PFPTPSPASLDVYVAR 16 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 PFPT(0.006)PS(0.295)PAS(0.699)LDVYVAR 130.24 5.36E-05 23874000 46584 30768 46763 44004 39243 39947 48918 54549 97845 TRUE FALSE 40427.80637 30565.88298 69377.74321 53995.78076 38462.14108 41483.78694 44173.93989 42884.12085 86277.87557 0.468576748 0.35427255 0.804119744 0.625835771 0.445793789 0.480816045 0.511996147 0.497046555 1 16.39670303 1.236538066 24.99600682 1.000000605 0.524680414 0.608933683 0.119989321 38.21373124 472146.3309 0.189993143 0.029863655 17.24003194 -1.236538066 -0.475320191 PFSAPKPQT(ph)SPSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PFSAPKPQTSPSPK 14 1 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 PFSAPKPQT(0.566)S(0.413)PS(0.02)PK 68.82 0.078774 440780000 460500 379190 307370 314430 359820 384040 402370 404200 627280 TRUE FALSE 399643.7582 376699.0759 456015.1601 385826.1373 352660.286 398814.2673 363348.2193 317764.9755 553123.673 0.722521522 0.681039511 0.824436166 0.697540453 0.637579448 0.721021874 0.656902311 0.574491729 1 19.07724256 1.225641294 24.99722806 1.000000746 0.686103366 0.695457225 0.064551842 397.0703277 768233.0982 0.310252413 0.017103864 16.81284827 -1.225641294 -0.313897381 PFSAPKPQTS(ph)PSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PFSAPKPQTSPSPK 14 1 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 PFSAPKPQT(0.215)S(0.774)PS(0.011)PK 97.081 0.0018872 669960000 393810 363800 271700 280750 311990 372760 355720 384010 531520 TRUE FALSE 341767.0107 361410.1738 403095.0288 344498.5785 305782.0094 387100.3184 321222.3292 301892.4499 468684.3111 0.729205144 0.771116432 0.860056587 0.735033306 0.652426382 0.825929755 0.685370347 0.644127492 1 18.83825698 1.225959766 24.99133384 1.000000618 0.735893927 0.588062622 0.068919832 471.218978 934513.0827 0.313067668 0.017859283 16.82518181 -1.225959766 -0.264106691 PFVPNVHAAEFVPSFLR ddPTM_MDA-MB-175_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 ; 101.96 0.00097119 1664950000 1043080 845305 670675 798380 853940 790151 977890 1192230 1239290 FALSE TRUE 905234.3352 839752.1358 995015.6733 979664.3815 836948.2647 820548.6203 883054.3783 937280.8924 1092782.548 0.828375542 0.768453099 0.910534008 0.896486115 0.76588729 0.750880055 0.808078771 0.857701191 1 20.05957492 1.240186493 2.719805119 1.039762475 0.818859504 0.540745119 0.052351872 0.392905135 3.358488615 0.198064667 0.014661957 17.3854723 -1.240186493 -0.220902971 PGATAFLEEATAEEPGAAPGS(ph)PPDS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PGATAFLEEATAEEPGAAPGSPPDSPGR 28 0 Q96C34;Q96C34-2;K7EQS2 Q96C34 RUNDC1 RUN domain-containing protein 1 2 PGATAFLEEATAEEPGAAPGS(1)PPDS(1)PGR 76.691 2.08E-06 0 14528 13357 11410 9149.2 11964 12986 14926 20199 11688 TRUE FALSE 12608.08799 13269.25699 16927.91416 11226.6657 11725.93981 13485.57982 13478.47882 15879.60104 10306.25796 1.223342948 1.287495136 1.642488888 1.089305716 1.137749497 1.308484601 1.307795601 1.540772714 1 13.33123299 -1.999972393 0.004954709 0.764203948 1.811537398 0 0.194801156 4341671.019 2139.251596 239391.0829 213526.6001 0.010000636 1.999972393 1.047333451 PGGYGYGYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PGGYGYGYGR 10 0 P98179 P98179 RBM3 RNA-binding protein 3 0 111.73 0.00399 192990000 492260 374020 361030 429650 415890 454120 459200 611230 668290 FALSE TRUE 427206.5938 371563.038 535625.3156 527208.5993 407614.6027 471590.2903 414666.8547 480523.2211 589285.5175 0.724956886 0.630531427 0.908940233 0.894657316 0.69170986 0.800274699 0.703677322 0.815433617 1 19.16860728 1.264890578 3.498408834 1.026287291 0.768389753 0.416970341 0.08680755 0.287149279 5.20079887 0.189848934 0.02264573 18.40308271 -1.264890578 -0.257897538 PGHLQEGFGCVVTNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 PGHLQEGFGCVVTNR 15 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;; 267.07 2.19E-25 3088130000 2171600 1628530 1421790 1573520 1836080 1675810 1797180 2097100 2078330 FALSE TRUE 1884617.558 1617832.079 2109372.4 1930811.766 1799545.6 1740279.495 1622889.76 1648651.485 1832632.195 1.028366501 0.882791475 1.151006953 1.053572982 0.981945862 0.949606528 0.885551266 0.899608492 1 20.80548584 2.82482492 2.577351617 0.92166769 1.026107248 0.278188679 0.071160496 0.360642115 4.697207194 0.025792172 0.025202513 668.0745372 -2.82482492 0.104439558 PGIGATHSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PGIGATHSSR 10 0 K7EM56;A0A0B4J2B4;S4R417;K7ELC2;P62841;K7EQJ5 K7EM56 RPS15 40S ribosomal protein S15 0 101.38 0.0033706 62906000 63335 72402 35264 51344 73446 75878 69209 79701 126350 FALSE TRUE 54965.11928 71926.38649 52317.78835 63002.43994 71984.56829 78797.07576 62497.12183 62657.56138 111413.0469 0.493345446 0.645583156 0.469584037 0.565485297 0.646105373 0.70725178 0.560949759 0.562389802 1 16.76555866 1.236800497 24.99912658 1.00000052 0.583471945 0.774044825 0.071079518 21.76447752 309030.1116 0.108397957 0.017371154 17.25045271 -1.236800497 -0.416528575 PGMYPDPHS(ph)PFAVS(ph)PIPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 PGMYPDPHSPFAVSPIPGR 19 0 P41162 P41162 ETV3 ETS translocation variant 3 2 PGMYPDPHS(1)PFAVS(1)PIPGR;PGMY(0.009)PDPHS(0.991)PFAVS(1)PIPGR 98.21 0.00052439 326010000 323500 458050 612300 683640 739560 673680 780200 1030560 1091470 TRUE FALSE 280748.6554 455041.0394 908410.328 838870.9108 724844.2029 699596.9055 704536.3241 810182.7638 962437.66 0.291705808 0.472800534 0.943864071 0.871610646 0.753133666 0.726901008 0.732033204 0.841802849 1 19.87633357 4.38557737 4.44661037 0.826284405 0.32950841 0.818761989 0.0908138 0.08198763 2.820725424 0.024187507 0.071354076 24298.38284 -4.38557737 -0.496775995 PGPTPSGTNVGSSGRS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 PGPTPSGTNVGSSGRSPSK 19 1 P60468 P60468 SEC61B Protein transport protein Sec61 subunit beta 1 PGPTPSGTNVGS(0.001)S(0.007)GRS(0.992)PS(0.001)K;PGPTPSGTNVGSS(0.003)GRS(0.997)PSK;PGPTPSGTNVGS(0.009)S(0.032)GRS(0.952)PS(0.007)K;PGPTPSGTNVGSSGRS(0.999)PS(0.001)K;PGPTPSGTNVGSSGRS(0.999)PS(0.001)K;PGPTPSGTNVGS(0.002)S(0.205)GRS(0.79)PS(0.002)K 253.13 4.37E-31 7657090000 2912460 1973750 1786999 2159230 2548170 1646340 2218570 4344250 1312324 TRUE FALSE 2527571.032 1960784.306 2651197.694 2649516.173 2497466.402 1709675.765 2003413.423 3415265.944 1157182.552 2.184245716 1.69444683 2.291079907 2.289626792 2.158230263 1.477446893 1.731285543 2.951363153 1 20.14218504 PGPTPSGTNVGSSGRS(ph)PSKAVAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 PGPTPSGTNVGSSGRSPSKAVAAR 24 2 P60468 P60468 SEC61B Protein transport protein Sec61 subunit beta 1 PGPTPSGTNVGSS(0.021)GRS(0.979)PSKAVAAR;PGPTPSGTNVGS(0.012)S(0.021)GRS(0.967)PSKAVAAR;PGPTPSGTNVGS(0.004)S(0.007)GRS(0.988)PS(0.001)KAVAAR;PGPTPSGTNVGSSGRS(0.998)PS(0.002)KAVAAR 296.35 2.94E-62 1373610000 84067 60932.2 56533.3 55441.9 83393 59636 59310.6 102012 45707.9 TRUE FALSE 72957.33295 60531.93237 83872.99297 68030.83077 81733.64246 61930.23551 53558.66714 80197.52766 40304.36413 1.810159632 1.501870422 2.080990354 1.687927157 2.027910481 1.536564013 1.328855281 1.989797616 1 15.29864844 1.226393041 24.96508674 0.999998283 1.740795823 0.479412969 0.244100768 499.7038653 1025212.477 0.956289708 0.057348609 16.84197588 -1.226393041 0.74079754 PGPYDRPGTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PGPYDRPGTAR 11 1 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 75.819 0.033784 132710000 142040 120940 142960 133360 98536 91396 100920 138050 242130 FALSE TRUE 123269.0541 120145.5372 212095.9342 163641.4263 96575.32638 94912.06326 91132.79393 108529.0818 213505.6672 0.577357293 0.562727626 0.99339721 0.766450036 0.452331442 0.444541189 0.426840164 0.508319443 1 17.70391484 3.24919364 24.98865145 0.542584835 0.732565842 0.126807651 0.201017885 390.387134 917443.0519 0.059284927 0.075728514 1774.980719 -3.24919364 0.189981007 PGS(ph)LPLNAEACWPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PGSLPLNAEACWPK 14 0 Q01581;D6RIW1 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 1 PGS(1)LPLNAEACWPK 90.444 0.0060314 75913000 130740 105340 84436 91549 112560 90215 123930 145180 117500 TRUE FALSE 113462.3777 104648.0146 125269.532 112336.5997 110320.2762 93685.62943 111911.2877 114134.3868 103609.2839 1.095098562 1.01002546 1.20905702 1.084232952 1.064772114 0.904220413 1.080127992 1.101584554 1 16.66079376 3.163763377 4.035705909 1.034784351 1.101464807 0.19886664 0.070949079 0.428802893 13.52645865 0.02264755 0.026518349 1458.019649 -3.163763377 0.066680457 PGS(ph)WLHRVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PGSWLHRVPR 10 1 Q96KV7-3;Q96KV7-5 Q96KV7-3 1 PGS(1)WLHRVPR 52.49 0.090706 300230000 229690 261350 99944 220670 325370 330110 272480 290460 295760 TRUE FALSE 199335.8845 259633.1746 148277.2527 270776.4962 318895.7736 342809.5453 246054.9315 228347.3894 260795.5897 0.764337636 0.995542812 0.568557363 1.038270994 1.222780546 1.314476007 0.943478116 0.87557995 1 17.99255995 3.576894487 11.26587144 1.056726965 0.798327686 0.413421375 0.161833795 0.725133221 78.60412271 0.048434012 0.071843761 3774.8047 -3.576894487 -0.25839928 PGSGAAAS(ph)GGRGDLPYGPGRRS(ph)SGGGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 PGSGAAASGGRGDLPYGPGRRSSGGGGR 28 3 P54826 P54826 GAS1 Growth arrest-specific protein 1 2 PGS(0.002)GAAAS(0.98)GGRGDLPY(0.115)GPGRRS(0.476)S(0.426)GGGGR;PGS(0.002)GAAAS(0.986)GGRGDLPY(0.056)GPGRRS(0.504)S(0.452)GGGGR 81.566 0.0073651 482220000 217971 195942 137048 200564 222662 253910 239500 232620 308620 TRUE FALSE 189165.5801 194654.8441 203324.8712 246105.1216 218231.4618 263678.082 216273.3269 182876.0233 272135.2952 0.695115935 0.715287019 0.747146272 0.90434841 0.801922667 0.968922763 0.794727221 0.67200406 1 18.05396456 3.937183567 5.471090752 0.836114499 0.710482748 0.314807742 0.093857389 0.296796482 17.87496173 0.026052305 0.047086467 8653.335999 -3.937183567 -0.125631751 PGWLSS(ph)PTLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 PGWLSSPTLGR 11 0 Q5XPI4;Q5XPI4-2;C9JS59;C9J266 Q5XPI4 RNF123 E3 ubiquitin-protein ligase RNF123 1 PGWLS(0.267)S(0.723)PT(0.009)LGR;PGWLS(0.039)S(0.959)PT(0.002)LGR;PGWLS(0.001)S(0.996)PT(0.004)LGR;PGWLS(0.137)S(0.848)PT(0.015)LGR;PGWLSS(1)PTLGR;PGWLSS(0.997)PT(0.002)LGR 266.93 4.36E-21 2377931000 3372020 2817940 2599150 2482130 2861920 2681580 3120910 3488600 3778760 TRUE FALSE 2926399.013 2799428.767 3856107.634 3045735.553 2804973.391 2784742.118 2818244.629 2742590.038 3332039.298 0.878260654 0.840154787 1.157281559 0.91407552 0.84181882 0.835747081 0.845801738 0.823096546 1 21.66797399 3.475356877 24.14238595 0.861703511 0.961550209 0.152505529 0.095407419 61.36595355 839664.4735 0.027293769 0.035515898 2987.836835 -3.475356877 0.099846698 PHYGSVLDNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PHYGSVLDNER 11 0 P46940;H0YLE8;A0A0J9YXZ5;A0A087X225 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 134.98 0.00012963 1027200000 378700 407680 303890 362800 334000 434140 363480 357600 586410 FALSE TRUE 328653.8355 405001.9232 450852.2205 445179.2851 327354.0535 450841.6467 328229.7655 281130.0228 517085.2778 0.635589234 0.783240097 0.871910766 0.860939779 0.633075563 0.871890317 0.634769118 0.543682125 1 18.9800427 2.220787914 24.99283178 0.684328644 0.778141093 0 0.144420051 638.8407479 898362.0051 0.057841926 0.03909049 166.2600528 -2.220787914 0.093812449 PIPEAEEAQRPEPVGTSSNADSAS(ph)PDLGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 PIPEAEEAQRPEPVGTSSNADSASPDLGPR 30 1 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 PIPEAEEAQRPEPVGTSSNADS(0.001)AS(0.999)PDLGPR;PIPEAEEAQRPEPVGTSSNADSAS(1)PDLGPR;PIPEAEEAQRPEPVGTSSNADSAS(1)PDLGPR;PIPEAEEAQRPEPVGT(0.013)S(0.01)S(0.008)NADS(0.036)AS(0.932)PDLGPR 310.71 1.89E-92 1150370000 491612 456629 390643 514937 509961 409701 551746 639017 604580 TRUE FALSE 426644.2286 453629.374 579559.2614 631861.3162 499813.7738 425462.4626 498237.7578 502368.1874 533107.2411 0.800297193 0.850915799 1.087134476 1.185242419 0.937548274 0.798080442 0.934591991 0.942339831 1 19.02406625 4.415088727 8.294813674 0.976082639 0.812733918 0.298625798 0.101570943 0.321628739 38.11315153 0.027926147 0.074567286 26006.90833 -4.415088727 -0.163348721 PIRPGQHPAAS(ph)PTHPSAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 PIRPGQHPAASPTHPSAIR 19 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 1 PIRPGQHPAAS(0.996)PT(0.004)HPSAIR;PIRPGQHPAAS(0.988)PT(0.012)HPSAIR;PIRPGQHPAAS(0.989)PT(0.011)HPSAIR;PIRPGQHPAAS(0.86)PT(0.14)HPSAIR 201.15 3.70E-16 2616740000 971240 906940 481857 987660 1044180 1062430 1071160 1283090 3119000 TRUE FALSE 842888.1732 900982.2514 714884.6569 1211923.298 1023402.861 1103302.37 967279.0681 1008711.189 2750275.373 0.306474101 0.327597105 0.259932029 0.440655256 0.372109233 0.401160691 0.351702625 0.366767342 1 21.39114465 1.238192168 6.902033509 1.0146786 0.353914528 0.944459851 0.049295851 0.024231477 6.373554425 0.074907258 0.012395269 17.30581944 -1.238192168 -0.660764072 HPNYS(ph)PPGSPIEK ddPTM_MDA-MB-175_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 191.35 2.34E-06 3806560000 6196940 4885430 2373790 2720870 3088170 2496370 3102140 3563120 2968370 TRUE FALSE 5377998.678 4853337.289 3521762.784 3338685.119 3026721.459 2592406.969 2801294.94 2801174.516 2617452.68 2.054668922 1.854221597 1.345492436 1.275547461 1.156361481 0.990431265 1.07023709 1.070191082 1 21.31973202 4.380837737 0.897207142 1.042504833 2.372984519 0.971663088 0.061208218 0.1907576 0.17686915 0.021532336 0.224737412 24034.64638 -4.380837737 1.330479686 up PIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 PISPGLSYASHTVGFTPPTSLTR 23 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 PIS(1)PGLSYASHTVGFTPPTSLTR;PIS(1)PGLSYASHTVGFTPPTSLTR;PIS(0.999)PGLS(0.001)YASHTVGFTPPTSLTR;PIS(0.918)PGLS(0.082)YASHTVGFTPPTSLTR 256.57 8.97E-44 3984780000 1285996 1156825 1008566 1412466 1126003 1081621 1215164 1553755 3346720 TRUE FALSE 1116048.37 1149225.74 1496311.891 1733187.993 1103597.743 1123231.66 1097317.582 1221496.585 2951074.574 0.378183723 0.389426194 0.507039674 0.58730742 0.373964709 0.38061785 0.371836616 0.413915865 1 21.49280895 1.237844673 24.9968176 1.000000663 0.425745613 0.869521613 0.069965142 6.372494386 222334.3692 0.106548348 0.018318188 17.29197796 -1.237844673 -0.574255051 PIT(ph)PVYTVAPNVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 PITPVYTVAPNVQR 14 0 B7Z8Z7;A0AV96;A0AV96-2 B7Z8Z7 RBM47 RNA-binding protein 47 1 PIT(1)PVYTVAPNVQR;PIT(0.999)PVYT(0.001)VAPNVQR;PIT(1)PVYTVAPNVQR 204.18 1.56E-07 419630000 278910 199947 216861 237081 216286 228125 214448 255790 565980 TRUE FALSE 242051.3368 198633.535 321735.705 290913.8646 211982.3318 236901.1164 193650.866 201091.2991 499070.4892 0.485004307 0.398006974 0.644669865 0.582911374 0.424754291 0.474684682 0.388023075 0.402931657 1 18.92888407 1.233964765 24.99955511 1.000000792 0.472325546 0.798431221 0.082869952 66.2810393 360496.4132 0.170255236 0.021779648 17.13818258 -1.233964765 -0.527675246 PKPS(ph)SSPVIFAGGQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PKPSSSPVIFAGGQDR 16 1 Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3 Q15366;Q15366-2 PCBP2 Poly(rC)-binding protein 2 1 PKPS(0.333)S(0.333)S(0.333)PVIFAGGQDR 76.704 0.015726 422840000 218480 172780 192010 188780 172710 129860 199890 236310 508990 TRUE FALSE 189607.3144 171644.9968 284866.6782 231645.3843 169273.4089 134855.7982 180504.6986 185776.9455 448817.782 0.422459452 0.382438049 0.634704527 0.516123455 0.377153971 0.300468929 0.402178135 0.4139251 1 18.77577031 1.237534562 24.99968821 1.000000673 0.430731174 0.799258489 0.089588024 12.04839475 293410.8525 0.139506078 0.023497981 17.2796349 -1.237534562 -0.569269498 PKPSSS(ph)PVIFAGGQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PKPSSSPVIFAGGQDR 16 1 Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3 Q15366;Q15366-2 PCBP2 Poly(rC)-binding protein 2 1 PKPS(0.021)S(0.112)S(0.867)PVIFAGGQDR 138.22 4.73E-06 316210000 324800 195850 226070 274160 201910 166620 254200 280300 645730 TRUE FALSE 281876.8571 194563.4485 335398.2082 336412.2183 197892.386 173029.9792 229547.7231 220360.0263 569392.535 0.495048389 0.341703546 0.589045672 0.590826535 0.347550018 0.303885226 0.403144947 0.387008984 1 19.11906405 1.23599025 24.9936549 1.000000756 0.429152532 0.763954856 0.099161638 35.57640518 345863.8994 0.168986674 0.025487815 17.21829921 -1.23599025 -0.570848224 PLEFWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PLEFWR 6 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 103.28 0.080999 85067000 150020 165660 164570 176020 182910 183920 191550 210140 389050 FALSE TRUE 130194.4769 164571.7686 244156.6025 215988.0313 179270.4489 190995.5214 172973.5105 165203.1963 343056.9522 0.37951272 0.479721421 0.711708656 0.629598176 0.522567602 0.556745812 0.504212229 0.481562013 1 18.38808858 1.23440151 24.99686379 1.000000678 0.536746514 0.729143413 0.089388277 70.13940998 421490.8029 0.172728726 0.022966692 17.15542611 -1.23440151 -0.463254165 PLELELCPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 PLELELCPGR 10 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;;; 164.57 1.42E-05 751580000 663299 548349 449840 454209 511843 472255 620979 692000 583823 FALSE TRUE 575642.3566 544746.8593 667384.1286 557344.0956 501658.3257 490422.9554 560756.5522 544021.1852 514804.11 1.118177469 1.058163384 1.296384616 1.082633345 0.974464492 0.952639938 1.089261995 1.056753772 1 18.97366405 3.48038876 24.89276497 1.022948885 1.154613146 0.463736503 0.069992221 118.6931202 904242.2489 0.020235742 0.026676258 3022.65625 -3.48038876 0.131664261 PLENLEEEGLPKNPDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PLENLEEEGLPKNPDLR 17 1 Q15008;Q15008-4;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 79.805 0.011639 78587000 124880 91024 68527 79915 82826 75637 113170 133380 47007 FALSE TRUE 108376.7916 90426.05735 101666.8864 98060.92217 81177.92465 78546.80433 102194.7908 104857.725 41449.88601 2.614646312 2.181575537 2.452766369 2.365770612 1.958459539 1.894982397 2.465502337 2.529747004 1 15.33908051 3.296184115 7.885096996 2.073443629 2.393202971 0.18025834 0.429112511 0.582122916 69.35795756 0.124929644 0.160883895 1977.807936 -3.296184115 0.319759342 PLHISTFINELDSGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 PLHISTFINELDSGFR 16 0 E9PGT1;Q15631 E9PGT1 TSN Translin 0 ; 209.6 1.18E-11 568550000 844770 737370 361541 610360 740130 675720 731120 892850 1147400 FALSE TRUE 733131.5041 732526.1679 536383.4369 748951.5668 725402.861 701715.3856 660216.0949 701920.9757 1011755.679 0.724613184 0.724014881 0.53015115 0.740249432 0.716974341 0.693562092 0.652544985 0.693765293 1 19.94842952 1.238955418 6.130046318 1.010890385 0.682055081 0.733050915 0.059867177 0.0656465 9.908468223 0.090359856 0.014461349 17.33626025 -1.238955418 -0.328835304 PLPKGT(ph)MMETLSR ddPTM_MDA-MB-175_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 53.981 0.075984 261680000 435690 420610 313420 349380 445100 411180 530730 593200 540160 TRUE FALSE 378112.4626 417846.9852 464990.9603 428712.0689 436243.3808 426998.3607 479259.8863 466348.7963 476302.9002 0.793848751 0.877271554 0.976250533 0.900082844 0.915894866 0.896484906 1.006208205 0.979101316 1 18.86151981 7.646741824 0.255657564 1.00372871 3.56E-29 0.636732299 0.03953494 50.21612044 0.944634131 0.132192841 20.49414413 44334500.92 -7.646741824 -1.00372871 PLPPAAIES(ph)PAVAAPAYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 PLPPAAIESPAVAAPAYSR 19 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 PLPPAAIES(1)PAVAAPAYSR;PLPPAAIES(1)PAVAAPAYSR;PLPPAAIES(1)PAVAAPAYSR;PLPPAAIES(1)PAVAAPAYSR 291.18 1.59E-49 855700000 155912 155336 125390 174571 154383 160716 175957 198926 437280 TRUE FALSE 135307.8342 154315.5876 186029.0234 214210.0137 151311.0803 166898.8485 158892.7172 156387.2229 385585.2566 0.350915477 0.400211328 0.48245886 0.555545136 0.392419258 0.432845514 0.412081931 0.405584032 1 18.55669036 1.237019278 24.9999992 1.000000699 0.430817584 0.911856632 0.055788492 11.26101839 182588.0503 0.0872682 0.014185573 17.25914504 -1.237019278 -0.569183115 PLPS(ph)PPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PLPSPPK 7 0 A0A2R8Y5E4;A0A2R8YFK2;A0A2R8Y6M6;A0A2R8Y4C2;A0A2R8YFS8;A0A2R8Y8C4;A0A2R8Y5C9;A0A2R8Y596;P56945-4;P56945-5;P56945-8;P56945;P56945-7;P56945-3;P56945-2;P56945-6 A0A2R8Y5E4 BCAR1 Breast cancer anti-estrogen resistance protein 1 1 PLPS(1)PPK 71.223 0.065483 0 617570 398610 567520 542400 469840 336800 646850 702480 1124600 TRUE FALSE 535956.5598 395991.5047 841974.5702 665560.2101 460491.1032 349756.9139 584118.5866 552260.1187 991651.0691 0.540468897 0.399325445 0.849063341 0.671163709 0.46436808 0.352701595 0.589036411 0.556909719 1 19.91947305 1.238078094 8.079500077 1.005332244 0.553538476 0.504305909 0.139313182 0.084290015 49.91624229 0.206625218 0.03540891 17.30127441 -1.238078094 -0.451793768 PLTS(ph)PESLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 PLTSPESLSR 10 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 PLT(0.073)S(0.927)PESLSR;PLT(0.023)S(0.977)PESLSR 160.91 7.59E-06 247830000 344757 291556 301076 321209 305303 261422 308608 356396 750280 TRUE FALSE 299196.4889 289640.7494 446677.3606 394144.4128 299228.0676 271479.0735 278679.2437 280183.4889 661582.7531 0.452243484 0.437799728 0.67516476 0.595759806 0.452291216 0.41034787 0.421231119 0.423504826 1 19.3355621 1.234573673 24.99662967 1.000000749 0.482609224 0.781691677 0.085772436 60.03273335 376328.9444 0.171716742 0.023140967 17.16222824 -1.234573673 -0.517391525 PLTS(ph)PLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 PLTSPLR 7 0 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 PLT(0.041)S(0.959)PLR;PLT(0.03)S(0.97)PLR;PLT(0.024)S(0.976)PLR;PLT(0.024)S(0.976)PLR;PLT(0.151)S(0.849)PLR;PLT(0.028)S(0.972)PLR 138.06 0.0029603 1449980000 3263490 2569520 2838280 3258440 2868820 2712680 3296180 3703780 5607920 TRUE FALSE 2832211.528 2552640.654 4210881.701 3998318.604 2811736.095 2817038.555 2976516.971 2911755.47 4944958.086 0.572747327 0.516210777 0.851550535 0.808564711 0.568606659 0.569678955 0.601929666 0.588833195 1 22.23752686 1.234089889 24.99481892 1.000000544 0.635472533 0.525860338 0.108989624 120.2908198 672431.6127 0.219382767 0.028332237 17.14312093 -1.234089889 -0.364528011 PMFIVNTNVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 PMFIVNTNVPR 11 0 P14174 P14174 MIF Macrophage migration inhibitory factor 0 ; 189.38 6.36E-06 1458650000 292260 225470 168218 169113 197528 183526 278160 264940 147967 FALSE TRUE 253637.1005 223988.8727 249568.7875 207512.6914 193597.5793 190586.364 251184.086 208284.6428 130474.5098 1.943959022 1.716725152 1.912778119 1.590446223 1.48379618 1.460717225 1.925158304 1.596362715 1 16.99340846 1.254594796 4.030224547 0.935429222 1.706044409 0.624603789 0.173611972 0.1541735 4.392752585 0.339868251 0.045091506 17.9719332 -1.254594796 0.770615188 PMGDLLDQIFIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PMGDLLDQIFIHR 13 0 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 0 113.77 0.00079592 25168000 50780 44414 45375 47197 41552 38242 45882 51615 95747 FALSE TRUE 44069.29434 44122.24151 67318.50177 57913.80021 40725.1965 39713.19449 41432.3707 40577.53392 84427.89874 0.521975496 0.522602625 0.797349014 0.685955722 0.482366577 0.470379994 0.490742649 0.480617598 1 16.36543219 1.232663642 24.99893181 1.000000721 0.55536447 0.635875058 0.105468761 141.8635627 601337.651 0.249750967 0.028420676 17.08691432 -1.232663642 -0.444636251 PMSS(ph)EELPLASSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PMSSEELPLASSWR 14 0 Q9H6S0 Q9H6S0 YTHDC2 Probable ATP-dependent RNA helicase YTHDC2 1 PMS(0.024)S(0.976)EELPLASSWR 74.475 0.034553 27641000 24448 25315 26289 24608 31918 29102 32915 37173 40795 TRUE FALSE 21217.13486 25148.7041 39002.44833 30195.62251 31282.89425 30221.57277 29722.90837 29223.84323 35972.26157 0.58981932 0.699113789 1.08423676 0.83941407 0.869639352 0.840135467 0.826272997 0.812399386 1 15.13459724 4.463157121 24.72620784 0.880641427 0.617142872 0.601707527 0.086614395 113.9110331 201701.7294 0.021088842 0.055854664 29050.73478 -4.463157121 -0.263498555 PNSSPS(ph)PSPGQASETPHPRPS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PNSSPSPSPGQASETPHPRPS 21 1 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 1 PNS(0.268)S(0.137)PS(0.595)PSPGQASETPHPRPS 210.13 1.34E-22 198950000 63816 60821 35223 59097 59341 58553 58795 83130 110520 TRUE FALSE 55382.55391 60421.46285 52256.96061 72515.87709 58160.2302 60805.5718 53093.06995 65353.29642 97454.4515 0.568291679 0.619996952 0.536219329 0.744100202 0.596793982 0.623938372 0.544798818 0.670603502 1 16.57244047 1.245043343 3.498979025 1.053804763 0.608526251 0.820278275 0.057669533 0.113336198 2.043289169 0.133920331 0.014016606 17.58099064 -1.245043343 -0.445278512 PPQDQS(ph)VIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 PPQDQSVIK 9 0 Q58EX2-2;Q58EX2-3;Q58EX2;Q58EX2-4 Q58EX2-2 SDK2 Protein sidekick-2 1 PPQDQS(1)VIK;PPQDQS(1)VIK;PPQDQS(1)VIK;PPQDQS(1)VIK 107.21 0.0029489 96450000 597147 444546 294920 377638 311138 371165 426065 500583 497628 TRUE FALSE 518232.511 441625.7481 437544.2984 463386.4797 304946.9625 385443.9577 384745.2819 393537.221 438798.9847 1.181024863 1.006442046 0.997140635 1.056033619 0.694958223 0.878406676 0.87681443 0.896850801 1 18.74320066 4.601118504 0.859239642 0.884591242 1.278624219 0.48751773 0.092640698 1.710062051 1.148145764 0.034338116 0.61458877 39913.37976 -4.601118504 0.394032977 PQEVPQSVTATAAS(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PQEVPQSVTATAASK 15 0 Q5T321;A0A0D9SF28;F5GXV7;Q8NFP9 Q5T321 NBEA Neurobeachin 1 PQEVPQSVTAT(0.398)AAS(0.602)K 68.044 0.044407 0 45520 39693 25658 42850 58768 64491 52422 55113 53661 TRUE FALSE 39504.41667 39432.25407 38066.29462 52579.74742 57598.63178 66972.0105 47338.12251 43327.51384 47317.25771 0.8348839 0.83335882 0.804490718 1.111217132 1.217285924 1.415382331 1.000440955 0.915681 1 15.53007884 3.737348486 24.91099779 1.100106433 0.825155901 0.492306831 0.136548565 105.3383931 2164864.036 0.04322106 0.068335807 5461.959627 -3.737348486 -0.274950532 PQS(ph)PS(ph)IPSS(ph)HLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PQSPSIPSSHLR 12 0 Q9P2P6;H3BN21 Q9P2P6 STARD9 StAR-related lipid transfer protein 9 3 PQS(0.999)PS(0.999)IPS(0.023)S(0.979)HLR 44.567 0.096015 74192000000 7212100 10009000 4170200 4568400 9849100 11345000 10519000 7407300 6732300 TRUE FALSE 6259002.712 9943250.22 6186922.668 5605725.044 9653122.179 11781449.49 9498868.999 5823306.539 5936415.163 1.054340463 1.674958699 1.042198448 0.944294644 1.6260861 1.984606731 1.600101869 0.980946645 1 22.50116056 3.229541777 24.99904015 1.420617457 1.204609543 0.116630369 0.349713527 588.761935 1631967.415 0.1176947 0.135340593 1696.452784 -3.229541777 -0.216007913 PQSPVIQAAAVS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PQSPVIQAAAVSPK 14 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 PQSPVIQAAAVS(1)PK 123.59 0.00010701 112200000 120030 76029 100920 83591 86940 71706 110280 111870 283810 TRUE FALSE 104167.7314 75529.56049 149725.2496 102571.6142 85210.0641 74464.57622 99585.06257 87947.47107 250258.3051 0.416240857 0.301806409 0.59828284 0.409862978 0.340488457 0.297550869 0.397929102 0.351426783 1 17.93305842 1.236487584 24.99656463 1.000000782 0.387899666 0.836532813 0.084853056 21.18872825 255427.3876 0.132489217 0.020737501 17.23802808 -1.236487584 -0.612101116 PQYQTWEEFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PQYQTWEEFSR 11 0 P49458;Q6P2S0;Q659G3;E9PE20;P49458-2 P49458 SRP9;DKFZp564M2223 Signal recognition particle 9 kDa protein 0 150.04 7.93E-05 553240000 186180 160190 116070 123420 138950 103610 242790 208070 176700 FALSE TRUE 161575.8413 159137.7013 172201.8402 151444.3974 136185.1669 107595.9437 219244.2632 163575.8497 155810.7273 1.037000751 1.021352664 1.105198873 0.971976705 0.874042303 0.69055543 1.407119182 1.049836892 1 17.24943504 1.068624657 10.1382523 0.994840074 1.025611573 0.000195603 0.179731152 3172.388492 146836.5864 501.9073172 0.044771814 11.71182721 -1.068624657 0.0307715 PRPPGRPVS(ph)GHGMDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 PRPPGRPVSGHGMDSR 16 2 P36507;G5E9C7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR 127.59 3.41E-05 6645420000 733025 731590 757054 984551 1033230 1011130 1114899 1309849 1504743 TRUE FALSE 636153.889 726784.1371 1123167.847 1208108.352 1012670.744 1050028.825 1006776.267 1029747.985 1326853.997 0.479445282 0.547749895 0.846489402 0.91050587 0.763211888 0.79136727 0.758769442 0.776082363 1 20.3395782 4.289652118 4.945048544 0.824753769 0.500067335 0.758202743 0.075580334 0.09286161 4.77363978 0.019228358 0.052183929 19482.83347 -4.289652118 -0.324686434 PS(ph)LQT(ph)RKGT(ph)IHNNHS(ph)VNIPVHQENDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PSLQTRKGTIHNNHSVNIPVHQENDK 26 2 A0A1B0GTF4;Q56UN5-3;Q56UN5 A0A1B0GTF4 MAP3K19 Mitogen-activated protein kinase kinase kinase 19 4 PS(1)LQT(1)RKGT(1)IHNNHS(1)VNIPVHQENDK 58.284 0.045687 104940000 68671 32200 108580 46749 12204 13940 33995 41098 36781 TRUE FALSE 59595.95336 31988.47608 161089.6512 57364.07496 11961.16428 14476.28082 30698.17013 32309.51252 32432.79208 1.837521519 0.986300409 4.966875833 1.768706031 0.368798476 0.446347042 0.946516416 0.996198923 1 14.98516561 3.473013954 16.5348635 0.80759058 2.591154432 0.412562156 1.011187507 1.74268499 7009.49592 0.287610898 0.376366392 2971.761511 -3.473013954 1.783563852 PS(ph)PS(ph)QWK ddPTM_MDA-MB-175_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 57.103 0.041203 0 145610 125870 104070 105340 100110 121120 117740 142750 120230 TRUE FALSE 126367.2696 125043.1517 154398.6001 129259.057 98118.00686 125779.5648 106321.5929 112224.0234 106016.5464 1.191957991 1.179468262 1.456363232 1.219234746 0.925497106 1.186414471 1.002877349 1.058551964 1 16.69392992 3.400252221 6.849725672 1.043828194 1.277812663 0.571802717 0.098433221 0.152239831 11.08309367 0.027425865 0.035515612 2513.345662 -3.400252221 0.233984469 PSATSHSGSGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 PSATSHSGSGSK 12 0 Q14444-2;Q14444;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ;; 106.67 0.0018972 93389000 199657 158164 65875 129055 97417 131164 207777 226911 230297 FALSE TRUE 173271.8216 157125.0103 97732.37034 158358.9102 95478.59229 136209.964 187626.8185 178387.8485 203071.551 0.853255026 0.77374211 0.481270615 0.779818293 0.470172172 0.670748627 0.923944381 0.878448249 1 17.63162862 2.242611662 8.170875413 0.922526605 0.662973109 0.494288631 0.124856081 0.098416768 53.88671476 0.048006973 0.034993784 174.8282708 -2.242611662 -0.259553495 PSMS(ph)PTPLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 PSMSPTPLDR 10 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 PS(0.006)MS(0.958)PT(0.036)PLDR;PSMS(0.992)PT(0.008)PLDR;PSMS(0.98)PT(0.02)PLDR;PS(0.001)MS(0.742)PT(0.258)PLDR;PSMS(0.984)PT(0.016)PLDR 215.71 0.00012409 1541700000 2147770 1527500 1561780 1675210 1504540 1340050 1631300 1948520 2975080 TRUE FALSE 1863936.753 1517465.752 2317062.032 2055592.034 1474602.598 1391602.591 1473096.777 1531844.161 2623369.432 0.710512492 0.578441501 0.883238938 0.783569409 0.562102531 0.530463828 0.561528529 0.583922395 1 21.32298956 3.244747134 24.97331519 0.627330722 0.737783391 0.073368218 0.152067878 348.6116965 1407243.689 0.04454268 0.05604812 1756.90037 -3.244747134 0.110452669 PSSS(ph)PVIFAGGQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 PSSSPVIFAGGQDR 14 0 Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3 Q15366;Q15366-2 PCBP2 Poly(rC)-binding protein 2 1 PSS(0.028)S(0.972)PVIFAGGQDR;PSS(0.029)S(0.971)PVIFAGGQDR 265.16 1.01E-24 743610000 1167580 872830 903290 907560 797020 757760 906120 1025130 2146090 TRUE FALSE 1013281.345 867096.3223 1340124.065 1113635.369 781160.8613 786911.5175 818244.6219 805913.9271 1892381.685 0.535452944 0.458203717 0.708167954 0.588483485 0.412792444 0.41583129 0.432388787 0.425872821 1 20.85177167 1.233867839 24.99968163 1.000000764 0.493826599 0.739985004 0.093657808 81.21891821 432621.3793 0.196379664 0.024941371 17.13435809 -1.233867839 -0.506174165 PSTQPRPDS(ph)WGEDNWEGLETDSR ddPTM_MDA-MB-175_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 312.69 1.93E-73 5484120000 954749 918962 946951 951707 1112648 1027538 1331880 1550870 1374810 TRUE FALSE 828576.5006 912925.2781 1404899.671 1167806.62 1090508.482 1067068.052 1202714.483 1219228.519 1212281.528 0.683485215 0.753063754 1.158888953 0.963313053 0.899550522 0.880214725 0.992108231 1.00573051 1 20.20929334 4.391873475 7.561622754 0.979814439 0.700742426 0.691824363 0.074788588 0.116409841 8.631921286 0.019079011 0.051080242 24653.21001 -4.391873475 -0.279072013 PT(ph)SPEKFSVPHVCAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PTSPEKFSVPHVCAR 15 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 PT(0.5)S(0.5)PEKFS(0.001)VPHVCAR 75.97 0.04434 144210000 222450 154850 150600 147360 162600 127940 191680 218420 178650 TRUE FALSE 193052.6689 153832.7802 223430.6637 180820.3403 159364.5781 132861.9346 173090.9031 171712.5827 157530.2005 1.225496243 0.976528816 1.418335424 1.147845554 1.011644609 0.843406116 1.098779171 1.090029608 1 17.26526891 3.323628833 4.787451474 1.017517679 1.197844818 0.349477517 0.125386109 0.25783348 10.39625584 0.036818415 0.047524402 2106.826795 -3.323628833 0.180327139 PTHSGGGGGGGGGGGGGGGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 PTHSGGGGGGGGGGGGGGGGR 21 0 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 0 ; 116.6 2.82E-05 9745700 17658 17782.8 13506.4 15946.4 11074.8 15108.2 15363.9 15121.9 26839 FALSE TRUE 15324.45056 17665.98362 20038.14022 19567.27385 10854.43315 15689.42223 13873.91134 11888.19936 23666.124 0.647526843 0.746467128 0.846701396 0.826805177 0.458648537 0.662948535 0.586235048 0.502329801 1 14.53053582 3.2697705 24.99737376 0.621430367 0.771119324 0.132899972 0.153353918 339.4080948 271844.746 0.042947418 0.05543934 1861.103391 -3.2697705 0.149688956 VEPVGEDLGS(ph)PPPPADFAPEDYSSFQHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VEPVGEDLGSPPPPADFAPEDYSSFQHIR 29 0 O95644-6;O95644;K7ER53;O95644-8;O95644-11;O95644-3;O95644-10;O95644-2;O95644-5;O95644-4 O95644-6 NFATC1 "Nuclear factor of activated T-cells, cytoplasmic 1" 1 VEPVGEDLGS(1)PPPPADFAPEDYSSFQHIR;VEPVGEDLGS(1)PPPPADFAPEDYSSFQHIR 118.83 5.50E-05 255510000 57585 87855 63304 98434 139367 141180 122235 155044 149274 TRUE FALSE 49974.99635 87277.87472 93918.02614 120784.9442 136593.8694 146611.286 110380.6685 121889.0472 131626.9978 0.379671323 0.663069706 0.713516435 0.917630473 1.037734444 1.113839018 0.838586843 0.926018592 1 17.0060959 4.398746633 1.078309694 0.973283994 0.2901462 0.853757047 0.081842739 0.410353772 0.585634146 0.028747662 0.283253682 25046.47618 -4.398746633 -0.683137794 down PTTLSEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PTTLSEER 8 0 Q6ZRI6;H3BMJ2;Q6ZRI6-2 Q6ZRI6 C15orf39 Uncharacterized protein C15orf39 0 87.323 0.015406 209860000 246200 201300 107910 131540 160140 213560 149350 184900 174410 FALSE TRUE 213664.0462 199977.647 160095.6369 161408.1675 156953.5273 221775.7914 134866.06 145360.5739 153791.4485 1.389310318 1.300317079 1.040991801 1.049526284 1.020560823 1.442055417 0.876941217 0.945179822 1 17.23061576 8 0.418255311 1.000937691 8.456366215 0.369221267 0.152970639 98.77434909 1.336509834 0.13842418 611.76277 100000000 -8 7.455428524 PVPDS(ph)PVSVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 PVPDSPVSVTR 11 0 G3XAC1;A0A0C4DFT5;Q9BXS9-5;Q9BXS9-7;Q9BXS9-4;Q9BXS9-2;Q9BXS9-3;Q9BXS9 G3XAC1 SLC26A6 Solute carrier family 26 member 6 1 PVPDS(1)PVSVTR;PVPDS(1)PVSVTR 123.92 0.00096098 296430000 420420 325950 285130 498890 492130 486280 288160 537280 571470 TRUE FALSE 364860.4318 323808.813 423019.8217 612170.5996 482337.5758 504987.5063 260214.2876 422386.8531 503911.4676 0.724056616 0.642590681 0.839472504 1.214837603 0.957187139 1.002135372 0.516388898 0.838216394 1 18.94281076 4.114301758 5.435761827 0.90166106 0.686479088 0.229148274 0.17556377 0.341670882 14.77174772 0.048750689 0.105228606 13010.73281 -4.114301758 -0.215181972 PVS(ph)SAASVYAGAGGSGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 PVS(0.436)S(0.436)AAS(0.128)VYAGAGGSGSR 327.7 8.67E-75 151280000 62141 51001 50147 41055 60950 55979 57315 60224 72695 TRUE FALSE 53928.9094 50665.97107 74398.25693 50377.16524 59737.21425 58132.54835 51756.60012 47345.56626 64101.07991 0.841310466 0.790407449 1.160639681 0.785901974 0.931922119 0.906888752 0.807421656 0.738607935 1 15.96806104 2.245327816 24.20099235 0.824026615 0.905458316 0.028602734 0.122929061 264.1388093 944623.8284 0.045091448 0.034086817 175.9251039 -2.245327816 0.081431701 PVSS(ph)AASVYAGAGGSGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 PVS(0.001)S(0.997)AAS(0.003)VYAGAGGSGSR 360.81 5.41E-91 341090000 387710 324980 313300 248730 374330 310570 399630 401890 442550 TRUE FALSE 336473.1412 322845.185 464812.9279 305207.9481 366881.5654 322517.8289 360873.9441 315948.951 390232.2432 0.862238185 0.827315504 1.191118715 0.782118734 0.9401621 0.826476629 0.924767111 0.809643377 1 18.57397346 PVSSAASVYAGAGGS(ph)GSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 PVS(0.002)S(0.191)AAS(0.112)VYAGAGGS(0.659)GS(0.036)R;PVSSAASVYAGAGGS(0.983)GS(0.017)R;PVSSAASVYAGAGGS(0.978)GS(0.022)R;PVSSAASVYAGAGGS(0.99)GS(0.01)R;PVSSAASVYAGAGGS(0.852)GS(0.148)R;PVSSAASVYAGAGGS(0.995)GS(0.005)R 407.92 3.04E-147 4800340000 1803987 1486648 1290938 1291144 1377700 1276945 1751825 1761433 1840330 TRUE FALSE 1565585.547 1476882.111 1915239.935 1584317.979 1350286.465 1326069.9 1581933.281 1384764.26 1622768.284 0.964762229 0.910100429 1.180230076 0.976305733 0.832088277 0.817165281 0.974836208 0.853334561 1 20.63002558 3.449236419 10.54306658 0.89325233 1.019289001 0.295544155 0.088174485 0.538448431 199.000718 0.024959605 0.032344167 2813.431974 -3.449236419 0.126036671 PVSVAGSPLS(ph)PGPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 PVSVAGSPLSPGPVR 15 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 PVSVAGS(0.014)PLS(0.986)PGPVR;PVSVAGS(0.008)PLS(0.992)PGPVR 160.98 1.76E-06 196250000 408190 272300 247180 230960 269350 233940 290960 330050 342440 TRUE FALSE 354246.6573 270511.2434 366717.0748 283402.998 263990.462 242939.8232 262742.744 259471.376 301957.1333 1.173168699 0.895859755 1.214467334 0.938553744 0.874264698 0.804550701 0.870132595 0.859298713 1 18.20398423 3.521033837 7.499906007 0.876822455 1.07563139 0.507024946 0.095381209 0.211054797 31.49297555 0.024513107 0.03594559 3319.203175 -3.521033837 0.198808935 PVVDPSRITR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PVVDPSRITR 10 1 Q9NQU5-2;Q9NQU5;H0YL16;H0YL47;H0YK38;H0YM99;H0YK74;H0YK91;H0YLZ9;H0YMS4 Q9NQU5-2 PAK6 Serine/threonine-protein kinase PAK 6 0 61.765 0.081594 269380000 28462 32189 9546.8 21637 35437 25388 34004 33128 24681 FALSE TRUE 24700.67459 31977.54834 14163.66441 26550.01155 34731.87303 26364.69279 30706.29731 26043.835 21763.2403 1.134972286 1.469337649 0.650806783 1.219947544 1.595896225 1.211432325 1.410924885 1.196689218 1 14.40960575 5.043012046 18.04555357 1.225164918 0.596569586 0.009794387 0.261019788 42447679.17 401003051.4 0.062712516 928303870.6 110410.9244 -5.043012046 -0.628595331 PWIS(ph)LPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 PWISLPR 7 0 P62701;C9JEH7;P22090;Q8TD47 P62701 RPS4X;RPS4Y1;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1;40S ribosomal protein S4, Y isoform 2" 1 PWIS(1)LPR;PWIS(1)LPR;PWIS(1)LPR;PWIS(1)LPR 82.452 0.015749 1545650000 2832710 3389050 2207840 1851150 2687300 4331300 1982670 2316130 2052650 TRUE FALSE 2458360.196 3366787.107 3275558.809 2271481.901 2633827.988 4497927.914 1790390.969 1820843.624 1809988.055 1.358219016 1.86011565 1.809712942 1.254970658 1.455163187 2.485059446 0.989172809 1.005997591 1 20.78754875 PWLHPEQSPLPSLALSELSVQHADS(ph)LENIDESAVAESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 PWLHPEQSPLPSLALSELSVQHADSLENIDESAVAESR 38 0 Q9Y365;F5H8H3;F5GY11 Q9Y365 STARD10 PCTP-like protein 1 PWLHPEQSPLPSLALS(0.004)ELS(0.017)VQHADS(0.977)LENIDES(0.002)AVAESR;PWLHPEQSPLPSLALSELSVQHADS(1)LENIDESAVAESR 333.53 4.46E-129 1069250000 114796 77369 82664 93893 80596 104746 89516 87584 211071 TRUE FALSE 99625.41774 76860.75794 122640.5869 115212.8407 78992.29728 108775.6464 80834.7521 68854.84318 186118.4268 0.535279711 0.412966944 0.658938446 0.619029736 0.424419541 0.584443186 0.434318909 0.369951779 1 17.50586137 1.229239966 24.99974114 1.000000977 0.50075777 0.725785088 0.095605418 210.1132896 563521.9325 0.302664166 0.024568662 16.95274253 -1.229239966 -0.499243207 PYHPPPLFPPS(ph)PQPPDSTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 PYHPPPLFPPSPQPPDSTPR 20 0 P54259 P54259 ATN1 Atrophin-1 1 PYHPPPLFPPS(1)PQPPDSTPR;PYHPPPLFPPS(1)PQPPDSTPR 111.58 0.00010695 336730000 369710 269480 256220 342410 262280 269070 285370 356550 674320 TRUE FALSE 320851.8868 267709.7681 380128.849 420159.4239 257061.1411 279421.297 257694.8613 280304.5572 594602.6578 0.539607219 0.45023305 0.63929894 0.706622176 0.432324238 0.469929445 0.433390026 0.471414908 1 19.18156639 1.235419735 24.99931891 1.000000665 0.515127332 0.735234937 0.090915345 49.36585872 392850.3872 0.164350572 0.023747949 17.19569505 -1.235419735 -0.484873332 PYQYPALT(ph)PEQK ddPTM_MDA-MB-175_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 144.8 0.00070826 132080000 236010 188600 181400 182850 173560 131630 242640 253120 280370 TRUE FALSE 204820.6805 187361.0742 269125.6467 224368.8872 170106.4956 136693.8913 219108.8101 198992.2578 247224.978 0.828478911 0.757856571 1.088585987 0.907549427 0.688063548 0.552912947 0.886272948 0.804903531 1 17.91546499 PYQYPALTPEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 PYQYPALTPEQK 12 0 P04075;J3KPS3;H3BQN4;H3BUH7;H3BR04;H3BMQ8 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 154.24 0.00065673 0 156490 128410 126150 130670 119570 98457 175280 186360 165410 FALSE TRUE 135809.45 127566.4663 187156.5619 160340.6207 117190.7909 102244.7045 158281.3726 146508.3643 145855.4182 0.931123791 0.874609033 1.28316496 1.099312063 0.803472318 0.701000386 1.085193642 1.004476666 1 17.15417945 QAAAQPHTEIPEGTTAEEAGIGDTPS(ph)LEDEAAGHVTQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QAAAQPHTEIPEGTTAEEAGIGDTPSLEDEAAGHVTQAR 39 0 P10636-8;P10636-5 P10636-8 MAPT Microtubule-associated protein tau 1 QAAAQPHTEIPEGTTAEEAGIGDT(0.014)PS(0.984)LEDEAAGHVT(0.002)QAR 107.15 2.19E-05 35842000 10256 10091 5943.2 6430.2 10042 8132.6 9023.3 9791.9 9540.1 TRUE FALSE 8900.643615 10024.71156 8817.351399 7890.275189 9842.183847 8445.466384 8148.221755 7697.978386 8412.280246 1.058053626 1.191675891 1.048152361 0.937947258 1.169978122 1.003944963 0.968610355 0.9150882 1 13.0382812 2.488456869 5.036846483 0.955119334 1.078751144 0.374221189 0.071640664 0.188179425 13.93990035 0.026342432 0.021623359 307.9334506 -2.488456869 0.12363181 QAALGIMQMVEDTLIEHAHTKPLLPSQLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QAALGIMQMVEDTLIEHAHTKPLLPSQLVR 30 1 A0A3B3ISG5;P14735;P14735-2 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 53.844 0.041934 242730000 33830 30935 18028 17562 39278 25343 64897 54181 34819 FALSE TRUE 29359.27979 30731.78595 26746.4011 21549.72052 38496.44465 26317.96161 58603.29893 42594.81479 30702.73749 0.956243065 1.00094612 0.871140598 0.701882708 1.253844048 0.857186159 1.908732046 1.387329544 1 14.90607967 2.273271693 24.99958109 1.442573646 0.94325166 0.45156679 0.255399265 151.9407294 109430.0938 0.093642127 0.072531645 187.6167866 -2.273271693 -0.499321987 QAAPPIELDAVWEDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QAAPPIELDAVWEDIR 16 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 78.505 0.048737 9387100 17674 15061 7535.7 13945 14654 15587 15779 19502 19956 FALSE TRUE 15338.33612 14962.0633 11179.98973 17111.42539 14362.41407 16186.64198 14248.75501 15331.64906 17596.82441 0.871653644 0.850270648 0.635341324 0.972415533 0.816193521 0.919861538 0.809734454 0.871273629 1 14.10302748 1.250405131 3.126698528 1.026156884 0.839183814 0.248737174 0.087198859 0.496321459 6.393642453 0.227639814 0.021451623 17.79939048 -1.250405131 -0.18697307 QAAPPIELDAVWEDIRER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QAAPPIELDAVWEDIRER 18 1 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;;; 252.77 1.57E-30 235828000 199977 175031.8 67583.2 75040.1 150936.9 154517.6 164513 176320.3 23142.6 FALSE TRUE 173549.5328 173882.0046 100266.6616 92079.10162 147933.551 160461.9921 148558.5546 138615.576 20406.70819 8.504533467 8.520825747 4.913416737 4.512197693 7.249260861 7.863198246 7.27988822 6.792647529 1 14.31675586 4.253301296 24.72510757 5.94135493 8.512682174 0.254716413 1.984292253 321.367074 539030.206 0.498549857 1.306476019 17918.48537 -4.253301296 2.571327244 QAAS(ph)PLEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QAASPLEPK 9 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 QAAS(1)PLEPK 132.79 0.0003096 334120000 974210 934180 605730 772330 917310 758040 1059100 1327700 1115700 TRUE FALSE 845465.6802 928043.3101 898663.054 947699.3308 899057.3257 787202.2893 956388.645 1043781.687 983803.217 0.859384952 0.943322093 0.913458137 0.96330172 0.9138589 0.800162345 0.97213409 1.060965922 1 19.90801025 2.003133303 24.98883129 1.029351385 0.903612564 0.578658258 0.046975853 60.70351941 484121.6505 0.019226079 0.012884023 100.7240786 -2.003133303 -0.12573882 QACTAQT(ph)PEPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QACTAQTPEPLR 12 0 F2Z2E2;Q86VI3 F2Z2E2 IQGAP3 Ras GTPase-activating-like protein IQGAP3 1 QACT(0.084)AQT(0.916)PEPLR 105.58 0.022518 240860000 237680 291300 161900 222020 282390 283600 220450 255100 260940 TRUE FALSE 206269.9858 289386.4311 240195.3815 272433.0344 276770.9915 294510.2755 199070.7929 200548.8502 230091.9705 0.896467553 1.257698956 1.043910316 1.184017999 1.202871143 1.279967636 0.865179226 0.871602993 1 17.81185111 2.224650966 24.99957656 0.901828578 1.149240878 0.471896312 0.115384208 181.3662338 325963.9187 0.044563883 0.030216656 167.7455338 -2.224650966 0.2474123 QACTAQT(ph)PEPLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QACTAQTPEPLRR 13 1 F2Z2E2;Q86VI3 F2Z2E2 IQGAP3 Ras GTPase-activating-like protein IQGAP3 1 QACTAQT(1)PEPLRR;QACTAQT(1)PEPLRR;QACTAQT(1)PEPLRR;QACTAQT(1)PEPLRR 153.22 2.67E-05 1442380000 876110 1019460 565850 663570 997800 1100360 845570 950050 766100 TRUE FALSE 760329.8437 1012763.1 839496.9527 814243.7105 977945.7322 1142691.561 763566.7515 746889.2008 675532.5307 1.125526617 1.499207002 1.242718765 1.205336047 1.447666378 1.691541871 1.130318255 1.10563025 1 19.36566572 2.026238689 24.99987225 1.077644181 1.368865846 0.420134938 0.161932448 206.4180869 196671.4952 0.066273932 0.044680647 106.2279227 -2.026238689 0.291221665 QADFEAHNILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QADFEAHNILR 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;; 211.26 9.94E-09 1497650000 3069540 2650540 1472990 1950640 2704260 2779630 2376800 2878260 2451160 FALSE TRUE 2663892.512 2633128.428 2185332.891 2393562.626 2650450.517 2886564.165 2146298.302 2262766.498 2161386.657 1.232492346 1.218258852 1.011079107 1.107419914 1.226273193 1.335514937 0.993019132 1.046905 1 21.04352575 2.199810668 24.99982824 1.019461862 1.179825033 0.4788472 0.085762379 159.1590348 102681.582 0.037349262 0.025181358 158.4202403 -2.199810668 0.160363171 QADLYISEGLHPR ddPTM_MDA-MB-175_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 ;;;;; 180.48 1.29E-05 4401210000 5326860 5201960 2698960 3789350 5165840 5448690 4904790 5819440 5373960 FALSE TRUE 4622901.954 5167787.982 4004186.083 4649779.834 5063049.891 5658304.63 4429124.221 4574998.043 4738656.571 0.975572271 1.09055972 0.845004491 0.981244318 1.068456812 1.194073583 0.934679303 0.965463096 1 22.17604668 5.077598094 19.37755283 1.006147994 0.000513825 0.011592094 0.094111051 1526.073289 576055.0375 0.022755516 33967.36778 119563.3554 -5.077598094 -1.005634168 QADVFPDRDHFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QADVFPDRDHFGR 13 1 Q9HCC0-2;Q9HCC0;D6R9R1;D6RDF7;A0A0G2JM88 Q9HCC0-2 MCCC2 "Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial" 0 ; 82.102 0.0079694 715710000 507550 419090 268250 413740 478520 485340 399650 513200 413760 FALSE TRUE 440475.9815 416336.9702 397976.5972 507685.9906 468998.3882 504011.3439 360892.0045 403456.1737 364845.7642 1.20729367 1.141131434 1.090807778 1.391508524 1.285470284 1.381436742 0.989163203 1.105826663 1 18.47692718 2.22391565 24.99902669 1.045343124 1.245539255 0.521542219 0.098062176 215.2054891 367353.7871 0.042272517 0.028639139 167.4617596 -2.22391565 0.200196131 QAEATRAS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QAEATRASPPR 11 1 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 QAEAT(0.002)RAS(0.998)PPR;QAEAT(0.008)RAS(0.992)PPR 94.45 0.0051444 567230000 764470 503410 300000 394320 382310 408310 389920 425750 382960 TRUE FALSE 663443.3526 500103.0666 445081.0034 483856.3828 374702.779 424017.9499 352105.6184 334706.6757 337686.9051 1.964670062 1.480966715 1.318028614 1.432855037 1.109615959 1.255654109 1.042698468 0.991174578 1 18.36532671 8 0.331433939 0.971485235 10.75702101 0.891106278 0.097214487 23.48561857 0.366174023 0.145539285 138.9662166 100000000 -8 9.785535771 QAEEECAHRGS(ph)PLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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;QAEEECAHRGS(1)PLPK 152.13 1.74E-06 2147670000 5401770 3889490 2585520 2946210 3535000 3458100 4629120 4959500 2896610 TRUE FALSE 4687912.408 3863939.684 3835886.12 3615192.011 3464660.416 3591135.345 4180188.655 3898949.52 2554176.066 1.835391252 1.512793004 1.501809594 1.415404388 1.356468907 1.405985826 1.636609438 1.526499904 1 21.28442655 5.817713464 1.034808844 1.419959943 4.768429394 0.405428673 0.16417709 16.0194076 2.47615746 0.050447881 99.25330175 657224.0756 -5.817713464 3.348469451 QAEEYLSFAFEHCHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QAEEYLSFAFEHCHR 15 0 Q5JVF3-3;Q5JVF3-2;Q5JVF3;Q5JVF3-4 Q5JVF3-3 PCID2 PCI domain-containing protein 2 0 96.247 0.002182 48320000 40557 40009 22523 26239 36702 40257 37399 42062 41573 FALSE TRUE 35197.28969 39746.17824 33415.19813 32196.96599 35971.70201 41805.71284 33772.05074 33067.36863 36658.2873 0.960145503 1.084234458 0.911531896 0.878299789 0.981270666 1.140416422 0.921266465 0.902043469 1 15.16185176 1.55569853 0.007865117 5.19E-05 1.919174806 0 0.083084028 84885.05673 224.4362138 28103.55288 26671.8238 35.94996984 -1.55569853 1.919122907 QAEILQESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QAEILQESR 9 0 E5RJD8;O75347;E5RIW3;O75347-2 E5RJD8 TBCA Tubulin-specific chaperone A 0 ;; 177.58 0.00012088 524130000 915790 898040 592350 664850 865950 869760 839110 1023910 922160 FALSE TRUE 794766.0312 892140.7161 878812.4413 815814.3541 848719.2892 903220.23 757733.2414 804954.8146 813143.2953 0.977399722 1.097150676 1.080759623 1.003284856 1.043751199 1.110776213 0.931856963 0.989929843 1 19.63315009 2.232114593 24.99999985 0.975509464 1.052923329 0.417946986 0.043516391 145.7042393 565087.5827 0.016930164 0.011724241 170.6532616 -2.232114593 0.077413865 QAEPELDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 121.64 0.001415 1443190000 1946160 2118170 1243120 1569440 2041990 2137390 1917940 2330910 1976990 FALSE TRUE 1688970.025 2104255.602 1844296.99 1925805.339 2001358.394 2219616.776 1731938.474 1832463.036 1743272.494 0.968850269 1.207072106 1.057951064 1.104707007 1.148046792 1.273247174 0.993498423 1.051162708 1 20.73336667 QAFEELRDDLVELSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QAFEELRDDLVELSK 15 1 Q15397 Q15397 KIAA0020 Pumilio domain-containing protein KIAA0020 0 ; 129.62 5.91E-05 71229000 128916 107480 70559 93591 97927 80138 103239 124349 145668 FALSE TRUE 111879.424 106773.9568 104681.5684 114842.267 95978.44429 83220.96072 93226.89767 97757.93404 128447.295 0.871014247 0.831266683 0.814976823 0.894080852 0.74722044 0.647899675 0.72579884 0.761074292 1 16.97081698 3.226357381 24.99021756 0.76426316 0.848589955 0.139828772 0.091222966 414.6432422 849119.5487 0.028113446 0.032106789 1684.059303 -3.226357381 0.084326794 QAFPNTNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QAFPNTNR 8 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 137.84 0.0032401 0 150571 147905 97457 111633 143452 140285 141550 170026 158943 FALSE TRUE 130672.6609 146933.4023 144587.5312 136980.9789 140597.5859 145681.8547 127822.5028 133667.263 140152.9396 0.932357617 1.048379026 1.031641088 0.977367861 1.003172579 1.039449156 0.912021561 0.953724292 1 17.09664248 2.244286656 24.99889257 0.953129922 1.007166476 0.266873606 0.039054079 164.4227861 717844.2812 0.014352171 0.010808187 175.5038534 -2.244286656 0.054036554 QAGAPGGSSGSGGS(ph)PELSALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QAGAPGGSSGSGGSPELSALR 21 0 Q9Y2J4;Q9Y2J4-2;Q9Y2J4-4 Q9Y2J4 AMOTL2 Angiomotin-like protein 2 1 QAGAPGGSSGSGGS(1)PELSALR;QAGAPGGSSGSGGS(1)PELSALR;QAGAPGGSSGSGGS(1)PELSALR 369.36 2.52E-112 371420000 416766 357064 222622 281083 353970 404454 373739 408784 403139 TRUE FALSE 361689.3171 354718.4231 330282.7438 344907.1912 346926.6895 420013.6071 337493.8493 321368.7228 355480.3667 1.017466367 0.99785658 0.929116696 0.970256654 0.975937695 1.181538128 0.94940222 0.904040709 1 18.43941036 2.031463261 24.99990024 0.939632264 1.009192651 0.138730035 0.069797333 337.8759692 268466.3116 0.029202058 0.019687816 107.5135647 -2.031463261 0.069560388 QAGEVTFADAHRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QAGEVTFADAHRPK 14 1 Q13243;Q13243-3 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 106.52 0.0005628 207220000 554890 426220 249220 325580 390470 346310 433540 525340 441230 FALSE TRUE 481559.8806 423420.1328 369743.6256 399507.9152 382700.4109 359632.7698 391495.3575 413000.1292 389068.2921 1.237725845 1.088292573 0.950330914 1.026832367 0.983632999 0.924343559 1.006238148 1.061510634 1 18.56966388 4.609840918 2.830551666 0.998639813 1.250931862 0.80197974 0.038869424 0.152110734 1.93254832 0.010721651 0.075470162 40723.10818 -4.609840918 0.252292049 QAGEVTYADAHK ddPTM_MDA-MB-175_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 ;;;; 210.41 4.39E-08 4788420000 5679710 4551780 3145870 3819830 4504620 3950190 5153720 5850100 5585190 FALSE TRUE 4929121.933 4521879.057 4667223.254 4687180.784 4414986.875 4102156.365 4653913.028 4599101.641 4924915.201 1.000854174 0.918163841 0.947675861 0.951728221 0.896459471 0.832939492 0.944973231 0.933843823 1 22.23166745 QAGGHKDPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QAGGHKDPEK 10 1 Q15813-2;Q15813;A0A2R8Y5Q8;A0A2R8YHI9;A0A2R8Y7E7;A0A2U3TZJ6;A0A2R8Y6Q1 Q15813-2 TBCE Tubulin-specific chaperone E 0 61.435 0.055043 65031000 155270 115560 135680 116300 77650 89478 142130 177760 175350 FALSE TRUE 134750.6761 114800.8788 201295.3018 142707.6925 76104.91692 92920.27656 128346.2545 139747.4073 154620.3228 0.871493952 0.742469532 1.301868333 0.922955599 0.492205136 0.60095772 0.830073642 0.903810087 1 17.23837043 3.45907059 24.92721189 0.772813344 0.9762325 0.195168545 0.197760228 408.3395636 563897.8342 0.060565684 0.078204148 2877.866145 -3.45907059 0.203419156 QAGPASVPLRTEEEFKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QAGPASVPLRTEEEFKK 17 2 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 155.2 6.15E-08 289490000 379280 309570 202190 241360 309180 248600 388410 401970 98986 FALSE TRUE 329157.187 307536.4143 299969.7603 296164.477 303027.9229 258163.8029 350742.058 316011.8436 87283.98785 3.771106192 3.523400132 3.436710074 3.393113494 3.471746999 2.957745278 4.018400931 3.620501898 1 16.4134294 1.237254443 24.99967406 0.999996952 3.525601553 0.895203393 0.27140601 9.907632982 189553.143 0.400887206 0.06629771 17.26849318 -1.237254443 2.525604601 QAHDLS(ph)PAAESSSTFSFSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QAHDLSPAAESSSTFSFSGR 20 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 QAHDLS(1)PAAESSSTFSFSGR;QAHDLS(1)PAAESSSTFSFSGR;QAHDLS(1)PAAESSSTFSFSGR;QAHDLS(1)PAAESSSTFSFSGR;QAHDLS(1)PAAESSSTFSFSGR;QAHDLS(1)PAAESSSTFSFSGR 285.77 2.53E-45 5837550000 2812520 2455700 1487170 1882080 2712240 2794810 2423460 2910750 2642270 TRUE FALSE 2440838.356 2439568.345 2206370.386 2309435.03 2658271.73 2902328.149 2188433.222 2288308.764 2329903.851 1.04761334 1.047068249 0.946979158 0.991214736 1.140936236 1.245685803 0.939280486 0.982147295 1 21.15183899 QAHELFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QAHELFR 7 0 E7EPM6;P33121-2;P33121;P33121-3;D6RER0;D6RG07 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 ; 103.56 0.0083479 344130000 283170 197599 149193 147222 240421 341140 219801 264440 244478 FALSE TRUE 245748.367 196300.9592 221343.2338 180651.0052 235637.0925 354263.8765 198484.7329 207891.5639 215576.0894 1.139961151 0.91058781 1.026752246 0.837991847 1.093057645 1.643335667 0.920717754 0.964353535 1 17.71783764 3.027665603 24.65280389 1.117420837 0.975891702 0.104607213 0.212205956 495.068253 441151.3232 0.067585067 0.07663251 1065.775182 -3.027665603 -0.141529135 QAHLCVLASNCDEPMYVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QAHLCVLASNCDEPMYVK 18 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 ; 243.29 4.42E-24 744020000 303360 320930 197452 204861 255180 268170 281940 309130 334630 FALSE TRUE 263270.2074 318821.7897 292940.4476 251377.8212 250102.4173 278486.6734 254597.5022 243024.9552 295070.4226 0.892228388 1.080493893 0.992781469 0.851924835 0.847602464 0.943797318 0.862836403 0.823616793 1 18.17069979 3.749691267 23.0188167 0.880584577 0.997700561 0.318158931 0.068092041 250.8005855 518665.2703 0.017268683 0.029491421 5619.417081 -3.749691267 0.117115984 QAHLTNQYMQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QAHLTNQYMQR 11 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;H0YB86 P11940-2 PABPC1 Polyadenylate-binding protein 1;Polyadenylate-binding protein 0 ;;; 205.07 0.0001355 287947000 848107 1035007 408059 536380 1101194 1486510 813801 888834 923681 FALSE TRUE 736027.5111 1028207.971 605397.6973 658173.2771 1079282.394 1543697.002 734878.7043 698763.766 814484.4844 0.903672845 1.262403386 0.743289417 0.808085715 1.325111054 1.895305596 0.902262374 0.857921519 1 19.63552769 3.242647912 24.99968472 1.166765226 0.939860506 0.144192855 0.318040825 278.6762979 1704494.731 0.103022167 0.128181303 1748.428641 -3.242647912 -0.226904721 QAHLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QAHLYR 6 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 126.04 0.041095 666050000 808450 673020 454386 486320 597190 658810 694420 677800 683340 FALSE TRUE 701611.2841 668598.8873 674128.5894 596746.3889 585307.0874 684154.847 627075.2553 532857.7446 602556.3237 1.164391206 1.109603967 1.118781038 0.990357856 0.971373238 1.135420574 1.040691518 0.884328525 1 19.20073658 8 0.151901584 0.872302962 1.954450673 0.45315264 0.06442116 138.4006032 1.758598033 1.109635281 32.32175046 99999999.97 -8 1.082147711 QAHTMDPQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 22 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 ;;;;;;;;;;;;;;;;;;;;; 158.41 8.00E-06 25925839000 4754619 4719491 3093037 3193593 4577877 4945169 4655335 5003428 4677304 FALSE TRUE 4126284.052 4688488.353 4588840.039 3918747.102 4486786.204 5135412.851 4203861.328 3933483.859 4124358.45 1.000466885 1.136780037 1.112619113 0.950147071 1.087874941 1.245142224 1.019276423 0.953720174 1 21.97573829 2.009028456 24.99334919 0.977437528 1.089622109 0.268496372 0.078468542 240.9500784 667016.1456 0.03240375 0.021812106 102.1006379 -2.009028456 0.112184582 QALDYVELSPLTQAS(ph)PQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QALDYVELSPLTQASPQR 18 0 Q9H2D6-3;Q9H2D6-2;Q9H2D6;Q9H2D6-5;Q9H2D6-7;F6WYE2;F6TR96;H0Y5J9;Q9H2D6-6 Q9H2D6-3 TRIOBP TRIO and F-actin-binding protein 1 QALDYVELS(0.001)PLT(0.159)QAS(0.841)PQR;QALDYVELSPLTQAS(1)PQR;QALDYVELSPLTQAS(1)PQR 382.09 5.62E-109 510320000 555867 518544 281775 365098 441396 488112 429191 485341 475471 TRUE FALSE 482407.7676 515137.6503 418042.3325 447999.0811 432613.0832 506889.9845 387568.1229 381554.6041 419261.36 1.150613468 1.228679052 0.99709244 1.068543691 1.031845823 1.209007156 0.924406969 0.910063842 1 18.67749035 0.552649002 0.056631309 2.04E-08 1.821376318 0.365664133 0.087292405 416.8963624 4.778104302 104.8427148 55.60137786 3.569842059 -0.552649002 1.821376297 QALQRYSEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QALQRYSEDR 10 1 B0QY60;Q9UH99-3;Q9UH99;Q9UH99-2 B0QY60 SUN2 SUN domain-containing protein 2 0 59.067 0.097589 184820000 267730 249540 185960 174690 258490 252350 258750 274650 268990 FALSE TRUE 232348.8022 247900.7553 275890.878 214356.0345 253346.5547 262058.0678 233656.4648 215918.2348 237190.3086 0.979588093 1.045155499 1.163162524 0.903730155 1.068115119 1.104843066 0.98510123 0.910316429 1 17.85568554 2.009662012 21.55758955 0.948439192 1.044328881 0.218467532 0.071818524 48.29239516 107746.4295 0.028529673 0.019184336 102.2496927 -2.009662012 0.095889689 QALQST(ph)PLGSSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QALQSTPLGSSSK 13 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 QALQS(0.007)T(0.992)PLGSSSK;QALQS(0.014)T(0.986)PLGSSSK 179.14 1.30E-05 147140000 492480 502970 322940 395130 443920 393730 516960 592900 620470 TRUE FALSE 427397.5202 499665.957 479114.8642 484850.3057 435086.8605 408877.0479 466825.2988 466112.949 547118.7434 0.781178721 0.913267847 0.875705448 0.88618844 0.795232965 0.747327802 0.853243111 0.851941109 1 19.06149446 1.207664085 3.335209295 1.033281164 0.83818656 0.505145858 0.050531555 0.35173849 5.125048649 0.186232722 0.013569404 16.13110376 -1.207664085 -0.195094604 QALTEFNTAIQEIVVTHWHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QALTEFNTAIQEIVVTHWHR 20 0 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 141.97 1.07E-07 74535000 90857 98554 73469 69661 66452 61911 73912 79406 86669 FALSE TRUE 78850.01725 97906.59228 108998.8541 85478.59475 65129.73521 64292.75623 66744.02562 62425.64484 76423.08955 1.031756472 1.281112722 1.426255531 1.118491744 0.852225886 0.841273974 0.873348958 0.816842726 1 16.22172096 3.369964504 3.894454285 0.867318487 1.253339435 0.719283569 0.106832372 0.110486738 3.13583626 0.031290361 0.041220902 2344.037222 -3.369964504 0.386020947 QALVAIFTHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QALVAIFTHLR 11 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 161.99 2.57E-05 78060000 202320 248590 144100 129940 165540 144150 231710 203340 249270 FALSE TRUE 175582.8994 246956.9959 213787.242 159444.863 162246.0779 149695.5438 209238.7999 159857.3234 219801.5846 0.798824539 1.123545112 0.972637401 0.72540361 0.738147899 0.68104852 0.951944001 0.727280123 1 17.74584226 3.757191596 21.82044232 0.797366083 0.980856828 0.258771849 0.127211683 186.3403274 218236.5917 0.031782398 0.054837892 5717.308088 -3.757191596 0.183490745 QAPQTIHLPSGEILDVFDAAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QAPQTIHLPSGEILDVFDAAER 22 0 P21399 P21399 ACO1 Cytoplasmic aconitate hydratase 0 ;; 189.09 2.26E-17 350324000 241533 281510 144955 186061 244591 225739 241090 300594 312176 FALSE TRUE 209613.8021 279660.7423 215055.7228 228308.9938 239724.1176 234423.3254 217709.1289 236314.3123 275270.9089 0.761481854 1.01594732 0.781251182 0.829397464 0.870866154 0.851609516 0.790890435 0.858479064 1 18.07049263 1.244588204 5.516125654 1.006770675 0.846332895 0.326895903 0.070090087 0.165101787 15.61664177 0.099617562 0.016125271 17.56257549 -1.244588204 -0.16043778 QAQAQES(ph)EEEEESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QAQAQESEEEEESR 14 0 H0YLQ7;Q9NVM6 H0YLQ7 DNAJC17 DnaJ homolog subfamily C member 17 1 QAQAQES(1)EEEEESR;QAQAQES(1)EEEEESR;QAQAQES(1)EEEEESR;QAQAQES(1)EEEEESR;QAQAQES(1)EEEEESR 371.03 4.09E-97 2447029000 1443502 1368345 879782.8 1012668.8 1306985 1358888 1314890 1401042 1322899 TRUE FALSE 1252739.553 1359356.252 1305248.705 1242610.729 1280978.556 1411165.301 1187372.17 1101440.071 1166507.387 1.073923378 1.165321597 1.118937367 1.065240342 1.098131542 1.209735417 1.017886542 0.944220399 1 20.15376401 2.044369947 7.756686796 0.97184294 1.119925935 0.684875525 0.043814115 0.113856982 17.04488791 0.017627444 0.011790493 110.7566846 -2.044369947 0.148082995 QAQEEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 186.91 0.000477 250767000 493400 456150 276851 315970 299393 493510 433952 461630 502900 FALSE TRUE 428195.9399 453153.5206 410737.0696 387715.8178 293435.6651 512495.649 391867.4018 362914.0169 443447.7349 0.96560633 1.021887102 0.926235579 0.87432134 0.661714204 1.155706995 0.883683399 0.818391861 1 18.75840455 4.06108504 4.674139145 0.890931258 0.992582161 0.084099222 0.12551879 0.471661181 20.79721743 0.031956784 0.069086342 11510.25751 -4.06108504 0.101650903 QAQEYEALLNIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QAQEYEALLNIK 12 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 240.37 7.72E-16 644100000 759967 699832 454685 574417 689695 584656 774332 928897 826355 FALSE TRUE 659535.4354 695234.7575 674572.1868 704847.1593 675971.4189 607148.0946 699237.4018 730259.6052 728664.2533 0.905129396 0.954122223 0.925765445 0.967314035 0.927685715 0.833234363 0.959615349 1.00218942 1 19.47489469 2.001380427 24.99844145 0.995146496 0.921145445 0.478368815 0.035498291 39.14063993 708798.0576 0.015033939 0.010051038 100.3183607 -2.001380427 -0.074001051 QAQQERDELADEIANSSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QAQQERDELADEIANSSGK 19 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 393.73 3.37E-127 6640650000 6914540 6324650 3461240 4100260 5663930 5129940 7182680 8158700 2532530 FALSE TRUE 6000766.02 6283102.958 5135107.241 5031286.702 5551228.874 5327292.111 6486104.799 6414025.496 2233137.188 2.68714616 2.813576788 2.299503706 2.253012814 2.485843191 2.385564191 2.904481119 2.872203969 1 21.09064045 4.242527634 24.98340355 2.402267091 2.750361573 0.088531017 0.525727662 285.0321765 1795002.156 0.1304628 0.319541436 17479.44481 -4.242527634 0.348094481 QAQTQT(ph)SPEHLVLQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QAQTQTSPEHLVLQQK 16 0 H0Y5D5;Q9BTG3;Q5SYW2;F5H2X7;Q9ULV3-5;Q9ULV3-2;Q9ULV3;A0A494C0L7;Q9ULV3-3;Q9ULV3-4 H0Y5D5 CIZ1 Cip1-interacting zinc finger protein 1 QAQT(0.272)QT(0.574)S(0.154)PEHLVLQQK 188.04 4.57E-09 186460000 365900 347470 195840 270320 312820 282570 324400 471610 405920 TRUE FALSE 317545.3879 345187.4467 290548.879 331700.2876 306595.494 293440.6507 292939.7379 370759.8716 357932.6 0.887165315 0.964392309 0.811741873 0.926711586 0.85657326 0.819820968 0.818421507 1.035837114 1 18.44932842 1.701858947 7.521922349 1.016302655 0.870686252 0.607735898 0.049486847 0.078086018 9.558072774 0.0289386 0.012819842 50.33371049 -1.701858947 -0.145616404 QAQTQTS(ph)PEHLVLQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QAQTQTSPEHLVLQQK 16 0 H0Y5D5;Q9BTG3;Q5SYW2;F5H2X7;Q9ULV3-5;Q9ULV3-2;Q9ULV3;A0A494C0L7;Q9ULV3-3;Q9ULV3-4 H0Y5D5 CIZ1 Cip1-interacting zinc finger protein 1 QAQT(0.041)QT(0.101)S(0.858)PEHLVLQQK 165.17 4.59E-09 370970000 299230 289830 160240 242050 261560 205670 300460 367100 330260 TRUE FALSE 259685.9973 287926.0876 237732.6 297011.152 256355.4677 213582.258 271321.4354 288598.5218 291217.039 0.891726659 0.988699317 0.816341656 1.019896202 0.88029007 0.733412642 0.931681183 0.991008365 1 18.15173524 1.84017218 4.150376128 0.993988241 0.891338265 0.22721143 0.079783817 0.335969458 9.24873295 0.046174746 0.02156217 69.21053072 -1.84017218 -0.102649976 QAQYLGMSCDGPFKPDHYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QAQYLGMSCDGPFKPDHYR 19 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;;; 234.28 2.36E-24 2348941000 1188045 1321930 885464 1207214 1063270 910998 1219100 1372941 2442650 FALSE TRUE 1031041.843 1313246.155 1313677.352 1481330.39 1042113.007 946044.6826 1100871.87 1079348.251 2153882.7 0.478689876 0.609711084 0.609911279 0.687748869 0.483829972 0.439227579 0.51111041 0.501117471 1 21.03850825 1.235531931 24.99973024 1.000000624 0.541025301 0.786568085 0.075275919 41.78291962 344826.8955 0.136333522 0.019839197 17.20013799 -1.235531931 -0.458975324 QAQYLGMSCDGPFKPDHYRY ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QAQYLGMSCDGPFKPDHYRY 20 2 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 173.77 2.47E-12 1435830000 958000 1100140 483490 467790 755430 623960 992850 1058570 306720 FALSE TRUE 831397.8727 1092913.108 717307.3812 574008.8692 740398.421 647964.145 896563.5598 832203.0433 270459.911 3.074015183 4.040943088 2.652176356 2.12234363 2.737553296 2.395786283 3.314959161 3.076992225 1 18.04505524 4.155334348 7.715391477 2.560430394 3.552697479 0.30873717 0.666105889 0.278014733 21.98202642 0.168258876 0.354160998 14299.94437 -4.155334348 0.992267085 QAREEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QAREEEAR 8 1 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 120.15 0.0037951 0 200950 219430 90591 93576 122050 192940 198520 223220 13881 FALSE TRUE 174393.9484 217988.5499 134401.1106 114823.861 119621.4438 200362.5266 179267.561 175486.1401 12240.00399 14.24786695 17.80951624 10.98047931 9.381031336 9.772990585 16.36948213 14.64603778 14.33709827 1 13.57931641 1.236082795 24.99969789 0.999983573 13.45067905 0.674028223 2.719443073 43.74062044 441220.1514 4.678603915 0.711108974 17.22196869 -1.236082795 12.45069548 QAREQTGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QAREQTGK 8 1 Q9Y5B6-2;Q9Y5B6 Q9Y5B6-2 PAXBP1 PAX3- and PAX7-binding protein 1 0 72.547 0.041835 1656400000 1144200 1029400 1502900 829450 378530 1167600 481540 478090 449380 FALSE TRUE 992991.071 1022637.804 2229707.467 1017789.3 370997.9936 1212518.328 434840.3249 375854.174 396254.8083 2.505940748 2.580758093 5.626953718 2.56852227 0.936261178 3.05994603 1.097375516 0.948516374 1 18.59606892 3.469452042 8.70703396 1.438488355 3.576237318 0.475886154 1.042050969 0.115043112 80.04052109 0.300295565 0.399195417 2947.487974 -3.469452042 2.137748963 QAS(ph)DTGSNDAHNKK ddPTM_MDA-MB-175_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(0.97)DT(0.03)GSNDAHNKK;QAS(0.982)DT(0.018)GSNDAHNKK;QAS(0.999)DT(0.001)GSNDAHNKK;QAS(0.943)DT(0.057)GSNDAHNKK;QAS(0.639)DT(0.361)GSNDAHNKK 265.38 4.33E-25 1048280000 1866380 1125485 445244 1174979 605511 312807 2106910 1531410 1248430 TRUE FALSE 1619733.154 1118091.615 660565.4877 1441775.94 593462.5158 324840.8877 1902582.192 1203929.889 1100842.028 1.471358391 1.015669448 0.60005475 1.309702849 0.539098709 0.295084017 1.728297199 1.093644555 1 20.07017602 2.229046677 24.99999254 1.25534021 0.870792245 0.186737381 0.394983032 359.1220158 943664.2369 0.160226444 0.109619509 169.4519913 -2.229046677 -0.384547965 VSS(ph)QAEDTSSSFDNLFIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.027)S(0.973)QAEDTSSSFDNLFIDR;VS(0.088)S(0.912)QAEDTSSSFDNLFIDR;VS(0.03)S(0.97)QAEDTSSSFDNLFIDR 318.9 8.16E-62 161757000 97023 109287 112774 137430 187282 204955 188451 217127 276214 TRUE FALSE 84201.16473 108569.0865 167311.8836 168635.582 183555.4546 212839.7515 170175.051 170696.0807 243560.2956 0.345709733 0.445758559 0.686942357 0.692377145 0.753634553 0.873868834 0.698697834 0.700837057 1 17.89391944 4.403728679 1.024345181 0.788523864 0.222855409 0.76079621 0.091111976 0.568136946 0.710123573 0.030477462 0.314111173 25335.45332 -4.403728679 -0.565668454 down QAS(ph)LDGLQQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QASLDGLQQLR 11 0 Q3MII6 Q3MII6 TBC1D25 TBC1 domain family member 25 1 QAS(1)LDGLQQLR;QAS(1)LDGLQQLR;QAS(1)LDGLQQLR 174.44 1.15E-05 670180000 572449 465680 310472 415424 540904 528232 512208 601921 526632 TRUE FALSE 496798.4142 462620.9174 460617.2977 509752.3686 530141.0687 548553.4269 462534.147 473204.8783 464374.1649 1.069823543 0.996224494 0.991909827 1.097719053 1.141624812 1.181274645 0.996037639 1.019016375 1 18.82492819 5.104054643 19.72055546 1.052693953 3.002695364 0.006179763 0.067059867 4702.73871 977644.9898 0.017349565 40001.30858 127073.3978 -5.104054643 1.950001411 QAS(ph)LPVSGSVAGDFVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QASLPVSGSVAGDFVK 16 0 Q9Y3S1;Q9Y3S1-4;Q9Y3S1-2;H0Y7T5;F8W9F9;H0Y7R3;H0Y493;H0Y7J9;E9PCD1 Q9Y3S1 WNK2 Serine/threonine-protein kinase WNK2 1 QAS(0.998)LPVS(0.002)GS(0.001)VAGDFVK 138.75 5.15E-06 58890000 220490 165980 84293 131450 136390 67146 257100 202300 161210 TRUE FALSE 191351.6878 164889.6665 125057.3767 161297.7316 133676.1058 69729.15007 232166.4816 159039.7193 142151.9375 1.346106787 1.159953705 0.879744441 1.134685425 0.940374843 0.490525499 1.633227698 1.118800926 1 17.11707424 1.225014264 22.47958757 0.999999193 1.088862019 0.008568553 0.297086635 1653.897 2743956.768 1.204081763 0.07184712 16.78859156 -1.225014264 0.088862825 QAS(ph)PLISPLLNDQACPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QASPLISPLLNDQACPR 17 0 C9JME2;Q9Y4F1;Q9Y4F1-2 C9JME2 FARP1 "FERM, RhoGEF and pleckstrin domain-containing protein 1" 1 QAS(1)PLISPLLNDQACPR;QAS(0.994)PLIS(0.006)PLLNDQACPR;QAS(1)PLISPLLNDQACPR 159.81 3.32E-09 268193000 159307 165763 93597 154339 209537 224158 115422 236490 175371 TRUE FALSE 138254.1763 164674.0919 138860.8223 189384.0289 205367.6237 232781.5033 104228.3922 185918.4539 154638.8402 0.894045611 1.064894769 0.897968596 1.224686041 1.328046844 1.50532365 0.67401173 1.202275274 1 17.2385432 3.739828724 24.98608255 1.152212787 0.963562168 0.159224287 0.219750334 235.4104905 4638363.174 0.059982812 0.096821815 5493.241905 -3.739828724 -0.188650619 QAS(ph)PQNLGTPGLLHPQTSPLLHSLVGQHILSVQQFTK ddPTM_MDA-MB-175_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(1)PQNLGTPGLLHPQTSPLLHSLVGQHILSVQQFTK 345.13 2.02E-131 1821670000 686050 677560 251858 542890 793990 718910 826460 924020 847280 TRUE FALSE 595386.7543 673109.0637 373657.3712 666161.4721 778191.1524 746566.9329 746310.0364 726425.5137 747115.5236 0.796913911 0.900943753 0.500133325 0.891644533 1.041594141 0.999265722 0.998921871 0.972306813 1 19.51097181 3.484338109 22.63774786 0.995360095 0.740557855 0.603461722 0.099678431 63.31252399 198598.3645 0.027208706 0.036736017 3050.268777 -3.484338109 -0.25480224 QAS(ph)PTEVVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QASPTEVVER 10 0 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;C9JW01;A0A0C4DG68 Q8TB72-3 PUM2 Pumilio homolog 2 1 QAS(0.901)PT(0.099)EVVER;QAS(0.992)PT(0.008)EVVER;QAS(0.905)PT(0.095)EVVER;QAS(0.905)PT(0.095)EVVER;QAS(0.923)PT(0.077)EVVER 187.1 1.33E-06 3165500000 1645950 1485470 944940 1104710 1539660 1595980 1403560 1659740 1477080 TRUE FALSE 1428433.537 1475711.85 1401916.145 1355551.29 1509023.778 1657378.383 1267442.967 1304817.517 1302461.285 1.096718615 1.133017823 1.076359168 1.040761292 1.15859396 1.272497235 0.973113736 1.001809061 1 20.31280906 2.165754411 25 0.99298623 1.124671133 0.529227354 0.061238659 35.82202444 12299.42376 0.026075826 0.017580323 146.4719325 -2.165754411 0.131684903 LFS(ph)QGQDVSNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LFSQGQDVSNK 11 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;H0Y8L4;H0Y8U8 P55196-5 MLLT4 Afadin 1 LFS(1)QGQDVSNK;LFS(1)QGQDVSNK;LFS(1)QGQDVSNK 148.85 3.63E-05 809160000 672300 1181430 1553940 1448960 2418800 2085660 2221300 2533790 2533410 TRUE FALSE 583453.8516 1173669.109 2305430.582 1777968.514 2370670.612 2165896.69 2005878.668 1991958.726 2233913.156 0.261180185 0.525387079 1.032014416 0.795898672 1.061218788 0.969552771 0.897921507 0.891690315 1 21.09114167 4.409498206 3.428800515 0.941010829 0.296395434 0.896042564 0.081030324 0.063195368 1.438439746 0.019947849 0.069841621 25674.27601 -4.409498206 -0.644615395 down QAS(ph)VHDS(ph)GEEGEA ddPTM_MDA-MB-175_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 176.18 2.49E-05 5274500000 5862900 5235500 3527500 4433100 5471300 5758700 6185300 6485700 6194300 TRUE FALSE 5088102.91 5201107.656 5233410.799 5439703.111 5362431.834 5980240.915 5585450.558 5098783.527 5462016.911 0.93154287 0.952232068 0.958146209 0.995914733 0.98176771 1.094877774 1.022598547 0.933498305 1 22.38100235 3.862151827 1.739186389 1.002709194 0.939370902 0.325176429 0.039815817 0.555648459 3.242441166 0.013423645 0.032722733 7280.342767 -3.862151827 -0.063338292 QAS(ph)VHDSGEEGEA ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 QASVHDSGEEGEA 13 0 Q8TE77;Q8TE77-3;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA 214.58 3.21E-11 27013357000 9727329 10369216 3687196 6650823 9880212 10027656 10025882 10351232 9714079 TRUE FALSE 8441837.827 10301099.94 5470336.319 8160994.014 9683615.112 10413426.42 9053573.507 8137701.59 8565691.647 0.98554071 1.202599902 0.638633346 0.952753654 1.130511757 1.215713435 1.056957673 0.950034384 1 23.03013831 3.334469235 8.17355043 1.061585686 0.940227829 0.14394984 0.151536427 0.561403059 42.37796639 0.045456361 0.058683592 2160.077013 -3.334469235 -0.121357857 QASALIDRPAPFFER ddPTM_MDA-MB-175_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 ; 177.04 7.02E-07 1236960000 618770 635680 375670 547950 589990 666460 502360 595350 538700 FALSE TRUE 536997.9767 631504.1762 557345.2685 672370.4224 578250.3533 692099.1475 453641.2045 468039.0355 475015.4997 1.130485168 1.329439095 1.173320174 1.415470491 1.217329442 1.457003293 0.955002952 0.985313186 1 18.85761506 2.220644954 24.98596576 0.980144274 1.286577374 0.675634125 0.100297305 126.620183 176588.7137 0.037505953 0.025344627 166.2053326 -2.220644954 0.306433099 QASASYDS(ph)EEEEEGLPMSYDEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QASASYDSEEEEEGLPMSYDEKR 23 1 Q15059 Q15059 BRD3 Bromodomain-containing protein 3 1 QASASYDS(1)EEEEEGLPMSYDEKR;QASAS(0.002)YDS(0.998)EEEEEGLPMSYDEKR 276.2 5.76E-52 380060000 347750 312310 172831 192676 284520 248140 329650 390040 111069 TRUE FALSE 301793.9564 310258.415 256412.6497 236426.0307 278858.6087 257686.1064 297680.5937 306632.9813 97938.54935 3.081462391 3.167888611 2.61809728 2.414024225 2.847281387 2.631099889 3.039462966 3.130871177 1 16.57958921 4.235545478 24.34643501 2.618617386 3.124675624 0.136134395 0.592309385 114.7274794 926442.5445 0.146695372 0.328293455 17200.67454 -4.235545478 0.506058238 QASCSGDEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QASCSGDEYR 10 0 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A087WT27;A0A494C1E2;A0A494C1Q4;J3KN95;A0A494C099;A0A494C163;D6RIS6 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 ;; 212.4 9.61E-08 748530000 580809 544900 329299 368141 481454 543102 495574 558395 537186 FALSE TRUE 504053.6191 541320.516 488549.0978 451733.0407 471874.0073 563995.4854 447513.3098 438986.5747 473680.483 1.06412157 1.142796749 1.031389545 0.953666146 0.996186299 1.190666505 0.944757755 0.926756728 1 18.8535547 -1.999999014 0.052213248 0.257205635 1.447361516 0.171203629 0.077638393 1640.190701 8.358989515 172.301015 52.10993017 0.010000023 1.999999014 1.190155881 QASDT(ph)GSNDAHNKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QASDTGSNDAHNKK 14 1 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0YA91;E7EQK6;P20810-5;E9PCH5;P20810-2;F8W7E0;E9PSG1;A0A0C4DGB5;H0Y944;E7EN75;D6RGF7;D6RBR1;E7EVY3 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 1 QAS(0.363)DT(0.623)GS(0.014)NDAHNKK 131.45 4.28E-05 474690000 88235 62735 30376 51354 35949 30070 90283 87595 53086 TRUE FALSE 76574.52119 62322.88965 45065.9352 63014.7106 35233.68523 31226.81236 81527.36856 68863.49092 46810.23356 1.635850013 1.331394546 0.962736816 1.346173813 0.752691934 0.66709371 1.741656949 1.47112043 1 15.51453634 4.623392096 3.472314397 1.172980242 1.645432717 0.188942386 0.325342058 0.509485309 9.924410628 0.087647796 0.510690867 42013.81275 -4.623392096 0.472452475 QASDTGSNDAHNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QASDTGSNDAHNK 13 0 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0YA91;E7EQK6;P20810-5;E9PCH5;P20810-2;F8W7E0;E9PSG1;A0A0C4DGB5;H0Y944;E7EN75;D6RGF7;D6RBR1;E7EVY3 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ;; 154.6 1.39E-06 201440000 313278 316135 167927 246864 203582 268920 313537 423667 501367 FALSE TRUE 271877.5186 314058.2884 249137.0589 302918.2443 199531.1165 279265.5264 283130.23 333069.109 442095.9644 0.614973989 0.710384879 0.563536153 0.685186631 0.451329875 0.63168531 0.640427085 0.75338645 1 18.75400004 1.184217158 1.522834621 1.202696326 0.609103854 0.759799999 0.069730858 0.624194333 1.163938619 0.590356235 0.01951649 15.2833007 -1.184217158 -0.593592472 QASDTGSNDAHNKK ddPTM_MDA-MB-175_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 ;;;; 324.84 6.83E-57 1500080000 1489790 1357541 798526 1142599 861096 956438 1668597 2052700 1660710 FALSE TRUE 1292910.477 1348623.224 1184695.845 1402043.566 843961.8743 993232.7888 1506776.72 1613746.079 1464382.756 0.88290474 0.920949949 0.809006962 0.957429716 0.576326012 0.678260369 1.028950057 1.101997461 1 20.48186126 2.135434725 7.130522709 1.059587191 0.806775673 0.495256898 0.113909962 0.187308064 11.43481966 0.049587943 0.033336613 136.5949756 -2.135434725 -0.252811518 QASEGPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QASEGPLK 8 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;; 123.98 0.0030808 5643300000 6567540 6777750 4416650 5185360 5776880 5651100 7589910 7999660 7940270 FALSE TRUE 5699622.949 6733226.514 6552556.713 6362775.241 5661931.39 5868501.474 6853841.696 6288994.962 7001580.326 0.81404807 0.961672394 0.935868248 0.908762729 0.808664777 0.838168128 0.978899245 0.898225068 1 22.73924916 -0.298430897 0.941421873 2.780309775 0.889140958 0.261496326 0.057811197 50.47552309 3.141073444 179.5351692 0.01988544 0.503001295 0.298430897 -1.891168817 SAEPSPTVMSTS(ph)LGSNLSELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SAEPSPTVMSTSLGSNLSELDR 22 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 SAEPSPTVMS(0.221)T(0.154)S(0.625)LGSNLSELDR;SAEPSPTVMS(0.063)T(0.027)S(0.91)LGS(0.001)NLSELDR;SAEPSPTVMS(0.023)T(0.203)S(0.774)LGSNLSELDR;SAEPSPTVMS(0.156)T(0.023)S(0.82)LGSNLSELDR;SAEPSPTVMS(0.065)T(0.174)S(0.761)LGSNLSELDR;SAEPSPTVMS(0.016)T(0.012)S(0.972)LGSNLSELDR 284.48 6.85E-46 959113000 840204 1082970 1026992 1182350 1814460 2258850 1914620 1962580 2126320 TRUE FALSE 729168.9126 1075855.899 1523648.766 1450820.639 1778355.796 2345749.421 1728940.447 1542897.54 1874948.872 0.388900691 0.573805459 0.812634835 0.773792107 0.948482288 1.251100473 0.922126717 0.822901127 1 20.83841982 4.410870489 0.967725505 0.96822946 0.242228346 0.745987204 0.117887367 0.70954661 0.766103244 0.044836677 0.485106992 25755.52988 -4.410870489 -0.726001114 down QATENAKEEVRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QATENAKEEVRR 12 2 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;;; 275.85 4.33E-28 953755000 1262304 1098764 363332 324299 934533 827946 1278334 1264768 72590.8 FALSE TRUE 1095487.328 1091546.147 539040.5705 397936.0445 915937.6217 859797.6184 1154361.365 994307.2056 64009.19832 17.11452974 17.05295763 8.421298573 6.216857186 14.30946873 13.43240723 18.03430438 15.53381751 1 15.96599162 7.999997766 0.039602739 4.74E-07 32.97447875 0.075267913 5.307389808 9020.783385 35.19563001 9272.073285 23011.01845 99999485.69 -7.999997766 32.97447827 QATVGDINTERPGMLDFTGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QATVGDINTERPGMLDFTGK 20 1 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ;;;;; 273.42 1.71E-44 2841980000 3250590 2961360 1982950 2372220 2277020 2119680 2532610 3265730 7285050 FALSE TRUE 2821016.296 2941906.631 2941911.253 2910868.808 2231711.757 2201225.461 2286997.872 2567379.053 6423819.688 0.439149359 0.457968432 0.457969152 0.453136755 0.347411955 0.342666134 0.356018379 0.399665492 1 22.61499997 1.238258934 24.99776608 1.000000664 0.404832311 0.9435089 0.045618202 1.752893122 145003.471 0.071881094 0.012668531 17.30848012 -1.238258934 -0.595168353 QATVSWDSGGSDEAPPKPSRPGYPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QATVSWDSGGSDEAPPKPSRPGYPSPR 27 2 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-6;B4DWJ1;E5RJQ2;E5RG80;E5RHK7 E7ESA6 PTK2 Focal adhesion kinase 1 1 QATVSWDSGGSDEAPPKPS(0.001)RPGYPS(0.999)PR;QATVSWDSGGSDEAPPKPS(0.008)RPGYPS(0.992)PR;QATVSWDSGGSDEAPPKPS(0.028)RPGYPS(0.972)PR;QATVSWDSGGSDEAPPKPS(0.001)RPGYPS(0.999)PR;QATVSWDSGGSDEAPPKPS(0.016)RPGYPS(0.984)PR;QATVSWDSGGSDEAPPKPSRPGYPS(1)PR 312.21 2.51E-82 10647810000 4317890 3609690 2688370 3242680 3322110 3079140 4062760 4519140 5365210 TRUE FALSE 3747269.896 3585977.709 3988474.724 3978980.055 3256006.511 3197596.508 3668754.161 3552757.079 4730940.986 0.792077075 0.757984029 0.84306161 0.84105468 0.688236552 0.67589017 0.775480855 0.750962037 1 22.17369573 1.236531043 24.99960044 1.000000299 0.764691626 0.645630564 0.05457321 37.0056024 455703.6741 0.090521909 0.014240999 17.23975315 -1.236531043 -0.235308673 QATYRERNKT(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QATYRERNKTR 11 3 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 QATYRERNKT(1)R;QATYRERNKT(1)R 79.659 0.027298 3875800000 3492800 3729200 1792660 2519900 4018200 4383500 2938300 3236700 2739200 TRUE FALSE 3031217.63 3704702.64 2659596.372 3092081.809 3938245.681 4552136.082 2653344.118 2544556.893 2415374.897 1.254967763 1.533800258 1.101111209 1.28016641 1.630490442 1.88464991 1.098522686 1.053483207 1 21.2038157 2.031984064 24.99960897 1.044193723 1.441012618 0.430923914 0.215865693 185.9332186 145329.6969 0.092907527 0.062637777 107.6425713 -2.031984064 0.396818894 QAVDFLSNEGHIYSTVDDDHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QAVDFLSNEGHIYSTVDDDHFK 22 0 Q5TEJ0;P15927;P15927-2;P15927-3 Q5TEJ0 RPA2 Replication protein A 32 kDa subunit 0 ;; 248.18 2.24E-31 1213670000 1332340 1549350 745360 808030 1434480 1632990 1311230 1279180 1028400 FALSE TRUE 1156267.893 1539172.218 1105818.589 991505.5615 1405936.655 1695812.182 1184067.116 1005637.312 906823.7236 1.275074596 1.697322399 1.219441618 1.09338291 1.550396861 1.870057143 1.305730194 1.108966699 1 19.79046261 1.767164164 3.233782471 1.038217652 1.44737635 0.331746943 0.228342361 0.266648431 5.539198863 0.16625169 0.064754836 58.5011178 -1.767164164 0.409158698 QAVEEMMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QAVEEMMDR 9 0 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 108.67 0.0059886 127740000 121440 132720 76443 82481 137530 123430 114810 145060 111320 FALSE TRUE 105391.3963 131848.1536 113411.0905 101209.5717 134793.4221 128178.432 103675.7439 114040.0479 98159.87642 1.073670833 1.34319804 1.155371162 1.031068654 1.37320285 1.305812891 1.056192689 1.161778641 1 16.58284581 1.124724356 1.133413653 0.875094343 1.206896282 0.208465768 0.118754319 3.395332131 3.057017171 1.44918809 0.037585884 13.32675322 -1.124724356 0.331801939 QAVEQQIQSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QAVEQQIQSHR 11 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ;;; 196.02 6.19E-08 3436710000 3584450 3365560 1812310 2361410 3388840 3505430 3134630 3522800 3253650 FALSE TRUE 3110755.851 3343451.415 2688749.178 2897604.232 3321408.714 3640286.16 2830634.065 2769476.634 2869007.204 1.084262126 1.165368777 0.937170591 1.00996757 1.157685735 1.268831307 0.986624942 0.965308359 1 21.45212016 2.046645395 24.99999788 0.978912034 1.099812885 0.285661869 0.08920037 159.2541068 85352.87413 0.038642221 0.026052568 111.3385073 -2.046645395 0.120900851 QAVPQANHTESCHECGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QAVPQANHTESCHECGR 17 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 0 97.579 0.0011796 53397000 41264 45087 12275 30466 52617 55243 48290 48754 43290 FALSE TRUE 35810.85785 44790.82053 18211.23106 37383.77094 51570.02464 57368.23396 43606.84323 38328.3365 38172.30552 0.938137149 1.173385257 0.477079674 0.979342757 1.350980087 1.502875794 1.142368601 1.004087544 1 15.2202387 3.461593229 16.67532787 1.184456793 0.866302985 0.328976655 0.223209895 6.257703601 6718.078651 0.068097847 0.08813411 2894.631133 -3.461593229 -0.318153807 QAVRVS(ph)PCHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QAVRVSPCHSR 11 1 A0A1B0GWK2;Q674X7-4;Q674X7-3;Q674X7-2;Q674X7;Q674X7-5 A0A1B0GWK2 KAZN Kazrin 1 QAVRVS(0.937)PCHS(0.063)R;QAVRVS(0.734)PCHS(0.266)R 75.01 0.023776 320340000 624790 711040 298740 427590 739300 804710 645690 764870 543430 TRUE FALSE 542222.4185 706369.1314 443211.6632 524680.8448 724589.3764 835667.7144 583071.0832 601308.5027 479186.3245 1.131548191 1.474101191 0.924925526 1.094941191 1.51212449 1.743930642 1.216794081 1.254853221 1 18.87022721 3.260044931 24.99868144 1.34446817 1.162541056 0.139447589 0.233269041 553.4866646 644021.0494 0.070824794 0.091347346 1819.88913 -3.260044931 -0.181927114 QAWRKGPDGPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QAWRKGPDGPQK 12 2 Q9BYZ6-2;E5RI44 Q9BYZ6-2 RHOBTB2 Rho-related BTB domain-containing protein 2 0 ; 54.776 0.074287 2117210000 8072700 5248100 5042900 4139400 1893610 2089550 4779100 5368000 5064400 FALSE TRUE 7005872.241 5213624.886 7481663.307 5079314.037 1855930.866 2169936.341 4315623.618 4220094.974 4465692.401 1.56882105 1.167484103 1.675364677 1.137407949 0.41559756 0.48591263 0.966395181 0.945003506 1 22.09045245 3.470984722 11.80708773 0.785798018 1.434694757 0.663759278 0.23049193 0.182890867 337.3461454 0.069790075 0.091958402 2957.908412 -3.470984722 0.648896739 QAYS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QAYSPR 6 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 QAY(0.001)S(0.999)PR;QAYS(1)PR 93.649 0.047601 984610000 1494130 1240110 712670 899110 944090 1270170 1213970 1287440 1194570 TRUE FALSE 1296676.935 1231963.636 1057319.596 1103266.668 925304.4561 1319034.262 1096239.376 1012130.975 1053349.295 1.231003752 1.169568007 1.003769215 1.047389192 0.878440286 1.252228741 1.040717814 0.960869276 1 20.00655249 4.348899121 3.926066046 1.024596037 1.21857481 0.378271847 0.094058743 0.222815349 6.178896865 0.023721469 0.071388025 22330.53464 -4.348899121 0.193978773 QAYVDKLEELMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QAYVDKLEELMK 12 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 129.71 0.00020927 359750000 966540 833820 659350 747550 716660 596470 1044360 1142600 1008060 FALSE TRUE 838809.2901 828342.5815 978213.8654 917292.6531 702399.8681 619416.5869 943078.1279 898263.8817 888888.2952 0.943661082 0.931886027 1.100491334 1.031954924 0.790200379 0.696844126 1.060963603 1.010547542 1 19.7616426 QCFHEEVEQGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QCFHEEVEQGVK 12 0 Q9Y3Q3;G3V1J9;F5H4M7;Q9Y3Q3-2 Q9Y3Q3 TMED3 Transmembrane emp24 domain-containing protein 3 0 151.66 6.92E-05 260130000 344480 311620 233660 262140 324050 287720 280540 391300 416120 FALSE TRUE 298956.0952 309572.9477 346658.7575 321662.8936 317602.039 298788.7746 253333.274 307623.5401 366926.7676 0.814756844 0.843691371 0.944762792 0.876640578 0.86557337 0.814300839 0.690419169 0.838378574 1 18.48513263 2.803822976 5.544756885 0.822628464 0.872820903 0.028654036 0.080755692 0.634645921 38.67175937 0.027281119 0.027128514 636.5360073 -2.803822976 0.050192439 QCVENADLPEGEKKPIDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QCVENADLPEGEKKPIDQR 19 2 A0A087WW66;Q99460-2;Q99460;C9J9M4;H7BZR6 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;; 177.61 2.24E-14 1067750000 1378260 1037660 780650 811170 973600 758950 1423210 1627500 650220 FALSE TRUE 1196119.449 1030843.543 1158174.951 995358.5465 954227.2648 788147.2976 1285187.313 1279471.79 573351.7323 2.086187904 1.797925226 2.020007765 1.736034776 1.664296471 1.374631405 2.241533845 2.23156523 1 19.12906093 7.83804864 0.894391518 1.795088286 98.5553413 0.064447473 0.375262293 2492.997508 7.805593622 0.126930186 490687.3701 68872942.81 -7.83804864 96.76025301 QDAAGKDS(ph)PNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QDAAGKDSPNR 11 1 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 QDAAGKDS(1)PNR 101.39 0.002012 139330000 540850 418800 268460 319030 292340 362570 451750 495580 419310 TRUE FALSE 469375.3022 416048.8752 398288.1539 391470.6376 286523.006 376518.3025 407939.3545 389604.0736 369739.6495 1.269475164 1.1252482 1.077212451 1.058773756 0.774931783 1.018333584 1.103315144 1.053725437 1 18.49615024 4.576692515 1.346161668 1.007418864 1.328347199 0.492410714 0.087761281 0.932455904 1.889119704 0.02732977 0.378030258 37730.49609 -4.576692515 0.320928335 QDAKDPTSLLGVLQAEADS(ph)TSEGLEDAVHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QDAKDPTSLLGVLQAEADSTSEGLEDAVHSR 31 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 QDAKDPTSLLGVLQAEADS(0.822)T(0.177)S(0.001)EGLEDAVHSR 233.08 6.83E-46 43409000 82590 77776 38192 43592 75407 66869 86647 107390 26902 TRUE FALSE 71675.52224 77265.08433 56661.77894 53490.22986 73906.54823 69441.4937 78243.98728 84425.48421 23721.67621 3.021520133 3.257151125 2.388607721 2.254909366 3.115570231 2.92734346 3.298417304 3.559001627 1 14.53391834 QDAKDPTSLLGVLQAEADSTSEGLEDAVHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QDAKDPTSLLGVLQAEADSTSEGLEDAVHSR 31 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 ; 185.5 1.34E-18 70850000 108582 81436 41273 54564 80223 69556 96874 107699 40497 FALSE TRUE 94232.61359 80901.04155 61232.76085 66953.59016 78626.71925 72231.86433 87479.17439 84668.40696 35709.49079 2.638867469 2.265533329 1.714747522 1.874952251 2.201843754 2.022763773 2.44974578 2.371033725 1 15.12401994 4.569185458 3.808058175 2.019719005 2.61907319 0.21922102 0.408605675 0.408599975 10.08595743 0.101112007 0.492194559 37083.9048 -4.569185458 0.599354185 QDAPPWGSGVELTHLGS(ph)PSAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QDAPPWGSGVELTHLGSPSAQR 22 0 Q8NDX1-2;Q8NDX1 Q8NDX1-2 PSD4 PH and SEC7 domain-containing protein 4 1 QDAPPWGSGVELTHLGS(0.993)PS(0.007)AQR;QDAPPWGSGVELTHLGS(0.993)PS(0.007)AQR 256.63 2.62E-37 204730000 148128 164773 93652 133083 171660 180116 130980 187678 192787 TRUE FALSE 128552.5095 163690.5953 138942.4204 163301.5292 168244.3018 187045.1791 118277.5798 147544.5202 169995.9405 0.75620929 0.962908849 0.817327873 0.96062017 0.989695997 1.100292034 0.695767084 0.867929668 1 17.37514077 5.95778228 12.65575144 0.902682745 0.63159158 0 0.12285362 0 0 0.027109475 0 907365.5358 -5.95778228 -0.271091164 QDATVWIPS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QDATVWIPSPSR 12 0 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 QDATVWIPS(0.996)PS(0.004)R 97.093 0.0053661 87513000 100370 96949 65674 87538 86321 93514 98837 97369 165170 TRUE FALSE 87105.85019 96312.13564 97434.16607 107414.8408 84603.38098 97111.54409 89251.80295 76547.39708 145643.7908 0.598074588 0.661285559 0.668989495 0.737517475 0.580892467 0.666774351 0.612808843 0.525579544 1 17.15208467 1.22840469 24.99997615 1.000000755 0.630587779 0.800774518 0.057763957 200.2113178 492808.6827 0.203738209 0.015143939 16.92016873 -1.22840469 -0.369412976 QDATVWIPS(ph)PSRQPVYYDELDAASSSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QDATVWIPSPSRQPVYYDELDAASSSLR 28 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 QDATVWIPS(0.865)PS(0.135)RQPVYYDELDAASSSLR;QDATVWIPS(0.833)PS(0.167)RQPVYYDELDAASSSLR 153.57 2.04E-08 215840000 163313 162880 79628 103385 144295 166836 149538 168065 83782 TRUE FALSE 141730.7733 161810.0306 118136.3671 126860.1444 141423.8118 173254.2889 135035.8278 132125.6076 73877.3874 1.918459467 2.190251121 1.599086964 1.717171503 1.914304455 2.345159933 1.827837076 1.788444506 1 16.17284523 1.146029042 2.276156783 0.561852248 1.933163751 0.649786756 0.212788009 0.568186319 2.449599746 1.74973652 0.058335197 13.99680918 -1.146029042 1.371311504 QDDFTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QDDFTAR 7 0 A0A2R8Y430;P48637;A0A2R8YF34;A0A2R8Y790;A0A2R8Y446;A0A0S2Z4J7 A0A2R8Y430 GSS Glutathione synthetase 0 78.77 0.080109 442040000 569640 540040 367140 448570 513400 533860 478800 570360 611200 FALSE TRUE 494360.6307 536492.4417 544690.132 550424.6745 503184.3445 554397.9397 432366.0497 448392.9525 538944.6323 0.917275358 0.995450014 1.010660649 1.021300968 0.933647567 1.028673274 0.802245767 0.831983335 1 19.03977754 2.244377491 24.99996015 0.865314041 0.985549217 0.391417925 0.061869451 121.1960406 520882.7848 0.023102311 0.017406518 175.5405648 -2.244377491 0.120235176 QDDS(ph)PPRPIIGPALPPGFIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QDDSPPRPIIGPALPPGFIK 20 1 A0A0A0MRI1;Q8IXQ4;Q8IXQ4-4 A0A0A0MRI1 GPALPP1 GPALPP motifs-containing protein 1 1 QDDS(1)PPRPIIGPALPPGFIK;QDDS(1)PPRPIIGPALPPGFIK;QDDS(1)PPRPIIGPALPPGFIK;QDDS(1)PPRPIIGPALPPGFIK;QDDS(1)PPRPIIGPALPPGFIK 218.93 5.79E-25 2641510000 6656440 5541960 3708870 4680730 5467410 4998220 6162310 7075520 6630200 TRUE FALSE 5776774.589 5505554.5 5502491.937 5743561.287 5358619.238 5190504.758 5564690.125 5562475.11 5846385.309 0.988093374 0.941702301 0.941178463 0.982412377 0.916569633 0.887814347 0.951817205 0.951438336 1 22.47911348 1.170448698 2.374668365 1.022681615 0.942520981 0.26624965 0.028730761 1.063125456 5.422779822 0.192227542 0.007813771 14.8063734 -1.170448698 -0.080160634 QDEEKPLHALLHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QDEEKPLHALLHGR 14 1 P24593;C9JXX4 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 0 ; 208.47 5.16E-09 186606000 304540 227534 158308 176155 229029 194835 297710 276070 287270 FALSE TRUE 264294.2674 226039.3142 234866.2783 216153.6851 224471.771 202330.4285 268838.13 217034.5789 253309.2679 1.04336596 0.892345219 0.927191809 0.853319292 0.886156961 0.798748622 1.061303964 0.856796835 1 17.95054034 1.211608174 24.01560336 1.00000073 0.912268729 0.095930331 0.0817438 4108.54612 3660539.277 1.461457751 0.018634968 16.27826725 -1.211608174 -0.087732 QDEFKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QDEFKR 6 1 P30040;F8W1G0 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 ;; 92.925 0.074083 748280000 1801570 1243540 991120 1328870 1255770 1463690 1471010 1511770 1206640 FALSE TRUE 1563487.96 1235371.104 1470428.947 1630610.244 1230782.634 1519999.101 1328351.677 1188489.75 1063992.394 1.469454076 1.161071368 1.381991973 1.53253938 1.156758865 1.428580797 1.248459749 1.11700963 1 20.02105641 1.658161454 1.703623634 0.987177935 1.348254331 0.511237977 0.120500438 0.340227679 1.778517499 0.170709284 0.033753261 45.51572386 -1.658161454 0.361076396 QDEHGYISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 QDEHGYISR 9 0 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;;;;;;;; 170.02 5.80E-05 3.50039E+11 138355990 135750110 84187340 100677240 135029620 151642020 146558310 153713670 146204900 FALSE TRUE 120071895.4 134858358.6 124900619.2 123537546.1 132342794.7 157475786.6 132345107.7 120843197.9 128920723.3 0.931362254 1.046056485 0.968817239 0.958244283 1.026543998 1.221493199 1.026561939 0.937345019 1 26.94190895 3.128585566 6.900673147 1.037762886 0.980895865 0.154616018 0.076582119 0.563729859 32.26640925 0.025734114 0.0292875 1344.576655 -3.128585566 -0.056867021 QDELGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QDELGER 7 0 Q15393 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ; 89.698 0.041136 323260000 704350 632210 424890 503960 513980 649720 608080 692790 701180 FALSE TRUE 611268.3629 628056.9709 630368.2252 618391.8205 503752.8036 674715.1488 549108.4952 544642.2498 618287.2992 0.988647775 1.015801185 1.01953934 1.00016905 0.814755219 1.091264772 0.888112203 0.880888627 1 19.23791784 3.441097744 24.99989187 0.930256402 1.008956468 0.185554348 0.073720937 260.5717863 180833.073 0.020365224 0.026291511 2761.199234 -3.441097744 0.078700066 QDELKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QDELKR 6 1 Q86VP6;Q86VP6-2;A0A0C4DGH5;O75155-2;O75155;P56385 Q86VP6 CAND1;CAND2;ATP5I "Cullin-associated NEDD8-dissociated protein 1;Cullin-associated NEDD8-dissociated protein 2;ATP synthase subunit e, mitochondrial" 0 ;; 132.29 0.023993 1360321000 3869720 3028750 2296200 2655090 2647750 2876430 3714700 4044050 4478790 FALSE TRUE 3358326.697 3008853.942 3406650 3257968.765 2595064.955 2987088.123 3354448.966 3179261.378 3949312.548 0.850357285 0.761867769 0.862593162 0.824945791 0.657092829 0.756356476 0.84937541 0.805016402 1 21.91317012 0.442372452 1.46758257 2.399677343 0.788799208 0.522054972 0.061056748 8.807292035 2.763902468 36.97399661 0.017831777 2.769315602 -0.442372452 -1.610878135 QDENDDDDDWNPCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QDENDDDDDWNPCK 14 0 Q14974;Q14974-2 Q14974 KPNB1 Importin subunit beta-1 0 ;; 462.33 7.79E-198 3038300000 4448940 3648590 2934530 2903260 3426380 2807410 4671380 4879930 4364180 FALSE TRUE 3861001.307 3624622.172 4353678.523 3562489.557 3358201.742 2915412.879 4218350.287 3836394.945 3848251.612 1.003313114 0.941888041 1.131339362 0.925742367 0.872656489 0.757594142 1.096173201 0.996918947 1 21.8757717 QDFVQHFSQIVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QDFVQHFSQIVR 12 0 P14324-2;P14324;A0A087WVN4;A0A087X1D8;A0A087WTP2 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 ;; 219.35 3.22E-11 6255210000 6443146 8759370 2314300 4344817 11286148 11520570 8671004 9622840 9340791 FALSE TRUE 5591667.931 8701829.122 3433503.221 5331374.106 11061575.74 11963773.78 7830091.367 7565070.551 8236533.329 0.678886093 1.056491703 0.416862663 0.647283741 1.342989252 1.45252539 0.950653759 0.918477501 1 22.97360582 3.254888672 24.99882501 1.108431887 0.705137531 0.475230695 0.225275175 251.3586599 384836.6976 0.070402933 0.090613362 1798.409847 -3.254888672 -0.403294356 QDGGQNESFKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QDGGQNESFKR 11 1 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 83.617 0.026575 149440000 241510 191860 131280 179640 202920 175750 241260 290040 206900 FALSE TRUE 209593.8416 190599.659 194767.4471 220430.0076 198882.289 182511.2162 217862.6423 228017.2031 182440.5177 1.148833846 1.0447222 1.067566841 1.208229457 1.090121271 1.000387515 1.194157115 1.249816685 1 17.47706664 2.17824026 24.99999781 1.171128644 1.095007793 0.063750215 0.084315654 137.974315 57182.38096 0.034155775 0.023027827 150.7440782 -2.17824026 -0.076120851 QDGPMPKPHSVSLNDTETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QDGPMPKPHSVSLNDTETR 19 1 Q9P0L0-2;Q9P0L0 Q9P0L0-2 VAPA Vesicle-associated membrane protein-associated protein A 0 226.45 9.01E-20 306520000 91862 67050 42355 58570 88198 87359 54568 116620 57781 FALSE TRUE 79722.20395 66609.54414 62838.01967 71869.21369 86443.03236 90719.75726 49276.00376 91681.72054 50950.196 1.564708484 1.30734618 1.233322432 1.410577767 1.696618249 1.780557571 0.967140612 1.799438034 1 15.63680008 1.205894476 24.23565198 0.999995241 1.464294277 0.244932736 0.259150163 4813.68135 3571057.795 9.323104976 0.060835905 16.06550849 -1.205894476 0.464299035 QDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPK 38 2 O43809;H3BND3 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 228.69 5.22E-40 306740000 188280 144190 79934 101840 130970 90578 183450 188250 101900 FALSE TRUE 163398.321 143242.8064 118590.3498 124964.3285 128363.9532 94062.59427 165659.0472 147994.2025 89853.49808 1.818497047 1.594181745 1.319818953 1.390756411 1.428591607 1.046843988 1.843657184 1.647061112 1 16.45528705 4.547122289 3.233318386 1.421101331 1.813727825 0.238395978 0.249590458 0.445786647 8.268496051 0.064422729 0.335718052 35247.01058 -4.547122289 0.392626494 QDHAQQLATAAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QDHAQQLATAAEER 14 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;;; 195.6 2.60E-08 2271340000 2551800 2663800 1527310 2019500 2760230 2797750 2547120 2923960 2408150 FALSE TRUE 2214573.165 2646301.322 2265922.225 2478058.341 2705306.823 2905381.253 2300100.694 2298693.908 2123461.25 1.042907265 1.24622068 1.067089039 1.16699014 1.274008095 1.368228995 1.08318468 1.082522183 1 21.01798635 2.025943517 24.99935483 1.057864767 1.195918956 0.320734196 0.096102866 264.2843655 254665.1747 0.040037652 0.02699252 106.1557485 -2.025943517 0.138054189 QDHPSSMGVYGQESGGFSGPGENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QDHPSSMGVYGQESGGFSGPGENR 24 0 B0QYK0;Q01844-6;Q01844-3;Q01844;Q01844-5;Q01844-4 B0QYK0 EWSR1 RNA-binding protein EWS 0 ;;;; 260.99 4.86E-44 1910450000 912787 904168 317449 463662 905884 912593 805944 956115 858847 FALSE TRUE 792159.8852 898228.4609 470968.3982 568943.5437 887858.6807 947701.0432 727783.6749 751657.2477 757315.0861 1.046010967 1.186069679 0.62189227 0.751263977 1.172376857 1.251395965 0.96100512 0.992529083 1 19.53053414 3.229128876 24.99986777 1.065307356 0.901690889 0.19903426 0.172931821 381.3663217 1010851.476 0.056321913 0.06469936 1694.840667 -3.229128876 -0.163616467 QDIAFAYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QDIAFAYQR 9 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;H0YKS4;H0YMM1;H0YMW4;H0YKX9;H0YMT9;H0YLV6;H0YKZ7;H0YKL9;H0YKV8 P07355-2 ANXA2 Annexin A2;Annexin 0 ; 131.5 0.00077069 557820000 695840 621900 401670 599370 720610 691030 477990 707690 766370 FALSE TRUE 603882.981 617814.698 595918.9555 735466.1193 706271.2708 717614.3713 431634.6034 556356.0007 675770.6117 0.893621253 0.914237298 0.881836152 1.08833694 1.045134634 1.061920064 0.638729468 0.823291204 1 19.36617409 2.260643911 24.99996326 0.813637752 0.981127452 0.318395741 0.110315576 270.7887012 306552.5816 0.042666064 0.033021745 182.2400857 -2.260643911 0.1674897 QDKPLS(ph)PAGSSQEAADTPDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QDKPLSPAGSSQEAADTPDTR 21 1 P13994 P13994 CCDC130 Coiled-coil domain-containing protein 130 1 QDKPLS(0.999)PAGSSQEAADTPDTR;QDKPLS(0.995)PAGS(0.002)S(0.003)QEAADTPDTR 143.35 8.35E-08 356990000 406250 251690 198175 236590 276280 250550 323910 366430 368010 TRUE FALSE 352563.0332 250036.6318 294013.0929 290311.3756 270782.5685 260188.8206 292497.2581 288071.7961 324504.277 1.086466522 0.770518756 0.906037651 0.894630352 0.834449922 0.801803979 0.901366419 0.887728811 1 18.30787797 1.127490238 2.471478118 1.06034022 0.877018026 0.147411208 0.084660709 1.526539756 7.671529037 0.68318613 0.020514869 13.41189789 -1.127490238 -0.183322195 QDLAYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QDLAYER 7 0 B0QY89;Q9Y262-2;Q9Y262;H7C3A0;C9JHP4;C9K0Q7 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ; 86.205 0.047104 552230000 868000 890610 496330 620210 857050 867930 831550 945030 789970 FALSE TRUE 753291.6008 884759.5243 736356.8481 761038.1598 839996.3818 901319.8287 750906.409 742942.6887 696580.6465 1.081413336 1.270146578 1.057102077 1.092534172 1.205885329 1.293920285 1.077989193 1.066556604 1 19.40993086 2.01902336 24.98988227 1.048304468 1.166690976 0.341972423 0.07879245 271.2835897 356368.0905 0.032352845 0.021809159 104.4776413 -2.01902336 0.118386508 QDLECDKISLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QDLECDKISLER 12 1 Q0VF96;Q0VF96-2;Q9P2M7 Q0VF96;Q9P2M7 CGNL1;CGN Cingulin-like protein 1;Cingulin 0 92.265 0.007143 614070000 277380 282150 145280 183460 271440 234000 300580 317530 85865 FALSE TRUE 240723.5302 280296.5381 215537.8939 225117.397 266038.8751 243002.1314 271429.7979 249628.6805 75714.13752 3.179373603 3.702036994 2.846732473 2.973254459 3.513727869 3.209468395 3.584928875 3.296989026 1 16.20827509 1.238553052 24.99754093 0.999998854 3.296488575 0.881956162 0.263082109 0.059936583 184033.1072 0.351665299 0.063132082 17.32020597 -1.238553052 2.296489721 QDLPALEEKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QDLPALEEKPR 11 1 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;;; 178.15 6.99E-06 2639130000 4269790 3416760 2673420 3220070 3697610 3450060 4205520 4599690 4666130 FALSE TRUE 3705526.433 3394315.079 3966294.854 3951236.109 3624034.795 3582786.041 3797669.318 3616082.088 4114505.427 0.900600692 0.824963082 0.96397852 0.960318604 0.880794754 0.87076955 0.922995336 0.878861908 1 21.9722876 QDLPDAMKPHEIQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QDLPDAMKPHEIQEK 15 1 P62330 P62330 ARF6 ADP-ribosylation factor 6 0 218.12 1.19E-12 516480000 1247700 987940 839730 893400 905490 603700 1220000 1435300 1219600 FALSE TRUE 1082813.284 981450.1571 1245826.237 1096260.125 887472.5206 626924.7296 1101684.588 1128372.265 1075420.277 1.006874528 0.912620096 1.158455223 1.019378328 0.825233203 0.582957884 1.024422369 1.049238412 1 20.03646915 5.479247562 4.385609829 0.952160434 7.936494612 0.013402715 0.155640686 8536.64887 1027.898993 0.041312573 589517.8322 301472.4028 -5.479247562 6.984334178 QDLPNAMNAAEITDKLGLHSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QDLPNAMNAAEITDKLGLHSLR 22 1 P61204;P61204-2;H0YGG7;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 287.1 1.66E-46 3510300000 2149200 1948000 819630 922830 1818700 1518400 2339800 2471800 310270 FALSE TRUE 1865177.775 1935203.46 1216005.809 1132372.656 1782511.428 1576813.831 2112886.556 1943224.806 273590.2341 6.817413571 7.073364539 4.444624325 4.138936684 6.515259707 5.763414166 7.722814242 7.10268337 1 18.06165721 4.270144177 24.90290645 5.565061749 6.945391563 0.105370078 1.88927252 518.2948225 408654.9489 0.474306576 1.254634398 18627.05414 -4.270144177 1.380329814 QDLPSLDEKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QDLPSLDEKPR 11 1 Q92598-2;Q92598;Q92598-4;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;; 157.52 2.79E-05 2291290000 2934150 2461710 1823330 2401310 2521940 2459220 3117950 3626650 3388480 FALSE TRUE 2546394.643 2445538.865 2705098.487 2946564.137 2471758.328 2553827.785 2815571.689 2851119.12 2987897.755 0.852236205 0.818481443 0.905351759 0.986166321 0.827256664 0.854723955 0.942325314 0.954222451 1 21.51069935 1.898616518 1.976478089 0.984101197 0.876413016 0.443701283 0.048635396 0.348029081 2.501366092 0.04345422 0.015145652 79.18018603 -1.898616518 -0.107688181 QDNCVHDLQAHNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QDNCVHDLQAHNK 13 0 Q9BZK7;A0A0D9SF63 Q9BZK7 TBL1XR1 F-box-like/WD repeat-containing protein TBL1XR1 0 146 2.43E-05 210040000 119920 92390 47398 59370 76676 69466 114950 134870 50638 FALSE TRUE 104072.2682 91783.08401 70319.83134 72850.86591 75150.29761 72138.40197 103802.1667 106029.1001 44651.63333 2.330760611 2.055536991 1.574854627 1.631538658 1.683035804 1.615582602 2.324711527 2.37458503 1 15.44642533 4.486272454 5.153102525 1.818890566 2.278391772 0.181332068 0.393503498 0.338149223 27.15761262 0.103812182 0.357132875 30638.84953 -4.486272454 0.459501206 QDPGTELLHCENEDLICFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QDPGTELLHCENEDLICFK 19 0 Q9NQE9 Q9NQE9 HINT3 Histidine triad nucleotide-binding protein 3 0 ; 187.33 1.86E-14 215045000 173382 147372 93115 118271 120599 119132 162420 188729 186215 FALSE TRUE 150469.1294 146403.9036 138145.7255 145126.2382 118199.3158 123715.0851 146668.5334 148370.772 164200.8748 0.916372276 0.891614638 0.841321495 0.883833526 0.719845835 0.75343743 0.89322626 0.903593067 1 17.32510229 1.439703164 1.754506278 1.017343062 0.836382454 0.405257239 0.062044343 0.656653365 2.804908256 0.183329409 0.01907554 27.52346855 -1.439703164 -0.180960608 QDPSVLHTEEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 QDPSVLHTEEMR 12 0 P50502;Q3KNR6;Q8NFI4;F8WAQ7 P50502 ST13;ST13P5 Hsc70-interacting protein;Putative protein FAM10A5 0 ;;;;;;;;; 204.13 1.17E-07 12969730000 11263580 11482640 5861480 8250440 11636670 11995780 11003770 12418270 11598340 FALSE TRUE 9775069.365 11407209.78 8696111.333 10123828.5 11405123.03 12457265.42 9936626.079 9762719.6 10227197.46 0.955791594 1.115379832 0.850292699 0.989892739 1.115175793 1.218052694 0.971588367 0.954584053 1 23.28590752 5.056259875 14.23402374 1.021569079 0.540115601 0.043431679 0.102175103 765603.7089 5541719.448 0.026061401 10132417.66 113830.8229 -5.056259875 -0.481453478 QDQVCIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QDQVCIAR 8 0 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ; 99.305 0.01607 198669000 235370 212921 144521 161950 209427 213700 229140 214600 220260 FALSE TRUE 204265.2581 211522.3079 214411.839 198723.2228 205259.8124 221921.1773 206918.0381 168709.46 194221.1137 1.051714998 1.089079884 1.103957417 1.023180328 1.05683573 1.142621279 1.065373553 0.868646342 1 17.56734052 1.757654146 25 0.930195595 1.07746023 0.63530372 0.044627627 4.314588046 5656.10741 0.022530078 0.010819277 57.23400619 -1.757654146 0.147264635 QDS(ph)DEDDGPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QDSDEDDGPQR 11 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 QDS(1)DEDDGPQR 107.69 0.0022696 144750000 123070 106660 127980 167010 118620 126950 126770 146560 590570 TRUE FALSE 106805.9877 105959.3434 189871.5561 204932.1731 116259.6941 131833.8486 114475.8649 115219.2845 520753.4874 0.205098939 0.203473133 0.364609284 0.393530102 0.223252838 0.2531598 0.219827361 0.221254946 1 18.99024107 1.236689751 24.99977852 1.000000929 0.261008332 0.924851754 0.066244224 13.18100506 176083.8208 0.109747495 0.017430126 17.24605436 -1.236689751 -0.738992597 QDS(ph)DEDDGPQRVEEVDQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QDSDEDDGPQRVEEVDQGR 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 QDS(1)DEDDGPQRVEEVDQGR;QDS(1)DEDDGPQRVEEVDQGR 168.55 9.59E-12 1016830000 550370 469250 427980 522580 639560 552560 582390 632540 675840 TRUE FALSE 477637.21 466167.4659 634952.5595 641239.7761 626834.0073 573817.3408 525909.9074 497276.2434 595942.9651 0.801481413 0.782235034 1.065458604 1.076008634 1.051835568 0.962872916 0.882483624 0.834435965 1 19.18481474 4.257447234 24.88817548 0.968564941 0.791858045 0.502060058 0.077798101 243.6144234 321021.3882 0.023412413 0.061714132 18090.36102 -4.257447234 -0.176706896 QDS(ph)DSDVVDIEEAEHDFMGEAHPVVFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QDSDSDVVDIEEAEHDFMGEAHPVVFSR 28 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 QDS(0.998)DS(0.002)DVVDIEEAEHDFMGEAHPVVFSR;QDS(0.984)DS(0.016)DVVDIEEAEHDFMGEAHPVVFSR;QDS(0.998)DS(0.002)DVVDIEEAEHDFMGEAHPVVFSR 267.73 4.62E-54 229558000 115812 98400 55596.4 67858 112567 99757 88870 122079 86112 TRUE FALSE 100507.1508 97753.60392 82483.005 83266.19604 110327.1369 103594.7163 80251.40108 95973.35587 75931.93746 1.323647916 1.28738456 1.086275522 1.096589904 1.452974079 1.364310194 1.056885992 1.263939247 1 16.2124192 0.544241598 1.398389626 4.27E-12 1.245183541 0.246398073 0.129467017 12.22582655 4.85692016 35.09285044 0.038537109 3.501398958 -0.544241598 1.245183541 QDS(ph)LEPVLRDPCYLINEGICNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QDSLEPVLRDPCYLINEGICNR 22 1 D6RD37;D6RAX8;D6RBL1;D6RDZ9;D6RCK9;Q99576-3;E7EWD5 D6RD37 TSC22D3 1 QDS(1)LEPVLRDPCYLINEGICNR;QDS(1)LEPVLRDPCYLINEGICNR 159.65 1.17E-11 188300000 85295 60226 31302 42030 69226 38594 78639 76668 34483 TRUE FALSE 74023.04964 59830.37144 46439.7519 51573.55389 67848.53804 40078.73615 71012.60188 60273.14483 30406.45902 2.434451495 1.967686254 1.527298916 1.696138108 2.231385706 1.318099425 2.335444644 1.982248074 1 14.8920902 8 0.036157596 2.52E-12 4.678095823 0.148114632 0.422346718 6231.695163 22.24424886 947.59925 2173.853819 99999999.97 -8 4.678095823 QDSGEWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QDSGEWR 7 0 Q96G03-2;Q96G03 Q96G03-2;Q96G03 PGM2 Phosphoglucomutase-2 0 84.227 0.050484 672020000 1647100 1529000 842060 1045800 1377000 1483700 1274600 1448300 1454300 FALSE TRUE 1429431.562 1518955.898 1249283.033 1283264.874 1349600.394 1540778.899 1150989.488 1138592.316 1282374.311 1.114675762 1.184487154 0.974195305 1.000694464 1.052423136 1.201504807 0.897545653 0.887878294 1 20.290386 -2 0.100622058 0.137950206 1.315847156 0.259108494 0.092242471 375.4255519 3.482164121 62.30880519 6.409395193 0.01 2 1.17789695 QDVEALWENMAVIDCFASDHAPHTLEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QDVEALWENMAVIDCFASDHAPHTLEEK 28 0 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 ; 161.72 5.21E-12 62897000 61800 59924 27711 39236 57543 54799 70436 77625 75546 FALSE TRUE 53632.97342 59530.3553 41112.13229 48145.13348 56398.00688 56907.15299 63605.12756 61025.49783 66615.03794 0.80511811 0.893647398 0.617159932 0.722736712 0.846625756 0.854268867 0.954816353 0.916091917 1 16.02356027 2.602522582 1.532011012 0.953145408 0.763219625 0.559220413 0.074075901 0.311536176 1.493715051 0.038561466 0.028968846 400.426289 -2.602522582 -0.189925783 QEAEDLSLSAPSSPEIS(ph)PQSS(ph)PRPHRPNNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QEAEDLSLSAPSSPEISPQSSPRPHRPNNDR 31 2 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 2 QEAEDLSLSAPS(0.152)S(0.152)PEIS(0.677)PQS(0.37)S(0.649)PRPHRPNNDR 90.182 0.0002964 111660000 38168 47193 26491 37251 46196 46591 44747 52539 54370 TRUE FALSE 33124.00209 46882.98608 39302.13621 45709.4089 45276.78998 48383.38592 40407.44283 41303.94371 47942.44054 0.690911888 0.977901533 0.819777545 0.953422654 0.944398939 1.009197391 0.842832413 0.861531938 1 15.54901573 4.748130914 24.58686844 0.917876945 0.690911734 0.554449325 0.065898427 838.9527484 2155281.138 0.015906046 0.198917323 55992.6361 -4.748130914 -0.226965211 QEAEDLSLSAPSSPEIS(ph)PQSSPRPHRPNNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QEAEDLSLSAPSSPEISPQSSPRPHRPNNDR 31 2 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 QEAEDLSLSAPS(0.008)S(0.027)PEIS(0.929)PQS(0.021)S(0.016)PRPHRPNNDR;QEAEDLSLSAPS(0.148)S(0.113)PEIS(0.512)PQS(0.113)S(0.113)PRPHRPNNDR 143.72 1.08E-08 344490000 50411 58452 24875 29873 56773 63155 50795 62025 45957 TRUE FALSE 43749.05862 58068.02496 36904.6332 36656.12123 55643.32837 65584.61372 45868.90872 48761.43643 40524.01581 1.079583495 1.432928692 0.91068549 0.904553028 1.37309512 1.618413486 1.131894453 1.203272564 1 15.30648953 3.220244849 24.9946771 1.265223147 1.094776064 0.152100343 0.214214277 537.2192894 733116.083 0.068259602 0.077546111 1660.522823 -3.220244849 -0.170447083 QEAGDS(ph)PPPAPGTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QEAGDSPPPAPGTPK 15 0 J3KR72;P49848-4;P49848-2;P49848;P49848-3 J3KR72 TAF6 Transcription initiation factor TFIID subunit 6 1 QEAGDS(1)PPPAPGTPK;QEAGDS(1)PPPAPGTPK 202.34 6.25E-09 365970000 758640 621210 408040 553620 653190 520280 696760 850040 745560 TRUE FALSE 658383.8019 617129.2306 605369.5088 679327.8826 640192.7969 540295.5083 629188.3224 668265.561 657420.7461 1.0014649 0.938712741 0.920825076 1.033322855 0.973794637 0.821841281 0.957055776 1.016496003 1 19.32645746 1.790668163 5.922625802 1.007856806 0.946981757 0.16154637 0.055531058 0.347583505 24.77961518 0.031004724 0.015099729 61.75443646 -1.790668163 -0.060875049 QEAGISEGQGTAGEEEEKKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QEAGISEGQGTAGEEEEKKK 20 2 O43583;F8VVL1 O43583 DENR Density-regulated protein 0 122.01 1.76E-05 153850000 166710 97669 94858 71837 79894 58948 161040 162520 37524 FALSE TRUE 144678.8511 97027.40591 140731.6461 88148.68881 78304.26571 61215.7677 145422.3656 127766.3627 33087.95547 4.372553368 2.932408622 4.253259051 2.664071792 2.366548933 1.850092181 4.395024217 3.861416063 1 15.01401853 3.72659454 24.22847791 2.869757358 3.760707191 0.208368851 1.024375313 1009.884664 2044778.058 0.293131612 0.438901977 5328.372037 -3.72659454 0.890949833 AALSS(ph)SELLELGDSLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AALSSSELLELGDSLMR 17 0 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 AALS(0.401)S(0.596)S(0.004)ELLELGDSLMR;AALS(0.333)S(0.644)S(0.023)ELLELGDSLMR 330.28 5.79E-72 160774000 120326 145161 140024 159929 232360 233100 216180 257330 256620 TRUE FALSE 104424.6142 144207.4278 207740.0748 196243.3238 227736.4906 242067.5078 195214.8969 202301.982 226282.6759 0.461478608 0.637288857 0.918055586 0.867248555 1.006424772 1.069757138 0.862703678 0.894023288 1 17.78776661 4.41723469 1.856987905 0.947691568 0.427947823 0.869731082 0.065674638 0.162949919 0.909358724 0.018968117 0.118652001 26135.73331 -4.41723469 -0.519743744 down QEALEWLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QEALEWLIR 9 0 Q9NQW7-4;Q9NQW7-3;Q5T6H7;Q9NQW7-2;Q9NQW7 Q9NQW7-4 XPNPEP1 Xaa-Pro aminopeptidase 1 0 ; 129.85 0.00087862 647340000 478530 490830 272580 299590 441920 445800 423610 436650 453070 FALSE TRUE 415291.0481 487605.7054 404400.5997 367616.4884 433126.6566 462950.2145 382528.3674 343275.7955 399508.5807 1.039504702 1.220513723 1.012245091 0.920171696 1.08414857 1.158799177 0.95749725 0.859245113 1 18.60786696 2.060008082 7.465399642 0.91619439 1.069753489 0.345796826 0.086763558 0.229699244 24.13922478 0.036740028 0.024625403 114.8174989 -2.060008082 0.153559099 QEARPEPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QEARPEPAR 9 1 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ;;; 126.33 0.0004346 1541890000 2655220 2585110 1394420 1747520 2365290 2556810 2418630 2560520 2492410 FALSE TRUE 2304325.95 2568128.242 2068766.176 2144321.125 2318225.357 2655172.135 2184071.635 2012972.724 2197760.129 1.048488376 1.168520717 0.941306628 0.975684788 1.054812728 1.208126447 0.993771616 0.915920121 1 21.0676025 2.009340699 24.99724183 0.952821781 1.063876751 0.248206517 0.080599192 259.209614 693684.5585 0.033902224 0.022824733 102.1740713 -2.009340699 0.11105497 QEDKDDLDVTELTNEDLLDQLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 318.17 1.75E-73 743919000 744379 559740 509154 594249 531743 348739 672113 1006224 785836 FALSE TRUE 646007.4291 556063.0311 755382.5774 729182.318 521162.3546 362155.215 606931.5847 791050.828 692935.3633 0.932276607 0.802474604 1.090119826 1.052309287 0.75210818 0.522639245 0.875884847 1.141593964 1 19.40236126 1.753694937 24.99989397 1.071900656 0.857811074 0.225764901 0.161338474 7.733329079 12794.99591 0.093057295 0.044687473 56.71460834 -1.753694937 -0.214089582 QEEAEEQGAGS(ph)PGQPAHLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QEEAEEQGAGSPGQPAHLAR 20 0 Q96S99 Q96S99 PLEKHF1 Pleckstrin homology domain-containing family F member 1 1 QEEAEEQGAGS(1)PGQPAHLAR;QEEAEEQGAGS(1)PGQPAHLAR;QEEAEEQGAGS(1)PGQPAHLAR;QEEAEEQGAGS(1)PGQPAHLAR 224.83 6.99E-27 1444880000 467645 400734 307662 427747 404543 453103 438167 436381 618310 TRUE FALSE 405844.5284 398101.552 456448.3723 524873.4941 396493.3858 470534.1656 395673.6318 343064.3191 545214.0962 0.744376441 0.730174724 0.837191069 0.96269245 0.727225119 0.863026413 0.725721574 0.629228631 1 19.05646334 2.221960418 24.9835495 0.750065247 0.811424647 0 0.116455364 790.614738 1189878.606 0.047167201 0.031899146 166.7095265 -2.221960418 0.0613594 QEEAEYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QEEAEYVR 8 0 P46108-2;P46108 P46108-2 CRK Adapter molecule crk 0 95.358 0.022582 205550000 145910 139480 88696 88715 155910 172280 140480 126560 117520 FALSE TRUE 126627.6238 138563.7467 131589.6823 108859.0967 152807.696 178907.7231 126856.2712 99496.12889 103626.9195 1.221956847 1.337140459 1.269840722 1.050490521 1.474594601 1.72645992 1.224163295 0.960137862 1 16.6610393 1.856428504 4.363524941 0.985367039 1.344222792 0.420117355 0.174610396 0.223047574 6.473875403 0.104247091 0.050151839 71.8502865 -1.856428504 0.358855753 QEESES(ph)PVERPLKENPPNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QEESESPVERPLKENPPNK 19 2 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;D6RBF8 H3BLV9 SRPK1 SRSF protein kinase 1 1 QEES(0.146)ES(0.854)PVERPLKENPPNK 145.13 6.70E-08 154050000 250180 196880 190010 205840 188020 146410 252080 265600 269490 TRUE FALSE 217118.0791 195586.6823 281899.4715 252579.1181 184278.7699 152042.4874 227633.3204 208803.5069 237631.1992 0.913676655 0.823068195 1.186289816 1.062903857 0.77548222 0.639825444 0.95792691 0.878687258 1 17.85836474 3.241115008 24.99990695 0.851459972 0.997655257 0.226362665 0.134195519 112.08794 1096998.513 0.041604284 0.051241394 1742.268193 -3.241115008 0.146195285 QEFAQHANAFHQWIQETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QEFAQHANAFHQWIQETR 18 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 171.85 7.08E-12 791100000 474740 459180 294280 375040 420220 509240 404600 488810 639570 FALSE TRUE 412001.9062 456163.6163 436594.7923 460198.5641 411858.4441 528830.7923 365361.9543 384281.7854 563960.7632 0.730550657 0.808857009 0.774158099 0.81601167 0.730296274 0.937708484 0.647849954 0.681398087 1 19.10523527 4.757378101 21.55728887 0.785071349 0.730550367 0.024056869 0.107348212 3003.828889 3440799.824 0.025505334 0.672334266 57197.63886 -4.757378101 -0.054520983 QEFEFWYPVDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QEFEFWYPVDLR 12 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRP1 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ;;; 235.49 1.11E-15 404804000 587432 507369 386976 470726 506557 529063 477954 558532 887246 FALSE TRUE 509801.3728 504036.0596 574118.888 577611.5329 496477.5068 549416.396 431602.0946 439094.2783 782356.7886 0.65162261 0.644253449 0.733832564 0.738296825 0.634592189 0.702258105 0.551669137 0.561245566 1 19.57746716 1.229652811 24.99826826 1.000000671 0.64924739 0.752140185 0.06272145 197.5047506 554221.9535 0.205270015 0.017397006 16.96886563 -1.229652811 -0.350753281 QEGGDNDLIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QEGGDNDLIER 11 0 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A096LNY6 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 0 ; 187.76 8.02E-06 309950000 261900 245010 173943 192518 242750 284010 246780 263090 271600 FALSE TRUE 227289.2514 243400.5132 258062.4166 236232.1544 237919.7499 294936.0485 222847.3136 206830.2509 239491.7574 0.949048326 1.016321045 1.077541956 0.986389498 0.993436069 1.231508139 0.930500974 0.863621584 1 17.86961648 2.033732425 24.99954607 0.914566599 1.041601392 0.280018221 0.082881425 197.098102 146071.2218 0.03304526 0.02227899 108.076787 -2.033732425 0.127034794 QEGHLDSES(ph)PTNIPLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QEGHLDSESPTNIPLTK 17 0 H7BXC7;Q9H7P9-3;Q9H7P9;E7ESZ3 H7BXC7 PLEKHG2 Pleckstrin homology domain-containing family G member 2 1 QEGHLDS(0.009)ES(0.907)PT(0.085)NIPLTK 80.412 0.0073908 109820000 194580 188170 116940 163940 200670 175080 226290 239900 242270 TRUE FALSE 168865.76 186933.8989 173492.5751 201165.0827 196677.0596 181815.4409 204344.4306 188599.2519 213629.1166 0.790462287 0.875039423 0.812120454 0.941655734 0.920647254 0.851079871 0.956538293 0.882834957 1 17.70474877 7.905839233 0.25902702 0.949827052 1.81E-17 0.491012452 0.046267383 72.44213133 1.209683896 0.131758888 29.25666734 80508036.1 -7.905839233 -0.949827052 QEHADGLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QEHADGLLK 9 0 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 93.096 0.0074213 0 223240 188900 155600 203260 183670 175060 211640 249890 341510 FALSE TRUE 193738.2684 187659.1035 230848.6805 249413.2896 180015.3263 181794.6715 191115.1854 196452.9681 301137.0768 0.643355745 0.623168377 0.766590029 0.828238396 0.597785328 0.603694083 0.63464515 0.652370576 1 18.20006082 1.236842019 24.98878087 1.000000415 0.668735697 0.66822626 0.073357166 29.23666755 424976.5881 0.119294202 0.01915364 17.25210206 -1.236842019 -0.331264718 QEIEAETDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QEIEAETDR 9 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 119.53 0.0018902 115490000 184620 128560 127380 126960 148640 179340 134550 139290 224030 FALSE TRUE 160221.9992 127715.4809 188981.3941 155788.2085 145682.3548 186239.3258 121501.3617 109503.9175 197545.4286 0.811064069 0.646511953 0.956647772 0.788619659 0.737462546 0.942767075 0.615055294 0.554322711 1 17.59182494 2.217984587 24.99920862 0.683455722 0.808111926 0.056359267 0.146531666 481.1815971 584615.7355 0.058302355 0.03935711 165.1903173 -2.217984587 0.124656204 QEIGNLDKHEELEELVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QEIGNLDKHEELEELVAR 18 1 O15270;H0YJV2 O15270 SPTLC2 Serine palmitoyltransferase 2 0 194.27 4.88E-15 54754000 102210 87630 53984 78362 101830 105360 74403 123160 95432 FALSE TRUE 88702.68953 87054.35276 80090.84297 96155.28979 99803.78223 109413.2674 67187.40851 96823.19243 84150.13768 1.054100349 1.034512303 0.951761283 1.142663487 1.186020427 1.300214954 0.798423037 1.150600523 1 16.36067801 3.731176885 24.95699193 1.095589104 1.01556341 0.079573304 0.132770327 1573.109671 5317111.568 0.036262021 0.054981019 5384.890604 -3.731176885 -0.080025694 QEKPAEKPAETPVAT(ph)SPTATDSTSGDSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 1 QEKPAEKPAETPVAT(0.466)S(0.259)PT(0.259)AT(0.009)DS(0.006)T(0.001)SGDSSR;QEKPAEKPAETPVAT(0.507)S(0.426)PT(0.059)AT(0.007)DSTSGDSSR 194.29 1.38E-18 3602100000 1181228 966492 827834 916135 975812 632948 1540382 1709636 1363055 TRUE FALSE 1025125.727 960143.0504 1228177.291 1124157.454 956395.2503 657297.9191 1390995.991 1344043.646 1201916.191 0.852909491 0.798843595 1.021849361 0.93530436 0.795725407 0.546875002 1.157315295 1.11825072 1 20.19690487 2.190360701 24.99999938 1.100082297 0.836646049 0.493327562 0.126925929 100.8440722 52304.33433 0.053816494 0.036283163 155.0103516 -2.190360701 -0.263436248 QEKPAEKPAETPVATS(ph)PTATDSTSGDSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 1 QEKPAEKPAETPVAT(0.005)S(0.994)PT(0.001)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.092)S(0.903)PT(0.005)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.155)S(0.706)PT(0.118)AT(0.02)DSTSGDSSR;QEKPAEKPAETPVAT(0.061)S(0.467)PT(0.467)AT(0.006)DSTSGDSSR;QEKPAEKPAETPVAT(0.031)S(0.841)PT(0.112)AT(0.016)DSTSGDSSR;QEKPAEKPAETPVAT(0.019)S(0.799)PT(0.158)AT(0.023)DSTSGDSSR;QEKPAEKPAETPVAT(0.008)S(0.991)PT(0.001)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.233)S(0.736)PT(0.03)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.243)S(0.751)PT(0.005)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.039)S(0.923)PT(0.039)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.015)S(0.982)PT(0.003)ATDSTSGDSSR 260.16 3.32E-58 29546180000 9941850 7616260 6514100 7970250 8118800 6083420 11764940 14169230 11706660 TRUE FALSE 8628009.333 7566228.287 9664340.548 9780017.08 7957251.764 6317453.104 10623977.93 11139250.43 10322711.99 0.835827769 0.732969039 0.936221078 0.947427099 0.770848956 0.611995482 1.029184766 1.079101155 1 23.29931871 2.096581786 11.05621196 1.047855088 0.813422158 0.552062708 0.097564295 0.293277134 31.26866733 0.041581447 0.028029078 124.9055643 -2.096581786 -0.23443293 QEKPAEKPAETPVATSPTATDSTSGDSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 ;;; 234.52 1.81E-45 2117220000 2526640 1549194 1216099 1365675 1384973 1044601 2048050 2321710 2083040 FALSE TRUE 2192738.122 1539017.243 1804208.544 1675772.382 1357414.747 1084787.476 1849430.426 1825230.384 1836785.384 1.193791142 0.837886264 0.98226421 0.912339785 0.739016522 0.590590216 1.006884333 0.993709118 1 20.80875164 4.744529487 23.90039188 0.88771504 1.193791396 0.348293054 0.133527871 471.0824132 1886192.574 0.035355538 0.304514956 55530.2319 -4.744529487 0.306076356 QELEEICHDLEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QELEEICHDLEAR 13 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 174.17 2.04E-05 117313000 156408 161136 120932 144150 158494 171861 146649 195516 318920 FALSE TRUE 135738.2865 160077.487 179415.1197 176881.4607 155340.2795 178472.6039 132427.0026 153706.4249 281217.6409 0.482680553 0.569229891 0.63799383 0.628984228 0.552384548 0.634642277 0.470905744 0.546574619 1 18.10132757 1.236984372 24.99915122 1.000000534 0.566238801 0.846573887 0.058140409 15.50743286 245865.2782 0.089623151 0.014522512 17.25775788 -1.236984372 -0.433761733 QELEIVIGDEHISFTTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QELEIVIGDEHISFTTSK 18 0 P61326;Q96A72;F5H6P7 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 157.85 1.35E-09 78968000 259100 191230 47942 144340 219500 191790 240690 293240 264660 FALSE TRUE 224859.2785 189973.7975 71126.91156 177114.6031 215132.3794 199168.2854 217347.9208 230532.908 233372.1963 0.963522142 0.814037835 0.304778858 0.75893618 0.921842374 0.853436221 0.93133597 0.987833648 1 17.83227316 3.298270094 4.209951588 0.94153549 0.681690003 0.316063038 0.168038984 0.254139989 9.054585244 0.051590906 0.065995282 1987.330483 -3.298270094 -0.259845487 QELGS(ph)PEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QELGSPEER 9 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GYF0 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 QELGS(1)PEER;QELGS(1)PEER;QELGS(1)PEER;QELGS(1)PEER;QELGS(1)PEER 158.53 7.00E-05 6724680000 4282970 4338590 2835630 3449570 4160800 4901580 4702940 4720650 4693920 TRUE FALSE 3716964.663 4310089.517 4206950.153 4232847.592 4078008.22 5090146.954 4246849.603 3711175.734 4139010.125 0.898032271 1.041333407 1.016414559 1.022671476 0.985261717 1.22979814 1.026054413 0.896633645 1 21.98085435 4.744618536 23.17289691 1.021541054 0.898032114 0.192461434 0.082457229 485.451143 1856802.933 0.021582915 0.186615075 55541.61907 -4.744618536 -0.12350894 QELS(ph)FAARSFYYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QELSFAARSFYYK 13 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 QELS(0.272)FAARS(0.272)FY(0.228)Y(0.228)K 62.924 0.044059 923540000 295900 276090 225260 243390 243900 198240 422560 310620 252470 TRUE FALSE 256796.0653 274276.3466 334196.4894 298655.4195 239046.8672 205866.4211 381580.1962 244196.3302 222623.2842 1.15350048 1.232020036 1.501174914 1.341528226 1.073772979 0.924729962 1.71401746 1.096903817 1 17.76424497 3.264545101 24.89143148 1.183314372 1.315561904 0.086050344 0.228510042 639.6285584 612717.6634 0.066737141 0.086129454 1838.844907 -3.264545101 0.132247533 QELSFAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 144.12 0.0013737 5822510000 6795550 7133480 4643880 5249030 7406920 8426860 7215570 7511130 8075870 FALSE TRUE 5897500.85 7086619.7 6889675.901 6440902.488 7259536.783 8751046.757 6515805.132 5904933.301 7121149.849 0.828166936 0.995151043 0.967494864 0.904475067 1.019433229 1.228881142 0.914993403 0.829210651 1 22.76367878 4.744199642 23.39057617 0.973272477 0.828166782 0.173513318 0.104124053 537.5389872 2229526.771 0.027634742 0.229047203 55488.07292 -4.744199642 -0.145105695 QELSHALYQHDAACR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QELSHALYQHDAACR 15 0 Q9UMS4;F5GY56;F5H2I0 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 ;; 241.87 3.88E-18 1651530000 1172440 987740 578300 744100 988830 959400 955280 1087660 1042350 FALSE TRUE 1017499.083 981251.4709 857967.8143 913059.2779 969154.2176 996308.7388 862637.0926 855072.3732 919124.5704 1.107030664 1.067593559 0.933461951 0.993401011 1.054431846 1.083975743 0.938542087 0.930311734 1 19.80990088 QELVDAFVEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QELVDAFVEHR 11 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ; 127.02 0.0002954 232400000 278680 246130 142220 172557 244320 264210 224860 242013 248320 FALSE TRUE 241851.7319 244513.1558 210998.0677 211738.7042 239458.51 274374.3297 203053.1118 190260.4033 218963.8925 1.104527916 1.116682541 0.963620373 0.967002832 1.09359816 1.253057418 0.927336053 0.868912226 1 17.74033346 2.046274706 24.99993723 0.917001481 1.075698713 0.397096987 0.086836357 117.9118076 63701.40668 0.037055419 0.024982747 111.2435158 -2.046274706 0.158697231 QEMQEVQSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 QEMQEVQSSR 10 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;; 287.77 1.62E-24 5643453000 3242761 2493981 1340848 1713664 2409709 2458829 2198668 2668837 2513196 FALSE TRUE 2814221.918 2477597.875 1989286.578 2102777.603 2361760.505 2553421.743 1985441.516 2098126.976 2216088.832 1.269904833 1.118004765 0.897656515 0.948868824 1.06573368 1.152219941 0.895921448 0.94677025 1 21.07958428 4.511252538 3.708227318 0.985837808 1.255392697 0.586867122 0.077648082 0.170449339 4.723446403 0.020786494 0.089793523 32452.82726 -4.511252538 0.269554889 QENGDLS(ph)PFSGTSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QENGDLSPFSGTSLR 15 0 P19174-2 P19174-2 PLCG1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1" 1 QENGDLS(0.999)PFS(0.001)GTSLR;QENGDLS(0.984)PFS(0.011)GT(0.004)S(0.001)LR 177.01 2.16E-11 0 292710 326260 232140 330170 380440 371090 341960 430410 536180 TRUE FALSE 254027.6319 324116.7766 344403.6805 405140.1448 372869.9883 385366.0724 308796.7718 338370.171 472793.4112 0.537290973 0.685535731 0.728444332 0.856907341 0.788653098 0.815083424 0.653132562 0.715682924 1 18.8508504 4.642252244 1.572061672 0.785098649 0.475708526 0.456117925 0.091973976 0.877114061 2.395142104 0.025870962 0.394954653 43878.54765 -4.642252244 -0.309390124 QENKRPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QENKRPSPR 9 2 Q9Y4B6-3;Q9Y4B6-2;Q9Y4B6 Q9Y4B6-3 VPRBP Protein VPRBP 1 QENKRPS(1)PR 59.116 0.082209 123810000 62350 54396 27842 33488 48678 45953 68416 74752 15666 TRUE FALSE 54110.28953 54038.66909 41306.48433 41091.96223 47709.40304 47720.84165 61781.02685 58766.86652 13813.98333 3.91706637 3.911881737 2.990193585 2.974664241 3.453703534 3.45453158 4.472354236 4.254157916 1 13.75384177 1.23120524 24.99999036 0.999995273 3.69251261 0.748323727 0.488122344 153.2960333 520988.5635 1.384271011 0.137067554 17.0296311 -1.23120524 2.692517337 QENLPDEIYHVYSFALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QENLPDEIYHVYSFALR 17 0 Q9BV86;S4R338 Q9BV86 NTMT1 "N-terminal Xaa-Pro-Lys N-methyltransferase 1;N-terminal Xaa-Pro-Lys N-methyltransferase 1, N-terminally processed" 0 87.85 0.004441 33022000 23009 22830 14420 17301 22952 20111 22361 25469 22192 FALSE TRUE 19968.30235 22680.02823 21393.56023 21229.45648 22495.3001 20884.68318 20192.43366 20022.65255 19568.48704 1.02043159 1.159007755 1.093265932 1.084879809 1.149567673 1.067261007 1.031885277 1.023209025 1 14.2562446 2.333617006 2.808643182 1.017668418 1.10364244 0.493721824 0.038260429 0.203059737 3.270175261 0.015478621 0.010843155 215.5842385 -2.333617006 0.085974021 QENLSWQHELHQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QENLSWQHELHQLR 14 0 Q14789;Q14789-2;Q14789-4;Q14789-3 Q14789 GOLGB1 Golgin subfamily B member 1 0 104.95 0.00059435 144820000 160330 183440 99135 129910 184060 223890 160310 208710 178330 FALSE TRUE 139141.9843 182234.9706 147077.0176 159408.0511 180397.5661 232503.1932 144763.1609 164078.9907 157248.0306 0.884856769 1.15890145 0.935318662 1.013736391 1.147216696 1.478576185 0.920603968 1.043440672 1 17.26268242 4.753700495 23.1304099 1.083054297 0.884856358 0.137330122 0.159093032 2144.22744 3275749.239 0.039412026 0.799841235 56715.33416 -4.753700495 -0.198197939 QENQEAVGGFFSQIGELYVVHHLWAYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QENQEAVGGFFSQIGELYVVHHLWAYK 27 0 Q9BPW8 Q9BPW8 NIPSNAP1 Protein NipSnap homolog 1 0 217.67 1.97E-34 145010000 126230 125120 89423 197660 108630 98562 119250 145660 182180 FALSE TRUE 109548.3857 124298.0785 132668.2619 242541.724 106468.4755 102353.7439 107685.1534 114511.7425 160642.8879 0.681937352 0.773754009 0.825858297 1.509819247 0.66276495 0.637150796 0.670338754 0.712834188 1 17.29349758 QENSADDLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QENSADDLHR 10 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 0 ; 164.9 6.02E-06 363812000 451690 371210 300045 262864 247710 268120 506190 503780 203196 FALSE TRUE 391998.0221 368771.4971 445147.7656 322551.2888 242781.0556 278434.7499 457099.7717 396050.5674 179174.4004 2.187801501 2.058170678 2.484438428 1.800208558 1.354998566 1.55398734 2.55114442 2.210419383 1 17.451005 3.712823486 22.98283215 1.819750961 2.224940248 0.209605083 0.440086814 537.4506516 479934.1424 0.129642107 0.192410792 5162.065204 -3.712823486 0.405189287 QEPCAQHNGSEPAS(ph)PKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QEPCAQHNGSEPASPKR 17 1 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 QEPCAQHNGS(0.009)EPAS(0.991)PKR;QEPCAQHNGS(0.001)EPAS(0.999)PKR;QEPCAQHNGS(0.002)EPAS(0.998)PKR 196.1 7.67E-12 688324000 999288 897788 569217 719056 962315 839940 1061947 1264740 945706 TRUE FALSE 867229.5589 891890.3715 844492.2451 882328.6549 943166.8142 872253.0353 958959.5434 994285.1932 833905.714 1.039961166 1.069533829 1.012695118 1.058067645 1.131023326 1.0459852 1.149961593 1.192323276 1 19.66952475 3.339982979 5.03798778 1.115364359 1.042485405 0.20899098 0.054944543 0.284742003 11.63891795 0.016398964 0.02122934 2187.675883 -3.339982979 -0.072878954 QEPES(ph)EEEEEEKQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QEPESEEEEEEKQEK 15 1 P49756 P49756 RBM25 RNA-binding protein 25 1 QEPES(1)EEEEEEKQEK;QEPES(1)EEEEEEKQEK;QEPES(1)EEEEEEKQEK;QEPES(1)EEEEEEKQEK;QEPES(1)EEEEEEKQEK;QEPES(1)EEEEEEKQEK 277.94 8.16E-34 3915040000 3993080 2227970 2674140 2485370 2325570 1829860 3370220 3791500 4440040 TRUE FALSE 3465384.361 2213334.318 3967363.048 3049711.245 2279295.707 1900255.898 3043376.583 2980717.23 3915143.529 0.885123198 0.565326482 1.01333783 0.778952603 0.58217424 0.485360469 0.777334614 0.761330257 1 21.90063377 1.135467859 2.196172212 1.141699069 0.719852449 0.229027317 0.155710676 1.48301596 5.704228089 1.382712686 0.042051625 13.66053972 -1.135467859 -0.42184662 QEPGGSHGS(ph)ETEDTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QEPGGSHGSETEDTGR 16 0 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 QEPGGS(0.044)HGS(0.905)ET(0.044)EDT(0.007)GR 165.17 4.19E-09 0 74121 74949 42029 63325 78815 74017 80330 77923 69540 TRUE FALSE 64325.72205 74456.65508 62354.36498 77703.90911 77246.7357 76864.48189 72539.60896 61259.77285 61319.06042 1.049033068 1.214249771 1.016883895 1.267206454 1.259750805 1.253516955 1.182986309 0.99903313 1 15.90404797 1.726071039 5.16428677 0.998334568 1.182797609 0.431683157 0.084710776 0.140779466 9.249359303 0.053221032 0.022347818 53.21953055 -1.726071039 0.184463041 QEPLGS(ph)DSEGVNCLAYDEAIMAQQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QEPLGSDSEGVNCLAYDEAIMAQQDR 26 0 J3KR44;Q96FW1;F5H6Q1;F5GYJ8;F5H3F0 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 1 QEPLGS(0.5)DS(0.5)EGVNCLAYDEAIMAQQDR 105.98 0.0019954 43173000 38274 32414 16470 20169 23970 24852 27111 32279 26943 TRUE FALSE 33215.99393 32201.0703 24434.94709 24748.67971 23493.0439 25808.07252 24481.77939 25376.38705 23757.82923 1.398107277 1.355387733 1.02850083 1.041706272 0.988854818 1.086297585 1.030472067 1.068127344 1 14.5361154 4.257619315 5.958965579 1.037476759 1.382919276 0.958565028 0.029571062 0.026052825 3.029745084 0.007093842 0.018005121 18097.53043 -4.257619315 0.345442517 QEPQGQEIQSENLIMEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QEPQGQEIQSENLIMEK 17 0 Q4VCS5 Q4VCS5 AMOT Angiomotin 0 ;; 67.605 0.027051 10881830000 8645660 9246330 4939410 6769360 8207720 8689870 9094190 10249100 6599490 FALSE TRUE 7503114.126 9185590.249 7328125.197 8306446.651 8044402.43 9024174.922 8212236.854 8057409.724 5819305.81 1.289348656 1.578468386 1.259278243 1.427394765 1.382364614 1.550730485 1.411205584 1.384599811 1 22.47241563 1.228381358 3.989313541 0.948332248 1.417614184 0.634453736 0.098092413 0.155795096 4.26259748 0.217717184 0.022814679 16.91925974 -1.228381358 0.469281936 QEPVKPEEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QEPVKPEEGR 10 1 P61586 P61586 RHOA Transforming protein RhoA 0 ;; 124.42 0.0003976 929730000 769380 651940 551600 803810 748690 646180 697850 1139830 1556570 FALSE TRUE 667704.4836 647657.3632 818355.605 986327.346 733792.5338 671038.9627 630172.6144 896086.2247 1372554.068 0.48646862 0.471862915 0.596228319 0.71860728 0.534618308 0.488898018 0.459124073 0.65286042 1 20.38843155 1.269648555 2.966485915 1.069750752 0.541971006 0.783373635 0.07642162 0.178640196 2.025330462 0.218220244 0.021462748 18.60580888 -1.269648555 -0.527779746 QEQEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QEQEEAR 7 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ; 160.78 0.0031029 244390000 463450 457480 286140 378090 261850 489200 446610 493730 716720 FALSE TRUE 402203.9083 454474.7838 424518.2611 463941.1132 256639.6973 508019.8406 403297.8309 388149.6817 631990.1781 0.636408479 0.719116846 0.671716548 0.734095449 0.406081781 0.803841354 0.638139397 0.614170434 1 19.26954261 1.234697224 24.99157859 1.000000501 0.65262585 0.524592201 0.103829247 87.64331649 566865.3806 0.173832286 0.023657074 17.16711136 -1.234697224 -0.347374651 QEQEEEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 150.24 0.0011453 124330000 144220 127450 106090 117440 86585 149010 131390 151220 149870 FALSE TRUE 125160.9616 126612.7726 157395.4788 144106.547 84862.1279 154742.5111 118647.818 118882.7798 132152.5393 0.947094639 0.958080512 1.191013655 1.090456133 0.642152836 1.170938613 0.897809597 0.899587555 1 17.01184462 QEQINTEPLEDTVLS(ph)PTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QEQINTEPLEDTVLSPTK 18 0 O15446;O15446-2 O15446 CD3EAP DNA-directed RNA polymerase I subunit RPA34 1 QEQINTEPLEDTVLS(0.819)PT(0.181)K;QEQINTEPLEDTVLS(0.998)PT(0.002)K 202.62 1.33E-15 174383000 432480 395550 266630 349780 397290 302590 418790 545020 460120 TRUE FALSE 375326.6722 392951.606 395573.1598 429202.8951 389384.7063 314230.8331 378175.8103 428471.7144 405725.1378 0.925076209 0.968516785 0.974978188 1.057866164 0.959725366 0.774491901 0.932098544 1.056064006 1 18.63014317 1.751716635 13.99926445 1.027509524 0.942839034 0.20229267 0.071144398 0.322389137 336.803253 0.04118156 0.019608182 56.45684899 -1.751716635 -0.08467049 QEQLS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 96.171 0.01356 634380000 1965450 1267800 844840 995830 1216730 1114340 1393460 1736000 1672610 TRUE FALSE 1705710.803 1259471.738 1253407.45 1221948.422 1192519.453 1157209.381 1258322.464 1364769.91 1474875.951 1.156511367 0.853950963 0.849839235 0.828509286 0.808555765 0.78461472 0.853171728 0.925345558 1 20.49216219 4.739503819 24.43045911 0.861768814 1.156511496 0.696789459 0.060843869 36.04444294 933411.659 0.016167717 0.094986224 54891.33828 -4.739503819 0.294742682 QEQLS(ph)PR ddPTM_MDA-MB-175_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 100.48 0.020521 0 2384500 2102900 1318810 1543790 1701070 2004660 1838640 2092980 2059150 TRUE FALSE 2069382.283 2089085.911 1956590.927 1894331.115 1667222.035 2081780.567 1660328.976 1645412.515 1815719.633 1.139703645 1.150555336 1.077584277 1.043294945 0.918215569 1.146531948 0.914419245 0.906204066 1 20.79211002 4.204931866 0.392469309 0.924654294 1.273508023 0.476117985 0.070171073 3.826446696 0.817033603 0.121011874 0.658501513 16029.93887 -4.204931866 0.348853729 QEQSYFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QEQSYFVR 8 0 O60664-4;O60664;O60664-3;O60664-2 O60664-4 PLIN3 Perilipin-3 0 ;;; 158.61 0.00084673 1483980000 1179060 1283390 696990 851880 1201510 1201940 1132650 1343370 1288730 FALSE TRUE 1023244.234 1274959.327 1034056.695 1045312.374 1177602.302 1248179.41 1022805.777 1056100.78 1136377.808 0.900443697 1.121950216 0.909958544 0.919863418 1.036277102 1.098384183 0.90005786 0.929357096 1 20.11601113 2.148142766 22.85608189 0.938473458 0.997836199 0.096063126 0.078616992 22.89981886 5777.167645 0.031567306 0.021282686 140.650981 -2.148142766 0.059362742 QERLS(ph)PEVAPPAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QERLSPEVAPPAHR 14 1 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 QERLS(1)PEVAPPAHR;QERLS(1)PEVAPPAHR;QERLS(1)PEVAPPAHR;QERLS(1)PEVAPPAHR;QERLS(1)PEVAPPAHR 126.84 0.00032474 2914770000 2963320 2592880 1628430 1938190 2771030 2653420 2562780 2920740 2217150 TRUE FALSE 2571709.754 2575847.201 2415944.195 2378285.663 2715891.924 2755498.784 2314241.99 2296162.48 1955041.053 1.315424937 1.317541234 1.235751132 1.216488861 1.389173859 1.409432697 1.183730637 1.174483 1 20.89876747 1.427240777 1.44504732 0.946126743 1.305624788 0.682834229 0.067042712 0.510887898 1.309997443 0.251044052 0.021204006 26.74488761 -1.427240777 0.359498045 QES(ph)DPEDDDVKKPALQSSVVATSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QESDPEDDDVKKPALQSSVVATSK 24 2 Q9H307 Q9H307 PNN Pinin 1 QES(1)DPEDDDVKKPALQSSVVATSK;QES(1)DPEDDDVKKPALQSSVVATSK 229.28 2.30E-33 2499930000 3564730 2204850 2303690 2034040 1846630 1046250 3230020 3685100 3045790 TRUE FALSE 3093641.899 2190366.195 3417762.189 2495899.87 1809885.676 1086499.915 2916773.158 2897070.042 2685720.176 1.151885415 0.815560093 1.272568237 0.929322382 0.673892125 0.404546953 1.086030177 1.078693927 1 21.35687757 3.490416665 24.28727103 0.866501412 1.06145768 0.170783596 0.229673957 980.1830007 1790538.323 0.070173938 0.098943042 3093.261704 -3.490416665 0.194956269 QES(ph)FTKEPASGPPAPGKPPHISSHPLLQDLAATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QESFTKEPASGPPAPGKPPHISSHPLLQDLAATR 34 2 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 QES(0.962)FT(0.038)KEPASGPPAPGKPPHISSHPLLQDLAATR 201.25 1.66E-27 353380000 63781 54608 13367 34346 78127 55576 89596 94550 86013 TRUE FALSE 55352.17925 54249.27645 19831.32591 42144.78425 76572.42555 57714.04468 80906.99371 74331.21829 75844.64113 0.729810023 0.715268418 0.261473001 0.555672538 1.009595726 0.760950857 1.066746345 0.980045751 1 16.21075963 3.242625294 24.99475769 0.963160061 0.55452944 0.639746398 0.148271888 65.96328858 405622.6529 0.044297915 0.055099677 1748.337583 -3.242625294 -0.408630622 QESCLGNS(ph)PPFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QESCLGNSPPFEK 13 0 Q86W56-3;Q86W56-2;Q86W56 Q86W56-3 PARG Poly(ADP-ribose) glycohydrolase 1 QESCLGNS(1)PPFEK;QES(0.001)CLGNS(0.999)PPFEK 137.17 6.70E-05 326700000 1225340 982660 713870 948400 985000 856260 982870 1291630 1508250 TRUE FALSE 1063408.214 976204.8418 1059099.92 1163748.715 965400.4271 889200.8763 887551.4187 1015424.976 1329946.403 0.79958727 0.734018183 0.796347821 0.875034297 0.725894235 0.668599031 0.667358787 0.763508194 1 20.34293668 1.241900605 6.342120675 1.007219956 0.750562692 0.609628367 0.061950746 0.088437494 15.62518235 0.098152875 0.016619489 17.45422639 -1.241900605 -0.256657264 QESCSPHHPQVLAQQGSGS(ph)SPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QESCSPHHPQVLAQQGSGSSPK 22 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 QESCSPHHPQVLAQQGS(0.002)GS(0.571)S(0.427)PK 127.63 1.15E-05 178390000 51049 49213 11983 29731 62920 47995 52862 70628 63011 TRUE FALSE 44302.74531 48889.71656 17778.01888 36481.87796 61668.0151 49841.39871 47735.45138 55524.75183 55561.91136 0.797358194 0.879914232 0.319967734 0.656598685 1.109897295 0.897042551 0.859139835 0.999331205 1 15.76180861 3.256811423 24.78461914 0.964015629 0.654385448 0.488318363 0.15721621 195.5000904 265487.5837 0.046206323 0.059531545 1806.389594 -3.256811423 -0.30963018 QESCSPHHPQVLAQQGSGSS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QESCSPHHPQVLAQQGSGSSPK 22 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 QESCSPHHPQVLAQQGS(0.004)GS(0.131)S(0.865)PK;QESCSPHHPQVLAQQGSGS(0.002)S(0.998)PK;QESCSPHHPQVLAQQGSGS(0.054)S(0.946)PK 170.97 1.09E-11 987089000 337369 282437 76283.2 182762 394101 292781 326430 386057 387422 TRUE FALSE 292784.8319 280581.6528 113174.0107 224260.9054 386259.1611 304044.4745 294772.8688 303501.7148 341621.4125 0.857044732 0.821323379 0.331284886 0.656460331 1.130664376 0.890004149 0.862864147 0.888415374 1 18.38203888 3.269889389 23.99456245 0.936059087 0.65363872 0.446767649 0.158156134 126.2355677 96682.02429 0.046812429 0.060426724 1861.612938 -3.269889389 -0.282420367 QESDKNGESAS(ph)PERDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QESDKNGESASPERDR 16 2 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 QESDKNGES(0.059)AS(0.941)PERDR 87.062 0.0034424 166170000 386110 250320 140550 186210 247450 177430 270470 298660 150070 TRUE FALSE 335084.5852 248675.6314 208520.4501 228491.8265 242526.2291 184255.8469 244239.861 234793.8832 132328.8956 2.532210246 1.879223962 1.575774129 1.726696392 1.832753369 1.392408258 1.845703163 1.774320583 1 17.0137686 4.720180297 2.265942694 1.627539283 2.74051854 0.577355754 0.252937847 0.424449427 2.63551789 0.062856518 0.928912047 52502.53793 -4.720180297 1.112979257 QESEQGPCRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QESEQGPCRR 10 1 P24593 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 0 79.659 0.042238 74601000 119360 115110 44887 47152 90962 109240 114030 108490 20408 FALSE TRUE 103586.2736 114353.8348 66594.50334 57858.58227 89152.03416 113442.5335 102971.3882 85290.25777 17995.38949 5.756267384 6.354618493 3.700642511 3.215189219 4.954159743 6.303977669 5.722098331 4.739561643 1 14.13533971 4.247746771 24.99521218 4.42186661 6.055443549 0.201454487 1.471266712 354.5302823 964644.0809 0.379318717 0.9740558 17690.77143 -4.247746771 1.633576939 QESRPGEWLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QESRPGEWLVR 11 1 Q9BUP3-3;Q9BUP3;E9PI87 Q9BUP3-3 HTATIP2 Oxidoreductase HTATIP2 0 ; 147.24 3.23E-05 637350000 187808 196659 121861 137765 184351 223270 181688 216270 177975 FALSE TRUE 162988.697 195367.1341 180793.3872 169046.6489 180682.7758 231859.3414 164067.9257 170022.3435 156934.9982 1.038574561 1.244892065 1.152027204 1.077176224 1.151322381 1.47742278 1.045451477 1.083393414 1 17.2598076 QETVADFT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QETVADFTPK 10 0 O75400-3;O75400;O75400-2;F5H578 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 QETVADFT(1)PK;QETVADFT(1)PK;QETVADFT(1)PK;QETVADFT(1)PK 173.06 3.94E-05 1019810000 2799650 1638450 1795280 2199620 1722300 1609870 1943170 2387560 4578900 TRUE FALSE 2429669.159 1627686.914 2663483.413 2699077.34 1688029.6 1671802.741 1754721.672 1876998.874 4037587.658 0.601762578 0.403133517 0.659671972 0.668487614 0.41807875 0.414059801 0.434596551 0.464881269 1 21.94506215 1.235865004 24.99699684 1.000000662 0.503333245 0.698222695 0.101591493 43.84453558 406498.0243 0.172595826 0.025818109 17.21333433 -1.235865004 -0.496667417 QEVGSHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QEVGSHGR 8 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 102.62 0.0049298 48776000 132370 81509 53326 62519 60988 75243 79488 88350 93861 FALSE TRUE 114876.9691 80973.56201 79114.63196 76714.89449 59774.45812 78137.6469 71779.26599 69457.04004 82764.85951 1.387992075 0.978356787 0.955896409 0.926901767 0.722220257 0.944092062 0.867267418 0.839209303 1 16.33673073 5.620522318 1.125402976 0.875886246 3.963344855 0.807673787 0.075418758 4.043756173 0.962389159 0.021467955 23.71137222 417371.046 -5.620522318 3.08745861 QEVPSWLENMAYEHHYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QEVPSWLENMAYEHHYK 17 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8Y7T2;A0A087WVZ1;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;; 172.2 9.43E-10 1025190000 1156780 967010 638884 760102 988720 833470 1057700 1169650 1098560 FALSE TRUE 1003908.592 960657.6476 947850.4393 932694.7765 969046.4064 865534.1302 955124.4168 919529.4497 968689.4883 1.036357475 0.99170855 0.97848738 0.962841847 1.000368455 0.893510398 0.985996471 0.949250984 1 19.88567476 5.504722058 0.820267103 0.962058627 1.228802517 0.352228584 0.030394539 7.915919122 1.662032924 0.010077508 2.57387226 319684.8517 -5.504722058 0.26674389 QEYDESGPSIVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 37 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 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 262.37 4.13E-24 2.63563E+11 73702646.8 60332097.4 32611626 59882382.3 66956338.6 66273756.8 54774766.3 72441955.7 84283971.6 FALSE TRUE 63962655.29 59935771.88 48382717.41 73479592.45 65624038.46 68823351.11 49462717.89 56950807.22 74320016.49 0.860638335 0.806455309 0.651005203 0.988691821 0.882992787 0.926040579 0.665536961 0.766291639 1 26.14724749 4.765069781 20.36726676 0.825744006 0.86063885 0 0.120351593 5362.592377 4119291.059 0.029403004 1.424922274 58219.67556 -4.765069781 0.034894844 QEYDESGPSIVHRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 3133310000 4107810 3230290 673620 1148290 3083390 2815890 3906930 4397550 455436 FALSE TRUE 3564952.501 3209070.012 999384.8851 1409026.795 3022036.572 2924219.11 3528036.53 3457168.154 401594.8749 8.876987042 7.990814158 2.488539938 3.508577631 7.525087496 7.281515012 8.785063631 8.6085963 1 18.61538133 4.458376205 24.99121369 6.036191878 8.655447965 0.155828796 2.631606534 435.0804402 580056.5838 0.69180693 1.830943936 28732.68459 -4.458376205 2.619256086 QEYLDTLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QEYLDTLYR 9 0 P60228;E5RGA2;H0YBR5 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 ;; 140.45 0.00025377 1285200000 1378060 1206440 809170 903200 1295300 1284150 1241370 1333520 1438550 FALSE TRUE 1195945.879 1198514.816 1200487.319 1108285.365 1269526.064 1333552.081 1120982.128 1048357.125 1268486.258 0.94281343 0.944838629 0.946393633 0.873707033 1.000819722 1.051294071 0.883716415 0.826463132 1 20.27467646 QFAEILHFTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QFAEILHFTLR 11 0 E5RI16;Q9NUQ9;A0A087X178;A0A1W2PRQ0 E5RI16 FAM49B Protein FAM49B 0 109.72 0.0018907 229850000 122410 141630 53979 88413 117040 114450 132550 126910 137400 FALSE TRUE 106233.2084 140699.6232 80083.42495 108488.523 114711.133 118852.9656 119695.3214 99771.28411 121156.7285 0.876824669 1.161302595 0.660990322 0.895439521 0.946799525 0.980985266 0.987937879 0.82348942 1 16.886515 3.243459298 23.6477127 0.936962594 0.90042601 0.031369493 0.127997851 369.5763871 1784050.201 0.03702574 0.046202076 1751.698259 -3.243459298 -0.036536584 QFAFVHMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QFAFVHMR 8 0 Q96PK6;Q96PK6-2;A0A0A6YYI9;F8WDX3;A0A0A0MSL8;B8ZZ74;Q96PK6-3;Q96PK6-4 Q96PK6 RBM14;RBM14-RBM4 RNA-binding protein 14 0 109.21 0.0036612 297440000 331040 520060 228160 240930 370360 397810 385600 397000 301930 FALSE TRUE 287292.2253 516643.6916 338498.9391 295636.8389 362990.5606 413114.0081 348204.5713 312104.6395 266236.1794 1.079087846 1.940546521 1.271423516 1.110430745 1.363415601 1.551682454 1.307878487 1.17228485 1 18.02234711 1.571047067 2.031935414 0.995075443 1.393512503 0.217427642 0.241106663 0.557238797 4.299599048 0.357606252 0.066300782 37.24320667 -1.571047067 0.39843706 SQSFT(ph)HSPSGDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQSFTHSPSGDPK 13 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 S(0.001)QS(0.399)FT(0.557)HS(0.044)PSGDPK 194.13 1.43E-05 195060000 167150 154470 126190 180750 247640 219200 300550 346400 344720 TRUE FALSE 145060.704 153455.2764 187215.9061 221792.0501 242712.4485 227632.7658 271402.7073 272325.0557 303967.5943 0.477224239 0.504840908 0.615907451 0.729656892 0.798481328 0.748871821 0.892867241 0.895901605 1 18.213558 4.418591152 0.241128989 1.10115526 2.57E-17 0.950164968 0.037842836 2.756507065 0.255461467 0.257803643 1.063830262 26217.49249 -4.418591152 -1.10115526 down QFCQEGQPHVLEALSPPQTSGLS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QFCQEGQPHVLEALSPPQTSGLSPSR 26 0 E9PR76;E9PSH4;Q9H063 E9PR76 MAF1 Repressor of RNA polymerase III transcription MAF1 homolog 1 QFCQEGQPHVLEALSPPQTS(0.001)GLS(0.941)PS(0.058)R;QFCQEGQPHVLEALSPPQTSGLS(0.973)PS(0.027)R;QFCQEGQPHVLEALSPPQTSGLS(0.944)PS(0.056)R;QFCQEGQPHVLEALSPPQTSGLS(0.974)PS(0.025)R;QFCQEGQPHVLEALSPPQT(0.005)S(0.075)GLS(0.911)PS(0.009)R 251.7 1.07E-52 4188780000 1392710 1431480 726994 1008050 1385630 1301730 1215540 1573100 1398820 TRUE FALSE 1208659.845 1422076.514 1078570.73 1236943.16 1358058.674 1351808.395 1097657.118 1236704.807 1233453.093 0.979899318 1.152923059 0.874431899 1.002829509 1.101021743 1.095954441 0.889905846 1.002636269 1 20.23427142 2.248098454 24.99997641 0.969097485 1.034199355 0.140269832 0.081774483 421.0307142 1103579.565 0.030517441 0.023324678 177.0510285 -2.248098454 0.06510187 QFCTGEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QFCTGEFR 8 0 C9JQD4;O43447;A6NM32 C9JQD4 PPIH Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase H 0 77.732 0.075497 58163000 108050 102420 64586 63699 95846 102100 88959 90573 111250 FALSE TRUE 93770.91874 101747.1963 95820.00563 78162.83153 93938.85212 106027.8531 80331.76987 71204.66879 98098.15174 0.955888741 1.037197893 0.97677687 0.796781898 0.957600632 1.08083436 0.818891778 0.725851278 1 16.58193833 2.198610055 24.86759348 0.821525011 0.962890854 0.22865751 0.099055518 180.0225639 112055.4225 0.040894734 0.02757166 157.9828903 -2.198610055 0.141365843 QFDHLNHLNPDKFESTDLDMLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QFDHLNHLNPDKFESTDLDMLIK 23 1 P80303-2;P80303;E9PKG6;Q2L696;E9PLR0;E9PLE9;A0A2R8Y6G7 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 54.637 0.066043 202870000 343320 342720 221620 259770 291110 267340 379090 473060 369740 FALSE TRUE 297949.3921 340468.6498 328796.1733 318754.7488 285317.4805 277624.7428 342325.9101 371899.8004 326029.7584 0.913871769 1.044287035 1.008485161 0.977686057 0.875127111 0.85153191 1.049983633 1.140692807 1 18.31464413 2.021057702 21.53454788 1.084878602 0.950835939 0.408776115 0.066713765 43.08658411 44061.41612 0.028796001 0.019408781 104.9681885 -2.021057702 -0.134042663 QFDTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QFDTDR 6 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;U3KQE2;K7EIV0;A0A075B7C0;U3KPR7 A0A0C4DGQ5 CAPNS1 Calpain small subunit 1 0 114.19 0.059325 734720000 1893700 1486300 970810 1105300 1279400 1440900 1357900 1636500 1515600 FALSE TRUE 1643442.747 1476536.397 1440296.963 1356275.258 1253942.443 1496332.355 1226211.067 1286547.21 1336427.495 1.229728327 1.104838387 1.077721739 1.014851359 0.938279441 1.119650981 0.917529063 0.962676401 1 20.34995014 8 0.466495919 0.970917453 7.655568881 0.672087068 0.054500055 57.87412434 0.696324042 0.037101635 370.9690465 100000000 -8 6.684651428 QFDVDILISGHTHKFEAFEHENK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QFDVDILISGHTHKFEAFEHENK 23 1 Q9UBQ0;F8VXU5;Q9UBQ0-2;Q05DG7 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 82.477 0.0029171 261610000 416060 303180 134540 242070 295120 232680 375850 483940 143140 FALSE TRUE 361076.6168 301188.3906 199603.994 297035.6933 289247.6894 241631.3502 339400.1248 380453.197 126218.1523 2.860734453 2.386252573 1.581420663 2.353351622 2.291648897 1.914394608 2.688996145 3.014251042 1 16.94555988 2.233352214 24.95823572 2.415822137 2.217094661 0 0.614637509 673.9330825 3229382.29 0.243525051 0.169757174 171.1402706 -2.233352214 -0.198727477 QFEDELHPDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QFEDELHPDLK 11 0 Q9Y3C6 Q9Y3C6 PPIL1 Peptidyl-prolyl cis-trans isomerase-like 1 0 ;;; 136.99 8.78E-05 1498360000 7113800 5632100 3849630 4550300 5365400 4683130 6381600 7603700 6838200 FALSE TRUE 6173693.306 5595102.364 5711323.944 5583515.162 5258639.037 4863293.041 5762713.414 5977707.927 6029795.786 1.02386441 0.927909097 0.947183644 0.92598744 0.872108977 0.806543574 0.955706233 0.991361588 1 22.52367771 2.00394242 24.99912508 0.988604826 0.914426269 0.258523139 0.05470332 153.7322848 974819.6139 0.02369947 0.015901892 100.9119085 -2.00394242 -0.074178557 QFEEIWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QFEEIWER 8 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;;; 211.79 6.56E-05 1118170000 1578820 1482280 820930 1059140 1407510 1446600 1359390 1526410 1399150 FALSE TRUE 1370174.937 1472542.805 1217934.494 1299633.925 1379503.305 1502251.638 1227556.567 1199999.1 1233744.081 1.110582785 1.193556126 0.987185684 1.053406411 1.118143808 1.217636349 0.994984767 0.972648314 1 20.23461173 2.087633986 11.70111359 0.984208809 1.108777697 0.45158565 0.064431641 0.447670022 57.01241839 0.027127154 0.018286945 122.3584553 -2.087633986 0.124568888 QFEHLDPQNQHTFEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QFEHLDPQNQHTFEAR 16 0 Q02818;C9JKZ2 Q02818 NUCB1 Nucleobindin-1 0 83.751 0.0044654 654040000 129910 137880 96318 115370 179150 158510 159420 180110 177260 FALSE TRUE 112742.0643 136974.2572 142897.707 141566.5218 175585.2655 164607.9823 143959.4729 141594.8781 156304.5247 0.721297509 0.876329444 0.914226298 0.905709685 1.123353696 1.05312359 0.921019229 0.905891102 1 17.25400002 4.823547006 1.073777995 0.980023092 0.563813317 0.609270999 0.067547113 1.633727569 1.379239883 0.023487631 0.808875168 66611.1614 -4.823547006 -0.416209774 QFFDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 128.86 0.038255 1080060000 2857500 2931200 1752220 2222700 2718200 2838300 2767500 3096600 3006000 FALSE TRUE 2479874.135 2911944.754 2599599.453 2727398.007 2664113.138 2947491.238 2499108.276 2434416.188 2650634.104 0.935577691 1.098584203 0.980746248 1.028960581 1.005085211 1.111994761 0.942834121 0.918427852 1 21.3379061 2.135397455 24.58560288 0.945933528 1.027146516 0.279742282 0.054792522 10.34035819 2443.336247 0.020609278 0.013894779 136.5832538 -2.135397455 0.081212988 QFGAQVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QFGAQVHR 8 0 Q8NFW8;Q8NFW8-2 Q8NFW8 CMAS N-acylneuraminate cytidylyltransferase 0 117.04 0.0021563 105150000 256940 227600 137370 179300 239620 261660 216790 266110 287610 FALSE TRUE 222984.728 226104.8806 203802.5915 220012.8054 234852.0308 271726.2295 195765.7392 209204.4474 253609.0734 0.87924586 0.891548861 0.803609227 0.867527342 0.926039544 1.071437334 0.771919303 0.824909159 1 17.95224684 4.793880379 15.55062013 0.886241742 0.879242345 0 0.089975334 6409.14156 1795664.993 0.022350717 4.716939199 62212.89036 -4.793880379 -0.006999397 QFGFIVLTTSAGIMDHEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QFGFIVLTTSAGIMDHEEAR 20 0 P62244 P62244 RPS15A 40S ribosomal protein S15a 0 ;;; 200.1 1.39E-21 1242220000 1713523 1911812 985558 1394151 1635464 1560441 1744022 1965986 1964357 FALSE TRUE 1487076.594 1899253.181 1462177.145 1710714.293 1602921.466 1620472.175 1574887.015 1545575.193 1732132.953 0.858523355 1.096482333 0.844148333 0.987634517 0.925403251 0.935535677 0.909218321 0.892295935 1 20.72411824 3.09808761 23.21320962 0.925860594 0.950878068 0.003197039 0.074136829 37.57851325 8842.836164 0.020652987 0.02341829 1253.393996 -3.09808761 0.025017473 QFGFIVLTTSAGIMDHEEARR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QFGFIVLTTSAGIMDHEEARR 21 1 P62244 P62244 RPS15A 40S ribosomal protein S15a 0 66.325 0.014813 23831000 19511 21135 13857 8629.5 14046 22628 14087 16587 6164.8 FALSE TRUE 16932.57192 20996.16279 20558.29155 10588.95987 13766.51208 23498.5138 12720.84491 13039.99913 5436.004367 3.114892994 3.862425667 3.781875466 1.947930714 2.532468915 4.322754769 2.340109398 2.398820577 1 12.4083309 1.228391894 1.268157704 1.00E-12 3.20461473 0.485593254 0.714013449 1.366296882 1.847623026 5.890787825 0.224618526 16.91967021 -1.228391894 3.20461473 QFHDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QFHDSK 6 0 Q02543;M0R3D6;M0R1A7;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ;;;; 94.662 0.044227 3183730000 7744710 8498560 1701360 4781910 5733540 8448960 9066240 10494900 9793200 FALSE TRUE 6721226.951 8442732.4 2524143.387 5867715.752 5619453.771 8773996.958 8186997.44 8250647.306 8635459.052 0.778328854 0.977681945 0.29229985 0.679490889 0.650741754 1.016042912 0.948067426 0.955438183 1 23.04184144 2.741140482 24.93773667 0.973083891 0.671394577 0.448038388 0.167650083 213.6940795 2065637.517 0.055828925 0.053397556 550.985896 -2.741140482 -0.301689315 QFKEEDGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QFKEEDGLR 9 1 O95292 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 0 89.561 0.010966 276280000 953670 668450 425090 636510 805240 794000 658150 1113200 721150 FALSE TRUE 827640.0932 664058.9079 630664.9458 781039.3239 789217.2994 824545.6938 594322.7143 875150.8429 635896.4685 1.301532772 1.044287774 0.991772996 1.228249192 1.241109738 1.296666572 0.934621819 1.376247371 1 19.27843237 4.777084807 21.82275845 1.154350519 1.301534774 0.100554843 0.146488642 9726.500982 5509175.446 0.034387233 6.667954643 59852.84613 -4.777084807 0.147184255 QFLDYFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QFLDYFK 7 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 106.36 0.017961 277590000 422610 450630 393220 409150 417100 356430 473620 526990 734080 FALSE TRUE 366761.0177 447669.7819 583382.5072 502053.761 408800.526 370142.0927 427688.4053 414297.2895 647297.8987 0.566603134 0.691597768 0.901258151 0.775614693 0.631549286 0.571826501 0.660728864 0.640041147 1 19.30407029 1.233879506 24.97741174 1.000000485 0.682520617 0.510832319 0.098411012 132.6086345 707482.8712 0.203817427 0.025923809 17.13481841 -1.233879506 -0.317479868 QFLEVELDQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QFLEVELDQAR 11 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 156.51 7.22E-05 286780000 250700 255160 172722 185758 250360 272130 246589 285580 265390 FALSE TRUE 217569.3598 253483.8372 256250.9369 227937.193 245378.3258 282599.0172 222674.8367 224510.9394 234015.8965 0.929720429 1.083190676 1.095015085 0.974024399 1.048554092 1.20760607 0.951537225 0.959383284 1 17.83624701 QFLEVWEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QFLEVWEK 8 0 C9JIF9;P13798;H7C393;H7C1U0;C9JLK2 C9JIF9 APEH Acylamino-acid-releasing enzyme 0 75.378 0.08967 302030000 141200 146180 97512 117670 126660 122780 142610 149660 142720 FALSE TRUE 122540.0622 145219.734 144669.1294 144388.772 124139.7138 127503.426 128779.7041 117656.3737 125847.8042 0.973716332 1.153931409 1.149556246 1.147328497 0.986427333 1.013155747 1.023297188 0.934910024 1 16.94132052 3.229080884 24.96996433 0.987937349 1.112648936 0.504528129 0.056191448 147.8893107 389545.0028 0.016848325 0.019355993 1694.653387 -3.229080884 0.124711587 QFLIS(ph)PPAS(ph)PPVGWK ddPTM_MDA-MB-175_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 166.77 1.97E-06 809270000 1545140 1421670 1002180 1404620 1299250 1182660 1498210 1745290 2601890 TRUE FALSE 1340945.834 1412330.956 1486837.6 1723560.439 1273397.467 1228157.695 1352913.825 1372073.315 2294297.528 0.584469023 0.615583175 0.648057883 0.751236672 0.555027171 0.535308817 0.58968543 0.598036348 1 21.12962106 1.23749729 24.9998814 1.000000462 0.609969038 0.812578566 0.058912038 11.82897387 277976.3675 0.09066832 0.015216847 17.278152 -1.23749729 -0.390031424 QFLISPPAS(ph)PPVGWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QFLISPPASPPVGWK 15 0 V9GYW9;E9PD55;E9PDJ2;P53805-4;P53805-3;P53805-2;P53805;H0YF64;Q9UKA8-6;Q9UKA8-5;Q9UKA8-2;Q9UKA8 V9GYW9 RCAN1;RCAN3 Calcipressin-1;Calcipressin-3 1 QFLISPPAS(1)PPVGWK;QFLISPPAS(1)PPVGWK 182.31 5.79E-07 490180000 1605250 1236910 1105460 1208340 1224780 1178880 1487630 1541350 1975180 TRUE FALSE 1393112.145 1228784.657 1640064.154 1482712.065 1200409.274 1224232.276 1343359.872 1211744.297 1741676.471 0.7998685 0.70551832 0.941658328 0.85131314 0.689226326 0.702904527 0.771302762 0.695734436 1 20.73204523 1.227443779 24.98739404 1.000000504 0.76761736 0.449479878 0.080073113 494.8387827 1112178.523 0.30537186 0.020435262 16.88277293 -1.227443779 -0.232383144 QFLPFLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QFLPFLQR 8 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 105.12 0.010352 392830000 358110 398860 253210 230920 371610 357690 423600 430840 305130 FALSE TRUE 310784.8562 396239.8624 375663.2029 283353.9154 364215.688 371450.5658 382519.3372 338708.2188 269057.879 1.155085505 1.472693771 1.396217068 1.053133684 1.353670405 1.380560076 1.421699073 1.258867497 1 18.03755703 1.265409456 3.65365242 0.967071776 1.322320959 0.383623837 0.126074325 0.268276059 5.536889188 0.250438919 0.031680085 18.42508313 -1.265409456 0.355249182 QFVEMTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QFVEMTR 7 0 B0YIW6;P48444;Q6P1Q5;E9PK34 B0YIW6 ARCN1 Coatomer subunit delta 0 ; 82.452 0.056881 300990000 552450 477790 307830 367070 482040 525810 569710 576390 525270 FALSE TRUE 479442.3328 474651.366 456697.6176 450418.8538 472448.3471 546038.2509 514459.6119 453133.484 463173.179 1.035125423 1.024781631 0.986019136 0.972463161 1.02002527 1.17890732 1.110728417 0.978324101 1 18.82119219 2.983610728 24.90199776 1.061928606 1.003653566 0.210618841 0.057359484 1308.415023 1988020.538 0.020319419 0.020885191 962.9655 -2.983610728 -0.05827504 QGAIYHGLATLLNQPS(ph)PMMQR ddPTM_MDA-MB-175_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 223.12 2.36E-25 6316320000 1832910 1920750 1096380 1361810 1752670 1748780 1742090 2016000 2023050 TRUE FALSE 1590686.299 1908132.467 1626593.035 1671029.774 1717795.296 1816056.698 1573142.38 1584894.089 1783887.334 0.891696616 1.069648531 0.911824982 0.936735041 0.962950554 1.018033294 0.88186196 0.888449656 1 20.76659307 2.224846105 24.99744301 0.91441584 0.966083016 0.092128508 0.05947146 449.1416134 818643.7561 0.023144251 0.015693701 167.8209227 -2.224846105 0.051667175 QGDETPSTNNGS(ph)DDEKTGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QGDETPSTNNGSDDEKTGLK 20 1 Q9Y3P9;Q9Y3P9-3;Q9Y3P9-4;C9JGR5;B5MCD9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 1 QGDETPS(0.001)T(0.001)NNGS(0.998)DDEKTGLK 175.76 8.86E-13 238870000 117270 72263 76314 66103 83978 56939 126610 154690 123870 TRUE FALSE 101772.4724 71788.29959 113219.7057 81112.69647 82307.0021 59129.48017 114331.3817 121610.7473 109226.2297 0.93175854 0.657244142 1.03656151 0.742611886 0.753546125 0.541348725 1.046739249 1.113384098 1 16.73695982 2.104309655 10.37546609 1.069292295 0.78102551 0.472713468 0.137348348 0.26453465 24.26048891 0.054304908 0.036601557 127.1480357 -2.104309655 -0.288266786 QGDTGDWIGTFLGHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QGDTGDWIGTFLGHK 15 0 Q9Y3F4;Q9Y3F4-2 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 ; 234.63 1.17E-17 2508700000 2501500 2203600 1282230 1877990 2134200 1919580 2386000 2884100 2521200 FALSE TRUE 2170920.437 2189124.407 1902320.717 2304416.333 2091733.595 1993427.485 2154606.087 2267357.659 2223146.608 0.976507995 0.984696375 0.855688379 1.03655617 0.940888733 0.896669377 0.96916959 1.019886701 1 21.08417166 1.902505435 4.874099565 1.008836248 0.948403179 0.207900275 0.048830597 0.33131836 12.3043374 0.024871204 0.012686606 79.89239394 -1.902505435 -0.060433069 QGEAEFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QGEAEFNR 8 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 106.6 0.0096883 1078400000 790540 646960 594640 740590 481640 536500 524670 665400 1792800 FALSE TRUE 686068.136 642710.0772 882209.893 908752.2787 472056.3063 557139.5022 473787.5842 523109.3881 1580857.226 0.433984881 0.406557953 0.558057918 0.574847787 0.298607805 0.352428728 0.299702956 0.330902361 1 20.59227565 1.234332082 24.99833527 1.000000876 0.40317746 0.788470578 0.096528732 63.49982124 375348.6898 0.198531594 0.026216131 17.1526838 -1.234332082 -0.596823416 QGFDFLCMPVFHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QGFDFLCMPVFHPR 14 0 O14744-2;O14744;G3V580;O14744-4;O14744-3;O14744-5;G3V2L6;C9JSX3 O14744-2 PRMT5 "Protein arginine N-methyltransferase 5;Protein arginine N-methyltransferase 5, N-terminally processed" 0 ; 136.51 2.66E-05 437410000 692610 760880 405050 462790 622420 642770 622980 716670 699120 FALSE TRUE 601079.8336 755881.7292 600933.5348 567873.5428 610035.0597 667497.7778 562563.4955 563415.6976 616470.83 0.975033699 1.226143545 0.974796382 0.921168554 0.9895603 1.082772688 0.912554931 0.913937319 1 19.23367311 4.058697013 18.65418978 0.964690606 1.100573871 0.323728496 0.077835229 7.605725032 2415.641287 0.019101335 0.03976321 11447.1405 -4.058697013 0.135883265 QGGDLGWMTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QGGDLGWMTR 10 0 Q9Y237;Q9Y237-2 Q9Y237 PIN4 Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4 0 ; 149.33 5.47E-05 408180000 403250 396500 237960 275560 344980 372810 367010 381150 367160 FALSE TRUE 349959.4908 393895.3654 353038.2519 338130.1097 338115.5729 387152.2419 331417.4267 299644.0386 323754.7631 1.080940053 1.216647322 1.0904496 1.044401962 1.044357061 1.195819448 1.023668111 0.925527815 1 18.30454189 2.017069307 8.455342612 0.962409133 1.109869673 0.532657288 0.059027105 0.127336506 50.91333837 0.024794586 0.016332447 104.0086134 -2.017069307 0.147460539 QGGDVLQNEEGETTSHLMGMFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QGGDVLQNEEGETTSHLMGMFYR 23 0 P39748;F5H1Y3 P39748 FEN1 Flap endonuclease 1 0 ; 296.78 1.05E-61 218018000 304960 224530 131775 197127 205492 218390 191161 236970 255590 FALSE TRUE 264658.7633 223055.0476 195501.8308 241887.6982 201403.1112 226791.6046 172622.2356 186295.8096 225374.4414 1.174306908 0.98970871 0.867453424 1.073270318 0.893637761 1.006288039 0.765935279 0.826605752 1 17.78196439 8 0.545524302 0.886227232 12.46366087 0.414141894 0.0925568 136.5357736 1.296537592 0.050691793 1846.281217 100000000 -8 11.57743364 QGGLGPMNIPLVSDPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QGGLGPMNIPLVSDPKR 17 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 136.36 1.69E-05 449950000 337020 241190 143850 152490 220010 203660 283340 278490 110630 FALSE TRUE 292481.9531 239605.607 213416.3411 187115.1852 215632.2314 211494.932 255861.7304 218937.0807 97551.44743 2.998232838 2.456197354 2.187731159 1.918117979 2.210446253 2.168034791 2.622838893 2.244324267 1 16.57387566 8 0.055346473 1.47E-10 6.448295134 0.357682839 0.414236438 1394.204109 7.5130025 230.9069166 819.5051768 99999999.98 -8 6.448295134 QGGS(ph)PDEPDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QGGSPDEPDSK 11 0 Q9ULX6;Q9ULX6-2;V9GZ50 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 1 QGGS(1)PDEPDSK 72.681 0.047863 184880000 267700 189130 139070 190940 164900 189760 251670 267720 376910 TRUE FALSE 232322.7667 187887.5926 206324.7172 234295.8453 161618.8126 197060.19 227263.0821 210470.1614 332352.1292 0.699025962 0.565326881 0.620801551 0.704962673 0.486287881 0.592925914 0.683802095 0.633274599 1 18.34235307 1.224499775 4.417789063 1.039292503 0.619604907 0.761796777 0.066155882 0.110096742 4.282829647 0.148597644 0.0162393 16.76871465 -1.224499775 -0.419687596 QGGSQPSSFS(ph)PGQSQVTPQDQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QGGSQPSSFSPGQSQVTPQDQEK 23 0 Q9H0L4 Q9H0L4 CSTF2T Cleavage stimulation factor subunit 2 tau variant 1 QGGSQPS(0.003)S(0.062)FS(0.935)PGQSQVTPQDQEK 227.48 5.40E-33 146330000 221870 145220 93448 100040 144160 103860 185010 183730 175750 TRUE FALSE 192549.3174 144266.0403 138639.7654 122755.611 141291.498 107855.5614 167067.7587 144440.7693 154973.0352 1.242469808 0.930910594 0.89460573 0.792109484 0.91171666 0.695963406 1.078044051 0.932038074 1 17.24165769 4.73958111 4.055034196 0.902548085 1.272376502 0.515494648 0.103383894 0.194645588 6.871065258 0.025440915 0.211741417 54901.10812 -4.73958111 0.369828418 QGIAVMTPTVPGS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QGIAVMTPTVPGSPK 15 0 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;E7EX50;H0Y7S5;Q9UPX8-2 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 QGIAVMTPTVPGS(1)PK;QGIAVMTPT(0.001)VPGS(0.999)PK;QGIAVMTPTVPGS(1)PK;QGIAVMTPT(0.002)VPGS(0.998)PK 195.38 1.32E-08 415680000 1093680 905460 626380 879120 1126230 878060 887780 1358950 1208910 TRUE FALSE 949147.417 899511.9736 929299.4631 1078737.633 1103820.226 911839.5364 801683.2322 1068349.118 1065994.037 0.890387173 0.843824583 0.871767975 1.011954659 1.035484429 0.855388965 0.752052267 1.002209281 1 20.02376794 3.959483228 24.0488676 0.937671809 0.864778425 0.142200286 0.085280642 689.3388309 409159.9232 0.024228399 0.041974618 9109.262716 -3.959483228 -0.072893384 QGIETPEDQNDLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QGIETPEDQNDLRK 14 1 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 0 135.47 5.25E-05 339060000 258220 212470 127700 144120 168880 147470 222140 239980 188170 FALSE TRUE 224095.5728 211074.2706 189456.1471 176844.6487 165519.6184 153143.2663 200596.897 188662.1445 165924.757 1.350585511 1.272108361 1.141819645 1.065812311 0.9975583 0.922968152 1.20896303 1.137034328 1 17.34016964 4.243990936 1.963767744 1.065729972 1.349105343 0.645504129 0.078413993 0.264167978 1.899482862 0.023851118 0.095252057 17538.43898 -4.243990936 0.283375371 QGLAET(ph)ASPVAVSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QGLAETASPVAVSLR 15 0 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 QGLAET(0.725)AS(0.275)PVAVSLR 153.36 2.98E-05 273990000 590900 582260 342240 525450 588550 555240 543240 656330 885490 TRUE FALSE 512811.0679 578435.0957 507748.4087 644761.4535 576839.0065 576600.4421 490556.6684 515978.9371 780808.381 0.65676942 0.740815685 0.650285552 0.825761441 0.738771535 0.738466 0.628267678 0.660826586 1 19.57460901 1.233372066 24.99999848 1.000000459 0.704613533 0.712023583 0.058960218 94.52371982 455391.9281 0.122593104 0.014876507 17.11480934 -1.233372066 -0.295386926 QGLAETAS(ph)PVAVSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QGLAETASPVAVSLR 15 0 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 QGLAET(0.008)AS(0.992)PVAVSLR 204.36 5.18E-09 271710000 563060 552790 307820 521340 557950 515760 507750 631000 859920 TRUE FALSE 488650.1944 549158.6861 456682.7816 639718.2152 546847.8866 535601.6209 458508.4832 496065.5604 758261.2372 0.64443515 0.724234155 0.602276312 0.843664668 0.721186657 0.706355006 0.60468406 0.654214585 1 19.53233545 1.234886867 24.99425103 1.000000445 0.687163006 0.661847022 0.070168682 66.89337961 455037.5056 0.124624443 0.017232431 17.17460933 -1.234886867 -0.31283744 QGLGPASTTSPSPGPRS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QGLGPASTTSPSPGPRSPK 19 1 P98171-2;P98171;E7EQN5;E9PCM6 P98171-2 ARHGAP4 Rho GTPase-activating protein 4 1 QGLGPASTTSPS(0.001)PGPRS(0.999)PK;QGLGPASTTSPSPGPRS(1)PK 172.2 5.34E-12 1221720000 634070 491770 280420 259761 564520 443740 635800 678700 107257 TRUE FALSE 550276.043 488539.5305 416032.0499 318743.7052 553287.1565 460810.9649 574140.2139 533565.2866 94577.19965 5.818273802 5.165510634 4.398862004 3.370196056 5.850111428 4.87232617 6.07059858 5.641584744 1 16.5292048 1.234421289 24.99592608 0.99999392 5.149614871 0.723877388 0.805201971 70.10278775 423267.2864 1.556276592 0.206850479 17.15620744 -1.234421289 4.149620952 QGLSMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QGLSMR 6 0 P61956;J3KRH1;A8MUA9;A8MU27;P55854 P61956;A8MUA9 SUMO2;SUMO3 Small ubiquitin-related modifier 2;Small ubiquitin-related modifier 3 0 97.071 0.096521 304690000 373370 367040 224480 240050 350820 371280 376090 375390 344740 FALSE TRUE 324028.2085 364628.8901 333039.2788 294557.0214 343839.3684 385563.3819 339616.8497 295115.7698 303985.2299 1.065934054 1.199495417 1.095577173 0.968984649 1.131105509 1.268362223 1.11721497 0.970822727 1 18.2136417 1.757608377 6.432809464 0.986689687 1.123490047 0.34003856 0.07838269 0.174464398 20.20848255 0.047008009 0.021447436 57.22797479 -1.757608377 0.136800359 QGMEYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QGMEYYR 7 0 C9JIF9;P13798 C9JIF9 APEH Acylamino-acid-releasing enzyme 0 ;; 94.114 0.033589 1091550000 1202440 1464800 723440 937890 1334890 1493700 1114460 1231120 1226750 FALSE TRUE 1043534.507 1455177.632 1073298.004 1150852.259 1308328.301 1551163.606 1006379.841 967854.5686 1081725.013 0.964694812 1.345238037 0.992209657 1.063904639 1.209483266 1.433972209 0.930347204 0.894732541 1 20.04490236 2.100165666 24.99985173 0.931316249 1.1668252 0.346449697 0.146445678 12.35006012 3063.471785 0.058423887 0.039389377 125.9405733 -2.100165666 0.235508951 QGMSMRES(ph)PVSAPLEGLICR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QGMSMRESPVSAPLEGLICR 20 1 O75376;O75376-2;A0A088AWL3 O75376 NCOR1 Nuclear receptor corepressor 1 1 QGMS(0.001)MRES(0.996)PVS(0.003)APLEGLICR 96.181 0.00067853 85379000 54553 53559 35581 32887 41404 47041 54704 50572 34352 TRUE FALSE 47343.68283 53207.1674 52788.09061 40354.496 40580.14141 48850.69771 49398.8145 39757.57135 30290.94569 1.562964831 1.756537017 1.742701966 1.332229651 1.33967892 1.612716163 1.630811233 1.312523279 1 14.886599 1.412697349 2.487195866 0.964037296 1.565685961 0.628046722 0.142682522 0.270207553 2.523502475 0.302075002 0.041755192 25.86409872 -1.412697349 0.601648665 QGNFFAS(ph)PMLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QGNFFASPMLK 11 0 Q9H0H5 Q9H0H5 RACGAP1 Rac GTPase-activating protein 1 1 QGNFFAS(1)PMLK 117.08 0.00094683 162120000 484220 419230 285520 352030 406110 367110 466900 524900 535030 TRUE FALSE 420229.1001 416476.0505 423598.427 431963.7919 398029.2055 381232.9593 421620.1099 412654.2198 471779.3629 0.890732264 0.882777169 0.897874007 0.915605526 0.843676593 0.808074683 0.893680697 0.874676283 1 18.84775279 1.238279413 24.99995308 1.000000138 0.875682339 0.623065459 0.030337516 4.8218297 427914.9471 0.044139714 0.007801931 17.30929635 -1.238279413 -0.124317799 QGPPCS(ph)DS(ph)EEEVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QGPPCSDSEEEVER 14 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 2 QGPPCS(1)DS(1)EEEVER 67.607 0.076183 264870000 256570 260950 152710 214840 204620 258450 249680 260680 230660 TRUE FALSE 222663.6244 259235.8023 226561.0668 263622.7056 200548.4623 268392.7387 225466.072 204935.6106 203391.6376 1.094753094 1.274564704 1.113915348 1.296133454 0.986021179 1.319585908 1.108531672 1.007591133 1 17.63390084 1.876241655 3.70732366 1.006188426 1.180524139 0.335968514 0.10123729 0.24046211 5.458937705 0.053756775 0.024866837 75.20412376 -1.876241655 0.174335713 QGPPHINHDDPSLVPNVPYFDLPAGLMAPLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QGPPHINHDDPSLVPNVPYFDLPAGLMAPLVK 32 0 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 135.92 1.94E-08 317120000 409880 369230 203960 255280 375650 304410 339620 447170 478420 FALSE TRUE 355713.3195 366804.5038 302595.7382 313245.2257 368175.2999 316120.8497 306683.7047 351546.1754 421861.7326 0.84319883 0.869489872 0.71728653 0.742530553 0.872739269 0.749347061 0.726976829 0.833320845 1 18.6864107 1.2691814 3.503075361 1.022853416 0.788671673 0.572208005 0.05704987 0.203198694 3.691788781 0.121128219 0.014839683 18.58580603 -1.2691814 -0.234181743 QGPPS(ph)PCQQLVLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QGPPSPCQQLVLTK 14 0 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 QGPPS(1)PCQQLVLTK;QGPPS(1)PCQQLVLTK;QGPPS(1)PCQQLVLTK;QGPPS(1)PCQQLVLTK 207.95 9.15E-09 895500000 723760 639100 417939 551600 713570 677180 633470 848790 739830 TRUE FALSE 628113.2822 634901.71 620055.6983 676849.2107 699371.3531 703231.5528 572036.1769 667282.8638 652368.1402 0.96282029 0.973226114 0.950469007 1.037526465 1.072050135 1.077967346 0.876860996 1.022862434 1 19.3153268 3.748173871 24.53033167 1.011844466 0.963277233 0.165600999 0.055178486 1114.887349 2844869.393 0.015300358 0.026075309 5599.817466 -3.748173871 -0.048567233 QGPVSQSATQQPVTADKQQGHEPVS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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(0.001)ADKQQGHEPVS(0.999)PR;QGPVSQSATQQPVTADKQQGHEPVS(1)PR;QGPVSQSATQQPVTADKQQGHEPVS(1)PR;QGPVSQSATQQPVTADKQQGHEPVS(1)PR;QGPVSQSATQQPVT(0.016)ADKQQGHEPVS(0.984)PR 264.31 1.79E-53 4332760000 2809374 2197784 932008.8 1121140.6 2114268 1859472 2563364 2779010 292515.4 TRUE FALSE 2438108.108 2183346.612 1382731.373 1375712.709 2072198.203 1931007.091 2314769.354 2184740.338 257934.5626 9.452428875 8.464730705 5.360783599 5.333572572 8.033813623 7.486422414 8.974250407 8.470134112 1 17.97664558 4.427332015 6.942450509 6.768715499 9.217680641 0.170458366 2.291470106 0.345887228 37.58519847 0.572026994 1.557197956 26750.50687 -4.427332015 2.448965142 QGQQQAGGDGKTEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QGQQQAGGDGKTEQK 15 1 Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 224.33 1.05E-12 185586000 249280 148726 91122 96565 118905 111335 217049 239497 30419 FALSE TRUE 216337.0164 147749.0091 135188.904 118491.5592 116539.0231 115618.1295 195999.6214 188282.4303 26822.90047 8.065384898 5.508315898 5.040055385 4.417552057 4.344758437 4.310426071 7.307174762 7.019465718 1 14.71117763 4.744113872 3.053544613 5.072116349 8.561522699 0.249368594 1.729206286 0.619343914 8.591002118 0.442465772 5.276154553 55477.11545 -4.744113872 3.48940635 QGQSQAASSSSVTS(ph)PIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QGQSQAASSSSVTSPIK 17 0 O60583-2;O60583 O60583-2 CCNT2 Cyclin-T2 1 QGQSQAASSSSVT(0.027)S(0.973)PIK;QGQSQAASSSSVT(0.002)S(0.998)PIK 258.43 3.83E-27 371090000 1129350 841220 483060 697270 945050 713870 995910 1235570 1127850 TRUE FALSE 980103.5361 835693.9704 716669.4317 855595.8106 926245.354 741333.0408 899326.8015 971352.9707 994516.8579 0.985507212 0.840301463 0.720620697 0.860313029 0.93135209 0.745420286 0.904285125 0.976708402 1 19.9236363 1.844237699 3.180047765 0.989882897 0.844609208 0.354059656 0.077352548 0.260167027 4.599562215 0.04995441 0.02115054 69.86146669 -1.844237699 -0.145273689 QGRPTLQEGPGLQQKPRPEAEPPS(ph)PPSGDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QGRPTLQEGPGLQQKPRPEAEPPSPPSGDLR 31 3 A0A0A0MRY0;Q8WUA7-3;Q8WUA7-4;Q8WUA7;F8WDP1;B0QYI1;Q8WUA7-2 A0A0A0MRY0 TBC1D22A TBC1 domain family member 22A 1 QGRPTLQEGPGLQQKPRPEAEPPS(0.988)PPS(0.012)GDLR;QGRPTLQEGPGLQQKPRPEAEPPS(0.855)PPS(0.145)GDLR 89.559 0.0031625 1072170000 260080 240620 129783 171919 244120 206850 254350 310440 212320 TRUE FALSE 225709.769 239039.3514 192546.4929 210955.8366 239262.4896 214807.6533 229683.1761 244054.8218 187219.7715 1.205587248 1.276784762 1.028451703 1.126781829 1.277976614 1.147355601 1.226810472 1.303573976 1 17.51437327 3.283476061 24.99992479 1.205683411 1.158432402 0.012237961 0.102789249 482.879496 268767.5541 0.029464112 0.038037854 1920.773084 -3.283476061 -0.047251009 QGS(ph)ESPAQAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QGSESPAQAGR 11 0 Q92817;K7EKI0 Q92817 EVPL Envoplakin 1 QGS(0.5)ES(0.5)PAQAGR 150.29 3.56E-05 65361000 72622 70566 43789 53863 64847 76057 70865 76405 74583 TRUE FALSE 63024.8187 70102.4473 64965.50687 66093.41739 63556.67157 78982.96201 63992.52321 60066.38533 65765.88271 0.958320882 1.065939427 0.987829923 1.004980313 0.966407945 1.20097167 0.973035267 0.913336564 1 16.00505173 2.014893812 24.99764216 0.948290331 1.031354781 0.170453409 0.071494918 336.1119937 564125.2292 0.028301222 0.019072892 103.4889099 -2.014893812 0.083064451 QGS(ph)FTIEKPSPNIPIELIPHINK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QGSFTIEKPSPNIPIELIPHINK 23 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 QGS(0.908)FT(0.082)IEKPS(0.01)PNIPIELIPHINK 119.35 0.00011777 125790000 273300 162590 138800 143010 170620 121480 260180 289300 221430 TRUE FALSE 237182.7125 161521.9356 205924.1443 175482.6063 167224.9958 126153.4142 234947.7836 227435.4463 195252.7977 1.214746807 0.827245179 1.054654001 0.898745669 0.856453776 0.646102979 1.203300472 1.164825544 1 17.57498369 2.185134021 24.9999999 1.134841325 0.915039759 0.280999031 0.15521231 113.8976995 53295.3462 0.06181505 0.041675732 153.1560019 -2.185134021 -0.219801566 QGS(ph)RLMDNFLIREMS(ph)GS(ph)TSELLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QGSRLMDNFLIREMSGSTSELLIK 24 2 Q9NS91;F8WE49 Q9NS91 RAD18 E3 ubiquitin-protein ligase RAD18 3 QGS(1)RLMDNFLIREMS(0.5)GS(0.5)T(0.5)S(0.5)ELLIK 40.381 0.070985 940580000 82707 95492 83389 63791 75833 133070 70395 115350 113600 TRUE FALSE 71777.0604 94864.70676 123716.1993 78275.72153 74324.07166 138189.289 63568.10373 90683.30015 100170.3374 0.716550051 0.947033915 1.235058227 0.781426154 0.741976852 1.379543012 0.634600076 0.905290952 1 16.61209583 QGSES(ph)PAQAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QGSESPAQAGR 11 0 Q92817;K7EKI0 Q92817 EVPL Envoplakin 1 QGS(0.006)ES(0.994)PAQAGR;QGS(0.307)ES(0.693)PAQAGR;QGS(0.107)ES(0.893)PAQAGR 210.96 1.15E-08 1071275000 816844 798334 473181 535782 634329 795681 814979 797450 762968 TRUE FALSE 708895.9958 793089.6914 702012.9143 657439.492 621707.0939 826291.3629 735942.462 626921.5233 672770.7922 1.053696153 1.178840848 1.043465207 0.977211704 0.924099413 1.228191492 1.093897759 0.93185009 1 19.35975555 1.7465446 12.49939866 0.967008202 1.071153863 0.196552181 0.08858585 0.157310087 175.1617045 0.049679381 0.023522797 55.78848914 -1.7465446 0.104145661 QGSGRES(ph)PSLASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 QGS(0.004)GRES(0.982)PS(0.014)LASR;QGSGRES(0.997)PS(0.003)LASR;QGSGRES(0.999)PS(0.001)LASR;QGSGRES(0.958)PS(0.042)LASR;QGSGRES(0.966)PS(0.034)LASR;QGS(0.01)GRES(0.988)PS(0.002)LASR;QGS(0.072)GRES(0.925)PS(0.003)LASR 213.47 1.49E-08 11675351000 7111219 6162921 3464394 4208618 5794652 6536009 6071281 6662354 4935145 TRUE FALSE 6171453.392 6122436.366 5139786.526 5164249.042 5679349.762 6787453.496 5482489.103 5237661.444 4351717.78 1.418164896 1.406901062 1.181093716 1.186715063 1.30508228 1.559718217 1.25984482 1.203584816 1 22.05315357 1.368117805 1.915832883 0.947236996 1.331086643 0.476118796 0.11243973 0.594765437 2.736433 0.381865769 0.033155047 23.34091111 -1.368117805 0.383849647 QGSIT(ph)SPQANEQSVT(ph)PQRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QGSITSPQANEQSVTPQRR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 QGSIT(0.585)S(0.415)PQANEQS(0.011)VT(0.989)PQRR;QGS(0.079)IT(0.503)S(0.418)PQANEQS(0.015)VT(0.985)PQRR 219.96 1.87E-19 5267200000 1621510 1399590 1012770 1041730 1426260 1433200 1263110 1433520 1467470 TRUE FALSE 1407223.345 1390396.001 1502548.96 1278270.718 1397880.216 1488336.131 1140613.787 1126972.904 1293987.368 1.087509337 1.07450508 1.161177455 0.987854093 1.08028892 1.15019371 0.881472118 0.870930375 1 20.3033921 2.231224706 24.99967789 0.90627242 1.087655064 0.662896014 0.057882128 92.17558281 314117.0654 0.022891198 0.015785694 170.3039443 -2.231224706 0.181382644 QGSITS(ph)PQANEQSVT(ph)PQRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QGSITSPQANEQSVTPQRR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 QGS(0.001)IT(0.197)S(0.802)PQANEQSVT(1)PQRR;QGS(0.008)IT(0.451)S(0.541)PQANEQS(0.066)VT(0.934)PQRR 171.89 8.14E-12 1732260000 1096490 894360 661010 765220 1007930 1030440 943370 1064720 1034450 TRUE FALSE 951586.0683 888484.8903 980676.6469 938974.8967 987874.165 1070081.694 851882.1226 837037.9137 912158.4994 1.043224471 0.974046606 1.075116493 1.029398835 1.083007137 1.173131308 0.933918966 0.917645249 1 19.79892501 2.185982983 24.99999667 0.942980074 1.058879625 0.488674082 0.053939616 81.57440759 38786.92219 0.02259057 0.015230571 153.4556853 -2.185982983 0.115899551 QGSITS(ph)PQANEQSVTPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QGSITSPQANEQSVTPQR 18 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QGSITS(1)PQANEQSVTPQR;QGSITS(1)PQANEQSVTPQR 386 1.83E-126 344310000 495360 386600 298720 397610 459040 408910 360880 449980 773530 TRUE FALSE 429896.9209 384060.3991 443181.9912 487893.4276 449906.0021 424641.0323 325881.9131 353755.2787 682084.1646 0.630269611 0.563068928 0.649746782 0.715297984 0.659604819 0.62256398 0.477773756 0.51863875 1 19.37959024 1.231339559 24.99940007 1.000000697 0.600493591 0.760844859 0.069629816 144.2930927 499500.6053 0.196194237 0.019651066 17.03489885 -1.231339559 -0.399507105 QGSITSPQANEQSVT(ph)PQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QGSITSPQANEQSVTPQR 18 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QGSITSPQANEQSVT(1)PQR 195.38 4.66E-18 0 104810 82216 69405 84029 100520 82930 71144 87901 181510 TRUE FALSE 90959.09295 81675.91768 102969.4901 103109.0688 98519.84866 86120.37076 64244.46583 69104.0552 160052.0946 0.568309294 0.510308334 0.643349844 0.644221927 0.615548637 0.538077124 0.40139722 0.431759768 1 17.28818203 1.230290174 24.9998276 1.000000851 0.539379928 0.754937702 0.08158732 181.3342657 548092.0079 0.259022388 0.023404754 16.99378714 -1.230290174 -0.460620923 QGSITSPQANEQSVT(ph)PQRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 QGSITSPQANEQSVTPQRR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QGSITSPQANEQSVT(1)PQRR;QGSITSPQANEQSVT(1)PQRR;QGSITSPQANEQSVT(1)PQRR;QGSITSPQANEQSVT(1)PQRR;QGSITSPQANEQS(0.021)VT(0.979)PQRR;QGSITSPQANEQS(0.022)VT(0.978)PQRR;QGSITSPQANEQS(0.26)VT(0.74)PQRR 328.64 1.96E-75 9158800000 734526 577750 392964 470485 619386 645820 566199 644721 631709 TRUE FALSE 637456.528 573954.7222 583002.7048 577315.8102 607061.4304 670665.1133 511289.1081 506852.4314 557029.0817 1.144386441 1.03038556 1.046628846 1.036419514 1.089819994 1.204003768 0.917885843 0.90992095 1 19.08739312 2.20937744 24.99991427 0.934763696 1.084463047 0.597220653 0.057475901 141.5129252 121226.7436 0.023726759 0.015999521 161.9486903 -2.20937744 0.149699351 QGTEIDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QGTEIDGR 8 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 134.77 0.0036035 0 3319000 2825000 1623260 2109900 2515700 2598500 2593000 3094600 2691800 FALSE TRUE 2880385.741 2806442.389 2408273.965 2588985.043 2465642.492 2698465.976 2341531.259 2432843.872 2373578.471 1.213520335 1.182367646 1.014617379 1.090751823 1.038787014 1.136876665 0.986498356 1.024968798 1 21.17863232 8 0.442963157 1.021473261 5.519812535 0.611424781 0.049035175 62.26901172 0.795698359 0.037288902 251.0688083 100000000 -8 4.498339274 QGTTPPIWHLTDK ddPTM_MDA-MB-175_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 97.797 0.0036135 435560000 929900 889880 505660 650850 931710 1009600 921020 996300 1000900 FALSE TRUE 807011.3589 884034.3197 750198.8673 798635.4401 913170.7939 1048439.965 831699.6222 783248.9982 882574.7422 0.914383021 1.001653772 0.850011712 0.904892698 1.034666811 1.187933344 0.942356021 0.887459113 1 19.75135893 4.764943175 21.42149923 0.969893956 0.914382506 0.037136234 0.094164464 5344.904865 4339332.791 0.024667987 1.339722616 58202.70574 -4.764943175 -0.05551145 QGVCCADRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QGVCCADRR 9 1 K7EQ05;P28799-3;P28799-2;P28799 K7EQ05 GRN Granulins;Acrogranin;Paragranulin;Granulin-1;Granulin-2;Granulin-3;Granulin-4;Granulin-5;Granulin-6;Granulin-7 0 95.09 0.013277 71435000 105670 113670 64757 74506 98942 106150 97680 101210 82730 FALSE TRUE 91705.44177 112923.2943 96073.7018 91423.72605 96973.24778 110233.6592 88207.00863 79567.02912 72949.75365 1.257104201 1.547959913 1.316984596 1.253242423 1.329315631 1.511090219 1.20914745 1.090710045 1 16.15461549 1.848066595 2.496952938 1.031108959 1.367502022 0.638382323 0.100122918 0.170926829 1.953975488 0.073459807 0.027760723 70.48011347 -1.848066595 0.336393063 QGVLTHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 QGVLTHGR 8 0 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ;;;;;;; 133.57 0.0009136 4360930000 8571830 9715530 5612040 6356240 8566840 9784400 9626900 9354410 9290940 FALSE TRUE 7439040.947 9651708.044 8326041.315 7799521.441 8396376.645 10160812.2 8693284.72 7354042.218 8192575.657 0.908022246 1.178104231 1.01629105 0.95202312 1.024876302 1.240246367 1.061117417 0.897647153 1 22.96588566 1.753956519 25 0.946241962 1.059753263 0.160447099 0.099761609 8.498755126 13822.10764 0.052501304 0.025211997 56.74877861 -1.753956519 0.113511301 QGVSYSVHAYTGQPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QGVSYSVHAYTGQPSPR 17 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 QGVSYSVHAYT(0.298)GQPS(0.702)PR;QGVSYSVHAYT(0.039)GQPS(0.961)PR 220.63 4.14E-15 334150000 96236 155471 66436 117309 198320 189221 192826 204681 174355 TRUE FALSE 83518.16877 154449.7008 98564.67182 143945.8014 194373.82 196500.4543 174125.7642 160911.561 153742.9505 0.543232509 1.00459696 0.641100431 0.936275783 1.264277935 1.278110337 1.132577225 1.046627247 1 17.23016074 3.46667651 5.25078808 1.136722932 0.75989585 0.635263077 0.143180256 0.116128903 9.785735527 0.040725055 0.055474665 2928.710944 -3.46667651 -0.376827081 QGVTEAAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QGVTEAAEK 9 0 O76070;F8W754;G4Y816;Q16143 O76070 SNCG;SNCB Gamma-synuclein;Beta-synuclein 0 ;;;; 176.33 0.00012386 668437000 1098637 1194890 774655 947069 1044313 1074434 1224310 1441850 1442090 FALSE TRUE 953449.3369 1187040.689 1149280.749 1162115.491 1023533.214 1115768.171 1105576.605 1133521.598 1271607.763 0.749798298 0.933495944 0.9038013 0.913894619 0.804912682 0.877446807 0.869432098 0.891408209 1 20.2782223 1.185633952 2.496523428 1.045571698 0.868979476 0.381994198 0.053543762 0.70333457 4.240724366 0.285358763 0.013431534 15.33324065 -1.185633952 -0.176592222 QGYACPYYHNS(ph)KDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QGYACPYYHNSKDR 14 1 Q9C0B0 Q9C0B0 UNK RING finger protein unkempt homolog 1 QGYACPY(0.01)Y(0.063)HNS(0.927)KDR;QGYACPYY(0.003)HNS(0.997)KDR;QGYACPY(0.003)Y(0.02)HNS(0.977)KDR 93.153 0.0028232 349250000 538190 496499 339451 383727 518810 442877 534640 645060 593420 TRUE FALSE 467066.8279 493237.4654 503610.639 470858.0802 508486.696 459914.7648 482790.6951 507118.9389 523266.5636 0.892598267 0.942612236 0.962436116 0.899843623 0.971754611 0.878930161 0.922647707 0.969140729 1 18.99718655 1.56049193 3.092029775 0.996417709 0.925746929 0.436533404 0.029407648 0.204290459 4.221313137 0.028182192 0.007452108 36.34895504 -1.56049193 -0.07067078 QGYACPYYHNS(ph)KDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QGYACPYYHNSKDRR 15 2 Q9C0B0 Q9C0B0 UNK RING finger protein unkempt homolog 1 QGYACPYYHNS(1)KDRR;QGYACPYYHNS(1)KDRR 171.79 5.55E-07 221970000 328430 263620 194680 204105 250790 213440 317920 390990 363820 TRUE FALSE 285027.1434 261888.2629 288827.8992 250450.1598 245799.7697 221651.1749 287088.1673 307379.8312 320809.6141 0.888461975 0.816335457 0.900309363 0.780681591 0.766185796 0.690911884 0.894886421 0.958137842 1 18.29135785 1.892132796 3.208418453 0.977261452 0.808078859 0.570225323 0.06113087 0.187900978 3.373967681 0.039770688 0.017717542 78.00685989 -1.892132796 -0.169182593 QGYGEGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QGYGEGFR 8 0 Q9Y6B6;Q9H029;Q9NR31;Q9NR31-2;H0Y5E8 Q9Y6B6;Q9NR31 SAR1B;DKFZp434B2017;SAR1A GTP-binding protein SAR1b;GTP-binding protein SAR1a 0 ;;; 157.8 0.0008635 3964170000 3387110 3445560 2194850 2577110 3578100 3556940 3598140 3890820 3815770 FALSE TRUE 2939494.832 3422925.889 3256286.801 3162282.214 3506902.81 3693777.783 3249192.937 3058798.421 3364674.018 0.87363436 1.017312783 0.967786711 0.93984802 1.042271195 1.097811486 0.965678375 0.909092056 1 21.68203531 4.748560468 23.66051394 0.987136468 0.873634226 0.325626925 0.053257103 940.2777472 2224679.285 0.014336952 0.179944382 56048.0449 -4.748560468 -0.113502243 QGYVIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QGYVIYR 7 0 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;; 122.79 0.010019 1046910000 1622130 1712960 863150 1006080 1375220 1364310 1389530 1536880 1562700 FALSE TRUE 1407761.411 1701707.453 1280572.227 1234525.841 1347855.813 1416795.889 1254773.594 1208230.172 1377959.386 1.021627651 1.234947467 0.929325087 0.895908728 0.978153512 1.028184069 0.910602741 0.876825677 1 20.39410194 4.219002843 24.99390411 0.939900462 1.128287553 0.548833582 0.068723149 143.4307432 183298.1591 0.017100299 0.035678853 16557.80802 -4.219002843 0.188387091 QHDYS(ph)DYEDSSLEFLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QHDYSDYEDSSLEFLER 17 0 A0A0A0MQS0;F8W9L8;A8MW92 A0A0A0MQS0 PHF20L1 PHD finger protein 20-like protein 1 1 QHDY(0.001)S(0.999)DYEDSSLEFLER 139.26 5.96E-07 46174000 21141 17517 13565 14794 19526 19465 17911 18130 19090 TRUE FALSE 18347.16329 17401.92967 20125.07937 18153.20381 19137.4708 20213.83115 16173.99398 14253.04059 16833.20195 1.089938999 1.033786069 1.195558601 1.078416564 1.136888327 1.200831025 0.960838825 0.846721891 1 14.03902201 2.09669935 5.755194045 0.910042316 1.119781975 0.666958236 0.062322846 0.105908256 5.201440145 0.025290776 0.016822978 124.9393811 -2.09669935 0.209739659 QHEAEEGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QHEAEEGVR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 176.48 5.31E-05 358890000 199588 189876 113966 154214 179066 213296 155186 178209 233120 FALSE TRUE 173211.9401 188628.6921 169080.3388 189230.6457 175502.9369 221501.6351 140136.0856 140100.3922 205560.8192 0.842631105 0.917629599 0.822531937 0.920557947 0.853776209 1.07754793 0.681725662 0.681552023 1 17.64920578 2.208682017 24.9979757 0.761214696 0.900842038 0.184268809 0.112207596 279.7129508 234020.2976 0.044547427 0.030038289 161.6895742 -2.208682017 0.139627341 QHEAEEGVRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 113.03 0.0010015 123237000 49389 48189 36652 28042 36687 46680 44499 40047 25963.7 FALSE TRUE 42862.11851 47872.44329 54377.02979 34409.3647 35957.00048 48475.80981 40183.49383 31483.2607 22894.30096 1.872174153 2.091020091 2.375133876 1.502966382 1.570565554 2.117374533 1.755174525 1.375157108 1 14.4827009 0.990664933 0.852066495 3.42E-11 1.947998165 0.593447973 0.256134897 2.502709705 1.075703804 5.101730119 0.101974111 9.787345801 -0.990664933 1.947998165 QHEAPSNRPLNELLT(ph)PQGPS(ph)PR ddPTM_MDA-MB-175_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 172.98 6.52E-11 338410000 257355 299498 169210 257898 359167 421920 287667 350270 334489 TRUE FALSE 223344.8847 297530.5779 251040.522 316457.6826 352020.2794 438151.5354 259769.0986 275367.4863 294946.0915 0.757239683 1.008762572 0.851140358 1.072933976 1.193507185 1.485530909 0.880734162 0.933619717 1 18.17009177 3.728067834 19.8084931 1.084715485 0.886019042 0.260181878 0.175470509 71.22699933 134465.9824 0.05249392 0.079340656 5346.478614 -3.728067834 -0.198696443 QHEAPSNRPLNELLT(ph)PQGPSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QHEAPSNRPLNELLTPQGPSPR 22 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 QHEAPSNRPLNELLT(0.999)PQGPSPR 89.659 0.0036596 142650000 97416 104290 83236 98365 113370 116240 119780 131640 131600 TRUE FALSE 84542.22878 103604.9121 123489.208 120700.2767 111114.1588 120711.828 108163.754 103489.8104 116042.3979 0.728546034 0.892819469 1.064173183 1.040139456 0.957530703 1.040239 0.932105472 0.891827576 1 16.82429249 4.620145369 3.280097126 0.980192874 0.72118525 0.7018168 0.053957764 0.171882068 2.991342548 0.015110225 0.092803616 41700.89431 -4.620145369 -0.259007625 QHEAPSNRPLNELLTPQGPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 QHEAPSNRPLNELLTPQGPSPR 22 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 QHEAPSNRPLNELLTPQGPS(1)PR;QHEAPSNRPLNELLTPQGPS(1)PR;QHEAPSNRPLNELLTPQGPS(1)PR;QHEAPSNRPLNELLTPQGPS(1)PR;QHEAPSNRPLNELLTPQGPS(1)PR;QHEAPSNRPLNELLT(0.01)PQGPS(0.99)PR;QHEAPSNRPLNELLT(0.003)PQGPS(0.997)PR 204.25 7.21E-23 6850350000 1384477 1500380 898388 1204612 1652070 1860270 1615180 1778980 1624960 TRUE FALSE 1201514.857 1490523.905 1332851.442 1478137.566 1619197.039 1931835.791 1458540.092 1398558.971 1432859.08 0.838543632 1.040244589 0.930204135 1.031600097 1.130046256 1.34823851 1.017922916 0.976061771 1 20.4504653 5.276248469 0.833248814 1.076197014 0.482815687 0.296184922 0.112471207 8.113062263 2.340892103 0.043824748 5.454647329 188907.1819 -5.276248469 -0.593381327 QHEVEIPS(ph)PTQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.995)PT(0.005)QK 74.12 0.024066 304150000 236210 221780 170240 212730 264630 222600 244040 329430 297520 TRUE FALSE 204994.25 220323.1126 252568.6334 261033.5979 259364.3807 231163.566 220373.0384 258983.9581 262347.5245 0.78138435 0.839813957 0.96272543 0.994991656 0.988629038 0.881134924 0.840004261 0.987178966 1 18.00111965 4.374948538 3.663912803 0.948443835 0.791770334 0.562190595 0.052483435 0.177125176 4.40921049 0.014522253 0.046346465 23710.92722 -4.374948538 -0.156673501 QHFISFDTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QHFISFDTDR 10 0 C9J0K6;P30626-3;P30626-2;P30626 C9J0K6 SRI Sorcin 0 ;;; 184.55 1.55E-06 5224930000 1766770 1844680 954570 1161150 1620990 1748360 1348600 1599670 1505550 FALSE TRUE 1533286.868 1832562.176 1416203.245 1424806.855 1588735.47 1815620.541 1217812.98 1257593.019 1327565.594 1.154961288 1.380392942 1.066767059 1.073247801 1.196728416 1.367631512 0.917327916 0.947292567 1 20.34035171 2.21822625 24.99952342 0.951729633 1.201651074 0.558852714 0.105365348 180.3844748 221767.0657 0.043718863 0.029514348 165.2822629 -2.21822625 0.249921441 QHFPATPLLDYALEVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QHFPATPLLDYALEVEK 17 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 162.15 2.88E-09 239600000 760100 716050 421670 523580 628050 508380 744480 877870 792920 FALSE TRUE 659650.8592 711346.2204 625591.0224 642466.8414 615553.0338 527937.7076 672280.4442 690144.3321 699181.9009 0.943461005 1.017397932 0.894747163 0.918883685 0.880390401 0.755079196 0.961524381 0.987074081 1 19.41530831 2.01454457 24.99239371 0.987119458 0.902412543 0.268315983 0.064631153 327.5642346 562861.9837 0.028281313 0.01905875 103.4057217 -2.01454457 -0.084706915 QHGCTANDANTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QHGCTANDANTK 12 0 Q8N6H7;G5E9L0;Q8N6H7-2;E9PIY6;H0YF45;E9PJT7;E9PK28;E9PN48;H0YDX1 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 0 131.13 0.00020417 96897000 109680 101530 67654 82128 76371 95532 108490 127220 122130 FALSE TRUE 95185.51011 100863.0427 100371.7007 100776.4176 74851.36652 99207.17786 97968.6565 100014.993 107691.9305 0.883868546 0.936588677 0.932026199 0.935784298 0.695050838 0.921212735 0.909712139 0.928713902 1 16.71655063 1.238103589 1.389819606 1.049676151 0.884981313 0.21062441 0.070751587 2.251007808 3.795618554 0.533327845 0.021566237 17.30229008 -1.238103589 -0.164694837 QHGDVVSAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QHGDVVSAIR 10 0 O14745;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;; 165.18 5.93E-06 3261960000 925830 885020 506264 664298 893140 875970 827740 899430 858990 FALSE TRUE 803479.2197 879206.2453 751094.9638 815137.0141 875368.2614 909669.1327 747465.9022 707093.8939 757441.1808 1.060781009 1.160758443 0.991621505 1.076172031 1.155691404 1.200976598 0.986830293 0.933529773 1 19.53077433 2.086350318 7.916767449 0.961499137 1.105315752 0.524456238 0.06037751 0.180853493 14.39562524 0.025335796 0.017038619 121.9973277 -2.086350318 0.143816615 QHHHLLQSPVSHHEPES(ph)PQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QHHHLLQSPVSHHEPESPQLR 21 0 Q9Y6D6 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 QHHHLLQSPVSHHEPES(1)PQLR;QHHHLLQSPVS(0.005)HHEPES(0.995)PQLR;QHHHLLQSPVSHHEPES(1)PQLR;QHHHLLQSPVSHHEPES(1)PQLR 243.28 1.96E-30 1316229000 377979 413331 145894 230266 329326 311273 291391 331267 183339 TRUE FALSE 328028.1175 410615.8014 216448.8264 282551.4147 322773.0569 323247.8737 263131.9457 260428.13 161664.8723 2.029062423 2.539919747 1.33887358 1.747760108 1.996556533 1.999493577 1.627638348 1.610913529 1 17.30264671 0.925459353 0.965724072 4.57E-18 1.937779471 0.484300156 0.30170156 3.197578358 1.57796819 7.523330762 0.105618558 8.422855552 -0.925459353 1.937779471 QHHPPYHQQHHQGPPPGGPGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QHHPPYHQQHHQGPPPGGPGGR 22 0 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;;; 168.2 3.37E-12 5512502000 2265025.3 1984661.4 1185461.1 1426111.6 1511329.4 1600895.2 1588185.9 1495471.2 1428158.8 FALSE TRUE 1965696.468 1971624.029 1758754.053 1749932.036 1481256.902 1662482.674 1434163.876 1175676.322 1259323.494 1.560914632 1.565621573 1.396586391 1.389581029 1.176232246 1.32013949 1.138836751 0.933577693 1 20.2642175 1.665620626 0.14465121 1.95E-09 2.104855187 0.890193809 0.07129746 10.04687036 0.549700422 5.8857344 2.507628118 46.30422562 -1.665620626 2.104855185 QHIAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QHIAEK 6 0 Q96TA1 Q96TA1 FAM129B Niban-like protein 1 0 68.422 0.096181 312900000 759020 752820 486940 590860 474210 596310 722820 799130 860000 FALSE TRUE 658713.5839 747874.6759 722425.8127 725023.7937 464774.1488 619250.4316 652721.0277 628242.2683 758331.7797 0.868635077 0.986210384 0.952651375 0.956077291 0.612890243 0.816595649 0.860732789 0.82845304 1 19.53246966 QHLLGTSPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QHLLGTSPER 10 0 Q8WUY1;H0YAR9 Q8WUY1 THEM6 Protein THEM6 0 ; 107.06 0.0023346 243680000 174477 160519 99743 159577 191582 188809 139363 179370 170647 FALSE TRUE 151419.4224 159464.5401 147979.0484 195811.3968 187769.893 196072.6044 125847.5977 141013.1214 150473.3061 1.006287602 1.059753017 0.983423919 1.301303214 1.247861816 1.303039121 0.836345004 0.937130479 1 17.19914805 2.228122328 24.99995039 0.923452086 1.149879465 0.447119307 0.118354865 206.9174233 495567.6827 0.051858479 0.035380328 169.0917148 -2.228122328 0.226427379 QHMDITGEENPLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QHMDITGEENPLNK 14 0 Q9H4A4;A6NKB8;C9JMZ3 Q9H4A4 RNPEP Aminopeptidase B 0 ;; 216.54 6.09E-12 1040790000 664150 577100 458680 516860 560470 514990 666150 734480 725890 FALSE TRUE 576380.8948 573308.9921 680499.1822 634220.9627 549317.7435 534801.9985 601546.8755 577417.1677 640076.1111 0.900488059 0.895688782 1.063153538 0.990852418 0.858206913 0.835528759 0.939805228 0.902107043 1 19.28788394 3.251551285 24.96629607 0.905372396 0.964956479 0.156688512 0.063701427 433.6830775 833475.4346 0.019167519 0.024590665 1784.64272 -3.251551285 0.059584083 QHPDPDSSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QHPDPDSSVK 10 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 116.03 0.0011449 623950000 972860 967650 533340 738660 892830 943000 973770 1032970 1116420 FALSE TRUE 844294.0861 961293.4434 791265.0079 906384.0427 875064.4298 979277.8202 879333.9353 812077.4041 984438.0994 0.857640604 0.976489476 0.803773247 0.920712072 0.888897362 0.994758148 0.89323436 0.824914644 1 19.90894097 QHPVPPPAQNQNQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QHPVPPPAQNQNQVR 15 0 Q15942;Q15942-2;H0Y2Y8 Q15942 ZYX Zyxin 0 69.714 0.048839 135100000 195510 196960 122680 150900 188770 201450 189260 212330 197640 FALSE TRUE 169672.8581 195666.1568 182008.4583 185164.1514 185013.8463 209199.9119 170905.5943 166924.8819 174275.2244 0.973591391 1.122742246 1.044373685 1.062481211 1.061618753 1.200399613 0.980664894 0.957823365 1 17.41100796 2.046286114 24.99997822 0.973902015 1.077829313 0.386285745 0.05817927 109.1506873 58953.8014 0.022476778 0.015153835 111.2464379 -2.046286114 0.103927299 QHS(ph)ITK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QHSITK 6 0 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 1 QHS(0.954)IT(0.046)K;QHS(1)ITK 117.7 0.014492 699930000 2070800 1882750 857840 1196900 1066660 935450 2612000 2086290 2066250 TRUE FALSE 1797138.533 1870382.091 1272694.293 1468674.438 1045435.553 971437.3668 2358688.642 1640153.119 1821980.279 0.986365524 1.026565497 0.698522541 0.806086902 0.573790817 0.533176664 1.294574189 0.900203552 1 20.79707591 2.240611099 24.99999999 1.040177403 0.771749554 0.363711168 0.182440867 66.72879419 813591.6339 0.07416499 0.054541391 174.0247823 -2.240611099 -0.268427849 QHSITK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QHSITK 6 0 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 ; 87.284 0.052615 246310000 803460 765760 476330 576610 485620 659460 791130 939230 863700 FALSE TRUE 697280.7253 760729.6721 706684.7812 707538.1134 475957.1121 684829.8529 714406.3344 738382.9736 761594.3699 0.915553939 0.998864622 0.927901793 0.929022248 0.624948307 0.899205509 0.938040462 0.969522626 1 19.53866329 -0.469140734 10.25275649 5.266366617 0.911666329 0 0.106662372 0 0 0 0.025008107 0.339515234 0.469140734 -4.354700288 QHSLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QHSLLK 6 0 K7EM56;A0A0B4J2B4;S4R417;K7ELC2;P62841;K7EQJ5;S4R456;K7EJ78 K7EM56 RPS15 40S ribosomal protein S15 0 81.635 0.06136 505180000 799470 707450 490280 667610 569560 597950 714790 749010 932550 FALSE TRUE 693818.0139 702802.7144 727381.0479 819201.0543 558226.8703 620953.5234 645469.7758 588840.0403 822305.0014 0.843747773 0.854674012 0.88456357 0.996225309 0.678856227 0.755137719 0.784951782 0.716084712 1 19.64931408 3.236292961 24.99999993 0.776393436 0.89120496 0.243448932 0.093295065 80.95444599 892490.8094 0.027067428 0.032177326 1723.030484 -3.236292961 0.114811524 QHTFVETESVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QHTFVETESVR 11 0 B0YIW6;P48444;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 ;; 131.17 0.00020886 2169140000 455936 437832 253686 317625 462620 404681 400207 434848 436203 FALSE TRUE 395682.9024 434955.8528 376369.3981 389746.6108 453414.7671 420249.3399 361394.9867 341859.1392 384635.5783 1.028721535 1.130825845 0.97850906 1.013287987 1.178816502 1.092590919 0.939577634 0.888787097 1 18.55313269 2.23024243 22.27993135 0.93140402 1.071349777 0.472644809 0.063187414 38.41803564 102897.1509 0.025846227 0.017816522 169.9191904 -2.23024243 0.139945757 QHTGERPFTCAECGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QHTGERPFTCAECGK 15 1 Q9BWE0;Q9BWE0-4 Q9BWE0 REPIN1 Replication initiator 1 0 73.834 0.021988 27126000 60650 48264 30526 43008 46853 41349 53705 56586 45407 FALSE TRUE 52634.94883 47946.95061 45288.4757 52773.62374 45920.71697 42939.72279 48496.69737 44485.52425 40039.03619 1.314590805 1.197505114 1.131108039 1.318054298 1.14689866 1.072446464 1.211235384 1.111053824 1 15.28911963 -1.745903437 0.248504171 4.54E-15 1.264654407 0.485842325 0.071361145 72.17384425 1.294321799 36.07254503 0.24272033 0.017951327 1.745903437 1.264654407 QHVIDGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QHVIDGEK 8 0 Q9UQ80;Q9UQ80-2;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;; 110.87 0.0033424 2180970000 6159060 5338590 3403210 4264280 4488120 4086430 5722600 6312460 5781700 FALSE TRUE 5345124.616 5303520.451 5049013.739 5232549.949 4398815.193 4243637.606 5167623.133 4962589.553 5098194.013 1.048434917 1.040274348 0.990353393 1.026353634 0.86281832 0.832380564 1.013618375 0.973401471 1 22.28155485 3.29602092 24.98940211 0.941648275 1.02477724 0.374716985 0.057478324 104.7383592 45549.55881 0.018153432 0.02343597 1977.064874 -3.29602092 0.083128965 QHVNDQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QHVNDQK 7 0 Q9P2M7 Q9P2M7 CGN Cingulin 0 63.486 0.079143 15266000 36477 33810 26781 28815 27234 38404 46374 46216 52969 FALSE TRUE 31656.47203 33587.89988 39732.38118 35357.88616 26692.09668 39881.42673 41876.65662 36333.06805 46707.06516 0.677766242 0.719118184 0.850671757 0.757013656 0.571478781 0.853862828 0.896580774 0.777892337 1 15.51135318 -2 0.501399861 8.422082326 0.728462044 0.434460591 0.090320204 121.1714582 1.356798412 978.7417736 0.060394485 0.01 2 -7.693620282 QHVPEQHPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QHVPEQHPK 9 0 Q9H3U1;A0A1W2PNX8;Q9H3U1-2 Q9H3U1;Q9H3U1-2 UNC45A Protein unc-45 homolog A 0 ;; 77.379 0.018949 214528000 535130 461010 331177 365074 423930 426913 483700 492770 460530 FALSE TRUE 464411.2147 457981.595 491335.3049 447969.6315 415494.6224 443336.6194 436790.8484 387394.9702 406086.668 1.143625859 1.127792737 1.209927199 1.103137992 1.023167356 1.091729067 1.07560992 0.953971161 1 18.63142814 2.325190609 0.452122929 0.926530601 1.173058227 0.662214306 0.04306324 1.282013048 0.561442121 0.185141635 0.06921632 211.441684 -2.325190609 0.246527626 QHWTMTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QHWTMTK 7 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 123.92 0.0041971 743390000 1781000 1488500 644110 1005800 1294100 1065100 1504800 1459900 1422600 FALSE TRUE 1545636.338 1478721.945 955603.7504 1234182.263 1268349.942 1106075.086 1358864.728 1147711.746 1254421.849 1.232150364 1.17880755 0.761788191 0.983865407 1.011103197 0.881740929 1.083259773 0.914932841 1 20.25859116 4.388814411 8.569305584 0.953767154 1.21878802 0.608667388 0.086202064 0.145294301 12.27115265 0.020037526 0.053328436 24480.16894 -4.388814411 0.265020866 QHYIDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 133.12 0.0033029 16947600000 32033500 30436300 18709700 20314500 24909000 21476400 32106800 33696300 32607000 FALSE TRUE 27800191.81 30236361.94 27757773.5 24927217.71 24413359.63 22302611.01 28993087.48 26490608.47 28752237.61 0.966887941 1.051617699 0.965412636 0.866966184 0.84909425 0.77568262 1.008376735 0.921340761 1 24.7771709 3.971846634 5.664404819 0.904853136 1.009714627 0.284281247 0.070622596 0.229028604 22.70624139 0.019491789 0.036445725 9372.309771 -3.971846634 0.104861491 QHYNCEHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 QHYNCEHSK 9 0 P50454;E9PR70;E9PPV6;E9PK86;E9PMI5;E9PQ34;E9PIG2;E9PRS3;E9PNX1 P50454 SERPINH1 Serpin H1 0 ;;;;;; 169.76 3.37E-05 2568313000 3517410 3962100 2452851 3149040 3122450 4018780 3641790 3273540 2887650 FALSE TRUE 3052575.357 3936072.704 3639057.948 3864077.662 3060319.354 4173385.067 3288609.766 2573518.946 2546275.307 1.198839477 1.545815841 1.429169084 1.517541191 1.201880781 1.639015646 1.291537391 1.010699408 1 21.27995698 1.831581112 3.428446195 1.001792028 1.424744402 0.598047775 0.138738217 0.140813288 2.869737111 0.080692903 0.034798338 67.85488401 -1.831581112 0.422952374 QIANS(ph)QDGYVWQVTDMNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 419.26 1.89E-148 89256000 163160 142300 84231 104920 116660 122110 122300 135970 143420 TRUE FALSE 141597.9926 141365.2219 124965.3933 128743.6896 114338.6942 126807.6507 110439.3648 106893.8736 126465.051 1.119661057 1.117820464 0.988141723 1.018017931 0.904112981 1.002709047 0.873279724 0.84524438 1 16.94837922 4.171721146 0.61934354 0.898859461 1.204702584 0.63953326 0.055160141 1.172304443 0.578953656 0.033707195 0.238107745 14849.8185 -4.171721146 0.305843124 QIAQEIIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QIAQEIIK 8 0 A8MY87;A0A2R8Y4X0;A0A0A0MQW1;A0A2R8Y5H9;Q8IVT5-4;Q8IVT5-3;Q8IVT5-2;Q8IVT5 A8MY87 KSR1 Kinase suppressor of Ras 1 0 83.005 0.018804 1727600000 345090 516170 148890 225580 466110 576100 277240 330110 415180 FALSE TRUE 299485.4822 512779.2453 220893.702 276801.3868 456835.3229 598262.9398 250353.3075 259518.5454 366097.8934 0.818047543 1.400661557 0.603373322 0.756085713 1.247850182 1.63416111 0.683842524 0.708877462 1 18.48186995 QIAQSKEDDDVIVNKPHVS(ph)DEEEEEPPFYHHPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QIAQSKEDDDVIVNKPHVSDEEEEEPPFYHHPFK 34 2 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;H7C1M2;H7C2G8;J3QSZ5 P18583-7 SON Protein SON 1 QIAQSKEDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;QIAQS(0.011)KEDDDVIVNKPHVS(0.989)DEEEEEPPFYHHPFK 126.52 4.29E-08 795200000 745150 523960 311327 310643 411892 283860 646890 759980 153809 TRUE FALSE 646676.5395 520518.0723 461885.7785 381179.241 403696.1551 294780.2779 584154.7074 597464.1912 135625.8752 4.76809118 3.837896503 3.405587449 2.810520045 2.976542303 2.17348111 4.307103688 4.405237497 1 17.04927292 4.602619669 1.749123261 3.153444996 5.055362398 0.252083014 0.981606313 1.130198711 4.308554022 0.275043136 3.276614503 40051.58144 -4.602619669 1.901917403 QIATLHAQVADMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QIATLHAQVADMK 13 0 P35579 P35579 MYH9 Myosin-9 0 ; 200.19 1.12E-07 1604740000 4047600 3889000 2638200 3441900 3309600 2975600 4109400 4708800 6093300 FALSE TRUE 3512699.405 3863452.903 3914042.344 4223436.001 3243745.435 3090073.257 3710871.021 3701859.764 5372957.016 0.653773964 0.719055241 0.728470809 0.786054307 0.60371699 0.575115946 0.69065712 0.68897997 1 22.35728487 1.237434694 6.277959129 1.010330081 0.681123389 0.73455244 0.060335859 0.071803136 12.02713592 0.100946872 0.015962862 17.27566183 -1.237434694 -0.329206692 QICLVMLETLSQS(ph)PQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 QICLVMLETLSQSPQGR 17 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLS(0.001)QS(0.999)PQGR;QICLVMLETLS(0.148)QS(0.852)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR 401.46 3.73E-140 5064174000 3137510 3356524 1834218 2219453 2566712 2567001 2724770 3229292 3382541 TRUE FALSE 2722880.104 3334474.773 2721251.96 2723413.726 2515639.453 2665755.19 2460522.225 2538733.036 2982660.856 0.91290302 1.11795304 0.912357151 0.913081928 0.843421218 0.893750687 0.824942004 0.851163829 1 21.50816851 4.051247095 10.03428435 0.881017029 1.015787114 0.366904777 0.068167149 0.3791514 71.15134424 0.016354194 0.034094578 11252.45009 -4.051247095 0.134770085 QICVVMLETLSQS(ph)PPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QICVVMLETLSQSPPK 16 0 F8VZX2;Q15366;Q15366-2;Q15366-5;Q15366-8 F8VZX2;Q15366;Q15366-2;Q15366-5 PCBP2 Poly(rC)-binding protein 2 1 QICVVMLETLSQS(1)PPK;QICVVMLETLSQS(1)PPK 238.94 8.68E-20 450620000 327508 264605 224822 246667 281234 206381 307178 354880 513706 TRUE FALSE 284226.988 262866.7923 333546.6712 302676.5124 275637.9936 214320.6106 277387.9248 278991.6737 452976.2619 0.627465525 0.580310304 0.736344703 0.668195086 0.608504279 0.473138724 0.612367464 0.615907934 1 18.78907592 1.238558551 10.6188701 1.001128443 0.614789227 0.770950477 0.065901977 0.034340898 109.9176071 0.095299473 0.016975041 17.32042527 -1.238558551 -0.386339215 QIDNPDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QIDNPDYK 8 0 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ;;;; 159.37 0.00083652 1515570000 4710320 3845620 2984667 3775370 3765580 4028440 4031600 4194950 3587760 FALSE TRUE 4087839.278 3820357.869 4428061.944 4632625.461 3690652.325 4183416.694 3640616.053 3297892.588 3163619.1 1.292140156 1.207590974 1.39968239 1.464343625 1.166591871 1.322351573 1.150775722 1.042443001 1 21.59314448 1.941511799 1.334499237 0.981371736 1.31841925 0.667293429 0.084884499 0.307960975 0.968851455 0.104639103 0.028619154 87.40007373 -1.941511799 0.337047514 QIDSS(ph)PVGGETDETTVSQNYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 QIDSSPVGGETDETTVSQNYR 21 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 QIDS(0.001)S(0.999)PVGGETDETTVSQNYR;QIDSS(1)PVGGETDETTVSQNYR;QIDS(0.182)S(0.818)PVGGETDETTVSQNYR;QIDS(0.038)S(0.962)PVGGETDETTVSQNYR;QIDS(0.025)S(0.975)PVGGETDETTVSQNYR;QIDS(0.085)S(0.915)PVGGETDETTVSQNYR;QIDS(0.245)S(0.755)PVGGETDETTVSQNYR;QIDS(0.229)S(0.771)PVGGETDETTVSQNYR 381.63 1.82E-113 12491900000 3508200 3404920 2181050 2714350 3445070 3637080 3074040 3775700 3369260 TRUE FALSE 3044582.481 3382552.856 3235813.075 3330684.654 3376519.847 3777000.821 2775920.074 2968295.938 2970949.921 1.024784181 1.138542536 1.089150999 1.121084078 1.136511869 1.271310834 0.934354381 0.999106689 1 21.50249286 2.211502451 24.99999374 0.980443886 1.12861113 0.564774826 0.063045943 159.9017952 147737.7398 0.025343752 0.017091395 162.7430499 -2.211502451 0.148167244 QIEAQEKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QIEAQEKPR 9 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;; 112.13 0.0018355 492950000 797840 594440 498020 600910 621770 620370 723990 821130 878160 FALSE TRUE 692403.4225 590535.0845 738864.1378 737355.7998 609397.9935 644236.0353 653777.5612 645537.7395 774344.9252 0.894179583 0.762625369 0.954179609 0.95223172 0.786985197 0.831975537 0.844297599 0.833656577 1 19.56261682 1.233184341 24.99582292 1.000000227 0.855791317 0.339525079 0.062412687 207.0283696 962426.977 0.12718381 0.015219733 17.10741304 -1.233184341 -0.14420891 QIEETLAHFHLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QIEETLAHFHLTK 13 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 248.68 1.15E-17 2114800000 1177890 937160 477580 899550 933800 1040090 774120 1184850 1128820 FALSE TRUE 1022228.852 931003.7343 708539.2854 1103806.576 915219.2069 1080102.935 699045.9615 931479.048 995372.1856 1.026981532 0.935332278 0.711833519 1.108938538 0.919474364 1.085124691 0.702296057 0.935809802 1 19.92487655 4.715475922 5.515946186 0.918828965 1.029537017 0.053747783 0.133558984 0.426579248 44.18174042 0.031116479 0.160534625 51936.88783 -4.715475922 0.110708052 QIEHCEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QIEHCEGR 8 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 134.51 0.00087357 292420000 614190 533240 330600 351720 449520 534640 483290 521480 532010 FALSE TRUE 533023.2353 529737.1113 490479.2658 431583.4017 440575.4315 555207.9468 436420.6102 409965.5602 469116.3839 1.136228138 1.129223215 1.045538554 0.919992174 0.939160188 1.183518559 0.930303492 0.87391013 1 18.83958636 7.999999661 0.337195302 0.938286538 3.395959812 0.320323742 0.086509708 92.42775633 1.432374443 0.132721642 140.6780161 99999921.9 -7.999999661 2.457673274 QIEIQFAQGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 138.99 0.00010706 223892000 176494 167869 104672 129852 166327 175116 158763 161994 186736 FALSE TRUE 153169.8707 166766.2575 155291.7293 159336.8813 163017.4181 181852.8258 143366.1887 127352.8437 164660.2828 0.930217464 1.012789816 0.943103745 0.967670397 0.990022702 1.104412204 0.870678625 0.773427821 1 17.32913308 2.070552146 12.86504002 0.855993935 0.988965067 0.321121616 0.072617626 0.753543332 135.5277027 0.028790987 0.019409651 117.6392225 -2.070552146 0.132971132 QIEYEYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QIEYEYK 7 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ; 112.94 0.01452 247091000 418530 359300 216690 311450 365450 334870 357780 494440 413270 FALSE TRUE 363220.2001 356939.7346 321482.0088 382169.4827 358178.26 347752.6656 323082.5507 388707.8537 364413.6914 0.9967249 0.979490461 0.88218971 1.048724271 0.982889141 0.954279913 0.886581812 1.066666437 1 18.47521764 1.681945022 11.78969093 1.032625371 0.963144971 0.250638143 0.051473834 0.156925923 28.34305521 0.027392622 0.012874648 48.07784817 -1.681945022 -0.0694804 QIEYYFSVDNLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QIEYYFSVDNLER 13 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 0 ; 117.93 0.0010874 94414000 109772 102655 61789 79259 101761 82585 100950 112577 120349 FALSE TRUE 95265.35207 101980.6525 91670.36707 97255.96735 99736.15519 85762.09839 91159.88454 88503.28463 106121.4783 0.897700952 0.960980323 0.863824822 0.916458844 0.939830059 0.808150242 0.859014461 0.833980887 1 16.69535715 2.770325249 24.94415987 0.867306883 0.915424942 0.10807253 0.055712602 1225.635615 962466.1135 0.017349652 0.017348354 589.2848135 -2.770325249 0.048118059 QIFDEYENETFLCHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QIFDEYENETFLCHR 15 0 S4R3N1;Q9Y3A3-2;Q9Y3A3-3;Q9Y3A3;B4DM50 S4R3N1 HSPE1-MOB4;MOB4 MOB-like protein phocein 0 ;;; 288.06 1.18E-34 1159097000 1003670 946260 633960 800508 948550 985590 941990 1075630 1085640 FALSE TRUE 871032.4665 940043.9558 940545.1765 982275.5764 929675.7108 1023506.285 850635.9548 845614.8951 957296.876 0.909887506 0.981977461 0.98250104 1.026092951 0.971146709 1.06916288 0.888581146 0.883336106 1 19.86860688 2.20822889 24.99999733 0.914031861 0.990182974 0.265093926 0.05103806 232.2797422 191447.8832 0.020369542 0.013734997 161.5209611 -2.20822889 0.076151113 QIFLGGVDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QIFLGGVDKR 10 1 P05141 P05141 SLC25A5 "ADP/ATP translocase 2;ADP/ATP translocase 2, N-terminally processed" 0 ; 154.05 2.43E-05 1837620000 1238870 1230940 802710 1238070 1493540 1291350 1280370 1771950 1282280 FALSE TRUE 1075150.191 1222853.874 1190903.241 1519192.716 1463821.476 1341029.07 1156199.914 1393032.282 1130690.319 0.950879452 1.081510873 1.053253239 1.343597527 1.294626346 1.186026843 1.02256108 1.232019288 1 20.10877242 3.970253905 24.34841972 1.181841829 1.0289918 0.298770261 0.10990761 613.6098137 502266.9532 0.02948903 0.051195935 9338.000754 -3.970253905 -0.152850029 QIGASSRPPPNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QIGASSRPPPNR 12 1 Q06787;Q06787-2;R9WNI0;G3V0J0;Q06787-9;Q06787-7;Q06787-6;Q06787-5;Q06787-8;Q06787-3;Q06787-4;A8MQB8 Q06787 FMR1 Fragile X mental retardation protein 1 0 93.959 0.0062736 38408000 23659 24335 16848 17876 21170 22640 21522 26108 23407 FALSE TRUE 20532.40321 24175.14178 24995.74915 21935.01902 20748.75842 23510.97545 19434.79975 20525.00737 20639.85113 0.994794152 1.171284698 1.211043093 1.062750835 1.005276554 1.139105864 0.941615307 0.994435825 1 14.33314494 2.655197611 0.926187389 0.978253066 1.121272544 0.299699507 0.074107733 0.682563007 1.303784427 0.060910185 0.039727907 452.0615933 -2.655197611 0.143019478 QIGLDQIWDDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QIGLDQIWDDLR 12 0 A0A590UJ56;A0A590UJR3;A0A590UJ21;A0A0C4DGX4;Q13616;A0A590UJC4;A0A590UK34;A0A590UJ50;A0A590UJM8;A0A590UJ59;A0A590UJ97 A0A590UJ56 CUL1 Cullin-1 0 ;;; 245.58 4.13E-16 270443000 289829 309447 191725 204623 293720 281193 248812 314097 322268 FALSE TRUE 251527.3633 307414.2223 284443.8513 251085.7796 287875.5467 292010.6767 224682.2505 246929.8009 284169.8442 0.885130384 1.081797483 1.000964237 0.883576441 1.013040449 1.027592064 0.790661835 0.86895146 1 18.11639394 2.254386428 24.9999246 0.878879093 0.984349174 0.246767464 0.078184988 294.5291467 465265.0524 0.028727243 0.022177339 179.6331261 -2.254386428 0.10547008 QIGNVAALPGIVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QIGNVAALPGIVHR 14 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ; 108.59 0.00081656 746330000 804060 719280 459160 596570 653570 715000 672590 745400 781410 FALSE TRUE 697801.4338 714555.0023 681211.3118 732030.3365 640565.2357 742506.5127 607362.3253 586002.0107 689032.6 1.012726297 1.037040921 0.988648885 1.062403051 0.929658823 1.077607232 0.881471102 0.850470661 1 19.39421272 2.224127406 24.99998903 0.896894755 1.015545788 0.448199014 0.055418633 181.4799634 314341.7629 0.021183788 0.014354785 167.5434315 -2.224127406 0.118651033 QIHKFEELNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QIHKFEELNR 10 1 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 100.93 0.0022094 363090000 367240 316150 164210 206450 276200 247750 340920 339300 272300 FALSE TRUE 318708.3035 314073.1898 243622.5052 253327.6279 270704.1604 257281.1028 307857.6309 266743.3354 240109.0042 1.327348404 1.308044198 1.014632942 1.055052595 1.127421944 1.071517929 1.282157793 1.110925999 1 17.87332998 4.257376799 23.55540129 1.104988306 1.317696837 0.582782377 0.078112711 92.94711967 116353.4768 0.020021076 0.052722721 18087.42732 -4.257376799 0.21270853 QIILEKEETEELKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QIILEKEETEELKR 14 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 134.44 2.18E-05 223930000 619300 450950 325830 327680 383490 246390 579730 613790 243640 FALSE TRUE 537457.9359 447987.6798 483402.4778 402084.7523 375859.2993 255868.7827 523507.8738 482535.785 214837.1568 2.501699166 2.085243012 2.250087858 1.871579192 1.749507883 1.190989429 2.436765975 2.246053673 1 17.71288401 3.72080944 3.461469117 1.815135898 2.270190917 0.238516066 0.436989953 0.443033457 11.31324085 0.127541642 0.214081564 5257.865105 -3.72080944 0.455055019 QILIACS(ph)PVSSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QILIACSPVSSVR 13 0 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 QILIACS(0.996)PVS(0.003)S(0.001)VR;QILIACS(0.997)PVS(0.002)S(0.001)VR;QILIACS(0.942)PVS(0.042)S(0.016)VR 142.91 4.26E-05 477705000 974460 1037060 536969 626400 843660 820180 770200 899160 898790 TRUE FALSE 845682.642 1030247.485 796649.0045 768633.6939 826872.8166 851732.8553 695506.1225 706881.6313 792536.0701 1.067058868 1.29993766 1.005189586 0.969840646 1.043325153 1.074692859 0.877570307 0.891923608 1 19.59611707 3.805276109 0.549842982 0.920646439 1.22272916 0.387427088 0.091745608 1.62249834 0.88160337 0.083928789 0.304768406 6386.694008 -3.805276109 0.302082721 QILSADLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QILSADLR 8 0 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 80.438 0.059203 153530000 324490 414570 248750 266030 378720 430370 417060 431100 421160 FALSE TRUE 281607.8243 411846.6624 369046.332 326436.1775 371184.213 446926.6124 376613.5854 338912.6198 371370.9446 0.75829256 1.108989996 0.993740457 0.879003008 0.999497183 1.203450671 1.014116992 0.912598642 1 18.50250142 3.01398413 24.41988257 1.022006607 0.950081775 0.135219873 0.112759225 494.1931146 862979.7798 0.034960877 0.0396223 1032.723668 -3.01398413 -0.071924831 QIMALRVMT(ph)S(ph)KMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QIMALRVMTSKMK 13 2 O75487-2;O75487 O75487-2 GPC4 Glypican-4;Secreted glypican-4 2 QIMALRVMT(1)S(1)KMK 48.899 0.075581 331140000 610890 655880 288320 456860 708830 619740 652750 825780 411940 TRUE FALSE 530159.3387 651571.4811 427752.5164 560597.0457 694725.6698 643581.7988 589446.4055 649193.3732 363240.9225 1.459525362 1.793772234 1.177600017 1.543320179 1.912575447 1.771776689 1.622742288 1.787225318 1 18.47056722 1.230507794 24.99443585 0.999998826 1.641237772 0.475438348 0.209006407 276.0351578 856690.9408 0.559641434 0.051754503 17.00230466 -1.230507794 0.641238947 QINWTVLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QINWTVLYR 9 0 C9JXB8;C9JNW5;P83731 C9JXB8 RPL24 60S ribosomal protein L24 0 ; 215.38 1.49E-06 1894670000 1592000 1859270 1171180 1266840 1386180 1390260 1575120 1637410 2012690 FALSE TRUE 1381613.166 1847056.333 1737566.565 1554495.384 1358597.73 1443744.202 1422365.105 1287262.614 1774752.081 0.778482348 1.04074048 0.979047487 0.875894386 0.765514093 0.813490637 0.801444393 0.725319681 1 20.75918607 3.476718855 4.89129622 0.807691417 0.94218396 0.210238696 0.096362257 0.226181266 15.29309185 0.026542282 0.036797128 2997.221606 -3.476718855 0.134492544 QIPFHDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QIPFHDVR 8 0 Q06787;Q06787-2;R9WNI0;G3V0J0;Q06787-9;Q06787-7;Q06787-6;Q06787-5;Q06787-8;Q06787-3;Q06787-4;A8MQB8;Q06787-10;Q06787-11;A0A087WXI3;Q8IXW7;A0A087WY29 Q06787 FMR1 Fragile X mental retardation protein 1 0 ; 115.71 0.0024106 416370000 503900 523410 283050 348110 493060 518050 426190 503250 442880 FALSE TRUE 437308.3383 519971.6852 419933.9267 427153.696 483249.0707 537979.7187 384858.1594 395633.9038 390523.2309 1.119801086 1.331474402 1.075311002 1.093798428 1.23744001 1.377586981 0.985493638 1.013086732 1 18.57504885 2.200818612 24.99970493 1.0017668 1.202011904 0.503894856 0.096471262 139.9966851 92730.64135 0.039752248 0.026801595 158.7883412 -2.200818612 0.200245104 QIQEDWELAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QIQEDWELAER 11 0 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3;Q3HKR1;A0A1W2PPY0;V9GYI8;E9PHB8 E9PFK9 RABGEF1;KCTD7 Rab5 GDP/GTP exchange factor 0 132.32 0.00043017 45300000 91810 88417 62727 66629 83153 81837 76438 90979 92034 FALSE TRUE 79677.07588 87836.18291 93061.98701 81758.13281 81498.41799 84985.32235 69025.05453 71523.84885 81153.84537 0.98180284 1.082341601 1.146735396 1.007446196 1.004245919 1.047212513 0.850545704 0.881336535 1 16.30837184 2.251548767 24.96254576 0.902021748 1.047732874 0.531817924 0.059196323 158.1243695 303906.6565 0.022710835 0.017479735 178.4632375 -2.251548767 0.145711125 QIQEEEDEKQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QIQEEEDEKQR 11 1 A0A087WV26;O43805 A0A087WV26 SSNA1 Sjoegren syndrome nuclear autoantigen 1 0 117.2 0.0008086 452670000 196850 183660 112470 136870 154330 154780 190390 225750 154080 FALSE TRUE 170835.7737 182453.5254 166860.8682 167948.4254 151259.1349 160734.4868 171926.0071 177475.1193 135864.8379 1.257395043 1.34290467 1.22813872 1.23614342 1.113305968 1.183046984 1.26541944 1.306262327 1 17.05181261 4.058019408 4.244368378 1.200616656 1.299932423 0.213081086 0.087334953 0.360941065 13.35446688 0.023069073 0.050397024 11429.29409 -4.058019408 0.099315767 QIQELVEAIVLPMNHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QIQELVEAIVLPMNHK 16 0 P17980;E9PM69;R4GNH3;E9PN50;E9PMD8 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ; 146.78 7.71E-06 172810000 632260 572750 350280 465420 544590 472420 617880 715140 694060 FALSE TRUE 548705.2391 568987.5675 519676.5796 571100.7245 533753.7245 490594.3031 557958.0927 562212.8762 612009.0175 0.896563978 0.929704549 0.849132226 0.933157369 0.872133758 0.801612867 0.911682797 0.918634955 1 19.22319338 1.249235978 1.81255916 1.03849558 0.883341765 0.471511369 0.038698867 0.808781858 2.552935137 0.217938762 0.010794701 17.75153764 -1.249235978 -0.155153815 QIS(ph)EETESVDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QISEETESVDNR 12 0 P46934-4;H0Y8X6;P46934-3;P46934-2;P46934 P46934-4 NEDD4 E3 ubiquitin-protein ligase NEDD4 1 QIS(0.999)EET(0.001)ESVDNR 130.27 0.00023023 75398000 59741 47361 30935 49341 55587 41687 61177 56264 55809 TRUE FALSE 51846.07549 47049.88247 45895.26947 60544.62818 54480.92745 43290.72587 55244.06396 44232.38145 49211.3236 1.053539545 0.956078379 0.932616035 1.230298715 1.107081124 0.879690338 1.12258846 0.898825275 1 15.5867027 1.712168835 14.21756358 0.950028574 1.036585424 0.115873271 0.10392823 0.299782427 138.1151596 0.056022223 0.026657614 51.54289819 -1.712168835 0.08655685 QIS(ph)LPDLSQEEPQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QISLPDLSQEEPQLK 15 0 H0YBZ4;Q15390-2;Q15390 H0YBZ4 MTFR1 Mitochondrial fission regulator 1 1 QIS(0.981)LPDLS(0.019)QEEPQLK;QIS(1)LPDLSQEEPQLK 237.73 1.00E-17 214090000 763020 514270 317978 446230 460340 486110 504880 623080 565010 TRUE FALSE 662184.9738 510891.7265 471753.2244 547553.3417 451180.1346 504810.9663 455916.8153 489839.1908 498215.1615 1.329114457 1.025443957 0.946886528 1.099029865 0.905592944 1.013238868 0.915100243 0.983188045 1 18.9264094 4.734883767 3.504360788 0.97990464 1.370055315 0.799868718 0.054364337 0.113735325 2.460303271 0.012451015 0.117137559 54310.4958 -4.734883767 0.390150676 QIS(ph)QDVK ddPTM_MDA-MB-175_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 110.39 0.0071486 1335870000 3511060 3232300 2173950 2818510 2742300 1900010 4632300 4083070 4347100 TRUE FALSE 3047064.525 3211066.808 3225279.491 3458495.774 2687733.595 1973104.614 4183060.259 3209937.255 3833190.79 0.794915957 0.837700752 0.841408547 0.902249839 0.701173968 0.514742084 1.09127369 0.837406075 1 21.87011438 2.209259634 24.9999752 0.952099154 0.775413564 0.394308483 0.121556025 255.981161 218404.6404 0.0508005 0.034255629 161.9047664 -2.209259634 -0.17668559 QIS(ph)QDVKLEPDILLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 109.03 0.00062528 59867000 102700 110520 36251 38838 82791 53177 140080 113690 8177.4 TRUE FALSE 89127.93479 109793.9868 53782.10485 47656.7615 81143.62108 55222.7536 126495.0632 89378.27824 7210.677088 12.36055002 15.2265849 7.458676099 6.609193689 11.25325959 7.658469923 17.54274413 12.39526845 1 12.81591902 4.246675142 24.99730243 9.806287301 13.79356785 0.15215065 4.35447316 391.4930718 1205991.135 1.110301867 2.830334376 17647.17295 -4.246675142 3.987280551 QISSLRDEVEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QISSLRDEVEAK 12 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 159 5.99E-05 1497070000 1165530 1263520 1093240 920450 921500 944080 1115790 1147510 966010 FALSE TRUE 1011502.257 1255219.854 1621934.521 1129452.241 903163.9529 980399.3685 1007580.858 902123.9164 851809.3983 1.187474873 1.473592398 1.904104984 1.325944798 1.060288786 1.150960967 1.182871262 1.059067813 1 19.70017112 3.449649685 5.378753695 1.101425073 1.532806754 0.552170005 0.177866551 0.131304102 10.5644197 0.051892176 0.069272024 2816.110458 -3.449649685 0.43138168 QIT(ph)MEELVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QITMEELVR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 QIT(1)MEELVR;QIT(1)MEELVR;QIT(1)MEELVR;QIT(1)MEELVR;QIT(1)MEELVR 171.26 0.00063812 1508585000 1728570 1381270 744096 1100981 1227760 956379 1446260 1466350 1871990 TRUE FALSE 1500135.095 1372196.346 1103943.314 1350975.563 1203329.978 993171.519 1306001.928 1152782.464 1650685.475 0.908795236 0.831288799 0.668778717 0.81843306 0.728988046 0.601672174 0.791187629 0.69836591 1 20.65463382 4.460364707 6.675772693 0.749879144 0.890946029 0.176485541 0.1059044 0.200569298 38.58963911 0.025027785 0.072176102 28864.5444 -4.460364707 0.141066885 QIT(ph)QEEDDSDEEVAPENFFSLPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QITQEEDDSDEEVAPENFFSLPEK 24 0 Q92733 Q92733 PRCC Proline-rich protein PRCC 1 QIT(0.794)QEEDDS(0.206)DEEVAPENFFSLPEK 95.138 0.026295 189500000 98250 82994 56125 53414 73393 97093 77413 76780 71220 TRUE FALSE 85266.01357 82448.80695 83267.23773 65542.46508 71932.62289 100828.2305 69905.49918 60361.1945 62800.45273 1.357729281 1.312869627 1.32590187 1.043662302 1.145415674 1.605533498 1.113136867 0.961158588 1 15.93848734 2.006934611 24.9994782 0.995607702 1.288327371 0.459337834 0.144891262 148.717079 536126.9952 0.060470328 0.040665155 101.6095694 -2.006934611 0.29271967 QITQEEDDS(ph)DEEVAPENFFSLPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QITQEEDDSDEEVAPENFFSLPEK 24 0 Q92733 Q92733 PRCC Proline-rich protein PRCC 1 QIT(0.16)QEEDDS(0.84)DEEVAPENFFSLPEK;QIT(0.072)QEEDDS(0.928)DEEVAPENFFSLPEK;QIT(0.325)QEEDDS(0.675)DEEVAPENFFSLPEK 123.43 7.28E-05 377550000 211902 186592 133366 153290 165794 154499 202764 240536 216531 TRUE FALSE 183898.6138 185366.2649 197862.2437 188096.8374 162495.0238 160442.6765 183099.9785 189099.2483 190932.9519 0.963158072 0.970844807 1.036291755 0.985146019 0.85105804 0.840308993 0.958975267 0.990396086 1 17.54270658 3.44150176 24.99835502 0.932417311 0.991930699 0.231096183 0.054749874 306.9784006 215441.509 0.01795432 0.023178999 2763.769122 -3.44150176 0.059513388 QITT(ph)SPITVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QITTSPITVR 10 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 QIT(0.058)T(0.47)S(0.47)PIT(0.002)VR 109.15 0.022999 418630000 700230 633960 401810 494870 605860 666040 622750 709270 649320 TRUE FALSE 607692.8313 629795.475 596126.66 607237.7971 593804.5713 691662.9898 562355.8009 557598.13 572558.1293 1.061364428 1.099967746 1.04116356 1.060569689 1.037107921 1.208022303 0.982181148 0.97387165 1 19.12706265 2.095796109 23.45717162 0.982736846 1.081402618 0.481405655 0.048501768 7.527846287 1835.320558 0.018993142 0.012805172 124.6798035 -2.095796109 0.098665772 QITTS(ph)PITVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QITTSPITVR 10 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 QIT(0.035)T(0.253)S(0.712)PITVR 114.87 0.0022836 954580000 1917400 1844100 1131100 1629500 1896800 2091200 1759300 2083700 2042200 TRUE FALSE 1664010.732 1831985.986 1678103.743 1999502.88 1859057.391 2171649.817 1588683.357 1638116.97 1800773.442 0.92405335 1.017332854 0.931879438 1.110357824 1.032366064 1.205953934 0.882222782 0.909674105 1 20.78018525 QITVNDLPVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QITVNDLPVGR 11 0 P32119;Q06830;A0A0A0MSI0;A0A0A0MRQ5 P32119;Q06830 PRDX2;PRDX1 Peroxiredoxin-2;Peroxiredoxin-1 0 ;;; 228.54 7.42E-12 1772530000 2156910 1959660 1098810 1442250 1840420 1972160 1783780 2008480 1948370 FALSE TRUE 1871868.879 1946786.864 1630198.191 1769734.906 1803799.243 2048030.271 1610789.29 1578982.182 1718035.918 1.089540014 1.133146778 0.948873172 1.030091913 1.049919401 1.192076516 0.937576027 0.919062381 1 20.71232877 2.174747028 24.99998579 0.944695824 1.067863564 0.423348528 0.066528541 59.50070837 23309.52095 0.027546955 0.018572158 149.536437 -2.174747028 0.12316774 QIYVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QIYVGR 6 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YAP2;H0YAW6 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ;;; 138.38 0.028678 1042030000 861830 830690 512938 539990 675190 835220 703040 730310 725140 FALSE TRUE 747936.9819 825233.1427 760996.5325 662602.9827 661755.04 867351.4539 634859.289 574138.8898 639414.7753 1.169721143 1.290606934 1.190145367 1.036264735 1.034938612 1.356477028 0.992875538 0.897913079 1 19.28639256 2.023707238 23.37436046 0.942783496 1.172323913 0.509119395 0.100499599 82.53480485 81375.22018 0.041769168 0.028158223 105.6105338 -2.023707238 0.229540416 QIYYSDKYDDEEFEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QIYYSDKYDDEEFEYR 16 1 P61024;Q5T179 P61024 CKS1B Cyclin-dependent kinases regulatory subunit 1;Cyclin-dependent kinases regulatory subunit 0 ;;;; 217.88 1.26E-14 2231820000 2178570 2312670 1664030 1789910 1856170 1563470 2373490 2542350 2577910 FALSE TRUE 1890666.455 2297477.918 2468760.474 2196336.423 1819235.849 1623617.703 2143309.305 1998688.237 2273152.417 0.831737652 1.010701219 1.086051448 0.966207284 0.800314064 0.714258178 0.942879716 0.879258347 1 21.11626299 3.373326682 7.20745362 0.867205888 0.987068145 0.224050607 0.097694562 0.325177981 19.99511831 0.029043541 0.037540789 2362.254484 -3.373326682 0.119862257 QKAEADKNDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 140.14 2.24E-05 6895890000 11370090 6931360 6727920 6992400 3547110 3413180 11324560 13120410 10366960 FALSE TRUE 9867503.798 6885827.44 9981564.616 8580131.292 3476529.451 3544487.243 10226305.91 10314712.42 9141389.799 1.079431467 0.753258267 1.091908871 0.938602497 0.380306444 0.387740521 1.118681747 1.128352762 1 23.12398209 QKDEEDKAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QKDEEDKAR 9 2 O00170 O00170 AIP AH receptor-interacting protein 0 ;;; 91.855 0.0058893 350561000 999561 643061 573898 615524 379361 487476 916052 1054054 673149 FALSE TRUE 867466.4813 638836.6899 851436.9924 755288.1319 371812.4583 506229.5172 827213.418 828652.7548 593570.0921 1.461438999 1.076261588 1.434433783 1.272449778 0.626400257 0.852855499 1.393623818 1.396048699 1 19.17905888 3.449558768 24.99976211 1.097229503 1.308296329 0.198518759 0.249710581 477.9299867 433491.0856 0.080429516 0.103836154 2815.520983 -3.449558768 0.211066826 QKDFLDGVYAFEYYPS(ph)TPGR ddPTM_MDA-MB-175_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(0.5)T(0.5)PGR 103.73 0.00017022 56456000 130760 149590 83120 93441 124140 118980 128580 133510 164030 TRUE FALSE 113479.7347 148607.3334 123317.11 114658.2072 121669.8569 123557.2376 116110.3314 104959.9255 144638.5603 0.784574559 1.027439247 0.852588064 0.792722266 0.841199308 0.854248254 0.802761941 0.725670425 1 17.1420927 4.013093646 24.96612996 0.823418583 0.914508606 0.078528266 0.090066314 401.0741763 764730.7652 0.021692561 0.045117537 10306.08325 -4.013093646 0.091090023 QKDFLDGVYAFEYYPST(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QKDFLDGVYAFEYYPSTPGR 20 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 1 QKDFLDGVYAFEYYPS(0.001)T(0.999)PGR;QKDFLDGVYAFEYYPS(0.001)T(0.999)PGR;QKDFLDGVYAFEYYPS(0.044)T(0.956)PGR;QKDFLDGVYAFEYYPS(0.289)T(0.711)PGR 276.65 2.41E-44 2467050000 4360320 4744920 2821810 3061280 3755070 3494880 4233590 4385420 4917370 TRUE FALSE 3784092.664 4713750.308 4186446.754 3756390.413 3680351.454 3629330.295 3823017.093 3447632.06 4336044.12 0.872706218 1.087108474 0.965499113 0.866317387 0.848780905 0.837014153 0.881683163 0.795110005 1 22.04794801 3.776331492 4.380734559 0.861315586 0.989329349 0.30066203 0.073106367 0.207128389 9.262358022 0.018481968 0.032084333 5974.911701 -3.776331492 0.128013763 QKDFLDGVYAFEYYPSTPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QKDFLDGVYAFEYYPSTPGR 20 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ; 212.39 1.62E-22 1520460000 2735800 2873700 1649910 1852510 2335900 2303500 2643200 2762300 2380300 FALSE TRUE 2374257.098 2854822.475 2447811.995 2273150.709 2289420.16 2392117.136 2386862.871 2171603.641 2098903.646 1.131189182 1.360149372 1.166233619 1.083018134 1.090769538 1.139698404 1.137195066 1.034637129 1 21.00120451 -1.999999962 0.071225226 0.076777303 1.59944192 0.446744922 0.071896444 494.0868252 3.372448957 80.39566571 15.84412904 0.010000001 1.999999962 1.522664616 QKDYDFEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QKDYDFEER 9 1 Q96NC0 Q96NC0 ZMAT2 Zinc finger matrin-type protein 2 0 72.006 0.042694 0 678030 531040 313050 412590 478290 415590 534870 671600 625180 FALSE TRUE 588426.6176 527551.5633 464442.0271 506274.8655 468772.9648 431578.0162 482998.3897 527983.5664 551271.9326 1.067398108 0.956971564 0.842491699 0.918375915 0.850347963 0.782876818 0.876152696 0.957755211 1 19.07240462 4.604266078 3.073091652 0.890937178 1.07312777 0.464151566 0.060962662 0.289111145 4.436053709 0.016719303 0.10565879 40203.70503 -4.604266078 0.182190592 QKEEEAR ddPTM_MDA-MB-175_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 ;;; 114.89 0.0052918 1139210000 2406750 1983270 1361840 1688180 1078193 1729320 2377600 2596410 2668370 FALSE TRUE 2088691.89 1970241.769 2020430.379 2071507.071 1056739.069 1795848.059 2147020.718 2041187.927 2352918.338 0.887702669 0.837360879 0.858691246 0.880399051 0.449118463 0.763242833 0.912492662 0.867513289 1 21.16601982 2.235134089 24.31975107 0.913753998 0.775232493 0.221130811 0.129360447 107.2475668 761168.9847 0.053895903 0.038021723 171.8438876 -2.235134089 -0.138521505 QKEELQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QKEELQR 7 1 P80303-2;P80303;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 ;; 90.657 0.015484 777640000 1147700 1119300 704199 864710 999270 1126890 1125850 1279930 1197930 FALSE TRUE 996028.5371 1111947.245 1044751.992 1061055.622 979386.482 1170242.187 1016665.24 1006226.93 1056312.08 0.942930177 1.05266925 0.989056181 1.004490663 0.927175312 1.107856484 0.962466736 0.952584893 1 20.0106047 QKEIEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QKEIEER 7 1 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 0 ;;; 94.302 0.013042 872110000 2246910 1970190 1221000 1534560 1607910 1790500 2160560 2460960 2051600 FALSE TRUE 1949975.151 1957247.692 1811479.684 1883005.302 1575915.737 1859381.694 1951029.224 1934702.855 1809062.185 1.077892826 1.081912887 1.001336327 1.040873729 0.871123033 1.027815245 1.078475488 1.069450719 1 20.78681057 4.246985247 24.44086472 1.01779913 1.079902904 0.190354522 0.056854649 269.8364353 782803.9964 0.015283768 0.039006357 17659.7783 -4.246985247 0.062103774 QKETS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QKETSPR 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QKET(0.011)S(0.989)PR;QKET(0.001)S(0.999)PR;QKET(0.096)S(0.904)PR 109.15 0.018661 602790000 2734740 2116290 1389100 1784760 1391250 1857160 2512300 2926040 2717950 TRUE FALSE 2373337.18 2102387.952 2060873.406 2190017.036 1363566.847 1928606.147 2268657.533 2300329.116 2396637.047 0.990278099 0.877224173 0.859902174 0.913787525 0.568950083 0.804713483 0.946600377 0.959815388 1 21.19258001 2.159745362 5.326579733 0.96936947 0.830388205 0.251403617 0.108426628 0.30006815 14.70653841 0.047450557 0.031729926 144.459252 -2.159745362 -0.138981265 QKFDNLYCCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QKFDNLYCCR 10 1 O43865-2;O43865;H0Y8B3;Q96HN2-4;Q96HN2-3;Q96HN2-2;Q96HN2 O43865-2 AHCYL1;AHCYL2 Putative adenosylhomocysteinase 2;Adenosylhomocysteinase;Putative adenosylhomocysteinase 3 0 116.55 0.00098122 705120000 696880 727230 384560 529290 668570 550930 747260 773810 629420 FALSE TRUE 604785.5423 722452.7782 570534.5023 649473.3842 655266.765 572124.6336 674790.8402 608336.7533 555010.6846 1.089682702 1.301691658 1.027970304 1.170199786 1.180638109 1.03083535 1.215815945 1.096081157 1 19.08215602 1.34051541 3.466937128 0.993977262 1.145266358 0.236749376 0.082665932 0.357482265 6.188200518 0.120565169 0.019494643 21.90359547 -1.34051541 0.151289096 QKFNDS(ph)EGDDTEETEDYR ddPTM_MDA-MB-175_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(1)EGDDTEETEDYR;QKFNDS(1)EGDDTEETEDYR 304.56 4.13E-50 19352640000 13418030 9691720 7157540 8003430 9824240 8575200 11087480 12968540 10496600 TRUE FALSE 11644803.34 9628054.453 10618950.28 9820731.106 9628756.845 8905093.493 10012217.9 10195318.64 9255703.906 1.258121852 1.040229306 1.147287164 1.061046378 1.040305194 0.96211953 1.081734895 1.101517372 1 23.14191128 7.62804642 1.14284258 1.052805534 199.9999953 0.588492333 0.052572732 1182.545174 1.958803419 0.015368918 616255.0161 42466495.24 -7.62804642 198.9471897 QKIDDRDS(ph)DEEGASDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QKIDDRDSDEEGASDR 16 2 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 QKIDDRDS(1)DEEGASDR;QKIDDRDS(0.999)DEEGAS(0.001)DR;QKIDDRDS(1)DEEGASDR 114.72 0.00029292 1299330000 1375941 1159165 621634 792834 1134770 1039216 1463951 1302113 1245147 TRUE FALSE 1194106.911 1151550.369 922258.2816 972859.0774 1112190.297 1079195.312 1321977.257 1023666.268 1097947.14 1.087581421 1.04882132 0.839984229 0.886070961 1.012972534 0.98292101 1.204044538 0.932345675 1 20.06637717 2.832103468 2.945429378 1.031957256 0.963063312 0.079867377 0.098711229 0.72015231 12.12471513 0.035747713 0.035252381 679.3654676 -2.832103468 -0.068893944 QKIPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QKIPAR 6 1 A0A3B3ISL2;A0A3B3IRU6;Q9GZU2-2;Q9GZU2-4;Q9GZU2 A0A3B3ISL2 PEG3 Paternally-expressed gene 3 protein 0 ;; 92.075 0.043018 3868380000 3667790 3589960 1898590 2600910 2861830 2791910 4498070 3998250 3771210 FALSE TRUE 3183082.259 3566377.316 2816754.474 3191486.368 2804885.182 2899316.584 4061847.864 3143255.352 3325381.85 0.957208045 1.072471517 0.847046926 0.959735306 0.843477624 0.871874785 1.221468104 0.945231403 1 21.66508858 QKLDILDQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QKLDILDQER 10 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;;; 176.78 2.19E-06 2197130000 4914000 4482470 3051770 3992850 4559890 4379030 4834940 5599590 5325820 FALSE TRUE 4264602.45 4453024.359 4527616.18 4899487.619 4469157.11 4547494.118 4366048.263 4402161.255 4696207.627 0.908094954 0.948217096 0.964100512 1.043285989 0.951652368 0.968333276 0.9296966 0.93738642 1 22.16306476 4.644472007 2.57717952 0.967044749 0.902131086 0.271639259 0.032363613 0.611579015 5.973151697 0.008757792 0.07802165 44103.39348 -4.644472007 -0.064913663 QKLDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QKLDPK 6 1 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 0 ; 95.793 0.039163 1314720000 1763830 1518400 1197200 1361650 1038330 1098240 1906740 2124030 1934450 FALSE TRUE 1530735.397 1508425.53 1776169.924 1670833.444 1017669.264 1140490.003 1721824.648 1669822.714 1705761.525 0.897391209 0.884312085 1.041276813 0.979523468 0.596606999 0.668610463 1.009416981 0.978930929 1 20.70198453 QKLDSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QKLDSQR 7 1 O15371-2;O15371;O15371-3 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ; 82.75 0.021562 213550000 784220 879130 461160 541960 727630 1045470 815290 853040 725780 FALSE TRUE 680583.34 873354.9371 684178.5185 665020.3013 713151.5866 1085689.907 736223.3013 670624.0344 639979.1152 1.063446172 1.364661622 1.069063821 1.03912813 1.114335718 1.69644584 1.150386448 1.047884249 1 19.2876653 1.778050017 4.068896594 1.022251033 1.224399092 0.1455613 0.195109712 0.394935519 12.84340898 0.123961585 0.053443968 59.98601578 -1.778050017 0.202148059 QKLEEDAEMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QKLEEDAEMK 10 1 P05455 P05455 SSB Lupus La protein 0 ; 103.75 0.0025289 675360000 1586990 1062490 897600 914690 930930 685480 1402890 1553710 1181780 FALSE TRUE 1377265.251 1055510.433 1331682.362 1122384.345 912406.3143 711850.8592 1266837.944 1221461.207 1042071.315 1.321661225 1.012896544 1.277918645 1.07707057 0.875569936 0.683111462 1.215692176 1.172147424 1 19.99102258 7.999976277 0.760805585 1.030685267 52.35089672 0.216967715 0.170446236 787.9999211 3.251693976 0.068019819 69396.88615 99994537.77 -7.999976277 51.32021146 QKLETQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QKLETQEK 8 1 O43633;M0R1L7;M0QXX8 O43633 CHMP2A Charged multivesicular body protein 2a 0 85.533 0.015208 3759000000 280350 247270 183120 251330 204350 212180 349420 405940 345320 FALSE TRUE 243301.0372 245645.6671 271677.4445 308398.3178 200283.8348 220342.7019 315533.3022 319132.89 304496.663 0.799026941 0.806726959 0.892218134 1.012813457 0.657753792 0.723629283 1.036245518 1.048066954 1 18.21606689 2.222239132 24.99953267 1.032602394 0.820273554 0.530431312 0.094251859 198.109972 303441.6573 0.040611444 0.027471473 166.8165487 -2.222239132 -0.21232884 QKLYTLQDK ddPTM_MDA-MB-175_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 ; 104.82 0.0029162 2829700000 3490300 3474900 1795840 1757360 2888300 2720700 4157200 3941300 832100 FALSE TRUE 3029048.012 3452073.153 2664314.231 2156395.448 2830828.481 2825367.09 3754035.384 3098483.666 733730.0859 4.128286505 4.704827046 3.631191199 2.938949198 3.858133304 3.850689979 5.116371069 4.222920289 1 19.48488992 4.226135306 24.3552291 3.669085381 4.416556734 0.096290669 1.069519098 405.3066119 794460.1086 0.276306 0.582107863 16831.98387 -4.226135306 0.747471353 QKPITPETAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QKPITPETAEK 11 1 A0A590UJK8;P60953-1;P60953 A0A590UJK8 CDC42 Cell division control protein 42 homolog 0 ; 155.02 2.89E-05 355510000 618770 591690 435950 549940 539640 364090 686960 890560 808380 FALSE TRUE 536997.9767 587803.1494 646776.8782 674812.2823 528902.2198 378096.7779 620338.7249 700120.6743 712814.2373 0.753349118 0.824623189 0.907356846 0.946687436 0.741991661 0.530428207 0.870267024 0.982192327 1 19.44316663 1.848175334 4.023977067 0.988156922 0.791112506 0.359011587 0.111907755 0.270804055 7.017138189 0.070668462 0.032870715 70.49776255 -1.848175334 -0.197044417 QKPQAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 QKPQAER 7 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;;;;; 116.37 0.0049893 7116690000 5797100 5097630 3010760 4204420 2903990 4336130 5669910 5995270 6152150 FALSE TRUE 5030998.547 5064143.333 4466773.606 5159097.822 2846206.281 4502943.727 5120043.001 4713228.166 5424849.836 0.927398675 0.933508482 0.823391198 0.951012098 0.524660842 0.830058686 0.943812853 0.868821868 1 22.37115177 1.112512876 1.21567676 1.10098459 0.836855898 0.131931228 0.123909924 4.468489614 4.549090335 1.623941619 0.039280326 12.95725113 -1.112512876 -0.264128691 QKS(ph)AEPS(ph)PTVMSTSLGSNLSELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QKSAEPSPTVMSTSLGSNLSELDR 24 1 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 2 QKS(0.996)AEPS(0.949)PT(0.052)VMS(0.001)T(0.001)S(0.001)LGSNLSELDR;QKS(1)AEPS(0.889)PT(0.111)VMSTSLGSNLSELDR;QKS(0.997)AEPS(0.932)PT(0.07)VMS(0.001)TSLGSNLSELDR 99.372 0.0027696 449082000 201188 197615 144963 166382 235105 196658 250850 309775 224879 TRUE FALSE 174600.4961 196316.8541 215067.5917 204161.5761 230426.8705 204223.5605 226522.6056 243532.0269 198294.0608 0.880512988 0.990028916 1.084589174 1.02958997 1.162046254 1.029902558 1.142356986 1.228135759 1 17.59728194 6.02056827 0.542802544 1.13162426 3.21E-19 0.518119606 0.068878232 11.57484921 0.908834182 0.038924043 11.20440771 1048499.603 -6.02056827 -1.13162426 QKS(ph)DAEEDGGT(ph)VSQEEEDRKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 2 QKS(1)DAEEDGGT(0.575)VS(0.425)QEEEDRKPK 141.78 2.27E-07 1038300000 1213100 722300 1029000 954830 986460 740000 1072700 2051600 1362900 TRUE FALSE 1052785.761 717555.1637 1526627.842 1171638.745 966831.376 768468.2788 968669.7191 1612881.306 1201779.515 0.876022389 0.597077213 1.270306095 0.974919884 0.804499797 0.639441985 0.806029482 1.342077549 1 20.1967408 1.751254669 25 1.18030932 0.853504934 0.302142749 0.201076498 4.299144901 8483.676894 0.108380109 0.052045431 56.39682683 -1.751254669 -0.326804386 RHT(ph)MDKDSR ddPTM_MDA-MB-175_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 152.4 0.0038394 485397000 589920 891257 1007110 1160560 1350430 1644340 1740460 1895320 1985530 TRUE FALSE 511960.5773 885402.2741 1494151.765 1424082.886 1323559.085 1707598.824 1571670.457 1490020.567 1750802.905 0.292414741 0.505712134 0.853409461 0.813388464 0.755972635 0.975323275 0.897685543 0.85104986 1 20.73958525 4.438361608 1.757188451 0.883032429 0.234706637 0.888714751 0.07248189 0.156192365 0.742529046 0.019912134 0.139919705 27438.57851 -4.438361608 -0.648325792 down QKS(ph)DAEEDGGTVS(ph)QEEEDRKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 2 QKS(1)DAEEDGGT(0.014)VS(0.986)QEEEDRKPK;QKS(1)DAEEDGGT(0.251)VS(0.749)QEEEDRKPK;QKS(1)DAEEDGGT(0.25)VS(0.75)QEEEDRKPK;QKS(1)DAEEDGGT(0.213)VS(0.787)QEEEDRKPK 193.05 1.23E-17 2092950000 1669350 910210 1251770 1193874 1234075 898817 1384000 2643380 1645400 TRUE FALSE 1448741.168 904230.7706 1857130.159 1464961.339 1209519.322 933395.0716 1249779.893 2078113.758 1450882.686 0.998523989 0.623228038 1.280000221 1.009703508 0.833643776 0.643329113 0.861392795 1.432309984 1 20.46849944 1.757251046 25 1.234514759 0.889975446 0.283896693 0.213003884 8.793991918 11777.29337 0.11233335 0.053944751 57.18090777 -1.757251046 -0.344539313 QKS(ph)DAEEDGGTVSQEEEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QKSDAEEDGGTVSQEEEDR 19 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 QKS(1)DAEEDGGTVSQEEEDR;QKS(1)DAEEDGGTVSQEEEDR;QKS(1)DAEEDGGTVSQEEEDR 227.58 7.49E-20 3000210000 838550 554631 641762 822680 845910 747740 551670 998030 1952990 TRUE FALSE 727733.4929 550987.5924 952120.2498 1009482.068 829078.046 776506.0417 498169.1283 784609.0512 1722109.747 0.422582529 0.319949175 0.552880124 0.586189161 0.481431597 0.450903924 0.289278386 0.455609204 1 20.71574566 1.239750399 7.942941133 1.006916212 0.442781921 0.788884815 0.090269666 0.043525282 24.03877493 0.133930946 0.023605283 17.36802353 -1.239750399 -0.564134291 QKS(ph)DAEEDGGTVSQEEEDRKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 QKS(1)DAEEDGGTVSQEEEDRKPK;QKS(1)DAEEDGGTVSQEEEDRKPK;QKS(1)DAEEDGGTVSQEEEDRKPK 197.36 1.11E-21 1589680000 1777430 950200 1151820 1151830 1109710 806560 1216130 2204590 1317630 TRUE FALSE 1542538.122 943958.0736 1708844.005 1413370.606 1087628.942 837588.8851 1098189.9 1733155.585 1161861.282 1.327643967 0.812453335 1.470781435 1.216471043 0.93610912 0.720902657 0.945198808 1.491706119 1 20.1480064 5.10864422 18.73315004 1.1003614 25.97830495 0.080223199 0.256439247 869.5901743 149919.053 0.063371888 132.3489327 128423.4166 -5.10864422 24.87794355 QKS(ph)EEPSVSIPFLQTALLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QKSEEPSVSIPFLQTALLR 19 1 Q5SW79;H0Y2V6;H0YB66 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 QKS(1)EEPSVSIPFLQTALLR 88.239 0.0015675 100400000 367750 158310 99629 132490 162510 109150 268770 241570 186570 TRUE FALSE 319150.9057 157270.0512 147809.9176 162573.8795 159276.3689 113349.0711 242704.7268 189912.1354 164513.9071 1.939963078 0.955968124 0.898464575 0.988207516 0.968163554 0.688993855 1.47528395 1.154383472 1 17.32785002 4.74152738 24.65248149 1.032222151 1.939963484 0.677672322 0.199949348 148.6087987 1234796.141 0.051105808 0.348529836 55147.69689 -4.74152738 0.907741332 QKS(ph)PAQSDSTTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QKSPAQSDSTTQR 13 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 QKS(1)PAQSDSTTQR 189.77 3.01E-06 195750000 72487 54464 40699 45541 61294 58760 71439 75741 69149 TRUE FALSE 62907.65929 54106.2224 60381.17253 55881.7801 60074.36932 61020.53522 64510.85678 59544.37657 60974.28399 1.031708044 0.887361341 0.99027276 0.91648112 0.985241078 1.000758537 1.058001055 0.976549008 1 15.89591329 3.018554145 6.944737033 1.006827455 0.953417186 0.244004838 0.043254132 0.207450549 43.24873273 0.012257507 0.013643602 1043.64824 -3.018554145 -0.053410269 QKS(ph)PEIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 QKSPEIHR 8 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR;QKS(1)PEIHR 128.36 0.00068842 63156880000 18378583 12942571 10065137 11753271 12727380 11968584 15643491 17220582 18508774 TRUE FALSE 15949806.69 12857550.4 14932670.92 14422030.82 12474130.04 12429023.17 14126387.65 13538094.55 16320687.82 0.977275398 0.787806895 0.914953529 0.883665626 0.764313991 0.761550206 0.865550999 0.829505147 1 23.96019852 4.756807175 23.64224559 0.847456624 0.977275634 0.228341938 0.072752832 2856.376077 3700907.085 0.01742935 0.519678058 57122.49592 -4.756807175 0.12981901 QKS(ph)PEIHRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 QKSPEIHRR 9 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 QKS(1)PEIHRR;QKS(1)PEIHRR;QKS(1)PEIHRR;QKS(1)PEIHRR;QKS(1)PEIHRR;QKS(1)PEIHRR;QKS(1)PEIHRR 136.53 9.92E-05 9178980000 6138760 4156270 2162023 2473775 3981930 3621990 5006130 5254270 1128779 TRUE FALSE 5327507.312 4128967.189 3207584.554 3035483.423 3902697.384 3761330.299 4520636.283 4130685.249 995336.0325 5.352471063 4.148314794 3.222614725 3.049707158 3.920984729 3.778955223 4.54181918 4.150040905 1 19.92482415 4.63544684 2.857485553 3.536052155 5.482694722 0.29083638 0.965754131 0.462043262 5.870688185 0.24213996 1.831651535 43196.32894 -4.63544684 1.946642567 QKSDAEEDGGTVS(ph)QEEEDRKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 QKSDAEEDGGT(0.124)VS(0.876)QEEEDRKPK;QKSDAEEDGGT(0.006)VS(0.994)QEEEDRKPK;QKSDAEEDGGT(0.009)VS(0.991)QEEEDRKPK;QKSDAEEDGGT(0.008)VS(0.992)QEEEDRKPK 203.78 6.89E-22 1018510000 1177370 625520 754220 702470 737240 538800 834540 1510980 755780 TRUE FALSE 1021777.571 621410.9179 1118963.315 861976.5501 722570.3664 559527.9847 753606.4392 1187868.685 666432.5494 1.533204782 0.932443829 1.679034609 1.293419043 1.084236307 0.83958682 1.130806771 1.782428974 1 19.34609934 5.047107112 19.60323369 1.257060971 3.849367579 0.082436227 0.306765382 373.6581442 219998.92 0.074950048 16204.55357 111456.9392 -5.047107112 2.592306607 QKSQT(ph)PPRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QKSQTPPRR 9 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QKS(0.001)QT(0.999)PPRR 115.18 0.07237 169770000 166900 119770 66054 80893 108040 98967 136880 167590 34742 TRUE FALSE 144843.7421 118983.223 97997.93534 99260.99202 105890.2154 102774.3245 123605.3987 131752.1827 30634.84034 4.728072369 3.883918495 3.198904719 3.240134139 3.456529044 3.35481835 4.0347982 4.300730189 1 14.90288571 4.613730246 2.669059005 3.380636297 4.824714552 0.220365888 0.883152805 0.603297412 6.645091476 0.220243585 1.681902756 41089.4422 -4.613730246 1.444078256 QKT(ph)VDIDDAQILPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QKTVDIDDAQILPR 14 1 Q6GYQ0-2;A0A1B0GUI1;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5 Q6GYQ0-2 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 1 QKT(1)VDIDDAQILPR;QKT(1)VDIDDAQILPR;QKT(1)VDIDDAQILPR 241.8 3.02E-17 1003810000 1401010 1388880 842800 956630 1374730 945770 1639980 1605320 1439650 TRUE FALSE 1215862.979 1379756.356 1250380.899 1173847.463 1347375.563 982154.3839 1480934.992 1262034.811 1269456.217 0.957782523 1.086887706 0.984973631 0.924685268 1.061380097 0.77368118 1.16659005 0.99415387 1 20.27577921 QKVDDCER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QKVDDCER 8 1 Q9Y3P9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 0 90.108 0.012248 81032000 172900 138640 91435 111570 115940 126540 161620 171620 128930 FALSE TRUE 150050.8269 137729.2647 135653.2718 136903.6737 113633.0208 131408.0757 145946.1173 134920.3985 113688.0423 1.319847047 1.211466588 1.193206155 1.20420469 0.999516031 1.155865411 1.283742022 1.186759802 1 16.79472099 4.926657975 1.056945722 1.149024487 1.456763847 0.304952077 0.08663906 3.639905237 2.573442215 0.028056421 1.379606557 84461.3415 -4.926657975 0.30773936 QKVDDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QKVDDDR 7 1 Q13618;Q13618-2;Q13618-3;A0A087WTG3 Q13618 CUL3 Cullin-3 0 ; 77.282 0.035083 231970000 786340 626590 450180 596240 404480 514890 742640 831630 874610 FALSE TRUE 682423.1767 622473.889 667888.5538 731625.405 396431.6394 534698.1515 670618.8871 653792.3963 771214.6022 0.88486807 0.80713447 0.866021665 0.948666432 0.514035443 0.693319538 0.869561968 0.847743798 1 19.55677284 1.203294811 1.596373779 1.091464764 0.790511912 0.219457785 0.120721771 1.990901359 4.27916314 0.978275344 0.035972699 15.96962841 -1.203294811 -0.300952853 QKVDSLLENLEK ddPTM_MDA-MB-175_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 ; 187.97 8.94E-06 5365100000 6851000 4520300 3639600 4344900 4368200 4166700 4942600 7318100 6417500 FALSE TRUE 5945622.992 4490605.852 5399722.734 5331475.953 4281281.366 4326995.645 4463267.413 5753181.265 5658830.461 1.050680531 0.793557235 0.954211788 0.942151561 0.756566466 0.764644863 0.788726123 1.016673199 1 22.43207248 1.666549331 7.232826682 1.00867487 0.860418598 0.281176607 0.095219366 0.152455262 15.02616728 0.057296108 0.024721325 46.40334955 -1.666549331 -0.148256272 QKWDQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QKWDQK 6 1 O15371-2;O15371;B0QYA5;B0QYA6 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ; 92.925 0.042137 791560000 625860 514960 377810 435650 407340 358130 597260 664980 582050 FALSE TRUE 543151.0153 511577.1939 560520.1797 534570.991 399234.7309 371907.4928 539337.8171 522779.2019 513240.7121 1.058277339 0.996758795 1.09211948 1.04155999 0.777870347 0.724625861 1.050847691 1.018584827 1 18.96927609 3.426115335 24.9998064 0.926480565 1.047659843 0.28436934 0.103744403 167.2430078 81970.99072 0.033673377 0.04347215 2667.566991 -3.426115335 0.121179277 QKYNVR ddPTM_MDA-MB-175_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 ; 90.285 0.044874 1730310000 1179090 1328740 684600 659770 803400 786750 1270360 1016520 725170 FALSE TRUE 1023270.269 1320011.419 1015674.85 809580.8625 787413.9118 817016.7816 1147160.683 799145.1086 639441.2287 1.600256948 2.06432016 1.588378735 1.266075483 1.231409356 1.277704259 1.794004877 1.249755369 1 19.28645224 3.975042036 4.485877374 1.327765005 1.836132871 0.487765964 0.225228677 0.165007953 8.114287545 0.059930332 0.116984465 9441.522573 -3.975042036 0.508367865 QKYPEQQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QKYPEQQGR 9 1 A0A0G2JKR7;P28702;P28702-3 A0A0G2JKR7 RXRB Retinoic acid receptor RXR-beta 0 73.067 0.041014 17271000 32334 26422 18427 22054 23433 22328 28834 32465 27766 FALSE TRUE 28060.97998 26248.43214 27338.35883 27061.69777 22966.72915 23186.97261 26037.68312 25522.61239 24483.53511 1.146116353 1.072085057 1.116601778 1.105301896 0.938047918 0.947043493 1.063477272 1.042439839 1 14.57952426 3.293542533 13.56693363 1.006077632 1.107835123 0.637801389 0.041624802 1.013431584 248.8301446 0.013091138 0.016897608 1965.814493 -3.293542533 0.101757491 QLAAENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLAAENR 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 107.9 0.017157 395040000 674190 748080 488830 568720 532630 748730 661820 713850 935420 FALSE TRUE 585094.0833 743165.8132 725229.823 697856.5683 522031.7051 777534.1276 597636.7983 561198.7327 824835.7132 0.709346205 0.900986465 0.87924154 0.846055229 0.632891734 0.942653325 0.724552524 0.680376375 1 19.65374727 QLADKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLADKER 7 1 Q9Y3D0;J3KS95 Q9Y3D0 FAM96B Mitotic spindle-associated MMXD complex subunit MIP18 0 ; 104.44 0.0074343 274720000 1558300 1560740 935360 1231480 1258580 1416880 1583600 1943810 1455200 FALSE TRUE 1352366.707 1550487.396 1387703.225 1511106.356 1233536.72 1471388.29 1430022.716 1528141.358 1283167.914 1.053928089 1.208327748 1.081466587 1.177637268 0.961321357 1.146684136 1.114447065 1.190913007 1 20.29127854 5.262572646 0.005482881 0.640642777 1.597357349 0 0.081699169 700720.809 837.9912894 71046.33151 75226.78558 183051.2275 -5.262572646 0.956714572 QLAEAHAQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLAEAHAQAK 10 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 88.596 0.013163 127950000 855790 823580 546190 647270 717530 752840 883230 972010 847050 FALSE TRUE 742695.1832 818169.8488 810329.3109 794242.5464 703252.5568 781802.242 797574.4905 764153.2257 746912.714 0.994353382 1.095402225 1.084904964 1.063367287 0.941545838 1.046711654 1.067828242 1.023082365 1 19.51058013 QLAEDFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QLAEDFLR 8 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;; 152.89 0.0010467 1326179000 2551461 2611073 1635102 1961859 2569859 2811092 2417183 2787109 2772042 FALSE TRUE 2214278.964 2593920.69 2425842.796 2407329.071 2518723.834 2919236.528 2182764.965 2191107.43 2444334.353 0.905882193 1.061197167 0.992434932 0.984860794 1.030433431 1.194286913 0.892989522 0.896402502 1 21.22101021 QLAPIWDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLAPIWDK 8 0 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ; 157.68 0.0008679 1298820000 2610900 2182600 1733510 2057190 2172600 2350700 2264300 2257000 2011640 FALSE TRUE 2265862.95 2168262.357 2571841.234 2524306.432 2129369.511 2441132.95 2044708.535 1774358.114 1773826.211 1.27738723 1.222364594 1.449883432 1.42308554 1.200438632 1.376196233 1.152710746 1.000299862 1 20.75843324 1.984825854 2.704982822 1.000374247 1.325230791 0.737519887 0.080410167 0.138546645 1.920721713 0.050575945 0.02350583 96.56635843 -1.984825854 0.324856544 QLAQYHAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLAQYHAK 8 0 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 86.011 0.016336 626280000 659620 796200 463080 531320 658990 699270 746310 773080 854700 FALSE TRUE 572449.5457 790969.7098 687027.0369 651964.3267 645877.3883 726171.3694 673932.9711 607762.8581 753658.3397 0.759561084 1.049507009 0.91158951 0.865066161 0.856989639 0.963528606 0.894215503 0.806416948 1 19.52355112 3.988879347 24.92806202 0.888968847 0.923537571 0 0.087610257 2246.076212 5034845.467 0.021576817 0.040636203 9747.188101 -3.988879347 0.034568724 QLCAEHGISPEGIVEEFATEGTDR ddPTM_MDA-MB-175_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 ;; 206.46 8.60E-25 120803000 103430 107092 63302 87805 107469 119721 93027 110201 154043 FALSE TRUE 89761.46344 106388.5056 93915.05893 107742.4673 105330.5772 124326.7443 84005.25586 86635.37374 135832.212 0.660826045 0.783234728 0.691404914 0.793202626 0.775446233 0.915296471 0.618448707 0.637811698 1 17.05146612 4.747276777 22.88082534 0.760690271 0.660825876 0.074279029 0.116946112 1088.707287 2857751.898 0.028369409 0.303615165 55882.6223 -4.747276777 -0.099864395 QLDDKDEEINQQSQLVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLDDKDEEINQQSQLVEK 18 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 257.47 1.15E-30 471110000 342520 249260 239410 212730 226560 170910 365020 391700 324570 FALSE TRUE 297255.1142 247622.5946 355189.4768 261033.5979 222051.8993 177485.0183 329620.4166 307938.0032 286199.7044 1.038628306 0.865209121 1.24105466 0.912068021 0.775863482 0.620143961 1.151714735 1.075955001 1 18.12666266 QLDDLKVELSQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QLDDLKVELSQLR 13 1 P42766;F2Z388 P42766 RPL35 60S ribosomal protein L35 0 ;;; 167.88 2.84E-05 5060748000 4950120 4740790 2995949 3438140 4377360 3862340 5441740 5848600 2773690 FALSE TRUE 4295949.1 4709647.438 4444799.957 4218822.236 4290259.1 4010926.719 4914000.892 4597922.404 2445787.528 1.756468643 1.925615935 1.817328736 1.72493407 1.754142194 1.639932608 2.009169168 1.879935338 1 21.22186765 1.235985368 24.99992435 0.999998919 1.819318486 0.854246873 0.105570749 26.25316244 254806.1789 0.178027538 0.026858006 17.21810563 -1.235985368 0.819319568 QLDMILDEQRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLDMILDEQRR 11 1 P49257 P49257 LMAN1 Protein ERGIC-53 0 ; 100.07 0.0068987 432040000 705730 695610 305600 405130 654780 585080 705840 708840 502380 FALSE TRUE 612465.9924 691040.4921 453389.1822 497120.9585 641751.1591 607588.4062 637387.7454 557260.0822 442989.2087 1.382575423 1.559948817 1.02347681 1.122196543 1.448683504 1.371564802 1.438833572 1.257954079 1 18.75691203 1.273858076 3.549498191 0.967033473 1.330433256 0.309351185 0.156642205 0.352398722 6.641093895 0.325526455 0.041637769 18.78702772 -1.273858076 0.363399783 QLDWRPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLDWRPER 8 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 67.563 0.0536 561050000 1395800 1276400 820120 997340 1263800 1326100 1231700 1369100 1347700 FALSE TRUE 1211341.493 1268015.244 1216732.775 1223801.29 1238652.853 1377115.925 1112249.924 1076328.619 1188376.441 1.019324729 1.067014795 1.023861407 1.029809451 1.042306806 1.158821294 0.935940738 0.905713528 1 20.18056048 2.189651892 24.99499687 0.938101078 1.053927681 0.557056015 0.045798022 75.8003501 38737.46618 0.018293572 0.012333547 154.7575665 -2.189651892 0.115826603 QLEAIDQLHLEYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QLEAIDQLHLEYAK 14 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ;;; 184.99 1.23E-06 2718950000 3232610 2574920 2286490 3478120 2149350 2215480 2310660 3049230 9345000 FALSE TRUE 2805412.398 2558005.181 3392244.212 4267880.306 2106582.14 2300710.949 2086572.549 2397175.894 8240244.746 0.340452557 0.310428302 0.411667895 0.517931255 0.255645579 0.279204201 0.253217303 0.290910764 1 22.97425576 1.23651454 24.99441404 1.000000855 0.330295058 0.872269793 0.080278486 19.45107913 237548.1901 0.134901984 0.021167915 17.23909805 -1.23651454 -0.669705798 QLEDTVALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLEDTVALR 9 0 Q9Y5S2 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 0 93.267 0.0095148 137530000 249950 256170 113940 142300 257300 335870 155250 208570 98524 FALSE TRUE 216918.4742 254487.2024 169041.7651 174611.3899 252180.2334 348791.1362 140193.8789 163968.9286 86876.60496 2.496857172 2.929294976 1.945768544 2.009878148 2.902740427 4.014787829 1.613712679 1.88737726 1 16.4066801 4.242751309 24.99723283 2.221043328 2.713076079 0.065480234 0.807412144 352.2987976 2101364.789 0.215332487 0.528932241 17488.44957 -4.242751309 0.492032751 QLEEAEEEAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QLEEAEEEAQR 11 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 355.77 1.09E-70 5154180000 2874420 2715090 1791290 2063450 2730400 2953020 2697000 2880700 3014170 FALSE TRUE 2494558.114 2697254.395 2657563.836 2531987.86 2676070.382 3066624.59 2435445.355 2264684.723 2657838.256 0.938566562 1.014830149 0.99989675 0.95264934 1.006859757 1.153804067 0.916325645 0.852077705 1 21.34182188 2.038489484 24.99981597 0.90609113 1.010174442 0.266247305 0.067446205 171.9689942 111697.1731 0.027256279 0.018376141 109.267117 -2.038489484 0.104083312 QLEEEDGSRDSPLFDFIESCLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLEEEDGSRDSPLFDFIESCLR 22 1 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ; 128.88 2.24E-06 20566000 49339 40541 11646.1 12605 33659 35919 26960 38500 5211.7 FALSE TRUE 42818.72614 40274.6835 17278.19291 15467.15791 32989.25175 37300.82717 24345.42335 30267.07461 4595.578763 9.317374013 8.763789193 3.759742527 3.365660497 7.178475977 8.116676722 5.29757504 6.586129009 1 12.16603085 4.310579695 7.485051809 5.324413078 9.115847335 0.390818535 2.052947952 0.254368331 22.26624001 0.516722729 1.377240899 20444.65068 -4.310579695 3.791434258 QLEEPGAGTPS(ph)PVR ddPTM_MDA-MB-175_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;QLEEPGAGT(0.003)PS(0.997)PVR 176.28 2.36E-06 442640000 561490 451110 273579 356730 423280 466590 456980 465590 477580 TRUE FALSE 487287.6739 448146.6287 405882.7195 437730.9988 414857.5561 484540.0192 412662.1499 366027.2017 421121.0365 1.157120238 1.064175356 0.963814876 1.039442253 0.985126651 1.150595618 0.979913408 0.869173397 1 18.68387542 5.99057053 0.029922889 1.68E-06 2.265223951 0.274848604 0.073593642 2372.774337 11.7787544 362.317656 546.6588445 978521.8549 -5.99057053 2.265222267 QLEEQLR ddPTM_MDA-MB-175_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 ; 113.5 0.014226 605770000 902060 781370 477980 610000 784620 773540 728620 817530 771490 FALSE TRUE 782850.4855 776237.129 709132.7267 748509.8233 769007.5971 803298.5843 657958.5445 642707.5715 680285.3311 1.150767847 1.141046401 1.042404847 1.100288054 1.130419196 1.180825968 0.967180262 0.944761767 1 19.37578046 2.223763597 24.96463243 0.965109982 1.120518878 0.780627487 0.038323311 105.45829 177921.3374 0.01630616 0.011045459 167.4031388 -2.223763597 0.155408896 QLEESVDALSEELVQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLEESVDALSEELVQLR 17 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 90.367 0.008887 17287000 19391 15979 7384.6 10429 10427 14149 14856 17238 10907 FALSE TRUE 16828.43022 15874.0329 10955.81726 12797.06385 10219.5231 14693.32119 13415.26741 13551.78785 9617.586885 1.749755986 1.650521392 1.13914409 1.330589887 1.062587032 1.527755492 1.394868335 1.40906321 1 13.23145924 4.342739672 5.851971152 1.291037995 1.722328389 0.543681442 0.164807548 0.153857874 7.313148942 0.040668355 0.110840649 22016.06364 -4.342739672 0.431290395 QLEGDCCSFITQLVNHFWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLEGDCCSFITQLVNHFWK 19 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 0 95.814 0.0013762 72900000 76736 78686 53131 55891 77462 69194 75422 74580 79659 FALSE TRUE 66595.14318 78169.10648 78825.32931 68581.90579 75920.65775 71855.93795 68107.58605 58631.64738 70241.80377 0.948084184 1.112857334 1.122199674 0.976368802 1.080847212 1.02297968 0.969616132 0.834711585 1 16.10004227 2.13449216 3.05176133 0.904988087 1.050592288 0.377276016 0.06743461 0.212333559 3.952426087 0.031460676 0.018760354 136.2988402 -2.13449216 0.145604202 QLEQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLEQER 6 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 108 0.071629 426380000 464350 437980 290100 377960 378420 480310 391500 467540 493110 FALSE TRUE 402984.971 435102.8805 430393.3303 463781.5948 370890.1824 498787.8365 353532.3903 367560.2094 434815.0976 0.926796179 1.000661851 0.989830695 1.066617966 0.852983681 1.147126306 0.813063742 0.845325315 1 18.73004251 2.203027293 24.99999923 0.874584377 0.993734174 0.247959927 0.09041012 217.3978866 152952.049 0.03435327 0.023161889 159.5979442 -2.203027293 0.119149797 QLFHPEQLITGK ddPTM_MDA-MB-175_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 ; 158.58 6.69E-05 18499200000 12590500 11360200 7035900 9379600 10461400 9849500 11063500 13324700 14875900 FALSE TRUE 10926633.52 11285574.1 10438484.77 11509381.54 10253238.61 10228416.64 9990563.473 10475316.6 13117288.05 0.83299486 0.860358792 0.795780708 0.877420813 0.781658417 0.779766107 0.761633307 0.798588592 1 23.64496614 1.236592724 24.9963562 1.000000242 0.809372568 0.725323248 0.036534401 29.05351947 368941.0354 0.059415557 0.009379889 17.2422018 -1.236592724 -0.190627674 QLFHPEQLITGKEDAANNYAR ddPTM_MDA-MB-175_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 ; 225.23 1.73E-25 2154500000 2522300 2123320 562650 631320 1697240 1486660 2368800 2486200 67082 FALSE TRUE 2188971.664 2109371.771 834749.422 774670.8551 1663468.245 1543852.772 2139074.141 1954545.478 59151.64238 37.0061012 35.66040918 14.11202442 13.09635412 28.12209734 26.09991388 36.16254857 33.04296211 1 15.85213061 7.999999935 0.064425129 9.999999373 59.03419183 0.079370274 11.50607143 3433.73221 21.3556877 3862.041615 16821.9987 99999985.03 -7.999999935 49.03419246 QLGEAHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QLGEAHGR 8 0 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ;; 148.52 0.00051989 161877000 320267 301858 195680 226513 337887 329243 310432 325698 315220 FALSE TRUE 277942.9045 299875.0749 290311.5025 277946.2387 331163.7098 341909.1913 280326.3524 256050.0173 277955.0507 0.999956302 1.078861759 1.044454856 0.999968297 1.191429006 1.230088068 1.008531242 0.921192173 1 18.08449207 2.008522056 24.98911243 0.957935359 1.091150345 0.349257471 0.075602024 198.9215817 583292.6578 0.032805965 0.022078869 101.9816551 -2.008522056 0.133214987 QLHDDYFYHDEL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QLHDDYFYHDEL 12 0 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 ;;; 174.05 3.14E-05 1786970000 1791310 1778280 1276980 1496010 1797910 2427890 1708670 1633870 1497040 FALSE TRUE 1554583.845 1766598.362 1894531.799 1835701.936 1762135.109 2521292.499 1542963.446 1284479.615 1320061.637 1.177660044 1.338269602 1.435184348 1.39061835 1.334888508 1.90998089 1.168857123 0.973045182 1 20.33217386 2.008739594 24.99703255 1.01050333 1.430733522 0.500804934 0.186964803 148.6870075 425273.643 0.07608983 0.05121312 102.0327504 -2.008739594 0.420230191 QLHDEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLHDEAR 7 0 P18206;P18206-2 P18206 VCL Vinculin 0 95.531 0.013398 81379000 29835 27733 18324 17227 20083 29086 27342 29030 25794 FALSE TRUE 25892.22916 27550.8201 27185.54769 21138.65365 19683.38759 30204.95724 24690.37705 22822.16041 22744.6627 1.138387036 1.21130924 1.195249542 0.92938963 0.86540688 1.328001986 1.085545975 1.003407292 1 14.47324042 3.769166018 24.28200432 1.040229214 1.184614728 0.241991302 0.121861483 753.5295157 597839.0676 0.033381984 0.057808737 5877.139757 -3.769166018 0.144385514 QLHFQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLHFQEK 7 0 Q9Y6Y8;Q9Y6Y8-2 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 96.253 0.0249 0 379210 381060 259240 311480 368940 336380 387760 461360 449920 FALSE TRUE 329096.4377 378556.7918 384609.3311 382206.2947 361598.8158 349320.7563 350155.0949 362701.7543 396730.9702 0.829520412 0.95419017 0.969446199 0.963389106 0.911445899 0.880497825 0.882600859 0.914225966 1 18.5978015 2.013800234 0.00384772 1.685916188 0.164827221 0.037144124 0.049688237 386891.7408 711.4591793 141856.8133 139401.0921 103.2286466 -2.013800234 -1.521088967 QLHLEGASLELS(ph)DDDTESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QLHLEGASLELSDDDTESK 19 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 1 QLHLEGASLELS(1)DDDTESK;QLHLEGASLELS(1)DDDTESK;QLHLEGASLELS(1)DDDTESK 366.69 4.70E-108 1988400000 1284660 988720 778280 972860 968840 833060 1128060 1388610 1635890 TRUE FALSE 1114888.926 982225.0332 1154658.811 1193762.732 949561.9795 865108.3573 1018660.915 1091666.558 1442496.948 0.772888239 0.680920008 0.800458409 0.827566903 0.658276595 0.599729766 0.706178905 0.75678951 1 20.46013684 1.229790827 3.385405681 1.046803323 0.720034415 0.624949316 0.067399363 0.237812325 3.798357583 0.206620415 0.018511056 16.97425911 -1.229790827 -0.326768908 QLHLNQLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLHLNQLIR 9 0 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 162.97 6.34E-05 271320000 172890 212560 119940 127030 180100 185450 176030 199470 179410 FALSE TRUE 150042.1485 211163.6794 177943.3852 155874.103 176516.3624 192584.3815 158958.6377 156814.8928 158200.3542 0.948431179 1.334786388 1.124797641 0.985295538 1.115777289 1.217344819 1.004793185 0.991242362 1 17.2713933 2.130682669 9.178309903 0.996084248 1.124431737 0.224576747 0.107159147 0.392631901 30.82472298 0.042642567 0.028732269 135.1084989 -2.130682669 0.128347489 QLICDPSYIPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QLICDPSYIPDR 12 0 P31150 P31150 GDI1 Rab GDP dissociation inhibitor alpha 0 ;; 141.88 0.00014166 364103000 314237 288557 180100 202900 249746 275759 289250 271803 302407 FALSE TRUE 272709.7843 286661.4501 267196.9624 248971.5461 244776.5432 286367.6272 261198.5795 213680.0436 266656.789 1.022699573 1.075020258 1.002025725 0.933677883 0.917946039 1.073918381 0.979530956 0.801329846 1 18.02462453 7.999995535 0.110317388 0.790223028 1.603696646 0.175575909 0.073176155 356.9941563 3.573899452 3.711504147 44.58856494 99998971.94 -7.999995535 0.813473618 QLIVGVNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLIVGVNK 8 0 A0A2U3TZH3;Q05639;A0A2R8Y488;P68104;Q5VTE0;A0A087WV01 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 75.109 0.09129 494570000 796000 720860 511110 590620 671770 518040 919550 980310 863470 FALSE TRUE 690806.5832 716124.6232 758284.5056 724729.2981 658403.0913 537969.334 830372.1825 770678.3353 761391.5603 0.907294773 0.940547099 0.995919242 0.951848347 0.864736524 0.706560674 1.090598092 1.012197108 1 19.53827905 QLIYNYPEQLFGAAGVMAIEHADFAGVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLIYNYPEQLFGAAGVMAIEHADFAGVER 29 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 188.44 5.18E-18 91978000 42588 54729 29502 33161 37861 34650 39630 41052 64315 FALSE TRUE 36959.8879 54369.4816 43769.26588 40690.71188 37107.64017 35983.00792 35786.6887 32273.34927 56711.75397 0.651714774 0.958698643 0.771784733 0.717500501 0.654320094 0.634489421 0.631027718 0.569076902 1 15.79136016 3.704725964 2.897239103 0.674869257 0.814820801 0.077818038 0.137209811 0.47489873 7.96812671 0.037753337 0.064716241 5066.709024 -3.704725964 0.139951544 QLKDSEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLKDSEER 8 1 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2 A0A2R8Y430 GSS Glutathione synthetase 0 91.867 0.011111 101030000 397790 349860 143090 151350 279590 258550 361680 358120 75664 FALSE TRUE 345221.0436 347561.7466 212288.8026 185716.3307 274026.706 268496.5858 326604.3293 281538.8249 66719.08812 5.174247031 5.20932999 3.181830097 2.78355619 4.107171032 4.024284405 4.895215724 4.219764281 1 16.02581195 4.248337295 24.59739851 3.62295397 5.191789775 0.306361143 1.061971325 223.0284997 561108.6504 0.268363648 0.690713602 17714.84249 -4.248337295 1.568835804 QLKPWCWYCNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLKPWCWYCNR 11 1 J3QRS9;O43670-2;O43670;O43670-4;O43670-3 J3QRS9 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 ; 107.06 0.0020507 995890000 858120 843870 497940 532450 753740 589440 893820 872910 653980 FALSE TRUE 744717.2678 838326.5624 738745.4495 653350.9105 738742.0487 612116.1382 807137.474 686244.9895 576667.2294 1.291415967 1.453744065 1.281060223 1.132977352 1.281054326 1.061472036 1.399658994 1.190019052 1 19.13737951 7.999999997 0.031696389 5.15E-05 3.030636741 0.289573638 0.119230595 3947.186896 12.3809019 410.4117376 850.2007917 99999999.31 -7.999999997 3.0305852 QLLCGAAIGTHEDDKYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLLCGAAIGTHEDDKYR 17 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 189.9 1.98E-10 550500000 799020 783070 622400 685380 735240 544930 760880 850120 1230480 FALSE TRUE 693427.4825 777925.9616 923394.7218 841006.0044 720610.1625 565893.8097 687089.9747 668328.4536 1085014.056 0.639095391 0.716973165 0.851044018 0.7751107 0.664148228 0.521554358 0.633254446 0.615962945 1 20.0492823 3.228870468 24.11789007 0.665805141 0.751049069 0.031769822 0.133464011 345.4253131 859729.6134 0.040396996 0.04641887 1693.832525 -3.228870468 0.085243928 QLLDS(ph)DEEQEEDEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLLDSDEEQEEDEGR 15 0 Q9UNS1-2;Q9UNS1 Q9UNS1-2 TIMELESS Protein timeless homolog 1 QLLDS(1)DEEQEEDEGR;QLLDS(1)DEEQEEDEGR 432.06 1.58E-153 1546660000 530040 509400 326601 451590 499400 536430 472790 577400 536790 TRUE FALSE 459993.871 506053.7179 484546.336 554130.4116 489462.9171 557066.8092 426938.8986 453927.5033 473331.2977 0.971822217 1.069132171 1.023693845 1.170703087 1.034081033 1.176906771 0.901987468 0.959005892 1 18.85249079 2.222750963 24.99999799 0.952624042 1.074392177 0.425340109 0.066146238 218.5713471 345626.9349 0.025745778 0.017421715 167.0132637 -2.222750963 0.121768135 QLLEEELAR ddPTM_MDA-MB-175_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 ; 122.13 0.0013826 280410000 276540 266380 177030 199124 251870 279540 234080 256010 259560 FALSE TRUE 239994.5383 264630.1322 262642.3001 244338.1476 246858.2798 290294.0847 211378.9576 201264.2538 228875.1125 1.04858294 1.156220654 1.147535428 1.067561016 1.078571965 1.268351467 0.923555887 0.879362774 1 17.80420107 2.207336996 24.85537453 0.922411498 1.125016318 0.643631549 0.067659706 104.6611212 83314.09919 0.026602551 0.01793745 161.189592 -2.207336996 0.202604821 QLLEELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLLEELER 8 0 Q9NWB6;Q9NWB6-2;Q9NWB6-3 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 0 ; 157.2 0.00088571 148714000 330610 327770 195612 231480 301420 329870 299590 326030 299460 FALSE TRUE 286919.0508 325616.8573 290210.6175 284041.072 295422.3317 342560.3124 270535.8079 256311.0217 264058.1799 1.086575129 1.233125432 1.099040437 1.075676095 1.118777429 1.297291046 1.024531063 0.970661169 1 18.01049631 2.021123598 24.97515549 0.987543269 1.149162467 0.532276679 0.068463227 164.4477445 194431.3865 0.027472543 0.018520169 104.9841165 -2.021123598 0.161619198 QLLGHMEDLEGDAQSVLDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLLGHMEDLEGDAQSVLDAR 20 0 Q9NX46 Q9NX46 ADPRHL2 Poly(ADP-ribose) glycohydrolase ARH3 0 ; 257.73 3.14E-36 158219000 167953 130613 77903 100673 135466 147130 127321 144376 130522 FALSE TRUE 145757.5855 129754.9946 115577.1514 123532.3433 132770.4916 152790.1863 114973.429 113502.3159 115091.8379 1.266445894 1.127403967 1.00421675 1.073337134 1.153604757 1.327550147 0.99897118 0.9861891 1 16.812426 2.053758568 24.99997922 0.992248023 1.147615242 0.419667651 0.090134981 94.61968471 44001.59527 0.038572724 0.026005721 113.1771017 -2.053758568 0.155367219 QLLHLAEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLLHLAEEK 9 0 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7BZC3;H7C2D1 Q00341 HDLBP Vigilin 0 80.706 0.023353 178820000 299070 305980 198010 225500 300470 245240 305070 337890 354640 FALSE TRUE 259547.1418 303969.9972 293768.2983 276703.2216 294491.2349 254674.5415 275484.3584 265634.853 312714.8632 0.829980191 0.972035656 0.93941265 0.884841925 0.941724457 0.814398583 0.880944243 0.849447481 1 18.25448827 QLLHSCTVIATNILLVDEIMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QLLHSCTVIATNILLVDEIMR 21 0 P40227;P40227-2;Q92526-3;Q92526;Q92526-2 P40227 CCT6A;CCT6B T-complex protein 1 subunit zeta;T-complex protein 1 subunit zeta-2 0 ;;;; 247.74 2.01E-30 2201330000 730603 915916 496070 563935 595290 563439 769172 764557 923521 FALSE TRUE 634051.9624 909899.2875 735971.1113 691985.061 583444.8937 585114.8629 694577.8178 601062.4353 814343.3995 0.778605147 1.117341024 0.903760148 0.849746018 0.716460518 0.718511212 0.85292988 0.738094563 1 19.63527777 3.722570272 3.088358779 0.796337171 0.957114864 0.194562905 0.115684069 0.325976945 6.353218952 0.030803592 0.05293674 5279.226211 -3.722570272 0.160777693 QLLLTADDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QLLLTADDR 9 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;; 214.93 1.53E-06 3478360000 3450720 4057840 2851850 3485280 3239120 3094840 3397590 3474900 7698910 FALSE TRUE 2994698.609 4031183.782 4231014.199 4276666.093 3174667.849 3213900.497 3068092.245 2731819.677 6788753.63 0.441126423 0.593803222 0.623238731 0.629963367 0.467636332 0.473415397 0.451937485 0.402403714 1 22.6947153 1.230804691 24.99999357 1.00000088 0.51000446 0.788736312 0.079625611 145.7523096 469770.1151 0.231032605 0.022000991 17.01393192 -1.230804691 -0.48999642 QLLLTADDRVNPCIGGVILFHETLYQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QLLLTADDRVNPCIGGVILFHETLYQK 27 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;; 254.55 4.68E-53 2203877000 3658136 4817953 1180683 2008980 2839933 2383070 3844604 4062143 1132379 FALSE TRUE 3174704.059 4786303.55 1751665.248 2465149.614 2783423.89 2474748.245 3471754.896 3193485.331 998510.4446 3.179440011 4.793443649 1.754278343 2.468827069 2.787576139 2.478440019 3.476933982 3.198249301 1 19.92941799 4.239201745 24.99991216 2.587099376 3.986441735 0.380852863 0.799046664 17.76950499 692755.908 0.198253137 0.464849827 17346.09597 -4.239201745 1.399342359 QLLS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLLSPK 6 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 QLLS(1)PK;QLLS(1)PK 101.65 0.038064 1473020000 3333900 2951800 2212300 3011300 4197500 3315300 4526300 5394200 4553000 TRUE FALSE 2893316.668 2932409.431 3282175.68 3695061.69 4113977.962 3442841.736 4087340.123 4240692.308 4014749.527 0.720671775 0.730409061 0.817529377 0.920371661 1.024715972 0.857548326 1.018080978 1.056278176 1 21.93687855 3.986127075 0.694294617 1.019655778 0.636416187 0.805949049 0.053676488 0.576187765 0.422795226 0.030197717 0.154533917 9685.612167 -3.986127075 -0.383239591 QLLSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLLSER 6 0 A0A087X1E4;P53365;P53365-2;P53365-3;E9PRV8;E9PPY7 A0A087X1E4 ARFIP2 Arfaptin-2 0 107.32 0.072981 269490000 252320 288520 212040 210930 208270 226500 309780 263050 355200 FALSE TRUE 218975.2727 286624.6931 314583.2532 258824.8804 204125.8345 235213.6016 279737.5833 206798.8046 313208.6606 0.699135433 0.915123779 1.004388744 0.826365656 0.651724745 0.750980516 0.893134892 0.660258896 1 18.25676458 4.776255041 22.23082084 0.822804391 0.699134154 0.099303848 0.124141966 12560.06991 7406854.028 0.030926707 5.854825526 59738.60011 -4.776255041 -0.123670237 QLLTLS(ph)SELSQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLLTLSSELSQAR 13 0 P15311;E7EQR4 P15311 EZR Ezrin 1 QLLTLS(0.843)S(0.152)ELS(0.004)QAR 153.72 4.81E-05 54400000 128170 123980 62833 134900 128340 90593 114190 134750 159810 TRUE FALSE 111232.0098 123165.5672 93219.24896 165531.1068 125786.2851 94078.17133 103115.8714 105934.7611 140917.4439 0.789341665 0.874026408 0.661516746 1.174667254 0.892623948 0.667611963 0.731746678 0.751750516 1 17.10449069 1.225390435 24.27267315 1.000000643 0.816423369 0.130825653 0.147456349 1015.30272 1871039.823 0.653809853 0.036601838 16.8031396 -1.225390435 -0.183577274 QLLTLSS(ph)ELSQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLLTLSSELSQAR 13 0 P15311;E7EQR4 P15311 EZR Ezrin 1 QLLT(0.035)LS(0.334)S(0.622)ELS(0.009)QAR 114.28 0.0007928 76360000 131690 102020 58785 107340 97812 90422 96529 125360 130860 TRUE FALSE 114286.8328 101349.8239 87213.62262 131713.1876 95865.73257 93900.59285 87167.63244 98552.73955 115389.8799 0.990440695 0.878325066 0.755816911 1.141462213 0.830798443 0.813768009 0.755418348 0.854084775 1 16.81615717 QLLTLSSELS(ph)QAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLLTLSSELSQAR 13 0 P15311;E7EQR4 P15311 EZR Ezrin 1 QLLTLS(0.072)S(0.088)ELS(0.84)QAR 135.47 8.77E-05 42182000 90030 86150 57384 81736 75606 64941 81735 90171 122980 TRUE FALSE 78132.30739 85584.07498 85135.09434 100295.4081 74101.58852 67439.32229 73808.35228 70888.63336 108441.4445 0.720502274 0.789219245 0.78507894 0.924880783 0.683332732 0.6218962 0.680628634 0.653704252 1 16.72655671 QLMEQDASS(ph)SPSAQVIGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLMEQDASSSPSAQVIGLK 19 0 Q9H4L5-5;Q9H4L5;Q9H4L5-7;Q9H4L5-3;Q9H4L5-6;Q9H4L5-2;Q9H4L5-8;Q9H4L5-4 Q9H4L5-5;Q9H4L5-6 OSBPL3 Oxysterol-binding protein-related protein 3 1 QLMEQDASS(0.511)S(0.465)PS(0.023)AQVIGLK;QLMEQDASS(0.69)S(0.302)PS(0.008)AQVIGLK 245.78 1.39E-24 359720000 683700 692010 517950 588260 718270 737260 801560 980820 991390 TRUE FALSE 593347.3127 687464.1407 768432.3524 721833.424 703977.8323 765622.8693 723824.8346 771079.2757 874189.0036 0.678740307 0.786402183 0.879023128 0.825717804 0.805292482 0.875809311 0.827995813 0.88205099 1 19.73758571 -1.999932373 0.037459712 2.126070365 6.83E-06 0.622740791 0.050401924 1513.868307 5.593381153 243.3494836 102.9586864 0.010001557 1.999932373 -2.126063534 QLNVNAKPFVPNVHAAEFVPSFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLNVNAKPFVPNVHAAEFVPSFLR 24 1 P15170-2;P15170-3 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 95.926 0.004039 637540000 1140200 1162000 625780 694170 939240 781320 1224700 1238900 544020 FALSE TRUE 989519.6811 1154366.745 928409.3011 851791.9082 920550.9616 811377.886 1105928.783 973970.8761 479706.5753 2.062760304 2.406401756 1.935369138 1.775651934 1.918987583 1.691404554 2.305427608 2.030347146 1 18.87179269 1.238175939 24.96377943 0.99999886 2.019079038 0.687068459 0.215433003 5.520396907 357768.6362 0.309291763 0.054262577 17.30517275 -1.238175939 1.019080178 QLPAHDQDPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QLPAHDQDPSK 11 0 Q9UGI8-2;Q9UGI8;F8W7T0 Q9UGI8-2 TES Testin 0 ;; 146.07 3.59E-05 964250000 1529320 1290553 858812 1134276 1218189 1094201 1440304 1657060 1516330 FALSE TRUE 1327216.487 1282075.272 1274136.356 1391830.702 1193949.422 1136295.621 1300623.54 1302710.614 1337071.195 0.992629631 0.958868366 0.952930824 1.040954818 0.89295875 0.849839279 0.972740677 0.974301607 1 20.35064486 1.680469589 2.845585705 0.992521921 0.948764228 0.086027512 0.051644569 0.617136481 11.17903355 0.046571068 0.01482027 47.91479002 -1.680469589 -0.043757693 QLPALDGSLMGPES(ph)PPAQEEEAPVSPHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLPALDGSLMGPESPPAQEEEAPVSPHK 28 0 A0A494C108;Q8N9T8 A0A494C108 KRI1 Protein KRI1 homolog 1 QLPALDGSLMGPES(1)PPAQEEEAPVSPHK;QLPALDGSLMGPES(1)PPAQEEEAPVSPHK 236.39 1.30E-44 386670000 276010 245160 144374 236873 255250 218440 267940 308800 457070 TRUE FALSE 239534.5792 243549.5278 214193.7493 290658.635 250171.0244 226843.5281 241955.22 242765.5231 403035.7053 0.594325952 0.604287721 0.531451051 0.721173413 0.620716778 0.5628373 0.600331973 0.602342472 1 18.62054813 1.238335472 24.99999999 1.000000438 0.604902409 0.868278921 0.048388818 1.791741587 198510.6647 0.065252841 0.011555031 17.31153076 -1.238335472 -0.395098029 QLPDKWQHDLFDSGFGGGAGVETGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLPDKWQHDLFDSGFGGGAGVETGGK 26 1 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 ; 238.2 3.23E-45 1460000000 1480430 1304370 824630 959730 1076520 804310 1374580 1624530 1117180 FALSE TRUE 1284787.425 1295801.508 1223423.826 1177651.365 1055099.358 835252.3262 1241273.443 1277136.902 985108.2531 1.304209381 1.315389962 1.241918157 1.19545376 1.071049151 0.847878721 1.260037604 1.296443206 1 19.90992274 3.741187636 2.185612219 1.122259993 1.304272228 0.315340494 0.126849762 0.482738346 4.502571863 0.041536365 0.079831475 5510.457227 -3.741187636 0.182012235 QLPLEPES(ph)PSGQVGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLPLEPESPSGQVGPR 16 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 QLPLEPES(0.999)PS(0.001)GQVGPR 238.45 9.02E-20 94369000 79606 84369 68322 98594 87098 93299 86213 104720 158940 TRUE FALSE 69085.8654 83814.77448 101362.7477 120981.2746 85364.9202 96888.2729 77852.07653 82326.44293 140150.2943 0.49294128 0.598034952 0.723243203 0.863225263 0.609095547 0.691316942 0.555489926 0.587415413 1 17.09661525 7.999999999 0.054084573 1.028014417 9.80E-05 0.139814369 0.141260304 3165.977041 16.68975992 84.90303455 292.8433225 99999999.86 -7.999999999 -1.027916401 QLPTAAPDKTEVTGDHIPTPQDLPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLPTAAPDKTEVTGDHIPTPQDLPQR 26 1 P56211;H3BMD8;P56211-2;H3BQ52 P56211 ARPP19 cAMP-regulated phosphoprotein 19 0 92.833 0.0054946 257090000 161460 135380 82665 107460 125180 133870 149530 171910 147960 FALSE TRUE 140122.6519 134490.6799 122642.0705 131860.4354 122689.1629 139020.0655 135028.6036 135148.3843 130468.3374 1.073997376 1.030830028 0.940014052 1.010670007 0.940375001 1.065546387 1.03495305 1.035871132 1 16.9933402 2.705417354 24.99745464 1.034451187 0.998287372 0.145763617 0.04196566 1279.940787 965361.2552 0.014467765 0.012760406 507.4781575 -2.705417354 -0.036163815 QLPTAAPDKTEVTGDHIPTPQDLPQRKPS(ph)LVASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLPTAAPDKTEVTGDHIPTPQDLPQRKPSLVASK 34 3 P56211;H3BMD8;P56211-2;H3BQ52 P56211 ARPP19 cAMP-regulated phosphoprotein 19 1 QLPTAAPDKTEVTGDHIPT(0.236)PQDLPQRKPS(0.761)LVAS(0.003)K 107.37 1.01E-05 856490000 610420 441900 196250 229990 342920 189720 699230 645910 81076 TRUE FALSE 529751.4504 438997.1298 291157.1564 282212.7447 336096.5629 197018.6512 631418.7822 507787.173 71491.28764 7.410014113 6.140568233 4.072624316 3.947512403 4.701224079 2.755841413 8.832108122 7.102783986 1 16.12547982 4.489917108 4.369923463 4.986578734 7.214050995 0.142023771 2.165837732 0.452254595 20.85332753 0.565894375 2.103089064 30897.05655 -4.489917108 2.227472262 QLQEERPELSESELTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLQEERPELSESELTR 16 1 E9PKP7;P17480-2;P17480;E9PLT2 E9PKP7 UBTF Nucleolar transcription factor 1 0 85.636 0.0064584 262400000 71151 74863 31313 44015 63076 80931 57709 63222 58581 FALSE TRUE 61748.21508 74371.22002 46456.07154 54009.27848 61820.91101 84044.46794 52112.39006 49702.46729 51655.62092 1.195382303 1.439750771 0.899342041 1.045564404 1.196789622 1.627014959 1.008842584 0.962188943 1 15.65663772 2.035402856 24.99947907 0.980529119 1.226201562 0.254459639 0.196709583 242.8835506 171509.5634 0.082652402 0.055724015 108.4932841 -2.035402856 0.245672443 QLQGPEKEPPKPEQVESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QLQGPEKEPPKPEQVESR 18 2 O60664-4;O60664;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 0 ;; 112.74 0.00015029 2044310000 1286912 948977 752229 834464 987957 685992 1294200 1478140 951601 FALSE TRUE 1116843.319 942743.1076 1116009.46 1023941.805 968298.5886 712382.5561 1168688.683 1162051.264 839103.8138 1.330995403 1.123511885 1.330001654 1.220280242 1.153967569 0.848980239 1.392781994 1.384871865 1 19.67848979 4.76708322 21.58369482 1.202117787 1.330996616 0.059512575 0.170127769 5337.120166 4038290.147 0.042683362 2.949248218 58490.21536 -4.76708322 0.128878829 QLRDELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLRDELR 7 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 0 89.752 0.01609 110160000 138290 144120 68455 81326 126440 138150 146710 158670 81914 FALSE TRUE 120014.6261 143173.2662 101560.067 99792.31129 123924.0914 143464.7199 132482.0868 124739.6553 72230.22024 1.661556973 1.982179561 1.406060602 1.381586695 1.715682037 1.986214626 1.834164237 1.72697321 1 16.14031495 1.238004135 24.98349668 0.999999182 1.715521405 0.549739435 0.202423988 11.17643514 501309.764 0.301175253 0.052277977 17.29832828 -1.238004135 0.715522223 QLS(ph)EEQPSGNGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QLSEEQPSGNGVK 13 0 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 1 QLS(1)EEQPSGNGVK;QLS(1)EEQPSGNGVK;QLS(1)EEQPSGNGVK;QLS(1)EEQPSGNGVK 241.33 7.30E-17 1005970000 2016710 1744720 1461270 1786240 1980550 1875660 2477840 2627680 2991370 TRUE FALSE 1750196.664 1733258.819 2167945.06 2191833.093 1941140.93 1947817.854 2237539.458 2065771.081 2637733.646 0.663522894 0.657101532 0.821896882 0.830953154 0.735912412 0.738443723 0.848281047 0.783161364 1 21.33086746 -0.880343493 0.84076076 10 0.745500263 0.594879015 0.063427759 60.46828185 1.441753659 1002.719983 0.024142895 0.131721451 0.880343493 -9.254499737 QLS(ph)ESES(ph)SLEMDDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLSESESSLEMDDER 15 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 QLS(1)ES(0.147)ES(0.803)S(0.05)LEMDDER;QLS(1)ES(0.001)ES(0.876)S(0.123)LEMDDER 286.6 6.58E-34 265700000 256750 258870 216868 319560 327940 313210 334290 359330 464150 TRUE FALSE 222819.837 257169.4659 321746.0902 392120.9822 321414.6356 325259.3914 301870.6073 282490.0758 409278.7158 0.544420778 0.628348008 0.786129544 0.958078119 0.785319693 0.794713673 0.737567324 0.690214431 1 18.64272412 4.318411051 3.239523473 0.809344527 0.560794514 0.528115409 0.093782384 0.205827308 4.178014427 0.025013168 0.079453485 20816.66008 -4.318411051 -0.248550014 QLS(ph)ESESS(ph)LEMDDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLSESESSLEMDDER 15 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 QLS(1)ESES(0.368)S(0.632)LEMDDER;QLS(1)ES(0.001)ES(0.155)S(0.845)LEMDDER 267.33 2.94E-25 479650000 626850 680750 549460 789180 836400 801470 813760 936720 1257980 TRUE FALSE 544010.1843 676278.1084 815180.6938 968375.3809 819757.2764 832303.0695 734841.6805 736409.7176 1109263.037 0.490424873 0.609664332 0.734884934 0.872989857 0.73901072 0.750320746 0.662459359 0.663872943 1 20.08117008 4.420822959 2.448856045 0.761527973 0.494192326 0.485363324 0.099872958 0.300980423 3.266427246 0.026553954 0.126219782 26352.569 -4.420822959 -0.267335646 QLS(ph)ESESSLEMDDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QLSESESSLEMDDER 15 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.996)ES(0.004)ESSLEMDDER;QLS(0.993)ES(0.007)ESSLEMDDER;QLS(0.74)ES(0.26)ESSLEMDDER;QLS(0.999)ES(0.001)ESSLEMDDER;QLS(1)ESESSLEMDDER;QLS(0.988)ES(0.012)ESSLEMDDER 340.42 2.53E-69 5976740000 2830547 2611969 1699500 2779516 2731322 2102524 2811365 2952230 3461828 TRUE FALSE 2456483.042 2594810.804 2521383.884 3410647.59 2676974.036 2183409.459 2538719.255 2320918.589 3052574.638 0.804724973 0.850040085 0.82598599 1.117301948 0.876956128 0.715268165 0.831664924 0.760315099 1 21.54159514 2.985452786 24.9243119 0.814569661 0.90402768 0.082523988 0.111471526 1401.349611 2400991.785 0.035190819 0.036502704 967.0585873 -2.985452786 0.089458019 QLS(ph)ESESSLEMDDERYFNEMSAQGLRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.877)ES(0.123)ES(0.001)SLEMDDERYFNEMSAQGLRPR;QLS(0.997)ES(0.003)ESSLEMDDERYFNEMSAQGLRPR;QLS(0.983)ES(0.017)ESSLEMDDERYFNEMSAQGLRPR;QLS(0.857)ES(0.095)ES(0.035)S(0.013)LEMDDERYFNEMSAQGLRPR;QLS(0.879)ES(0.064)ES(0.025)S(0.031)LEMDDERYFNEMSAQGLRPR;QLS(0.662)ES(0.105)ES(0.116)S(0.116)LEMDDERYFNEMSAQGLRPR 359.65 1.25E-111 981130000 136762 135582 62789.7 80994.9 116887.4 119485.4 135787 142156 77447.6 TRUE FALSE 118688.5552 134691.3529 93155.00894 99386.02997 114561.5694 124082.0807 122618.3976 111757.0457 68291.83296 1.737961189 1.972290786 1.364072465 1.455313552 1.677529574 1.816938795 1.795506027 1.636462822 1 16.05942544 1.240629496 5.07542389 0.959049922 1.684798622 0.605498899 0.173470223 0.121971886 8.244141985 0.311834408 0.045556843 17.40321542 -1.240629496 0.7257487 QLS(ph)LEGSGLGVEDLKDNTPSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLSLEGSGLGVEDLKDNTPSGK 22 1 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 QLS(0.999)LEGS(0.001)GLGVEDLKDNTPSGK;QLS(1)LEGSGLGVEDLKDNTPSGK 209.68 3.27E-23 376220000 632900 291580 203292 272830 292060 207829 488000 530430 320540 TRUE FALSE 549260.6614 289664.5918 301604.6912 334780.2214 286248.5774 215824.3161 440673.8351 417001.6723 282646.1264 1.943280343 1.024831281 1.067075268 1.18445006 1.012745446 0.763584907 1.559100918 1.475348973 1 18.1086374 4.74502388 24.70805279 1.166134061 1.943280757 0.536980744 0.234123869 584.7226689 2235233.911 0.062816199 0.577603631 55593.48247 -4.74502388 0.777146696 QLS(ph)LPLTQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QLSLPLTQSK 10 0 Q9C0I1-3;Q9C0I1-2;Q9C0I1 Q9C0I1-3 MTMR12 Myotubularin-related protein 12 1 QLS(0.996)LPLT(0.004)QSK;QLS(1)LPLTQSK;QLS(0.982)LPLT(0.018)QSK;QLS(1)LPLTQSK 205.87 1.69E-07 1495160000 2933020 2334020 1323200 1790160 2247410 1624830 3044330 2848240 2429410 TRUE FALSE 2545413.976 2318687.669 1963103.946 2196643.189 2202690.938 1687338.262 2749091.345 2239166.041 2142207.917 1.188219853 1.082382177 0.916392816 1.025410825 1.028233964 0.787663162 1.283298098 1.045260837 1 21.03066708 -1.403773003 10.55840713 0.097568752 1.040243538 0 0.134945658 0 0 0 0.029342665 0.039466353 1.403773003 0.942674787 QLS(ph)MTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QLSMTLR 7 0 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;E5RIY8;E5RIU4;E5RJQ8;E5RGV7 E5RJM2 CDK16 Cyclin-dependent kinase 16 1 QLS(0.964)MT(0.036)LR;QLS(0.977)MT(0.023)LR;QLS(0.886)MT(0.114)LR;QLS(0.966)MT(0.034)LR;QLS(0.912)MT(0.088)LR;QLS(0.846)MT(0.154)LR 96.665 0.01318 1228130000 1513220 1628220 831742 912070 1360179 1325063 1440859 1534990 1524747 TRUE FALSE 1313244.143 1617524.116 1233975.213 1119169.434 1333114.099 1376039.031 1301124.716 1206744.334 1344493.147 0.976757781 1.20307353 0.917799556 0.832409921 0.991536552 1.023463031 0.967743658 0.897545917 1 20.35863097 4.214710673 24.99989183 0.944085176 1.089915755 0.372807386 0.076866637 198.6028901 208178.9329 0.01913232 0.039861281 16394.97178 -4.214710673 0.145830579 QLS(ph)PQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QLSPQSK 7 0 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 QLS(0.991)PQS(0.009)K;QLS(0.912)PQS(0.088)K;QLS(0.977)PQS(0.023)K;QLS(0.994)PQS(0.006)K;QLS(0.997)PQS(0.003)K;QLS(0.972)PQS(0.028)K 136.52 0.0031181 8712110000 9218150 6805620 4564900 5715980 4957530 5772300 7888330 8742390 7985170 TRUE FALSE 7999948.122 6760913.434 6772500.909 7013880.622 4858884.852 5994364.116 7123320.971 6872897.932 7041172.299 1.136167073 0.96019713 0.961842804 0.996123987 0.690067598 0.851330412 1.011666903 0.976101371 1 22.74738422 5.266312388 1.292769731 0.924171787 1.606184284 0.320386451 0.095662731 6.442478607 3.646795707 0.029308887 8.110379794 184634.3016 -5.266312388 0.682012497 QLS(ph)SGVSEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 33 QLSSGVSEIR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 QLS(0.499)S(0.499)GVS(0.002)EIR;QLS(0.914)S(0.082)GVS(0.004)EIR;QLS(0.901)S(0.099)GVSEIR;QLS(0.949)S(0.051)GVSEIR;QLS(0.5)S(0.5)GVSEIR;QLS(0.896)S(0.104)GVSEIR;QLS(0.5)S(0.5)GVSEIR;QLS(0.968)S(0.032)GVSEIR;QLS(0.799)S(0.2)GVS(0.001)EIR;QLS(0.499)S(0.499)GVS(0.001)EIR;QLS(0.959)S(0.04)GVSEIR;QLS(0.934)S(0.065)GVS(0.001)EIR;QLS(0.967)S(0.032)GVS(0.001)EIR;QLS(0.921)S(0.058)GVS(0.021)EIR;QLS(0.976)S(0.022)GVS(0.002)EIR;QLS(0.973)S(0.027)GVSEIR;QLS(0.967)S(0.032)GVSEIR;QLS(0.987)S(0.013)GVSEIR;QLS(0.958)S(0.042)GVS(0.001)EIR;QLS(0.981)S(0.018)GVSEIR;QLS(0.964)S(0.035)GVS(0.001)EIR;QLS(0.813)S(0.184)GVS(0.002)EIR;QLS(0.921)S(0.076)GVS(0.003)EIR;QLS(0.952)S(0.047)GVS(0.001)EIR;QLS(0.968)S(0.032)GVSEIR;QLS(0.5)S(0.5)GVS(0.001)EIR;QLS(0.498)S(0.498)GVS(0.005)EIR;QLS(0.496)S(0.496)GVS(0.009)EIR;QLS(0.915)S(0.08)GVS(0.005)EIR;QLS(0.491)S(0.491)GVS(0.019)EIR;QLS(0.913)S(0.086)GVS(0.001)EIR;QLS(0.499)S(0.499)GVS(0.002)EIR;QLS(0.5)S(0.5)GVSEIR 208 1.28E-07 5.75366E+11 58792119 47168228.9 29702127.9 44575019 49283488 47346546 68735443 58435956 55761119 TRUE FALSE 51022591.51 46858377.7 44066176.3 54696458.35 48302843.01 49167998.26 62069490.32 45939881.56 49169103.04 1.037696203 0.953004525 0.896216802 1.112415216 0.982382025 0.999977531 1.262367757 0.934324174 1 25.5512487 3.739389709 24.9999884 1.045255071 0.961375715 0.15280996 0.095536932 150.2314331 4529907.205 0.025493458 0.041162012 5487.691751 -3.739389709 -0.083879356 QLS(ph)SGVSEIRHTADRWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QLSSGVSEIRHTADRWR 17 2 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 QLS(0.897)S(0.103)GVSEIRHTADRWR;QLS(0.972)S(0.028)GVSEIRHTADRWR;QLS(0.827)S(0.173)GVSEIRHTADRWR 171.06 8.41E-10 336879000 12020.7 11352 8857.7 15200.6 18509 21139.6 15727 12621.3 20228 TRUE FALSE 10432.13404 11277.42796 13141.31335 18652.12856 18140.70711 21952.85409 14201.79796 9922.333214 17836.66888 0.584870085 0.63226088 0.736758272 1.045718159 1.017045684 1.23077096 0.796213579 0.556288468 1 14.12255859 3.996575057 3.984590121 0.907328253 0.616087779 0.376938213 0.177110286 0.290018049 10.60118326 0.055531017 0.114333931 9921.447924 -3.996575057 -0.291240474 QLS(ph)TCQRANSLGDLYAQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLSTCQRANSLGDLYAQK 18 1 Q13009;Q13009-2 Q13009 TIAM1 T-lymphoma invasion and metastasis-inducing protein 1 1 QLS(0.834)T(0.163)CQRANS(0.003)LGDLYAQK 65.184 0.020466 934870000 486550 552460 458660 579260 691900 724720 623170 862270 965860 TRUE FALSE 422251.1847 548830.8539 680469.5101 710789.8364 678132.5437 752600.4474 562735.0693 677880.2707 851677.1311 0.495787863 0.644411871 0.798975909 0.834576638 0.796231951 0.883668728 0.66073756 0.795935744 1 19.69994709 4.484672504 2.030941203 0.816996647 0.475691986 0.634805695 0.084279724 0.295509257 1.925661995 0.022476053 0.154255222 30526.18301 -4.484672504 -0.341304661 QLSES(ph)ESSLEMDDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QLSESESSLEMDDER 15 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.017)ES(0.981)ES(0.001)S(0.001)LEMDDER;QLS(0.237)ES(0.758)ESS(0.004)LEMDDER;QLSES(0.999)ES(0.001)SLEMDDER;QLSES(0.992)ES(0.003)S(0.005)LEMDDER;QLSES(0.999)ESSLEMDDER 383.17 2.98E-114 2135520000 1020757 1143960 1037949 1414210 1509530 1531220 1545270 1673670 2382490 TRUE FALSE 885861.3762 1136445.251 1539904.608 1735327.995 1479493.306 1590127.024 1395409.953 1315768.695 2100834.746 0.421671137 0.540949379 0.732996544 0.826018324 0.704240688 0.756902477 0.664216905 0.626307565 1 21.00253125 4.37530182 2.866184395 0.7434377 0.434514839 0.56747168 0.102736102 0.204534406 3.194347056 0.026553791 0.09970854 23730.22304 -4.37530182 -0.308922861 QLSES(ph)ESSLEMDDERYFNEMSAQGLRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.029)ES(0.656)ES(0.138)S(0.177)LEMDDERYFNEMSAQGLRPR;QLSES(0.957)ES(0.041)S(0.002)LEMDDERYFNEMSAQGLRPR;QLS(0.023)ES(0.35)ES(0.35)S(0.278)LEMDDERYFNEMSAQGLRPR 250.03 2.09E-46 506681000 56350 79197 56129.3 73687 107843 136374 79361 109081 60980 TRUE FALSE 48903.20473 78676.74969 83273.61722 90418.75959 105697.1353 141620.396 71664.58243 85754.87702 53771.01387 0.909471502 1.463181444 1.548671138 1.681552068 1.965689833 2.633768379 1.332773502 1.59481607 1 15.71454105 4.86431132 1.376706537 1.708502764 0.399745004 0.25346206 0.420390478 2.560275621 3.511840446 0.123951456 5.037261505 73166.33822 -4.86431132 -1.30875776 QLSESESS(ph)LEMDDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLSESESSLEMDDER 15 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLSESES(0.056)S(0.944)LEMDDER 419.86 7.20E-135 186090000 143320 164990 141660 188480 208240 216870 185760 219150 370160 TRUE FALSE 124379.8989 163906.1698 210167.2498 231277.2647 204096.4314 225213.1292 167745.0238 172286.4779 326400.1065 0.381065742 0.502163347 0.64389455 0.70856982 0.625295235 0.68999098 0.513924538 0.527838302 1 18.316282 4.44597677 2.448530079 0.652577534 0.380891231 0.351317173 0.133816663 0.404812798 4.320746783 0.034802665 0.176258353 27923.94477 -4.44597677 -0.271686303 QLSESESS(ph)LEMDDERYFNEMSAQGLRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.001)ES(0.28)ES(0.28)S(0.44)LEMDDERYFNEMSAQGLRPR 208.37 9.79E-26 200240000 38190 62831 52284 51935 82470 98947 47819 74590 53161 TRUE FALSE 33143.09474 62418.25902 77568.71728 63727.63553 80829.00835 102753.5551 43181.52074 58639.50896 46876.36714 0.707032067 1.33155069 1.65475104 1.359483241 1.724301888 2.192011911 0.921178909 1.250939707 1 15.51657315 TAS(ph)FSESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 TASFSESR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 TAS(1)FSESR;TAS(1)FSESR;TAS(0.975)FS(0.025)ESR;T(0.002)AS(0.995)FS(0.003)ESR;TAS(0.953)FS(0.046)ESR;TAS(0.922)FS(0.077)ESR;T(0.014)AS(0.976)FS(0.009)ESR;T(0.029)AS(0.97)FS(0.001)ESR;TAS(0.999)FS(0.001)ESR;TAS(1)FSESR 196.37 0.00016011 52646900000 9864608 12739979 11604535 15121597 18803260 20083800 20819070 21038740 24451780 TRUE FALSE 8560975.059 12656289.24 17216526.94 18555186.72 18429111.91 20856436.78 18800039.8 16539769.17 21561118.42 0.397056168 0.586995952 0.798498789 0.860585539 0.854738217 0.967317018 0.871941772 0.76711091 1 24.36192868 4.455820066 1.486511677 0.878450719 0.328633697 0.875086603 0.063183794 0.233585759 0.709855276 0.018613241 0.163228369 28564.0685 -4.455820066 -0.549817021 down QLSILVHPDKNQDDADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QLSILVHPDKNQDDADR 17 1 O75937 O75937 DNAJC8 DnaJ homolog subfamily C member 8 0 ;; 194.51 4.23E-11 793240000 1433360 1165980 579700 824290 1014060 902640 1279330 1444300 608760 FALSE TRUE 1243937.844 1158320.601 860044.859 1011457.643 993882.19 937365.1449 1155260.774 1135447.685 536793.0863 2.317350719 2.157853054 1.602190641 1.884259818 1.851518239 1.746231777 2.152152856 2.115242751 1 19.03400656 4.404755861 6.062581388 1.824209904 2.279957284 0.263417838 0.322044167 0.263148945 16.2987831 0.079236712 0.217735607 25395.44695 -4.404755861 0.45574738 QLSSGVS(ph)EIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLSSGVSEIR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 QLS(0.016)S(0.016)GVS(0.968)EIR 105.95 0.0035798 0 637150 765340 432200 480170 736210 744270 707800 667970 829430 TRUE FALSE 552949.0132 760312.4311 641213.3656 589199.9374 721560.8614 772902.5485 639157.6649 525129.8136 731375.7303 0.756039598 1.039564754 0.876722236 0.805604989 0.986580264 1.056779049 0.873911505 0.718002788 1 19.48025323 2.001153917 24.99994332 0.825988249 0.925126477 0.033067357 0.11612482 76.45904915 1656483.543 0.046419583 0.031011742 100.2660525 -2.001153917 0.099138228 QLSSGVSEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 QLSSGVSEIR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;;;;; 243.1 4.99E-12 18872350000 9846570 9767740 5728190 7457130 8759000 9923490 9913300 10530170 10188000 FALSE TRUE 8545320.826 9703575.073 8498361.844 9150385.342 8584713.037 10305253.08 8951909.692 8278375.091 8983586.246 0.95121487 1.080144923 0.945987672 1.018567095 0.95559978 1.147120181 0.996473952 0.921500041 1 23.09886005 1.989417466 24.99602322 0.956296104 1.018324874 0.110540415 0.064292444 906.2419471 2140549.418 0.026409136 0.016525434 97.59272992 -1.989417466 0.06202877 QLSSTS(ph)PLAPYPTSQMVSSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QLSSTSPLAPYPTSQMVSSDR 21 0 Q6UUV7;Q6UUV7-3 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 QLSST(0.004)S(0.996)PLAPYPTSQMVSSDR;QLSSTS(1)PLAPYPTSQMVSSDR;QLSSTS(1)PLAPYPTSQMVSSDR;QLSST(0.002)S(0.998)PLAPYPTSQMVSSDR 269.28 1.48E-37 940880000 685050 907030 609108 755930 1073320 1166970 913750 1171600 1125080 TRUE FALSE 594518.9068 901071.6602 903674.6661 927575.4602 1051963.032 1211864.091 825134.6656 921062.4574 992074.3241 0.599268515 0.908270316 0.910894118 0.934985855 1.060367158 1.221545666 0.831726662 0.92842082 1 19.92008868 5.164014801 1.222940609 0.987205812 1.06E-19 0.584229322 0.102342997 2.941223463 1.864017173 0.031486322 4.716665758 145886.3978 -5.164014801 -0.987205812 QLT(ph)QPETHFGR ddPTM_MDA-MB-175_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 219.95 3.50E-11 7936440000 5518830 5120950 2153500 3270080 4515620 2745360 5799070 4310910 4290740 TRUE FALSE 4789502.633 5087310.142 3194939.803 4012601.644 4425767.997 2850975.776 5236677.084 3389055.444 3783493.605 1.265894206 1.344606513 0.844441708 1.060554626 1.169756965 0.753529958 1.384085089 0.895747634 1 21.85128758 4.257183923 24.96231748 1.022274497 1.305250571 0.319494222 0.175617831 270.7229964 362865.4978 0.040201599 0.10594859 18079.39623 -4.257183923 0.282976074 QLTAHLQDVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLTAHLQDVNR 11 0 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 100.07 0.0043025 190560000 122970 137440 76852 91805 138060 153160 112460 139820 98773 FALSE TRUE 106719.2029 136537.1476 114017.8843 112650.7284 135312.8761 159052.1643 101553.6465 109920.5811 87096.16846 1.225303074 1.567659634 1.309103331 1.293406247 1.553603086 1.82616718 1.165994421 1.262059893 1 16.41032163 2.097834407 21.9529466 1.16819216 1.460084048 0.405417706 0.181705455 6.057952881 1348.637732 0.074710501 0.050369803 125.2663453 -2.097834407 0.291891888 QLTQPETHFGR ddPTM_MDA-MB-175_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 ;;; 174.21 1.13E-05 3225520000 2298540 2266860 1443970 2009830 2187360 2462790 2072940 2397850 2732720 FALSE TRUE 1994782.115 2251968.847 2142278.722 2466192.62 2143835.815 2557535.125 1871906.598 1885088.438 2409660.955 0.827826882 0.934558384 0.889037405 1.023460423 0.889683593 1.06136721 0.776834016 0.782304429 1 21.20039874 2.211735792 24.99999806 0.835132807 0.937024724 0.15502693 0.089924193 326.7552582 304524.56 0.035434753 0.023897503 162.8305132 -2.211735792 0.101891918 QLTSNTVQQHPS(ph)TPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLTSNTVQQHPSTPKR 16 1 O94916-2;O94916;O94916-4;O94916-5 O94916-2 NFAT5 Nuclear factor of activated T-cells 5 1 QLTSNTVQQHPS(0.5)T(0.5)PKR 57.496 0.055406 39941000 133850 131050 127280 154900 96349 158680 139530 202890 196460 TRUE FALSE 116161.3834 130189.1239 188833.0337 190072.4125 94431.8434 164784.5223 125998.4021 159503.5524 173234.7226 0.670543305 0.751518645 1.090041482 1.097195814 0.545109214 0.951221094 0.727327641 0.920736617 1 17.4023686 4.462264312 24.9461878 0.894093852 0.690787036 0.197726073 0.164939857 320.0269374 537355.2513 0.040729183 0.107848891 28991.0745 -4.462264312 -0.203306815 QLVAGNS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLVAGNSPK 9 0 Q96EU6-2;Q96EU6 Q96EU6-2 RRP36 Ribosomal RNA processing protein 36 homolog 1 QLVAGNS(1)PK 117.2 0.0012484 117330000 363540 276780 215730 243800 296520 257500 329450 370100 401980 TRUE FALSE 315497.2679 274961.814 320057.7496 299158.5162 290619.8321 267406.1916 297499.9897 290956.9951 354458.3823 0.890082683 0.77572383 0.90294874 0.843987704 0.81989832 0.754407865 0.839308659 0.820849526 1 18.43525672 1.236897728 24.99868407 1.000000212 0.829025795 0.584056664 0.044822169 30.06628808 451852.7163 0.064919808 0.010464894 17.25431521 -1.236897728 -0.170974417 QLVARPDVVEMHDVTAQDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLVARPDVVEMHDVTAQDPK 20 1 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 0 142.43 1.08E-07 269430000 282990 231820 161240 209120 216930 158440 257610 279900 270650 FALSE TRUE 245592.1545 230297.1592 239216.2033 256603.8922 212613.5174 164535.2893 232627.0219 220045.5632 238654.0653 1.029071741 0.964983181 1.002355451 1.075212743 0.890885798 0.689430072 0.974745691 0.922027299 1 17.86456139 3.219560865 24.79407447 0.894394131 1.01301485 0.331793823 0.086243978 277.9054301 362656.7114 0.027075955 0.030753409 1657.90967 -3.219560865 0.118620719 QLVEILTTHCDSYWVEMASLQVFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 281.23 2.75E-53 86093000 177138 156580 89212 129710 106008 101024 165267 182397 177393 FALSE TRUE 153728.7645 155551.4157 132355.2216 159162.638 103898.6482 104910.4587 149239.4318 143392.821 156421.8016 0.982783492 0.994435648 0.846143058 1.017522087 0.664221017 0.670689492 0.95408332 0.916706108 1 17.25508208 4.212861966 1.585066695 0.862032031 1.002390539 0.132762208 0.121637121 1.060497264 4.67459195 0.037577257 0.171336465 16325.32991 -4.212861966 0.140358508 QLVHELDEAEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QLVHELDEAEYR 12 0 Q06323;Q06323-3;Q06323-2;H0YKK6 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;;;;; 231.06 4.33E-12 10700500000 4732195 4574360 3280321 3935413 4401595 4614518 3985295 4695020 5833490 FALSE TRUE 4106823.441 4544310.728 4866695.208 4829008.671 4314011.871 4792041.493 3598801.704 3691026.51 5143861.458 0.798393089 0.883443453 0.946117085 0.938790578 0.838671863 0.931603919 0.699630372 0.717559472 1 22.29442036 2.253260634 24.98078002 0.782940263 0.891731047 0.139651609 0.092308882 333.6514203 566996.9904 0.034361267 0.026500339 179.1680778 -2.253260634 0.108790784 QLVYVEQAGSS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLVYVEQAGSSPK 13 0 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 QLVYVEQAGS(0.261)S(0.739)PK;QLVYVEQAGS(0.001)S(0.999)PK 205.12 7.60E-08 317504000 478280 452140 281644 402310 491210 430580 455210 590840 530250 TRUE FALSE 415074.0862 449169.8626 417847.9804 493660.6344 481435.882 447144.6912 411063.8043 464493.4639 467564.4491 0.887736625 0.960658714 0.893669271 1.055813023 1.029667424 0.956327394 0.879159665 0.993431953 1 18.83480571 3.778151218 24.99953483 0.980479747 0.91868525 0.305674644 0.05037396 817.5426806 516235.9163 0.01409344 0.024410172 5999.999551 -3.778151218 -0.061794497 QLWGLLIEETEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QLWGLLIEETEKR 13 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 184.21 1.56E-05 261481000 377910 382540 293050 310880 318010 311330 396070 477180 448740 FALSE TRUE 327968.236 380027.0696 434769.9602 381470.0555 311682.2232 323307.0666 357659.1924 375138.7704 395690.4684 0.828850483 0.960415021 1.098762783 0.964061775 0.787692017 0.817070646 0.903886297 0.948061175 1 18.59401279 4.749228695 22.70038735 0.932294335 0.828850265 0.125561498 0.087773501 1068.075767 2272566.125 0.023467332 0.301715116 56134.34955 -4.749228695 -0.10344407 QLWWGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLWWGHR 7 0 P26640;A0A140T936;H0Y426 P26640 VARS Valine--tRNA ligase 0 94.407 0.014223 252790000 316120 407530 217350 171950 260610 226440 319780 252850 303110 FALSE TRUE 274343.9411 404852.9086 322461.187 210993.8756 255424.3709 235151.2933 288767.7848 198779.9952 267276.6811 1.026441738 1.514733373 1.206469587 0.78942119 0.955655278 0.879804749 1.080407702 0.743723674 1 18.02797445 3.859901542 5.225601401 0.903596669 1.289805136 0.533291669 0.150516309 0.148376581 5.712336617 0.036887274 0.065564801 7242.717431 -3.859901542 0.386208467 QLYQTLTDYDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QLYQTLTDYDIR 12 0 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YF43;A0A2R8Y4H0;A0A2R8Y4D6;V9GYA2;A0A2R8YDY7 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 133.85 0.00036247 77971000 191070 171840 107580 145270 137360 157090 153130 180390 195120 FALSE TRUE 165819.6154 170711.1717 159606.0478 178255.7738 134626.8047 163133.354 138279.4762 141815.0023 172053.1359 0.963769794 0.992200292 0.927655558 1.036050711 0.782472252 0.948156819 0.803702156 0.824251192 1 17.39249466 3.245775633 24.99997557 0.864504262 0.977063203 0.370381027 0.069705591 169.0291999 585681.6941 0.019272516 0.024360925 1761.066003 -3.245775633 0.112558941 QMDTVLS(ph)SSPDVLFDPINGLTPDEEALSNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QMDTVLSSSPDVLFDPINGLTPDEEALSNER 31 0 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 QMDT(0.015)VLS(0.398)S(0.324)S(0.264)PDVLFDPINGLTPDEEALSNER 76.611 0.0093492 24759000 11404 11805 6633.7 7860.1 13530 13733 11316 14035 12696 TRUE FALSE 9896.932506 11727.45218 9841.779508 9644.855839 13260.77947 14261.3174 10218.57606 11033.72447 11195.09334 0.884041982 1.047552871 0.879115449 0.861525272 1.184517097 1.273889994 0.912772743 0.98558575 1 13.45057894 3.256119892 24.9998488 1.058865545 0.924526792 0.30835242 0.113042713 382.5799507 544691.2083 0.035504967 0.045729719 1803.515554 -3.256119892 -0.134338753 QMDTVLSS(ph)SPDVLFDPINGLTPDEEALSNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QMDTVLSSSPDVLFDPINGLTPDEEALSNER 31 0 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 QMDTVLS(0.068)S(0.511)S(0.421)PDVLFDPINGLTPDEEALSNER 110.65 6.55E-05 70560000 19400 19201 11070 13252 17574 20519 17408 21037 18294 TRUE FALSE 16836.24085 19074.86737 16423.48903 16261.06914 17224.31178 21308.37921 15719.77484 16538.40126 16131.30416 1.043699919 1.182475216 1.01811291 1.008044296 1.067756928 1.320933447 0.974488776 1.025236465 1 13.97757546 QMDTVLSSS(ph)PDVLFDPINGLTPDEEALSNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QMDTVLSSSPDVLFDPINGLTPDEEALSNER 31 0 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 QMDT(0.002)VLS(0.14)S(0.201)S(0.657)PDVLFDPINGLTPDEEALSNER;QMDTVLS(0.007)S(0.033)S(0.959)PDVLFDPINGLTPDEEALSNER;QMDTVLS(0.002)S(0.055)S(0.943)PDVLFDPINGLTPDEEALSNER;QMDTVLS(0.003)S(0.132)S(0.865)PDVLFDPINGLTPDEEALSNER 146.26 1.10E-08 128498000 99111.2 82494 67152.4 81834.8 95374.4 116382.8 98617.6 102195.2 109273.6 TRUE FALSE 86013.4038 81952.09148 99627.52525 100416.6421 93476.63604 120860.1216 89053.68033 80341.55176 96355.39949 0.892668229 0.850518932 1.033958925 1.042148573 0.970123486 1.254316024 0.924220965 0.833804355 1 16.55607789 7.039044286 12.70467108 0.972976647 0.308919519 0 0.12091559 0 0 0.028634067 0 10940679.26 -7.039044286 -0.664057128 QMEDGHTLFDYEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QMEDGHTLFDYEVR 14 0 A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2 A0A087WVR3 UHRF1 E3 ubiquitin-protein ligase UHRF1 0 142.1 9.49E-06 102300000 133890 148580 91747 114320 135290 154470 131960 152640 132610 FALSE TRUE 116196.0973 147603.9682 136116.1561 140278.1033 132597.9937 160412.5609 119162.5395 119999.1238 116932.9969 0.993698104 1.262295264 1.164052575 1.199645156 1.133965581 1.371833145 1.019066839 1.02622123 1 16.83532257 2.078384177 24.99999556 1.017269395 1.188639968 0.423183168 0.094915452 28.21273356 8996.662317 0.035887976 0.024195665 119.7799636 -2.078384177 0.171370573 QMEKDETVSDCSPHIANIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QMEKDETVSDCSPHIANIGR 20 1 P47756-2;B1AK88;B1AK87;P47756;B1AK85 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;;;; 207.67 3.87E-22 3178550000 3878610 3194457 1729110 2221374 3093995 2779805 3716280 4272010 1957275 FALSE TRUE 3366041.861 3173472.402 2565313.38 2725770.918 3032430.553 2886745.897 3355875.738 3358473.906 1725888.179 1.95032442 1.8387474 1.486372878 1.579343871 1.757026086 1.672614676 1.944434047 1.945939457 1 20.71890756 4.464748939 23.39549028 1.675759854 1.922430317 0.132801502 0.26964789 198.1330245 374661.71 0.067053819 0.177767181 29157.4097 -4.464748939 0.246670463 QMEQISQFLQAAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QMEQISQFLQAAER 14 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ; 152.74 1.53E-05 62022000 65485 63131 32037 37971 53422 56088 47953 63505 71118 FALSE TRUE 56830.99133 62716.2883 47530.20036 46592.8959 52359.00672 58245.74165 43302.52544 49924.94995 62710.51106 0.906243473 1.000092126 0.757930362 0.742983833 0.834931909 0.928803492 0.690514632 0.796117734 1 15.93641966 4.240795906 24.99999447 0.813808262 0.953167817 0.257515708 0.092131551 72.05381803 805815.9511 0.022942613 0.054967035 17409.88516 -4.240795906 0.139359554 QMGFPLIYVEAEQVEDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QMGFPLIYVEAEQVEDDR 18 0 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ;;; 198.16 4.10E-15 172244000 120864 123319 96561 96098 121633 137559 110880 127517 162608 FALSE TRUE 104891.5162 122508.9094 143258.2226 117918.5197 119212.7413 142850.9837 100126.8747 100248.4819 143384.6675 0.731539278 0.854407319 0.999118142 0.82239281 0.831419031 0.996277958 0.698309494 0.699157613 1 17.12953124 2.22059642 24.99954576 0.77412088 0.873309175 0.069927152 0.114572031 484.2888793 673946.891 0.046175414 0.031202714 166.1867597 -2.22059642 0.099188295 QMGFPLIYVEAEQVEDDRLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QMGFPLIYVEAEQVEDDRLLR 21 1 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 60.034 0.054717 15560000 12458 13506 5762.6 4299 10432 15195 11463 14294 3320.4 FALSE TRUE 10811.64374 13417.2782 8549.412635 5275.153656 10224.42361 15779.56148 10351.32002 11237.33934 2927.866095 3.692670152 4.582613331 2.920014905 1.801705913 3.492107658 5.389440969 3.535448579 3.838064643 1 11.51563386 4.234679835 24.99954042 3.268283454 4.137641766 0.101014481 1.190643416 246.6454637 1588902.445 0.311141569 0.689048727 17166.42398 -4.234679835 0.869358312 QMGYTEAIEVIQAASS(ph)PVK ddPTM_MDA-MB-175_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(0.169)S(0.831)PVK 122.49 3.47E-05 23694000 54281 63439 44397 57701 54818 45190 60333 84734 92309 TRUE FALSE 47107.62832 63022.26503 65867.5377 70802.89395 53727.22905 46928.48854 54481.91495 66614.2935 81396.33518 0.578743849 0.774264159 0.809219943 0.869853585 0.660069387 0.576543016 0.66934113 0.81839426 1 16.31267622 1.358405221 2.729442507 1.022778559 0.712596475 0.50151406 0.09403302 0.333820398 3.460388268 0.207443465 0.026630029 22.82470751 -1.358405221 -0.310182084 QMIAVADENQNHHLEPEEVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QMIAVADENQNHHLEPEEVLK 21 0 A0A5F9UP49;Q9BRK5;Q9BRK5-2;Q9BRK5-5 A0A5F9UP49 SDF4 45 kDa calcium-binding protein 0 72.876 0.0087939 113710000 68193 60728 53964 54779 65779 54821 59814 64386 74481 FALSE TRUE 59181.12227 60329.07377 80061.1709 67217.40919 64470.12659 56929.99934 54013.24749 50617.55495 65675.94103 0.901108097 0.918587124 1.219033479 1.02347082 0.981639937 0.866831879 0.82242061 0.770716859 1 16.00307735 2.781563291 2.848185377 0.842970144 1.021630609 0.323555841 0.102488925 0.290260402 4.693654492 0.03763192 0.035920541 604.7324743 -2.781563291 0.178660464 QMKEMELLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QMKEMELLR 9 1 Q6ZUX3 Q6ZUX3 FAM179A Protein FAM179A 0 ; 67.993 0.054109 898060000 1049610 924970 679500 680470 678780 735890 987860 878600 536110 FALSE TRUE 910901.3791 918893.8112 1008108.473 834981.1138 665273.606 764200.1645 892057.4892 690718.2273 472731.6865 1.926888772 1.943795682 2.132517243 1.766289711 1.407296411 1.616562177 1.88702707 1.461121069 1 18.85066204 0.482105994 0.400611143 1.17E-34 1.961995058 0.62768477 0.200758279 9.77059492 0.845407801 10.35160485 0.259019442 3.034631726 -0.482105994 1.961995058 QMNPHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QMNPHIR 7 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;; 140.12 0.002646 788190000 1351710 1319410 507493 618040 1145760 1256670 1158440 1261720 268462 FALSE TRUE 1173078.099 1310742.709 752918.3123 758375.4281 1122961.618 1305014.908 1046094.667 991910.9967 236724.7282 4.9554523 5.536991082 3.180564692 3.203617273 4.743744459 5.512795043 4.419034188 4.190145256 1 17.85285089 1.22648183 3.851910299 0.528787076 4.481832769 0.649505078 0.803382065 0.190072917 4.599370955 2.189337045 0.217884802 16.84541948 -1.22648183 3.953045694 QMQVLHPAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QMQVLHPAAR 10 0 P50991 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;;; 101.97 0.0048947 1181787000 1427665 1293688 829061 916507 1230168 1190689 1365099 1443969 1095156 FALSE TRUE 1238995.453 1285189.678 1229997.673 1124613.922 1205690.064 1236495.576 1232711.909 1135187.466 965687.9053 1.283018505 1.330854069 1.273701023 1.164572856 1.248529734 1.280429805 1.276511699 1.175522092 1 19.88119748 1.280190531 2.139363068 0.935804724 1.264358084 0.802207907 0.041914524 0.291486867 1.456761311 0.181157742 0.012281622 19.06296852 -1.280190531 0.32855336 QMVEHGGFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QMVEHGGFYR 10 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 161.67 7.00E-06 949130000 930820 956890 599810 653730 898950 975890 808830 831570 979200 FALSE TRUE 807809.7786 950604.1266 889880.1222 802169.3881 881062.6538 1013433.12 730389.7911 653745.2268 863440.0915 0.935571311 1.10094972 1.030621732 0.929038848 1.02040971 1.173715617 0.845906738 0.757140227 1 19.71973656 2.184067982 16.95645957 0.843721482 1.029630901 0.403964375 0.092389756 3.76982329 1172.032771 0.036924963 0.024895609 152.7805195 -2.184067982 0.185909418 QMVEILHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QMVEILHK 8 0 O76003 O76003 GLRX3 Glutaredoxin-3 0 ; 90.629 0.013061 996870000 1455590 1522870 931730 1112870 1385520 1258260 1480930 1663950 1627810 FALSE TRUE 1263230.094 1512866.167 1382317.744 1365564.143 1357950.863 1306666.076 1337309.637 1308127.241 1435372.156 0.880071477 1.053988793 0.96303787 0.951365914 0.946061868 0.910332607 0.931681467 0.911350576 1 20.45299341 3.483549782 2.251027354 0.93400301 0.973945229 0.043076344 0.048137076 0.65611783 6.654623889 0.013961636 0.021333934 3044.736981 -3.483549782 0.039942219 QMVIDVLHPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QMVIDVLHPGK 11 0 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4 E7ETK0 RPS24 40S ribosomal protein S24 0 127.87 0.00027769 1211600000 2026300 2034100 1281300 1537600 1765000 1604500 2117500 2283300 2549300 FALSE TRUE 1758519.321 2020737.863 1900940.966 1886735.581 1729879.953 1666226.153 1912145.176 1795034.064 2247924.658 0.782285703 0.898934871 0.84564265 0.839323317 0.769545343 0.741228647 0.850626897 0.79852946 1 21.10016225 1.23502356 24.99956809 1.000000257 0.817086244 0.617201084 0.045587619 72.7285817 513957.2939 0.081753317 0.011433248 17.18001583 -1.23502356 -0.182914013 QNAQCLHGDIAQSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QNAQCLHGDIAQSQR 15 0 Q9BQ39;A0A087WVC1 Q9BQ39 DDX50 ATP-dependent RNA helicase DDX50 0 ; 121.19 0.00097982 67619000 83497 80323 42766 49947 71595 68521 75032 79733 78472 FALSE TRUE 72462.6599 79795.35292 63447.78064 61288.22974 70170.39957 71157.04721 67755.40819 62682.71843 69195.12956 1.04722197 1.153193201 0.916939979 0.885730399 1.014094489 1.028353407 0.979193314 0.905883389 1 16.07838287 4.23586919 24.99999979 0.95900934 1.100207598 0.53968245 0.053236977 48.98767254 455052.9019 0.01398283 0.031392104 17213.50023 -4.23586919 0.141198257 QNAVLQAAQDDLGHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QNAVLQAAQDDLGHLR 16 0 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 ; 157.8 3.19E-08 269110000 176117 163121 94621 115501 157936 151066 135469 159457 185735 FALSE TRUE 152842.6922 162049.4474 140380.0321 141727.2674 154793.3826 156877.6068 122331.2372 125358.3614 163777.6199 0.933233077 0.989448055 0.857138064 0.865364068 0.945143681 0.957869621 0.746935004 0.765418142 1 17.3213787 2.251343342 24.99989602 0.81867268 0.922803804 0.205307007 0.07799728 290.5874989 568318.357 0.02951569 0.022711226 178.3788427 -2.251343342 0.104131124 QNEEFRPFIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QNEEFRPFIR 10 1 O15258;Q5T092;A0A0A0MR06;Q5T091 O15258 RER1 Protein RER1 0 ; 149.33 2.15E-05 1556650000 1206700 1213000 676260 755460 1271090 1385980 1097700 1362510 882810 FALSE TRUE 1047231.538 1205031.723 1003301.598 926998.7395 1245797.796 1439299.547 991245.223 1071147.84 778445.2075 1.345286126 1.547998127 1.288853202 1.190833639 1.60036671 1.848941369 1.273365438 1.376009293 1 19.57023597 1.034050489 1.663862277 0.60860133 1.452031208 0.345096173 0.190263041 2.197836218 3.597527286 3.565624117 0.055276638 10.8155968 -1.034050489 0.843429878 QNEHCLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QNEHCLK 7 0 Q9ULV0;A0A0A0MR36;Q9ULV0-2;Q9ULV0-3 Q9ULV0 MYO5B Unconventional myosin-Vb 0 75.38 0.043628 28426000 97199 82368 62184 57089 62962 75128 89042 96231 96324 FALSE TRUE 84353.90588 81826.91918 92256.39039 70051.93 61709.17938 78018.22277 80406.72054 75652.74952 84936.68645 0.993138647 0.963387231 1.086178355 0.824754684 0.726531514 0.918545637 0.946666557 0.890695796 1 16.37410021 3.733562758 24.9942431 0.883891627 1.009149993 0.378083106 0.078324396 474.4493134 2372718.013 0.022545226 0.034623166 5414.554854 -3.733562758 0.125258366 QNGDDPLLTYR ddPTM_MDA-MB-175_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 ;;; 209.97 3.34E-08 1465490000 1434500 1359550 808660 1010710 1312280 1423800 1244490 1451940 1563060 FALSE TRUE 1244927.19 1350619.027 1199730.681 1240207.153 1286168.195 1478574.507 1123799.551 1141453.93 1378276.827 0.903249018 0.979933058 0.870456977 0.899824425 0.933171167 1.072770345 0.815365628 0.828174651 1 20.39443425 QNGS(ph)NDSDRYS(ph)DNEEDSKIELK ddPTM_MDA-MB-175_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(0.537)NDS(0.463)DRY(0.331)S(0.668)DNEEDSKIELK 55.158 0.051478 111880000 105070 81605 73591 100720 110030 75624 100330 183750 134420 TRUE FALSE 91184.73329 81068.93138 109179.8537 123590.0154 107840.6183 78533.30422 90600.01204 144456.4924 118529.0207 0.769303017 0.683958501 0.921123393 1.042698359 0.909824595 0.662566043 0.764369869 1.218743659 1 16.85488081 1.747112835 17.52397137 1.108579233 0.82621935 0.476745919 0.125110287 0.224900529 464.9879822 0.071357469 0.034165059 55.86153114 -1.747112835 -0.282359883 QNGSNDSDRYS(ph)DNEEDSKIELK ddPTM_MDA-MB-175_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(1)DNEEDSKIELK;QNGSNDSDRYS(1)DNEEDSKIELK;QNGSNDSDRYS(1)DNEEDSKIELK 246.31 3.12E-31 3668370000 3467810 2403700 2206480 2929210 3194210 2230660 2888890 5273690 3756180 TRUE FALSE 3009530.122 2387909.936 3273541.108 3594331.901 3130651.47 2316474.934 2608725.892 4145952.433 3312128.679 0.908639251 0.720959289 0.988349616 1.085202976 0.945208285 0.699391587 0.787628183 1.251748599 1 21.65932729 1.74309161 25 1.12835873 0.87866325 0.381147549 0.132083251 0.84844641 4708.85456 0.073514172 0.035302283 55.34668451 -1.74309161 -0.24969548 QNGSNDSDRYS(ph)DNEEGK ddPTM_MDA-MB-175_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 318.64 1.25E-58 2096150000 2078569 1523487 1429642 1671916 1776721 1459876 1983832 2451411 3285768 TRUE FALSE 1803880.84 1513479.114 2121021.653 2051550.081 1741367.728 1516038.374 1791440.278 1927195.835 2897328.25 0.622601474 0.522370606 0.73206122 0.708083415 0.601025351 0.523253923 0.618307669 0.665163098 1 21.46629171 1.218857244 3.247129211 1.074784326 0.619071207 0.762344408 0.066421909 0.191281008 2.632064452 0.229006129 0.017934982 16.55225787 -1.218857244 -0.455713119 QNGSNDSDRYS(ph)DNEEGKKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QNGSNDSDRYSDNEEGKKK 19 3 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 QNGSNDS(0.175)DRYS(0.825)DNEEGKKK;QNGS(0.003)NDS(0.029)DRY(0.003)S(0.965)DNEEGKKK;QNGSNDSDRYS(1)DNEEGKKK;QNGS(0.001)NDS(0.006)DRY(0.001)S(0.993)DNEEGKKK;QNGSNDS(0.002)DRYS(0.998)DNEEGKKK 196.2 4.68E-15 725880000 1230700 689728 602238 497122 598253 411933 1169330 1324730 276611 TRUE FALSE 1068059.877 685197.1314 893482.3112 610001.1481 586348.9358 427780.3291 1055928.557 1041446.799 243910.3627 4.378903237 2.809216975 3.663158471 2.50092346 2.403952539 1.753842372 4.32916644 4.269793161 1 17.89599153 6.344245172 1.593884883 2.972838112 199.7813022 0.159006704 1.055060509 460.3978313 10.53590793 0.296430391 324031.8504 2209251.57 -6.344245172 196.8084641 QNLFQEAEEFLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 QNLFQEAEEFLYR 13 0 A0A087X1Z3;Q9UL46 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;;;;;;; 333.38 3.84E-62 1844038000 918075 1115043 559622 697241 828978 803816 830640 1005880 1304391 FALSE TRUE 796749.0626 1107718.209 830257.071 855560.2257 812482.9597 834739.3217 750084.6606 790780.3898 1150187.382 0.692712401 0.963076301 0.721845052 0.743844211 0.706391821 0.725742027 0.652141271 0.687523096 1 20.13343749 QNPEQS(ph)ADEDAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QNPEQSADEDAEK 13 0 Q99613-2;Q99613;B5ME19;H3BPE3 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 1 QNPEQS(1)ADEDAEK 146.67 4.45E-05 168970000 125140 99625 100010 109330 101790 91225 126430 126530 300200 TRUE FALSE 108602.4319 98970.55682 148375.1705 134155.0475 99764.57815 94734.48478 114168.8381 99472.54416 264710.698 0.41026839 0.373881968 0.560518225 0.506798737 0.37688155 0.357879321 0.431296653 0.375778331 1 18.01405698 1.235648172 24.99980201 1.000000778 0.423952532 0.888029255 0.064259964 26.65663308 228772.0171 0.113043179 0.016628923 17.20474232 -1.235648172 -0.576048246 QNPHDGVVT(ph)PAAS(ph)PSLPQPGLQMPGQWGPVQGGPQPSGQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QNPHDGVVTPAASPSLPQPGLQMPGQWGPVQGGPQPSGQHR 41 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 2 QNPHDGVVT(1)PAAS(0.984)PS(0.016)LPQPGLQMPGQWGPVQGGPQPSGQHR;QNPHDGVVT(1)PAAS(0.972)PS(0.028)LPQPGLQMPGQWGPVQGGPQPSGQHR 250.85 2.16E-55 4645600000 158184 194742 59413 167214 210917 222028 173836 219680 190301 TRUE FALSE 137279.5836 193462.727 88145.32552 205182.4944 206720.1644 230569.5608 156977.4115 172703.1416 167803.8326 0.818095639 1.152910062 0.525287916 1.222752134 1.231915631 1.374042281 0.935481682 1.029196645 1 17.35641614 3.682448328 24.99992369 1.12343075 0.864175404 0.339093732 0.195566435 365.6722194 162919.1056 0.054006741 0.080104977 4813.359813 -3.682448328 -0.259255346 QNPHDGVVT(ph)PAASPSLPQPGLQMPGQWGPVQGGPQPSGQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QNPHDGVVTPAASPSLPQPGLQMPGQWGPVQGGPQPSGQHR 41 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 QNPHDGVVT(0.945)PAAS(0.055)PSLPQPGLQMPGQWGPVQGGPQPSGQHR;QNPHDGVVT(1)PAASPSLPQPGLQMPGQWGPVQGGPQPSGQHR 207.61 2.67E-35 638710000 24401.5 20111.7 17018.6 19401.6 24418.7 19683.4 24491.1 27723.7 22368.6 TRUE FALSE 21176.77995 19979.58492 25248.85188 23807.02981 23932.81564 20440.63313 22115.95689 21795.2025 19724.20959 1.073644034 1.012947304 1.280094483 1.206995378 1.213372609 1.036322041 1.121259475 1.104997511 1 14.26767987 2.73263753 24.80417064 1.077007506 1.158955477 0.236008049 0.080875274 776.2606861 3250746.607 0.0290748 0.026335181 540.3031877 -2.73263753 0.081947971 QNPHDGVVTPAAS(ph)PSLPQPGLQMPGQWGPVQGGPQPSGQHR ddPTM_MDA-MB-175_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(0.976)PS(0.024)LPQPGLQMPGQWGPVQGGPQPSGQHR 166.68 1.11E-19 359960000 11175 8107.4 2701.7 4216.8 17633 11455 13884 13707 8748.2 TRUE FALSE 9698.195436 8054.141956 4008.251157 5174.28889 17282.1378 11895.68126 12537.53182 10775.86472 7713.997762 1.257220411 1.044094412 0.519607508 0.67076619 2.240360748 1.542090318 1.625296274 1.396923496 1 12.91326301 3.271630061 24.99999675 1.544318637 0.859911672 0.476716034 0.357834158 174.182934 131678.513 0.105694053 0.136441483 1869.089343 -3.271630061 -0.684406965 QNRDEVLDNLLAFVCDIRPEIHENYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QNRDEVLDNLLAFVCDIRPEIHENYR 26 2 O75348 O75348 ATP6V1G1 V-type proton ATPase subunit G 1 0 ; 131.57 3.75E-05 426950000 388590 401140 170406 179901 337530 327820 320090 384070 100693 FALSE TRUE 337236.8469 398504.8849 252814.9116 220750.2717 330813.8134 340431.4475 289047.7211 301939.6193 88789.18825 3.798174683 4.488214081 2.847361447 2.486229191 3.725834416 3.834154296 3.255438266 3.400634979 1 16.43809639 4.233690854 24.99835505 3.038568517 4.143194486 0.267147451 0.817781189 155.9766153 800704.1348 0.206399478 0.452728307 17127.37689 -4.233690854 1.104625968 QNTASPGS(ph)PVNSHLPGS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QNTASPGSPVNSHLPGSPK 19 0 Q8NDX1-2;Q8NDX1 Q8NDX1-2 PSD4 PH and SEC7 domain-containing protein 4 2 QNT(0.012)AS(0.033)PGS(0.954)PVNSHLPGS(1)PK 127.59 1.22E-05 402240000 180920 163460 127970 148220 213890 178610 223150 254420 220180 TRUE FALSE 157010.9636 162386.2205 189856.72 181875.6164 209634.0075 185481.2423 201508.9473 200014.2629 194150.5712 0.808707194 0.836393215 0.977883912 0.936776108 1.07974963 0.955347394 1.037900358 1.030201774 1 17.56681643 4.271253323 1.190650811 1.01768636 0.771088356 0.776795084 0.040435492 0.31172275 0.644541766 0.011708969 0.078886963 18674.68665 -4.271253323 -0.246598005 QNTAWEFEES(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QNTAWEFEESPR 12 0 A0A1B0GU24;Q9HCJ0-2;Q9HCJ0 A0A1B0GU24 TNRC6C Trinucleotide repeat-containing gene 6C protein 1 QNTAWEFEES(1)PR 218.79 3.51E-11 338450000 168900 156500 121530 127820 153810 179430 173120 170910 207060 TRUE FALSE 146579.4371 155471.9412 180302.3145 156843.4846 150749.4819 186332.7882 156330.849 134362.2265 182581.6027 0.802816028 0.851520301 0.987516332 0.859032248 0.825655377 1.020545255 0.856224542 0.735902328 1 17.47818188 2.008317371 24.97738188 0.833179937 0.893406269 0 0.093122187 489.311407 1469414.681 0.037203834 0.025036637 101.9336019 -2.008317371 0.060226331 QNVAYEYLCHLEEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QNVAYEYLCHLEEAK 15 0 P46940;A0A0J9YXZ5;A0A087X225 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 193.69 8.26E-08 255500000 466890 467990 369440 480800 433040 353180 536840 585910 1167520 FALSE TRUE 405189.3036 464915.7429 548102.4197 589972.9886 424423.3512 366767.0631 484777.3394 460617.7061 1029497.116 0.393579834 0.451594993 0.532398208 0.573069103 0.412262788 0.356258466 0.470887516 0.447420104 1 19.97350836 1.237964935 24.99996288 1.00000062 0.456733029 0.881192298 0.062923108 4.960026193 207988.312 0.094105778 0.016284732 17.29676697 -1.237964935 -0.543267591 QNVAYEYLCHLEEAKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QNVAYEYLCHLEEAKR 16 1 P46940;A0A0J9YXZ5;A0A087X225 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 206.74 1.25E-11 2711100000 3187200 3002800 1797730 2038140 2831700 2319540 3209200 3835900 1691720 FALSE TRUE 2766003.445 2983074.409 2667118.241 2500930.838 2775354.71 2408774.205 2897972.278 3015622.636 1491726.789 1.85422925 1.999745819 1.787940165 1.676534106 1.860498002 1.614755613 1.94269641 2.02156498 1 20.5085519 1.2313857 24.99998552 0.999998526 1.848742474 0.808956423 0.128999558 114.7881189 399927.6714 0.332657558 0.033556805 17.03670879 -1.2313857 0.848743948 QPAQELS(ph)PTPGGTAHQALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QPAQELSPTPGGTAHQALK 19 0 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 QPAQELS(0.817)PT(0.183)PGGTAHQALK;QPAQELS(1)PTPGGTAHQALK;QPAQELS(0.977)PT(0.023)PGGTAHQALK;QPAQELS(0.999)PT(0.001)PGGTAHQALK 258.05 3.32E-31 3079350000 2639170 2590670 1605990 2191150 2631010 2391240 2804550 3301420 2695480 TRUE FALSE 2290396.998 2573651.718 2382652.136 2688684.097 2578658.048 2483232.55 2532565.173 2595437.025 2376823.425 0.963637843 1.082811492 1.002452311 1.13120902 1.084917803 1.04476947 1.065525165 1.091977215 1 21.1806033 5.568091679 1.711218187 1.066858544 4.60E-14 0.356058643 0.040660747 16.96199348 5.383179184 0.01023896 57.92225402 369906.2586 -5.568091679 -1.066858544 QPAQSQNLS(ph)PLSGFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QPAQSQNLSPLSGFSR 16 0 Q9P2M7;Q9P2M7-2;A6PVU7 Q9P2M7 CGN Cingulin 1 QPAQSQNLS(0.934)PLS(0.066)GFSR;QPAQSQNLS(0.998)PLS(0.002)GFSR;QPAQSQNLS(1)PLSGFSR;QPAQSQNLS(0.968)PLS(0.032)GFSR;QPAQSQNLS(1)PLSGFSR;QPAQS(0.016)QNLS(0.978)PLS(0.005)GFS(0.001)R 242.95 5.93E-20 7026570000 2078695 2213279 1515193 2000394 2541525 2715028 2303034 2777260 2557742 TRUE FALSE 1803990.189 2198739.825 2247945.403 2454614.032 2490953.625 2819476.884 2079686.117 2183364.562 2255368.655 0.799864885 0.974891542 0.99670863 1.088342709 1.104455194 1.25011797 0.922104736 0.968074358 1 21.10493184 4.821656807 1.540560022 1.046137801 0.671356138 0.437721283 0.089369851 1.475447966 2.827433924 0.027027425 0.887407793 66321.87666 -4.821656807 -0.374781663 QPASAQSTPSTTPHSS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QPASAQSTPSTTPHSSPK 18 0 A0A087WT18;Q96A73-2;Q96A73 A0A087WT18 KIAA1191 Putative monooxygenase p33MONOX 1 QPASAQSTPSTTPHS(0.063)S(0.937)PK;QPASAQSTPSTTPHS(0.25)S(0.75)PK 194.97 2.95E-15 463410000 216480 174804 89750 159531 224292 221980 189480 253070 230100 TRUE FALSE 187871.6195 173655.701 133153.4002 195754.9518 219829.028 230519.7142 171104.2588 198952.9499 202897.8401 0.925941939 0.855877524 0.656258342 0.964795642 1.083446861 1.136136856 0.843302514 0.980557259 1 17.63039398 3.502542164 23.96132708 1.001411677 0.815930346 0.447538656 0.099727144 430.9614082 406215.6133 0.028239278 0.04166174 3180.84249 -3.502542164 -0.185481331 QPCT(ph)PPPQPQQQQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QPCTPPPQPQQQQVK 15 0 P35321 P35321 SPRR1A Cornifin-A 1 QPCT(1)PPPQPQQQQVK;QPCT(1)PPPQPQQQQVK;QPCT(1)PPPQPQQQQVK;QPCT(1)PPPQPQQQQVK 177.63 8.33E-06 1236350000 1271390 1282020 835740 1065100 1328140 1154080 1578380 1780830 1605120 TRUE FALSE 1103372.59 1273598.326 1239906.659 1306947.234 1301712.612 1198478.204 1425308.951 1400013.363 1415364.542 0.779567777 0.899837666 0.876033433 0.923399729 0.919701302 0.846762914 1.00702604 0.989153904 1 20.43274225 -1.999965116 0.034444354 2.280710827 1.22E-05 0.642710542 0.042745997 1456.026576 4.955065699 243.0919185 110.1848207 0.010000803 1.999965116 -2.280698615 QPDISCILGTGGKS(ph)PR ddPTM_MDA-MB-175_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(0.011)GGKS(0.989)PR 208.08 9.56E-12 3767370000 2593380 2385630 1718930 2084430 2591770 2381880 2915670 3318290 2412690 TRUE FALSE 2250658.262 2369958.639 2550210.297 2557731.69 2540198.848 2473512.465 2632908.772 2608699.506 2127464.537 1.057906359 1.113982677 1.198708723 1.202244101 1.19400291 1.162657437 1.237580569 1.226201171 1 21.02070365 4.447022808 3.215283264 1.183664431 1.063309927 0.245812655 0.066483226 0.310276448 6.282443566 0.016484107 0.065660792 27991.28316 -4.447022808 -0.120354504 QPDKEFSFMDEEEEDEIRV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QPDKEFSFMDEEEEDEIRV 19 2 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 0 ;; 131.65 6.03E-05 256669000 303634 249967 185870 229756 238633 238707 312180 359839 239990 FALSE TRUE 263507.9976 248324.9503 275757.3537 281925.6114 233884.6702 247890.2128 281904.8316 282890.2301 211618.6556 1.245202115 1.173454909 1.303086219 1.332234205 1.105217636 1.171400565 1.332136011 1.336792493 1 17.69110729 QPDPDENKPMEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QPDPDENKPMEDK 13 1 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;A0A0C4DGD1;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ;; 107.61 0.0011689 579850000 1112790 875360 1016470 1030370 847600 556490 1186920 1459760 1824170 FALSE TRUE 965731.982 869609.7025 1508038.292 1264331.257 830734.4183 577898.5304 1071812.681 1147601.684 1608518.701 0.600385921 0.540627661 0.937532334 0.786022106 0.516459285 0.359273741 0.666335232 0.713452497 1 20.61730128 1.213136398 2.272038787 1.119343381 0.63066654 0.36015303 0.154704096 0.851683467 4.288770871 0.870231712 0.044575897 16.33564918 -1.213136398 -0.488676842 QPEKEEEEEAGES(ph)VEDIFSEVVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QPEKEEEEEAGESVEDIFSEVVGR 24 1 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 QPEKEEEEEAGES(1)VEDIFSEVVGR 88.668 0.0064371 23872000 72379 47770 42928 45294 49082 45497 54859 60905 60925 TRUE FALSE 62813.93176 47456.19572 63688.12439 55578.69498 48105.36423 47247.29903 49538.78262 47880.93971 53722.51591 1.169229153 0.883357656 1.185501522 1.034551231 0.895441388 0.879469218 0.922123281 0.891263912 1 15.71323925 3.315586981 5.060806789 0.912857117 1.0668205 0.42798504 0.086984943 0.190229093 8.696018188 0.02361385 0.03041432 2068.173557 -3.315586981 0.153963383 QPEKEEEEEAGESVEDIFSEVVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QPEKEEEEEAGESVEDIFSEVVGR 24 1 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 0 94.542 0.0068105 17601000 37491 26068 25334 21683 25184 21829 24867 31277 28183 FALSE TRUE 32536.46936 25896.75759 37585.60714 26606.45655 24682.88767 22668.77576 22455.40217 24588.65695 24851.23785 1.309249445 1.042071134 1.512423943 1.070629025 0.993225683 0.912178938 0.903592904 0.989433891 1 14.60103009 3.507280556 8.055292235 0.963243092 1.268513229 0.623042326 0.116216892 0.169665852 40.21389341 0.03051943 0.04417084 3215.737249 -3.507280556 0.305270137 QPEWLEEQQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QPEWLEEQQGR 11 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 127.03 0.00068671 236240000 110220 120570 89978 93274 106920 85658 151210 118680 107450 FALSE TRUE 95654.14774 119777.9677 133491.6618 114453.2873 104792.5012 88953.31869 136545.6775 93301.20557 94747.38341 1.009570336 1.264182328 1.408921882 1.207983621 1.106020002 0.938847232 1.441155128 0.984736488 1 16.53179848 3.28844922 4.687633551 1.098321337 1.24195185 0.126667603 0.166080349 0.410157806 19.08588298 0.048690601 0.062006467 1942.894504 -3.28844922 0.143630513 QPEYSPES(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QPEYSPESPR 10 0 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 QPEYSPES(1)PR;QPEYSPES(1)PR;QPEYSPES(1)PR;QPEYSPES(1)PR 187.45 1.29E-06 1616420000 1450010 1004230 657880 875840 1041110 1185040 941640 1092650 1223080 TRUE FALSE 1258387.505 997633.147 976032.9685 1074712.858 1020393.948 1230629.256 850319.8977 858995.3005 1078488.876 1.166806198 0.925028685 0.905000497 0.996498789 0.94613303 1.141068103 0.78843641 0.796480446 1 20.04057986 4.738846428 22.74501266 0.926827927 1.166806403 0.330333803 0.101708775 8.283810631 657955.0464 0.026480752 0.149792977 54808.31221 -4.738846428 0.239978476 QPGITFIAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QPGITFIAAK 10 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;A0A1B0GU92;A0A1B0GU03;C9JH19;F8WD96;F8W787 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 93.058 0.021042 104250000 152690 178020 115770 136070 168120 168190 178450 185220 163300 FALSE TRUE 132511.6296 176850.5749 171756.7592 166966.7732 164774.7409 174660.3781 161143.9465 145612.1444 143994.86 0.920252498 1.228172831 1.192797848 1.159532869 1.144309879 1.212962588 1.119095129 1.011231542 1 17.13565779 1.775695269 3.474471345 1.001884164 1.150893113 0.300086099 0.085041037 0.23786442 5.601726293 0.053784592 0.021837532 59.66165129 -1.775695269 0.14900895 QPGS(ph)PSPPSIPETGQGVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QPGSPSPPSIPETGQGVTK 19 0 F8VSJ1;F8VRY0;H0YI55;Q96PM9-1;Q96PM9;F8VQ24 F8VSJ1 ZNF385A Zinc finger protein 385A 1 QPGS(1)PSPPSIPETGQGVTK 206.74 3.67E-16 133010000 86393 72966 69723 101900 90004 69670 85327 112710 194000 TRUE FALSE 74975.94616 72486.68154 103441.276 125037.9524 88213.09649 72350.24998 77052.00067 88607.84361 171065.541 0.438287838 0.423736313 0.604687977 0.730935942 0.515668416 0.422938773 0.450423856 0.517975994 1 17.38418965 1.238805592 9.739266394 1.002291196 0.514363111 0.721091462 0.095168304 0.043631825 79.93326897 0.14215665 0.025319449 17.3302805 -1.238805592 -0.487928085 QPGTCS(ph)PDLAAPLDENGAVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QPGTCSPDLAAPLDENGAVDR 21 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 QPGT(0.001)CS(0.999)PDLAAPLDENGAVDR;QPGTCS(1)PDLAAPLDENGAVDR 217.54 6.05E-25 348060000 230869 196595 146994 203280 212773 197499 184044 210823 393550 TRUE FALSE 200359.0767 195303.5545 218080.7901 249437.8309 208539.2336 205096.9143 166195.4412 165740.1421 347024.9673 0.577362137 0.562793957 0.628429683 0.718789293 0.60093438 0.591014865 0.478914939 0.477602933 1 18.40467994 1.230306868 24.99935354 1.000000782 0.576383296 0.784146216 0.069320879 165.7387345 501957.3666 0.218022205 0.019700113 16.99444039 -1.230306868 -0.423617486 QPGVDS(ph)LSPVASLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QPGVDSLSPVASLPK 15 0 Q9UBW7;Q9UBW7-2;A0A087X151 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 1 QPGVDS(0.709)LS(0.291)PVASLPK;QPGVDS(0.69)LS(0.31)PVASLPK 102.38 0.0028842 49766000 81867 67682 51510 59714 73187 66310 78178 98266 98314 TRUE FALSE 71048.06853 67237.39249 76420.40829 73272.97637 71730.72189 68860.98861 70596.30959 77252.58061 86691.43092 0.819551226 0.775594448 0.881522054 0.845215907 0.827425746 0.794322898 0.814340112 0.8911213 1 16.40360178 1.343122894 2.241725781 1.026754698 0.823079929 0.800375167 0.0284735 0.224055774 1.423758737 0.084461612 0.0079601 22.03549921 -1.343122894 -0.203674769 QPGVDSLS(ph)PVASLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QPGVDSLSPVASLPK 15 0 Q9UBW7;Q9UBW7-2;A0A087X151 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 1 QPGVDSLS(1)PVASLPK;QPGVDS(0.001)LS(0.999)PVASLPK 244.1 5.42E-18 338850000 467350 413290 266470 375120 369210 344810 418270 529890 547930 TRUE FALSE 405588.5134 410575.0708 395335.7833 460296.7294 361863.4433 358075.0638 377706.2398 416577.1471 483154.3396 0.839459527 0.849780364 0.818239123 0.952690873 0.74896035 0.74111942 0.781750693 0.862203054 1 18.88212459 1.273783515 3.149080121 1.023458336 0.819674846 0.477496883 0.059358476 0.303352288 4.070088942 0.147069049 0.016037121 18.78380259 -1.273783515 -0.20378349 QPGYQPPNPHPGPS(ph)SPPAAPASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QPGYQPPNPHPGPSSPPAAPASK 23 0 Q9BUL9 Q9BUL9 RPP25 Ribonuclease P protein subunit p25 1 QPGYQPPNPHPGPS(0.5)S(0.5)PPAAPASK 141.78 1.16E-07 575810000 377940 247180 138720 247590 264020 222820 257900 345640 340440 TRUE FALSE 327994.2714 245556.2583 205805.456 303809.0937 258766.5185 231392.0296 232888.8977 271727.5758 300193.571 1.092609246 0.817993062 0.685575828 1.012043971 0.861998868 0.770809411 0.775795754 0.905174534 1 18.19553355 1.357013398 3.667228341 1.002295404 0.853177413 0.122180627 0.117861089 0.499410362 9.789958684 0.164379087 0.029493451 22.75167619 -1.357013398 -0.149117991 QPGYQPPNPHPGPSS(ph)PPAAPASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QPGYQPPNPHPGPSSPPAAPASK 23 0 Q9BUL9 Q9BUL9 RPP25 Ribonuclease P protein subunit p25 1 QPGYQPPNPHPGPS(0.232)S(0.768)PPAAPAS(0.001)K;QPGYQPPNPHPGPS(0.12)S(0.88)PPAAPASK 138.4 2.44E-06 810930000 425000 272410 158366 262587 297950 249553 280140 370850 373600 TRUE FALSE 368835.1732 270620.5208 234952.3273 322211.3917 292021.3779 259153.4654 252972.0659 291546.6135 329433.4336 1.119604556 0.821472544 0.713201222 0.978077386 0.886435158 0.78666413 0.767900401 0.884994004 1 18.32962745 2.972031339 24.04675859 0.85311725 0.893515854 0.027033961 0.12029545 2272.9956 1954264.997 0.038986516 0.039086807 937.6296645 -2.972031339 0.040398604 QPHVGDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QPHVGDYR 8 0 Q06323;Q06323-3;Q06323-2;H0YKK6 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;;;;; 111.61 0.0032009 8650080000 7504110 7247450 4430030 5392460 7017110 7952710 6916340 7553110 6647640 FALSE TRUE 6512422.851 7199841.024 6572407.326 6616900.462 6877483.24 8258655.9 6245594.411 5937936.205 5861763.572 1.111000601 1.228272163 1.12123378 1.128824181 1.173278853 1.408902935 1.065480437 1.012994832 1 22.48290335 2.016837584 24.99971954 1.016969151 1.193355429 0.47871104 0.084679037 196.1567766 291244.0636 0.034661134 0.023362442 103.9531331 -2.016837584 0.176386278 QPLFS(ph)PETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QPLFSPETR 9 0 Q9BQ89 Q9BQ89 FAM110A Protein FAM110A 1 QPLFS(0.998)PET(0.002)R 86.114 0.01506 130450000 168920 156520 106350 122520 166300 176620 145500 154910 150520 TRUE FALSE 146596.794 155491.8098 157781.2157 150340.0386 162990.9554 183414.6857 131389.4324 121783.702 132725.6971 1.104509505 1.171527543 1.188776697 1.132712368 1.228028626 1.381907873 0.989932133 0.917559332 1 17.01808819 2.082391159 9.176990597 0.953162909 1.197206483 0.675250856 0.076033843 0.162858513 16.50557725 0.031554636 0.021253505 120.8902174 -2.082391159 0.244043573 QPLLLS(ph)EDEEDTKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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(0.998)EDEEDT(0.002)KR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR 264.92 6.16E-25 75553570000 10062870 8580640 6708580 7625730 8960170 7351260 10853730 12296590 11240210 TRUE FALSE 8733036.233 8524273.211 9952871.727 9357268.548 8781880.147 7634067.729 9801136.935 9667059.921 9911405.179 0.8811098 0.860046891 1.00418372 0.944091012 0.886037851 0.770230617 0.98887461 0.975347062 1 23.24065818 QPLLLSEDEEDT(ph)KR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QPLLLSEDEEDTKR 14 1 Q99613-2;Q99613;B5ME19;H3BPE4 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 1 QPLLLS(0.119)EDEEDT(0.881)KR 228.55 3.12E-12 540420000 919770 759050 535800 629670 735070 658770 944880 1070200 920420 TRUE FALSE 798220.0641 754063.7506 794914.6721 772646.1974 720443.5451 684113.3082 853245.683 841346.0583 811608.9961 0.983503224 0.929097329 0.979430583 0.951993141 0.887673188 0.842909962 1.051301411 1.036639641 1 19.63042533 2.210218121 24.99993253 1.031756135 0.930546165 0.547291921 0.042932439 165.631213 146096.3493 0.018446988 0.012439686 162.2624842 -2.210218121 -0.10120997 QPPGPVPT(ph)PPLPSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QPPGPVPTPPLPSER 15 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QQI0 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 QPPGPVPT(1)PPLPSER 113.01 0.0080296 301220000 194230 200110 138620 186910 235310 255800 238230 256620 237660 TRUE FALSE 168562.0134 198795.4642 205657.0957 229350.7722 230627.7914 265640.7915 215126.4913 201743.81 209564.1055 0.804345825 0.948614095 0.981356493 1.094418205 1.100511897 1.267587266 1.026542645 0.962683039 1 17.67703211 4.537259449 1.386834668 1.067747358 0.757690135 0.522819394 0.083066314 0.827264429 1.903647704 0.027223006 0.324530925 34455.57077 -4.537259449 -0.310057223 QPPGTQQSHSS(ph)PGEITSSPQGLDNPALLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QPPGTQQSHSSPGEITSSPQGLDNPALLR 29 0 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 1 QPPGTQQS(0.006)HS(0.156)S(0.838)PGEITSSPQGLDNPALLR;QPPGTQQS(0.002)HS(0.117)S(0.881)PGEITSSPQGLDNPALLR;QPPGTQQS(0.012)HS(0.255)S(0.733)PGEITSSPQGLDNPALLR 234.28 2.10E-45 995640000 156549 141026 94571 117260 119870 152592 127388 159750 181634 TRUE FALSE 135860.653 140099.5909 140305.8519 143885.6752 117484.8215 158462.313 115033.9314 125588.7057 160161.4354 0.848273198 0.874739856 0.876027688 0.898379031 0.733540014 0.989391189 0.71823739 0.784138237 1 17.28916728 QPPGVPNGPSS(ph)PTNESAPELPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QPPGVPNGPSSPTNESAPELPQR 23 0 Q8TF74;Q8TF74-2 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 1 QPPGVPNGPS(0.081)S(0.72)PT(0.193)NES(0.006)APELPQR;QPPGVPNGPS(0.24)S(0.722)PT(0.035)NES(0.003)APELPQR 120.32 6.46E-05 770970000 435520 522010 377210 603450 739000 753340 651120 858360 723690 TRUE FALSE 377964.9285 518580.8819 559630.0177 740472.5457 724295.3458 782321.4773 587974.4826 674806.3938 638136.1926 0.592295082 0.812649224 0.876975831 1.160367574 1.135016873 1.225947511 0.92139341 1.057464537 1 19.28350483 4.303850794 1.589546509 1.076634539 0.594243886 0.751761666 0.093309495 0.261604706 1.093235878 0.027705724 0.153471397 20130.32535 -4.303850794 -0.482390653 QPPLLGDHPAEYGEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QPPLLGDHPAEYGEGR 16 0 A0A3B3ITJ4 A0A3B3ITJ4 0 164.57 7.33E-09 159880000 106560 107870 68617 73774 95662 103670 92242 104590 126480 FALSE TRUE 92477.82601 107161.3949 101800.4107 90525.51426 93758.51336 107658.252 83296.38504 82224.24242 111527.6785 0.829191706 0.960850224 0.912781581 0.811686529 0.840674841 0.965305236 0.74686738 0.737254138 1 16.76704227 3.348468165 0.907035371 0.827392921 0.903377765 0 0.091208083 1.686744751 3.116035304 0.047919903 0.082910234 2230.838673 -3.348468165 0.075984844 QPPMFS(ph)PLISAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QPPMFSPLISAR 12 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3;F8W719;E7EPJ2 A0A087WVF7 ITSN2 Intersectin-2 1 QPPMFS(1)PLISAR;QPPMFS(1)PLISAR 147.12 6.85E-05 196335000 140557 146087 86982 107636 139121 157707 126624 154594 123067 TRUE FALSE 121982.0363 145127.3449 129046.7861 132076.3989 136352.7643 163774.0903 114344.024 121535.2762 108518.1595 1.124070266 1.337355385 1.189172271 1.217090297 1.256497207 1.509186031 1.053685619 1.119953349 1 16.72757696 QPPPASS(ph)PTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QPPPASSPTK 10 0 A0A0J9YWL0;Q9Y4K1;A0A494C1M5 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 QPPPAS(0.062)S(0.929)PT(0.01)K 66.56 0.068099 0 83750 68354 47169 64091 62027 62351 73276 93650 107540 TRUE FALSE 72682.2253 67904.97807 69980.08617 78643.84112 60792.78405 64749.68332 66169.7048 73623.67629 94826.74371 0.766473913 0.716095222 0.737978374 0.82934242 0.641093237 0.682820909 0.697795814 0.77640203 1 16.53300638 1.23882187 2.972067005 1.053406527 0.724367998 0.74721054 0.050023221 0.202874704 2.220039272 0.161269035 0.013217441 17.33093007 -1.23882187 -0.329038529 QPPTAAGRPVDAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QPPTAAGRPVDASPR 15 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 QPPTAAGRPVDAS(1)PR 79.461 0.012037 469150000 208350 212720 125990 142000 165080 207960 192280 219770 195580 TRUE FALSE 180816.0196 211322.6283 186919.1854 174243.2703 161795.231 215960.3558 173632.7152 172773.8958 172458.7552 1.048459496 1.225351697 1.083848629 1.010347489 0.938167684 1.252243503 1.006807193 1.001827339 1 17.39589185 2.605224333 0.024120934 3.67E-05 2.105684766 0.103838853 0.095733377 1048.635302 23.75287966 1058.509787 1013.107367 402.9251099 -2.605224333 2.105648024 QPPTAAGRPVDASPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QPPTAAGRPVDASPR 15 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 90.453 0.0054793 161480000 93743 101540 58937 73629 106810 111830 93603 108840 88692 FALSE TRUE 81354.62504 100872.9771 87439.13033 90347.5898 104684.69 116132.1725 84525.39547 85565.41299 78206.9328 1.040248251 1.289821419 1.118048326 1.155237606 1.33856023 1.484934498 1.080791593 1.094089871 1 16.25500888 2.038877609 24.99997898 1.063867334 1.239497765 0.317180849 0.124332699 192.3982308 123719.5845 0.052055492 0.035095751 109.3648115 -2.038877609 0.175630431 QPS(ph)EEEIIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 QPSEEEIIK 9 0 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 1 QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK 162.32 6.70E-05 58586520000 13619550 10559660 5743338 8710910 9320130 5156463 15022380 13081360 10133240 TRUE FALSE 11819691.96 10490292.9 8520835.467 10688855.25 9134677.648 5354835.468 13565511.9 10284012.96 8935299.911 1.322808644 1.174028069 0.953614938 1.196250306 1.022313491 0.599289954 1.518193237 1.150942113 1 23.09108472 4.58395056 3.734870677 1.080946579 1.318100114 0.11539448 0.228215581 0.595365477 13.70153383 0.056683183 0.286879115 38366.35666 -4.58395056 0.237153534 QPS(ph)LTLELFPNHTDNLNSSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QPSLTLELFPNHTDNLNSSQR 21 0 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;A0A0J9YW54 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 QPS(0.999)LT(0.001)LELFPNHTDNLNSSQR 158.8 1.50E-11 96867000 23216 19267 7208.1 14148 21115 18800 25145 19504 17880 TRUE FALSE 20147.94678 19140.43381 10693.96127 17360.51964 20694.85281 19523.24817 22706.44177 15333.22138 15766.24677 1.277916493 1.214013334 0.678281992 1.101119366 1.312604903 1.238293961 1.440193224 0.972534656 1 13.94455164 3.470407673 24.85824827 1.187932969 1.042004186 0.084964021 0.205741312 396.1269207 1466724.106 0.06185934 0.08006242 2953.980834 -3.470407673 -0.145928783 QPS(ph)PSPS(ph)PTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QPSPSPSPTER 11 0 P29590-2;P29590-5;P29590-9;P29590-3;P29590-8;P29590;P29590-4;P29590-14;P29590-10;P29590-12;P29590-13;P29590-11;H3BT57 P29590-2;P29590-12 PML Protein PML 2 QPS(0.93)PS(0.071)PS(0.997)PT(0.002)ER;QPS(0.882)PS(0.12)PS(0.993)PT(0.005)ER 157.82 4.45E-05 340730000 366280 316220 272140 300690 350890 320040 299000 354230 616880 TRUE FALSE 317875.17 314142.73 403747.8143 368966.2603 343907.9755 332352.1459 270003.026 278480.6711 543953.1492 0.584379685 0.577517991 0.742247407 0.67830522 0.632238229 0.610994065 0.496371841 0.51195709 1 19.05312287 1.230590283 24.99902387 1.000000724 0.601744712 0.748855974 0.072012121 171.9060594 539140.8077 0.217448405 0.020252183 17.00553436 -1.230590283 -0.398256012 QPS(ph)PSPSPTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QPSPSPSPTER 11 0 P29590-2;P29590-5;P29590-9;P29590-3;P29590-8;P29590;P29590-4;P29590-14;P29590-10;P29590-12;P29590-13;P29590-11;H3BT57 P29590-2;P29590-12 PML Protein PML 1 QPS(0.96)PS(0.039)PSPTER 148.48 3.65E-05 189090000 56015 52992 47083 55809 54249 51263 43951 58031 106760 TRUE FALSE 48612.47583 52643.89206 69852.49628 68481.28644 53169.55104 53235.12078 39688.63878 45621.52225 94138.95442 0.51639065 0.559214752 0.742014788 0.727448981 0.564798615 0.565495135 0.421596342 0.484618961 1 16.52250421 1.231496212 24.99985034 1.000000742 0.570719678 0.6517541 0.098151587 180.950388 640298.6965 0.268010497 0.027338261 17.04104458 -1.231496212 -0.429281064 QPS(ph)SPSHNTNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QPSSPSHNTNLR 12 0 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 QPS(0.579)S(0.42)PS(0.001)HNTNLR;QPS(0.521)S(0.457)PS(0.022)HNTNLR;QPS(0.498)S(0.498)PS(0.004)HNTNLR 147.1 4.21E-05 1006560000 595220 647690 276999 482260 677970 695850 625690 709330 647260 TRUE FALSE 516560.1689 643435.2817 410956.6429 591764.5039 664479.7234 722619.7998 565010.6801 557645.2995 570741.6602 0.905068273 1.127366945 0.720039681 1.036834255 1.164239042 1.26610663 0.989958714 0.977053785 1 19.12247835 3.496688987 24.8959323 1.072128513 0.928472128 0.244874712 0.129381621 1195.440512 1520950.228 0.037031644 0.054006551 3138.260474 -3.496688987 -0.143656385 QPS(ph)SPYEDKDKDKK ddPTM_MDA-MB-175_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(0.584)S(0.416)PYEDKDKDKK;QPS(0.582)S(0.418)PYEDKDKDKK 97.284 0.016774 1463040000 1788790 818440 1406150 751610 627040 402850 1475720 1534630 867380 TRUE FALSE 1552396.869 813063.6138 2086168.843 922274.5381 614563.1308 418347.9002 1332604.902 1206461.317 764839.3245 2.029703259 1.063051529 2.727590981 1.205840898 0.803519264 0.546974883 1.74233314 1.577404925 1 19.54479718 3.539432769 24.99977056 1.187453243 1.871460918 0.334229452 0.5232628 305.9860819 122762.4013 0.146307436 0.217008738 3462.842736 -3.539432769 0.684007675 QPS(ph)VETLDSPTGSHVEWCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QPSVETLDSPTGSHVEWCK 19 0 F8WA39;Q13613;Q13613-2;E9PPP8;Q8NEC6 F8WA39 MTMR1 Myotubularin-related protein 1 1 QPS(0.649)VET(0.348)LDS(0.002)PTGSHVEWCK;QPS(0.998)VET(0.002)LDSPTGSHVEWCK 192.99 4.04E-15 775780000 1029590 836640 366040 569880 770700 665880 1245300 1098070 898730 TRUE FALSE 893527.0729 831144.0568 543058.1683 699279.9641 755364.5778 691496.8345 1124530.998 863256.2757 792483.1632 1.12750291 1.048784498 0.685261459 0.882390941 0.953161673 0.872569749 1.418996705 1.089305509 1 19.59602076 2.282982711 24.99999001 1.163140498 0.921754926 0.348349244 0.155235364 144.1163421 81105.59755 0.058663718 0.04544049 191.8592361 -2.282982711 -0.241385572 TTS(ph)FAESCKPVQQPSAFGSMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TTSFAESCKPVQQPSAFGSMK 21 1 A0A3B3ITW1;P49841;P49841-2 A0A3B3ITW1 GSK3B Glycogen synthase kinase-3 beta 1 TT(0.002)S(0.998)FAESCKPVQQPSAFGSMK;TT(0.002)S(0.998)FAESCKPVQQPSAFGSMK 352.15 1.25E-95 2740200000 1984430 2016740 2231330 2152770 3164700 2762000 3914200 4611900 4602300 TRUE FALSE 1722182.548 2003491.902 3310408.651 2641589.332 3101728.662 2868255.927 3534601.486 3625681.075 4058221.337 0.424368807 0.493687193 0.815728955 0.650922932 0.764307416 0.706776612 0.870973068 0.893416296 1 21.95241612 4.466807349 0.213206248 1.114500662 2.15E-18 0.78357338 0.082607327 8.626253008 0.666685321 0.825108402 3.100533158 29295.93401 -4.466807349 -1.114500662 down QPSS(ph)PSHNTNLR ddPTM_MDA-MB-175_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(0.204)S(0.795)PSHNTNLR 101.75 0.001606 625070000 157300 178780 87361 128440 162970 206730 171120 208200 164890 TRUE FALSE 136512.4065 177605.5824 129609.0718 157604.2651 159727.2158 214683.0369 154524.8087 163678.0502 145396.892 0.938894942 1.221522551 0.891415697 1.083958968 1.098560042 1.476531127 1.062779311 1.125732799 1 17.14963691 3.214851549 3.636572136 1.161477152 1.034173971 0.141848943 0.150741939 0.47547607 13.31383175 0.045984696 0.055847059 1640.029082 -3.214851549 -0.127303181 QPSS(ph)PYEDKDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QPSSPYEDKDK 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QPS(0.202)S(0.798)PYEDKDK;QPS(0.007)S(0.993)PYEDKDK;QPS(0.025)S(0.975)PYEDKDK;QPS(0.001)S(0.999)PYEDKDK;QPS(0.09)S(0.91)PYEDKDK;QPS(0.157)S(0.843)PYEDKDK 174.62 6.54E-06 3003090000 3537230 2057320 2842900 2964270 1854960 1592926 2736180 3332620 6728020 TRUE FALSE 3069776.093 2043805.329 4217735.949 3637352.81 1818049.925 1654206.894 2470825.685 2619965.147 5932641.14 0.517438359 0.344501763 0.710937313 0.613108517 0.30644866 0.278831444 0.416479882 0.44161868 1 22.50024309 1.237972608 24.99479997 1.000000628 0.450908384 0.621670812 0.133925041 10.20866176 433570.7135 0.198771467 0.034422462 17.29707261 -1.237972608 -0.549092244 QPSS(ph)PYEDKDKDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QPSSPYEDKDKDK 13 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QPS(0.096)S(0.904)PYEDKDKDK 112.3 0.00047572 182240000 207740 121460 186920 163830 113830 64766 201220 234170 339270 TRUE FALSE 180286.6327 120662.1213 277315.1372 201030.1055 111565.0057 67257.58993 181705.7154 184094.5678 299161.8871 0.602639041 0.403333869 0.926973485 0.671977662 0.372925197 0.224820048 0.607382568 0.615367718 1 18.19056686 1.157965916 2.27940165 1.201146296 0.541125889 0.360564852 0.18910307 1.001108312 4.46464168 1.466331463 0.053140146 14.38685664 -1.157965916 -0.660020407 QPSS(ph)PYEDKDKDKK ddPTM_MDA-MB-175_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(0.203)S(0.797)PYEDKDKDKK 150.45 3.98E-05 511760000 815600 356880 602350 332040 247850 159120 601600 652030 379740 TRUE FALSE 707816.3935 354535.6318 893648.4747 407434.7569 242918.2699 165241.4494 543256.9246 512598.4586 334847.5698 2.11384659 1.058797088 2.668821743 1.216776807 0.725459259 0.4934826 1.622400679 1.530841209 1 18.35314497 3.512397413 24.59623042 1.127862329 1.872399592 0.378665338 0.510142544 604.1445787 421236.9272 0.142569334 0.211350275 3253.849132 -3.512397413 0.744537263 QPT(ph)PPSEAAASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QPTPPSEAAASK 12 0 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 1 QPT(0.997)PPS(0.003)EAAASK 107.5 0.020207 156200000 341640 299490 229890 387360 395520 304950 279960 546760 512770 TRUE FALSE 296491.4084 297522.6305 341065.5729 475316.0084 387649.9258 316681.6238 252809.5223 429839.6289 452150.9147 0.655735505 0.658016208 0.754317998 1.051233101 0.857346327 0.700389214 0.55912642 0.950655223 1 18.78644486 3.998593559 12.39651058 0.843645306 0.669112155 0.246293507 0.141795552 0.180827517 1312.348254 0.039282031 0.077457996 9967.667877 -3.998593559 -0.174533152 QPTAEGSGSDAHSVESLTAQNLSLHSGT(ph)ATPPLTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QPTAEGSGSDAHSVESLTAQNLSLHSGTATPPLTSR 36 0 Q9UDT6;Q9UDT6-2 Q9UDT6 CLIP2 CAP-Gly domain-containing linker protein 2 1 QPTAEGSGSDAHS(0.009)VES(0.072)LT(0.008)AQNLS(0.045)LHS(0.18)GT(0.453)AT(0.199)PPLT(0.017)S(0.017)R 61.063 0.039506 152900000 33353 37401 11373 23902 38776 33056 34120 36435 28359 TRUE FALSE 28945.31654 37155.31037 16873.02084 29329.31442 38004.43346 34327.68571 30811.04765 28643.65879 25006.43133 1.157514888 1.48583018 0.674747253 1.172870852 1.519786369 1.372754283 1.232124938 1.145451681 1 14.61001156 1.365104789 2.413704664 0.976238309 1.232771002 0.091725296 0.232595284 1.161900727 9.18327211 0.563195401 0.06341078 23.17953874 -1.365104789 0.256532693 QPYAVSELAGHQTSAESWGTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QPYAVSELAGHQTSAESWGTGR 22 0 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 ;;; 281.95 1.02E-45 5278070000 1581090 1684760 537663 974960 1561620 1788200 1470950 1596900 1500030 FALSE TRUE 1372144.951 1673692.701 797678.6252 1196339.569 1530546.817 1856993.211 1328297.495 1255415.362 1322698.162 1.037383274 1.265362536 0.603069278 0.904469064 1.157139899 1.403943291 1.004233266 0.949132159 1 20.33505245 3.243594218 24.99546095 1.091323474 0.949948868 0.118673804 0.202135944 327.1358193 1624454.837 0.06289368 0.078647848 1752.242532 -3.243594218 -0.141374606 QQAAYYAQTS(ph)PQGMPQHPPAPQGQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QQAAYYAQTSPQGMPQHPPAPQGQ 24 0 Q96AE4 Q96AE4 FUBP1 Far upstream element-binding protein 1 1 QQAAYYAQT(0.001)S(0.999)PQGMPQHPPAPQGQ;QQAAYYAQT(0.018)S(0.982)PQGMPQHPPAPQGQ;QQAAYYAQT(0.026)S(0.974)PQGMPQHPPAPQGQ 178.95 2.51E-17 776400000 473510 385965 223532 282685 354816 383906 345462 414912 352061 TRUE FALSE 410934.4538 383429.5705 331632.8229 346872.9498 347755.8558 398675.1122 311959.1484 326186.2976 310440.7496 1.323712993 1.235113531 1.06826447 1.117356372 1.120200412 1.284222876 1.004891106 1.050719978 1 18.24395842 8 0.32898542 1.044767055 3.756603828 0.484932444 0.081172098 74.00027221 1.156552152 0.131506735 120.1019606 100000000 -8 2.711836773 QQAGAQGPGS(ph)ADLEDGEMGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QQAGAQGPGSADLEDGEMGKR 21 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 QQAGAQGPGS(1)ADLEDGEMGKR 96.679 0.00076145 99487000 61164 54528 37659 39697 56197 43290 62368 75967 53147 TRUE FALSE 53081.02243 54169.80198 55871.01836 48710.81058 55078.78965 44955.39431 56319.56096 59722.04823 46864.02221 1.132660406 1.155893144 1.192194262 1.039407381 1.175289424 0.959273067 1.201765412 1.27436881 1 15.51619316 QQALTVSTDPEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QQALTVSTDPEHR 13 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ;; 143.58 4.09E-05 1185030000 768800 758270 504158 714310 742010 659140 669430 782410 1378150 FALSE TRUE 667201.1321 753288.8744 747970.4951 876505.003 727245.4527 684497.5423 604508.7816 615097.7102 1215226.677 0.549034303 0.619875196 0.615498745 0.721268731 0.598444279 0.563267377 0.497445286 0.506158828 1 20.21279402 1.232140914 24.98141915 1.000000704 0.582398078 0.808083823 0.063727982 105.2085222 409365.2942 0.164229658 0.017803836 17.06636047 -1.232140914 -0.417602625 QQASKS(ph)PYNGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QQASKSPYNGVR 12 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 1 QQAS(0.093)KS(0.907)PYNGVR;QQAS(0.01)KS(0.99)PYNGVR;QQAS(0.015)KS(0.985)PYNGVR;QQAS(0.001)KS(0.999)PYNGVR;QQAS(0.098)KS(0.902)PYNGVR 182.7 1.00E-05 3168556000 4129360 3399060 1722503 2193656 3323270 2848330 3839140 4185780 1709367 TRUE FALSE 3583654.614 3376731.351 2555511.212 2691759.123 3257143.429 2957907.098 3466820.794 3290683.521 1507287.581 2.377552008 2.240270135 1.695437052 1.785829829 2.160930317 1.962403948 2.300039381 2.183182269 1 20.52352327 1.235371227 24.99998384 0.999998512 2.083957499 0.71104824 0.217995115 53.3465667 418083.8631 0.391452084 0.056313778 17.19377452 -1.235371227 1.083958986 QQDAQEFFLHLINMVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QQDAQEFFLHLINMVER 17 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;; 204.29 8.92E-12 1166260000 1209030 1199370 794950 858430 1034610 992949 1149980 1315500 1143200 FALSE TRUE 1049253.622 1191491.259 1179390.479 1053349.652 1014023.285 1031148.391 1038455.117 1034190.562 1008052.198 1.040872312 1.181973772 1.169969651 1.044935623 1.005923391 1.022911703 1.030160063 1.025929574 1 19.94313891 3.606230838 4.837393568 1.019896492 1.135334192 0.649078996 0.038228868 0.12983033 4.5389947 0.010262366 0.015420017 4038.599971 -3.606230838 0.1154377 QQDKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QQDKER 6 1 Q16849-3;Q16849-2;Q16849 Q16849-3 PTPRN Receptor-type tyrosine-protein phosphatase-like N 0 ;; 83.287 0.052129 262896000 673981 605061 283327 401892 391595 495527 696598 757940 601318 FALSE TRUE 584912.7032 601086.3145 420344.8849 493147.7211 383803.0256 514590.2443 629042.0332 595860.4293 530230.8711 1.103128345 1.133631305 0.792758226 0.930062258 0.723841343 0.970502233 1.186354978 1.123775438 1 19.01626114 2.374256589 6.43886547 1.109815399 0.930568826 0.257379025 0.129541177 0.284012168 15.49298909 0.051204509 0.039432038 236.7317941 -2.374256589 -0.179246573 QQDLHLES(ph)PQRQPEYSPES(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QQDLHLESPQRQPEYSPESPR 21 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 2 QQDLHLES(1)PQRQPEYSPES(1)PR;QQDLHLES(0.998)PQRQPEY(0.006)S(0.088)PES(0.908)PR 155.55 1.33E-08 230500000 419030 319790 221677 287070 333410 412810 292430 366520 299700 TRUE FALSE 363654.1238 317689.2784 328880.7387 352253.6311 326775.7933 428691.0678 264070.1836 288142.5503 264269.8074 1.3760714 1.202139895 1.244488509 1.332931804 1.236523372 1.622171946 0.999244621 1.090334734 1 18.01165208 2.181674412 24.999999 1.041182172 1.320869425 0.593666201 0.118739844 58.91876141 25892.67983 0.046637055 0.031442711 151.9408012 -2.181674412 0.279687253 QQDVIYELIQTELHHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QQDVIYELIQTELHHVR 17 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 0 ; 85.51 0.0029022 295520000 228340 232840 156277 185130 211725 244080 244450 255230 274840 FALSE TRUE 198164.2905 231310.4587 231853.0799 227166.596 207512.0867 253469.9155 220743.2766 200651.0507 242348.7283 0.817682403 0.95445295 0.95669196 0.937354191 0.856254077 1.045889192 0.910849742 0.827943485 1 17.88672499 4.747501437 23.58832382 0.928144673 0.817682274 0.248795222 0.063356575 852.1779253 2248167.288 0.015619586 0.176144491 55911.53776 -4.747501437 -0.110462399 QQEEIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QQEEIRR 7 1 Q92828 Q92828 CORO2A Coronin-2A 0 86.095 0.057868 0 127400 121150 87227 88287 105560 132830 113630 132360 76529 FALSE TRUE 110563.7672 120354.1577 129410.269 108333.9127 103459.5625 137940.0561 102610.1801 104055.844 67481.8288 1.638422805 1.783504683 1.917705422 1.605379028 1.533146987 2.044106665 1.520560155 1.541983166 1 16.04221145 0.890938193 1.253663815 1.47E-10 1.740548302 0.666545719 0.161469301 1.868000612 1.359087233 5.250945769 0.047195195 7.779258326 -0.890938193 1.740548302 QQEELLAEENQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QQEELLAEENQR 12 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 106.49 0.0017692 0 62842 56512 32089 32690 57507 58522 65200 76477 52782 FALSE TRUE 54537.27048 56140.76895 47607.34773 40112.76414 56362.72321 60773.37921 58876.91404 60122.98869 46542.17209 1.171781806 1.206234398 1.022886247 0.861858447 1.211003283 1.305770154 1.265022911 1.291795935 1 15.50625092 3.030926302 24.99997677 1.235087059 1.068141488 0.25632532 0.124179876 259.1513884 209489.2191 0.038604766 0.043773323 1073.807177 -3.030926302 -0.166945571 QQEGFKPNYMENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QQEGFKPNYMENR 13 1 Q8WXF1 Q8WXF1 PSPC1 Paraspeckle component 1 0 ;;;;; 192.32 2.57E-06 1816910000 1457410 1266200 874520 1076810 1286770 1152670 1363360 1545980 1548300 FALSE TRUE 1264809.576 1257882.249 1297440.797 1321316.169 1261165.795 1197013.961 1231141.557 1215384.208 1365261.738 0.926422781 0.921348789 0.950323854 0.967811616 0.923753856 0.876765185 0.901762294 0.890220662 1 20.38074613 3.004596292 24.97404299 0.910275475 0.941309956 0.084225298 0.035042457 248.839451 1352057.054 0.010549441 0.011921049 1010.639555 -3.004596292 0.031034481 QQEKEDKDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QQEKEDKDEK 10 2 Q06323;Q06323-3;Q06323-2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;; 106.49 0.0013551 562250000 2243000 1280730 1703890 1268673 616672 666311 2199810 2470260 1596870 FALSE TRUE 1946581.867 1272316.8 2527896.903 1556744.595 604401.4337 691944.4153 1986472.765 1942014.123 1408089.848 1.382427315 0.903576432 1.795266763 1.105571919 0.429234991 0.491406437 1.41075711 1.379183385 1 20.42530796 3.488851212 24.93095426 0.987366072 1.337352237 0.196871291 0.378638729 1154.18357 2453109.44 0.117573752 0.163854746 3082.131842 -3.488851212 0.349986165 QQELTHQEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QQELTHQEHR 10 0 P18206;P18206-2;P18206-3 P18206 VCL Vinculin 0 ; 134.13 0.0001034 2544500000 600340 598920 349110 485910 558360 696850 529040 604970 659260 FALSE TRUE 521003.5479 594985.6551 517940.7637 596243.2922 547249.7284 723658.2704 477733.7822 475601.8734 581323.0338 0.896237578 1.023502632 0.890968934 1.025666037 0.941386624 1.244847061 0.821804323 0.818136984 1 19.14898055 QQFS(ph)PSMTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QQFSPSMTER 10 0 Q8TDB6 Q8TDB6 DTX3L E3 ubiquitin-protein ligase DTX3L 1 QQFS(0.946)PS(0.054)MTER;QQFS(0.942)PS(0.058)MTER 264.98 1.46E-17 1119510000 943640 1163900 684380 956180 1314290 1364650 1211340 1423960 1337490 TRUE FALSE 818935.5831 1156254.264 1015348.457 1173295.283 1288138.2 1417148.969 1093864.433 1119457.235 1179373.456 0.694381902 0.980397056 0.860921918 0.99484627 1.09222248 1.201611721 0.927496229 0.949196567 1 20.1695892 5.395086709 0.955196283 1.016316247 8.65E-16 0.540292981 0.090463691 5.542255957 1.651033505 0.031295897 7.846639003 248362.8924 -5.395086709 -1.016316247 QQGHEPVS(ph)PR ddPTM_MDA-MB-175_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 157.42 9.66E-06 2212030000 2455360 2026450 1413790 1691910 1922420 2172290 1961600 2190120 2340680 TRUE FALSE 2130877.955 2013138.117 2097503.573 2076084.025 1884167.603 2255859.402 1771364.334 1721779.882 2063967.477 1.032418378 0.975372984 1.016248365 1.005870513 0.912886285 1.092972359 0.858232677 0.834208824 1 20.97698881 2.215876992 24.98560386 0.882663532 1.000803877 0.394645623 0.062224989 204.903467 225695.7555 0.024197038 0.016326115 164.3906044 -2.215876992 0.118140345 QQHNQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QQHNQLK 7 0 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 60.788 0.095399 75608000 49951 53455 31774 36021 29720 46489 51518 52714 54068 FALSE TRUE 43349.84879 53103.85059 47140.01268 44200.1186 29128.63015 48277.46191 46521.79229 41441.52132 47676.14263 0.90925663 1.113845367 0.988754754 0.927090913 0.610968684 1.012612582 0.975787673 0.869229745 1 15.54097989 3.734164908 4.281559289 0.892707871 1.017334762 0.140324529 0.122393624 0.365771618 17.04050399 0.033490402 0.055328833 5422.067352 -3.734164908 0.12462689 QQHQGILSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QQHQGILSR 9 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 0 75.509 0.03806 55813000 76948 85573 47407 64702 71469 89068 68385 75844 86932 FALSE TRUE 66779.12684 85010.86533 70333.18377 79393.57801 70046.90673 92494.50359 61753.03323 59625.35082 76654.99799 0.871164681 1.109006165 0.917529001 1.035726046 0.913794385 1.206633697 0.805596958 0.777840355 1 16.22609224 QQKPTLSGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QQKPTLSGQR 10 1 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;C9IZ80;C9JFN4;C9J188;C9JWF5;C9JV57 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 ; 103.89 0.0025121 1152160000 779240 903770 510330 596810 902080 817180 936680 1000310 987620 FALSE TRUE 676261.4597 897833.0754 757127.295 732324.8322 884130.3729 848617.4434 845840.9178 786401.4909 870864.6887 0.776540223 1.030967367 0.869397169 0.840916898 1.015232773 0.974453844 0.971265604 0.90301226 1 19.73208905 3.239751393 24.99930905 0.964038815 0.889559255 0.299925827 0.069395107 49.21569221 1033224.712 0.019787735 0.024134854 1736.806327 -3.239751393 -0.07447956 QQLS(ph)PSPGQEAGILPETEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QQLSPSPGQEAGILPETEK 19 0 E5RJM0;B7ZLQ8;Q17RY0-2;Q17RY0 E5RJM0 CPEB4 Cytoplasmic polyadenylation element-binding protein 4 1 QQLS(1)PSPGQEAGILPETEK;QQLS(0.997)PS(0.003)PGQEAGILPETEK;QQLS(0.938)PS(0.062)PGQEAGILPETEK;QQLS(0.963)PS(0.037)PGQEAGILPETEK 246.66 1.18E-24 668550000 813030 786700 601804 674000 856640 762490 1037530 1213530 1135350 TRUE FALSE 705586.0255 781532.1159 892838.4273 827042.0014 839594.54 791823.4837 936910.5003 954026.0532 1001130.216 0.704789461 0.780649813 0.891830466 0.82610832 0.838646688 0.790929562 0.935852784 0.952949015 1 19.93319821 -2 0.215222243 2.199516675 0.727867094 0.711848201 0.047923027 54.42979252 0.834034937 26.74078971 0.257575363 0.01 2 -1.471649581 QQLSAEELDAQLDAYNAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QQLSAEELDAQLDAYNAR 18 0 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 ;; 341.07 4.50E-75 259322000 293026 283361 165986 201355 275634 291965 248656 292730 277960 FALSE TRUE 254301.8717 281499.5829 246257.3848 247075.7303 270149.4227 303197.0825 224541.3794 230131.9675 245099.8855 1.037543821 1.148509647 1.004722562 1.008061386 1.102201342 1.237034778 0.916121927 0.938931355 1 17.90301028 2.191875935 24.99998928 0.947545573 1.085351361 0.45265166 0.071378734 112.0467239 60001.01895 0.029598316 0.019955244 155.5521201 -2.191875935 0.137805788 QQLVASHLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QQLVASHLEK 10 0 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18;F8VX93 Q13561 DCTN2 Dynactin subunit 2 0 ;;; 113.63 0.0014628 804620000 2258370 2050410 1390960 1634080 1712520 1507600 2001160 2246240 2214680 FALSE TRUE 1959920.683 2036940.722 2063632.908 2005122.839 1678444.202 1565598.348 1807087.811 1765899.056 1952863.053 1.003613991 1.04305354 1.056721773 1.026760599 0.859478702 0.801693874 0.925353065 0.904261593 1 20.89715935 3.250977849 23.46454913 0.896136968 1.03501619 0.629810891 0.051164692 71.18443661 134513.8072 0.015406973 0.019721859 1782.287862 -3.250977849 0.138879222 QQNDELTTLADEAQSLKDEIDVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QQNDELTTLADEAQSLKDEIDVLR 24 1 Q86VS8 Q86VS8 HOOK3 Protein Hook homolog 3 0 ; 164.66 1.39E-11 120576000 74873 65676 47288 50661 58303 56378 76760 82482 75107 FALSE TRUE 64978.34335 65244.57003 70156.63497 62164.35435 57142.88437 58546.89814 69315.82701 64843.86618 66227.93602 0.98113194 0.985151795 1.059320872 0.938642484 0.862821459 0.88402118 1.046625203 0.97910142 1 16.01515228 -1.007141156 12.32910069 9.259656665 0.971058283 0 0.062400602 0 0 0 0.014882068 0.098369133 1.007141156 -8.288598382 QQNELAELHANLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QQNELAELHANLAR 14 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 193.06 3.02E-07 1221410000 1211190 1294090 680950 974580 1276020 1358790 1090740 1322110 1199790 FALSE TRUE 1051128.173 1285589.038 1010259.698 1195873.285 1250629.698 1411063.531 984960.2027 1039387.065 1057952.193 0.993549784 1.215167421 0.95491999 1.130366091 1.182123074 1.333768709 0.931006343 0.982451827 1 20.01284301 QQPGPSEHIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QQPGPSEHIER 11 0 P50552;K7EQD0 P50552 VASP Vasodilator-stimulated phosphoprotein 0 ;;;; 200.82 4.56E-08 3606494000 1082262 971721 503728 682338 970744 1044633 930762 1040050 1082523 FALSE TRUE 939238.3346 965337.7008 747332.5457 837273.2718 951428.0936 1084820.707 840496.8445 817643.4012 954548.3642 0.98396097 1.01130308 0.782917423 0.877140754 0.996731155 1.136475372 0.88051782 0.85657619 1 19.86445877 QQPPEPEWIGDGES(ph)TSPSDKVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QQPPEPEWIGDGESTSPSDKVVK 23 1 Q5STZ8;Q8NE71;Q8NE71-2;A0A0G2JIC2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 QQPPEPEWIGDGES(0.424)T(0.318)S(0.24)PS(0.019)DKVVK 85.814 0.0042312 717790000 115610 91805 59695 72815 95714 57438 140120 135840 38561 TRUE FALSE 100331.8456 91201.92691 88563.70167 89348.75866 93809.47866 59647.67703 126531.184 106791.6731 34002.36251 2.950731602 2.682223239 2.604633771 2.627722078 2.758910609 1.754221549 3.721246838 3.140713328 1 15.05334737 4.73724352 2.814928752 2.621516401 3.010540415 0.019704266 0.73634281 2.570186135 28.35716048 0.183027709 2.298876928 54606.39673 -4.73724352 0.389024014 QQPPEPEWIGDGEST(ph)SPSDKVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QQPPEPEWIGDGESTSPSDKVVK 23 1 Q5STZ8;Q8NE71;Q8NE71-2;A0A0G2JIC2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 QQPPEPEWIGDGES(0.018)T(0.49)S(0.49)PS(0.002)DKVVK 175.76 1.85E-12 115500000 132020 107710 71390 65333 107100 71242 145460 181550 38919 TRUE FALSE 114573.2225 107002.4459 105914.4428 80167.8562 104968.9195 73982.72584 131353.3116 142726.9453 34318.04016 3.338571258 3.117964937 3.086261404 2.336026645 3.058709619 2.155796937 3.827529515 4.158948025 1 15.06667954 4.451853859 2.364575095 2.947767054 3.326655675 0.022462819 0.885972155 2.103589919 20.5636057 0.237933536 1.267309556 28304.39384 -4.451853859 0.378888621 QQPPEPEWIGDGESTS(ph)PSDKVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QQPPEPEWIGDGESTSPSDKVVK 23 1 Q5STZ8;Q8NE71;Q8NE71-2;A0A0G2JIC2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 QQPPEPEWIGDGES(0.296)T(0.223)S(0.478)PS(0.003)DKVVK;QQPPEPEWIGDGES(0.023)T(0.164)S(0.798)PS(0.015)DKVVK 212.78 1.50E-25 665490000 1103720 841750 539049 569782 793680 554505 1118030 1265940 262075 TRUE FALSE 957860.6055 836220.4888 799734.8994 699159.7117 777887.3208 575837.1662 1009603.623 995228.5826 231092.7921 4.144917706 3.618548555 3.460665702 3.025450104 3.366125416 2.491800636 4.368823509 4.306618885 1 17.81811274 4.654888464 1.647165995 3.287515487 4.35741189 0.094750555 0.952450265 2.480479919 7.480133043 0.261521563 4.01846974 45173.99128 -4.654888464 1.069896403 QQPQQQPSGNNRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QQPQQQPSGNNRR 13 1 B4DT96;C9JYA1;O15504-2;O15504 B4DT96 NUPL2 Nucleoporin-like protein 2 0 70.488 0.071916 1908400 2745.9 3221.4 2238.9 2102.5 1954.1 2587 1884.8 3152.3 0 FALSE TRUE 2383.022358 3200.238411 3321.639529 2579.90476 1915.217233 2686.523564 1702.012386 2478.205176 0 0 QQQQEALRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QQQQEALRR 9 1 Q6Y7W6;I1E4Y6;Q6Y7W6-3;Q6Y7W6-4;Q6Y7W6-5 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 0 96.143 0.012134 52528000 62863 75745 65835 29885 41154 87907 45685 34009 30258 FALSE TRUE 54555.49528 75247.42611 97673.0262 36670.84601 40335.11592 91288.83917 41254.47573 26736.44001 26680.93371 2.04473711 2.820269595 3.660779914 1.374421391 1.511758035 3.421500918 1.546215593 1.002080373 1 14.70352153 2.012689647 22.93489966 1.083076222 2.451473457 0.424187915 0.727353547 78.80682766 142431.7761 0.303866517 0.204648551 102.9650056 -2.012689647 1.368397235 QQQQMEQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QQQQMEQER 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 ; 224.36 7.28E-07 217104000 103836 109644 63805 72165 105805 137278 99279 117436 107300 FALSE TRUE 90113.80951 108923.7413 94661.31141 88551.16622 103699.6875 142559.1735 89650.93786 92323.22529 94615.11624 0.952425079 1.1512298 1.000488243 0.93590929 1.096016066 1.506727246 0.947532925 0.975776694 1 16.52978307 QQQQQQGEDGS(ph)PQAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QQQQQQGEDGSPQAHR 16 0 A0A087WUX9;E9PEG3;A0A087WZ66;F5GZG9;P10275-3;P10275-4;P10275 A0A087WUX9 AR Androgen receptor 1 QQQQQQGEDGS(1)PQAHR;QQQQQQGEDGS(1)PQAHR 279.48 1.31E-35 696080000 409530 384270 191308 254714 381200 383540 316730 394630 390570 TRUE FALSE 355409.5729 381745.7051 283825.1887 312550.7068 373614.8658 398295.032 286013.5733 310241.4455 344397.2595 1.031975613 1.108445827 0.824121507 0.907529599 1.08483693 1.156498842 0.830475753 0.900824373 1 18.39371414 3.826091603 0.018466551 1.23E-05 1.989339038 0.026720645 0.113846111 5294.604176 54.36473216 2825.362259 3030.759544 6700.259188 -3.826091603 1.989326781 QQQQQQQHQQPNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 161.99 4.12E-05 358599000 205511 204976 100557 97953 169925 225855 156968 168714 93594 FALSE TRUE 178352.2007 203629.4992 149186.7015 120194.7258 166543.825 234543.788 141745.2675 132635.824 82529.42394 2.161074101 2.467356361 1.807678939 1.456386341 2.017993305 2.841941417 1.717511898 1.607133768 1 16.33262095 1.478299424 1.824656821 0.924591113 2.087573383 0.462204118 0.380709258 0.504943854 2.554715629 0.915987921 0.113402709 30.08149554 -1.478299424 1.16298227 QQQQQQQQHSENKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QQQQQQQQHSENKR 14 1 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 0 ;;;; 182.33 9.97E-07 159289300 138765 120524 80729.2 97862 99740 103161 131261 156669 157567 FALSE TRUE 120426.8537 119732.2699 119770.1111 120083.0628 97755.36914 107129.6704 118531.3284 123166.5535 138939.6088 0.866756821 0.861757644 0.862030001 0.864282431 0.703581722 0.771052052 0.853114022 0.88647546 1 17.08409841 1.294546195 1.772779996 1.048869233 0.822771226 0.53546663 0.051925806 0.713086218 2.346350674 0.267781486 0.015918926 19.70362781 -1.294546195 -0.226098007 QQQQQQQQQQQQQQHSAVLALS(ph)PSQSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QQQQQQQQQQQQQQHSAVLALSPSQSPR 28 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 QQQQQQQQQQQQQQHSAVLALS(0.995)PS(0.003)QS(0.003)PR 191.99 1.60E-31 0 25764 20355 9069.8 11161 17309 16937 15248 18157 14683 TRUE FALSE 22359.22212 20221.28666 13455.98562 13695.27564 16964.58476 17588.57735 13769.25131 14274.26685 12947.19247 1.726955259 1.561827919 1.039297566 1.057779567 1.310290614 1.358485818 1.063493212 1.102499008 1 13.66035167 4.348819683 4.557377781 1.138927834 1.687843835 0.768550315 0.117888504 0.098943103 3.400681328 0.032004109 0.091612871 22326.45048 -4.348819683 0.548916001 QQS(ph)GSELEELMNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QQSGSELEELMNK 13 0 Q9H6S3;Q9H6S3-3;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 QQS(0.97)GS(0.03)ELEELMNK;QQS(0.968)GS(0.032)ELEELMNK 179.14 4.85E-07 38770000 117745 88792 40117 115107 97517 48968 101928 114651 92110 TRUE FALSE 102184.6999 88208.71951 59517.71538 141243.8037 95576.60249 50851.83065 92043.03825 90133.77587 81220.86073 1.25810905 1.086035271 0.732788533 1.739008949 1.176749441 0.626093225 1.133243817 1.109736773 1 16.3095627 2.963295029 24.99475868 0.993570652 1.198900669 0.143946155 0.277549968 1323.161792 901025.156 0.089766556 0.089794867 918.9566593 -2.963295029 0.205330017 QQS(ph)LFS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QQSLFSSPR 9 0 Q5T7B8-4;Q5T7B8-2;Q5T7B8 Q5T7B8-4 KIF24 Kinesin-like protein KIF24 2 QQS(0.947)LFS(0.982)S(0.071)PR;QQS(0.979)LFS(0.993)S(0.028)PR 75.652 0.055049 3085800000 115652 208516 45363 71834.6 98917 47963 78139 132526 83209 TRUE FALSE 100368.2952 207146.2447 67300.69853 88145.74385 96948.74523 49808.16765 70561.09181 104186.3462 73372.12681 1.36793493 2.823228025 0.91725157 1.201351899 1.321329358 0.678843177 0.961687972 1.419971735 1 16.16294448 4.217125379 24.99997471 1.096260299 2.095581931 0.527221754 0.402642265 148.2674259 172925.0214 0.094872403 0.197783484 16486.38278 -4.217125379 0.999321632 QQS(ph)LGGFFK ddPTM_MDA-MB-175_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 114.76 0.0016629 287580000 591760 451530 217694 359180 398860 234340 607230 500850 483880 TRUE FALSE 513557.4167 448563.8697 322971.5465 440737.3087 390923.4664 243355.2114 548340.9281 393747.1251 426676.2576 1.203623139 1.051297938 0.756947547 1.032954848 0.916206279 0.570350956 1.285145162 0.92282408 1 18.70278231 4.476642303 24.99340697 0.933860728 1.165541908 0.193491007 0.18345938 22.50501095 1174492.541 0.044020922 0.118879664 29966.93342 -4.476642303 0.23168118 QQS(ph)PQEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 QQSPQEPK 8 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK 166.69 0.0003325 24404080000 29845250 24247730 19579670 23466080 19904770 21044430 32570870 36962670 33313440 TRUE FALSE 25901124.59 24088445.07 29048463.9 28794412.12 19508704.02 21854022.84 29412152.04 29058490.66 29375163.07 0.881735517 0.82002762 0.988878388 0.980229865 0.664122407 0.743962605 1.001259192 0.989219722 1 24.80809352 2.209369147 24.88364652 0.995426441 0.849551244 0.349473297 0.096622243 247.6291897 211084.3702 0.042622797 0.028741422 161.9455977 -2.209369147 -0.145875196 QQS(ph)PS(ph)PIR ddPTM_MDA-MB-175_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 55.353 0.065743 578190000 654050 536490 471600 540980 504740 612970 580770 781490 792870 TRUE FALSE 567615.6353 532965.7619 699667.3374 663817.7774 494696.6615 636551.3525 524447.0148 614374.4451 699137.8118 0.811879469 0.762318606 1.000757398 0.949480583 0.707581042 0.910480512 0.750133959 0.878760145 1 19.41521734 1.279927354 4.174650819 1.009221651 0.84445291 0.2250749 0.091563003 0.314973331 9.440926028 0.141955681 0.022848299 19.05142013 -1.279927354 -0.164768741 QQSHFAMMHGGTGFAGIDSS(ph)SPEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QQSHFAMMHGGTGFAGIDSSSPEVK 25 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 QQSHFAMMHGGTGFAGIDS(0.024)S(0.775)S(0.201)PEVK;QQSHFAMMHGGTGFAGIDS(0.028)S(0.871)S(0.101)PEVK;QQSHFAMMHGGTGFAGIDS(0.108)S(0.496)S(0.396)PEVK 91.615 0.0059934 536870000 288351 268354 205533 279791 384439 377060 448292 501707 474379 TRUE FALSE 250244.6848 266591.1649 304929.4463 343321.8229 376789.416 391565.7422 404816.7108 394420.8623 418298.455 0.598244344 0.637322853 0.728975789 0.820758047 0.900766932 0.936091772 0.967770036 0.94291733 1 18.67417314 3.796915338 0.804928939 0.971762815 0.554436224 0.99010338 0.013974027 0.076247807 0.088562023 0.006477449 0.023176095 6264.91724 -3.796915338 -0.417326591 QQSHFAMMHGGTGFAGIDSSS(ph)PEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QQSHFAMMHGGTGFAGIDSSSPEVK 25 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 QQSHFAMMHGGTGFAGIDS(0.009)S(0.202)S(0.788)PEVK 104.9 0.0071639 550770000 148190 153500 107400 147360 173510 153770 269650 293060 286190 TRUE FALSE 128606.316 152491.6484 159338.9992 180820.3403 170057.4905 159685.6314 243499.3845 230391.3996 252356.9442 0.509620674 0.604269674 0.631403268 0.716526113 0.673876802 0.632776847 0.96490067 0.91295843 1 17.94510626 1.487587447 0.372703803 1.335027439 0.527660716 0.827412532 0.068931984 2.559433098 0.398923987 0.9679189 0.124881019 30.731761 -1.487587447 -0.807366723 QQSNEHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QQSNEHLR 8 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ; 119.07 0.0017654 87229000 331730 299380 198151 242710 184650 198888 341170 320590 318310 FALSE TRUE 287891.04 297413.3531 293977.4864 297821.0151 180975.8263 206539.3501 308083.3859 252034.3233 280679.7544 1.025692219 1.059618118 1.047376883 1.061070528 0.644776915 0.735854107 1.097633089 0.897942653 1 18.09856548 QQSNEHLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QQSNEHLRR 9 1 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ; 118.03 0.0016916 146257000 75399 63383 31132 52883 53013 72702 43639 63053 50274 FALSE TRUE 65434.83111 62966.6329 46187.53933 64890.89342 51958.14502 75498.89298 39406.8965 49569.60663 44330.66499 1.476062476 1.420385481 1.041886905 1.463792466 1.172058778 1.703085054 0.888930868 1.118178729 1 15.43601738 2.21340394 24.99999567 1.021770051 1.360451882 0.476110332 0.185420097 204.1284411 202855.5414 0.071338227 0.048117989 163.4571567 -2.21340394 0.338681831 QQSSSSKGDS(ph)PELKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QQSSSSKGDSPELKPR 16 2 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 QQS(0.001)SS(0.001)S(0.001)KGDS(0.996)PELKPR;QQS(0.301)S(0.138)S(0.065)S(0.065)KGDS(0.431)PELKPR 136.49 8.95E-06 447920000 1270590 854620 634550 601230 689400 593480 937580 1043240 558880 TRUE FALSE 1102678.312 849005.9449 941420.5024 737748.4607 675682.2888 616311.5596 846653.6359 820151.2445 492809.8431 2.237533052 1.722786095 1.910311889 1.497024605 1.371081155 1.250607244 1.718012836 1.664234706 1 18.91067155 5.198916425 0.66225371 1.437448056 3.209771703 0.576095477 0.225630839 4.620946854 1.013635637 0.105090064 7.065567122 158094.3776 -5.198916425 1.772323647 QQTEKPES(ph)EDEWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QQTEKPESEDEWER 14 1 O60231;A0A140T947;A2AB15 O60231 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 1 QQTEKPES(1)EDEWER;QQTEKPES(1)EDEWER 235.21 1.89E-17 3945400000 2747500 2093620 1487070 1745920 2428040 2084980 2749000 2790900 2764800 TRUE FALSE 2384410.914 2079866.872 2206222.026 2142357.821 2379726.754 2165190.53 2482402.403 2194087.754 2437948.494 0.978039905 0.853121745 0.90495022 0.87875434 0.976118552 0.888119883 1.018234146 0.899972973 1 21.21723622 3.241352575 24.99998756 0.95063701 0.900190756 0.206808873 0.05043013 114.7529525 1027519.66 0.01349078 0.016640852 1743.221505 -3.241352575 -0.050446254 QRDELNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QRDELNR 7 1 P43034;I3L495 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ;;; 153.73 0.0015747 629757000 409190 357676 232270 266220 296938 390332 335959 355883 376037 FALSE TRUE 355114.5047 355326.4028 344596.5489 326669.3199 291029.5147 405348.3246 303377.7479 279780.1899 331582.3342 1.070969313 1.071608364 1.039248818 0.985183124 0.877699095 1.222466588 0.914939418 0.843772907 1 18.33900762 -1.999999999 0.078007325 0.237974369 1.308894078 0.13391152 0.10191854 801.8555343 5.94741006 98.01394253 16.60257328 0.01 1.999999999 1.070919709 QREELLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QREELLSR 8 1 O14653-3;O14653-2;E7EQ34;A0A1W2PS81;A0A1W2PQM3;A0A1W2PQP2;A0A1W2PRC2;I3L4Z6;A0A1W2PPG1;A0A1W2PPP5;A0A1W2PPG5;I3L0K1;A0A1W2PRV0;A0A1W2PRL0;A0A1W2PS12;A0A1W2PNV3;A0A1X7SBU8;A0A1W2PPJ0;O14653;I3NI02;A0A1W2PRE6;A0A1W2PRD0;A0A1W2PQ38;A0A1W2PQ06;I3L1K7;A0A1W2PQE0;A0A1W2PR23;A0A1W2PPW8;A0A1W2PQ77;A0A1W2PRP7;A0A1W2PR02 O14653-3 GOSR2 Golgi SNAP receptor complex member 2 0 ; 166.19 0.00029177 223617000 157605 152458 93716 100977 171329 185986 136614 159395 143394 FALSE TRUE 136777.0999 151456.4934 139037.3711 123905.3712 167919.8881 193141.0018 123365.1953 125309.6197 126442.1247 1.081736805 1.197832556 1.099612739 0.979937434 1.328037539 1.527505191 0.975665314 0.991043293 1 16.94811766 QREESYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QREESYSR 8 1 P23246;P23246-2;H0Y9K7;H0Y9U2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;; 179.51 0.00022251 1900028000 1134709 944092 472906 675967 837684 966447 917513 912537 686576 FALSE TRUE 984754.3307 937890.1975 701604.9234 829455.6389 821015.7273 1003626.841 828532.7305 717398.0639 605409.7674 1.626591416 1.549182468 1.15889264 1.370073103 1.356132278 1.657764535 1.368548667 1.184979336 1 19.20755243 1.584169751 2.347007888 1.008409328 1.439790724 0.523939521 0.14477998 0.252223433 2.844614852 0.187695476 0.041433803 38.38572527 -1.584169751 0.431381396 QREFESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QREFESR 7 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 150.4 0.0017797 3256000000 423630 469020 231280 284730 384360 466530 427980 484590 332740 FALSE TRUE 367646.2222 465938.9767 343127.7816 349382.2983 376711.988 484477.711 386474.5655 380964.1996 293403.8563 1.253038139 1.588046533 1.169472637 1.190789728 1.283936731 1.651231573 1.317210245 1.298429422 1 18.16252831 1.186179919 2.513147685 0.8789064 1.354119914 0.327283472 0.156520713 0.795403476 4.887167039 0.871896245 0.041436574 15.35252872 -1.186179919 0.475213514 QRELEIEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QRELEIEER 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 176.48 4.84E-05 221400000 524210 489330 250740 282800 530980 566940 470500 500450 234075 FALSE TRUE 454934.3203 486115.559 371998.7027 347014.0623 520414.5368 588750.5487 424870.9824 393432.662 206402.9202 2.204107965 2.355177721 1.802293797 1.681245895 2.521352588 2.852433232 2.058454319 1.90613903 1 17.65510386 1.199806247 1.99910003 0.524155765 2.214982303 0.56653602 0.333046968 0.709280376 2.534839279 2.321190289 0.097790572 15.84186276 -1.199806247 1.690826538 QRELEQLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 112.3 0.002179 283020000 316840 329880 198637 302200 373430 321030 360050 333280 576380 FALSE TRUE 274968.7912 327712.9966 294698.5176 370819.1288 365999.4736 333380.2318 325132.4064 262010.6656 508241.013 0.541020469 0.644798409 0.579840096 0.729612761 0.72012975 0.655949094 0.639720916 0.515524444 1 18.95515327 1.227517638 24.99674051 1.000000796 0.629468314 0.742600151 0.06876611 270.1922429 611563.054 0.264963035 0.017899107 16.88564437 -1.227517638 -0.370532482 QRHS(ph)YPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QRHSYPER 8 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 QRHS(1)YPER;QRHS(1)YPER 128.01 0.00069743 865350000 515780 564150 357430 412950 497690 604430 540400 587930 614260 TRUE FALSE 447618.3662 560444.0615 530284.3435 506716.609 487786.9427 627682.8132 487992.0912 462205.7448 541642.8826 0.826408655 1.034711393 0.979029469 0.935517894 0.900569284 1.158849924 0.900948036 0.853340383 1 19.04698244 QRIDEFEAL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QRIDEFEAL 9 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;; 102.51 0.029133 2737840000 4778100 4858100 2885310 4069240 5112100 5261300 4454000 5284500 4843700 FALSE TRUE 4146661.979 4826186.821 4280655.567 4993223.136 5010379.212 5463705.616 4022051.766 4154450.799 4271083.304 0.970868907 1.129967851 1.002241179 1.169076504 1.173093301 1.279231808 0.941693589 0.972692524 1 22.02617061 2.192543938 24.99999797 0.970477806 1.120355892 0.394198588 0.087236241 129.076711 70124.01927 0.03620514 0.024409584 155.7915644 -2.192543938 0.149878086 QRLEAEAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QRLEAEAGR 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 108.43 0.0023825 1172510000 999190 1012010 577620 694620 965940 1064660 897740 973410 721950 FALSE TRUE 867144.5099 1005362.04 856958.964 852344.0876 946719.6838 1105618.159 810677.313 765253.8466 636601.8934 1.362145666 1.579263351 1.346145798 1.338896564 1.487145567 1.736749718 1.273444709 1.202091691 1 19.28003192 1.689590918 2.078826104 1.031452126 1.466349125 0.589199656 0.129609524 0.22130326 1.923477017 0.144364549 0.037006402 48.93176918 -1.689590918 0.434897 QRPDLGS(ph)AQK ddPTM_MDA-MB-175_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 130.65 0.00016406 1665750000 1713490 1536120 986030 1227130 1469730 1363840 1767650 1986350 1693730 TRUE FALSE 1487047.955 1526029.127 1462877.406 1505768.622 1440485.248 1416307.807 1596223.575 1561584.51 1493499.169 0.99568047 1.021781035 0.979496632 1.008215239 0.964503549 0.948315096 1.068781027 1.0455878 1 20.510265 2.230951538 24.99999543 1.040955538 0.987635113 0.459313829 0.026404253 152.3561072 500568.9911 0.010943181 0.007533585 170.1968579 -2.230951538 -0.053320425 QRPDLGSAQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QRPDLGSAQK 10 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RFR3 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ; 103.91 0.0025097 274860000 229890 201409 124086 174798 206328 174169 206920 252910 219312 FALSE TRUE 199509.454 200085.931 184094.4046 214488.5575 202222.4765 180869.3941 186852.9302 198827.1646 193385.1852 1.031668759 1.034649737 0.951957124 1.109126107 1.045697871 0.935280507 0.966221534 1.028140622 1 17.56111775 2.788589261 24.99963682 0.988038109 1.034168444 0.252787625 0.044130352 609.1486731 304394.1431 0.014589442 0.014589437 614.5953377 -2.788589261 0.046130335 QRPGQQVATCVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QRPGQQVATCVR 12 1 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ; 131.69 0.00017713 333820000 148379 147472 91545 116456 138074 143698 145185 186260 164147 FALSE TRUE 128770.3392 146503.2467 135816.4682 142899.1147 135326.5975 149226.155 131104.981 146429.7485 144741.7287 0.889655944 1.012170078 0.938336646 0.987269643 0.934952199 1.030982264 0.905785652 1.011662289 1 17.14312138 4.305422613 0.010644119 1.907668441 1.61E-07 0.137572509 0.045071914 14707.79632 57.84905604 5019.627711 5351.203372 20203.31395 -4.305422613 -1.90766828 QRPQATAEQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QRPQATAEQIR 11 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5;Q5VU81;Q5VU80;Q5VU79;Q5VU78;Q5VU77 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 0 ; 224.24 5.80E-12 772050000 230020 279220 139754 201121 274760 249720 259470 268760 287580 FALSE TRUE 199622.2742 277385.7854 207339.5018 246788.597 269292.8136 259326.89 234306.6393 211287.7655 253582.62 0.787208028 1.093867495 0.817640822 0.973207852 1.061952959 1.022652459 0.923985403 0.833210752 1 17.95209634 4.785727387 22.48449017 0.953875371 0.787205501 0.272867583 0.089767163 16302.25876 7770599.891 0.022345038 11.86062744 61055.86484 -4.785727387 -0.166669869 QRQEEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QRQEEEAR 8 1 A2A3N6;H0Y3Y9;Q5VWC4;P55036-2;P55036 A2A3N6;Q5VWC4 PIPSL;PSMD4 Putative PIP5K1A and PSMD4-like protein;26S proteasome non-ATPase regulatory subunit 4 0 136.21 0.00073033 74176000 46682 48023 28001 32765 30052 51661 43221 49705 51089 FALSE TRUE 40512.85542 47707.53375 41542.37726 40204.79403 29454.024 53648.4321 39029.43407 39075.97255 45049.31662 0.899300111 1.059006825 0.922153328 0.892461796 0.653817332 1.190882262 0.866371279 0.867404336 1 15.4592176 4.022573265 24.48892662 0.905392044 0.982010192 0.037301228 0.137294283 597.9548139 648688.2284 0.033680477 0.070103692 10533.51372 -4.022573265 0.076618148 QRQELEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QRQELEK 7 1 P35579 P35579 MYH9 Myosin-9 0 ;;; 147.52 0.0019572 3842460000 922660 924180 494084 734999 819040 898690 1142330 1334560 1067231 FALSE TRUE 800728.1433 918109.0007 733024.675 901891.7567 802742.7064 933263.1858 1031547.012 1049174.73 941064.167 0.850875181 0.975607225 0.778931661 0.958374347 0.85301591 0.991710468 1.096149496 1.114881181 1 19.84393357 2.495325393 3.358705333 1.0797998 0.887310475 0.651310437 0.062699844 0.132868824 3.131171279 0.022464044 0.01810522 312.8422446 -2.495325393 -0.192489325 QRS(ph)APDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QRSAPDLK 8 1 O43896 O43896 KIF1C Kinesin-like protein KIF1C 1 QRS(1)APDLK 89.266 0.0084952 116630000 307730 261160 217890 251640 169220 207060 267120 250140 174190 TRUE FALSE 267062.7008 259444.4228 323262.3328 308778.7081 165852.8531 215025.7322 241214.7435 196649.5076 153597.4566 1.738718249 1.689119263 2.104607328 2.010311335 1.079789058 1.399930291 1.57043449 1.280291431 1 17.2287948 3.244178824 24.99998798 1.297382307 1.887285438 0.71095096 0.195747961 81.99442056 364857.7608 0.059688805 0.074896739 1754.602825 -3.244178824 0.589903131 QRS(ph)DDESPSTSSGSSDADQRDPAAPEPEEQEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QRSDDESPSTSSGSSDADQRDPAAPEPEEQEER 33 2 R4GN77;R4GND1;A0A1B0GX65;Q969T4;R4GMM6;R4GNG6 R4GN77 UBE2E3 Ubiquitin-conjugating enzyme E2 E3 1 QRS(0.688)DDES(0.188)PS(0.038)T(0.038)S(0.038)S(0.007)GS(0.002)SDADQRDPAAPEPEEQEER;QRS(0.587)DDES(0.408)PS(0.002)T(0.002)SSGSSDADQRDPAAPEPEEQEER 129.34 3.92E-08 1122350000 101791 104971 71926 80773 128140 89888 108586 135264 89389 TRUE FALSE 88339.06144 104281.4386 106709.6542 99113.74419 125590.2647 93346.04953 98055.34643 106338.8462 78821.53425 1.120747804 1.323006962 1.353813462 1.257445001 1.593349659 1.184270903 1.244017227 1.349109063 1 16.26630221 1.233980445 24.95752883 0.999999526 1.308714249 0.363765826 0.125838994 148.6656988 809979.8894 0.229038854 0.029299084 17.13880133 -1.233980445 0.308714722 QRS(ph)PIALPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QRSPIALPVK 10 1 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 QRS(1)PIALPVK;QRS(1)PIALPVK;QRS(1)PIALPVK;QRS(1)PIALPVK 84.753 0.0089062 3584760000 6962900 6413900 4473060 5828700 6176200 5587980 7913100 8259300 9729400 TRUE FALSE 6042735.123 6371766.669 6636246.777 7152195.421 6053305.704 5802953.207 7145688.78 6493112.969 8579201.416 0.70434704 0.742699275 0.773527331 0.833666804 0.705579157 0.676397828 0.832908383 0.756843517 1 23.03241193 -0.0527822 1.47530415 9.999999996 0.749450826 0.682578628 0.052463339 29.37636042 2.108040267 854.2405365 0.014916786 0.88555961 0.0527822 -9.25054917 QRS(ph)PIALPVKQEPPQIDAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QRSPIALPVKQEPPQIDAVK 20 2 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 QRS(1)PIALPVKQEPPQIDAVK;QRS(1)PIALPVKQEPPQIDAVK 140.8 1.04E-07 399740000 926310 673640 407900 502130 622020 515230 923600 998870 441371 TRUE FALSE 803895.7865 669214.8145 605161.8043 616146.2911 609643.019 535051.2315 834029.4142 785269.4237 389192.6232 2.065547337 1.719495115 1.554915916 1.583139696 1.566430047 1.374772284 2.142973336 2.017688355 1 18.57012484 4.721318623 3.849200687 1.659600081 2.098806478 0.15604763 0.316917926 0.50828072 14.97566329 0.080861102 0.613087748 52640.33245 -4.721318623 0.439206397 QRS(ph)PLLNQPVPELSHASLIANQSPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QRSPLLNQPVPELSHASLIANQSPFR 26 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 QRS(1)PLLNQPVPELSHASLIANQSPFR;QRS(0.98)PLLNQPVPELS(0.02)HASLIANQSPFR;QRS(1)PLLNQPVPELSHASLIANQSPFR;QRS(1)PLLNQPVPELSHASLIANQSPFR;QRS(1)PLLNQPVPELSHASLIANQSPFR 150.36 8.32E-08 3850300000 598981 550613 193929 347720 751424 686043 529622 640320 530591 TRUE FALSE 519824.1432 546995.9869 287713.7131 426675.1406 736472.1325 712435.5181 478259.34 503392.551 467865.1364 1.111055522 1.169131753 0.614950101 0.911961818 1.574112015 1.522736923 1.022216239 1.075935161 1 18.8357332 QRS(ph)PS(ph)PAPAPAPAAAAGPPTR ddPTM_MDA-MB-175_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 142.9 8.09E-08 4468210000 1290920 1236520 694420 772770 1225750 1236210 1033900 1263640 1071180 TRUE FALSE 1120321.651 1228397.219 1030243.835 948239.2395 1201359.973 1283767.799 933632.5371 993420.4197 944546.3207 1.186094982 1.300515593 1.090728757 1.003909728 1.271891009 1.359136943 0.988445476 1.051743464 1 19.84926202 2.204694092 24.99999711 1.020345548 1.19563087 0.430030307 0.102100447 199.0144925 146909.591 0.0440871 0.029725365 160.2116497 -2.204694092 0.175285322 QRS(ph)SPVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QRSSPVTK 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QRS(0.591)S(0.36)PVT(0.049)K;QRS(0.605)S(0.395)PVTK 94.692 0.026778 318220000 620320 448120 290341 403039 283719 386421 555960 633090 526830 TRUE FALSE 538343.1403 445176.2702 430750.8787 494555.165 278073.547 401286.8659 502043.0848 497708.6302 464548.7576 1.158851749 0.958298269 0.927245788 1.06459259 0.598588506 0.863820771 1.080711285 1.071380823 1 18.8254705 2.229961827 24.97381443 1.056257026 0.921041734 0.13410458 0.145231206 356.5572203 1035553.391 0.060269637 0.041357607 169.8094391 -2.229961827 -0.135215292 QRSS(ph)PVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QRSSPVTK 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QRS(0.133)S(0.867)PVTK;QRS(0.034)S(0.966)PVTK;QRS(0.279)S(0.721)PVTK;QRS(0.048)S(0.952)PVTK 104.14 0.0028081 4354580000 3834540 2732780 1890590 2448840 1768780 2315580 3371710 3810530 3301130 TRUE FALSE 3327795.824 2714828.188 2804885.648 3004886.55 1733584.739 2404661.861 3044722.083 2995677.813 2910874.172 1.143229019 0.932650478 0.963588765 1.032296957 0.595554681 0.826096121 1.045982033 1.029133393 1 21.47302105 4.738609584 10.22170893 0.932323573 1.143676928 0.201339398 0.134387602 0.135949179 522.420948 0.035083193 0.197151177 54778.43045 -4.738609584 0.211353354 QRT(ph)LEDEEEQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QRTLEDEEEQER 12 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 QRT(1)LEDEEEQER;QRT(1)LEDEEEQER 242.9 4.15E-16 2157000000 612740 477100 268930 586370 487960 288710 637820 583180 685520 TRUE FALSE 531764.8565 473965.8987 398985.4475 719514.2706 478250.5507 299816.8605 575964.3146 458471.4953 604478.6065 0.879708315 0.784090443 0.660048914 1.1903056 0.791178622 0.495992509 0.952828286 0.758457769 1 19.20533176 1.227644586 24.09507369 1.000000638 0.813324271 0.094456245 0.180902465 777.194431 1715325.635 0.59826898 0.042858441 16.89058089 -1.227644586 -0.186676367 QRT(ph)LEDEEEQERER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QRTLEDEEEQERER 14 2 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 QRT(1)LEDEEEQERER;QRT(1)LEDEEEQERER 229.59 5.85E-11 2161350000 497210 447400 193132 322510 393780 258290 505290 494360 225789 TRUE FALSE 431502.4387 444460.9999 286531.2812 395740.8248 385944.5484 268226.5834 456287.0536 388644.9611 199096.4816 2.167303185 2.232390027 1.439157934 1.987683667 1.938480003 1.347219103 2.291788633 1.952043341 1 17.6031082 4.267381086 24.9901471 1.766438962 2.199847299 0.218350622 0.374372633 349.8113268 303314.633 0.09049432 0.239335848 18508.92032 -4.267381086 0.433408336 QRVEQFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QRVEQFAR 8 1 P34897-3;P34897-2;P34897 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial" 0 ;; 163.32 0.00030698 512020000 488530 568700 361456 503400 591340 594720 520920 603680 587410 FALSE TRUE 423969.5227 564964.1723 536257.3306 617704.664 579573.4909 617599.2632 470401.2586 474587.7298 517967.059 0.818526034 1.090733788 1.03531165 1.192555884 1.118938899 1.192352395 0.908168291 0.916250796 1 18.98250082 2.215586753 24.9892056 0.93483064 1.081036214 0.255041557 0.106804127 296.9481665 322995.0104 0.043516069 0.029359965 164.280779 -2.215586753 0.146205574 QRWDEAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QRWDEAFR 8 1 P27695;G3V3M6;G3V5Q1;H7C4A8 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ;;; 191.17 0.0001665 2456890000 1832410 1609230 967470 1114660 1726010 1624860 1630300 1682080 1326140 FALSE TRUE 1590252.376 1598658.862 1435341.728 1367760.59 1691665.778 1687369.416 1472193.757 1322380.282 1169365.24 1.359927866 1.367116798 1.227453732 1.169660721 1.446653039 1.442978941 1.25896829 1.130853079 1 20.15729418 1.617491954 2.197086883 1.006191961 1.329951542 0.630762839 0.086607685 0.216407238 2.131340485 0.114916153 0.02608696 41.44689055 -1.617491954 0.32375958 GTEPSPGGTPQPSRPVS(ph)PAGPPEGVPEEAQPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 GTEPSPGGTPQPSRPVSPAGPPEGVPEEAQPPR 33 1 I3L1Q2;Q8WUZ0;Q8WUZ0-2 I3L1Q2 BCL7C B-cell CLL/lymphoma 7 protein family member C 1 GTEPSPGGTPQPS(0.002)RPVS(0.998)PAGPPEGVPEEAQPPR;GTEPSPGGTPQPSRPVS(0.999)PAGPPEGVPEEAQPPR;GTEPSPGGTPQPSRPVS(1)PAGPPEGVPEEAQPPR;GTEPSPGGTPQPSRPVS(1)PAGPPEGVPEEAQPPR 387.16 1.72E-166 2489500000 133939 188662 181058 219495 316642 311197 289889 321208 297741 TRUE FALSE 116238.6218 187422.6669 268618.2544 269334.6945 310341.4437 323168.95 261775.6094 252520.1688 262542.3982 0.442742287 0.713875809 1.023142381 1.025871236 1.182062196 1.230920995 0.997079372 0.961826244 1 18.0021909 4.468188468 1.923613453 1.063950295 0.398594179 0.862676331 0.08393391 0.185537321 1.07377152 0.026211928 0.181871718 29389.24764 -4.468188468 -0.665356116 down QS(ph)LGELIGTLNAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QSLGELIGTLNAAK 14 0 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 1 QS(1)LGELIGTLNAAK 136.85 2.59E-05 56522000 273340 249910 206010 226650 239250 218130 259120 287680 563460 TRUE FALSE 237217.4264 248268.3248 305637.1251 278114.3466 234489.3931 226521.6022 233990.5823 226161.8707 496848.4007 0.477444279 0.499686271 0.615151673 0.559756953 0.471953603 0.45591694 0.470949654 0.455192913 1 18.9224462 1.235415195 24.99999631 1.000000685 0.50030736 0.906252113 0.050462583 27.8904344 221635.9225 0.095561951 0.013788382 17.19551529 -1.235415195 -0.499693326 QS(ph)PALQHRPMGQSQANHIPGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QSPALQHRPMGQSQANHIPGDR 22 1 Q5TCQ9;Q5TCQ9-1;Q5TCQ9-3;Q5TCQ9-2 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 1 QS(0.999)PALQHRPMGQS(0.001)QANHIPGDR;QS(0.999)PALQHRPMGQS(0.001)QANHIPGDR;QS(1)PALQHRPMGQSQANHIPGDR 135.75 3.36E-06 438540000 197620 163204 80147 149139 204418 204795 184939 214746 193251 TRUE FALSE 171504.0163 162131.9022 118906.3573 183003.2894 200350.4817 212673.5962 167003.6442 168824.2391 170405.0869 1.006448923 0.951449896 0.69778643 1.073930906 1.175730639 1.248047227 0.980039078 0.990723001 1 17.37860888 3.583290347 24.84129874 1.074037334 0.89084791 0.38969575 0.113621436 34.09202901 7961.270543 0.033515717 0.049711844 3830.807655 -3.583290347 -0.183189424 QS(ph)PECENFLDVGLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QSPECENFLDVGLGR 15 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36;A0A087X047 Q12802-2 AKAP13 A-kinase anchor protein 13 1 QS(1)PECENFLDVGLGR 102.16 0.00165 47958000 42827 47892 39309 49864 54049 49572 48285 58275 87679 TRUE FALSE 37167.30344 47577.3943 58318.96388 61186.38332 52973.53065 51479.06692 43602.32813 45813.34475 77313.6885 0.480733802 0.61538125 0.75431615 0.791404271 0.685176605 0.665846733 0.563966472 0.592564469 1 16.23843625 4.588133925 3.132126972 0.700747987 0.477077168 0.281842401 0.121649244 0.417711803 6.788235677 0.031109142 0.184825729 38737.70833 -4.588133925 -0.223670818 QS(ph)PGPALAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QSPGPALAR 9 0 P85037 P85037 FOXK1 Forkhead box protein K1 1 QS(1)PGPALAR;QS(1)PGPALAR 90.614 0.011865 1156730000 1259560 1233830 761270 895840 1324210 1280220 1291280 1478280 1345470 TRUE FALSE 1093105.955 1225724.889 1129422.718 1099254.164 1297860.812 1329470.892 1166051.864 1162161.326 1186410.069 0.921355932 1.033137632 0.951966565 0.926538127 1.093939478 1.120582947 0.982840499 0.979561246 1 20.17817132 3.254802087 24.99995161 1.028725982 0.963149933 0.330425939 0.053902029 375.3726386 577795.3656 0.01704988 0.021945766 1798.051335 -3.254802087 -0.065576049 QS(ph)PLTYEDHGAPFAGHLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QSPLTYEDHGAPFAGHLPR 19 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 QS(0.961)PLT(0.039)YEDHGAPFAGHLPR;QS(0.705)PLT(0.292)Y(0.003)EDHGAPFAGHLPR 179.79 2.26E-14 910810000 406440 307240 217889 212334 301700 373730 318980 332260 317450 TRUE FALSE 352727.9242 305221.7202 323260.8492 260547.68 295696.7603 388107.6349 288045.3687 261208.7847 279921.4226 1.260096212 1.09038357 1.154827116 0.930788639 1.056356307 1.386487791 1.029022238 0.93315039 1 18.09466238 2.009775321 24.9963159 0.967585995 1.136861855 0.286491001 0.120723094 255.6775417 653786.2951 0.050003136 0.03366944 102.2763736 -2.009775321 0.16927586 QS(ph)PS(ph)SSPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QSPSSSPTR 9 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 QS(0.942)PS(0.752)S(0.289)S(0.017)PTR 75.849 0.054233 102350000 292490 237460 156390 200080 181440 260140 249990 298310 345770 TRUE FALSE 253836.7054 235900.1096 232020.7271 245511.222 177829.699 270147.7541 225746.0083 234518.728 304893.4645 0.832542297 0.773713238 0.760989507 0.805236093 0.583251921 0.886039832 0.740409469 0.769182535 1 18.2179457 1.238880633 8.552085135 1.002114084 0.766345539 0.465259456 0.077817891 0.073291166 60.75890097 0.100778189 0.017707138 17.33327524 -1.238880633 -0.235768546 QS(ph)PSFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QSPSFK 6 0 Q6IN85-2;Q6IN85;Q6IN85-4 Q6IN85-2 SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3A 1 QS(0.992)PS(0.008)FK;QS(0.577)PS(0.423)FK 94.114 0.047046 1420870000 4355800 3555000 2383700 2963500 2935700 3109800 4246600 5117200 4549600 TRUE FALSE 3780169.994 3531646.971 3536465.293 3636407.969 2877285.314 3229436.018 3834765.386 4022926.602 4011751.471 0.942274221 0.880325463 0.881526515 0.906438994 0.717214248 0.804994039 0.955883088 1.002785599 1 21.9358008 2.080750443 5.090239932 0.99565513 0.854248209 0.514986977 0.060834448 0.168479788 7.666211803 0.027787214 0.018187504 120.4343694 -2.080750443 -0.14140692 QS(ph)PSPS(ph)TRPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QSPSPSTRPIR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 QS(0.577)PS(0.477)PS(0.916)T(0.03)RPIR 123.36 0.0044418 1401000000 846710 690870 495070 628310 795690 770270 751270 864040 845160 TRUE FALSE 734815.1282 686331.6295 734487.5079 770977.3886 779857.3257 799902.7853 678411.951 679271.77 745246.1476 0.986003256 0.920946229 0.985563643 1.034527171 1.046442613 1.073340383 0.910319299 0.911473038 1 19.50735749 2.21368481 24.99999883 0.933268255 1.00581592 0.301551574 0.047720025 285.2548499 286676.7337 0.021252151 0.014334835 163.5629031 -2.21368481 0.072547665 QS(ph)PSPSTRPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QSPSPSTRPIR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QS(0.742)PS(0.258)PSTRPIR;QS(0.967)PS(0.033)PSTRPIR;QS(0.972)PS(0.028)PSTRPIR;QS(0.955)PS(0.045)PSTRPIR 98.439 0.0033428 1733360000 2922870 2396180 1552970 2014300 2580370 2410480 2664350 2953130 2210560 TRUE FALSE 2536605.324 2380439.336 2303991.486 2471677.602 2529025.685 2503212.725 2405961.747 2321626.131 1949230.115 1.301337028 1.221220274 1.182000765 1.268027609 1.297448498 1.284205854 1.23431386 1.191047744 1 20.89447299 1.114516904 1.769917317 0.839196892 1.255403884 0.831192901 0.036216852 0.552914556 1.2355201 0.436272777 0.010697798 13.01717982 -1.114516904 0.416206992 QS(ph)PSS(ph)SPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QSPSSSPTR 9 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 QS(0.994)PS(0.157)S(0.437)S(0.394)PT(0.018)R 67.252 0.089802 203210000 563190 461070 333530 411880 329750 501440 440000 520660 605650 TRUE FALSE 488763.0146 458041.2008 494826.2236 505403.6492 323188.6201 520730.7213 397328.8677 409320.9108 534050.747 0.915199571 0.857673551 0.926552816 0.946358847 0.605164625 0.975058502 0.743990847 0.766445723 1 19.02661731 QS(ph)PSSS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QSPSSSPTR 9 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 QS(0.997)PS(0.021)S(0.282)S(0.7)PT(0.001)R 96.067 0.011138 264910000 411900 325760 218450 270950 252970 361680 319230 370950 436730 TRUE FALSE 357466.3714 323620.0611 324093.1507 332473.3387 247936.3919 375594.0636 288271.1237 291625.2292 385100.2769 0.928242312 0.840352709 0.841581194 0.863342248 0.643822939 0.975314966 0.748561196 0.757270889 1 18.55487464 5.332664382 1.184660282 0.819170819 1.198274164 0.065058086 0.104822135 13.96394944 6.153679136 0.028985375 9.194612321 215111.8732 -5.332664382 0.379103344 QSAEEQAQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QSAEEQAQAR 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 88.596 0.026948 0 59992 61401 44382 38752 69981 71980 59962 70419 58570 FALSE TRUE 52063.9052 60997.65279 65845.28365 47551.23389 68588.51502 74749.11718 54146.89447 55360.44485 51645.92132 1.00809326 1.181073959 1.274936761 0.920716151 1.328052889 1.447338246 1.048425376 1.071922882 1 15.6563668 2.074680563 25 1.046758945 1.195049327 0.18898669 0.14942406 66.16801645 22148.14307 0.061776906 0.041649975 118.7628369 -2.074680563 0.148290382 QSAGPNS(ph)PTGGGGGGGSGGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.99)PT(0.01)GGGGGGGSGGTR;QSAGPNS(0.624)PT(0.376)GGGGGGGSGGTR;QSAGPNS(0.982)PT(0.018)GGGGGGGSGGTR;QSAGPNS(0.964)PT(0.036)GGGGGGGSGGTR 265.7 6.62E-37 689418000 516881 519761 373260 421928 584787 684095 568920 666596 874216 TRUE FALSE 448573.8662 516346.6558 553769.7845 517733.2012 573150.8828 710412.5773 513746.226 524049.6329 770867.1804 0.581908113 0.669825709 0.718372501 0.671624392 0.743514444 0.92157585 0.666452327 0.679818322 1 19.55612278 6.635930617 0.272111535 0.822034403 7.97E-12 0.349137375 0.102284593 57.73455606 1.815442917 0.306532135 18.78036702 4324447.384 -6.635930617 -0.822034403 QSANDFFSYYDSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QSANDFFSYYDSHR 14 0 Q92621 Q92621 NUP205 Nuclear pore complex protein Nup205 0 130.06 6.43E-05 123150000 139980 120630 70507 83192 123510 121190 110470 140840 135330 FALSE TRUE 121481.2883 119837.5736 104604.421 102082.0151 121052.3926 125852.2577 99756.6364 110722.462 119331.4416 1.018015761 1.004241397 0.876587257 0.855449442 1.014421606 1.054644577 0.835962719 0.92785657 1 16.86461469 4.38310444 8.855416905 0.935521894 1.014539718 0.158878105 0.070272774 0.453211381 37.4038077 0.01806383 0.048019872 24160.41779 -4.38310444 0.079017824 QSAPS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QSAPSPTR 8 0 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 QSAPS(0.969)PT(0.031)R 74.094 0.034941 0 1126500 1018800 691840 687670 777870 1124200 871160 1036000 1111400 TRUE FALSE 977630.1708 1012107.436 1026416.138 843815.9839 762391.9089 1167448.701 786675.0373 814459.4622 980011.5581 0.997570042 1.032750509 1.047351054 0.861026563 0.777941752 1.191260135 0.802720163 0.831071282 1 19.90243924 3.744233104 24.7446637 0.9017925 1.02657654 0.170839155 0.11858658 685.8007205 2991605.185 0.031492828 0.052627683 5549.234843 -3.744233104 0.12478404 QSDEVGDRDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QSDEVGDRDHR 11 1 P40222 P40222 TXLNA Alpha-taxilin 0 ;; 136.27 6.16E-05 657712000 354689 316548 193232 222641 297851 338283 309443 362831 204536 FALSE TRUE 307815.95 314468.5753 286679.6415 273195.0419 291924.3478 351296.9659 279433.2655 285242.4142 180355.9871 1.706713234 1.743599314 1.58952107 1.514754494 1.618600816 1.947797639 1.549342886 1.581552233 1 17.46048779 1.051608056 1.985879881 0.464870399 1.670513886 0.744807271 0.121562524 0.745906973 1.834390374 1.997750851 0.033398262 11.26180638 -1.051608056 1.205643487 QSDS(ph)VKGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QSDSVKGK 8 1 F8WBN3;B9A031;C9JQZ0;B8ZZY7;F8WBV6;P84101-4;P84101;P84101-3;P84101-2 F8WBN3 SERF2 Small EDRK-rich factor 2 1 QS(0.009)DS(0.991)VKGK;QS(0.002)DS(0.998)VKGK 103.08 0.0029317 966950000 2147200 1782520 709290 1050930 1032400 614750 3389500 2528400 828580 TRUE FALSE 1863442.08 1770810.509 1052305.016 1289559.719 1011857.26 638399.8303 3060786.812 1987721.336 730626.2163 2.55047251 2.423688706 1.440278206 1.765006087 1.384917811 0.873770768 4.189264967 2.72057215 1 19.478774 2.263548302 24.99994951 2.718800297 1.742195536 0.180600014 0.894910325 353.6888112 353861.3144 0.338805703 0.26232731 183.4629201 -2.263548302 -0.976604762 QSEPFFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QSEPFFK 7 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 98.299 0.026439 137830000 365460 337470 228450 305880 346550 316130 411920 410650 452610 FALSE TRUE 317163.535 335253.1373 338929.1841 375334.7291 339654.333 328291.7257 371972.0618 322835.6932 399102.9614 0.794691009 0.840016662 0.849227435 0.940445863 0.851044382 0.822574016 0.9320203 0.808903277 1 18.60640146 4.246793301 0.019032085 1.686311356 1.60E-05 0.229148665 0.057828097 3844.659402 28.23582959 1183.585992 1320.108387 17651.97491 -4.246793301 -1.686295387 QSFDDNDS(ph)EELEDKDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 227.6 1.03E-15 3577550000 4593520 2890709 3136211 2760460 2701711 2122380 4364420 4694430 4201180 TRUE FALSE 3986474.694 2871719.742 4652893.13 3387264.634 2647952.237 2204029.332 3941159.22 3690562.677 3704521.286 1.076110619 0.775193209 1.256003885 0.914359609 0.714789316 0.594956585 1.063878141 0.996232007 1 21.82085569 5.196111623 8.196666391 0.922404409 7.301409633 0.067321937 0.187035166 47200.16144 34788.06036 0.048188463 5447908.687 157076.6475 -5.196111623 6.379005225 QSFTMVADT(ph)PENLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QSFTMVADTPENLR 14 0 Q14847;Q14847-2;C9J9W2;F6S2S5 Q14847 LASP1 LIM and SH3 domain protein 1 1 QSFTMVADT(1)PENLR;QSFTMVADT(1)PENLR;QSFTMVADT(1)PENLR;QSFTMVADT(1)PENLR 327.42 2.81E-67 893240000 1637480 1422980 792010 906550 1119610 1230280 1156280 1352680 1352110 TRUE FALSE 1421082.869 1413632.351 1175028.685 1112396.033 1097331.951 1277609.668 1044144.144 1063419.909 1192265.096 1.191918537 1.185669492 0.985543139 0.933010651 0.920375808 1.071581875 0.875765085 0.891932434 1 20.18527362 4.197331565 3.722867687 0.943190367 1.195483183 0.757805271 0.0554444 0.099261489 2.831417093 0.014800146 0.037347687 15751.84992 -4.197331565 0.252292817 QSHAASAAPQASS(ph)PPDYTMAWAEYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QSHAASAAPQASSPPDYTMAWAEYYR 26 0 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 1 QSHAASAAPQAS(0.434)S(0.564)PPDY(0.001)TMAWAEYYR;QSHAASAAPQAS(0.028)S(0.972)PPDYTMAWAEYYR;QSHAASAAPQAS(0.005)S(0.995)PPDYTMAWAEYYR 256.12 8.19E-53 1218060000 548458 447452 273231 354513 453056 437003 432506 482950 499408 TRUE FALSE 475977.8857 444512.6583 405366.4255 435010.595 444041.072 453814.7882 390561.6347 379674.9008 440368.5552 1.080862564 1.009410534 0.920516283 0.987833009 1.008339644 1.030534044 0.886897191 0.862175322 1 18.74835193 8 0.210220105 0.895136702 1.694438516 0.280556879 0.057124258 129.3137658 1.955894912 0.349790321 33.44851833 100000000 -8 0.799301814 QSHSES(ph)PSLQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 QSHSESPSLQSK 12 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QSHSES(0.982)PS(0.017)LQSK;QSHSES(0.779)PS(0.22)LQSK;QSHSES(0.999)PSLQSK;QSHSES(0.999)PS(0.001)LQSK;QSHSES(1)PSLQSK;QSHSES(0.989)PS(0.011)LQSK;QS(0.002)HSES(0.998)PSLQSK;QS(0.051)HS(0.097)ES(0.852)PSLQSK 309.06 3.23E-46 10782380000 10627920 7532940 4748200 6418870 7544620 6609860 8574520 9977130 9135960 TRUE FALSE 9223413.444 7483455.621 7044445.402 7876372.54 7394496.823 6864145.591 7742964.37 7843598.392 8055917.217 1.14492406 0.928938992 0.874443619 0.977712696 0.917896327 0.852062578 0.961152425 0.973644364 1 22.94161743 4.739757238 24.93638485 0.936109614 1.144924129 0.670695394 0.046065822 63.45337046 1322149.476 0.011698626 0.070468285 54923.37776 -4.739757238 0.208814515 QSHSGS(ph)IS(ph)PYPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QSHSGSISPYPK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 QSHS(0.012)GS(0.988)IS(0.999)PY(0.001)PK;QS(0.001)HS(0.147)GS(0.852)IS(1)PYPK 139.93 8.66E-05 294620000 700540 511150 333500 398610 528250 432640 550580 633570 601730 TRUE FALSE 607961.8641 507792.222 494781.7155 489120.4929 517738.8585 449283.9408 497184.8363 498085.9859 530594.1649 1.145813325 0.957025643 0.932505007 0.921835416 0.975771866 0.846756279 0.93703412 0.938732498 1 19.01724928 4.74330042 3.523698712 0.934391263 1.172256675 0.734785426 0.039285764 0.14837158 3.231152922 0.009443132 0.094548613 55373.30176 -4.74330042 0.237865411 QSHSGSIS(ph)PYPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 QSHSGSISPYPK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QSHSGSIS(1)PYPK;QSHSGSIS(1)PYPK;QSHSGSIS(1)PYPK;QSHSGS(0.003)IS(0.997)PYPK;QSHSGSIS(1)PYPK;QSHSGS(0.001)IS(0.999)PYPK;QSHSGS(0.026)IS(0.974)PYPK;QSHSGS(0.043)IS(0.957)PYPK 221.73 2.78E-11 11003440000 17693800 13307780 7865890 11095220 14207280 11688530 15210230 17189970 17146300 TRUE FALSE 15355519.5 13220360.32 11669860.71 13614559.28 13924582.92 12138195.31 13735144.24 13514028.69 15119283.95 1.015624784 0.874403865 0.771852738 0.90047646 0.92098164 0.802828716 0.908452033 0.893827296 1 23.84988648 1.015769892 1.900300211 1.113821512 0.879031299 0.224499426 0.065915244 2.561328434 5.234147852 1.331441509 0.017610188 10.36978834 -1.015769892 -0.234790213 QSHSS(ph)SS(ph)PHPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QSHSSSSPHPK 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 QS(0.003)HS(0.085)S(0.907)S(0.053)S(0.952)PHPK;QS(0.003)HS(0.103)S(0.89)S(0.112)S(0.892)PHPK;QS(0.024)HS(0.167)S(0.791)S(0.233)S(0.785)PHPK 99.796 0.0023809 2201870000 4462060 3054080 1977440 2647500 1985650 2561750 3500990 4270250 4218030 TRUE FALSE 3872387.466 3034017.547 2933736.598 3248655.34 1946139.45 2660302.18 3161464.529 3357090.269 3719379.299 1.041138092 0.815732224 0.788770481 0.873440184 0.523243072 0.715254339 0.849997883 0.902594223 1 21.82663045 1.602167924 2.058574529 0.995463444 0.786908549 0.210149688 0.12913931 0.548917615 4.527384761 0.183110744 0.037555488 40.00994223 -1.602167924 -0.208554895 QSHSSS(ph)SPHPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QSHSSSSPHPK 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QSHS(0.008)S(0.105)S(0.729)S(0.158)PHPK;QSHS(0.002)S(0.12)S(0.727)S(0.151)PHPK;QSHSS(0.012)S(0.494)S(0.494)PHPK;QSHS(0.006)S(0.074)S(0.46)S(0.46)PHPK;QS(0.024)HS(0.017)S(0.092)S(0.513)S(0.354)PHPK 136.6 0.00016004 1338463000 2971390 2527835 529165 1656179 1887957.3 2514931 2800735 3245447 3284707 TRUE FALSE 2578713.283 2511229.485 785070.964 2032239.755 1850390.643 2611682.023 2529120.151 2551433.415 2896392.68 0.890318948 0.867019691 0.271051287 0.701645108 0.63886042 0.901701638 0.873196569 0.880900381 1 21.46582578 2.734194811 23.25456436 0.904965131 0.663689018 0.329149264 0.169822337 175.3651281 934080.3463 0.058622781 0.053578513 542.2440692 -2.734194811 -0.241276113 QSHSSSS(ph)PHPK ddPTM_MDA-MB-175_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(0.002)S(0.018)S(0.979)PHPK;QSHSSS(0.035)S(0.965)PHPK;QSHS(0.002)S(0.017)S(0.098)S(0.883)PHPK;QS(0.011)HS(0.008)S(0.006)S(0.124)S(0.852)PHPK;QS(0.044)HS(0.034)S(0.03)S(0.215)S(0.677)PHPK 157.37 1.97E-05 3339145000 3341329 2980380 618581 1855122 2135483.1 2921569 3325462 3848483 3785365 TRUE FALSE 2899763.907 2960801.688 917728.8406 2276355.804 2092991.164 3033963.65 3002959.207 3025514.859 3337863.462 0.868748509 0.887034991 0.274944991 0.681979904 0.627045171 0.908953792 0.899665083 0.906422595 1 21.67049351 2.731156107 20.50193082 0.92254265 0.659067795 0.374081162 0.167333111 54.82631171 151802.5986 0.05820925 0.052639219 538.4632977 -2.731156107 -0.263474855 QSHVWEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QSHVWEQK 8 0 Q8TE77;Q8TE77-3;E9PIT5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ; 111.61 0.0032009 502630000 976570 858800 566250 671900 784660 719200 948860 1029010 993800 FALSE TRUE 847513.8002 853158.4863 840090.394 824465.1643 769046.8012 746868.0894 856839.7032 808964.2193 876314.0961 0.967134734 0.97357613 0.958663563 0.940832936 0.87759264 0.852283551 0.977776926 0.923144136 1 19.74108854 3.70351363 3.317268474 0.925044115 0.968411654 0.15623375 0.042315395 0.463126025 10.49320017 0.012396377 0.020624645 5052.585024 -3.70351363 0.04336754 QSIAIDDCTFHQCVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QSIAIDDCTFHQCVR 15 0 A0A087WY71;Q96CW1-2;Q96CW1;E9PFW3;C9JJ47 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 ; 204.13 5.06E-09 562600000 502960 506120 319040 425470 467440 525270 487630 530660 583740 FALSE TRUE 436492.5617 502795.2644 473328.8111 522079.4664 458138.8585 545477.4768 440339.7177 417182.4886 514730.9222 0.848001437 0.97681185 0.919565526 1.014276477 0.890055054 1.059733257 0.855475548 0.810486549 1 18.97345893 QSIDALKDWFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QSIDALKDWFR 11 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 83.204 0.01372 270920000 1386080 1395330 724700 892720 1265290 1066150 1341040 1438000 842820 FALSE TRUE 1202906.016 1386163.985 1075167.344 1095425.72 1240113.204 1107165.48 1210986.147 1130494.891 743182.7797 1.618587041 1.865172368 1.446706481 1.473965423 1.668651694 1.489762022 1.629459374 1.521153236 1 19.50335755 1.227764295 3.410348649 0.899776329 1.596097696 0.710041649 0.119281506 0.184460735 3.005395631 0.344171815 0.030576892 16.89523726 -1.227764295 0.696321367 QSIRNS(ph)QK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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;QS(0.003)IRNS(0.997)QK 113.63 0.0017029 558979000 932380 726178 292095 534225 402939 272910 1342800 921460 649055 TRUE FALSE 809163.6207 721407.6889 433353.119 655528.9514 394921.3022 283409.0243 1212575.463 724412.9498 572324.4573 1.413819749 1.260487263 0.75718085 1.145379938 0.690030449 0.495189434 2.118685384 1.265738237 1 19.12647373 2.254139547 24.99982395 1.448080253 0.960879305 0.271765245 0.38649665 323.4685611 519075.959 0.146166806 0.112813668 179.53104 -2.254139547 -0.487200948 QSLEDFPEWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QSLEDFPEWER 11 0 Q86W56-3;Q86W56-2;Q86W56;Q86W56-5;Q86W56-4 Q86W56-3 PARG Poly(ADP-ribose) glycohydrolase 0 110.08 0.0025398 0 94639 73712 47485 54132 68169 70345 76491 95048 87620 FALSE TRUE 82132.21637 73227.78102 70448.90483 66423.49796 66812.57027 73051.21767 69072.91459 74722.72486 77261.66342 1.063039711 0.947789341 0.911822264 0.859721303 0.864757078 0.945504076 0.894012781 0.967138443 1 16.23746512 4.723758501 2.94903029 0.920153231 1.084554615 0.516209931 0.043112217 0.331651711 4.280663378 0.011695486 0.127040376 52936.89942 -4.723758501 0.164401384 QSLGES(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QSLGESPR 8 0 O14639-3;F8W8M4;O14639-5;O14639-2;O14639;J3QSX6;A0A0A0MRL6;A0A3B3IS55;O14639-4;O14639-6;A0A494C1P1;A0A494C1G0;H0Y7N6;F6XFR5 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 QSLGES(1)PR;QSLGES(1)PR;QSLGES(1)PR 116.6 0.0023495 786130000 1112490 1027110 535340 631162 815650 950090 860830 954150 876320 TRUE FALSE 965471.6278 1020362.847 794232.2146 774476.9788 799420.1608 986640.5771 777346.8391 750112.4477 772722.4479 1.249441673 1.320477811 1.027836342 1.002270584 1.034550197 1.276836955 1.005984544 0.970739817 1 19.55959078 4.235631611 24.99996001 1.043004959 1.284959789 0.568822964 0.086668937 51.92234861 443189.3138 0.023412325 0.052400316 17204.08623 -4.235631611 0.24195483 QSLGHPPPEPGPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QSLGHPPPEPGPDR 14 0 P13861-2;P13861;C9J830 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 0 76.391 0.014339 0 164610 185370 52365 97687 199630 192970 156820 183000 180830 FALSE TRUE 142856.3714 184152.2923 77688.88915 119868.3264 195657.7536 200393.6808 141611.6205 143866.8741 159452.4834 0.895918134 1.154903883 0.487222823 0.751749511 1.227059933 1.256761115 0.888111728 0.902255462 1 17.28276704 3.261770149 24.99494057 1.033356689 0.822250665 0.246328564 0.200035013 405.7439952 436953.1642 0.061633205 0.079517911 1827.132947 -3.261770149 -0.211106024 QSLS(ph)SADNLESDAQGHQVAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QSLSSADNLESDAQGHQVAAR 21 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 QS(0.043)LS(0.585)S(0.372)ADNLESDAQGHQVAAR 113.05 0.00013542 110450000 43500 33556 24509 25191 36650 41109 40701 32829 40568 TRUE FALSE 37751.36479 33335.56843 36361.63438 30911.00157 35920.7367 42690.48983 36753.82328 25808.77383 35772.09726 1.055329927 0.931887448 1.016480362 0.86410929 1.004155178 1.193401928 1.027443905 0.721477794 1 15.12654708 1.765269958 25 0.845050757 1.011094655 0.257745491 0.106820304 20.91337758 19590.48116 0.056777044 0.027268097 58.24651663 -1.765269958 0.166043898 QSMAFSILNT(ph)PK ddPTM_MDA-MB-175_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 197.47 2.17E-06 926160000 1297420 1795720 871470 920440 1199540 1037610 1050820 1303230 1305910 TRUE FALSE 1125962.66 1783923.797 1292915.807 1129439.97 1175671.501 1077527.528 948911.6381 1024544.406 1151526.807 0.977799781 1.5491813 1.122783941 0.98081952 1.020967548 0.935738118 0.824046502 0.889726926 1 20.13511657 3.839445665 3.035578324 0.928965445 1.274714259 0.446063311 0.147848731 0.200429939 3.543971791 0.038259588 0.073145891 6909.484794 -3.839445665 0.345748814 QSMDMS(ph)PIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QSMDMSPIK 9 0 Q14562;F5H658 Q14562 DHX8 ATP-dependent RNA helicase DHX8 1 QSMDMS(1)PIK;QS(0.075)MDMS(0.925)PIK;QSMDMS(1)PIK;QSMDMS(1)PIK;QSMDMS(1)PIK;QSMDMS(1)PIK 160.56 6.84E-05 1758789000 4568240 4311060 2834560 3482890 4499900 3624310 4929310 5682760 5458310 TRUE FALSE 3964535.51 4282740.363 4205362.697 4273733.407 4410360.794 3763739.551 4451266.275 4467545.997 4813034.81 0.823708048 0.88982119 0.873744501 0.887949823 0.916336775 0.781988849 0.92483567 0.928218094 1 22.19851543 1.515755777 1.64916732 1.008477528 0.868561039 0.530648638 0.04070179 0.439372047 1.819210109 0.089153801 0.011355335 32.79108427 -1.515755777 -0.139916489 QSNASS(ph)DVEVEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QSNASSDVEVEEK 13 0 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 QSNAS(0.026)S(0.974)DVEVEEK;QSNAS(0.12)S(0.88)DVEVEEK;QSNAS(0.069)S(0.931)DVEVEEK;QSNAS(0.059)S(0.941)DVEVEEK;QSNAS(0.015)S(0.985)DVEVEEK 360.12 1.79E-76 3170190000 4886240 4486090 3813420 5110970 4855940 3458917 5244970 6640890 9309500 TRUE FALSE 4240511.004 4456620.579 5657602.667 6271493.855 4759316.294 3591983.775 4736313.617 5220787.353 8208941.515 0.516572203 0.542898323 0.689200021 0.763983254 0.579772226 0.437569663 0.576970077 0.635987885 1 22.96876478 1.229084287 3.607817035 1.061332768 0.590725075 0.676559376 0.089042257 0.198201663 3.875793679 0.258962513 0.024716052 16.94666665 -1.229084287 -0.470607693 QSNVIADHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QSNVIADHR 9 0 P49750;P49750-1;H0YIQ2;P49750-3;F8VU51;H0YI23 P49750 YLPM1 YLP motif-containing protein 1 0 ; 70.977 0.050884 246590000 447860 415950 407170 366900 233731 359140 337930 361300 361220 FALSE TRUE 388674.1663 413217.5971 604078.7739 450210.2527 229080.2104 372956.3482 305157.6006 284038.8066 318516.9831 1.220261986 1.297317314 1.896535525 1.413457607 0.719208779 1.17091511 0.95805755 0.89175404 1 18.28101077 3.335285609 6.886556286 0.954034686 1.484795333 0.599537334 0.206695663 0.148687923 9.079041263 0.059690755 0.077078918 2164.141281 -3.335285609 0.530760647 QSPAS(ph)PPPLGGGAPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QSPASPPPLGGGAPVR 16 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 QS(0.022)PAS(0.978)PPPLGGGAPVR;QS(0.098)PAS(0.902)PPPLGGGAPVR 196.24 4.87E-11 678540000 707370 641510 374950 623150 736540 745170 574490 812450 752370 TRUE FALSE 613889.2623 637295.8786 556277.0741 764645.7318 721884.295 773837.1721 518776.0482 638713.89 663425.6757 0.925332384 0.960613829 0.838491928 1.15257181 1.088116305 1.166426324 0.781965587 0.962751237 1 19.33957532 6.865180041 13.22390106 0.983745969 0.38767879 0 0.124380115 0 0 0.028470771 0 7331283.962 -6.865180041 -0.596067179 QSPGST(ph)SPKPPHTLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QSPGSTSPKPPHTLSR 16 1 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 1 QSPGS(0.071)T(0.464)S(0.464)PKPPHTLSR 68.458 0.071746 156320000 99349 78454 56805 69108 78582 78274 83868 109550 84787 TRUE FALSE 86219.77793 77938.63051 84276.088 84800.02765 77018.37194 81285.25143 75734.49427 86123.58502 74763.57745 1.153232374 1.042467912 1.127234556 1.134242509 1.030158997 1.08723063 1.012986495 1.151945746 1 16.19004798 3.248737083 24.99957747 1.066677014 1.110088177 0.224201494 0.051279872 402.6167402 989066.0233 0.014239369 0.018174916 1773.115732 -3.248737083 0.043411162 QSPS(ph)PS(ph)TRPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QSPSPSTRPIR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 QS(0.171)PS(0.89)PS(0.914)T(0.025)RPIR;QS(0.363)PS(0.727)PS(0.776)T(0.135)RPIR 117.48 0.010153 298120000 807260 684210 464030 586850 754940 703050 714000 824830 774540 TRUE FALSE 700578.5457 679715.3795 688436.4601 720103.2619 739918.171 730096.7884 644756.3899 648446.5233 682974.7636 1.025775158 0.995227665 1.007996923 1.054362914 1.083375566 1.068995265 0.944041309 0.94944434 1 19.38147275 2.23227097 24.99999381 0.960507359 1.03855289 0.578551115 0.030024023 112.6123922 447604.1516 0.013496138 0.009352227 170.7147199 -2.23227097 0.07804553 QSPS(ph)SSPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QSPSSSPTR 9 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 QS(0.004)PS(0.598)S(0.199)S(0.199)PTR 150.04 9.04E-05 284750000 248360 259840 212940 243780 241480 380710 361290 405160 450130 TRUE FALSE 215538.5967 258133.0939 315918.4962 299133.9749 236675.0204 395356.1601 326252.1514 318519.687 396916.1442 0.543033081 0.650346673 0.795932594 0.753645271 0.596284691 0.996069739 0.821967451 0.802486096 1 18.59847472 5.817518169 0.19635006 1.001942132 4.95E-14 0.53703552 0.102593329 38.79881719 1.326872362 0.954911315 10.36133146 656928.5985 -5.817518169 -1.001942132 QSPSS(ph)SPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QSPSSSPTR 9 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 QS(0.006)PS(0.1)S(0.447)S(0.447)PTR 145.28 0.00010233 280020000 325990 417640 351030 518380 448650 763700 679660 758500 878450 TRUE FALSE 282909.5955 414896.4953 520789.2821 636086.1019 439722.7428 793080.0332 613746.6778 596300.6777 774600.6417 0.365232844 0.535626325 0.672332624 0.821179415 0.567676709 1.023856669 0.79233949 0.769816917 1 19.56309317 4.840899946 0.570889494 0.862264373 7.93E-12 0.659464495 0.118878094 2.832604774 0.672250459 0.068650969 1.668753753 69326.60716 -4.840899946 -0.862264373 QSQQPMKPISPVKDPVS(ph)PASQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QSQQPMKPISPVKDPVSPASQK 22 2 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 QSQQPMKPIS(0.006)PVKDPVS(0.977)PAS(0.017)QK 59.65 0.031977 291710000 870230 599440 503500 473440 506860 339730 800140 833000 794050 TRUE FALSE 755226.9006 595502.2392 746994.2841 580941.7881 496774.4777 352799.6329 722542.546 654869.4324 700178.3136 1.078620811 0.850500833 1.066862926 0.829705486 0.709497092 0.503871123 1.031940767 0.935289511 1 19.41736285 3.717848882 23.57733238 0.838767275 0.983845451 0.183300504 0.161669048 785.6118863 894305.9303 0.047793684 0.071005375 5222.144466 -3.717848882 0.145078177 QSS(ph)LSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QSSLSEK 7 0 A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;Q7Z4S6-3;H0YHT2;H0YI78 A0A1B0GV47 KIF21A Kinesin-like protein KIF21A 1 QS(0.001)S(0.999)LS(0.001)EK;QS(0.001)S(0.996)LS(0.003)EK;QS(0.01)S(0.98)LS(0.01)EK 112.3 0.0066989 464690000 2824330 2243580 1217960 1883790 1320180 1226530 3292260 3109030 2600840 TRUE FALSE 2451087.635 2228841.775 1806969.53 2311533.311 1293911.001 1273715.403 2972977.132 2444188.129 2293371.658 1.068770352 0.97186244 0.787909593 1.007919193 0.56419595 0.555389877 1.296334644 1.065761897 1 21.12903874 2.227098981 24.99994791 1.116571763 0.827274037 0.362738111 0.184096956 254.9055081 555991.3231 0.078310162 0.053308627 168.6937455 -2.227098981 -0.289297726 QSS(ph)PPRNNYSDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QSSPPRNNYSDLR 13 1 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 QS(0.044)S(0.956)PPRNNYSDLR;QS(0.12)S(0.879)PPRNNYS(0.001)DLR 75.376 0.019111 1091840000 1979730 1716130 726040 934360 1644040 1786870 1527220 1900600 442280 TRUE FALSE 1718103.665 1704856.629 1077155.372 1146520.719 1611326.821 1855612.045 1379110.439 1494171.48 389994.1622 4.405459955 4.371492689 2.761978195 2.93984072 4.131669077 4.758050824 3.536233546 3.831266273 1 18.573093 4.273396426 20.97010381 3.413900707 4.388494387 0.165768508 0.999350914 66.0922332 39779.89215 0.248563844 0.657412585 18767.06793 -4.273396426 0.97459368 QSS(ph)PSGSEQLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 QSSPSGSEQLVR 12 0 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;H7BZT5;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 1 QSS(1)PSGSEQLVR;QSS(1)PSGSEQLVR;QSS(0.998)PS(0.002)GSEQLVR;QSS(0.999)PS(0.001)GSEQLVR;QSS(0.932)PS(0.067)GS(0.001)EQLVR;QSS(1)PSGSEQLVR;QSS(0.952)PS(0.002)GS(0.046)EQLVR;QSS(1)PSGSEQLVR 325.27 2.19E-47 9297250000 6439130 6530640 4408430 5665910 6674060 7029500 6475910 7201610 8001700 TRUE FALSE 5588182.656 6487739.796 6540361.493 6952441.464 6541259.264 7299929.414 5847877.245 5661601.744 7055748.142 0.79200427 0.919497078 0.926955067 0.985358508 0.927082307 1.034607425 0.828810372 0.802409841 1 22.75036763 -1.630590993 12.23375413 9.614851111 0.908138555 0 0.083130726 0 0 0 0.019320196 0.023410409 1.630590993 -8.706712555 QSSGASSSS(ph)FSSSR ddPTM_MDA-MB-175_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 QSSGAS(0.003)S(0.005)S(0.047)S(0.945)FSSSR;QSSGAS(0.063)S(0.063)S(0.191)S(0.684)FSSSR 129.05 7.36E-05 393770000 680270 657250 225833 487390 556520 324380 825290 604220 599290 TRUE FALSE 590370.5959 652932.4815 335046.5942 598059.3488 545446.3408 336859.1085 745253.5028 475012.255 528442.6189 1.117189596 1.235578771 0.634026443 1.131739431 1.032177045 0.63745636 1.410282737 0.898890888 1 19.0113873 QSSLAEPVS(ph)PSK ddPTM_MDA-MB-175_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(0.952)PS(0.048)K 242.19 2.92E-16 601850000 1168630 1034090 793630 1055910 1340180 1147750 1470050 1758760 1843280 TRUE FALSE 1014192.585 1027296.995 1177432.123 1295670.504 1313513.04 1191904.685 1327484.777 1382662.861 1625369.538 0.623976616 0.632039035 0.724408877 0.797154415 0.808131941 0.733313045 0.816727978 0.850676002 1 20.63233633 -2 0.074794142 2.162016907 0.17869538 0.804606248 0.048244998 240.21954 1.714848496 52.71677635 9.592776579 0.01 2 -1.983321528 QSTIVCHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QSTIVCHNR 9 0 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 ;;;;; 133.13 0.0002855 1519320000 1322320 1353330 618692 796480 1168830 1172580 1179760 1233640 1123630 FALSE TRUE 1147572.062 1344439.886 917893.5206 977332.9574 1145572.57 1217689.911 1065347.057 969835.6862 990795.7414 1.158232735 1.356929415 0.926420535 0.98641215 1.156214669 1.229001963 1.075243879 0.978845231 1 19.91822814 8 0.029113716 1.53E-14 2.62726709 0.156788854 0.121440345 6259.916038 18.05776098 582.1011857 1136.624643 99999999.99 -8 2.62726709 QSVDHFAK ddPTM_MDA-MB-175_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 ; 98.033 0.0078096 652400000 639200 581530 242670 451610 610910 560490 693980 723680 761410 FALSE TRUE 554728.1005 577709.8911 360026.0237 554154.9529 598754.0862 582052.413 626677.9264 568926.6637 671396.9772 0.826229666 0.860459476 0.536234204 0.825376002 0.891803369 0.866927366 0.933394024 0.847377458 1 19.35680652 3.481497396 17.12518009 0.89641791 0.74090394 0.39710307 0.093604452 3.256101141 12740.45022 0.026143055 0.035060856 3030.382127 -3.481497396 -0.155513971 QSVEHFTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QSVEHFTK 8 0 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;C9IZ80 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 ;; 87.308 0.015416 946480000 1626480 1708100 650110 1196240 1671680 1555190 1791010 1913340 1860020 FALSE TRUE 1411536.547 1696879.379 964505.3705 1467864.575 1638416.839 1615019.166 1617318.126 1504187.131 1640130.555 0.860624505 1.034600187 0.588066217 0.89496813 0.998955134 0.984689396 0.98609109 0.917114267 1 20.64537923 3.47448873 22.42402432 0.968685778 0.830625696 0.283777959 0.108758713 29.81790803 253981.3777 0.030546677 0.039762554 2981.870165 -3.47448873 -0.138060082 QSVENDIHGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QSVENDIHGLR 11 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 193.49 9.30E-07 504640000 533070 637720 466020 953220 423380 502750 397080 609480 1327050 FALSE TRUE 462623.4489 633530.7753 691388.8307 1169663.17 414955.5663 522091.1178 358571.2427 479147.445 1170167.661 0.395348004 0.541401712 0.590845956 0.999568873 0.354612061 0.446167789 0.306427237 0.409469054 1 20.15828382 1.231824129 24.97827191 1.000000853 0.504311333 0.390016164 0.194353848 264.6824945 981326.1283 0.474287416 0.049890328 17.05391636 -1.231824129 -0.495689519 QSVFPFESGKPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QSVFPFESGKPFK 13 1 P17931;G3V3R6 P17931 LGALS3 Galectin-3;Galectin 0 ; 162.41 3.69E-05 1031380000 2106500 1663630 1078390 1356330 1381850 1159070 1537290 2197700 2881900 FALSE TRUE 1828120.688 1652701.505 1599903.011 1664305.457 1354353.889 1203660.173 1388203.852 1727738.958 2541205.065 0.71939125 0.65036133 0.629584378 0.654927648 0.532957339 0.473657238 0.546277776 0.679889625 1 21.27708137 1.250588907 3.058546084 1.067388168 0.599204708 0.759173355 0.070177915 0.192435051 2.325856643 0.218006583 0.019989613 17.80692408 -1.250588907 -0.46818346 TPTVPDS(ph)PGYMGPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TPTVPDSPGYMGPTR 15 0 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 TPTVPDS(1)PGYMGPTR;TPTVPDS(0.999)PGYMGPTR;TPT(0.001)VPDS(0.998)PGYMGPTR;TPTVPDS(0.988)PGY(0.012)MGPTR 198.44 8.31E-09 941090000 376256 499243 368744 551894 707256 761899 736732 867796 847930 TRUE FALSE 326532.8163 495963.4399 547069.8318 677209.9679 693182.9893 791209.7475 665283.844 682224.5786 747688.6814 0.436722963 0.663328805 0.731681307 0.905737889 0.927101087 1.05820747 0.889787234 0.912444705 1 19.51207817 4.469587337 0.922104376 0.956990904 0.295161602 0.917115146 0.052412735 0.399962519 0.36237911 0.019247491 0.245059468 29484.06347 -4.469587337 -0.661829302 down QTDFEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QTDFEHR 7 0 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ;; 120.87 0.0044934 2194900000 2272900 2148010 1321330 1480010 1890820 2143710 1881730 2075600 2317570 FALSE TRUE 1972530.506 2133899.581 1960329.608 1816068.891 1853196.381 2226179.911 1699240.114 1631749.092 2043589.515 0.965228336 1.044191882 0.959258008 0.888666182 0.906833964 1.089347883 0.831497765 0.798472042 1 20.96267401 3.215685512 0.426300888 0.863028943 1.020790189 0.08413464 0.086334208 2.859200044 1.775864124 0.210851987 0.288593848 1643.181408 -3.215685512 0.157761246 QTDPST(ph)PQQESSKPLGGIQPSSQTIQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QTDPSTPQQESSKPLGGIQPSSQTIQPK 28 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 QTDPS(0.004)T(0.959)PQQES(0.033)S(0.004)KPLGGIQPSSQTIQPK 188.49 1.12E-17 272410000 289480 182890 143080 177770 197000 146940 238180 309110 240370 TRUE FALSE 251224.4846 181688.5835 212273.9666 218135.3955 193080.0854 152592.8769 215081.3403 243009.232 211953.7324 1.185279833 0.857208701 1.001510868 1.029165153 0.910953929 0.719934842 1.014756088 1.146520183 1 17.69338985 2.000784093 24.99939001 1.08279954 0.943570407 0.14262474 0.124077992 40.65923471 1296321.478 0.050224397 0.033519603 100.1807072 -2.000784093 -0.139229133 QTDVGITHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QTDVGITHFR 10 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;; 120.96 0.0005277 525740000 772990 730240 357496 540127 715700 769250 591180 754390 775820 FALSE TRUE 670837.413 725443.0054 530382.2614 662771.0907 701458.9702 798843.5453 533847.4546 593069.5692 684103.4434 0.980608151 1.060428817 0.775295412 0.968817066 1.02536974 1.167723322 0.780360718 0.866929665 1 19.38385497 2.206068021 24.99974566 0.874948079 0.989302128 0.189386587 0.110119785 329.7422217 253700.8172 0.045895072 0.03094498 160.719296 -2.206068021 0.114354049 QTELVEVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QTELVEVAK 9 0 F8W8N9;A6H8Z2-3;A6H8Z2 F8W8N9 FAM221B Protein FAM221B 0 74.127 0.09764 450160000 767360 732410 525650 646330 715790 644700 804230 844540 1003500 FALSE TRUE 665951.4318 727598.7505 779856.0982 793089.105 701547.1794 669502.0262 726235.8984 663941.6932 884867.3732 0.752600279 0.822268707 0.881325407 0.896280199 0.792827491 0.756612851 0.82072853 0.750329047 1 19.75510171 1.227226512 24.99835143 1.000000414 0.810150582 0.586790892 0.050332178 406.1926768 895834.6963 0.201678145 0.013188294 16.87432897 -1.227226512 -0.189849833 QTFLSHGDDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QTFLSHGDDFR 11 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 0 ; 141.32 3.82E-05 358310000 539010 539700 285960 360630 473770 515780 468650 509660 528040 FALSE TRUE 467778.4628 536154.6752 424251.2125 442516.5534 464342.9039 535622.3904 423200.3951 400673.1752 465615.7127 1.004644925 1.151496095 0.911161717 0.950390078 0.997266396 1.150352911 0.908904883 0.860523312 1 18.82878022 2.102170234 24.59085041 0.909446414 1.023566606 0.2540789 0.08304907 12.16035335 2901.053954 0.034048759 0.022955668 126.5232192 -2.102170234 0.114120192 QTFT(ph)PPPQLQQQQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QTFTPPPQLQQQQVK 15 0 B1AN48;Q9UBC9 B1AN48 SPRR3 Small proline-rich protein 3 1 QTFT(1)PPPQLQQQQVK;QTFT(1)PPPQLQQQQVK 264 4.77E-24 863820000 1181990 1153240 696530 872470 1009430 863220 1151880 1338960 1314240 TRUE FALSE 1025787.027 1145664.291 1033374.238 1070577.648 989344.3179 896428.632 1040170.855 1052633.824 1158872.044 0.885159869 0.988602923 0.891706934 0.923810056 0.853713162 0.77353547 0.89757179 0.908326186 1 20.14428985 5.132133274 13.15740878 0.901337787 0.000261503 0.006775041 0.063780658 1025385.567 918057.5766 0.016097099 27242963.91 135560.5348 -5.132133274 -0.901076284 QTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSER 39 1 O00487 O00487 PSMD14 26S proteasome non-ATPase regulatory subunit 14 0 ; 71.359 0.0020484 399355000 78553 82549 55673.2 52229 54133 50699 65644 93846 84801 FALSE TRUE 68172.02202 82006.73018 82596.94574 64088.39272 53055.85921 52649.42334 59277.85498 73777.76321 74775.92239 0.911684134 1.09669968 1.104592803 0.85707258 0.709531324 0.70409594 0.79273987 0.986651329 1 16.19028618 3.700187758 9.243101252 0.842313837 1.04349279 0.412992159 0.110070865 0.480028172 112.5028631 0.034061151 0.050856195 5014.039583 -3.700187758 0.201178953 QTLENER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QTLENER 7 0 P35579 P35579 MYH9 Myosin-9 0 ;;; 168.08 0.0024716 3499570000 2572150 2638630 1991970 2455240 2263710 2783870 2573040 2903230 4372400 FALSE TRUE 2232233.861 2621296.666 2955293.355 3012739.768 2218666.6 2890967.28 2323506.977 2282396.857 3855499.853 0.578973919 0.679885038 0.766513673 0.781413535 0.575454982 0.749829436 0.602647404 0.591984683 1 21.87848648 1.230674869 24.9952572 1.000000605 0.666411022 0.639674225 0.078817413 197.1853206 624961.7106 0.210925825 0.019790408 17.00884679 -1.230674869 -0.333589583 QTLPS(ph)SPTTTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QTLPSSPTTTK 11 0 F8VW64;F8VWX1;F8W659;J3KQU3;P51513-2;P51513 F8VW64 NOVA1 RNA-binding protein Nova-1 1 QTLPS(0.604)S(0.381)PT(0.01)T(0.002)T(0.003)K;QTLPS(0.53)S(0.465)PT(0.003)T(0.001)T(0.001)K 134.04 0.00015638 313130000 928660 848620 559190 721590 879550 784860 916420 1103890 1126380 TRUE FALSE 805935.2281 843045.3593 829616.1544 885438.0383 862048.6758 815054.0721 827545.7295 867831.714 993220.6396 0.811436247 0.848799678 0.83527881 0.891481714 0.867932704 0.820617333 0.833194254 0.873755216 1 19.92175472 1.234469132 2.982383268 1.030666887 0.846036066 0.819040844 0.022867323 0.170618286 1.87260138 0.076712342 0.006132122 17.15809752 -1.234469132 -0.184630822 QTLPSS(ph)PTTTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QTLPSSPTTTK 11 0 F8VW64;F8VWX1;F8W659;J3KQU3;P51513-2;P51513 F8VW64 NOVA1 RNA-binding protein Nova-1 1 QTLPS(0.18)S(0.459)PT(0.194)T(0.082)T(0.084)K;QTLPS(0.02)S(0.925)PT(0.045)T(0.009)T(0.002)K 154.7 3.34E-05 345920000 1175690 1020740 721280 886820 1057820 971630 1229970 1420620 1497450 TRUE FALSE 1020319.588 1014034.692 1070093.421 1088186.035 1036771.452 1009009.235 1110687.699 1116831.468 1320423.167 0.772721665 0.767961906 0.810417029 0.824119163 0.785181204 0.764155962 0.841160415 0.845813294 1 20.33256893 -0.718137054 0.948472018 9.999895765 0.789415812 0.891814946 0.022678584 24.17015514 0.647005122 453.2994283 0.007834855 0.191365192 0.718137054 -9.210479953 QTPMAS(ph)SPRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QTPMASSPRPK 11 1 Q5SSJ5;Q5SSJ5-2;Q5SWC8;B0QZK4 Q5SSJ5 HP1BP3 Heterochromatin protein 1-binding protein 3 1 QT(0.001)PMAS(0.611)S(0.388)PRPK;QTPMAS(0.579)S(0.421)PRPK 76.759 0.021543 410754000 461840 430460 312813 347520 432950 312680 502270 551780 527930 TRUE FALSE 400806.6738 427632.2799 464090.4131 426429.7275 424335.1421 324709.0019 453559.9327 433786.141 465518.7168 0.860989385 0.918614579 0.996931802 0.916031326 0.911531861 0.69752083 0.974310841 0.931833942 1 18.82847965 QTPMASS(ph)PRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QTPMASSPRPK 11 1 Q5SSJ5;Q5SSJ5-2;Q5SWC8;B0QZK4 Q5SSJ5 HP1BP3 Heterochromatin protein 1-binding protein 3 1 QTPMAS(0.054)S(0.946)PRPK 152.07 2.01E-05 297190000 248360 201070 155890 201300 220540 175520 279450 297970 292000 TRUE FALSE 215538.5967 199749.1579 231278.9254 247008.2417 216151.6855 182272.368 252348.982 234251.4343 257480.0926 0.837107811 0.775784861 0.898240027 0.959329473 0.839488922 0.707908585 0.980071816 0.909784644 1 17.97410137 2.168973555 24.99999998 0.952839462 0.84210201 0.418050852 0.070040592 55.76215731 20032.05115 0.029674809 0.020006757 147.5616678 -2.168973555 -0.110737453 QTPS(ph)PDVVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QTPSPDVVLR 10 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3;D6RJ93;D6R8Y0;Q9UPQ0-7;Q6NVB9 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 QTPS(1)PDVVLR;QTPS(1)PDVVLR;QTPS(1)PDVVLR;QTPS(1)PDVVLR;QT(0.004)PS(0.996)PDVVLR;QT(0.002)PS(0.998)PDVVLR 200.98 2.62E-07 4889050000 3566890 3287160 2111010 2563950 3336500 3690180 3400390 3501460 3729180 TRUE FALSE 3095516.449 3265566.43 3131901.497 3146134.035 3270110.178 3832143.612 3070620.701 2752700.027 3288320.589 0.941366988 0.99308031 0.952431922 0.95676013 0.994462094 1.165380172 0.933796027 0.837114251 1 21.64891953 2.011999603 24.99947241 0.900482198 1.000264808 0.188212237 0.073724153 284.346385 592393.3666 0.030332162 0.020433685 102.8015359 -2.011999603 0.09978261 QTQDWVLQSFEEPRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QTQDWVLQSFEEPRR 15 1 Q9P2M7;Q9P2M7-2;A6PVU7 Q9P2M7 CGN Cingulin 0 ; 163.02 2.50E-06 325420000 200248 232010 109375 163815 220890 204356 182653 191599 127430 FALSE TRUE 173784.7194 230485.911 162269.1158 201011.6995 216494.7212 212217.7076 164939.3402 150627.0449 112365.3706 1.546603892 2.051218359 1.444120328 1.788911463 1.926703219 1.888639769 1.467884094 1.340511264 1 16.77783796 1.629140672 1.494920705 0.968331145 1.775706114 0.653275556 0.186302695 0.319395027 1.159168315 0.336003872 0.054301702 42.57362912 -1.629140672 0.807374969 QTQT(ph)PDLLPEALEAQVLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QTQTPDLLPEALEAQVLPR 19 0 H0Y5D5;Q9BTG3;Q5SYW2;F5H2X7;Q9ULV3-5;Q9ULV3-2;Q9ULV3;A0A494C0L7;Q9ULV3-3;Q9ULV3-4 H0Y5D5 CIZ1 Cip1-interacting zinc finger protein 1 QTQT(1)PDLLPEALEAQVLPR 171.79 1.07E-10 17991000 41103 38884 19526 28805 44167 36533 30545 36845 30445 TRUE FALSE 35671.13441 38628.56844 28968.83891 35345.61551 43288.16311 37938.44815 27582.7506 28965.98348 26845.82678 1.328740392 1.438904034 1.079081644 1.316614899 1.612472712 1.413197234 1.027450219 1.07897528 1 14.71241022 2.235057122 24.99983763 1.044203251 1.364277562 0.578546235 0.132446272 68.91358358 491737.0487 0.055706569 0.039251369 171.8134356 -2.235057122 0.320074311 QTS(ph)IETDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QTSIETDR 8 0 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 QT(0.006)S(0.994)IETDR;QT(0.001)S(0.999)IETDR;QT(0.012)S(0.988)IETDR;QT(0.119)S(0.881)IETDR 179.19 0.00025765 1704680000 2616300 2060670 1321330 1852900 2080030 2171210 2536410 2567780 2324690 TRUE FALSE 2270549.326 2047133.323 1960329.608 2273629.265 2038641.473 2254737.854 2290429.349 2018680.229 2049867.796 1.107656469 0.998666025 0.956320018 1.109158975 0.994523391 1.099943059 1.117354667 0.984785572 1 20.96709944 4.757744495 23.37182251 1.033756143 1.107656631 0.145458829 0.057115363 3669.901337 4470884.487 0.01395655 0.437057938 57245.91411 -4.757744495 0.073900489 QTS(ph)PDPCPQLPLVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QTSPDPCPQLPLVPR 15 0 Q5D1E8;A0A1W2PQC8 Q5D1E8 ZC3H12A Ribonuclease ZC3H12A 1 QT(0.086)S(0.914)PDPCPQLPLVPR;QT(0.036)S(0.964)PDPCPQLPLVPR 134.88 3.40E-05 72339000 153649 168546 96817 123438 171458 175599 155130 183260 197656 TRUE FALSE 133343.8954 167438.8102 143638.025 151466.4845 168046.3213 182354.4072 140085.5165 144071.2751 174289.3329 0.76507204 0.960694539 0.824135492 0.86905195 0.964180185 1.046274056 0.803752669 0.826621301 1 17.41112475 3.45169942 24.37649536 0.912462438 0.858632329 0.137380342 0.086788292 479.7553355 460025.4586 0.026147696 0.033757707 2829.433035 -3.45169942 -0.053830109 QTTFLGS(ph)PGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QTTFLGSPGPR 11 0 E9PNH0;H0YCD7;Q9H0X9-3;Q9H0X9-2;Q9H0X9 E9PNH0 OSBPL5 Oxysterol-binding protein;Oxysterol-binding protein-related protein 5 1 QTTFLGS(1)PGPR;QTTFLGS(1)PGPR;QTTFLGS(1)PGPR 176.56 8.93E-06 1146900000 802930 934510 530420 842620 1225250 1275000 684520 1278030 1137850 TRUE FALSE 696820.7661 928371.1423 786932.8861 1033949.75 1200869.922 1324050.075 618135.3558 1004733.23 1003334.669 0.694504822 0.925285621 0.784317447 1.030513329 1.196878727 1.319649481 0.61608093 1.001393913 1 19.93637148 3.735564698 24.38570338 1.01823682 0.813760923 0.244509019 0.186424117 309.2732808 2517381.356 0.052804849 0.082357567 5439.571609 -3.735564698 -0.204475897 QTVAVGVIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QTVAVGVIK 9 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 0 109.66 0.0060157 0 424570 358450 211800 285530 285590 276230 419440 454550 348130 FALSE TRUE 368461.9988 356095.3183 314227.1884 350363.9506 279907.3177 286856.7468 378762.7734 357348.0198 306974.468 1.200301775 1.160016078 1.023626461 1.141345575 0.911826054 0.934464513 1.233857577 1.164096878 1 18.22775914 4.390165215 5.423968832 1.070846783 1.190997981 0.197995066 0.100857341 0.3562524 16.58052697 0.027392891 0.076447172 24556.42918 -4.390165215 0.120151198 QTVEDEKLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QTVEDEKLR 9 1 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 ;; 181.53 4.32E-05 2008880000 1778820 1696200 993010 980670 1537430 1497300 1954500 2037690 467580 FALSE TRUE 1543744.43 1685057.551 1473232.957 1203346.112 1506838.151 1554902.1 1764952.891 1601945.851 412303.2251 3.744196834 4.086937594 3.57317835 2.918594954 3.654684367 3.77125864 4.280715705 3.885358526 1 18.65334622 4.057917299 6.426723627 3.407628901 3.903969483 0.06853897 0.899343846 0.694011934 57.76208444 0.230084686 0.485008429 11426.60722 -4.057917299 0.496340583 QVAEQGGDLS(ph)PAANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QVAEQGGDLSPAANR 15 0 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 QVAEQGGDLS(1)PAANR;QVAEQGGDLS(1)PAANR;QVAEQGGDLS(1)PAANR 289.95 7.29E-44 1878990000 1732260 1816320 1055080 1398200 1754040 1991720 1607340 1909050 1747300 TRUE FALSE 1503337.452 1804388.474 1565320.217 1715682.68 1719138.036 2068342.757 1451460.414 1500814.514 1540736.185 0.975726712 1.171120983 1.01595603 1.11354734 1.115790005 1.342437971 0.94205642 0.974089224 1 20.55518842 QVAGDAPVEQATAETAS(ph)PVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QVAGDAPVEQATAETASPVHR 21 0 Q92766;Q92766-2;A0A087X055;Q92766-4 Q92766 RREB1 Ras-responsive element-binding protein 1 1 QVAGDAPVEQATAET(0.242)AS(0.758)PVHR;QVAGDAPVEQATAET(0.042)AS(0.958)PVHR 184.66 2.50E-17 175130000 360860 273070 145888 281660 344460 258190 269430 324540 295580 TRUE FALSE 313171.4367 271276.1852 216439.9248 345615.2079 337605.9199 268122.7364 243300.7201 255139.6466 260636.8691 1.201562303 1.040820457 0.830427121 1.326041128 1.295311446 1.028721444 0.933485431 0.9789085 1 17.99168165 2.487668001 24.22951199 0.97238587 1.130190453 0.241923472 0.137792014 548.5502716 1260215.493 0.052097423 0.043059587 307.3746171 -2.487668001 0.157804584 QVDDLEVWSHTNDTIGSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QVDDLEVWSHTNDTIGSVR 19 0 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 170.06 1.29E-11 157810000 120030 123450 93189 94563 126920 130780 118370 114780 122340 FALSE TRUE 104167.7314 122639.0488 138255.5121 116034.9745 124394.5403 135811.1912 106890.4956 90235.19022 107877.1046 0.965614824 1.136840382 1.281601992 1.075621884 1.153113451 1.258943608 0.990854325 0.836462849 1 16.71902918 2.04542969 6.379922776 0.908212424 1.147546236 0.508936016 0.095728382 0.130876466 13.00648798 0.03918963 0.025899295 111.0272773 -2.04542969 0.239333812 QVDEAEEEIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QVDEAEEEIER 11 0 Q9P2M7 Q9P2M7 CGN Cingulin 0 ; 252.14 5.19E-20 279320000 282780 310430 196331 240270 287300 301820 279670 303940 334530 FALSE TRUE 245409.9065 308390.7649 291277.3283 294826.9758 281583.2921 313431.2107 252547.6464 238944.7963 294982.2445 0.831948062 1.045455347 0.987440206 0.999473634 0.954577088 1.062542633 0.856145247 0.810031114 1 18.17026859 2.215834327 24.99282567 0.870973238 0.983238974 0.223459436 0.07798386 269.1800841 296023.6889 0.030137285 0.020334363 164.3744555 -2.215834327 0.112265737 QVDGDNSHVEMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QVDGDNSHVEMK 12 0 P02786;F8WBE5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 138.02 8.19E-05 240690000 622330 518220 352490 403720 557970 505960 563080 642840 619440 FALSE TRUE 540087.5137 514815.7787 522955.343 495390.7965 546867.4886 525424.6086 508472.5883 505373.6686 546210.5089 0.988790045 0.942522654 0.957424536 0.906959475 1.001202796 0.961945257 0.930909567 0.925236077 1 19.05909755 4.74635606 23.51064558 0.950487115 0.988790089 0.114596789 0.030151482 880.3300936 2654877.044 0.007148204 0.072280919 55764.275 -4.74635606 0.038302974 QVDLESNPQNRSPES(ph)RPSVVYPSTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QVDLESNPQNRSPESRPSVVYPSTK 25 2 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 QVDLES(0.003)NPQNRS(0.148)PES(0.838)RPS(0.011)VVYPSTK 149.54 1.49E-07 287920000 128990 102350 60957 65196 112450 90846 138310 141540 50858 TRUE FALSE 111943.6447 101677.6561 90436.00909 79999.74826 110212.465 94340.90441 124896.7175 111272.7725 44845.62518 2.496199891 2.267281495 2.016607166 1.783891917 2.457596802 2.10368133 2.785036823 2.4812403 1 15.45267963 QVEDEKNSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QVEDEKNSFR 10 1 P35579 P35579 MYH9 Myosin-9 0 70.728 0.048437 290940000 583180 682120 465280 467200 627700 617670 730670 839600 716150 FALSE TRUE 506111.2854 677639.1088 690290.9643 573284.9007 615209.9981 641432.1646 659809.7359 660058.0738 631487.5628 0.801458833 1.073083856 1.093118859 0.907832449 0.974223459 1.015747898 1.04484993 1.045243189 1 19.26839479 2.583526563 3.902683602 1.033511051 0.979294922 0.101185841 0.081602334 0.628315201 16.94992713 0.029207023 0.025103708 383.2891832 -2.583526563 -0.054216129 QVEDLQATFSSIHSFQDLSSSILAQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QVEDLQATFSSIHSFQDLSSSILAQSR 27 0 O60664-4;O60664;O60664-3;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 0 ; 349.34 3.81E-110 1112920000 347890 354920 134840 334610 443720 416780 385690 482110 420830 FALSE TRUE 301915.4551 352588.5072 200049.075 410588.3147 434890.8401 432813.7963 348285.8432 379014.5283 371079.9568 0.813612941 0.950168557 0.53909965 1.106468585 1.17195993 1.166362635 0.938573579 1.021382377 1 18.50137055 3.706008859 24.99625558 1.06307837 0.785881108 0.570929583 0.122149719 480.4453738 368930.4458 0.033796914 0.05013291 5081.698081 -3.706008859 -0.277197262 QVEEALHQLHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 QVEEALHQLHAR 12 0 F5H169;F5H5V4;F5GX23;J3KN29;O00233-2;O00233 F5H169 PSMD9 26S proteasome non-ATPase regulatory subunit 9 0 ;;;;; 195.77 1.24E-07 3206640000 975718 923507 593167 686737 903560 978350 881045 1013546 931490 FALSE TRUE 846774.3941 917440.4217 880024.5452 842671.132 885580.9238 1015987.758 795601.3915 796807.0753 821370.3134 1.030928901 1.11696321 1.071410216 1.025933271 1.078174983 1.236942389 0.968626914 0.970094807 1 19.64767328 QVEEELTHLQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QVEEELTHLQK 11 0 P67936-2;A0A2R8YHD2;K7ELP0 P67936-2 TPM4 Tropomyosin alpha-4 chain 0 107.65 0.0021693 145600000 479160 540630 392660 446530 491670 471760 565220 579290 626630 FALSE TRUE 415837.792 537078.5659 582551.6894 547921.4613 481886.7289 489908.9125 510405.0514 455413.3415 552550.5153 0.752578779 0.971999032 1.054295803 0.991622388 0.872113437 0.886631899 0.923725591 0.824202184 1 19.07574684 3.227487855 24.82782466 0.892637251 0.952698778 0.041212858 0.088123285 488.3085697 1094903.737 0.026574722 0.030416251 1688.448641 -3.227487855 0.060061527 QVEELFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QVEELFER 8 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 ;;; 171.99 0.0006658 764340000 1038656 910644 593249 681695 850828 998408 830582 991705 937068 FALSE TRUE 901394.978 904661.9196 880146.2007 836484.2688 833898.1874 1036817.402 750032.2855 779636.6032 826288.8886 1.090895679 1.094849431 1.065179761 1.01233876 1.009209005 1.254788024 0.907711934 0.943539982 1 19.65628674 QVELALWDTAGQEDYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 ;;;;;; 411.28 3.90E-140 1798573000 1985110 1949721 1251512 1585409 1995204 1934536 1537803 2332597 2164282 FALSE TRUE 1722772.684 1936913.154 1856747.389 1945400.345 1955503.344 2008958.852 1388667.102 1833789.284 1908423.048 0.90272054 1.014928612 0.972922325 1.019375839 1.024669738 1.052680041 0.727651609 0.960892443 1 20.86394958 QVELYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QVELYR 6 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 101.69 0.084302 188970000 341220 328040 237160 263100 306310 381850 321920 358950 360170 FALSE TRUE 296126.9125 325885.0836 351851.3693 322840.8762 300215.0303 396540.0166 290700.2479 282191.3359 317591.1129 0.932415614 1.026115248 1.107875362 1.016529944 0.945287881 1.248586628 0.91532866 0.888536626 1 18.27681102 QVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHR 37 1 P13010;C9JZ81 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 209.1 7.01E-31 70166000 106710 83789 60226 83235 77481 74203 90815 116050 125180 FALSE TRUE 92608.00313 83238.58454 89351.49504 102134.7789 75939.27969 77057.63743 82007.77528 91233.6106 110381.363 0.838982239 0.754099988 0.809479903 0.925290068 0.687971933 0.698103695 0.742949471 0.82653093 1 16.75213708 1.259999867 3.095159002 1.033615378 0.778984221 0.499732252 0.068951877 0.307142177 3.881461865 0.188048806 0.018544557 18.19700302 -1.259999867 -0.254631158 QVFEQDAS(ph)GDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QVFEQDASGDER 12 0 Q96HP0 Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 1 QVFEQDAS(1)GDER;QVFEQDAS(1)GDER 207.55 0.00012101 126420000 420230 459440 302810 298960 453350 508710 444600 483970 489000 TRUE FALSE 364695.5408 456421.9084 449249.9288 366843.4373 444329.222 528280.4029 401482.7604 380476.7818 431190.9771 0.845786578 1.058514516 1.041881562 0.850767889 1.030469666 1.225165718 0.931101952 0.882385769 1 18.71796746 2.044851945 24.9999135 0.924974956 1.012319069 0.079782196 0.110511714 275.3943945 153500.2061 0.045301972 0.030542563 110.8796751 -2.044851945 0.087344112 QVFGEATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QVFGEATK 8 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;A0A1B0GU92;A0A1B0GU03;C9JH19;F8WD96;F8W787 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ;;; 103.55 0.011055 676190000 1868150 1828570 1248820 1677490 1652530 1685830 1882210 2046490 2392400 FALSE TRUE 1621269.244 1816558.003 1852753.529 2058389.743 1619647.886 1750684.971 1699673.564 1608864.039 2109573.197 0.768529505 0.861102144 0.878259892 0.975737531 0.767760933 0.829876381 0.805695468 0.762649071 1 21.00851972 QVHPDTGISS(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QVHPDTGISSK 11 0 Q16778;P33778;P23527;P06899;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;P57053;Q99880;Q96A08 Q16778;P58876;Q99880 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;H2BFS;HIST1H2BL;HIST1H2BA Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type F-S;Histone H2B type 1-L;Histone H2B type 1-A 1 QVHPDTGIS(0.138)S(0.862)K 130.27 0.00014666 394030000 634770 633420 434040 425410 665410 522140 615300 701790 645360 TRUE FALSE 550883.5362 629259.0223 643943.1958 522005.8425 652169.6429 542227.0637 555628.3007 551717.6698 569066.276 0.968048116 1.10577458 1.131578558 0.917302368 1.146034602 0.952836403 0.976385922 0.969513909 1 19.11823716 2.687324253 24.999422 0.974035748 1.053381924 0.238303846 0.070232369 495.5102592 241770.1678 0.022689054 0.020009906 486.7705022 -2.687324253 0.079346177 QVHPDTGISSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 17 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 ;;;;;;;;;;;;;;;; 184.31 4.96E-06 1.44619E+11 159492208 129143887 65893678 118052270 116104213 114998321 121556529 162166974 138642467 FALSE TRUE 138414908.6 128295532.3 97760081.08 144857842.2 113793966.3 119422380.8 109767995.5 127488828.6 122252312.5 1.132206874 1.049432356 0.799658338 1.184908811 0.930812383 0.976851713 0.89788073 1.042833677 1 26.86528651 4.475130675 24.99996865 0.979813531 1.111513308 0.208942498 0.099135201 79.19135863 994595.9356 0.022923586 0.06157537 29862.81027 -4.475130675 0.131699777 QVHQCIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QVHQCIER 8 0 E7EQY1;Q96C01;C9JF51 E7EQY1 FAM136A Protein FAM136A 0 ; 135.79 0.00081866 700090000 308500 247350 155176 207750 215780 286670 202865 269010 270340 FALSE TRUE 267730.9434 245725.1416 230219.6326 254922.8128 211486.4002 297698.3804 183191.1835 211484.3049 238380.7132 1.123123342 1.030809659 0.96576451 1.069393616 0.887179157 1.248835849 0.768481565 0.887170368 1 17.86290799 2.215312429 24.99999619 0.88076027 1.042203104 0.344582187 0.108962518 258.9717766 278483.7891 0.041838617 0.028227367 164.1770428 -2.215312429 0.161442835 QVIDVLETDKHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QVIDVLETDKHFR 13 1 P80303-2;P80303;E9PKG6;Q2L696;E9PLR0;E9PLE9;A0A2R8Y6G7;E9PM22 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 ;; 145.71 2.52E-05 784790000 1563860 1498380 815900 899410 1447860 1384690 1523520 1772620 622710 FALSE TRUE 1357191.939 1488537.043 1210471.969 1103634.787 1419050.419 1437959.92 1375769.265 1393559.008 549093.9332 2.47169356 2.710896903 2.204489789 2.009919834 2.584349112 2.618786756 2.505526253 2.537924612 1 19.06669345 1.236629159 24.99999761 0.999998159 2.457011922 0.83221717 0.205377292 21.00633751 271822.7514 0.33433137 0.052876223 17.24364839 -1.236629159 1.457013763 QVKPYVEEGLHPQIIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QVKPYVEEGLHPQIIIR 17 1 Q99832-3;Q99832;Q99832-4;F8WAM2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 192.55 1.08E-10 2047840000 4408700 4008500 2448920 3261700 3593000 3218600 4650600 5371500 4235900 FALSE TRUE 3826079.125 3982167.9 3633225.903 4002318.837 3521506.33 3342421.625 4199585.528 4222846.526 3735136.728 1.024347809 1.066137116 0.972715638 1.071532083 0.9428052 0.894859243 1.124345863 1.130573479 1 21.83272962 2.202656252 24.99957744 1.096113775 0.998653532 0.300650024 0.063519908 202.3440849 140887.199 0.026436697 0.017824318 159.4616496 -2.202656252 -0.097460243 QVLGQMVIDEELLGDGHSYSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QVLGQMVIDEELLGDGHSYSPR 22 0 P28070 P28070 PSMB4 Proteasome subunit beta type-4 0 ;; 213.14 1.25E-23 672910000 823430 772960 410030 591480 593290 698830 651210 742550 890290 FALSE TRUE 714611.6392 767882.3749 608321.8795 725784.5742 581484.6898 725714.4423 588055.7544 583761.461 785040.9304 0.910285835 0.978143107 0.774891927 0.924518132 0.740706207 0.924428796 0.749076553 0.743606401 1 19.58240835 4.243842946 24.99985097 0.826570285 0.944214493 0.187964896 0.090971203 183.374402 867834.8779 0.021708018 0.053965122 17532.4636 -4.243842946 0.117644208 QVLQLQASHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QVLQLQASHR 10 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 89.827 0.011248 284850000 165520 177560 122770 155910 162850 152810 160980 191020 197070 FALSE TRUE 143646.1126 176393.5967 182141.9826 191311.7484 159609.6036 158688.6996 145368.1844 150171.8595 173772.6091 0.826632652 1.015082858 1.048162789 1.100931553 0.918496905 0.913197427 0.836542566 0.86418602 1 17.40684117 3.02199605 24.40634364 0.893819499 1.00344404 0.236298317 0.080767089 228.8262664 253898.4439 0.024714026 0.028020802 1051.952306 -3.02199605 0.109624541 QVNELVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QVNELVR 7 0 M0R1K3;Q15102;M0R389 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 127.12 0.0090405 155390000 297730 305820 191340 243350 308990 352870 312590 348790 282660 FALSE TRUE 258384.2261 303811.0483 283872.664 298606.3369 302841.7035 366445.1372 282275.0699 274203.9728 249244.2568 1.036670732 1.218928982 1.138933621 1.198047011 1.215039846 1.470224999 1.132523868 1.100141589 1 17.92720074 1.641631904 2.50668578 1.018874004 1.212307718 0.273064058 0.109787483 0.342132857 4.694994656 0.113406256 0.030536469 43.8159169 -1.641631904 0.193433713 QVNYEVDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QVNYEVDRR 9 1 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 99.568 0.0084163 307590000 239260 257120 152490 179320 242400 239320 234350 295010 276570 FALSE TRUE 207641.1848 255430.9618 226234.674 220037.3467 237576.7142 248526.7953 211622.7731 231924.4073 243874.2097 0.851427402 1.047388168 0.927669532 0.902257549 0.97417728 1.019077809 0.867753804 0.951000139 1 17.89577767 QVQDESQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QVQDESQR 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 117.89 0.0046364 90567000 168200 153890 110900 123530 128250 193450 170290 183670 187110 FALSE TRUE 145971.9438 152879.0865 164531.6109 151579.3745 125698.0759 200892.1467 153775.302 144393.5998 164990.069 0.884731698 0.926595688 0.997221299 0.918718172 0.761852375 1.217601447 0.932027624 0.875165401 1 17.33201966 QVQEFLKDGDDVIIIGVFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QVQEFLKDGDDVIIIGVFK 19 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;; 217.09 3.36E-19 368544000 1204300 1064370 784423 904820 756665 750188 1190400 1168960 552958 FALSE TRUE 1045148.704 1057378.083 1163772.587 1110273.21 741608.8469 779048.2178 1074955.191 918987.0009 487587.9352 2.143508131 2.168589514 2.386795289 2.27707277 1.520974564 1.597759423 2.204638617 1.884761567 1 18.8953029 3.249508163 24.84749166 1.712051192 2.248806006 0.474209899 0.310272928 204.4266734 463981.5056 0.092562211 0.118307241 1776.266653 -3.249508163 0.536754815 QVQPEGPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 ;;;;;; 195.88 7.11E-05 6537820000 4230200 4546380 3176050 3467590 4641980 5431200 4665550 4748500 5428580 FALSE TRUE 3671168.352 4516514.53 4711998.403 4254959.308 4549613.68 5640141.778 4213085.679 3733070.228 4786819.457 0.766932696 0.943531414 0.98436936 0.888890702 0.950446057 1.17826499 0.880143009 0.77986443 1 22.19063596 4.73926093 23.37224796 0.940261774 0.76693258 0.23618199 0.102336394 41.19168553 1373995.299 0.02686532 0.155133385 54860.64761 -4.73926093 -0.173329194 QVS(ph)ASELHTSGILGPETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 QVSASELHTSGILGPETLR 19 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 QVS(1)ASELHTSGILGPETLR;QVS(0.998)AS(0.002)ELHTSGILGPETLR;QVS(1)ASELHTSGILGPETLR;QVS(0.995)AS(0.005)ELHTSGILGPETLR;QVS(0.998)AS(0.002)ELHTSGILGPETLR;QVS(0.998)AS(0.002)ELHTSGILGPETLR;QVS(0.999)AS(0.001)ELHTSGILGPETLR;QVS(1)ASELHTSGILGPETLR;QVS(1)ASELHTSGILGPETLR;QVS(0.999)AS(0.001)ELHTSGILGPETLR;QVS(0.997)AS(0.003)ELHTSGILGPETLR 320.79 6.12E-62 62194910000 9735940 10409540 1982661 6051890 11733940 8718450 11890750 11587230 10825630 TRUE FALSE 8449310.861 10341159.05 2941482.491 7426064.122 11500457.55 9053854.413 10737586.9 9109391.036 9545836.354 0.885130495 1.083316188 0.308142983 0.777937506 1.204761649 0.948461096 1.124845063 0.954278986 1 23.18644017 3.336741376 8.235958985 1.035476854 0.751126731 0.319622654 0.20462436 0.311816141 23.27958496 0.058963192 0.076123286 2171.407713 -3.336741376 -0.284350123 QVSASELHTSGILGPETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QVSASELHTSGILGPETLR 19 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 122.19 2.99E-05 0 79099 112000 62409 78506 132160 167920 86578 106730 118510 FALSE TRUE 68645.86674 111264.2646 92590.20115 96331.98719 129530.2746 174379.9911 78181.67889 83906.62007 104499.8828 0.656898983 1.064730999 0.886031627 0.921838232 1.239525549 1.66870992 0.748150876 0.802935064 1 16.6731418 4.742461519 23.2366221 1.026294885 0.656898602 0.173346682 0.262079683 302.7360211 1803105.417 0.068645173 0.49330483 55266.44364 -4.742461519 -0.369396283 QVVESAYEVIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QVVESAYEVIK 11 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 122.51 0.0009056 39681000 76427 68116 23716 41530 52217 72782 78779 92570 14289 FALSE TRUE 66326.97831 67668.54151 35185.13693 50960.02125 51177.98386 75581.97064 71139.02471 72774.62588 12599.7707 5.264141697 5.370616905 2.792522004 4.044519735 4.06181867 5.998678265 5.646057092 5.775869071 1 13.62110986 QVVGAGLQTAGESGSSPEGLLASELVHRPEPCT(ph)SPEAMGPSGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QVVGAGLQTAGESGSSPEGLLASELVHRPEPCTSPEAMGPSGHR 44 1 P98171-2;P98171;E7EQN5;E9PCM6 P98171-2 ARHGAP4 Rho GTPase-activating protein 4 1 QVVGAGLQTAGESGSSPEGLLASELVHRPEPCT(0.5)S(0.5)PEAMGPSGHR 250.29 8.67E-56 254940000 12717 15390 9178.8 8211.8 14616 6172.6 9630.1 11264 9983.1 TRUE FALSE 11036.41623 15288.90208 13617.69838 10076.4147 14325.1702 6410.063916 8696.174384 8855.281257 8802.909291 1.253723725 1.736801047 1.5469543 1.144668696 1.627322255 0.728175618 0.987875042 1.005949393 1 13.10376469 2.742371578 24.99987063 0.947667885 1.464268569 0.668839445 0.185621947 198.2382143 1300443.42 0.059377782 0.05723992 552.5499931 -2.742371578 0.516600684 QVVGAGLQTAGESGSSPEGLLASELVHRPEPCTSPEAMGPS(ph)GHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QVVGAGLQTAGESGSSPEGLLASELVHRPEPCTSPEAMGPSGHR 44 1 P98171-2;P98171;E7EQN5;E9PCM6 P98171-2 ARHGAP4 Rho GTPase-activating protein 4 1 QVVGAGLQTAGES(0.002)GS(0.161)S(0.161)PEGLLAS(0.161)ELVHRPEPCT(0.161)S(0.161)PEAMGPS(0.193)GHR 86.146 6.63E-05 423790000 3431.8 10354 5097.8 4618.5 8942.7 12203 5467.9 8363.2 7344.6 TRUE FALSE 2978.278935 10285.98389 7563.113131 5667.201014 8764.757766 12672.45731 4937.6239 6574.794762 6476.329755 0.459871416 1.588242767 1.16780853 0.87506369 1.353352608 1.956734414 0.762410823 1.015203829 1 12.66096073 QVVPPFKPNISGEFGLDNFDSQFTNEPVQLT(ph)PDDDDIVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QVVPPFKPNISGEFGLDNFDSQFTNEPVQLTPDDDDIVR 39 1 P41743 P41743 PRKCI Protein kinase C iota type 1 QVVPPFKPNISGEFGLDNFDSQFTNEPVQLT(1)PDDDDIVR;QVVPPFKPNISGEFGLDNFDSQFTNEPVQLT(1)PDDDDIVR 235.05 6.84E-50 192421000 309671 253832 161494 196561 220897 218325 270574 302577 283229 TRUE FALSE 268747.1927 252164.5609 239593.0386 241193.1793 216501.5819 226724.104 244333.7751 237873.2632 249745.9903 1.076082112 1.009684122 0.959346888 0.965753961 0.866887119 0.907818795 0.978329121 0.95246079 1 17.93010199 4.558280043 1.578370632 0.943637812 1.100036995 0.578753684 0.036660653 0.56521624 1.761250804 0.010857972 0.122999475 36164.29831 -4.558280043 0.156399183 QVVQGLLSETYLEAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QVVQGLLSETYLEAHR 16 0 P33993;P33993-3;P33993-2 P33993 MCM7 DNA replication licensing factor MCM7 0 168.05 6.11E-09 503060000 634880 592420 387820 456140 574400 501140 510480 764100 692700 FALSE TRUE 550978.9994 588528.354 575371.0492 559713.5587 562970.5638 520419.1801 460973.7282 600703.1612 610809.7951 0.902046765 0.963521474 0.941980718 0.91634673 0.921679004 0.852015119 0.754692757 0.983453713 1 19.22036367 3.295937071 2.417733541 0.897890967 0.937063096 0.046771462 0.06893966 1.010330234 12.07671702 0.023567379 0.031083342 1976.683201 -3.295937071 0.039172129 DLLVGPGVELLLT(ph)PR ddPTM_MDA-MB-175_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 193.27 1.12E-06 328049000 95829 150482 147473 196896 219049 229162 248595 272423 361387 TRUE FALSE 83164.95485 149493.4738 218791.4361 241604.2462 214690.3535 237978.0104 224486.2952 214167.4614 318664.2406 0.260979879 0.469125351 0.686589232 0.758178093 0.673719628 0.746798605 0.704460264 0.672078741 1 18.28167761 4.485448549 1.641804721 0.745237546 0.199189304 0.765382321 0.092936854 0.289862869 1.098096056 0.025039187 0.216620499 30580.77933 -4.485448549 -0.546048242 down LS(ph)SLRAS(ph)TSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 LSSLRASTSK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 LS(0.739)S(0.261)LRAS(0.932)T(0.05)S(0.018)K 105.53 0.0014438 3880100000 727880 2436100 2848200 3680800 4500000 3259700 4770600 5286500 6426700 TRUE FALSE 631688.8138 2420097.099 4225599.047 4516581.898 4410458.804 3385102.768 4307947.946 4156023.115 5666942.847 0.111469064 0.427055145 0.745657608 0.79700502 0.778278328 0.597341964 0.760189058 0.7333801 1 22.43413922 4.502647116 2.081882364 0.767695853 0.068489125 0.835547496 0.098426503 0.16769258 1.139933574 0.02607581 0.183814638 31816.11265 -4.502647116 -0.699206728 down QWADDWLVHLISPNVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QWADDWLVHLISPNVYR 17 0 Q9H7Z7;A6NHH0;X6RJ95 Q9H7Z7 PTGES2 Prostaglandin E synthase 2;Prostaglandin E synthase 2 truncated form 0 103.13 0.00091398 369820000 173990 181280 113230 106080 131210 161290 116050 156740 166700 FALSE TRUE 150996.7807 180089.1597 167988.4067 130167.0853 128599.1777 167494.9307 104795.4889 123222.3708 146992.9159 1.027238488 1.225155366 1.142833352 0.885533051 0.874866499 1.13947621 0.712928839 0.838287818 1 17.1653871 3.739999121 24.55153093 0.897197193 1.141083718 0.436437199 0.118958085 86.66860702 1479193.259 0.03207656 0.051944226 5495.397611 -3.739999121 0.243886525 QWDSVVLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QWDSVVLER 9 0 Q9BRX2 Q9BRX2 PELO Protein pelota homolog 0 75.378 0.03843 463350000 212650 216930 141450 159400 221070 235840 207380 237230 273290 FALSE TRUE 184547.7637 215504.9725 209855.6931 195594.2063 216671.1395 244912.9174 187268.3195 186500.2106 240981.9675 0.765815657 0.894278417 0.87083567 0.811654948 0.899117647 1.016312216 0.777105115 0.773917702 1 17.87856567 3.230742676 24.91592867 0.875806104 0.842347725 0.079034905 0.085725803 774.7023331 2468986.585 0.027336949 0.031561575 1701.15026 -3.230742676 -0.033458379 QWDYYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QWDYYAR 7 0 Q6UN15;Q6UN15-5;Q6UN15-3;H0Y8P7 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 0 ; 121.62 0.010284 632140000 1325600 1238430 703710 940790 1195890 1216800 1087740 1268060 1262700 FALSE TRUE 1150418.601 1230294.672 1044026.51 1154410.749 1172094.129 1263611.083 982251.1422 996895.2371 1113425.044 1.033225009 1.104964073 0.937671121 1.036810474 1.052692442 1.134886528 0.882188834 0.89534113 1 20.08657301 2.223601679 24.99793407 0.91766974 1.04694942 0.48953732 0.059535507 191.4162952 319874.0715 0.024191272 0.016385432 167.3407378 -2.223601679 0.129279681 QWGWTQGR ddPTM_MDA-MB-175_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 0 141.52 0.0014708 2528000000 1359500 1404300 1244200 875150 1358300 1244100 1290800 1461200 1282400 FALSE TRUE 1179838.63 1395075.061 1845899.282 1073866.183 1331272.487 1291961.332 1165618.415 1148733.751 1130796.133 1.043369884 1.233710498 1.6323891 0.949654984 1.177287796 1.142523656 1.030794483 1.015862822 1 20.10890742 2.866698584 0.945422148 1.009233817 1.261797575 0.214794532 0.173491792 0.832492729 1.712818788 0.115391356 0.102005949 735.6963208 -2.866698584 0.252563758 QWHNDCFNCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QWHNDCFNCK 10 0 Q14192 Q14192 FHL2 Four and a half LIM domains protein 2 0 85.958 0.016389 0 190690 177170 111670 122880 182250 142590 162580 223010 207910 FALSE TRUE 165489.8334 176006.1586 165673.9855 150781.7821 178623.5816 148075.5296 146813.0166 175321.047 183331.1167 0.902682733 0.9600452 0.903687211 0.822456029 0.974322225 0.807694473 0.800807955 0.956308183 1 17.48409215 1.537545885 6.356658697 0.989515245 0.88350294 0.327765294 0.059001056 0.146296443 11.62371286 0.041566676 0.015236396 34.47830324 -1.537545885 -0.106012304 LSS(ph)LRASTS(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSSLRASTSK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 LS(0.079)S(0.921)LRAS(0.005)T(0.064)S(0.931)K;LS(0.074)S(0.926)LRAS(0.014)T(0.065)S(0.921)K 149.37 0.00028063 2263410000 786420 2337280 2629070 3465500 4516600 3092000 4540700 5068100 6073300 TRUE FALSE 682492.6045 2321926.254 3900497.046 4252394.742 4426728.497 3210951.241 4100343.613 3984326.255 5355321.393 0.127441951 0.433573652 0.728340422 0.794050334 0.826603703 0.599581427 0.765657803 0.743993864 1 22.35254173 4.503554455 1.869875671 0.778048897 0.065346636 0.834804313 0.097889516 0.197095853 1.019440295 0.026253121 0.208830681 31882.65317 -4.503554455 -0.712702261 down QWLQEIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 182.09 0.00053604 716030000 679340 695870 448880 535970 702240 750600 578840 739000 767050 FALSE TRUE 589563.4978 691298.7842 665959.8694 657670.1803 688266.7979 779476.0677 522704.1859 580970.6009 676370.2228 0.871657974 1.022071583 0.984608498 0.972352357 1.017588851 1.152439953 0.772807803 0.858953545 1 19.36745362 2.223825444 24.99996265 0.869089355 1.0026718 0.317763008 0.086890798 266.934091 452881.691 0.034940846 0.023669394 167.4269803 -2.223825444 0.133582445 QWSGS(ph)QDSQMGFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QWSGSQDSQMGFPR 14 0 Q96HB5-2;Q96HB5;Q96HB5-5;Q96HB5-3;Q96HB5-4 Q96HB5-2 CCDC120 Coiled-coil domain-containing protein 120 1 QWS(0.001)GS(0.988)QDS(0.011)QMGFPR 149 7.98E-06 65349000 66702 58362 30592 33797 48864 60779 38994 52350 61685 TRUE FALSE 57887.1617 57978.61618 45386.39352 41471.1254 47891.702 63117.20746 35212.36788 41155.35989 54392.66957 1.064245645 1.06592702 0.834421143 0.762439603 0.880480814 1.160399149 0.647373408 0.756634308 1 15.73112461 4.240919671 24.68579404 0.849686085 1.06508644 0.259465953 0.140443993 66.3639536 694401.3365 0.036337528 0.087157135 17414.8473 -4.240919671 0.215400354 QWTEILHFTEHSGLTTGVAFGHHAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QWTEILHFTEHSGLTTGVAFGHHAK 25 0 Q9UMS4;H0YGZ5 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 ; 120.64 5.87E-05 75315000 90633 66512 31661 59788.2 53901.3 52672 77528 88115 91162 FALSE TRUE 78655.61942 66075.07829 46972.3655 73364.02462 52828.76959 54698.32592 70009.34649 69272.29296 80384.93221 0.978487103 0.82198338 0.584342914 0.91265891 0.657197414 0.680454961 0.870926237 0.861757186 1 16.29463748 1.415670121 1.486344674 1.038490305 0.771484897 0.250768678 0.119639715 1.128841148 3.04828248 0.42161783 0.034913555 26.04174733 -1.415670121 -0.267005408 QWTSLS(ph)LR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QWTSLSLR 8 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 QWTSLS(1)LR;QWTS(0.001)LS(0.999)LR;QWTS(0.006)LS(0.994)LR;QWTSLS(1)LR 126.39 0.0012811 873570000 1513870 778570 386547 1525080 720610 474639 683356 873200 1131720 TRUE FALSE 1313808.244 773455.5224 573482.4221 1871372.723 706271.2708 492898.6695 617084.2403 686472.9753 997929.3509 1.316534325 0.775060401 0.574672367 1.87525572 0.707736745 0.493921407 0.618364657 0.687897369 1 19.92857816 3.046199287 24.99996757 0.680522923 1.097330882 0.259746444 0.360717056 179.2647477 97004.92485 0.107480399 0.121871277 1112.241991 -3.046199287 0.416807959 QWYESHYALPLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QWYESHYALPLGR 13 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ;;;; 203.32 8.68E-08 7879859000 7552990 7081500 4298122 5042076 6423150 6459330 5598560 6563800 7298450 FALSE TRUE 6554843.235 7034981.16 6376708.176 6186956.419 6295341.882 6707824.605 5055612.513 5160182.45 6435635.555 1.018523062 1.093129202 0.99084358 0.96135904 0.978200494 1.042294043 0.785565383 0.801813963 1 22.6176512 2.245200416 24.99974425 0.846621297 1.01257186 0.524686561 0.067449694 110.1344619 414672.677 0.026007379 0.01966732 175.8735039 -2.245200416 0.165950563 QYADKLEFMHILTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QYADKLEFMHILTR 14 1 P42574 P42574 CASP3 Caspase-3;Caspase-3 subunit p17;Caspase-3 subunit p12 0 218.63 3.19E-12 456660000 1776700 1639900 898960 1113100 1315000 1255100 1726600 1817400 1519600 FALSE TRUE 1541904.593 1629127.389 1333700.063 1365846.368 1288834.073 1303384.509 1559154.598 1428763.153 1339954.619 1.15071404 1.215807883 0.995332263 1.019322855 0.961849046 0.972707949 1.163587614 1.06627727 1 20.35375271 4.239559632 24.99996976 1.032220903 1.183260994 0.548394749 0.059249926 20.96864205 524661.8776 0.016244028 0.038262472 17360.39616 -4.239559632 0.151040092 QYAENYTRPSS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QYAENYTRPSSR 12 1 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 QYAENYTRPS(0.188)S(0.812)R;QYAENYTRPS(0.07)S(0.93)R;QYAENYT(0.001)RPS(0.229)S(0.771)R;QYAENYTRPS(0.081)S(0.919)R 113.31 0.00071417 2595150000 2021870 1862570 1263540 1511170 1698430 1708340 1628800 2016910 2165290 TRUE FALSE 1754674.757 1850334.655 1874592.17 1854304.245 1664634.566 1774060.945 1470839.227 1585609.492 1909311.883 0.919008975 0.969110742 0.981815589 0.97118981 0.871850524 0.92916247 0.770350428 0.830461229 1 20.86462135 3.233686911 23.36465997 0.868315719 0.962450133 0.280650513 0.061885768 60.98711185 292373.851 0.018900855 0.02215029 1712.722136 -3.233686911 0.094134414 QYDISDPQRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QYDISDPQRPR 11 1 Q13228;Q13228-4;Q13228-2;Q13228-3;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 103.44 0.0024934 1559450000 1665590 1733640 887260 1104500 1517090 1688600 1463720 1734900 1598330 FALSE TRUE 1445478.061 1722251.605 1316341.904 1355293.606 1486902.877 1753561.535 1321768.66 1363905.136 1409377.248 1.025614727 1.221994755 0.933988331 0.961625858 1.05500701 1.244210191 0.937838795 0.967736025 1 20.4266264 QYDPPAESQQSES(ph)PPRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QYDPPAESQQSESPPRR 17 1 Q6P597;Q6P597-3;K7ENJ3;K7EL76 Q6P597 KLC3 Kinesin light chain 3 1 QYDPPAESQQS(0.01)ES(0.99)PPRR;QYDPPAESQQS(0.002)ES(0.998)PPRR;QYDPPAESQQS(0.09)ES(0.91)PPRR 173.78 8.79E-10 3098060000 1866540 1863630 1193130 1336690 1823390 2086240 1676400 2040530 1725160 TRUE FALSE 1619872.01 1851387.692 1770131.659 1640205.895 1787108.106 2166499.003 1513822.986 1604178.539 1521213.55 1.064855102 1.217046543 1.163631272 1.078221986 1.174791078 1.424191234 0.995141666 1.054538686 1 20.53679126 QYECSLEQALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QYECSLEQALR 11 0 Q8TE77;Q8TE77-2;Q8TE77-3;E9PIT5;Q8TE77-5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ; 136.36 0.00023453 518650000 432280 390900 212717 306316 387040 359200 435610 443070 434580 FALSE TRUE 375153.1027 388332.1522 315587.6527 375869.7295 379338.6612 373018.6564 393364.6092 348322.9285 383204.4475 0.978989428 1.01338112 0.823549034 0.980859518 0.989911948 0.973419434 1.026513684 0.908974128 1 18.54775478 QYEMGECTR ddPTM_MDA-MB-175_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 ;; 158.57 0.0012697 611000000 631540 582490 345038 401672 519730 599350 537470 599050 541730 FALSE TRUE 548080.3889 578663.5848 511899.5309 492877.7668 509388.3898 622407.3823 485346.2421 470947.8193 477687.2965 1.147362287 1.211385752 1.071620566 1.03180003 1.066363693 1.302959879 1.016033388 0.985891446 1 18.86570699 2.029530658 24.9999827 0.994645129 1.133110037 0.41544775 0.077304759 197.0454686 166813.4109 0.032311318 0.02178396 107.036194 -2.029530658 0.138464908 QYLPHVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QYLPHVAR 8 0 Q5T8U5;O15260-3;O15260-2;O15260 Q5T8U5 SURF4 Surfeit locus protein 4 0 84.476 0.022049 0 202450 164780 117540 193820 193320 209340 112710 223570 285600 FALSE TRUE 175695.7196 163697.5493 174382.7371 237829.7934 189473.3102 217393.4453 101779.4015 175761.2953 251836.6934 0.697657348 0.650014687 0.692443721 0.94438102 0.75236578 0.863231813 0.404148419 0.697917738 1 17.94212898 3.979700908 24.65927287 0.753445129 0.673184234 0.062511133 0.161770531 2314.215064 2811314.39 0.044367109 0.078129318 9543.351226 -3.979700908 -0.080260895 QYMEGFNDELEAFKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QYMEGFNDELEAFKER 16 1 Q16543;K7EKQ2;K7EQA9;K7EL68 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;;; 234.04 1.05E-19 593917000 484398 400032 183503 203024 367398 321420 461934 538891 68426 FALSE TRUE 420383.577 397404.1635 272245.6646 249123.7022 360087.4986 333785.2354 417135.7118 423653.3533 60336.75623 6.967288321 6.58643567 4.512103096 4.128887892 5.967962501 5.532038118 6.913459354 7.021480434 1 15.88074952 4.373510882 6.571567965 5.316608236 6.870460092 0.137631765 1.7203567 0.447401788 24.13874235 0.430295798 1.162658531 23632.56613 -4.373510882 1.553851857 QYNEEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QYNEEGR 7 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;Q9BUJ2-5 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ; 118.05 0.011849 494910000 728920 640730 377580 493940 556900 817150 506780 653860 660130 FALSE TRUE 632591.3752 636521.0024 560178.9509 606096.6264 545818.7796 848586.2893 457632.5536 514037.1273 582090.1834 1.086758364 1.093509254 0.962357667 1.041241793 0.937687656 1.457826147 0.786188406 0.883088466 1 19.15088316 QYNGVPLDGRPMNIQLVTSQIDAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QYNGVPLDGRPMNIQLVTSQIDAQR 25 1 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 ; 184.59 1.69E-17 1040900000 600030 617650 322586 377483 604210 567230 500190 582020 411370 FALSE TRUE 520734.5152 613592.6165 478589.6686 463196.2846 592187.4031 589051.7051 451681.6508 457559.5523 362738.3072 1.435565268 1.691557258 1.319380002 1.276943392 1.632547187 1.623902669 1.245199754 1.261404002 1 18.46856958 1.557659837 1.380182852 0.963091927 1.487661844 0.537706743 0.145803004 0.561926099 1.534020007 0.374390138 0.046157265 36.11268973 -1.557659837 0.524569917 QYPWGVAEVENGEHCDFTILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 QYPWGVAEVENGEHCDFTILR 21 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4 E7EPK1 7-Sep Septin-7 0 ;;;; 302.11 3.39E-55 1940390000 1465980 1649520 866120 1030550 1350400 1408220 1262440 1551930 1582070 FALSE TRUE 1272247.029 1638684.195 1284978.529 1264552.128 1323529.682 1462395.135 1140008.763 1220061.847 1395039.487 0.911979224 1.174650761 0.921105489 0.906463323 0.948739942 1.048282252 0.817187452 0.87457155 1 20.41187453 4.11736089 21.49613897 0.923716383 1.044526043 0.214740728 0.088526993 3.816461239 690.2372056 0.021814812 0.045411377 13102.7028 -4.11736089 0.12080966 QYPWGVVQVENENHCDFVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QYPWGVVQVENENHCDFVK 19 0 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;E7EW69;E7EX04;B5ME97;Q9P0V9;Q9P0V9-2;Q9P0V9-3;A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599;Q92599-3 D6RGI3;E7EW69;A0A087X142 SEPT11;SEPT10;SEPT8 Septin-11;Septin-10;Septin-8 0 291.7 1.47E-49 305750000 342430 301990 199670 237820 270250 231150 312160 345940 366480 FALSE TRUE 297177.0079 300006.2078 296231.0799 291820.6659 264872.5537 240042.4901 281886.7712 271963.4231 323155.1519 0.919610924 0.928365852 0.91668376 0.903035784 0.819645152 0.742808798 0.872295458 0.841587768 1 18.30186747 3.389199276 5.602734482 0.849437159 0.920344532 0.192723876 0.062907844 0.325489781 16.2274143 0.018577793 0.024147515 2450.187251 -3.389199276 0.070907373 QYQDFLEDLEEDEAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QYQDFLEDLEEDEAIR 16 0 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 0 114.74 0.0035273 0 22369 21271 16111 21160 21876 22159 21483 24457 31626 FALSE TRUE 19412.87997 21131.2694 23902.33349 25964.70141 21440.7104 23011.47107 19399.58197 19227.06087 27887.21031 0.69612126 0.757740526 0.85710737 0.931061269 0.768836688 0.825162173 0.69564441 0.689458023 1 14.767316 4.506441931 4.524950897 0.807171348 0.705550939 0.147148578 0.096209199 0.456179459 22.03595327 0.025035651 0.097176604 32095.33629 -4.506441931 -0.101620409 QYQDFLEDLEEDEAIRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 QYQDFLEDLEEDEAIRK 17 1 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 0 ; 250.55 3.84E-21 174951000 350630 300520 198072 239556 292150 246135 305330 379400 292190 FALSE TRUE 304293.3571 298545.8643 293860.2817 293950.8512 286336.7866 255603.9727 275719.1436 298268.2625 257647.6311 1.181044653 1.158737083 1.140551072 1.140902596 1.111350356 0.99206801 1.070140418 1.157659635 1 17.9750398 3.120413511 3.361373949 1.070872085 1.155339365 0.484687186 0.047269616 0.257792521 5.725039946 0.015892559 0.018444888 1319.512508 -3.120413511 0.08446728 QYSLQNWEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QYSLQNWEAR 10 0 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2;A0A2R8Y6Q7 A0A2R8Y430 GSS Glutathione synthetase 0 ;;; 261.03 5.63E-17 2758640000 1047769 1090496 648602 635530 941258 907816 864675 840700 1071080 FALSE TRUE 909303.6719 1083332.46 962268.0966 779836.8 922528.8073 942740.269 780818.9516 660922.8473 944458.1426 0.962778159 1.147041262 1.018857325 0.825697577 0.976781041 0.998181101 0.826737487 0.699790512 1 19.84912733 3.196959829 0.589062344 0.812480124 1.071669279 0.247757483 0.108764508 1.104570128 1.082928794 0.128015401 0.177491077 1573.837284 -3.196959829 0.259189155 QYTS(ph)PEEIDAQLQAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QYTSPEEIDAQLQAEK 16 0 Q13442;F8WBW6 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 QYT(0.028)S(0.972)PEEIDAQLQAEK 229.6 3.18E-15 71981000 187420 166920 117420 150480 158620 143460 188710 204890 178860 TRUE FALSE 162651.9721 165823.4915 174204.7047 184648.7839 155463.7723 148978.999 170408.9332 161075.868 157715.3746 1.031300674 1.051409807 1.104551191 1.17077225 0.985723635 0.944606697 1.080483965 1.021307329 1 17.26696378 3.204707833 24.99999209 1.010748274 1.087861803 0.411692172 0.049184059 207.3868851 153152.7351 0.015646523 0.0177425 1602.167187 -3.204707833 0.077113528 QYVETHWCAQSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QYVETHWCAQSEK 13 0 Q96P70 Q96P70 IPO9 Importin-9 0 202.4 9.42E-08 157640000 336040 288220 189320 270700 294420 200630 334810 352050 349980 FALSE TRUE 291631.4626 286326.6638 280875.7852 332166.5724 288561.618 208348.3659 302340.1777 276766.8472 308605.7631 0.944996813 0.927807248 0.910144329 1.07634598 0.935049349 0.675127917 0.979697121 0.896829808 1 18.23540548 2.991518728 24.94568646 0.887597895 0.964201878 0.124646257 0.096342642 859.2437486 2527275.771 0.02977347 0.032156051 980.6606031 -2.991518728 0.076603983 QYYTLLNQAPDMLHR ddPTM_MDA-MB-175_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 ; 165.34 1.43E-06 1428450000 1028710 987980 550680 686930 849780 810110 879370 945930 985330 FALSE TRUE 892763.3671 981489.8943 816990.6899 842907.9556 832871.0406 841275.4559 794088.8327 743650.2307 868845.4099 1.027528438 1.129648477 0.940317668 0.970147216 0.958595201 0.968268286 0.913958713 0.855906266 1 19.72873998 4.224394662 24.89584772 0.936760489 1.078588438 0.596310792 0.045786511 128.6448529 226086.9539 0.012362008 0.025929975 16764.65661 -4.224394662 0.141827949 RAAATQPDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RAAATQPDAK 10 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 112.85 0.0025121 122050000 145850 133730 79897 90599 108530 114960 161480 174610 73331 FALSE TRUE 126575.553 132851.5188 118535.4564 111170.8877 106370.4653 119382.5856 145819.6945 137271.0103 64661.89272 1.957498422 2.054556606 1.833157853 1.719264361 1.645025545 1.846258756 2.25511021 2.122904303 1 15.98062812 4.226507984 22.58816522 1.82734411 2.006027333 0.059734867 0.334142512 226.2197805 423974.8548 0.087364916 0.184702771 16846.43398 -4.226507984 0.178683223 RAADEDWDS(ph)ELEDDLLGEDLLSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RAADEDWDSELEDDLLGEDLLSGK 24 1 Q96EV2;A8MTF7;Q96EV2-2 Q96EV2 RBM33 RNA-binding protein 33 1 RAADEDWDS(1)ELEDDLLGEDLLSGK 147.55 1.08E-07 15378000 9831 8284 5858.3 7652.9 6674.5 6942.6 10121 8855.7 7573.4 TRUE FALSE 8531.808441 8229.581859 8691.393475 9390.607912 6541.690508 7209.686314 9139.466978 6961.97747 6678.08128 1.277583798 1.232327298 1.301480637 1.406183531 0.979576354 1.079604457 1.368576781 1.04251164 1 12.70521794 3.242339973 24.99997408 1.107477823 1.299038115 0.453031779 0.114249867 102.6539249 679038.0688 0.034426329 0.042734256 1747.189348 -3.242339973 0.191560292 RAAEDDEDDDVDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RAAEDDEDDDVDTK 14 1 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;; 296.85 1.87E-43 10958900000 15703690 11089608 8176905 9300874 10661314 8287300 13052229 15691375 12625208 FALSE TRUE 13628407.58 11016759.63 12131283.61 11412779.6 10449174.71 8606117.794 11786425.84 12335896.57 11132670.29 1.224181371 0.989588243 1.089701149 1.025161017 0.938604525 0.773050631 1.058724055 1.108080653 1 23.40829634 7.420132131 1.220449357 0.998208842 199.9316289 0.355128968 0.094519769 1774.321858 3.903140415 0.029070405 986695.5495 26310683.52 -7.420132131 198.9334201 RAAEDDEDDDVDTKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RAAEDDEDDDVDTKK 15 2 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;; 189.81 1.36E-07 8411980000 6815590 4651554 3813880 3816173 4025995 2708435 5995365 7178083 4084279 FALSE TRUE 5914892.513 4620997.635 5658285.125 4682693.406 3945885.576 2812630.247 5413935.425 5643105.81 3601440.189 1.642368664 1.283097148 1.571117338 1.300228009 1.095641013 0.780973749 1.503269564 1.566902548 1 21.78014251 3.570683498 5.631382215 1.236183182 1.475005787 0.236566392 0.244458666 0.456478217 21.85362781 0.074311491 0.110567388 3721.204161 -3.570683498 0.238822605 RAAEEAEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 127.17 0.00058218 328990000 400700 395250 203280 248860 334440 385730 342200 381850 220840 FALSE TRUE 347746.4798 392653.5767 301586.8879 305367.4666 327785.2983 400569.2827 309013.4967 300194.3491 194732.5468 1.785764555 2.016373653 1.548723585 1.568137795 1.68325893 2.05702277 1.586861065 1.541572552 1 17.5711345 1.085244853 1.485927996 0.440570831 1.759446406 0.657353678 0.171684054 1.115616874 1.622244098 2.455516888 0.050737575 12.16871875 -1.085244853 1.318875575 RAAPT(ph)TPPPPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RAAPTTPPPPVK 12 1 Q9NZQ3-5;Q9NZQ3-4;Q9NZQ3-3;Q9NZQ3-2;Q9NZQ3;C9JC20;C9JMQ4;C9JSC3 Q9NZQ3-5 NCKIPSD NCK-interacting protein with SH3 domain 1 RAAPT(0.5)T(0.5)PPPPVK;RAAPT(0.592)T(0.408)PPPPVK;RAAPT(0.615)T(0.385)PPPPVK 104.41 0.0012544 1836570000 1761420 1614750 994420 1308840 1696680 1463370 1873800 2144640 1585200 TRUE FALSE 1528643.884 1604142.601 1475324.838 1606032.126 1662919.387 1519666.791 1692079.164 1686025.426 1397799.462 1.093607435 1.147619987 1.055462445 1.148971773 1.1896695 1.087185131 1.210530702 1.206199796 1 20.41472597 3.527615346 24.1262036 1.151721712 1.103510256 0.062515448 0.066167438 574.1538811 274329.9188 0.017811503 0.026418053 3369.887059 -3.527615346 -0.048211455 RAAS(ph)SDQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RAASSDQLR 9 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 RAAS(0.941)S(0.059)DQLR;RAAS(0.778)S(0.222)DQLR;RAAS(0.932)S(0.068)DQLR;RAAS(0.975)S(0.025)DQLR 147.96 5.58E-05 4412020000 1182946 1015225 700330 911293 886990 1022955 988918 1104753 996414 TRUE FALSE 1026616.689 1008555.92 1039011.93 1118216.004 869340.6344 1062308.741 893012.8846 868510.1681 878619.072 1.168443438 1.14788758 1.182551078 1.272697167 0.989439749 1.209066334 1.016382313 0.988494554 1 19.74487829 2.18375927 0.987266502 0.965730024 1.174843655 0.482599533 0.074496954 0.545757562 0.983668395 0.090897639 0.029741913 152.6719562 -2.18375927 0.209113631 RAAS(ph)SDQLRDNS(ph)PPPAFKPEPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RAASSDQLRDNSPPPAFKPEPPK 23 3 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 2 RAAS(0.991)S(0.009)DQLRDNS(1)PPPAFKPEPPK;RAAS(0.995)S(0.005)DQLRDNS(1)PPPAFKPEPPK 141.14 2.68E-07 2512500000 2471400 1877330 1134530 1226670 1573480 1208960 2610100 2812300 807670 TRUE FALSE 2144798.228 1864997.696 1683192.503 1505204.172 1542170.826 1255469.474 2356972.904 2210911.53 712188.1727 3.011561144 2.6186867 2.363409794 2.113492234 2.165397974 1.762833927 3.309480548 3.104392371 1 19.44189895 6.509695521 6.730673946 2.447135132 2.648926435 0 0.689911824 0 0 0.154764187 0 3233668.685 -6.509695521 0.201791303 RAAVAASSS(ph)S ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RAAVAASSSS 10 1 P61927 P61927 RPL37 60S ribosomal protein L37 1 RAAVAASS(0.039)S(0.48)S(0.48) 74.306 0.044898 153690000 372070 339670 192890 219400 258860 445330 364500 373920 261540 TRUE FALSE 322900.0068 337438.6854 286172.2492 269218.1233 253709.1925 462462.1333 329150.8461 293960.1178 230621.0391 1.400132477 1.463173901 1.240876592 1.167361505 1.100112953 2.005290302 1.427236853 1.274645709 1 17.81516461 4.261206533 24.85864658 1.330243047 1.431653231 0.02813981 0.272174759 1215.697973 1334457.986 0.069922231 0.184696765 18247.63278 -4.261206533 0.101410185 RADAGEKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RADAGEKPK 9 2 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A0U1RQX5;A0A0U1RQX9 P47897 QARS Glutamine--tRNA ligase 0 ; 150.61 4.77E-05 295160000 482490 408900 298989 355280 262820 299560 545640 587280 546590 FALSE TRUE 418727.724 406213.909 443581.0805 435951.7541 257590.3962 311084.267 492723.9168 461694.7422 481972.7529 0.868778829 0.84281509 0.920344724 0.904515352 0.534450121 0.64543953 1.02230658 0.95792706 1 18.87859206 2.217331829 24.99860266 0.987222729 0.788688896 0.402341735 0.119025321 275.5087282 324431.225 0.053480676 0.036096144 164.9422175 -2.217331829 -0.198533833 RADDFPVRDDPS(ph)DVT(ph)DEDEGPAEPPPPPK ddPTM_MDA-MB-175_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 177.1 1.49E-17 2165160000 905330 770600 681880 827500 722440 693600 878980 1013600 1382870 TRUE FALSE 785688.3467 765537.8779 1011639.449 1015396.523 708064.8574 720283.2408 793736.6549 796849.5278 1219388.684 0.644329701 0.627804643 0.829628372 0.832709485 0.580671993 0.590692082 0.650929983 0.653482797 1 20.21772663 1.23608009 24.98873645 1.000000427 0.676527264 0.574518139 0.08755037 54.21355396 546025.9729 0.151283419 0.0229602 17.2218614 -1.23608009 -0.323473163 RADDFPVRDDPS(ph)DVT(ph)DEDEGPAEPPPPPKLPLPAFR ddPTM_MDA-MB-175_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 154.4 2.29E-13 490050000 297965 231004 129581 156369 224326 223074 193636 294534 94430 TRUE FALSE 258588.1703 229486.5195 192246.805 191874.9714 219862.3515 231655.8011 174857.2105 231550.1962 83266.59298 3.105545226 2.756045508 2.308810751 2.304345171 2.640462923 2.782097752 2.099968358 2.780829477 1 16.34545017 1.234031387 24.99988956 0.999997644 2.576477371 0.745486126 0.293078283 70.33197213 388160.3803 0.546835605 0.07038704 17.14081183 -1.234031387 1.576479726 RADDNATIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RADDNATIR 9 1 O75821;K7ENA8;K7ER90;K7EL20 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 77.192 0.053391 124540000 56398 51503 39992 42201 42385 61612 52097 54682 52319 FALSE TRUE 48944.86141 51164.6734 59332.26497 51783.38205 41541.62142 63982.25351 47044.64096 42988.67984 46133.90742 1.060930325 1.109047039 1.286088005 1.122458186 0.900457467 1.3868813 1.019741088 0.93182395 1 15.49353987 2.014190728 24.99965997 0.965464262 1.142594175 0.263306176 0.128850087 281.4698682 495860.7391 0.050825371 0.034249745 103.321506 -2.014190728 0.177129913 RADLNQGIGEPQS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RADLNQGIGEPQSPSR 16 1 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 RADLNQGIGEPQS(0.991)PS(0.009)R;RADLNQGIGEPQS(0.996)PS(0.004)R;RADLNQGIGEPQS(0.994)PS(0.006)R;RADLNQGIGEPQS(0.985)PS(0.015)R 169.86 3.35E-09 2652430000 1802290 1558160 1076440 1166350 1566350 1527010 1742440 2017640 1515870 TRUE FALSE 1564112.81 1547924.344 1597009.984 1431187.594 1535182.7 1585755.063 1573458.437 1586183.387 1336665.575 1.170160165 1.158049083 1.194771537 1.070714785 1.148516673 1.18635139 1.177151911 1.186671832 1 20.35020713 RADS(ph)GEEENTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RADSGEEENTK 11 1 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 1 RADS(0.948)GEEENT(0.052)K;RADS(0.993)GEEENT(0.007)K 192.3 1.54E-06 364276000 727070 510760 375350 440180 375287 440700 579360 656820 695180 TRUE FALSE 630985.8573 507404.7839 556870.5155 540129.5967 367819.5229 457654.0142 523173.7564 516364.1544 612996.6124 1.029346402 0.827744842 0.908439793 0.881129823 0.600035164 0.746584899 0.853469246 0.842360535 1 19.22551958 7.614117054 1.078024294 0.820740898 135.7511253 0.253073102 0.104912194 1559.914948 3.699568552 0.032549025 518825.5552 41126055.23 -7.614117054 134.9303844 RADSGEEENT(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RADSGEEENTK 11 1 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 1 RADS(0.16)GEEENT(0.84)K 140.16 7.49E-05 294630000 659230 479180 317930 406980 321900 404500 529030 575280 630560 TRUE FALSE 572111.0852 476032.235 471682.0114 499391.0293 315494.8198 420061.3767 477724.752 452260.8488 556015.9151 1.028947319 0.856148578 0.848324659 0.898159595 0.567420484 0.755484448 0.859192586 0.81339551 1 19.08476665 5.236687303 1.212795689 0.80953969 1.453410206 0.259823688 0.109964613 6.277997687 3.430486396 0.032530102 6.807457726 172459.5716 -5.236687303 0.643870516 RAEATAASTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RAEATAASTSR 11 1 O95721 O95721 SNAP29 Synaptosomal-associated protein 29 0 ;;; 152.4 5.29E-05 287215000 100117.5 106453 66655.4 75605 104215 110682 103934 108447 91876 FALSE TRUE 86886.71871 105753.7032 98890.17439 92772.2708 102141.3254 114940.0082 93854.49668 85256.45299 81014.52395 1.072483235 1.305367212 1.220647479 1.145131345 1.26077795 1.418758052 1.158489763 1.052360106 1 16.30589295 1.789284462 3.119660523 1.018656407 1.238775761 0.462140316 0.092382498 0.199419564 3.685407029 0.063502189 0.025056015 61.55799444 -1.789284462 0.220119354 RAEDGSVIDYELIDQDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RAEDGSVIDYELIDQDAR 18 1 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;H0YL33;H0YNP5;H0YN28;H0YNA0 P07355-2 ANXA2 Annexin A2;Annexin 0 ;;;;; 254.2 2.54E-30 5145210000 3386240 2862330 2015710 3116230 3182820 3270350 1605960 3633710 3419080 FALSE TRUE 2938739.804 2843527.166 2990514.098 3823817.65 3119488.109 3396162.481 1450214.246 2856669.394 3014880.257 0.974745115 0.943164213 0.991918034 1.268314932 1.034697183 1.126466788 0.481018854 0.947523334 1 21.52366927 RAEEQMLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RAEEQMLK 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 102.07 0.0080756 1436840000 1427390 1346380 1159290 1462020 1654910 1627520 1738100 1937220 3092720 FALSE TRUE 1238756.795 1337535.541 1719926.522 1793993.987 1621980.529 1690131.748 1569539.33 1522960.578 2727102.165 0.454239233 0.490460372 0.630679167 0.657838936 0.59476339 0.619753733 0.575533748 0.558453804 1 21.37893732 1.237101529 24.99966155 1.000000517 0.576238854 0.824939654 0.061840027 16.12747391 276225.7363 0.098151253 0.016078217 17.26241404 -1.237101529 -0.423761663 RAEILDEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RAEILDEMR 9 1 Q9Y6K5 Q9Y6K5 OAS3 2-5-oligoadenylate synthase 3 0 90.05 0.018748 85460000 70955 87048 60660 47035 80614 87612 70514 76949 73391 FALSE TRUE 61578.11697 86476.17596 89995.3789 57715.01563 79009.93912 90982.49033 63675.56313 60494.05517 64714.79959 0.951530676 1.336265839 1.390646026 0.891836427 1.220894442 1.405899283 0.983941286 0.934779302 1 15.98180806 2.090047284 11.03636192 0.961736463 1.201313743 0.285971333 0.168872493 0.492877173 56.77786647 0.068043301 0.045865644 123.0402724 -2.090047284 0.23957728 RAEISNAIDQYVTGTIGEDEDLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RAEISNAIDQYVTGTIGEDEDLIK 24 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 175.11 3.32E-12 74388000 105460 103690 69969 76307 87573 70109 142130 111970 83634 FALSE TRUE 91523.1938 103008.8536 103806.2424 93633.67063 85830.46863 72806.1386 128346.2545 88026.08685 73746.8838 1.241044897 1.396789237 1.407601747 1.269662741 1.163852141 0.987243594 1.740361733 1.193624494 1 16.17029447 1.473948007 25 1.048402896 1.314653839 0.212218141 0.193315139 0.647195387 5096.654225 0.125295788 0.047360495 29.78159871 -1.473948007 0.266250943 RAELPGSS(ph)SPLLAQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RAELPGSSSPLLAQPR 16 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 RAELPGS(0.113)S(0.584)S(0.303)PLLAQPR 80.238 0.0098758 162320000 72417 70035 43267 60676 84433 81969 71273 79395 61393 TRUE FALSE 62846.90997 69574.93547 64191.06592 74453.41317 82752.94849 85122.40047 64360.95543 62416.9971 54135.18948 1.160925279 1.285207203 1.185754895 1.375323775 1.528635058 1.572404222 1.18889314 1.152983812 1 15.72427907 1.733536016 2.259124496 1.038515158 1.34805599 0.410817797 0.135819709 0.306620175 3.161252748 0.139414639 0.041718536 54.14221466 -1.733536016 0.309540832 RAELPGSSS(ph)PLLAQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RAELPGSSSPLLAQPR 16 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 RAELPGS(0.005)S(0.054)S(0.941)PLLAQPR;RAELPGSS(0.017)S(0.983)PLLAQPR;RAELPGSS(0.023)S(0.977)PLLAQPR 214.55 1.04E-14 1354800000 802222 869430 561101 588062 855589 964216 683696 877745 695277 TRUE FALSE 696206.3301 863718.6571 832451.3204 721590.4651 838564.4528 1001310.013 617391.2672 690046.0624 613082.1451 1.13558409 1.408813915 1.357813675 1.176988224 1.367784822 1.633239561 1.007028621 1.12553606 1 19.22572086 2.196508276 24.99993135 1.059587021 1.343276696 0.51645451 0.137693819 119.6178824 71111.4754 0.055313212 0.037292515 157.2201752 -2.196508276 0.283689675 RAELYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RAELYEK 7 1 Q99614;H0YB37 Q99614 TTC1 Tetratricopeptide repeat protein 1 0 ; 109.11 0.019245 371320000 573430 489690 298160 367700 528780 515260 605260 695930 596170 FALSE TRUE 497649.7726 486473.1941 442351.1733 451191.9049 518258.3125 535082.3856 546561.9784 547110.7852 525691.4618 0.946657515 0.925396796 0.841465395 0.858282734 0.985860244 1.017863946 1.039701076 1.040745047 1 19.00385678 3.076826542 4.166833598 1.026503545 0.892062581 0.793161042 0.031883628 0.099626786 3.344249378 0.010832747 0.012305106 1193.511319 -3.076826542 -0.134440964 RAEPPKPEVVDSTESIPVS(ph)DEDSDAMVDDPNDEDFVPFRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RAEPPKPEVVDSTESIPVSDEDSDAMVDDPNDEDFVPFRPR 41 3 A6NHN7;A6NHB5;Q14202-2;Q14202;A6NL54;Q14202-3 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 1 RAEPPKPEVVDSTES(0.002)IPVS(0.993)DEDS(0.005)DAMVDDPNDEDFVPFRPR 89.628 0.00017938 85250000 62928 52010 39076 53269 61597 55994 57668 83381 58867 TRUE FALSE 54611.90536 51668.34289 57973.2843 65364.54062 60371.34021 58148.12541 52075.36624 65550.62202 51907.81032 1.052094184 0.995386678 1.116850893 1.259242881 1.163049257 1.120219193 1.003227952 1.262827725 1 15.66366401 4.131858123 5.532567484 1.143701843 1.024890183 0.202497572 0.088581892 0.276688657 12.32634977 0.02204263 0.047633358 13547.46765 -4.131858123 -0.11881166 RAEPQGREAPGPAGGGGGGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RAEPQGREAPGPAGGGGGGSR 21 2 Q9BQ61;K7EN60;K7ELS0;K7ERU7 Q9BQ61 C19orf43 Uncharacterized protein C19orf43 0 ; 144.5 7.14E-08 62214000 16287 10308.3 26964 15046.5 9342.2 6336.4 8896 11847.1 10951 FALSE TRUE 14134.63168 10240.5841 40003.88059 18463.0378 9156.308498 6580.165408 8033.267289 9313.689859 9656.385255 1.463760125 1.060498709 4.142738668 1.912003023 0.948212841 0.681431533 0.831912468 0.964511006 1 13.23726752 3.28594426 4.586817457 0.875446961 2.238462555 0.384855078 0.796362248 0.213059961 9.574207422 0.239033829 0.303905509 1931.720372 -3.28594426 1.363015594 RAEVLGHKT(ph)PEPAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RAEVLGHKTPEPAPR 15 2 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EJ51;K7ER34 Q9UHD8 9-Sep Septin-9 1 RAEVLGHKT(1)PEPAPR;RAEVLGHKT(1)PEPAPR;RAEVLGHKT(1)PEPAPR;RAEVLGHKT(1)PEPAPR;RAEVLGHKT(1)PEPAPR 139.11 1.05E-05 4508710000 3464330 3530060 1991870 2101740 3324260 3001830 3595140 4055400 2496320 TRUE FALSE 3006510.013 3506870.803 2955144.994 2578972.19 3258113.73 3117312.343 3246483.876 3188184.269 2201207.893 1.365845553 1.593157472 1.342510629 1.171616819 1.480148122 1.416182611 1.474864726 1.448379446 1 21.06986398 1.235721787 24.99957109 0.999999443 1.414581207 0.583195155 0.109325479 58.35707223 513810.6896 0.18289046 0.027012348 17.20765885 -1.235721787 0.414581764 RAFS(ph)TEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RAFSTEK 7 1 Q9NZ32;H0YJD9 Q9NZ32 ACTR10 Actin-related protein 10 1 RAFS(0.855)T(0.145)EK 73.067 0.030564 943870000 793550 590150 395110 467300 592680 390960 982710 860540 681710 TRUE FALSE 688680.3569 586273.2658 586186.5176 573407.6072 580886.8276 406000.4842 887406.9355 676520.2177 601119.0204 1.145663893 0.975303136 0.975158825 0.953900289 0.966342451 0.675407815 1.476258287 1.125434722 1 19.19729114 2.239012035 24.99999994 1.196399527 0.952092483 0.348354046 0.162354692 13.6133198 754000.5221 0.061993834 0.045025606 173.3852044 -2.239012035 -0.244307044 RAFST(ph)EK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RAFSTEK 7 1 Q9NZ32;H0YJD9 Q9NZ32 ACTR10 Actin-related protein 10 1 RAFS(0.35)T(0.65)EK 82.008 0.015034 885170000 848280 625550 465560 509950 548590 430390 1049600 900550 679570 TRUE FALSE 736177.6487 621440.7209 690706.3732 625741.9416 537674.1323 446947.3818 947809.9535 707974.3906 599232.0088 1.228535255 1.037061959 1.152652667 1.044239848 0.897272049 0.745867002 1.581707819 1.181469581 1 19.19275516 1.212343869 22.96833495 0.99999862 1.113383667 0.023333964 0.218871794 4846.032614 4244950.33 3.515144743 0.055265502 16.30586599 -1.212343869 0.113385047 RAGAES(ph)PTMSVDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RAGAESPTMSVDGR 14 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 RAGAES(0.479)PT(0.479)MS(0.041)VDGR 90.56 0.0060421 398780000 258000 257510 108820 137220 242830 250330 239630 274450 59664 TRUE FALSE 223904.6463 255818.3999 161445.716 168377.8983 237998.1581 259960.3571 216390.7195 215761.0033 52610.58989 4.255885493 4.862488719 3.068692374 3.200456384 4.523769047 4.941217303 4.113063928 4.101094546 1 15.68306561 1.238433836 8.261950334 0.966431799 4.13095781 0.722263313 0.610658923 0.051703036 34.88364426 0.913124484 0.158162604 17.31545212 -1.238433836 3.16452601 RAGAESPT(ph)MSVDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RAGAESPTMSVDGR 14 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 RAGAES(0.337)PT(0.623)MS(0.04)VDGR 150.31 1.40E-05 404620000 332850 314130 151450 167880 335610 313940 282790 352810 59677 TRUE FALSE 288863.0292 312066.4593 224691.7266 205999.7199 328932.0176 326017.4749 255365.0693 277364.3271 52622.05304 5.489391091 5.930336072 4.269915626 3.914703208 6.250839688 6.195453352 4.852814639 5.270876202 1 15.68337992 4.246655598 24.95224201 4.717186309 5.709863839 0.088847472 1.476522023 505.6362897 1558553.529 0.365890697 0.932686105 17646.37882 -4.246655598 0.99267753 RAGDLLEDS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 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;RAGDLLEDS(1)PK;RAGDLLEDS(1)PK;RAGDLLEDS(1)PK 171.11 9.14E-06 52723153700 42462616 33732697 30975576 33709751 40789078 31650508 44695824 50157018 67997779 TRUE FALSE 36851073.71 33511104.69 45955468.16 41364065.19 39977455.15 32868123.52 40361229.87 39431330.02 59959159.03 0.614602911 0.558898844 0.766446176 0.68987067 0.666744761 0.548175192 0.673145363 0.657636476 1 25.83747681 1.235773035 5.672316636 1.016298375 0.647386728 0.755990805 0.063059943 0.075090336 8.003469664 0.107872371 0.015902504 17.20968953 -1.235773035 -0.368911646 RAGDLLEDS(ph)PKRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RAGDLLEDSPKRPK 14 3 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK 209.31 3.77E-08 14386670000 9386680 6842030 4810140 4370010 6654790 4696950 10069930 10373610 2616820 TRUE FALSE 8146206.455 6797084.254 7136339.793 5362287.562 6522372.699 4877644.706 9093349.739 8155294.229 2307462.521 3.530374332 2.945696493 3.092721866 2.323889343 2.826642964 2.113856525 3.94084396 3.53431276 1 21.13787578 4.923593558 1.483720307 2.799218096 4.081346965 0.088316428 0.806306203 5.68018443 8.229715715 0.22477881 12.15659745 83867.47299 -4.923593558 1.282128868 RAGDLLEDSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RAGDLLEDSPK 11 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;; 91.914 0.016653 538580000 1119540 978440 713000 793020 951590 811720 1078280 1355530 1066120 FALSE TRUE 971589.9524 972012.5632 1057809.185 973087.3116 932655.2208 842947.3937 973708.5716 1065660.458 940084.5081 1.033513417 1.033962963 1.12522776 1.035106209 0.992097213 0.896671934 1.035767065 1.133579427 1 19.84243093 1.982859824 24.70636983 1.078833755 1.019523825 0.077365348 0.064011271 1302.112699 1876901.989 0.030395651 0.018094556 96.13019516 -1.982859824 -0.05930993 RAGELTEDEVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RAGELTEDEVER 12 1 P62269 P62269 RPS18 40S ribosomal protein S18 0 ;;;;; 237.65 6.61E-16 6087420000 4100800 4050040 2288250 2610290 3779870 3975510 3894570 4423950 2415120 FALSE TRUE 3558868.89 4023435.021 3394855.354 3202996.24 3704657.982 4128450.442 3516875.201 3477922.72 2129607.265 1.671138594 1.889284981 1.594122733 1.504031421 1.739596799 1.938597088 1.651419611 1.633128689 1 21.02215597 1.179605572 2.751643193 0.767798391 1.714720841 0.750334499 0.127979519 0.302465387 2.334927759 0.708771123 0.034528041 15.12187251 -1.179605572 0.94692245 RAHT(ph)PTPGIYMGRPTHSGGGGGGGGGGGGGGGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RAHTPTPGIYMGRPTHSGGGGGGGGGGGGGGGGR 34 2 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 RAHT(0.983)PT(0.016)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;RAHT(0.986)PT(0.013)PGIY(0.001)MGRPTHSGGGGGGGGGGGGGGGGR 145.62 2.22E-10 596990000 34356 25717 13666.7 17484.9 23035 24164 24240 21795 17643.5 TRUE FALSE 29815.76755 25548.06333 20275.96183 21455.11378 22576.64857 25093.60472 21889.20853 17134.30886 15557.70553 1.916463035 1.642148534 1.30327456 1.37906671 1.451155411 1.612937375 1.406968945 1.101339065 1 13.92534169 0.507791924 0.431727513 6.34E-42 1.61943272 0.599166897 0.16714849 8.708449639 0.840684668 8.228854858 0.179558836 3.219525906 -0.507791924 1.61943272 RAHTPT(ph)PGIYMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RAHTPTPGIYMGR 13 1 Q13595;Q13595-3;Q13595-4;Q13595-2 Q13595 TRA2A Transformer-2 protein homolog alpha 1 RAHT(0.392)PT(0.608)PGIYMGR 90.926 0.0051576 126080000 51418 44461 24502 28728 41339 47570 38518 44340 22496 TRUE FALSE 44622.98102 44168.93276 36351.24915 35251.13148 40516.43478 49400.04868 34782.53029 34858.23605 19836.54851 2.249533532 2.226644053 1.83253902 1.777079892 2.04251434 2.490355047 1.753456771 1.757273249 1 14.2758734 1.026889381 1.335647634 0.035501394 2.068735257 0.691657619 0.224348131 1.337217121 1.406696148 4.283285777 0.069062708 10.63872005 -1.026889381 2.033233863 RALEQQVEEMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RALEQQVEEMK 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 77.74 0.050972 448280000 288400 244330 170130 218470 297340 284390 342500 395430 417620 FALSE TRUE 250287.2093 242724.9801 252405.4371 268076.9526 291423.5157 295330.6673 309284.4027 310870.3717 368249.4394 0.679667591 0.659131975 0.685419746 0.72797654 0.791375314 0.801985382 0.839877457 0.844184236 1 18.4903238 -2 0.203316756 2.39201032 0.59779653 0.925050402 0.027834693 26.49533762 0.39673994 14.72368959 0.179190563 0.01 2 -1.79421379 RALIVLAHSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RALIVLAHSER 11 1 P15559-2;P15559;B4DLR8;P15559-3;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ; 181.31 4.08E-06 5295200000 2587800 3666700 2150680 2089900 4180000 4633300 4799300 4743100 2158800 FALSE TRUE 2245815.673 3642613.206 3190756.042 2564443.737 4096826.178 4811546.049 4333864.625 3728824.976 1903589.123 1.179779631 1.913550126 1.676178962 1.347162424 2.15215885 2.527617956 2.276680704 1.95883919 1 20.86029069 3.231151566 24.9990145 2.029281386 1.567124453 0.204270301 0.43707998 277.4743697 936229.8123 0.134702834 0.155757372 1702.752653 -3.231151566 -0.462156933 RALS(ph)SDSILSPAPDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RALSSDSILSPAPDAR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 RALS(0.848)S(0.131)DS(0.021)ILSPAPDAR;RALS(0.984)S(0.016)DSILSPAPDAR;RALS(0.898)S(0.102)DSILSPAPDAR;RALS(0.81)S(0.15)DS(0.039)ILSPAPDAR;RALS(0.802)S(0.181)DS(0.017)ILSPAPDAR;RALS(0.92)S(0.079)DS(0.001)ILSPAPDAR;RALS(0.832)S(0.164)DS(0.004)ILSPAPDAR 340.75 4.97E-72 12140620000 3083050 3089540 1315940 1496230 2644970 2765370 2642130 3054230 676156 TRUE FALSE 2675617.131 3069244.608 1952332.986 1835971.89 2592340.272 2871755.573 2385896.639 2401106.683 596221.608 4.487621876 5.147825183 3.27450894 3.07934477 4.347947537 4.816590903 4.001694349 4.02720507 1 19.18548914 4.239644445 24.99993061 3.641296829 4.817723726 0.206197141 1.04372151 47.5589515 1096875.912 0.263192318 0.620873301 17363.78681 -4.239644445 1.176426897 RALSS(ph)DSILS(ph)PAPDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RALSSDSILSPAPDAR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 2 RALS(0.464)S(0.489)DS(0.148)ILS(0.899)PAPDAR 150.69 4.78E-07 82187000 89863 141340 100250 104420 187370 219650 161430 197000 82250 TRUE FALSE 77987.37687 140411.5282 148731.2353 128130.157 183641.7036 228100.0776 145774.5434 154873.0831 72526.4987 1.075294937 1.936003126 2.05071578 1.766666794 2.532063547 3.145058451 2.009948723 2.135399969 1 16.14622058 3.335825852 9.829436006 2.197996394 1.745461914 0.129027404 0.583264341 0.72607 67.32168402 0.173041191 0.223384497 2166.835051 -3.335825852 -0.45253448 RALSSDS(ph)ILSPAPDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RALSSDSILSPAPDAR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 RALS(0.237)S(0.07)DS(0.691)ILS(0.002)PAPDAR 253.34 1.58E-26 444460000 371690 367290 150470 179100 313040 344690 277730 350160 46750 TRUE FALSE 322570.2248 364877.2478 223237.7953 219767.3924 306811.1165 357950.4473 250795.7873 275281.0089 41223.26826 7.824955138 8.851245018 5.415334706 5.33114917 7.442668411 8.683213691 6.083840461 6.677806505 1 15.33117127 4.240281683 24.99990855 6.042119465 8.338100581 0.209449788 2.005290293 74.04592202 1075492.962 0.503183221 1.197242391 17389.28329 -4.240281683 2.295981116 RAPEEELPPLDPEEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RAPEEELPPLDPEEIR 16 1 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67;K7EKR9;Q8IY67-3 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 0 ; 95.814 0.005812 161249000 115323 102057 63238 72861 96949 105791 91867 114776 114802 FALSE TRUE 100082.7734 101386.5808 93820.10832 89405.20366 95019.90458 109860.8482 82957.75248 90232.04559 101230.2383 0.9886648 1.001544425 0.926799244 0.883186735 0.938651396 1.085257232 0.819495774 0.891354669 1 16.62728077 4.236071851 24.68968826 0.928534309 0.995104626 0.105635484 0.070856553 108.3006614 1074448.246 0.018302855 0.041195411 17221.5347 -4.236071851 0.066570317 RAPFDLFENK ddPTM_MDA-MB-175_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 ; 174.57 4.92E-06 6694200000 5737900 4566100 3402900 4502700 4532800 3713000 5432100 6138000 5759200 FALSE TRUE 4979621.977 4536104.988 5048553.822 5525106.854 4442606.148 3855841.513 4905295.778 4825436.466 5078353.937 0.980558275 0.893223482 0.994131934 1.087971993 0.874812233 0.759269945 0.965922391 0.950196959 1 22.27592952 5.092899443 17.34799564 0.940909663 2.601894598 0.02026071 0.0871138 15146224.62 27299268.52 0.022157944 971469658 123850.9787 -5.092899443 1.660984934 RAPFDLFENKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RAPFDLFENKK 11 2 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 111.94 0.00089614 1442600000 3146800 2091600 1410800 1852100 1899300 1427300 2800500 3155400 1920100 FALSE TRUE 2730942.407 2077860.142 2093067.599 2272647.613 1861507.646 1482209.155 2528907.941 2480642.265 1693107.965 1.612975937 1.227246097 1.236228074 1.342293379 1.099461868 0.87543688 1.493648363 1.465141217 1 20.69124254 4.7398287 23.11542355 1.239847281 1.61297626 0.286781932 0.193180736 57.35497893 1045129.951 0.049615433 0.297778157 54932.41597 -4.7398287 0.373128979 RAPFDLFENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 RAPFDLFENR 10 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;; 253.71 6.95E-17 52988119000 11193698 13158595 8831506 9933157 13447303 12591745 12376440 13599819 12398788 FALSE TRUE 9714422.448 13072155.32 13102451.84 12188632.12 13179727.98 13076157.58 11176174.75 10691603.54 10933017.41 0.888539923 1.195658512 1.198429615 1.114846127 1.205497759 1.196024582 1.022240644 0.977918825 1 23.38218829 2.112901113 5.620055753 0.99121764 1.141008227 0.312778671 0.09327727 0.223724249 10.16216599 0.037813226 0.025168854 129.6883943 -2.112901113 0.149790586 RAPFDLFENRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RAPFDLFENRK 11 2 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 96.82 0.0037838 2734600000 837920 641470 329890 558290 591250 594330 692690 994930 369320 FALSE TRUE 727186.749 637256.1413 489425.9074 685058.2774 579485.2818 617194.2597 625513.0304 782171.9621 325659.4103 2.2329671 1.956817832 1.5028766 2.103603506 1.779421271 1.895213957 1.920758346 2.401809796 1 18.31300439 4.681898664 4.286043599 1.866718148 2.244044032 0.101326387 0.37115892 0.492292265 17.29455341 0.087541537 0.477194182 48072.71646 -4.681898664 0.377325884 RAPS(ph)PDGFSPYSPEETNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RAPSPDGFSPYSPEETNR 18 1 Q13233 Q13233 MAP3K1 Mitogen-activated protein kinase kinase kinase 1 1 RAPS(1)PDGFSPYSPEETNR;RAPS(1)PDGFSPYSPEETNR 136.11 4.28E-06 397430000 118945 121205 81483 74629 104611 103579 110966 114648 103065 TRUE FALSE 103226.1169 120408.7964 120888.4513 91574.65508 102529.4458 107563.7512 100204.5344 90131.41739 90880.77311 1.135841095 1.324909464 1.330187313 1.00763508 1.128175325 1.18356994 1.102593332 0.991754519 1 16.47168749 1.104823808 0.255613922 0.682711567 1.304655903 0.439276342 0.090883087 15.39701436 1.124786781 3.286417995 0.452280737 12.72986529 -1.104823808 0.621944336 RAPS(ph)PGAYK ddPTM_MDA-MB-175_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 100.93 0.0026498 3428080000 3255880 2737950 1839600 2283280 2445940 2170160 3032190 3471110 3088040 TRUE FALSE 2825607.209 2719964.226 2729236.713 2801733.622 2397270.579 2253647.459 2738128.681 2728840.139 2722975.429 1.037691041 0.99889415 1.002299427 1.028923578 0.880386416 0.827641497 1.005564961 1.002153787 1 21.37675253 3.280945178 24.99986564 0.949430472 1.014615646 0.289110217 0.056983245 240.7805713 142019.0358 0.018539038 0.023933585 1909.612187 -3.280945178 0.065185174 RAPS(ph)PLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RAPSPLPK 8 1 Q9BSL1 Q9BSL1 UBAC1 Ubiquitin-associated domain-containing protein 1 1 RAPS(1)PLPK;RAPS(1)PLPK 62.166 0.049833 1874020000 3060000 2761700 2037120 2344100 2591300 2432000 3310400 3622100 3585400 TRUE FALSE 2655613.247 2743558.211 3022278.046 2876363.732 2539738.2 2525560.614 2989357.918 2847542.102 3161538.097 0.83997509 0.867792235 0.955951804 0.909798852 0.803323611 0.798839216 0.94553911 0.900682521 1 21.59219517 1.049240716 1.250349986 1.103133958 0.871024201 0.373945676 0.051980826 2.698024273 2.604437752 0.91519477 0.016824984 11.20058524 -1.049240716 -0.232109758 RAPS(ph)PVVSPTEMNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RAPSPVVSPTEMNK 14 1 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 RAPS(1)PVVSPTEMNK;RAPS(1)PVVSPTEMNK;RAPS(1)PVVSPTEMNK;RAPS(1)PVVSPTEMNK;RAPS(1)PVVSPTEMNK;RAPS(1)PVVSPTEMNK;RAPS(1)PVVSPTEMNK 181.4 1.01E-06 3867040000 3992370 3180749 2443412 3409696 3427989 2786696 3101377 4361080 4582860 TRUE FALSE 3464768.189 3159854.45 3625054.216 4183919.591 3359778.726 2893901.998 2800605.936 3428496.98 4041079.512 0.85738679 0.781933254 0.89705095 1.03534701 0.831406241 0.716121024 0.693034108 0.848411166 1 21.94630931 3.013896757 24.99744364 0.804489155 0.891305711 0.116020469 0.102349358 506.0124768 910207.1876 0.032848746 0.037230696 1032.515922 -3.013896757 0.086816557 RAPS(ph)VANVGSHCDLSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RAPSVANVGSHCDLSLK 17 1 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 1 RAPS(1)VANVGSHCDLSLK;RAPS(0.952)VANVGS(0.048)HCDLSLK;RAPS(1)VANVGSHCDLSLK 233.1 1.98E-20 577360000 683251 559526 521265 614652 543234 608988 754061 729210 1741690 TRUE FALSE 592957.6492 555850.4369 773350.4975 754218.131 532424.7062 632416.1624 680932.2803 573274.1162 1535789.392 0.386093075 0.361931421 0.503552441 0.491094765 0.346678203 0.411785734 0.44337608 0.373276518 1 20.55054896 1.23605121 24.99618389 1.00000077 0.415418291 0.92549621 0.052187035 17.22233988 171514.7032 0.085551783 0.012976612 17.22071623 -1.23605121 -0.584582479 RAPS(ph)WR ddPTM_MDA-MB-175_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 70.856 0.054983 2805540000 814780 866700 566420 639600 800240 839070 893080 894690 902060 TRUE FALSE 707104.7586 861006.5906 840342.6066 784830.9557 784316.7896 871349.5659 806469.2391 703367.506 795419.4944 0.888970868 1.082455983 1.056477258 0.986688108 0.986041699 1.095459153 1.01389172 0.884272401 1 19.6013564 1.841966742 8.803425334 0.936364551 1.020936388 0.180538956 0.064281891 0.422833457 32.83217828 0.029058863 0.016195197 69.49710955 -1.841966742 0.084571837 RAQAEQAALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RAQAEQAALR 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 ; 105.13 0.0041521 377780000 221353 271150 152970 156237 225896 275810 249409 254067 161454 FALSE TRUE 192100.6402 269368.7978 226946.8037 191712.9988 221401.1116 286420.5892 225221.3536 199736.7492 142367.092 1.349333174 1.892072065 1.594095942 1.346610344 1.555142473 2.01184547 1.581976216 1.40296993 1 17.11925618 1.333262996 2.146152857 0.893906179 1.629359439 0.477816601 0.20634899 0.487038205 2.734386249 0.652071686 0.055974005 21.5408579 -1.333262996 0.73545326 RAQQQAEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RAQQQAEAER 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 168.22 8.02E-06 226370000 149847 137159 71290 84259 117652 156616 129946 143667 78987 FALSE TRUE 130044.3393 136257.9935 105766.0825 103391.2938 115310.9554 162641.1189 117343.8569 112944.9301 69649.24684 1.867132025 1.956345541 1.518553139 1.484456738 1.655595152 2.335145407 1.684782855 1.621624572 1 16.08782013 1.181071524 2.165486394 0.683632393 1.784376094 0.507897892 0.242029067 0.730731673 3.035729877 1.67862308 0.067937181 15.17300232 -1.181071524 1.100743701 RAQS(ph)IER ddPTM_MDA-MB-175_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 68.335 0.066447 203740000 543030 540970 371110 468600 606090 734070 465390 732410 563150 TRUE FALSE 471267.2096 537416.3325 550580.0373 575002.7921 594029.9948 762310.1479 420256.5494 575789.8211 496575.0485 0.949035218 1.082245945 1.108754938 1.157937343 1.196254215 1.535135827 0.846310242 1.159522257 1 18.92165225 4.768290966 1.513242141 1.147415765 0.863642948 0.116028243 0.171946695 2.830738882 5.720252411 0.047163572 1.227376334 58653.09936 -4.768290966 -0.283772816 RAQS(ph)LKAPSIATIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RAQSLKAPSIATIK 14 2 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 RAQS(0.999)LKAPS(0.001)IATIK;RAQS(1)LKAPSIATIK 120.4 6.86E-05 713060000 740940 708750 350900 502860 752470 671190 826790 912980 408870 TRUE FALSE 643022.9017 704094.1746 520596.4137 617042.0487 737497.3192 697011.1136 746608.0331 717746.3318 360533.8544 1.783529879 1.952921109 1.443959859 1.711467706 2.045570229 1.933275073 2.070840294 1.990787614 1 18.45977521 RAQS(ph)TDSLGTSGSLQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RAQSTDSLGTSGSLQSK 17 1 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 RAQS(0.919)T(0.08)DS(0.001)LGTSGSLQSK;RAQS(0.659)T(0.078)DS(0.238)LGT(0.026)SGSLQSK 319.31 1.15E-58 590620000 1086160 889830 351050 407230 778490 636070 1013950 1096360 98574 TRUE FALSE 942621.204 883984.6481 520818.9542 499697.7956 762999.5721 660540.0245 915617.2851 861911.9459 86920.69402 10.84461203 10.17001369 5.991886743 5.748893302 8.778111826 7.599341353 10.53393896 9.916072986 1 16.40741207 4.360788515 6.63062134 7.556510703 10.66565146 0.20643793 2.681287473 0.355895163 18.79392914 0.673792975 1.816906598 22950.3078 -4.360788515 3.10914076 RAQST(ph)DSLGTSGSLQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RAQSTDSLGTSGSLQSK 17 1 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 RAQS(0.337)T(0.66)DS(0.003)LGTSGSLQSK;RAQS(0.376)T(0.615)DS(0.009)LGTSGSLQSK 145.55 2.76E-07 392270000 221660 200972 79039 90715 178116 149094 210502 251740 42967 TRUE FALSE 192367.0694 199651.8017 117262.5248 111313.2272 174571.8401 154829.7427 190087.5484 197907.36 37887.49021 5.07732416 5.26959692 3.095019599 2.93799422 4.607638012 4.086566352 5.017158629 5.223554238 1 15.20943395 4.262638936 24.88470122 3.932879068 5.17346211 0.179593197 1.23074025 435.5812876 450160.5673 0.308719658 0.815846538 18307.91704 -4.262638936 1.240583042 RAS(ph)AAAAAGGGATGHPGGGQGAENPAGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RASAAAAAGGGATGHPGGGQGAENPAGLK 29 1 Q07617 Q07617 SPAG1 Sperm-associated antigen 1 1 RAS(1)AAAAAGGGATGHPGGGQGAENPAGLK;RAS(1)AAAAAGGGATGHPGGGQGAENPAGLK;RAS(1)AAAAAGGGATGHPGGGQGAENPAGLK;RAS(1)AAAAAGGGATGHPGGGQGAENPAGLK 234.71 1.49E-45 1206480000 564308 442648 333705 437912 594829 415426 543553 651476 583994 TRUE FALSE 489733.268 439740.2161 495085.8542 537346.6127 582993.0667 431407.707 490839.3137 512162.9272 514954.8946 0.951021678 0.853939288 0.96141596 1.043482873 1.132124527 0.837758242 0.953169528 0.994578229 1 18.97408655 4.033149404 8.869963762 0.991322473 0.903424039 0.192370786 0.076292505 0.470023846 114.3023758 0.019868609 0.041268098 10793.1796 -4.033149404 -0.087898434 RAS(ph)AGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RASAGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK 35 1 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 RAS(1)AGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK;RAS(1)AGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK;RAS(1)AGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK;RAS(0.629)AGPAPGPVVT(0.017)AEGLHPS(0.341)LPS(0.01)PT(0.003)GNSTPLGSSK;RAS(1)AGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK 220.03 7.00E-37 3870990000 2029671 1858085 617181.1 1505316 2324523 2196645 2351798 2738683 2402177 TRUE FALSE 1761444.835 1845879.117 915651.9443 1847121.005 2278269.54 2281151.355 2123720.992 2153036.953 2118194.372 0.83157847 0.871439912 0.432279472 0.872026208 1.07557152 1.076932025 1.002609119 1.01644919 1 21.01440355 3.473801684 7.672214413 1.027250545 0.715099832 0.612193662 0.117529723 0.080595438 36.09293028 0.033179588 0.044717054 2977.156631 -3.473801684 -0.312150713 RAS(ph)AILPGVLGSETLSNEVFQES(ph)EEEKQPEVPSSLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RASAILPGVLGSETLSNEVFQESEEEKQPEVPSSLAK 37 2 Q9BZQ8 Q9BZQ8 FAM129A Protein Niban 2 RAS(1)AILPGVLGSETLSNEVFQES(1)EEEKQPEVPSSLAK 147.73 1.70E-13 54311000 44338 46723 33226 32356 44034 31688 48522 70922 52308 TRUE FALSE 38478.62096 46416.07354 49294.20473 39702.92433 43157.80955 32907.05786 43816.34391 55755.88222 46124.20783 0.834239172 1.00632782 1.068727401 0.860782791 0.935686738 0.713444402 0.949964151 1.208820375 1 15.49323651 1.898355565 6.846551677 1.111161306 0.908434553 0.367650838 0.107407692 0.250348882 14.54512581 0.053025772 0.028853724 79.13262366 -1.898355565 -0.202726753 RAS(ph)AILPGVLGSETLSNEVFQESEEEKQPEVPSSLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RASAILPGVLGSETLSNEVFQESEEEKQPEVPSSLAK 37 2 Q9BZQ8 Q9BZQ8 FAM129A Protein Niban 1 RAS(1)AILPGVLGSETLSNEVFQESEEEKQPEVPSSLAK;RAS(0.998)AILPGVLGSET(0.001)LS(0.001)NEVFQESEEEKQPEVPSSLAK 226.86 9.32E-40 1185100000 486270 422505 392073 375062 431123 312047 597452 692437 554778 TRUE FALSE 422008.1874 419729.5368 581680.8142 460225.5596 422544.4958 324051.65 539511.197 544364.7361 489192.7768 0.862662344 0.858004363 1.189062557 0.940785681 0.863758657 0.662421167 1.102860105 1.112781631 1 18.90004358 RAS(ph)APHGPLDMAPFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RASAPHGPLDMAPFAR 16 1 Q8N4B1-2;Q8N4B1;Q8N4B1-4 Q8N4B1-2 FAM109A Sesquipedalian-1 1 RAS(1)APHGPLDMAPFAR;RAS(1)APHGPLDMAPFAR 148.33 5.77E-07 856070000 403710 378420 258340 308820 408410 438860 437470 397200 358160 TRUE FALSE 350358.7006 375934.1341 383274.0881 378942.301 400283.44 455743.2282 395044.2267 312261.871 315818.7328 1.109366432 1.190347801 1.213588835 1.19987278 1.267446793 1.443053185 1.250857488 0.988737648 1 18.26873722 1.726612288 5.68270067 0.994547189 1.244064885 0.589856329 0.084654902 0.103131415 8.509619381 0.055794846 0.023849442 53.28589788 -1.726612288 0.249517696 RAS(ph)CTSSTSGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RASCTSSTSGSK 12 1 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 1 RAS(0.993)CT(0.007)SSTSGSK;RAS(0.999)CT(0.001)SSTSGSK;RAS(0.977)CT(0.005)S(0.009)S(0.009)T(0.001)S(0.001)GSK;RAS(0.962)CT(0.007)S(0.002)S(0.029)T(0.001)SGSK;RAS(0.993)CT(0.007)SSTSGSK;RAS(0.989)CT(0.005)S(0.005)S(0.001)TSGSK 139.66 6.25E-05 1593280000 1920890 1788780 1322960 1559090 1183750 1603890 2321420 2424100 3179130 TRUE FALSE 1667039.52 1777029.386 1962747.881 1913105.214 1160195.691 1665592.686 2096289.046 1905725.079 2803296.873 0.594671059 0.633906956 0.700156983 0.68244831 0.413868293 0.59415494 0.747794165 0.679815648 1 21.41869311 -0.301005927 1.052655913 9.99999997 0.612655352 0.650167451 0.086930666 27.18827225 1.534694187 554.2715357 0.0287575 0.500027711 0.301005927 -9.387344617 RAS(ph)DGGANIQLHAQQLLK ddPTM_MDA-MB-175_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 194.68 2.85E-15 198500000 228020 202250 127550 142170 174730 163120 217420 253050 178920 TRUE FALSE 197886.5793 200921.4064 189233.6066 174451.8714 171253.2149 169395.332 196334.6419 198937.2267 157768.2814 1.254286207 1.273522185 1.199440121 1.105747428 1.085473032 1.073697009 1.244449392 1.260945641 1 17.26744766 4.03630737 3.945452041 1.145474182 1.262372092 0.32852684 0.078136672 0.304445686 10.31772891 0.022555549 0.048861105 10871.94808 -4.03630737 0.11689791 RAS(ph)DTSLTQGIVAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RASDTSLTQGIVAFR 15 1 Q9H0K1 Q9H0K1 SIK2 Serine/threonine-protein kinase SIK2 1 RAS(0.833)DT(0.141)S(0.025)LT(0.001)QGIVAFR;RAS(0.999)DT(0.001)SLTQGIVAFR 241.13 4.41E-18 248418000 260870 254820 128005 154675 224163 226122 226408 249550 191137 TRUE FALSE 226395.3685 253146.0706 189908.6462 189796.3228 219702.5949 234821.0597 204450.987 196185.6745 168541.0016 1.343265831 1.501985085 1.126780097 1.126113652 1.303555768 1.393257768 1.213063795 1.164023428 1 17.36274008 1.369683844 1.521240354 0.931109794 1.291718772 0.411716219 0.113389327 0.95275919 2.515468932 0.496587545 0.035341179 23.42522896 -1.369683844 0.360608978 RAS(ph)FAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 RASFAEK 7 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 RAS(1)FAEK;RAS(1)FAEK;RAS(1)FAEK;RAS(1)FAEK;RAS(1)FAEK;RAS(1)FAEK;RAS(1)FAEK;RAS(1)FAEK;RAS(1)FAEK 145.46 0.0013998 15301890000 10479924.7 9483001.8 7769427.1 8605271.4 9071714.3 9813717.2 13153651.9 13162002.3 13062796.4 TRUE FALSE 9094976.098 9420707.337 11526748.03 10559229.79 8891204.934 10191257.25 11878012.76 10347410.53 11518527.49 0.789595381 0.817874276 1.00071368 0.916716985 0.77190465 0.884770841 1.031209308 0.898327546 1 23.45745296 7.999963902 0.042396321 1.45393783 4.94E-06 0.276837272 0.07669335 2377.605144 9.912919617 104.1423235 275.4499231 99991688.52 -7.999963902 -1.453932885 RAS(ph)FAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RASFAK 6 1 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;F6UYG0;K7ENT7;Q96J92-2;Q96J92-3;Q96J92;Q9Y3S1;Q9Y3S1-4;Q9Y3S1-2;H0Y7T5;F8W9F9;A6PVV2;Q9Y3S1-3 F5GWT4;Q9Y3S1 WNK1;WNK4;WNK2 Serine/threonine-protein kinase WNK1;Serine/threonine-protein kinase WNK4;Serine/threonine-protein kinase WNK2 1 RAS(1)FAK 87.258 0.032245 2935100000 3621800 3087900 2141300 2514600 2413500 2391000 3224100 3611000 3502100 TRUE FALSE 3143169.954 3067615.382 3176839.842 3085578.363 2365476.072 2482983.317 2911427.278 2838815.751 3088085.728 1.017837661 0.993371186 1.02874082 0.999188052 0.766000779 0.804052587 0.942793541 0.919280098 1 21.55828137 3.439559832 24.9994811 0.88990959 1.011762522 0.463942471 0.065969241 160.9203678 107102.0815 0.0204123 0.02635223 2751.438637 -3.439559832 0.121852932 RAS(ph)GQAFELILS(ph)PR ddPTM_MDA-MB-175_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 186.96 3.51E-06 1197693000 513884 583741 410231 494300 684012 691097 694590 836900 719115 TRUE FALSE 445972.9274 579906.3669 608620.0837 606538.3699 670401.4994 717683.9488 627228.7687 657935.4478 634102.0439 0.70331413 0.914531616 0.959814102 0.95653117 1.057245448 1.131811442 0.989160617 1.03758607 1 19.2743555 5.422437459 0.802862897 1.037683134 1.40E-20 0.840340865 0.044984055 2.598913568 0.590587485 0.016790867 3.104774238 264507.1761 -5.422437459 -1.037683134 VTGPPPGT(ph)PQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VTGPPPGTPQPR 12 0 F5GYK2;Q9NRL3;Q9NRL3-3;R4GN16;M0QZM0 F5GYK2 STRN4 Striatin-4 1 VTGPPPGT(1)PQPR;VTGPPPGT(1)PQPR;VTGPPPGT(1)PQPR;VTGPPPGT(1)PQPR;VTGPPPGT(1)PQPR 228.7 1.11E-10 1494530000 450193 624211 496733 690785 998280 977020 792164 996060 1022620 TRUE FALSE 390698.8544 620110.5168 736954.7403 847638.2922 978416.1811 1014606.592 715340.0572 783060.3203 901727.0286 0.433278411 0.687692059 0.817270323 0.940016508 1.085046971 1.125181523 0.793300006 0.868400631 1 19.78233124 4.50503266 1.361629084 0.957708123 0.341976713 0.767429707 0.097129897 0.463375159 1.059838006 0.031992629 0.351314071 31991.3568 -4.50503266 -0.61573141 down RAS(ph)HTLLPSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RASHTLLPSHR 11 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 RAS(0.729)HT(0.271)LLPSHR;RAS(0.541)HT(0.459)LLPSHR 90.759 0.0052889 467330000 629250 307080 224000 262740 322330 381780 390990 410970 388000 TRUE FALSE 546093.0182 305062.7713 332327.1492 322399.1327 315916.2636 396467.3236 353071.85 323087.2637 342131.082 1.596151437 0.891654653 0.971344513 0.942326347 0.923377852 1.158817028 1.031978293 0.944337655 1 18.38418965 4.743859364 24.99951782 0.984255819 1.596151693 0.872590357 0.073632948 197.7323137 932873.6029 0.018392911 0.153213467 55444.61394 -4.743859364 0.611895874 RAS(ph)ISEPSDTDPEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RASISEPSDTDPEPR 15 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 RAS(0.974)IS(0.026)EPSDTDPEPR;RAS(0.999)IS(0.001)EPSDTDPEPR;RAS(0.989)IS(0.011)EPSDTDPEPR;RAS(1)ISEPSDTDPEPR 190.31 1.36E-07 3703400000 1814610 1490890 1027160 1052960 1328670 1609130 1390360 1528250 1463370 TRUE FALSE 1574804.691 1481096.245 1523898.012 1292050.661 1302232.066 1671034.272 1255523.101 1201445.63 1290372.066 1.220426831 1.147805571 1.180975668 1.001300862 1.009191148 1.295001897 0.972993088 0.931084656 1 20.29935568 -1.999997076 0.086518614 9.40E-07 1.484415045 0.340116499 0.098305914 439.3726616 3.575566884 80.71660463 11.31975185 0.010000067 1.999997076 1.484414105 RAS(ph)LSDIGFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RASLSDIGFGK 11 1 Q07002;A0A0A0MSJ6;Q07002-3;D6R9B0;D6RA44 Q07002 CDK18 Cyclin-dependent kinase 18 1 RAS(0.987)LS(0.013)DIGFGK;RAS(0.973)LS(0.027)DIGFGK;RAS(0.964)LS(0.036)DIGFGK;RAS(0.945)LS(0.055)DIGFGK;RAS(1)LSDIGFGK;RAS(0.997)LS(0.003)DIGFGK 176.25 5.43E-06 4129230000 11685640 11184740 7865670 8426030 10904330 10234030 13834770 14846320 13284930 TRUE FALSE 10141353.07 11111266.71 11669534.32 10339288.9 10687355.17 10627739.76 12493076.13 11671550 11714400.71 0.865716763 0.948513456 0.99616998 0.882613558 0.912326241 0.907237171 1.06647164 0.996342049 1 23.48177981 2.251552441 24.98563511 1.017711003 0.921697929 0.59134764 0.039960401 159.9020272 307520.5055 0.015017791 0.011556688 178.4647469 -2.251552441 -0.096013074 RAS(ph)LSDLTDLEDIEGLTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RASLSDLTDLEDIEGLTVR 19 1 J3KSI3;J3KSU7;K7EN88;Q8WZ73-3;Q8WZ73-2;Q8WZ73 J3KSI3 RFFL;hCG_2039718 E3 ubiquitin-protein ligase rififylin 1 RAS(0.494)LS(0.494)DLT(0.013)DLEDIEGLTVR;RAS(0.942)LS(0.058)DLTDLEDIEGLTVR;RAS(0.994)LS(0.006)DLTDLEDIEGLTVR;RAS(0.774)LS(0.176)DLT(0.049)DLEDIEGLTVR;RAS(0.712)LS(0.288)DLTDLEDIEGLTVR 285.02 3.51E-40 570700000 369571 286820 206313.5 240628.1 331904.4 342262 264964 371098 291132 TRUE FALSE 320731.256 284935.8605 306087.3987 295266.3879 325300.1518 355429.0406 239267.8321 291741.5806 256714.7066 1.249368453 1.109931972 1.192325141 1.150173248 1.267166015 1.384529329 0.932037884 1.136442802 1 17.96980642 2.226879107 24.99999998 1.042714029 1.217276329 0.531722583 0.088819131 197.4650708 422598.0497 0.036302978 0.024698838 168.6083613 -2.226879107 0.174562299 RAS(ph)LSEIGFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RASLSEIGFGK 11 1 Q00537;Q00537-2;F5H6Z0 Q00537 CDK17 Cyclin-dependent kinase 17 1 RAS(0.892)LS(0.108)EIGFGK;RAS(0.996)LS(0.004)EIGFGK;RAS(1)LSEIGFGK 187.08 2.29E-06 856290000 3735660 3198030 2453570 2928830 3083670 2597960 4032360 4084310 3635540 TRUE FALSE 3241983.066 3177021.93 3640124.659 3593865.616 3022311 2697905.202 3641302.348 3210912.091 3205750.603 1.011302334 0.991038394 1.135498393 1.121068374 0.942777956 0.841582998 1.135865761 1.001610072 1 21.61223076 3.234500585 24.99985218 0.990745863 1.064518518 0.185098678 0.083187387 208.4645905 1283628.821 0.026106521 0.03066907 1715.934023 -3.234500585 0.073772654 RAS(ph)LTLEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RASLTLEEK 9 1 Q6P3W7;A0A0U1RQQ9 Q6P3W7 SCYL2 SCY1-like protein 2 1 RAS(0.998)LT(0.002)LEEK;RAS(1)LTLEEK;RAS(1)LTLEEK 166.6 3.71E-05 687810000 956400 869030 735170 943520 986420 997710 1356700 1418400 1411910 TRUE FALSE 830009.3168 863321.2847 1090700.671 1157760.637 966792.1719 1036092.549 1225127.443 1115086.198 1244995.608 0.666676502 0.693433197 0.876067886 0.929931503 0.776542636 0.832205786 0.984041578 0.895654724 1 20.24770922 5.976922136 0.376990176 0.947385928 3.46E-16 0.647194112 0.066688498 12.71706194 0.751744192 0.086812893 6.506407 948248.4389 -5.976922136 -0.947385928 RAS(ph)MQPIQIAEGTGITTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RASMQPIQIAEGTGITTR 18 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 RAS(1)MQPIQIAEGTGITTR;RAS(1)MQPIQIAEGTGITTR 169.28 1.14E-11 871500000 194299 233480 132347 114669 189436 215860 212860 229360 232410 TRUE FALSE 168621.8949 231946.2545 196350.4519 140706.3491 185666.5942 224164.2739 192216.87 180313.1489 204934.7546 0.822807704 1.131805364 0.958112021 0.686590956 0.90597905 1.093832397 0.937941787 0.879856368 1 17.64480514 RAS(ph)PGLSMPS(ph)SSPPIKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RASPGLSMPSSSPPIKK 17 2 P57682;P57682-2 P57682 KLF3 Krueppel-like factor 3 2 RAS(1)PGLS(0.002)MPS(0.401)S(0.328)S(0.269)PPIKK 92.034 0.001828 132370000 277200 224550 157300 183020 235730 162360 252850 300800 175890 TRUE FALSE 240567.3177 223074.9163 233370.8061 224577.4883 231039.4342 168606.0943 228328.6459 236476.2608 155096.4846 1.551081692 1.438297695 1.504681468 1.447985677 1.489649716 1.087104551 1.472171639 1.524704196 1 17.24280646 2.886454536 19.41598936 1.324915971 1.482656298 0.282378003 0.160597724 7.47318044 1257.798382 0.052175166 0.052175362 769.9358395 -2.886454536 0.157740326 RAS(ph)PNLFSEAQYQEAPVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RASPNLFSEAQYQEAPVEK 19 1 F6VUX8;Q9HC77-2;Q9HC77 F6VUX8 CENPJ Centromere protein J 1 RAS(0.999)PNLFS(0.001)EAQYQEAPVEK 153.59 2.71E-08 80769000 169930 167400 113220 131710 153720 148410 179630 203340 174610 TRUE FALSE 147473.32 166300.3384 167973.5707 161616.7686 150661.2727 154119.4287 162209.5102 159857.3234 153967.8047 0.957819203 1.080098133 1.09096555 1.049678982 0.978524524 1.000984777 1.053528759 1.038251625 1 17.23226918 3.416673466 24.99996776 1.019044455 1.050616886 0.106882399 0.040821235 155.9977993 64516.39453 0.011894672 0.015355961 2610.198078 -3.416673466 0.031572431 RAS(ph)PPGT(ph)PTPEADATLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RASPPGTPTPEADATLLK 18 1 Q8IYK8;Q8IYK8-2 Q8IYK8 REM2 GTP-binding protein REM 2 2 RAS(1)PPGT(0.857)PT(0.144)PEADATLLK;RAS(1)PPGT(0.991)PT(0.009)PEADATLLK;RAS(1)PPGT(0.998)PT(0.002)PEADATLLK 172.61 8.96E-12 449167000 511690 500867 363679 447986 559400 489044 609980 752640 710600 TRUE FALSE 444068.87 497576.7717 539555.3808 549708.0683 548269.0344 507857.8391 550824.2335 591693.7931 626593.6775 0.708703081 0.794097977 0.861092922 0.877295907 0.874999308 0.810505847 0.879077229 0.944302208 1 19.25717069 -1.999929026 0.040448599 2.230344637 8.22E-06 0.725932276 0.041760437 1010.044742 4.02224191 175.8284601 69.4867499 0.010001634 1.999929026 -2.230336415 RAS(ph)PS(ph)PPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RASPSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RAS(1)PS(1)PPPK 81.709 0.013711 429100000 1140400 936200 576230 699910 775130 742130 946000 1092500 1196200 TRUE FALSE 989693.2506 930050.0406 854896.7554 858835.263 759706.4295 770680.2213 854257.0656 858877.3768 1054786.599 0.938287661 0.881742375 0.810492621 0.814226559 0.72024657 0.730650373 0.809886158 0.814266486 1 20.00851972 4.44238406 2.295129555 0.80685852 0.940395835 0.23258222 0.07514628 0.521402492 4.780317718 0.02028755 0.108628172 27693.89618 -4.44238406 0.133537315 RAS(ph)PS(ph)PPPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RASPSPPPKR 10 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RAS(1)PS(1)PPPKR;RAS(1)PS(1)PPPKR 79.639 0.014161 2369600000 529820 417050 275920 331570 387010 331000 439420 479830 489740 TRUE FALSE 459802.9446 414310.3711 409355.8349 406858.0362 379309.2582 343733.7842 396805.116 377222.0885 431843.4951 1.064744403 0.959399356 0.947926366 0.942142329 0.878348898 0.795968419 0.918863247 0.873515736 1 18.72014903 5.08929121 0.820023928 0.892390847 1.255988282 0.491936947 0.052229197 3.427699442 1.210605213 0.019013307 1.289978348 122826.255 -5.08929121 0.363597435 RAS(ph)PSKPASAPASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RASPSKPASAPASR 14 2 E7EVA0;P27816-4;H0Y2V1;F8W9U4;H7C4C5;B5MEG9;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 RAS(0.995)PS(0.005)KPASAPASR;RAS(0.992)PS(0.008)KPASAPASR;RAS(0.993)PS(0.007)KPASAPASR;RAS(0.826)PS(0.161)KPAS(0.003)APAS(0.01)R 132.25 4.06E-05 2670690000 1084000 1017690 681290 893450 1021130 811720 991530 1372200 1086450 TRUE FALSE 940746.6535 1011004.727 1010764.123 1096321.478 1000811.511 842947.3937 895371.5732 1078765.708 958011.1187 0.981978847 1.055316277 1.055065127 1.144372395 1.0446763 0.879893121 0.934615012 1.126047169 1 19.86968287 2.983801366 24.94323555 0.997959767 1.063101757 0.183256557 0.072781164 1477.573932 2275225.107 0.025272173 0.025959949 963.3882966 -2.983801366 0.06514199 RAS(ph)PSPPPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RASPSPPPKR 10 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RAS(0.995)PS(0.005)PPPKR 79.492 0.014006 42716000 130480 116410 76426 85675 80449 124690 129670 134290 99723 TRUE FALSE 113236.7374 115645.295 113385.8692 105128.8182 78848.2223 129486.905 117094.6234 105573.1285 87933.86054 1.287748959 1.315139519 1.289444914 1.195544214 0.896676454 1.472548847 1.331621546 1.200596993 1 16.42413119 0.494054223 0.021893353 2.67E-05 2.311415218 0.077992743 0.159588982 10535.64703 45.55855065 2725.873606 2117.713638 3.11927901 -0.494054223 2.311388493 RAS(ph)QEANLLTLAQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RASQEANLLTLAQK 14 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2;H7C1L3 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 RAS(1)QEANLLTLAQK;RAS(1)QEANLLTLAQK;RAS(1)QEANLLTLAQK;RAS(1)QEANLLTLAQK 300.14 8.61E-44 2300050000 2640120 2570140 2006090 2829210 3256670 2578700 3376730 4170970 4590330 TRUE FALSE 2291221.453 2553256.581 2976241.834 3471625.372 3191868.639 2677904.258 3049255.244 3279040.524 4047666.417 0.566059852 0.630797185 0.735298201 0.857685643 0.788570082 0.661592133 0.753336597 0.810106414 1 21.94865897 -1.999999902 0.054493921 2.153230092 7.59E-12 0.539248846 0.083123488 901.6549939 4.786729947 175.4283338 50.38510623 0.010000002 1.999999902 -2.153230092 RAS(ph)SLNVLNVGGK ddPTM_MDA-MB-175_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(0.667)S(0.333)LNVLNVGGK;RAS(0.5)S(0.5)LNVLNVGGK 170.16 1.67E-05 1550020000 4254000 5641700 1826500 2066380 3168450 3046100 4085200 4205500 1740360 TRUE FALSE 3691823.122 5604639.301 2709801.509 2535583.162 3105404.044 3163285.438 3689017.933 3306186.552 1534616.623 2.405697335 3.652142962 1.765784019 1.652258371 2.023569924 2.061287093 2.403869394 2.154405538 1 20.54944686 4.223002242 24.99981138 1.925444725 3.028920249 0.504429617 0.476419526 168.7987182 271233.4703 0.117972849 0.246948349 16710.99242 -4.223002242 1.103475524 RAS(ph)TAFCPPAASSEAPDGPSSTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RASTAFCPPAASSEAPDGPSSTAR 24 1 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 1 RAS(0.785)T(0.215)AFCPPAASSEAPDGPSSTAR;RAS(0.91)T(0.09)AFCPPAASSEAPDGPSSTAR 136.34 1.31E-05 1006540000 294270 288640 206720 196439 249340 327860 299100 270740 283770 TRUE FALSE 255381.4739 286743.9048 306690.4834 241043.4773 244378.6218 340472.9864 270093.328 212844.3579 250223.0339 1.020615368 1.145953274 1.225668471 0.963314502 0.976643189 1.360678036 1.079410332 0.850618565 1 17.93285507 1.8618479 6.241854876 0.922451917 1.117033922 0.284041997 0.122987855 0.273217738 12.54560394 0.061691676 0.032761765 72.75249633 -1.8618479 0.194582005 RAS(ph)VCAEAYNPDEEEDDAESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RASVCAEAYNPDEEEDDAESR 21 1 P31323 P31323 PRKAR2B cAMP-dependent protein kinase type II-beta regulatory subunit 1 RAS(1)VCAEAYNPDEEEDDAESR;RAS(1)VCAEAYNPDEEEDDAESR;RAS(1)VCAEAYNPDEEEDDAESR;RAS(1)VCAEAYNPDEEEDDAESR;RAS(1)VCAEAYNPDEEEDDAESR;RAS(1)VCAEAYNPDEEEDDAESR 259.84 8.78E-37 4430890000 1848208 1958761 934289 1182395 1468198 1601792 1322806 1657835 2236084 TRUE FALSE 1603962.63 1945893.77 1386114.285 1450875.857 1438983.732 1663413.975 1194520.478 1303319.887 1971736.697 0.81347709 0.986893318 0.702991575 0.735836513 0.729805219 0.843628856 0.605821497 0.661000979 1 20.91103548 4.227339358 24.99525767 0.739562817 0.900185218 0.209976764 0.115084103 256.3648794 571054.3642 0.0286711 0.060558184 16878.71415 -4.227339358 0.160622401 RAS(ph)WASENGETDAEGTQMTPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RASWASENGETDAEGTQMTPAK 22 1 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 1 RAS(0.992)WAS(0.008)ENGETDAEGTQMTPAK;RAS(0.997)WAS(0.002)ENGET(0.001)DAEGTQMTPAK 198.99 1.12E-22 320460000 305610 197086 162794 193467 237620 197420 267560 322260 304930 TRUE FALSE 265222.8642 195791.3291 241521.7229 237396.6393 232891.8269 205014.8751 241612.0724 253347.2068 268881.5228 0.986393046 0.728169519 0.898245891 0.88290425 0.866150357 0.762472903 0.89858191 0.942226168 1 18.03661109 1.672852853 2.306035495 0.991435615 0.851832822 0.31400803 0.071520025 0.308290493 3.454532258 0.068826836 0.018573683 47.08177772 -1.672852853 -0.139602793 RASEDTTS(ph)GSPPKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RASEDTTSGSPPKK 14 2 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 RASEDT(0.046)T(0.283)S(0.335)GS(0.335)PPKK 51.888 0.083977 392150000 143730 99494 80397 87732 103510 69938 138700 156670 120980 TRUE FALSE 124735.7163 98840.41736 119277.2581 107652.8915 101450.3535 72628.56012 125248.8953 123167.3397 106677.8822 1.169274396 0.926531492 1.118106731 1.009139751 0.950997071 0.680821166 1.174084944 1.154572411 1 16.70290156 RASEDTTSGS(ph)PPKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RASEDTTSGSPPKK 14 2 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 RAS(0.004)EDT(0.135)T(0.107)S(0.107)GS(0.646)PPKK;RASEDTTS(0.017)GS(0.983)PPKK 101.15 0.00078378 1424750000 231965 159385 135505 141017 156495 106286 218225 244789 187616 TRUE FALSE 201310.2375 158337.9894 201035.6712 173037.0652 153381.0557 110374.8912 197061.5731 192442.7773 165436.2502 1.21684478 0.95709368 1.21518513 1.045944072 0.927130877 0.667174764 1.191163199 1.163244313 1 17.33591587 4.754824113 23.37414864 1.032846833 1.216845133 0.126799642 0.15888352 3154.545966 4533574.267 0.04083185 0.947093517 56862.25944 -4.754824113 0.1839983 RASGQAFELILS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RASGQAFELILSPR 14 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 RASGQAFELILS(1)PR;RASGQAFELILS(1)PR;RASGQAFELILS(1)PR;RASGQAFELILS(1)PR 155.49 3.57E-06 970210000 720410 701000 385025 529820 927560 827870 874600 1068270 509671 TRUE FALSE 625205.9932 696395.0848 571224.3778 650123.7288 909103.3707 859718.6946 789781.4266 839828.7738 449418.275 1.391145016 1.549547768 1.271030596 1.446589436 2.022844689 1.912958913 1.757341591 1.868701876 1 18.77769927 3.391569586 10.53009072 1.745090063 1.408578438 0.212548036 0.281864184 0.543237497 62.78321806 0.079756464 0.102972861 2463.596541 -3.391569586 -0.336511625 RASLS(ph)DLTDLEDIEGLTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RASLSDLTDLEDIEGLTVR 19 1 J3KSI3;J3KSU7;K7EN88;Q8WZ73-3;Q8WZ73-2;Q8WZ73 J3KSI3 RFFL;hCG_2039718 E3 ubiquitin-protein ligase rififylin 1 RAS(0.387)LS(0.607)DLT(0.006)DLEDIEGLTVR;RAS(0.41)LS(0.59)DLTDLEDIEGLTVR 157.07 5.87E-09 200398000 84253 66694 49571 51316 77169 83868 65232 75338 60386 TRUE FALSE 73118.75258 66255.88272 73543.70141 62968.08212 75633.48788 87094.45623 58905.81068 59227.55498 53247.23587 1.373193395 1.244306519 1.381174068 1.18256058 1.420420922 1.635661548 1.106269832 1.112312292 1 15.70041901 2.038249539 24.87969546 1.077712056 1.361764585 0.576757093 0.121158423 111.6554437 72626.64139 0.050374994 0.033962734 109.2067641 -2.038249539 0.284052529 RASS(ph)LNFLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RASSLNFLNK 10 1 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 RAS(0.005)S(0.995)LNFLNK;RAS(0.023)S(0.977)LNFLNK 112.44 0.0017169 1347780000 4089300 3952200 2169100 2244100 3383200 3172800 4373000 4603400 3024800 TRUE FALSE 3548888.644 3926237.738 3218084.015 2753657.204 3315880.939 3294859.669 3948907.133 3618998.734 2667211.59 1.330561346 1.472038346 1.206534955 1.032410482 1.243201309 1.235319943 1.480537633 1.356847259 1 21.34690085 4.230815427 24.99383102 1.242443243 1.401299855 0.20361954 0.142991193 289.2703777 933489.0271 0.039053586 0.083760401 17014.35252 -4.230815427 0.158856612 RASS(ph)LNVLNVGGK ddPTM_MDA-MB-175_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(0.191)S(0.809)LNVLNVGGK;RAS(0.33)S(0.67)LNVLNVGGK 189.59 3.14E-06 1927400000 4556700 5634200 2135020 2206470 3441870 3359820 4522600 4640800 2094930 TRUE FALSE 3954520.55 5597188.569 3167522.813 2707482.737 3373383.521 3489074.449 4083998.948 3648401.035 1847269.762 2.140737986 3.029978991 1.714705063 1.46566722 1.826145585 1.888773649 2.210829751 1.975023416 1 20.81696313 4.220623332 24.99736935 1.774207838 2.585358486 0.458037462 0.385904345 190.8921735 266027.762 0.097308581 0.203227015 16619.70581 -4.220623332 0.811150648 RASS(ph)PFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RASSPFR 7 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 RAS(0.478)S(0.522)PFR 76.605 0.024688 1248800000 754210 803670 442630 522800 643220 1119300 604690 614070 724830 TRUE FALSE 654539.2376 798390.6389 656687.3485 641509.7305 630421.1804 1162360.195 546047.2569 482755.9092 639141.4231 1.024091404 1.249161156 1.027452336 1.003705451 0.986356317 1.818627542 0.854344965 0.755319389 1 19.28577567 2.058796196 24.99999979 0.843547401 1.177826297 0.259042088 0.249711409 93.76855229 39869.50284 0.100466206 0.06773431 114.4975506 -2.058796196 0.334278896 RASSLS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RASSLSR 7 1 Q9Y259;Q9Y259-2 Q9Y259 CHKB Choline/ethanolamine kinase 1 RAS(0.045)S(0.013)LS(0.942)R;RAS(0.026)S(0.43)LS(0.544)R 108.15 0.007752 447570000 1041250 1164430 799870 865080 879250 1382130 1245560 1359220 1107670 TRUE FALSE 903646.1743 1156780.783 1186689.807 1061509.636 861754.6452 1435301.435 1124765.783 1068561.38 976722.5145 0.925182087 1.18434946 1.214971284 1.086807788 0.882292189 1.469507884 1.151571471 1.094027592 1 19.89758923 RASVFVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RASVFVK 7 1 P50502;Q3KNR6;Q8NFI4;F6VDH7;Q8IZP2;H7C3I1 P50502 ST13;ST13P5;ST13P4 Hsc70-interacting protein;Putative protein FAM10A5;Putative protein FAM10A4 0 87.696 0.05418 0 1008500 922060 620960 684120 977160 897650 1032600 1180300 838450 FALSE TRUE 875224.1698 916002.9271 921258.333 839459.9021 957716.4278 932183.1764 932458.6109 927902.0301 739329.3962 1.183808157 1.23896457 1.246072911 1.135434228 1.295385295 1.260849604 1.26122215 1.255059024 1 19.49585775 1.235895565 24.99874706 0.999999685 1.236922391 0.729560277 0.044868596 37.94659221 355874.5857 0.072152012 0.010803957 17.21454566 -1.235895565 0.236922706 RAT(ph)LDEEDLVDSLSEGDAYPNGLQVNFHSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RATLDEEDLVDSLSEGDAYPNGLQVNFHSPR 31 1 B4DKB2;A0A3B3ISF9;P42892-3;P42892-4;P42892;E9PN99;E9PHZ1 B4DKB2 ECE1 Endothelin-converting enzyme 1 1 RAT(1)LDEEDLVDSLSEGDAYPNGLQVNFHSPR;RAT(1)LDEEDLVDSLSEGDAYPNGLQVNFHSPR 101.36 0.00015264 71871000 32047 34484 21560.8 27226.4 32103 34330 28415.1 38747 31055 TRUE FALSE 27811.90775 34257.47233 31987.675 33408.57025 31464.21311 35650.69731 25659.40798 30461.25558 27383.71328 1.01563683 1.251016324 1.168127736 1.22001607 1.149011925 1.301894194 0.937031721 1.112385865 1 14.74103047 2.234195978 24.99996262 1.033144454 1.186603693 0.455999928 0.085736631 99.25813728 568525.5922 0.031511822 0.022070021 171.4730917 -2.234195978 0.153459239 RAT(ph)SLPSIPNPFPELCSPPSQS(ph)PILGGPSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RATSLPSIPNPFPELCSPPSQSPILGGPSSAR 32 1 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 RAT(0.524)S(0.465)LPS(0.011)IPNPFPELCS(0.011)PPS(0.326)QS(0.663)PILGGPSSAR 124 1.29E-07 97142000 34571 17137 9724.8 16073 21199 21069 22506 22037 10424 TRUE FALSE 30002.35476 17024.42592 14427.74581 19722.62031 20777.18138 21879.53806 20323.37158 17324.55904 9191.686595 3.264075036 1.852154743 1.569651626 2.145702 2.260431876 2.380361628 2.211060111 1.884807414 1 13.16611389 1.222438064 2.191982481 0.611983498 2.20162685 0.447081255 0.433624099 0.685827105 3.222145322 2.204661374 0.114686313 16.6892978 -1.222438064 1.589643352 RAT(ph)SLPSIPNPFPELCSPPSQSPILGGPSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RATSLPSIPNPFPELCSPPSQSPILGGPSSAR 32 1 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 RAT(0.5)S(0.5)LPSIPNPFPELCSPPSQSPILGGPSSAR 173.22 9.58E-15 317160000 198080 107610 63619 64777 114510 109470 101000 140880 49865 TRUE FALSE 171903.2261 106903.1028 94385.36119 79485.6079 112231.475 113681.3817 91205.03555 110753.9083 43970.01651 3.909555642 2.431272747 2.14658462 1.807722949 2.552454694 2.58542959 2.074255204 2.518850734 1 15.42423245 4.745985002 2.926911094 2.159746681 4.2262101 0.595091858 0.464512451 0.288784765 3.515504147 0.111736873 1.42067823 55716.65068 -4.745985002 2.06646342 RATVVESSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RATVVESSEK 10 1 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;; 134.98 0.00025074 733210000 1244660 957790 736330 895930 867090 852320 1110690 1253430 1190090 FALSE TRUE 1080175.027 951498.2144 1092421.651 1099364.6 849836.6054 885109.3019 1002975.455 985393.7487 1049398.916 1.029327371 0.906707831 1.040997503 1.047613623 0.809831793 0.843444079 0.955761855 0.939007782 1 20.00113177 3.265678033 24.99997418 0.913437042 1.001546013 0.345080707 0.06584176 294.9129758 271882.8925 0.019938331 0.025733691 1843.648111 -3.265678033 0.088108971 RAVS(ph)PSNPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 RAVSPSNPK 9 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 RAVS(0.881)PS(0.119)NPK;RAVS(0.988)PS(0.012)NPK;RAVS(0.983)PS(0.017)NPK;RAVS(0.951)PS(0.049)NPK;RAVS(1)PSNPK;RAVS(1)PSNPK;RAVS(0.5)PS(0.5)NPK;RAVS(0.963)PS(0.037)NPK 146.9 9.92E-05 9902183000 6695570 5962350 4449110 5075030 5562960 5886710 6662840 7135190 5898140 TRUE FALSE 5810733.46 5923182.93 6600714.477 6227393.128 5452267.98 6113175.543 6016678.802 5609385.145 5200868.608 1.117262115 1.138883401 1.269156169 1.197375592 1.048337959 1.17541434 1.156860374 1.078547752 1 22.31032116 1.41547027 1.805929816 0.974010837 1.160547192 0.464340186 0.056232971 0.570809478 2.50171306 0.168562877 0.016506889 26.02976634 -1.41547027 0.186536355 RAVVVS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RAVVVSPK 8 1 O75909;G3V5E1;O75909-1 O75909 CCNK Cyclin-K 1 RAVVVS(1)PK 68.515 0.030018 0 418310 278480 247680 270530 311980 269640 346600 392060 486570 TRUE FALSE 363029.2736 276650.6465 367458.8764 331957.9713 305772.2084 280013.2253 312986.7853 308221.02 429048.2489 0.846126921 0.644800782 0.856451174 0.773707787 0.712675577 0.65263808 0.729490882 0.718383121 1 18.71078037 1.235959158 24.99951317 1.000000347 0.737965844 0.573046156 0.069976623 50.46021621 484812.257 0.108322938 0.016329767 17.21706653 -1.235959158 -0.262034503 RCDIIIISGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RCDIIIISGR 10 1 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 0 ;;; 187.85 1.90E-06 1305590000 568378 625637 365149 415415 587520 614400 554120 703100 541944 FALSE TRUE 493265.4072 621527.1494 541736.2778 509741.325 575829.5015 638036.3656 500381.5277 552747.5365 477875.9977 1.032203772 1.300603404 1.133633579 1.066681163 1.204976823 1.335150476 1.047094916 1.156675663 1 18.86627678 0.380847539 1.179688521 0.099609808 1.170675264 0.196017245 0.100743114 16.57717941 4.049968901 35.86578439 0.029578704 2.403518886 -0.380847539 1.071065455 RCEAFGWHAIIVDGHSVEELCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RCEAFGWHAIIVDGHSVEELCK 22 1 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 172.61 1.91E-12 939071000 704172 822621 349454 315929 498273 530816 682397 670002 220118 FALSE TRUE 611113.8861 817217.1485 518451.1233 387665.5081 488358.3422 551236.835 616218.244 526727.2863 194095.9008 3.148515159 4.210378195 2.671108051 1.997288487 2.516067264 2.840023065 3.174813283 2.713747607 1 17.56641012 4.122904251 6.480461694 2.474486801 3.668497015 0.405054512 0.637404001 0.207420017 10.84042498 0.162695415 0.345402104 13271.0184 -4.122904251 1.194010213 RCPT(ph)PEIQK ddPTM_MDA-MB-175_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 158.01 3.94E-05 3454310000 4360150 4129890 3179800 3934390 4089130 3564000 4507910 5080670 8324910 TRUE FALSE 3783945.13 4102760.481 4717561.916 4827753.383 4007764.313 3701109.386 4070733.582 3994208.258 7340748.624 0.515471286 0.55890219 0.642654061 0.657664992 0.545961253 0.504186913 0.554539297 0.544114567 1 22.80749577 1.236765298 24.99999716 1.000000542 0.566494786 0.885422236 0.049126832 16.0915996 224011.4414 0.081800607 0.013053489 17.24905466 -1.236765298 -0.433505756 RCQYVTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RCQYVTEK 8 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;P09972 H3BPS8;P04075;P09972 ALDOA;ALDOC Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase C 0 ;;;; 194.84 0.00026176 2125890000 2943491 2510174 1686813 1984433 2584953 2345436 3090191 3232872 2674138 FALSE TRUE 2554501.206 2493684.502 2502561.409 2435028.843 2533517.493 2435666.441 2790504.752 2541547.481 2358004.452 1.0833318 1.057540201 1.061304785 1.032665074 1.074432871 1.032935472 1.183417932 1.077838288 1 21.16913501 RCS(ph)DGGAHGYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RCSDGGAHGYGR 12 1 A0A2R8YGX0;P10071 A0A2R8YGX0 GLI3 Transcriptional activator GLI3;Transcriptional repressor GLI3R 1 RCS(1)DGGAHGYGR 85.576 0.0071027 55413000 35202 45931 24672 24395 42420 55777 36752 40066 27183 TRUE FALSE 30549.96651 45629.27624 36603.46172 29934.2576 41575.92499 57922.77728 33187.7967 31498.19769 23969.45671 1.274537295 1.903642489 1.527087667 1.248850067 1.734537645 2.416524412 1.384586939 1.314097273 1 14.54890959 1.680740081 2.456517338 1.071852075 1.674464728 0.289128734 0.339611848 0.337698283 4.37818676 0.331096091 0.095425915 47.94464205 -1.680740081 0.602612653 RCS(ph)DPSLNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RCSDPSLNEK 10 1 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 RCS(1)DPSLNEK;RCS(1)DPSLNEK;RCS(1)DPSLNEK;RCS(1)DPSLNEK 141.34 2.31E-05 1783910000 2288060 2059650 1530320 1743490 1966690 1713520 2422040 2751460 2465910 TRUE FALSE 1985687.074 2046120.024 2270387.871 2139376.052 1927556.717 1779440.223 2187150.934 2163081.691 2174392.929 0.913214464 0.941007486 1.044147928 0.983895792 0.886480402 0.818361851 1.005867387 0.994797979 1 21.05218124 RCS(ph)EDFSPLSPDVPMTVNTVDHSHSTTVEKPNNETGDITR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RCSEDFSPLSPDVPMTVNTVDHSHSTTVEKPNNETGDITR 40 2 Q7Z3T8 Q7Z3T8 ZFYVE16 Zinc finger FYVE domain-containing protein 16 1 RCS(0.802)EDFS(0.192)PLS(0.006)PDVPMTVNTVDHSHSTTVEKPNNETGDITR 44.099 0.031101 194140000 28635 28424 14535 26288 41822 35692 39252 49691 37054 TRUE FALSE 24850.8122 28237.28087 21564.17462 32257.09219 40989.82402 37065.09434 35445.34708 39064.96635 32673.51833 0.760579621 0.864225291 0.659989365 0.987254934 1.254527401 1.134407809 1.084834107 1.195615542 1 14.99583419 3.512634536 4.95395167 1.137655098 0.775466653 0.809678751 0.082191866 0.076478956 4.666482185 0.021907303 0.031689343 3255.62621 -3.512634536 -0.362188446 RCS(ph)QVK ddPTM_MDA-MB-175_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 70.525 0.055517 86120000 67076 67776 51547 65788 44820 47361 70790 61340 147270 TRUE FALSE 58211.73665 67330.77499 76475.30161 80726.17091 43928.16969 49183.00832 63924.7967 48222.91835 129859.9084 0.448265653 0.518487775 0.588906173 0.621640443 0.338273531 0.378738973 0.492259678 0.371345698 1 16.98659657 1.232078736 24.99754756 1.000000889 0.469225264 0.767135068 0.091813339 114.1387328 440136.9802 0.223373559 0.024026004 17.06391723 -1.232078736 -0.530775626 RCS(ph)SSLGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RCSSSLGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR 36 2 Q96HP0 Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 1 RCS(0.837)S(0.158)S(0.006)LGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR;RCS(0.742)S(0.212)S(0.046)LGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR 230.71 4.39E-40 629380000 126394 117746 77769 85438 128648 138304 133366 127760 95160 TRUE FALSE 109690.7127 116972.5188 115378.3485 104838.0037 126088.1565 143624.6444 120432.1858 100439.5182 83910.29321 1.307237866 1.394018711 1.375020204 1.249405761 1.502654224 1.711645126 1.435249255 1.196986858 1 16.35656018 1.529927269 2.859827408 1.013744504 1.428733262 0.569872234 0.123999984 0.20000499 3.301996126 0.157717315 0.036087175 33.87874152 -1.529927269 0.414988758 RCS(ph)VTSMESTVSSGTQTTVQDDPEQFEVIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RCSVTSMESTVSSGTQTTVQDDPEQFEVIK 30 1 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 RCS(0.936)VT(0.027)S(0.027)MES(0.004)T(0.004)VS(0.001)S(0.001)GT(0.001)QTTVQDDPEQFEVIK;RCS(0.999)VT(0.001)SMESTVSSGTQTTVQDDPEQFEVIK;RCS(0.999)VT(0.001)SMESTVSSGTQTTVQDDPEQFEVIK 291.17 4.50E-81 1008750000 1102847 866312 633750 658079 908623 810993 1109542 1298249 961983 TRUE FALSE 957102.9747 860621.1394 940233.6198 807505.8951 890543.18 842192.4255 1001938.788 1020628.554 848258.4656 1.128315264 1.014574183 1.108428218 0.951957367 1.049848856 0.99284883 1.181171575 1.203204678 1 19.6941444 2.234911682 24.99978499 1.145977194 1.039214852 0.224654694 0.073813793 108.9910533 746714.0127 0.028300136 0.01992089 171.7559069 -2.234911682 -0.106762342 RCSS(ph)SLGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RCSSSLGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR 36 2 Q96HP0 Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 1 RCS(0.349)S(0.515)S(0.136)LGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR;RCS(0.305)S(0.579)S(0.116)LGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR 257.72 2.51E-62 504290000 79580 70994 54922 48082 65254 84843 78304 79740 70943 TRUE FALSE 69063.30137 70527.63574 81482.4629 58999.75299 63955.57307 88106.96511 70710.09013 62688.22154 62556.19936 1.104020098 1.1274284 1.302548169 0.943147979 1.022369865 1.408444982 1.130345047 1.002110457 1 15.93286524 1.752988415 4.939717334 1.000729466 1.151414284 0.182476061 0.129938643 0.293967903 16.69459758 0.07983083 0.034719794 56.62241843 -1.752988415 0.150684818 RDAYVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RDAYVSR 7 1 P00390-5;P00390-4;P00390-2;P00390-3;P00390;A0A2R8YF59;H0YC68 P00390-5 GSR "Glutathione reductase, mitochondrial" 0 ;; 136.27 0.0048048 262923000 396319 454640 233416 326149 375681 525398 367527 364697 426496 FALSE TRUE 343944.44 451653.4399 346296.7583 400206.1153 368205.6831 545610.401 331884.2881 286709.3846 376076.1287 0.91456068 1.200962798 0.920815579 1.064162505 0.979072201 1.450797749 0.882492301 0.762370602 1 18.52066521 2.032879445 24.99999155 0.851676914 1.087059108 0.254905143 0.164935425 211.2261249 160605.638 0.064090525 0.043209524 107.8647262 -2.032879445 0.235382194 RDDFCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDDFCK 6 1 P32456;H3BNS1;Q9H0R5-4;P32455;Q9H0R5 P32456 GBP2;GBP3;GBP1 Interferon-induced guanylate-binding protein 2;Guanylate-binding protein 3;Interferon-induced guanylate-binding protein 1 0 ; 117.17 0.0368 734470000 954670 991980 646830 702290 753410 794760 1052530 1151760 1086430 FALSE TRUE 828507.9407 985463.6181 959639.1515 861755.6783 738418.615 825334.9315 950455.8026 905465.087 957993.4831 0.864836719 1.028674657 1.001717828 0.899542318 0.770797117 0.861524578 0.992131804 0.945168316 1 19.86965632 2.222775919 24.82682332 0.97257393 0.908273247 0.184733152 0.073153 488.7592804 768734.394 0.033077751 0.022386985 167.0228613 -2.222775919 -0.064300683 RDDGLSAAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RDDGLSAAAR 10 1 F8WBN3;B9A031;C9JQZ0;B8ZZY7;F8WBV6;P84101-4;P84101;P84101-3;P84101-2 F8WBN3 SERF2 Small EDRK-rich factor 2 0 ;;;;; 231.07 1.37E-09 3768480000 1571730 1690040 1052934 1198031 1622090 1655770 1505400 1801730 1807170 FALSE TRUE 1364021.898 1678938.016 1562136.404 1470062.249 1589813.583 1719468.543 1359406.54 1416444.061 1593528.421 0.855975883 1.053597786 0.980300309 0.922520257 0.997668797 1.079032241 0.85307957 0.888872794 1 20.60379332 2.216425756 24.99985602 0.906214933 0.982789735 0.162166724 0.071599145 373.9814943 422384.0745 0.028286126 0.019087441 164.5984557 -2.216425756 0.076574802 RDDGSWEVIEGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RDDGSWEVIEGYR 13 1 P00367;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 ;; 214.11 8.50E-10 705931000 372597 434572 280766 427076 454316 494564 346790 476662 424248 FALSE TRUE 323357.3624 431717.2679 416545.3767 524050.1332 445276.0005 513590.1971 313158.3592 374731.5407 374093.8847 0.864374895 1.15403455 1.113478177 1.400851911 1.190278747 1.372891186 0.837111677 1.001704535 1 18.51304086 2.228179225 24.99995558 0.953272161 1.188471457 0.347701076 0.152384906 237.3964394 571681.4582 0.061912481 0.042251228 169.1138688 -2.228179225 0.235199296 RDDGTGQLLLPLSDAR ddPTM_MDA-MB-175_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 ;;;;; 194.94 2.13E-10 2744597000 2740460 2474210 1576513 1870940 2503100 2676510 2520120 2698890 2234790 FALSE TRUE 2378301.268 2457956.752 2338919.96 2295765.523 2453293.207 2779477.072 2275719.15 2121753.376 1970595.672 1.206894596 1.247316629 1.186910127 1.165010943 1.244950064 1.410475579 1.154838196 1.076706605 1 20.91020036 1.748412668 2.688606641 1.021538944 1.239022984 0.597178195 0.068870645 0.173817121 2.559801102 0.05712897 0.019711631 56.02897377 -1.748412668 0.217484039 RDDMESLGYVLMYFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RDDMESLGYVLMYFNR 16 1 P48729-2;A0A5F9W493;U3KPX3;A0A590UJ43;P48729;E7ETM0;P48729-3;D6REM4;H0Y9X2;U3KQK7 P48729-2 CSNK1A1 Casein kinase I isoform alpha 0 ;; 211.12 1.27E-11 753730000 499046 500184 286497 382895 456757 432417 518187 532683 419963 FALSE TRUE 433095.8067 496898.2584 425047.9075 469837.1619 447668.4293 449052.3618 467933.3045 418772.8858 370315.4526 1.169532094 1.341824261 1.147799544 1.268748465 1.20888401 1.212621182 1.263607287 1.130854473 1 18.49839523 1.394724619 2.460731274 0.981246807 1.231444996 0.651662585 0.054665365 0.218753609 1.919722874 0.10227682 0.013122879 24.81559077 -1.394724619 0.25019819 RDDNSAANNSANEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDDNSAANNSANEK 14 1 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77;H0YEC5;H0YD99;H0YEN8;H0YDC0;H0YCF8;H0YEI7 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 ; 222.45 6.24E-12 399250000 258970 234350 154945 176104 182350 215480 237870 284690 264870 FALSE TRUE 224746.4584 232810.5394 229876.9203 216091.1048 178721.5918 223769.655 214801.404 223811.259 233557.3703 0.96227517 0.996802366 0.984241773 0.92521638 0.765214951 0.958092886 0.919694393 0.958271018 1 17.83341745 3.724412058 7.254729319 0.919819891 0.982777679 0.175024123 0.061387433 0.284477145 89.56828516 0.01753277 0.027274747 5301.662266 -3.724412058 0.062957787 RDDNSAANNSANEKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDDNSAANNSANEKER 16 2 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77;H0YEC5;H0YD99;H0YEN8;H0YDC0;H0YCF8;H0YEI7 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 99.451 0.0013441 25396000 28133 21685 11960 14287 21948 24033 25712 27651 16498 FALSE TRUE 24415.15277 21542.54981 17743.896 17531.08171 21511.27774 24957.56506 23218.4542 21738.04883 14547.62523 1.678291293 1.480829308 1.219710827 1.205082028 1.478679674 1.715576574 1.596030543 1.49426786 1 13.82849605 3.045399911 24.99826389 1.485645206 1.383502611 0.007720975 0.2250959 494.4964288 272278.214 0.070684728 0.080148906 1110.196646 -3.045399911 -0.102142595 RDDSNESDVVESLDEIYHTGTFAQIHEMQDLGDKLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDDSNESDVVESLDEIYHTGTFAQIHEMQDLGDKLR 36 2 K7EKE6;K7EJE8;P36776-2;P36776;K7EQF8 K7EKE6 LONP1 "Lon protease homolog, mitochondrial" 0 111.1 5.12E-06 26684000 8015.3 6688.1 2386 3623.6 6870.9 5983.1 7221.8 10724 2910.1 FALSE TRUE 6956.057797 6644.165431 3539.877581 4446.393763 6734.182533 6213.273729 6521.430948 8430.756054 2566.071293 2.710781191 2.589236491 1.379493076 1.732763145 2.624316226 2.421317656 2.541406766 3.285472261 1 11.32534554 3.216724951 24.9889046 2.503232414 2.086110636 0.018794008 0.680028406 649.0204199 742741.8624 0.207448554 0.235417558 1647.118901 -3.216724951 -0.417121777 RDEFEFLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDEFEFLEK 9 1 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 162.26 0.00010248 382090000 1024800 1010300 673270 814250 1004600 773460 1161700 1338100 1087500 FALSE TRUE 889370.0835 1003663.273 998865.624 999137.9075 984610.4255 803215.5067 1049038.513 1051957.728 958936.9889 0.927454143 1.046641525 1.041638435 1.041922378 1.026772809 0.837610308 1.093959796 1.097004016 1 19.87107649 RDELLAQHAAGALGLPDLVAVLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDELLAQHAAGALGLPDLVAVLTR 24 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 202.74 8.28E-25 1402220000 659320 723010 429340 496870 667230 718580 582670 687040 739410 FALSE TRUE 572189.1915 718260.4997 636970.2601 609691.9277 653953.4284 746224.2376 526162.7531 540121.8426 651997.7921 0.877593756 1.101630264 0.97695156 0.935113485 1.002999452 1.144519577 0.80700082 0.828410539 1 19.31450755 2.216048398 24.99995887 0.865063395 1.006050925 0.304460601 0.090444019 256.3630604 284690.6255 0.035813681 0.024164906 164.4554983 -2.216048398 0.14098753 RDELSEEINNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDELSEEINNLR 12 1 A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7;A0A087WYS2;B4DSP0;A0A087WZG9;Q86TG7-2 A0A087WXK2;B4DSP0 PEG10 Retrotransposon-derived protein PEG10 0 248.67 1.39E-16 131940000 64429 62388 42096 44948 60958 66614 54720 64698 96860 FALSE TRUE 55914.54441 61978.16912 62453.7664 55154.13039 59745.05506 69176.68368 49413.26282 50862.83618 85409.32114 0.654665599 0.725660482 0.731228929 0.645762426 0.699514459 0.809943022 0.578546488 0.595518563 1 16.38210591 1.229458585 24.99780916 1.000000623 0.677991462 0.687892129 0.067704373 226.6093322 622313.0455 0.213446473 0.01773259 16.96127851 -1.229458585 -0.322009162 RDELTLEGIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RDELTLEGIK 10 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ;; 193.22 9.58E-07 1224670000 1710790 1326370 1014120 1271150 1394510 1130750 1606840 1832620 1693530 FALSE TRUE 1484704.767 1317656.988 1504551.824 1559784.036 1366761.979 1174250.684 1451008.904 1440728.474 1493322.813 0.994228947 0.882365807 1.00751948 1.044505597 0.915248845 0.786334123 0.971664594 0.964780329 1 20.51009464 1.788786169 0.003077177 0.468369666 1.428106116 0.000916589 0.074442973 2273324.822 2680.91146 421792.4508 414369.3842 61.48740559 -1.788786169 0.959736451 RDENWDKEIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDENWDKEIEK 11 2 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 98.531 0.0030661 103510000 199070 196910 142910 141750 168470 121970 208230 252630 156840 FALSE TRUE 172762.3951 195616.4852 212021.754 173936.504 165117.7766 126662.2648 188035.8866 198607.0405 138298.5539 1.249198855 1.414450692 1.53307282 1.257688523 1.193922655 0.915861094 1.359637403 1.4360746 1 17.07742655 3.539767194 8.176924198 1.214175263 1.400332692 0.253127055 0.165442398 0.571084814 69.00981748 0.048701952 0.072081642 3465.510304 -3.539767194 0.186157429 RDEQDDDDKGDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDEQDDDDKGDSK 13 2 Q9H4A6;D6REM1 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 0 ; 177.93 8.45E-06 1502560000 1909560 1338540 1369340 1130740 712560 704920 1787530 2019370 1925510 FALSE TRUE 1657206.808 1329747.043 2031557.404 1387491.799 698381.4501 732038.7285 1614175.616 1587543.44 1697878.401 0.976045638 0.783181553 1.196527032 0.817191501 0.411325952 0.431149091 0.950701543 0.935015982 1 20.69530171 3.49303863 24.83981315 0.754901674 0.972013584 0.195679291 0.22105606 1309.368867 2043328.688 0.068214922 0.097899549 3111.993133 -3.49303863 0.217111909 RDFNHINVELSLLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDFNHINVELSLLGK 15 1 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 73.022 0.025322 208420000 511280 441410 307290 397660 473830 402260 550150 630310 473520 FALSE TRUE 443713.0526 438510.3486 455896.4718 487954.7809 464401.71 417735.2025 496796.5377 495523.1116 417541.005 1.062681383 1.05022104 1.091860359 1.168639187 1.112230187 1.000465098 1.189814968 1.186765145 1 18.67155836 4.040108589 5.173181514 1.11913387 1.058273622 0.083561279 0.067045846 0.404956935 26.13128493 0.01781123 0.037602507 10967.52388 -4.040108589 -0.060860248 RDGPEETDWWWAALHGQEGYVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RDGPEETDWWWAALHGQEGYVPR 23 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 0 ;; 95.71 0.0024967 110860000 130810 116702 81339 88315 128374 131665 114738 150499 96426 FALSE TRUE 113523.1271 115935.3769 120674.8125 108368.2706 125819.6086 136730.2377 103610.7264 118315.96 85026.62813 1.335147936 1.363518458 1.419259062 1.274521558 1.479767119 1.608087263 1.218567979 1.391516548 1 16.37562711 0.760908976 1.700120098 2.31E-16 1.395403254 0.548776587 0.108648269 3.302466061 2.816295617 11.56804122 0.029544462 5.766455913 -0.760908976 1.395403254 RDGSYGSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDGSYGSGR 9 1 Q08170;A0A0D9SEM4;A0A0D9SGD2 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 0 ; 108.7 0.0041198 128347000 286647 254627 126632 172133 174525 272649 229723 285319 172842 FALSE TRUE 248765.8727 252954.3385 187871.6588 211218.4285 171052.294 283137.9835 207444.4988 224305.7522 152408.8157 1.632227582 1.659709364 1.232682361 1.385867528 1.122325459 1.857753321 1.361105642 1.471737388 1 17.21758683 7.999969775 0.030463965 6.99E-07 3.449651143 0.139090302 0.23980619 7811.490577 23.56358769 938.3696264 1889.825943 99993040.66 -7.999969775 3.449650444 RDHALLEEQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RDHALLEEQSK 11 1 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;;;; 107.85 0.0013907 2142260000 1691550 1304020 1128908 1670370 1107620 1090080 1174686 1534580 3946150 FALSE TRUE 1468007.382 1295453.807 1674851.685 2049653.039 1085580.529 1132016.083 1060765.133 1206422.009 3479640.642 0.421884767 0.372295286 0.481328924 0.589041585 0.311980644 0.325325572 0.304849047 0.346708794 1 21.73050689 1.236018598 25 1.000000802 0.391173492 0.826194396 0.087315443 30.00109408 294989.182 0.153055019 0.023149362 17.21942312 -1.236018598 -0.60882731 RDHHSTHYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RDHHSTHYR 9 1 P05060 P05060 CHGB Secretogranin-1;PE-11;GAWK peptide;CCB peptide 0 ;;; 105.52 0.0049459 5002300000 3958370 4663000 3157540 2986920 3743040 3762900 5566550 4395160 4204360 FALSE TRUE 3435261.375 4632368.446 4684536.905 3665145.838 3668560.827 3907661.198 5026706.838 3455289.237 3707325.35 0.926614486 1.249517646 1.26358937 0.988622657 0.989543803 1.054037838 1.355885001 0.932016727 1 21.8219473 3.724383571 24.79471207 1.056990382 1.156868229 0.08188415 0.145459552 1758.554076 3075594.557 0.04015449 0.059911327 5301.314521 -3.724383571 0.099877847 RDHRPPCAQEAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RDHRPPCAQEAPR 13 2 Q13501;Q13501-2;E7EMC7;C9JRJ8;E9PFW8;E3W990 Q13501 SQSTM1 Sequestosome-1 0 ;;; 170.79 1.47E-05 88145000 177044 155301.3 97959.2 113777.2 146111.3 161852.7 139842.8 161759.4 156131.6 FALSE TRUE 153647.1868 154281.1155 145332.5968 139612.0522 143203.971 168079.2781 126280.8668 127168.4111 137673.9001 1.116022621 1.120627188 1.055629256 1.014077847 1.040167896 1.220850706 0.917246237 0.923692951 1 17.07089556 2.205215594 24.99900095 0.940889303 1.087846854 0.569350344 0.060240641 135.5585161 101628.2951 0.024816852 0.016732689 160.4041478 -2.205215594 0.146957552 RDIEDIPYV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDIEDIPYV 9 1 Q96EI5;Q96EI5-2;A2RQR6 Q96EI5 TCEAL4 Transcription elongation factor A protein-like 4 0 124.08 0.0015493 0 133770 129160 74861 92551 123360 115280 102030 135760 123090 FALSE TRUE 116091.9556 128311.5395 111064.03 113566.1191 120905.3773 119714.8962 92135.1463 106728.7805 108538.4404 1.069592995 1.182176001 1.023269079 1.046321641 1.113940618 1.102972327 0.848871109 0.983327014 1 16.72784656 2.26318901 24.99994911 0.948278935 1.090023925 0.587091128 0.057542808 153.0488547 155357.3833 0.021179287 0.016397879 183.3112041 -2.26318901 0.141744989 RDINVSVGSQQPDTKDS(ph)PVCPHFTTNGNENSSIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDINVSVGSQQPDTKDSPVCPHFTTNGNENSSIEK 35 2 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 RDINVSVGSQQPDT(0.141)KDS(0.851)PVCPHFT(0.008)TNGNENSSIEK;RDINVSVGSQQPDT(0.032)KDS(0.903)PVCPHFT(0.032)T(0.032)NGNENSSIEK 97.718 0.00011026 216640000 139543 109861 78480 79610 105995 87700 153694 165781 116512 TRUE FALSE 121102.039 109139.3159 116433.1905 97686.66726 103885.9069 91073.87575 138788.7795 130330.0233 102738.0841 1.178745351 1.062306318 1.133301166 0.95083209 1.01117232 0.886466558 1.350899044 1.268565833 1 16.64861155 2.233793134 24.99996963 1.225438205 1.037549243 0.303462174 0.119806409 133.4932396 700008.9292 0.048210283 0.033690994 171.31411 -2.233793134 -0.187888962 RDNYVPEVSALDQEIIEVDPDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RDNYVPEVSALDQEIIEVDPDTK 23 1 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 ;;; 230.9 4.92E-33 776168000 1024947 865018 667543 834075 887857 728387 1026291 1265490 1168211 FALSE TRUE 889497.6571 859335.6398 990369.0276 1023464.477 870190.3828 756408.5192 926761.4568 994874.8116 1030106.426 0.863500736 0.834220249 0.961423987 0.993552171 0.844757746 0.73430133 0.899675444 0.965798083 1 19.97436197 1.704738355 3.409047336 0.990173887 0.874677137 0.294275191 0.070297083 0.276132906 7.233942617 0.056545897 0.020524079 50.66853588 -1.704738355 -0.115496751 RDPFIGEHTEEILEEFGFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDPFIGEHTEEILEEFGFSR 20 1 D6RB81;Q9UHK6;Q9UHK6-5 D6RB81 AMACR Alpha-methylacyl-CoA racemase 0 ; 104.06 0.00017934 46117000 40348 28275 20269.6 23894.7 26648 32001 23549 28554 22849.3 FALSE TRUE 35015.90957 28089.25966 30072.04636 29320.35684 26117.75694 33232.09918 21265.2216 22447.94931 20148.08178 1.737927707 1.394140641 1.492551335 1.455243092 1.29629 1.649392708 1.05544646 1.114148213 1 14.29835487 2.225589081 24.9857638 1.06848966 1.487039154 0.736964565 0.125745001 113.1620143 217970.8254 0.048274829 0.032775213 168.1082709 -2.225589081 0.418549494 RDPHLACVAYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RDPHLACVAYER 12 1 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ;;; 94.023 0.0044421 3868090000 1542900 1557860 752281 795970 1472680 1644520 1418070 1559180 1148990 FALSE TRUE 1339001.856 1547626.315 1116086.608 976707.1541 1443376.549 1707785.749 1280545.79 1225761.491 1013157.711 1.321612461 1.527527549 1.101592176 0.96402282 1.424631657 1.685607018 1.263915554 1.209842729 1 19.95042734 1.371878582 2.181489882 0.962469104 1.328455155 0.213464714 0.201292473 0.873530607 5.520576915 0.572683032 0.058424724 23.5439096 -1.371878582 0.365986051 RDPMYNEYLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDPMYNEYLDR 11 1 Q7L5D6;Q7L5D6-2 Q7L5D6 GET4 Golgi to ER traffic protein 4 homolog 0 ; 186.58 6.36E-06 507430000 375390 347800 223860 227760 348730 356070 313040 341990 351260 FALSE TRUE 325781.2604 345515.2789 332119.4448 279476.3891 341790.9553 369768.2433 282681.429 268858.0999 309734.443 1.051808308 1.115521011 1.072271594 0.90230969 1.103496763 1.193823457 0.912657392 0.868027777 1 18.2406723 2.20004676 24.78551586 0.914037525 1.068695066 0.427308548 0.079268424 134.8672151 86792.5202 0.033151884 0.022351481 158.5063846 -2.20004676 0.154657541 RDPSSNDINGGMEPTPSTVS(ph)TPS(ph)PSADLLGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDPSSNDINGGMEPTPSTVSTPSPSADLLGLR 32 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 2 RDPSSNDINGGMEPT(0.001)PS(0.005)T(0.006)VS(0.528)T(0.489)PS(0.928)PS(0.043)ADLLGLR 68.807 0.013438 48751000 29480 31808 15112 24403 32985 32950 27586 30798 32310 TRUE FALSE 25584.14331 31599.05115 22420.21375 29944.07413 32328.66303 34217.60782 24910.71397 24212.08737 28490.34861 0.89799334 1.109114233 0.78694066 1.051025192 1.134723323 1.20102454 0.874356236 0.849834718 1 14.79818565 0.915764948 20.85889976 1.951740179 0.983352556 0 0.135916979 5396.054251 1418269.338 15147.29019 0.03376663 8.236921899 -0.915764948 -0.968387624 RDPSSNDINGGMEPTPSTVS(ph)TPSPSADLLGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDPSSNDINGGMEPTPSTVSTPSPSADLLGLR 32 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 1 RDPSSNDINGGMEPTPS(0.004)T(0.004)VS(0.522)T(0.106)PS(0.361)PS(0.003)ADLLGLR;RDPSSNDINGGMEPTPST(0.001)VS(0.562)T(0.219)PS(0.219)PSADLLGLR 222.75 3.27E-36 549770000 144536 131973 76917 114430 127861 142165 133788 151840 126995 TRUE FALSE 125435.2014 131106.0607 114114.3185 140413.0805 125316.8163 147634.1795 120813.2604 119370.1976 111981.7958 1.12013922 1.170780123 1.019043477 1.253892023 1.119082038 1.318376603 1.078865181 1.065978598 1 16.7729047 2.017929236 24.99813802 1.048117943 1.165165839 0.328096721 0.081318709 272.7510943 380286.2129 0.031936094 0.021526299 104.2147607 -2.017929236 0.117047895 RDPSSNDINGGMEPTPSTVSTPS(ph)PSADLLGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 RDPSSNDINGGMEPTPSTVSTPSPSADLLGLR 32 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 1 RDPSSNDINGGMEPTPSTVS(0.015)T(0.051)PS(0.931)PS(0.003)ADLLGLR;RDPSSNDINGGMEPTPSTVS(0.001)T(0.015)PS(0.984)PSADLLGLR;RDPSSNDINGGMEPTPSTVST(0.001)PS(0.995)PS(0.003)ADLLGLR;RDPSSNDINGGMEPTPSTVS(0.002)T(0.009)PS(0.988)PSADLLGLR;RDPSSNDINGGMEPTPSTVST(0.001)PS(0.994)PS(0.005)ADLLGLR;RDPSSNDINGGMEPTPS(0.037)T(0.037)VS(0.175)T(0.147)PS(0.595)PS(0.007)ADLLGLR;RDPSSNDINGGMEPTPSTVS(0.012)T(0.283)PS(0.703)PS(0.001)ADLLGLR;RDPSSNDINGGMEPTPSTVS(0.003)T(0.005)PS(0.992)PSADLLGLR;RDPSSNDINGGMEPTPSTVS(0.001)T(0.005)PS(0.991)PS(0.003)ADLLGLR;RDPSSNDINGGMEPTPSTVS(0.061)T(0.205)PS(0.698)PS(0.037)ADLLGLR;RDPSSNDINGGMEPTPSTVS(0.075)T(0.198)PS(0.722)PS(0.004)ADLLGLR;RDPSSNDINGGMEPTPSTVS(0.074)T(0.044)PS(0.876)PS(0.006)ADLLGLR 307.02 6.12E-91 6523159000 1221336 1113862 698393 794282 1082645 1256868 1004448 1267295 1082307 TRUE FALSE 1059933.353 1106544.967 1036138.191 974635.8679 1061102.483 1305220.525 907036.7876 996293.8264 954357.8994 1.110624592 1.159465404 1.085691428 1.021247761 1.111849636 1.367642607 0.950415759 1.04394151 1 19.86417088 RDPTEEIEILLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDPTEEIEILLR 12 1 B4DG22;B1AXG1;B7ZB17;P51812;A0A2R8Y603 B4DG22 RPS6KA3 Ribosomal protein S6 kinase alpha-3 0 97.551 0.0077891 44233000 15412 15140 12442 15794 13948 17321 15843 20455 19253 FALSE TRUE 13375.26515 15040.54434 18458.99282 19380.2691 13670.46209 17987.35008 14306.5483 16080.85743 16976.93227 0.787849356 0.885940057 1.087298489 1.141564847 0.805237476 1.059517102 0.842705152 0.947218094 1 14.05128817 4.473648645 24.46437181 0.975409494 0.812371973 0.279425139 0.103156086 87.52863909 616642.9609 0.025506078 0.068269831 29761.07708 -4.473648645 -0.163037521 RDPYGFGDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDPYGFGDSR 10 1 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 0 72.848 0.074974 159140000 383920 366930 195510 269900 344520 353230 330390 380680 361140 FALSE TRUE 333183.9993 364519.6127 290059.2899 331184.9202 337664.726 366818.9867 298348.8287 299274.5445 318446.4406 1.046279552 1.144681071 0.910857378 1.040001953 1.060350134 1.15190167 0.936888565 0.939795539 1 18.28069122 2.201930856 24.99999917 0.95399869 1.05536855 0.326001383 0.067604279 198.6072115 135549.1063 0.027572242 0.018589774 159.1955253 -2.201930856 0.10136986 RDQALTEEHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RDQALTEEHAR 11 1 P12814-3;P12814;P12814-2;P12814-4;H9KV75;H0YJ11 P12814-3 ACTN1 Alpha-actinin-1 0 ;;;; 199.4 3.27E-08 2282324000 1466766 1197261 1030928 1434096 1208933 1410391 1102113 1358817 2905313 FALSE TRUE 1272929.157 1189396.114 1529488.229 1759729.416 1184877.599 1464649.654 995230.2509 1068244.559 2561850.207 0.496878839 0.46427231 0.597024847 0.686897856 0.46250854 0.571715571 0.388481047 0.416981663 1 21.28875469 1.232088257 24.99994218 1.000000824 0.507652967 0.750702567 0.088618635 120.3225716 464710.0764 0.217800198 0.023494658 17.06429135 -1.232088257 -0.492347857 RDRS(ph)PIRGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDRSPIRGSPR 11 3 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 2 RDRS(1)PIRGS(1)PR 89.466 0.01753 396770000 204960 184750 120230 144340 192410 163580 162980 216020 189540 TRUE FALSE 177874.0167 183536.3651 178373.6301 177114.6031 188581.4174 169873.0285 147174.2247 169825.8041 167132.7971 1.064267575 1.098146912 1.067256895 1.059723801 1.128332803 1.016395533 0.88058255 1.016112977 1 17.35063534 2.482592879 24.9686018 0.969117024 1.081152002 0.647074191 0.040073421 147.0475061 671025.335 0.014203291 0.011348279 303.8035742 -2.482592879 0.112034978 RDS(ph)ASYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RDSASYR 7 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 1 RDS(1)ASYR;RDS(1)ASYR;RDS(0.59)AS(0.41)YR 179.31 0.00043057 2706230000 529605 493569 401996 442367 439068 650420 743520 777050 810570 TRUE FALSE 459616.3574 490326.7127 596402.6102 542813.1885 430331.4058 675442.0783 671413.5448 610883.9045 714745.338 0.643049115 0.686015965 0.834426723 0.759449778 0.602076548 0.94501082 0.9393745 0.854687498 1 19.44706978 2.722556907 24.99194813 0.922687449 0.714163714 0.71524994 0.07172878 487.330614 761031.2416 0.025135955 0.022236542 527.906376 -2.722556907 -0.208523736 RDS(ph)AYGSFSTSSSTPDHTLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RDSAYGSFSTSSSTPDHTLSK 21 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 RDS(1)AYGSFSTSSSTPDHTLSK;RDS(1)AYGSFSTSSSTPDHTLSK;RDS(1)AYGSFSTSSSTPDHTLSK 201.66 3.20E-22 629060000 272478 326807 141683 265606 389906 362944 389469 479080 429530 TRUE FALSE 236469.3419 324660.1833 210201.3727 325915.9018 382147.6334 376906.6905 351698.3563 376632.4702 378751.4527 0.624339102 0.857185315 0.554984994 0.860500731 1.008966779 0.995129359 0.928572957 0.994405348 1 18.5308919 3.494085831 4.921794304 0.980347501 0.6960898 0.758437491 0.078674397 0.085898381 5.742907244 0.020579324 0.029158232 3119.506041 -3.494085831 -0.284257701 RDS(ph)DGVDGFEAEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RDSDGVDGFEAEGK 14 1 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 RDS(1)DGVDGFEAEGK;RDS(1)DGVDGFEAEGK;RDS(1)DGVDGFEAEGK 182.22 9.48E-07 1261560000 1358210 926810 887290 1027660 945770 950000 1276310 1343240 2118680 TRUE FALSE 1178719.107 920721.7241 1316386.412 1261005.91 926951.0274 986547.1147 1152533.653 1055998.579 1868212.064 0.630934319 0.492835766 0.704623654 0.67498007 0.496170133 0.528070198 0.616918001 0.565245563 1 20.8332268 1.236686391 24.9999554 1.000000519 0.5874768 0.767855756 0.071065518 23.43535142 312511.7832 0.108669433 0.017280759 17.24592096 -1.236686391 -0.412523718 RDS(ph)DGVDGFEAEGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDSDGVDGFEAEGKK 15 2 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 RDS(1)DGVDGFEAEGKK 123.43 8.09E-05 421470000 593040 367670 355290 330080 304790 297980 551520 535250 471140 TRUE FALSE 514668.2614 365254.7516 527109.4324 405029.709 298725.2753 309443.4834 498033.6753 420790.9528 415442.3659 1.23884395 0.879194761 1.268790753 0.974935977 0.719053471 0.744852978 1.198803291 1.012874438 1 18.66428882 7.999994127 0.948236448 0.970512798 164.2877274 0.166597686 0.174299823 2577.159128 4.519750595 0.057479042 912860.4731 99998647.62 -7.999994127 163.3172146 RDS(ph)DTYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDSDTYR 7 1 H3BUL5;H3BVF8;P49761-3;P49761-1;P49761;H3BRT8;H3BQR7;H3BV35;H3BRK0;H3BQG1;P49761-2 H3BUL5 CLK3 Dual specificity protein kinase CLK3 1 RDS(0.977)DT(0.023)YR 94.801 0.0085347 315680000 139010 100610 105070 98770 82446 111620 120250 105940 141900 TRUE FALSE 120639.4763 99949.08629 155882.2034 121197.2381 80805.4859 115914.0936 108588.1735 83285.55543 125124.7437 0.964153634 0.798795533 1.245814368 0.96861128 0.645799412 0.926388261 0.867839328 0.665620188 1 16.93300759 3.449709518 24.06950964 0.810161223 1.003292658 0.248068933 0.150166161 181.2046937 159109.9877 0.042116027 0.054373129 2816.498457 -3.449709518 0.193131436 RDS(ph)EEFGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RDSEEFGVK 9 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 RDS(1)EEFGVK;RDS(1)EEFGVK;RDS(1)EEFGVK 145.06 6.01E-05 617850000 1434400 1087270 931210 1093970 1201090 1071890 1394660 1511050 1853780 TRUE FALSE 1244840.406 1080127.652 1381546.271 1342372.609 1177190.659 1113126.302 1259406.088 1187923.717 1634628.24 0.761543435 0.660778778 0.845174601 0.821209726 0.720158033 0.680966029 0.770454136 0.726724088 1 20.64053113 1.235622773 24.98486534 1.000000344 0.74797127 0.661338288 0.056587497 51.19641513 435317.7215 0.094929444 0.013945544 17.20373615 -1.235622773 -0.252029074 RDS(ph)FDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RDSFDDR 7 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RDS(1)FDDR;RDS(1)FDDR;RDS(1)FDDR;RDS(1)FDDR 133.12 0.0020226 1217890000 1857190 1427020 1379420 1750360 1420570 1635800 1861490 1896470 4172960 TRUE FALSE 1611757.636 1417645.812 2046512.126 2147805.991 1392303.436 1698730.285 1680962.986 1490924.649 3679637.423 0.438020775 0.385267799 0.556172223 0.583700442 0.378380606 0.461656976 0.45682843 0.405182489 1 21.81113218 1.23516792 24.99295729 1.000000758 0.457931968 0.866318298 0.066892505 34.20907026 251966.2891 0.118937682 0.016820699 17.18572746 -1.23516792 -0.54206879 RDS(ph)FDDRGPSLNPVLDYDHGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 RDSFDDRGPSLNPVLDYDHGSR 22 2 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(0.785)FDDRGPS(0.215)LNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(0.999)FDDRGPS(0.001)LNPVLDYDHGSR;RDS(0.953)FDDRGPS(0.047)LNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(0.98)FDDRGPS(0.02)LNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(0.993)FDDRGPS(0.007)LNPVLDYDHGSR 274.99 1.05E-45 48376802000 7341353 6152328 2281566 4933482 7829552 7736232 7785705 8956888 6420961 TRUE FALSE 6371174.6 6111912.952 3384938.949 6053704.492 7673759.233 8033849.851 7030648.527 7041527.204 5661882.305 1.125274998 1.079484281 0.597846929 1.06920352 1.355337116 1.418936216 1.241751091 1.243672479 1 22.43285033 3.460801548 8.694802123 1.254766145 0.929633325 0.413777187 0.174196475 0.177792285 78.23678085 0.050789153 0.066691087 2889.359277 -3.460801548 -0.32513282 RDS(ph)FDNCSLGESSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDSFDNCSLGESSK 14 1 Q5UIP0-2;Q5UIP0 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 RDS(1)FDNCSLGESSK;RDS(1)FDNCSLGESSK 238.72 1.51E-17 471970000 584530 354530 208974 278080 332950 181285 558100 473750 395070 TRUE FALSE 507282.8795 352201.0691 310034.5254 341222.3142 326324.9464 188259.1513 503975.5479 372442.2492 348365.2747 1.456180958 1.01101084 0.889969661 0.979495774 0.936732132 0.54040734 1.446687097 1.069114164 1 18.4102413 4.73696554 5.864432013 0.993139214 1.469395038 0.314685114 0.218714396 0.173360802 27.38419721 0.05387151 0.331237895 54571.45582 -4.73696554 0.476255824 RDS(ph)FIGTPYWMAPEVVMCETMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDSFIGTPYWMAPEVVMCETMK 22 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 RDS(0.777)FIGT(0.118)PY(0.105)WMAPEVVMCETMK 63.427 0.0069368 0 61451 49818 41049 31209 41505 33905 51458 65196 51131 TRUE FALSE 53330.09465 49490.74228 60900.4337 38295.48045 40679.1317 35209.34729 46467.61108 51254.34276 45086.35143 1.182843432 1.097687897 1.350750987 0.849380782 0.90224936 0.780931394 1.030635871 1.136803958 1 15.46040315 3.733237016 24.98836675 0.965464524 1.199153484 0.527521584 0.115404793 419.8054988 1970519.573 0.035410734 0.054312908 5410.495204 -3.733237016 0.23368896 RDS(ph)FIGTPYWMAPEVVMCETSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 RDSFIGTPYWMAPEVVMCETSK 22 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 RDS(1)FIGTPYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(0.836)FIGT(0.093)PY(0.071)WMAPEVVMCETSK;RDS(0.999)FIGT(0.001)PYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(0.999)FIGT(0.001)PYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(0.994)FIGT(0.005)PY(0.001)WMAPEVVMCETSK;RDS(0.999)FIGT(0.001)PYWMAPEVVMCETSK;RDS(0.995)FIGT(0.005)PY(0.001)WMAPEVVMCETSK;RDS(0.955)FIGT(0.045)PYWMAPEVVMCETSK 316.55 1.33E-67 5153777000 3953443 3251221 2203840 2429549 2998509 2736533 3629704 4073048 2977254 TRUE FALSE 3430985.491 3229863.515 3269624.395 2981215.234 2938844.537 2841809.195 3277695.865 3202058.382 2625286.424 1.306899491 1.230289955 1.245435304 1.135577134 1.119437678 1.082475866 1.248509814 1.219698678 1 21.3240434 3.813298655 4.089109993 1.147429168 1.261910215 0.40667637 0.071073648 0.275282487 8.819673515 0.020105888 0.036040603 6505.76924 -3.813298655 0.114481047 RDS(ph)FLGGGPGPEEPEDLALQLQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDSFLGGGPGPEEPEDLALQLQQK 24 1 A0A2R8Y2X6;A1A5D9 A0A2R8Y2X6 CCDC64B Bicaudal D-related protein 2 1 RDS(1)FLGGGPGPEEPEDLALQLQQK 66.644 0.022337 20949000 20179 21048 14728 20313 20535 20018 22113 27556 25346 TRUE FALSE 17512.29402 20909.7343 21850.51006 24925.37711 20126.39368 20788.10541 19968.48466 21663.36384 22349.62475 0.783560987 0.93557429 0.977667871 1.115248126 0.900524904 0.93013219 0.893459505 0.969294298 1 14.44796299 4.726553236 3.19449472 0.966398665 0.759498488 0.467631455 0.0618513 0.312503805 5.100974357 0.015958816 0.158908314 53278.6529 -4.726553236 -0.206900178 RDS(ph)GDNSAPSGQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RDSGDNSAPSGQER 14 1 Q8IXQ3 Q8IXQ3 C9orf40 Uncharacterized protein C9orf40 1 RDS(0.973)GDNS(0.027)APSGQER;RDS(1)GDNSAPSGQER;RDS(1)GDNSAPSGQER 123.42 0.00010913 176481000 103409 97390 79549.9 89253.2 90660.6 104704 103091 115933.4 159593 TRUE FALSE 89743.23864 96750.23868 118020.4977 109519.5032 88856.63143 108732.0306 93093.25069 91141.9446 140726.0973 0.637715678 0.687507438 0.838653952 0.778245864 0.631415445 0.772650082 0.661520872 0.647654886 1 17.10253037 1.231357572 24.99817569 1.00000051 0.70744778 0.638619719 0.069285531 175.1457252 607789.9342 0.174752796 0.017540003 17.03560542 -1.231357572 -0.29255273 RDS(ph)GIGEETATGLGSHVEVTPHTAPPGVSAGPDAISEVLSTLSLEVNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDSGIGEETATGLGSHVEVTPHTAPPGVSAGPDAISEVLSTLSLEVNK 48 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 RDS(0.165)GIGEET(0.165)AT(0.165)GLGS(0.165)HVEVT(0.165)PHT(0.165)APPGVS(0.008)AGPDAISEVLSTLSLEVNK;RDS(0.161)GIGEET(0.161)AT(0.161)GLGS(0.161)HVEVT(0.161)PHT(0.161)APPGVS(0.034)AGPDAISEVLSTLSLEVNK 87.578 7.85E-06 62617000 24859 24857 18227.2 21426.1 22072 18245.6 28719 26986 47308 TRUE FALSE 21573.82017 24693.71273 27041.93489 26291.22348 21632.81038 18947.52004 25933.8358 21215.25391 41715.30213 0.517168019 0.591958142 0.648249767 0.630253699 0.518582134 0.454210303 0.621686395 0.508572462 1 15.34828907 1.234225798 24.99999812 1.000000645 0.562833895 0.830361447 0.062307622 53.42654173 308083.6088 0.119708849 0.015645572 17.14848659 -1.234225798 -0.43716675 RDS(ph)ICSSVSLESSAAETQEEMLQVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RDSICSSVSLESSAAETQEEMLQVLK 26 1 Q08378;Q08378-4;Q08378-2 Q08378 GOLGA3 Golgin subfamily A member 3 1 RDS(0.859)ICS(0.039)S(0.039)VS(0.059)LES(0.004)S(0.001)AAETQEEMLQVLK;RDS(0.571)ICS(0.101)S(0.101)VS(0.163)LES(0.054)S(0.011)AAETQEEMLQVLK;RDS(0.556)ICS(0.116)S(0.116)VS(0.15)LES(0.031)S(0.031)AAETQEEMLQVLK 212.39 4.26E-26 382376000 138074 116440 92609 108594 140134 126765 159561 169145 180865 TRUE FALSE 119827.1711 115675.098 137395.0222 133251.9275 137345.6076 131641.7316 144086.7988 132974.658 159483.3457 0.751345982 0.725311458 0.861500751 0.835522523 0.861190909 0.825426197 0.903459845 0.833783975 1 17.28304625 8 0.147160874 0.988376764 0.073418067 0.596698147 0.048116735 117.0124857 1.455534268 0.844606366 22.27595668 100000000 -8 -0.914958698 RDS(ph)IVAELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDSIVAELDR 10 1 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 1 RDS(1)IVAELDR;RDS(1)IVAELDR 133.93 0.00011279 665680000 474700 451990 350950 362050 483290 452380 451350 505040 487410 TRUE FALSE 411967.1923 449020.8479 520670.5939 444258.9861 473673.4745 469783.3513 407578.1465 397041.1262 429788.9451 0.958533711 1.044747319 1.21145646 1.033667783 1.102107162 1.093055921 0.948321615 0.923804883 1 18.71326885 2.235000156 24.93560323 0.950004346 1.078303815 0.407089072 0.065967968 79.39458361 556027.8365 0.026172398 0.018437582 171.7909005 -2.235000156 0.128299469 RDS(ph)LASLFPSEEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDSLASLFPSEEEER 15 1 Q6P597;Q6P597-3;Q6P597-2;K7ENJ3;K7EL76 Q6P597 KLC3 Kinesin light chain 3 1 RDS(1)LASLFPSEEEER 93.804 0.0028882 99261000 281730 289830 303970 300950 174590 271730 173900 189500 488330 TRUE FALSE 244498.6667 287926.0876 450970.9087 369285.2972 171116.0006 282183.6289 157035.2048 148976.8997 430600.1837 0.567809016 0.66866225 1.047307748 0.857605991 0.397389521 0.655326309 0.364689126 0.345975003 1 18.71598941 3.24600264 24.99015738 0.517871864 0.795723249 0.20041192 0.224619301 237.3493965 797009.6453 0.065631934 0.083035079 1761.986757 -3.24600264 0.277851385 RDS(ph)LEEGELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDSLEEGELR 10 1 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;A0A087X1I0;A0A087WYI9;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;J3KS35;E7ESP2;E9PFJ2 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 RDS(1)LEEGELR;RDS(1)LEEGELR 124.48 0.00046006 321990000 441450 376550 336660 404250 415170 418470 413540 461100 585730 TRUE FALSE 383111.264 374076.4183 499469.9021 496041.1411 406908.9293 434568.8117 373434.9545 362497.3533 516485.6667 0.741765529 0.724272603 0.967054721 0.960416083 0.787841668 0.841395686 0.723030625 0.701853656 1 18.97836879 1.217719956 24.55242576 1.000000893 0.805037475 0.295166096 0.094226712 1884.356709 2219816.762 1.077676441 0.025398994 16.50896915 -1.217719956 -0.194963418 RDS(ph)LGAYASQDANEQGQDLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDSLGAYASQDANEQGQDLGK 21 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RDS(0.999)LGAY(0.001)ASQDANEQGQDLGK;RDS(1)LGAYASQDANEQGQDLGK 324.87 9.80E-68 1451980000 543330 503320 519520 617370 568120 445670 644300 750500 1481290 TRUE FALSE 471527.5639 500013.6578 770761.6097 757553.2944 556815.5235 462815.2133 581815.8852 590011.4154 1306173.584 0.360999158 0.38280797 0.590091255 0.579979035 0.426295196 0.354329026 0.445435348 0.451709805 1 20.31691521 1.238561095 18.77429131 1.000012798 0.451691718 0.821222203 0.080791775 0.016784275 8430.026879 0.11733675 0.021075751 17.32052673 -1.238561095 -0.548321079 RDS(ph)LGAYASQDANEQGQDLGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RDSLGAYASQDANEQGQDLGKR 22 2 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RDS(1)LGAYASQDANEQGQDLGKR;RDS(0.996)LGAYAS(0.004)QDANEQGQDLGKR;RDS(1)LGAYASQDANEQGQDLGKR;RDS(1)LGAYASQDANEQGQDLGKR 238.1 1.20E-30 2295980000 1057796 1016589 769701 833751 1135913 944451 1327250 1515850 701080 TRUE FALSE 918005.5785 1009910.96 1141930.978 1023066.908 1113310.554 980784.6411 1198533.499 1191697.274 618199.1211 1.48496746 1.633633769 1.847189585 1.654914853 1.800893136 1.586518983 1.938749924 1.927691634 1 19.23771208 1.230067338 24.99869023 0.9999986 1.748327838 0.70658048 0.148470119 189.099713 556542.9926 0.431445015 0.038119614 16.98506988 -1.230067338 0.748329238 RDS(ph)LGTYSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RDSLGTYSSR 10 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RDS(1)LGTYSSR;RDS(1)LGTYSSR;RDS(1)LGTYSSR;RDS(1)LGTYSSR 177.21 1.44E-06 3053410000 472118 442100 292151 341346 460819 514835 458051 456527 568613 TRUE FALSE 409726.4101 439195.816 433436.2008 418853.8264 451649.6035 534641.0356 413629.2845 358902.2537 501392.2189 0.81717744 0.875952596 0.864465352 0.835381585 0.90079101 1.066312989 0.824961515 0.715811375 1 18.93558008 4.740553022 20.71091014 0.873279719 0.817177295 0.034516676 0.09587537 80.62253016 837226.5996 0.024734467 0.153456297 55024.10939 -4.740553022 -0.056102423 RDS(ph)LTGSSDLYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RDSLTGSSDLYK 12 1 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;Q14671-4;E9PR38;H0YDK8 Q5T1Z4 PUM1 Pumilio homolog 1 1 RDS(1)LTGSSDLYK;RDS(0.987)LT(0.012)GS(0.001)SDLYK;RDS(0.917)LT(0.082)GS(0.001)SDLYK;RDS(0.926)LT(0.074)GSSDLYK;RDS(0.862)LT(0.112)GS(0.014)S(0.012)DLYK;RDS(0.813)LT(0.185)GS(0.002)SDLYK 217.16 3.96E-11 2016890000 4419610 3325990 3276750 3813080 3833530 3243940 4784430 5131660 7176830 TRUE FALSE 3835547.341 3304141.353 4861397.26 4678898.093 3757250.253 3368736.471 4320436.715 4034294.444 6328393.333 0.606085485 0.522113778 0.768188228 0.739350076 0.593713136 0.532320969 0.682706729 0.637491103 1 22.59340784 1.23824701 9.556267256 1.00192269 0.636809093 0.675671722 0.079412549 0.049283975 77.66564371 0.114418145 0.020086629 17.30800492 -1.23824701 -0.365113597 RDS(ph)LTGSSDLYKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RDSLTGSSDLYKR 13 2 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;Q14671-4;E9PR38;H0YDK8 Q5T1Z4 PUM1 Pumilio homolog 1 1 RDS(1)LTGSSDLYKR;RDS(1)LTGSSDLYKR;RDS(1)LTGSSDLYKR 176.21 8.84E-06 1115870000 1610350 1170630 684300 760390 1213980 1069460 1697490 1815180 353815 TRUE FALSE 1397538.167 1162940.054 1015229.769 933048.1713 1189824.173 1110602.818 1532867.681 1427017.883 311987.3938 4.479469989 3.727522578 3.254073046 2.990659847 3.813693107 3.559768248 4.913235957 4.573960074 1 18.25112821 4.722695782 4.379130103 3.6173631 4.530059616 0.069397803 1.054807297 0.625939978 28.81341467 0.259630933 1.722329215 52807.52125 -4.722695782 0.912696516 RDS(ph)PLQGSGQQNSQAGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDSPLQGSGQQNSQAGQR 18 1 O95819-3;O95819-6;E7EN19;O95819;H7C360;O95819-2;A0A0D9SEY1;H7C0P6;A0A0D9SG62;G5E948;E7ENQ1;G3XAA2;C9J840;E7EX83;O95819-4;O95819-5 O95819-3 MAP4K4 Mitogen-activated protein kinase kinase kinase kinase 4 1 RDS(1)PLQGSGQQNSQAGQR 127.35 1.57E-05 162240000 76375 65696 71349 58598 50000 80561 48379 56547 57353 TRUE FALSE 66281.85024 65264.43865 105853.615 71903.57151 49005.09782 83660.2338 43687.21203 44454.8641 50572.79368 1.310622677 1.290504912 2.09309408 1.421783657 0.969001201 1.654253754 0.863848106 0.879027257 1 15.62607386 2.344916333 1.03681502 0.85137177 1.509861083 0.357183621 0.30835701 0.624371648 1.34191474 0.305760824 0.132932534 221.2668399 -2.344916333 0.658489313 RDS(ph)PPPPAR ddPTM_MDA-MB-175_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 127.56 0.00027075 8553077000 2178886 1928243 1454638 1443151 1825411 1981914 1926879 2184713 2217675 TRUE FALSE 1890940.695 1915576.245 2158105.802 1770840.492 1789088.892 2058159.514 1740010.571 1717529.126 1955503.988 0.966983809 0.979581866 1.103605933 0.905567313 0.914899128 1.052495687 0.889801597 0.8783051 1 20.89910905 3.701679329 24.9964216 0.934211098 1.013009783 0.241247396 0.063292984 782.3207109 530220.6025 0.017689507 0.026238475 5031.289748 -3.701679329 0.078798685 RDS(ph)PTYDPYKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RDSPTYDPYKR 11 2 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 RDS(0.995)PT(0.004)Y(0.001)DPYKR;RDS(0.972)PT(0.027)Y(0.001)DPYKR;RDS(0.836)PT(0.163)YDPYKR;RDS(0.992)PT(0.007)Y(0.001)DPYKR 97.797 0.0047242 2261120000 1922530 1326950 1183940 1397810 1341540 1110070 1621500 1903550 2877870 TRUE FALSE 1668462.789 1318233.178 1756497.344 1715204.125 1314845.979 1152775.111 1464247.18 1496490.646 2537651.487 0.65748303 0.519469748 0.69217438 0.675902161 0.518134971 0.454268491 0.577008776 0.589714803 1 21.27506252 1.238384237 7.287581854 1.007646079 0.582669131 0.749771278 0.075246868 0.054473134 18.81673674 0.114258228 0.01926217 17.31347472 -1.238384237 -0.424976948 RDS(ph)QDGSSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 RDSQDGSSYR 10 1 Q14847;Q14847-2;C9J9W2;Q14847-3;J3KSN1 Q14847 LASP1 LIM and SH3 domain protein 1 1 RDS(1)QDGSSYR;RDS(1)QDGSSYR;RDS(1)QDGSSYR;RDS(1)QDGSSYR;RDS(1)QDGSSYR;RDS(1)QDGSSYR;RDS(0.333)QDGS(0.333)S(0.333)YR;RDS(1)QDGSSYR 207.8 7.68E-08 10808662000 1837909 1040703 772145 914706 855871 948491 1092531 1197403 1666823 TRUE FALSE 1595024.669 1033866.553 1145556.905 1122403.978 838840.8416 984980.0625 986577.5118 941347.6867 1469773.084 1.085218315 0.703419164 0.779410725 0.763658003 0.570728129 0.670157913 0.671244781 0.640471442 1 20.48716201 4.739392269 24.48873303 0.712164711 1.085218472 0.490196387 0.114834407 43.50798817 1280842.243 0.027094464 0.158543353 54877.24103 -4.739392269 0.373053761 RDS(ph)QGTYSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDSQGTYSSR 10 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RDS(0.435)QGT(0.081)YS(0.048)S(0.435)R 75.819 0.040094 54507000 95801 94136 79281 93121 88899 121100 101140 110510 233370 TRUE FALSE 83140.65512 93517.61442 117621.5568 114265.5463 87130.08383 125758.7954 91331.45837 86878.29649 205781.2645 0.404024416 0.454451549 0.571585353 0.555276724 0.42341116 0.611128499 0.443827861 0.422187592 1 17.65075211 1.234174917 24.99854498 1.000000761 0.486642357 0.838518891 0.070922884 51.48983281 293454.2911 0.134154956 0.01747712 17.14647764 -1.234174917 -0.513358404 RDS(ph)SASTISSAYLSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDSSASTISSAYLSSR 16 1 A0A2R8YGX0;P10071 A0A2R8YGX0 GLI3 Transcriptional activator GLI3;Transcriptional repressor GLI3R 1 RDS(0.947)S(0.053)ASTISSAYLSSR 135.55 1.36E-05 307830000 79484 74628 46047 48286 85055 70974 73838 83627 61971 TRUE FALSE 68979.98801 74137.76375 68315.48322 59250.07431 83362.57191 73704.41571 66677.20212 65744.01684 54644.85898 1.26233262 1.356719829 1.250172194 1.084275363 1.525533663 1.348789567 1.220191677 1.203114402 1 15.73779815 1.146427386 1.414257744 0.821335106 1.299953843 0.415175657 0.111193003 1.63049342 2.411427129 1.198844424 0.032934506 14.00965325 -1.146427386 0.478618737 RDS(ph)SDDWEIPDGQITVGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RDSSDDWEIPDGQITVGQR 19 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 RDS(0.855)S(0.145)DDWEIPDGQITVGQR;RDS(0.862)S(0.138)DDWEIPDGQITVGQR;RDS(0.861)S(0.139)DDWEIPDGQITVGQR;RDS(0.5)S(0.5)DDWEIPDGQITVGQR;RDS(0.795)S(0.205)DDWEIPDGQITVGQR 334.62 2.26E-75 4665200000 2648790 2391680 1678589 1861549 2567840 2461230 2564300 2864760 2775300 TRUE FALSE 2298745.69 2375968.897 2490360.255 2284242.152 2516745.008 2555915.111 2315614.581 2252153.368 2447207.196 0.939334313 0.97088996 1.017633594 0.933407746 1.028415172 1.044421214 0.946227432 0.920295336 1 21.22270482 RDS(ph)SDTTPLLNGSSQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDSSDTTPLLNGSSQDR 17 1 B4DQA8;E9PCW1 B4DQA8 GOSR1 Golgi SNAP receptor complex member 1 1 RDS(0.654)S(0.067)DT(0.03)T(0.03)PLLNGS(0.161)S(0.058)QDR 256.33 4.55E-27 858720000 597110 464940 380340 395720 541210 629570 501080 654740 583600 TRUE FALSE 518200.4006 461885.7785 564273.6962 485574.2742 530440.9799 653789.9653 452485.3387 514728.9462 514607.4728 1.00698188 0.897549692 1.09651283 0.943581856 1.030768125 1.270463411 0.879282487 1.000236051 1 18.97311288 4.24614574 24.9987388 1.025959341 0.952265817 0.086929389 0.105623339 472.8315356 1558301.781 0.026054579 0.066191778 17625.67425 -4.24614574 -0.073693525 RDS(ph)SESQLASTESDKPTTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDSSESQLASTESDKPTTGR 20 2 Q96B23-2;Q96B23;A0A087WVF1;K7EQH1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 RDS(0.817)S(0.183)ESQLASTESDKPTTGR;RDS(0.976)S(0.024)ESQLASTESDKPTTGR 238.07 6.69E-30 1018960000 1116180 453080 423020 505430 501180 450020 675410 725910 718460 TRUE FALSE 968673.985 450103.6876 627593.8869 620195.6065 491207.4985 467332.5606 609908.8422 570679.7955 633524.4773 1.529023771 0.710475607 0.990638735 0.978960764 0.77535678 0.737670883 0.962723405 0.900801494 1 19.27304084 4.748283816 24.99864236 0.885893719 1.529024115 0.781904763 0.107361412 621.3542376 1597488.497 0.025824275 0.330962597 56012.35286 -4.748283816 0.643130396 RDS(ph)SGGTKDGDRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RDSSGGTKDGDRPK 14 3 Q9Y478;F5H4Y8 Q9Y478 PRKAB1 5-AMP-activated protein kinase subunit beta-1 1 RDS(0.828)S(0.114)GGT(0.058)KDGDRPK;RDS(0.963)S(0.019)GGT(0.019)KDGDRPK;RDS(0.864)S(0.113)GGT(0.024)KDGDRPK 118.48 0.0013427 288235000 643530 453260 131596 106885 320681 259810 770610 802590 34783.2 TRUE FALSE 558485.88 450282.5052 195236.2658 131154.8729 314300.0755 269805.0588 695876.3608 630962.3743 30671.16972 18.20882233 14.68096944 6.365465274 4.276161427 10.24741079 8.796699352 22.68828894 20.57183929 1 14.90459557 -1.957063771 1.25E-12 9.874519435 15.144131 0 7.170248385 0 0.459100464 341705213.8 341705214.6 0.011039165 1.957063771 5.26961156 RDS(ph)SSHEETPGSHPLYGHGECK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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)HEET(0.001)PGSHPLYGHGECK;RDS(0.333)S(0.333)S(0.333)HEETPGSHPLYGHGECK 215.93 5.23E-26 1007990000 535420 402920 226410 320640 440860 385880 499810 586580 532580 TRUE FALSE 464662.8904 400273.192 335902.6333 393446.2127 432087.7485 400725.0533 451338.5031 461144.4318 469618.9991 0.989446533 0.852336027 0.715266277 0.837798755 0.92008149 0.853298214 0.961073773 0.981954377 1 18.84113125 2.148538084 1.278502902 1.004058841 0.84834905 0.391674069 0.069413755 0.512874779 1.592071419 0.069448377 0.025543593 140.7790676 -2.148538084 -0.155709791 RDS(ph)TEAPKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RDSTEAPKPK 10 2 Q8N201 Q8N201 INTS1 Integrator complex subunit 1 1 RDS(0.824)T(0.176)EAPKPK;RDS(0.98)T(0.02)EAPKPK;RDS(0.969)T(0.031)EAPKPK;RDS(0.966)T(0.034)EAPKPK 150.21 1.15E-05 402501000 1049550 633980 559143 603661 558610 539070 790090 912360 938300 TRUE FALSE 910849.3083 629815.3436 829546.425 740731.4564 547494.7539 559808.3717 713467.1934 717258.914 827375.2429 1.100890214 0.76122092 1.002624181 0.89527873 0.661724844 0.676607593 0.862326012 0.866908842 1 19.65818226 4.749667591 24.33392966 0.839908433 1.100890436 0.331865213 0.115955669 1478.621758 3239376.505 0.029486282 0.427787244 56191.10734 -4.749667591 0.260982002 RDS(ph)TSSLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDSTSSLQR 9 1 Q96CC6;F8WCF7;B8ZZ07;A0A1B0GXG1;F8WBS4 Q96CC6 RHBDF1 Inactive rhomboid protein 1 1 RDS(0.376)T(0.305)S(0.305)S(0.013)LQR 87.777 0.014016 197690000 225480 198470 133290 180090 252550 240150 206690 267980 212590 TRUE FALSE 195682.2467 197166.2375 197749.4898 220982.187 247524.7491 249388.7259 186645.2356 210674.5624 187457.8524 1.043873299 1.051789696 1.054901074 1.178836652 1.320428811 1.330372256 0.995665069 1.123850294 1 17.51620673 3.74809795 21.45712196 1.158390985 1.050348091 0.176195822 0.110089388 196.7913821 442730.8723 0.031911201 0.054080737 5598.838626 -3.74809795 -0.108042894 RDSFDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDSFDDR 7 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 117.81 0.0082532 142640000 330310 301900 230430 298470 278240 325690 309810 324530 549870 FALSE TRUE 286658.6966 299916.799 341866.7187 366242.1753 272703.5684 338219.505 279764.6739 255131.785 484864.995 0.59121343 0.618557335 0.705076098 0.755348765 0.562431958 0.697553976 0.576994992 0.526191389 1 18.88722358 1.228811458 24.99887925 1.000000745 0.627932861 0.727826284 0.071262907 229.289582 587904.3318 0.240138727 0.018600012 16.93602392 -1.228811458 -0.372067885 RDSFDDRGPSLNPVLDYDHGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDSFDDRGPSLNPVLDYDHGSR 22 2 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 145.13 5.71E-08 486760000 114284 107886 51337 60123 96573 112167 78677 103345 63550 FALSE TRUE 99181.07984 107177.2898 76163.74491 73774.84607 94651.38624 116482.1371 71046.91665 81245.47598 56037.1914 1.769915254 1.912609949 1.359164209 1.316533613 1.689081553 2.078657659 1.267852918 1.44984918 1 15.77409703 1.242825428 1.244329073 0.72733738 1.650851517 0.392901814 0.254537448 1.673112175 2.221433851 2.034429754 0.081746952 17.49143448 -1.242825428 0.923514137 RDSFIGT(ph)PYWMAPEVVMCETMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDSFIGTPYWMAPEVVMCETMK 22 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 RDS(0.343)FIGT(0.35)PY(0.307)WMAPEVVMCETMK 78.413 0.0051119 28424000 34859 31807 22417 25963 28095 25928 36043 42573 29240 TRUE FALSE 30252.29483 31598.05772 33257.93618 31858.29597 27535.96447 26925.46694 32547.55541 33469.09525 25783.28051 1.173329934 1.225525112 1.289903206 1.235618406 1.067977539 1.0442995 1.262351212 1.298092973 1 14.65414821 3.376586924 23.53013063 1.159306822 1.234942141 0.173600716 0.096455282 18.62700828 4324.418644 0.030309102 0.039128882 2380.054623 -3.376586924 0.07563532 RDSGDNS(ph)APSGQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDSGDNSAPSGQER 14 1 Q8IXQ3 Q8IXQ3 C9orf40 Uncharacterized protein C9orf40 1 RDS(0.031)GDNS(0.969)APSGQER 200.81 1.98E-08 179740000 106560 104680 78786 100720 98026 109450 117120 117950 169820 TRUE FALSE 92477.82601 103992.3502 116887.1731 123590.0154 96075.47438 113660.6123 105761.7204 92727.31039 149744.0731 0.61757253 0.69446722 0.78057963 0.825341617 0.641597844 0.759032461 0.706283182 0.619238602 1 17.19213938 RDSIVAELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDSIVAELDR 10 1 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 0 ; 210.95 1.09E-07 894790000 624000 578830 360370 436460 652850 682150 579140 707760 678510 FALSE TRUE 541536.819 575027.6276 534646.1374 535564.9139 639859.5623 708392.7519 522975.0919 556411.0318 598297.3208 0.905129942 0.961106807 0.893612789 0.895148441 1.069467537 1.184014582 0.874105689 0.929990847 1 19.19050308 3.261949988 24.99394285 0.999644334 0.915693801 0.246988642 0.083375317 437.5150205 467526.6668 0.026490759 0.03417875 1827.889712 -3.261949988 -0.083950533 RDSLGT(ph)YSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDSLGTYSSR 10 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RDS(0.296)LGT(0.704)YSSR 159.36 1.49E-05 724800000 534520 561970 426300 497910 567210 591930 581560 656820 897670 TRUE FALSE 463881.8277 558278.3821 632460.1059 610968.0756 555923.6307 614701.9301 525160.4007 516364.1544 791548.4752 0.586043486 0.705299043 0.799016265 0.771864383 0.702324176 0.776581535 0.663459557 0.65234685 1 19.59431818 -1.877168661 0.025126526 1.697391265 1.39E-06 0.177052611 0.101785476 11893.53799 30.4077706 1359.768347 773.8421419 0.013268791 1.877168661 -1.697389875 RDSS(ph)DDWEIPDGQITVGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDSSDDWEIPDGQITVGQR 19 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 RDS(0.388)S(0.612)DDWEIPDGQITVGQR;RDS(0.495)S(0.505)DDWEIPDGQITVGQR 191.18 6.25E-15 2000340000 1117880 1062400 720840 882350 1108480 1001460 1126710 1255330 1205290 TRUE FALSE 970149.3257 1055421.024 1069440.635 1082701.053 1086423.417 1039986.814 1017441.838 986887.4485 1062801.989 0.912822271 0.993055183 1.006246362 1.018723209 1.022225615 0.978532996 0.957320223 0.928571322 1 20.0194414 0.932098689 22.61512846 1.778673565 0.97731422 0.037859795 0.036136948 1013.061892 746086.3184 49754.08899 0.009364566 8.552610396 -0.932098689 -0.801359345 RDSSGGT(ph)KDGDRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDSSGGTKDGDRPK 14 3 Q9Y478;F5H4Y8 Q9Y478 PRKAB1 5-AMP-activated protein kinase subunit beta-1 1 RDS(0.281)S(0.281)GGT(0.437)KDGDRPK 106.36 0.00097345 124820000 221150 155260 48454 39769 113360 98098 276190 279250 18613 TRUE FALSE 191924.4672 154240.0868 71886.51647 48799.15928 111104.3578 101871.8935 249405.1363 219534.5606 16412.59234 11.69373266 9.397667572 4.379961128 2.973275535 6.769458197 6.20693498 15.19596241 13.37598327 1 14.00251551 4.479053778 24.79014389 7.855530947 11.119718 0.089079403 4.365248516 179.8114277 2306531.365 1.206505476 3.305881661 30133.79141 -4.479053778 3.264187056 RDVEQLEQLIESHDVVFLLMDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RDVEQLEQLIESHDVVFLLMDTR 23 1 O95352-3;O95352-2;O95352 O95352-3 ATG7 Ubiquitin-like modifier-activating enzyme ATG7 0 132.1 1.83E-05 99360000 40486 29959 21766 18016 29301 28336 32447 42764 26011 FALSE TRUE 35135.67252 29762.19736 32292.1104 22106.80816 28717.96743 29426.10426 29300.29493 33619.25139 22936.00921 1.5319 1.297618826 1.407921932 0.963847196 1.252090857 1.282965314 1.277480082 1.4657847 1 14.48532677 4.917508033 1.471771874 1.249575993 1.736993305 0.266635022 0.15467631 2.800384331 4.034674911 0.043006622 2.252442601 82700.48051 -4.917508033 0.487417312 RDVQEIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RDVQEIFR 8 1 O00148;O00148-2;O00148-3;K7EQN7;Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;F6S4E6;A0A0A0MT12;F6TRA5;A0A140T9K1;A0A140T973;A0A140T9L4 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ;;; 204.07 0.00014514 1995740000 1272320 1492940 894040 844520 1391810 1738230 1114830 1349790 1279650 FALSE TRUE 1104179.688 1483132.779 1326400.734 1036281.174 1364115.704 1805100.833 1006713.958 1061147.913 1128371.235 0.978560649 1.314401443 1.175500308 0.918386735 1.208924565 1.599740207 0.892183288 0.940424463 1 20.10581036 RDVYLS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RDVYLSPR 8 1 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 1 RDVYLS(1)PR;RDVYLS(1)PR;RDVYLS(1)PR;RDVYLS(1)PR;RDVYLS(1)PR;RDVYLS(1)PR 127.56 0.00071735 3444000000 2862750 2842910 1747080 2060340 2795540 2930890 2779460 3026250 2865620 TRUE FALSE 2484430.334 2824234.737 2591973.732 2528171.687 2739914.223 3043643.235 2509908.397 2379109.988 2526849.668 0.983212561 1.117690052 1.025772829 1.000523189 1.084320234 1.204520899 0.993295497 0.941532066 1 21.2689084 2.018435494 24.99975851 0.966836905 1.069760092 0.315611876 0.063795666 253.4176331 343649.9047 0.026066635 0.01757107 104.336315 -2.018435494 0.102923187 RDWGDHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDWGDHGR 8 1 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 ; 101.43 0.0086583 200375000 287490 267390 149305 172817 212967 280670 230290 259150 236250 FALSE TRUE 249497.4681 265633.4975 221509.3974 212057.7412 208729.3734 291467.5565 207956.5112 203732.7892 208320.7941 1.197659932 1.275117535 1.063309106 1.017938426 1.001961298 1.399128482 0.998251337 0.977976251 1 17.66844733 -2 0.200730414 1.17E-10 1.225220655 0.181892136 0.128802284 178.9278508 2.664178779 66.77516703 0.855320654 0.01 2 1.225220655 RDYDDMS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 15 RDYDDMSPR 9 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 RDYDDMS(1)PR;RDYDDMS(1)PR;RDY(0.01)DDMS(0.99)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 158.25 4.10E-05 18121508000 13880144 12843186 7395122 8680398 12124666 11716671 12200481 14075619 12093354 TRUE FALSE 12045847.8 12758818.27 10971427.73 10651415.04 11883408.87 12167418.92 11017280.23 11065657.41 10663691.47 1.129613309 1.196472939 1.028858324 0.998848764 1.11438041 1.141013781 1.033158195 1.037694822 1 23.34620361 8 0.327313881 1.03415325 2.32798222 0.280951576 0.056770602 108.0831126 1.691915867 0.093805216 83.10292862 100000000 -8 1.29382897 RDYDDMSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 RDYDDMSPR 9 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;; 201.84 3.34E-05 2575796000 914006 881374 623995 654560 782720 823154 970839 1039020 796538 FALSE TRUE 793217.7913 875584.1962 925761.0691 803187.8523 767145.4034 854821.267 876687.1832 816833.6587 702372.1851 1.129341122 1.246610009 1.318049161 1.143535962 1.092220648 1.21704886 1.248180383 1.162964132 1 19.42187619 1.257915832 3.514813207 0.975880592 1.200355689 0.473978645 0.065488798 0.259068878 4.759832811 0.151393973 0.017401074 18.1098908 -1.257915832 0.224475097 RDYEVDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RDYEVDGR 8 1 A0A590UJD9;A0A0C4DFT3;A0A590UJ18;F8VYC1;E9PIW2;E9PN83;A0A3B3ISW2;B7Z2T4;A0A3B3ITF1;F8W750;Q15700-2;Q15700-4;Q15700;Q15700-3;B5MCC5;H7C325;Q15700-5;A0A590UJ08;Q12959-4;Q12959-2;A0A590UJC5;Q12959;Q12959-3;Q12959-5;Q12959-7;Q12959-6;A0A590UKA8;A0A590UJR5;A0A590UJ68;A0A590UJS9;A0A590UK48;A0A590UJ81;C9JUA9;Q12959-8;A0A590UJX2;A0A590UK81;A0A590UJ29;Q12959-9;A0A590UJR4 A0A590UJD9;A0A590UJ08;Q12959 DLG1;DLG2 Disks large homolog 2;Disks large homolog 1 0 ; 126.31 0.0019634 704720000 810330 803880 535480 626330 799310 914310 646060 780170 794190 FALSE TRUE 703242.8374 798599.2593 794439.9191 768547.7994 783405.2948 949484.0973 583405.2006 613336.7168 700301.7629 1.004199724 1.140364485 1.134425131 1.097452327 1.118668175 1.355821372 0.83307687 0.875817753 1 19.41761719 2.212214771 24.99999999 0.894397133 1.138350271 0.579376984 0.095816402 148.7463577 141146.7074 0.038264981 0.025807092 163.0101966 -2.212214771 0.243953138 RDYYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RDYYDR 6 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 ;; 105.04 0.05342 1063190000 1020000 849850 558230 649370 770870 903990 760820 849860 812130 FALSE TRUE 885204.4156 844267.2794 828191.8952 796819.3835 755531.1952 938767.0803 687035.7935 668124.0526 716120.9166 1.236110265 1.178945147 1.156497284 1.112688325 1.055032995 1.310905824 0.959385179 0.932976593 1 19.44984368 2.207461593 24.4159289 0.957434642 1.16607739 0.668902429 0.069707568 87.88224252 68995.80777 0.02777654 0.018729515 161.235843 -2.207461593 0.208642748 REALEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 REALEK 6 1 O43707;O43707-2;F5GXS2;O43707-3;Q9Y2J4;Q9Y2J4-2;Q9Y2J4-4;Q9Y2J4-3;Q4VCS5;E7ERM3;Q4VCS5-2;A6NP16 O43707;Q9Y2J4;Q4VCS5 ACTN4;AMOTL2;AMOT Alpha-actinin-4;Angiomotin-like protein 2;Angiomotin 0 ; 96.19 0.068129 586900000 979810 836310 672780 918630 573080 707830 825860 1080480 1774610 FALSE TRUE 850325.626 830816.2245 998138.6583 1127218.982 561676.8292 735060.6781 745768.2243 849427.7603 1564817.627 0.543402382 0.530934858 0.637862611 0.720351664 0.35894076 0.469742074 0.476584754 0.542828599 1 20.5775631 1.239080188 7.554448214 1.007277407 0.533508435 0.696653768 0.096430016 0.059099299 24.75013931 0.144043499 0.024801822 17.34124157 -1.239080188 -0.473768973 RECPSDECGAGVFMASHFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RECPSDECGAGVFMASHFDR 20 1 P62979 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ; 123.53 1.85E-05 1028660000 596194 536256 330509 346104 499850 507561 503064 615333 419752 FALSE TRUE 517405.4523 532733.299 490344.2579 424692.2031 489903.9629 527087.2001 454276.9307 483748.8265 370129.3967 1.397904238 1.439316368 1.324791444 1.14741549 1.323601873 1.424061976 1.22734626 1.306972185 1 18.4976702 0.687649771 1.548319844 3.60E-14 1.329929476 0.569447991 0.088266089 4.151211907 2.605297446 13.12236258 0.025899583 4.871354904 -0.687649771 1.329929476 REDEGEPGDEGQLEDEGS(ph)QEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 REDEGEPGDEGQLEDEGSQEK 21 1 Q969E4 Q969E4 TCEAL3 Transcription elongation factor A protein-like 3 1 REDEGEPGDEGQLEDEGS(1)QEK;REDEGEPGDEGQLEDEGS(1)QEK 277.75 4.57E-45 781080000 655180 460670 465410 499790 514550 467280 572750 635360 949460 TRUE FALSE 568596.303 457643.8284 690483.8327 613274.9583 504311.4617 485256.564 517204.7932 499493.2084 837215.9204 0.679151327 0.546625807 0.824738058 0.732517076 0.602367262 0.579607425 0.617767508 0.596612172 1 19.67524022 1.233775288 24.99928436 1.000000538 0.645174523 0.648085936 0.081635394 98.3143376 513546.4774 0.164138858 0.020630582 17.13070704 -1.233775288 -0.354826015 REDEGEPGDEGQLEDEGS(ph)QEKQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 REDEGEPGDEGQLEDEGSQEKQGR 24 2 Q969E4 Q969E4 TCEAL3 Transcription elongation factor A protein-like 3 1 REDEGEPGDEGQLEDEGS(1)QEKQGR 108.5 0.0012096 150610000 68579 61867 43588 25398 59072 42930 65774 75831 19939 TRUE FALSE 59516.11139 61460.5916 64667.30259 31165.00408 57896.58277 44581.54488 59395.2476 59615.13077 17581.83413 3.385091165 3.495687147 3.678074887 1.772568427 3.292977418 2.535659507 3.378216809 3.390723079 1 14.10179796 3.839255007 24.99588709 2.728043306 3.517233619 0.244384565 0.757255146 67.13661407 16653.55687 0.195888975 0.339289653 6906.45215 -3.839255007 0.789190313 REDEGEPGDEGQLEDEGSQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 REDEGEPGDEGQLEDEGSQEK 21 1 Q969E4 Q969E4 TCEAL3 Transcription elongation factor A protein-like 3 0 213.48 7.19E-32 0 70034 58595 43309 50344 73783 48926 69482 71603 71358 FALSE TRUE 60778.82946 58210.08559 64253.37726 61775.37466 72314.86265 50808.21488 62743.64633 56291.25567 62922.13853 0.965937123 0.925112956 1.021156921 0.981774875 1.149275348 0.80747756 0.997163285 0.894617649 1 15.94128008 0.932096475 21.68788985 2.009214646 0.966018638 0.012669418 0.088032921 1291.629243 632594.4164 34723.50747 0.019869734 8.552566796 -0.932096475 -1.043196009 REDIFYTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 REDIFYTSK 9 1 S4R3P0;P52895;B4DK69;H0Y804;Q04828;A6NHU4;P52895-2;S4R3D5;P17516;A0A0A0MSS8;P42330;S4R3Z2 S4R3P0;A0A0A0MSS8 AKR1C2;AKR1C1;AKR1C3;AKR1C4 Aldo-keto reductase family 1 member C2;Aldo-keto reductase family 1 member C1;Aldo-keto reductase family 1 member C4;Aldo-keto reductase family 1 member C3 0 ;;; 192.5 5.56E-05 2194380000 3798580 3887060 2613910 3167040 3737270 3586580 4459740 4707760 4920900 FALSE TRUE 3296588.029 3861525.647 3878005.619 3886164.837 3662905.639 3724558.053 4027235.101 3701042.16 4339156.808 0.759730098 0.889925351 0.893723318 0.895603687 0.844151479 0.858359865 0.928114673 0.852940404 1 22.04898329 -1.056255995 0.019880121 1.934787542 1.91E-06 0.352507014 0.049599605 8018.133549 19.53563865 1143.571291 789.0012881 0.087850453 1.056255995 -1.934785629 REDLVEEIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 REDLVEEIK 9 1 B3KWE1;P12081-4;P12081;B4DDD8;P12081-3;P12081-2;B4E1C5 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 ; 141.1 0.00017242 435260000 830410 721040 547570 570880 653310 547370 936110 861800 811380 FALSE TRUE 720669.2145 716303.4408 812376.6835 700507.0294 640310.4092 568427.6781 845326.1963 677510.7765 715459.5807 1.007281521 1.001179466 1.135461325 0.979100774 0.894963778 0.794493069 1.181514958 0.946958843 1 19.44851074 3.507111289 24.04141073 0.966455402 1.045625731 0.125847018 0.10217319 979.0812081 784873.807 0.028351748 0.041971034 3214.484151 -3.507111289 0.079170329 REDS(ph)FESLDSLGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 REDSFESLDSLGSR 14 1 E9PMS6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 REDS(0.997)FES(0.003)LDSLGSR;REDS(0.654)FES(0.345)LDSLGSR;REDS(1)FESLDSLGSR;REDS(1)FESLDSLGSR 204.18 1.48E-08 1379130000 1303100 1010529 676587 858932 1058030 988890 1212820 1205950 1064937 TRUE FALSE 1130892.033 1003890.768 1003786.736 1053965.639 1036977.273 1026933.238 1095200.903 948066.9772 939041.361 1.204304816 1.06905916 1.068948374 1.122384681 1.104293502 1.09359745 1.166296767 1.009611521 1 19.84082918 1.636096495 6.530861494 1.001988232 1.113016983 0.559404044 0.041692061 0.088108607 7.723806196 0.02511478 0.010240642 43.26099412 -1.636096495 0.111028751 REDS(ph)MEDRGEEDDSLAIKPPQQMSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 REDSMEDRGEEDDSLAIKPPQQMSR 25 3 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;Q9UQ88-9;A0A087X1I0;A0A087WYI9;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;J3KS35;E7ESP2;E9PFJ2 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 REDS(1)MEDRGEEDDSLAIKPPQQMSR 148.75 1.14E-06 307260000 176350 133670 88929 102730 124270 124480 152720 177460 94087 TRUE FALSE 153044.9007 132791.913 131935.3618 126056.4166 121797.2701 129268.8261 137909.2379 139511.56 82964.14204 1.844711425 1.60059406 1.590269707 1.519408428 1.468071231 1.558128885 1.662275225 1.681588655 1 16.3402003 1.234477371 24.98900999 0.999999107 1.610231613 0.780920592 0.102440065 58.61184833 358647.8314 0.194294034 0.025967855 17.15842305 -1.234477371 0.610232506 REDS(ph)PGPEVQPMDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 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 226.79 2.40E-12 16061690000 19745490 15335730 11503410 13294350 14633750 13294310 18481400 20645570 18718120 TRUE FALSE 17136073.47 15234988.58 17066497.55 16313035.36 14342567.01 13805750.71 16689076.67 16230675.52 16505285.18 1.038217352 0.92303698 1.03400198 0.988352227 0.868968143 0.83644424 1.011135312 0.98336232 1 23.97642473 4.755925034 22.77545309 0.957461845 1.03821758 0.144077013 0.063100668 2284.953377 2996810.362 0.016320272 0.408099333 57006.58614 -4.755925034 0.080755735 REDS(ph)YHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 REDSYHVR 8 1 B1AVT0;P49760-3;P49760;P49760-2 B1AVT0 CLK2 Dual specificity protein kinase CLK2 1 REDS(1)YHVR 117.45 0.0012724 493100000 124040 122300 87762 79221 122600 122600 107070 127820 148800 TRUE FALSE 107647.7997 121496.6032 130203.9967 97209.33887 120160.4999 127316.5013 96686.36788 100486.6877 131209.0335 0.820429789 0.925977427 0.992340186 0.740873828 0.915794413 0.970333352 0.736888043 0.765851901 1 17.00150752 2.239854183 24.99999935 0.815941145 0.894192393 0.065529582 0.099158061 74.4301903 1438518.882 0.038071029 0.027827877 173.7217451 -2.239854183 0.078251248 REDYVGGQSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 REDYVGGQSHR 11 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 0 ; 107.37 0.0014321 60439000 77291 63167 42216 51616 64933 63155 60530 66565 58193 FALSE TRUE 67076.79852 62752.05182 62631.7988 63336.2017 63640.96034 65584.61372 54659.80992 52330.59276 51313.48983 1.307196192 1.2229153 1.220571803 1.234299244 1.240238396 1.278116416 1.065213263 1.019821356 1 15.64705053 2.147636986 4.443224801 1.020036069 1.246730739 0.934226057 0.027962924 0.048437961 1.717182671 0.0121407 0.007981329 140.4872741 -2.147636986 0.226694669 REEAAVDAQQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 166.6 8.25E-05 597090000 1122220 947060 647380 769760 900490 858310 1060580 1170310 1163480 FALSE TRUE 973915.7837 940838.7005 960455.1334 944545.773 882572.0108 891329.7411 957725.1148 920048.3139 1025934.72 0.949296056 0.917055133 0.936175679 0.920668494 0.860261373 0.868797716 0.933514673 0.896790308 1 19.9685075 1.233742691 24.91672161 1.000000144 0.90925294 0.494444909 0.028480449 129.9682328 672068.1822 0.057367286 0.007239354 17.12942128 -1.233742691 -0.090747204 REEDEENDNDNES(ph)DHDEADS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 REEDEENDNDNESDHDEADS 20 1 H0YBP8;Q9NRG0 H0YBP8 CHRAC1 Chromatin accessibility complex protein 1 1 REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(0.998)DHDEADS(0.002);REEDEENDNDNES(0.998)DHDEADS(0.002);REEDEENDNDNES(0.998)DHDEADS(0.002);REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS 349.3 2.85E-95 4701641000 2920442.2 2778192 2037246.7 2147804.8 2644547.7 2738958.8 2718449.2 2952419.6 2922420.5 TRUE FALSE 2534498.364 2759941.874 3022466.018 2635496.707 2591926.375 2844328.317 2454814.415 2321067.644 2576935.278 0.983532022 1.071017149 1.172891708 1.022725223 1.005817413 1.103763972 0.952610039 0.900708553 1 21.29722487 2.167937593 6.967779852 0.939214156 1.061291306 0.435518368 0.057972329 0.18590498 14.97285481 0.023957076 0.016136683 147.210095 -2.167937593 0.122077151 REEDEPEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 REEDEPEER 9 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 129.88 0.0006044 244960000 177416 141251 90973 108276 134170 149818 131774 143102 159511 FALSE TRUE 153970.0261 140323.1129 134967.8471 132861.7207 131500.2795 155581.5954 118994.5778 112500.7509 140653.7913 1.094673842 0.99764899 0.959574896 0.944601062 0.934921685 1.106131544 0.846010454 0.799841582 1 17.10178892 8 0.203375642 0.851410759 1.903107636 0.238230161 0.083213589 140.3585495 2.094734313 0.548215568 45.73501796 100000000 -8 1.051696877 REEDEPEERS(ph)GDETPGSEVPGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 REEDEPEERSGDETPGSEVPGDK 23 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 REEDEPEERS(0.962)GDET(0.037)PGS(0.002)EVPGDK 46.578 0.08416 806820000 292630 205160 142340 125830 156270 166460 229410 242430 114340 TRUE FALSE 253958.2041 203812.2905 211176.1001 154401.6247 153160.5327 172863.8239 207161.8535 190588.2311 100822.8555 2.518855501 2.021488972 2.094526079 1.531414916 1.519105287 1.714530134 2.054711232 1.890327647 1 16.62146319 4.559082779 1.145970507 1.680081096 2.715382297 0.482905801 0.295674779 1.18458358 1.64369691 0.093911137 1.371478244 36231.20505 -4.559082779 1.035301201 REEEEFNTGPLSVLTQSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 REEEEFNTGPLSVLTQSVK 19 1 P62316;P62316-2;K7ERG4 P62316 SNRPD2 Small nuclear ribonucleoprotein Sm D2 0 195.93 1.38E-15 109550000 159050 156450 98942 111030 122830 118750 134910 156450 136840 FALSE TRUE 138031.1395 155422.2696 146790.6821 136241.0585 120385.9233 123318.3893 121826.449 122994.385 120662.9311 1.143939885 1.288069735 1.216535027 1.1291045 0.997704284 1.022007241 1.009642712 1.019322039 1 16.88062301 3.46118279 2.667369668 1.011028583 1.223078431 0.875265064 0.035775176 0.081381052 1.169641048 0.010195072 0.014841809 2891.896795 -3.46118279 0.212049848 REEEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 REEEMR 6 1 Q15233;Q15233-2;H7C367;P49755 Q15233;P49755 NONO;TMED10 Non-POU domain-containing octamer-binding protein;Transmembrane emp24 domain-containing protein 10 0 ; 104.21 0.054559 227714000 88772 107627 52056 66117 82563 94570 102244 102773 87628 FALSE TRUE 77040.55528 106919.9912 77230.45572 81129.87539 80920.15783 98208.16909 92328.39262 80795.79373 77268.71767 0.997047157 1.383742275 0.99950482 1.049970516 1.047256384 1.270995198 1.194900024 1.045646882 1 16.23759684 1.571441219 5.1072934 1.010570449 1.137553481 0.129201933 0.123176038 0.283413931 15.4417225 0.086262075 0.030891381 37.2770228 -1.571441219 0.126983032 REEGDPS(ph)PHSGGVCKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 REEGDPSPHSGGVCKPK 17 2 O75376;O75376-2;E7EVK1;J3KRE4 O75376 NCOR1 Nuclear receptor corepressor 1 1 REEGDPS(0.999)PHS(0.001)GGVCKPK;REEGDPS(1)PHSGGVCKPK 64.723 0.023355 137928000 232880 171703 123723 136516 139264 115067 215840 225400 208400 TRUE FALSE 202104.318 170575.0717 183555.8566 167514.0443 136492.9189 119493.7019 194907.87 177199.9641 183763.1894 1.099808501 0.928233082 0.998871739 0.911575625 0.742765291 0.650259186 1.06064697 0.96428433 1 17.48748828 5.274583056 1.095956628 0.898686513 1.487258981 0.205934236 0.122598729 9.171723816 4.023535747 0.040410639 8.290342386 188184.1563 -5.274583056 0.588572468 REELITNWEQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 REELITNWEQIR 12 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 202.13 2.25E-07 202560000 79958 82199 51184 64811 66574 83586 69886 68930 142710 FALSE TRUE 69391.34771 81659.02936 75936.7536 79527.32812 65249.30765 86801.60751 63108.46648 54189.85591 125838.9864 0.551429646 0.648916776 0.60344378 0.631976865 0.51851425 0.689783111 0.501501707 0.430628516 1 16.94121943 1.226949553 24.98838773 1.000000959 0.569356694 0.75550009 0.07650109 283.988686 611137.6593 0.318231328 0.020287992 16.86357128 -1.226949553 -0.430644265 REELSNVLAAMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 REELSNVLAAMR 12 1 Q9Y3U8 Q9Y3U8 RPL36 60S ribosomal protein L36 0 ; 215.34 6.68E-11 518350000 332840 371650 281070 284950 330400 386090 362660 375580 495540 FALSE TRUE 288854.3507 369208.6067 416996.3921 349652.2527 323825.6864 400943.1321 327489.289 295265.1398 436957.8257 0.661057735 0.844952499 0.954317253 0.800196797 0.741091399 0.917578559 0.749475738 0.675729149 1 18.73713451 3.514565255 24.99558738 0.796546628 0.831704058 0 0.115594839 3226.321137 2153708.661 0.031779657 0.047120753 3270.131783 -3.514565255 0.03515743 REEQT(ph)DT(ph)SDGESVTHHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 REEQTDTSDGESVTHHIR 18 1 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 2 REEQT(1)DT(0.539)S(0.461)DGESVTHHIR;REEQT(1)DT(0.536)S(0.465)DGESVTHHIR;REEQT(1)DT(0.661)S(0.339)DGESVTHHIR 104.97 0.0002171 700909000 314743 270251 249519 184898 270867 336694 312827 294541 225117 TRUE FALSE 273148.9151 268475.7034 370187.223 226881.9169 265477.2766 349646.8361 282489.0857 231555.6993 198503.9247 1.376037857 1.352495694 1.864886165 1.142959351 1.337390568 1.761410192 1.423090682 1.166504388 1 17.59880801 1.629147628 2.891073911 1.025316059 1.472594882 0.381161218 0.208329445 0.230729776 4.386438476 0.19008783 0.055376702 42.57431093 -1.629147628 0.447278823 REEQTDT(ph)SDGESVTHHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 REEQTDTSDGESVTHHIR 18 1 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 1 REEQT(0.029)DT(0.485)S(0.485)DGESVTHHIR;REEQT(0.015)DT(0.493)S(0.493)DGESVTHHIR 131.56 1.27E-05 545830000 262660 237160 120792 183885 262680 276020 238640 275320 289970 TRUE FALSE 227948.8155 235602.0803 179207.4152 225638.8998 257453.1819 286638.668 215496.7295 216444.9605 255690.0769 0.891504349 0.921436151 0.700877474 0.882470303 1.006895477 1.121039469 0.84280443 0.846512947 1 17.96403665 3.470471261 23.51456424 0.947393276 0.8371865 0.253464108 0.097869091 132.6819044 469161.4455 0.030448425 0.039429889 2954.413375 -3.470471261 -0.110206776 REEQTDTS(ph)DGESVTHHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 REEQTDTSDGESVTHHIR 18 1 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 1 REEQTDT(0.093)S(0.906)DGESVTHHIR;REEQT(0.073)DT(0.183)S(0.744)DGESVTHHIR 209.75 2.29E-16 2628000000 899420 791240 337790 529470 818050 787350 760270 777240 501950 TRUE FALSE 780559.3682 786042.2923 501146.3738 649694.2559 801772.4055 817639.864 686539.1324 611033.2745 442610.0428 1.763537409 1.775925118 1.132252605 1.46787057 1.811464558 1.847314306 1.551115126 1.380522843 1 18.75567666 1.341010992 1.944606645 0.881332334 1.619722788 0.476417443 0.210340119 0.621050782 2.800422731 0.785188627 0.062161193 21.92860438 -1.341010992 0.738390454 REERPENK ddPTM_MDA-MB-175_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 ;; 122.94 0.00076996 193626000 202696 192232 127751 152078 143163 144595 197881 232475 236228 FALSE TRUE 175909.21 190969.2153 189531.8109 186609.6343 140314.3364 150157.6632 178690.5311 182762.0304 208301.395 0.844493673 0.916792782 0.909892183 0.895863584 0.673612082 0.720867295 0.857846061 0.877392254 1 17.66831298 1.244586713 2.034198032 1.051361705 0.830275919 0.314632233 0.078557515 1.056581534 4.338576813 0.440487394 0.023794285 17.5625152 -1.244586713 -0.221085785 REESPMDVDQPS(ph)PSAQDTQSIASDGTPQGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 REESPMDVDQPSPSAQDTQSIASDGTPQGEK 31 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 REESPMDVDQPS(0.988)PS(0.012)AQDTQSIASDGTPQGEK;REESPMDVDQPS(0.992)PS(0.008)AQDTQSIASDGTPQGEK 327.5 8.57E-106 922930000 803940 554690 443530 501600 540780 497040 611670 740140 808070 TRUE FALSE 697697.2921 551046.2049 658022.5915 615495.9465 530019.536 516161.4504 552350.3375 581866.8208 712540.8852 0.979168082 0.773353805 0.923487487 0.863804393 0.743844384 0.724395556 0.775184062 0.816608328 1 19.44261327 4.750347776 23.95947109 0.822558213 0.979168252 0.24037434 0.084265531 1533.308289 3116612.644 0.020865223 0.316983967 56279.1819 -4.750347776 0.156610039 REFDRHS(ph)GSDR ddPTM_MDA-MB-175_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(0.817)GS(0.183)DR 61.409 0.045652 110080000 84868 65865 45514 66223 56674 77483 73756 79794 65515 TRUE FALSE 73652.47877 65432.32848 67524.72264 81259.94431 55546.29828 80463.82115 66603.15447 62730.67406 57769.89133 1.274928463 1.132637209 1.168856667 1.40661411 0.961509482 1.392833175 1.152904271 1.085871422 1 15.81803016 1.653218841 2.422217498 1.012601699 1.215230417 0.252123435 0.128124386 0.359286246 4.544409283 0.121491653 0.032672184 45.00065563 -1.653218841 0.202628718 REFEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 REFEER 6 1 P25325-2;P25325;B1AH49 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase 0 ;; 130.04 0.025549 1580900000 881990 926750 532700 693900 826130 972510 832390 991930 921120 FALSE TRUE 765432.7868 920662.1182 790315.5018 851460.6006 809691.6293 1009923.089 751664.9459 779813.4887 812226.2429 0.942388643 1.133504521 0.973023845 1.048304716 0.996879424 1.243401205 0.925437897 0.960093934 1 19.63152212 REFITGDVEPTDAESEWHS(ph)ENEEEEKLAGDMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 REFITGDVEPTDAESEWHSENEEEEKLAGDMK 32 2 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;A8MXH2;E9PKT8 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 REFIT(0.001)GDVEPT(0.013)DAES(0.105)EWHS(0.881)ENEEEEKLAGDMK 84.436 0.00010579 60501000 39759 36227 21592 26337 28773 26567 42467 52305 27489 TRUE FALSE 34504.74741 35989.02245 32033.96342 32317.21839 28200.47359 27589.04968 38348.55688 41119.98279 24239.28174 1.423505358 1.484739641 1.321572304 1.333258087 1.163420348 1.138195842 1.582083054 1.696419194 1 14.56505933 2.220909406 24.99920556 1.488966337 1.313502913 0.036817055 0.207077788 509.4905915 721580.231 0.08597942 0.058108006 166.3065698 -2.220909406 -0.175463423 REGDVAACYANPSLAQEELGWTAALGLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 REGDVAACYANPSLAQEELGWTAALGLDR 29 1 Q14376;Q14376-2;Q5QPP4;Q5QPP9 Q14376 GALE UDP-glucose 4-epimerase 0 140.35 1.38E-07 38565000 19138 19861 13765 13562 18910 17381 24506 22891 21911 FALSE TRUE 16608.86481 19730.53178 20421.80004 16641.45938 18533.728 18049.65832 22129.41189 17995.93779 19320.70654 0.859640654 1.021211711 1.056990333 0.861327682 0.95926761 0.93421316 1.145372807 0.931432696 1 14.23786023 REGGDGEEQDVGDAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 REGGDGEEQDVGDAGR 16 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 125.12 0.00012629 315690000 114230 105670 71962 79566 94634 111240 99174 112720 97288 FALSE TRUE 99134.21608 104975.8468 106763.0639 97632.67639 92750.96855 115519.4748 89556.12074 88615.70519 85786.72347 1.155589257 1.223684069 1.244517328 1.138086087 1.081180919 1.346589194 1.043939168 1.032976918 1 16.38846677 2.036179448 24.64418998 1.02472815 1.19362253 0.572171482 0.070511026 100.0076724 68121.32614 0.027839037 0.018769019 108.6874622 -2.036179448 0.16889438 REGS(ph)YDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 REGSYDR 7 1 Q9HCD5;Q5JY17 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 REGS(1)YDR;REGS(1)YDR;REGS(1)YDR;REGS(1)YDR 104.43 0.0049933 500823000 805952 709102 457879 528560 524114 725101 684795 812500 735184 TRUE FALSE 699443.4012 704443.8623 679310.8159 648577.6265 513685.1568 752996.1047 618383.6863 638753.1979 648271.385 1.078936102 1.086649632 1.047880304 1.000472397 0.79239215 1.161544566 0.953896317 0.985317589 1 19.30623837 3.830057193 3.249069125 0.980144866 1.079225675 0.192445927 0.087995573 0.411205544 8.308856637 0.023346908 0.043694935 6761.720152 -3.830057193 0.099080809 REGTGTEMPMIGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 REGTGTEMPMIGDR 14 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 155.26 4.76E-07 450970000 262900 260700 155644 196969 255480 257460 240800 277220 251080 FALSE TRUE 228157.0989 258987.4445 230913.959 241693.8219 250396.4478 267364.6528 217447.2531 217938.6603 221397.6084 1.030531 1.169784292 1.042983078 1.091673138 1.130980816 1.207622136 0.98215719 0.984376759 1 17.75628011 2.206301438 24.99473903 0.987635064 1.111642953 0.550671135 0.052548413 138.4604375 107279.5934 0.020822756 0.014039907 160.8056995 -2.206301438 0.124007888 REIEIAEQDMSALISLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 REIEIAEQDMSALISLR 17 1 O43865-2;O43865 O43865-2 AHCYL1 Putative adenosylhomocysteinase 2 0 63.691 0.077293 0 7643.7 9103.8 5625.1 5338.8 7094.5 6951.6 8517 9082.2 7657 FALSE TRUE 6633.565678 9043.996538 8345.417175 6551.056138 6953.33333 7219.03255 7691.022651 7140.042208 6751.798183 0.982488738 1.339494501 1.236028825 0.970268358 1.029849107 1.069201471 1.139107308 1.057502315 1 12.72105607 3.749951431 24.90880352 1.052052208 1.201353077 0.312502769 0.097741421 795.8147777 1740238.518 0.024949526 0.042731416 5622.784401 -3.749951431 0.14930087 RELDDLEQWIQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RELDDLEQWIQER 13 1 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 136.6 0.0001129 25701000 22116 23098 13707 16703 26561 25310 22592 22395 21298 FALSE TRUE 19193.31457 22946.26772 20335.75105 20495.67144 26032.48807 26283.69208 20401.03132 17606.00353 18780.1747 1.021998723 1.221834625 1.082830771 1.091346154 1.386168578 1.399544599 1.086306791 0.937478155 1 14.19692286 2.001430101 24.99857442 0.978558976 1.203300088 0.382534512 0.122184013 47.37188827 828065.5874 0.053401509 0.035695081 100.3298357 -2.001430101 0.224741112 RELGCSSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RELGCSSVR 9 1 Q9HA64;I3L3W5;I3L139;I3L407 Q9HA64 FN3KRP Ketosamine-3-kinase 0 94.616 0.0097865 0 88124 102080 63015 70528 92194 91649 82492 99428 111500 FALSE TRUE 76478.19012 101409.4298 93489.26477 86542.46035 90359.51977 95174.79633 74491.93854 78166.09595 98318.59702 0.777860877 1.031436908 0.950880786 0.880224728 0.9190481 0.968024354 0.757658681 0.795028594 1 16.58517671 2.252923411 24.99996598 0.835371867 0.92563717 0.111297355 0.089653905 381.8212442 664599.8279 0.032470063 0.025032202 179.0290104 -2.252923411 0.090265304 RELGSIDGVQQISLEDALSSQEVEVAYICSESSSHEDYIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RELGSIDGVQQISLEDALSSQEVEVAYICSESSSHEDYIR 40 1 P53004;C9J1E1 P53004 BLVRA Biliverdin reductase A 0 ; 309.04 1.03E-110 118078000 67193 62405 24391 43706 59755 65325 55665 71559 62570 FALSE TRUE 58313.2748 61995.05745 36186.56918 53630.1153 58565.99241 67838.09502 50266.61687 56256.66472 55173.04588 1.056915997 1.123647543 0.655874052 0.972034704 1.061496451 1.229551386 0.911071993 1.019640367 1 15.75167601 3.383823312 6.210078667 1.039668161 0.939747489 0.094206224 0.142724862 0.53357544 29.35314173 0.042183803 0.054657521 2420.044277 -3.383823312 -0.099920672 RENIRDFLSELELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RENIRDFLSELELK 14 2 A6ND36 A6ND36 FAM83G Protein FAM83G 0 58.32 0.061749 21570000000 22150000 28149000 13142000 17458000 24755000 23490000 31910000 25915000 20665000 FALSE TRUE 19222821.38 27964087.37 19497515.16 21422105.73 24262423.93 24393675.5 28815373.11 20373278.92 18222007.24 1.054923375 1.534632656 1.069998211 1.175617233 1.331490193 1.338693108 1.581350108 1.118058985 1 24.11917855 1.522330915 7.551060826 1.029074226 1.299877606 0.263036063 0.17192797 0.141161539 15.33011593 0.112111023 0.041786591 33.29131234 -1.522330915 0.270803381 REPAEQPGDGER ddPTM_MDA-MB-175_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 1645960000 1099240 944250 614293 746120 962390 993560 967510 1047160 996790 FALSE TRUE 953972.6489 938047.1596 911367.1495 915537.9497 943240.3219 1031782.896 873681.0291 823232.983 878950.6217 1.085354086 1.067235333 1.036880943 1.041626147 1.073143699 1.173880387 0.994004677 0.936608909 1 19.74542259 2.017634747 24.91600055 0.964235585 1.075880565 0.596591794 0.040156092 142.5294881 201378.0796 0.016603866 0.011191806 104.1441181 -2.017634747 0.11164498 REPEDEGEDDD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 REPEDEGEDDD 11 1 P39687 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ; 151.22 0.00068719 703520000 743650 630350 423730 503500 560720 611880 601320 673050 734070 FALSE TRUE 645374.7683 626209.1893 628647.2453 617827.3705 549562.769 635419.4195 543004.079 529123.4952 647289.0809 0.997042569 0.967433575 0.971200139 0.954484463 0.849022153 0.981662503 0.838889601 0.817445421 1 19.30405064 3.387195528 5.642701371 0.88746624 0.975223333 0.286697688 0.058570039 0.243948352 12.12911845 0.017197842 0.022342977 2438.908617 -3.387195528 0.087757092 REPHPAEAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 REPHPAEAEK 10 1 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WWC8;Q9P2K5-4 A0A0A0MQW0 MYEF2 Myelin expression factor 2 0 83.045 0.010512 131260000 463980 436310 275430 302590 248750 392970 429510 490860 547460 FALSE TRUE 402663.8674 433443.8509 408628.8693 371297.6843 243800.3617 408087.8102 387856.1863 385893.4089 482739.9025 0.834121781 0.897882791 0.846478336 0.769146454 0.505034617 0.845357527 0.803447538 0.799381627 1 18.88088656 1.214370133 3.636975517 1.036342675 0.784334001 0.283153695 0.106275287 0.472339826 9.206600502 0.339050293 0.028423303 16.38212112 -1.214370133 -0.252008673 REPLGVCVGIGAWNYPFQIASWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 REPLGVCVGIGAWNYPFQIASWK 23 1 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ; 175.12 3.03E-12 491270000 402920 381720 199267 265840 360810 345210 413800 480980 286470 FALSE TRUE 349673.1011 379212.4562 295633.1877 326203.0351 353630.5869 358490.4521 373669.7397 378126.17 252603.8429 1.384274669 1.501214122 1.170343191 1.291362124 1.399941437 1.419180516 1.479271793 1.496913767 1 17.94651706 3.211398861 24.88186063 1.388314772 1.336652796 0 0.160208741 1074.414354 984226.8328 0.048626147 0.055150924 1627.042365 -3.211398861 -0.051661976 REPLPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 REPLPSR 7 1 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39;Q8IZ40 P38159;Q96E39;Q8IZ40 RBMX;RBMXL1;RCOR2 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1;REST corepressor 2" 0 ;;;;; 121.09 0.00717 6353830000 2305690 2190830 1407640 1687050 2018460 2227400 1986550 2270810 2583530 FALSE TRUE 2000987.225 2176438.293 2088379.412 2070120.487 1978296.595 2313089.519 1793894.687 1785214.953 2278108.027 0.878354846 0.955370978 0.916716586 0.908701635 0.86839455 1.015355502 0.787449351 0.783639288 1 21.11940473 2.21902504 24.99996367 0.838840754 0.921721219 0.145306303 0.071863475 356.2042853 455836.4343 0.028477907 0.019231344 165.5865431 -2.21902504 0.082880466 REPLQMEDSNMEQGVEGVEPGMPES(ph)PGHLTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 REPLQMEDSNMEQGVEGVEPGMPESPGHLTGR 32 1 Q8TBE0-3;Q8TBE0-2;Q8TBE0 Q8TBE0-3 BAHD1 Bromo adjacent homology domain-containing 1 protein 1 REPLQMEDSNMEQGVEGVEPGMPES(1)PGHLTGR;REPLQMEDSNMEQGVEGVEPGMPES(1)PGHLTGR 142.91 2.68E-10 151873000 89891 108226 45012 75306 82367 103988 84946 105202 102496 TRUE FALSE 78011.6766 107515.0563 66779.95376 92405.37828 80728.05785 107988.4856 76707.94999 82705.37098 90379.03964 0.863161159 1.189601668 0.738887623 1.022420449 0.893216593 1.194839933 0.84873606 0.915094598 1 16.46370061 REPPPYGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 REPPPYGYR 9 1 Q13573;G3V3A4;G3V5R3 Q13573 SNW1 SNW domain-containing protein 1 0 89.827 0.018991 109350000 76900 66830 45473 39285 74055 88307 54529 61689 57046 FALSE TRUE 66737.47016 66390.98933 67463.8949 48205.25968 72581.45039 91704.22743 49240.78597 48497.28741 50302.08687 1.326733627 1.319845626 1.341174872 0.958315304 1.442911317 1.823070038 0.978901454 0.964120784 1 15.61833063 2.084985862 24.99999989 0.976935863 1.354185583 0.435928269 0.207427948 23.14440952 6804.825563 0.087357988 0.058896736 121.614641 -2.084985862 0.377249719 REPPS(ph)PQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 REPPSPQGR 9 1 A0A0A0MRB5;Q8WXG6-6;Q8WXG6-8;Q8WXG6-5;Q8WXG6-4;Q8WXG6-7;Q8WXG6-3;Q8WXG6-2;Q8WXG6 A0A0A0MRB5 MADD MAP kinase-activating death domain protein 1 REPPS(1)PQGR;REPPS(1)PQGR 97.463 0.0024544 0 175188 142662 94402 88778 116045 155346 128192 139932 116698 TRUE FALSE 152036.4619 141724.8439 140055.123 108936.4018 113735.9315 161322.2611 115759.9596 110008.6308 102902.0954 1.47748655 1.377278503 1.361052197 1.058641239 1.10528295 1.567725716 1.124952404 1.069061134 1 16.65091283 7.999980247 0.049599936 1.06E-06 3.421098993 0.371941367 0.15591697 1326.803155 6.437952373 125.1692226 389.9938185 99995451.84 -7.999980247 3.42109793 REQEEELR ddPTM_MDA-MB-175_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 ; 144.65 0.0018274 0 146022 139573 77346 97376 122334 136119 145292 153593 130391 FALSE TRUE 126724.8227 138656.1358 114750.7843 119486.7091 119899.7927 141355.586 131201.6042 120748.3322 114976.3245 1.102181891 1.205953803 0.998038377 1.039228812 1.042821583 1.229432117 1.141118441 1.050201706 1 16.81097729 1.508600339 3.96322689 1.007273561 1.107153058 0.202992113 0.072032828 0.322927223 10.44646022 0.068900146 0.019542466 32.25524453 -1.508600339 0.099879497 REQEVAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 REQEVAEER 9 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 77.64 0.039314 0 104560 117700 90978 89928 89409 124620 83950 114900 112560 FALSE TRUE 90742.13108 116926.821 134975.2651 110347.5269 87629.93583 129414.212 75808.54192 90329.52915 99253.28503 0.914248139 1.178064997 1.359907282 1.111777074 0.882892045 1.303878375 0.763788744 0.910091078 1 16.59882723 2.230927339 24.9999939 0.889896808 1.12658842 0.330340469 0.156932001 199.8078452 654390.3101 0.063007051 0.043394698 170.1873748 -2.230927339 0.236691612 REQEVNILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 REQEVNILK 9 1 P35579 P35579 MYH9 Myosin-9 0 ; 112.83 0.0030439 799280000 529140 464400 375550 397930 448970 387010 507040 532150 589700 FALSE TRUE 459212.8083 461349.3258 557167.2361 488286.0885 440036.3754 401898.5251 457867.3388 418353.8637 519986.3378 0.883124757 0.887233553 1.071503606 0.93903638 0.846246033 0.772902086 0.880537248 0.804547799 1 18.98811419 3.266365897 6.261154523 0.850765113 0.950886275 0.218163457 0.07792128 0.2332066 28.39798469 0.022572482 0.028476793 1846.570516 -3.266365897 0.100121162 RES(ph)AASGLGGLLEEEGAGAGAAQEEVLEPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RESAASGLGGLLEEEGAGAGAAQEEVLEPGR 31 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RES(0.999)AAS(0.001)GLGGLLEEEGAGAGAAQEEVLEPGR;RES(0.985)AAS(0.015)GLGGLLEEEGAGAGAAQEEVLEPGR 294.34 1.65E-81 587600000 202673 168665 143233 143223 177171 192072 203269 203812 189688 TRUE FALSE 175889.2495 167557.0285 212500.9579 175743.9712 173645.6437 199461.1341 183556.0037 160228.3899 167263.3007 1.051571078 1.00175608 1.270457757 1.050702518 1.038157462 1.192497896 1.097407518 0.957941097 1 17.35176141 1.764466246 7.410314762 0.980126729 1.102527178 0.286963243 0.079451489 0.18981874 31.75687765 0.043269758 0.020287592 58.13882445 -1.764466246 0.122400449 RES(ph)CGSSVLTDFEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RESCGSSVLTDFEGK 15 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;H7BZT5;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 1 RES(0.883)CGS(0.101)S(0.016)VLTDFEGK;RES(0.943)CGS(0.055)S(0.002)VLTDFEGK;RES(0.988)CGS(0.011)SVLTDFEGK;RES(0.973)CGS(0.026)S(0.001)VLTDFEGK;RES(0.997)CGS(0.003)SVLTDFEGK 205.84 2.57E-09 7062710000 6212630 5475880 5052980 6297250 5925340 4970070 7155350 8059590 10956700 TRUE FALSE 5391615.205 5439908.584 7496618.029 7727136.86 5807437.327 5161271.809 6461425.258 6336109.398 9661411.408 0.558056683 0.563055267 0.775934044 0.799793791 0.601096163 0.534215095 0.668786887 0.655816126 1 23.20380253 1.23667569 6.02756794 1.013273468 0.646921871 0.615214525 0.088341899 0.100854392 14.02948588 0.151878104 0.023343634 17.24549603 -1.23667569 -0.366351597 RES(ph)CGSSVLTDFEGKDVATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.96)CGS(0.04)SVLTDFEGKDVATK;RES(0.993)CGS(0.007)SVLTDFEGKDVATK;RES(0.981)CGS(0.019)SVLTDFEGKDVATK;RES(0.967)CGS(0.001)S(0.031)VLT(0.001)DFEGKDVATK 280.35 5.45E-45 4066870000 3012960 2429280 1449618 1559468 2246250 1714160 3808960 3891560 526371 TRUE FALSE 2614789.702 2413321.9 2150658.113 1913569.044 2201554.02 1780104.844 3439567.645 3059380.178 464144.02 5.63357404 5.199510918 4.633600824 4.122791551 4.743256241 3.835242441 7.410561156 6.591445858 1 18.82421301 4.56181203 3.646443416 4.903626269 5.612612418 0.019016551 1.707189273 1.520703938 35.22384396 0.434009119 2.143738299 36459.61096 -4.56181203 0.708986149 RES(ph)DESGESAPDEGGEGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RESDESGESAPDEGGEGAR 19 1 Q7Z3C6;H7C152;Q7Z3C6-2 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 RES(0.997)DES(0.003)GESAPDEGGEGAR;RES(1)DESGESAPDEGGEGAR 182.35 1.80E-14 928700000 410430 337360 378480 236410 264834 315491 320080 323720 343570 TRUE FALSE 356190.6356 335143.8599 561514.1939 290090.5038 259564.3215 327628.1429 289038.6909 254494.9972 302953.546 1.175726907 1.10625495 1.85346632 0.957541206 0.856779282 1.0814468 0.954069344 0.840046273 1 18.20873707 3.529201847 24.99986325 0.937454613 1.360300905 0.490723706 0.206219315 279.1086705 133977.65 0.054785795 0.08125958 3382.219952 -3.529201847 0.422846291 RES(ph)EDDPES(ph)EPDDHEK ddPTM_MDA-MB-175_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 155.91 7.50E-07 520160000 1043210 806080 689200 722060 821160 675240 962510 1153120 1106180 TRUE FALSE 905347.1553 800784.8074 1022499.425 886014.759 804820.5226 701216.9197 869165.9283 906534.2616 975408.6606 0.928172152 0.820973649 1.048277985 0.90835236 0.82511111 0.718895524 0.891078748 0.929389187 1 19.89564726 1.459211467 2.515065906 1.001470012 0.875231388 0.182586821 0.084355044 0.631959328 6.699604564 0.146113109 0.023825007 28.78799822 -1.459211467 -0.126238624 RES(ph)FLYR ddPTM_MDA-MB-175_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 145.99 0.0013778 961400000 166694 194988 101997 114311 173666 138475 239324 168230 168255 TRUE FALSE 144664.9656 193707.111 151323.0904 140267.0597 170210.3864 143802.2229 216114.3953 132255.3237 148364.0856 0.975067281 1.305619957 1.019944212 0.945424623 1.147247905 0.969252244 1.456648989 0.891424115 1 17.17878238 1.606662641 25 0.945700936 1.114043878 0.160367061 0.162840546 0.210062077 4126.999851 0.091055405 0.03854468 40.42617399 -1.606662641 0.168342942 RES(ph)LSTSSDLYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RESLSTSSDLYK 12 1 Q8TB72-3;Q8TB72;Q8TB72-4 Q8TB72-3 PUM2 Pumilio homolog 2 1 RES(0.934)LS(0.042)T(0.009)S(0.009)S(0.007)DLYK 71.601 0.01651 0 290230 272900 175070 229990 277890 269070 312180 323620 374560 TRUE FALSE 251875.3702 271107.3019 259734.4376 282212.7447 272360.5327 279421.297 281904.8316 254416.3814 330279.9435 0.762611763 0.820840948 0.786406934 0.854465281 0.824635398 0.846013518 0.853533002 0.770305271 1 18.33332984 RES(ph)PSEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RESPSEER 8 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 RES(0.996)PS(0.004)EER;RES(0.997)PS(0.003)EER 147.28 0.00033064 252100000 231600 176523 146052 183129 136154 186160 164852 187664 307740 TRUE FALSE 200993.4732 175363.4088 216683.2357 224711.2384 133444.8018 193321.6957 148864.6784 147533.514 271359.3278 0.740691226 0.646240578 0.798510364 0.828094764 0.491764196 0.71241957 0.548588765 0.543683223 1 18.04984498 3.263870131 24.9999354 0.639193763 0.748954366 0.083093893 0.146798295 506.971492 500766.8878 0.041278977 0.053269745 1835.989237 -3.263870131 0.109760602 RES(ph)PSPAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RESPSPAPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RES(1)PSPAPK;RES(0.999)PS(0.001)PAPK;RES(0.999)PS(0.001)PAPK;RES(0.995)PS(0.005)PAPK;RES(0.99)PS(0.01)PAPK;RES(0.992)PS(0.008)PAPK 108.72 0.0015718 2731430000 3651570 2919870 2653560 3420960 2482380 2566050 3237840 3890100 9446400 TRUE FALSE 3169005.773 2900689.182 3936830.492 4197741.254 2432985.495 2664767.604 2923834.775 3058232.388 8329657.353 0.380448515 0.348236315 0.472628144 0.503951252 0.292087104 0.319913232 0.351015012 0.367149843 1 22.98982572 1.237911133 24.99966596 1.000000713 0.378760949 0.901746575 0.064375929 4.866352815 187167.5623 0.096857506 0.016716687 17.29462436 -1.237911133 -0.621239764 RES(ph)PSPAPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 RESPSPAPKPR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RES(0.997)PS(0.003)PAPKPR;RES(0.977)PS(0.023)PAPKPR;RES(0.991)PS(0.009)PAPKPR;RES(0.668)PS(0.332)PAPKPR;RES(0.975)PS(0.025)PAPKPR;RES(0.938)PS(0.062)PAPKPR;RES(0.997)PS(0.003)PAPKPR;RES(0.5)PS(0.5)PAPKPR;RES(1)PSPAPKPR;RES(0.978)PS(0.022)PAPKPR 164.53 1.79E-05 48147820000 16455720 12986840 7928450 10200150 12011440 10258100 13601200 15730320 12818260 TRUE FALSE 14281054.91 12901528.59 11762674.94 12516249.96 11772435.84 10652735.74 12282157.72 12366513.48 11302899.91 1.263485922 1.141435269 1.040677617 1.107348562 1.041541192 0.94247811 1.08663775 1.094100946 1 23.43018963 4.76906395 1.411737312 1.046794122 1.368291569 0.684835641 0.048354342 0.819835235 1.40104342 0.014160432 0.381682465 58757.58667 -4.76906395 0.321497447 RES(ph)QEEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 187.58 0.00012342 1396358000 3038640 2554270 1854880 2102620 1885820 2698400 2961300 2646900 3248030 TRUE FALSE 2637076.025 2537490.832 2751906.172 2580052.008 1848295.872 2802209.194 2674113.582 2080881.033 2864051.594 0.920750182 0.885979442 0.960843785 0.90083992 0.645343078 0.978407372 0.933682056 0.726551518 1 21.44962605 3.45935663 24.99966174 0.845156586 0.920865383 0.067897724 0.108718254 570.964028 803499.3105 0.030518002 0.03940699 2879.762222 -3.45935663 0.075708796 RES(ph)VNLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RESVNLGK 8 1 P46013 P46013 MKI67 Antigen KI-67 1 RES(1)VNLGK 90.685 0.0062913 0 146500 134100 69530 98081 115560 124220 123550 146000 132730 TRUE FALSE 127139.6538 133219.0883 103154.9406 120351.7901 113260.5821 128998.8238 111568.14 114779.0362 117038.8106 1.086303365 1.138247113 0.881373794 1.028306675 0.967718157 1.102188437 0.953257637 0.980692093 1 16.83662749 4.267120698 24.99996941 0.990015682 1.112275363 0.452072678 0.056995179 184.6772354 161653.5205 0.013320349 0.035228267 18497.82633 -4.267120698 0.122259681 RES(ph)VVNLENFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RESVVNLENFR 11 1 Q9UIK4 Q9UIK4 DAPK2 Death-associated protein kinase 2 1 RES(1)VVNLENFR 102.15 0.0017803 100360000 136060 118030 91973 103810 135780 136320 117850 144700 191720 TRUE FALSE 118079.3263 117254.6532 136451.4504 127381.6471 133078.2436 141564.3186 106420.9251 113757.0311 169055.08 0.698466596 0.693588463 0.807141971 0.753491981 0.78718867 0.837385772 0.62950445 0.672899218 1 17.36713384 4.260293611 24.02515225 0.766693116 0.696027396 0.100173446 0.099604736 428.4902637 473669.4317 0.024941983 0.065839073 18209.31507 -4.260293611 -0.07066572 RESAAS(ph)GLGGLLEEEGAGAGAAQEEVLEPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RESAASGLGGLLEEEGAGAGAAQEEVLEPGR 31 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RES(0.38)AAS(0.62)GLGGLLEEEGAGAGAAQEEVLEPGR 160.23 1.27E-12 129600000 28647 18357 14584 18677 26676 25769 20084 21430 28873 TRUE FALSE 24861.22637 18236.41166 21636.87118 22917.89831 26145.19979 26760.3501 18136.25677 16847.36127 25459.66683 0.976494568 0.716286343 0.849848952 0.900164895 1.026926234 1.051087993 0.712352479 0.661727484 1 14.63592592 2.214280294 24.95275315 0.761061205 0.911620672 0.168063684 0.12840438 347.9767835 357611.0442 0.05440039 0.036696631 163.7873267 -2.214280294 0.150559467 RESCGSS(ph)VLTDFEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RESCGSSVLTDFEGK 15 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;H7BZT5;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 1 RES(0.222)CGS(0.093)S(0.684)VLT(0.001)DFEGK 231.42 2.08E-13 480170000 534730 462280 382670 467800 471360 384450 561610 597490 836920 TRUE FALSE 464064.0757 459243.2522 567730.492 574021.1399 461980.8582 399240.0403 507145.1486 469721.4132 737980.271 0.628829921 0.622297465 0.769303075 0.777827216 0.626007058 0.540990127 0.687206919 0.636495895 1 19.49322272 1.235916661 24.9957807 1.000000449 0.662151616 0.694812606 0.070579746 44.4841107 420463.6031 0.121529033 0.018252532 17.2153819 -1.235916661 -0.337848833 RESPSEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RESPSEER 8 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 0 81.972 0.03444 242210000 70982 78298 56080 56701 58528 84820 54398 69137 81073 FALSE TRUE 61601.54885 77783.65528 83200.47558 69575.82867 57363.40731 88083.08029 49122.49033 54352.59057 71488.6423 0.861697004 1.088056127 1.163827888 0.973243112 0.802412879 1.232126915 0.687136988 0.760296864 1 16.12542643 2.22090319 24.99998295 0.798884368 1.0178015 0.293136351 0.148834463 282.7071685 400263.3812 0.059414126 0.040154914 166.3041894 -2.22090319 0.218917132 RET(ph)DDEGEDD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RETDDEGEDD 10 1 Q92688 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 1 RET(1)DDEGEDD;RET(1)DDEGEDD 155.47 2.45E-05 320490000 674460 615360 406030 474870 341810 564200 530430 624380 1003970 TRUE FALSE 585328.4021 611317.6596 602387.4661 582696.4914 335008.6497 585905.1391 478988.9802 490861.1959 885281.8103 0.661177486 0.690534531 0.680447129 0.658204523 0.378420347 0.661828959 0.541058197 0.55446886 1 19.75577725 1.234615265 24.99749117 1.000000578 0.599723304 0.635232202 0.094446567 77.84724316 493164.0639 0.174038333 0.023533877 17.16387192 -1.234615265 -0.400277274 RET(ph)PS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RETPSPR 7 1 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RET(1)PS(1)PR 64.82 0.062548 65021000 44297 40063 32795 38308 31954 41268 37779 45988 78817 TRUE FALSE 38443.03922 39799.82352 48654.77169 47006.4169 31318.17792 42855.60666 34115.19839 36153.82408 69499.34405 0.553142476 0.572664736 0.700075265 0.676357706 0.450625518 0.616633254 0.490870797 0.520203817 1 16.08471174 1.234419571 24.99983724 1.000000626 0.571084021 0.751639551 0.077210869 64.53883575 389572.7949 0.147581012 0.019657644 17.15613957 -1.234419571 -0.428916605 RET(ph)PS(ph)PRPMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RETPSPRPMR 10 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RET(1)PS(1)PRPMR 82.069 0.013519 670780000 764910 678110 423430 558790 592870 618240 586700 688460 562670 TRUE FALSE 663825.2055 673655.4508 628202.1643 685671.8101 581073.0469 642024.0929 529801.9243 541238.1866 496151.7936 1.33794781 1.357760789 1.266149135 1.381979908 1.171159823 1.294007401 1.067822249 1.090872176 1 18.92042204 2.056791416 0.630228272 0.940174936 1.345613889 0.791790288 0.060331128 0.606795334 0.383424167 0.165200318 0.037471465 113.9702277 -2.056791416 0.405438953 REVADAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 REVADAQR 8 1 Q9P2M7 Q9P2M7 CGN Cingulin 0 88.496 0.023368 48503000 36682 41921 23604 29369 40338 52605 36091 38280 33740 FALSE TRUE 31834.38076 41645.61819 35018.97335 36037.68033 39535.35272 54628.74839 32590.90037 30094.1199 29751.29564 1.070016619 1.39979175 1.177057086 1.211297846 1.328861546 1.836180483 1.095444742 1.011523003 1 14.86066488 2.020456567 24.99980015 1.020654062 1.3382604 0.337654979 0.201761561 257.6621186 314885.4425 0.083015037 0.055961963 104.8229957 -2.020456567 0.317606338 REVLYDS(ph)EGLS(ph)GEER ddPTM_MDA-MB-175_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 124.2 6.55E-05 294750000 483550 451010 292290 353060 450320 451830 424840 485660 437130 TRUE FALSE 419647.6423 448047.2856 433642.4217 433227.6692 441359.513 469212.1925 383639.0822 381805.3884 385452.9894 1.088712901 1.162391518 1.125020258 1.123944245 1.145041095 1.217300697 0.99529409 0.990536846 1 18.55619539 2.219126075 24.99821289 0.994290079 1.142892231 0.821397477 0.032630929 90.34536132 116208.3433 0.012952668 0.00874724 165.6250699 -2.219126075 0.148602152 RFDAMPFTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RFDAMPFTLR 10 1 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 199.19 4.54E-07 2716000000 1456680 1735370 881420 894990 1593710 1613550 1406210 1596940 872800 FALSE TRUE 1264176.047 1723970.24 1307677.66 1098211.159 1561998.289 1675624.313 1269835.971 1255446.808 769618.5783 1.642600741 2.240031996 1.699124342 1.426955104 2.029574562 2.17721396 1.649954934 1.631258449 1 19.5537841 1.066528595 1.509757719 0.328222587 1.857692137 0.524607813 0.251635576 1.474605639 2.131534547 3.869478433 0.072732407 11.6554379 -1.066528595 1.52946955 RFDAQTGADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RFDAQTGADR 10 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;;;; 202.05 3.70E-07 2923510000 1993040 2014880 1230000 1313360 1872970 1991380 1971550 2035360 1765600 FALSE TRUE 1729654.714 2001644.121 1824832.114 1611578.461 1835701.561 2067989.677 1780349.384 1600114.103 1556872.779 1.110980125 1.285682521 1.172113829 1.035138184 1.179095419 1.328297151 1.143541982 1.027774475 1 20.57021963 1.758570328 3.551086868 1.008542832 1.185329766 0.424094693 0.081274012 0.200531063 5.167152527 0.056342071 0.022525135 57.35487377 -1.758570328 0.176786934 RFDDAVVQSDMK ddPTM_MDA-MB-175_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 ;;;;;;;;;;;;;;;;; 215.25 6.71E-11 43549300000 34350940 29423410 19051380 23973170 27350940 23849900 32503600 38098820 28101450 FALSE TRUE 29811376.24 29230125.68 28264691.09 29416644.66 26806709.81 24767421.09 29351405.87 29951683.83 24779328.59 1.203074415 1.17961734 1.140656051 1.18714454 1.081817439 0.999519458 1.18451175 1.208736698 1 24.56263376 3.248166267 24.98775235 1.111094242 1.175125041 0.245118641 0.068884853 400.3421305 1041427.349 0.021572441 0.027476361 1770.786765 -3.248166267 0.064030798 RFDEATQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RFDEATQLR 9 1 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ;;;;; 167.93 9.56E-05 1612730000 612395 704819 343673 461315 587611 652628 549730 594483 481634 FALSE TRUE 531465.4491 700188.9976 509874.4123 566063.6215 575918.6907 677735.0215 496417.2692 467357.4367 424695.7772 1.251402716 1.648683682 1.200563885 1.332868495 1.356073504 1.595812951 1.168877337 1.100452281 1 18.69607024 2.053121799 7.362225676 1.079913458 1.39519367 0.528973211 0.139596282 0.162837913 18.78115027 0.055351155 0.037031315 113.0112813 -2.053121799 0.315280213 RFDEDDDKSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RFDEDDDKSFR 11 2 Q13136-2;A0A2R8Y7R9;Q13136 Q13136-2 PPFIA1 Liprin-alpha-1 0 64.121 0.039544 82165000 108400 96364 48724 70390 81846 86298 82068 85482 97284 FALSE TRUE 94074.66535 95730.97854 72287.08937 86373.12534 80217.42473 89617.9399 74109.05799 67202.33952 85783.19635 1.096656098 1.115964229 0.842671904 1.006876976 0.93511816 1.044702736 0.863911129 0.783397476 1 16.38840745 8 0.325103794 0.874068092 3.351393269 0.313289016 0.090990705 86.44603913 1.355958602 0.148159026 126.0731336 100000000 -8 2.477325177 RFDEILEASDGIMVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 33 RFDEILEASDGIMVAR 16 1 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 342.97 3.75E-72 18866908100 9153538.1 7733823.7 5156022 5543968.7 7114238.9 8100505.7 7525132.1 7995852.3 5824192 FALSE TRUE 7943874.848 7683019.703 7649491.485 6802811.528 6972679.465 8412137.396 6795345.947 6286001.509 5135662.657 1.546806202 1.496013312 1.489484804 1.324621959 1.357698107 1.637984805 1.323168284 1.223990345 1 22.29211901 1.51221064 1.609756981 0.954128675 1.464198913 0.728472829 0.094390302 0.31380186 1.213023085 0.228814654 0.028170953 32.52450081 -1.51221064 0.510070238 RFDIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RFDIYR 6 1 Q969X5;F2Z2U2;F2Z2P5;A0A1B0GTQ3 Q969X5 ERGIC1 Endoplasmic reticulum-Golgi intermediate compartment protein 1 0 ;; 124.12 0.029649 881780000 404954 609784 310600 369550 638453 643630 498124 679992 524785 FALSE TRUE 351438.3029 605778.2888 460807.1989 453461.9757 625749.0344 668390.8626 449816.0111 534581.0025 462745.5151 0.759463445 1.309095969 0.99581127 0.979938132 1.35225305 1.444402681 0.972059148 1.155237566 1 18.81985948 4.754266191 24.33109006 1.148280659 0.759463023 0.344034466 0.16991183 2518.67317 3901836.136 0.041729107 0.972003643 56789.25761 -4.754266191 -0.388817636 RFDSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RFDSEK 6 1 P17980;E9PM69;E9PKD5;R4GNH3 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ;;; 140.98 0.018777 2562280000 3184010 2769320 1899930 2273720 1902280 2310110 3253910 3583430 3162900 FALSE TRUE 2763235.011 2751128.155 2818742.503 2790002.878 1864428.35 2398981.427 2938346.309 2817141.381 2788985.565 0.990767054 0.9864261 1.010669448 1.000364761 0.668496952 0.860162726 1.053553789 1.010095361 1 21.41130904 2.229632688 24.9916881 1.020246902 0.918937197 0.182738186 0.101410414 364.0754605 1019136.027 0.044676277 0.03062283 169.6807942 -2.229632688 -0.101309705 TGQIWPNDGEGAFHGDADGSFGT(ph)PPGYGCAADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TGQIWPNDGEGAFHGDADGSFGTPPGYGCAADR 33 0 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 TGQIWPNDGEGAFHGDADGS(0.226)FGT(0.774)PPGYGCAADR;TGQIWPNDGEGAFHGDADGS(0.034)FGT(0.966)PPGYGCAADR 156.92 1.13E-10 486830000 141344 181163 153756 197482 298910 333350 314440 324350 447510 TRUE FALSE 122665.0323 179972.9283 228112.9159 242323.3064 292962.2758 346174.1902 283945.6572 254990.2766 394605.8776 0.310854549 0.456082736 0.578077846 0.61408945 0.742417416 0.877265672 0.719567734 0.646189758 1 18.59005292 4.510139347 0.631669303 0.793828792 0.084253755 0.75671223 0.096660569 1.479592122 0.565110768 0.054261609 0.736160412 32369.75016 -4.510139347 -0.709575038 down RFDYDWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RFDYDWER 8 1 Q93008;Q93008-3;O00507;O00507-2 Q93008 USP9X;USP9Y Probable ubiquitin carboxyl-terminal hydrolase FAF-X;Probable ubiquitin carboxyl-terminal hydrolase FAF-Y 0 ;;; 147.4 0.00086235 1141070000 366782 471699 349955 280733.6 454818 532558 421886 470617 462023 FALSE TRUE 318310.8294 468600.3782 519194.4085 344478.4546 445768.0116 553045.8509 380971.5607 369979.2169 407403.1673 0.781316531 1.150212899 1.274399539 0.845546825 1.094169234 1.357490308 0.935121745 0.908140257 1 18.63609767 RFEDLGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RFEDLGSR 8 1 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 ; 134.51 0.0014007 349230000 327240 394380 217560 212598 347260 417440 300200 293110 298780 FALSE TRUE 283994.4049 391789.2918 322772.7437 260871.6253 340350.2054 433499.1869 271086.6502 230430.7075 263458.5688 1.077947118 1.487100206 1.225136632 0.990180834 1.291854757 1.645416921 1.028953628 0.874637362 1 18.00721658 2.017440193 24.99496266 0.935393498 1.284231404 0.400350576 0.18620338 217.9970569 312428.1358 0.076215679 0.051372781 104.0974745 -2.017440193 0.348837907 RFEEALQTIFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RFEEALQTIFNR 12 1 J3QRN6;O94832;K7EIG7 J3QRN6 MYO1D Unconventional myosin-Id 0 179.67 3.27E-05 184370000 144410 132970 95073 122100 139040 149920 114390 131860 114500 FALSE TRUE 125325.8526 132096.5113 141050.6208 149824.6712 136273.376 155687.5194 103296.4754 103662.7651 100963.9404 1.241293199 1.308353366 1.397039579 1.483942391 1.349723232 1.542011125 1.023102654 1.02673058 1 16.6234806 2.222420164 24.99933072 1.018989612 1.386643041 0.813856813 0.083513739 97.24663629 150620.4481 0.034537486 0.023365409 166.8860995 -2.222420164 0.367653429 RFEEELAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RFEEELAAR 9 1 Q02818 Q02818 NUCB1 Nucleobindin-1 0 ; 160.53 0.00010458 250330000 192602 225545 134823 155844 210474 254335 175717 229752 190852 FALSE TRUE 167149.1577 224063.38 200023.8538 191230.7621 206285.9792 264119.432 158675.9924 180621.3227 168289.694 0.99322278 1.331414745 1.188568646 1.136318913 1.225779038 1.569433195 0.942874092 1.073276197 1 17.3605873 RFEELGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RFEELGVK 8 1 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 ;;; 138.26 0.0011432 2668040000 3433990 2785850 1509960 2210640 2440680 2438940 2492740 3124330 3688380 FALSE TRUE 2980179.521 2767549.568 2240181.707 2712599.6 2392115.243 2532767.6 2250994.458 2456216.343 3252343.918 0.916317461 0.850940011 0.68878992 0.834044513 0.735505009 0.778751468 0.692114523 0.75521421 1 21.63304839 4.469249043 23.70728523 0.775583214 0.899973152 0.194402136 0.088555726 116.5683969 351049.7065 0.021125585 0.056171502 29461.10577 -4.469249043 0.124389938 RFEETGQELAELLEEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RFEETGQELAELLEEEK 17 1 P36405 P36405 ARL3 ADP-ribosylation factor-like protein 3 0 102.78 0.0014932 23633000 45293 42354 43025 48059 43997 33436 51772 60384 82532 FALSE TRUE 39307.41529 42075.77379 63832.03391 58971.53049 43121.54578 34722.30456 46751.15941 47471.35151 72775.16098 0.54012131 0.578161192 0.877112919 0.810324975 0.592531094 0.477117523 0.642405441 0.652301566 1 16.15115851 1.23856101 8.738728799 1.002884346 0.649416188 0.465308986 0.119132037 0.085758529 79.9729937 0.179325994 0.031399081 17.32052335 -1.23856101 -0.353468159 RFEIACYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RFEIACYK 8 1 Q9Y3A5;A0A087X020;F8WE72 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ; 134.05 0.0014321 1120540000 1228900 1346030 914820 929260 1224660 1127260 1403130 1447820 1407750 FALSE TRUE 1066497.751 1337187.84 1357230.012 1140262.686 1200291.662 1170626.422 1267054.669 1138214.96 1241327.399 0.859159117 1.077224141 1.093369898 0.918583354 0.966942052 0.943044053 1.020725612 0.916933728 1 20.24345224 3.713059104 24.99399437 0.959670639 1.0166484 0.096109126 0.069567379 1485.355748 1455793.725 0.018336062 0.027206431 5164.866538 -3.713059104 0.056977762 RFEKPLEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RFEKPLEEK 9 2 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 118.28 0.00057101 1622700000 1287500 930470 709270 904830 882420 748680 1145300 1421400 1267600 FALSE TRUE 1117353.613 924357.6813 1052275.344 1110285.481 864861.5684 777482.2041 1034228.982 1117444.671 1117745.772 0.999649152 0.826983832 0.94142637 0.993325592 0.773755169 0.695580537 0.925281051 0.999730618 1 20.09216066 1.998036887 24.99962011 0.988644021 0.86868811 0.238360522 0.093657629 108.8920523 1386713.782 0.040762962 0.027013051 99.5489967 -1.998036887 -0.11995591 RFFPYYVYNIIGGLDEEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RFFPYYVYNIIGGLDEEGK 19 1 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 89.661 0.0037853 150640000 258500 209100 115740 132540 180500 161120 235470 260820 131400 FALSE TRUE 224338.57 207726.4083 171712.2511 162635.2327 176908.4031 167318.3907 212634.1556 205045.6727 115866.0417 1.936189126 1.792815266 1.481989448 1.40364882 1.526835651 1.444067547 1.835172347 1.769678758 1 16.82209827 4.383996491 3.884072427 1.533812348 1.909539242 0.313062662 0.226402477 0.286910034 7.953844187 0.058868484 0.184110906 24210.09487 -4.383996491 0.375726894 RFIGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RFIGSPR 7 1 P23443-5;P23443;P23443-3;P23443-2;P23443-4;K7ERJ3 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 1 RFIGS(1)PR;RFIGS(1)PR 89.886 0.010746 825540000 52666 36702 26148 31783 51283 57287 46430 50846 45744 TRUE FALSE 45706.05466 36460.90215 38793.26026 38999.81592 50262.56863 59490.86796 41927.22575 39972.97858 40336.19643 1.133127531 0.903925143 0.9617481 0.966868951 1.246090933 1.474875502 1.039444208 0.990995238 1 15.29978743 3.262182325 24.92914574 1.138287392 0.983048671 0.211793083 0.150923543 417.126863 440211.3535 0.048299986 0.062319628 1828.867848 -3.262182325 -0.155238721 RFNDGSDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RFNDGSDEK 9 1 P25705;P25705-2;P25705-3;K7EK77;K7ENJ4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ; 100.82 0.0070581 272680000 376670 349970 266700 367180 345660 332720 373220 408050 358460 FALSE TRUE 326892.1051 347671.024 395677.0121 450553.831 338782.0423 345519.9537 337025.1818 320791.6829 316083.2672 1.034196173 1.099934923 1.251812586 1.425427657 1.071812644 1.093129531 1.066254424 1.014896125 1 18.26994514 3.028395664 24.99945604 1.045800101 1.205193908 0.354203762 0.103659187 249.4832946 219642.6778 0.033411187 0.037884139 1067.568287 -3.028395664 0.159393807 RFPEEPHVPLEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RFPEEPHVPLEQR 13 1 Q8TCD5;J3KSX6;J3KRC4;Q8TCD5-2 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 0 ; 82.55 0.0078189 592990000 377810 385910 266790 330260 385750 444210 324140 414710 421560 FALSE TRUE 327881.4513 383374.9318 395810.5364 405250.5807 378074.3297 461299.0461 292704.9527 326027.4938 371723.657 0.882056993 1.031343915 1.064797811 1.09019314 1.017084392 1.240973065 0.787426216 0.877069532 1 18.50387098 2.21755805 24.99934988 0.881656206 1.053762226 0.378015457 0.100406477 238.8354119 284283.5913 0.040117453 0.027078164 165.0281572 -2.21755805 0.17210602 RFPELESLVPNALDYIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RFPELESLVPNALDYIR 17 1 Q8WWY3-4;Q8WWY3;E7EVX8;Q8WWY3-3;Q8WWY3-2;E7EU94;E7ESX0;E7EN72 Q8WWY3-4 PRPF31 U4/U6 small nuclear ribonucleoprotein Prp31 0 ; 120.9 9.95E-05 237380000 393050 331240 132203 160394 291680 292790 263460 294120 176630 FALSE TRUE 341107.4466 329064.0626 196136.813 196813.9092 285876.1387 304053.8208 237909.6898 231224.7268 155749.0026 2.19010999 2.112784397 1.259313445 1.263660799 1.83549258 1.952203967 1.527519828 1.484598443 1 17.2488634 4.269275115 13.1190202 1.500827094 2.151922038 0.508100131 0.275904734 1.14781851 486.5646167 0.072357111 0.190192317 18589.81704 -4.269275115 0.651094944 RFPGYDSESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RFPGYDSESK 10 1 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;;;; 196.11 5.44E-07 8756990000 14826780 12953110 8777880 10342150 11935600 10910350 14933430 17076100 14361120 FALSE TRUE 12867383.46 12868020.17 13022892.13 12690493.23 11698104.91 11330078.22 13485188.26 13424508.9 12663364.75 1.016110939 1.016161219 1.028391141 1.00214228 0.923775406 0.894713091 1.06489772 1.060105996 1 23.59415746 RFPQHTIMAGNVVTGEMVEELILSGADIIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RFPQHTIMAGNVVTGEMVEELILSGADIIK 30 1 A0A087WWM4;Q9P2T1;Q9P2T1-3;F8WAN9;H0YNJ6;Q9P2T1-2;H0YNH0;H0YLB8 A0A087WWM4 GMPR2 GMP reductase;GMP reductase 2 0 135.35 2.67E-06 171570000 252240 235120 146340 183790 226170 191500 283210 304500 216580 FALSE TRUE 218905.8449 233575.4812 217110.5135 225522.3286 221669.6595 198867.1289 255744.3378 239385.0446 190976.1591 1.146246976 1.223060943 1.136846162 1.180892576 1.160719016 1.041319135 1.339142744 1.253481302 1 17.54303302 2.24551415 24.9999574 1.215095564 1.153126081 0.044484354 0.095254029 418.6311429 1505102.038 0.035805826 0.027113864 176.0006006 -2.24551415 -0.061969483 RFS(ph)DFLGLYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RFSDFLGLYEK 11 1 Q13596-2;Q13596;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 1 RFS(1)DFLGLYEK 141.97 2.32E-05 118030000 510050 495320 279810 399210 305830 284430 469760 450900 584890 TRUE FALSE 442645.6002 492066.2103 415127.0519 489856.732 299744.5813 295372.2062 424202.7475 354478.5439 515744.9705 0.858264502 0.954088238 0.804907611 0.949804186 0.581187599 0.572709814 0.822504865 0.687313622 1 18.97629832 3.258417383 24.99991687 0.7257949 0.890013547 0.276610895 0.127497264 318.8746545 401464.6834 0.036328356 0.046835224 1813.081736 -3.258417383 0.164218648 RFS(ph)DQAAGPAIPTSNSYSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RFSDQAAGPAIPTSNSYSK 19 1 Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7 Q7KZI7-12 MARK2 Serine/threonine-protein kinase MARK2 1 RFS(1)DQAAGPAIPTSNSYSK 145.2 7.82E-08 156900000 331950 249920 195720 278870 286930 253130 372390 347100 308990 TRUE FALSE 288081.9664 248278.2591 290370.8466 342191.6958 281220.6544 262868.0749 336275.6751 272875.3661 272461.5542 1.057330702 0.91124144 1.065731448 1.255926535 1.032148022 0.964789604 1.234213304 1.00151879 1 18.05569315 4.06316073 11.0634548 1.082269706 0.985045249 0.13195235 0.10193626 1.043831463 177.6080953 0.025605033 0.053364049 11565.40193 -4.06316073 -0.097224457 RFS(ph)DQAGPAIPTSNSYSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RFSDQAGPAIPTSNSYSK 18 1 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 RFS(1)DQAGPAIPTSNSYSK;RFS(1)DQAGPAIPTSNSYSK;RFS(1)DQAGPAIPTSNSYSK;RFS(1)DQAGPAIPTSNSYSK;RFS(1)DQAGPAIPTSNSYSK 241.84 3.17E-24 3211190000 4405450 3288460 2391420 3314390 3687920 3124190 4588910 4257510 3771790 TRUE FALSE 3823258.621 3266857.89 3547918.711 4066972.907 3614537.607 3244379.611 4143878.215 3347074.618 3325893.283 1.149543384 0.982249763 1.06675663 1.222821227 1.086787007 0.975491194 1.245944431 1.006368615 1 21.66531045 1.596458805 25 1.003147079 1.099113627 0.184127725 0.087916789 1.405566839 3067.891315 0.054855323 0.021134181 39.48742417 -1.596458805 0.095966548 RFS(ph)DSEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RFSDSEER 8 1 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 RFS(0.775)DS(0.225)EER 126.66 0.00074096 661170000 360520 334230 202850 260080 350530 385800 324100 331770 369230 TRUE FALSE 312876.3686 332034.4211 300948.9385 319135.1391 343555.1388 400641.9756 292668.8319 260823.5673 325580.05 0.960981389 1.019824222 0.924346988 0.980204835 1.055209429 1.230548296 0.898915127 0.801104267 1 18.31265278 2.029332048 24.99997066 0.875444369 1.025933131 0.282906824 0.094535057 222.5488101 189679.487 0.039467356 0.026608502 106.9872557 -2.029332048 0.150488762 RFS(ph)DSEGEETVPEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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(0.998)DS(0.002)EGEETVPEPR;RFS(0.999)DS(0.001)EGEETVPEPR;RFS(0.998)DS(0.002)EGEETVPEPR;RFS(0.99)DS(0.01)EGEETVPEPR;RFS(0.993)DS(0.007)EGEETVPEPR;RFS(0.996)DS(0.004)EGEETVPEPR 268.25 8.51E-26 3938750000 1601870 1451180 1245452 1451570 1573220 1842770 1308611 1695770 2017560 TRUE FALSE 1390178.821 1441647.103 1847756.753 1781171.154 1541916 1913662.554 1181702.107 1333142.782 1779046.355 0.781417987 0.810348251 1.038622039 1.001194347 0.866709288 1.075667617 0.664233455 0.749358092 1 20.76267267 1.168719914 22.13148991 1.00002353 0.871111988 0.083295825 0.131741926 40567.19481 12846838.67 167.833146 0.034379805 14.74755123 -1.168719914 -0.128911542 RFS(ph)EGVLQSPSQDQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RFSEGVLQSPSQDQEK 16 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RFS(1)EGVLQSPSQDQEK;RFS(1)EGVLQSPSQDQEK;RFS(1)EGVLQSPSQDQEK;RFS(1)EGVLQSPSQDQEK;RFS(1)EGVLQSPSQDQEK;RFS(1)EGVLQSPSQDQEK 306.06 9.70E-47 15593450000 8742710 6508500 5136240 5168850 6340150 5535850 7732790 7695600 6729340 TRUE FALSE 7587338.722 6465745.235 7620142.844 6342516.393 6213993.419 5748817.732 6982865.216 6049955.827 5933805.091 1.278663287 1.089645705 1.284191632 1.068878451 1.047218998 0.968824834 1.176793829 1.01957441 1 22.50052611 3.613600993 6.187117091 1.047160959 1.204013369 0.531727258 0.075361355 0.188341957 8.692368489 0.019586156 0.02919447 4107.721513 -3.613600993 0.156852409 RFS(ph)FCCSPEPEAEAEAAAGPGPCER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RFSFCCSPEPEAEAEAAAGPGPCER 25 1 Q13501;E7EMC7;E3W990;D6RBF1;C9J6J8 Q13501 SQSTM1 Sequestosome-1 1 RFS(0.863)FCCS(0.137)PEPEAEAEAAAGPGPCER;RFS(0.994)FCCS(0.006)PEPEAEAEAAAGPGPCER;RFS(0.999)FCCS(0.001)PEPEAEAEAAAGPGPCER 221.91 6.66E-34 1107790000 470060 419500 259936 259567 361146 423655 375358 408237 416332 TRUE FALSE 407940.38 416744.2769 385641.919 318505.6546 353959.9012 439953.282 338955.8389 320938.6945 367113.7052 1.11120989 1.13519128 1.050469959 0.867594018 0.964169673 1.198411489 0.923299332 0.874221501 1 18.48586745 3.991685033 5.943497932 0.966476957 1.117500066 0.322162829 0.091578233 0.184261488 26.1255975 0.025613648 0.04961602 9810.36201 -3.991685033 0.151023108 RFS(ph)FFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RFSFFK 6 1 O15020;A4QPE4 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 1 RFS(1)FFK;RFS(1)FFK 112.41 0.016548 569070000 655210 816720 510990 613390 654360 613150 718120 790170 1835780 TRUE FALSE 568622.3384 811354.9125 758106.4732 752669.5746 641339.5162 636738.2773 648476.8329 621198.2946 1618756.18 0.351271146 0.501221199 0.468326535 0.464967846 0.396192783 0.39335033 0.40060192 0.383750377 1 20.62645427 1.236306967 24.99999929 1.000000747 0.421238521 0.941271625 0.045532051 13.75670482 152568.5948 0.074845548 0.011570536 17.2308605 -1.236306967 -0.578762226 RFS(ph)FSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 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(0.998)FS(0.002)QR;RFS(1)FSQR;RFS(1)FSQR;RFS(1)FSQR;RFS(1)FSQR 157.99 0.00088104 17451258000 2905262 2923170 1954557 2131137 2843026 3153611 2722335 2697377 2671984 TRUE FALSE 2521324.266 2903967.504 2899787.303 2615044.228 2786455.345 3274932.456 2458323.371 2120563.92 2356105.095 1.070123854 1.23252885 1.23075465 1.109901351 1.182653248 1.389977239 1.043384429 0.900029427 1 21.16797246 2.009513702 24.80209321 0.951523826 1.201542426 0.60329236 0.087145174 107.745558 280889.9945 0.034651989 0.023329334 102.2147808 -2.009513702 0.2500186 RFS(ph)IPESGQGGTEMDGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 236.78 4.82E-24 906690000 298241 320676 226415 303119 297573 320383 320671 328993 515987 TRUE FALSE 258827.6962 318569.4582 335910.0513 371946.8018 291651.8795 332708.3413 289572.3758 258640.4072 454987.6047 0.568867577 0.70017173 0.738283962 0.817487769 0.641010604 0.731247045 0.636440142 0.568455941 1 18.79546772 -1.999997286 0.016432414 1.543509761 4.19E-08 0.071729587 0.123178869 56355.35728 92.16475491 5226.748605 3580.866 0.010000062 1.999997286 -1.543509719 RFS(ph)LSVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RFSLSVPR 8 1 Q07002;A0A0A0MSJ6;Q07002-3;D6R9B0;D6R9X1 Q07002 CDK18 Cyclin-dependent kinase 18 1 RFS(1)LSVPR;RFS(1)LSVPR;RFS(1)LSVPR;RFS(1)LSVPR 160.77 0.00021525 3435750000 659110 743620 461000 448428 639990 827890 658410 655700 862510 TRUE FALSE 572006.9435 738735.1113 683941.142 550250.4312 627255.4511 859739.464 594557.4995 515483.6577 760545.0504 0.752101329 0.971323278 0.899277619 0.723494855 0.824744637 1.130425428 0.781751849 0.677781885 1 19.53667418 RFS(ph)MEDVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RFSMEDVSK 9 1 Q07002 Q07002 CDK18 Cyclin-dependent kinase 18 1 RFS(1)MEDVSK;RFS(1)MEDVSK;RFS(1)MEDVSK;RFS(1)MEDVSK;RFS(1)MEDVSK;RFS(0.984)MEDVS(0.016)K 122.66 0.00035496 4188120000 6964310 6188610 5156670 5322310 6364560 5862560 8280250 8613990 9111710 TRUE FALSE 6043958.788 6147956.613 7650452.86 6530821.832 6237917.708 6088096.477 7477232.629 6771955.273 8034534.024 0.752247582 0.765191434 0.952196212 0.812843883 0.776388237 0.757741079 0.93063675 0.842856008 1 22.93778292 -1.136363703 0.79631102 9.999936106 0.811699203 0.418690244 0.06779437 111.2934662 1.852847249 1761.199029 0.025801118 0.073052704 1.136363703 -9.188236903 RFS(ph)NVGLVHTSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RFSNVGLVHTSER 13 1 A0A087X165;Q9C0H9;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 RFS(1)NVGLVHTSER;RFS(1)NVGLVHTSER;RFS(1)NVGLVHTSER;RFS(1)NVGLVHTSER;RFS(1)NVGLVHTSER 172.95 1.38E-05 4413133000 2165788 2173556 982061 1360348 2516616 2702458 1938142 2091246 2114860 TRUE FALSE 1879573.628 2159277.768 1456988.984 1669235.805 2466540.265 2806423.308 1750181.287 1644049.317 1864843.66 1.007898768 1.157886751 0.781292832 0.895107639 1.322652573 1.50491077 0.938513681 0.881601687 1 20.83062326 2.044834842 24.99999727 0.925653695 1.108733782 0.134511806 0.204293587 263.2975494 146814.1034 0.090713181 0.061158778 110.8753088 -2.044834842 0.183080087 RFS(ph)TEEFVLL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RFSTEEFVLL 10 1 Q96DT6 Q96DT6 ATG4C Cysteine protease ATG4C 1 RFS(0.5)T(0.5)EEFVLL 65.179 0.073878 58834000 133420 156850 102760 140360 174220 176550 199400 198260 197980 TRUE FALSE 115788.209 155819.642 152455.0797 172230.8833 170753.3629 183341.9927 180062.2187 155863.6419 174575.0299 0.663257563 0.892565461 0.873292588 0.986572268 0.978108742 1.050218882 1.031431693 0.8928175 1 17.41348769 5.37415579 0.891041664 0.9842148 3.69E-18 0.812238807 0.04840435 2.736198862 0.764685171 0.017291031 3.428026738 236676.855 -5.37415579 -0.9842148 RFSDIQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RFSDIQIR 8 1 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ;; 219.19 1.05E-05 1318730000 743390 760550 409464 476604 690060 762240 725860 755959 521924 FALSE TRUE 645149.128 755553.897 607482.16 584824.2226 676329.1561 791563.866 655466.2089 594303.0507 460222.7393 1.401819321 1.641713528 1.319974239 1.270741692 1.469569185 1.719958182 1.424236903 1.291337867 1 18.81197274 1.347115878 2.079942991 0.923771117 1.46765942 0.554218107 0.133670948 0.451772537 2.422095682 0.435635978 0.038123019 22.23903189 -1.347115878 0.543888304 RFSDS(ph)EER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RFSDSEER 8 1 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 RFS(0.249)DS(0.751)EER;RFS(0.207)DS(0.793)EER;RFS(0.019)DS(0.981)EER 139.64 0.00070164 1452690000 2074880 1921880 1325720 1503640 1753850 1985290 1906600 2101300 2054480 TRUE FALSE 1800679.351 1909255.044 1966842.626 1845064.444 1718951.816 2061665.391 1721698.225 1651953.347 1811601.715 0.99397088 1.053904414 1.085692628 1.01847135 0.948857468 1.138034577 0.95037348 0.911874467 1 20.78883438 2.045766529 24.99914148 0.944086716 1.03800543 0.348476787 0.05473632 117.4156366 64135.68341 0.021451311 0.014462463 111.1134235 -2.045766529 0.093918714 RFSEGTSADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RFSEGTSADR 10 1 A0A087X2I1;P62333;H0YJX2 A0A087X2I1;H0YJX2 PSMC6 26S protease regulatory subunit 10B 0 83.182 0.025305 154780000 295920 287780 160620 212050 239010 299310 254340 304040 283840 FALSE TRUE 256813.4222 285889.5542 238296.3692 260199.1935 234254.1686 310824.6494 229674.1459 239023.412 250284.7586 1.026084943 1.142257147 0.952101001 1.03961262 0.935950595 1.241884049 0.917651348 0.955005864 1 17.93321091 RFVEVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RFVEVGR 7 1 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ;;; 122.18 0.0070011 1575650000 1085080 1412180 799300 811980 1371000 1633250 1173670 1107740 1041440 FALSE TRUE 941683.9288 1402903.297 1185844.153 996352.4693 1343719.782 1696082.184 1059847.664 870858.4214 918322.1496 1.025439634 1.527680996 1.291316075 1.08497053 1.463233554 1.846935942 1.154113145 0.94831473 1 19.80864082 2.005948011 24.99690099 0.994689995 1.37862419 0.348004406 0.22839195 160.56635 674787.3385 0.094561054 0.063552499 101.3790019 -2.005948011 0.383934195 RFVNVVPTFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RFVNVVPTFGK 11 1 P62861;E9PR30 P62861 FAU 40S ribosomal protein S30 0 ; 101.93 0.0047091 769500000 2062010 1862850 1069420 1494340 1863920 1842970 2075480 2422400 1965980 FALSE TRUE 1789510.154 1850612.816 1586595.089 1833652.737 1826831.639 1913870.248 1874200.269 1904388.611 1733564.084 1.032272283 1.067519126 0.915221481 1.057735767 1.053801042 1.104008941 1.081125461 1.098539494 1 20.72530974 3.498538325 24.91677884 1.072545807 1.007126252 0.267884084 0.047234145 919.3093534 1069529.664 0.012697156 0.018616794 3151.652492 -3.498538325 -0.065419556 RGAAAADLLS(ph)SSPESQHGGTQSPGGGQPLLQPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 34 1 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 RGAAAADLLS(0.194)S(0.194)S(0.194)PES(0.194)QHGGT(0.194)QS(0.029)PGGGQPLLQPTK;RGAAAADLLS(0.364)S(0.296)S(0.296)PES(0.021)QHGGT(0.021)QS(0.002)PGGGQPLLQPTK 67.809 0.002319 811950000 419004 422735 149933.5 291479 458947 464172 525599 599326 503405 TRUE FALSE 363631.5598 419958.026 222441.8421 357663.7619 449814.8526 482028.9972 474626.4899 471164.7989 443893.0344 0.819187353 0.946079333 0.501115865 0.805743128 1.013340642 1.085912506 1.069236174 1.061437694 1 18.75985254 3.239927546 4.03953629 1.055175421 0.756914681 0.612975614 0.110554843 0.139255596 5.114279945 0.033519562 0.041235532 1737.510934 -3.239927546 -0.29826074 RGAAAADLLSSS(ph)PESQHGGTQSPGGGQPLLQPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 34 1 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 RGAAAADLLS(0.029)S(0.181)S(0.789)PES(0.001)QHGGTQSPGGGQPLLQPTK 192.06 8.75E-21 743410000 224620 206740 88595 159160 252690 272720 285100 351870 272630 TRUE FALSE 194935.8979 205381.9113 131439.8383 195299.7106 247661.9634 283211.7149 257451.0459 276625.3388 240399.992 0.810881466 0.854334102 0.546754753 0.81239483 1.030207869 1.178085376 1.070927847 1.150687804 1 17.87507732 3.230263527 3.345820075 1.104418335 0.739988141 0.764081694 0.09228358 0.106275166 2.487119631 0.027973686 0.034493642 1699.274447 -3.230263527 -0.364430193 RGAAGDWGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGAAGDWGER 10 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 ; 129.82 0.00046984 332510000 538830 516640 281750 348180 407700 515470 501070 535020 329460 FALSE TRUE 467622.2503 513246.1578 418005.2424 427239.5906 399587.5677 535300.4645 452476.3085 420610.1365 290511.6141 1.609650794 1.766697553 1.438858972 1.470645474 1.375461593 1.842612957 1.557515385 1.447825547 1 18.14823632 1.209188389 2.294603257 0.809390134 1.578659971 0.623560847 0.141199359 0.465550689 2.382772207 0.756896985 0.03826467 16.18782082 -1.209188389 0.769269837 RGADDDRPSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RGADDDRPSWR 11 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 147.33 1.99E-05 860370000 160439 151358 86835 71074.1 143143 143587 136190 158212 29374.9 FALSE TRUE 139236.5796 150363.7193 128828.6964 87212.5607 140294.7344 149110.8848 122982.3148 124379.595 25902.23279 5.375466308 5.805048568 4.973652175 3.366990075 5.416318181 5.756680748 4.747942611 4.801887005 1 14.66078884 3.998714852 10.3856517 4.381094295 5.541420781 0.155024868 1.326350254 0.189800663 548.4879413 0.341830647 0.670236577 9970.452123 -3.998714852 1.160326487 RGAEDDRGPWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RGAEDDRGPWR 11 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 110.93 0.00097197 435039000 269082 248567 138345 141693 241116 259937 207362 245630 113311 FALSE TRUE 233522.1319 246934.147 205249.1047 173866.5613 236318.2633 269936.9446 187252.0652 193103.936 99915.50266 2.337196188 2.471429762 2.054226814 1.740135981 2.365181148 2.70165227 1.87410422 1.932672417 1 16.60842092 1.051915145 1.443103094 4.17E-13 2.240287126 0.660905741 0.276370044 1.266240255 1.624383221 4.720972613 0.083299994 11.2697724 -1.051915145 2.240287126 RGAEGPEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGAEGPEAER 10 1 Q9Y446;Q9Y446-2;E9PQ15 Q9Y446 PKP3 Plakophilin-3 0 79.283 0.044044 137980000 130390 140130 81433 112180 111940 127050 138330 156080 144210 FALSE TRUE 113158.6311 139209.4768 120814.2712 137652.1836 109712.613 131937.6957 124914.7779 122703.5066 127161.6581 0.889880117 1.094744115 0.950084113 1.082497552 0.862780611 1.037558787 0.982330521 0.964941072 1 16.95630421 RGAT(ph)PPAPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGATPPAPPR 10 1 Q6SPF0 Q6SPF0 SAMD1 Atherin 1 RGAT(1)PPAPPR 61.375 0.053911 393920000 232450 193430 146940 145450 208660 239500 193190 196030 200930 TRUE FALSE 201731.1435 192159.3456 218000.6755 178476.6456 204508.0742 248713.72 174454.4635 154110.51 177176.2843 1.138589989 1.08456584 1.230416793 1.007339364 1.154263253 1.403764172 0.984637782 0.86981455 1 17.43482598 2.019399263 24.99101754 0.926093602 1.163408606 0.485979355 0.106543561 179.0366182 230642.2484 0.042907363 0.028923833 104.5681111 -2.019399263 0.237315004 RGAYGGGYGGYDDYNGYNDGYGFGSDR ddPTM_MDA-MB-175_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 ;; 206.03 4.64E-25 723990000 314898 250310 118438 139615 255616 236625 241970 264403 116368 FALSE TRUE 273283.4315 248665.6971 175715.013 171316.7196 250529.7417 245728.1169 218503.7866 207862.476 102611.1076 2.663292872 2.423379914 1.712436568 1.669572853 2.441546023 2.394751627 2.129436001 2.025730751 1 16.64682738 1.185081236 2.677567803 0.615796309 2.187998532 0.587373548 0.314382169 0.463129692 3.365060009 1.756790818 0.087441608 15.31373881 -1.185081236 1.572202223 RGDDSFGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RGDDSFGDK 9 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;; 147.74 0.00014699 2559310000 2210920 1915150 1694340 2123280 1703170 1646520 2162080 2527810 4164960 FALSE TRUE 1918741.32 1902569.254 2513728.491 2605403.176 1669280.249 1709862.69 1952401.814 1987257.503 3672583.174 0.522450066 0.518046607 0.684457879 0.709419788 0.454524832 0.46557494 0.531615411 0.541106194 1 21.80836373 1.237569093 24.99813796 1.000000526 0.553834149 0.741386099 0.08289409 13.66932468 344450.2509 0.1285801 0.02169988 17.28100887 -1.237569093 -0.446166377 RGDDSFGDKYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RGDDSFGDKYR 11 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;; 208.95 1.00E-08 6327410000 3700973 3393457 1773063 1962441 3190852 2839180 3638833 4175146 1181546 FALSE TRUE 3211880.041 3371165.158 2630522.197 2408043.223 3127360.288 2948405.092 3285939.536 3282323.519 1041864.978 3.082817936 3.235702542 2.524820637 2.311281475 3.001694418 2.829930129 3.153901518 3.150430803 1 19.99073689 4.243210444 24.93772127 2.666643285 3.159260397 0.118332362 0.627709717 270.6941382 1451722.848 0.155035584 0.382631717 17506.9481 -4.243210444 0.492617112 RGDDWNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGDDWNDR 8 1 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;A0A087X0F4 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 88.136 0.023777 875410000 365150 310340 270260 312730 292580 321650 277990 367530 660760 FALSE TRUE 316894.5023 308301.3561 400958.64 383740.1263 286758.2304 334024.0836 251030.5726 288936.5696 582645.7055 0.543888849 0.529140356 0.688168875 0.658616587 0.492165698 0.573288502 0.430846002 0.495904401 1 19.15225935 1.23445236 24.99988254 1.000000657 0.548986343 0.773291827 0.076306742 62.95980248 383074.8005 0.15269587 0.020342115 17.15743491 -1.23445236 -0.451014315 RGDDWNDREWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RGDDWNDREWDR 12 2 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;;;; 162.93 3.45E-05 2148380000 1033009 859296 468518 581505 824415 910208 858153 992964 686946 FALSE TRUE 896494.2433 853651.228 695094.8719 713544.598 808010.7544 945224.2907 774929.4541 780626.3759 605736.0265 1.480008129 1.409279275 1.147521101 1.177979461 1.333932141 1.560455792 1.279318747 1.288723704 1 19.20832969 1.12581165 2.195820101 0.820024585 1.337423517 0.419892426 0.124885883 1.07835737 4.044059168 1.245831718 0.035430385 13.36015972 -1.12581165 0.517398933 RGDIIGVQGNPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGDIIGVQGNPGK 13 1 Q15046;Q15046-2;H3BVA8;J3KRL2;H3BPV7 Q15046 KARS Lysine--tRNA ligase 0 102.73 0.0018774 0 332160 274140 148990 197380 266750 245600 267960 335330 229500 FALSE TRUE 288264.2144 272339.1563 221042.0623 242198.1458 261442.1969 255048.3909 241973.2804 263622.289 202368.7714 1.424450089 1.34575683 1.092273579 1.196815813 1.291909789 1.260314964 1.195704647 1.302682658 1 17.62662715 4.426927212 7.078191201 1.207956041 1.405667613 0.437466057 0.091931425 0.169303831 18.96145967 0.022234082 0.060365623 26725.58452 -4.426927212 0.197711573 RGDLPFVVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RGDLPFVVPR 10 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 187.42 1.98E-06 19669340000 4278060 4356720 2472500 2955294 4444110 4554250 4228380 4421330 4080340 FALSE TRUE 3712703.532 4328100.419 3668209.27 3626338.672 4355680.906 4729454.944 3818312.358 3475862.986 3597966.854 1.031889309 1.202929486 1.019522808 1.007885514 1.210595062 1.314479854 1.061241672 0.966063093 1 21.77875047 2.000116792 24.99999988 0.990520927 1.132440018 0.288581235 0.09619314 5.096586814 1090755.303 0.041613084 0.027739518 100.0268959 -2.000116792 0.141919091 RGDQGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 86.794 0.031772 193934000 350420 340110 226526 267791 242876 298560 410480 455130 493680 FALSE TRUE 304111.1091 337875.795 336074.7313 328597.0395 238043.2428 310045.7964 370671.7128 357803.9913 435317.7128 0.698595762 0.776159079 0.772021724 0.754844174 0.546826458 0.712228764 0.851496968 0.821937589 1 18.7317092 1.274494111 1.099809535 1.116553435 0.715549373 0.60325766 0.072959107 1.211325087 1.279376883 0.572391417 0.025420461 18.81456194 -1.274494111 -0.401004062 RGDS(ph)ES(ph)EEDEQDSEEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGDSESEEDEQDSEEVR 17 1 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 2 RGDS(1)ES(0.922)EEDEQDS(0.079)EEVR;RGDS(1)ES(0.997)EEDEQDS(0.003)EEVR 194.96 2.99E-11 525320000 746890 717990 486520 540060 725590 661340 637700 812790 871710 TRUE FALSE 648186.5941 713273.4764 721802.6993 662688.8773 711152.1786 686782.1777 575855.9522 638981.1836 768657.4369 0.843271089 0.927947148 0.939043408 0.86213812 0.925187404 0.893482772 0.749171119 0.83129513 1 19.55198126 2.447144609 24.99831041 0.845491142 0.902028102 0.053064645 0.067473403 416.9518184 347704.3987 0.024910228 0.019295635 279.9913464 -2.447144609 0.056536961 RGDS(ph)QECSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGDSQECSPR 10 1 Q13111;Q13111-2;Q13111-3 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 RGDS(0.5)QECS(0.5)PR 74.392 0.013534 0 33582 41214 23643 29401 36538 44286 35986 47785 41738 TRUE FALSE 29144.05361 40943.26252 35076.83388 36076.94642 35810.96529 45989.71108 32496.08326 37566.54961 36803.78119 0.791876614 1.112474349 0.953076905 0.980251084 0.973024079 1.249592015 0.882955017 1.020725273 1 15.16756637 2.94393682 24.99999598 1.031037622 0.970739597 0.090871041 0.117021985 905.3265591 403706.9114 0.035841791 0.035841934 878.8946483 -2.94393682 -0.060298025 RGDSQECS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGDSQECSPR 10 1 Q13111;Q13111-2;Q13111-3 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 RGDS(0.472)QECS(0.528)PR 135.5 0.00015092 52392000 103480 114010 69464 78647 85667 119640 104570 122130 118270 TRUE FALSE 89804.85582 113261.0608 103057.0227 96505.00339 83962.3943 124242.6282 94428.81749 96013.44992 104288.2553 0.861121471 1.086038504 0.988193948 0.925367896 0.805099232 1.191338639 0.905459749 0.920654484 1 16.67021717 RGDTVATLSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGDTVATLSER 11 1 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ; 161.25 4.25E-05 523300000 378140 312080 271400 231030 192527 225325 227550 261360 171257 FALSE TRUE 328167.8409 310029.9259 402649.9478 283488.8926 188696.0894 233993.3986 205482.236 205470.1979 151011.1926 2.173135881 2.053026141 2.666358307 1.877270736 1.249550356 1.549510302 1.36070865 1.360628934 1 17.20429596 3.416227712 3.938598683 1.330276781 2.277135797 0.828098459 0.207746419 0.084797182 2.677097161 0.059782154 0.080330171 2607.520386 -3.416227712 0.946859017 RGDTYELQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGDTYELQVR 10 1 A0A087WU53;Q9H0U3 A0A087WU53 MAGT1 Magnesium transporter protein 1 0 167.18 8.53E-06 364940000 75851 71722 46381 66650 95398 84680 50018 97352 81338 FALSE TRUE 65827.09817 71250.85346 68811.00674 81783.90118 93499.76644 87937.6944 45167.26206 76534.03239 71722.3143 0.917804993 0.993426581 0.959408622 1.140285307 1.303635659 1.226085567 0.629751877 1.06708816 1 16.13013442 2.298057994 24.99999998 0.922736807 1.09175861 0.232659923 0.161721512 124.598143 52353.55015 0.063144228 0.048911282 198.636015 -2.298057994 0.169021802 RGEAHLAVNDFELAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 RGEAHLAVNDFELAR 15 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;;;;; 200.77 4.38E-09 7949950000 2790163 2477871 1467755 1870631 2364598 2513964 2724224 2862680 1518098 FALSE TRUE 2421435.89 2461593.702 2177566.227 2295386.359 2317547.126 2610677.822 2460029.176 2250518.159 1338630.184 1.808890849 1.838890032 1.626712331 1.714727777 1.731282586 1.950260687 1.837721281 1.681209782 1 20.35232602 1.232287785 3.474940226 0.877736723 1.782884569 0.890077641 0.086195642 0.102583221 1.785842303 0.250236228 0.023553093 17.072133 -1.232287785 0.905147846 RGEDVETSKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RGEDVETSKK 10 2 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 ;;; 135.99 7.29E-05 1208970000 2123010 1780450 1217430 1453200 1428260 1230580 2283500 2915860 1742830 FALSE TRUE 1842448.849 1768754.107 1806183.22 1783171.271 1399840.42 1277921.209 2062046.521 2292326.03 1536794.623 1.198890744 1.150937204 1.175292517 1.160318526 0.910883211 0.831549766 1.341784055 1.491628091 1 20.55149295 2.183930356 24.99998844 1.325017459 1.076410375 0.232852921 0.169445728 111.3194223 50941.14809 0.071624988 0.048289591 152.7321116 -2.183930356 -0.248607084 RGEEGHDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGEEGHDPK 9 1 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 71.349 0.032348 99555000 139310 107190 106240 130620 89890 97042 130490 153270 315310 FALSE TRUE 120899.8305 106485.8618 157618.0194 160279.2674 88101.36487 100775.2685 117835.0999 120494.4032 278034.411 0.434837652 0.382995261 0.566901121 0.576472771 0.316872162 0.362456101 0.423814806 0.433379461 1 18.08490392 1.238335841 24.99967304 1.000000624 0.437021114 0.825717968 0.081255787 2.267156678 251591.1498 0.117788097 0.020862536 17.31154548 -1.238335841 -0.56297951 RGEEGHDPKEPEQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RGEEGHDPKEPEQLR 15 2 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;; 177.74 4.45E-07 2199450000 1986540 1733270 1224310 1235200 1587040 1333840 1918860 2304260 1133140 FALSE TRUE 1724013.706 1721884.035 1816390.411 1515671.039 1555461.009 1385153.688 1732769.253 1811511.931 999181.4801 1.725426001 1.723294586 1.817878381 1.516912662 1.556735228 1.386288393 1.734188721 1.812995904 1 19.93038721 3.732189709 24.49594644 1.545756626 1.75230915 0.211800977 0.220358367 711.7145974 2736521.525 0.060743239 0.092689704 5397.463436 -3.732189709 0.206552524 RGEEGHDPKEPEQLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RGEEGHDPKEPEQLRK 16 3 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;; 153.95 2.41E-07 822320000 1931000 1397200 959470 926110 1335740 911500 1966600 2250040 391397 FALSE TRUE 1675813.457 1388021.701 1423472.901 1136397.43 1309161.387 946565.9948 1775879.435 1768886.456 345126.4925 4.855650011 4.021776743 4.124496183 3.292698343 3.793279901 2.742663966 5.145590017 5.125327942 1 18.3967657 4.918678403 1.468641119 3.778645216 5.660867319 0.088407241 1.192947895 5.654131827 8.090490526 0.333155695 17.5433692 82923.64867 -4.918678403 1.882222103 RGEFCIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGEFCIAK 8 1 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 111.06 0.005301 2375600000 2403900 2455500 1573290 1900470 2314000 2154800 2576000 2939300 2495100 FALSE TRUE 2086218.524 2439369.659 2334138.306 2332000.76 2267955.927 2237696.55 2326179.916 2310753.569 2200132.12 0.948224202 1.108737805 1.060908245 1.059936691 1.030827152 1.017073716 1.057291012 1.050279457 1 21.06915873 3.224761645 24.75616756 1.034756143 1.050219064 0.011890376 0.042584523 918.4514311 1647751.434 0.012242495 0.013965771 1677.882889 -3.224761645 0.015462921 RGEGDAPFSEPGT(ph)TSTQRPSSPETATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGEGDAPFSEPGTTSTQRPSSPETATK 27 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RGEGDAPFS(0.011)EPGT(0.899)T(0.069)S(0.011)T(0.001)QRPS(0.002)S(0.007)PETATK 218.25 5.26E-34 1858800000 908960 696720 475750 616270 686870 602170 766680 890990 876750 TRUE FALSE 788838.633 692143.2004 705824.2913 756203.5226 673202.6308 625335.8696 692327.4916 700458.7222 773101.6138 1.020355693 0.895281019 0.912977387 0.978142471 0.870781562 0.808866336 0.895519398 0.906037072 1 19.56029852 3.23108582 24.99965847 0.89304256 0.944894867 0.182866174 0.057228664 325.3529714 1088150.283 0.017594674 0.020331851 1702.494901 -3.23108582 0.051852306 RGEGDAPFSEPGTT(ph)STQRPSSPETATK ddPTM_MDA-MB-175_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(0.01)EPGT(0.392)T(0.569)S(0.019)T(0.003)QRPS(0.004)S(0.004)PETATK;RGEGDAPFS(0.041)EPGT(0.041)T(0.182)S(0.182)T(0.182)QRPS(0.182)S(0.182)PET(0.007)AT(0.002)K 173.64 4.27E-12 2564650000 1034660 771230 535475 675550 740730 672150 869740 1053050 1062820 TRUE FALSE 897927.0595 766163.7393 794432.5011 828943.9526 725990.9222 698008.0454 785392.7487 827863.4523 937174.6304 0.95812139 0.817525053 0.847688867 0.884513863 0.774659171 0.744800406 0.838043117 0.883360929 1 19.83795837 1.277195031 2.277532812 1.036733432 0.833787975 0.438007708 0.057722216 0.54491492 3.154423867 0.217860669 0.015706002 18.93193615 -1.277195031 -0.202945457 RGEGDAPFSEPGTTSTQRPS(ph)S(ph)PETATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGEGDAPFSEPGTTSTQRPSSPETATK 27 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RGEGDAPFSEPGTT(0.004)S(0.005)T(0.005)QRPS(0.977)S(0.99)PET(0.017)AT(0.002)K 126.5 3.67E-05 208570000 219130 146150 108800 132170 152000 119340 172460 187910 218000 TRUE FALSE 190171.4153 145189.931 161416.0439 162181.2186 148975.4974 123931.087 155734.8557 147726.9088 192228.2883 0.989299842 0.755299505 0.839710145 0.843690697 0.774992581 0.644707853 0.810155764 0.768497239 1 17.55246113 4.746779412 24.32213474 0.798460605 0.989299982 0.295760884 0.089102647 900.674141 2665302.151 0.021175524 0.227706929 55818.66071 -4.746779412 0.190839377 RGEGDAPFSEPGTTSTQRPS(ph)SPETATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RGEGDAPFSEPGTTSTQRPSSPETATK 27 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RGEGDAPFSEPGT(0.001)T(0.027)S(0.189)T(0.189)QRPS(0.52)S(0.074)PETATK;RGEGDAPFSEPGT(0.001)T(0.003)S(0.018)T(0.115)QRPS(0.432)S(0.432)PETATK;RGEGDAPFSEPGTTSTQRPS(0.5)S(0.5)PETATK 187.77 4.85E-18 8785680000 1263020 910230 702400 820800 950270 733450 1044890 1299880 1207060 TRUE FALSE 1096108.707 904250.6392 1042082.989 1007175.185 931361.4862 761666.2961 943556.7286 1021910.778 1064362.742 1.029826265 0.849569986 0.979067519 0.946270614 0.875041421 0.715607815 0.886499209 0.960115135 1 20.02155848 4.755009863 23.4210431 0.90257935 1.029826504 0.197702807 0.081203295 2500.406787 3560028.665 0.021036758 0.506813315 56886.58494 -4.755009863 0.127247154 RGEGDAPFSEPGTTSTQRPSS(ph)PETATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RGEGDAPFSEPGTTSTQRPSSPETATK 27 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RGEGDAPFSEPGTTST(0.001)QRPS(0.204)S(0.795)PETATK;RGEGDAPFSEPGTTSTQRPS(0.216)S(0.784)PET(0.001)ATK;RGEGDAPFS(0.001)EPGT(0.138)T(0.138)S(0.197)T(0.197)QRPS(0.047)S(0.282)PET(0.001)ATK 177.86 1.11E-17 2353210000 611020 422750 334366 367475 445538 358684 508547 581150 542300 TRUE FALSE 530272.1589 419972.9274 496066.516 450915.8153 436672.6655 372482.8056 459228.1902 456875.595 478189.9118 1.108915403 0.878255515 1.037383901 0.942963881 0.913178331 0.778943253 0.960346881 0.955427088 1 18.86722417 4.750656001 23.95744579 0.934407937 1.108915597 0.384472985 0.069815049 1183.766397 2344619.207 0.017249774 0.269880618 56319.1383 -4.750656001 0.174507659 RGEIIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGEIIAK 7 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 117.4 0.0084017 1551280000 3239800 2545300 1537930 1924240 2327100 1940740 2636900 3073000 2723300 FALSE TRUE 2811652.221 2528579.757 2281678.092 2361168.102 2280795.263 2015401.524 2381173.844 2415862.864 2401354.576 1.170860917 1.052980589 0.950162927 0.983265081 0.949795289 0.839276941 0.991596105 1.00604171 1 21.19541701 4.588351551 2.173031723 0.961405483 1.193982561 0.674484388 0.047687413 0.302230845 2.058021367 0.013516216 0.120250759 38757.12479 -4.588351551 0.232577078 RGELQTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGELQTK 7 1 O75152;E9PBY7;E9PQ61 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 0 98.458 0.018035 92188000 194190 168730 115670 115160 110990 204250 166100 178830 163900 FALSE TRUE 168527.2995 167621.6015 171608.3989 141308.8381 108781.5161 212107.6297 149991.6476 140588.5962 144523.9287 1.166085789 1.159819021 1.187404746 0.977753922 0.752688618 1.467629835 1.03783262 0.972770374 1 17.14094885 3.749535146 23.88692742 1.034792476 1.169974788 0.118798513 0.175015155 924.9735121 2013266.639 0.046672748 0.079776455 5617.397366 -3.749535146 0.135182312 RGERPDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGERPDYK 8 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L0N7 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ; 66.504 0.034596 152526000 160315 122372 96260 119391 102206 112609 139112 167842 242899 FALSE TRUE 139128.9666 121568.1303 142811.658 146500.5513 100172.3006 116941.1411 125620.9397 131950.2944 214183.7569 0.64957758 0.567588 0.666771654 0.683994685 0.467693265 0.545985105 0.586510114 0.616061163 1 17.70848955 1.236220647 5.00644025 1.026716643 0.594493333 0.802195366 0.062807462 0.077797873 4.973178955 0.117796995 0.016196264 17.22743608 -1.236220647 -0.43222331 RGES(ph)LDNLDSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RGESLDNLDSPR 12 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 RGES(1)LDNLDSPR;RGES(1)LDNLDSPR;RGES(1)LDNLDSPR;RGES(1)LDNLDSPR 256.4 3.83E-21 4025070000 2884710 3167130 2090520 2452050 3317680 2798250 3459680 3876770 3603040 TRUE FALSE 2503488.265 3146324.914 3101502.464 3008825.43 3251664.659 2905900.488 3124160.766 3047752.905 3177092.716 0.787980864 0.990315737 0.976207729 0.947037339 1.023471755 0.914641387 0.983339501 0.959289885 1 21.59927576 4.741942582 24.99542696 0.972421945 0.787980795 0.794447038 0.029769054 132.5952325 979940.8887 0.006560713 0.046105756 55200.4454 -4.741942582 -0.184441149 RGESLDNLDS(ph)PR ddPTM_MDA-MB-175_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 RGESLDNLDS(1)PR;RGESLDNLDS(1)PR 105 0.0012724 811490000 652390 776720 562310 718520 929480 1003460 892970 1139400 984910 TRUE FALSE 566175.0086 771617.6752 834244.9968 881670.9479 910985.1665 1042063.756 806369.9068 895748.1768 868475.0618 0.651918556 0.888474188 0.960586013 1.015194318 1.048947985 1.19987758 0.92848942 1.031403452 1 19.7281249 4.959134267 1.088673686 1.037980653 0.307008926 0.76636279 0.067482309 1.247516588 0.893435118 0.020864 1.173016794 91019.46254 -4.959134267 -0.730971727 RGEVPAELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RGEVPAELR 9 1 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ;;;;; 161.51 0.00010339 2086350000 1757990 1979610 1441366 1668640 1913140 2088350 1825950 2052790 3542120 FALSE TRUE 1525667.167 1966605.812 2138415.419 2047530.216 1875072.257 2168690.176 1648869.65 1613816.833 3123374.609 0.488467558 0.629641352 0.684649037 0.655550637 0.600335372 0.694342001 0.527912869 0.51669013 1 21.57467418 1.231132773 24.99669204 1.000000705 0.600755926 0.761470236 0.070407786 139.6752808 470004.2815 0.186310378 0.018272721 17.02678973 -1.231132773 -0.399244779 RGFAFVTFDDHDSVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGFAFVTFDDHDSVDK 16 1 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;A0A2R8Y4L2;H0YH80 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ; 138.55 3.90E-06 462280000 1256610 1171770 371030 761740 1216280 1065240 1276380 1529330 1031190 FALSE TRUE 1090545.805 1164072.566 550461.349 934704.7095 1192078.408 1106220.472 1152596.864 1202294.681 909283.8929 1.199345785 1.280208057 0.605378973 1.027956963 1.311007945 1.21658426 1.267587464 1.32224346 1 19.79437127 3.254037684 22.30164931 1.238792111 1.016017916 0.19489923 0.195134063 101.837064 146738.4921 0.056987429 0.073180367 1794.889365 -3.254037684 -0.222774195 RGFEGSCSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGFEGSCSQK 10 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 105.46 0.0040826 118080000 164920 158910 97880 128520 158210 136290 176750 208020 140310 FALSE TRUE 143125.4041 157866.1097 145215.0954 157702.4303 155061.9305 141533.1645 159608.8122 163536.5418 123722.7116 1.156824016 1.275967101 1.173714134 1.274644147 1.253302069 1.143954595 1.290052652 1.321798881 1 16.91675083 1.226430704 24.99917406 0.999999451 1.240941626 0.603670841 0.060062029 402.1534628 828766.8642 0.246199089 0.014807337 16.84343651 -1.226430704 0.240942175 RGFGFVTFDDHDPVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGFGFVTFDDHDPVDK 16 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ; 99.055 0.0016385 1886520000 1608280 1106580 780820 867180 1098060 907810 1327510 1531070 1129450 FALSE TRUE 1395741.723 1099310.803 1158427.164 1064086.473 1076210.754 942734.0381 1198768.285 1203662.595 995927.7077 1.401448832 1.103805823 1.163163907 1.068437463 1.08061132 0.946588825 1.203669981 1.208584304 1 19.9256815 4.738901052 23.92539529 1.106573495 1.401448978 0.568086149 0.083083268 12.47771523 876235.6782 0.021119609 0.120128114 54815.20616 -4.738901052 0.294875483 RGGADVNIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGGADVNIR 9 1 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ; 128.03 0.00068734 453370000 738280 666760 281100 382200 613390 652830 578440 655830 269790 FALSE TRUE 640714.4274 662380.0097 417040.9002 468984.3516 601184.7391 677944.7925 522342.9778 515585.8582 237895.7335 2.693257327 2.784329083 1.753040687 1.971386139 2.527093404 2.849755994 2.195680309 2.167276607 1 17.85996987 1.083740885 1.986388121 0.04099441 2.393409783 0.608222357 0.349421906 0.952767865 2.547670822 4.818465709 0.10028771 12.12665117 -1.083740885 2.352415373 RGGDGYDGGYGGFDDYGGYNNYGYGNDGFDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RGGDGYDGGYGGFDDYGGYNNYGYGNDGFDDR 32 1 P31942;P31942-3;P31942-4;P31942-5 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;; 312.45 7.43E-104 1120470000 629047 458623 268125 343684 465866 441652 459439 530366 430641 FALSE TRUE 545916.8451 455610.2753 397791.1468 421722.7051 456596.1781 458642.6382 414882.6765 416951.3582 379731.1116 1.437640553 1.199823405 1.047560062 1.110582442 1.202419723 1.207808958 1.092569621 1.098017375 1 18.53461868 4.681113285 3.015391995 1.113748753 1.46988743 0.730736155 0.06275165 0.175846433 2.495974047 0.016565708 0.1392544 47985.86025 -4.681113285 0.356138677 RGGGS(ph)GGGEES(ph)EGEEVDED ddPTM_MDA-MB-175_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 149.67 5.57E-08 629050000 1186740 922870 717960 721750 1054870 964480 1021650 1157500 1057040 TRUE FALSE 1029909.302 916807.6062 1065167.857 885634.3688 1033880.151 1001584.17 922570.5402 909977.6327 932077.9354 1.104960501 0.983616897 1.142788405 0.950172014 1.109220712 1.074571269 0.989799785 0.976289212 1 19.83009106 2.228021889 23.41380377 0.986157428 1.058263062 0.258366025 0.057489917 123.4656039 274296.957 0.021237619 0.014511135 169.0526133 -2.228021889 0.072105635 RGGGSGGGEES(ph)EGEEVDED ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RGGGSGGGEESEGEEVDED 19 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 RGGGS(0.001)GGGEES(0.999)EGEEVDED;RGGGSGGGEES(1)EGEEVDED;RGGGSGGGEES(1)EGEEVDED 298.22 9.24E-50 6312353000 6038197 4728319 3299309 3509249 4853600 4645416 5109039 5363429 4946006 TRUE FALSE 5240233.968 4697258.361 4894865.868 4306077.621 4757022.856 4824128.16 4613565.184 4216501.447 4361294.805 1.201531701 1.077032985 1.122342352 0.987339268 1.090736368 1.106122923 1.057843001 0.966800374 1 22.05632508 8 0.142147894 0.923200131 1.754765137 0.509788551 0.049127025 146.4590562 1.778730437 1.026578798 24.36493031 100000000 -8 0.831565006 RGGPNYQEGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RGGPNYQEGLR 11 1 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 ;;;;; 176.62 1.35E-05 2839030000 1648060 1652240 768948 939660 1623290 1801640 1618360 1779000 843859 FALSE TRUE 1430264.695 1641386.327 1140813.825 1153024.165 1590989.705 1870950.257 1461411.696 1398574.694 744098.9503 1.922143143 2.205871042 1.53314801 1.549557575 2.138142655 2.514383679 1.964001825 1.87955472 1 19.50513496 1.224594455 3.621345964 0.848999299 1.97459201 0.525732439 0.288818132 0.271922986 5.34275954 0.857434384 0.078929285 16.77237078 -1.224594455 1.12559271 RGGRIPT(ph)MGCLDLPGEDMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGGRIPTMGCLDLPGEDMR 19 2 A0A140T901;A0A140T8Y9;Q9H2S5-2;Q9H2S5 A0A140T901 RNF39 RING finger protein 39 1 RGGRIPT(1)MGCLDLPGEDMR 40.113 0.072738 317360000 30171 31652 21230 23652 31742 33518 26617 29946 45971 TRUE FALSE 26183.82591 31444.07593 31496.89901 29022.5481 31110.3963 34807.45915 24035.68744 23542.28094 40536.36075 0.645934302 0.775700515 0.777003619 0.715963337 0.767468903 0.858672523 0.592941423 0.580769475 1 15.30692895 2.235855997 24.99807587 0.68912729 0.757198444 0 0.125985931 224.7687545 2077430.469 0.049219575 0.034873859 172.1297732 -2.235855997 0.068071154 RGILTLK ddPTM_MDA-MB-175_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 ; 151.56 0.0030031 26945000000 7854200 7746000 4055600 5545600 7312700 6826000 8659600 9457100 7221500 FALSE TRUE 6816247.57 7695116.016 6016901.725 6804813.239 7167191.577 7088600.637 7819793.325 7434772.76 6367782.497 1.070427197 1.208445172 0.944897494 1.068631544 1.125539633 1.11319767 1.228024564 1.167560727 1 22.60235963 3.120127458 3.73825858 1.140981685 1.073786904 0.081070537 0.084164548 0.516779562 13.71032315 0.026508288 0.030639988 1318.643682 -3.120127458 -0.067194781 RGIQYLQEQGMLGTTPEDIAQFLHQEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGIQYLQEQGMLGTTPEDIAQFLHQEER 28 1 Q9Y6D6;E5RIF2 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 0 53.197 0.051243 235950000 176570 146160 206280 167800 84359 89922 135350 128370 139850 FALSE TRUE 153235.8271 145199.8653 306037.698 205901.5547 82680.42095 93381.35753 122223.7778 100919.0745 123317.0923 1.242616285 1.177451257 2.481713542 1.669691936 0.670470082 0.757245859 0.99113412 0.818370532 1 16.91201325 3.246310742 24.94746189 0.850076746 1.669541921 0.545659859 0.36029267 132.8989882 427795.9377 0.107649544 0.136345799 1763.23721 -3.246310742 0.819465174 RGKNENESEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGKNENESEKR 11 3 P47813;O14602;A6NJH9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 ; 75.78 0.016275 39054000 48609 32396 14230.6 11110.6 26159 21519.2 45403 55066 5576.2 FALSE TRUE 42185.19749 32183.18854 21112.56576 13633.43154 25638.48708 22347.05755 40999.82405 43290.56442 4916.987988 8.579479468 6.545305504 4.293800556 2.772720124 5.214266771 4.544867224 8.33840232 8.804285169 1 12.26355912 4.610623577 3.416968197 5.426021765 8.622774456 0.182146061 2.328178918 0.542849276 10.28986692 0.625557046 3.599569383 40796.56303 -4.610623577 3.196752691 RGLDEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGLDEDR 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 121.67 0.0070797 606050000 710960 658600 471030 543860 641320 748200 615230 771140 674540 FALSE TRUE 617004.8347 654273.6132 698821.6835 667351.7254 628558.9867 776983.7381 555565.0893 606237.712 594796.6496 1.037337441 1.099995458 1.174891762 1.121982993 1.056762823 1.306301471 0.934042062 1.01923525 1 19.182037 2.192442485 24.99997128 0.989578361 1.129339678 0.457364738 0.076092159 112.6419556 61060.76897 0.029563919 0.019932069 155.7551751 -2.192442485 0.139761317 RGLEVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RGLEVSK 7 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;;; 127.46 0.0061773 2747980000 5167470 4896980 2984410 3370260 4409500 4318260 5155050 5787690 4940720 FALSE TRUE 4484575.747 4864811.416 4427680.658 4135529.044 4321759.577 4484386.256 4655114.044 4550037.533 4356633.71 1.029367178 1.116644579 1.016307763 0.949248736 0.991995165 1.029323683 1.068511689 1.04439295 1 22.05478239 4.203034514 24.68817083 1.017273443 1.073005882 0.291740671 0.037830565 189.2741963 131532.2909 0.01046961 0.021795645 15960.05977 -4.203034514 0.055732438 RGLLSNHTGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGLLSNHTGSPR 12 1 Q13111 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 RGLLSNHT(0.086)GS(0.914)PR 57.788 0.067824 185170000 192250 178310 137550 134850 159770 169510 182550 210570 155470 TRUE FALSE 166843.6754 177138.6699 204069.6401 165469.7536 156590.8896 176031.1594 164846.3291 165541.2442 137090.5137 1.217032972 1.292129303 1.488575938 1.207010967 1.142244531 1.284050622 1.202463428 1.207532452 1 17.06476922 0.114243336 0.692934589 4.63E-32 1.285182566 0.452614301 0.090985333 12.95304757 1.456074917 18.6972818 0.041390444 1.30089827 -0.114243336 1.285182566 KPVTVS(ph)PTTPT(ph)SPTEGEAS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 2 KPVTVS(0.895)PT(0.137)T(0.074)PT(0.804)S(0.089)PT(0.001)EGEAS 142.39 3.45E-07 479890000 350940 433510 361930 509500 598800 578510 683100 786950 752620 TRUE FALSE 304562.3898 430662.2443 536960.5586 625189.7622 586885.0515 600765.654 616853.0671 618666.8666 663646.121 0.458922881 0.648933567 0.809106754 0.942052914 0.884334336 0.905250005 0.929490956 0.932224038 1 19.34005463 4.520140054 1.14982261 0.935174566 0.328967792 0.964903678 0.030666233 0.187012073 0.274158808 0.009605109 0.125159237 33123.79239 -4.520140054 -0.606206774 down RGLLYDS(ph)DEEDEERPARK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGLLYDSDEEDEERPARK 18 3 P49736 P49736 MCM2 DNA replication licensing factor MCM2 1 RGLLYDS(1)DEEDEERPARK;RGLLYDS(1)DEEDEERPARK 158.89 2.45E-10 357620000 221861 161867 106347 104142 172169 148078 209926 222808 83715 TRUE FALSE 192541.5067 160803.685 157776.7649 127789.0328 168743.1737 153774.6565 189567.4088 175162.2431 73818.30807 2.608316443 2.178371318 2.137366312 1.731129257 2.285925784 2.083150651 2.568027008 2.372883471 1 16.17169105 4.764735076 2.483820268 2.087520525 2.744176732 0.142383476 0.429945356 1.307643326 9.541521345 0.107941043 1.871368389 58174.82379 -4.764735076 0.656656207 RGMDDDRGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGMDDDRGPR 10 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 93.096 0.035832 174174000 139261 126126 61030 67414 118402 125935 97969 114141 71301 FALSE TRUE 120857.306 125297.47 90544.31213 82721.37906 116046.0318 130779.8009 88467.98146 89732.8354 62871.87701 1.922279273 1.992901691 1.440140114 1.315713527 1.845754213 2.080100152 1.407115322 1.427233282 1 15.94012721 1.435989155 1.441982728 0.879458187 1.735117063 0.473065559 0.251744522 0.793747901 2.052895978 0.924327724 0.080343704 27.28909634 -1.435989155 0.855658876 RGNDAVMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGNDAVMAR 9 1 P21399 P21399 ACO1 Cytoplasmic aconitate hydratase 0 ; 86.898 0.01451 99130000 42947 38221 23533 25480 31603 44202 39023 41565 31497 FALSE TRUE 37271.44514 37969.92373 34913.63751 31265.62344 30974.16213 45902.47954 35238.55547 32676.64821 27773.46054 1.341980596 1.367129734 1.257086327 1.125737406 1.115243168 1.652746134 1.268785192 1.176542194 1 14.76141933 1.430450982 2.412199203 0.986994947 1.302942341 0.307056091 0.14837779 0.505517995 4.572159882 0.290691856 0.041177581 26.94331212 -1.430450982 0.315947394 RGNDPLT(ph)SSPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RGNDPLTSSPGR 12 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RGNDPLT(0.38)S(0.253)S(0.367)PGR;RGNDPLT(0.858)S(0.138)S(0.004)PGR;RGNDPLT(0.785)S(0.136)S(0.079)PGR 82.705 0.027532 3778880000 1690300 1565400 927580 1270530 1558080 1658010 1528730 1828680 1224510 TRUE FALSE 1466922.572 1555116.784 1376160.791 1559023.255 1527077.256 1721794.718 1380474 1437631.013 1079749.823 1.358576349 1.440256578 1.274518191 1.443874518 1.414288036 1.594623756 1.278512828 1.331448251 1 20.04226565 0.841767918 1.3939236 0.321367283 1.409727374 0.661394866 0.089862269 2.040905303 1.596692528 4.157773967 0.025444833 6.946530036 -0.841767918 1.088360092 RGNDPLTSS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGNDPLTSSPGR 12 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RGNDPLT(0.05)S(0.471)S(0.478)PGR;RGNDPLT(0.057)S(0.12)S(0.823)PGR 99.069 0.0024523 6160400000 1586000 1457510 947230 1098910 1464850 1499330 1317180 1628080 1419310 TRUE FALSE 1376406.082 1447935.521 1405313.596 1348434.311 1435702.351 1557010.195 1189440.086 1279927.762 1251520.789 1.099786831 1.156940847 1.122884741 1.077436606 1.147166203 1.244094552 0.950395788 1.022697963 1 20.25525082 2.22299878 24.99989816 0.995935321 1.138607184 0.694462365 0.04695113 138.2333802 222068.4979 0.01913987 0.012954664 167.1085921 -2.22299878 0.142671863 RGNGLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGNGLIK 7 1 P62249;M0R210;M0R3H0;M0R1M5;Q6IPX4 P62249 RPS16 40S ribosomal protein S16 0 ; 153.15 0.0028312 1430690000 2133600 1859530 1085990 1525720 1971890 1670560 2059800 2368900 1964920 FALSE TRUE 1851639.354 1847314.625 1611178.396 1872158.045 1932653.247 1734827.524 1860040.913 1862329.17 1732629.396 1.068687486 1.066191437 0.929903648 1.080530002 1.11544526 1.001268666 1.073536509 1.074857193 1 20.72453167 4.434213456 24.99999688 1.043913748 1.068066958 0.041496843 0.0527449 510.640412 297520.565 0.013114697 0.034698339 27177.74731 -4.434213456 0.02415321 RGNVAGDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 RGNVAGDSK 9 1 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;;;;;;;; 166.66 9.71E-05 17769779000 10496880 8807710 6028080 7641240 4630990 7081010 10428750 11765910 13287610 FALSE TRUE 9109690.712 8749851.573 8943279.651 9376300.331 4538842.359 7353421.037 9417371.43 9249861.709 11716763.88 0.777492045 0.746780567 0.763289227 0.800246589 0.387380202 0.627598295 0.803751917 0.789455331 1 23.48207082 1.216224881 1.408692237 1.139367146 0.689658199 0.383424961 0.121805126 1.553567805 2.59425967 1.027442668 0.038113437 16.45223412 -1.216224881 -0.449708946 RGNVCGDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RGNVCGDSK 9 1 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ;;; 140.49 0.00017475 2889890000 2643590 2033210 1129250 1411810 1147230 1641480 2315250 2653900 2084280 FALSE TRUE 2294232.883 2019853.71 1675359.077 1732383.039 1124402.368 1704628.798 2090717.411 2086384.138 1837878.793 1.248304781 1.099013557 0.911572125 0.942599178 0.611793537 0.927497942 1.137570889 1.13521313 1 20.80961019 2.24259247 24.89901368 1.102097536 0.944878246 0.126053492 0.163627719 186.2768887 1150376.615 0.067153334 0.050062076 174.8205452 -2.24259247 -0.15721929 RGPAEESSSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RGPAEESSSWR 11 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 128.57 0.00042197 802479000 989675 915782 533128 577068 788644 765417 925196 1102449 534227 FALSE TRUE 858886.9412 909766.1677 790950.484 708100.1093 772951.5274 794863.0873 835470.6343 866698.8606 471071.2927 1.823263176 1.931270663 1.679046243 1.503169733 1.640837681 1.687351999 1.77355455 1.839846482 1 18.84558589 1.233530303 24.99958126 0.999998869 1.734275002 0.791000972 0.118699759 78.91232769 392131.5425 0.261087643 0.032161218 17.12104634 -1.233530303 0.734276133 RGPCIIYNEDNGIIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGPCIIYNEDNGIIK 15 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ; 224.34 1.84E-12 2868200000 2930700 2544250 1575200 2006820 2434060 2193490 2940400 3360000 2428670 FALSE TRUE 2543400.57 2527536.654 2336971.989 2462499.153 2385626.968 2277874.98 2655240.461 2641490.148 2141555.399 1.187641735 1.180234074 1.091249841 1.149864792 1.1139693 1.063654473 1.239865409 1.233444696 1 21.03022757 2.234688452 24.9999802 1.176956208 1.131598216 0.006185073 0.07517176 289.3083096 1867841.517 0.029916007 0.021047999 171.667646 -2.234688452 -0.045357992 RGPDHQPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGPDHQPAK 9 1 C9J6P4;Q7Z2W4;Q7Z2W4-4 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 0 56.563 0.078623 29057000 25967 29958 18830 22702 24654 24247 32300 36486 37498 FALSE TRUE 22535.39516 29761.20393 27936.25098 27856.83608 24163.43363 25179.79778 29167.55097 28683.75283 33065.02916 0.681547718 0.900080982 0.84488814 0.842486361 0.730785191 0.761523532 0.882126879 0.867495162 1 15.01301855 1.059459898 1.158782743 1.157947157 0.803565923 0.48150529 0.065599584 2.137308141 1.811505678 1.026462142 0.0204596 11.4672663 -1.059459898 -0.354381234 RGPEEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGPEEDR 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 139.97 0.0042586 398920000 451540 438650 283990 329960 332220 482340 430710 484990 495350 FALSE TRUE 391867.8449 435768.4793 421328.5139 404882.4611 325609.472 500895.9319 388939.8105 381278.6627 436790.2873 0.897153294 0.997660644 0.96460138 0.926949323 0.745459506 1.14676527 0.890449769 0.872910121 1 18.73658125 3.705069754 8.745451084 0.92320527 0.957583234 0.00681518 0.103490553 1.817162028 453.3133448 0.027686828 0.041526964 5070.721455 -3.705069754 0.034377963 RGPEVTSQGVQTS(ph)SPACK ddPTM_MDA-MB-175_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(0.139)S(0.849)S(0.011)PACK 213.48 4.74E-17 575090000 519310 415540 382930 405510 402240 444830 514630 567400 702730 TRUE FALSE 450681.8677 412810.2904 568116.2288 497587.2433 394236.211 461942.8979 464721.2618 446065.9255 619654.06 0.727312055 0.666194764 0.916828059 0.803008123 0.636219847 0.745485147 0.749968881 0.71986283 1 19.24110349 1.234985529 24.9275042 1.000000373 0.745847572 0.525693635 0.075938838 83.46041975 581837.931 0.134249473 0.018719 17.17851146 -1.234985529 -0.2541528 RGPEVTSQGVQTSS(ph)PACK ddPTM_MDA-MB-175_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 RGPEVTSQGVQTS(0.007)S(0.993)PACK 175.28 2.29E-12 542130000 571600 443480 411760 465570 468980 389910 568600 611240 733360 TRUE FALSE 496061.6118 440566.7507 610888.5133 571284.7843 459648.2155 404910.09 513457.2595 480531.0827 646663.0162 0.767109916 0.681292636 0.944678291 0.883435066 0.710800222 0.626153158 0.794010554 0.743093498 1 19.30265458 1.234631441 24.75306517 1.000000381 0.768866725 0.382340457 0.092341927 118.1730172 744345.4824 0.173089488 0.023529812 17.16451124 -1.234631441 -0.231133656 RGPFELEAFYSDPQGVPYPEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGPFELEAFYSDPQGVPYPEAK 22 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 154.11 6.46E-13 194650000 711480 566000 374720 471810 523300 477800 663550 748310 625130 FALSE TRUE 617456.1153 562281.9087 555935.8454 578941.6717 512887.3538 496181.2752 599199.0231 588289.7299 551227.8436 1.120146819 1.020053532 1.008540936 1.050276539 0.930445296 0.900138266 1.087026046 1.067235149 1 19.07228924 4.740299731 4.05519594 1.011192212 1.1298094 0.275485411 0.057159934 0.370246505 13.06103575 0.015429278 0.129299732 54992.02741 -4.740299731 0.118617188 RGPGLYYVDSEGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RGPGLYYVDSEGNR 14 1 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;;; 227.47 3.24E-12 6361050000 4350970 4106100 2236680 2770730 3905130 3662990 4358160 4231350 3294620 FALSE TRUE 3775978.291 4079126.759 3318345.929 3399866.594 3827425.553 3803907.596 3935506.314 3326508.731 2905133.777 1.299760555 1.404109784 1.142235155 1.170296054 1.317469641 1.309374331 1.354673009 1.14504494 1 21.47017317 1.463902158 3.232921138 1.006414715 1.281724001 0.589886786 0.078568713 0.185548928 3.475021944 0.101456223 0.021616146 29.1006144 -1.463902158 0.275309286 RGPLSQNGSFGPSPVSGGECS(ph)PPLTVEPPVRPLSATLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGPLSQNGSFGPSPVSGGECSPPLTVEPPVRPLSATLNR 39 2 Q5JRA6-2;Q5JRA6;Q5JRA6-4 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 1 RGPLSQNGSFGPSPVSGGECS(0.966)PPLT(0.034)VEPPVRPLSATLNR 170.51 1.17E-18 1437600000 133190 160800 88964 104590 204580 211570 112370 206960 115640 TRUE FALSE 115588.604 159743.6942 131987.288 128338.7581 200509.2583 219709.2348 101472.3747 162703.2146 101969.1709 1.133564223 1.566588144 1.294384241 1.258603526 1.966371369 2.154663344 0.995127976 1.595611821 1 16.63777351 0.825553737 1.824718669 1.28E-20 1.512385689 0.146910389 0.360040092 7.340564898 8.266953033 28.54451774 0.099603248 6.691966177 -0.825553737 1.512385689 RGPNYTSGYGTNSELS(ph)NPS(ph)ETESER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGPNYTSGYGTNSELSNPSETESER 25 1 B4DXZ6;P51114;P51114-3;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 2 RGPNYTSGYGTNS(0.001)ELS(0.999)NPS(0.999)ET(0.001)ESER;RGPNYTSGYGTNS(0.004)ELS(0.995)NPS(0.966)ET(0.029)ES(0.006)ER 103.1 0.016635 625880000 372310 316760 222000 254900 321800 335770 281000 287950 385510 TRUE FALSE 323108.2902 314679.1827 329359.9425 312778.9409 315396.8096 348687.2892 253748.6633 226374.1333 339935.447 0.950498964 0.925702764 0.968889669 0.920112756 0.927813832 1.0257456 0.746461322 0.66593271 1 18.37490128 2.228616025 24.99928311 0.772937005 0.949945901 0.365895741 0.089306501 176.0835605 442644.8628 0.035352484 0.024153263 169.2840437 -2.228616025 0.177008896 RGPNYTSGYGTNSELSNPS(ph)ETESER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.996)ET(0.004)ESER;RGPNYTSGYGTNSELSNPS(1)ETESER;RGPNYTSGYGTNSELS(0.002)NPS(0.988)ET(0.01)ESER 243.74 6.15E-39 1385920000 340732 315008 252502 272341 356527 360803 281355 323809 418535 TRUE FALSE 295703.4029 312938.6917 374612.8118 334180.1865 349432.8102 374683.3249 254069.2354 254564.9652 369056.2691 0.801242053 0.847943032 1.015056085 0.905499282 0.946828003 1.015247149 0.688429534 0.689772771 1 18.49348127 2.235546967 24.99999581 0.766937803 0.923216964 0.230605805 0.107886492 94.85735294 786881.5779 0.042989731 0.030392094 172.0073349 -2.235546967 0.156279161 RGPNYTSGYGTNSELSNPSETESER ddPTM_MDA-MB-175_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 0 242.5 1.86E-38 262330000 119610 106220 68376 87184 123380 129730 93958 117190 128640 FALSE TRUE 103803.2354 105522.2338 101442.8623 106980.4597 120924.9794 134720.797 84845.96762 92129.83047 113432.3257 0.915111585 0.930265981 0.894302939 0.943121452 1.066053954 1.187675525 0.747987552 0.812200842 1 16.79147231 2.202480294 24.99998207 0.840421832 0.983788679 0.265627777 0.10561256 234.9886543 162821.5959 0.045399413 0.030609357 159.3970555 -2.202480294 0.143366847 RGPPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGPPEK 6 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 133.47 0.023172 405730000 662970 608570 461340 542000 433590 526890 618900 750110 993450 FALSE TRUE 575356.8347 604572.2636 684445.5671 665069.384 424962.4073 547159.7992 558879.1733 589704.8139 876005.4727 0.656795936 0.690146674 0.781325675 0.759206882 0.485113873 0.624607741 0.637985938 0.673174806 1 19.74058036 1.238745987 6.402812068 1.009977243 0.662770729 0.635500648 0.080120306 0.085260187 15.70989147 0.129122467 0.020989076 17.32790217 -1.238745987 -0.347206515 RGPPPPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RGPPPPPR 8 1 P38159;P38159-2;H3BT71;H0Y6E7 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 0 ;;; 113.5 0.0045486 409492000 438185 341052 219553 241565 376201 334824 363809 407813 355676 FALSE TRUE 380277.742 338811.607 325729.5652 296416.0253 368715.3361 347704.8959 328526.8592 320605.3636 313628.3885 1.212510589 1.080296362 1.038584443 0.945118606 1.17564401 1.108652497 1.047503578 1.022245993 1 18.25869663 RGPRT(ph)PPITTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGPRTPPITTK 11 2 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 RGPRT(1)PPITTK;RGPRT(1)PPITTK 112.42 0.072818 495450000 778210 630430 446700 488210 651320 593250 735350 844520 538350 TRUE FALSE 675367.5768 626288.6638 662725.6141 599065.5423 638360.0063 616072.7114 664035.8702 663925.9701 474706.8763 1.422704432 1.319316604 1.39607334 1.26196938 1.344745649 1.297796055 1.398833477 1.398601965 1 18.85667742 1.234187591 24.99567306 0.999999474 1.354255539 0.827184792 0.050993877 52.32764418 299059.1821 0.094370259 0.012343336 17.14697801 -1.234187591 0.354256065 RGPS(ph)VTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGPSVTR 7 1 P51788-4;P51788-5;P51788-3;P51788 P51788-4 CLCN2 Chloride channel protein 2 1 RGPS(0.998)VT(0.002)R;RGPS(0.999)VT(0.001)R 77.192 0.023713 92058000 157062 141408 69142 105273 116263 110254 144268 184683 141081 TRUE FALSE 136305.8588 140479.0815 102579.3025 129176.8436 113949.5938 114495.5427 130276.9116 145189.9777 124402.5649 1.095683669 1.129229784 0.824575462 1.038377655 0.915974633 0.9203632 1.047220463 1.167097943 1 16.92465671 0.928958301 22.95627839 0.079159917 1.021548953 0.001237096 0.105093032 950.7090484 2640365.623 351446.0476 0.026422496 8.490989452 -0.928958301 0.942389036 RGQAALDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RGQAALDR 8 1 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ;;;;; 148.62 0.0008311 4264640000 4784440 5310540 2858350 3292630 4681200 5522790 4869580 5482680 4354530 FALSE TRUE 4152164.132 5275654.713 4240657.621 4040271.966 4588053.279 5735255.305 4397328.881 4310251.548 3839742.424 1.081365277 1.373960576 1.104412003 1.052224738 1.194885691 1.493656259 1.145214547 1.122536637 1 21.87257811 1.494743149 2.239468689 0.999622518 1.213837 0.197258918 0.135090761 0.626160992 5.441332871 0.231826525 0.037426868 31.24231085 -1.494743149 0.214214483 RGQPAS(ph)PSAHMVSHSHSPSVVS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(0.998)PS(0.002)AHMVSHSHSPSVVS;RGQPAS(0.939)PS(0.061)AHMVSHSHSPSVVS;RGQPAS(0.979)PS(0.021)AHMVSHSHSPSVVS;RGQPAS(0.928)PS(0.072)AHMVSHSHSPSVVS;RGQPAS(0.975)PS(0.025)AHMVSHSHSPSVVS 150.03 2.77E-08 1592770000 551180 558183 118905.4 320349 634356 590162 475034 609946 480857 TRUE FALSE 478340.1665 554516.2591 176408.4492 393089.1367 621733.5567 612865.914 428965.2758 479513.7945 424010.6333 1.128132478 1.307788569 0.416047229 0.927073771 1.466315955 1.445402228 1.011685185 1.130900399 1 18.69374092 3.331229807 24.99999998 1.197682634 0.93291772 0.191691096 0.270285674 31.46466119 8474.62633 0.081173694 0.104794936 2144.024813 -3.331229807 -0.264764914 RGQS(ph)SPPPAPPICLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RGQSSPPPAPPICLR 15 1 O43379-4;O43379;H7C3R4;O43379-3;O43379-2 O43379-4 WDR62 WD repeat-containing protein 62 1 RGQS(0.575)S(0.425)PPPAPPICLR;RGQS(0.565)S(0.435)PPPAPPICLR;RGQS(0.5)S(0.5)PPPAPPICLR;RGQS(0.572)S(0.428)PPPAPPICLR 113.86 0.00039937 2099530000 1748890 1684710 1035670 1282280 1670440 1593760 1645450 1810130 1763800 TRUE FALSE 1517769.755 1673643.029 1536523.476 1573441.272 1637201.512 1655072.979 1485874.512 1423047.786 1555285.573 0.975878502 1.076100144 0.987936558 1.011673547 1.052669388 1.064160182 0.955370858 0.914975237 1 20.56874807 2.159549862 7.390760483 0.947082177 1.028689673 0.438573008 0.037546943 0.18052534 14.30726274 0.014807313 0.009970343 144.3942376 -2.159549862 0.081607495 RGRS(ph)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RGRSPQPPAEEDEDDFDDTLVAIDTYNCDLHFK 33 2 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;M0QYZ0;M0R0K8;M0QYI8 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 1 RGRS(0.888)PQPPAEEDEDDFDDT(0.112)LVAIDTYNCDLHFK;RGRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;RGRS(0.999)PQPPAEEDEDDFDDT(0.001)LVAIDTYNCDLHFK 175.42 2.14E-15 355597000 469036 411346 131777 132177 352185 386190 368598 458619 29316.3 TRUE FALSE 407051.7042 408643.841 195504.798 162189.808 345177.2075 401046.9792 332851.4227 360546.8958 25850.56041 15.74633964 15.80792968 7.562884319 6.274131217 13.35279398 15.51405358 12.87598479 13.94735317 1 14.65790794 1.234375705 24.98467634 0.999982894 12.56222572 0.554716025 3.275533186 105.3729162 629008.8443 6.488365147 0.8597587 17.15440683 -1.234375705 11.56224282 RGRS(ph)PS(ph)PKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGRSPSPKPR 10 3 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RGRS(1)PS(1)PKPR 74.987 0.057918 290010000 367270 246020 178060 198230 199830 206350 303650 321700 162100 TRUE FALSE 318734.339 244403.8784 264170.4116 243241.1513 195853.774 214288.418 274202.0697 252906.9585 142936.7227 2.229898189 1.709874648 1.848163346 1.70174009 1.370213129 1.499183793 1.918345857 1.76936307 1 17.12501709 7.99999987 0.683679113 1.578147483 71.62308968 0.400470913 0.256452521 313.6484581 1.788044728 0.105980832 33475.41219 99999970.11 -7.99999987 70.0449422 RGS(ph)ALGPDEAGGELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RGSALGPDEAGGELER 16 1 O75145-2;O75145;R4GN36;R4GNF1 O75145-2 PPFIA3 Liprin-alpha-3 1 RGS(1)ALGPDEAGGELER;RGS(1)ALGPDEAGGELER;RGS(1)ALGPDEAGGELER;RGS(1)ALGPDEAGGELER;RGS(1)ALGPDEAGGELER 193.39 2.34E-10 2677100000 1102070 1028100 802856 798631 1142980 1054575 1205650 1203130 1234260 TRUE FALSE 956428.6572 1021346.343 1191119.847 979972.3749 1120236.934 1095145.183 1088726.249 945850.0123 1088347.189 0.878790029 0.938437985 1.09443003 0.900422572 1.029301078 1.006246163 1.000348289 0.869070111 1 20.05370743 7.872230372 19.72757103 0.966476995 0.03431486 0 0.071877957 0 0 0.0158728 0 74512712.19 -7.872230372 -0.932162135 RGS(ph)ASGSEPAGDSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RGSASGSEPAGDSDR 15 1 P50747;A0A0C4DG27 P50747 HLCS Biotin--protein ligase;Biotin--[methylmalonyl-CoA-carboxytransferase] ligase;Biotin--[propionyl-CoA-carboxylase [ATP-hydrolyzing]] ligase;Biotin--[methylcrotonoyl-CoA-carboxylase] ligase;Biotin--[acetyl-CoA-carboxylase] ligase 1 RGS(0.999)AS(0.001)GSEPAGDSDR;RGS(0.968)AS(0.03)GS(0.002)EPAGDSDR;RGS(0.922)AS(0.055)GS(0.022)EPAGDS(0.001)DR;RGS(0.979)AS(0.021)GSEPAGDSDR;RGS(0.457)AS(0.457)GS(0.083)EPAGDS(0.003)DR;RGS(0.999)AS(0.001)GSEPAGDSDR;RGS(1)ASGSEPAGDSDR 240.94 4.50E-18 1684122800 1059855.1 968928.5 763532.4 796945.6 995862.8 1032598.8 1184574.3 1223028.6 1101609.5 TRUE FALSE 919792.5632 962563.5449 1132779.223 977904.279 976047.0787 1072323.544 1069694.467 961493.4515 971378.4799 0.946894112 0.990925334 1.166156391 1.006718081 1.004806158 1.103919395 1.101212853 0.989823711 1 19.889674 4.466852971 24.996675 1.050560458 0.957901856 0.289129125 0.056918415 226.9524142 552484.0969 0.014333346 0.038007127 29299.01168 -4.466852971 -0.092658603 RGS(ph)DAS(ph)DFDISEIQSVCSDVETVPQTHRPTPR ddPTM_MDA-MB-175_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 193.4 1.28E-20 420440000 39625 28984 21636 23160 32320 31753 40205 31319 32425 TRUE FALSE 34388.45585 28793.6022 32099.24197 28418.83198 31676.89523 32974.55846 36305.92529 24621.67557 28591.75344 1.202740361 1.007059684 1.122674831 0.993952051 1.107903204 1.15328913 1.269804084 0.861146051 1 14.80331148 1.692279443 10.49681649 0.932940456 1.113581905 0.448519969 0.087896627 0.1017258 17.97679768 0.047542361 0.02211951 49.23562357 -1.692279443 0.180641449 RGS(ph)DASDFDISEIQSVCSDVETVPQTHRPTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RGSDASDFDISEIQSVCSDVETVPQTHRPTPR 32 2 F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A0U1RQJ2;A0A494C073;H0YC65;A0A494C1U5 F6QMI7 DST Dystonin 1 RGS(0.639)DAS(0.361)DFDISEIQSVCSDVETVPQTHRPTPR;RGS(0.787)DAS(0.213)DFDISEIQSVCSDVETVPQTHRPTPR;RGS(0.999)DAS(0.001)DFDISEIQSVCSDVETVPQTHRPTPR;RGS(0.5)DAS(0.5)DFDISEIQSVCSDVETVPQTHRPTPR 204.08 3.02E-27 1306591000 145957 124397 92481 123953 150862 145278 165395 185565 153497 TRUE FALSE 126668.4126 123579.8279 137205.1209 152098.4232 147860.1414 150866.9387 149355.0184 145883.3688 135350.7595 0.935852987 0.913033871 1.013700414 1.123735276 1.092421955 1.114636809 1.103466422 1.077817142 1 17.04634346 4.038422394 3.495618993 1.086855707 0.925305002 0.787827974 0.034340654 0.097978073 2.504361229 0.009279397 0.020631128 10925.02387 -4.038422394 -0.161550705 RGS(ph)DELTVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RGSDELTVPR 10 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 RGS(1)DELTVPR;RGS(1)DELTVPR;RGS(1)DELTVPR;RGS(1)DELTVPR 165.02 3.66E-06 3719120000 2068980 1253580 985110 1041400 1129740 1158310 1356050 1407900 1215740 TRUE FALSE 1795559.051 1245345.15 1461512.491 1277865.787 1107260.384 1202870.935 1224540.48 1106831.541 1072016.602 1.674935861 1.161684575 1.36333009 1.192020519 1.032876153 1.122063719 1.142277533 1.032476119 1 20.03189582 8 0.510895552 1.058476189 19.96895301 0.776671167 0.094317101 55.5309154 0.588451306 0.054360013 1130.668644 100000000 -8 18.91047682 RGS(ph)DPASGEVEASQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RGSDPASGEVEASQLR 16 1 Q8WWA1-3;Q8WWA1-2;Q8WWA1 Q8WWA1-3 TMEM40 Transmembrane protein 40 1 RGS(0.563)DPAS(0.435)GEVEAS(0.002)QLR;RGS(1)DPASGEVEASQLR;RGS(1)DPASGEVEASQLR;RGS(0.999)DPAS(0.001)GEVEASQLR 248.98 1.81E-20 3746360000 1752370 1795680 1529100 2185130 2807400 2194410 1519420 2630800 3059580 TRUE FALSE 1520789.865 1783884.06 2268577.875 2681297.164 2751538.233 2278830.373 1372066.882 2068223.893 2697879.938 0.563698126 0.661216993 0.840874289 0.993853406 1.01988906 0.844674494 0.508572254 0.766610798 1 21.36339472 4.364369704 3.427278962 0.838173673 0.580819322 0.319070838 0.148314263 0.330915153 7.304730732 0.042444685 0.138777967 23140.3383 -4.364369704 -0.257354351 RGS(ph)DPASGEVEASQLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGSDPASGEVEASQLRR 17 2 Q8WWA1-3;Q8WWA1-2;Q8WWA1 Q8WWA1-3 TMEM40 Transmembrane protein 40 1 RGS(1)DPASGEVEASQLRR;RGS(1)DPASGEVEASQLRR 127.01 2.18E-05 796920000 35143 39020 23943 19429.7 32064 37362 32528 38035 25324 TRUE FALSE 30498.76351 38763.67505 35521.91488 23841.51035 31425.98913 38799.34032 29373.43957 29901.51124 22330.22557 1.365806333 1.735928503 1.590754862 1.067678886 1.407329677 1.737525678 1.315411682 1.339059973 1 14.4467102 1.035599798 1.344297325 0.585451088 1.473853703 0.352363011 0.198127268 2.570137813 2.782691999 3.598517253 0.060233573 10.85424944 -1.035599798 0.888402616 RGS(ph)FDATGSGFSMTFSSSSYSSSGYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGSFDATGSGFSMTFSSSSYSSSGYGR 27 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 RGS(0.989)FDAT(0.009)GS(0.002)GFSMTFSSSSYSSSGYGR;RGS(0.969)FDAT(0.015)GS(0.015)GFSMTFSSSSYSSSGYGR 166.88 5.17E-12 816290000 176057 157014 109981 102187 159984 152623 157944 179659 116176 TRUE FALSE 152790.6214 155982.5647 163168.1795 125390.1202 156800.6314 158494.5056 142626.6152 141240.321 102441.8056 1.491487 1.522645601 1.592788984 1.224013179 1.530631273 1.547166263 1.392269634 1.378737129 1 16.64444506 0.767223161 1.367371713 1.50E-11 1.478466432 0.678043411 0.101867406 2.434318205 1.577845954 6.953543268 0.029275783 5.850906543 -0.767223161 1.478466432 RGS(ph)FSSENYWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RGSFSSENYWR 11 1 Q6P6C2-3;Q6P6C2;Q6P6C2-1;K7ER58 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 RGS(0.999)FS(0.001)SENYWR;RGS(1)FSSENYWR;RGS(0.675)FS(0.24)S(0.085)ENYWR;RGS(0.999)FS(0.001)SENYWR 196.18 3.76E-08 1423780000 589961 534697 405296 539866 726244 688524 699546 786230 650986 TRUE FALSE 511996.1591 531184.5402 601298.5012 662450.8266 711793.1653 715011.9638 631704.1366 618100.8329 574027.1767 0.891937141 0.925364794 1.047508769 1.154040877 1.23999907 1.245606468 1.100477751 1.076779738 1 19.13075952 4.121366756 2.508806039 1.135999441 0.897719166 0.626501631 0.072170771 0.206929377 2.588757598 0.022166092 0.061162262 13224.11922 -4.121366756 -0.238280275 RGS(ph)GDTSISIDTEASIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 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(0.956)GDT(0.038)S(0.006)IS(0.001)IDTEASIR;RGS(0.953)GDT(0.04)S(0.007)ISIDTEASIR;RGS(0.974)GDT(0.023)S(0.003)ISIDTEASIR;RGS(0.888)GDT(0.101)S(0.011)IS(0.001)IDTEASIR;RGS(0.863)GDT(0.12)S(0.013)IS(0.003)IDTEASIR;RGS(0.925)GDT(0.07)S(0.004)ISIDTEASIR;RGS(0.939)GDT(0.058)S(0.003)ISIDTEASIR;RGS(0.97)GDT(0.028)S(0.002)ISIDTEASIR;RGS(0.827)GDT(0.168)S(0.004)IS(0.001)IDTEASIR;RGS(0.93)GDT(0.016)S(0.016)IS(0.038)IDTEASIR;RGS(0.999)GDT(0.001)SISIDTEASIR;RGS(0.992)GDT(0.008)SISIDTEASIR;RGS(0.924)GDT(0.072)S(0.004)ISIDTEASIR 126.19 2.87E-05 265023600 235890 196468.6 140666 143868 203206.9 201712 206744.2 222615.5 203366.6 TRUE FALSE 204716.5388 195177.9848 208692.5481 176535.4283 199163.4803 209471.9912 186694.1793 175010.9077 179324.8322 1.141596154 1.08840467 1.163768261 0.984444966 1.110629676 1.168114804 1.041094962 0.975943519 1 17.45221576 2.014957632 6.412696046 0.992302016 1.105595661 0.493166263 0.051567977 0.121642099 20.69108763 0.021904252 0.013982797 103.5041186 -2.014957632 0.113293645 RGS(ph)GDTSSLIDPDTSLSELR ddPTM_MDA-MB-175_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(0.996)GDT(0.003)SSLIDPDTSLSELR;RGS(0.998)GDT(0.002)SSLIDPDTSLSELR;RGS(0.879)GDT(0.039)S(0.069)S(0.013)LIDPDTSLSELR;RGS(0.997)GDT(0.002)SSLIDPDTSLSELR;RGS(0.994)GDT(0.006)SSLIDPDTSLSELR 169.44 6.60E-12 4287540000 3344000 2938100 2238150 2590660 3316670 3042930 3291360 3800380 3546740 TRUE FALSE 2902081.927 2918799.428 3320526.826 3178908.949 3250674.756 3159993.486 2972164.414 2987698.312 3127448.438 0.927939176 0.933284588 1.061736714 1.016454471 1.039401551 1.010406262 0.950348015 0.95531497 1 21.57655467 4.374743965 11.94177205 0.999310899 0.929290312 0.449179899 0.033758706 0.444219382 47.86077594 0.00967775 0.025621095 23699.76092 -4.374743965 -0.070020586 RGS(ph)GDTSSLIDPDTSLSELRDIYDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGSGDTSSLIDPDTSLSELRDIYDLK 26 2 C9JSU1;Q9Y608-4;Q9Y608 C9JSU1 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 RGS(0.999)GDT(0.001)SSLIDPDTSLSELRDIYDLK;RGS(0.976)GDT(0.019)S(0.004)S(0.001)LIDPDTSLSELRDIYDLK 156.67 1.28E-08 140305000 347790 308940 131231 122882 283090 238691 413320 418690 26295 TRUE FALSE 301828.6703 306910.5528 194694.7505 150784.2362 277457.0629 247873.5972 373236.29 329156.4017 23186.43506 13.01746774 13.23664255 8.396924757 6.503122877 11.96635283 10.69045744 16.09718308 14.19607632 1 14.5009934 4.257160301 24.27744715 10 13.1270596 0.09709301 4.149270357 478.7114389 624828.0046 1.082730684 2.852162728 18078.4129 -4.257160301 3.127059598 RGS(ph)GHLPSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGSGHLPSAR 10 1 Q8N4Y2 Q8N4Y2 CRACR2B EF-hand calcium-binding domain-containing protein 4A 1 RGS(1)GHLPSAR 85.287 0.008785 93244000 92301 79040 68089 75293 66107 64457 71981 89704 90567 TRUE FALSE 80103.18899 78520.78104 101017.0681 92389.42643 64791.60004 66936.7025 65000.2937 70521.49768 79860.27243 1.00304177 0.983227062 1.264922659 1.156888445 0.811312034 0.838172729 0.813925269 0.883061071 1 16.28519037 3.238890387 24.99999353 0.865306317 1.105170702 0.605786241 0.093241195 6.200205558 470013.8396 0.028997188 0.035147267 1733.366452 -3.238890387 0.239864385 RGS(ph)GSALGGPLDPQFVGPSDTSLGAAPGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RGSGSALGGPLDPQFVGPSDTSLGAAPGHR 30 1 P98174 P98174 FGD1 "FYVE, RhoGEF and PH domain-containing protein 1" 1 RGS(0.895)GS(0.105)ALGGPLDPQFVGPSDTSLGAAPGHR;RGS(0.5)GS(0.5)ALGGPLDPQFVGPSDTSLGAAPGHR;RGS(0.5)GS(0.5)ALGGPLDPQFVGPSDTSLGAAPGHR 239.39 7.09E-46 1054340000 294226 270956 154392 170296 288268 284130 281286 310280 242165 TRUE FALSE 255343.2886 269176.0722 229056.4876 208964.3096 282532.0308 295060.665 254006.927 243929.0366 213536.5296 1.195782703 1.260562175 1.072680576 0.978588113 1.323108657 1.381780745 1.189524469 1.142329311 1 17.70412337 1.284868409 2.384248748 0.961261103 1.199858305 0.234751787 0.114167182 0.862738826 5.678468512 0.413667462 0.032779549 19.26940964 -1.284868409 0.238597202 RGS(ph)GSPEDTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGSGSPEDTPR 11 1 Q96HP0 Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 1 RGS(0.735)GS(0.2)PEDT(0.064)PR;RGS(0.667)GS(0.329)PEDT(0.004)PR 78.529 0.007841 0 967230 926360 595510 695010 896840 989600 871820 1010820 866670 TRUE FALSE 839408.1049 920274.6802 883500.6279 852822.6431 878994.6386 1027670.552 787271.0306 794664.0092 764213.2599 1.098395106 1.204211872 1.156091728 1.115948503 1.150195482 1.344743158 1.030171906 1.039845879 1 19.54361576 2.063495979 24.99999788 1.026437105 1.175422111 0.539881257 0.06737746 46.28621677 18223.62133 0.026827528 0.018087113 115.7433315 -2.063495979 0.148985006 RGS(ph)GVFCANCLTTK ddPTM_MDA-MB-175_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 211.13 2.61E-09 2057910000 1782230 2019090 1449760 1552290 2260080 1741870 2654660 2970770 2056490 TRUE FALSE 1546703.79 2005826.465 2150868.785 1904761.17 2215108.83 1808880.866 2397211.482 2335493.954 1813374.095 0.852942476 1.106129436 1.186114212 1.050396151 1.221539911 0.997522172 1.32196191 1.287927274 1 20.79024515 4.749688764 2.590557376 1.166991815 0.781932734 0.405928747 0.111718998 0.506771802 4.299946976 0.028677785 0.430856115 56193.84694 -4.749688764 -0.385059081 RGS(ph)HPYIDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RGSHPYIDFR 10 1 Q13946-3;Q13946-2;Q13946;E5RG23 Q13946-3 PDE7A "High affinity cAMP-specific 3,5-cyclic phosphodiesterase 7A" 1 RGS(0.999)HPY(0.001)IDFR;RGS(0.996)HPY(0.004)IDFR;RGS(0.985)HPY(0.015)IDFR;RGS(1)HPYIDFR;RGS(1)HPYIDFR 122.64 0.00029598 2660260000 2579890 2347370 1922450 1988620 2312470 2415600 2652310 2601420 2736890 TRUE FALSE 2238951 2331949.972 2852153.25 2440166.565 2266456.371 2508529.695 2395089.384 2045126.577 2413337.982 0.92774034 0.966275751 1.181829181 1.011116795 0.939137571 1.039444004 0.992438441 0.847426507 1 21.20259854 1.938086155 9.193278125 0.914634552 1.013624926 0.166932854 0.078836746 0.680846 96.9855865 0.037280443 0.021033383 86.71338807 -1.938086155 0.098990374 RGS(ph)IGENQIKDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGSIGENQIKDEK 13 2 Q05682-5;Q05682-4;C9J813;E9PGZ1 Q05682-5 CALD1 Caldesmon 1 RGS(1)IGENQIKDEK;RGS(1)IGENQIKDEK 103.73 0.0012505 522990000 290490 222670 225443 216597 211849 138624 348030 407190 265350 TRUE FALSE 252101.0105 221207.2661 334467.9889 265778.6593 207633.6194 143956.955 314278.1042 320115.5873 233980.6253 1.077443956 0.945408475 1.429468737 1.135900287 0.887396634 0.615251604 1.343180034 1.368128608 1 17.83602955 0.94701627 17.84402379 0.000122171 1.11338399 0.013640189 0.246493455 29833542.64 222936859.7 1198451283 0.064596164 8.851487693 -0.94701627 1.11326182 RGS(ph)ISSMSSVSSVLDEKDDDRIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RGSISSMSSVSSVLDEKDDDRIR 23 3 Q9H1K0 Q9H1K0 RBSN Rabenosyn-5 1 RGS(0.951)IS(0.043)S(0.006)MSSVSSVLDEKDDDRIR;RGS(0.825)IS(0.039)S(0.13)MS(0.006)SVSSVLDEKDDDRIR;RGS(0.988)IS(0.011)S(0.002)MSSVSSVLDEKDDDRIR 228.93 3.39E-32 1074610000 367370 315643 217935 222867 304182 282387 396091 450608 107983 TRUE FALSE 318821.1237 313569.5203 323329.0949 273472.3587 298129.3733 293250.6106 357678.1558 354248.9858 95217.37275 3.348350353 3.293196517 3.395694353 2.872084692 3.131039691 3.079801533 3.756437984 3.720423864 1 16.5389372 3.762591126 22.99961396 3.076079997 3.340492062 0.039818146 0.762901531 1466.027491 1403123.002 0.200363641 0.346674262 5788.8344 -3.762591126 0.264412064 RGS(ph)KGHMNYEGPGMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGSKGHMNYEGPGMAR 16 2 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 RGS(1)KGHMNYEGPGMAR 53.278 0.079709 37386000 66795 53407 61596 48118 40812 39025 65479 76529 55169 TRUE FALSE 57967.87151 53056.1659 91384.03163 59043.92734 39999.92105 40526.317 59128.85666 60163.8689 48646.98367 1.191602585 1.090636292 1.87851383 1.213722268 0.82224874 0.833069472 1.215468097 1.236744077 1 15.57006273 3.478314626 24.9993634 1.050304245 1.388760874 0.318998541 0.242985436 58.33429408 1222035.588 0.07269809 0.095139082 3008.254856 -3.478314626 0.33845663 RGS(ph)LEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RGSLEK 6 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 RGS(1)LEK;RGS(1)LEK;RGS(1)LEK;RGS(1)LEK;RGS(1)LEK;RGS(1)LEK 105.1 0.020375 2893220000 4271690 2640500 2156110 2405170 1855749 2171880 3387490 3880230 4276690 TRUE FALSE 3707175.343 2623154.382 3198812.008 2951300.609 1818823.226 2255433.629 3058971.741 3050473.01 3771104.58 0.98304761 0.695593115 0.84824272 0.78260906 0.482305167 0.598083023 0.811160676 0.808907031 1 21.84655573 1.2247926 1.687232118 1.104840935 0.73034525 0.260880281 0.135912063 1.50168014 3.819779577 0.943610495 0.039539017 16.78002486 -1.2247926 -0.374495685 RGS(ph)LGEEGSEPPPPPPLPLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RGSLGEEGSEPPPPPPLPLAR 21 1 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;Q14934-12;Q14934-13;Q14934-18 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 RGS(0.991)LGEEGS(0.009)EPPPPPPLPLAR;RGS(0.996)LGEEGS(0.004)EPPPPPPLPLAR;RGS(1)LGEEGSEPPPPPPLPLAR;RGS(1)LGEEGSEPPPPPPLPLAR;RGS(0.994)LGEEGS(0.006)EPPPPPPLPLAR;RGS(0.99)LGEEGS(0.01)EPPPPPPLPLAR 178.85 3.65E-17 1838270000 388939 378723 254616 258891 395422 381155 380474 416115 378954 TRUE FALSE 337539.7257 376235.1437 377749.1492 317676.1585 387553.8758 395818.2795 343575.69 327132.0455 334154.4898 1.010130751 1.125931733 1.130462588 0.950686488 1.159804485 1.184536768 1.028194145 0.978984438 1 18.35015573 2.01083901 24.91018829 0.992670547 1.094344789 0.29202249 0.068873908 239.1510773 549614.4372 0.028124457 0.01894199 102.5271794 -2.01083901 0.101674241 RGS(ph)LPAGASWQNTDLFEMIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGSLPAGASWQNTDLFEMIEK 21 1 J3KPC5;P47736-3 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 RGS(1)LPAGASWQNTDLFEMIEK;RGS(1)LPAGASWQNTDLFEMIEK 202.98 3.73E-22 151742000 235200 142099 119535 127183 144882 125112 175718 198788 182330 TRUE FALSE 204117.7241 141165.5423 177342.5258 156061.844 141999.1317 129925.1396 158676.8954 156278.7332 160775.1551 1.269584992 0.878030826 1.103046834 0.970683834 0.883215641 0.808117022 0.986949105 0.972032856 1 17.29468496 4.746965429 24.75663119 0.952556171 1.269585175 0.609624328 0.080286984 680.0910225 2003177.7 0.02000678 0.222003985 55842.57406 -4.746965429 0.317029004 RGS(ph)LPDQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RGSLPDQK 8 1 X6RKU3;Q6P3S6 X6RKU3 FBXO42 F-box only protein 42 1 RGS(1)LPDQK;RGS(1)LPDQK;RGS(1)LPDQK 101.35 0.0033429 664167000 1556573 1264784 1001393 1048135 1239432 1054102 1500606 1722230 1482560 TRUE FALSE 1350867.934 1256475.551 1485670.004 1286130.071 1214769.728 1094653.986 1355077.461 1353944.517 1307293.446 1.033331834 0.9611274 1.136447222 0.983811305 0.929224982 0.837343742 1.036551866 1.035685233 1 20.31815159 5.397676009 5.439644304 0.993608157 6.823561364 0.028203543 0.077299505 15873.89826 2144.789495 0.019805571 1139868.043 249848.076 -5.397676009 5.829953207 RGS(ph)LSNAGDPEIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RGSLSNAGDPEIVK 14 1 O43847;O43847-2;F5H7V1 O43847 NRD1 Nardilysin 1 RGS(0.819)LS(0.181)NAGDPEIVK;RGS(0.999)LS(0.001)NAGDPEIVK;RGS(0.999)LS(0.001)NAGDPEIVK;RGS(1)LSNAGDPEIVK;RGS(0.996)LS(0.004)NAGDPEIVK;RGS(0.996)LS(0.004)NAGDPEIVK 193.54 1.51E-07 13532330000 20947400 15820400 13227800 13890300 15809000 14054400 21314100 22142200 21442400 TRUE FALSE 18179148.02 15716474.75 19624808.32 17044304.91 15494431.83 14595081.86 19247061.86 17407262.84 18907503.9 0.961477946 0.831229486 1.037937553 0.901457168 0.819485846 0.771920077 1.0179589 0.920653669 1 24.17245558 2.19443756 24.99999857 0.968870893 0.889118973 0.232041608 0.078297319 232.9354552 131978.9028 0.032508712 0.021917498 156.4723338 -2.19443756 -0.07975192 RGS(ph)LTLTISGESPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RGSLTLTISGESPK 14 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(0.883)LT(0.111)LT(0.007)ISGESPK;RGS(0.855)LT(0.144)LT(0.001)ISGESPK;RGS(0.843)LT(0.157)LTISGESPK;RGS(0.883)LT(0.117)LTISGESPK;RGS(0.999)LT(0.001)LTISGESPK 262.37 9.08E-25 3697580000 7842690 5587320 4460510 5191870 6017710 4613990 7405220 8331890 7340710 TRUE FALSE 6806258.646 5550616.527 6617627.556 6370763.436 5897969.344 4791493.181 6687062.904 6550180.162 6472899.626 1.051500724 0.857516237 1.022359057 0.984220953 0.911178866 0.740239067 1.033086142 1.011939091 1 22.6259807 RGS(ph)MEQAPAVALPPTHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RGSMEQAPAVALPPTHK 17 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 RGS(1)MEQAPAVALPPTHK;RGS(1)MEQAPAVALPPTHK;RGS(1)MEQAPAVALPPTHK;RGS(1)MEQAPAVALPPTHK 140.66 4.00E-07 1306684000 1473750 1194478 821141 1203795 1309130 924678 1511900 1528890 1759460 TRUE FALSE 1278990.203 1186631.395 1218247.534 1477135.054 1283080.874 960250.961 1365276.171 1201948.771 1551458.643 0.82437918 0.764848873 0.785227205 0.952094379 0.827015841 0.618934295 0.879995208 0.77472176 1 20.56519381 1.233424835 24.94382489 1.000000314 0.803495191 0.343570368 0.085401818 187.3944217 910043.1882 0.167748964 0.020489357 17.11688902 -1.233424835 -0.196505123 RGS(ph)MFYDEDGDLAHEFYEETIVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 RGSMFYDEDGDLAHEFYEETIVTK 24 1 O75896 O75896 TUSC2 Tumor suppressor candidate 2 1 RGS(0.408)MFY(0.364)DEDGDLAHEFY(0.166)EET(0.062)IVTK;RGS(0.455)MFY(0.41)DEDGDLAHEFY(0.064)EET(0.071)IVTK;RGS(0.482)MFY(0.429)DEDGDLAHEFY(0.074)EET(0.015)IVTK;RGS(0.552)MFY(0.448)DEDGDLAHEFYEETIVTK;RGS(0.553)MFY(0.447)DEDGDLAHEFYEETIVTK;RGS(0.54)MFY(0.46)DEDGDLAHEFYEETIVTK;RGS(1)MFYDEDGDLAHEFYEETIVTK;RGS(0.466)MFY(0.411)DEDGDLAHEFY(0.096)EET(0.027)IVTK 205.03 6.24E-25 664321000 637414 610163 407688 424300 509727 369326 635455 686463 719943 TRUE FALSE 553178.1249 606154.7991 604847.2804 520643.8 499584.43 383534.2102 573828.6719 539668.2295 634832.1587 0.871376973 0.954826864 0.952767235 0.82012827 0.786955139 0.604150569 0.903906118 0.850095922 1 19.27601569 3.73148873 23.6266457 0.823663023 0.929174008 0.173643803 0.101287968 443.49187 1481675.619 0.028815525 0.043866709 5388.75861 -3.73148873 0.105510985 RGS(ph)MNNELLSPEFGPVRDPLADGVEGLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RGSMNNELLSPEFGPVRDPLADGVEGLGR 29 2 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 1 RGS(1)MNNELLSPEFGPVRDPLADGVEGLGR;RGS(1)MNNELLSPEFGPVRDPLADGVEGLGR;RGS(1)MNNELLSPEFGPVRDPLADGVEGLGR;RGS(0.724)MNNELLS(0.276)PEFGPVRDPLADGVEGLGR;RGS(0.72)MNNELLS(0.28)PEFGPVRDPLADGVEGLGR;RGS(1)MNNELLSPEFGPVRDPLADGVEGLGR 219.73 1.11E-34 2209440000 341436.9 304867.9 248287.2 286048.7 320119.5 355971 317323.5 362935.3 441939.9 TRUE FALSE 296315.1486 302865.2027 368359.7204 351000.4293 313749.7483 369665.4347 286549.5158 285324.4105 389694.2685 0.760378513 0.7771867 0.945253113 0.900707189 0.805117687 0.948603725 0.735318784 0.732175024 1 18.57198319 4.446524946 24.96836994 0.850393717 0.764580353 0.153212975 0.089964481 365.8872163 298584.8732 0.023328523 0.061722843 27959.2132 -4.446524946 -0.085813365 RGS(ph)MSYLAAVEEEVEESSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGSMSYLAAVEEEVEESSVK 20 1 Q8WXH0;Q8WXH0-2;G3V5X4;A0A0A0MRE3;A0A0C4DGK3;Q8WXH0-7 Q8WXH0 SYNE2 Nesprin-2 1 RGS(0.581)MS(0.236)Y(0.183)LAAVEEEVEESSVK;RGS(0.937)MS(0.063)YLAAVEEEVEESSVK 189.86 1.25E-17 108983000 167819 138735 93518 129727 151836 126404 148803 207130 177327 TRUE FALSE 145641.294 137823.6407 138743.6176 159183.4981 148814.7607 131266.8437 134372.108 162836.8614 156363.6041 0.931427072 0.881430442 0.887314017 1.01803421 0.951722503 0.839497429 0.859356682 1.041398747 1 17.25454522 1.701490867 8.33861655 1.01916683 0.911052578 0.44490752 0.051328582 0.110120234 15.79145428 0.031116922 0.014043769 50.291069 -1.701490867 -0.108114252 RGS(ph)PSAAFTFPDTDDFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RGSPSAAFTFPDTDDFGK 18 1 Q9ULT0;Q9ULT0-4;H7C055;Q9ULT0-3 Q9ULT0 TTC7A Tetratricopeptide repeat protein 7A 1 RGS(0.997)PS(0.003)AAFTFPDTDDFGK;RGS(0.992)PS(0.008)AAFTFPDTDDFGK;RGS(0.994)PS(0.006)AAFTFPDTDDFGK 248.7 9.44E-25 455950000 1054310 891500 742360 790540 990790 819280 1106610 1288290 1130010 TRUE FALSE 914980.2622 885643.6778 1101367.779 970044.1896 971075.2174 850798.2317 999291.1325 1012799.209 996421.5051 0.918266273 0.888824331 1.105323172 0.973527954 0.974562685 0.853853743 1.002879933 1.016436522 1 19.92639663 4.044008998 0.011430136 1.918254337 2.47E-07 0.051926127 0.069031703 16804.30249 87.08769438 7107.943906 7509.189939 11066.46713 -4.044008998 -1.91825409 RGS(ph)PTTGFIEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RGSPTTGFIEQK 12 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(0.812)PT(0.184)T(0.004)GFIEQK;RGS(0.99)PT(0.005)T(0.004)GFIEQK;RGS(0.511)PT(0.485)T(0.005)GFIEQK;RGS(0.975)PT(0.021)T(0.003)GFIEQK;RGS(0.867)PT(0.127)T(0.006)GFIEQK;RGS(0.636)PT(0.023)T(0.341)GFIEQK 221.85 2.78E-11 7629700000 5284490 3700060 2982580 3277390 3800920 2969330 4565940 5279550 4609290 TRUE FALSE 4586131.257 3675754.062 4424965.664 4021571.491 3725289.128 3083562.047 4123135.842 4150559.318 4064384.987 1.128370288 0.90438137 1.088717156 0.989466181 0.916568962 0.758678633 1.014455042 1.021202305 1 21.95460563 4.753200258 23.63560105 0.965891509 1.128370534 0.255968909 0.089054532 1921.807853 3102630.54 0.022694372 0.454091489 56650.04483 -4.753200258 0.162479025 RGS(ph)PVPPVPER ddPTM_MDA-MB-175_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 85.734 0.0091848 8490630000 2918160 2501090 1638470 1847340 2765450 2445040 2381420 2750930 3150640 TRUE FALSE 2532517.762 2484660.175 2430839.572 2266806.782 2710422.956 2539102.271 2150470.255 2162665.027 2778174.928 0.911576063 0.894349794 0.874977147 0.815933784 0.975612776 0.913946147 0.774058621 0.778448112 1 21.40570601 2.264977036 24.99699462 0.832555761 0.896366404 0.065698156 0.073134945 424.3044231 401504.0832 0.027323021 0.021157922 184.067467 -2.264977036 0.063810643 RGS(ph)PVPPVPERR ddPTM_MDA-MB-175_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 111.92 0.00069355 934679000 156155 149716 155813 112530 153715 150000 131487 145041 76902 TRUE FALSE 135518.7211 148732.5057 231164.688 138081.6564 150656.3722 155770.5971 118735.411 114025.1109 67810.73317 1.998484823 2.193347554 3.408969011 2.036280246 2.221718675 2.29713778 1.750982557 1.681520101 1 16.04922602 1.148009989 0.666734063 1.09E-15 2.451992966 0.560597463 0.400557031 2.691350652 0.863824502 5.249850935 0.199735961 14.06079865 -1.148009989 2.451992966 RGS(ph)QNSSEHRPPASSTSEDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGSQNSSEHRPPASSTSEDVK 21 2 O15014 O15014 ZNF609 Zinc finger protein 609 1 RGS(1)QNSSEHRPPASSTSEDVK;RGS(0.983)QNS(0.017)S(0.001)EHRPPASSTSEDVK 142.65 7.53E-08 174172000 111000 81784 57427 74545 110335 91209 140022 144967 135877 TRUE FALSE 96331.06876 81246.75552 85198.88928 91471.5816 108139.5494 94717.86925 126442.688 113966.9352 119813.7759 0.804006618 0.678108631 0.711094268 0.76344795 0.902563571 0.790542394 1.055326794 0.951200598 1 16.87043427 2.752683187 0.933209343 1.003186342 0.722253104 0.718636884 0.066072557 0.281349563 0.55654204 0.046593671 0.035020973 565.8263749 -2.752683187 -0.280933238 RGS(ph)RPEMTPVSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGSRPEMTPVSLR 13 2 A0A5E8;Q99501;Q99501-4;Q99501-2 A0A5E8 GAS2L1 GAS2-like protein 1 1 RGS(1)RPEMTPVSLR;RGS(0.997)RPEMT(0.001)PVS(0.001)LR 91.518 0.0051151 792630000 371140 414980 320962 324363 465500 424123 523180 614740 575825 TRUE FALSE 322092.9087 412253.9691 476180.2968 398014.5767 456237.4607 440439.2863 472442.0841 483282.6349 507751.6245 0.634351311 0.811920532 0.937821316 0.783876521 0.898544561 0.86743058 0.93045903 0.951809136 1 18.95376342 5.8834694 0.476769793 0.943635362 2.59E-86 0.696509432 0.057769756 8.888013917 0.700487239 0.043344579 5.915345177 764661.8091 -5.8834694 -0.943635362 RGS(ph)RS(ph)SPEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGSRSSPEPK 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RGS(0.999)RS(0.841)S(0.16)PEPK 86.539 0.066349 3392200000 10467000 6797800 5636000 5044600 4940700 5461500 8177500 9473900 7762300 TRUE FALSE 9083759.43 6753144.804 8361588.451 6190053.532 4842389.736 5671607.439 7384447.309 7447980.211 6844649.737 1.327132838 0.986631174 1.221624009 0.904363813 0.707470787 0.82861909 1.078864163 1.088146289 1 22.70654529 5.92019993 0.935707843 0.963133436 3.869657479 0.391015508 0.140593762 19.82173748 2.455507786 0.050194141 96.89366265 832146.7662 -5.92019993 2.906524042 RGS(ph)S(ph)PGSLEIPK ddPTM_MDA-MB-175_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(1)S(1)PGSLEIPK 134.14 0.00098544 117700000 349290 289240 304820 233500 315430 235240 359700 435680 396560 TRUE FALSE 303130.4415 287339.9634 452231.9716 286519.7438 309153.5601 244289.835 324816.3494 342513.2225 349679.1286 0.866881712 0.821724661 1.293276992 0.819379026 0.884106413 0.698611427 0.928898304 0.979507195 1 18.41567216 1.757012254 4.082619168 0.991276497 0.90138595 0.056097062 0.152671442 0.665011335 23.43432296 0.099185414 0.041453335 57.14947611 -1.757012254 -0.089890548 RGS(ph)SDPTVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RGSSDPTVQR 10 1 H7BXG1;A0A2R8YDG4;H7BZJ9;H7BZI2;Q2KHT3;Q2KHT3-2 H7BXG1;Q2KHT3 CLEC16A Protein CLEC16A 1 RGS(0.974)S(0.026)DPTVQR;RGS(0.499)S(0.499)DPT(0.002)VQR;RGS(0.911)S(0.081)DPT(0.008)VQR 147.96 2.75E-05 732289000 1446780 1197720 879557 938775 1221300 1261020 1434730 1377430 1258770 TRUE FALSE 1255584.357 1189852.098 1304913.707 1151938.212 1196998.519 1309532.255 1295590.105 1082877.314 1109959.645 1.131198205 1.0719778 1.175640676 1.037819904 1.078416252 1.179801682 1.16724073 0.975600617 1 20.08207579 1.691340518 7.264017701 0.988680386 1.117891537 0.571232934 0.047532506 0.0873517 9.345268403 0.028267759 0.012380171 49.12929342 -1.691340518 0.129211151 RGS(ph)SGSVDETLFALPAASEPVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGSSGSVDETLFALPAASEPVIR 23 1 Q9NQC3-5;Q9NQC3 Q9NQC3-5 RTN4 Reticulon-4 1 RGS(0.598)S(0.197)GS(0.197)VDET(0.009)LFALPAASEPVIR;RGS(0.342)S(0.138)GS(0.226)VDET(0.294)LFALPAASEPVIR 192.1 6.23E-18 265100000 303070 174440 141588 218644 246700 230330 150921 291890 339650 TRUE FALSE 263018.5316 173294.0922 210060.4304 268290.462 241791.1527 239190.9441 136284.7046 229471.595 299496.9639 0.878200995 0.578617192 0.701377495 0.895803612 0.80732422 0.7986423 0.455045363 0.766190054 1 18.19218185 3.979010326 0.01013215 1.482856704 2.60E-07 0.004169721 0.157056501 66431.95193 323.1538858 23108.7809 24187.94992 9528.188193 -3.979010326 -1.482856444 RGS(ph)SGSVVVDLLYWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGSSGSVVVDLLYWR 15 1 Q9NQC3-2;F8W914 Q9NQC3-2 RTN4 Reticulon-4;Reticulon 1 RGS(0.647)S(0.303)GS(0.05)VVVDLLYWR;RGS(0.612)S(0.321)GS(0.067)VVVDLLYWR 126.48 5.15E-05 303413000 158857 123690 104565 129623 142554 144241 114655 172356 167335 TRUE FALSE 137863.645 122877.4722 155132.9837 159055.8833 139717.4543 149790.0446 103535.7757 135499.0107 147552.8469 0.934334022 0.83276924 1.051372352 1.077958756 0.94689772 1.01516201 0.70168606 0.918308345 1 17.17087223 RGS(ph)SPGSLEIPK ddPTM_MDA-MB-175_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 1 RGS(0.798)S(0.202)PGSLEIPK 131.48 0.00012122 573210000 984030 873490 676490 638520 894150 731980 974540 1081200 951070 TRUE FALSE 853987.9423 867751.9867 1003642.827 783505.7252 876358.1644 760139.7443 880029.2608 849993.7939 838635.5881 1.018306347 1.034718773 1.196756781 0.934262433 1.044980891 0.906400533 1.049358355 1.013543673 1 19.67768453 3.709306526 24.99788675 0.996038165 1.078406545 0.310946429 0.064065217 878.4471273 750640.7653 0.016879305 0.025040383 5120.431093 -3.709306526 0.08236838 RGSDAS(ph)DFDISEIQSVCSDVETVPQTHRPTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGSDASDFDISEIQSVCSDVETVPQTHRPTPR 32 2 F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A0U1RQJ2;A0A494C073;H0YC65;A0A494C1U5 F6QMI7 DST Dystonin 1 RGS(0.421)DAS(0.579)DFDISEIQSVCSDVETVPQTHRPTPR 134.05 2.45E-08 138810000 21695 23969 16643 22713 31122 22835 23815 30009 23723 TRUE FALSE 18827.95078 23811.54606 24691.61047 27870.3338 30502.73309 23713.47723 21505.42497 23591.80888 20918.49397 0.900062443 1.138301165 1.180372282 1.332329844 1.458170609 1.133613025 1.028057995 1.12779672 1 14.35249137 2.48081616 24.55319525 1.068768245 1.21352479 0.177398072 0.144857516 229.4706541 1524893.161 0.056242082 0.044560716 302.5632384 -2.48081616 0.144756546 RGSDIIIVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGSDIIIVGR 10 1 P11172-2;P11172-3;P11172;P11172-4 P11172-2 UMPS Uridine 5-monophosphate synthase;Orotate phosphoribosyltransferase;Orotidine 5-phosphate decarboxylase 0 141.1 6.11E-05 97149000 47697 55689 19203 39289 58228 60533 46508 56737 43569 FALSE TRUE 41393.7206 55323.17529 28489.63503 48210.16794 57069.37672 62861.74368 41997.66132 44604.23408 38418.32245 1.077447373 1.440020588 0.741563744 1.254874364 1.485472896 1.636243846 1.093167495 1.161014621 1 15.2295069 RGSDPAS(ph)GEVEASQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGSDPASGEVEASQLR 16 1 Q8WWA1-3;Q8WWA1-2;Q8WWA1 Q8WWA1-3 TMEM40 Transmembrane protein 40 1 RGS(0.006)DPAS(0.994)GEVEASQLR 203.13 3.03E-11 1671900000 798280 760270 690740 932100 1209900 1226200 672130 1336100 1487600 TRUE FALSE 692785.2754 755275.7363 1024784.174 1143747.551 1185825.357 1273372.707 606946.9361 1050385.413 1311737.623 0.528143177 0.575782629 0.781241734 0.871933176 0.904011089 0.9707526 0.462704527 0.800758776 1 20.32304775 4.242550869 3.580356418 0.817594369 0.538054473 0.38186055 0.146652041 0.250952139 6.757927084 0.039399727 0.107860525 17480.37997 -4.242550869 -0.279539896 RGSFSS(ph)ENYWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGSFSSENYWR 11 1 Q6P6C2-3;Q6P6C2;Q6P6C2-1;K7ER58 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 RGS(0.314)FS(0.314)S(0.371)ENYWR 124.43 0.00036996 481330000 567000 536960 427500 498160 704120 727170 740090 790200 679270 TRUE FALSE 492069.5134 533432.6744 634240.4299 611274.8419 690109.3896 755144.7004 668316.1857 621221.8793 598967.4744 0.821529606 0.890587047 1.058889601 1.020547639 1.152165049 1.260744085 1.115780429 1.037154613 1 19.19211814 4.318288454 1.449479125 1.104730864 0.790572697 0.650664012 0.073570909 0.407477113 1.334146329 0.023875048 0.149794916 20810.7846 -4.318288454 -0.314158167 RGSGDT(ph)SSLIDPDTSLSELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGSGDTSSLIDPDTSLSELR 20 1 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 RGS(0.369)GDT(0.462)S(0.118)S(0.041)LIDPDT(0.007)S(0.002)LS(0.001)ELR 100.39 0.00094762 0 201160 181780 128670 145980 193300 170400 201040 214440 189750 TRUE FALSE 174576.1963 180585.8752 190895.2424 179126.9902 189453.7082 176955.3983 181543.1717 168583.6748 167317.9712 1.04337983 1.079297543 1.140912964 1.070578306 1.132297427 1.057599474 1.085018964 1.00756466 1 17.35223288 1.730795758 2.682641033 0.997405272 1.090225857 0.566516341 0.030141682 0.166581666 2.503561838 0.024074058 0.008066952 53.80167024 -1.730795758 0.092820586 RGSGS(ph)ALGGPLDPQFVGPSDTSLGAAPGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGSGSALGGPLDPQFVGPSDTSLGAAPGHR 30 1 P98174 P98174 FGD1 "FYVE, RhoGEF and PH domain-containing protein 1" 1 RGS(0.465)GS(0.535)ALGGPLDPQFVGPSDTSLGAAPGHR 138.69 3.29E-07 625240000 97287 75828 48790 62347 86851 75776 89454 112350 74356 TRUE FALSE 84430.27646 75329.88088 72385.00719 76503.83926 85122.83502 78691.15175 80778.76485 88324.82681 65565.71839 1.287719841 1.148921765 1.104006926 1.166826829 1.298282656 1.200187441 1.23202745 1.347119028 1 16.00065407 3.339300962 21.87644455 1.232488838 1.169660348 0.018004411 0.100692293 13.61274048 2926.588715 0.028196855 0.036401956 2184.243048 -3.339300962 -0.062828489 RGSISS(ph)MS(ph)S(ph)VSSVLDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGSISSMSSVSSVLDEK 17 1 Q9H1K0 Q9H1K0 RBSN Rabenosyn-5 3 RGS(0.226)IS(0.39)S(0.445)MS(0.549)S(0.546)VS(0.446)S(0.398)VLDEK 79.511 0.0049659 95621000 196960 168240 105510 134670 142370 146940 169340 191850 189840 TRUE FALSE 170931.237 167134.8204 156534.9889 165248.8818 139537.1155 152592.8769 152917.4329 150824.3705 167397.3315 1.021110883 0.998431808 0.93511042 0.987165568 0.833568339 0.911560988 0.913499824 0.900996265 1 17.352917 4.212879069 1.233043087 0.914732603 1.031063831 0.377923076 0.045544981 0.674628179 1.596124987 0.013937853 0.080136071 16325.97281 -4.212879069 0.116331228 RGSLT(ph)LTISGESPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGSLTLTISGESPK 14 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(0.392)LT(0.608)LTISGESPK 162.37 2.61E-06 413400000 418200 293020 241380 273250 302510 270990 386410 443390 414750 TRUE FALSE 362933.8104 291095.1323 358112.1754 335295.5889 296490.6429 281415.1607 348936.0177 348574.499 365718.7275 0.992385085 0.795953585 0.979201087 0.916812741 0.810706755 0.769485234 0.954110335 0.953121819 1 18.48037498 2.030892017 24.99957803 0.967333661 0.875829267 0.256443054 0.073899197 267.8587169 216765.3984 0.029999065 0.020225116 107.3722409 -2.030892017 -0.091504393 RGSPT(ph)TGFIEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGSPTTGFIEQK 12 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(0.013)PT(0.897)T(0.09)GFIEQK 208.83 1.20E-07 1016600000 1960200 1413700 1118100 1308000 1564100 1134500 1783000 2088500 1823300 TRUE FALSE 1701154.603 1404413.312 1658816.9 1605001.392 1532977.47 1178144.949 1610084.934 1641890.528 1607751.551 1.058095452 0.87352633 1.031761965 0.998289437 0.95349152 0.732790429 1.001451333 1.021233988 1 20.61661305 2.031066519 24.99992847 1.011896954 0.938965729 0.106789252 0.090401954 413.1640444 332480.8415 0.037028123 0.024964109 107.4153924 -2.031066519 -0.072931225 RGSS(ph)GSVDETLFALPAASEPVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGSSGSVDETLFALPAASEPVIR 23 1 Q9NQC3-5;Q9NQC3 Q9NQC3-5 RTN4 Reticulon-4 1 RGS(0.228)S(0.324)GS(0.324)VDET(0.124)LFALPAASEPVIR 110.01 0.00067248 83906000 55672 41648 31263 37151 42944 52707 31716 54876 57037 TRUE FALSE 48314.80415 41374.41155 46381.89137 45586.70237 42089.49842 54734.6724 28640.1872 43141.19445 50294.15084 0.960644595 0.822648576 0.922212436 0.906401671 0.836866668 1.088291014 0.569453639 0.857777569 1 15.61810301 2.26395687 24.99999777 0.809238168 0.913605526 0.150466703 0.126165078 441.287027 434400.3235 0.045473763 0.035210607 183.6355966 -2.26395687 0.104367359 RGSS(ph)PGSLEIPK ddPTM_MDA-MB-175_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 1 RGS(0.464)S(0.536)PGSLEIPK 104.78 0.0012869 519970000 1068200 878230 810770 743820 962190 754410 1134800 1304400 1233100 TRUE FALSE 927034.6635 872460.8493 1202861.084 912715.6996 943044.3015 783432.6409 1024747.271 1025464.211 1087324.323 0.852583396 0.80239247 1.106257865 0.839414405 0.867307281 0.720514224 0.942448586 0.943107948 1 20.0523509 2.024915134 24.99485861 0.960076805 0.86848932 0.181930506 0.097627895 407.7306725 409033.6031 0.040286442 0.027160028 105.9046756 -2.024915134 -0.091587485 RGSSGSVDET(ph)LFALPAASEPVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGSSGSVDETLFALPAASEPVIR 23 1 Q9NQC3-5;Q9NQC3 Q9NQC3-5 RTN4 Reticulon-4 1 RGS(0.148)S(0.127)GS(0.181)VDET(0.544)LFALPAASEPVIR 152.95 3.30E-08 79934000 107370 56073 45287 66621 78388 85407 61119 95264 116500 TRUE FALSE 93180.78246 55704.65277 67187.94468 81748.31629 76828.23216 88692.66256 55191.68879 74892.53495 102727.5027 0.907067533 0.542256468 0.654040475 0.795778288 0.747883771 0.863377968 0.537263024 0.729040743 1 16.64846295 3.740341599 24.25541171 0.760824562 0.685234992 0.046877958 0.145574314 350.8738134 4778534.28 0.038443738 0.062502512 5499.732913 -3.740341599 -0.07558957 RGT(ph)GQS(ph)DDSDIWDDTALIK ddPTM_MDA-MB-175_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(0.669)GQS(0.8)DDS(0.532)DIWDDTALIK 94.389 0.0013886 93462000 121130 106780 73434 79353 106390 98257 121760 136140 97493 TRUE FALSE 105122.3636 106078.5551 108946.928 97371.31148 104273.0471 102037.0104 109951.7339 107027.5204 85967.4886 1.222815338 1.233938049 1.267303835 1.13265274 1.21293583 1.18692557 1.278992044 1.244976702 1 16.39150354 1.23526162 24.99942811 0.999999691 1.223791554 0.742373802 0.041199201 49.0858876 371905.039 0.072109663 0.010276757 17.18943572 -1.23526162 0.223791864 RGT(ph)GQSDDSDIWDDTALIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGTGQSDDSDIWDDTALIK 19 1 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 1 RGT(0.564)GQS(0.424)DDS(0.012)DIWDDTALIK 99.366 0.00047338 294190000 53629 43632 32890 41474 53696 41963 59650 68974 39710 TRUE FALSE 46541.79177 43345.37852 48795.71401 50891.30559 52627.55465 43577.34376 53865.15218 54224.44686 35015.52904 1.329175741 1.237890151 1.39354496 1.453392452 1.502977567 1.24451479 1.538321815 1.548582824 1 15.09570726 4.156778548 6.707260738 1.408800825 1.284256338 0.042448771 0.16517884 0.494405626 32.71191754 0.041206823 0.087589217 14347.57646 -4.156778548 -0.124544488 RGT(ph)SLMEDDEEPIVEDVMMSSEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGTSLMEDDEEPIVEDVMMSSEGR 24 1 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 1 RGT(0.5)S(0.5)LMEDDEEPIVEDVMMSSEGR 54.235 0.064031 15612000 9436.5 9173.7 3864.3 6226.3 6484.5 7636.7 6331.6 9800.5 7456.3 TRUE FALSE 8189.442616 9113.437361 5733.088405 7640.076578 6355.471137 7930.488791 5717.562407 7704.739343 6574.824708 1.245575811 1.386111077 0.871975856 1.162019813 0.966637351 1.206190148 0.869614425 1.171854716 1 12.68273672 4.25283721 24.99971993 1.046920798 1.315843535 0.473793574 0.122378506 188.2058238 329560.9665 0.026993823 0.070687576 17899.34793 -4.25283721 0.268922738 RGT(ph)SPRPPEGGLGYSQLGDDDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGTSPRPPEGGLGYSQLGDDDLK 23 2 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12;Q9UQ88-8;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;Q9UQ88-5;Q9UQ88-10 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 RGT(0.5)S(0.5)PRPPEGGLGYSQLGDDDLK;RGT(0.5)S(0.5)PRPPEGGLGYSQLGDDDLK 149.85 4.31E-06 498490000 406840 279100 285830 329010 258140 254110 324540 421970 647170 TRUE FALSE 353075.0632 277266.5737 424058.344 403716.7491 253003.519 263885.7761 293066.1608 331734.9993 570662.2999 0.618711037 0.485868041 0.743098579 0.707452988 0.443350681 0.462420202 0.513554445 0.581315779 1 19.12227773 1.239304927 6.389957147 1.0127983 0.566279408 0.649231556 0.099494607 0.081496348 14.89731844 0.158551003 0.02596554 17.35021764 -1.239304927 -0.446518893 RGTFS(ph)DQELDAQSLDDEDDNMHHAVY(ph)PAVNRFSPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGTFSDQELDAQSLDDEDDNMHHAVYPAVNRFSPSPR 37 2 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 3 RGT(0.425)FS(0.575)DQELDAQS(0.003)LDDEDDNMHHAVY(0.533)PAVNRFS(0.496)PS(0.967)PR 83.15 0.00070215 108830000 44779 35628 16334 19234 29997 32247 31625 37127 21566 TRUE FALSE 38861.34169 35393.95732 24233.17703 23601.37367 29400.11839 33487.56296 28558.01237 29187.67997 19016.49205 2.043559958 1.861224312 1.274324254 1.241100284 1.546032692 1.760974783 1.50174976 1.534861419 1 14.21496352 4.373261476 4.96660519 1.437479585 2.001081746 0.543923941 0.208469439 0.155708216 6.030765002 0.053900447 0.152506535 23618.99837 -4.373261476 0.563602161 RGTGGVDTAATGGVFDISNLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RGTGGVDTAATGGVFDISNLDR 22 1 P12532;P12532-2 P12532 CKMT1A "Creatine kinase U-type, mitochondrial" 0 ; 152.95 6.01E-08 327300000 148331 159344 82474 96725 151258 164739 139310 172976 75471 FALSE TRUE 128728.6825 158297.2588 122358.7023 118687.8896 148248.2617 171076.6159 125799.7376 135986.4285 66548.90436 1.934347136 2.37866063 1.838628351 1.783468725 2.22765894 2.570690195 1.890335218 2.043405971 1 16.02212729 1.202798125 3.550530638 0.787708705 2.09554773 0.650250241 0.249334419 0.23692073 4.140293418 0.881421943 0.064396976 15.951375 -1.202798125 1.307839025 RGTGQS(ph)DDS(ph)DIWDDTALIK ddPTM_MDA-MB-175_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(0.006)GQS(0.994)DDS(0.999)DIWDDTALIK;RGT(0.028)GQS(0.972)DDS(1)DIWDDTALIK;RGT(0.489)GQS(0.707)DDS(0.804)DIWDDTALIK 220.05 1.05E-18 369837000 509100 449970 301131 314694 461120 402946 497940 596510 332387 TRUE FALSE 441821.1451 447014.1174 446758.9588 386150.0825 451944.6142 418447.5934 449649.8554 468950.9785 293092.5875 1.507445647 1.525163503 1.524292929 1.317502042 1.541985821 1.427697633 1.534156354 1.600009685 1 18.16099696 1.23144158 24.99926532 0.999999134 1.499145376 0.80655889 0.076530365 110.4407896 387790.369 0.18927425 0.019133075 17.03890102 -1.23144158 0.499146243 RGTGQS(ph)DDSDIWDDTALIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGTGQSDDSDIWDDTALIK 19 1 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 1 RGT(0.301)GQS(0.699)DDSDIWDDTALIK 269.28 2.65E-32 640800000 171940 150290 105430 117830 160530 114210 182500 221700 92918 TRUE FALSE 149217.6934 149302.7351 156416.3006 144585.1024 157335.7671 118603.7326 164801.1781 174291.1803 81933.33989 1.821208479 1.822246418 1.909067796 1.764667504 1.920289924 1.447563748 2.011405593 2.127231485 1 16.322163 RGTLVAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RGTLVAER 8 1 Q9BR76;A0A087WW53;F5H390 Q9BR76 CORO1B Coronin-1B;Coronin 0 ;;;;;; 128.86 0.0017887 3330490000 3654790 5261900 2704350 3051800 4441880 5000750 4634470 5077060 4477320 FALSE TRUE 3171800.241 5227334.232 4012182.706 3744757.834 4353495.278 5193132.088 4185019.813 3991370.229 3948016.33 0.803390862 1.324040682 1.016252814 0.948516298 1.102704476 1.31537756 1.060031029 1.010981185 1 21.91269653 1.817628446 4.492426104 1.006757696 1.094199352 0.038025279 0.154305715 0.698396104 23.48895412 0.085083047 0.039929767 65.70954296 -1.817628446 0.087441655 RGVFNVQMEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGVFNVQMEPK 11 1 P05198 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 87.184 0.022309 435090000 333130 345040 244420 280010 337580 292710 377040 438730 373170 FALSE TRUE 289106.0265 342773.4095 362622.3295 343590.5502 330862.8185 303970.7431 340474.7188 344911.0037 329054.2677 0.878596799 1.041692642 1.102013756 1.044175943 1.005496208 0.923770858 1.034706893 1.048188817 1 18.32796601 4.742173625 24.77244067 1.026503892 0.878596736 0.507406717 0.04531387 283.4426842 1943318.692 0.011819405 0.084086013 55229.8197 -4.742173625 -0.147907156 RGVTIKPTVDDD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RGVTIKPTVDDD 12 2 P41091;Q2VIR3 P41091 EIF2S3;EIF2S3L Eukaryotic translation initiation factor 2 subunit 3;Putative eukaryotic translation initiation factor 2 subunit 3-like protein 0 ;; 123.99 0.0013148 2841860000 2215020 1904560 1336910 1665460 1978170 1708040 2179820 2356480 2005150 FALSE TRUE 1922299.495 1892048.82 1983444.148 2043628.148 1938808.287 1773749.404 1968421.392 1852565.09 1768103.451 1.087209854 1.070100745 1.12179191 1.155830642 1.09654686 1.003193225 1.113295373 1.047769625 1 20.75377126 2.975556582 23.35923475 1.048993417 1.109316845 0.41798481 0.037976651 359.6399249 343688.3882 0.012357898 0.012432329 945.2715383 -2.975556582 0.060323428 RGWVTFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RGWVTFDR 8 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 81.099 0.038062 432630000 505980 466860 265870 264480 530890 687440 462630 435750 366790 FALSE TRUE 439113.461 463793.1659 394445.6213 324534.2263 520326.3277 713886.2616 417764.2138 342568.2535 323428.504 1.357683245 1.433989769 1.219575938 1.003418753 1.60878315 2.207245968 1.291674075 1.059177683 1 18.3030873 3.222059303 24.99964373 1.414667111 1.264111919 0.060167595 0.347510155 1056.153187 1600077.793 0.118759131 0.135043207 1667.47489 -3.222059303 -0.150555192 RHDS(ph)LHDPAAPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RHDSLHDPAAPSR 13 1 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 RHDS(1)LHDPAAPSR;RHDS(1)LHDPAAPSR 59.342 0.04708 999630000 197896 204023 154357 180044 212896 269154 190041 210562 262993 TRUE FALSE 171743.5422 202682.7595 229004.5615 220925.742 208659.7861 279508.5285 171610.8531 165534.9549 231902.2671 0.74058587 0.874000768 0.987504626 0.952667452 0.899774671 1.205285882 0.740013693 0.713813439 1 17.8231574 RHEAFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RHEAFEK 7 1 Q01082;A0A087WUZ3;Q01082-2;P11277-3;P11277;P11277-2;H0YJE6;Q01082-3 Q01082;Q01082-3 SPTBN1;SPTB "Spectrin beta chain, non-erythrocytic 1;Spectrin beta chain, erythrocytic" 0 88.37 0.029916 71885000 90630 109500 63583 88597 96119 145990 78309 87986 175850 FALSE TRUE 78653.01587 108780.6873 94331.95147 108714.303 94206.41995 151606.3298 70714.60523 69170.87861 155061.2133 0.507238491 0.701533833 0.608352982 0.701105716 0.607543421 0.977719228 0.456043157 0.446087562 1 17.24247833 4.748471668 22.75987702 0.662161331 0.507238195 0.070812387 0.186139031 1256.032765 2884153.474 0.045034471 0.535596412 56036.58597 -4.748471668 -0.154923136 RHEDGEFWMSFSDFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RHEDGEFWMSFSDFLR 16 1 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 124.92 5.18E-05 215560000 105920 145400 65882 74992 126840 126630 108330 124270 42498 FALSE TRUE 91922.40363 144444.8578 97742.75556 92020.07978 124316.1322 131501.538 97824.17327 97695.82757 37473.93485 2.452969083 3.854542054 2.608286425 2.455575592 3.317402687 3.509146786 2.610459074 2.607034141 1 15.19359985 1.147213112 1.843026392 3.58E-12 3.012566998 0.631724141 0.470210302 0.732104345 1.926180211 4.201678703 0.125550667 14.03502247 -1.147213112 3.012566998 RHEGLPGLAVQWGAIGDVGILVETMSTNDTIVSGTLPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 21 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 ;;;;;;;;;;;;;;;;;;;; 394.91 3.73E-180 17881460100 3159346.5 3159215 2029975.7 2201962.7 2908220.9 3503922 3139355.3 3424273.7 2086123.4 FALSE TRUE 2741830.855 3138461.909 3011678.738 2701951.986 2850352.994 3638720.147 2834901.106 2692019.417 1839504.268 1.490527042 1.706145489 1.637223023 1.468847902 1.54952236 1.978098235 1.541122331 1.463448312 1 20.81088559 1.197797493 1.912818202 0.740660462 1.632449152 0.651129755 0.143870872 0.58657503 1.880904535 0.982165999 0.039493696 15.76875818 -1.197797493 0.891788691 RHEHPPNPPVS(ph)PGK ddPTM_MDA-MB-175_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 112.56 0.00027577 615082000 634921 492189 384927 432187 541329 440112 573406 675985 693437 TRUE FALSE 551014.5812 488955.7781 571078.9847 530321.6639 530557.612 457043.3934 517797.1744 531430.8683 611459.6678 0.901146241 0.79965336 0.933960185 0.867304406 0.867690283 0.747462862 0.846821469 0.869118433 1 19.22189782 1.227683943 3.415173345 1.025005958 0.850729309 0.450623782 0.050918764 0.311327987 5.094436838 0.145536951 0.012941174 16.89211163 -1.227683943 -0.174276649 RHEILQWVLQTDSQQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RHEILQWVLQTDSQQ 15 1 Q96AG4 Q96AG4 LRRC59 Leucine-rich repeat-containing protein 59 0 77.562 0.016968 0 181330 172390 115100 126210 169910 142730 120270 227180 183010 FALSE TRUE 157366.7811 171257.5587 170762.745 154867.9095 166529.1234 148220.9155 108606.2339 178599.3249 161374.7663 0.975163495 1.06124125 1.05817501 0.959678598 1.031940292 0.9184888 0.673006297 1.106736382 1 17.30005548 2.737690668 24.90183178 0.9294403 1.018760601 0.145794193 0.111162595 164.050166 4695768.651 0.038353711 0.035851327 546.6264817 -2.737690668 0.089320301 RHES(ph)EEGDSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RHESEEGDSHR 11 1 Q6UN15;Q6UN15-5;Q6UN15-3;H0Y8P7 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 RHES(1)EEGDSHR;RHES(1)EEGDSHR;RHES(1)EEGDSHR;RHES(1)EEGDSHR;RHES(1)EEGDSHR 148.7 1.63E-05 917489500 624777.5 531240.4 338244.5 451390 452600.5 597278.8 517724.5 578680.9 677796.3 TRUE FALSE 542211.5704 527750.6468 501820.6716 553884.9986 443594.6355 620256.5019 467515.6577 454934.4928 597667.9936 0.907211991 0.883016411 0.839631161 0.926743618 0.74220912 1.037794409 0.78223305 0.761182626 1 19.18898476 8 0.627761998 0.855850456 4.821052265 0 0.098051617 1033.571592 7.33420252 0.042410935 5661.850848 99999999.93 -8 3.96520181 RHES(ph)EEGDSHRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 133.25 7.91E-05 333580000 114634 118074 59063 64254 91859 122658 106007 112648 70746 TRUE FALSE 99484.82645 117298.3641 87626.06435 78843.85276 90031.18562 127376.7326 95726.45746 88559.10183 62382.48847 1.594755658 1.880309154 1.404658046 1.263877968 1.443212476 2.041866808 1.534508478 1.419614767 1 15.92885348 1.267735726 2.140487797 0.849708316 1.595152032 0.412339437 0.224545756 0.697241096 3.400380373 0.993708837 0.063552445 18.52404067 -1.267735726 0.745443716 RHGAPAAPS(ph)PPPR ddPTM_MDA-MB-175_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 118.21 0.00027313 1000150000 424498 380847 218487 307540 389419 404498 346513 417985 323681 TRUE FALSE 368399.5138 378345.191 324148.044 377371.6575 381670.3238 420059.2998 312908.2226 328602.1605 285415.8009 1.290746737 1.325593011 1.135704621 1.32218208 1.337243147 1.471745077 1.096324105 1.151310332 1 18.12270568 2.202638635 24.94213073 1.097444793 1.307743938 0.600595888 0.088555263 127.658793 88637.94434 0.036907241 0.024883826 159.4551812 -2.202638635 0.210299145 RHNS(ph)WSSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RHNSWSSSSR 10 1 Q96F86;H3BPW9;H3BQ37 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 1 RHNS(1)WSSSSR;RHNS(0.998)WS(0.002)SSSR;RHNS(1)WSSSSR;RHNS(1)WSSSSR;RHNS(0.998)WSS(0.001)S(0.001)SR 167.89 3.13E-06 2487710000 294689 357974 159681 277706 468440 561906 464053 470618 262516 TRUE FALSE 255745.102 355622.4452 236903.2657 340763.3918 459118.9605 583522.8874 419049.2115 369980.0031 231481.6575 1.104818 1.536287795 1.023421329 1.472096733 1.983392401 2.520816956 1.810291217 1.598312398 1 17.82053835 3.443520185 5.66365252 1.795811632 1.250747982 0.299873882 0.392813435 0.241684694 21.09488931 0.120704997 0.159707882 2776.643897 -3.443520185 -0.54506365 RHPKGEEGS(ph)DDDETENGPKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RHPKGEEGSDDDETENGPKPK 21 3 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 RHPKGEEGS(1)DDDETENGPKPK 173.36 3.15E-12 166170000 255070 154730 115120 95849 136600 85302 275210 284780 40622 TRUE FALSE 221361.8532 153713.5684 170792.4171 117612.9804 133881.9273 88583.62314 248520.1766 223882.0132 35819.71344 6.179889005 4.291312065 4.768112323 3.283470724 3.737660478 2.473041089 6.938083885 6.250245791 1 15.12846618 4.739363063 21.86733682 4.328774989 6.179891884 0.113881587 1.721160222 30.87185285 840286.7166 0.431561272 2.508215443 54873.55065 -4.739363063 1.851116895 RHPQHLHQQHHGDAAQHTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RHPQHLHQQHHGDAAQHTR 19 1 Q9NR09;A0A3B3IUB9 Q9NR09 BIRC6 Baculoviral IAP repeat-containing protein 6 0 ;;; 166.91 7.73E-12 58554100 44143.9 50099.3 24140.9 25652.5 27843.9 39109.7 38428.3 43784.1 22103.7 FALSE TRUE 38310.17177 49770.1944 35815.51999 31477.2922 27289.86087 40614.27547 34701.52938 34421.21094 19490.62577 1.965569101 2.553545227 1.837576711 1.61499649 1.40015314 2.083785095 1.780421511 1.766039293 1 14.25049279 7.999999973 0.062935432 3.60E-07 5.523002626 0.362531806 0.326871809 887.6218785 5.40083234 114.5627629 482.55218 99999993.74 -7.999999973 5.523002266 RHPTGTT(ph)PPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RHPTGTTPPVK 11 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 RHPT(0.281)GT(0.281)T(0.438)PPVK;RHPT(0.249)GT(0.373)T(0.378)PPVK 53.363 0.081149 345110000 954830 837650 468030 656800 749100 643630 842690 1038250 888800 TRUE FALSE 828646.7963 832147.422 694370.8735 805936.4786 734194.3756 668390.8626 760966.0535 816228.3172 783727.0765 1.057315513 1.061782152 0.885985561 1.028338184 0.936798533 0.852836252 0.970957973 1.041470101 1 19.57999182 4.27845571 24.99125406 0.965258739 1.059549157 0.332719145 0.058470925 202.0669834 126576.5395 0.015507035 0.041026582 18986.97199 -4.27845571 0.094290418 RHQDGLPYIDDS(ph)PSSSPHLSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RHQDGLPYIDDSPSSSPHLSSK 22 1 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 RHQDGLPYIDDS(0.984)PS(0.015)S(0.001)SPHLSSK;RHQDGLPYIDDS(0.994)PS(0.005)S(0.001)SPHLSSK 129.51 7.07E-06 437690000 246557 307143 81060 152240 358400 307946 292923 339259 122285 TRUE FALSE 213973.8678 305125.3574 120260.8871 186808.4188 351268.5412 319792.8819 264515.3725 266711.103 107828.6066 1.984388693 2.829725497 1.115296682 1.732456949 3.257656314 2.965751779 2.453109438 2.473472591 1 16.71838045 RHQDGLPYIDDSPSS(ph)SPHLSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RHQDGLPYIDDSPSSSPHLSSK 22 1 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 RHQDGLPYIDDS(0.152)PS(0.223)S(0.446)S(0.179)PHLSSK 144.4 4.72E-08 411170000 161130 169120 47933 90231 201990 157790 196870 208930 86064 TRUE FALSE 139836.2622 168009.0396 71113.55913 110719.3276 197970.7942 163860.2834 177777.5777 164251.9454 75889.61196 1.842627187 2.213860833 0.937065789 1.458952349 2.608667894 2.159192532 2.342581193 2.164353475 1 16.2116148 3.272151608 24.99976389 2.095417378 1.607745899 0.149130578 0.519376952 343.7302349 255815.6821 0.150768844 0.194629883 1871.335292 -3.272151608 -0.487671479 RHQYS(ph)DYDYHSSSEK ddPTM_MDA-MB-175_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 RHQYS(1)DYDYHSSSEK 128.14 3.47E-05 142590000 125840 140470 42903 84799 152440 143680 154120 167860 106680 TRUE FALSE 109209.9252 139547.2433 63651.0343 104053.909 149406.7422 149207.4626 139173.4661 131964.4453 94068.41193 1.160962781 1.483465496 0.676646209 1.106151437 1.588277501 1.586159047 1.479492034 1.402856098 1 16.52142273 3.259330666 24.15309974 1.424144527 1.102984701 0.26594006 0.250888452 220.5885775 256515.8703 0.073144213 0.094306591 1816.898499 -3.259330666 -0.321159826 RHQYSDYDYHSS(ph)SEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.037)S(0.77)S(0.193)EK;RHQYSDYDYHSS(0.987)S(0.013)EK;RHQYSDYDYHS(0.148)S(0.519)S(0.333)EK 168.09 5.99E-07 574990000 597630 506000 256773 348689 437650 371354 482480 462810 417506 TRUE FALSE 518651.6813 502676.0527 380949.2817 427864.1668 428941.6212 385640.2287 435689.1639 363841.6831 368148.9163 1.408809474 1.365415 1.034769532 1.162204064 1.165130745 1.047511514 1.183459042 0.988300296 1 18.48992993 8 0.430910113 1.042224701 9.083960747 0.678950253 0.081741723 52.35686142 0.688530928 0.066319731 363.9090311 100000000 -8 8.041736046 RHS(ph)ASNLHALAHPAPSPGSCSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RHSASNLHALAHPAPSPGSCSPK 23 1 P47974 P47974 ZFP36L2 "Zinc finger protein 36, C3H1 type-like 2" 1 RHS(0.5)AS(0.5)NLHALAHPAPSPGSCSPK 104.29 0.00062338 727030000 624850 612480 256470 473030 573270 497910 657670 752270 668750 TRUE FALSE 542274.4893 608456.5786 380499.7498 580438.6913 561863.0486 517064.9199 593889.2646 591402.9147 589691.1368 0.919590707 1.031822492 0.645252618 0.984309675 0.952809044 0.876840243 1.007119198 1.002902838 1 19.16959998 2.231018285 24.86180816 1.003406929 0.902094007 0.181413908 0.101706519 274.4825383 904766.8335 0.03993607 0.02752101 170.2230175 -2.231018285 -0.101312922 RHS(ph)DENDGGQPHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RHSDENDGGQPHK 13 1 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RHS(1)DENDGGQPHK;RHS(1)DENDGGQPHK;RHS(1)DENDGGQPHK 179.14 6.58E-06 1814370000 969220 752470 505530 606850 685210 655670 795780 971750 960250 TRUE FALSE 841135.1213 747526.975 750005.9989 744644.5676 671575.6616 680894.0492 718605.3781 763948.8247 846730.3389 0.993391972 0.882839483 0.885767244 0.879435321 0.793139953 0.804145095 0.848682686 0.90223391 1 19.69154306 4.985423706 1.796812825 0.868795146 1.1122156 0.299924163 0.056840118 2.662237862 5.018484712 0.016025977 1.353920457 96699.38355 -4.985423706 0.243420454 RHS(ph)DENDGGQPHKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RHSDENDGGQPHKR 14 2 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RHS(1)DENDGGQPHKR;RHS(1)DENDGGQPHKR;RHS(1)DENDGGQPHKR 119.23 0.00010397 450789000 92738 73700 47681.5 53787 70367.4 56406.4 75060 91436 62326.8 TRUE FALSE 80482.43833 73215.85985 70740.43289 66000.16043 68967.22641 58576.39071 67780.69275 71883.12296 54958.59671 1.464419457 1.332200315 1.287158645 1.200906944 1.254894239 1.065827627 1.233304648 1.30795048 1 15.74605755 5.112315831 0.699879987 1.183079669 1.795688099 0.545369159 0.088604949 4.083900716 1.069941068 0.037861092 2.224913048 129513.736 -5.112315831 0.612608429 RHS(ph)GSYLVTSV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RHSGSYLVTSV 11 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 RHS(0.972)GS(0.027)YLVTSV;RHS(0.995)GS(0.005)YLVTSV 111.79 0.0017081 504740000 414240 536840 276390 368930 547760 564250 475140 559160 521050 TRUE FALSE 359497.1344 533313.4627 410053.1285 452701.1952 536860.6477 585957.0626 429060.9959 439587.9854 459452.0626 0.782447536 1.160759753 0.892482942 0.985306699 1.168480221 1.275338845 0.933853672 0.956765724 1 18.80955482 4.757574925 23.72738976 1.038539592 0.782447072 0.319200671 0.120735675 2919.545569 3643095.331 0.03091396 1.001501412 57223.56686 -4.757574925 -0.256092519 RHS(ph)HSHS(ph)PMSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RHSHSHSPMSTR 12 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 2 RHS(0.972)HS(0.034)HS(0.992)PMST(0.001)R;RHS(0.992)HS(0.015)HS(0.993)PMSTR 97.081 0.0021485 106187000 53534 52537 33722 28566 35576 33960 34635 35603 33248 TRUE FALSE 46459.34626 52191.88099 50030.07199 35052.3469 34868.1072 35266.46318 31276.10303 27989.57551 29317.45932 1.584698925 1.78023206 1.706494122 1.195613389 1.18932909 1.20291676 1.066808099 0.954706723 1 14.83947246 3.648586728 2.693211992 1.073339807 1.710869189 0.904622291 0.090511874 0.085400713 1.205592338 0.030051361 0.050017438 4452.323663 -3.648586728 0.637529382 RHS(ph)LENK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RHSLENK 7 1 O14578-4 O14578-4 CIT Citron Rho-interacting kinase 1 RHS(1)LENK;RHS(1)LENK;RHS(1)LENK 101.12 0.0056939 409878000 573290 490260 372450 414430 395800 457800 528970 647950 626690 TRUE FALSE 497528.274 487039.4498 552568.0658 508532.6657 387924.3544 475411.8622 477670.5708 509390.9349 552603.4221 0.90033513 0.881354386 0.999936019 0.920248854 0.701994122 0.860312917 0.864400313 0.921801991 1 19.07588497 1.348174367 2.433794748 1.015053977 0.875210627 0.226868895 0.073563123 0.727123828 5.668745748 0.195360413 0.020842348 22.29330032 -1.348174367 -0.13984335 RHS(ph)MQTEQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RHSMQTEQIR 10 1 Q69YU3 Q69YU3 ANKRD34A Ankyrin repeat domain-containing protein 34A 1 RHS(1)MQTEQIR;RHS(1)MQTEQIR 186.39 8.24E-07 303980000 177868 169198 100790 104197 158060 182410 156623 189564 174489 TRUE FALSE 154362.2931 168086.5272 149532.3811 127856.5214 154914.9152 189427.4307 141433.7256 149027.2138 153861.1092 1.003257379 1.092456229 0.971866002 0.830986609 1.006849073 1.231158619 0.919229858 0.968582734 1 17.23126909 2.615325313 0.004593661 1.15E-05 1.997227735 0 0.104803281 184384.5425 811.5321286 177132.249 175691.077 412.4063205 -2.615325313 1.997216188 RHS(ph)MREEDFIQPSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RHSMREEDFIQPSSR 15 2 Q14289 Q14289 PTK2B Protein-tyrosine kinase 2-beta 1 RHS(1)MREEDFIQPSSR;RHS(1)MREEDFIQPSSR 95.094 0.0022008 309870000 260173 320329 179401 170346 282958 340084 267910 271755 177571 TRUE FALSE 225790.4789 318224.7377 266159.9237 209025.6629 277327.6894 353167.2515 241928.1294 213642.308 156578.7587 1.442024964 2.032362119 1.699846939 1.334955422 1.771170571 2.255524661 1.545089075 1.364439914 1 17.25652899 1.559135941 2.124125968 1.0053141 1.750173349 0.455874123 0.265894623 0.324430564 2.760684106 0.400248487 0.074816427 36.23564041 -1.559135941 0.744859249 RHS(ph)PESPSIAVVESELVAEYITTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RHSPESPSIAVVESELVAEYITTER 25 1 Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-7 EMSY Protein EMSY 1 RHS(0.332)PES(0.332)PS(0.332)IAVVES(0.004)ELVAEYITTER;RHS(0.333)PES(0.333)PS(0.333)IAVVESELVAEYITTER;RHS(0.554)PES(0.222)PS(0.222)IAVVES(0.002)ELVAEYITTER;RHS(0.551)PES(0.224)PS(0.224)IAVVESELVAEYITTER 187.81 6.14E-18 88503000 48336.7 43474.7 29029.9 32646.9 38603.5 39307 38824.5 50490.6 41546.9 TRUE FALSE 41948.88263 43189.11183 43068.85674 40059.87762 37835.36588 40819.16573 35059.30597 39693.57811 36635.27281 1.145040815 1.178894233 1.175611738 1.093478349 1.032757858 1.114203951 0.956982254 1.083479801 1 15.16094574 3.529902595 2.701537082 1.040764206 1.168313275 0.647349872 0.043311622 0.163385697 2.357961595 0.012007829 0.018342102 3387.681679 -3.529902595 0.127549068 RHS(ph)PESPSIAVVESELVAEYITTVSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RHSPESPSIAVVESELVAEYITTVSHR 27 1 Q7Z589-4;E9PMC9 Q7Z589-4 EMSY;C11orf30 Protein EMSY 1 RHS(0.76)PES(0.201)PS(0.04)IAVVESELVAEYITTVSHR;RHS(0.98)PES(0.012)PS(0.008)IAVVESELVAEYITTVSHR 128.92 2.61E-05 50912000 19840.3 20519.8 11081.5 17020.3 17539.7 18368.7 16962.7 20333 18028.8 TRUE FALSE 17218.35409 20385.00408 16440.55047 20885.01925 17190.69429 19075.35578 15317.65996 15984.94618 15897.4558 1.083088659 1.282280909 1.034162363 1.313733437 1.08134877 1.199899909 0.963529017 1.00550342 1 13.95650828 2.237852863 24.99999922 0.991885008 1.16795763 0.473121116 0.087560212 14.52611102 513066.1692 0.030578674 0.022005419 172.9230403 -2.237852863 0.176072622 RHS(ph)PPIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RHSPPIEK 8 1 Q8IZD4;Q8IZD4-2;F5GZK9 Q8IZD4 DCP1B mRNA-decapping enzyme 1B 1 RHS(1)PPIEK;RHS(1)PPIEK;RHS(1)PPIEK;RHS(1)PPIEK;RHS(1)PPIEK;RHS(1)PPIEK;RHS(1)PPIEK 150.09 0.00030307 4136354000 5638580 4647880 3144905 3699410 4385920 3940120 5191800 5556190 5532490 TRUE FALSE 4893427.367 4617347.77 4665791.577 4539417.582 4298648.773 4091698.966 4688300.035 4368042.007 4878445.335 1.003071067 0.94647935 0.956409523 0.93050496 0.881151366 0.838730105 0.961023382 0.895375823 1 22.21799003 4.512912028 1.108007957 0.914105352 1.018218857 0.25569516 0.044442805 1.635554555 2.206047695 0.01398105 0.182610713 32577.07055 -4.512912028 0.104113505 RHS(ph)VADPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RHSVADPR 8 1 A0A0D9SGD0;A0A0D9SF89;Q9H2X9 A0A0D9SGD0 SLC12A5 Solute carrier family 12 member 5 1 RHS(1)VADPR;RHS(1)VADPR 76.143 0.022397 391400000 786310 940390 564140 543790 778030 946890 868060 820910 859290 TRUE FALSE 682397.1412 934212.5162 836959.9909 667265.8308 762548.7252 983317.471 783875.6748 645364.7848 757705.7151 0.900609732 1.232949016 1.104597701 0.880639828 1.006391677 1.297756439 1.034538422 0.851735406 1 19.5312781 1.982085502 23.81058185 0.923635167 1.076071068 0.163587942 0.133085309 633.9839967 842640.5777 0.05976548 0.035447948 95.95895334 -1.982085502 0.152435901 RHS(ph)VSEMTSCPEPQGFSDPPGQGPTGTFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RHSVSEMTSCPEPQGFSDPPGQGPTGTFR 29 1 P85299;P85299-5;P85299-2;P85299-4;P85299-3 P85299 PRR5 Proline-rich protein 5 1 RHS(0.589)VS(0.282)EMT(0.064)S(0.064)CPEPQGFSDPPGQGPTGTFR;RHS(0.447)VS(0.447)EMT(0.053)S(0.053)CPEPQGFSDPPGQGPTGTFR;RHS(0.672)VS(0.202)EMT(0.063)S(0.063)CPEPQGFSDPPGQGPTGTFR;RHS(0.446)VS(0.446)EMT(0.054)S(0.054)CPEPQGFSDPPGQGPTGTFR;RHS(0.25)VS(0.25)EMT(0.25)S(0.25)CPEPQGFSDPPGQGPTGTFR 167.23 1.88E-12 1175130000 258172 249594 158857 165743 251934 248738 246824 256746 248530 TRUE FALSE 224053.9161 247954.4006 235680.7765 203377.4814 246921.0063 258307.1118 222887.0465 201842.8659 219149.0665 1.022381339 1.131441737 1.075435913 0.928032615 1.126726252 1.178682236 1.017056792 0.921030005 1 17.74155301 2.000562358 24.99986892 0.959125008 1.076894831 0.325182979 0.069980167 20.33790549 904105.5175 0.029343999 0.019583887 100.1295717 -2.000562358 0.117769823 RHS(ph)VTDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RHSVTDKR 8 2 Q17R89-3;Q17R89 Q17R89-3 ARHGAP44 Rho GTPase-activating protein 44 1 RHS(0.956)VT(0.044)DKR 77.744 0.016916 26294000 52142 51879 38153 40513 40115 45434 55560 59432 53398 TRUE FALSE 45251.30259 51538.20343 56603.91841 49712.09585 39316.78998 47181.87538 50171.79975 46722.9293 47085.34927 0.961048464 1.094569845 1.202155645 1.055786919 0.835011115 1.002050024 1.065550124 0.992302914 1 15.52299061 3.466179617 24.99528118 0.984394229 1.093819548 0.27474815 0.080887331 279.2108004 637831.9878 0.023681742 0.030601529 2925.362012 -3.466179617 0.109425319 RHS(ph)VTLPSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RHSVTLPSSK 10 1 Q07352;G3V2D5;G3V515;G3V2P5 Q07352 ZFP36L1 "Zinc finger protein 36, C3H1 type-like 1" 1 RHS(0.999)VT(0.001)LPSSK;RHS(0.978)VT(0.022)LPSSK;RHS(0.997)VT(0.003)LPSSK;RHS(0.994)VT(0.006)LPSSK;RHS(0.984)VT(0.016)LPSSK;RHS(1)VTLPSSK 130.72 0.0001649 3579770000 4123390 3926530 2511140 2915290 4001080 3716250 4806690 5145150 4985660 TRUE FALSE 3578473.564 3900736.366 3725535.703 3577251.152 3921466.336 3859216.542 4340537.944 4044899.712 4396260.954 0.813981154 0.887284992 0.847432794 0.813703097 0.892000356 0.877840643 0.987324908 0.920077255 1 22.06784559 2.492383233 1.590240617 0.962940156 0.846588866 0.710925435 0.033980954 0.207660614 1.077689902 0.017010865 0.011493035 310.7300344 -2.492383233 -0.11635129 RHS(ph)VVAGGGGGEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 171.47 1.84E-06 905084000 492777 471355 247419.5 286057.5 360373 357174 384629 331705 356963 TRUE FALSE 427655.2709 468258.638 367072.3978 351011.2275 353202.2824 370914.7149 347327.7388 260772.4671 314763.2408 1.35865697 1.487653504 1.166185724 1.115159529 1.122120491 1.178392731 1.103457119 0.828471795 1 18.26390754 8 0.120517669 0.569168398 3.379959334 0.699336648 0.098197149 114.7734494 1.233065705 3.611181835 54.0747059 100000000 -8 2.810790935 RHS(ph)WGPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RHSWGPGK 8 1 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36;H0YLH1 Q12802-2 AKAP13 A-kinase anchor protein 13 1 RHS(1)WGPGK;RHS(1)WGPGK;RHS(1)WGPGK;RHS(1)WGPGK 138.76 0.0004235 848471000 1455570 1417380 881790 1044280 1279010 1210450 1563280 1782390 1536070 TRUE FALSE 1263212.737 1408069.137 1308226.593 1281399.735 1253560.203 1257016.795 1411673.346 1401239.769 1354477.554 0.932619911 1.039566239 0.965853283 0.946047227 0.925493523 0.928045497 1.042227198 1.034524171 1 20.36930506 2.230155123 24.99987024 1.028139856 0.958628968 0.47640292 0.034160049 166.5718177 495417.8807 0.014488728 0.009948421 169.8850346 -2.230155123 -0.069510888 RHS(ph)YAGEQPETVPYLLLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RHSYAGEQPETVPYLLLNR 19 1 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 RHS(0.989)Y(0.009)AGEQPET(0.002)VPYLLLNR 66.075 0.016963 774780000 154240 159740 102170 99576 149560 155630 142110 158820 116200 TRUE FALSE 133856.7932 158690.6574 151579.7537 122186.2527 146584.0486 161617.1868 128328.1941 124857.5789 102462.9684 1.306391912 1.548761079 1.479361336 1.192491831 1.430605134 1.577322904 1.252434866 1.218562969 1 16.64474307 1.495339558 1.478866996 0.949930838 1.417570234 0.562392751 0.118359141 0.517648102 1.563607658 0.32893036 0.035567829 31.28524481 -1.495339558 0.467639396 RHSPESPS(ph)IAVVESELVAEYITTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RHSPESPSIAVVESELVAEYITTER 25 1 Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-7 EMSY Protein EMSY 1 RHS(0.073)PES(0.343)PS(0.584)IAVVESELVAEYITTER 246.35 4.11E-39 29858000 13667 16496 9810 8610 13379 12409 15090 17100 13085 TRUE FALSE 11860.87132 16387.63669 14554.14881 10565.0321 13112.78408 12886.38226 13626.57412 13443.29807 11538.10621 1.027973838 1.420305585 1.261398409 0.915664313 1.136476285 1.11685419 1.181006127 1.165121713 1 13.49411883 DSGRGDS(ph)VSDSGSDALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DSGRGDSVSDSGSDALR 17 1 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 1 DSGRGDS(0.751)VS(0.235)DS(0.013)GS(0.001)DALR;DSGRGDS(0.556)VS(0.443)DS(0.001)GSDALR;DS(0.006)GRGDS(0.984)VS(0.01)DSGSDALR;DS(0.016)GRGDS(0.976)VS(0.008)DSGSDALR 240.61 6.59E-20 2154120000 619000 1210030 1144100 1330820 2146130 2340440 2304610 2726390 2333130 TRUE FALSE 537197.5817 1202081.233 1697390.587 1633003.021 2103426.212 2430478.241 2081109.277 2143372.715 2057310.029 0.261116494 0.584297561 0.825053377 0.793756409 1.022415767 1.181386474 1.011568139 1.041832628 1 20.97232779 4.525713499 0.814275841 1.054540249 1.53E-14 0.921647609 0.074966863 0.501420836 0.322432503 0.030356338 0.452962318 33551.62036 -4.525713499 -1.054540249 down RHT(ph)PLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 88.496 0.010879 820740000 1431750 1346770 844360 1150810 1012670 1134670 1373680 1687370 1800870 TRUE FALSE 1242540.61 1337922.979 1252695.32 1412119 992519.8483 1178321.489 1240460.725 1326539.057 1587973.2 0.782469509 0.842534987 0.788864271 0.88925871 0.625023047 0.742028574 0.781159736 0.835366149 1 20.59875513 1.219406107 2.198775924 1.072205578 0.778738951 0.511858276 0.067880959 0.605344864 2.847096479 0.361036827 0.018527911 16.5731899 -1.219406107 -0.293466626 RHT(ph)VEDAVVSQGPEAAGPLSTPQEVSASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RHTVEDAVVSQGPEAAGPLSTPQEVSASR 29 1 Q96NW4 Q96NW4 ANKRD27 Ankyrin repeat domain-containing protein 27 1 RHT(0.999)VEDAVVS(0.001)QGPEAAGPLSTPQEVSASR;RHT(0.992)VEDAVVS(0.008)QGPEAAGPLSTPQEVSASR;RHT(0.995)VEDAVVS(0.005)QGPEAAGPLSTPQEVSASR 173.96 8.91E-13 389190000 221403 194517 111521 144408 211603 182353 233690 233025 197568 TRUE FALSE 192144.0326 193239.205 165452.9286 177198.0435 207392.5143 189368.2379 211026.7798 183194.4172 174211.7361 1.102933918 1.109220362 0.949723206 1.017141827 1.190462359 1.087000464 1.211323556 1.051561859 1 17.41048229 RHVTLPS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RHVTLPSSPR 10 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 RHVTLPS(0.5)S(0.5)PR;RHVT(0.001)LPS(0.5)S(0.5)PR 84.892 0.0075879 187450000 385320 387840 172376 227070 410400 446500 374770 365760 377070 TRUE FALSE 334398.9857 385292.2535 255737.6102 278629.714 402233.8429 463677.1439 338424.8631 287545.0703 332493.2142 1.005731761 1.158797344 0.769151367 0.838001205 1.209750533 1.394546187 1.01783991 0.864814854 1 18.34296537 1.988141502 24.92214168 0.928324127 1.063167549 0.080950385 0.179523615 1430.641855 3006673.334 0.085188997 0.052684255 97.3064217 -1.988141502 0.134843422 RHVTLPSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RHVTLPSSPR 10 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 RHVTLPS(0.22)S(0.78)PR 90.861 0.0064575 239430000 189090 156340 72538 97826 173700 193760 150280 168410 161980 TRUE FALSE 164101.2774 155312.9922 107617.6194 120038.8885 170243.7098 201214.0726 135705.8687 132396.8321 142830.9089 1.148919927 1.087390631 0.7534617 0.840426553 1.191924851 1.408757209 0.950115558 0.926948047 1 17.12394869 1.990588747 0.004734949 0.526123465 1.52154885 0 0.187855616 1297088.619 2860.310105 303986.3879 297345.2598 97.85629023 -1.990588747 0.995425386 RIACDEEFS(ph)DS(ph)EDEGEGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RIACDEEFSDSEDEGEGGR 19 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 2 RIACDEEFS(1)DS(1)EDEGEGGR 130.11 1.46E-06 0 229940 197580 155770 173710 183270 196560 192860 205370 298910 TRUE FALSE 199552.8464 196282.084 231100.893 213153.5105 179623.2856 204121.7904 174156.4669 161453.2237 263573.2003 0.757105981 0.744696668 0.876799662 0.80870707 0.681492979 0.774440611 0.660751801 0.612555539 1 18.00784416 3.255107701 24.81538889 0.724233996 0.798816056 0.030796494 0.109414795 554.3477906 831340.7633 0.031265141 0.040244078 1799.317073 -3.255107701 0.07458206 RIDFIPVS(ph)PAPS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RIDFIPVSPAPSPTR 15 1 Q96E09 Q96E09 FAM122A Protein FAM122A 2 RIDFIPVS(1)PAPS(0.996)PT(0.004)R;RIDFIPVS(1)PAPS(0.973)PT(0.027)R;RIDFIPVS(0.997)PAPS(0.501)PT(0.501)R;RIDFIPVS(1)PAPS(0.913)PT(0.087)R 119.62 0.00069352 1041060000 1043550 968220 571038 588259 753110 842130 731620 824190 664720 TRUE FALSE 905642.2235 961859.6991 847193.8868 721832.1969 738124.5844 874527.286 660667.605 647943.3824 586137.5589 1.545101845 1.641013589 1.445384064 1.231506472 1.259302656 1.492017143 1.127154531 1.105445936 1 19.16087976 1.755495239 0.109743244 2.33E-17 2.290281156 0.726261913 0.109754003 30.77241787 1.338616505 18.54801827 10.0360434 56.95019809 -1.755495239 2.290281156 RIDFIPVSPAPS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RIDFIPVSPAPSPTR 15 1 Q96E09 Q96E09 FAM122A Protein FAM122A 1 RIDFIPVSPAPS(0.952)PT(0.048)R;RIDFIPVSPAPS(0.778)PT(0.222)R 158.5 1.11E-06 1732350000 467190 479510 409610 431990 663910 721470 701480 690510 534760 TRUE FALSE 405449.6578 476360.0672 607698.7661 530079.9321 650699.4899 749225.4178 633450.5776 542849.8101 471541.282 0.859839156 1.010219222 1.28874987 1.124143214 1.379941725 1.588886162 1.343361868 1.151224359 1 18.84702455 4.435982133 1.969813218 1.276965479 0.831122675 0.437408091 0.160399446 0.4474927 2.840285067 0.047061217 0.290785976 27288.65516 -4.435982133 -0.445842803 RIDFTPVS(ph)PAPS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RIDFTPVSPAPSPTR 15 1 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3;Q7Z309-5 G1UD79 SPACIA2;FAM122B Protein FAM122B 2 RIDFT(0.009)PVS(0.991)PAPS(0.939)PT(0.061)R;RIDFT(0.034)PVS(0.966)PAPS(0.963)PT(0.037)R;RIDFT(0.001)PVS(0.999)PAPS(0.993)PT(0.007)R 98.292 0.010444 938920000 1176180 1070700 640660 697710 943440 992200 929820 1000310 755170 TRUE FALSE 1020744.833 1063666.501 950485.3189 856135.7193 924667.3898 1030370.576 839646.1995 786401.4909 665894.6629 1.532892347 1.597349492 1.427380893 1.285692418 1.388609102 1.547347701 1.260929463 1.180969806 1 19.34493445 0.393939359 0.518856326 7.75E-16 1.494200665 0.741140251 0.09345139 5.576341255 0.618521175 6.110695534 0.067613748 2.477076154 -0.393939359 1.494200665 RIDFTPVSPAPS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RIDFTPVSPAPSPTR 15 1 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3;Q7Z309-5 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 RIDFTPVSPAPS(0.959)PT(0.041)R;RIDFTPVS(0.002)PAPS(0.972)PT(0.026)R;RIDFTPVSPAPS(0.993)PT(0.007)R 109.37 0.00061579 592657000 181661 175951 118703 169193 219007 232770 212797 242029 192042 TRUE FALSE 157654.0386 174795.1663 176108.1678 207610.8566 214649.1892 241724.8125 192159.9797 190272.9818 169339.0135 0.930996557 1.032220294 1.03997398 1.22600724 1.267570802 1.427460852 1.134764965 1.12362165 1 17.36955486 3.892242872 3.138058385 1.197628451 0.987128008 0.408772237 0.111967123 0.286287582 5.340566188 0.033549791 0.066154873 7802.663393 -3.892242872 -0.210500443 RIDIS(ph)PSTFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 RIDISPSTFR 10 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 RIDIS(0.576)PS(0.158)T(0.267)FR;RIDIS(0.999)PS(0.001)TFR;RIDIS(0.954)PS(0.036)T(0.01)FR;RIDIS(0.998)PS(0.002)T(0.001)FR;RIDIS(0.979)PS(0.019)T(0.002)FR;RIDIS(0.939)PS(0.054)T(0.007)FR;RIDIS(0.999)PS(0.001)TFR;RIDIS(0.997)PS(0.002)TFR 142.39 2.19E-05 34065360000 858243 803302 502474 541194 740299 833401 759148 873796 499435 TRUE FALSE 744824.013 798025.0563 745472.1071 664080.3693 725568.4983 865462.4758 685525.9438 686941.5253 440392.3633 1.69127368 1.812077417 1.692745309 1.507928894 1.647550137 1.965207728 1.556625412 1.559839776 1 18.74842993 0.963521637 1.557815586 0.193901156 1.704996983 0.75167662 0.125341415 1.160177499 1.428420705 3.35727433 0.035864851 9.194362811 -0.963521637 1.511095827 RIDIS(ph)PSTFRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RIDISPSTFRK 11 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 RIDIS(0.998)PS(0.002)TFRK;RIDIS(0.985)PS(0.006)T(0.009)FRK;RIDIS(0.951)PS(0.038)T(0.011)FRK 108.66 0.0010608 1976130000 1904070 1500190 526442 643250 1347450 1119690 1577840 1674210 394614 TRUE FALSE 1652442.325 1490335.153 781031.112 789309.744 1320638.381 1162765.199 1424821.32 1316193.22 347963.1825 4.748899908 4.283025412 2.244579747 2.268371436 3.795339415 3.341632843 4.094747351 3.782564612 1 18.40857514 1.23530118 24.99724055 0.999996479 3.544575067 0.503762893 0.801234377 85.69613329 657108.4687 1.447512196 0.207126788 17.19100158 -1.23530118 2.544578588 RIDIS(ph)PSTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 RIDISPSTLR 10 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 RIDIS(0.881)PS(0.109)T(0.01)LR;RIDIS(0.999)PS(0.001)TLR;RIDIS(0.984)PS(0.015)T(0.001)LR;RIDIS(0.917)PS(0.042)T(0.041)LR;RIDIS(0.992)PS(0.007)T(0.001)LR;RIDIS(0.996)PS(0.003)T(0.001)LR;RIDIS(0.582)PS(0.209)T(0.209)LR;RIDIS(0.97)PS(0.021)T(0.008)LR;RIDIS(0.999)PSTLR;RIDIS(0.959)PS(0.038)T(0.003)LR 146.37 1.76E-05 52154310000 1711658 1362974 914431 1026521 1334745 1445771 1283235 1424717 975244 TRUE FALSE 1485458.059 1354020.534 1356652.89 1259608.282 1308186.186 1501390.746 1158787.067 1120052.357 859951.7653 1.727373695 1.574530792 1.577591843 1.464742946 1.521232049 1.745901115 1.347502399 1.302459512 1 19.71389622 1.389306544 1.16055742 0.821305805 1.589503506 0.784832941 0.101554388 0.547020918 0.769937225 0.496371737 0.032527747 24.5079251 -1.389306544 0.768197701 RIDIS(ph)PSTLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(0.838)PS(0.081)T(0.081)LRK;RIDIS(0.937)PS(0.015)T(0.048)LRK;RIDIS(0.962)PS(0.034)T(0.004)LRK;RIDIS(0.992)PS(0.006)T(0.001)LRK;RIDIS(0.996)PS(0.003)T(0.001)LRK 116.19 0.00053351 4742090000 5282100 4035170 1733360 1961379 3915990 3510880 4660400 4978060 861392 TRUE FALSE 4584057.102 4008662.703 2571618.694 2406740.08 3838069.461 3645945.825 4208435.125 3913540.608 759559.2191 6.03515432 5.277617073 3.385672413 3.168600972 5.053022021 4.800081065 5.540628064 5.152383791 1 19.53480292 4.43945899 6.257204064 4.233626433 5.862043389 0.20547799 1.328723392 0.273988005 29.2542676 0.334943141 0.939010409 27507.99836 -4.43945899 1.628416956 RIDT(ph)PSLEEPSDLEELEQFAK ddPTM_MDA-MB-175_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(1)PSLEEPSDLEELEQFAK;RIDT(0.962)PS(0.038)LEEPSDLEELEQFAK;RIDT(0.99)PS(0.01)LEEPSDLEELEQFAK;RIDT(0.881)PS(0.094)LEEPS(0.025)DLEELEQFAK 295.3 4.39E-55 609879000 685131 568503 361976 355494 439971 430738 572506 591480 461892 TRUE FALSE 594589.2024 564768.4664 537028.8043 436214.3461 431216.4379 447308.7696 516984.4562 464996.6049 407287.6539 1.45987534 1.386657466 1.318549185 1.071022757 1.058751557 1.098262531 1.269334956 1.141690892 1 18.63568856 3.939909565 2.948405345 1.118222108 1.420628515 0.775373091 0.072667295 0.131644542 2.250908241 0.021354023 0.0447483 8707.822441 -3.939909565 0.302406408 RIEELNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RIEELNK 7 1 Q9BTC8;E7EV10;E7EQY4;Q9BTC8-2;E9PCS8;H7C3F3;H0YIT0;E9PF88;E7ESY4;Q13330-3;Q13330;Q13330-2;O94776 Q9BTC8;E7ESY4;O94776 MTA3;MTA1;MTA2 Metastasis-associated protein MTA3;Metastasis-associated protein MTA1;Metastasis-associated protein MTA2 0 ;;; 129.47 0.0058649 737500000 1035970 995430 641330 785190 928450 867640 1106500 1280600 1064120 FALSE TRUE 899063.9397 988890.9548 951479.3331 963479.3904 909975.6615 901018.6722 999191.8003 1006753.656 938320.9458 0.958162496 1.053894149 1.014023333 1.026812195 0.969791483 0.96024572 1.064872105 1.072931027 1 19.83972194 2.217665242 24.99313793 1.052347765 1.000604959 0.28576809 0.035601397 289.9017973 346751.8449 0.014668805 0.009901342 165.0688941 -2.217665242 -0.051742807 RIEGLIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RIEGLIER 8 1 Q13618;Q13618-2;Q13618-3;A0A087WTG3;H7C399 Q13618 CUL3 Cullin-3 0 ; 89.913 0.021757 522735000 422984 353419 236764 259987 344039 389260 329411 393702 395634 FALSE TRUE 367085.5927 351097.3673 351263.8623 319021.022 337193.297 404235.0841 297464.7719 309511.8911 348862.5992 1.052235446 1.006405869 1.00688312 0.914460371 0.966550435 1.158722904 0.852670285 0.887202847 1 18.41229941 7.999999999 0.073623817 0.757336559 1.484811699 0.089141352 0.083086161 1140.936674 8.02908553 16.96089322 90.79905023 99999999.76 -7.999999999 0.727475139 RIENAK ddPTM_MDA-MB-175_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 2829700000 4375760 3721540 2378570 2919890 1788060 3009140 4041640 4650840 4287760 FALSE TRUE 3797492.229 3697092.959 3528854.408 3582895.652 1752481.104 3124903.563 3649682.375 3656294.059 3780865.897 1.004397493 0.977842922 0.933345563 0.947638914 0.463513161 0.826504734 0.965303312 0.967052035 1 21.85028525 3.4497165 24.99976295 0.853198357 0.967132746 0.139177174 0.149923294 522.2343302 476402.2504 0.047304389 0.061071123 2816.543739 -3.4497165 0.113934389 RIEQHYFEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RIEQHYFEDR 10 1 C9JNK6;O75431-2;O75431 C9JNK6 MTX2 Metaxin-2 0 102.4 0.0019166 133160000 151620 108240 83838 128530 121650 183360 95419 130540 130450 FALSE TRUE 131583.0328 107528.9643 124382.3372 157714.701 119229.403 190413.9778 86165.28007 102625.0369 115028.3496 1.143918289 0.934804026 1.081318976 1.371094182 1.036521896 1.655365642 0.749078643 0.892171688 1 16.81162994 RIESLIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 272100000 129120 115500 86901 89808 115380 125690 110150 117820 132820 FALSE TRUE 112056.4649 114741.2729 128926.6143 110200.279 113084.1637 130525.3756 99467.66995 92625.10988 117118.1709 0.956781206 0.97970513 1.100825032 0.940932378 0.965556095 1.114475872 0.849293232 0.790868822 1 16.8376054 2.211388639 24.99614332 0.860191962 1.007356639 0.374333684 0.077576923 195.4240928 179773.8081 0.030886035 0.020829013 162.7004067 -2.211388639 0.147164677 RIESLIDRDYMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RIESLIDRDYMER 13 2 Q13619;A0A0A0MR50;Q13619-2;A0A669KAX4;Q13620-1;K4DI93;Q13620;Q13620-3 Q13619;A0A669KAX4 CUL4A;CUL4B Cullin-4A;Cullin-4B 0 ; 83.692 0.0056731 135796000 109275 123247 70881 71054 109615 118802 94409 108527 72055 FALSE TRUE 94834.03188 122437.3823 105159.2887 87187.89669 107433.876 123372.3898 85253.22971 85319.34561 63536.73999 1.492585737 1.927032806 1.655094182 1.372243787 1.690893741 1.941748819 1.341794208 1.342834801 1 15.95530345 1.598536017 1.49723897 0.9773932 1.670125313 0.563330744 0.190293629 0.419513073 1.486858028 0.38417252 0.05727023 39.67674325 -1.598536017 0.692732113 RIEYIEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RIEYIEAR 8 1 Q8WUW1;Q8WUW1-2 Q8WUW1 BRK1 Protein BRICK1 0 ;; 144.77 0.0009301 2632720000 2769820 2890020 1647240 2202240 2871630 2801280 2663710 3040320 2720830 FALSE TRUE 2403781.269 2871035.268 2443850.774 2702292.251 2814490.181 2909047.054 2405383.814 2390171.228 2399176.577 1.00191928 1.196675266 1.018620637 1.126341544 1.173106727 1.212518946 1.002587236 0.996246483 1 21.19410791 2.158476052 10.906111 0.998642521 1.122788661 0.417115233 0.067932557 0.414829713 53.94907842 0.02686924 0.018114043 144.0376581 -2.158476052 0.12414614 RIILLAEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RIILLAEGR 9 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 185.29 6.90E-05 2438300000 856700 1571400 1000900 1039150 1770390 1814680 1683110 1646140 1093290 FALSE TRUE 743484.9244 1561077.37 1484938.588 1275104.89 1735162.703 1884491.914 1519882.251 1294125.771 964042.5017 0.77121592 1.619303472 1.540324815 1.3226646 1.799881955 1.954780946 1.57657183 1.342394935 1 19.87873723 4.742982074 24.64827673 1.525195791 0.771215551 0.444371194 0.262887012 383.5475294 2138066.123 0.067681114 0.519916794 55332.72693 -4.742982074 -0.75398024 RIILLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RIILLVK 7 1 P52209-2;P52209;K7EM49;K7EPF6;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 131.04 0.014642 0 256500 268980 133470 174430 231170 204860 306560 331550 227790 FALSE TRUE 222602.8751 267213.0527 198016.5384 214036.9975 226570.1693 212741.0968 276829.8584 260650.6126 200860.9257 1.108243798 1.33033865 0.985839021 1.065597984 1.127995246 1.059146253 1.378216582 1.297667088 1 17.61583741 2.261176859 24.99986665 1.246744027 1.115511532 0.137552963 0.128928747 387.145036 427946.7795 0.048086953 0.037219588 182.4638605 -2.261176859 -0.131232494 RINPPSSGGTSS(ph)SPIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RINPPSSGGTSSSPIK 16 1 A0A0C4DG88;P14859-4;P14859-5;P14859-3;P14859;P14859-2;P14859-6;A0A0A0MT46 A0A0C4DG88 POU2F1 "POU domain protein;POU domain, class 2, transcription factor 1" 1 RINPPSSGGT(0.008)S(0.057)S(0.467)S(0.467)PIK 74.364 0.019899 204000000 248510 208500 132710 162300 210690 200890 240790 283500 185120 TRUE FALSE 215668.7739 207130.3498 196888.9999 199152.6956 206497.6812 208618.3683 217438.2229 222875.7312 163235.3245 1.321213864 1.268906411 1.206166622 1.220034305 1.265030604 1.278022199 1.33205373 1.365364586 1 17.31659377 1.228139981 24.99868004 0.999999412 1.282958267 0.770531573 0.048378469 247.8391584 594515.1381 0.190572137 0.013838741 16.90985879 -1.228139981 0.282958854 RINPPSSGGTSSS(ph)PIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RINPPSSGGTSSSPIK 16 1 A0A0C4DG88;P14859-4;P14859-5;P14859-3;P14859;P14859-2;P14859-6;A0A0A0MT46 A0A0C4DG88 POU2F1 "POU domain protein;POU domain, class 2, transcription factor 1" 1 RINPPS(0.002)S(0.001)GGT(0.004)S(0.02)S(0.139)S(0.835)PIK 65.784 0.034541 189940000 176790 144020 107380 118510 152950 152510 205880 185430 132450 TRUE FALSE 153426.7536 143073.9231 159309.3272 145419.5068 149906.5942 158377.1584 185913.7893 145777.2375 116791.9119 1.313676188 1.225032803 1.364044176 1.245116245 1.28353575 1.356062726 1.591837879 1.24817922 1 16.83358084 1.298219172 4.221495137 0.986315174 1.336845778 0.525024251 0.101081899 0.163413591 4.722928363 0.149204366 0.026235444 19.87097479 -1.298219172 0.350530604 RIPADTFAALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RIPADTFAALK 11 1 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 132.56 0.0002884 1267660000 1902690 2054170 1528150 1998470 1839690 1645940 2007100 2258100 3552100 FALSE TRUE 1651244.696 2040676.022 2267168.451 2452253.158 1803083.768 1709260.377 1812451.751 1775222.888 3132174.785 0.527187916 0.651520481 0.723832036 0.782923472 0.575665118 0.545710407 0.578656006 0.566770059 1 21.57873329 1.233612607 24.99818428 1.000000582 0.620455837 0.686272927 0.080944973 99.84437945 504370.8418 0.173360397 0.02153918 17.12429129 -1.233612607 -0.379544746 RIPHS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RIPHSPAR 8 1 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 RIPHS(1)PAR;RIPHS(1)PAR;RIPHS(1)PAR;RIPHS(1)PAR 120.86 0.00089316 3907560000 703131 906300 600579 589865 788514 909320 811640 807730 755440 TRUE FALSE 610210.4568 900346.4556 891021.0132 723802.8638 772824.1141 944302.1288 732927.2777 635003.2253 666132.7438 0.916049335 1.35160216 1.337602785 1.086574516 1.160165329 1.417588518 1.100272107 0.953268296 1 19.34545017 2.001220928 24.96857487 0.989338349 1.219273066 0.313426934 0.143489802 42.20473182 863097.0845 0.057146949 0.038182865 100.2815246 -2.001220928 0.229934717 RIPLAEWESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RIPLAEWESR 10 1 P31930 P31930 UQCRC1 "Cytochrome b-c1 complex subunit 1, mitochondrial" 0 113.38 0.0039108 0 86548 91907 60110 112220 92889 141870 68364 106230 87161 FALSE TRUE 75110.46252 91303.25687 89179.39706 137701.2662 91040.69063 147327.8307 61734.0698 83513.54118 76856.92587 0.977276435 1.187963945 1.160330003 1.79165722 1.184547646 1.916910272 0.803233659 1.086610481 1 16.22988765 RIPSIVSS(ph)PLNSPLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RIPSIVSSPLNSPLDR 16 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 RIPSIVS(0.026)S(0.974)PLNSPLDR;RIPSIVS(0.066)S(0.934)PLNSPLDR 100.9 0.0011617 219576000 129316 141495 79906 82443 131652 124963 135788 154532 64576 TRUE FALSE 112226.563 140565.51 118548.8089 101162.9432 129032.3828 129770.4075 122619.3007 121486.5344 56941.89885 1.97089604 2.468577847 2.08192581 1.776599398 2.266035826 2.278996839 2.153410813 2.133517442 1 15.79720298 1.238430378 7.84115142 0.984496482 2.147701639 0.790093462 0.184854493 0.042380693 21.47609608 0.261415149 0.044850828 17.31531426 -1.238430378 1.163205157 RIPYAPSGEIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RIPYAPSGEIPK 12 1 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ; 96.756 0.0085067 1438650000 1295060 1302050 857670 924680 1230790 983080 1280440 1525650 1252440 FALSE TRUE 1123914.54 1293496.748 1272442.081 1134642.727 1206299.687 1020899.724 1156263.126 1199401.62 1104377.97 1.017690112 1.171244613 1.152179883 1.027404347 1.092288799 0.924411525 1.046981339 1.086042689 1 20.07480258 3.72765814 24.62887482 1.034736044 1.119458843 0.292578171 0.061133546 709.9457112 1603779.74 0.016582661 0.024866126 5341.437359 -3.72765814 0.084722799 RIQLVEEELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RIQLVEEELDR 11 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;H0YL80;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5;H0YKP3;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;H7BYY1;P09493-3;P67936;P67936-2 TPM3;TPM1;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain 0 ;;;;;; 269.81 9.85E-22 11448870000 4368900 4461560 2691770 2959280 4317900 4477790 4305850 4686100 2442030 FALSE TRUE 3791538.796 4432251.719 3993518.975 3631229.754 4231982.238 4650053.479 3888269.33 3684013.982 2153335.995 1.760774354 2.058318687 1.854573083 1.686327522 1.965314399 2.15946489 1.805695599 1.710840292 1 21.03814202 1.113386806 1.874578157 0.440556135 1.908716179 0.804386718 0.138637026 0.529663421 1.339253455 1.547754541 0.03835186 12.98335124 -1.113386806 1.468160044 RIQPQPPDEDGDHS(ph)DKEDEQPQVVVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RIQPQPPDEDGDHSDKEDEQPQVVVLK 27 2 Q96AT1 Q96AT1 KIAA1143 Uncharacterized protein KIAA1143 1 RIQPQPPDEDGDHS(1)DKEDEQPQVVVLK;RIQPQPPDEDGDHS(1)DKEDEQPQVVVLK 70.091 0.010119 257670000 295330 217830 196436 173086 220450 145773 291790 341990 104604 TRUE FALSE 256301.3922 216399.0604 291433.1066 212387.8218 216063.4763 151380.9816 263492.2507 268858.0999 92237.83429 2.778701324 2.346098671 3.159583146 2.302610674 2.342460423 1.641202689 2.85666129 2.914835349 1 16.49307102 3.52960488 23.57076629 2.278355815 2.721787616 0.165381478 0.588770546 415.8236813 186747.3167 0.162967798 0.241716377 3385.36017 -3.52960488 0.443431801 RIS(ph)ACLSDYSLASDSGVFEPLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RISACLSDYSLASDSGVFEPLTK 23 1 Q9ULE0 Q9ULE0 WWC3 Protein WWC3 1 RIS(0.73)ACLS(0.222)DYS(0.047)LASDSGVFEPLTK;RIS(0.823)ACLS(0.172)DYS(0.005)LASDSGVFEPLTK;RIS(0.575)ACLS(0.204)DY(0.001)S(0.219)LASDSGVFEPLTK;RIS(0.9)ACLS(0.1)DYSLASDSGVFEPLTK 163.49 9.43E-12 196866000 329735 221474 154059 193807 230002 209857 256986 309338 248785 TRUE FALSE 286159.6843 220019.1227 228562.4477 237813.8415 225425.4102 217930.3346 232063.5373 243188.476 219373.9207 1.304438027 1.002941106 1.041885229 1.084057033 1.027585273 0.993419518 1.057844691 1.108556911 1 17.7430325 4.744316376 24.98613871 1.045436738 1.304438139 0.832020123 0.037323065 269.2674788 1168874.04 0.009547828 0.083472117 55502.9895 -4.744316376 0.259001402 RIS(ph)FSASHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 154.28 4.66E-05 1599980000 666086 661492 393655 475077 597003 706727 579491 612998 638153 TRUE FALSE 578061.0475 657146.6155 584027.8747 582950.4939 585123.8083 733915.245 523292.052 481913.1481 562711.2793 1.027278231 1.167822007 1.037881941 1.035967316 1.039829536 1.304248328 0.929947686 0.85641281 1 19.10203536 2.037490059 24.99996382 0.910518889 1.098115902 0.444653128 0.090792626 129.1134342 86097.81338 0.03571672 0.024080147 109.0159537 -2.037490059 0.187597014 RIS(ph)GLIYEETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RISGLIYEETR 11 1 P62805 P62805 HIST1H4A Histone H4 1 RIS(1)GLIYEETR;RIS(1)GLIYEETR;RIS(1)GLIYEETR;RIS(1)GLIYEETR;RIS(1)GLIYEETR;RIS(1)GLIYEETR 197.29 3.53E-08 939465000 766257 694474 612366 1464369 822683 1523812 584581 1044672 722421 TRUE FALSE 664994.196 689911.9546 908508.2458 1796876.363 806313.2179 1582434.034 527888.4246 821277.0224 637017.2124 1.043918725 1.083035028 1.426191048 2.820765794 1.265763628 2.484130731 0.828687851 1.289254052 1 19.28097283 4.168395853 4.832544896 1.591574413 1.061175497 0.114520209 0.618868225 0.44922557 19.54680335 0.161954473 0.364436147 14736.55106 -4.168395853 -0.530398916 RIS(ph)HEGSPVKPVAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RISHEGSPVKPVAIR 15 2 Q96II8-3;Q96II8;Q96II8-2 Q96II8-3 LRCH3 Leucine-rich repeat and calponin homology domain-containing protein 3 1 RIS(1)HEGSPVKPVAIR;RIS(1)HEGSPVKPVAIR 147.06 1.97E-06 266620000 263490 186937 150772 173635 177173 167324 241170 234430 187113 TRUE FALSE 228669.1289 185708.9985 223685.8435 213061.4806 173647.6039 173761.0626 217781.3705 184298.9688 164992.7143 1.385934705 1.125558782 1.355731642 1.291338721 1.052456193 1.053143851 1.319945377 1.11701277 1 17.33204279 3.252658702 24.97145387 1.122663423 1.282641621 0.406901579 0.107766584 267.0669397 473043.9265 0.030885387 0.039676517 1789.199227 -3.252658702 0.159978197 RIS(ph)IVENCFGAAGQPLTIPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RISIVENCFGAAGQPLTIPGR 21 1 Q9H8W4 Q9H8W4 PLEKHF2 Pleckstrin homology domain-containing family F member 2 1 RIS(1)IVENCFGAAGQPLTIPGR;RIS(1)IVENCFGAAGQPLTIPGR 295.01 4.70E-55 1798240000 514430 467500 394110 361090 465580 578640 525340 530510 472490 TRUE FALSE 446446.7721 464428.9617 584702.9142 443081.0034 456315.8689 600900.6552 474392.6077 417064.5649 416632.7705 1.071559425 1.114720192 1.403401162 1.063480923 1.095247185 1.442278903 1.138634887 1.001036391 1 18.66841679 1.816875043 4.178681415 1.001355577 1.199348215 0.271429869 0.131094938 0.276115691 8.187529676 0.076575688 0.035034004 65.59565042 -1.816875043 0.197992638 RIS(ph)LDQQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 70.488 0.060263 1639910000 2498200 2164800 1433680 1721230 2252000 2228200 2516200 2559900 2054400 TRUE FALSE 2168056.54 2150579.286 2127012.443 2112061.579 2207189.606 2313920.296 2272179.311 2012485.306 1811531.172 1.196808851 1.187161071 1.174151721 1.165898556 1.218411054 1.277328445 1.25428662 1.110930541 1 20.7887782 1.451978145 3.087972827 1.002145487 1.208953431 0.795921928 0.035014401 0.130570326 2.15001977 0.053057495 0.010464918 28.31249517 -1.451978145 0.206807944 RIS(ph)LSDMPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 198.33 1.63E-05 5197900000 1362474 1151546 1154852 1360461 1668411 1888250 1883045 1950629 2152480 TRUE FALSE 1182419.609 1143981.419 1713342.29 1669374.463 1635212.885 1960892.199 1700427.586 1533502.168 1898016.267 0.622976541 0.60272477 0.902701584 0.879536436 0.861537867 1.033127183 0.895897267 0.807949961 1 20.85606093 4.237327476 24.99632594 0.902863353 0.612850569 0.784759624 0.06490875 13.62118391 276133.6924 0.016816074 0.038448339 17271.39734 -4.237327476 -0.290012784 RIS(ph)QSQPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RISQSQPVR 9 1 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 RIS(0.676)QS(0.324)QPVR;RIS(1)QSQPVR;RIS(1)QSQPVR;RIS(1)QSQPVR;RIS(0.996)QS(0.004)QPVR;RIS(0.869)QS(0.131)QPVR;RIS(1)QSQPVR 204.32 1.03E-05 6239610000 2948830 2353310 1853079 2044480 2715360 3286810 3058860 2902580 3154390 TRUE FALSE 2559134.644 2337850.952 2749234.203 2508710.432 2661329.649 3413255.708 2762212.228 2281885.855 2781481.608 0.920061681 0.84050563 0.988406393 0.901933137 0.956802893 1.227135818 0.993072261 0.820385024 1 21.40742214 3.003367052 24.08604601 0.991460471 0.915022994 0.154775898 0.103290256 167.7511466 1199965.904 0.034902641 0.039361504 1007.783056 -3.003367052 -0.076437477 RIS(ph)QVSSGETEYNPTEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RISQVSSGETEYNPTEAR 18 1 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 RIS(0.999)QVS(0.001)SGETEYNPTEAR;RIS(0.524)QVS(0.43)S(0.046)GETEYNPTEAR;RIS(1)QVSSGETEYNPTEAR;RIS(0.984)QVS(0.008)S(0.008)GETEYNPTEAR;RIS(1)QVSSGETEYNPTEAR 247.28 2.43E-24 3981410000 982825 1070975 617048 674890 1109120 1216899 1041450 1034823 918308 TRUE FALSE 852942.1861 1063939.695 915454.4767 828134.0895 1087050.682 1263713.892 940450.3393 813534.1545 809746.6744 1.053344476 1.31391672 1.130544287 1.022707614 1.342457729 1.56062869 1.161413031 1.004677364 1 19.62711111 1.823666696 4.216014616 1.004147362 1.239251778 0.273627113 0.154514085 0.291311789 8.580526395 0.094493654 0.043679723 66.62952182 -1.823666696 0.235104416 RIS(ph)SSSVQPCSEEVSTPQDSLAQCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RISSSSVQPCSEEVSTPQDSLAQCK 25 1 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 RIS(0.905)S(0.063)S(0.021)S(0.011)VQPCSEEVSTPQDSLAQCK 225.72 4.34E-34 805990000 739650 667510 445670 507480 658180 554430 917190 863830 626380 TRUE FALSE 641903.3785 663125.0829 661197.5027 622711.0903 645083.5057 575759.2809 828241.055 679106.6768 552330.07 1.162173514 1.200595656 1.19710575 1.127425654 1.167931172 1.042418858 1.49954004 1.229530518 1 19.07517115 RISAVSVAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RISAVSVAER 10 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;; 155.47 2.03E-05 1415440000 890020 965380 436982 460239 967420 973680 903020 995370 294137 FALSE TRUE 772401.602 959038.3552 648307.9568 564743.2993 948170.2347 1011138.1 815445.2594 782517.8715 259364.4589 2.978054916 3.697647546 2.499602141 2.177412054 3.655744656 3.898522195 3.144013111 3.017058986 1 17.98462127 4.238833107 24.99999997 2.863121642 3.337851139 0.067021072 0.825656379 23.81231506 2183636.807 0.212663965 0.49605478 17331.37848 -4.238833107 0.474729496 RITEAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RITEAEK 7 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 93.162 0.024272 268440000 521450 507840 242033 384100 365880 489960 454310 529350 479990 FALSE TRUE 452539.0613 504503.9656 359080.9684 471315.7756 358599.7038 508809.0782 410251.0861 416152.6219 423246.129 1.06921016 1.191987194 0.848397525 1.113573742 0.847260446 1.202158847 0.969296724 0.983240232 1 18.69113735 4.267081593 24.99853388 0.998814931 1.130598672 0.207952751 0.109931792 315.7797593 276774.6636 0.024597455 0.065052941 18496.16083 -4.267081593 0.131783742 RITINK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RITINK 6 1 Q9Y2J8 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 85.357 0.087878 657830000 1183100 957020 899440 779880 930100 826320 1093100 1227400 981300 FALSE TRUE 1026750.337 950733.2726 1334412.192 956963.6737 911592.8297 858109.0651 987091.3302 964930.0616 865291.8319 1.186594279 1.098742918 1.542152767 1.105943265 1.053509112 0.991699024 1.140761179 1.115149856 1 19.72282726 3.503704396 24.99689229 1.070614751 1.269109087 0.404765341 0.119627575 762.060775 716585.7313 0.032165498 0.0475358 3189.366264 -3.503704396 0.198494337 RIVDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RIVDGK 6 1 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 98.503 0.063914 6028420000 15080000 13404620 8986150 11351330 11103580 12647720 17252900 18696600 14062500 FALSE TRUE 13087139.79 13316564.17 13331882.2 13928822.97 10882640.48 13134285.97 15579716.41 14698477.59 12400047.27 1.055410476 1.073912371 1.075147691 1.123287893 0.877628951 1.059212573 1.256423953 1.185356577 1 23.56384228 2.422300836 13.66621129 1.159523392 1.041271961 0.228106676 0.089083815 1.786906742 443.3320439 0.033376535 0.025851283 264.4239789 -2.422300836 -0.118251431 RIVNAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RIVNAK 6 1 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 122.51 0.030768 968120000 1935250 1565030 1161560 1456780 1328950 1505780 1913050 2213700 1569690 FALSE TRUE 1679501.809 1554749.215 1723294.301 1787564.164 1302506.495 1563708.331 1727522.705 1740317.482 1384123.036 1.213404997 1.123273852 1.245044159 1.291477793 0.941033753 1.129746626 1.248099092 1.257343051 1 20.40054076 5.282553144 7.275889784 1.16665682 6.530469183 0.015792259 0.114749503 119556.8315 28566.73247 0.02845495 10551130.95 191669.5592 -5.282553144 5.363812363 RIVSQLLTLMDGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RIVSQLLTLMDGLK 14 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 141.85 1.53E-05 104124000 390050 320640 163758 213709 292710 254030 362360 394920 168880 FALSE TRUE 338503.9042 318533.6947 242951.9165 262234.8948 286885.6437 263802.6985 327218.383 310469.4313 148915.1988 2.273132004 2.139027428 1.631478308 1.760967966 1.926503446 1.771496131 2.197347119 2.084874034 1 17.18413148 4.393748828 5.974340858 1.825361877 2.241238979 0.230735872 0.323789111 0.2986049 16.30814936 0.080355056 0.220523183 24759.89669 -4.393748828 0.415877103 RKAS(ph)PEPPDSAEGALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RKASPEPPDSAEGALK 16 2 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 RKAS(1)PEPPDSAEGALK;RKAS(0.991)PEPPDS(0.009)AEGALK 102.33 0.00079603 529390000 1520020 1038980 821880 872820 978610 780180 1439370 1638080 1016800 TRUE FALSE 1319145.506 1032154.872 1219343.917 1071007.121 959137.5756 810194.0294 1299780.119 1287789.34 896595.0623 1.471283483 1.151194018 1.359971707 1.194527124 1.069755585 0.903634275 1.449684672 1.436310988 1 19.77409703 4.74854255 23.68118025 1.218388385 1.471283772 0.176905424 0.181038324 1403.655442 3329892.084 0.046908814 0.590703328 56045.73254 -4.74854255 0.252895387 RKAS(ph)VHSSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RKASVHSSGR 10 2 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 1 RKAS(1)VHSSGR 51.726 0.080743 12551000 31888 16889 5883.5 7857 17692 19427 24738 21365 10888 TRUE FALSE 27673.92001 16778.05505 8728.780279 9641.051937 17339.96381 20174.36926 22338.91257 16796.26101 9600.833044 2.882449875 1.747562422 0.909169052 1.004189105 1.806089507 2.101314456 2.326768153 1.749458712 1 13.22894388 3.029251313 24.98795014 1.850213207 1.568570159 0.007596873 0.626704285 818.1563663 698905.2195 0.198351233 0.224906281 1069.673687 -3.029251313 -0.281643048 RKDDSYFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RKDDSYFDR 9 2 Q9HCD5;Q5JY17 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 0 ; 187.99 2.24E-05 629250000 465080 435240 253120 277130 445160 360990 440220 497030 393970 FALSE TRUE 403618.4996 432380.8798 375529.6786 340056.6022 436302.1869 374877.5189 397527.5322 390744.0024 347395.3154 1.161842091 1.244636472 1.080986594 0.978875037 1.25592421 1.079109309 1.144308845 1.124782014 1 18.40621877 5.254344247 0.015985322 4.43E-07 2.344216526 0.131458373 0.084434737 12288.4066 43.0432298 2903.468304 3427.230351 179615.6799 -5.254344247 2.344216083 RKDGVFLYFEDNAGVIVNNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RKDGVFLYFEDNAGVIVNNK 20 2 J3KTJ3;P62829;J3KT29 J3KTJ3 RPL23 60S ribosomal protein L23 0 ;; 174.23 2.09E-12 111764000 598456 535578 394026 442916 487086 377030 645778 734129 326976 FALSE TRUE 519368.5233 532059.7529 584578.2915 543486.8473 477393.9416 391534.5881 583150.549 577141.2263 288321.2698 1.801353482 1.845371149 2.027523991 1.885004349 1.655770807 1.357980243 2.022572075 2.001729622 1 18.13731774 3.247787981 13.46801871 1.675511316 1.896506056 0.158971043 0.300622956 1.834279728 2659.242318 0.090136034 0.112702707 1769.245016 -3.247787981 0.22099474 RKDPELWGSVLLESNPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RKDPELWGSVLLESNPYR 18 2 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 164.57 1.71E-11 842850000 1825100 1596600 728680 797310 1389400 1421600 1686000 1963300 392240 FALSE TRUE 1583908.411 1586111.829 1081072.085 978351.4216 1361753.658 1476289.872 1522491.98 1543463.573 345869.834 4.579492789 4.585863447 3.125661676 2.828669416 3.937185393 4.268339492 4.401921849 4.462556203 1 18.39986967 4.25777032 23.82616029 3.60237399 4.582680081 0.162993056 1.029187583 293.7427177 364323.3711 0.256953508 0.677033667 18103.82404 -4.25777032 0.980306091 RKDPLTHTS(ph)NSLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RKDPLTHTSNSLPR 14 2 A0A2R8Y7K2;A0A2R8Y481;A0A2R8YGN6;A0A2R8Y4I8;A0A2U3TZR0;Q9UBP0-4;Q9UBP0-3;Q9UBP0-2;Q9UBP0;A0A2R8Y5N9;A0A2R8YFW8;A0A2R8YCL5 A0A2R8Y7K2 SPAST Spastin 1 RKDPLT(0.002)HT(0.267)S(0.715)NS(0.016)LPR 75.239 0.016075 57211000 115930 113180 30495 58172 96985 101070 108590 104850 70145 TRUE FALSE 100609.5568 112436.5131 45242.484 71380.8417 95055.18825 104958.2283 98058.95851 82428.64344 61852.53801 1.626603532 1.817815675 0.731457196 1.15404871 1.53680336 1.696910615 1.585366772 1.332663882 1 15.91654517 7.999998139 0.020185087 5.08E-10 3.153714734 0.03944442 0.332773616 42750.71674 85.80058986 5309.641532 8447.617535 99999571.54 -7.999998139 3.153714734 RKDREDS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RKDREDSPER 10 3 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 1 RKDREDS(1)PER;RKDREDS(1)PER;RKDREDS(1)PER;RKDREDS(1)PER;RKDREDS(1)PER;RKDREDS(1)PER;RKDREDS(1)PER 169.19 2.60E-05 4644647000 1365890 1162759 591829.6 629860 915023 1028762 1275585 1312224 359779.7 TRUE FALSE 1185384.176 1155120.76 878040.3741 772879.3398 896815.8325 1068339.14 1151878.963 1031615.109 317246.9537 3.73647142 3.641077545 2.767687329 2.436207285 2.8268698 3.367531594 3.630859018 3.251773097 1 18.27524679 4.251218042 11.78963963 2.85886825 3.689493754 0.215817531 0.719336095 0.796560323 718.6054525 0.181931318 0.45578973 17832.73854 -4.251218042 0.830625505 RKDS(ph)AQDDQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 177.3 6.33E-06 4194240000 4845740 3228370 3253040 3145800 1878287 2379440 5499090 5630840 5186370 TRUE FALSE 4205363.181 3207162.625 4826221.025 3860101.971 1840912.764 2470978.597 4965789.098 4426728.685 4573243.247 0.919558168 0.701288441 1.05531693 0.844062247 0.402539875 0.540312086 1.085835332 0.967962657 1 22.12478623 2.220048456 24.99975576 1.010351574 0.745110904 0.32956921 0.184171059 317.6063734 428908.4245 0.080962786 0.054695223 165.9772083 -2.220048456 -0.265240669 RKDS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RKDSPSR 7 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;Q7Z6E9-4 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 RKDS(0.956)PS(0.044)R;RKDS(0.552)PS(0.448)R;RKDS(0.582)PS(0.418)R 82.645 0.018844 1553920000 1475960 1102940 650580 831800 664040 934720 1199480 1354880 1473350 TRUE FALSE 1280908.146 1095694.715 965202.6641 1020672.903 650826.9032 970679.2832 1083154.614 1065149.456 1299172.241 0.985941745 0.843379099 0.742936643 0.785633245 0.500955056 0.747152111 0.833726722 0.819867776 1 20.30916128 0.987060578 1.417369999 1.241191631 0.764794205 0.251220727 0.120067721 3.47974798 3.786304625 2.840391019 0.03658964 9.70645349 -0.987060578 -0.476397426 RKEDEVEEWQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 RKEDEVEEWQHR 12 2 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;;;;; 208.95 3.66E-08 21275190000 14861090 12686150 9799550 12612180 12982130 11108890 13592600 17276140 15192740 FALSE TRUE 12897159.3 12602813.85 14538645.16 15475968.23 12723811.01 11536256.19 12274391.74 13581771.9 13396671.58 0.962713703 0.940742166 1.085243082 1.155209944 0.949774049 0.861128536 0.916226965 1.013816889 1 23.67537127 3.0881418 22.14050241 0.949549472 1.035171482 0.268232363 0.072024805 13.97748568 3504.540029 0.023978787 0.027189504 1225.016109 -3.0881418 0.085622011 RKEEEVQQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RKEEEVQQQK 10 2 Q96CS3 Q96CS3 FAF2 FAS-associated factor 2 0 67.726 0.034934 73075000 35912 32189 23276 32649 33638 27448 21678 54176 37666 FALSE TRUE 31166.13821 31977.54834 34532.35145 40062.45446 32968.66961 28503.94232 19575.6709 42590.884 33213.16839 0.938366911 0.962797285 1.039718676 1.206222002 0.992638499 0.85821208 0.589394865 1.282349323 1 15.01946774 3.00259907 24.95809248 0.95170471 1.040168175 0.06421995 0.181227732 303.3173777 2912608.418 0.058519734 0.065978953 1006.002522 -3.00259907 0.088463465 RKEEWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RKEEWER 7 2 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 0 ; 133.58 0.0018322 262519000 354080 260080 164076 215958 210267 237130 310250 334190 277980 FALSE TRUE 307287.4309 258371.5174 243423.7024 264994.5646 206083.0981 246252.5445 280162.0028 262726.0692 245117.5211 1.253633072 1.054072007 0.993089769 1.081091892 0.840752212 1.004630528 1.142970121 1.071837166 1 17.90311409 4.731085081 3.760993934 1.025623391 1.275604572 0.463311569 0.078426643 0.24856173 6.801235264 0.020384247 0.171059675 53837.52433 -4.731085081 0.249981182 RKEQEEEEQKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 179.35 9.12E-06 386540000 281350 180226 160653 168724 178777 143302 269640 292580 176161 FALSE TRUE 244168.8846 179042.0835 238345.3282 207035.363 175219.6875 148814.9207 243490.3543 230014.0439 155335.4473 1.571881299 1.152615753 1.534391102 1.332827546 1.128008388 0.958022932 1.567513137 1.480756955 1 17.24502756 4.760313313 22.96817679 1.29590062 1.571882174 0.153804624 0.215154575 3901.733348 4119550.12 0.053675584 2.147116339 57585.52265 -4.760313313 0.275981554 RKFS(ph)NSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RKFSNSLK 8 2 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;Q9BV36-3;Q9BV36 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 RKFS(1)NSLK;RKFS(0.998)NS(0.002)LK 123.67 0.0010535 1631070000 2793480 2155660 1164450 1416470 1821550 1329120 3057100 2953390 1941030 TRUE FALSE 2424314.54 2141499.328 1727581.915 1738101.163 1785304.719 1380252.106 2760622.913 2321830.532 1711563.645 1.416432598 1.251194681 1.009358852 1.015504839 1.043084039 0.806427567 1.612924486 1.356555182 1 20.70688351 1.187919325 22.59204963 0.999989234 1.19106983 0.060353563 0.234151318 17656.6609 7874728.623 46.96619291 0.061171628 15.41414092 -1.187919325 0.191080595 RKGS(ph)GS(ph)EQEGEDEEGGER ddPTM_MDA-MB-175_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 129.84 0.00010004 803160000 2555370 2049610 1377380 1465760 2095490 1774650 2321020 2744770 2123690 TRUE FALSE 2217671.38 2036145.977 2043485.575 1798583.211 2053793.849 1842921.934 2095927.838 2157822.295 1872629.788 1.184255102 1.087319015 1.091238422 0.960458507 1.096743127 0.984135757 1.11924303 1.152295189 1 20.83663428 4.798173555 2.084377232 1.064956899 1.229324637 0.290604263 0.061354383 1.261843743 5.33394542 0.016583318 0.412336697 62830.93971 -4.798173555 0.164367738 RKGS(ph)QITQQSTNQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RKGSQITQQSTNQSR 15 2 P50750;P50750-2 P50750 CDK9 Cyclin-dependent kinase 9 1 RKGS(1)QITQQSTNQSR 81.016 0.012014 35466000 17290 14767 5973.7 8718.6 13667 13780 19404 19683 2702.6 TRUE FALSE 15005.08269 14669.9946 8862.601301 10698.29139 13395.05344 14310.12552 17522.20307 15473.94362 2383.101707 6.296450819 6.155840753 3.718935401 4.489229878 5.62084841 6.004832054 7.352687893 6.493194805 1 11.21862481 4.439632664 24.99702365 5.243029465 6.261311042 0.065644554 1.752213609 489.9166545 326671.005 0.4440836 1.174940447 27519.001 -4.439632664 1.018281577 RKHDNEGSGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RKHDNEGSGSK 11 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 161.99 1.44E-05 23342000 19694 14651 7602 9336.9 9018.3 11508 15422 20998 12178 FALSE TRUE 17091.388 14554.75662 11278.35263 11456.98585 8838.853474 11950.72021 13926.37681 16507.74111 10738.33071 1.59162429 1.355402157 1.050289186 1.066924288 0.823112429 1.112902976 1.296884701 1.537272556 1 13.39048212 4.527575407 3.369898523 1.159578369 1.579139379 0.385799788 0.190233192 0.335995558 7.113099416 0.056164847 0.269691742 33695.77166 -4.527575407 0.419561011 RKHS(ph)PS(ph)PPPPTPTESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RKHSPSPPPPTPTESR 16 2 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 2 RKHS(1)PS(1)PPPPTPTESR;RKHS(1)PS(1)PPPPTPTESR 141.31 8.67E-07 107484000 207146 134567 97124 103441 126885 127480 151410 164942 116386 TRUE FALSE 179771.1313 133683.0205 144093.4913 126928.86 124360.2367 132384.2381 136726.2815 129670.4369 102626.9797 1.75169465 1.302610882 1.404050784 1.236798164 1.211769431 1.289955512 1.332264498 1.263512161 1 16.64705053 7.846248695 0.913579538 1.238439395 199.9999998 0.711539091 0.100982227 406.1399729 1.153814892 0.032246137 167967.6757 70185709.66 -7.846248695 198.7615604 RKLEEQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RKLEEQAR 8 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ;;;;;; 158.37 0.00020552 3163338000 2456850 2845380 1505743 1844548 2671570 2475870 3304770 3729120 1399325 FALSE TRUE 2132171.048 2826688.511 2233925.351 2263380.816 2618410.984 2571118.321 2984273.914 2931676.708 1233898.393 1.727995644 2.290860032 1.810461351 1.834333223 2.122063696 2.083735854 2.418573468 2.375946614 1 20.23479217 3.222569656 24.07063002 2.082621094 1.935162266 0 0.417357434 729.6336873 1098287.127 0.125038149 0.142284757 1669.435545 -3.222569656 -0.147458828 RKLESTESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 174.98 3.05E-05 877770000 1129970 987590 572490 680520 962400 964880 1144230 1293670 551510 FALSE TRUE 980641.6015 981102.4563 849348.0789 835042.4671 943250.1229 1001999.558 1033262.751 1017028.738 486311.1161 2.016490204 2.017437858 1.746511751 1.717095167 1.939602225 2.060408502 2.124694905 2.091312956 1 18.89152004 1.234071439 24.99989442 0.999998558 1.967054029 0.832830258 0.135753282 61.36129875 341672.6396 0.294830351 0.038079629 17.14239268 -1.234071439 0.967055471 RKPAAPPPS(ph)PAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RKPAAPPPSPAAR 13 2 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 RKPAAPPPS(1)PAAR;RKPAAPPPS(1)PAAR 90.561 0.0054611 97932000 87593 88217 53574 77471 101419 88354 94390 117431 96332 TRUE FALSE 76017.36312 87637.49672 79482.56559 95061.97462 99400.96032 91753.03555 85236.07233 92319.2945 84943.7407 0.89491424 1.031712237 0.935708328 1.119116886 1.170197586 1.080162409 1.003441473 1.086828691 1 16.37422002 3.743354415 24.97868221 1.077159795 0.96187166 0.482876883 0.059584192 375.9005983 1958670.525 0.016159631 0.026909221 5538.018664 -3.743354415 -0.115288135 RKPDTIEVQQMK ddPTM_MDA-MB-175_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 ; 162.49 3.52E-05 1509940000 1990690 1650190 1125240 1833540 1542780 1195880 1587760 2570600 2455100 FALSE TRUE 1727615.273 1639349.793 1669409.828 2249873.281 1512081.696 1241886.277 1433779.28 2020897.194 2164860.875 0.798026004 0.757254109 0.771139544 1.039269224 0.698465991 0.573656391 0.662296269 0.9334998 1 21.04584288 1.592770997 5.344056974 0.983445718 0.759665143 0.352763281 0.119362318 0.164268345 9.792219552 0.089228479 0.033048637 39.15353668 -1.592770997 -0.223780575 RKPEEES(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RKPEEESPR 9 2 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33 P49321 NASP Nuclear autoantigenic sperm protein 1 RKPEEES(1)PR;RKPEEES(1)PR 133.32 0.00022071 527420000 1246100 794020 743060 913450 713430 789690 847390 1103680 2124060 TRUE FALSE 1081424.728 788804.0303 1102406.301 1120862.784 699234.1388 820069.8853 765210.2482 867666.6208 1872956.047 0.577389272 0.421154587 0.588591656 0.598445856 0.373331846 0.437847907 0.408557504 0.463260535 1 20.83688561 1.237500246 24.99970416 1.000000617 0.479151107 0.805068932 0.07983487 11.53009103 271706.1774 0.118239629 0.019862073 17.27826961 -1.237500246 -0.520849509 RKPFTFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RKPFTFK 7 2 Q9Y2J8 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ; 119.41 0.0026934 1558210000 2188600 2302700 1395110 1505220 1895430 1571960 2157100 2531000 2272300 FALSE TRUE 1899370.965 2287573.412 2069789.862 1847003.207 1857714.651 1632434.318 1947904.774 1989765.346 2003671.283 0.947945395 1.141690971 1.032998716 0.921809492 0.927155401 0.814721623 0.972167836 0.993059772 1 20.93421441 3.815039835 5.239551385 0.940483989 1.053635662 0.327674128 0.068921334 0.253374149 12.49077433 0.018895469 0.033295385 6531.904635 -3.815039835 0.113151673 RKPNAGGS(ph)PAPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 171.87 1.92E-05 991390000 1478220 1286320 742160 919050 1239930 1024710 1274030 1431090 968420 TRUE FALSE 1282869.482 1277870.079 1101071.058 1127734.349 1215257.819 1064131.257 1150474.767 1125062.54 853934.4908 1.502304328 1.496449778 1.289409282 1.320633329 1.423127689 1.246150926 1.347263495 1.317504507 1 19.70376587 0.694007819 1.401051593 7.85E-21 1.377220848 0.669308623 0.082247619 3.256435674 1.85042769 9.388683998 0.024847775 4.943195871 -0.694007819 1.377220848 RKPQEESER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RKPQEESER 9 2 P26358;P26358-2;K7EJL0;K7ENQ6;K7ERQ1;K7ELB1 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 ; 201.84 1.17E-05 132420000 108606 105622 67247 78943 82206 78374 109370 122705 99785 FALSE TRUE 94253.44193 104928.1621 99767.87413 96868.21472 80570.26143 81389.09849 98763.31423 96465.49064 87988.53098 1.07120145 1.1925209 1.13387362 1.10091865 0.915690494 0.924996674 1.122456679 1.096341643 1 16.42502786 3.463105253 24.90810959 1.024754594 1.135008444 0.387382096 0.070324736 270.9334416 481479.3206 0.02245519 0.029002848 2904.726538 -3.463105253 0.11025385 RKPS(ph)PEPEGEVGPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RKPSPEPEGEVGPPK 15 2 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK 198.77 6.11E-09 21091890000 13703050 10518280 9619790 10177790 9851540 7433060 14198590 16321740 15717180 TRUE FALSE 11892157.22 10449184.73 14271952.62 12488812.78 9655513.628 7719014.628 12821612.93 12831462.92 13859112.89 0.858074923 0.753957689 1.029788323 0.90112642 0.696690597 0.556963111 0.925139512 0.925850235 1 23.72433158 2.029226414 24.99985203 0.947988946 0.802227863 0.245323988 0.125389073 321.0066384 274583.179 0.055025649 0.037097704 106.9612363 -2.029226414 -0.145761083 RKPS(ph)SEEGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RKPSSEEGKR 10 3 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 RKPS(0.98)S(0.02)EEGKR 118.37 0.0046112 147580000 160140 111500 117460 110710 97516 87542 180250 200330 181270 TRUE FALSE 138977.0933 110767.5492 174264.0489 135848.3976 95575.62239 90909.79739 162769.3827 157490.9885 159840.4671 0.869473768 0.692988147 1.09023736 0.849899904 0.597943838 0.568753327 1.018323993 0.985301103 1 17.28627318 2.186016037 24.99995034 0.998608154 0.783588208 0.337084367 0.147272018 124.4317088 59201.75016 0.063850069 0.043047753 153.4673653 -2.186016037 -0.215019947 RKPS(ph)VPDSASPADDSFVDPGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RKPSVPDSASPADDSFVDPGER 22 2 P16333-2;P16333;C9JAB9;C9K098;C9JVV5;H7C5C7;C9J869 P16333-2 NCK1 Cytoplasmic protein NCK1 1 RKPS(0.881)VPDS(0.106)AS(0.013)PADDSFVDPGER;RKPS(0.469)VPDS(0.469)AS(0.063)PADDSFVDPGER;RKPS(0.977)VPDS(0.021)AS(0.002)PADDSFVDPGER;RKPS(0.903)VPDS(0.087)AS(0.01)PADDSFVDPGER;RKPS(0.974)VPDS(0.013)AS(0.013)PADDSFVDPGER;RKPS(0.999)VPDS(0.001)ASPADDSFVDPGER 260.14 1.58E-37 4634050000 2913137 2380876 1854311 2280654 2505728 2282495 3340017 3189432 2908236 TRUE FALSE 2528158.565 2365235.869 2751062.002 2798511.348 2455868.915 2370304.06 3016102.665 2507396.787 2564427.653 0.985856849 0.922325052 1.072778169 1.091281068 0.957667459 0.924301396 1.176130924 0.977760782 1 21.29020544 4.244791449 24.99658909 1.02791456 0.95409095 0.149708036 0.073770871 282.4275172 1132999.151 0.018227415 0.045758846 17570.79652 -4.244791449 -0.073823609 RKPVLPALTINPTIAEGPS(ph)PTSEGASEANLVDLQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RKPVLPALTINPTIAEGPSPTSEGASEANLVDLQK 35 2 P36507 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 RKPVLPALTINPTIAEGPS(0.459)PT(0.459)S(0.081)EGASEANLVDLQK 252.15 5.28E-60 3011500000 392560 300610 244830 290390 344720 317610 463990 506280 396050 TRUE FALSE 340682.2014 298635.2731 363230.6069 356327.4878 337860.7464 329828.6622 418992.3212 398015.9619 349229.4202 0.97552549 0.855126332 1.040091659 1.020324942 0.967446403 0.944446954 1.199762383 1.139697685 1 18.41381558 2.25126695 24.99981961 1.122292138 0.967812464 0.498994633 0.068755255 172.3631199 339125.9535 0.026051928 0.020041081 178.3474689 -2.25126695 -0.154479675 RKPYHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RKPYHK 6 2 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 71.067 0.050175 139540000 288710 293490 170780 178060 157190 230570 239930 333480 203950 FALSE TRUE 250556.242 291562.0449 253369.7792 218491.2445 154062.2265 239440.1771 216661.6255 262167.8971 179839.2633 1.393223245 1.621236873 1.408867978 1.214925153 0.856666246 1.331412132 1.204751518 1.457790097 1 17.45634851 3.852701645 3.678050811 1.201535511 1.507694911 0.397739785 0.173052651 0.263186202 6.412679605 0.048381002 0.0897463 7123.634774 -3.852701645 0.3061594 RKQEEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RKQEEEER 8 2 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;Q5JVM0 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;;;;; 209.03 2.84E-05 602153000 682086 578175 387231 476952 385202 494832 625742 735398 604569 FALSE TRUE 591946.6069 574376.9304 574497.2068 585251.2414 377537.2338 513868.5072 565057.6372 578138.8606 533097.5415 1.110390802 1.077433088 1.077658706 1.097831439 0.708195413 0.963929614 1.059951684 1.084489827 1 19.02404 RKQEELQQLEQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 236.92 5.60E-17 1417980000 1433600 1241100 781400 843490 1267500 1131640 1417030 1547450 598000 FALSE TRUE 1244146.128 1232947.132 1159287.654 1035017.296 1242279.23 1175174.923 1279606.649 1216539.86 527305.1212 2.359442527 2.338204358 2.198513929 1.962843247 2.355902076 2.228643106 2.426691108 2.307089028 1 19.00827848 1.237613114 25 0.999998506 2.272398983 0.907239529 0.127839993 6.819172037 179827.6104 0.190809285 0.032295234 17.2827606 -1.237613114 1.272400477 RKQEQEAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RKQEQEAAK 9 2 P49589-3;P49589;B4DKY1;P49589-2 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 0 77.14 0.018811 30569000 53995 61790 37115 45012 48274 67655 42439 62387 44888 FALSE TRUE 46859.42394 61384.09742 55063.93814 55232.66257 47313.44185 70257.73163 38323.27231 49046.02555 39581.39178 1.183875095 1.550832213 1.3911572 1.39541992 1.195345583 1.775019232 0.96821437 1.239118266 1 15.27253472 2.204338993 24.9999954 1.100325029 1.409441659 0.442776219 0.18186355 173.3852485 126662.3484 0.068415205 0.046128145 160.0807068 -2.204338993 0.30911663 RKRET(ph)DDEGEDD ddPTM_MDA-MB-175_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 133.16 0.00039414 7050630000 6474900 5070830 2796003 3340670 4141630 4082820 6152540 7092790 2720757 TRUE FALSE 5619225.56 5037519.384 4148159.403 4099220.182 4059219.666 4239888.727 5555867.618 5576052.055 2399112.207 2.342210399 2.099743134 1.729039347 1.708640459 1.69196741 1.767274042 2.315801488 2.324214782 1 21.1940692 4.484076953 3.825048726 1.859996782 2.312132884 0.18401237 0.371645116 0.429995079 13.56532321 0.097249169 0.379992474 30484.35096 -4.484076953 0.452136102 RKS(ph)ELPQDPHTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RKSELPQDPHTK 12 2 H0YJ75;Q13362-3;Q13362;Q13362-4;Q13362-5 H0YJ75 PPP2R5C Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform 1 RKS(0.999)ELPQDPHT(0.001)K;RKS(1)ELPQDPHTK 97.836 0.0024511 937860000 1634210 1170730 1023387 1052785 1164020 979250 1731900 1708320 2161080 TRUE FALSE 1418245.008 1163039.398 1518300.376 1291835.925 1140858.279 1016922.381 1563940.605 1343009.062 1905599.584 0.744251321 0.610327273 0.796757298 0.677915726 0.598687305 0.533649561 0.820707885 0.704769813 1 20.86181357 -0.208545469 1.191634027 9.999999987 0.671850918 0.555533526 0.088470851 33.09190827 2.0269222 769.269836 0.026361643 0.618663552 0.208545469 -9.328149069 RKS(ph)ELPQDVYTIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RKSELPQDVYTIK 13 2 E9PFR3;Q14738;H0Y8C4;Q14738-2;Q14738-3 E9PFR3 PPP2R5D Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform 1 RKS(1)ELPQDVYTIK;RKS(1)ELPQDVYTIK;RKS(1)ELPQDVYTIK;RKS(1)ELPQDVYTIK 165.8 2.27E-05 1875660000 4212200 3417410 2151890 2573070 2986030 2018250 4753540 4529990 4054710 TRUE FALSE 3655547.098 3394960.809 3192551.202 3157324.87 2926613.845 2095893.383 4292542.422 3561286.891 3575366.803 1.022425754 0.949541962 0.892929699 0.88307719 0.818549258 0.586203738 1.200587984 0.996061967 1 21.76965983 2.20892968 24.99999983 1.056699778 0.863739645 0.377378756 0.124914925 239.025369 201667.0554 0.052195266 0.035195636 161.7818063 -2.20892968 -0.192960133 RKS(ph)EPAVGPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RKSEPAVGPPR 11 2 O94875-12;O94875-10;O94875-3;H7BXR3;O94875-9;O94875-5;O94875-4;O94875-11;O94875-2;O94875-8;H7BZK1;H7BZX1;H7C1R7;O94875-7;O94875 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 RKS(1)EPAVGPPR;RKS(1)EPAVGPPR;RKS(1)EPAVGPPR;RKS(1)EPAVGPPR 115.1 0.00092023 1136200000 2184710 1965920 1330320 1382450 1850370 1609200 2236870 2315060 2335720 TRUE FALSE 1895995.038 1953005.742 1973667.202 1696356.402 1813551.257 1671106.965 2019938.692 1820002.435 2059593.842 0.920567443 0.948248 0.958279813 0.823636373 0.880538298 0.811376948 0.980746131 0.883670555 1 20.97392843 -0.167679463 1.675736489 9.999929396 0.899311504 0.230613576 0.055263028 185.20912 6.960506445 6271.402578 0.015414816 0.679705113 0.167679463 -9.100617893 RKS(ph)HEAEVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RKSHEAEVLK 10 2 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 RKS(1)HEAEVLK;RKS(1)HEAEVLK;RKS(1)HEAEVLK;RKS(1)HEAEVLK;RKS(1)HEAEVLK 168.89 2.50E-06 5830810000 2042510 1692780 1459640 1723700 1710060 1371050 2383730 2905620 2352770 TRUE FALSE 1772587.128 1681660.017 2165526.786 2115092.43 1676033.152 1423795.181 2152556.231 2284275.775 2074628.211 0.854411947 0.810583799 1.043814393 1.019504323 0.807871571 0.686289318 1.037562403 1.101053077 1 20.98442139 2.033158435 24.99917217 1.061213715 0.878043737 0.381069441 0.105213273 192.5508009 145169.2138 0.04584978 0.030911724 107.9340405 -2.033158435 -0.183169978 RKS(ph)ISGK ddPTM_MDA-MB-175_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 73.841 0.072862 0 850000 853980 471540 529640 431830 562660 993040 931810 422560 TRUE FALSE 737670.3464 848370.1492 699578.3212 649902.857 423237.4279 584305.8943 896735.1336 732549.6829 372605.4382 1.979762695 2.276859279 1.877531162 1.744211948 1.135886341 1.568162551 2.406661422 1.966019837 1 18.50728921 3.998096858 3.590924007 1.698708899 2.126979009 0.194279509 0.40059763 0.438630257 12.22349646 0.114415224 0.241315296 9956.274411 -3.998096858 0.42827011 MAGNEALS(ph)PTSPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MAGNEALSPTSPFR 14 0 Q86WR7;Q86WR7-2;D3DRR9 Q86WR7 PROSER2;C10orf47 Proline and serine-rich protein 2 1 MAGNEALS(0.684)PT(0.315)S(0.001)PFR;MAGNEALS(0.999)PT(0.001)SPFR 197.17 2.50E-08 131450000 194863 275310 226360 306200 441000 415390 413950 496380 414500 TRUE FALSE 169111.3608 273501.4705 335828.4531 375727.39 432224.9628 431370.3221 373805.1927 390232.9998 365498.2822 0.462687156 0.748297554 0.918823616 1.027986747 1.182563596 1.180225306 1.022727632 1.067673964 1 18.4795051 4.527535487 1.201301184 1.086846012 0.312089076 0.917592053 0.061533812 0.299191755 0.484896743 0.020468357 0.264702299 33692.67455 -4.527535487 -0.774756936 down RKS(ph)LS(ph)DSESDDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RKSLSDSESDDSK 13 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 RKS(0.999)LS(0.96)DS(0.032)ES(0.007)DDS(0.001)K 89.507 0.036489 922370000 2843900 1854800 1719700 1576800 1653800 1302600 2409600 3053700 2290500 TRUE FALSE 2468071.409 1842615.697 2551352.672 1934836.54 1620892.616 1352711.865 2175917.363 2400690.019 2019719.699 1.221987096 0.912312583 1.263221165 0.957972802 0.802533449 0.669752276 1.077336307 1.188625342 1 20.94572366 7.999985437 0.940326429 0.985917166 139.2472656 0.144886072 0.173455115 2949.312516 5.360533089 0.061540803 876746.4788 99996646.85 -7.999985437 138.2613484 RKS(ph)LSDS(ph)ESDDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RKSLSDSESDDSK 13 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 RKS(0.993)LS(0.043)DS(0.482)ES(0.482)DDSK 95.414 0.023155 734460000 2118400 1576900 1246800 1213100 1370100 1040800 2027500 2387000 1737600 TRUE FALSE 1838448.073 1566541.24 1849756.65 1488552.896 1342837.691 1080840.249 1830873.362 1876558.626 1532182.907 1.199888123 1.022424433 1.20726882 0.97152428 0.876421271 0.70542508 1.194944385 1.224761493 1 20.5471571 RKS(ph)LSDSESDDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RKSLSDSESDDSK 13 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 RKS(0.686)LS(0.261)DS(0.047)ES(0.006)DDSK;RKS(0.991)LS(0.009)DSESDDSK;RKS(0.992)LS(0.005)DS(0.002)ESDDSK;RKS(0.839)LS(0.16)DSESDDSK;RKS(0.977)LS(0.023)DSESDDSK 219.23 1.80E-11 2819340000 3473160 2059010 2038770 1850824 1886040 1583540 3217310 3360660 2121670 TRUE FALSE 3014173.106 2045484.228 3024725.991 2271081.877 1848511.494 1644459.808 2905295.771 2642009.012 1870848.59 1.611126161 1.093345682 1.616766855 1.213931416 0.988060447 0.878991393 1.552929397 1.412198201 1 20.83526137 4.754934786 23.26795162 1.244572193 1.611126903 0.194198124 0.246031393 2312.3728 3285773.678 0.061859621 1.458804271 56876.75182 -4.754934786 0.36655471 RKS(ph)LVGTPYWMAPELISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RKSLVGTPYWMAPELISR 18 2 O96013;O96013-4;O96013-2;O96013-3;M0R1R1 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 RKS(1)LVGTPYWMAPELISR 168.54 1.61E-11 2212000000 713240 838130 360630 356160 601810 621630 819580 763160 109130 TRUE FALSE 618983.5269 832624.2688 535031.8742 437031.5716 589835.1584 645544.5083 740097.2577 599964.1729 96228.77572 6.432416107 8.652549745 5.559998766 4.541589231 6.12950912 6.708435221 7.69101812 6.234768846 1 16.55418075 4.217125414 24.47373056 5.646390152 7.542482769 0.176595335 1.860989187 308.2774776 351977.8967 0.476773622 0.994098244 16486.3841 -4.217125414 1.896092617 RKS(ph)PENTEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RKSPENTEGK 10 2 Q15651;A0A087WZE9;Q15651-2 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 RKS(0.965)PENT(0.035)EGK;RKS(1)PENTEGK;RKS(0.951)PENT(0.049)EGK;RKS(1)PENTEGK;RKS(1)PENTEGK;RKS(1)PENTEGK 229.89 7.37E-10 3539260000 5391240 2969080 2859864 2863210 2040490 2017240 3971740 4160680 4524180 TRUE FALSE 4678773.974 2949575.918 4242903.796 3513345.592 1999888.241 2094844.528 3586561.266 3270950.96 3989336.594 1.172820058 0.739365017 1.063561245 0.880684171 0.501308474 0.525111 0.899037016 0.819923534 1 21.92771742 7.999981831 0.881402754 0.781858748 158.4574301 0.272482023 0.183310265 1254.875606 2.992213466 0.064143505 397580.7657 99995816.54 -7.999981831 157.6755714 RKS(ph)PPKEYIDEEGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RKSPPKEYIDEEGVR 15 3 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3;Q9H0E3-2 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 RKS(1)PPKEYIDEEGVR;RKS(1)PPKEYIDEEGVR 109.65 0.0054337 2564700000 2213550 1338280 1087880 1102280 1312610 1096680 1835250 2121590 1389510 TRUE FALSE 1921023.759 1329488.751 1613982.407 1352569.521 1286491.629 1138869.989 1657267.737 1667904.489 1225243.711 1.567870736 1.085081065 1.31727459 1.103918763 1.049988356 0.929504864 1.352602525 1.361283861 1 20.22463731 4.746196168 24.56398194 1.169742564 1.567870983 0.426839263 0.150650313 823.176949 2648123.952 0.039022125 0.398785606 55743.74824 -4.746196168 0.398128418 RKS(ph)QEALHEQSSYILSSAETPARPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RKSQEALHEQSSYILSSAETPARPR 25 3 Q9NVE5;Q9NVE5-3 Q9NVE5 USP40 Ubiquitin carboxyl-terminal hydrolase 40 1 RKS(1)QEALHEQSSYILSSAETPARPR;RKS(1)QEALHEQSSYILSSAETPARPR;RKS(1)QEALHEQSSYILSSAETPARPR;RKS(1)QEALHEQSSYILSSAETPARPR 233.17 1.68E-38 2578460000 423581 401035 236180 283433 411691 378830 465228 493924 377852 TRUE FALSE 367603.6976 398400.5747 350397.438 347790.7947 403499.1546 393403.8352 420110.2602 388302.1963 333182.767 1.103309457 1.195741839 1.051667351 1.043843887 1.211044491 1.180744847 1.260900328 1.165433014 1 18.34595426 3.228675525 24.99978675 1.172002292 1.102221194 0.142969942 0.077346581 389.9895656 986295.3966 0.023868948 0.027385965 1693.072381 -3.228675525 -0.069781098 RKS(ph)QMEEVQDELIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RKSQMEEVQDELIHR 15 2 A0A2R8Y4W2;A0A2R8YE63;Q12929-2;Q12929 A0A2R8Y4W2 EPS8 Epidermal growth factor receptor kinase substrate 8 1 RKS(1)QMEEVQDELIHR;RKS(1)QMEEVQDELIHR 192.98 5.83E-08 585580000 489620 434950 254370 306620 365790 294090 563320 492080 352380 TRUE FALSE 424915.4765 432092.7848 377384.1828 376242.7574 358511.4947 305403.8326 508689.3131 386852.5214 310722.0378 1.367509944 1.390608751 1.214539482 1.21086602 1.153801311 0.982884364 1.637120163 1.245011535 1 18.24526504 4.23790724 24.99182663 1.223158182 1.379059392 0.135007733 0.177850034 36.75665206 1406218.103 0.045652771 0.105146221 17294.46932 -4.23790724 0.15590121 RKS(ph)QVNGEAGSYEMTNQHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RKSQVNGEAGSYEMTNQHVK 20 2 Q05D32-2;Q05D32;H0YMH7 Q05D32-2 CTDSPL2 CTD small phosphatase-like protein 2 1 RKS(1)QVNGEAGSYEMTNQHVK;RKS(1)QVNGEAGSYEMTNQHVK;RKS(0.988)QVNGEAGS(0.012)YEMTNQHVK 202.2 6.18E-22 708578000 329965 261945 210891 247810 325074 244387 382905 433887 286637 TRUE FALSE 286359.2892 260224.266 312878.593 304079.048 318605.6634 253788.726 345770.932 341103.6416 252751.1004 1.132969505 1.029567292 1.23789211 1.203077049 1.260551044 1.004105326 1.368029383 1.349563428 1 17.94735785 4.229891143 24.98656552 1.220119338 1.081268393 0.130407039 0.125315066 291.1162337 839042.8606 0.032173476 0.06866452 16978.18036 -4.229891143 -0.138850944 RKS(ph)TITALLFGEDDLEALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RKSTITALLFGEDDLEALK 19 2 Q96HU1;Q96HU1-2 Q96HU1 SGSM3 Small G protein signaling modulator 3 1 RKS(0.515)T(0.201)IT(0.284)ALLFGEDDLEALK 126.86 1.93E-05 648270000 999050 786760 583570 557670 751080 563120 1078300 1055400 659260 TRUE FALSE 867023.0112 781591.7218 865786.4039 684297.497 736134.9775 584783.5908 973726.632 829710.9231 581323.0338 1.49146509 1.344504993 1.489337861 1.177138109 1.266309667 1.005952898 1.675018149 1.427280315 1 19.14898055 3.753982219 24.60427728 1.29200366 1.432042879 0.142954022 0.200117171 1751.216949 2793956.386 0.054891731 0.094600034 5675.213698 -3.753982219 0.140039218 RKS(ph)VEEESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RKSVEEESK 9 2 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 RKS(1)VEEESK;RKS(1)VEEESK 136.24 0.00015609 71854000 164893 121377 115995 145461 92684 97682 159076 199856 175221 TRUE FALSE 143101.9723 120579.6665 172090.57 178490.1433 90839.76973 101439.8897 143648.834 157118.3497 154506.573 0.926186954 0.780417714 1.113807436 1.155226861 0.587934662 0.656540934 0.929726362 1.016903984 1 17.23730869 1.997435601 24.99088543 0.998756173 0.87016658 0.094983185 0.175573674 261.9331034 2552628.962 0.078758182 0.052068124 99.4112651 -1.997435601 -0.128589593 RKS(ph)YTSDLQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RKSYTSDLQK 10 2 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;E9PJ10;E9PK58;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 RKS(0.968)YT(0.027)S(0.005)DLQK;RKS(0.999)YT(0.001)SDLQK;RKS(0.994)YT(0.006)SDLQK 195.1 2.04E-07 1610010000 976890 1110070 565635 593204 897240 657269 1371480 1118170 748990 TRUE FALSE 847791.5114 1102777.877 839177.9779 727900.0348 879386.6794 682554.5637 1238474.081 879058.0471 660445.2555 1.283666594 1.669749109 1.270624584 1.102135308 1.331505787 1.033476368 1.875210807 1.331008195 1 19.33307946 4.182124147 24.99921455 1.30140468 1.476715244 0.086524064 0.260096592 208.261016 92250.88144 0.066452662 0.138332405 15209.82253 -4.182124147 0.175310564 RKSLVGT(ph)PYWMAPELISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RKSLVGTPYWMAPELISR 18 2 O96013;O96013-4;O96013-2;O96013-3;M0R1R1 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 RKS(0.382)LVGT(0.612)PY(0.006)WMAPELISR 165.71 1.31E-09 1719000000 605310 673210 257620 262840 560750 570120 686350 676800 79686 TRUE FALSE 525316.7498 668787.6392 382205.8937 322521.8393 549592.1721 592052.8853 619787.8826 532071.5869 70265.61186 7.476157055 9.517993532 5.439444468 4.590038153 7.82163789 8.425926561 8.820643075 7.572289955 1 16.10053118 4.240573312 24.99654763 6.571758319 8.49707516 0.126559812 2.342768599 122.788308 1524856.003 0.60020524 1.433630014 17400.96415 -4.240573312 1.92531684 RKST(ph)ITALLFGEDDLEALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RKSTITALLFGEDDLEALK 19 2 Q96HU1;Q96HU1-2 Q96HU1 SGSM3 Small G protein signaling modulator 3 1 RKS(0.411)T(0.443)IT(0.147)ALLFGEDDLEALK 162.47 4.43E-11 649410000 905510 835900 514950 602000 780630 418410 1172200 1205800 641180 TRUE FALSE 785844.5592 830408.9179 763981.5424 738693.301 765096.9903 434506.5034 1058520.224 947949.0535 565380.4308 1.38993944 1.468761338 1.351269872 1.306542039 1.353242788 0.768520592 1.872226499 1.676656994 1 19.10886242 2.201987829 24.99999756 1.564533288 1.290663659 0.127692263 0.288289099 312.6047166 213684.561 0.117009908 0.078890683 159.2164108 -2.201987829 -0.273869629 RKT(ph)DTVVESSVSGDHSGTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RKTDTVVESSVSGDHSGTLR 20 2 Q9NXL2-1;Q9NXL2 Q9NXL2-1 ARHGEF38 Rho guanine nucleotide exchange factor 38 1 RKT(0.979)DT(0.021)VVESSVSGDHSGTLR;RKT(0.974)DT(0.026)VVESSVSGDHSGTLR;RKT(0.952)DT(0.048)VVESSVSGDHSGTLR;RKT(0.986)DT(0.014)VVESSVSGDHSGTLR 338.11 1.86E-78 1223810000 435866 441671 183599 318367 474499 394067 481055 554881 427118 TRUE FALSE 378265.2038 438769.6341 272388.0905 390657.0933 465057.3982 409227.0125 434402.3601 436224.0162 376624.5966 1.004356081 1.165005255 0.723235001 1.037258577 1.234803575 1.086564755 1.153409427 1.158246222 1 18.5227677 3.472110878 24.98152924 1.131064955 0.966940657 0.27617478 0.120729281 167.7151942 836215.5272 0.033565756 0.043490004 2965.588423 -3.472110878 -0.164124298 RKT(ph)SDANETEDHLESLICK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RKTSDANETEDHLESLICK 19 2 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RKT(0.5)S(0.5)DANET(0.001)EDHLESLICK;RKT(0.5)S(0.5)DANET(0.001)EDHLESLICK 169.56 6.62E-10 382940000 307580 284329 151592 174966 354150 229111 465850 572090 131172 TRUE FALSE 266932.5237 282461.2241 224902.3982 214694.7045 347103.1079 237925.0484 420671.9387 449753.0055 115664.9956 2.307807322 2.442063155 1.944429229 1.856177 3.000934778 2.05701861 3.636985732 3.888410692 1 16.81959279 3.229713629 24.96892615 2.899178768 2.14556588 0.086753221 0.822451775 353.1816118 996785.3562 0.252970949 0.291089557 1697.124209 -3.229713629 -0.753612888 RKVDWLTEK ddPTM_MDA-MB-175_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 ; 163.38 3.55E-05 5104000000 5413700 4130600 3015200 3712100 3942600 3184200 5585900 5991100 3900200 FALSE TRUE 4698265.828 4103465.817 4473360.805 4554989.041 3864149.974 3306698.234 5044180.278 4709949.888 3439122.799 1.366123312 1.193172229 1.300727269 1.324462459 1.123585926 0.961494668 1.466705486 1.369520707 1 21.7136092 4.75180285 22.44790481 1.23603552 1.366123674 0.068781318 0.159373391 1750.250546 2966754.102 0.039840249 0.641223337 56468.05771 -4.75180285 0.130088154 RKVMDS(ph)DEDDDY ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RKVMDSDEDDDY 12 2 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 1 RKVMDS(1)DEDDDY;RKVMDS(0.832)DEDDDY(0.168);RKVMDS(1)DEDDDY;RKVMDS(1)DEDDDY;RKVMDS(1)DEDDDY;RKVMDS(1)DEDDDY;RKVMDS(1)DEDDDY 164.8 4.43E-05 4801580000 6748200 5465060 2880179 3675237 5916460 4554870 6473940 8186670 1409485 TRUE FALSE 5856408.272 5429159.661 4273043.198 4509755.733 5798734.021 4730098.796 5846098.295 6436014.329 1242857.289 4.712052079 4.368288869 3.43808033 3.628538669 4.665647515 3.80582617 4.703756696 5.178401725 1 20.24522922 4.469301792 23.82214029 3.972292396 4.626111699 0.055473694 1.142300265 306.4540479 933623.1309 0.276826055 0.736003347 29464.68432 -4.469301792 0.653819303 RKVS(ph)LVLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RKVSLVLEK 9 2 Q9P2M7;Q9P2M7-2;H0Y4A8 Q9P2M7 CGN Cingulin 1 RKVS(1)LVLEK 96.756 0.0071096 0 1495900 1295300 1282400 1132700 1106900 947560 2252300 1864200 1547400 TRUE FALSE 1298213.025 1286791.089 1902572.929 1389896.847 1084874.856 984013.2464 2033872.293 1465555.337 1364468.135 0.951442538 0.943071557 1.394369631 1.018636355 0.795089917 0.721169825 1.490597135 1.074085426 1 20.37990727 1.228043088 21.73072057 0.999999461 1.058898368 0.002429324 0.237901602 919.063551 1898183.703 0.718383811 0.059207786 16.90608657 -1.228043088 0.058898907 RKVTGTEGSSSTLVDYTSTSSTGGS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RKVTGTEGSSSTLVDYTSTSSTGGSPVR 28 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 RKVTGTEGSSSTLVDYTSTSS(0.001)T(0.003)GGS(0.995)PVR 65.345 0.0076438 68518000 31027 25368 16293 9831.8 30345 26080 33112 30976 6374 TRUE FALSE 26926.70334 25201.35594 24172.3493 12064.26046 29741.19387 27083.31448 29900.80334 24352.02346 5620.472981 4.790825154 4.483849673 4.300767814 2.146484913 5.291582037 4.81868956 5.319979908 4.332735614 1 12.45647583 4.203699053 3.933390558 4.01635218 4.66374094 0.046249655 1.363783249 0.893470804 29.21035105 0.356403709 0.888905824 15984.49991 -4.203699053 0.64738876 RLAAAEETAVS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RLAAAEETAVSPR 13 1 Q9BUH6 Q9BUH6 C9orf142 Protein PAXX 1 RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR 170.16 1.67E-05 8277360000 3293370 3721890 2043680 2584670 3545490 3791900 3345220 3904440 2107740 TRUE FALSE 2858142.81 3697440.66 3032010.484 3171558.828 3474941.686 3937776.847 3020801.079 3069505.89 1858565.378 1.537822045 1.989405755 1.631371443 1.706455347 1.869690314 2.118718498 1.62534023 1.651545825 1 20.82575801 0.996276546 1.659472771 0.185529584 1.800406064 0.659480724 0.175456386 1.192363611 1.780203923 3.816718766 0.047481133 9.914630795 -0.996276546 1.614876481 AS(ph)GQAFELILSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 ASGQAFELILSPR 13 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 AS(1)GQAFELILSPR;AS(1)GQAFELILSPR;AS(1)GQAFELILSPR;AS(1)GQAFELILSPR;AS(1)GQAFELILSPR;AS(1)GQAFELILSPR 281.1 2.05E-32 1233275000 313870 457504 380195 534251 718499 625155 653870 824703 757539 TRUE FALSE 272391.2843 454498.6261 564058.5737 655560.8551 704202.2756 649205.1174 590457.788 648346.6813 667983.6024 0.407781394 0.680403867 0.844419791 0.981402616 1.054220902 0.971887805 0.883940543 0.97060269 1 19.34945316 4.538836493 1.373180253 0.974088454 0.29051965 0.946316764 0.044638078 0.200201859 0.448317655 0.0142491 0.172136462 34580.91599 -4.538836493 -0.683568804 down RLAEINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLAEINR 7 1 Q9BQI0-3;Q9BQI0;Q9BQI0-2;Q5JUP3;Q9BQI0-4 Q9BQI0-3 AIF1L Allograft inflammatory factor 1-like 0 ; 150.17 0.0031543 158907000 189903 182128 129027 133220 184194 200169 180553 187409 149500 FALSE TRUE 164806.8374 180931.5892 191424.8888 163469.6371 180528.8998 207869.631 163042.9978 147333.0438 131826.2803 1.250181959 1.372500148 1.452099599 1.240038305 1.36944545 1.576845152 1.23680193 1.117630289 1 17.00827848 1.760286102 2.484606392 1.030209263 1.373841746 0.630608997 0.099743065 0.165418989 2.035868635 0.082523095 0.027611674 57.58191477 -1.760286102 0.343632483 RLAPEYEAAATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RLAPEYEAAATR 12 1 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 221.86 4.20E-11 1758410000 939890 944790 491416 627827 934880 1083710 841000 833780 435490 FALSE TRUE 815681.1551 938583.6123 729066.4213 770384.7161 916277.7171 1125401.025 759439.9494 655482.6355 384006.8683 2.124131682 2.44418444 1.898576514 2.006174315 2.38609721 2.930679417 1.977672829 1.706955499 1 18.55077259 1.442656737 1.868593488 0.871490197 2.27690699 0.664571477 0.292757192 0.342899994 1.723610465 0.770566949 0.086191845 27.71128962 -1.442656737 1.405416793 RLDAAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RLDAAYR 7 1 A0A024R7W5;A0A087X0Q1;A0A087WY31;Q7Z739;Q9Y5A9;Q9Y5A9-2 A0A024R7W5;Q9Y5A9 YTHDF3;YTHDF2 YTH domain-containing family protein 3;YTH domain-containing family protein 2 0 ;; 131.03 0.0056209 629380000 480460 600230 348772 364665 447020 529370 476440 535930 584000 FALSE TRUE 416965.9937 596287.0496 517439.3058 447467.7618 438125.1766 549735.2064 430234.9221 421325.5401 514960.1853 0.809705305 1.157928451 1.004814198 0.868936618 0.850794273 1.067529534 0.835472206 0.818171098 1 18.97410137 3.750020394 22.13491659 0.897486298 1.007527302 0.100350277 0.112702683 282.8014485 546231.2901 0.028917604 0.049359472 5623.677333 -3.750020394 0.110041005 RLDADLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLDADLAR 8 1 A0A1B0GW41;Q8WYH8-2;Q8WYH8;E9PEN0 A0A1B0GW41 ING5 Inhibitor of growth protein 5 0 95.775 0.01509 86359000 52229 56422 37494 43726 47003 64087 44235 46597 44361 FALSE TRUE 45326.80532 56051.36017 55626.22381 53654.65661 46067.73226 66552.46836 39945.09651 36632.59417 39116.69312 1.15875862 1.432926858 1.422058446 1.37165625 1.177700071 1.701382787 1.021177746 0.93649517 1 15.25549679 2.07960722 10.34484722 0.968248116 1.372434906 0.606580376 0.149050815 0.227309844 27.85280389 0.056592055 0.038139057 120.1177587 -2.07960722 0.40418679 RLDDNIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLDDNIR 7 1 E7EVT8;F6VX93;Q5VIR6-2;Q5VIR6-3;Q5VIR6-1;Q5VIR6;I3L0S6 E7EVT8 VPS53 Vacuolar protein sorting-associated protein 53 homolog 0 75.854 0.067891 101370000 117370 125240 66290 79825 101370 134700 119390 113950 119370 FALSE TRUE 101859.2571 124417.2902 98348.06573 97950.4863 99352.93533 139881.9962 107811.5762 89582.67926 105258.2146 0.967708388 1.182019766 0.934350503 0.930573321 0.943897212 1.328941373 1.024258074 0.851075421 1 16.6835733 1.913328441 8.16836423 0.920548243 1.049984987 0.128410584 0.129987441 0.603371429 51.73024663 0.062668662 0.03490742 81.90839964 -1.913328441 0.129436744 RLDECEEAFQGTK ddPTM_MDA-MB-175_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 ;;; 199.87 1.83E-07 1900470000 2355690 2119620 1379880 1805610 2111660 1915480 2230450 2725010 2149330 FALSE TRUE 2044379.598 2105696.077 2047194.583 2215601.348 2069642.097 1989169.755 2014141.302 2142287.818 1895238.656 1.078692434 1.11104534 1.080177727 1.169035541 1.092021889 1.049561621 1.062737559 1.130352534 1 20.8539481 2.998361543 24.97516297 1.071640348 1.110570848 0.231661491 0.040144891 111.2833763 1696327.667 0.012115001 0.013533112 996.2344215 -2.998361543 0.0389305 RLDEEEEDNEGGEWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RLDEEEEDNEGGEWER 16 1 Q99613-2;Q99613 Q99613-2 EIF3C Eukaryotic translation initiation factor 3 subunit C 0 ;; 220.64 1.81E-14 2002570000 1429010 1177770 508880 564230 1099610 915990 1371520 1441990 565860 FALSE TRUE 1240162.708 1170033.151 754976.0701 692347.0452 1077729.912 951228.728 1238510.201 1133631.66 498964.6754 2.485471956 2.344921813 1.513085209 1.387567255 2.159932287 1.906404952 2.482160086 2.271967768 1 18.92857816 RLDEELEDAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLDEELEDAEK 11 1 Q15008;Q15008-4;Q15008-3;Q15008-2;C9J0E9;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 163.51 3.83E-05 1737130000 2012700 1817910 1410170 1557160 1773680 1469950 2004940 2314500 2080800 FALSE TRUE 1746716.595 1805968.03 2092132.929 1910736.978 1738387.238 1526499.928 1810501.227 1819562.186 1834810.194 0.951987623 0.984280573 1.140244879 1.041381274 0.947447994 0.831966125 0.986751236 0.991689599 1 20.8071994 3.237947462 24.99098691 0.953244084 1.034157759 0.250366193 0.066729274 24.66661645 1005380.964 0.021121918 0.025425639 1729.607111 -3.237947462 0.080913675 RLDEVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RLDEVSR 7 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;; 131.03 0.0056209 768280000 956240 718402 448905 590458 531648 692180 710213 871438 800680 FALSE TRUE 829870.4612 713682.77 665996.9595 724530.5135 521069.245 718808.6125 641336.6526 685087.7652 706024.5225 1.175413084 1.010846999 0.943305704 1.026211541 0.738032785 1.018107147 0.908377304 0.970345566 1 19.42935877 4.878632833 1.520131882 0.939952179 1.331207192 0.447058332 0.081512888 1.422089391 2.372231236 0.021215596 0.918665521 75619.33144 -4.878632833 0.391255013 RLDFDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLDFDYK 7 1 Q99961-3;Q99961-2;Q99961;Q99962;M0R0I3 Q99961-3 SH3GL1;SH3GL2 Endophilin-A2;Endophilin-A1 0 ; 136.27 0.0048048 1473030000 2406500 2444400 1860210 2120900 2150800 2007670 2589400 2985600 3783900 FALSE TRUE 2088474.928 2428342.575 2759813.778 2602482.761 2108003.288 2084906.364 2338280.387 2347152.674 3336571.653 0.625934386 0.727795722 0.82714057 0.779987074 0.631787208 0.624864856 0.700803289 0.703462391 1 21.66993506 1.238366589 24.90638379 1.000000335 0.705103119 0.66744194 0.065927546 2.943288225 376789.7108 0.097232202 0.017259411 17.31277119 -1.238366589 -0.294897216 RLDINEGAARPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RLDINEGAARPR 12 2 Q9BUP0;H7C0I0 Q9BUP0 EFHD1 EF-hand domain-containing protein D1 0 ;; 190.85 3.44E-06 1686610000 787564 711735 442088 480380 715830 775980 628438 750748 483579 FALSE TRUE 683485.422 707059.5659 655883.2355 589457.6211 701586.3835 805832.4527 567492.1795 590206.3825 426410.8415 1.602880029 1.658165077 1.538148592 1.382370155 1.64532961 1.889802918 1.330857765 1.384126118 1 18.70188459 1.280392238 1.328405185 0.781368805 1.598439488 0.623256954 0.146894638 0.865116195 1.417668257 0.962819217 0.045328943 19.07182433 -1.280392238 0.817070682 RLDLDACK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RLDLDACK 8 1 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39 B7ZC38 SH3GLB2 Endophilin-B2 0 ;; 182.76 0.00036371 1287550000 1549450 2378240 1512510 1538560 2066660 1815450 2425590 2525350 2480570 FALSE TRUE 1344686.257 2362617.185 2243964.895 1887913.563 2025537.509 1885291.536 2190356.655 1985323.555 2187319.84 0.614764349 1.080142529 1.025897015 0.863117286 0.926036271 0.861918546 1.001388372 0.907651235 1 21.06073276 4.752611137 24.89072918 0.951457296 0.614764106 0.697451856 0.070974975 1391.507832 2465034.343 0.017328999 0.354179365 56573.25113 -4.752611137 -0.336693189 RLDLPIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLDLPIER 8 1 P17812;B4E1E0;P17812-2;A0A3B3IRI2;A0A3B3IRQ8;A0A3B3ITF6;A0A3B3ITB8;A0A3B3ISY3 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ; 169.41 0.00048296 307850000 171943 195570 121765 141320 173117 214190 171479 215560 188306 FALSE TRUE 149220.2969 194285.2878 180650.9613 173408.8659 169672.3104 222430.0279 154848.993 169464.1715 166044.6792 0.898675571 1.170078371 1.087965975 1.044350634 1.02184732 1.339579377 0.932574255 1.020593808 1 17.34121197 RLDLTTSAFHWSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLDLTTSAFHWSDR 14 1 Q17RN3;Q17RN3-2 Q17RN3 FAM98C Protein FAM98C 0 ; 146.2 5.43E-06 509150000 256880 297620 88452 202975 397230 388590 313620 336370 293420 FALSE TRUE 222932.6571 295664.9146 131227.6831 249063.576 389325.9002 403539.3088 283205.1807 264439.8931 258732.2219 0.861634688 1.142744852 0.507194976 0.962630685 1.504744548 1.55967937 1.094587982 1.022060149 1 17.98110021 3.46349104 24.6993111 1.216695678 0.845607823 0.381159166 0.236509523 236.0519188 427747.8047 0.073238752 0.094601028 2907.307981 -3.46349104 -0.371087854 RLDPDAIPSPIQVIEDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RLDPDAIPSPIQVIEDDR 18 1 P53992;G5EA31 P53992 SEC24C Protein transport protein Sec24C 0 ;; 178.77 1.40E-13 149367000 98692 87854 84297 88233 99108 102161 105351 97923 215612 FALSE TRUE 85649.60215 87276.88129 125063.3112 108267.6512 97135.9447 106091.1998 95134.07624 76982.92849 190122.595 0.450496703 0.459055807 0.657803514 0.569462305 0.510912155 0.558014684 0.500382799 0.404912044 1 17.53657047 1.230631747 24.99999765 1.000000881 0.513947207 0.824086501 0.070584451 128.4009197 404819.2063 0.198932867 0.018594627 17.00715804 -1.230631747 -0.486053674 RLDQELDFILSQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLDQELDFILSQQK 14 1 P37198;M0QXN5 P37198 NUP62 Nuclear pore glycoprotein p62 0 147.12 6.09E-06 0 299560 258110 149320 201330 221270 241940 300870 306200 271180 FALSE TRUE 259972.387 256414.4584 221531.6514 247045.0536 216867.1599 251247.5884 271691.6737 240721.5129 239121.4093 1.087198289 1.072319117 0.926440054 1.03313649 0.906933263 1.05071139 1.136208065 1.006691595 1 17.86738378 1.501687133 25 1.00162363 1.028314402 0.025768305 0.068867078 3.781783871 3836.405489 0.046519313 0.017583964 31.74586267 -1.501687133 0.026690772 RLDQLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLDQLER 7 1 Q96CT7;M0R2F5 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 83.313 0.035871 379760000 71400 67404 37317 41054 60050 73617 66215 64390 58979 FALSE TRUE 61964.3091 66961.21869 55363.62602 50375.93817 58855.12249 76449.09363 59793.47949 50620.69958 52006.56981 1.191470795 1.287553071 1.064550618 0.968645661 1.131686299 1.469989155 1.149729346 0.973352016 1 15.66640626 1.781685341 5.231527424 0.987638357 1.182479317 0.272972617 0.132046068 0.262419434 14.93652474 0.080568454 0.037476464 60.49024469 -1.781685341 0.19484096 RLDQVEQELNELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RLDQVEQELNELR 13 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ;;; 274.45 5.77E-32 370207000 252754 230806 170472 189290 227186 242713 204838 246643 235798 FALSE TRUE 219351.9185 229289.8202 252912.8294 232271.1876 222665.4431 252050.3262 184972.8423 193900.3138 207922.2291 1.054970984 1.102767228 1.216381868 1.117106087 1.070907349 1.212233667 0.889625141 0.932561731 1 17.66568448 2.231900751 24.99994248 0.936898102 1.128648371 0.699296739 0.058199416 81.89646044 307420.9547 0.023072828 0.01596076 170.5692543 -2.231900751 0.191750269 RLDVTVQSFGWSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLDVTVQSFGWSDR 14 1 Q52LJ0;Q52LJ0-1;Q8NCA5;E9PH82 Q52LJ0;Q8NCA5 FAM98B;FAM98A Protein FAM98B;Protein FAM98A 0 ; 137.79 3.08E-05 1979690000 669420 584460 350990 446710 526420 516990 543230 606050 396810 FALSE TRUE 580954.4509 580620.6438 520729.938 548142.333 515945.2719 536878.9398 490547.6382 476450.9238 349899.5738 1.660346266 1.659392258 1.488226843 1.566570451 1.474552444 1.534380091 1.40196695 1.361679063 1 18.41658138 0.590048204 0.722993449 2.61E-28 1.579736276 0.885487561 0.064049875 2.204196749 0.453079608 3.534324397 0.027912566 3.89088329 -0.590048204 1.579736276 RLDYITAEIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLDYITAEIK 10 1 O15212 O15212 PFDN6 Prefoldin subunit 6 0 95.094 0.012277 273290000 394630 394030 250500 317750 391220 386810 433720 456130 530010 FALSE TRUE 342478.6456 391441.591 371642.6379 389899.994 383435.4874 401690.831 391657.9012 358590.1491 467352.8216 0.732805345 0.837571901 0.795207862 0.834273328 0.820441152 0.859502313 0.838034742 0.767279307 1 18.83415258 RLDYITAEIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLDYITAEIKR 11 2 O15212 O15212 PFDN6 Prefoldin subunit 6 0 ; 118.87 0.00037289 644320000 763760 620330 426820 509880 613980 569240 571610 733130 624770 FALSE TRUE 662827.1809 616255.0114 633231.5796 625656.047 601762.9992 591139.0311 516175.3502 576355.8547 550910.4023 1.203148784 1.118612044 1.149427524 1.13567659 1.092306474 1.07302209 0.936949725 1.046188005 1 19.07145818 2.806886894 1.477913325 1.002699013 1.151935988 0.76683055 0.036931053 0.183530479 0.820296774 0.015852147 0.014449287 641.0426048 -2.806886894 0.149236975 RLEAAYLDLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 RLEAAYLDLQR 11 1 E5RJD8;O75347;E5RIW3;E5RHG6;O75347-2 E5RJD8 TBCA Tubulin-specific chaperone A 0 ;;;;;;; 174.89 1.68E-05 10638980000 4860770 5828810 3327450 3646950 5669660 5928080 5105600 5674020 4664080 FALSE TRUE 4218406.929 5790520.163 4936615.95 4475045.738 5556844.859 6156137.074 4610459.698 4460674.978 4112697.776 1.025703117 1.407961508 1.20033521 1.08810469 1.351143498 1.496861041 1.121030513 1.084610448 1 21.97165363 2.016379307 24.99626897 1.064690252 1.265656841 0.302564485 0.141014216 283.7405648 433011.4619 0.057264394 0.038596032 103.8434974 -2.016379307 0.200966589 RLEAEQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RLEAEQAR 8 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 ;; 179.51 0.00039119 480780000 498027 614900 364951 400394 534860 671420 582130 579090 532970 FALSE TRUE 432211.4701 610860.6814 541442.5243 491309.5773 524217.3324 697249.9619 525675.1222 455256.11 469962.8938 0.91967148 1.299806196 1.152096328 1.045422062 1.11544409 1.483627689 1.118546015 0.9687065 1 18.84218733 1.840064762 4.844122378 0.986992556 1.175757177 0.201033044 0.148536613 0.322204198 11.24292977 0.079906318 0.039249915 69.19341444 -1.840064762 0.188764621 RLEAFLTQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLEAFLTQK 9 1 P36507;A0A1B0GUL7;Q02750;Q02750-2 P36507;Q02750 MAP2K2;MAP2K1 Dual specificity mitogen-activated protein kinase kinase 2;Dual specificity mitogen-activated protein kinase kinase 1 0 115.39 0.0032716 0 1163300 1277600 772980 885960 1122500 977750 1493600 1292400 1377700 FALSE TRUE 1009566.958 1269207.361 1146795.713 1087130.759 1100164.446 1015364.675 1348750.902 1016030.317 1214829.875 0.831035668 1.0447614 0.943996963 0.894883128 0.905611945 0.835808121 1.110238503 0.836356051 1 20.21232286 0.945339181 21.09137027 2.008154671 0.929099518 0.060602846 0.091320266 23.89612142 208101.5857 25235.4347 0.01985659 8.817372341 -0.945339181 -1.079055153 RLEAGAMVLADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLEAGAMVLADR 12 1 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 0 115.83 0.0014555 152830000 184920 187320 129110 143980 170270 177800 182550 225610 191710 FALSE TRUE 160482.3535 186089.4826 191548.0278 176672.8596 166881.9601 184640.0811 164846.3291 177365.0572 169046.2622 0.949339852 1.100819859 1.133110105 1.045115445 0.987196984 1.092245866 0.975155126 1.049210168 1 17.36705859 3.479081312 24.99811132 1.02371549 1.069071238 0.090509108 0.056808726 158.1333249 2016815.206 0.015565826 0.020424525 3013.570197 -3.479081312 0.045355748 RLEDLSESIVNDFAYMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLEDLSESIVNDFAYMK 17 1 P49755 P49755 TMED10 Transmembrane emp24 domain-containing protein 10 0 ; 214.5 9.49E-15 468650000 1273680 1357200 661370 587690 1216440 1209390 1212210 1581470 207542 FALSE TRUE 1105359.961 1348284.464 981210.7441 721133.9968 1192235.224 1255916.016 1094650.061 1243284.948 183006.6212 6.03999983 7.367408103 5.361613355 3.940480361 6.514710868 6.862680747 5.981477903 6.793661013 1 17.48153632 4.22101195 24.50839034 5.451360927 6.703703932 0.098077572 1.769863999 448.3100968 626110.4375 0.44420733 0.928220215 16634.58422 -4.22101195 1.252343004 RLEEAALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLEEAALR 8 1 Q96A33;A0A087WYW6 Q96A33 CCDC47 Coiled-coil domain-containing protein 47 0 136.57 0.0025434 0 53632 59432 43524 60247 75644 85768 43248 70112 62871 FALSE TRUE 46544.39531 59041.58728 64572.35198 73927.00217 74138.83239 89067.55046 39053.81562 55119.09441 55438.462 0.839568661 1.06499324 1.164757276 1.333496628 1.337317626 1.606602118 0.704453446 0.994239242 1 15.75859961 2.216607335 24.99999997 0.911158671 1.224580724 0.342041804 0.212214962 294.0934159 334905.735 0.090731282 0.061226392 164.6672887 -2.216607335 0.313422054 RLEEALMADMLAHVEELAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLEEALMADMLAHVEELAR 19 1 O95983-2;O95983;K7EIE8 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 0 ; 170.91 7.33E-12 103601000 155312 177916 113434 132938 155590 174022 151467 193820 134904 FALSE TRUE 134787.1257 176747.2581 168291.0618 163123.6047 152494.0634 180716.7389 136777.7537 152373.1013 118955.8028 1.133085755 1.485822918 1.414736044 1.371295901 1.281938836 1.519192294 1.149819937 1.28092197 1 16.86006612 0.470253371 0.878446372 1.90E-16 1.365288807 0.427700704 0.123918004 6.9719401 1.5587116 12.70485841 0.041191882 2.952931487 -0.470253371 1.365288807 RLEEEGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLEEEGDR 8 1 Q13619;A0A0A0MR50;Q13619-2 Q13619 CUL4A Cullin-4A 0 81.525 0.036294 269080000 196600 175930 122940 113850 146710 183200 152270 181710 133250 FALSE TRUE 170618.8119 174774.3042 182394.1952 139701.3826 143790.758 190247.8225 137502.8788 142852.7306 117497.3368 1.452107908 1.487474602 1.552326207 1.188974886 1.22377887 1.619167104 1.170263791 1.215795476 1 16.84226853 0.179691906 0.48281781 7.03E-18 1.44509085 0.470852388 0.143651515 12.25959062 1.052791269 12.50846363 0.109413923 1.51248789 -0.179691906 1.44509085 RLEEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLEEELR 7 1 Q07065 Q07065 CKAP4 Cytoskeleton-associated protein 4 0 137.9 0.0045498 245370000 200490 205740 133070 151630 235310 253850 157720 242520 178350 FALSE TRUE 173994.7385 204388.4804 197423.0971 186059.909 230627.7914 263615.7738 142424.3387 190658.9853 157265.6662 1.1063746 1.299638283 1.25534773 1.183093001 1.466485324 1.676244918 0.905628941 1.212336996 1 17.26284421 2.206440451 24.99999969 1.069796343 1.325733154 0.383695594 0.172855117 233.6903449 181885.9653 0.072082966 0.04860272 160.8571801 -2.206440451 0.255936811 RLEEFEGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLEEFEGER 9 1 Q08378;Q08378-4;Q08378-2 Q08378 GOLGA3 Golgin subfamily A member 3 0 ; 141.88 0.0024479 0 630630 642560 376220 422970 607040 724440 528660 582510 459520 FALSE TRUE 547290.6477 638338.9811 558161.2504 519011.8032 594961.0917 752309.6756 477390.6346 457944.7696 405196.0691 1.350681039 1.575382956 1.377509046 1.280890519 1.468328883 1.856655908 1.17817193 1.130180682 1 18.62826065 2.022970931 24.99689158 1.098325031 1.477720277 0.565689161 0.159451914 166.0722134 180718.4959 0.065859729 0.04439969 105.4316325 -2.022970931 0.379395246 TSS(ph)LTQFPPSQSEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 TSSLTQFPPSQSEER 15 0 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3 Q9H6Z4 RANBP3 Ran-binding protein 3 1 T(0.004)S(0.069)S(0.928)LTQFPPSQSEER;T(0.002)S(0.047)S(0.944)LT(0.007)QFPPSQSEER;T(0.015)S(0.015)S(0.969)LTQFPPSQSEER;TSS(1)LTQFPPSQSEER;TS(0.002)S(0.997)LTQFPPSQSEER;TSS(1)LTQFPPSQSEER;T(0.015)S(0.015)S(0.97)LTQFPPSQSEER;T(0.001)S(0.068)S(0.931)LT(0.001)QFPPSQSEER;TS(0.02)S(0.979)LTQFPPSQSEER;T(0.006)S(0.006)S(0.988)LTQFPPSQSEER;T(0.193)S(0.119)S(0.687)LTQFPPSQSEER;TS(0.015)S(0.985)LTQFPPSQSEER;TS(0.005)S(0.992)LT(0.003)QFPPSQSEER;T(0.002)S(0.002)S(0.997)LTQFPPSQSEER 419.37 2.95E-134 2990770000 2826286 4117170 3579433 4713150 6870060 6738920 6486160 7576400 8065880 TRUE FALSE 2452785.144 4090124.039 5310458.771 5783342.743 6733359.247 6998170.613 5857133.202 5956245.82 7112340.855 0.344863273 0.575074244 0.746654144 0.813141954 0.946714926 0.983947586 0.823516943 0.837452245 1 22.76189304 4.54718154 1.029646702 0.903711382 0.164570955 0.909100197 0.059983355 0.414004167 0.449006843 0.021145124 0.314995971 35251.81971 -4.54718154 -0.739140427 down RLEELLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLEELLR 7 1 P42285;H0YAC4 P42285 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 167.24 0.0017534 98895000 76266 75763 40951 52790 70055 73991 78499 74422 67310 FALSE TRUE 66187.25487 75265.30786 60755.04057 64776.77634 68661.04256 76837.48165 70886.17906 58507.43445 59352.68848 1.115151757 1.268102756 1.02362744 1.0913874 1.156831212 1.294591427 1.194321283 0.985758791 1 15.85702576 1.707112041 6.366120445 0.993487114 1.164009346 0.442835731 0.079297149 0.122037109 11.70899959 0.049599432 0.021291801 50.94622869 -1.707112041 0.170522232 RLEEPEEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLEEPEEPK 9 1 O75822;O75822-2 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 0 ; 116.75 0.0020266 528550000 1286240 1105480 764980 861800 1040510 894690 1268600 1385140 1200000 FALSE TRUE 1116260.125 1098218.029 1134926.887 1057484.862 1019805.887 929109.3032 1145571.367 1088938.59 1058137.367 1.054929312 1.037878505 1.072570464 0.999383345 0.963774571 0.87806114 1.082630104 1.029108908 1 20.0130955 3.710040604 12.80088116 0.995720184 1.053398287 0.244993334 0.051827515 3.237169574 1451.782764 0.015361627 0.022899203 5129.093353 -3.710040604 0.057678103 RLEEPSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 153.24 0.00071218 375800000 334330 295826 203061 244884 289931 320980 273457 330100 284946 FALSE TRUE 290147.4434 293882.6995 301261.9788 300488.655 284161.9403 333328.3083 246937.1822 259510.6838 251260.0085 1.154769695 1.169635794 1.19900489 1.195927107 1.130947746 1.326626988 0.982795407 1.032837201 1 17.93882154 2.215055466 24.99999573 1.010032291 1.192102397 0.743025409 0.052873142 110.1668159 117172.1607 0.020156311 0.013598251 164.0799314 -2.215055466 0.182070106 RLEEQAAQHK ddPTM_MDA-MB-175_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 ;;; 133.42 0.00012829 1197620000 1686220 1445800 978540 1137040 1404970 1373720 1589130 1776440 1662520 FALSE TRUE 1463381.755 1436302.445 1451765.217 1395222.311 1377013.846 1426567.897 1435016.417 1396562.13 1465978.78 0.99822847 0.979756641 0.990304387 0.951734316 0.939313628 0.973116335 0.978879393 0.952648258 1 20.48343279 3.756201702 24.45710666 0.964560228 0.988462518 0.290932457 0.017167707 793.7014068 1100362.088 0.00449971 0.007773408 5704.291386 -3.756201702 0.02390229 RLEEWLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RLEEWLGR 8 1 P56192;P56192-2 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ;; 207.29 0.0001035 1728730000 1547890 1345000 822301 899764 1246830 1418700 1334220 1360460 1296330 FALSE TRUE 1343332.415 1336164.606 1219968.514 1104069.168 1222020.522 1473278.307 1204827.55 1069536.216 1143079.344 1.175187376 1.168916763 1.067264946 0.965872731 1.069060104 1.288867929 1.054019177 0.935662272 1 20.12449412 1.995691276 24.97234641 0.972717102 1.117479629 0.358403312 0.085191252 198.1399066 1148373.344 0.037754997 0.024758309 99.01278497 -1.995691276 0.144762526 RLEFENQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLEFENQK 8 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 83.783 0.028728 722650000 151470 127850 119470 117470 129530 105690 130560 178290 162050 FALSE TRUE 131452.8557 127010.1449 177246.0916 144143.3589 126952.6064 109755.9627 117898.3113 140164.071 142892.6336 0.919941444 0.888850193 1.240414479 1.008752903 0.888447523 0.768100915 0.825083199 0.980904805 1 17.12457202 3.259038748 6.66900129 0.892111468 1.022403164 0.221831375 0.113226454 0.261482627 43.78047966 0.035276294 0.044213239 1815.677652 -3.259038748 0.130291696 RLEFLYDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLEFLYDK 8 1 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;O94979-7;H7BXG7;H0Y8W8 D6REX3 SEC31A Protein transport protein Sec31A 0 ; 121.8 0.0022735 2048570000 3092900 3624500 2253500 2497000 3267400 3023700 3479000 3954100 3708300 FALSE TRUE 2684165.429 3600690.421 3343300.138 3063982.014 3202385.133 3140023.696 3141607.115 3108546.486 3269908.999 0.820868541 1.101159213 1.022444398 0.937023634 0.979349925 0.960278618 0.960762858 0.950652293 1 21.64081906 3.735527286 24.92594455 0.963400232 0.993457566 0.002809594 0.070471211 977.3000612 8030818.553 0.017950224 0.027863353 5439.103038 -3.735527286 0.030057333 RLEHSEWDSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLEHSEWDSSR 11 1 Q14789;Q14789-2;Q14789-4;Q14789-3 Q14789 GOLGB1 Golgin subfamily B member 1 0 108.56 0.0013282 138210000 126680 115230 66318 87342 127380 151270 101290 133570 110180 FALSE TRUE 109938.917 114473.0465 98389.60662 107174.336 124845.3872 157089.4548 91466.91139 105007.0949 97154.64592 1.131586822 1.178256021 1.012711288 1.103131353 1.28501716 1.61690111 0.941456896 1.080824226 1 16.56799537 RLEIS(ph)PDSS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RLEISPDSSPER 12 1 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 2 RLEIS(1)PDS(0.383)S(0.617)PER;RLEIS(0.999)PDS(0.363)S(0.637)PER;RLEIS(0.988)PDS(0.271)S(0.741)PER;RLEIS(0.998)PDS(0.017)S(0.986)PER 161.24 4.40E-05 2193390000 2890010 2678290 1658020 2097200 2543950 2721710 2259930 2689140 2341340 TRUE FALSE 2508087.856 2660696.137 2459844.018 2573401.314 2493330.372 2826415.945 2040762.336 2114088.338 2064549.452 1.214835447 1.288753889 1.191467715 1.246471142 1.207687406 1.369023126 0.988478302 1.02399501 1 20.97739555 2.223219176 24.9999617 1.007637129 1.249504378 0.844179491 0.050383332 81.62388986 133010.8629 0.019208087 0.013004066 167.193418 -2.223219176 0.241867249 RLELLPSAES(ph)PVCWLEQPESHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLELLPSAESPVCWLEQPESHQR 23 1 O95402;B8ZZF3 O95402 MED26 Mediator of RNA polymerase II transcription subunit 26 1 RLELLPS(0.037)AES(0.963)PVCWLEQPESHQR 130.46 1.62E-05 76966000 18750 19229 10788 11126 18140 19401 22989 24403 15642 TRUE FALSE 16272.13999 19102.68343 16005.11288 13652.32835 17779.04949 20147.36902 20759.53032 19184.60835 13792.82058 1.179754344 1.384972952 1.160394481 0.989814104 1.289007523 1.460714211 1.505096815 1.390912631 1 13.75162989 3.005561231 24.95499451 1.364156654 1.185562286 0.170548559 0.163728283 238.5579199 1070472.249 0.050888435 0.057529375 1012.887545 -3.005561231 -0.178594368 RLETYYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLETYYK 7 1 P00568;Q5T9B7 P00568 AK1 Adenylate kinase isoenzyme 1 0 106.04 0.012492 808170000 520900 535440 300600 377330 454580 492980 522850 560240 503930 FALSE TRUE 452061.7452 531922.6594 445971.1654 463008.5436 445534.7474 511945.2596 472144.0875 440437.0358 444355.9695 1.017341448 1.197064282 1.003634915 1.041976648 1.002652778 1.152106182 1.062535714 0.991180644 1 18.76135634 1.764138972 5.377559901 0.995863382 1.070684005 0.187303017 0.062785512 0.270683585 18.37471972 0.035498175 0.016025257 58.09502883 -1.764138972 0.074820623 RLFDANKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLFDANKDR 9 2 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41;A0A2R8YF08;K7ELR7;K7ENA0;K7ERK8;A0A0J9YXM3;A0A0J9YXH9;K7EIL4;A0A0J9YYI8 P06744 GPI Glucose-6-phosphate isomerase 0 ; 94.692 0.0048088 436300000 1242440 1132470 436090 526640 943520 838820 1252150 1264370 149581 FALSE TRUE 1078248.406 1125030.73 646984.5826 646221.6612 924745.798 871089.9482 1130716.686 993994.3148 131897.7046 8.174883782 8.529570197 4.905199713 4.899415522 7.011083331 6.604284365 8.572679027 7.536100177 1 17.00905993 4.256656983 24.80082624 6.135726374 8.352229076 0.196387091 2.064698887 412.4637627 565265.2563 0.517525133 1.363047682 18057.47337 -4.256656983 2.216502702 RLFDDEAS(ph)VDEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLFDDEASVDEPR 13 1 A0A2R8Y549;Q8NI35-3;Q8NI35;A0A0X1KG69;A0A087WUZ6;Q8NI35-4;Q8NI35-2;Q8NI35-5;A0A0U1RR46 A0A2R8Y549 INADL InaD-like protein 1 RLFDDEAS(1)VDEPR;RLFDDEAS(1)VDEPR 80.859 0.010195 619480000 531730 671640 429900 512480 578010 691180 461140 553040 518110 TRUE FALSE 461460.5333 667227.9526 637801.0779 628846.4168 566508.7319 717770.1419 416418.7138 434776.6998 456859.626 1.010070724 1.460466004 1.396054809 1.376454344 1.240006119 1.571095586 0.911480661 0.951663651 1 18.80139143 2.221083465 24.99824005 0.952027546 1.347064735 0.606427663 0.147303791 148.0358837 211739.8212 0.056217729 0.037998435 166.3732365 -2.221083465 0.395037188 RLFDDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLFDDTR 7 1 Q15042-4;Q15042;Q15042-3 Q15042-4 RAB3GAP1 Rab3 GTPase-activating protein catalytic subunit 0 99.136 0.017237 99460000 209490 230520 146180 157020 218780 260940 221830 226510 179000 FALSE TRUE 181805.3657 229005.6989 216873.1369 192673.7909 214426.706 270978.5307 200316.9607 178072.5992 157838.8239 1.151841868 1.450883206 1.374016427 1.220699611 1.358516876 1.716805308 1.269123501 1.128192638 1 17.26809259 1.705159716 2.830816567 1.03204942 1.379148099 0.422279537 0.150745028 0.216612597 3.783676823 0.124465283 0.041247979 50.71771939 -1.705159716 0.347098679 RLGDS(ph)SGPALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLGDSSGPALK 11 1 Q9UHD8 Q9UHD8 9-Sep Septin-9 1 RLGDS(0.678)S(0.322)GPALK 57.095 0.048769 0 136740 104000 61545 95426 100020 63661 175420 131540 91701 TRUE FALSE 118669.4625 103316.8172 91308.36786 117093.9318 98029.79769 66110.07986 158407.7954 103411.1946 80860.21225 1.467587819 1.27772132 1.129212567 1.448103196 1.212336636 0.817584793 1.959032644 1.278888489 1 16.30314237 RLGDSS(ph)LSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLGDSSLSR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 RLGDS(0.201)S(0.799)LSR 96.64 0.004429 306950000 84433 84858 73584 103120 112230 154590 102920 124680 117220 TRUE FALSE 73274.96512 84300.56221 109169.4685 126534.9721 109996.8426 160537.1773 92938.83424 98018.15226 103362.3851 0.708913257 0.815582594 1.056181786 1.224187812 1.064186381 1.553148925 0.899155279 0.948296154 1 16.65735174 4.287664638 3.094833217 1.103161387 0.728612755 0.392669583 0.181285283 0.27483925 5.205460308 0.049692048 0.154767597 19393.87706 -4.287664638 -0.374548632 RLGDSSLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RLGDSSLSR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 103.69 0.0066059 0 652020 678020 373787 450264 558700 654530 621700 706560 505442 FALSE TRUE 565853.905 673566.042 554551.6434 552503.3231 547582.9631 679710.1926 561407.6297 555467.6425 445689.2226 1.26961541 1.511290845 1.244256346 1.239660497 1.228620607 1.525076574 1.259639231 1.246311587 1 18.76567855 1.134766688 1.709574381 0.808285278 1.330617103 0.474002901 0.10788699 1.159547641 2.512497703 1.097300106 0.029702089 13.63850252 -1.134766688 0.522331825 RLGGLRPES(ph)PESLTSVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLGGLRPESPESLTSVSR 18 2 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 RLGGLRPES(0.984)PES(0.005)LT(0.01)S(0.001)VSR 95.195 0.0019256 0 83027 70953 29813 37089 64798 77041 66565 90946 34558 TRUE FALSE 72054.77159 70486.90507 44230.66652 45510.62432 63508.64658 80004.81712 60109.53655 71497.90564 30472.59261 2.364576343 2.313124649 1.451490101 1.493493675 2.084123507 2.625468012 1.972577041 2.346302022 1 14.89522463 RLIELYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLIELYK 7 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ; 155.75 0.002549 3085000000 3174500 3363400 2056720 2700000 3541000 3215700 4401400 4846700 3204600 FALSE TRUE 2754981.782 3341305.604 3051356.671 3313076.267 3470541.028 3339410.06 3974552.905 3810270.922 2825755.839 0.974953938 1.182446678 1.079837341 1.172456665 1.228181494 1.181775868 1.406545056 1.348407697 1 21.43020538 3.844149332 0.755649612 1.270244291 1.018590579 0.262375229 0.116752758 1.318089987 1.295776412 0.060230782 0.237618268 6984.725325 -3.844149332 -0.251653712 RLIISDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLIISDR 7 1 P30520;G3V2N1;Q8N142;Q8N142-2 P30520;Q8N142 ADSS;ADSSL1 Adenylosuccinate synthetase isozyme 2;Adenylosuccinate synthetase isozyme 1 0 ; 127.46 0.0061773 1074770000 1091320 1146860 679040 761520 1108350 1285150 1152280 1204530 861650 FALSE TRUE 947099.2969 1139326.201 1007426.015 934434.7551 1086296.003 1334590.552 1040532.063 946950.6332 759786.7186 1.246533104 1.499534242 1.325932647 1.229864556 1.429738079 1.756533142 1.369505464 1.246337439 1 19.53523497 1.405986663 2.265346906 0.96697202 1.415073816 0.442475354 0.14789627 0.428229103 3.176498796 0.343648199 0.041581073 25.46752039 -1.405986663 0.448101796 RLIVDVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLIVDVIR 8 1 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 143.7 0.00095755 839290000 588710 632690 398010 467440 710290 683560 633530 744680 415490 FALSE TRUE 510910.4819 628533.8177 590488.9673 573579.3964 696156.6187 709856.9955 572090.3581 585435.9771 366371.2455 1.394515776 1.71556536 1.611723012 1.565568814 1.900139891 1.937534684 1.561504526 1.597931017 1 18.48294675 1.064925847 2.048202827 0.490711177 1.684292395 0.626984418 0.160420463 0.898101422 2.445485878 2.412730653 0.044107778 11.61250321 -1.064925847 1.193581218 RLKS(ph)EDELRPEVDEHTQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLKSEDELRPEVDEHTQK 18 3 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;H0YCR2;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 RLKS(1)EDELRPEVDEHTQK;RLKS(1)EDELRPEVDEHTQK 202.43 9.24E-16 1294640000 1100700 983020 946030 903600 1357960 1121430 1971920 2194220 817380 TRUE FALSE 955239.7062 976562.4769 1403533.272 1108776.191 1330939.253 1164572.138 1780683.502 1725003.128 720750.2676 1.325340758 1.35492489 1.947322582 1.538363897 1.84660251 1.6157776 2.470597074 2.393343723 1 19.45913994 4.473073265 0.574511279 2.001293828 0.959262964 0.132426997 0.431974409 5.019759171 1.648304035 0.284725769 3.389801596 29721.67391 -4.473073265 -1.042030864 RLLAEK ddPTM_MDA-MB-175_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 ; 131.3 0.024675 4357600000 6478500 5751400 3714900 4442300 5351000 4935000 6879200 7154800 5156600 FALSE TRUE 5622349.811 5713618.675 5511438.066 5450992.111 5244525.569 5124852.643 6212056.243 5624801.699 4546992.622 1.236498556 1.256570914 1.212106226 1.198812614 1.153405339 1.127086202 1.366190086 1.237037789 1 22.11648123 1.236780363 24.98961343 0.999999717 1.225498333 0.546626192 0.063933705 38.03318495 533717.3704 0.101959226 0.016268366 17.249653 -1.236780363 0.225498616 RLLEDGEDFNLGDALDSSNSMQTIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RLLEDGEDFNLGDALDSSNSMQTIQK 26 1 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;; 311.89 9.78E-82 2917170000 2488830 2314810 905557 1027705 2088460 1918980 2656590 3022970 268665 FALSE TRUE 2159924.81 2299603.861 1343487.394 1261061.128 2046903.732 1992804.402 2398954.311 2376531.39 236903.7298 9.117310275 9.706912859 5.671026773 5.323095289 8.640234301 8.411874327 10.12628342 10.03163349 1 17.85394139 4.277818043 24.99871157 7.509146444 9.412115999 0.098602919 2.708155242 451.7366514 287654.1655 0.683353467 1.807921558 18959.11422 -4.277818043 1.902969555 RLLS(ph)FQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RLLSFQR 7 1 Q13946-3;Q13946-2;Q13946;A1E5M1;Q9NP56 Q13946-3;A1E5M1 PDE7A;PDE7B "High affinity cAMP-specific 3,5-cyclic phosphodiesterase 7A;cAMP-specific 3,5-cyclic phosphodiesterase 7B" 1 RLLS(1)FQR;RLLS(1)FQR;RLLS(1)FQR 133.23 0.0020165 708370000 486420 534490 389725 375226 505510 612540 599080 557100 379442 TRUE FALSE 422138.3646 530978.9 578197.3136 460426.7983 495451.34 636104.8102 540981.3138 437968.5004 334584.799 1.261678253 1.586978552 1.728103952 1.376113917 1.480794529 1.901176658 1.616873556 1.308991029 1 18.35201238 1.447958884 2.705952956 0.99100275 1.572712189 0.520850535 0.176755214 0.254458476 3.104489731 0.279399513 0.047591208 28.05168049 -1.447958884 0.581709439 RLNHS(ph)PPQSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RLNHSPPQSSSR 12 1 A0A087X0H9;Q5T8P6-3;Q5T8P6-2;Q5T8P6 A0A087X0H9 RBM26 RNA-binding protein 26 1 RLNHS(0.989)PPQS(0.004)S(0.007)SR;RLNHS(0.999)PPQS(0.001)SSR;RLNHS(0.703)PPQS(0.278)S(0.018)S(0.001)R;RLNHS(1)PPQSSSR 147.1 4.00E-05 3327360000 538770 542937 293618 338644 439222 493352 570004 531641 424716 TRUE FALSE 467570.1794 539370.4111 435612.6469 415538.296 430482.3415 512331.5707 514725.0998 417953.7094 374506.5583 1.248496639 1.440216197 1.163164268 1.109562134 1.149465428 1.36801762 1.374408774 1.116011723 1 18.51463146 1.518244202 4.521899216 1.020722759 1.261078635 0.413896168 0.106650895 0.171175053 7.421404292 0.093340103 0.029444731 32.97951027 -1.518244202 0.240355876 RLNHYVLYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLNHYVLYK 9 1 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 78.905 0.018468 659120000 1289290 1555190 925700 1069590 1531140 1251470 1630020 1655680 1318970 FALSE TRUE 1118907.06 1544973.854 1373371.616 1312456.757 1500673.31 1299614.861 1471940.911 1301625.717 1163042.869 0.962051434 1.32838943 1.180843503 1.128468083 1.290299222 1.117426447 1.265594717 1.119155408 1 20.14947284 1.359103471 3.323490838 0.993448595 1.187395476 0.236258586 0.103372239 0.354397057 5.68165134 0.147404693 0.024007498 22.86143413 -1.359103471 0.193946881 RLNKHEENLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLNKHEENLK 10 2 P42766 P42766 RPL35 60S ribosomal protein L35 0 91.584 0.0060356 704070000 677260 582590 384600 420810 569620 480340 843990 865040 181280 FALSE TRUE 587758.375 578762.9279 570593.8464 516361.3422 558285.6764 498818.9906 762139.9797 680057.9277 159849.2849 3.676953421 3.620678868 3.569573969 3.230301233 3.492575376 3.120558161 4.767866057 4.254369534 1 17.28635276 4.119947163 4.067094894 3.493945464 3.649069367 0 0.979383798 2.698222459 80.38637969 0.25636945 0.585544386 13180.96366 -4.119947163 0.155123904 RLNNLSPAPHLASGSPPPGLPSGLPSGLQSGS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLNNLSPAPHLASGSPPPGLPSGLPSGLQSGSPSR 35 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 RLNNLSPAPHLASGSPPPGLPSGLPSGLQS(0.011)GS(0.887)PS(0.102)R;RLNNLSPAPHLASGSPPPGLPSGLPSGLQS(0.123)GS(0.719)PS(0.158)R 193.05 2.89E-21 1398920000 461280 329910 115122 210252 332360 431470 333790 356170 199667 TRUE FALSE 400320.6793 327742.7995 170795.3843 257992.9301 325746.6863 448068.9301 301419.0972 280005.8172 176062.5947 2.273740654 1.861512947 0.970083308 1.465347767 1.850175426 2.544941081 1.711999631 1.590376523 1 17.42572891 3.225296158 24.79689101 1.759067971 1.610260698 0.006746265 0.490681365 1233.368158 2305680.663 0.157589318 0.179718222 1679.949234 -3.225296158 -0.148807273 RLNS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RLNSSPR 7 1 Q9UBS0 Q9UBS0 RPS6KB2 Ribosomal protein S6 kinase beta-2 1 RLNS(0.83)S(0.17)PR;RLNS(0.645)S(0.355)PR;RLNS(0.551)S(0.449)PR 74.301 0.024914 258926000 205190 228506 166074 165239 191022 293057 192680 230733 219675 TRUE FALSE 178073.6216 227004.929 246387.9419 202759.0405 187221.0359 304331.0924 173993.9233 181392.5435 193705.2718 0.919301886 1.171908885 1.271973342 1.046739919 0.966525249 1.57110382 0.898240516 0.936435761 1 17.56350369 RLNSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLNSSPR 7 1 Q9UBS0 Q9UBS0 RPS6KB2 Ribosomal protein S6 kinase beta-2 1 RLNS(0.222)S(0.778)PR 65.803 0.042627 131540000 78777 104400 66855 74682 77819 135210 85265 99504 95610 TRUE FALSE 68366.41985 103714.1895 99186.30162 91639.68954 76270.55415 140411.6162 76996.01342 78225.84394 84307.09472 0.810921312 1.230195274 1.176488194 1.086974825 0.904675394 1.665478056 0.913280355 0.927867865 1 16.36336642 RLNVWDLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLNVWDLSK 9 1 Q09028-3;Q09028;Q09028-2;Q09028-4;H0YF10;H0YCT5;H0YDK2;H0YEU5;Q16576;E9PC52;Q16576-2;Q5JP02 Q09028-3;Q16576 RBBP4;RBBP7 Histone-binding protein RBBP4;Histone-binding protein RBBP7 0 ; 166.66 9.71E-05 2620700000 2762650 4558600 2716700 3014000 4263700 3415600 4439600 4834100 4059400 FALSE TRUE 2397558.803 4528654.256 4030505.207 3698374.766 4178860.712 3547000.342 4009048.275 3800365.334 3579502.356 0.66980227 1.265163088 1.125995964 1.0332092 1.167441811 0.990919963 1.120001575 1.061702146 1 21.7713276 4.753701957 24.99111716 1.092035182 0.669801965 0.726335032 0.082104442 1470.269531 2426671.514 0.019162354 0.437906912 56715.52505 -4.753701957 -0.422233217 RLPDAHSDYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RLPDAHSDYAR 11 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ;;; 182.71 3.68E-06 3663960000 1298010 1117820 822462 835500 899622 1054970 1005690 1004970 965740 FALSE TRUE 1126474.69 1110476.967 1220207.374 1025213.045 881721.2823 1095555.379 908158.3386 790064.9862 851571.3174 1.322818966 1.304032844 1.432889236 1.20390744 1.035405097 1.286510426 1.066450126 0.92777313 1 19.69976783 2.436378497 0.436564871 0.843639538 1.392073975 0.665316533 0.094725277 1.197904437 0.554007071 0.390851253 0.174037135 273.1357183 -2.436378497 0.548434437 RLPDGLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLPDGLTR 8 1 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 96.331 0.014458 159760000 82251 69031 42570 56495 65346 65404 58655 75746 62660 FALSE TRUE 71381.32195 68577.53082 63156.99439 69323.05322 64045.74245 67920.1342 52966.64713 59548.30736 55252.40618 1.291913364 1.241168223 1.143063239 1.254661254 1.159148476 1.22927016 0.958630597 1.077750481 1 15.75374967 2.248147973 24.99997537 1.023569559 1.216168909 0.779233888 0.051982316 87.79116677 228924.3914 0.018801078 0.014372648 177.0712173 -2.248147973 0.192599349 RLPDLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLPDLIK 7 1 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 80.684 0.046895 266000000 628880 468760 347690 505530 553460 495490 587240 714960 617310 FALSE TRUE 545771.9146 465680.6847 515834.047 620318.313 542447.2288 514551.8209 530289.5552 562071.3678 544332.315 1.002644707 0.855508063 0.94764546 1.139594869 0.996536884 0.945289866 0.974201863 1.032588645 1 19.05412816 3.983615601 24.98083614 1.012941457 0.922201465 0.273340179 0.061337236 828.6399786 1263411.034 0.015894155 0.028541807 9629.763052 -3.983615601 -0.090739993 RLPLNFLSGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLPLNFLSGEK 11 1 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ; 123.84 0.00057988 694870000 1503280 1379290 1100710 1142160 1307770 1203410 1524490 1714480 1800670 FALSE TRUE 1304617.739 1370229.353 1633017.038 1401504.885 1281747.936 1249705.961 1376645.194 1347851.794 1587796.844 0.82165281 0.862975234 1.028479836 0.882672673 0.807249328 0.787069181 0.867015953 0.848881769 1 20.5985949 4.663613703 5.026684721 0.881172555 0.821845145 0.066159795 0.075674829 0.612315426 26.60238858 0.019188463 0.087922393 46090.74232 -4.663613703 -0.05932741 RLPLSFVLDVLEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLPLSFVLDVLEGR 14 1 C9K0I3;B5MC20;P0C869-8;P0C869-7;P0C869-6;P0C870 C9K0I3 JMJD7 JmjC domain-containing protein 7 0 ; 102.08 0.001915 81414000 157169 182885 106533 123848 173430 179292 171258 186570 155998 FALSE TRUE 136398.7184 181683.6164 158052.7151 151969.5813 169979.0823 186189.4793 154649.4255 146673.4574 137556.0942 0.991586155 1.320796563 1.149005546 1.104782614 1.235707392 1.353553112 1.124264443 1.066281056 1 17.06966053 1.746192525 2.728219042 1.019502086 1.195761203 0.279860244 0.104033562 0.298035326 4.539950944 0.080009792 0.027748882 55.74328064 -1.746192525 0.176259117 RLPS(ph)SPASPSPK ddPTM_MDA-MB-175_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(0.631)S(0.369)PASPSPK;RLPS(0.5)S(0.5)PASPSPK 122.08 0.00022349 1538840000 1690730 1548140 980960 1368410 1577040 1297600 1466060 2183370 1454080 TRUE FALSE 1467295.747 1537970.166 1455355.537 1679128.405 1545659.989 1347519.512 1323881.727 1716473.317 1282180.319 1.144375503 1.199496002 1.135063076 1.309588348 1.20549346 1.050959441 1.032523825 1.338714447 1 20.29016774 RLPSS(ph)PASPSPK ddPTM_MDA-MB-175_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(0.197)S(0.803)PASPSPK;RLPS(0.107)S(0.893)PASPSPK 140.93 3.68E-05 676950000 1563410 1423440 848190 1331050 1399050 1242730 1250540 1737880 1278930 TRUE FALSE 1356801.407 1414089.329 1258377.521 1633285.246 1371211.642 1290538.627 1129262.823 1366247.886 1127736.352 1.203119332 1.25391837 1.115843715 1.448286422 1.21589735 1.144362 1.001353571 1.211495828 1 20.1049984 2.697767536 3.50849064 1.095968801 1.253180003 0.383307822 0.101342183 0.26926973 6.89916735 0.034982079 0.031591276 498.6175216 -2.697767536 0.157211201 RLPSSPAS(ph)PSPK ddPTM_MDA-MB-175_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 RLPSSPAS(0.87)PS(0.129)PK 118.64 0.00036967 730070000 686450 620370 451570 691170 750890 608770 777510 1028300 820270 TRUE FALSE 595733.8933 616294.7486 669950.7624 848110.7124 735948.7581 632189.7758 702107.1999 808406.0472 723298.6151 0.823634777 0.852061287 0.926243668 1.172559569 1.017489516 0.874037033 0.970701706 1.117665692 1 19.46423186 4.000368657 5.465296372 1.026964976 0.846963392 0.487889276 0.079966321 0.145236624 14.87165493 0.022362757 0.044431145 10008.49224 -4.000368657 -0.180001584 RLPVTNEMVHNLVAIELAYINTK ddPTM_MDA-MB-175_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 0 104.44 0.0010624 67237000 70892 57210 40576 49854 39924 46314 63791 64066 61686 FALSE TRUE 61523.44258 56834.18374 60198.68932 61174.11267 39129.59051 48095.72955 57604.55864 50365.98446 54393.55135 1.131079715 1.044869885 1.106724746 1.124657448 0.719379219 0.884217492 1.059032867 0.925955067 1 15.731148 RLQDFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLQDFLR 7 1 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 84.368 0.061845 0 152790 212020 130900 168220 209520 200930 184900 192800 155340 FALSE TRUE 132598.4144 210627.2267 194203.6778 206416.9221 205350.9619 208659.9071 166968.4265 151571.2204 136975.8822 0.968042054 1.537695712 1.417794686 1.506958151 1.49917605 1.523333187 1.218962228 1.106554073 1 17.06356237 1.905739478 2.390129841 1.043033966 1.422513723 0.432097618 0.167805842 0.260032814 2.707285675 0.117116215 0.046324433 80.48954606 -1.905739478 0.379479757 RLQGQLQGGS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLQGQLQGGSR 11 1 Q9UP83-3;Q9UP83;Q9UP83-2;U3KQU7 Q9UP83-3 COG5 Conserved oligomeric Golgi complex subunit 5 1 RLQGQLQGGS(1)R 74.769 0.024451 81098000 32713 28878 17159 17376 24795 28773 27287 28075 25561 TRUE FALSE 28389.89417 28688.29852 25457.14979 21321.48638 24301.62801 29879.91593 24640.71094 22071.37973 22539.2077 1.259578178 1.272817523 1.129460722 0.945973197 1.078193534 1.32568617 1.093237671 0.979243815 1 14.46014918 7.999999997 0.403449857 1.048811518 5.191410375 0.294587735 0.10921822 118.2566612 1.650629229 0.113264051 387.7864075 99999999.36 -7.999999997 4.142598856 RLQSIGTENTEENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RLQSIGTENTEENR 14 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;; 310.9 1.63E-55 14783460000 3216490 2820813 2288387 2959357 3070565 3188761 2762230 3294134 6108050 FALSE TRUE 2791422.697 2802282.894 3395058.607 3631324.238 3009466.764 3311434.699 2494349.36 2589709.079 5385963.287 0.518277335 0.520293724 0.630353091 0.674220013 0.558761099 0.614826823 0.463120379 0.480825609 1 22.36077297 1.232607864 24.99996451 1.00000072 0.556137739 0.81326379 0.066620846 92.08993611 386713.6386 0.160438674 0.018159231 17.08471995 -1.232607864 -0.443862981 RLQSIGTENTEENRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RLQSIGTENTEENRR 15 2 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;; 268.93 5.24E-26 3811460000 1174186 1201138 448419 392172 1052472 1040367 1195895 1139378 143082.2 FALSE TRUE 1019014.345 1193247.645 665275.9283 481220.6466 1031529.866 1080390.592 1079917.287 895730.8813 126167.1853 8.076698727 9.457670332 5.27297115 3.814150608 8.175896639 8.563166318 8.559414909 7.099555079 1 16.9449772 4.244660767 24.99042775 6.378453106 8.767184968 0.172905733 2.379528512 287.6980239 1178576.698 0.611644309 1.532716212 17565.51015 -4.244660767 2.388731861 RLQTQVFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLQTQVFK 8 1 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 ; 123.86 0.0021318 2544200000 2803970 2944340 1844050 2078000 2870530 2485070 3181580 3422800 2426310 FALSE TRUE 2433418.26 2924998.437 2735838.748 2549841.66 2813412.069 2580672.251 2873030.861 2690860.856 2139474.396 1.13739069 1.367157486 1.278743393 1.191807514 1.315001514 1.206217871 1.342867607 1.257720523 1 21.02882498 1.240575532 6.892124314 0.994154919 1.267658402 0.578204087 0.070263375 0.071078863 18.74133744 0.091526137 0.015720955 17.40105311 -1.240575532 0.273503483 RLREEFSFIPSAALDLLDHMLTLDPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLREEFSFIPSAALDLLDHMLTLDPSK 27 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 0 ; 56.95 0.039705 3162490000 1883650 1421400 487652 798250 1531520 1558670 1857610 2026150 296645 FALSE TRUE 1634720.88 1412062.73 723482.1383 979504.863 1501045.748 1618633.043 1677459.268 1592873.59 261575.966 6.249507188 5.398289266 2.765858612 3.744628674 5.738469673 6.188003692 6.412895242 6.089525785 1 17.99687046 4.478736665 24.99656571 4.816551826 6.036703358 0.08012839 1.727724996 162.2473094 2510516.718 0.444674211 1.215348525 30111.79636 -4.478736665 1.220151532 RLS(ph)AEGGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSAEGGDK 9 1 S4R3H3;S4R393;S4R410;A7E2V4-5;A7E2V4;A7E2V4-3;A7E2V4-4;A7E2V4-2;H7BZ52;H0YCW2 S4R3H3 ZSWIM8 Zinc finger SWIM domain-containing protein 8 1 RLS(1)AEGGDK 78.692 0.0098196 0 182840 149680 143340 143380 148000 169520 191900 217050 218670 TRUE FALSE 158677.2307 148696.7422 212659.7034 175936.6204 145055.0896 176041.5441 173289.5675 170635.5466 192819.0817 0.822933235 0.771172339 1.102897605 0.912444032 0.752285968 0.912988188 0.898715864 0.884951557 1 17.5568883 -1.931754574 0.014254864 1.942204172 4.75E-06 0.065410812 0.099783249 55238.41473 79.49130615 6363.896592 4604.332066 0.011701605 1.931754574 -1.942199419 RLS(ph)APLPSSCGDPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RLSAPLPSSCGDPEK 15 1 H0YKX0;Q96EP0-3;Q96EP0 H0YKX0 RNF31 E3 ubiquitin-protein ligase RNF31 1 RLS(1)APLPSSCGDPEK;RLS(1)APLPSSCGDPEK;RLS(1)APLPSSCGDPEK;RLS(1)APLPSSCGDPEK;RLS(1)APLPSSCGDPEK;RLS(1)APLPSSCGDPEK 177.02 4.72E-07 4323630000 4231990 3317420 2939320 3154070 3248760 2989410 4505430 4451150 4880840 TRUE FALSE 3672721.799 3295627.65 4360784.983 3870249.8 3184116.032 3104414.537 4068494.092 3499306.211 4303832.655 0.853360735 0.765742517 1.013232933 0.899256572 0.739832676 0.721313951 0.94531884 0.813067443 1 22.03719055 1.231370682 24.95362427 1.000000278 0.844697969 0.223979841 0.091308442 411.1394675 1426785.582 0.222376489 0.022434816 17.03611966 -1.231370682 -0.155302308 RLS(ph)AQAHPAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLSAQAHPAGK 11 1 H7C3T2;Q2TAZ0-3;Q2TAZ0 H7C3T2;Q2TAZ0 ATG2A Autophagy-related protein 2 homolog A 1 RLS(1)AQAHPAGK;RLS(1)AQAHPAGK 139.66 2.39E-05 407510000 886510 740030 566780 720730 865660 763440 1146030 897670 794840 TRUE FALSE 769355.4574 735168.6942 840876.7038 884382.7622 848435.0596 792810.0308 1034888.187 705710.2562 700874.9207 1.097707215 1.048929948 1.199752879 1.261826805 1.210537051 1.131171922 1.476566155 1.006898999 1 19.41879748 4.235392005 24.98591473 1.185567649 1.073318565 0.10494208 0.134092271 176.1055222 1388720.03 0.034505906 0.076974163 17194.59714 -4.235392005 -0.112249083 RLS(ph)AS(ph)STGSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 2 RLS(0.971)AS(0.861)S(0.155)T(0.011)GS(0.002)T(0.001)R 54.871 0.086167 141030000 271600 287030 203770 213800 274640 310770 274570 313190 292660 TRUE FALSE 235707.3719 285144.481 302313.8536 262346.5577 269175.2013 322725.523 247942.2437 246216.7557 258062.0682 0.91337473 1.104945345 1.171477295 1.016602554 1.043063799 1.250573264 0.960785308 0.954098979 1 17.97735857 RLS(ph)ASSTGSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.611)AS(0.055)S(0.126)T(0.126)GS(0.028)T(0.055)R;RLS(0.969)AS(0.005)S(0.012)T(0.003)GS(0.009)T(0.001)R;RLS(0.873)AS(0.079)S(0.046)T(0.002)GST(0.001)R;RLS(0.456)AS(0.133)S(0.133)T(0.133)GS(0.072)T(0.072)R 135.02 0.00013641 748959000 701455 674791 479220 531958 656166 865237 715665 741456 745832 TRUE FALSE 608755.9445 670358.2535 710972.3949 652747.1944 643109.5804 898523.2273 646259.9185 582901.4044 657660.5906 0.925638472 1.019307319 1.081062793 0.992528979 0.97787459 1.366241554 0.982664809 0.88632558 1 19.3269837 2.008984503 24.99953731 0.934878717 1.062818357 0.14602373 0.121043728 324.4654287 902827.2022 0.049620219 0.033402043 102.0903054 -2.008984503 0.12793964 RLS(ph)DCESTDVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSDCESTDVKR 12 2 Q7Z333-3;Q7Z333;Q7Z333-4 Q7Z333-3 SETX Probable helicase senataxin 1 RLS(1)DCESTDVKR 69.331 0.026227 58497000 68438 53179 38198 43406 52697 55087 67996 74397 44524 TRUE FALSE 59393.7449 52829.66365 56670.68056 53261.99572 51648.4328 57206.23254 61401.75839 58487.78051 39260.42344 1.512814679 1.345621341 1.443455663 1.356633247 1.315534278 1.457096677 1.563960676 1.489738912 1 15.26078811 1.234260396 24.99932331 0.999999357 1.436045545 0.755306607 0.077919241 69.81419555 405810.6206 0.157033057 0.020612245 17.14985276 -1.234260396 0.436046188 RLS(ph)DEHEPEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSDEHEPEQR 11 1 Q9UK59;Q9UK59-2 Q9UK59 DBR1 Lariat debranching enzyme 1 RLS(1)DEHEPEQR 101.2 0.0021185 222750000 141600 122920 93960 104900 119150 126390 121800 130970 128620 TRUE FALSE 122887.2012 122112.5304 139399.3703 128719.1483 116779.1481 131252.3051 109987.8547 102963.0847 113414.6901 1.083521024 1.076690597 1.229112121 1.134942468 1.029665099 1.157277818 0.969784907 0.907846105 1 16.79124799 2.169618529 5.901933254 0.945942034 1.118213273 0.631196654 0.057275631 0.121507858 7.614537359 0.023896048 0.016067039 147.7809755 -2.169618529 0.172271238 RLS(ph)DPLLPSPEDETGSLVHLEDPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RLSDPLLPSPEDETGSLVHLEDPER 25 1 Q8WYL5-2;Q8WYL5-5;Q8WYL5-4;Q8WYL5 Q8WYL5-2 SSH1 Protein phosphatase Slingshot homolog 1 1 RLS(1)DPLLPSPEDETGSLVHLEDPER;RLS(0.999)DPLLPSPEDETGSLVHLEDPER;RLS(1)DPLLPSPEDETGSLVHLEDPER;RLS(1)DPLLPSPEDETGSLVHLEDPER 96.242 0.0043778 174134000 49704.6 50304.2 37769.7 46191.2 55054 55286.8 50789.3 57330 71902 TRUE FALSE 43136.01117 49973.7484 56035.25325 56679.61795 53958.53311 57413.71897 45863.7615 45070.42564 63401.82747 0.680359114 0.78820675 0.883811327 0.893974515 0.851056433 0.905553062 0.723382327 0.710869504 1 15.9522368 4.647795185 3.243398408 0.836401261 0.672122164 0.278079961 0.085726724 0.431345906 7.320563086 0.022868176 0.153876825 44442.16271 -4.647795185 -0.164279097 RLS(ph)EDYGVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLSEDYGVLK 10 1 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 1 RLS(1)EDYGVLK;RLS(1)EDYGVLK 137.93 4.78E-05 532670000 1838730 1272570 665000 1114750 939720 662590 1444330 1836380 1199230 TRUE FALSE 1595737.172 1264210.404 986596.2243 1367871.025 921021.4105 688080.2661 1304259.099 1443684.428 1057458.396 1.509030689 1.195517865 0.932988218 1.29354595 0.870976498 0.650692518 1.233390462 1.365239932 1 20.01216947 4.669634765 3.244160283 1.074977912 1.54025811 0.313167663 0.21249994 0.399463068 6.837341413 0.057758916 0.41933565 46734.19489 -4.669634765 0.465280198 RLS(ph)EGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSEGR 6 1 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 1 RLS(1)EGR 73.233 0.08845 1291900000 1899100 1579600 1163300 1135700 1182900 2007600 1636200 1743200 1956700 TRUE FALSE 1648129.123 1569223.504 1725875.771 1393578.043 1159362.604 2084833.671 1477521.576 1370430.246 1725381.155 0.955226107 0.909493823 1.000286671 0.807692862 0.671945791 1.208332237 0.856345029 0.794276813 1 20.71848367 3.751758375 24.50112608 0.881927738 0.950451349 0.042378259 0.142441113 2225.443663 4131436.812 0.037718987 0.064796293 5646.227529 -3.751758375 0.068523612 RLS(ph)EQLAHTPTAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RLSEQLAHTPTAFK 14 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;F8W860;Q9UBF8-3 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 RLS(1)EQLAHTPTAFK;RLS(0.999)EQLAHT(0.001)PTAFK;RLS(1)EQLAHTPTAFK;RLS(1)EQLAHTPTAFK;RLS(1)EQLAHTPTAFK 182.34 9.39E-07 6137070000 5002800 4765580 3570750 3942560 4332330 4199260 5522910 5861930 7053860 TRUE FALSE 4341667.305 4734274.591 5297576.643 4837778.506 4246125.109 4360808.249 4987299.038 4608401.887 6219960.707 0.698021661 0.761142202 0.851705805 0.777782808 0.682661082 0.701099003 0.801821631 0.740905305 1 22.56847404 1.236681752 24.99819343 1.00000031 0.754184356 0.698061967 0.051261056 29.68095754 394792.7957 0.081806116 0.012987921 17.24573675 -1.236681752 -0.245815953 RLS(ph)EQLAHTPTAFKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLSEQLAHTPTAFKR 15 2 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;F8W860;Q9UBF8-3 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 RLS(1)EQLAHTPTAFKR;RLS(1)EQLAHTPTAFKR 137.99 6.96E-06 1212590000 838640 850930 439400 467640 736730 757700 959130 1002260 328060 TRUE FALSE 727811.5992 845340.1848 651895.3097 573824.8094 722070.5144 786849.2093 866113.7202 787934.4986 289277.1205 2.515966689 2.922250413 2.253532213 1.983650862 2.496120374 2.720053379 2.994062298 2.723805108 1 18.1420927 4.231709907 24.95970699 2.393360841 2.719108565 0.070319482 0.557646385 470.6808052 1714889.991 0.14414576 0.31095002 17049.43167 -4.231709907 0.325747724 RLS(ph)ESQLSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RLSESQLSFR 10 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 1 RLS(1)ESQLSFR;RLS(0.705)ES(0.294)QLS(0.001)FR;RLS(1)ESQLSFR 216.88 4.60E-09 982630000 615920 517460 350311 385577 516994 647110 555860 569120 635550 TRUE FALSE 534524.6115 514060.7712 519722.5713 473128.151 506706.8309 672004.7404 501952.7828 447418.1169 560416.003 0.953799693 0.917284247 0.927387099 0.844244541 0.904161959 1.199117685 0.895678889 0.798367845 1 19.09613863 2.017125488 24.99877736 0.873454003 0.955244136 0.055413472 0.104496402 532.9189956 777920.9268 0.043573249 0.02937003 104.0220691 -2.017125488 0.081790133 RLS(ph)ESSALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RLSESSALK 9 1 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 RLS(0.85)ES(0.15)SALK;RLS(0.431)ES(0.42)S(0.149)ALK;RLS(0.988)ES(0.009)S(0.003)ALK;RLS(0.928)ES(0.068)S(0.004)ALK 162.34 6.76E-05 1362970000 1385410 1021860 1181070 1621750 1342780 1379610 1678240 1919100 3913510 TRUE FALSE 1202324.558 1015147.334 1752239.402 1989993.124 1316061.305 1432684.489 1515484.543 1508715.399 3450859.306 0.348413091 0.294172333 0.507769007 0.576665969 0.381372055 0.415167459 0.439161498 0.437199916 1 21.71852422 1.238001644 6.944683648 1.012764812 0.426904992 0.842122356 0.078253448 0.044618912 12.07946203 0.122883726 0.020308145 17.29822908 -1.238001644 -0.58585982 RLS(ph)EVIYEPFQLLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLSEVIYEPFQLLSK 15 1 A0A087WVA8;Q8IWB9;Q8IWB9-2 A0A087WVA8 TEX2 Testis-expressed sequence 2 protein 1 RLS(1)EVIYEPFQLLSK;RLS(1)EVIYEPFQLLSK 163.79 1.61E-06 204108000 393290 310890 238330 370290 438650 370480 392480 528770 403570 TRUE FALSE 341315.73 308847.7431 353587.1852 454370.004 429921.7232 384732.6053 354417.35 415696.6504 355860.4143 0.95912812 0.867890135 0.99361202 1.276820871 1.208118987 1.081133472 0.995944858 1.168145244 1 18.44095193 3.98907598 20.8554415 1.121709913 0.917819169 0.499840057 0.088291257 46.54747107 88872.07129 0.023453668 0.044151542 9751.602276 -3.98907598 -0.203890745 RLS(ph)FAVPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSFAVPFR 9 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 1 RLS(1)FAVPFR 113.69 0.0010773 129340000 74917 68430 48010 47399 78109 65555 66735 74060 58699 TRUE FALSE 65016.52863 67980.47882 71227.79658 58161.6674 76554.78372 68076.94327 60263.04997 58222.84534 51759.67109 1.256123296 1.313386994 1.376125371 1.123686959 1.479043087 1.315250693 1.164285798 1.12486892 1 15.65954083 1.779650261 1.542700538 1.013318109 1.311731241 0.562502177 0.092782184 0.327755746 1.382469421 0.117848912 0.027567174 60.20745383 -1.779650261 0.298413133 RLS(ph)FLVSYIASK ddPTM_MDA-MB-175_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(0.978)FLVS(0.021)YIASK 140.89 3.68E-05 234183700 963004 934193 657498 738482 810989 820049 1133361 1172188 1004421 TRUE FALSE 835740.5815 928056.2247 975466.232 906165.6251 794851.9056 851596.8157 1023447.825 921524.7182 885679.4936 0.943615142 1.047846576 1.101376106 1.023130412 0.897448695 0.961518046 1.155551 1.040472005 1 19.75642519 2.280062824 24.99939593 1.063919521 0.999754869 0.188081045 0.067739911 273.7855962 164917.2313 0.026819343 0.020773964 190.5736376 -2.280062824 -0.064164653 RLS(ph)GDLSSMPGPGTLSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLSGDLSSMPGPGTLSVR 18 1 A0A0C4DG26;Q9NP71-6;Q9NP71-4;Q9NP71-2;Q9NP71-3;Q9NP71 A0A0C4DG26 MLXIPL Carbohydrate-responsive element-binding protein 1 RLS(1)GDLSSMPGPGTLSVR;RLS(0.994)GDLS(0.006)SMPGPGTLSVR 95.666 0.0010633 217450000 149555 162371 109186 122900 166797 182424 147821 164071 182988 TRUE FALSE 129790.9278 161304.3742 161988.7148 150806.3234 163478.066 189441.9693 133485.3422 128985.6935 161355.3671 0.804379366 0.999683972 1.003925173 0.934622294 1.013155428 1.174066737 0.827275501 0.799388925 1 17.29988204 RLS(ph)GEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSGEER 7 1 Q99549-2;Q99549;A0A0A0MT47 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 RLS(1)GEER 112.83 0.0038376 570890000 258620 249390 142800 211880 237080 308200 226280 278710 262540 TRUE FALSE 224442.7117 247751.7407 211858.5576 259990.5924 232362.5718 320056.6534 204335.4004 219110.0354 231502.8203 0.969503142 1.070188866 0.915144608 1.123055832 1.003713784 1.382517297 0.882647564 0.946468104 1 17.82067024 RLS(ph)GLSSVGHNWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSGLSSVGHNWR 13 1 Q14D93;A0A0G2JR24;Q8WYQ4 Q14D93 C22orf15 Uncharacterized protein C22orf15 1 RLS(0.987)GLS(0.007)S(0.007)VGHNWR 56.599 0.056865 154220000 154160 84889 365310 126010 19856 23691 75882 90644 60394 TRUE FALSE 133787.3654 84331.35857 541975.1379 154622.4964 19460.90445 24602.4081 68522.97532 71260.48599 53254.29012 2.512236387 1.583559904 10.17711694 2.903474933 0.365433553 0.461979834 1.286712773 1.338117283 1 15.70061013 3.477118338 21.57231227 1.016495347 4.790240012 0.383493157 2.245950429 0.048799427 136838.5521 0.641447006 0.840392209 2999.979853 -3.477118338 3.773744664 RLS(ph)IIGPTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RLSIIGPTSR 10 1 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 1 RLS(1)IIGPTSR;RLS(1)IIGPTSR;RLS(1)IIGPTSR;RLS(1)IIGPTSR 191.06 5.11E-07 1990600000 542100 558480 407191 401088 619030 696980 530508 573420 630070 TRUE FALSE 470460.1115 554811.3081 604109.9296 492161.1606 606712.5141 723793.2716 479059.4158 450798.5954 555583.8424 0.846785086 0.998609509 1.08734251 0.885844985 1.092026923 1.302761557 0.862263045 0.811396158 1 19.08364512 RLS(ph)LESEGAGEGAAASPELSALEEAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RLSLESEGAGEGAAASPELSALEEAFR 27 1 O94811 O94811 TPPP Tubulin polymerization-promoting protein 1 RLS(0.995)LES(0.005)EGAGEGAAASPELSALEEAFR;RLS(0.995)LES(0.005)EGAGEGAAASPELSALEEAFR;RLS(0.969)LES(0.031)EGAGEGAAASPELSALEEAFR;RLS(0.995)LES(0.005)EGAGEGAAASPELSALEEAFR 227.49 7.38E-35 408570000 130724 122172 89522.9 113305 127600 148661 126364 150754 182514 TRUE FALSE 113448.4922 121369.4441 132816.4739 139032.632 125061.0096 154380.0849 114109.2387 118516.4303 160937.4028 0.704923095 0.75414069 0.825267909 0.863892604 0.777078587 0.959255475 0.709028708 0.736413215 1 17.29614013 4.406731401 2.853853964 0.825900385 0.709225517 0.200601713 0.090491523 0.494837887 7.630105177 0.023391083 0.093771523 25511.23019 -4.406731401 -0.116674868 RLS(ph)LESEGAGEGAAASPELSALEEAFRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLSLESEGAGEGAAASPELSALEEAFRR 28 2 O94811 O94811 TPPP Tubulin polymerization-promoting protein 1 RLS(0.534)LES(0.068)EGAGEGAAAS(0.264)PELS(0.134)ALEEAFRR;RLS(1)LESEGAGEGAAASPELSALEEAFRR 208.7 9.23E-26 102521000 31627.8 30245.4 17491.6 26088.6 38681.2 30542.9 29565.3 40623.1 27541.3 TRUE FALSE 27448.1061 30046.71598 25950.59627 32012.41537 37911.5198 31717.90513 26698.06176 31936.16619 24285.39889 1.130230812 1.237233785 1.068567841 1.318175399 1.561082854 1.306048349 1.099346232 1.315035686 1 14.56780156 3.725474322 24.69463372 1.275116889 1.154533104 0.121560189 0.15187184 1446.664479 2729945.555 0.042904473 0.064090804 5314.645759 -3.725474322 -0.120583785 RLS(ph)LGAQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLSLGAQK 8 1 Q9H788-2;Q9H788 Q9H788-2 SH2D4A SH2 domain-containing protein 4A 1 RLS(1)LGAQK;RLS(1)LGAQK 132.69 0.00058281 357250000 543420 470000 169558 389920 351810 200053 313390 336780 456110 TRUE FALSE 471605.6701 466912.5391 251556.8159 478457.2956 344809.6693 207749.1684 282997.486 264762.2178 402189.1954 1.172596568 1.160927604 0.625468856 1.189632394 0.857332005 0.516545871 0.703642687 0.658302662 1 18.6175148 3.001002052 24.87450731 0.706142892 1.017452366 0.361694558 0.197918578 34.51728197 856795.7145 0.058594781 0.065897819 1002.309975 -3.001002052 0.311309474 RLS(ph)LGQGDSTEAATEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RLSLGQGDSTEAATEER 17 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RLS(0.981)LGQGDS(0.014)T(0.005)EAATEER;RLS(1)LGQGDSTEAATEER;RLS(1)LGQGDSTEAATEER;RLS(1)LGQGDSTEAATEER;RLS(0.858)LGQGDS(0.136)T(0.005)EAATEER;RLS(1)LGQGDSTEAATEER 239.58 2.90E-20 7905370000 2036280 1543435 1210135 1386300 1646813 1744398 1715880 1712059 1855530 TRUE FALSE 1767180.439 1533296.074 1795360.334 1701080.603 1614044.643 1811506.12 1549474.222 1345948.506 1636171.357 1.080070514 0.937124383 1.097293585 1.039671423 0.98647653 1.107161614 0.947012191 0.822620748 1 20.64189242 2.029706116 8.022053966 0.894435134 1.036028197 0.415949604 0.066090393 0.159577036 36.4538979 0.025481616 0.016949024 107.0794461 -2.029706116 0.141593063 RLS(ph)LGQGDSTEAATEERGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSLGQGDSTEAATEERGPR 20 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RLS(1)LGQGDSTEAATEERGPR 240.8 5.34E-30 237170000 81066 64641 31134 38422 65097 70233 53537 60910 30888 TRUE FALSE 70352.9227 64216.36901 46190.50654 47146.30234 63801.69706 72934.90896 48344.98998 47884.8705 27236.45583 2.583042491 2.357735875 1.695907383 1.730999901 2.342510988 2.677841398 1.775010313 1.758116798 1 14.73325136 1.245066107 1.407248873 0.512716504 2.18139757 0.558635087 0.337156288 1.052951925 1.848928404 2.542852211 0.106222165 17.58191219 -1.245066107 1.668681065 RLS(ph)LLCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSLLCR 7 1 O15068-4;O15068-10;A2A3G7;O60423;O60423-3;O60423-1 O15068-4 MCF2L;ATP8B3 Guanine nucleotide exchange factor DBS;Phospholipid-transporting ATPase IK 1 RLS(1)LLCR 89.047 0.014262 0 16146 16826 14967 16417 21629 22828 22630 22433 22460 TRUE FALSE 14012.26519 16715.4689 22205.09126 20144.73077 21198.62522 23706.20793 20435.34608 17635.87752 19804.80439 0.707518485 0.844010805 1.121197202 1.017163834 1.070377915 1.196992784 1.031837815 0.890484813 1 14.27356283 4.42816587 4.249361547 1.036669211 0.731901648 0.674681457 0.080665827 0.12834066 4.811222886 0.023238759 0.073724983 26801.91773 -4.42816587 -0.304767563 RLS(ph)LPADIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 RLSLPADIR 9 1 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;E5RIY8;E5RIU4;H0YBX5;Q00537;Q00537-2;F5H6Z0;F8VQZ9;F8VZY6 E5RJM2;Q00537 CDK16;CDK17 Cyclin-dependent kinase 16;Cyclin-dependent kinase 17 1 RLS(1)LPADIR;RLS(1)LPADIR;RLS(1)LPADIR;RLS(1)LPADIR;RLS(1)LPADIR;RLS(1)LPADIR;RLS(1)LPADIR;RLS(1)LPADIR 117.93 0.00065622 9331494000 4618016 4736230 3517389 3838953 4894130 5498770 4711360 5219140 5847790 TRUE FALSE 4007733.485 4705117.393 5218410.085 4710645.953 4796746.388 5710311.24 4254453.032 4103067.526 5156470.928 0.777224102 0.912468519 1.012011928 0.913540679 0.93023823 1.107406852 0.825070691 0.795712336 1 22.2979526 RLS(ph)LPGLLSQVS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RLSLPGLLSQVSPR 14 1 Q96Q42;Q96Q42-3 Q96Q42 ALS2 Alsin 2 RLS(1)LPGLLS(0.004)QVS(0.996)PR;RLS(1)LPGLLS(0.002)QVS(0.998)PR;RLS(1)LPGLLSQVS(1)PR;RLS(1)LPGLLSQVS(1)PR 204.81 4.59E-08 716367000 477904 439308 300530 324705 452416 459772 438895 476857 435293 TRUE FALSE 414747.7755 436422.1568 445867.3132 398434.2331 443413.8067 477459.7264 396331.0305 374884.8415 383833.1574 1.080541812 1.137010048 1.161617501 1.038040162 1.155225384 1.243925172 1.032560691 0.976686965 1 18.55011982 2.016278963 24.51154454 0.99206192 1.134060839 0.587882437 0.05340603 122.4083274 184311.6495 0.021913788 0.014769222 103.8195072 -2.016278963 0.141998919 RLS(ph)LPMDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 RLSLPMDIR 9 1 Q07002;A0A0A0MSJ6;Q07002-3;D6R9B0;D6RA44;D6RGH0 Q07002 CDK18 Cyclin-dependent kinase 18 1 RLS(1)LPMDIR;RLS(1)LPMDIR;RLS(1)LPMDIR;RLS(1)LPMDIR;RLS(1)LPMDIR;RLS(1)LPMDIR;RLS(1)LPMDIR;RLS(1)LPMDIR;RLS(1)LPMDIR 97.86 0.0039233 3491180000 2109770 2280830 1604630 1666450 2400030 2718090 2474290 2497740 2677570 TRUE FALSE 1830958.549 2265847.078 2380634.435 2044842.943 2352274.099 2822656.681 2234333.737 1963617.738 2361030.725 0.7754912 0.959685553 1.008303031 0.866080615 0.996291185 1.195518826 0.946338272 0.831678181 1 21.17098539 4.736653323 5.552896703 0.96848262 0.768869643 0.294039248 0.09695037 0.211274827 26.05147545 0.02550079 0.160645674 54532.23822 -4.736653323 -0.199612977 RLS(ph)LQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RLSLQPR 7 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 RLS(1)LQPR;RLS(1)LQPR;RLS(1)LQPR 123.86 0.0025739 694540000 587533 813450 226615 211078 429452 505650 575357 506013 584122 TRUE FALSE 509889.0254 808106.3934 336206.772 259006.486 420906.7454 525102.6827 519558.9667 397806.0577 515067.7626 0.989945523 1.568932191 0.652742797 0.50285905 0.817187128 1.019482718 1.008719637 0.772337325 1 18.97440272 4.229397849 24.99996251 0.825122764 1.279438905 0.441927914 0.212419114 156.9667609 428276.6185 0.054663418 0.116386511 16958.90663 -4.229397849 0.454316141 RLS(ph)LTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSLTLR 7 1 Q00537;Q00537-2;F8VQZ9;F8VZY6;F8VUX2;F8W1S5 Q00537 CDK17 Cyclin-dependent kinase 17 1 RLS(0.998)LT(0.002)LR 128.6 0.0022918 324900000 136900 134750 71317 85108 109570 142130 113800 98350 120120 TRUE FALSE 118808.3181 133864.8184 105806.1397 104433.0722 107389.7714 147597.8331 102763.6935 77318.61786 105919.5504 1.121684502 1.263834843 0.998929275 0.985965969 1.013880544 1.393489988 0.970205152 0.729974944 1 16.69260938 2.003777976 24.99849719 0.847016958 1.123319226 0.388466111 0.139903855 96.35419361 637562.4816 0.057146507 0.038332394 100.8737059 -2.003777976 0.276302268 RLS(ph)MEIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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;RLS(1)MEIEK 147.39 0.00032956 2256940000 2466280 2428660 1503600 2020980 2361370 1941320 2923570 2969950 2798700 TRUE FALSE 2140354.849 2412705.973 2230745.989 2479874.398 2314383.357 2016003.837 2640042.631 2334849.305 2467840.874 0.867298565 0.977658648 0.903926186 1.004876134 0.937817094 0.816909979 1.069778307 0.946110152 1 21.23481794 2.220370085 24.99971681 0.995652441 0.924988041 0.309093274 0.06031533 348.9617141 479583.4094 0.023659361 0.015985276 166.1001731 -2.220370085 -0.070664399 RLS(ph)MSEVKDDNSATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLSMSEVKDDNSATK 15 2 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 RLS(0.998)MS(0.002)EVKDDNSATK;RLS(0.998)MS(0.002)EVKDDNSATK 224.59 5.81E-13 415350000 460900 352320 351310 354730 371930 333380 621330 680430 482070 TRUE FALSE 399990.8972 350005.5867 521204.6911 435276.8682 364529.3207 346205.3443 561073.5122 534925.3396 425080.2338 0.94097741 0.823387114 1.226132503 1.023987553 0.857554155 0.814447055 1.319923788 1.258410288 1 18.69737565 2.234292291 24.99976597 1.211749158 0.954114484 0.392658517 0.142862024 107.9184073 632072.6273 0.058747198 0.041185489 171.5111232 -2.234292291 -0.257634674 RLS(ph)NLPGYLQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSNLPGYLQK 11 1 Q6ZN28 Q6ZN28 MACC1 Metastasis-associated in colon cancer protein 1 1 RLS(1)NLPGYLQK 115.06 0.0003554 0 301060 312670 246550 271750 305260 286780 392950 455530 395230 TRUE FALSE 261274.1582 310616.0502 365782.4047 333454.9909 299185.9232 297812.6122 354841.7695 358118.4544 348506.3596 0.74969696 0.891277997 1.049571678 0.956811782 0.858480527 0.854539964 1.01817875 1.02758083 1 18.41082546 4.619907744 3.34986742 0.966755726 0.744245358 0.518067569 0.066218288 0.237581125 4.314910014 0.018448305 0.11070613 41678.0838 -4.619907744 -0.222510368 RLS(ph)NPCIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSNPCIQR 9 1 Q5RGS4;Q9HB21-2 Q5RGS4 PLEKHA1 Pleckstrin homology domain-containing family A member 1 1 RLS(1)NPCIQR 98.407 0.002362 0 134400 147490 90467 91954 113090 115340 159220 149460 95464 TRUE FALSE 116638.6995 146521.1285 134217.1438 112833.5611 110839.7303 119777.2044 143778.8689 117499.1421 84178.35467 1.385613914 1.740603378 1.594437719 1.340410627 1.316724836 1.422897904 1.7080266 1.395835575 1 16.36116169 1.273178503 3.827757324 0.958270146 1.500787572 0.537834121 0.145034481 0.18948378 4.463039511 0.272981204 0.038278726 18.75765324 -1.273178503 0.542517427 RLS(ph)NSSLCSIEEEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLSNSSLCSIEEEHR 15 1 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 RLS(0.991)NS(0.007)S(0.002)LCSIEEEHR;RLS(0.937)NS(0.058)S(0.005)LCSIEEEHR 183.27 2.41E-07 619970000 249460 290470 202567 247440 332010 339170 324670 354080 334650 TRUE FALSE 216493.2289 288561.8834 300529.0787 303625.0339 325403.6506 352218.0894 293183.5534 278362.7475 295088.0582 0.733656354 0.977883975 1.018438633 1.028930265 1.102734053 1.193603331 0.993545978 0.94332095 1 18.17078601 4.844208269 1.941355512 1.037298916 0.580469666 0.667309912 0.067672884 0.780734713 2.481117221 0.020460983 0.699661745 69856.7327 -4.844208269 -0.45682925 RLS(ph)NVS(ph)LTGVSTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSNVSLTGVSTIR 14 1 F8WBA3;Q15139;A0A494C0Q1 F8WBA3 PRKD1 Serine/threonine-protein kinase;Serine/threonine-protein kinase D1 2 RLS(1)NVS(0.98)LT(0.02)GVSTIR 136.66 1.72E-05 99812000 222670 252530 136860 178720 219260 171500 221430 247830 226560 TRUE FALSE 193243.5953 250871.1138 203045.9538 219301.1076 214897.155 178097.716 199955.7527 194833.4831 199776.3349 0.967299733 1.255759917 1.016366397 1.097733161 1.075688745 0.891485551 1.000898093 0.975258072 1 17.60802617 2.8830949 7.289855449 0.971642552 1.09104538 0.344224411 0.07901145 0.276063531 15.63076212 0.023433681 0.023475066 764.0027109 -2.8830949 0.119402828 RLS(ph)NVSLTGVSTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RLSNVSLTGVSTIR 14 1 F8WBA3;Q15139;A0A494C0Q1 F8WBA3 PRKD1 Serine/threonine-protein kinase;Serine/threonine-protein kinase D1 1 RLS(1)NVSLTGVSTIR;RLS(1)NVSLTGVSTIR;RLS(1)NVSLTGVSTIR;RLS(1)NVSLTGVSTIR 219.96 2.95E-12 2874170000 1609260 1657710 988590 1123570 1522690 1822300 1371850 1648170 1719920 TRUE FALSE 1396592.214 1646820.394 1466675.431 1378693.741 1492391.448 1892405.06 1238808.198 1295721.672 1516593.017 0.920874749 1.085868374 0.967085707 0.909072985 0.984042147 1.247800194 0.81683628 0.854363469 1 20.53240255 RLS(ph)PAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLSPAER 7 1 P41212 P41212 ETV6 Transcription factor ETV6 1 RLS(1)PAER;RLS(1)PAER 90.827 0.010322 866380000 243638 251204 158008 160540 221978 250150 198281 238838 218813 TRUE FALSE 211440.621 249553.8244 234421.1973 196993.0607 217561.0721 259773.4324 179051.7391 187764.3523 192945.1764 1.095858549 1.293392398 1.214962725 1.020979453 1.127579741 1.34635878 0.927992824 0.973148725 1 17.55783145 2.214455929 24.99999967 0.966690979 1.179741372 0.540003689 0.094003429 178.5494361 185179.8398 0.03856518 0.026015487 163.853578 -2.214455929 0.213050393 RLS(ph)PEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLSPEK 6 1 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 1 RLS(1)PEK;RLS(1)PEK 80.455 0.039488 1052340000 1425060 1328390 1119900 1438180 1201190 1333730 1380660 1734160 2663100 TRUE FALSE 1236734.71 1319663.719 1661487.386 1764740.75 1177288.669 1385039.456 1246763.806 1363323.379 2348271.352 0.526657496 0.561972413 0.707536369 0.751506315 0.501342687 0.589812355 0.530928338 0.580564669 1 21.1631677 1.237347875 24.98774632 1.000000489 0.594699089 0.72358576 0.078900255 17.21315543 354513.5177 0.12110591 0.020140212 17.27220863 -1.237347875 -0.4053014 RLS(ph)PEKQNCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RLSPEKQNCR 10 2 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 1 RLS(1)PEKQNCR;RLS(1)PEKQNCR;RLS(1)PEKQNCR;RLS(1)PEKQNCR 130.61 0.00014192 1130780000 898730 935240 484810 516000 950720 814020 985860 1161310 243960 TRUE FALSE 779960.5534 929096.3469 719265.7376 633165.6866 931802.5321 845335.8761 890251.4489 912972.8938 215119.3267 3.625711205 4.318981288 3.343566329 2.943323114 4.331561214 3.929613806 4.138407564 4.244030082 1 17.71477762 4.227497 24.96836903 3.5647747 3.972346356 0.036011348 0.986859688 854.7010839 1928902.406 0.247547377 0.523141763 16884.84195 -4.227497 0.407571656 RLS(ph)PISGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLSPISGSR 9 1 E9PQ01 E9PQ01 PCF11 1 RLS(1)PISGSR;RLS(1)PISGSR 98.902 0.0034913 553850000 227610 206240 110598 146960 178235 195539 158433 213680 204610 TRUE FALSE 197530.7618 204885.1959 164083.5627 180329.5141 174688.4722 203061.5119 143068.192 167986.1949 180421.2389 1.09483098 1.135593554 0.909447046 0.999491608 0.968225655 1.125485631 0.792967574 0.931077715 1 17.46100965 7.999999998 0.357102419 0.928951195 3.383951427 0.244546765 0.091500688 104.8466058 1.584793865 0.113837351 172.5487638 99999999.64 -7.999999998 2.455000232 RLS(ph)PPSSSAASSYSFSDLNSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RLSPPSSSAASSYSFSDLNSTR 22 1 P50402 P50402 EMD Emerin 1 RLS(0.936)PPS(0.019)S(0.019)S(0.026)AASSYSFSDLNSTR;RLS(0.879)PPS(0.064)S(0.018)S(0.039)AASSYSFSDLNSTR;RLS(0.996)PPS(0.002)S(0.001)S(0.001)AASSYSFSDLNSTR 165.4 7.88E-12 2550630000 454040 481674 376957 557083 749353 690159 472361 865789 745407 TRUE FALSE 394037.4636 478509.8518 559254.666 683577.2096 734442.3414 716709.8633 426551.5029 680646.7599 657285.8336 0.599491794 0.728008771 0.850854586 1.039999913 1.117386537 1.090408201 0.648958917 1.035541503 1 19.32616137 4.227323387 2.056731536 0.980757249 0.617240433 0.520016639 0.129981156 0.296531695 2.382856114 0.036935299 0.137490409 16878.09346 -4.227323387 -0.363516817 RLS(ph)PQPQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSPQPQIR 9 1 A0A0A0MR27;J3QT39;Q49A88-5;Q49A88-6;Q49A88;C9JU82;Q49A88-2;Q49A88-3 A0A0A0MR27 CCDC14 Coiled-coil domain-containing protein 14 1 RLS(1)PQPQIR 84.352 0.0095248 161430000 153010 156550 109790 125670 183550 141990 196780 200620 185950 TRUE FALSE 132789.3408 155521.6127 162884.8112 154205.2942 179897.7141 147452.4472 177696.3059 157718.9742 163967.2028 0.809853059 0.948492199 0.993398731 0.940464261 1.097156694 0.899280128 1.083730788 0.961893424 1 17.32304775 5.198966859 1.239649361 0.999042746 0.471176325 0.496867574 0.059156179 3.109408843 1.887439281 0.015269989 2.766241424 158112.7379 -5.198966859 -0.52786642 RLS(ph)PSAS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSPSASPPR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RLS(0.539)PS(0.52)AS(0.941)PPR 137.58 5.85E-05 2625200000 987120 830020 570390 644030 843700 868530 754150 920410 721570 TRUE FALSE 856669.591 824567.544 846232.5118 790266.8549 826912.0207 901942.9111 681012.6491 723587.4841 636266.8166 1.34639992 1.29594617 1.3299963 1.242036885 1.299630908 1.417554535 1.070325579 1.137239072 1 19.27927236 2.224758872 24.99985813 1.083412785 1.31646838 0.821606776 0.055345677 95.32287574 172662.1756 0.022085866 0.014977939 167.7872177 -2.224758872 0.233055596 RLS(ph)QPAGGLLDSITNIFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSQPAGGLLDSITNIFGR 19 1 Q676U5-3;Q676U5;Q676U5-4 Q676U5-3 ATG16L1 Autophagy-related protein 16-1 1 RLS(1)QPAGGLLDSITNIFGR 88.222 0.0015871 50694000 34930 47283 21011 22610 29727 24340 41818 44928 22543 TRUE FALSE 30313.912 46972.39486 31171.98988 27743.94607 29135.49086 25276.37555 37762.4968 35320.49683 19877.99222 1.524998685 2.363035177 1.568165916 1.395711688 1.465715981 1.271575885 1.899713833 1.776864405 1 14.27888442 4.035298513 24.5225327 1.516217078 1.949413863 0.263822555 0.317913147 193.1594453 134188.6161 0.07948831 0.165467017 10846.7221 -4.035298513 0.433196784 RLS(ph)QPESAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RLSQPESAEK 10 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 RLS(1)QPESAEK;RLS(1)QPESAEK;RLS(1)QPESAEK;RLS(1)QPESAEK;RLS(1)QPESAEK 205.31 1.81E-07 4119890000 6769540 4666380 3970430 4859470 5380500 4858430 6767870 7520300 7075440 TRUE FALSE 5874928.137 4635726.243 5890543.228 5962886.936 5273438.577 5045336.946 6111523.009 5912142.368 6238989.544 0.941647377 0.743025166 0.9441502 0.955745621 0.845239207 0.808678539 0.979569362 0.947612162 1 22.57288096 2.216304558 24.85962899 0.970030025 0.872891746 0.3444724 0.066595768 262.7072858 293437.0078 0.026919 0.018164881 164.5525278 -2.216304558 -0.097138279 RLS(ph)QRPTPEELEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSQRPTPEELEQR 14 2 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 RLS(0.999)QRPT(0.001)PEELEQR 211.06 2.28E-09 110900000 48214 55171 21169 25441 49106 36395 48988 48552 50707 TRUE FALSE 41842.39774 54808.57807 31406.39921 31217.76789 48128.88667 37795.1392 44237.1513 38169.53263 44712.47623 0.935810344 1.225800553 0.70240796 0.698189197 1.076408438 0.845292911 0.9893693 0.853666266 1 15.44838983 4.244959334 24.99974726 0.883361156 1.080805377 0.26387741 0.138852678 199.975929 781283.8506 0.033624656 0.084537389 17577.59017 -4.244959334 0.197444221 RLS(ph)QRPTTEELEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSQRPTTEELEQR 14 2 J3KP75;O75167-5;O75167-2;O75167;O75167-4 J3KP75 PHACTR2 Phosphatase and actin regulator;Phosphatase and actin regulator 2 1 RLS(0.993)QRPT(0.006)T(0.001)EELEQR 124.43 7.65E-05 362920000 190160 174580 80964 116990 130490 96266 153010 147850 121180 TRUE FALSE 165029.8742 173433.1725 120118.4612 143554.3676 127893.5043 99969.41531 138171.1138 116233.4281 106854.2384 1.544439197 1.623081826 1.124133801 1.343459742 1.196896877 0.935568086 1.293080328 1.087775551 1 16.70528461 4.350689944 0.780124989 1.099418718 1.766906918 0.620366053 0.136493786 1.051308812 0.725446962 0.055062701 0.559123493 22422.8052 -4.350689944 0.6674882 RLS(ph)QSDEDVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 RLSQSDEDVIR 11 1 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y917;Q9H7D7-3;Q9H7D7-4 A0A499FIZ0 WDR26 WD repeat-containing protein 26 1 RLS(1)QSDEDVIR;RLS(0.956)QS(0.044)DEDVIR;RLS(1)QSDEDVIR;RLS(1)QSDEDVIR;RLS(1)QSDEDVIR;RLS(1)QSDEDVIR;RLS(1)QSDEDVIR;RLS(0.992)QS(0.008)DEDVIR 233.02 1.12E-15 6710770000 3486290 3582130 2468767 2654968 3531730 3920200 3609246 3654383 4124340 TRUE FALSE 3025567.943 3558598.752 3662670.979 3257819.063 3461455.483 4071012.631 3259221.878 2872921.634 3636765.224 0.831939308 0.978506594 1.007123296 0.895801313 0.951795145 1.11940485 0.896187045 0.789966208 1 21.79422436 2.016515832 24.99986083 0.868909412 0.966772073 0.100556469 0.089393318 363.6981942 550524.5333 0.035660153 0.024035737 103.8761469 -2.016515832 0.097862662 RLS(ph)S(ph)LRAS(ph)TSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RLSSLRASTSK 11 2 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 3 RLS(1)S(1)LRAS(0.802)T(0.163)S(0.035)K;RLS(1)S(1)LRAS(0.518)T(0.442)S(0.041)K;RLS(1)S(1)LRAS(0.851)T(0.127)S(0.021)K;RLS(1)S(1)LRAS(0.838)T(0.138)S(0.024)K 82.007 0.013285 2601570000 852460 1358010 1967070 2126370 2457930 2252970 3064900 3123500 5482600 TRUE FALSE 739805.2511 1349089.143 2918351.631 2609194.808 2409022.002 2339643.214 2767666.47 2455563.832 4834453.274 0.153027697 0.279057231 0.603657015 0.539708352 0.498302883 0.483951976 0.572487997 0.507929996 1 22.20492131 -2 0.119871491 2.43710373 6.49E-11 0.575349051 0.143262314 195.8044167 2.095413238 79.56580801 5.39560476 0.01 2 -2.43710373 RLS(ph)S(ph)LRAST(ph)SK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSSLRASTSK 11 2 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 3 RLS(1)S(1)LRAS(0.131)T(0.785)S(0.085)K 104.88 0.0040663 464930000 234250 380660 555830 609200 685220 665090 931250 912730 1545000 TRUE FALSE 203293.269 378159.4194 824631.2471 747528.171 671585.4626 690676.4427 840937.5183 717549.7924 1362351.86 0.149222293 0.277578378 0.605299755 0.548704188 0.492960359 0.506973612 0.617268962 0.526699316 1 20.37766793 -2 0.123196514 2.561098524 4.09E-12 0.613684659 0.138195908 170.2998645 1.861762434 74.7927645 4.723368897 0.01 2 -2.561098524 RLS(ph)SAHNGGSAFGAAGYGGAQPTPPMPTRPVSFHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLSSAHNGGSAFGAAGYGGAQPTPPMPTRPVSFHER 36 2 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 RLS(0.333)S(0.333)AHNGGS(0.333)AFGAAGYGGAQPTPPMPTRPVSFHER;RLS(0.435)S(0.435)AHNGGS(0.131)AFGAAGYGGAQPTPPMPTRPVSFHER 108.99 9.23E-06 1211980000 225536 264455 57335 142044 288344 286142 289520 242676 223964 TRUE FALSE 195730.8462 262717.7777 85062.39777 174297.2612 282606.5185 297150.0679 261442.395 190781.6259 197487.2311 0.991106337 1.330302604 0.430723532 0.882574839 1.4310116 1.504654586 1.323844552 0.966045374 1 17.59139985 3.260430932 24.80056914 1.229110164 0.904653267 0.274538201 0.271028191 333.0835943 377708.5724 0.083604794 0.107837667 1821.507366 -3.260430932 -0.324456897 RLS(ph)SAS(ph)TGKPPLSVEDDFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSSASTGKPPLSVEDDFEK 20 2 O75152;A0A1B0GTU1;A0A494C0C4 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 2 RLS(0.994)S(0.008)AS(0.979)T(0.019)GKPPLSVEDDFEK 194.19 2.48E-18 50557000 54340 51039 58989 56107 64478 60488 89863 107040 106360 TRUE FALSE 47158.83132 50703.72145 87516.27771 68846.95189 63195.01395 62815.0125 81148.10009 84150.32899 93786.24197 0.502833148 0.540630698 0.933146226 0.734083704 0.673819663 0.66976788 0.865245247 0.897256647 1 16.51708868 -2 0.074380442 2.524144518 1.10E-06 0.543921206 0.11208994 441.9137794 3.13873034 122.9287826 22.57664981 0.01 2 -2.524143419 RLS(ph)SASTGKPPLSVEDDFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RLSSASTGKPPLSVEDDFEK 20 2 O75152;A0A1B0GTU1;A0A494C0C4 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 RLS(0.791)S(0.206)AS(0.003)T(0.001)GKPPLSVEDDFEK;RLS(0.531)S(0.467)AS(0.001)TGKPPLSVEDDFEK;RLS(0.874)S(0.124)AS(0.002)TGKPPLSVEDDFEK 190.5 9.41E-18 1603120000 663968 559866 512620 558283 588353 525845 1010140 1106480 1034240 TRUE FALSE 576222.9465 556188.2034 760524.7466 685049.688 576645.9264 546074.5974 912176.7783 869867.8626 911973.3254 0.631841887 0.609873324 0.833933105 0.751172944 0.632305694 0.598783519 1.000223091 0.953830379 1 19.7986321 2.231229671 24.99999217 0.978904065 0.681864381 0.803293793 0.071879772 75.98320605 259115.1412 0.030900306 0.021307371 170.3058912 -2.231229671 -0.297039684 RLS(ph)SGQNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSSGQNK 8 1 P49454 P49454 CENPF Centromere protein F 1 RLS(0.969)S(0.031)GQNK 52.49 0.087335 89022000 81606 83658 56218 63296 67243 92429 71904 83624 85313 TRUE FALSE 70821.56034 83108.44509 83405.21284 77668.32422 65904.99586 95984.80344 64930.76115 65741.65836 75227.39433 0.941433117 1.104763043 1.108707986 1.032447354 0.876077079 1.275928859 0.863126548 0.873905828 1 16.1989705 RLS(ph)STSLASGHSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RLSSTSLASGHSVR 14 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3;M0QZ82 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 RLS(0.929)S(0.068)T(0.002)SLASGHSVR;RLS(0.651)S(0.339)T(0.009)SLASGHSVR;RLS(0.766)S(0.217)T(0.018)SLASGHSVR;RLS(0.523)S(0.459)T(0.019)SLASGHSVR;RLS(0.77)S(0.163)T(0.066)S(0.001)LASGHSVR 212.78 1.20E-09 11578100000 2384434 2532880 1089558 1658604 2848970 2858470 2426330 2626370 2395730 TRUE FALSE 2069325.006 2516241.345 1616471.893 2035215.388 2792281.071 2968437.191 2191024.89 2064741.214 2112509.529 0.979557714 1.19111479 0.765190344 0.963411223 1.321783894 1.40517103 1.037166867 0.977387882 1 21.01052642 5.042815349 13.65710928 1.076740771 0.606439698 0.02888527 0.185060796 1108610.579 11560127.57 0.048317847 12585299.45 110360.9293 -5.042815349 -0.470301073 RLS(ph)TIFEECDEELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RLSTIFEECDEELER 15 1 Q5T5P2;Q5T5P2-3;A0A0U1RRK8 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 RLS(0.95)T(0.05)IFEECDEELER;RLS(0.999)T(0.001)IFEECDEELER;RLS(0.987)T(0.013)IFEECDEELER;RLS(0.681)T(0.319)IFEECDEELER;RLS(0.86)T(0.14)IFEECDEELER 288.25 5.79E-35 1699675000 680165 484143 387295 409347 457431 398761 607892 700592 684161 TRUE FALSE 590279.4719 480962.6328 574592.1574 502295.4928 448329.018 414101.5937 548938.7274 550775.8528 603280.266 0.978449827 0.797245758 0.952446466 0.8326072 0.743152136 0.686416608 0.909923229 0.912968456 1 19.20246887 1.636165152 2.135489808 0.987104072 0.832550682 0.254449075 0.088875671 0.448601626 4.151972742 0.110629892 0.025660469 43.26783369 -1.636165152 -0.15455339 RLS(ph)TSPDVIQGHQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RLSTSPDVIQGHQPR 15 1 Q9Y385 Q9Y385 UBE2J1 Ubiquitin-conjugating enzyme E2 J1 1 RLS(0.972)T(0.027)S(0.001)PDVIQGHQPR;RLS(0.889)T(0.107)S(0.004)PDVIQGHQPR;RLS(0.706)T(0.114)S(0.18)PDVIQGHQPR 243.16 3.56E-18 2633810000 592296 507551 369880 530193 755136 781350 469108 829142 683457 TRUE FALSE 514022.5829 504216.8641 548755.2052 650581.4241 740110.271 811409.0401 423613.9784 651836.4357 602659.4921 0.852923732 0.836652987 0.910555981 1.079517427 1.228073698 1.346380586 0.702907668 1.081599882 1 19.20098357 3.864891184 3.574040508 1.068578909 0.849601698 0.265599576 0.16394604 0.357100672 8.250542483 0.046332684 0.086975142 7326.409418 -3.864891184 -0.218977212 RLS(ph)VELTSSLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RLSVELTSSLFR 12 1 A0A2R8Y804;A0A2R8Y543;A0A2R8Y5C3;A0A2R8Y750;A0A2R8Y5Z1;B4DGU4;A0A2R8YCH5;A0A2R8Y5A3;P35222;A0A2R8Y6G0;A0A2R8Y7Z0;A0A2R8YG06 A0A2R8Y804 CTNNB1 Catenin beta-1 1 RLS(1)VELTSSLFR;RLS(1)VELTSSLFR;RLS(1)VELTSSLFR;RLS(1)VELTSSLFR;RLS(1)VELTSSLFR 241.8 1.77E-16 1047614000 351691 304042 232657 368497 378569 469465 242016 424841 386682 TRUE FALSE 305214.1433 302044.7281 345170.7034 452169.876 371036.2176 487525.6223 218545.3256 333992.0583 340968.8945 0.895137792 0.885842471 1.012323144 1.326132334 1.088182012 1.429824334 0.64095385 0.979538203 1 18.37928061 2.224289844 24.99997735 0.88590003 1.101127629 0.242063076 0.193588294 381.3622549 668076.7329 0.080986312 0.054891014 167.6061091 -2.224289844 0.2152276 RLS(ph)YNTASNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RLSYNTASNK 10 1 P49207 P49207 RPL34 60S ribosomal protein L34 1 RLS(0.575)Y(0.002)NT(0.423)AS(0.001)NK;RLS(0.986)Y(0.003)NT(0.011)ASNK;RLS(0.995)YNT(0.005)ASNK;RLS(1)YNTASNK;RLS(0.964)YNT(0.035)AS(0.001)NK 151.08 2.07E-05 2503927000 3390740 3120460 1045800 3217420 2022940 976224 3471720 3902190 3947830 TRUE FALSE 2942645.118 3099961.493 1551552.378 3947984.386 1982687.452 1013779.969 3135033.129 3067737.035 3481122.035 0.845315128 0.890506412 0.445704679 1.134112607 0.569554136 0.291222186 0.90058122 0.881249495 1 21.73112096 2.040889373 24.99987802 0.919776888 0.69837194 0.175663466 0.236291648 264.417094 161664.2715 0.096274352 0.064908083 109.8725927 -2.040889373 -0.221404948 RLSEDYGVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RLSEDYGVLK 10 1 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ;;;;; 180.19 3.25E-06 3801430000 6805480 5982410 3263870 3628350 5481390 5019540 6674310 7159610 2796670 FALSE TRUE 5906118.575 5943111.155 4842288.449 4452222.323 5372321.063 5212644.952 6027036.443 5628583.118 2466050.859 2.394970304 2.409971041 1.963580123 1.805405719 2.178511868 2.113762145 2.444003303 2.282427833 1 21.23377112 1.236110536 24.99842997 0.999998431 2.198086762 0.77646348 0.202191387 33.84890051 345288.0597 0.352112906 0.053579934 17.2230688 -1.236110536 1.198088331 RLSELLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RLSELLR 7 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;; 179.21 0.0011295 7771790000 4098915 3842482 2267643 2804479 3916628 4286797 3511853 4114252 2996770 FALSE TRUE 3557232.997 3817240.483 3364282.74 3441278.821 3838694.766 4451712.855 3171274.037 3234451.227 2642495.265 1.346164379 1.444559063 1.273146175 1.302283817 1.452678011 1.684662567 1.200105854 1.224014011 1 21.33346946 1.590531315 1.779515134 1.008228516 1.403263357 0.507966046 0.127000994 0.372683688 2.076696522 0.217889637 0.03754607 38.95213934 -1.590531315 0.395034841 RLSESQLS(ph)FR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSESQLSFR 10 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 1 RLS(0.286)ES(0.325)QLS(0.389)FR 107.71 0.0023809 278060000 358790 295210 214730 211730 276510 389810 362000 332870 372410 TRUE FALSE 311374.9924 293270.7461 318574.1462 259806.5326 271007.992 404806.2429 326893.2957 261688.3409 328384.1141 0.94820358 0.89307227 0.970126546 0.791166568 0.825277413 1.23272176 0.995460139 0.796897078 1 18.32502481 RLSNS(ph)SLCSIEEEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLSNSSLCSIEEEHR 15 1 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 RLS(0.125)NS(0.657)S(0.217)LCS(0.001)IEEEHR;RLS(0.331)NS(0.573)S(0.096)LCSIEEEHR 124.73 5.81E-05 378130000 88245 79098 62292 69300 105910 103466 107115 112466 93320 TRUE FALSE 76583.19967 78578.40003 92416.61955 85035.62418 103802.5982 107446.404 96727.00379 88416.02111 82287.81591 0.930674837 0.954921444 1.123089956 1.03339265 1.26145769 1.305738921 1.17547176 1.074472814 1 16.32839121 4.226731919 1.50945779 1.151641786 0.907976185 0.429127679 0.093981717 0.534690515 2.074829531 0.030138688 0.148050508 16855.12274 -4.226731919 -0.243665601 RLSPS(ph)AS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLSPSASPPR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RLS(0.296)PS(0.841)AS(0.863)PPR;RLS(0.269)PS(0.737)AS(0.994)PPR 132.9 0.00014125 2613850000 1465560 1321130 831000 918220 1335500 1210340 1128150 1367150 1183400 TRUE FALSE 1271882.533 1312451.41 1232874.38 1126715.885 1308926.163 1256902.563 1018742.187 1074795.612 1043499.8 1.218862268 1.257739973 1.181480226 1.079747102 1.25436168 1.20450676 0.976274443 1.0299912 1 19.99299889 2.243008333 24.9989716 1.006825998 1.198337433 0.771956487 0.050542799 52.23237933 293581.0243 0.019915951 0.014888745 174.9880264 -2.243008333 0.191511435 RLSQPESAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RLSQPESAEK 10 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 ;; 108.56 0.0052034 158167000 408960 329141 291219 259112 286380 268920 342139 419260 257504 FALSE TRUE 354914.8998 326978.8511 432053.4825 317947.3399 280681.5983 279265.5264 308958.4124 329604.5117 227062.1705 1.563073669 1.440041071 1.90279817 1.400265571 1.236144258 1.229907764 1.360677614 1.45160469 1 17.79272784 3.4902812 22.89708429 1.289606678 1.621737045 0.526835643 0.162288778 173.5628655 301982.6187 0.044679277 0.062882628 3092.297008 -3.4902812 0.332130367 RLSS(ph)AS(ph)TGKPPLSVEDDFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSSASTGKPPLSVEDDFEK 20 2 O75152;A0A1B0GTU1;A0A494C0C4 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 2 RLS(0.475)S(0.523)AS(0.525)T(0.476)GKPPLS(0.001)VEDDFEK 49.618 0.078213 90261000 22217 17501 17534 15497 21622 19909 28235 32347 28606 TRUE FALSE 19280.96716 17386.03478 26013.50105 19015.83071 21191.7645 20674.91211 25496.77405 25429.84577 25224.23127 0.764382746 0.689259252 1.031290142 0.753871565 0.840135197 0.819644884 1.0108048 1.008151468 1 14.62252268 2.239478211 24.70206341 1.006887524 0.818650318 0.508674365 0.087955778 16.58113016 446397.0035 0.033310308 0.024280572 173.571418 -2.239478211 -0.188237205 TSFGS(ph)LTDSSEEALEGMVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TSFGSLTDSSEEALEGMVR 19 0 G3V160;Q969H4-2;Q969H4 G3V160 CNKSR1 Connector enhancer of kinase suppressor of ras 1 1 TS(0.001)FGS(0.999)LTDSSEEALEGMVR;T(0.015)S(0.015)FGS(0.95)LT(0.019)DS(0.001)S(0.001)EEALEGMVR;TSFGS(1)LTDSSEEALEGMVR;TSFGS(1)LTDSSEEALEGMVR 198.42 7.78E-16 68147000 62957 83569 66225 87503 125364 130969 129280 145260 135723 TRUE FALSE 54637.07294 83020.02974 98251.63151 107371.8935 122869.5017 136007.4622 116742.4455 114197.2794 119677.9816 0.456534044 0.693695103 0.820966649 0.897173333 1.026667563 1.136445154 0.975471377 0.954204591 1 16.86879822 4.547906799 0.917850124 1.012167439 0.264353317 0.918539208 0.05497624 0.477996542 0.39469961 0.021778772 0.337635153 35310.73834 -4.547906799 -0.747814122 down RLSS(ph)LRAST(ph)SK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSSLRASTSK 11 2 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 RLS(0.487)S(0.606)LRAS(0.2)T(0.586)S(0.121)K 62.915 0.086025 2084300000 507140 1904400 1814200 2129800 3171100 2601400 3562200 3795500 2225800 TRUE FALSE 440120.1641 1891889.871 2691553.188 2613403.642 3108001.314 2701477.541 3216738.392 2983861.862 1962668.46 0.224245803 0.963937573 1.371374353 1.331556346 1.583559006 1.376430914 1.638961678 1.520308663 1 20.90438506 4.634861592 1.778434593 1.439306261 5.31E-17 0.822987637 0.175337752 0.269969859 1.023171974 0.046277724 0.611286338 43138.15749 -4.634861592 -1.439306261 RLSS(ph)T(ph)SSEETQLFHIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSSTSSEETQLFHIPR 17 1 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 2 RLS(0.351)S(0.524)T(0.541)S(0.49)S(0.091)EET(0.003)QLFHIPR 91.589 0.0030453 95149000 78574 79225 53724 72646 86155 114110 61792 101200 71638 TRUE FALSE 68190.24682 78704.56576 79705.1061 89141.38462 84440.68406 118499.8855 55799.42135 79559.16754 63169.03725 1.079488461 1.245935813 1.261774907 1.411156296 1.336741665 1.875917233 0.883334997 1.259464621 1 15.94692996 RLSSTS(ph)S(ph)EETQLFHIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSSTSSEETQLFHIPR 17 1 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 2 RLS(0.283)S(0.25)T(0.313)S(0.429)S(0.68)EET(0.044)QLFHIPR 109.85 0.0020534 113340000 98177 89440 60104 85601 106380 145080 75744 120980 85851 TRUE FALSE 85202.6607 88852.46275 89170.49544 105038.0154 104263.2461 150661.3215 68398.35854 95109.36847 75701.79258 1.125503872 1.17371676 1.177917885 1.387523489 1.377288999 1.990194899 0.903523631 1.256368776 1 16.20803984 RLST(ph)EHSSVSEYHPADGYAFSSNIYTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLSTEHSSVSEYHPADGYAFSSNIYTR 27 1 A0A2R8Y4W2;A0A2R8YE63;Q12929-2;Q12929 A0A2R8Y4W2 EPS8 Epidermal growth factor receptor kinase substrate 8 1 RLS(0.48)T(0.52)EHSSVSEYHPADGYAFSSNIYTR 290.08 1.37E-70 504590000 77989 109840 24489 63812 151010 147600 103390 131770 126260 TRUE FALSE 67682.55605 109118.4538 36331.96231 78301.48991 148005.1964 153278.2675 93363.25371 103592.0109 111333.6866 0.607925221 0.980102762 0.326333955 0.703304564 1.329383773 1.376746537 0.838589438 0.930464211 1 16.76453065 3.363593493 7.762524821 1.068388803 0.646979189 0.485911353 0.224946703 0.227096116 14.56346522 0.06823377 0.088140041 2309.901672 -3.363593493 -0.421409614 RLSYNTASNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RLSYNTASNK 10 1 P49207 P49207 RPL34 60S ribosomal protein L34 0 ; 135.08 0.00024622 1739910000 2275370 2849800 1661770 1789620 2592000 2267580 3161400 3005800 2186350 FALSE TRUE 1974674.089 2831079.476 2465407.53 2195980.574 2540424.271 2354815.27 2854807.915 2363033.061 1927882.194 1.024271139 1.468491947 1.278816485 1.139063674 1.31772796 1.221451849 1.48079998 1.225714449 1 20.87858547 1.273623818 4.492899879 0.985273866 1.282800778 0.282662173 0.136163188 0.217858686 8.373313316 0.188093379 0.031749461 18.77689675 -1.273623818 0.297526911 RLT(ph)VMS(ph)LQESGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RLTVMSLQESGLK 13 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 2 RLT(1)VMS(1)LQESGLK;RLT(1)VMS(1)LQESGLK;RLT(1)VMS(1)LQESGLK;RLT(1)VMS(1)LQESGLK 67.456 0.022222 3697610000 2294190 2550920 1122830 2117790 3106740 3668130 2408330 2465580 2075820 TRUE FALSE 1991006.979 2534162.839 1665834.344 2598666.588 3044921.952 3809245.335 2174770.527 1938334.904 1830418.924 1.087732951 1.384471503 0.910083654 1.419711386 1.663510966 2.081078426 1.188127209 1.058956984 1 20.80374244 2.011025415 24.99982035 1.060645243 1.428614548 0.222019252 0.31121064 339.7570597 770386.7221 0.137180827 0.092395606 102.5711949 -2.011025415 0.367969305 RLTAEDLFEAR ddPTM_MDA-MB-175_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 ; 147.33 5.67E-05 289950000 442530 460810 209624 228460 450180 575520 377690 398590 197103 FALSE TRUE 384048.5393 457782.9088 310998.8676 280335.3348 441222.2988 597660.6268 341061.6819 313354.6303 173801.7079 2.209693702 2.633937919 1.789389019 1.61296076 2.538653412 3.438750022 1.962360935 1.802943332 1 17.40708273 4.243414253 24.99484148 2.052729872 2.421815753 0.061824156 0.640200561 427.0058326 2198886.468 0.171141245 0.423448007 17515.16581 -4.243414253 0.369085881 RLTELETAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLTELETAVR 10 1 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18;F8VRV7 Q13561 DCTN2 Dynactin subunit 2 0 132.56 0.0003532 145230000 120630 114830 68887 83504 107200 129520 122570 132230 72876 FALSE TRUE 104688.4399 114075.6742 102200.9836 102464.8595 105066.9297 134502.7182 110683.1803 103953.6435 64260.6823 1.6291212 1.775201727 1.590412363 1.594518698 1.635011114 2.093079522 1.722409042 1.617686582 1 15.97164868 1.217849646 3.017150872 0.840389765 1.72124894 0.703622718 0.145622287 0.246132567 2.710246091 0.543686148 0.039063949 16.51389982 -1.217849646 0.880859175 RLTLEDLEDSWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RLTLEDLEDSWDR 13 1 Q6P2Q9;I3L3Z8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;; 202.13 1.54E-07 509320000 732330 665010 320149 349411 624520 656270 589050 725930 267008 FALSE TRUE 635550.735 660641.5055 474974.1272 428750.108 612093.2739 681517.1316 531924.0217 570695.5187 235442.6184 2.699386964 2.805955481 2.017366824 1.82103865 2.599755635 2.894620932 2.259251215 2.423926146 1 17.84501597 1.238076084 8.626104928 0.987342615 2.429814885 0.641697517 0.338120866 0.060729903 51.78409517 0.504739121 0.087341718 17.30119433 -1.238076084 1.44247227 RLVEVDSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RLVEVDSSR 9 1 Q03252 Q03252 LMNB2 Lamin-B2 0 86.014 0.024188 0 120390 117410 65710 75474 145490 144830 98918 108330 79666 FALSE TRUE 104480.1565 116638.726 97487.57579 92611.52525 142595.0336 150401.7038 89324.94759 85164.47253 70247.97624 1.48730486 1.660385569 1.387763477 1.318351506 2.02988102 2.141011199 1.271566134 1.212340584 1 16.10016904 2.021382986 24.98438621 1.15752211 1.66179395 0.463055416 0.261714302 222.2444066 259674.5307 0.115562125 0.07790492 105.0468383 -2.021382986 0.50427184 RMDEISDHAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RMDEISDHAK 10 1 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 169.52 2.99E-06 579210000 1122520 1137660 374660 808550 1172550 1030700 1243720 1421480 945690 FALSE TRUE 974176.1379 1130186.637 555846.8292 992143.6354 1149218.549 1070351.696 1123104.226 1117507.564 833891.6055 1.168228738 1.355316002 0.666569642 1.1897753 1.378139007 1.283562143 1.346822799 1.340111301 1 19.66950034 3.481816973 24.96501881 1.284904326 1.06516702 0.183367316 0.197325087 307.3286708 1633931.314 0.055181388 0.073186366 3032.612866 -3.481816973 -0.219737306 RMEDEGGFPVPQENGQPES(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RMEDEGGFPVPQENGQPESPR 21 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR 194.89 1.26E-18 4575470000 1950740 1840020 1349800 1602630 2006970 2068780 1959930 2278500 1983850 TRUE FALSE 1692944.766 1827932.787 2002567.795 1966531.636 1967035.224 2148367.305 1769856.29 1791260.506 1749321.513 0.967772221 1.044938151 1.144768289 1.124168211 1.124456087 1.228114609 1.01173871 1.023974434 1 20.73836404 RMEDEGGFPVPQENGQPES(ph)PRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RMEDEGGFPVPQENGQPESPRR 22 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RMEDEGGFPVPQENGQPES(1)PRR;RMEDEGGFPVPQENGQPES(1)PRR;RMEDEGGFPVPQENGQPES(1)PRR 163.49 7.84E-12 1462300000 368710 362108 265808 285603 415120 408630 402300 441430 285138 TRUE FALSE 319984.0393 359729.2887 394353.6379 350453.5263 406859.9242 424350.2605 363285.0079 347033.6297 251429.3105 1.272660052 1.430737284 1.568447359 1.393845155 1.618188124 1.687751757 1.444879307 1.380243334 1 17.93979332 1.172176938 1.99677825 0.775607796 1.497703318 0.627986849 0.117512769 0.637046236 2.133597386 0.911876352 0.032914604 14.86541156 -1.172176938 0.722095522 RMEEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 122.19 0.0069993 632000000 503934 456120 324652 333387 385725 507300 430332 490493 429730 FALSE TRUE 437337.8451 453123.7177 481654.7931 409087.6139 378049.8272 526816.1593 388598.4689 385604.889 378927.809 1.154145552 1.195804866 1.27109909 1.079592482 0.997682984 1.390281069 1.025521114 1.017620982 1 18.5315635 2.043927101 24.99987024 1.013518614 1.176075098 0.364836665 0.103878214 140.1269861 79748.73871 0.041534292 0.028002391 110.6438046 -2.043927101 0.162556483 RMEEEQHHWDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RMEEEQHHWDDR 12 1 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 ;;; 150.49 2.77E-05 940737000 314835 257073 191143 214980 254934 282145 255378 263332 243961 FALSE TRUE 273228.7571 255384.2705 283580.3941 263794.4948 249861.3122 292999.3007 230611.4809 207020.5011 215120.2085 1.270121292 1.187170059 1.318241536 1.226265522 1.161496235 1.362025924 1.072012167 0.962347994 1 17.71478353 2.056774441 5.571556564 0.98876877 1.247995188 0.797416904 0.058862907 0.073710469 4.762990911 0.023530074 0.015418449 113.9657731 -2.056774441 0.259226418 RMEEEQHHWDDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RMEEEQHHWDDRR 13 2 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 ;; 82.102 0.0079658 1285670000 889340 750400 330071 381443 533870 666580 698150 747460 263362 FALSE TRUE 771811.4657 745470.573 489694.4396 468055.4631 523247.0315 692223.7639 630443.5205 587621.4957 232227.6444 3.323512443 3.21008541 2.108682801 2.015502781 2.253164273 2.980798284 2.71476517 2.530368412 1 17.8251802 4.248777781 22.54862775 2.302049298 3.266801694 0.39518232 0.527764553 67.86580594 149764.0444 0.133512185 0.342841788 17732.81899 -4.248777781 0.964752396 RMEEETKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RMEEETKR 8 2 F5GWE5;Q00169 F5GWE5 PITPNA Phosphatidylinositol transfer protein alpha isoform 0 99.815 0.0036816 40837000 69972 68558 43524 43259 54730 57694 75102 74852 45577 FALSE TRUE 60725.02291 68107.63798 64572.35198 53081.61712 53640.98008 59913.52551 67818.6196 58845.4823 40188.93898 1.510988457 1.694686143 1.606719501 1.320801655 1.334719986 1.490796399 1.687494652 1.464220848 1 15.29451087 1.247193743 4.807417977 0.96698549 1.519224846 0.626652336 0.125304697 0.123784996 6.703650488 0.226810138 0.033900667 17.66825841 -1.247193743 0.552239356 RMEELHNQEMQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RMEELHNQEMQK 12 1 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;;; 142.1 2.91E-05 394962000 392858 295742 194997.3 233871 286300 263260 296092 382912 197332 FALSE TRUE 340940.8199 293799.2513 289298.6465 286974.985 280603.1901 273387.7826 267377.0434 301029.2486 174003.6358 1.959389058 1.688466164 1.662601159 1.649247062 1.612628316 1.571161323 1.536617567 1.730017004 1 17.40875793 1.235211087 24.97073324 0.99999906 1.66607624 0.772400606 0.115249769 45.20161713 336921.1863 0.19762478 0.028055357 17.18743572 -1.235211087 0.66607718 RMEELHNQEVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RMEELHNQEVQK 12 1 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;;;; 149.23 4.36E-05 2677960000 1835314 1624170 1052991 1244769 1510378 1390973 1816151 1867852 1383615 FALSE TRUE 1592772.605 1613500.72 1562220.97 1527412.827 1480324.433 1444484.631 1640020.956 1468426.385 1220045.611 1.305502508 1.322492131 1.28046112 1.251930922 1.213335321 1.183959533 1.344229216 1.203583188 1 20.21850365 1.277384529 3.258465835 0.968507152 1.26795148 0.756957734 0.048243504 0.153633605 2.270365671 0.110886373 0.012904529 18.9401986 -1.277384529 0.299444328 RMFIVIS(ph)EPDMIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RMFIVISEPDMIK 13 1 C9JS68;A0A498U6I9;A0A0A0MSK3;Q53F23;A0A0C4DH47;P24557-4;P24557-2;P24557;P24557-3 C9JS68 TBXAS1 Thromboxane-A synthase 1 RMFIVIS(1)EPDMIK 40.066 0.085497 17668000 15084 14370 16439 14887 15149 19240 20339 23896 25349 TRUE FALSE 13090.61118 14275.60252 24388.95539 18267.32088 14847.56454 19980.17525 18366.52691 18786.02636 22352.2701 0.585650188 0.63866455 1.091117604 0.817246785 0.664253093 0.893876781 0.821685083 0.840452727 1 14.44813374 4.446431147 24.34654372 0.860823962 0.598903661 0.480897851 0.113607116 108.4578789 86039.75001 0.027776477 0.073491636 27953.17522 -4.446431147 -0.261920301 RMGESDDSILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RMGESDDSILR 11 1 Q8WVC2;P63220 Q8WVC2 RPS21 40S ribosomal protein S21 0 ;;; 196.02 9.93E-08 1774350000 1563610 1587230 806420 857130 1473620 1727120 1486070 1430210 489524 FALSE TRUE 1356974.977 1576803.382 1196407.409 1051754.467 1444297.845 1793563.424 1341951.16 1124370.721 431653.0304 3.143670683 3.652941763 2.771687733 2.436573806 3.345969432 4.155104442 3.108865375 2.604802103 1 18.71951259 1.237051431 2.098707866 0.306511828 3.235571267 0.699361065 0.461318612 0.436996632 1.904232518 2.48050197 0.133247182 17.26042286 -1.237051431 2.929059439 RMHS(ph)QPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RMHSQPR 7 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 RMHS(1)QPR;RMHS(1)QPR 114.39 0.0036229 869510000 592510 592310 338300 333130 397460 623880 514180 538040 373520 TRUE FALSE 514208.3023 588419.0766 501903.0115 408772.2581 389551.3236 647881.0673 464314.9027 422984.333 329362.8911 1.561221122 1.786537259 1.523860232 1.241099921 1.182741997 1.967073659 1.409736541 1.284250122 1 18.32931849 1.482736482 2.094199563 0.978524176 1.529565699 0.363500272 0.229405798 0.490553036 3.534240834 0.453717665 0.065632093 30.39040458 -1.482736482 0.551041523 RMIDVQNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RMIDVQNR 8 1 Q13630;E9PP14;A0A0J9YX13;E9PKL9 Q13630 TSTA3 GDP-L-fucose synthase 0 80.455 0.040736 212820000 232080 279750 103030 141300 307490 377540 248230 265250 75109 FALSE TRUE 201410.04 277912.3038 152855.6526 173384.3246 301371.5506 392064.2081 224156.6928 208528.3517 66229.69958 3.0410834 4.196188501 2.307962343 2.617924069 4.550398877 5.919764253 3.384534344 3.148562548 1 16.01519069 5.060406122 14.60564503 3.439929417 0.000175963 0.005561323 1.331369893 5081279.587 32157333.13 0.335492311 506060041.5 114922.7797 -5.060406122 -3.439753454 RMKVT(ph)NEDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RMKVTNEDFK 10 2 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 1 RMKVT(1)NEDFK 71.349 0.082403 795460000 663890 783250 882490 638350 398060 741660 546570 410930 574590 TRUE FALSE 576155.2544 778104.7792 1309265.116 783297.1241 390139.3848 770192.1401 493563.7255 323055.8174 506662.6248 1.1371576 1.535745368 2.584096501 1.545993499 0.770018086 1.520128193 0.974146703 0.637615252 1 18.95066588 3.373709539 5.343089097 0.967620828 1.781214007 0.426259407 0.419139606 0.194645568 8.519941423 0.125990602 0.163666003 2364.337873 -3.373709539 0.813593179 RMNS(ph)TGGQTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RMNSTGGQTPR 11 1 Q96ST2;Q96ST2-3;Q96ST2-2;A0A1B0GW95 Q96ST2 IWS1 Protein IWS1 homolog 1 RMNS(0.97)T(0.03)GGQTPR 70.889 0.030952 138280000 90415 97945 60172 70853 119730 129220 123580 116200 68508 TRUE FALSE 78466.42867 97301.59285 89271.38046 86941.25657 117347.6072 134191.177 111595.2306 91351.53427 60409.06228 1.298918171 1.610711856 1.477781265 1.439208842 1.942549724 2.221374938 1.847325987 1.512215731 1 15.88247737 3.27573297 24.91127892 1.717165336 1.469167856 0.127221848 0.321159229 388.4956952 260350.1766 0.099879066 0.12894002 1886.830857 -3.27573297 -0.247997481 RMS(ph)ADMSEIEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RMSADMSEIEAR 12 1 O43318;O43318-3;Q9UG54;O43318-2;O43318-4 O43318 MAP3K7;DKFZp586F0420 Mitogen-activated protein kinase kinase kinase 7 1 RMS(0.997)ADMS(0.003)EIEAR;RMS(1)ADMSEIEAR;RMS(1)ADMSEIEAR 195.89 1.30E-07 1230060000 1304410 1373200 918690 1094650 1484760 1633270 1410560 1515800 1401980 TRUE FALSE 1132028.914 1364179.359 1362971.557 1343207.013 1455216.181 1696102.954 1273764.108 1191657.966 1236239.522 0.915703546 1.10349114 1.102514143 1.08652651 1.177131256 1.371985707 1.030353816 0.963937769 1 20.23752686 2.013739996 24.99989854 0.984718765 1.131002473 0.236139989 0.110938595 310.9721141 565811.176 0.046820828 0.031550019 103.2143295 -2.013739996 0.146283708 RMS(ph)DEFVDSFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RMSDEFVDSFK 11 1 Q92934;F5H1R6;F5H3B1 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 RMS(1)DEFVDSFK;RMS(1)DEFVDSFK;RMS(1)DEFVDSFK 184.87 2.89E-06 549521000 1854230 714240 642900 721280 712340 813000 978120 1010040 1380060 TRUE FALSE 1609188.807 709548.1104 953808.5904 885057.6481 698165.8277 844276.6361 883262.0729 794050.8061 1216910.879 1.322355511 0.583073192 0.783794941 0.727298657 0.573719768 0.693786744 0.725823138 0.652513524 1 20.21479208 4.745930521 24.77779577 0.709957764 1.322355841 0.716724056 0.119420223 403.183981 1355476.713 0.027252054 0.27442827 55709.66173 -4.745930521 0.612398076 RMS(ph)FQKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RMSFQKPK 8 2 Q8N573-2;Q8N573-3;Q8N573-5;Q8N573-8;Q8N573;E5RII8 Q8N573-2 OXR1 Oxidation resistance protein 1 1 RMS(1)FQKPK;RMS(1)FQKPK 120.77 0.00076276 1935830000 5339500 4545900 3424000 4041300 4227700 3486400 5357400 5552800 5511200 TRUE FALSE 4633871.546 4516037.684 5079857.853 4958938.932 4143577.041 3620524.064 4837840.173 4365376.932 4859672.214 0.953535823 0.929288537 1.045308743 1.020426628 0.852645376 0.745014047 0.995507507 0.898286292 1 22.21242758 3.243263969 24.99987429 0.897917534 0.987162609 0.244033285 0.077704186 182.1069349 967951.6582 0.023442229 0.029259613 1750.91059 -3.243263969 0.089245075 RMS(ph)PKPELTEEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RMSPKPELTEEQK 13 2 P41208 P41208 CETN2 Centrin-2 1 RMS(1)PKPELTEEQK;RMS(1)PKPELTEEQK 199.08 6.30E-08 569420000 571090 431430 516780 534420 418410 321880 517640 635680 1482640 TRUE FALSE 495619.0095 428595.9079 766696.5365 655768.2291 410084.4596 334262.9319 467439.3525 499744.7789 1307363.988 0.379097951 0.32783212 0.586444589 0.501595757 0.313672752 0.255677023 0.35754339 0.382253744 1 20.31822943 1.238248876 24.91086941 1.000000716 0.387727143 0.806295079 0.094268454 3.289908048 262448.0962 0.140284076 0.024732992 17.30807928 -1.238248876 -0.612273572 RMS(ph)PKPELTEEQKQEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RMSPKPELTEEQKQEIR 17 3 P41208 P41208 CETN2 Centrin-2 1 RMS(0.998)PKPELT(0.002)EEQKQEIR 108.25 0.0036726 600190000 778840 556780 557450 581970 507460 393900 772870 822980 601160 TRUE FALSE 675914.3207 553122.4755 827034.6846 714115.1834 497362.5388 409053.5879 697917.1864 646992.1314 530091.5496 1.275089786 1.043447072 1.560173304 1.347154437 0.938257814 0.771665929 1.316597457 1.220529042 1 19.01588202 3.25434721 24.99033217 1.076951762 1.305801065 0.300745581 0.192235312 370.1561311 585957.4326 0.059382775 0.076400856 1796.169055 -3.25434721 0.228849303 RMS(ph)VGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RMSVGDR 7 1 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 RMS(1)VGDR;RMS(1)VGDR 65.627 0.042921 423690000 1205870 1425860 790900 867360 1024560 1825250 1005300 1019420 1085000 TRUE FALSE 1046511.224 1416493.432 1173381.885 1064307.345 1004173.261 1895468.549 907806.1607 801424.9661 956732.536 1.093838858 1.480553215 1.226447143 1.112439793 1.049586193 1.981189598 0.948860968 0.837668769 1 19.86775614 2.036239824 24.99999385 0.903044892 1.317968462 0.323502941 0.269330799 180.9645884 124837.462 0.106612191 0.071877678 108.7025729 -2.036239824 0.414923571 RMSADMS(ph)EIEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RMSADMSEIEAR 12 1 O43318;O43318-3;Q9UG54;O43318-2;O43318-4 O43318 MAP3K7;DKFZp586F0420 Mitogen-activated protein kinase kinase kinase 7 1 RMS(0.118)ADMS(0.882)EIEAR 113.65 0.0012101 792940000 451340 459290 310070 330580 503990 515050 459760 539000 438970 TRUE FALSE 391694.2755 456272.8937 460020.8891 405643.2416 493961.585 534864.3068 415172.546 423739.0445 387075.4667 1.011932579 1.17876986 1.188452715 1.047969392 1.276137672 1.381808853 1.072588117 1.094719456 1 18.56225535 2.042463856 24.99988123 1.062982647 1.183372523 0.236408825 0.105792797 212.4471533 125073.7793 0.044345388 0.029897637 110.2716457 -2.042463856 0.120389875 RMYDMILLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RMYDMILLR 9 1 J3KPJ6;A0A087X170;Q8NET8-3;Q8NET8;Q8NET8-2 J3KPJ6 TRPV3 Transient receptor potential cation channel subfamily V member 3 0 68.735 0.091764 1660000000 59621 40192 37388 45826 47275 58135 53377 68457 25090 FALSE TRUE 51741.93379 39927.97611 55468.96186 56231.49371 46334.31999 60371.49107 48200.50676 53818.00328 22123.88878 2.338735938 1.80474493 2.507197645 2.541664093 2.094311739 2.728792016 2.1786634 2.432574301 1 14.43331737 1.235799111 24.99999999 0.999998227 2.327300656 0.723245038 0.258234356 39.35243365 356188.671 0.404518514 0.060128975 17.21072284 -1.235799111 1.327302429 RMYEQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RMYEQQR 7 1 Q9NZZ3-2;Q9NZZ3 Q9NZZ3-2 CHMP5 Charged multivesicular body protein 5 0 ; 119.29 0.0077202 62950000 48863 56998 33230 40251 47848 61258 71487 65979 55848 FALSE TRUE 42405.63075 56623.57639 49300.13915 49390.60475 46895.91841 63614.6349 64554.20174 51869.9043 49245.71306 0.86110299 1.149817372 1.001105194 1.002942219 0.95228428 1.291780156 1.310859316 1.053287709 1 15.58771052 2.758199031 24.9886327 1.160455624 1.003090049 0.345638401 0.11612867 1049.747411 1335735.283 0.038678738 0.038628341 573.0585956 -2.758199031 -0.157365575 RMYS(ph)FDDVLEEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RMYSFDDVLEEGK 13 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;E9PJ10;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 RMYS(1)FDDVLEEGK;RMYS(1)FDDVLEEGK 150.59 6.67E-07 147230000 188338 228841 170191 211830 256250 195025 291704 335220 242308 TRUE FALSE 163448.6561 227337.7284 252495.9369 259929.2391 251151.1263 202527.7379 263414.591 263535.8117 213662.6243 0.764984782 1.064003258 1.181750611 1.216540516 1.175456527 0.947885661 1.232852923 1.23342027 1 17.70497504 4.714150415 2.785411704 1.150855466 0.704788491 0.596074663 0.096458667 0.273267867 3.031451101 0.024486767 0.27108972 51778.61326 -4.714150415 -0.446066975 RNAEQYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNAEQYK 7 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 110.81 0.010776 198770000 137475 158508 108545 136859 117821 142914 151639 178193 302671 FALSE TRUE 119307.3304 157466.7505 161037.7251 167934.9277 115476.5926 148411.9941 136933.0731 140087.8136 266889.5792 0.447028808 0.590007115 0.603387084 0.629229992 0.432675539 0.556080138 0.513070138 0.524890534 1 18.02588345 1.237473868 24.99785027 1.000000547 0.539294627 0.841688137 0.063092128 10.19974028 234507.4257 0.090472867 0.01516798 17.27722017 -1.237473868 -0.46070592 RNAEQYKDQADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNAEQYKDQADK 12 2 P35579;P35579-2 P35579 MYH9 Myosin-9 0 124.51 0.0001809 203740000 265200 257750 276040 143100 165180 190860 265240 253510 98039 FALSE TRUE 230153.1481 256056.8233 409533.8673 175593.0421 161893.2412 198202.5077 239517.0656 199298.8593 86448.94111 2.662301529 2.961942853 4.737291886 2.031176321 1.872703576 2.292711804 2.770618848 2.305393875 1 16.39956067 3.667008065 24.99997435 2.120941756 3.40467489 0.475242589 0.694006113 136.2807083 47615.16226 0.19011722 0.281989446 4645.239011 -3.667008065 1.283733134 LSS(ph)LRAS(ph)TSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LSSLRASTSK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 LS(0.009)S(0.991)LRAS(0.981)T(0.018)SK;LS(0.436)S(0.564)LRAS(0.965)T(0.03)S(0.005)K;LS(0.439)S(0.561)LRAS(0.896)T(0.089)S(0.015)K 127.79 0.001661 3078880000 1024790 3770600 4158500 5462000 6844600 4892700 7188400 8000300 10160000 TRUE FALSE 889361.405 3745830.68 6169564.509 6702230.581 6708405.851 5080925.335 6491270.074 6289498.103 8958896.374 0.099271313 0.41811296 0.688652291 0.748108952 0.748798242 0.567137415 0.724561353 0.702039385 1 23.09488959 4.553818154 1.742470312 0.736889133 0.003010013 0.803785661 0.105752988 0.266287636 1.077125378 0.028563499 0.288260838 35794.65278 -4.553818154 -0.73387912 down RNAET(ph)PEATTQQETDTDLPEAPPPPLEPAVIARPGCVNLSLHGIVEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNAETPEATTQQETDTDLPEAPPPPLEPAVIARPGCVNLSLHGIVEDR 48 2 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 1 RNAET(0.563)PEAT(0.182)T(0.182)QQET(0.037)DT(0.037)DLPEAPPPPLEPAVIARPGCVNLSLHGIVEDR 48.874 0.015359 55291000 15939 17002 2064.7 4505.3 15241 16119 16100 16953 1892.5 TRUE FALSE 13832.62077 16890.31274 3063.195826 5528.297224 14937.73392 16739.10836 14538.62448 13327.73288 1668.770806 8.289107597 10.12140953 1.835600081 3.312795984 8.951339432 10.03080129 8.712175708 7.98655683 1 10.70457011 5.999694493 15.30040728 6.889051687 8.848992786 0 3.400459473 0 0 0.776371983 0 999296.7924 -5.999694493 1.959941098 RNALFPEVFS(ph)PTPDENSDQNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RNALFPEVFSPTPDENSDQNSR 22 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 RNALFPEVFS(1)PTPDENSDQNSR;RNALFPEVFS(0.992)PT(0.008)PDENSDQNSR;RNALFPEVFS(1)PTPDENSDQNSR 199.03 1.11E-22 337928000 194413 191166 118921 136371 233661 278884 214453 245752 162695 TRUE FALSE 168720.8295 189910.218 176431.5934 167336.1199 229011.6032 289612.8479 193655.3811 193199.8472 143461.3824 1.176071404 1.323772396 1.229819415 1.166419262 1.596329265 2.01875127 1.349878119 1.346702813 1 17.13030291 3.248228114 24.99129473 1.4672655 1.231559921 0.177479615 0.254574757 399.0169961 1031486.983 0.079024476 0.100715254 1771.038956 -3.248228114 -0.235705579 RNDFQLIGIQDGYLSLLQDSGEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RNDFQLIGIQDGYLSLLQDSGEVR 24 1 P63241;P63241-2;I3L397;I3L504 P63241 EIF5A Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A 0 ;;;; 313.21 2.52E-73 5328653000 1894138 1763600 887620 1021535 1555740 1679446 1628695 1871877 1117149 FALSE TRUE 1643822.864 1752014.795 1316876.001 1253490.135 1524783.818 1744055.374 1470744.41 1471590.671 985080.9179 1.668718614 1.778549116 1.33682013 1.272474283 1.547876718 1.770469149 1.493018881 1.493877958 1 19.90988271 1.187702027 2.925889699 0.842905732 1.548548668 0.524356798 0.163829421 0.460256122 4.313090609 0.829414534 0.045326678 15.40643044 -1.187702027 0.705642936 RNDYVHALVAYFNIEFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNDYVHALVAYFNIEFTR 18 1 E9PKG1;Q99873-2;Q99873-3;Q99873;Q99873-5 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ; 175.39 2.26E-12 25589000 26730.6 33497 13596.1 18435.3 26057.9 21264.8 29288.5 29588.9 14971.9 FALSE TRUE 23198.08348 33276.956 20171.21944 22621.31663 25539.39877 22082.87062 26448.10578 23261.544 13201.93904 1.757172444 2.520611245 1.527898241 1.713484403 1.934518763 1.672699029 2.003350091 1.761979352 1 13.68846222 1.240844838 3.778025276 0.892756832 1.875748837 0.512257889 0.266362452 0.212970707 4.907833459 0.588615368 0.065247676 17.41184683 -1.240844838 0.982992006 RNEFLGELQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RNEFLGELQK 10 1 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;H0Y961;B1AMS2;Q14141-2;Q14141-4;Q14141 D6RGI3;B1AMS2 SEPT11;SEPT6 Septin-11;Septin-6 0 ;; 175.97 4.23E-06 1354030000 1924540 1738780 1074990 1316610 1577450 1481120 1760780 1997040 1835510 FALSE TRUE 1670207.163 1727357.84 1594858.76 1615566.424 1546061.831 1538099.645 1590019.827 1569988.537 1618518.099 1.031936043 1.067246539 0.985382098 0.99817631 0.955232958 0.950313528 0.982392367 0.970016052 1 20.62624207 4.160779625 5.517821385 0.975276789 1.049310416 0.736387209 0.01799061 0.090331927 4.646267451 0.004641337 0.010120604 14480.36887 -4.160779625 0.074033627 RNEIWLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNEIWLLK 8 1 Q9NRV9;A0A3B3IRV5 Q9NRV9 HEBP1 Heme-binding protein 1 0 ; 131.62 0.0015993 2667100000 3814700 3822000 2071030 2848200 3549200 3540700 3794800 4343100 4215400 FALSE TRUE 3310577.73 3796893.03 3072587.035 3494927.342 3478577.864 3676913.02 3426780.88 3414361.863 3717060.214 0.890644095 1.021477407 0.826617504 0.940239636 0.935841139 0.989199208 0.921906206 0.91856512 1 21.82573063 3.497937923 24.74734585 0.947322156 0.917045973 0.09797015 0.053659095 2020.505115 2402019.165 0.014177512 0.020756917 3147.298415 -3.497937923 -0.030276183 RNELVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RNELVIR 7 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;; 155.75 0.002549 16492800000 9924340 10957260 12899350 8178650 9232540 12792370 10179040 9804860 9841540 FALSE TRUE 8612813.324 10885281.04 19137518.81 10035737.49 9048830.517 13284500.75 9191878.268 7708166.991 8678084.353 0.992478636 1.254341465 2.205269968 1.156446178 1.04272212 1.530810282 1.059205914 0.888233702 1 23.04894518 2.086881137 5.358727733 0.946324669 1.371709927 0.22272171 0.339885043 0.297713594 14.06657479 0.146529978 0.096690048 122.1465308 -2.086881137 0.425385258 RNEVLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RNEVLDR 7 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 112.84 0.010043 1949210000 2266550 1862290 1180660 1305540 1644540 2126910 1620210 1895520 1824760 FALSE TRUE 1967019.675 1850056.494 1751631.125 1601982.811 1611816.871 2208733.604 1463082.284 1490177.799 1609038.952 1.22248108 1.14978975 1.088619467 0.995614686 1.001726447 1.372703626 0.909289537 0.926129102 1 20.61776782 -2 0.126942547 0.09662346 1.302633268 0.207310364 0.126980135 309.1383358 3.458155442 65.96315297 3.845713887 0.01 2 1.206009808 RNFAELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNFAELK 7 1 P18124 P18124 RPL7 60S ribosomal protein L7 0 139.88 0.0042686 365390000 615960 697280 494460 523580 719280 711490 856220 897400 855100 FALSE TRUE 534559.3254 692699.5218 733582.5099 642466.8414 704967.7352 738861.4807 773183.9162 705497.9936 754011.0521 0.708954231 0.918686165 0.97290684 0.852065549 0.934956767 0.979908025 1.025427829 0.935660017 1 19.52422614 5.323966239 1.383328576 0.958670933 9.82E-14 0.730972985 0.046798433 3.053910027 1.667137648 0.013526539 6.086310648 210846.4238 -5.323966239 -0.958670933 LNT(ph)SDFQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 LNTSDFQK 8 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 LNT(0.986)S(0.014)DFQK;LNT(0.915)S(0.085)DFQK;LNT(0.864)S(0.136)DFQK;LNT(0.996)S(0.004)DFQK;LNT(0.911)S(0.089)DFQK;LNT(0.932)S(0.068)DFQK 201.09 0.0012806 11194610000 2521470 5130680 6006870 5961140 10528010 8212100 11479560 12119310 11867840 TRUE FALSE 2188251.351 5096976.225 8911812.424 7314707.947 10318523.2 8528024.801 10366274.04 9527689.869 10464837.48 0.209105144 0.487057371 0.851595875 0.698979603 0.986018486 0.814921858 0.990581465 0.910447954 1 23.31904657 4.554029113 1.059575141 0.925073019 2.57E-22 0.879848557 0.087712677 0.400729926 0.462049992 0.026066001 0.390716183 35812.04429 -4.554029113 -0.925073019 down RNLADCLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNLADCLR 8 1 P49721 P49721 PSMB2 Proteasome subunit beta type-2 0 ; 135.71 0.0013181 220006000 212900 347250 148990 164111 318420 351730 305400 334770 107637 FALSE TRUE 184764.7256 344968.8919 221042.0623 201374.9108 312084.065 365261.2807 275782.355 263182.0407 94912.27648 1.946689432 3.63460771 2.328909078 2.121695088 3.2881317 3.848409228 2.905655256 2.772897779 1 16.53430709 5.002342061 21.05325593 2.769414602 1.025056037 0.08437516 0.812734979 2923.104495 156149.1608 0.18996977 131374.9745 100540.7361 -5.002342061 -1.744358564 RNLDIERPTYTNLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RNLDIERPTYTNLNR 15 2 P68363;F8VQQ4;F8VVB9;C9JDS9;P68366-2;P68366;Q9BQE3;F5H5D3 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA1A;TUBA4A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 ;;; 284.26 3.26E-34 8203370000 1752140 1412120 707240 1079680 1730160 1716540 1745020 1810690 698493 FALSE TRUE 1520590.26 1402843.691 1049263.63 1324837.846 1695733.201 1782576.405 1575788.229 1423488.034 615917.9533 2.46881951 2.27764702 1.703576952 2.150997286 2.753180342 2.894178348 2.55843854 2.311165029 1 19.23237866 1.239329452 5.224666739 0.921787657 2.395016104 0.642007056 0.326781555 0.116258312 8.835805593 0.61984253 0.091069566 17.35119744 -1.239329452 1.473228447 RNPAGSVVMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RNPAGSVVMER 11 1 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;; 157.22 4.92E-05 866310000 998213 805640 549898 642201 746662 682607 845881 944415 867381 FALSE TRUE 866296.6229 800347.6978 815830.5121 788022.5525 731804.887 708867.333 763847.5908 742459.2017 764840.2063 1.132650475 1.046424719 1.06666792 1.030310052 0.956807554 0.926817559 0.998702192 0.970737672 1 19.54479884 3.562960114 2.046237825 0.970625869 1.083305599 0.744617789 0.029821831 0.166383562 1.375972221 0.009146292 0.015283155 3655.612163 -3.562960114 0.112679731 RNPDELAEALDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNPDELAEALDER 13 1 O14908;O14908-2;K7EM11 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 ; 212.87 1.67E-08 387650000 478490 492840 322490 360660 526320 554810 455620 541620 485720 FALSE TRUE 415256.3342 489602.5016 478447.2427 442553.3653 515847.2617 576153.8997 411434.0425 425798.7779 428298.7349 0.969548356 1.143133196 1.117087686 1.033281981 1.204409959 1.34521504 0.960623997 0.994163053 1 18.70825789 RNPDTQWITKPVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNPDTQWITKPVHK 14 2 P61313;A0A2R8YEM3;E7EQV9;E7ENU7 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 185.12 7.29E-07 4228600000 5233500 4542600 2941000 3612900 4358400 3882800 5424800 6395100 4605300 FALSE TRUE 4541879.715 4512759.361 4363277.437 4433264.165 4271676.367 4032173.829 4898703.731 5027557.632 4060866.68 1.118450831 1.111279861 1.074469511 1.091703942 1.051912486 0.992934303 1.206319763 1.238050403 1 21.95335623 2.220447184 24.99995197 1.169283038 1.075073554 0.177046126 0.071110364 320.2307383 441975.5528 0.029060939 0.019636586 166.129663 -2.220447184 -0.094209484 RNPLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNPLPK 6 1 P22059 P22059 OSBP Oxysterol-binding protein 1 0 99.511 0.062077 277490000 511850 443890 279050 345840 422740 377950 462080 507520 520860 FALSE TRUE 444207.7256 440974.0574 413999.5134 424368.2578 414328.3011 392489.9811 417267.5527 398990.7975 459284.5242 0.967173293 0.960132628 0.901400965 0.923976828 0.902116835 0.85456827 0.908516466 0.868722495 1 18.80902865 4.256947496 5.998132094 0.903228452 0.964710788 0.253439783 0.038592809 0.191567214 22.95445604 0.009359704 0.023708041 18069.5566 -4.256947496 0.061482336 RNPPGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNPPGGK 7 1 Q9UK76;Q9UK76-3 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 0 74.415 0.074148 20762000 72294 62747 38374 45767 44833 51903 62157 84139 69257 FALSE TRUE 62740.16473 62334.81083 56931.79475 56159.09685 43940.91101 53899.742 56129.02371 66146.52962 61069.51636 1.027356502 1.020718921 0.932245712 0.919592952 0.719522826 0.88259651 0.919100511 1.083134984 1 15.8981648 1.752023843 24.99845316 1.041715092 0.913003017 0.263004259 0.086245915 5.57958598 10379.35715 0.049989243 0.024005716 56.49679905 -1.752023843 -0.128712075 RNPS(ph)PDHSYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNPSPDHSYK 10 1 Q15696 Q15696 ZRSR2 U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 1 RNPS(0.997)PDHS(0.003)YK 116.84 0.00063531 253500000 516910 384400 285520 395590 398590 343590 438220 462430 791300 TRUE FALSE 448599.0338 381874.8511 423598.427 485414.7557 390658.8388 356808.1296 395721.4918 363542.9431 697753.4155 0.642919151 0.547291984 0.607089005 0.695682379 0.559880941 0.511367084 0.567136589 0.521019224 1 19.41235776 1.233796285 24.99801481 1.00000064 0.578459494 0.847647154 0.055738977 56.77851114 297875.2958 0.113122989 0.014253141 17.1315353 -1.233796285 -0.421541146 RNPS(ph)PDHSYKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RNPSPDHSYKR 11 2 Q15696 Q15696 ZRSR2 U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 1 RNPS(0.941)PDHS(0.059)YKR;RNPS(0.999)PDHS(0.001)YKR;RNPS(1)PDHSYKR;RNPS(0.999)PDHS(0.001)YKR;RNPS(1)PDHSYKR 140.1 2.02E-05 1600262000 1286236 1051390 561791 637601 917252 801002 1053577 1260310 428146 TRUE FALSE 1116256.654 1044483.35 833475.0067 782378.0522 899000.4798 831817.0653 951401.2647 990802.5142 377531.0676 2.956727934 2.766615623 2.207699122 2.07235409 2.381262251 2.203307586 2.520060854 2.624426436 1 18.52623585 4.309290872 3.840760497 2.213132031 2.91412553 0.303994297 0.445714717 0.286855817 8.149132986 0.111052904 0.324879309 20384.0686 -4.309290872 0.700993499 RNQKPEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RNQKPEVR 8 2 C9JXB8;C9JNW5;P83731 C9JXB8 RPL24 60S ribosomal protein L24 0 ;;; 133.86 0.00050689 1686180000 3250420 3026480 1872440 2169690 2556290 2646960 3514120 3559140 2913550 FALSE TRUE 2820868.761 3006598.854 2777958.247 2662351.276 2505424.83 2748790.264 3173321.183 2798045.608 2569113.438 1.097993074 1.170286531 1.081290614 1.036291834 0.975209889 1.069937288 1.235181419 1.089109405 1 21.29283916 4.128724868 8.039322159 1.07527643 1.133810389 0.121110264 0.071188658 0.568190472 37.8358599 0.019708272 0.041352591 13450.08002 -4.128724868 0.058533959 RNQSFCPTVNLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNQSFCPTVNLDK 13 1 P46776;E9PLL6;E9PJD9 P46776 RPL27A 60S ribosomal protein L27a 0 121.31 0.00039784 316150000 351010 350610 238420 260510 292060 298680 370660 379240 395400 FALSE TRUE 304623.1392 348306.8198 353720.7095 319662.7771 286248.5774 310170.4129 334713.4503 298142.4772 348656.2624 0.873706203 0.998997745 1.014525616 0.916842207 0.821005122 0.88961664 0.960009862 0.855118664 1 18.41144587 5.115200269 10.66625432 0.925323178 6.56E-05 0.066619519 0.0643969 336256.002 745858.6185 0.016296961 7042245.885 130376.7854 -5.115200269 -0.925257596 TVAISDAAQLPHDYCT(ph)TPGGTLFS(ph)TTPGGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDYCT(0.536)T(0.463)PGGT(0.009)LFS(0.597)T(0.385)T(0.009)PGGTR 136.39 2.49E-06 3261000000 364110 692300 547060 723550 1203000 1299800 1075100 1375200 1319700 TRUE FALSE 315991.941 687752.2357 811620.0458 887843.0863 1179062.654 1349804.147 970836.9675 1081124.182 1163686.569 0.271543858 0.591011578 0.697455885 0.762957234 1.013213252 1.159937893 0.834277024 0.929051009 1 20.1502711 4.570250282 0.800395038 0.976310658 6.07E-11 0.850374693 0.097113684 0.812483047 0.481138165 0.040937755 0.678351549 37174.94053 -4.570250282 -0.976310658 down RNS(ph)CNVGGGGGGFKHPAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNSCNVGGGGGGFKHPAFK 19 2 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 RNS(1)CNVGGGGGGFKHPAFK 101.71 0.00022608 503880000 792690 380670 285590 335910 509260 552900 791740 896700 191970 TRUE FALSE 687934.0081 378169.3537 423702.2792 412183.4996 499126.7224 574170.4208 714957.1767 704947.6831 169275.5253 4.063989799 2.234046257 2.503033315 2.434985795 2.948605367 3.391928158 4.22362994 4.164498571 1 17.36901387 2.824370263 3.80308402 3.444490658 2.743662495 0.003014949 1.014691639 0.607147847 16.49945685 0.338460584 0.335200801 667.375506 -2.824370263 -0.700828163 RNS(ph)EGSELSCTEGSLTSSLDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNSEGSELSCTEGSLTSSLDSR 22 1 Q5T5U3;A0A087WW76;A0A452Q6Z5 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 RNS(0.944)EGS(0.055)ELSCTEGSLTSSLDSR 108.75 0.00025227 90083000 41075 30869 18564 27090 30862 30483 41956 46336 37314 TRUE FALSE 35646.83468 30666.21951 27541.61249 33241.19854 30247.90658 31655.70074 37887.11358 36427.40699 32902.78143 1.083398823 0.932025141 0.837060312 1.010285365 0.919311537 0.962098016 1.15148665 1.10712242 1 15.00592193 2.299414738 8.240349974 1.093082093 0.950937666 0.407391429 0.072850483 0.227867386 27.55589467 0.026869821 0.020716366 199.2575278 -2.299414738 -0.142144427 RNS(ph)FSENEK ddPTM_MDA-MB-175_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(0.999)FS(0.001)ENEK;RNS(0.983)FS(0.017)ENEK 221.56 2.54E-07 2379170000 1612320 1410900 1065380 1236750 1566840 1379540 1873450 2214750 1820110 TRUE FALSE 1399247.827 1401631.705 1580601.331 1517572.99 1535662.949 1432611.796 1691763.107 1741142.948 1604938.669 0.871838815 0.873324154 0.98483597 0.945564475 0.956835908 0.892627129 1.05409829 1.084865722 1 20.61408674 -0.419092047 0.06736477 1.754957222 0.500471432 0.529538171 0.049377236 310.2489714 3.01116624 47.00381114 16.42732047 0.380985066 0.419092047 -1.254485791 RNS(ph)FTPLSSSNTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RNSFTPLSSSNTIR 14 1 O60825 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 RNS(0.878)FT(0.005)PLS(0.082)S(0.029)S(0.002)NT(0.004)IR;RNS(0.999)FT(0.001)PLSSSNTIR;RNS(0.999)FT(0.001)PLSSSNTIR;RNS(0.999)FT(0.001)PLSSSNTIR;RNS(0.99)FT(0.008)PLSS(0.001)S(0.001)NTIR;RNS(1)FTPLSSSNTIR 174.59 2.67E-06 7423480000 2071540 2154780 1475024 1753890 2027810 2211880 2227490 2450760 2308540 TRUE FALSE 1797780.74 2140625.108 2188350.54 2152137.531 1987460.548 2296972.455 2011468.363 1926684.046 2035627.031 0.883158218 1.051580214 1.07502529 1.057235681 0.976338257 1.128385711 0.988132075 0.946481854 1 20.95704182 2.014615082 24.99140272 0.968784799 1.032994473 0.115360516 0.065770463 393.4777396 672833.8923 0.025835674 0.017411152 103.422512 -2.014615082 0.064209674 RNS(ph)GSSLVSSSSASSNLSHLEEDSWILWGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNSGSSLVSSSSASSNLSHLEEDSWILWGR 30 1 O60447-2;O60447 O60447-2 EVI5 Ecotropic viral integration site 5 protein homolog 1 RNS(0.535)GS(0.424)S(0.04)LVSSSSASSNLSHLEEDSWILWGR 135.92 1.66E-06 62185000 39738 38589 23324 36408 40248 44273 45531 43866 45697 TRUE FALSE 34486.52262 38335.50632 34603.56441 44674.99286 39447.14354 45976.21096 41115.41063 34485.59727 40294.75272 0.855856415 0.951377133 0.858761056 1.108704976 0.978964775 1.140997471 1.020366372 0.855833451 1 15.29830436 3.76397139 24.94630063 1.004362371 0.894936087 0.353613905 0.080663239 1077.492909 1057794.39 0.023275454 0.040291789 5807.261598 -3.76397139 -0.109426283 RNS(ph)GSSLVSSSSASSNLSHLEEDTWILWGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RNSGSSLVSSSSASSNLSHLEEDTWILWGR 30 1 Q96CN4;Q96CN4-2 Q96CN4 EVI5L EVI5-like protein 1 RNS(0.371)GS(0.258)S(0.371)LVSSSSASSNLSHLEEDTWILWGR;RNS(0.688)GS(0.311)S(0.001)LVSSSSASSNLSHLEEDTWILWGR;RNS(0.373)GS(0.313)S(0.313)LVSSSSASSNLSHLEEDTWILWGR;RNS(0.602)GS(0.381)S(0.017)LVSSSSASSNLSHLEEDTWILWGR 187.43 1.80E-18 696716000 101282 92168 44368 60843.7 104720 99809 102394 107760 74353 TRUE FALSE 87897.32708 91562.54234 65824.5132 74659.19202 102636.2769 103648.7168 92463.84564 84716.36259 65563.07304 1.340652947 1.396556599 1.003987613 1.138738448 1.565458605 1.580900833 1.410303717 1.292135323 1 16.00059586 1.24882432 3.666744477 0.958372117 1.34614465 0.281862173 0.173237933 0.403950906 8.466169901 0.425722417 0.04846532 17.73471935 -1.24882432 0.387772534 RNS(ph)LDGGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RNSLDGGGR 9 1 O43896 O43896 KIF1C Kinesin-like protein KIF1C 1 RNS(1)LDGGGR;RNS(1)LDGGGR;RNS(1)LDGGGR;RNS(1)LDGGGR 120.84 0.00038632 1695640000 2342349 2249175 1476532 1756113 1818145 2379681 2315327 2526699 2289125 TRUE FALSE 2032801.645 2234400.021 2190587.814 2154865.297 1781967.472 2471228.868 2090786.944 1986384.082 2018507.25 1.007081666 1.106956649 1.085251397 1.067553905 0.882814501 1.224285356 1.035808488 0.984085681 1 20.94485734 1.993969346 24.95578673 0.99661838 1.06352085 0.103682962 0.084478168 576.2231546 2384505.948 0.034369391 0.022283928 98.62098722 -1.993969346 0.06690247 RNS(ph)LEGYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNSLEGYSR 9 1 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 RNS(0.99)LEGYS(0.01)R;RNS(0.957)LEGYS(0.043)R 116.06 0.0014563 780630000 769940 814110 555050 790070 1036020 1040930 975320 1133390 1077620 TRUE FALSE 668190.4782 808762.0578 823474.0365 969467.469 1015405.229 1080975.251 880733.6165 891023.3686 950224.9912 0.703191859 0.851126907 0.866609534 1.020250444 1.068594531 1.137599264 0.926868504 0.937697258 1 19.85790963 4.276468646 1.416357068 1.008011378 0.705200685 0.707707147 0.066181103 0.375686056 1.200853256 0.022127229 0.128771544 18900.29775 -4.276468646 -0.302810693 RNS(ph)LIELPDDYSCLLNQASHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNSLIELPDDYSCLLNQASHFR 22 1 Q8IWV7 Q8IWV7 UBR1 E3 ubiquitin-protein ligase UBR1 1 RNS(1)LIELPDDYSCLLNQASHFR;RNS(1)LIELPDDYSCLLNQASHFR 229.95 1.13E-26 182302000 45932 55219 44860 44539 55784 62058 61774 66096 58591 TRUE FALSE 39861.96982 54856.26275 66554.44605 54652.26069 54674.00754 64445.41142 55783.16699 51961.88476 51664.43873 0.771555267 1.061779903 1.288206118 1.057831306 1.058252231 1.247384333 1.079720759 1.005757268 1 15.65688398 4.723549166 4.68381519 1.101093049 0.755542554 0.547390301 0.094408139 0.13691456 8.094569768 0.024037959 0.150421509 52911.38943 -4.723549166 -0.345550496 RNS(ph)LPQIPMLNLEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 RNSLPQIPMLNLEAR 15 1 Q14289;Q14289-2;H0YB74 Q14289 PTK2B Protein-tyrosine kinase 2-beta 1 RNS(1)LPQIPMLNLEAR;RNS(1)LPQIPMLNLEAR;RNS(1)LPQIPMLNLEAR;RNS(1)LPQIPMLNLEAR;RNS(1)LPQIPMLNLEAR;RNS(1)LPQIPMLNLEAR;RNS(1)LPQIPMLNLEAR;RNS(1)LPQIPMLNLEAR 195.09 1.52E-08 2135450000 905764 987674 624842 702512 1056143 1115387 960311 1131369 1052908 TRUE FALSE 786064.9925 981185.9045 927017.6812 862028.0868 1035127.821 1158296.66 867180.187 889434.5437 928434.4157 0.846656456 1.056817679 0.998474061 0.928474938 1.114917546 1.247580486 0.934024173 0.95799394 1 19.82444048 4.74503873 24.16799309 1.025009895 0.846656326 0.265292874 0.095481805 734.0488734 2738407.077 0.024715849 0.223278612 55595.38344 -4.74503873 -0.178353569 RNS(ph)LTASLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNSLTASLDK 10 1 A0A0U1RR07;Q9HCH5-7;Q9HCH5-8;A0A0U1RQP0;A0A0U1RRJ3;Q9HCH5-11 A0A0U1RR07 SYTL2 Synaptotagmin-like protein 2 1 RNS(0.969)LT(0.031)ASLDK;RNS(0.997)LT(0.003)ASLDK 125.47 0.00025007 553070000 708400 668540 445590 568690 679600 583380 751020 875630 817720 TRUE FALSE 614783.1451 664148.3167 661078.8144 697819.7564 666077.2896 605823.0061 678186.196 688383.3387 721050.0731 0.852621986 0.921084875 0.916827886 0.967782658 0.923760103 0.840195471 0.940553536 0.954695609 1 19.45973992 1.576056937 2.036717 0.998618984 0.908868684 0.405770402 0.037313195 0.391758185 3.059683678 0.056592678 0.010671539 37.67531892 -1.576056937 -0.0897503 RNS(ph)PAFLSTDLGDEDVGLGPPAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RNSPAFLSTDLGDEDVGLGPPAPR 24 1 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;A0A590UJF3 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 RNS(1)PAFLSTDLGDEDVGLGPPAPR;RNS(1)PAFLSTDLGDEDVGLGPPAPR;RNS(1)PAFLSTDLGDEDVGLGPPAPR;RNS(1)PAFLSTDLGDEDVGLGPPAPR 265.45 1.55E-44 1211590000 257261 218058 159030 202918 235978 309554 188666 242171 240863 TRUE FALSE 223263.307 216625.5626 235937.4399 248993.6333 231282.4995 321462.7427 170369.2004 190384.6162 212388.4505 1.051202674 1.019949824 1.110876977 1.172350157 1.08895987 1.513560374 0.802158497 0.89639816 1 17.69634579 RNS(ph)PMAQT(ph)PPCHLPNIPGVTSPGTLIEDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSK 30 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK;RNS(1)PMAQT(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(0.999)PMAQT(0.999)PPCHLPNIPGVT(0.001)S(0.001)PGTLIEDSK 234.95 1.84E-45 2533930000 343403 410198 628475 823794 790216 811184 1087347 1208067 2656450 TRUE FALSE 298021.4235 407503.3823 932407.6121 1010849.019 774492.2476 842390.7734 981896.2553 949731.2732 2342407.507 0.127228684 0.173967758 0.398055253 0.431542768 0.330639415 0.359626056 0.419182509 0.405450918 1 21.15956065 0.127015942 1.279961418 10 0.313266646 0.820475646 0.09917632 9.295106038 1.265487457 224.974019 0.031556488 1.339725866 -0.127015942 -9.686733354 RNS(ph)PMAQTPPCHLPNIPGVTSPGTLIEDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSK 30 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 RNS(0.951)PMAQT(0.049)PPCHLPNIPGVTSPGTLIEDSK;RNS(0.518)PMAQT(0.482)PPCHLPNIPGVTSPGTLIEDSK 213.09 7.50E-27 528290000 95310 120227 144953 217070 180666 154919 243400 276900 546620 TRUE FALSE 82714.54202 119437.2209 215052.7556 266359.0612 177071.1001 160878.8342 219795.1055 217687.0898 481999.2063 0.171607216 0.247795472 0.446168278 0.55261307 0.367368032 0.333774064 0.456007194 0.45163371 1 18.87867125 0.746404443 1.560533849 2.592701246 0.36713547 0.771962406 0.10698697 2.223770496 1.637416452 11.3467911 0.032147728 5.577048781 -0.746404443 -2.225565776 RNS(ph)PMAQTPPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 44 2 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 RNS(0.983)PMAQT(0.017)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 172.77 6.60E-21 382850000 70796 88934 69256 120720 158820 122220 190390 206230 131410 TRUE FALSE 61440.12923 88349.7867 102748.4332 148131.3211 155659.7927 126921.8825 171926.0071 162129.3194 115874.8595 0.530228295 0.762458631 0.886718946 1.278373253 1.343343961 1.095335805 1.483721386 1.399175974 1 16.82220806 4.048686924 1.486582629 1.299604261 0.558715998 0.761162081 0.147537777 0.21164128 0.857311893 0.044576253 0.158864637 11186.31189 -4.048686924 -0.740888263 RNS(ph)PSGTTTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNSPSGTTTK 10 1 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 RNS(0.746)PS(0.108)GT(0.108)T(0.035)T(0.002)K;RNS(0.486)PS(0.486)GT(0.026)T(0.002)T(0.001)K 112.5 0.0017083 56937000 266510 224377 156963 206670 145181 190927 245570 299220 337670 TRUE FALSE 231290.0282 222903.0527 232870.8318 253597.5823 142292.1821 198272.0852 221754.6592 235234.1315 297751.0373 0.77679 0.748622254 0.782099145 0.851710155 0.477889795 0.66589889 0.744765362 0.790036313 1 18.18374701 1.173054185 1.913013956 1.130767865 0.717830112 0.441502906 0.09854308 1.004943201 3.051242928 0.79579651 0.028025212 14.8954691 -1.173054185 -0.412937753 RNS(ph)RDGDPLPSSLSCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNSRDGDPLPSSLSCK 16 2 P53602;H3BP35 P53602 MVD Diphosphomevalonate decarboxylase 1 RNS(0.987)RDGDPLPS(0.012)S(0.001)LSCK;RNS(1)RDGDPLPSSLSCK 131.4 2.34E-05 521240000 854970 633310 288130 253560 580870 575760 838210 764780 79444 TRUE FALSE 741983.5483 629149.7449 427470.6317 311134.6734 569311.8235 597909.8598 756920.5232 601237.7485 70052.22082 10.59186332 8.981153453 6.102171019 4.441467662 8.126963239 8.535202064 10.80508961 8.582707892 1 16.09614317 4.459795301 4.540471033 7.202473767 10.30455768 0.176107188 2.686848163 0.354976723 18.1067798 0.694647002 2.291521931 28826.72473 -4.459795301 3.10208391 RNS(ph)SEASSGDFLDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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(0.996)S(0.004)EASSGDFLDLK;RNS(0.999)S(0.001)EASSGDFLDLK;RNS(0.995)S(0.005)EASSGDFLDLK;RNS(0.675)S(0.319)EAS(0.005)SGDFLDLK;RNS(0.748)S(0.239)EAS(0.011)S(0.001)GDFLDLK;RNS(1)SEASSGDFLDLK;RNS(0.96)S(0.04)EASSGDFLDLK;RNS(0.983)S(0.017)EASSGDFLDLK;RNS(0.884)S(0.116)EASSGDFLDLK;RNS(0.863)S(0.129)EAS(0.008)SGDFLDLK 321.54 7.21E-57 23676140000 17710255 13150014 13473828 16852239 14449899 11670073 16966836 20738350 32786020 TRUE FALSE 15369799.93 13063630.69 19989816.29 20678797.44 14162374.28 12119028.26 15321394.86 16303615.24 28910094.07 0.531641298 0.451870916 0.691447639 0.715279493 0.489876451 0.419197123 0.529966967 0.563941964 1 24.78506997 1.23817116 6.011877445 1.016718376 0.548396144 0.697745656 0.09331526 0.082065974 11.33264226 0.157893693 0.024767101 17.30498231 -1.23817116 -0.468322232 RNS(ph)SIVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.98)S(0.02)IVGR;RNS(0.96)S(0.04)IVGR 138.25 0.00043703 318810000 163323 169327 102312 104412 142498 175714 161457 153888 135048 TRUE FALSE 141739.4517 168214.6798 151790.4254 128120.3404 139662.5686 182473.8313 145798.925 120980.2488 119082.7793 1.190259856 1.412586109 1.274663107 1.075893099 1.172819189 1.532327616 1.224349363 1.015934037 1 16.86160527 1.764053264 4.141271105 1.004531565 1.276093399 0.428812828 0.126171251 0.184913913 6.578494217 0.081789647 0.034709164 58.08356494 -1.764053264 0.271561834 RNS(ph)SS(ph)PVSPASVPGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 2 RNS(0.991)S(0.012)S(0.947)PVS(0.05)PASVPGQR;RNS(0.982)S(0.068)S(0.95)PVSPASVPGQR 146.28 7.61E-07 469610000 567670 423430 291368 374970 490420 492380 450000 549090 649370 TRUE FALSE 492650.9712 420648.4604 432274.5394 460112.6696 480661.6015 511322.1772 406359.0693 431671.3765 572602.2184 0.860372097 0.734625971 0.754929907 0.803546781 0.839433705 0.892979735 0.709670791 0.753876535 1 19.12717373 3.492606062 9.306163585 0.821518097 0.778536047 0.064985196 0.084031269 0.919642241 504.8234426 0.023955014 0.033714318 3108.895057 -3.492606062 -0.04298205 RNS(ph)SSSSSPSERPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNSSSSSSPSERPR 14 2 G3V1D0;B7WPE2;H0Y3M3;Q32P44;Q32P44-2 G3V1D0 EML3 Echinoderm microtubule-associated protein-like 3 1 RNS(0.891)S(0.06)S(0.004)S(0.034)S(0.006)S(0.006)PSERPR;RNS(0.915)S(0.056)S(0.001)S(0.024)S(0.004)S(0.001)PSERPR 182.79 1.17E-06 2661910000 810510 816680 531500 522510 893650 926360 996570 868310 849500 TRUE FALSE 703399.0499 811315.1753 788535.1778 641153.8816 875868.1134 961997.6686 899922.7948 682628.6637 749073.0778 0.939025939 1.083092157 1.052681242 0.855929682 1.169269247 1.284250759 1.201381843 0.911297821 1 19.51474695 4.743653186 22.87958395 1.066129892 0.939025767 0.091640509 0.128886849 497.0568437 2232888.986 0.033874896 0.267274599 55418.29825 -4.743653186 -0.127104125 RNS(ph)TDSRPVSVTYR ddPTM_MDA-MB-175_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(0.997)T(0.003)DSRPVSVTYR;RNS(0.818)T(0.182)DSRPVSVTYR;RNS(0.961)T(0.028)DS(0.011)RPVSVTYR;RNS(0.893)T(0.102)DS(0.006)RPVSVTYR 152.66 3.92E-06 2888100000 630300 621202 354480 453794 589712 578604 540855 653271 607356 TRUE FALSE 547004.258 617121.2832 525907.7137 556834.8635 577977.885 600863.2703 488402.9653 513574.0804 535555.0656 1.02137818 1.152302205 0.981986256 1.039734099 1.079212806 1.121944892 0.911956579 0.958956629 1 19.03067539 2.234500506 24.99999845 0.95550912 1.06558685 0.494042167 0.052048536 83.29911864 512902.3434 0.020220068 0.014199188 171.5933711 -2.234500506 0.11007773 RNS(ph)TIVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.999)T(0.001)IVLR;RNS(0.97)T(0.03)IVLR;RNS(1)TIVLR;RNS(0.973)T(0.027)IVLR 156.58 0.00023927 1366810000 344726 332956 205837 257528 332674 324574 328705 314929 350582 TRUE FALSE 299169.5857 330768.7901 305380.4617 316003.6685 326054.4383 337060.5718 296827.2397 247583.8841 309136.5953 0.967758558 1.069976169 0.987849599 1.022213718 1.054726109 1.090328925 0.9601815 0.800888306 1 18.23788492 1.997822689 10.08159116 0.884454275 1.03187942 0.457354645 0.059505103 0.070823416 148.6276751 0.023939259 0.015252803 99.49991014 -1.997822689 0.147425145 RNS(ph)TSSTNQNMFCEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNSTSSTNQNMFCEER 16 1 O75140;O75140-9;O75140-4;O75140-1;A0A2R8Y7U0;O75140-8;H0Y770;A0A2R8Y6H3 O75140 DEPDC5 DEP domain-containing protein 5 1 RNS(0.884)T(0.076)S(0.03)S(0.007)T(0.003)NQNMFCEER 107.25 0.0010648 0 88469 57388 46329 41231 63894 53976 81339 89372 76501 TRUE FALSE 76777.5975 57011.01445 68733.85936 50593.12873 62622.63441 56052.49165 73450.7563 70260.49329 67457.13893 1.138168602 0.84514427 1.018926395 0.75000407 0.928332203 0.83093491 1.08885075 1.041557564 1 16.04168351 2.228364691 24.99675716 1.04496203 0.9125881 0.229369742 0.107523219 276.0182289 676691.599 0.040906123 0.027931206 169.1861047 -2.228364691 -0.13237393 RNS(ph)TTFPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNSTTFPSR 9 1 Q96E09 Q96E09 FAM122A Protein FAM122A 1 RNS(0.807)T(0.134)T(0.055)FPS(0.003)R;RNS(0.979)T(0.018)T(0.003)FPSR 115.05 0.00094245 1286650000 608859 611750 388726 407781 607526 679638 630240 674890 597912 TRUE FALSE 528396.7405 607731.374 576715.1938 500373.9086 595437.4212 705784.1136 569119.4218 530570.0255 527227.5245 1.002217669 1.152692805 1.093863971 0.949066362 1.129374688 1.338670841 1.079456962 1.00633977 1 19.00806616 1.796437893 4.509920936 1.003712757 1.112692943 0.154344182 0.101541744 0.384248348 14.36733894 0.061967395 0.028350313 62.5803364 -1.796437893 0.108980186 RNS(ph)TTIMSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNSTTIMSR 9 1 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 RNS(0.954)T(0.039)T(0.007)IMSR;RNS(0.993)T(0.006)T(0.001)IMSR 67.997 0.025457 374560000 271420 276610 160450 225351 277710 284540 286830 311640 289620 TRUE FALSE 235551.1593 274792.9307 238044.1567 276520.3888 272184.1143 295486.4379 259013.2707 244998.2112 255381.4535 0.922350296 1.076009737 0.932112154 1.082773964 1.065794366 1.157039534 1.014221147 0.959342222 1 17.96229423 4.754069677 23.94372972 1.031852707 0.92235015 0.230176472 0.064891373 2832.524693 4372874.137 0.016690434 0.377387044 56763.56683 -4.754069677 -0.109502557 RNS(ph)VERPAEPVAGAATPSLVEQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RNSVERPAEPVAGAATPSLVEQQK 24 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 RNS(1)VERPAEPVAGAATPSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK;RNS(0.999)VERPAEPVAGAAT(0.001)PSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK 203.84 6.01E-25 3029136000 1055216 725753 588131 677870 878771 728702 1056211 1218876 1079143 TRUE FALSE 915766.532 720985.4808 872553.1188 831790.7441 861285.1764 756735.6375 953779.8198 958228.8527 951567.9439 0.9623764 0.757681556 0.916963549 0.874126487 0.905122101 0.795251293 1.002324454 1.00699993 1 19.85994715 2.217341846 24.90297671 1.003886358 0.867657185 0.544972177 0.057939445 155.574328 182585.1754 0.021618804 0.014591479 164.9460218 -2.217341846 -0.136229174 RNS(ph)VTPLASPEPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNSVTPLASPEPTK 14 1 Q5W015;Q5VX20;A0A1W2PR17;Q16875-3;Q16875-2;Q16875;Q16875-4;Q9H178 Q5W015 PFKFB3 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 RNS(0.998)VT(0.002)PLASPEPTK 147.1 4.98E-06 309820000 589410 515260 399730 617850 548520 480710 826180 847790 911220 TRUE FALSE 511517.9751 511875.2231 593040.765 758142.2857 537605.5252 499203.2248 746057.1908 666496.706 803496.6097 0.636614976 0.637059593 0.738075006 0.943553808 0.669082506 0.621288527 0.928513178 0.829495356 1 19.61593241 -2 0.379486743 4.950758067 0.68752066 0.434615811 0.106298351 83.13285469 1.236804118 257.7753666 0.122804524 0.01 2 -4.263237407 RNSFT(ph)PLSSSNTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNSFTPLSSSNTIR 14 1 O60825 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 RNS(0.145)FT(0.775)PLS(0.076)S(0.003)SNTIR 243.55 2.97E-17 2309600000 519290 662050 424170 489080 756820 831350 734590 813790 777370 TRUE FALSE 450664.5108 657700.95 629300.0308 600133.0891 741760.7627 863332.5725 663349.5749 639767.3414 685470.2042 0.6574531 0.959488751 0.918055996 0.875505727 1.082119628 1.259474981 0.967729262 0.933326259 1 19.38673443 5.345212444 0.912655664 1.019363943 1.35E-11 0.522790121 0.104862697 5.39452177 1.624385034 0.037781401 7.103607373 221417.7553 -5.345212444 -1.019363943 RNSFTPLSS(ph)SNTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNSFTPLSSSNTIR 14 1 O60825 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 RNS(0.001)FT(0.001)PLS(0.008)S(0.906)S(0.084)NT(0.001)IR 252.68 3.49E-24 2222700000 520480 684500 410480 458340 757330 831310 741240 803070 749150 TRUE FALSE 451697.2493 680003.4744 608989.501 562413.1023 742260.6147 863291.0336 669354.6589 631339.73 660586.3404 0.683782303 1.029393787 0.921892361 0.851384699 1.12363906 1.306855714 1.013273539 0.955726286 1 19.33338761 3.241931547 24.99983092 1.070728284 0.886474664 0.397613844 0.126526472 109.3031538 810619.1039 0.039234723 0.048585273 1745.546999 -3.241931547 -0.18425362 RNSGSS(ph)LVSSSSASSNLSHLEEDSWILWGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNSGSSLVSSSSASSNLSHLEEDSWILWGR 30 1 O60447-2;O60447 O60447-2 EVI5 Ecotropic viral integration site 5 protein homolog 1 RNS(0.309)GS(0.309)S(0.38)LVS(0.001)S(0.001)SSASSNLSHLEEDSWILWGR 114.57 6.62E-05 58307000 16834 20167 9960.3 14321 13808 15122 24220 21603 19641 TRUE FALSE 14609.34425 20034.52165 14777.1344 17572.80193 13533.24781 15703.75313 21871.14813 16983.36656 17319.06336 0.843541244 1.156790136 0.853229421 1.014650826 0.781407605 0.906732241 1.26283666 0.98061692 1 14.08007329 RNSLEGYS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNSLEGYSR 9 1 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 RNS(0.312)LEGYS(0.688)R 94.66 0.00908 731060000 458600 462120 350040 472500 575970 602020 611470 632910 650800 TRUE FALSE 397994.8481 459084.3033 519320.5148 579788.3467 564509.3239 625180.099 552169.7335 497567.1218 573863.1654 0.693536146 0.799989145 0.904955303 1.010325077 0.983700223 1.089423641 0.962197553 0.867048369 1 19.13034725 4.338034174 1.826780817 0.975889183 0.68888335 0.763739734 0.055588449 0.242010903 1.387912724 0.017579038 0.091781692 21778.8114 -4.338034174 -0.287005832 RNSS(ph)EASSGDFLDLK ddPTM_MDA-MB-175_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(0.356)S(0.637)EAS(0.007)SGDFLDLK 151.96 1.78E-06 306860000 362920 223630 217540 247590 229930 238320 268660 332520 538210 TRUE FALSE 314959.2025 222160.9598 322743.0716 303809.0937 225354.8429 247488.3246 242605.3946 261413.1857 474583.4269 0.663654027 0.468117821 0.680055504 0.640159509 0.474847688 0.521485392 0.511196516 0.550826621 1 18.8563022 1.237864482 24.99913913 1.000000507 0.559647781 0.767314163 0.075460041 7.965965374 285859.1302 0.104942415 0.018051393 17.29276668 -1.237864482 -0.440352726 RNSSEAS(ph)SGDFLDLK ddPTM_MDA-MB-175_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(0.08)S(0.001)EAS(0.907)S(0.013)GDFLDLK 322.14 1.10E-56 4770100000 1669100 1245400 1241700 1518800 1274400 905330 1593800 1795800 2809300 TRUE FALSE 1448524.206 1237218.885 1842190.273 1863666.753 1249041.933 940158.6309 1439233.521 1411782.145 2477187.754 0.584745425 0.499444938 0.743661949 0.752331651 0.504217709 0.379526594 0.580994928 0.569913258 1 21.24027179 1.238013896 24.95749733 1.000000492 0.576564175 0.593627808 0.110026195 9.999719963 456048.9709 0.164552049 0.028592952 17.29871707 -1.238013896 -0.423436317 RNSSS(ph)PVSPASVPGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 RNS(0.045)S(0.045)S(0.911)PVSPASVPGQR;RNS(0.013)S(0.057)S(0.931)PVSPASVPGQR 138.05 5.34E-06 917110000 456720 445780 171716 176840 342040 429850 415350 399350 59594 TRUE FALSE 396363.2948 442851.6418 254758.432 216994.2248 335234.0732 446386.6076 375069.4209 313952.1102 52548.86521 7.542756504 8.427425408 4.848029181 4.129379844 6.379473122 8.494695478 7.137536071 5.974479353 1 15.68137199 4.24417015 24.98723879 5.662029611 7.985091642 0.21436617 1.998636285 232.030152 1033530.028 0.5163905 1.288187319 17545.67781 -4.24417015 2.323062031 RNSSSSSS(ph)PSERPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNSSSSSSPSERPR 14 2 G3V1D0;B7WPE2;H0Y3M3;Q32P44;Q32P44-2 G3V1D0 EML3 Echinoderm microtubule-associated protein-like 3 1 RNS(0.142)S(0.004)S(0.055)S(0.091)S(0.109)S(0.597)PS(0.001)ERPR 113.66 0.00041176 294520000 95602 101050 80579 82054 119640 142480 124550 105130 136190 TRUE FALSE 82967.95348 100386.1959 119547.2739 100685.6148 117259.3981 147961.2978 112471.1602 82648.76762 120089.7733 0.690882755 0.835926267 0.995482551 0.838419559 0.976431171 1.232089075 0.936559018 0.688224861 1 16.87375377 4.584495667 2.945384869 0.934719434 0.683622805 0.271515414 0.137056883 0.49379134 7.053768496 0.038383952 0.240149305 38414.54265 -4.584495667 -0.251096629 RNST(ph)DSRPVSVTYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNSTDSRPVSVTYR 14 2 A0A088AWN2;Q8TBZ3-4;Q8TBZ3-5;Q8TBZ3-6;Q8TBZ3;Q8TBZ3-2;Q8TBZ3-7 A0A088AWN2 WDR20 WD repeat-containing protein 20 1 RNS(0.374)T(0.593)DS(0.004)RPVS(0.011)VT(0.017)YR;RNS(0.346)T(0.588)DS(0.066)RPVSVTYR 94.387 0.0067293 993840000 506200 453460 274470 345530 468450 447560 413040 501290 440190 TRUE FALSE 439304.3875 450481.1914 407204.61 423987.8676 459128.7615 464777.9228 372983.4444 394093.0345 388151.2397 1.13178664 1.160581612 1.049087491 1.092326455 1.18286048 1.197414501 0.960922976 1.015307937 1 18.56625937 2.230939232 24.99999892 0.995618655 1.13304671 0.699270371 0.044350066 103.8848207 340763.7671 0.019041197 0.013116081 170.1920352 -2.230939232 0.137428055 RNST(ph)TFPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNSTTFPSR 9 1 Q96E09 Q96E09 FAM122A Protein FAM122A 1 RNS(0.366)T(0.629)T(0.005)FPSR 126.65 0.00027399 756840000 126010 128960 95496 106960 162840 169980 170120 169710 148070 TRUE FALSE 109357.4592 128112.8533 141678.185 131246.9028 159599.8026 176519.2406 153621.7886 133418.8372 130565.3333 0.837568874 0.981216453 1.085113341 1.005220141 1.222375025 1.351961016 1.176589411 1.021854989 1 16.99441237 4.647029747 1.065232415 1.137262897 0.720283464 0.457121594 0.106300592 1.627665335 1.699746728 0.037997195 0.743949893 44363.90299 -4.647029747 -0.416979433 RNSTIPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RNSTIPTK 8 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 0 ; 90.827 0.020717 1283900000 1632540 1393570 856070 1127180 1310540 1400940 1554630 1865480 1811550 FALSE TRUE 1416795.703 1384415.547 1270068.315 1383123.447 1284462.818 1454835.068 1403862.222 1466561.619 1597390.623 0.886943796 0.86667314 0.795089377 0.865864258 0.804100637 0.910757236 0.878847166 0.918098303 1 20.60728572 -0.038558194 0.667494211 1.748646716 0.846198519 0.674679739 0.033034615 8.811585988 0.804890484 8.88951958 0.014577882 0.915043639 0.038558194 -0.902448196 RNT(ph)IDSTSSFSQFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNTIDSTSSFSQFR 14 1 Q8TDN4-2;Q8TDN4;Q8TDN4-4 Q8TDN4-2 CABLES1 CDK5 and ABL1 enzyme substrate 1 1 RNT(0.747)IDS(0.089)T(0.089)S(0.056)S(0.015)FS(0.004)QFR 162.64 8.52E-06 215340000 179380 224940 172430 233750 362680 337340 311300 368400 296520 TRUE FALSE 155674.4785 223462.3543 255817.7247 286826.5101 355463.3776 350317.6881 281110.1739 289620.5269 261465.7434 0.59539149 0.854652512 0.978398629 1.096994606 1.359502675 1.339822508 1.075131948 1.107680582 1 17.99626241 4.400256885 1.316202482 1.167277924 0.534793439 0.73462539 0.11367129 0.436948681 1.032811252 0.037647693 0.317878656 25133.72653 -4.400256885 -0.632484485 RNTIDST(ph)SSFSQFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RNTIDSTSSFSQFR 14 1 Q8TDN4-2;Q8TDN4;Q8TDN4-4 Q8TDN4-2 CABLES1 CDK5 and ABL1 enzyme substrate 1 1 RNTIDS(0.076)T(0.308)S(0.308)S(0.308)FSQFR 281.14 5.10E-33 210900000 165710 217630 167650 209290 298520 312110 310050 317080 294920 TRUE FALSE 143811.0036 216200.3742 248726.1008 256812.4933 292580.036 324117.0737 279981.3987 249274.9095 260054.8936 0.55300249 0.831364376 0.956436917 0.987531862 1.125070296 1.246340991 1.076624227 0.958547275 1 17.98845666 4.791897553 1.065579018 1.068013667 0.253704977 0.814266892 0.079519262 0.938226434 0.813064068 0.028767107 0.89011212 61929.49707 -4.791897553 -0.81430869 RPAAAAAAGSAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RPAAAAAAGSASPR 14 1 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 RPAAAAAAGS(0.034)AS(0.966)PR;RPAAAAAAGS(0.006)AS(0.994)PR;RPAAAAAAGS(0.01)AS(0.99)PR;RPAAAAAAGSAS(1)PR;RPAAAAAAGSAS(1)PR 173.19 2.90E-06 1233840000 806474 607606 395303 472783 583159 638807 563917 643381 611078 TRUE FALSE 699896.4176 603614.5962 586472.853 580135.6062 571555.2768 663382.3187 509228.4161 505798.9799 538837.055 1.298901794 1.12021731 1.08840483 1.076643859 1.060720067 1.231137155 0.945050849 0.938686334 1 19.03948954 8 0.094222764 0.683453812 2.226419227 0.502092423 0.080535025 287.873199 2.524199667 6.985025977 59.04226683 99999999.94 -8 1.542965415 RPADESNLSPSEVVQWSNHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RPADESNLSPSEVVQWSNHR 20 1 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30 E9PP16 PPFIBP2 Liprin-beta-2 0 ;; 164.02 1.22E-11 432990000 272260 296381 94733 159006 273577 301356 251431 291454 252207 FALSE TRUE 236280.1512 294434.0537 140546.1957 195110.7426 268133.3529 312949.3603 227047.2603 229128.8302 222391.3758 1.062451951 1.323945466 0.631976825 0.877330525 1.205682334 1.407200973 1.020935545 1.030295484 1 17.76274132 3.234669095 24.99982674 1.125334297 0.974502615 0.128634948 0.204981455 244.2587021 1569158.753 0.064937157 0.076397769 1716.599947 -3.234669095 -0.150831681 RPAEAT(ph)SSPTS(ph)PERPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 2 RPAEAT(0.468)S(0.17)S(0.364)PT(0.375)S(0.623)PERPR 119.16 0.00023862 736060000 573880 518260 316170 370580 538000 557430 527950 563280 567670 TRUE FALSE 498040.304 514855.5159 469070.8695 454725.853 527294.8526 578874.6928 476749.4903 442826.9554 500560.6993 0.994964856 1.028557609 0.937090887 0.90843299 1.053408414 1.156452541 0.952430926 0.884661852 1 18.9331855 2.016347645 24.99935039 0.929428594 1.011378964 0.159440803 0.071862773 378.4859727 578790.88 0.031114873 0.020971546 103.8359272 -2.016347645 0.08195037 RPAEATS(ph)SPTS(ph)PERPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 2 RPAEAT(0.182)S(0.533)S(0.305)PT(0.327)S(0.653)PERPR 135.23 0.00011789 8056000000 601150 541360 342280 387120 520280 549130 505900 566800 516190 TRUE FALSE 521706.5044 537803.7705 507807.7529 475021.5128 509927.4459 570255.3864 456837.8959 445594.2308 455166.6062 1.146188005 1.181553662 1.11565248 1.043621185 1.12030944 1.252849789 1.003671819 0.978969513 1 18.79603519 2.105726485 9.261588171 0.989047104 1.13812688 0.639092126 0.052810221 0.177566339 14.20867857 0.022345021 0.015054378 127.563517 -2.105726485 0.149079776 RPAEATSS(ph)PT(ph)SPERPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 2 RPAEAT(0.018)S(0.082)S(0.883)PT(0.671)S(0.345)PERPR;RPAEAT(0.092)S(0.106)S(0.804)PT(0.538)S(0.461)PERPR 81.665 0.013405 818370000 513210 493677 312924 353949 448266 528419 467356 528207 464506 TRUE FALSE 445387.9982 490434.0033 464255.0931 434318.5302 439346.3836 548747.6209 422031.8871 415254.0436 409592.6298 1.087392608 1.197370186 1.133455681 1.060367054 1.072642308 1.339739978 1.030369827 1.01382206 1 18.64383023 2.032123464 24.99986097 1.012157262 1.146118715 0.389071918 0.079321929 188.3232933 146560.5773 0.031861153 0.021480614 107.6771282 -2.032123464 0.133961453 RPAEATSS(ph)PTS(ph)PERPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 2 RPAEAT(0.171)S(0.277)S(0.552)PT(0.245)S(0.755)PERPR 122.47 0.00045825 7269600000 834780 728700 457390 520090 721110 719390 629390 720130 691430 TRUE FALSE 724461.7079 723913.1217 678585.3339 638184.3836 706761.3218 747065.3988 568351.8547 566135.8036 609689.9331 1.188246137 1.187346358 1.113000719 1.04673597 1.159214354 1.225320213 0.932198194 0.928563476 1 19.2177162 2.22755301 24.98410267 0.947482673 1.148449485 0.767626517 0.051718938 101.9351554 231361.5005 0.022281462 0.015181318 168.8701971 -2.22755301 0.200966811 RPAEATSSPT(ph)SPERPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 RPAEATSSPT(0.5)S(0.5)PERPR;RPAEATSS(0.003)PT(0.498)S(0.498)PERPR;RPAEAT(0.018)S(0.044)S(0.151)PT(0.675)S(0.112)PERPR;RPAEAT(0.004)SS(0.002)PT(0.962)S(0.031)PERPR;RPAEAT(0.026)S(0.026)S(0.078)PT(0.723)S(0.148)PERPR 177.29 4.78E-09 14155260000 816072 796729 571420 596534 819053 891352 767129 893911 845289 TRUE FALSE 708226.0175 791495.2347 847760.6233 731986.1622 802755.4478 925642.8882 692732.9477 702755.0891 745359.8974 0.950179933 1.061896726 1.137384271 0.982057345 1.077003808 1.241873746 0.929393908 0.942839951 1 19.50757767 RPAEATSSPTS(ph)PERPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 RPAEATSS(0.002)PT(0.175)S(0.823)PERPR;RPAEATSS(0.002)PT(0.008)S(0.99)PERPR;RPAEAT(0.024)S(0.024)S(0.094)PT(0.375)S(0.483)PERPR;RPAEAT(0.007)S(0.005)S(0.026)PT(0.291)S(0.671)PERPR;RPAEAT(0.142)S(0.142)S(0.114)PT(0.074)S(0.528)PERPR 112.74 0.0003732 1549916000 598362 513012 265166.4 367723 459549 511420 482174 558404 517573 TRUE FALSE 519286.9456 509641.9904 393401.758 451220.1274 450404.874 531094.6583 435412.8397 438993.6501 456386.1096 1.13782373 1.116690407 0.861993277 0.988680676 0.986894352 1.16369593 0.954044899 0.96189091 1 18.79989536 4.439065974 23.70424028 0.990178148 1.132540471 0.382823032 0.07362289 83.22967859 51842.61554 0.018491985 0.048925542 27483.11621 -4.439065974 0.142362322 RPAEDMEEEQAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RPAEDMEEEQAFK 13 1 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;; 209.19 6.40E-08 3780060000 2070970 1753090 1530260 1967290 1581020 1494660 1801620 2362870 4099160 FALSE TRUE 1797286.067 1741573.836 2270298.854 2413993.263 1549560.795 1552160.537 1626899.17 1857588.638 3614561.975 0.497234818 0.481821545 0.628097919 0.667852227 0.428699468 0.429418709 0.450095802 0.513918049 1 21.7853894 1.238722562 10.68310321 1.00137461 0.511575967 0.789258332 0.079225194 0.032634927 110.6646914 0.117394848 0.021004466 17.32696756 -1.238722562 -0.489798643 RPAEDMEEEQAFKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 RPAEDMEEEQAFKR 14 2 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;; 249.41 2.35E-18 12008560000 9720820 7641370 5028211 5462170 7301550 6443630 8349230 10039640 5726096 FALSE TRUE 8436189.008 7591173.337 7459870.658 6702439.183 7156263.44 6691520.616 7539522.96 7892741.115 5049163.454 1.670809251 1.503451692 1.477446853 1.327435573 1.417316652 1.325273122 1.4932222 1.563177977 1 22.26761295 4.750699516 1.176270105 1.386623351 1.807530128 0.303960171 0.150526923 2.285639523 2.621005709 0.044759364 1.192973694 56324.78155 -4.750699516 0.420906777 RPAEDYVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RPAEDYVPR 9 1 Q969E4;Q5H9L2 Q969E4 TCEAL3;TCEAL5 Transcription elongation factor A protein-like 3;Transcription elongation factor A protein-like 5 0 ;; 113.44 0.0028849 1033790000 654680 600270 436600 471690 543030 590840 624150 700610 561120 FALSE TRUE 568162.3793 596326.7868 647741.2203 578794.4238 532224.7654 613569.9971 563620.0291 550790.0037 494785.0328 1.148301467 1.205223981 1.30913665 1.169789677 1.075668685 1.240073883 1.139121016 1.113190511 1 18.91644233 -0.07445812 0.668714641 2.83E-10 1.199124561 0.499479259 0.060629031 14.05936221 1.23163055 19.07601062 0.027973857 0.842445627 0.07445812 1.199124561 RPAEEQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RPAEEQKR 8 2 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDQ3;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 0 ;; 87.308 0.0086709 68332000 109202 104367 124276 75334 69785 82483 92317 99823 69641 FALSE TRUE 94770.67902 103681.4063 184376.2893 92439.73611 68396.41503 85656.17438 83364.11155 78476.62827 61408.12032 1.543292296 1.688398957 3.002474076 1.505334077 1.113800824 1.394867225 1.357542148 1.277951969 1 15.90614182 3.491842557 24.61586857 1.258076354 2.074891971 0.489244528 0.395643314 467.3221667 781420.4141 0.108523294 0.154568298 3103.43431 -3.491842557 0.816815617 RPAEPGPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPAEPGPAR 9 1 A0A0A0MTR2;Q8N543;H3BR79;H3BR02 A0A0A0MTR2 OGFOD1 Prolyl 3-hydroxylase OGFOD1 0 ; 105.98 0.0048277 80904000 134225 119779 73632 78548 109659 110553 108960 118227 92103 FALSE TRUE 116486.8262 118992.1639 109240.6815 96383.52393 107477.0004 114806.0454 98393.07597 92945.07609 81214.68826 1.434307373 1.465155705 1.345085277 1.186774535 1.323368996 1.413611847 1.211518237 1.144436777 1 16.30945305 0.078799297 0.460726845 2.95E-17 1.393945603 0.715828584 0.077905236 8.786718718 0.665201823 8.342726049 0.069301192 1.1989451 -0.078799297 1.393945603 RPAETNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RPAETNLR 8 1 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ;;;;;; 169.21 0.00048479 9244620000 3275370 3511400 2471020 2498930 3061820 3948990 3295900 3294680 3659310 FALSE TRUE 2842521.556 3488333.382 3666013.537 3066350.25 3000895.772 4100910.201 2976264.125 2590138.321 3226710.54 0.880934785 1.081080357 1.136145772 0.950302239 0.930017036 1.270925963 0.922383365 0.802717904 1 21.62163273 2.018160578 24.98524292 0.879852253 1.043294725 0.211223907 0.120226836 288.3530314 396713.2774 0.047513269 0.032027446 104.2702892 -2.018160578 0.163442472 RPAGGRPS(ph)PSAMGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 RPAGGRPSPSAMGK 14 2 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 RPAGGRPS(1)PSAMGK;RPAGGRPS(1)PSAMGK;RPAGGRPS(0.992)PS(0.008)AMGK;RPAGGRPS(0.999)PS(0.001)AMGK;RPAGGRPS(0.999)PS(0.001)AMGK;RPAGGRPS(0.998)PS(0.002)AMGK;RPAGGRPS(0.952)PS(0.048)AMGK;RPAGGRPS(0.999)PS(0.001)AMGK;RPAGGRPS(0.974)PS(0.026)AMGK;RPAGGRPS(0.971)PS(0.029)AMGK 114.28 0.00038346 3222390000 5552940 5135840 3557900 4201550 4865020 4688090 5633000 6178350 5956380 TRUE FALSE 4819104.91 5102102.329 5278512.34 5155576.144 4768215.62 4868443.856 5086712.527 4857157.932 5252223.542 0.917536139 0.971417589 1.00500527 0.981598765 0.907847045 0.926930055 0.968487439 0.924781265 1 22.32449689 3.296734959 24.99999874 0.943786717 0.971649759 0.10516633 0.033077352 158.4118057 68074.77732 0.009434063 0.012179315 1980.318109 -3.296734959 0.027863041 RPAMLDNEADGNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPAMLDNEADGNK 13 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 94.023 0.0030271 0 232810 158040 117000 146260 175440 146680 176830 204410 207040 FALSE TRUE 202043.5686 157001.8248 173581.5913 179470.5684 171949.0872 152322.8745 159681.0538 160698.5122 182563.9671 1.106700144 0.859982544 0.950798748 0.98305581 0.941856654 0.834353443 0.874658107 0.880231268 1 17.47804252 2.984601487 21.82768223 0.892027966 0.964831629 0.197770597 0.072321991 214.69747 304339.5755 0.021841678 0.022600286 965.1648278 -2.984601487 0.072803662 RPAPAVS(ph)PGSWKPGPPGS(ph)PRPWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPAPAVSPGSWKPGPPGSPRPWK 23 3 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 RPAPAVS(1)PGS(0.001)WKPGPPGS(0.999)PRPWK;RPAPAVS(1)PGS(0.006)WKPGPPGS(0.994)PRPWK 140.35 2.81E-07 2974700000 2610900 1958280 1423420 1583220 1881220 1309120 2346700 2725800 1891300 TRUE FALSE 2265862.95 1945415.93 2111790.673 1942714.299 1843787.403 1359482.694 2119117.395 2142908.882 1667712.669 1.35866507 1.16651745 1.266279685 1.164897488 1.105578579 0.815178009 1.270672961 1.2849389 1 20.66943932 5.402656617 0.791972062 1.127376065 1.791282483 0.228282199 0.139252295 12.30733188 2.814165953 0.0545958 9.190079958 252729.8951 -5.402656617 0.663906418 RPAPAVS(ph)PGSWKPGPPGSPRPWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPAPAVSPGSWKPGPPGSPRPWK 23 3 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 RPAPAVS(0.998)PGS(0.002)WKPGPPGSPRPWK 216.67 1.39E-31 1668100000 2383600 1730900 1270900 1426000 1537100 1349000 2008200 2404200 1518600 TRUE FALSE 2068601.221 1719529.604 1885511.491 1749795.095 1506514.717 1400896.903 1813445.073 1890080.54 1339072.838 1.544801121 1.284119545 1.40807239 1.306721371 1.125043145 1.046169307 1.354254243 1.411484488 1 20.35280301 7.999999473 0.644988816 1.229644698 27.17441668 0.353827073 0.138447658 299.4884558 1.989845611 0.063515833 11076.972 99999878.64 -7.999999473 25.94477198 RPAS(ph)PS(ph)SPEHLPATPAESPAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 2 RPAS(0.999)PS(0.983)S(0.018)PEHLPATPAESPAQR 161.5 6.05E-11 1914500000 636320 523280 326800 398620 398840 531580 437790 521930 488540 TRUE FALSE 552228.6998 519842.5392 484841.5731 489132.7635 390903.8643 552030.2266 395333.1932 410319.3312 430785.3577 1.28191149 1.206732146 1.125482945 1.135444264 0.907421428 1.281450766 0.917703413 0.95249136 1 18.71660969 8 0.206418313 0.901196256 2.817169117 0.45075063 0.104944146 87.69529125 1.316849044 0.598762296 53.08135604 99999999.93 -8 1.915972862 RPAS(ph)PSHNGSSGGGYGASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPASPSHNGSSGGGYGASK 19 1 K7ELX9;K7EQ79;K7ENM4;K7ENP7;Q6PI98;Q6PI98-3;Q6PI98-4 K7ELX9 INO80C INO80 complex subunit C 1 RPAS(0.718)PS(0.094)HNGS(0.094)S(0.094)GGGYGASK 81.949 0.0024222 24771000 61084 54220 31891 50579 55853 43909 61922 69498 114620 TRUE FALSE 53011.59463 53863.82525 47313.59427 62063.735 54741.63457 45598.20764 55916.81397 54636.39353 101069.7542 0.524505032 0.532937135 0.468128123 0.614068328 0.541622318 0.451155818 0.553249728 0.540581047 1 16.6249918 1.236603989 5.916058483 1.018888652 0.52764993 0.917599974 0.04444029 0.03567198 4.569596646 0.070842263 0.010785609 17.24264906 -1.236603989 -0.491238722 RPAS(ph)PSS(ph)PEHLPATPAESPAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 2 RPAS(0.978)PS(0.116)S(0.906)PEHLPATPAESPAQR;RPAS(0.998)PS(0.245)S(0.755)PEHLPAT(0.002)PAESPAQR;RPAS(0.977)PS(0.308)S(0.715)PEHLPATPAESPAQR;RPAS(0.995)PS(0.296)S(0.71)PEHLPATPAESPAQR 163.49 5.26E-11 5497180000 1118550 1028810 662350 740480 1055100 1067910 915310 1019000 1041810 TRUE FALSE 970730.7835 1022051.679 982664.6754 908617.3015 1034105.574 1108993.189 826543.3771 801094.7799 918648.4086 1.056694568 1.112560224 1.069685275 0.989080581 1.125681561 1.207200903 0.899738539 0.872036322 1 19.80915328 2.215042064 24.99441894 0.912106948 1.089987141 0.608298059 0.063865526 148.6641447 157992.0858 0.026629591 0.017964913 164.0748682 -2.215042064 0.177880192 RPAS(ph)PSSPEHLPATPAESPAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 1 RPAS(0.969)PS(0.03)S(0.001)PEHLPATPAESPAQR;RPAS(0.953)PS(0.038)S(0.01)PEHLPATPAESPAQR;RPAS(0.954)PS(0.044)S(0.002)PEHLPATPAESPAQR;RPAS(0.333)PS(0.333)S(0.333)PEHLPATPAESPAQR 174.89 9.93E-13 2018960000 904586 807260 415182 576241 813875 901898 739493 917077 816456 TRUE FALSE 785042.6682 801957.0559 615965.4039 707085.3263 797680.4798 936594.5997 667777.0827 720967.2203 719935.5018 1.090434721 1.113929031 0.855584149 0.982150935 1.10798881 1.300942372 0.927551261 1.001433071 1 19.45750814 RPAS(ph)VSSSAAVEHEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 RPASVSSSAAVEHEQR 16 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 RPAS(0.997)VS(0.003)SSAAVEHEQR;RPAS(0.971)VS(0.027)S(0.002)SAAVEHEQR;RPAS(0.993)VS(0.006)S(0.001)SAAVEHEQR;RPAS(0.993)VS(0.002)S(0.002)S(0.002)AAVEHEQR;RPAS(0.964)VS(0.036)SSAAVEHEQR;RPAS(0.995)VS(0.005)SSAAVEHEQR;RPAS(0.873)VS(0.127)SSAAVEHEQR;RPAS(0.997)VS(0.003)SSAAVEHEQR 286.95 2.72E-36 11046351000 1715162 1786066 1117812 1339452 1869026 1955596 1685466 1946120 1836832 TRUE FALSE 1488498.996 1774333.215 1658389.622 1643595.049 1831836.039 2030829.044 1522009.767 1529957.383 1619683.813 0.919005909 1.095481229 1.023897139 1.014762903 1.130983729 1.253842896 0.939695609 0.944602502 1 20.62728077 RPASPS(ph)HNGSSGGGYGASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPASPSHNGSSGGGYGASK 19 1 K7ELX9;K7EQ79;K7ENM4;K7ENP7;Q6PI98;Q6PI98-3;Q6PI98-4 K7ELX9 INO80C INO80 complex subunit C 1 RPAS(0.39)PS(0.594)HNGS(0.008)S(0.008)GGGYGASK 208.16 1.74E-16 107810000 40429 36886 22495 37833 36945 33247 39929 46796 90810 TRUE FALSE 35086.20522 36643.69344 33373.65724 46423.56089 36209.86678 34526.0336 36056.69173 36789.03957 80074.54525 0.438169272 0.457619751 0.416782351 0.579754287 0.452201966 0.431173646 0.45028906 0.459434886 1 16.28905608 1.238446783 24.99993035 1.000000591 0.461199763 0.936008306 0.044317027 0.607844516 132905.5417 0.059515687 0.010615106 17.31596833 -1.238446783 -0.538800828 RPASPS(ph)S(ph)PEHLPATPAESPAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 2 RPAS(0.099)PS(0.933)S(0.967)PEHLPATPAESPAQR 87.237 0.010026 2329800000 254800 247810 165780 190350 252950 245330 249010 268940 242580 TRUE FALSE 221127.5344 246182.1198 245951.7625 233571.8768 247916.7899 254768.0038 224861.0485 211429.2739 213902.4687 1.033777383 1.150908268 1.149831341 1.091955031 1.159017899 1.191047515 1.051231666 0.988437745 1 17.70659361 2.029045137 5.351414012 1.000078536 1.130889989 0.639948169 0.042590424 0.102717339 8.08412981 0.018352363 0.011630977 106.9165995 -2.029045137 0.130811453 RPASPSS(ph)PEHLPATPAESPAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 1 RPAS(0.286)PS(0.286)S(0.429)PEHLPATPAESPAQR 128.91 9.77E-06 501720000 153760 128010 79806 67747 120400 123760 96909 118480 117350 TRUE FALSE 133440.2264 127169.0939 118400.4485 83129.9918 118004.2756 128521.1273 87510.7801 93143.97401 103477.0167 1.289563912 1.228959801 1.144219773 0.803366723 1.140391165 1.242025828 0.845702581 0.900141664 1 16.65895084 7.999999997 0.334526494 0.932601385 5.059284285 0.379845585 0.136031126 84.574301 1.314437413 0.211670534 213.7748287 99999999.4 -7.999999997 4.1266829 RPASVSSSAAVEHEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RPASVSSSAAVEHEQR 16 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 0 ;;;;; 171.26 3.24E-09 986763000 773460 753096 463537 616133 793728 856685 691375 809296 998095 FALSE TRUE 671245.3013 748148.8628 687705.0436 756035.4147 777934.3657 889642.2263 624325.5589 636234.3483 880101.3461 0.762690915 0.850071263 0.781393014 0.859032222 0.883914528 1.010840661 0.709379166 0.722910323 1 19.74731014 4.744002045 22.44875922 0.839348391 0.762690785 0.059606534 0.100838574 522.6743801 2156002.142 0.025410714 0.203664 55462.83247 -4.744002045 -0.076657606 RPATADS(ph)PKPSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RPATADSPKPSAK 13 2 Q03111 Q03111 MLLT1 Protein ENL 1 RPATADS(1)PKPSAK;RPATADS(1)PKPSAK;RPATADS(1)PKPSAK;RPATADS(0.996)PKPS(0.004)AK 159.04 2.41E-05 2951060000 8134330 5086250 5023400 4717730 4907300 4090030 7424710 7834970 7147970 TRUE FALSE 7059357.681 5052838.089 7452733.042 5788962.702 4809654.331 4247376.101 6704662.767 6159522.637 6302945.13 1.120009382 0.80166303 1.18242074 0.918453609 0.76308047 0.673871661 1.063734909 0.977245162 1 22.58759467 4.76886302 22.92417815 0.928685963 1.120010345 0.147436305 0.14857033 8329.821632 6301292.255 0.037157665 3.653401428 58730.40823 -4.76886302 0.191324382 RPDADLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RPDADLK 7 1 P27824;P27824-2;P27824-3;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 ;;; 113.94 0.0096466 3393280000 4670330 3441730 2746760 3903450 4369840 3870770 3201790 6033900 5549100 FALSE TRUE 4053134.057 3419121.049 4075102.323 4789787.983 4282888.733 4019681.027 2891280.899 4743597.441 4893091.72 0.828338051 0.698764962 0.8328277 0.97888784 0.87529296 0.821501263 0.590890395 0.96944789 1 22.2223149 1.584054602 11.75410898 0.988352334 0.808825634 0.350965973 0.102356897 0.122236531 41.32620626 0.068577448 0.026468991 38.375549 -1.584054602 -0.1795267 RPDDVPLSLS(ph)PSKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RPDDVPLSLSPSKR 14 2 Q9UFC0;F8WDB4 Q9UFC0 LRWD1 Leucine-rich repeat and WD repeat-containing protein 1 1 RPDDVPLS(0.001)LS(0.762)PS(0.237)KR;RPDDVPLS(0.157)LS(0.812)PS(0.031)KR;RPDDVPLS(0.003)LS(0.561)PS(0.436)KR;RPDDVPLS(0.001)LS(0.633)PS(0.365)KR 182.49 7.91E-07 3689090000 2653580 2196900 1489840 1820150 2164740 1822930 2253810 2851620 2215850 TRUE FALSE 2302902.68 2182468.419 2210331.607 2233442.877 2121665.909 1893059.297 2035235.853 2241823.254 1953894.737 1.178621671 1.116983621 1.131243953 1.143072262 1.085865 0.968864525 1.041630245 1.147361325 1 20.89792132 3.1042228 4.442864271 1.053812078 1.139498251 0.487642487 0.048617081 0.232259707 8.036927268 0.016165962 0.018504199 1271.226098 -3.1042228 0.085686173 RPDHSGGS(ph)PS(ph)PPTSEPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RPDHSGGSPSPPTSEPAR 18 1 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 2 RPDHS(0.015)GGS(0.985)PS(0.994)PPT(0.003)S(0.003)EPAR;RPDHS(0.267)GGS(0.735)PS(0.988)PPT(0.008)S(0.001)EPAR;RPDHS(0.473)GGS(0.541)PS(0.985)PPTSEPAR 144.22 3.49E-07 1177800000 658979 616085 342214 431037 584307 606033 509716 674982 594373 TRUE FALSE 571893.2555 612037.8971 507709.835 528910.5388 572680.4339 629347.4817 460283.8208 530642.352 524106.9011 1.091176732 1.167773017 0.968714272 1.009165378 1.092678674 1.200799838 0.878225072 1.012469691 1 18.99950158 -1.999999584 0.153778767 0.493097879 1.146034675 0.133158024 0.088720746 291.5233771 3.738485703 41.68107094 1.38240397 0.01000001 1.999999584 0.652936796 RPDHSGGS(ph)PSPPTSEPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPDHSGGSPSPPTSEPAR 18 1 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 RPDHS(0.007)GGS(0.993)PSPPTSEPAR;RPDHS(0.001)GGS(0.998)PS(0.001)PPTSEPAR 151.89 2.72E-08 503140000 234071 220637 122296 149594 206476 198614 204930 234873 200280 TRUE FALSE 203137.9243 219187.621 181438.7547 183561.6041 202367.5316 206254.8091 185055.9201 184647.2367 176603.1266 1.150251008 1.241131034 1.027381328 1.03940178 1.145888725 1.1679001 1.047863216 1.045549081 1 17.43015136 -1.999999961 0.276273435 2.39E-08 1.156571214 0.331114749 0.0631479 101.010695 1.634271896 54.79607241 0.165259813 0.010000001 1.999999961 1.156571191 RPDLLTMVVDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RPDLLTMVVDYR 12 1 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 ;;; 159.02 9.79E-05 3215948000 2652687 3123652 1984283 2330812 2906214 3148430 2767515 3208782 3064482 FALSE TRUE 2302127.692 3103132.524 2943888.896 2860058.489 2848386.027 3269552.139 2499121.821 2522608.94 2702202.429 0.851944942 1.148371599 1.089440548 1.058417555 1.054097945 1.209958256 0.924846264 0.933538107 1 21.36570432 2.182506736 24.99999913 0.947618103 1.072138695 0.256215009 0.092834914 105.0384434 46846.05545 0.035806186 0.024140539 152.2322746 -2.182506736 0.124520592 RPDPDS(ph)DEDEDYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 RPDPDSDEDEDYER 14 1 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 1 RPDPDS(1)DEDEDYER;RPDPDS(1)DEDEDYER;RPDPDS(0.992)DEDEDY(0.008)ER;RPDPDS(1)DEDEDYER;RPDPDS(1)DEDEDYER;RPDPDS(1)DEDEDYER;RPDPDS(1)DEDEDYER;RPDPDS(1)DEDEDYER;RPDPDS(1)DEDEDYER;RPDPDS(1)DEDEDYER 239.19 2.51E-17 10734089000 5130859 4999698 3406775 4220265 4624534 5042741 4034231 4569815 5608580 TRUE FALSE 4452802.983 4966854.655 5054302.785 5178540.671 4532514.821 5236738.509 3642991.899 3592595.625 4945540.062 0.900367387 1.004309862 1.021992082 1.047113279 0.916485311 1.058881021 0.736621654 0.726431407 1 22.23769664 2.237650814 24.9999902 0.797795697 0.992606704 0.438454328 0.089683415 18.95672641 520870.7387 0.034375956 0.02469965 172.8426092 -2.237650814 0.194811007 RPDPDS(ph)DEDEDYERER ddPTM_MDA-MB-175_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 245.12 3.34E-20 6407480000 1816745 1770284 859890 915675 1469809 1671783 1560256 1725955 454919 TRUE FALSE 1576657.545 1758654.888 1275735.68 1123593.004 1440562.677 1736097.574 1408942.613 1356872.955 401138.9941 3.930451959 4.384153408 3.180283391 2.801006685 3.591180857 4.327920246 3.512355154 3.382550624 1 18.61374269 4.231130829 24.86633993 3.208246593 4.157302726 0.196577605 0.860818337 249.6064389 835404.487 0.220495302 0.474005209 17026.71354 -4.231130829 0.949056132 RPDQQLQGEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RPDQQLQGEGK 11 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;;;; 186.76 6.23E-06 4037330000 6292520 5133880 3393090 4263910 4648050 4088360 5606450 6409340 5641010 FALSE TRUE 5460947.539 5100155.204 5033999.673 5232095.935 4555562.899 4245641.855 5062737.342 5038752.519 4974136.224 1.097868513 1.025334847 1.012034944 1.051860202 0.915850048 0.853543543 1.017812363 1.012990455 1 22.24601459 4.575080036 0.941188638 0.973047556 1.133246203 0.344507069 0.055342963 2.235805907 1.900369869 0.021030126 0.347831481 37590.66735 -4.575080036 0.160198648 RPDS(ph)PTRPTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RPDSPTRPTLR 11 2 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 RPDS(0.882)PT(0.112)RPT(0.006)LR;RPDS(0.995)PT(0.004)RPT(0.001)LR;RPDS(0.998)PT(0.002)RPTLR;RPDS(0.999)PT(0.001)RPTLR;RPDS(0.922)PT(0.069)RPT(0.01)LR;RPDS(0.953)PT(0.035)RPT(0.012)LR 135.58 9.21E-05 7087230000 2734273 2706535 1804900 2077579 2617264 2843926 2512464 2823145 2660152 TRUE FALSE 2372931.895 2688755.593 2677755.677 2549325.066 2565185.567 2953333.673 2268805.628 2219437.411 2345671.861 1.011621418 1.146262458 1.141573006 1.086820841 1.093582444 1.259056615 0.967230611 0.946184097 1 21.16156978 2.151298328 14.06366346 0.965582483 1.122033561 0.564724875 0.062846034 0.607751399 95.97146756 0.024566715 0.016562818 141.6766658 -2.151298328 0.156451078 RPDTTAPLTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPDTTAPLTDR 11 1 Q96JB2;Q96JB2-2;A0A087WYY9 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 0 ; 114.02 0.0021065 470270000 277690 257350 199773 224190 262660 307750 258090 290540 363190 FALSE TRUE 240992.5629 255659.4509 296383.891 275095.766 257433.5799 319589.3416 233060.4715 228410.282 320254.0919 0.752504243 0.798301903 0.925464806 0.858992197 0.803841657 0.997924303 0.727736124 0.713215811 1 18.28885748 4.471878779 24.88755095 0.844689778 0.763953621 0.107164525 0.098372573 296.1923658 1406118.218 0.025278496 0.067369035 29640.03954 -4.471878779 -0.080736157 RPDYAPMES(ph)S(ph)DEEDEEFQFIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 RPDYAPMESSDEEDEEFQFIK 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 RPDY(0.006)APMES(0.997)S(0.997)DEEDEEFQFIK;RPDY(0.008)APMES(0.996)S(0.996)DEEDEEFQFIK;RPDY(0.01)APMES(0.995)S(0.995)DEEDEEFQFIK;RPDY(0.057)APMES(0.971)S(0.971)DEEDEEFQFIK;RPDY(0.047)APMES(0.976)S(0.976)DEEDEEFQFIK;RPDY(0.027)APMES(0.987)S(0.987)DEEDEEFQFIK;RPDY(0.017)APMES(0.991)S(0.991)DEEDEEFQFIK;RPDY(0.013)APMES(0.994)S(0.994)DEEDEEFQFIK 139.19 1.41E-06 339640000 604289 517587 376784 493143 524760 508479 538304 659017 813767 TRUE FALSE 524430.6776 514186.9369 558998.0027 605118.6554 514318.3027 528040.5162 486099.3609 518091.343 717564.3923 0.730848246 0.716572537 0.779021379 0.843295266 0.716755609 0.735878929 0.677429602 0.722013729 1 19.45274878 1.236259959 24.99984148 1.000000338 0.739254194 0.772846228 0.044257068 31.38323828 340943.1795 0.075439228 0.011623863 17.22899555 -1.236259959 -0.260746144 RPDYAPMES(ph)S(ph)DEEDEEFQFIKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPDYAPMESSDEEDEEFQFIKK 22 2 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 RPDYAPMES(1)S(1)DEEDEEFQFIKK 112.39 0.00020602 121540000 86604 57814 38196 43378 59796 49580 71235 90213 41470 TRUE FALSE 75159.06197 57434.21603 56667.71336 53227.63789 58606.17659 51487.37468 64326.64066 70921.65199 36567.46384 2.055353423 1.570637118 1.549675788 1.455601026 1.602686389 1.408010545 1.759122288 1.939474181 1 15.15827295 4.738782841 24.99999977 1.573717637 2.055353564 0.297266686 0.244981116 25.35979325 2851224.171 0.059430673 0.336111409 54800.28799 -4.738782841 0.481635928 RPEGPGAQAPS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPEGPGAQAPSSPR 14 1 P40222 P40222 TXLNA Alpha-taxilin 1 RPEGPGAQAPS(0.823)S(0.177)PR 131.11 3.56E-05 8852200000 2457700 2559800 1692500 1994000 2792400 2603100 2613000 3137600 2766700 TRUE FALSE 2132908.718 2542984.505 2510998.661 2446768.176 2736836.703 2703242.941 2359591.662 2466648.657 2439623.878 0.874277686 1.042367444 1.02925647 1.002928443 1.121827314 1.108057257 0.967194855 1.011077437 1 21.21822731 4.74039425 24.77207261 1.034021347 0.874277624 0.530435063 0.047609511 124.9993143 1688570.87 0.012357004 0.077023227 55003.99705 -4.74039425 -0.159743723 RPEGPGAQAPSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RPEGPGAQAPSSPR 14 1 P40222 P40222 TXLNA Alpha-taxilin 1 RPEGPGAQAPS(0.078)S(0.922)PR;RPEGPGAQAPS(0.013)S(0.987)PR;RPEGPGAQAPS(0.005)S(0.995)PR;RPEGPGAQAPS(0.013)S(0.987)PR;RPEGPGAQAPS(0.013)S(0.987)PR;RPEGPGAQAPS(0.211)S(0.789)PR 226.73 2.43E-12 24545150000 7310260 7893120 5173820 6476940 8632870 9232090 7957080 9241410 8810080 TRUE FALSE 6344190.619 7841269.575 7675896.657 7947628.221 8461092.777 9587254.476 7185403.606 7265206.388 7768562.379 0.816649247 1.009359157 0.988071703 1.023050062 1.089145245 1.234109222 0.924933502 0.935206031 1 22.88921621 5.063558656 1.751831703 1.02470269 0.544584881 0.362335161 0.087036749 3.407005048 4.999380234 0.025565909 3.58960773 115760.0368 -5.063558656 -0.480117809 RPELEDSTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 179.94 3.29E-06 5421700000 2775930 2778330 1827060 1977550 2439940 2970070 2365230 2697330 2572920 FALSE TRUE 2409083.817 2760078.967 2710632.327 2426582.952 2391389.968 3084330.515 2135850.359 2120526.97 2268752.329 1.061854036 1.216562483 1.194767843 1.069567146 1.054055102 1.359483129 0.941420679 0.934666576 1 21.11346769 2.172068831 24.99999933 0.952968395 1.154721562 0.513671439 0.091920983 42.56360007 16002.61762 0.036141823 0.024366818 148.6171166 -2.172068831 0.201753167 RPELLTHSTTEVTQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RPELLTHSTTEVTQPR 16 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 ;;; 188.47 7.62E-10 1580910000 827590 760260 396625 664350 795890 901970 697370 854510 821780 FALSE TRUE 718221.8847 755265.802 588434.1766 815200.8215 780053.3461 936669.3696 629739.1647 671779.6863 724630.1046 0.991156564 1.042277704 0.812047654 1.124988896 1.076484873 1.292617245 0.869049134 0.92706566 1 19.46688522 RPENPKPQDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPENPKPQDGK 11 2 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 78.705 0.016396 71217000 121560 76312 71540 87105 65719 64128 108240 117670 155870 FALSE TRUE 105495.538 75810.70145 106136.9833 106883.5216 64411.32048 66595.04566 97742.90146 92507.18621 137443.2262 0.767557201 0.551578303 0.772224185 0.777655797 0.468639469 0.484527667 0.7111511 0.673057442 1 17.06847628 1.101422095 2.331550177 1.211042193 0.641100577 0.474071489 0.115344602 0.948234744 3.834785036 1.300818149 0.031290017 12.63054513 -1.101422095 -0.569941616 RPENSLLEETLHFDHAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPENSLLEETLHFDHAVR 18 1 O00566;U3KQ48 O00566 MPHOSPH10 U3 small nucleolar ribonucleoprotein protein MPP10 0 ; 208.34 2.61E-16 176187000 112224 102805 60917 72412 99302 99911 92572 110402 90291 FALSE TRUE 97393.31406 102129.6672 90376.66496 88854.25135 97326.08448 103754.6408 83594.38169 86793.39145 79616.90084 1.223274368 1.282763661 1.135144222 1.116022483 1.222429955 1.303173569 1.049957745 1.090137779 1 16.28078709 2.215869504 24.96685833 1.055884061 1.209308411 0.62624074 0.060651682 168.0948204 184951.983 0.026009479 0.017549071 164.38777 -2.215869504 0.15342435 RPEPSTLENITDDKYATVSS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RPEPSTLENITDDKYATVSSPSK 23 2 Q01804-5;Q01804-3;Q01804 Q01804-5 OTUD4 OTU domain-containing protein 4 1 RPEPSTLENITDDKYAT(0.004)VS(0.126)S(0.865)PS(0.004)K;RPEPSTLENITDDKYATVS(0.164)S(0.835)PSK;RPEPSTLENITDDKYATVS(0.014)S(0.972)PS(0.014)K 244.04 1.05E-37 1078350000 1464290 1171400 1017420 1006400 1071750 993830 1445290 1602730 1561520 TRUE FALSE 1270780.366 1163704.996 1509447.715 1234918.502 1050424.272 1032063.283 1305125.998 1259998.662 1376918.884 0.922915925 0.845151453 1.096250282 0.896870916 0.762880286 0.749545449 0.947859756 0.915085613 1 20.39301214 1.305175926 1.764059094 1.026156873 0.885187757 0.116018445 0.097035682 2.011830914 6.686318236 0.466563567 0.028893458 20.19184137 -1.305175926 -0.140969116 RPES(ph)PPSILTPPVVPTADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RPESPPSILTPPVVPTADK 19 1 P55198;Q6P2C6 P55198 MLLT6 Protein AF-17 1 RPES(0.812)PPS(0.187)ILT(0.001)PPVVPTADK;RPES(0.982)PPS(0.017)ILT(0.001)PPVVPTADK;RPES(0.997)PPS(0.003)ILTPPVVPTADK;RPES(0.953)PPS(0.046)ILT(0.002)PPVVPTADK 176.48 3.43E-13 463572000 1646280 633310 545336 650280 596330 566568 655140 844660 1415550 TRUE FALSE 1428719.927 629149.7449 809062.3136 797936.0129 584464.1997 588364.2376 591604.6236 664036.0322 1248205.292 1.144619348 0.504043485 0.648180487 0.639266648 0.468243648 0.471368165 0.473964201 0.531992643 1 20.2514238 4.743157494 24.60240906 0.577473891 1.144619637 0.541034527 0.159412323 290.7338799 1555934.72 0.037854986 0.293464599 55355.08141 -4.743157494 0.567145746 RPES(ph)PSEIS(ph)PIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RPESPSEISPIK 12 1 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 2 RPES(0.98)PS(0.02)EIS(1)PIK;RPES(0.992)PS(0.008)EIS(1)PIK;RPES(0.996)PS(0.009)EIS(0.995)PIK 143.46 0.00021776 398730000 985800 881270 736370 931370 947060 790270 914320 1153160 2230420 TRUE FALSE 855524.0323 875480.8793 1092480.995 1142851.794 928215.3589 820672.1983 825649.3871 906565.7079 1966742.289 0.434995493 0.445142653 0.555477452 0.581088738 0.471955764 0.417274903 0.41980558 0.46094789 1 20.9073765 1.237731809 24.99933867 1.000000613 0.473504191 0.902002986 0.054555469 6.546033194 197326.921 0.086557489 0.014783343 17.28748472 -1.237731809 -0.526496421 RPES(ph)PSEISPIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RPESPSEISPIK 12 1 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 1 RPES(0.981)PS(0.019)EISPIK;RPES(0.995)PS(0.005)EISPIK;RPES(0.999)PS(0.001)EISPIK;RPES(0.996)PS(0.004)EISPIK;RPES(0.998)PS(0.002)EISPIK 201.04 9.37E-08 6403450000 5231530 4316500 3001480 3554170 4171470 3734730 4683760 5341760 4942730 TRUE FALSE 4540170.055 4288144.627 4453005.767 4361198.621 4088465.908 3878407.48 4229529.676 4199466.194 4358406.09 1.041704229 0.983879092 1.021705109 1.000640723 0.938064472 0.889868314 0.970430379 0.963532564 1 22.05536919 3.33643914 5.283884016 0.952137403 1.012167138 0.480837935 0.030964473 0.196590087 8.632174516 0.009383195 0.012133596 2169.897101 -3.33643914 0.060029735 RPFDPNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RPFDPNDR 8 1 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2;F8WEA1 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ;;;; 133.13 0.0014951 4983310000 1339420 1443351 788444 1347439 1097588 1186580 1127916 1252320 1550900 FALSE TRUE 1162412.253 1433869.532 1169738.156 1653395.619 1075748.146 1232228.5 1018530.88 984521.1136 1367554.369 0.849993448 1.048491793 0.855350385 1.20901637 0.786621849 0.901045347 0.744782733 0.719913691 1 20.38316676 RPFGISALIVGFDFDGTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RPFGISALIVGFDFDGTPR 19 1 O14818;H0Y586;O14818-2 O14818 PSMA7 Proteasome subunit alpha type-7 0 ;; 157.97 1.02E-09 1550460000 1785675 1713048 1194126 1312724 1668462 1616461 1681198 1919400 1745249 FALSE TRUE 1549693.524 1701794.875 1771609.328 1610798.048 1635262.87 1678647.301 1518155.677 1508951.247 1538927.651 1.006995698 1.105831631 1.151197281 1.046701608 1.062598927 1.090790265 0.986502306 0.980521239 1 20.55349398 2.234717054 24.98102223 0.987135385 1.079939808 0.548609208 0.037714898 69.08312691 448994.7317 0.015071868 0.01059884 171.678952 -2.234717054 0.092804423 RPFGVSLLYIGWDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPFGVSLLYIGWDK 14 1 P25789;H0YN18;P25789-2;H0YMZ1;H0YL69;H0YLC2;H0YMI6;H0YMA1;H0YKT8;H0YMV3;H0YKS0 P25789 PSMA4 Proteasome subunit alpha type-4;Proteasome subunit alpha type;Proteasome subunit beta type 0 ; 87.932 0.010818 299720000 643870 593520 449490 726410 479680 395660 829190 802970 1085060 FALSE TRUE 558780.9481 589621.128 666864.8675 891352.493 470135.3065 410881.2962 748775.2814 631261.1142 956785.4429 0.584019074 0.616252194 0.696984755 0.931611679 0.491369627 0.429439327 0.782594768 0.659772908 1 19.86783591 0.693022203 1.637527593 2.140214155 0.643808732 0.375798907 0.141329278 6.079871457 4.113276757 23.08317819 0.040401259 4.931990175 -0.693022203 -1.496405423 RPFLEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPFLEPK 7 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;P78347-5 A0A494C1K3 GTF2I General transcription factor II-I 0 80.229 0.048871 460230000 456740 480440 394240 379000 471710 441170 443660 579520 504320 FALSE TRUE 396380.6518 477283.958 584895.7827 465057.7427 462323.8939 458142.0954 400633.9215 455594.1578 444699.8641 0.891344216 1.073272102 1.315259639 1.045778918 1.039631291 1.030227649 0.900908576 1.024498082 1 18.76247244 2.965978641 1.994339304 0.98486817 1.096776957 0.143412642 0.106923057 0.600407377 4.800162872 0.040026339 0.042656517 924.6526968 -2.965978641 0.111908787 RPFSWEDVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPFSWEDVDR 10 1 O95696-2;O95696;J3KQ61 O95696-2 BRD1 Bromodomain-containing protein 1 0 110.08 0.0031009 157010000 126770 132050 81970 90055 121940 126000 122090 125630 111030 FALSE TRUE 110017.0233 131182.5549 121610.9662 110503.3642 119513.6326 130847.3015 110249.7306 98765.00215 97904.15989 1.123721642 1.339907875 1.242142993 1.128689162 1.220720679 1.336483574 1.126098531 1.008792704 1 16.57908254 1.929010442 3.472430917 1.009056589 1.232508615 0.627707262 0.071914924 0.14954157 3.292269742 0.041104195 0.019563985 84.92008921 -1.929010442 0.223452027 RPGAPSLS(ph)PAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPGAPSLSPAPR 12 1 Q5QP82-2;Q5QP82 Q5QP82-2 DCAF10 DDB1- and CUL4-associated factor 10 1 RPGAPS(0.003)LS(0.997)PAPR;RPGAPS(0.001)LS(0.999)PAPR 138.28 4.73E-05 661270000 318434 369060 217105 288109 347142 359899 314338 335717 368881 TRUE FALSE 276352.1401 366635.6206 322097.7042 353528.5519 340234.5534 373744.5474 283853.5491 263926.5321 325272.3084 0.849602419 1.127165182 0.990240164 1.086869502 1.045999135 1.149020491 0.872664355 0.811401786 1 18.31128848 2.214758923 24.8293549 0.876419463 1.045316569 0.344212941 0.094299649 195.8654285 204320.3731 0.036076699 0.024338136 163.9679334 -2.214758923 0.168897106 RPGFS(ph)PTSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RPGFSPTSHR 10 1 Q8WUA4;H0Y4Q6 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 RPGFS(0.933)PT(0.034)S(0.034)HR;RPGFS(0.943)PT(0.047)S(0.011)HR;RPGFS(0.578)PT(0.329)S(0.092)HR 97.631 0.0036305 1305440000 625830 513020 356307 450530 527950 527470 496100 579060 587720 TRUE FALSE 543124.9798 509649.9378 528618.257 552829.7224 517444.8279 547762.1122 447988.2984 455232.5252 518240.4111 1.048017422 0.983423768 1.020025157 1.066743755 0.998464838 1.056965263 0.864441075 0.878419582 1 18.98326199 2.241450759 24.99998221 0.904737615 1.026799013 0.603470155 0.043560072 45.22352665 391192.1924 0.016435417 0.012160906 174.3615654 -2.241450759 0.122061398 RPGGS(ph)SPLNAVPCEGPPGSEPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPGGSSPLNAVPCEGPPGSEPPR 23 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 RPGGS(0.5)S(0.5)PLNAVPCEGPPGSEPPR 96.707 0.0021619 238410000 128940 116270 91736 111460 114700 108870 94966 104800 160550 TRUE FALSE 111900.2523 115506.2147 136099.8364 136768.6966 112417.6944 113058.2993 85756.21194 82389.33555 141569.9619 0.790423694 0.815894934 0.961360974 0.966085565 0.794078722 0.798603728 0.605751466 0.581969045 1 17.11115566 2.691727081 2.320343614 0.697203417 0.880046996 0.171426667 0.127950054 0.399478684 4.249437486 0.050441541 0.044683876 491.7304252 -2.691727081 0.18284358 RPGHGS(ph)LTNISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPGHGSLTNISR 12 1 G5EA48;Q7Z6B7-2;Q7Z6B7 G5EA48 SRGAP1 SLIT-ROBO Rho GTPase-activating protein 1 1 RPGHGS(0.999)LT(0.001)NISR 91.355 0.0018781 0 132310 95049 60893 87164 113570 111440 102710 121700 122560 TRUE FALSE 114824.8983 94424.61686 90341.05847 106955.9184 111310.1792 115727.1689 92749.20001 95675.40207 108071.0964 1.062494062 0.873726833 0.835940982 0.989681071 1.029971777 1.070842924 0.85822392 0.885300559 1 16.7216212 2.193807772 24.9999974 0.906078153 0.968968697 0.105022778 0.082721925 317.4954898 177358.2222 0.035725632 0.02408633 156.2455913 -2.193807772 0.062890544 RPGQAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPGQAAK 7 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 0 ; 80.462 0.047856 70765000 234660 175736 131463 137330 82634 124210 159775 189696 184115 FALSE TRUE 203649.0864 174581.5786 195038.9465 168512.8755 80989.74507 128988.4391 144280.0451 149130.9866 162349.1344 1.254389727 1.075346532 1.201355013 1.037965962 0.498861576 0.794512638 0.888702275 0.918581963 1 17.30874017 3.467727618 24.99891153 0.830128329 1.158995157 0.590416612 0.137035701 151.4501465 403046.4812 0.041149725 0.053192804 2935.807789 -3.467727618 0.328866828 RPGQSFHVNSEVNSVLS(ph)PR ddPTM_MDA-MB-175_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 250.75 9.07E-26 2350140000 563560 706980 347500 695280 1242140 1389350 1031950 1164380 1263210 TRUE FALSE 489084.1181 702335.8018 515552.1623 853153.9507 1217423.844 1442799.194 931871.6478 915386.3982 1113874.753 0.439083584 0.630533909 0.46284572 0.765933466 1.092962958 1.29529751 0.836603618 0.821803704 1 20.08715559 3.499250245 3.842440774 0.985932477 0.527338625 0.718655444 0.141934576 0.140276785 4.52792236 0.045822416 0.06597767 3156.82309 -3.499250245 -0.458593852 RPGRS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 87.639 0.015116 7347030000 5389080 3802240 2704110 3133270 2337980 3240440 4522990 5114430 3803990 TRUE FALSE 4676899.424 3777262.835 4011826.641 3844726.843 2291458.772 3365101.824 4084351.126 4020748.945 3354286.636 1.394305237 1.126100195 1.19602976 1.146212969 0.683143399 1.003224289 1.217651194 1.198689731 1 21.67757455 5.281988539 1.062812041 1.062864689 2.034982268 0.3210853 0.154123868 7.101130252 2.939878359 0.051534695 10.28055396 191420.5407 -5.281988539 0.972117579 RPGS(ph)VSSTDQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPGSVSSTDQER 12 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 RPGS(0.517)VS(0.046)S(0.046)T(0.391)DQER;RPGS(0.974)VS(0.016)S(0.007)T(0.003)DQER 134.14 0.00015972 1379480000 640760 534350 390783 430002 576450 664870 565820 577260 578020 TRUE FALSE 556081.9425 530839.8197 579766.9659 527640.5263 564979.7728 690447.9791 510946.8635 453817.4412 509687.1341 1.091026054 1.041501314 1.137495783 1.035224339 1.108483489 1.354650594 1.002471574 0.890384338 1 18.95925241 2.011636956 24.99745538 0.94008207 1.124373834 0.424738166 0.09155427 189.3876119 406823.5944 0.037668856 0.02537469 102.7157298 -2.011636956 0.184291764 RPGTEAASYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPGTEAASYR 10 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 0 ; 124.42 0.00069904 84087000 47058 52569 33740 37005 38778 54382 50489 49547 46469 FALSE TRUE 40839.16607 52223.67078 50056.77685 45407.55084 38006.39367 56474.11073 45592.58455 38951.75963 40975.48776 0.996673092 1.274510046 1.221627358 1.108163766 0.92753975 1.37824133 1.112679483 0.95061125 1 15.3224735 1.827799599 5.062359889 0.97656771 1.154641652 0.234164135 0.128841807 0.287372507 11.30875864 0.068220027 0.033604428 67.26661901 -1.827799599 0.178073942 RPGTQGHLGPEKEEEES(ph)DGEPEDSSTS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RPGTQGHLGPEKEEEESDGEPEDSSTS 27 2 Q8IYB7;H7C1Q8 Q8IYB7 DIS3L2 DIS3-like exonuclease 2 1 RPGTQGHLGPEKEEEES(1)DGEPEDSSTS;RPGTQGHLGPEKEEEES(1)DGEPEDSSTS;RPGTQGHLGPEKEEEES(0.993)DGEPEDS(0.002)S(0.002)T(0.002)S(0.002);RPGTQGHLGPEKEEEES(1)DGEPEDSSTS;RPGTQGHLGPEKEEEES(0.839)DGEPEDS(0.043)S(0.039)T(0.039)S(0.039) 160.56 7.22E-12 2402700000 2079980 1677750 1315704 1432923 1817060 1452502 2156540 2334240 1793272 TRUE FALSE 1805105.373 1666728.75 1951982.855 1758290.068 1780904.061 1508380.692 1947399.083 1835080.941 1581273.427 1.141551703 1.054042091 1.234437272 1.111945624 1.126246752 0.95390251 1.231538486 1.160508303 1 20.59265542 3.508518629 24.85040783 1.10714821 1.140876501 0.049713784 0.088156595 2867.209048 2269332.785 0.024368535 0.036110727 3224.917645 -3.508518629 0.03372829 RPGYGAYDAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPGYGAYDAFK 11 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ; 147.62 5.65E-05 3697700000 2025560 3625400 2374200 2729000 3360100 2984900 3424100 3932500 4808600 FALSE TRUE 1757877.114 3601584.509 3522371.061 3348661.16 3293240.584 3099731.034 3092031.309 3091565.478 4240132.786 0.414580675 0.849403707 0.830721876 0.789753842 0.776683361 0.731045746 0.72922983 0.729119967 1 22.01567801 4.743874335 24.9170492 0.792272642 0.414580509 0.691155854 0.081550071 328.7319857 1541438.184 0.019648076 0.16409072 55446.52524 -4.743874335 -0.377692134 RPHGSTLSVSAS(ph)PEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPHGSTLSVSASPEK 15 1 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 RPHGSTLSVS(0.212)AS(0.788)PEK;RPHGSTLS(0.003)VS(0.203)AS(0.795)PEK 162.85 9.63E-07 258170000 303480 322510 81629 253170 526160 479990 341080 526620 480100 TRUE FALSE 263374.3491 320391.4106 121105.0574 310656.118 515690.4454 498455.5259 308002.1141 414006.4112 423343.1249 0.622129742 0.756812599 0.286068322 0.733816377 1.218138231 1.177426765 0.727547221 0.977945281 1 18.69146793 3.455372977 9.186911117 0.999029479 0.564257925 0.603896147 0.173786221 0.177365775 68.52541309 0.05083713 0.066294396 2853.467808 -3.455372977 -0.434771554 RPHS(ph)PEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RPHSPEK 7 1 Q53F19;Q53F19-2 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 RPHS(1)PEK;RPHS(1)PEK;RPHS(1)PEK;RPHS(1)PEK;RPHS(1)PEK;RPHS(1)PEK 125.75 0.0024618 1905440000 4213180 2567705 1761938 2153205 1681936 2097005 2820560 3300370 3295900 TRUE FALSE 3656397.588 2550837.577 2614017.11 2642123.105 1648468.764 2177678.139 2547022.525 2594611.559 2906262.457 1.258109907 0.877703791 0.899442892 0.909113731 0.567212627 0.749305395 0.876391091 0.892765742 1 21.47073356 5.340454773 1.414872704 0.833153794 2.558206889 0.553879727 0.116188943 4.862178878 2.62242974 0.034273463 18.126658 219005.3744 -5.340454773 1.725053095 RPHT(ph)PAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPHTPAER 8 1 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 RPHT(1)PAER;RPHT(1)PAER 96.229 0.005326 670860000 189046 201620 125753 145684 177494 181055 166670 162116 180855 TRUE FALSE 164063.0921 200295.5449 186567.5714 178763.7788 173962.2167 188020.303 150506.3691 127448.755 159474.5279 1.028773023 1.25597202 1.169889473 1.120955059 1.090846412 1.178998963 0.943764318 0.799179384 1 17.28296648 2.140979261 4.628768763 0.882033997 1.144092723 0.660829994 0.076467999 0.106700532 3.942601503 0.031105378 0.020492168 138.350031 -2.140979261 0.262058726 RPHT(ph)PTPGIYMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 15 RPHTPTPGIYMGR 13 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 1 RPHT(0.923)PT(0.077)PGIYMGR;RPHT(0.999)PT(0.001)PGIYMGR;RPHT(0.972)PT(0.028)PGIYMGR;RPHT(0.998)PT(0.002)PGIYMGR;RPHT(0.991)PT(0.009)PGIYMGR;RPHT(0.893)PT(0.107)PGIYMGR;RPHT(0.953)PT(0.047)PGIYMGR;RPHT(0.946)PT(0.054)PGIYMGR;RPHT(0.947)PT(0.052)PGIYMGR;RPHT(0.654)PT(0.346)PGIYMGR;RPHT(0.858)PT(0.142)PGIYMGR;RPHT(0.991)PT(0.009)PGIYMGR;RPHT(0.994)PT(0.006)PGIYMGR;RPHT(0.999)PT(0.001)PGIYMGR;RPHT(0.987)PT(0.013)PGIYMGR 197.14 7.98E-08 74060330000 3091130 2710578 2438297 2771083 2726116 2858085 2494437 2895886 6036310 TRUE FALSE 2682629.339 2692772.035 3617465.585 3400299.749 2671871.625 2968037.379 2252526.884 2276623.315 5322704.308 0.503997439 0.505902992 0.679629259 0.638829353 0.50197634 0.55761831 0.423192188 0.427719291 1 22.34372799 1.231119358 24.99644865 1.000000836 0.527403713 0.769148723 0.080935496 144.5634365 485571.269 0.227464477 0.02235137 17.02626379 -1.231119358 -0.472597123 RPHTPT(ph)PGIYMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPHTPTPGIYMGR 13 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 1 RPHT(0.297)PT(0.703)PGIYMGR 90.926 0.0051576 249620000 120460 113450 103860 123010 120500 109450 93235 126810 283440 TRUE FALSE 104540.9058 112704.7395 154087.0434 150941.3006 118102.2858 113660.6123 84193.08405 99692.66834 249932.0461 0.418277317 0.450941531 0.616515752 0.60392936 0.472537586 0.454766062 0.336863901 0.398879095 1 17.93117637 1.234057207 24.99976435 1.000000795 0.467513628 0.792796273 0.085295295 69.79494133 387402.7039 0.184189292 0.023754129 17.14183091 -1.234057207 -0.532487167 RPILQLS(ph)PPGPR ddPTM_MDA-MB-175_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 120.7 0.00023844 4711300000 1643090 1232541 1685367 967562 1259914 1313830 1209039 1313426 1235341 TRUE FALSE 1425951.493 1224444.357 2500416.118 1187261.74 1234844.176 1364373.89 1091786.584 1032560.071 1089300.394 1.309052582 1.124064917 2.295433043 1.089930516 1.133612163 1.252523085 1.002282373 0.947911225 1 20.05497043 3.52592587 24.99557856 1.06173781 1.557923515 0.373184571 0.308393376 407.3310932 208615.942 0.083083415 0.123229883 3356.803119 -3.52592587 0.496185705 RPIS(ph)DDDCPSASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPISDDDCPSASK 13 1 Q96PU4 Q96PU4 UHRF2 E3 ubiquitin-protein ligase UHRF2 1 RPIS(0.982)DDDCPS(0.017)AS(0.001)K;RPIS(0.99)DDDCPS(0.01)ASK 159.22 4.87E-05 159800000 435870 436540 302381 337198 425673 353821 465020 570950 504900 TRUE FALSE 378268.6751 433672.34 448613.463 413763.9596 417202.9401 367432.7228 419922.432 448856.7856 445211.2972 0.849638537 0.974082066 1.007641688 0.929365365 0.937089743 0.825299639 0.94319806 1.008188221 1 18.76413068 1.801953982 4.694753446 1.003731631 0.925066843 0.288634047 0.052908753 0.274572361 10.83185422 0.031361197 0.014640862 63.38025493 -1.801953982 -0.078664788 RPISADSAIMNPASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPISADSAIMNPASK 15 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;J3KSQ2;J3QL20 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 158.17 2.95E-06 1320300000 1372270 1091950 799630 849830 1067840 980440 1152140 1223240 1209430 FALSE TRUE 1190921.043 1084776.909 1186333.743 1042796.89 1046592.073 1018158.161 1040405.64 961659.6453 1066452.563 1.116712626 1.017182523 1.112411169 0.977818354 0.981377053 0.954714908 0.975576107 0.901736916 1 20.02438836 3.617425853 4.666565419 0.95746959 1.075170301 0.685509797 0.037170028 0.124820332 4.205496485 0.010049527 0.015163317 4144.058267 -3.617425853 0.117700711 RPKEEDPATGTGDPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPKEEDPATGTGDPPR 16 2 P45974-2;P45974;F5H571 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 64.52 0.033698 101674000 411490 344430 160336 175804 304870 265640 402170 418210 37894 FALSE TRUE 357110.5539 342167.4167 237875.0259 215722.9852 298803.6835 275859.3427 363167.6153 328779.046 33414.21449 10.68738438 10.24017538 7.118977044 6.456024434 8.942412325 8.255748247 10.86865637 9.839496485 1 15.02817434 4.305978551 6.76866173 7.930947705 10.52777012 0.161529234 2.673940693 0.437621215 34.73340927 0.6650041 1.778080688 20229.19266 -4.305978551 2.596822418 RPKS(ph)ESQGNATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RPKSESQGNATK 12 2 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 1 RPKS(0.887)ES(0.113)QGNATK;RPKS(0.991)ES(0.009)QGNATK;RPKS(0.863)ES(0.137)QGNATK 169.64 2.26E-05 282698000 294468 111459 105303 110949 112366 143792 267551 253609 116457 TRUE FALSE 255553.3077 110726.8185 156227.883 136141.6662 110130.1364 149323.7713 241603.9452 199376.6889 102689.5861 2.488600036 1.078267258 1.521360528 1.325759226 1.072456717 1.454127696 2.352759947 1.941547302 1 16.64793036 2.411422748 24.99999366 1.837148727 1.44555126 0.049673994 0.51204568 125.2253239 47649.71191 0.184752762 0.143108883 257.8830203 -2.411422748 -0.391597467 RPLDDGVGNQLGALVHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RPLDDGVGNQLGALVHQR 18 1 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ;;; 216.29 5.87E-19 1642880000 986380 937250 659575 671190 978920 971600 846960 992620 879940 FALSE TRUE 856027.3838 931093.143 978547.6761 823593.948 959441.4072 1008978.081 764821.9496 780355.9376 775914.4956 1.103249635 1.19999452 1.261154008 1.061449364 1.236529814 1.300372768 0.985703907 1.005724138 1 19.56553815 2.220122986 24.99999307 0.998453781 1.193062637 0.638965446 0.06967832 150.3753926 203895.7875 0.028117808 0.018996444 166.0056945 -2.220122986 0.194608856 RPLDS(ph)PEAEELPAMK ddPTM_MDA-MB-175_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 202.95 3.46E-09 1186810000 2814380 2259390 1655180 2063650 2249330 2111710 2601930 3062260 2972720 TRUE FALSE 2442452.552 2244547.918 2455630.584 2532233.273 2204572.734 2192948.85 2349595.229 2407419.53 2621288.428 0.931775583 0.856276591 0.936802894 0.96602619 0.841026386 0.83659197 0.896351277 0.918410772 1 21.32184468 1.22978212 2.411240423 1.029203906 0.893859332 0.377912404 0.042160375 0.666782618 4.051467876 0.192997599 0.011620661 16.97391879 -1.22978212 -0.135344574 RPLEDGDQPDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPLEDGDQPDAK 12 1 Q96AE4;E9PEB5;Q96AE4-2 Q96AE4 FUBP1 Far upstream element-binding protein 1 0 ; 135.04 0.00021603 519490000 1656750 987200 703000 901970 924670 740130 1083560 1372380 1285290 FALSE TRUE 1437806.29 980715.0182 1042973.151 1106776.074 906270.8761 768603.28 978476.518 1078907.217 1133344.48 1.268640131 0.86532827 0.920261376 0.976557519 0.799642908 0.678172694 0.863353142 0.951967593 1 20.112155 4.740045128 24.82020768 0.881732297 1.268640271 0.629696589 0.093201471 85.09346575 1422565.796 0.024627501 0.150810438 54959.79801 -4.740045128 0.386907974 RPLEEDFRRS(ph)PTEDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPLEEDFRRSPTEDFR 16 3 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 RPLEEDFRRS(0.989)PT(0.011)EDFR;RPLEEDFRRS(0.989)PT(0.011)EDFR 152.81 2.83E-06 2359500000 1759960 1742960 656030 604630 1364120 1555880 1552660 1604310 189145 TRUE FALSE 1527376.827 1731510.381 973288.3023 741920.4827 1336976.681 1615735.71 1402083.272 1261240.791 166784.4936 9.157786759 10.38172281 5.835604266 4.448378064 8.016192946 9.687565527 8.406556522 7.562098635 1 17.34762564 4.241841536 24.99945723 6.733442989 9.769755563 0.238439445 2.438289259 131.824943 1004415.473 0.62707015 1.522658552 17451.85261 -4.241841536 3.036312574 RPLEMEQQQAYRPEMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPLEMEQQQAYRPEMK 16 2 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0QYZ0;M0R0K8;M0QZV6;M0R203 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ; 174.78 2.11E-09 419820000 938150 700580 659800 672720 668750 647240 808850 919450 834630 FALSE TRUE 814171.1005 695977.8439 978881.4869 825471.3579 655443.1834 672139.7416 730407.8515 722832.7727 735960.9922 1.106269366 0.945672191 1.330072514 1.121623791 0.890595005 0.913281748 0.992454572 0.9821618 1 19.48926978 3.255948355 24.00897894 0.959642394 1.12761858 0.431475598 0.097018422 152.1323081 210062.0819 0.02813614 0.036221886 1802.803344 -3.255948355 0.167976186 RPLEQQQPHHIPTSAPVYQQPQQQPVAQSYGGYKEPAAPVSIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPLEQQQPHHIPTSAPVYQQPQQQPVAQSYGGYKEPAAPVSIQR 44 2 Q14847;Q14847-2;C9J9W2;Q14847-3;J3KSN1 Q14847 LASP1 LIM and SH3 domain protein 1 0 95.371 1.83E-05 544830000 79023 21327 16079 17301 20773 18345 23833 28024 17820 FALSE TRUE 68579.91033 21186.90153 23854.85818 21229.45648 20359.65794 19050.74402 21521.67933 22031.28568 15713.3399 4.364438799 1.348338524 1.518127803 1.351046729 1.295692582 1.212393046 1.369643848 1.402075295 1 13.93970224 4.738676352 7.835865673 1.324185591 4.391692003 0.980477118 0.135351804 0.011522055 8.050816624 0.032331491 0.186789278 54786.85262 -4.738676352 3.067506412 RPLFLAPDFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPLFLAPDFDR 11 1 H3BS72;Q9P035;H3BPZ1 H3BS72 HACD3 Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3 0 ; 127.56 0.00045558 1239420000 911150 1235430 639510 682140 1231290 1369040 655730 951640 926920 FALSE TRUE 790739.2189 1227314.379 948779.175 837030.3129 1206789.738 1421707.855 592137.4055 748139.1917 817340.5736 0.96745377 1.501594829 1.160812525 1.024090006 1.476483338 1.739431396 0.724468385 0.91533348 1 19.64057783 2.211952256 24.99999549 0.880831054 1.307844747 0.422157569 0.238068162 215.3571798 202338.131 0.097490671 0.06574916 162.9116926 -2.211952256 0.427013693 RPLFLAPDFDRWLDES(ph)DAEMELR ddPTM_MDA-MB-175_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 198.21 2.51E-24 874100000 437634 469232 325058 506310 490645 541226 341922 688648 379407 TRUE FALSE 379799.5581 466149.5841 482257.1361 621275.424 480882.1244 562047.3144 308762.4571 541385.9843 334553.9367 1.135241635 1.393346582 1.441492935 1.857026195 1.43738295 1.679990139 0.922907858 1.618232294 1 18.35187929 1.223477768 24.76091352 0.999998674 1.439931575 0.212258735 0.263674008 1190.431133 1954157.203 1.403456168 0.061946018 16.72929997 -1.223477768 0.439932901 RPLHSAQAVDVASASNFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPLHSAQAVDVASASNFR 18 1 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ; 159.19 2.83E-11 1110530000 772440 647860 512960 562410 718620 787640 670880 734820 701540 FALSE TRUE 670360.0969 643604.165 761029.1717 690113.7864 704320.868 817941.0205 605818.1609 577684.4614 618604.7404 1.083664662 1.040412598 1.23023495 1.115597313 1.138563645 1.322235293 0.979329968 0.933850686 1 19.23865836 2.046540305 20.61933207 0.960517353 1.150772534 0.546917926 0.078918298 14.71902367 6520.757239 0.03203757 0.021599628 111.3115691 -2.046540305 0.190255181 RPLIDQVVQTALSETQDPEEVSVTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPLIDQVVQTALSETQDPEEVSVTVK 26 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 132.93 8.27E-05 73764000 85183 64130 44824 48915 61051 60437 71804 75898 69243 FALSE TRUE 73925.85072 63708.72581 66501.03633 60021.89837 59836.20454 62762.0505 64840.45913 59667.80334 61057.17142 1.21076442 1.043427403 1.089160123 0.983044202 0.980002892 1.027922667 1.061963036 0.977244801 1 15.89787314 7.999998692 0.857603583 1.007521334 75.83643924 0.762662457 0.034286691 335.8451529 0.896205107 0.011450679 49058.2401 99999698.73 -7.999998692 74.8289179 RPLPVES(ph)PDTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RPLPVESPDTQR 12 1 P57682 P57682 KLF3 Krueppel-like factor 3 1 RPLPVES(0.988)PDT(0.012)QR;RPLPVES(0.997)PDT(0.003)QR;RPLPVES(0.994)PDT(0.006)QR;RPLPVES(0.992)PDT(0.008)QR;RPLPVES(0.999)PDT(0.001)QR 152.17 4.26E-05 3760270000 4000930 3866790 2729180 3455200 3903110 3734250 3446100 4183700 5269020 TRUE FALSE 3472196.963 3841388.802 4049020.577 4239755.969 3825445.747 3877909.014 3111897.752 3289048.313 4646122.458 0.74733221 0.826794566 0.871483826 0.912536423 0.823363091 0.83465493 0.669783842 0.707912532 1 22.14759575 2.435067983 24.94556715 0.767300008 0.840668374 0.021000727 0.095744895 316.2518319 187595.464 0.03579147 0.02772398 272.3127544 -2.435067983 0.073368366 RPLQEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPLQEDR 7 1 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785;O95785-2 M0QXA7 WIZ Protein Wiz 0 ; 81.548 0.043137 112280000 127421 119248 76481 97493 92200 133582 110355 121061 115225 FALSE TRUE 110581.992 118464.652 113467.4674 119630.2757 90365.40039 138720.986 99652.78909 95173.04725 101603.2318 1.088370813 1.165953582 1.116770259 1.177425891 0.889394942 1.365320606 0.98080334 0.936712795 1 16.63258677 2.036196446 24.99995056 0.962311924 1.129390758 0.300839845 0.115865208 183.7785501 126930.3743 0.043534943 0.029351173 108.6917162 -2.036196446 0.167078834 RPLRPQVVTDDDGQAPEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPLRPQVVTDDDGQAPEAK 19 2 Q9HDC9;Q9HDC9-2 Q9HDC9 APMAP Adipocyte plasma membrane-associated protein 0 57.989 0.046382 226870000 247790 208940 165670 267620 299680 218100 233490 380770 299670 FALSE TRUE 215043.9237 207567.4594 245788.5661 328387.2113 293716.9543 226490.4481 210846.1757 299345.2987 264243.354 0.813810151 0.785516291 0.930159879 1.242745395 1.111539609 0.857128267 0.797924234 1.132839461 1 18.01150766 4.06107361 4.985840878 1.022419807 0.805537773 0.338883741 0.1282259 0.241321154 12.04569007 0.035532449 0.076294703 11509.9546 -4.06107361 -0.216882035 RPLS(ph)ASLGQLNEVGLPSAAILPDEGAVDLPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPLSASLGQLNEVGLPSAAILPDEGAVDLPSR 32 1 Q5TC82-2;Q5TC82 Q5TC82-2 RC3H1 Roquin-1 1 RPLS(0.981)AS(0.019)LGQLNEVGLPSAAILPDEGAVDLPSR 207.05 2.50E-27 225390000 28502 32269 27423 32385 43963 53068 35242 49231 41535 TRUE FALSE 24735.38849 32057.02281 40684.85452 39738.50922 43088.22231 55109.5603 31824.23626 38703.33377 36624.77962 0.675373033 0.87528234 1.110855955 1.08501702 1.176477313 1.504706946 0.868926355 1.056752673 1 15.16053246 4.479063815 2.175963286 1.11408393 0.655598044 0.456907312 0.161616483 0.384834232 2.995942395 0.044247975 0.277237147 30134.48787 -4.479063815 -0.458485886 YSYLTEPGMS(ph)PQS(ph)PCER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSYLTEPGMSPQSPCER 17 0 Q12955-4;Q12955-5;Q12955-6;H0Y3A4;H0YA66 Q12955-4 ANK3 Ankyrin-3 2 YSYLTEPGMS(1)PQS(1)PCER;YSYLT(0.001)EPGMS(0.999)PQS(1)PCER 216.16 7.87E-15 156004000 144233 204735 143054 209576 295740 294282 301866 318540 291070 TRUE FALSE 125172.2436 203390.0823 212235.3929 257163.434 289855.3526 305603.219 272591.0818 250422.6999 256660.0362 0.487696665 0.792449363 0.826912503 1.001961341 1.129335743 1.190692651 1.062070612 0.975698062 1 17.96949915 4.571458485 0.992345766 1.064095157 0.311247611 0.86824236 0.072742195 0.586933624 0.5670856 0.027647677 0.446209441 37278.50477 -4.571458485 -0.752847546 down RPLS(ph)SSHEASEGQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RPLSSSHEASEGQAK 15 1 Q8IZ21-3;Q8IZ21;Q8IZ21-2;A0A0J9YVR0 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 RPLS(0.446)S(0.121)S(0.432)HEASEGQAK;RPLS(0.787)S(0.139)S(0.073)HEASEGQAK;RPLS(0.875)S(0.11)S(0.014)HEASEGQAK 205.24 2.75E-09 809280000 547390 559340 282347 444490 607840 588750 617770 778950 757920 TRUE FALSE 475051.0246 555665.6587 418890.9536 545418.2481 595745.1732 611399.5935 557858.7605 612377.6043 668319.561 0.710814186 0.831437072 0.626782423 0.816103972 0.891407656 0.914831211 0.834718588 0.916294599 1 19.35017858 3.402172974 3.465539552 0.906621313 0.731796755 0.645489791 0.063526209 0.150521656 3.619591014 0.018301759 0.024733292 2524.486044 -3.402172974 -0.174824558 RPLSAS(ph)LGQLNEVGLPSAAILPDEGAVDLPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPLSASLGQLNEVGLPSAAILPDEGAVDLPSR 32 1 Q5TC82-2;Q5TC82 Q5TC82-2 RC3H1 Roquin-1 1 RPLS(0.158)AS(0.842)LGQLNEVGLPSAAILPDEGAVDLPSR;RPLS(0.18)AS(0.82)LGQLNEVGLPSAAILPDEGAVDLPSR 265.48 7.47E-60 735410000 227480 201118 131472 140248 160481 205885 153234 189749 168580 TRUE FALSE 197417.9416 199796.8426 195052.2989 172093.452 157287.7421 213805.5292 138373.3903 149172.653 148650.6644 1.328066325 1.344069624 1.312152217 1.157703886 1.058103189 1.438308601 0.930862911 1.003511512 1 17.18156639 0.206641835 0.165062764 0.17222721 1.537755432 0.480658541 0.125685973 48.93689476 1.424713764 15.36341019 2.039720971 1.609317876 -0.206641835 1.365528222 RPLSSS(ph)HEASEGQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPLSSSHEASEGQAK 15 1 Q8IZ21-3;Q8IZ21;Q8IZ21-2;A0A0J9YVR0 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 RPLS(0.262)S(0.262)S(0.474)HEAS(0.003)EGQAK 177.4 4.62E-07 230710000 156040 160650 80841 134120 184180 181730 190250 234150 213240 TRUE FALSE 135418.9186 159594.6796 119935.978 164573.9959 180515.1783 188721.2707 171799.5843 184078.8447 188031.0101 0.720194603 0.848767868 0.637852118 0.875249225 0.960028765 1.003670993 0.913676867 0.97898131 1 17.52061109 3.481084646 4.036325946 0.967844689 0.746217589 0.780682696 0.05675082 0.092715164 3.485523832 0.015416326 0.021758284 3027.503443 -3.481084646 -0.2216271 RPLT(ph)PFHHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPLTPFHHR 9 1 Q9UHV7;J3QRB7 Q9UHV7 MED13 Mediator of RNA polymerase II transcription subunit 13 1 RPLT(1)PFHHR 72.531 0.035432 73793000 48451 47876 34028 40443 43179 46912 43855 42955 39541 TRUE FALSE 42048.07759 47561.4994 50484.05462 49626.20128 42319.82238 48716.735 39601.94885 33769.40753 34866.50803 1.205973296 1.364102748 1.447924024 1.423320088 1.213767159 1.397235851 1.13581632 0.968534259 1 15.08955426 2.034550229 3.110882509 0.989052425 1.346004188 0.774136128 0.080925555 0.110566858 2.144588368 0.043761008 0.023280562 108.2804941 -2.034550229 0.356951763 RPMEEDGEEKS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 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(0.963)PS(0.037)K;RPMEEDGEEKS(0.984)PS(0.016)K;RPMEEDGEEKS(0.833)PS(0.167)K;RPMEEDGEEKS(0.987)PS(0.013)K;RPMEEDGEEKS(0.5)PS(0.5)K;RPMEEDGEEKS(0.909)PS(0.091)K;RPMEEDGEEKS(0.5)PS(0.5)K;RPMEEDGEEKS(0.595)PS(0.405)K;RPMEEDGEEKS(0.962)PS(0.038)K;RPMEEDGEEKS(0.972)PS(0.028)K;RPMEEDGEEKS(0.905)PS(0.095)K 212.92 9.19E-10 13984860000 6704625 4476324 4169568 3957256 4488928 3498196 5745320 7119321 6514270 TRUE FALSE 5818591.819 4446918.733 6185985.031 4855811.458 4399607.115 3632773.864 5188139.751 5596909.607 5744160.422 1.01295775 0.774163395 1.076917178 0.845347466 0.765926923 0.63242904 0.903202447 0.974365128 1 22.45366461 1.812843606 3.868323518 0.987148781 0.848722273 0.161244364 0.124578232 0.398789963 10.42606958 0.07793815 0.03452859 64.98956136 -1.812843606 -0.138426508 RPMEEDGEEKS(ph)PSKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RPMEEDGEEKSPSKK 15 3 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 RPMEEDGEEKS(0.996)PS(0.004)KK;RPMEEDGEEKS(0.996)PS(0.004)KK;RPMEEDGEEKS(0.991)PS(0.009)KK;RPMEEDGEEKS(0.988)PS(0.012)KK 149.44 1.86E-05 1561060000 2050660 1166430 1340950 1086660 1123620 792740 1764560 2091480 1816310 TRUE FALSE 1779660.085 1158767.645 1989437.905 1333402.762 1101262.16 823237.2208 1593433.243 1644233.278 1601587.901 1.111184771 0.723511737 1.242165918 0.832550471 0.687606443 0.514013137 0.994908392 1.026626935 1 20.61107155 RPMEEDGEEKSPS(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPMEEDGEEKSPSK 14 2 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 RPMEEDGEEKS(0.356)PS(0.644)K 83.729 0.0043906 2262700000 1130500 688840 711650 640910 779080 583050 935410 1151800 1149200 TRUE FALSE 981101.5607 684314.9647 1055806.32 786438.4112 763577.8322 605480.3108 844694.0822 905496.5333 1013342.885 0.968183203 0.675304455 1.041904311 0.776083222 0.753523653 0.597507832 0.833571829 0.893573682 1 19.95069099 1.498556796 2.417226217 0.999534711 0.799403011 0.195986705 0.127913559 0.538233261 5.65917609 0.192394952 0.034046296 31.51786534 -1.498556796 -0.200131701 RPMEEDGEEKSPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPMEEDGEEKSPSK 14 2 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 86.548 0.0041036 97062000 294470 203660 183130 164690 196470 158480 266270 324970 180080 FALSE TRUE 255555.0434 202322.1441 271692.2805 202085.3816 192560.6314 164576.8282 240447.1764 255477.6944 158791.1475 1.609378403 1.274139945 1.711003949 1.272648915 1.212666036 1.036435788 1.514235397 1.608891291 1 17.27677096 3.694091569 24.99358637 1.311554775 1.505771063 0.22519614 0.216036513 872.8578436 490584.5675 0.06256409 0.092797998 4944.149206 -3.694091569 0.194216288 RPMS(ph)DPSWNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RPMSDPSWNR 10 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 RPMS(0.995)DPS(0.005)WNR;RPMS(0.862)DPS(0.138)WNR;RPMS(0.975)DPS(0.025)WNR;RPMS(0.972)DPS(0.028)WNR 122.97 0.00029067 2271810000 1995130 2182570 1476540 1627990 2202720 2340140 2200050 2306390 2511970 TRUE FALSE 1731468.515 2168232.554 2190599.683 1997650.012 2158890.182 2430166.7 1986689.49 1813186.447 2215007.768 0.78169862 0.978882596 0.988980587 0.901870432 0.974664835 1.097136875 0.896922132 0.818591462 1 21.07888033 6.345466829 15.61222347 0.934712216 0.530507845 0 0.092219797 0 0 0.021087724 0 2215474.875 -6.345466829 -0.404204371 RPMS(ph)SPEMK ddPTM_MDA-MB-175_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(0.5)S(0.5)PEMK 45.879 0.068551 47137000 130970 112760 81375 94136 122160 100370 118990 154620 134770 TRUE FALSE 113661.9827 112019.2721 120728.2222 115511.0176 119729.255 104231.2988 107450.3681 121555.7163 118837.6441 0.956447626 0.942624477 1.015908916 0.972006963 1.007502765 0.877089912 0.904177871 1.022872147 1 16.85863238 1.64503365 10.59141045 1.011263074 0.955637781 0.244694927 0.041982855 0.158442393 32.09043784 0.024745305 0.011362974 44.16046619 -1.64503365 -0.055625293 RPMSDPSWNR ddPTM_MDA-MB-175_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 0 ; 113.69 0.0023332 851470000 427280 423190 270360 275750 410940 476940 419710 440640 432710 FALSE TRUE 370813.8654 420410.037 401107.0003 338363.2521 402763.098 495288.1904 379006.5888 346412.5651 381555.5167 0.971847737 1.101831892 1.051241517 0.886799528 1.055581902 1.298076345 0.993319641 0.907895574 1 18.54153346 2.007299573 24.99995526 0.948340465 1.061791134 0.155841088 0.105725108 292.0977745 1000387.584 0.04462657 0.030018513 101.6949934 -2.007299573 0.113450669 RPMSS(ph)PEMK ddPTM_MDA-MB-175_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(0.137)S(0.863)PEMK 99.844 0.0031006 383960000 440960 419400 288300 348480 390320 360760 459300 543660 482900 TRUE FALSE 382686.0187 416644.9338 427722.8443 427607.7102 382553.3956 374638.6706 414757.1567 427402.5398 425812.1121 0.89872037 0.978471307 1.004487266 1.004216879 0.89840891 0.879821546 0.97403795 1.003735046 1 18.69985746 2.001880158 24.99107007 0.998159978 0.94715928 0.234395712 0.043223289 97.43733881 1295125.902 0.019391304 0.012973916 100.4338609 -2.001880158 -0.051000698 RPNEDS(ph)DEDEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RPNEDSDEDEEK 12 1 Q12996;E9PLP8;H0YE74 Q12996 CSTF3 Cleavage stimulation factor subunit 3 1 RPNEDS(1)DEDEEK;RPNEDS(1)DEDEEK;RPNEDS(1)DEDEEK;RPNEDS(1)DEDEEK;RPNEDS(1)DEDEEK 174.87 1.79E-05 2295290000 3211310 2015450 2089280 2089680 2042930 1927720 2492650 2817460 5427300 TRUE FALSE 2786927.247 2002210.376 3099662.796 2564173.783 2002279.69 2001880.636 2250913.187 2214968.104 4785690.777 0.582345868 0.418374373 0.647693915 0.535800139 0.418388856 0.418305471 0.470342379 0.46283143 1 22.19029575 1.236661486 24.99777342 1.000000643 0.490642811 0.813857947 0.075993672 20.75123403 273067.0269 0.11747924 0.018631901 17.24493201 -1.236661486 -0.509357832 RPNEDS(ph)DEDEEKGAVVPPVHDIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 RPNEDSDEDEEKGAVVPPVHDIYR 24 2 Q12996;E9PLP8;H0YE74 Q12996 CSTF3 Cleavage stimulation factor subunit 3 1 RPNEDS(1)DEDEEKGAVVPPVHDIYR;RPNEDS(1)DEDEEKGAVVPPVHDIYR;RPNEDS(1)DEDEEKGAVVPPVHDIYR;RPNEDS(1)DEDEEKGAVVPPVHDIYR;RPNEDS(1)DEDEEKGAVVPPVHDIYR;RPNEDS(1)DEDEEKGAVVPPVHDIYR;RPNEDS(1)DEDEEKGAVVPPVHDIYR;RPNEDS(1)DEDEEKGAVVPPVHDIYR;RPNEDS(1)DEDEEKGAVVPPVHDIYR;RPNEDS(1)DEDEEKGAVVPPVHDIYR 223.05 4.15E-33 22741640000 10639970 7292440 5483820 5651250 7225180 6293850 8321780 9838000 6292670 TRUE FALSE 9233871.006 7244535.481 8135813.694 6934452.686 7081413.054 6535978.482 7514735.056 7734220.259 5548757.721 1.664133031 1.305613949 1.466240572 1.249730667 1.276215941 1.177917439 1.354309457 1.393865194 1 22.40373338 7.999999986 0.744353323 1.265267773 65.16561584 0.507666087 0.122894735 334.3269204 1.48114598 0.044935184 35791.48951 99999996.72 -7.999999986 63.90034807 RPNKPLFTALVTQCQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPNKPLFTALVTQCQK 16 2 Q8NCW5-2;Q8NCW5;Q5T3I4;Q5T3I3 Q8NCW5-2 APOA1BP NAD(P)H-hydrate epimerase 0 51.695 0.093294 702330000 393960 326850 295950 413010 335320 281310 415790 487130 914780 FALSE TRUE 341897.1878 324702.9008 439072.4099 506790.233 328647.788 292132.1777 375466.7498 382961.0403 806635.7505 0.423855734 0.402539685 0.544325502 0.628276434 0.407430228 0.362161208 0.465472488 0.474763287 1 19.62155782 1.238133798 6.880830531 1.012329054 0.464181445 0.829988898 0.076310088 0.047493335 12.30121458 0.121401508 0.020050597 17.30349364 -1.238133798 -0.548147609 RPNKQEES(ph)ESPVERPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPNKQEESESPVERPLK 17 3 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;D6RBF8 H3BLV9 SRPK1 SRSF protein kinase 1 1 RPNKQEES(0.608)ES(0.392)PVERPLK 115.42 0.0017448 125890000 118740 84683 79780 99966 87024 83293 122360 138030 131030 TRUE FALSE 103048.2082 84126.7118 118361.8748 122664.8082 85292.39266 86497.33561 110493.546 108513.3587 115539.7827 0.891885079 0.728119007 1.024425285 1.061667292 0.738208007 0.748636821 0.956324683 0.939186107 1 16.81803016 2.055132456 24.99867411 0.960003048 0.868175104 0.146379878 0.113159262 191.8450644 86987.07525 0.048786502 0.032891847 113.5357036 -2.055132456 -0.091827944 RPNKQEESES(ph)PVERPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RPNKQEESESPVERPLK 17 3 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;D6RBF8 H3BLV9 SRPK1 SRSF protein kinase 1 1 RPNKQEES(0.111)ES(0.889)PVERPLK;RPNKQEES(0.005)ES(0.995)PVERPLK;RPNKQEES(0.012)ES(0.988)PVERPLK 207.43 3.36E-11 832260000 939290 705400 583865 694840 604129 562570 868360 969680 921870 TRUE FALSE 815160.4466 700766.181 866224.0669 852614.042 592108.0149 584212.4319 784146.5809 762321.4781 812887.5788 1.002796042 0.862070229 1.065613609 1.048870796 0.728400864 0.718687857 0.96464333 0.937794472 1 19.63269632 4.768584617 21.56588382 0.916602131 1.002796884 0.050319534 0.118778602 6412.88116 4605797.058 0.030656864 2.444225516 58692.77147 -4.768584617 0.086194753 RPNPCAYT(ph)PPSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RPNPCAYTPPSLK 13 1 Q9UD71;J3KSJ8;Q9UD71-2 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 1 RPNPCAY(0.007)T(0.973)PPS(0.019)LK;RPNPCAYT(1)PPSLK;RPNPCAY(0.007)T(0.992)PPS(0.001)LK 125.52 0.00011672 853010000 1301700 1343900 903960 1099210 1214540 1156860 1373570 1722520 1960120 TRUE FALSE 1129677.047 1335071.832 1341118.08 1348802.431 1190373.03 1201365.153 1240361.393 1354172.503 1728396.847 0.653598188 0.77243362 0.775931802 0.780377743 0.688715113 0.695074835 0.717636922 0.78348471 1 20.72100307 1.222808628 2.655629221 1.069166244 0.729821168 0.809675892 0.041465367 0.223314079 1.729114735 0.17387779 0.011211401 16.70354409 -1.222808628 -0.339345076 RPNT(ph)SPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPNTSPDR 8 1 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RPNT(0.5)S(0.5)PDR;RPNT(0.755)S(0.245)PDR 78.513 0.058866 607580000 703860 598987 406434 489848 477709 586520 567053 626230 663050 TRUE FALSE 610843.1176 595052.215 602986.8418 601075.4753 468203.5255 609083.8039 512060.2873 492315.5878 584664.9843 1.044774587 1.017766124 1.031337361 1.028068195 0.80080651 1.04176549 0.875818291 0.842047328 1 19.15725067 3.329682953 13.25531511 0.907111253 1.029832797 0.415515317 0.069638556 0.649129753 91.44958646 0.019324971 0.024947741 2136.40189 -3.329682953 0.122721544 RPNT(ph)SPDRGS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPNTSPDRGSR 11 2 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 2 RPNT(0.772)S(0.228)PDRGS(1)R 89.502 0.013448 621530000 528770 443950 323400 359850 423630 530530 465230 508900 533530 TRUE FALSE 458891.7048 441033.6632 479797.3217 441559.4425 415200.5918 550939.8324 420112.0662 400075.6953 470456.6912 0.975417532 0.937458583 1.01985439 0.938576177 0.882547957 1.171074496 0.892987759 0.850398565 1 18.84370239 RPNT(ph)SPDRGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPNTSPDRGSR 11 2 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RPNT(0.607)S(0.312)PDRGS(0.081)R 96.135 0.011638 538080000 397900 315860 81952 96446 293870 350780 302020 340700 29757 TRUE FALSE 345316.5068 313785.0949 121584.2613 118345.5384 288022.5619 364274.7336 272730.1469 267843.9563 26239.16136 13.16034846 11.95865564 4.633694639 4.510263753 10.97682041 13.88286495 10.39401157 10.20779409 1 14.67943399 4.452421396 23.83101028 8.462969576 12.85992865 0.19876071 3.77920398 203.4277385 196271.5853 0.980213665 2.593724045 28341.40628 -4.452421396 4.396959074 RPNTS(ph)PDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RPNTSPDR 8 1 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RPNT(0.292)S(0.708)PDR;RPNT(0.136)S(0.864)PDR;RPNT(0.156)S(0.844)PDR;RPNT(0.159)S(0.841)PDR;RPNT(0.005)S(0.995)PDR 99.283 0.0042406 5920762000 4929546 4109754 2662736 3156688 3387882 4224072 3493062 4301753 4622774 TRUE FALSE 4278094.006 4082756.755 3950444.036 3873462.257 3320469.776 4386574.783 3154305.385 3381856.597 4076274.924 1.049510665 1.001590136 0.969130912 0.950245587 0.814584354 1.076123388 0.77382057 0.829643893 1 21.95881993 4.372522784 0.619530443 0.878960154 1.115563041 0.235271 0.089556098 3.280023076 1.360216653 0.051211219 0.525799587 23578.85893 -4.372522784 0.236602887 RPNTSPDRGS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RPNTSPDRGSR 11 2 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RPNT(0.002)S(0.001)PDRGS(0.997)R;RPNT(0.002)S(0.001)PDRGS(0.996)R;RPNT(0.109)S(0.007)PDRGS(0.884)R;RPNTS(0.001)PDRGS(0.999)R 118.16 0.00059647 2125209000 1430732 1103388 256920 332760 957291 1051056 983881 1045183 45116.7 TRUE FALSE 1241657.141 1096139.772 381167.3713 408318.2439 938242.782 1091490.804 888464.3721 821678.7491 39783.05512 31.21070359 27.55293097 9.581148812 10.2636221 23.58398014 27.436073 22.3327336 20.65398815 1 15.27986645 8 0.071871039 2.29E-09 64.62133649 0.173480128 8.659611245 1487.89408 10.24183052 2008.695448 10340.00115 99999999.97 -8 64.62133649 RPPDEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RPPDEQR 7 1 B8ZZU8;Q15370;Q15370-2;I3L0M9;A0A0B4J296 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 ;;;;; 147.06 0.0034908 2382713000 852594 832573 529152 585255 603499 855579 719598 812393 802344 FALSE TRUE 739921.5427 827103.7731 785051.6771 718146.0928 591490.5506 888493.6778 649811.4967 638669.079 707491.8064 1.045837614 1.169064809 1.109626529 1.015059237 0.836038729 1.255835997 0.918472116 0.902722934 1 19.43235391 3.332095452 0.378837828 0.918058275 1.160639598 0.142141897 0.117271047 3.555122413 1.705627523 0.343553341 0.539860987 2148.302591 -3.332095452 0.242581323 RPPEEDFRHS(ph)PEEDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RPPEEDFRHSPEEDFR 16 2 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 RPPEEDFRHS(1)PEEDFR;RPPEEDFRHS(1)PEEDFR;RPPEEDFRHS(1)PEEDFR;RPPEEDFRHS(1)PEEDFR;RPPEEDFRHS(1)PEEDFR 191.8 3.33E-10 6586310000 2354090 2248930 1515460 1745090 2159610 2369930 2000350 2268310 2135520 TRUE FALSE 2042991.042 2234156.631 2248341.525 2141339.357 2116637.986 2461102.741 1806356.365 1783249.559 1883061.258 1.084930739 1.186449257 1.193982147 1.137158628 1.124040961 1.306969027 0.959265853 0.94699498 1 20.8446485 2.212132445 24.99712931 0.963825076 1.170101052 0.723317786 0.059295697 105.7399504 100013.5109 0.02307039 0.015559154 162.9792988 -2.212132445 0.206275976 RPPEEDFRHS(ph)PEEDFRQS(ph)PQEHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RPPEEDFRHSPEEDFRQSPQEHFR 24 3 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 2 RPPEEDFRHS(1)PEEDFRQS(1)PQEHFR;RPPEEDFRHS(1)PEEDFRQS(1)PQEHFR;RPPEEDFRHS(1)PEEDFRQS(1)PQEHFR;RPPEEDFRHS(1)PEEDFRQS(1)PQEHFR;RPPEEDFRHS(1)PEEDFRQS(1)PQEHFR;RPPEEDFRHS(1)PEEDFRQS(1)PQEHFR 195.2 2.96E-19 6013390000 1199548 1155349 799625 885073 1098516 1271218 1031232 1206837 1020522 TRUE FALSE 1041024.693 1147759.436 1186326.325 1086042.352 1076657.681 1320122.579 931223.2794 948764.2992 899877.0517 1.156852139 1.275462502 1.318320455 1.206878595 1.196449758 1.467003272 1.0348339 1.054326585 1 19.77936838 2.192300779 24.75956834 1.035058906 1.266364139 0.639586647 0.085021671 69.09383462 36980.40441 0.033240059 0.02241054 155.704362 -2.192300779 0.231305233 RPPES(ph)PPIVEEWNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RPPESPPIVEEWNSR 15 1 Q9BTL3;A0A3B3IU46 Q9BTL3 FAM103A1 RNMT-activating mini protein 1 RPPES(1)PPIVEEWNSR;RPPES(1)PPIVEEWNSR;RPPES(1)PPIVEEWNSR;RPPES(1)PPIVEEWNSR;RPPES(1)PPIVEEWNSR 172.3 6.33E-07 5655510000 636519 558217 339640 446460 509629 577743 517989 591685 553321 TRUE FALSE 552401.4014 554550.0358 503891.04 547835.5667 499488.38 599969.1471 467754.5065 465157.7672 487908.0217 1.132183479 1.136587248 1.032758261 1.122825496 1.023734716 1.229676743 0.958694028 0.953371838 1 18.89624968 2.198337398 24.9998866 0.966580957 1.106782046 0.567623264 0.058332387 103.3746522 64249.62544 0.022228818 0.01498687 157.8837373 -2.198337398 0.14020109 KPVTVSPTTPTS(ph)PTEGEAS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 KPVTVSPT(0.001)T(0.003)PT(0.001)S(0.953)PT(0.036)EGEAS(0.007);KPVTVSPTT(0.001)PT(0.015)S(0.984)PTEGEAS;KPVTVSPT(0.019)T(0.129)PT(0.099)S(0.75)PT(0.002)EGEAS(0.001);KPVTVSPT(0.001)T(0.005)PT(0.151)S(0.281)PT(0.281)EGEAS(0.281) 278.98 1.52E-39 3037190000 1428740 1775000 1367520 2001940 2413610 2309000 2661850 3063630 2916350 TRUE FALSE 1239928.389 1763339.908 2028857.246 2456511.075 2365583.883 2397828.724 2403704.197 2408496.566 2571582.425 0.482165525 0.685702271 0.788952835 0.955252708 0.919894249 0.932433159 0.934717928 0.936581516 1 21.29422497 4.572890477 1.01284961 0.94988422 0.319692863 0.968948431 0.027919615 0.222841457 0.225634663 0.008955569 0.144088527 37401.62548 -4.572890477 -0.630191357 down RPPS(ph)PDVIVLS(ph)DNEQPSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.239)S(0.761)PR;RPPS(1)PDVIVLS(1)DNEQPS(0.07)S(0.93)PR;RPPS(1)PDVIVLS(1)DNEQPS(0.27)S(0.73)PR;RPPS(1)PDVIVLS(1)DNEQPS(0.247)S(0.753)PR 214.46 5.14E-25 6428720000 1600260 1541690 1097640 1216910 1618540 1676680 1522160 1749290 1634230 TRUE FALSE 1388781.586 1531562.537 1628462.375 1493228.015 1586334.221 1741182.965 1374541.157 1375217.946 1441033.191 0.96374018 1.062822526 1.130065834 1.036220417 1.100831147 1.208287897 0.953858083 0.954327739 1 20.45867213 2.17133047 24.99998924 0.965608005 1.083450109 0.416690399 0.063678417 50.77290609 18879.34867 0.025984168 0.017518526 148.3646616 -2.17133047 0.117842104 RPPS(ph)PDVIVLS(ph)DNEQPSSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JHD7;C9JJK9;C9JMI3;C9JGN4 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 2 RPPS(1)PDVIVLS(1)DNEQPSSPR;RPPS(1)PDVIVLS(1)DNEQPSSPR 202.14 4.16E-21 811870000 344030 372580 234130 288160 419830 391000 327130 459870 348120 TRUE FALSE 298565.5638 370132.4974 347356.0511 353591.1322 411476.2044 406042.023 295404.983 361530.3792 306965.6502 0.972635093 1.205778227 1.131579546 1.151891529 1.340463352 1.322760455 0.96233889 1.177755163 1 18.2277177 1.014247532 1.077792126 0.871300557 1.175669494 0.128424595 0.123979847 5.858817303 4.023995786 2.311176703 0.040479733 10.3335021 -1.014247532 0.304368937 RPPS(ph)PDVIVLSDNEQPS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JHD7;C9JJK9;C9JMI3;C9JGN4 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 2 RPPS(1)PDVIVLSDNEQPS(0.558)S(0.442)PR 170 3.48E-11 151960000 132780 113370 74183 76027 91769 133210 109530 113660 105420 TRUE FALSE 115232.7866 112625.265 110058.1469 93290.09235 89942.97644 138334.6749 98907.79746 89354.6935 92957.36769 1.239630483 1.211579757 1.183963678 1.003579325 0.967572326 1.488151809 1.06401246 0.961243802 1 16.5042816 2.006656122 24.99836372 0.988285901 1.175095466 0.267900598 0.140210527 218.840364 821894.313 0.058200498 0.039134103 101.5444336 -2.006656122 0.186809566 RPPS(ph)PDVIVLSDNEQPSS(ph)PR ddPTM_MDA-MB-175_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)PDVIVLSDNEQPS(0.021)S(0.979)PR;RPPS(1)PDVIVLSDNEQPS(0.339)S(0.661)PR;RPPS(1)PDVIVLSDNEQPS(0.055)S(0.945)PR;RPPS(1)PDVIVLSDNEQPS(0.411)S(0.589)PR 224.12 2.10E-24 2966960000 1023590 890310 705889 709200 847240 1038360 886290 928570 1007860 TRUE FALSE 888319.9881 884461.495 1047259.281 870234.6994 830381.5816 1078306.381 800337.7322 730002.5316 888711.939 0.999558967 0.995217298 1.178401274 0.979208967 0.934365282 1.213336216 0.900559222 0.821416366 1 19.76135634 2.041029539 24.99871057 0.88686261 1.045889808 0.319391227 0.096769585 144.9667574 88325.57309 0.038089368 0.025681201 109.9080591 -2.041029539 0.159027198 RPPS(ph)PEPSTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 RPPSPEPSTK 10 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 RPPS(0.999)PEPS(0.001)TK;RPPS(0.998)PEPS(0.002)TK;RPPS(0.973)PEPS(0.025)T(0.002)K;RPPS(1)PEPSTK;RPPS(0.999)PEPS(0.001)TK;RPPS(0.997)PEPS(0.003)TK;RPPS(0.985)PEPS(0.007)T(0.007)K;RPPS(0.992)PEPS(0.006)T(0.002)K;RPPS(0.913)PEPS(0.034)T(0.053)K 98.407 0.0057178 64122100000 14501200 12818741 9395295 10837255 11799902 12000871 13657128 15810160 15034160 TRUE FALSE 12584829.68 12734533.85 13938891.09 13298019.38 11565107.04 12462552.27 12332661.83 12429280.32 13256838.73 0.949308499 0.960601098 1.051449095 1.003106371 0.872388001 0.940084776 0.930286781 0.937574981 1 23.66023345 3.298736207 24.99999879 0.936021715 0.993246283 0.313961795 0.040380614 88.81350746 36896.71845 0.011780412 0.015208442 1989.464558 -3.298736207 0.057224568 RPPSAFFLFCSEHRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPPSAFFLFCSEHRPK 16 2 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 ; 132.59 2.30E-05 1372100000 2192280 1757770 644880 1118520 1346850 1032450 1691810 1989620 1172100 FALSE TRUE 1902564.643 1746223.093 956746.125 1372497.062 1320050.32 1072169.02 1527738.527 1564155.246 1033535.673 1.840831132 1.689562478 0.925702082 1.327962931 1.277217956 1.03737979 1.478167195 1.513402282 1 19.97915675 4.398473279 7.348998596 1.262256661 1.803710522 0.56687728 0.196824764 0.154351102 11.8985903 0.050361305 0.135179308 25030.71636 -4.398473279 0.541453861 RPPSAFFLFCSEYRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPPSAFFLFCSEYRPK 16 2 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ; 212.32 2.71E-12 11877100000 5011800 4295700 2489820 2896920 3487240 2802920 4663000 4900700 2704600 FALSE TRUE 4349477.932 4267481.264 3693905.28 3554709.963 3417850.747 2910750.146 4210782.978 3852723.442 2384865.269 1.823783502 1.789401405 1.548894744 1.49052863 1.433142069 1.220509261 1.765627196 1.61548893 1 21.18547633 4.17073907 2.164565344 1.454264603 1.834878056 0.360600805 0.207088968 0.398927107 3.641385483 0.057902846 0.188227856 14816.27637 -4.17073907 0.380613453 RPPSGFFLFCSEFRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPPSGFFLFCSEFRPK 16 2 O15347;E7ES08;E7EQU1;E9PES6 O15347 HMGB3 High mobility group protein B3 0 ; 170.09 3.04E-09 1094830000 1079810 1071710 577190 713260 847670 669830 1164200 1264950 664280 FALSE TRUE 937110.3726 1064669.866 856321.0146 875216.5845 830803.0254 695598.7935 1051296.063 994450.2864 585749.5752 1.599848147 1.817619528 1.461923407 1.494182193 1.418358733 1.187536147 1.794787581 1.697739663 1 19.15992448 4.222921482 24.77972088 1.471435338 1.708733811 0.180222364 0.232321042 362.6766843 574652.1808 0.060547029 0.126749743 16707.88519 -4.222921482 0.237298473 RPPT(ph)PCS(ph)DPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPPTPCSDPER 11 1 Q9BW71;Q9BW71-2;Q9BW71-3 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 RPPT(1)PCS(1)DPER;RPPT(1)PCS(1)DPER 102.5 0.0063349 959440000 972770 887670 582340 709420 815140 873980 809940 835440 856940 TRUE FALSE 844215.9798 881838.8373 863961.5718 870504.6538 798920.3088 907602.5761 731392.1435 656787.6574 755633.5294 1.11722938 1.1670192 1.143360555 1.152019623 1.057285414 1.201114748 0.967919123 0.869188081 1 19.52732719 2.125797499 5.441715847 0.923826484 1.137369295 0.780379978 0.048532627 0.079017983 3.461715548 0.018985322 0.012632917 133.597244 -2.125797499 0.213542812 RPPT(ph)PGPDTSVSGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPPTPGPDTSVSGPR 15 1 Q9H6K5-2;Q9H6K5 Q9H6K5-2 PRR36 Proline-rich protein 36 1 RPPT(1)PGPDTSVSGPR 64.2 0.039055 187170000 94758 91148 65424 80855 94960 103040 85715 89500 91886 TRUE FALSE 82235.49021 90549.24279 97063.26523 99214.36354 93070.48179 107004.0155 77402.37249 70361.12149 81023.34176 1.014960485 1.117569836 1.197966699 1.224515817 1.148687277 1.320656655 0.955309554 0.868405573 1 16.30604997 2.113689044 7.472404598 0.921307006 1.170513381 0.625926837 0.083555975 0.133375843 8.201943543 0.034263453 0.023037725 129.9238986 -2.113689044 0.249206375 RPPVVVNLSTS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPPVVVNLSTSPR 13 1 C9J069 C9J069 C9orf172 Uncharacterized protein C9orf172 1 RPPVVVNLS(0.018)T(0.171)S(0.811)PR 60.158 0.057539 158000000 229570 235120 156310 167640 231890 292280 206030 229960 222410 TRUE FALSE 199231.7428 233575.4812 231902.0388 205705.2242 227275.8427 303524.2007 186049.2423 180784.8436 196116.9432 1.015882359 1.19100103 1.182468149 1.048890631 1.158879182 1.547669446 0.948664808 0.921821647 1 17.58135465 2.088559966 21.90544464 0.948753329 1.188002799 0.374319416 0.1424332 8.052924642 1987.3413 0.057784396 0.038958244 122.61962 -2.088559966 0.239249469 RPQHNSSGAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RPQHNSSGASPR 12 1 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 1 RPQHNSS(0.025)GAS(0.975)PR;RPQHNSSGAS(1)PR;RPQHNSS(0.005)GAS(0.995)PR;RPQHNS(0.026)S(0.095)GAS(0.879)PR 149.22 3.87E-05 1714980000 478278 521149 243763 356258 560770 708890 481167 543460 957871 TRUE FALSE 415072.3505 517725.5379 361647.6021 437151.824 549611.7741 736161.457 434503.4984 427245.3082 844632.5816 0.49142356 0.612959468 0.428171503 0.517564481 0.650711074 0.871575965 0.514429005 0.505835694 1 19.68796437 3.20738244 5.118690229 0.678370836 0.512895203 0.274279852 0.154667156 0.312938687 20.44122825 0.048078641 0.056749325 1612.064594 -3.20738244 -0.165475633 RPQLDLDILSSLIDLCDSPVS(ph)PAEASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPQLDLDILSSLIDLCDSPVSPAEASR 27 1 Q9BQ89 Q9BQ89 FAM110A Protein FAM110A 1 RPQLDLDILSSLIDLCDS(0.001)PVS(0.999)PAEASR 141.69 1.27E-07 103750000 44951 45880 35824 47963 60913 59044 59691 67706 54741 TRUE FALSE 39010.61146 45578.61126 53148.60622 58853.73222 59700.95047 61315.46089 53902.17601 53227.59879 48269.58134 0.808182097 0.944251224 1.101078666 1.219271653 1.236823457 1.270271239 1.116690357 1.102715153 1 15.55882669 4.368859103 2.183431402 1.157790438 0.810266808 0.705038149 0.07691609 0.213080442 1.828977766 0.022781437 0.107096571 23380.78576 -4.368859103 -0.34752363 RPQS(ph)PGAS(ph)PSQAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPQSPGASPSQAER 14 1 Q96T58;A0A669KB49 Q96T58 SPEN Msx2-interacting protein 2 RPQS(1)PGAS(0.978)PS(0.022)QAER 129.77 0.00023084 672420000 352510 320310 223150 313330 321200 350820 279670 314390 397790 TRUE FALSE 305924.9104 318205.8625 331066.0864 384476.3654 314808.7484 364316.2724 252547.6464 247160.1451 350763.7194 0.872168053 0.90718009 0.943843585 1.096112124 0.897495183 1.038637271 0.719993638 0.704634292 1 18.42014001 2.235387503 24.99999044 0.782955519 0.95958818 0.311535111 0.103594637 83.3414373 656608.4795 0.040719186 0.028751426 171.9441891 -2.235387503 0.176632661 RPQS(ph)PGASPS(ph)QAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPQSPGASPSQAER 14 1 Q96T58;A0A669KB49 Q96T58 SPEN Msx2-interacting protein 2 RPQS(0.993)PGAS(0.355)PS(0.652)QAER 202.65 1.08E-08 333420000 311010 278000 216970 241850 274840 289800 244670 266620 352640 TRUE FALSE 269909.2405 276173.7997 321897.4177 296765.7389 269371.2217 300948.7935 220941.9411 209605.3878 310951.3009 0.868011292 0.888157724 1.035202029 0.954380117 0.866281057 0.96783256 0.71053551 0.674077861 1 18.24632913 2.24256019 24.99999675 0.766191868 0.931073432 0.276608967 0.099444423 105.1848217 657480.6127 0.037942995 0.028286096 174.8075516 -2.24256019 0.164881564 RPQS(ph)PSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPQSPSPR 8 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 RPQS(0.97)PS(0.03)PR;RPQS(0.935)PS(0.065)PR 83.883 0.010931 261300000 286807 346539 165846 147661 280127 516120 225977 218187 135544 TRUE FALSE 248904.7283 344262.5625 246049.6803 181189.6869 274553.0208 535975.4704 204061.7853 171529.408 119520.1427 2.082533727 2.880372752 2.058646139 1.515976159 2.297127618 4.484394497 1.707342216 1.435150629 1 16.86689425 4.177390399 24.91009999 2.069366842 2.481458794 0.03098499 0.95368881 277.783266 113118.7097 0.260871027 0.543046855 15044.93788 -4.177390399 0.412091952 RPQYS(ph)NPPVQGEVMEGADNQGAGEQGRPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPQYSNPPVQGEVMEGADNQGAGEQGRPVR 30 2 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 RPQYS(1)NPPVQGEVMEGADNQGAGEQGRPVR 121.09 9.73E-06 125690000 22545 14672 12945 16854 23728 28285 17414 19795 19614 TRUE FALSE 19565.62113 14575.61867 19205.2453 20680.9583 23255.85922 29373.14225 15725.19296 15561.99329 17295.25526 1.131271024 0.842752445 1.110434336 1.195759067 1.344638103 1.698335284 0.909220056 0.899783961 1 14.07808869 RPQYSNPPVQGEVMEGADNQGAGEQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPQYSNPPVQGEVMEGADNQGAGEQGR 27 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 149.73 1.69E-07 55981000 30501 28768 22876 29177 28657 28519 24813 30891 64549 FALSE TRUE 26470.21557 28579.02111 33938.91012 35802.08379 28086.78177 29616.14438 22406.63908 24285.20004 56918.09075 0.465058037 0.502107866 0.596276327 0.629010624 0.493459661 0.520329196 0.393664629 0.426669267 1 15.79659965 1.233296663 24.99996196 1.000000778 0.501606592 0.832184829 0.070090602 74.87920373 355581.8708 0.161973778 0.019518256 17.11183813 -1.233296663 -0.498394186 RPQYSNPPVQGEVMEGADNQGAGEQGRPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RPQYSNPPVQGEVMEGADNQGAGEQGRPVR 30 2 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;;;;; 258.24 1.86E-58 4192330000 977293 854775 518846 585505 832756 925785 817487 883546 692484 FALSE TRUE 848141.2539 849159.9267 769761.661 718452.8591 816185.7849 961400.548 738207.2366 694606.5637 610619.3304 1.388985267 1.390653529 1.260624456 1.176596978 1.336652386 1.574467922 1.208948358 1.137544341 1 19.21991374 1.710013646 2.305538351 1.028538253 1.343164481 0.545876507 0.107405081 0.225237108 2.475299803 0.108249681 0.031499658 51.28774989 -1.710013646 0.314626227 RPRDS(ph)PTLSNSGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RPRDSPTLSNSGIR 14 2 Q9HD20;Q9HD20-2;Q9HD20-3 Q9HD20 ATP13A1 Manganese-transporting ATPase 13A1 1 RPRDS(1)PTLSNSGIR;RPRDS(0.999)PT(0.001)LSNSGIR;RPRDS(0.5)PT(0.5)LSNSGIR;RPRDS(0.797)PT(0.034)LS(0.073)NS(0.096)GIR 152.89 5.15E-06 703836000 339319 274810 191150 261818 279930 308385 271053 403274 276146 TRUE FALSE 294477.1344 273004.755 283590.7794 321267.7785 274359.9407 320248.7705 244766.3218 317036.9934 243500.3345 1.20935002 1.121167885 1.164642258 1.319373048 1.126733322 1.315188216 1.005199119 1.301998184 1 17.89356423 1.216388956 24.73394001 0.999999129 1.193714267 0.276826619 0.099246335 2088.477649 2329692.334 1.104974361 0.021807153 16.45845088 -1.216388956 0.193715138 RPRPPNAPS(ph)QDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPRPPNAPSQDGK 13 2 P16989;P16989-2 P16989;P16989-2 YBX3 Y-box-binding protein 3 1 RPRPPNAPS(1)QDGK 76.586 0.02226 50458000 45227 27466 17190 24563 24870 13793 37004 34583 31463 TRUE FALSE 39250.13736 27285.57404 25503.1415 30140.40457 24375.13566 14323.62564 33415.35778 27187.69458 27743.47998 1.414751768 0.983495007 0.919248108 1.08639596 0.878589696 0.516287994 1.204440027 0.97996699 1 14.75986114 4.738250083 4.227205696 0.946248283 1.451393627 0.412097824 0.176548188 0.224395429 9.212303921 0.043532519 0.343317228 54733.10463 -4.738250083 0.505145344 RPS(ph)ADSESPGTPSPDGAAWEPPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPSADSESPGTPSPDGAAWEPPAR 24 1 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 RPS(0.972)ADS(0.011)ES(0.017)PGTPSPDGAAWEPPAR 169.68 5.46E-12 140660000 53293 31268 17618 26013 31829 35177 38352 40655 23359 TRUE FALSE 46250.19502 31062.59845 26138.12373 31919.64923 31195.66517 36530.28195 34632.62894 31961.24463 20597.52563 2.245424807 1.508074271 1.268993383 1.549683676 1.514534597 1.773527685 1.681397541 1.551703112 1 14.33018342 7.999999998 0.039307279 3.04E-11 4.038647482 0.231659011 0.282232661 3890.416473 15.06835963 491.5265557 1211.659917 99999999.62 -7.999999998 4.038647482 RPS(ph)ASSPNNNTAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPSASSPNNNTAAK 14 1 O75151;E7ET14;A0A087WW48 O75151 PHF2 Lysine-specific demethylase PHF2 1 RPS(0.54)AS(0.331)S(0.129)PNNNTAAK;RPS(0.427)AS(0.427)S(0.146)PNNNTAAK 130.39 3.82E-05 440840000 452210 363840 234120 303100 330580 241760 332580 408540 364820 TRUE FALSE 392449.3027 361449.9111 347341.2151 371923.4876 324002.1048 251060.6636 300326.4428 321176.9003 321691.3952 1.21995586 1.123592102 1.079734243 1.156149941 1.007183001 0.780439475 0.933585565 0.998400657 1 18.29531782 3.099983842 4.441899357 0.935268528 1.137846679 0.683371957 0.069457999 0.138027491 4.812124395 0.022750008 0.026013579 1258.878575 -3.099983842 0.202578151 RPS(ph)DSSRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RPSDSSRPK 9 2 Q13573;G3V4X8 Q13573 SNW1 SNW domain-containing protein 1 1 RPS(0.999)DS(0.001)S(0.001)RPK;RPS(0.998)DS(0.001)S(0.001)RPK;RPS(0.957)DS(0.032)S(0.011)RPK 73.881 0.033602 206550000 349186 337359 191679 242511 246897 312826 290859 386094 346817 TRUE FALSE 303040.1854 335142.8665 284375.6055 297576.8291 241984.2327 324860.6186 262651.5389 303530.8027 305816.6894 0.990921019 1.095894626 0.929889098 0.973056211 0.791272161 1.062272368 0.858852862 0.992525304 1 18.22230762 4.224292246 24.97680805 0.943564177 1.043407828 0.213604545 0.079308976 289.3907002 506581.1515 0.018786128 0.039396898 16760.70361 -4.224292246 0.099843651 RPS(ph)EGPQPLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPSEGPQPLVR 11 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 RPS(1)EGPQPLVR;RPS(1)EGPQPLVR 177.21 4.95E-06 757950000 278530 294850 188726 229960 294180 299720 280170 243350 211970 TRUE FALSE 241721.5548 292913.1109 279994.5249 282175.9327 288326.3936 311250.4223 252999.1565 191311.4963 186911.1481 1.293243112 1.567124882 1.498008694 1.509679522 1.542585322 1.665231986 1.353579811 1.02354246 1 17.51199309 1.834787022 3.063671803 1.002193344 1.515771348 0.825334277 0.093775007 0.088315332 1.475376686 0.060561217 0.024979243 68.35763385 -1.834787022 0.513578005 RPS(ph)GRSPTSTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPSGRSPTSTEK 12 2 A1L390-3;A1L390;A1L390-2;A0A0U1RR71 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 RPS(0.744)GRS(0.245)PT(0.007)S(0.003)T(0.001)EK 73.296 0.031172 120820000 113270 104020 42473 31386 82026 70137 99052 113830 6905.1 TRUE FALSE 98301.08251 103336.6858 63013.08486 38512.671 80393.84308 72835.21577 89445.95229 89488.34033 6088.786944 16.14460867 16.97163765 10.34903757 6.325179606 13.20358945 11.96218827 14.69027462 14.69723627 1 12.57193912 8 0.430361342 10 150.6483243 0.201236452 4.347911605 168.7960903 2.222620835 3.768275997 20484.8815 100000000 -8 140.6483243 RPS(ph)GSQHSPSLQT(ph)FAPEADGTIFFPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPSGSQHSPSLQTFAPEADGTIFFPER 27 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 2 RPS(0.959)GS(0.095)QHS(0.351)PS(0.06)LQT(0.535)FAPEADGTIFFPER 167.99 6.48E-12 131870000 30156 31899 21874 35961 41303 57703 33777 57494 46222 TRUE FALSE 26170.80819 31689.45337 32452.33956 44126.49468 40481.15111 59922.87175 30501.31174 45199.35552 40757.68782 0.642107283 0.777508614 0.796226217 1.082654514 0.993215103 1.470222551 0.748357264 1.108977421 1 15.31478459 3.883464917 2.226617126 1.068641001 0.703509746 0.432942362 0.17858747 0.295848694 2.856693582 0.048992514 0.107926715 7646.539167 -3.883464917 -0.365131256 RPS(ph)HEGYLAAPGLEGPGPDGDGQMQLVTSL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPSHEGYLAAPGLEGPGPDGDGQMQLVTSL 30 1 O94910-2;O94910 O94910-2 LPHN1 Latrophilin-1 1 RPS(1)HEGYLAAPGLEGPGPDGDGQMQLVTSL;RPS(1)HEGYLAAPGLEGPGPDGDGQMQLVTSL 136.63 1.72E-06 276530000 110295 106846 67878 105180 120608 144945 80619 133172 112629 TRUE FALSE 95719.2363 106144.1216 100704.0278 129062.7266 118208.1368 150521.1279 72800.58179 104694.2041 99314.12793 0.963802817 1.068771622 1.013994987 1.299540451 1.190244925 1.5156064 0.73303349 1.054172315 1 16.59971134 2.214797321 24.99997634 0.946963927 1.169474626 0.304899642 0.174433935 320.9570873 337657.7022 0.072005097 0.048576076 163.9824312 -2.214797321 0.222510698 RPS(ph)HPKQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPSHPKQPR 9 2 Q8TBE0-3;Q8TBE0-2;Q8TBE0 Q8TBE0-3 BAHD1 Bromo adjacent homology domain-containing 1 protein 1 RPS(1)HPKQPR 57.836 0.058844 7723100 4959.3 6105.2 4185.8 4473.5 4456.8 4586.9 6824.9 5234.8 2826.1 TRUE FALSE 4303.91594 6065.094539 6210.066881 5489.276548 4368.1184 4763.361011 6163.022248 4115.378757 2492.001678 1.727091911 2.433824421 2.491999478 2.202757967 1.752855321 1.911459793 2.473121228 1.651434987 1 11.28308932 1.40891964 3.022093052 0.976398555 2.144008386 0.633216821 0.281620135 0.190280842 2.7122981 0.442495974 0.075256175 25.64009557 -1.40891964 1.167609831 RPS(ph)ILPEGSSDSR ddPTM_MDA-MB-175_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 114.29 0.00046217 1096990000 1436430 1512750 944000 929440 1385080 1649450 1398030 1345630 1444990 TRUE FALSE 1246602.136 1502812.646 1400521.557 1140483.558 1357519.618 1712905.409 1262449.266 1057877.496 1274164.928 0.978367956 1.179449075 1.09916819 0.89508315 1.065419074 1.344335706 0.990805223 0.83025162 1 20.2811206 2.003284309 24.99992287 0.905259141 1.094155409 0.267845302 0.123986806 113.1097836 860978.2566 0.051203578 0.034330119 100.7591069 -2.003284309 0.188896268 RPS(ph)LEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPSLEHR 7 1 Q8WU20 Q8WU20 FRS2 Fibroblast growth factor receptor substrate 2 1 RPS(1)LEHR 64.439 0.045271 0 128870 131250 84878 111110 119540 169770 106390 161360 137010 TRUE FALSE 111839.503 130387.8101 125925.2847 136339.2237 117161.3879 176301.1618 96072.31418 126854.4197 120812.8339 0.92572535 1.079254628 1.042317117 1.128516063 0.969776009 1.459291667 0.79521613 1.050007815 1 16.88241419 RPS(ph)LGELLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RPSLGELLLR 10 1 Q8N612;Q8N612-2 Q8N612 FAM160A2 FTS and Hook-interacting protein 1 RPS(1)LGELLLR;RPS(1)LGELLLR;RPS(1)LGELLLR 180.11 1.25E-06 402777000 234421 196572 151284 189533 221013 222519 237570 207738 289951 TRUE FALSE 203441.6709 195280.7056 224445.4484 232569.3645 216615.2737 231079.4499 214530.498 163314.8453 255673.3231 0.795709417 0.763789915 0.877860254 0.909634848 0.847234553 0.903807433 0.839080493 0.638763729 1 17.96394211 0.952142279 18.23831879 2.341977228 0.820161204 0.334046977 0.07895355 7570986.274 66715821.06 416807995.9 0.021390558 8.956581435 -0.952142279 -1.521816024 RPS(ph)LPALHFIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPSLPALHFIK 11 1 P00519-2;R4GRW0 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 RPS(1)LPALHFIK;RPS(1)LPALHFIK 135.47 7.32E-05 1397570000 2024760 2047640 1381240 1668880 2000130 1738740 2346460 2261200 2044010 TRUE FALSE 1757182.836 2034188.918 2049212.284 2047824.711 1960331.326 1805630.453 2118900.67 1777659.977 1802369.466 0.974929319 1.128619274 1.136954616 1.136184755 1.087641221 1.001809278 1.175619489 0.986290552 1 20.78146335 1.627690981 10.10392261 0.992628485 1.092657586 0.304837488 0.061747038 0.108017924 27.77152531 0.034217185 0.015199571 42.43175365 -1.627690981 0.100029101 RPS(ph)PAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPSPAEK 7 1 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 RPS(1)PAEK 55.806 0.076817 269590000 456340 478820 302290 350300 383480 565980 416940 512480 473950 TRUE FALSE 396033.5128 475674.5999 448478.4551 429840.969 375849.4983 587753.6168 376505.223 402890.1401 417920.1709 0.947629572 1.138194883 1.073119907 1.028524103 0.899333233 1.406377719 0.900902252 0.96403612 1 18.67286787 RPS(ph)PLAHQPVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RPSPLAHQPVPR 12 1 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 RPS(1)PLAHQPVPR;RPS(1)PLAHQPVPR;RPS(1)PLAHQPVPR 152.34 4.27E-05 595670000 170274 206507 138616 146301 173843 193853 158457 176963 198756 TRUE FALSE 147771.8595 205150.4419 205651.1612 179520.8781 170383.8644 201310.6503 143089.8645 139120.8396 175259.2921 0.843161339 1.170553866 1.173410886 1.024315892 0.972181631 1.148644662 0.816446665 0.793800077 1 17.41913141 2.229661113 24.99984667 0.851955272 1.060784871 0.36877093 0.113310731 177.481683 498563.9726 0.044755599 0.030676575 169.6919 -2.229661113 0.2088296 RPS(ph)PPEPWDEEDGASCSTFFGSEER ddPTM_MDA-MB-175_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 233.58 1.41E-38 1722010000 219919 223519 162291 178650 206959 239452 189753 220217 308144 TRUE FALSE 190856.1469 222050.689 240775.4704 219215.213 202840.9208 248663.8734 171350.7833 173125.3083 271715.5674 0.702411528 0.817217398 0.886130569 0.806781942 0.746519321 0.91516241 0.630625565 0.637156384 1 18.0517377 2.235698437 24.9996546 0.725962492 0.812696299 0.028675563 0.117644326 174.1282253 1520888.123 0.045893158 0.032488558 172.0673368 -2.235698437 0.086733807 RPS(ph)PQPSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RPSPQPSPR 9 1 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RPS(1)PQPSPR;RPS(1)PQPSPR;RPS(1)PQPSPR 107.34 0.0017082 1272640000 845130 655963 442685 535591 511618 663649 627432 736146 720819 TRUE FALSE 733443.9292 651653.9359 656768.9467 657205.1225 501437.8028 689180.0065 566583.7412 578726.9066 635604.599 1.153931124 1.025250505 1.033297978 1.033984215 0.788914686 1.084290465 0.891409128 0.910514033 1 19.27777004 5.286151598 0.628199611 0.93577551 1.455920654 0.384765465 0.081587176 6.467017694 1.201518256 0.037164119 2.814753636 193264.282 -5.286151598 0.520145144 RPS(ph)PTSGDSRPAAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RPSPTSGDSRPAAGR 15 2 Q8N1G1 Q8N1G1 REXO1 RNA exonuclease 1 homolog 1 RPS(0.942)PT(0.021)S(0.021)GDS(0.016)RPAAGR;RPS(0.87)PT(0.107)S(0.023)GDSRPAAGR;RPS(0.677)PT(0.226)S(0.085)GDS(0.012)RPAAGR;RPS(0.792)PT(0.157)S(0.05)GDSRPAAGR;RPS(0.978)PT(0.007)S(0.012)GDS(0.003)RPAAGR;RPS(0.901)PT(0.076)S(0.023)GDSRPAAGR;RPS(0.86)PT(0.069)S(0.069)GDS(0.002)RPAAGR 136.62 1.71E-05 2126800000 397158.2 404630.1 236569 270736.1 370395.2 436687.6 384732 411647.2 325121.4 TRUE FALSE 344672.7376 401972.0582 350974.5597 332210.8694 363025.0602 453487.2545 347420.7499 323619.6497 286685.9185 1.202266018 1.402133946 1.224247642 1.158797304 1.266281449 1.581826052 1.211851463 1.128829945 1 18.12911152 1.640626207 2.504748308 1.020859961 1.301736826 0.405739546 0.121292896 0.262295881 3.592423844 0.126319613 0.033916212 43.71456959 -1.640626207 0.280876865 RPS(ph)QEQSASASSGQPQAPLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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(0.999)QEQS(0.001)ASASSGQPQAPLNR 347.4 1.77E-95 6184940000 1009767 784237 597934 649185 918562 1029266 857831 912233 1026189 TRUE FALSE 876323.7325 779085.2955 887096.8824 796592.3764 900284.4133 1068862.529 774638.6817 717159.072 904874.1055 0.968448237 0.860987502 0.980353927 0.880335034 0.994927811 1.181227889 0.856073433 0.792551215 1 19.78735756 RPS(ph)QGPPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 126.12 0.00029552 7257983000 2465842 2472744 1791844 1770549 2617421 3059143 2518542 2752468 2656361 TRUE FALSE 2139974.732 2456500.382 2658385.752 2172579.212 2565339.443 3176830.211 2274294.184 2163874.138 2342329.029 0.91360979 1.048742662 1.134932676 0.927529474 1.095208833 1.356269837 0.97095419 0.923813056 1 21.15951232 2.03234269 24.99999352 0.953739572 1.081771534 0.162406179 0.122270875 311.7635785 240983.2686 0.050729817 0.034201786 107.7314958 -2.03234269 0.128031962 RPS(ph)QGPPARS(ph)PSQDFSFIEDTEILDSAMYR ddPTM_MDA-MB-175_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 70.647 0.0033147 22608000 13373 12190 4878.2 4106.1 12056 9233.7 8804.9 10895 2185.5 TRUE FALSE 11605.72417 12109.92309 7237.313837 5038.452763 11816.10919 9588.926414 7951.002153 8565.189035 1927.13268 6.022275627 6.283907286 3.755482906 2.614481512 6.131445599 4.975747915 4.125819793 4.444524824 1 10.91224019 1.195503641 2.802282203 1.56E-13 4.809906458 0.519928781 1.148862402 0.468715275 3.965542984 5.539039967 0.310979558 15.68569048 -1.195503641 4.809906458 RPS(ph)QGPPARSPSQDFSFIEDTEILDSAMYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPSQGPPARSPSQDFSFIEDTEILDSAMYR 30 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RPS(0.332)QGPPARS(0.332)PS(0.332)QDFS(0.003)FIEDTEILDSAMYR 105.56 0.00016818 29532000 22359 9602.1 5265.6 5141.1 15666 10619 12526 19957 6203 TRUE FALSE 19404.2015 9539.023173 7812.061772 6308.465332 15354.27725 11027.5198 11311.23045 15689.35086 5469.688406 3.5475881 1.743979266 1.428246217 1.153350038 2.807157576 2.01611481 2.067984428 2.868417667 1 12.41724293 3.215702037 24.99665516 2.228407534 1.913692905 0.00575419 0.805298498 988.0376308 1080450.438 0.240206548 0.272547836 1643.243931 -3.215702037 -0.31471463 RPS(ph)QNAISFFNVGHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPSQNAISFFNVGHSK 16 1 Q9BXB4 Q9BXB4 OSBPL11 Oxysterol-binding protein-related protein 11 1 RPS(0.994)QNAIS(0.006)FFNVGHSK;RPS(1)QNAISFFNVGHSK 265.63 2.52E-27 2398300000 1989370 1711130 1133570 1180390 1734900 1755410 1983950 2057040 1416710 TRUE FALSE 1726469.714 1699889.474 1681768.244 1448415.591 1700378.884 1822941.759 1791546.834 1617158.004 1249228.158 1.382029138 1.360751808 1.346245866 1.159448402 1.361143578 1.459254458 1.434123001 1.294525739 1 20.25260556 1.253353351 3.651920365 0.958912964 1.354191959 0.664684737 0.079203643 0.174029304 3.601620375 0.184942331 0.021633523 17.92063322 -1.253353351 0.395278995 RPS(ph)RHDNSAIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RPSRHDNSAIGR 12 2 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 RPS(1)RHDNSAIGR;RPS(1)RHDNSAIGR;RPS(1)RHDNSAIGR 149.59 3.52E-05 278846000 102361 89107 38214 60335 77345 101626 94648 95233 64355 TRUE FALSE 88833.7345 88521.65025 56694.41822 74034.98391 75805.98582 105535.618 85469.05153 74868.16405 56747.02521 1.565434209 1.559934638 0.999072956 1.304649603 1.335858321 1.859755953 1.506141533 1.319331961 1 15.79225715 1.292725133 2.935382518 0.944741818 1.438933759 0.290683705 0.219899362 0.505091861 5.705833607 0.556808247 0.060596628 19.62118052 -1.292725133 0.494191941 RPS(ph)SMYSTGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RPSSMYSTGGK 11 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 RPS(0.499)S(0.499)MY(0.002)STGGK;RPS(0.518)S(0.482)MYSTGGK;RPS(0.793)S(0.207)MYSTGGK;RPS(0.5)S(0.5)MYSTGGK;RPS(0.5)S(0.5)MYSTGGK 162.48 2.66E-05 1234063000 1904510 1857820 1299091 1411241 1753230 1826809 2042220 2146100 2506070 TRUE FALSE 1652824.178 1845615.858 1927335.753 1731684.839 1718344.153 1897087.524 1844165.819 1687173.216 2209805.26 0.747950151 0.835193893 0.87217448 0.783636853 0.777599811 0.858486292 0.834537709 0.763494072 1 21.07548781 1.229702534 24.99994741 1.000000361 0.810729961 0.680048957 0.041130656 208.9058103 589544.8008 0.11750318 0.00999505 16.97080854 -1.229702534 -0.189270399 RPS(ph)SNLNNNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPSSNLNNNVR 11 1 Q9NW75-2;Q9NW75 Q9NW75-2 GPATCH2 G patch domain-containing protein 2 1 RPS(0.937)S(0.063)NLNNNVR;RPS(0.96)S(0.04)NLNNNVR 151.99 3.51E-05 68277000 109439 95050 87303 100901 108345 111748 126533 122241 163157 TRUE FALSE 94976.35887 94425.61029 129523.0228 123812.1142 106189.1465 116047.0179 114261.8491 96100.71343 143868.7653 0.660159685 0.656331554 0.900285913 0.86059065 0.738097295 0.806617181 0.794208867 0.667974826 1 17.13439388 4.264057381 24.94505856 0.806067126 0.658245386 0.355773257 0.090245094 265.5089986 259759.0621 0.02234041 0.059058963 18367.81012 -4.264057381 -0.14782174 RPS(ph)STALHQHHF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPSSTALHQHHF 12 1 Q9UGP4 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 RPS(0.494)S(0.494)T(0.012)ALHQHHF 118.51 0.00029063 487020000 64850 72276 48321 50828 57088 77087 74188 72826 85930 TRUE FALSE 56279.90819 71801.2142 71689.19722 62369.27426 55952.06049 80052.58677 66993.25918 57252.72663 75771.45329 0.742758727 0.947602442 0.946124089 0.823123638 0.73843193 1.056500612 0.88414906 0.755597579 1 16.2093668 RPS(ph)STSVPLGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPSSTSVPLGDK 12 1 Q9NXR1;Q9NXR1-1;I3L533;I3L2R9;I3L2T8 Q9NXR1 NDE1 Nuclear distribution protein nudE homolog 1 1 RPS(0.691)S(0.229)T(0.076)S(0.004)VPLGDK 82.877 0.0084336 466250000 885320 661340 586570 631140 709290 590060 912700 933230 809400 TRUE FALSE 768322.7189 656995.614 870237.214 774449.9834 695176.5167 612759.99 824186.4945 733666.0269 713713.6541 1.07651397 0.920531098 1.219308625 1.085099015 0.974027206 0.858551587 1.154785942 1.027955711 1 19.44498585 3.25339266 24.90254687 1.010329054 1.074585576 0.111510079 0.100239272 616.1675344 1034519.192 0.0293492 0.03772499 1792.22553 -3.25339266 0.064256522 RPS(ph)TS(ph)SASGQWSPTPEWVLSWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPSTSSASGQWSPTPEWVLSWK 22 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 2 RPS(0.814)T(0.194)S(0.542)S(0.447)AS(0.003)GQWSPTPEWVLSWK;RPS(0.761)T(0.276)S(0.433)S(0.456)AS(0.075)GQWSPTPEWVLSWK 175.39 5.38E-12 1128380000 876920 880260 594970 653800 818960 711710 890410 1032180 1011860 TRUE FALSE 761032.8002 874477.5141 882699.4821 802255.2827 802664.2983 739089.9442 804058.1752 811456.3394 892239.0635 0.852947188 0.980093284 0.989308267 0.899148351 0.899606766 0.828354165 0.901168989 0.909460673 1 19.76707079 4.794871382 20.94287839 0.920726366 0.85294379 0.155829674 0.052138595 15827.69541 5885100.209 0.013361386 12.1478349 62355.01413 -4.794871382 -0.067782576 RPS(ph)TSSASGQWSPTPEWVLSWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPSTSSASGQWSPTPEWVLSWK 22 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 RPS(0.239)T(0.239)S(0.239)S(0.239)AS(0.043)GQWSPTPEWVLSWK;RPS(0.395)T(0.062)S(0.101)S(0.166)AS(0.276)GQWSPTPEWVLSWK 227.96 2.46E-26 18058300000 4228990 3917030 2600580 2785180 3747380 3562690 4078880 4428420 3952360 TRUE FALSE 3670118.257 3891298.772 3858229.186 3417597.688 3672814.47 3699748.99 3683310.845 3481436.845 3485116.503 1.053083377 1.116547687 1.107058884 0.980626526 1.053857013 1.061585455 1.056868785 0.998944179 1 21.73277545 -1.999999975 0.148075204 0.659428593 1.12380494 0.332953878 0.036279331 178.3730723 2.230260482 17.36164882 0.64834413 0.010000001 1.999999975 0.464376347 RPS(ph)VGSQSNQAGQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RPSVGSQSNQAGQGK 15 1 Q9UPP1-4;Q9UPP1-3;Q9UPP1-2;Q9UPP1;H0Y3N9 Q9UPP1-4 PHF8 Histone lysine demethylase PHF8 1 RPS(1)VGSQSNQAGQGK;RPS(0.691)VGS(0.308)QSNQAGQGK;RPS(1)VGSQSNQAGQGK;RPS(1)VGSQSNQAGQGK 211.35 8.72E-10 520766000 338139 367082 357320 449992 583810 504369 653060 693880 687120 TRUE FALSE 293453.0744 364670.6142 530121.1472 552169.5613 572193.3232 523772.4018 589726.3417 545499.1618 605889.4564 0.484334347 0.601876481 0.874946975 0.911337135 0.944385675 0.864468586 0.973323327 0.900327867 1 19.20869507 4.300820925 2.329468423 0.929563939 0.485625404 0.947885187 0.037896661 0.058743262 0.604950164 0.009484772 0.036531487 19990.37426 -4.300820925 -0.443938535 RPSANCDPFSVTEALIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPSANCDPFSVTEALIR 17 1 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ; 146.58 6.92E-07 3311000000 1460100 1458270 1095060 1230940 1524930 1673860 1580340 1426310 1501350 FALSE TRUE 1267144.086 1448690.528 1624634.679 1510443.741 1494586.876 1738254.477 1427078.87 1121304.706 1323862.113 0.957157149 1.0942911 1.227193272 1.140937357 1.128959626 1.313017768 1.077966395 0.846995087 1 20.33632144 1.92659716 5.907573349 0.923007983 1.148347141 0.459568627 0.097272141 0.183991966 11.32469539 0.048382271 0.025938602 84.44951504 -1.92659716 0.225339158 RPSAPVDFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPSAPVDFSK 10 1 Q14696 Q14696 MESDC2 LDLR chaperone MESD 0 71.085 0.078962 0 245130 259950 209400 242350 267700 283000 225990 258910 287650 FALSE TRUE 212735.4494 258242.3713 310666.5404 297379.2716 262373.2937 293887.1931 204073.5246 203544.1113 253644.3447 0.838715524 1.01812785 1.224811619 1.172426186 1.034414128 1.158658568 0.80456564 0.802478414 1 17.95244747 2.234084175 24.99988281 0.852467554 1.08142007 0.397245408 0.118551154 104.7845983 585188.6856 0.048567453 0.033998158 171.428954 -2.234084175 0.228952516 RPSDSSRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPSDSSRPK 9 2 Q13573;G3V4X8 Q13573 SNW1 SNW domain-containing protein 1 0 71.349 0.028027 116940000 68145 63140 41738 46831 51851 57019 66232 72586 60422 FALSE TRUE 59139.46559 62725.22918 61922.63641 57464.69432 50819.26654 59212.55783 59808.83083 57064.04876 53278.97999 1.109996205 1.177297861 1.162233894 1.078562208 0.953833323 1.111368082 1.122559607 1.071042441 1 15.70127884 3.666722419 5.105284047 1.05899915 1.152506496 0.422838895 0.051791454 0.219523581 10.7445558 0.014824174 0.022498785 4642.184732 -3.666722419 0.093507346 RPSENLGQVLFGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RPSENLGQVLFGER 14 1 Q99805 Q99805 TM9SF2 Transmembrane 9 superfamily member 2 0 ;; 133.16 7.41E-05 1726720000 1411069 1438462 1132242 1278482 1538750 1642131 1594084 1829784 2093675 FALSE TRUE 1224592.656 1429012.648 1679798.018 1568780.878 1508131.886 1705304.842 1439489.979 1438498.931 1846163.127 0.663317688 0.774044627 0.909886019 0.849752038 0.816900665 0.923702146 0.779719819 0.779183004 1 20.8160986 4.563588208 3.291095531 0.852963612 0.664627045 0.471769513 0.068766538 0.249272016 4.662356689 0.017128333 0.09167646 36609.02879 -4.563588208 -0.188336567 RPSGRS(ph)PTSTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPSGRSPTSTEK 12 2 A1L390-3;A1L390;A1L390-2;A0A0U1RR71 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 RPS(0.115)GRS(0.58)PT(0.028)S(0.059)T(0.219)EK 101.53 0.0020636 106060000 139240 113450 35814 39474 90893 88128 121500 138290 7251.3 TRUE FALSE 120839.0812 112704.7395 53133.77019 48437.17502 89084.40713 91518.34119 109716.9487 108717.7597 6394.059575 18.898648 17.62647629 8.309864738 7.575339963 13.93237052 14.31302604 17.15920026 17.00293193 1 12.64251647 8 0.156228181 10 31.97367359 0.107657422 5.337958406 549.3025573 7.108755247 84.43652586 2691.85151 100000000 -8 21.97367359 RPSGSQHSPS(ph)LQTFAPEADGTIFFPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPSGSQHSPSLQTFAPEADGTIFFPER 27 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 RPS(0.042)GS(0.042)QHS(0.335)PS(0.494)LQT(0.088)FAPEADGTIFFPER;RPS(0.101)GS(0.101)QHS(0.303)PS(0.492)LQT(0.003)FAPEADGTIFFPER 231.94 9.96E-36 346340000 100537 153932 69437 146629 194887 198867 136272 191419 199245 TRUE FALSE 87250.78072 152920.8106 103016.9655 179923.3555 191009.13 206517.5422 123056.3624 150485.5365 175690.4831 0.496616431 0.870398942 0.586354842 1.024092782 1.087191102 1.175462316 0.700415642 0.856537781 1 17.42267652 3.736073541 24.99647454 0.957738346 0.673050953 0.477915681 0.157902516 222.7072971 2238333.626 0.044977482 0.070384127 5445.948632 -3.736073541 -0.284687392 RPSQEQS(ph)ASASSGQPQAPLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPSQEQSASASSGQPQAPLNR 21 1 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 RPS(0.139)QEQS(0.855)AS(0.007)ASSGQPQAPLNR 223.78 3.63E-25 1447200000 162690 157750 107640 123530 153450 167060 153090 153630 154710 TRUE FALSE 141190.1043 156713.7299 159695.064 151579.3745 150396.6452 173486.9063 138243.3554 120777.42 136420.36 1.034963581 1.148756167 1.170610193 1.111119883 1.102450141 1.271708316 1.013363074 0.885332805 1 17.05769945 2.009450607 24.07305975 0.938937485 1.13903474 0.624646786 0.065187221 68.88811692 175474.243 0.025344308 0.017058087 102.199932 -2.009450607 0.200097255 RPSS(ph)EDFVFL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPSSEDFVFL 10 1 Q86TL0;K7EQ67;K7EN30;Q86TL0-2 Q86TL0 ATG4D "Cysteine protease ATG4D;Cysteine protease ATG4D, mitochondrial" 1 RPS(0.387)S(0.613)EDFVFL 69.451 0.060316 26343000 52389 58696 45895 55728 68234 77050 57725 68263 88225 TRUE FALSE 45465.66091 58310.42211 68089.97551 68381.89415 66876.2769 80014.16336 52126.83838 53665.48867 77795.14101 0.584428029 0.749538099 0.875247151 0.878999553 0.859645937 1.02852392 0.670052624 0.689830855 1 16.24739243 4.628891997 2.722657834 0.839055527 0.564450712 0.365290175 0.113808831 0.446371831 5.078505085 0.030914719 0.242737922 42549.25856 -4.628891997 -0.274604816 RPSS(ph)MYSTGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RPSSMYSTGGK 11 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 RPS(0.475)S(0.516)MYS(0.008)TGGK;RPS(0.231)S(0.747)MYS(0.022)TGGK;RPS(0.418)S(0.574)MY(0.006)S(0.001)TGGK;RPS(0.393)S(0.607)MYSTGGK;RPS(0.007)S(0.993)MYSTGGK;RPS(0.074)S(0.926)MYSTGGK 183.87 3.16E-06 4306370000 3485160 3592090 2586630 2899120 3526430 3540280 4114650 4239490 4879260 TRUE FALSE 3024587.276 3568493.324 3837532.92 3557409.506 3456260.942 3676476.862 3715611.876 3332908.055 4302439.441 0.702993573 0.829411633 0.891943506 0.826835463 0.803325878 0.854509846 0.863605851 0.774655425 1 22.03672346 7.999728902 0.027409009 1.441931906 1.26E-06 0.267976114 0.066100595 7058.05076 19.18362333 367.690279 690.4343582 99937596.89 -7.999728902 -1.441930643 RPSS(ph)TALHQHHF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPSSTALHQHHF 12 1 Q9UGP4 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 RPS(0.323)S(0.663)T(0.014)ALHQHHF 136.6 5.03E-05 344620000 168010 187780 123440 118730 186380 228580 172370 190030 209520 TRUE FALSE 145807.0528 186546.4608 183135.9969 145689.4612 182671.4026 237373.6205 155653.5839 149393.5633 184750.7843 0.789209385 1.009719453 0.991259645 0.788572897 0.988744937 1.284831463 0.842505673 0.808622079 1 17.49522096 RPSS(ph)TSVPLGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPSSTSVPLGDK 12 1 Q9NXR1;Q9NXR1-1;I3L533;I3L2R9;I3L2T8 Q9NXR1 NDE1 Nuclear distribution protein nudE homolog 1 1 RPS(0.209)S(0.557)T(0.221)S(0.013)VPLGDK;RPS(0.081)S(0.918)T(0.002)SVPLGDK 201.76 1.53E-07 761740000 1363460 1080690 941080 945830 1097880 947060 1528380 1389870 1366220 TRUE FALSE 1183275.306 1073590.876 1396189.436 1160595.158 1076034.336 983494.011 1380157.943 1092657.116 1204707.028 0.982210014 0.891163454 1.158945207 0.963383736 0.893191715 0.816376088 1.145637828 0.906989908 1 20.20025091 5.112803701 19.34094974 0.971125471 2.666891898 0.000818592 0.10911402 11319.45241 1721595.982 0.024838666 95916.98966 129659.3084 -5.112803701 1.695766428 RPSVGS(ph)QSNQAGQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPSVGSQSNQAGQGK 15 1 Q9UPP1-4;Q9UPP1-3;Q9UPP1-2;Q9UPP1;H0Y3N9 Q9UPP1-4 PHF8 Histone lysine demethylase PHF8 1 RPS(0.275)VGS(0.725)QSNQAGQGK 182.76 3.27E-07 154080000 106600 116480 115330 147130 176660 169500 207050 234890 229150 TRUE FALSE 92512.53991 115714.8352 171103.9738 180538.1152 173144.8116 176020.7747 186970.3229 184660.6014 202060.148 0.457846541 0.572675198 0.84679723 0.893486999 0.856897381 0.871130584 0.925320132 0.913889271 1 17.62442528 4.295512273 2.210134388 0.908501957 0.454654761 0.947445504 0.038552616 0.069893849 0.641878223 0.010932044 0.04355493 19747.50686 -4.295512273 -0.453847197 RPT(ph)PAMLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RPTPAMLFR 9 1 Q9UD71;J3KSJ8;J3KT77 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 1 RPT(1)PAMLFR;RPT(1)PAMLFR;RPT(1)PAMLFR 86.803 0.01399 737290000 175996 225744 150665 138974 215927 214702 156552 169677 232432 TRUE FALSE 152737.6827 224261.0728 223527.0979 170530.1708 211630.4752 222961.7249 141369.6111 133392.894 204954.1537 0.74522853 1.09420116 1.090619994 0.832040569 1.032574707 1.08786146 0.689762118 0.650842598 1 17.6449417 2.232343909 24.99831776 0.749483447 0.98622799 0.285622412 0.146417612 156.1999928 628095.8684 0.057243086 0.039683143 170.7433934 -2.232343909 0.236744543 RPTETNPVTSNS(ph)DEECNETVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPTETNPVTSNSDEECNETVK 21 1 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 RPTETNPVTS(0.002)NS(0.998)DEECNETVK;RPTETNPVTSNS(1)DEECNETVK 324.63 1.13E-67 790740000 449850 311300 262950 286650 309660 285900 337450 429810 484360 TRUE FALSE 390401.1827 309255.0498 390113.4995 351738.2637 303498.3718 296898.758 304724.1509 337898.4763 427099.5126 0.914075458 0.724081954 0.913401884 0.823551077 0.710603414 0.695151245 0.713473422 0.791146949 1 18.70421273 4.761654191 22.77425653 0.790781723 0.914075923 0.123032395 0.097684949 3954.065969 3899181.329 0.024032698 1.08290055 57763.59195 -4.761654191 0.123294199 RPTETNPVTSNS(ph)DEECNETVKEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPTETNPVTSNSDEECNETVKEK 23 2 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 RPTETNPVTSNS(1)DEECNETVKEK 181.21 2.25E-17 225800000 91936 66708 37646 33545 70122 50321 87066 103430 31312 TRUE FALSE 79786.42466 66269.79076 55851.73152 41161.90495 68726.70939 52256.88143 78622.35272 81312.29939 27610.33103 2.889730825 2.400180957 2.02285628 1.490815337 2.48916644 1.892656824 2.847570086 2.944995455 1 14.75292056 2.258537074 24.99535839 2.430331282 2.179965541 0 0.642464005 1032.938136 1292451.813 0.239632464 0.185361803 181.3581487 -2.258537074 -0.250365741 RPTPNDDTLDEGVGLVHSNIATEHIPS(ph)PAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RPTPNDDTLDEGVGLVHSNIATEHIPSPAK 30 1 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 1 RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAK;RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAK;RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAK;RPTPNDDTLDEGVGLVHSNIAT(0.001)EHIPS(0.999)PAK;RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAK;RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAK;RPTPNDDTLDEGVGLVHSNIAT(0.001)EHIPS(0.999)PAK 255.98 1.85E-58 8829150000 2956450 2384774 1721951 2216425 2478720 2147358 2880920 3488550 3310230 TRUE FALSE 2565747.642 2369108.263 2554692.263 2719698.172 2429398.322 2229968.252 2601528.822 2742550.73 2918898.38 0.879012322 0.811644653 0.875224804 0.931755004 0.832299726 0.76397598 0.891270775 0.939584176 1 21.47699255 1.639732651 2.317960538 0.993140991 0.850922879 0.553174329 0.045219436 0.220759218 2.50756998 0.051995043 0.013074113 43.6247199 -1.639732651 -0.142218112 RPTPNDDTLDEGVGLVHSNIATEHIPS(ph)PAKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPTPNDDTLDEGVGLVHSNIATEHIPSPAKK 31 2 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 1 RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAKK;RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAKK 214.42 4.45E-35 2581840000 589090 428180 344570 395220 420160 322170 622460 648250 359110 TRUE FALSE 511240.2639 425367.2574 511205.2045 484960.7416 411799.638 334564.0884 562093.925 509626.7822 316656.4249 1.614495155 1.343308469 1.614384438 1.531504506 1.30046197 1.056552345 1.775090858 1.609399785 1 18.27255883 7.999999052 0.574304474 1.417200198 9.401571262 0.056619323 0.246185155 739.4142232 6.369792726 0.127321609 7340.033239 99999781.74 -7.999999052 7.984371063 RPTPNDDTLDEGVGLVHSNIATEHIPSPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPTPNDDTLDEGVGLVHSNIATEHIPSPAK 30 1 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 142.59 1.97E-08 625810000 140470 108020 67970 104320 107990 105600 121710 157250 112010 FALSE TRUE 121906.5336 107310.4095 100840.5193 128007.4504 105841.2103 109662.5003 109906.5829 123623.3112 98768.3054 1.234267745 1.086486288 1.020980556 1.296037731 1.071611079 1.110300515 1.112771779 1.251649613 1 16.59176054 3.540752719 0.004981481 0.724208725 1.553000748 0.007395727 0.098510515 372654.0664 1433.26332 118485.6478 119965.8266 3473.383358 -3.540752719 0.828792023 RPTPQDS(ph)PIFLPVDDTSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 RPTPQDSPIFLPVDDTSFR 19 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPT(0.001)PQDS(0.999)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR 202.58 3.34E-16 22526190000 2060884 2137458 1620656 1677321 2257589 2702839 2133895 2381918 2700920 TRUE FALSE 1788532.958 2123416.898 2404410.662 2058182.369 2212667.396 2806818.965 1926950.191 1872563.372 2381620.314 0.75097317 0.891584979 1.009569262 0.864194161 0.929059675 1.178533349 0.809092104 0.786256046 1 21.183512 5.906178579 13.82522029 0.90861086 0.644158436 0 0.126406718 0 0 0.028773193 0 805709.6751 -5.906178579 -0.264452425 RPTPQDSPIFLPVDDT(ph)SFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPTPQDSPIFLPVDDTSFR 19 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 RPTPQDSPIFLPVDDT(0.5)S(0.5)FR 102.21 0.00023245 71245000 35450 32917 23915 29303 30194 30308 29040 34867 39630 TRUE FALSE 30765.19268 32700.76606 35480.37399 35956.69402 29593.19847 31473.96837 26223.70527 27410.96339 34944.98655 0.880389313 0.93577847 1.015320866 1.028951434 0.846851048 0.900671927 0.750428255 0.784403318 1 15.09279787 3.21398019 21.3675141 0.84171894 0.966601246 0.314337318 0.078043754 48.16807392 41871.17625 0.024403683 0.027698985 1636.741861 -3.21398019 0.124882306 RPTPQDSPIFLPVDDTSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 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 ;;;;;;;;;;; 272.74 4.78E-38 41910498000 7976028 7748784 5978255 5646546 8298338 9966672 7623636 8732050 9439324 FALSE TRUE 6921975.691 7697881.728 8869359.114 6928680.571 8133217.309 10350096.32 6884296.954 6864769.06 8323417.87 0.831626598 0.924846241 1.065590993 0.832432143 0.977148743 1.243491133 0.827099764 0.824753625 1 22.98874464 RPTWAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RPTWAEER 8 1 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;A0A0G2JQ95;A0A096LP11 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;;; 118.71 0.0029406 3795980000 3267590 4267670 2486240 2973210 4015590 4436190 3728360 4132870 4244730 FALSE TRUE 2835769.702 4239635.395 3688593.98 3648322.773 3935687.615 4606853.1 3366784.221 3249087.913 3742922.855 0.757635092 1.132707127 0.985484907 0.974725613 1.051501131 1.230817005 0.899506709 0.868061683 1 21.83573388 RPVDSYDIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPVDSYDIPK 10 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDQ3;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 0 ; 120.77 0.00085417 455170000 656000 650700 467810 584030 633370 555820 732960 938810 836800 FALSE TRUE 569307.9379 646425.5089 694044.4807 716642.9378 620767.1762 577202.7551 661877.652 738052.7873 737874.4573 0.77155122 0.876064353 0.940599683 0.971226109 0.841291049 0.782250625 0.897005779 1.000241681 1 19.49301585 1.784643265 4.044233555 1.001234666 0.86971787 0.44902041 0.0611695 0.202388417 6.340168359 0.040493333 0.017588814 60.90364213 -1.784643265 -0.131516796 RPVGASFSFGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPVGASFSFGGK 12 1 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-7;H7BXG7;O94979-5;H0YAB3 D6REX3 SEC31A Protein transport protein Sec31A 0 70.622 0.075018 478020000 800120 750090 494750 595160 699070 711430 790100 915540 738070 FALSE TRUE 694382.1148 745162.6094 734012.7548 730300.1745 685159.8747 738799.1725 713476.2236 719758.8957 650816.2054 1.066940419 1.14496628 1.12783417 1.122129671 1.052770151 1.135188654 1.09627913 1.105932658 1 19.31189065 1.236674273 6.407094726 0.996703256 1.107797762 0.570894043 0.029002257 0.089828651 16.45735888 0.043309334 0.006821679 17.24543975 -1.236674273 0.111094506 RPVHLDQAAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPVHLDQAAFR 11 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 78.908 0.018563 71188000 77519 68204 55694 59565 68278 76900 75826 79437 109210 FALSE TRUE 67274.66774 67755.96343 82627.80469 73090.14364 66919.40138 79858.39276 68472.40619 62450.01573 96299.31821 0.698599627 0.70359754 0.858031045 0.758989212 0.694910438 0.82927267 0.711037289 0.648499043 1 16.55523796 1.226339495 24.99978248 1.0000006 0.737278628 0.625859567 0.063693181 408.3175513 835210.675 0.27182477 0.016220248 16.8398995 -1.226339495 -0.262721972 RPWILTSLHNGVIQLWDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPWILTSLHNGVIQLWDYR 19 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1;A0A3B3ITX2;A0A3B3IS23;A0A3B3IU84 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 181.88 1.98E-14 87312000 49439 56183 20686 36282 51799 45863 56133 57343 56570 FALSE TRUE 42905.51089 55813.93017 30689.81879 44520.38264 50768.30124 47627.37929 50689.2303 45080.64569 49882.35904 0.860133957 1.118911199 0.615243933 0.892507562 1.017760632 0.954794043 1.016175483 0.903739249 1 15.60624207 3.390617763 7.312374731 0.970147966 0.868080907 0.157043813 0.123319701 0.461994358 33.1455931 0.034691229 0.044860074 2458.203107 -3.390617763 -0.102067059 RPWRPEEAVEDPDEEDEDNT(ph)SEAENGFSLEEVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPWRPEEAVEDPDEEDEDNTSEAENGFSLEEVLR 34 2 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 1 RPWRPEEAVEDPDEEDEDNT(0.485)S(0.485)EAENGFS(0.031)LEEVLR 87.25 0.026757 39452000 10127 8704.9 8101.9 11869 9967.4 11252 6513.1 10698 11567 TRUE FALSE 8788.691291 8647.716939 12020.00594 14564.03786 9769.068241 11684.87172 5881.460564 8410.315952 10199.56244 0.861673365 0.847851758 1.17848251 1.427908104 0.957792876 1.145624804 0.576638518 0.824576153 1 13.31621964 2.259320125 24.99919885 0.796116881 1.075910745 0.297886473 0.194848298 292.4541613 352180.9677 0.075981044 0.058788854 181.6854402 -2.259320125 0.279793864 RPWRPEEAVEDPDEEDEDNTS(ph)EAENGFSLEEVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPWRPEEAVEDPDEEDEDNTSEAENGFSLEEVLR 34 2 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 1 RPWRPEEAVEDPDEEDEDNT(0.196)S(0.759)EAENGFS(0.045)LEEVLR;RPWRPEEAVEDPDEEDEDNT(0.031)S(0.969)EAENGFSLEEVLR 264.36 3.71E-60 240900000 71571 50484 40485.3 60333.3 52179.1 60885 32802 57807 67769 TRUE FALSE 62112.71101 50152.36728 60064.1265 74032.8979 51140.838 63227.28535 29620.86709 45445.4229 59757.42602 1.039414097 0.839265856 1.005132424 1.238890341 0.855807243 1.058065743 0.495685123 0.760498334 1 15.86683039 2.271547144 24.99998276 0.743136163 1.002219318 0.35293408 0.161942028 195.9888654 148536.2838 0.059688633 0.04623153 186.8732521 -2.271547144 0.259083155 RPYDLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RPYDLDR 7 1 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 ;;; 105.14 0.012819 1938900000 1144595 1329131 856372 939315 1086683 1362970 1081857 1197481 1943610 FALSE TRUE 993333.8707 1320399.851 1270516.364 1152600.827 1065060.134 1415404.338 976938.6747 941409.007 1713838.64 0.579595913 0.77043417 0.741327879 0.672525873 0.621447148 0.825867911 0.570029553 0.549298507 1 20.70879985 1.225935983 24.99951705 1.000000782 0.665693003 0.570651171 0.090960099 484.928214 960203.8942 0.406456418 0.023170654 16.82426047 -1.225935983 -0.334307779 RPYGVGLLIAGYDDMGPHIFQTCPSANYFDCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RPYGVGLLIAGYDDMGPHIFQTCPSANYFDCR 32 1 P25786;P25786-2;F5GX11 P25786 PSMA1 Proteasome subunit alpha type-1 0 ; 220.82 4.13E-36 939020000 305190 258780 156830 202132 226610 228620 224730 273960 206260 FALSE TRUE 264858.3682 257080.0571 232673.5126 248029.16 222100.9044 237415.1593 202935.7192 215375.786 181876.1778 1.456256512 1.413489443 1.279296252 1.363725382 1.221165449 1.305366993 1.115790543 1.184189093 1 17.47259706 -0.889606549 0.138907921 5.26E-15 1.644438638 0.818439922 0.058719361 47.05798972 0.78383183 14.86956065 1.344825993 0.128941718 0.889606549 1.644438638 RPYPDPEDEIPDEMIQCVVCEDWFHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RPYPDPEDEIPDEMIQCVVCEDWFHGR 27 1 E9PCJ7;Q8N806;H0YJA0;H0YJM2 E9PCJ7 UBR7 Putative E3 ubiquitin-protein ligase UBR7 0 ;;; 246.37 1.11E-45 414366000 139032 160118 100623 115836 140252 150355 135994 161487 139006 FALSE TRUE 120658.5689 159066.1743 149284.6194 142138.3342 137461.2596 156139.2541 122805.3228 126954.2617 122572.869 0.984382351 1.29772743 1.217925472 1.159623132 1.121465628 1.273848408 1.001896454 1.035745208 1 16.90328015 2.220271472 24.99908218 1.016936284 1.180075408 0.442080985 0.086335272 211.0266331 288446.1375 0.033060495 0.022336198 166.0624617 -2.220271472 0.163139123 RPYTVILIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RPYTVILIER 10 1 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 110.98 0.0029094 1012900000 259820 250680 211290 265110 237830 292180 335660 314990 244980 FALSE TRUE 225484.1287 249033.2666 313470.5507 325307.2775 233097.6483 303420.3537 303107.7449 247631.8398 216018.7435 1.043817426 1.152831752 1.451126628 1.505921534 1.079062143 1.404601975 1.403154837 1.146344228 1 17.72079697 1.486446622 3.844689628 1.017265856 1.29643217 0.272008292 0.157655536 0.272383436 7.895996983 0.159414161 0.041725162 30.65113932 -1.486446622 0.279166314 RQAMPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RQAMPFK 7 1 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ; 89.55 0.028526 978870000 1346340 1811790 1075800 1162780 1845900 1654780 2185000 1899500 1577410 FALSE TRUE 1168417.758 1799888.232 1596060.478 1426806.971 1809170.201 1718440.457 1973099.036 1493306.707 1390930.387 0.840026049 1.294017479 1.147476893 1.025793228 1.300690688 1.235461152 1.418546216 1.073602763 1 20.40761879 4.749801548 24.39312832 1.187750419 0.840025762 0.407221413 0.131539271 1274.467148 2765554.93 0.032399811 0.473280615 56208.44204 -4.749801548 -0.347724657 RQAT(ph)VSWDSGGSDEAPPKPSRPGYPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQATVSWDSGGSDEAPPKPSRPGYPSPR 28 3 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-6;B4DWJ1;E5RJQ2;E5RG80;E5RHK7 E7ESA6 PTK2 Focal adhesion kinase 1 2 RQAT(0.494)VS(0.494)WDS(0.011)GGS(0.002)DEAPPKPS(0.09)RPGY(0.001)PS(0.909)PR 68.811 0.023894 71506000 30383 29921 16504 20610 33458 36225 39193 45258 12933 TRUE FALSE 26367.80957 29724.44698 24485.3896 25289.8155 32792.25126 37618.59919 35392.06889 35579.9289 11404.07547 2.312139167 2.606475821 2.147073619 2.217612078 2.875485289 3.298697845 3.103457968 3.119931027 1 13.47726187 3.236105115 24.98811967 2.797321475 2.328817935 0.053733102 0.650505685 151.3409702 1540106.284 0.192522582 0.228647957 1722.285379 -3.236105115 -0.468503541 RQATVSWDSGGSDEAPPKPSRPGYPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RQATVSWDSGGSDEAPPKPSRPGYPSPR 28 3 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-6;B4DWJ1;E5RJQ2;E5RG80;E5RHK7 E7ESA6 PTK2 Focal adhesion kinase 1 1 RQATVSWDSGGSDEAPPKPS(0.002)RPGYPS(0.998)PR;RQATVSWDSGGSDEAPPKPS(0.213)RPGYPS(0.787)PR;RQATVSWDSGGSDEAPPKPS(0.017)RPGYPS(0.983)PR 223.28 1.10E-33 1928230000 1272990 1108370 536810 579770 1053790 1009350 1313490 1308760 313270 TRUE FALSE 1104761.146 1101089.044 796413.1115 711415.6397 1032821.641 1048180.348 1186107.942 1028891.859 276235.5775 3.999344169 3.9860508 2.883093911 2.575394691 3.738916073 3.794516105 4.293827583 3.724689876 1 18.07553962 4.262716019 23.2957899 3.281878986 3.992699903 0.115532396 0.916333949 276.0732876 266237.8886 0.230541969 0.608984362 18311.16683 -4.262716019 0.710820916 RQAVDVSPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RQAVDVSPLR 10 1 M0R0F0;M0R0R2;P46782;M0QZN2 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;;;; 214.67 1.37E-08 2742690000 1613708 1608986 1004028 1103251 1664910 1787954 1520638 1659449 1311551 FALSE TRUE 1400452.399 1598416.465 1489579.299 1353761.002 1631781.548 1856737.747 1373166.761 1304588.745 1156500.935 1.210939271 1.382114287 1.28800527 1.170566284 1.410964314 1.605478812 1.187346002 1.128048154 1 20.141335 1.785217104 2.620615755 1.044326338 1.339578017 0.458764651 0.124639885 0.238584819 3.168635058 0.099440319 0.035653732 60.98416816 -1.785217104 0.295251679 RQCEEVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQCEEVAR 8 1 P51570;P51570-2;K7EII7 P51570 GALK1 Galactokinase 0 152.11 0.00074131 129220000 86007 102210 58363 53385 77971 96360 80707 100400 78099 FALSE TRUE 74640.95704 101538.5758 86587.54201 65506.88019 76419.52965 100067.0316 72880.04756 78930.24131 68866.22519 1.08385434 1.47443214 1.25732958 0.951219266 1.109680826 1.453063984 1.058284338 1.146138635 1 16.07150898 1.443747274 1.423110507 0.974451038 1.212832842 0.131039583 0.164803326 1.779688905 4.506025687 0.570731023 0.050443173 27.7809616 -1.443747274 0.238381804 RQDEDYDEQVEES(ph)LQDEDDNDVYILTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQDEDYDEQVEESLQDEDDNDVYILTK 27 1 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 1 RQDEDYDEQVEES(1)LQDEDDNDVYILTK 169.22 3.94E-12 100950000 241860 185820 148440 181000 175530 156820 206040 228460 273470 TRUE FALSE 209897.5882 184599.3362 220226.0805 222098.8164 172037.2964 162852.9669 186058.2725 179605.6069 241140.6881 0.870436216 0.76552546 0.913268027 0.921034182 0.713431225 0.675344207 0.771575606 0.744816681 1 17.87951557 3.238407137 24.99998344 0.770512626 0.863541792 0.165007141 0.094911662 7.231653621 1177990.863 0.028235976 0.034097257 1731.438766 -3.238407137 0.093029166 RQDEDYDEQVEESLQDEDDNDVYILTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RQDEDYDEQVEESLQDEDDNDVYILTK 27 1 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ;; 278.24 9.07E-61 553200000 213865 193820 130595 151883 177785 174029 195299 229066 217064 FALSE TRUE 185602.1984 192546.7837 193751.1788 186370.3565 174247.4263 180724.0082 176358.933 180082.0185 191402.9412 0.969693554 1.005976097 1.012268556 0.973706858 0.910369638 0.944207059 0.921401374 0.940852932 1 17.54625347 3.458569348 8.084201325 0.941421377 0.996375566 0.473420694 0.025521215 0.140126919 46.70457154 0.007232667 0.009503032 2874.546561 -3.458569348 0.054954189 RQDLEDSLQAQQYFADANEAESWMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RQDLEDSLQAQQYFADANEAESWMR 25 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 262.18 6.36E-45 1128620000 538330 463207 291725 350847 492257 521772 435789 546910 349056 FALSE TRUE 467188.3265 460164.1627 432804.1858 430512.1737 482462.0488 541844.9065 393526.2499 429957.5526 307790.9973 1.517875216 1.495054003 1.406162589 1.398715939 1.567498897 1.760431303 1.278550228 1.396913998 1 18.23159151 0.796102878 1.224403897 0.124902063 1.502134829 0.615309384 0.122357091 2.757953474 1.616950733 6.349309667 0.037599121 6.25320804 -0.796102878 1.377232766 RQDLLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RQDLLSR 7 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 122.18 0.0070006 1393920000 1348900 1663060 1074020 1048360 1359520 2104900 1252200 1290250 1269040 FALSE TRUE 1170639.447 1652135.249 1593419.664 1286406.161 1332468.212 2185876.865 1130761.837 1014340.078 1119015.537 1.046133328 1.476418508 1.423947758 1.1495874 1.190750412 1.953392775 1.010496994 0.906457547 1 20.09379864 2.031083765 24.99999454 0.950125338 1.371886949 0.372932667 0.245972789 187.6560419 150926.9233 0.097351518 0.06563374 107.4196578 -2.031083765 0.421761611 RQDS(ph)AGPVLDGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RQDSAGPVLDGAR 13 1 Q0VF96 Q0VF96 CGNL1 Cingulin-like protein 1 1 RQDS(1)AGPVLDGAR;RQDS(1)AGPVLDGAR;RQDS(1)AGPVLDGAR 152.89 2.78E-05 1105160000 667880 624150 417118 485760 697070 696550 801320 801120 649020 TRUE FALSE 579617.9658 620049.9176 618837.66 596059.2324 683199.6708 723346.7292 723608.1097 629806.7223 572293.595 1.012798275 1.083447243 1.081328999 1.041527002 1.193792272 1.26394343 1.264400154 1.100495843 1 19.12639593 3.240964049 24.99948516 1.168983924 1.058720043 0.324001494 0.078535357 83.81760827 871825.235 0.024979962 0.030742926 1741.66269 -3.240964049 -0.11026388 RQEAIAQNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RQEAIAQNR 9 1 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;; 204.52 6.84E-05 265353000 260986 243149 146325 174962 218423 238238 213344 245056 235192 FALSE TRUE 226496.0388 241551.7382 217088.2594 214689.7962 214076.8096 247403.17 192653.9317 192652.6814 207387.8697 1.092137352 1.16473417 1.046774142 1.035209034 1.032253284 1.192949088 0.928954678 0.928948649 1 17.66197199 2.214529597 24.99898103 0.94671317 1.089597373 0.587730625 0.055661966 158.028663 164392.7796 0.022862144 0.015422251 163.8813743 -2.214529597 0.142884203 RQEEEEAMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQEEEEAMR 9 1 A0A024R7W5;A0A087X0Q1;A0A087WY31;Q7Z739 A0A024R7W5 YTHDF3 YTH domain-containing family protein 3 0 98.04 0.0085863 0 79979 64892 44778 49324 69029 79529 71726 92258 62437 FALSE TRUE 69409.57251 64465.72018 66432.79057 60523.76807 67655.45795 82588.53209 64770.02356 72529.34465 55055.76899 1.260713887 1.170916715 1.206645403 1.099317459 1.228853201 1.500088612 1.1764439 1.317379559 1 15.74860612 3.004387828 24.99778854 1.264932929 1.182407066 0.046159587 0.129023674 328.0997641 1869184.881 0.037801765 0.042702389 1010.154557 -3.004387828 -0.082525864 RQEEGYYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQEEGYYSR 9 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;H0Y8L4;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 0 81.017 0.036037 152790000 48445 43544 28884 31997 48513 61204 47184 44377 44376 FALSE TRUE 42042.87051 43257.9566 42852.39901 39262.40789 47547.68621 63558.55748 42608.10294 34887.32389 39129.91983 1.074443052 1.105495661 1.095131275 1.003385851 1.215123527 1.624295622 1.088888071 0.891576677 1 15.25598453 1.994413021 24.98622314 0.953700335 1.186914347 0.253003477 0.169799484 338.9998664 1516083.732 0.076212561 0.049610088 98.72178985 -1.994413021 0.233214013 RQEELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQEELER 7 1 A0A087WXB0;O15126-2;O15126;A0A087WZA6 A0A087WXB0 SCAMP1 Secretory carrier-associated membrane protein 1 0 124.08 0.0067043 235030000 235080 228360 141310 168690 184870 248730 183680 221360 235150 FALSE TRUE 204013.5824 226859.8881 209647.9887 206993.6428 181191.4487 258298.804 165866.7419 174023.8866 207350.8349 0.983905285 1.09408717 1.011078585 0.998277354 0.873839977 1.245709014 0.799932838 0.839272659 1 17.66171433 2.176955759 24.99999849 0.867980247 1.027188754 0.317025658 0.106246999 75.45176897 30618.34153 0.04118731 0.027768487 150.298885 -2.176955759 0.159208507 RQEELQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RQEELQR 7 1 Q9NYJ1;Q9NYJ1-2 Q9NYJ1 COA4 "Cytochrome c oxidase assembly factor 4 homolog, mitochondrial" 0 ; 155.88 0.0025357 155078000 206393 204301 154954 140608 151520 182619 140542 178632 173217 FALSE TRUE 179117.6421 202958.9333 229890.2727 172535.1955 148505.0484 189644.4711 126912.2585 140432.9369 152739.4836 1.172700325 1.328791538 1.505113591 1.129604418 0.972276748 1.241620481 0.830906688 0.919427862 1 17.22071353 3.495087787 4.562364341 0.986991225 1.335487795 0.59317214 0.129246602 0.136619019 7.17026197 0.038042472 0.054103119 3126.711326 -3.495087787 0.34849657 RQEQIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RQEQIAK 7 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ;;; 143.89 0.0038344 4155330000 2453440 2502030 1562170 1943130 1912860 2040690 2910830 2894610 2774000 FALSE TRUE 2129211.688 2485594 2317640.637 2384347.365 1874797.828 2119196.665 2628538.155 2275620.177 2446060.88 0.870465533 1.016161953 0.947499163 0.974770246 0.766455914 0.866371186 1.074600463 0.930320335 1 21.22202888 2.258239775 24.99943633 0.989822012 0.910457246 0.25188642 0.075859891 401.241081 509715.9738 0.029362683 0.022712499 181.2340415 -2.258239775 -0.079364767 RQEQIQAMPLADSQAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RQEQIQAMPLADSQAVR 17 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 205.62 1.24E-11 1835800000 860010 793330 503803 599884 820850 889910 767355 855070 601336 FALSE TRUE 746357.4995 788118.563 747443.8159 736096.8309 804516.691 924145.4135 692937.0302 672219.9347 530246.7431 1.4075664 1.486324194 1.4096151 1.388215657 1.51724966 1.742859198 1.306819965 1.267749295 1 19.01630433 1.475216731 1.701070362 0.956866332 1.480509407 0.659060873 0.110891673 0.365001683 1.535522753 0.286133021 0.032767126 29.86872824 -1.475216731 0.523643075 RQEQPSIES(ph)TSPISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQEQPSIESTSPISR 15 1 Q5T5P2;Q5T5P2-3 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 RQEQPS(0.001)IES(0.364)T(0.364)S(0.271)PISR 69.763 0.029824 492270000 98767 92168 60721 90630 103410 105690 99602 113380 72723 TRUE FALSE 85714.69071 91562.54234 90085.8787 111208.9267 101352.3433 109755.9627 89942.61337 89134.56932 64125.76979 1.336665291 1.427858763 1.404831147 1.73423145 1.580524392 1.711573414 1.402597016 1.389996091 1 15.96861662 1.073634533 1.528944305 0.598021895 1.528130548 0.605691509 0.130639705 1.255605446 1.889305507 2.015821541 0.039217249 11.84771321 -1.073634533 0.930108653 RQEQPSIESTS(ph)PISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RQEQPSIESTSPISR 15 1 Q5T5P2;Q5T5P2-3 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 RQEQPSIES(0.011)T(0.04)S(0.949)PISR;RQEQPSIES(0.186)T(0.046)S(0.768)PISR 131.98 3.08E-05 1154040000 320910 356960 201399 266140 348980 364140 347290 383550 292320 TRUE FALSE 278500.9304 354615.1063 298796.23 326571.1547 342035.9808 378148.7014 313609.8693 301530.8173 257762.2626 1.080456571 1.375744854 1.159193076 1.266947114 1.326943585 1.467044468 1.216663239 1.169802027 1 17.97568154 1.388379885 1.932296586 0.962119193 1.280476189 0.394791262 0.107629934 0.581150553 2.845058647 0.30795289 0.029178013 24.45568798 -1.388379885 0.318356997 RQEQTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RQEQTLR 7 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;; 161.02 0.002124 1760335000 1515252 1574947 980734 1181075 1275411 1715360 1327206 1509408 1719077 FALSE TRUE 1315007.609 1564601.069 1455020.243 1449256.13 1250032.816 1781351.009 1198493.766 1186632.845 1515849.675 0.867505288 1.032161101 0.959871065 0.956068503 0.824641676 1.175150174 0.790641569 0.782816967 1 20.53169526 RQEVSSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RQEVSSPR 8 1 E7EV32;E7EMT6;E7ENY2;E7EVA2;E7EW82;H7C3L4;E7EQA9;Q92844 E7EV32 TANK TRAF family member-associated NF-kappa-B activator 0 ; 115.71 0.0038652 48087000 43972 46466 28796 33476 44090 55557 44806 45283 47557 FALSE TRUE 38160.98879 46160.76179 42721.84192 41077.23745 43212.69526 57694.31374 40460.72102 35599.58284 41934.86564 0.910006225 1.100772855 1.018766634 0.979548565 1.030471771 1.375807764 0.964846802 0.848925645 1 15.35586261 2.012080831 24.99986625 0.911636034 1.071513977 0.196248124 0.126579229 303.762233 628598.0649 0.05168575 0.034819734 102.820765 -2.012080831 0.159877943 RQEYLDQQLQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQEYLDQQLQK 11 1 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 0 171.49 2.32E-05 276200000 460200 445970 261030 322500 414850 378980 454080 550100 467540 FALSE TRUE 399383.404 443040.3937 387264.9811 395728.5541 406595.2966 393559.6058 410043.3915 432465.3959 412267.9538 0.968747147 1.074641843 0.939352616 0.959881918 0.986240364 0.954620902 0.994604086 1.048991055 1 18.6532228 1.946680502 7.754899649 1.026401265 0.981665289 0.181237498 0.038059793 0.471358833 61.74318271 0.017909282 0.010013421 88.4464695 -1.946680502 -0.044735975 RQGLEQFINK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQGLEQFINK 10 1 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 0 127.42 0.00057157 500410000 685200 705170 466830 596660 669110 611470 739030 793840 677010 FALSE TRUE 594649.0839 700537.6918 692590.5495 732140.7724 655796.0201 634993.6466 667358.9843 624083.4937 596974.6491 0.996104416 1.1734798 1.160167439 1.226418531 1.098532444 1.063686117 1.117901716 1.045410378 1 19.18731014 3.00481784 24.98564369 1.06297731 1.145444304 0.262518848 0.064251173 180.6000639 936591.3292 0.019336576 0.021846837 1011.155248 -3.00481784 0.082466994 RQGSVVS(ph)SR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQGSVVSSR 9 1 Q9BZ67-2;Q9BZ67-3;Q9BZ67 Q9BZ67-2 FRMD8 FERM domain-containing protein 8 1 RQGS(0.048)VVS(0.879)S(0.073)R 100.88 0.0019925 0 250480 264550 135730 143510 189850 205300 195010 204340 174440 TRUE FALSE 217378.4334 262812.1536 201369.482 176096.1389 186072.3564 213198.0238 176097.9602 160643.4812 153817.9019 1.413219337 1.70859276 1.309142041 1.144835138 1.209692462 1.386041684 1.144846978 1.044374414 1 17.23086389 7.999999954 0.089947416 0.409475 3.641836748 0.594311818 0.131926642 248.3939039 2.091845342 13.33611414 102.5933142 99999989.35 -7.999999954 3.232361748 RQGYGEGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQGYGEGFR 9 1 Q9Y6B6;Q9H029;Q9NR31;Q9NR31-2;H0Y5E8 Q9Y6B6;Q9NR31 SAR1B;DKFZp434B2017;SAR1A GTP-binding protein SAR1b;GTP-binding protein SAR1a 0 68.49 0.092873 121460000 407330 409720 259730 264420 304260 345190 413340 442830 375500 FALSE TRUE 353500.3085 407028.5223 385336.2967 324460.6024 298205.8213 358469.6827 373254.3504 348134.2506 331108.8178 1.067625776 1.229289286 1.1637754 0.979921358 0.900627846 1.082634057 1.127286047 1.051419449 1 18.33694591 3.752221353 24.35901085 1.030350245 1.161136091 0.418646217 0.071695479 588.5008651 1049375.794 0.02015972 0.034657592 5652.249875 -3.752221353 0.130785846 RQIQAAYSILSEVQQAVSQGSSDSQILDLSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQIQAAYSILSEVQQAVSQGSSDSQILDLSNR 32 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 178.28 3.19E-19 128660000 65463 51792 30096 32552 52260 50343 50726 53786 28500 FALSE TRUE 56811.89869 51451.77494 44650.52627 39943.42913 51220.12824 52279.72779 45806.60033 42284.28246 25130.76247 2.260651612 2.047362272 1.776727878 1.589423687 2.038144617 2.080308063 1.822730225 1.682570615 1 14.61716682 1.040097512 1.514918287 0.176871452 1.94427027 0.726984359 0.183234301 1.090460663 1.502327341 3.382839843 0.055511341 10.96724417 -1.040097512 1.767398818 RQLEEAEEEAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RQLEEAEEEAQR 12 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 265.13 2.16E-21 1235570000 774700 756660 421460 491209 697507 790100 693430 710330 537550 FALSE TRUE 672321.4322 751689.4506 625279.4657 602745.5111 683627.9753 820495.6583 626181.2653 558431.4573 474001.4514 1.418395303 1.585837867 1.319150952 1.271611109 1.442248696 1.730998198 1.321053477 1.17812183 1 18.85453195 1.659188712 2.346073541 1.024686929 1.452856792 0.57581752 0.132484979 0.205719506 2.408836786 0.144031625 0.038254076 45.62351182 -1.659188712 0.428169863 RQLHLEGASLELS(ph)DDDTESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RQLHLEGASLELSDDDTESK 20 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 1 RQLHLEGASLELS(1)DDDTESK;RQLHLEGAS(0.053)LELS(0.947)DDDTESK 207.83 3.85E-22 427560000 345941 263011 180972 221860 261689 257387 315724 350101 339730 TRUE FALSE 300224.0203 261283.2634 268490.6645 272236.7039 256481.9009 267288.8444 285105.1351 275234.6256 299567.5064 1.002191539 0.872201617 0.896260972 0.908765798 0.856173969 0.892249122 0.951722496 0.918773297 1 18.19252162 -1.053718499 0.963821805 9.999816864 0.903973788 0.312057291 0.040955748 195.4719211 2.497634357 3804.189969 0.01306579 0.088365248 1.053718499 -9.095843076 RQLS(ph)PQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RQLSPQSK 8 1 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RQLS(0.999)PQS(0.001)K;RQLS(1)PQSK 92.838 0.0070403 1484640000 1127530 842020 608280 592960 742940 771940 968110 1064990 841720 TRUE FALSE 978524.0537 836488.7152 902446.2426 727600.6308 728156.9475 801637.0313 874222.8412 837250.1763 742212.8205 1.318387431 1.12702003 1.215886088 0.980312669 0.981062207 1.080063574 1.177860065 1.128045964 1 19.5014734 5.011838292 1.132793586 1.077443358 1.550770446 0.501225902 0.076738494 2.675294047 1.912096748 0.024572049 1.739341775 102763.3591 -5.011838292 0.473327088 RQMPDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RQMPDNR 7 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1;A0A5F9ZGZ7 E7EPK1 7-Sep Septin-7 0 ; 95.531 0.021483 61041000 190782 190513 102792 123539 166933 211770 187730 195214 113734 FALSE TRUE 165569.6753 189261.5076 152502.555 151590.4181 163611.3599 219916.9289 169523.9735 153469.0053 100288.4961 1.650933874 1.887170662 1.520638567 1.511543438 1.631407053 2.192843023 1.690363104 1.530275268 1 16.6137966 1.251028162 2.25103484 0.80851414 1.728320636 0.574426313 0.196854256 0.476561997 2.541327834 0.878150935 0.054803791 17.8249435 -1.251028162 0.919806496 RQPEAVHLLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RQPEAVHLLDK 11 1 Q92621 Q92621 NUP205 Nuclear pore complex protein Nup205 0 ; 76.533 0.022779 142378000 408420 346760 233070 257700 334660 302810 388400 468720 407850 FALSE TRUE 354446.2622 344482.1107 345783.4316 316214.7237 328000.9208 314459.2966 350733.0278 368487.8756 359634.4376 0.985573752 0.957867419 0.961485874 0.879267085 0.912039801 0.874385942 0.975248728 1.024617881 1 18.45617165 2.005773276 23.47289937 1.00982716 0.928006416 0.499654688 0.035193908 56.37878234 229222.0444 0.015398174 0.010339625 101.3382209 -2.005773276 -0.081820744 RQPMPS(ph)PSEGSLSSGGMDQGSDAPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RQPMPSPSEGSLSSGGMDQGSDAPAR 26 1 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 1 RQPMPS(0.998)PS(0.002)EGSLSSGGMDQGSDAPAR;RQPMPS(0.996)PS(0.004)EGSLSSGGMDQGSDAPAR 290.1 1.99E-70 827660000 262300 300620 242832 244321 388310 483940 411960 453710 331960 TRUE FALSE 227636.3904 298645.2074 360266.3674 299797.8173 380583.3907 502557.485 372008.1826 356687.6473 292716.067 0.777669613 1.020255603 1.23077073 1.024193241 1.300179367 1.716877007 1.270884057 1.21854482 1 18.15914241 4.893957998 0.885748626 1.285482884 0.376877244 0.410247528 0.191331685 3.024412798 1.558984355 0.070316787 2.840838845 78335.38785 -4.893957998 -0.90860564 RQPPVS(ph)PLTLS(ph)PGPEAHQGFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQPPVSPLTLSPGPEAHQGFSR 22 1 Q6UUV7;Q6UUV7-3 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 2 RQPPVS(0.972)PLT(0.294)LS(0.734)PGPEAHQGFSR 66.294 0.022471 371710000 37249 38529 30052 30001 56730 44280 50391 52121 17739 TRUE FALSE 32326.45027 38275.90046 44585.24772 36813.18559 55601.18399 45983.48025 45504.08858 40975.32976 15641.91563 2.066655456 2.447008498 2.850370043 2.353495982 3.554627535 2.939760151 2.909112263 2.619585141 1 13.93312959 4.617206233 3.138371205 2.658964021 2.044506398 0.057363609 0.652556046 0.822621394 13.07263892 0.162122449 1.037206647 41419.63172 -4.617206233 -0.614457622 RQPQEEVVHEDQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RQPQEEVVHEDQGK 14 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDQ3;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 0 ; 170.11 2.09E-06 480370000 754430 720140 534830 652760 732250 615950 849840 991950 921510 FALSE TRUE 654730.164 715409.3529 793475.5769 800979.1348 717679.6576 639645.9951 767422.6476 779829.2119 812570.1376 0.805752185 0.880427818 0.976501031 0.985735382 0.883221798 0.787188657 0.944438655 0.959706954 1 19.63213282 RQQEEMMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RQQEEMMR 8 1 Q15233;Q15233-2;H7C367 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ; 191.17 0.00029273 660960000 300240 330330 164537 162967 253360 325100 263590 231500 115580 FALSE TRUE 260562.5233 328160.0405 244107.6435 199971.1481 248318.6317 337606.8074 238027.0824 181995.5265 101916.2641 2.556633386 3.219898644 2.395178491 1.96211223 2.436496608 3.3125901 2.335516167 1.785735851 1 16.63702477 1.512352409 2.012255785 0.92944685 2.62782847 0.64895185 0.396214148 0.274272026 1.889118705 0.759967628 0.116335946 32.53511972 -1.512352409 1.698381619 RQQEGFK ddPTM_MDA-MB-175_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 ;;; 143.89 0.0038344 2861810000 2922430 2444740 1489570 1952080 2086270 2162250 2730950 3030050 2625240 FALSE TRUE 2536223.471 2428680.342 2209931.034 2395329.6 2044757.309 2245433.157 2466102.889 2382097.387 2314887.118 1.095614318 1.049157137 0.954660388 1.034750067 0.883307567 0.969996826 1.065323173 1.02903393 1 21.14251041 4.453309784 5.240447701 0.995384832 1.086105913 0.329874518 0.05009604 0.201232491 15.41014909 0.013272699 0.040357343 28399.4405 -4.453309784 0.090721081 RQQEQQVPILEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 RQQEQQVPILEK 12 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;; 112.15 0.0020916 20815750000 5728940 5288180 3725960 3917580 5461030 5304710 6335950 6781420 5641100 FALSE TRUE 4971846.064 5253441.597 5527846.719 4807126.415 5352366.187 5508785.626 5721490.544 5331266.106 4974215.584 0.999523639 1.056134683 1.111300189 0.966408941 1.076022158 1.107468209 1.150229709 1.071780267 1 22.24603761 3.020606874 24.99896706 1.087595586 1.038123016 0.166368283 0.052231541 435.9262857 528834.7601 0.015932072 0.018063386 1048.592806 -3.020606874 -0.049472571 RQQEVETELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RQQEVETELK 10 1 P08621;P08621-2;M0QYR1;P08621-3;M0QX04 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ; 147.83 4.20E-05 447170000 733170 524470 371820 405010 484530 434600 622990 700040 581160 FALSE TRUE 636279.7269 521024.722 551633.3957 496973.7107 474888.801 451319.3432 562572.5257 550341.8937 512455.9269 1.241628194 1.016721038 1.076450416 0.9697882 0.926691987 0.880698846 1.097796896 1.073930195 1 18.96706841 5.67466091 1.340520205 1.004159977 3.156874838 0.54408738 0.067938165 12.83496917 2.92853595 0.021209844 67.63145397 472781.9741 -5.67466091 2.152714861 RQQQLTAMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RQQQLTAMK 9 1 P35579;P35579-2;P35749;P35749-2;P35749-4;P35749-3 P35579;P35749 MYH9;MYH11 Myosin-9;Myosin-11 0 ; 130.53 0.00057479 1755970000 1913350 2605200 1341970 1579470 2539700 2908900 2306800 2377400 2019740 FALSE TRUE 1660495.95 2588086.27 1990951.181 1938112.804 2489164.939 3020807.265 2083086.891 1869011.511 1780968.638 0.932355525 1.453190255 1.11790356 1.088235224 1.397646699 1.696159719 1.169637043 1.049435386 1 20.76423068 1.854478534 4.0125885 1.030254068 1.287255774 0.190097127 0.212667048 0.369767929 9.483899301 0.124784269 0.058286348 71.52840394 -1.854478534 0.257001706 RQQVLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RQQVLDR 7 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3;A0A0D9SFF6 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;;;; 143.89 0.0038344 1118205000 1246900 1377470 740477 880236 1236490 1570550 1288070 1381270 1299650 FALSE TRUE 1082119.006 1368421.309 1098574.154 1080107.037 1211886.268 1630970.075 1163153.17 1085896.16 1146006.858 0.944251772 1.194077766 0.958610454 0.942496138 1.057486053 1.42317654 1.014961788 0.947547698 1 20.12818425 2.010175293 24.99892862 0.973395406 1.089629336 0.101094276 0.143186387 456.4195943 1121339.717 0.060067366 0.040447777 102.3706103 -2.010175293 0.11623393 RQS(ph)FASLALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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;RQS(1)FASLALR;RQS(1)FASLALR 232.13 2.21E-10 5799930000 1205112 1499685 869867 834967 1464839 1728255 1278214 1122593 1361529 TRUE FALSE 1045853.396 1489833.47 1290537.591 1024559.019 1435691.57 1794742.088 1154253.003 882535.223 1200570.593 0.871130279 1.240937834 1.074936866 0.853393399 1.195841026 1.494907587 0.961420353 0.735096485 1 20.1952888 2.006508105 24.99281276 0.848516059 1.125619917 0.239553829 0.192022863 197.1983329 757289.5106 0.079120863 0.053197273 101.5098311 -2.006508105 0.277103858 RQS(ph)FAVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 RQSFAVLR 8 1 Q8TE77;Q8TE77-2;A0A087WWG1;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 RQS(1)FAVLR;RQS(1)FAVLR;RQS(1)FAVLR;RQS(1)FAVLR;RQS(1)FAVLR;RQS(1)FAVLR;RQS(1)FAVLR;RQS(1)FAVLR;RQS(1)FAVLR 173.71 0.00016916 18560174000 3697872 4673410 1807421 2414515 3052050 2125292 3121967 2874045 3290117 TRUE FALSE 3209188.846 4642710.062 2681495.841 2962767.534 2991320.176 2207053.358 2819199.121 2259452.843 2901163.116 1.106173185 1.600292667 0.924283032 1.021234386 1.031076177 0.760747766 0.971747884 0.778809309 1 21.46819998 4.21529266 24.89104995 0.917192682 1.353232786 0.585955058 0.14883987 117.9190926 126144.9159 0.035393198 0.073750171 16416.95697 -4.21529266 0.436040104 RQS(ph)GLYDSQNPPTVNNCAQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RQSGLYDSQNPPTVNNCAQDR 21 1 Q96RU3-5;Q96RU3-2;Q96RU3;H0Y7W6;Q96RU3-3;B7ZL14;Q96RU3-4 Q96RU3-5 FNBP1 Formin-binding protein 1 1 RQS(1)GLYDSQNPPTVNNCAQDR;RQS(1)GLYDSQNPPTVNNCAQDR;RQS(0.999)GLY(0.001)DSQNPPTVNNCAQDR 237.67 4.44E-30 819390000 218519 225282 167339 179670 265571 273420 243396 248631 229234 TRUE FALSE 189641.1605 223802.1077 248264.7001 220466.8196 260286.6567 283938.6443 219791.4934 195463.1955 202134.2177 0.938194249 1.107195557 1.228217088 1.090695193 1.287692206 1.404703506 1.087354214 0.966997066 1 17.62495404 2.000477253 24.99884384 0.994951487 1.182331296 0.292279983 0.123427089 19.79193178 1036676.699 0.053252651 0.035533383 100.1099519 -2.000477253 0.18737981 RQS(ph)ILFSTEV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RQSILFSTEV 10 1 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 RQS(1)ILFSTEV;RQS(1)ILFSTEV;RQS(1)ILFSTEV;RQS(1)ILFSTEV 148.76 2.60E-05 539707000 689280 851860 615517 608640 953350 1155230 924710 1139140 1217910 TRUE FALSE 598189.9016 846264.0756 913183.08 746841.0145 934380.2002 1199672.446 835031.7665 895543.7758 1073930.067 0.557010107 0.788006688 0.850318943 0.695427977 0.87005684 1.117086189 0.777547619 0.833893941 1 20.03446862 3.130020217 5.535641658 0.911422916 0.737228546 0.410590786 0.117400287 0.249747912 11.25117708 0.036464291 0.041688332 1349.02568 -3.130020217 -0.17419437 RQS(ph)LELQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RQSLELQK 8 1 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 RQS(1)LELQK;RQS(1)LELQK 129.87 0.00065676 314490000 840210 674260 468990 755390 786000 654890 720530 895850 775030 TRUE FALSE 729174.1197 669830.7417 695795.1327 926912.8449 770360.1378 680084.0421 650653.1115 704279.449 683406.8363 1.066969309 0.980134681 1.018127264 1.35631193 1.127235048 0.995137897 0.952072875 1.030542002 1 19.38238515 2.73355938 22.92879469 0.996107645 1.111161592 0.244446976 0.100705467 215.3419331 987256.3757 0.036562136 0.033323437 541.4512738 -2.73355938 0.115053946 RQS(ph)LTSPDSQSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RQSLTSPDSQSAR 13 1 Q15751 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 RQS(1)LTSPDSQSAR;RQS(0.994)LT(0.006)SPDSQSAR;RQS(0.999)LT(0.001)SPDSQSAR;RQS(0.996)LT(0.004)SPDSQSAR 125.98 0.00011878 1191590000 620950 483334 378645 396176 600520 612390 566290 538830 731120 TRUE FALSE 538889.8842 480158.9471 561758.9885 486133.816 588570.8269 635949.0396 511371.283 423605.3977 644687.8265 0.835892756 0.744792948 0.871365901 0.754060797 0.912954771 0.986444933 0.793207599 0.65707057 1 19.29824122 6.394332261 14.41915716 0.826927702 0.826133624 0 0.108985088 0 0 0.024934787 0 2479318.16 -6.394332261 -0.000794078 SNTEPQSPPIAS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SNTEPQSPPIASPK 14 0 A0A2R8Y7M0;P82094;P82094-2;F8WF45 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 SNTEPQSPPIAS(1)PK;SNTEPQSPPIAS(1)PK 257.46 2.52E-24 604150000 404250 511710 415360 503020 907830 656620 908040 1034790 878430 TRUE FALSE 350827.3383 508348.5433 616229.4853 617238.3792 889765.9591 681880.5963 819978.4206 813508.2112 774583.0061 0.452924135 0.656286724 0.795562878 0.796865377 1.148703176 0.880319592 1.058606262 1.05025311 1 19.56306032 4.57546882 0.661159401 1.04051795 0.165052995 0.838979216 0.083879224 0.965749138 0.380993744 0.039148895 0.62186224 37624.33392 -4.57546882 -0.875464954 down RQS(ph)LYENQV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RQSLYENQV 9 1 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 RQS(1)LYENQV;RQS(1)LYENQV 116.54 0.0013744 518710000 374780 357870 245070 294740 441820 497600 395200 422170 443420 TRUE FALSE 325251.8734 355519.1284 363586.6717 361665.2218 433028.6464 516742.994 356873.5648 331892.2308 390999.3927 0.831847516 0.909257495 0.92989063 0.924976428 1.107491864 1.321595388 0.912721532 0.848830553 1 18.57680684 3.416011321 8.754983675 1.019256167 0.898006153 0.223838671 0.127141665 0.605831775 79.60745582 0.042094515 0.054404652 2606.22149 -3.416011321 -0.121250014 RQS(ph)MLF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RQSMLF 6 1 Q00537 Q00537 CDK17 Cyclin-dependent kinase 17 1 RQS(1)MLF;RQS(1)MLF 89.698 0.052827 213530000 278830 311280 203639 196089 278710 385380 263770 285130 300880 TRUE FALSE 241981.909 309235.1812 302119.5015 240614.0045 273164.2163 400205.818 238189.626 224157.1684 265310.3092 0.912071264 1.165560366 1.138740151 0.906915397 1.029602721 1.508444279 0.8977775 0.844886763 1 18.01732121 RQS(ph)PEPSPVTLGR ddPTM_MDA-MB-175_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(0.999)PEPS(0.001)PVTLGR;RQS(1)PEPSPVTLGR;RQS(1)PEPSPVTLGR 185.63 5.20E-06 2372610000 1802030 1509980 1101790 1314690 1563530 1503740 1369680 1584960 2058370 TRUE FALSE 1563887.17 1500060.842 1634619.329 1613210.458 1532418.812 1561589.851 1236848.644 1246028.638 1815031.844 0.861630707 0.826465303 0.90060091 0.888805595 0.844293073 0.860364988 0.681447352 0.686505112 1 20.79156343 2.343062053 10.82132074 0.763476058 0.864255447 0.111388248 0.089664433 0.544854474 52.37861959 0.033241754 0.025732917 220.3241242 -2.343062053 0.100779389 RQS(ph)PLPPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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 97.734 0.0056803 15779450000 12878420 10552290 6980385 8701960 9529270 8874050 11600410 12939320 13770420 TRUE FALSE 11176504.17 10482971.31 10356122.53 10677873.02 9339656.171 9215440.446 10475404.02 10172347.11 12142496.63 0.920445317 0.863329151 0.852882471 0.879380356 0.769170991 0.758941157 0.862705944 0.837747575 1 23.53356175 1.237873557 24.89432817 1.00000019 0.840881031 0.512278155 0.048077768 13.99823175 506804.7605 0.071089202 0.012250831 17.29312806 -1.237873557 -0.159119159 RQS(ph)PLPPQKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RQSPLPPQKK 10 2 Q01105;B2REB7 Q01105 SET Protein SET 1 RQS(1)PLPPQKK;RQS(1)PLPPQKK;RQS(1)PLPPQKK;RQS(1)PLPPQKK 61.641 0.07109 2949690000 5207050 4001220 2937640 3508990 3413910 2981840 4945150 5573920 4282080 TRUE FALSE 4518925.15 3974935.722 4358292.53 4305759.811 3345979.87 3096553.314 4465570.114 4381980.584 3775857.381 1.196794448 1.05272401 1.154252423 1.140339631 0.88615102 0.820092764 1.182663873 1.160525979 1 21.84837284 RQS(ph)PS(ph)PSTRPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RQSPSPSTRPIR 12 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RQS(1)PS(0.981)PS(0.016)T(0.003)RPIR;RQS(0.999)PS(0.973)PS(0.015)T(0.013)RPIR;RQS(1)PS(0.964)PS(0.032)T(0.004)RPIR 79.317 0.012528 1827470000 106676 90597 63017.3 62010 79603.6 116012 99322 88823 41308.3 TRUE FALSE 92578.49632 90001.86234 93492.67706 76090.31826 78019.6441 120475.0567 89689.76773 69828.89267 36424.87983 2.54162805 2.470889753 2.566725751 2.088965526 2.141932779 3.307493594 2.462321582 1.917065835 1 15.15263659 1.368111902 2.233454004 0.814693654 2.50989415 0.688772896 0.327504731 0.287164972 1.903662499 0.884425601 0.091495396 23.34059385 -1.368111902 1.695200496 RQS(ph)PSPS(ph)TRPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RQSPSPSTRPIR 12 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RQS(0.991)PS(0.189)PS(0.795)T(0.024)RPIR;RQS(1)PS(0.033)PS(0.866)T(0.101)RPIR;RQS(0.989)PS(0.076)PS(0.66)T(0.275)RPIR 106.82 0.0092508 4881270000 5140820 4398680 2994050 3288060 4559880 4688620 4283440 4809500 4474890 TRUE FALSE 4461447.612 4369784.781 4441982.594 4034664.278 4469147.309 4868994.245 3868032.648 3781025.853 3945873.602 1.130661562 1.107431515 1.125728557 1.022502159 1.132612891 1.233945822 0.980272821 0.95822275 1 21.91191331 2.139154817 10.44193047 0.974255939 1.120245257 0.639825298 0.051497557 0.218039347 21.216614 0.021387827 0.014416791 137.7700503 -2.139154817 0.145989318 RQS(ph)PSPSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RQSPSPSTR 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RQS(0.981)PS(0.019)PSTR;RQS(0.998)PS(0.002)PSTR;RQS(0.996)PS(0.004)PSTR 104.24 0.0020161 523414000 102868 90202 68297 94091 72388 108318 93278 98559 182138 TRUE FALSE 89273.73317 89609.45712 101325.6576 115455.7996 70947.62042 112485.0636 84231.91392 77482.92484 160605.8531 0.555856038 0.557946397 0.630896419 0.718876662 0.441749905 0.700379602 0.524463538 0.482441476 1 17.29316495 1.230876767 24.99868401 1.00000076 0.57493864 0.697580143 0.087610565 158.6774349 516198.7495 0.219503061 0.021053142 17.01675582 -1.230876767 -0.42506212 RQS(ph)PSPSTRPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQSPSPSTRPIR 12 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RQS(0.481)PS(0.156)PS(0.156)T(0.207)RPIR 58.885 0.081078 69882000 38468 42561 33471 37369 30250 39934 41871 39240 40833 TRUE FALSE 33384.35633 42281.41399 49657.68755 45854.2026 29648.08418 41470.28682 37810.35686 30848.83137 36005.76926 0.927194642 1.174295533 1.37915919 1.273523759 0.823425934 1.151767833 1.050119402 0.856774678 1 15.13594047 3.251452484 24.9847482 0.975757344 1.201141026 0.346779946 0.144205096 256.9832442 498036.8837 0.042774537 0.054864592 1784.236764 -3.251452484 0.225383682 RQS(ph)SPSCGPVAETSSIGNGDGISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RQSSPSCGPVAETSSIGNGDGISK 24 1 Q9Y4K4 Q9Y4K4 MAP4K5 Mitogen-activated protein kinase kinase kinase kinase 5 1 RQS(0.967)S(0.033)PSCGPVAETSSIGNGDGISK;RQS(0.71)S(0.29)PSCGPVAETSSIGNGDGISK;RQS(0.963)S(0.037)PSCGPVAETSSIGNGDGISK;RQS(0.988)S(0.012)PSCGPVAETSSIGNGDGISK 263.16 2.28E-44 1897500000 912739 809559 578150 608447 782031 672456 1027005 905580 898026 TRUE FALSE 792118.2286 804240.9536 857745.2738 746604.1909 766470.1131 698325.8175 927406.2132 711928.7642 791862.3893 1.000323085 1.015632217 1.083199916 0.942845879 0.967933474 0.881877744 1.171170933 0.899056167 1 19.59489021 3.726608813 24.84879166 0.976785861 1.031309791 0.096391327 0.08062447 1659.549145 3450334.726 0.021158374 0.031650592 5328.547145 -3.726608813 0.05452393 RQS(ph)SSYDDPWK ddPTM_MDA-MB-175_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(0.903)S(0.072)S(0.025)YDDPWK;RQS(0.592)S(0.051)S(0.354)Y(0.003)DDPWK 99.451 0.0029188 370350000 1645110 1447600 1455080 1712620 1406050 1532120 1521650 1952390 4562000 TRUE FALSE 1427704.545 1438090.62 2158761.555 2101496.547 1378072.356 1591061.648 1374080.617 1534886.592 4022685.557 0.354913285 0.357495161 0.536646856 0.522411339 0.342575212 0.395522251 0.341582905 0.381557686 1 21.93972754 1.237233702 24.9991162 1.00000072 0.404296085 0.87660385 0.070264088 11.81150108 222442.07 0.110974985 0.018319859 17.26766847 -1.237233702 -0.595704635 RQS(ph)VS(ph)PPYKEPSAYQSSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RQSVSPPYKEPSAYQSSTR 19 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 RQS(1)VS(0.996)PPY(0.004)KEPSAYQSSTR;RQS(1)VS(0.976)PPY(0.023)KEPS(0.001)AYQSSTR 84.365 0.0017207 797650000 455600 299230 229601 263720 300290 264620 323690 377090 497370 TRUE FALSE 395391.3057 297264.3384 340636.8116 323601.6567 294314.8165 274800.1026 292298.5936 296452.238 438571.4852 0.901543577 0.677801336 0.776696213 0.737853845 0.671076042 0.626579958 0.666478792 0.675949641 1 18.74245249 1.234522756 24.99681043 1.000000422 0.709549623 0.565275919 0.077837209 88.25445854 546271.8465 0.139946914 0.018772757 17.16021622 -1.234522756 -0.290450799 RQS(ph)VSGLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RQSVSGLHR 9 1 Q8N1G4;J3KRP5 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 RQS(1)VSGLHR;RQS(1)VSGLHR;RQS(1)VSGLHR;RQS(0.999)VS(0.001)GLHR 133.88 0.00016209 1615720000 339745 375446 171790 343141 352530 302455 348859 365274 561600 TRUE FALSE 294846.8374 372979.6705 254868.2186 421056.4086 345515.3427 314090.6396 315026.7079 287162.9977 495208.2878 0.595399642 0.753177359 0.514668726 0.850261232 0.697717206 0.634259659 0.63614991 0.579883263 1 18.91767593 1.23047093 24.99931559 1.000000625 0.658083901 0.568030602 0.093812455 222.1358236 686404.0322 0.238845907 0.021961811 17.00086153 -1.23047093 -0.341916724 RQSPS(ph)PSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQSPSPSTR 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RQS(0.316)PS(0.534)PS(0.126)T(0.024)R 63.624 0.079282 107640000 98133 79309 71079 75223 72467 92834 73853 88057 200630 TRUE FALSE 85164.47541 78788.01396 105453.0421 92303.53186 71025.04848 96405.38405 66690.74743 69226.69581 176911.75 0.481395246 0.445352069 0.596077096 0.521749018 0.401471629 0.544934885 0.376971837 0.391306376 1 17.43267035 1.233602912 24.99999274 1.000000817 0.466868001 0.848619616 0.070350678 60.20318268 303547.8986 0.146546275 0.018145362 17.12390901 -1.233602912 -0.533132816 RQSS(ph)GSATNVASTPDNR ddPTM_MDA-MB-175_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(0.112)S(0.872)GS(0.014)ATNVAS(0.001)T(0.001)PDNR;RQS(0.118)S(0.821)GS(0.018)AT(0.001)NVAS(0.021)T(0.021)PDNR;RQS(0.033)S(0.933)GS(0.031)AT(0.003)NVASTPDNR 240.01 2.80E-20 1294220000 1059930 968650 484651 571000 972300 1010330 1016750 966500 945140 TRUE FALSE 919857.565 962286.8744 719029.8447 700654.2772 952953.1323 1049198.049 918145.7415 759821.4963 833406.6259 1.103732004 1.154642697 0.862759933 0.840711191 1.143443192 1.258926935 1.101677996 0.91170561 1 19.66866104 -1.999873994 0.007638474 0.000111765 1.987703548 0.004975656 0.136607156 533166.032 405.3635011 57588.73367 48287.22802 0.010002902 1.999873994 1.987591783 RQSS(ph)SYDDPWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQSSSYDDPWK 11 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;H0YCF0;H7C1V2;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 RQS(0.23)S(0.601)S(0.167)Y(0.002)DDPWK 92.935 0.0058954 142470000 286610 250760 248510 299000 245670 263800 252900 330570 783220 TRUE FALSE 248733.7623 249112.741 368690.2672 366892.5199 240781.6476 273948.5567 228373.7969 259880.178 690628.6238 0.360155594 0.360704339 0.533847359 0.5312443 0.34864128 0.396665512 0.330675256 0.376295116 1 19.3975506 1.236909474 24.99998669 1.000000737 0.404570113 0.872292024 0.071574582 15.39639741 233043.089 0.116747303 0.018821489 17.25478188 -1.236909474 -0.595430624 RQSS(ph)TPSAPELGQQPDVNISEWK ddPTM_MDA-MB-175_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(0.104)S(0.861)T(0.035)PSAPELGQQPDVNISEWK;RQS(0.048)S(0.466)T(0.466)PS(0.02)APELGQQPDVNISEWK 234.74 2.74E-37 826600000 822900 706250 430980 408110 607510 615690 865470 818390 252340 TRUE FALSE 714151.68 701610.5972 639403.3695 500777.6131 595421.7396 639375.9927 781536.8526 643383.6672 222508.6527 3.209545658 3.153183433 2.873611259 2.250598379 2.675948699 2.873488222 3.512388589 2.891499542 1 17.76350191 4.099905724 3.793763594 2.647002486 3.18160961 0.133157972 0.644467205 0.539860741 14.67617447 0.171405931 0.393711643 12586.52157 -4.099905724 0.534607124 RQSSS(ph)YDDPWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQSSSYDDPWK 11 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;H0YCF0;H7C1V2;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 RQS(0.273)S(0.273)S(0.414)Y(0.039)DDPWK 68.069 0.035677 166130000 208020 191560 189040 235400 208550 202310 201710 274770 610500 TRUE FALSE 180529.6299 190301.6297 280460.3763 288851.1679 204400.263 210092.9966 182148.1952 216012.5738 538327.3855 0.335352863 0.353505385 0.520984783 0.536571565 0.379695086 0.39026994 0.338359519 0.40126618 1 19.03812429 1.238160674 24.99396035 1.000000667 0.408077502 0.877695294 0.069566466 3.376823034 210763.603 0.104177644 0.018252236 17.30456452 -1.238160674 -0.591923165 RQT(ph)IEER ddPTM_MDA-MB-175_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 130.94 0.0020595 936360000 1071010 739430 320008 895900 610280 350382 686460 684850 547048 TRUE FALSE 929473.3149 734572.6356 474764.9392 1099327.788 598136.622 363861.4223 619887.2149 538400.157 482376.6086 1.926862328 1.522819769 0.984220484 2.278982372 1.239978497 0.75430984 1.285068977 1.116140682 1 18.87980042 3.01421147 24.99143882 1.065488917 1.635291079 0.429757621 0.347658391 238.0397333 418599.4477 0.101232662 0.114738624 1033.264408 -3.01421147 0.569802162 RQTIEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RQTIEER 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 160.88 0.0021324 1040900000 2150810 2438580 1188020 1342790 1966980 2579690 1786130 2046970 1843690 FALSE TRUE 1866575.009 2422560.807 1762550.446 1647690.993 1927840.946 2678932.344 1612911.388 1609241.395 1625731.069 1.148145007 1.490136256 1.084158678 1.013507723 1.185830168 1.647832409 0.992114513 0.989857072 1 20.63265719 2.089466291 22.38162675 0.992630729 1.255105462 0.313282051 0.186600411 10.88654447 2717.292388 0.077053365 0.051949395 122.8757811 -2.089466291 0.262474733 RQVDEGVWPPPNNLLSQS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQVDEGVWPPPNNLLSQSPK 20 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;Q9C0H9-4 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 RQVDEGVWPPPNNLLS(0.009)QS(0.991)PK 157.9 9.46E-10 136610000 163150 100840 78737 80752 123000 112340 138540 157900 106950 TRUE FALSE 141589.3141 100177.5754 116814.4766 99087.97582 120552.5406 116661.7925 125104.4121 124134.3138 94306.49284 1.501373976 1.062255338 1.238668442 1.050701525 1.278305841 1.237049422 1.326572629 1.316285974 1 16.52506948 4.757813895 24.19863833 1.206713024 1.50137439 0.409860679 0.11613088 3192.841364 4012848.64 0.028157983 0.987646426 57255.0627 -4.757813895 0.294661366 RQVEEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RQVEEAER 8 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 185.81 0.00033798 1957804000 1274290 1254395 765679 834953 1072687 1374228 1083982 1252238 1053446 FALSE TRUE 1105889.348 1246154.797 1135963.925 1024541.84 1051342.627 1427095.44 978857.5925 984456.6486 928908.814 1.190525196 1.341525431 1.222901439 1.102952006 1.13180391 1.536313811 1.053771455 1.059799018 1 19.82517746 2.047256881 24.9999996 1.040952851 1.248639047 0.414460766 0.121258114 115.0764041 60877.60468 0.049056983 0.033074198 111.4953822 -2.047256881 0.207686196 RQVS(ph)ASELHTSGILGPETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RQVSASELHTSGILGPETLR 20 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 RQVS(0.931)AS(0.065)ELHT(0.004)SGILGPETLR;RQVS(0.848)AS(0.148)ELHT(0.003)SGILGPETLR;RQVS(0.661)AS(0.339)ELHTSGILGPETLR 202.47 7.09E-22 2558470000 479460 576890 245623 224206 590150 446490 619290 573670 119499 TRUE FALSE 416098.1462 573100.3716 364407.1044 275115.3991 578407.1696 463666.7592 559231.3511 450995.1348 105371.9644 3.948850615 5.43883162 3.458292788 2.610897507 5.489194143 4.400285807 5.307211976 4.280029679 1 16.68513154 4.226481363 24.98557363 3.957107411 4.693841451 0.061521476 1.349335773 690.5757778 1428442.926 0.345536832 0.727973678 16845.40135 -4.226481363 0.73673404 RQVSAS(ph)ELHTSGILGPETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQVSASELHTSGILGPETLR 20 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 RQVS(0.196)AS(0.8)ELHT(0.004)S(0.001)GILGPETLR 153.27 3.36E-08 573010000 175560 204210 44063 76951 219330 157080 218300 204480 33883 TRUE FALSE 152359.3012 202868.5311 65372.01418 94423.90067 214965.7621 163122.9692 197129.2996 160753.5433 29877.39034 5.09948491 6.790035166 2.188009509 3.160379792 7.194931005 5.459746229 6.597942369 5.380441245 1 14.86676652 6.050312757 16.55367508 4.910000013 5.522182774 0 2.052709183 0 0 0.455235193 0 1122826.765 -6.050312757 0.612182761 RQWTSLS(ph)LR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RQWTSLSLR 9 1 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 RQWTSLS(1)LR;RQWTSLS(1)LR 156.01 4.41E-05 320080000 372970 215450 120701 376070 205146 124687 183421 263720 252490 TRUE FALSE 323681.0695 214034.6948 179072.4073 461462.4414 201063.996 129483.7896 165632.8597 207325.5303 222640.9198 1.453825603 0.961344819 0.8043104 2.072675776 0.903086441 0.581581273 0.74394617 0.931210356 1 17.76435925 3.025963302 24.99979805 0.816600981 1.288617969 0.330044021 0.348167462 277.7008458 267393.3694 0.104685634 0.118699097 1061.605847 -3.025963302 0.472016989 RQYEEK ddPTM_MDA-MB-175_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 0 128.86 0.026366 158890000 287340 275610 183190 191200 162820 231450 284840 311050 275410 FALSE TRUE 249367.291 273799.4998 271781.2967 234614.8823 159580.2006 240354.0313 257216.2606 244534.3781 242851.3435 1.026831012 1.127436628 1.119126181 0.96608435 0.657110635 0.989716704 1.059151071 1.006930308 1 17.88971394 3.699899031 7.186901761 0.949214504 1.094735959 0.272779007 0.111287875 0.338253364 53.15084334 0.033059904 0.049822399 5010.707269 -3.699899031 0.145521456 RQYHES(ph)EEES(ph)EEEEAA ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RQYHESEEESEEEEAA 16 1 Q8N9N8;E9PNH5 Q8N9N8 EIF1AD Probable RNA-binding protein EIF1AD 2 RQYHES(1)EEES(1)EEEEAA 76.526 0.017687 250290000 312220 297980 167470 203140 276630 279920 258160 280280 264940 TRUE FALSE 270959.3359 296022.5498 248459.0522 249266.0418 271125.6042 290688.7035 233123.6829 220344.3031 233619.095 1.159833857 1.267116242 1.063522021 1.066976318 1.160545563 1.244284863 0.997879402 0.943177625 1 17.83379867 2.123668874 6.541597705 0.968847949 1.156151129 0.628246427 0.065363796 0.137622128 7.349799584 0.02815089 0.018879737 132.9440405 -2.123668874 0.18730318 RRDDGLSAAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRDDGLSAAAR 11 2 F8WBN3;B9A031;C9JQZ0;B8ZZY7;F8WBV6;P84101-4;P84101;P84101-3;P84101-2 F8WBN3 SERF2 Small EDRK-rich factor 2 0 91.961 0.041124 78927000 23975 20611 16344 16484 16157 27246 17571 20779 19843 FALSE TRUE 20806.64301 20475.60498 24248.01307 20226.94414 15835.50731 28294.17125 15866.96712 16335.57255 17497.18315 1.189142437 1.170222933 1.385823813 1.156011455 0.905031809 1.617070074 0.906829802 0.933611566 1 14.09483506 RRDEDMLYS(ph)PELAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RRDEDMLYSPELAQR 15 2 Q9Y2W2 Q9Y2W2 WBP11 WW domain-binding protein 11 1 RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR 222.13 7.53E-13 3288490000 1105849 1020753 660960 712374 965141 1050873 943240 1089736 719092 TRUE FALSE 959708.2528 1014047.606 980602.4668 874129.4047 945936.5824 1091300.764 851764.73 856704.4367 634081.763 1.513540223 1.59923793 1.546492147 1.378575218 1.491821146 1.721072625 1.343304255 1.351094586 1 19.27430936 1.018353858 1.163487831 0.511553977 1.530468435 0.733359921 0.100127574 1.312060786 1.047151398 1.858742934 0.03129251 10.43167044 -1.018353858 1.018914458 GGSFWSSIPAS(ph)PASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GGSFWSSIPASPASR 15 0 O75962-5;O75962;E7EPJ7;O75962-4 O75962-5 TRIO Triple functional domain protein 1 GGSFWSSIPAS(0.995)PAS(0.005)R 113.65 0.0015143 0 88438 139140 131420 143680 195120 227620 176100 204500 212860 TRUE FALSE 76750.69423 138225.9802 194975.1516 176304.74 191237.4937 236376.6887 159021.8491 160769.2664 187695.9333 0.408909734 0.736435669 1.038781971 0.939310388 1.018868605 1.25935967 0.847231191 0.856541021 1 17.51803787 4.578347289 2.440030171 0.982816793 0.36846811 0.728754442 0.116025209 0.220616166 2.036421993 0.032294269 0.243083568 37874.53324 -4.578347289 -0.614348683 down QPSGS(ph)FSTPGSATYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 QPSGSFSTPGSATYVR 16 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 QPSGS(0.985)FS(0.012)T(0.003)PGSATYVR;QPS(0.011)GS(0.987)FS(0.002)T(0.001)PGSATYVR;QPS(0.001)GS(0.714)FS(0.205)T(0.08)PGSATYVR;QPS(0.018)GS(0.981)FS(0.001)TPGSATYVR 185.99 1.65E-09 1017430000 262650 378467 320866 392004 610721 686938 511629 645774 611893 TRUE FALSE 227940.137 375980.8254 476037.8708 481014.4996 598568.847 713364.9494 462011.2983 507680.2555 539555.7066 0.42245895 0.696834119 0.88227752 0.891501088 1.109373582 1.322134009 0.856280997 0.94092278 1 19.04141239 4.579152585 1.114869755 1.023066587 0.233873152 0.714326282 0.126642119 0.773915277 0.979745848 0.042930377 0.674728388 37944.82767 -4.579152585 -0.789193435 down RRDS(ph)DGVDGFEAEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RRDSDGVDGFEAEGK 15 2 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 RRDS(1)DGVDGFEAEGK;RRDS(1)DGVDGFEAEGK;RRDS(1)DGVDGFEAEGK 224.1 9.28E-13 5114810000 4098990 2614710 2302850 2760160 2726150 2820050 3730340 4018190 4802550 TRUE FALSE 3557298.086 2597533.798 3416515.963 3386896.514 2671904.949 2928539.148 3368572.201 3158931.338 4234798.01 0.840016 0.61337844 0.806771882 0.799777582 0.630940352 0.691541637 0.795450502 0.745946166 1 22.01386173 0.937062677 1.985253499 1.360731977 0.732806378 0.52841519 0.076362561 1.748926263 3.121471846 2.75926921 0.0196699 8.650927585 -0.937062677 -0.627925599 RRDS(ph)DGVDGFEAEGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRDSDGVDGFEAEGKK 16 3 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 RRDS(1)DGVDGFEAEGKK 93.776 0.023855 1062000000 234740 136420 138660 126830 127550 126480 186180 219570 140130 TRUE FALSE 203718.5142 135523.848 205716.4398 155628.69 125012.0045 131345.7674 168124.2923 172616.6642 123563.991 1.648688364 1.096790796 1.664857521 1.259498732 1.011718734 1.062977704 1.360625299 1.396981942 1 16.91489885 3.495940637 24.69430574 1.198386315 1.43767979 0.308065196 0.202933696 969.2429761 1271813.133 0.056071389 0.081555413 3132.857469 -3.495940637 0.239293475 RRDS(ph)EEFGVK ddPTM_MDA-MB-175_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 207.31 1.06E-07 8429620000 4713270 4185350 3317520 3845170 4292880 3932030 5593480 5468540 4819700 TRUE FALSE 4090399.428 4157856.16 4921883.768 4718274.618 4207460.087 4083297.738 5051025.171 4299135.277 4249920.557 0.962464915 0.978337384 1.158111947 1.110203016 0.990009114 0.960793898 1.188498727 1.011580151 1 22.01900444 4.443730625 24.86753024 1.058891517 0.966432774 0.202813941 0.074061416 239.4782296 178350.09 0.018482201 0.04889981 27779.89661 -4.443730625 -0.092458743 RRDS(ph)GDNSAPSGQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RRDSGDNSAPSGQER 15 2 Q8IXQ3 Q8IXQ3 C9orf40 Uncharacterized protein C9orf40 1 RRDS(0.999)GDNS(0.001)APSGQER;RRDS(0.946)GDNS(0.054)APSGQER 115.63 0.00040327 1016520000 125227 104755 70210 72082 105667 131793 106599 108733 70145 TRUE FALSE 108677.9347 104066.8575 104163.7908 88449.3198 103564.4334 136863.162 96261.04539 85481.29411 61852.53801 1.757048913 1.682499391 1.684066559 1.430003079 1.674376457 2.212733162 1.556299038 1.382017567 1 15.91654517 1.491262533 2.065685077 0.972214039 1.72192496 0.587450259 0.198292746 0.312295867 2.210806088 0.389390119 0.05712933 30.99292272 -1.491262533 0.749710922 RRDS(ph)GIGEETATGLGSHVEVTPHTAPPGVSAGPDAISEVLSTLSLEVNK ddPTM_MDA-MB-175_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(0.143)GIGEET(0.143)AT(0.143)GLGS(0.143)HVEVT(0.143)PHT(0.143)APPGVS(0.143)AGPDAIS(0.001)EVLSTLSLEVNK;RRDS(0.162)GIGEET(0.162)AT(0.162)GLGS(0.162)HVEVT(0.162)PHT(0.162)APPGVS(0.029)AGPDAISEVLSTLSLEVNK;RRDS(0.159)GIGEET(0.159)AT(0.159)GLGS(0.159)HVEVT(0.159)PHT(0.159)APPGVS(0.038)AGPDAIS(0.01)EVLSTLSLEVNK 99.805 1.05E-06 2802936000 58908 50608 34620 51633.5 50098.7 47899.9 58217 72052 60507 TRUE FALSE 51123.15855 50275.55272 51362.3478 63357.67534 49101.83389 49742.64015 52571.1243 56644.24051 53353.93139 0.958189157 0.942302683 0.962672224 1.187497785 0.920303952 0.93231443 0.985328034 1.061669478 1 15.70330696 RRDS(ph)LDSSTEASGSDVVLGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RRDSLDSSTEASGSDVVLGGR 21 2 Q9Y2I9 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 RRDS(0.612)LDS(0.171)S(0.171)T(0.046)EASGSDVVLGGR;RRDS(0.408)LDS(0.293)S(0.102)T(0.197)EASGSDVVLGGR 134.03 7.03E-06 988780000 343370 264210 156640 218697 328060 255735 294640 348510 174559 TRUE FALSE 297992.7845 262474.3871 232391.6279 268355.4964 321532.2478 265573.2909 266065.8581 273983.8486 153922.8339 1.935988164 1.705233593 1.50979307 1.74344176 2.088918452 1.725366434 1.728566525 1.780007824 1 17.23184774 1.23817681 24.99999974 0.999999134 1.771486371 0.723065163 0.151116243 5.137143163 334178.3207 0.214460749 0.037635339 17.30520745 -1.23817681 0.771487237 RRDS(ph)YYDR ddPTM_MDA-MB-175_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 134.98 0.00067219 2802160000 1661330 1073340 635253 890877 939701 1134887 1207450 1220200 1235430 TRUE FALSE 1441781.031 1066289.159 942463.4756 1093164.239 921002.7886 1178546.837 1090351.685 959269.7256 1089378.873 1.32348907 0.978804698 0.865138382 1.003474793 0.845438453 1.081852115 1.000892997 0.880565751 1 20.05507436 4.733949643 4.779722826 0.950579837 1.343234288 0.712549431 0.07327359 0.089016338 5.837052634 0.017146372 0.116077066 54193.80481 -4.733949643 0.392654451 RRDSGIGEETATGLGSHVEVTPHTAPPGVS(ph)AGPDAISEVLSTLSLEVNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRDSGIGEETATGLGSHVEVTPHTAPPGVSAGPDAISEVLSTLSLEVNK 49 2 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 RRDS(0.139)GIGEET(0.139)AT(0.139)GLGS(0.139)HVEVT(0.139)PHT(0.139)APPGVS(0.16)AGPDAIS(0.003)EVLS(0.001)T(0.001)LSLEVNK 64.687 0.00023697 1576500000 39595 36616 27919 29007 24820 33287 47511 33905 38694 TRUE FALSE 34362.42043 36375.46709 41420.72178 35593.48269 24326.13056 34567.57243 42903.39053 26654.6796 34119.6394 1.00711558 1.066115226 1.213984746 1.043196333 0.712965641 1.013128305 1.257439741 0.78121223 1 15.05831478 3.468141765 24.9612845 0.950123562 1.098745286 0.158850464 0.152175434 344.7411607 958310.8518 0.044117717 0.05704084 2938.608734 -3.468141765 0.148621724 RRDSLDS(ph)STEASGSDVVLGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRDSLDSSTEASGSDVVLGGR 21 2 Q9Y2I9 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 RRDS(0.233)LDS(0.368)S(0.368)T(0.032)EASGSDVVLGGR 129.47 1.30E-05 354440000 161540 173650 82634 85825 146070 114660 147740 156430 103600 TRUE FALSE 140192.0797 172509.2817 122596.0788 105312.878 143163.4928 119071.0444 133412.1975 122978.6618 91352.52602 1.534627293 1.888390932 1.342010825 1.152818456 1.567154178 1.303423666 1.460410602 1.34619881 1 16.479157 8 0.199248267 1.151076066 3.718777814 0.335470611 0.19687138 130.4658468 1.929916407 1.315699801 101.052826 100000000 -8 2.567701748 RREDS(ph)YHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RREDSYHVR 9 2 B1AVT0;P49760-3;P49760;P49760-2 B1AVT0 CLK2 Dual specificity protein kinase CLK2 1 RREDS(1)YHVR;RREDS(1)YHVR;RREDS(1)YHVR;RREDS(1)YHVR 134.99 0.00012179 526062000 251840 232012 144689 140535.6 199249 230121 183844.2 208489 122178.1 TRUE FALSE 218558.7059 230487.8979 214661.0844 172446.3559 195284.3347 238973.9038 166015.0178 163905.2498 107734.3442 2.028681824 2.139409671 1.992503746 1.60066279 1.81264699 2.218177551 1.540966523 1.521383464 1 16.71711871 0.955740957 0.840546817 4.37E-13 1.962659932 0.714089651 0.194495182 2.043414762 0.82089022 4.194731655 0.076433201 9.031106365 -0.955740957 1.962659932 RREEEGLQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RREEEGLQLR 10 2 C9JYI4;P52294;C9J352;C9JWD9;F2Z3G4;C9J4U1 C9JYI4 KPNA1 "Importin subunit alpha-5;Importin subunit alpha-5, N-terminally processed" 0 ; 182.28 1.01E-06 351970000 267940 270280 154659 174689 261160 310140 216100 245670 144093 FALSE TRUE 232531.0501 268504.5129 229452.6097 214354.8074 255963.427 322071.2865 195142.6553 193135.3823 127058.4897 1.830110296 2.113235515 1.805881766 1.687056158 2.014532264 2.53482697 1.535849007 1.520050984 1 16.95513325 1.563185318 1.707849248 0.981715921 1.970730558 0.594391288 0.258539726 0.344269778 1.667741971 0.496822893 0.075889381 36.57508281 -1.563185318 0.989014637 RREEEMMIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RREEEMMIR 9 2 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;; 163.64 3.54E-05 1543066000 351810 331368 176116 198837 286207 371706 283064 291222 218608 FALSE TRUE 305317.4171 329191.2218 261286.2867 243985.9799 280512.0407 386005.7703 255612.4968 228946.4416 192764.4113 1.58388893 1.707738579 1.355469534 1.265721085 1.455206585 2.002474252 1.32603573 1.18770078 1 17.5564792 1.765584492 2.714693587 1.060302143 1.544317038 0.457674286 0.207731204 0.23560197 3.449931218 0.167649673 0.059676648 58.28871646 -1.765584492 0.484014896 RREEGPPPPS(ph)PDGAS(ph)SDAEPEPPSGR ddPTM_MDA-MB-175_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(0.6)S(0.4)DAEPEPPSGR 101.27 6.13E-08 0 96507 94334 54230 61827 100400 90269 90240 115290 68520 TRUE FALSE 83753.35543 93714.31374 80455.80939 75865.76532 98402.23643 93741.70684 81488.53869 90636.13069 60419.64366 1.386194131 1.551057042 1.331616748 1.255647348 1.628646421 1.551510422 1.348709356 1.500110315 1 15.88273005 1.234262981 24.96203498 0.999999329 1.445380728 0.5921189 0.115855315 91.52008885 531505.2212 0.214384376 0.028127568 17.14995483 -1.234262981 0.445381398 RREEGPPPPSPDGAS(ph)SDAEPEPPSGR ddPTM_MDA-MB-175_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 1 RREEGPPPPS(0.145)PDGAS(0.751)S(0.104)DAEPEPPSGR;RREEGPPPPS(0.051)PDGAS(0.583)S(0.366)DAEPEPPSGR 167.86 7.83E-12 1741770000 237660 222360 135745 156518 238190 251420 236560 266730 145061 TRUE FALSE 206252.6288 220899.3025 201391.736 192057.8041 233450.485 261092.2901 213618.4476 209691.8652 127912.0538 1.612456549 1.726962361 1.574454713 1.501483233 1.825085893 2.041185973 1.670041573 1.639344056 1 16.9647927 1.211514853 3.290283998 0.855373688 1.709827284 0.68949945 0.147935151 0.239170958 3.373336156 0.546913722 0.040752964 16.27476975 -1.211514853 0.854453596 RREEGPPPPSPDGASS(ph)DAEPEPPSGR ddPTM_MDA-MB-175_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(0.14)S(0.86)DAEPEPPSGR;RREEGPPPPSPDGAS(0.114)S(0.886)DAEPEPPSGR;RREEGPPPPS(0.001)PDGAS(0.12)S(0.879)DAEPEPPSGR;RREEGPPPPS(0.001)PDGAS(0.151)S(0.848)DAEPEPPSGR 206.93 1.47E-25 2146190000 271951 266908 169987 191136 253531 273185 250694 260920 149418 TRUE FALSE 236011.9863 265154.6638 252193.2818 234536.3501 248486.2291 283694.6037 226381.7345 205124.2885 131753.9743 1.79130829 2.012498411 1.914122767 1.780108353 1.885986594 2.153214773 1.718215604 1.556873632 1 17.00748695 1.246814524 1.452584735 0.619654231 1.915579363 0.859685488 0.117124582 0.41683271 0.788708474 0.800083143 0.034074386 17.65283754 -1.246814524 1.295925132 RREPGGYDSSSTLMSSELETTSFFDS(ph)DEDDSTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RREPGGYDSSSTLMSSELETTSFFDSDEDDSTSR 34 2 Q92997-2;Q92997 Q92997-2 DVL3 Segment polarity protein dishevelled homolog DVL-3 1 RREPGGYDSSSTLMSSELETTSFFDS(1)DEDDSTSR;RREPGGYDSSSTLMSSELETTSFFDS(1)DEDDSTSR 262.66 4.77E-60 337710000 89283 84874 73202 57171 85329 76619 78501 101589 77020 TRUE FALSE 77484.02534 84316.45711 108602.732 70152.54935 83631.11984 79566.58251 70887.9851 79864.98292 67914.78334 1.140900722 1.241503734 1.599102974 1.032949616 1.231412599 1.171564991 1.043778418 1.175958738 1 16.05143803 3.664346388 25 1.119813923 1.318628566 0.367113334 0.134234 147.4381198 49665.84504 0.035798976 0.053098468 4616.856631 -3.664346388 0.198814644 ASTSKSES(ph)SQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 ASTSKSESSQK 11 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 1 AST(0.002)S(0.011)KS(0.296)ES(0.594)S(0.096)QK 73.466 0.036616 0 32079 55203 59592 79085 90904 73726 136590 144110 107060 TRUE FALSE 27839.67887 54840.36786 88410.89052 97042.45799 89095.18825 76562.28693 123343.5228 113293.198 94403.48876 0.294900954 0.580914631 0.936521432 1.027954149 0.943770081 0.811011202 1.306556828 1.200095457 1 16.52655256 4.580954677 0.945499023 1.09281252 1.20E-22 0.78566008 0.13461047 0.794347898 0.677978312 0.050508182 0.847587812 38102.60575 -4.580954677 -1.09281252 down RRES(ph)LSYIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RRESLSYIPK 10 2 A1L390-3;A1L390;A1L390-2;G3V311 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 RRES(0.983)LS(0.017)YIPK;RRES(0.994)LS(0.006)YIPK 134.06 0.00014233 1124270000 1685580 1845030 931690 967040 1231870 1219250 1584040 1721720 1742940 TRUE FALSE 1462826.332 1832909.876 1382258.4 1186621.212 1207358.197 1266155.336 1430420.045 1353543.576 1536891.619 0.951808387 1.192608414 0.899385736 0.772091667 0.785584476 0.823841656 0.930722783 0.880702035 1 20.551584 4.099222718 7.297914651 0.863869958 1.070454482 0.483914793 0.087262813 0.17483831 11.18528506 0.02213834 0.04659753 12566.74255 -4.099222718 0.206584524 RRES(ph)QEEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 162.49 3.33E-05 1057035000 750410 613649 492261 536824 529025 703380 729757 664424 705382 TRUE FALSE 651241.4172 609617.8993 730320.0661 658718.094 518498.4375 730439.4837 658985.2785 522342.0982 621992.5435 1.047024476 0.980104835 1.174162092 1.059045001 0.833608767 1.174354084 1.059474563 0.83978836 1 19.24653776 1.75572101 25 0.913595896 1.04633074 0.207146121 0.103072498 9.124311074 13311.02971 0.053415229 0.02565093 56.97981176 -1.75572101 0.132734844 RRET(ph)PS(ph)PRPMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RRETPSPRPMR 11 3 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RRET(1)PS(1)PRPMR;RRET(1)PS(1)PRPMR;RRET(1)PS(1)PRPMR;RRET(1)PS(1)PRPMR;RRET(1)PS(1)PRPMR;RRET(1)PS(1)PRPMR 108.71 0.0038374 8497100000 5242980 4510050 2493700 3249890 4435170 4616110 4231680 4410950 2763330 TRUE FALSE 4550106.909 4480423.185 3699661.661 3987827.196 4346918.794 4793694.739 3821292.325 3467702.669 2436652.275 1.867359966 1.838761825 1.518337967 1.636600854 1.783971738 1.967328202 1.568255087 1.423142195 1 21.21646895 1.362649731 1.533130301 0.817376052 1.75222019 0.775416119 0.131497559 0.427886021 1.136771486 0.582869572 0.040618361 23.0488749 -1.362649731 0.934844138 RRFS(ph)DSEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RRFSDSEER 9 2 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 RRFS(0.5)DS(0.5)EER;RRFS(0.997)DS(0.003)EER 135.94 0.00016286 1035670000 582080 564850 331330 366360 567370 627460 570860 643840 461520 TRUE FALSE 505156.6532 561139.4632 491562.2962 449547.6375 556080.447 651598.7922 515498.0851 506159.8264 406959.6314 1.241294257 1.378857803 1.207889575 1.104649215 1.366426555 1.601138644 1.266705701 1.2437593 1 18.63452617 1.207240032 2.216095353 0.893454359 1.312374944 0.357182147 0.129936026 0.880419688 4.110743369 0.762529373 0.036809028 16.11536076 -1.207240032 0.418920585 RRGDDWNDREWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RRGDDWNDREWDR 13 3 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;; 172.57 1.01E-05 716990000 190476 185496 66800.4 78090.4 153986 160636 177836 194361 37485.6 FALSE TRUE 165304.114 184277.4646 99105.29687 95822.01886 150921.9799 166815.7709 160589.4921 152798.4127 33054.09507 5.001017684 5.57502676 2.998275907 2.89894546 4.565908688 5.046750501 4.858384165 4.622677231 1 15.0125414 4.25530139 24.99674708 3.904596351 5.288022922 0.209373336 1.229334888 434.0228331 648056.6194 0.311317965 0.818792456 18001.19724 -4.25530139 1.383426571 RRGDS(ph)ES(ph)EEDEQDSEEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RRGDSESEEDEQDSEEVR 18 2 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 2 RRGDS(1)ES(1)EEDEQDSEEVR;RRGDS(1)ES(0.995)EEDEQDS(0.005)EEVR 151.47 2.34E-07 2787200000 1349830 1312270 790250 908420 1314270 1271300 1216420 1431760 1060060 TRUE FALSE 1171446.545 1303649.612 1172417.543 1114690.645 1288118.598 1320207.734 1098451.776 1125589.266 934740.9144 1.253231272 1.394664117 1.25427006 1.19251295 1.378048803 1.412378246 1.175140361 1.20417246 1 19.83420702 1.134550304 1.194188455 0.803897639 1.307348147 0.598416695 0.078244193 1.379038134 1.40405917 0.930048276 0.024674731 13.63170891 -1.134550304 0.503450509 RRGEEGHDPKEPEQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RRGEEGHDPKEPEQLR 16 3 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 155.92 1.28E-07 349350000 334340 288820 110610 131176 249080 217125 318030 365630 45464 FALSE TRUE 290156.1219 286922.7224 164101.366 160961.5157 244123.7953 225477.9392 287187.4995 287442.8698 40089.29771 7.237745195 7.157090265 4.093395877 4.015074468 6.089500421 5.624392347 7.163694949 7.170064986 1 15.29092952 4.292378297 14.19630966 5.352518367 7.198949659 0.18262567 1.811159655 3.305838416 867.4045501 0.456490564 1.207621616 19605.51691 -4.292378297 1.846431293 RRGS(ph)QEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 99.53 0.008238 853420000 698990 593270 391890 490860 746290 539440 717460 812670 700510 TRUE FALSE 606616.7005 589372.7703 581409.3148 602317.2653 731440.2891 560192.6059 647880.8396 638886.8447 617696.5058 0.982062704 0.954146194 0.941254013 0.975102271 1.18414186 0.906905901 1.048865962 1.034305421 1 19.23653864 3.455049359 24.99995485 1.033994078 0.958574161 0.220932811 0.067448692 334.2153462 378551.1153 0.018297302 0.023623545 2851.342311 -3.455049359 -0.075419918 RRHEGLPGLAVQWGAIGDVGILVETMSTNDTIVSGTLPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 381.61 1.87E-163 1328533000 352891 370151 151986 148200 340526 405968 500667 435298 58610.9 FALSE TRUE 306255.5602 367719.4537 225486.938 181851.0751 333750.1988 421585.8517 452112.3914 342212.9102 51681.98617 5.925769943 7.115041061 4.362969666 3.518654923 6.457766498 8.157307466 8.747968584 6.621512359 1 15.65737389 6.383468511 17.14907574 5.972389268 5.786347122 0 2.304058861 0 0 0.527656112 0 2418068.006 -6.383468511 -0.186042146 RRHS(ph)DENDGGQPHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRHSDENDGGQPHK 14 2 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RRHS(1)DENDGGQPHK 83.404 0.004057 273040000 328270 313730 170860 249110 243380 402260 297560 346710 279160 TRUE FALSE 284888.2878 311669.087 253488.4675 305674.2329 238537.2142 417735.2025 268702.677 272568.7646 246158.0228 1.157339032 1.266134182 1.029779426 1.241780501 0.96904099 1.697020466 1.091586104 1.107291818 1 17.90922524 2.033876327 24.99997274 1.072746582 1.224109258 0.132252966 0.194219516 381.8890106 281823.9514 0.076549043 0.051609093 108.1126037 -2.033876327 0.151362676 RRHT(ph)MDKDSR ddPTM_MDA-MB-175_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 169.17 2.50E-06 545940000 176920 241429 171597 233744 342496 372417 383681 434309 145779 TRUE FALSE 153539.5737 239843.037 254581.8832 286819.1478 335680.9997 386744.123 346471.6757 341435.4001 128545.1727 1.194440604 1.865826868 1.980485753 2.231271247 2.611385497 3.008624244 2.69533012 2.656151087 1 16.97191591 4.527104906 1.048182247 2.462237825 0.885298612 0.316234582 0.541121276 1.511749617 1.751279067 0.176474791 2.46884271 33659.28653 -4.527104906 -1.576939213 RRKDS(ph)AQDDQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RRKDSAQDDQAK 12 3 Q13045-3;Q13045;Q13045-2;J3KS54 Q13045-3 FLII Protein flightless-1 homolog 1 RRKDS(1)AQDDQAK;RRKDS(1)AQDDQAK;RRKDS(1)AQDDQAK;RRKDS(1)AQDDQAK 156 0.00034827 370800000 804120 493311 303407 324732 447271 431682 1105750 1066790 181547 TRUE FALSE 697853.5046 490070.4076 450135.64 398467.3638 438371.1822 448289.0859 998514.5352 838665.2603 160084.7205 4.359276154 3.06131907 2.811858863 2.489103036 2.738369914 2.800324007 6.237413116 5.238883872 1 17.28847609 RRKEDEVEEWQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RRKEDEVEEWQHR 13 3 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;; 245.15 2.62E-17 3340260000 1899380 1525930 586787 673511 1501910 1270390 1832860 2274700 156382 FALSE TRUE 1648372.121 1515906.065 870559.1559 826441.9665 1472024.929 1319262.725 1655109.519 1788273.107 137894.6981 11.95384698 10.99321501 6.313217026 5.99328312 10.67499294 9.567175123 12.00270599 12.9683964 1 17.07320746 4.458781499 24.28346713 8.984207596 11.71369146 0.105574309 3.465204254 381.7895958 505523.2969 0.879087088 2.326847191 28759.51109 -4.458781499 2.72948386 RRLS(ph)EQLAHTPTAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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;RRLS(0.997)EQLAHT(0.003)PTAFK;RRLS(0.999)EQLAHT(0.001)PTAFK;RRLS(0.998)EQLAHT(0.002)PTAFK 117.29 0.00019896 1015960000 1129160 1023310 556269 735736 955150 897220 1209050 1246390 563893 TRUE FALSE 979938.6451 1016587.809 825282.549 902796.1038 936144.3837 931736.634 1091796.517 979859.1979 497230.2119 1.970794657 2.044501289 1.659759462 1.81565014 1.882718228 1.873853623 2.195756595 1.970634878 1 18.92355443 1.237049989 24.9968126 0.999998858 1.930221193 0.810412798 0.140853922 17.3342147 286735.2824 0.224261046 0.036561153 17.26036553 -1.237049989 0.930222335 RRLS(ph)ESSALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRLSESSALK 10 2 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 RRLS(0.924)ES(0.063)S(0.012)ALK 63.185 0.063183 157890000 78189 65990 39367 49120 99196 101090 80894 80157 66900 TRUE FALSE 67856.12554 65556.50734 58405.01287 60273.44675 97222.19367 104978.9977 73048.91233 63016.04933 58991.15821 1.150276204 1.111293783 0.990063844 1.021736962 1.648080774 1.779571734 1.238302731 1.068228718 1 15.84821111 RRLS(ph)PEKQNCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRLSPEKQNCR 11 3 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 1 RRLS(1)PEKQNCR 87.566 0.075314 48562000 41652 40188 13385 15395 39258 33564 44691 53165 2482.3 TRUE FALSE 36147.58267 39924.00238 19858.03077 18890.67005 38476.84261 34855.2288 40356.8737 41796.07848 2188.845322 16.51445276 18.23975499 9.072377373 8.630427129 17.57860285 15.92402554 18.4375174 19.09503521 1 11.09595429 1.229780314 24.98647191 0.99997244 15.5068937 0.600731361 3.698375922 265.2372109 754738.3263 11.56596213 0.992382288 16.97384822 -1.229780314 14.50692126 RRNDLDDPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RRNDLDDPER 10 2 Q15393 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ;;; 133.07 0.00011638 414539000 234241 205379 134774.5 148308.8 162611.1 229867 189645.1 231531 158478.7 FALSE TRUE 203285.4584 204029.8518 199951.899 181984.5798 159375.4573 238710.1322 171253.3474 182019.8974 139743.5286 1.454703916 1.460030771 1.430849077 1.302275544 1.140485422 1.708201693 1.225483205 1.302528276 1 17.09242195 0.81750808 1.210139738 0.349837483 1.39696363 0.399865381 0.151145656 3.926697611 2.354614183 6.694848951 0.044699864 6.569133383 -0.81750808 1.047126147 ASTSKS(ph)ESSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 ASTSKSESSQK 11 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 1 AS(0.002)T(0.004)S(0.006)KS(0.988)ESSQK;AS(0.001)T(0.004)S(0.11)KS(0.872)ES(0.012)S(0.001)QK;AST(0.006)S(0.033)KS(0.8)ES(0.161)S(0.001)QK 181.08 1.68E-05 201061000 151754 226130 284422 325941 364047 321556 594060 644670 493220 TRUE FALSE 131699.3244 224644.5371 421969.4305 399950.8857 356803.1769 333926.4674 536448.1526 506812.3373 434912.0935 0.302818262 0.516528605 0.970240738 0.919613163 0.820402979 0.767802212 1.233463407 1.165321326 1 18.7303643 4.586490888 0.723490056 1.059374411 1.58E-50 0.724915675 0.146926701 1.440306013 0.676238006 0.071647488 1.209190196 38591.43143 -4.586490888 -1.059374411 down RRPENPKPQDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RRPENPKPQDGK 12 3 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ; 119.25 0.00023546 322230000 458537 311086 270062 304086 295698 232717 408663 459098 463511 FALSE TRUE 397940.1737 309042.4556 400664.8865 373133.374 289814.1883 241669.7736 369030.9252 360923.4654 408715.2576 0.973636698 0.756131438 0.980303228 0.91294212 0.709085807 0.591291294 0.902904695 0.883068245 1 18.64073658 1.406424622 1.977750629 1.015440221 0.824248656 0.160920794 0.121302369 1.050356679 5.643739216 0.335884747 0.034917849 25.49321579 -1.406424622 -0.191191565 RRPESAPAESS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRPESAPAESSPSK 14 2 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 1 RRPES(0.414)APAES(0.159)S(0.417)PS(0.01)K 60.09 0.075374 48159000 41812 36351 31192 33077 45732 45272 52735 57847 50874 TRUE FALSE 36286.43826 36112.20789 46276.55553 40587.6384 44822.02267 47013.64313 47620.76782 45476.86922 44859.73368 0.808886618 0.805002726 1.031583376 0.904767708 0.999159357 1.048014317 1.061548162 1.013757004 1 15.45313343 4.551466196 0.763445798 1.028185173 0.67767022 0.707215155 0.050694229 1.113184547 0.605866853 0.020275898 0.320016913 35601.32784 -4.551466196 -0.350514954 RRPGAALEDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RRPGAALEDSR 11 2 Q9H5N1;Q9H5N1-2 Q9H5N1 RABEP2 Rab GTPase-binding effector protein 2 0 ; 112.13 0.00088155 37452000 44143 44382 30804 31788 40803 43920 40323 45403 32016 FALSE TRUE 38309.39071 44090.45172 45700.91743 39005.95125 39991.10013 45609.63082 36412.48167 35693.92178 28231.10495 1.356992253 1.561768545 1.618814337 1.381665766 1.416561633 1.615580789 1.289800088 1.264347316 1 14.78499798 1.243972452 1.030304156 0.745646695 1.493737795 0.704104876 0.101367579 0.993092616 0.869307233 0.839415846 0.033744105 17.53769255 -1.243972452 0.7480911 RRPGGEGPQCEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRPGGEGPQCEK 12 2 Q9NWY4 Q9NWY4 C4orf27 UPF0609 protein C4orf27 0 75.695 0.018626 16176000 28799 25206 15232 18188 25870 21614 24143 31819 19827 FALSE TRUE 24993.13918 25040.42013 22598.24615 22317.86339 25355.23761 22445.50457 21801.61558 25014.75447 17483.07465 1.429562001 1.432266385 1.292578485 1.276541103 1.450273372 1.283841945 1.247012669 1.430798356 1 14.09367131 1.230715691 24.99997555 0.999999365 1.352526277 0.67835809 0.076878101 175.0564977 557818.6391 0.197955157 0.018670094 17.01044563 -1.230715691 0.352526913 RRPPS(ph)PEPSTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RRPPSPEPSTK 11 2 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 RRPPS(1)PEPSTK;RRPPS(0.988)PEPS(0.008)T(0.003)K;RRPPS(0.995)PEPS(0.005)TK;RRPPS(0.998)PEPS(0.002)TK;RRPPS(0.984)PEPS(0.007)T(0.009)K;RRPPS(1)PEPSTK 103.76 0.0021191 835746000 1186123 1027867 646541 794977 980910 927540 1107696 1377999 1109494 TRUE FALSE 1029373.84 1021114.874 959210.3901 975488.6783 961391.8101 963223.064 1000271.812 1083324.637 978330.8833 1.052173511 1.043731616 0.980456006 0.997094843 0.982685742 0.984557557 1.0224269 1.107319268 1 19.89996296 1.984132447 23.58257042 1.062389649 1.005543766 0.219297086 0.035288453 376.9761963 560264.8029 0.015813323 0.009465236 96.41230079 -1.984132447 -0.056845883 RRPS(ph)PQPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RRPSPQPSPR 10 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RRPS(1)PQPS(1)PR;RRPS(1)PQPS(1)PR;RRPS(1)PQPS(1)PR;RRPS(1)PQPS(1)PR;RRPS(1)PQPS(1)PR;RRPS(1)PQPS(1)PR 94.717 0.038926 9599060000 1696187 1385220 854858 1083171 1260923 1482366 1298549 1418799 1256763 TRUE FALSE 1472031.59 1376120.399 1268270.188 1329121.531 1235833.099 1539393.579 1172615.918 1115399.875 1108189.91 1.328320694 1.241773081 1.144452027 1.199362599 1.115181692 1.389106294 1.058136252 1.006506074 1 20.07977371 2.050929567 11.00916515 1.012271026 1.22525895 0.620003579 0.079751706 0.35327664 74.95892894 0.0317839 0.021414915 112.4422602 -2.050929567 0.212987924 RRPS(ph)PQPSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RRPSPQPSPR 10 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RRPS(1)PQPSPR;RRPS(1)PQPSPR 109 0.0016358 183698000 55931 71574 67978 60935 54881 62421 67671 58465 56022 TRUE FALSE 48539.57664 71103.82568 100852.3882 74771.22308 53788.97547 64822.37626 61108.27684 45962.71473 49399.14298 0.98259957 1.439373669 2.041581738 1.513613771 1.088864548 1.312216617 1.237031113 0.930435468 1 15.59219839 2.348197822 0.911668692 0.941139281 1.493699919 0.296219413 0.278007636 0.855658492 1.416247209 0.343233469 0.139834049 222.9450438 -2.348197822 0.552560638 RRQEIEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RRQEIEQK 8 2 Q9H307 Q9H307 PNN Pinin 0 ; 101.72 0.0029211 72055000 119949 99136 93639 80178 86799 91760 107554 120370 76876 FALSE TRUE 104097.4357 98484.76909 138923.1336 98383.64034 85071.86972 95290.06658 97123.42963 94629.81222 67787.80686 1.535636578 1.452838994 2.049382331 1.451347151 1.254973035 1.405711012 1.432756629 1.395970995 1 16.04873818 3.487458729 24.53345593 1.32815126 1.67226186 0.438286345 0.1953994 383.0260872 909017.8941 0.054048115 0.074503149 3072.265391 -3.487458729 0.3441106 RRS(ph)GEQITSSPVSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRSGEQITSSPVSPK 15 2 A0A087WZV0;O43314-2;O43314;A0A087WWN8 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 RRS(0.804)GEQIT(0.189)S(0.007)S(0.001)PVSPK 64.422 0.051048 114800000 193340 273770 64333 119520 178010 77465 125150 83013 50644 TRUE FALSE 167789.6291 271971.5868 95444.65398 146658.8427 174467.9493 80445.12868 113012.9723 65261.31596 44656.92401 3.757303774 6.090244522 2.137286795 3.284123257 3.906851023 1.801403264 2.530693163 1.461392996 1 15.44659626 2.87313747 0.293786211 2.70E-14 5.65230098 0.55388511 0.98759241 1.918130813 0.800977196 7.117071101 6.152834857 746.6850736 -2.87313747 5.65230098 RRS(ph)GLEEPGKDGDGQTLANGLGPGGDSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRSGLEEPGKDGDGQTLANGLGPGGDSNR 29 3 O75145-2;O75145;R4GN36 O75145-2 PPFIA3 Liprin-alpha-3 1 RRS(1)GLEEPGKDGDGQTLANGLGPGGDSNR 130.37 7.90E-05 71815000 137260 117260 69171 78956 112230 125480 111010 114010 92425 TRUE FALSE 119120.7432 116489.7113 102622.327 96884.16657 109996.8426 130307.2968 100244.2673 89629.84873 81498.62179 1.461628928 1.429345783 1.25919095 1.188782883 1.349677334 1.598889575 1.23001181 1.099771343 1 16.31448804 1.79323927 2.757397192 1.032867215 1.369012651 0.581079948 0.11475652 0.190684392 2.765146444 0.090155299 0.033618766 62.12111891 -1.79323927 0.336145436 RRS(ph)LEPAENVHGAGGGAFPASQTPSKPASADGHR ddPTM_MDA-MB-175_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 148.2 7.12E-11 7104880000 2238332 2304660 720073 1548401 2432081 1996755 2575760 3092159 1050740 TRUE FALSE 1942530.755 2289520.537 1068302.711 1899989.113 2383687.346 2073571.457 2325963.192 2430924.861 926522.7142 2.096581903 2.471089485 1.153023768 2.050666523 2.572724133 2.238014703 2.510422201 2.623707788 1 19.82146682 3.469906024 24.84380782 2.273677983 1.903072112 0.039000808 0.55918463 414.9582021 1428794.642 0.157776959 0.204141319 2950.570693 -3.469906024 -0.370605871 RRS(ph)PGLCSDSLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRSPGLCSDSLEK 13 2 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 RRS(0.999)PGLCS(0.001)DSLEK 118.31 0.0003448 269830000 334270 244910 146620 164040 232380 189520 311280 313400 95030 TRUE FALSE 290095.3726 243301.1701 217525.9224 201287.7892 227756.0926 196810.957 281092.1135 246381.8489 83795.66166 3.461937848 2.903505567 2.595909121 2.402126616 2.717993845 2.348701032 3.354494826 2.940269747 1 16.35458793 4.64878715 2.015741401 2.566690277 3.625902664 0.208010305 0.606828628 1.059607297 5.440541873 0.158151108 1.930106329 44543.78837 -4.64878715 1.059212387 RRS(ph)PPADAIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 106.58 0.0018214 16638257100 9008612 6860111 4726848 5686739 6366775 5639033 7547890 8548180 7550007 TRUE FALSE 7818101.099 6815046.479 7012767.503 6978000.006 6240088.634 5855970.248 6815896.79 6720218.229 6657453.773 1.174338023 1.023671618 1.053370814 1.048148473 0.937308594 0.879611102 1.023799342 1.009427697 1 22.66653908 7.999999931 0.697462228 0.98174434 24.05932209 0.587836508 0.049131778 228.8552697 1.233929581 0.021065081 8230.542516 99999984 -7.999999931 23.07757775 RRS(ph)PQEGPTWSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RRSPQEGPTWSR 12 2 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 RRS(0.998)PQEGPT(0.001)WS(0.001)R;RRS(1)PQEGPTWSR;RRS(1)PQEGPTWSR;RRS(0.999)PQEGPT(0.001)WSR;RRS(1)PQEGPTWSR;RRS(1)PQEGPTWSR 177.76 1.80E-05 4470830000 802226 703552 429010 516106 642283 746110 634149 766167 613855 TRUE FALSE 696209.8015 698930.3206 636480.671 633295.7555 629502.8249 774813.3345 572649.3276 602328.1494 541285.7612 1.286214882 1.291240913 1.175868121 1.169984139 1.162976878 1.431431214 1.057942715 1.112772943 1 19.04603091 2.135615574 24.94321702 1.068576982 1.243479917 0.547854106 0.083438282 8.750203124 2103.564983 0.033797509 0.022786277 136.6518685 -2.135615574 0.174902934 RRS(ph)PS(ph)LSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RRSPSLSSK 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRS(0.999)PS(0.927)LS(0.073)SK;RRS(1)PS(0.98)LS(0.02)SK;RRS(1)PS(0.687)LS(0.313)SK 120.9 0.0030945 5307830000 6731000 5334420 3767770 4244120 4712180 4572080 5938800 7009500 6328100 TRUE FALSE 5841481.296 5299377.844 5589876.174 5207812.313 4618416.837 4747970.876 5362856.09 5510572.973 5579999.227 1.046860592 0.949709423 1.001770063 0.933299827 0.827673383 0.850890956 0.961085454 0.987558017 1 22.41183349 5.094114991 1.083306369 0.932882928 1.17955009 0.269603595 0.057790316 5.596880318 3.233566325 0.020056272 1.897208557 124198.111 -5.094114991 0.246667162 RRS(ph)PS(ph)PAPPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RRSPSPAPPPR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRS(1)PS(1)PAPPPR;RRS(1)PS(1)PAPPPR 88.716 0.062821 5976900000 2623110 2338960 1413460 1756990 2199590 2501690 2127520 2369470 2371960 TRUE FALSE 2276459.367 2323595.218 2097013.984 2155941.433 2155822.462 2597931.633 1921193.438 1862777.28 2091549.591 1.088408029 1.110944358 1.002612605 1.030786668 1.030729786 1.242108552 0.918550268 0.890620661 1 20.99614077 RRS(ph)PS(ph)PKPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RRSPSPKPTK 10 3 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BUL0;H3BV80 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 2 RRS(1)PS(0.83)PKPT(0.171)K;RRS(1)PS(0.985)PKPT(0.016)K;RRS(1)PS(0.999)PKPT(0.001)K;RRS(0.999)PS(0.968)PKPT(0.033)K;RRS(0.997)PS(0.938)PKPT(0.065)K 112.08 0.0023941 5908060000 4310000 2817330 2562910 2445370 2173430 1796730 3340070 4039950 3537940 TRUE FALSE 3740422.58 2798822.774 3802341.848 3000628.634 2130182.995 1865851.366 3016150.525 3176038.131 3119688.764 1.198972995 0.897148077 1.218820894 0.961835895 0.682819075 0.598088946 0.966811357 1.018062497 1 21.57297067 3.481377334 24.98456302 0.865248304 1.085219248 0.344833159 0.157282434 244.1501951 1433244.706 0.048923037 0.064762946 3029.544485 -3.481377334 0.219970944 RRS(ph)PS(ph)PYYSR ddPTM_MDA-MB-175_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(0.898)PS(0.836)PY(0.173)Y(0.028)S(0.066)R;RRS(0.818)PS(0.497)PY(0.278)Y(0.194)S(0.213)R 98.421 0.026503 15810900000 2425990 2334060 1579280 1909260 2240590 2236620 2172520 2195280 2261260 TRUE FALSE 2105389.275 2318727.406 2343025.09 2342786.664 2196006.643 2322664.219 1961829.345 1725836.456 1993936.419 1.055895893 1.16288934 1.175075127 1.174955551 1.101342361 1.164863732 0.983897644 0.865542371 1 20.92718798 2.125586145 4.218713769 0.92353419 1.141707784 0.768287311 0.049364997 0.086357856 2.751083412 0.020658342 0.013362455 133.5322434 -2.125586145 0.218173594 RRS(ph)PSLSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 RRSPSLSSK 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RRS(0.987)PS(0.013)LSSK;RRS(0.967)PS(0.033)LSSK;RRS(1)PSLSSK;RRS(0.999)PS(0.001)LSSK;RRS(0.992)PS(0.008)LSSK;RRS(0.996)PS(0.004)LSSK;RRS(0.855)PS(0.145)LSSK;RRS(0.999)PS(0.001)LSSK 170 4.57E-05 26864470000 5280740 4063280 2633420 3182980 3650810 3488940 4523030 5091260 3841800 TRUE FALSE 4582876.829 4036588.046 3906950.72 3905724.258 3578166.024 3623161.779 4084387.247 4002533.669 3387626.781 1.352828138 1.191568112 1.153300223 1.152938181 1.056245642 1.069528025 1.205678049 1.181515535 1 21.69184351 5.132793395 1.153230881 1.120689554 1.684499163 0.605829241 0.060915357 2.683911951 1.626556325 0.01892067 2.266616314 135766.7417 -5.132793395 0.563809609 RRS(ph)QS(ph)IEQESQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRSQSIEQESQEK 13 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 2 RRS(0.916)QS(0.865)IEQES(0.219)QEK 98.062 0.017176 195230000 358030 236440 181330 209890 232150 210400 289520 318650 295650 TRUE FALSE 310715.4284 234886.8101 269021.7945 257548.7325 227530.6692 218494.2241 261442.395 250509.1772 260698.5938 1.19185694 0.900989939 1.031926527 0.987917613 0.872772906 0.838110482 1.002853108 0.960914954 1 17.99202328 4.74585306 24.935039 0.950742223 1.191857058 0.602476149 0.061876828 626.4529223 2141975.617 0.015568799 0.154488865 55699.7261 -4.74585306 0.241114835 RRS(ph)QSIEQES(ph)QEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RRSQSIEQESQEK 13 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 2 RRS(1)QS(0.004)IEQES(0.996)QEK;RRS(0.999)QS(0.061)IEQES(0.94)QEK 209.23 1.94E-07 3972600000 5285300 3373300 2591400 2899800 3188200 2983500 4250600 4630400 4063900 TRUE FALSE 4586834.214 3351140.57 3844609.708 3558243.911 3124761.058 3098277.176 3838377.466 3640224.994 3583470.372 1.279997806 0.935166256 1.072873307 0.992960327 0.871992994 0.864602426 1.071134143 1.015837894 1 21.772926 4.744157157 24.56518698 0.981950843 1.27999797 0.638213539 0.071387871 340.5732368 1494838.266 0.018419832 0.156233666 55482.64502 -4.744157157 0.298047128 RRS(ph)QVIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRSQVIEK 8 2 A0A494BZV2;A0A1W2PPU9 A0A494BZV2 1 RRS(1)QVIEK 68.536 0.044302 107490000 126070 93912 65634 94355 92143 93203 134250 118570 81974 TRUE FALSE 109409.5301 93295.08589 97374.82193 115779.7449 90309.53457 96788.57972 121230.4557 93214.72821 72283.12711 1.513624748 1.290689676 1.347130732 1.601753404 1.249386104 1.339020372 1.677161193 1.289577969 1 16.1413713 1.326860967 3.795713105 0.985458892 1.422109186 0.498600172 0.136475042 0.190735462 4.031957334 0.195471272 0.033562186 21.22564845 -1.326860967 0.436650294 RRS(ph)S(ph)SPFLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRSSSPFLSK 10 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 RRS(0.96)S(0.525)S(0.514)PFLSK 82.822 0.082944 387450000 1535800 905050 673300 775590 971170 789920 890380 1257100 1061200 TRUE FALSE 1332840.139 899104.667 998910.1321 951699.5637 951845.6171 820308.7335 804031.0846 988278.9478 935746.1449 1.424360812 0.960842502 1.067501199 1.017048875 1.017204957 0.876635974 0.859240606 1.056140015 1 19.83575767 4.740347707 24.98086608 0.98348263 1.424360961 0.804711775 0.068507742 71.77487615 1003226.526 0.01768235 0.11053788 54998.10259 -4.740347707 0.440878332 RRS(ph)VSQDLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRSVSQDLIK 10 2 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 RRS(0.915)VS(0.085)QDLIK 56.65 0.096652 666550000 595650 488870 357690 404490 381750 337590 697860 634450 316320 TRUE FALSE 516933.3433 485658.5808 530670.0804 496335.6367 374153.9219 350577.3057 630181.6446 498777.8048 278925.01 1.853305817 1.741179756 1.90255467 1.779459063 1.341414031 1.256887311 2.259322836 1.788214706 1 18.08951777 3.453478067 24.83091896 1.5988544 1.82619297 0.138005188 0.337920597 560.6952163 588859.9105 0.102197499 0.131943531 2841.0447 -3.453478067 0.22733857 RRSPS(ph)LSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRSPSLSSK 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RRS(0.056)PS(0.944)LSSK 156.02 5.66E-05 3626900000 1570200 1156100 730750 790090 1069100 842520 1209300 1487100 1061300 TRUE FALSE 1362694.092 1148505.503 1084143.144 969492.0103 1047827.002 874932.2896 1092022.272 1169095.238 935834.323 1.456127498 1.227253024 1.158477647 1.035965434 1.11967148 0.934922206 1.166897009 1.249254498 1 19.83589362 4.737885875 1.577101702 1.102630107 1.588751754 0.634120284 0.088480065 0.773851406 1.823352332 0.026090976 0.58176907 54687.22353 -4.737885875 0.486121648 RRSPS(ph)PY(ph)YSR ddPTM_MDA-MB-175_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(0.277)PS(0.938)PY(0.71)Y(0.043)S(0.032)R;RRS(0.064)PS(0.941)PY(0.948)Y(0.041)S(0.006)R 106.66 0.0039177 15985800000 3547300 3513700 2189370 2817900 3378600 3277000 3342500 3304700 3292900 TRUE FALSE 3078515.317 3490618.273 3248156.655 3457747.264 3311372.47 3403068.311 3018344.864 2598015.622 2903617.113 1.060234596 1.20216204 1.118658738 1.19084133 1.14043014 1.172010006 1.039512011 0.89475145 1 21.46941979 2.030736785 3.848080058 0.94432504 1.14957812 0.758408717 0.047056046 0.085511333 2.739151496 0.020832146 0.012030001 107.3338691 -2.030736785 0.20525308 RRSQFFEQGS(ph)SDSVVPDLPVPTISAPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRSQFFEQGSSDSVVPDLPVPTISAPSR 28 2 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 RRS(0.402)QFFEQGS(0.463)S(0.135)DSVVPDLPVPTISAPSR 117.24 0.0001965 442260000 126070 170260 97490 97947 196740 216520 203420 213180 87919 TRUE FALSE 109409.5301 169141.5508 144636.4901 120187.3634 192825.2589 224849.6645 183692.3597 167593.116 77525.31598 1.411274868 2.181758935 1.865667856 1.550298272 2.487255376 2.900338575 2.369449997 2.161785655 1 16.24237988 3.239805524 24.99997634 2.230773321 1.79103048 0.141182443 0.5178267 69.0526656 1386681.024 0.15667501 0.191154338 1737.02282 -3.239805524 -0.439742841 RRSQFFEQGSSDS(ph)VVPDLPVPTISAPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RRSQFFEQGSSDSVVPDLPVPTISAPSR 28 2 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 RRS(0.23)QFFEQGS(0.23)S(0.23)DS(0.31)VVPDLPVPTISAPSR 99.614 0.00079439 515830000 119120 148680 87825 89124 190280 199050 187270 201930 77046 TRUE FALSE 103377.9902 147703.3113 130297.4638 109360.9664 186493.8003 206707.5823 169108.5842 158748.8409 67937.70965 1.521658453 2.174099069 1.917896032 1.609724068 2.745070466 3.042604518 2.489171111 2.33668226 1 16.05192496 3.248029392 24.99956752 2.372932615 1.840152001 0.172806044 0.553656245 364.1363743 961391.5537 0.164195487 0.209162522 1770.228758 -3.248029392 -0.532780614 RRSS(ph)PSARPPDVPGQQPQAAK ddPTM_MDA-MB-175_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(0.675)PS(0.118)ARPPDVPGQQPQAAK 152.4 2.93E-07 330460000 437280 324320 155900 177770 365590 300300 385300 466900 78407 TRUE FALSE 379492.3401 322189.5206 231293.7615 218135.3955 358315.4743 311852.7353 347933.6653 367057.0684 69137.81378 5.488925948 4.660105707 3.345401725 3.155080897 5.182626622 4.510595841 5.032465539 5.309063859 1 16.07718736 4.578307332 3.978122636 4.144982748 5.441841997 0.119269808 1.286721934 0.576188074 14.99379034 0.315878707 1.517691869 37871.04877 -4.578307332 1.296859249 RRVEHHDHAVVSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RRVEHHDHAVVSGR 14 2 O95831-3;O95831;E9PMA0;O95831-5;O95831-2 O95831-3 AIFM1 "Apoptosis-inducing factor 1, mitochondrial" 0 ;;; 127.71 4.68E-05 587760000 597055 484569 246975 312201 510613 650192 437859 545251 191806 FALSE TRUE 518152.669 481385.8343 366412.9361 383091.0087 500452.8003 675205.307 395395.5016 428653.3168 169130.9132 3.06361894 2.846232101 2.166445679 2.265056113 2.958967056 3.992205176 2.337807407 2.534446889 1 17.36778085 4.464326855 22.69486449 2.527883798 3.009272678 0.069524866 0.738116244 205.6659089 364814.2906 0.187658555 0.497580422 29129.0858 -4.464326855 0.48138888 RRVS(ph)EVEEEKEPVPQPLPSDDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RRVSEVEEEKEPVPQPLPSDDTR 23 3 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 1 RRVS(1)EVEEEKEPVPQPLPSDDTR;RRVS(1)EVEEEKEPVPQPLPSDDTR;RRVS(1)EVEEEKEPVPQPLPSDDTR;RRVS(1)EVEEEKEPVPQPLPSDDTR;RRVS(1)EVEEEKEPVPQPLPSDDTR 222.47 8.92E-32 5514780000 2536320 1945810 2009820 2407210 2930560 2949790 3977130 4252870 3122670 TRUE FALSE 2201138.886 1933027.846 2981775.674 2953803.822 2872247.59 3063270.33 3591428.545 3343426.846 2753511.51 0.799393385 0.702022795 1.082899296 1.072740685 1.043121694 1.112495923 1.304308528 1.214241101 1 21.39284121 4.178636891 5.027642896 1.136075298 0.749782859 0.743899341 0.08958344 0.094051554 4.709741343 0.02549274 0.057273755 15088.18121 -4.178636891 -0.38629244 RRVS(ph)HS(ph)PPPK ddPTM_MDA-MB-175_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 80.96 0.012037 362338000 690619 534015 362275 446506 487654 438307 592606 735054 576554 TRUE FALSE 599351.9493 530507.0203 537472.4017 547892.0117 477950.6395 455168.9539 535135.1613 577868.4223 508394.4429 1.178911292 1.043494923 1.057195666 1.077690796 0.940117749 0.895306706 1.052598369 1.136653695 1 18.95558874 TIS(ph)QSSSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TISQSSSLK 9 0 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 T(0.002)IS(0.786)QS(0.041)S(0.085)S(0.085)LK;TIS(0.983)QS(0.014)S(0.003)SLK;TIS(1)QSSSLK;TIS(1)QSSSLK;TIS(1)QSSSLK;TIS(1)QSSSLK 261.35 3.74E-15 4094530000 2034800 2241001 2267540 2922460 4125810 3846300 5114590 5396710 5482970 TRUE FALSE 1765896.024 2226279.717 3364129.928 3586049.21 4043714.453 3994269.65 4618577.849 4242665.564 4834779.533 0.365248511 0.460471817 0.695818683 0.741719283 0.83638032 0.826153421 0.955281997 0.877530306 1 22.20501867 4.586768802 0.534016386 0.945001072 2.36E-21 0.952367971 0.044193084 0.705473889 0.184149716 0.029877019 0.413302679 38616.13478 -4.586768802 -0.945001072 down RS(ph)AS(ph)PERMD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RSASPERMD 9 2 Q16629;Q16629-4;C9JAB2;H7BZZ6 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 2 RS(1)AS(1)PERMD;RS(1)AS(1)PERMD;RS(1)AS(1)PERMD 95.273 0.0046255 2939310000 3699890 3177180 2194140 2608240 2982110 3088630 2965870 3347190 3086810 TRUE FALSE 3210940.162 3156308.895 3255233.443 3200480.756 2922771.845 3207451.595 2678240.384 2631419.466 2721890.838 1.179672644 1.159601572 1.195945626 1.175829946 1.073802007 1.178390973 0.983963187 0.966761572 1 21.37617778 2.233984438 24.99485666 0.98008827 1.158859438 0.858643055 0.033833691 38.61873268 210930.3625 0.013743095 0.009613853 171.3895891 -2.233984438 0.178771168 RS(ph)ASASHQADIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RSASASHQADIK 12 1 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 RS(0.787)AS(0.187)AS(0.026)HQADIK;RS(0.43)AS(0.43)AS(0.141)HQADIK;RS(0.451)AS(0.451)AS(0.098)HQADIK 159.18 4.38E-05 508969000 945300 853520 491920 803476 1061290 931830 794399 1504740 917630 TRUE FALSE 820376.2099 847913.1709 729814.1574 985917.5062 1040172.405 967678.1031 717358.3073 1182963.061 809148.8268 1.013875548 1.047907558 0.901952933 1.218462505 1.285514322 1.195921036 0.886559164 1.461984522 1 19.62604556 3.726221506 24.22159214 1.192148346 0.993911566 0.232321995 0.157871856 654.2713433 1284330.654 0.041968847 0.062797701 5323.797225 -3.726221506 -0.19823678 RS(ph)ASPHDVDLCLVSPCEFEHR ddPTM_MDA-MB-175_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(0.78)AS(0.22)PHDVDLCLVSPCEFEHR 151.05 3.08E-08 464790000 103680 110900 55541 63598 106800 139990 110250 111890 27570 TRUE FALSE 89978.42531 110171.4906 82400.81337 78038.89793 104674.889 145375.5059 99557.97197 87963.19423 24310.70601 3.701185201 4.531809589 3.389486646 3.210063003 4.305711604 5.979896505 4.095231621 3.618290403 1 14.56930417 4.234799001 24.97228151 3.767153066 4.116497263 0.017374312 1.236983826 615.7672448 4088012.536 0.325668073 0.722527911 17171.13494 -4.234799001 0.349344197 RS(ph)ASPHDVDLCLVSPCEFEHRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSASPHDVDLCLVSPCEFEHRK 22 2 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 RS(0.827)AS(0.173)PHDVDLCLVSPCEFEHRK;RS(0.5)AS(0.5)PHDVDLCLVSPCEFEHRK 100.94 0.00036979 578090000 536710 471980 144975 146662 419290 370740 539550 550110 45126 TRUE FALSE 465782.4137 468879.5323 215085.3949 179963.8487 410946.9493 385002.6077 487224.524 432473.2575 39791.25569 11.70564752 11.78348168 5.405343239 4.522698406 10.32756927 9.675558136 12.24451241 10.86855014 1 15.28016381 4.28046605 24.3110123 8.292737889 11.74458314 0.180376214 3.400022373 220.5277943 127932.4611 0.876712174 2.319508056 19075.06602 -4.28046605 3.451845251 RS(ph)ATLSGSATNLASLTAALAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSATLSGSATNLASLTAALAK 21 1 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 RS(0.2)AT(0.2)LS(0.2)GS(0.2)AT(0.2)NLAS(0.002)LTAALAK 78.794 0.005103 47089000 45334 49047 36232 45091 56609 54946 64976 83641 52251 TRUE FALSE 39342.99704 48724.80703 53753.91639 55329.60072 55482.59165 57059.80817 58674.63752 65755.02304 46073.9463 0.85390986 1.057534918 1.166687916 1.200886947 1.204207499 1.238439785 1.27348843 1.427162818 1 15.49166355 5.478649371 0.679298129 1.26406288 3.39E-19 0.559289665 0.104693343 5.340240476 0.910486452 0.044347955 6.534085738 301057.4449 -5.478649371 -1.26406288 RS(ph)DSMTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSDSMTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR 38 1 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 RS(0.707)DS(0.128)MT(0.164)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR;RS(0.385)DS(0.385)MT(0.229)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR 195.99 1.38E-30 857400000 188131 180597 85938 96145 155680 160006 186209 210831 69374 TRUE FALSE 163269.0117 179410.6464 127497.9042 117976.1917 152582.2726 166161.5344 168150.4798 165746.4313 61172.68475 2.668985551 2.932855524 2.084229338 1.928576328 2.494287658 2.716270097 2.748783718 2.70948434 1 15.90059997 4.246592282 24.97539644 2.324318385 2.800920637 0.14881822 0.528512283 385.5144458 1198773.871 0.132882278 0.3385464 17643.80635 -4.246592282 0.476602252 RS(ph)ET(ph)PPHWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSETPPHWR 9 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 RS(1)ET(1)PPHWR;RS(1)ET(1)PPHWR 93.348 0.0081883 1526360000 882440 715800 470300 639500 718900 676080 634740 796280 682860 TRUE FALSE 765823.3182 711097.8627 697738.6531 784708.2491 704595.2965 702089.2351 573183.0125 626001.7187 602133.0687 1.271850622 1.18096464 1.158778166 1.303214007 1.170165422 1.166003449 0.951920833 1.039640158 1 19.19972283 2.364732893 4.446850636 1.004704819 1.21259522 0.804991614 0.049405501 0.089477589 3.069023905 0.018731749 0.014204034 231.5969808 -2.364732893 0.207890401 RS(ph)FSSQRPVDR ddPTM_MDA-MB-175_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(0.559)FS(0.404)S(0.037)QRPVDR 71.692 0.038067 260460000 240150 241940 136620 135890 239520 273480 208390 249810 175110 TRUE FALSE 208413.569 240350.6802 202689.889 166745.9014 234754.0206 284000.9526 188180.3699 196390.0755 154408.6953 1.349752801 1.556587728 1.312684422 1.079899685 1.520341974 1.839280826 1.218716145 1.271884819 1 17.23639447 1.434371986 1.763876748 0.960830337 1.424205693 0.299525425 0.20334546 0.814856058 3.492474582 0.585461887 0.060060385 27.18766975 -1.434371986 0.463375356 RS(ph)LSVEHLETK ddPTM_MDA-MB-175_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(0.746)LS(0.254)VEHLETK 97.45 0.0038329 188410000 239690 200320 119070 171210 196750 200110 197880 279880 194720 TRUE FALSE 208014.3592 199004.0847 176652.6503 210085.8473 192835.0599 207808.3612 178689.6281 220029.84 171700.4234 1.211495901 1.159019184 1.028842252 1.22356045 1.123090183 1.210296149 1.040705809 1.281475232 1 17.38953407 1.201665281 24.5405077 0.999998219 1.158235465 0.285393099 0.079438319 7085.51483 4712465.829 4.607528659 0.017999921 15.90982053 -1.201665281 0.158237246 RS(ph)LTNSHLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSLTNSHLEK 10 1 F8VX12;F8VX04;Q9H2H9 F8VX12 SLC38A1 Sodium-coupled neutral amino acid transporter 1 1 RS(0.793)LT(0.202)NS(0.004)HLEK;RS(0.862)LT(0.138)NSHLEK 102.63 0.0017895 537080000 711280 581880 460750 652150 640030 727520 618320 806720 720820 TRUE FALSE 617282.5458 578057.592 683570.2411 800230.625 627294.6552 755508.1652 558355.4216 634209.2059 635605.4808 0.971172472 0.909459735 1.075463101 1.259005231 0.986924553 1.188643251 0.878462251 0.997803237 1 19.27777204 -1.2124978 7.050208175 0.140010526 1.028680523 0 0.117583066 0 0 0 0.02657181 0.06130589 1.2124978 0.888669997 RS(ph)NSAPLIHGLSDTSPVFQAEAPSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSNSAPLIHGLSDTSPVFQAEAPSAR 26 1 Q96E09 Q96E09 FAM122A Protein FAM122A 1 RS(0.49)NS(0.49)APLIHGLS(0.009)DT(0.011)S(0.001)PVFQAEAPSAR 92.349 0.0044312 159580000 60339 64290 31925 27376 60526 60370 67030 59644 17246 TRUE FALSE 52365.04827 63867.67476 47364.03678 33592.13922 59321.65102 62692.47296 60529.44092 46889.59475 15207.19753 3.443438423 4.199831997 3.114580231 2.208963167 3.900893042 4.122552683 3.980315295 3.083381712 1 13.89246669 4.218251279 24.17263196 3.147978147 3.821635152 0.096052073 0.942595412 396.1737062 471536.4517 0.248005559 0.517407943 16529.17887 -4.218251279 0.673657005 RS(ph)NSPDKFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSNSPDKFK 9 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 RS(0.895)NS(0.105)PDKFK;RS(0.5)NS(0.5)PDKFK 116.71 0.00099948 1892520000 6240700 2816050 2703050 3257050 2853530 2216880 4192900 5010500 3792200 TRUE FALSE 5415975.683 2797551.182 4010254.021 3996612.983 2796750.336 2302164.808 3786273.203 3939043.567 3343890.436 1.61966302 0.836615683 1.199277936 1.195198545 0.836376188 0.688468971 1.132295832 1.177982246 1 21.67309615 4.750049853 24.57815179 1.023792728 1.619663468 0.542220625 0.17603368 1196.75124 2560068.843 0.045362767 0.682185591 56240.58799 -4.750049853 0.59587074 RS(ph)NSSEALLVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSNSSEALLVDR 12 1 Q96HB5-2;Q96HB5;Q96HB5-5;Q96HB5-3;Q96HB5-4 Q96HB5-2 CCDC120 Coiled-coil domain-containing protein 120 1 RS(0.494)NS(0.494)S(0.012)EALLVDR 56.407 0.073818 82931000 32535 36246 17335 24978 27796 35091 29944 20956 23152 TRUE FALSE 28235.41732 36007.89764 25718.26398 30649.63666 27242.91398 36440.97348 27040.03549 16474.72248 20414.99693 1.383072327 1.763796377 1.2597731 1.501329477 1.334455943 1.78500999 1.324518224 0.806991181 1 14.31734173 1.88108187 4.412646722 0.908258809 1.501264068 0.663728587 0.174056605 0.118620653 3.540736337 0.089348957 0.04384572 76.04696215 -1.88108187 0.593005259 RS(ph)PASIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSPASIDR 8 1 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 RS(1)PASIDR 61.815 0.051192 415520000 368790 394650 223540 222150 390010 426160 282880 294010 317790 TRUE FALSE 320053.4671 392057.5182 331644.6917 272592.5529 382249.564 442554.651 255446.3411 231138.2495 280221.2282 1.142145687 1.399099992 1.183510235 0.97277624 1.364099239 1.579304515 0.911588115 0.82484204 1 18.09620673 2.116885175 10.67766153 0.890569514 1.265389041 0.509562096 0.166670056 0.266762972 23.6318693 0.069812967 0.047058085 130.8835829 -2.116885175 0.374819527 RS(ph)PERPTGDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RSPERPTGDLR 11 2 Q5T200;Q5T200-2;Q5T9K0 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 RS(0.999)PERPT(0.001)GDLR;RS(1)PERPTGDLR;RS(1)PERPTGDLR;RS(0.98)PERPT(0.02)GDLR 94.551 0.0066305 3268940000 3885480 3554683 2131533 2763110 3595520 3530557 3510140 3793473 3429847 TRUE FALSE 3372003.973 3531332.053 3162349.488 3390516.357 3523976.187 3666379.812 3169727.163 2982268.32 3024374.395 1.11494264 1.167623975 1.045621036 1.121063703 1.165191781 1.212277097 1.048060441 0.986077757 1 21.52820531 2.035105797 6.716113632 0.999076894 1.135452099 0.669432752 0.04309308 0.105621871 14.17402121 0.018789298 0.012388862 108.4190998 -2.035105797 0.136375205 RS(ph)PESCSKPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RSPESCSKPEK 11 2 Q03111 Q03111 MLLT1 Protein ENL 1 RS(0.998)PES(0.002)CSKPEK;RS(0.996)PES(0.003)CS(0.001)KPEK;RS(0.908)PES(0.091)CSKPEK 131.96 0.00015161 1888810000 2539580 1833840 1564250 1663740 1672910 1397330 2434180 2705420 2309470 TRUE FALSE 2203968.069 1821793.384 2320726.532 2041517.596 1639622.364 1451086.189 2198113.598 2126886.987 2036447.088 1.082261396 0.894594019 1.139595792 1.00248988 0.805138702 0.712557767 1.079386551 1.04441063 1 20.9576229 7.999967978 0.796141201 0.959260793 25.31589423 0.070153542 0.128516017 1966.993161 6.940730453 0.049502158 86372.26858 99992626.96 -7.999967978 24.35663343 RS(ph)PGGGSEANGLALVSGFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSPGGGSEANGLALVSGFK 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 RS(0.984)PGGGS(0.016)EANGLALVSGFK;RS(0.956)PGGGS(0.044)EANGLALVSGFK 142.23 9.63E-08 1334890000 1049650 1011880 811140 925230 1005050 971220 1148950 1329850 1183380 TRUE FALSE 910936.093 1005232.894 1203410.017 1135317.613 985051.4713 1008583.462 1037525.006 1045471.926 1043482.165 0.872977157 0.963344586 1.153263619 1.088008642 0.944004129 0.966555535 0.994291078 1.001906848 1 19.99297451 4.565337059 4.663139865 1.01801829 0.883215001 0.377666997 0.060524735 0.25832027 9.245399202 0.016037617 0.069970651 36756.74614 -4.565337059 -0.134803289 RS(ph)PLGQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RSPLGQK 7 1 A0A2R8Y6S3;C9J167;Q68D20;P54278-3;P54278 A0A2R8Y6S3 PMS2;PMS2CL Protein PMS2CL;Mismatch repair endonuclease PMS2 1 RS(1)PLGQK;RS(1)PLGQK;RS(1)PLGQK;RS(1)PLGQK 101.66 0.0054471 1519836000 3617450 2495430 1664300 1990110 1954180 1953450 2836900 3277360 2953380 TRUE FALSE 3139394.817 2479037.356 2469161.047 2441994.892 1915295.641 2028600.486 2561777.875 2576522.068 2604234.781 1.205496079 0.951925446 0.948133043 0.937701512 0.73545429 0.778962212 0.983696974 0.989358597 1 21.31242809 5.016695632 1.654469936 0.909470045 1.524564877 0.522533964 0.087967803 2.113807207 3.134474899 0.026735646 2.583177646 103919.161 -5.016695632 0.615094833 RS(ph)PPWEP ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 104.01 0.0087355 4110130000 3018460 2357920 1577040 1928290 2532430 2514460 2346620 2678120 2594170 TRUE FALSE 2619562.863 2342430.668 2339701.819 2366137.717 2482039.598 2611192.903 2119045.154 2105424.879 2287490.178 1.14516901 1.024017804 1.022824859 1.034381585 1.085049292 1.141509996 0.926362515 0.920408271 1 21.12533412 2.221982911 24.99913799 0.942042813 1.069324147 0.604503733 0.047980703 162.1701799 244550.2845 0.019897993 0.013458081 166.7181608 -2.221982911 0.127281334 RS(ph)PRPDHPGTPPHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSPRPDHPGTPPHK 14 2 P30291 P30291 WEE1 Wee1-like protein kinase 1 RS(1)PRPDHPGTPPHK 93.152 0.0022201 65112000 62849 52397 38516 42734 57628 56467 59561 63521 56575 TRUE FALSE 54543.34541 52052.80066 57142.46643 52437.40785 56481.31555 58639.32203 53784.78339 49937.52847 49886.76795 1.093342937 1.043418983 1.145443347 1.051128586 1.132190316 1.175448409 1.078137262 1.001017515 1 15.60636958 1.804412351 3.813400866 0.999751255 1.105639882 0.538842586 0.039924827 0.163684215 4.270638259 0.024911684 0.010871889 63.74004282 -1.804412351 0.105888627 RS(ph)PSPKPT(ph)K ddPTM_MDA-MB-175_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(0.866)PS(0.258)PKPT(0.876)K 71.548 0.054374 314440000 1062200 621910 602630 633360 489720 494070 917880 1058300 926890 TRUE FALSE 921827.5787 617824.6323 894063.8837 777174.0683 479975.5301 513077.1926 828864.1389 831990.7807 817314.1201 1.127874285 0.755920664 1.093904855 0.950887852 0.587259559 0.627760099 1.014131677 1.017957185 1 19.64053113 2.096487783 24.68149812 1.012459139 0.852526086 0.146165884 0.174535884 24.9051175 6347.171075 0.074093696 0.04995396 124.8785316 -2.096487783 -0.159933053 RS(ph)PTEDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RSPTEDFR 8 1 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 RS(1)PTEDFR;RS(1)PTEDFR;RS(1)PTEDFR;RS(1)PTEDFR 118.28 0.0011743 2005440000 2402180 2200580 1611560 1903970 2236890 2203180 1931990 2463690 2877590 TRUE FALSE 2084725.827 2186124.245 2390915.806 2336295.489 2192380.265 2287937.76 1744625.907 1936849.066 2537404.588 0.821597721 0.861559191 0.94226826 0.920742202 0.864024711 0.901684253 0.687563156 0.763318974 1 21.27492214 RS(ph)PTSSAIPLQSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSPTSSAIPLQSPR 14 1 Q9ULD2;Q9ULD2-2;Q9ULD2-4;Q9ULD2-7;Q9ULD2-3;Q9ULD2-6 Q9ULD2 MTUS1 Microtubule-associated tumor suppressor 1 1 RS(0.922)PT(0.029)S(0.042)S(0.008)AIPLQSPR 78.932 0.012557 185430000 96178 101370 53440 84879 102400 110710 93989 109430 96560 TRUE FALSE 83467.83362 100704.0938 79283.76275 104152.0742 100362.4403 114969.0853 84873.96125 86029.24609 85144.7868 0.980304687 1.182739397 0.931164029 1.223234894 1.17872678 1.350277447 0.996819235 1.010387709 1 16.37763058 RS(ph)PVPAQIAITVPK ddPTM_MDA-MB-175_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 120.31 8.37E-05 2936090000 4906730 3992880 2842210 3616520 4266360 3767760 4750950 5375450 5316780 TRUE FALSE 4258293.198 3966650.508 4216712.263 4437706.141 4181467.783 3912708.165 4290203.6 4225951.849 4688236.325 0.908293205 0.84608587 0.899423999 0.946561955 0.891906357 0.834579977 0.915099688 0.901394801 1 22.16061386 1.023267465 1.998229051 1.099752757 0.890154474 0.522703265 0.032166608 1.337685408 3.088437076 0.645395894 0.008797772 10.55036452 -1.023267465 -0.209598283 RS(ph)PVSTRPLPSASQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RSPVSTRPLPSASQK 15 2 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 RS(1)PVSTRPLPSASQK;RS(1)PVSTRPLPSASQK;RS(1)PVSTRPLPSASQK;RS(1)PVSTRPLPSASQK 195.55 4.89E-09 2513800000 2787390 2342090 1632800 1981000 2335450 1997120 2786870 3006780 2472710 TRUE FALSE 2419029.349 2326704.657 2422427.541 2430816.328 2288979.114 2073950.499 2516599.776 2363803.496 2180389.041 1.109448499 1.067105279 1.111007025 1.114854405 1.049803073 0.951183692 1.15419759 1.084120059 1 21.05615414 3.230250154 24.93888262 1.055534668 1.098954139 0.183889499 0.053831163 385.6700943 1157354.663 0.016776088 0.019319855 1699.222122 -3.230250154 0.043419471 RS(ph)S(ph)DGSLSHEEDLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSDGSLSHEEDLAK 15 1 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 2 RS(0.663)S(0.726)DGS(0.581)LS(0.03)HEEDLAK 107.72 0.003972 811310000 434030 447680 298130 326670 467440 355600 507760 600800 508940 TRUE FALSE 376671.8358 444739.1606 442306.6652 400845.4163 458138.8585 369280.1621 458517.5134 472323.5954 448773.693 0.83933582 0.991009873 0.985589557 0.89320168 1.020868348 0.822864994 1.021712102 1.052476121 1 18.77562858 2.037209689 24.99992056 1.032118853 0.933077332 0.338049807 0.064799959 169.5900162 113941.0418 0.024564006 0.016561005 108.9455985 -2.037209689 -0.099041521 RS(ph)S(ph)LSSHSHQSQIYR ddPTM_MDA-MB-175_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 2 RS(1)S(1)LSSHSHQSQIYR;RS(1)S(0.973)LS(0.026)S(0.001)HSHQSQIYR 150.98 3.15E-06 1202110000 283970 249180 141467 187169 306640 304280 244730 270200 296170 TRUE FALSE 246442.645 247543.1202 209880.9144 229668.5821 300538.4639 315985.8485 220996.1223 212419.8327 261157.12 0.943656619 0.947870463 0.803657639 0.879426845 1.150795597 1.209945371 0.84621902 0.813379443 1 17.99455851 RS(ph)S(ph)SPAELDLKDDLQQTQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSSSPAELDLKDDLQQTQGK 20 2 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 2 RS(0.719)S(0.791)S(0.489)PAELDLKDDLQQTQGK;RS(0.712)S(0.778)S(0.511)PAELDLKDDLQQTQGK 254.11 2.17E-36 294110000 294310 230940 202793 177835 210245 169727 322160 343380 293580 TRUE FALSE 255416.1878 229422.9399 300864.3731 218215.1548 206061.5358 176256.5075 290916.9728 269950.8592 258873.3068 0.986645518 0.886236371 1.162207015 0.842941891 0.795993756 0.680860107 1.123781267 1.042791404 1 17.98188669 RS(ph)SAIGIENIQEVQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.66)S(0.34)AIGIENIQEVQEK 225.34 4.27E-15 1575910000 1515880 1095680 870470 954470 1139660 1082780 1329850 1480130 1238460 TRUE FALSE 1315552.617 1088482.406 1291432.204 1171197.002 1116982.996 1124435.247 1200881.352 1163615.718 1092050.67 1.204662617 0.996732511 1.182575351 1.072474963 1.022830741 1.029654831 1.099657173 1.065532718 1 20.05860837 4.756958026 24.20787088 1.063413386 1.204662806 0.411321048 0.054623947 2838.368749 3734717.133 0.012855435 0.418406134 57142.34072 -4.756958026 0.141249419 RS(ph)SDGSLSHEEDLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RSSDGSLSHEEDLAK 15 1 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 1 RS(0.484)S(0.484)DGS(0.026)LS(0.005)HEEDLAK;RS(0.372)S(0.372)DGS(0.128)LS(0.128)HEEDLAK;RS(0.49)S(0.49)DGS(0.011)LS(0.009)HEEDLAK 151.58 1.83E-06 1340620000 1430780 1272380 722802 1027340 1390740 1167710 1563110 1848140 1430990 TRUE FALSE 1241698.798 1264021.652 1072351.465 1260613.249 1363066.995 1212632.559 1411519.833 1452929.643 1261819.992 0.984053831 1.001744829 0.849845042 0.999043648 1.080238864 0.961018661 1.118638032 1.151455558 1 20.26707468 2.867345609 1.063000462 1.097249847 0.952386278 0.333838412 0.069579208 0.517398082 1.295044974 0.040850453 0.037075939 736.7932001 -2.867345609 -0.144863569 RS(ph)SDPALIGLSTSVSDSNFSSEEPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RSSDPALIGLSTSVSDSNFSSEEPSR 26 1 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 RS(0.5)S(0.5)DPALIGLSTSVSDSNFSSEEPSR;RS(0.645)S(0.355)DPALIGLSTSVSDSNFSSEEPSR;RS(0.5)S(0.5)DPALIGLSTSVSDSNFSSEEPSR;RS(0.63)S(0.37)DPALIGLSTSVSDSNFSSEEPSR;RS(0.5)S(0.5)DPALIGLSTSVSDSNFSSEEPSR 364.94 1.21E-126 4206500000 976160 895170 598115 679508 937870 995860 842460 968720 875330 TRUE FALSE 847157.9827 889289.5693 887365.4146 833800.677 919208.2219 1034171.379 760758.3589 761566.7666 771849.4846 1.097568891 1.152154127 1.149661213 1.080263307 1.190916416 1.339861462 0.985630455 0.98667782 1 19.55796001 2.152043612 25 0.989698513 1.163839068 0.591119527 0.069572727 16.26211557 4696.346085 0.028979225 0.019537794 141.920003 -2.152043612 0.174140556 RS(ph)SDPLGDTASNLGSAVDELMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.646)S(0.354)DPLGDTASNLGSAVDELMR 219.09 6.90E-26 138699000 141220 120468 89045 93559 126612 144221 131207 138742 113826 TRUE FALSE 122557.4192 119676.6378 132107.4598 114803.0009 124092.6689 149769.2752 118482.5653 109073.103 100369.62 1.221060907 1.19235918 1.316209625 1.143802288 1.236356867 1.492177367 1.180462429 1.086714317 1 16.61496313 1.720001441 2.824804099 1.023117838 1.2621645 0.480261489 0.095078353 0.201125936 3.429263364 0.077517096 0.026305778 52.4809201 -1.720001441 0.239046662 RS(ph)SDSWEVWGSASTNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 RSSDSWEVWGSASTNR 16 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 RS(0.498)S(0.498)DS(0.003)WEVWGSASTNR;RS(0.498)S(0.498)DS(0.005)WEVWGSASTNR;RS(0.499)S(0.499)DS(0.001)WEVWGSASTNR;RS(0.67)S(0.33)DSWEVWGSASTNR;RS(0.499)S(0.499)DS(0.001)WEVWGSASTNR;RS(0.499)S(0.499)DS(0.002)WEVWGSASTNR;RS(0.497)S(0.497)DS(0.007)WEVWGSASTNR;RS(0.498)S(0.498)DS(0.004)WEVWGSASTNR 292.53 8.79E-46 9914580000 3271650 2995940 1894900 2148910 2948760 3038260 3294350 3247280 2525470 TRUE FALSE 2839293.163 2976259.473 2811279.978 2636852.86 2890085.445 3155143.828 2974864.444 2552874.442 2226911.814 1.274991289 1.336496333 1.262411902 1.184084993 1.297799683 1.416824775 1.335869892 1.146374287 1 21.086613 1.492235604 2.93019633 1.005579012 1.300353413 0.733819349 0.060394965 0.146831915 2.365970902 0.083141389 0.017526913 31.06244266 -1.492235604 0.294774401 RS(ph)SEASQSDGLPSLLSLTPAQQYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RSSEASQSDGLPSLLSLTPAQQYR 24 1 A0A2R8YGX0;P10071 A0A2R8YGX0 GLI3 Transcriptional activator GLI3;Transcriptional repressor GLI3R 1 RS(0.457)S(0.457)EAS(0.062)QS(0.024)DGLPSLLSLTPAQQYR;RS(0.498)S(0.498)EAS(0.002)QS(0.002)DGLPSLLSLTPAQQYR;RS(0.285)S(0.285)EAS(0.215)QS(0.215)DGLPSLLSLTPAQQYR 184.19 1.63E-17 214203000 123796 113823 76878 86149 118899 118159 122255 136278 105740 TRUE FALSE 107436.0449 113075.2892 114056.4579 105710.4472 116533.1425 122704.6532 110398.7289 107136.0102 93239.53766 1.152258448 1.212739703 1.2232628 1.133751301 1.249825401 1.316015247 1.184033423 1.149040556 1 16.50865423 1.238675187 1.903833992 0.927949737 1.21350204 0.635999592 0.050318244 0.560587433 1.941662389 0.289899216 0.014264378 17.32507754 -1.238675187 0.285552303 RS(ph)SFSEGQTLTVTSGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSFSEGQTLTVTSGAK 17 1 E9PEM3;H7C357;H0Y6E6;Q92622-3;Q92622-2;Q92622;H7C3H3 E9PEM3 KIAA0226 Run domain Beclin-1 interacting and cysteine-rich containing protein 1 RS(0.428)S(0.428)FS(0.143)EGQTLTVTSGAK 198.64 8.58E-12 418000000 324890 246070 190590 221730 281360 222930 286610 355240 271610 TRUE FALSE 281954.9633 244453.55 282759.9615 272077.1854 275761.4865 231506.2614 258814.6063 279274.6905 239500.5752 1.177262155 1.020680429 1.180623308 1.136018923 1.151402189 0.966620899 1.080642942 1.166071064 1 17.8696696 RS(ph)SFSMEEES ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSSFSMEEES 10 1 P19532 P19532 TFE3 Transcription factor E3 1 RS(0.631)S(0.369)FS(0.001)MEEES;RS(0.5)S(0.5)FS(0.001)MEEES 118.87 0.0008138 268950000 404680 416860 287130 385070 471590 494200 495980 538570 501910 TRUE FALSE 351200.5127 414121.6192 425987.0284 472506.0289 462206.2817 513212.1938 447879.9359 423400.9967 442574.7716 0.793539386 0.935709954 0.962519908 1.067629832 1.044357499 1.159605623 1.011987046 0.956676756 1 18.75556169 4.667117804 1.328972328 1.033275537 0.715292129 0.67030806 0.05470261 0.810647246 1.401919277 0.017834345 0.337184834 46464.12939 -4.667117804 -0.317983408 RS(ph)SGFISELPSEEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RSSGFISELPSEEGK 15 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 RS(0.489)S(0.489)GFIS(0.023)ELPSEEGK;RS(0.499)S(0.499)GFIS(0.002)ELPSEEGK;RS(0.5)S(0.5)GFIS(0.001)ELPSEEGK;RS(0.5)S(0.5)GFISELPSEEGK;RS(0.5)S(0.5)GFISELPSEEGK;RS(0.5)S(0.5)GFISELPSEEGK 203.71 3.23E-09 2793050000 3644800 3905930 3079120 3636780 4572680 3993930 5196170 6044820 5271960 TRUE FALSE 3163130.445 3880271.689 4568192.731 4462566.484 4481692.614 4147579.072 4692246.233 4752182.284 4648714.895 0.680431155 0.834697713 0.982678619 0.959957017 0.964071301 0.892199063 1.009364166 1.022257203 1 22.14840052 4.557770543 1.993396713 0.979489189 0.646052528 0.875491341 0.036683939 0.179978859 1.023813987 0.010852192 0.095804817 36121.89645 -4.557770543 -0.333436661 RS(ph)SGREEDDEELLR ddPTM_MDA-MB-175_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(0.5)S(0.5)GREEDDEELLR 117.29 0.00024557 1184000000 213600 209310 146410 145880 208910 217760 246050 240820 185480 TRUE FALSE 185372.2188 207935.0288 217214.3657 179004.2836 204753.0997 226137.3681 222188.1089 189322.5171 163552.7657 1.133409258 1.271363575 1.328099618 1.094474208 1.251908513 1.38265695 1.358510252 1.157562309 1 17.31939663 1.390855332 3.368965785 0.998043558 1.26104697 0.459542379 0.090549215 0.244293547 4.220334036 0.133576542 0.024087421 24.59548166 -1.390855332 0.263003412 RS(ph)SITEPEGPGGPNIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSITEPEGPGGPNIQK 17 1 Q96KQ4;A0A3B3ISJ2;H0YJL1 Q96KQ4 PPP1R13B Apoptosis-stimulating of p53 protein 1 1 RS(0.429)S(0.429)IT(0.141)EPEGPGGPNIQK 129.02 2.14E-05 218530000 178410 144170 64588 115620 122940 97102 91413 125230 120420 TRUE FALSE 154832.6665 143222.9378 95822.97283 141873.2881 120493.7345 100837.5768 82547.78133 98450.53904 106184.0848 1.458153233 1.348817368 0.902423118 1.336106898 1.13476266 0.949648688 0.777402579 0.927168504 1 16.69620802 7.999999979 0.264166991 0.83687586 5.177175127 0.575593165 0.146034752 59.96132449 0.95908546 0.420159155 114.807229 99999995.1 -7.999999979 4.340299268 RS(ph)SLDAEIDSLTSILADLECSSPY(ph)KPRPPQSSTGSTASPPVSTPVTGHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 49 3 Q93052;A0A087WZF1;C9JUT4 Q93052 LPP Lipoma-preferred partner 2 RS(0.272)S(0.284)LDAEIDS(0.203)LT(0.203)S(0.038)ILADLECS(0.09)S(0.088)PY(0.146)KPRPPQS(0.122)S(0.119)T(0.115)GS(0.108)T(0.105)AS(0.1)PPVS(0.003)T(0.003)PVTGHK 60.267 0.0047528 433060000 57068 29341 16989 23426 28547 16280 32149 36341 38025 TRUE FALSE 49526.31921 29148.25704 25204.93722 28745.23134 27978.97055 16906.30213 29031.19493 28569.75996 33529.72782 1.477086825 0.869325787 0.751719112 0.857305836 0.83445266 0.504218293 0.865834494 0.852072528 1 15.03315315 4.736633202 4.078513774 0.80777768 1.533333881 0.734948198 0.125090351 0.117032471 4.227416012 0.031043714 0.249835661 54529.71172 -4.736633202 0.725556201 RS(ph)SLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RSSLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 49 3 Q93052;A0A087WZF1;C9JUT4 Q93052 LPP Lipoma-preferred partner 1 RS(0.5)S(0.5)LDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK;RS(0.461)S(0.461)LDAEIDS(0.034)LT(0.034)S(0.01)ILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK;RS(0.5)S(0.5)LDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK;RS(0.5)S(0.5)LDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK;RS(0.492)S(0.492)LDAEIDS(0.014)LT(0.001)SILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 208.03 1.85E-39 12703551000 838305 754604 514406.8 728494 750665 645080 995581 1122882 1138863 TRUE FALSE 727520.8703 749646.9566 763175.6491 893909.697 735728.2352 669896.645 899029.7079 882762.4226 1004227.914 0.724457925 0.746490858 0.759962593 0.890146236 0.732630736 0.667076304 0.895244691 0.879045893 1 19.9376553 1.708473691 1.584082475 0.987365059 0.761245583 0.591755492 0.065583456 0.33193457 1.468868763 0.096717788 0.020035374 51.10621188 -1.708473691 -0.226119476 RS(ph)SLLSLMTGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RSSLLSLMTGK 11 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 RS(0.5)S(0.5)LLSLMTGK;RS(0.5)S(0.5)LLSLMTGK;RS(0.5)S(0.5)LLS(0.001)LMTGK;RS(0.481)S(0.481)LLS(0.038)LMTGK 188.9 1.81E-06 4829110000 8199020 7114410 5350660 6791410 7613640 7069320 9120810 9354000 9557750 TRUE FALSE 7115498.733 7067674.972 7938257.073 8333503.441 7462143.46 7341281.315 8236275.25 7353719.893 8427843.683 0.844284612 0.838610116 0.941908437 0.988806123 0.885415504 0.871074689 0.977269579 0.87255058 1 23.00673213 4.242710301 24.99312106 0.928701856 0.841447325 0.400671624 0.046658158 103.3155446 622235.6963 0.011339961 0.027825707 17486.79832 -4.242710301 -0.087254531 RS(ph)SLPLDHGSPAQENPESEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RSSLPLDHGSPAQENPESEK 20 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5;A0A0A0MRX3 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 RS(0.448)S(0.448)LPLDHGS(0.105)PAQENPESEK;RS(0.444)S(0.444)LPLDHGS(0.113)PAQENPESEK;RS(0.46)S(0.46)LPLDHGS(0.08)PAQENPESEK 149.34 4.71E-08 1079880000 654850 765570 182530 566640 936870 754140 977060 1125050 1049520 TRUE FALSE 568309.9133 760540.9203 270802.1185 695304.2726 918228.12 783152.2538 882304.8716 884466.8126 925446.9412 0.614092379 0.821809319 0.29261766 0.751317273 0.992199638 0.846242198 0.953382449 0.955718554 1 19.81979075 3.44700445 5.49340677 0.941786776 0.58793 0.623617696 0.132785614 0.113525078 9.46049669 0.036873421 0.049030669 2799.009998 -3.44700445 -0.353856776 RS(ph)SLSLEEADSEVEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSSLSLEEADSEVEGR 16 1 Q5JTZ5 Q5JTZ5 C9orf152 Uncharacterized protein C9orf152 1 RS(0.686)S(0.308)LS(0.006)LEEADSEVEGR;RS(0.652)S(0.346)LS(0.002)LEEADSEVEGR 203.23 7.85E-13 304350000 359443 351680 204719 283618 362518 358568 327350 390832 333931 TRUE FALSE 311941.6968 349369.7909 303721.7931 348017.8017 355304.6011 372362.343 295603.6474 307255.6183 294454.0576 1.059390043 1.186500175 1.031474301 1.181908664 1.206655476 1.264585538 1.00390414 1.043475579 1 18.16768303 2.20863535 24.9993575 1.021064917 1.154458278 0.479460924 0.068342512 185.4808318 154948.0595 0.028209802 0.019021897 161.6722006 -2.20863535 0.133393361 RS(ph)SLSSHSHQSQIYR ddPTM_MDA-MB-175_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(0.453)S(0.453)LS(0.08)S(0.013)HSHQSQIYR;RS(0.5)S(0.5)LSSHSHQSQIYR;RS(0.5)S(0.5)LSSHSHQSQIYR 224.12 5.53E-13 3634490000 301056 401626 61414.6 123100 502567 571337 429689 422748 82160 TRUE FALSE 261270.6868 398987.6924 91114.90598 151051.7365 492566.9 593316.7041 388017.8269 332346.63 72447.1384 3.606363103 5.507294024 1.257674326 2.084992448 6.798983519 8.18964996 5.355875132 4.587436266 1 16.14464109 5.018247557 15.13114353 4.449803341 2.014703561 0.00817788 2.336817807 1681662.02 32872776.23 0.600816694 91080015.05 104291.1741 -5.018247557 -2.43509978 RS(ph)SLYGIAK ddPTM_MDA-MB-175_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(0.647)S(0.353)LYGIAK;RS(0.612)S(0.387)LY(0.001)GIAK 89.43 0.0074189 293310000 872180 1041800 600240 724020 1148130 1017210 1136100 1162170 1016150 TRUE FALSE 756919.2032 1034956.347 890518.0717 888419.807 1125284.459 1056342.727 1025921.197 913648.9895 896021.9046 0.844755245 1.155056971 0.993857479 0.991515723 1.255867132 1.178925115 1.144973345 1.019672605 1 19.77317448 RS(ph)SPAAFINPPIGTVTPALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSSPAAFINPPIGTVTPALK 20 1 F6VRR5;Q9BY77-2;Q9BY77;Q6R954;F8WEE2;Q8WUT1;F8WCX5 F6VRR5 POLDIP3;PDIP46 Polymerase delta-interacting protein 3 1 RS(0.5)S(0.5)PAAFINPPIGTVTPALK;RS(0.625)S(0.375)PAAFINPPIGTVTPALK 176.7 4.77E-14 1571550000 1527700 1387090 846550 1008580 1293620 1137950 1568070 1741910 1219170 TRUE FALSE 1325810.574 1377978.114 1255944.412 1237593.504 1267879.493 1181727.673 1415998.813 1369416.102 1075041.111 1.233264998 1.281791087 1.168275704 1.151205745 1.179377681 1.099239518 1.317157826 1.273826729 1 20.0359604 4.234577578 24.92727113 1.184192 1.257528049 0.131599288 0.087812875 211.4718535 1323499.501 0.022979976 0.05083303 17162.38253 -4.234577578 0.073336049 RS(ph)SPPGHYYQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RSSPPGHYYQK 11 1 D6RDK6;D6RBN5;Q9NX40;D6RI08;D6RDK1;D6RIV2;D6R9T5;D6RG39;D6RIT9;Q9NX40-3;Q9NX40-2;Q9NX40-4 D6RDK6 OCIAD1 OCIA domain-containing protein 1 1 RS(0.5)S(0.5)PPGHYYQK;RS(0.82)S(0.18)PPGHYYQK;RS(0.5)S(0.5)PPGHYYQK;RS(0.762)S(0.238)PPGHYYQK 160.79 1.66E-05 2667180000 1716910 1630150 1162080 1747560 1858290 2003450 1570240 2364000 2024570 TRUE FALSE 1490015.993 1619441.437 1724065.775 2144370.208 1821313.665 2080524.018 1417958.366 1858476.997 1785227.641 0.834636412 0.907134418 0.965740018 1.201174662 1.020213682 1.165411049 0.794273141 1.041030821 1 20.76767662 4.243473651 2.859901004 1.029414 0.854729484 0.282062904 0.108963733 0.349176198 5.693051648 0.028511298 0.08667644 17517.56151 -4.243473651 -0.174684517 RS(ph)SPPPPPSGSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSPPPPPSGSSSR 14 1 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 RS(0.5)S(0.5)PPPPPSGSSSR 53.188 0.092246 147040000 160750 118030 88020 95162 86382 103080 139200 153280 133970 TRUE FALSE 139506.4802 117254.6532 130586.7664 116769.9866 84663.1672 107045.5543 125700.4054 120502.2648 118132.2192 1.180935067 0.992571323 1.105428877 0.988468576 0.716681425 0.906150371 1.064065386 1.020062652 1 16.85004297 5.069352056 0.998968213 0.961811026 1.407538275 0.300435518 0.103401293 5.110388864 2.643369221 0.036048617 2.848615047 117314.5978 -5.069352056 0.445727249 RS(ph)SPSARPPDVPGQQPQAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RSSPSARPPDVPGQQPQAAK 20 2 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 RS(0.495)S(0.495)PS(0.009)ARPPDVPGQQPQAAK;RS(0.491)S(0.491)PS(0.017)ARPPDVPGQQPQAAK;RS(0.443)S(0.443)PS(0.113)ARPPDVPGQQPQAAK 175.21 1.18E-12 5411800000 2755320 2026770 1330850 1643320 1962540 1661260 2086930 2600650 2191590 TRUE FALSE 2391197.481 2013456.014 1974453.511 2016460.923 1923489.294 1725169.747 1884539.85 2044521.236 1932502.727 1.237357882 1.041890387 1.021708008 1.043445318 0.995335876 0.89271271 0.975180952 1.057965511 1 20.88203902 RS(ph)SPVPPVPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RSSPVPPVPER 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RS(0.5)S(0.5)PVPPVPER;RS(0.57)S(0.43)PVPPVPER;RS(0.5)S(0.5)PVPPVPER 121.99 0.00024512 5780110000 3843970 3634780 2414550 2805910 3643130 3844450 3542310 3677860 4018360 TRUE FALSE 3335979.625 3610902.891 3582234.456 3443034.751 3570638.841 3992348.479 3198777.321 2891378.26 3543314.059 0.941485731 1.019075033 1.01098418 0.971699007 1.007711646 1.126727243 0.902764268 0.816009592 1 21.75666791 2.031136135 24.64919875 0.884219885 1.011333822 0.363438206 0.06488979 140.7003429 111386.0433 0.025697159 0.017324793 107.4326121 -2.031136135 0.127113937 RS(ph)SQPSPTAVPASDSPPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSSQPSPTAVPASDSPPTK 19 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 RS(0.396)S(0.396)QPS(0.091)PT(0.118)AVPASDSPPTK;RS(0.498)S(0.498)QPS(0.004)PTAVPASDSPPTK 140.21 1.09E-07 591250000 861920 622800 570120 682060 665210 652840 852320 845020 1048530 TRUE FALSE 748015.0882 618708.7858 845831.9389 836932.1476 651973.6225 677955.1772 769662.1376 664319.049 924573.9779 0.809037574 0.669182565 0.914834247 0.905208418 0.705161121 0.73326223 0.832450573 0.718513677 1 19.81842923 1.22747272 24.99608101 1.000000463 0.784907694 0.400196767 0.082342784 526.934807 1187820.558 0.299917418 0.020128297 16.883898 -1.22747272 -0.215092769 RS(ph)SQPSPTAVPASDSPPTKQEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSQPSPTAVPASDSPPTKQEVK 23 2 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 RS(0.499)S(0.499)QPS(0.002)PTAVPASDSPPTKQEVK 104.87 0.0008321 145000000 225470 148790 84061 96117 130350 111110 248550 218180 12062 TRUE FALSE 195673.5682 147812.5887 124713.1808 117941.8339 127756.29 115384.4736 224445.6593 171523.9049 10636.0441 18.39721295 13.89732755 11.7255231 11.08888162 12.01163598 10.84843881 21.1023626 16.12666356 1 13.37667404 1.23407629 24.98972492 0.999979813 14.4065468 0.613453654 3.342787111 101.2041633 563905.7111 6.781844615 0.875939652 17.14258414 -1.23407629 13.40656698 RS(ph)SRSS(ph)PELTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSSRSSPELTR 11 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RS(0.641)S(0.348)RS(0.036)S(0.651)PELT(0.323)R;RS(0.967)S(0.034)RS(0.176)S(0.737)PELT(0.086)R 159.6 0.00074738 5129520000 4746110 4073360 2308080 3019080 4097310 3914540 4096850 4012250 3290460 TRUE FALSE 4118899.538 4046601.83 3424275.208 3704608.258 4015781.547 4065134.887 3699538.118 3154261.561 2901465.567 1.419592769 1.394675117 1.180188125 1.276805866 1.384052802 1.401062598 1.275058425 1.087127001 1 21.46835038 1.700663905 2.503150593 1.009445249 1.337087372 0.750202104 0.071185558 0.133293604 1.779194265 0.069672183 0.021163185 50.19539833 -1.700663905 0.327642123 RS(ph)SSLKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSSLKER 8 2 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 RS(0.333)S(0.333)S(0.333)LKER 65.241 0.051018 2897600000 1852500 1525000 659890 1076100 881820 704790 1790100 1625200 528100 TRUE FALSE 1607687.431 1514982.175 979015.0112 1320444.952 864273.5073 731903.7274 1616496.378 1277663.627 465668.6196 3.452428108 3.25334822 2.102385624 2.835589294 1.855984 1.571726538 3.471344878 2.743718545 1 18.82894414 4.300135733 5.957925485 2.324457374 3.385929125 0.305163962 0.695732138 0.264924221 18.0508686 0.176291099 0.473774675 19958.86006 -4.300135733 1.061471751 RS(ph)SSSGDQSSDSLNSPTLLAL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSSSSGDQSSDSLNSPTLLAL 21 1 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 1 RS(0.433)S(0.433)S(0.113)S(0.02)GDQSSDSLNSPTLLAL;RS(0.426)S(0.426)S(0.073)S(0.073)GDQS(0.001)S(0.001)DSLNSPTLLAL 117.55 0.00010985 103108000 190137 133999 84249 120366 158315 163069 147266 168875 155728 TRUE FALSE 165009.9137 133118.7517 124992.0982 147696.94 155164.8412 169342.3699 132984.166 132762.3954 137318.0132 1.201662548 0.969419442 0.910238178 1.075583141 1.129967129 1.233213079 0.968439339 0.966824325 1 17.06716136 RS(ph)STSGDTEEEEEEEVVPFSSDEQK ddPTM_MDA-MB-175_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(0.422)S(0.422)T(0.113)S(0.036)GDT(0.007)EEEEEEEVVPFSSDEQK 176.18 4.73E-13 441480000 439960 359640 300770 305870 345200 284910 451790 497980 514480 TRUE FALSE 381818.1713 357277.5012 446223.378 375322.4584 338331.1954 295870.6721 407975.4753 391490.8523 453658.7605 0.84164179 0.787546791 0.983610186 0.82732329 0.74578345 0.652187719 0.899300335 0.862963281 1 18.79124799 1.213094669 1.617343588 1.075754006 0.815221008 0.302479492 0.086772569 1.563789339 3.529729267 0.667546572 0.025845371 16.33407966 -1.213094669 -0.260532998 RS(ph)STSSEPTPTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RSSTSSEPTPTVK 13 1 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 RS(0.499)S(0.499)T(0.002)SSEPTPTVK;RS(0.489)S(0.489)T(0.016)S(0.005)SEPTPTVK;RS(0.458)S(0.458)T(0.062)S(0.021)S(0.001)EPTPTVK;RS(0.489)S(0.489)T(0.02)S(0.002)SEPTPTVK;RS(0.47)S(0.47)T(0.037)S(0.021)S(0.001)EPTPTVK;RS(0.485)S(0.485)T(0.029)S(0.001)SEPTPTVK 174.78 1.19E-05 7623250000 6425980 5713980 4126950 4795780 5816860 5465790 7887810 7955230 5747010 TRUE FALSE 5576770.462 5676444.489 6122756.824 5884735.148 5701115.866 5676062.478 7122851.4 6254065.972 5067605.025 1.10047457 1.120143433 1.208215083 1.161245819 1.125011882 1.12006805 1.40556562 1.234126563 1 22.27287265 RS(ph)SVFAAEIMDAFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSVFAAEIMDAFDR 15 1 Q9UMX3 Q9UMX3 BOK Bcl-2-related ovarian killer protein 1 RS(0.5)S(0.5)VFAAEIMDAFDR 118.32 0.00018409 22496000 22242 17443 13200 20780 24220 29268 15006 26624 28820 TRUE FALSE 19302.66335 17328.41578 19583.56415 25498.4166 23738.06939 30393.9589 13550.72043 20930.66479 25412.93243 0.759560645 0.681873917 0.770614104 1.003363806 0.934094066 1.196003609 0.53322144 0.823622573 1 14.63327524 3.945924229 7.456167548 0.893985445 0.721808556 0.19645022 0.168048116 0.480167282 59.00411639 0.046135341 0.081296459 8829.25843 -3.945924229 -0.172176889 RS(ph)SVSTIQVEWPEPDLAPAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSSVSTIQVEWPEPDLAPAIK 21 1 Q96B33 Q96B33 CLDN23 Claudin-23 1 RS(0.49)S(0.49)VS(0.014)T(0.005)IQVEWPEPDLAPAIK;RS(0.499)S(0.499)VS(0.002)TIQVEWPEPDLAPAIK 199.1 5.02E-22 173914000 338020 249070 187896 270190 307310 272500 204559 385270 243950 TRUE FALSE 293349.8006 247433.8428 278763.1341 331540.7691 301195.1322 282983.2513 184720.8997 302883.0087 215110.5089 1.363716734 1.150263853 1.295906627 1.54125789 1.400187902 1.315524996 0.858725595 1.408034457 1 17.71471848 2.447479555 24.99808529 1.137427036 1.347857183 0.330807361 0.167307072 280.0071913 236140.0751 0.061787681 0.04786108 280.2073706 -2.447479555 0.210430148 RS(ph)TSPIIGSPPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSTSPIIGSPPVR 13 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 RS(0.401)T(0.401)S(0.197)PIIGSPPVR 66.022 0.029521 0 365010 327010 121610 129440 192010 207950 195690 213250 80830 TRUE FALSE 316773.0037 324861.8498 180421.0028 158831.3304 188189.3767 215949.9711 176712.0139 167648.147 71274.36948 4.44441678 4.557905628 2.531358805 2.228449463 2.640351336 3.029840497 2.47932062 2.352151948 1 16.12109575 7.999999989 0.374671928 1.995925385 41.26301413 0.670191037 0.599712059 50.87254398 0.748592299 0.690871791 1430.277595 99999997.51 -7.999999989 39.26708875 RS(ph)WGQQAQEYQEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSWGQQAQEYQEQK 14 1 Q5VZK9;Q5VZK9-2 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 RS(1)WGQQAQEYQEQK;RS(1)WGQQAQEYQEQK 266.28 4.61E-25 1094290000 558730 656920 499930 550210 768160 671700 849980 926910 798920 TRUE FALSE 484892.4149 652604.6493 741697.8202 675143.5899 752875.1189 697540.7336 767549.0704 728697.5097 704472.5877 0.688305583 0.926373376 1.052841279 0.958367439 1.068707473 0.990160222 1.089537171 1.034387317 1 19.42618404 4.712052189 2.173846272 1.029931292 0.608223707 0.882386077 0.039110482 0.175867098 0.99145846 0.009481901 0.140920436 51529.05627 -4.712052189 -0.421707584 RS(ph)YDVPPPPMEPDHPFYSNISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RSYDVPPPPMEPDHPFYSNISK 22 1 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 1 RS(0.839)Y(0.161)DVPPPPMEPDHPFYSNISK;RS(0.99)Y(0.01)DVPPPPMEPDHPFYSNISK;RS(0.991)Y(0.009)DVPPPPMEPDHPFYSNISK;RS(0.735)Y(0.265)DVPPPPMEPDHPFYSNISK;RS(0.998)Y(0.002)DVPPPPMEPDHPFYSNISK;RS(0.525)Y(0.475)DVPPPPMEPDHPFYSNISK 173.96 1.49E-12 1872460000 1564554 1660962 921505 1193250 1662771 1281594 1746206 2039290 1788558 TRUE FALSE 1357794.225 1650051.031 1367147.9 1464195.65 1629685.11 1330897.75 1576859.211 1603203.703 1577116.711 0.860934524 1.046245354 0.866865395 0.928400314 1.033331965 0.843880317 0.999836727 1.01654094 1 20.588858 2.033700384 24.96533266 1.009073177 0.935730543 0.216543244 0.067251353 258.6071441 191575.7259 0.025399445 0.017124238 108.0688137 -2.033700384 -0.073342634 RSAPGGGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RSAPGGGSK 9 1 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 0 ;;; 163.9 0.00010049 414006000 779040 578700 318651 403916 389198 553380 725570 838040 548190 FALSE TRUE 676087.8902 574898.4816 472751.6894 495631.3013 381453.7213 574668.8867 655204.3331 658831.6676 483383.6027 1.398657063 1.189321438 0.978005226 1.025337431 0.789132522 1.188846464 1.355454197 1.362958247 1 18.88280901 2.484436533 24.56039963 1.270332944 1.065600208 0.140048924 0.182837858 437.5203224 1468945.567 0.06837959 0.055272885 305.0960137 -2.484436533 -0.204732736 RSAS(ph)PDDDLGSSNWEAADLGNEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RSASPDDDLGSSNWEAADLGNEER 24 1 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 RS(0.034)AS(0.966)PDDDLGSSNWEAADLGNEER;RS(0.003)AS(0.997)PDDDLGSSNWEAADLGNEER;RS(0.21)AS(0.79)PDDDLGSSNWEAADLGNEER;RS(0.038)AS(0.962)PDDDLGSSNWEAADLGNEER;RS(0.101)AS(0.899)PDDDLGSSNWEAADLGNEER 365.67 8.44E-119 9054220000 2560620 2222190 1389811 1566127 2051199 2162860 2224560 2517670 1281654 TRUE FALSE 2222227.579 2207592.288 2061928.248 1921740.072 2010384.153 2246066.624 2008822.514 1979285.863 1130138.324 1.966332379 1.953382378 1.824491926 1.700446778 1.778883266 1.987426296 1.777501453 1.751366024 1 20.10806793 1.160232744 2.567005003 0.66420185 1.853113381 0.89055264 0.093352534 0.226059023 1.373694031 0.64863165 0.025796871 14.46214609 -1.160232744 1.188911531 RSAS(ph)PHDVDLCLVSPCEFEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RSASPHDVDLCLVSPCEFEHR 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 RS(0.227)AS(0.773)PHDVDLCLVSPCEFEHR;RS(0.184)AS(0.816)PHDVDLCLVSPCEFEHR;RS(0.148)AS(0.852)PHDVDLCLVSPCEFEHR;RS(0.152)AS(0.848)PHDVDLCLVSPCEFEHR;RS(0.063)AS(0.937)PHDVDLCLVSPCEFEHR 173.07 2.25E-12 1853460000 629833 610324 289430 299748 599165 628956 611624 674948 221764 TRUE FALSE 546598.9733 606314.7415 429399.3161 367810.3648 587242.7887 653152.3443 552308.7986 530615.6227 195547.3126 2.79522621 3.100603805 2.195884518 1.88092774 3.003072663 3.340124371 2.824425411 2.713489721 1 17.57715818 4.251292711 24.99321086 2.504223567 2.947915077 0.089624647 0.657164744 678.0273727 1330948.687 0.16692986 0.435358725 17835.80483 -4.251292711 0.44369151 RSCFESS(ph)PDPELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSCFESSPDPELK 13 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RS(0.02)CFES(0.128)S(0.853)PDPELK 122.93 0.00014045 155970000 333420 224990 165890 202140 260240 197190 283130 340380 224210 TRUE FALSE 289357.7022 223512.0259 246114.9589 248038.9765 255061.7332 204776.0269 255672.0962 267592.3858 197704.1492 1.463589426 1.130537861 1.244864915 1.254596717 1.290118261 1.035770001 1.293205515 1.353499089 1 17.59298362 4.751791905 24.2002527 1.217396344 1.463589678 0.331581344 0.115225171 1794.185606 3281504.002 0.027406194 0.490489174 56466.63465 -4.751791905 0.246193333 RSDAEEVDFAGWLCSTIGLNQPS(ph)TPTHAAGV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSDAEEVDFAGWLCSTIGLNQPSTPTHAAGV 31 1 Q02750;Q02750-2;H3BRW9 Q02750 MAP2K1 Dual specificity mitogen-activated protein kinase kinase 1 1 RSDAEEVDFAGWLCSTIGLNQPS(0.537)T(0.461)PT(0.002)HAAGV 148.1 8.80E-09 77045000 36811 45256 37380 44197 54495 61276 66879 70940 62424 TRUE FALSE 31946.33308 44958.71036 55457.09303 54232.60436 53410.65612 63633.32737 60393.08487 55770.03306 55044.30583 0.580374893 0.816773137 1.007499181 0.98525367 0.970321186 1.15603833 1.09717225 1.01318442 1 15.74830571 4.974814757 0.994495439 1.049376515 0.126639622 0.884356436 0.054278497 0.935429516 0.547421148 0.018263453 1.027732276 94365.82836 -4.974814757 -0.922736893 RSDAEEVDFAGWLCSTIGLNQPST(ph)PTHAAGV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RSDAEEVDFAGWLCSTIGLNQPSTPTHAAGV 31 1 Q02750;Q02750-2;H3BRW9 Q02750 MAP2K1 Dual specificity mitogen-activated protein kinase kinase 1 1 RSDAEEVDFAGWLCSTIGLNQPS(0.144)T(0.83)PT(0.026)HAAGV;RSDAEEVDFAGWLCSTIGLNQPS(0.032)T(0.964)PT(0.004)HAAGV;RSDAEEVDFAGWLCSTIGLNQPS(0.118)T(0.846)PT(0.036)HAAGV;RSDAEEVDFAGWLCSTIGLNQPS(0.034)T(0.962)PT(0.003)HAAGV;RSDAEEVDFAGWLCSTIGLNQPS(0.129)T(0.866)PT(0.005)HAAGV;RSDAEEVDFAGWLCSTIGLNQPS(0.026)T(0.974)PTHAAGV;RSDAEEVDFAGWLCSTIGLNQPS(0.155)T(0.824)PT(0.021)HAAGV 225.73 2.13E-35 907153000 378110 431203 321292 398764 518945 592059 579377 609625 565459 TRUE FALSE 328141.8055 428370.3991 476669.8859 489309.4609 508619.0098 614835.8928 523189.1077 479261.4379 498611.0812 0.658111739 0.859127314 0.955995372 0.981344939 1.020071613 1.233097129 1.049292981 0.961192914 1 18.92755542 4.857614366 0.950688462 1.045345439 0.381908974 0.749883648 0.072448565 1.379113787 0.858992432 0.026584545 0.993448146 72046.74519 -4.857614366 -0.663436465 RSDS(ph)ASSEPVGIYQGFEK ddPTM_MDA-MB-175_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(0.112)DS(0.868)AS(0.019)S(0.002)EPVGIYQGFEK;RS(0.253)DS(0.531)AS(0.188)S(0.028)EPVGIYQGFEK;RS(0.008)DS(0.949)AS(0.038)S(0.005)EPVGIYQGFEK;RS(0.014)DS(0.871)AS(0.058)S(0.058)EPVGIYQGFEK 245.94 1.84E-24 1955220000 1736590 1569490 812700 1370520 1644290 1112020 2268000 2273100 1198670 TRUE FALSE 1507095.232 1559179.917 1205724.438 1681717.513 1611571.846 1154800.129 2048049.709 1787015.254 1056964.598 1.42587106 1.475148666 1.1407425 1.591082157 1.524716957 1.092562732 1.937671056 1.690704928 1 20.01149563 2.248070696 24.99999069 1.590060527 1.385548378 0.065664175 0.278122831 451.1086256 1185871.023 0.103234169 0.0788982 177.0397126 -2.248070696 -0.204512149 RSDS(ph)LLSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RSDSLLSFR 9 1 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 RSDS(1)LLSFR;RS(0.005)DS(0.995)LLSFR;RSDS(1)LLSFR;RSDS(1)LLSFR 200.98 1.36E-05 473383000 188105 164162.8 96531.9 109179.9 142053.2 173481 123341.8 148928 131614.3 TRUE FALSE 163246.4477 163084.4038 143215.0497 133970.865 139226.6192 180154.9263 111380.1312 117080.9062 116055.0074 1.406629936 1.405233668 1.23402732 1.154373844 1.199660595 1.552323595 0.959718445 1.008839763 1 16.82444925 2.211438305 24.99999287 0.992302556 1.311365605 0.650719202 0.115685152 142.3400575 131200.9407 0.048636072 0.032799767 162.7190144 -2.211438305 0.319063049 RSDS(ph)PEIPFQAAAGPSDGLDAS(ph)SPGNSFVGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 32 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 RS(0.03)DS(0.97)PEIPFQAAAGPSDGLDAS(0.562)S(0.438)PGNSFVGLR;RS(0.211)DS(0.789)PEIPFQAAAGPS(0.001)DGLDAS(0.732)S(0.251)PGNS(0.017)FVGLR 216.32 3.05E-35 125217000 80789 75555 52904 58552 75826 87356 77536 101390 60423 TRUE FALSE 70112.52896 75058.67423 78488.55135 71847.12651 74317.21095 90716.64185 70016.57065 79708.53752 53279.86177 1.315929258 1.408762556 1.473137293 1.348485603 1.394846167 1.702644092 1.314128234 1.496034991 1 15.70130272 1.233609763 24.99999897 0.999999335 1.434532047 0.589444841 0.113217497 106.6688767 538575.1973 0.211584831 0.026259955 17.12417917 -1.233609763 0.434532712 RSDS(ph)PEIPFQAAAGPSDGLDASSPGNSFVGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RSDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 32 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 RS(0.049)DS(0.951)PEIPFQAAAGPSDGLDASSPGNSFVGLR;RS(0.039)DS(0.961)PEIPFQAAAGPSDGLDASSPGNSFVGLR;RS(0.149)DS(0.851)PEIPFQAAAGPSDGLDASSPGNSFVGLR;RS(0.146)DS(0.854)PEIPFQAAAGPSDGLDASSPGNSFVGLR;RS(0.042)DS(0.958)PEIPFQAAAGPSDGLDASSPGNSFVGLR;RS(0.007)DS(0.993)PEIPFQAAAGPSDGLDASSPGNSFVGLR 241.72 5.20E-47 3791500000 940121 923931 559993 575561 933214 967994 934382 1042605 468884 TRUE FALSE 815881.6279 917861.6364 830807.4879 706250.9219 914644.8672 1005233.356 843765.7775 819652.0343 413453.0677 1.973335529 2.219989905 2.009436023 1.708176761 2.212209653 2.431311881 2.040777644 1.982454838 1 18.65736405 1.215743961 3.408874853 0.797800492 2.087211944 0.763965286 0.187993566 0.178520347 2.838393922 0.627001118 0.05019064 16.43402566 -1.215743961 1.289411452 RSDS(ph)PENKYSDSTGHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RSDSPENKYSDSTGHSK 17 2 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5;Q9BTA9-3;A0A494C0B7;A0A494C0C1;A0A494C0S5;C9JVK6;C9JD58;J3QTA0;E9PMZ7;C9JMU2 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 RS(0.001)DS(0.947)PENKYS(0.05)DS(0.001)T(0.001)GHSK;RSDS(1)PENKYSDSTGHSK;RS(0.002)DS(0.998)PENKYSDSTGHSK;RS(0.008)DS(0.866)PENKY(0.001)S(0.088)DS(0.019)T(0.019)GHSK;RS(0.029)DS(0.794)PENKY(0.001)S(0.146)DS(0.015)T(0.015)GHSK 226.99 9.91E-16 849748000 1139702 867450 308432 438015 719937 655499 1131757 1178699 306265.4 TRUE FALSE 989087.4931 861751.6638 457590.7468 537473.0004 705611.6622 680716.4707 1021999.38 926643.3915 270059.0533 3.662485967 3.190974912 1.694409949 1.990205452 2.612805065 2.520620814 3.784355191 3.431262089 1 18.04291539 2.373337314 19.09351404 2.958724633 2.568042972 0 0.908551447 9.208467047 1658.811999 0.346858828 0.268673783 236.2312317 -2.373337314 -0.390681661 RSDS(ph)VSASER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RSDSVSASER 10 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 RS(0.001)DS(0.998)VS(0.001)ASER;RSDS(0.999)VS(0.001)ASER;RSDS(0.987)VS(0.013)ASER 165.02 3.66E-06 848600000 344466 292768 208147 215168 255276 257121 293231 266504 215551 TRUE FALSE 298943.9453 290844.7877 308807.5854 264025.183 250196.507 267012.6112 264793.5028 209514.1935 190068.8063 1.572819607 1.530207893 1.624714709 1.389103179 1.316347021 1.404820793 1.393145503 1.102307094 1 17.53616225 0.3137729 0.357025931 6.82E-18 1.590140521 0.84710557 0.076582585 6.23978294 0.424453557 4.83246889 0.124583392 2.059552657 -0.3137729 1.590140521 RSDSAS(ph)SEPVGIYQGFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSDSASSEPVGIYQGFEK 18 1 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 1 RS(0.004)DS(0.333)AS(0.632)S(0.031)EPVGIYQGFEK 230.03 9.53E-20 867650000 718380 674150 346790 544660 689880 462700 951620 985350 438150 TRUE FALSE 623444.2629 669721.4643 514498.8039 668333.3776 676152.7377 480500.3684 859332.0389 774640.5705 386352.4061 1.613667349 1.733447116 1.33168267 1.729854317 1.750093249 1.243684162 2.224218163 2.005010343 1 18.55955786 2.249177017 24.99906079 1.817693449 1.57965301 0.038058104 0.352728608 520.7526918 1226248.046 0.130597796 0.100085587 177.4912782 -2.249177017 -0.238040439 RSDSMT(ph)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSDSMTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR 38 1 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 RS(0.326)DS(0.252)MT(0.422)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR;RS(0.255)DS(0.255)MT(0.49)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR 208.9 6.46E-31 1052830000 205810 209914 107088 115475 153863 179694 188417 206509 96955 TRUE FALSE 178611.687 208535.0611 158876.115 141695.3637 150801.4273 186606.9445 170144.3483 162348.6574 85493.09035 2.089194417 2.439203686 1.858350357 1.657389657 1.763901933 2.182713757 1.990153212 1.898968171 1 16.3835202 1.226286444 3.732749979 0.857104673 1.991135354 0.670037725 0.218173731 0.191401124 4.167474622 0.619157509 0.059661054 16.83784256 -1.226286444 1.13403068 RSDSVS(ph)ASER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSDSVSASER 10 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 RSDS(0.336)VS(0.664)ASER 189.52 1.06E-06 306330000 529780 482020 240060 331290 451360 467010 545240 471560 351360 TRUE FALSE 459768.2307 478853.5789 356153.819 406514.458 442378.8191 484976.1769 492362.7087 370720.5637 309822.6211 1.483972439 1.545573326 1.149541043 1.312087725 1.427845448 1.565334949 1.589176113 1.196557444 1 18.24108296 1.512443717 4.109411875 1.030185326 1.431087443 0.56026688 0.13112334 0.14339806 5.045712224 0.124778323 0.036622703 32.54196073 -1.512443717 0.400902117 RSDSVSASER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSDSVSASER 10 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 142.97 5.58E-05 263980000 98217 87028 49631 59053 87671 100130 82268 93375 66739 FALSE TRUE 85237.3746 86456.30734 73632.71761 72461.88622 85926.51863 103982.0659 74289.66202 73407.4829 58849.19145 1.448403495 1.469116316 1.251210353 1.231314899 1.460113835 1.766924291 1.262373538 1.247383033 1 15.84473497 1.463726864 1.85794322 0.971426897 1.420396536 0.44005431 0.152614271 0.533313984 2.750443436 0.379047339 0.045421591 29.08887087 -1.463726864 0.448969639 RSEACPCQPDSGS(ph)PLPAEEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSEACPCQPDSGSPLPAEEEK 21 1 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 RSEACPCQPDS(0.011)GS(0.989)PLPAEEEK 153.06 2.86E-08 554560000 215500 174870 127060 203200 212010 187940 197380 304110 236160 TRUE FALSE 187021.129 173721.2675 188506.641 249339.6657 207791.4158 195170.1734 178238.118 239078.4431 208241.4338 0.898097586 0.834230077 0.90523119 1.197358571 0.99783896 0.937230261 0.855920528 1.148082966 1 17.66789762 3.980121237 24.63239088 1.023116971 0.867055488 0.333167175 0.096909066 690.9531487 856185.5426 0.026152638 0.046135211 9552.592176 -3.980121237 -0.156061483 RSECNMCNTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSECNMCNTPK 11 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 0 ; 135.26 0.00019831 222827000 259490 190381 108112 135992 181563 161953 207848 245940 189179 FALSE TRUE 225197.739 189130.3747 160395.3248 166871.0621 177950.2515 168183.4367 187690.933 193347.6449 166814.4741 1.349989203 1.133776764 0.961519231 1.000339227 1.066755463 1.008206498 1.125147766 1.159057965 1 17.34788495 4.676338598 3.370761429 1.057542237 1.37016112 0.705485723 0.0614489 0.167067555 3.161609507 0.017106315 0.121242958 47461.18726 -4.676338598 0.312618883 RSEEVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSEEVVR 7 1 O14907;A0A087X282 O14907 TAX1BP3 Tax1-binding protein 3 0 126.52 0.0063237 242980000 268810 240840 155340 161210 198840 230330 211150 218710 217370 FALSE TRUE 233286.0774 239257.9062 230462.9436 197815.1944 194883.473 239190.9441 190672.7055 171940.5685 191672.7662 1.217106019 1.248262395 1.202377094 1.032046432 1.016750981 1.247913039 0.994782458 0.897052679 1 17.54828584 2.477832733 0.063967112 2.48E-08 2.10282033 0.522942516 0.086650473 63.58945665 3.240205997 57.01926513 48.94650964 300.4918744 -2.477832733 2.102820305 RSELIAK ddPTM_MDA-MB-175_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 ;;; 125.31 0.0065119 3686680000 5338420 4350390 2548440 3164350 3739540 3520820 4504010 4970520 4742990 FALSE TRUE 4632934.271 4321812.002 3780874.108 3882864.032 3665130.47 3656268.224 4067211.803 3907612.979 4182279.125 1.107753484 1.03336288 0.904022423 0.92840863 0.876347647 0.874228648 0.972486934 0.934326204 1 21.99585792 4.422058517 3.36137309 0.926593779 1.098571387 0.713333583 0.039143771 0.127465797 2.816329452 0.010434432 0.037966067 26427.64822 -4.422058517 0.171977608 RSES(ph)PPAELPSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSESPPAELPSLR 13 1 Q14669-3;Q14669;Q14669-2;G5E9G6;H7C1L9 Q14669-3;H7C1L9 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 RS(0.062)ES(0.938)PPAELPSLR;RS(0.377)ES(0.623)PPAELPSLR 113.88 0.00048194 353870000 347100 352750 263390 273410 341770 340490 297720 319210 316930 TRUE FALSE 301229.8556 350432.762 390766.285 335491.9193 334969.4457 353588.8706 268847.1602 250949.4256 279462.8964 1.077888548 1.253950941 1.398276086 1.200488235 1.198618671 1.265244421 0.96201379 0.89797046 1 18.09229723 2.218412868 7.767729233 0.941006138 1.238079046 0.717783793 0.082334488 0.085386776 23.30962061 0.033434927 0.023144658 165.3533006 -2.218412868 0.297072908 RSET(ph)PPHWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSETPPHWR 9 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 RS(0.008)ET(0.992)PPHWR;RS(0.005)ET(0.995)PPHWR 78.705 0.017004 622060000 367760 351090 229000 239560 341450 399130 273800 319150 325540 TRUE FALSE 319159.5842 348783.6667 339745.166 293955.7594 334655.813 414484.7894 247246.9181 250902.2561 287055.0321 1.111841106 1.215041117 1.18355412 1.024039737 1.165824583 1.443921001 0.861322362 0.874056289 1 18.13096782 2.201765469 24.99984066 0.901827861 1.182778637 0.580804567 0.111457199 117.5595894 79873.07895 0.04546121 0.030650877 159.1349122 -2.201765469 0.280950776 RSFS(ph)KEVEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.03)FS(0.97)KEVEER 58.674 0.086286 620550000 135300 113070 98906 106540 139630 143170 162470 174540 118400 TRUE FALSE 117419.7622 112327.2357 146737.2724 130731.5354 136851.6362 148677.8425 146713.6844 137215.9793 104402.8869 1.124679266 1.075901626 1.405490565 1.252183146 1.310803181 1.424077887 1.405264632 1.31429296 1 16.67180208 4.250500729 24.99288916 1.311322525 1.100290329 0.32121703 0.121117233 248.8110205 520798.2356 0.029874535 0.077707647 17803.30899 -4.250500729 -0.211032196 RSFS(ph)SQRPVDR ddPTM_MDA-MB-175_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(0.291)FS(0.678)S(0.031)QRPVDR 91.093 0.0086618 233520000 263220 292760 174410 154690 295280 343340 236970 284840 198600 TRUE FALSE 228434.8101 290836.8403 258755.2594 189814.7288 289404.5057 356548.512 213988.6859 223929.1826 175121.7342 1.304434376 1.66076953 1.477573646 1.083901605 1.652590451 2.036003775 1.221942478 1.27870583 1 17.41799862 1.749480651 2.304168618 1.086610619 1.521229073 0.281125365 0.261527422 0.383277767 4.069371558 0.240755118 0.075159555 56.16692545 -1.749480651 0.434618454 RSGS(ph)FGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSGSFGK 7 1 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 RS(0.015)GS(0.985)FGK;RS(0.087)GS(0.913)FGK 72.321 0.031803 609850000 1886540 1756030 1216770 1338680 1268760 1810090 2060220 2426650 2008040 TRUE FALSE 1637228.959 1744494.523 1805204.042 1642647.754 1243514.158 1879725.334 1860420.182 1907729.782 1770651.799 0.924647613 0.985227318 1.019513855 0.927707952 0.702291754 1.061600782 1.050697931 1.07741668 1 20.7558491 RSGS(ph)PLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RSGSPLEK 8 1 B1AKL4;Q9NRA8;Q9NRA8-3;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 RS(0.104)GS(0.896)PLEK;RS(0.128)GS(0.872)PLEK;RS(0.293)GS(0.707)PLEK;RS(0.288)GS(0.712)PLEK 88.338 0.0089953 1763330000 2991640 2633510 1569310 1916840 1906070 2131090 2922280 3313000 2718080 TRUE FALSE 2596287.194 2616210.299 2328233.565 2352087.819 1868142.936 2213074.411 2638877.735 2604540.732 2396751.679 1.083252478 1.091565022 0.971412093 0.981364836 0.779447847 0.923364081 1.101022588 1.086696112 1 21.19264901 0.905784 21.12412902 0.511643566 1.004994192 0 0.099295439 17999.78507 4086755.662 860527.9867 0.026122418 8.049779788 -0.905784 0.493350626 RSIQFVDWCPTGFK ddPTM_MDA-MB-175_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 98.312 0.0042137 577550000 358160 279020 177660 141530 482200 408040 534810 512770 184300 FALSE TRUE 310828.2485 277187.0992 263576.9702 173666.5497 472605.1634 423737.5628 482944.2085 403118.1259 162512.264 1.912644874 1.705638039 1.62188972 1.068636578 2.90811999 2.607418988 2.971740081 2.480539721 1 17.31018907 3.235703195 24.99999889 2.458491725 1.589568248 0.326829359 0.577900417 85.37555526 746963.3112 0.173597739 0.205604859 1720.692218 -3.235703195 -0.868923477 RSIS(ph)QQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSISQQK 7 1 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 RS(0.021)IS(0.979)QQK 66.758 0.070978 37414000 72541 56747 39522 42763 48402 49239 66355 70851 70160 TRUE FALSE 62954.52305 56374.22522 58634.97139 52472.99274 47438.8949 51133.25619 59919.90231 55700.06501 61865.76473 1.017598721 0.911234598 0.947777364 0.848174964 0.766803661 0.826519423 0.968547024 0.900337453 1 15.91685365 4.985950046 1.373932622 0.888652851 1.137114503 0.243984927 0.068539096 3.658872516 4.005225576 0.020663249 1.477456973 96816.64881 -4.985950046 0.248461652 RSIS(ph)SPNVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RSISSPNVNR 10 1 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 RS(0.234)IS(0.646)S(0.121)PNVNR;RSIS(0.92)S(0.08)PNVNR;RSIS(0.956)S(0.044)PNVNR;RSIS(0.652)S(0.347)PNVNR;RS(0.052)IS(0.897)S(0.052)PNVNR;RS(0.231)IS(0.505)S(0.263)PNVNR;RS(0.001)IS(0.913)S(0.085)PNVNR 170.63 2.61E-06 6281590000 2190656 2453945 1259495 1369527 2355178 2350151 2104300 2208763 1455927 TRUE FALSE 1901155.259 2437824.874 1868590.995 1680499.037 2308314.566 2440562.83 1900225.31 1736436.221 1283808.969 1.480870835 1.898900018 1.455505484 1.308994623 1.798020283 1.9010327 1.480146467 1.352565891 1 20.29199911 1.429319156 1.779299316 0.920036115 1.633777793 0.517826983 0.19589436 0.504162433 2.187279966 0.561839927 0.057062894 26.87318586 -1.429319156 0.713741677 RSLS(ph)GSSPCPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSLSGSSPCPK 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RS(0.061)LS(0.313)GS(0.313)S(0.313)PCPK 69.602 0.057258 23217000 131050 113130 59626 70225 106840 83358 123560 143310 82346 TRUE FALSE 113731.4105 112386.8416 88461.33304 86170.65957 104714.093 86564.8362 111577.1702 112664.2717 72611.14969 1.566307805 1.547790416 1.218288561 1.186741429 1.442121403 1.192170026 1.53663963 1.551611181 1 16.14790348 4.284993227 12.2330303 1.335297459 1.557411491 0.257450057 0.172427804 1.427150986 371.1285429 0.044005105 0.116302053 19274.94852 -4.284993227 0.222114031 RSNS(ph)PDKFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RSNSPDKFK 9 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 RS(0.022)NS(0.978)PDKFK;RS(0.016)NS(0.984)PDKFK;RSNS(1)PDKFK;RS(0.005)NS(0.995)PDKFK 136.93 0.00014086 16244700000 18056700 11346800 11163700 11379900 10222000 7748900 16206600 18982000 14358700 TRUE FALSE 15670461.35 11272262.12 16562502.66 13963880.23 10018602.2 8047005.197 14634886.43 14922847.02 12661230.84 1.237672825 0.890297497 1.308127374 1.102884893 0.791281853 0.635562632 1.15588181 1.178625301 1 23.59391433 4.766037565 22.46849846 1.022069601 1.237674023 0.114306398 0.197562128 5990.387855 4898151.712 0.05145912 3.526586662 58349.55729 -4.766037565 0.215604422 RSNVSSPATPTAS(ph)SSSSTTPTRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSNVSSPATPTASSSSSTTPTRK 23 2 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 RSNVSSPATPTAS(0.164)S(0.164)S(0.132)S(0.132)S(0.132)T(0.132)T(0.132)PT(0.01)RK 75.226 0.0091048 58547000 24088 24173 13750 20166 27454 22456 25904 31293 16340 TRUE FALSE 20904.70977 24014.20597 20399.54599 24744.99852 26907.71911 23319.89685 23391.83407 24601.23547 14408.30381 1.450879301 1.666692088 1.415818701 1.717412323 1.867514696 1.618503965 1.623496726 1.707434531 1 13.81461289 1.234896714 24.99994925 0.999999093 1.640174887 0.704042787 0.129010083 59.72932879 407489.3848 0.227742836 0.031515794 17.17499875 -1.234896714 0.640175794 RSNVSSPATPTASS(ph)SSSTTPTRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSNVSSPATPTASSSSSTTPTRK 23 2 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 RSNVSSPATPT(0.001)AS(0.035)S(0.16)S(0.16)S(0.16)S(0.16)T(0.16)T(0.16)PT(0.006)RK 82.486 0.0045216 77814000 27122 23070 13807 16715 26428 24353 29706 36341 17873 TRUE FALSE 23537.75898 22918.45165 20484.11138 20510.39622 25902.13451 25289.87567 26825.11669 28569.75996 15760.0743 1.493505585 1.454209619 1.299747133 1.301414945 1.643528705 1.604679977 1.702093288 1.812793481 1 13.94398672 3.232001576 24.99349918 1.598954517 1.385756322 0.100504562 0.223093833 270.655603 1031342.996 0.066289521 0.076918563 1706.088581 -3.232001576 -0.213198195 RSPLSDPPSQDPT(ph)PAATPETPPVISAVVHATDEEK ddPTM_MDA-MB-175_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 1 RS(0.001)PLS(0.001)DPPS(0.054)QDPT(0.295)PAAT(0.295)PET(0.295)PPVIS(0.05)AVVHAT(0.012)DEEK 47.006 0.064444 26943000 21688 23598 13239 20839 29843 27502 34657 41944 33955 TRUE FALSE 18821.87585 23442.98318 19641.42468 25570.81345 29249.18269 28560.01974 31295.96947 32974.60201 29940.87858 0.628634721 0.782975794 0.656006958 0.854043524 0.976897943 0.953880483 1.045258889 1.101323794 1 14.86982894 3.345195037 1.069547019 1.054305775 0.673326605 0.879062424 0.055386753 0.156038671 0.387215433 0.023393384 0.038756694 2214.088809 -3.345195037 -0.380979169 SPLDPMT(ph)SPGSGLILQANFVHSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPLDPMTSPGSGLILQANFVHSQR 24 0 Q08499-10;A0A087WSZ7;A0A1B0GW84;Q08499-2;Q08499-9;Q08499-6;Q08499-11;Q08499;A0A1W2PQN6;Q08499-7;Q08499-12 Q08499-10 PDE4D "cAMP-specific 3,5-cyclic phosphodiesterase 4D" 1 SPLDPMT(0.526)S(0.464)PGS(0.011)GLILQANFVHSQR;S(0.002)PLDPMT(0.537)S(0.455)PGS(0.007)GLILQANFVHSQR;S(0.003)PLDPMT(0.744)S(0.249)PGS(0.004)GLILQANFVHSQR 101.49 0.013706 988638000 202299 292708 242126 334584 408538 483915 415015 494035 439011 TRUE FALSE 175564.6746 290785.1819 359218.9435 410556.411 400408.8931 502531.5232 374766.9092 388389.4598 387111.6197 0.453524683 0.751166245 0.927946683 1.060563388 1.034349972 1.298156649 0.968110721 1.00330096 1 18.56239009 4.590023513 1.291188673 1.059906343 0.286438025 0.828118498 0.090875316 0.43412885 0.778254896 0.02785132 0.414503288 38906.62086 -4.590023513 -0.773468317 down RSQS(ph)FSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSQSFSK 7 1 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 RSQS(0.989)FS(0.011)K;RS(0.004)QS(0.987)FS(0.009)K 70.441 0.034924 314160000 415770 378060 292631 377870 400240 382730 465330 512570 420800 TRUE FALSE 360824.9411 375576.499 434148.3304 463671.1589 392276.0071 397453.8708 420202.3682 402960.8943 371053.5034 0.972433727 1.012189605 1.170042397 1.249607279 1.057195266 1.071149759 1.132457622 1.085991348 1 18.5012677 4.389897409 6.038506119 1.110108252 0.982005906 0.350538792 0.067276719 0.213020559 11.45212336 0.017528478 0.047976226 24541.29122 -4.389897409 -0.128102346 RSQS(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RSQSPVK 7 1 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3;Q7Z309-5 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 RS(0.205)QS(0.795)PVK;RS(0.035)QS(0.965)PVK;RS(0.132)QS(0.868)PVK 53.756 0.084382 331650000 1168240 1081630 934090 864600 545350 815470 1105110 1277800 1248400 TRUE FALSE 1013854.124 1074524.701 1385819.048 1060920.645 534498.602 846841.6586 997936.6023 1004552.414 1100815.574 0.921002707 0.976116914 1.258902109 0.963758753 0.48554782 0.769285681 0.906542954 0.912552872 1 20.07014136 3.469561623 24.9991869 0.82188986 1.055570291 0.321552071 0.159432124 223.8840872 740365.8629 0.048401316 0.062611604 2948.231778 -3.469561623 0.233680431 RSQS(ph)VTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSQSVTR 7 1 Q9H3Q1;J3KRZ9 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 RS(0.007)QS(0.938)VT(0.055)R;RS(0.016)QS(0.804)VT(0.18)R 95.523 0.014198 15806000 115694 94813 56061 51706 54322 98951 91309 89183 89155 TRUE FALSE 100404.7448 94190.16716 83172.28711 63446.63758 53241.09848 102757.709 82453.86723 70111.90947 78615.19747 1.277167113 1.198116524 1.057967032 0.807053084 0.67723672 1.307097257 1.048828597 0.891836588 1 16.26252061 4.185147295 3.000377165 0.956628614 1.253387586 0.333341872 0.163617353 0.300209276 5.397944117 0.044798738 0.122254708 15316.06833 -4.185147295 0.296758972 RSS(ph)DGS(ph)LSHEEDLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RSSDGSLSHEEDLAK 15 1 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 2 RS(0.197)S(0.811)DGS(0.87)LS(0.122)HEEDLAK;RS(0.499)S(0.603)DGS(0.871)LS(0.027)HEEDLAK;RS(0.117)S(0.892)DGS(0.985)LS(0.007)HEEDLAK 154.08 8.89E-06 2569440000 1770190 1754270 1203650 1303600 1667460 1419450 2021010 2321420 1946320 TRUE FALSE 1536254.906 1742746.085 1785739.166 1599602.304 1634280.808 1474057.16 1825012.761 1825002.398 1716228.267 0.895134369 1.015451219 1.040502129 0.932045192 0.952251422 0.858893417 1.063385796 1.063379758 1 20.71081002 2.190872962 24.99999936 1.047536746 0.955594322 0.385741527 0.054900291 125.2926141 65683.04197 0.022910709 0.015446437 155.193298 -2.190872962 -0.091942424 RSS(ph)DGSLSHEEDLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSDGSLSHEEDLAK 15 1 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 1 RS(0.268)S(0.555)DGS(0.174)LS(0.003)HEEDLAK 157.88 1.15E-06 476490000 580430 556830 268650 442610 575610 475330 672710 788080 513180 TRUE FALSE 503724.7049 553172.1471 398570.0386 543111.3654 564156.4872 493616.2527 607470.6877 619555.2248 452512.445 1.113173152 1.222446262 0.880793541 1.200213102 1.246720379 1.090834646 1.342439737 1.369145162 1 18.78759794 3.500220598 24.6337858 1.232805044 1.079390967 0.171149659 0.13589326 993.9282573 1059950.203 0.037480208 0.055139173 3163.884333 -3.500220598 -0.153414077 RSS(ph)DPALIGLSTSVSDSNFSSEEPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSDPALIGLSTSVSDSNFSSEEPSR 26 1 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 RS(0.132)S(0.868)DPALIGLSTSVSDSNFSSEEPSR 303.57 4.70E-71 2025000000 260550 241430 154410 184620 211190 246150 231720 266770 214340 TRUE FALSE 226117.6574 239844.0304 229083.1925 226540.7927 206987.7322 255619.5498 209247.8301 209723.3115 189000.9694 1.196383585 1.269009525 1.212074167 1.198622385 1.095167569 1.352477454 1.107125698 1.10964146 1 17.52803411 1.606926023 1.6070739 0.997486048 1.214413387 0.497177572 0.070304832 0.406256428 1.753610412 0.121532128 0.019849391 40.45069832 -1.606926023 0.216927339 RSS(ph)DTEEESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSSDTEEESR 10 1 Q96IZ7-2;Q96IZ7;C9J713;C9J8Q2;C9JVB3;F8WDM0;C9J367 Q96IZ7-2 RSRC1 Serine/Arginine-related protein 53 1 RS(0.244)S(0.755)DTEEESR;RS(0.203)S(0.784)DT(0.014)EEESR 187.63 7.40E-07 972520000 404610 358960 209435 249260 214614 338410 340480 372730 333020 TRUE FALSE 351139.7633 356601.9681 310718.4665 305858.2927 210343.6013 351428.8517 307460.302 293024.5901 293650.755 1.195773406 1.21437443 1.058122485 1.04157162 0.716305331 1.196757869 1.047027112 0.997867654 1 18.16374182 4.113403795 2.779889226 1.000454533 1.209813823 0.336224694 0.117277281 0.303622443 4.6702448 0.031028576 0.080549781 12983.85914 -4.113403795 0.209359291 RSS(ph)GREEDDEELLR ddPTM_MDA-MB-175_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(0.063)S(0.937)GREEDDEELLR 193.06 2.38E-07 1370100000 300360 285220 181880 213680 306020 243350 340720 294780 275610 TRUE FALSE 260666.665 283346.371 269837.7764 262199.3099 299930.8007 252711.832 307677.0268 231743.591 243027.6998 1.072580061 1.165901547 1.110316958 1.078886523 1.23414245 1.039847854 1.26601629 0.953568631 1 17.89076123 1.645075974 9.612046778 0.976948976 1.135418044 0.467321405 0.071432768 0.081147178 13.86249015 0.036233939 0.016361115 44.16477012 -1.645075974 0.158469068 RSS(ph)ITEPEGPGGPNIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSITEPEGPGGPNIQK 17 1 Q96KQ4;A0A3B3ISJ2;H0YJL1 Q96KQ4 PPP1R13B Apoptosis-stimulating of p53 protein 1 1 RS(0.341)S(0.603)IT(0.056)EPEGPGGPNIQK 124.82 3.00E-05 147860000 115750 106280 38434 71770 72981 62635 54332 79538 54716 TRUE FALSE 100453.3442 105581.8397 57020.81095 88066.47544 71528.82088 65044.60898 49062.891 62529.41767 48247.53681 2.082040885 2.188336372 1.181838799 1.825305109 1.482538293 1.348143621 1.016899395 1.296012642 1 15.55816767 8 0.216958275 0.897892885 7.737877509 0.663057876 0.242232484 55.55261621 0.850078604 1.173191139 128.2227441 100000000 -8 6.839984624 RSS(ph)LLNAK ddPTM_MDA-MB-175_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(0.063)S(0.937)LLNAK;RS(0.322)S(0.678)LLNAK 93.336 0.0068238 1291870000 1650580 1321390 2193100 1234230 1327130 1114380 1614050 1885580 1618810 TRUE FALSE 1432451.671 1312709.702 3253690.495 1514480.786 1300722.709 1157250.92 1457519.679 1482363.391 1427436.126 1.003513674 0.91962763 2.279394809 1.060979723 0.911230062 0.810719933 1.021075236 1.038479665 1 20.44499476 3.499581386 24.95174701 0.966147908 1.405634178 0.23763463 0.364833233 1092.150031 1213305.185 0.099948612 0.146925558 3159.231026 -3.499581386 0.43948627 RSS(ph)LPLDHGSPAQENPES(ph)EKSSPAVSR ddPTM_MDA-MB-175_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(0.468)S(0.532)LPLDHGSPAQENPES(0.528)EKS(0.279)S(0.193)PAVS(0.001)R 109.27 0.00083729 175900000 65121 72579 14528 40988 86474 68437 86436 91998 75060 TRUE FALSE 56515.09485 72102.22377 21553.78939 50294.95186 84753.33658 71069.81567 78053.45002 72324.94363 66186.49231 0.853876567 1.08937974 0.32565239 0.759897528 1.280523165 1.073781269 1.179295764 1.092744775 1 16.01424919 3.255711318 24.54347646 1.122681058 0.750103416 0.460383164 0.197930766 178.8895664 255997.6479 0.057108104 0.073527838 1801.819647 -3.255711318 -0.372577643 RSS(ph)LPLDHGSPAQENPESEKS(ph)SPAVSR ddPTM_MDA-MB-175_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(0.359)S(0.641)LPLDHGSPAQENPES(0.365)EKS(0.406)S(0.229)PAVSR 195.07 2.50E-19 284070000 165530 174600 61517 109230 213770 175710 218340 230760 210750 TRUE FALSE 143654.7911 173453.0411 91266.82696 134032.341 209516.3952 182469.6774 197165.4204 181413.7698 185835.3751 0.773021773 0.933369338 0.491116543 0.721242341 1.127430098 0.981888821 1.060968184 0.97620687 1 17.50366563 3.25064764 24.99281769 1.022667005 0.727195327 0.629718098 0.114092527 148.0092702 306042.9199 0.032928631 0.042180422 1780.933242 -3.25064764 -0.295471678 RSS(ph)LS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSLSPGR 8 1 Q9BUQ8;F8VVA2;F8W1J5 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 2 RS(0.178)S(0.832)LS(0.99)PGR 84.169 0.011791 464710000 752360 643310 393550 458990 538290 626900 570970 699220 646060 TRUE FALSE 652933.7198 639084.0543 583872.0963 563210.6947 527579.0821 651017.2487 515597.4173 549697.2443 569683.5228 1.146134114 1.121822957 1.024906063 0.988637853 0.926091525 1.142770016 0.905059382 0.964916875 1 19.11980115 4.191489052 2.351721775 0.984430123 1.146199019 0.475952615 0.062758156 0.251837256 2.734243796 0.016564342 0.052516289 15541.36111 -4.191489052 0.161768895 RSS(ph)LSLEEADSEVEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSLSLEEADSEVEGR 16 1 Q5JTZ5 Q5JTZ5 C9orf152 Uncharacterized protein C9orf152 1 RS(0.088)S(0.885)LS(0.028)LEEADSEVEGR 169.77 1.43E-12 0 157520 143290 82707 97748 159090 136580 128190 181470 134740 TRUE FALSE 136703.3329 142348.7186 122704.3818 119943.1774 155924.4203 141834.321 115758.1535 142664.0527 118811.1907 1.150593072 1.198108677 1.032767883 1.00952761 1.312371498 1.193779139 0.974303455 1.200762755 1 16.8583112 1.218030405 24.4002436 0.999999357 1.13205613 0.142997257 0.10301447 2400.809979 2853168.725 0.995126394 0.024889416 16.52077458 -1.218030405 0.132056773 RSS(ph)LSSHSHQSQIYR ddPTM_MDA-MB-175_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(0.028)S(0.971)LSSHSHQSQIYR;RS(0.017)S(0.979)LS(0.004)SHSHQSQIYR 257.93 3.93E-25 662410000 134449 158567 34988 52928 246120 241160 170340 184776 39279 TRUE FALSE 116681.224 157525.3629 51908.31383 64946.11135 241222.6935 250437.5813 153820.453 145263.0903 34635.48137 3.368835061 4.548092208 1.498703404 1.875132344 6.964612126 7.230665531 4.44112358 4.194054322 1 15.0799631 4.775954893 20.21140781 4.061658596 3.368817416 0.00631512 2.097386587 10528.59156 5689273.146 0.539181057 70.34119836 59697.32796 -4.775954893 -0.69284118 RSS(ph)LSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSLSSR 7 1 Q8WUM0 Q8WUM0 NUP133 Nuclear pore complex protein Nup133 1 RS(0.041)S(0.959)LSSR 82.261 0.015294 57211000 57895 52120 30910 36823 48937 69701 41338 49764 41931 TRUE FALSE 50244.02906 51777.62029 45858.17939 45184.22495 47963.24944 72382.44257 37329.04712 39122.35586 36973.96495 1.358902924 1.400380521 1.240282979 1.222055168 1.297216826 1.957659739 1.009603573 1.058105505 1 15.17422214 RSS(ph)LVG ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSLVG 6 1 Q9H0B6;Q9H0B6-2 Q9H0B6 KLC2 Kinesin light chain 2 1 RS(0.021)S(0.979)LVG 80.165 0.069098 3075300000 2146700 1802300 1219300 1367000 1418200 2175700 2365800 2076400 2047900 TRUE FALSE 1863008.156 1790460.573 1808957.558 1677398.243 1389980.595 2259400.587 2136365.08 1632378.019 1805799.595 1.03168046 0.99150569 1.001748789 0.928895016 0.769731369 1.251191214 1.18305768 0.903964107 1 20.78420636 2.740284604 24.99994238 1.06557098 0.949601869 0.254585952 0.11674695 288.0629975 4177302.69 0.041703375 0.039560971 549.9011199 -2.740284604 -0.115969111 RSS(ph)NPPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RSSNPPAR 8 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 RS(0.016)S(0.984)NPPAR;RS(0.033)S(0.967)NPPAR;RS(0.152)S(0.848)NPPAR 147.83 0.00032529 656747000 177218 208065 132991 172013 150805 284508 265575 288619 306247 TRUE FALSE 153798.1923 206698.2073 197305.8924 211071.1807 147804.2755 295453.2069 239819.5774 226900.0729 270042.8285 0.569532593 0.765427501 0.730646666 0.78162113 0.547336422 1.094097586 0.888079786 0.840237358 1 18.04282871 2.74116635 24.9999833 0.931247327 0.692299349 0.643908357 0.10125654 165.9782278 1592437.873 0.032876022 0.031457013 551.0187158 -2.74116635 -0.238947979 RSS(ph)PESDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSSPESDR 8 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 RS(0.14)S(0.818)PES(0.043)DR;RS(0.032)S(0.755)PES(0.213)DR 101.5 0.0056662 243210000 509850 472790 285470 367270 341460 483390 456370 540980 519350 TRUE FALSE 442472.0307 469684.2114 423524.2468 450664.2669 334665.6141 501986.3261 412111.3076 425295.6369 457953.0346 0.966195215 1.02561655 0.924820265 0.984084028 0.730785886 1.096152418 0.899898628 0.928688326 1 18.80484012 4.226886916 24.86804338 0.934852841 0.995905886 0.062873946 0.092768913 497.5319315 1059880.561 0.022169683 0.04676343 16861.1393 -4.226886916 0.061053044 RSS(ph)PPPPPSGSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSPPPPPSGSSSR 14 1 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 RS(0.204)S(0.796)PPPPPSGSSSR 95.414 0.002314 562370000 104730 85662 50586 60185 52017 72402 84349 93824 81276 TRUE FALSE 90889.66515 85099.28068 75049.5588 73850.92412 50981.96347 75187.35179 76168.84696 73760.46774 71667.64387 1.268210593 1.187415633 1.047188867 1.03046396 0.711366535 1.049111534 1.062806629 1.029201795 1 16.12903431 4.264650215 1.972710438 0.983607187 1.267885949 0.516023662 0.099525792 0.322414607 2.320537638 0.028627098 0.11855746 18392.90024 -4.264650215 0.284278762 RSS(ph)PSARPPDVPGQQPQAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSPSARPPDVPGQQPQAAK 20 2 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 RS(0.192)S(0.659)PS(0.149)ARPPDVPGQQPQAAK 71.656 0.013487 263310000 159520 135720 81749 109340 168760 142770 136970 183080 146890 TRUE FALSE 138439.0278 134828.4464 121283.0898 134167.3182 165402.0062 148262.4543 123686.6705 143929.7667 129524.8315 1.068822296 1.040946703 0.936369408 1.035842445 1.276990707 1.144664328 0.954926318 1.111213696 1 16.98286918 5.166932152 9.98053945 1.065204583 1.232917239 0 0.098739879 4887418.798 3855479.952 0.024830124 18196039.62 146869.6813 -5.166932152 0.167712655 RSS(ph)PVPPVPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSPVPPVPER 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RS(0.376)S(0.624)PVPPVPER 97.767 0.0036882 648420000 556380 461580 298270 373260 489920 547770 485160 535410 564510 TRUE FALSE 482852.9733 458547.8506 442514.3697 458014.3879 480171.5505 568843.0664 438109.2579 420916.7381 497774.2709 0.970023968 0.921196368 0.888986023 0.920124672 0.964637143 1.14277314 0.880136406 0.845597619 1 18.92513214 RSS(ph)PVPPVPERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSPVPPVPERR 12 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RS(0.203)S(0.797)PVPPVPERR 84.375 0.0064032 146450000 75029 78392 53851 57319 67113 62858 67322 79130 57527 TRUE FALSE 65113.72755 77877.03779 79893.52372 70334.15502 65777.5826 65276.18793 60793.1228 62208.66529 50726.22359 1.283630496 1.535242174 1.574994511 1.386544277 1.296717515 1.286833186 1.198455522 1.226361059 1 15.63044414 1.421525988 0.426879612 0.786968355 1.486388556 0.685369188 0.092312727 3.226297797 0.590459417 1.17618449 0.11721122 26.39526268 -1.421525988 0.699420201 RSS(ph)RDMAGGAGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSRDMAGGAGPR 13 2 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 RS(0.187)S(0.813)RDMAGGAGPR 67.646 0.041412 33841000 16227 15732 7934.8 9186.6 10238 17266 15201 14598 9753.1 TRUE FALSE 14082.56084 15628.65546 11772.09582 11272.55794 10034.28383 17930.23419 13726.80936 11476.3313 8600.099629 1.637488104 1.817264466 1.368832494 1.310747366 1.166763673 2.0848868 1.596122133 1.334441669 1 13.07013766 1.401897442 2.666580158 0.973790757 1.562819407 0.334822782 0.259143853 0.436062181 4.658840421 0.493199096 0.07134929 25.22884929 -1.401897442 0.589028651 RSS(ph)RS(ph)SPELTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSRSSPELTR 11 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RS(0.386)S(0.615)RS(0.831)S(0.168)PELTR 87.138 0.068606 120980000 316850 265890 182410 209750 269330 285880 273700 311670 245330 TRUE FALSE 274977.4697 264143.3511 270624.0861 257376.9433 263970.8599 296877.9886 247156.6161 245021.7959 216327.3669 1.271117352 1.221035299 1.250993298 1.189756742 1.220237937 1.372355208 1.142512016 1.132643546 1 17.72285666 1.512676364 1.578601811 0.980205892 1.245939405 0.672057479 0.056032246 0.356164571 1.308798059 0.133575631 0.016178118 32.55939782 -1.512676364 0.265733513 RSS(ph)SEGLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RSSSEGLSK 9 1 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 RS(0.107)S(0.886)S(0.007)EGLSK;RS(0.038)S(0.955)S(0.007)EGLSK;RS(0.094)S(0.89)S(0.016)EGLSK 175.34 0.00039561 237850000 913720 744440 533700 650690 489790 642430 936930 940270 869880 TRUE FALSE 792969.5869 739549.7246 791799.1051 798439.1097 480044.1373 667144.6978 846066.6728 739200.5777 767043.7774 1.033799648 0.964155823 1.032273683 1.0409303 0.625836688 0.869760915 1.103022667 0.963700638 1 19.54894939 RSS(ph)VTVEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSVTVEER 9 1 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 RS(0.25)S(0.75)VTVEER 101.33 0.0024859 108970000 109250 96750 74139 83094 100050 123690 106720 118510 104590 TRUE FALSE 94812.3357 96114.44288 109992.8684 101961.7627 98059.20074 128448.4343 96370.31083 93167.55875 92225.48935 1.028049147 1.042167882 1.192651502 1.105570309 1.063254871 1.392765007 1.044942255 1.010214848 1 16.49287792 2.01825077 24.99999949 1.012359357 1.138113649 0.233807385 0.10325897 334.9905416 458869.9807 0.04225238 0.028481085 104.2919457 -2.01825077 0.125754292 RSSLDAEIDS(ph)LTSILADLECSSPYKPRPPQS(ph)STGSTASPPVSTPVTGHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 49 3 Q93052;A0A087WZF1;C9JUT4 Q93052 LPP Lipoma-preferred partner 2 RS(0.29)S(0.322)LDAEIDS(0.274)LT(0.108)S(0.007)ILADLECS(0.002)S(0.002)PYKPRPPQS(0.361)S(0.16)T(0.144)GS(0.117)T(0.106)AS(0.107)PPVS(0.001)TPVTGHK 149.11 9.20E-16 669400000 423970 286870 194730 208870 216880 175470 277790 329430 337380 TRUE FALSE 367941.2903 284985.5321 288902.0793 256297.1259 212564.5123 182220.4444 250849.9686 258983.9581 297495.3207 1.236796899 0.957949629 0.971114701 0.861516495 0.714513801 0.61251533 0.843206434 0.870548006 1 18.18250745 4.938637389 0.989106523 0.81446744 1.57787291 0.601159327 0.106170561 2.0755448 1.261960838 0.0372622 1.846310555 86823.51996 -4.938637389 0.76340547 RSSLPLDHGS(ph)PAQENPESEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSLPLDHGSPAQENPESEK 20 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5;A0A0A0MRX3 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 RS(0.2)S(0.311)LPLDHGS(0.489)PAQENPESEK 155.11 1.59E-08 809100000 410240 501020 80566 352190 623790 505390 625250 729140 677940 TRUE FALSE 356025.7446 497728.7666 119527.9871 432160.1224 611377.7994 524832.6803 564613.3512 573219.0852 597794.7055 0.595565236 0.832608188 0.19994822 0.722923971 1.022722004 0.877948024 0.94449373 0.958889532 1 19.18929059 3.433426536 5.49151027 0.951582507 0.554211906 0.60275935 0.155869442 0.124751069 8.96018047 0.043496004 0.057312493 2712.854714 -3.433426536 -0.397370601 RSSPS(ph)ARPPDVPGQQPQAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSPSARPPDVPGQQPQAAK 20 2 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 RS(0.297)S(0.297)PS(0.407)ARPPDVPGQQPQAAK 123.41 1.50E-05 890320000 363670 297140 177100 228410 277220 238900 270570 347920 276470 TRUE FALSE 315610.0881 295188.0678 262746.1524 280273.9815 271703.8644 248090.6376 244330.163 273520.0155 243786.0316 1.294619245 1.210848981 1.077773614 1.149672029 1.114517771 1.017657312 1.002232004 1.121967546 1 17.89525594 8 0.441493224 1.043785157 6.653005217 0.745906444 0.047308061 49.31736406 0.632459189 0.037589453 246.87309 99999999.92 -8 5.60922006 RSSQTQNKASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSQTQNKASR 11 2 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 61.435 0.049117 19984000 9527.6 8211.7 8274.9 7308.4 7913.1 8633.3 8629.1 12370 7748 FALSE TRUE 8268.50352 8157.756802 12276.66932 8967.883922 7755.644792 8965.428637 7792.25121 9724.771763 6832.040267 1.210253921 1.194044017 1.796925785 1.312621643 1.135187219 1.312262265 1.14054527 1.423406681 1 12.73810076 3.47982311 24.97081289 1.230164074 1.408938536 0.167837179 0.197287097 202.5637134 1872125.926 0.055726248 0.073304793 3018.721931 -3.47982311 0.178774462 RSSS(ph)LSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSSSLSK 7 1 Q6P597;Q6P597-3;Q6P597-2 Q6P597 KLC3 Kinesin light chain 3 1 RS(0.103)S(0.111)S(0.784)LS(0.002)K 61.593 0.05546 64784000 145170 130930 92271 100310 98128 115940 170760 185220 118500 TRUE FALSE 125985.4167 130069.9122 136893.5642 123086.9186 96175.44478 120400.2868 154199.7215 145612.1444 104491.065 1.205705164 1.244794588 1.310098277 1.177965969 0.920417883 1.152254375 1.475721599 1.3935368 1 16.67302006 1.212042298 23.99984892 0.999998015 1.242215686 0.196510289 0.148752489 3112.398352 2816560.841 3.056752716 0.040943354 16.29454724 -1.212042298 0.242217671 RST(ph)SPIIGS(ph)PPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSTSPIIGSPPVR 13 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 2 RS(0.151)T(0.585)S(0.264)PIIGS(1)PPVR;RS(0.435)T(0.49)S(0.075)PIIGS(1)PPVR 99.011 0.0026457 1029090000 631410 685460 559660 669380 1127530 1227760 1042420 1139430 789580 TRUE FALSE 547967.5687 680957.1681 830313.448 821372.9598 1105094.359 1274992.722 941326.2688 895771.7616 696236.7519 0.787042004 0.97805404 1.192573425 1.179732264 1.587239335 1.83126317 1.352020367 1.286590745 1 19.40921845 4.183409966 1.338508083 1.39828363 0.773103505 0.475111877 0.218954521 0.558897431 1.655988317 0.073052911 0.366783297 15254.92111 -4.183409966 -0.625180125 RSTAPSAAASASASAAASS(ph)PAGGGAEALELLEHCGVCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSTAPSAAASASASAAASSPAGGGAEALELLEHCGVCR 38 1 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 RSTAPSAAASASASAAAS(0.014)S(0.986)PAGGGAEALELLEHCGVCR 141.09 2.25E-13 263340000 69346 64664 21082 20175 55956 65412 65283 60784 12165 TRUE FALSE 60181.7504 64239.21793 31277.32572 24756.04211 54842.58508 67928.44197 58951.86471 47785.81462 10726.86756 5.610375077 5.988627861 2.915793035 2.307853805 5.112637476 6.332551567 5.495720385 4.454778094 1 13.38894122 4.264122855 24.98117 4.142555959 5.799503438 0.184143697 1.580574943 446.1848963 436034.5557 0.414548643 1.095931506 18370.57944 -4.264122855 1.656947479 RSVPTWLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RSVPTWLK 8 1 P62277;J3KMX5;E9PS50 P62277 RPS13 40S ribosomal protein S13 0 78.516 0.04878 255960000 476650 550060 263450 286180 567660 509480 492310 527680 337610 FALSE TRUE 413659.4948 546446.6196 390855.3012 351161.543 556364.6766 529080.0253 444565.852 414839.7384 297698.1304 1.38952668 1.835572897 1.312924944 1.179589346 1.868888716 1.777236641 1.493344454 1.393491245 1 18.18349064 1.234231171 1.933415946 0.809506573 1.559365439 0.373623435 0.225384868 0.939163326 3.341639926 1.293546814 0.063170747 17.14869874 -1.234231171 0.749858866 RSVSDNDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RSVSDNDIR 9 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;; 110.54 0.0036403 3297880000 6270850 4103510 2220940 2741080 4210120 4426710 4309480 4626020 3095440 FALSE TRUE 5442141.284 4076553.773 3294994.013 3363484.109 4126346.849 4597008.398 3891547.293 3636781.623 2729500.61 1.99382307 1.493516344 1.207178339 1.232270877 1.511758904 1.684193945 1.425736004 1.332398172 1 21.38020559 4.702152996 3.365002915 1.359389088 2.053012933 0.550222539 0.183857664 0.228091285 4.378812953 0.04812766 0.385668311 50367.80161 -4.702152996 0.693623845 RSYS(ph)PDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RSYSPDGK 8 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RS(0.007)YS(0.992)PDGK;RS(0.287)Y(0.006)S(0.708)PDGK;RS(0.002)YS(0.998)PDGK;RS(0.013)YS(0.987)PDGK;RS(0.121)Y(0.001)S(0.879)PDGK 144.7 0.00061568 1863630000 2093780 1561035 1162250 1387968 1429337 1308537 1803292 2052707 1881266 TRUE FALSE 1817081.668 1550780.458 1724317.987 1703127.348 1400895.99 1358877.265 1628409.019 1613751.582 1658864.877 1.095376539 0.934844351 1.039456566 1.026682385 0.844490718 0.819160912 0.981640544 0.97280472 1 20.66176495 4.743194812 23.81433309 0.952859491 1.095376653 0.281690391 0.071756464 368.1177626 1891561.185 0.018753964 0.143805644 55359.83816 -4.743194812 0.142517162 RSYS(ph)SPDITQAIQEEEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RSYSSPDITQAIQEEEKR 18 2 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 RS(0.002)YS(0.886)S(0.111)PDITQAIQEEEKR;RS(0.005)YS(0.498)S(0.498)PDITQAIQEEEKR 258.34 6.14E-31 331862000 318484 285619 189481 192949 278990 230230 332601 378519 161957 TRUE FALSE 276395.5325 283742.75 281114.6454 236761.0195 273438.6448 239087.0971 300345.4062 297575.6575 142810.628 1.935398901 1.986846175 1.968443451 1.657866945 1.914693946 1.674154791 2.103102623 2.083708067 1 17.12374382 1.232332923 24.99987026 0.999998481 1.920464581 0.79117907 0.147797223 99.09838429 397772.1412 0.346015154 0.038182873 17.07390743 -1.232332923 0.920466099 RT(ph)ASPPPPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RTASPPPPPK 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RT(0.595)AS(0.405)PPPPPK;RT(0.602)AS(0.398)PPPPPK 81.431 0.012323 518890000 1141470 940040 611800 828530 878210 799820 1032540 1197270 1074750 TRUE FALSE 990621.8474 933864.8153 907668.5263 1016660.4 860735.3392 830589.593 932404.4297 941243.1277 947694.2794 1.045296853 0.985407252 0.957765121 1.072772541 0.908241569 0.876432 0.983866264 0.993192792 1 19.8540622 3.227795392 24.99991441 0.956020574 1.009064129 0.287575241 0.048615661 351.5468124 816389.2081 0.015730332 0.018002173 1689.644708 -3.227795392 0.053043554 RT(ph)FEDISEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RTFEDISEK 9 1 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2;A0A2R8Y6Q7;A0A2R8Y7I7 A0A2R8Y430 GSS Glutathione synthetase 1 RT(1)FEDISEK;RT(1)FEDISEK 104.44 0.0063066 46121000 187815 225160 139108 165752 194680 288340 166723 186745 197289 TRUE FALSE 162994.7719 223680.9091 206381.0941 203388.525 190806.2489 299432.6264 150554.2291 146811.035 173965.7192 0.936936154 1.285775785 1.186331969 1.169129906 1.096803725 1.721216271 0.865424693 0.843907844 1 17.40844352 RT(ph)GTPSDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RTGTPSDPR 9 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 RT(0.497)GT(0.497)PS(0.005)DPR;RT(0.498)GT(0.498)PS(0.003)DPR;RT(0.496)GT(0.496)PS(0.008)DPR;RT(0.499)GT(0.499)PS(0.001)DPR 64.439 0.040732 2791073000 3554840 3067130 1700516 2121590 2625210 3352830 2177980 2997200 2188290 TRUE FALSE 3085058.887 3046981.821 2522891.225 2603329.436 2572973.457 3481815.54 1966759.835 2356272.104 1929592.849 1.598813391 1.579080179 1.307473349 1.349159973 1.333428168 1.804430163 1.019261569 1.221123982 1 20.87986504 2.21166009 24.99965453 1.106966298 1.476650033 0.596506981 0.160003082 165.2871336 153606.2315 0.065149137 0.043936383 162.8021329 -2.21166009 0.369683735 RT(ph)HSDAS(ph)DDEAFTTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTHSDASDDEAFTTSK 16 1 Q13017-2;Q13017;H0YK04 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 2 RT(0.511)HS(0.511)DAS(0.978)DDEAFTTSK 110.26 0.0007866 210720000 230750 211340 128090 171950 250010 208350 268350 298180 203960 TRUE FALSE 200255.8029 209951.6936 190034.7524 210993.8756 245035.2901 216365.3593 242325.4583 234416.5274 179848.0812 1.113472001 1.167383562 1.056640422 1.173178353 1.362457072 1.203045136 1.347389734 1.303414115 1 17.45641924 3.469827039 24.75196839 1.257600865 1.117474181 0.244840106 0.10365432 193.169003 655490.0596 0.028930403 0.037435848 2950.034122 -3.469827039 -0.140126684 RT(ph)NSDSALHQSTMTPTQPESFSSGSQDVHQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTNSDSALHQSTMTPTQPESFSSGSQDVHQK 31 1 M0QXN6;M0QX46;Q6UUV9;Q6UUV9-2;Q6UUV9-3 M0QXN6 CRTC1 CREB-regulated transcription coactivator 1 1 RT(0.237)NS(0.182)DS(0.182)ALHQS(0.182)T(0.182)MT(0.035)PTQPESFSSGSQDVHQK 115.76 2.20E-05 196370000 87471 115600 14844 57988 139930 135410 109890 133050 70220 TRUE FALSE 75911.48573 114840.616 22022.60805 71155.06169 137145.6668 140619.3103 99232.88471 104598.2929 61918.67159 1.225986989 1.854700901 0.355669905 1.149169707 2.214932317 2.271032416 1.60263265 1.689285157 1 15.9180869 3.278076287 21.0663055 1.761590884 1.140491096 0.271772004 0.49542244 42.73388216 22780.58193 0.145881264 0.188319783 1897.039119 -3.278076287 -0.621099789 RT(ph)PDSTFSETFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RTPDSTFSETFK 12 1 Q9NZI5-3;Q9NZI5;B7Z1S6 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 RT(0.915)PDS(0.085)TFSETFK;RT(0.933)PDS(0.062)T(0.005)FSETFK;RT(0.999)PDS(0.001)TFSETFK 204.13 6.86E-08 1569250000 1543840 1152540 844750 991370 1187750 967790 1363800 1653570 1514210 TRUE FALSE 1339817.632 1144968.889 1253273.926 1216475.711 1164116.099 1005021.508 1231538.886 1299966.924 1335201.819 1.003457016 0.857524962 0.938640068 0.911080028 0.871865273 0.752711308 0.9223616 0.973610809 1 20.34862639 1.76673364 3.469006681 0.990008701 0.887241831 0.276106192 0.063804104 0.272264599 6.539734111 0.043348528 0.017374754 58.44315326 -1.76673364 -0.102766871 RT(ph)PDYFL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RTPDYFL 7 1 P67775;P62714;P67775-2;H0YBN9 P67775 PPP2CA;PPP2CB Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform 1 RT(1)PDYFL;RT(1)PDYFL;RT(1)PDYFL;RT(1)PDYFL 116.73 0.010426 376401000 776340 833370 532390 691520 863150 774840 762630 925390 1153520 TRUE FALSE 673744.702 827895.5376 789855.5847 848540.1852 845975.0037 804648.5962 688670.26 727502.5499 1017152.18 0.662383383 0.813934782 0.776536295 0.8342313 0.831709375 0.791079852 0.677057252 0.715234716 1 19.95610411 4.74459191 24.08280929 0.792393132 0.662383286 0.202060479 0.08587446 741.5684071 2960920.433 0.021043159 0.18238893 55538.21411 -4.74459191 -0.130009847 RT(ph)PS(ph)DDEEDNLFAPPK ddPTM_MDA-MB-175_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 2 RT(1)PS(1)DDEEDNLFAPPK 117.35 0.00030915 90604000 214480 139710 112500 131030 150930 134660 170730 186920 187410 TRUE FALSE 186135.9246 138792.2358 166905.3763 160782.3642 147926.7883 139840.4573 154172.6309 146948.6126 165254.6033 1.126358485 0.839869105 1.009989271 0.97293728 0.895144736 0.846212175 0.932940008 0.889225532 1 17.33433093 3.266996027 8.693114257 0.90796455 0.978558394 0.177070871 0.078542537 0.444697791 121.0613278 0.021167672 0.026975255 1849.251701 -3.266996027 0.070593843 RT(ph)PTMPQEEAAACPPHILPPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTPTMPQEEAAACPPHILPPEK 22 1 Q9NYV4 Q9NYV4 CDK12 Cyclin-dependent kinase 12 1 RT(0.999)PT(0.001)MPQEEAAACPPHILPPEK 167 8.43E-12 319800000 296280 208350 143850 173000 194040 167030 228230 263970 232420 TRUE FALSE 257125.8473 206981.3351 213416.3411 212282.2941 190178.9836 173455.7522 206096.2897 207522.0697 204943.5724 1.254617768 1.009943043 1.041341959 1.035808499 0.927957786 0.846358586 1.00562456 1.012581499 1 17.64486722 7.963152712 0.964144898 0.972992327 199.9947592 0.696830091 0.056541102 769.3097025 1.355819831 0.019163118 337691.9987 91865556.8 -7.963152712 199.0217669 RT(ph)PTMPQEEAAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTPTMPQEEAAEK 13 1 Q9NYV4-2 Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 RT(0.996)PT(0.004)MPQEEAAEK 166.52 1.96E-05 467520000 876490 552360 443020 431530 529390 476060 663310 766900 698020 TRUE FALSE 760659.6258 548731.5108 657265.9538 529515.482 518856.1747 494374.3363 598982.2983 602904.403 615500.8708 1.235838423 0.891520283 1.067855441 0.860300135 0.842982032 0.803206559 0.97316239 0.979534606 1 19.23140137 6.827803943 1.535352159 0.925036833 199.6970934 0.568538066 0.082727666 747.3207773 3.51363404 0.023420138 521510.8748 6726729.179 -6.827803943 198.7720566 RT(ph)SFSTSDVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RTSFSTSDVSK 11 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 RT(0.499)S(0.499)FS(0.001)TSDVSK;RT(0.548)S(0.436)FS(0.004)T(0.004)S(0.007)DVSK 88.075 0.0161 336848000 627180 589490 432080 524240 622070 620240 743700 789830 700170 TRUE FALSE 544296.5739 585617.6014 641035.3332 643276.7045 609692.0241 644101.0341 671576.0885 620931.001 617396.7002 0.881599422 0.948527262 1.038287592 1.04191795 0.987520704 1.043253121 1.08775458 1.005724522 1 19.23583825 4.457182126 2.731520673 1.029914425 0.883545896 0.753723359 0.028420875 0.144537477 1.985365406 0.007573295 0.035570616 28653.79346 -4.457182126 -0.14636853 RT(ph)SLGEVSKGDTMENLDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTSLGEVSKGDTMENLDGK 19 2 Q9ULJ8;Q9ULJ8-4;Q9ULJ8-5;Q9ULJ8-3 Q9ULJ8 PPP1R9A Neurabin-1 1 RT(0.5)S(0.5)LGEVS(0.001)KGDTMENLDGK 122.84 0.0015442 381810000 425310 305020 214300 240690 290830 222050 412270 502670 175810 TRUE FALSE 369104.2059 303016.3035 317936.1968 295342.3432 285043.052 230592.4072 372288.1189 395177.9323 155025.9421 2.380918967 1.954616753 2.050858021 1.905115616 1.838679696 1.487443999 2.401456904 2.549108407 1 17.24215013 4.739321642 23.05818688 1.963090368 2.380919112 0.09181376 0.436651265 62.4663426 1891508.535 0.107257072 0.622342685 54868.31738 -4.739321642 0.417828745 RT(ph)SMGGTQQQFVEGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RTSMGGTQQQFVEGVR 16 1 A0A2R8Y804;A0A2R8Y543;A0A2R8Y5C3;A0A2R8Y750;A0A2R8Y5Z1;B4DGU4;A0A2R8YCH5;A0A2R8Y5A3;P35222;A0A2R8Y6G0 A0A2R8Y804 CTNNB1 Catenin beta-1 1 RT(0.5)S(0.5)MGGTQQQFVEGVR;RT(0.5)S(0.5)MGGTQQQFVEGVR 283.52 6.89E-36 785680000 148901 111880 84694 111679 105630 138007 109806 148804 121475 TRUE FALSE 129223.3556 111145.0529 125652.3017 137037.4239 103528.1697 143316.2186 99157.03102 116983.4226 107114.3639 1.20640548 1.037629771 1.173066778 1.279356184 0.96651995 1.337973857 0.925711804 1.092135717 1 16.70879243 2.21290214 24.99999942 1.020561537 1.157246918 0.30457526 0.113268127 299.3182215 291634.4937 0.042591706 0.028726211 163.2684012 -2.21290214 0.13668538 RT(ph)SNERPGSGQGQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RTSNERPGSGQGQGR 15 2 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 RT(0.651)S(0.349)NERPGSGQGQGR;RT(0.808)S(0.192)NERPGSGQGQGR;RT(0.748)S(0.252)NERPGSGQGQGR 152.66 4.49E-06 1753457000 217185 196776 118024 134468 176629 181921 183333 216603 167278 TRUE FALSE 188483.452 195483.3655 175100.8012 165001.0146 173114.4285 188919.6186 165553.3939 170284.1341 147502.5854 1.277831514 1.325287723 1.187103268 1.118631339 1.17363657 1.280788524 1.122376218 1.15444847 1 17.17038072 -0.759307157 0.400743632 2.17E-42 1.248920743 0.541565741 0.064242508 28.07887873 1.036286836 23.25152351 0.070824368 0.174057541 0.759307157 1.248920743 RT(ph)SPQVLGSILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RTSPQVLGSILK 12 1 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 RT(0.78)S(0.22)PQVLGSILK;RT(0.968)S(0.032)PQVLGSILK;RT(0.5)S(0.5)PQVLGSILK;RT(0.5)S(0.5)PQVLGSILK 157.91 4.03E-05 4071390000 5073980 4918530 3146320 4126670 4892450 4455090 5395540 6575070 5210660 TRUE FALSE 4403440.687 4886219.853 4667890.876 5063693.496 4795099.817 4626480.195 4872281.361 5169042.448 4594661.711 0.958381915 1.063455845 1.01593788 1.102081897 1.043624127 1.006925098 1.060422218 1.125010452 1 22.13152721 5.663312963 1.479658107 1.058755734 1.18E-14 0.328660502 0.040480325 19.06550698 4.527464553 0.011256486 55.97452735 460588.3651 -5.663312963 -1.058755734 RT(ph)SPSDGAMANYESTEVMGDGESAHDSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.491)S(0.491)PS(0.017)DGAMANYESTEVMGDGESAHDSPR;RT(0.499)S(0.499)PS(0.001)DGAMANYESTEVMGDGESAHDSPR 291.82 8.40E-81 1197120000 88418 128657 33805 61494 157086 161291 130665 146269 133128 TRUE FALSE 76733.33728 127811.8437 50153.21107 75457.15258 153960.2959 167495.9691 117993.1284 114990.5126 117389.7595 0.653662957 1.088781886 0.42723668 0.642791611 1.311530892 1.426836292 1.005139877 0.979561702 1 16.84094703 3.248486812 24.95978707 1.127632838 0.710959778 0.514135102 0.212848225 186.4088027 468729.179 0.065270776 0.083238477 1772.094234 -3.248486812 -0.416673061 RT(ph)SSEELRDATSLLAAGEGGLLDEVEPLRPDELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RTSSEELRDATSLLAAGEGGLLDEVEPLRPDELER 35 3 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RT(0.2)S(0.2)S(0.2)EELRDAT(0.2)S(0.2)LLAAGEGGLLDEVEPLRPDELER;RT(0.296)S(0.296)S(0.296)EELRDAT(0.056)S(0.056)LLAAGEGGLLDEVEPLRPDELER;RT(0.324)S(0.324)S(0.324)EELRDAT(0.013)S(0.013)LLAAGEGGLLDEVEPLRPDELER;RT(0.305)S(0.305)S(0.305)EELRDAT(0.043)S(0.043)LLAAGEGGLLDEVEPLRPDELER 157.15 3.89E-12 214996000 98717.9 92275.5 37323.4 29299.5 72974.2 90584.5 99827.2 88925.6 17151.4 TRUE FALSE 85672.0794 91669.33616 55373.12108 35952.39929 71522.15619 94069.34433 90145.97351 69909.55246 15123.78103 5.664726249 6.061271052 3.661327876 2.377209721 4.729118733 6.219962068 5.960544742 4.622491711 1 13.88453125 4.247699402 24.97959241 4.269117896 5.862999395 0.177614042 1.553407544 386.1238039 1055392.549 0.407610643 1.046266893 17688.84198 -4.247699402 1.593881499 RT(ph)SSEQAVALPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RTSSEQAVALPR 12 1 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;Q14934-12;Q14934-13;Q14934-18 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 RT(0.649)S(0.344)S(0.007)EQAVALPR;RT(0.684)S(0.313)S(0.003)EQAVALPR 176.33 1.48E-05 574190000 253830 244160 169258 222920 267470 283150 276500 285360 314410 TRUE FALSE 220285.7224 242556.0969 251111.7349 273537.3931 262147.8703 294042.9637 249685.0726 224337.9847 277240.808 0.794564566 0.874893197 0.905753149 0.986641884 0.945560187 1.060604916 0.900607217 0.809180965 1 18.0807801 4.557388869 1.787427259 0.936691325 0.776665405 0.353583679 0.066673469 0.837560016 3.600431032 0.020236532 0.201156876 36090.16512 -4.557388869 -0.16002592 RT(ph)SSLDTITGPYLTGQWPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RTSSLDTITGPYLTGQWPR 19 1 Q86VQ1;H7C2L5;H7C0Q2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 RT(0.333)S(0.333)S(0.333)LDT(0.001)ITGPYLTGQWPR;RT(0.331)S(0.331)S(0.331)LDT(0.008)ITGPYLTGQWPR 202.44 3.24E-16 178499000 74590 60783 41414 43526 60545 75428 64145 64824 41907 TRUE FALSE 64732.74251 60383.71247 61441.94892 53409.24355 59340.27295 78329.76397 57924.22777 50961.89206 36952.8022 1.751768165 1.634076684 1.662714199 1.445336764 1.605839596 2.119724603 1.567519222 1.379107646 1 15.17339615 1.447553419 2.06556405 0.950462546 1.687697891 0.626268503 0.173626706 0.316081163 2.052508868 0.392525542 0.0496045 28.02550318 -1.447553419 0.737235345 KRS(ph)EGFSMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 KRSEGFSMDR 10 2 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;K7ERA4 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 1 KRS(0.997)EGFS(0.003)MDR;KRS(0.861)EGFS(0.139)MDR;KRS(0.942)EGFS(0.058)MDR;KRS(0.967)EGFS(0.033)MDR;KRS(0.997)EGFS(0.003)MDR;KRS(1)EGFSMDR;KRS(0.962)EGFS(0.038)MDR;KRS(0.986)EGFS(0.014)MDR;KRS(0.968)EGFS(0.032)MDR 214.18 4.58E-09 19161080000 12326390 12510280 13782090 16802640 20341070 21274820 27903830 27763830 26762870 TRUE FALSE 10697426.33 12428099.15 20447154.82 20617936.22 19936322.5 22093276.09 25197720.86 21826751.01 23598994 0.4533001 0.52663682 0.866441799 0.873678608 0.844795439 0.936195674 1.067745552 0.924901757 1 24.49222202 4.593720177 0.779147542 0.9740566 0.154109314 0.887052568 0.065612069 0.663050599 0.361789196 0.026224472 0.45793249 39239.20291 -4.593720177 -0.819947285 down RT(ph)SVPS(ph)PEQPQPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTSVPSPEQPQPYR 14 1 Q8TEH3 Q8TEH3 DENND1A DENN domain-containing protein 1A 2 RT(0.534)S(0.472)VPS(0.994)PEQPQPYR 71.535 0.035617 141190000 104190 120800 78678 91245 131390 120280 128700 145780 128280 TRUE FALSE 90421.02752 120006.4568 116726.944 111963.5718 128775.5961 124907.2494 116218.6938 114606.0815 113114.8845 0.799373379 1.060925424 1.031932662 0.98982174 1.138449609 1.104251222 1.027439442 1.01318303 1 16.78742926 4.740870185 24.59302319 1.044893171 0.799373271 0.738947731 0.046018862 93.04472255 990690.115 0.011899886 0.077073788 55064.30792 -4.740870185 -0.2455199 RT(ph)SVPSPEQPQPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTSVPSPEQPQPYR 14 1 Q8TEH3 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 RT(0.529)S(0.471)VPSPEQPQPYR 144.68 8.35E-06 0 132680 130630 95114 97005 106200 120010 108060 134780 244620 TRUE FALSE 115146.0018 129771.8829 141111.4485 119031.4679 104086.8278 124626.8624 97580.35783 105958.3459 215701.3023 0.533821542 0.601627721 0.654198408 0.551834721 0.482550762 0.577775197 0.452386503 0.491227196 1 17.71867536 1.234757797 24.99991553 1.000000656 0.541239781 0.853837823 0.059394237 44.16966988 290330.4951 0.116736094 0.01596903 17.16950591 -1.234757797 -0.458760875 RTAQEVETYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RTAQEVETYR 10 1 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;; 198.81 4.65E-07 1074810000 648420 592580 397501 471210 550650 575080 510720 651520 560320 FALSE TRUE 562729.6541 588687.303 589733.8132 578205.4325 539693.1423 597203.6997 461190.453 512197.5181 494079.6079 1.138945314 1.191482695 1.193600796 1.170267753 1.092320213 1.208719587 0.933433491 1.036670022 1 18.91438399 2.242807409 24.99999683 0.997391855 1.165167306 0.803781183 0.040904168 43.29712644 254883.347 0.015101497 0.011275381 174.9070879 -2.242807409 0.167775452 RTDALTS(ph)SPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RTDALTSSPGR 11 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RTDALT(0.042)S(0.479)S(0.479)PGR;RTDALT(0.013)S(0.493)S(0.493)PGR;RTDALT(0.235)S(0.382)S(0.382)PGR;RTDALT(0.112)S(0.444)S(0.444)PGR 145.49 2.22E-05 7212375000 2272318 1799314 1304232 1376543 1933835 1866014 1602708 2074297 1874690 TRUE FALSE 1972025.419 1787494.188 1934962.958 1689108.127 1895355.467 1937800.766 1447277.625 1630724.729 1653066.284 1.192949997 1.081320335 1.170529565 1.021803024 1.146569551 1.172246258 0.875510945 0.98648478 1 20.65671314 2.246077744 24.99999957 0.957496211 1.126203586 0.666477971 0.0589134 96.77457596 321847.967 0.021308085 0.016177588 176.2291491 -2.246077744 0.168707375 RTDALTSS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RTDALTSSPGR 11 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RTDALT(0.04)S(0.341)S(0.618)PGR;RTDALT(0.001)S(0.004)S(0.995)PGR;RTDALT(0.005)S(0.156)S(0.84)PGR;RTDALT(0.026)S(0.223)S(0.751)PGR;RTDALT(0.025)S(0.19)S(0.785)PGR;RTDALT(0.088)S(0.332)S(0.58)PGR 206.7 2.70E-08 18227270000 4070690 3608380 2387164 3226447 3555440 3936690 3362720 3909650 3917740 TRUE FALSE 3532738.003 3584676.314 3541604.495 3959061.105 3484693.7 4088137.012 3036603.932 3073601.772 3454589.24 1.022621723 1.037656307 1.025188307 1.146029478 1.008714338 1.183393083 0.879005786 0.889715552 1 21.72008275 2.218298322 24.99994078 0.914162938 1.067654483 0.539856806 0.064070249 167.1671054 206251.8617 0.024894327 0.016806532 165.3096941 -2.218298322 0.153491545 RTDDIPVWDQEFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RTDDIPVWDQEFLK 14 1 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2;E5RGM3 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ;; 197.47 3.75E-08 1823830000 2445620 2047470 1479090 1875630 1960520 1756890 2345300 2661830 2223250 FALSE TRUE 2122425.121 2034020.035 2194382.871 2301520.459 1921509.488 1824478.695 2117853.167 2092618.369 1960419.918 1.082638011 1.037543037 1.119343285 1.173993611 0.980151992 0.93065709 1.080305881 1.067433742 1 20.90273128 3.222507376 24.99877471 1.019767322 1.099817178 0.41406234 0.05363911 298.2570496 464457.0887 0.017837157 0.020288141 1669.196157 -3.222507376 0.080049855 RTDEAAFQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RTDEAAFQK 9 1 P26447 P26447 S100A4 Protein S100-A4 0 ;;;;; 204.52 2.64E-05 10064410000 9349660 7836400 5653600 5998630 6693040 7511230 8577840 8708180 7637110 FALSE TRUE 8114078.742 7784922.172 8387699.87 7360710.625 6559861.599 7800191.879 7745962.397 6846003.474 6734259.556 1.204895457 1.156017541 1.245526669 1.093024491 0.974102876 1.158285007 1.150232232 1.016593349 1 22.6830879 7.9999999 0.058039567 0.605821635 2.094964039 0.424066857 0.068354123 870.9743933 4.910027827 32.2167811 121.5166098 99999976.87 -7.9999999 1.489142404 RTDLCDHALHISHDEL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RTDLCDHALHISHDEL 16 1 Q9Y2B0;H0YI18 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;; 148.72 3.68E-07 1183170000 521741 513199 186158 341807 597798 770461 497267 472975 403637 FALSE TRUE 452791.6049 509827.762 276184.6315 419419.5035 585902.9894 800101.1332 449042.1229 371832.9769 355919.4937 1.272174222 1.432424385 0.775975007 1.17841116 1.64616718 2.247983455 1.261639587 1.044710907 1 18.44119143 3.396072894 11.97619754 1.417508515 1.152428078 0.112162404 0.382101829 1.557115174 222.7210012 0.12276302 0.158487834 2489.275094 -3.396072894 -0.265080437 RTEARS(ph)S(ph)DEENGPPS(ph)SPDLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTEARSSDEENGPPSSPDLDR 21 2 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 3 RT(0.047)EARS(0.977)S(0.977)DEENGPPS(0.605)S(0.395)PDLDR 71.927 0.01077 191440000 115950 132570 63959 83163 140310 145880 110000 152330 103930 TRUE FALSE 100626.9137 131699.1389 94889.78633 102046.4302 137518.1055 151492.098 99332.21693 119755.4149 91643.5138 1.098025485 1.437080853 1.035422829 1.113515032 1.500576525 1.653058593 1.083897952 1.306752764 1 16.48374516 0.691802296 1.764749577 8.96E-11 1.287799995 0.148623721 0.204311084 11.48161066 8.3568213 41.23721102 0.056997066 4.918155951 -0.691802296 1.287799995 RTEEGPTLSYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RTEEGPTLSYGR 12 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;; 240.92 5.06E-16 4446970000 2159400 1847220 1149360 1326900 1873800 2070980 1796470 1979060 1509650 FALSE TRUE 1874029.819 1835085.49 1705194.34 1628192.925 1836515.046 2150651.941 1622248.616 1555853.42 1331180.897 1.407795006 1.378539532 1.28096365 1.223119209 1.379613432 1.615597058 1.218653768 1.168776854 1 20.3442752 1.65769231 2.088939906 1.022140983 1.367896444 0.56095322 0.109046772 0.24980974 2.200028353 0.133925687 0.032083644 45.46658237 -1.65769231 0.34575546 RTEEPDRDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RTEEPDRDER 10 2 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 ; 117.25 0.00055258 228857000 68681 54018 34408 44018 56645 54853 52037 63985 57692 FALSE TRUE 59604.63183 53663.1522 51047.82389 54012.95967 55517.87532 56963.2304 46990.45975 50302.30568 50871.71748 1.171665412 1.054872036 1.003461774 1.061748302 1.091330863 1.119742624 0.923704999 0.988806908 1 15.63457618 -1.999871387 0.03334627 3.57E-07 1.75357247 0.349191121 0.05752631 2964.6647 9.773809219 376.1092368 174.8187005 0.010002962 1.999871387 1.753572113 RTEISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTEISK 6 1 Q9H4A5;Q5T5I6;Q9H4A5-2 Q9H4A5 GOLPH3L Golgi phosphoprotein 3-like 0 98.457 0.063998 165020000 217780 228610 139170 177970 161620 189490 248440 283760 259600 FALSE TRUE 188999.8212 227108.2459 206473.0775 218380.8086 158404.0782 196779.8029 224346.327 223080.1322 228910.3837 0.825649838 0.992127321 0.901982139 0.954001322 0.691991668 0.859636857 0.980061819 0.974530419 1 17.80442338 2.233201855 24.3793832 0.982511181 0.873466808 0.31196889 0.079697873 126.7892725 576810.2412 0.032892918 0.022924888 171.0810296 -2.233201855 -0.109044374 RTEITIVKPQESAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTEITIVKPQESAHR 15 2 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EJ51;K7ER34 Q9UHD8 9-Sep Septin-9 0 118.2 0.00018606 1004200000 1474500 1187300 613130 1119400 1323200 1323100 1435400 1650000 1149600 FALSE TRUE 1279641.089 1179500.548 909641.7188 1373576.879 1296870.909 1374000.513 1296195.129 1297160.34 1013695.598 1.262352418 1.163564832 0.897351948 1.355019083 1.279349453 1.355436993 1.278682804 1.279634975 1 19.95119306 3.697034818 24.99984328 1.266511159 1.113336639 0.219577769 0.13276249 706.0845252 425084.9941 0.035993759 0.053387735 4977.769909 -3.697034818 -0.153174519 RTELFIAAEGIHTGQFVYCGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTELFIAAEGIHTGQFVYCGK 21 1 P62917;E9PKZ0;G3V1A1;E9PKU4 P62917 RPL8 60S ribosomal protein L8 0 153.11 3.00E-08 70688000 98449 91860 45223 64438 76752 71787 100720 102580 50286 FALSE TRUE 85438.71521 91256.56561 67092.99406 79069.63277 75224.78536 74548.69234 90952.1899 80644.06528 44341.24637 1.926845143 2.058051433 1.513105732 1.783207268 1.696496863 1.681249366 2.05118704 1.818714445 1 15.4363617 1.238460477 24.97105716 0.999999298 1.816360504 0.70188429 0.167151067 1.345335006 333765.6459 0.230004981 0.041061653 17.31651434 -1.238460477 0.816361205 RTELSIDISSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RTELSIDISSK 11 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 0 ; 145 5.84E-05 1338830000 1837030 1758790 1103270 1501070 1726670 1435250 1908950 2297000 1940570 FALSE TRUE 1594261.831 1747236.393 1636815.062 1841910.886 1692312.645 1490464.996 1723820.323 1805804.425 1711158.025 0.931685915 1.021084182 0.956554005 1.076411914 0.988986768 0.871027091 1.007399841 1.055311315 1 20.70654157 2.003754327 24.9999093 1.031531215 0.977446399 0.14253338 0.05502212 195.4111036 1301231.645 0.022708501 0.015231658 100.8682131 -2.003754327 -0.054084816 RTES(ph)FHSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTESFHSYR 9 1 Q9Y597-3;Q9Y597-2;Q9Y597 Q9Y597-3 KCTD3 BTB/POZ domain-containing protein KCTD3 1 RT(0.017)ES(0.982)FHS(0.001)YR 81.278 0.013313 181040000 120670 120170 76747 80149 114720 127690 109010 106600 105400 TRUE FALSE 104723.1538 119380.5954 113862.1059 98348.05545 112437.2964 132602.3169 98438.22698 83804.41956 92939.73207 1.126785621 1.284494723 1.225117647 1.058191726 1.209787181 1.426755963 1.059161941 0.901707135 1 16.50400787 2.00741317 24.99529813 0.95481319 1.219037851 0.576377445 0.098205004 113.9012359 384043.9054 0.040203319 0.027043889 101.7215969 -2.00741317 0.264224661 RTETVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RTETVQK 7 1 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ;; 126.52 0.0063237 447860000 678710 700070 364913 425580 412100 551800 544350 510990 667850 FALSE TRUE 589016.7539 695471.1941 541386.1474 522214.4436 403900.0163 573028.1031 491559.0208 401718.765 588897.5338 1.000202446 1.180971483 0.919321472 0.886766226 0.685857884 0.973052306 0.834710612 0.682153927 1 19.16765711 3.998926128 2.978968527 0.825855946 1.089808879 0.431036448 0.11300629 0.210326913 3.798259056 0.029708451 0.066079072 9975.303727 -3.998926128 0.263952933 RTFEDISEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTFEDISEK 9 1 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2;A0A2R8Y6Q7;A0A2R8Y7I7 A0A2R8Y430 GSS Glutathione synthetase 0 87.066 0.021988 495790000 1104100 1070200 561180 652520 948180 915530 914950 1056600 723930 FALSE TRUE 958190.3876 1063169.786 832568.525 800684.6391 929313.0731 950751.0315 826218.2898 830654.3125 638347.8201 1.501047481 1.665502336 1.304255296 1.254307783 1.455809895 1.489393402 1.294307373 1.301256598 1 19.2839832 0.560485692 0.869610355 2.08E-17 1.44347245 0.582719019 0.116099232 5.270543153 1.325721362 9.664320499 0.044572664 3.634843296 -0.560485692 1.44347245 RTFQEQVSDTENNLNQGPS(ph)LMEAIFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTFQEQVSDTENNLNQGPSLMEAIFK 26 1 Q8IV33-3 Q8IV33-3 1 RTFQEQVS(0.07)DT(0.07)ENNLNQGPS(0.86)LMEAIFK 43.256 0.08161 963310000 265480 174660 226920 249840 222830 189130 273710 320240 634170 TRUE FALSE 230396.1454 173512.647 336659.271 306569.9906 218396.119 196405.9535 247165.6463 251759.1681 559199.145 0.412010904 0.310287754 0.602038243 0.548230435 0.390551597 0.351227206 0.441999328 0.450213793 1 19.09300263 1.238027198 6.731334037 1.014052774 0.438393862 0.809900036 0.085540523 0.051110668 11.89629922 0.134312402 0.02198924 17.29924694 -1.238027198 -0.575658911 RTGAPAQADSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RTGAPAQADSR 11 1 P20290 P20290 BTF3 Transcription factor BTF3 0 ; 100.04 0.0069399 123302000 160971 191008 90444 94216 161570 195218 179019 181652 69960 FALSE TRUE 139698.2745 189753.2559 134183.0209 115609.1828 158355.0731 202728.1628 161657.7649 142807.1334 61689.4085 2.264542292 3.075945458 2.175138718 1.87405238 2.566973439 3.286271788 2.62051086 2.314937635 1 15.91273519 1.227427541 3.081669013 0.68979091 2.556424977 0.583231988 0.408972252 0.297746908 3.554814434 1.395084501 0.110286281 16.88214169 -1.227427541 1.866634067 RTGS(ph)NAAQYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTGSNAAQYK 10 1 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 RT(0.088)GS(0.912)NAAQYK 83.617 0.0094821 60356000 87859 80943 53877 56548 76906 68457 86028 104780 70594 TRUE FALSE 76248.21054 80411.2801 79932.09741 69388.08768 75375.72106 71090.58509 77685.0178 82373.6124 62248.45774 1.224901199 1.291779476 1.284081571 1.114695692 1.210884957 1.142045726 1.247983012 1.323303667 1 15.92575047 3.782343653 24.97851882 1.193745923 1.269406653 0.178410839 0.087671476 958.4929116 546823.8725 0.023482179 0.040671694 6058.200645 -3.782343653 0.075660729 RTHEHVSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RTHEHVSEK 9 1 P20810-6;P20810-10;P20810-7;P20810-9;H0YA91;P20810-5;F8W7E0;E9PSG1 P20810-6;P20810-5 CAST Calpastatin 0 ;;; 107.83 0.0017591 244507000 543886 573508 269216 394094 469749 485803 569491 604586 512227 FALSE TRUE 472010.0871 569740.5882 399409.7581 483579.066 460401.9139 504492.1558 514261.8505 475299.9888 451672.1076 1.045028194 1.261403081 0.884291395 1.070641861 1.019327752 1.116943347 1.138573407 1.052312022 1 18.7849163 4.260187951 24.99999901 1.049707862 1.153215461 0.222790161 0.086299402 376.2768161 434947.5996 0.020453168 0.054005323 18204.88548 -4.260187951 0.103507599 RTHS(ph)DAS(ph)DDEAFTTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTHSDASDDEAFTTSK 16 1 Q13017-2;Q13017;H0YK04 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 2 RT(0.199)HS(0.927)DAS(0.874)DDEAFTTSK 88.768 0.0069482 0 311760 291970 218650 257220 342570 301420 383450 430060 266200 TRUE FALSE 270560.1261 290052.0298 324389.8713 315625.7324 335753.5272 313015.8224 346263.078 338095.0157 234730.1393 1.152643316 1.235682945 1.381969407 1.344632323 1.430380983 1.333513555 1.47515389 1.440356218 1 17.84064357 4.412246368 3.176089109 1.362312023 1.161753633 0.18336661 0.132016036 0.361892799 7.03256658 0.03283927 0.122216623 25837.25481 -4.412246368 -0.20055839 RTIQEVLEEQS(ph)EDEDREAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RTIQEVLEEQSEDEDREAK 19 2 P18858;P18858-3;P18858-2;M0R0Q7 P18858 LIG1 DNA ligase 1;DNA ligase 1 RTIQEVLEEQS(1)EDEDREAK;RTIQEVLEEQS(1)EDEDREAK 157.83 1.10E-09 161741000 115370 92982 52990 65591 88025 84577 104505 120628 78675 TRUE FALSE 100123.5622 92371.19512 78616.14124 80484.43905 86273.47472 87830.73192 94370.12118 94832.64093 69374.13113 1.443240594 1.331493362 1.133219832 1.160150588 1.243597193 1.266044425 1.360307072 1.366974107 1 16.08211018 4.485726186 5.587794269 1.239159569 1.420468522 0.304785109 0.109070515 0.215969434 23.46055826 0.028309267 0.0948564 30600.33537 -4.485726186 0.181308952 RTIQFVDWCPTGFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTIQFVDWCPTGFK 14 1 Q9BQE3;F5H5D3;A0A1W2PQM2 Q9BQE3 TUBA1C Tubulin alpha-1C chain 0 107.35 0.0014253 321250000 599940 447130 275420 290300 490210 455910 631060 653010 316350 FALSE TRUE 520656.4089 444192.7736 408614.0332 356217.052 480455.7801 473449.1527 569859.8983 513368.8932 278951.4634 1.866476708 1.592365812 1.464821257 1.27698578 1.722363361 1.697245632 2.042863986 1.840352035 1 18.08965459 RTLEGELHDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 155.99 2.03E-05 1487120000 1503660 1400540 775750 954170 1389740 1410230 1287660 1460110 833310 FALSE TRUE 1304947.521 1391339.761 1150905.295 1170828.882 1362086.893 1464482.461 1162782.931 1147876.839 734797.0411 1.7759292 1.893502127 1.566290051 1.593404459 1.853691314 1.993043492 1.582454564 1.562168565 1 19.48698629 1.001379372 1.423166192 0.246370317 1.762813024 0.747827972 0.137952473 1.172288173 1.323004003 3.026767539 0.041806055 10.03181171 -1.001379372 1.516442707 RTLS(ph)MDKGF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTLSMDKGF 9 2 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 1 RTLS(1)MDKGF 166.7 4.77E-05 332770000 844870 616380 224910 439780 614820 324210 1028600 824660 248480 TRUE FALSE 733218.2889 612330.9592 333677.2283 539638.7706 602586.2849 336682.5685 928846.5303 648312.8765 219104.9775 3.34642461 2.794692144 1.522910306 2.462923375 2.750217233 1.536626746 4.239276264 2.958914416 1 17.74126273 3.265679658 22.79765018 2.63739662 2.478460759 0 0.962725547 865.367727 727457.5362 0.281713581 0.363523528 1843.65501 -3.265679658 -0.158935861 RTNPPGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RTNPPGGK 8 1 A6NGP5;Q9H910;Q9H910-3;H3BMV3;H3BTV5;Q9H910-2;H3BU16;H3BMT0 A6NGP5;Q9H910-2 HN1L Hematological and neurological expressed 1-like protein 0 ;; 87.308 0.024719 258966000 335809 272619 163198 213111 171741 235873 303017 331457 307098 FALSE TRUE 291430.9898 270828.1478 242121.0987 261501.1097 168323.6901 244947.1869 273630.458 260577.5 270793.2243 1.076212267 1.000128968 0.894118009 0.965685572 0.621594911 0.904554342 1.010477491 0.962274816 1 18.04683212 4.472602585 2.653989865 0.910004376 1.076240482 0.209991667 0.10948801 0.536705408 6.812519776 0.029958451 0.150610019 29689.47955 -4.472602585 0.166236106 RTNS(ph)DSALHQSTMTPTQPESFSSGSQDVHQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTNSDSALHQSTMTPTQPESFSSGSQDVHQK 31 1 M0QXN6;M0QX46;Q6UUV9;Q6UUV9-2;Q6UUV9-3 M0QXN6 CRTC1 CREB-regulated transcription coactivator 1 1 RT(0.101)NS(0.741)DS(0.158)ALHQSTMTPTQPESFSSGSQDVHQK 243.63 2.29E-46 326910000 108460 127920 16097 67240 152010 136120 136020 163020 71430 TRUE FALSE 94126.7362 127079.6851 23881.56304 82507.8697 148985.2984 141356.6245 122828.8013 128159.4416 62985.62677 1.494416123 2.017598167 0.379158933 1.309947585 2.365385661 2.244267966 1.950108424 2.03474107 1 15.94273502 3.301044984 11.16605512 1.951797328 1.284637279 0.247161295 0.534487842 0.77842295 135.7910474 0.154423048 0.199296694 2000.069024 -3.301044984 -0.667160049 RTNS(ph)SSSSPVVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RTNSSSSSPVVLK 13 1 Q7Z589-4;E9PMC9;Q7Z589-6;Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-4;Q7Z589-7 EMSY;C11orf30 Protein EMSY 1 RT(0.037)NS(0.906)S(0.024)S(0.01)S(0.01)S(0.014)PVVLK;RT(0.033)NS(0.587)S(0.248)S(0.071)S(0.021)S(0.04)PVVLK 110.35 0.0002286 0 127121 127222 88117 110017 167776 157613 179978 213144 104539 TRUE FALSE 110321.6378 126386.2703 130730.6759 134998.0414 164437.5858 163676.4741 162523.7613 167564.8143 92180.51851 1.196799926 1.371073545 1.41820287 1.464496442 1.783864839 1.775608087 1.763103136 1.817789887 1 16.49217426 3.7476572 1.609409649 1.665339447 1.283577485 0.232996124 0.24290499 0.516516387 2.593839096 0.075402222 0.167659293 5593.159442 -3.7476572 -0.381761962 RTNS(ph)TGGSSGSSVGGGSGK ddPTM_MDA-MB-175_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(0.182)NS(0.661)T(0.117)GGS(0.03)S(0.01)GS(0.001)SVGGGSGK 99.996 0.00043304 153610000 88603 78940 55365 49139 76452 84136 105650 116210 64642 TRUE FALSE 76893.88906 78421.43794 82139.69918 60296.76099 74930.75478 87372.76636 95404.07926 91359.39585 57000.0964 1.349013316 1.375812374 1.441044917 1.057836123 1.314572422 1.532852958 1.673752946 1.602793708 1 15.79867674 2.748995278 20.29317958 1.496613264 1.304973734 0.092939861 0.204730965 103.168098 200637.7507 0.066950102 0.065913456 561.0418758 -2.748995278 -0.19163953 S(ph)LPTTVPESPNYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLPTTVPESPNYR 13 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 1 S(0.999)LPT(0.001)TVPESPNYR;S(0.996)LPT(0.003)T(0.002)VPESPNYR;S(1)LPTTVPESPNYR;S(0.981)LPT(0.01)T(0.01)VPESPNYR 164.11 3.94E-05 3629940000 264223 425795 341751 521425 578939 662735 574983 653834 641180 TRUE FALSE 229305.2611 422997.9246 507022.9267 639822.5157 567419.2466 688230.8443 519221.2372 514016.6872 565380.4308 0.405576933 0.748165132 0.896781882 1.131667247 1.003606095 1.217288054 0.918357284 0.90915189 1 19.10886242 4.606696345 1.57434871 1.016287561 0.273635321 0.816957427 0.094718117 0.357749579 1.03415324 0.028295596 0.379206526 40429.31142 -4.606696345 -0.74265224 down RTPDGTENGDFLALDLGGTNFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RTPDGTENGDFLALDLGGTNFR 22 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;; 189.19 3.56E-17 391060000 445840 422190 184907 205588 384240 451080 330576 436710 130994 FALSE TRUE 386921.1144 419416.6061 274328.6437 252269.8976 376594.3758 468433.3395 298516.7904 343322.965 115508.0385 3.349733224 3.631059893 2.374974479 2.184002956 3.260330454 4.055417661 2.584381089 2.972286339 1 16.81763373 1.170242034 3.066057352 0.369863718 3.059453773 0.559067939 0.570879531 0.44275799 4.498486703 3.208687582 0.153875391 14.79932932 -1.170242034 2.689590055 RTPEPLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RTPEPLSR 8 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 0 ; 72.243 0.074813 282450000 482480 441530 393180 360080 319680 427720 433680 449580 402340 FALSE TRUE 418719.0456 438629.5604 583323.1631 441841.6675 313318.9934 444174.6652 391621.7804 353440.8156 354775.8235 1.180235568 1.236356965 1.644202125 1.245410871 0.883146406 1.251986848 1.103857012 0.996237038 1 18.43654817 3.467279469 22.54391958 1.056027251 1.359029468 0.469376836 0.151154375 53.54712094 122654.9066 0.043220806 0.055904755 2932.779884 -3.467279469 0.303002217 RTPS(ph)DDEEDNLFAPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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(0.076)PS(0.924)DDEEDNLFAPPK;RT(0.015)PS(0.985)DDEEDNLFAPPK;RT(0.017)PS(0.983)DDEEDNLFAPPK;RT(0.019)PS(0.981)DDEEDNLFAPPK;RT(0.017)PS(0.983)DDEEDNLFAPPK;RT(0.224)PS(0.776)DDEEDNLFAPPK;RT(0.107)PS(0.893)DDEEDNLFAPPK;RT(0.019)PS(0.981)DDEEDNLFAPPK 241.65 3.98E-20 5819430000 6646240 5510900 3778210 4578390 5326770 4488230 6421820 7376990 6435040 TRUE FALSE 5767922.545 5474698.535 5605364.993 5617983.426 5220777.699 4660895.112 5799032.885 5799478.096 5674296.902 1.016499955 0.964824124 0.987851903 0.990075691 0.92007482 0.821404871 1.021982632 1.022061093 1 22.43601021 RTPS(ph)EADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RTPSEADR 8 1 P49757-3;P49757;G3V3Z8;P49757-8;P49757-7;P49757-6;P49757-5;P49757-4;P49757-2;P49757-9 P49757-3 NUMB Protein numb homolog 1 RT(0.006)PS(0.994)EADR;RT(0.014)PS(0.986)EADR 111.52 0.0019703 404070000 398310 370230 292800 377030 387830 490880 464230 472320 419690 TRUE FALSE 345672.3243 367797.9348 434399.0594 462640.424 380112.9418 509764.4712 419209.0461 371318.0436 370074.7263 0.934060879 0.993847752 1.173814445 1.250127045 1.027124834 1.377463617 1.132768644 1.003359638 1 18.49745709 4.362381869 4.666310735 1.133812103 0.948033002 0.284156001 0.116109013 0.276339864 9.747713195 0.030653069 0.087755651 23034.66334 -4.362381869 -0.185779102 RTPS(ph)EAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RTPSEAER 8 1 A0A0C4DGH3;Q9Y6R0 A0A0C4DGH3 NUMBL Numb-like protein 1 RT(0.045)PS(0.955)EAER;RT(0.083)PS(0.917)EAER 84.507 0.0094403 215070000 354460 375110 226690 265610 320330 397150 299050 362620 331830 TRUE FALSE 307617.2129 372645.8777 336318.0422 325920.8101 313956.0597 412428.6175 270048.177 285076.5349 292601.4354 1.051318195 1.273561345 1.149406672 1.113872902 1.072981953 1.409523562 0.922921573 0.974282763 1 18.15857732 2.181562073 24.99999762 0.965731143 1.173721913 0.479822969 0.104326058 67.97426657 29813.35473 0.040188357 0.027094997 151.9015036 -2.181562073 0.20799077 RTPS(ph)TKPTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RTPSTKPTVR 10 2 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 RT(0.012)PS(0.983)T(0.005)KPTVR;RT(0.002)PS(0.992)T(0.006)KPTVR;RT(0.023)PS(0.953)T(0.023)KPTVR;RT(0.184)PS(0.796)T(0.02)KPTVR 122.97 0.00024762 588830000 686990 650620 369975 495795 566250 480670 805250 812370 820160 TRUE FALSE 596202.5309 646346.0344 548896.1475 608372.8325 554982.7328 499161.6859 727156.9789 638650.9974 723201.6191 0.824393247 0.893728688 0.758980806 0.841221613 0.767396972 0.690210963 1.005469235 0.883088451 1 19.46403838 2.225898678 24.99452344 0.94801074 0.799505669 0.603685767 0.063311817 168.9613405 333525.0847 0.025681713 0.017443417 168.2281534 -2.225898678 -0.148505071 RTQAPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RTQAPTK 7 1 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 0 ;;; 140.35 0.0042171 1721140000 2043350 2366580 1406090 1682500 1502530 2013370 2535980 2847860 2579840 FALSE TRUE 1773316.12 2351033.78 2086079.827 2064537.34 1472632.593 2090825.647 2290041.05 2238867.301 2274854.254 0.779529553 1.033487651 0.917016914 0.907547082 0.647352502 0.919103122 1.006675942 0.984180546 1 21.11734269 2.468039145 12.60483697 0.990194111 0.863976519 0.293010319 0.098830396 0.77848082 1064.772829 0.037403442 0.029355272 293.7914447 -2.468039145 -0.126217591 RTQAPTKAS(ph)E ddPTM_MDA-MB-175_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;RTQAPTKAS(1)E;RTQAPT(0.001)KAS(0.999)E 173.59 2.65E-06 1301598000 1609172 1045076 915598 1040725 1170767 1328555 1763934 1725098 1352344 TRUE FALSE 1396515.843 1038210.827 1358384.255 1277037.518 1147471.027 1379665.371 1592867.952 1356199.217 1192471.433 1.171110523 0.870637902 1.139133582 1.070916655 0.962262907 1.156979809 1.335770324 1.137301222 1 20.18552327 2.620288341 7.366072289 1.172500095 1.040462583 0.191371275 0.115661219 0.391726687 22.29940397 0.038987551 0.034306197 417.1462473 -2.620288341 -0.132037512 RTQSSGQDGRPQEEPPAEEDLQQITVQVEPACS(ph)VEIVVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTQSSGQDGRPQEEPPAEEDLQQITVQVEPACSVEIVVPK 40 2 O60331-4;O60331;O60331-2;O60331-3 O60331-4 PIP5K1C Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma 1 RT(0.182)QS(0.182)S(0.182)GQDGRPQEEPPAEEDLQQIT(0.202)VQVEPACS(0.251)VEIVVPK 51.632 0.017059 33312000 15546 11610 12025 17303 19425 15246 19060 25304 19065 TRUE FALSE 13491.55671 11533.73315 17840.33022 21231.91061 19038.4805 15832.52349 17211.56413 19892.93652 16811.15742 0.802535862 0.68607609 1.061219628 1.262965427 1.132490764 0.941786642 1.023817915 1.183317485 1 14.03713143 4.200494522 7.040902981 1.095684205 0.744303 0.687293626 0.095877293 0.095404473 13.35939093 0.02527506 0.054595765 15866.98904 -4.200494522 -0.351381204 RTS(ph)FSFQK ddPTM_MDA-MB-175_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(0.224)S(0.775)FSFQK;RT(0.032)S(0.968)FSFQK 187.35 0.00012414 1649770000 1123940 1054590 654440 800760 1008730 912540 1168250 1333890 1134850 TRUE FALSE 975408.4813 1047662.329 970929.373 982584.7969 988658.2465 947646.0043 1054953.295 1048648.004 1000689.326 0.97473657 1.046940646 0.970260547 0.981907942 0.987977208 0.946993217 1.054226589 1.047925642 1 19.93256271 2.221133252 24.99975262 1.037782014 0.986978845 0.390832791 0.028773363 239.1949425 343125.3157 0.011628175 0.007860105 166.3923105 -2.221133252 -0.05080317 RTS(ph)FSTSDVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RTSFSTSDVSK 11 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 RT(0.23)S(0.764)FS(0.006)TSDVSK;RT(0.032)S(0.688)FS(0.063)T(0.026)S(0.081)DVS(0.11)K;RT(0.016)S(0.978)FS(0.003)T(0.003)S(0.001)DVSK 156.72 1.89E-05 1263803000 2542800 2412430 1864020 2119830 2742170 2426840 3232220 3374850 3035840 TRUE FALSE 2206762.537 2396582.588 2765466.307 2601169.801 2687606.182 2520202.105 2918759.802 2653164.591 2676946.454 0.824358117 0.895267287 1.033067472 0.971692877 1.003982048 0.941446588 1.090331784 0.991116048 1 21.35215685 4.413152366 3.61403041 1.004360879 0.83478672 0.713463824 0.039304251 0.110063412 2.803827839 0.009592384 0.032627019 25891.21112 -4.413152366 -0.169574159 RTS(ph)NERPGSGQGQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RTSNERPGSGQGQGR 15 2 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 RT(0.443)S(0.557)NERPGSGQGQGR;RT(0.376)S(0.603)NERPGS(0.021)GQGQGR 75.017 0.026053 1413700000 107803 107343 56800 66817 95087 90440 90070 107136 88660 TRUE FALSE 93556.56041 106637.8568 84268.66998 81988.82108 93194.95473 93919.28532 81335.02526 84225.80013 78178.7158 1.196701167 1.364026713 1.077897854 1.048735839 1.192075794 1.201340855 1.040373002 1.077349497 1 16.25448827 7.999999972 0.054011593 0.484497298 2.345273633 0.385165715 0.084731775 1021.388787 5.377418299 49.6289728 170.8952356 99999993.52 -7.999999972 1.860776335 RTS(ph)PSDGAMANYESTEVMGDGESAHDSPR ddPTM_MDA-MB-175_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(0.321)S(0.584)PS(0.093)DGAMANYES(0.001)T(0.001)EVMGDGESAHDSPR 185.02 4.71E-18 186610000 29867 44449 14819 19740 56758 66220 52499 47193 42464 TRUE FALSE 25920.00028 44157.01159 21985.51797 24222.26871 55628.62685 68767.52625 47407.65506 37101.14421 37443.9543 0.692234588 1.179282809 0.587158017 0.646893982 1.485650431 1.836545513 1.266096382 0.990844715 1 15.19244518 3.241547484 24.99941421 1.297510662 0.791653464 0.4678964 0.285270491 83.94496987 702595.3983 0.092958447 0.114829721 1744.00403 -3.241547484 -0.505857198 RTS(ph)SEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RTSSEELR 8 1 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RT(0.216)S(0.771)S(0.013)EELR;RT(0.125)S(0.857)S(0.019)EELR;RT(0.027)S(0.963)S(0.01)EELR 114.71 0.0015949 1647330000 1857640 1625680 1096440 1481360 1339760 1882430 1713040 1796010 2395820 TRUE FALSE 1612148.167 1615000.801 1626682.051 1817725.429 1313101.397 1954848.3 1546909.644 1411947.238 2112588.889 0.763114951 0.764465254 0.769994607 0.860425537 0.621560306 0.925333041 0.73223411 0.668349268 1 21.01058061 1.224288351 24.98606279 1.000000615 0.761221413 0.430757494 0.085528362 723.2271915 1266059.542 0.419980623 0.019945431 16.76055329 -1.224288351 -0.238779202 RTS(ph)SEELRDATSLLAAGEGGLLDEVEPLRPDELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTSSEELRDATSLLAAGEGGLLDEVEPLRPDELER 35 3 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RT(0.217)S(0.652)S(0.131)EELRDATSLLAAGEGGLLDEVEPLRPDELER 334.01 5.31E-117 44986000 15840 13403 7129.8 6308.4 14078 12789 15886 15201 3049 TRUE FALSE 13746.70387 13314.95481 10577.79513 7740.818638 13797.87534 13281.00111 14345.37817 11950.38444 2688.550693 5.113053624 4.952465595 3.934385598 2.879178978 5.132086732 4.939836596 5.335729098 4.444916911 1 11.39261296 4.281891416 6.909459915 4.109653009 5.048691721 0.101381003 1.272618985 0.548690644 65.32274102 0.320765837 0.845412258 19137.77375 -4.281891416 0.939038712 RTSS(ph)PPRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RTSSPPRK 8 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RT(0.287)S(0.287)S(0.425)PPRK;RT(0.154)S(0.154)S(0.692)PPRK 63.073 0.059553 618300000 76915 65982 41533 52680 46382 52576 64260 76932 64290 TRUE FALSE 66750.48787 65548.5599 61618.49772 64641.79916 45459.08894 54598.63274 58028.07509 60480.69049 56689.70944 1.177470983 1.15626911 1.086943262 1.140273955 0.801893137 0.963113646 1.023608617 1.066872473 1 15.79079925 3.372048832 22.43753268 0.98518581 1.137668545 0.571160664 0.07223868 4.306597756 904.5507325 0.022428725 0.028955343 2355.314097 -3.372048832 0.152482735 RTT(ph)PLSAEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTTPLSAEIR 10 1 A0A2R8Y8C6;Q8WXX7-2;Q8WXX7;A0A087WVB5;Q75MD7;A0A2R8Y568;A0A024RDL5;A0A2R8Y522;Q8WXX7-5 A0A2R8Y8C6 AUTS2 Autism susceptibility gene 2 protein 1 RT(0.083)T(0.917)PLSAEIR 115.12 0.00074168 227060000 126140 130770 77994 72076 118740 133210 87107 103890 97560 TRUE FALSE 109470.2794 129910.9633 115712.1593 88441.95741 116377.3063 138334.6749 78659.37655 81673.93197 86026.56794 1.272517107 1.510126073 1.345074691 1.02807725 1.35280657 1.608045958 0.91436144 0.949403585 1 16.39249466 2.215831996 24.99883413 0.951831854 1.344819455 0.605938145 0.151276737 162.6792072 178926.8036 0.06358462 0.042902131 164.3735731 -2.215831996 0.392987601 RTTWAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RTTWAEER 8 1 Q9BX40;Q9BX40-2 Q9BX40 LSM14B Protein LSM14 homolog B 0 108.15 0.0062 172100000 198220 244990 121210 147020 203760 242650 190720 215900 154290 FALSE TRUE 172024.7248 243380.6446 179827.5614 180403.1381 199705.5746 251984.9025 172224.0038 169731.4651 136050.012 1.26442271 1.78890572 1.321775418 1.326006043 1.467883551 1.852149065 1.265887458 1.247566705 1 17.05377756 1.645087992 1.957790787 1.027930134 1.495348351 0.38326931 0.201245621 0.361010403 2.688577289 0.255646295 0.055947617 44.16599223 -1.645087992 0.467418217 RTVQS(ph)LEIDLDSMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RTVQSLEIDLDSMR 14 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 RT(0.006)VQS(0.994)LEIDLDSMR;RT(0.031)VQS(0.969)LEIDLDSMR 161.86 2.77E-06 62435000 58695 59249 35450 39585 65579 67265 64805 65289 30026 TRUE FALSE 50938.30704 58859.78942 52593.73857 48573.37927 64274.1062 69852.72808 58520.22107 51327.45543 26476.36049 1.923916509 2.223107268 1.986441399 1.834594271 2.427603531 2.638305522 2.210281927 1.938614465 1 14.6924172 1.226773418 2.611553229 0.699091864 2.183199422 0.709499348 0.235461925 0.306101566 2.283007399 1.026407932 0.066577287 16.8567334 -1.226773418 1.484107559 RTVQSLEIDLDSMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RTVQSLEIDLDSMR 14 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 199.84 3.22E-08 2869710000 1790380 1780500 898097 1023617 1853880 1977520 1771570 1873430 975749 FALSE TRUE 1553776.747 1768803.778 1332419.713 1256044.885 1816991.415 2053596.474 1599763.414 1472811.574 860397.0648 1.805883365 2.05579941 1.548610249 1.459843294 2.111805688 2.386800883 1.859331557 1.711781262 1 19.71464308 1.211682838 2.469153664 0.733468291 1.891284674 0.523024661 0.265463993 0.531737917 3.30723452 1.363656519 0.075547664 16.28106603 -1.211682838 1.157816383 RVAFISLS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVAFISLSPVR 11 1 Q6ZU65;Q6ZU65-2 Q6ZU65 UBN2 Ubinuclein-2 1 RVAFISLS(1)PVR;RVAFIS(0.01)LS(0.99)PVR 198.85 3.20E-08 716090000 410270 809000 346880 364950 760120 756500 652740 739710 246850 TRUE FALSE 356051.78 803685.6257 514632.3282 447817.4754 744995.0991 785603.0445 589437.3753 581528.7729 217667.6742 1.635758646 3.692259903 2.364302968 2.057344882 3.422626267 3.609185642 2.707969281 2.671635901 1 17.73176764 RVATPVDWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVATPVDWK 9 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 112.89 0.0030283 1106800000 1955100 1875400 1360500 1550200 1946500 1677500 2216200 2591200 1879100 FALSE TRUE 1696728.581 1863080.374 2018442.351 1902196.603 1907768.458 1742034.51 2001273.265 2037092.045 1656954.939 1.024004058 1.124400145 1.218163695 1.148007444 1.151370151 1.051346944 1.207801865 1.229419097 1 20.66010294 4.692538423 3.824524835 1.152840496 1.016563157 0.201022019 0.072260079 0.328228629 8.927533696 0.017619688 0.113917832 49264.99268 -4.692538423 -0.136277339 RVDAENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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 ;;;;;;;;; 148.04 0.0033842 3503950000 2154671 1985776 1326799.8 1566923.7 1253817.3 2127179 1829364.9 2064454.7 2063809.3 FALSE TRUE 1869925.768 1972731.307 1968444.621 1922717.675 1228868.789 2209012.953 1651953.374 1622987.128 1819828.116 1.027528783 1.084020677 1.081665133 1.056538064 0.675266405 1.21385802 0.907752419 0.891835396 1 20.79537076 3.434460801 24.99984819 0.936500762 1.06682405 0.183264982 0.130845181 222.7149545 130514.465 0.035663142 0.046040955 2719.323034 -3.434460801 0.130323287 RVDIIPGFEFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RVDIIPGFEFDR 12 1 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ;;;;; 138.31 0.00012309 3244260000 1085060 1121958 688868 751025 1086313 1182186 964249 1023410 1039305 FALSE TRUE 941666.5718 1114587.784 1022006.869 921556.7049 1064697.497 1227665.46 870736.2804 804561.7357 916439.5469 1.027527211 1.216215284 1.115192892 1.005583738 1.161776028 1.339603321 0.950129535 0.877921232 1 19.80568019 2.035834442 24.76114918 0.92537605 1.141091674 0.487166305 0.097313355 117.9023444 81468.53812 0.039500072 0.026630836 108.6011546 -2.035834442 0.215715625 RVEDVLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RVEDVLGK 8 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 77.677 0.052261 1112550000 1431750 1504690 1033070 1071620 1435840 1381210 1539910 1704030 1594900 FALSE TRUE 1242540.61 1494805.592 1532666.107 1314947.7 1407269.593 1434346.042 1390569.765 1339636.445 1406352.739 0.883519885 1.062895212 1.089816278 0.935005609 1.000651938 1.019904895 0.988777372 0.952560768 1 20.42352706 1.997231766 23.59277212 0.972225024 1.003018036 0.019235872 0.059136007 178.4416011 1520807.97 0.024115748 0.015871358 99.36461776 -1.997231766 0.030793012 RVEELVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVEELVAK 8 1 Q9NWB6;Q9NWB6-2;Q9NWB6-3 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 0 104.89 0.0072051 222290000 259120 234280 147490 206610 194480 215770 235460 290880 252290 FALSE TRUE 224876.6355 232740.9993 218816.6573 253523.9583 190610.2285 224070.8115 212625.1254 228677.5756 222464.5636 1.010842499 1.046193585 0.983602304 1.139615021 0.856811644 1.007220242 0.955770762 1.027928097 1 17.76321602 3.251225697 24.99999686 0.97769442 1.040753954 0.271285983 0.060507272 359.3254084 709279.4038 0.016709204 0.0214253 1783.305286 -3.251225697 0.063059534 RVEHHDHAVVSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RVEHHDHAVVSGR 13 1 O95831-3;O95831;E9PMA0;O95831-5;O95831-2 O95831-3 AIFM1 "Apoptosis-inducing factor 1, mitochondrial" 0 ;; 77.078 0.01748 52598000 38648.2 30145.8 26733.2 38239.4 36753.5 50225.4 24079.8 32790.2 33711.3 FALSE TRUE 33540.74245 29947.77025 39661.46494 46922.24022 36022.17726 52157.60364 21744.5447 25778.2709 29725.98852 1.1283306 1.00746087 1.334235358 1.578492173 1.211807548 1.754612924 0.731499465 0.867196423 1 14.85943717 2.21206542 24.99999448 0.860818886 1.326219054 0.501805888 0.220408755 185.5491772 175076.7276 0.091340947 0.061602235 162.9541479 -2.21206542 0.465400169 RVEIQMPKPAEAPTAPS(ph)PAQTLENSEPAPVSQLQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVEIQMPKPAEAPTAPSPAQTLENSEPAPVSQLQSR 36 2 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;K7EJ51 Q9UHD8 9-Sep Septin-9 1 RVEIQMPKPAEAPT(0.002)APS(0.998)PAQTLENSEPAPVSQLQSR;RVEIQMPKPAEAPT(0.003)APS(0.996)PAQTLENSEPAPVSQLQSR 315.88 5.39E-110 458720000 457530 394340 234083 257870 338720 367460 476840 471980 161719 TRUE FALSE 397066.2513 391749.5546 347286.3218 316423.3248 331980.1347 381596.424 430596.1302 371050.75 142600.7641 2.784460896 2.747177108 2.435374902 2.218945508 2.328038962 2.675977415 3.019592027 2.602024978 1 17.12162219 4.231033714 4.59669029 2.393926882 2.775238251 0.098024621 0.526261852 0.512012729 26.85977148 0.136066944 0.338422075 17022.9065 -4.231033714 0.381311369 RVEISAPSNFEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVEISAPSNFEHR 13 1 O96013;O96013-4;O96013-2;O96013-3;M0R2X4;M0R0L9;M0R3G6 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ; 159.02 3.00E-05 421380000 288310 270920 145681 216136 271780 296130 263450 272280 259560 FALSE TRUE 250209.103 269140.3087 216132.8189 265212.9822 266372.1097 307522.3127 237900.6595 214055.0409 228875.1125 1.093212365 1.175926494 0.944326434 1.158767239 1.163831693 1.343624955 1.039434375 0.935248217 1 17.80420107 2.007250421 24.99889936 0.970301643 1.14437412 0.374359598 0.097769311 173.8403141 599385.8163 0.040898842 0.027510701 101.6834847 -2.007250421 0.174072477 RVELLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVELLK 6 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31;A0A3B3IRR8 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ; 114.72 0.040155 1180520000 1360740 1285850 796840 1020750 1203340 1135810 1193550 1624270 1326130 FALSE TRUE 1180914.761 1277403.167 1182194.489 1252526.889 1179395.888 1179505.346 1077799.705 1276932.501 1169356.422 1.009884359 1.09239847 1.010978746 1.071124992 1.008585463 1.008679068 0.921703327 1.09199597 1 20.1572833 3.213632228 24.75242476 1.010705757 1.046895496 0.146729529 0.04710529 437.143303 434056.5787 0.014049933 0.015938086 1635.431008 -3.213632228 0.036189739 RVELSGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RVELSGPK 8 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 0 ;; 110.76 0.0053949 1865630000 3313640 2713320 2204840 2327020 2308140 2202980 2795600 3091350 2821970 FALSE TRUE 2875734.078 2695496.022 3271107.999 2855405.457 2262212.53 2287730.066 2524483.142 2430288.859 2488359.921 1.155674488 1.083242018 1.31456385 1.147505002 0.909117893 0.919372654 1.014516879 0.976662917 1 21.24676374 3.32265298 5.955762228 0.967497603 1.182393599 0.726533473 0.06458244 0.110035475 6.116272485 0.018861333 0.024333659 2102.098102 -3.32265298 0.214895995 RVES(ph)EES(ph)GDEEGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 92.812 0.02366 858640000 2332190 1385670 1609170 1334270 1404410 1209370 2022960 2161670 2963400 TRUE FALSE 2023985.182 1376567.443 2387369.994 1637236.397 1376464.989 1255895.246 1826773.651 1699413.693 2613070.228 0.774562107 0.526800783 0.913626419 0.6265566 0.526761575 0.480620549 0.699090913 0.650351328 1 21.31731447 1.236566454 6.651989612 1.009492793 0.646041229 0.425318961 0.127864538 0.120155879 26.18339111 0.195805605 0.031183654 17.24115888 -1.236566454 -0.363451565 IADPEHDHTGFLTEY(ph)VATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 IADPEHDHTGFLTEYVATR 19 0 P27361;E9PQW4;P27361-3;P27361-2;E9PJF0;B3KR49 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 1 IADPEHDHTGFLT(0.017)EY(0.983)VATR;IADPEHDHTGFLTEY(1)VATR;IADPEHDHTGFLT(0.004)EY(0.996)VATR;IADPEHDHTGFLTEY(1)VATR;IADPEHDHTGFLTEY(1)VATR;IADPEHDHTGFLT(0.001)EY(0.998)VAT(0.001)R;IADPEHDHTGFLT(0.001)EY(0.999)VATR;IADPEHDHTGFLT(0.002)EY(0.998)VATR 327.7 2.68E-75 12372860000 2750070 4454690 3753010 5181950 6849950 6940770 6780760 7430550 7295600 TRUE FALSE 2386641.282 4425426.848 5567978.189 6358590.949 6713649.397 7207785.913 6123162.939 5841584.707 6433122.479 0.370992669 0.68791273 0.865517205 0.988414408 1.04360665 1.120417952 0.951818181 0.90804811 1 22.61708773 4.609934595 1.303169234 0.99701453 0.189206543 0.928975479 0.057078026 0.305190901 0.545013055 0.019603843 0.309187502 40731.89306 -4.609934595 -0.807807987 down RVGDPPQPLPEEPMEVQGAERAS(ph)PEPQRENAS(ph)PAPGTTAEEAMSR ddPTM_MDA-MB-175_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(0.992)PEPQRENAS(0.942)PAPGT(0.029)T(0.028)AEEAMS(0.009)R 56.221 0.0076413 95530000 33384 34988 12876 16211 26521 32808 28223 28048 15835 TRUE FALSE 28972.21982 34758.16152 19102.87667 19891.95532 25993.28399 34070.14499 25485.9378 22050.15347 13963.00434 2.074927366 2.489303926 1.368106476 1.424618573 1.861582461 2.440029679 1.825247431 1.57918403 1 13.76932177 1.340904466 2.042878226 0.838341467 1.924136468 0.4036378 0.362115279 0.658477836 3.339012215 1.259733074 0.105296706 21.92322625 -1.340904466 1.085795001 RVGDPPQPLPEEPMEVQGAERAS(ph)PEPQRENASPAPGTTAEEAMSR ddPTM_MDA-MB-175_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 1 RVGDPPQPLPEEPMEVQGAERAS(0.967)PEPQRENAS(0.025)PAPGT(0.002)T(0.002)AEEAMS(0.003)R 63.052 0.0025342 146170000 32836 34234 11926 11480 20280 18433 22683 27688 3744.6 TRUE FALSE 28496.6394 34009.1146 17693.45349 14086.70946 19876.46768 19142.12944 20483.20615 21767.13667 3301.917654 8.630330127 10.29980701 5.358538687 4.266220705 6.019673947 5.797276445 6.203427311 6.592271204 1 11.68908843 4.230787032 24.98412909 5.270757109 9.465068763 0.555725191 1.636531485 113.5319666 364893.2635 0.405880457 0.87053923 17013.24013 -4.230787032 4.194311655 RVGEYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVGEYQR 7 1 P31350;P31350-2 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 0 ; 122.74 0.0069128 108982000 186200 170774 143166 134964 138040 176874 152753 214410 161529 FALSE TRUE 161593.1982 169652.1743 212401.5565 165609.639 135293.2741 183678.4572 137939.0376 168560.09 142433.2256 1.134518983 1.191099714 1.49123602 1.162717746 0.949871587 1.289575915 0.968447053 1.183432372 1 17.1199262 3.484710024 24.94039775 1.090336244 1.274634808 0.298206945 0.135251991 418.9487333 1376870.242 0.036274031 0.048965987 3052.882043 -3.484710024 0.184298564 RVGFQYEGTYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVGFQYEGTYK 11 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 150.51 5.43E-05 1432610000 1729540 1752480 956690 1084920 1632370 1632450 2075210 2222710 941200 FALSE TRUE 1500976.907 1740967.843 1419348.484 1331267.668 1599889.031 1695251.408 1873956.454 1747400.764 829932.4082 1.808553193 2.097722449 1.710197686 1.604067578 1.927734132 2.04263792 2.257962739 2.105473586 1 19.66263432 1.23307824 24.98550505 0.999998479 1.955955088 0.694657448 0.196616318 112.0153388 510445.2093 0.452338058 0.053490107 17.10323408 -1.23307824 0.955956609 RVGMADANS(ph)PPKPLSKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVGMADANSPPKPLSKPR 18 3 P26358;P26358-2;K7EJL0 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 RVGMADANS(1)PPKPLSKPR;RVGMADANS(1)PPKPLSKPR 143.93 5.63E-07 1459680000 2081920 1657840 1134990 1312850 1719430 1241010 2161740 2519230 1362960 TRUE FALSE 1806788.997 1646949.54 1683874.96 1610952.658 1685216.707 1288752.458 1952094.788 1980512.269 1201832.421 1.503361837 1.370365377 1.401089645 1.340413713 1.402206062 1.072322925 1.624265374 1.647910502 1 20.19680432 4.74397953 21.25099281 1.385872731 1.503362236 0.032057576 0.204263292 339.6189565 1331470.852 0.050308143 0.393016496 55459.95714 -4.74397953 0.117489506 RVHNNS(ph)PDTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVHNNSPDTSR 11 1 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 1 RVHNNS(1)PDTSR 88.087 0.00811 75091000 46376 43076 21600 24231 34810 40882 38299 40891 22650 TRUE FALSE 40247.2941 42793.03092 32045.83225 29733.0189 34117.3491 42454.75699 34584.76887 32146.77786 19972.3428 2.015151377 2.142614482 1.604510425 1.488709622 1.708229697 2.125677364 1.73163305 1.609564696 1 14.28571595 1.157844474 1.816155982 0.574168448 1.828912258 0.600885805 0.213478665 0.859965114 2.241449334 2.01376682 0.06328531 14.3828342 -1.157844474 1.254743809 RVIISAPSADAPMFVMGVNHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RVIISAPSADAPMFVMGVNHEK 22 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;; 311.27 2.17E-67 25513790000 5381020 4993360 2975540 3317900 4746500 4118770 5751020 6601440 2180170 FALSE TRUE 4669904.573 4960558.289 4414521.097 4071279.906 4652053.936 4277221.747 5193286.966 5189773.428 1922432.786 2.429164029 2.580354603 2.296320125 2.117774902 2.419878588 2.224900541 2.701414064 2.699586412 1 20.87450173 1.232291401 24.99982753 0.99999762 2.442153441 0.848175206 0.190595685 86.59649353 345288.146 0.471038788 0.051841097 17.07227513 -1.232291401 1.442155821 RVIISAPSADAPMFVMGVNHEKYDNSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVIISAPSADAPMFVMGVNHEKYDNSLK 28 2 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 322.77 1.62E-83 3367900000 2344500 1556660 684850 1104640 1745740 1194550 2980600 3378800 354200 FALSE TRUE 2034668.385 1546434.198 1016045.751 1355465.395 1711003.189 1240505.111 2691541.871 2656269.914 312326.8795 6.514547797 4.9513324 3.2531486 4.339893504 5.478245075 3.971816686 8.617708072 8.504775247 1 18.25269721 2.264019806 24.99803908 6.661522259 4.706798579 0.044801419 2.260479152 433.2960099 425446.3125 0.83852948 0.649276929 183.6622101 -2.264019806 -1.954723679 RVLPPNWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVLPPNWK 8 1 P62277 P62277 RPS13 40S ribosomal protein S13 0 77.046 0.05488 355550000 419300 931180 289340 1020800 495120 540890 572310 563900 547010 FALSE TRUE 363888.4426 925063.0173 429265.7918 1252588.242 485268.0807 561698.3883 516807.4643 443314.3733 482343.101 0.754418259 1.917852697 0.889959431 2.59688226 1.006064106 1.164520415 1.071451967 0.919085133 1 18.87970021 RVLQALEGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVLQALEGLK 10 1 P39019;A0A075B6E2 P39019 RPS19 40S ribosomal protein S19 0 ; 184.24 2.53E-06 5379000000 6063900 9038600 5362600 6430200 8953200 7451400 10067800 11422500 8851000 FALSE TRUE 5262540.251 8979224.841 7955971.297 7890275.189 8775048.837 7738060.18 9091426.306 8979887.265 7804644.863 0.674283115 1.150497556 1.019389279 1.010971713 1.124336724 0.991468583 1.164873798 1.150582432 1 22.89590156 4.744543129 24.86272187 1.081446669 0.674282922 0.774168685 0.06822747 290.9141619 1208973.257 0.016647164 0.146900479 55531.97624 -4.744543129 -0.407163747 RVLVDVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVLVDVER 8 1 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ; 110.76 0.0053949 695650000 557500 461780 264240 344670 486850 499950 456940 519770 335800 FALSE TRUE 483824.9625 458746.5368 392027.3478 422932.5915 477162.6375 519183.4 412626.0291 408621.2304 296102.1065 1.633980143 1.549284948 1.32396001 1.428333612 1.61148005 1.753393132 1.393526152 1.380001092 1 18.17573523 1.125342793 1.525149402 0.666461782 1.531990794 0.651554389 0.122675899 1.036391208 1.724420829 1.488511357 0.037387666 13.34574411 -1.125342793 0.865529012 RVLVWDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVLVWDLR 8 1 O43684;O43684-2;J3QT28 O43684 BUB3 Mitotic checkpoint protein BUB3 0 80.239 0.041632 472020000 195060 383270 202280 170250 382440 384640 345950 369390 267130 FALSE TRUE 169282.3268 380752.2741 300103.2846 208907.8646 374830.1922 399437.3497 312399.8222 290398.8231 235550.1957 0.71866774 1.616437944 1.274052368 0.886893191 1.591296458 1.695763183 1.326255838 1.232853245 1 17.84567501 4.757475754 24.09911135 1.324693076 0.718666858 0.354005734 0.258624853 3157.092952 4022234.544 0.064363499 2.113954221 57210.50135 -4.757475754 -0.606026219 RVMGLVPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVMGLVPAK 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 78.334 0.048206 256620000 428420 446240 310560 344280 506450 458940 528320 576880 446780 FALSE TRUE 371803.2115 443308.6201 460747.8548 422454.036 496372.6359 476595.7188 477083.6077 453518.7013 393962.1774 0.94375357 1.125256803 1.169523069 1.072321305 1.259949976 1.209749936 1.210988351 1.151173202 1 18.5876976 4.747963239 2.895402144 1.159209606 0.903367238 0.440563076 0.073399134 0.397744104 4.670617232 0.018458942 0.241093749 55971.02225 -4.747963239 -0.255842368 RVNALK ddPTM_MDA-MB-175_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 1267050000 1494220 1494160 840160 1233230 1175370 1280460 1548150 1765540 1422670 FALSE TRUE 1296755.041 1484344.765 1246464.186 1513253.72 1151982.437 1329720.125 1398010.651 1387993.01 1254483.573 1.03369631 1.183231727 0.99360742 1.206276234 0.918292165 1.059974122 1.114411285 1.106425815 1 20.25866215 5.080328998 17.29597382 1.075865178 0.00011792 0.018347054 0.08727862 26776767.3 55090769.59 0.019634792 1091673035 120317.5551 -5.080328998 -1.075747259 RVNNGNTAPEDS(ph)SPAKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVNNGNTAPEDSSPAKK 17 2 G3V167;Q9UGN5-2;Q9UGN5;E9PJ27 G3V167 PARP2 Poly [ADP-ribose] polymerase 2 1 RVNNGNTAPEDS(0.5)S(0.5)PAKK 50.883 0.081389 35426000 104160 72364 55950 58060 68875 64039 96481 121660 71076 TRUE FALSE 90394.99209 71888.63612 83007.60714 71243.41039 67504.52225 66502.62177 87124.28747 95643.95576 62673.47625 1.442316551 1.147034446 1.324445557 1.13673941 1.077082784 1.061096747 1.390130127 1.526067509 1 15.9355674 1.003217792 13.51126806 0.761563246 1.263593111 0.213995108 0.158471267 53695.7445 1607078.378 401193.4171 0.042800918 10.07436756 -1.003217792 0.502029864 RVNNGNTAPEDSS(ph)PAKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVNNGNTAPEDSSPAKK 17 2 G3V167;Q9UGN5-2;Q9UGN5;E9PJ27 G3V167 PARP2 Poly [ADP-ribose] polymerase 2 1 RVNNGNTAPEDS(0.21)S(0.79)PAKK;RVNNGNTAPEDS(0.129)S(0.871)PAKK 102.07 0.00050392 169441000 387700 270600 244433 234233 301180 219890 352580 456770 276620 TRUE FALSE 336464.4627 268822.4108 362641.6164 287419.1827 295187.1072 228349.3106 318386.8459 359093.2901 243918.2987 1.379414601 1.10210022 1.486733953 1.178342028 1.210188447 0.936171299 1.305301191 1.472186761 1 17.89603847 RVNQAIWLLCTGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVNQAIWLLCTGAR 14 1 M0R0F0;M0R0R2;P46782;M0QZN2 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 121.42 0.00018388 506780000 373460 365770 184280 181300 300580 355250 323790 392730 207800 FALSE TRUE 324106.3148 363367.2328 273398.4244 222466.936 294599.0461 368916.6974 292388.8956 308747.7457 183234.1207 1.768809835 1.983076249 1.492071582 1.214113044 1.60777395 2.013362445 1.595712057 1.684990462 1 17.48332865 1.237567054 24.96903893 0.999999203 1.665974412 0.456492047 0.229713291 24.53374524 616228.982 0.348450429 0.058871826 17.28092772 -1.237567054 0.665975208 RVNTTQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RVNTTQK 7 1 P36578;H3BM89;H3BTP7 P36578 RPL4 60S ribosomal protein L4 0 ;;; 113.7 0.0097347 2050730000 1605100 1534960 984339 1235440 784313 1272320 1741230 1925020 1979330 FALSE TRUE 1392981.968 1524876.747 1460368.633 1515965.535 768706.7058 1321266.974 1572365.783 1513369.454 1745335.862 0.798116854 0.87368671 0.836726423 0.86858098 0.440434831 0.757027345 0.90089582 0.867093541 1 20.73507326 2.225346023 7.149226099 0.910880196 0.76089415 0.261247362 0.126529821 0.231549765 57.06794915 0.053410902 0.03745636 168.0142135 -2.225346023 -0.149986045 RVPFSLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVPFSLLR 8 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ; 182.98 0.00036186 702130000 274350 1080000 248500 171179 635210 809660 852580 764710 79946 FALSE TRUE 238093.9524 1072905.409 368675.4312 210047.8083 622570.5638 840808.1441 769896.9228 601182.7175 70494.87495 3.37746471 15.21962284 5.229818925 2.979618141 8.831430145 11.92722371 10.92131766 8.528034384 1 16.10523076 RVPGS(ph)SGHLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RVPGSSGHLHK 11 1 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 1 RVPGS(0.5)S(0.5)GHLHK;RVPGS(0.5)S(0.5)GHLHK;RVPGS(0.5)S(0.5)GHLHK 101.36 0.0015723 1176770000 1419850 1431430 467930 901810 1219670 965490 1166970 1514760 1071380 TRUE FALSE 1232213.225 1422026.842 694222.5131 1106579.744 1195400.953 1002633.025 1053797.429 1190840.362 944722.6769 1.304312107 1.50523204 0.734842648 1.171327598 1.265345887 1.061298781 1.1154569 1.260518447 1 19.84953136 RVPGSS(ph)GHLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RVPGSSGHLHK 11 1 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 1 RVPGS(0.145)S(0.855)GHLHK;RVPGS(0.231)S(0.769)GHLHK;RVPGS(0.109)S(0.891)GHLHK 102.64 0.0013363 3099600000 3568300 3770100 1296570 2360860 3393300 2493770 3048140 3929400 2732270 TRUE FALSE 3096740.114 3745333.965 1923595.589 2896929.346 3325779.969 2589706.946 2752531.852 3089128.389 2409264.153 1.28534686 1.554555137 0.798416224 1.202412505 1.380413171 1.074895396 1.142478233 1.282187503 1 21.20016115 4.277544035 24.99999997 1.150688969 1.419950952 0.332387686 0.170487225 191.9636185 123102.976 0.040713598 0.107714217 18947.15617 -4.277544035 0.269261983 RVPLS(ph)PLSLLAGPADAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RVPLSPLSLLAGPADAR 17 1 Q53ET0;H0YDQ8;Q5T4K5 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 RVPLS(0.816)PLS(0.184)LLAGPADAR;RVPLS(0.999)PLS(0.001)LLAGPADAR;RVPLS(1)PLSLLAGPADAR 149.85 1.89E-07 393507000 268578 332214 156403.2 200426.4 373892 388294 353882 401274 81188.2 TRUE FALSE 233084.7368 330031.6644 232040.3107 245936.2774 366452.2807 403231.9214 319562.5781 315464.6778 71590.22349 3.25581798 4.610010254 3.24122903 3.435333283 5.118747545 5.632499828 4.463773998 4.406532938 1 16.12747496 4.767986515 21.59757334 4.089505617 3.255810231 0.026303779 1.275593035 6394.238718 4692648.938 0.308564989 23.00081385 58611.99651 -4.767986515 -0.833695386 RVPPPALS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RVPPPALSR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 RVPPPALS(1)R;RVPPPALS(1)R;RVPPPALS(1)R 100.04 0.0030205 805300000 265128 261873 220430 222599 286360 363252 298149 295496 358150 TRUE FALSE 230090.6631 260152.739 327030.6853 273143.5052 280661.9963 377226.5395 269234.5559 232306.48 315809.915 0.728573272 0.823763684 1.035530139 0.864898447 0.888705461 1.194473389 0.852520909 0.735589571 1 18.26869694 4.471264116 23.16751248 0.92134271 0.752370768 0.237629637 0.123775891 84.25890391 333285.2806 0.032699775 0.087245399 29598.11925 -4.471264116 -0.168971943 RVPS(ph)PGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVPSPGK 7 1 D6RIF6;H0Y9L2 D6RIF6 SLAIN2 1 RVPS(1)PGK;RVPS(1)PGK 69.276 0.036861 503850000 1019740 902280 844070 906920 777290 926990 1115070 1228160 1644670 TRUE FALSE 884978.7753 896352.8633 1252265.075 1112850.047 761823.4497 962651.9051 1006930.683 965527.5416 1450238.986 0.610229613 0.618072519 0.863488768 0.767356317 0.525308902 0.663788461 0.694320517 0.665771332 1 20.46785923 1.237215141 24.99586977 1.00000039 0.678223796 0.55583747 0.090991221 27.59916875 512531.2111 0.138505698 0.022825171 17.2669305 -1.237215141 -0.321776595 RVPS(ph)PTPAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 RVPSPTPAPK 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RVPS(0.995)PT(0.005)PAPK;RVPS(0.972)PT(0.028)PAPK;RVPS(0.986)PT(0.014)PAPK;RVPS(0.899)PT(0.101)PAPK;RVPS(0.856)PT(0.144)PAPK;RVPS(0.984)PT(0.016)PAPK;RVPS(0.975)PT(0.025)PAPK;RVPS(0.985)PT(0.015)PAPK;RVPS(0.998)PT(0.002)PAPK;RVPS(0.97)PT(0.03)PAPK 155.86 1.27E-05 22143432000 23322539 17123774 10994266 13801352 15066382 13399199 18139542 21728865 18046878 TRUE FALSE 20240406.38 17011286.8 16311129.81 16935159.91 14766590.48 13914674.86 16380372.01 17082316.31 15913396.64 1.271909878 1.068991566 1.024993606 1.064207742 0.927934545 0.874400052 1.029344795 1.07345507 1 23.92373847 5.351241354 1.130855484 0.997836408 1.961569692 0.683260724 0.058781743 3.809046433 1.525375121 0.019673546 6.099809834 224512.928 -5.351241354 0.963733284 RVPTTLSIKPLGAIS(ph)PVLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVPTTLSIKPLGAISPVLNR 20 2 Q8NEN9 Q8NEN9 PDZD8 PDZ domain-containing protein 8 1 RVPTTLSIKPLGAIS(1)PVLNR 117.03 4.49E-05 288130000 150090 133630 99667 144750 213520 180180 126390 237400 160260 TRUE FALSE 130255.2262 132752.1757 147866.2946 177617.6999 209271.3697 187111.6412 114132.7173 186633.8574 141314.2454 0.921741654 0.939411136 1.046365101 1.256898761 1.480893658 1.324081947 0.807651889 1.320700945 1 17.10854738 3.978594278 3.400829054 1.202775066 0.93453413 0.269155113 0.184718579 0.321847543 7.756153507 0.050765118 0.106064663 9519.064675 -3.978594278 -0.268240936 RVPVLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVPVLGK 7 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 73.975 0.091622 0 392370 367120 213580 264620 347950 327330 385310 410240 385010 FALSE TRUE 340517.3104 364708.3645 316868.0024 324706.0155 341026.4758 339922.5969 347942.6955 322513.3685 339494.5564 1.003012578 1.074268667 0.933352233 0.956439534 1.004512353 1.001260817 1.024884461 0.949980971 1 18.37302892 4.24640389 24.99996906 0.981635104 1.038640608 0.345531679 0.032699092 194.5703493 620166.7717 0.008093569 0.020596962 17636.15431 -4.24640389 0.057005505 RVQS(ph)LPSVPLSCAAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVQSLPSVPLSCAAYR 16 1 Q96AD5-2;Q96AD5 Q96AD5-2 PNPLA2 Patatin-like phospholipase domain-containing protein 2 1 RVQS(1)LPSVPLSCAAYR;RVQS(0.997)LPS(0.003)VPLSCAAYR 164.18 4.58E-09 1138620000 296750 290430 118309 121602 289480 248170 345270 339900 43418 TRUE FALSE 257533.7356 288522.1462 175523.6281 149213.5927 283719.9144 257717.2605 311785.7685 267215.0301 38285.1735 6.726722438 7.536132654 4.584637134 3.897425009 7.410699454 6.731516065 8.143773164 6.979595641 1 15.22449817 4.267397454 24.88972174 5.855257372 7.131428306 0.076774678 2.082662754 659.3730888 569108.3974 0.525225203 1.389074162 18509.61792 -4.267397454 1.276170934 RVS(ph)EVEEEKEPVPQPLPSDDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVSEVEEEKEPVPQPLPSDDTR 22 2 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 1 RVS(1)EVEEEKEPVPQPLPSDDTR;RVS(1)EVEEEKEPVPQPLPSDDTR 199.04 1.43E-22 1421380000 773840 583630 629700 835310 889290 841120 1111730 1240540 1556790 TRUE FALSE 671575.0833 579796.0961 934225.0262 1024979.902 871594.8689 873478.4307 1003914.596 975260.1749 1372748.06 0.489219474 0.422361621 0.680550972 0.746662795 0.634927045 0.636299155 0.731317439 0.710443674 1 20.38863544 -2 0.080362374 2.317599881 3.20E-13 0.6377725 0.093368896 325.8497515 2.482634645 88.16556996 14.17216535 0.01 2 -2.317599881 RVS(ph)GDAAQDLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVSGDAAQDLDR 12 1 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 RVS(1)GDAAQDLDR 69.289 0.030857 123930000 332280 304880 202860 256330 302370 271460 360420 374470 310600 TRUE FALSE 288368.3561 302877.2232 300963.7745 314533.6443 296353.4286 281903.2419 325466.5239 294392.5046 273881.2218 1.052895683 1.105870717 1.098884299 1.14843085 1.082050922 1.029290143 1.188349174 1.074891161 1 18.06319083 1.296781989 4.376029193 0.996341522 1.101452388 0.332096584 0.044576576 0.212530611 6.769712571 0.059205656 0.010747353 19.8053257 -1.296781989 0.105110866 RVS(ph)GPDPKPGSNCSPAQSVLSEVPSVPTNGMAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVSGPDPKPGSNCSPAQSVLSEVPSVPTNGMAK 33 2 P22314;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 RVS(0.997)GPDPKPGS(0.001)NCS(0.001)PAQS(0.001)VLSEVPSVPTNGMAK 198.06 3.53E-27 1789400000 3033300 2027900 1857100 2163600 2105000 1730900 3109300 3672900 3116800 TRUE FALSE 2632441.72 2014578.591 2755199.772 2654878.449 2063114.618 1797488.843 2807760.565 2887478.918 2748335.455 0.957831299 0.733017721 1.002497627 0.965995051 0.750677875 0.654028183 1.021622219 1.050628268 1 21.39012668 2.050662262 24.9993983 1.031089539 0.846665636 0.367458513 0.111289379 108.4927869 53535.46351 0.046612861 0.031426376 112.3730743 -2.050662262 -0.184423903 RVS(ph)HS(ph)PPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RVSHSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RVS(1)HS(1)PPPK;RVS(1)HS(1)PPPK;RVS(1)HS(1)PPPK;RVS(1)HS(1)PPPK;RVS(1)HS(1)PPPK;RVS(1)HS(1)PPPK;RVS(1)HS(1)PPPK 100.22 0.016818 13184044000 9169760 7398920 5291653 6145050 6419090 6074340 7980090 9047620 8948910 TRUE FALSE 7957952.983 7350316.007 7850714.09 7540377.524 6291362.668 6308023.79 7206182.1 7112856.872 7890980.054 1.008487276 0.931483283 0.994897216 0.955569203 0.797285334 0.799396748 0.91321763 0.901390806 1 22.91177306 3.452880906 24.85588455 0.882246617 0.97387944 0.36087061 0.060287245 248.1795733 254480.6343 0.018203088 0.023501162 2837.140909 -3.452880906 0.091632823 RVS(ph)HS(ph)PPPKQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RVSHSPPPKQR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RVS(1)HS(1)PPPKQR;RVS(1)HS(1)PPPKQR;RVS(1)HS(1)PPPKQR;RVS(1)HS(1)PPPKQR 65.472 0.03505 416317000 308537 265731 102793 116054 177699 217565 280388 308434 129784 TRUE FALSE 267763.0537 263985.3956 152504.0386 142405.8345 174163.1376 225934.8663 253196.0149 242477.7893 114441.0834 2.339745883 2.306736251 1.332598697 1.244359371 1.521858518 1.974246133 2.21245734 2.118800191 1 16.80424553 2.701241452 24.69409231 1.908262349 1.728865943 0 0.483952479 2394.741113 1584597.026 0.176697299 0.155836947 502.6219516 -2.701241452 -0.179396405 RVS(ph)ISSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVSISSSK 8 1 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 RVS(1)ISSSK 70.685 0.031049 132490000 123630 108990 74923 100740 115200 115370 141670 133950 124130 TRUE FALSE 107291.9823 108274.0375 111156.0134 123614.5567 112907.7454 119808.3586 127930.8652 105305.8349 109455.4928 0.980233879 0.989206067 1.015536183 1.129359099 1.031540241 1.094585164 1.16879347 0.962088171 1 16.73998483 3.98761137 19.11770816 1.061097338 0.989132158 0.241784682 0.05950543 41.1556034 63520.21257 0.016353325 0.030420853 9718.77147 -3.98761137 -0.07196518 RVS(ph)LHCLLDQFDKDLPVYLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVSLHCLLDQFDKDLPVYLK 20 2 Q8IWF6 Q8IWF6 DENND6A Protein DENND6A 1 RVS(1)LHCLLDQFDKDLPVYLK 93.397 0.0007911 223690000 237270 164930 158600 178860 175060 128500 202340 221560 177100 TRUE FALSE 205914.1683 163846.564 235299.4905 219472.8967 171576.6485 133443.4782 182717.0979 174181.1182 156163.4398 1.318581152 1.049199251 1.506751458 1.405405113 1.098699214 0.854511647 1.170037611 1.115377059 1 17.25269721 3.133804863 6.140282798 1.051883564 1.31290848 0.48565513 0.139798112 0.200707725 10.28299821 0.043574521 0.049708639 1360.833096 -3.133804863 0.261024915 RVS(ph)LSEIGFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RVSLSEIGFGK 11 1 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;H0YBX5 E5RJM2 CDK16 Cyclin-dependent kinase 16 1 RVS(0.995)LS(0.005)EIGFGK;RVS(0.999)LS(0.001)EIGFGK;RVS(0.874)LS(0.126)EIGFGK;RVS(0.977)LS(0.023)EIGFGK 201.16 2.72E-08 5237170000 7809310 6740250 5395040 6262220 7115200 6588980 8989770 9811940 9240960 TRUE FALSE 6777289.897 6695972.854 8004099.389 7684152.763 6973621.441 6842462.324 8117943.489 7713732.988 8148504.236 0.831721958 0.821742575 0.982278361 0.943013901 0.85581614 0.839720043 0.996249527 0.946644042 1 22.95810383 -2 0.245869769 1.766160752 0.85121026 0.348663704 0.057007523 106.4199984 1.696288646 38.89733009 0.207585062 0.01 2 -0.914950491 RVS(ph)LVGADDLR ddPTM_MDA-MB-175_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 125.86 0.0001957 2428830000 1822788 1943358 1201650 1976096 2282220 2407100 1830131 2488020 2351590 TRUE FALSE 1581901.947 1930591.953 1782771.959 2424798.8 2236808.287 2499702.695 1652645.177 1955976.285 2073587.709 0.762881618 0.931039447 0.859752376 1.169373636 1.078714094 1.205496485 0.796997962 0.943281191 1 20.98369764 4.439281253 1.569670061 1.012295398 0.760680921 0.303069818 0.122916428 0.893672637 3.182518363 0.036907061 0.292507573 27496.74288 -4.439281253 -0.251614477 RVS(ph)PLNLS(ph)SVTP ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVSPLNLSSVTP 12 1 Q9UJX2-3;Q9UJX2 Q9UJX2-3 CDC23 Cell division cycle protein 23 homolog 2 RVS(0.996)PLNLS(0.394)S(0.303)VT(0.306)P 59.261 0.067026 87466000 186300 196540 129400 143310 204060 224990 192100 210100 204110 TRUE FALSE 161679.983 195248.9158 191978.2728 175850.7259 199999.6052 233645.5109 173470.1716 165171.75 179980.3483 0.898320203 1.084834637 1.066662414 0.977055148 1.111230238 1.298172345 0.963828402 0.917721026 1 17.45747986 2.035438129 24.9997585 0.949320104 1.07544201 0.206943765 0.103104028 243.5036703 171778.2534 0.042581117 0.028708076 108.5020962 -2.035438129 0.126121907 RVS(ph)PLNLSSVTP ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RVSPLNLSSVTP 12 1 Q9UJX2-3;Q9UJX2 Q9UJX2-3 CDC23 Cell division cycle protein 23 homolog 1 RVS(0.996)PLNLS(0.002)S(0.002)VTP;RVS(0.998)PLNLS(0.002)SVTP;RVS(0.986)PLNLS(0.014)SVTP;RVS(0.999)PLNLS(0.001)SVTP;RVS(0.989)PLNLS(0.01)S(0.001)VTP 100.11 0.0036195 1976990000 3716870 3741470 2351910 2677760 3968040 4225070 3322740 3804650 3444240 TRUE FALSE 3225676.212 3716892.037 3489301.543 3285786.335 3889083.767 4387611.177 3000501.186 2991055.205 3037065.871 1.062102815 1.223843076 1.148905454 1.081894985 1.280539815 1.444687525 0.987960523 0.984850291 1 21.53424677 2.103430217 24.32688478 0.989438435 1.203914491 0.476734653 0.106668063 7.511949482 1747.627878 0.044745149 0.030167173 126.8908238 -2.103430217 0.214476056 RVS(ph)QDLEVEKPDASPTSLQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVSQDLEVEKPDASPTSLQLR 21 2 O94885 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 RVS(0.986)QDLEVEKPDAS(0.011)PT(0.002)SLQLR;RVS(1)QDLEVEKPDASPTSLQLR 162.44 1.46E-11 879520000 752140 656230 473380 598270 695350 580710 798310 932660 805330 TRUE FALSE 652742.7933 651919.1819 702308.1514 734116.3475 681513.8954 603050.2895 720890.0191 733217.917 710124.8048 0.91919447 0.918034657 0.988992564 1.033784966 0.959710027 0.849217328 1.015159609 1.032519794 1 19.43771308 2.04489524 24.99996892 1.020160464 0.948820839 0.319420029 0.048599054 155.7634025 86736.33824 0.020955832 0.01412841 110.8907294 -2.04489524 -0.071339626 RVS(ph)RT(ph)PEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 74.46 0.055333 6143080000 6610390 4854380 3633870 4020690 3997650 4269710 5463740 6240200 5626180 TRUE FALSE 5736810.213 4822491.258 5391221.687 4933649.117 3918104.586 4433968.507 4933867.336 4905781.791 4961059.41 1.156367973 0.972068838 1.086707746 0.994474911 0.789771753 0.893754366 0.994518898 0.988857699 1 22.2422168 5.764877654 0.795011992 0.949909038 1.930148153 0.402162714 0.075899676 13.01302287 1.861978833 0.029507449 16.46811356 581939.2556 -5.764877654 0.980239115 RVS(ph)S(ph)SSELDLPSGDHCEAGLLQLDVPLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 2 RVS(0.499)S(0.499)S(0.499)S(0.499)ELDLPS(0.002)GDHCEAGLLQLDVPLLR;RVS(0.48)S(0.52)S(0.52)S(0.48)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.497)S(0.497)S(0.497)S(0.497)ELDLPS(0.011)GDHCEAGLLQLDVPLLR 131.79 1.23E-05 55432000 56427.8 60343.7 48176.4 48537.7 65009.3 81287.9 69051 77188.8 73573.5 TRUE FALSE 48970.72326 59947.29826 71474.66818 59558.92664 63715.74212 84415.09811 62354.44465 60682.5758 64875.72465 0.754838941 0.924032812 1.101716683 0.918046418 0.98211993 1.301181583 0.961136773 0.935366443 1 15.98539113 4.61340691 3.097807958 1.020783749 0.744850998 0.384642723 0.11032376 0.325932066 5.0499688 0.028479584 0.182931837 41058.86216 -4.61340691 -0.275932751 RVS(ph)SDLQHATAQLSLEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVSSDLQHATAQLSLEHR 18 1 P50548;P50548-2 P50548 ERF ETS domain-containing transcription factor ERF 1 RVS(0.837)S(0.163)DLQHATAQLSLEHR 196.2 9.31E-16 530300000 395210 259030 268900 251660 243870 200700 312840 401380 331820 TRUE FALSE 342981.9972 257328.4149 398940.9394 308803.2494 239017.4641 208421.0589 282500.825 315548.0105 292592.6176 1.172216852 0.879476786 1.363468917 1.05540342 0.816895061 0.712325077 0.965509066 1.078455134 1 18.15853384 4.76774064 21.29297372 0.990846721 1.172218909 0.1028055 0.173734362 3463.956275 2527370.31 0.044752749 3.132665601 58578.8228 -4.76774064 0.181372188 RVS(ph)SSS(ph)ELDLPSGDHCEAGLLQLDVPLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 2 RVS(0.835)S(0.206)S(0.452)S(0.507)ELDLPS(0.001)GDHCEAGLLQLDVPLLR 122.37 9.45E-05 90928000 41745 35747 20547 30657 50138 62470 47138 43790 48455 TRUE FALSE 36228.29248 35512.1756 30483.59793 37618.14041 49140.35189 64873.26132 42566.56402 34425.84927 42726.7051 0.847907471 0.831147066 0.713455387 0.880436259 1.150108621 1.518330542 0.996251967 0.80572207 1 15.38285045 3.393051544 5.161267428 1.070699528 0.800121497 0.364062917 0.182175278 0.281194263 12.7935482 0.061193275 0.079843983 2472.017515 -3.393051544 -0.270578031 RVS(ph)SSSELDLPSGDHCEAGLLQLDVPLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 RVS(0.861)S(0.061)S(0.061)S(0.016)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.767)S(0.204)S(0.015)S(0.015)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.93)S(0.062)S(0.004)S(0.004)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.851)S(0.106)S(0.042)S(0.001)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.732)S(0.179)S(0.044)S(0.044)ELDLPSGDHCEAGLLQLDVPLLR 279.29 1.29E-71 3209450000 582415 567519 290984 430900 619194 642942 603821 682105 556272 TRUE FALSE 505447.3821 563790.9303 431704.8357 528742.4309 606873.2508 667676.3948 545262.5324 536242.1539 490510.1579 1.030452426 1.149397054 0.880113956 1.077943897 1.237228712 1.361187702 1.111623324 1.093233535 1 18.90392349 3.469718743 23.45073274 1.158486364 1.023945442 0.246991423 0.113199989 127.6391944 404349.0947 0.034508263 0.044669442 2949.298589 -3.469718743 -0.134540923 RVS(ph)TDLPEGQDVYTAACNSVIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RVSTDLPEGQDVYTAACNSVIHR 23 1 Q15751;H0YNB1 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 RVS(0.963)T(0.037)DLPEGQDVYTAACNSVIHR;RVS(0.991)T(0.009)DLPEGQDVYTAACNSVIHR;RVS(0.949)T(0.051)DLPEGQDVYTAACNSVIHR;RVS(0.971)T(0.029)DLPEGQDVYTAACNSVIHR;RVS(0.825)T(0.175)DLPEGQDVYTAACNSVIHR 303.42 2.54E-62 2980170000 1074980 1040300 661219 707721 1092890 1255410 1101240 1124160 1122180 TRUE FALSE 932918.6693 1033466.201 980986.72 868419.8699 1071143.627 1303706.435 994441.9143 883767.1322 989517.1588 0.942801912 1.044414634 0.991379191 0.877619819 1.082491211 1.317517765 1.004976928 0.893129669 1 19.9163652 4.751296449 22.16839848 1.020121409 0.942801672 0.043145386 0.12056289 1868.53527 3252132.699 0.031795676 0.48024863 56402.2526 -4.751296449 -0.077319737 RVS(ph)VCAETYNPDEEEEDTDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 260.76 8.01E-37 10178910000 5157100 5582380 3188530 3349810 4316170 5592550 3997400 5080250 5680150 TRUE FALSE 4475576.169 5545708.978 4730513.773 4110435.559 4230286.661 5807699.017 3609732.763 3993878.072 5008649.138 0.893569513 1.107226485 0.944468986 0.820667499 0.844596326 1.15953401 0.720699866 0.797396256 1 22.25599012 3.999325094 24.98323727 0.879711115 1.006760446 0.10544043 0.130151788 47.49910085 1758590.843 0.033214458 0.067849613 9984.47178 -3.999325094 0.127049331 RVS(ph)VELTNSLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RVSVELTNSLFK 12 1 P14923 P14923 JUP Junction plakoglobin 1 RVS(1)VELTNSLFK;RVS(1)VELTNSLFK;RVS(1)VELTNSLFK;RVS(1)VELTNSLFK;RVS(1)VELTNSLFK 221.85 1.60E-11 5716352000 5259600 4644080 4190427 8032630 6359020 6263160 4893610 8394960 11047850 TRUE FALSE 4564530.534 4613572.733 6216931.513 9856561.413 6232487.943 6504107.818 4419028.455 6599763.134 9741785.759 0.468551726 0.473585937 0.638171652 1.011781788 0.639768529 0.667650468 0.453615853 0.677469542 1 23.21575483 4.147752292 4.373453998 0.716939285 0.470270885 0.299805579 0.165880912 0.281497766 9.600871152 0.044356225 0.101010285 14052.45789 -4.147752292 -0.2466684 RVSEVEEEKEPVPQPLPS(ph)DDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVSEVEEEKEPVPQPLPSDDTR 22 2 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 1 RVS(0.491)EVEEEKEPVPQPLPS(0.508)DDT(0.001)R 152.35 3.30E-08 978590000 607140 488600 492770 632610 679350 646970 849070 990560 1146100 TRUE FALSE 526904.9107 485390.3544 731075.2202 776253.7693 665832.2641 671859.3545 766727.3221 778736.4525 1010609.364 0.52137347 0.480294733 0.723400402 0.768104668 0.658842366 0.664806184 0.758678229 0.770561288 1 19.94679402 -2 0.100725536 2.20724451 0.214872667 0.673313091 0.0822742 199.4886448 1.851914456 56.05463891 5.75303919 0.01 2 -1.992371842 RVSEYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVSEYQR 7 1 Q7LG56;A0A0C4DGZ6;H0YAV1;Q7LG56-2;Q7LG56-6;Q7LG56-4;Q7LG56-3 Q7LG56 RRM2B Ribonucleoside-diphosphate reductase subunit M2 B 0 113.71 0.0097317 46207000 49826 59118 27885 35070 49057 54052 51671 53303 46628 FALSE TRUE 43241.36786 58729.64997 41370.27927 43033.17951 48080.86168 56131.41542 46659.95437 41904.56825 41115.69096 1.051699895 1.428399927 1.006191999 1.046636418 1.1694042 1.365206667 1.134845439 1.01918677 1 15.32740145 1.77679448 3.861287583 1.007077972 1.179839142 0.206186141 0.133886252 0.317264486 9.265534203 0.084618537 0.035782686 59.81284772 -1.77679448 0.17276117 RVSS(ph)SSELDLPSGDHCEAGLLQLDVPLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 RVS(0.183)S(0.271)S(0.271)S(0.271)ELDLPS(0.003)GDHCEAGLLQLDVPLLR;RVS(0.204)S(0.265)S(0.265)S(0.265)ELDLPSGDHCEAGLLQLDVPLLR 118.23 4.90E-05 1601020000 74468 79731 43011.8 51285 71622 80279 70922 81442 72430 TRUE FALSE 64626.86512 79207.24181 63812.45035 62930.04309 70196.86233 83367.38508 64043.99536 64026.26208 63867.40791 1.011891154 1.240182503 0.999139505 0.985323268 1.099103042 1.30531969 1.002764907 1.002487249 1 15.96279228 2.075140463 25 1.001719998 1.106446308 0.192516401 0.101444996 61.98999349 20622.53985 0.041711267 0.028121725 118.8886684 -2.075140463 0.10472631 RVSVCAETYNPDEEEEDTDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVSVCAETYNPDEEEEDTDPR 21 1 P13861-2;P13861 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 0 83.395 0.005131 211150000 174720 165610 95860 115620 184620 180650 168010 194830 87019 FALSE TRUE 151630.3093 164522.097 142218.2166 141873.2881 180946.4232 187599.7224 151716.4161 153167.1207 76731.71295 1.976110053 2.144121259 1.853447697 1.848952443 2.358169996 2.444878593 1.977232232 1.996138425 1 16.22753534 1.197220223 3.14796152 0.735057562 2.090343751 0.74989924 0.195438419 0.237355859 2.82432271 0.851968798 0.053698718 15.74781207 -1.197220223 1.355286189 RVT(ph)LPAITPIILQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVTLPAITPIILQK 14 1 Q14449-2 Q14449-2 GRB14 Growth factor receptor-bound protein 14 1 RVT(1)LPAITPIILQK;RVT(1)LPAITPIILQK 131.11 3.41E-05 264947000 348770 355310 230615 267602 331160 317070 348010 394580 404880 TRUE FALSE 302679.1608 352975.9452 342141.1854 328365.1241 324570.5639 329267.8881 314260.0438 310202.1376 357015.5476 0.847803864 0.98868508 0.958336934 0.919750208 0.90912165 0.922278848 0.880241899 0.868875711 1 18.44562738 3.499279239 5.949981087 0.908287106 0.937720485 0.001588014 0.049505598 0.512575972 62.82493523 0.013614566 0.019373331 3157.033854 -3.499279239 0.029433379 RVTIMPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVTIMPK 7 1 K7EK07;Q71DI3;Q16695;P84243;P68431;Q6NXT2;Q5TEC6;A0A590UJL8 K7EK07;Q5TEC6 H3F3B;HIST2H3A;HIST3H3;H3F3A;HIST1H3A;H3F3C;HIST2H3PS2 Histone H3;Histone H3.2;Histone H3.1t;Histone H3.3;Histone H3.1;Histone H3.3C 0 84.568 0.034394 792390000 915560 764980 584080 1531300 667150 1946900 853010 1334200 1306300 FALSE TRUE 794566.4263 759954.796 866543.0416 1879005.069 653875.0203 2021798.503 770285.2215 1048891.713 1151870.702 0.689805223 0.659757032 0.752291937 1.631263879 0.567663557 1.755230426 0.668725422 0.910598482 1 20.13554735 3.973985187 24.84419242 1.061018447 0.682591712 0.196308226 0.369883745 1059.267073 1011605.011 0.091616859 0.159445137 9418.574706 -3.973985187 -0.378426735 RVTSIADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVTSIADR 8 1 B1ALA9;P60891;A0A2R8Y7H4;P60891-2;P11908;P11908-2 B1ALA9;P11908 PRPS1;PRPS2 Ribose-phosphate pyrophosphokinase 1;Ribose-phosphate pyrophosphokinase 2 0 ; 103.26 0.0077091 509470000 888930 906760 526800 647680 879430 1008980 757690 865440 685290 FALSE TRUE 771455.6482 900803.4339 781562.242 794745.6432 861931.0636 1047796.113 684209.3404 680372.3909 604275.7969 1.276661505 1.490715727 1.293386639 1.3152035 1.426386872 1.733970017 1.132279903 1.125930236 1 19.20484763 2.032750813 24.99812274 1.089103454 1.416704984 0.586956615 0.133602316 129.3168698 98704.79908 0.054490149 0.036736983 107.8327828 -2.032750813 0.32760153 RVVFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVVFLK 6 1 Q02878;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ; 121.87 0.03121 1293710000 1346060 1302720 699380 800360 1232330 1413840 1677900 1945330 1124300 FALSE TRUE 1168174.761 1294162.347 1037602.507 982093.9707 1207809.044 1468231.34 1515177.516 1529336.318 991386.5348 1.178324215 1.305406419 1.046617511 0.990626699 1.218302853 1.480987776 1.528341835 1.542623653 1 19.91908814 2.88253716 4.573917552 1.423892792 1.133484893 0.323052153 0.17272045 0.243605409 8.065288821 0.057324534 0.057766692 763.0221749 -2.88253716 -0.290407899 RVVLGDGVQLPPGDYSTT(ph)PGGT(ph)LFSTTPGGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.039)S(0.13)T(0.391)T(0.416)PGGT(0.382)LFS(0.255)T(0.152)T(0.227)PGGT(0.009)R;RVVLGDGVQLPPGDY(0.016)S(0.158)T(0.159)T(0.658)PGGT(0.398)LFS(0.212)T(0.199)T(0.196)PGGT(0.004)R 60.632 0.014979 476850000 183295 146516 120950 162811 215780 226450 192238 222333 247665 TRUE FALSE 159072.1013 145553.5267 179441.8246 199779.726 211486.4002 235161.678 173594.7883 174788.8181 218386.3258 0.728397718 0.666495607 0.821671521 0.914799611 0.968404956 1.07681503 0.794897701 0.800365213 1 17.736523 4.025134799 3.154682113 0.911915239 0.697735271 0.539921262 0.086177521 0.217381921 4.45830037 0.025679421 0.057797174 10595.82554 -4.025134799 -0.214179969 RVVLGDGVQLPPGDYSTT(ph)PGGTLFS(ph)TTPGGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.097)S(0.279)T(0.299)T(0.321)PGGT(0.059)LFS(0.315)T(0.295)T(0.277)PGGT(0.058)R;RVVLGDGVQLPPGDY(0.002)S(0.097)T(0.144)T(0.757)PGGT(0.062)LFS(0.647)T(0.158)T(0.133)PGGT(0.001)R 108.33 3.89E-06 727180000 508684 412930 294208 382478 550234 635972 592433 664612 330414 TRUE FALSE 441460.1206 410217.4356 436487.9729 469325.4757 539285.4199 660438.2544 534978.9388 522489.8958 291352.8333 1.51520792 1.40797476 1.498142194 1.61084919 1.850970227 2.266798805 1.836189244 1.793323545 1 18.15240782 3.492120338 3.260790532 1.785896488 1.470378359 0.135441456 0.309833967 0.455352155 9.997244929 0.093555179 0.135734408 3105.419942 -3.492120338 -0.315518129 RVVLGDGVQLPPGDYSTT(ph)PGGTLFSTT(ph)PGGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.007)S(0.033)T(0.44)T(0.52)PGGTLFS(0.047)T(0.334)T(0.591)PGGT(0.028)R;RVVLGDGVQLPPGDYS(0.001)T(0.011)T(0.981)PGGT(0.008)LFS(0.365)T(0.227)T(0.401)PGGT(0.006)R;RVVLGDGVQLPPGDYS(0.014)T(0.074)T(0.912)PGGT(0.001)LFS(0.038)T(0.032)T(0.929)PGGT(0.002)R;RVVLGDGVQLPPGDY(0.021)S(0.053)T(0.198)T(0.684)PGGT(0.052)LFS(0.266)T(0.264)T(0.387)PGGT(0.075)R;RVVLGDGVQLPPGDY(0.007)S(0.033)T(0.11)T(0.788)PGGT(0.062)LFS(0.001)T(0.034)T(0.96)PGGT(0.004)R;RVVLGDGVQLPPGDY(0.001)S(0.01)T(0.129)T(0.856)PGGT(0.004)LFS(0.016)T(0.028)T(0.956)PGGT(0.001)R 158.89 5.14E-14 2490228000 1492696 1255226 871160 1092319 1829450 1907190 1738950 1820970 951707 TRUE FALSE 1295432.442 1246980.338 1292455.89 1340346.724 1793047.524 1980560.833 1570306.897 1431569.736 839197.2826 1.543656621 1.485920371 1.540109717 1.59717715 2.136622176 2.360065832 1.871201122 1.705879852 1 19.67865048 3.454978227 24.1928452 1.835758005 1.527688824 0.133820424 0.347081129 327.8077971 358151.593 0.10619621 0.137111085 2850.875335 -3.454978227 -0.30806918 RVWGSPGGEGTGDLDEFDF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RVWGSPGGEGTGDLDEFDF 19 1 Q13438-4;Q13438;Q13438-8;Q13438-6;Q13438-5;Q13438-3;Q13438-2;Q13438-7;B4E321 Q13438-4 OS9 Protein OS-9 0 85.837 0.060946 63389000 113090 95305 53795 81133 98895 118340 75850 86218 68860 FALSE TRUE 98144.86997 94678.93518 79810.44193 99555.48769 96927.18298 122892.6164 68494.07867 67780.95165 60719.44925 1.616366274 1.559285144 1.31441314 1.639598002 1.596311959 2.023941553 1.128041831 1.116297208 1 15.88987108 2.107468133 9.694206478 1.083323349 1.606887883 0.685408629 0.173576156 0.172524249 14.34512207 0.072032599 0.048540385 128.0761114 -2.107468133 0.523564534 RVYATILNAGTNTDGFK ddPTM_MDA-MB-175_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 ; 280.69 9.96E-36 5035200000 4035300 3760000 2902000 2914600 3919200 3762800 4788500 5293800 3596800 FALSE TRUE 3502024.881 3735300.312 4305416.907 3576404.477 3841215.588 3907557.351 4324112.007 4161762.066 3171590.401 1.104185736 1.177737299 1.35749462 1.127637565 1.211132303 1.23204981 1.363389171 1.31220036 1 21.59677503 2.672144195 4.19202657 1.254352051 1.199653792 0 0.115450607 0.848084744 29.6005315 0.040947433 0.03632584 470.0501494 -2.672144195 -0.054698259 RWDDSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RWDDSQK 7 1 Q16543;K7EKQ2 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;;; 201.3 0.00053652 2149020000 3421090 2936220 1978730 2369350 2428700 2428030 3299930 3611300 3091330 FALSE TRUE 2968984.289 2916931.777 2935650.446 2907347.131 2380373.622 2521437.885 2979903.297 2839051.598 2725876.489 1.089185185 1.070089488 1.076956516 1.066573318 0.873250725 0.925000782 1.093190872 1.041518796 1 21.37828876 3.443615186 24.99874889 0.995785967 1.076859633 0.35250257 0.059460684 255.2314766 190426.516 0.019131188 0.024698393 2777.25135 -3.443615186 0.081073666 RWDQTADQTPGAT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RWDQTADQTPGATPK 15 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 RWDQTADQT(0.003)PGAT(0.997)PK;RWDQTADQTPGAT(1)PK;RWDQTADQT(0.04)PGAT(0.96)PK;RWDQTADQT(0.009)PGAT(0.991)PK 173.56 5.64E-07 1924840000 1944460 1624580 1067550 1318240 1875580 1453240 1927840 2312990 1700350 TRUE FALSE 1687494.684 1613908.027 1583820.751 1617566.54 1838259.628 1509147.083 1740878.374 1818375.088 1499336.56 1.125494255 1.076414776 1.056347716 1.078854864 1.226048691 1.006543243 1.161099129 1.212786466 1 20.51589283 RWESER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RWESER 6 1 Q9Y2T2;H0YBA0;E7ER80;E5RJ52;P53677-2;P53677 Q9Y2T2 AP3M1;AP3M2 AP-3 complex subunit mu-1;AP-3 complex subunit mu-2 0 ; 95.541 0.069313 110620000 360720 362700 223890 315530 275250 442910 297490 347130 432070 FALSE TRUE 313049.9381 360317.3998 332163.9529 387175.9091 269773.0635 459949.0343 268639.4656 272898.9509 380991.1768 0.821672409 0.945736861 0.871841589 1.016233269 0.708082181 1.20724327 0.70510679 0.7162868 1 18.53939806 RWQS(ph)PVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RWQSPVTK 8 1 A9Z1X7 A9Z1X7 SRRM1 1 RWQS(1)PVTK;RWQS(1)PVTK;RWQS(1)PVTK;RWQS(0.999)PVT(0.001)K;RWQS(0.998)PVT(0.002)K;RWQS(0.848)PVT(0.152)K 125.72 0.00076557 4540370000 6547900 5230640 3397350 4482640 5384520 4441320 5793560 6990750 5824160 TRUE FALSE 5682578.425 5196279.581 5040319.823 5500491.925 5277378.587 4612180.454 5231701.443 5495832.515 5135634.44 1.106499789 1.011808695 0.981440537 1.071044287 1.027600124 0.898074134 1.018705966 1.070137016 1 22.29211108 4.739086162 22.13617371 1.01306227 1.106499911 0.278874814 0.048599316 13.12997783 552192.3961 0.012334653 0.070719596 54838.57519 -4.739086162 0.093437641 RWS(ph)AEVTSSTYSDEDRPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RWSAEVTSSTYSDEDRPPK 19 2 Q9UJM3 Q9UJM3 ERRFI1 ERBB receptor feedback inhibitor 1 1 RWS(0.999)AEVT(0.001)SSTYSDEDRPPK 129.66 9.95E-06 215850000 85480 71272 58803 65599 63477 61205 71921 86511 102130 TRUE FALSE 74183.60142 70803.80954 87240.32748 80494.25557 62213.93189 63559.59595 64946.11249 68011.29588 90056.30775 0.823746868 0.786217105 0.968730894 0.893821406 0.690833696 0.70577617 0.721172277 0.755208575 1 16.45853971 3.256433733 24.97189278 0.764726397 0.86946408 0.180970133 0.097606809 390.9296752 546194.145 0.028637173 0.036890687 1804.819327 -3.256433733 0.104737682 RWS(ph)APAAAGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RWSAPAAAGQR 11 1 C9JI98 C9JI98 TMEM238 Transmembrane protein 238 1 RWS(1)APAAAGQR;RWS(1)APAAAGQR;RWS(1)APAAAGQR 134.81 8.16E-05 1105310000 329648 313137 171731 344699 324654 327780 231203 392550 362245 TRUE FALSE 286084.1816 311079.9824 254780.686 422968.1763 318194.0206 340389.9087 208780.9686 308606.2373 319420.8088 0.895634141 0.973887655 0.797633338 1.324172267 0.996159335 1.065647257 0.653623568 0.966143184 1 18.28509878 1.261392269 8.828221637 1.000145804 0.95638947 0.005298849 0.173120421 1.566920736 578.9091198 0.180316864 0.042241818 18.2554385 -1.261392269 -0.043756334 RWS(ph)APESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RWSAPESR 8 1 P54253 P54253 ATXN1 Ataxin-1 1 RWS(1)APESR;RWS(1)APESR;RWS(1)APESR;RWS(1)APESR 116.03 0.0014398 1965220000 1365370 1384340 837630 960140 1336590 1335260 1162530 1423340 1285460 TRUE FALSE 1184932.895 1375246.179 1242710.67 1178154.462 1309994.474 1386628.316 1049788.02 1118969.817 1133494.383 1.045380474 1.213280101 1.096353619 1.039400353 1.155713247 1.223321736 0.926151938 0.987186028 1 20.11234581 2.227382766 24.9999912 0.972587893 1.128413456 0.580904894 0.063176757 152.0870551 340149.8303 0.02537622 0.017286443 168.8040128 -2.227382766 0.155825563 RWS(ph)GNEPTDEFSDLPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 202.62 6.39E-12 217367000 176564 158137 120982 148272 179895 181016 146539 186734 183652 TRUE FALSE 153230.62 157098.1876 179489.2999 181939.4238 176315.4415 187979.8027 132327.6703 146802.3873 161940.8698 0.946213394 0.970095985 1.108363195 1.123492939 1.088764323 1.160792843 0.817135727 0.906518456 1 17.30510761 2.237145662 24.99999481 0.903818883 1.067449293 0.477129814 0.078123922 33.02823548 583534.6224 0.03241236 0.023203483 172.6416834 -2.237145662 0.163630411 RWS(ph)IVSSPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RWSIVSSPER 10 1 Q12923-3;Q12923;Q12923-4;Q12923-2 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 RWS(1)IVSSPER;RWS(1)IVSSPER;RWS(1)IVSSPER;RWS(1)IVSSPER 134.04 0.00011094 1605330000 428948 492039 345205 370093 495013 610945 506668 519016 493023 TRUE FALSE 372261.435 488806.7634 512147.2926 454128.2722 485163.2098 634448.4495 457531.4153 408028.4674 434738.3826 0.856288402 1.124369927 1.178058605 1.044601283 1.115988901 1.459379882 1.052429308 0.938560945 1 18.72978795 2.001520462 24.99817417 0.974072872 1.137953685 0.167770151 0.147412306 78.81629505 1295815.863 0.06114492 0.040881468 100.3507128 -2.001520462 0.163880813 RWSEPSS(ph)QK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RWSEPSSQK 9 1 Q9BQK8-2;Q9BQK8 Q9BQK8-2 LPIN3 Phosphatidate phosphatase LPIN3 1 RWS(0.139)EPS(0.257)S(0.604)QK 119.74 0.00082374 174410000 174100 157390 107320 116300 161520 135510 188140 196660 192960 TRUE FALSE 151092.2439 156356.0947 159220.311 142707.6925 158306.068 140723.1574 169894.2118 154605.7894 170148.4886 0.888002269 0.918939075 0.935772702 0.838724421 0.930399496 0.827060872 0.998505559 0.908652147 1 17.37643481 0.215651269 0.756123562 1.363159121 0.896866932 0.293071875 0.047882563 14.3162866 1.955882748 8.117379788 0.017853539 1.643051853 -0.215651269 -0.466292188 RWST(ph)ELVPEGLQS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RWSTELVPEGLQSPR 15 1 H3BRD5;B2RTY4-5;B2RTY4-2;B2RTY4;B2RTY4-4;H3BV44;H3BMM1 H3BRD5 MYO9A Unconventional myosin-IXa 2 RWS(0.47)T(0.53)ELVPEGLQS(1)PR 60.464 0.084215 73692000 88498 84801 61897 63749 88959 105480 89672 105890 104070 TRUE FALSE 76802.76507 84243.93665 91830.59623 78224.18479 87188.88995 109537.8839 80975.62324 83246.24754 91766.96316 0.836932622 0.918020317 1.00069342 0.852422071 0.950111968 1.193652706 0.882404958 0.907148332 1 16.48568724 3.004110828 24.98935959 0.982492269 0.909090806 0.177180003 0.092783112 271.5922741 1650962.806 0.029286585 0.033070041 1009.51047 -3.004110828 -0.073401463 RY(ph)GCVFQGT(ph)NQQIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RYGCVFQGTNQQIK 14 1 H0YL25;Q13114 H0YL25 TRAF3 TNF receptor-associated factor 3 2 RY(1)GCVFQGT(1)NQQIK;RY(1)GCVFQGT(1)NQQIK;RY(1)GCVFQGT(1)NQQIK 79.022 0.028812 998490000 1099880 1123900 573200 766100 1142200 1153930 972120 1152430 1391630 TRUE FALSE 954528.0713 1116517.027 850401.4372 940054.7141 1119472.455 1198322.434 877843.952 905991.8127 1227113.087 0.777864796 0.909872968 0.693009835 0.766070156 0.912281408 0.976537898 0.715373311 0.738311589 1 20.22683678 5.052053242 14.87765281 0.826142821 0.490689767 0.018140526 0.109844799 4711913.26 37595863.59 0.027068199 45061132.55 112733.5652 -5.052053242 -0.335453054 RYDDPEVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RYDDPEVQK 9 1 P38646;D6RJI2;A0A3B3ITI4 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ; 88.392 0.020548 726080000 1132620 1133130 913990 1453020 1308770 1355410 1217470 1529660 1389020 FALSE TRUE 982941.3973 1125686.394 1355998.621 1782950.399 1282728.038 1407553.5 1099399.947 1202554.113 1224811.638 0.802524541 0.919068989 1.107107884 1.455693548 1.047285964 1.149199972 0.897607365 0.981827797 1 20.22412847 2.239818884 24.99526112 0.961806557 1.08962723 0.099487819 0.169033542 81.49684529 1618975.405 0.069926204 0.051107816 173.7076258 -2.239818884 0.127820673 RYDEIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RYDEIVK 7 1 A0A2U3TZH3;Q05639;A0A2R8Y488 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ; 127.56 0.013952 421730000 910110 635740 491190 644480 704310 601040 714100 879610 878750 FALSE TRUE 789836.6576 631563.7821 728731.1269 790819.0343 690295.609 624162.3977 644846.6919 691512.2466 774865.1761 1.019321402 0.815062803 0.940461837 1.020589205 0.890858991 0.805510968 0.832205023 0.892429119 1 19.56358578 3.021019594 24.91831487 0.87589918 0.940829925 0.149051084 0.075187094 458.3410161 543350.5388 0.022951014 0.026021668 1049.589782 -3.021019594 0.064930745 RYDFQNPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RYDFQNPSR 9 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 0 ; 117.99 0.001704 447810000 341370 355194 188883 210535 344860 423650 282140 333440 292750 FALSE TRUE 296257.0896 352860.7072 280227.4506 258340.1896 337997.9607 439948.0896 254778.1062 262136.4508 258141.4285 1.14765418 1.366927848 1.085557836 1.00076997 1.309351864 1.704290908 0.986971009 1.015476099 1 17.97780217 RYDQDLCYTDILFTEQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RYDQDLCYTDILFTEQER 18 1 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;; 163.42 5.32E-11 363394000 272056 246792 181610 201970 227016 262697 247809 283777 251655 FALSE TRUE 236103.1103 245170.8071 269437.2034 247830.3754 222498.8257 272803.1236 223776.5213 223093.4969 221904.6326 1.063984593 1.104847629 1.214202697 1.116832815 1.002677696 1.229371016 1.008435555 1.005357546 1 17.75958026 2.094438995 15.05108231 1.004212772 1.119736341 0.420238995 0.064981916 0.9315656 144.6101492 0.025790351 0.017387777 124.2908034 -2.094438995 0.115523569 RYDSNSGGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RYDSNSGGER 10 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 196.16 5.43E-07 325240000 201926 217991 112297 116118 175278 194287 176641 207200 118921 FALSE TRUE 175240.9675 216559.0028 166604.2048 142484.3667 171790.3107 201761.3466 159510.383 162891.8924 104862.2949 1.671153275 2.065175124 1.588790375 1.358775972 1.638246721 1.924059996 1.521141448 1.553388591 1 16.6781365 0.885716965 1.427425771 1.43E-11 1.693118804 0.543995797 0.195447655 2.474151908 2.208170645 7.788950073 0.05863622 7.686293524 -0.885716965 1.693118804 RYEEIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RYEEIVK 7 1 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;;; 138.54 0.00445 3400460000 2438250 2203570 1595080 2149080 2220150 2090880 2574040 3186850 2754350 FALSE TRUE 2116029.085 2189094.604 2366466.023 2637061.461 2175973.359 2171317.507 2324409.997 2505366.928 2428733.881 0.871247814 0.901331604 0.974362009 1.085776207 0.895929099 0.894012112 0.95704598 1.031552673 1 21.21177299 4.302969867 3.946289831 0.97905497 0.879100299 0.309265959 0.057072547 0.276968763 8.414210259 0.015617839 0.045005077 20089.53417 -4.302969867 -0.09995467 RYEPSDKDRQS(ph)PPPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RYEPSDKDRQSPPPAK 16 3 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RYEPS(0.061)DKDRQS(0.939)PPPAK 113.36 0.0036874 282430000 162420 102630 81069 96946 99934 88339 133880 162200 131760 TRUE FALSE 140955.7855 101955.8168 120274.2396 118959.071 97945.50892 91737.45849 120896.3382 127514.7922 116183.4829 1.213217077 0.877541405 1.035209451 1.023889696 0.843024382 0.789591224 1.040563901 1.097529434 1 16.82604546 2.025691081 24.98381159 1.059725954 0.956551653 0.092036701 0.119536949 427.3974519 415629.3178 0.048478876 0.032683227 106.0940628 -2.025691081 -0.1031743 RYESQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 RYESQLR 7 1 O15212 O15212 PFDN6 Prefoldin subunit 6 0 ;;;; 225.57 2.67E-05 905005000 778198 819558 495298 557554 813671 896974 713804 811933 758227 FALSE TRUE 675357.1626 814174.2695 734825.7695 684155.1574 797480.539 931481.1702 644579.3979 638307.4464 668590.2678 1.010121139 1.217747713 1.099067403 1.023280162 1.192779161 1.393201808 0.964087318 0.954706458 1 19.35076283 RYGDFFIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RYGDFFIR 8 1 B0QY89;Q9Y262-2;Q9Y262;B0QY90;H0Y7E6 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ; 138.06 0.0011567 773890000 377040 518270 238110 240710 440030 474580 413760 435940 166811 FALSE TRUE 327213.2087 514865.4502 353260.7924 295366.8845 431274.2639 492837.3997 373633.6189 342717.6235 147090.7936 2.224566206 3.500324103 2.401651278 2.00805827 2.932027582 3.350565916 2.540156387 2.329973312 1 17.16634743 4.104821675 22.66620157 2.414622405 2.884658836 0.081025907 0.678893119 14.50337049 3097.319451 0.174991851 0.364275402 12729.80276 -4.104821675 0.470036431 RYIGIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RYIGIVK 7 1 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 146.94 0.0035031 4537100000 5404500 4753100 2815000 3620000 4910900 4096600 5317700 6415800 4495300 FALSE TRUE 4690281.632 4721876.573 4176343.416 4441976.328 4813182.698 4254198.853 4801990.272 5043831.098 3963870.755 1.183257962 1.191228692 1.053602318 1.120615833 1.214263278 1.073243583 1.211439668 1.272450947 1 21.91847849 2.184600004 24.99938847 1.186543232 1.140378088 0 0.085055219 293.666295 136049.7015 0.034185025 0.023047564 152.967794 -2.184600004 -0.046165144 RYLSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RYLSPK 6 1 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3KTB5;J3QR64;J3QLN6;J3KS25;Q14240;Q14240-2;E7EQG2 P60842;Q14240 EIF4A1;EIF4A2 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 83.377 0.091487 471430000 994710 876870 569040 690150 808520 791310 955500 1091200 996450 FALSE TRUE 863256.5532 871109.7832 844229.6473 846859.1058 792432.0338 821752.2077 862835.7571 857855.3717 878650.8162 0.982479658 0.991417486 0.960824974 0.963817583 0.901873667 0.935243208 0.982000746 0.976332527 1 19.74493041 2.124661442 8.84393097 0.984258067 0.955705392 0.240999652 0.02519332 0.44932823 33.00619701 0.011451146 0.007713934 133.2482278 -2.124661442 -0.028552675 RYPSS(ph)ISSS(ph)PQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RYPSSISSSPQK 12 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 2 RYPS(0.151)S(0.845)IS(0.003)S(0.081)S(0.919)PQK;RYPS(0.036)S(0.942)IS(0.028)S(0.113)S(0.881)PQK 165.58 6.65E-05 564190000 1664800 1305520 1113370 1112090 1150340 1127470 1318640 1409430 2213460 TRUE FALSE 1444792.462 1296943.953 1651799.456 1364607.032 1127450.485 1170844.5 1190758.496 1108034.363 1951787.28 0.740240741 0.664490422 0.846300964 0.699157662 0.577650288 0.599883252 0.610086205 0.56770242 1 20.8963644 1.229100573 24.99841878 1.000000673 0.658459418 0.610561168 0.084461348 289.9135694 766048.5975 0.283099705 0.022674626 16.94730218 -1.229100573 -0.341541255 RYPSS(ph)ISSS(ph)PQKDLTQAK ddPTM_MDA-MB-175_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(0.003)PS(0.41)S(0.583)IS(0.004)S(0.257)S(0.743)PQKDLTQAK;RY(0.001)PS(0.437)S(0.549)IS(0.013)S(0.302)S(0.698)PQKDLTQAK 170.55 8.30E-12 990020000 1250890 932160 643210 489790 749960 696710 1050700 1195970 338880 TRUE FALSE 1085581.717 926036.5796 954268.5074 601004.3055 735037.2633 723512.8845 948803.2757 940221.1225 298817.9925 3.632919518 3.098998732 3.193477406 2.011272148 2.459815948 2.421249399 3.175187906 3.14646757 1 18.18890749 3.886322355 6.50917431 2.50743082 3.3133041 0.320072638 0.626477571 0.34012031 17.11915477 0.168923423 0.296502205 7697.015397 -3.886322355 0.80587328 RYPSSISS(ph)SPQKDLTQAK ddPTM_MDA-MB-175_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 1 RYPS(0.001)S(0.005)IS(0.121)S(0.838)S(0.035)PQKDLTQAK 183.63 4.91E-14 1623200000 2032100 1452500 917140 911180 1410200 1076500 1866700 2267700 352290 TRUE FALSE 1763552.836 1442958.432 1360671.972 1118077.346 1382139.779 1117913.652 1685667.721 1782770.002 310642.6775 5.677110596 4.645074667 4.380183632 3.59923934 4.449291353 3.598712387 5.426388076 5.738973204 1 18.24489652 4.725134635 2.05673622 4.239357534 6.058383262 0.128866285 1.292258902 1.67586779 7.962100431 0.335515103 5.644431602 53104.90487 -4.725134635 1.819025728 RYPSSISSS(ph)PQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 RYPSSISSSPQK 12 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 RYPSSIS(0.003)S(0.122)S(0.874)PQK;RYPSSIS(0.002)S(0.026)S(0.972)PQK;RYPSSIS(0.001)S(0.124)S(0.875)PQK;RYPSSISS(0.067)S(0.933)PQK;RYPSSISS(0.117)S(0.883)PQK;RYPSSIS(0.001)S(0.099)S(0.9)PQK;RYPSSISS(0.108)S(0.892)PQK 183.41 9.58E-06 24428110000 5785220 5402320 4492570 5725560 5680340 4762330 6298090 7320700 10367430 TRUE FALSE 5020688.519 5366831.804 6665191.879 7025635.908 5567312.347 4945539.917 5687302.201 5755225.275 9141804.236 0.549201054 0.587064836 0.729089325 0.768517431 0.608994921 0.540980729 0.622120323 0.629550264 1 23.12404749 1.238345015 24.99999964 1.000000406 0.631834656 0.726862955 0.071374582 2.976688858 344355.9928 0.105403368 0.018686702 17.31191118 -1.238345015 -0.36816575 RYPSSISSS(ph)PQKDLTQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RYPSSISSSPQKDLTQAK 18 2 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 RYPSSIS(0.003)S(0.331)S(0.666)PQKDLTQAK;RYPSSISS(0.016)S(0.984)PQKDLTQAK;RYPSSISS(0.002)S(0.998)PQKDLTQAK 272.1 4.46E-39 3814900000 6350000 4672600 2668040 2999010 4494800 3392340 6505300 7397000 1476090 TRUE FALSE 5510831.411 4641905.383 3958313.068 3679981.057 4405362.274 3522845.515 5874417.007 5815209.114 1301588.322 4.233928131 3.566339145 3.041140583 2.827300304 3.384604948 2.706574311 4.513268066 4.46777911 1 20.31184178 RYS(ph)ASLPAPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RYSASLPAPVK 11 1 Q5VTQ0-2;Q5VTQ0-3;Q5VTQ0-4;Q5VTQ0;Q5VTQ0-5;Q5VTQ0-6;Q5VTQ0-7 Q5VTQ0-2 TTC39B Tetratricopeptide repeat protein 39B 1 RYS(0.979)AS(0.021)LPAPVK;RYS(0.906)AS(0.094)LPAPVK 130.47 0.00013692 572990000 829550 860080 614370 707630 817480 759650 963710 1016550 1034630 TRUE FALSE 719922.8657 854430.0778 911481.3869 868308.2069 801213.7474 788874.2271 870249.5525 799168.6933 912317.2201 0.78911463 0.936549326 0.999083835 0.951761282 0.878218376 0.864692905 0.95388921 0.875976772 1 19.79917602 RYS(ph)DFEWLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RYSDFEWLK 9 1 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 1 RYS(1)DFEWLK;RY(0.001)S(0.999)DFEWLK;RYS(1)DFEWLK;RYS(1)DFEWLK 190.26 2.28E-05 1712000000 2944840 2757410 2527590 2936510 2828100 2533240 3061840 3818200 5285500 TRUE FALSE 2555671.933 2739296.392 3749940.978 3603289.477 2771826.343 2630695.382 2764903.228 3001707.643 4660654.211 0.548350471 0.58774933 0.804595408 0.773129547 0.594729027 0.564447664 0.593243588 0.644052853 1 22.15210105 1.238849053 9.337926429 1.002110573 0.640841314 0.637556328 0.08558162 0.055209388 77.58090284 0.127529134 0.022644305 17.33201488 -1.238849053 -0.361269258 RYS(ph)DFEWLKNELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RYSDFEWLKNELER 14 2 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 1 RYS(1)DFEWLKNELER;RYS(1)DFEWLKNELER 120.92 6.14E-05 65885000 102631 100457 43094 47458 90092 83115 120574 117720 10832.3 TRUE FALSE 89068.05332 99797.09135 63934.40254 58234.06425 88299.34546 86312.48783 108880.752 92546.4941 9551.717834 9.3248204 10.44807783 6.693497824 6.096711111 9.244341907 9.036331405 11.39907543 9.688989531 1 13.2215445 4.254419167 24.9589704 8.041975315 9.886449514 0.085686002 2.83313585 725.824696 1142318.175 0.71119929 1.868095435 17964.66682 -4.254419167 1.844474199 RYS(ph)DFEWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RYSDFEWLR 9 1 O60493-4;O60493;O60493-3 O60493-4 SNX3 Sorting nexin-3 1 RYS(1)DFEWLR;RYS(1)DFEWLR;RYS(1)DFEWLR;RYS(1)DFEWLR 223.36 2.14E-07 711527000 259892 226826 185239 213625 217688 260658 241548 256789 350614 TRUE FALSE 225546.6137 225335.9651 274821.2 262131.8213 213356.4347 270685.6819 218122.7121 201876.6707 309164.8123 0.729535202 0.728853854 0.888914873 0.847870815 0.690105815 0.875538454 0.705522438 0.65297428 1 18.2380166 4.813847859 0.003104147 1.309932537 0.242810171 0 0.109559829 3852568.284 3236.358416 549119.3086 563526.1032 65140.01565 -4.813847859 -1.067122367 RYS(ph)DHAGPAIPSVVAYPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RYSDHAGPAIPSVVAYPK 18 1 H0YIY6;P27448-6;P27448-7;J3KNR0;P27448-8;P27448-3;P27448-4;P27448-2;P27448 H0YIY6;J3KNR0 MARK3 MAP/microtubule affinity-regulating kinase 3 1 RY(0.424)S(0.512)DHAGPAIPS(0.064)VVAYPK;RY(0.447)S(0.548)DHAGPAIPS(0.006)VVAYPK 113.69 0.00011278 430260000 870470 830430 580610 826360 970950 801740 1115560 1080190 990210 TRUE FALSE 755435.184 824974.8507 861394.938 1013997.668 951629.9946 832583.4566 1007373.163 849199.7745 873148.5019 0.865185226 0.944827654 0.986538872 1.161311811 1.089883328 0.953541642 1.153724894 0.972571988 1 19.73586752 4.295347152 2.29016112 1.050228591 0.87835059 0.441130127 0.070585178 0.304404319 3.026195581 0.018784274 0.072612016 19740.00018 -4.295347152 -0.171878001 RYS(ph)FRVPEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 RYSFRVPEEER 11 2 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;H0Y6R0;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 1 RY(0.041)S(0.959)FRVPEEER;RYS(1)FRVPEEER;RYS(1)FRVPEEER;RYS(1)FRVPEEER;RYS(1)FRVPEEER;RYS(1)FRVPEEER 157.07 1.61E-05 3409340000 2049133 2279645 1278107 1593266 2281520 2519179 2610437 2414536 1200930 TRUE FALSE 1778334.882 2264669.862 1896203.82 1955041.397 2236122.216 2616093.446 2357277.222 1898206.266 1058957.424 1.67932614 2.138584434 1.790632728 1.846194524 2.111626177 2.47044252 2.226035881 1.792523688 1 20.01421315 RYS(ph)GDSDSSASSAQSGPLGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RYSGDSDSSASSAQSGPLGTR 21 1 A0A5E8;Q99501 A0A5E8 GAS2L1 GAS2-like protein 1 1 RYS(0.972)GDS(0.027)DS(0.001)SASSAQSGPLGTR 137.42 2.03E-06 311320000 104620 104570 58883 63903 101350 98922 106460 116330 95984 TRUE FALSE 90794.20193 103883.0728 87359.01575 78413.15285 99333.33329 102727.5934 96135.52559 91453.73478 84636.88087 1.072749858 1.227397226 1.032162514 0.926465532 1.173641234 1.213745028 1.13585856 1.080542357 1 16.36899884 1.301577781 3.067876627 0.988278618 1.112007346 0.136323836 0.088468494 0.716889537 9.139820675 0.19979281 0.024029338 20.02524235 -1.301577781 0.123728729 RYS(ph)GNMEYVISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RYSGNMEYVISR 12 1 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 RYS(1)GNMEYVISR;RYS(1)GNMEYVISR 228.32 6.64E-12 1023870000 403130 444370 327450 366000 475220 513460 459630 490260 482560 TRUE FALSE 349855.3491 441450.9042 485805.9153 449105.894 465764.0518 533213.1385 415055.1533 385421.7142 425512.3065 0.822197957 1.037457431 1.14169651 1.055447485 1.09459596 1.253108618 0.975424558 0.905782767 1 18.69884133 2.020099814 24.9999454 0.944494114 1.073801779 0.176378652 0.108900965 342.7082946 426255.4227 0.044807615 0.030205504 104.7369238 -2.020099814 0.129307665 RYS(ph)PPIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 RYSPPIQR 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RYS(1)PPIQR;RYS(1)PPIQR;RYS(1)PPIQR;RYS(1)PPIQR;RYS(1)PPIQR;RYS(1)PPIQR;RY(0.001)S(0.999)PPIQR;RYS(1)PPIQR;RY(0.004)S(0.996)PPIQR;RY(0.086)S(0.914)PPIQR;RYS(1)PPIQR;RYS(1)PPIQR;RYS(1)PPIQR 130.01 0.00065316 78863606000 2554741.1 2078186.9 1674621.2 3402310.6 2160084 2555829.1 2061435.1 2162232.3 1910045.4 TRUE FALSE 2217125.591 2064535.153 2484473.614 4174857.223 2117102.555 2654153.499 1861517.441 1699855.749 1684242.009 1.316393713 1.225794834 1.475128634 2.478775141 1.257006145 1.575874183 1.105255321 1.009270485 1 20.68366802 2.186749528 3.364120784 1.013445796 1.569557782 0.323899164 0.352594465 0.289272878 6.708375607 0.164224946 0.105753109 153.726779 -2.186749528 0.556111985 RYS(ph)PS(ph)PPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 RYSPSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RY(0.039)S(0.964)PS(0.997)PPPK;RY(0.016)S(0.984)PS(1)PPPK 85.845 0.0097175 1209970000 1301670 1012430 725310 839490 997390 834200 1117200 1292220 1256480 TRUE FALSE 1129651.011 1005779.281 1076072.342 1030109.035 977543.8904 866292.2138 1008854.116 1015888.809 1107940.366 1.0195955 0.907791892 0.971236698 0.929751336 0.882307316 0.781894261 0.910567163 0.916916506 1 20.0794488 7.999987086 0.773186715 0.902460875 23.8983012 0.253672533 0.057306754 665.287095 2.603809481 0.021731313 26719.33593 99997026.41 -7.999987086 22.99584033 RYS(ph)PS(ph)PPPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RYSPSPPPKR 10 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RY(0.044)S(0.959)PS(0.997)PPPKR;RY(0.199)S(0.866)PS(0.935)PPPKR;RY(0.149)S(0.858)PS(0.993)PPPKR 72.891 0.025007 1047310000 726770 596400 403730 446870 563640 533480 625100 714340 605100 TRUE FALSE 630725.5031 592482.2091 598975.1784 548338.6635 552424.6667 554003.3208 564477.8982 561583.95 533565.7673 1.182095145 1.110420206 1.12258922 1.027687114 1.035345033 1.038303719 1.057934997 1.052511207 1 19.02530658 4.189370918 1.213956766 1.037522746 1.179921078 0.819594187 0.022965368 0.279177581 0.646145773 0.007181355 0.039843082 15465.74758 -4.189370918 0.142398332 RYS(ph)PSPPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RYSPSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RY(0.176)S(0.804)PS(0.019)PPPK 67.153 0.037795 283550000 298780 246580 174600 227960 256710 221130 282020 351740 284650 TRUE FALSE 259295.466 244960.1997 259037.144 279721.8022 251601.9732 229637.0142 254669.7438 276523.1382 250999.0013 1.033053776 0.975940934 1.0320246 1.114433925 1.002402288 0.914892143 1.01462453 1.101690193 1 17.9373221 1.951640199 23.24136792 1.058123387 1.01135674 0.073765517 0.055215842 391.5435568 188170.9566 0.026424123 0.015248526 89.46232869 -1.951640199 -0.046766647 RYS(ph)SSGTPSSASPALSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 RYSSSGTPSSASPALSR 17 1 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;Q14934-12;Q14934-13;Q14934-18 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 RY(0.041)S(0.727)S(0.158)S(0.063)GT(0.011)PSSASPALSR 56.29 0.068564 166180000 152020 145350 95783 106670 145420 154890 135170 152890 136950 TRUE FALSE 131930.1718 144395.1863 142103.9792 130891.0538 142526.4265 160848.7185 122061.2342 120195.6633 120759.927 1.092499599 1.195721046 1.176747806 1.083894774 1.180246047 1.331970982 1.010775985 0.995327393 1 16.88178226 2.088441428 12.92754146 0.999048792 1.1736068 0.60303568 0.066886389 0.424349322 59.97745468 0.027186382 0.018328297 122.5861563 -2.088441428 0.174558008 RYTCGEAPDYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 RYTCGEAPDYDR 12 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;; 134.4 0.00023433 2302940000 1638500 1709420 1029150 1115280 1522710 1872750 1771870 1704910 867930 FALSE TRUE 1421968.074 1698190.707 1526850.382 1368521.37 1492411.05 1944795.904 1600034.32 1340328.264 765324.3041 1.857994142 2.218916475 1.995037103 1.788158775 1.950037444 2.541139611 2.090661843 1.751320658 1 19.54571169 1.276948716 2.357498889 0.774082588 2.067073901 0.720828374 0.208841816 0.295227693 1.860837124 0.767818313 0.057737975 18.92120173 -1.276948716 1.292991313 S(ph)AEDVSTVPTQPDNPFSHPDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAEDVSTVPTQPDNPFSHPDK 21 0 A0A0U1RR07;Q9HCH5-7;Q9HCH5-13;Q9HCH5;Q9HCH5-15;Q9HCH5-12 A0A0U1RR07;Q9HCH5-12 SYTL2 Synaptotagmin-like protein 2 1 S(1)AEDVSTVPTQPDNPFSHPDK 157.68 2.17E-09 223990000 190430 162420 139230 126030 139600 158580 185210 196450 188630 TRUE FALSE 165264.193 161353.0523 206562.0937 154647.0377 136822.2331 164680.6752 167248.3627 154440.6963 166330.3763 0.993589967 0.970075677 1.241878353 0.929758239 0.82259318 0.990081781 1.005519055 0.928517687 1 17.34369214 S(ph)AEPSPT(ph)VMSTSLGSNLSELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAEPSPTVMSTSLGSNLSELDR 22 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 2 S(0.999)AEPS(0.151)PT(0.85)VMSTSLGSNLSELDR 160.52 3.27E-11 34667000 31546 26234 19352 23377 32028 24867 29841 38583 37912 TRUE FALSE 27377.11617 26061.66713 28710.69193 28685.10515 31390.70546 25823.64958 26947.02441 30332.3257 33430.08655 0.818936443 0.779587187 0.858827927 0.858062545 0.938995638 0.772467326 0.806071033 0.90733614 1 15.02885947 1.420982671 2.85923932 1.003669328 0.83528927 0.566475032 0.047484287 0.238251949 3.091402274 0.078009594 0.012970737 26.36226192 -1.420982671 -0.168380058 S(ph)AEPSPTVMSTSLGSNLSELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAEPSPTVMSTSLGSNLSELDR 22 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 S(0.877)AEPS(0.123)PTVMSTSLGSNLSELDR 112.56 0.00030287 42505000 15956 12136 7092.9 11321 15982 12200 12397 19140 14492 TRUE FALSE 13847.37417 12056.27782 10523.05016 13891.60608 15663.98947 12669.34189 11194.74085 15047.05995 12778.77227 1.083623206 0.943461356 0.823478965 1.087084564 1.225782034 0.99143655 0.876041971 1.177504351 1 13.64146161 3.687468255 24.99846628 1.064524649 0.949514722 0.167680335 0.114608075 593.4945377 290384.6439 0.031990144 0.047449103 4869.31931 -3.687468255 -0.115009927 S(ph)AFSPYQTPVAHFPPPPEEPTATAAFGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAFSPYQTPVAHFPPPPEEPTATAAFGAR 29 0 A0A0A0MQV9;Q9UPS6-2;Q9UPS6 A0A0A0MQV9 SETD1B Histone-lysine N-methyltransferase;Histone-lysine N-methyltransferase SETD1B 1 S(0.505)AFS(0.477)PY(0.013)QT(0.005)PVAHFPPPPEEPTATAAFGAR 58.172 0.029018 120490000 56872 41193 20969 25669 35341 42077 39001 37235 35640 TRUE FALSE 49356.2211 40922.40047 31109.67854 31497.53878 34637.78324 43695.72942 35218.68902 29272.58501 31426.6798 1.570519744 1.302154753 0.989912989 1.002254739 1.102177623 1.390402349 1.120662101 0.931456495 1 14.93970224 4.532136878 3.009668836 1.076196069 1.567997416 0.618120561 0.126687261 0.207658319 3.348993409 0.03571554 0.189562752 34051.54942 -4.532136878 0.491801347 S(ph)AGEEEDGPVLTDEQK ddPTM_MDA-MB-175_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 453.68 1.49E-182 3447290000 5072390 4416600 3336780 3829350 4847170 3271680 5384320 7104290 5736120 TRUE FALSE 4402060.81 4387587.064 4950457.969 4698862.445 4750720.8 3397543.647 4862149.475 5585092.869 5058002.428 0.870316073 0.867454519 0.97873776 0.928995688 0.939248422 0.671716492 0.961278596 1.104209211 1 22.2701363 1.99821336 24.99997764 1.051506881 0.879868267 0.425330006 0.084798902 59.77255931 836384.9023 0.035360981 0.023435225 99.58945589 -1.99821336 -0.171638614 S(ph)AKPETVIDSLLQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAKPETVIDSLLQ 13 1 J3KPF9;A0A087X011;E9PES4;Q9Y496;H7C2F6 J3KPF9 KIF3A Kinesin-like protein;Kinesin-like protein KIF3A 1 S(1)AKPETVIDSLLQ;S(1)AKPETVIDSLLQ 141.1 0.00010439 137997000 640010 475160 287150 458560 428210 274000 737300 569710 581280 TRUE FALSE 555431.0569 472038.6427 426016.7005 562683.0567 419689.4588 284540.9573 665796.7595 447881.95 512561.7406 1.083637371 0.920940065 0.83115197 1.09778591 0.81880762 0.555134991 1.298959143 0.873810732 1 18.96736627 0.876737595 8.501554553 1.723771343 0.935180062 0.010498045 0.198209719 19699.1165 54879.58539 267830.1405 0.04668216 7.529005159 -0.876737595 -0.78859128 TVAISDAAQLPHDYCTT(ph)PGGTLFS(ph)TTPGGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDYCT(0.116)T(0.883)PGGT(0.001)LFS(0.582)T(0.266)T(0.151)PGGTR;TVAISDAAQLPHDYCT(0.01)T(0.99)PGGTLFS(0.637)T(0.233)T(0.13)PGGTR 223.33 8.61E-35 6727300000 511430 859060 685000 885430 1397720 1572760 1325900 1521180 1467480 TRUE FALSE 443843.2297 853416.7783 1016268.291 1086480.414 1369908.107 1633265.095 1197314.422 1195887.495 1293996.186 0.343001961 0.65952032 0.785371937 0.839631852 1.058664717 1.262186946 0.925284352 0.924181623 1 20.30340193 4.610118068 0.889748705 1.016780632 0.076111697 0.815318235 0.105489321 0.862206357 0.620141874 0.041697831 0.76245012 40749.1044 -4.610118068 -0.940668936 down S(ph)APASPT(ph)HPGLMSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 S(0.787)APAS(0.214)PT(0.691)HPGLMS(0.308)PR;S(0.999)APAS(0.255)PT(0.598)HPGLMS(0.149)PR;S(1)APAS(0.151)PT(0.849)HPGLMSPR 193.06 1.92E-07 2214740000 2115220 1721380 772690 951050 1249250 1254770 1106160 1288230 1201730 TRUE FALSE 1835688.318 1710072.141 1146365.468 1167000.438 1224392.369 1303041.814 998884.7735 1012752.04 1059662.848 1.732332431 1.613788899 1.081820949 1.101294096 1.155454653 1.22967585 0.94264395 0.955730439 1 20.01517389 4.269466822 3.930508988 1.056711146 1.706496094 0.892555488 0.087890396 0.068764777 2.254045571 0.026172293 0.072407866 18598.0248 -4.269466822 0.649784948 S(ph)APELPEGILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SAPELPEGILK 11 0 Q3KR16-2;Q3KR16;Q3KR16-3 Q3KR16-2 PLEKHG6 Pleckstrin homology domain-containing family G member 6 1 S(1)APELPEGILK;S(1)APELPEGILK;S(1)APELPEGILK;S(1)APELPEGILK;S(1)APELPEGILK;S(1)APELPEGILK 196.27 6.41E-08 1381295000 1797241 1743805 1323215 1604703 1870508 1578191 2125473 2477520 2215357 TRUE FALSE 1559731.048 1732349.83 1963126.2 1969075.342 1833288.55 1638905.029 1919344.956 1947721.628 1953460.019 0.798445339 0.886810998 1.004948236 1.007993674 0.93848276 0.838975466 0.982536083 0.997062448 1 20.8976003 4.510038773 3.390341877 0.966262363 0.804545184 0.545734443 0.050526649 0.205689782 4.565466851 0.013842701 0.063059648 32362.2548 -4.510038773 -0.161717179 S(ph)APPNLWAAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SAPPNLWAAQR 11 0 Q92934;F5H1R6;F5H3B1 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 S(1)APPNLWAAQR;S(1)APPNLWAAQR;S(1)APPNLWAAQR;S(1)APPNLWAAQR 129.54 0.00025481 1347200000 172288 105845 66955 114980 157559 165822 150015 159699 224195 TRUE FALSE 149519.7043 105149.6972 99334.66195 141087.9664 154423.8842 172201.2796 135466.5684 125548.6116 197690.9225 0.756330652 0.531889355 0.502474573 0.713679539 0.781137961 0.87106316 0.685244252 0.635075248 1 17.5928871 3.537421194 5.43279007 0.768677822 0.591070648 0.353085028 0.119129611 0.260762663 15.8445228 0.033684559 0.049645863 3446.840554 -3.537421194 -0.177607174 S(ph)AQLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAQLER 6 0 Q8N3R9-2;Q8N3R9;G3V2B0;G3V2H1 Q8N3R9-2 MPP5 MAGUK p55 subfamily member 5 1 S(1)AQLER;S(1)AQLER 98.044 0.04236 3185100000 708020 616860 471290 504600 501720 729390 549790 650820 695130 TRUE FALSE 614453.3631 612807.806 699207.4204 619177.1423 491736.7536 757450.1053 496471.4504 511647.2077 612952.5233 1.002448542 0.999763901 1.140720356 1.010155141 0.802242808 1.235740251 0.809967219 0.834725673 1 19.22541581 S(ph)ARHT(ph)PAR ddPTM_MDA-MB-175_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 92.039 0.027638 1511120000 133246 137504 76748 87775 108540 128368 139887 164262 75914 TRUE FALSE 115637.2035 136600.7272 113863.5895 107705.6553 106380.2664 133306.4 126320.7803 129135.8496 66939.5334 1.727487445 2.04065849 1.700991682 1.608999194 1.589199401 1.991445014 1.887087852 1.929141765 1 16.03057087 1.233663509 24.99996614 0.999998755 1.815020983 0.730841015 0.154330176 84.69164919 432303.2292 0.31820606 0.039640766 17.1262985 -1.233663509 0.815022227 S(ph)AS(ph)APTLAETEKETAEHLDLAGASSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASAPTLAETEKETAEHLDLAGASSR 26 1 Q86W92-2 Q86W92-2 PPFIBP1 Liprin-beta-1 2 S(0.411)AS(0.411)APT(0.398)LAET(0.39)EKET(0.39)AEHLDLAGASSR 50.215 0.071118 45154000 5156.8 2859.4 3515 1353.1 4473 2814.8 2641.9 5963.8 3447.9 TRUE FALSE 4475.315814 2840.616413 5214.865757 1660.342036 4383.996051 2923.087177 2385.688945 4688.48778 3040.29319 1.472001394 0.934323184 1.715250942 0.546112474 1.441964895 0.961449109 0.784690421 1.542116989 1 11.56999474 4.766531544 22.44377506 1.13983845 1.472003276 0.085537725 0.358463189 6290.815633 5047393.923 0.080181732 5.817395932 58415.96352 -4.766531544 0.332164827 S(ph)AS(ph)PERMD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 103.91 0.0031458 3501063000 4651480 3623388 2747485 3132316 3648442 3869280 3600946 4366890 4768320 TRUE FALSE 4036775.133 3599585.726 4076177.936 3843556.222 3575845.142 4018133.705 3251726.811 3433064.557 4204614.642 0.960082071 0.856103599 0.969453394 0.914128059 0.850457283 0.955648507 0.773370948 0.816499216 1 22.00354215 3.013327712 1.357222958 0.860507997 0.923259303 0.051820488 0.071934691 0.945750965 3.67439126 0.030637591 0.033759824 1031.163929 -3.013327712 0.062751306 S(ph)AS(ph)PPPATSSSSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASPPPATSSSSSSR 15 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 S(1)AS(0.985)PPPAT(0.014)SSSSSSR 91.592 0.0081412 256380000 373300 347960 235180 226460 357900 333080 357450 398090 398640 TRUE FALSE 323967.4592 345674.2278 348913.8346 277881.2042 350778.4902 345893.8031 322784.554 312961.5514 351513.2333 0.921636594 0.983388945 0.992605119 0.790528429 0.997909771 0.984013603 0.918271415 0.890326513 1 18.42321948 S(ph)AS(ph)PYPSHS(ph)LSSPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASPYPSHSLSSPQR 15 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 3 S(0.865)AS(0.626)PY(0.069)PS(0.438)HS(0.389)LS(0.445)S(0.169)PQR 101.68 0.0011214 353000000 548420 478610 283610 343300 541600 446440 461080 603050 515960 TRUE FALSE 475944.9075 475465.9794 420764.7446 421251.512 530823.2196 463614.8357 416364.5326 474092.4504 454963.7966 1.046116001 1.045063328 0.924831267 0.925901171 1.166737274 1.019014786 0.915159702 1.042044343 1 18.79539222 4.408909723 24.99999997 1.001348754 1.045875956 0.064449109 0.073256989 144.8336524 53080.34131 0.018475056 0.048880408 25639.51014 -4.408909723 0.044527201 S(ph)ASASHQADIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASASHQADIK 11 0 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 S(0.472)AS(0.472)AS(0.057)HQADIK 127.32 0.00018618 756440000 1438400 1288100 882950 1336600 1437400 1384600 1109900 2308100 2180500 TRUE FALSE 1248311.796 1279638.386 1309947.573 1640095.459 1408798.552 1437866.458 1002262.069 1814530.777 1922723.774 0.649241359 0.665534178 0.68129785 0.853006282 0.7327098 0.747827887 0.521272001 0.943729308 1 20.87472008 1.600735052 6.896337567 0.984505806 0.701494846 0.657145165 0.083960494 0.070510156 7.155534213 0.054945562 0.021527685 39.87815452 -1.600735052 -0.28301096 S(ph)ASDNTLVAMDFSGHAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SASDNTLVAMDFSGHAGR 18 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 1 S(0.5)AS(0.5)DNT(0.001)LVAMDFSGHAGR;S(0.592)AS(0.408)DNTLVAMDFSGHAGR;S(0.582)AS(0.418)DNTLVAMDFSGHAGR;S(0.578)AS(0.421)DNT(0.001)LVAMDFSGHAGR;S(0.333)AS(0.333)DNT(0.333)LVAMDFSGHAGR 251.44 5.27E-26 1022198000 689344 291399.7 190742.4 279111.2 384301.7 414538 341717.6 383337.5 381771.4 TRUE FALSE 598245.4438 289485.4762 282986.0626 342487.6639 376654.848 430485.5451 308577.8797 301363.7588 336638.82 1.777113655 0.859928977 0.840622192 1.017374241 1.118869321 1.278775707 0.916643778 0.895213923 1 18.36084203 4.744322751 24.93248848 0.989091444 1.777114008 0.780541275 0.131007185 312.645852 1352763.776 0.034904674 0.302984786 55503.80426 -4.744322751 0.788022564 S(ph)ASNGHVPGTPVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASNGHVPGTPVYR 14 0 A0A087WX19;A0A087WX45;Q6IPM2-2;Q6IPM2-3;Q6IPM2-4;Q6IPM2;C9JP75 A0A087WX19 IQCE IQ domain-containing protein E 1 S(0.5)AS(0.5)NGHVPGTPVYR 59.733 0.063478 260570000 329840 330360 163970 223570 310470 245740 358060 352050 289600 TRUE FALSE 286250.8083 328189.8434 243266.4404 274334.9856 304292.2544 255193.7768 323335.3963 276766.8472 255363.8179 1.120952885 1.285185372 0.952626893 1.074290742 1.191602855 0.999334122 1.266175447 1.083813868 1 17.9621946 7.999987911 0.010138524 9.96E-10 2.364306202 0.038146325 0.109847543 133621.3021 135.0216813 14006.6472 17688.58415 99997216.37 -7.999987911 2.364306201 S(ph)ASPHDVDLCLVSPCEFEHR ddPTM_MDA-MB-175_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(0.5)AS(0.5)PHDVDLCLVSPCEFEHR;S(0.59)AS(0.41)PHDVDLCLVSPCEFEHR;S(0.57)AS(0.43)PHDVDLCLVSPCEFEHR 229.89 3.43E-25 4124690000 437593 440826 275138 353332 426424 474468 400964 447359 626461 TRUE FALSE 379763.9763 437930.185 408195.6571 433561.4309 417938.9967 492721.091 362078.573 351694.7592 552401.4942 0.687478184 0.792775164 0.738947417 0.784866506 0.756585565 0.891961908 0.655462697 0.636665112 1 19.0753577 4.752253786 22.25314602 0.766219101 0.687477943 0.055298763 0.106147425 1752.255922 2847398.094 0.025598806 0.426161526 56526.71998 -4.752253786 -0.078741158 S(ph)ASPHDVDLCLVSPCEFEHRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SASPHDVDLCLVSPCEFEHRK 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 S(0.562)AS(0.438)PHDVDLCLVSPCEFEHRK;S(0.5)AS(0.5)PHDVDLCLVSPCEFEHRK;S(0.5)AS(0.5)PHDVDLCLVSPCEFEHRK;S(0.5)AS(0.5)PHDVDLCLVSPCEFEHRK 152.5 2.44E-08 1158367000 1204650 1078630 599249 691075 1157630 1056140 1287160 1504120 670977 TRUE FALSE 1045452.45 1071544.409 889047.8208 847994.1412 1134595.428 1096770.389 1162331.421 1182475.643 591654.8634 1.766997138 1.811097102 1.502646012 1.433258127 1.917664331 1.853733413 1.964543002 1.998590253 1 19.17439631 3.219949938 24.869569 1.800030789 1.632552608 0.020050902 0.303646113 691.423686 923951.2056 0.091691361 0.104154221 1659.395614 -3.219949938 -0.16747818 S(ph)ASPTVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASPTVPR 8 0 Q92817;K7EKI0;K7EQ87 Q92817 EVPL Envoplakin 1 S(0.517)AS(0.453)PT(0.03)VPR 88.948 0.014951 5215200000 1738200 1850700 1147900 1372400 1725600 2072900 1768200 2058200 2022100 TRUE FALSE 1508492.466 1838542.63 1703028.279 1684024.396 1691263.936 2152645.804 1596720.236 1618069.947 1783049.642 0.84601821 1.031122514 0.955121069 0.94446299 0.948523191 1.207283159 0.895499597 0.907473303 1 20.76591544 4.753973452 23.16627137 0.979243139 0.846017936 0.196072753 0.088206646 1868.775948 2808731.246 0.021754218 0.458005936 56750.99135 -4.753973452 -0.133225203 S(ph)ASTESGFHNHTDTAEGDVIAAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASTESGFHNHTDTAEGDVIAAAR 24 0 Q02410-2;Q02410 Q02410-2 APBA1 Amyloid beta A4 precursor protein-binding family A member 1 1 S(0.509)AS(0.356)T(0.1)ES(0.021)GFHNHT(0.012)DT(0.001)AEGDVIAAAR 92.449 0.014364 513290000 38954 48715 27178 37884 52721 51719 53035 54385 47969 TRUE FALSE 33806.1302 48394.98796 40321.3717 46486.14122 51671.95525 53708.6634 47891.67386 42755.19097 42298.15947 0.799234071 1.144139333 0.953265395 1.099010969 1.22161238 1.269763604 1.132240137 1.010804998 1 15.36830727 4.743563429 24.37382878 1.101922987 0.799233891 0.489485487 0.097750092 363.6359623 1771559.853 0.026040061 0.207755403 55406.84599 -4.743563429 -0.302689096 S(ph)AT(ph)PPATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SATPPATR 8 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)AT(1)PPATR 80.758 0.052768 0 444360 347260 285370 289790 348350 367170 305800 402950 704540 TRUE FALSE 385636.7001 344978.8262 423375.8865 355591.2487 341418.5165 381295.2675 276143.5631 316782.2783 621250.0838 0.620743096 0.555297834 0.681490269 0.572380202 0.549566954 0.613754875 0.444496621 0.509911043 1 19.24481462 1.234228718 24.98788442 1.000000648 0.563969496 0.816921391 0.064172037 56.75900741 327361.9201 0.127572881 0.016704881 17.1486019 -1.234228718 -0.436031152 S(ph)ATLSGSATNLASLTAALAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SATLSGSATNLASLTAALAK 20 0 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 S(0.795)AT(0.205)LSGSATNLASLTAALAK;S(0.985)AT(0.015)LSGSATNLASLTAALAK 291.28 1.89E-54 41312000 66162 81091 56337 65968 89078 75238 100874 114086 116582 TRUE FALSE 57418.52407 80558.30788 83581.76164 80947.04266 87305.52208 78132.45455 91091.25501 89689.59672 102799.8088 0.558546993 0.783642585 0.813053668 0.787424059 0.849277086 0.760044746 0.886103351 0.872468517 1 16.64947806 6.11012951 0.331650752 0.916755131 1.99E-79 0.682690075 0.063460883 15.45860081 0.750982838 0.110673558 6.69587174 1288633.775 -6.11012951 -0.916755131 S(ph)ATPVNCEQPDILVSSTPINEGQTVLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SATPVNCEQPDILVSSTPINEGQTVLDK 28 0 A0A2R8Y7M0;P82094;P82094-2;F8WF45 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 S(0.5)AT(0.5)PVNCEQPDILVSSTPINEGQTVLDK 132.12 1.27E-05 59932000 88392 87975 69148 66421 85549 76186 100040 127510 125210 TRUE FALSE 76710.77324 87397.08643 102588.2041 81502.90323 83846.74227 79116.92472 90338.1362 100242.9788 110407.8164 0.694794768 0.791584231 0.929175192 0.73819867 0.759427593 0.716588076 0.818222288 0.907933714 1 16.75248279 1.582640793 2.07267384 1.002106862 0.777269481 0.593286155 0.063606892 0.25859666 2.128808729 0.094215822 0.01841588 38.25082384 -1.582640793 -0.224837381 S(ph)AVFPGEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 125.23 0.00053238 2240150000 3532100 3425710 2718510 2760370 3400850 3252680 4248000 4677720 5192430 TRUE FALSE 3065324.036 3403206.285 4033190.529 3387154.198 3333179.739 3377812.704 3836029.614 3677425.98 4578586.841 0.669491296 0.743287482 0.880881082 0.739781578 0.727993124 0.737741321 0.83781956 0.803179258 1 22.12647096 -0.606452169 0.981158341 9.999999998 0.757052082 0.631697785 0.057403021 46.11231296 1.474191961 891.6670611 0.019112979 0.247484401 0.606452169 -9.242947916 S(ph)AVLLVDETATTPIFANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SAVLLVDETATTPIFANR 18 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;A0A087WY36;A0A087WX73 Q12802-2 AKAP13 A-kinase anchor protein 13 1 S(1)AVLLVDETATTPIFANR;S(1)AVLLVDETATTPIFANR;S(1)AVLLVDETATTPIFANR;S(1)AVLLVDETATTPIFANR 380.5 2.35E-108 1000770000 288175 315000 211525 234156 343217 348926 317234 365747 388547 TRUE FALSE 250091.9436 312930.7443 313819.1975 287324.6987 336387.6532 362349.409 286468.6955 287534.8503 342613.4163 0.729953737 0.913363953 0.915957118 0.838626525 0.981828607 1.057604261 0.836128073 0.839239903 1 18.38622212 4.738582977 7.317354793 0.915599088 0.727684714 0.39630961 0.07434649 0.119073003 56.83265888 0.018955861 0.110780244 54775.07457 -4.738582977 -0.187914374 S(ph)CETSSQDLGFSYYPAENLIEYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SCETSSQDLGFSYYPAENLIEYK 23 0 S5FZ81;Q8WUB8-3;Q8WUB8-2;Q8WUB8 S5FZ81 PHF10 PHD finger protein 10 1 S(0.889)CET(0.109)S(0.002)SQDLGFSYYPAENLIEYK;S(0.851)CET(0.142)S(0.003)S(0.004)QDLGFSYYPAENLIEYK;S(0.907)CET(0.092)S(0.001)SQDLGFSYYPAENLIEYK 274.97 6.64E-52 277022000 314404 237949 188109 218945 235353 199575 276786 344130 387192 TRUE FALSE 272854.7148 236385.8974 279079.1416 268659.8086 230669.9358 207252.7794 249943.3363 270540.4775 341418.6029 0.799179402 0.692363847 0.817410473 0.786892707 0.675622048 0.607034232 0.732072987 0.792401103 1 18.38118214 1.228019328 2.371822884 1.077287989 0.728081096 0.645527497 0.062643839 0.406971691 2.361125561 0.3012277 0.017619475 16.90516164 -1.228019328 -0.349206893 S(ph)CHDLDLLGQSPGWGQTQAVETNIVCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SCHDLDLLGQSPGWGQTQAVETNIVCK 27 0 Q9P0V3;Q9P0V3-2 Q9P0V3 SH3BP4 SH3 domain-binding protein 4 1 S(0.999)CHDLDLLGQS(0.001)PGWGQTQAVETNIVCK;S(1)CHDLDLLGQSPGWGQTQAVETNIVCK;S(1)CHDLDLLGQSPGWGQTQAVETNIVCK 260.9 3.00E-53 497760000 245773 171311 109143 160125 178225 180032 168602 195224 213127 TRUE FALSE 213293.4753 170185.6468 161924.9199 196483.8286 174678.6712 186957.9475 152251.004 153476.8668 187931.3689 1.134954088 0.90557339 0.861617307 1.04550842 0.929481184 0.994820336 0.810141516 0.816664444 1 17.51984637 4.739578248 24.06828037 0.911866258 1.134954202 0.423765413 0.078027998 52.48097638 1240942.339 0.020089503 0.118571109 54900.74631 -4.739578248 0.223087944 S(ph)CLWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SCLWLR 6 0 Q99956 Q99956 DUSP9 Dual specificity protein phosphatase 9 1 S(1)CLWLR 94.407 0.089389 0 369830 315780 337420 250720 379340 428300 377280 328520 366480 TRUE FALSE 320956.0285 313705.6204 500597.4406 307649.808 371791.8762 444776.9781 340691.4437 258268.5545 323155.1519 0.993194837 0.970758531 1.549093176 0.952018887 1.150505799 1.37635738 1.054265859 0.799209151 1 18.30186747 1.994346449 24.63587346 0.897704868 1.167866065 0.248657615 0.190093907 251.1051036 1094213.932 0.077838071 0.050631823 98.70665817 -1.994346449 0.270161197 S(ph)CNITECQDPDLLHNWPDAFTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SCNITECQDPDLLHNWPDAFTLR 23 0 Q6ZN28 Q6ZN28 MACC1 Metastasis-associated in colon cancer protein 1 1 S(0.95)CNIT(0.05)ECQDPDLLHNWPDAFTLR;S(0.993)CNIT(0.007)ECQDPDLLHNWPDAFTLR;S(0.987)CNIT(0.013)ECQDPDLLHNWPDAFTLR;S(0.791)CNIT(0.209)ECQDPDLLHNWPDAFTLR 216.21 1.67E-32 573150000 326866 333696 212222 203410 293385 323130 290680 271456 331008 TRUE FALSE 283669.8299 331503.929 314853.269 249597.3494 287547.2125 335561.0202 262489.8983 213407.2469 291876.6113 0.971882703 1.135767362 1.078720448 0.855146797 0.985167024 1.149667384 0.899318027 0.731155696 1 18.15499908 2.016013829 19.32735158 0.837033318 1.026369225 0.30978246 0.106282 16.03509159 19351.96197 0.043274085 0.029136844 103.7561454 -2.016013829 0.189335907 S(ph)CPELTSGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SCPELTSGPR 10 0 Q13111;Q13111-2;Q13111-3 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 S(1)CPELTSGPR;S(1)CPELTSGPR 234.9 4.42E-12 736110000 215300 221490 120673 162464 211172 189741 179753 207140 196031 TRUE FALSE 186847.5595 220035.0176 179030.8664 199353.9343 206970.0904 197040.459 162320.5817 162844.723 172856.4385 1.080940699 1.272935041 1.035719977 1.153291923 1.197352509 1.139908127 0.939048514 0.942080749 1 17.39921482 2.249066472 11.59755692 0.955651377 1.150035398 0.647489658 0.064742908 0.196672019 212.2401447 0.023215925 0.017387587 177.4461054 -2.249066472 0.194384021 S(ph)CSPLAFSAFGDLTIK ddPTM_MDA-MB-175_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 80.534 0.016047 22805000 55342 60141 38473 46667 61159 46361 62420 78360 56202 TRUE FALSE 48028.41448 59745.92981 57078.67148 57263.45561 59942.05556 48144.53767 56366.51801 61603.3238 49557.86359 0.969138115 1.205579206 1.151758114 1.155486768 1.209536716 0.971481299 1.137387973 1.243058505 1 15.59682637 4.752621352 24.17629913 1.141401775 0.969137928 0.258767269 0.087104273 2170.387413 3731702.923 0.020714076 0.41259239 56574.5818 -4.752621352 -0.172263847 S(ph)DDELLDDFFHDQSTATSQAGTLSSIPTALTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDDELLDDFFHDQSTATSQAGTLSSIPTALTR 32 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 S(1)DDELLDDFFHDQSTATSQAGTLSSIPTALTR;S(1)DDELLDDFFHDQSTATSQAGTLSSIPTALTR 131.56 4.88E-08 60176000 19063.6 11812.8 10699.1 12634.7 19068.7 13928.8 15045.6 21360.8 24523 TRUE FALSE 16544.29696 11735.20094 15873.22055 15503.60174 18689.27018 14464.64995 13586.48003 16792.95915 21623.91888 0.765092445 0.542695383 0.734058458 0.716965404 0.864286917 0.668918989 0.628307945 0.776591849 1 14.40034038 1.279936069 3.17985294 1.035788234 0.703377391 0.550146519 0.08421426 0.241440334 3.339211363 0.190143542 0.021692969 19.05180242 -1.279936069 -0.332410843 S(ph)DEDRYQNGAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDEDRYQNGAER 12 1 Q9HCG8 Q9HCG8 CWC22 Pre-mRNA-splicing factor CWC22 homolog 1 S(1)DEDRYQNGAER;S(1)DEDRYQNGAER 180.74 1.15E-05 297510000 142065 122806 95334 110130 144305 126338 129745 139663 149394 TRUE FALSE 123290.7503 121999.2793 141437.8413 135136.6997 141433.6128 131198.3046 117162.3499 109797.1543 131732.8115 0.935915273 0.926111558 1.073672076 1.025839335 1.073639978 0.995942492 0.889393831 0.833483724 1 17.00725521 2.263592708 5.6915815 0.890968991 1.009487267 0.335029952 0.063362521 0.167877849 15.8340884 0.025471344 0.018839274 183.48168 -2.263592708 0.118518276 S(ph)DSDLLTCSPTEDATMGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SDSDLLTCSPTEDATMGSR 19 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 S(0.991)DS(0.009)DLLTCSPTEDATMGSR;S(1)DSDLLTCSPTEDATMGSR;S(0.975)DS(0.025)DLLTCSPTEDATMGSR 425.24 4.06E-169 362782000 81479 64568 58759 70974 76786 70845 67321 81855 135599 TRUE FALSE 70711.34371 64143.84856 87175.04894 87089.73147 75258.10883 73570.45299 60792.21978 64350.94525 119568.6407 0.591387033 0.536460465 0.729079535 0.728365991 0.629413435 0.615298899 0.508429463 0.538192497 1 16.86747954 1.232357884 24.96803765 1.000000657 0.607451031 0.730955723 0.074429405 121.4895052 488986.1672 0.18412495 0.020408456 17.07488878 -1.232357884 -0.392549627 S(ph)DSEATISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDSEATISR 9 0 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2;H0Y4T4 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 S(0.995)DS(0.005)EATISR;S(0.986)DS(0.014)EATISR 169.58 0.00062512 352740000 617850 516350 357490 391920 465260 495870 560450 551370 627960 TRUE FALSE 536199.5571 512958.0629 530373.3597 480911.4261 456002.2363 514946.4398 506097.6453 433463.8163 553723.2842 0.968352916 0.926379796 0.957831059 0.868504973 0.823520067 0.929970717 0.913990182 0.782816668 1 19.07880566 3.737907625 24.97780264 0.87658023 0.948407114 0.193075555 0.059746254 83.7360343 3203021.091 0.015805041 0.025119453 5468.996245 -3.737907625 0.071826884 S(ph)DSELEVKPAESLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SDSELEVKPAESLLR 15 1 Q92539 Q92539 LPIN2 Phosphatidate phosphatase LPIN2 1 S(0.996)DS(0.004)ELEVKPAESLLR;S(0.995)DS(0.005)ELEVKPAESLLR;S(0.998)DS(0.002)ELEVKPAESLLR 122.49 6.58E-05 287285000 287849 174440 158660 194290 193047 162914 180619 279694 328021 TRUE FALSE 249809.0253 173294.0922 235388.5067 238406.514 189205.7424 169181.407 163102.5972 219883.6147 289242.7311 0.863665698 0.599130327 0.813809584 0.824243753 0.654141737 0.584911525 0.563895233 0.760204462 1 18.14192118 1.273538813 3.926644397 1.023430821 0.697383913 0.440012998 0.105276408 0.213840082 5.4338355 0.187669449 0.027202111 18.77322188 -1.273538813 -0.326046907 S(ph)DSELEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDSELEVR 8 0 Q9BQK8-2;Q9BQK8 Q9BQK8-2 LPIN3 Phosphatidate phosphatase LPIN3 1 S(0.999)DS(0.001)ELEVR;S(0.998)DS(0.002)ELEVR 159.34 0.00037737 632290000 537560 445560 406370 506680 501320 478650 488900 581470 1206550 TRUE FALSE 466520.084 442633.087 602891.8912 621729.4381 491344.7128 497063.9752 441486.5532 457127.1655 1063913.034 0.438494566 0.416042546 0.566674035 0.584379943 0.461827891 0.467203577 0.414964888 0.429665914 1 20.0209488 1.235775972 24.9999954 1.000000707 0.471901048 0.888599491 0.058707084 26.19774033 235152.3027 0.106277261 0.015785441 17.2098059 -1.235775972 -0.528099659 S(ph)DSENVYEVIQDLHVPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDSENVYEVIQDLHVPPR 18 0 A0A0G2JRG8;A0A0G2JNY3;A0A0G2JP16 A0A0G2JRG8 1 S(0.681)DS(0.317)ENVY(0.002)EVIQDLHVPPR 114.92 0.0001315 30282000 22880 18983 17327 20077 21643 17046 20635 22478 39615 TRUE FALSE 19856.35003 18858.29942 25706.39516 24635.78971 21212.34664 17701.77065 18633.82088 17671.25462 34931.75983 0.56843257 0.539861133 0.735903238 0.705254755 0.607251016 0.506752902 0.53343493 0.505879312 1 15.09225171 1.231717148 24.99960308 1.000000706 0.586321993 0.732854066 0.078198873 141.0914638 515368.2905 0.206296232 0.021463642 17.04971594 -1.231717148 -0.413678713 S(ph)DSLLSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SDSLLSFR 8 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 S(0.994)DS(0.006)LLSFR;S(0.999)DS(0.001)LLSFR;S(1)DSLLSFR 197.27 0.00015252 123315000 145439 140154 96194 109061 159939 153247 158282 184099 157807 TRUE FALSE 126218.8677 139233.3191 142713.7401 133824.9669 156756.5268 159142.5113 142931.836 144730.8615 139151.2362 0.907062496 1.000589883 1.025601669 0.961723162 1.12651911 1.14366581 1.027168999 1.040097562 1 17.0862942 5.307382636 0.799482308 1.056038362 0.656151002 0.432111143 0.052540319 5.9044975 1.539050527 0.020333994 2.587744757 202947.0001 -5.307382636 -0.39988736 S(ph)DSPEIPFQAAAGPSDGLDASSPGNSFVGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 31 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 S(0.55)DS(0.45)PEIPFQAAAGPSDGLDASSPGNSFVGLR;S(0.545)DS(0.455)PEIPFQAAAGPSDGLDASSPGNSFVGLR;S(0.5)DS(0.5)PEIPFQAAAGPSDGLDASSPGNSFVGLR 201.9 6.09E-26 830162000 648147 583667 400615 477988 635725 581242 578720 712253 834820 TRUE FALSE 562492.7318 579832.853 594353.754 586522.481 623075.3163 603602.7559 522595.8235 559943.2387 736128.5306 0.764122987 0.787678821 0.807404861 0.796766402 0.846421909 0.819969246 0.709924696 0.760659607 1 19.48959816 3.410811533 0.013873661 1.593079741 1.61E-06 0.107496807 0.072332455 5830.666341 74.31867798 4209.755247 4321.537174 2575.203376 -3.410811533 -1.593078131 S(ph)EAEDEDDEDYVPYVPLR ddPTM_MDA-MB-175_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 294.93 2.88E-49 882690000 599470 423009 316710 416902 516234 425258 386931 551772 662670 TRUE FALSE 520248.5206 420230.226 469872.0153 511565.971 505961.9534 441617.9504 349406.4912 433779.8517 584329.9075 0.890333549 0.719166041 0.804121113 0.875474564 0.865884061 0.75576818 0.597960992 0.742354355 1 19.15642361 2.685674931 11.28607778 0.752523349 0.825751107 0.04728631 0.10818196 2.610657189 552.8247383 0.037918932 0.033450634 484.9253978 -2.685674931 0.073227758 S(ph)EAEEGEVR ddPTM_MDA-MB-175_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 175.33 5.66E-05 456120000 452260 333420 337750 513550 347450 374010 318490 397140 952180 TRUE FALSE 392492.6951 331229.7421 501087.0297 630159.3766 340536.4248 388398.4067 287602.8888 312214.7015 839614.3651 0.467467818 0.394502233 0.596806165 0.750534296 0.405586706 0.462591426 0.342541649 0.371854883 1 19.67936732 1.232001963 24.97633018 1.000000901 0.470539715 0.653188773 0.1204324 153.2604533 583582.8385 0.299061554 0.032043602 17.06090102 -1.232001963 -0.529461186 S(ph)EDEDS(ph)LEEAGSPAPGPCPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEDEDSLEEAGSPAPGPCPR 20 0 Q8TBB5-3;Q8TBB5;Q8TBB5-2 Q8TBB5-3 KLHDC4 Kelch domain-containing protein 4 2 S(1)EDEDS(1)LEEAGSPAPGPCPR;S(1)EDEDS(1)LEEAGSPAPGPCPR 199.91 2.06E-21 315800000 367710 269060 209090 242650 293690 286550 275470 338360 392660 TRUE FALSE 319116.1918 267292.5271 310206.6234 297747.3912 287846.1436 297573.7639 248754.9618 266004.3471 346240.1821 0.921661345 0.771985867 0.895929009 0.859944647 0.831348175 0.859443182 0.718446254 0.768265386 1 18.40141364 S(ph)EEHS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEEHSPPR 8 0 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 2 S(1)EEHS(1)PPR 72.152 0.068556 169450000 339430 292090 211700 225220 253660 302610 278990 334610 342570 TRUE FALSE 294573.4655 290171.2416 314078.8281 276359.6433 248612.6623 314251.6025 251933.5927 263056.2554 302071.7649 0.975177093 0.960603656 1.039749042 0.914880752 0.823025159 1.040321007 0.834019005 0.870840264 1 18.20453181 3.614737751 7.406593303 0.905222244 0.988384898 0.211483272 0.069797722 0.374934029 20.97425769 0.018623138 0.027677631 4118.487493 -3.614737751 0.083162654 S(ph)EEKEAGEI ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SEEKEAGEI 9 1 Q9NQ29-3;Q9NQ29;B8ZZ08 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 1 S(1)EEKEAGEI;S(1)EEKEAGEI;S(1)EEKEAGEI;S(1)EEKEAGEI 100.93 0.0056572 833610000 2503750 1851430 1550520 1512750 1951130 1521930 2371610 2715900 2456520 TRUE FALSE 2172873.094 1839267.834 2300356.658 1856243.008 1912306.33 1580479.632 2141611.627 2135125.92 2166113.004 1.003120839 0.849109825 1.061974446 0.856946524 0.882828517 0.729638587 0.988688782 0.985694613 1 21.04667708 2.067672731 24.99999838 0.990455064 0.896668374 0.200600483 0.08863291 82.04456677 30308.1178 0.035719815 0.024082292 116.8618428 -2.067672731 -0.093786691 S(ph)EETQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEETQER 7 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(1)EETQER;S(1)EETQER 163.91 0.0012769 204845000 134738 102403 90695 115610 89789 102513 140428 148739 265240 TRUE FALSE 116932.0319 101730.308 134555.4054 141861.0175 88002.37457 106456.7414 126809.3142 116932.3223 233883.6294 0.499958173 0.434961217 0.575309207 0.606545306 0.376265645 0.4551697 0.542189783 0.499959414 1 17.83543136 1.23843832 10.77919971 1.001347633 0.499367762 0.84696899 0.066953188 0.025896859 90.61162238 0.093458642 0.016608474 17.31563092 -1.23843832 -0.501979871 S(ph)EGSPVLPHEPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEGSPVLPHEPAK 13 0 Q9UKE5-6;Q9UKE5-2;Q9UKE5-4;Q9UKE5;Q9UKE5-8;Q9UKE5-5;Q9UKE5-7;Q9UKE5-3 Q9UKE5-6 TNIK TRAF2 and NCK-interacting protein kinase 1 S(0.561)EGS(0.439)PVLPHEPAK 112.5 0.00018516 0 733730 524130 288330 365860 399210 274490 368380 490880 671240 TRUE FALSE 636765.7215 520686.9555 427767.3524 448934.1048 391266.502 285049.8079 332654.5643 385909.132 591886.7719 1.075823539 0.879707032 0.722718217 0.758479706 0.66104958 0.481595166 0.562023989 0.651998237 1 19.17496169 4.723699661 1.063931473 0.659543015 1.285133499 0.472660205 0.134987452 1.533066453 1.4485511 0.04368006 1.083527534 52929.72784 -4.723699661 0.625590484 GRLPNNSS(ph)RPS(ph)TPTINVLESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GRLPNNSSRPSTPTINVLESK 21 2 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 2 GRLPNNS(0.456)S(0.54)RPS(0.544)T(0.46)PTINVLESK 120.08 2.34E-05 348130000 412990 291870 164310 152810 172340 181740 181590 190320 185340 TRUE FALSE 358412.3251 289952.6868 243770.8656 187507.8461 168910.7712 188731.6554 163979.4297 149621.5491 163429.3163 2.193072413 1.774177934 1.491598148 1.147332989 1.033540218 1.154821299 1.003366063 0.915512299 1 17.31830728 4.612243487 0.739479615 0.974543305 2.81535883 0.979496758 0.058463122 0.319211452 0.153063041 0.026473704 0.47682871 40949.01756 -4.612243487 1.840815525 up S(ph)EPDDELLFDFLNSSQKEPTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEPDDELLFDFLNSSQKEPTGR 22 1 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 1 S(1)EPDDELLFDFLNSSQKEPTGR;S(1)EPDDELLFDFLNSSQKEPTGR 170.16 4.52E-12 142138000 87153 62624 44638 45283 73402 57712 72765 107086 32105 TRUE FALSE 75635.51023 62212.61882 66225.08611 55565.19726 71941.44381 59932.21798 65708.2615 84186.49224 28309.58347 2.67172812 2.197581567 2.339316867 1.962769862 2.541239926 2.117029311 2.321060695 2.973780675 1 14.7890029 1.222996936 24.99797529 0.999996192 2.389803737 0.697783636 0.287601532 534.8978887 859090.4351 1.769186026 0.072832599 16.71078825 -1.222996936 1.389807544 S(ph)ESELIDELSEDFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SESELIDELSEDFDR 15 0 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;D6RC54;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 1 S(1)ESELIDELSEDFDR;S(0.999)ES(0.001)ELIDELSEDFDR;S(1)ESELIDELSEDFDR;S(1)ESELIDELSEDFDR;S(0.897)ES(0.103)ELIDELSEDFDR;S(1)ESELIDELSEDFDR;S(0.999)ES(0.001)ELIDELSEDFDR;S(1)ESELIDELSEDFDR 358.01 1.10E-82 1780866000 456875 482155 388315 518574 517731 522049 571569 695270 858485 TRUE FALSE 396497.8112 478987.6921 576105.4328 636324.1526 507429.166 542132.5628 516138.3264 546591.9211 756995.8813 0.52377803 0.632748082 0.761041701 0.840591301 0.670319586 0.716163161 0.681824484 0.722054022 1 19.52992593 -2 0.046675517 1.951048035 1.76E-14 0.388920607 0.09893686 1771.455468 8.105329212 288.0267225 98.7772873 0.01 2 -1.951048035 S(ph)ESELIDELSEDFDRSECK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.933)ES(0.067)ELIDELSEDFDRSECK;S(1)ESELIDELSEDFDRSECK;S(0.546)ES(0.454)ELIDELSEDFDRSECK;S(0.975)ES(0.025)ELIDELSEDFDRSECK 310.77 9.79E-62 447981000 538851 630636 356872 372590 634636 493823 839527 1031292 213571 TRUE FALSE 467640.4751 626493.3106 529456.4929 457192.2542 622007.9852 512820.6904 758109.8008 810758.2313 188322.8797 2.483184602 3.326697806 2.811429465 2.427704244 3.302880597 2.723092867 4.025585219 4.305149925 1 17.52284876 2.292210913 24.99980316 3.397335323 2.867894083 0 0.92686352 270.2689097 125937.6215 0.339869078 0.263261198 195.9796209 -2.292210913 -0.52944124 S(ph)ESNEDLFGLVPFDEITGSQQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SESNEDLFGLVPFDEITGSQQQK 23 0 H0Y9P1;Q9NSY1 H0Y9P1 BMP2K BMP-2-inducible protein kinase 1 S(0.5)ES(0.5)NEDLFGLVPFDEITGSQQQK;S(0.5)ES(0.5)NEDLFGLVPFDEITGSQQQK;S(0.5)ES(0.5)NEDLFGLVPFDEITGSQQQK;S(0.5)ES(0.5)NEDLFGLVPFDEITGSQQQK;S(0.5)ES(0.5)NEDLFGLVPFDEITGSQQQK 133.84 1.38E-05 153873000 287583 209936 153229 183922 214352 178260 243448 290372 250582 TRUE FALSE 249578.1779 208556.9166 227331.0569 225684.3012 210086.8146 185117.7775 219838.4504 228278.2075 220958.4814 1.129525223 0.943873778 1.028840601 1.021387818 0.950797694 0.837794396 0.994931034 1.033127156 1 17.75341578 4.747224203 24.33306423 0.979571637 1.129525334 0.409949265 0.057639215 884.2040864 2483346.265 0.015090646 0.169259011 55875.85777 -4.747224203 0.149953698 S(ph)ESSDFEVVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SESSDFEVVPK 11 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.998)ES(0.001)S(0.001)DFEVVPK 111.94 0.0016713 45284000 108850 90706 62617 90791 81427 52367 84321 113370 133220 TRUE FALSE 94465.19671 90110.14631 92898.79064 111406.4842 79806.76201 54381.59238 76143.5624 89126.70775 117470.8834 0.804158392 0.767084947 0.790823973 0.9483753 0.679374835 0.462936779 0.648190941 0.758713182 1 16.84194369 3.189405763 24.98713328 0.698982519 0.820660639 0.147790675 0.138726407 223.634864 113680.4652 0.044459789 0.050412762 1546.698853 -3.189405763 0.12167812 S(ph)ET(ph)PPHWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SETPPHWR 8 0 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 S(1)ET(1)PPHWR;S(1)ET(1)PPHWR;S(1)ET(1)PPHWR 116.55 0.0039937 1539710000 1541950 1101030 872340 1024770 1352750 1170830 1082160 1317080 1997380 TRUE FALSE 1338177.401 1093797.261 1294206.542 1257459.691 1325832.922 1215872.588 977212.2898 1035432.692 1761252.012 0.759787578 0.621033932 0.734821896 0.713957845 0.752778656 0.690345606 0.554839559 0.587895818 1 20.74816992 2.481693613 24.8120437 0.672896493 0.713003887 0 0.125106805 970.7253148 5267727.005 0.045516085 0.036214296 303.1751583 -2.481693613 0.040107395 S(ph)ETEDSILHQLFIVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SETEDSILHQLFIVR 15 0 Q9UKG1 Q9UKG1 APPL1 DCC-interacting protein 13-alpha 1 S(0.995)ET(0.005)EDSILHQLFIVR;S(0.886)ET(0.108)EDS(0.007)ILHQLFIVR 243.01 3.81E-18 57708000 27424 34040 28112 39451 41959 45588 36554 49639 81360 TRUE FALSE 23799.84892 33816.389 41707.05723 48408.95252 41124.09799 47341.79986 33008.99871 39024.08614 71741.71349 0.331743525 0.471362996 0.581350169 0.674767164 0.573224363 0.659892238 0.46010887 0.543952524 1 16.13052458 -2 0.071737238 1.877289521 2.99E-13 0.381470285 0.138786366 800.4853382 5.499950531 161.3943437 31.44476486 0.01 2 -1.877289521 S(ph)FAGNLNTYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SFAGNLNTYK 10 0 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 1 S(1)FAGNLNTYK;S(1)FAGNLNTYK;S(1)FAGNLNTYK;S(1)FAGNLNTYK 203.88 2.07E-07 2005980000 1144110 1266360 819340 1062650 971410 725150 981930 1073240 2194980 TRUE FALSE 992912.9647 1258041.198 1215575.565 1303940.924 952080.8415 753046.9897 886702.5797 843735.978 1935491.965 0.513002886 0.649985234 0.628044749 0.673699993 0.491906378 0.389072651 0.45812775 0.435928432 1 20.88426889 1.231702953 24.9978787 1.000000808 0.52790929 0.709714979 0.094462575 152.3496589 555301.3449 0.25390617 0.026384702 17.04915868 -1.231702953 -0.472091517 S(ph)FDAVLEALSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFDAVLEALSR 11 0 Q6P1N0-2;Q6P1N0;K7EJY5 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 S(1)FDAVLEALSR 67.519 0.062677 35673000 21326 14549 7306.6 12267 13957 6951.1 14874 16184 11435 TRUE FALSE 18507.71507 14453.42666 10840.0962 15052.40984 13679.28301 7218.513315 13431.52177 12723.17754 10083.16733 1.835506093 1.433421284 1.075068562 1.492825553 1.356645443 0.715897404 1.332073676 1.261823506 1 13.29966127 7.999999937 0.779665299 1.168848198 148.0813782 0.48604106 0.217043743 409.3897046 1.55507591 0.078143784 106001.6917 99999985.57 -7.999999937 146.91253 S(ph)FDAVVFDVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFDAVVFDVLK 11 0 Q86X27;Q86X27-3;Q86X27-2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 S(1)FDAVVFDVLK 125.54 0.0003421 44513000 147060 129180 84070 98131 101970 87852 144870 143920 141060 TRUE FALSE 127625.6484 128331.4081 124726.5332 120413.1434 99940.9965 91231.72329 130820.5297 113143.828 124384.0475 1.026061227 1.031735264 1.002753454 0.968075455 0.803487252 0.733468038 1.051746846 0.909632949 1 16.92444194 3.471365424 24.85595362 0.902351748 1.015351183 0.280687517 0.08865967 200.6915049 866659.3042 0.026813762 0.03471815 2960.502444 -3.471365424 0.112999435 S(ph)FDEVEGVFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFDEVEGVFGR 11 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;C9JW88;Q6Y7W6-4;Q6Y7W6-5;E7ESB6 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 S(1)FDEVEGVFGR;S(1)FDEVEGVFGR 163.51 2.50E-05 95970000 98956 65961 53443 63802 74197 67097 109574 81387 110211 TRUE FALSE 85878.71388 65527.69785 79288.21356 78289.21925 72720.62486 69678.26501 98947.53035 63983.0234 97181.98113 0.883689681 0.674278267 0.815873608 0.805593983 0.748293295 0.716987493 1.018167454 0.658383608 1 16.56840122 1.21330289 24.76730901 1.000001111 0.788739243 0.282130426 0.105172534 2814.709394 2759891.625 1.672001126 0.02346479 16.34191286 -1.21330289 -0.211261868 S(ph)FDGNTLLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SFDGNTLLNR 10 0 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 S(1)FDGNTLLNR;S(1)FDGNTLLNR;S(1)FDGNTLLNR;S(1)FDGNTLLNR 227.48 2.66E-09 1735740000 1804830 1514150 861108 1153600 1432890 829387 2084070 1662960 1657390 TRUE FALSE 1566317.143 1504203.449 1277542.709 1415542.512 1404378.292 861294.0546 1881957.212 1307348.945 1461455.242 1.071751702 1.029250438 0.874157943 0.968584238 0.960945126 0.589340015 1.287728257 0.894552845 1 20.47897422 4.417164848 7.020306451 0.943445297 1.061561058 0.07224634 0.168447988 0.523034104 48.88836239 0.03982946 0.107778075 26131.53057 -4.417164848 0.118115761 S(ph)FDYNYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 SFDYNYR 7 0 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 1 S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR 154.35 0.0017667 44256350000 10787560 8957360 7036466 8270383 9380660 9386560 8982742 10465870 15298670 TRUE FALSE 9361956.614 8898518.512 10439324.49 10148299.87 9194003.219 9747667.037 8111597.063 8227825.146 13490078.66 0.693988289 0.659634294 0.77385201 0.752278776 0.681538147 0.722580445 0.601300946 0.609916766 1 23.68539542 1.230243005 25 1.000000585 0.68412435 0.76169891 0.055020412 173.3878986 521105.613 0.168927443 0.015193764 16.99194154 -1.230243005 -0.315876235 S(ph)FDYNYRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SFDYNYRR 8 1 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 1 S(1)FDYNYRR;S(1)FDYNYRR;S(1)FDYNYRR;S(1)FDYNYRR;S(1)FDYNYRR;S(1)FDYNYRR 147.41 0.00032937 2788380000 5668540 4559420 1522250 1645360 4426820 4365090 4810050 5266010 845479 TRUE FALSE 4919428.077 4529468.87 2258415.192 2018964.136 4338734.943 4533017.837 4343572.091 4139914.742 745527.4358 6.598587578 6.075522714 3.029285152 2.708101726 5.819685145 6.080283058 5.826173368 5.553001195 1 19.50790192 4.42941357 12.37762448 4.545588828 6.468050724 0.199020885 1.663236077 1.41306302 364.2525027 0.427650831 1.132600026 26879.02861 -4.42941357 1.922461896 S(ph)FEEEGEHLGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFEEEGEHLGSR 12 0 Q9BXW6-4;Q9BXW6 Q9BXW6-4 OSBPL1A Oxysterol-binding protein-related protein 1 1 S(1)FEEEGEHLGSR 207.4 5.08E-08 609320000 121770 137240 96706 136180 187660 145750 150700 197920 162950 TRUE FALSE 105677.786 136338.4614 143473.3451 167101.7504 183925.9332 151357.0968 136085.1372 155596.3482 143686.2366 0.735476052 0.948862359 0.998518358 1.162962816 1.280052547 1.053386186 0.947099321 1.082889718 1 17.13256235 4.636594067 1.63464285 1.082036976 0.657626843 0.592778694 0.091548368 0.622954554 1.895573416 0.027287425 0.393829522 43310.58675 -4.636594067 -0.424410133 S(ph)FEEKVENLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SFEEKVENLK 10 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 1 S(1)FEEKVENLK;S(1)FEEKVENLK;S(1)FEEKVENLK;S(1)FEEKVENLK 160.84 1.91E-05 1102380000 2307880 1077610 813720 1101580 968140 678980 1828950 1666580 1232480 TRUE FALSE 2002887.811 1070531.109 1207237.714 1351710.576 948875.9081 705100.8 1651578.711 1310194.836 1086777.618 1.84296012 0.985050751 1.110841531 1.243778444 0.873109541 0.648799523 1.519702543 1.205577677 1 20.05162533 4.743552793 24.83550047 1.091581466 1.842960462 0.520097066 0.231742072 430.3973773 2141101.157 0.058298253 0.471441515 55405.48913 -4.743552793 0.751378997 S(ph)FEERVETTVTSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFEERVETTVTSLK 14 1 Q16890-5;E9PPQ1;J3KNE7;Q16890;E9PNK6 Q16890-5 TPD52L1 Tumor protein D53 1 S(1)FEERVETTVTSLK;S(1)FEERVETTVTSLK 161.51 2.78E-06 92096000 159087 90374 44869 54740 83903 56559 154417 134911 41696 TRUE FALSE 138063.2499 89780.32724 66567.79848 67169.55365 82233.49445 58734.86133 139441.6631 106061.3325 36766.74638 3.755111982 2.441889372 1.810543631 1.826910463 2.236626913 1.597499564 3.792602741 2.884708139 1 15.16611389 1.230339 24.92558415 0.999997066 2.53022234 0.289341748 0.759837531 428.9566933 1300365.337 2.1194259 0.193143175 16.99569779 -1.230339 1.530225273 S(ph)FEMTEFNQALEEIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFEMTEFNQALEEIK 15 0 Q9BVS4-2;Q9BVS4;H0Y919 Q9BVS4-2 RIOK2 Serine/threonine-protein kinase RIO2 1 S(1)FEMTEFNQALEEIK;S(1)FEMTEFNQALEEIK 170.16 1.21E-06 83335000 52627 38417 39453 44050 42095 31013 49056 60173 89525 TRUE FALSE 45672.20861 38164.6362 58532.60276 54052.22576 41257.39186 32206.09018 44298.55667 47305.47222 78941.45649 0.578557967 0.483454928 0.741468493 0.684712801 0.522632767 0.40797436 0.561157073 0.599247522 1 16.26849552 1.234213013 4.466632384 1.03889026 0.569465176 0.674724687 0.093527925 0.135346584 5.585493936 0.203825007 0.025081559 17.14798177 -1.234213013 -0.469425084 S(ph)FEVEEVETPNSTPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 SFEVEEVETPNSTPPR 16 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 1 S(1)FEVEEVETPNSTPPR;S(0.999)FEVEEVET(0.001)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 398.32 5.47E-122 19318580000 2112124 1584035 968554 1335834 1751434 1187307 2718036 2149080 1829338 TRUE FALSE 1833001.462 1573629.37 1436949.954 1639155.527 1716583.89 1232983.469 2454441.287 1689515.966 1613075.746 1.136339361 0.975545863 0.890813688 1.016167735 1.064168186 0.764367992 1.521590845 1.047387868 1 20.62138275 2.267798662 24.9999965 1.173851137 0.976768502 0.265136922 0.168093282 286.3187503 244816.0479 0.060341429 0.046732892 185.2672529 -2.267798662 -0.197082635 S(ph)FEVEEVETPNSTPPRR ddPTM_MDA-MB-175_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(1)FEVEEVETPNSTPPRR;S(1)FEVEEVETPNSTPPRR;S(1)FEVEEVETPNSTPPRR;S(1)FEVEEVETPNSTPPRR;S(1)FEVEEVETPNSTPPRR 261.58 1.64E-27 6936650000 463693 387398 200809 241579 375547 284488 538903 474249 259642 TRUE FALSE 402414.7952 384853.157 297920.9041 296433.2043 368074.3494 295432.4374 486640.27 372834.542 228947.4185 1.757673433 1.680967444 1.301263434 1.294765436 1.607680715 1.290394272 2.125554737 1.628472355 1 17.80465677 4.456984407 23.99102154 1.505965831 1.738497113 0.102946142 0.297880123 335.3857501 399577.9837 0.075753437 0.20048706 28640.75135 -4.456984407 0.232531281 S(ph)FGHFPGPEFLDVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFGHFPGPEFLDVEK 15 0 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 S(1)FGHFPGPEFLDVEK;S(1)FGHFPGPEFLDVEK 258.9 4.96E-25 177095000 543660 417520 388760 451910 489530 488420 615790 637640 1034380 TRUE FALSE 471813.9535 414777.2836 576765.6363 554523.0725 479789.3107 507209.8334 556070.7806 501285.6481 912096.7748 0.517284971 0.454751398 0.63235136 0.607965172 0.526028952 0.556092125 0.60966204 0.549596997 1 19.79882738 1.237846625 24.99999996 1.000000509 0.558664867 0.878622479 0.051774288 5.824410946 203792.833 0.07494551 0.012882815 17.29205566 -1.237846625 -0.441335642 S(ph)FGNPFEGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SFGNPFEGSR 10 0 Q96RR4-6;Q96RR4-5;Q96RR4-2;Q96RR4-3;Q96RR4-4;Q96RR4-7;Q96RR4;F5GZ00 Q96RR4-6 CAMKK2 Calcium/calmodulin-dependent protein kinase kinase 2 1 S(1)FGNPFEGSR;S(1)FGNPFEGSR;S(1)FGNPFEGSR;S(1)FGNPFEGSR 133.88 0.00019459 502181000 577251 539067 414042 465997 563571 607839 584197 573149 741446 TRUE FALSE 500965.8178 535525.8334 614274.0961 571808.7412 552357.0397 631222.9597 527541.6649 450585.5466 653793.0985 0.766245191 0.819105975 0.939554268 0.874601984 0.844849909 0.965478163 0.806893903 0.689186759 1 19.31847462 1.182534247 24.11606847 1.000006392 0.837670636 0.291332706 0.07928249 28273.84474 12168096.01 42.99846886 0.021304223 15.22419182 -1.182534247 -0.162335756 S(ph)FKPWLEIFKQNQQK ddPTM_MDA-MB-175_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 62.891 0.036746 145490000 387700 307600 156460 257050 323050 256370 333380 422260 209570 TRUE FALSE 336464.4627 305579.3553 232124.5793 315417.1313 316621.937 266232.7198 301048.8589 331962.985 184794.8733 1.820745655 1.653613814 1.256120233 1.706850009 1.713369702 1.440693213 1.629097461 1.796386334 1 17.49556521 1.228685064 24.9981132 0.999998742 1.623734434 0.579942403 0.167707 308.6840307 781320.2002 0.538285523 0.0412575 16.93109567 -1.228685064 0.623735692 S(ph)FLESNYFTKPNLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFLESNYFTKPNLK 14 1 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 1 S(1)FLESNYFTKPNLK 65.225 0.035585 235940000 115310 106150 100070 130730 141060 108680 165790 160360 170700 TRUE FALSE 100071.4913 105452.6937 148464.1867 160414.2446 138253.182 112860.9899 149711.7113 126068.2619 150520.0405 0.664838323 0.70058906 0.986341661 1.065733467 0.918503487 0.749807066 0.994629757 0.837551342 1 17.19959606 4.273223838 8.726515306 0.927736335 0.681111512 0.577623104 0.089861128 0.202233283 45.52227053 0.02282607 0.059650999 18759.6114 -4.273223838 -0.246624823 S(ph)FLNYYADLETSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFLNYYADLETSAR 14 0 H0YAJ5;G5E9Y1;Q92870-2;Q92870;Q92870-4 H0YAJ5 APBB2 Amyloid beta A4 precursor protein-binding family B member 2 1 S(1)FLNYYADLETSAR 158.64 5.29E-06 32258000 17560 19423 15607 14643 23197 27885 22888 23750 33298 TRUE FALSE 15239.40151 19295.40903 23154.5974 17967.91695 22735.42508 28957.75399 20668.32528 18671.24732 29361.54837 0.519025813 0.657165923 0.788602737 0.611953999 0.774326503 0.986247511 0.70392491 0.63590813 1 14.84164043 5.449850708 0.698675273 0.78577123 5.01E-16 0.338232133 0.12601648 10.02003731 1.829286415 0.053593916 7.798799764 281741.4259 -5.449850708 -0.78577123 S(ph)FNDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SFNDFR 6 0 P42356 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 1 S(1)FNDFR;S(1)FNDFR;S(1)FNDFR;S(1)FNDFR;S(1)FNDFR 127.68 0.017785 4134180000 6497520 7082530 5108560 5946050 8270000 8342600 7535720 7970900 8516900 TRUE FALSE 5638856.269 7036004.394 7579076.703 7296191.532 8105443.18 8663545.22 6804907.034 6266385.065 7510041.784 0.750842197 0.936879527 1.009192348 0.971524759 1.079280703 1.153594809 0.906107746 0.834400826 1 22.8403895 7.413253226 10.44193269 0.958914535 0.123087918 0 0.114908261 0 0 0.027349039 0 25897224.76 -7.413253226 -0.835826617 S(ph)FPLFDNSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SFPLFDNSK 9 0 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 S(1)FPLFDNSK;S(1)FPLFDNSK;S(1)FPLFDNSK;S(1)FPLFDNSK 167.2 6.31E-05 235680000 699690 653058 484552 568660 688252 573152 710510 861550 827440 TRUE FALSE 607224.1937 648768.019 718882.9679 697782.9444 674557.1317 595201.5283 641604.8496 677314.2371 729620.9858 0.832246064 0.889184976 0.985282745 0.956363589 0.92453088 0.815768104 0.879367318 0.928309698 1 19.4767877 -1.998314578 0.00838306 1.912397974 0.002706144 0.082856091 0.057735843 172316.1101 144.0473508 18066.46047 14896.24306 0.010038884 1.998314578 -1.90969183 S(ph)FQGDDSDLLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SFQGDDSDLLLK 12 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 S(1)FQGDDSDLLLK;S(1)FQGDDSDLLLK;S(1)FQGDDSDLLLK;S(1)FQGDDSDLLLK 188.47 9.61E-06 283489000 645158 537901 433683 606797 674211 521102 1058180 954520 964980 TRUE FALSE 559898.7357 534367.4929 643413.5494 744579.5332 660795.5202 541149.1311 955557.8665 750403.3261 850901.1637 0.658006781 0.628001836 0.756155447 0.875048202 0.776583167 0.635971784 1.122995134 0.881892467 1 19.69863204 -1.999746542 0.06868234 2.594693513 3.88E-08 0.487501247 0.115377375 502.0407145 3.313747289 135.7662301 28.32694575 0.010005838 1.999746542 -2.594693474 S(ph)FS(ph)PEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFSPEER 7 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83 Q9UDY2-7 TJP2 Tight junction protein ZO-2 2 S(1)FS(1)PEER;S(1)FS(1)PEER 101.38 0.013306 389620000 912560 743810 618370 792110 847470 818230 718250 845990 1556510 TRUE FALSE 791962.8839 738923.8631 917415.8003 971970.6821 830607.005 849707.8376 648594.2255 665081.622 1372501.161 0.57702165 0.538377587 0.668426247 0.708174761 0.605177634 0.61909444 0.472563699 0.484576364 1 20.38837594 1.230407088 24.99570639 1.000000771 0.581099932 0.759158543 0.07358745 171.9132966 526980.073 0.225757194 0.020657021 16.99836256 -1.230407088 -0.418900839 S(ph)FSEDTLMDGPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SFSEDTLMDGPAR 13 0 Q9BRG2;M0QZQ6 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 S(0.984)FS(0.016)EDTLMDGPAR;S(0.947)FS(0.053)EDTLMDGPAR;S(0.976)FS(0.024)EDTLMDGPAR;S(0.998)FS(0.002)EDTLMDGPAR;S(0.86)FS(0.14)EDTLMDGPAR;S(0.994)FS(0.006)EDTLMDGPAR 182.37 1.18E-05 1616650000 1731393 1962030 1158302 1481997 2099930 1836650 2087990 2380700 1951190 TRUE FALSE 1502585.028 1949141.296 1718460.721 1818507.07 2058145.501 1907307.114 1885497.051 1871605.832 1720522.541 0.873330626 1.132877512 0.998801632 1.056950448 1.196232803 1.1085627 1.095886282 1.087812445 1 20.71441536 4.746444746 24.62077234 1.086102487 0.873330497 0.562918955 0.058504151 622.3473846 1943427.082 0.014264062 0.152284683 55775.66354 -4.746444746 -0.21277199 S(ph)FSEDVFQSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFSEDVFQSVK 11 0 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 S(0.999)FS(0.001)EDVFQSVK 106.32 0.0024618 35306000 107580 81038 63380 77552 107400 94709 109680 139440 124800 TRUE FALSE 93363.03043 80505.65604 94030.77999 95161.36691 105262.9501 98352.51651 99043.25048 109621.8411 110046.2862 0.84839783 0.731561771 0.854465728 0.864739468 0.956533417 0.893737717 0.900014475 0.996143032 1 16.74775093 2.538582464 0.159587803 1.215833289 0.616307853 0.679344552 0.044866797 6.730643063 0.967643759 2.034112567 1.473110939 345.6069476 -2.538582464 -0.599525436 S(ph)FSEDVISHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFSEDVISHK 10 0 F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A494C1D7;H0YC82;Q03001-10 F6QMI7 DST Dystonin 1 S(0.964)FS(0.036)EDVISHK;S(0.933)FS(0.067)EDVISHK 156.36 7.13E-06 299890000 358980 332220 218391 309750 327120 287240 335980 435490 465500 TRUE FALSE 311539.8835 330037.6249 324005.6181 380083.4717 320610.952 298290.3087 303396.7113 342363.8525 410469.1203 0.758984947 0.804049826 0.789354429 0.925973363 0.781084218 0.726705844 0.739146251 0.834079436 1 18.64691417 1.264104121 3.472768628 1.024120298 0.792189462 0.595378642 0.054246148 0.20986472 3.718729 0.124417857 0.014631246 18.369787 -1.264104121 -0.231930836 S(ph)FSIS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.963)FS(0.04)IS(0.996)PVR;S(0.998)FS(0.057)IS(0.945)PVR 92.943 0.016695 106685000 553140 383210 292160 397630 466400 463030 429050 504400 513700 TRUE FALSE 480041.1475 380692.6683 433449.5532 487917.9689 457119.5525 480843.0637 387440.797 396537.9852 452970.9712 1.059761393 0.840435022 0.9569036 1.077150634 1.009158603 1.061531741 0.855332508 0.875415889 1 18.78905907 2.230810681 24.99801932 0.900704267 0.99538504 0.229921951 0.077059225 255.4315055 823904.9851 0.031815725 0.021899399 170.1416661 -2.230810681 0.094680773 S(ph)FSKEVEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SFSKEVEER 9 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 S(0.998)FS(0.002)KEVEER;S(0.998)FS(0.002)KEVEER;S(1)FSKEVEER;S(1)FSKEVEER;S(0.999)FS(0.001)KEVEER 160.52 3.95E-05 3753300000 17899220 9528780 3358850 2743450 3789870 3004980 4282870 4523440 820318 TRUE FALSE 15533792.73 9466184.817 4983201.095 3366392.254 3714459.002 3120583.525 3867517.927 3556137.557 723340.9405 21.47506363 13.08675382 6.889145651 4.653949562 5.135142771 4.314125401 5.346742746 4.9162675 1 19.46431628 4.658913577 1.256978628 4.272939168 27.83297007 0.957172278 1.203232248 0.225855232 0.344973541 0.350636815 6.650798697 45594.61755 -4.658913577 23.5600309 S(ph)FSLDEPPLFIPDNIATIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SFSLDEPPLFIPDNIATIR 19 0 Q92576-2;Q92576;E7EVH3;D6R9X2;E9PE34;A0A1B0GX99 Q92576-2 PHF3 PHD finger protein 3 1 S(0.82)FS(0.18)LDEPPLFIPDNIATIR;S(0.875)FS(0.125)LDEPPLFIPDNIATIR;S(0.795)FS(0.205)LDEPPLFIPDNIATIR;S(0.833)FS(0.167)LDEPPLFIPDNIATIR 316.96 1.03E-61 162633000 137765 130587 110383 132916 196483 200242 181025 228069 244648 TRUE FALSE 119559.0062 129729.1654 163764.588 163096.6093 192573.3727 207945.4393 163469.2234 179298.2192 215725.9921 0.554216972 0.601360847 0.75913239 0.756035968 0.8926758 0.963933169 0.757763224 0.831138693 1 17.71884049 4.126745846 1.069184929 0.87474777 0.513109681 0.742623374 0.07192685 0.417207459 0.737511771 0.025360058 0.137832388 13388.92923 -4.126745846 -0.361638089 S(ph)FTLDDESLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SFTLDDESLK 10 0 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 S(1)FTLDDESLK;S(1)FTLDDESLK;S(0.993)FT(0.007)LDDESLK 256.92 3.67E-17 184979000 526630 439500 390664 543350 569050 411380 648550 783360 948160 TRUE FALSE 457034.5112 436612.8956 579590.4171 666725.9221 557727.0183 427206.0548 585653.7208 615844.5601 836069.6049 0.546646486 0.522220749 0.693232254 0.79745265 0.667082041 0.510969484 0.700484406 0.736594844 1 19.67326353 1.074879326 1.51489764 1.281247304 0.632511063 0.634005974 0.088149335 1.247694493 1.847387122 1.384434908 0.027127849 11.88172034 -1.074879326 -0.648736242 S(ph)GAAETALLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGAAETALLVR 11 0 Q8WZ26 Q8WZ26 PP6455 Putative uncharacterized protein PP6455 1 S(0.5)GAAET(0.5)ALLVR 61.962 0.0881 18159000 8588.3 6962.3 4796.1 9892.1 6500.7 6977.6 8942.3 8520.9 5548.2 TRUE FALSE 7453.334395 6916.564193 7115.510002 12138.2525 6371.348788 7246.032787 8075.077122 6698.771845 4892.298117 1.523483283 1.413765888 1.454430992 2.481094203 1.30232227 1.48111023 1.650569309 1.369248497 1 12.2562966 0.826014356 1.10500363 9.10E-11 1.631505139 0.272243895 0.324019048 5.404189436 2.858251705 12.93820359 0.103022712 6.69906753 -0.826014356 1.631505139 S(ph)GAEVEAGDAAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGAEVEAGDAAER 13 0 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67;K7EKR9;Q8IY67-3 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 S(1)GAEVEAGDAAER 100.22 0.0026219 219520000 346370 298110 180400 217240 330650 291170 322260 381870 257250 TRUE FALSE 300596.3269 296151.6958 267642.0434 266567.6623 324070.7119 302371.4983 291007.2748 300210.0722 226838.1981 1.325157445 1.305563606 1.179880839 1.175144506 1.428642595 1.332983161 1.282884793 1.323454668 1 17.79130408 1.235005355 24.99701344 0.999999586 1.293526846 0.611425237 0.073709024 74.42270657 523182.7675 0.134068063 0.018745798 17.17929569 -1.235005355 0.29352726 S(ph)GAKCDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGAKCDFR 8 1 B5MCA9;Q8N7S2 B5MCA9 DNAJC5G DnaJ homolog subfamily C member 5G 1 S(1)GAKCDFR 84.244 0.046272 95152000 13767 9870.3 3657.3 7603.1 9879.5 15327 3905.9 8727.2 14309 TRUE FALSE 11947.65607 9805.461349 5425.982513 9329.500061 9682.917279 15916.63961 3527.106419 6860.956195 12617.40632 0.946918548 0.777137638 0.430039453 0.739415045 0.767425335 1.261482685 0.279542905 0.543769141 1 13.62312775 4.636660266 4.233995114 0.695578092 0.945959697 0.057323301 0.27656935 0.610879318 17.11694508 0.068659268 0.341274663 43317.18905 -4.636660266 0.250381605 S(ph)GASEANLIVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGASEANLIVAK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 S(0.996)GAS(0.004)EANLIVAK 84.566 0.01276 59446000 105460 110710 66425 85689 98195 77219 99701 101810 131480 TRUE FALSE 91523.1938 109982.7387 98548.35218 105145.9971 96241.11162 80189.6649 90032.01237 80038.72379 115936.5842 0.789424619 0.948645671 0.850019456 0.906926816 0.830118571 0.691668341 0.776562575 0.690366413 1 16.82297636 2.99387876 16.81907313 0.771574002 0.876298838 0.138694576 0.094040643 5.775440865 15873.84726 0.027632571 0.02999599 986.0041879 -2.99387876 0.104724836 S(ph)GCCDDSALAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGCCDDSALAR 11 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 S(1)GCCDDSALAR;S(1)GCCDDSALAR 236.34 1.58E-15 241370000 211540 245860 160690 153378 246070 235180 227990 271530 276780 TRUE FALSE 183584.453 244244.9295 238400.2215 188204.8191 241173.6884 244227.5268 205879.5649 213465.4225 244059.3837 0.752212229 1.000760248 0.976812355 0.771143548 0.988176258 1.000688943 0.843563406 0.874645422 1 17.8968727 S(ph)GDEEFKGEDELCDSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGDEEFKGEDELCDSGR 17 1 O43823;M0QYL4 O43823 AKAP8 A-kinase anchor protein 8 1 S(1)GDEEFKGEDELCDSGR;S(1)GDEEFKGEDELCDSGR;S(1)GDEEFKGEDELCDSGR;S(1)GDEEFKGEDELCDSGR 184.95 8.53E-14 779630000 740605 465699 529135 501583 517830 485960 568470 670333 981284 TRUE FALSE 642732.1728 462639.7926 785026.4559 615475.0864 507526.1961 504655.1957 513339.8669 526987.5045 865277.7234 0.742804484 0.534672025 0.907253746 0.711303515 0.586547166 0.583229155 0.593266015 0.609038567 1 19.72280374 1.234009935 24.99988784 1.000000517 0.654087693 0.496855322 0.107913985 121.4924277 667352.9339 0.206621389 0.026543159 17.13996515 -1.234009935 -0.345912824 S(ph)GDETPGSEVPGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGDETPGSEVPGDK 14 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.998)GDET(0.002)PGSEVPGDK;S(1)GDETPGSEVPGDK;S(1)GDETPGSEVPGDK;S(1)GDETPGSEVPGDK 325.24 8.31E-57 2124720000 3473550 1918560 2294720 2671130 2088750 1739710 2529910 3166400 5761200 TRUE FALSE 3014511.567 1905956.853 3404454.267 3277650.892 2047187.962 1806637.769 2284559.718 2489290.001 5080117.499 0.593394064 0.375179679 0.670152662 0.645191945 0.402980435 0.355629131 0.449706078 0.490006383 1 22.27643044 1.238291741 24.98148885 1.000000568 0.493919457 0.676202984 0.10918898 3.942324353 365595.8385 0.155203816 0.027446301 17.30978769 -1.238291741 -0.506081111 S(ph)GDLGDMEPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SGDLGDMEPLK 11 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;H0YC95 O60716-13 CTNND1 Catenin delta-1 1 S(1)GDLGDMEPLK;S(1)GDLGDMEPLK;S(1)GDLGDMEPLK;S(1)GDLGDMEPLK;S(1)GDLGDMEPLK 270.02 3.79E-22 920900000 2198980 1234040 1390420 1885810 1361090 1129190 1417630 1877060 4008890 TRUE FALSE 1908379.221 1225933.51 2062831.763 2314011.983 1334006.972 1172630.67 1280148.461 1475665.326 3534963.591 0.53985824 0.346802302 0.583551063 0.65460702 0.377375025 0.33172355 0.362139079 0.417448522 1 21.75326393 1.236702167 24.99882803 1.000000695 0.446998558 0.714678989 0.108842497 28.10020588 377880.6391 0.176505778 0.028035777 17.24654741 -1.236702167 -0.553002137 S(ph)GEGEVSGLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SGEGEVSGLMR 11 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 S(1)GEGEVSGLMR;S(1)GEGEVSGLMR;S(1)GEGEVSGLMR 210.15 1.44E-08 1342850000 626660 363432 286000 316871 299664 304420 397979 411004 430810 TRUE FALSE 543845.2932 361044.5913 424310.5566 388821.4036 293701.2727 316131.2344 359383.0578 323113.993 379880.1326 1.431623416 0.950417146 1.116959062 1.023537085 0.773141966 0.832186807 0.946043309 0.850568285 1 18.53518474 7.999999998 0.747467309 0.894161882 88.76316964 0.711910082 0.099167708 207.4060344 0.906359139 0.03666453 30673.2205 99999999.61 -7.999999998 87.86900776 S(ph)GEQITSSPVSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGEQITSSPVSPK 13 0 A0A087WZV0;O43314-2;O43314;A0A087WWN8 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 S(1)GEQITSSPVSPK;S(1)GEQITSSPVSPK 225.37 1.32E-11 490810000 852210 531760 367240 355080 369680 238804 409870 459570 461250 TRUE FALSE 739588.2893 528266.8335 544838.4923 435706.3411 362324.0913 247990.9444 370120.8705 361294.5319 406721.5505 1.818414314 1.298841512 1.339585994 1.071264457 0.890840652 0.609731508 0.910010473 0.88830929 1 18.63368191 4.560856817 0.757706439 0.848429066 2.158457264 0.84635545 0.12989258 0.851873079 0.45204763 0.056621104 0.911936604 36379.50765 -4.560856817 1.310028198 S(ph)GGGAGSNGSVLDPAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGGGAGSNGSVLDPAER 17 0 Q15149-3;Q15149-2;H0YDN1;E9PMV1 Q15149-3 PLEC Plectin 1 S(1)GGGAGSNGSVLDPAER 178.57 7.60E-14 0 156030 174440 110000 144640 200990 187160 179310 198920 201660 TRUE FALSE 135410.2402 173294.0922 163196.3679 177482.7227 196990.6922 194360.1663 161920.5438 156382.506 177819.9845 0.761501811 0.974547898 0.917761681 0.998103352 1.107809635 1.093016439 0.910586874 0.879442805 1 17.44005795 4.745376703 4.865346175 0.979611937 0.748775176 0.475854133 0.073563174 0.20159153 13.95504566 0.020681823 0.157694511 55638.66526 -4.745376703 -0.23083676 S(ph)GGGDLTLGLEPSEEEAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SGGGDLTLGLEPSEEEAPR 19 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 S(1)GGGDLTLGLEPSEEEAPR;S(1)GGGDLTLGLEPSEEEAPR;S(1)GGGDLTLGLEPSEEEAPR;S(1)GGGDLTLGLEPSEEEAPR;S(0.997)GGGDLT(0.003)LGLEPSEEEAPR;S(0.999)GGGDLT(0.001)LGLEPSEEEAPR 396.67 2.37E-127 1194090000 1003360 528874 500692 598719 605679 728807 478685 674489 715651 TRUE FALSE 870763.4338 525399.7919 742828.3259 734667.2998 593627.1729 756844.6769 432262.2024 530254.7762 631047.5541 1.379869755 0.832583517 1.177135259 1.164202753 0.940701171 1.199346503 0.684991487 0.840277049 1 19.2673892 2.245252591 24.99999902 0.834916157 1.099824533 0.377247166 0.164974214 154.9271551 578781.7639 0.058233704 0.044048161 175.894634 -2.245252591 0.264908376 S(ph)GHFDVTTVASIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGHFDVTTVASIK 13 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 S(0.92)GHFDVT(0.067)T(0.013)VASIK 81.448 0.0096895 341830000 142130 140380 98308 141170 142540 143140 165380 200780 198980 TRUE FALSE 123347.1604 139457.8345 145850.0776 173224.8061 139703.7329 148646.6884 149341.4731 157844.7595 175456.8111 0.703005826 0.794827135 0.831259138 0.987278893 0.79622861 0.847198165 0.851158027 0.899621727 1 17.42075643 4.440164666 1.77466619 0.888401804 0.694122423 0.499939215 0.062942587 0.447567835 2.177560837 0.017298459 0.120886168 27552.73187 -4.440164666 -0.194279381 S(ph)GLEEPGKDGDGQTLANGLGPGGDSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGLEEPGKDGDGQTLANGLGPGGDSNR 27 1 O75145-2;O75145;R4GN36 O75145-2 PPFIA3 Liprin-alpha-3 1 S(1)GLEEPGKDGDGQTLANGLGPGGDSNR;S(1)GLEEPGKDGDGQTLANGLGPGGDSNR 196.06 3.90E-25 241540000 127538 102923 112275 123563 127673 108721 157457 167130 228540 TRUE FALSE 110683.5302 102246.892 166571.5655 151619.8677 125132.5571 112903.5672 142186.8444 131390.5501 201522.2616 0.549237237 0.50737269 0.826566575 0.752372798 0.620936646 0.560253574 0.705563957 0.651990252 1 17.62057969 1.237777758 8.195106192 1.003943132 0.6505758 0.56822216 0.09671152 0.074739268 47.50715495 0.144259689 0.024632316 17.28931385 -1.237777758 -0.353367331 S(ph)GLSRSSNLRVT(ph)RT(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SGLSRSSNLRVTRTR 15 3 Q9NSI6-3;Q9NSI6-2;Q9NSI6 Q9NSI6-3 BRWD1 Bromodomain and WD repeat-containing protein 1 3 S(0.788)GLS(0.138)RS(0.037)S(0.037)NLRVT(0.999)RT(0.999)R;S(0.811)GLS(0.138)RS(0.026)S(0.026)NLRVT(0.999)RT(0.999)R;S(0.631)GLS(0.109)RS(0.131)S(0.131)NLRVT(1)RT(1)R 47.559 0.06687 386612000 54868.8 30900.2 15948.7 16911.6 29791.1 39728.2 44926.2 34377.2 14609.2 TRUE FALSE 47617.74906 30697.21455 23661.54467 20751.63726 29198.3154 41256.56956 40569.26404 27025.9033 12882.11702 3.696422645 2.382932441 1.836774548 1.610887188 2.266577407 3.202623412 3.149269951 2.097939591 1 13.65308208 4.729225633 4.345400892 2.226856111 3.792379674 0.343640842 0.654925216 0.253978663 11.51628033 0.171621064 1.211295312 53607.50976 -4.729225633 1.565523564 S(ph)GNSDSIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGNSDSIER 9 0 C9J8U3;A0A0A0MRW7;Q7Z2E3-4;Q7Z2E3-5;Q7Z2E3-10;Q7Z2E3-8;Q7Z2E3-7;Q7Z2E3;A0A5F9ZI51;A0A5F9ZGW5;Q7Z2E3-13;Q7Z2E3-9;Q7Z2E3-11 C9J8U3 APTX Aprataxin 1 S(1)GNSDSIER;S(0.99)GNS(0.01)DSIER;S(1)GNSDSIER;S(0.984)GNS(0.016)DSIER 212.93 2.85E-06 993140000 953580 862930 644220 776200 733225 878040 916950 1025340 1178030 TRUE FALSE 827561.9869 857261.356 955766.9468 952448.0735 718635.257 911818.767 828024.3301 806079.0202 1038764.635 0.796679015 0.825270063 0.92009962 0.916904601 0.691817215 0.8777915 0.797124105 0.77599775 1 19.98643737 1.228542437 24.87098543 1.000000381 0.824894294 0.392700506 0.068309658 428.432601 1063540.318 0.221228291 0.016737712 16.92553625 -1.228542437 -0.175106087 S(ph)GREGGPGEGQVRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGREGGPGEGQVRR 14 2 P35916-3 P35916-3 1 S(1)GREGGPGEGQVRR 58.98 0.082327 2063500000 1594200 1841200 1511800 1609800 1594800 2071700 1072300 1060200 1860500 TRUE FALSE 1383522.431 1829105.036 2242911.537 1975329.694 1563066.6 2151399.64 968308.511 833484.4805 1640553.809 0.843326456 1.114931449 1.367167309 1.204062727 0.952767651 1.311386208 0.590232704 0.508050681 1 20.64575148 2.230543633 24.99976493 0.655007665 1.137266123 0.510565076 0.198154059 127.5805977 397836.9125 0.079334212 0.054552555 170.0370778 -2.230543633 0.482258457 S(ph)GSFDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGSFDSR 7 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 S(0.5)GS(0.5)FDSR;S(0.748)GS(0.252)FDSR 81.548 0.02822 465760000 1781610 1484900 1013290 1126770 1174090 1486870 1672080 1779950 1786400 TRUE FALSE 1546165.724 1475145.594 1503320.433 1382620.35 1150727.906 1544070.851 1509921.939 1399321.544 1575213.827 0.981559264 0.936473239 0.954359597 0.877735026 0.730521715 0.980229366 0.95855046 0.88833752 1 20.58711625 1.22880793 24.07540669 1.000000288 0.911654672 0.119742509 0.073583975 580.0311783 1431693.295 0.226648734 0.018305353 16.93588633 -1.22880793 -0.088345617 S(ph)GSLDDSFSDFQELPASSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGSLDDSFSDFQELPASSK 19 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 S(0.5)GS(0.5)LDDSFSDFQELPASSK;S(0.5)GS(0.5)LDDSFSDFQELPASSK 145.43 1.32E-07 56521000 132742 84420 71246 82140 114986 88433 124869 152110 126041 TRUE FALSE 115199.8084 83865.43946 105700.8039 100791.1424 112698.0036 91835.07473 112759.2236 119582.4602 111140.5766 1.036523401 0.754588846 0.951055026 0.906879787 1.014013127 0.826296548 1.014563961 1.07595681 1 16.7620261 2.06533943 8.279225118 1.043981353 0.913579444 0.300483996 0.083342406 0.268894024 30.39921419 0.031615961 0.021257535 116.2356718 -2.06533943 -0.130401909 S(ph)GSMDPSGAHPSVR ddPTM_MDA-MB-175_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(0.636)GS(0.364)MDPSGAHPSVR 190.96 3.50E-07 1146700000 1876100 1460000 435020 877650 1872800 1723500 1962500 2040800 2199100 TRUE FALSE 1628168.632 1450409.164 645397.1271 1076933.847 1835534.944 1789804.16 1772177.052 1604390.802 1939124.903 0.839640927 0.747970985 0.332829064 0.555371057 0.946579017 0.92299581 0.913905571 0.827378782 1 20.8869743 3.236772751 24.99569938 0.909743961 0.607731128 0.546860316 0.13672441 38.59940179 539649.9279 0.042801097 0.051069086 1724.935064 -3.236772751 -0.302012834 S(ph)GSNIEQYIHDLDSNSFELDLQFSEDEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGSNIEQYIHDLDSNSFELDLQFSEDEKR 29 1 E9PER6;O15530-5;O15530-2;O15530;O15530-3;O15530-4 E9PER6 PDPK1 3-phosphoinositide-dependent protein kinase 1 1 S(0.498)GS(0.498)NIEQY(0.005)IHDLDSNSFELDLQFSEDEKR;S(0.5)GS(0.5)NIEQY(0.001)IHDLDSNSFELDLQFSEDEKR 72.878 0.003197 34057000 28417 25008 17099.8 20425.7 23800 27564 29949 28589 25858 TRUE FALSE 24661.62145 24843.7208 25369.32048 25063.66737 23326.42656 28624.40492 27044.55059 22475.46483 22801.0967 1.081598038 1.089584467 1.112635976 1.099230783 1.023039675 1.25539597 1.186107447 0.985718587 1 14.4768156 1.661539673 7.379228838 0.992446577 1.119817723 0.418916227 0.062581338 0.118969063 12.09948014 0.038881662 0.016795771 45.87115476 -1.661539673 0.127371146 S(ph)GSPRPTEPTDFLMLFEGSPSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SGSPRPTEPTDFLMLFEGSPSGK 23 1 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 S(0.5)GS(0.5)PRPTEPTDFLMLFEGSPSGK;S(0.571)GS(0.429)PRPTEPTDFLMLFEGSPSGK;S(0.53)GS(0.469)PRPT(0.001)EPTDFLMLFEGSPSGK 257.19 8.06E-44 890540000 668052 607623 436979 480737 669256 507150 654695 882791 630758 TRUE FALSE 579767.2356 603631.4845 648303.506 589895.6835 655939.115 526660.3887 591202.7797 694013.0145 556190.5078 1.042389662 1.085296272 1.165614114 1.060600056 1.17934252 0.946906467 1.062950143 1.247797301 1 19.0852196 S(ph)GSPSDNSGAEEMEVSLAKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSPSDNSGAEEMEVSLAKPK 21 1 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 1 S(0.526)GS(0.464)PS(0.01)DNS(0.001)GAEEMEVSLAKPK 96.338 0.001962 501460000 319680 214200 179250 174490 232040 202570 325190 347670 297680 TRUE FALSE 277433.478 212792.9061 265935.8996 214110.6214 227422.858 210362.999 293653.1239 273323.4761 262488.6095 1.056935303 0.810674819 1.013133103 0.815694905 0.866410388 0.801417629 1.118727111 1.041277473 1 18.00189529 2.233342536 24.99999948 1.053547588 0.890850528 0.418331696 0.088490791 114.7461441 549745.2093 0.033289745 0.023195051 171.1364568 -2.233342536 -0.162697059 S(ph)GSSPGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSSPGLR 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.662)GS(0.169)S(0.169)PGLR 74.301 0.043356 209610000 162680 168260 92730 120910 123450 130570 127360 165850 147790 TRUE FALSE 141181.4258 167154.689 137574.5382 148364.4635 120993.5865 135593.1124 115008.6468 130384.2681 130318.4346 1.083357288 1.28266342 1.055679794 1.13847641 0.928445672 1.040475301 0.882520168 1.000505175 1 16.99168165 3.4437168 1.716954473 0.969419996 1.164678939 0.527352024 0.076285095 0.252539179 1.511765145 0.022995441 0.036502329 2777.901227 -3.4437168 0.195258943 S(ph)GSTESLNPRPQTTISPADLHGMWYPTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSTESLNPRPQTTISPADLHGMWYPTVR 29 1 Q96JB2 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 1 S(0.527)GS(0.455)T(0.009)ES(0.002)LNPRPQT(0.003)T(0.004)ISPADLHGMWYPTVR 165.37 2.88E-12 187530000 307830 227100 133850 142820 263130 236920 275420 300890 131130 TRUE FALSE 267149.4856 225608.1651 198580.3077 175249.4639 257894.2278 246034.4657 248709.8108 236547.015 115627.9608 2.310422875 1.95115579 1.717407333 1.515632228 2.230379452 2.127811163 2.15094869 2.045759637 1 16.81913078 1.236953316 24.99421451 0.999998763 1.999562551 0.639298413 0.237476 28.7844206 447463.8793 0.376944398 0.061012881 17.25652387 -1.236953316 0.999563789 S(ph)GTPTQDEMMDKPTSSSVDTMSLLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SGTPTQDEMMDKPTSSSVDTMSLLSK 26 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 S(0.535)GT(0.462)PT(0.003)QDEMMDKPTSSSVDTMSLLSK;S(0.345)GT(0.345)PT(0.309)QDEMMDKPTSSSVDTMSLLSK;S(0.5)GT(0.5)PTQDEMMDKPTSSSVDTMSLLSK 119.5 0.00056656 690250000 523450 333120 326251 289918 362785 250228 483170 555778 456431 TRUE FALSE 454274.7562 330931.7128 484027.0748 355748.313 355566.2883 259854.4331 436312.2478 436929.1998 402472.2471 1.128710761 0.822247286 1.202634662 0.883907687 0.88345542 0.645645594 1.084080333 1.085613239 1 18.61852978 S(ph)GTTPKPVINSTPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGTTPKPVINSTPGR 15 1 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 1 S(0.357)GT(0.322)T(0.322)PKPVINSTPGR 75.239 0.011277 0 562640 417930 287710 350280 507620 405980 557780 657200 544530 TRUE FALSE 488285.6985 415184.5903 426847.5183 429816.4277 497519.3551 421598.3133 503686.5815 516662.8943 480156.2837 1.016930768 0.864686362 0.88897622 0.895159435 1.036161292 0.878043936 1.049005498 1.076030684 1 18.87314453 2.222973024 24.82589791 1.049140727 0.928402612 0.437488887 0.059481443 184.6956465 294156.8373 0.023512888 0.015916527 167.0986819 -2.222973024 -0.120738116 S(ph)GYTLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGYTLIR 7 0 Q9Y487 Q9Y487 ATP6V0A2 V-type proton ATPase 116 kDa subunit a isoform 2 1 S(0.374)GY(0.252)T(0.374)LIR 52.683 0.092902 215600000 24822 26938 13983 17156 28814 40131 22177 20032 21686 TRUE FALSE 21541.70981 26761.0425 20745.22557 21051.53201 28240.65777 41674.86554 20026.27795 15748.31269 19122.30578 1.126522609 1.399467345 1.084870507 1.100888787 1.476843749 2.179384955 1.047273178 0.823557204 1 14.22296887 2.015969018 24.99962168 0.910047122 1.391360921 0.30702173 0.31488564 278.8545292 436547.2712 0.134850753 0.090886964 103.7454402 -2.015969018 0.481313799 S(ph)HESLLSPCSTVECLDLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SHESLLSPCSTVECLDLGR 19 0 Q9UJF2;Q9UJF2-2 Q9UJF2 RASAL2 Ras GTPase-activating protein nGAP 1 S(0.502)HES(0.454)LLS(0.044)PCSTVECLDLGR;S(0.963)HES(0.037)LLSPCSTVECLDLGR;S(0.778)HES(0.221)LLS(0.001)PCSTVECLDLGR;S(0.97)HES(0.03)LLSPCSTVECLDLGR 237.5 2.06E-24 572000000 238588 280565 86623 179225 261635 279011 252531 261732 208859 TRUE FALSE 207057.9913 278721.95 128514.1725 219920.7755 256428.9754 289744.7337 228040.5825 205762.6486 184167.927 1.124289092 1.513411997 0.697809736 1.194131786 1.392364999 1.573263806 1.238220934 1.117255605 1 17.49066231 1.547319894 2.971890191 1.013229593 1.25222523 0.106287488 0.240100915 0.572610987 10.62800677 0.263508459 0.065290543 35.26305172 -1.547319894 0.238995637 S(ph)HNNFVAILDLPEGEHQYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SHNNFVAILDLPEGEHQYK 19 0 Q9Y478 Q9Y478 PRKAB1 5-AMP-activated protein kinase subunit beta-1 1 S(1)HNNFVAILDLPEGEHQYK;S(1)HNNFVAILDLPEGEHQYK;S(1)HNNFVAILDLPEGEHQYK 159.66 5.51E-11 334931000 609300 449220 315039 382332 498420 422641 547180 580590 611160 TRUE FALSE 528779.4612 446269.0442 467392.9141 469146.3242 488502.4171 438900.2728 494114.5678 456435.3467 538909.361 0.981202962 0.828096664 0.867294109 0.870547736 0.906464895 0.814423175 0.916878799 0.846961251 1 19.03968312 1.230313203 24.99826966 1.000000229 0.875881106 0.3845845 0.047967404 299.9699237 909148.9194 0.115687658 0.010476263 16.99468828 -1.230313203 -0.124119123 S(ph)HS(ph)GTSPDNTAPPPPPPRPQPSHSR ddPTM_MDA-MB-175_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(0.481)HS(0.519)GT(0.519)S(0.481)PDNTAPPPPPPRPQPSHSR 61.186 0.091535 190890000 18410 21617 11949 16661 20001 20655 27337 29136 29861 TRUE FALSE 15977.07186 21474.9965 17727.57637 20444.1347 19603.01923 21449.61122 24685.86195 22905.49314 26330.8666 0.606781087 0.815582595 0.673262169 0.776432277 0.744488191 0.814618506 0.937525617 0.869910341 1 14.68446738 -2 0.18228945 2.301041765 0.599604427 0.739293602 0.059233993 56.53477378 0.802805402 25.89773779 0.479497475 0.01 2 -1.701437338 S(ph)HSDNDRFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHSDNDRFK 9 1 O75494-2;O75494 O75494-2 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.998)HS(0.002)DNDRFK;S(0.976)HS(0.024)DNDRFK 90.614 0.0068501 247150000 857720 658580 334040 379860 504770 479700 644900 704890 269513 TRUE FALSE 744370.1288 654253.7446 495582.8613 466113.0188 494726.0646 498154.3694 582357.6973 554154.759 237651.4802 3.132192269 2.752996717 2.085334629 1.961330173 2.081729364 2.09615513 2.450469473 2.33179595 1 17.85848786 4.36735849 2.773511276 2.053773364 3.097776683 0.511195171 0.389186656 0.235512079 3.440361588 0.100610101 0.381921277 23300.1378 -4.36735849 1.044003319 S(ph)HSDNDRPNCSWNTQYSSAYYTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SHSDNDRPNCSWNTQYSSAYYTSR 24 1 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.87)HS(0.13)DNDRPNCSWNTQYSSAYYTSR;S(0.429)HS(0.429)DNDRPNCS(0.142)WNTQYSSAYYTSR;S(0.393)HS(0.393)DNDRPNCS(0.214)WNTQYSSAYYTSR 277.5 2.63E-52 2333120000 504838 433396.4 304937.5 323107 363529 424456 383817.6 398642 531791 TRUE FALSE 438122.3792 430549.3905 452406.295 396473.3827 356295.4841 440785.097 346595.0282 313395.5105 468923.2738 0.934315705 0.918165966 0.964776799 0.845497344 0.759816166 0.939994071 0.739129507 0.66833004 1 18.83899236 3.570725902 4.271419604 0.801905907 0.936023268 0.225187666 0.096146466 0.303113875 9.649011181 0.027662889 0.04145292 3721.567517 -3.570725902 0.134117362 S(ph)HSGTSPDNTAPPPPPPRPQPSHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHSGTSPDNTAPPPPPPRPQPSHSR 25 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.274)HS(0.242)GT(0.242)S(0.242)PDNTAPPPPPPRPQPSHSR 52.359 0.075468 29094000 8952.7 7262.7 5094.4 5911.4 3642.9 5584.4 5665.9 6858 4844 TRUE FALSE 7769.578012 7214.990845 7558.06888 7253.67372 3570.413417 5799.235482 5116.42189 5391.470069 4271.347838 1.818999132 1.689160218 1.769481008 1.698216581 0.835898539 1.357706209 1.197847163 1.26224093 1 12.06047567 3.330086753 7.992962761 1.164383069 1.747394599 0.811551089 0.14645484 0.101519893 7.777056014 0.040054928 0.051706073 2138.389206 -3.330086753 0.58301153 S(ph)HSLSRPGPTEGDAEGEAEGPVGSTLGSYATLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHSLSRPGPTEGDAEGEAEGPVGSTLGSYATLTR 34 1 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 S(0.436)HS(0.436)LS(0.103)RPGPT(0.025)EGDAEGEAEGPVGSTLGSYATLTR 189.3 2.04E-20 165470000 71095 76893 34971 46839 73209 73866 72871 82421 50671 TRUE FALSE 61699.61562 76387.88482 51883.09257 57474.51084 71752.28413 76707.67282 65803.98164 64795.91055 44680.7321 1.380899836 1.709638164 1.161196116 1.286337715 1.60588873 1.716795343 1.472759701 1.45019805 1 15.4473652 1.23362148 4.621005435 0.959934496 1.478451877 0.42142952 0.174376337 0.209084031 9.78510363 0.357269344 0.044907624 17.12464115 -1.23362148 0.518517381 S(ph)HSQASLAGPGPVDPSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHSQASLAGPGPVDPSNR 18 0 Q9P2M7;Q9P2M7-2;A6PVU7;A2A3M4 Q9P2M7 CGN Cingulin 1 S(0.417)HS(0.417)QAS(0.166)LAGPGPVDPSNR;S(0.527)HS(0.416)QAS(0.057)LAGPGPVDPSNR 121.56 2.45E-05 2367200000 766650 907750 393920 487360 746490 694730 743620 779310 759590 TRUE FALSE 665335.2601 901786.9305 584421.0296 598022.5368 731636.3095 721456.7127 671503.8469 612660.6211 669792.1355 0.993345883 1.346368347 0.872540895 0.892847953 1.092333383 1.07713524 1.002555586 0.91470262 1 19.35335391 4.225171727 24.99999976 0.978901921 1.169857204 0.343012902 0.109885379 218.630018 408232.4218 0.02727399 0.057286242 16794.67974 -4.225171727 0.190955283 S(ph)HSVGGPLQNIDFTQRPFHGISTVSLPNSLQEVVDPLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHSVGGPLQNIDFTQRPFHGISTVSLPNSLQEVVDPLGK 39 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.511)HS(0.46)VGGPLQNIDFT(0.02)QRPFHGIS(0.004)T(0.004)VSLPNSLQEVVDPLGK 125.44 7.37E-09 533970000 231300 265800 121620 154400 207090 129580 280450 279960 201070 TRUE FALSE 200733.119 264053.9423 180435.8388 189458.8799 202969.3142 134565.0264 253252.0022 220092.7327 177299.7337 1.132168192 1.489308172 1.017688155 1.068579608 1.144780705 0.75896914 1.428383433 1.241359635 1 17.43583084 4.223107927 24.99476816 1.114199495 1.310738303 0.175148022 0.191548316 393.8847033 637112.0847 0.049194164 0.102987507 16715.0595 -4.223107927 0.196538808 S(ph)HWIFEARK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHWIFEARK 9 1 I3L3Y3;A0A087WYU4;A6NH52-2;A6NH52 I3L3Y3 TVP23A Golgi apparatus membrane protein TVP23 homolog;Golgi apparatus membrane protein TVP23 homolog A 1 S(1)HWIFEARK 74.941 0.04202 468940000 764740 691860 441990 614210 540650 744600 592740 650940 833710 TRUE FALSE 663677.6714 687315.1261 655737.8424 753675.7681 529892.1228 773245.2438 535256.166 511741.5466 735149.7536 0.90277888 0.934932132 0.891978592 1.025200327 0.720794804 1.051820041 0.728091336 0.696105173 1 19.48767864 2.213863352 24.99441524 0.781408165 0.916155537 0.154721956 0.119014103 331.6023834 335589.4909 0.045853685 0.030929734 163.6301587 -2.213863352 0.134747372 S(ph)IAEELELSILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SIAEELELSILK 12 0 Q9UBT7-3;Q9UBT7-2;Q9UBT7 Q9UBT7-3 CTNNAL1 Alpha-catulin 1 S(1)IAEELELSILK;S(1)IAEELELSILK 165.7 5.65E-05 15923000 33644 29589 17915 24582.3 27980 23951.6 34997 37823 38273 TRUE FALSE 29197.86016 29394.62791 26578.75392 30164.08693 27423.25274 24873.03355 31602.99633 29734.84579 33748.40954 0.865162553 0.870992983 0.787555748 0.893792844 0.812579115 0.737013503 0.936429205 0.881073988 1 15.04253189 1.181800192 1.197800143 1.085599515 0.834953458 0.465419374 0.054265468 1.585606778 1.754556749 0.521690739 0.016611095 15.19848125 -1.181800192 -0.250646057 S(ph)IAIGS(ph)QPVLTVGT(ph)T(ph)HIS(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SIAIGSQPVLTVGTTHISK 19 0 Q96DZ1;Q96DZ1-3 Q96DZ1 ERLEC1 Endoplasmic reticulum lectin 1 5 S(0.999)IAIGS(0.999)QPVLT(0.013)VGT(0.996)T(0.996)HIS(0.995)K;S(0.998)IAIGS(0.999)QPVLT(0.055)VGT(0.984)T(0.984)HIS(0.978)K 50.364 0.044995 954470000 80201 93692 47676 36134 73852 111220 49047 68660 48164 TRUE FALSE 69602.23465 93076.53108 70732.27307 44338.77697 72382.48969 115498.7054 44290.42949 53977.59331 42470.10679 1.638852358 2.191577515 1.665460212 1.043999658 1.704316169 2.719529431 1.04286127 1.27095497 1 15.37416012 S(ph)IDAALFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SIDAALFR 8 0 Q5FWE3-2;Q5FWE3 Q5FWE3-2 PRRT3 Proline-rich transmembrane protein 3 1 S(1)IDAALFR;S(1)IDAALFR;S(1)IDAALFR;S(1)IDAALFR;S(1)IDAALFR;S(1)IDAALFR 146.88 0.00057291 529346000 563157 678797 451175 767660 929274 1067156 411797 891288 833326 TRUE FALSE 488734.3756 674337.9378 669364.7391 941968.9359 910783.2655 1108210.182 371860.9903 700692.9972 734811.1496 0.665115623 0.917702376 0.91093438 1.281919765 1.239479376 1.50815646 0.506063348 0.953568815 1 19.48701399 4.61310089 1.723664184 1.052044822 0.5996606 0.190944176 0.262753927 1.387753184 5.015195923 0.075961923 0.954410621 41029.94079 -4.61310089 -0.452384222 S(ph)IDKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SIDKDR 6 1 Q8TF01 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 S(1)IDKDR 88.177 0.031249 136390000 361710 225230 200460 224510 152520 214610 310840 364850 514050 TRUE FALSE 313909.107 223750.4493 297403.1265 275488.4269 149485.1504 222866.1856 280694.7846 286829.6668 453279.5946 0.692528653 0.493625683 0.656114085 0.607767105 0.329785749 0.49167487 0.619253079 0.632787512 1 18.79004169 0.967595855 1.628742566 1.516381688 0.545908755 0.645900294 0.102606156 1.424109181 1.920357276 2.757350356 0.029238085 9.28102314 -0.967595855 -0.970472933 S(ph)IDQDYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SIDQDYER 8 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 S(1)IDQDYER;S(1)IDQDYER;S(1)IDQDYER;S(1)IDQDYER;S(1)IDQDYER;S(1)IDQDYER;S(1)IDQDYER 209.97 4.50E-05 10221292000 5372770 4757950 3590840 4165260 5272700 5037510 5385270 6155560 8693790 TRUE FALSE 4662744.832 4726694.713 5327382.235 5111045.945 5167783.586 5231306.269 4863007.344 4839241.397 7666020.05 0.608235408 0.6165774 0.694934555 0.666714398 0.674115584 0.682401851 0.634358808 0.631258641 1 22.87004634 1.236504056 24.99999955 1.000000444 0.65184248 0.936135751 0.028640796 13.28797867 161489.9292 0.047436198 0.007443695 17.23868189 -1.236504056 -0.348157964 S(ph)IEALLEAGQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SIEALLEAGQAR 12 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 S(1)IEALLEAGQAR;S(1)IEALLEAGQAR 96.464 0.0057373 37113000 23422 15078.6 11289.7 14990.2 18012.8 17536.4 13474.5 17104.6 31055 TRUE FALSE 20326.72336 14979.54768 16749.43668 18393.95402 17654.38052 18211.03666 12167.74506 13446.9144 27383.71328 0.74229244 0.547023975 0.611656882 0.67171146 0.644703673 0.665031673 0.444342407 0.491055185 1 14.74103047 1.22959236 24.9923797 1.000000784 0.59364616 0.662941722 0.088948959 230.7645209 643036.6591 0.277323086 0.023371448 16.96650385 -1.22959236 -0.406354624 S(ph)IEEGDGAFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SIEEGDGAFGR 11 0 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 S(1)IEEGDGAFGR 134.98 0.00013597 138400000 95682 64657 29347 59657 61653 36617 104990 73889 54107 TRUE FALSE 83037.38127 64232.26391 43539.30736 73203.03365 60426.22592 38025.67968 94808.08596 58088.41235 47710.5321 1.740441316 1.346291083 0.912572244 1.534316018 1.266517544 0.797008082 1.98715214 1.217517596 1 15.54202016 4.711803298 4.49514827 1.269456482 1.762182051 0.172001891 0.335445622 0.324811921 15.67720005 0.079147759 0.473228369 51499.5339 -4.711803298 0.492725569 S(ph)IEVENDFLPVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SIEVENDFLPVEK 13 0 Q5JPT1;Q5VSN0;Q5JPT2;Q96B97-2;Q96B97 Q5JPT1 SH3KBP1 SH3 domain-containing kinase-binding protein 1 1 S(1)IEVENDFLPVEK;S(1)IEVENDFLPVEK;S(1)IEVENDFLPVEK;S(1)IEVENDFLPVEK;S(1)IEVENDFLPVEK;S(1)IEVENDFLPVEK 360.07 1.82E-76 935874000 1289838 1270419 923620 1117175 1442812 1160670 1638320 1943667 1651915 TRUE FALSE 1119382.64 1262073.534 1370285.721 1370846.659 1414102.864 1205321.726 1479435.979 1528028.938 1456627.491 0.768475569 0.866435339 0.94072488 0.941109973 0.970806107 0.82747424 1.015658422 1.04901833 1 20.47420055 7.28323971 0.227005442 1.052059159 1.65E-21 0.581769334 0.056599946 51.70698381 1.081928195 0.283603324 18.28003069 19197280.48 -7.28323971 -1.052059159 S(ph)IHEVDISNLEAALR ddPTM_MDA-MB-175_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 359.91 4.59E-83 2146450000 867772 744735 573600 762832 732658 702161 826514 826018 1151572 TRUE FALSE 753093.7315 739842.7867 850994.8786 936044.6648 718079.5392 729173.588 746358.7995 649380.4788 1015434.47 0.741646806 0.728597274 0.838059869 0.921816909 0.707164825 0.718090246 0.735014244 0.639509981 1 19.95366571 S(ph)INRNS(ph)VRS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SINRNSVRSR 10 2 A0A499FJE4;Q96MK2;Q96MK2-2 A0A499FJE4 FAM65C Protein FAM65C 3 S(1)INRNS(1)VRS(1)R 81.565 0.01275 423800000 229840 243510 122720 132600 273990 303490 168220 189390 211060 TRUE FALSE 199466.0617 241910.3668 182067.8025 162708.8567 268538.1351 315165.4567 151906.0503 148890.4223 186108.7272 1.071771671 1.299833545 0.97828729 0.874267742 1.442909954 1.693448026 0.816222068 0.800018487 1 17.50578618 S(ph)IPLSIK ddPTM_MDA-MB-175_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 143.7 0.0025214 256800000 1265710 1091180 738090 1237500 950100 677150 1268740 1120340 2192150 TRUE FALSE 1098443.217 1084011.967 1095032.793 1518493.289 931194.8688 703200.3987 1145697.79 880764.0095 1932996.524 0.568259282 0.560793542 0.566494962 0.785564418 0.481736442 0.36378772 0.592705561 0.45564697 1 20.88240761 1.231589335 24.9596158 1.000000799 0.545496012 0.632113477 0.108633336 163.472414 585234.176 0.264387849 0.027157009 17.04469897 -1.231589335 -0.454504788 S(ph)IPMPASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SIPMPASR 8 0 P35568 P35568 IRS1 Insulin receptor substrate 1 1 S(1)IPMPASR;S(1)IPMPASR 85.733 0.018462 0 250422 282940 120877 162789 219046 189137 307940 240756 267450 TRUE FALSE 217328.0982 281081.3485 179333.5215 199752.7305 214687.4132 196413.2228 278076.0262 189272.203 235832.3657 0.921536353 1.191869266 0.760427946 0.84701152 0.910339056 0.832851005 1.179125797 0.802570938 1 17.8474022 4.240912955 24.99999985 0.905796307 1.056702751 0.182887003 0.133628058 96.88408957 1029594.684 0.031702554 0.076037351 17414.57801 -4.240912955 0.150906443 S(ph)IPQLDLGWPDTIAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SIPQLDLGWPDTIAYR 16 0 A6ND36 A6ND36 FAM83G Protein FAM83G 1 S(1)IPQLDLGWPDTIAYR;S(1)IPQLDLGWPDTIAYR;S(1)IPQLDLGWPDTIAYR;S(1)IPQLDLGWPDTIAYR 249.47 1.46E-20 427438000 263551 199314 123989 163268 188876 187205 201853 219295 239376 TRUE FALSE 228722.0676 198004.6932 183950.4951 200340.4948 185117.7371 194406.8975 182277.3271 172400.4708 211077.242 1.083594164 0.938067465 0.871484265 0.949133563 0.877014193 0.92102254 0.863557461 0.816764845 1 17.68741151 4.717031374 2.626876824 0.892136414 1.117690007 0.559487297 0.050547042 0.319546387 2.993603926 0.012776721 0.155163361 52123.23642 -4.717031374 0.225553593 S(ph)IQDLTVTGTEPGQVS(ph)SR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SIQDLTVTGTEPGQVSSR 18 0 O43318;O43318-3;Q9UG54;O43318-2;O43318-4 O43318 MAP3K7;DKFZp586F0420 Mitogen-activated protein kinase kinase kinase 7 2 S(1)IQDLTVTGTEPGQVS(0.594)S(0.406)R;S(1)IQDLTVTGTEPGQVS(0.584)S(0.416)R 230.91 1.58E-19 288620000 421380 414610 255790 287410 408210 418070 360940 388670 403810 TRUE FALSE 365693.5654 411886.3996 379490.8996 352670.8333 400087.4196 434153.4234 325936.0944 305555.9451 356072.0418 1.027021283 1.156750183 1.065769999 0.990447976 1.123613687 1.219285348 0.915365589 0.858129562 1 18.44180964 2.173504972 11.81246522 0.910005738 1.094747805 0.554798341 0.072501414 0.458287201 81.64531452 0.029685474 0.02001574 149.1093825 -2.173504972 0.184742067 S(ph)IQDLTVTGTEPGQVSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SIQDLTVTGTEPGQVSSR 18 0 O43318;O43318-3;Q9UG54;O43318-2;O43318-4 O43318 MAP3K7;DKFZp586F0420 Mitogen-activated protein kinase kinase kinase 7 1 S(0.983)IQDLT(0.015)VT(0.002)GTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR;S(0.994)IQDLT(0.006)VTGTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR 360.75 5.52E-91 7190640000 2737046 2254795 1754312 2066869 2751547 2572478 2661396 2995186 2945425 TRUE FALSE 2375338.436 2239983.103 2602703.151 2536183.197 2696796.598 2671442.893 2403294.226 2354688.782 2597220.212 0.914569518 0.862454055 1.00211108 0.976499099 1.038339601 1.028577739 0.925333252 0.906618843 1 21.30853691 4.238547759 25 0.976085798 0.888511773 0.447047454 0.042998468 0.356518476 695888.0004 0.01252255 0.029099424 17319.99485 -4.238547759 -0.087574025 S(ph)IQEIQELDKDDESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SIQEIQELDKDDESLR 16 1 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 1 S(1)IQEIQELDKDDESLR;S(1)IQEIQELDKDDESLR 97.974 0.0017511 70256000 118170 72767 38057 93433 74902 44531 87541 81808 74840 TRUE FALSE 102553.5351 72288.98879 56461.49249 114648.3907 73411.59674 46244.13639 79051.28729 64313.99583 65992.50046 1.554018023 1.09541218 0.855574377 1.737294236 1.112423324 0.700748359 1.197882892 0.974565222 1 16.01001446 3.004586415 24.99770862 0.98144433 1.28297502 0.270438872 0.263259252 191.93183 1046087.477 0.077828446 0.087922249 1010.61657 -3.004586415 0.30153069 S(ph)IQFVDWCPTGFK ddPTM_MDA-MB-175_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 197.15 1.43E-07 901800000 1917560 1520070 1009370 1177740 1403880 1181940 1813900 2030240 1875790 TRUE FALSE 1664149.588 1510084.56 1497504.708 1445163.868 1375945.535 1227409.997 1637988.257 1596088.975 1654036.243 1.006114343 0.912969451 0.905363903 0.87371959 0.831871454 0.74206959 0.990297682 0.964966144 1 20.65755942 S(ph)ISEIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SISEIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE 35 1 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 1 S(0.5)IS(0.5)EIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE;S(0.5)IS(0.5)EIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE;S(0.5)IS(0.5)EIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE;S(0.5)IS(0.5)EIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE;S(0.5)IS(0.5)EIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE 213.61 4.31E-29 1248931000 266383.4 288295.2 135707.8 181927 240399.6 150546.9 301416 290280.5 230072.2 TRUE FALSE 231180.1588 286401.3698 201336.546 223236.3059 235616.1183 156338.5367 272184.7227 228206.274 202873.3266 1.13952959 1.411725113 0.992424925 1.100372876 1.161395252 0.770621448 1.34164864 1.124870765 1 17.63021967 4.23022796 24.99834693 1.083251472 1.27562737 0.222786879 0.158066074 248.9273934 746800.9312 0.038745629 0.082829077 16991.35288 -4.23022796 0.192375898 S(ph)ISESSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SISESSR 7 0 Q9H307 Q9H307 PNN Pinin 1 S(0.994)IS(0.006)ESSR;S(0.982)IS(0.018)ESSR;S(0.999)IS(0.001)ESSR 184.04 0.00066496 5045400000 1904000 1813150 1335840 1789270 1816840 2327770 2407290 2820880 2390160 TRUE FALSE 1652381.576 1801239.298 1981856.692 2195551.101 1780688.439 2417320.818 2173831.386 2217656.764 2107598.008 0.784011737 0.854640824 0.940339042 1.041731437 0.84488998 1.146955354 1.031426002 1.052219995 1 21.00716829 5.259083108 0.504109712 1.048883017 0.414987067 0.577888785 0.072540785 5.367623736 0.742294109 0.048875003 2.239500397 181586.312 -5.259083108 -0.63389595 S(ph)ISGTSTSEKPNSMDTANTSPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SISGTSTSEKPNSMDTANTSPFK 23 1 Q9UJF2;Q9UJF2-2 Q9UJF2 RASAL2 Ras GTPase-activating protein nGAP 1 S(0.972)IS(0.019)GT(0.002)S(0.002)T(0.002)S(0.002)EKPNSMDTANTSPFK 71.068 0.013615 134690000 102530 93851 77308 92496 84755 75538 110360 109450 125640 TRUE FALSE 88980.40072 93234.4866 114694.4074 113498.6305 83068.54132 78443.99574 99657.30419 86044.96924 110786.9823 0.803166571 0.841565359 1.035269713 1.024476235 0.74980417 0.70806149 0.899539838 0.776670394 1 16.75742885 3.229897165 24.99989082 0.820063755 0.927876343 0.175356867 0.106418685 320.8853954 925968.6595 0.032819107 0.037784464 1697.841578 -3.229897165 0.107812587 S(ph)ISKDSLASNIVNLTPQNQPHPTATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SISKDSLASNIVNLTPQNQPHPTATK 26 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 S(0.536)IS(0.439)KDS(0.024)LASNIVNLTPQNQPHPTATK 174.46 1.54E-12 521260000 355030 305600 169700 290190 388080 262330 519790 567550 431270 TRUE FALSE 308111.886 303592.4935 251767.4876 356082.0748 380357.9673 272422.0049 469380.8458 446183.8492 380285.7519 0.810211491 0.798327289 0.662048174 0.936353973 1.000189898 0.716361324 1.234284596 1.173285738 1 18.53672436 2.236085241 24.99999993 1.147755668 0.825790708 0.638143049 0.111750509 40.18217251 405809.1595 0.045181381 0.032073191 172.2206568 -2.236085241 -0.32196496 S(ph)ISLGDSEGPIVATLAQPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SISLGDSEGPIVATLAQPLR 20 0 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 S(0.5)IS(0.5)LGDSEGPIVATLAQPLR 68.82 0.021617 12950000 9818.9 10189 6273.8 8789.7 10833 9808.7 12503 12665 11100 TRUE FALSE 8521.307487 10122.06779 9307.830665 10785.53573 10617.44449 10186.04704 11290.46098 9956.688309 9787.770645 0.870607598 1.034154575 0.950965343 1.101939974 1.084766376 1.040691226 1.153527335 1.017258033 1 13.25676458 5.803036505 0.847168316 1.062629293 4.73E-11 0.524415612 0.054520369 9.782007522 1.391636924 0.018308992 14.75095314 635384.3371 -5.803036505 -1.062629293 S(ph)ISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 43 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 S(0.535)IS(0.465)LLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.517)IS(0.482)LLEPS(0.001)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 214.53 4.44E-44 373110000 287320 361339 36520.9 188727 362354 215364 334953 320699 301595 TRUE FALSE 249349.934 358965.3403 54182.5294 231580.3499 355143.8643 223649.1924 302469.3096 252120.0145 265940.7827 0.9376145 1.349794254 0.203739076 0.870796677 1.335424604 0.840973657 1.137355868 0.948030656 1 18.02074551 3.454316525 24.95654082 1.041302742 0.824814314 0.108922391 0.301907544 527.8710977 577678.0662 0.085454895 0.110328454 2846.534982 -3.454316525 -0.216488427 S(ph)ISQDSLDELSMEDYWIELENIKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SISQDSLDELSMEDYWIELENIKK 24 1 Q8N392;Q8N392-2 Q8N392 ARHGAP18 Rho GTPase-activating protein 18 1 S(0.5)IS(0.5)QDSLDELSMEDYWIELENIKK 102.6 0.0020712 15885000 18259 12968 7655.6 7177.8 14438 10359 21251 23045 8021.6 TRUE FALSE 15846.02689 12882.81235 11357.87377 8807.629196 14150.71205 10757.51743 19190.08129 18117.00609 7073.295586 2.240260808 1.821330976 1.605740016 1.245194561 2.000582596 1.52086355 2.713032568 2.561324614 1 12.78816684 2.262538616 24.99899562 2.215242093 1.726125701 0.075110665 0.525042684 412.6675261 430237.8345 0.194965252 0.150938703 183.036885 -2.262538616 -0.489116393 S(ph)ISTVNLSENSSVVIPPPDYLECLSMGAAADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SISTVNLSENSSVVIPPPDYLECLSMGAAADR 32 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 S(0.33)IS(0.33)T(0.33)VNLS(0.004)ENS(0.005)S(0.001)VVIPPPDYLECLSMGAAADR 57.427 0.025885 22391000 25669 25927 17820 17207 26619 25853 21228 28348 35751 TRUE FALSE 22276.77661 25756.68383 26437.8116 21114.11234 26089.33398 26847.58164 19169.31183 22286.0008 31524.55751 0.706648352 0.817035539 0.838641798 0.669767128 0.827587635 0.851640237 0.608075524 0.706940955 1 14.9441885 S(ph)ISVSEHVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SISVSEHVVR 10 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9 P49815 TSC2 Tuberin 1 S(0.698)IS(0.302)VSEHVVR;S(0.665)IS(0.334)VSEHVVR 142.08 2.34E-05 239130000 118794 168716 108634 154957 260652 313780 238486 240693 314410 TRUE FALSE 103095.0719 167607.6935 161169.7658 190142.3552 255465.5352 325851.3196 215357.6644 189222.675 277240.808 0.3718611 0.604556359 0.58133493 0.685838267 0.921457187 1.175336784 0.776789196 0.682521005 1 18.0807801 3.565213848 2.143762051 0.884149243 0.513240864 0.607776683 0.143803538 0.260693573 2.361866552 0.048399869 0.07993484 3674.631961 -3.565213848 -0.370908379 S(ph)ITST(ph)PLSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SITSTPLSGK 10 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 2 S(0.992)IT(0.008)S(0.286)T(0.712)PLS(0.002)GK 188.88 5.69E-06 182920000 490360 468800 487260 527580 683570 655030 738690 830010 994670 TRUE FALSE 425557.6836 465720.4219 722900.5658 647375.1026 669968.2944 680229.428 667051.9575 652518.8206 877081.2457 0.485197564 0.530988918 0.824211633 0.738101636 0.763861156 0.775560339 0.760536109 0.743966222 1 19.74235096 4.275326549 6.341557697 0.78928238 0.502483577 0.715051789 0.076619535 0.093820456 10.23355312 0.018462392 0.048365986 18850.65949 -4.275326549 -0.286798803 S(ph)ITSTPLSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SITSTPLSGK 10 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 1 S(0.87)IT(0.108)S(0.02)T(0.002)PLSGK 160.72 7.65E-06 127290000 243520 198060 146740 173410 206670 163950 247820 256160 286130 TRUE FALSE 211338.215 196758.9308 217703.9548 212785.3909 202557.6713 170257.2626 223786.4545 201382.1774 252304.0374 0.837633108 0.779848523 0.86286354 0.843368949 0.802831669 0.674809901 0.886971358 0.798172632 1 17.94480377 1.236205124 24.99643848 1.000000246 0.810966791 0.5149473 0.057704111 52.09637181 552719.8415 0.088989932 0.013662865 17.22682032 -1.236205124 -0.189033455 S(ph)IVVIHPDTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SIVVIHPDTGR 11 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 1 S(1)IVVIHPDTGR 77.42 0.02104 171190000 101470 99723 110270 92392 111560 117630 136170 122620 121800 TRUE FALSE 88060.48241 99067.91305 163596.9408 113371.0157 109340.1743 122155.3022 122964.2544 96398.66723 107400.9428 0.819922807 0.92241195 1.523235613 1.055586784 1.018056001 1.137376443 1.144908519 0.897558855 1 16.71264713 1.740483912 12.27594068 0.950489636 1.09696132 0.089266077 0.184411672 0.176196125 200.8329207 0.101171039 0.047823326 55.01535405 -1.740483912 0.146471684 FVS(ph)EGDGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 FVSEGDGGR 9 0 Q53EL6;Q53EL6-2 Q53EL6 PDCD4 Programmed cell death protein 4 1 FVS(1)EGDGGR;FVS(1)EGDGGR;FVS(1)EGDGGR;FVS(1)EGDGGR;FVS(1)EGDGGR;FVS(1)EGDGGR 199.59 2.57E-05 12659440000 3014060 6252670 5900870 7003010 10315100 11695200 10399400 12077500 12662400 TRUE FALSE 2615744.334 6211595.799 8754550.469 8593150.455 10109849.69 12145121.91 9390867.789 9494820.612 11165465.5 0.234270961 0.556322153 0.784073935 0.769618648 0.905457072 1.087739863 0.841063706 0.850373915 1 23.41254006 4.617095406 1.0301247 0.9186763 5.49E-17 0.886126134 0.080761014 0.510972524 0.511392515 0.027361172 0.495718679 41409.0632 -4.617095406 -0.9186763 down S(ph)KDEYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SKDEYEK 7 1 Q13247;Q13247-3;A0A590UJP7 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 S(1)KDEYEK;S(1)KDEYEK;S(1)KDEYEK;S(1)KDEYEK;S(0.998)KDEY(0.002)EK 142.07 0.0015226 3108560000 6427940 3524940 5019860 5363670 2671170 2792640 5050840 6625560 23351800 TRUE FALSE 5578471.443 3501784.437 7447481.086 6581573.252 2618018.943 2900074.668 4561010.314 5208735.554 20591176.81 0.270915621 0.170062375 0.361683121 0.319630748 0.127142755 0.140840647 0.22150314 0.252959586 1 24.29552295 1.237851707 6.152262225 1.026530055 0.230118558 0.913969284 0.073975788 0.036517432 5.588207722 0.122008853 0.019249975 17.29225803 -1.237851707 -0.796411497 S(ph)KDEYEKS(ph)R ddPTM_MDA-MB-175_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 90.707 0.0060324 255330000 313740 198960 216180 249410 228370 207800 226220 321680 552800 TRUE FALSE 272278.4641 197653.0187 320725.3711 306042.3525 223825.8838 215794.2005 204281.2192 252891.2353 487448.6138 0.558578805 0.405484831 0.657967552 0.627845364 0.459178419 0.442701434 0.419082573 0.518805938 1 18.89489061 1.239403953 7.606379647 1.00741074 0.507868421 0.767087053 0.084649268 0.048123864 20.95632976 0.12487249 0.021659074 17.35417423 -1.239403953 -0.49954232 S(ph)KDRDPNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SKDRDPNR 8 2 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 1 S(1)KDRDPNR;S(1)KDRDPNR;S(1)KDRDPNR 69.65 0.04203 908504000 2558880 1887380 1177816 1480723 1115411 1497257 2171660 2586280 2781160 TRUE FALSE 2220717.525 1874981.677 1747411.757 1816943.789 1093216.503 1554857.446 1961052.747 2033224.148 2452374.433 0.905537709 0.764557668 0.712538727 0.74089167 0.445778788 0.634021226 0.799654702 0.829083896 1 21.22574784 1.440040719 1.598104489 1.041007736 0.699089298 0.388613038 0.117247291 0.762677031 2.576408048 0.379542899 0.036338086 27.54486947 -1.440040719 -0.341918438 S(ph)KDVEFQDGWPR ddPTM_MDA-MB-175_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 112.34 0.00077795 678200000 1054650 826670 635330 649900 966630 873930 1019680 1063000 939140 TRUE FALSE 915275.3304 821239.5503 942577.7131 797469.7281 947395.9542 907550.6526 920791.5905 835685.7223 828115.9391 1.105250228 0.991696345 1.138219504 0.96299285 1.144037821 1.095922213 1.111911445 1.00914097 1 19.65947324 1.628830131 6.408965809 1.002245917 1.076106016 0.215323241 0.058636107 0.183742292 15.69687306 0.034919488 0.01404407 42.54319782 -1.628830131 0.073860098 S(ph)KEDSRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKEDSRR 7 2 P62995 P62995 TRA2B Transformer-2 protein homolog beta 1 S(0.993)KEDS(0.007)RR 68.525 0.048996 1169700000 1525600 1170300 787790 826260 975530 853890 1462500 1846500 907160 TRUE FALSE 1323988.095 1162612.222 1168767.879 1013874.962 956118.8616 886739.7008 1320666.975 1451640.344 799916.5782 1.655157713 1.453416836 1.461112209 1.267475871 1.195273217 1.108540222 1.651005881 1.814739667 1 19.60949003 4.804773766 1.821997157 1.395289166 1.767631201 0.116780807 0.244894119 3.002125856 8.910686561 0.072044361 2.021074422 63793.10862 -4.804773766 0.372342035 S(ph)KGDS(ph)DPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKGDSDPK 8 1 Q9BVI0 Q9BVI0 PHF20 PHD finger protein 20 2 S(1)KGDS(1)DPK 47.894 0.097679 428150000 215800 251310 186520 117650 186960 311540 133630 111560 124720 TRUE FALSE 187281.4832 249659.1281 276721.6959 144364.2307 183239.8618 323525.1454 120670.5832 87703.76216 109975.7437 1.702934456 2.270129028 2.516206634 1.312691561 1.666184339 2.941786385 1.097247258 0.797482783 1 16.74682583 2.06722681 10.2464138 0.903111148 2.044739205 0.564715904 0.458800133 0.281127884 40.99595383 0.185955313 0.125300139 116.7419143 -2.06722681 1.141628057 S(ph)KNES(ph)KEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKNESKEDK 9 2 Q96GA3 Q96GA3 LTV1 Protein LTV1 homolog 2 S(1)KNES(1)KEDK 47.261 0.09765 8029700 13916 13980 11885 13430 12789 10805 14932 20021 30078 TRUE FALSE 12076.96534 13888.16446 17632.62575 16479.48676 12534.52392 11220.67534 13483.89694 15739.66495 26522.2131 0.455352851 0.523642744 0.664824828 0.621346593 0.472604751 0.423067083 0.508400143 0.593452171 1 14.69491354 1.225943326 3.231661302 1.088156568 0.528410792 0.8067637 0.072570175 0.171287201 2.353936015 0.24866993 0.020514791 16.82454492 -1.225943326 -0.559745776 S(ph)KNPSGKNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKNPSGKNR 9 2 A0A0U1RRM7;Q8WXE1-3;A0A1W2PQ89;A0A0U1RQR9 A0A0U1RRM7 ATRIP ATR-interacting protein 1 S(0.5)KNPS(0.5)GKNR 47.823 0.09308 119210000 105460 83974 50116 79448 83359 87333 93396 103240 146550 TRUE FALSE 91523.1938 83422.36926 74352.26523 97487.88269 81700.31899 90692.75702 84338.4703 81162.92941 129225.026 0.708246666 0.645558928 0.57537048 0.754404048 0.632232947 0.701820382 0.65264812 0.628074391 1 16.97952597 1.235269009 24.99997578 1.00000047 0.660173063 0.820312358 0.049662997 35.89331615 272566.3146 0.080086255 0.011437943 17.18972816 -1.235269009 -0.339827407 S(ph)KPIPIMPASPQKGHAVNLLDVPVPVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.896)KPIPIMPAS(0.104)PQKGHAVNLLDVPVPVAR 81.068 0.002575 1390100000 1258500 879360 645250 889720 986890 803110 1097900 1342200 1313500 TRUE FALSE 1092186.036 873583.4263 957295.0582 1091744.525 967252.8198 834006.1614 991425.827 1055180.975 1158219.526 0.942987069 0.754246847 0.826522983 0.94260587 0.835120457 0.720076067 0.85599129 0.911037114 1 20.14347729 1.464784941 2.259634575 1.006417039 0.834931102 0.362305971 0.06950013 0.42587312 3.557217995 0.127716248 0.018870362 29.15982688 -1.464784941 -0.171485936 S(ph)KPLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SKPLTR 6 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 1 S(0.991)KPLT(0.009)R;S(0.991)KPLT(0.009)R;S(1)KPLTR;S(0.999)KPLT(0.001)R;S(1)KPLTR 96.948 0.025211 8662460000 9730480 7062070 5174590 5568200 4386760 6402550 8383140 9261890 9593870 TRUE FALSE 8444572.414 7015678.797 7677039.032 6832544.915 4299472.059 6648860.242 7570144.373 7281306.9 8459693.618 0.998212559 0.829306487 0.907484287 0.807658672 0.508230233 0.78594575 0.894848527 0.860705745 1 23.01217398 1.212502156 1.383810366 1.085899297 0.805806689 0.17071794 0.126131843 2.681081019 4.275414607 1.091196975 0.039672873 16.31181006 -1.212502156 -0.280092609 S(ph)KS(ph)EMLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKSEMLSR 8 1 E9PR23;E9PRA4;E9PNU3;E9PQC8;Q71H61 E9PR23 ILDR2 Immunoglobulin-like domain-containing receptor 2 2 S(1)KS(1)EMLSR 91.656 0.0082862 292770000 11605 14876 11638 16241 15421 15352 14723 14700 12317 TRUE FALSE 10071.36985 14778.27858 17266.17573 19928.76728 15114.15227 15942.60137 13295.16573 11556.5194 10860.89829 0.92730542 1.360686582 1.58975577 1.834909668 1.39161162 1.467889759 1.224131317 1.064048211 1 13.40685581 1.962243328 2.038889157 1.016724391 1.452273879 0.345290056 0.225307662 0.380182744 2.924936445 0.181287605 0.070260535 91.67339763 -1.962243328 0.435549488 S(ph)KS(ph)ISSSNPDLAVAPGSVDDEVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKSISSSNPDLAVAPGSVDDEVSR 24 1 K7ESB7;K7EKT0;K7EP20;Q96HP0 K7ESB7;Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 2 S(0.4)KS(0.458)IS(0.477)S(0.35)S(0.316)NPDLAVAPGSVDDEVSR 80.79 0.0096127 186270000 242450 164060 112250 124850 188230 135830 264720 230240 167290 TRUE FALSE 210409.6182 162982.2791 166534.4755 153199.1007 184484.5913 141055.468 239047.4951 181004.9677 147513.1668 1.426378559 1.104865976 1.128946514 1.038545264 1.250631352 0.956222899 1.620516327 1.22704279 1 17.17048421 S(ph)KS(ph)PFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SKSPFR 6 1 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 2 S(1)KS(1)PFR;S(1)KS(1)PFR;S(1)KS(1)PFR 64.711 0.060292 1470680000 838840 688560 510920 515200 664980 697680 751970 864430 913530 TRUE FALSE 727985.1687 684036.804 758002.6209 632184.0343 651748.199 724520.2011 679044.0651 679578.3715 805533.5241 0.903730443 0.84917236 0.940994506 0.784801644 0.809088858 0.899428986 0.842974308 0.843637603 1 19.61958511 1.235212993 24.99950966 1.000000198 0.857340318 0.481040989 0.045913507 83.26551971 621710.771 0.076932221 0.010917782 17.18751115 -1.235212993 -0.14265988 S(ph)KS(ph)PTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKSPTLR 7 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(0.999)KS(0.942)PT(0.059)LR;S(1)KS(0.976)PT(0.024)LR 72.243 0.029664 829560000 1465780 1109640 747890 804280 934020 886820 1213980 1504440 1284400 TRUE FALSE 1272073.459 1102350.702 1109572.106 986904.0667 915434.8294 920936.5392 1096248.406 1182727.214 1132559.695 1.123184468 0.973326798 0.979702977 0.871392537 0.808288369 0.813146135 0.967938742 1.044295695 1 20.11115566 4.859300784 1.59737646 0.927797828 1.237726531 0.396691177 0.07681134 1.855688265 3.599083528 0.024960649 0.976194494 72327.05536 -4.859300784 0.309928704 S(ph)KSDATASISLSSNLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKSDATASISLSSNLK 16 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 S(0.5)KS(0.5)DATASISLSSNLK;S(0.499)KS(0.499)DAT(0.001)ASISLSSNLK 267.24 1.64E-27 901610000 907860 947220 841350 975810 950410 702510 1231310 1350650 1933040 TRUE FALSE 787884.0008 940997.6495 1248229.674 1197382.575 931498.7004 729536.0143 1111897.746 1061824.008 1704518.213 0.462232668 0.552060777 0.732306446 0.702475671 0.546487971 0.428001302 0.652323769 0.622946707 1 20.70093258 1.133469517 2.503571083 1.195142712 0.584985867 0.646205075 0.096129367 0.563593291 2.976742089 0.841569277 0.026649678 13.59782716 -1.133469517 -0.610156846 S(ph)KSDLSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKSDLSER 8 1 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 S(0.528)KS(0.472)DLSER 133.07 0.00056637 913840000 1346100 1149500 834370 1066900 904320 928780 1259100 1433600 1346700 TRUE FALSE 1168209.474 1141948.859 1237874.123 1309155.952 886325.8013 964510.7676 1136992.676 1127035.796 1187494.66 0.983759771 0.961645468 1.042425001 1.102452074 0.746382978 0.812223246 0.957471822 0.949087044 1 20.1794896 3.26280204 24.99996751 0.900832068 1.019636917 0.384677308 0.081038296 292.6974531 301854.2738 0.025381257 0.032750667 1831.479407 -3.26280204 0.118804849 S(ph)KSEDMDNVQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKSEDMDNVQSK 12 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 S(0.5)KS(0.5)EDMDNVQSK 137.91 0.00012717 246220000 600160 368060 353300 382890 428330 303470 608890 680040 721720 TRUE FALSE 520847.3354 365642.1896 524157.0617 469831.0266 419807.071 315144.6873 549839.9415 534618.7381 636399.0838 0.818428795 0.57454858 0.823629504 0.738264775 0.659660081 0.495199782 0.863986067 0.840068365 1 19.27957223 1.731219122 1.936092121 0.964389755 0.690954 0.441165639 0.11067315 0.312078353 2.263501055 0.118713046 0.031140068 53.85414336 -1.731219122 -0.273435755 S(ph)KSEEAHAEDSVMDHHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SKSEEAHAEDSVMDHHFR 18 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR 257.66 6.23E-31 5543970000 2418790 1325210 637723 1341770 1280179 851007 1660416 1444046 1349738 TRUE FALSE 2099140.773 1316504.608 946127.9759 1646439.386 1254705.943 883745.79 1499389.112 1135248 1190173.511 1.763726678 1.106145109 0.794949616 1.383360805 1.054221028 0.742535254 1.259807161 0.953850837 1 20.18274048 4.729215012 4.50661158 1.031672576 1.806895464 0.594441932 0.189617956 0.12346518 6.409396568 0.044036024 0.299970448 53606.19875 -4.729215012 0.775222888 S(ph)KSHESQLGNR ddPTM_MDA-MB-175_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 S(0.498)KS(0.481)HES(0.022)QLGNR 64.394 0.041533 27123000 32983 29367 13630 22097 26607 25080 34033 38963 35815 TRUE FALSE 28624.21298 29174.08624 20221.51359 27114.46158 26077.57276 26044.84383 30732.4849 30631.06566 31580.9915 0.906374741 0.923786267 0.640306483 0.858569041 0.825736353 0.824700004 0.973132363 0.969920962 1 14.94676885 2.232155705 7.504568501 0.978869404 0.826494699 0.466728728 0.076079921 0.115956876 39.97268949 0.030361778 0.021575689 170.6694171 -2.232155705 -0.152374706 S(ph)KSIS(ph)SSNPDLAVAPGSVDDEVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKSISSSNPDLAVAPGSVDDEVSR 24 1 K7ESB7;K7EKT0;K7EP20;Q96HP0 K7ESB7;Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 2 S(0.471)KS(0.471)IS(0.424)S(0.341)S(0.293)NPDLAVAPGSVDDEVSR 113.65 0.00079049 162590000 268830 190120 111660 141380 206450 143120 296970 256770 174260 TRUE FALSE 233303.4344 188871.0892 165659.1495 173482.4899 202342.0489 148625.919 268169.8951 201861.7337 153659.1813 1.518317567 1.229155899 1.078094703 1.129008292 1.316823682 0.967243986 1.745225328 1.313697834 1 17.22937445 S(ph)KSISS(ph)SNPDLAVAPGSVDDEVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKSISSSNPDLAVAPGSVDDEVSR 24 1 K7ESB7;K7EKT0;K7EP20;Q96HP0 K7ESB7;Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 2 S(0.489)KS(0.489)IS(0.377)S(0.439)S(0.206)NPDLAVAPGSVDDEVSR 109.77 0.0011879 179510000 154030 101580 71754 76906 116230 89437 165720 145470 93634 TRUE FALSE 133674.5452 100912.7143 106454.4744 94368.68273 113917.2504 92877.69926 149648.4999 114362.3725 82564.69519 1.619027902 1.222225965 1.289346181 1.142966525 1.379733192 1.124908159 1.812499877 1.385124384 1 16.33323739 S(ph)KSISSSNPDLAVAPGSVDDEVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKSISSSNPDLAVAPGSVDDEVSR 24 1 K7ESB7;K7EKT0;K7EP20;Q96HP0 K7ESB7;Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 1 S(0.342)KS(0.342)IS(0.105)S(0.105)S(0.105)NPDLAVAPGSVDDEVSR 81.967 0.0092446 165270000 286830 270020 164810 174940 267220 221010 352480 338260 220570 TRUE FALSE 248924.6888 268246.2208 244512.6673 214662.8008 261902.8448 229512.3977 318296.5439 265925.7313 194494.4659 1.279854867 1.37919719 1.257170306 1.103696189 1.346582504 1.180045904 1.636532651 1.367266313 1 17.56936958 S(ph)KSLCHDEIENLLDSDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 116.72 9.19E-05 225770000 152810 149720 81473 105810 159600 113920 178320 183960 157510 TRUE FALSE 132615.7713 148736.4795 120873.6153 129835.7777 156424.2723 118302.5761 161026.5538 144621.5856 138889.3472 0.954830403 1.070899118 0.870287158 0.934814514 1.126251043 0.851775737 1.159387362 1.04127198 1 17.08357642 2.227443092 24.99990482 1.06540426 0.974037521 0.207038593 0.090592813 355.8304099 800147.2737 0.035058942 0.023882345 168.8274623 -2.227443092 -0.091366739 S(ph)KSLDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SKSLDSR 7 1 Q9P2M7;Q9P2M7-2;A6PVU7 Q9P2M7 CGN Cingulin 1 S(0.521)KS(0.479)LDSR;S(0.5)KS(0.5)LDSR;S(0.5)KS(0.5)LDSR 121.73 0.0026704 4145154000 11243230 10494440 6592710 8099500 6193180 8643030 11862400 13264270 11506110 TRUE FALSE 9757408.669 10425501.33 9780966.607 9938615.268 6069947.835 8975532.957 10711986.27 10427809.08 10145870.78 0.961712294 1.02756102 0.964034218 0.979572427 0.598267804 0.884648854 1.055797625 1.027788477 1 23.27438936 2.241460742 24.97777131 1.029010703 0.900764776 0.202623597 0.117061409 126.0866992 1085955.161 0.048342882 0.035775058 174.3655732 -2.241460742 -0.128245927 S(ph)KSLTNLVAAGDDVLEDQEILMHHPPQVDELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 56.952 0.020899 10534000 14638 14181 9790.2 14725 10838 10547 15017 14901 19579 TRUE FALSE 12703.55121 14087.84408 14524.77347 18068.53631 10622.345 10952.74991 13560.65365 11714.53711 17264.39292 0.7358238 0.81600576 0.841313884 1.046578144 0.615274748 0.634412688 0.785469475 0.678537448 1 14.07551198 4.761238238 20.66328392 0.789528229 0.735823221 0.014369547 0.141624063 3513.228553 3200599.961 0.034774376 1.213069883 57708.29432 -4.761238238 -0.053705008 S(ph)KSMSDVSAEDVQNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKSMSDVSAEDVQNLR 16 1 E9PMS6;E9PJ10 E9PMS6 LMO7 1 S(0.706)KS(0.293)MS(0.001)DVSAEDVQNLR;S(0.5)KS(0.5)MS(0.001)DVSAEDVQNLR 144.92 1.93E-06 1315400000 1313290 1520090 717360 808150 1442030 1069980 1427970 1886080 635360 TRUE FALSE 1139735.399 1510104.429 1064277.695 991652.8093 1413336.424 1111142.823 1289485.689 1482756.469 560248.4646 2.034339175 2.695419129 1.899653034 1.770023252 2.522695757 1.983303647 2.301631813 2.646605146 1 19.09570726 1.226956744 24.99993398 0.99999725 2.24545196 0.598853968 0.316634189 376.5412274 811186.0389 1.212754126 0.077470494 16.86385053 -1.226956744 1.24545471 S(ph)KSPASVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKSPASVDR 9 1 Q13243;Q13243-3 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 1 S(0.567)KS(0.433)PASVDR 79.492 0.016224 107340000 151370 130160 78217 103810 115580 119550 156950 178750 137800 TRUE FALSE 131366.071 129304.9704 116043.0028 127381.6471 113280.1841 124149.1659 141729.0132 140525.7035 121509.441 1.081118224 1.064155751 0.955012235 1.04832716 0.932274753 1.021724443 1.166403302 1.156500288 1 16.89070889 2.299456257 8.574922763 1.120126056 1.013667166 0.304090841 0.063518511 0.287907618 36.88962174 0.023719982 0.018302943 199.2765783 -2.299456257 -0.106458889 S(ph)KSPLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SKSPLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 36 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.392)KS(0.353)PLPPEEEAKDEEEDQT(0.216)LVNLDT(0.019)Y(0.006)T(0.007)S(0.007)DLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQT(0.001)LVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 256.84 2.45E-62 12430162000 249459.2 158128.1 139635.7 139039.7 141951.9 105599.9 224844.1 268302.3 235634.5 TRUE FALSE 216492.5347 157089.3461 207163.9916 170610.789 139127.3349 109662.3965 203038.7538 210927.9411 207778.0578 1.041941276 0.756043962 0.997044605 0.821120337 0.669595896 0.527786224 0.977190546 1.015159845 1 17.66468378 2.032264188 24.999235 1.00491692 0.799557376 0.286686748 0.145673981 235.8450416 182738.6761 0.061456777 0.041433873 107.7120243 -2.032264188 -0.205359544 S(ph)KSPPKVPIVIQDDSLPAGPPPQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKSPPKVPIVIQDDSLPAGPPPQIR 25 2 Q7Z422-5;Q7Z422;Q7Z422-4;Q7Z422-2;Q7Z422-3 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 S(0.5)KS(0.5)PPKVPIVIQDDSLPAGPPPQIR;S(0.5)KS(0.5)PPKVPIVIQDDSLPAGPPPQIR 200.06 3.57E-25 3502500000 2116570 1463210 1272670 1410820 1650400 1142650 1975040 2296040 2705830 TRUE FALSE 1836859.912 1453598.077 1888137.469 1731168.244 1617560.269 1186608.485 1783500.925 1805049.714 2385949.86 0.769865261 0.609232449 0.791356726 0.725567739 0.677952331 0.497331694 0.747501427 0.756532962 1 21.18613229 1.139906748 1.823908443 1.174157548 0.683086105 0.56959882 0.084895567 0.87339908 2.208151286 0.815426233 0.023283977 13.80087898 -1.139906748 -0.491071443 S(ph)KSVIEQVSWDT ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKSVIEQVSWDT 12 1 Q6WCQ1 Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 S(0.607)KS(0.393)VIEQVSWDT 110.77 0.0038235 303070000 673800 615710 434620 449370 582390 564080 701930 756460 818220 TRUE FALSE 584755.6228 611665.3605 644803.6857 551406.3267 570801.5784 585780.5226 633856.9366 594696.9158 721490.9637 0.810482254 0.847779655 0.893709995 0.764259505 0.791141687 0.811902785 0.878537596 0.824261073 1 19.4606218 -0.080331501 1.582417748 10 0.825311144 0.648793828 0.039327523 44.34471944 2.585082288 1398.814472 0.01126587 0.831129121 0.080331501 -9.174688856 S(ph)KSYNTPLLNPVQEHEAEGAAAGGTSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKSYNTPLLNPVQEHEAEGAAAGGTSIR 28 1 P85299;P85299-5;P85299-2;P85299-4;P85299-3 P85299 PRR5 Proline-rich protein 5 1 S(0.5)KS(0.5)YNTPLLNPVQEHEAEGAAAGGTSIR;S(0.5)KS(0.5)YNTPLLNPVQEHEAEGAAAGGTSIR 269.96 2.29E-55 1130690000 297140 318050 208410 253220 344180 263650 306260 390830 380950 TRUE FALSE 257872.1961 315960.7086 309197.7731 310717.4712 337331.4914 273792.7861 276558.9523 307254.0459 335914.525 0.767672062 0.940598531 0.920465625 0.924989687 1.004218235 0.815066827 0.82330156 0.914679251 1 18.35773465 4.745453509 24.21150201 0.913010938 0.767671956 0.36555706 0.061904598 634.7251953 2229400.925 0.015540872 0.146791053 55648.50592 -4.745453509 -0.145338981 S(ph)KTFDWAEFRPIQQALAQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKTFDWAEFRPIQQALAQER 20 2 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 S(0.547)KT(0.453)FDWAEFRPIQQALAQER 55.881 0.058789 0 147480 111220 75293 88793 124630 120860 116970 134330 129570 TRUE FALSE 127990.1443 110489.3885 111704.9466 108954.8078 122150.1068 125509.5624 105626.2674 105604.5749 114252.3822 1.120240487 0.967064199 0.977703436 0.9536327 1.069125251 1.098529063 0.924499475 0.92430961 1 16.80186472 2.208945706 24.98831866 0.943287545 1.023927821 0.292096523 0.058807906 268.1644047 226268.6323 0.024603367 0.016590371 161.7877764 -2.208945706 0.080640276 S(ph)KTLAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKTLAFR 7 1 Q53EV4-2 Q53EV4-2 1 S(0.902)KT(0.098)LAFR;S(0.908)KT(0.092)LAFR 75.243 0.026645 712140000 686990 736510 218748 198798 654610 851480 439850 421200 47203 TRUE FALSE 596202.5309 731671.8173 324535.2645 243938.1243 641584.5417 884236.9866 397193.4147 331129.6578 41622.71511 14.3239702 17.57866625 7.797070988 5.860697066 15.41428857 21.24409674 9.542707957 7.955503548 1 15.34508346 4.241931578 24.9984894 10 15.95131933 0.177875328 5.461141631 162.1747058 1202608.392 1.471653487 3.578250472 17455.47123 -4.241931578 5.951319334 S(ph)KTPPKSYSTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKTPPKSYSTAR 12 2 Q05519-2;Q05519;Q5T757;Q5T760 Q05519-2;Q5T760 SRSF11 Serine/arginine-rich splicing factor 11 1 S(0.484)KT(0.484)PPKS(0.02)Y(0.001)S(0.008)T(0.003)AR 48.214 0.093185 147440000 395180 260130 172850 205650 261930 181130 337310 335230 178390 TRUE FALSE 342955.9617 258421.1889 256440.8381 252345.9757 256718.1055 188098.1883 304597.7281 263543.6733 157300.9374 2.180253769 1.642845829 1.630256261 1.604224233 1.632018917 1.195785552 1.936401226 1.675410697 1 17.26316774 7.362253794 1.054912258 1.542663843 199.9993201 0.384164506 0.259176889 583.8109821 2.772000235 0.076935291 277696.193 23027871.3 -7.362253794 198.4566562 S(ph)KTPPPPPQTAQTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKTPPPPPQTAQTK 14 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 S(0.623)KT(0.377)PPPPPQTAQTK 130.56 3.72E-05 199470000 314730 263340 230320 256960 269930 211580 355180 461540 410860 TRUE FALSE 273137.6331 261610.1022 341703.5224 315306.6954 264558.9211 219719.6195 320734.6983 362843.2627 362288.5989 0.753922795 0.722104154 0.943180446 0.870319122 0.730243574 0.606476771 0.885301661 1.001531 1 18.46677988 2.001756569 24.96932587 0.983637327 0.776515253 0.531299039 0.089249658 45.37316284 644965.5357 0.039609863 0.02649348 100.4052841 -2.001756569 -0.207122074 S(ph)LAIPDDDRFEDLEEANPFSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLAIPDDDRFEDLEEANPFSFR 22 1 Q96C92-4 Q96C92-4 SDCCAG3 Serologically defined colon cancer antigen 3 1 S(1)LAIPDDDRFEDLEEANPFSFR 180.42 3.23E-17 39379000 22686 24719 13219 15152 24610 17976 19472 21966 19269 TRUE FALSE 19687.98762 24556.61926 19611.75261 18592.49318 24120.30915 18667.54835 17583.60844 17268.74184 16991.04077 1.158727584 1.445268691 1.154240807 1.094252756 1.419589858 1.098670093 1.034875301 1.01634397 1 14.05248661 2.51509901 7.68764384 1.024194763 1.251767872 0.500017833 0.110235426 0.213706792 38.32304387 0.037348917 0.032337303 327.4153302 -2.51509901 0.227573109 S(ph)LALVAHTGYLPHQQDPHHVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLALVAHTGYLPHQQDPHHVHR 22 0 Q9Y485;F5H269;E7EMZ0 Q9Y485 DMXL1 DmX-like protein 1 1 S(0.969)LALVAHT(0.028)GY(0.003)LPHQQDPHHVHR 90.972 0.001041 632600000 267810 247300 170980 188650 251290 229170 264500 276010 184660 TRUE FALSE 232418.23 245675.47 253666.4999 231485.8658 246289.8206 237986.3182 238848.8307 216987.4094 162829.7052 1.427369961 1.508787784 1.557863779 1.421643954 1.512560748 1.461565738 1.46686276 1.332603343 1 17.31300439 1.082220391 1.534039996 0.633271317 1.485991087 0.93366644 0.040501418 0.371424881 0.572763793 0.544833415 0.011067374 12.08426918 -1.082220391 0.85271977 S(ph)LDADEFR ddPTM_MDA-MB-175_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 88.681 0.01515 1055740000 1805510 1695410 930000 1444680 1670230 1511530 1913150 2150900 1396450 TRUE FALSE 1566907.279 1684272.74 1379751.111 1772716.675 1636995.691 1569679.537 1727613.007 1690946.773 1231363.272 1.272497982 1.367811416 1.120506955 1.439637445 1.329417344 1.274749356 1.403008395 1.373231452 1 20.23182501 1.23351805 24.99699184 0.999999497 1.326220737 0.567017869 0.088545862 114.7260769 568653.3257 0.168601208 0.020748272 17.12056333 -1.23351805 0.32622124 S(ph)LDDLSAPPHHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLDDLSAPPHHR 12 0 A6NKD9 A6NKD9 CCDC85C Coiled-coil domain-containing protein 85C 1 S(1)LDDLSAPPHHR 111.12 0.00091247 1269200000 254570 229500 155700 162280 243870 259050 201710 258500 231660 TRUE FALSE 220927.9295 227992.3994 230997.0408 199128.1543 239017.4641 269015.8211 182148.1952 203221.7866 204273.4187 1.081530484 1.116113887 1.130822807 0.974811875 1.170085984 1.316939927 0.891688191 0.994851841 1 17.64014196 2.20604344 24.9999989 0.966049483 1.125579809 0.446590433 0.088756779 189.7131405 145854.8044 0.036868206 0.024858582 160.7101993 -2.20604344 0.159530326 S(ph)LDEIAMDLTETGTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLDEIAMDLTETGTQR 16 0 E9PGA7;Q9Y2L6-2;Q9Y2L6;C9JYK2 E9PGA7 FRMD4B FERM domain-containing protein 4B 1 S(1)LDEIAMDLTETGTQR 197.88 4.42E-11 17673000 14731 11271 8459.1 9758 16623 13345 11558 14143 13740 TRUE FALSE 12784.26103 11196.96006 12549.94905 11973.70304 16292.23482 13858.39079 10437.10694 11118.62951 12115.67285 1.055183743 0.924171542 1.035844167 0.988282136 1.344723898 1.143839963 0.861454998 0.917706317 1 13.56458691 2.237901899 24.99997316 0.921873097 1.08041628 0.288648616 0.115073463 23.88656146 906480.7737 0.048514242 0.034922905 172.9425663 -2.237901899 0.158543183 S(ph)LDFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLDFFR 6 0 Q6P3S1 Q6P3S1 DENND1B DENN domain-containing protein 1B 1 S(1)LDFFR;S(1)LDFFR;S(1)LDFFR;S(1)LDFFR;S(1)LDFFR;S(1)LDFFR 138.83 0.01273 591994000 593592 490533 337641 338260 475592 499194 419015 440808 491249 TRUE FALSE 515147.3132 487310.6564 500925.3169 415067.103 466128.6497 518398.3162 378378.9898 346544.6396 433174.1029 1.189238484 1.124976431 1.156406428 0.958199256 1.076076909 1.196743556 0.873503257 0.800012368 1 18.72458747 2.22493113 24.90889464 0.871444014 1.110026457 0.618409426 0.083003652 136.9826536 250343.8189 0.034117123 0.023142099 167.8537816 -2.22493113 0.238582443 S(ph)LDGAEFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLDGAEFSR 9 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 S(1)LDGAEFSR;S(1)LDGAEFSR 122.51 0.0006124 988780000 567790 478350 368160 550220 537570 515340 494170 622990 940380 TRUE FALSE 492755.1129 475207.6874 546203.4074 675155.8606 526873.4087 535165.4633 446245.4695 489768.4366 829209.3477 0.594246934 0.573085299 0.658703871 0.814216413 0.63539251 0.645392463 0.538157789 0.590645098 1 19.66137685 1.23481976 24.99996338 1.000000526 0.630297363 0.709371987 0.074178352 66.05232751 441358.1291 0.142709267 0.019619858 17.17195572 -1.23481976 -0.369703164 S(ph)LDLPSIGGSSVGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLDLPSIGGSSVGK 14 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 S(0.999)LDLPS(0.001)IGGSSVGK 130.95 6.20E-05 159980000 164350 127170 121510 170480 174920 136860 169610 203490 568450 TRUE FALSE 142630.7311 126334.6119 180272.6424 209190.0896 171439.4342 142125.0928 153161.2483 159975.2471 501248.4886 0.284550945 0.252039886 0.359647254 0.417338096 0.34202484 0.283542187 0.305559521 0.319153575 1 18.93516646 1.238448093 24.99950736 1.000000745 0.321350918 0.955868052 0.045885747 0.544430689 120415.9896 0.067925749 0.012115273 17.31602055 -1.238448093 -0.678649827 MAGNEALSPTS(ph)PFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 MAGNEALSPTSPFR 14 0 Q86WR7;Q86WR7-2;D3DRR9 Q86WR7 PROSER2;C10orf47 Proline and serine-rich protein 2 1 MAGNEALSPT(0.001)S(0.999)PFR;MAGNEALSPT(0.05)S(0.95)PFR;MAGNEALSPT(0.001)S(0.999)PFR;MAGNEALSPT(0.053)S(0.947)PFR 157.98 5.40E-06 458630000 930940 1309620 876640 1287520 1815310 1874850 1752220 2064860 1904370 TRUE FALSE 807913.9203 1301017.02 1300586.036 1579871.095 1779188.883 1946976.693 1582289.974 1623305.758 1679237.548 0.481119495 0.774766513 0.774509859 0.940826446 1.059521855 1.159440899 0.942266909 0.966692151 1 20.6793749 4.619937798 0.885190999 1.018246719 0.279350641 0.848123432 0.073203213 0.770455732 0.541996098 0.028493734 0.534645115 41680.96816 -4.619937798 -0.738896078 down S(ph)LDT(ph)ITLSGDERDFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLDTITLSGDERDFGR 16 1 Q8N9U0;Q8N9U0-2;H0YJ73 Q8N9U0 TC2N Tandem C2 domains nuclear protein 2 S(0.999)LDT(0.456)IT(0.409)LS(0.137)GDERDFGR 77.871 0.052058 98120000 60446 49520 32756 42851 65944 70056 41917 86582 31216 TRUE FALSE 52457.90795 49194.69986 48596.91116 52580.97449 64631.84342 72751.09965 37851.89579 68067.11308 27525.68004 1.905780634 1.787229227 1.765511736 1.910251605 2.34805619 2.643026423 1.375148434 2.472858544 1 14.74849059 3.472133964 24.61207848 2.030157792 1.819879716 0.009933066 0.49151857 431.7937315 2130869.685 0.134270811 0.173991841 2965.746071 -3.472133964 -0.210278077 S(ph)LDTITLS(ph)GDERDFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLDTITLSGDERDFGR 16 1 Q8N9U0;Q8N9U0-2;H0YJ73 Q8N9U0 TC2N Tandem C2 domains nuclear protein 2 S(0.989)LDT(0.198)IT(0.104)LS(0.709)GDERDFGR 114.37 0.00033499 80331000 60933 53551 34796 36687 68772 59742 39006 81294 32731 TRUE FALSE 52880.54967 53199.21995 51623.46199 45017.34408 67403.57175 62040.3134 35223.20412 63909.91073 28861.57847 1.832212667 1.843254 1.788656918 1.559767222 2.335408364 2.14958144 1.220418494 2.214359509 1 14.81686258 1.223617026 24.96506016 0.999997672 1.864369068 0.415883239 0.323244755 809.4688769 1352235.931 1.703853753 0.075390305 16.73466512 -1.223617026 0.864371396 S(ph)LDTITLSGDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLDTITLSGDER 12 0 Q8N9U0;Q8N9U0-2;H0YJ73 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 S(0.999)LDT(0.001)ITLSGDER;S(0.998)LDT(0.002)ITLSGDER 183.06 1.69E-05 390540000 560270 408630 515230 497790 431360 408270 464310 606760 519110 TRUE FALSE 486228.9 405945.6826 764396.9513 610820.8277 422776.7799 423976.4111 419281.2877 477009.0958 457741.4072 1.062234905 0.88684501 1.669931842 1.334423363 0.923614891 0.926235653 0.9159785 1.042092955 1 18.80417328 3.232556592 24.99875853 0.96646006 1.24407731 0.318899669 0.200843639 185.9282575 774141.8083 0.063153347 0.073451355 1708.270306 -3.232556592 0.27761725 S(ph)LEDLRAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SLEDLRAPK 9 1 Q8TEH3;Q8TEH3-7;Q8TEH3-6 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 S(1)LEDLRAPK;S(1)LEDLRAPK;S(1)LEDLRAPK;S(1)LEDLRAPK;S(1)LEDLRAPK 145.91 5.82E-05 1630940000 5438350 3859050 2422640 2567860 3977400 3256730 4865410 5189230 1924900 TRUE FALSE 4719658.268 3833699.646 3594236.807 3150931.86 3898257.522 3382018.51 4393563.287 4079553.547 1697340.515 2.780619579 2.258650879 2.117569678 1.856393477 2.296685602 1.992539789 2.588498447 2.403497419 1 20.69484459 4.736877845 2.375956404 2.100765301 2.940291989 0.221653587 0.428363559 0.955265172 6.538556783 0.10775321 1.652064498 54560.43767 -4.736877845 0.839526688 S(ph)LEELLLDANQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLEELLLDANQLR 13 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JPP5;Q14160-3;Q5T0G3;Q9BTT6-2;Q9BTT6 A0A0G2JNZ2 SCRIB;LRRC1 Protein scribble homolog;Leucine-rich repeat-containing protein 1 1 S(1)LEELLLDANQLR;S(1)LEELLLDANQLR;S(1)LEELLLDANQLR;S(1)LEELLLDANQLR 262.37 4.34E-24 122222000 110128 95914 63415 99079 118807 111093 88613 133734 121395 TRUE FALSE 95574.30577 95283.93462 94082.70611 121576.4013 116442.9731 115366.8196 80019.3249 105136.0248 107043.8214 0.892852147 0.890139509 0.87891767 1.135762902 1.087806579 1.077753186 0.747538007 0.982177425 1 16.707842 S(ph)LEGGGCPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLEGGGCPAR 10 0 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 S(1)LEGGGCPAR;S(1)LEGGGCPAR 126.03 0.00041277 1645210000 357800 306970 252110 277550 400570 389350 445200 416330 406380 TRUE FALSE 310515.8235 304953.4939 374031.2393 340571.9696 392599.4407 404328.5464 402024.5725 327301.0694 358338.2193 0.866543971 0.851021402 1.043793877 0.950420444 1.095611407 1.128343349 1.121913742 0.913385879 1 18.4509624 4.239332151 25 1.032182747 0.858782626 0.529509381 0.069450628 16.77402616 543437.1182 0.019297934 0.045311117 17351.3053 -4.239332151 -0.173400121 S(ph)LEGIFDDIVPDGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLEGIFDDIVPDGKR 15 1 Q13009 Q13009 TIAM1 T-lymphoma invasion and metastasis-inducing protein 1 1 S(1)LEGIFDDIVPDGKR;S(1)LEGIFDDIVPDGKR 184.01 2.95E-07 79281000 135801 103930 69737 71870 99759 89184 107907 117846 76020 TRUE FALSE 117854.5538 103247.277 103462.0465 88189.18196 97773.99108 92614.96619 97442.19575 92645.54998 67033.0022 1.758157175 1.540245455 1.543449391 1.315608418 1.458594839 1.381632377 1.453645108 1.382088627 1 16.03258393 8 0.048919154 1.09E-09 3.951649502 0.631761204 0.117347821 880.7658231 4.217235681 96.78453728 296.9310082 99999999.99 -8 3.951649501 S(ph)LEGLNQELEEVFVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SLEGLNQELEEVFVK 15 0 Q9C073;D6RJ87;D6RFX7;K7ENS5 Q9C073 FAM117A Protein FAM117A 1 S(1)LEGLNQELEEVFVK;S(1)LEGLNQELEEVFVK;S(1)LEGLNQELEEVFVK;S(1)LEGLNQELEEVFVK;S(1)LEGLNQELEEVFVK 221.47 1.61E-12 311830700 248622.3 178969.6 163559.5 180013.9 206547.2 180278.1 213269.8 264151.3 308666.2 TRUE FALSE 215766.2331 177793.9369 242657.4213 220888.8073 202437.3148 187213.5152 192586.9276 207664.6001 272176.0335 0.79274516 0.65323142 0.89154588 0.811565973 0.743773477 0.687839825 0.707582241 0.762979008 1 18.05418051 1.239956936 6.60284018 1.006376226 0.754123819 0.565639314 0.067104494 0.088034493 18.81424187 0.100010667 0.016753809 17.37628519 -1.239956936 -0.252252407 S(ph)LEGLNQELEEVFVKEQGEEELLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLEGLNQELEEVFVKEQGEEELLR 24 1 Q9C073;D6RJ87;D6RFX7;K7ENS5 Q9C073 FAM117A Protein FAM117A 1 S(1)LEGLNQELEEVFVKEQGEEELLR 127.76 4.99E-05 24146000 15857 10281 5956.6 4765.4 9865.5 10259 12397 14876 4298.2 TRUE FALSE 13761.45727 10213.46343 8837.231684 5847.456905 9669.195852 10653.67037 11194.74085 11694.88317 3790.071693 3.630922682 2.694794258 2.331679293 1.542835434 2.551190752 2.810941648 2.953701607 3.085662783 1 11.88800942 3.001452572 24.87635882 2.614320079 2.482574926 0 0.763882811 466.3053792 7985496.27 0.235914964 0.265556622 1003.35027 -3.001452572 -0.131745153 S(ph)LELSSLAGPGEDPLSADSLGKPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLELSSLAGPGEDPLSADSLGKPTR 25 1 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 S(0.999)LELS(0.001)S(0.001)LAGPGEDPLSADSLGKPTR;S(1)LELSSLAGPGEDPLSADSLGKPTR;S(1)LELSSLAGPGEDPLSADSLGKPTR;S(1)LELSSLAGPGEDPLSADSLGKPTR;S(0.98)LELS(0.019)S(0.001)LAGPGEDPLSADSLGKPTR;S(0.976)LELS(0.024)SLAGPGEDPLSADSLGKPTR 296.35 3.20E-63 3405212000 869439 833729 660493 785131 941577 787833 1060872 1238414 1122078 TRUE FALSE 754540.4333 828252.1793 979909.624 963406.9935 922841.4599 818141.4453 957988.7967 973588.8034 989427.2171 0.762603272 0.837102684 0.990380704 0.973701731 0.932702723 0.826883909 0.968225636 0.983992341 1 19.91623406 4.412688427 4.0330519 0.952304153 0.775724514 0.639329825 0.049496408 0.135333539 4.292922334 0.013522717 0.043020762 25863.56737 -4.412688427 -0.176579639 S(ph)LENPT(ph)PPFTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLENPTPPFTPK 12 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 2 S(1)LENPT(1)PPFTPK;S(1)LENPT(1)PPFTPK;S(1)LENPT(1)PPFTPK;S(1)LENPT(0.997)PPFT(0.003)PK 199.58 9.02E-07 553651000 2279670 1826550 1373360 1623590 1970060 1522680 2218180 2536100 2321580 TRUE FALSE 1978405.834 1814551.273 2037521.49 1992250.925 1930859.66 1581258.485 2003061.245 1993774.751 2047125.457 0.966431162 0.886389872 0.995308559 0.973194348 0.943205339 0.772428714 0.97847508 0.973938722 1 20.96516809 2.045679409 24.99991662 0.982439566 0.923328213 0.179307143 0.061856913 224.560977 122899.0928 0.025739983 0.017353885 111.0911364 -2.045679409 -0.059111353 S(ph)LEPAENVHGAGGGAFPASQTPSKPASADGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SLEPAENVHGAGGGAFPASQTPSKPASADGHR 32 1 P12931;P12931-2 P12931 SRC Proto-oncogene tyrosine-protein kinase Src 1 S(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;S(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;S(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;S(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;S(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR 248.61 1.55E-47 8230060000 2445260 2430710 1047590 2565460 3023580 2242140 2765890 3545440 5119140 TRUE FALSE 2122112.696 2414742.506 1554208.028 3147986.904 2963416.674 2328396.577 2497654.414 2787275.247 4513961.101 0.470122061 0.534949782 0.344311347 0.697389019 0.656500268 0.515821143 0.553317664 0.617478792 1 22.10596256 1.171604848 2.417218081 1.178697247 0.541167397 0.692121657 0.095876583 0.427889812 2.290876603 0.622409216 0.025850825 14.84584247 -1.171604848 -0.63752985 S(ph)LEQYDQVLDGAHGASLTDLANLSEGVSLAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLEQYDQVLDGAHGASLTDLANLSEGVSLAER 32 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4;M0R2S2;M0R3I1 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 S(0.995)LEQY(0.005)DQVLDGAHGAS(0.001)LTDLANLSEGVSLAER 85.864 0.00012027 41934000 15706 12582 11078 14128 15756 15824 15147 15353 16502 TRUE FALSE 13630.41231 12499.34801 16435.35785 17335.97833 15442.48643 16432.75952 13678.04627 12069.88043 14551.15236 0.936723908 0.858993687 1.129488404 1.191381817 1.061255222 1.129309838 0.939997461 0.829479352 1 13.82884579 2.067630067 6.684246324 0.897280367 1.052287626 0.250750506 0.103942853 0.264635778 20.77071926 0.046254686 0.030899286 116.8503634 -2.067630067 0.155007259 S(ph)LESCLLDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLESCLLDLR 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 S(1)LESCLLDLR;S(1)LESCLLDLR;S(1)LESCLLDLR 169.65 4.79E-06 454150000 202135 225346 137924 172934 258732 234315 240484 286652 245147 TRUE FALSE 175422.3476 223865.6873 204624.5077 212201.3078 253583.7394 243329.2497 217161.8987 225353.7005 216166.0009 0.811516829 1.035619322 0.946608194 0.981659035 1.173097242 1.125659209 1.004607097 1.042502982 1 17.72178011 5.629123708 0.906916958 1.053351016 1.41E-10 0.532336534 0.066821091 8.081258493 1.584192205 0.023046636 12.33273725 425719.6618 -5.629123708 -1.053351016 S(ph)LESVLSLGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLESVLSLGPR 11 0 Q13470-2;Q13470 Q13470-2 TNK1 Non-receptor tyrosine-protein kinase TNK1 1 S(0.93)LES(0.07)VLSLGPR 255.3 1.93E-20 79689000 37432 27850 28927 36620 39287 33977 34856 41236 73218 TRUE FALSE 32485.26636 27667.05152 42916.19396 44935.1307 38505.26556 35284.11718 31475.67048 32418.0023 64562.25145 0.503161919 0.428532941 0.664725796 0.695996959 0.596405248 0.546513115 0.487524363 0.502120071 1 15.97840327 1.234600665 24.99945545 1.000000646 0.552861921 0.748295764 0.081451452 65.14104376 411181.1985 0.161726851 0.021848523 17.16329492 -1.234600665 -0.447138725 S(ph)LESVLSLGPRPT(ph)GGGSSPPEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLESVLSLGPRPTGGGSSPPEIR 23 1 Q13470-2;Q13470 Q13470-2 TNK1 Non-receptor tyrosine-protein kinase TNK1 2 S(0.996)LES(0.065)VLS(0.17)LGPRPT(0.298)GGGS(0.246)S(0.224)PPEIR;S(1)LES(0.048)VLS(0.005)LGPRPT(0.4)GGGS(0.259)S(0.288)PPEIR 88.668 0.013934 365150000 303300 244760 183284 206840 295260 289360 273540 319170 232430 TRUE FALSE 263218.1365 243152.1554 271920.7554 253806.1834 289384.9037 300491.8664 247012.1329 250917.9793 204952.3902 1.284289177 1.186383605 1.326750838 1.238366545 1.411961595 1.466154487 1.205217137 1.224274472 1 17.64492929 1.140741471 1.515862235 0.819175818 1.30905313 0.559926627 0.085184389 1.187777851 2.01215638 0.950491569 0.025667318 13.82743009 -1.140741471 0.489877312 S(ph)LESVLSLGPRPTGGGS(ph)SPPEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLESVLSLGPRPTGGGSSPPEIR 23 1 Q13470-2;Q13470 Q13470-2 TNK1 Non-receptor tyrosine-protein kinase TNK1 2 S(0.999)LESVLS(0.001)LGPRPT(0.002)GGGS(0.647)S(0.351)PPEIR;S(1)LES(0.04)VLS(0.002)LGPRPT(0.161)GGGS(0.426)S(0.372)PPEIR;S(0.999)LES(0.014)VLS(0.012)LGPRPT(0.188)GGGS(0.415)S(0.372)PPEIR;S(1)LES(0.005)VLS(0.002)LGPRPT(0.259)GGGS(0.395)S(0.339)PPEIR 128.01 2.50E-05 820943000 847100 755150 494749 546247 812900 775240 773600 880490 645303 TRUE FALSE 735153.5887 750189.3699 734011.2712 670280.7302 796724.8804 805063.9844 698576.3911 692204.0655 569016.0145 1.291973459 1.318397639 1.289965928 1.177964615 1.400180065 1.414835372 1.227691969 1.216493118 1 19.11810973 1.127185257 1.47826347 0.805663362 1.308739265 0.663415581 0.068705442 1.003359824 1.569264348 0.814784329 0.020575816 13.40248275 -1.127185257 0.503075902 S(ph)LGGAVGSVASGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLGGAVGSVASGAR 14 0 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 S(1)LGGAVGSVASGAR;S(1)LGGAVGSVASGAR;S(1)LGGAVGSVASGAR 153.51 6.69E-06 1034840000 386578 289141 200191 349680 437100 289627 340846 407760 412600 TRUE FALSE 335490.7378 287241.6137 297004.0372 429080.1885 428402.5652 300769.1381 307790.8074 320563.6972 363822.898 0.922126506 0.789509443 0.816342343 1.17936554 1.177503031 0.826691062 0.845990753 0.881098191 1 18.47287682 6.273093519 13.9300221 0.932695101 0.440749843 0 0.14176495 0 0 0.033972942 0 1875398.303 -6.273093519 -0.491945258 S(ph)LGSPLLHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLGSPLLHER 10 0 E7EV32;E7EMT6;E7ENY2;E7EVA2;E7EW82;H7C3L4;E7EQA9;Q92844 E7EV32 TANK TRAF family member-associated NF-kappa-B activator 1 S(0.563)LGS(0.437)PLLHER 90.731 0.0068478 361630000 330640 360970 182320 192140 313560 387260 258840 279880 257320 TRUE FALSE 286945.0863 358598.7643 270490.5618 235768.3237 307320.7695 402158.1428 233737.7366 220029.84 226899.9227 1.264632807 1.580427 1.192113944 1.039085077 1.354433116 1.772403172 1.030135814 0.96972197 1 17.79169659 2.035554067 24.99997454 0.98786688 1.357412005 0.429219502 0.199917245 163.3306803 114845.9309 0.083971656 0.056613472 108.5310656 -2.035554067 0.369545125 S(ph)LGSVQAPSYGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLGSVQAPSYGAR 13 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.999)LGS(0.001)VQAPSYGAR 117.76 0.00050474 168870000 83266 94999 65336 62840 90787 101530 88900 97427 129390 TRUE FALSE 72262.18713 94374.94531 96932.70814 77108.78245 88980.51632 105435.9248 80278.49168 76592.99423 114093.6616 0.633358472 0.8271708 0.849588897 0.675837565 0.779890093 0.924117285 0.703619207 0.671316821 1 16.79985912 4.747767622 23.36956493 0.789305522 0.633358263 0.191660753 0.10638575 904.1721399 2294877.084 0.025624265 0.291915256 55945.81727 -4.747767622 -0.155947258 S(ph)LHGPCPVTTFGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLHGPCPVTTFGPK 14 0 O95544;O95544-2 O95544 NADK NAD kinase 1 S(0.999)LHGPCPVT(0.001)TFGPK;S(1)LHGPCPVTTFGPK 98.531 0.0016367 585480000 709870 655840 320200 605940 566820 361770 946780 780500 847960 TRUE FALSE 616058.8809 651531.7439 475049.791 743527.9382 555541.391 375687.526 854961.4213 613596.1489 747715.1348 0.823921909 0.87136359 0.635335262 0.994400011 0.74298535 0.502447401 1.143432012 0.820628232 1 19.51212921 2.221852405 24.99994382 0.959622165 0.77070195 0.322747639 0.152313561 331.1398037 495469.8077 0.060217356 0.040722559 166.6680695 -2.221852405 -0.188920215 S(ph)LHS(ph)AHSLASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLHSAHSLASR 11 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 2 S(1)LHS(1)AHSLASR;S(1)LHS(0.999)AHS(0.001)LASR;S(1)LHS(0.999)AHS(0.001)LASR;S(1)LHS(0.999)AHS(0.001)LASR;S(1)LHS(0.998)AHS(0.002)LASR;S(1)LHS(1)AHSLASR 147.1 1.87E-05 6945640000 5935840 5223950 3006168 4376940 4951960 4274980 4729900 5751510 4187080 TRUE FALSE 5151403.704 5189633.528 4459960.9 5370791.124 4853425.684 4439441.247 4271195.026 4521594.345 3692088.172 1.395254789 1.405609315 1.207977895 1.454675748 1.31454761 1.202420159 1.156850765 1.224671279 1 21.81600558 -0.608764287 0.30158625 5.47E-11 1.406582177 0.666577039 0.078379517 21.92410633 0.757370117 13.82605157 0.167300733 0.246170333 0.608764287 1.406582177 S(ph)LHSAHSLASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLHSAHSLASR 11 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 S(0.999)LHS(0.001)AHSLASR;S(1)LHSAHSLASR;S(0.998)LHS(0.002)AHSLASR;S(1)LHSAHSLASR;S(1)LHSAHSLASR;S(0.999)LHS(0.001)AHSLASR 199.13 3.30E-08 3130566000 794634 820046 414961 596165 880750 803720 717041 812540 723212 TRUE FALSE 689621.1036 814659.0638 615637.5276 731533.3751 863224.7982 834639.6285 647502.4742 638784.6442 637714.7012 1.081394395 1.277466338 0.965380799 1.147117 1.353622233 1.308797848 1.0153482 1.001677777 1 19.28255161 2.145863843 8.941824142 1.003732869 1.188239271 0.373733145 0.111900349 0.310508061 26.9916135 0.047762147 0.032182497 139.9148604 -2.145863843 0.184506402 S(ph)LIVEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 105.4 0.0083246 659010000 2100500 1737710 1575040 1961980 1634850 1578990 1823010 2165370 4476100 TRUE FALSE 1822913.603 1726294.869 2336734.612 2407477.546 1602319.684 1639734.767 1646214.771 1702322.476 3946940.557 0.461854841 0.437375441 0.592036941 0.609960427 0.40596499 0.415444505 0.417086284 0.431301777 1 21.91230336 1.236004874 24.99888299 1.000000699 0.470201227 0.8409325 0.072251694 28.9236096 282855.2572 0.127923727 0.019308847 17.218879 -1.236004874 -0.529799472 S(ph)LLQSEQQPSWTDDLPLCHLSGVGSASNR ddPTM_MDA-MB-175_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(1)LLQSEQQPSWTDDLPLCHLSGVGSASNR;S(0.999)LLQS(0.001)EQQPSWTDDLPLCHLSGVGSASNR;S(1)LLQSEQQPSWTDDLPLCHLSGVGSASNR 361.66 6.47E-121 1487090000 86864 114771 37783.8 68608 182770 196325 122525 159820 135928 TRUE FALSE 75384.70231 114017.0617 56056.17206 84186.49501 179133.2346 203877.7498 110642.5444 125643.7367 119858.7467 0.628946192 0.951261922 0.467685285 0.702380905 1.49453619 1.700983494 0.923107803 1.048265064 1 16.87097567 3.261873143 24.09038282 1.210349187 0.69069735 0.525186832 0.257355782 141.8981355 146631.2686 0.080225267 0.103492448 1827.566307 -3.261873143 -0.519651837 S(ph)LNLVDSPQPLLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLNLVDSPQPLLEK 14 0 P46019 P46019 PHKA2 "Phosphorylase b kinase regulatory subunit alpha, liver isoform" 1 S(1)LNLVDSPQPLLEK 168.42 3.66E-06 28771000 118280 80072 66396 91148 82994 69846 125610 98844 116160 TRUE FALSE 102648.9983 79546.00176 98505.32768 111844.5465 81342.58178 72533.02082 113428.3615 77706.9798 102427.6971 1.00216056 0.776606367 0.961705969 1.091936553 0.79414635 0.708138744 1.107399314 0.758652025 1 16.64424636 S(ph)LPAFPTSSLLTQSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLPAFPTSSLLTQSQK 16 0 Q99698 Q99698 LYST Lysosomal-trafficking regulator 1 S(0.998)LPAFPT(0.001)SSLLTQSQK;S(1)LPAFPTSSLLTQSQK 185.02 1.81E-09 211942000 265440 243870 193642 249719 278980 227208 285650 332320 491460 TRUE FALSE 230361.4315 242268.0019 287287.9189 306421.5157 273428.8438 235948.8388 257947.707 261255.9541 433360.1587 0.531570397 0.559045397 0.662931082 0.707082803 0.630950581 0.544463615 0.595227092 0.602861036 1 18.725207 1.238250432 24.99999947 1.000000437 0.606375027 0.843862227 0.053489437 3.025143263 243423.2013 0.07968205 0.014037482 17.30814132 -1.238250432 -0.39362541 S(ph)LPAGDALYLSFNPPQPSR ddPTM_MDA-MB-175_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 277.98 1.66E-39 6631904000 396939 405747 307253 344499 427082 489080 461234 475977 431457 TRUE FALSE 344482.5054 403081.6212 455841.5785 422722.7633 418583.9038 507895.2241 416503.5977 374193.0226 380450.645 0.905459118 1.059484657 1.198162191 1.11111065 1.100231815 1.334983212 1.09476381 0.983552078 1 18.53734978 1.800354435 4.938777308 0.992622989 1.124900932 0.184522814 0.107124768 0.321697099 14.21162161 0.061865714 0.029258299 63.14724891 -1.800354435 0.132277942 S(ph)LPEEDVAEIQHAEEFLIKPESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLPEEDVAEIQHAEEFLIKPESK 23 1 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 S(1)LPEEDVAEIQHAEEFLIKPESK;S(1)LPEEDVAEIQHAEEFLIKPESK 326.01 6.09E-75 352850000 208672 182574 141231 152860 164989 122862 204710 275136 257071 TRUE FALSE 181095.4665 181374.6594 209530.784 187569.1993 161706.0417 127588.5806 184857.2557 216300.3075 226680.3592 0.798902327 0.800133986 0.924344679 0.827461188 0.713365914 0.562856796 0.815497453 0.95420842 1 17.79029987 1.72727328 3.597578521 0.986249152 0.773514681 0.456336409 0.091855951 0.193273732 5.501043105 0.070867132 0.027172145 53.36706024 -1.72727328 -0.212734471 S(ph)LPELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLPELDR 7 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 S(1)LPELDR;S(1)LPELDR 139.78 0.0027993 231810000 309710 273150 263150 314240 207299 258450 223310 264470 461240 TRUE FALSE 268781.0388 271355.6597 390410.2202 385592.9949 203174.1555 268392.7387 201653.4306 207915.1486 406712.7326 0.66086212 0.667192438 0.959916395 0.948072101 0.499551991 0.659907392 0.495812927 0.511208851 1 18.63365063 4.443936817 24.99181046 0.699326249 0.662441662 0.003531279 0.193923911 1782.205117 1342209.71 0.051724504 0.136851264 27793.08893 -4.443936817 -0.036884587 S(ph)LPGSALELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLPGSALELR 10 0 O75145-2;O75145;R4GN36 O75145-2 PPFIA3 Liprin-alpha-3 1 S(0.997)LPGS(0.003)ALELR;S(0.997)LPGS(0.003)ALELR 115.65 0.0012537 172140000 166023 152311 129210 101136 132123 153267 113890 140547 161308 TRUE FALSE 144082.6399 151310.459 191696.3882 124100.4746 129494.0108 159163.2807 102844.9653 110492.1178 142238.352 1.012966179 1.063781019 1.347712382 0.872482511 0.910401512 1.11898991 0.72304666 0.776809603 1 17.11795099 3.067599497 0.970905897 0.840248622 1.117989963 0.27147955 0.152352496 0.64816862 1.40701596 0.086104734 0.100279471 1168.421386 -3.067599497 0.27774134 S(ph)LPGSPEFLHQEACPFVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLPGSPEFLHQEACPFVGR 19 0 Q96S53-3;Q96S53-2;Q96S53 Q96S53-3 TESK2 Dual specificity testis-specific protein kinase 2 1 S(0.999)LPGS(0.001)PEFLHQEACPFVGR;S(0.967)LPGS(0.033)PEFLHQEACPFVGR;S(1)LPGSPEFLHQEACPFVGR 267.8 6.80E-32 594689000 61222.7 54478.5 38435 41966 47200 66547.4 50242 54161 71355 TRUE FALSE 53131.96508 54120.62715 57022.29456 51495.02171 46260.81235 69107.52154 45369.53857 42579.09163 62919.49319 0.844443628 0.860156756 0.906273901 0.818427154 0.735238159 1.09834835 0.721072855 0.676723373 1 15.94121943 S(ph)LPITIEMLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLPITIEMLK 10 0 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 S(1)LPITIEMLK 142.08 3.82E-05 159290000 232930 288870 169380 230250 224600 220880 192950 254780 375020 TRUE FALSE 202147.7103 286972.3939 251292.7345 282531.7817 220130.8994 229377.3965 174237.7387 200297.2797 330685.5628 0.611298868 0.867810471 0.759914441 0.854381967 0.665680405 0.693642004 0.526898535 0.605703128 1 18.33510054 3.212147319 24.79618212 0.673700944 0.779138739 0.050457592 0.139511739 440.8934076 413898.7683 0.041656654 0.047248271 1629.848809 -3.212147319 0.105437795 S(ph)LPNLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLPNLSR 7 0 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 S(1)LPNLSR;S(1)LPNLSR;S(1)LPNLSR;S(0.999)LPNLS(0.001)R;S(0.999)LPNLS(0.001)R;S(1)LPNLSR 109.88 0.015928 1817090000 2310160 1672233 1269251 1370089 1461376 1743034 1756620 1680878 1924533 TRUE FALSE 2004866.503 1661247.991 1883065.029 1681188.648 1432297.477 1810089.646 1586263.263 1321435.32 1697016.901 1.181406326 0.978922479 1.109632454 0.990672896 0.844008964 1.0666303 0.934736279 0.778681296 1 20.6945695 7.999999997 0.248551074 0.855205775 2.709574758 0.396226563 0.091937642 83.14230243 1.319246889 0.308756724 62.53805194 99999999.3 -7.999999997 1.854368983 S(ph)LPRPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 70.256 0.034835 250220000 354500 379730 259980 258050 331900 368050 369610 415560 640830 TRUE FALSE 307651.9268 377235.5286 385707.1976 316644.1965 325295.8394 382209.1217 333765.2791 326695.7279 565071.8074 0.544447489 0.667588656 0.682580855 0.560360988 0.575671685 0.676390357 0.590659939 0.578149049 1 19.10807469 1.235645589 24.99806317 1.000000526 0.610729767 0.858558104 0.049811392 28.70067666 246078.8832 0.082351662 0.012100448 17.20463997 -1.235645589 -0.389270759 S(ph)LPS(ph)SPERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLPSSPERR 9 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 2 S(1)LPS(0.59)S(0.41)PERR;S(0.994)LPS(0.568)S(0.438)PERR 142.12 0.00036778 2814640000 1357720 1161750 917170 1065780 1290400 1402180 1059480 1444130 1495090 TRUE FALSE 1178293.862 1154118.388 1360716.48 1307781.638 1264723.565 1456122.772 956731.7927 1135314.038 1318342.163 0.893769383 0.875431599 1.032142123 0.991989542 0.959328769 1.104510507 0.725708256 0.861167965 1 20.33029343 2.238636634 25 0.856366918 0.974109431 0.256512342 0.091182054 2.743080732 902596.6272 0.035801785 0.025927778 173.2353962 -2.238636634 0.117742513 S(ph)LPSASTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLPSASTSK 9 0 C9J0A7;Q9UQN3;Q9UQN3-2 C9J0A7 CHMP2B Charged multivesicular body protein 2b 1 S(0.88)LPS(0.117)AS(0.002)TSK 83.081 0.017245 0 368880 346170 247130 336960 409160 378690 525930 593230 656840 TRUE FALSE 320131.5734 343895.9865 366642.8946 413471.9181 401018.5165 393258.4493 474925.3895 466372.381 579189.1235 0.552723731 0.59375422 0.633027935 0.713880668 0.692379225 0.678981068 0.819983267 0.805216055 1 19.14367498 -2 0.265346355 3.443301894 0.552135726 0.898579361 0.041060836 24.15983282 0.389770345 30.98450585 0.114534264 0.01 2 -2.891166168 S(ph)LPSHMEEAPNVFQLYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLPSHMEEAPNVFQLYQR 18 0 Q5THJ4-2;Q5THJ4;H3BLS7 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 S(1)LPSHMEEAPNVFQLYQR;S(0.999)LPS(0.001)HMEEAPNVFQLYQR;S(0.955)LPS(0.045)HMEEAPNVFQLYQR;S(0.998)LPS(0.002)HMEEAPNVFQLYQR 303.84 5.39E-50 561400000 292346 263796 240321 275955 286546 310449 242163 316746 542890 TRUE FALSE 253711.7354 262063.1067 356541.0394 338614.8005 280844.2952 322392.1739 218678.0695 249012.3328 478710.1627 0.529990285 0.547435854 0.744795217 0.70734826 0.586668755 0.673460058 0.456806825 0.520173483 1 18.86879291 1.232114072 24.9948057 1.000000679 0.594537956 0.667015797 0.089739763 147.4429784 571616.8955 0.221306426 0.023889464 17.06530567 -1.232114072 -0.405462723 S(ph)LPSHMEEAPNVFQLYQRPTSASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLPSHMEEAPNVFQLYQRPTSASR 24 1 Q5THJ4-2;Q5THJ4;H3BLS7 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 S(0.942)LPS(0.058)HMEEAPNVFQLYQRPTSASR;S(1)LPSHMEEAPNVFQLYQRPTSASR 268.83 4.65E-45 352593000 44317 55351 36151 33606 49837 65118 66568 63732 43088 TRUE FALSE 38460.39617 54987.39564 53633.74452 41236.75594 48845.3412 67623.1316 60112.24561 50103.40776 37994.18573 1.012270573 1.447258168 1.411630319 1.085343853 1.285600422 1.779828421 1.582143279 1.318712503 1 15.21349104 2.972087081 24.989839 1.432082082 1.256208759 0.117485742 0.233892154 1667.23001 1492635.889 0.077677871 0.077859616 937.7500186 -2.972087081 -0.175873324 S(ph)LPSS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLPSSPER 8 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 2 S(1)LPS(0.186)S(0.814)PER;S(1)LPS(0.37)S(0.63)PER;S(1)LPS(0.072)S(0.928)PER;S(1)LPS(0.407)S(0.593)PER 125.54 0.0018385 2306680000 3500840 2986220 2312020 2859230 3021680 3240770 2811870 3633740 5980900 TRUE FALSE 3038195.124 2966603.324 3430120.605 3508461.872 2961554.48 3365444.519 2539175.28 2856692.979 5273844.815 0.57608732 0.562512442 0.650402263 0.665256942 0.561555105 0.638138708 0.48146568 0.541671793 1 22.33042369 1.235140774 24.99875933 1.000000583 0.58262006 0.84883293 0.055081078 38.53092505 281611.9939 0.102114192 0.014418385 17.18465328 -1.235140774 -0.417380523 S(ph)LPSS(ph)PERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLPSSPERR 9 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 2 S(1)LPS(0.036)S(0.964)PERR;S(1)LPS(0.203)S(0.797)PERR 133.04 0.0010084 3604080000 1286840 1046400 780370 955290 1221370 1242840 1030550 1244850 1283510 TRUE FALSE 1116780.834 1039526.13 1157759.542 1172203.195 1197067.127 1290652.859 930607.4196 978648.5149 1131774.91 0.986751715 0.918491937 1.022959187 1.035721136 1.057690108 1.140379459 0.82225486 0.86470243 1 20.11015563 2.224497777 24.99963903 0.886146285 1.023674698 0.432373577 0.070595938 221.2081738 393240.7566 0.030116854 0.02041682 167.6863753 -2.224497777 0.137528413 S(ph)LPSS(ph)PLLTHQSISVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLPSSPLLTHQSISVR 16 0 J3QQY7;J3KTM5 J3QQY7 TANC2 2 S(0.949)LPS(0.27)S(0.781)PLLTHQSISVR 88.951 0.0031457 159390000 101390 123750 80117 78689 123290 149610 91134 110990 102900 TRUE FALSE 87991.05461 122937.0781 118861.8492 96556.54014 120836.7702 155365.5935 82295.83871 87255.65223 90735.27922 0.969755704 1.354898328 1.309984939 1.064156533 1.331750684 1.712295315 0.906988323 0.961650782 1 16.46937598 S(ph)LPSSPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLPSSPER 8 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 S(0.966)LPS(0.03)S(0.004)PER;S(0.998)LPS(0.002)SPER;S(1)LPSSPER;S(0.962)LPS(0.038)SPER 152.37 0.00048061 1401400000 1236710 1090280 923190 965150 1026510 1080120 1122010 1317440 1545790 TRUE FALSE 1073275.64 1083117.879 1369647.772 1184302.059 1006084.459 1121672.915 1013197.643 1035715.708 1363048.467 0.787408273 0.794629028 1.004841577 0.868862764 0.738113489 0.822914916 0.743332073 0.759852443 1 20.37840543 3.325474497 17.51833049 0.80151014 0.869070744 0.059668065 0.094068322 5.685722034 1138.46855 0.027095798 0.034980374 2115.799437 -3.325474497 0.067560604 LSEEAECPNPST(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSEEAECPNPSTPSK 15 0 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 LSEEAECPNPS(0.016)T(0.983)PS(0.001)K;LSEEAECPNPS(0.17)T(0.829)PS(0.002)K 298.93 3.85E-43 304740000 285120 390010 322030 455190 525180 417070 623810 715530 642310 TRUE FALSE 247440.6696 387447.9986 477764.7851 558547.8466 514729.9455 433114.9528 563313.0022 562519.4778 566376.8435 0.43688345 0.684081638 0.84354576 0.986177053 0.908811777 0.764711619 0.994590454 0.993189401 1 19.11140276 4.628111052 1.270520876 0.944814391 0.270138208 0.84555947 0.070697058 0.456704436 0.7472128 0.022486609 0.382625466 42472.81559 -4.628111052 -0.674676182 down VADPDHDHTGFLTEY(ph)VATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 VADPDHDHTGFLTEYVATR 19 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 1 VADPDHDHTGFLT(0.084)EY(0.915)VATR;VADPDHDHTGFLTEY(1)VATR;VADPDHDHTGFLT(0.207)EY(0.793)VATR;VADPDHDHTGFLTEY(1)VATR;VADPDHDHTGFLT(0.173)EY(0.827)VATR;VADPDHDHTGFLTEY(1)VATR;VADPDHDHTGFLTEY(1)VATR;VADPDHDHTGFLT(0.328)EY(0.672)VATR;VADPDHDHTGFLTEY(1)VATR 251.35 4.36E-26 28450330000 4369040 8082050 5910020 9521470 12780300 12079570 11851340 14100300 12180500 TRUE FALSE 3791660.294 8028958.481 8768125.44 11683465.29 12525997.03 12544278.87 10701998.87 11085060.57 10740535.17 0.353023405 0.747538028 0.816358338 1.087791726 1.166235838 1.167937973 0.996412069 1.032077117 1 23.35656254 4.631973801 1.124703449 1.072794047 0.109523362 0.903329583 0.075887824 0.430296091 0.520961114 0.025670088 0.470788169 42852.26684 -4.631973801 -0.963270685 down S(ph)LPVSICR ddPTM_MDA-MB-175_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 160.36 0.00037112 2241350000 888300 955560 620340 739840 1081200 956280 983230 1154340 1037250 TRUE FALSE 770908.9043 949282.8634 920338.4989 907831.9797 1059686.235 993068.7104 887876.5059 907493.3741 914627.4866 0.842866539 1.037890155 1.006244086 0.992570192 1.15859872 1.085763029 0.970752048 0.99219998 1 19.80282475 4.740361825 24.41881671 1.028495587 0.842866454 0.531619908 0.055321378 102.6277197 1391157.239 0.014544116 0.09059244 54999.89046 -4.740361825 -0.185629133 GAS(ph)TVSSSSSTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 GASTVSSSSSTK 12 0 Q5VTQ0-2;Q5VTQ0-3;Q5VTQ0-4;Q5VTQ0 Q5VTQ0-2 TTC39B Tetratricopeptide repeat protein 39B 1 GAS(0.985)T(0.015)VSSSSSTK;GAS(0.5)T(0.5)VSSSSSTK;GAS(0.863)T(0.137)VSSSSSTK;GAS(0.88)T(0.119)VSSSSSTK;GAS(0.963)T(0.037)VSSSSSTK 248.91 8.32E-17 792968000 561544 961336 962675 1035114 1317170 1531416 1758820 2034410 2130320 TRUE FALSE 487334.5376 955020.9205 1428227.85 1270152.454 1290960.894 1590330.564 1588249.907 1599367.253 1878475.996 0.259430804 0.508401982 0.760312004 0.676161131 0.68723843 0.846606807 0.845499176 0.851417456 1 20.84113125 4.650976192 0.548709685 0.888477239 1.48E-33 0.854246578 0.079345022 1.558567151 0.404785785 0.055239796 0.885255054 44768.87617 -4.650976192 -0.888477239 down S(ph)LQEEHVAVAQLR ddPTM_MDA-MB-175_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 147.17 2.75E-05 475880000 486940 301080 151152 252340 258770 156268 357090 281570 252330 TRUE FALSE 422589.6453 299102.1857 224249.6128 309637.6538 253620.9833 162279.7311 322459.4668 221358.4467 222499.8349 1.899280714 1.344280484 1.007864176 1.391630938 1.139870434 0.729347647 1.449257106 0.994870162 1 17.76344474 4.69226772 2.431441281 1.108528757 2.036722529 0.600153835 0.205448258 0.31999982 2.519792869 0.050360724 0.594487734 49234.29462 -4.69226772 0.928193772 S(ph)LQLMDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLQLMDNR 8 0 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 S(1)LQLMDNR;S(1)LQLMDNR;S(1)LQLMDNR;S(1)LQLMDNR;S(1)LQLMDNR;S(1)LQLMDNR 121.02 0.0015221 2895020000 5410170 5621080 4088620 3882990 6223330 7318450 5201880 5984000 6073570 TRUE FALSE 4695202.327 5584154.755 6065890.308 4764682.227 6099497.909 7599995.507 4697402.478 4704368.168 5355559.474 0.876696889 1.042683735 1.132634291 0.889670304 1.138909565 1.41908526 0.877107705 0.878408351 1 22.35260586 S(ph)LQLPAS(ph)PAPDPSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLQLPASPAPDPSPR 15 0 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 2 S(1)LQLPAS(1)PAPDPSPR 79.837 0.012644 0 53445 50200 36683 44601 62784 53185 56552 69008 94817 TRUE FALSE 46382.10784 49870.23289 54423.0215 54728.33873 61534.72123 55231.06137 51067.59574 54251.17622 83607.84228 0.554757862 0.596477932 0.650932018 0.654583796 0.735992217 0.66059666 0.610799111 0.648876645 1 16.35135065 1.238873595 7.152238197 1.007018083 0.640969879 0.852579353 0.047166484 0.041033601 12.93893483 0.0730225 0.012350195 17.33299433 -1.238873595 -0.366048204 S(ph)LQLPASPAPDPSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLQLPASPAPDPSPR 15 0 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 S(1)LQLPASPAPDPSPR;S(0.996)LQLPAS(0.004)PAPDPSPR;S(1)LQLPASPAPDPSPR;S(1)LQLPASPAPDPSPR;S(1)LQLPASPAPDPSPR;S(1)LQLPASPAPDPSPR 211.9 1.20E-09 1976679000 1009248 951436 794649 874778 1048020 1056919 1040582 1115704 1956570 TRUE FALSE 875873.3197 945185.9543 1178943.914 1073409.715 1027166.452 1097579.358 939666.5178 877119.382 1725266.524 0.50767421 0.54784924 0.683340167 0.622170372 0.595366825 0.636179595 0.544650061 0.508396454 1 20.71838782 1.232449525 24.9999985 1.000000686 0.58129239 0.845801724 0.056263328 82.98450789 339449.2042 0.133765006 0.014918894 17.07849216 -1.232449525 -0.418708296 S(ph)LQLPASPAPDPSPRPAYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLQLPASPAPDPSPRPAYK 19 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 S(1)LQLPASPAPDPSPRPAYK;S(1)LQLPASPAPDPSPRPAYK 175.47 1.52E-12 1551370000 2292760 1981480 947170 1054130 1875890 1829090 2618500 2645070 556660 TRUE FALSE 1989765.957 1968463.527 1405224.58 1293486.328 1838563.459 1899456.276 2364558.273 2079442.364 490852.2889 4.053695993 4.010297134 2.862825766 2.635184468 3.745655262 3.869710539 4.817250171 4.236391296 1 18.90492942 3.09293026 21.18282768 3.735036042 3.371248896 0 1.085035352 28.91754392 6561.729877 0.334810674 0.379640488 1238.597674 -3.09293026 -0.363787146 S(ph)LQQLAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SLQQLAEER 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 S(1)LQQLAEER;S(1)LQQLAEER;S(1)LQQLAEER;S(1)LQQLAEER;S(1)LQQLAEER 184.43 4.62E-05 3447110000 987410 819062 696698 686754 767502 969820 818590 793390 1339660 TRUE FALSE 856921.2667 813681.5278 1033623.483 842691.9921 752230.2118 1007129.603 739203.2678 623729.7227 1181286.921 0.72541332 0.688809394 0.874997822 0.713367749 0.636788742 0.852569842 0.625760985 0.528008659 1 20.17192799 2.196777352 24.99880526 0.674517656 0.744991695 0 0.13924531 488.747876 292413.0152 0.055683696 0.037542312 157.3176143 -2.196777352 0.070474039 S(ph)LQTLPTDSSTFDTDTFCPPRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLQTLPTDSSTFDTDTFCPPRPK 23 1 B0QY95;Q9NQG6 B0QY95 MIEF1 Mitochondrial dynamics protein MID51 1 S(0.999)LQT(0.001)LPTDSSTFDTDTFCPPRPK 199.92 1.53E-24 527030000 362780 305590 233510 297000 308410 216240 307780 354130 592390 TRUE FALSE 314837.7038 303582.5592 346436.217 364438.3894 302273.2444 224558.8927 277931.543 278402.0553 522358.3291 0.602723622 0.581176833 0.663215647 0.697678909 0.578670287 0.429894347 0.532070664 0.53297141 1 18.99468029 1.235103806 24.99988975 1.000000594 0.575106368 0.766710986 0.073267794 52.99389705 383193.6897 0.141547093 0.019925117 17.18319054 -1.235103806 -0.424894226 S(ph)LQTLPTDSSTFDTDTFCPPRPKPVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLQTLPTDSSTFDTDTFCPPRPKPVAR 27 2 B0QY95;Q9NQG6 B0QY95 MIEF1 Mitochondrial dynamics protein MID51 1 S(1)LQTLPTDSSTFDTDTFCPPRPKPVAR;S(1)LQTLPTDSSTFDTDTFCPPRPKPVAR 231.45 1.67E-35 407800000 641000 602020 266760 297130 503640 474500 572220 650850 160843 TRUE FALSE 556290.2259 598065.291 395766.0283 364597.9078 493618.5494 492754.322 516726.1925 511670.7924 141828.3238 3.922278788 4.216825491 2.790458335 2.570698843 3.480394721 3.474301246 3.643321579 3.607677076 1 17.11378615 4.242831896 24.99709242 3.061075878 4.069552473 0.252240951 0.788069614 159.4888099 933352.7921 0.196269396 0.482562525 17491.69501 -4.242831896 1.008476595 S(ph)LQTLPTDSSTFDTGETSYLLPEPGSHPCWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLQTLPTDSSTFDTGETSYLLPEPGSHPCWR 31 0 Q9NQG6-2 Q9NQG6-2 MIEF1 Mitochondrial dynamics protein MID51 1 S(0.738)LQT(0.218)LPT(0.027)DS(0.005)S(0.005)T(0.005)FDTGETSYLLPEPGSHPCWR 56.547 0.03054 45753000 10265 10449 5112.7 8479.3 12159 12858 9420.3 13211 14443 TRUE FALSE 8908.454242 10380.35983 7585.218821 10404.65466 11917.05969 13352.65558 8506.720756 10385.93046 12735.56499 0.699494231 0.815068655 0.595593429 0.816976292 0.935730743 1.048454119 0.667950009 0.815506062 1 13.63657534 3.488348662 22.65122522 0.874762493 0.713175561 0.353552054 0.115589316 201.4215034 406365.9232 0.033456165 0.046452044 3078.56737 -3.488348662 -0.161586932 S(ph)LS(ph)PGVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.996)PGVS(0.004)R 120.32 0.0022297 1687390000 2250610 1821810 1406250 1866810 2134570 1831430 1752320 2210120 3532410 TRUE FALSE 1953186.186 1809842.41 2086317.204 2290697.743 2092096.233 1901886.297 1582380.276 1737503.037 3114812.514 0.627063805 0.581043771 0.669805067 0.735420746 0.671660405 0.610594149 0.508017824 0.557819461 1 21.5707139 1.233123326 25 1.000000604 0.617236108 0.777853977 0.063772774 93.46836686 429708.9967 0.151164488 0.01796798 17.10500973 -1.233123326 -0.382764495 S(ph)LS(ph)PKPR ddPTM_MDA-MB-175_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 135.43 0.0017515 1660110000 3803650 2680610 2167120 2160340 2842920 2349620 3163530 3797010 4088220 TRUE FALSE 3300988.015 2663000.896 3215146.481 2650878.216 2786351.454 2440011.402 2856731.348 2985048.96 3604915.289 0.915690869 0.738713862 0.891878511 0.735351042 0.772931187 0.676856793 0.792454501 0.828049682 1 21.78153393 1.207661295 2.440726226 1.066872232 0.784743222 0.462832564 0.070780203 0.540786524 3.233884282 0.3367986 0.017970421 16.13100013 -1.207661295 -0.28212901 S(ph)LSAPLHPEFEEVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSAPLHPEFEEVYR 15 0 Q53HC0-2;Q53HC0 Q53HC0-2 CCDC92 Coiled-coil domain-containing protein 92 1 S(0.553)LS(0.447)APLHPEFEEVYR;S(0.544)LS(0.456)APLHPEFEEVYR 108.49 0.00069226 135764000 269710 226717 98941 180969 189053 141337 298750 228510 219056 TRUE FALSE 234067.1401 225227.6811 146789.1985 222060.7774 185291.2152 146774.3258 269777.271 179644.9148 193159.4492 1.211781982 1.166019483 0.759937964 1.1496242 0.959265601 0.759860967 1.39665583 0.930034308 1 17.55943273 4.450004882 24.98290276 1.002697107 1.200341862 0.164956656 0.183180775 319.7253345 294569.6508 0.043096738 0.114029133 28184.14613 -4.450004882 0.197644756 S(ph)LSDPIPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSDPIPQR 9 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 S(0.62)LS(0.38)DPIPQR 73.067 0.047173 164390000 281760 237860 149050 188220 248960 231310 216210 266080 231460 TRUE FALSE 244524.7021 236297.482 221131.0785 230958.2278 244006.1831 240208.6454 195241.9875 209180.8626 204097.0625 1.198080458 1.157770127 1.083460369 1.131609759 1.195539907 1.176933379 0.956613413 1.024908738 1 17.63889589 2.2429787 24.99999987 0.998762074 1.154480113 0.814536166 0.036712756 47.3530651 267952.2465 0.014772473 0.011038238 174.9760871 -2.2429787 0.155718038 S(ph)LSDSESDDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 S(0.95)LS(0.042)DS(0.008)ESDDSK;S(0.977)LS(0.009)DS(0.014)ESDDSK;S(0.998)LS(0.002)DSESDDSK;S(0.988)LS(0.01)DS(0.003)ESDDSK;S(0.974)LS(0.026)DSESDDSK;S(0.982)LS(0.018)DSESDDSK 343.61 2.00E-58 4471010000 8020490 4985280 4961190 5404910 4509810 4647090 6667340 7406920 10648260 TRUE FALSE 6960561.925 4952531.367 7360438.078 6632177.424 4420073.604 4825866.559 6020742.393 5823007.799 9389434.833 0.741318519 0.527457877 0.783906402 0.706344689 0.470749697 0.513967736 0.641225217 0.620165953 1 23.16260689 1.238374943 24.99999867 1.000000411 0.62218502 0.576575752 0.1007819 3.295648496 442542.6955 0.138930179 0.024676818 17.31310419 -1.238374943 -0.377815391 S(ph)LSGS(ph)SPCPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)LS(0.009)GS(0.783)S(0.208)PCPK 116.74 0.001536 369230000 748860 584080 411910 475510 577210 514540 678510 823700 738600 TRUE FALSE 649896.2536 580243.14 611111.0538 583481.8132 565724.6503 534334.6868 612708.2046 647558.165 651283.5494 0.997869905 0.890922457 0.938317964 0.895895211 0.868630339 0.820433262 0.940770276 0.994279935 1 19.31292626 1.881949688 3.793997368 0.995322302 0.9001646 0.416342432 0.045715629 0.222767857 5.277198878 0.027058315 0.012674154 76.19907294 -1.881949688 -0.095157703 S(ph)LSGSS(ph)PCPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)LSGS(0.129)S(0.871)PCPK;S(1)LSGSS(1)PCPK;S(0.998)LS(0.094)GS(0.179)S(0.729)PCPK;S(1)LSGS(0.005)S(0.995)PCPK 185.37 2.13E-06 2894640000 5113300 3974750 2921910 3132340 4068400 3395110 4779120 5431270 4881190 TRUE FALSE 4437564.45 3948639.606 4334955.449 3843585.672 3987446.8 3525722.079 4315641.678 4269835.177 4304141.279 1.03099879 0.917404739 1.007159191 0.892997098 0.926420984 0.819146457 1.002671938 0.992029513 1 22.037294 S(ph)LSLESTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSLESTDR 9 0 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 1 S(0.973)LS(0.026)LESTDR 101.48 0.004147 366850000 87950 87879 79647 82266 96826 95608 86681 102640 108040 TRUE FALSE 76327.18466 87301.71706 118164.5556 100945.7527 94899.35204 99286.10163 78274.68996 80691.23475 95267.63428 0.801186943 0.916383804 1.240343129 1.059601757 0.996134235 1.042180824 0.821629408 0.846995261 1 16.53969854 2.246498689 24.9972529 0.877848068 1.017270695 0.17833824 0.119500998 268.6789904 846081.3061 0.046944393 0.035691834 176.4000441 -2.246498689 0.139422627 S(ph)LSLSLADSGHLPDVHGFNSYGSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSLSLADSGHLPDVHGFNSYGSHR 25 0 Q9Y446;Q9Y446-2;E9PKC4;E9PRW6 Q9Y446 PKP3 Plakophilin-3 1 S(0.976)LS(0.024)LS(0.001)LADSGHLPDVHGFNSYGSHR;S(0.867)LS(0.128)LS(0.005)LADSGHLPDVHGFNSYGSHR 236.06 3.32E-38 2634400000 289930 347970 95689 198910 358870 304570 257980 276310 283610 TRUE FALSE 251615.0159 345684.1622 141964.5205 244075.5556 351729.1891 316287.005 232961.1393 217223.2567 250081.9489 1.006130259 1.382283542 0.567672001 0.9759823 1.406455727 1.264733446 0.931539203 0.868608301 1 17.9320414 2.047966503 22.3341449 0.917465343 1.097435734 0.096479008 0.239804636 92.64340645 43135.35974 0.101075535 0.068145009 111.6777107 -2.047966503 0.179970391 S(ph)LSPILPGR ddPTM_MDA-MB-175_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(0.953)LS(0.047)PILPGR 81.95 0.020803 161780000 41528 38185 26756 32153 43257 42555 38734 44333 51008 TRUE FALSE 36039.96958 37934.16022 39695.29109 39453.83008 42396.27033 44192.11839 34977.58264 34852.73295 44977.89235 0.801281868 0.843395683 0.882551161 0.877182723 0.942602423 0.982529774 0.777661665 0.774885863 1 15.45692844 4.546364669 2.360944883 0.879339539 0.796868495 0.124998999 0.074927144 1.053151512 9.318451698 0.021209498 0.149272047 35185.5763 -4.546364669 -0.082471043 S(ph)LSPNHNTLQTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSPNHNTLQTLK 13 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.5)LS(0.5)PNHNTLQTLK;S(0.591)LS(0.409)PNHNTLQTLK 204.05 5.22E-08 1998900000 2981710 2762440 1370750 2156610 3049290 2692160 3019770 3620900 3484300 TRUE FALSE 2587669.469 2744293.35 2033649.285 2646301.262 2988615.095 2795729.137 2726913.17 2846598.713 3072390.023 0.842233391 0.893211255 0.661911173 0.861316839 0.972732977 0.90995255 0.887554363 0.926509555 1 21.55092994 3.473323952 16.01835255 0.93099632 0.800709286 0.491331147 0.065319228 1.112575808 4686.326359 0.018450861 0.024181885 2973.883503 -3.473323952 -0.130287033 S(ph)LSPSHLTEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSPSHLTEDR 11 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 S(0.525)LS(0.475)PSHLTEDR 248.56 3.15E-16 825990000 391800 346600 187750 272920 333910 380870 328050 361120 318880 TRUE FALSE 340022.6373 344323.1618 278546.528 334890.6573 327265.8443 395522.3154 296235.7615 283897.2982 281182.3697 1.20926016 1.224554591 0.990625864 1.191008731 1.163891764 1.406639811 1.053536044 1.009655401 1 18.10114661 2.021382369 24.99978372 1.013340773 1.191175009 0.416558372 0.099455334 225.0323173 263101.6675 0.041018137 0.027651743 105.0466891 -2.021382369 0.177834237 S(ph)LSPVFNHTMVYDGFGPADLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSPVFNHTMVYDGFGPADLR 21 0 A0A087X1N4;Q8IYJ3-2;Q8IYJ3 A0A087X1N4 SYTL1 Synaptotagmin-like protein 1 1 S(0.492)LS(0.492)PVFNHT(0.015)MVYDGFGPADLR 87.729 0.00165 84330000 23166 21595 16589 14157 24397 24195 22722 29414 26147 TRUE FALSE 20104.5544 21453.14102 24611.49589 17371.56323 23911.54743 25125.79731 20518.42394 23124.045 23055.93145 0.871990553 0.930482513 1.067469165 0.753453109 1.03711045 1.089775851 0.889941228 1.002954275 1 14.49285033 S(ph)LSQSFENLLDEPAYGLIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSQSFENLLDEPAYGLIQK 20 0 Q8TC07-2;Q8TC07-3;C9JA93 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 S(0.453)LS(0.361)QS(0.186)FENLLDEPAYGLIQK 161.65 1.43E-11 135850000 176500 151340 96758 112990 139860 126530 151470 180960 157300 TRUE FALSE 153175.0778 150345.8376 143550.4924 138646.1064 137077.0596 131397.691 136780.4627 142263.1122 138704.1732 1.104329266 1.083931609 1.034939967 0.999581363 0.988269181 0.94732327 0.986130839 1.025658486 1 17.08165167 4.122057575 1.728043454 0.991687556 1.105451891 0.834250991 0.019045508 0.179478336 1.005595317 0.006405056 0.022836937 13245.17116 -4.122057575 0.113764334 S(ph)LSS(ph)SPVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSSSPVKK 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 2 S(0.997)LS(0.248)S(0.475)S(0.28)PVKK;S(0.999)LS(0.114)S(0.443)S(0.443)PVKK 113.77 0.0061135 1422060000 4443900 2988000 2664800 2495010 2667630 2066180 3938100 4392700 4176400 TRUE FALSE 3856627.356 2968371.631 3953506.193 3061540.154 2614549.382 2145667.282 3556183.668 3453355.289 3682670.75 1.047236535 0.806037746 1.073543214 0.831336919 0.709960124 0.582638913 0.965653437 0.937731208 1 21.81232099 7.999956694 0.946409014 0.857218291 118.7831683 0.127416922 0.144560197 3184.614017 5.628326309 0.049293353 812856.8048 99990029 -7.999956694 117.92595 S(ph)LSSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLSSLR 6 0 O94915;H0Y9X0;A0A286YEZ9;A0A2C9F2R7;C9J1G1;Q70YC5-2;Q70YC5;Q70YC5-4;Q70YC5-3;Q8TF61 O94915;Q8TF61 FRYL;ZNF365;FBXO41 Protein furry homolog-like;Protein ZNF365;F-box only protein 41 1 S(1)LSSLR;S(1)LSSLR;S(0.994)LS(0.006)SLR;S(0.983)LS(0.017)SLR;S(1)LSSLR;S(1)LSSLR 178.87 0.0035641 2859530000 1199175 1288618 864221 1066648 1336410 1298850 1276050 1375730 2085100 TRUE FALSE 1040700.985 1280152.984 1282161.166 1308846.731 1309818.056 1348817.6 1152298.867 1081540.845 1838601.853 0.566028465 0.696264382 0.697356616 0.711870669 0.712398964 0.733610486 0.62672561 0.58824092 1 20.81017767 1.230066892 24.99956636 1.000000621 0.667857475 0.777233585 0.056096667 164.8420879 485141.3683 0.166873372 0.014728651 16.98505245 -1.230066892 -0.332143146 S(ph)LSSPTVTLSAPLEGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSSPTVTLSAPLEGAK 17 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-2;Q96PU5-4;Q96PU5-5;Q96PU5-6;Q96PU5-9 Q96PU5-7;Q96PU5-5 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 S(0.931)LS(0.067)S(0.002)PTVTLSAPLEGAK 244.56 1.68E-20 84789000 300990 129610 115230 162340 167580 167700 168260 221890 238300 TRUE FALSE 261213.4089 128758.5834 170955.6134 199201.7782 164245.4859 174151.5275 151942.1711 174440.5502 210128.4455 1.243113032 0.612761319 0.813576729 0.948000057 0.781643273 0.828786065 0.723091872 0.830161523 1 17.68091195 4.756839361 24.82309022 0.81706595 1.243113431 0.610716874 0.106851887 2542.316299 3452481.523 0.025180557 0.821338504 57126.72941 -4.756839361 0.426047482 S(ph)LSSS(ph)PVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSSSPVKK 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 2 S(0.998)LS(0.066)S(0.182)S(0.755)PVKK;S(0.527)LS(0.473)S(0.029)S(0.971)PVKK 175.57 3.60E-05 733790000 2570500 1818070 1525310 1396700 1514900 1132990 2219210 2526500 2228060 TRUE FALSE 2230801.912 1806126.978 2262955.018 1713842.082 1484756.454 1176576.858 2003991.356 1986227.636 1964661.285 1.135463873 0.919307054 1.151829598 0.872334634 0.755731517 0.598870079 1.020018754 1.010977135 1 20.90584918 3.717781293 23.59276451 0.882744512 1.053910862 0.288929335 0.141507442 601.5947398 683048.0526 0.042871862 0.063691215 5221.331815 -3.717781293 0.171166349 S(ph)LSTNGENMGLAVQYLDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSTNGENMGLAVQYLDPR 19 0 J3KRN4;J3QRB6;Q99759;Q99759-2 J3KRN4 MAP3K3 Mitogen-activated protein kinase kinase kinase 3 1 S(0.451)LS(0.451)T(0.099)NGENMGLAVQYLDPR 60.034 0.069129 60351000 18068 17910 9709.2 14985 16777 16239 18627 18118 17145 TRUE FALSE 15680.26802 17792.34803 14404.6016 18387.57328 16443.17052 16863.72484 16820.55641 14243.60669 15118.13763 1.037182516 1.176887555 0.95280265 1.216259154 1.087645246 1.115463111 1.112607705 0.942153527 1 13.88399281 1.751488739 9.454797468 0.972893789 1.101777853 0.352113351 0.072518659 0.110366913 44.05112785 0.036309562 0.016923974 56.42723099 -1.751488739 0.128884064 S(ph)LSTSGESLYHVLGLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSTSGESLYHVLGLDK 17 0 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 S(0.421)LS(0.421)T(0.052)S(0.052)GES(0.052)LY(0.001)HVLGLDK 85.808 0.0031853 20727000 41211 29117 17454 37712 35282 30587 31145 46215 55973 TRUE FALSE 35764.86193 28925.72851 25894.81278 46275.08599 34579.95723 31763.70168 28124.56269 36332.2819 49355.9357 0.724631423 0.586063826 0.52465448 0.937578942 0.700624084 0.643563965 0.569831415 0.736127912 1 15.59093598 1.265858799 3.617396158 1.03430957 0.670357649 0.454972233 0.112913124 0.244734775 4.899401062 0.232473462 0.029115371 18.44415653 -1.265858799 -0.363951921 S(ph)LSVEHLETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSVEHLETK 10 0 J3KN34;P26045-2;P26045 J3KN34 PTPN3 Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 3 1 S(0.593)LS(0.407)VEHLETK 133.32 0.0020868 0 535810 454660 306110 408660 468820 463200 432750 566660 563970 TRUE FALSE 465001.3509 451673.3085 454145.8199 501452.499 459491.3992 481019.6037 390781.9716 445484.1688 497298.1091 0.935055538 0.908254627 0.913226517 1.008353923 0.923975762 0.967266102 0.785810291 0.895809094 1 18.92375142 1.230893767 24.79056801 1.000000171 0.914273798 0.171621041 0.05682958 483.7711766 1564114.912 0.149775467 0.014459493 17.01742195 -1.230893767 -0.085726373 S(ph)LTAHSLLPLAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLTAHSLLPLAEK 13 0 F2Z2E2;Q86VI3 F2Z2E2 IQGAP3 Ras GTPase-activating-like protein IQGAP3 1 S(0.625)LT(0.297)AHS(0.078)LLPLAEK 138.05 3.45E-05 111200000 690170 679350 387500 502430 722380 683310 722480 843000 517780 TRUE FALSE 598962.2858 674887.3051 574896.2961 616514.4107 708006.0513 709597.3779 652414.0008 662731.0102 456568.6383 1.311877855 1.478172718 1.259167293 1.350321417 1.550711091 1.554196496 1.428950537 1.451547379 1 18.80047224 1.236571673 24.99273511 0.999999456 1.427129716 0.659715465 0.095462122 33.67699704 423066.56 0.153174255 0.024139862 17.24136605 -1.236571673 0.42713026 S(ph)LTNSHLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLTNSHLEK 9 0 F8VX12;F8VX04;Q9H2H9 F8VX12 SLC38A1 Sodium-coupled neutral amino acid transporter 1 1 S(0.864)LT(0.033)NS(0.103)HLEK;S(0.993)LT(0.006)NS(0.001)HLEK;S(0.997)LT(0.003)NSHLEK;S(0.994)LT(0.006)NSHLEK 170.95 0.0003406 896440000 2920330 2133110 1834570 3114170 2755590 2991410 2373510 3617790 3593390 TRUE FALSE 2534400.991 2119097.46 2721774.188 3821289.896 2700759.15 3106491.478 2143327.366 2844153.762 3168583.528 0.799852984 0.66878384 0.858987672 1.205993108 0.852355359 0.980403846 0.676430761 0.897610474 1 21.59540662 4.029531195 9.621275002 0.922815581 0.741119879 0.268105165 0.135177035 0.487514531 149.458586 0.035077666 0.072754017 10703.63263 -4.029531195 -0.181695702 S(ph)LTRS(ph)PPAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLTRSPPAIR 10 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.989)LT(0.097)RS(0.914)PPAIR;S(0.844)LT(0.207)RS(0.949)PPAIR 108.66 0.0012073 675650000 766150 439250 272710 333410 527350 504260 568520 641450 233773 TRUE FALSE 664901.3363 436364.5378 404593.4682 409115.8364 516856.7667 523659.2085 513385.0179 504280.9093 206136.6223 3.225537166 2.116870516 1.962744241 1.984682934 2.507350519 2.540350195 2.490508539 2.446343128 1 17.65324131 4.741005093 24.13208625 2.187290566 3.225537765 0.35455565 0.458527557 166.6914501 1645425.565 0.110224547 0.717281918 55081.41553 -4.741005093 1.038247199 S(ph)LVESVSSSPNKESNEEEQVWHFLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLVESVSSSPNKESNEEEQVWHFLGK 26 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;Q9H2U2-4 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 1 S(0.22)LVES(0.194)VS(0.194)S(0.194)S(0.194)PNKES(0.003)NEEEQVWHFLGK 51.296 0.071504 489120000 48136 31454 21198 27511 29365 29511 40087 42597 43864 TRUE FALSE 41774.70564 31247.3766 31449.4237 33757.79303 28780.69395 30646.30727 36199.36891 33487.96304 38678.44789 1.080051241 0.80787566 0.813099424 0.872780447 0.744101574 0.792335498 0.935905417 0.865804211 1 15.23924228 0.1962332 1.157607715 2.255330064 0.850796536 0.16709487 0.093082654 26.65970137 4.334527261 79.91719351 0.027762459 1.571206257 -0.1962332 -1.404533529 S(ph)LVGTPYWMAPELISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 21 SLVGTPYWMAPELISR 16 0 O96013;O96013-4;O96013-2;O96013-3;M0R1R1 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(0.999)LVGT(0.001)PYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(0.878)LVGT(0.122)PYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR 440.58 6.66E-182 20855836800 4358496.8 4029173.1 2684406 3131097.9 4115659.2 3930242.9 3823372.2 4365649.4 4365971.8 TRUE FALSE 3782510.405 4002705.197 3982593.72 3842061.534 4033765.634 4081441.888 3452582.153 3432089.249 3849831.588 0.982513214 1.039709168 1.034485179 0.997981716 1.047777167 1.060161151 0.896813815 0.89149075 1 21.87636391 2.235586771 24.9999987 0.92017061 1.027628913 0.604509248 0.036987146 45.89260631 385793.8449 0.014478533 0.010242471 172.0231003 -2.235586771 0.107458303 S(ph)MDDLLSACDTSSPLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SMDDLLSACDTSSPLTR 17 0 J3QR65;Q9NYA4 J3QR65 MTMR4 Myotubularin-related protein 4 1 S(1)MDDLLSACDTSSPLTR 78.441 0.016422 37551000 22325 16788 12012 14115 24315 18233 21555 25775 23611 TRUE FALSE 19374.69469 16677.71852 17821.04338 17320.02648 23831.17907 18934.43531 19464.59942 20263.21683 20819.73448 0.930592785 0.801053373 0.855968812 0.831904293 1.144643756 0.909446532 0.934911031 0.973269705 1 14.34566405 S(ph)MDELNHDFQALALEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SMDELNHDFQALALEGR 17 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4;E9PR38 Q5T1Z4 PUM1 Pumilio homolog 1 1 S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR 252.84 3.46E-27 590396000 303779 250451 167502.1 184061.2 269340 282347 256561 286727 283384 TRUE FALSE 263633.8355 248805.7709 248506.6758 225855.1087 263980.661 293209.0718 231679.7537 225412.6624 249882.6664 1.055030504 0.995690396 0.994493453 0.90384464 1.056418458 1.173386998 0.92715416 0.902074024 1 17.9308913 S(ph)MDLGIADETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SMDLGIADETK 11 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 S(1)MDLGIADETK;S(1)MDLGIADETK;S(1)MDLGIADETK;S(1)MDLGIADETK 190.85 2.19E-06 446148000 1733820 1091930 826800 969270 1019710 814950 1287270 1434900 1437460 TRUE FALSE 1504691.294 1084757.04 1226643.245 1189357.568 999419.766 846301.6538 1162430.754 1128057.801 1267525.116 1.187109647 0.855807136 0.967746698 0.938330572 0.788481233 0.667680382 0.917086958 0.889968796 1 20.2735829 7.096446653 1.336382698 0.869644686 199.9999999 0.491026516 0.096845417 868.666352 3.205493956 0.028416607 528492.3349 12486670.53 -7.096446653 199.1303552 S(ph)MDSSDLSDGAVTLQEYLELKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SMDSSDLSDGAVTLQEYLELKK 22 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 S(0.894)MDS(0.081)S(0.025)DLSDGAVTLQEYLELKK;S(0.926)MDS(0.037)S(0.037)DLSDGAVTLQEYLELKK;S(0.979)MDS(0.018)S(0.004)DLSDGAVTLQEYLELKK 219.38 6.75E-26 271983000 467422 291948 234279 280117 269422 198066 351010 443231 386708 TRUE FALSE 405650.9984 290030.1744 347577.108 343721.8462 264061.0293 205685.7272 316969.1042 348449.4999 340991.8208 1.189620905 0.850548772 1.019312156 1.008006132 0.774391095 0.603198419 0.929550461 1.021870551 1 18.37937761 4.745584048 24.19930665 0.905454455 1.189621115 0.318674507 0.132540798 751.3872507 2588808.506 0.035317762 0.336996465 55665.2352 -4.745584048 0.28416666 S(ph)MGETESGDAFLDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SMGETESGDAFLDLK 15 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B1AKL5;B1AKL6 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 S(0.991)MGET(0.009)ESGDAFLDLK;S(0.892)MGET(0.031)ES(0.077)GDAFLDLK;S(0.993)MGET(0.006)ES(0.001)GDAFLDLK;S(1)MGETESGDAFLDLK;S(0.996)MGET(0.003)ESGDAFLDLK;S(0.994)MGET(0.006)ESGDAFLDLK 176.19 8.53E-07 128440000 262566 256773 204521 250344 277598 225853 319899 387244 362604 TRUE FALSE 227867.2378 255086.2413 303428.0397 307188.4315 272074.3429 234541.7111 288875.2442 304434.8841 319737.3682 0.712670024 0.797799277 0.948991484 0.960752361 0.850930701 0.733544885 0.903476643 0.952140458 1 18.28652784 -1.999955126 0.032374413 2.143341418 9.17E-06 0.311404929 0.082096677 3972.938449 12.7219627 609.6068229 289.7111435 0.010001033 1.999955126 -2.143332252 S(ph)MGYDDLDYGMMSDYGTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 17 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(0.996)MGY(0.004)DDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(0.988)MGY(0.012)DDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(0.846)MGY(0.154)DDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(0.993)MGY(0.007)DDLDYGMMSDYGTAR;S(0.94)MGY(0.06)DDLDYGMMSDYGTAR;S(0.996)MGY(0.004)DDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR 343.26 4.04E-76 5870043000 3061454 3028007 2097054 2290162 3212684 3569772 2534354 3193684 3163354 TRUE FALSE 2656875.097 3008115.823 3111196.329 2810178.285 3148757.874 3707103.439 2288572.739 2510739.53 2789385.894 0.952494634 1.078415084 1.115369636 1.007454111 1.128835519 1.329003437 0.820457558 0.900104763 1 21.41151611 2.204022992 24.99999928 0.901848107 1.098400021 0.43018487 0.105731674 171.0961462 123846.5336 0.04331374 0.029203634 159.9642712 -2.204022992 0.196551914 S(ph)MPSMGYMTHTVSAPSLHGK ddPTM_MDA-MB-175_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(0.997)MPS(0.003)MGYMTHTVSAPSLHGK 202.73 1.89E-21 437420000 330900 375080 250760 286110 363800 326100 387720 398590 333770 TRUE FALSE 287170.7266 372616.0748 372028.3747 351075.6484 356561.0918 338645.278 350118.9741 313354.6303 294312.0908 0.975735403 1.266057652 1.264060792 1.192868589 1.211506774 1.150633251 1.189618045 1.064701859 1 18.16698729 1.57624801 2.25081216 0.995459466 1.187751978 0.367780297 0.081121221 0.31828425 3.205485302 0.103772687 0.021553266 37.6918982 -1.57624801 0.192292511 S(ph)MPVLGSVSSVTK ddPTM_MDA-MB-175_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(1)MPVLGSVSSVTK;S(0.979)MPVLGS(0.021)VSSVTK;S(1)MPVLGSVSSVTK;S(1)MPVLGSVSSVTK;S(1)MPVLGSVSSVTK 236.42 1.08E-16 2401570000 3015900 3360820 1693710 1912730 2786250 2130440 2984470 3467080 3388130 TRUE FALSE 2617341.174 3338742.552 2512793.821 2347044.581 2730809.076 2212399.405 2695036.559 2725671.923 2987589.131 0.876071327 1.117537387 0.841077441 0.785598179 0.914051081 0.740530009 0.902077374 0.912331583 1 21.51055032 4.206739689 24.99853695 0.870040015 0.996804717 0.246340473 0.091613088 228.5331091 179535.719 0.022694463 0.047248983 16096.80524 -4.206739689 0.126764702 S(ph)MSAPSDLEMIGNEDLEFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SMSAPSDLEMIGNEDLEFTR 20 0 F8VWT9;J3KPF0;Q9Y4D8-4;Q9Y4D8;Q9Y4D8-2 F8VWT9 HECTD4 Probable E3 ubiquitin-protein ligase HECTD4 1 S(0.779)MS(0.221)APSDLEMIGNEDLEFTR;S(0.5)MS(0.5)APSDLEMIGNEDLEFTR 156.08 8.82E-08 46596000 76357 61416 37676 47449 66748 59471 70333 71806 64153 TRUE FALSE 66266.22899 61012.55425 55896.23962 58223.02066 65419.84539 61758.88785 63512.11649 56450.84569 56568.90542 1.171424981 1.078552852 0.988108912 1.029240715 1.156462988 1.091746206 1.122739003 0.997912993 1 15.78772164 1.663762391 6.636711356 0.99812862 1.086700524 0.329354537 0.054287383 0.158558262 13.8392307 0.034833008 0.014674048 46.10652501 -1.663762391 0.088571905 S(ph)MSDVSAEDVQNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SMSDVSAEDVQNLR 14 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;E9PJ10;E9PK58;E9PLU6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.995)MS(0.005)DVSAEDVQNLR;S(0.983)MS(0.017)DVSAEDVQNLR;S(1)MSDVSAEDVQNLR;S(0.998)MS(0.002)DVSAEDVQNLR;S(0.991)MS(0.009)DVSAEDVQNLR;S(0.953)MS(0.047)DVSAEDVQNLR;S(1)MSDVSAEDVQNLR 380.52 7.31E-98 6635440000 3661440 4073340 2915600 3599180 3995190 3657260 3426170 4570120 7495160 TRUE FALSE 3177571.427 4046581.961 4325593.912 4416428.829 3915693.535 3797957.159 3093900.561 3592835.403 6609090.723 0.480787987 0.612275142 0.654491532 0.668235467 0.59247084 0.574656533 0.468128021 0.543620228 1 22.65602037 1.235980161 24.99896981 1.000000562 0.575117142 0.809137882 0.064970197 32.69324057 316659.5973 0.114760054 0.017319477 17.21789919 -1.235980161 -0.42488342 S(ph)MSIDDTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SMSIDDTPR 9 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GUE9;Q96N67-7;A0A0C4DGY6;A0A1B0GVW2 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 S(0.985)MS(0.015)IDDTPR;S(0.998)MS(0.002)IDDTPR 219.72 5.06E-07 800630000 776860 787480 572330 630970 891390 953830 878880 920670 878100 TRUE FALSE 674195.9827 782306.992 849110.7023 774241.3823 873653.083 990524.4573 793646.3529 723791.8852 774292.0183 0.87072573 1.010351358 1.09662851 0.999934603 1.128325053 1.279264714 1.02499617 0.934778957 1 19.56251824 4.687653782 2.927928154 1.059784228 0.849179915 0.301311477 0.093356259 0.509603035 6.664960234 0.026310946 0.237309227 48713.99891 -4.687653782 -0.210604313 S(ph)MSVDLSHIPLKDPLLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SMSVDLSHIPLKDPLLFK 18 1 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 S(0.5)MS(0.5)VDLSHIPLKDPLLFK;S(0.5)MS(0.5)VDLSHIPLKDPLLFK 181.29 4.48E-14 412590000 1088030 983910 552850 686450 763990 546810 1149250 940300 940360 TRUE FALSE 944244.0788 977446.6304 820210.1092 842318.9642 748788.0937 567846.1345 1037795.912 739224.1624 829191.7121 1.138752432 1.178794501 0.989168243 1.015831384 0.903033741 0.684818874 1.251575356 0.8914997 1 19.66134617 4.171235813 4.272958678 0.958745652 1.160224574 0.257284924 0.139281099 0.270638254 9.556369931 0.035026453 0.081740568 14833.2328 -4.171235813 0.201478922 S(ph)MVWPGDGLVPDTAEPHVAPSPTLPSTEDVIR ddPTM_MDA-MB-175_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(1)MVWPGDGLVPDTAEPHVAPSPTLPSTEDVIR 198.39 5.83E-27 225398000 5318.2 2453.8 8336.4 3682.6 2984 7696.8 8423.2 8233.9 9803.1 TRUE FALSE 4615.386395 2437.680826 12367.91092 4518.790615 2924.624238 7992.900876 7606.31936 6473.144561 8644.188686 0.53392939 0.282002269 1.430777528 0.522754741 0.338334151 0.924655993 0.879934443 0.748843506 1 13.07751485 -2 0.066325378 2.300127793 1.94E-12 0.100405668 0.325393858 1785.499223 11.408503 418.1515868 91.97664002 0.01 2 -2.300127793 S(ph)NENLDKIDMSLDDIIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SNENLDKIDMSLDDIIK 17 1 H9KVD1;Q96QD9-4;Q96QD9 H9KVD1 FYTTD1 UAP56-interacting factor 1 S(1)NENLDKIDMSLDDIIK;S(1)NENLDKIDMSLDDIIK 123.12 3.31E-05 43661000 154446 84798 95417 75773 80004 66964 133028 131323 111164 TRUE FALSE 134035.5698 84240.95635 141560.9804 92978.41777 78412.07693 69540.14841 120126.965 103240.5984 98022.31856 1.367398484 0.859405874 1.444170903 0.948543343 0.799941055 0.709431785 1.22550626 1.05323563 1 16.58082265 S(ph)NGDLSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SNGDLSPK 8 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 S(1)NGDLSPK;S(1)NGDLSPK;S(1)NGDLSPK;S(1)NGDLSPK 140.91 0.00067349 1481350000 5266590 2914660 2393660 2764130 2256600 2519440 3390300 3969070 4454220 TRUE FALSE 4570596.788 2895513.407 3551241.982 3391767.964 2211698.075 2616364.487 3061509.228 3120315.268 3927647.186 1.163698411 0.737213214 0.90416522 0.863562281 0.56311017 0.666140405 0.779476639 0.794448972 1 21.90523391 4.74289431 24.6099189 0.783645814 1.163698601 0.485388996 0.12131423 325.3444369 1847461.668 0.030397654 0.231266374 55321.54621 -4.74289431 0.380052787 S(ph)NMSPHGLPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNMSPHGLPAR 11 0 E7ESY4;Q13330-3;Q13330;H0Y4T7 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 S(0.79)NMS(0.21)PHGLPAR 116.19 0.0034248 234770000 296240 262330 131070 168180 257180 274180 254580 277790 247630 TRUE FALSE 257091.1334 260606.737 194455.8904 206367.8395 252062.6212 284727.882 229890.8708 218386.7703 218355.4635 1.177397301 1.19349767 0.8905474 0.945100416 1.154368282 1.303965 1.052828572 1.000143375 1 17.7363191 2.002843145 24.9888609 1.00800311 1.1056223 0.129914871 0.118668559 200.6642305 1763660.16 0.053242758 0.03566705 100.6568058 -2.002843145 0.09761919 S(ph)NNSYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNNSYLR 7 0 F5GYN7;Q5FWF4-4;Q5FWF4-2;Q5FWF4-3;Q5FWF4 F5GYN7 ZRANB3 DNA annealing helicase and endonuclease ZRANB3;DNA annealing helicase ZRANB3;Endonuclease ZRANB3 1 S(0.5)NNS(0.5)YLR 63.287 0.084275 102010000 29060 22621 11485 13867 19814 21487 18126 17067 27116 TRUE FALSE 25219.64737 22472.40116 17039.18442 17015.71429 19419.74017 22313.61879 16368.14331 13417.35487 23910.37737 1.054757396 0.939859744 0.712627164 0.711645577 0.812188777 0.933219014 0.684562316 0.561151949 1 14.54534928 4.402768116 3.718892139 0.755035724 1.035992069 0.361772376 0.125829894 0.224305104 5.940071329 0.033304327 0.109374568 25279.47884 -4.402768116 0.280956345 S(ph)NPEGAEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNPEGAEDR 9 0 M0R3H9;M0QXG9;M0R3F4;M0R2A4;M0R2K3;M0R193;M0R0I0;J3KQS6;Q9NWV8-3;Q9NWV8;M0R2I2 M0R3H9 BABAM1 BRISC and BRCA1-A complex member 1 1 S(1)NPEGAEDR 179.68 5.19E-05 192900000 94994 93960 85387 112760 101820 132440 132820 146800 224420 TRUE FALSE 82440.30222 93342.77057 126680.4388 138363.8814 99793.98121 137535.0525 119939.1368 115407.9624 197889.3233 0.41659803 0.471691797 0.640158027 0.699198315 0.504291892 0.695009969 0.606092006 0.583194487 1 17.59433425 1.238477262 10.80984684 1.001103574 0.582521884 0.676073149 0.091941153 0.042423153 152.0797624 0.128603239 0.022879969 17.31718362 -1.238477262 -0.41858169 S(ph)NPQHRESWPGMGSGEAPTPLQPPEEVTPHPATPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNPQHRESWPGMGSGEAPTPLQPPEEVTPHPATPAR 36 1 O43896 O43896 KIF1C Kinesin-like protein KIF1C 1 S(0.477)NPQHRES(0.477)WPGMGS(0.036)GEAPT(0.01)PLQPPEEVTPHPATPAR 60.065 0.015362 227750000 14985 20051 10304 16315 28120 20025 18790 23685 17336 TRUE FALSE 13004.69428 19919.28366 15287.04886 20019.57011 27560.46702 20795.37471 16967.74869 18620.14707 15286.55783 0.850727445 1.303058797 1.000032122 1.309619231 1.802921712 1.360370002 1.10997838 1.218073243 1 13.89997596 3.726845303 23.65338305 1.303180443 1.076451394 0.196788254 0.235155795 672.0105314 1356799.408 0.068156424 0.102160476 5331.449541 -3.726845303 -0.226729049 S(ph)NPSIQATLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SNPSIQATLNK 11 0 Q6UUV7;Q6UUV7-3 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 S(0.997)NPS(0.003)IQATLNK;S(1)NPSIQATLNK 225.36 5.80E-12 457790000 948760 831740 435080 540650 750230 568200 789820 933490 771390 TRUE FALSE 823378.9621 826276.2452 645486.1433 663412.8458 735301.8908 590059.0217 713223.378 733870.4279 680197.153 1.210500454 1.214759929 0.948969193 0.97532435 1.081012891 0.867482346 1.048553901 1.078908409 1 19.37559344 4.248239039 24.99836071 1.006952669 1.212630325 0.658635564 0.06347794 123.7046322 319509.5506 0.016149348 0.041582039 17710.83507 -4.248239039 0.205677656 S(ph)NSAPLIHGLSDTSPVFQAEAPSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SNSAPLIHGLSDTSPVFQAEAPSAR 25 0 Q96E09 Q96E09 FAM122A Protein FAM122A 1 S(0.5)NS(0.5)APLIHGLSDTSPVFQAEAPSAR;S(0.5)NS(0.5)APLIHGLSDTSPVFQAEAPSAR 221.5 7.26E-34 1791950000 292720 252562 126760 193449 267780 266193 236756 298460 294090 TRUE FALSE 254036.3103 250902.9036 188061.56 237374.5521 262451.7019 276433.617 213795.4396 234636.6516 259323.0152 0.979613437 0.967530411 0.725201964 0.915362456 1.012064825 1.065981809 0.82443681 0.904804579 1 17.98439073 4.447490038 24.99997329 0.917612221 0.976593858 0.048451707 0.096381277 587.814901 495941.3699 0.024835221 0.065709595 28021.41342 -4.447490038 0.058981637 S(ph)NSDNNLNASAPDWAVCSTATSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SNSDNNLNASAPDWAVCSTATSHR 24 0 Q9UPX8;Q9UPX8-3;A0A2R8Y2H5;A0A087X158 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 S(0.614)NS(0.386)DNNLNASAPDWAVCSTATSHR;S(0.585)NS(0.415)DNNLNASAPDWAVCSTATSHR;S(0.624)NS(0.376)DNNLNASAPDWAVCSTATSHR 236.27 1.35E-37 1999420000 684819 584276 346609 480619 579758 515510 473163 661159 680780 TRUE FALSE 594318.434 580437.8525 514230.2717 589750.8898 568221.9501 535342.0033 427275.7251 519775.293 600298.9639 0.990037414 0.966914633 0.85662362 0.982428632 0.946564935 0.891792316 0.711771552 0.86586072 1 19.19532165 2.479622713 24.99103945 0.846928456 0.943601602 0.216306593 0.077343382 142.1110532 1419804.839 0.028752595 0.022676174 301.7329321 -2.479622713 0.096673146 S(ph)NSDVTISDIDAEDVLDQNAVNPNTGAALHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SNSDVTISDIDAEDVLDQNAVNPNTGAALHR 31 0 Q9P2F8 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 S(0.499)NS(0.499)DVT(0.002)ISDIDAEDVLDQNAVNPNTGAALHR;S(0.561)NS(0.436)DVT(0.003)ISDIDAEDVLDQNAVNPNTGAALHR 133.85 1.67E-06 873390000 762210 676270 589270 662510 758600 716810 900630 1048880 1064870 TRUE FALSE 661482.0173 671827.5378 874242.943 812943.0213 743505.3442 744386.1445 813287.0412 824585.1744 938982.2817 0.704466985 0.715484787 0.931053716 0.865770353 0.791820419 0.792758457 0.866136728 0.878169046 1 19.84073841 -1.999957089 0.037167633 2.11668728 8.27E-06 0.468129329 0.066618811 2117.23348 7.763005206 337.7807041 143.8677157 0.010000988 1.999957089 -2.11667901 S(ph)NSELEDEILCLEK ddPTM_MDA-MB-175_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(0.965)NS(0.035)ELEDEILCLEK 139.88 1.18E-05 0 36038 36757 26295 30947 37968 34111 29873 54888 46583 TRUE FALSE 31275.48699 36515.54085 39011.34995 37973.98935 37212.51108 35423.27224 26975.92106 43150.62834 41076.01081 0.76140517 0.888974857 0.949735604 0.924480946 0.905942674 0.862383458 0.656731765 1.050506792 1 15.32600846 1.611783181 25 1.025267147 0.860268019 0.410683802 0.086616911 0.346865633 2205.079464 0.049366859 0.022293791 40.90563894 -1.611783181 -0.164999128 S(ph)NSGRELTDEEILASVMIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 SNSGRELTDEEILASVMIK 19 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 S(0.467)NS(0.467)GRELT(0.065)DEEILASVMIK;S(0.458)NS(0.458)GRELT(0.084)DEEILASVMIK;S(0.644)NS(0.343)GRELT(0.013)DEEILASVMIK;S(0.646)NS(0.353)GRELT(0.001)DEEILASVMIK;S(0.492)NS(0.492)GRELT(0.017)DEEILASVMIK;S(0.483)NS(0.483)GRELT(0.033)DEEILASVMIK;S(0.443)NS(0.443)GRELT(0.114)DEEILASVMIK;S(0.499)NS(0.499)GRELT(0.002)DEEILASVMIK;S(0.441)NS(0.441)GRELT(0.118)DEEILASVMIK;S(0.497)NS(0.497)GRELT(0.006)DEEILASVMIK;S(0.491)NS(0.491)GRELT(0.019)DEEILASVMIK;S(0.494)NS(0.494)GRELT(0.011)DEEILASVMIK;S(0.469)NS(0.469)GRELT(0.062)DEEILASVMIK 262.55 1.97E-31 1349278000 2882763 2547630 1481286 1618664 2474621 2196712 3208321 3591447 947947 TRUE FALSE 2501798.566 2530894.451 2197640.864 1986206.401 2425380.884 2281220.932 2897178.523 2823444.008 835881.7856 2.993005242 3.027813854 2.629128786 2.376180981 2.901583604 2.729119083 3.466014661 3.377803006 1 19.6729394 1.230834313 24.99847742 0.999996492 2.950984407 0.78001255 0.323308355 149.8168801 484692.3113 0.948321244 0.090532875 17.01509246 -1.230834313 1.950987915 S(ph)NSLDKHQQSSTLGNSVVR ddPTM_MDA-MB-175_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(0.571)NS(0.429)LDKHQQSSTLGNSVVR;S(0.642)NS(0.358)LDKHQQSSTLGNSVVR 245.49 8.38E-25 1015240000 573380 511190 292970 420190 636040 512050 671390 718790 432010 TRUE FALSE 497606.3802 507831.9592 434651.2719 515600.5617 623384.0484 531748.8948 606278.7011 565082.3521 380938.2699 1.306265134 1.333108273 1.141001853 1.35350161 1.636443743 1.395892555 1.591540543 1.483396121 1 18.53919771 3.476610338 24.99973124 1.445611727 1.264061444 0.139999094 0.176972636 29.32559887 1434868.177 0.049845422 0.064965747 2996.472788 -3.476610338 -0.181550283 S(ph)NSLPHSAVSNAGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNSLPHSAVSNAGSK 15 0 A0A088AWN2;Q8TBZ3-4;Q8TBZ3-5;Q8TBZ3-6;Q8TBZ3;Q8TBZ3-2;Q8TBZ3-7 A0A088AWN2 WDR20 WD repeat-containing protein 20 1 S(0.707)NS(0.293)LPHSAVSNAGSK 270.35 1.46E-33 1421700000 1286100 1353100 878520 1251800 1659800 1239800 1928700 2088400 1790500 TRUE FALSE 1116138.626 1344211.397 1303375.21 1536040.323 1626773.227 1287495.908 1741654.971 1641811.912 1578829.13 0.706940736 0.851397641 0.825532786 0.972898393 1.030366869 0.815475142 1.103130756 1.039892083 1 20.59042361 5.989495469 0.353390374 1.050140474 4.88E-14 0.625846983 0.075951751 13.12743905 0.725277619 0.111092159 6.907296573 976102.5981 -5.989495469 -1.050140474 S(ph)NTLDIMDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SNTLDIMDGR 10 0 O94915;H0Y9X0;A0A286YEZ9;A0A2C9F2R7 O94915 FRYL Protein furry homolog-like 1 S(0.967)NT(0.033)LDIMDGR;S(0.969)NT(0.031)LDIMDGR 85.271 0.015475 155010000 510050 416950 295640 376430 399600 385410 455690 471120 477090 TRUE FALSE 442645.6002 414211.028 438612.4929 461904.1849 391648.7418 400236.9721 411497.2539 370374.6543 420688.9637 1.052192091 0.984601603 1.04260518 1.097970769 0.930969851 0.95138453 0.978150818 0.880400215 1 18.68239445 3.220430117 24.99912843 0.942116354 1.039951126 0.570803356 0.041170066 170.0624752 234489.0348 0.012400955 0.014089735 1661.231345 -3.220430117 0.097834772 S(ph)PAFALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPAFALK 7 0 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 S(1)PAFALK;S(1)PAFALK 97.635 0.012433 761120000 1047250 1565270 908020 718910 1094410 1005380 1200260 1245170 1727780 TRUE FALSE 908853.2591 1554987.638 1347141.509 882149.5034 1072633.382 1044057.619 1083858.97 978900.0854 1523523.817 0.596546801 1.020652005 0.884227404 0.579019175 0.704047663 0.685291301 0.711415836 0.642523651 1 20.53898062 3.768200224 24.92689122 0.709569343 0.852493088 0.106450551 0.149556666 1196.740409 1006454.015 0.037340562 0.064663531 5864.084555 -3.768200224 0.142923745 S(ph)PAFRGPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPAFRGPDR 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 S(1)PAFRGPDR 101.71 0.0023 268730000 103990 127680 45446 56608 110240 128880 115060 131420 67095 TRUE FALSE 90247.45802 126841.2617 67423.83761 69461.7116 108046.4397 133838.097 103901.4989 103316.8557 59163.10553 1.525400961 2.143925011 1.139626411 1.174071425 1.826246927 2.262188501 1.756187373 1.746305485 1 15.85241016 S(ph)PAGGESATVAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPAGGESATVAAK 13 0 Q147X3 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 S(1)PAGGESATVAAK;S(1)PAGGESATVAAK;S(1)PAGGESATVAAK 265.77 2.48E-24 931860000 722250 512023 483311 759760 554526 481537 575102 725120 1623440 TRUE FALSE 626802.8326 508659.4872 717041.8162 932275.1202 543492.0175 500062.04 519328.6966 570058.7309 1431518.773 0.437858619 0.355328548 0.500895853 0.651248966 0.379661118 0.349322726 0.362781618 0.398219529 1 20.44911516 1.236774223 24.99963319 1.000000716 0.427622154 0.795891701 0.090804454 21.96262984 307264.7927 0.148209482 0.023677534 17.24940912 -1.236774223 -0.572378562 S(ph)PAKSPNPSTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPAKSPNPSTPR 12 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 S(0.999)PAKS(0.001)PNPSTPR 52.522 0.089661 92784000 126920 120640 69259 78139 96604 97568 113000 138750 46626 TRUE FALSE 110147.2004 119847.5079 102752.8841 95881.65423 94681.7694 101321.5041 102041.2774 109079.3923 41113.9274 2.679072699 2.915009961 2.49922327 2.332096696 2.302912307 2.464408304 2.481915104 2.653100766 1 15.32733957 1.235942289 24.99433746 0.999997959 2.537481058 0.881755096 0.177338537 25.22736474 240768.3935 0.316853187 0.047635351 17.21639782 -1.235942289 1.537483099 S(ph)PAMSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPAMSR 6 0 Q9BQI6 Q9BQI6 ANKRD32 Ankyrin repeat domain-containing protein 32 1 S(1)PAMSR;S(1)PAMSR 119.41 0.022069 2513300000 909840 776090 537130 738820 603370 879690 649860 830970 984430 TRUE FALSE 789602.3388 770991.8137 796887.8646 906580.3732 591364.1175 913532.2435 586836.6772 653273.5321 868051.8069 0.909625822 0.888186405 0.918018784 1.0443851 0.681254405 1.052393689 0.676038772 0.752574359 1 19.72742162 3.24829511 24.99964224 0.82173356 0.934775212 0.146564082 0.127290376 379.0994632 973579.381 0.035697592 0.045496064 1771.312184 -3.24829511 0.113041652 S(ph)PAPGLASGDRPPSVSSVHSEGDCNRR ddPTM_MDA-MB-175_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(0.023)GDRPPSVSSVHSEGDCNRR 57.262 0.035878 128060000 8773.3 6488.1 5505.7 6610.3 11250 9026.2 7239.3 9998.9 9037.7 TRUE FALSE 7613.886176 6445.479244 8168.274935 8111.269647 11026.14701 9373.443755 6537.2338 7860.713047 7969.273402 0.955405316 0.808791331 1.024971101 1.017817966 1.383582474 1.17619804 0.820304872 0.986377634 1 12.96023248 4.114005468 5.889943485 1.055930465 0.883559778 0.198980682 0.14820988 0.364876698 17.26459248 0.041706375 0.089212298 13001.85946 -4.114005468 -0.172370687 S(ph)PARTPPS(ph)EEDSAEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPARTPPSEEDSAEAER 17 1 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 2 S(0.999)PART(0.009)PPS(0.728)EEDS(0.264)AEAER;S(0.995)PART(0.25)PPS(0.693)EEDS(0.062)AEAER 127.49 0.00047942 530160000 423460 367670 304290 372540 376770 373890 355460 391980 622400 TRUE FALSE 367498.6881 365254.7516 451445.6618 457130.9009 369273.0141 388273.7902 320987.5439 308158.1274 548820.581 0.669615355 0.665526702 0.822574221 0.832933233 0.672848335 0.707469442 0.584867906 0.561491566 1 19.06597506 S(ph)PCGLTEQYLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPCGLTEQYLHK 12 0 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 S(1)PCGLTEQYLHK 164.15 3.74E-05 223730000 204130 274560 161440 228510 312790 211520 279250 351710 262960 TRUE FALSE 177153.7033 272756.3973 239512.924 280396.6881 306566.091 219657.3113 252168.378 276499.5535 231873.1684 0.764011225 1.176317205 1.032947993 1.209267506 1.322128356 0.947316642 1.087527202 1.192460324 1 17.82297636 4.743485124 24.74779082 1.125874934 0.764011052 0.506281869 0.110695428 376.3342518 1891171.106 0.026263547 0.210713997 55396.85689 -4.743485124 -0.361863882 S(ph)PCPQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPCPQEK 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(1)PCPQEK 68.847 0.064345 1031700000 1595000 1378900 1022700 1156800 820190 1085200 1383100 1474300 2979600 TRUE FALSE 1384216.709 1369841.915 1517281.141 1419469.121 803869.8237 1126948.346 1248967.175 1159032.418 2627355.082 0.526847977 0.521376773 0.577493751 0.540265429 0.305961622 0.428928832 0.475370529 0.441140379 1 21.32517976 1.236314207 24.99574753 1.000000679 0.47502962 0.825243337 0.07560549 25.77101854 286685.2418 0.127808199 0.019777806 17.23114777 -1.236314207 -0.524971059 S(ph)PDALESAQSEEEVDELSLIDHNEIMSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPDALESAQSEEEVDELSLIDHNEIMSR 28 0 Q13905-2;Q13905;Q13905-4;Q13905-3;H0Y6R4 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 S(1)PDALESAQSEEEVDELSLIDHNEIMSR;S(1)PDALESAQSEEEVDELSLIDHNEIMSR 215.92 2.26E-34 85324000 18238.9 16951.6 10413.1 15611.4 17190.6 18187.6 17103.5 23190.4 21588.5 TRUE FALSE 15828.58315 16840.24382 15448.90999 19156.20698 16848.54069 18887.28874 15444.8052 18231.31343 19036.33212 0.831493328 0.884637004 0.811548669 1.006297161 0.885072848 0.992170583 0.811333039 0.95771146 1 14.21646791 3.753480467 24.99253518 0.935261541 0.8467674 0.365882482 0.06125059 953.4518332 1597141.495 0.015418162 0.026571014 5668.660759 -3.753480467 -0.088494141 S(ph)PDEVTLTSIVPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPDEVTLTSIVPTR 14 0 A0A0C4DGG1;Q9UKS6;H0YDM6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 S(1)PDEVTLTSIVPTR;S(1)PDEVTLTSIVPTR;S(1)PDEVTLTSIVPTR;S(1)PDEVTLTSIVPTR 135.14 3.64E-05 290575000 74362.4 73207.3 63007.4 84742.8 82388.4 82445.6 68825.5 86034 172871 TRUE FALSE 64535.22043 72726.39643 93477.98939 103984.948 80749.03203 85617.33558 62150.8136 67636.29862 152434.3873 0.423363924 0.477099674 0.613234264 0.682162009 0.529729764 0.561666807 0.40772174 0.443707616 1 17.21782887 1.233212054 24.9971931 1.000000758 0.517409174 0.757288621 0.085874038 93.93825716 438983.6672 0.194268112 0.023258886 17.10850471 -1.233212054 -0.482591583 S(ph)PDKPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPDKPGK 7 1 P55317-2;P55317;P55318;Q9Y261;Q9Y261-2 P55317-2 FOXA1;FOXA3;FOXA2 Hepatocyte nuclear factor 3-alpha;Hepatocyte nuclear factor 3-gamma;Hepatocyte nuclear factor 3-beta 1 S(1)PDKPGK 50.805 0.094201 122970000 494970 379770 337840 343680 229880 198440 466520 604250 791310 TRUE FALSE 429558.4604 377275.2659 501220.554 421717.7968 225305.8378 206074.1152 421276.9622 475035.8398 697762.2333 0.615622973 0.540693159 0.718325713 0.604386103 0.322897725 0.295335725 0.603754319 0.680799013 1 19.41237599 1.278870776 1.863550081 1.133899633 0.521981854 0.573488686 0.129503129 0.640016102 2.293512673 0.679078139 0.039472437 19.00512699 -1.278870776 -0.611917778 S(ph)PDLEASLDTLENNCHVGSDIDFRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SPDLEASLDTLENNCHVGSDIDFRPK 26 1 Q13111;Q13111-2;Q13111-3;K7EJF1 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 S(1)PDLEASLDTLENNCHVGSDIDFRPK;S(0.969)PDLEAS(0.021)LDT(0.009)LENNCHVGS(0.001)DIDFRPK;S(1)PDLEASLDTLENNCHVGSDIDFRPK;S(1)PDLEASLDTLENNCHVGSDIDFRPK;S(1)PDLEASLDTLENNCHVGSDIDFRPK 278.5 6.04E-61 891700000 591173 492537 514511 627239 546320 415196 601926 747528 1333184 TRUE FALSE 513047.9902 489301.492 763330.2405 769663.2017 535449.3009 431168.8588 543551.3092 587674.9545 1175576.506 0.43642246 0.416222585 0.649324171 0.654711282 0.455478055 0.366772266 0.46237 0.499903623 1 20.164937 1.238713217 8.220011356 1.005520412 0.493668078 0.745839624 0.093082803 0.049786249 32.82767117 0.142239917 0.024751232 17.32659473 -1.238713217 -0.511852334 S(ph)PDNSIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SPDNSIK 7 0 Q9UKL0 Q9UKL0 RCOR1 REST corepressor 1 1 S(1)PDNSIK;S(1)PDNSIK;S(1)PDNSIK;S(1)PDNSIK;S(1)PDNSIK;S(1)PDNSIK 146.88 0.002296 4490200000 8860990 6903030 5162840 6221130 4167100 5400620 8002820 9358460 13843100 TRUE FALSE 7689987.721 6857683.541 7659606.693 7633732.651 4084182.863 5608385.346 7226707.748 7357226.157 12206584.49 0.629986851 0.561801997 0.627497946 0.625378267 0.334588506 0.459455743 0.592033566 0.602726026 1 23.54115624 1.129458037 2.312732274 1.232679074 0.542559327 0.703396239 0.091474316 0.541589354 2.323966141 0.86538052 0.02579114 13.47280539 -1.129458037 -0.690119747 KPVTVS(ph)PTTPTS(ph)PTEGEAS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 2 KPVTVS(0.635)PT(0.329)T(0.036)PT(0.002)S(0.995)PT(0.003)EGEAS 177.07 2.74E-14 291700000 271040 364820 285630 393810 521950 475780 512320 629990 569240 TRUE FALSE 235221.3773 362423.4734 423761.6234 483230.5795 511564.2162 494083.5645 462635.2853 495271.5411 501945.0957 0.468619734 0.72203808 0.844238996 0.96271601 1.019163691 0.984337866 0.921685039 0.986704612 1 18.93717004 4.668802996 1.089327525 0.981908334 0.255367245 0.971643846 0.028625172 0.244579508 0.261913723 0.009620819 0.199938848 46644.77428 -4.668802996 -0.726541089 down S(ph)PDPGIVPQEAPVGNSLSELSEENFDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPDPGIVPQEAPVGNSLSELSEENFDGK 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 1 S(1)PDPGIVPQEAPVGNSLSELSEENFDGK;S(1)PDPGIVPQEAPVGNSLSELSEENFDGK 169.13 2.94E-12 348200000 629470 582230 410260 555290 589280 391380 734520 955490 706130 TRUE FALSE 546283.9446 578405.2928 608663.1082 681377.0816 577554.4809 406436.6419 663286.3635 751165.8991 622652.1158 0.877350178 0.928938131 0.977533189 1.094314247 0.927571699 0.65275076 1.065259953 1.206397409 1 19.24806681 2.016222273 24.9995636 1.123307654 0.917572593 0.335763592 0.119684388 242.7691955 374121.3841 0.050101569 0.033768586 103.8059562 -2.016222273 -0.205735061 S(ph)PDPYR ddPTM_MDA-MB-175_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 103.75 0.036105 464390000 504070 412410 307850 399480 370540 407930 419660 474670 517930 TRUE FALSE 437455.8723 409700.8516 456727.2897 490188.0397 363166.9789 423623.3311 378961.4378 373165.5144 456700.9054 0.957860751 0.89708789 1.000057771 1.073323994 0.795196538 0.927572786 0.829780351 0.8170895 1 18.80089012 3.230596532 24.9999986 0.866194238 0.977295496 0.352649915 0.072264816 195.0053644 612138.4174 0.0216317 0.024960325 1700.577903 -3.230596532 0.111101258 S(ph)PDQCSSQGSMESLEPSGAYPPCHLSPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPDQCSSQGSMESLEPSGAYPPCHLSPAK 29 0 A0A2R8Y5P9;Q8TF72;Q8TF72-2 A0A2R8Y5P9;Q8TF72-2 SHROOM3 Protein Shroom3 1 S(0.986)PDQCS(0.006)S(0.006)QGS(0.002)MESLEPSGAYPPCHLSPAK;S(1)PDQCSSQGSMESLEPSGAYPPCHLSPAK 132.12 7.42E-06 208157000 106571 98086 50033 60617 101750 101389 114012 112359 111599 TRUE FALSE 92487.37233 97441.66661 74229.12615 74381.01632 99725.37407 105289.5004 102955.1338 88331.90223 98405.89335 0.939856031 0.990201535 0.754315861 0.755859368 1.013408554 1.069951167 1.046229349 0.897628173 1 16.5864571 3.210684824 24.9992058 0.998250924 0.861801087 0.425099521 0.083769926 242.3687886 217357.2585 0.027878216 0.031617633 1624.369491 -3.210684824 -0.136449836 RAS(ph)GQAFELILSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 RASGQAFELILSPR 14 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR 228.86 9.20E-13 10797082000 1095779 1609040 1185288 1576133 2422707 2528699 2128700 2650370 2174407 TRUE FALSE 950969.0288 1598470.11 1758497.241 1934018.087 2374499.871 2625979.687 1922259.002 2083609.001 1917351.082 0.495980646 0.833686707 0.91714932 1.008692725 1.238427273 1.369587298 1.00255974 1.086712298 1 20.8706831 4.675255774 0.997738315 1.126590725 0.230412745 0.751191979 0.116311667 0.943098337 0.817403083 0.041181637 0.889617268 47342.99992 -4.675255774 -0.89617798 down S(ph)PDSTANVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPDSTANVR 9 0 B7ZM87;O75044;A0A075B7B5;E9PDX4;A0A087WW56;A0A286YEY3;P0DMP2 B7ZM87 SRGAP2;SRGAP2B SLIT-ROBO Rho GTPase-activating protein 2;SLIT-ROBO Rho GTPase-activating protein 2B 1 S(0.995)PDS(0.004)T(0.001)ANVR 77.358 0.023291 0 663380 600350 391170 411910 606940 593780 619510 731790 375660 TRUE FALSE 575712.6522 596406.2613 580341.1204 505440.4612 594863.0815 616623.1008 559430.0156 575302.4033 331249.9028 1.73800097 1.800472261 1.751973708 1.525858444 1.795813603 1.861504247 1.688845826 1.736762482 1 18.33756051 1.23855371 24.9945587 0.999999235 1.73661659 0.873310231 0.088265748 0.058987761 196856.797 0.120802742 0.021681879 17.32023221 -1.23855371 0.736617355 S(ph)PEAQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPEAQPK 7 0 P55265-5;P55265;P55265-4 P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 1 S(1)PEAQPK;S(1)PEAQPK 84.615 0.022464 2476700000 4184700 3512500 2634700 3033900 2023100 2605700 4139300 4898300 4840100 TRUE FALSE 3631681.292 3489426.156 3908849.733 3722793.365 1982844.268 2705942.965 3737871.323 3850836.664 4267908.892 0.850927558 0.817596215 0.915870004 0.872275735 0.46459386 0.634020789 0.875808603 0.902277148 1 22.02509795 1.803311079 2.455387878 0.965072041 0.762382581 0.260668771 0.133154119 0.423359323 4.851588518 0.116319046 0.041104719 63.57861741 -1.803311079 -0.202689461 S(ph)PEASQTDS(ph)PVESPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPEASQTDSPVESPR 15 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 S(1)PEASQTDS(1)PVESPR;S(1)PEASQT(0.002)DS(0.998)PVESPR;S(1)PEASQT(0.004)DS(0.996)PVESPR 294.93 7.32E-44 1019720000 764570 615370 413880 540970 580840 613370 589270 663230 678930 TRUE FALSE 663530.1373 611327.594 614033.7523 663805.5067 569282.4204 636966.7408 532122.6861 521403.4258 598667.6688 1.108344699 1.021146833 1.025667134 1.10880467 0.950915591 1.063973844 0.88884487 0.870939676 1 19.19139583 2.238166819 24.9999789 0.908427088 1.042867852 0.525619151 0.056251034 7.326603619 465058.3652 0.021097557 0.015222683 173.0480937 -2.238166819 0.134440764 S(ph)PEAVGPELEAEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPEAVGPELEAEEK 14 0 Q96N64-3;Q96N64-2;Q96N64 Q96N64-3 PWWP2A PWWP domain-containing protein 2A 1 S(1)PEAVGPELEAEEK 247.79 7.63E-18 206400000 320170 243590 173100 189730 222990 161440 255810 309220 277920 TRUE FALSE 277858.7233 241989.8413 256811.739 232811.0963 218552.9353 167650.7013 231001.5856 243095.7094 245064.6142 1.133818214 0.987453215 1.047934806 0.949998828 0.891817597 0.684108156 0.942615017 0.991965773 1 17.90280266 3.647583887 2.691878134 0.905993589 1.053538533 0.363488547 0.093069662 0.363710458 5.128151358 0.029619239 0.049265525 4442.054543 -3.647583887 0.147544944 S(ph)PEAVGSECPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPEAVGSECPSR 12 0 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 S(1)PEAVGSECPSR 145.31 6.69E-05 179030000 24086 13081 9530.4 24851 19806 23126 20682 23630 27539 TRUE FALSE 20902.97407 12995.07005 14139.33332 30493.79937 19411.89935 24015.67218 18676.26282 18576.90839 24283.37079 0.860793761 0.535142759 0.582264029 1.255748209 0.799390641 0.988976052 0.769096802 0.765005342 1 14.56768108 S(ph)PEDQLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPEDQLGK 8 0 Q9UK61-3;Q9UK61;Q9UK61-2 Q9UK61-3 FAM208A Protein FAM208A 1 S(1)PEDQLGK;S(1)PEDQLGK;S(1)PEDQLGK;S(1)PEDQLGK 145.46 0.00059692 849230000 1558080 1092680 974790 1065840 1153550 992340 1345200 1606130 1747350 TRUE FALSE 1352175.78 1085502.113 1446201.704 1307855.262 1130596.612 1030515.962 1214742.711 1262671.598 1540780.274 0.877591571 0.704514545 0.938616446 0.848826588 0.733781858 0.668827334 0.788394511 0.819501405 1 20.55522971 1.224335715 3.242058751 1.039141087 0.791993871 0.387699157 0.080495537 0.400605806 5.543874236 0.257902282 0.021082499 16.76238127 -1.224335715 -0.247147216 S(ph)PEIHR ddPTM_MDA-MB-175_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 98.009 0.042402 5395700000 676910 573640 516130 563370 449310 542820 539580 592720 1253440 TRUE FALSE 587454.6284 569871.7211 765732.1944 691291.7691 440369.6101 563702.6367 487251.6146 465971.4406 1105259.751 0.531508207 0.515599813 0.692807454 0.625456386 0.398430875 0.510018243 0.440848058 0.421594508 1 20.07595403 1.231882039 24.99970937 1.000000823 0.513898969 0.742254252 0.089424604 129.8533826 486030.8106 0.227023043 0.023988698 17.05619054 -1.231882039 -0.486101854 SSS(ph)NASSVSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSSNASSVSTR 11 0 P98177-2;P98177 P98177-2 FOXO4 Forkhead box protein O4 1 SS(0.002)S(0.996)NAS(0.001)S(0.001)VSTR;S(0.002)S(0.086)S(0.911)NAS(0.001)SVSTR;S(0.001)S(0.024)S(0.974)NAS(0.001)SVSTR 125.82 0.00033607 146224000 136468 206174 193337 232346 260003 351641 292923 355929 400696 TRUE FALSE 118433.408 204819.6294 286835.4199 285103.7105 254829.449 365168.8568 264515.3725 279816.3532 353326.1754 0.335195681 0.57968994 0.811814804 0.806913641 0.721230033 1.033517702 0.748643579 0.791949119 1 18.43064111 4.681696752 1.292143064 0.846540716 0.132142546 0.748022044 0.099400904 0.616721908 0.975153286 0.028122208 0.568455844 48050.37171 -4.681696752 -0.71439817 down S(ph)PENSTLEEILGQYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPENSTLEEILGQYQR 16 0 Q86SQ7-3;Q86SQ7-4;Q86SQ7;Q86SQ7-2 Q86SQ7-3 SDCCAG8 Serologically defined colon cancer antigen 8 1 S(1)PENSTLEEILGQYQR;S(1)PENSTLEEILGQYQR;S(1)PENSTLEEILGQYQR 171.78 5.04E-09 66407000 29686.4 36388.5 24531.4 25313.3 33640.5 38048.8 36075.7 38535.5 47924.3 TRUE FALSE 25763.26702 36149.46155 36394.86709 31061.07165 32971.11987 39512.56196 32577.08417 30294.98321 42258.74385 0.609655297 0.855431521 0.861238735 0.735021177 0.780220065 0.935015061 0.770895706 0.716892658 1 15.36696226 4.744670045 24.57850399 0.81950672 0.609655179 0.376923036 0.088522491 623.0926459 2506640.377 0.021164499 0.186975434 55548.20697 -4.744670045 -0.209851541 S(ph)PEPDGPAPAFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SPEPDGPAPAFLR 13 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 S(1)PEPDGPAPAFLR;S(1)PEPDGPAPAFLR;S(1)PEPDGPAPAFLR;S(1)PEPDGPAPAFLR;S(1)PEPDGPAPAFLR;S(1)PEPDGPAPAFLR 221.75 1.95E-11 1999420000 853489 731562 617515 783970 736583 717266 713946 783048 1699950 TRUE FALSE 740698.2662 726756.3211 916147.3195 961982.3707 721926.4394 744859.6872 644707.6268 615599.2789 1498983.848 0.494133587 0.484832657 0.611178914 0.641756329 0.481610553 0.496909749 0.430096447 0.410677727 1 20.51555341 1.231936444 24.99965144 1.000000837 0.504094909 0.825888661 0.071217739 104.1382322 392981.1531 0.187107272 0.019856484 17.05832734 -1.231936444 -0.495905928 S(ph)PEPEATLTFPFLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 SPEPEATLTFPFLDK 15 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;H0Y8P3 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 S(1)PEPEATLTFPFLDK;S(1)PEPEATLTFPFLDK;S(1)PEPEATLTFPFLDK;S(1)PEPEATLTFPFLDK;S(1)PEPEATLTFPFLDK;S(1)PEPEATLTFPFLDK;S(1)PEPEATLTFPFLDK;S(0.911)PEPEAT(0.089)LTFPFLDK;S(0.996)PEPEAT(0.004)LTFPFLDK;S(1)PEPEATLTFPFLDK 207.08 3.75E-09 4881946000 942034 821794 852328 1004047 876717 702856 1030566 1200182 1892042 TRUE FALSE 817541.8201 816395.5811 1264516.672 1232031.217 859272.047 729895.3251 930621.8679 943532.4191 1668366.95 0.490025183 0.489338141 0.757936779 0.73846537 0.515037802 0.43749088 0.557804066 0.565542502 1 20.67000521 1.238102646 25 1.000000484 0.571194066 0.62901551 0.104020626 8.015546709 437076.6247 0.155937025 0.027236974 17.30225252 -1.238102646 -0.428806418 S(ph)PEPEVLSTQEDLFDQSNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPEPEVLSTQEDLFDQSNK 19 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 S(1)PEPEVLSTQEDLFDQSNK;S(1)PEPEVLSTQEDLFDQSNK;S(1)PEPEVLSTQEDLFDQSNK 250.38 1.78E-25 461770000 507870 394620 405890 497280 417360 337456 493380 607720 1048610 TRUE FALSE 440753.6927 392027.7152 602179.7616 610195.0244 409055.3526 350438.1507 445532.0835 477763.8073 924644.5204 0.476673665 0.423976681 0.651255427 0.659923907 0.442392015 0.378997704 0.481841479 0.516699982 1 19.8185393 1.23846662 6.586748124 1.013337356 0.50371184 0.749758309 0.090094049 0.064162826 13.4933675 0.146451026 0.02396213 17.31675929 -1.23846662 -0.509625516 S(ph)PEPGQTWTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPEPGQTWTR 10 0 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 S(1)PEPGQTWTR;S(1)PEPGQTWTR;S(1)PEPGQTWTR;S(1)PEPGQTWTR 136.53 0.00012087 3898090000 587923 433552 363081 586615 518176 468341 401378 596109 1126220 TRUE FALSE 510227.4859 430703.9684 538668.186 719814.9016 507865.3114 486358.3813 362452.4233 468635.7293 993079.5546 0.513783094 0.433705403 0.542421988 0.724831055 0.511404458 0.489747653 0.364978235 0.471901498 1 19.92154977 1.236337205 24.99486694 1.000000642 0.503617174 0.740239067 0.091840485 33.02936935 371215.9687 0.156623427 0.024255997 17.23206027 -1.236337205 -0.496383468 S(ph)PERPTGDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPERPTGDLR 10 1 Q5T200;Q5T200-2;Q5T9K0 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 S(1)PERPTGDLR;S(1)PERPTGDLR;S(1)PERPTGDLR;S(1)PERPTGDLR 116.51 0.00065442 3733230000 3732760 3371200 2344300 2653290 3531010 3137750 3212140 3567980 3421500 TRUE FALSE 3239466.308 3349054.365 3478011.321 3255760.047 3460749.809 3258461.273 2900627.157 2804995.243 3017014.168 1.073732548 1.110055896 1.152799134 1.079133165 1.147077745 1.080028496 0.961423114 0.929725579 1 21.52469004 2.292131745 3.847619396 0.954873662 1.11275909 0.835670056 0.030196952 0.072862017 2.210614185 0.011694763 0.008453215 195.9438988 -2.292131745 0.157885428 S(ph)PESCSKPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPESCSKPEK 10 1 Q03111 Q03111 MLLT1 Protein ENL 1 S(0.999)PESCSKPEK;S(0.995)PES(0.004)CS(0.001)KPEK;S(0.994)PES(0.006)CSKPEK;S(1)PESCSKPEK 144.28 8.54E-05 2280160000 4348320 3068810 2395040 2657380 2250528 1899889 3765510 4615030 3993600 TRUE FALSE 3773678.495 3048650.785 3553289.355 3260778.745 2205746.896 1972978.959 3400331.42 3628141.749 3521481.158 1.071616836 0.865729688 1.009032619 0.925967966 0.626369075 0.560269634 0.965596937 1.030288559 1 21.74775093 3.467472164 24.97822053 0.8492862 0.969989022 0.149629324 0.158096291 524.7649317 1358432.186 0.052154992 0.067416513 2934.081442 -3.467472164 0.120702822 S(ph)PESDRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPESDRPR 8 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 S(1)PESDRPR;S(1)PESDRPR;S(1)PESDRPR 137.46 0.00045253 425383000 103475 63378.4 62797.3 81932.2 54474.7 70624.4 61860.8 80489 156312 TRUE FALSE 89800.51658 62962.06312 93166.28432 100536.1583 53390.76005 73341.36637 55861.54914 63277.05372 137832.9734 0.651516936 0.456799716 0.675936113 0.729405713 0.3873584 0.532103201 0.405284365 0.459085023 1 17.07256154 1.233249071 24.9999979 1.000000734 0.530332039 0.608842052 0.116467147 120.5785808 567467.0353 0.243840228 0.029281867 17.109963 -1.233249071 -0.469668695 S(ph)PETALEAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPETALEAFK 10 0 Q68DA7-5;Q68DA7-3 Q68DA7-5 FMN1 Formin-1 1 S(1)PETALEAFK;S(1)PETALEAFK;S(1)PETALEAFK;S(1)PETALEAFK 143.97 3.46E-05 321033000 524466 484474 464004 581130 608340 506818 643920 769020 983830 TRUE FALSE 455156.4893 481291.4584 688397.8864 713084.4485 596235.2242 526315.6164 581472.7375 604571.0575 867522.7382 0.524662316 0.554788292 0.793521433 0.821977819 0.687284838 0.606687979 0.670268008 0.696893615 1 19.72654205 -1.999999999 0.04725385 1.897855781 1.13E-12 0.30987193 0.115797237 2091.589481 9.684644073 332.8116891 112.6467204 0.01 1.999999999 -1.897855781 S(ph)PFEGAVTESQSLFSDNFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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(0.998)PFEGAVT(0.002)ESQSLFSDNFR;S(0.924)PFEGAVT(0.076)ESQSLFSDNFR;S(0.999)PFEGAVT(0.001)ESQSLFSDNFR;S(1)PFEGAVTESQSLFSDNFR;S(1)PFEGAVTESQSLFSDNFR 385.59 8.04E-127 1790617000 310875 306440 203882 240716 335264 321656 295762 376882 330517 TRUE FALSE 269792.0811 304426.9755 302480.0171 295374.2469 328592.9023 334030.3145 267079.0468 296288.7172 291443.6568 0.925709223 1.044548297 1.037867904 1.013486621 1.127466303 1.146123124 0.916400273 1.016624347 1 18.15285748 7.036646574 19.28405578 1.026956287 0.349630801 0 0.073196815 0 0 0.016595642 0 10880442.91 -7.036646574 -0.677325486 S(ph)PFLKPDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPFLKPDER 9 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 S(1)PFLKPDER 69.672 0.067352 0 234410 196210 133750 143370 185960 157960 205820 228280 197470 TRUE FALSE 203432.1246 194921.0836 198431.9474 175924.3498 182259.7598 164036.8234 185859.6081 179464.0985 174125.3216 1.16830868 1.119429856 1.139592712 1.010331801 1.046715999 0.942061855 1.067389891 1.030660543 1 17.40976649 3.741263067 24.73885641 1.019083094 1.14014237 0.746082422 0.034684025 101.9939197 933670.1371 0.009011576 0.014776056 5511.414407 -3.741263067 0.121059275 S(ph)PGAAGLTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPGAAGLTSR 10 0 Q53T59;F6TR53 Q53T59 HS1BP3 HCLS1-binding protein 3 1 S(1)PGAAGLTSR 103.65 0.002923 233240000 218440 202540 116720 108820 180840 186590 160220 206690 152950 TRUE FALSE 189572.6005 201209.5014 173166.1824 133529.2442 177241.6378 193768.238 144681.8891 162490.952 134868.4252 1.405611434 1.491894793 1.283963849 0.990070463 1.314181859 1.43672055 1.072763242 1.204810923 1 17.04119311 8 0.211393987 1.065818472 3.062402143 0.33962121 0.144890156 124.2833046 1.883825921 0.82645383 80.8946023 100000000 -8 1.996583672 S(ph)PGAFDMSGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 SPGAFDMSGVR 11 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR 169.33 1.78E-05 8659920000 1404263 1735850 1583916 2049120 2463870 2440560 2247880 2720990 3399790 TRUE FALSE 1218686.087 1724447.087 2349903.075 2514404.015 2414843.807 2534449.922 2029880.944 2139127.463 2997870.699 0.406517228 0.575223971 0.783857381 0.838729974 0.805519667 0.84541669 0.67710757 0.713548941 1 21.51550673 4.437902649 2.365969952 0.797857608 0.40380826 0.716701261 0.086494738 0.193388762 1.913393834 0.023345161 0.119806791 27409.59694 -4.437902649 -0.394049348 S(ph)PGAPGPLTLK ddPTM_MDA-MB-175_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 156.14 3.27E-05 20554600000 16247200 18740400 14167900 19865400 23693800 20007300 27194700 34067300 29440100 TRUE FALSE 14100091.35 18617293.08 21019543.83 24376142.69 23222339.74 20776993.78 24557362.18 26782273.01 25959724.92 0.543152572 0.717160646 0.80969825 0.938998498 0.894552612 0.800354928 0.945979291 1.031685547 1 24.62977176 5.287502493 0.499958459 0.979552369 3.69E-22 0.835927587 0.058916642 3.510771679 0.469229368 0.047405485 2.256968669 193866.3765 -5.287502493 -0.979552369 S(ph)PGASNFSTLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SPGASNFSTLPK 12 0 Q9Y4E8 Q9Y4E8 USP15 Ubiquitin carboxyl-terminal hydrolase 15 1 S(0.994)PGAS(0.006)NFSTLPK;S(1)PGASNFSTLPK;S(1)PGASNFSTLPK;S(1)PGASNFSTLPK;S(1)PGASNFSTLPK;S(1)PGASNFSTLPK 183.28 1.66E-05 3673460000 1759820 1715580 1265040 1595110 1752400 1514420 1971830 2441780 2509860 TRUE FALSE 1527255.328 1704310.242 1876817.575 1957304.105 1717530.669 1572680.717 1780602.23 1919624.349 2213147.21 0.690083028 0.770084445 0.84803106 0.884398515 0.776058032 0.710608273 0.804556616 0.867373097 1 21.07766799 1.326440788 1.941469112 1.045154371 0.785812277 0.60167707 0.056836926 0.503947049 2.196499816 0.225515527 0.016784374 21.20512263 -1.326440788 -0.259342094 S(ph)PGDFTSAAQLASTPFHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPGDFTSAAQLASTPFHK 18 0 A0A590UJ99;O43683-2;O43683-3;O43683 A0A590UJ99 BUB1 Mitotic checkpoint serine/threonine-protein kinase BUB1 1 S(1)PGDFTSAAQLASTPFHK 167.34 1.51E-11 389560000 182060 181880 110790 164410 213830 185930 186650 259510 224690 TRUE FALSE 158000.3097 180685.2183 164368.4146 201741.8033 209575.2014 193082.8474 168548.7117 204015.806 198127.4042 0.797468227 0.911964799 0.829609691 1.018242803 1.057779979 0.974538824 0.850708727 1.02972028 1 17.59606892 3.74076556 24.9754198 0.986485602 0.852909289 0.543427669 0.061305709 161.8522726 1833293.679 0.016862349 0.027512816 5505.104401 -3.74076556 -0.133576313 S(ph)PGDGHNAPVEGPEGEYVELLEVTLPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPGDGHNAPVEGPEGEYVELLEVTLPVR 28 0 Q8TER5;Q8TER5-4;Q8TER5-3;G3V485;G3V3N2;G3V5C1 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 S(1)PGDGHNAPVEGPEGEYVELLEVTLPVR;S(1)PGDGHNAPVEGPEGEYVELLEVTLPVR 145.52 6.10E-08 48179000 9758.2 9552 9411.1 8064.6 9436.6 9322.1 9639 12671.6 9139.8 TRUE FALSE 8468.629146 9489.252283 13962.33944 9895.79069 9248.830122 9680.727219 8704.211264 9961.876951 8059.303256 1.05078924 1.177428368 1.732449939 1.227871737 1.147596737 1.201186618 1.080020318 1.236071734 1 12.9764394 3.482489644 24.91804179 1.149158656 1.334979372 0.176129751 0.182835946 392.1234707 1820092.588 0.052309985 0.069633209 3037.313663 -3.482489644 0.185820716 S(ph)PGEPGGAAPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPGEPGGAAPER 12 0 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 S(1)PGEPGGAAPER;S(1)PGEPGGAAPER;S(1)PGEPGGAAPER 93.096 0.0077255 174525000 81537 66996 42281.8 46188 63581 62219 73671 78605 61144 TRUE FALSE 70761.67886 66555.89886 62729.4199 56675.69134 62315.86249 64612.60519 66526.39776 61795.93245 53915.62598 1.312452143 1.234445444 1.163473831 1.051192309 1.155803375 1.198402208 1.233898273 1.146159974 1 15.71841584 4.424371936 2.401673487 1.140878868 1.310146907 0.446618866 0.067011908 0.339185761 3.509529337 0.018363357 0.089730817 26568.79978 -4.424371936 0.169268039 S(ph)PGETSKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPGETSKPR 9 1 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 S(0.996)PGET(0.004)SKPR;S(0.999)PGET(0.001)SKPR;S(0.994)PGET(0.006)SKPR;S(0.999)PGET(0.001)SKPR 115.33 0.00090479 1162110000 1222870 1186650 1248250 1687410 858600 1000960 1392970 1600700 5256700 TRUE FALSE 1061264.631 1178854.818 1851907.875 2070562.231 841515.5398 1039467.579 1257879.984 1258402.762 4635258.914 0.228954768 0.254323402 0.399526307 0.44669829 0.181546609 0.224252323 0.271372108 0.271484891 1 22.1442185 1.237849334 24.99946401 1.000000823 0.286097098 0.886666587 0.080360083 5.769087562 202621.2461 0.120578712 0.020718926 17.29216355 -1.237849334 -0.713903725 S(ph)PGETSKPRPFAGGGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPGETSKPRPFAGGGYR 17 2 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 S(1)PGETSKPRPFAGGGYR;S(0.984)PGET(0.013)S(0.004)KPRPFAGGGYR;S(0.999)PGET(0.001)SKPRPFAGGGYR;S(0.98)PGET(0.018)S(0.002)KPRPFAGGGYR 175.33 6.49E-10 4893560000 1993270 1950780 1369280 1659820 1885000 1599530 2126190 2474090 1625080 TRUE FALSE 1729854.319 1937965.198 2031468.388 2036707.5 1847492.188 1661064.954 1919992.421 1945025.107 1432964.894 1.207185415 1.352416382 1.417667939 1.421324073 1.289279449 1.159180495 1.339874012 1.357343167 1 20.45057183 3.007589857 23.1739388 1.245601216 1.354779388 0.215191029 0.11514959 137.8647136 420928.8819 0.03536281 0.040005715 1017.629895 -3.007589857 0.109178172 S(ph)PGEYINIDFGEPGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPGEYINIDFGEPGAR 16 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 S(1)PGEYINIDFGEPGAR;S(1)PGEYINIDFGEPGAR;S(1)PGEYINIDFGEPGAR;S(1)PGEYINIDFGEPGAR 238.45 9.02E-20 567660000 295116 251452 227801 265010 265346 281584 265258 306623 487030 TRUE FALSE 256115.6729 249800.1953 337966.3255 325184.5709 260066.1337 292416.7187 239533.32 241054.0576 429453.8682 0.596375285 0.58166945 0.786967706 0.757204894 0.605574086 0.680903679 0.557762632 0.561303729 1 18.71214364 1.230862892 24.99850859 1.000000646 0.639818863 0.669882964 0.079204039 188.2893548 611422.0439 0.220561447 0.021095151 17.01621217 -1.230862892 -0.360181782 S(ph)PGGGS(ph)EANGLALVSGFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPGGGSEANGLALVSGFK 18 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 S(1)PGGGS(1)EANGLALVSGFK;S(1)PGGGS(1)EANGLALVSGFK 125.79 7.76E-05 0 83736 81590 57416 61604 85326 71784 86149 100797 103652 TRUE FALSE 72670.07544 81054.02992 85182.56964 75592.12976 83628.17954 74545.57693 77794.28324 79242.34595 91398.37864 0.795091516 0.88682131 0.931992131 0.827062043 0.914985373 0.81561159 0.851156053 0.866999471 1 16.47988095 1.238898189 6.549385016 1.003731054 0.862939667 0.511918635 0.042579109 0.096736705 19.8340282 0.06073408 0.009982317 17.33397594 -1.238898189 -0.140791387 S(ph)PGGGSEANGLALVSGFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SPGGGSEANGLALVSGFK 18 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK 449.39 7.04E-191 7669890000 5774970 5209870 4053370 5266340 5267470 4450250 6345770 7185170 7392270 TRUE FALSE 5011793.083 5175646.021 6013593.29 6462142.988 5162657.653 4621453.997 5730358.202 5648677.311 6518364.262 0.768872816 0.794009941 0.922561712 0.991374941 0.79201736 0.708989834 0.879109846 0.866578958 1 22.63607854 1.107647025 1.926279125 1.100065322 0.8380993 0.2882736 0.0801512 1.806040205 4.785670107 0.968273133 0.023359255 12.81288785 -1.107647025 -0.261966022 S(ph)PGGGSEANGLALVSGFKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPGGGSEANGLALVSGFKR 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 S(1)PGGGSEANGLALVSGFKR;S(1)PGGGSEANGLALVSGFKR;S(1)PGGGSEANGLALVSGFKR;S(1)PGGGSEANGLALVSGFKR 226.24 9.48E-20 2754080000 2203910 1911430 845940 984960 1781600 1669770 2175750 2560860 305314 TRUE FALSE 1912657.71 1898873.69 1255039.413 1208610.222 1746149.646 1734007.132 1964746.1 2013240.018 269220.1267 7.10443804 7.053238231 4.66175924 4.489301141 6.485955069 6.440852522 7.297916852 7.478044239 1 18.03842674 4.326769099 11.62166213 5.736683636 7.086883157 0.101723779 1.876033458 1.336411165 168.0715589 0.467119488 1.236735081 21221.15898 -4.326769099 1.350199521 S(ph)PGGPGSHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SPGGPGSHVR 10 0 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 S(1)PGGPGSHVR;S(1)PGGPGSHVR;S(1)PGGPGSHVR;S(1)PGGPGSHVR;S(1)PGGPGSHVR;S(1)PGGPGSHVR 147.26 1.75E-05 1896217000 1219405 1135054 880777 912401 1044552 1215009 1170595 1170561 1722359 TRUE FALSE 1058257.54 1127597.756 1306723.703 1119575.592 1023767.459 1261751.182 1057070.877 920245.6395 1518743.681 0.696797987 0.742454286 0.860397788 0.737172181 0.674088374 0.830786128 0.696016642 0.605925576 1 20.53444698 3.567414433 22.67901695 0.737296501 0.769914004 0 0.113038109 172.0922988 43210.54801 0.030672116 0.045494065 3693.298701 -3.567414433 0.032617503 S(ph)PGHMVILDQTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 SPGHMVILDQTK 12 0 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 1 S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK 272.96 6.05E-28 9147370000 11554690 8866310 7009420 8555230 8343280 7349230 9645070 10840200 13441000 TRUE FALSE 10027708.44 8808066.626 10399198.96 10497825.73 8177265.051 7631959.634 8709692.596 8522107.589 11852020.29 0.846075875 0.74317006 0.877419942 0.885741458 0.689946933 0.643937442 0.734869869 0.719042609 1 23.49862967 4.760177368 22.03459463 0.777479448 0.846076155 0.023084351 0.107044719 4382.952173 4467303.336 0.026491317 0.963860734 57567.49982 -4.760177368 0.068596707 S(ph)PGIISQASAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPGIISQASAPR 12 0 Q08495;Q08495-2;Q08495-3;Q08495-4;E5RGQ0;E5RFK4;E5RGQ7;E5RJC0 Q08495 DMTN Dematin 1 S(1)PGIISQASAPR;S(1)PGIISQASAPR;S(1)PGIISQASAPR;S(1)PGIISQASAPR 202.58 1.42E-07 883180000 69179 103300 74246 92946 149907 131598 142944 139036 130020 TRUE FALSE 60036.81987 102621.4155 110151.6139 114050.8099 146924.144 136660.6602 129081.3129 109304.2334 114649.1837 0.523656758 0.895090677 0.960771027 0.994780828 1.281510598 1.191989823 1.125880784 0.953379953 1 16.80686656 4.98327744 1.089498218 1.088703463 2.61E-17 0.765287789 0.098629707 1.481341359 1.024976971 0.034109158 2.101961443 96222.67813 -4.98327744 -1.088703463 S(ph)PGKAEAESDALPDDTVIESEALPSDIAAEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPGKAEAESDALPDDTVIESEALPSDIAAEAR 32 1 G3V529;Q9GZR7;Q9GZR7-2;A0A1W2PRR2;F5GYL3 G3V529 DDX24 ATP-dependent RNA helicase DDX24 1 S(0.906)PGKAEAES(0.094)DALPDDTVIESEALPSDIAAEAR;S(0.936)PGKAEAES(0.064)DALPDDTVIESEALPSDIAAEAR;S(0.998)PGKAEAES(0.002)DALPDDTVIESEALPSDIAAEAR;S(1)PGKAEAESDALPDDTVIESEALPSDIAAEAR 218.63 4.55E-36 526506000 699950 588038 421891 447953 623186 411946 684090 783430 431865 TRUE FALSE 607449.8341 584175.1397 625918.8987 549667.5752 610785.8178 427793.8292 617747.0571 615899.5912 380810.4117 1.595150278 1.534031428 1.643649647 1.443415301 1.6039105 1.12337745 1.622190566 1.61733916 1 18.5387134 S(ph)PGLCSDSLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPGLCSDSLEK 11 0 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 S(1)PGLCSDSLEK;S(1)PGLCSDSLEK;S(1)PGLCSDSLEK;S(1)PGLCSDSLEK 215.14 1.37E-11 1217030000 2085810 1444450 1188920 1515080 1499260 1207210 1594520 2031810 2849680 TRUE FALSE 1810164.924 1434961.313 1763885.689 1859102.071 1469427.659 1253652.15 1439883.696 1597323.243 2512794.077 0.720379334 0.571062041 0.701961894 0.739854526 0.584778384 0.498907635 0.573020969 0.635676141 1 21.26086102 1.239387488 6.661257421 1.009542749 0.623866204 0.705084216 0.075562623 0.067118191 14.94313375 0.117490656 0.019578084 17.3535163 -1.239387488 -0.385676546 S(ph)PGLLDTTPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPGLLDTTPIR 11 0 Q8IY92-2;Q8IY92 Q8IY92-2 SLX4 Structure-specific endonuclease subunit SLX4 1 S(1)PGLLDTTPIR;S(1)PGLLDTTPIR 107.09 0.002354 469850000 333410 356520 238780 268020 349040 360920 279790 345380 372350 TRUE FALSE 289349.0237 354177.9966 354254.8067 328878.0374 342094.7869 374804.8259 252656.0089 271523.1748 328331.2072 0.881271769 1.078721696 1.078955637 1.001665484 1.041919804 1.141544933 0.76951567 0.826979491 1 18.32479236 2.235214295 24.99999991 0.853474336 1.039704573 0.458484508 0.087691475 69.35681703 518147.1299 0.033988588 0.023976094 171.875627 -2.235214295 0.186230237 S(ph)PGLLSSDNPQLSALLMGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPGLLSSDNPQLSALLMGK 19 0 H0Y6I7;F5H5V6;F5H6S1;F8W8R6;A0A087X0R0;O15550 H0Y6I7 KDM6A Lysine-specific demethylase 6A 1 S(0.928)PGLLS(0.072)SDNPQLSALLMGK;S(0.999)PGLLS(0.001)SDNPQLSALLMGK 272.13 2.54E-39 314820000 471990 348710 290698 418580 391970 322740 394060 505840 842370 TRUE FALSE 409615.3256 346419.301 431280.5251 513624.9866 384170.5639 335156.0166 355844.1219 397670.0525 742785.9782 0.551458075 0.466378353 0.580625561 0.691484494 0.517202229 0.451214787 0.479066827 0.535376359 1 19.50258706 1.238742552 10.11780432 1.001793891 0.532599365 0.821158822 0.068328506 0.030753459 72.08814898 0.100039961 0.017846038 17.32776511 -1.238742552 -0.469194526 S(ph)PGLVPPS(ph)PEFAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPGLVPPSPEFAPR 14 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 2 S(1)PGLVPPS(1)PEFAPR;S(1)PGLVPPS(1)PEFAPR;S(1)PGLVPPS(1)PEFAPR;S(1)PGLVPPS(1)PEFAPR 144.97 1.27E-05 617890000 1657140 1307190 978430 1165160 1390010 1214160 1307640 1496870 1677810 TRUE FALSE 1438144.75 1298602.983 1451602.021 1429727.386 1362351.521 1260869.521 1180825.274 1176775.999 1479461.213 0.972073304 0.87775399 0.981169366 0.966383825 0.920843013 0.852249123 0.798145476 0.795408483 1 20.49664044 2.807895225 3.446928755 0.844458738 0.946068577 0.28728522 0.063086619 0.27250844 6.377334668 0.021506142 0.021045942 642.532685 -2.807895225 0.101609839 S(ph)PGMLEPLGSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SPGMLEPLGSSR 12 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR 179.43 2.17E-05 7270500000 2414662 1758699 1412911 1948435 1989677 2004748 1790224 2214676 3953490 TRUE FALSE 2095558.299 1747145.99 2096199.486 2390856.947 1950086.32 2081871.953 1616608.352 1741084.772 3486112.916 0.601116014 0.501173092 0.60129994 0.685823152 0.559387021 0.597190052 0.463728052 0.499434417 1 21.73318787 1.233755954 24.99999483 1.000000668 0.559908493 0.820454682 0.0641298 65.36275511 340059.2127 0.134928171 0.016938404 17.12994441 -1.233755954 -0.440092175 S(ph)PGNLTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPGNLTER 8 0 Q9H0F6-2;Q9H0F6 Q9H0F6-2 SHARPIN Sharpin 1 S(1)PGNLTER;S(1)PGNLTER;S(1)PGNLTER;S(1)PGNLTER 110.54 0.0035728 3935690000 994100 1197190 830250 994720 1060090 1260120 978500 1156010 1440380 TRUE FALSE 862727.1663 1189325.58 1231761.677 1220586.379 1038996.283 1308597.632 883605.2206 908806.2576 1270099.917 0.679259289 0.936403163 0.969814784 0.961016029 0.81804295 1.030310776 0.695697408 0.715539183 1 20.27651057 2.226135221 24.99983067 0.780867231 0.903173557 0.104298966 0.125601039 395.011384 794754.2617 0.049695606 0.033768372 168.3198056 -2.226135221 0.122306326 S(ph)PGNLTEREELAGSLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPGNLTEREELAGSLAR 17 1 Q9H0F6-2;Q9H0F6 Q9H0F6-2 SHARPIN Sharpin 1 S(1)PGNLTEREELAGSLAR;S(1)PGNLTEREELAGSLAR;S(0.971)PGNLT(0.029)EREELAGSLAR;S(1)PGNLTEREELAGSLAR 296.17 2.30E-46 3969010000 189891 202581 86688.7 75595.5 173407 214478 195972 216303 65976.8 TRUE FALSE 164796.4232 201250.2321 128611.6453 92760.61368 169956.54 222729.1074 176966.6656 170048.2867 58177.09787 2.83266834 3.459269016 2.210692008 1.594452406 2.921365042 3.828467139 3.041861353 2.922942068 1 15.82816371 S(ph)PGNTSQPPAFFSK ddPTM_MDA-MB-175_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(0.999)PGNT(0.001)SQPPAFFSK;S(1)PGNTSQPPAFFSK;S(1)PGNTSQPPAFFSK;S(1)PGNTSQPPAFFSK;S(1)PGNTSQPPAFFSK 269.23 2.12E-25 4577280000 5459610 4321520 3203100 3702250 4209320 3934870 4801160 5396890 5571160 TRUE FALSE 4738108.706 4293131.651 4752129.874 4542902.448 4125562.767 4086246.995 4335544.242 4242807.072 4912543.811 0.964491898 0.873912135 0.967346055 0.92475561 0.839801725 0.831798586 0.882545664 0.863668037 1 22.22803884 3.381420957 8.751317914 0.878496321 0.93189615 0.177797131 0.052026423 0.439224995 35.93079679 0.014689476 0.018970822 2406.694453 -3.381420957 0.053399828 S(ph)PGPGPSQSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPGPGPSQSPR 11 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 S(1)PGPGPSQSPR 128.1 0.0010406 0 46032 51439 31861 34203 50349 56998 37509 37561 35349 TRUE FALSE 39948.75457 51101.09382 47269.08617 41969.31391 49347.15341 59190.74994 33871.38295 29528.87245 31170.08149 1.281637797 1.639427662 1.516489015 1.346461475 1.583157664 1.898960385 1.086663279 0.947346655 1 14.92787431 2.085420006 7.631909328 0.983928546 1.539275404 0.699510815 0.16580175 0.12046662 9.235153023 0.067412241 0.04530452 121.7362742 -2.085420006 0.555346857 S(ph)PGPPALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SPGPPALK 8 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 S(1)PGPPALK;S(1)PGPPALK;S(1)PGPPALK;S(1)PGPPALK;S(1)PGPPALK;S(1)PGPPALK 103.55 0.0049845 3209920000 4657380 3484080 2815930 3227330 3056390 2742590 3616060 4283380 5958000 TRUE FALSE 4041895.433 3461192.849 4177723.167 3960144.603 2995573.819 2848099.212 3265375.058 3367412.52 5253652.027 0.769349666 0.65881654 0.795203631 0.753788904 0.570188852 0.542117978 0.621543841 0.640966037 1 22.32488922 1.236098798 24.99573523 1.00000044 0.664681455 0.609350594 0.083226568 49.72668406 504782.5455 0.14446173 0.021966549 17.22260329 -1.236098798 -0.335318985 S(ph)PGPPALKHPATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPGPPALKHPATK 13 1 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 S(1)PGPPALKHPATK;S(1)PGPPALKHPATK 138.66 2.81E-05 511860000 1280050 912190 490710 531900 821380 621450 1154310 1247970 210680 TRUE FALSE 1110888.149 906197.7638 728018.9973 652676.0246 805036.145 645357.5836 1042365.194 981101.3272 185773.6504 5.979793942 4.877967149 3.918849609 3.51328632 4.333424806 3.473891923 5.610942088 5.281165144 1 17.50318636 4.572406122 2.63718323 4.085875166 6.064053276 0.221554416 1.251860273 0.596731513 6.699915063 0.32072307 2.173921181 37359.93589 -4.572406122 1.97817811 S(ph)PGPPPPVGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPGPPPPVGVK 11 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 S(1)PGPPPPVGVK;S(1)PGPPPPVGVK 109.24 0.0020516 783330000 872630 645680 517600 668330 636970 522690 729050 865670 996100 TRUE FALSE 757309.7345 641438.4856 767913.0913 820084.5413 624295.5432 542798.2225 658346.8432 680553.2072 878342.1928 0.862203525 0.73028313 0.874275536 0.933673172 0.710765745 0.617980358 0.749533438 0.77481557 1 19.74442358 4.803252089 19.96126912 0.792875495 0.86221133 0.028158444 0.111954026 28274.47211 8720029.421 0.028029648 43.02309718 63569.98204 -4.803252089 0.069335835 ELFDDPS(ph)YVNVQNLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ELFDDPSYVNVQNLDK 16 0 P29353-2;P29353-7;P29353;P29353-6;H0Y539;X6R6D0;P29353-5;P29353-3;Q5T188 P29353-2 SHC1 SHC-transforming protein 1 1 ELFDDPS(0.855)Y(0.145)VNVQNLDK;ELFDDPS(0.971)Y(0.029)VNVQNLDK 309.33 1.36E-57 441360000 456330 570880 583600 796460 1001890 842930 1133450 1428120 1226060 TRUE FALSE 396024.8343 567129.8517 865830.912 977308.4161 981954.3492 875358.0625 1023528.193 1122727.652 1081116.584 0.366310942 0.524577886 0.800867293 0.903980598 0.908277945 0.809679618 0.946732488 1.038488974 1 20.04409068 4.681708757 0.779856402 0.967747712 6.26E-14 0.917887803 0.060703881 0.697870853 0.349280092 0.02701119 0.582904424 48051.70001 -4.681708757 -0.967747712 down S(ph)PGRPTQGALGEQQDLSNTTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPGRPTQGALGEQQDLSNTTSK 22 1 A0A2R8YGX0;P10071 A0A2R8YGX0 GLI3 Transcriptional activator GLI3;Transcriptional repressor GLI3R 1 S(1)PGRPTQGALGEQQDLSNTTSK 140.71 7.73E-08 282280000 48970 55552 32183 46563 55495 46322 51081 64966 75187 TRUE FALSE 42498.49043 55187.07525 47746.80645 57135.84082 54390.75807 48104.03731 46127.17248 51073.52647 66298.47851 0.641017583 0.832403345 0.72017952 0.861797165 0.820392252 0.725567741 0.695750091 0.770357444 1 16.01668814 1.2406932 6.715882514 1.005746145 0.760857981 0.562528067 0.06696935 0.083670907 19.42860458 0.093942685 0.016013617 17.40576839 -1.2406932 -0.244888165 S(ph)PGSGSQSSGWHEVEPGMPS(ph)PTTLKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPGSGSQSSGWHEVEPGMPSPTTLKK 26 1 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;A0A590UJA3;S4R3W2 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 2 S(0.981)PGS(0.003)GS(0.004)QS(0.005)S(0.006)GWHEVEPGMPS(0.734)PT(0.129)T(0.138)LKK 82.384 0.016016 98384000 98426 60397 27709 58418 54960 54190 65110 97077 64535 TRUE FALSE 85418.75472 60000.24813 41109.16508 71682.69976 53866.40353 56274.72437 58795.64222 76317.839 56905.74582 1.501056765 1.054379435 0.722407983 1.259674199 0.946589887 0.988911112 1.033210994 1.34112712 1 15.79628671 0.951011141 20.36869509 0.000118784 1.100490289 0.022170463 0.2184372 209.5291024 244394.5458 37390.56122 0.051000659 8.933283993 -0.951011141 1.100371506 S(ph)PGSGSQSSGWHEVEPGMPSPTTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPGSGSQSSGWHEVEPGMPSPTTLK 25 0 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;A0A590UJA3;S4R3W2 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 1 S(0.999)PGS(0.001)GSQSSGWHEVEPGMPSPTTLK 190.82 5.11E-18 276420000 601930 319490 103050 283970 363400 303150 344330 429140 515950 TRUE FALSE 522383.4254 317391.2492 152885.3247 348449.7287 356169.051 314812.3767 310936.9296 337371.7506 454954.9788 1.148209053 0.697632214 0.336044953 0.765899364 0.782866586 0.691963802 0.683445493 0.74154975 1 18.79536426 1.238484856 4.297678162 1.026873204 0.715011245 0.156217842 0.194453667 0.405108209 14.56651852 0.391028873 0.048536261 17.31748641 -1.238484856 -0.311861959 S(ph)PGSISYLPSFFTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPGSISYLPSFFTK 14 0 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 S(1)PGSISYLPSFFTK;S(1)PGSISYLPSFFTK 242.79 1.76E-17 1875800000 2168050 1794490 1103780 1303960 1624070 1548600 1840700 2052940 1868380 TRUE FALSE 1881536.699 1782701.877 1637571.7 1600044.048 1591754.184 1608175.644 1662189.197 1613934.757 1647502.245 1.142054104 1.082063398 0.993972363 0.97119385 0.966162073 0.976129562 1.008914678 0.979625225 1 20.651849 4.386172846 2.404609148 0.983179708 1.140661308 0.945565028 0.013103025 0.068957414 0.731636524 0.003686639 0.01644639 24331.72202 -4.386172846 0.157481599 S(ph)PGSNSKVPEIEVTVEGPNNNNPQTSAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPGSNSKVPEIEVTVEGPNNNNPQTSAVR 29 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 S(0.738)PGS(0.26)NS(0.002)KVPEIEVTVEGPNNNNPQTSAVR;S(1)PGSNSKVPEIEVTVEGPNNNNPQTSAVR 380.32 1.90E-137 1070710000 427790 289550 87939 78237 289170 228175 339310 450160 14595.5 TRUE FALSE 371256.4676 287647.927 130466.5945 96001.90663 283416.0828 236953.0399 306403.7684 353896.7871 12870.03662 28.84657431 22.35020269 10.13723569 7.459334381 22.021389 18.41121723 23.80752888 27.49772962 1 13.65172854 7.99999994 0.046021365 9.999999991 33.29593418 0.032116082 8.913322328 13903.58157 62.76505316 9333.688423 26810.51084 99999986.18 -7.99999994 23.29593419 S(ph)PGSTPTTPTSSQAPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658;P35658-5;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 S(0.774)PGS(0.225)T(0.001)PTTPTSSQAPQK;S(0.851)PGS(0.148)T(0.001)PTTPTSSQAPQK 321.02 1.50E-58 564110000 785260 529220 392790 393420 425120 336990 467380 540920 597510 TRUE FALSE 681485.9014 525743.519 582744.5578 482752.024 416660.9437 349954.2234 422053.5595 425248.4674 526873.0485 1.293453714 0.997856164 1.10604359 0.916258718 0.790818481 0.664209764 0.801053614 0.807117518 1 19.00709586 3.836464262 1.312206743 0.802714614 1.184959451 0.661533716 0.105243383 0.300114745 0.973111265 0.034715211 0.098487359 6862.214075 -3.836464262 0.382244837 S(ph)PGVVISDDEPGYDLDLFCIPNHYAEDLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPGVVISDDEPGYDLDLFCIPNHYAEDLER 30 0 P00492 P00492 HPRT1 Hypoxanthine-guanine phosphoribosyltransferase 1 S(1)PGVVISDDEPGYDLDLFCIPNHYAEDLER;S(1)PGVVISDDEPGYDLDLFCIPNHYAEDLER 215.72 1.16E-34 119115000 41893 43711 27898.4 28236.8 38590 36584 42454 45017 39206 TRUE FALSE 36356.73391 43423.85956 41390.15955 34648.39701 37822.1345 37991.41015 38336.81761 35390.46487 34571.11134 1.051650713 1.256073579 1.197247006 1.002235556 1.094038723 1.098935171 1.108926388 1.023700526 1 15.07727936 -2 0.1942838 0.300821812 1.19230466 0.289861756 0.069460932 131.2410249 1.924833101 34.1626992 0.497368379 0.01 2 0.891482848 S(ph)PGYEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPGYEPR 7 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 S(1)PGYEPR;S(1)PGYEPR 108.3 0.0076397 381890000 469360 359310 232420 293910 314330 328470 344750 353360 331720 TRUE FALSE 407332.8868 356949.669 344819.0894 360646.7576 308075.448 341106.4534 311316.1981 277796.7139 292504.4395 1.39256993 1.220322227 1.178850789 1.232961654 1.053233409 1.16615821 1.064312728 0.94971794 1 18.158099 8 0.111807806 0.681087792 2.736388652 0.805804164 0.056918138 100.0538336 1.012628242 2.577890624 31.98687364 100000000 -8 2.05530086 S(ph)PHEAGFCVYLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SPHEAGFCVYLK 12 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(1)PHEAGFCVYLK;S(1)PHEAGFCVYLK;S(1)PHEAGFCVYLK;S(1)PHEAGFCVYLK;S(1)PHEAGFCVYLK 183.28 1.02E-05 2348430000 3716260 3149310 2522470 2992900 3100360 3016870 3094570 3732850 5808910 TRUE FALSE 3225146.825 3128621.975 3742344.929 3672483.689 3038668.902 3132930.941 2794459.078 2934609.077 5122187.277 0.629642504 0.610798045 0.730614624 0.716975677 0.593236588 0.611639281 0.545559724 0.572921082 1 22.28832857 1.233785855 24.9917164 1.000000572 0.624223364 0.804845971 0.057802501 71.2007129 372628.1055 0.126475466 0.015927594 17.13112387 -1.233785855 -0.375777208 S(ph)PHGQTRPPASLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPHGQTRPPASLK 13 1 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C103 Q9H8V3-2 ECT2 Protein ECT2 1 S(0.999)PHGQT(0.001)RPPASLK;S(1)PHGQTRPPASLK 93.495 0.0033839 231660000 253764 210001 152574 183320 184759 183757 226693 285129 286627 TRUE FALSE 220228.4444 208621.4896 226359.2967 224945.6079 181082.6574 190826.2507 204708.3478 224156.3822 252742.2826 0.871355763 0.825431691 0.89561309 0.890019689 0.71647156 0.755023056 0.809948955 0.88689704 1 17.94730751 1.344706517 2.474855522 1.020931579 0.822575794 0.501412257 0.056222039 0.393421538 3.169431154 0.151554634 0.016300348 22.11599672 -1.344706517 -0.198355785 S(ph)PHKDLGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPHKDLGHR 9 1 O94888;C9JAT7 O94888 UBXN7 UBX domain-containing protein 7 1 S(1)PHKDLGHR;S(1)PHKDLGHR;S(1)PHKDLGHR 87.18 0.008235 866980000 616481 550887 375110 407536 471166 487142 583271 559847 566940 TRUE FALSE 535011.4739 547268.187 556514.4507 500073.2776 461790.7184 505882.668 526705.4682 440128.0758 499916.9991 1.070200603 1.094718099 1.113213697 1.000312609 0.923734779 1.011933319 1.053585834 0.8804023 1 18.93132906 3.61922447 4.417923213 0.969581455 1.092421822 0.558224195 0.04824276 0.166212097 5.236298922 0.013852672 0.020993166 4161.256344 -3.61922447 0.122840367 S(ph)PHLWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPHLWK 6 0 P00519-2;P00519 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 S(1)PHLWK 91.065 0.031122 108770000 275360 240470 218020 250680 229920 206920 213960 268350 517050 TRUE FALSE 238970.4783 238890.3367 323455.2012 307600.7254 225345.0418 214880.3463 193210.1921 210965.4408 455924.938 0.524144346 0.523968568 0.709448364 0.674674052 0.494259083 0.471306411 0.423776319 0.462719679 1 18.7984368 1.233290971 24.99956514 1.000000729 0.53300908 0.722743346 0.090395016 103.0415484 488781.3617 0.208565839 0.02515537 17.11161383 -1.233290971 -0.466991649 S(ph)PHPDILIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPHPDILIR 9 0 H0Y4T1;Q5T0A6;Q5T0A3;Q86SQ9-3;Q86SQ9-4;Q86SQ9;Q86SQ9-2 H0Y4T1 DHDDS Dehydrodolichyl diphosphate syntase complex subunit DHDDS 1 S(1)PHPDILIR 54.416 0.087075 74829000 1439.3 0 0 1110 2374.6 1765 1306.3 1184.4 0 TRUE FALSE 1249.092858 0 0 1362.042465 2327.350106 1832.900692 1179.615227 931.125277 0 0 S(ph)PHS(ph)KSPAEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPHSKSPAEQR 11 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 2 S(1)PHS(0.628)KS(0.373)PAEQR 55.66 0.070514 249750000 587410 492860 263270 244260 326420 338350 431720 466780 266700 TRUE FALSE 509782.2802 489622.3702 390588.2526 299722.9663 319924.8806 351366.5434 389851.8608 366962.7295 235171.0298 2.16770867 2.081984208 1.660868913 1.274489322 1.360392396 1.494089403 1.65773761 1.560407886 1 17.84335082 4.150756959 2.895759669 1.429077245 2.152709722 0.734539953 0.179760039 0.137409269 2.286850695 0.049301496 0.131164875 14150.01691 -4.150756959 0.723632477 S(ph)PHSKS(ph)PAEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPHSKSPAEQR 11 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 2 S(0.996)PHS(0.163)KS(0.841)PAEQR 61.495 0.049474 86776000 226050 173580 93943 94059 124970 135320 152480 171670 92448 TRUE FALSE 196176.9198 172439.7416 139374.149 115416.5336 122483.3415 140525.848 137692.5131 134959.7064 81518.90276 2.406520612 2.115334428 1.709715714 1.415825405 1.502514599 1.723843712 1.689086928 1.655563334 1 16.31484701 4.316672007 2.111396923 1.53478786 2.40064759 0.703174948 0.205739617 0.203220171 1.664789842 0.055866369 0.241898497 20733.47071 -4.316672007 0.86585973 S(ph)PHSTVPEHHPHPISPYEHLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPHSTVPEHHPHPISPYEHLLR 22 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.999)PHS(0.001)T(0.001)VPEHHPHPISPYEHLLR;S(0.998)PHS(0.001)T(0.001)VPEHHPHPISPYEHLLR;S(0.996)PHS(0.002)T(0.002)VPEHHPHPISPYEHLLR;S(0.999)PHSTVPEHHPHPISPYEHLLR 205.72 4.99E-23 1405070000 103417 99294 51576 72608 103904 108630 90632 96307 183492 TRUE FALSE 89750.18142 98641.73118 76518.32611 89094.75614 101836.5137 112809.0664 81842.52259 75712.49751 161799.7848 0.554699016 0.609653043 0.472919826 0.550648175 0.629398326 0.697213946 0.505825905 0.46793942 1 17.30385016 1.231289333 24.99788383 1.000000772 0.558917941 0.791003774 0.070902983 125.7344304 432223.5103 0.187628892 0.018752402 17.03292889 -1.231289333 -0.441082831 S(ph)PIALPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPIALPVK 8 0 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 S(1)PIALPVK;S(1)PIALPVK;S(1)PIALPVK;S(1)PIALPVK 115.71 0.0025286 529010000 1260180 1073280 769614 1092960 1054570 901200 1071240 1336140 2100410 TRUE FALSE 1093644.02 1066229.553 1141801.905 1341133.273 1033586.12 935869.7472 967351.3097 1050416.859 1852101.923 0.590488032 0.575686219 0.616489779 0.724114184 0.558061145 0.505301428 0.522299177 0.567148517 1 20.82073206 1.237409949 24.99851826 1.0000005 0.581018406 0.829936795 0.059398051 12.42490942 269813.3619 0.094566069 0.015805849 17.27467755 -1.237409949 -0.418982094 S(ph)PIEPSALEPAYYQGVYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPIEPSALEPAYYQGVYSR 19 0 P55317-2;P55317 P55317-2 FOXA1 Hepatocyte nuclear factor 3-alpha 1 S(0.919)PIEPS(0.081)ALEPAYYQGVYSR;S(0.999)PIEPS(0.001)ALEPAYYQGVYSR;S(1)PIEPSALEPAYYQGVYSR;S(1)PIEPSALEPAYYQGVYSR 258.82 5.06E-31 631322000 120461 110941 98935 134282 119597 113259.9 110771 124937 365145 TRUE FALSE 104541.7736 110212.2213 146780.2969 164772.7805 117217.2537 117617.0816 100028.4455 98220.19481 321977.9741 0.324686103 0.342297393 0.455870615 0.511751715 0.364053641 0.365295427 0.310668597 0.305052528 1 18.29660247 1.234846679 24.99969854 1.000000893 0.371933682 0.90198606 0.065010998 34.99777635 235545.6052 0.129230745 0.017825023 17.17302015 -1.234846679 -0.628067211 S(ph)PILEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPILEEK 7 0 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2;A0A0A0MR81 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 S(1)PILEEK;S(1)PILEEK 94.85 0.014579 708430000 1891430 1416380 1172290 1399900 1373770 1210430 1661350 1969570 2142940 TRUE FALSE 1641472.733 1407075.707 1739213.365 1717768.691 1346434.665 1256996.025 1500232.533 1548392.783 1889604.074 0.868686068 0.744640491 0.920411524 0.909062758 0.712548561 0.665216615 0.793940145 0.819427098 1 20.84965255 1.231841831 3.897302628 1.025042848 0.800296749 0.363538439 0.081672513 0.316621241 8.037149298 0.207418598 0.021971415 17.0546115 -1.231841831 -0.224746099 S(ph)PILLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SPILLPK 7 0 Q8TD16;Q8TD16-2 Q8TD16 BICD2 Protein bicaudal D homolog 2 1 S(1)PILLPK;S(1)PILLPK;S(1)PILLPK;S(1)PILLPK;S(1)PILLPK;S(1)PILLPK 109.71 0.0073072 2900943000 3114310 2705340 2434680 3139870 2625460 2321390 3193480 3644490 6820420 TRUE FALSE 2702746.043 2687568.443 3612099.392 3852825.473 2573218.483 2410695.375 2883776.801 2865144.175 6014117.717 0.449400256 0.446876594 0.600603374 0.640630206 0.427863006 0.400839406 0.479501223 0.476403075 1 22.51992168 1.237552901 24.99962627 1.0000006 0.49115686 0.82045177 0.074938548 11.05334538 274074.157 0.116497696 0.019632944 17.28036458 -1.237552901 -0.508843741 S(ph)PIRQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SPIRQDR 7 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(1)PIRQDR;S(1)PIRQDR;S(1)PIRQDR;S(1)PIRQDR;S(1)PIRQDR;S(1)PIRQDR;S(1)PIRQDR 107.95 0.0044585 11358360000 2107521 1668196 1226545 1400014 1196712 1572760 1540648 1799565 1948045 TRUE FALSE 1829006.76 1657237.511 1819706.265 1717908.577 1172899.773 1633265.095 1391236.194 1414742.029 1717749.339 1.064769299 0.964772608 1.059354949 1.000092701 0.682811948 0.950816896 0.809918049 0.823602138 1 20.7120881 3.445424175 24.99413544 0.850411317 1.024242633 0.479483919 0.087761045 153.3789114 120943.5745 0.023529179 0.030376264 2788.843703 -3.445424175 0.173831316 S(ph)PISPELHSAPLTPVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPISPELHSAPLTPVAR 17 0 A0A1W2PRB5;A0A0J9YVS1;A0A0G2JNB1;A0A0G2JNT7;Q7Z3B3;A0A0G2JQF5;A0A3B3IT55;A0A0G2JQF4;Q7Z3B3-4;Q7Z3B3-2 A0A1W2PRB5;Q7Z3B3-4 KANSL1 KAT8 regulatory NSL complex subunit 1 1 S(0.999)PIS(0.001)PELHSAPLTPVAR;S(0.998)PIS(0.002)PELHSAPLTPVAR 145.52 3.04E-07 557810000 274170 239300 153282 216053 245860 230310 228540 286140 292530 TRUE FALSE 237937.7398 237728.0225 227409.6879 265111.1358 240967.867 239170.1747 206376.226 224951.1877 257947.4367 0.922427231 0.921614208 0.881612513 1.027771934 0.934174304 0.927205084 0.800070854 0.872081501 1 17.97671758 2.451197997 24.99415107 0.880283714 0.937758968 0.105064601 0.060181847 403.2155616 388761.4242 0.022461802 0.017399301 282.6168148 -2.451197997 0.057475254 S(ph)PISVPGGSALISNLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPISVPGGSALISNLGK 17 0 P51610-2;P51610;A6NEM2;P51610-4 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 1 S(1)PISVPGGSALISNLGK;S(0.998)PIS(0.002)VPGGSALISNLGK 220.97 4.02E-15 505870000 918710 824790 637910 943650 821990 607700 846870 1111250 1898980 TRUE FALSE 797300.1458 819371.9002 946405.4097 1157920.155 805634.0072 631078.6122 764740.6777 873617.8353 1674484.748 0.476146556 0.489327778 0.565192016 0.691508332 0.481123527 0.376879284 0.456702086 0.521723376 1 20.6752858 1.239059776 6.57460989 1.01320387 0.506756103 0.785944916 0.080844266 0.05797605 12.1121017 0.131470224 0.021693056 17.34042653 -1.239059776 -0.506447767 S(ph)PKPAAPAAPPFSSSSGVLGTGLCELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPKPAAPAAPPFSSSSGVLGTGLCELDR 28 1 H3BS04;H3BN49;H3BSN4;H3BQC4;O43294-2;O43294 H3BS04 TGFB1I1 Transforming growth factor beta-1-induced transcript 1 protein 1 S(1)PKPAAPAAPPFSSSSGVLGTGLCELDR 109.59 0.00042393 67434000 35382 27183 23032 35348 41523 30424 36724 59061 53490 TRUE FALSE 30706.17905 27004.43308 34170.35224 43374.30366 40696.77354 31594.43097 33162.51213 46431.26476 47166.47314 0.651017068 0.572534499 0.724462737 0.919600317 0.862832661 0.669849341 0.703095015 0.984412479 1 15.52547411 -2 0.249814773 2.9668884 0.634380981 0.471489208 0.107511592 83.30834018 1.332156913 79.33536541 0.392851946 0.01 2 -2.332507419 S(ph)PKPGPAPHDQELGFFLETGLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPKPGPAPHDQELGFFLETGLQR 23 1 Q86TV6;Q86TV6-2;G3V3H1 Q86TV6 TTC7B Tetratricopeptide repeat protein 7B 1 S(1)PKPGPAPHDQELGFFLETGLQR;S(1)PKPGPAPHDQELGFFLETGLQR;S(1)PKPGPAPHDQELGFFLETGLQR 240.16 1.83E-37 268133000 256769 216682 165532 200329 233621 205851 258975 313226 251489 TRUE FALSE 222836.3261 215258.6017 245583.8289 245816.7613 228972.3992 213770.2212 233859.6444 246245.0574 221758.2569 1.004861461 0.970690357 1.10743939 1.108489779 1.032531561 0.963978632 1.054570178 1.110421144 1 17.7586283 4.256841701 24.9988646 1.05697144 0.987775877 0.241767386 0.048463443 357.0534012 488252.0089 0.012759108 0.033617776 18065.15536 -4.256841701 -0.069195563 S(ph)PLAEHRPDAYQDVSIHGTLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPLAEHRPDAYQDVSIHGTLPR 22 1 O75815 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 S(1)PLAEHRPDAYQDVSIHGTLPR 195.21 5.42E-19 69833000 21572 24733 15604 28790 39238 35335 35016 32664 41007 TRUE FALSE 18721.20554 24570.52729 23150.14659 35327.20953 38457.24057 36694.36031 31620.15371 25679.05779 36159.19918 0.517743921 0.67950972 0.64022841 0.976990927 1.063553437 1.014800138 0.87447052 0.710166662 1 15.14207511 3.765423563 8.91339199 0.920222245 0.618607343 0.680346656 0.105217299 0.260454359 81.3470549 0.03254282 0.055573634 5826.71214 -3.765423563 -0.301614902 S(ph)PLAQMEEER ddPTM_MDA-MB-175_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 149.57 0.00016223 143840000 71338 71059 55002 61578 82146 82774 77273 99628 110111 TRUE FALSE 61910.50255 70592.20875 81601.15117 75560.22606 80511.45532 85958.36934 69779.07635 78323.32751 97093.80302 0.637635983 0.72705164 0.840436244 0.778218833 0.82921312 0.885312622 0.718676931 0.806676895 1 16.5670916 4.518227403 2.09295564 0.828416213 0.622057136 0.452944765 0.07335368 0.430092933 2.910148777 0.019190927 0.141108913 32978.23455 -4.518227403 -0.206359077 S(ph)PLAQMEEERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPLAQMEEERR 11 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2 E7EPK1 7-Sep Septin-7 1 S(1)PLAQMEEERR;S(1)PLAQMEEERR;S(1)PLAQMEEERR;S(1)PLAQMEEERR 161.09 1.64E-05 3426370000 710521 697965 461600 493947 714018 719882 625238 679618 669959 TRUE FALSE 616623.8496 693380.022 684831.304 606105.2159 699810.4388 747576.3264 564602.515 534286.9795 590757.2102 1.043785567 1.173714023 1.159243243 1.025980226 1.184599065 1.265454426 0.955726829 0.904410425 1 19.17220581 2.145280055 8.60002346 0.941420719 1.140782368 0.604753858 0.071771756 0.167002194 13.75454501 0.029249431 0.019704778 139.7269099 -2.145280055 0.199361649 S(ph)PLELEPEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPLELEPEAK 10 0 Q92466-4;Q92466;A0A087WTQ7;A0A087WV56;A0A087WW71;A0A087X0X5;Q92466-3;Q92466-2;Q92466-5 Q92466-4 DDB2 DNA damage-binding protein 2 1 S(1)PLELEPEAK 185.99 1.46E-06 66802000 232280 197110 154940 197630 192390 140350 218190 248860 343660 TRUE FALSE 201583.6095 195815.1714 229869.5022 242504.9121 188561.8154 145749.3553 197029.9674 195643.2256 303032.9063 0.665220197 0.646184514 0.758562841 0.800259335 0.622248645 0.480968741 0.650193307 0.645617098 1 18.20911494 1.237289738 24.99760607 1.000000412 0.658115722 0.620381059 0.083913809 23.75004153 466961.9783 0.133814989 0.022150539 17.26989662 -1.237289738 -0.34188469 S(ph)PLFIFMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPLFIFMR 8 0 C9J417;O43521-11;O43521-10;O43521-14;O43521-19;O43521-4;O43521-8;O43521-12;O43521 C9J417 BCL2L11 Bcl-2-like protein 11 1 S(1)PLFIFMR;S(1)PLFIFMR 94.85 0.01056 98952000 45292 49063 32630 37874 52357 45520 34716 55900 49192 TRUE FALSE 39306.54744 48740.70192 48409.97714 46473.87057 51315.19813 47271.18386 31349.24766 43946.22001 43376.5778 0.90616986 1.123664069 1.116039568 1.071404729 1.18301629 1.089785923 0.722722936 1.013132484 1 15.40462862 2.380556705 22.04943155 0.922433497 1.089399067 0.365846308 0.104708338 6.516900909 1479.505983 0.037709732 0.029209785 240.190986 -2.380556705 0.16696557 S(ph)PLGGGGGSGASSQAACLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPLGGGGGSGASSQAACLK 19 0 J3QQY0;Q68DK7;J3KSZ8;Q68DK7-2 J3QQY0;Q68DK7 MSL1 Male-specific lethal 1 homolog 1 S(1)PLGGGGGSGASSQAACLK 164.74 2.43E-11 75409000 54664 55178 31789 41194 52501 39639 48813 61126 55661 TRUE FALSE 47440.0139 54815.53208 47162.26673 50547.72731 51456.33282 41163.93798 44079.12277 48054.68058 49080.81999 0.966569302 1.116842223 0.960910326 1.029887588 1.048400023 0.838697031 0.898092631 0.979092863 1 15.58287173 2.775934163 24.99667056 0.93390736 1.02641493 0.377244614 0.060829936 627.6160291 419769.3282 0.019559431 0.019559017 596.944786 -2.775934163 0.09250757 S(ph)PLLAGGS(ph)PPQPVVPAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPLLAGGSPPQPVVPAHK 18 0 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4;C9JIY9 Q8NFH5-2 NUP35 Nucleoporin NUP53 2 S(1)PLLAGGS(1)PPQPVVPAHK 98.121 0.00039754 0 68762 57283 48773 50232 65918 51089 67794 77272 88556 TRUE FALSE 59674.92748 56906.7042 72359.78594 61637.94335 64606.36077 53054.42689 61219.34831 60747.98413 78087.01056 0.76421068 0.728760184 0.92665586 0.789349508 0.827363736 0.679427046 0.783988885 0.777952488 1 16.25279496 1.237380761 24.98181215 1.000000259 0.785237286 0.529044032 0.063833968 24.02195311 508407.3921 0.092244201 0.015389944 17.27351659 -1.237380761 -0.214762973 S(ph)PLLLGAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPLLLGAQR 9 0 Q96DR7;Q96DR7-4;Q96DR7-3 Q96DR7 ARHGEF26 Rho guanine nucleotide exchange factor 26 1 S(1)PLLLGAQR 99.34 0.0056675 111280000 37936 35293 28107 32867 35585 47963 32111 39086 57093 TRUE FALSE 32922.66148 35061.15796 41699.63921 40329.95469 34876.92812 49808.16765 28996.88016 30727.76307 50343.53058 0.653960124 0.696438203 0.828301844 0.801095081 0.692778749 0.989365805 0.575980267 0.610361703 1 15.61951878 4.441664532 8.877708111 0.763149097 0.664400375 0.084196039 0.139998362 0.704285945 164.0733365 0.035203883 0.094449366 27648.05167 -4.441664532 -0.098748722 S(ph)PLPTKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPLPTKR 7 1 D6R9T3;Q96FZ2;E7EMP6 D6R9T3 HMCES Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein 1 S(0.999)PLPT(0.001)KR 57.598 0.070203 343000000 467580 405910 262130 301590 365840 368400 391200 502810 332290 TRUE FALSE 405788.1183 403243.5505 388896.9448 370070.619 358560.4998 382572.5864 353261.4842 395287.9944 293007.0547 1.384909038 1.376224715 1.32726137 1.263009245 1.223726507 1.305677048 1.205641566 1.3490733 1 18.16057588 1.232974396 24.99924268 0.999999522 1.301079368 0.718605836 0.059838195 104.6824899 468420.8393 0.130293182 0.015208524 17.09914505 -1.232974396 0.301079846 S(ph)PLSGIPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPLSGIPVR 9 0 Q5M775-4;Q5M775;J3KSG2 Q5M775-4 SPECC1 Cytospin-B 1 S(0.999)PLS(0.001)GIPVR;S(1)PLSGIPVR;S(0.999)PLS(0.001)GIPVR;S(1)PLSGIPVR 99.788 0.0053498 485780000 228377 284488 171467 215355 316438 348505 276146 315506 283575 TRUE FALSE 198196.4008 282619.1796 254389.0147 264254.6442 310141.5029 361912.2129 249365.4034 248037.4972 250051.0865 0.792623634 1.130245757 1.017348168 1.056802623 1.240312558 1.44735309 0.997257828 0.991947288 1 17.93186335 4.74141998 23.89204168 1.105667923 0.792623421 0.330143343 0.142017623 196.9935912 1645854.259 0.037569531 0.251797347 55134.06069 -4.74141998 -0.313044502 S(ph)PLSPTETFSWPDVR ddPTM_MDA-MB-175_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(0.999)PLS(0.001)PTETFSWPDVR;S(1)PLSPTETFSWPDVR;S(0.998)PLS(0.002)PTETFSWPDVR;S(1)PLSPTETFSWPDVR 265.12 3.67E-25 392679000 175691.3 155358.9 94310.2 106280.6 117298.9 137185.4 129243 132285.3 125193.1 TRUE FALSE 152473.2496 154338.3372 139918.9282 130413.2346 114964.8814 142463.0111 116709.0338 103997.118 110392.9143 1.381186922 1.398081916 1.267462944 1.181355121 1.041415403 1.290508652 1.057214899 0.942063344 1 16.75228805 7.999999609 0.095997531 0.488956701 3.192362435 0.740634604 0.08155289 157.070429 1.399568096 6.527279202 57.36749007 99999910.04 -7.999999609 2.703405734 S(ph)PLSSILFSALDSDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPLSSILFSALDSDTR 16 0 A0A1W2PRB5;A0A0J9YVS1;A0A0G2JNB1;A0A0G2JNT7;Q7Z3B3;A0A0G2JQF5;A0A3B3IT55;A0A0G2JQF4;A0A1W2PPV8;A0A1W2PRR3;I3L233 A0A1W2PRB5 KANSL1 KAT8 regulatory NSL complex subunit 1 1 S(1)PLSSILFSALDSDTR 100.45 0.0028479 0 12384 22909 15294 11950 16025 15693 18650 20562 15965 TRUE FALSE 10747.42302 22758.50927 22690.22956 14663.43014 15706.13385 16296.71986 16841.32587 16164.97631 14077.63589 0.76343948 1.616642841 1.611792615 1.041611693 1.11567979 1.157631863 1.196317763 1.148273506 1 13.78111746 3.706331518 24.81781131 1.121542319 1.359226956 0.154869888 0.238937309 972.6851167 749009.7052 0.063394225 0.094037789 5085.474936 -3.706331518 0.237684638 S(ph)PLTQEQLIPNLAMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPLTQEQLIPNLAMK 15 0 Q9UNE7;Q9UNE7-2;H3BTA3 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 1 S(0.997)PLT(0.003)QEQLIPNLAMK 101.56 0.0026777 0 96682 82466 66709 79750 94670 81411 102360 123120 112610 TRUE FALSE 83905.22874 81924.27542 98969.69553 97858.4564 92786.25222 84542.93385 92433.14295 96791.74612 99297.37409 0.844989402 0.825039697 0.996700028 0.985509006 0.934428056 0.851411577 0.930871977 0.974766423 1 16.59946795 4.249657985 24.99979378 0.950915495 0.835014483 0.560673966 0.043518456 173.7666098 391448.0057 0.011819463 0.030645095 17768.79532 -4.249657985 -0.115901013 S(ph)PMDSLLHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SPMDSLLHPR 10 0 E9PAK5;O75064 E9PAK5 DENND4B DENN domain-containing protein 4B 1 S(1)PMDSLLHPR;S(1)PMDSLLHPR;S(1)PMDSLLHPR;S(1)PMDSLLHPR;S(1)PMDSLLHPR 213.63 1.20E-08 372727000 249008 256607 134828 189578 274027 271455 248514 279309 284704 TRUE FALSE 216100.9619 254921.3317 200031.2718 232624.5824 268574.3988 281898.0495 224413.1505 219580.9439 251046.6175 0.860800134 1.015434242 0.796789353 0.926619067 1.069818831 1.122891248 0.893910274 0.87466203 1 17.93759576 3.467608393 24.96240921 0.978668041 0.896492811 0.205719996 0.090016537 410.9102609 1078252.775 0.028213809 0.036472024 2935.001945 -3.467608393 -0.08217523 S(ph)PNELVDDLFK ddPTM_MDA-MB-175_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 198.85 5.48E-08 736340000 707546 595574 531151 607864 580680 449044 647088 797311 1477537 TRUE FALSE 614042.0034 591661.6352 788017.4002 745888.8118 569125.6041 466319.0133 584333.5054 626812.2473 1302864.259 0.471301595 0.454123775 0.604834613 0.57249925 0.436826477 0.35791834 0.448499144 0.481103264 1 20.31325535 1.23865368 9.682270067 1.002551412 0.478015598 0.850188079 0.068813365 0.03013843 52.75593468 0.104101408 0.018467515 17.32421959 -1.23865368 -0.524535814 S(ph)PNSHDSEPWTLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPNSHDSEPWTLLR 14 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 S(0.999)PNS(0.001)HDSEPWTLLR;S(0.996)PNS(0.004)HDSEPWTLLR;S(0.999)PNS(0.001)HDSEPWTLLR;S(1)PNSHDSEPWTLLR 223.18 2.33E-12 1510310000 313403 379363 132989 315609 455247 488026 352828 447277 541591 TRUE FALSE 271985.9995 376870.9395 197302.9252 387272.8472 446188.4754 506800.676 318610.7949 351630.2943 477564.729 0.569526983 0.789151536 0.413143838 0.810932684 0.934299475 1.061218816 0.667157299 0.736298711 1 18.86533676 3.509482424 19.835471 0.85658442 0.610723423 0.44631781 0.14583309 56.9565861 34909.82364 0.04108906 0.060786524 3232.082396 -3.509482424 -0.245860998 S(ph)PPADAIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 113.47 0.0018826 561450000 1098760 751190 614580 754050 702970 645440 869620 990950 1497400 TRUE FALSE 953556.0821 746255.3834 911792.9436 925268.5774 688982.2723 670270.4945 785284.3862 779043.0541 1320379.078 0.722183574 0.565182678 0.690553917 0.700759799 0.521806414 0.507634895 0.594741616 0.590014691 1 20.33252075 1.2370066 24.99616134 1.000000483 0.607553258 0.73490587 0.073272625 21.17014969 340404.4372 0.112316216 0.018271344 17.25864121 -1.2370066 -0.392447226 S(ph)PPAPGLQPMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 110.93 0.0018127 2188160000 139888 131799 66099.1 99096.7 131707.8 140975 114682 119696 111277 TRUE FALSE 121401.4464 130933.2037 98064.84585 121598.1203 129087.0725 146398.3995 103560.1573 94099.94188 98121.95983 1.237250526 1.334392463 0.999417929 1.239254908 1.315577804 1.492004437 1.055422838 0.959010012 1 16.58228843 2.019322357 24.44250373 0.985768891 1.262073615 0.521208057 0.121108009 142.065717 179710.1458 0.051131059 0.034466694 104.5495956 -2.019322357 0.276304724 S(ph)PPAS(ph)PESWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPPASPESWK 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 S(1)PPAS(0.964)PES(0.036)WK;S(1)PPAS(0.999)PES(0.001)WK;S(1)PPAS(0.859)PES(0.141)WK;S(1)PPAS(0.949)PES(0.051)WK 148.13 3.75E-05 718440000 2232130 1645280 1342110 1697950 1562180 1154040 1586560 2105060 2953580 TRUE FALSE 1937148.365 1634472.047 1991158.885 2083495.499 1531095.674 1198436.666 1432695.655 1654909.301 2604411.137 0.743795147 0.627578351 0.76453324 0.799987172 0.58788555 0.460156482 0.55010349 0.63542552 1 21.31252578 3.227556216 24.98625887 0.628729431 0.728556674 0.073658217 0.14567058 539.2534794 1224409.826 0.045284526 0.051831459 1688.714435 -3.227556216 0.099827243 DVPSPGGLSAPSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 DVPSPGGLSAPSSPR 15 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 DVPSPGGLSAPS(0.001)S(0.999)PR;DVPSPGGLSAPSS(1)PR;DVPSPGGLSAPSS(1)PR;DVPSPGGLSAPS(0.017)S(0.983)PR 313.66 3.22E-56 4083340000 1323250 2117520 1721550 2343520 2723030 2787350 2656050 3281620 3462240 TRUE FALSE 1148379.16 2103609.872 2554097.338 2875652.034 2668847.031 2894581.158 2398466.68 2579871.101 3052937.931 0.376155423 0.689044428 0.8366031 0.941929413 0.874189745 0.948129711 0.785625759 0.845045382 1 21.54176683 4.691182577 1.647634255 0.888129542 0.222266581 0.885177996 0.059990004 0.286973187 0.816572495 0.016682613 0.296084773 49111.42972 -4.691182577 -0.665862961 down S(ph)PPEGDTTLFLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPPEGDTTLFLSR 13 0 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 S(1)PPEGDTTLFLSR;S(1)PPEGDTTLFLSR;S(1)PPEGDTTLFLSR 180.84 1.32E-05 2248520000 565570 300475 946065 438884 269231 211956 319266 408412 374130 TRUE FALSE 490828.4915 298501.1599 1403585.198 538539.3201 263873.8298 220110.0845 288303.6325 321076.2721 329900.7776 1.48780641 0.904821026 4.254567717 1.632428162 0.799858163 0.667200866 0.873910133 0.973251031 1 18.33167265 3.429071036 5.773938213 0.885755869 2.218401601 0.348094061 0.849869575 0.212046016 16.24264585 0.245861442 0.322256924 2685.783711 -3.429071036 1.332645732 S(ph)PPETAAPVEDMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPPETAAPVEDMAR 14 0 Q9Y3L3;Q6ZT62-2;Q6ZT62;A0A2R8Y5V0;A0A3B3IU28 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 S(0.991)PPET(0.009)AAPVEDMAR;S(0.997)PPET(0.003)AAPVEDMAR 129.92 6.83E-05 1255590000 118851 92592 62396 70356 94527 76416 74787 104462 105130 TRUE FALSE 103144.5392 91983.75706 92570.9143 86331.40512 92646.09764 79355.77297 67534.16825 82123.61422 92701.65116 1.112650508 0.992255865 0.998589703 0.931282281 0.999400728 0.856034083 0.728510953 0.885891602 1 16.50030742 4.123518772 0.633824564 0.863916566 1.138971575 0.466221512 0.076105978 1.705309903 0.920481361 0.048389973 0.314967577 13289.81 -4.123518772 0.275055009 S(ph)PPGS(ph)GASTPVGPWDQAVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPPGSGASTPVGPWDQAVQR 20 0 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 2 S(1)PPGS(1)GASTPVGPWDQAVQR;S(1)PPGS(1)GASTPVGPWDQAVQR;S(1)PPGS(0.708)GAS(0.289)T(0.004)PVGPWDQAVQR 242.9 1.20E-29 728090000 378240 289465 204759 228624 271175 262508 268990 272580 351240 TRUE FALSE 328254.6257 287563.4854 303781.1373 280536.5735 265779.148 272606.8526 242903.3912 214290.8882 309716.8073 1.059854092 0.928472329 0.98083517 0.905784145 0.858136019 0.880181011 0.784275782 0.691892991 1 18.24059015 3.560020292 0.747115191 0.800858973 1.027878867 0.39102373 0.082981057 0.788817629 0.927929097 0.049201675 0.121871378 3630.950197 -3.560020292 0.227019894 S(ph)PPGSGAS(ph)TPVGPWDQAVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPPGSGASTPVGPWDQAVQR 20 0 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 2 S(1)PPGSGAS(0.852)T(0.148)PVGPWDQAVQR;S(1)PPGS(0.225)GAS(0.767)T(0.008)PVGPWDQAVQR 298.96 1.41E-54 384480000 462330 378990 305173 370164 426080 397960 363500 467300 565150 TRUE FALSE 401231.9191 376500.3897 452755.6835 454215.3938 417601.8416 413269.7787 328247.8259 367371.5315 498338.6108 0.805139137 0.755511176 0.908530212 0.911459365 0.837988132 0.829295121 0.658684314 0.737192591 1 18.92676683 1.226706365 24.96754291 1.000000452 0.802124987 0.390886721 0.076211583 656.7114608 1383082.53 0.339117174 0.021035895 16.85413101 -1.226706365 -0.197875464 S(ph)PPGSGAST(ph)PVGPWDQAVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPPGSGASTPVGPWDQAVQR 20 0 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 2 S(0.999)PPGS(0.001)GAS(0.34)T(0.659)PVGPWDQAVQR 175.8 7.40E-12 208380000 380780 345420 282460 340800 387720 378560 386870 441760 468330 TRUE FALSE 330458.9582 343150.9133 419058.6008 418183.8488 380005.1306 393123.4482 349351.4069 347293.0618 412964.5609 0.800211421 0.830945185 1.014756811 1.012638585 0.920188235 0.951954442 0.845959775 0.84097546 1 18.65565845 4.402885459 8.474792166 0.929030179 0.807819063 0.407409379 0.062093178 0.277311599 27.88872621 0.01740504 0.046372244 25286.31006 -4.402885459 -0.121211117 S(ph)PPGSGASTPVGPWDQAVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 SPPGSGASTPVGPWDQAVQR 20 0 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 S(0.998)PPGS(0.002)GASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR;S(0.983)PPGS(0.017)GASTPVGPWDQAVQR;S(0.973)PPGS(0.025)GAS(0.001)TPVGPWDQAVQR;S(0.867)PPGS(0.133)GASTPVGPWDQAVQR;S(0.975)PPGS(0.025)GASTPVGPWDQAVQR;S(0.84)PPGS(0.16)GASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR;S(0.591)PPGS(0.407)GAS(0.002)TPVGPWDQAVQR 299.06 9.99E-55 32307710000 506458 436725 374276 411665 482747 505008 460637 500750 679514 TRUE FALSE 439528.2921 433856.1247 555277.1255 505139.8302 473141.2792 524435.9845 415964.4946 393668.5093 599182.629 0.733546453 0.724079944 0.926724338 0.843048189 0.789644519 0.875252317 0.694219883 0.657009216 1 19.19263627 LDS(ph)PPPSPITEASEAAEAAEAGNLAVSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 LDSPPPSPITEASEAAEAAEAGNLAVSSR 29 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 LDS(0.864)PPPS(0.119)PIT(0.017)EASEAAEAAEAGNLAVSSR;LDS(0.894)PPPS(0.096)PIT(0.011)EASEAAEAAEAGNLAVSSR;LDS(0.884)PPPS(0.099)PIT(0.016)EAS(0.001)EAAEAAEAGNLAVSSR;LDS(0.849)PPPS(0.13)PIT(0.02)EAS(0.001)EAAEAAEAGNLAVSSR 176.71 1.14E-14 141646000 172255 106194 52956.2 54490.3 70645 69778 74629 84145 73001 TRUE FALSE 149491.0653 105496.4046 78565.99545 66863.15545 69239.30271 72462.40481 67391.49107 66151.24657 64370.90494 2.322339036 1.638883354 1.220520288 1.038717034 1.075630407 1.125701198 1.046924711 1.027657552 1 15.97412113 4.691474296 1.342685138 1.047450725 2.806580746 0.992550147 0.035691354 0.09847376 0.168470234 0.011278126 0.231204484 49144.42935 -4.691474296 1.759130021 up S(ph)PPKVPIVIQDDSLPAGPPPQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 176.97 3.39E-17 241918000 166378 130905 135600 152604 160131 112062 159175 195007 297459 TRUE FALSE 144390.7258 130045.0764 201176.6136 187255.0706 156944.7064 116373.0977 143738.233 153306.2706 262293.7359 0.550492467 0.495799398 0.766989775 0.71391362 0.598354764 0.443674712 0.548004826 0.584483156 1 18.00082383 1.238246448 24.99975236 1.000000459 0.588206298 0.652828494 0.094486698 5.148714905 409049.2961 0.140186132 0.024684213 17.30798254 -1.238246448 -0.411794161 S(ph)PPLGLISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPPLGLISR 9 0 Q16584;Q16584-2;E9PID4 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 S(1)PPLGLISR;S(1)PPLGLISR 84.882 0.015935 993310000 69780 79486 54862 43990 68591 114707 49598 56201 66412 TRUE FALSE 60558.3962 78963.85123 81393.4467 53978.60185 67226.1733 119119.8525 44787.99359 44182.85351 58560.84902 1.034110625 1.348406872 1.389895264 0.921752378 1.147971288 2.034120996 0.764811207 0.75447768 1 15.83764885 S(ph)PPLMAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPPLMAK 7 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(1)PPLMAK;S(1)PPLMAK;S(1)PPLMAK 73.039 0.052422 2505320000 2679810 2458570 2141960 2802660 2552240 2111390 2780520 3393040 5420300 TRUE FALSE 2325666.319 2442419.492 3177819.02 3439046.789 2501455.417 2192616.54 2510865.598 2667464.801 4779518.309 0.486590106 0.511017917 0.664882696 0.719538365 0.523369774 0.458752619 0.52533863 0.558103271 1 22.1884338 1.238589558 13.63463974 1.000246468 0.557656311 0.754798547 0.079533935 0.028227519 619.2887328 0.117108706 0.021028829 17.32166191 -1.238589558 -0.442590157 S(ph)PPLPAVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SPPLPAVIR 9 0 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 S(1)PPLPAVIR;S(1)PPLPAVIR;S(1)PPLPAVIR;S(1)PPLPAVIR;S(1)PPLPAVIR;S(1)PPLPAVIR;S(1)PPLPAVIR 101.54 0.0041031 17235600000 823096 580114.4 387458.7 466345.4 596715.3 709656.3 554760 575709 717348 TRUE FALSE 714321.7781 576303.5903 574835.0233 572236.2507 584841.833 736957.2371 500959.4606 452598.1105 632543.9366 1.129284049 0.911088633 0.908766949 0.904658503 0.924586893 1.16506885 0.791975753 0.715520432 1 19.27080617 8 0.163995614 0.785164437 1.776575241 0.11943227 0.127317862 270.8871328 3.613840305 1.694153263 63.45748964 100000000 -8 0.991410803 S(ph)PPPPHRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPPPPHRPR 9 1 O43281-3;O43281-2;O43281 O43281-3 EFS Embryonal Fyn-associated substrate 1 S(1)PPPPHRPR;S(1)PPPPHRPR 80.24 0.014942 105874000 18467.5 11832.3 7885.7 7605.9 10997.3 13723.6 11214.6 12349.3 9886.6 TRUE FALSE 16026.97308 11754.57284 11699.2509 9332.935844 10778.47525 14251.55577 10127.00982 9708.498297 8717.817411 1.838415779 1.348338958 1.34199311 1.070558765 1.236373135 1.634761902 1.161645093 1.113638637 1 13.08975127 6.459084341 0.994132643 1.208114684 19.77727294 0.558189838 0.172533052 42.0439452 1.79711761 0.056467285 1624.144586 2877957.269 -6.459084341 18.56915826 S(ph)PPPPPPPPSDEALLHCVLEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPPPPPPPPSDEALLHCVLEGK 22 0 Q9BRK4 Q9BRK4 LZTS2 Leucine zipper putative tumor suppressor 2 1 S(1)PPPPPPPPSDEALLHCVLEGK 89.039 0.0016688 46518000 38199 30229 21785 40169 38523 26394 38616 38628 87354 TRUE FALSE 33150.90537 30030.42371 32320.29887 49289.98539 37756.46767 27409.39426 34871.02626 30367.7028 77027.10963 0.430379713 0.389868241 0.419596412 0.639904387 0.49017116 0.355840877 0.452711084 0.394246947 1 16.23307867 1.235279514 24.99992939 1.000000766 0.446374184 0.833218528 0.077811485 38.14120314 290562.9105 0.139100004 0.019859981 17.19014397 -1.235279514 -0.553626581 S(ph)PPPVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPPPVSK 7 0 Q01130;Q01130-2 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 S(1)PPPVSK 63.48 0.083058 2199700000 732970 464100 440030 624950 408770 436940 588640 675330 1307200 TRUE FALSE 636106.1574 461051.2965 652829.9798 766854.4493 400636.2767 453749.3645 531553.7834 530915.9349 1152664.305 0.551857253 0.399987485 0.566366094 0.665288624 0.347574116 0.393652655 0.46115229 0.460598921 1 20.13654098 1.23740423 24.99917028 1.000000623 0.477966473 0.751665394 0.093772778 14.76423743 319035.9773 0.139309524 0.023265855 17.27445007 -1.23740423 -0.52203415 S(ph)PPREGSQGELTPANSQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPPREGSQGELTPANSQSR 19 1 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;J3QQX0 Q13098-7 GPS1 COP9 signalosome complex subunit 1 1 S(0.999)PPREGS(0.001)QGELTPANSQSR;S(0.996)PPREGS(0.004)QGELTPANSQSR;S(0.992)PPREGS(0.008)QGELTPANSQSR 137.86 1.85E-06 1754240000 75855.3 68672 29803 39760 53574 62542 56237 53990 34310 TRUE FALSE 65830.82991 68220.88911 44215.83049 48788.11569 52507.98222 64948.03121 50783.1444 42444.65865 30253.91089 2.175944464 2.254944472 1.461491397 1.612621782 1.73557668 2.146764809 1.678564619 1.402947831 1 14.88483403 1.523396168 1.773742367 0.936347702 1.874910129 0.573207392 0.255389059 0.393668653 1.995135275 0.55923033 0.078273296 33.37307067 -1.523396168 0.938562427 S(ph)PPRPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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;S(1)PPRPPR 89.698 0.010708 6558470000 694248 693025 563523.2 495372 409565.7 560960 851109 680411 724218 TRUE FALSE 602501.3678 688472.4731 836044.9044 607853.7839 401416.1439 582540.4942 768568.5802 534910.4026 638601.7731 0.943469613 1.078093582 1.309180368 0.951851075 0.628586015 0.91221246 1.203517767 0.837627494 1 19.28455703 3.502880834 24.82121971 0.915355739 1.110946345 0.22501373 0.165635117 1034.67755 996984.1086 0.046537511 0.068721204 3183.323927 -3.502880834 0.195590607 S(ph)PPSLALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPPSLALR 8 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 S(0.998)PPS(0.002)LALR;S(1)PPSLALR;S(0.999)PPS(0.001)LALR 108.57 0.0059872 693360000 106665 84711 71607 86493 110321 109958 84982 112866 162228 TRUE FALSE 92568.95 84154.52786 106236.3847 106132.5576 108125.8279 114188.1554 76740.45872 88730.48422 143049.5907 0.647110905 0.58828919 0.742654238 0.741928426 0.755862547 0.798241749 0.536460527 0.620277792 1 17.12615584 4.235400085 24.99799383 0.722774786 0.617700034 0.140490764 0.120809575 171.3868223 1355617.415 0.031343772 0.069978298 17194.91703 -4.235400085 -0.105074751 S(ph)PPSSSEIFTPAHEENVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SPPSSSEIFTPAHEENVR 18 0 I3L3A7;I3L2L5;I3L317;I3L4Q0;C9JLW8 I3L3A7 FAM195B Protein FAM195B 1 S(0.915)PPS(0.05)S(0.023)S(0.012)EIFTPAHEENVR;S(0.997)PPS(0.003)S(0.001)SEIFTPAHEENVR;S(0.967)PPS(0.032)S(0.001)S(0.001)EIFTPAHEENVR;S(0.862)PPS(0.132)S(0.003)S(0.002)EIFTPAHEENVR;S(0.884)PPS(0.083)S(0.019)S(0.014)EIFTPAHEENVR 204.86 6.61E-16 5598400000 291590 241112 217030 264809 277273 264526 260146 323565 411619 TRUE FALSE 253055.6427 239528.1194 321986.4339 324937.9308 271755.8098 274702.4864 234917.081 254373.1427 362957.8707 0.697203899 0.659933669 0.887117927 0.895249716 0.74872549 0.756843999 0.64722961 0.700833797 1 18.46944258 4.272761664 24.93770431 0.786848273 0.678568602 0.18853707 0.103911592 357.8399424 260913.4433 0.027134457 0.071783012 18739.65813 -4.272761664 -0.10827967 S(ph)PPSTGSTYGSSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SPPSTGSTYGSSQK 14 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.737)PPS(0.262)T(0.001)GSTYGSSQK;S(0.994)PPS(0.006)TGSTYGSSQK;S(0.998)PPS(0.002)TGSTYGSSQK;S(1)PPSTGSTYGSSQK;S(0.922)PPS(0.069)T(0.008)GSTYGSSQK;S(0.995)PPS(0.003)T(0.002)GSTYGSSQK;S(0.999)PPS(0.001)TGSTYGSSQK 183.06 1.52E-06 4705842000 1000875 690560 891394 1201726 798972 642313 841606 1072550 4597420 TRUE FALSE 868606.8329 686023.6659 1322475.12 1474596.256 783074.0204 667023.1967 759987.1797 843193.5291 4053918.245 0.21426353 0.16922484 0.326221458 0.363745928 0.193164729 0.1645379 0.187469784 0.207994705 1 21.95088556 1.237668768 24.99998135 1.000000903 0.227811211 0.931371119 0.065830399 5.676909497 159041.8699 0.102460053 0.017404121 17.28497548 -1.237668768 -0.772189692 S(ph)PPSTGSTYGSSQKEESAASGGAAYTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPPSTGSTYGSSQKEESAASGGAAYTK 27 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.801)PPS(0.151)T(0.045)GS(0.002)TYGSSQKEESAASGGAAYTK;S(0.882)PPS(0.116)T(0.003)GSTYGSSQKEESAASGGAAYTK;S(0.999)PPS(0.001)TGSTYGSSQKEESAASGGAAYTK;S(0.84)PPS(0.08)T(0.08)GS(0.001)TYGSSQKEESAASGGAAYTK 280.86 2.59E-61 3146460000 1907730 1228200 1244650 1468140 1241330 840970 1607620 2003770 1694070 TRUE FALSE 1655618.647 1220131.873 1846566.903 1801503.626 1216629.962 873322.6601 1451713.26 1575279.379 1493798.974 1.10832761 0.816797905 1.236154887 1.205987992 0.814453606 0.584631985 0.971826387 1.054545763 1 20.51055458 3.230876076 24.99906498 0.897755461 1.082482718 0.268469855 0.168534305 293.9171029 956158.7303 0.055571729 0.064176957 1701.672876 -3.230876076 0.184727257 S(ph)PPSTGSTYGSSQKEESAASGGAAYTKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPPSTGSTYGSSQKEESAASGGAAYTKR 28 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.978)PPS(0.017)T(0.004)GSTYGSSQKEESAASGGAAYTKR;S(0.975)PPS(0.02)T(0.004)GS(0.001)T(0.001)YGSSQKEESAASGGAAYTKR 133.29 8.64E-06 577800000 754250 460210 200708 216776 422380 298823 625240 704290 26098.2 TRUE FALSE 654573.9515 457186.8502 297771.0601 265998.304 413975.4644 310318.9142 564604.321 553683.0643 23012.90053 28.44378312 19.86654614 12.93931027 11.55866049 17.98884343 13.48456331 24.53425288 24.05968181 1 14.49015521 8 0.097209506 10 40.90550549 0.11507025 7.427877639 1267.207543 11.4134087 592.7256651 5349.829114 99999999.99 -8 30.90550549 S(ph)PPVTLGPNLAPTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPPVTLGPNLAPTSR 15 0 B4DF95;Q15735;C9K0M5 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 S(1)PPVTLGPNLAPTSR;S(0.997)PPVT(0.003)LGPNLAPTSR;S(0.999)PPVT(0.001)LGPNLAPTSR;S(1)PPVTLGPNLAPTSR 114.69 0.00061496 593262000 174638 138249 90122 121214 132346 146682 143209 162327 144957 TRUE FALSE 151559.1458 137340.8332 133705.3006 148737.4913 129712.5735 152324.9515 129320.6132 127614.6343 127820.3486 1.185720016 1.074483325 1.046040807 1.163644858 1.014803785 1.191711282 1.011737291 0.998390598 1 16.963758 2.092881071 10.14187412 1.000884529 1.10576935 0.441937481 0.057694641 0.295445813 29.6999426 0.021711224 0.014631903 123.8457395 -2.092881071 0.104884821 S(ph)PPYTAFLGNLPYDVTEESIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPPYTAFLGNLPYDVTEESIK 21 0 E7EX17;P23588-2;P23588;F8VX11;F8VP89;F8W0K0;F8VSC7;F8VYE9;F8VRU1 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.502)PPY(0.452)T(0.046)AFLGNLPYDVTEESIK;S(0.367)PPY(0.316)T(0.316)AFLGNLPYDVTEESIK;S(0.488)PPY(0.435)T(0.076)AFLGNLPYDVTEESIK 84.493 0.001957 171178000 76662 70222 69160.5 90850 68698 57260.5 80579 100628 213526 TRUE FALSE 66530.92246 69760.70706 102606.7491 111478.8811 67331.04421 59463.34849 72764.46098 79109.48529 188283.1995 0.353355597 0.370509463 0.544959664 0.592080873 0.357605163 0.315818664 0.386462845 0.42016221 1 17.52254475 1.238599069 12.19433647 1.000715061 0.419134471 0.816035522 0.086897917 0.026414338 233.3083973 0.127948205 0.022935337 17.32204125 -1.238599069 -0.58158059 S(ph)PQEGPTWSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPQEGPTWSR 10 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 S(1)PQEGPTWSR;S(1)PQEGPTWSR 75.589 0.040429 359060000 209320 182779 153855 162094 201953 182250 156384 204838 276230 TRUE FALSE 181657.8317 181578.3127 228259.7926 198899.9202 197934.5304 189261.2754 141217.9037 161034.9878 243574.4041 0.745800169 0.745473702 0.93712553 0.816587937 0.812624509 0.777016272 0.579773167 0.661132636 1 17.89400301 2.467937835 24.96080404 0.715873218 0.81308319 0.037914207 0.118670799 427.5838989 1162174.354 0.044391662 0.034434003 293.7229189 -2.467937835 0.097209972 S(ph)PQESTGDPGNSSSVSEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPQESTGDPGNSSSVSEGK 19 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 S(1)PQESTGDPGNSSSVSEGK 194.48 2.23E-21 0 222990 202820 167130 231500 227490 165360 251910 317000 369150 TRUE FALSE 193521.3065 201487.6621 247954.627 284065.6133 222963.3941 171721.5062 227479.807 249212.0169 325509.5075 0.594518139 0.618991634 0.761743117 0.872679927 0.684967379 0.527546822 0.698842282 0.765605954 1 18.31234016 1.230559723 2.202201843 1.096489234 0.683198698 0.537159887 0.093493591 0.596458216 2.884880768 0.49624619 0.027117425 17.00433778 -1.230559723 -0.413290536 S(ph)PQFINLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPQFINLK 8 0 Q92576-2;Q92576 Q92576-2 PHF3 PHD finger protein 3 1 S(1)PQFINLK 71.379 0.051287 296840000 417310 392610 300250 322870 401190 289920 528580 464950 458620 TRUE FALSE 362161.4262 390030.9191 445451.9043 396182.5683 393207.1039 301073.41 477318.393 365524.0607 404402.4661 0.895547027 0.964462267 1.101506399 0.979673967 0.972316286 0.74448955 1.180305347 0.903862096 1 18.62543227 2.208613466 24.99999849 1.00852553 0.95417883 0.101979905 0.110921872 721.3358776 602169.243 0.044754961 0.030178301 161.6640544 -2.208613466 -0.0543467 S(ph)PQGQLDTSESKPDSFFLEPLMPAVLKPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPQGQLDTSESKPDSFFLEPLMPAVLKPAK 30 2 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 S(0.752)PQGQLDT(0.083)S(0.083)ES(0.083)KPDSFFLEPLMPAVLKPAK;S(1)PQGQLDTSESKPDSFFLEPLMPAVLKPAK 282.32 6.30E-72 1390640000 551660 430288 411008 442977 370568 268355 616340 704070 691700 TRUE FALSE 478756.7333 427461.4098 609772.8435 543561.6983 363194.4218 278678.7905 556567.4417 553510.1096 609928.014 0.784939734 0.700839115 0.999745592 0.891189921 0.595470963 0.456904395 0.912513328 0.907500716 1 19.21827945 2.034278394 24.99999648 0.936003058 0.743497143 0.290307196 0.149059557 255.5564775 186382.0318 0.065963378 0.044472281 108.2127401 -2.034278394 -0.192505915 S(ph)PQHFHRPDQGINIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPQHFHRPDQGINIYR 16 1 O14639-3;O14639-5;J3QSX6;O14639-4;H0Y7N6;F6XFR5 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 S(1)PQHFHRPDQGINIYR;S(1)PQHFHRPDQGINIYR;S(1)PQHFHRPDQGINIYR;S(1)PQHFHRPDQGINIYR 163.7 4.61E-09 1885790000 186760 193446 112206 120956 189740 153796 202604 220930 145970 TRUE FALSE 162079.1928 192175.2405 166469.1969 148420.9085 185964.5452 159712.6316 182955.4953 173685.8388 128713.5929 1.259223592 1.493045421 1.293330356 1.153109824 1.444793367 1.240837335 1.421415494 1.349397798 1 16.97380489 1.237155962 24.98097186 0.999999589 1.335837387 0.509391495 0.102298132 28.39044356 504717.8011 0.143594311 0.023570018 17.26457777 -1.237155962 0.335837798 S(ph)PQLSDFGLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPQLSDFGLER 11 0 Q8IX90-3;Q8IX90 Q8IX90-3 SKA3 Spindle and kinetochore-associated protein 3 1 S(1)PQLSDFGLER;S(1)PQLSDFGLER 164.93 2.33E-05 333820000 288390 230102 180225 210923 277180 243710 271470 310270 312740 TRUE FALSE 250278.5308 228590.4448 267382.4128 258816.2909 271664.6603 253085.6814 245142.8812 243921.175 275768.2335 0.907568387 0.828922323 0.969591056 0.938528298 0.985119486 0.91774777 0.888945322 0.884515131 1 18.07309675 4.236812319 24.99999976 0.933551519 0.868245358 0.32589246 0.042341106 56.18355464 803454.8707 0.011148035 0.025301143 17250.92228 -4.236812319 -0.065306161 S(ph)PQMVSAIVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPQMVSAIVR 10 0 A0A2R8Y804;A0A2R8Y543;A0A2R8Y5C3;A0A2R8Y750;A0A2R8Y5Z1;B4DGU4;A0A2R8YCH5;A0A2R8Y5A3;P35222;A0A2R8Y7Z0 A0A2R8Y804 CTNNB1 Catenin beta-1 1 S(1)PQMVSAIVR;S(1)PQMVSAIVR 91.307 0.01074 346499000 84793 70228 53954 69332 73019 67379 61999 88228 93855 TRUE FALSE 73587.39021 69766.66764 80046.33487 85074.89027 71566.06476 69971.11373 55986.34652 69361.12879 82759.56882 0.889170778 0.843004243 0.967215465 1.02797648 0.864746709 0.845474605 0.676493937 0.838104038 1 16.33663851 3.010051936 24.78483388 0.827802213 0.930315253 0.185402241 0.090172757 301.9611445 744532.175 0.02848756 0.032265301 1023.415372 -3.010051936 0.102513039 S(ph)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.998)PQPPAEEDEDDFDDT(0.002)LVAIDTYNCDLHFK 181.06 1.15E-17 63273000 141626 100790 79397 107021 95677 95604 77900 126923 151937 TRUE FALSE 122909.7653 100127.9039 117793.6548 131321.7538 93773.21489 99281.94774 70345.26999 99781.50417 133975.1809 0.917406973 0.747361587 0.879219971 0.980194636 0.69992975 0.741047312 0.525061952 0.744776036 1 17.03160624 3.216110818 24.98698667 0.726151239 0.871366539 0.220008398 0.127405132 350.1405108 389710.8677 0.039239332 0.044525277 1644.791368 -3.216110818 0.1452153 S(ph)PQPPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPQPPSR 7 0 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 S(1)PQPPSR;S(1)PQPPSR 87.435 0.020291 4859100000 2615300 2036980 1355440 1685630 1844010 2067020 1998120 2224200 2239790 TRUE FALSE 2269681.479 2023598.944 2010935.318 2068378.055 1807317.809 2146539.597 1804342.63 1748572.139 1975004.578 1.149203148 1.024604685 1.018192738 1.0472776 0.915095504 1.086852973 0.913589087 0.88535093 1 20.91342457 7.999999989 0.272982467 0.918534433 2.423287349 0.449452521 0.060894001 71.97775675 1.153535163 0.154775283 50.00193871 99999997.52 -7.999999989 1.504752916 S(ph)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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 345.24 9.04E-120 7169299000 1670710 1169146 1104273 1307060 1201337 1098534 1270899 1522795 2910220 TRUE FALSE 1449921.44 1161465.803 1638303.116 1603847.95 1177432.744 1140795.314 1147647.411 1197157.14 2566177.107 0.565012226 0.452605473 0.638421686 0.624995035 0.458827546 0.444550499 0.447220657 0.466513841 1 21.29118931 1.235555278 24.99998748 1.000000667 0.50888882 0.8123563 0.073651777 37.75317913 313993.5822 0.132548863 0.019337296 17.20106267 -1.235555278 -0.491111847 S(ph)PQQSAALPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPQQSAALPR 10 0 A0A0A6YYG7;Q6IBW4-2;Q6IBW4;Q6IBW4-4;E5RJN3 A0A0A6YYG7 NCAPH2 Condensin-2 complex subunit H2 1 S(1)PQQSAALPR;S(1)PQQSAALPR;S(1)PQQSAALPR 123.28 0.00048919 1127080000 332256 297028 213592 250226 293507 330760 269983 321398 378320 TRUE FALSE 288347.5278 295076.8035 316885.8056 307043.6378 287666.7849 343484.5512 243800.0902 252669.5388 333595.4406 0.864362916 0.884534882 0.949910482 0.920407177 0.862322292 1.029644022 0.730825607 0.757413046 1 18.34774005 2.22688462 24.99990706 0.810305143 0.915941838 0.18327455 0.085454726 305.7212939 654585.4798 0.034010881 0.02314528 168.6105013 -2.22688462 0.105636695 S(ph)PQREPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SPQREPQR 8 1 O96013;O96013-4;O96013-2;O96013-3 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 S(1)PQREPQR;S(1)PQREPQR;S(1)PQREPQR;S(1)PQREPQR;S(1)PQREPQR;S(1)PQREPQR 127.7 0.0007057 6379600000 718414 624644 500559 538689 608623 650220 657100 730971 619794 TRUE FALSE 623473.7697 620540.6724 742631.0067 661006.5708 596512.5931 675234.3841 593374.5431 574658.5401 546522.6594 1.140801317 1.135434482 1.358829307 1.209476971 1.091469096 1.235510317 1.085727248 1.051481636 1 19.05992179 1.837750411 1.103640872 0.980389487 1.202332426 0.48262565 0.073638486 0.634889952 1.216128172 0.137752189 0.02671578 68.82566424 -1.837750411 0.221942939 S(ph)PQRPGWSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPQRPGWSR 9 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(1)PQRPGWSR;S(1)PQRPGWSR;S(1)PQRPGWSR;S(1)PQRPGWSR 90.697 0.0068159 2461480000 219065 199564 107728 132395 148170 175619 170021 195588 215019 TRUE FALSE 190115.0052 198253.0509 159825.6211 162457.3083 145221.7069 182375.1766 153532.3896 153763.0283 189599.6988 1.002717865 1.045640116 0.842963476 0.856843705 0.76593849 0.961895919 0.809771274 0.810987724 1 17.53259715 4.236846869 24.9990661 0.856143063 1.024179029 0.465451101 0.070946038 33.05361845 482196.5403 0.017162641 0.03896764 17252.29472 -4.236846869 0.168035966 S(ph)PQTLAPVGEDAMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPQTLAPVGEDAMK 14 0 Q92797 Q92797 SYMPK Symplekin 1 S(0.99)PQT(0.01)LAPVGEDAMK;S(1)PQTLAPVGEDAMK;S(1)PQTLAPVGEDAMK 169.64 3.46E-06 473130000 947910 676120 665000 686350 681120 566540 800230 930270 1303620 TRUE FALSE 822641.2918 671678.5232 986596.2243 842196.2577 667567.0446 588335.1604 722623.8178 731338.9999 1149507.529 0.715646719 0.584318507 0.858277305 0.732658323 0.580741777 0.511814969 0.628637742 0.636219408 1 20.13258448 1.236832677 24.99707565 1.000000432 0.653438759 0.558364356 0.096110912 36.27629982 524628.0499 0.153257534 0.024606411 17.25173098 -1.236832677 -0.346561673 S(ph)PRPDHPGTPPHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPRPDHPGTPPHK 13 1 P30291 P30291 WEE1 Wee1-like protein kinase 1 S(1)PRPDHPGTPPHK 131.48 7.85E-05 248510000 297920 324280 160380 172090 257520 289100 272700 314720 247130 TRUE FALSE 258549.1172 322149.7833 237940.3044 211165.6647 252395.8558 300221.8641 246253.596 247419.5772 217914.5729 1.186470063 1.478330609 1.091897165 0.969029569 1.158233029 1.377704391 1.130046479 1.135397114 1 17.73340315 7.999999999 0.026484819 2.78E-08 2.769529249 0.123670144 0.145292325 9283.150458 24.38878664 939.1498676 1726.595408 99999999.67 -7.999999999 2.769529221 S(ph)PRPSPVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPRPSPVPK 9 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.999)PRPS(0.001)PVPK 71.241 0.030364 310510000 236600 197090 166820 209920 168990 135460 165770 225220 584670 TRUE FALSE 205332.7105 195795.3028 247494.71 257585.5444 165627.4296 140671.2339 149693.6509 177058.4557 515550.9787 0.39827819 0.379778743 0.480058656 0.499631569 0.321262953 0.272856109 0.290356642 0.343435398 1 18.97575557 1.237056431 24.99997585 1.000000771 0.370664056 0.877722496 0.073517189 14.15910239 235246.4844 0.12426857 0.020256463 17.26062156 -1.237056431 -0.629336715 S(ph)PRPTGSDLLPGAPILSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.704)PRPT(0.284)GS(0.012)DLLPGAPILSLR;S(0.806)PRPT(0.193)GS(0.002)DLLPGAPILSLR 135.98 1.77E-05 801630000 265986 260707 216213 280865 283134 326730 287422 313396 358326 TRUE FALSE 230835.2762 258994.3986 320774.33 344639.691 277500.1873 339299.5145 259547.8587 246378.7043 315965.1085 0.730572047 0.819693034 1.015220736 1.09075237 0.878262124 1.073851211 0.821444684 0.779765543 1 18.26940573 4.441171834 5.315514257 0.935552204 0.749367787 0.345416694 0.102625883 0.212125198 15.07820192 0.028285443 0.083275872 27616.70331 -4.441171834 -0.186184416 S(ph)PS(ph)PAPAPAPAAAAGPPTR ddPTM_MDA-MB-175_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 156.96 1.58E-08 704220000 558200 428960 345830 362170 505610 432550 435000 547020 614600 TRUE FALSE 484432.4557 426142.1335 513074.5447 444406.2339 495549.3502 449190.4784 392813.767 430044.0299 541942.6882 0.893881339 0.786323246 0.94673211 0.820024412 0.914394383 0.828852364 0.724825292 0.793523078 1 19.04778077 2.50102172 24.12884535 0.818210235 0.869019658 0.023848679 0.081876022 1310.260976 1322781.724 0.027681553 0.024260758 316.9725982 -2.50102172 0.050809423 S(ph)PS(ph)PAPPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 76.143 0.05302 2273400000 1392070 1111460 793290 891320 1131340 1074620 1092310 1268380 1494510 TRUE FALSE 1208104.422 1104158.746 1176927.697 1093707.829 1108828.547 1115961.327 986377.9443 997146.8075 1317830.73 0.916737176 0.837860827 0.893079567 0.829930433 0.841404379 0.846816895 0.74848607 0.756657729 1 20.32973364 3.669150262 1.063433944 0.818743479 0.887508472 0.045579924 0.071652086 1.376682791 3.048036496 0.027817636 0.071420376 4668.208681 -3.669150262 0.068764993 S(ph)PS(ph)PAPPPRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSPAPPPRR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 S(1)PS(1)PAPPPRR 104.59 0.009313 857810000 353930 287560 224440 180550 308880 253640 303400 315050 221900 TRUE FALSE 307157.2538 285670.9994 332979.9347 221546.637 302733.8923 263397.6949 273976.3147 247679.0092 195667.2348 1.569794013 1.459983833 1.701766446 1.132262319 1.547187462 1.346151261 1.400215601 1.265817496 1 17.57804267 0.409946621 0.628619248 6.97E-32 1.488452402 0.516047983 0.145605041 7.39251374 1.047618803 10.04742434 0.068974993 2.570079873 -0.409946621 1.488452402 S(ph)PS(ph)PGPNHTSNSSNASNATVVPQNSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSPGPNHTSNSSNASNATVVPQNSSAR 28 0 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 2 S(0.971)PS(0.605)PGPNHT(0.13)S(0.116)NS(0.147)S(0.032)NASNATVVPQNSSAR 102.32 0.00059589 330940000 39347 39768 18551 28222 66435 61300 51574 50545 87770 TRUE FALSE 34147.19426 39506.76139 27522.32565 34630.23645 65113.07348 63658.25067 46572.36142 39736.34509 77393.93059 0.441212819 0.510463302 0.355613489 0.447454163 0.841320152 0.822522518 0.601757283 0.513429733 1 16.23993281 3.257181401 24.28419958 0.71729106 0.43787895 0.554726944 0.138815474 156.7127272 204374.3436 0.042251328 0.054435502 1807.929123 -3.257181401 -0.27941211 S(ph)PS(ph)PKPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSPKPTK 8 1 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BUL0;H3BV80 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 2 S(1)PS(0.894)PKPT(0.107)K 72.652 0.025947 486750000 1266300 760290 770100 721840 543480 545380 1045800 1258200 1327300 TRUE FALSE 1098955.247 755295.6049 1142522.936 885744.8046 532665.8113 566361.1215 944378.477 989143.7213 1170388.106 0.93896652 0.645337731 0.976191513 0.756795801 0.455118955 0.483908815 0.806893433 0.845141638 1 20.15855558 1.541517501 2.114220269 0.996742363 0.709668226 0.22641091 0.167813882 0.585438288 4.795982419 0.279180984 0.049253958 34.79505288 -1.541517501 -0.287074137 S(ph)PS(ph)PLRGNVVPS(ph)PLPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPSPLRGNVVPSPLPTR 17 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 3 S(1)PS(1)PLRGNVVPS(1)PLPTR;S(1)PS(1)PLRGNVVPS(0.975)PLPT(0.025)R 108.57 0.0010926 256455000 219828 212365 143599 148390 251280 230376 233617 282850 100675 TRUE FALSE 190777.1728 210969.9603 213043.9567 182084.2175 246280.0196 239238.7138 210960.8593 222364.7286 88773.31619 2.149037357 2.376501965 2.3998648 2.051114291 2.77425729 2.694939471 2.376399445 2.504859998 1 16.43783847 1.236611016 24.99998378 0.999998199 2.42498416 0.808278776 0.216670579 21.98485355 281838.1398 0.338821796 0.053486541 17.24292804 -1.236611016 1.424985961 S(ph)PPASPESWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPPASPESWK 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 S(0.931)PPAS(0.069)PESWK 112.83 0.0016451 343630000 237750 258580 234660 355220 441290 394720 514010 631160 562870 TRUE FALSE 206330.7351 256881.371 348142.3609 435878.1302 432509.1924 409905.1338 464161.3893 496191.3457 496328.1498 0.415714352 0.517563574 0.701435857 0.878205539 0.871417816 0.825875248 0.935190538 0.999724368 1 18.92093476 4.695110522 0.539160126 0.982324484 2.64E-17 0.945050111 0.046020453 0.95978755 0.23298427 0.034943577 0.597659697 49557.6292 -4.695110522 -0.982324484 down S(ph)PS(ph)PSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSPSFR 7 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 S(1)PS(0.937)PS(0.063)FR 70.1 0.084711 589760000 686290 660090 414550 505370 589070 614710 677440 667330 643860 TRUE FALSE 595595.0377 655753.8253 615027.7666 620121.9826 577348.6595 638358.2915 611741.9731 524626.6727 567743.6043 1.049056358 1.155017547 1.083284359 1.0922571 1.016917945 1.124377777 1.077496899 0.924055628 1 19.11488002 1.762831785 14.34149291 0.961943185 1.087200057 0.606118076 0.041358264 0.308968339 184.921561 0.020925187 0.009999652 57.92043103 -1.762831785 0.125256872 S(ph)PS(ph)PSPTPEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSPSPTPEAK 11 0 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 S(1)PS(0.911)PS(0.078)PT(0.011)PEAK 138.24 0.0018606 0 600410 367100 280980 348810 388040 323780 407870 503570 592640 TRUE FALSE 521064.2973 364688.4959 416862.8678 428012.6417 380318.7632 336236.0261 368314.8302 395885.4743 522578.7743 0.997101916 0.6978632 0.797703405 0.819039469 0.727773078 0.643416921 0.704802507 0.757561336 1 18.995289 4.74851417 24.4168419 0.761984992 0.997102096 0.354868042 0.09650102 1147.864778 2815721.804 0.023376182 0.302370773 56042.07019 -4.74851417 0.235117104 S(ph)PS(ph)PYYSR ddPTM_MDA-MB-175_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(0.999)PS(0.904)PY(0.096)YSR;S(0.997)PS(0.939)PY(0.064)YSR;S(1)PS(0.999)PY(0.001)YSR;S(0.998)PS(0.941)PY(0.06)Y(0.001)SR;S(0.999)PS(0.994)PY(0.007)YSR;S(0.999)PS(0.955)PY(0.046)YSR 90.827 0.018889 6850310000 6060340 4961930 3556110 3915570 4971770 4696890 4681600 5143100 7705540 TRUE FALSE 5259450.714 4929334.755 5275856.69 4804660.014 4872841.504 4877582.398 4227579.153 4043288.089 6794599.839 0.77406335 0.725478302 0.776477911 0.70712921 0.717163868 0.717861613 0.622196929 0.595073762 1 22.69595716 3.716904679 19.69427417 0.705594976 0.755353627 0 0.109453177 199.1507183 181110.4317 0.029907052 0.044484439 5210.80329 -3.716904679 0.049758651 S(ph)PSAGDVHILTGFAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPSAGDVHILTGFAK 15 0 A0A3B3ITL0;A0A3B3IRJ9;Q9Y2H2-4;Q9Y2H2 A0A3B3ITL0 INPP5F Phosphatidylinositide phosphatase SAC2 1 S(0.945)PS(0.055)AGDVHILTGFAK;S(0.975)PS(0.025)AGDVHILTGFAK 151.04 1.98E-06 244780000 356540 321390 285970 402880 378500 312640 412840 480150 731310 TRUE FALSE 309422.3356 319278.7679 424266.0485 494360.0616 370968.5905 324667.4631 372802.8403 377473.659 644855.3649 0.479832149 0.495116867 0.657924353 0.766621616 0.575274101 0.503473307 0.578118537 0.585361741 1 19.29861609 1.238559536 9.625972638 1.00210618 0.583260628 0.709459433 0.084405726 0.045804765 76.87754988 0.124971275 0.022110883 17.32046453 -1.238559536 -0.418845552 S(ph)PSAQCPFPGGTVLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSAQCPFPGGTVLSR 16 0 P78411-3;P78411-2;P78411;H0YML8 P78411-3 IRX5 Iroquois-class homeodomain protein IRX-5 1 S(0.936)PS(0.064)AQCPFPGGTVLSR 127.2 7.08E-05 81309000 44359 41403 24265 29784 36869 29322 37843 46198 49602 TRUE FALSE 38496.84576 41131.02097 35999.63516 36546.91242 36135.37903 30450.03631 34172.99168 36318.91721 43738.10807 0.880167146 0.940393236 0.823072528 0.835585123 0.826176088 0.696190065 0.781309325 0.830372387 1 15.4166032 4.224761404 23.83362453 0.820855783 0.910280169 0.167608548 0.075536928 194.6696223 336231.242 0.01972163 0.041447903 16778.81958 -4.224761404 0.089424386 S(ph)PSASSLSSMSSVASSVSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSASSLSSMSSVASSVSSR 20 0 J3KP58;P30622-2;P30622-1;P30622;F5H0N7;F5H6A0;F5H1T5 J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 1 S(0.892)PS(0.101)AS(0.005)S(0.002)LSSMSSVASSVSSR 82.55 0.0039303 91882000 33040 23808 16854 23943 29784 29434 28888 30595 31825 TRUE FALSE 28673.68029 23651.60368 25004.65077 29379.6241 29191.35667 30566.34503 26086.44621 24052.49734 28062.68476 1.021772526 0.842813291 0.89102846 1.046928487 1.04021967 1.089216705 0.929577709 0.857098939 1 14.77636542 5.048467699 15.49378257 0.957639277 1.383161173 0.045919942 0.083277951 7260430.078 63099640.2 0.022331023 91064169.89 111806.6665 -5.048467699 0.425521896 S(ph)PSDSSTASTPVAEQIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPSDSSTASTPVAEQIER 18 0 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 S(0.956)PS(0.029)DS(0.011)S(0.003)T(0.001)ASTPVAEQIER;S(0.921)PS(0.079)DSSTASTPVAEQIER 254.53 1.63E-30 434240000 188188 86634 75044 84678 80440 89227 87592 105291 162862 TRUE FALSE 163318.479 86064.89555 111335.5294 103905.4341 78839.40138 92659.62043 79097.34132 82775.33903 143608.6399 1.137246889 0.599301655 0.775270412 0.723531914 0.54898787 0.64522316 0.550784001 0.576395258 1 17.13178302 4.743337306 24.60902566 0.66308313 1.137247132 0.526871258 0.136334434 313.4068453 1614571.595 0.032281989 0.255709157 55378.00503 -4.743337306 0.474164001 S(ph)PSELFAQHIVTIVHHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSELFAQHIVTIVHHVK 18 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.991)PS(0.009)ELFAQHIVTIVHHVK 228.62 3.89E-19 580530000 627830 436380 311100 402520 410420 342370 511490 555360 527290 TRUE FALSE 544860.6748 433513.391 461549.0006 493918.3181 402253.445 355541.1954 461885.7785 436600.5858 464954.3769 1.171858363 0.932378342 0.992675891 1.062294158 0.865146055 0.764679747 0.993400216 0.939018122 1 18.82672963 4.740168516 24.72026889 0.942850592 1.171858452 0.433434537 0.081974147 125.0580777 1922475.811 0.020731274 0.128460831 54975.41496 -4.740168516 0.22900786 S(ph)PSFGDPQLS(ph)PEARPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPSFGDPQLSPEARPR 16 1 O95425-2;O95425-3 O95425-2 SVIL Supervillin 2 S(0.989)PS(0.015)FGDPQLS(0.996)PEARPR;S(0.999)PS(0.001)FGDPQLS(1)PEARPR;S(0.998)PS(0.005)FGDPQLS(0.997)PEARPR 104.06 0.00079152 1171690000 549600 490200 349263 376400 524840 494430 456350 565220 364030 TRUE FALSE 476968.9675 486979.8439 518167.755 461867.3729 514396.7108 513451.042 412093.2472 444352.1015 320994.7881 1.48590876 1.517095797 1.614255976 1.43886253 1.602507984 1.599561928 1.283800431 1.384296936 1 18.29219035 0.650246325 0.869075961 1.88E-11 1.538849046 0.780185145 0.087190667 2.552370219 0.726907212 4.802822349 0.03041409 4.469370155 -0.650246325 1.538849046 S(ph)PSFGDPQLSPEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSFGDPQLSPEAR 14 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 S(0.967)PS(0.033)FGDPQLSPEAR 116.87 0.00096109 0 189300 147620 122440 148420 153700 146660 160920 184170 194920 TRUE FALSE 164283.5254 146650.2745 181652.3935 182121.0295 150641.6707 152302.1051 145314.0032 144786.6787 171876.7797 0.955821523 0.853229126 1.05687571 1.059602291 0.876451554 0.886112164 0.845454537 0.842386499 1 17.39101513 3.200025873 24.90631412 0.880573632 0.977620813 0.281634176 0.071455304 196.789124 127190.8386 0.022345834 0.025338271 1584.987614 -3.200025873 0.097047181 S(ph)PSFNMQLISQV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSFNMQLISQV 12 0 Q8IXS8 Q8IXS8 FAM126B Protein FAM126B 1 S(0.649)PS(0.351)FNMQLISQV 81.017 0.019701 26636000 50269 51547 35697 39002 58021 63022 52194 54855 53853 TRUE FALSE 43625.82428 51208.38436 52960.1886 47858.00021 56866.49562 65446.49712 47132.23391 43124.68513 47486.55969 0.918698355 1.078376381 1.115266908 1.007822014 1.197528227 1.378210962 0.992538399 0.908145071 1 15.53523162 2.01827795 24.99986371 0.948360427 1.11906048 0.255886503 0.121009019 299.6181211 409804.4174 0.051232608 0.034534397 104.298473 -2.01827795 0.170700053 S(ph)PSGHPHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SPSGHPHVR 9 0 Q8WX93-8;Q8WX93-3;Q8WX93-2;Q8WX93-9;Q8WX93-5;Q8WX93;Q8WX93-4;Q8WX93-7 Q8WX93-8 PALLD Palladin 1 S(0.975)PS(0.025)GHPHVR;S(0.987)PS(0.013)GHPHVR;S(0.998)PS(0.002)GHPHVR;S(0.984)PS(0.016)GHPHVR;S(0.998)PS(0.002)GHPHVR;S(0.999)PS(0.001)GHPHVR 152.69 5.14E-05 4976930000 837164 949761 428367 664300 791107 958312 842276 1036581 865515 TRUE FALSE 726530.6563 943521.9575 635526.714 815139.4682 775365.5185 995178.8828 760592.2032 814916.2198 763194.8027 0.951959649 1.236279328 0.83271887 1.068062132 1.015947063 1.303964439 0.996589862 1.067769614 1 19.54169182 3.50658183 24.97735136 1.077504395 1.016661179 0.056030366 0.130799043 2502.979244 2122077.217 0.03447466 0.05103173 3210.567682 -3.50658183 -0.060843216 S(ph)PSGLRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPSGLRPR 8 1 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;H3BQK4 P49815 TSC2 Tuberin 1 S(0.988)PS(0.012)GLRPR;S(0.862)PS(0.138)GLRPR;S(0.999)PS(0.001)GLRPR;S(0.996)PS(0.004)GLRPR 78.77 0.018026 918260000 246047 296224 216927 201260 271488 303628 268776 290973 296806 TRUE FALSE 213531.2655 294278.085 321833.6228 246959.1591 266085.92 315308.7656 242710.1449 228750.6883 261717.9328 0.815883204 1.124409328 1.229696488 0.943608091 1.016689675 1.204765613 0.927373001 0.87403521 1 17.99765326 2.04986913 24.99050776 0.919824928 1.060487681 0.174843856 0.123589335 154.6967498 77521.17551 0.049371289 0.033286109 112.1680397 -2.04986913 0.140662753 S(ph)PSLDNPTPFPNLGPSENPLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.889)PS(0.111)LDNPTPFPNLGPSENPLKR;S(0.552)PS(0.448)LDNPTPFPNLGPSENPLKR 140.57 7.88E-08 961400000 651240 475050 375449 524670 480910 367350 556620 613120 1098240 TRUE FALSE 565176.984 471929.3653 557017.3922 643804.3426 471340.8319 381482.1922 502639.0781 482009.0593 968407.3183 0.583614945 0.487325278 0.57518916 0.664807391 0.486717544 0.393927416 0.519036844 0.497733805 1 19.88525446 1.236665043 24.99884669 1.000000601 0.523693098 0.811470755 0.071786913 21.84074178 287955.5719 0.115735999 0.018348622 17.24507322 -1.236665043 -0.476307502 QAS(ph)TDAGTAGALTPQHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.5)T(0.5)DAGTAGALTPQHVR;QAS(0.756)T(0.244)DAGTAGALTPQHVR;QAS(0.87)T(0.13)DAGT(0.001)AGALTPQHVR 184.57 1.16E-14 1446180000 1147300 559180 243395 246726 459680 498000 474135 476030 300438 TRUE FALSE 995681.3981 555506.7098 361101.6361 302748.9093 450533.2673 517158.3822 428153.4607 374234.689 264920.5619 3.758414941 2.096880309 1.363056282 1.142791285 1.700635331 1.952126247 1.616157906 1.412629832 1 18.0152003 4.702313361 2.470545296 1.477251664 4.165157512 0.876311113 0.272433597 0.164519384 1.331838276 0.074282892 0.902763045 50386.40356 -4.702313361 2.687905847 up ASS(ph)LNENVDHSALLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASSLNENVDHSALLK 15 0 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 1 AS(0.122)S(0.878)LNENVDHSALLK;AS(0.113)S(0.887)LNENVDHSALLK 284.65 3.43E-34 1576290000 2559000 1062150 353220 677980 729040 490750 1065190 1093020 1055650 TRUE FALSE 2220821.666 1055172.667 524038.3734 831925.7213 714533.5303 509629.4701 961888.0377 859286.1789 930852.2596 2.385793925 1.133555466 0.562966215 0.89372477 0.767612178 0.547486956 1.03334125 0.923117681 1 19.82819268 4.713571199 3.23545544 0.830127207 2.563944687 0.897877465 0.165007369 0.089274297 1.527991112 0.041711017 0.376135365 51709.60242 -4.713571199 1.73381748 up S(ph)PSLSSK ddPTM_MDA-MB-175_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(0.974)PS(0.026)LSSK;S(0.994)PS(0.006)LSSK;S(0.998)PS(0.002)LSSK;S(0.98)PS(0.02)LSSK;S(0.974)PS(0.026)LSSK 110.79 0.007053 5601160000 5882160 4681090 3688780 4710790 3328640 3696130 5069850 6101760 11645100 TRUE FALSE 5104817.653 4650339.612 5472686.346 5780446.869 3262406.576 3838322.513 4578176.727 4796946.108 10268429.54 0.497137136 0.452877394 0.532962351 0.562933879 0.31771232 0.373798398 0.445849748 0.467154796 1 23.29171222 1.238165804 6.58728224 1.014748155 0.453979393 0.853735455 0.070741319 0.045371714 9.53277612 0.113855886 0.018542513 17.30476893 -1.238165804 -0.560768762 S(ph)PSMPSLNQTWPELNQSSEDTAIVHPVPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPSMPSLNQTWPELNQSSEDTAIVHPVPIR 30 0 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2 E9PMG1 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.585)PS(0.414)MPS(0.001)LNQTWPELNQSSEDTAIVHPVPIR;S(0.85)PS(0.149)MPS(0.001)LNQTWPELNQSSEDTAIVHPVPIR 179.1 5.02E-18 306125000 68009 58769 53784 64713 59915 69470 67166 71547 96850 TRUE FALSE 59021.43834 58382.94257 79794.1223 79407.07573 58722.80872 72142.55585 60652.25166 56247.23083 85400.50333 0.691113472 0.683636984 0.934351897 0.929819763 0.687616658 0.844755628 0.710209534 0.658628798 1 16.38195695 S(ph)PSMSISEPISVTLPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPSMSISEPISVTLPPR 17 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.979)PS(0.021)MSISEPISVTLPPR;S(0.73)PS(0.269)MSISEPISVTLPPR 159.4 3.38E-09 97559000 70751 63611 30173.4 49449.2 55576 47738.8 88775 67609 48283 TRUE FALSE 61401.07609 63193.13515 44765.35716 60677.39664 54470.14633 49575.34253 80165.61416 53151.34148 42575.03874 1.442184855 1.484276633 1.05144607 1.425187115 1.279391586 1.164422723 1.882925219 1.248415575 1 15.37772022 1.346139842 4.815936129 1.007762703 1.382964591 0.236558416 0.220715487 0.2817376 9.090239828 0.247359429 0.053902664 22.18910788 -1.346139842 0.375201887 S(ph)PSPAVPLR ddPTM_MDA-MB-175_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(0.896)PS(0.104)PAVPLR;S(0.596)PS(0.404)PAVPLR;S(0.876)PS(0.124)PAVPLR 140.45 0.00011442 1074560000 1255350 1128820 668000 814470 1103950 1130780 891150 1169590 1035490 TRUE FALSE 1089452.317 1121404.707 991047.0343 999407.8619 1081983.555 1174281.838 804726.4102 919482.2803 913075.5518 1.193167767 1.228162012 1.085394338 1.094551113 1.184987981 1.286073026 0.881336061 1.007016647 1 19.80037471 2.234187245 24.99998646 0.968605644 1.173186554 0.697758826 0.066893169 65.15265475 372433.5449 0.027540292 0.01929356 171.4696435 -2.234187245 0.20458091 S(ph)PSPFTHTHLAQGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSPFTHTHLAQGYR 15 0 P38398-7;P38398;P38398-4;P38398-8;Q5YLB2 P38398-7 BRCA1 Breast cancer type 1 susceptibility protein 1 S(0.974)PS(0.026)PFTHTHLAQGYR 124.68 6.13E-05 119730000 63115 69148 45276 50257 70945 59750 53948 78098 51505 TRUE FALSE 54774.19284 68693.76223 67171.62504 61668.61998 69533.3333 62048.62116 48716.13126 61397.35046 45416.13757 1.206051324 1.512540826 1.479025488 1.357856993 1.53102701 1.366224089 1.072661258 1.351884016 1 15.4709174 2.391125791 6.236828101 1.183934977 1.425174296 0.482955821 0.128637867 0.185241071 10.84132373 0.045529215 0.035077924 246.1080337 -2.391125791 0.241239319 S(ph)PSPGPNHTSNSSNASNATVVPQNSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSPGPNHTSNSSNASNATVVPQNSSAR 28 0 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 S(0.951)PS(0.049)PGPNHTSNSSNASNATVVPQNSSAR 142.72 7.46E-08 273510000 23426 30152 17638 21031 46514 49750 28950 33780 52491 TRUE FALSE 20330.19475 29953.92953 26167.7958 25806.40999 45588.4624 51663.91469 26142.43346 26556.40988 46285.57378 0.439233936 0.647154763 0.565355329 0.557547587 0.984938906 1.116199076 0.564807376 0.573751338 1 15.49827499 3.270702302 24.44241154 0.805843911 0.560027187 0.38135564 0.182657634 215.0024103 163498.65 0.058251999 0.0751957 1865.100771 -3.270702302 -0.245816725 S(ph)PSPRPNMPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSPRPNMPVR 11 1 Q9H6S0 Q9H6S0 YTHDC2 Probable ATP-dependent RNA helicase YTHDC2 1 S(0.932)PS(0.068)PRPNMPVR 54.309 0.080236 212110000 75207 56607 51213 48200 61186 62673 55031 70450 94863 TRUE FALSE 65268.2044 56235.14489 75979.7781 59144.54669 59968.51831 65084.07086 49694.10209 55384.81574 83648.40421 0.780268375 0.672279949 0.908323103 0.707061267 0.716911684 0.778067095 0.594083086 0.662114433 1 16.3520504 S(ph)PSPSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPSPSFR 7 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 S(0.995)PS(0.005)PSFR;S(0.996)PS(0.004)PSFR 122.44 0.0045536 1188000000 249470 257900 185961 191116 222820 245920 224180 243560 235860 TRUE FALSE 216501.9074 256205.8379 275892.3616 234511.8088 218386.3179 255380.7015 202439.0581 191476.5894 207976.8995 1.040990167 1.231895651 1.326552912 1.127585849 1.05005084 1.227928208 0.973372805 0.920662775 1 17.66606377 2.193495221 7.803311257 0.954609753 1.170417506 0.546361943 0.086958444 0.171023687 25.25390629 0.036379716 0.02464265 156.1331855 -2.193495221 0.215807753 S(ph)PSPVLR ddPTM_MDA-MB-175_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(0.805)PS(0.195)PVLR 81.548 0.02822 350370000 221420 194140 143710 138870 195270 226050 195840 189010 216070 TRUE FALSE 192158.786 192864.6816 213208.6367 170402.556 191384.509 234746.2898 176847.4669 148591.6824 190526.4507 1.008567499 1.012272473 1.119050063 0.894377423 1.004503618 1.232092913 0.92820428 0.779900543 1 17.53963178 2.011080572 24.99727985 0.868175906 1.041795544 0.304833571 0.101351964 212.5714695 479550.0451 0.040452414 0.027246803 102.5842228 -2.011080572 0.173619637 S(ph)PSPVQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPSPVQGK 8 0 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 S(0.982)PS(0.018)PVQGK;S(0.878)PS(0.122)PVQGK 121.64 0.0014944 813700000 2912000 2033100 1259750 1560680 1535070 1729030 2147350 2630650 2353670 TRUE FALSE 2527171.822 2019744.432 1868969.314 1915056.248 1504525.11 1795546.903 1939100.328 2068105.969 2075421.814 1.217666599 0.97317298 0.900525041 0.922731097 0.724924977 0.865147938 0.934316251 0.996475008 1 20.98497315 4.743135443 2.522002552 0.908553178 1.287176493 0.618189743 0.076545575 0.397973997 3.17375924 0.021848384 0.324761206 55352.27083 -4.743135443 0.378623315 S(ph)PSPYYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.696)PS(0.304)PYYSR;S(0.999)PS(0.001)PYYSR;S(0.98)PS(0.02)PYYSR 116.52 0.0023665 1995350000 427010 323749 269223 352929 325830 323629 331588 411780 530220 TRUE FALSE 370579.5466 321622.2715 399420.1433 433066.9236 319346.6205 336079.217 299430.6468 323724.0515 467537.9956 0.792619103 0.687906169 0.854305205 0.926271079 0.683038862 0.718827604 0.640441311 0.69240159 1 18.83472409 3.189270287 24.99988756 0.73073112 0.808967577 0.071693984 0.113177474 271.3658718 137634.6882 0.034692583 0.039337762 1546.216442 -3.189270287 0.078236457 S(ph)PSQDFSFIEDTEILDSAMYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SPSQDFSFIEDTEILDSAMYR 21 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 S(0.458)PS(0.458)QDFS(0.084)FIEDTEILDSAMYR;S(0.459)PS(0.459)QDFS(0.081)FIEDTEILDSAMYR;S(0.444)PS(0.444)QDFS(0.112)FIEDTEILDSAMYR;S(0.473)PS(0.473)QDFS(0.053)FIEDTEILDSAMYR;S(0.496)PS(0.496)QDFS(0.008)FIEDTEILDSAMYR;S(0.497)PS(0.497)QDFS(0.006)FIEDTEILDSAMYR;S(0.43)PS(0.43)QDFS(0.141)FIEDTEILDSAMYR 193.06 5.54E-18 477141000 235617 218255 152519.9 183500 203357 223102 223732 274887 251940 TRUE FALSE 204479.6165 216821.2685 226279.0338 225166.4796 199310.5936 231684.8783 202034.5051 216104.5542 222155.9402 0.920432811 0.975986815 1.018559457 1.013551469 0.897165268 1.042893015 0.909426527 0.972760638 1 17.76121319 S(ph)PSQESIGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSQESIGAR 10 0 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 S(0.997)PS(0.003)QESIGAR 104.39 0.0028192 195480000 28847 18827 18791 26696 22942 21340 18865 33130 29756 TRUE FALSE 25034.79586 18703.3242 27878.39045 32757.73482 22485.49909 22160.96361 17035.4752 26045.40732 26238.27958 0.954132522 0.71282586 1.062508324 1.24847114 0.856973073 0.844604294 0.649260374 0.992649203 1 14.67938551 S(ph)PSQGSYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPSQGSYSR 9 0 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 S(1)PSQGSYSR;S(0.953)PS(0.047)QGSYSR;S(0.999)PS(0.001)QGSYSR;S(0.993)PS(0.007)QGSYSR 119.05 0.00093378 2197799000 1726864 1574402 1147358.7 1436687.4 1814390 2201566 1893321 2204242 2112753 TRUE FALSE 1498654.547 1564059.65 1702225.205 1762909.233 1778287.189 2286261.669 1709707.021 1732882.002 1862985.747 0.804436936 0.839544614 0.91370812 0.946281653 0.954536121 1.227202984 0.917724155 0.930163854 1 20.82918521 4.02005097 1.322644066 0.997933921 0.800967509 0.427466086 0.085712958 0.567492329 1.771601885 0.028548628 0.106868668 10472.51449 -4.02005097 -0.196966412 S(ph)PSSDLDTDAEGDDFELLDQSELSQLDPASSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPSSDLDTDAEGDDFELLDQSELSQLDPASSR 32 0 K7EQI9;Q86VR2-2;Q86VR2 K7EQI9 FAM134C Protein FAM134C 1 S(0.348)PS(0.348)S(0.303)DLDT(0.001)DAEGDDFELLDQSELSQLDPASSR;S(0.333)PS(0.333)S(0.333)DLDT(0.002)DAEGDDFELLDQSELSQLDPASSR 197.35 6.21E-27 320810000 68472 55346 38856 60670 67896 76913 44050 83626 62237 TRUE FALSE 59423.25171 54982.42848 57646.89157 74446.05078 66545.00244 79871.89288 39778.03778 65743.23068 54879.41276 1.082796785 1.001877129 1.05042836 1.356538765 1.212567684 1.455407208 0.724826229 1.197957984 1 15.74397742 2.241851737 24.99999867 1.010471766 1.186375391 0.245322915 0.177051087 149.3864952 1134782.497 0.068837792 0.051056914 174.522625 -2.241851737 0.175903626 S(ph)PSSDSWTCADTSTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSSDSWTCADTSTER 16 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7;H0YIQ0 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 S(0.986)PS(0.014)SDSWTCADTSTER 163.23 8.18E-09 156510000 113070 93649 73947 84646 107650 82569 114560 129820 144500 TRUE FALSE 98127.51302 93033.81355 109708.0165 103866.168 105507.9756 85745.48286 103449.9888 102059.0033 127417.3746 0.770126628 0.730150137 0.861013004 0.815164873 0.828050146 0.672949691 0.811898606 0.800981841 1 16.95920249 1.199623503 3.262914008 1.048782632 0.784682226 0.617792742 0.052897202 0.286498889 3.821642232 0.204534841 0.0135711 15.83519817 -1.199623503 -0.264100406 S(ph)PSSESSPQHPTPPARPR ddPTM_MDA-MB-175_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(0.725)PS(0.076)S(0.076)ES(0.064)S(0.059)PQHPTPPARPR 52.453 0.079825 208090000 59924 49922 34881 45653 68301 64165 64391 67388 50813 TRUE FALSE 52004.89157 49594.05909 51749.56827 56019.21141 66941.94373 66633.46907 58146.37073 52977.60061 44805.94503 1.16066945 1.106863365 1.154971025 1.250262914 1.494041554 1.487156872 1.297737849 1.182378825 1 15.45140255 3.69712811 4.035911176 1.294432274 1.135333566 0.192487468 0.140865141 0.3947994 14.07852844 0.043751022 0.069863823 4978.839312 -3.69712811 -0.159098708 S(ph)PSSKPSLAVAVDSAPEVAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSSKPSLAVAVDSAPEVAVK 21 1 O60508;Q5SRN1 O60508 CDC40 Pre-mRNA-processing factor 17 1 S(0.826)PS(0.086)S(0.086)KPS(0.001)LAVAVDSAPEVAVK 176.09 5.21E-13 191820000 419750 291220 271460 349940 277490 239310 340460 488060 801370 TRUE FALSE 364278.974 289306.9566 402738.964 429399.2255 271968.4919 248516.4106 307442.2416 383692.1671 706632.9515 0.515513709 0.40941617 0.56994082 0.607669405 0.384879436 0.351690945 0.435080534 0.54298652 1 19.4306015 1.230088222 3.294753451 1.093033486 0.468124494 0.812126173 0.079800727 0.154496976 2.268779304 0.252094121 0.021955341 16.98588665 -1.230088222 -0.624908992 S(ph)PSSQTPNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSSQTPNSR 10 0 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 1 S(0.955)PS(0.043)S(0.002)QTPNSR 78.83 0.030238 358840000 229020 213360 215740 232600 210280 196700 223770 256390 212630 TRUE FALSE 198754.4267 211958.4241 320072.5856 285415.3851 206095.8394 204267.1763 202068.8198 201562.9937 187493.1236 1.060062486 1.130486388 1.707116397 1.522271215 1.099218123 1.089464895 1.077739897 1.075042059 1 17.51647816 3.13840377 7.426663501 1.068225003 1.363327276 0.38270084 0.181107643 0.259074145 16.8710978 0.058950588 0.067045583 1375.320037 -3.13840377 0.295102273 S(ph)PSSVTGNALWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSSVTGNALWK 12 0 Q9NYB0;A0A590UJT3 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 S(0.992)PS(0.008)SVTGNALWK 227.06 2.91E-06 0 240420 173780 120630 177520 177100 130290 191050 215540 253830 TRUE FALSE 208647.8879 172638.4277 178967.0715 217828.6292 173576.0565 135302.3406 172522.0004 169448.4483 223822.5066 0.932202445 0.771318445 0.799593724 0.973220399 0.775507607 0.604507307 0.770798268 0.757066172 1 17.77199559 3.042180135 24.98640293 0.768110486 0.859290418 0.125201552 0.110688209 292.4644772 173246.4506 0.033520882 0.038009085 1101.996297 -3.042180135 0.091179932 S(ph)PSTLLPK ddPTM_MDA-MB-175_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(0.713)PS(0.287)TLLPK 137.28 0.00079199 430220000 536750 441100 353700 415210 375040 372870 481340 575130 644320 TRUE FALSE 465817.1275 438202.3851 524750.5031 509489.7766 367577.4378 387214.5502 434659.7209 452142.9252 568149.2236 0.819885178 0.771280443 0.92361387 0.89675345 0.646973405 0.681536706 0.765044997 0.795817201 1 19.11591038 1.238929366 5.616557781 1.00974361 0.785622738 0.388392423 0.083833702 0.170375704 17.50565132 0.147404825 0.022548415 17.33522032 -1.238929366 -0.224120872 S(ph)PSTTYLHTPTPSEDAAIPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPSTTYLHTPTPSEDAAIPSK 21 0 Q13111 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 S(0.919)PS(0.027)T(0.027)T(0.027)YLHTPTPSEDAAIPSK;S(0.957)PS(0.036)T(0.005)T(0.001)YLHTPTPSEDAAIPSK;S(0.974)PS(0.024)T(0.002)T(0.001)YLHTPTPSEDAAIPSK 226.81 1.47E-25 3736980000 1182160 1128490 718875 972840 1175990 985570 1178190 1555140 1440060 TRUE FALSE 1025934.561 1121076.875 1066525.354 1193738.191 1152590.1 1023485.516 1063929.315 1222585.413 1269817.747 0.807938433 0.882864393 0.839904275 0.940086239 0.907681517 0.806009774 0.837859856 0.962803848 1 20.27619002 1.619431263 4.367286082 0.991322975 0.863416018 0.591056387 0.042215074 0.113306819 4.790052525 0.031707146 0.011332085 41.63238227 -1.619431263 -0.127906957 S(ph)PSVAAMASPQLCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SPSVAAMASPQLCR 14 0 P25325-2 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 1 S(0.999)PS(0.001)VAAMASPQLCR;S(0.99)PS(0.01)VAAMASPQLCR;S(0.542)PS(0.458)VAAMASPQLCR;S(1)PSVAAMASPQLCR;S(1)PSVAAMASPQLCR;S(0.998)PS(0.002)VAAMASPQLCR;S(0.996)PS(0.004)VAAMASPQLCR 225.09 3.05E-12 1831060000 1158047 1055620 796660 935610 1154170 1091732 1255305 1343399 1867359 TRUE FALSE 1005008.155 1048685.563 1181927.441 1148054.55 1131204.275 1133731.636 1133565.714 1056123.578 1646601.946 0.610352828 0.636878612 0.717797913 0.697226523 0.68699316 0.688528056 0.688427289 0.641395803 1 20.65106041 1.235232649 24.99998231 1.000000454 0.67265497 0.910255438 0.032466409 27.35402904 205451.6438 0.058210398 0.00828817 17.18828907 -1.235232649 -0.327345483 S(ph)PSWQRPNQGVPSTGR ddPTM_MDA-MB-175_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(0.973)PS(0.027)WQRPNQGVPSTGR;S(0.993)PS(0.007)WQRPNQGVPSTGR;S(0.998)PS(0.002)WQRPNQGVPSTGR;S(0.969)PS(0.031)WQRPNQGVPSTGR;S(0.998)PS(0.002)WQRPNQGVPSTGR 166.61 4.01E-09 5097160000 413887 377862 407113 317710 300701 453220 336590 342679 325602 TRUE FALSE 359190.7843 375379.7996 603994.2085 389850.9114 294717.6384 470655.6667 303947.5536 269399.7626 287109.7025 1.251057631 1.307443797 2.10370532 1.357846524 1.026498359 1.639288615 1.058646054 0.93831647 1 18.13124256 2.121612791 5.988107162 0.975434148 1.446725949 0.362631514 0.281719796 0.227436191 11.02959274 0.119660782 0.079989332 132.3161302 -2.121612791 0.4712918 S(ph)PSWTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPSWTR 6 0 D3DX86;H3BLZ2;Q9H9R9;Q9H9R9-2;Q9H9R9-3 D3DX86 MGC3101;DBNDD1 Dysbindin domain-containing protein 1 1 S(0.993)PS(0.007)WTR;S(0.993)PS(0.007)WTR 81.1 0.065842 1985000000 1346350 1370380 919770 1024210 1374790 1536680 1445430 1469930 1709350 TRUE FALSE 1168426.436 1361377.884 1364573.848 1256772.535 1347434.369 1595797.074 1305252.421 1155596.909 1507272.59 0.775192519 0.903206157 0.90532652 0.833805738 0.893955332 1.058731569 0.865969719 0.766680769 1 20.52350892 3.03233942 18.01633036 0.902360005 0.86180431 0.102590386 0.085383163 37.25593167 20750.5862 0.027764316 0.031478272 1077.306847 -3.03233942 -0.040555694 S(ph)PSYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SPSYGR 6 0 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 1 S(0.999)PS(0.001)YGR;S(1)PSYGR;S(1)PSYGR;S(0.999)PS(0.001)YGR;S(0.999)PS(0.001)YGR 161.6 0.0088654 32707840000 4370220 3346620 2091940 2843360 2089230 3051510 3127730 3820220 3680740 TRUE FALSE 3792684.354 3324635.833 3103609.181 3488988.346 2047658.411 3168903.564 2824403.226 3003295.682 3245607.11 1.168559294 1.024349442 0.956249193 1.074987892 0.630901505 0.976366965 0.870223391 0.925341725 1 21.63005694 4.753644327 0.978211831 0.901699738 1.308536126 0.348257556 0.114262199 2.278881508 1.717324677 0.036249701 0.989597793 56707.99948 -4.753644327 0.406836388 S(ph)PSYTNDSTATFIIDGMHCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPSYTNDSTATFIIDGMHCK 20 0 Q04656-5;Q04656;Q04656-2;Q04656-3 Q04656-5 ATP7A Copper-transporting ATPase 1 1 S(0.743)PS(0.235)Y(0.022)TNDSTATFIIDGMHCK;S(0.995)PS(0.005)YTNDSTATFIIDGMHCK 201.79 7.89E-22 426700000 464870 384460 321600 446320 496460 500160 416240 680740 549280 TRUE FALSE 403436.2517 381934.4569 477126.8357 547663.7776 486581.4173 519401.4788 375873.1089 535169.0485 484344.7441 0.832952678 0.788559103 0.985097581 1.130731332 1.004617936 1.072379715 0.77604457 1.104934151 1 18.88567476 4.188817397 5.600620094 1.014085049 0.810362222 0.427599395 0.09637426 0.158685178 10.93668893 0.024026266 0.053201846 15446.04862 -4.188817397 -0.203722827 S(ph)PTAALNESLVECPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPTAALNESLVECPK 15 0 Q53EZ4 Q53EZ4 CEP55 Centrosomal protein of 55 kDa 1 S(0.995)PT(0.005)AALNESLVECPK;S(0.87)PT(0.13)AALNESLVECPK;S(0.999)PT(0.001)AALNESLVECPK 240.53 7.99E-18 472080000 234170 254926 179127 240560 276001 213575 283625 359818 364397 TRUE FALSE 203223.8412 253251.3743 265753.4163 295182.8247 270509.1201 221791.3685 256119.0912 282873.7208 321318.4018 0.632468729 0.788163308 0.827071885 0.918661437 0.841872481 0.690254175 0.797088152 0.880353317 1 18.29364408 -1.999915363 0.035488953 2.048638863 2.77E-05 0.343677529 0.085329194 3239.284209 11.35178609 491.2695075 217.4248655 0.010001949 1.999915363 -2.048611127 S(ph)PTEDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SPTEDFR 7 0 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 S(0.981)PT(0.019)EDFR;S(0.969)PT(0.031)EDFR;S(0.989)PT(0.011)EDFR;S(0.988)PT(0.012)EDFR;S(0.991)PT(0.009)EDFR;S(0.988)PT(0.012)EDFR 122.19 0.0045789 4736070000 5754360 4903870 3803910 4373960 4901810 4854510 4675430 5500740 6497090 TRUE FALSE 4993906.746 4871656.155 5643493.599 5367134.47 4804273.571 5041266.141 4222007.518 4324449.558 5729011.422 0.871687343 0.85034848 0.985072848 0.936834311 0.838586838 0.879953934 0.736952191 0.754833468 1 22.44985478 2.894272439 2.077625866 0.816223545 0.909763362 0.106230273 0.081559423 0.533220105 4.569539632 0.030787967 0.031226282 783.9212537 -2.894272439 0.093539817 S(ph)PTESVNTPVGK ddPTM_MDA-MB-175_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(1)PTESVNTPVGK;S(0.999)PT(0.001)ESVNTPVGK 193.62 2.70E-06 316620000 416210 357860 318250 399530 370370 346430 400950 445240 817610 TRUE FALSE 361206.794 355509.1941 472156.7645 490249.3929 363000.3616 359757.3863 362065.9307 350028.8909 720953.0772 0.501012903 0.493110031 0.654906372 0.680001804 0.503500676 0.499002498 0.502204571 0.485508561 1 19.45954584 1.234452629 24.99999851 1.00000067 0.539682276 0.810711021 0.069867988 56.75223456 345329.3958 0.140382569 0.018717115 17.15744553 -1.234452629 -0.460318394 S(ph)PTFSEELPVLGDGQQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SPTFSEELPVLGDGQQLR 18 0 Q8N0Z3 Q8N0Z3 SPICE1 Spindle and centriole-associated protein 1 1 S(0.984)PT(0.016)FSEELPVLGDGQQLR;S(0.93)PT(0.07)FSEELPVLGDGQQLR;S(0.94)PT(0.06)FSEELPVLGDGQQLR;S(0.992)PT(0.008)FSEELPVLGDGQQLR;S(0.931)PT(0.069)FSEELPVLGDGQQLR 346.42 3.08E-90 670438000 214868 228383 139255 174175 233550 211237 217322 269657 207012 TRUE FALSE 186472.6494 226882.737 206599.1838 213724.0958 228902.8119 219363.4241 196246.1459 211992.949 182539.2772 1.021548087 1.24292558 1.131806737 1.170838951 1.253992102 1.201732731 1.075089969 1.161355256 1 17.4778474 0.334142139 1.191555292 3.60E-09 1.168433508 0.315720754 0.071221992 13.48178481 2.991892645 32.95422348 0.020506435 2.158450725 -0.334142139 1.168433505 S(ph)PTGPSNSFLANMGGTVAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 SPTGPSNSFLANMGGTVAHK 20 0 H0Y6J6;Q5W012;Q96I25 H0Y6J6 RBM17 Splicing factor 45 1 S(0.567)PT(0.432)GPSNSFLANMGGTVAHK;S(0.843)PT(0.157)GPSNSFLANMGGTVAHK;S(0.975)PT(0.025)GPSNSFLANMGGTVAHK;S(0.979)PT(0.021)GPSNSFLANMGGTVAHK;S(0.905)PT(0.095)GPSNSFLANMGGTVAHK;S(0.877)PT(0.123)GPSNSFLANMGGTVAHK;S(0.8)PT(0.2)GPSNSFLANMGGTVAHK;S(0.978)PT(0.021)GPSNSFLANMGGTVAHK;S(0.834)PT(0.166)GPSNSFLANMGGTVAHK;S(0.992)PT(0.008)GPSNSFLANMGGTVAHK;S(0.855)PT(0.145)GPSNSFLANMGGTVAHK;S(0.707)PT(0.293)GPSNSFLANMGGTVAHK;S(0.761)PT(0.239)GPSNSFLANMGGTVAHK 336.76 3.00E-80 37831960000 8559490 6898574 5073279 7065488 7327683 6102556 7686919 9275486 11446328 TRUE FALSE 7428331.71 6853256.813 7526733.693 8669815.04 7181876.445 6337325.278 6941442.779 7291995.501 10093156.14 0.735977092 0.679000376 0.745726469 0.858979581 0.711559035 0.627883408 0.68773758 0.722469305 1 23.26687404 1.238809355 9.348136044 1.00163738 0.720091342 0.686824691 0.059170487 0.048375271 68.33747514 0.087054423 0.015445843 17.33043064 -1.238809355 -0.281546038 S(ph)PTKTDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPTKTDPK 8 1 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 S(0.976)PT(0.019)KT(0.004)DPK;S(0.707)PT(0.291)KT(0.002)DPK;S(0.987)PT(0.012)KT(0.001)DPK;S(0.842)PT(0.152)KT(0.006)DPK 99.343 0.014505 1533260000 3600960 2139210 2448220 2637120 1287030 1429740 2969510 3677930 5619520 TRUE FALSE 3125084.012 2125157.389 3632187.381 3235918.402 1261420.621 1484743.023 2681527.377 2891433.291 4955186.747 0.630669271 0.428875337 0.733007163 0.653036619 0.254565708 0.299634121 0.541155665 0.583516513 1 22.240508 1.172456047 2.385975029 1.194987759 0.500784078 0.51324098 0.149919607 0.649638071 3.37093582 1.018467778 0.042131392 14.87496824 -1.172456047 -0.694203681 S(ph)PTMEQAVQTASAHLPAPAAVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 SPTMEQAVQTASAHLPAPAAVGR 23 0 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.963)PT(0.037)MEQAVQTASAHLPAPAAVGR;S(0.922)PT(0.078)MEQAVQTASAHLPAPAAVGR;S(0.864)PT(0.134)MEQAVQT(0.002)ASAHLPAPAAVGR;S(0.961)PT(0.039)MEQAVQTASAHLPAPAAVGR;S(0.969)PT(0.031)MEQAVQTASAHLPAPAAVGR;S(0.968)PT(0.032)MEQAVQTASAHLPAPAAVGR;S(0.829)PT(0.171)MEQAVQTASAHLPAPAAVGR;S(0.982)PT(0.018)MEQAVQTASAHLPAPAAVGR;S(0.966)PT(0.034)MEQAVQTASAHLPAPAAVGR;S(0.974)PT(0.026)MEQAVQTASAHLPAPAAVGR;S(0.942)PT(0.058)MEQAVQTASAHLPAPAAVGR;S(0.957)PT(0.043)MEQAVQTASAHLPAPAAVGR;S(0.933)PT(0.067)MEQAVQTASAHLPAPAAVGR;S(0.974)PT(0.026)MEQAVQTASAHLPAPAAVGR 256.73 8.87E-44 30318203000 2465792.1 2306727.5 1360331 2175129 2445014 2327648.3 2153938.6 2832972 4006846 TRUE FALSE 2139931.426 2291574.455 2018191.622 2669025.284 2396363.005 2417194.436 1945049.966 2227162.984 3533161.23 0.605670471 0.6485904 0.571214131 0.75542131 0.678248981 0.684144956 0.550512654 0.63035985 1 21.75252816 1.237625466 24.99629439 1.000000423 0.640044254 0.788457893 0.058517063 10.61113713 283477.6101 0.085257924 0.014455415 17.28325214 -1.237625466 -0.359956169 S(ph)PTPESSTIASYVTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPTPESSTIASYVTLR 16 0 Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;A0JP02;B4DJX4;Q9HAU0-5;Q9HAU0-8;H0YGJ6 Q9HAU0 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 S(0.984)PT(0.016)PESSTIASYVTLR 86.497 0.0071216 89416000 28391 29606 17325 26331 23307 29899 19595 29546 37654 TRUE FALSE 24639.05742 29411.51624 25703.42795 32309.85599 22843.2363 31049.23388 17694.67992 23227.81783 33202.58702 0.742082459 0.885820018 0.774139314 0.973112607 0.687995676 0.935145019 0.53293076 0.699578554 1 15.01900803 S(ph)PTPPPTLHLVPEPAAPPPPPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPTPPPTLHLVPEPAAPPPPPPR 23 0 A0A087WWH3;Q9NZM4-2;Q9NZM4 A0A087WWH3 GLTSCR1 Glioma tumor suppressor candidate region gene 1 protein 1 S(0.901)PT(0.096)PPPT(0.003)LHLVPEPAAPPPPPPR 58.294 0.048712 82673000 107970 82386 68719 70935 92737 82359 83008 95171 142360 TRUE FALSE 93701.49094 81844.80094 101951.7383 87041.87592 90891.71514 85527.40402 74957.89694 74819.42227 125530.363 0.746444834 0.651992068 0.812167955 0.693393008 0.724061597 0.681328421 0.597129612 0.596026495 1 16.93767684 2.746718388 21.38137765 0.688075889 0.724540651 0 0.119479676 471.5641379 1235955.81 0.038419732 0.0376203 558.1081799 -2.746718388 0.036464762 S(ph)PTQIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPTQIVK 7 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.98)PT(0.02)QIVK 79.974 0.032697 115950000 192390 173170 152950 212060 168340 157070 184270 210660 501950 TRUE FALSE 166965.174 172032.4349 226917.1316 260211.4641 164990.3634 163112.5845 166399.5238 165611.9984 442610.0428 0.377228616 0.388677206 0.512679582 0.587902304 0.372766877 0.368524364 0.375950628 0.374171353 1 18.75567666 1.23583103 24.99999384 1.000000774 0.419669853 0.860519309 0.073418173 28.85029027 264184.1415 0.131108172 0.019548169 17.2119878 -1.23583103 -0.580330921 S(ph)PTTTQSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPTTTQSPK 9 0 Q14669-3;Q14669;Q14669-2;Q14669-4 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 S(0.49)PT(0.402)T(0.088)T(0.02)QSPK;S(0.93)PT(0.051)T(0.015)T(0.004)QSPK;S(0.985)PT(0.012)T(0.002)TQSPK;S(0.995)PT(0.004)T(0.001)TQSPK 83.862 0.016421 173134000 290881 242545 187642 264198 226891 234349 303311 351980 527349 TRUE FALSE 252440.3389 240951.7059 278386.2988 324188.1939 222376.313 243364.5577 273895.9459 276711.8161 465006.402 0.542874975 0.518168578 0.59867197 0.697169313 0.478222046 0.523357435 0.58901543 0.595070982 1 18.82689105 1.226006544 4.043181048 1.053527632 0.565647817 0.841884203 0.05897837 0.100516423 2.868395164 0.147887095 0.015311757 16.82699415 -1.226006544 -0.487879815 S(ph)PTVEPSTLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPTVEPSTLPR 11 0 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 S(0.977)PT(0.023)VEPSTLPR;S(0.992)PT(0.007)VEPS(0.001)TLPR 115.65 0.0011487 894960000 365400 314310 200433 251930 305940 266556 276010 328310 326800 TRUE FALSE 317111.4642 312245.2769 297363.0692 309134.557 299852.3926 276810.5818 249242.5927 258103.4614 288166.0763 1.100446896 1.08356015 1.031915599 1.072765264 1.040554101 0.960593923 0.864926906 0.895676079 1 18.13654098 2.696320147 2.5941894 0.912656432 1.068933661 0.760191082 0.038430597 0.130188399 1.735952726 0.014641947 0.013117035 496.9585276 -2.696320147 0.15627723 S(ph)PTVLCQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPTVLCQK 8 0 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 S(0.986)PT(0.014)VLCQK 79.974 0.02461 0 100430 106310 67413 85684 98520 80049 99976 124670 156140 TRUE FALSE 87157.92104 105611.6426 100014.1523 105139.8618 96559.64475 83128.53683 90280.34291 98010.29068 137681.3071 0.633041063 0.767073213 0.726417801 0.763646598 0.701327194 0.603775041 0.655719682 0.711863453 1 17.07097317 1.239645768 5.557904423 1.014126176 0.695816306 0.770340112 0.052354739 0.073415266 7.215652254 0.089304804 0.013701526 17.36383971 -1.239645768 -0.31830987 S(ph)PVFTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPVFTPR 7 0 P52735-3 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 1 S(1)PVFTPR;S(1)PVFTPR;S(1)PVFTPR;S(1)PVFTPR 119.07 0.0051031 870160000 587450 620920 476540 627950 645620 688580 591810 763700 1194510 TRUE FALSE 509816.9941 616841.1356 706996.3379 770535.6451 632773.4251 715070.1182 534416.3573 600388.6981 1053296.389 0.484020452 0.585629214 0.671222598 0.73154684 0.600755335 0.678887848 0.507375097 0.570009263 1 20.00648002 1.235435337 24.98557413 1.000000545 0.605389306 0.72991513 0.075757415 48.83055681 390314.9462 0.133769103 0.019329107 17.19631283 -1.235435337 -0.394611238 S(ph)PVGKS(ph)PPSTGSTYGSSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPVGKSPPSTGSTYGSSQK 19 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 S(1)PVGKS(0.996)PPS(0.003)T(0.001)GSTYGSSQK 63.272 0.02258 327510000 143730 75765 127150 139380 94417 61562 118510 156930 452960 TRUE FALSE 124735.7163 75267.29473 188640.1653 171028.3593 92538.28642 63930.32998 107016.9184 123371.7407 399411.5848 0.312298694 0.188445447 0.472295177 0.428200798 0.231686536 0.160061281 0.267936441 0.308883732 1 18.60751665 1.238512367 7.046103914 1.014722542 0.294435119 0.840189539 0.096480565 0.043605224 12.72641369 0.150155472 0.025134266 17.31858345 -1.238512367 -0.720287424 S(ph)PVGKSPPS(ph)TGSTYGSSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPVGKSPPSTGSTYGSSQK 19 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 S(1)PVGKS(0.409)PPS(0.476)T(0.086)GS(0.024)T(0.005)YGSSQK;S(1)PVGKS(0.297)PPS(0.53)T(0.1)GS(0.033)T(0.039)YGS(0.001)SQK 122.79 1.85E-05 729810000 821810 502110 717010 835810 607180 400583 673220 911300 2740160 TRUE FALSE 713205.7263 498811.6063 1063758.434 1025593.435 595098.3059 415993.6872 607931.228 716425.5867 2416221.406 0.295173995 0.206442839 0.440257019 0.424461696 0.246292953 0.17216704 0.251604106 0.296506597 1 21.20432123 1.238669291 8.974935346 1.005112826 0.290608649 0.872937757 0.084938039 0.02906887 31.85086076 0.126624393 0.022296648 17.32484234 -1.238669291 -0.714504177 S(ph)PVGLDCCNCCLDLAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPVGLDCCNCCLDLAHR 17 0 D6RD37;D6RAX8;D6RBL1;D6RDZ9;D6RCK9;Q99576-3;D6R8Z7;D6RDZ7 D6RD37 TSC22D3 1 S(1)PVGLDCCNCCLDLAHR;S(1)PVGLDCCNCCLDLAHR 134.86 1.00E-05 304750000 137439 142326 111828 135465 156450 162251 159664 190198 196455 TRUE FALSE 119276.0879 141391.0511 165908.3948 166224.3987 153336.9511 168492.901 144179.8099 149525.6378 173230.3137 0.688540506 0.816202708 0.957733039 0.959557223 0.885162347 0.972652519 0.832301269 0.863160925 1 17.40233188 4.549571201 3.009578198 0.91521925 0.687815913 0.674969584 0.053186425 0.18108826 2.846682537 0.013930881 0.077588244 35446.32385 -4.549571201 -0.227403337 S(ph)PVGSGAPQAAAPAPAAHVAGNPGGDAAPAATGTAAAASLATAAGSEDAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPVGSGAPQAAAPAPAAHVAGNPGGDAAPAATGTAAAASLATAAGSEDAEK 51 0 P16989;P16989-3;P16989-2 P16989;P16989-2 YBX3 Y-box-binding protein 3 1 S(0.839)PVGS(0.161)GAPQAAAPAPAAHVAGNPGGDAAPAATGTAAAASLATAAGSEDAEK 231.02 1.76E-51 103980000 90158 60023 71949 87054 75023 61240 77862 95126 223800 TRUE FALSE 78243.39187 59628.70496 106743.7771 106820.9412 73530.18908 63595.94243 70310.95522 74784.04517 197342.619 0.396485018 0.302158273 0.54090585 0.541296866 0.372601668 0.322261571 0.356288751 0.37895537 1 17.59034303 1.237313407 24.99993312 1.00000072 0.40046717 0.844744082 0.080652644 12.60993701 252657.1715 0.126826989 0.021039328 17.27083785 -1.237313407 -0.59953355 S(ph)PVIGSEVFLPNSNHVASGAGEAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SPVIGSEVFLPNSNHVASGAGEAEER 26 0 P29590-2;P29590-5;P29590-9;P29590-3;P29590-8;P29590;H3BVD2;P29590-12;P29590-13;P29590-11 P29590-2;P29590-12 PML Protein PML 1 S(1)PVIGSEVFLPNSNHVASGAGEAEER;S(1)PVIGSEVFLPNSNHVASGAGEAEER;S(1)PVIGSEVFLPNSNHVASGAGEAEER;S(1)PVIGSEVFLPNSNHVASGAGEAEER;S(1)PVIGSEVFLPNSNHVASGAGEAEER;S(1)PVIGSEVFLPNSNHVASGAGEAEER 292.91 1.76E-70 4213290000 467224 356026 235829 347877 448387 409605 437434 477560 694474 TRUE FALSE 405479.1646 353687.2418 349876.6932 426867.7898 439464.976 425362.7694 395011.718 375437.5104 612374.0749 0.662142931 0.577567301 0.571344718 0.697070316 0.71764138 0.694612634 0.645049708 0.613085246 1 19.22405368 1.235290327 24.99969219 1.000000489 0.646280657 0.835927028 0.049102982 39.44267356 301468.0088 0.092144688 0.013183806 17.19057196 -1.235290327 -0.353719831 S(ph)PVLEEAPFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPVLEEAPFSR 11 0 K7EL81;Q9BZL4-3 K7EL81 PPP1R12C Protein phosphatase 1 regulatory subunit 12C 1 S(1)PVLEEAPFSR;S(1)PVLEEAPFSR 101.3 0.0035524 460000000 150515 171603 142923 195259 211881 197353 197851 249160 309360 TRUE FALSE 130624.0614 170475.7286 212041.0408 239595.5403 207664.9826 204945.2976 178663.4405 195879.073 272787.8132 0.478848596 0.624938946 0.777311267 0.87832201 0.761269282 0.751299316 0.654953894 0.71806387 1 18.05741967 4.480493641 2.548964949 0.778668035 0.477837337 0.552743623 0.094007735 0.265722305 3.040774378 0.025067907 0.133915722 30233.86301 -4.480493641 -0.300830698 S(ph)PVPAQIAITVPK ddPTM_MDA-MB-175_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 183.41 1.06E-06 841370000 850795 686640 434804 547995 634414 553164 751503 914888 826038 TRUE FALSE 738360.2851 682129.4166 645076.6687 672425.6403 621790.4026 574444.577 678622.3547 719246.3209 728384.7287 1.01369545 0.936496044 0.885626295 0.923173721 0.853656561 0.788655438 0.931681195 0.987453872 1 19.47434115 1.811547234 3.741026874 0.994176017 0.89782137 0.2988114 0.057745625 0.278116233 6.867982863 0.037872403 0.016545631 64.7958563 -1.811547234 -0.096354648 S(ph)PVPSAFSDQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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;S(1)PVPSAFSDQSR;S(1)PVPSAFSDQSR;S(1)PVPSAFSDQSR;S(0.999)PVPS(0.001)AFSDQSR 171.99 3.88E-05 23272710000 2677046 2108044 1594106 2152261 1965566 1967741 1913410 2361429 3785700 TRUE FALSE 2323267.588 2094196.12 2365020.994 2640964.755 1926455.082 2043441.27 1727847.793 1856455.785 3338158.859 0.695972746 0.627350647 0.708480661 0.791144121 0.57710108 0.612146203 0.517605023 0.556131647 1 21.67062118 3.217106296 24.99451457 0.628391752 0.700334064 0.018412963 0.138299606 763.143063 889067.3289 0.041751829 0.047385297 1648.565837 -3.217106296 0.071942312 S(ph)PVQLEEAPFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPVQLEEAPFSR 12 0 Q9BZL4-5;Q9BZL4-2;Q9BZL4-4;Q9BZL4 Q9BZL4-5 PPP1R12C Protein phosphatase 1 regulatory subunit 12C 1 S(1)PVQLEEAPFSR;S(1)PVQLEEAPFSR;S(1)PVQLEEAPFSR 151.07 7.20E-05 369010000 127966 172198 133170 182739 175449 178421 205276 224210 243105 TRUE FALSE 111054.9689 171066.82 197571.4574 224232.6829 171957.9082 185284.9713 185368.3651 176264.4363 214365.4038 0.518063861 0.798015057 0.921657384 1.046030185 0.802171923 0.864341764 0.86473079 0.822261583 1 17.70971256 4.697248799 2.736488904 0.893207283 0.464980075 0.720330607 0.075287606 0.217485689 2.345071271 0.019380679 0.200863036 49802.23108 -4.697248799 -0.428227208 S(ph)PVREPIDNLTPEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPVREPIDNLTPEER 15 1 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23;H0Y4X3;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 1 S(1)PVREPIDNLTPEER;S(1)PVREPIDNLTPEER 177.09 4.65E-07 440190000 131255 106563 79879 93234 97762 124293 88939 115365 180094 TRUE FALSE 113909.3192 105862.9806 118508.7516 114404.2047 95816.72747 129074.6321 80313.70947 90695.09252 158803.4925 0.717297318 0.666628794 0.746260361 0.720413657 0.603366626 0.812794669 0.505742715 0.571115226 1 17.27688312 S(ph)PVSPLAAQGIPLPAQLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPVSPLAAQGIPLPAQLTK 19 0 K7EIF1;K7EPF0;K7EQS3;K7EM48;K7EN63;Q96SI1-2;Q96SI1 K7EIF1 KCTD15 BTB/POZ domain-containing protein KCTD15 1 S(0.918)PVS(0.082)PLAAQGIPLPAQLTK;S(0.881)PVS(0.119)PLAAQGIPLPAQLTK 325.35 1.19E-62 1013700000 1195080 839410 632420 754410 815710 734220 889100 1105530 1084570 TRUE FALSE 1037147.15 833895.8604 938260.4273 925710.3209 799478.9669 762465.9185 802875.2188 869121.0127 956353.3701 1.084481095 0.871953701 0.981081321 0.967958445 0.835966068 0.797263796 0.839517321 0.90878648 1 19.86718426 3.253927033 24.47046125 0.873655355 0.969247101 0.312147623 0.073413074 247.7241718 394488.7827 0.021348638 0.02745038 1794.432116 -3.253927033 0.095591746 S(ph)PVSTRPLPSASQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SPVSTRPLPSASQK 14 1 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.945)PVS(0.053)T(0.002)RPLPSASQK;S(0.919)PVS(0.078)T(0.003)RPLPSASQK;S(0.976)PVS(0.023)T(0.001)RPLPSASQK;S(0.992)PVS(0.004)T(0.004)RPLPSASQK;S(0.983)PVS(0.01)T(0.007)RPLPSASQK;S(0.997)PVST(0.003)RPLPSASQK;S(0.96)PVS(0.019)T(0.009)RPLPS(0.012)ASQK;S(1)PVSTRPLPSASQK 194.77 2.77E-07 67865480000 17015730 14235690 9877496 12230212 13926211 11597655 17022500 18299010 16289637 TRUE FALSE 14767058.17 14142174.82 14654286.1 15007268.56 13649106.65 12043824.29 15371660.57 14385909.11 14363894.67 1.02806784 0.984564085 1.020216761 1.044791048 0.950237172 0.838479018 1.070159655 1.001532624 1 23.77594364 4.744840518 21.56558283 0.990398004 1.028067952 0.037050201 0.06249637 474.4743849 1629027.931 0.015525448 0.130082484 55570.01549 -4.744840518 0.037669948 S(ph)PVTTLLECMHK ddPTM_MDA-MB-175_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 138.19 5.08E-05 128080000 158370 316800 117510 131020 156330 122020 175190 252550 294860 TRUE FALSE 137441.0032 314718.9199 174338.229 160770.0935 153219.3389 126714.1884 158200.1008 198544.1478 260001.9867 0.528615204 1.210448135 0.670526527 0.618341789 0.589300646 0.487358539 0.608457277 0.763625503 1 17.98816312 4.079042571 24.99999999 0.668751218 0.887273501 0.124919584 0.210078538 55.11654414 17429.01948 0.051654248 0.107526904 11996.16888 -4.079042571 0.218522283 S(ph)PVVELSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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;S(1)PVVELSK;S(1)PVVELSK 123.79 0.0013977 3368320000 3237553 2966075 2985689 3744730 3245090 2772513 3773410 4492420 9208720 TRUE FALSE 2809702.168 2946590.658 4429578.187 4595028.181 3180519.058 2879173.369 3407465.279 3531750.943 8120075.612 0.346019212 0.362877244 0.545509475 0.565884901 0.391685892 0.354574699 0.419634674 0.434940647 1 22.95306173 1.238546881 8.556267469 1.005187375 0.429829712 0.851898483 0.074997682 0.03389997 27.96138569 0.112948909 0.019713638 17.31995986 -1.238546881 -0.575357664 S(ph)PYKFPSS(ph)PLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPYKFPSSPLR 11 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 2 S(1)PYKFPS(0.03)S(0.97)PLR;S(0.999)PY(0.001)KFPS(0.43)S(0.57)PLR 135.02 0.001538 426158000 1004820 923430 697580 856750 1044030 811710 1010330 1265440 1325200 TRUE FALSE 872030.4911 917363.9275 1034932.021 1051288.182 1023255.846 842937.0089 912348.3521 994835.5037 1168536.366 0.746258753 0.785053811 0.885665223 0.899662358 0.875673086 0.721361383 0.780761625 0.85135177 1 20.1562712 1.256106207 3.43110781 1.023499193 0.817334829 0.49125853 0.059207221 0.280739899 4.790735153 0.148933205 0.016407689 18.03458724 -1.256106207 -0.206164364 S(ph)PYNGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPYNGVR 7 0 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 1 S(0.99)PY(0.01)NGVR 80.787 0.030383 202240000 127550 103230 83971 91597 126390 115970 127590 129970 203310 TRUE FALSE 110693.9443 102551.8753 124579.6565 112395.4988 123875.0863 120431.4409 115216.3414 102176.9269 179274.9234 0.617453586 0.572036922 0.694908435 0.626944899 0.690978325 0.671769585 0.64267963 0.56994545 1 17.45181418 1.232244267 24.99999089 1.000000604 0.63549144 0.875919584 0.043073766 73.2413211 289859.5613 0.100132703 0.01096148 17.07042239 -1.232244267 -0.364509164 S(ph)PYQEFTDHLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPYQEFTDHLVK 12 0 P15880;H0YEN5;E9PQD7 P15880 RPS2 40S ribosomal protein S2 1 S(1)PYQEFTDHLVK;S(1)PYQEFTDHLVK;S(1)PYQEFTDHLVK;S(0.999)PY(0.001)QEFTDHLVK 173.28 2.16E-05 541058000 476349 399115 378744 447632 446110 361717 464796 544200 870330 TRUE FALSE 413398.2727 396493.1873 561905.8652 549273.6872 437233.2838 375632.4871 419720.1555 427827.065 767440.5789 0.538671376 0.516643501 0.732181593 0.715721454 0.56972917 0.489461331 0.546908995 0.557472561 1 19.54969552 1.236362009 24.99519009 1.000000537 0.583771209 0.729841998 0.079665013 33.95320739 385908.0344 0.136503506 0.021172037 17.23304449 -1.236362009 -0.416229328 S(ph)PYSGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPYSGPK 7 0 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23 Q14498-2 RBM39 RNA-binding protein 39 1 S(0.999)PY(0.001)SGPK;S(0.816)PY(0.022)S(0.162)GPK 86.744 0.020824 913640000 1706110 1318700 1050190 1118580 1024040 1096850 1395820 1629410 2244630 TRUE FALSE 1480643.241 1310037.373 1558065.397 1372570.685 1003663.608 1139046.529 1260453.591 1280973.352 1979272.398 0.748074516 0.661878261 0.787190989 0.693472352 0.507087154 0.575487502 0.636826741 0.647194066 1 20.91653875 1.237892953 24.96782147 1.000000403 0.653836923 0.649621105 0.079097174 10.91732243 407946.4342 0.119707917 0.020637032 17.2939004 -1.237892953 -0.34616348 S(ph)QAELETLVLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQAELETLVLSR 12 0 Q00G26 Q00G26 PLIN5 Perilipin-5 1 S(1)QAELETLVLSR 188.44 9.65E-06 23727000 7800.8 6080.7 5972.9 6614.2 6055.2 6871.5 7760.1 9272.7 13107 TRUE FALSE 6769.904515 6040.755481 8861.414418 8116.055202 5934.713367 7135.851051 7007.526696 7289.805265 11557.50539 0.585758283 0.522669493 0.766723797 0.702232439 0.51349432 0.617421391 0.606318272 0.630742104 1 13.49654242 1.238051658 6.051073872 1.013861643 0.618176855 0.720214226 0.074837019 0.073483093 10.44316569 0.120158023 0.018872693 17.30022128 -1.238051658 -0.395684788 S(ph)QDDAMVDYFFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SQDDAMVDYFFQR 13 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4;E9PR38;E9PMX1;E9PM68;E9PL65 Q5T1Z4 PUM1 Pumilio homolog 1 1 S(1)QDDAMVDYFFQR;S(1)QDDAMVDYFFQR;S(1)QDDAMVDYFFQR 110.38 0.0011148 65947000 69875 65057 56694 58248 102549 100009 103602 102151 108334 TRUE FALSE 60640.84171 64629.63628 84111.40803 71474.09866 100508.4755 103856.4109 93554.69399 80306.80359 95526.87793 0.634803974 0.676559704 0.880499916 0.748209302 1.052148649 1.0871957 0.97935467 0.840672336 1 16.54361909 4.063936912 1.080209305 0.967961564 0.604795622 0.656033173 0.091113199 0.495219013 0.935897331 0.033699523 0.161209964 11586.09038 -4.063936912 -0.363165942 S(ph)QDVELWEGEVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SQDVELWEGEVVK 13 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 S(1)QDVELWEGEVVK;S(1)QDVELWEGEVVK;S(1)QDVELWEGEVVK 269.91 2.17E-25 271240000 571677 292583 208781 282254 294202 231236 438031 417216 440000 TRUE FALSE 496128.436 290661.003 309748.1899 346344.0847 288347.9558 240131.7985 395550.821 327997.6052 387983.7012 1.278735252 0.749157766 0.798353614 0.892676892 0.743196054 0.618922387 1.019503705 0.845390165 1 18.56563652 4.745380351 24.70332733 0.8342963 1.278735494 0.578354524 0.119497331 506.8974417 1836093.333 0.029008683 0.276318136 55639.13267 -4.745380351 0.444439193 S(ph)QEADVQDWEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 229.68 8.00E-12 3820812000 4592060 2842525 1830475 2412861 2759771 2278927 3663050 3298746 3056102 TRUE FALSE 3985207.636 2823852.266 2715698.833 2960737.968 2704856.957 2366598.796 3307807.975 2593334.839 2694813.103 1.478843795 1.047884272 1.007750344 1.098680263 1.003727106 0.878205169 1.227472128 0.962343116 1 21.36175379 4.738414724 5.146328077 1.027189341 1.499187984 0.711638759 0.090244139 0.083539028 7.403451331 0.020806626 0.140242339 54753.85784 -4.738414724 0.471998643 S(ph)QEDLNEPIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQEDLNEPIKR 11 1 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 S(1)QEDLNEPIKR;S(1)QEDLNEPIKR 101.01 0.0022072 641950000 820960 591420 470860 520970 587690 521130 798690 822950 812720 TRUE FALSE 712468.056 587534.9231 698569.4709 639264.201 575996.1188 541178.2083 721233.1667 646968.5467 716641.1675 0.994176847 0.819845342 0.974782782 0.892028298 0.803744112 0.755159252 1.006407669 0.90277893 1 19.4508914 2.198501276 24.9995075 0.957309212 0.873163634 0.251018263 0.077545882 245.8664122 153434.1581 0.031568446 0.02128373 157.9433248 -2.198501276 -0.084145578 S(ph)QEELREDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SQEELREDK 9 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 S(1)QEELREDK;S(1)QEELREDK;S(1)QEELREDK;S(1)QEELREDK;S(1)QEELREDK;S(1)QEELREDK 162.48 3.86E-05 4284820000 5174710 4116770 3385530 3487580 3792080 3083040 4695980 5655610 5005430 TRUE FALSE 4490858.962 4089726.667 5022783.632 4279488.343 3716625.027 3201646.544 4240564.582 4446201.814 4413693.768 1.017483133 0.926599552 1.138000028 0.969593399 0.842066809 0.725389371 0.960774536 1.00736527 1 22.0735551 3.47647902 24.99865633 0.913791468 1.023370095 0.24941796 0.09520409 36.60222018 1424672.978 0.030023107 0.039117467 2995.566878 -3.47647902 0.109578627 S(ph)QEEPKDTFEHDPSESIDEFNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQEEPKDTFEHDPSESIDEFNK 22 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 S(0.999)QEEPKDT(0.001)FEHDPSESIDEFNK 159.66 1.17E-11 149120000 296540 170940 179980 164830 177510 149220 267890 289780 275550 TRUE FALSE 257351.4877 169817.0839 267018.93 202257.1708 173977.8983 154960.59 241910.069 227812.8021 242974.7929 1.059169491 0.698908236 1.098957331 0.832420385 0.716032705 0.637764058 0.995617966 0.937598503 1 17.89044713 S(ph)QESDGVEYIFISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQESDGVEYIFISK 14 0 S4R337;Q5T2T1-2;Q5T2T1;U5GXS2 S4R337 MPP7 MAGUK p55 subfamily member 7 1 S(1)QESDGVEYIFISK;S(1)QESDGVEYIFISK;S(1)QESDGVEYIFISK;S(0.999)QES(0.001)DGVEYIFISK 295.82 1.34E-43 415131000 693141 603492 413222 546111 635859 508644 765724 890910 734069 TRUE FALSE 601540.6607 599527.6213 613057.5413 670113.8493 623206.6499 528211.8638 691464.2043 700395.8296 647288.1991 0.929324313 0.926214354 0.947116821 1.035263504 0.962796249 0.816038149 1.068247815 1.082046344 1 19.30404868 2.148791315 24.9999744 1.057513168 0.941859783 0.465206473 0.057201958 17.20647411 4787.113794 0.023650357 0.015945071 140.8611778 -2.148791315 -0.115653385 S(ph)QESGYYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQESGYYDR 9 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 S(0.998)QES(0.002)GYYDR;S(0.985)QES(0.013)GY(0.002)YDR 116.03 0.0014482 445920000 291663 304342 155836 213722 300210 345879 298755 302574 220076 TRUE FALSE 253118.9956 302342.7574 231198.8108 262250.8466 294236.4084 359185.1889 269781.7861 237870.9047 194058.866 1.30434131 1.557995074 1.191384942 1.351398429 1.516222445 1.85090842 1.390205929 1.225766746 1 17.56613482 1.531861947 2.46574085 1.008350946 1.460476519 0.422340907 0.175941901 0.309767017 3.64239663 0.250771723 0.050061546 34.02999983 -1.531861947 0.452125573 S(ph)QFFEQGSSDSVVPDLPVPTISAPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQFFEQGSSDSVVPDLPVPTISAPSR 26 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.999)QFFEQGSSDSVVPDLPVPTISAPSR;S(0.994)QFFEQGS(0.006)SDSVVPDLPVPTISAPSR;S(1)QFFEQGSSDSVVPDLPVPTISAPSR;S(0.992)QFFEQGS(0.003)S(0.004)DS(0.001)VVPDLPVPTISAPSR 131.94 3.83E-05 298115000 75878 92537 68345 95821 116124 117404 112260 111392 183780 TRUE FALSE 65850.53005 91929.11835 101396.8706 117578.6226 113813.3596 121920.6079 101373.0425 87571.68765 162053.7378 0.406349961 0.56727552 0.625699055 0.72555329 0.702318633 0.75234678 0.625552017 0.540386719 1 17.30611277 4.671291742 1.264168018 0.699290689 0.300498558 0.425766557 0.118428441 1.363699695 2.075563592 0.034817876 0.686683119 46912.8418 -4.671291742 -0.398792131 AS(ph)SLNENVDHSALLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ASSLNENVDHSALLK 15 0 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 1 AS(0.557)S(0.443)LNENVDHSALLK;AS(0.563)S(0.437)LNENVDHSALLK 168.27 8.14E-07 313950000 378710 165251 55719 114778 123679 93987 178479 174625 171245 TRUE FALSE 328662.514 164165.4553 82664.89477 140840.0992 121218.0299 97602.74071 161170.1341 137282.8027 151000.6112 2.17656413 1.087184045 0.547447418 0.932712113 0.802765161 0.64637315 1.067347561 0.909153954 1 17.20419486 4.715110369 3.534725242 0.854002429 2.301808537 0.875470196 0.156706906 0.083393118 1.864407828 0.038331683 0.310239634 51893.19 -4.715110369 1.447806108 up S(ph)QGLSGDK ddPTM_MDA-MB-175_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 132.5 0.0010065 894951000 1578100 1824180 1229257 1369930 942669 1347740 1495090 1686220 2646530 TRUE FALSE 1369550.087 1812196.841 1823729.797 1680993.545 923911.7312 1399588.43 1350096.402 1325634.975 2333660.238 0.586867816 0.776546993 0.781488996 0.720324886 0.395906703 0.599739588 0.57853169 0.56804969 1 21.1541631 -0.32768811 10.5355589 1.032817264 0.65512061 0 0.164070204 0 0 0 0.036539524 0.470231686 0.32768811 -0.377696654 S(ph)QHSSGNGNDFEMITK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQHSSGNGNDFEMITK 16 0 Q99442 Q99442 SEC62 Translocation protein SEC62 1 S(0.444)QHS(0.235)S(0.321)GNGNDFEMITK 71.853 0.025432 150610000 133530 136160 67135 147150 193490 172920 126590 225410 202210 TRUE FALSE 115883.6722 135265.556 99601.71055 180562.6565 189639.9276 179572.3443 114313.3213 177207.8256 178304.9642 0.649918373 0.758619126 0.558603127 1.012661972 1.063570655 1.007107935 0.641111266 0.993846843 1 17.44398734 3.733614297 24.99610967 0.94466078 0.666004097 0.555912501 0.125014961 330.7687443 1671532.797 0.035175898 0.054079749 5415.197458 -3.733614297 -0.278656683 S(ph)QPWDLTPMLSSSEPWGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQPWDLTPMLSSSEPWGR 18 0 Q9H201 Q9H201 EPN3 Epsin-3 1 S(1)QPWDLTPMLSSSEPWGR;S(1)QPWDLTPMLSSSEPWGR;S(0.999)QPWDLTPMLS(0.001)SSEPWGR;S(0.998)QPWDLT(0.002)PMLSSSEPWGR 264.66 5.82E-31 380757000 203923 198194 187669 242929 337436 367898 354602 399860 404752 TRUE FALSE 176974.0589 196892.0506 278426.3561 298089.7424 330721.6838 382051.2741 320212.7526 314353.0507 356902.6797 0.49586083 0.551668737 0.780118424 0.835212957 0.92664388 1.070463451 0.897199071 0.880780864 1 18.44517121 4.119405033 1.234412484 0.945791757 0.450092431 0.896626134 0.058177655 0.192836118 0.486724862 0.019677548 0.093546826 13164.52013 -4.119405033 -0.495699325 S(ph)QS(ph)T(ph)PHQEKVITESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQSTPHQEKVITESK 15 1 Q9ULI3-2;Q9ULI3 Q9ULI3-2 HEG1 Protein HEG homolog 1 3 S(0.999)QS(0.999)T(0.999)PHQEKVIT(0.002)ESK 89.468 0.0053469 125620000 197340 107940 109960 116540 155710 141230 163750 184930 156090 TRUE FALSE 171261.019 107230.935 163137.0238 143002.1882 152611.6756 146663.2095 147869.5502 145384.1586 137637.218 1.244292942 0.77908386 1.185268245 1.038979066 1.108796573 1.065578131 1.074342771 1.056285216 1 17.07051111 5.055868681 22.63628081 1.047036094 4.872498094 0.27400539 0.10444201 1465.850619 610578.354 0.022321219 7776.529465 113728.3349 -5.055868681 3.825462 S(ph)QSDRTEYNQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQSDRTEYNQK 11 1 Q9NXL2-1;Q9NXL2 Q9NXL2-1 ARHGEF38 Rho guanine nucleotide exchange factor 38 1 S(0.5)QS(0.5)DRTEYNQK 52.928 0.085533 97125000 43870 41198 31275 32404 38800 34737 45997 45793 44526 TRUE FALSE 38072.46835 40927.36763 46399.69461 39761.82346 38027.95591 36073.35487 41536.21802 36000.52331 39262.187 0.969698105 1.042411815 1.181790882 1.01272564 0.968564382 0.918781087 1.057919112 0.916926082 1 15.26085292 3.483318508 20.27065232 0.971174231 1.068219231 0.299015833 0.064395711 26.58542775 86958.89314 0.017917833 0.024119398 3043.116006 -3.483318508 0.097045 S(ph)QSFTHSPSGDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQSFTHSPSGDPK 13 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 S(0.499)QS(0.499)FT(0.002)HSPSGDPK;S(0.623)QS(0.375)FT(0.002)HSPSGDPK 157.42 3.07E-05 1626210000 1699870 1757320 1289590 1925300 2583500 2258800 3100900 3345800 3296600 TRUE FALSE 1475227.873 1745776.049 1913240.037 2362468.791 2532093.405 2345697.498 2800175.195 2630326.707 2906879.703 0.507495329 0.600567009 0.658176544 0.812716394 0.871069209 0.806946877 0.963292424 0.904862593 1 21.47103994 5.005922041 0.353165447 0.995700655 4.33E-09 0.93293852 0.041194536 2.35988819 0.240264731 0.071344652 1.056127228 101372.9398 -5.005922041 -0.99570065 S(ph)QSS(ph)HSYDDSTLPLIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQSSHSYDDSTLPLIDR 17 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;H0YC95 O60716-13 CTNND1 Catenin delta-1 2 S(0.711)QS(0.3)S(0.617)HS(0.314)Y(0.058)DDSTLPLIDR 81.477 0.0048666 107010000 69920 56137 39074 60349 61029 71986 62668 71914 72688 TRUE FALSE 60679.89485 55768.23235 57970.31709 74052.16283 59814.6423 74755.348 56590.46701 56535.75074 64094.90745 0.946719439 0.870088351 0.904444977 1.15535174 0.933219887 1.166322739 0.882916744 0.882063068 1 15.96792211 6.813096421 8.109681285 0.966176148 0.417970564 0 0.108272052 0 0 0.024422709 0 6502740.473 -6.813096421 -0.548205585 S(ph)RADLTAEMISAPLGDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 SRADLTAEMISAPLGDFR 18 1 Q9H3Q1;Q9H3Q1-2;J3KRZ9;J3QQS6;J3QR93 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 S(0.83)RADLT(0.17)AEMISAPLGDFR;S(0.848)RADLT(0.152)AEMISAPLGDFR;S(0.995)RADLT(0.005)AEMISAPLGDFR;S(0.999)RADLT(0.001)AEMISAPLGDFR;S(0.985)RADLT(0.015)AEMISAPLGDFR;S(0.999)RADLT(0.001)AEMISAPLGDFR;S(0.5)RADLT(0.5)AEMISAPLGDFR;S(0.929)RADLT(0.071)AEMISAPLGDFR;S(0.904)RADLT(0.096)AEMISAPLGDFR 256.89 7.98E-31 1661947000 1084611 1198194 668323 611479 1145082 1325682 1218996 1344754 1299095 TRUE FALSE 941276.9083 1190322.985 991526.2382 750324.6528 1122297.109 1376681.844 1100777.956 1057188.822 1145517.469 0.821704543 1.039113778 0.865570596 0.65500935 0.97972937 1.201799083 0.96094384 0.922891925 1 20.12756803 3.024341466 24.99991875 1.010393327 0.85522608 0.340679835 0.116417858 307.1763186 315483.372 0.036966209 0.04191413 1057.648765 -3.024341466 -0.155167247 S(ph)RAS(ph)PATHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRASPATHR 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)RAS(0.978)PAT(0.022)HR 60.157 0.055516 102650000 14739 14335 5644.2 7420.8 6842 12081 9686.1 12902 12598 TRUE FALSE 12791.20381 14240.83244 8373.753999 9105.80606 6705.857586 12545.76389 8746.743513 10143.0077 11108.67879 1.151460407 1.281955551 0.753802874 0.819701985 0.603659329 1.129365978 0.78737928 0.913070572 1 13.43939962 4.242400253 24.99999923 0.858479016 1.216708082 0.516324504 0.14428051 72.74416369 473620.7925 0.035057596 0.085730202 17474.31875 -4.242400253 0.358229066 S(ph)RAS(ph)PVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SRASPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)RAS(0.999)PVS(0.001)R;S(1)RAS(0.998)PVS(0.002)R;S(1)RAS(0.999)PVS(0.001)R;S(1)RAS(1)PVSR 92.856 0.0065329 1985220000 174275 171487 79118.2 96403.1 120066 148466.6 154893 178713 154443 TRUE FALSE 151244.1172 170360.4906 117380.0262 118292.8973 117676.9215 154178.2062 139871.5007 140496.6157 136184.9245 1.110579 1.250949701 0.861916446 0.868619619 0.864096536 1.132123888 1.027070369 1.031660562 1 17.05520748 4.246227439 24.99996358 0.976466399 1.180764378 0.471209814 0.092869021 165.0510759 538185.5246 0.024976611 0.063454564 17628.99029 -4.246227439 0.204297979 S(ph)RASPVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRASPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.848)RAS(0.151)PVSR 64.439 0.040564 148110000 92025 73590 48436 64636 58148 71704 71226 84212 69859 TRUE FALSE 79863.66309 73106.58244 71859.81161 79312.5917 56990.96856 74462.49928 64318.51348 66203.91914 61600.3486 1.2964807 1.186788453 1.166548782 1.287534787 0.925172825 1.208799966 1.044125804 1.074732865 1 15.91065089 7.999999929 0.16115656 0.942023796 2.266324432 0.429723359 0.091642425 130.6660694 1.724545954 1.133684639 40.03959856 99999983.73 -7.999999929 1.324300636 S(ph)RDDLYDQDDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRDDLYDQDDSR 12 1 S4R3V8;Q86X29-6;Q86X29-5;Q86X29-2;Q86X29-3;Q86X29-4;Q86X29 S4R3V8 LSR Lipolysis-stimulated lipoprotein receptor 1 S(1)RDDLYDQDDSR 136.26 6.85E-05 227890000 318180 331820 228260 333070 294650 339620 345670 390180 614870 TRUE FALSE 276131.7068 329640.2526 338647.2995 408698.6342 288787.0415 352685.4012 312146.9766 306743.0434 542180.7691 0.509298231 0.60798957 0.624602197 0.75380511 0.532639772 0.650494118 0.575724914 0.565757882 1 19.04841442 1.235150181 24.99978465 1.000000551 0.604459058 0.772358738 0.067805877 45.54642403 333818.0291 0.114716427 0.016183825 17.18502551 -1.235150181 -0.395541493 S(ph)RDDLYDQDDSRDFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRDDLYDQDDSRDFPR 16 2 S4R3V8;Q86X29-6;Q86X29-5;Q86X29-2;Q86X29-3;Q86X29-4;Q86X29 S4R3V8 LSR Lipolysis-stimulated lipoprotein receptor 1 S(1)RDDLYDQDDSRDFPR 178.84 2.14E-09 748070000 316610 253140 136500 266810 328320 290500 174400 358310 195920 TRUE FALSE 274769.1863 251477.1067 202511.8566 327393.2884 321787.0743 301675.723 157486.7148 281688.1949 172758.5608 1.590480871 1.455656412 1.172224726 1.895091548 1.862640398 1.746227345 0.911600063 1.630531035 1 17.39839768 2.26417805 24.99984905 1.263209703 1.616026255 0.341219183 0.280240629 304.8387887 297488.815 0.10671011 0.082627507 183.7291435 -2.26417805 0.352816552 S(ph)RDKEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRDKEER 7 2 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 1 S(1)RDKEER;S(1)RDKEER 84.479 0.016944 5624800000 11344000 7202000 5263200 6123000 4312900 5046200 8903100 10209500 10518900 TRUE FALSE 9844861.658 7154689.588 7808501.124 7513320.734 4227081.728 5240330.579 8039678.732 8026277.875 9275367.625 1.06139854 0.77136453 0.841853546 0.810029428 0.455731988 0.564972817 0.866777367 0.865332588 1 23.14497303 5.499513961 1.480452307 0.76524511 2.698231364 0.248942438 0.156456863 16.19376702 6.071531413 0.04702571 79.51887985 315874.059 -5.499513961 1.932986254 S(ph)RDREQDRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRDREQDRK 9 3 O95232;J3KPP4;H0YA81;H0YBV7;H0YAR4;H0YAX1;H0YAY6 O95232 LUC7L3 Luc7-like protein 3 1 S(1)RDREQDRK 108.17 0.014671 271490000 161340 90003 42663 59833 60284 72951 113990 136110 16705 TRUE FALSE 140018.5102 89411.76437 63294.9695 73418.99714 59084.46634 75757.47218 102935.2673 107003.9357 14730.15393 9.505570062 6.069981671 4.296965924 4.984265439 4.011123483 5.143019722 6.988064608 7.264278175 1 13.84648489 4.704951396 3.205192656 5.136794464 9.976920556 0.41000895 1.736479276 0.332459087 5.55037307 0.441267054 3.836107472 50693.39714 -4.704951396 4.840126092 S(ph)RDRHDDYYR ddPTM_MDA-MB-175_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 156.2 5.93E-06 1572450000 192733 177846 50737 68408 123376 152525 142678 158757 36740 TRUE FALSE 167262.8457 176677.7179 75273.58291 83941.08195 120921.059 158392.7354 128841.1095 124808.051 32396.63905 5.16296908 5.453581701 2.323499755 2.591042911 3.732518635 4.889171842 3.976989999 3.85249997 1 14.98355653 4.255524418 24.99861003 3.353808492 5.30827699 0.395125802 1.073095385 271.4585817 400026.4783 0.274531379 0.722252683 18010.44394 -4.255524418 1.954468499 S(ph)RECDITK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRECDITK 8 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 S(1)RECDITK;S(1)RECDITK;S(1)RECDITK 127.78 0.00070363 1230800000 1768880 1237470 907100 943140 1105910 940140 1558270 1760730 1387940 TRUE FALSE 1535118.026 1229340.978 1345776.594 1157294.352 1083904.555 976307.7942 1407149.215 1384211.592 1223859.314 1.254325565 1.004478998 1.099617071 0.945610609 0.885644732 0.797728777 1.149763865 1.131021822 1 20.2230063 5.765200818 1.421545947 1.005298929 4.316630471 0.341314644 0.109282039 28.71033841 5.127521591 0.033957206 261.3950418 582372.4451 -5.765200818 3.311331542 S(ph)REDLSALTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SREDLSALTR 10 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 S(1)REDLSALTR;S(1)REDLSALTR;S(1)REDLSALTR 168.93 2.90E-06 4309750000 499340 447830 312883 354557 449700 446020 441840 493190 456898 TRUE FALSE 433350.9538 444888.1752 464194.2653 435064.5859 440751.8498 463178.678 398990.4248 387725.1565 402884.0389 1.075622045 1.104258626 1.152178345 1.079875458 1.093991837 1.149657552 0.990335646 0.96237408 1 18.62000513 2.187131272 7.851169732 0.979115329 1.108879512 0.826538246 0.026975181 0.087170201 11.49838102 0.010777062 0.007284744 153.861964 -2.187131272 0.129764183 S(ph)REDLSAQPVQTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SREDLSAQPVQTK 13 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 S(0.999)REDLS(0.001)AQPVQTK;S(0.988)REDLS(0.012)AQPVQTK;S(1)REDLSAQPVQTK;S(1)REDLSAQPVQTK 217.91 1.51E-11 5089490000 7989000 5900820 4573400 5587360 6566750 5115670 7459440 8605120 7514380 TRUE FALSE 6933233.408 5862057.125 6785111.537 6856055.485 6436084.523 5312473.135 6736024.657 6764982.053 6626038.557 1.046361766 0.884700123 1.024007252 1.034714095 0.971332187 0.801757051 1.016599073 1.020969316 1 22.65971517 S(ph)REDLTAVVSVSTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SREDLTAVVSVSTK 14 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 S(0.997)REDLT(0.003)AVVSVSTK;S(0.962)REDLT(0.038)AVVSVSTK;S(0.975)REDLT(0.021)AVVS(0.004)VSTK;S(1)REDLTAVVSVSTK 238.21 6.72E-17 1892300000 2613400 2195340 1656070 1944180 2459280 2029000 2778120 3225140 2985440 TRUE FALSE 2268032.568 2180918.667 2456950.991 2385635.784 2410345.139 2107056.943 2508698.35 2535468.909 2632504.684 0.8615493 0.828457659 0.933313056 0.906222807 0.91560906 0.800400074 0.952970137 0.963139372 1 21.32800467 2.024556747 23.61766364 0.972672192 0.878067794 0.566554469 0.040631235 88.63738965 85247.10928 0.016742736 0.01128715 105.8173173 -2.024556747 -0.094604398 S(ph)REEDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SREEDFR 7 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 S(1)REEDFR 84.054 0.05742 112930000 270010 244270 166640 202530 236270 222460 223080 261140 308470 TRUE FALSE 234327.4944 242665.3743 247227.6614 248517.532 231568.6893 231018.1802 201445.7359 205297.2432 272003.028 0.861488551 0.89214218 0.908915107 0.913657226 0.851345998 0.84932209 0.740601079 0.754760874 1 18.05326319 2.848520717 2.350169892 0.81270362 0.893909055 0.092076286 0.07194701 0.496046166 5.384322451 0.026406409 0.026098146 705.5384995 -2.848520717 0.081205435 S(ph)RENLSAVMLYNPGLEFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRENLSAVMLYNPGLEFER 19 1 Q96L93-5;Q96L93-6;Q96L93-4;Q96L93;Q96L93-2;A0A1B0GTU3 Q96L93-5 KIF16B Kinesin-like protein KIF16B 1 S(0.532)RENLS(0.468)AVMLYNPGLEFER;S(0.938)RENLS(0.062)AVMLYNPGLEFER;S(0.724)RENLS(0.276)AVMLYNPGLEFER 207.47 1.91E-16 1541640000 375458 289993 217429 242004 304107 290930 303444 333015 332828 TRUE FALSE 325840.274 288088.0169 322578.3917 296954.707 298055.8657 302122.2654 274016.0476 261802.3338 293481.453 1.110258487 0.981622566 1.099144046 1.011834663 1.015586718 1.029442448 0.933674155 0.892057509 1 18.16290981 2.25489808 4.903311282 0.9302902 1.039581862 0.498272009 0.046641307 0.131733788 8.245806882 0.017446636 0.012601425 179.8448805 -2.25489808 0.109291663 S(ph)RERPSAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRERPSAPR 9 2 Q8N5F7;A0A494C050 Q8N5F7 NKAP NF-kappa-B-activating protein 1 S(0.996)RERPS(0.004)APR 61.48 0.070009 285080000 51932 52675 26947 40455 48758 45764 46138 65018 46008 TRUE FALSE 45069.05462 52328.97446 39978.65933 49640.92607 47787.81119 47524.57069 41663.54386 51114.40667 40568.98665 1.110923845 1.289876301 0.985448803 1.2236176 1.177939484 1.171450771 1.026980147 1.25993797 1 15.30808965 1.210549136 24.46809131 0.999998889 1.156788579 0.208611833 0.095330844 3708.679804 3239308.432 1.968748733 0.02121939 16.23862063 -1.210549136 0.156789691 S(ph)RERPSQPEGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRERPSQPEGLR 12 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 S(0.999)RERPS(0.001)QPEGLR;S(0.999)RERPS(0.001)QPEGLR 131.72 0.00015258 4051400000 520160 505400 390810 484330 660010 673800 678720 747360 860060 TRUE FALSE 451419.5381 502079.9941 579807.0232 594304.529 646877.0923 699721.522 612897.8389 587542.88 758384.6866 0.595238203 0.662038676 0.764528917 0.783645213 0.852966975 0.922647219 0.808162203 0.774729356 1 19.53257031 4.293065536 0.94201746 0.858440387 0.53949313 0.706151443 0.062826796 0.68447458 0.774567022 0.023274868 0.195052576 19636.56577 -4.293065536 -0.318947257 S(ph)RERPSQPEGLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SRERPSQPEGLRK 13 3 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 S(1)RERPSQPEGLRK;S(0.99)RERPS(0.01)QPEGLRK;S(0.993)RERPS(0.007)QPEGLRK;S(1)RERPSQPEGLRK 121.32 0.0013705 3597510000 752158 749440 537185 624792 902950 865570 1132350 1209550 626011 TRUE FALSE 652758.4146 744516.8793 796969.4628 766660.5729 884983.0616 898869.038 1022534.871 950897.1452 552004.6927 1.182523307 1.348750996 1.443772985 1.388866042 1.603216555 1.628372095 1.852402497 1.722625111 1 19.07432101 4.112062606 0.908934895 1.602548747 1.167280469 0.195198281 0.227346141 1.447677301 1.751129284 0.088747428 0.5240599 12943.8242 -4.112062606 -0.435268278 S(ph)RES(ph)SPSHGLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRESSPSHGLLK 12 1 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 2 S(0.754)RES(0.857)S(0.329)PS(0.059)HGLLK 61.641 0.047466 308320000 788790 583240 388970 417710 566740 461870 600400 693760 613280 TRUE FALSE 684549.403 579408.658 577077.193 512557.4398 555462.9828 479638.4378 542173.3004 545404.8228 540778.7371 1.265858578 1.071433876 1.067122565 0.947813597 1.027153889 0.886940268 1.002578806 1.008554489 1 19.0446789 5.319798632 0.956264392 0.981557126 1.835333054 0.80618092 0.043547459 2.227916945 0.744517108 0.013603258 2.561193225 208832.7617 -5.319798632 0.853775928 S(ph)RESASPTIPNLDLLEAHTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRESASPTIPNLDLLEAHTK 20 1 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 S(0.331)RES(0.331)AS(0.331)PT(0.008)IPNLDLLEAHTK 122.41 1.84E-05 87614000 74599 66121 39642 56015 82241 59554 88612 104820 34968 TRUE FALSE 64740.55314 65686.6468 58813.00379 68734.06189 80604.565 61845.08092 80018.42188 82405.05871 30834.12288 2.09963985 2.130323183 1.907399929 2.229155736 2.614135169 2.005735048 2.595125608 2.672528064 1 14.91224019 3.502683215 21.92161462 2.276618299 2.056580356 0 0.483596253 600.1194214 514650.0228 0.130150266 0.191772836 3181.875738 -3.502683215 -0.220037943 S(ph)RESLNVDVVK ddPTM_MDA-MB-175_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(0.995)RES(0.005)LNVDVVK;S(0.987)RES(0.013)LNVDVVK;S(1)RESLNVDVVK;S(0.999)RES(0.001)LNVDVVK;S(0.996)RES(0.004)LNVDVVK;S(0.995)RES(0.005)LNVDVVK 169.15 1.04E-05 9880530000 7437340 5768910 4556960 5187840 5871310 4771620 7198410 8393730 7590700 TRUE FALSE 6454476.675 5731013.65 6760721.098 6365818.363 5754482.418 4955187.309 6500309.306 6598796.16 6693336.093 0.964313847 0.856226786 1.010067477 0.951068088 0.859733074 0.740316524 0.971161348 0.985875514 1 22.67429403 2.025794808 24.99945085 0.987905913 0.897239613 0.250143773 0.07302254 313.8213346 304143.6145 0.031117813 0.020978961 106.1194053 -2.025794808 -0.0906663 S(ph)RESMIQLF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRESMIQLF 9 1 P30520;G3V5D8;G3V232;Q8N142;Q8N142-2 P30520;Q8N142 ADSS;ADSSL1 Adenylosuccinate synthetase isozyme 2;Adenylosuccinate synthetase isozyme 1 1 S(0.72)RES(0.28)MIQLF;S(0.748)RES(0.252)MIQLF 80.763 0.061008 53194000 132685 143088 88705 101863 132629 140630 141740 143202 175942 TRUE FALSE 115150.3411 142148.0455 131603.0347 124992.551 129989.9424 146040.1271 127994.0766 112579.3667 155142.3372 0.742223839 0.916242775 0.848272864 0.80566371 0.837875365 0.941329941 0.825010625 0.725652125 1 17.24323292 2.97895215 24.58418368 0.85037941 0.834078995 0.030518415 0.08370314 5666.856898 6618970.423 0.027255899 0.027545665 952.6911922 -2.97895215 -0.016300415 S(ph)RGQNRPTNVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRGQNRPTNVK 11 2 Q9BX40;Q9BX40-2;Q5TBQ1;Q5TBQ0;Q5TBP9;Q9BX40-3 Q9BX40 LSM14B Protein LSM14 homolog B 1 S(1)RGQNRPTNVK;S(1)RGQNRPTNVK;S(1)RGQNRPTNVK 105.14 0.0019737 522630000 433605 378804 259128 313691 387560 367015 463031 560400 538880 TRUE FALSE 376303.0006 376315.6116 384443.1675 384919.336 379848.3142 381134.3045 418126.3249 440562.821 475174.2203 0.791926381 0.791952921 0.809057291 0.810059384 0.799387463 0.802093818 0.879943202 0.927160612 1 18.85809704 1.620433599 1.109105204 1.033418124 0.797812806 0.974190154 0.011240268 0.126121366 0.207219501 0.031654259 0.003857661 41.72857933 -1.620433599 -0.235605318 S(ph)RGSPSSYNSSSSSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRGSPSSYNSSSSSPR 16 1 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 1 S(0.39)RGS(0.39)PS(0.212)S(0.008)YNSSSSSPR 119.56 0.00011207 410500000 101270 87239 53926 51438 77787 82356 71414 71658 62036 TRUE FALSE 87886.91291 86665.92126 80004.79397 63117.78408 76239.19089 85524.28861 64488.28127 56334.49434 54702.17475 1.606643855 1.58432314 1.462552345 1.153844145 1.393714075 1.563453172 1.178897943 1.029840122 1 15.73931057 0.358729084 0.287706376 1.60E-16 1.613957205 0.650469596 0.135133284 14.28116105 0.78824747 8.872354859 0.416465844 2.284173476 -0.358729084 1.613957205 S(ph)RKSPHKDLGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRKSPHKDLGHR 12 3 O94888;C9JAT7 O94888 UBXN7 UBX domain-containing protein 7 1 S(0.591)RKS(0.409)PHKDLGHR 95.347 0.0043516 302660000 569220 430830 202280 164780 312700 238800 478770 542210 67758 TRUE FALSE 493996.1348 427999.8494 300103.2846 202195.8175 306477.8818 247986.7905 432338.9591 426262.611 59747.72643 8.268032347 7.163449974 5.02284024 3.38415919 5.129532119 4.150564471 7.236073821 7.134373749 1 15.8665962 4.352612745 3.407672056 5.013053676 8.069417577 0.32307837 1.796569444 0.312218894 6.827273198 0.475671713 1.537074761 22522.30031 -4.352612745 3.056363901 S(ph)RLSAIEIDIPVVSHTT ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRLSAIEIDIPVVSHTT 17 1 P56749 P56749 CLDN12 Claudin-12 1 S(0.681)RLS(0.319)AIEIDIPVVSHTT 238.79 1.77E-20 76220000 91323 98464 61832 91828 137050 151880 79888 137550 103310 TRUE FALSE 79254.43417 97817.1835 91734.16202 112678.9509 134322.9731 157722.9219 72140.47406 108136.0029 91096.80949 0.870002304 1.073771782 1.006996431 1.23691435 1.474507986 1.731377013 0.791909996 1.187044898 1 16.47511291 3.752597814 5.948707408 1.234808286 0.990712353 0.18140104 0.253686167 0.327093812 47.31670875 0.072204477 0.120244516 5657.151559 -3.752597814 -0.244095933 S(ph)RLTPVSPESSSTEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRLTPVSPESSSTEEK 16 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 S(0.614)RLT(0.386)PVSPESSSTEEK;S(0.632)RLT(0.367)PVS(0.001)PESSSTEEK 136.68 9.76E-06 900630000 482680 314450 263480 303290 321720 300351 405890 386870 412600 TRUE FALSE 418892.615 312384.3572 390899.8093 372156.63 315318.4014 311905.6973 366526.8503 304140.8611 363822.898 1.151364077 0.858616538 1.074423329 1.022906013 0.866681023 0.857300898 1.007432056 0.835958547 1 18.47287682 3.250621848 24.89811707 0.908023148 1.018212158 0.274738934 0.090798328 279.3665824 576695.63 0.024258364 0.031072213 1780.827478 -3.250621848 0.11018901 S(ph)RNSPLLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRNSPLLER 9 1 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 S(0.828)RNS(0.172)PLLER 78.324 0.018225 746040000 348270 400390 191410 193590 344310 462930 237280 311080 440410 TRUE FALSE 302245.2371 397759.8117 283976.5162 237547.5683 337458.9046 480739.2167 214268.6221 244557.9628 388345.2315 0.778290069 1.024242811 0.731247594 0.611691735 0.868966263 1.237917136 0.551747787 0.6297437 1 18.56698023 S(ph)RPTS(ph)FADELAAR ddPTM_MDA-MB-175_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(0.999)RPT(0.127)S(0.874)FADELAAR;S(1)RPT(0.416)S(0.585)FADELAAR 127.91 0.0020493 341220000 508900 446100 373460 416310 611880 640340 607540 641340 671170 TRUE FALSE 441647.5756 443169.5397 554066.5051 510839.5484 599704.7851 664974.2942 548620.8643 504194.4319 591825.0472 0.746246847 0.748818493 0.936199824 0.863159731 1.013314303 1.123599444 0.926998387 0.851931554 1 19.17481123 4.204322164 1.623382597 0.961331612 0.720073645 0.55446119 0.078250433 0.390922763 1.833468909 0.024870538 0.109034775 16007.45037 -4.204322164 -0.241257967 S(ph)RPTSFADELAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRPTSFADELAAR 13 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;A0A0A0MT65 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 S(0.593)RPT(0.348)S(0.059)FADELAAR;S(0.996)RPT(0.003)SFADELAAR;S(0.98)RPT(0.014)S(0.006)FADELAAR 122.29 0.00014337 511645000 406560 423480 246719 310402 455550 530970 417880 466830 462500 TRUE FALSE 352832.0659 420698.132 366033.1336 380883.5183 446485.4463 551396.7595 377354.0619 367002.0374 407823.7769 0.865158154 1.031568427 0.897527693 0.933941422 1.09479994 1.352046621 0.925287056 0.899903483 1 18.63758636 4.744173619 23.15441916 1.010038404 0.865157979 0.110030141 0.134362841 601.2080742 2479841.948 0.035147162 0.292142868 55484.74812 -4.744173619 -0.144880426 S(ph)RPVSMDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRPVSMDAR 9 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 S(0.509)RPVS(0.491)MDAR 72.652 0.027945 234860000 166260 192350 124680 171680 215800 256350 176920 214150 247070 TRUE FALSE 144288.3198 191086.4402 184975.665 210662.568 211506.0022 266211.9504 159762.3256 168355.689 217861.6661 0.662293291 0.877099876 0.849050998 0.966955646 0.970827067 1.221931124 0.73332004 0.772764168 1 17.73305284 5.126137653 1.365456513 0.921731115 0.276930481 0.28154795 0.134466482 5.160263988 4.238753849 0.040802243 5.92789485 133701.9227 -5.126137653 -0.644800634 S(ph)RQTPS(ph)PDVVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRQTPSPDVVLR 12 1 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3;D6RJ93;D6R8Y0;Q9UPQ0-7;Q6NVB9 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 2 S(0.518)RQT(0.486)PS(0.997)PDVVLR 89.232 0.0054279 1139100000 795840 803410 471320 552220 825610 808290 704180 831610 828960 TRUE FALSE 690667.7276 798132.3468 699251.9285 677609.9912 809181.9763 839385.4393 635888.732 653776.6731 730961.2932 0.944875924 1.091894132 0.956619639 0.927012138 1.107010705 1.1483309 0.86993489 0.894406693 1 19.47943549 2.210133724 24.99972693 0.913667393 1.027716779 0.288971796 0.079407352 264.0232741 232190.5157 0.033182106 0.022376089 162.2309548 -2.210133724 0.114049385 S(ph)RS(ph)FDYNYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSFDYNYR 9 1 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 2 S(1)RS(1)FDYNYR 55.196 0.074015 169040000 282150 269760 149420 191640 272190 265310 227790 280270 300060 TRUE FALSE 244863.1626 267987.9288 221680.0118 235154.791 266773.9515 275516.6474 205698.9609 220336.4416 264587.2486 0.925453376 1.012852774 0.837833316 0.888760862 1.008264582 1.041307353 0.777433387 0.83275533 1 18.01338401 2.234458803 24.99872567 0.858430952 0.949596738 0.179578994 0.081575269 167.3434501 1019867.112 0.033314559 0.02337569 171.5768945 -2.234458803 0.091165786 S(ph)RS(ph)PATAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRSPATAK 8 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)RS(0.999)PAT(0.002)AK;S(1)RS(0.999)PAT(0.002)AK 83.182 0.010439 1782570000 1661810 1162080 937170 1044400 878470 861270 1333390 1665490 1729340 TRUE FALSE 1442197.598 1154446.22 1390388.547 1281546.983 860990.1657 894403.6142 1204078.043 1309337.924 1524899.395 0.945765735 0.757063858 0.911790346 0.84041412 0.564620963 0.586532867 0.789611463 0.85863889 1 20.54028263 7.999986643 0.974126472 0.778926544 131.1184182 0.112664747 0.133737586 3824.704637 5.976807501 0.046685936 1111717.239 99996924.44 -7.999986643 130.3394917 S(ph)RS(ph)PHEAGFCVYLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 157.97 2.93E-06 627343000 1170370 978430 668827 721890 956930 840650 947620 1215770 1187630 TRUE FALSE 1015702.639 972002.6289 992273.9743 885806.1579 937888.9652 872990.3495 855719.9583 955787.0466 1047229.734 0.969894767 0.928165614 0.947522728 0.845856576 0.895590465 0.833618757 0.817127255 0.912681349 1 19.99814654 3.760506762 23.23777984 0.881301114 0.946491528 0.256835956 0.051436209 480.2888306 508552.0964 0.014099842 0.024383686 5761.117887 -3.760506762 0.065190413 S(ph)RS(ph)PLAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SRSPLAIR 8 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)RS(1)PLAIR;S(1)RS(1)PLAIR;S(1)RS(1)PLAIR;S(1)RS(1)PLAIR;S(1)RS(1)PLAIR 92.856 0.0065329 6862030000 620074 457213 310467 362205 489847 546370 448704 488740 440883 TRUE FALSE 538129.6498 454209.5377 460609.8796 444449.1812 480100.0031 567389.2074 405188.7551 384226.7544 388762.314 1.384212488 1.168347654 1.184811035 1.143241423 1.234944813 1.459475847 1.042253173 0.988333335 1 18.56852885 2.028886454 23.78955591 0.999921274 1.248257446 0.600576474 0.097095535 80.67293642 66437.99802 0.039900241 0.026900055 106.8775412 -2.028886454 0.248336172 S(ph)RS(ph)PLDKDTYPPSASVVGASVGGHR ddPTM_MDA-MB-175_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(0.99)RS(0.99)PLDKDT(0.008)Y(0.012)PPSASVVGASVGGHR;S(0.686)RS(0.698)PLDKDT(0.26)Y(0.354)PPS(0.001)AS(0.001)VVGASVGGHR 114.35 0.00097783 2965430000 267960 217041 107891 151807 272680 209001 258450 294710 274520 TRUE FALSE 232548.4071 215615.2434 160067.4485 186277.0996 267254.2015 217041.4037 233385.5588 231688.5599 242066.5583 0.960679611 0.890727099 0.66125387 0.769528434 1.104052552 0.896618704 0.964137964 0.957127501 1 17.88504426 3.258781212 24.99996147 0.975072761 0.81418197 0.435481114 0.092228892 242.9533005 300376.2232 0.027182291 0.035048239 1814.601275 -3.258781212 -0.16089079 S(ph)RS(ph)PLGFYVHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRSPLGFYVHLK 12 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 2 S(1)RS(1)PLGFYVHLK;S(0.999)RS(0.999)PLGFY(0.002)VHLK 112.82 0.00070156 1126480000 1345640 1050480 712770 796110 1089960 845060 1112960 1414380 1346360 TRUE FALSE 1167810.265 1043579.328 1057467.956 976878.9433 1068271.928 877570.005 1005025.311 1111925.844 1187194.855 0.983671939 0.879029524 0.890728217 0.822846342 0.899828638 0.739196267 0.846554638 0.936599278 1 20.17912531 1.523032663 3.257662594 0.993321946 0.862573643 0.343055857 0.061838182 0.250055749 5.430183972 0.065136761 0.016433724 33.34514903 -1.523032663 -0.130748303 S(ph)RS(ph)PLLNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SRSPLLNDR 9 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(1)RS(1)PLLNDR;S(1)RS(1)PLLNDR;S(1)RS(1)PLLNDR;S(1)RS(1)PLLNDR 88.282 0.0073344 1717120000 1118470 943070 677500 865580 1109890 954560 988000 1068190 1457610 TRUE FALSE 970661.3557 936874.9111 1005141.266 1062123.169 1087805.36 991282.5409 892183.9121 839765.8812 1285293.006 0.755206284 0.728919325 0.782032783 0.826366566 0.846348152 0.771250241 0.694148266 0.653365324 1 20.29366586 4.227620887 23.88954017 0.779969103 0.742062811 0.033298699 0.093566383 542.3063408 1184273.363 0.024823019 0.052574601 16889.65924 -4.227620887 -0.037906292 S(ph)RS(ph)PPPVSK ddPTM_MDA-MB-175_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 92.65 0.0056518 27917210000 9028220 5738520 5036160 6046850 6682870 5151300 7226880 8820600 12734000 TRUE FALSE 7835117.852 5700823.284 7471663.821 7419879.713 6549893.962 5349473.844 6526018.29 6934383.332 11228601.03 0.697782193 0.50770557 0.665413599 0.660801795 0.583322352 0.47641499 0.581196026 0.617564318 1 23.42067486 1.236104559 4.83872511 1.029376814 0.593444603 0.773843159 0.068246701 0.08493602 4.751380786 0.126165613 0.016899877 17.22283174 -1.236104559 -0.435932211 S(ph)RS(ph)PQWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SRSPQWR 7 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)RS(1)PQWR;S(1)RS(1)PQWR;S(1)RS(1)PQWR;S(1)RS(1)PQWR;S(1)RS(1)PQWR 76.302 0.023402 3480740000 976151 1467931 701913 735900 1393073 1850587 964973 1088953 1030053 TRUE FALSE 847150.1721 1458288.065 1041360.475 902997.3425 1365353.573 1921780.279 871390.067 856088.8752 908281.3078 0.932695812 1.605546709 1.146517566 0.994182457 1.503227647 2.115842595 0.959383464 0.94253715 1 19.79277966 S(ph)RS(ph)PT(ph)PPSSAGLGSNSAPPIPDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRSPTPPSSAGLGSNSAPPIPDSR 24 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 3 S(0.984)RS(0.943)PT(0.494)PPS(0.419)S(0.159)AGLGSNSAPPIPDSR;S(0.997)RS(0.974)PT(0.754)PPS(0.222)S(0.053)AGLGSNSAPPIPDSR;S(0.933)RS(0.851)PT(0.467)PPS(0.348)S(0.384)AGLGS(0.013)NS(0.005)APPIPDSR 91.779 0.007495 749910000 469170 399880 264127 276067 465420 379381 393764 442290 414024 TRUE FALSE 407167.9958 397253.162 391859.7007 338752.2318 456159.0526 393976.0326 355576.8279 347709.7254 365078.5544 1.115288726 1.088130643 1.073357216 0.927888608 1.249481919 1.079154138 0.973973474 0.952424406 1 18.4778474 2.246042446 6.087080757 0.969991396 1.088570034 0.323031236 0.077381722 0.174605064 24.26973987 0.030065962 0.021813422 176.2148262 -2.246042446 0.118578638 S(ph)RS(ph)PVDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRSPVDLR 8 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(1)RS(1)PVDLR;S(1)RS(1)PVDLR;S(1)RS(1)PVDLR 78.324 0.017594 1796230000 1537240 1193910 864320 1009790 1444230 1267500 1165010 1394180 1279490 TRUE FALSE 1334089.839 1186067.127 1282308.043 1239078.253 1415492.649 1316261.545 1052027.51 1096045.457 1128230.15 1.182462496 1.051263456 1.136566013 1.098249549 1.254613386 1.166660495 0.932458249 0.971473291 1 20.10562997 2.241292667 24.99998693 0.967225565 1.145915407 0.704979036 0.054975479 38.85395689 355542.9613 0.021748701 0.016074852 174.2981056 -2.241292667 0.178689842 S(ph)RS(ph)RS(ph)PPPVSK ddPTM_MDA-MB-175_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(0.994)RS(0.998)PPPVS(0.008)K;S(1)RS(1)RS(1)PPPVS(0.001)K;S(1)RS(1)RS(0.999)PPPVS(0.001)K 77.505 0.021417 6599300000 9316780 6725360 4895240 5504220 7167630 5641250 6350160 9120900 10328940 TRUE FALSE 8085543.917 6681180.667 7262594.438 6754037.278 7025008.186 5858272.538 5734322.461 7170466.514 9107864.48 0.887754087 0.733561713 0.797398167 0.74156102 0.771312331 0.643210332 0.629601206 0.787282961 1 23.11868139 1.264755727 4.103105657 1.020040326 0.740249741 0.544729027 0.072990396 0.164250881 4.877267824 0.129797363 0.018827308 18.39736932 -1.264755727 -0.279790585 S(ph)RS(ph)RT(ph)PLISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSRTPLISR 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(1)RS(0.989)RT(0.877)PLIS(0.134)R 74.301 0.067867 1297100000 705640 625800 364300 424480 643840 585560 483390 677960 645220 TRUE FALSE 612387.8861 621689.0786 540476.6985 520864.6718 631028.8437 608086.8721 436510.9122 532983.5299 568942.8266 1.076361029 1.092709231 0.949966628 0.91549563 1.10912523 1.068801369 0.767231595 0.936796291 1 19.11792416 2.273936023 24.99982357 0.903140482 1.032030678 0.365595595 0.083162114 196.6524371 138973.7155 0.031914803 0.024720117 187.903999 -2.273936023 0.128890196 S(ph)RSCHDLSVL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSCHDLSVL 10 1 Q8IYK8 Q8IYK8 REM2 GTP-binding protein REM 2 1 S(0.498)RS(0.498)CHDLS(0.003)VL 58.32 0.067747 132030000 314940 402130 215410 232480 374360 378690 362390 386490 330240 TRUE FALSE 273319.881 399488.3816 319582.9965 285268.1372 366910.9684 393258.4493 327245.4736 303842.1212 291199.4034 0.938600416 1.371872253 1.09747133 0.979631599 1.259999039 1.350478211 1.123784835 1.043416015 1 18.15164787 1.745840474 3.318675376 1.014410972 1.172124538 0.14746718 0.140619492 0.386730957 8.887842672 0.098067579 0.037468994 55.69811205 -1.745840474 0.157713566 S(ph)RSDIDVNAAASAK ddPTM_MDA-MB-175_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 230.27 5.91E-13 1727090000 2433370 1851140 1253691 1507736 1798490 1607520 2050090 2358030 2229800 TRUE FALSE 2111793.989 1838979.739 1859980.161 1850090.503 1762703.568 1669362.335 1851272.587 1853783.635 1966195.584 1.074050825 0.935298479 0.945979218 0.940949373 0.896504693 0.849031677 0.941550577 0.942827687 1 20.90697541 4.742156359 4.786028062 0.929426953 1.082541047 0.576501864 0.038389163 0.143133503 9.374144684 0.009905243 0.073392698 55227.62397 -4.742156359 0.153114094 S(ph)RSDNALHLASER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRSDNALHLASER 13 1 A0A1X7SBR1;Q7Z3G6 A0A1X7SBR1 PRICKLE2 Prickle-like protein 2 1 S(0.734)RS(0.266)DNALHLASER;S(0.909)RS(0.091)DNALHLASER 131.25 8.03E-05 468970000 132309 157460 110519 99247 131413 157641 120073 144489 154364 TRUE FALSE 114824.0304 156425.6349 163966.3581 121782.5482 128798.1384 163705.5513 108428.3389 113591.1518 136115.2638 0.843579384 1.149214501 1.204614042 0.894701629 0.946243168 1.202697969 0.796592064 0.834521777 1 17.05446933 2.218332235 24.99775036 0.864828487 1.041723932 0.250543306 0.132430105 311.8212861 385338.3472 0.053509063 0.036125085 165.3226032 -2.218332235 0.176895445 S(ph)RSESETSTMAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRSESETSTMAAK 13 1 Q96B23-2;Q96B23;A0A087WVF1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 S(0.333)RS(0.333)ES(0.333)ET(0.002)STMAAK;S(0.437)RS(0.437)ES(0.126)ETSTMAAK;S(0.478)RS(0.478)ES(0.043)ETSTMAAK 179.1 8.50E-06 1760620000 1441223 968045 912856 1154131 1372100 1237619 1741366 1885920 1874460 TRUE FALSE 1250761.729 961685.8487 1354316.215 1416194.083 1344797.894 1285231.004 1572488.593 1482630.684 1652863.474 0.756724163 0.581830178 0.819375729 0.856812499 0.813617044 0.777578441 0.951372341 0.89700735 1 20.65653613 -1.999954852 0.057025928 2.405678144 3.23E-05 0.616155389 0.071210967 543.8320569 3.014599666 121.3104637 32.90317683 0.01000104 1.999954852 -2.405645876 S(ph)RSGEGEVSGLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSGEGEVSGLMR 13 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 S(0.5)RS(0.5)GEGEVSGLMR 73.688 0.054834 481590000 873860 534530 359040 398290 527260 556960 601090 573060 460890 TRUE FALSE 758377.1869 531018.6372 532672.9449 488727.832 516768.5576 578386.6116 542796.3843 450515.5786 406404.1092 1.866066729 1.306627136 1.310697734 1.202566167 1.271563318 1.423181012 1.33560752 1.108540904 1 18.63255546 4.922921828 1.953847961 1.234196158 2.319484089 0.733480975 0.118258538 0.836744833 2.214530078 0.033496075 1.925829342 83737.85415 -4.922921828 1.08528793 S(ph)RSHSDNDRPNCSWNTQYSSAYYTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSHSDNDRPNCSWNTQYSSAYYTSR 26 2 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.483)RS(0.483)HS(0.033)DNDRPNCSWNTQYSSAYYTSR 217.17 1.97E-34 663880000 124670 119880 53913 59570 136760 134460 87280 92223 56062 TRUE FALSE 108194.5436 119092.5004 79985.50713 73096.27897 134038.7436 139632.7632 78815.59903 72501.82913 49434.41423 2.188648239 2.409101074 1.618012641 1.478651666 2.711445977 2.824606408 1.594346778 1.466626646 1 15.59322812 1.824077563 2.423813818 1.171919878 2.172117086 0.452852543 0.441072436 0.280975772 3.084608261 0.369003995 0.132981618 66.69258688 -1.824077563 1.000197208 S(ph)RSPAPPADKEAFAAEAQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSPAPPADKEAFAAEAQK 19 2 Q9Y618;Q9Y618-4;Q9Y618-5 Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.5)RS(0.5)PAPPADKEAFAAEAQK 101.3 0.00026026 166650000 231070 191940 154690 167640 184450 137290 225950 286270 201590 TRUE FALSE 200533.514 190679.1335 229498.6014 205705.2242 180779.8059 142571.6351 204037.4038 225053.3883 177758.2599 1.128124871 1.072687895 1.291071377 1.157218935 1.016998063 0.802053504 1.147836415 1.266064308 1 17.43955707 3.326097225 8.156265827 1.069531309 1.165896469 0.153261515 0.128975586 0.659115823 54.05592414 0.041780274 0.053928028 2118.835423 -3.326097225 0.09636516 S(ph)RSPATAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSPATAK 8 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.6)RS(0.4)PATAK 60.434 0.05591 282050000 505850 411170 319130 347120 208020 254090 475280 591210 521820 TRUE FALSE 439000.6408 408468.9972 473462.3354 425938.9014 203880.809 263865.0067 429187.4188 464784.3423 460131.0341 0.954077444 0.887723207 1.028972837 0.925690444 0.443092932 0.573456227 0.932750428 1.010113007 1 18.81168524 2.0128688 24.97363536 0.995474775 0.80128021 0.194404275 0.175934923 391.0141811 758812.6685 0.080314929 0.054112353 103.0074888 -2.0128688 -0.194194566 S(ph)RSPHEAGFCVYLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRSPHEAGFCVYLK 14 1 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(0.5)RS(0.5)PHEAGFCVYLK;S(0.5)RS(0.5)PHEAGFCVYLK 69.108 0.028941 648200000 714930 636980 376040 500500 656440 579950 685800 742500 622570 TRUE FALSE 620450.1891 632795.6364 557894.2018 614146.1747 643378.1283 602261.0518 619291.2216 583722.1531 548970.4838 1.130206828 1.15269519 1.016255369 1.118723488 1.171972168 1.097073649 1.128095662 1.063303348 1 19.06636906 1.40254246 2.320306406 0.98937312 1.115578575 0.460116654 0.041220785 0.396486682 3.087861734 0.090753778 0.011157682 25.26634719 -1.40254246 0.126205455 S(ph)RSPIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSPIQR 7 1 Q9Y252 Q9Y252 RNF6 E3 ubiquitin-protein ligase RNF6 1 S(0.63)RS(0.37)PIQR 62.823 0.050349 97607000 13423 17916 8870.3 8975.8 14323 16532 9150.7 15498 12199 TRUE FALSE 11649.11654 17798.30862 13160.00675 11013.89258 14038.00032 17167.99674 8263.266522 12183.87331 10756.84812 1.082948873 1.654602577 1.223407322 1.02389589 1.305029147 1.596006242 0.768186594 1.132662019 1 13.39296779 2.232059463 24.99972049 0.993191235 1.312027506 0.367616053 0.213834535 177.4540245 682379.0111 0.084501929 0.05849963 170.6316 -2.232059463 0.318836271 S(ph)RSPITTNHRPS(ph)PDPEQRPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRSPITTNHRPSPDPEQRPLR 21 3 P41212 P41212 ETV6 Transcription factor ETV6 2 S(0.5)RS(0.5)PIT(0.021)T(0.067)NHRPS(0.913)PDPEQRPLR;S(0.5)RS(0.5)PIT(0.002)T(0.001)NHRPS(0.997)PDPEQRPLR 112.99 0.00030394 662300000 165762 139587 100888 134761 156061 158478 144430 163336 160557 TRUE FALSE 143856.1317 138670.0438 149677.7743 165360.5447 152955.6914 164574.7512 130423.2008 128407.8675 141576.1344 1.01610439 0.979473302 1.057224616 1.167997315 1.080377651 1.16244699 0.921223068 0.906988088 1 17.11121856 2.218742609 24.99333678 0.934392871 1.076179352 0.510956609 0.061859514 196.1830914 247413.0227 0.026954353 0.018199576 165.4788938 -2.218742609 0.141786481 S(ph)RSPITTNHRPSPDPEQRPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRSPITTNHRPSPDPEQRPLR 21 3 P41212 P41212 ETV6 Transcription factor ETV6 1 S(0.497)RS(0.497)PIT(0.002)T(0.003)NHRPSPDPEQRPLR;S(0.499)RS(0.499)PIT(0.001)T(0.001)NHRPSPDPEQRPLR;S(0.5)RS(0.5)PITTNHRPSPDPEQRPLR 90.468 0.0015401 506700000 311821 321836 147773 221719 333174 285708 240880 325855 271833 TRUE FALSE 270613.0648 319721.8381 219236.5171 272063.6877 326544.4892 296699.3716 217519.4947 256173.4441 239697.2124 1.128978773 1.33385714 0.914639411 1.13503067 1.362320763 1.23780902 0.907476113 1.068737686 1 17.87085361 2.247349102 24.99988153 1.004518632 1.185625252 0.333264145 0.128530548 231.3333019 658056.2145 0.049225393 0.037533672 176.7457996 -2.247349102 0.18110662 S(ph)RSPLGFYVHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRSPLGFYVHLK 12 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 S(0.5)RS(0.5)PLGFYVHLK;S(0.606)RS(0.394)PLGFYVHLK 87.429 0.0063914 953410000 1084440 863490 525660 661290 797440 729550 931820 1027950 846960 TRUE FALSE 941128.5064 857817.6773 779870.9342 811446.0017 781572.5042 757616.2606 841452.2398 808130.892 746833.3537 1.260158644 1.148606544 1.044236884 1.086515483 1.046515264 1.01443817 1.126693439 1.082076595 1 19.51042683 4.577363776 2.358237116 1.062035554 1.275909546 0.761563427 0.03697515 0.199660551 1.695590012 0.009662674 0.075348304 37788.8587 -4.577363776 0.213873992 S(ph)RSPLHPMSEIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSPLHPMSEIPR 13 1 Q9NVW2-2;Q9NVW2 Q9NVW2-2 RLIM E3 ubiquitin-protein ligase RLIM 1 S(0.61)RS(0.39)PLHPMSEIPR 94.203 0.0031871 273220000 179950 185060 125860 144190 218870 177780 164730 218190 181380 TRUE FALSE 156169.1516 183844.3287 186726.317 176930.5433 214514.9152 184619.3116 148754.51 171531.7665 159937.463 0.976438844 1.149476334 1.167495804 1.10624828 1.341242453 1.154321871 0.930079214 1.072492731 1 17.28714838 2.263515958 23.69665287 1.012832327 1.156824375 0.351251247 0.094194339 137.8554408 130901.6295 0.035043855 0.027129355 183.4492573 -2.263515958 0.143992048 S(ph)RSPLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRSPLLK 7 1 A0A0U1RQD2;Q6ZUS6-6;Q6ZUS6;Q6ZUS6-5;Q6ZUS6-4 A0A0U1RQD2 CCDC149 Coiled-coil domain-containing protein 149 1 S(0.5)RS(0.5)PLLK;S(0.5)RS(0.5)PLLK 80.231 0.018455 663890000 1104690 1267480 695440 933900 1199050 1218970 1212650 1548750 1458530 TRUE FALSE 958702.4176 1259153.84 1031757.11 1145956.269 1175191.251 1265864.565 1095047.39 1217561.865 1286104.245 0.745431345 0.97904493 0.802234433 0.89102907 0.913760495 0.9842628 0.851445281 0.946705424 1 20.29457615 8 0.241856087 0.966707499 0.035519634 0.34711675 0.066839714 113.7212694 1.794844863 0.232527024 41.37871888 100000000 -8 -0.931187864 S(ph)RSPLLVTVVESDPRPQGQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRSPLLVTVVESDPRPQGQPR 21 2 A0A2R8YH03;Q5VWN6;Q5VWN6-2 A0A2R8YH03 FAM208B Protein FAM208B 1 S(0.5)RS(0.5)PLLVTVVESDPRPQGQPR;S(0.5)RS(0.5)PLLVTVVESDPRPQGQPR;S(0.5)RS(0.5)PLLVTVVESDPRPQGQPR 110.94 0.00013578 1510750000 585483 470927 311096 475440 616337 655724 408412 617095 520928 TRUE FALSE 508109.9381 467833.4495 461543.0662 583395.9186 604073.0995 680950.1266 368804.2671 485134.0365 459344.4853 1.10616314 1.018480606 1.004786344 1.270061876 1.315076416 1.482438885 0.802892554 1.056144249 1 18.80921698 2.216226205 24.99995883 0.968243206 1.190883223 0.359664154 0.154310786 309.4077287 346332.039 0.06810791 0.045957947 164.5228427 -2.216226205 0.222640017 S(ph)RSPNRFDAHDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSPNRFDAHDPR 13 2 Q96T58;A0A669KB49;F6WRY4 Q96T58 SPEN Msx2-interacting protein 1 S(0.58)RS(0.42)PNRFDAHDPR 60.918 0.046004 1048100000 295480 268770 123440 131720 259070 253000 228380 246440 135540 TRUE FALSE 256431.5693 267004.4322 183135.9969 161629.0392 253915.0139 262733.0737 206231.7428 193740.7238 119516.6156 2.145572547 2.234036086 1.532305746 1.352356226 2.124516433 2.19829747 1.725548717 1.621035894 1 16.86685167 1.172568848 1.586451244 0.531388778 1.904354444 0.492091688 0.292254914 1.233358292 2.457353452 2.808680477 0.089276618 14.87883226 -1.172568848 1.372965666 S(ph)RSPPPVS(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSPPPVSK 9 1 Q01130;Q01130-2 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 2 S(1)RS(0.077)PPPVS(0.923)K 125.53 0.0059671 5262200000 1639100 1049900 935980 1117200 1215700 880820 1271400 1632700 2320100 TRUE FALSE 1422488.782 1043003.138 1388623.059 1370877.335 1191509.948 914705.7154 1148099.824 1283559.811 2045820.421 0.695314587 0.509821452 0.678760973 0.670086837 0.582411797 0.447109485 0.561192865 0.627405904 1 20.96424808 1.235684409 4.149187493 1.043239491 0.589765978 0.732742405 0.076851097 0.123041625 3.896481954 0.169049831 0.019749416 17.20617791 -1.235684409 -0.453473513 S(ph)RSPPRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSPPRPK 8 2 Q8WUQ7-2;Q8WUQ7 Q8WUQ7-2 CACTIN Cactin 1 S(0.5)RS(0.5)PPRPK 58.37 0.054985 237740000 161630 134840 84281 100840 112550 113400 141540 174640 153120 TRUE FALSE 140270.186 133954.2272 125039.5735 123737.2632 110310.4752 117762.5714 127813.4726 137294.5951 135018.328 1.038897371 0.992118841 0.926093334 0.9164479 0.817003712 0.872196931 0.946637945 1.016858948 1 17.04279573 1.847285891 4.299862033 1.007856527 0.923608271 0.231260065 0.059919672 0.338374167 9.714498033 0.037650429 0.017900982 70.3535297 -1.847285891 -0.084248256 S(ph)RSPQWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRSPQWR 7 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.603)RS(0.397)PQWR;S(0.53)RS(0.47)PQWR 54.608 0.080324 700860000 148668 140814 85787 89112 114654 146891 121369 127370 111490 TRUE FALSE 129021.1471 139888.9836 127273.8801 109346.2416 112372.6097 152541.9918 109598.6531 100132.9167 98309.77921 1.312393825 1.422940675 1.29462075 1.112262101 1.1430461 1.551646164 1.114829612 1.018544823 1 16.58504731 2.012847109 24.99573624 1.027424049 1.297919795 0.506746458 0.1245049 184.9953217 359931.3234 0.052369326 0.035284406 103.0023442 -2.012847109 0.270495746 S(ph)RSSPSTDHYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSSPSTDHYK 11 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 S(0.4)RS(0.4)S(0.2)PSTDHYK 128.54 0.00015923 480350000 463220 467320 253540 398180 459430 455920 479030 645570 685530 TRUE FALSE 402004.3034 464250.1441 376152.792 488592.8548 450288.2419 473459.5374 432573.7443 507519.8793 604487.4244 0.665033361 0.76800629 0.622267357 0.808276293 0.744909197 0.783241335 0.715604208 0.839587159 1 19.2053528 -0.812989373 0.831198246 10 0.72355231 0.716219225 0.054956864 34.27377208 0.937569662 557.0868679 0.019003337 0.153819228 0.812989373 -9.27644769 S(ph)RSSSS(ph)PPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSSSSPPPK 10 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.55)RS(0.194)S(0.255)S(0.036)S(0.963)PPPK 77.192 0.019197 513280000 873210 569900 390040 506330 361100 491340 633400 723310 902070 TRUE FALSE 757813.0861 566156.2894 578664.6486 621299.9653 353914.8165 510242.1677 571972.9655 568635.7853 795428.3122 0.952710728 0.711762808 0.727488121 0.781088573 0.444936157 0.641468452 0.719075442 0.714879992 1 19.60137239 -1.910078714 16.84652257 9.965769953 0.729240846 0 0.154592212 0 0 0 0.034138881 0.012300458 1.910078714 -9.236529107 S(ph)RSVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSVEK 6 1 Q8TF01 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 S(0.728)RS(0.272)VEK 67.563 0.059619 390050000 788770 613290 405510 489880 389790 502350 716930 852260 712060 TRUE FALSE 684532.046 609261.2576 601615.9923 601114.7413 382033.9416 521675.7296 647402.2389 670010.8313 627881.078 1.090225634 0.970344989 0.958168694 0.957370372 0.608449522 0.830851172 1.031090539 1.067098301 1 19.26013181 2.17911043 9.070167556 1.040434651 0.897379645 0.193201378 0.124781734 0.531455479 75.34594759 0.054983255 0.037094061 151.0464177 -2.17911043 -0.143055006 S(ph)RSVSPCS(ph)NVESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSVSPCSNVESR 13 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.755)RS(0.238)VS(0.342)PCS(0.524)NVES(0.141)R 100.36 0.029147 213310000 717680 623760 496540 462960 577740 613390 573880 666460 472780 TRUE FALSE 622836.7696 619662.4795 736668.4048 568082.1439 566244.1043 636987.5102 518225.2059 523942.7154 416888.487 1.494012881 1.486398639 1.767063442 1.362671701 1.358262754 1.527956588 1.243078718 1.256793439 1 18.669302 0.312400991 0.443095262 3.66E-18 1.557199332 0.675147262 0.116262094 7.474057888 0.646834737 7.236226859 0.104464902 2.053056924 -0.312400991 1.557199332 S(ph)RT(ph)SPAPWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRTSPAPWK 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.958)RT(0.839)S(0.203)PAPWK 74.987 0.090599 2298600000 2283800 1634300 1283600 1508700 1652800 1363000 1732000 2167700 2984300 TRUE FALSE 1981990.044 1623564.176 1904353.253 1851273.394 1619912.514 1415435.492 1564030.907 1704154.224 2631499.454 0.753178968 0.616973024 0.723676097 0.703505141 0.615585351 0.537881735 0.594349698 0.647598168 1 21.32745366 1.238831999 9.733949752 1.001679069 0.644849403 0.747039379 0.064132082 0.038574033 70.51089277 0.091974632 0.016390688 17.3313343 -1.238831999 -0.356829667 S(ph)RT(ph)SVQTEDDQLIAGQSAR ddPTM_MDA-MB-175_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(0.998)RT(0.777)S(0.225)VQTEDDQLIAGQSAR;S(0.697)RT(0.822)S(0.481)VQTEDDQLIAGQSAR;S(0.939)RT(0.583)S(0.478)VQTEDDQLIAGQSAR 305.69 4.31E-50 3034350000 716030 593620 440673 606400 689890 763460 495290 784670 704450 TRUE FALSE 621404.8213 589720.4711 653783.9368 744092.3882 676162.5387 792830.8002 447256.852 616874.4268 621170.7235 1.000376865 0.94936939 1.052502818 1.197887087 1.08852931 1.276349271 0.720022427 0.993083549 1 19.24463031 2.240339126 24.99999999 0.915169864 1.090151468 0.360664372 0.118755151 56.1595518 789437.9801 0.046770964 0.034333985 173.915835 -2.240339126 0.174981604 S(ph)RTGSESSQTGTSTTSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.327)RT(0.327)GS(0.327)ES(0.017)S(0.002)QTGTSTTSSR;S(0.333)RT(0.333)GS(0.333)ES(0.002)SQTGTSTTSSR 88.765 0.0018266 128318000 35058.3 30213.5 12271.8 14388.6 43650.5 48750 60058 62412 4635.97 TRUE FALSE 30425.25683 30015.02553 18206.48353 17655.75155 42781.94045 50625.44405 54233.5844 49065.67949 4087.910908 7.442739706 7.342387397 4.453737847 4.319015738 10.4654777 12.38418478 13.26682152 12.00262936 1 11.99714804 3.228968375 24.99155125 10 5.890697619 0.236356798 3.506104903 293.882071 765676.4379 1.084921726 1.245760171 1694.214425 -3.228968375 -4.109302381 S(ph)RTPS(ph)ASNDDQQE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRTPSASNDDQQE 13 1 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 2 S(0.989)RT(0.011)PS(0.909)AS(0.091)NDDQQE;S(0.999)RT(0.001)PS(0.982)AS(0.018)NDDQQE 210.57 3.45E-07 324520000 390410 477400 422640 441470 702640 861070 668400 790230 790960 TRUE FALSE 338816.3293 474263.928 627030.1176 541712.5109 688658.8387 894195.9201 603578.6709 621245.4641 697453.6099 0.485790488 0.67999351 0.899027704 0.776700419 0.98739017 1.28208659 0.865403322 0.890733742 1 19.41173774 4.701961084 0.883688279 0.981741835 0.218363016 0.637005426 0.12606957 1.505586746 0.964263345 0.047429234 1.106835269 50345.54938 -4.701961084 -0.76337882 S(ph)RTPSLPTPPTREPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRTPSLPTPPTREPK 15 2 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 S(0.499)RT(0.499)PS(0.002)LPTPPTREPK 57.804 0.062149 135040000 258250 198860 106230 114010 175520 182500 215880 223850 55114 TRUE FALSE 224121.6082 197553.6756 157603.1833 139897.713 172027.4954 189520.8931 194943.9908 175981.4195 48598.48571 4.611699417 4.065017103 3.2429649 2.87864346 3.539770692 3.899728363 4.011318213 3.62112969 1 15.56862374 4.413388018 3.010988154 3.283243886 4.556899509 0.250203576 0.84893777 0.401630322 6.959839389 0.218355471 0.849418299 25905.26373 -4.413388018 1.273655622 S(ph)RTPSNDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRTPSNDGK 9 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 S(0.5)RT(0.5)PSNDGK 77.662 0.019359 101220000 347600 172850 128920 140230 127210 159320 218790 219800 253330 TRUE FALSE 301663.7793 171714.537 191266.1432 172071.3648 124678.7699 165449.1435 197571.7795 172797.4805 223381.616 1.350441387 0.768704874 0.856230457 0.770302265 0.558142483 0.740656937 0.884458547 0.773552827 1 17.76915093 4.739809639 24.90925692 0.788813966 1.350441577 0.705490314 0.112940894 57.55990939 1147782.508 0.02784727 0.167103273 54930.00507 -4.739809639 0.561627611 S(ph)RTPSRHS(ph)CSGS(ph)SPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRTPSRHSCSGSSPPR 16 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(0.498)RT(0.498)PS(0.006)RHS(0.584)CS(0.585)GS(0.674)S(0.155)PPR 58.952 0.069841 543690000 259800 247180 101030 156390 248570 249190 242600 237470 184380 TRUE FALSE 225466.7718 245556.2583 149888.4459 191900.7398 243623.9433 258776.5005 219072.6893 186688.8885 162582.8064 1.386781153 1.510345797 0.921920646 1.180326161 1.498460684 1.591659698 1.347452994 1.148269565 1 17.31081517 1.558552049 2.98786214 1.016149925 1.346485303 0.282863812 0.188790892 0.332140939 6.351350233 0.211425124 0.054094204 36.18695573 -1.558552049 0.330335378 S(ph)RTS(ph)PAPWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRTSPAPWK 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.997)RT(0.017)S(0.986)PAPWK 109.51 0.029145 811630000 1689200 1235600 961570 1121000 1216600 994580 1322400 1599600 2207800 TRUE FALSE 1465967.94 1227483.262 1426588.468 1375540.183 1192392.04 1032842.136 1194153.852 1257537.988 1946796.399 0.753015539 0.630514451 0.732787706 0.70656602 0.612489339 0.530534234 0.613394319 0.645952493 1 20.89267058 1.238228428 24.97865195 1.000000396 0.649302298 0.736984862 0.065081163 4.279773997 321321.5059 0.094794225 0.01670137 17.3072644 -1.238228428 -0.350698098 S(ph)RTS(ph)PVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRTSPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.772)RT(0.231)S(0.994)PVS(0.003)R;S(0.865)RT(0.21)S(0.924)PVS(0.001)R 77.813 0.018347 264450000 22002.5 24160 10446.6 12254 17968.2 23150.8 16745.8 22678 19131.3 TRUE FALSE 19094.81388 24001.29137 15498.6107 15036.45799 17610.66797 24041.42626 15121.79489 17828.48618 16869.61951 1.131905427 1.422752384 0.918729121 0.891333559 1.043927989 1.425131506 0.896392173 1.056839852 1 14.04213981 4.234656294 24.99999597 1.037290843 1.277328905 0.270479522 0.166582033 122.1281499 782026.5343 0.04226361 0.093572732 17165.49353 -4.234656294 0.240038062 S(ph)RTS(ph)PVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRTSPVTR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.933)RT(0.068)S(0.999)PVTR;S(0.927)RT(0.086)S(0.987)PVTR;S(0.984)RT(0.034)S(0.982)PVTR 99.732 0.0037582 3994420000 333436 321866 194387 168219 206638 210087 303499 266816 224556 TRUE FALSE 289371.5878 319751.6411 288393.2034 206415.695 202526.3081 218169.1828 274065.7137 209759.4748 198009.2455 1.461404426 1.614831874 1.456463322 1.042454833 1.022812382 1.101813111 1.384105641 1.059341821 1 17.59520827 3.829287609 4.64192491 1.112037524 1.535493475 0.743824627 0.11350707 0.115351706 4.258506307 0.031604282 0.056386143 6749.748786 -3.829287609 0.423455951 S(ph)RTS(ph)VQTEDDQLIAGQSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 2 S(0.94)RT(0.353)S(0.707)VQTEDDQLIAGQSAR;S(0.783)RT(0.274)S(0.943)VQTEDDQLIAGQSAR 227.66 6.93E-20 2819970000 417920 360780 244582 331490 371880 483990 261730 445780 402250 TRUE FALSE 362690.8131 358410.0124 362862.6733 406759.871 364480.3156 502609.4085 236347.4649 350453.4161 354696.4632 1.022538567 1.010469654 1.023023094 1.146782991 1.027583732 1.417012743 0.666337247 0.988037526 1 18.43622542 2.222114954 24.99999945 0.897199051 1.097731549 0.329665073 0.149158516 304.240697 462490.4069 0.058866796 0.039818244 166.7688578 -2.222114954 0.200532498 S(ph)RTSPITR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRTSPITR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.516)RT(0.301)S(0.181)PIT(0.001)R 69.721 0.03221 2337900000 161760 121760 68467 80825 132650 125770 100640 144470 104200 TRUE FALSE 140383.0062 120960.1505 101577.8702 99177.55158 130010.5245 130608.4533 90879.94829 113576.2148 91881.59471 1.527868629 1.316478571 1.105530118 1.079406076 1.414978973 1.421486574 0.989098509 1.236114971 1 16.48748828 7.999999999 0.036791276 6.55E-12 3.113822537 0.257613519 0.161496206 3502.353016 12.71623484 351.772601 818.7543381 99999999.81 -7.999999999 3.113822537 S(ph)RTSPVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRTSPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.333)RT(0.333)S(0.333)PVSR 62.408 0.048346 853180000 221140 185110 111110 118490 140640 208640 161020 186450 149350 TRUE FALSE 191915.7887 183894.0002 164843.1676 145394.9655 137841.5392 216666.5158 145404.3052 146579.1185 131694.0131 1.457285598 1.396373273 1.251713451 1.104036258 1.046680376 1.64522677 1.104107178 1.113027957 1 17.00683024 8 0.043045983 2.55E-09 3.259816105 0.252726289 0.178529119 2335.859537 9.883679461 227.5754879 610.9015873 99999999.91 -8 3.259816102 S(ph)RTSPVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRTSPVTR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.382)RT(0.382)S(0.235)PVTR 80.763 0.014902 4273700000 398180 324380 160910 219440 262030 336820 289340 284550 262240 TRUE FALSE 345559.5041 322249.1264 238726.6142 269267.2059 256816.1157 349777.6834 261279.8513 223701.1969 231238.2859 1.494387068 1.393580328 1.0323836 1.164457714 1.110612434 1.512628767 1.129916053 0.967405531 1 17.81902076 8 0.050019107 5.85E-11 3.314537137 0.338642752 0.16224769 1424.939654 6.970249406 129.5681664 407.5598207 99999999.99 -8 3.314537137 S(ph)RTSVQT(ph)EDDQLIAGQSAR ddPTM_MDA-MB-175_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(0.962)RT(0.038)S(0.012)VQT(0.985)EDDQLIAGQS(0.003)AR 250.55 5.97E-24 949780000 948220 700940 505960 778260 909650 1026200 624740 904120 839270 TRUE FALSE 822910.3245 696335.479 750643.9483 954975.828 891549.7447 1065678.578 564152.811 710780.9739 740052.4567 1.111962155 0.940927191 1.014311812 1.290416401 1.204711553 1.440004108 0.762314625 0.960446746 1 19.49726801 2.217464422 24.99999762 0.912546581 1.157153159 0.399094879 0.149717356 271.1419413 321313.7487 0.064732837 0.043692989 164.992583 -2.217464422 0.244606578 S(ph)RTSVQTEDDQLIAGQSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 1 S(0.444)RT(0.278)S(0.278)VQTEDDQLIAGQSAR;S(0.584)RT(0.318)S(0.098)VQTEDDQLIAGQSAR;S(0.528)RT(0.236)S(0.236)VQTEDDQLIAGQSAR 332.03 1.61E-75 6385620000 1117680 1012460 477155 956620 1088820 1083310 804370 1109070 783760 TRUE FALSE 969975.7562 1005809.084 707908.754 1173835.192 1067154.612 1124985.637 726362.3212 871904.0113 691104.7857 1.403514744 1.455364084 1.024314646 1.698490904 1.544128523 1.627807621 1.051016194 1.261608991 1 19.39854494 2.228453523 24.99813901 1.134783801 1.453779995 0.43231888 0.190487671 217.0084887 536728.0029 0.078010767 0.05328084 169.220714 -2.228453523 0.318996194 S(ph)RYMELYDLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRYMELYDLNR 11 1 J3QKP7;J3QLW0;H3BRL0;Q9BXC9 J3QKP7 BBS2 Bardet-Biedl syndrome 2 protein 1 S(0.385)RY(0.308)MELY(0.308)DLNR;S(0.403)RY(0.299)MELY(0.299)DLNR;S(0.401)RY(0.3)MELY(0.3)DLNR 104.52 0.0039265 3157440000 1128520 1081350 724300 895130 1140350 1178100 1073060 1139770 1279430 TRUE FALSE 979383.2227 1074246.541 1074573.903 1098382.948 1117659.266 1223422.269 968994.8064 896039.0552 1128177.243 0.868111131 0.952196605 0.952486774 0.973590767 0.990677017 1.084423815 0.858902989 0.794236066 1 20.10556231 S(ph)S(ph)KASLGSLEGEAEAEASSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSKASLGSLEGEAEAEASSPK 21 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 S(0.568)S(0.614)KAS(0.517)LGS(0.301)LEGEAEAEASSPK 96.351 0.00073485 101080000 214360 106250 78146 95089 104880 93485 123480 168170 103600 TRUE FALSE 186031.7829 105552.0368 115937.667 116680.4108 102793.0932 97081.42844 111504.9286 132208.1542 91352.52602 2.036416408 1.155436432 1.269123822 1.277254345 1.125235368 1.062712031 1.220600387 1.447230416 1 16.479157 4.741052555 24.97799708 1.214252508 2.036416701 0.815750876 0.125410948 99.897558 1001266.303 0.031655191 0.208672531 55087.43556 -4.741052555 0.822164193 S(ph)SAQLSDGNVGSGATGSRPEGLAAVDIGSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSAQLSDGNVGSGATGSRPEGLAAVDIGSER 31 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;H7BZT5;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 1 S(0.5)S(0.5)AQLSDGNVGSGATGSRPEGLAAVDIGSER 88.161 0.00037327 91639000 23566 25048 18495 31751 27467 40935 26084 34695 32571 TRUE FALSE 20451.69339 24883.45804 27439.24386 38960.54983 26920.46044 42509.79594 23554.37769 27275.74425 28720.49349 0.71209408 0.866400783 0.955389011 1.356541797 0.937325832 1.480120666 0.820124407 0.949696225 1 14.80979292 4.306063477 2.434761169 1.071802828 0.739067129 0.282392518 0.199369639 0.417801351 4.729585988 0.052768904 0.198080323 20233.14887 -4.306063477 -0.332735699 S(ph)SASSSPKRPSVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSASSSPKRPSVER 14 2 S4R3M9;O75764;S4R419;O75764-2 S4R3M9 TCEA3 Transcription elongation factor A protein 3 1 S(0.228)S(0.228)AS(0.191)S(0.191)S(0.161)PKRPSVER 56.514 0.06478 69918000 93974 85451 43405 48170 97987 82240 96066 123610 30053 TRUE FALSE 81555.0978 84889.66675 64395.80318 59107.73473 96037.25041 85403.82602 86749.53411 97176.96343 26500.16858 3.077531283 3.203363273 2.43001485 2.230466367 3.624024131 3.222765386 3.2735465 3.667031897 1 14.69371392 3.241085384 24.99989896 3.083138377 2.746964819 0.005249058 0.796764843 267.011033 2643885.409 0.230398291 0.283664132 1742.149353 -3.241085384 -0.336173558 S(ph)SDEDAAGEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSDEDAAGEPK 11 0 E9PHH9;Q9BUI4 E9PHH9 POLR3C DNA-directed RNA polymerase III subunit RPC3 1 S(0.984)S(0.016)DEDAAGEPK 177.64 8.28E-06 134300000 210360 147360 135050 137180 151570 117160 205210 244790 238620 TRUE FALSE 182560.393 146391.9825 200360.6317 168328.8157 148554.0535 121667.221 185308.7658 192443.5635 210410.6154 0.867638701 0.695744282 0.952236328 0.800001537 0.706019766 0.578237085 0.88070065 0.914609575 1 17.68284797 1.845596525 2.919790002 0.960980579 0.769633935 0.359702963 0.104005673 0.288497266 4.389389349 0.072209244 0.029476173 70.08039249 -1.845596525 -0.191346644 S(ph)SDELDAWTDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSDELDAWTDFR 12 0 O43524;O43524-2 O43524 FOXO3 Forkhead box protein O3 1 S(0.982)S(0.018)DELDAWTDFR;S(0.988)S(0.012)DELDAWTDFR;S(0.92)S(0.08)DELDAWTDFR;S(0.992)S(0.008)DELDAWTDFR 258.23 3.30E-21 496556000 1055130 604677 485389 569625 625242 569492 598994 744126 761544 TRUE FALSE 915691.8971 600704.837 720124.7439 698967.0624 612800.9075 591400.7258 540903.6541 585000.4457 671515.1359 1.363620637 0.894551448 1.072387956 1.040880577 0.91256455 0.880696047 0.805497338 0.871164944 1 19.35706039 8 0.858334133 0.906050171 156.9864108 0.672458463 0.090241367 450.8221508 1.20033457 0.03122003 137478.7292 100000000 -8 156.0803606 S(ph)SDIVSSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.986)S(0.014)DIVSSVR;S(0.997)S(0.003)DIVSSVR;S(0.928)S(0.072)DIVSSVR 183.07 4.78E-05 1737490000 1737420 1253870 841110 951920 1287990 983150 1815930 1622970 1630400 TRUE FALSE 1507815.545 1245633.245 1247873.609 1168067.985 1262361.519 1020972.417 1639821.388 1275910.495 1437655.969 1.048801366 0.866433467 0.867991812 0.812480879 0.878069264 0.710164628 1.140621556 0.887493616 1 20.45528705 2.238219731 25 0.989449161 0.86258182 0.303918601 0.102231881 12.23399092 897075.6656 0.038422972 0.027734954 173.0691778 -2.238219731 -0.126867342 S(ph)SDKLNLVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSDKLNLVTK 10 1 A0A088AWN2;Q8TBZ3-4;Q8TBZ3-5;Q8TBZ3-6;Q8TBZ3;Q8TBZ3-2;Q8TBZ3-7 A0A088AWN2 WDR20 WD repeat-containing protein 20 1 S(0.965)S(0.035)DKLNLVTK 80.507 0.014413 422050000 251500 208280 188760 214920 253940 183810 325190 363160 310710 TRUE FALSE 218263.6378 206911.795 280044.9674 263720.8708 248887.0908 190881.2896 293653.1239 285501.0601 273978.2178 0.796645951 0.755212574 1.022143182 0.962561451 0.908419264 0.696702428 1.071811935 1.042057513 1 18.06370167 -2 0.074902973 1.95334853 0.481271235 0.247823527 0.111550556 731.8745419 5.231545244 119.3365033 21.66272361 0.01 2 -1.472077295 S(ph)SDPLGDTASNLGSAVDELMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SSDPLGDTASNLGSAVDELMR 21 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 S(0.5)S(0.5)DPLGDTASNLGSAVDELMR;S(0.5)S(0.5)DPLGDTASNLGSAVDELMR;S(0.5)S(0.5)DPLGDTASNLGSAVDELMR;S(0.5)S(0.5)DPLGDTASNLGSAVDELMR;S(0.5)S(0.5)DPLGDTASNLGSAVDELMR 124.2 2.64E-05 77600000 67063.8 52010 43204.6 45866.1 54227.1 59259.1 54467 65992.1 70493.2 TRUE FALSE 58201.14891 51668.34289 64098.48907 56280.69902 53148.0868 61538.83592 49184.79872 51880.20297 62159.5742 0.936318333 0.831220991 1.031192538 0.905422853 0.855026558 0.990013795 0.791266661 0.834629317 1 15.923689 2.24061437 24.9999787 0.863324558 0.921383997 0.074906925 0.077799162 121.7562942 1482148.402 0.029223906 0.021497281 174.0260928 -2.24061437 0.058059439 S(ph)SDSEEAFETPESTTPVK ddPTM_MDA-MB-175_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(0.426)S(0.426)DS(0.148)EEAFETPESTTPVK 107.98 0.0004244 84790000 164780 151510 99138 145690 159370 164060 152480 171600 194950 TRUE FALSE 143003.9055 150514.7208 147081.4684 178771.1412 156198.8488 170371.4944 137692.5131 134904.6754 171903.2331 0.831886073 0.875578185 0.855606179 1.039952176 0.908644043 0.991089529 0.800988501 0.784771019 1 17.39123715 -1.414205464 15.9634523 8.175076499 0.891659683 0 0.087356774 0 0 0 0.020365462 0.038529603 1.414205464 -7.283416816 S(ph)SDSWEVWGSASTNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSDSWEVWGSASTNR 15 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 S(0.979)S(0.021)DSWEVWGSASTNR;S(0.58)S(0.419)DSWEVWGSASTNR 198.89 8.07E-09 764760000 541092 509824 434428 492581 481214 556337 566139 594887 1293990 TRUE FALSE 469585.3212 506474.9326 644518.8339 604429.0447 471638.7829 577739.6444 511234.9269 467675.0445 1141015.976 0.411550172 0.443880667 0.564863987 0.529728818 0.41334985 0.50633791 0.448052383 0.409875983 1 20.12188756 1.234859105 24.99999782 1.000000757 0.46649914 0.909704593 0.052876284 31.15746791 210405.6213 0.09799064 0.013530421 17.17351149 -1.234859105 -0.533501618 S(ph)SEDIIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSEDIIK 7 0 O14639-3;F8W8M4;O14639-5;O14639-2;O14639;J3QSX6;A0A0A0MRL6;A0A3B3IS55;O14639-4;O14639-6 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 S(0.993)S(0.007)EDIIK;S(0.981)S(0.019)EDIIK 103.55 0.0087605 677620000 1032830 835540 891130 643540 653590 564840 809120 867780 848390 TRUE FALSE 896338.8986 830051.2827 1322083.449 789665.5929 640584.8377 586569.7603 730651.6669 682212.0001 748094.3007 1.198162983 1.109554346 1.767268441 1.055569588 0.856288889 0.784085322 0.97668391 0.911933161 1 19.51286061 3.489470078 24.4307568 0.910353421 1.346445841 0.572574261 0.178419727 308.2295769 609796.9055 0.048739153 0.068252647 3086.526983 -3.489470078 0.43609242 S(ph)SEDLAGPLPSSVSSSSTTSSKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSEDLAGPLPSSVSSSSTTSSKPK 24 1 Q9NRF2-2;Q9NRF2-3;Q9NRF2 Q9NRF2-2 SH2B1 SH2B adapter protein 1 1 S(0.974)S(0.026)EDLAGPLPSSVSSSSTTSSKPK;S(0.853)S(0.147)EDLAGPLPSSVSSSSTTSSKPK 252.44 5.64E-44 986470000 878090 707340 613090 670470 706620 521680 946960 1079890 1031410 TRUE FALSE 762048.1817 702693.437 909582.3747 822710.461 692559.6445 541749.3672 855123.965 848963.9272 909477.8848 0.83789633 0.772633891 1.00011489 0.904596445 0.761491462 0.595670743 0.940236128 0.93346297 1 19.79467903 2.037619425 24.99999463 0.954440854 0.816331423 0.302606944 0.104432786 221.9027197 147464.6179 0.045373813 0.030590957 109.048432 -2.037619425 -0.138109431 S(ph)SEHLLRPSQVCPQRPLSQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSEHLLRPSQVCPQRPLSQER 21 2 Q0VF96 Q0VF96 CGNL1 Cingulin-like protein 1 1 S(0.863)S(0.137)EHLLRPSQVCPQRPLSQER 125.82 1.17E-05 347610000 123280 127300 52132 72055 122570 139420 138560 158640 64242 TRUE FALSE 106988.2356 126463.7579 77343.20957 88416.18904 120131.0968 144783.5776 125122.4725 124716.0705 56647.38394 1.888670371 2.232473048 1.365344773 1.560816809 2.120682165 2.555874032 2.208795249 2.201621008 1 15.78972171 3.217776789 24.77115929 2.081701926 1.767123739 0.062595726 0.45488504 529.5278092 631114.4661 0.139652182 0.158525874 1651.11297 -3.217776789 -0.314578186 S(ph)SEMLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSEMLVK 7 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 S(0.995)S(0.005)EMLVK 98.033 0.021588 0 101940 90036 62937 73554 75422 78008 96024 97268 98873 TRUE FALSE 88468.37072 89444.54759 93373.54371 90255.5599 73921.24976 81009.01824 86711.60726 76467.99514 87184.34658 1.014727691 1.02592439 1.070989775 1.03522666 0.847872957 0.9291693 0.994577704 0.877083997 1 16.41178151 3.318068595 11.00333301 0.928032902 1.03867917 0.554410602 0.047631021 0.328770526 43.56440126 0.013209779 0.017051891 2080.025191 -3.318068595 0.110646268 S(ph)SESDHFSYVQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSESDHFSYVQLR 13 0 Q96JQ2 Q96JQ2 CLMN Calmin 1 S(0.499)S(0.499)ES(0.002)DHFSYVQLR 79.471 0.013152 99643000 127820 119520 62157 98993 148090 149870 131910 157060 166470 TRUE FALSE 110928.2631 118734.8653 92216.3331 121470.8737 145143.2987 155635.5959 119117.3885 123473.9412 146790.1062 0.75569305 0.808875123 0.628218996 0.827514039 0.988781209 1.06025944 0.811481043 0.841159833 1 17.16339521 3.472332082 7.285795731 0.923204188 0.736661663 0.55479634 0.085341547 0.111553093 37.89476483 0.025976599 0.034994396 2967.099306 -3.472332082 -0.186542524 S(ph)SFSHYSGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSFSHYSGLK 10 0 Q8NC51;Q8NC51-3 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 S(0.488)S(0.488)FS(0.024)HYSGLK 173.72 2.14E-06 753010000 599710 580480 197150 585750 746530 600440 861320 832060 1601500 TRUE FALSE 520456.804 576666.7887 292492.3994 718753.4901 731675.5136 623539.3153 777789.319 654130.4441 1412172.494 0.368550447 0.408354355 0.207122289 0.508970039 0.518120496 0.441546141 0.550775009 0.4632086 1 20.42948489 0.096520808 1.320197183 10 0.417155431 0.768934492 0.097344603 11.92437709 1.478033684 300.2598363 0.029330995 1.248880281 -0.096520808 -9.582844569 S(ph)SFSQHAR ddPTM_MDA-MB-175_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(0.841)S(0.159)FSQHAR;S(0.82)S(0.18)FSQHAR 149.95 0.0003201 3020700000 2423400 2368500 901630 1371600 2405900 2500400 2434800 2541200 2415200 TRUE FALSE 2103141.55 2352941.168 1337661.284 1683042.744 2358027.297 2596592.006 2198673.471 1997784.156 2129677.807 0.987539778 1.104834337 0.628105002 0.790280454 1.107222552 1.219241707 1.032397231 0.93806873 1 21.02220376 3.232765427 24.99994675 1.05019001 0.876086999 0.2873833 0.141752109 210.6374665 908670.8448 0.046236892 0.053835414 1709.091944 -3.232765427 -0.17410301 MGLAMGGGGGAS(ph)FDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 MGLAMGGGGGASFDR 15 0 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 1 MGLAMGGGGGAS(1)FDR;MGLAMGGGGGAS(1)FDR 94.487 0.0038748 0 644330 353910 182049 209655 327240 239296 434410 375160 296000 TRUE FALSE 559180.158 351585.1419 270088.5053 257260.3721 320728.5642 248501.872 392280.9851 294934.9535 261007.2172 2.142393471 1.347032261 1.034793245 0.985644669 1.228811094 0.952088125 1.50295072 1.129987732 1 17.99373017 4.716090489 2.92627296 1.134864967 2.28760399 0.799706394 0.160080074 0.157028846 2.000462809 0.039662308 0.415711556 52010.43539 -4.716090489 1.152739023 up S(ph)SGFISELPSEEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSGFISELPSEEGK 14 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 S(0.539)S(0.461)GFISELPSEEGK 361.49 1.25E-82 297660000 374960 385640 307910 337080 458300 394500 518160 602810 549520 TRUE FALSE 325408.086 383106.7054 456816.3059 413619.1659 449180.7266 409676.6703 467908.923 473903.7726 484556.3716 0.67155878 0.790633924 0.942751623 0.853603812 0.926993747 0.845467513 0.965643938 0.978015769 1 18.88630499 5.787858063 0.519434129 0.95946278 1.87E-35 0.758290828 0.049294683 6.40522887 0.594666801 0.031963716 4.70963469 613561.4464 -5.787858063 -0.95946278 S(ph)SGPYGGGGQYFAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSGPYGGGGQYFAK 14 0 F8W6I7;P09651-2;P09651;P09651-3;Q32P51;H0YH80 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 1 S(0.987)S(0.013)GPYGGGGQYFAK;S(0.963)S(0.037)GPYGGGGQYFAK 227.74 2.01E-12 235800000 390850 351150 279160 369400 364430 286970 388740 417560 1081740 TRUE FALSE 339198.1822 348843.2725 414162.7097 453277.9159 357178.556 298009.9216 351040.0546 328268.0435 953857.9295 0.355606607 0.365718271 0.43419748 0.475204852 0.374456767 0.312425899 0.36802132 0.344147732 1 19.86341488 1.236624179 24.9999895 1.000000785 0.37873727 0.948017208 0.045720383 11.45257991 147815.7931 0.077523136 0.012257263 17.24345066 -1.236624179 -0.621263515 S(ph)SGPYGGGGQYFAKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.982)S(0.018)GPYGGGGQYFAKPR 197.67 2.59E-11 319350000 309750 216670 166800 181660 267290 214120 286130 319030 239110 TRUE FALSE 268815.7527 215246.6805 247465.0379 222908.6795 261971.4519 222357.335 258381.1566 250807.9172 210842.6882 1.274958857 1.020887574 1.173695138 1.057227459 1.242497211 1.054612502 1.225468897 1.189549988 1 17.68580747 2.540084304 0.003056929 0.001141751 2.277968183 0.018887634 0.097663305 486495.5689 1279.572925 478028.5328 474995.2754 346.8041644 -2.540084304 2.276826432 S(ph)SGREEDDEELLR ddPTM_MDA-MB-175_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(0.981)S(0.019)GREEDDEELLR;S(0.987)S(0.013)GREEDDEELLR 233.49 7.43E-17 2119700000 352500 387960 293750 334710 460590 441240 432060 511400 458550 TRUE FALSE 305916.2319 385411.4652 435808.4825 410711.0212 451425.1601 458214.7883 390158.8877 402041.0897 404340.7414 0.756580281 0.953184841 1.077824809 1.015754732 1.116447377 1.133239225 0.964925984 0.99431259 1 18.62521205 4.669242926 2.656614201 1.039314838 0.722143285 0.736133614 0.054229929 0.219560724 2.255797369 0.015090637 0.142931797 46692.04824 -4.669242926 -0.317171552 S(ph)SIPGCGVTFEIVSNIPEDAQGVEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSIPGCGVTFEIVSNIPEDAQGVEER 26 0 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 S(0.343)S(0.343)IPGCGVT(0.313)FEIVS(0.001)NIPEDAQGVEER 84.933 0.0088229 26935000 5905.9 9242.3 4971.5 6293.1 10599 6205.8 9560.4 11475 9392.4 TRUE FALSE 5125.420351 9181.586723 7375.734029 7722.044539 10388.10064 6444.541142 8633.233879 9021.160549 8282.041172 0.618859559 1.108613992 0.890569592 0.932384225 1.25429232 0.7781344 1.042404125 1.089243625 1 13.01577066 4.747221858 24.68577204 1.013406957 0.61885932 0.476525885 0.129472783 812.8711989 2316738.176 0.029786369 0.337106251 55875.5561 -4.747221858 -0.394547637 S(ph)SITEPEGPGGPNIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSITEPEGPGGPNIQK 16 0 Q96KQ4;A0A3B3ISJ2;H0YJL1 Q96KQ4 PPP1R13B Apoptosis-stimulating of p53 protein 1 1 S(0.749)S(0.251)ITEPEGPGGPNIQK 219.41 1.31E-14 230130000 478130 372050 266710 527660 338200 268970 222360 374280 862190 TRUE FALSE 414943.9091 369605.9791 395691.8481 647473.2678 331470.4817 279317.4499 200795.5614 294243.1347 760262.8804 0.545790042 0.486155498 0.520467141 0.851643931 0.435994562 0.36739588 0.264113331 0.387028148 1 19.53613883 1.232644487 24.98451259 1.000000858 0.475441703 0.525994858 0.15431777 173.8787069 734234.3139 0.363017082 0.041235683 17.08616069 -1.232644487 -0.524559155 S(ph)SITEPEGPNGPNIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSITEPEGPNGPNIQK 16 0 Q13625-2;Q13625;Q13625-3 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 S(0.5)S(0.5)ITEPEGPNGPNIQK 244.67 4.76E-20 242830000 182800 135820 116990 202190 156380 129170 145420 193750 359440 TRUE FALSE 158642.5168 134927.7895 173566.7553 248100.3298 153268.344 134139.2535 131317.1908 152318.0703 316947.4127 0.500532614 0.425710336 0.547620042 0.782780739 0.483576574 0.423222428 0.414318545 0.480578368 1 18.27388397 1.236797976 24.99652381 1.000000618 0.50563355 0.680654498 0.106056321 29.23097744 414408.8362 0.172811654 0.027649426 17.25035256 -1.236797976 -0.494367068 S(ph)SLETLEDIEENAPLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSLETLEDIEENAPLRR 17 1 Q8TDN4-2;Q8TDN4;V9GYB4 Q8TDN4-2 CABLES1 CDK5 and ABL1 enzyme substrate 1 1 S(0.932)S(0.054)LET(0.014)LEDIEENAPLRR;S(0.959)S(0.041)LETLEDIEENAPLRR 74.364 0.014887 58114000 16481.4 11968.5 7152 8814 13292.6 11943.3 10145 12275.5 13482.4 TRUE FALSE 14303.34123 11889.87814 10610.73112 10815.35341 13028.10327 12402.76648 9161.139461 9650.479853 11888.52603 1.203121497 1.000113732 0.892518643 0.909730389 1.095855216 1.04325519 0.770586651 0.81174738 1 13.53728224 7.345474801 1.009320034 0.916712568 69.31405479 0.411186219 0.099656904 433.1058504 2.516975612 0.034558338 67673.9488 22155155.44 -7.345474801 68.39734222 S(ph)SLGSHQLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSLGSHQLPR 10 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 S(0.5)S(0.5)LGSHQLPR;S(0.5)S(0.5)LGSHQLPR;S(0.5)S(0.5)LGSHQLPR;S(0.499)S(0.499)LGS(0.001)HQLPR 171.32 2.61E-06 839830000 445376 427068 246923 348701 485864 500917 480372 560694 526410 TRUE FALSE 386518.4332 424262.5622 366335.7887 427878.8916 476196.257 520187.6011 433785.5974 440793.9514 464178.4095 0.832693691 0.914007531 0.789213331 0.921798349 1.025890578 1.120663069 0.934523426 0.949621832 1 18.82431989 3.458345126 4.764793006 0.998510206 0.851872517 0.614340965 0.05814861 0.142095708 8.409051605 0.017869636 0.024306673 2873.062847 -3.458345126 -0.146637689 S(ph)SLPSLDDQEQASSGWGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSLPSLDDQEQASSGWGSR 19 0 R4GMM2;Q9NPB6-2;Q9NPB6 R4GMM2 PARD6A Partitioning defective 6 homolog alpha 1 S(0.5)S(0.5)LPS(0.001)LDDQEQASSGWGSR 217.67 3.72E-19 120330000 68861 67793 39180 67472 89529 87182 58089 97989 83690 TRUE FALSE 59760.84438 67347.66332 58127.57905 82792.54884 87747.54806 90535.94795 52455.53772 77034.8149 73796.26354 0.809808539 0.912616169 0.787676452 1.121907057 1.189051367 1.226836477 0.710815632 1.043885032 1 16.17126015 3.743037496 24.77233451 1.040387941 0.84429196 0.328239629 0.142529996 457.387496 2530895.287 0.040085456 0.066457397 5533.978868 -3.743037496 -0.196095981 S(ph)SLQVDWHEEEWEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSLQVDWHEEEWEK 14 0 Q96PE3-2;Q96PE3-4;Q96PE3-3;Q96PE3 Q96PE3-2 INPP4A "Type I inositol 3,4-bisphosphate 4-phosphatase" 1 S(0.5)S(0.5)LQVDWHEEEWEK 163.45 2.76E-06 125830000 107270 113060 91067 86636 129130 113340 142360 160020 180300 TRUE FALSE 93093.99771 112317.3014 135107.3058 106308.0279 126560.5656 117700.2631 128553.9491 125800.9683 158985.1394 0.585551568 0.70646415 0.849810909 0.668666445 0.796052802 0.74032242 0.808590976 0.791275013 1 17.2785324 -1.19768787 0.704995174 10 0.723191775 0.5801651 0.071979647 64.07842643 1.187895759 887.7706056 0.029553347 0.063432544 1.19768787 -9.276808225 S(ph)SLSSHSHQSQIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSLSSHSHQSQIYR 14 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 S(0.457)S(0.457)LS(0.075)S(0.01)HSHQSQIYR 112.3 0.0010056 108270000 44984 37407 25842 43552 71183 66754 41943 47834 56342 TRUE FALSE 39039.25043 37161.27095 38339.27764 53441.14725 69766.59757 69322.06958 37875.37432 37605.07134 49681.31295 0.785793453 0.747992932 0.771704195 1.075679045 1.404282484 1.395334895 0.762366614 0.756925876 1 15.60041568 3.744047915 22.200956 1.042468709 0.766446341 0.292756375 0.215784013 160.6976862 650149.2204 0.068740074 0.114398128 5546.869068 -3.744047915 -0.276022368 S(ph)SLVTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.75)S(0.25)LVTSK;S(0.551)S(0.449)LVTSK 201.21 0.00035305 3721130000 5969910 5341070 3103040 4080640 3989910 3827210 7406590 6717410 5704160 TRUE FALSE 5180971.268 5305984.159 4603680.523 5007211.681 3910518.597 3974445.245 6688300.042 5280944.146 5029820.703 1.030050885 1.054905229 0.915277262 0.995505004 0.777466798 0.790176326 1.329729316 1.049926918 1 22.26207554 2.252409246 24.99981847 1.119054288 0.928786339 0.36783763 0.123036285 263.2716304 475262.9546 0.047696651 0.036750349 178.817182 -2.252409246 -0.19026795 S(ph)SLYGIAK ddPTM_MDA-MB-175_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(0.546)S(0.454)LYGIAK;S(0.689)S(0.311)LYGIAK 178.32 0.00026248 452470000 1459050 1505260 929780 1286030 1789690 1462510 2072130 2188920 2222170 TRUE FALSE 1266232.846 1495371.848 1379424.718 1578042.767 1754078.67 1518773.706 1871175.152 1720836.492 1959467.594 0.646212701 0.76315212 0.703979347 0.805342621 0.89518126 0.775095087 0.954940596 0.878216357 1 20.90203028 5.670723148 0.111931236 1.242728475 4.08E-13 0.760096905 0.053798428 55.14487881 1.144933616 3.167351752 12.14117192 468514.6201 -5.670723148 -1.242728475 S(ph)SMEMEGIFNHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSMEMEGIFNHK 12 0 O75962-5;O75962;E7EPJ7;O75962-4;O75962-2;E7EWP2 O75962-5 TRIO Triple functional domain protein 1 S(0.5)S(0.5)MEMEGIFNHK;S(0.5)S(0.5)MEMEGIFNHK;S(0.5)S(0.5)MEMEGIFNHK 260.97 1.57E-21 536620000 782790 637180 459120 564630 761920 706170 728780 845710 912510 TRUE FALSE 679342.3182 632994.3226 681151.9677 692837.8713 746759.2827 733336.8169 658103.0278 664861.4978 804634.1073 0.844287251 0.78668592 0.846536285 0.861059536 0.928073115 0.911391663 0.817891041 0.826290474 1 19.61797337 3.8248098 2.629267967 0.882784387 0.816200663 0.248779479 0.053924671 0.462183574 6.225676965 0.015779887 0.030934712 6680.512793 -3.8248098 -0.066583724 S(ph)SPAAFINPPIGTVTPALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPAAFINPPIGTVTPALK 19 0 F6VRR5;Q9BY77-2;Q9BY77;Q6R954;F8WEE2;Q8WUT1;F8WCX5 F6VRR5 POLDIP3;PDIP46 Polymerase delta-interacting protein 3 1 S(0.5)S(0.5)PAAFINPPIGTVTPALK;S(0.5)S(0.5)PAAFINPPIGTVTPALK 223.29 8.27E-26 148280000 401040 361130 217700 280500 380210 295570 402480 456280 527700 TRUE FALSE 348041.5479 358757.7133 322980.4482 344191.8122 372644.5649 306940.7692 363447.5515 358708.0728 465315.9072 0.7479683 0.770998171 0.694110051 0.739694919 0.800842093 0.659639536 0.781076997 0.77089149 1 18.82785098 1.067005945 2.099236654 1.190417513 0.740142528 0.791777043 0.041147213 0.543259283 1.569890059 0.561163538 0.010386774 11.66825588 -1.067005945 -0.450274984 S(ph)SPAFGDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSPAFGDRR 9 1 P13716;P13716-2 P13716 ALAD Delta-aminolevulinic acid dehydratase 1 S(0.5)S(0.5)PAFGDRR;S(0.5)S(0.5)PAFGDRR;S(0.5)S(0.5)PAFGDRR 140.24 6.71E-05 669050000 792900 605780 328933 390160 572220 662750 515340 573600 428380 TRUE FALSE 688116.256 601800.5913 488006.099 478751.7912 560833.9415 688246.4214 465362.4061 450940.1038 377737.4044 1.821678891 1.593171829 1.291918919 1.267419603 1.484719106 1.822023483 1.231973325 1.193792562 1 18.52702412 2.02248137 22.49364374 1.141381796 1.522251327 0.504388296 0.190521659 66.65991719 66695.46605 0.082444893 0.055575618 105.312851 -2.02248137 0.380869531 S(ph)SPAPHSGPCPSR ddPTM_MDA-MB-175_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 119.45 0.00022418 344620000 223730 235210 134838 189613 282120 300060 257950 292740 269130 TRUE FALSE 194163.5136 233664.89 200046.1078 232667.5297 276506.364 311603.5024 232934.0487 230139.8291 237313.758 0.818172175 0.984624288 0.842960431 0.980421581 1.165151006 1.313044406 0.981544647 0.969770278 1 17.85643622 3.472624951 6.582260913 1.075137016 0.894766387 0.420843534 0.108969047 0.166778282 35.61603203 0.034403192 0.046604672 2969.100864 -3.472624951 -0.18037063 S(ph)SPATSLFVELDEEEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPATSLFVELDEEEVK 17 0 A0A087WTL4;A0A087WX97;Q9BXK5-4;Q9BXK5 A0A087WTL4 BCL2L13 Bcl-2-like protein 13 1 S(0.5)S(0.5)PATSLFVELDEEEVK;S(0.499)S(0.499)PAT(0.001)SLFVELDEEEVK 140.22 7.02E-07 51562000 152049 122039 119698 156064 138525 138764 109921 194689 258704 TRUE FALSE 131955.3394 121237.3178 177584.3532 191500.7165 135768.6235 144102.3409 99260.87834 153056.2724 228120.3078 0.578446262 0.531462187 0.778467971 0.839472462 0.595162372 0.631694487 0.435125129 0.670945405 1 17.79943536 1.250422965 5.251395319 1.017328528 0.629860133 0.507283221 0.114408664 0.132813423 10.04495683 0.181842533 0.030140146 17.80012143 -1.250422965 -0.387468395 S(ph)SPELTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SSPELTR 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.888)S(0.112)PELTR;S(0.763)S(0.237)PELTR;S(0.705)S(0.295)PELTR;S(0.5)S(0.5)PELTR;S(0.591)S(0.409)PELTR 182.73 0.00068499 6531120000 3805340 3374240 2200430 2555390 2907580 2910300 2891030 3510420 3775470 TRUE FALSE 3302454.677 3352074.395 3264565.308 3135630.356 2849724.847 3022261.124 2610658.356 2759744.001 3329138.238 0.991984845 1.006889518 0.98060371 0.941874483 0.855994748 0.907820856 0.784184425 0.828966478 1 21.66671735 3.468270106 1.946485459 0.862682174 0.998022262 0.468414069 0.0565926 0.271562081 2.070509119 0.018178094 0.028432917 2939.477268 -3.468270106 0.135340088 S(ph)SPEQPRPSTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPEQPRPSTSK 12 1 P29590-2;P29590-5;P29590-9;P29590-3;P29590-8;P29590;P29590-4;H3BVD2;H3BRN3;P29590-12;P29590-13;P29590-11;H3BT57;H3BUJ5 P29590-2;P29590-12 PML Protein PML 1 S(0.609)S(0.391)PEQPRPSTSK 164.64 0.00014928 274090000 348310 279500 184800 213200 270220 230020 343260 371340 317710 TRUE FALSE 302279.951 277663.9461 274169.8981 261610.3186 264843.1507 238869.0182 309970.698 291931.8308 280150.6857 1.07899058 0.991123564 0.978651533 0.933820019 0.945359637 0.852644774 1.10644276 1.042052887 1 18.0958435 2.213085617 24.99998466 1.050320016 0.963214686 0.30609252 0.061082892 282.2723481 277006.9312 0.02546965 0.017178884 163.3373921 -2.213085617 -0.08710533 S(ph)SPGAGPSDHHSASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPGAGPSDHHSASR 15 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 S(0.5)S(0.5)PGAGPSDHHSASR;S(0.5)S(0.5)PGAGPSDHHSASR 225.01 6.80E-13 1700940000 492800 610810 105003 287547 733130 738920 536750 598980 589240 TRUE FALSE 427675.2314 606797.5489 155782.802 352838.9412 718542.1473 767346.7305 484696.0676 470892.7883 519580.7185 0.823116055 1.167860021 0.299824063 0.679083978 1.38292689 1.476857596 0.932859997 0.906293809 1 18.98698837 3.260719366 24.9984792 1.111934902 0.741238188 0.337523766 0.275057716 325.0088289 366657.6305 0.085409952 0.110173832 1822.717513 -3.260719366 -0.370696714 S(ph)SPGAVAGLSNAPGTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPGAVAGLSNAPGTPR 17 0 V9GYB2;Q9BWG4-2;Q9BWG4;U3KPY3 V9GYB2 SSBP4 Single-stranded DNA-binding protein 4 1 S(0.857)S(0.143)PGAVAGLSNAPGTPR;S(0.839)S(0.161)PGAVAGLSNAPGTPR 260.58 3.14E-27 1406440000 1205350 1321730 764800 956940 1498250 1268650 1233520 1551210 1343690 TRUE FALSE 1046059.944 1313047.469 1134659.838 1174227.853 1468437.756 1317455.786 1113893.42 1219495.813 1184840.499 0.882869842 1.1082061 0.95764775 0.991042975 1.239354797 1.1119267 0.940120988 1.029248928 1 20.17626143 4.754112925 23.41604751 1.04424752 0.882869551 0.254531573 0.088250532 1852.85336 2789600.9 0.022206104 0.480614009 56769.21969 -4.754112925 -0.161377969 S(ph)SPGGQDEGGFMAQGK ddPTM_MDA-MB-175_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(0.5)S(0.5)PGGQDEGGFMAQGK 190.11 3.56E-09 397970000 770090 680090 523592 596560 740770 610690 797880 926300 892920 TRUE FALSE 668320.6553 675622.444 776802.8425 732018.0658 726030.1263 634183.6395 720501.7204 728217.9535 787360.0148 0.848812034 0.858085795 0.986591683 0.929712015 0.92210693 0.805455735 0.915085484 0.924885617 1 19.58666392 1.241455841 2.026844832 1.031961012 0.89647529 0.30762344 0.049707267 1.036296995 4.19035188 0.264798356 0.014030914 17.43636056 -1.241455841 -0.135485722 S(ph)SPGPDTLVVLEFNPASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 246.69 2.73E-24 260918000 368790 332033 241023 312364 356760 277231 356310 478180 520330 TRUE FALSE 320053.4671 329851.8534 357582.529 383291.0204 349661.174 287896.256 321755.111 375924.9282 458817.1802 0.697562081 0.718917834 0.779357322 0.835389425 0.762092592 0.627474882 0.701270844 0.8193349 1 18.80755989 1.312275036 2.649857936 1.035331136 0.734972367 0.702735101 0.055315613 0.249496103 2.237597026 0.155113775 0.016012339 20.52461578 -1.312275036 -0.300358769 S(ph)SPGQTPEEGAQALAEFAALHGPALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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)PGQTPEEGAQALAEFAALHGPALR;S(0.5)S(0.5)PGQTPEEGAQALAEFAALHGPALR 309.19 6.82E-82 14811042000 1046852 972165 587404 671918 1001908 986955 977104 1130821 1001108 TRUE FALSE 908507.8558 965778.7841 871474.5391 824487.2515 981971.991 1024923.797 882344.6045 889003.7292 882758.1527 1.029169601 1.094046859 0.987217775 0.93398996 1.112390736 1.161047105 0.999531527 1.007075071 1 19.75165871 S(ph)SPIAQPASSFQVETASQGHSISHHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPIAQPASSFQVETASQGHSISHHK 26 0 Q8IZH2-2;Q8IZH2;H7C5E4 Q8IZH2-2 XRN1 5-3 exoribonuclease 1 1 S(0.5)S(0.5)PIAQPASSFQVETASQGHSISHHK;S(0.5)S(0.5)PIAQPASSFQVETASQGHSISHHK 240.75 7.27E-45 313680000 158988 197169 27296 138190 249670 219980 207969 250240 429910 TRUE FALSE 137977.333 195873.7839 40496.4369 169568.1516 244702.0555 228442.7729 187800.1984 196728.1234 379086.5296 0.363973189 0.516699404 0.106826367 0.447307246 0.645504486 0.602613797 0.49540193 0.518953083 1 18.53216767 -0.033467496 1.177610631 10 0.442261717 0.573198332 0.14671433 22.10336217 2.105783662 497.5108994 0.047297701 0.925832676 0.033467496 -9.557738283 S(ph)SPIMR ddPTM_MDA-MB-175_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(0.631)S(0.369)PIMR;S(0.843)S(0.157)PIMR;S(0.834)S(0.166)PIMR 150.02 0.011082 1895500000 1537550 1511290 956870 1100560 1347420 1508380 1464220 1630370 1484460 TRUE FALSE 1334358.872 1501362.236 1419615.533 1350458.969 1320608.978 1566408.355 1322220.17 1281728.063 1308968.83 1.01939698 1.146980892 1.08452967 1.031696812 1.008892609 1.196673533 1.010123495 0.97918914 1 20.31999931 2.021930011 24.99775816 0.990072488 1.080975367 0.333477453 0.057143706 240.9561295 274661.881 0.022621615 0.015250378 105.1792358 -2.021930011 0.090902878 S(ph)SPINPAQSGSPNHVDSAYFPGSSTSSSSDNDEGSGGATNHISGNK ddPTM_MDA-MB-175_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(0.5)S(0.5)PINPAQSGSPNHVDSAYFPGSSTSSSSDNDEGSGGATNHISGNK;S(0.5)S(0.5)PINPAQSGSPNHVDSAYFPGSSTSSSSDNDEGSGGATNHISGNK 383.28 1.54E-205 812800000 82000 97538 10824.4 46083 138353 103114 110280 130181 116772 TRUE FALSE 71163.49224 96897.26646 16059.11605 56546.84948 135600.046 107080.8623 99585.06257 102342.8062 102967.3472 0.691126791 0.941048489 0.155963191 0.549172636 1.316922789 1.039949705 0.967151872 0.993934573 1 16.65182738 3.258353108 24.9643676 1.046469537 0.579210157 0.555069167 0.212887776 189.5612084 239092.9759 0.062480595 0.0805504 1812.813423 -3.258353108 -0.46725938 S(ph)SPKEELHPAAPSQLAPSFSSSSSSSSGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPKEELHPAAPSQLAPSFSSSSSSSSGPR 30 1 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 S(0.5)S(0.5)PKEELHPAAPSQLAPSFSSSSSSSSGPR;S(0.5)S(0.5)PKEELHPAAPS(0.001)QLAPSFSSSSSSSSGPR 211.73 2.39E-26 981380000 565340 473180 301780 362800 577170 401810 618810 692410 547770 TRUE FALSE 490628.8866 470071.6494 447721.8174 445179.2851 565685.4462 417267.8907 558797.9014 544343.5098 483013.2546 1.015766921 0.973206522 0.926934847 0.92167095 1.171159261 0.863884969 1.156899725 1.12697427 1 18.88170325 2.582573314 1.02439283 1.095619345 0.969859138 0.135726631 0.097149641 0.892709218 2.009187448 0.072834227 0.044665803 382.4488101 -2.582573314 -0.125760207 S(ph)SPLKLEFDFTEDTGNIEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPLKLEFDFTEDTGNIEAR 20 1 O75410-3;E7ET87;E7EVI4;O75410-2;O75410;O75410-9;O75410-7;H0YAY0;E5RFM9;R4GMT7 O75410-3 TACC1 Transforming acidic coiled-coil-containing protein 1 1 S(0.5)S(0.5)PLKLEFDFTEDTGNIEAR 75.646 0.0074037 51260000 34393 26979 26169 33287 32680 28339 32561 39351 65124 TRUE FALSE 29847.87791 26801.77317 38824.41593 40845.32211 32029.73194 29429.21967 29403.23923 30936.09488 57425.11491 0.519770452 0.466725634 0.676087736 0.711279763 0.557765222 0.512479944 0.512027521 0.538720644 1 15.80939422 1.236709529 24.99986903 1.00000055 0.562032206 0.767574232 0.075770448 25.31452537 341787.921 0.126144132 0.020063679 17.24683979 -1.236709529 -0.437968345 S(ph)SPLLNYNTGVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPLLNYNTGVYR 13 0 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 S(0.595)S(0.405)PLLNYNTGVYR 111.66 0.0010091 119980000 284340 265500 197860 303050 293250 264430 277860 369530 283180 TRUE FALSE 246763.7486 263755.913 293545.7578 371862.1343 287414.8987 274602.7932 250913.18 290508.8852 249702.783 0.988229869 1.056279429 1.175580641 1.489219022 1.151028015 1.099718593 1.004847351 1.163418692 1 17.92985237 1.233677774 24.08137878 0.99999964 1.144037181 0.091961504 0.138998523 267.3773428 1318404.098 0.282074378 0.035774331 17.12686105 -1.233677774 0.144037541 S(ph)SPLPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPLPAK 7 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 S(0.929)S(0.071)PLPAK 102.95 0.0089018 656680000 1307400 922670 716940 986030 841350 777050 1157400 1363100 2266200 TRUE FALSE 1134623.777 916608.92 1063654.582 1209923.182 824608.7811 806943.6163 1045155.526 1071611.673 1998292.418 0.567796669 0.458696091 0.532281748 0.605478543 0.412656713 0.403816583 0.523024317 0.536263694 1 20.93033628 1.224495356 3.899782328 1.067424441 0.499126643 0.858200473 0.063359326 0.099764179 2.507906217 0.167065295 0.016491727 16.76854403 -1.224495356 -0.568297798 S(ph)SPNPFITGLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSPNPFITGLTR 12 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 S(0.58)S(0.42)PNPFITGLTR;S(0.58)S(0.42)PNPFITGLTR;S(0.625)S(0.375)PNPFITGLTR 155.17 7.56E-05 790770000 887220 880550 509925 594340 890810 969370 879370 995130 969340 TRUE FALSE 769971.6291 874765.6091 756526.4356 729293.9809 873084.6238 1006662.291 794088.8327 782329.1936 854745.7295 0.90081951 1.023422029 0.885089459 0.85322916 1.02145538 1.177733046 0.929035157 0.915277101 1 19.70513578 3.215184394 24.99722323 0.999499042 0.921156531 0.23434866 0.082391337 447.0192724 478015.9133 0.02727201 0.030941564 1641.286486 -3.215184394 -0.07834251 S(ph)SPNVANQPPS(ph)PGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPNVANQPPSPGGK 15 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 2 S(0.768)S(0.232)PNVANQPPS(1)PGGK 197.41 1.23E-08 503150000 653640 594790 533400 613390 671920 558230 787770 926210 1064400 TRUE FALSE 567259.8179 590882.7853 791354.0241 752669.5746 658550.1066 579705.4693 711372.1867 728147.1993 938567.8446 0.60438872 0.629557883 0.843150582 0.801934116 0.701654239 0.617648977 0.757933687 0.775806676 1 19.84010151 1.048599102 1.647309454 1.242415948 0.709044935 0.582167602 0.077726532 1.36795343 2.267779742 1.373670862 0.023176977 11.18405006 -1.048599102 -0.533371014 S(ph)SPPAPPLPPGSGSPGTPQALPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPPAPPLPPGSGSPGTPQALPR 23 0 Q9Y3L3;A0A2R8Y5V0 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 S(0.367)S(0.367)PPAPPLPPGS(0.209)GS(0.057)PGTPQALPR 234.38 4.79E-37 631370000 143910 139960 77203 88081 138290 151430 126390 143650 150450 TRUE FALSE 124891.9289 139040.5935 114538.629 108081.1373 135538.2996 157255.6101 114132.7173 112931.5654 132663.9724 0.941415568 1.04806596 0.863374034 0.814698485 1.021666223 1.185367868 0.860314335 0.851260243 1 17.01741711 S(ph)SPPAS(ph)PTIIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPPASPTIIPR 12 0 G3V4P9;G3V347;A0A087WW79;J3KPI6;P80192;P80192-4 G3V4P9 MAP3K9 Mitogen-activated protein kinase kinase kinase 9 2 S(0.569)S(0.431)PPAS(0.99)PT(0.01)IIPR 101.39 0.003944 46760000 121630 105870 66234 81269 101040 94593 112870 134180 120240 TRUE FALSE 105556.2873 105174.533 98264.98394 99722.36857 99029.50168 98232.05392 101923.8848 105486.6512 106025.3642 0.995575805 0.991975211 0.92680638 0.940552002 0.934017086 0.926495794 0.961316055 0.994919018 1 16.69404991 1.765046726 3.526778916 0.998771039 0.95133439 0.363450102 0.024193062 0.238841453 5.964186466 0.017691269 0.007119833 58.21658502 -1.765046726 -0.047436649 S(ph)SPPLPPPAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSPPLPPPAEER 12 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 S(0.611)S(0.389)PPLPPPAEER;S(0.638)S(0.362)PPLPPPAEER;S(0.601)S(0.399)PPLPPPAEER 142.47 6.44E-05 1927490000 827990 730050 419765 471834 724870 748800 728350 791570 761460 TRUE FALSE 718569.0236 725254.2535 622764.758 578971.1212 710446.5052 777606.8205 657714.7291 622298.9155 671441.0663 1.070189269 1.080145809 0.92750472 0.862281368 1.058092126 1.158116266 0.9795569 0.926810925 1 19.35690125 2.010849539 24.99917192 0.956679506 1.022278569 0.094631881 0.083485546 511.7472066 1179147.873 0.037024806 0.024937773 102.5296651 -2.010849539 0.065599062 S(ph)SPPSAGNSPSSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPPSAGNSPSSLK 14 0 P57682;P57682-2 P57682 KLF3 Krueppel-like factor 3 1 S(0.599)S(0.401)PPSAGNSPSSLK;S(0.606)S(0.394)PPSAGNSPSSLK 210.34 5.65E-09 162616000 248104 224890 176768 237220 258070 189958 276070 299830 318660 TRUE FALSE 215316.4278 223412.6828 262253.5961 291084.4267 252934.9119 197265.8072 249296.7739 235713.6878 280988.3778 0.766282326 0.795095813 0.933325421 1.035930486 0.900161472 0.702042585 0.887213827 0.838873442 1 18.10015093 4.350367446 5.824189949 0.891142585 0.774080788 0.22882541 0.090271656 0.329240407 15.22027743 0.023729091 0.064793969 22406.16065 -4.350367446 -0.117061797 S(ph)SPPSAGNSPSSLKFPSSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPPSAGNSPSSLKFPSSHR 20 1 P57682;P57682-2 P57682 KLF3 Krueppel-like factor 3 1 S(0.498)S(0.498)PPS(0.005)AGNSPSSLKFPSSHR 84.602 0.0016707 125670000 85180 87406 18229 45709 97223 72736 81638 105000 18370 TRUE FALSE 73923.24718 86831.82423 27044.60537 56087.92707 95288.45251 75534.20099 73720.75933 82546.56711 16198.31953 4.563636805 5.360545215 1.669593276 3.462576903 5.882613462 4.663088715 4.551136258 5.095995728 1 13.98355653 S(ph)SPPVLQGPAPAGFSQHPGLLVPHTHAR ddPTM_MDA-MB-175_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 140.24 6.10E-08 3740360000 690420 720080 359332 546371 832100 726910 732660 935570 850070 TRUE FALSE 599179.2477 715349.7471 533106.1571 670432.8863 815542.838 754874.6981 661606.746 735505.6361 749575.693 0.799357894 0.954339573 0.711210572 0.894416525 1.088005982 1.00706934 0.882641676 0.981229305 1 19.51571464 3.47154 24.94629634 0.983789407 0.829557561 0.51113468 0.07629754 120.621486 539133.4044 0.021437419 0.027761822 2961.692738 -3.47154 -0.154231846 S(ph)SPQLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPQLAK 7 0 Q13370-2;Q13370 Q13370-2 PDE3B "cGMP-inhibited 3,5-cyclic phosphodiesterase B" 1 S(0.595)S(0.405)PQLAK;S(0.661)S(0.339)PQLAK 98.933 0.011432 2759890000 6313900 4343900 3343200 3960100 3888900 4675500 6197500 7699400 8611300 TRUE FALSE 5479502.118 4315364.635 4959982.702 4859301.231 3811518.499 4855369.51 5596467.404 6052943.227 7593281.924 0.721625006 0.568313501 0.65320671 0.639947427 0.501959303 0.639429638 0.737028792 0.79714454 1 22.85629214 1.276770504 1.092102785 1.174552851 0.615555175 0.803619725 0.060385345 0.672702857 0.701570945 0.440260717 0.019692631 18.91343903 -1.276770504 -0.558997676 S(ph)SPQLDPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPQLDPLR 9 0 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.5)S(0.5)PQLDPLR;S(0.5)S(0.5)PQLDPLR 76.143 0.024576 2950500000 726183 684263 495611 639443 745318 762790 668266 725352 1403330 TRUE FALSE 630216.0766 679768.0313 735290.1373 784638.3064 730487.63 792135.0249 603457.6662 570241.1195 1237429.926 0.509294355 0.549338607 0.594207496 0.634087062 0.590326462 0.64014536 0.487670173 0.460826999 1 20.2389154 1.23088169 24.99996304 1.000000792 0.55714188 0.84532888 0.059384272 119.598624 389339.6159 0.172267134 0.016524546 17.01694873 -1.23088169 -0.442858912 S(ph)SPQLDPLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSPQLDPLRK 10 1 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.936)S(0.064)PQLDPLRK;S(0.844)S(0.156)PQLDPLRK;S(0.929)S(0.071)PQLDPLRK 145.81 1.82E-05 18481770000 7916330 5993200 5425640 6786600 6481490 5567490 7278450 8744390 12095100 TRUE FALSE 6870166.933 5953830.275 8049497.652 8327601.257 6352521.03 5781674.943 6572587.039 6874470.247 10665231.06 0.644164847 0.558246722 0.754741984 0.780817707 0.595629011 0.542104987 0.616262977 0.644568337 1 23.34641189 1.238712661 9.000033208 1.002545962 0.641465454 0.687395233 0.075859671 0.050795387 56.67828005 0.112293301 0.019798035 17.32657252 -1.238712661 -0.361080507 S(ph)SPSARPPDVPGQQPQAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPSARPPDVPGQQPQAAK 19 1 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 S(0.471)S(0.471)PS(0.058)ARPPDVPGQQPQAAK;S(0.52)S(0.48)PSARPPDVPGQQPQAAK 141.08 1.02E-07 1069040000 891810 682770 509150 692640 719280 553270 758480 923600 1491700 TRUE FALSE 773955.0489 678284.8389 755376.643 849914.4983 704967.7352 574554.6549 684922.7263 726095.3275 1315352.925 0.588401055 0.515667564 0.57427678 0.646149396 0.535953296 0.43680646 0.520714033 0.552015595 1 20.32701851 1.238653769 7.455723007 1.007575264 0.54408971 0.874695917 0.053976561 0.035230684 13.71808668 0.082599324 0.014071063 17.32422313 -1.238653769 -0.463485554 S(ph)SPSHSTTSGETDPTTIFPCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPSHSTTSGETDPTTIFPCK 21 0 Q05GC8;Q96PN7-2;Q96PN7-3;Q96PN7-4;Q96PN7-5;Q96PN7 Q05GC8;Q96PN7 BCAR2;TRERF1 Transcriptional-regulating factor 1 1 S(0.459)S(0.459)PS(0.014)HS(0.015)T(0.015)T(0.017)S(0.017)GET(0.003)DPTTIFPCK 72.227 0.010281 80416000 114890 107610 46998 88959 120250 92350 117380 126740 125570 TRUE FALSE 99706.99541 106903.1028 69726.39 109158.5006 117857.2603 95902.76426 105996.5057 99637.63729 110725.2576 0.900490074 0.965480732 0.629724342 0.985850048 1.064411705 0.866132681 0.957292924 0.899863675 1 16.75662483 S(ph)SPSIICMPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.639)S(0.361)PSIICMPK;S(0.658)S(0.342)PSIICMPK;S(0.898)S(0.102)PSIICMPK;S(0.601)S(0.399)PSIICMPK 152.7 1.84E-05 1173780000 2174880 2035840 1470320 1839800 2004530 1523590 1965200 2386720 3315940 TRUE FALSE 1887464.098 2022466.433 2181371.67 2257554.71 1964643.775 1582203.493 1774615.206 1876338.501 2923933.351 0.645522271 0.691693753 0.746040148 0.772095133 0.671918111 0.5411216 0.60692738 0.641717261 1 21.479479 1.236256026 24.99236601 1.000000437 0.663966943 0.722282836 0.06535329 37.54996614 407119.3748 0.1166619 0.017971173 17.22883952 -1.236256026 -0.336033494 S(ph)SPSPALEQPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPSPALEQPFR 12 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 S(0.635)S(0.365)PSPALEQPFR 144.92 6.66E-05 211390000 202760 192830 200160 194180 193980 212110 241190 254590 358780 TRUE FALSE 175964.7523 191563.287 296958.0455 238271.5369 190120.1775 220270.009 217799.4309 200147.9097 316365.4371 0.556207258 0.605512691 0.938655146 0.75315287 0.600951163 0.696251812 0.688442558 0.632647838 1 18.27123247 1.232433556 24.99998323 1.000000513 0.687238222 0.465311353 0.106412026 199.23548 812851.0843 0.239295247 0.026689404 17.07786421 -1.232433556 -0.312762291 S(ph)SPSPQKR ddPTM_MDA-MB-175_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(0.633)S(0.367)PSPQKR;S(0.68)S(0.32)PSPQKR;S(0.5)S(0.5)PS(0.001)PQKR 131.22 0.00062119 1052246000 720348 665728 433036 484074 415921 584586 702819 808246 632078 TRUE FALSE 625152.1867 661354.7889 642453.658 593990.4003 407644.9858 607075.4017 634659.7216 635408.8827 557354.4589 1.12164203 1.18659639 1.152684163 1.065731853 0.731392706 1.089208836 1.138700357 1.140044495 1 19.0882356 3.693769198 5.145148802 1.035478723 1.157396065 0.208581904 0.115864629 0.369562217 23.8217481 0.034900465 0.053748277 4940.480592 -3.693769198 0.121917342 S(ph)SPSTDHYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPSTDHYK 9 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 S(0.487)S(0.487)PS(0.023)T(0.003)DHYK 98.04 0.0040472 144050000 261460 227020 164650 219260 225680 211300 261460 286180 541000 TRUE FALSE 226907.3985 225528.6907 244275.2907 269046.3342 221189.4095 219428.8477 236103.6494 224982.6341 477043.5963 0.475653379 0.47276327 0.512060727 0.56398689 0.463667076 0.459976508 0.494930969 0.471618602 1 18.86376159 1.237338149 24.99999967 1.000000612 0.489570318 0.964959254 0.030582481 5.360618794 109580.6921 0.046770448 0.007777552 17.2718218 -1.237338149 -0.510430294 S(ph)SPSVLIHSLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPSVLIHSLGK 12 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 1 S(0.5)S(0.5)PSVLIHSLGK 188.4 5.85E-05 0 376730 323360 192280 318900 367590 337070 391900 456780 499320 TRUE FALSE 326944.176 321235.8269 285267.2511 391311.1191 360275.6782 350037.301 353893.5983 359101.1517 440290.9584 0.742563911 0.729598963 0.647906221 0.888755746 0.818267265 0.795013603 0.803772123 0.81559965 1 18.74809769 -0.770680173 0.907370778 10 0.766582848 0.563461575 0.062171693 62.94913533 1.632433426 1128.541827 0.022517541 0.169558602 0.770680173 -9.233417152 S(ph)SPTQETQAPFIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPTQETQAPFIAK 14 0 O15231-5 O15231-5 ZNF185 Zinc finger protein 185 1 S(0.499)S(0.499)PT(0.002)QETQAPFIAK 89.386 0.0064719 64862000 366710 329690 232370 284870 343210 334380 353100 412830 422960 TRUE FALSE 318248.3444 327524.2447 344744.9092 349554.0875 336380.7925 347243.815 318856.4163 324549.5171 372958.1506 0.853308458 0.878179614 0.924352796 0.937247482 0.901926374 0.931053027 0.854938861 0.870203578 1 18.50865423 4.439509167 4.192002398 0.910150398 0.857579806 0.221092608 0.03972228 0.331139343 12.58177389 0.010229087 0.033443468 27511.17677 -4.439509167 -0.052570592 S(ph)SPVESLKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSPVESLKK 9 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 S(0.638)S(0.362)PVESLKK;S(0.833)S(0.167)PVESLKK;S(0.95)S(0.05)PVESLKK 135.8 0.00012911 5522300000 10592800 7717600 6674600 7553300 7637600 5547970 11695900 12794000 10684200 TRUE FALSE 9192934.641 7666902.577 9902458.885 9268392.21 7485626.703 5761403.996 10561633.42 10058102.66 9421126.047 0.975778755 0.81379896 1.051090797 0.983788155 0.794557536 0.61154091 1.121058498 1.067611516 1 23.16746808 S(ph)SPVPEMLEESQELLEPVVDDVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPVPEMLEESQELLEPVVDDVPK 24 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.5)S(0.5)PVPEMLEES(0.001)QELLEPVVDDVPK;S(0.499)S(0.499)PVPEMLEES(0.001)QELLEPVVDDVPK 147.93 5.68E-07 56630000 207446 184370 146589 156731 180225 147702 240936 272732 220154 TRUE FALSE 180031.4855 183158.8613 217479.9307 192319.169 176638.8751 153384.1915 217570.0638 214410.3842 194127.6449 0.927387161 0.943497055 1.120293458 0.990684089 0.909910977 0.790120292 1.120757757 1.104481458 1 17.56664606 2.155568171 24.99822583 1.083109484 0.954950919 0.323300418 0.086593742 33.38869938 10053.62294 0.037301772 0.025148854 143.076455 -2.155568171 -0.128158566 GYYS(ph)PYSVSGS(ph)GSTAGSR ddPTM_MDA-MB-175_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(0.002)S(0.003)VS(0.002)GS(0.427)GS(0.274)T(0.265)AGS(0.031)R 184.15 8.73E-14 218290000 1304000 764260 409380 274320 261110 332260 256840 270940 308250 TRUE FALSE 1131673.096 759239.5257 607357.5373 336608.5487 255914.4219 345042.2572 231931.6963 213001.5895 271809.0362 4.163485924 2.793282874 2.234500905 1.238400877 0.941522863 1.269428942 0.853289131 0.783644254 1 18.05223389 4.720779454 0.759330157 0.871190964 6.101386706 0.977012885 0.164308263 0.351470384 0.159970167 0.066709072 1.568487279 52575.02087 -4.720779454 5.230195743 up S(ph)SQASQNRHSMEISPPVLISSSNPTAAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSQASQNRHSMEISPPVLISSSNPTAAAR 29 1 Q7Z6J0;H0YA90;Q7Z6J0-3 Q7Z6J0 SH3RF1 E3 ubiquitin-protein ligase SH3RF1 1 S(0.322)S(0.214)QAS(0.214)QNRHS(0.214)MEIS(0.037)PPVLISSSNPTAAAR;S(0.234)S(0.234)QAS(0.234)QNRHS(0.234)MEIS(0.064)PPVLIS(0.001)SSNPTAAAR 169.01 1.96E-12 1628570000 892920 724290 344736 603000 933650 866130 901600 1051170 839780 TRUE FALSE 774918.3596 719532.0913 511451.4827 739920.3663 915072.1917 899450.5816 814162.9708 826385.4757 740502.1651 1.046476832 0.97168128 0.690681954 0.999214319 1.235745464 1.214649496 1.099474126 1.115979824 1 19.49814443 3.470216148 17.33611953 1.131198691 0.89900832 0.486921131 0.108920674 3.332175058 8363.355583 0.031811296 0.041400725 2952.678404 -3.470216148 -0.232190371 S(ph)SS(ph)PFLSK ddPTM_MDA-MB-175_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(0.405)S(0.595)PFLSK;S(0.992)S(0.091)S(0.917)PFLSK 97.813 0.011645 426090000 1417460 799750 639030 737730 1068420 825470 932700 1157790 1738870 TRUE FALSE 1230139.07 794496.3896 948067.0454 905242.872 1047160.532 857226.3651 842246.8976 910205.6184 1533302.77 0.802280602 0.518160148 0.61831692 0.590387554 0.682944395 0.559071817 0.549302404 0.593624193 1 20.54821117 1.237373032 24.99536425 1.000000471 0.607047941 0.694495441 0.080276 15.57662208 327701.9199 0.107992828 0.018005854 17.27320918 -1.237373032 -0.39295253 S(ph)SS(ph)PVTELASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSSPVTELASR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.999)S(0.001)S(0.999)PVT(0.001)ELASR;S(0.998)S(0.002)S(1)PVTELASR;S(0.998)S(0.126)S(0.875)PVTELASR;S(0.994)S(0.083)S(0.922)PVT(0.001)ELASR 171.26 3.45E-05 497140000 1279570 1008190 760210 815230 1192680 1022570 1001990 1181640 1492860 TRUE FALSE 1110471.582 1001567.134 1127850.099 1000340.432 1168948.001 1061908.93 904817.164 928955.4815 1316375.791 0.843582501 0.760851985 0.856784291 0.759920106 0.888004785 0.806691324 0.687354758 0.705691709 1 20.32813997 2.459502678 24.97387525 0.770078012 0.819984193 0 0.092793136 760.0451862 1077336.873 0.033869679 0.026241057 288.0730816 -2.459502678 0.049906182 S(ph)SSAPLIHGLSDLSQVFQPYTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSAPLIHGLSDLSQVFQPYTLR 23 0 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 S(0.321)S(0.321)S(0.321)APLIHGLS(0.036)DLSQVFQPYTLR 62.7 0.027963 10567000 8416.9 7082.9 5694.2 7628.5 12063 8512.5 9309.4 9477.1 8670.1 TRUE FALSE 7304.585339 7036.371964 8447.934166 9360.667519 11822.9699 8839.981383 8406.575821 7450.495916 7645.130655 0.955455919 0.920373017 1.105008475 1.224396016 1.546470614 1.156289118 1.099598712 0.974541346 1 12.90032544 4.147306373 4.265094289 1.158317115 0.937289858 0.262363541 0.155796679 0.330863988 10.85197649 0.046173859 0.105837846 14038.03668 -4.147306373 -0.221027258 S(ph)SSAPNVHINTIEPVNIDDLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSAPNVHINTIEPVNIDDLIR 22 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 S(0.333)S(0.333)S(0.333)APNVHINTIEPVNIDDLIR;S(0.362)S(0.362)S(0.276)APNVHINTIEPVNIDDLIR 234.37 1.25E-30 190899000 76298 68589 46995 60236 73376 69129 71467 75368 88278 TRUE FALSE 66215.02599 68138.43434 69721.93919 73913.50445 71915.96116 71788.43736 64536.14134 59251.13971 77841.87541 0.85063503 0.875344202 0.895686786 0.949533963 0.923872412 0.92223417 0.829067144 0.761173076 1 16.24825885 1.185378607 23.92521734 1.000004614 0.874208522 0.341946906 0.054036984 19417.62761 8733983.187 22.15711978 0.015530731 15.32422806 -1.185378607 -0.125796092 S(ph)SSDALSASFNGEMLGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSSDALSASFNGEMLGNR 18 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.87)S(0.065)S(0.065)DALSASFNGEMLGNR;S(0.966)S(0.029)S(0.005)DALSASFNGEMLGNR;S(0.695)S(0.304)S(0.001)DALSASFNGEMLGNR;S(0.821)S(0.156)S(0.023)DALSASFNGEMLGNR 344.29 4.31E-76 414967000 248022 215408 143736 172340 235022 227194 222205 253992 227810 TRUE FALSE 215245.2643 213992.9707 213247.2104 211472.4311 230345.522 235934.3002 200655.5933 199677.7874 200878.5613 1.071519344 1.065285261 1.061572768 1.052737682 1.146690421 1.174512096 0.998890036 0.994022389 1 17.61596408 2.140361753 12.06242472 0.996615047 1.092854213 0.587530387 0.03857044 0.367755115 42.77594552 0.017229102 0.011615273 138.1534559 -2.140361753 0.096239166 S(ph)SSDPGIPGGPQAIPATNSPDHSDHTLSVSSDSGHSTASAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSDPGIPGGPQAIPATNSPDHSDHTLSVSSDSGHSTASAR 41 0 Q68CZ2;E9PCX8;C9JHU5 Q68CZ2 TNS3 Tensin-3 1 S(0.333)S(0.333)S(0.333)DPGIPGGPQAIPATNSPDHSDHTLSVSSDSGHSTASAR;S(0.333)S(0.333)S(0.333)DPGIPGGPQAIPAT(0.001)NSPDHSDHTLSVSSDSGHSTASAR 73.176 0.0033988 588330000 95161 141491 24293 94969 221747 209814 143171 174382 310210 TRUE FALSE 82585.23274 140561.5363 36041.17606 116533.163 217334.6685 217885.6803 129286.2985 137091.7663 273537.3272 0.30191577 0.513866015 0.131759626 0.426022891 0.79453386 0.796548254 0.472645908 0.501181202 1 18.06137819 3.395896177 5.706055984 0.671045133 0.3267342 0.518083527 0.176924215 0.188603073 10.10184459 0.052604123 0.068399434 2488.262398 -3.395896177 -0.344310933 S(ph)SSDPPAVHPPLPPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSDPPAVHPPLPPLR 16 0 O43150 O43150 ASAP2 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2" 1 S(0.333)S(0.333)S(0.333)DPPAVHPPLPPLR;S(0.355)S(0.355)S(0.29)DPPAVHPPLPPLR 88.551 0.0039238 600990000 970400 752060 580490 748040 923070 1024190 971980 1055110 1149230 TRUE FALSE 842159.1813 747119.6683 861216.9056 917893.9151 904702.713 1063591.252 877717.5292 829482.9374 1013369.339 0.831048611 0.73726295 0.849854908 0.90578418 0.892767009 1.049559338 0.866137839 0.818539604 1 19.95072865 3.951846675 3.224309837 0.911796361 0.7841096 0.402755351 0.06889202 0.268862344 5.584384182 0.019479508 0.040151771 8950.487185 -3.951846675 -0.127686761 S(ph)SSEAKPTSLGLAGGHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSEAKPTSLGLAGGHK 17 1 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 S(0.623)S(0.02)S(0.356)EAKPTSLGLAGGHK;S(0.954)S(0.026)S(0.02)EAKPTSLGLAGGHK 146.19 2.70E-07 267940000 298320 313910 255620 371110 395470 324660 620700 679990 918160 TRUE FALSE 258896.2562 311847.9045 379238.687 455376.1976 387600.9207 337149.8803 560504.6095 534579.4302 809616.1708 0.319776538 0.385179936 0.468417876 0.562459365 0.478746516 0.416431752 0.692309059 0.660287491 1 19.62687858 -1.520501569 0.482003287 10 0.408350912 0.844516651 0.077167227 24.82081301 0.472937979 226.2819636 0.054792524 0.03016466 1.520501569 -9.591649088 S(ph)SSEDAESLAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSSEDAESLAPR 12 0 Q4G0J3;Q4G0J3-3;H0YA82 Q4G0J3 LARP7 La-related protein 7 1 S(0.826)S(0.116)S(0.059)EDAESLAPR;S(0.786)S(0.107)S(0.107)EDAESLAPR;S(0.796)S(0.102)S(0.102)EDAESLAPR;S(0.787)S(0.107)S(0.107)EDAESLAPR 300.75 1.77E-36 3640060000 2331400 1701830 1482780 1722300 2244380 2240160 2333350 2555010 2705290 TRUE FALSE 2023299.583 1690650.567 2199857.368 2113374.539 2199721.229 2326340.405 2107062.076 2008640.995 2385473.698 0.84817518 0.708727398 0.922188901 0.885934957 0.922131831 0.97521109 0.883288748 0.842030242 1 21.18584435 4.222098625 24.99868373 0.910915876 0.778451288 0.517050693 0.055954473 168.3184896 255604.2558 0.01403574 0.02935098 16676.25874 -4.222098625 -0.132464588 S(ph)SSETILSSLAGSDIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSETILSSLAGSDIVK 17 0 Q01850 Q01850 CDR2 Cerebellar degeneration-related protein 2 1 S(0.333)S(0.333)S(0.333)ET(0.002)ILSSLAGSDIVK 183.31 7.33E-10 61199000 241210 219440 133080 173320 198690 153760 251200 275590 238090 TRUE FALSE 209333.4874 217998.4842 197437.9331 212674.955 194736.4577 159675.2467 226838.6627 216657.2231 209943.2714 0.997095482 1.038368521 0.940434679 1.013011532 0.927567035 0.760563773 1.080475983 1.031979838 1 17.67964003 S(ph)SSFSDTLEESSPIAAIFDTENLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSFSDTLEESSPIAAIFDTENLEK 25 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 S(0.198)S(0.198)S(0.198)FS(0.198)DT(0.198)LEES(0.004)S(0.004)PIAAIFDTENLEK 130.71 5.68E-05 27366000 25126 19271 17582 19717 24702 19100 25682 31107 31359 TRUE FALSE 21805.53544 19144.40753 26084.71401 24194.04621 24210.47853 19834.78936 23191.36359 24455.01012 27651.77474 0.788576344 0.692339197 0.943328747 0.874954553 0.875548812 0.717306196 0.838693495 0.884392063 1 14.75508446 1.320642834 2.005556996 1.037010317 0.819104084 0.380976154 0.074131456 0.720990972 3.354948675 0.27743476 0.020881451 20.92390955 -1.320642834 -0.217906233 S(ph)SSISGVDMAGLQTSFLSQDESHDHSFGPMPISANGSNLYDAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSSISGVDMAGLQTSFLSQDESHDHSFGPMPISANGSNLYDAVR 44 0 A0A2R8Y7M0;P82094;P82094-2 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 S(0.326)S(0.326)S(0.326)IS(0.022)GVDMAGLQTSFLSQDESHDHSFGPMPISANGSNLYDAVR;S(0.332)S(0.332)S(0.332)IS(0.005)GVDMAGLQTSFLSQDESHDHSFGPMPISANGSNLYDAVR;S(0.333)S(0.333)S(0.333)IS(0.001)GVDMAGLQTSFLSQDESHDHSFGPMPISANGSNLYDAVR 159.61 2.81E-20 221253000 7255.1 11845.6 5955 9324 13921.1 17038.5 13287 13356.4 14237.1 TRUE FALSE 6296.320153 11767.78547 8834.857918 11441.15671 13644.09735 17693.98212 11998.42879 10500.2378 12554.00626 0.501538714 0.937372918 0.703748089 0.911355027 1.086832129 1.40942913 0.955745006 0.836405334 1 13.61586021 3.534793034 3.387146251 1.038869658 0.737243764 0.430622078 0.178538996 0.286332058 6.504425656 0.055617957 0.082922791 3426.044768 -3.534793034 -0.301625894 S(ph)SSKDSRPSQAAGDNQGDEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSKDSRPSQAAGDNQGDEAK 21 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.532)S(0.173)S(0.221)KDS(0.072)RPS(0.002)QAAGDNQGDEAK;S(0.366)S(0.366)S(0.266)KDS(0.003)RPSQAAGDNQGDEAK 280.36 2.99E-45 345230000 239970 166301 196391 153634 183501 128458 262620 320110 195422 TRUE FALSE 208257.3565 165208.5578 291366.3445 188518.9478 179849.6891 133399.8624 237151.1528 251656.9676 172319.4338 1.20855409 0.958734335 1.690850173 1.094008631 1.043699397 0.774142878 1.376229875 1.460409671 1 17.39472589 0.964075128 17.73073766 0.095281852 1.208727002 0.054307883 0.261533569 14282670.78 194322853.5 513018051.9 0.065586292 9.206088119 -0.964075128 1.11344515 S(ph)SSLEGFHNHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSLEGFHNHFK 12 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 S(0.337)S(0.337)S(0.326)LEGFHNHFK;S(0.475)S(0.475)S(0.049)LEGFHNHFK 192.18 7.38E-06 1210810000 1280270 1181450 853000 1052110 1263260 1053030 1847560 1874450 1390440 TRUE FALSE 1111079.076 1173688.977 1265513.653 1291007.656 1238123.598 1093540.746 1668383.916 1473613.454 1226063.767 0.906216386 0.957282165 1.032176047 1.052969422 1.009836218 0.891911803 1.360764391 1.201906046 1 20.22560258 2.250784703 24.99999374 1.197763246 0.981974542 0.50340119 0.099159807 174.8949636 357685.0989 0.037443285 0.028782989 178.1495392 -2.250784703 -0.215788703 S(ph)SSLESLQTAVAEVTLNGDIPFHR ddPTM_MDA-MB-175_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(0.316)S(0.316)S(0.316)LES(0.053)LQTAVAEVTLNGDIPFHR;S(0.307)S(0.307)S(0.307)LES(0.076)LQT(0.004)AVAEVTLNGDIPFHR 120.64 8.56E-05 39615000 14914.6 14145.8 13000.5 13668.4 17389 17826.1 10877.1 15893.1 30582 TRUE FALSE 12943.59782 14052.87531 19287.58528 16772.01913 17042.99292 18511.8816 9822.240516 12494.48425 26966.6308 0.479985724 0.521120915 0.715238972 0.621954565 0.63200305 0.686473655 0.364236845 0.463331305 1 14.71888766 1.230954472 24.99982281 1.000000787 0.558474323 0.621034667 0.107874097 206.5807567 678930.7178 0.298848037 0.028873862 17.01980076 -1.230954472 -0.441526464 S(ph)SSLESLQTAVAEVTLNGDIPFHRPRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSLESLQTAVAEVTLNGDIPFHRPRPR 28 2 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 S(0.333)S(0.333)S(0.333)LESLQTAVAEVTLNGDIPFHRPRPR;S(0.333)S(0.333)S(0.333)LES(0.002)LQTAVAEVTLNGDIPFHRPRPR 152.49 2.19E-08 244534000 33406.7 28177 24469.4 20756.5 31903.9 22974.9 32764.9 36763.2 28403.3 TRUE FALSE 28991.91995 27991.90343 36302.88369 25469.58057 31269.07481 23858.75927 29587.36504 28901.67577 25045.49423 1.157570287 1.117642286 1.449477633 1.01693264 1.248491027 0.952616828 1.181344827 1.153967077 1 14.61226346 S(ph)SSLKER ddPTM_MDA-MB-175_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(0.469)S(0.266)S(0.266)LKER;S(0.333)S(0.333)S(0.333)LKER 107.47 0.0045247 3255700000 2771670 2203630 944920 1761920 1133600 1050240 2247370 2427460 1834060 TRUE FALSE 2405386.787 2189154.209 1401886.473 2161990.865 1111043.578 1090643.412 2029420.403 1908366.57 1617239.516 1.487341091 1.353636358 0.866839116 1.336840241 0.687000019 0.674385829 1.25486694 1.180014803 1 20.62510193 4.374561858 5.285209799 1.019845542 1.455713594 0.389082533 0.220540931 0.212109025 8.903614992 0.057704622 0.161022844 23689.82531 -4.374561858 0.435868052 S(ph)SSLSDLTHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSSLSDLTHR 10 0 Q5T9C2-3;Q5T9C2;Q5T9C2-2 Q5T9C2-3 FAM102A Protein FAM102A 1 S(0.333)S(0.333)S(0.333)LS(0.001)DLTHR;S(0.472)S(0.472)S(0.056)LSDLTHR;S(0.333)S(0.333)S(0.333)LSDLTHR 153.34 1.06E-05 2118830000 1654890 1492620 1148100 1454800 1487330 1712710 1787170 1619190 2045070 TRUE FALSE 1436192.094 1482814.881 1703325 1785134.575 1457735.043 1778599.062 1613850.528 1272938.819 1803304.154 0.79642255 0.82227664 0.944557797 0.989924285 0.808368926 0.986300097 0.894940837 0.705892467 1 20.78221132 0.959450923 22.87221521 2.118683947 0.867782943 0.174693 0.089751777 390.4710411 313410.958 55740.66566 0.022271613 9.108585151 -0.959450923 -1.250901004 S(ph)SSLVDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSLVDIR 8 0 Q96Q42;Q96Q42-3 Q96Q42 ALS2 Alsin 1 S(0.333)S(0.333)S(0.333)LVDIR 64.654 0.069547 88683000 244350 215890 143180 216720 228680 233690 196080 234390 481490 TRUE FALSE 212058.5284 214471.8044 212422.3269 265929.5884 224129.7154 242680.2055 177064.1918 184267.5225 424568.8007 0.499467997 0.50515206 0.500324863 0.626352167 0.527899636 0.571592178 0.417044756 0.434010983 1 18.69563883 1.233299779 24.9876121 1.000000773 0.507919939 0.868288712 0.059941831 62.43293017 296506.6163 0.13417614 0.016197665 17.11196089 -1.233299779 -0.492080834 S(ph)SSPAGETEGDREPQARPGEGTAPLPPPGQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SSSPAGETEGDREPQARPGEGTAPLPPPGQK 31 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 S(0.333)S(0.333)S(0.333)PAGETEGDREPQARPGEGTAPLPPPGQK;S(0.327)S(0.327)S(0.327)PAGET(0.02)EGDREPQARPGEGTAPLPPPGQK;S(0.333)S(0.333)S(0.333)PAGET(0.001)EGDREPQARPGEGTAPLPPPGQK;S(0.333)S(0.333)S(0.333)PAGETEGDREPQARPGEGTAPLPPPGQK;S(0.333)S(0.333)S(0.333)PAGET(0.002)EGDREPQARPGEGTAPLPPPGQK 241.83 3.11E-46 1960570000 1183600 926605 580277 600551 848917 761197 1041438 1239635 534755 TRUE FALSE 1027184.261 920518.0707 860900.8981 736915.2834 832025.2126 790480.7412 940439.5031 974548.7021 471536.8731 2.178375266 1.952165617 1.825733993 1.562794609 1.764496607 1.676392211 1.994413495 2.066749724 1 18.84701107 4.494646094 1.939699926 1.740371502 2.205999364 0.229470709 0.2904241 0.827116711 4.745985727 0.077999723 0.580006243 31235.32968 -4.494646094 0.465627862 S(ph)SSPATEQSWMENDFDELREEGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSPATEQSWMENDFDELREEGFR 24 1 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.333)S(0.333)S(0.333)PATEQSWMENDFDELREEGFR 81.292 0.0098107 270210000 38516 30497 14351 29289 32529 28571 40040 49135 38758 TRUE FALSE 33426.01301 30296.6632 21291.1916 35939.5151 31881.73654 29670.14486 36156.92696 38627.86262 34176.07339 0.978053056 0.886487539 0.622985308 1.051598722 0.93286716 0.868155464 1.057960244 1.130260407 1 15.06069903 2.202263534 6.06828971 1.078719332 0.886867004 0.335844463 0.113858038 0.193416942 19.09526187 0.046727202 0.031904677 159.3175189 -2.202263534 -0.191852328 S(ph)SSPATEQSWMENDFDELREEGFRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SSSPATEQSWMENDFDELREEGFRR 25 2 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.455)S(0.455)S(0.089)PATEQSWMENDFDELREEGFRR;S(0.333)S(0.333)S(0.333)PATEQSWMENDFDELREEGFRR;S(0.332)S(0.332)S(0.332)PAT(0.003)EQSWMENDFDELREEGFRR;S(0.333)S(0.333)S(0.333)PAT(0.001)EQSWMENDFDELREEGFRR;S(0.333)S(0.333)S(0.333)PATEQSWMENDFDELREEGFRR;S(0.333)S(0.333)S(0.333)PATEQSWMENDFDELREEGFRR 235.7 1.06E-38 1099613000 145662.7 142911 73780.4 72232.4 140433.4 154678 151534.2 162874 68570.3 TRUE FALSE 126413.0051 141972.2082 109460.8482 88633.87042 137639.0501 160628.5627 136838.4366 128044.6626 60463.99725 2.090715316 2.348045361 1.810347532 1.465894986 2.276380265 2.656598473 2.263139105 2.11770092 1 15.88378874 1.238912785 8.424432915 0.989016114 2.132478009 0.554747571 0.317771774 0.072893556 55.44797216 0.478861271 0.083994959 17.33455852 -1.238912785 1.143461894 S(ph)SSPELVTHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SSSPELVTHLK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.388)S(0.388)S(0.225)PELVTHLK;S(0.592)S(0.204)S(0.204)PELVTHLK;S(0.717)S(0.235)S(0.048)PELVTHLK;S(0.396)S(0.396)S(0.207)PELVTHLK;S(0.333)S(0.333)S(0.333)PELVTHLK;S(0.407)S(0.407)S(0.186)PELVTHLK;S(0.333)S(0.333)S(0.333)PELVTHLK 271.32 3.15E-27 24593956100 25438361 25717467 18032309 22902852 28404662 24159847 30905297 36561265 33334980 TRUE FALSE 22076617.14 25548527.27 26752793.95 28103294.59 27839464.8 25089291.95 27908106.05 28742923 29394156.64 0.75105462 0.869170277 0.910139871 0.956084399 0.947108813 0.853546923 0.949444014 0.977844792 1 24.80902605 5.754283388 0.76534343 0.951568042 3.13E-16 0.735166166 0.037508526 6.093921994 0.855892986 0.015052018 7.108757381 567915.063 -5.754283388 -0.951568042 S(ph)SSPELVTHLKWDDPYYDIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSPELVTHLKWDDPYYDIAR 21 1 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.365)S(0.365)S(0.27)PELVTHLKWDDPYYDIAR;S(0.333)S(0.333)S(0.333)PELVTHLKWDDPYYDIAR 225.3 1.72E-25 250250000 239240 260510 52040 52715 225757 199904 308510 364180 24168 TRUE FALSE 207623.8278 258798.6927 77206.71806 64684.74645 221264.8774 207594.4362 278590.7477 286302.9411 21310.88657 9.742618034 12.1439665 3.622876871 3.035291199 10.38271574 9.741238851 13.07269628 13.43458612 1 14.37930299 6.323686222 10.4743007 8.907010537 9.70815701 0 4.432476323 0 0 1.029293668 0 2107105.216 -6.323686222 0.801146474 S(ph)SSPGKPQAVSSLNSSHSR ddPTM_MDA-MB-175_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(0.346)S(0.346)S(0.307)PGKPQAVSSLNSSHSR;S(0.333)S(0.333)S(0.333)PGKPQAVSSLNSSHSR 236.5 2.07E-24 4342980000 2655220 2471040 759650 1651126 2953560 2285810 2744490 3378190 2794610 TRUE FALSE 2304325.95 2454807.576 1127019.281 2026039.394 2894789.935 2373746.59 2478329.782 2655790.358 2464234.389 0.935108267 0.996174547 0.457350683 0.822178037 1.174721831 0.963279548 1.005719989 1.077734476 1 21.23270806 3.347846639 7.367979779 1.040918727 0.787975261 0.390069556 0.150101065 0.235274844 14.48077523 0.043650705 0.056379224 2227.64837 -3.347846639 -0.252943465 S(ph)SSPHDKNLPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 116.58 0.0004993 140490000 610910 518830 190610 239900 482730 398670 654690 674690 103820 TRUE FALSE 530176.6957 515421.7716 282789.6336 294372.9616 473124.6174 414007.0929 591198.2646 530412.7939 91546.51787 5.791336557 5.630162496 3.089026651 3.215556074 5.168133408 4.522368545 6.457900074 5.793915555 1 16.48221739 4.437135713 24.73506012 4.451252005 5.75104871 0.12680446 1.550760539 283.9337209 175640.9179 0.396637041 1.049406818 27361.23606 -4.437135713 1.299796705 S(ph)SSPPPRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSPPPRK 8 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.333)S(0.333)S(0.333)PPPRK 54.608 0.079126 118830000 457010 360900 194840 278940 199760 253420 438170 466170 328540 TRUE FALSE 396614.9706 358529.2241 289065.2757 342277.5903 195785.1668 263169.2314 395676.3408 366483.1732 289700.3755 1.369052318 1.237586329 0.997807736 1.181488252 0.675819514 0.908418676 1.365812316 1.265042106 1 18.14420203 4.450356157 4.061813984 1.077513483 1.348389294 0.22972592 0.192238702 0.349470757 12.6683178 0.053587857 0.183104066 28206.95186 -4.450356157 0.270875811 S(ph)SSSESLSDKGSELKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSSESLSDKGSELKK 16 2 Q86X27;Q86X27-3;Q86X27-2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 S(0.346)S(0.346)S(0.297)S(0.009)ES(0.002)LSDKGSELKK 71.073 0.021736 112110000 137220 95065 78705 89729 80104 56102 135790 158300 56095 TRUE FALSE 119086.0293 94440.51176 116767.0013 110103.3409 78510.08712 58260.28024 122621.1067 124448.7769 49463.513 2.407553004 1.90929649 2.360669394 2.225950689 1.587232333 1.17784356 2.479021389 2.515971255 1 15.59407709 3.277576549 24.71066938 1.873325365 2.212884422 0.15818704 0.501129338 379.8250496 240558.7243 0.154057531 0.198883634 1894.857474 -3.277576549 0.339559057 S(ph)SSSPELQTLQDILGDPGDKADVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSSPELQTLQDILGDPGDKADVGR 25 1 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;H3BQK4;A0A2R8Y670 P49815 TSC2 Tuberin 1 S(0.329)S(0.329)S(0.329)S(0.012)PELQT(0.001)LQDILGDPGDKADVGR;S(0.33)S(0.33)S(0.33)S(0.011)PELQTLQDILGDPGDKADVGR 127.59 7.27E-05 255560000 113718 84143 66141 51618 89417 76088 109282 118752 73223 TRUE FALSE 98689.87818 83590.25909 98127.00883 63338.65583 87637.77664 79015.1546 98683.84846 93357.80893 64566.66036 1.528495939 1.294635012 1.519778293 0.980980826 1.357322435 1.223776391 1.528402552 1.445913548 1 15.97850179 6.396830775 1.214858696 1.307286121 12.41510924 0.126961169 0.189782547 194.9588437 7.201319099 0.053867336 5698.867756 2493622.888 -6.396830775 11.10782312 S(ph)SSSQTLTQFDSNIAPADPDTAIVHPVPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSSQTLTQFDSNIAPADPDTAIVHPVPIR 30 0 Q96D71;Q96D71-3;H0YE73 Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.304)S(0.304)S(0.304)S(0.086)QTLTQFDSNIAPADPDTAIVHPVPIR;S(0.325)S(0.325)S(0.325)S(0.022)QT(0.003)LTQFDSNIAPADPDTAIVHPVPIR 140.61 3.51E-08 264254000 14262.2 10106.8 4104.7 3793.8 12146.6 11251.3 11212 7134.4 9545.4 TRUE FALSE 12377.41413 10040.40777 6089.746649 4655.240275 11904.90642 11684.14479 10124.66197 5608.76408 8416.953686 1.47053371 1.192879056 0.723509583 0.553078994 1.414396095 1.388167884 1.202889114 0.666365088 1 13.03908246 4.512733141 4.786185947 0.985885649 1.425565231 0.220195748 0.289618011 0.327782603 17.90901074 0.078083138 0.303908199 32563.65473 -4.512733141 0.439679582 S(ph)SSTGNLLDKDDLAIPPPDYGAASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSSTGNLLDKDDLAIPPPDYGAASR 25 1 Q9UQB8;Q9UQB8-2;Q9UQB8-4;Q9UQB8-5;Q9UQB8-3;I3L4C2;Q9UQB8-6;B4DWA1;I3L3C6 Q9UQB8 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 1 S(0.345)S(0.345)S(0.302)T(0.007)GNLLDKDDLAIPPPDYGAASR;S(0.333)S(0.333)S(0.333)T(0.002)GNLLDKDDLAIPPPDYGAASR;S(0.348)S(0.348)S(0.29)T(0.014)GNLLDKDDLAIPPPDYGAASR;S(0.333)S(0.333)S(0.333)T(0.002)GNLLDKDDLAIPPPDYGAASR 158.73 1.48E-11 871205000 1441270 929990 599958 743320 855520 686660 760530 1042350 890160 TRUE FALSE 1250802.518 923880.8345 890099.6955 912102.1669 838496.8258 713076.2545 686773.9177 819451.5641 784926.2989 1.593528615 1.177028768 1.133991429 1.162022687 1.068249117 0.908462687 0.874953379 1.043985359 1 19.58219767 8 0.566019111 0.974780164 30.58553883 0.862590281 0.073678439 56.1883443 0.498082833 0.040214481 2032.579112 99999999.97 -8 29.61075866 S(ph)SSTSDILEPFTVER ddPTM_MDA-MB-175_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 S(0.323)S(0.323)S(0.323)T(0.031)S(0.001)DILEPFTVER 127.36 0.00036086 0 56168 60638 40907 40293 51743 64440 58406 63061 65562 TRUE FALSE 48745.25649 60239.66499 60689.76203 49442.14149 50713.41553 66919.0485 52741.79511 49575.89589 57811.33505 0.843178184 1.042004391 1.04979001 0.855232654 0.877222702 1.157542002 0.912308893 0.85754629 1 15.81906477 2.048171664 24.99966365 0.908493362 0.97370868 0.038510757 0.103064573 301.3525456 156391.6672 0.041711847 0.028122112 111.7304798 -2.048171664 0.065215318 S(ph)SSVPHPFQVTLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSVPHPFQVTLLR 14 0 Q5VV41;Q5VV41-2 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 S(0.5)S(0.5)SVPHPFQVTLLR;S(0.5)S(0.5)SVPHPFQVTLLR 195.97 1.64E-08 2820490000 1729620 2132400 1289000 1453050 2233430 2462750 2059060 2115940 2112710 TRUE FALSE 1501046.335 2118392.124 1912364.711 1782987.211 2188989.113 2557493.586 1859372.678 1663462.697 1862947.831 0.805737182 1.137118329 1.026526175 0.957078444 1.175013641 1.372820829 0.998080916 0.892919635 1 20.82915584 4.749927543 23.66408946 1.060610419 0.805736861 0.272249398 0.134990237 1298.362699 2702868.546 0.036290826 0.52024654 56224.75131 -4.749927543 -0.254873557 S(ph)STDSLPGPISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSTDSLPGPISR 12 0 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 S(0.481)S(0.481)T(0.038)DS(0.001)LPGPISR 81.565 0.01815 174380000 360680 282940 221380 264800 383920 336810 339850 401660 392040 TRUE FALSE 313015.2242 281081.3485 328440.1085 324926.8872 376280.7431 349767.2986 306891.3993 315768.1347 345693.4778 0.905470436 0.813094162 0.950090556 0.939927734 1.088480886 1.011784489 0.887755827 0.91343388 1 18.39913386 4.124853296 6.176285859 0.966523493 0.860135386 0.37478426 0.059729444 0.235947567 11.73327051 0.016669035 0.035539956 13330.71046 -4.124853296 -0.106388107 S(ph)STPLHSPS(ph)PIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SSTPLHSPSPIR 12 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 2 S(0.977)S(0.011)T(0.013)PLHS(0.21)PS(0.79)PIR;S(0.999)S(0.003)T(0.002)PLHS(0.171)PS(0.825)PIR;S(0.999)S(0.003)T(0.003)PLHS(0.304)PS(0.692)PIR;S(0.999)S(0.048)T(0.039)PLHS(0.153)PS(0.76)PIR;S(0.997)S(0.066)T(0.05)PLHS(0.034)PS(0.852)PIR 117.41 0.0010773 892081000 1231148 1487544 851162 1127304 1446413 1659692 1049658 1294062 1400268 TRUE FALSE 1068448.672 1477772.226 1262786.79 1383275.603 1417632.211 1723541.425 947862.3287 1017336.912 1234729.912 0.865329868 1.196838443 1.022723089 1.120306222 1.148131423 1.395885374 0.767667746 0.823934774 1 20.23576407 2.209239815 24.99999983 0.851539774 1.124347594 0.420896988 0.144077412 186.4906264 159007.4879 0.057180554 0.038557753 161.897378 -2.209239815 0.272807819 S(ph)STPLHSPSPIR ddPTM_MDA-MB-175_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 164.68 0.00010285 0 241680 242910 94527 167490 243410 233810 214970 226060 208050 TRUE FALSE 209741.3757 241314.3082 140240.5734 205521.1644 238566.6172 242804.822 194122.2425 177718.8282 183454.566 1.143287846 1.315390036 0.764443079 1.120283724 1.300412535 1.323514739 1.058148874 0.968734832 1 17.48506329 2.007019717 24.82846034 0.991526457 1.157674545 0.178305112 0.159714528 272.7717138 964778.6487 0.068072437 0.045779305 101.6294831 -2.007019717 0.166148088 S(ph)STPPGESYFGVSSLQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSTPPGESYFGVSSLQLK 18 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.333)S(0.333)T(0.333)PPGESYFGVSSLQLK;S(0.333)S(0.333)T(0.333)PPGESYFGVSSLQLK 104.24 0.00053741 92965000 248550 186376 113121 156522 195685 144516 204493 284570 224990 TRUE FALSE 215703.4878 185151.6838 167826.694 192062.7124 191791.2514 150075.624 184661.3003 223716.92 198391.9385 1.087259338 0.933262133 0.845935048 0.968097362 0.966729056 0.756460294 0.930790342 1.127651263 1 17.59799388 1.756690225 25 1.067482673 0.920618571 0.282907702 0.090131152 8.163839579 11272.11705 0.047333639 0.022730123 57.10711554 -1.756690225 -0.146864102 S(ph)STPSHGQTTATEPTPAQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSTPSHGQTTATEPTPAQK 19 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 S(0.331)S(0.331)T(0.331)PS(0.008)HGQTTATEPTPAQK 90.819 0.0011239 0 147190 128730 55849 106430 133930 104150 140670 149770 151570 TRUE FALSE 127738.4686 127884.3642 82857.7632 130596.5582 131265.055 108156.7179 127027.8451 117742.851 133651.5673 0.955757356 0.956848968 0.619953547 0.977141988 0.982143777 0.809243918 0.95044037 0.880968726 1 17.02811723 S(ph)STPTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSTPTPR 7 0 Q04724;A0A669KBK8;A0A669KAE5;F6T2C8 Q04724 TLE1 Transducin-like enhancer protein 1 1 S(0.452)S(0.204)T(0.204)PT(0.141)PR 67.032 0.069507 46727000 74599 66867 37183 48287 46629 66447 58998 68802 67859 TRUE FALSE 64740.55314 66427.74627 55164.82317 59251.30137 45701.17413 69003.25909 53276.38304 54089.22772 59836.78633 1.081952376 1.110148963 0.921921556 0.990215301 0.763763847 1.153191261 0.890361704 0.903946068 1 15.86874507 4.239883479 24.99163133 0.941884898 1.096050719 0.285759546 0.098308327 38.97726512 736285.8394 0.023238174 0.054972767 17373.34641 -4.239883479 0.154165822 S(ph)STSPSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SSTSPSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNR 39 0 Q9BPZ3;D6RA77;D6R9Y1 Q9BPZ3 PAIP2 Polyadenylate-binding protein-interacting protein 2 1 S(0.245)S(0.245)T(0.245)S(0.245)PS(0.02)IINEDVIINGHS(0.002)HEDDNPFAEYMWMENEEEFNR;S(0.25)S(0.25)T(0.25)S(0.25)PSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNR;S(0.236)S(0.236)T(0.236)S(0.236)PS(0.042)IINEDVIINGHS(0.013)HEDDNPFAEYMWMENEEEFNR;S(0.249)S(0.249)T(0.249)S(0.249)PS(0.003)IINEDVIINGHSHEDDNPFAEYMWMENEEEFNR;S(0.25)S(0.25)T(0.25)S(0.25)PS(0.002)IINEDVIINGHSHEDDNPFAEYMWMENEEEFNR;S(0.239)S(0.239)T(0.239)S(0.239)PS(0.043)IINEDVIINGHS(0.001)HEDDNPFAEYMWMENEEEFNR 241.63 3.20E-50 360287000 94032.6 94684 64209.1 78033.8 92808.1 97356.3 102637.6 112941 93282.9 TRUE FALSE 81605.95366 94062.01457 95260.83553 95752.56696 90961.40039 101101.6599 92683.82135 88789.44606 82255.10183 0.992108111 1.143540187 1.158114614 1.164092741 1.105845089 1.229123271 1.126785078 1.079439987 1 16.32781754 1.408812295 2.268962107 0.98905298 1.136714756 0.334338796 0.059445957 0.485644497 3.637553967 0.128341725 0.015715703 25.63375887 -1.408812295 0.147661776 S(ph)STSSEPTPTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSTSSEPTPTVK 12 0 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 S(0.525)S(0.475)TSSEPTPTVK 283.35 3.48E-28 209020000 440730 392970 363330 466100 419540 368780 538070 535840 1383500 TRUE FALSE 382486.4138 390388.5542 539037.6033 571935.1289 411191.9748 382967.2052 485888.0542 421254.7859 1219944.206 0.313527792 0.320005253 0.441854308 0.468820726 0.337058017 0.313921902 0.398287112 0.3453066 1 20.21838374 1.23724573 24.9999993 1.000000761 0.369168587 0.931338131 0.053982809 8.310177269 157939.5584 0.083470648 0.013780165 17.26814674 -1.23724573 -0.630832175 S(ph)STVTGGEEPTPSVAYVHTTPGLPSGWEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSTVTGGEEPTPSVAYVHTTPGLPSGWEER 30 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-4 Q96PU5-7 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 S(0.236)S(0.236)T(0.236)VT(0.191)GGEEPT(0.062)PS(0.039)VAY(0.001)VHTTPGLPSGWEER 51.783 0.02623 0 12246 11835 8278.8 9937.1 12444 16332 12984 15215 17700 TRUE FALSE 10627.66007 11757.25511 12282.45537 12193.47043 12196.38875 16960.30261 11724.81368 11961.39065 15607.52616 0.680931748 0.753306769 0.786957218 0.781255806 0.781442787 1.086674623 0.751228193 0.766386071 1 13.92995426 2.976992673 24.95876036 0.873543971 0.756894782 0.315436887 0.102816035 1163.813888 1262526.999 0.033903536 0.034140048 948.4024626 -2.976992673 -0.116649188 S(ph)SWHQSSFHSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSWHQSSFHSTR 12 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 1 S(0.5)S(0.5)WHQSSFHSTR 85.576 0.0074693 207430000 333500 263030 225410 282270 340530 333600 313370 543250 413580 TRUE FALSE 289427.13 261302.1386 334419.03 346363.7177 333754.1192 346433.8079 282979.4256 427080.2151 364687.0436 0.793631513 0.716510617 0.917002772 0.949756027 0.915179536 0.94994822 0.77595141 1.171086888 1 18.47629942 2.836140141 0.065210461 1.849767464 1.71E-15 0.406824264 0.098920403 46.53628106 3.872182634 55.80710404 53.14384324 685.7094596 -2.836140141 -1.849767464 S(ph)TAALEEDAQILK ddPTM_MDA-MB-175_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(0.989)T(0.011)AALEEDAQILK;S(0.981)T(0.019)AALEEDAQILK;S(0.686)T(0.314)AALEEDAQILK;S(0.992)T(0.008)AALEEDAQILK;S(0.993)T(0.007)AALEEDAQILK;S(0.992)T(0.008)AALEEDAQILK 310.9 1.45E-50 1066900000 1354520 1684740 1220800 1377880 1874510 1729280 1963700 2207660 2353370 TRUE FALSE 1175516.75 1673672.832 1811182.963 1690748.714 1837210.918 1795806.521 1773260.676 1735569.089 2075157.28 0.566471159 0.806528184 0.872793104 0.814756901 0.885335746 0.865383332 0.854518688 0.836355445 1 20.98478925 4.784307774 2.207748912 0.8694009 0.464055109 0.794505555 0.049150428 0.319105495 1.617846343 0.012100888 0.264713272 60856.61252 -4.784307774 -0.405345791 S(ph)TCGDSEVEEESPGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STCGDSEVEEESPGKR 16 1 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 1 S(0.955)T(0.044)CGDS(0.001)EVEEESPGKR 127.4 4.07E-05 332580000 55254 43259 30995 51390 46477 49885 50569 67669 82210 TRUE FALSE 47952.0439 42974.82878 45984.28567 63058.88495 45552.19863 51804.10823 45664.82616 53198.51095 72491.22745 0.661487543 0.592827992 0.634342765 0.86988298 0.628382223 0.714625894 0.629935894 0.733861363 1 16.1455188 1.244549143 3.295655668 1.049809591 0.678343072 0.636728013 0.076371295 0.21157653 3.168340765 0.200921654 0.019469293 17.56099596 -1.244549143 -0.371466519 S(ph)TCMKETQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STCMKETQK 9 1 H0Y8A5;A0A3B3IS43;Q8IV35-2;Q8IV35 H0Y8A5 WDR49 WD repeat-containing protein 49 1 S(0.98)T(0.02)CMKETQK 56.258 0.07456 601370000 986090 737360 610480 719620 689300 585740 794960 972200 1251900 TRUE FALSE 855775.7081 732516.2336 905710.1699 883020.7197 675584.2786 608273.7968 717864.9016 764302.5957 1103901.808 0.775228106 0.6635701 0.82046262 0.799908754 0.611996713 0.551021651 0.650297786 0.692364656 1 20.07418042 1.238561249 24.36934719 1.000000043 0.692359518 0.562944565 0.084246357 0.022312326 340299.0505 0.122947911 0.022082872 17.32053285 -1.238561249 -0.307640525 S(ph)TDKEAQGQQFHHHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STDKEAQGQQFHHHR 15 1 A6ND36 A6ND36 FAM83G Protein FAM83G 1 S(0.944)T(0.056)DKEAQGQQFHHHR 105.99 0.00076807 32087000 31031 16551 9893.2 13717 19125 8676.8 26542 22777 15640 TRUE FALSE 26930.17473 16442.27539 14677.58461 16831.6545 18744.44992 9010.602111 23967.96093 17906.3158 13791.05702 1.952727387 1.192241854 1.064282788 1.220476029 1.359174275 0.65336559 1.737935018 1.298400534 1 13.75144542 4.739443665 23.83255556 1.210244693 1.952727799 0.42844193 0.275773537 38.44491261 1037251.067 0.064796407 0.380735142 54883.73582 -4.739443665 0.742483106 S(ph)TDSSSVSGSLQQETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STDSSSVSGSLQQETK 16 0 Q9H8G2;A0A3B3ISJ3 Q9H8G2 CAAP1 Caspase activity and apoptosis inhibitor 1 1 S(0.866)T(0.132)DS(0.002)S(0.001)SVSGSLQQETK 139.12 2.35E-05 0 120150 110070 71237 103730 137490 109430 124500 150280 140880 TRUE FALSE 104271.8731 109346.9429 105687.4515 127283.4819 134754.218 113639.8429 112426.0092 118143.7915 124225.3269 0.839376926 0.880230672 0.850772174 1.024617806 1.084756397 0.914788037 0.905016811 0.95104432 1 16.92259981 3.752200455 24.60018752 0.97397294 0.859136983 0.544600366 0.052919419 583.0196023 1051503.63 0.01543209 0.026536444 5651.977904 -3.752200455 -0.114835956 S(ph)TELVLSPDMPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 STELVLSPDMPR 12 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 S(0.993)T(0.007)ELVLSPDMPR;S(0.993)T(0.007)ELVLSPDMPR;S(0.991)T(0.009)ELVLSPDMPR;S(0.995)T(0.005)ELVLSPDMPR 292.39 3.88E-36 1018220000 903340 746634 498519 521797 785883 743905 731083 856430 796720 TRUE FALSE 783961.3302 741729.3121 739604.4558 640278.984 770245.4659 772523.5067 660182.6832 673289.1092 702532.6692 1.115907295 1.055793338 1.052768773 0.911386775 1.09638384 1.099626452 0.939718126 0.958374092 1 19.42220579 8 0.271240478 0.971000033 1.923603403 0.251667577 0.061771379 121.9795643 1.954400977 0.170104662 53.17006058 100000000 -8 0.952603371 S(ph)TENVNKLPELSSFGKPSSSVQGTGLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STENVNKLPELSSFGKPSSSVQGTGLIR 28 2 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 S(0.541)T(0.459)ENVNKLPELSSFGKPSSSVQGTGLIR;S(0.958)T(0.042)ENVNKLPELSSFGKPSSSVQGTGLIR 176.6 4.57E-14 2439500000 2313900 1527590 1149280 1385680 1531470 1079960 2345900 2407200 1376230 TRUE FALSE 2008112.252 1517555.161 1705075.652 1700319.823 1500996.743 1121506.76 2118394.979 1892439.013 1213533.657 1.654764366 1.250525811 1.405050154 1.401131162 1.236881016 0.924166176 1.745641719 1.559445015 1 20.21078269 4.750331426 23.37397785 1.345400842 1.654764825 0.152193605 0.24271378 1588.040019 3153312.821 0.060606224 0.888349908 56277.06327 -4.750331426 0.309363983 S(ph)TGDIAGTVVPETNKEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.993)T(0.007)GDIAGTVVPETNKEPR;S(0.992)T(0.008)GDIAGTVVPETNKEPR;S(0.987)T(0.013)GDIAGTVVPETNKEPR;S(0.975)T(0.025)GDIAGTVVPETNKEPR 216.31 5.47E-19 1403490000 896070 856460 807650 704980 883100 868760 882760 1031180 1453280 TRUE FALSE 777652.0791 850833.8579 1198232.241 865056.4839 865528.0378 902181.7594 797150.0711 810670.1817 1281474.894 0.606841447 0.663948909 0.935041527 0.675047547 0.675415525 0.704018287 0.622056721 0.632607151 1 20.28937378 1.232044644 24.97384615 1.000000528 0.690012462 0.529585936 0.092003944 187.6657754 719199.5193 0.215882265 0.023182945 17.06257779 -1.232044644 -0.309988066 S(ph)TMVGTPYWMAPEVVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STMVGTPYWMAPEVVTR 17 0 Q13177;H7C1X3;A0A087X294;O75914-2;O75914;O75914-4;O75914-3;H0YCG5;E9PM17;B3KNX7;Q13153;Q13153-2 Q13177;E9PM17 PAK2;PAK3;PAK1 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34;Non-specific serine/threonine protein kinase;Serine/threonine-protein kinase PAK 3;Serine/threonine-protein kinase PAK 1 1 S(0.844)T(0.156)MVGTPYWMAPEVVTR 132.84 2.34E-05 24126000 19089 21085 11514 12306 21011 22761 21097 22831 19482 TRUE FALSE 16566.34028 20946.49125 17082.20891 15100.26539 20592.92221 23636.6304 19051.01619 17948.76832 17178.86015 0.964344557 1.219317874 0.994373827 0.879002754 1.198736239 1.375913779 1.108980224 1.044817186 1 14.06834669 3.200314135 24.99996667 1.141838463 1.027485642 0.197769603 0.130200549 333.2822864 217850.1421 0.0424989 0.048190201 1586.039997 -3.200314135 -0.114352821 S(ph)TNTAVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 STNTAVSR 8 0 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 S(0.978)T(0.022)NTAVSR;S(0.976)T(0.024)NTAVSR;S(0.985)T(0.015)NTAVSR 130.09 0.0011147 1989700000 887090 754660 533750 702560 581380 824740 805600 854830 1537010 TRUE FALSE 769858.8089 749702.5888 791873.2853 862086.986 569811.6755 856468.2815 727473.036 672031.2568 1355306.429 0.568033024 0.553160948 0.584276196 0.63608271 0.420430143 0.631937002 0.536759083 0.495851892 1 20.37018764 1.234209574 24.9993113 1.000000663 0.551699875 0.833351166 0.062771713 48.82782889 280507.7401 0.111928193 0.01461438 17.14784599 -1.234209574 -0.448300788 S(ph)TPDLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 STPDLLR 7 0 Q9P2M7;Q9P2M7-2;H0Y4A8 Q9P2M7 CGN Cingulin 1 S(0.982)T(0.018)PDLLR;S(0.993)T(0.007)PDLLR;S(0.991)T(0.009)PDLLR 165.72 0.0012064 690050000 1198110 1207540 825740 835130 1076620 1055330 992230 1100540 1405390 TRUE FALSE 1039776.728 1199607.59 1225070.626 1024759.031 1055197.368 1095929.228 896003.6873 865198.0854 1239246.395 0.839039542 0.968013782 0.988560976 0.826921131 0.851483105 0.884351354 0.723023033 0.698164698 1 20.24103163 3.169043289 1.23651095 0.79347739 0.929666214 0.137456732 0.095304317 0.647042663 2.133232452 0.040946485 0.05337139 1475.853636 -3.169043289 0.136188824 S(ph)TPDSTYSESFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STPDSTYSESFK 12 0 Q6ISB3;Q6ISB3-2 Q6ISB3 GRHL2 Grainyhead-like protein 2 homolog 1 S(0.75)T(0.178)PDS(0.072)TYSESFK;S(0.947)T(0.053)PDSTYSESFK 300.27 1.89E-36 1655040000 2631500 1948150 1513220 1801500 1979340 1518870 2328100 2742600 2944300 TRUE FALSE 2283740.608 1935352.474 2245018.253 2210558.109 1939955.007 1577301.912 2102321.22 2156116.333 2596228.208 0.879637853 0.745447749 0.864723003 0.851449846 0.747220526 0.607535927 0.809759795 0.830480281 1 21.30798577 1.204949307 2.22932154 1.074740629 0.782956387 0.421540729 0.078117543 0.746018402 3.517279912 0.452914981 0.021698998 16.03058263 -1.204949307 -0.291784242 S(ph)TPLSQPSANGVQTEGLDYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STPLSQPSANGVQTEGLDYDR 21 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 1 S(0.5)T(0.5)PLSQPSANGVQTEGLDYDR 325.1 1.44E-67 598530000 113940 117500 99446 112940 159080 179450 152530 154940 211350 TRUE FALSE 98882.54031 116728.1348 147538.4182 138584.7532 155914.6192 186353.5576 137737.6641 121807.2867 186364.4438 0.530586942 0.626343375 0.791666131 0.743622283 0.836611405 0.999941587 0.739076947 0.653597244 1 17.50776711 4.43685774 1.507280123 0.814758485 0.489622547 0.479645265 0.108557904 0.64959513 2.090259477 0.032693983 0.268081297 27343.72893 -4.43685774 -0.325135938 S(ph)TPPYLFPEYPEASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 68.972 0.053541 79377000 75724 69085 61103 77154 81330 69769 65357 90095 102640 TRUE FALSE 65716.88154 68631.17609 90652.61518 94672.99493 79711.69212 72453.05858 59018.6882 70828.88537 90506.01613 0.726105118 0.758305127 1.001619771 1.046040904 0.88073363 0.800533066 0.652096852 0.782587594 1 16.46572607 1.228293622 24.73918759 1.000000397 0.830728919 0.164014536 0.119904385 836.2914446 2014953.993 0.440914429 0.032726786 16.91584208 -1.228293622 -0.169271478 S(ph)TPVRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STPVRDR 7 1 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 S(0.5)T(0.5)PVRDR 73.233 0.029946 44560000 119330 98880 59031 73090 63688 91396 95240 117190 77257 TRUE FALSE 103560.2382 98230.45077 87578.58905 89686.20161 62420.7334 94912.06326 86003.63946 92129.83047 68123.76547 1.520177833 1.441941004 1.285580567 1.31651856 0.916284251 1.393229846 1.262461622 1.352388991 1 16.05587056 4.25982512 1.747409151 1.22167814 1.528425381 0.367496722 0.14860359 0.49873608 2.706940881 0.041151004 0.188693667 18189.68255 -4.25982512 0.306747241 S(ph)TSATDTHHVEMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 STSATDTHHVEMAR 14 0 H3BTL2;H3BS02;O14874-2;O14874-3;O14874;H3BQP2;H3BNP3 H3BTL2 BCKDK "[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial" 1 S(0.952)T(0.046)S(0.001)ATDTHHVEMAR;S(0.799)T(0.2)S(0.001)ATDTHHVEMAR;S(0.974)T(0.025)S(0.001)ATDTHHVEMAR;S(0.976)T(0.022)S(0.001)ATDTHHVEMAR 177.04 1.38E-06 2494610000 722254 640637 458161 715794 778300 828980 640441 744261 751194 TRUE FALSE 626806.3039 636428.6134 679729.1921 878325.9679 762813.3527 860871.397 578331.1304 585106.577 662388.7011 0.946281697 0.960808378 1.026178724 1.325997811 1.15160985 1.299646862 0.873099329 0.883328137 1 19.33731854 2.208662238 24.99951253 0.90951257 1.118007581 0.345878244 0.129192112 238.6586464 199552.6511 0.056708786 0.038238742 161.6822105 -2.208662238 0.208495011 S(ph)TSFRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STSFRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR 40 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.315)T(0.315)S(0.315)FRGGMGS(0.053)GGLAT(0.004)GIAGGLAGMGGIQNEKETMQSLNDR 62.018 0.0084317 124560000 36591 50473 7611.5 10582 24938 18943 47369 39977 0 TRUE FALSE 31755.40664 50141.43954 11292.44686 12984.80484 24441.78259 19671.74947 42775.16167 31428.22965 0 0 S(ph)TSNFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STSNFK 6 0 A0A087X1U1;F5GXM9;E7EUN2;Q9UPQ3-2;Q9UPQ3;H7C211;H7C0A7 A0A087X1U1 AGAP1 "Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1" 1 S(0.976)T(0.016)S(0.008)NFK 90.601 0.051236 179930000 502320 514710 311560 459250 349420 450510 717800 679040 791900 TRUE FALSE 435937.1393 511328.8361 462231.4581 563529.7317 342467.2256 467841.4112 648187.8665 533832.5803 698282.4841 0.624299118 0.732266451 0.661954823 0.80702258 0.49044224 0.669988754 0.92826024 0.764493729 1 19.41345126 2.249290186 24.90450115 0.871135524 0.665891229 0.547720219 0.098944448 159.125194 369347.0771 0.035885367 0.027507339 177.5375352 -2.249290186 -0.205244295 S(ph)TSTPNVHMVSTTLPVDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 STSTPNVHMVSTTLPVDSR 19 0 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 S(0.36)T(0.36)S(0.272)T(0.008)PNVHMVSTTLPVDSR;S(0.343)T(0.343)S(0.263)T(0.052)PNVHMVSTTLPVDSR;S(0.325)T(0.325)S(0.325)T(0.024)PNVHMVSTTLPVDSR;S(0.348)T(0.348)S(0.285)T(0.018)PNVHMVSTTLPVDSR;S(0.33)T(0.33)S(0.33)T(0.009)PNVHMVSTTLPVDSR 211.71 7.48E-17 1291060000 882571 803256 475727 581633 852750 957197 779717 923072 813840 TRUE FALSE 765937.0062 797979.3584 705790.1684 713701.6624 835781.9434 994020.988 704100.1654 725680.2362 717628.7623 1.067316482 1.1119668 0.983503178 0.994527672 1.164643876 1.385146527 0.981148196 1.011219553 1 19.45287819 S(ph)TTELDDYSTNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 STTELDDYSTNK 12 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.972)T(0.006)T(0.022)ELDDYSTNK;S(0.937)T(0.051)T(0.008)ELDDYS(0.003)TNK;S(0.87)T(0.115)T(0.015)ELDDYSTNK;S(0.93)T(0.061)T(0.009)ELDDYSTNK;S(0.991)T(0.009)TELDDYSTNK 378.66 5.39E-87 3141340000 4534140 4599040 3727600 4510030 5170600 3704610 5804500 7027420 9135600 TRUE FALSE 3934941.911 4568828.603 5530279.828 5534101.243 5067715.176 3847128.744 5241580.483 5524660.92 8055599.775 0.488472866 0.567161817 0.686513727 0.686988107 0.629092224 0.477571981 0.650675385 0.685816212 1 22.94156058 1.092287509 1.817704415 1.273475097 0.599531132 0.752976972 0.072129127 0.717120475 1.613250358 0.955529168 0.020739291 12.36765918 -1.092287509 -0.673943965 S(ph)TTPAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STTPAPK 7 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.993)T(0.007)TPAPK;S(0.983)T(0.016)TPAPK 99.442 0.011041 378220000 1994570 1168230 815520 1056910 805480 965490 1460710 1798530 1454260 TRUE FALSE 1730982.521 1160555.82 1209908.2 1296897.569 789452.5239 1002633.025 1319050.569 1413928.356 1282339.039 1.349863388 0.905030405 0.943516623 1.011353105 0.615634789 0.781878266 1.028628567 1.102616634 1 20.29034632 4.740896692 23.84646798 0.931807565 1.349863676 0.482262048 0.138574446 114.585134 1169527.117 0.037756512 0.243480846 55067.66886 -4.740896692 0.418056112 S(ph)TTPPPAEPVSLPQEPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STTPPPAEPVSLPQEPPK 18 0 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 S(0.333)T(0.333)T(0.333)PPPAEPVSLPQEPPK;S(0.484)T(0.484)T(0.032)PPPAEPVSLPQEPPK 181.51 7.67E-14 743110000 676130 501780 400750 428800 489130 465790 589500 667890 650400 TRUE FALSE 586777.7074 498483.7741 594554.0404 526165.5938 479397.27 483709.2427 532330.3807 525066.921 573510.4529 1.023133414 0.869179928 1.036692596 0.91744726 0.835899795 0.843418355 0.928196475 0.915531562 1 19.12946026 4.756654439 23.55082318 0.917302488 1.023133614 0.215124405 0.062907127 2885.109671 3755107.312 0.015551582 0.448237354 57102.41009 -4.756654439 0.105831126 S(ph)TTPPPAEPVSLPQEPPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 STTPPPAEPVSLPQEPPKPR 20 1 Q9UN86-2 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 S(0.333)T(0.333)T(0.333)PPPAEPVSLPQEPPKPR;S(0.477)T(0.477)T(0.045)PPPAEPVSLPQEPPKPR;S(0.333)T(0.333)T(0.333)PPPAEPVSLPQEPPKPR 203.4 6.45E-22 26750820000 17558810 11676840 8263490 10829470 11864470 10806990 13529300 16466870 15120190 TRUE FALSE 15238368.77 11600134.07 12259741.4 13288466.68 11628390.26 11222741.9 12217230.57 12945558 13332698.36 1.142932087 0.870051489 0.919524396 0.996682466 0.872170805 0.841745729 0.916335931 0.97096309 1 23.66846546 4.74748933 24.96525484 0.924826773 1.142932201 0.62470677 0.053456598 840.5281615 2350119.825 0.013734038 0.161530189 55909.97907 -4.74748933 0.218105429 S(ph)TTPTSSPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STTPTSSPFR 10 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;H7C5N8;A0A2R8YET2;A0A2R8Y7F4;A0A2R8Y424 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.595)T(0.202)T(0.202)PTSSPFR 211.53 6.00E-08 463600000 847520 861650 484280 572760 847400 856760 727340 801510 749980 TRUE FALSE 735518.0847 855989.7644 718479.4278 702813.9121 830538.3979 889720.1116 656802.6787 630113.3239 661318.2188 1.112199942 1.294368944 1.086435255 1.062746938 1.255883135 1.345373659 0.99317191 0.952814101 1 19.33498512 2.117058304 8.778202059 0.973231818 1.189331062 0.547376168 0.090402615 0.19417324 14.0456629 0.03795485 0.025565158 130.9357694 -2.117058304 0.216099243 S(ph)VAS(ph)NQSEMEFSSLQDMPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVASNQSEMEFSSLQDMPK 19 0 Q8N163-2;Q8N163;H0YB24;G3V119;A0A087X2B6 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 2 S(0.973)VAS(0.514)NQS(0.514)EMEFSSLQDMPK 107.87 0.00015103 35502000 47370 38569 23515 33548 37622 25892 40938 52727 39326 TRUE FALSE 41109.93448 38315.6377 34886.93265 41165.58615 36873.39581 26888.08199 36967.83906 41451.74137 34676.92508 1.185512683 1.104931813 1.006056119 1.187117544 1.063340989 0.7753883 1.066064508 1.19536958 1 15.08168836 3.006952818 24.88117011 1.029817624 1.113268822 0.164917517 0.113813462 419.6703802 1501807.049 0.037626516 0.04257186 1016.138292 -3.006952818 0.083451197 S(ph)VAS(ph)SQPAKPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVASSQPAKPTK 12 1 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 2 S(0.999)VAS(0.985)S(0.016)QPAKPTK 97.797 0.056427 36004000 145280 145710 89761 102410 130320 88389 152470 175210 171790 TRUE FALSE 126080.8799 144752.8214 133169.7198 125663.7557 127726.887 91789.38203 137683.4829 137742.705 151481.1819 0.832320413 0.955582862 0.879117248 0.829566776 0.843186496 0.605945774 0.908914765 0.909305719 1 17.20877906 1.606674204 2.303304102 0.986668827 0.832350394 0.262631653 0.090686981 0.433317319 4.765866293 0.113032304 0.026037665 40.42725033 -1.606674204 -0.154318433 S(ph)VASSQPAKPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVASSQPAKPTK 12 1 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 S(0.992)VAS(0.008)SQPAKPTK;S(0.998)VAS(0.002)SQPAKPTK 156.72 3.91E-05 1286530000 1474140 1195250 923970 1113080 1218460 930820 1556170 1838400 1643780 TRUE FALSE 1279328.664 1187398.324 1370804.982 1365821.826 1194215.03 966629.2477 1405252.873 1445272.466 1449454.201 0.882627863 0.819203755 0.945738735 0.942300782 0.823906702 0.666891887 0.969504847 0.997114959 1 20.46707832 2.027587678 24.99998468 0.993839125 0.850398129 0.430632599 0.077440154 204.1021527 184956.7251 0.033176338 0.022366993 106.5583969 -2.027587678 -0.143440995 S(ph)VDALDDLTPPSTAESGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SVDALDDLTPPSTAESGSR 19 0 S4R3V8;Q86X29-6;Q86X29-5;Q86X29-2;Q86X29-3;Q86X29-4;Q86X29 S4R3V8 LSR Lipolysis-stimulated lipoprotein receptor 1 S(1)VDALDDLTPPSTAESGSR;S(1)VDALDDLTPPSTAESGSR;S(1)VDALDDLTPPSTAESGSR;S(1)VDALDDLTPPSTAESGSR 279.54 1.42E-39 730150000 563296 519576 356039 743540 735600 638980 364072 721650 1161500 TRUE FALSE 488855.0064 516162.871 528220.6513 912372.1213 720962.9992 663561.9741 328764.3535 567330.7634 1024188.793 0.477309466 0.503972387 0.515745393 0.89082416 0.703935645 0.64789029 0.320999757 0.553931821 1 19.96605025 3.966659911 24.89309954 0.652979611 0.495445225 0.175478536 0.182585841 1238.075871 924401.1454 0.051117745 0.088618758 9261.043222 -3.966659911 -0.157534387 S(ph)VDEVFDEVVQIFDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVDEVFDEVVQIFDK 15 0 P30085;P30085-3;A0A494BXC7;P30085-2 P30085 CMPK1 UMP-CMP kinase 1 S(1)VDEVFDEVVQIFDK;S(1)VDEVFDEVVQIFDK 256.45 9.82E-25 250510000 142484 77868 47431 110170 80408 56766 92032 103390 147529 TRUE FALSE 123654.3784 77356.47998 70368.79025 135185.7823 78808.03812 58949.82475 83106.75081 81280.85308 130088.2897 0.950541964 0.594645991 0.540931012 1.03918487 0.605804245 0.453152431 0.638848823 0.624812989 1 16.98913157 4.750054129 23.32470201 0.676609982 0.950542388 0.159490186 0.188627827 1253.126766 2542944.102 0.045129607 0.644403657 56241.14183 -4.750054129 0.273932406 S(ph)VDEVNYWDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVDEVNYWDK 10 0 F5H5P2;P12694;P12694-2;F5GXU9 F5H5P2 BCKDHA "2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial" 1 S(1)VDEVNYWDK 132.06 0.00024512 254220000 394890 274750 231530 289210 283770 242230 299040 349040 424230 TRUE FALSE 342704.286 272945.1492 343498.6824 354879.5508 278123.5322 251548.7448 270039.1468 274400.5122 374078.0127 0.916130525 0.729647667 0.918254136 0.948677919 0.743490723 0.67244996 0.721879228 0.7335382 1 18.51297965 3.216652487 24.998728 0.760159403 0.870430914 0.188469095 0.104342606 376.5739125 429696.2137 0.031658806 0.035926621 1646.844097 -3.216652487 0.110271511 ELFDDPSY(ph)VNVQNLDK ddPTM_MDA-MB-175_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(0.02)Y(0.98)VNVQNLDK;ELFDDPS(0.112)Y(0.888)VNVQNLDK;ELFDDPS(0.088)Y(0.912)VNVQNLDK 277.11 2.62E-34 525490000 456608 536252 557010 702950 925850 783950 1038670 1357890 1165350 TRUE FALSE 396266.0959 532729.3253 826381.8991 862565.5414 907427.3964 814109.0638 937939.9433 1067515.791 1027583.651 0.385629039 0.518429157 0.804199151 0.839411508 0.883069126 0.792255758 0.912762618 1.038860233 1 19.97082441 4.723823995 0.616993371 0.967492654 1.25E-20 0.894423211 0.065811612 1.176058752 0.35531903 0.039317421 0.813580692 52944.8833 -4.723823995 -0.967492654 down S(ph)VDFDSLTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 SVDFDSLTVR 10 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 S(1)VDFDSLTVR;S(0.998)VDFDS(0.002)LTVR;S(1)VDFDSLTVR;S(1)VDFDSLTVR;S(1)VDFDSLTVR;S(1)VDFDSLTVR;S(1)VDFDSLTVR;S(1)VDFDSLTVR;S(1)VDFDSLTVR 270.93 1.05E-23 12854660000 3748040 4344820 2796752 3115312 4609210 4603670 4501910 5002960 4691290 TRUE FALSE 3252727.018 4316278.591 4149270.622 3822691.204 4517495.739 4780776.164 4065315.461 3933115.937 4136691.041 0.786311326 1.043413334 1.003040977 0.92409396 1.092055388 1.155700563 0.982745731 0.950787936 1 21.98004578 4.742966415 24.57575749 1.015046658 0.786311209 0.543370803 0.066944423 311.0075674 1734735.674 0.017586317 0.13366823 55330.73184 -4.742966415 -0.228735449 S(ph)VDIHDSIQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SVDIHDSIQPR 11 0 Q9Y6D6;E5RIF2;E5RHL7 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 S(1)VDIHDSIQPR;S(1)VDIHDSIQPR;S(1)VDIHDSIQPR;S(1)VDIHDSIQPR;S(1)VDIHDSIQPR;S(1)VDIHDSIQPR 187.97 2.16E-06 8320910000 5109700 6052460 1554322 3199660 8477340 8012630 6339460 6878200 7088140 TRUE FALSE 4434440.199 6012700.992 2305997.318 3926191.707 8308657.52 8320881.061 5724660.145 5407350.456 6250188.164 0.709489072 0.962003196 0.368948463 0.628171761 1.329345182 1.331300889 0.915918048 0.865150027 1 22.57546819 3.262000388 24.99938631 1.059659803 0.666913325 0.501517583 0.207564984 231.3506501 246742.4092 0.065469377 0.084469879 1828.101849 -3.262000388 -0.392746478 S(ph)VDLDLLCGHYNNDGNAPSFGLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVDLDLLCGHYNNDGNAPSFGLLR 24 0 Q06190 Q06190 PPP2R3A Serine/threonine-protein phosphatase 2A regulatory subunit B subunit alpha 1 S(1)VDLDLLCGHYNNDGNAPSFGLLR 189.45 9.12E-18 121690000 59325 43294 28373 17476 44927 28913 70293 64730 23678 TRUE FALSE 51485.05094 43009.59886 42094.2777 21444.1929 44033.0406 30025.30182 63475.99568 50887.99323 20878.81381 2.465899232 2.059963715 2.016124004 1.027079081 2.108981908 1.438075079 3.040210821 2.437302889 1 14.34975213 4.716943678 2.629577266 1.946950171 2.555676195 0.075176164 0.620764699 1.505111474 14.14282698 0.162795928 1.973468408 52112.71237 -4.716943678 0.608726024 S(ph)VEDDAEGHLIYHVGDWLQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SVEDDAEGHLIYHVGDWLQER 21 0 B1AVT0;P49760-3;P49760 B1AVT0 CLK2 Dual specificity protein kinase CLK2 1 S(1)VEDDAEGHLIYHVGDWLQER;S(1)VEDDAEGHLIYHVGDWLQER;S(1)VEDDAEGHLIYHVGDWLQER;S(1)VEDDAEGHLIYHVGDWLQER;S(1)VEDDAEGHLIYHVGDWLQER 204.61 8.69E-22 190592000 118491.4 112297 92929.2 102815.4 124082.7 122493.3 117038.3 142369.6 134936.3 TRUE FALSE 102832.4613 111559.3136 137870.0719 126161.208 121613.697 127205.6965 105687.9437 111924.969 118984.2843 0.864252467 0.937597047 1.15872506 1.060318249 1.022098824 1.069096623 0.888251287 0.940670187 1 16.86041151 0.915946378 20.85228167 1.407908413 0.9927917 0.000667879 0.089436009 5038.361385 2131685.31 266967.4849 0.022494728 8.240363656 -0.915946378 -0.415116713 S(ph)VEDVRPHHTDANNQSACFEAPDQK ddPTM_MDA-MB-175_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(0.49)VEDVRPHHT(0.49)DANNQS(0.02)ACFEAPDQK;S(0.882)VEDVRPHHT(0.105)DANNQS(0.014)ACFEAPDQK;S(0.995)VEDVRPHHT(0.005)DANNQSACFEAPDQK;S(0.98)VEDVRPHHT(0.02)DANNQSACFEAPDQK;S(0.682)VEDVRPHHT(0.318)DANNQSACFEAPDQK;S(0.948)VEDVRPHHT(0.052)DANNQSACFEAPDQK 181.63 1.43E-17 6277610000 4793590 3768930 2049860 2927100 3894350 3023090 4549170 4880390 4494080 TRUE FALSE 4160104.936 3744171.651 3041179.152 3591742.793 3816860.054 3139390.228 4107992.194 3836756.578 3962794.982 1.049790604 0.944831026 0.767432877 0.906366039 0.963173738 0.792216161 1.036640102 0.968194569 1 21.9180869 2.205259519 24.99997344 0.996109215 0.902419601 0.240069309 0.081668009 285.2647996 214153.5641 0.033256368 0.022422919 160.4203719 -2.205259519 -0.093689615 S(ph)VENLPECGITHEQR ddPTM_MDA-MB-175_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 308.45 2.78E-56 13459530000 4592090 4489850 3020450 3299440 4700950 4443440 4655410 5084740 4710300 TRUE FALSE 3985233.672 4460355.88 4481149.723 4048628.281 4607410.292 4614382.012 4203929.055 3997407.92 4153453.7 0.959498759 1.073890839 1.078897237 0.974761866 1.109296173 1.110974708 1.012152622 0.962429874 1 21.98588004 2.004998571 24.85882899 0.981159316 1.053413847 0.249919256 0.050790133 153.4921746 763341.0945 0.020515962 0.013777661 101.1576125 -2.004998571 0.072254532 S(ph)VEPQDAGPLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVEPQDAGPLER 12 0 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 1 S(1)VEPQDAGPLER 68.751 0.049037 0 1259600 626660 941430 707690 656190 510920 1114400 1203500 1279600 TRUE FALSE 1093140.669 622543.4292 1396708.697 868381.8309 643133.1028 530575.423 1006325.66 946140.8906 1128327.146 0.968815359 0.551740186 1.237857923 0.769618842 0.56998815 0.470231905 0.891874013 0.838534191 1 20.10575399 3.512830769 24.98277852 0.752539389 0.902871417 0.106117348 0.221340906 1542.89539 1079423.203 0.061793434 0.091612379 3257.097573 -3.512830769 0.150332028 S(ph)VGGSGGGSFGDNLVTR ddPTM_MDA-MB-175_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(0.914)VGGS(0.042)GGGS(0.044)FGDNLVTR;S(0.969)VGGS(0.026)GGGS(0.005)FGDNLVTR 215.67 5.81E-15 569580000 815950 712330 445470 477910 654390 679170 689550 715260 759050 TRUE FALSE 708120.1401 707650.6573 660900.782 586426.7699 641368.9193 705298.1094 622677.5471 562307.2152 669315.9737 1.057975856 1.057274419 0.987427176 0.876158336 0.95824535 1.053759565 0.930319269 0.84012221 1 19.35232792 4.081209735 3.703199938 0.936364927 1.057343136 0.381600873 0.059112271 0.235356537 6.311566581 0.016822425 0.03836275 12056.18031 -4.081209735 0.120978209 S(ph)VHREESCSDSGTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SVHREESCSDSGTK 14 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 S(1)VHREESCSDSGTK;S(1)VHREESCSDSGTK;S(1)VHREESCSDSGTK;S(1)VHREESCSDSGTK 256.84 1.52E-24 1545190000 668964 723193 507202 505923 622116 695619 730626 813227 748679 TRUE FALSE 580558.7125 718442.2976 752486.5837 620800.5497 609737.1087 722379.9131 659770.003 639324.7346 660171.0215 0.879406538 1.08826694 1.139835829 0.940363223 0.923604776 1.094231479 0.999392554 0.968422899 1 19.33248029 S(ph)VHS(ph)EHS(ph)AR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVHSEHSAR 9 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 3 S(1)VHS(1)EHS(1)AR;S(1)VHS(1)EHS(1)AR 122.97 0.00038199 399785000 621060 596390 408950 445910 429920 508640 461200 581640 572400 TRUE FALSE 538985.3474 592472.2748 606719.5879 547160.6808 421365.4331 528207.7099 416472.895 457260.8123 504731.5241 1.067865433 1.173836479 1.202063986 1.084062823 0.834830822 1.046512224 0.825137474 0.90594859 1 18.94515667 3.397994401 5.392134475 0.920133228 1.149608951 0.670852451 0.073918414 0.110045365 5.507283628 0.020509895 0.026735771 2500.313124 -3.397994401 0.229475723 S(ph)VHSEHSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVHSEHSAR 9 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 S(1)VHSEHSAR 74.76 0.025881 80547000 17005 15275 9743.2 12067 13688 22675 12004 12590 11706 TRUE FALSE 14757.74616 15174.65752 14455.04411 14806.99678 13415.63558 23547.32192 10839.85393 9897.726475 10322.13002 1.429719074 1.470109124 1.400393532 1.434490436 1.299696435 2.281246398 1.050156694 0.958884112 1 13.33345309 2.034902785 24.99969062 0.984908193 1.536794253 0.480023408 0.270043745 141.7884431 101557.7353 0.106811932 0.072012292 108.3684308 -2.034902785 0.55188606 S(ph)VKEDSNLTLQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVKEDSNLTLQEK 13 1 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 1 S(1)VKEDSNLTLQEK 210.17 1.94E-08 398530000 461920 305740 144240 338960 255510 101770 610310 433900 220860 TRUE FALSE 400876.1016 303731.5738 213994.9465 415926.0487 250425.8509 105685.1578 551122.2301 341113.8616 194750.1824 2.058411944 1.559595837 1.098817695 2.135690162 1.285882497 0.542670392 2.829893268 1.751545788 1 17.57126515 2.24141268 24.99999919 1.878177186 1.46014527 0.088129897 0.625375932 189.8561489 1664222.377 0.238451494 0.176389987 174.3462777 -2.24141268 -0.418031916 S(ph)VKHDSIPAADTFEDLSDVEGGGSEPTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVKHDSIPAADTFEDLSDVEGGGSEPTQR 29 1 O95671;O95671-2;O95671-3 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 1 S(0.481)VKHDS(0.481)IPAADT(0.036)FEDLS(0.001)DVEGGGSEPTQR 45.511 0.069876 39781000 47206 58142 10824 23932 52071 22244 71344 64935 15738 TRUE FALSE 40967.6075 57760.06137 16058.5226 29366.12638 51034.88898 23099.74107 64425.06986 51049.15557 13877.47157 2.9520945 4.162145899 1.157164871 2.116100633 3.677535113 1.664549695 4.642421319 3.678563153 1 13.76045712 3.2456144 24.9980421 3.090689875 2.60584505 0.008631186 1.264172932 740.8380513 2625455.649 0.370013782 0.467293036 1760.412322 -3.2456144 -0.484844825 S(ph)VPILS(ph)RQRDADVEKIHY(ph)PHVYDS(ph)QAEAMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVPILSRQRDADVEKIHYPHVYDSQAEAMK 30 3 Q8N3C0;Q8N3C0-4 Q8N3C0 ASCC3 Activating signal cointegrator 1 complex subunit 3 4 S(1)VPILS(1)RQRDADVEKIHY(0.503)PHVY(0.503)DS(0.994)QAEAMK 44.596 0.046743 65171000 6645.5 7205.1 6876.8 6423.4 4024.5 6741.3 8566 7540.6 4750.1 TRUE FALSE 5767.280337 7157.769224 10202.44348 7881.931146 3944.420324 7000.642173 7735.270638 5928.101371 4188.548589 1.376916183 1.708890101 2.435794468 1.881780998 0.941715308 1.671376617 1.846766362 1.415311592 1 12.03223469 3.382682189 24.99985484 1.428572797 1.882767959 0.279948262 0.372182614 22.26942373 5881.056457 0.110112473 0.142154605 2413.693876 -3.382682189 0.454195162 S(ph)VPNTPLRPNQQSVVNSSFSELFVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVPNTPLRPNQQSVVNSSFSELFVK 25 1 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 1 S(1)VPNTPLRPNQQSVVNSSFSELFVK 211.63 7.46E-26 512240000 263060 183460 118710 143780 189810 140410 193130 206790 211390 TRUE FALSE 228295.9545 182254.8392 176118.5531 176427.4465 186033.1524 145811.6636 174400.2823 162569.5677 186399.715 1.224765577 0.977763508 0.944843467 0.946500624 0.998033459 0.78225261 0.935625263 0.872155667 1 17.50804013 7.890701418 0.970012281 0.912326872 199.9988154 0.688728571 0.062676902 588.8769965 1.17946498 0.019000944 259965.5515 77750182.64 -7.890701418 199.0864885 S(ph)VQEGENPDDGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVQEGENPDDGVR 13 0 H7C5M1;Q5TCT4;A2A2V2;P42696-2;P42696 H7C5M1 RBM34 RNA-binding protein 34 1 S(1)VQEGENPDDGVR;S(1)VQEGENPDDGVR 218.12 2.59E-11 1368840000 566870 311700 332190 360990 468500 476210 546060 519540 749300 TRUE FALSE 491956.6932 309652.4222 492838.1951 442958.2969 459177.7666 494530.1068 493103.1852 408440.4141 660718.6076 0.744578233 0.46866006 0.745912389 0.670418983 0.694967209 0.748473104 0.746313453 0.618176043 1 19.33367645 1.23206411 24.99958866 1.00000054 0.677739507 0.578478072 0.085915345 158.05855 608176.4555 0.186942174 0.020115031 17.06334257 -1.23206411 -0.322261033 S(ph)VS(ph)FY(ph)T(ph)RK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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;S(1)VS(1)FY(1)T(1)RK 56.013 0.037362 1626200000 2258720 1903300 1428210 1742690 2906800 1814450 3007600 2892100 2829500 TRUE FALSE 1960224.429 1890797.097 2118897.133 2138394.4 2848960.367 1884253.066 2715923.415 2273646.921 2494999.733 0.785661178 0.757834589 0.849257459 0.857071995 1.141868005 0.75521173 1.088546575 0.911281429 1 21.25060823 3.463971385 24.86067799 0.970722675 0.803535274 0.394175709 0.104619491 211.6501031 400136.5707 0.02763982 0.035703603 2910.525343 -3.463971385 -0.1671874 S(ph)VS(ph)PCSNVESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SVSPCSNVESR 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)VS(0.997)PCS(0.003)NVESR;S(1)VS(0.998)PCS(0.002)NVESR;S(1)VS(1)PCSNVESR;S(1)VS(0.79)PCS(0.21)NVESR;S(1)VS(0.941)PCS(0.059)NVESR;S(1)VS(1)PCSNVESR;S(1)VS(1)PCSNVESR 207.04 3.56E-08 9134870000 6775070 5496290 3552069 3923440 5660490 5241550 5082600 5996380 6204700 TRUE FALSE 5879727.334 5460184.509 5269861.449 4814317.018 5547857.324 5443195.82 4589690.234 4714100.801 5471187.434 1.074671158 0.997988933 0.963202506 0.879940063 1.014013391 0.994883814 0.83888375 0.861622976 1 22.38342255 8 0.467553628 0.910715155 5.09295339 0.3549583 0.060499837 113.9549363 1.367206688 0.045038553 458.3401041 100000000 -8 4.182238235 S(ph)VS(ph)PPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVSPPPK 7 0 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 2 S(1)VS(1)PPPK;S(1)VS(1)PPPK 81.338 0.040164 1256330000 4914800 3824200 2708000 3229900 3511500 3033900 4417900 5452900 6614700 TRUE FALSE 4265296.727 3799078.578 4017597.858 3963298.161 3441628.02 3150616.096 3989452.738 4286839.77 5832717.701 0.731270901 0.651339354 0.688803756 0.679494254 0.590055648 0.540162624 0.683978369 0.734964383 1 22.47573682 1.162477329 1.910825387 1.171683608 0.647688145 0.805923702 0.053555177 0.461984163 1.366059919 0.468126461 0.015536731 14.53708499 -1.162477329 -0.523995463 S(ph)VS(ph)PPPKR ddPTM_MDA-MB-175_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 86.014 0.057161 5935850000 5509790 4443050 3035270 3664870 4190430 3585780 4854200 5992190 6289510 TRUE FALSE 4781657.291 4413863.312 4503136.724 4497034.748 4107048.641 3723727.277 4383440.431 4710806.8 5545971.293 0.862185727 0.795868402 0.811965387 0.810865133 0.740546322 0.671429238 0.79038282 0.849410599 1 22.40300872 1.283098122 2.18113077 1.049787293 0.780519987 0.652709147 0.050000779 0.401568007 2.115994428 0.206471649 0.014517815 19.19102285 -1.283098122 -0.269267306 S(ph)VS(ph)PSPSVLSEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SVSPSPSVLSEGR 13 0 C9IYE1;A0A087X1P3;Q86UW7-3;Q86UW7-2;Q86UW7 C9IYE1 CADPS2 Calcium-dependent secretion activator 2 2 S(1)VS(0.707)PS(0.289)PS(0.004)VLSEGR;S(1)VS(0.532)PS(0.468)PS(0.001)VLSEGR;S(0.992)VS(0.874)PS(0.131)PS(0.002)VLSEGR;S(1)VS(0.767)PS(0.233)PSVLSEGR 196.74 2.04E-07 1427860000 1411150 1572880 1028810 1316680 1837510 1634940 1618380 2038890 2278330 TRUE FALSE 1224662.952 1562547.648 1526345.957 1615652.318 1800947.146 1697837.2 1461429.757 1602889.24 2008988.423 0.609591841 0.777778324 0.759758463 0.804211861 0.896444761 0.84512045 0.727445584 0.797858874 1 20.93803782 5.548782438 0.835063737 0.835350992 6.19E-11 0.498775516 0.072720188 7.611561854 1.538144456 0.025874403 8.056628794 353820.0488 -5.548782438 -0.835350992 S(ph)VS(ph)PYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVSPYSR 7 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 S(1)VS(0.995)PY(0.004)SR;S(1)VS(0.974)PY(0.025)S(0.002)R 83.869 0.032109 320930000 1124700 753410 536050 612630 789670 785120 751050 867640 809660 TRUE FALSE 976068.0454 748460.8001 795285.573 751737.005 773957.112 815324.0744 678213.2866 682101.938 713942.9172 1.367151381 1.048348239 1.113934397 1.052937128 1.084060215 1.142001769 0.9499545 0.955401225 1 19.4454492 8 0.911682387 1.022986791 178.0945333 0.70587199 0.064686097 583.1583302 1.212202335 0.022911546 214973.3156 100000000 -8 177.0715465 S(ph)VS(ph)RS(ph)PVPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVSRSPVPEK 10 1 Q13243;Q13243-3 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 3 S(1)VS(1)RS(1)PVPEK;S(1)VS(1)RS(1)PVPEK 121.24 0.00042423 669780000 3328800 2557850 2057470 2459400 2508600 2502100 2465900 3184300 5564700 TRUE FALSE 2888890.646 2541047.315 3052469.374 3017844.36 2458683.768 2598357.406 2226757.398 2503362.225 4906847.505 0.588746775 0.517857405 0.622083603 0.615027134 0.501071974 0.52953702 0.453806114 0.510177303 1 22.22636501 1.236389325 24.99999709 1.000000592 0.538952298 0.880656335 0.052940369 19.99327074 230143.522 0.089826856 0.013967709 17.23412842 -1.236389325 -0.461048294 S(ph)VSGS(ph)PEPAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVSGSPEPAAK 11 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 S(0.994)VS(0.006)GS(1)PEPAAK;S(0.998)VS(0.002)GS(1)PEPAAK 173.06 1.85E-05 1160000000 4004490 3369410 2288030 2810270 3202110 2901130 3803330 4570600 4032000 TRUE FALSE 3475286.5 3347276.124 3394528.961 3448384.756 3138394.276 3012738.348 3434483.642 3593212.758 3555341.553 0.977483161 0.941478076 0.954768736 0.96991659 0.88272652 0.847383663 0.966006666 1.010651918 1 21.76155673 2.001333264 24.99986909 1.000759566 0.92848127 0.395428434 0.039082212 44.81450962 840300.7576 0.017401745 0.011629168 100.307467 -2.001333264 -0.072278296 S(ph)VSHGSNHTQKPDEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SVSHGSNHTQKPDEQR 16 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.872)VS(0.125)HGS(0.003)NHTQKPDEQR;S(0.978)VS(0.022)HGSNHTQKPDEQR;S(0.995)VS(0.005)HGSNHTQKPDEQR;S(0.981)VS(0.019)HGSNHTQKPDEQR;S(0.99)VS(0.01)HGSNHTQKPDEQR;S(0.883)VS(0.117)HGSNHTQKPDEQR;S(0.756)VS(0.244)HGSNHTQKPDEQR;S(0.844)VS(0.156)HGSNHTQKPDEQR 276.08 1.67E-35 5132669000 1532310 1571904 397007 1195601 2420271 2176259 2426576 2547176 2815669 TRUE FALSE 1329811.351 1561578.059 589000.9131 1467080.481 2372112.342 2259981.092 2191247.033 2002482.235 2482803.818 0.53560871 0.628957491 0.23723216 0.590896659 0.955416745 0.910253591 0.882569544 0.806540662 1 21.24353884 3.355282557 4.65111446 0.894843779 0.473690551 0.780179975 0.110005085 0.09759982 3.531998921 0.031910696 0.041501094 2266.11819 -3.355282557 -0.421153228 S(ph)VSKESVASMGADSGDDFASDGSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVSKESVASMGADSGDDFASDGSSSR 26 1 Q92805;Q5T165 Q92805 GOLGA1 Golgin subfamily A member 1 1 S(0.512)VS(0.437)KES(0.049)VAS(0.002)MGADSGDDFASDGSSSR 102.4 1.26E-08 0 80957 76822 60038 61570 89167 70909 105550 103650 84768 TRUE FALSE 70258.32733 76317.35122 89072.57762 75550.40954 87392.75115 73636.91511 95313.77725 81485.25411 74746.82361 0.939950675 1.021011296 1.191657027 1.01075077 1.169183477 0.985151095 1.275154885 1.090150058 1 16.18972465 4.460239585 6.74539314 1.106328452 0.958680847 0.257971082 0.091588446 0.161964379 32.28148514 0.02121304 0.061010461 28856.22961 -4.460239585 -0.147647605 S(ph)VSPPPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVSPPPKR 8 1 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 S(0.91)VS(0.09)PPPKR;S(0.853)VS(0.147)PPPKR 52.79 0.086172 766100000 2395000 1901320 1183940 1400890 1579390 1507270 1966110 2329500 1693720 TRUE FALSE 2078494.682 1888830.104 1756497.344 1718983.486 1547963.229 1565255.652 1775436.955 1831354.553 1493490.351 1.391702786 1.264708608 1.176102238 1.150983992 1.036473539 1.048052069 1.188783679 1.226224563 1 20.51025649 4.521196521 1.380943896 1.120205298 1.443862272 0.646965962 0.069570865 0.620241833 1.441159051 0.022071085 0.251360598 33204.46758 -4.521196521 0.323656974 S(ph)VSQDLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(0.998)VS(0.002)QDLIK;S(0.999)VS(0.001)QDLIK;S(0.993)VS(0.007)QDLIK;S(1)VSQDLIK;S(0.999)VS(0.001)QDLIK 187.42 0.00021226 3178680000 5500550 5000150 3677430 4256300 4746270 3630280 6139760 6288870 8998570 TRUE FALSE 4773638.381 4967303.685 5455847.448 5222757.968 4651828.513 3769939.221 5544327.02 4944044.091 7934769.306 0.601610229 0.626017404 0.687587407 0.658211697 0.586258823 0.475116424 0.698738275 0.623086053 1 22.91975685 1.236778304 7.189262486 1.007559975 0.620936697 0.7871561 0.062159821 0.051653244 16.38416454 0.095926125 0.015667744 17.24957123 -1.236778304 -0.386623278 S(ph)VSSFPVPQDNVDTHPGSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVSSFPVPQDNVDTHPGSGK 20 0 Q676U5-3;Q676U5;E7EVC7;Q676U5-2;Q676U5-4;Q676U5-5;C9JAY7 Q676U5-3 ATG16L1 Autophagy-related protein 16-1 1 S(0.987)VS(0.013)S(0.001)FPVPQDNVDTHPGSGK 250.7 5.46E-31 1941500000 1687000 1372200 979710 1321400 1446400 1210900 2225400 2016500 1939700 TRUE FALSE 1464058.676 1363185.928 1453501.033 1621444.066 1417619.47 1257484.107 2009581.051 1585287.167 1710390.876 0.855979003 0.797002572 0.849806353 0.947996209 0.828827778 0.735202768 1.17492503 0.926856656 1 20.70589463 2.249263436 24.99976798 1.017495791 0.839458056 0.571267157 0.080450691 158.4371963 370079.712 0.029641438 0.022723746 177.5266 -2.249263436 -0.178037735 S(ph)VSSSPWLPQDGFDPSDYAEPMDAVVKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SVSSSPWLPQDGFDPSDYAEPMDAVVKPR 29 1 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 S(0.664)VS(0.112)S(0.112)S(0.112)PWLPQDGFDPSDYAEPMDAVVKPR;S(0.601)VS(0.219)S(0.169)S(0.011)PWLPQDGFDPSDYAEPMDAVVKPR;S(0.982)VS(0.017)SS(0.001)PWLPQDGFDPSDYAEPMDAVVKPR;S(0.994)VS(0.005)S(0.001)SPWLPQDGFDPSDYAEPMDAVVKPR 220.24 1.23E-34 627304000 359391 355228 270838 313327 401249 388814 477035 533536 526403 TRUE FALSE 311896.5688 352894.4839 401816.1627 384472.6843 393264.9299 403771.9262 430772.2191 419443.4784 464172.237 0.671941456 0.760266245 0.865661775 0.828297459 0.847239233 0.869875219 0.928043913 0.903637583 1 18.82430071 6.674306228 0.237662452 0.985758623 4.05E-18 0.851681184 0.034511952 18.73315073 0.524232301 0.153823703 6.23010825 4723960.181 -6.674306228 -0.985758623 S(ph)VVDMDLDDTDDGDDNAPLFYQPGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVVDMDLDDTDDGDDNAPLFYQPGKR 26 1 E7EMW7;O95071-2;O95071;E7ET84 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 S(1)VVDMDLDDTDDGDDNAPLFYQPGKR;S(1)VVDMDLDDTDDGDDNAPLFYQPGKR 234.95 4.09E-45 158726000 152067 124222 85994 89099 116038 104592 154796 151823 63241 TRUE FALSE 131970.9607 123405.9775 127580.986 109330.2897 113729.0708 108615.7219 139783.9077 119356.8329 55764.72102 2.366567217 2.212975789 2.287844065 1.960563735 2.039444809 1.947749759 2.50667277 2.140364566 1 15.76706508 1.240493183 6.908965317 0.97435671 2.183413139 0.818555255 0.175118208 0.044643412 11.91301742 0.25473792 0.043736781 17.39775389 -1.240493183 1.209056429 S(ph)VVGTPAYLAPEVLLNQGYNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SVVGTPAYLAPEVLLNQGYNR 21 0 Q9BZL6-2;Q9BZL6;Q9BZL6-3 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 S(0.855)VVGT(0.143)PAY(0.002)LAPEVLLNQGYNR;S(0.911)VVGT(0.089)PAYLAPEVLLNQGYNR;S(1)VVGTPAYLAPEVLLNQGYNR 307.92 1.97E-66 202792000 106608.7 85292.2 37035.5 68082.5 80263.4 41872 128935.8 95500.1 90278.8 TRUE FALSE 92520.09018 84731.90992 54945.99168 83541.6722 78666.31537 43482.84293 116431.626 75078.1468 79606.14311 1.162222996 1.064389086 0.69022301 1.049437505 0.98819403 0.546224716 1.462595993 0.943120014 1 16.28059215 0.915846002 18.12106881 1.385207212 0.988511337 0.000220087 0.247443661 2710.950138 729795.2432 98042.89439 0.055765567 8.238459325 -0.915846002 -0.396695876 S(ph)VVGTPAYLAPEVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SVVGTPAYLAPEVLR 15 0 F8WBA3;Q15139;H0Y5M6;O94806 F8WBA3;O94806 PRKD1;PRKD3 Serine/threonine-protein kinase;Serine/threonine-protein kinase D1;Serine/threonine-protein kinase D3 1 S(1)VVGTPAYLAPEVLR;S(1)VVGTPAYLAPEVLR;S(1)VVGTPAYLAPEVLR;S(1)VVGTPAYLAPEVLR 250.31 9.32E-19 242297000 196844 170404 71470.7 140314 165237 81251 238798 189740 196689 TRUE FALSE 170830.5667 169284.6049 106034.1696 172174.4383 161949.107 84376.77855 215639.4067 149165.5776 173436.6505 0.984973857 0.97606016 0.611371179 0.992722344 0.93376519 0.486499124 1.243332399 0.860057993 1 17.40404927 2.208658543 24.99999561 1.006831513 0.839549061 0.197143737 0.1904247 392.7509381 328361.4733 0.074853972 0.050473948 161.6808347 -2.208658543 -0.167282452 S(ph)WASPVYTEADGTFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SWASPVYTEADGTFSR 16 0 E9PMS6;E9PJ10;E9PK58;E9PLU6;Q8WWI1-3;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(1)WASPVYTEADGTFSR;S(0.961)WAS(0.039)PVYTEADGTFSR;S(1)WASPVYTEADGTFSR;S(0.997)WAS(0.003)PVYTEADGTFSR;S(1)WASPVYTEADGTFSR;S(0.942)WAS(0.058)PVYTEADGTFSR;S(0.997)WAS(0.003)PVYTEADGTFSR 378.79 8.62E-105 12252190000 1558320 1923740 1111320 1250160 1945640 1846700 1649270 2190620 2105310 TRUE FALSE 1352384.064 1911102.825 1648758.069 1534027.935 1906925.571 1917743.744 1489324.049 1722172.96 1856422.65 0.728489314 1.029454594 0.888137229 0.826335498 1.02720443 1.03303186 0.802254836 0.927683661 1 20.82409377 4.756311645 24.45213702 0.934362709 0.728489083 0.388274517 0.083672434 3171.239647 4368303.291 0.020259349 0.600606909 57057.35633 -4.756311645 -0.205873626 S(ph)WDNILAPGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SWDNILAPGPR 11 0 C9J069 C9J069 C9orf172 Uncharacterized protein C9orf172 1 S(1)WDNILAPGPR;S(1)WDNILAPGPR;S(1)WDNILAPGPR;S(1)WDNILAPGPR 144.47 3.85E-05 238360000 180013 168996 120104 133851 166057 178277 166270 193713 180877 TRUE FALSE 156223.826 167885.8541 178186.6961 164243.9153 162752.7906 185135.4316 150145.161 152288.9824 159493.9271 0.979497018 1.052615966 1.117200506 1.029781624 1.020432524 1.160767904 0.941384814 0.954826213 1 17.28314197 2.196862031 24.99986686 0.962199145 1.059132842 0.423274657 0.052027379 132.1207916 79210.44687 0.020626113 0.013906284 157.3482913 -2.196862031 0.096933697 S(ph)WEDS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SWEDSPER 8 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IU26;B1AN86 Q9UDY2-7 TJP2 Tight junction protein ZO-2 2 S(1)WEDS(1)PER;S(1)WEDS(1)PER 112.59 0.0044028 314170000 802280 849720 563090 600580 880660 864450 875340 948380 1093890 TRUE FALSE 696256.6653 844138.1334 835402.2074 736950.8683 863136.589 897705.9509 790449.6615 745576.3173 964571.5704 0.721829967 0.875143078 0.866086284 0.764018857 0.894839342 0.930678426 0.819482645 0.772961116 1 19.87952876 4.743768404 24.19185996 0.855839967 0.721829878 0.281032527 0.070713299 516.1145357 2397397.293 0.017010115 0.139345374 55433.00274 -4.743768404 -0.13401009 S(ph)WGEQCPETSGTDSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SWGEQCPETSGTDSGR 16 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 S(1)WGEQCPETSGTDSGR 154.31 3.85E-07 398220000 100830 80297 57000 63537 91852 85268 87818 98892 117170 TRUE FALSE 87505.06003 79769.52372 84565.39065 77964.04695 90024.32491 88548.31514 79301.42388 77744.71538 103318.2961 0.846946411 0.772075487 0.818493857 0.754600588 0.871329942 0.857043897 0.767544829 0.752477715 1 16.65673623 3.23503969 24.99709678 0.831737221 0.797637031 0.0853159 0.071720958 331.193108 2351331.122 0.021643831 0.025517182 1718.065394 -3.23503969 -0.03410019 S(ph)WGHES(ph)PEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SWGHESPEER 10 0 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 2 S(1)WGHES(1)PEER 73.386 0.065998 163410000 533750 470020 298160 423760 511280 457980 476590 502540 688730 TRUE FALSE 463213.5851 466932.4077 442351.1733 519981.1848 501106.5283 475598.787 430370.3752 395075.7318 607309.124 0.762731148 0.76885459 0.728378936 0.856205126 0.825125967 0.783124719 0.708651259 0.65053482 1 19.21207152 S(ph)WGQQAQEYQEQK ddPTM_MDA-MB-175_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 351.62 5.86E-76 1805500000 912778 933561 749504 887955 1122481 1000369 1263090 1453520 1434040 TRUE FALSE 792152.0746 927428.3763 1111966.641 1089578.754 1100145.824 1038853.843 1140595.726 1142696.059 1264509.425 0.626450115 0.73342939 0.879366037 0.861661236 0.870017892 0.821546935 0.902006504 0.903667491 1 20.27014636 5.530181693 0.651088135 0.906859739 5.80E-21 0.803342231 0.045214194 3.733556544 0.571062521 0.020834357 3.170286939 338985.9455 -5.530181693 -0.906859739 S(ph)WHEESPFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SWHEESPFEK 10 0 Q9BY84 Q9BY84 DUSP16 Dual specificity protein phosphatase 16 1 S(1)WHEESPFEK;S(1)WHEESPFEK 271.01 6.43E-24 449300000 1240990 976210 749540 851290 882580 979900 1189880 1265950 1341980 TRUE FALSE 1076990.027 969797.2122 1112020.051 1044588.406 865018.3847 1017597.387 1074485.621 995236.4441 1183332.653 0.91013294 0.819547411 0.939735795 0.882751273 0.731001872 0.859941948 0.908016539 0.841045366 1 20.17442426 1.233700763 24.95379627 1.000000218 0.860409077 0.359724014 0.05804396 168.6267773 865738.0001 0.112124626 0.01399658 17.12776765 -1.233700763 -0.139591141 S(ph)WRT(ph)S(ph)QRDT(ph)SDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SWRTSQRDTSDVK 13 2 Q5T321;A0A0D9SF28;F5GXV7;Q8NFP9;Q8NFP9-3 Q5T321 NBEA Neurobeachin 4 S(0.981)WRT(0.987)S(0.939)QRDT(0.584)S(0.509)DVK 56.599 0.046075 161970000 651990 514930 367110 400480 465610 412710 501110 601590 690780 TRUE FALSE 565827.8696 511547.3909 544645.6239 491415.105 456345.272 428587.2208 452512.4293 472944.6601 609116.7753 0.92893168 0.839818261 0.894156336 0.806766658 0.749191765 0.70362078 0.742899305 0.776443334 1 19.21635931 3.638722415 4.152007984 0.783409629 0.882923562 0.208944206 0.081896898 0.34673339 10.43595539 0.023247635 0.035657346 4352.335992 -3.638722415 0.099513932 S(ph)WS(ph)TATSPLGGERPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SWSTATSPLGGERPFR 16 1 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;D6RD46;H0Y8P3;D6RJ93;Q6NVB9 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 2 S(1)WS(0.381)T(0.327)AT(0.051)S(0.242)PLGGERPFR;S(0.971)WS(0.252)T(0.252)AT(0.263)S(0.263)PLGGERPFR 71.742 0.022642 389090000 195896 255600 182649 238460 309040 325290 310020 361290 381040 TRUE FALSE 170007.8473 253920.9468 270978.6673 292605.9876 302890.7086 337804.1168 279954.3081 284030.9451 335993.8853 0.505984944 0.755730857 0.806498806 0.870867002 0.901476848 1.005387692 0.833212509 0.845345578 1 18.35807545 5.128886502 0.925699458 0.904813799 7.07E-21 0.830822575 0.057748206 1.642369808 0.682681042 0.019775004 1.768555108 134550.8673 -5.128886502 -0.904813799 S(ph)WSTATSPLGGERPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.976)WS(0.019)T(0.003)AT(0.002)SPLGGERPFR;S(0.99)WS(0.01)TATSPLGGERPFR;S(0.978)WS(0.02)T(0.003)ATSPLGGERPFR 192.62 3.06E-10 2547190000 272406 315263 212272 197824 259068 255718 304943 340808 309103 TRUE FALSE 236406.8569 313192.0166 314927.4492 242742.9628 253913.0537 265555.6369 275369.6748 267928.8614 272561.1955 0.867353317 1.149070454 1.155437584 0.890599861 0.931581817 0.9742973 1.010304032 0.983004426 1 18.05622065 3.73467221 24.99431965 0.968675358 1.06646545 0.205000268 0.084858117 491.7182255 3160725.569 0.022732143 0.035253955 5428.4046 -3.73467221 0.097790092 S(ph)WTSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SWTSPK 6 0 O75494-2;O75494 O75494-2 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.978)WT(0.014)S(0.008)PK;S(0.999)WT(0.001)SPK;S(1)WTSPK 102.51 0.037212 4563360000 4060310 2941630 2211950 2674340 3021340 2542300 3290230 3986990 4509910 TRUE FALSE 3523729.746 2922306.239 3281656.419 3281589.772 2961221.245 2640103.926 2971144.001 3134403.215 3976753.578 0.886081996 0.734847202 0.825209899 0.82519314 0.744632824 0.663884215 0.747128014 0.788181403 1 21.92315974 1.238946532 4.832375352 1.015952618 0.771874077 0.572234436 0.060663892 0.134999121 7.524143778 0.111711714 0.015430655 17.33590553 -1.238946532 -0.244078541 S(ph)YDNLTTACDNTVPLASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SYDNLTTACDNTVPLASR 18 0 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 S(0.992)YDNLT(0.008)TACDNTVPLASR;S(1)YDNLTTACDNTVPLASR;S(0.863)YDNLT(0.137)TACDNTVPLASR;S(1)YDNLTTACDNTVPLASR;S(0.806)YDNLT(0.193)T(0.001)ACDNTVPLASR 305.98 3.96E-50 3298920000 1391091 1326766 925514 1244081 1622441 1417924 1344190 1669301 2042367 TRUE FALSE 1207254.8 1318050.387 1373095.666 1526568.606 1590157.598 1472472.454 1213830.661 1312333.972 1800920.7 0.670354225 0.73187586 0.762440937 0.847660092 0.882969249 0.817622038 0.674005613 0.728701698 1 20.78030323 4.338729005 1.958673623 0.80701867 0.674012553 0.248145619 0.087902086 0.683842531 4.6361835 0.025342033 0.123661739 21813.68337 -4.338729005 -0.133006116 S(ph)YDVPPPPMEPDHPFYSNISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 SYDVPPPPMEPDHPFYSNISK 21 0 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 1 S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(0.999)Y(0.001)DVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK 260.08 9.02E-37 13719240000 10601240 10416030 6565760 8225470 11235610 8592160 11576870 13876890 12230100 TRUE FALSE 9200259.274 10347606.41 9740983.497 10093188.68 11012043.34 8922705.955 10454146.93 10909425.06 10784271.51 0.85311829 0.959509078 0.903258369 0.935917523 1.021120744 0.827381427 0.969388328 1.011605193 1 23.36242539 2.006772139 24.96672692 1.001791122 0.921562155 0.329468315 0.053278183 180.4115286 665117.6369 0.020679169 0.013904185 101.5715639 -2.006772139 -0.080228967 S(ph)YEDLTESEDGAASGDSHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYEDLTESEDGAASGDSHK 19 0 A0A0A0MSQ9;Q86VX9-5;Q86VX9 A0A0A0MSQ9 MON1A Vacuolar fusion protein MON1 homolog A 1 S(1)YEDLTESEDGAASGDSHK 172.61 4.30E-15 0 99065 82130 54164 55304 87419 73977 88572 93474 98429 TRUE FALSE 85973.30925 81590.48262 80357.89157 67861.61847 85679.53293 76822.94306 79982.30107 73485.31252 86792.83575 0.990557671 0.940060109 0.925858579 0.781880415 0.987172872 0.885130004 0.921531142 0.846674865 1 16.40528834 4.479124627 2.265593069 0.899730348 0.990772654 0.151807176 0.06291376 0.641114308 5.513213365 0.015541196 0.093294971 30138.70776 -4.479124627 0.091042305 S(ph)YEDMIGEEVPSDQYYWAPLAQHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 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(0.959)Y(0.041)EDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(0.999)Y(0.001)EDMIGEEVPSDQYYWAPLAQHER;S(0.999)Y(0.001)EDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(0.998)Y(0.002)EDMIGEEVPSDQYYWAPLAQHER;S(0.999)Y(0.001)EDMIGEEVPSDQYYWAPLAQHER 257.04 4.17E-45 4366239000 1407639 1282740 919655 1108878 1273805 1327459 1168524 1359596 1488402 TRUE FALSE 1221615.94 1274313.596 1364403.234 1360665.698 1248458.773 1378527.207 1055200.722 1068856.976 1312444.811 0.93079414 0.970946424 1.039589035 1.036741268 0.951246683 1.050350609 0.803996262 0.814401464 1 20.32382533 2.238705124 25 0.857766242 0.997160362 0.438437811 0.065317978 3.120744042 540060.2711 0.025321472 0.018346072 173.2627184 -2.238705124 0.13939412 S(ph)YELPDGQVITIGNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SYELPDGQVITIGNER 16 0 P60709;A0A2R8Y793;P63267-2;A0A2R8YEA7;Q562R1;Q9BYX7;P63261;P68133;P68032;P63267;P62736;Q6S8J3;A5A3E0 P60709;P63261;P68133;Q6S8J3 ACTB;ACTG2;ACTBL2;POTEKP;ACTG1;ACTA1;ACTC1;ACTA2;POTEE;POTEF "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Beta-actin-like protein 2;Putative beta-actin-like protein 3;Putative beta-actin-like protein 3, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F" 1 S(1)YELPDGQVITIGNER;S(1)YELPDGQVITIGNER;S(1)YELPDGQVITIGNER;S(1)YELPDGQVITIGNER 248.95 1.82E-20 395637000 578160 470549 387049 446418 472546 483299 480732 568710 726170 TRUE FALSE 501754.6911 467457.9326 574227.191 547784.03 463143.2591 501891.8253 434110.6846 447095.7922 640323.0099 0.783596222 0.730034569 0.89677738 0.855480783 0.723296293 0.783810386 0.677955778 0.698234774 1 19.28844033 3.236747188 24.99813402 0.759811137 0.816034198 0.023695882 0.09810176 144.1784616 1987506.276 0.02925835 0.034900546 1724.833538 -3.236747188 0.056223061 S(ph)YENLAAEIMPVEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SYENLAAEIMPVEYR 15 0 Q9UJC3;Q9UJC3-2 Q9UJC3 HOOK1 Protein Hook homolog 1 1 S(1)YENLAAEIMPVEYR;S(1)YENLAAEIMPVEYR;S(1)YENLAAEIMPVEYR 163.45 4.44E-09 32961000 60139 48448 32357 40465 47749 47196 44286 54680 58084 TRUE FALSE 52191.47878 48129.7419 48004.95343 49653.19672 46798.88832 49011.66066 39991.15054 42987.10752 51217.37569 1.019018996 0.939715111 0.937278663 0.969459994 0.913730696 0.956934244 0.780812176 0.839307109 1 15.64434571 2.283188673 24.9991291 0.862419207 0.953118178 0.288197895 0.060303679 144.258667 80808.24444 0.022233169 0.017221647 191.9502461 -2.283188673 0.090698972 S(ph)YHDLSQASLYPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SYHDLSQASLYPHR 14 0 Q12923-3;Q12923;Q12923-4 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 S(0.996)Y(0.004)HDLSQASLYPHR;S(1)YHDLSQASLYPHR 166.52 2.44E-06 462260000 150781 174271 110410 118783 198900 209000 133982 132311 300230 TRUE FALSE 130854.9088 173126.2023 163804.6453 145754.4956 194942.2791 217040.3652 120988.4463 104017.3223 264737.1514 0.494282378 0.65395507 0.618744458 0.550563058 0.736361625 0.819833424 0.457013478 0.392907915 1 18.01420114 4.746323244 22.46888229 0.627544678 0.494282098 0.057940142 0.175871003 836.6590594 2421447.098 0.043474666 0.42267752 55760.06144 -4.746323244 -0.133262579 S(ph)YHDLSQASLYPHRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYHDLSQASLYPHRK 15 1 Q12923-3;Q12923;Q12923-4 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 S(0.539)Y(0.46)HDLSQASLYPHRK 55.186 0.066105 66085000 81911 84666 56057 56908 67175 75874 67026 84196 56709 TRUE FALSE 71086.25381 84109.82347 83166.3527 69829.83118 65838.34893 78792.92188 60525.82884 66191.34061 50004.92662 1.421585004 1.682030735 1.663163178 1.396459027 1.316637247 1.57570318 1.210397313 1.323696385 1 15.60978262 0.132498078 0.379370906 6.22E-14 1.588571252 0.613928973 0.129153532 11.56151166 0.748747184 9.830537586 0.162526689 1.356744525 -0.132498078 1.588571252 S(ph)YS(ph)PAHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SYSPAHNR 8 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 S(0.999)Y(0.001)S(1)PAHNR;S(0.998)Y(0.003)S(0.999)PAHNR;S(0.999)Y(0.001)S(1)PAHNR;S(0.999)Y(0.002)S(0.999)PAHNR 112.13 0.0045326 4422760000 4217650 3358940 2554540 3174340 3270900 3396210 3245230 3749450 5663770 TRUE FALSE 3660276.866 3336874.902 3789924.088 3895122.414 3205815.489 3526864.396 2930508.094 2947659.296 4994205.563 0.732904727 0.66814929 0.758864256 0.779928332 0.641906996 0.706191275 0.586781633 0.590215853 1 22.25182377 3.232885478 24.9294162 0.681859539 0.731896668 0 0.119228544 533.2501423 2342424.635 0.035495422 0.041357514 1709.564448 -3.232885478 0.050037129 S(ph)YS(ph)PDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SYSPDGK 7 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 2 S(1)Y(0.001)S(0.999)PDGK;S(0.998)Y(0.004)S(0.997)PDGK 88.681 0.026943 312010000 1074110 723190 662090 703560 680540 672530 843300 1041200 1812520 TRUE FALSE 932163.6421 718439.3173 982278.9386 863314.0512 666998.5855 698402.6643 761516.8958 818547.4826 1598245.95 0.583241673 0.449517371 0.614598109 0.540163453 0.417331629 0.436980719 0.476470405 0.512153641 1 20.60805801 1.238545702 6.781033847 1.012056444 0.50016162 0.860188962 0.062872949 0.040404452 9.770946419 0.095285119 0.015768242 17.31991285 -1.238545702 -0.511894825 S(ph)YSAGEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYSAGEAR 8 0 H7C3Q2 H7C3Q2 HECW1 1 S(0.377)Y(0.246)S(0.377)AGEAR 70.268 0.054306 330760000 46811 39643 29362 41109 50860 54547 46149 58479 59621 TRUE FALSE 40624.80775 39382.58252 43561.56141 50443.42676 49847.98551 56645.45839 41673.47708 45973.72093 52572.6733 0.772736199 0.749107474 0.828597039 0.959498987 0.948172927 1.077469621 0.792683241 0.874479421 1 15.68202548 3.945211127 3.473821432 0.931221571 0.763113486 0.510258724 0.074696679 0.214296329 5.156545362 0.021389773 0.042860365 8814.772882 -3.945211127 -0.168108085 S(ph)YSHDVLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SYSHDVLPK 9 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 S(0.5)Y(0.001)S(0.5)HDVLPK;S(0.5)Y(0.001)S(0.5)HDVLPK 94.616 0.0055403 580950000 1936940 1799970 1372390 1969940 2162990 2149510 2866370 2845130 2969260 TRUE FALSE 1680968.471 1788145.879 2036082.394 2417244.986 2119950.731 2232203.041 2588389.879 2236721.09 2618237.465 0.642022923 0.682957868 0.777653831 0.923233671 0.809686195 0.85255943 0.988600122 0.854285037 1 21.32016452 5.751277715 0.38703707 0.944427883 3.40E-15 0.756107991 0.057860695 7.604816722 0.534111414 0.068242744 3.860651915 563998.196 -5.751277715 -0.944427883 S(ph)YSPAHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SYSPAHNR 8 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.581)YS(0.418)PAHNR;S(0.571)Y(0.005)S(0.424)PAHNR 90.108 0.0086507 731519000 595613 570632 337442 379840 449725 607217 492881 469459 394586 TRUE FALSE 516901.233 566883.4808 500630.0799 466088.4775 440776.3524 630577.0309 445081.4765 369068.8462 347938.4926 1.485610946 1.629263484 1.438846493 1.339571469 1.266822619 1.812323282 1.279195852 1.060730141 1 18.40847277 1.883846331 3.431796929 1.035602 1.48488969 0.608332583 0.152343739 0.162028397 3.253075105 0.092331859 0.041839558 76.53257589 -1.883846331 0.44928769 S(ph)YSPDGKESPSDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYSPDGKESPSDKK 14 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 S(0.497)Y(0.007)S(0.497)PDGKESPSDKK 64.507 0.031705 3671200000 814280 430240 381110 274590 371650 249330 712280 776080 185590 TRUE FALSE 706670.8349 427413.7251 565416.0707 336939.8563 364254.8921 258921.8864 643203.1952 610121.3315 163649.7616 4.318190432 2.611758923 3.455037546 2.058908323 2.225819876 1.582170874 3.930364388 3.728213994 1 17.32025198 6.558032604 1.331094454 2.661526564 199.9997276 0.246759139 0.93749609 303.2826944 5.781880332 0.273385095 178024.6694 3614369.959 -6.558032604 197.3382011 S(ph)YSPYDYQPCLAGPNQDFHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYSPYDYQPCLAGPNQDFHSK 21 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7 E9PGF5 TNS1 Tensin-1 1 S(0.536)Y(0.001)S(0.461)PY(0.001)DY(0.001)QPCLAGPNQDFHSK 105.17 0.00025568 351080000 163640 160990 95219 136410 153300 157770 157850 201070 180380 TRUE FALSE 142014.5594 159932.4461 141267.2269 167383.9754 150249.6299 163839.514 142541.7313 158072.7452 159055.6819 0.892860649 1.00551231 0.88816209 1.052360868 0.944635414 1.030076462 0.896175035 0.993820173 1 17.27917238 4.753419465 23.65706086 0.974258589 0.892860526 0.193806866 0.053359217 2051.716112 3266459.117 0.011684058 0.238858064 56678.64575 -4.753419465 -0.081398063 S(ph)YSTLTTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SYSTLTTVR 9 0 Q96NY8-2;Q96NY8 Q96NY8-2 PVRL4 Nectin-4;Processed poliovirus receptor-related protein 4 1 S(0.514)YS(0.076)T(0.41)LTTVR;S(0.754)YS(0.123)T(0.123)LTTVR;S(1)YSTLTTVR;S(0.985)YS(0.011)T(0.004)LTTVR 187.41 4.25E-05 1391930000 391473 433606 295600 427810 522740 589920 331108 545147 428884 TRUE FALSE 339738.8512 430757.6136 438553.1487 524950.7992 512338.4967 612614.6041 298997.1971 428571.5564 378181.8221 0.898347914 1.139022524 1.159635718 1.388091041 1.354741203 1.619894369 0.79061758 1.133242084 1 18.52872049 2.215613814 24.99973078 0.99999956 1.260031553 0.301931031 0.203306785 330.6219979 360198.3021 0.085727583 0.05783974 164.2910154 -2.215613814 0.260031993 S(ph)YT(ph)PEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SYTPEYR 7 0 Q13595 Q13595 TRA2A Transformer-2 protein homolog alpha 2 S(0.997)Y(0.003)T(1)PEYR;S(0.999)Y(0.003)T(0.998)PEYR;S(0.999)Y(0.011)T(0.99)PEY(0.001)R;S(0.996)Y(0.018)T(0.985)PEY(0.001)R 114.4 0.031371 2758480000 4582080 3491820 2835270 3285810 4006100 3712430 3537280 4041270 6788700 TRUE FALSE 3976546.518 3468882.005 4206416.055 4031903.381 3926386.448 3855249.584 3194235.13 3177075.86 5986147.62 0.664291423 0.579484875 0.702691668 0.673538916 0.655912065 0.644028485 0.53360447 0.530737974 1 22.51319643 1.230373344 24.99784379 1.000000702 0.618907476 0.804462501 0.05837536 149.0781856 455137.3048 0.177751016 0.016198232 16.99704187 -1.230373344 -0.381093226 S(ph)YTSDLQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SYTSDLQK 8 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;E9PJ10;E9PK58;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.984)YT(0.016)SDLQK;S(0.799)YT(0.189)S(0.012)DLQK;S(0.763)YT(0.235)S(0.001)DLQK;S(0.984)YT(0.016)SDLQK;S(0.999)YT(0.001)SDLQK;S(1)YTSDLQK 192.64 0.00018341 2513640000 3222140 3881940 2364820 2580520 3402840 2381980 4321940 3926610 7463710 TRUE FALSE 2796326.035 3856439.281 3508454.862 3166466.507 3335130.142 2473616.312 3902798.924 3086935.008 6581358.706 0.424885827 0.585964001 0.533089749 0.481126565 0.506754044 0.375851921 0.593008085 0.469042206 1 22.64995403 1.236441244 24.99970328 1.00000064 0.499532129 0.850873263 0.066268634 19.36876561 228412.8887 0.096732417 0.015097221 17.23618886 -1.236441244 -0.500468511 SAAAGALGS(ph)PGLPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SAAAGALGSPGLPLR 15 0 O75145-2;O75145;A0A0C4DGR8;A0A0C4DGR7 O75145-2 PPFIA3 Liprin-alpha-3 1 SAAAGALGS(1)PGLPLR;SAAAGALGS(1)PGLPLR;SAAAGALGS(1)PGLPLR;SAAAGALGS(1)PGLPLR;SAAAGALGS(1)PGLPLR 206.28 4.17E-09 1126318000 2134230 2220230 1432230 1802290 2379270 2505040 2082350 2493380 3186470 TRUE FALSE 1852186.098 2205645.163 2124861.219 2211527.491 2331927.182 2601410.51 1880404.018 1960190.091 2809769.147 0.659195116 0.784991595 0.756240498 0.787085122 0.829935507 0.925844927 0.669237905 0.697633858 1 21.42202017 5.594271353 1.15095054 0.798746143 1.37E-08 0.181293659 0.097986335 20.214125 5.154728307 0.029485596 31.17007537 392890.3419 -5.594271353 -0.798746129 SAAAGALGS(ph)PGLPLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SAAAGALGSPGLPLRK 16 1 O75145-2;O75145;A0A0C4DGR8;A0A0C4DGR7 O75145-2 PPFIA3 Liprin-alpha-3 1 SAAAGALGS(1)PGLPLRK;SAAAGALGS(1)PGLPLRK;SAAAGALGS(1)PGLPLRK 170.14 3.30E-09 4408580000 2684910 2749730 1446825 1891263 2677470 2595770 2947180 3296860 2088041 TRUE FALSE 2330092.341 2731666.843 2146514.409 2320703.17 2624193.585 2695630.952 2661362.937 2591852.145 1841195.172 1.265532507 1.483637848 1.165826656 1.260433009 1.425266384 1.464065838 1.445454006 1.407700924 1 20.81221113 1.234977179 24.95067042 0.999999464 1.369772315 0.550178239 0.103557497 80.90646859 563243.1403 0.186489002 0.026015847 17.1781812 -1.234977179 0.369772851 SAAEMYGSSFDLDYDFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SAAEMYGSSFDLDYDFQR 18 0 B4DY08;G3V4W0;G3V5X6;G3V3K6;G3V251;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ;;; 314.39 6.76E-61 934640000 1051890 840556 579180 613768 889110 1160960 741433 1062420 970310 FALSE TRUE 912880.0714 835034.3323 859273.3852 753133.4053 871418.4505 1205622.882 669528.9418 835229.7508 855601.0572 1.066945937 0.975962249 1.004292103 0.880238984 1.018486879 1.409094662 0.782524678 0.976190648 1 19.70657874 SAAEMYGSVTEHPS(ph)PSPLLSSSFDLDYDFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SAAEMYGSVTEHPSPSPLLSSSFDLDYDFQR 31 0 P07910;G3V2Q1;G3V576;G3V555;G3V575 P07910 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 SAAEMYGS(0.002)VT(0.001)EHPS(0.99)PS(0.006)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.922)PS(0.078)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.998)PS(0.002)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.99)PS(0.01)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.868)PS(0.131)PLLSSSFDLDYDFQR;SAAEMYGSVT(0.004)EHPS(0.876)PS(0.12)PLLSSSFDLDYDFQR 335.91 4.72E-106 1772390000 646814 594207 379437 514400 651300 866128 583511 787632 853340 TRUE FALSE 561335.8911 590303.6151 562934.0023 631202.3821 638340.4042 899448.5046 526922.193 619203.0262 752459.1173 0.746001847 0.784499253 0.748125698 0.838852726 0.848338986 1.195345347 0.700266873 0.822905872 1 19.52125367 3.441008356 2.557579678 0.900245524 0.763043734 0.231023428 0.127545852 0.500272094 6.613675752 0.039955357 0.057712397 2760.630971 -3.441008356 -0.137201791 SAAEMYGSVTEHPSPS(ph)PLLSSSFDLDYDFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 SAAEMYGSVTEHPSPSPLLSSSFDLDYDFQR 31 0 P07910;G3V2Q1;G3V576;G3V555;G3V575 P07910 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 SAAEMYGS(0.004)VT(0.004)EHPS(0.142)PS(0.848)PLLSSSFDLDYDFQR;SAAEMYGS(0.001)VT(0.001)EHPS(0.026)PS(0.971)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.04)PS(0.96)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.003)PS(0.997)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.006)PS(0.992)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.001)PS(0.999)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.034)PS(0.966)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.045)PS(0.955)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.001)PS(0.995)PLLS(0.004)SSFDLDYDFQR;SAAEMYGS(0.013)VT(0.012)EHPS(0.466)PS(0.475)PLLS(0.011)S(0.011)S(0.012)FDLDYDFQR;SAAEMYGS(0.005)VT(0.017)EHPS(0.201)PS(0.775)PLLSSSFDLDYDFQR 311.32 8.79E-93 1935937000 524008 511949 263398.3 458896 676408 842217 560271 753853 745524 TRUE FALSE 454759.0151 508585.9733 390778.5989 563095.3506 662948.8042 874617.633 505936.0047 592647.4024 657389.002 0.691765475 0.773645394 0.594440427 0.856563388 1.008457401 1.330441535 0.769614343 0.901517063 1 19.3263878 3.485951237 4.139048235 0.986496363 0.696387332 0.492992075 0.145399676 0.19998239 8.033546603 0.044050894 0.062360732 3061.619651 -3.485951237 -0.290109031 SAAEMYGSVTEHPSPSPLLSSSFDLDYDFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SAAEMYGSVTEHPSPSPLLSSSFDLDYDFQR 31 0 P07910;G3V2Q1;G3V576;G3V555;G3V575 P07910 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ;; 305.51 4.50E-82 889870000 461820 444460 140653 292019 539300 643480 372140 577280 505310 FALSE TRUE 400789.3169 441540.313 208673.2613 358326.3772 528568.9851 668235.092 336049.9201 453833.1644 445572.8275 0.899492276 0.99094982 0.468325823 0.804192615 1.186268445 1.499721372 0.754197517 1.018538691 1 18.76530173 3.288467159 8.822147993 1.07751971 0.780977595 0.302836823 0.226191123 0.414984305 67.7253619 0.067871218 0.08738647 1942.974762 -3.288467159 -0.296542115 SAAMLGNSEDHTALSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAAMLGNSEDHTALSR 16 0 O60749;O60749-2 O60749 SNX2 Sorting nexin-2 0 ; 156.86 1.23E-07 1022930000 512520 438030 261660 381130 434220 467960 460860 500580 595110 FALSE TRUE 444789.1834 435152.5521 388199.6512 467671.3917 425579.8715 485962.724 416165.8681 393534.8625 524756.7738 0.84761018 0.829246184 0.739770634 0.89121554 0.811004055 0.926072322 0.793064309 0.749937652 1 19.00128936 3.714095572 24.99043266 0.846474936 0.807912679 0.086213352 0.07602053 2573.152508 2628409.76 0.021004107 0.031169908 5177.207504 -3.714095572 -0.038562257 SAAS(ph)PVVSSMPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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(0.999)PVVS(0.001)SMPER;SAAS(1)PVVSSMPER;SAAS(1)PVVSSMPER;SAAS(1)PVVSSMPER 281.94 1.84E-32 3266700000 2532170 2223870 1392860 1770350 2224770 2223510 2150780 2386560 2703160 TRUE FALSE 2197537.319 2209261.252 2066451.755 2172335.026 2180501.43 2309049.869 1942197.687 1876212.716 2383595.504 0.921942215 0.926860807 0.866947329 0.911368989 0.914795076 0.968725551 0.814818489 0.787135532 1 21.184708 2.228450878 24.99738774 0.848425848 0.915995099 0.110335178 0.060757397 320.5534597 792594.7669 0.024382678 0.016652312 169.2196833 -2.228450878 0.067569251 SAAS(ph)REDLVGPEVGAS(ph)PQSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAASREDLVGPEVGASPQSGR 21 1 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 2 S(0.392)AAS(0.608)REDLVGPEVGAS(0.992)PQS(0.008)GR 71.425 0.0096121 397440000 143380 140050 107310 119940 150730 145400 132270 137750 200640 TRUE FALSE 124431.9697 139130.0023 159205.4749 147174.2102 147730.7679 150993.6321 119442.4758 108293.2345 176920.5678 0.703321108 0.786398123 0.899869794 0.831866029 0.835011835 0.853454372 0.67511922 0.612100876 1 17.43274225 2.246372819 24.92101532 0.727456004 0.821950438 0.021721166 0.112049553 338.3752664 1079423.826 0.042105741 0.031995781 176.348926 -2.246372819 0.094494434 SAAS(ph)REDLVGPEVGASPQSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SAASREDLVGPEVGASPQSGR 21 1 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 S(0.023)AAS(0.641)REDLVGPEVGAS(0.298)PQS(0.037)GR;S(0.187)AAS(0.813)REDLVGPEVGASPQSGR;S(0.224)AAS(0.776)REDLVGPEVGASPQSGR 157.88 6.83E-13 1120170000 489050 418590 390358 436122 515580 591120 497610 568040 613190 TRUE FALSE 424420.8034 415840.2547 579136.4345 535150.1658 505320.9667 613860.7689 449351.8588 446569.0665 540699.3767 0.784947832 0.76907848 1.071087668 0.989736976 0.934569168 1.135308815 0.831056735 0.825910082 1 19.04446717 4.263303142 24.86378396 0.954785129 0.777012896 0.407083663 0.095355021 247.413579 248621.4016 0.025641381 0.067774146 18335.93844 -4.263303142 -0.177772233 SAATWDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAATWDER 8 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 111.82 0.0073532 685430000 1669590 1594170 1016300 1215950 1545550 1868400 1530160 1733920 1608820 FALSE TRUE 1448949.451 1583697.792 1507786.079 1492050.032 1514796.579 1940278.557 1381765.319 1363134.701 1418627.132 1.021374411 1.116359441 1.062848753 1.051756306 1.067790503 1.367715669 0.974015855 0.960883005 1 20.43606401 SAAVETASLS(ph)PSLVPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAAVETASLSPSLVPAR 17 0 Q2KHT3;Q2KHT3-3 Q2KHT3 CLEC16A Protein CLEC16A 1 SAAVETAS(0.018)LS(0.905)PS(0.077)LVPAR;SAAVETASLS(0.972)PS(0.028)LVPAR 293.59 4.88E-46 322140000 281640 341870 221524 294510 401970 439770 401350 474490 370660 TRUE FALSE 244420.5604 339624.2335 328653.7474 361382.9968 393971.5834 456688.2365 362427.1388 373024.006 326840.9971 0.747827117 1.039111484 1.005546276 1.105684416 1.205392185 1.397279535 1.108879064 1.141301151 1 18.31822943 5.325229628 0.842677415 1.165675387 4.21E-11 0.591443831 0.105564987 4.233292352 1.166710974 0.038698209 5.775262733 211460.6815 -5.325229628 -1.165675387 SACGVCPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SACGVCPGR 9 0 P49207 P49207 RPL34 60S ribosomal protein L34 0 ;;; 116.88 0.0028881 282819000 332989 339164 187201 255207 315292 329534 339489 365427 380637 FALSE TRUE 288983.66 336936.0094 277732.0297 313155.6499 309018.3061 342211.3862 306565.409 287283.2798 335638.5275 0.860996686 1.003865712 0.827473627 0.93301461 0.920687826 1.019583147 0.913379675 0.855930581 1 18.3565488 SACKEDIPSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SACKEDIPSEK 11 1 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 97.86 0.0054281 563680000 1598100 1137000 1075000 967240 1030800 790960 1732500 1845600 1194800 FALSE TRUE 1386907.036 1129530.972 1594873.596 1186866.625 1010289.097 821388.743 1564482.417 1450932.802 1053552.105 1.316410483 1.072116857 1.513806093 1.126538137 0.958936052 0.779637513 1.484959699 1.377181817 1 20.00683024 SACMLSSPESSLT(ph)PPLSTNLHLESELDALASLENHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SACMLSSPESSLTPPLSTNLHLESELDALASLENHVK 37 0 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 1 SACMLSSPESSLT(1)PPLSTNLHLESELDALASLENHVK 218.63 7.88E-39 96616000 88335 76080 31632 58748 72792 65588 86618 100660 86834 TRUE FALSE 76661.30594 75580.22547 46929.341 72087.63131 71343.58162 68111.2128 78217.79969 79134.64234 76568.58344 1.001210973 0.98709186 0.612905958 0.941477928 0.9317605 0.88954516 1.021539072 1.033513208 1 16.22446495 2.238616392 11.82234974 1.021675641 0.889309652 0.228920727 0.107298047 0.113788121 685.8992394 0.042447015 0.030716827 173.2273223 -2.238616392 -0.132365989 SADEADELPPDLPKPPS(ph)PAPSSEDPGLAQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SADEADELPPDLPKPPSPAPSSEDPGLAQPR 31 1 Q8TBE0-3;Q8TBE0-2;Q8TBE0 Q8TBE0-3 BAHD1 Bromo adjacent homology domain-containing 1 protein 1 SADEADELPPDLPKPPS(0.953)PAPS(0.023)S(0.023)EDPGLAQPR 74.284 0.0021231 103190000 80471 68960 54188 56084 82862 61414 92110 99459 90678 TRUE FALSE 69836.55346 68506.99722 80393.49805 68818.72939 81213.20832 63776.63632 83177.18638 78190.46684 79958.15014 0.873413821 0.85678567 1.005444697 0.860684361 1.015696438 0.79762521 1.040259013 0.977892394 1 16.28695747 -2 0.168935544 1.515923105 0.847106358 0.198676702 0.074838741 195.8289655 2.663801892 32.08890552 0.779050704 0.01 2 -0.668816747 SADLHPLSELPENRPCENGSTHSAGEFFTGPVQPGS(ph)PHNIGTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SADLHPLSELPENRPCENGSTHSAGEFFTGPVQPGSPHNIGTSR 44 1 Q8IZD4;Q8IZD4-2;F5GZK9 Q8IZD4 DCP1B mRNA-decapping enzyme 1B 1 SADLHPLSELPENRPCENGSTHSAGEFFTGPVQPGS(1)PHNIGTSR;SADLHPLSELPENRPCENGSTHSAGEFFTGPVQPGS(1)PHNIGTSR;SADLHPLSELPENRPCENGSTHSAGEFFTGPVQPGS(1)PHNIGTSR 300.99 2.09E-97 1380490000 288370 318513 96289 187505 343916 327874 267280 312435 283915 TRUE FALSE 250261.1739 316420.6671 142854.6825 230080.8761 337072.7445 340487.5249 241359.2267 245623.2066 250350.8921 0.99964163 1.263908686 0.570617829 0.919033578 1.346401211 1.360041189 0.964083749 0.981115763 1 17.93359207 SADTLWDIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SADTLWDIQK 10 0 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 ;;;; 200.6 5.98E-07 510830000 1645972 1757273 1093173 1378623 1695501 1531972 2000800 2217261 2059038 FALSE TRUE 1428452.63 1745729.358 1621835.119 1691660.423 1661763.847 1590907.954 1806762.724 1743116.99 1815620.873 0.786757109 0.961505446 0.8932675 0.931725587 0.915259277 0.876233567 0.995121146 0.960066617 1 20.79203155 0.94909193 0.026313308 1.974389364 6.15E-07 0.458319509 0.046378219 1556.368788 9.84188022 417.4511353 325.6933894 8.893893618 -0.94909193 -1.974388748 SADTLWGIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SADTLWGIQK 10 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 152.81 4.04E-05 329100000 286080 215790 356370 192200 192270 150350 202340 237290 264070 FALSE TRUE 248273.8032 214372.4613 528711.724 235841.9476 188444.2032 156134.0618 182717.0979 186547.3801 232851.9454 1.066230315 0.920638481 2.270591826 1.012840787 0.809287648 0.670529342 0.784692168 0.8011416 1 17.82905341 3.48940776 24.56032701 0.812250008 1.414704408 0.373863923 0.358128627 483.1300745 965760.4944 0.0989746 0.138528635 3086.084123 -3.48940776 0.6024544 SAEDWWWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAEDWWWDR 9 0 Q8N531-2;Q8N531 Q8N531-2 FBXL6 F-box/LRR-repeat protein 6 0 108.98 0.0058716 92586000 94895 111120 67149 84200 100740 112970 90520 105510 103020 FALSE TRUE 82354.38532 110390.0454 99622.481 103318.8969 98735.47109 117316.029 81741.38433 82947.50758 90841.09296 0.906576337 1.215199441 1.096667574 1.137358585 1.086903161 1.291442289 0.899828279 0.913105566 1 16.47105744 2.208299017 24.99999767 0.930956501 1.124480577 0.425289873 0.10110202 172.5773229 142570.0278 0.038379113 0.025878688 161.5470445 -2.208299017 0.193524076 SAEFLLHMLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAEFLLHMLK 10 0 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2;J3KRB3;A0A087WWH0;J3QS96;A0A087WY81 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 0 ; 134.23 0.00017623 848970000 2437100 3002500 1854050 2335780 3035100 2637800 3229200 3417700 4028400 FALSE TRUE 2115031.06 2982776.38 2750674.781 2866154.549 2974707.448 2739277.873 2916032.681 2686851.452 3552167.141 0.595419916 0.83970609 0.774365246 0.806874912 0.837434538 0.771156808 0.820916518 0.756397811 1 21.76026804 4.742218232 24.84092394 0.816648645 0.595419824 0.524462486 0.068461439 262.817564 1784859.333 0.015442522 0.111351777 55235.49266 -4.742218232 -0.221228822 SAEPS(ph)PTVMSTSLGSNLSELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAEPSPTVMSTSLGSNLSELDR 22 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 S(0.165)AEPS(0.835)PTVMSTSLGSNLSELDR;SAEPS(0.997)PT(0.003)VMSTSLGSNLSELDR 159.18 2.09E-11 233420000 50877 51943 32343 46520 53877 44027 56743 67576 52719 TRUE FALSE 44153.47554 51601.78301 47984.18298 57083.07701 52804.95311 45720.74718 51240.07259 53125.39828 46486.61988 0.949810411 1.11003517 1.032214928 1.227946389 1.135917243 0.983524879 1.102254213 1.142810521 1 15.50452791 4.741827172 24.21157688 1.096691286 0.949810328 0.272294235 0.072583752 275.342887 2040678.72 0.017363506 0.121957744 55185.77831 -4.741827172 -0.146880958 SAEPSANTTLVS(ph)ETEEEGSVPAFGAAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.043)T(0.032)LVS(0.766)ET(0.156)EEEGS(0.003)VPAFGAAAK;S(0.001)AEPS(0.005)ANT(0.118)T(0.096)LVS(0.342)ET(0.342)EEEGS(0.096)VPAFGAAAK 107.19 0.00054205 131731000 250870 175649 184317 256520 200820 175402 200519 248260 632880 TRUE FALSE 217716.8939 174495.1502 273453.3177 314766.7867 196824.0749 182149.8284 181072.6982 195171.531 558061.6474 0.390130544 0.312680778 0.490005574 0.56403587 0.352692352 0.326397324 0.324467197 0.349731131 1 19.09006498 1.236438979 24.99999293 1.000000784 0.387110336 0.852115268 0.080021549 22.21774041 261733.7121 0.135739214 0.021184362 17.23609895 -1.236438979 -0.612890449 STS(ph)LNERPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 STSLNERPK 9 1 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7 P49815 TSC2 Tuberin 1 S(0.017)T(0.202)S(0.781)LNERPK;S(0.056)T(0.056)S(0.889)LNERPK;S(0.001)T(0.022)S(0.977)LNERPK;S(0.007)T(0.003)S(0.99)LNERPK 126.12 0.00029219 1809680000 1165160 1320160 1355630 1657730 2174200 2096900 2668210 3008150 3110350 TRUE FALSE 1011181.154 1311487.782 2011217.202 2034142.933 2130937.674 2177569.1 2409447.405 2364880.532 2742647.966 0.368687913 0.478183055 0.733312196 0.741671173 0.776963613 0.793965951 0.878511364 0.862261785 1 21.38713803 4.728597472 0.52032303 0.906819952 6.55E-26 0.916481846 0.053842658 1.250558606 0.277815902 0.040087155 0.70062896 53530.02824 -4.728597472 -0.906819952 down SAEVGPSSEPEVQTLPYLPHYIPGVDPETSHGGHPHGNMPGLDRPLS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SAEVGPSSEPEVQTLPYLPHYIPGVDPETSHGGHPHGNMPGLDRPLSR 48 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 SAEVGPSSEPEVQTLPY(0.002)LPHY(0.001)IPGVDPET(0.149)S(0.149)HGGHPHGNMPGLDRPLS(0.699)R;SAEVGPS(0.001)S(0.003)EPEVQT(0.015)LPY(0.001)LPHY(0.001)IPGVDPET(0.179)S(0.179)HGGHPHGNMPGLDRPLS(0.622)R;SAEVGPSSEPEVQTLPYLPHYIPGVDPET(0.168)S(0.168)HGGHPHGNMPGLDRPLS(0.664)R;SAEVGPSSEPEVQT(0.001)LPY(0.036)LPHY(0.152)IPGVDPET(0.141)S(0.141)HGGHPHGNMPGLDRPLS(0.53)R;SAEVGPSSEPEVQTLPY(0.001)LPHYIPGVDPET(0.131)S(0.131)HGGHPHGNMPGLDRPLS(0.737)R;SAEVGPSSEPEVQT(0.002)LPY(0.004)LPHY(0.022)IPGVDPET(0.153)S(0.153)HGGHPHGNMPGLDRPLS(0.667)R 127.33 3.61E-11 5217352000 625418 803981 248909 402848 761528 693088 645484 739953 452953 TRUE FALSE 542767.4267 798699.5959 369282.225 494320.7955 746375.0827 719751.5438 582885.061 581719.8093 399405.4123 1.358938587 1.999721514 0.924579922 1.237641705 1.868715495 1.802057563 1.459381979 1.456464513 1 18.60749436 1.151829273 2.388450833 0.768276645 1.528853557 0.209113941 0.315562033 1.341551889 6.620662769 2.359897968 0.084313775 14.18499781 -1.151829273 0.760576911 SAFPYAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAFPYAHR 8 0 Q9HAB8;Q5VVM3 Q9HAB8 PPCS Phosphopantothenate--cysteine ligase 0 95.531 0.0095844 88825000 200930 217640 113340 139840 217340 245410 197180 208890 224820 FALSE TRUE 174376.5914 216210.3085 168151.6031 171592.8093 213015.3592 254851.0815 178057.5139 164220.4991 198242.0357 0.879614612 1.090638056 0.848213662 0.865572272 1.07452165 1.285555208 0.898182433 0.828383841 1 17.59690338 2.04580994 24.99952146 0.890334915 1.008126165 0.099694103 0.135996999 251.1029049 137031.4592 0.057650838 0.038868168 111.1245306 -2.04580994 0.11779125 SAFS(ph)PYQTPVAHFPPPPEEPTATAAFGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAFSPYQTPVAHFPPPPEEPTATAAFGAR 29 0 A0A0A0MQV9;Q9UPS6-2;Q9UPS6 A0A0A0MQV9 SETD1B Histone-lysine N-methyltransferase;Histone-lysine N-methyltransferase SETD1B 1 S(0.077)AFS(0.805)PY(0.011)QT(0.107)PVAHFPPPPEEPTATAAFGAR 53.288 0.046254 114090000 38271 30323 15410 13374 23842 25624 30376 25719 26638 TRUE FALSE 33213.39038 30123.80622 22862.32754 16410.77111 23367.59085 26609.77186 27430.1402 20219.192 23488.88599 1.414004496 1.282470622 0.973325323 0.698661108 0.994836062 1.132866492 1.1677923 0.860798252 1 14.51969067 4.324962088 3.754456173 0.971128925 1.384585632 0.590810843 0.130977415 0.160600104 4.252382961 0.035796585 0.10725639 21133.04551 -4.324962088 0.413456708 SAFSS(ph)LQNIPESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAFSSLQNIPESLR 14 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 SAFS(0.02)S(0.98)LQNIPESLR;SAFS(0.008)S(0.992)LQNIPESLR 244.18 1.48E-17 181883000 446820 439730 241571 258757 381390 456260 376670 442180 718300 TRUE FALSE 387771.6049 436841.3847 358395.5436 317511.7317 373801.0852 473812.6174 340140.6014 347623.248 633383.3923 0.612222565 0.689695041 0.565842976 0.501294691 0.590165593 0.748066058 0.537021661 0.548835433 1 19.27271951 1.234389845 24.99645094 1.000000591 0.596977551 0.749441793 0.072831663 64.7921733 388262.2127 0.138666794 0.018397229 17.15496535 -1.234389845 -0.40302304 SAGGRPGS(ph)GPQLGTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SAGGRPGSGPQLGTGR 16 1 O14908;O14908-2;K7EM11;K7ESN1 O14908 GIPC1 PDZ domain-containing protein GIPC1 1 SAGGRPGS(1)GPQLGTGR;SAGGRPGS(1)GPQLGTGR;SAGGRPGS(1)GPQLGTGR;SAGGRPGS(1)GPQLGTGR 213.5 1.06E-12 3073730000 1082040 1175180 669585 966180 1470350 1365830 1464780 1650630 1411240 TRUE FALSE 939045.6725 1167460.165 993398.5456 1185565.936 1441092.912 1418374.364 1322725.861 1297655.62 1244404.815 0.754614303 0.938167509 0.79829211 0.952717252 1.158057968 1.139801411 1.062938559 1.042792188 1 20.24702445 3.470769058 4.729337377 1.077162245 0.844285883 0.760274926 0.06418994 0.093920738 5.643020044 0.018657885 0.025741709 2956.439921 -3.470769058 -0.232876361 SAGGRPGSGPQLGTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAGGRPGSGPQLGTGR 16 1 O14908;O14908-2;K7EM11;K7ESN1 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 ; 177.04 2.75E-09 229960000 138475 152095 80908 89010 156418 152521 126260 152967 131370 FALSE TRUE 120175.1779 151095.8779 120035.3794 109221.0809 153305.5878 158388.5816 114015.3246 120256.1974 115839.5883 1.03742753 1.304354411 1.036220702 0.942864893 1.323430013 1.367309604 0.984251812 1.038126941 1 16.82176885 SAGGS(ph)SPEGGEDS(ph)DREDGNYCPPVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAGGSSPEGGEDSDREDGNYCPPVKR 26 2 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7EID7;K7ENB9 Q9H6Z4 RANBP3 Ran-binding protein 3 2 S(0.001)AGGS(0.51)S(0.489)PEGGEDS(1)DREDGNYCPPVKR 193.05 1.86E-18 370850000 851320 739720 493250 484990 690160 603860 845180 981360 561970 TRUE FALSE 738815.905 734860.7306 731787.3498 595114.3921 676427.1663 627090.8849 763214.5737 771503.801 495534.5468 1.490947321 1.482965689 1.476763537 1.200954396 1.365045425 1.265483686 1.54018439 1.556912239 1 18.91862611 3.953887417 24.95821679 1.357559381 1.485183823 0.160673513 0.16125873 901.6915729 488036.8039 0.043958739 0.076142455 8992.644342 -3.953887417 0.127624443 SAGGSS(ph)PEGGEDS(ph)DREDGNYCPPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAGGSSPEGGEDSDREDGNYCPPVK 25 1 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7EID7;K7ENB9 Q9H6Z4 RANBP3 Ran-binding protein 3 2 S(0.003)AGGS(0.139)S(0.858)PEGGEDS(1)DREDGNYCPPVK;S(0.283)AGGS(0.351)S(0.371)PEGGEDS(0.985)DREDGNY(0.01)CPPVK 131.95 4.30E-05 137480000 240540 236170 195773 209098 247370 209457 252060 291860 520000 TRUE FALSE 208752.0295 234618.5837 290449.4776 256576.8968 242447.821 217514.9463 227615.26 229448.0103 458526.1924 0.455267405 0.511679785 0.63344141 0.559568681 0.528754573 0.474378454 0.496406233 0.500403279 1 18.80664462 1.23704025 24.99994818 1.000000587 0.521335494 0.903764115 0.049224418 11.95338635 196486.5778 0.078883701 0.012859299 17.25997849 -1.23704025 -0.478665093 SAGGSS(ph)PEGGEDS(ph)DREDGNYCPPVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAGGSSPEGGEDSDREDGNYCPPVKR 26 2 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7EID7;K7ENB9 Q9H6Z4 RANBP3 Ran-binding protein 3 2 S(0.002)AGGS(0.144)S(0.854)PEGGEDS(1)DREDGNYCPPVKR;SAGGS(0.09)S(0.91)PEGGEDS(1)DREDGNYCPPVKR 150.82 9.54E-08 806280000 909430 851590 509730 557220 818250 685200 940960 1061490 609870 TRUE FALSE 789246.5213 845995.8492 756237.1329 683745.3176 801968.4259 711560.0874 849705.844 834498.624 537771.8634 1.467623308 1.573150079 1.406241539 1.271441227 1.491280003 1.323163475 1.580048905 1.551770706 1 19.03663475 1.231638275 24.97874725 0.999999199 1.461161365 0.665095315 0.102137195 155.0099899 559290.4278 0.252858669 0.026099999 17.04661982 -1.231638275 0.461162165 SAGGSSPEGGEDS(ph)DREDGNYCPPVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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;SAGGSSPEGGEDS(1)DREDGNYCPPVKR;SAGGSSPEGGEDS(1)DREDGNYCPPVKR;SAGGSSPEGGEDS(1)DREDGNYCPPVKR 324.97 4.74E-83 4351570000 1792510 1741470 954301 1176880 1572580 1424560 1911580 2068080 1169660 TRUE FALSE 1555625.262 1730030.169 1415804.156 1444108.591 1541288.735 1479363.745 1726195.266 1625837.186 1031384.127 1.50828893 1.677386847 1.372722459 1.400165616 1.494388651 1.434347985 1.673668636 1.576364366 1 19.97615032 1.234840666 24.99998552 0.99999926 1.520814442 0.712723081 0.103163409 62.48040575 419837.0792 0.191222955 0.026365454 17.17278238 -1.234840666 0.520815182 SAHAGTYEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAHAGTYEVR 10 0 A6NLM8;P51571 A6NLM8 SSR4 Translocon-associated protein subunit delta 0 ; 143.89 3.32E-05 563960000 181611 189446 110958 159439 226009 259186 152241 248101 209281 FALSE TRUE 157610.6462 188201.5168 164617.6599 195642.0618 221511.8631 269157.0531 137476.6913 195046.5319 184540.0386 0.854072902 1.019841104 0.892043056 1.060160512 1.200345815 1.458529299 0.744969451 1.056933408 1 17.49357434 3.656378639 5.725732567 1.083841277 0.932208866 0.156673642 0.180185455 0.4872469 26.32033095 0.051589353 0.077448472 4532.926102 -3.656378639 -0.151632411 SAHATAPVNIAGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAHATAPVNIAGSR 14 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 163.99 2.23E-07 0 30441 28339 9620.6 16645 31054 36864 29251 33596 27274 FALSE TRUE 26418.14472 28152.83924 14273.15434 20424.50165 30436.08616 38282.18193 26414.24252 26411.75684 24049.69879 1.098481314 1.170610887 0.593485784 0.849262264 1.265549578 1.591794653 1.098319058 1.098215702 1 14.5537312 3.236868621 24.99726006 1.207322493 0.921401225 0.295024735 0.217095307 62.55246423 924143.4775 0.069201825 0.082615177 1725.315887 -3.236868621 -0.285921268 SAICIQSWWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAICIQSWWR 10 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 144.65 7.40E-05 357260000 455220 420030 296958 357960 420330 385830 486270 521770 423530 FALSE TRUE 395061.5236 417270.7953 440567.8821 439240.2891 411966.2554 400673.1298 439111.6102 410193.5459 373460.7659 1.05783943 1.117308251 1.179689869 1.17613503 1.103104511 1.072865389 1.175790472 1.098357802 1 18.51059716 1.27821203 3.603996135 0.988318175 1.127364355 0.465330536 0.042206837 0.232604941 4.566631465 0.082194478 0.010972509 18.97632149 -1.27821203 0.139046179 SAIDHAGNYIGISLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAIDHAGNYIGISLR 15 0 O75165;A0A3B3IRM0 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 106.19 0.0012561 236080000 248060 268420 126680 188870 249160 246600 211330 274010 277610 FALSE TRUE 215278.2425 266656.7313 187942.8717 231755.8202 244202.2035 256086.8616 190835.2491 215415.0938 244791.2621 0.879435976 1.089322916 0.767767894 0.946748745 0.997593629 1.046143802 0.779583583 0.879995029 1 17.90119254 2.242733817 24.99847193 0.880709611 0.953748713 0.08905553 0.101902488 247.2511666 1481105.919 0.03812681 0.028455796 174.8774521 -2.242733817 0.073039102 SAIRHS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAIRHSPSK 9 1 O94964-2;H0YDM2;O94964 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 S(0.001)AIRHS(0.988)PS(0.011)K 55.261 0.078516 52089000 54405 68324 30886 40455 54915 48004 58632 86267 46604 TRUE FALSE 47215.24141 67875.17515 45822.57291 49640.92607 53822.29894 49850.74494 52945.87766 67819.47338 41094.52821 1.148942291 1.65168401 1.115052901 1.207969241 1.309719354 1.213075003 1.288392396 1.650328555 1 15.32665869 1.954379434 24.95730152 1.400939542 1.280217221 0 0.215005311 1283.78796 702309.3534 0.09383139 0.054147741 90.02837968 -1.954379434 -0.120722322 SAIVHLINYQDDAELATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SAIVHLINYQDDAELATR 18 0 P14923;C9JTX4;C9J826;C9JK18;C9JKY1 P14923 JUP Junction plakoglobin 0 ;; 257.81 1.23E-30 684660000 578600 474730 296547 503260 539010 634080 434810 612440 564770 FALSE TRUE 502136.544 471611.4674 439958.1211 617532.8748 528284.7556 658473.4679 392642.1931 481474.472 498003.534 1.008299158 0.947004258 0.883443773 1.240017053 1.060805234 1.322226496 0.788432544 0.966809348 1 18.92579645 2.199083307 24.99998766 0.923080684 1.068940236 0.224209223 0.138404145 263.5154933 166875.9763 0.057542508 0.038795751 158.1551387 -2.199083307 0.145859552 SAKPGDDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAKPGDDVR 9 1 P55809;E9PDW2 P55809 OXCT1 "Succinyl-CoA:3-ketoacid coenzyme A transferase 1, mitochondrial" 0 75.294 0.035266 68977000 273430 217290 135520 255260 252590 235660 226890 315850 297560 FALSE TRUE 237295.5327 215862.6077 201057.9253 313220.6844 247563.9532 244725.9927 204886.2427 248307.9354 262382.7958 0.904386783 0.822701073 0.76627709 1.193754657 0.943522049 0.932705942 0.780867671 0.946357533 1 18.0013136 SAKSEES(ph)LTSLHAVDGDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAKSEESLTSLHAVDGDSK 19 1 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.002)AKS(0.051)EES(0.896)LT(0.051)S(0.001)LHAVDGDSK 186.83 1.19E-14 291020000 490390 386570 157650 260660 377720 250420 481120 564080 377200 TRUE FALSE 425583.719 384030.5962 233890.0673 319846.8369 370204.111 260053.8194 434461.0565 443455.8817 332607.8457 1.27953602 1.154604743 0.703200692 0.96163347 1.113034812 0.781863154 1.306226122 1.333269457 1 18.34346267 2.213921094 24.99670089 1.242064532 0.996095026 0.216371527 0.189455207 309.4766036 313960.4768 0.077995932 0.05261069 163.651916 -2.213921094 -0.245969506 SALS(ph)PSKS(ph)PAK ddPTM_MDA-MB-175_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 S(0.121)ALS(0.866)PS(0.028)KS(0.986)PAK 58.885 0.058886 210810000 881460 668730 678460 578100 737280 525860 966970 1116200 983330 TRUE FALSE 764972.8277 664337.0686 1006565.525 709366.4407 722609.5705 546090.1745 873193.3982 877509.3163 867081.8476 0.882238314 0.766175731 1.160865642 0.818107821 0.833381038 0.629802338 1.007048413 1.012025934 1 19.72580866 2.082724467 24.99999987 1.007783648 0.853628046 0.243196112 0.131110589 38.70326354 11692.30358 0.053856384 0.036309963 120.9830328 -2.082724467 -0.154155602 SALSGHLETVILGLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SALSGHLETVILGLLK 16 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;A6NMY6;H0YNP5;H0YKS4;H0YMM1;H0YMW4;H0YKX9;H0YMT9;H0YLV6;H0YKZ7;H0YKL9 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 ; 125.28 7.79E-05 553410000 1272360 1039180 499950 1127690 1193410 1022140 732490 1548090 1672340 FALSE TRUE 1104214.402 1032353.558 741727.4922 1383749.25 1169663.476 1061462.387 661453.2325 1217043.001 1474637.87 0.748803774 0.700072593 0.502989586 0.938365464 0.793186924 0.719812239 0.448552994 0.825316524 1 20.49192928 1.451816076 5.585554322 0.968507199 0.696112297 0.341205274 0.138013963 0.194384614 12.54455436 0.119828151 0.035105896 28.30193154 -1.451816076 -0.272394902 SALSPS(ph)KSPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SALSPSKSPAK 11 1 P49792;Q7Z3J3 P49792 RANBP2;RGPD4 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 4 1 SALS(0.193)PS(0.641)KS(0.166)PAK 127.3 0.00017535 424560000 830620 642650 673350 594690 746570 491760 893400 1049700 999130 TRUE FALSE 720851.4625 638428.3898 998984.3122 729723.4538 731714.7176 510678.3254 806758.2055 825229.8238 881013.9896 0.818206602 0.724651819 1.133902894 0.828276806 0.830537002 0.579648373 0.915715545 0.936681861 1 19.7488054 2.015997178 24.99415499 0.952532467 0.823266801 0.175840916 0.13669821 438.140452 684552.4949 0.057099962 0.038484068 103.7521675 -2.015997178 -0.129265666 SALSPSKS(ph)PAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SALSPSKSPAK 11 1 P49792;Q7Z3J3 P49792 RANBP2;RGPD4 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 4 1 SALSPS(0.004)KS(0.996)PAK;SALS(0.094)PS(0.385)KS(0.521)PAK 112.42 0.00092535 870270000 1068550 864430 771260 759110 970660 713350 1248050 1446540 1302390 TRUE FALSE 927338.4101 858751.5024 1144243.916 931477.5278 951345.7651 740793.0361 1127014.303 1137208.678 1148422.938 0.807488582 0.747765892 0.996361077 0.811092758 0.828393211 0.645052456 0.981358231 0.990235078 1 20.13122262 2.056718506 21.25069162 0.991833081 0.813268209 0.505316303 0.085923898 16.23747598 6083.200945 0.034912002 0.023537692 113.9510957 -2.056718506 -0.178564872 SALSS(ph)SLRDLSEAGVHH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SALSSSLRDLSEAGVHH 17 1 A0A0C4DGT3 A0A0C4DGT3 IQSEC1 1 SALS(0.002)S(0.499)S(0.499)LRDLSEAGVHH 200.99 7.18E-12 442000000 235280 266390 91243 122080 258830 299870 215630 249620 70581 TRUE FALSE 204187.1519 264640.0665 135368.42 149800.1299 253679.7894 311406.1929 194718.2358 196240.7055 62236.99459 3.280800322 4.252134415 2.175047508 2.406930651 4.076028913 5.003554478 3.128657434 3.15311989 1 15.92548477 4.266562985 24.99749107 3.103296157 3.766466636 0.072658525 1.0955714 726.9039666 648889.3287 0.281505524 0.744457856 18474.08702 -4.266562985 0.663170478 SALSSS(ph)LR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(0.003)S(0.997)LR;SALSS(0.003)S(0.997)LR;SALSS(0.001)S(0.999)LR;SALSS(0.012)S(0.988)LR;SALS(0.01)S(0.412)S(0.578)LR 135.43 0.00087502 2743890000 6042190 6075590 4606650 5717280 6725880 7549630 5871930 7078350 12412400 TRUE FALSE 5243699.283 6035679.049 6834441.348 7015475.807 6592048.147 7840069.151 5302471.132 5564699.936 10945020.21 0.479094527 0.551454354 0.624433872 0.640974221 0.602287435 0.716313812 0.484464261 0.508422993 1 23.38377128 1.232929353 24.99998457 1.000000675 0.576472834 0.762144198 0.074451659 95.15253418 422384.4558 0.165590951 0.019307569 17.09737168 -1.232929353 -0.423527841 SALSSS(ph)LRDLSEAGVHH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SALSSSLRDLSEAGVHH 17 1 A0A0C4DGT3 A0A0C4DGT3 IQSEC1 1 SALS(0.001)S(0.341)S(0.657)LRDLSEAGVHH;SALS(0.001)S(0.374)S(0.625)LRDLSEAGVHH;SALS(0.001)S(0.027)S(0.972)LRDLSEAGVHH 210.61 1.95E-12 2200000000 1373350 1410300 490631 680312 1379860 1622190 1302360 1456770 405733 TRUE FALSE 1191858.318 1401035.646 727901.7927 834787.2375 1352403.486 1684596.699 1176057.328 1145251.072 357767.707 3.331374785 3.916048372 2.034565386 2.333321933 3.780116146 4.70863263 3.287209284 3.201102419 1 18.44866365 SALVQIYELEEHKIETWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SALVQIYELEEHKIETWR 18 1 F8VZX1;H0YIC9;F8VYY9;P54619-2;P54619;P54619-3;F8VSL2;F8VPF5;F8VVA3 F8VZX1 PRKAG1 5-AMP-activated protein kinase subunit gamma-1 0 100.97 0.0004523 153020000 157630 157740 128520 148520 155510 152830 180750 195380 181580 FALSE TRUE 136798.7961 156703.7956 190672.7019 182243.736 152415.6553 158709.469 163220.8928 153599.5074 160113.8193 0.854384692 0.978702502 1.190857246 1.138213658 0.951920677 0.99122905 1.019405405 0.959314494 1 17.28873831 1.845049931 6.231235648 0.978487554 1.024423624 0.024411185 0.093600711 0.927993228 45.16244685 0.050414599 0.026575787 69.99224623 -1.845049931 0.04593607 SAMDSPVPASMFAPEPS(ph)SPGAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SAMDSPVPASMFAPEPSSPGAAR 23 0 O00178;F8WAZ4 O00178 GTPBP1 GTP-binding protein 1 1 SAMDSPVPASMFAPEPS(0.5)S(0.5)PGAAR;SAMDSPVPASMFAPEPS(0.5)S(0.5)PGAAR;SAMDSPVPASMFAPEPS(0.5)S(0.5)PGAAR;SAMDSPVPASMFAPEPS(0.5)S(0.5)PGAAR;SAMDSPVPASMFAPEPS(0.5)S(0.5)PGAAR;SAMDSPVPASMFAPEPS(0.5)S(0.5)PGAAR 188.56 2.19E-17 946806000 876285 897955 494314 624018 944531 924362 876323 991818 935130 TRUE FALSE 760481.717 892056.2745 733365.9038 765710.8244 925736.681 959922.8043 791337.3303 779725.439 824579.9967 0.922265541 1.081831087 0.889381148 0.928607082 1.122676617 1.164135448 0.959685335 0.945603146 1 19.65329994 4.801638969 21.0995651 1.005752966 0.922261064 0.088916041 0.088072726 36585.10493 12234150.14 0.022802487 40.13013664 63334.29912 -4.801638969 -0.083491902 SAMDSPVPASMFAPEPSS(ph)PGAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 SAMDSPVPASMFAPEPSSPGAAR 23 0 O00178;F8WAZ4 O00178 GTPBP1 GTP-binding protein 1 1 SAMDSPVPASMFAPEPS(0.002)S(0.998)PGAAR;SAMDSPVPASMFAPEPS(0.225)S(0.775)PGAAR;SAMDSPVPASMFAPEPS(0.002)S(0.998)PGAAR;SAMDSPVPASMFAPEPS(0.003)S(0.997)PGAAR;SAMDSPVPASMFAPEPS(0.079)S(0.921)PGAAR;SAMDSPVPASMFAPEPSS(1)PGAAR;SAMDSPVPASMFAPEPS(0.27)S(0.73)PGAAR;SAMDSPVPASMFAPEPS(0.002)S(0.998)PGAAR;SAMDSPVPASMFAPEPS(0.124)S(0.876)PGAAR;SAMDSPVPASMFAPEPS(0.328)S(0.672)PGAAR;SAMDSPVPASMFAPEPS(0.139)S(0.861)PGAAR;SAMDSPVPASMFAPEPS(0.002)S(0.998)PGAAR;SAMDSPVPASMFAPEPS(0.232)S(0.768)PGAAR 381.01 2.62E-119 6371570000 3497932 3669341 2247078 2724039 3834860 3887010 3664079 4147140 3755348 TRUE FALSE 3035671.424 3645236.857 3333772.437 3342573.689 3758553.789 4036545.79 3308737.183 3260306.384 3311395.038 0.916734908 1.100816066 1.006757695 1.009415564 1.135036366 1.218986483 0.999197361 0.984571864 1 21.6590077 4.751768016 24.12950314 1.052961437 0.916734762 0.253637429 0.075273081 2250.47096 4111421.018 0.019942918 0.35351526 56463.52875 -4.751768016 -0.136226674 SAMPFTAS(ph)PASSTTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAMPFTASPASSTTAR 16 0 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 SAMPFT(0.001)AS(0.999)PASSTTAR 313.32 1.04E-57 709060000 396220 374840 220640 246330 371440 452880 374070 406960 399150 TRUE FALSE 343858.5231 372377.6514 327342.242 302262.9914 364049.0707 470302.5867 337792.749 319934.771 351962.9417 0.976973659 1.058002441 0.930047466 0.858792093 1.034339209 1.336227571 0.959739532 0.909001298 1 18.42506401 SAMPFTASPAS(ph)STTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAMPFTASPASSTTAR 16 0 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 SAMPFTAS(0.427)PAS(0.474)S(0.072)T(0.021)T(0.006)AR 188.9 1.16E-09 701690000 303750 307870 175220 203800 302590 337350 293160 325530 272700 TRUE FALSE 263608.6679 305847.5817 259956.9781 250075.9049 296569.051 350328.0728 264729.3883 255917.9428 240461.7167 1.096260442 1.271917983 1.081074284 1.039982199 1.233331672 1.456897496 1.100921145 1.064277284 1 17.8754477 2.011155646 24.999905 1.050490605 1.196771531 0.253174864 0.11806766 315.8228887 707759.7308 0.050584982 0.034070804 102.6019573 -2.011155646 0.146280926 SAMYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAMYSR 6 0 Q02878;F8VZ45;U3KQR5;F8VZA3;F8VWR1;F8VU16 Q02878 RPL6 60S ribosomal protein L6 0 99.919 0.088987 293520000 256250 261410 174290 205040 230840 328200 267930 314010 269970 FALSE TRUE 222385.9132 259692.7805 258577.227 251597.4658 226246.7356 340826.0664 241946.1898 246861.4051 238054.4542 0.934180854 1.090896541 1.086210413 1.056890394 0.950399086 1.431714721 1.01634809 1.036995531 1 17.8609321 4.740625987 22.83826252 1.082830941 0.934180673 0.114639441 0.130549819 130.1337955 1438600.296 0.030965688 0.194986108 55033.35468 -4.740625987 -0.148650268 SANAEDAQEFSDVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SANAEDAQEFSDVER 15 0 Q9HCY8 Q9HCY8 S100A14 Protein S100-A14 0 ;; 344.55 7.19E-70 975920000 551832 575597 358668 574881 683499 760301 437890 788973 681315 FALSE TRUE 478906.003 571815.8654 532121.0445 705416.5176 669898.7071 789550.2715 395423.4952 620257.2637 600770.7169 0.797152707 0.951803824 0.885730662 1.174185921 1.115065512 1.314228955 0.65819369 1.032435913 1 19.19645497 3.80502011 20.05232484 1.036666747 0.885582881 0.181107113 0.169610014 52.54823938 15852.9517 0.045813299 0.079351563 6382.930411 -3.80502011 -0.151083865 SANMDHWQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SANMDHWQQR 10 0 Q9NZL9;Q9NZL9-2;Q9NZL9-3;Q9NZL9-4;H7C0X7 Q9NZL9 MAT2B Methionine adenosyltransferase 2 subunit beta 0 ;; 145.99 2.95E-05 687130000 694570 597757 339905 490586 619427 681000 596345 647370 637835 FALSE TRUE 602780.8147 593830.2949 504284.1949 601981.0494 607101.6146 707198.5107 538511.5537 508934.9633 562430.8729 1.071742046 1.055828055 0.896615423 1.070320067 1.079424413 1.257396321 0.957471539 0.904884472 1 19.10131626 2.033255103 24.99999791 0.941306787 1.067126474 0.280075925 0.088417261 228.7318198 171951.4865 0.037482284 0.025270405 107.9580677 -2.033255103 0.125819687 SANPPHTIQASEEQSST(ph)PAPVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SANPPHTIQASEEQSSTPAPVKK 23 1 Q9Y450;Q9Y450-4;J3QT46;B7Z524;H0YDX7;E9PHZ9;E9PS53 Q9Y450 HBS1L HBS1-like protein 1 SANPPHTIQASEEQS(0.037)S(0.249)T(0.714)PAPVKK 113.13 0.00060686 171330000 54992 44377 22714 34248 38489 36257 50882 56910 51967 TRUE FALSE 47724.66787 44085.48457 33698.56637 42024.53185 37723.1442 37651.83025 45947.47147 44740.23937 45823.52046 1.041488462 0.962071096 0.735398896 0.917095226 0.823226671 0.821670397 1.002704965 0.976359715 1 15.48380068 2.223703489 24.99730427 0.989953853 0.879120187 0.277121043 0.083143194 318.7248977 536254.5139 0.03460666 0.023440708 167.3799714 -2.223703489 -0.110833666 SANPTRPS(ph)SPVTSHISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SANPTRPSSPVTSHISK 17 1 Q92560;F8W6N3;H0Y8E8 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 SANPT(0.01)RPS(0.829)S(0.16)PVTSHISK 187.79 2.71E-10 546710000 227000 216840 94857 159080 240560 213470 280450 339470 206050 TRUE FALSE 197001.3749 215415.5638 140730.1625 195201.5454 235773.3266 221682.329 253252.0022 266876.9823 181691.0037 1.084265983 1.185614914 0.774557681 1.074359992 1.297660984 1.220106249 1.393860989 1.468850833 1 17.47112746 3.279720455 4.341589019 1.3078381 1.016548605 0.366526623 0.159214012 0.202770913 8.259123847 0.047877181 0.060618598 1904.234615 -3.279720455 -0.291289495 SANPTRPSS(ph)PVTSHISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SANPTRPSSPVTSHISK 17 1 Q92560;F8W6N3;H0Y8E8 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 S(0.008)ANPT(0.034)RPS(0.049)S(0.883)PVT(0.027)SHISK 153.65 1.01E-07 582680000 520090 509710 138290 414450 694140 580780 642820 852360 679440 TRUE FALSE 451358.7888 506361.6814 205167.5066 508557.207 680327.9721 603122.9824 580479.4153 670089.4471 599117.3772 0.753372888 0.845179427 0.342449601 0.848844027 1.135550391 1.006685844 0.968890968 1.118461044 1 19.19247915 3.475069646 8.197590743 1.042823629 0.654817748 0.643195103 0.13600865 0.068615361 44.40732366 0.037642016 0.050722956 2985.861409 -3.475069646 -0.388005881 SANTS(ph)PESSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SANTSPESSSR 11 0 P20749;H7C0A2 P20749 BCL3 B-cell lymphoma 3 protein 1 SANT(0.162)S(0.837)PESSSR;SANT(0.183)S(0.817)PESSSR;SANT(0.056)S(0.942)PES(0.001)SSR;SANT(0.088)S(0.911)PESSSR 123.81 0.00037985 450612000 908585 978250 736712 928050 935627 1324880 1115570 1269130 1693050 TRUE FALSE 788513.1902 971823.8113 1092988.387 1138777.937 917009.8532 1375848.991 1007382.193 997736.4259 1492899.558 0.528175647 0.650963962 0.73212453 0.762796084 0.614247522 0.921595149 0.674782297 0.668321201 1 20.50968567 5.517929147 0.697742493 0.767470249 1.48E-21 0.333934057 0.114739024 10.42758058 1.762424488 0.046093852 8.094363501 329555.942 -5.517929147 -0.767470249 SANTSPES(ph)SSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SANTSPESSSR 11 0 P20749;H7C0A2 P20749 BCL3 B-cell lymphoma 3 protein 1 SANT(0.026)S(0.465)PES(0.505)S(0.004)SR 128.46 0.00027838 633020000 326480 356170 268510 355530 322210 479630 448840 500670 567740 TRUE FALSE 283334.8408 353830.2958 398362.3341 436258.5204 315798.6514 498081.6765 405311.5659 393605.6167 500622.424 0.565965141 0.706780757 0.7957341 0.87143224 0.630812038 0.994924823 0.809615284 0.786232494 1 18.93336339 5.503361517 0.637334008 0.854097935 2.02E-13 0.455610174 0.102979319 7.9280586 1.213230619 0.045623255 6.135222487 318684.9227 -5.503361517 -0.854097935 SAPAS(ph)PNHAGVLSAHSSGAQT(ph)PESLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAPASPNHAGVLSAHSSGAQTPESLSR 27 0 Q01167;Q01167-2 Q01167 FOXK2 Forkhead box protein K2 2 S(0.17)APAS(0.83)PNHAGVLSAHSS(0.004)GAQT(0.579)PES(0.322)LS(0.094)R 77.099 0.031641 71494000 54539 48905 25910 37671 72646 56179 71237 74370 65592 TRUE FALSE 47331.53297 48583.73983 38440.16266 46224.77632 71200.48673 58340.24248 64328.4467 58466.55425 57837.78848 0.818349633 0.839999957 0.664620202 0.799214104 1.231037503 1.008687296 1.112221757 1.010871193 1 15.81972477 3.332849646 8.029104897 1.064205202 0.773662549 0.763283569 0.080778492 0.115171065 8.636825168 0.022651704 0.029242423 2152.036566 -3.332849646 -0.290542653 SAPAS(ph)PTHPGLMSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 S(0.053)APAS(0.923)PT(0.024)HPGLMSPR;SAPAS(0.5)PT(0.5)HPGLMS(0.001)PR;SAPAS(0.771)PT(0.214)HPGLMS(0.015)PR;S(0.029)APAS(0.913)PT(0.058)HPGLMSPR;S(0.002)APAS(0.966)PT(0.032)HPGLMSPR;S(0.283)APAS(0.709)PT(0.008)HPGLMSPR;SAPAS(0.901)PT(0.099)HPGLMSPR;SAPAS(0.987)PT(0.012)HPGLMSPR;SAPAS(0.997)PT(0.003)HPGLMSPR 247.45 3.00E-18 5079350000 2616559 2442830 1541208 2337753 3415935 3451619 3410550 3795954 3303092 TRUE FALSE 2270774.099 2426782.889 2286541.344 2868575.549 3347964.577 3584405.016 3079795.386 2984218.777 2912604.227 0.779637026 0.83320036 0.785050479 0.984883398 1.149474599 1.230652961 1.057402636 1.024587807 1 21.47387825 3.579068327 3.416786363 1.087613501 0.802700221 0.801278248 0.066384066 0.119863727 2.607673245 0.021506116 0.032862776 3793.746664 -3.579068327 -0.28491328 SAPASPT(ph)HPGLMSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 SAPAS(0.195)PT(0.805)HPGLMSPR;SAPAS(0.102)PT(0.898)HPGLMSPR 217.69 2.28E-11 438240000 243720 234430 145231 208985 333840 337170 301250 361020 303440 TRUE FALSE 211511.7845 232890.0139 215465.1974 256438.2384 327197.2371 350141.1481 272034.8214 283818.6825 267567.6689 0.790498289 0.870396692 0.805273665 0.958405175 1.222857898 1.308607836 1.016695412 1.060736088 1 18.02954428 3.469777522 4.532358538 1.11531921 0.832124341 0.680978139 0.093964089 0.127623008 6.699596996 0.029820956 0.041233083 2949.697782 -3.469777522 -0.283194869 SAPGGGGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAPGGGGKR 9 1 Q14847;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ; 116.05 0.0022073 207556000 628040 158134 56197 81366 89146 194424 261200 449300 59646 FALSE TRUE 545042.9227 157095.2073 83374.05717 99841.3939 87372.16901 201903.6171 235868.8642 353220.6915 52594.71783 10.36307343 2.986900849 1.585217311 1.898315991 1.661234676 3.838857312 4.484649294 6.715896691 1 15.68263029 2.324497021 4.372549668 4.636952615 3.387729583 0 2.88451358 0.88330114 30.9475306 1.130771503 0.8458522 211.1042718 -2.324497021 -1.249223033 SAPTAPT(ph)PPPPPPPATPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAPTAPTPPPPPPPATPR 18 0 A6NHN7;A6NHB5;Q14202-2;Q14202 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 1 SAPTAPT(1)PPPPPPPATPR;SAPTAPT(1)PPPPPPPATPR 129.05 0.000246 580870000 862960 822950 514260 588660 836230 932520 840250 850800 881340 TRUE FALSE 748917.6495 817543.9873 762957.8561 722324.2501 819590.6591 968394.6478 758762.6843 668863.0409 777148.9892 0.963673195 1.051978448 0.981739495 0.929454017 1.054612012 1.246086222 0.976341338 0.860662563 1 19.56783168 2.00163653 24.99969094 0.919815585 1.038451728 0.197119909 0.090782669 73.99726287 1130372.873 0.038678993 0.02586309 100.3775359 -2.00163653 0.118636143 SAQGSSS(ph)PVPSMVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SAQGSSSPVPSMVQK 15 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 SAQGSSS(0.999)PVPSMVQK;SAQGSS(0.037)S(0.963)PVPSMVQK;SAQGSS(0.184)S(0.816)PVPSMVQK;SAQGSS(0.021)S(0.979)PVPSMVQK 345.11 2.69E-71 1599770000 3330690 2938700 1874370 2508190 2928090 2500740 3189940 3775160 4216570 TRUE FALSE 2890530.878 2919395.486 2780821.601 3077712.875 2869826.738 2596945.086 2880580.11 2967871.412 3718091.898 0.777423194 0.785186479 0.747916318 0.827766758 0.771854708 0.69846178 0.774746883 0.798224329 1 21.826131 1.208860379 3.028587724 1.054339706 0.769145368 0.833273313 0.032185324 0.174332024 1.903879087 0.126454666 0.008500058 16.17559927 -1.208860379 -0.285194338 SAQSLEYCAELLGLDQDDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAQSLEYCAELLGLDQDDLR 20 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ; 246.27 1.17E-29 162799000 267380 243330 149103 181017 225070 248940 228810 255960 241370 FALSE TRUE 232045.0555 241731.5492 221209.7095 222119.6765 220591.5473 258516.8829 206620.0414 201224.9459 212835.5136 1.090255342 1.135766983 1.039345858 1.043621305 1.036441446 1.21463227 0.970796828 0.945448166 1 17.69937937 2.054225054 24.99997984 0.965615529 1.088366663 0.520323014 0.054654257 66.92256753 30853.68077 0.0219495 0.014798347 113.2987332 -2.054225054 0.122751134 SAS(ph)ADNLTLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SASADNLTLPR 11 0 Q8ND76-3;Q8ND76-2;Q8ND76 Q8ND76-3 CCNY Cyclin-Y 1 S(0.008)AS(0.992)ADNLTLPR;S(0.001)AS(0.999)ADNLTLPR;S(0.013)AS(0.986)ADNLTLPR 138.35 6.24E-05 2209580000 2901810 2608830 1894980 2218420 3040510 3069080 2593590 3502100 3232070 TRUE FALSE 2518328.456 2591692.424 2811398.666 2722146.167 2980009.8 3187149.494 2342064.041 2753203.168 2849978.367 0.883630727 0.909372666 0.98646316 0.955146256 1.045625411 1.118306557 0.821783094 0.966043532 1 21.44251954 4.327997479 3.783156721 0.980454147 0.888703338 0.196869421 0.074390032 0.395288161 10.55752505 0.01961012 0.058760628 21281.26695 -4.327997479 -0.091750809 SAS(ph)ASHQADIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SASASHQADIK 11 0 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 S(0.011)AS(0.494)AS(0.494)HQADIK;SAS(0.5)AS(0.5)HQADIK;SAS(0.5)AS(0.5)HQADIK 214.42 1.42E-11 476801000 661050 572530 370070 581240 679570 617500 523020 1017960 938810 TRUE FALSE 573690.5676 568769.0127 549037.0898 713219.4257 666047.8866 641255.6246 472297.6009 800277.1758 827824.9513 0.693009515 0.687064351 0.663228487 0.861558261 0.804575757 0.77462708 0.570528347 0.966722705 1 19.65896621 1.616302431 7.102245584 0.991574175 0.72947819 0.646100507 0.080370253 0.072279843 7.894869756 0.052331315 0.021125981 41.33352375 -1.616302431 -0.262095984 SAS(ph)ASPLTPCSVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SASASPLTPCSVTR 14 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 SAS(0.991)AS(0.009)PLTPCSVTR;S(0.011)AS(0.989)ASPLTPCSVTR 201.48 1.86E-08 232238000 309220 210784 154550 138452 169892 190767 188174 200663 192824 TRUE FALSE 268355.7935 209399.346 229290.8969 169889.6427 166511.4816 198105.9299 169924.9144 157752.779 170028.5664 1.578298278 1.231553912 1.348543376 0.999182939 0.979314742 1.165133213 0.999390385 0.927801618 1 17.37541763 8 0.41277672 0.9617069 11.75623595 0.798959791 0.091469572 37.15565933 0.508713556 0.081391661 327.3734189 100000000 -8 10.79452905 SAS(ph)DNTLVAMDFSGHAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASDNTLVAMDFSGHAGR 18 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 1 S(0.144)AS(0.807)DNT(0.049)LVAMDFSGHAGR 261.74 5.42E-31 450920000 296290 106570 74554 115440 122620 144180 139550 137740 148020 TRUE FALSE 257134.5258 105869.9347 110608.5638 141652.4164 120180.1019 149726.6979 126016.4625 108285.3729 130521.2442 1.9700588 0.811131822 0.847437246 1.085282455 0.920770428 1.147144274 0.965486218 0.829637915 1 16.99392512 4.743250891 24.99940215 0.948238417 1.970059214 0.897800501 0.108064324 148.2184252 789985.1914 0.026944226 0.212476709 55366.98713 -4.743250891 1.021820797 SAS(ph)EPSLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SASEPSLHR 9 0 Q96II5;P10398;P04049;P04049-2;H7C155 Q96II5;P04049 ARAF;RAF1 Serine/threonine-protein kinase A-Raf;RAF proto-oncogene serine/threonine-protein kinase 1 SAS(0.539)EPS(0.46)LHR;S(0.143)AS(0.857)EPSLHR;S(0.015)AS(0.985)EPSLHR;S(0.09)AS(0.91)EPSLHR;S(0.106)AS(0.891)EPS(0.002)LHR;S(0.111)AS(0.889)EPSLHR;S(0.001)AS(0.872)EPS(0.127)LHR 149.96 5.56E-05 5718640000 5473620 4995910 2553200 3575540 5415620 5830490 5337830 5640310 5822600 TRUE FALSE 4750267.249 4963091.538 3787936.06 4387421.006 5307859.757 6054792.723 4820168.068 4434173.599 5134258.861 0.925209924 0.966661727 0.737776603 0.854538332 1.03381226 1.179292452 0.938824512 0.863644339 1 22.29172461 3.247506266 24.7977459 0.989668039 0.868356979 0.303964697 0.098103235 270.4914209 749809.7116 0.031745872 0.040368128 1768.097728 -3.247506266 -0.12131106 SAS(ph)EPSLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASEPSLNR 9 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0 P15056 BRAF Serine/threonine-protein kinase B-raf 1 SAS(0.96)EPS(0.04)LNR 129.39 0.0004098 1711100000 981720 963140 618920 712910 1051900 937700 950720 1069700 987120 TRUE FALSE 851983.2146 956813.0699 918231.7822 874787.1116 1030969.248 973773.9258 858519.3207 840952.9794 870423.7981 0.978814247 1.099249667 1.054924951 1.005012861 1.184445152 1.118735411 0.986323355 0.966141989 1 19.73135848 2.182279025 9.20495182 0.980126308 1.075731629 0.348934169 0.057418939 0.356900134 54.62784313 0.023730395 0.016014029 152.1524763 -2.182279025 0.09560532 TNS(ph)MGSATGPLPGTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 TNSMGSATGPLPGTK 15 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 T(0.011)NS(0.989)MGSATGPLPGTK;T(0.053)NS(0.946)MGS(0.001)ATGPLPGTK;T(0.14)NS(0.859)MGS(0.001)ATGPLPGTK;TNS(1)MGSATGPLPGTK;T(0.002)NS(0.998)MGSATGPLPGTK;TNS(0.997)MGS(0.003)ATGPLPGTK;TNS(0.994)MGS(0.006)ATGPLPGTK 265.22 3.61E-25 1494727000 1311280 1484650 1500820 1830420 2784600 2105310 3020530 3543350 3193080 TRUE FALSE 1137991.026 1474897.236 2226621.572 2246044.837 2729191.908 2186302.638 2727599.466 2785632.177 2815597.72 0.40417387 0.523830953 0.790816655 0.797715107 0.969311734 0.776496807 0.968746155 0.989357307 1 21.42500979 4.731144454 0.616420084 0.970034362 4.97E-18 0.887319894 0.067742886 1.080537442 0.323787242 0.035720217 0.749964724 53844.88502 -4.731144454 -0.970034362 down SAS(ph)LSSLLITPFPSPNSSLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SASLSSLLITPFPSPNSSLTR 21 0 A0A087WX11;J3KNG8;Q8TF40-3;Q8TF40;Q8TF40-2 A0A087WX11 FNIP1 Folliculin-interacting protein 1 1 S(0.131)AS(0.865)LS(0.004)SLLITPFPSPNSSLTR;S(0.111)AS(0.889)LSSLLITPFPSPNSSLTR 168.64 1.11E-11 174266000 384840 354330 177577 225950 329510 281360 314270 392830 330880 TRUE FALSE 333982.4189 352002.3829 263453.8312 277255.4009 322953.3957 292184.1013 283792.1438 308826.3615 291763.7433 1.144701583 1.20646376 0.902969739 0.950273662 1.106900371 1.001440748 0.972677895 1.058480941 1 18.15444109 4.254018498 24.9997996 1.005073711 1.175582763 0.619487904 0.057392434 161.7959388 261665.4183 0.014449177 0.037935434 17948.10074 -4.254018498 0.170509052 SAS(ph)LSYPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASLSYPDR 9 0 Q6P4Q7;Q6P4Q7-2 Q6P4Q7 CNNM4 Metal transporter CNNM4 1 S(0.004)AS(0.995)LS(0.001)YPDR 141.1 0.0001128 385330000 321340 304670 221290 332920 335100 421980 288670 408380 411400 TRUE FALSE 278874.1048 302668.6027 328306.5842 408514.5744 328432.1656 438213.8437 260674.8278 321051.115 362764.7607 0.768746403 0.83433849 0.905012338 1.126114272 0.905358517 1.207983496 0.718578142 0.885011858 1 18.46867479 4.253821615 2.976317399 0.958553229 0.786222397 0.216837309 0.133138989 0.426226424 7.551784548 0.035251572 0.106528074 17939.96597 -4.253821615 -0.172330832 SAS(ph)MKLPDNTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SASMKLPDNTVK 12 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 SAS(1)MKLPDNTVK;S(0.001)AS(0.999)MKLPDNTVK;SAS(1)MKLPDNTVK;SAS(1)MKLPDNTVK;S(0.025)AS(0.975)MKLPDNTVK;S(0.015)AS(0.985)MKLPDNTVK 199.15 1.06E-07 4940290000 9075100 8375400 3604830 4542500 5064640 2919910 8633000 8931900 7173300 TRUE FALSE 7875802.542 8320381.446 5348137.845 5573944.053 4963863.573 3032240.827 7795772.989 7021882.693 6325280.646 1.245130925 1.315416961 0.845517874 0.881216876 0.784765744 0.479384394 1.232478593 1.110129824 1 22.59269806 4.242407958 24.99922464 0.920353181 1.280274078 0.375314754 0.200615887 115.0276663 747396.0913 0.055629024 0.13608503 17474.62876 -4.242407958 0.359920898 SAS(ph)PCIADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASPCIADK 9 0 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 S(0.011)AS(0.989)PCIADK 89.266 0.010711 0 119410 122170 90953 92975 100890 96199 139760 150970 146260 TRUE FALSE 103629.666 121367.4572 134938.175 114086.3948 98882.48639 99899.83778 126206.0967 118686.2403 128969.3094 0.803521911 0.94105689 1.046281287 0.884601114 0.766713312 0.774601634 0.978574649 0.920267317 1 16.97666827 2.150002653 23.14060257 0.957208906 0.876698416 0.219955995 0.084650596 23.82704641 6217.356437 0.037888619 0.025544516 141.2546172 -2.150002653 -0.08051049 SAS(ph)PDDDLGSSNWEAADLGNEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SASPDDDLGSSNWEAADLGNEER 23 0 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 S(0.12)AS(0.88)PDDDLGSSNWEAADLGNEER;S(0.085)AS(0.915)PDDDLGSSNWEAADLGNEER;S(0.426)AS(0.574)PDDDLGSSNWEAADLGNEER;S(0.174)AS(0.826)PDDDLGSSNWEAADLGNEER;S(0.114)AS(0.886)PDDDLGSSNWEAADLGNEER;S(0.154)AS(0.846)PDDDLGSSNWEAADLGNEER;S(0.185)AS(0.815)PDDDLGSSNWEAADLGNEER;S(0.06)AS(0.94)PDDDLGSSNWEAADLGNEER 309.04 2.59E-73 3554580000 2174997 2005850 1311565 1549782 1966323 1983934 1789466 2067933 2191489 TRUE FALSE 1887565.636 1992673.439 1945842.221 1901683.69 1927197.019 2060257.225 1615923.863 1625721.621 1932413.667 0.976791703 1.031183681 1.006949109 0.98409762 0.99730045 1.066157449 0.836220469 0.841290687 1 20.88197253 2.234942468 24.99999987 0.879489193 1.00940777 0.538317549 0.050996679 62.86631432 434374.2943 0.019964519 0.014056475 171.7680829 -2.234942468 0.129918577 SAS(ph)PDDDLGSSNWEAADLGNEERK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SASPDDDLGSSNWEAADLGNEERK 24 1 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 SAS(1)PDDDLGSSNWEAADLGNEERK;S(0.001)AS(0.999)PDDDLGSSNWEAADLGNEERK;S(0.001)AS(0.999)PDDDLGSSNWEAADLGNEERK;S(0.004)AS(0.995)PDDDLGSSNWEAADLGNEERK 292.78 4.53E-62 3020940000 2416840 1994460 922340 855270 1683590 1444990 2213210 2409440 345914 TRUE FALSE 2097448.471 1981358.261 1368386.709 1049472.125 1650089.853 1500579.7 1998573.235 1894200.006 305020.441 6.876419376 6.495821246 4.486213136 3.440661623 5.409768105 4.919603734 6.552260001 6.210075627 1 18.2185464 4.297045988 5.896501518 4.828544112 6.745860408 0.228452464 1.56267718 0.325164596 22.49677714 0.394772101 1.05978036 19817.36865 -4.297045988 1.917316296 SAS(ph)PDDDLGSSNWEAADLGNEERKQKFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SASPDDDLGSSNWEAADLGNEERKQKFLR 29 3 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 SAS(1)PDDDLGSSNWEAADLGNEERKQKFLR;S(0.151)AS(0.849)PDDDLGSSNWEAADLGNEERKQKFLR;S(0.13)AS(0.588)PDDDLGS(0.152)S(0.13)NWEAADLGNEERKQKFLR 298.69 3.46E-80 1678690000 25761.2 26045.5 19979.1 17878.2 29258 37115 29306 48288 35021.7 TRUE FALSE 22356.79215 25874.4054 29641.05959 21937.71856 28675.82304 38542.83807 26463.90863 37961.98698 30881.47452 0.723954814 0.837861721 0.95983304 0.710384426 0.928576873 1.248089305 0.85695094 1.229280258 1 14.91445402 2.992767245 22.52782704 1.085458647 0.820797289 0.506064903 0.128168266 71.20736179 221792.868 0.036612633 0.039794173 983.4838772 -2.992767245 -0.264661357 SAS(ph)PDGGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SASPDGGPR 9 0 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 S(0.069)AS(0.931)PDGGPR;S(0.037)AS(0.963)PDGGPR;S(0.03)AS(0.97)PDGGPR;S(0.016)AS(0.984)PDGGPR 107.58 0.0030666 1003550000 3383610 3133070 1834230 2237100 2240930 3207520 2922710 3467780 3173740 TRUE FALSE 2936457.366 3112488.657 2721269.763 2745067.747 2196339.877 3330915.37 2639266.034 2726222.233 2798544.073 1.049280372 1.112181397 0.972387675 0.980891376 0.784815183 1.190231522 0.943085392 0.974157334 1 21.41624504 4.229204576 24.91405205 0.976523734 1.080730884 0.160164482 0.09781644 289.1224954 769906.3696 0.023800514 0.050628637 16951.36113 -4.229204576 0.104207149 SAS(ph)PDYNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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;SAS(1)PDYNR 161.28 0.00036549 1588940000 2268210 2119750 1208930 1587400 1862420 1894690 2013030 2124700 1949700 TRUE FALSE 1968460.302 2105825.223 1793572.592 1947843.432 1825361.486 1967579.95 1817806.66 1670349.439 1719208.687 1.14498043 1.224880515 1.043254728 1.132988361 1.06174515 1.144468362 1.057350788 0.971580386 1 20.71331325 -2 0.190131146 0.100173938 1.20982197 0.548206953 0.051146274 76.31686892 1.107549892 24.05123677 0.380427696 0.01 2 1.109648032 SAS(ph)PHDVDLCLVS(ph)PCEFEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SASPHDVDLCLVSPCEFEHR 20 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 2 S(0.025)AS(0.975)PHDVDLCLVS(1)PCEFEHR;S(0.389)AS(0.611)PHDVDLCLVS(1)PCEFEHR 186.26 1.77E-17 114430000 65261 70171 63431 58797 82601 94732 77864 82670 112837 TRUE FALSE 56636.5935 69710.04208 94106.44376 72147.75751 80957.40171 98376.40134 70312.76126 64991.66384 99497.5384 0.569226077 0.700620771 0.945816804 0.72512103 0.813662358 0.988732012 0.7066784 0.653198711 1 16.60237321 4.475784587 6.678784639 0.812458654 0.599144248 0.337699169 0.119798228 0.152386869 35.9397261 0.030288154 0.092734581 29907.80821 -4.475784587 -0.213314406 SAS(ph)PHDVDLCLVSPCEFEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SASPHDVDLCLVSPCEFEHR 20 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 S(0.144)AS(0.856)PHDVDLCLVSPCEFEHR;S(0.133)AS(0.867)PHDVDLCLVSPCEFEHR;S(0.009)AS(0.991)PHDVDLCLVSPCEFEHR;S(0.054)AS(0.946)PHDVDLCLVSPCEFEHR 252.18 2.91E-36 2642150000 498730 464306 314717 368370 455432 480975 394377 558110 703610 TRUE FALSE 432821.5669 461255.9433 466915.1939 452014.0387 446369.7942 499478.4195 356130.3792 438762.5197 620430.0274 0.697615441 0.743445551 0.752567047 0.728549585 0.719452274 0.805051976 0.574005711 0.707190981 1 19.24290899 1.237707453 24.98451166 1.000000336 0.714203019 0.699488005 0.058493534 11.90845048 348523.5514 0.083791525 0.014265686 17.28651524 -1.237707453 -0.285797316 SAS(ph)PHDVDLCLVSPCEFEHRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASPHDVDLCLVSPCEFEHRK 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 S(0.233)AS(0.767)PHDVDLCLVSPCEFEHRK 123.74 1.22E-05 593030000 225560 182720 81458 81705 167540 169940 196170 263720 76094 TRUE FALSE 195751.6745 181519.7003 120851.3613 100257.369 164206.2818 176477.7018 177145.4636 207325.5303 67098.25401 2.917388498 2.705282022 1.801110372 1.49418745 2.447251187 2.630138509 2.640090509 3.08987966 1 16.03398761 3.029983664 24.99133735 2.491253724 2.200108679 0 0.67089053 812.0144331 676807.5523 0.206700274 0.234373153 1071.479001 -3.029983664 -0.291145046 SAS(ph)PSPPESLVEEERPSGPGGGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASPSPPESLVEEERPSGPGGGGK 24 1 K7EMK7;Q04725;Q04725-3 K7EMK7 TLE2 Transducin-like enhancer protein 2 1 S(0.018)AS(0.981)PS(0.001)PPESLVEEERPSGPGGGGK 199.03 1.02E-24 140660000 79926 72464 55779 64592 74447 71130 93815 108710 101870 TRUE FALSE 69363.57659 71987.97921 82753.91097 79258.60083 72965.65035 73866.41713 84716.83574 85463.21248 89827.04465 0.772190345 0.80140652 0.921258306 0.882346749 0.812290448 0.822318239 0.943110575 0.951419618 1 16.45486225 2.158289218 4.541571781 0.965119004 0.838729742 0.664527389 0.043550274 0.14151257 5.368053289 0.019933732 0.013187821 143.9757065 -2.158289218 -0.126389262 SAS(ph)PTVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SASPTVPR 8 0 Q92817;K7EKI0;K7EQ87 Q92817 EVPL Envoplakin 1 S(0.147)AS(0.797)PT(0.056)VPR;S(0.004)AS(0.974)PT(0.022)VPR;S(0.006)AS(0.944)PT(0.05)VPR;S(0.005)AS(0.982)PT(0.014)VPR;S(0.228)AS(0.737)PT(0.036)VPR;S(0.147)AS(0.787)PT(0.066)VPR;S(0.014)AS(0.923)PT(0.063)VPR 133.13 0.00097808 13500020000 6994820 6941630 4302680 5196630 6604350 7220490 6653360 7229000 7275140 TRUE FALSE 6070436.814 6896029.975 6383470.44 6376604.267 6472936.356 7498266.923 6008118.171 5683134.606 6415081.237 0.946275907 1.074971574 0.995072424 0.994002107 1.009018611 1.168849878 0.93656151 0.885902204 1 22.6130361 2.041150151 24.99999897 0.9277299 1.030960373 0.294510583 0.065174793 149.8957073 91065.70688 0.025646531 0.017290866 109.938587 -2.041150151 0.103230473 SAS(ph)QS(ph)SLDKLDQELK ddPTM_MDA-MB-175_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(0.013)AS(0.986)QS(0.559)S(0.441)LDKLDQELK;S(0.457)AS(0.542)QS(0.625)S(0.375)LDKLDQELK 149.94 1.86E-06 135682000 834300 576200 778660 667280 651100 458060 913250 1070200 1323490 TRUE FALSE 724045.1412 572414.9043 1155222.58 818796.1227 638144.3839 475681.8646 824683.1556 841346.0583 1167028.52 0.620417692 0.490489216 0.989883761 0.701607637 0.546811301 0.407600891 0.706652101 0.720930161 1 20.15440839 1.166100853 1.910609447 1.172562082 0.636196629 0.350628367 0.15482508 1.256004174 3.743477887 1.298500424 0.043971375 14.65888214 -1.166100853 -0.536365453 SAS(ph)QSS(ph)LDKLDQELK ddPTM_MDA-MB-175_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(0.064)AS(0.936)QS(0.043)S(0.957)LDKLDQELK;S(0.048)AS(0.759)QS(0.399)S(0.794)LDKLDQELK;S(0.084)AS(0.914)QS(0.276)S(0.727)LDKLDQELK 222.11 1.73E-11 363410000 1959660 1375370 1633410 1425340 1453390 1051200 2106090 2458160 2923600 TRUE FALSE 1700685.966 1366335.104 2423332.539 1748985.232 1424470.383 1091640.344 1901841.716 1932501.613 2577975.339 0.659698307 0.530003171 0.940013856 0.678433655 0.552553921 0.423448715 0.737726885 0.749619899 1 21.29780703 1.233612481 1.718207455 1.133361627 0.641135706 0.406472902 0.136035235 1.075057213 2.902918151 0.894415929 0.039523654 17.12428633 -1.233612481 -0.492225921 SAS(ph)QSSLDKLDQELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SASQSSLDKLDQELK 15 1 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 S(0.006)AS(0.97)QS(0.023)S(0.001)LDKLDQELK;SAS(0.996)QS(0.004)SLDKLDQELK 246.1 2.29E-18 1759410000 1117510 896490 1030190 1057910 853450 714950 1508990 1568640 1729470 TRUE FALSE 969828.2221 890600.8982 1528393.33 1298124.635 836468.0147 742454.5891 1362648.382 1233198.543 1525014.027 0.635947083 0.583995217 1.002215916 0.851221439 0.548498571 0.48685099 0.893531704 0.808647345 1 20.54039108 1.563701268 1.630754733 0.995202119 0.703402854 0.255837541 0.160204869 0.826041146 3.541130317 0.341523348 0.049970013 36.61856048 -1.563701268 -0.291799265 SAS(ph)SDTSEELNSQDSPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SASSDTSEELNSQDSPPK 18 0 O14745;O14745-2;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 SAS(0.995)S(0.005)DTSEELNSQDSPPK;SAS(0.994)S(0.006)DTSEELNSQDSPPK;SAS(0.858)S(0.139)DT(0.003)SEELNSQDSPPK;S(0.182)AS(0.812)S(0.005)DTSEELNSQDSPPK;S(0.001)AS(0.855)S(0.1)DT(0.044)SEELNSQDSPPK 586.4 0 2542789000 1482090 972428 937099 1356516 994188 710211 1338645 1454974 3123310 TRUE FALSE 1286228.051 966040.0564 1390283.211 1664533.691 974405.6039 737533.2767 1208823.414 1143839.133 2754075.85 0.467027098 0.350767411 0.50480934 0.604389197 0.353804927 0.26779701 0.438921613 0.415325937 1 21.39313686 1.238030361 24.98284887 1.000000658 0.424108301 0.794523762 0.091837494 5.887887151 277139.4667 0.134024702 0.02330732 17.29937294 -1.238030361 -0.575892357 SAS(ph)SSWLEGTSTQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.003)AS(0.967)S(0.027)S(0.004)WLEGTSTQAK;S(0.153)AS(0.838)S(0.009)SWLEGTSTQAK 180.74 1.71E-11 76747000 392440 317540 194243 225190 292180 228436 360450 387930 364050 TRUE FALSE 340578.0597 315454.0588 288179.5645 276322.8313 286366.1896 237224.0807 325493.6145 304974.1884 321012.4237 1.060949778 0.982684892 0.897720908 0.860785474 0.892071984 0.738987227 1.013959556 0.950038584 1 18.29226961 4.506715168 2.778846417 0.909001916 1.060646377 0.303827786 0.076647574 0.407849172 5.610547494 0.020639548 0.109367583 32115.53548 -4.506715168 0.15164446 SAS(ph)TDLGTADVVLGR ddPTM_MDA-MB-175_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(0.982)T(0.018)DLGTADVVLGR 223.9 1.26E-12 84594000 281610 179140 105630 147860 195810 121210 325860 274900 212350 TRUE FALSE 244394.525 177963.2175 156713.0213 181433.8729 191913.7641 125873.0271 294258.1474 216114.7743 187246.2249 1.305204017 0.950423527 0.836935545 0.968958776 1.024927281 0.672232656 1.571503765 1.154174266 1 17.51457711 2.244729324 24.99999704 1.237351798 0.957149623 0.286339559 0.209884036 183.1461177 742241.8619 0.077575881 0.058539085 175.6828321 -2.244729324 -0.280202176 SAS(ph)TLCLPSVGAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SASTLCLPSVGAAR 14 0 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 SAS(0.939)T(0.061)LCLPSVGAAR;SAS(0.939)T(0.061)LCLPSVGAAR 284.91 1.45E-33 353620000 264090 269530 194023 212730 264650 263750 229420 234280 709950 TRUE FALSE 229189.8374 267759.4397 287853.1718 261033.5979 259383.9828 273896.6332 207170.8837 184181.0452 626020.5198 0.36610595 0.427716714 0.459814276 0.41697291 0.414337829 0.437520216 0.330933056 0.294209278 1 19.25585042 1.232938521 24.99996265 1.000000969 0.391778303 0.934185779 0.050593706 49.48378812 220017.7669 0.123649136 0.014445692 17.09773261 -1.232938521 -0.608222666 SAS(ph)TLCLPSVGAARPQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SASTLCLPSVGAARPQVK 18 1 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 SAS(0.69)T(0.31)LCLPSVGAARPQVK;SAS(0.96)T(0.04)LCLPSVGAARPQVK;S(0.007)AS(0.823)T(0.17)LCLPSVGAARPQVK 336.49 2.48E-75 3621200000 2492580 2364580 1367413 1487166 1833030 1691440 2123940 2155770 2269450 TRUE FALSE 2163179.238 2349046.918 2028698.501 1824849.77 1796556.289 1756510.791 1917960.626 1694775.362 2001158.206 1.080963629 1.173843683 1.013762177 0.911896803 0.89775825 0.87774709 0.958425286 0.84689724 1 20.9324038 3.974365253 3.050434166 0.908927136 1.126790306 0.765978473 0.048096861 0.101658978 1.912679728 0.01210645 0.026000732 9426.820843 -3.974365253 0.21786317 SAS(ph)VNKEPVSLPGIMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 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 SAS(1)VNKEPVSLPGIMR;SAS(1)VNKEPVSLPGIMR;SAS(1)VNKEPVSLPGIMR;S(0.003)AS(0.997)VNKEPVSLPGIMR;SAS(1)VNKEPVSLPGIMR;SAS(1)VNKEPVSLPGIMR;S(0.145)AS(0.855)VNKEPVSLPGIMR;S(0.001)AS(0.999)VNKEPVSLPGIMR;S(0.021)AS(0.979)VNKEPVSLPGIMR 275.23 1.79E-35 22249240000 7174610 9447490 5897590 8458550 11866930 8450130 14633110 15690420 13217400 TRUE FALSE 6226467.11 9385428.816 8749684.25 10379193.06 11630801.31 8775211.969 13213993.24 12335145.79 11654854.03 0.534238103 0.805280683 0.750733062 0.890546808 0.997936249 0.75292337 1.133775954 1.058369822 1 23.4744276 5.302152241 0.32861541 1.090164727 5.19E-17 0.68135616 0.100032263 8.313274326 0.642119718 0.201429453 3.881819426 200517.4812 -5.302152241 -1.090164727 SAS(ph)WGSADQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SASWGSADQLK 11 0 Q86VQ1;H7C0Q2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 S(0.001)AS(0.999)WGSADQLK;SAS(1)WGSADQLK;SAS(0.97)WGS(0.029)ADQLK;S(0.002)AS(0.994)WGS(0.004)ADQLK;S(0.001)AS(0.994)WGS(0.005)ADQLK 247.69 4.05E-16 1478670000 2964760 2697540 1982990 2497900 2837780 2331020 3286640 3880730 3828640 TRUE FALSE 2572959.454 2679819.682 2941970.597 3065086.373 2781313.73 2420695.848 2967902.159 3050866.089 3376022.541 0.762127451 0.793780151 0.87143097 0.90789867 0.823843353 0.717025973 0.879112068 0.903686528 1 21.68689311 1.49564254 1.785767395 1.012017255 0.820074031 0.536266724 0.055267606 0.4418368 2.179939048 0.129954324 0.016709862 31.30707832 -1.49564254 -0.191943224 SAS(ph)WGSTDHRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASWGSTDHRK 11 1 Q9C073;D6RJ87 Q9C073 FAM117A Protein FAM117A 1 S(0.003)AS(0.886)WGS(0.063)T(0.048)DHRK 94.688 0.0050946 269600000 181510 179160 84376 121450 198530 190460 190890 222370 146260 TRUE FALSE 157522.9936 177983.0862 125180.5158 149027.0787 194579.6414 197787.1194 172377.5172 174817.906 128969.3094 1.221399062 1.380042174 0.970622518 1.155523585 1.508728257 1.533598345 1.33657781 1.355500055 1 16.97666827 5.059313156 12.81503329 1.290746177 0.822677124 0.006547921 0.19033841 21512649.5 150863497.1 0.048125877 244927088.2 114633.9233 -5.059313156 -0.468069053 SAS(ph)WGSTDQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SASWGSTDQLK 11 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 SAS(1)WGSTDQLK;S(0.011)AS(0.977)WGS(0.005)T(0.007)DQLK 194.06 7.14E-07 507230000 1215470 955210 668150 859560 1094850 836830 1141610 1403550 1266770 TRUE FALSE 1054842.56 948935.1626 991269.5748 1054736.236 1073064.627 869023.3916 1030896.838 1103411.755 1117013.894 0.944341486 0.849528522 0.887428151 0.944246299 0.960654682 0.777987988 0.922904221 0.987822767 1 20.0912157 1.783367069 3.829764571 0.995224624 0.894135039 0.367891378 0.05302553 0.217628883 6.11565916 0.033321202 0.014178793 60.72493649 -1.783367069 -0.101089585 SASEPS(ph)LNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASEPSLNR 9 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0 P15056 BRAF Serine/threonine-protein kinase B-raf 1 SAS(0.068)EPS(0.932)LNR 157.97 7.06E-05 1565100000 736600 598040 344380 399210 572310 591800 614030 632670 664360 TRUE FALSE 639256.4437 594111.4359 510923.3199 489856.732 560922.1507 614566.9289 554481.4651 497378.4439 585820.1176 1.09121627 1.014153352 0.872150519 0.836189672 0.957498955 1.049071055 0.946504649 0.849029299 1 19.16009821 4.455205843 4.556595139 0.925801428 1.077278157 0.396959081 0.066080073 0.18406618 9.324263847 0.017716974 0.0575844 28523.69887 -4.455205843 0.151476728 SASNKS(ph)PLVLEANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SASNKSPLVLEANR 14 1 Q92560;F8W6N3 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 S(0.003)AS(0.011)NKS(0.987)PLVLEANR;SAS(0.004)NKS(0.996)PLVLEANR 122.94 6.41E-05 606410000 392520 350490 218772 290994 397750 300849 364540 431200 436060 TRUE FALSE 340647.4875 348187.6081 324570.8709 357068.6353 389835.5532 312422.8557 329186.9669 338991.2356 384509.4836 0.885927401 0.905537114 0.844116686 0.928634144 1.013851595 0.812523147 0.856121841 0.88161996 1 18.55265966 3.713249943 24.65180813 0.908035807 0.881228044 0.064269501 0.061989676 2566.907403 2500087.649 0.017647952 0.026188222 5167.136603 -3.713249943 -0.026807763 SASPDDDLGSS(ph)NWEAADLGNEERKQKFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASPDDDLGSSNWEAADLGNEERKQKFLR 29 3 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 SAS(0.005)PDDDLGS(0.15)S(0.844)NWEAADLGNEERKQKFLR 194.34 4.57E-18 462220000 8577 11000 0 0 8362.1 13885 0 24793 6296.4 TRUE FALSE 7443.527719 10927.74028 0 0 8195.71057 14419.16493 0 19491.20989 5552.046765 1.34068174 1.968236353 0 0 1.476160219 2.597089964 0 3.510635035 1 12.438804 1.740699035 24.99999997 2.349777114 1.084144347 0.181797479 1.053339078 0.512289033 6047.788687 0.549194591 0.263730235 55.04261201 -1.740699035 -1.265632768 SASQS(ph)S(ph)LDKLDQELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASQSSLDKLDQELK 15 1 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 2 S(0.036)AS(0.277)QS(0.749)S(0.937)LDKLDQELK 111.22 0.010277 93939000 595430 426640 527440 486520 461070 321800 650960 803340 956940 TRUE FALSE 516742.4169 423837.3737 782511.7482 596991.802 451895.6091 334179.8542 587829.9994 631551.9926 843811.6433 0.612390717 0.50228908 0.92735358 0.707494151 0.535540855 0.396036079 0.696636511 0.748451384 1 19.68656147 1.289887569 1.878388598 1.098110385 0.622969703 0.419516801 0.140705216 0.810234876 3.026905891 0.666071724 0.040968565 19.49339886 -1.289887569 -0.475140682 SASQS(ph)SLDKLDQELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASQSSLDKLDQELK 15 1 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 S(0.005)AS(0.041)QS(0.477)S(0.477)LDKLDQELK 93.776 0.0028623 71272000 102700 57727 63442 73583 60810 45305 78899 106640 135480 TRUE FALSE 89127.93479 57347.78754 94122.7634 90291.1448 59599.99997 47047.91267 71247.38712 83835.86587 119463.7087 0.746067034 0.480043589 0.78787746 0.755803965 0.498896281 0.393825984 0.596393565 0.701768485 1 16.86621289 1.249166127 2.515725391 1.091029903 0.604897666 0.477964946 0.128227508 0.475618051 3.355007622 0.497576668 0.035195539 17.74868276 -1.249166127 -0.486132237 SASQS(ph)SLDKLDQELKEQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SASQSSLDKLDQELKEQQK 19 2 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 SASQS(0.614)S(0.386)LDKLDQELKEQQK;S(0.003)AS(0.003)QS(0.577)S(0.417)LDKLDQELKEQQK 182.39 1.53E-14 855280000 1344530 807420 681170 513460 630300 406060 1244760 1380840 200969 TRUE FALSE 1166846.954 802116.0049 1010586.09 630048.9407 617758.2632 421681.391 1124043.367 1085558.112 177210.6738 6.584518467 4.526341376 5.702738266 3.55536677 3.486010464 2.379548489 6.342977784 6.125805453 1 17.43510598 5.558475645 0.97216225 4.223398362 14.52849153 0.185814894 1.659133347 17.47630822 4.103711667 0.547374692 276.1486326 361805.9001 -5.558475645 10.30509317 SASQSS(ph)LDKLDQELK ddPTM_MDA-MB-175_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(0.017)S(0.983)LDKLDQELK;SASQS(0.124)S(0.876)LDKLDQELK;SASQS(0.055)S(0.945)LDKLDQELK;SASQS(0.34)S(0.66)LDKLDQELK 291.97 3.73E-44 3343840000 3602100 2579840 2966570 2756230 2404130 1581470 3562500 3966930 5146400 TRUE FALSE 3126073.358 2562892.861 4401213.175 3382074.148 2356292.517 1642310.174 3217009.298 3118632.89 4537998.455 0.688866113 0.564762832 0.969857795 0.745278823 0.519236077 0.36190188 0.708904891 0.687226521 1 22.11362469 1.156103293 2.547638336 1.142043302 0.649014049 0.320994011 0.157833192 0.964927364 5.683746209 1.14756322 0.043975957 14.32528573 -1.156103293 -0.493029253 AVLS(ph)PGSVFS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AVLSPGSVFSPGR 13 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 2 AVLS(0.991)PGS(0.009)VFS(1)PGR;AVLS(0.739)PGS(0.338)VFS(0.923)PGR;AVLS(0.996)PGS(0.061)VFS(0.943)PGR;AVLS(0.997)PGS(0.04)VFS(0.963)PGR 188.9 8.36E-06 248733000 398381 578250 449446 610260 843350 863440 839570 940310 948690 TRUE FALSE 345733.9415 574451.4377 666799.5889 748828.8602 826568.985 896657.0955 758148.6306 739232.024 836536.949 0.413291896 0.686701811 0.797095203 0.89515336 0.988084251 1.071867891 0.906294255 0.883681259 1 19.67406974 4.733606725 0.967968232 0.958937959 0.127799408 0.912333742 0.055594907 0.611096848 0.461057634 0.020752504 0.533272682 54151.03035 -4.733606725 -0.831138552 down SASS(ph)GAEGDVSSEREP ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SASSGAEGDVSSEREP 16 1 Q8TEA8 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1 1 SAS(0.005)S(0.995)GAEGDVSSEREP;SAS(0.024)S(0.976)GAEGDVSSEREP;SAS(0.003)S(0.997)GAEGDVSSEREP;SAS(0.001)S(0.999)GAEGDVSSEREP 358.82 3.32E-87 2817240000 3357850 3538850 2096080 2438370 3703200 3403480 3399800 4244340 3359380 TRUE FALSE 2914101.615 3515603.061 3109751.299 2992039.177 3629513.565 3534414.078 3070087.919 3336720.92 2962237.923 0.983750019 1.186806446 1.04979795 1.010060385 1.225260651 1.193156718 1.036408283 1.126418946 1 21.49825609 4.769809924 23.38848663 1.104145734 0.98374952 0.182267444 0.079694626 9962.274174 7455938.743 0.019073317 2.234775475 58858.59949 -4.769809924 -0.120396214 SASSASSLFS(ph)PSSTLFSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SASSASSLFSPSSTLFSSSR 20 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4;E9PR38;H0YDK8 Q5T1Z4 PUM1 Pumilio homolog 1 1 SASSASSLFS(1)PSSTLFSSSR 349.98 4.66E-95 71038000 63348 63956 33899 52837 71894 65741 63370 71408 61638 TRUE FALSE 54976.4013 63535.86882 50292.66979 64834.44841 70463.45006 68270.09881 57224.38715 56137.9549 54351.22586 1.011502509 1.168986859 0.925327239 1.192879229 1.296446381 1.256091242 1.052862861 1.032873758 1 15.73002495 2.021316002 24.80563288 1.02600996 1.143595622 0.20077926 0.107963736 355.0943656 413224.8149 0.046700276 0.031482406 105.0306377 -2.021316002 0.117585662 SASSGAEGDVSS(ph)EREP ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SASSGAEGDVSSEREP 16 1 Q8TEA8 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1 1 SASSGAEGDVS(0.009)S(0.991)EREP;SASSGAEGDVS(0.006)S(0.994)EREP 251.04 9.68E-21 538530000 1433850 1460530 865800 995330 1563750 1579480 1392690 1541360 1453710 TRUE FALSE 1244363.09 1450935.682 1284503.776 1221334.889 1532634.434 1640243.618 1257627.138 1211752.159 1281854.06 0.970752544 1.131903957 1.002067097 0.952787784 1.195638788 1.279586865 0.981100094 0.945312104 1 20.28980059 2.035489548 24.99969393 0.967086136 1.089220677 0.219646437 0.100657711 254.1419211 179022.6891 0.043055406 0.029027833 108.5149432 -2.035489548 0.122134542 SASYKPVFVTEITDDLHFYVQDVETGTQLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SASYKPVFVTEITDDLHFYVQDVETGTQLEK 31 1 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 374.09 2.05E-137 2381901000 1948141 1545037 1065908 1445463 1417468 1171202 2101934 2386993 1999472 FALSE TRUE 1690689.231 1534887.55 1581384.674 1773677.467 1389263.16 1216258.899 1898088.764 1876553.123 1763096.698 0.958931653 0.870563453 0.896935872 1.006001241 0.787967649 0.689842423 1.076565322 1.064350653 1 20.74968017 2.190884464 24.99998426 1.051825963 0.872371932 0.476684937 0.088098511 104.6252941 54861.66131 0.037307298 0.025152645 155.1974082 -2.190884464 -0.179454032 SAT(ph)FPNAGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SATFPNAGPR 10 0 Q86X27;Q86X27-3 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 S(0.158)AT(0.842)FPNAGPR;S(0.006)AT(0.994)FPNAGPR;SAT(1)FPNAGPR;S(0.002)AT(0.998)FPNAGPR 219.33 7.11E-08 2145250000 1163540 1301340 763313 831508 1176510 1085770 1075130 1176220 1222840 TRUE FALSE 1009775.241 1292791.412 1132453.72 1020314.6 1153099.753 1127540.274 970864.0581 924694.5064 1078277.248 0.936470878 1.198941565 1.050243545 0.946245135 1.069390785 1.04568679 0.900384442 0.857566556 1 20.04029674 2.239878166 24.99997998 0.905663446 1.045716248 0.336777481 0.079671965 33.57449181 637083.5076 0.030083046 0.021992274 173.7313385 -2.239878166 0.140052802 SAT(ph)PVNCEQPDILVSSTPINEGQTVLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SATPVNCEQPDILVSSTPINEGQTVLDK 28 0 A0A2R8Y7M0;P82094;P82094-2;F8WF45 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 S(0.017)AT(0.983)PVNCEQPDILVSSTPINEGQTVLDK 275.73 5.55E-61 431670000 495070 460590 372690 398430 467320 384880 573480 709430 598100 TRUE FALSE 429645.2452 457564.354 552924.1306 488899.6211 458021.2463 399686.5827 517863.9979 557723.9153 527393.2994 0.814658142 0.86759607 1.048409472 0.927011439 0.868462392 0.757852978 0.981931319 1.057510431 1 19.00851972 2.012124721 24.94833269 1.028920457 0.88763478 0.410962296 0.076004999 213.4166735 439133.2824 0.032808541 0.02210286 102.8311566 -2.012124721 -0.141285677 SATDGNTST(ph)TPPTSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SATDGNTSTTPPTSAK 16 0 A0A669KAX4;Q13620-1;K4DI93;Q13620;A0A669KAU9 A0A669KAX4 CUL4B Cullin-4B 1 SATDGNT(0.003)S(0.112)T(0.479)T(0.406)PPTSAK 195.89 3.78E-12 0 499990 421690 216050 319250 370250 294760 399260 501050 404220 TRUE FALSE 433915.0547 418919.8906 320532.5026 391740.5919 362882.7494 306099.6079 360539.8267 393904.3567 356433.5721 1.217379867 1.175309857 0.89927697 1.099056381 1.01809363 0.858784447 1.011520392 1.105126979 1 18.4432737 4.366626528 6.925993515 1.008606659 1.206418471 0.536864538 0.076244716 0.164432577 9.181109275 0.019646987 0.052817359 23260.90072 -4.366626528 0.197811812 SATLS(ph)GSATNLASLTAALAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SATLSGSATNLASLTAALAK 20 0 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 S(0.016)AT(0.016)LS(0.482)GS(0.482)AT(0.003)NLASLTAALAK 81.723 0.0036366 0 19566 18046 13815 14538 18612 19352 17496 19823 19560 TRUE FALSE 16980.30353 17927.45464 20495.98021 17839.0751 18241.65761 20096.48396 15799.24061 15584.00571 17247.63908 0.984500165 1.039414992 1.188335407 1.034290839 1.05763215 1.165173034 0.916023378 0.903544284 1 14.07411127 2.220176223 24.99883994 0.931297889 1.078532419 0.500119219 0.065024137 185.7069219 252519.8003 0.02627167 0.017749068 166.026045 -2.220176223 0.14723453 SATLSGS(ph)ATNLASLTAALAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SATLSGSATNLASLTAALAK 20 0 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 SATLSGS(0.817)AT(0.183)NLASLTAALAK;SATLS(0.003)GS(0.997)ATNLASLTAALAK;SATLS(0.011)GS(0.986)AT(0.003)NLASLTAALAK;SATLSGS(0.996)AT(0.004)NLASLTAALAK 442.96 1.31E-197 2768320000 1280710 1358410 819807 900445 1271050 1183050 1333070 1572030 1453100 TRUE FALSE 1111460.929 1349486.515 1216268.407 1104904.8 1245758.592 1228562.699 1203789.077 1235863.618 1281316.173 0.867436899 1.053203373 0.949233634 0.862320185 0.972249174 0.958828683 0.939494171 0.964526667 1 20.28919508 1.28179433 2.219689761 1.012439291 0.946241525 0.102145023 0.053337711 1.508706498 8.275058465 0.192948868 0.013773646 19.13349602 -1.28179433 -0.066197766 SATREPPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SATREPPYR 9 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;; 93.111 0.0087741 183839000 228527 200794 96306 124918 175755 182274 179112 204139 116989 FALSE TRUE 198326.5779 199474.971 142879.9037 153282.5412 172257.8194 189286.1987 161741.7458 160485.4635 103158.6937 1.922538672 1.933670967 1.385049564 1.485890676 1.669833275 1.834903021 1.567892535 1.555714383 1 16.65450588 0.895287239 1.538950983 7.80E-10 1.685299206 0.594086903 0.177354641 2.172737744 2.24387263 7.321981265 0.053299906 7.857551553 -0.895287239 1.685299205 SATRPS(ph)PS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SATRPSPSPER 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.002)AT(0.103)RPS(0.904)PS(0.99)PER;S(0.048)AT(0.147)RPS(0.807)PS(0.998)PER;S(0.025)AT(0.033)RPS(0.944)PS(0.999)PER;S(0.176)AT(0.176)RPS(0.656)PS(0.992)PER;S(0.001)AT(0.002)RPS(0.997)PS(1)PER;S(0.118)AT(0.175)RPS(0.707)PS(1)PER;S(0.004)AT(0.042)RPS(0.954)PS(1)PER 133.13 0.0020101 20439066000 6981088 5558711 3399690 4060000 6110675 5917221 5487588 6158195 5674309 TRUE FALSE 6058519.533 5522195.461 5043791.455 4981885.053 5989084.523 6144860.321 4955402.56 4841312.922 5003498.654 1.210856633 1.103666823 1.008052925 0.995680302 1.196979341 1.228112716 0.990387507 0.967585535 1 22.25450581 2.106197027 10.57876365 0.980764178 1.115137574 0.405746935 0.078201801 0.369682957 34.11326113 0.03447662 0.023238399 127.7018024 -2.106197027 0.134373396 SATRPS(ph)PSPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SATRPSPSPER 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.001)AT(0.001)RPS(0.969)PS(0.029)PER 99.927 0.0026709 409440000 397050 356190 244220 295840 335890 394780 347310 403660 343340 TRUE FALSE 344578.8365 353850.1644 362325.6089 363014.9936 329206.4462 409967.4421 313627.9297 317340.4503 302750.7363 1.138160193 1.168783828 1.196778621 1.199055692 1.087384461 1.35414185 1.035927884 1.048190515 1 18.20777094 2.062804863 24.99999993 1.03189139 1.186458223 0.55617904 0.068415741 44.26688361 17620.39928 0.025861906 0.017436091 115.5592894 -2.062804863 0.154566833 SATRPSPS(ph)PER ddPTM_MDA-MB-175_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(0.012)PS(0.988)PER;S(0.005)AT(0.004)RPS(0.129)PS(0.863)PER 86.214 0.0088643 1325390000 817880 721040 395370 471230 718070 769410 703550 759210 851620 TRUE FALSE 709795.0858 716303.4408 586572.2544 578229.9738 703781.8119 799009.7006 635319.8293 596858.8497 750942.4538 0.945205697 0.953872613 0.781114786 0.770005705 0.937198061 1.064009228 0.84602998 0.794813034 1 19.51834283 1.20334615 23.89934097 1.000001623 0.882631645 0.128332847 0.09244108 7709.507479 5231731.37 4.658472036 0.024158954 15.97151635 -1.20334615 -0.117369978 SATTT(ph)PSGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SATTTPSGSPR 11 0 A0A096LNZ0;A0A096LP60;A0A096LP25;Q2M2I8;Q2M2I8-2 A0A096LNZ0;A0A096LP25;Q2M2I8 AAK1 AP2-associated protein kinase 1 2 SATT(0.002)T(0.997)PS(0.001)GS(0.999)PR 137.39 0.00042097 103120000 199760 182740 107490 126270 168900 185970 191330 213870 187290 TRUE FALSE 173361.2099 181539.5689 159472.5235 154941.5334 165539.2204 193124.3862 172774.846 168135.5648 165148.7896 1.049727402 1.099248559 0.965629382 0.938193576 1.002364116 1.169396317 1.046176884 1.01808536 1 17.33340687 SATTTGS(ph)PGTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.154)GS(0.846)PGTEK;SATTTGS(1)PGTEK;SATTTGS(1)PGTEK;SATTT(0.033)GS(0.967)PGTEK 369.8 1.76E-86 1684310000 3719940 3303600 2222550 2308080 2527220 2717600 3540640 4085060 3834230 TRUE FALSE 3228340.504 3281898.434 3297382.614 2832164.841 2476933.266 2822147.831 3197269.278 3211501.709 3380951.697 0.954861469 0.97070255 0.975282379 0.837682728 0.732614213 0.83471995 0.945671386 0.949880979 1 21.68899797 2.073489965 6.809319829 0.96449489 0.883449098 0.212030597 0.074427426 0.393963582 29.5707927 0.035254185 0.023591599 118.4376999 -2.073489965 -0.081045792 SATTTPSGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SATTTPSGSPR 11 0 A0A096LNZ0;A0A096LP60;A0A096LP25;Q2M2I8;Q2M2I8-2 A0A096LNZ0;A0A096LP25;Q2M2I8 AAK1 AP2-associated protein kinase 1 1 SATTTPSGS(1)PR;SATTTPSGS(1)PR;SATTTPSGS(1)PR 228.93 3.05E-12 1293350000 732160 758080 431689 652790 803520 835850 985570 1007230 884640 TRUE FALSE 635403.2009 753100.1226 640455.2443 801015.9468 787531.5241 868005.6904 889989.5731 791841.7028 780058.867 0.814558013 0.965440115 0.821034503 1.026866023 1.009579607 1.112743829 1.140926167 1.01510506 1 19.57322348 3.618973617 4.618945386 1.056680506 0.877477439 0.674632011 0.060201146 0.137770194 4.592804469 0.016874043 0.02548645 4158.853454 -3.618973617 -0.179203066 SAVADKHELLSLASSNHLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAVADKHELLSLASSNHLGK 20 1 A0A087WZK9;B3KS98;O15372;E5RJT0 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 206.74 4.75E-22 500260000 591510 633940 143700 406600 713440 505630 752640 849530 756980 FALSE TRUE 513340.4548 629775.6064 213193.8006 498924.7445 699243.9398 525081.9133 679649.0886 667864.6205 667490.6868 0.769060101 0.943497219 0.319395918 0.74746323 1.04757108 0.786650546 1.018215088 1.000560208 1 19.34838818 3.35465695 5.69804093 0.967674925 0.677886367 0.405069688 0.167380641 0.21022583 9.669797865 0.048265848 0.06248793 2262.85617 -3.35465695 -0.289788558 SAVEDEGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAVEDEGLK 9 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ; 147.51 0.00021457 353370000 544280 477060 431000 475930 473350 420770 537860 620220 1033960 FALSE TRUE 472352.019 473926.1614 639433.0416 583997.1806 463931.2611 436957.2942 485698.42 487590.7796 911726.4267 0.518085256 0.519811807 0.701343103 0.640539929 0.508849198 0.479263605 0.532723859 0.534799437 1 19.79824147 1.236989006 24.99806651 1.000000548 0.554916888 0.814829515 0.066753101 18.27449582 290577.7125 0.108705577 0.017637895 17.25794205 -1.236989006 -0.445083661 SAVENCQDSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAVENCQDSWR 11 0 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 357.62 8.40E-71 1944800000 681680 644000 374240 471140 638010 660440 650390 683100 644870 FALSE TRUE 591594.2608 639769.5216 555223.7158 578119.5379 625314.8492 685847.5542 587315.2779 537024.3809 568634.2032 1.040377553 1.125098557 0.976416319 1.016680908 1.099678573 1.206131376 1.032852534 0.944410973 1 19.11714135 1.995142591 24.99695508 0.974353899 1.077083669 0.318342889 0.063380087 240.0347302 1235255.845 0.027774003 0.01814787 98.88777166 -1.995142591 0.10272977 SAVGFDYQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAVGFDYQGK 10 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ; 161.63 1.63E-05 256560000 296000 276050 168809 215140 298710 241230 295090 336070 323970 FALSE TRUE 256882.85 274236.6094 250445.597 263990.8252 292766.2554 250510.2742 266472.2172 264204.0458 285670.6357 0.899227355 0.959974793 0.876693527 0.924109069 1.024838464 0.876919931 0.932795268 0.924855455 1 18.12399322 3.379461953 0.00813546 1.860314505 3.72E-07 0.092716285 0.046225616 14367.51099 112.1351883 12728.51033 12910.41316 2395.862846 -3.379461953 -1.860314132 SAVGFEYQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAVGFEYQGK 10 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ; 123.63 0.0010634 205900000 215904 200020 125581 157618 192205 180121 215560 259270 238160 FALSE TRUE 187371.7394 198706.0554 186312.3916 193407.5759 188380.4965 187050.3714 194655.0244 203827.1281 210004.9961 0.892225151 0.946196801 0.887180758 0.920966546 0.897028642 0.890694864 0.926906635 0.970582281 1 17.68006413 1.671653299 2.149194644 0.998830267 0.906976947 0.77692721 0.017693489 0.130895101 1.237198005 0.018651894 0.004731641 46.95191374 -1.671653299 -0.09185332 SAVGHEYQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SAVGHEYQSK 10 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;; 193.83 5.30E-07 7952860000 13320100 12791900 5880300 9560660 11703400 10976100 13970700 16188600 14209500 FALSE TRUE 11559815.04 12707869.17 8724032.748 11731553.98 11470525.24 11398357.67 12615823.66 12726793.87 12529669.1 0.922595397 1.014222249 0.696270004 0.93630198 0.915469128 0.909709393 1.006876045 1.01573264 1 23.57884498 2.26567283 4.041721378 1.010643512 0.89606238 0.293863817 0.07940075 0.261806262 9.394567277 0.032062176 0.022868652 184.3626024 -2.26567283 -0.114581132 SAVGNAAHTSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAVGNAAHTSDR 12 0 A0A2R8Y5E4;A0A2R8YFK2;A0A2R8Y6M6;A0A2R8Y4C2;A0A2R8YFS8;A0A2R8Y8C4;A0A2R8Y5C9;A0A2R8Y596;P56945-4;P56945-5;P56945-8;P56945;P56945-7;P56945-3;P56945-2;P56945-6 A0A2R8Y5E4 BCAR1 Breast cancer anti-estrogen resistance protein 1 0 ; 84.859 0.011999 136504000 138829 135798 66982 85633 147655 174042 137053 157133 134980 FALSE TRUE 120482.3959 134905.934 99374.71924 105077.2815 144716.9544 180737.5084 123761.6212 123531.3308 119022.8182 1.012263008 1.133445973 0.834921579 0.882833083 1.215875717 1.518511418 1.039814239 1.037879397 1 16.86087866 3.233842802 24.99787803 1.155458687 0.968482744 0.261945484 0.163682457 191.9470269 1017052.986 0.053550224 0.062713459 1713.337035 -3.233842802 -0.186975943 SAVRPAS(ph)LNLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SAVRPASLNLNR 12 1 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A0U1RRC1;A0A0U1RQJ5 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 SAVRPAS(1)LNLNR;SAVRPAS(1)LNLNR 119.45 0.00031289 558450000 371600 356500 356790 386800 415290 434690 391390 444790 460200 TRUE FALSE 322492.1185 354158.128 529334.8374 474628.8519 407026.5415 451412.8056 353433.058 349675.1199 405795.6803 0.794715504 0.872749872 1.304436846 1.169625196 1.003033204 1.112414024 0.870963086 0.86170242 1 18.63039398 2.230772617 24.96149053 0.898977816 1.05094405 0.148974357 0.146895217 307.9033044 986857.1521 0.062661437 0.04312025 170.1267546 -2.230772617 0.151966234 SAVSDKQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SAVSDKQDR 9 1 O95757;E9PDE8;D6RJ96 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 61.56 0.080597 48364000 149020 127250 68413 89532 102540 103880 150440 178800 78218 FALSE TRUE 129326.6294 126414.0864 101497.7556 109861.609 100499.6546 107876.3308 135850.352 140565.0114 68971.15715 1.875082785 1.832854364 1.471597111 1.592863069 1.45712583 1.564078889 1.969669027 2.038025999 1 16.07370555 4.390493644 9.082926649 1.640999165 1.864511865 0.108915612 0.288175817 0.697553434 64.89259527 0.07487312 0.198938767 24575.00662 -4.390493644 0.223512699 SAYQEYDS(ph)DSDVPEELKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SAYQEYDSDSDVPEELKR 18 1 Q96JG6;Q96JG6-3;H0Y7Q2 Q96JG6 CCDC132 Coiled-coil domain-containing protein 132 1 SAYQEYDS(0.993)DS(0.007)DVPEELKR;SAYQEYDS(1)DSDVPEELKR;SAYQEYDS(0.989)DS(0.011)DVPEELKR 238.63 4.22E-24 1895410000 1617910 1200040 1009240 1126270 1240850 1076890 1225010 1540550 1719620 TRUE FALSE 1404099.094 1192156.858 1497311.84 1382006.817 1216159.513 1118318.655 1106208.719 1211115.371 1516328.483 0.925986098 0.786212797 0.987458758 0.911416513 0.802042253 0.73751741 0.729531056 0.798715704 1 20.53215089 3.234465945 24.47712076 0.801601107 0.90049244 0.194781609 0.088231825 122.7295301 733652.5437 0.026596596 0.03126618 1715.797161 -3.234465945 0.098891333 SCAHDWVYE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 148.38 0.00020972 23035070000 4723050 5353170 2326840 2911480 4909290 5348480 4987370 5285920 5211050 FALSE TRUE 4098886.976 5318004.674 3452107.607 3572576.033 4811604.734 5554239.487 4503695.625 4155567.143 4595005.605 0.892030898 1.157344545 0.751273862 0.777491115 1.047137947 1.208755759 0.980128429 0.904366066 1 22.13163519 3.196229107 24.99959506 1.018051475 0.903073688 0.199846882 0.131441749 290.9435147 171820.5721 0.042642424 0.04835235 1571.19145 -3.196229107 -0.114977788 SCATFSSSHR ddPTM_MDA-MB-175_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 ;;; 182.64 1.76E-06 1426500000 983160 1178910 270609 667214 1279551 1341610 1137510 1208500 1069654 FALSE TRUE 853232.915 1171165.663 401476.4175 818715.1364 1254090.438 1393222.605 1027194.455 950071.6796 943200.7227 0.904614357 1.241692923 0.425653212 0.868017927 1.329611405 1.477122071 1.089051811 1.007284724 1 19.8472053 3.26517841 20.72979571 1.166905674 0.856232407 0.304879178 0.240037713 46.08114024 35885.77163 0.072705188 0.093785405 1841.528352 -3.26517841 -0.310673266 SCDEPLT(ph)PPPHS(ph)PTSMLQLIHDPVS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 3 S(0.02)CDEPLT(0.967)PPPHS(0.762)PT(0.126)S(0.126)MLQLIHDPVS(0.999)PR;S(0.002)CDEPLT(0.847)PPPHS(0.877)PT(0.137)S(0.137)MLQLIHDPVS(0.999)PR;S(0.094)CDEPLT(0.905)PPPHS(0.78)PT(0.11)S(0.11)MLQLIHDPVS(1)PR 75.893 0.021718 115928000 149237 129834 80375 93640 135085 146048 137460 141281 131676 TRUE FALSE 129514.9523 128981.1119 119244.6188 114902.3932 132397.0728 151666.5611 124129.1504 111069.1576 116109.4133 1.115456092 1.110858356 1.027002165 0.98960446 1.140278545 1.306238287 1.069070516 0.956590465 1 16.82512541 1.887723184 5.277387935 0.981014865 1.112088374 0.308649299 0.083033539 0.291909289 11.36931604 0.046737592 0.024129807 77.21882409 -1.887723184 0.131073508 SCDEPLT(ph)PPPHSPT(ph)SMLQLIHDPVSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 2 SCDEPLT(0.999)PPPHS(0.416)PT(0.452)S(0.133)MLQLIHDPVSPR 120.59 0.00017332 169100000 181980 159640 95168 102490 166650 159190 154380 185590 151930 TRUE FALSE 157930.8819 158591.3143 141191.5631 125761.921 163333.991 165314.1423 139408.2514 145903.0228 133969.0085 1.178861318 1.183791058 1.05391213 0.93873891 1.219192356 1.233973022 1.040600755 1.089080411 1 17.03153977 1.390309921 1.507684434 0.980999468 1.124181637 0.15927879 0.090155242 1.799147495 4.819733466 0.367154841 0.028032134 24.56461271 -1.390309921 0.143182169 SCDEPLT(ph)PPPHSPTS(ph)MLQLIHDPVSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 2 SCDEPLT(0.952)PPPHS(0.069)PT(0.452)S(0.526)MLQLIHDPVSPR 134.78 4.33E-05 207620000 161810 140360 71275 85476 146050 151500 132650 148300 117860 TRUE FALSE 140426.3985 139437.9659 105743.8284 104884.6322 143143.8907 157328.303 119785.6234 116587.1991 103926.7251 1.351205847 1.341694986 1.017484466 1.00921714 1.377354003 1.513838745 1.152596922 1.121821158 1 16.66520717 1.647822682 2.373082219 1.021947959 1.254852229 0.227463935 0.157815975 0.469372873 5.651661555 0.181708285 0.047481835 44.44497666 -1.647822682 0.232904269 SCDEPLT(ph)PPPHSPTSMLQLIHDPVSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 S(0.003)CDEPLT(0.996)PPPHS(0.001)PTSMLQLIHDPVSPR 88.293 0.013961 75662000 127310 98632 50481 71649 103180 109390 95881 109690 96459 TRUE FALSE 110485.6609 97984.0799 74893.78045 87918.00054 101126.9199 113598.3041 86582.47538 86233.64711 85055.72691 1.29897968 1.151998619 0.880526017 1.033651745 1.188948981 1.335575019 1.017949979 1.013848805 1 16.37612076 2.047607703 24.9999955 1.010307241 1.1365705 0.203682666 0.127030575 212.544597 111611.5283 0.055798278 0.037619177 111.5854843 -2.047607703 0.126263259 SCDEPLTPPPHS(ph)PTSMLQLIHDPVS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 2 S(0.012)CDEPLT(0.122)PPPHS(0.72)PT(0.128)S(0.061)MLQLIHDPVS(0.957)PR 66.593 0.011591 18857000 15255 16354 8131.9 10179 17358 17232 18668 19372 13230 TRUE FALSE 13239.0131 16246.5695 12064.51404 12490.29753 17012.60976 17894.92619 16857.58023 15229.44855 11665.96447 1.134840855 1.392646921 1.034163448 1.070661372 1.458311467 1.533943142 1.445022422 1.305459878 1 13.51001797 3.239156941 24.99999969 1.35966686 1.165982011 0.235776758 0.169475069 25.03225141 1049413.402 0.052193065 0.063372093 1734.430654 -3.239156941 -0.193684849 SCDEPLTPPPHS(ph)PTSMLQLIHDPVSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 SCDEPLTPPPHS(0.806)PT(0.161)S(0.033)MLQLIHDPVSPR;SCDEPLTPPPHS(0.715)PT(0.142)S(0.142)MLQLIHDPVSPR;SCDEPLTPPPHS(0.99)PT(0.005)S(0.005)MLQLIHDPVSPR 133.23 5.46E-05 612050000 361391 324266 159263 227313 343695 366752 299029 361348 301835 TRUE FALSE 313632.2637 322135.8753 236283.1195 278927.8909 336856.1419 380861.1868 270029.2136 284076.5422 266152.4102 1.178393476 1.210343634 0.887773736 1.04800062 1.265651293 1.430989058 1.014566103 1.067345368 1 18.02189311 SCDEPLTPPPHSPTSMLQLIHDPVS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 SCDEPLTPPPHS(0.048)PT(0.048)S(0.048)MLQLIHDPVS(0.857)PR 79.021 0.021978 55316000 125030 114740 49275 74960 106410 106420 99268 121240 104000 TRUE FALSE 108506.9687 113986.2654 73104.55481 91980.81369 104292.6492 110514.0463 89641.00464 95313.76949 91705.23848 1.183214509 1.242963513 0.797168799 1.003005011 1.137259451 1.205100691 0.977490557 1.039349235 1 16.48471653 SCELFSIIDVDADQEPSQS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SCELFSIIDVDADQEPSQSPPR 22 0 Q8IY92-2;Q8IY92 Q8IY92-2 SLX4 Structure-specific endonuclease subunit SLX4 1 SCELFSIIDVDADQEPS(0.127)QS(0.873)PPR 118.67 5.88E-05 8649700 14077 11400 7793.2 13131 12433 9973.8 11428 15356 19885 TRUE FALSE 12216.68878 11325.11265 11562.01759 16112.59424 12185.60762 10357.49854 10319.71432 12072.2389 17534.21795 0.69673417 0.645886385 0.659397392 0.918922891 0.694961569 0.590702053 0.588547168 0.688495999 1 14.09788547 1.239409484 8.925782578 1.002301484 0.683475007 0.538490986 0.091506607 0.067221001 72.66608807 0.132412737 0.023662217 17.35439523 -1.239409484 -0.318826477 SCFESS(ph)PDPELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SCFESSPDPELK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SCFESS(1)PDPELK;SCFES(0.002)S(0.998)PDPELK;SCFES(0.001)S(0.999)PDPELK;SCFES(0.001)S(0.999)PDPELK;SCFESS(1)PDPELK;SCFES(0.05)S(0.95)PDPELK 284.92 2.52E-28 28744200000 95068400 66500500 47105700 55090700 66128200 54154000 78720500 90795600 78097600 TRUE FALSE 82504870.07 66063653.84 69886174.08 67599885.44 64812378.2 56237339.42 71086198.03 71379667.51 68864990.7 1.19806696 0.959321321 1.014828774 0.981629196 0.941151339 0.816631773 1.032254522 1.036516041 1 26.0372674 4.741257167 24.67288549 0.976278493 1.198067056 0.556671777 0.06311179 177.9359984 1627971.649 0.01654418 0.110003334 55113.39534 -4.741257167 0.221788563 SCGYSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SCGYSVR 7 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 103.02 0.019706 285530000 403290 419850 240537 247820 385050 454100 370750 432890 363260 FALSE TRUE 349994.2047 417091.9777 356861.4977 304091.3187 377388.2583 471569.5208 334794.7221 340319.8423 320315.8166 1.09265352 1.302127326 1.114092652 0.949348433 1.178175534 1.472201797 1.045201968 1.062450946 1 18.28913551 2.060659486 24.99999764 1.041110517 1.182789359 0.208941175 0.136425098 117.4503224 48404.66166 0.057562432 0.03880858 114.9898443 -2.060659486 0.141678841 SCLLLQFTDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SCLLLQFTDKR 11 1 P61019;E9PKL7;A0A3B3ITL1;Q8WUD1;E9PE37;H0YD31;H0YDL5 P61019 RAB2A;RAB2B Ras-related protein Rab-2A;Ras-related protein Rab-2B 0 ; 191.79 2.69E-06 1962530000 1444270 1347930 771200 1191100 1653270 1437510 1501120 2252980 1706630 FALSE TRUE 1253406.06 1339075.359 1144154.9 1461557.46 1620373.162 1492811.94 1355541.613 1771197.76 1504874.146 0.832897597 0.88982548 0.760299393 0.971215742 1.07674995 0.991984575 0.900767428 1.176974011 1 20.52121141 3.546644579 4.909326123 1.035666487 0.835368149 0.594091358 0.075906679 0.150820737 6.907494533 0.021612338 0.031991419 3520.82613 -3.546644579 -0.200298339 SCLLLR ddPTM_MDA-MB-175_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 0 110.54 0.066582 266840000 472930 415070 263400 339400 488010 514240 406940 496520 477940 FALSE TRUE 410431.1022 412343.3778 390781.121 416465.9574 478299.5558 534023.1456 367475.0214 390343.0619 421438.4777 0.973881418 0.978418914 0.92725544 0.988201077 1.134921421 1.26714378 0.871954131 0.926216002 1 18.68496251 3.470484668 24.89314445 1.027929243 0.961045211 0.099949355 0.108388778 495.6234769 1859021.861 0.035121936 0.045452377 2954.504581 -3.470484668 -0.066884032 SCPETLTHAVGMSES(ph)PIGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SCPETLTHAVGMSESPIGPK 20 0 Q68CZ2;E9PCX8;Q68CZ2-2 Q68CZ2 TNS3 Tensin-3 1 SCPETLTHAVGMSES(1)PIGPK;SCPETLTHAVGMS(0.002)ES(0.998)PIGPK 255.2 2.43E-36 717510000 503040 598060 364220 469980 639380 593480 669460 761560 762790 TRUE FALSE 436561.9895 594131.3045 540358.0102 576696.1422 626657.5889 616311.5596 604535.8722 598706.3205 672613.8352 0.649052943 0.883317103 0.803370347 0.857395599 0.93167514 0.916293313 0.898785961 0.89011895 1 19.35941893 5.736122225 0.646611394 0.919518528 1.82E-24 0.727993955 0.048451231 5.934018812 0.724512761 0.020873453 5.390455937 544655.9162 -5.736122225 -0.919518528 SCS(ph)FSSESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.002)CS(0.995)FS(0.004)SESR;S(0.001)CS(0.977)FS(0.022)SESR 201.61 2.22E-05 1422730000 1505620 1463590 836900 1062850 1519300 1243970 1837600 1635170 1410980 TRUE FALSE 1306648.502 1453975.581 1241627.639 1304186.337 1489068.902 1291826.331 1659389.835 1285501.62 1244175.552 1.050212328 1.168625745 0.997952128 1.048233375 1.19683183 1.03829908 1.333726444 1.033215625 1 20.24675863 5.040188009 15.63964323 1.10395428 0.821802607 0.023107342 0.105444148 23240175.38 256801338.2 0.024717194 185741994.6 109695.2973 -5.040188009 -0.282151673 SCS(ph)PLAFSAFGDLTIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SCSPLAFSAFGDLTIK 16 0 E9PLZ8;Q96EY5;Q96EY5-2 E9PLZ8 MVB12A Multivesicular body subunit 12A 1 S(0.142)CS(0.842)PLAFS(0.016)AFGDLTIK;S(0.126)CS(0.874)PLAFSAFGDLTIK 118.21 0.0003041 209150000 373100 407500 258450 328720 423120 359360 493510 612470 473470 TRUE FALSE 323793.8897 404823.1057 383437.2845 403360.9002 414700.7398 373184.8117 445649.4762 481498.0567 417496.916 0.775559956 0.969643344 0.918419442 0.966141029 0.993302523 0.893862439 1.06743178 1.153297278 1 18.67140601 7.593371543 0.120284996 1.262492939 3.99E-15 0.526604767 0.069111416 151.2140664 1.808838684 2.669510088 31.88767793 39207715.92 -7.593371543 -1.262492939 SCS(ph)VTDAVAEQGHLPPPSAPAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SCSVTDAVAEQGHLPPPSAPAGR 23 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-4 Q96PU5-7 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 S(0.195)CS(0.803)VT(0.002)DAVAEQGHLPPPSAPAGR;S(0.423)CS(0.55)VT(0.027)DAVAEQGHLPPPSAPAGR 171.25 4.12E-12 624930000 517860 247670 231060 242970 370360 447860 318130 399700 444410 TRUE FALSE 449423.4889 246043.0395 342801.3888 298140.0521 362990.5606 465089.464 287277.8016 314227.2655 391872.3561 1.146861936 0.627865262 0.874778186 0.760809094 0.926297951 1.186839176 0.733090245 0.801861271 1 18.58002428 3.194596312 24.97314251 0.911769738 0.838112969 0.037715038 0.174647377 521.1584094 296032.8699 0.052347108 0.05935636 1565.295412 -3.194596312 -0.073656769 SCSFS(ph)SESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SCSFSSESR 9 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 SCS(0.301)FS(0.698)SESR 223.36 3.66E-07 920130000 861400 858450 452540 620650 866580 799040 1059300 908200 865080 TRUE FALSE 747563.8075 852810.7854 671389.8577 761578.0685 849336.7534 829779.5858 956569.249 713988.4976 762811.2279 0.980011542 1.117984049 0.880152039 0.998383402 1.113429801 1.087791521 1.254005203 0.935996314 1 19.54096655 3.273112197 15.23371542 1.074120592 0.994827926 0.15201899 0.098439441 6.620623194 2915.823871 0.029102811 0.037531692 1875.478964 -3.273112197 -0.079292665 SCTKPS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SCTKPSPSK 9 1 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 S(0.002)CT(0.02)KPS(0.953)PS(0.026)K;SCT(0.006)KPS(0.978)PS(0.017)K;SCTKPS(0.998)PS(0.001)K;SCTKPS(0.999)PS(0.001)K;SCTKPS(0.999)PS(0.001)K 117.07 0.00073333 3727630000 5154570 4238192 3360933 3610619 3581669 3023309 5902940 6853730 5638750 TRUE FALSE 4473380.514 4210351.038 4986291.44 4430465.229 3510400.794 3139617.654 5330473.787 5388113.175 4972143.399 0.899688556 0.846787934 1.002845461 0.891057412 0.706013587 0.631441494 1.072067589 1.083660052 1 22.24543647 2.194328153 24.98703296 1.059364363 0.835463803 0.501066365 0.104359769 117.0772107 66136.36741 0.046311087 0.031223108 156.4329204 -2.194328153 -0.22390056 SCTPS(ph)PDQISHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SCTPSPDQISHR 12 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 S(0.015)CT(0.015)PS(0.97)PDQISHR 70.451 0.021809 0 293910 227910 135980 177970 220660 222830 223090 275830 281260 TRUE FALSE 255069.0488 226412.8442 201740.3828 218380.8086 216269.2977 231402.4143 201454.7661 216845.901 248009.7632 1.028463741 0.912919077 0.813437262 0.880533112 0.87201929 0.93303752 0.812285627 0.874344212 1 17.92003739 4.691582806 3.705647211 0.879469728 1.037844752 0.405951914 0.054310099 0.218896057 5.443068161 0.012964531 0.086791529 49156.70978 -4.691582806 0.158375024 SCTPSPDQISHRAS(ph)LEDAPVDDLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SCTPSPDQISHRASLEDAPVDDLTR 25 1 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 SCTPSPDQIS(0.379)HRAS(0.62)LEDAPVDDLTR;SCTPSPDQIS(0.282)HRAS(0.718)LEDAPVDDLTR 197.81 4.79E-25 157594000 48294 48214 20043.2 28994 49082 53696 47000 56130 31265 TRUE FALSE 41911.82554 47897.27906 29736.15856 35577.53085 48105.36423 55761.71987 42441.94723 44127.0363 27568.88732 1.520258147 1.737367145 1.078612939 1.290495711 1.744914971 2.022632224 1.539487131 1.600609985 1 14.75075342 3.243148371 24.99958162 1.602816039 1.40687015 0.07523207 0.299484993 314.4449439 1713463.55 0.090333076 0.112715546 1750.444603 -3.243148371 -0.195945889 SCYDLSCHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SCYDLSCHAR 10 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;;;;; 196.27 3.36E-07 2914310000 3121944 3058425 968117 1952920 3227176 3255402 2650719 2978414 2928435 FALSE TRUE 2709371.19 3038334.005 1436301.619 2396360.335 3162961.511 3380639.421 2393652.679 2341503.344 2582238.75 1.049233418 1.176627841 0.556223401 0.928016565 1.224891196 1.309189331 0.926967996 0.906772599 1 21.30019097 3.434164355 24.99957014 1.055588472 0.917259624 0.115043514 0.197144162 354.9763987 206583.9453 0.060988677 0.078736098 2717.467479 -3.434164355 -0.138328848 SCYLSSLDLLLEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SCYLSSLDLLLEHR 14 0 Q9BQ69 Q9BQ69 MACROD1 O-acetyl-ADP-ribose deacetylase MACROD1 0 ; 117.77 0.00028435 615490000 809490 854260 519890 655160 883370 1054770 776270 842200 996960 FALSE TRUE 702513.8455 848648.3098 771310.5429 803924.0915 865792.6653 1095347.684 700987.4549 662102.084 879100.5245 0.799128002 0.965359804 0.877386057 0.914484827 0.98486196 1.24598684 0.797391692 0.753158559 1 19.74566862 SDAEEDGGTVS(ph)QEEEDRKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDAEEDGGTVSQEEEDRKPK 20 2 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 SDAEEDGGTVS(1)QEEEDRKPK;SDAEEDGGTVS(1)QEEEDRKPK 266.74 4.65E-37 1345080000 898810 531100 648130 744420 686200 600040 637770 1109020 1403760 TRUE FALSE 780029.9812 527611.1691 961567.8359 913451.9387 672545.9625 623123.9271 575919.1636 871864.7034 1237809.092 0.630169859 0.426245996 0.776830484 0.73795866 0.543335775 0.503408749 0.465273011 0.704361205 1 20.23935739 1.30349557 3.162875726 1.039776514 0.586118801 0.582158575 0.111189938 0.228833899 3.155331441 0.236553945 0.029885694 20.11386682 -1.30349557 -0.453657713 SDALETLGFLNHYQMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SDALETLGFLNHYQMK 16 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0;M0R076 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;; 255.91 1.27E-26 7313420000 3546600 3098310 1834490 2443080 2884000 2543270 3397340 3881630 3433620 FALSE TRUE 3077907.824 3077956.998 2721655.5 2997818.654 2826614.042 2641111.243 3067866.49 3051573.631 3027701.355 1.016582372 1.016598613 0.898918084 0.990130235 0.933584165 0.872315639 1.013265884 1.007884621 1 21.52979148 SDATADDLIDVVEGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDATADDLIDVVEGNR 16 0 Q9Y295 Q9Y295 DRG1 Developmentally-regulated GTP-binding protein 1 0 182.08 3.60E-12 0 22915 25491 17905 22478 25805 22809 25484 30356 25559 FALSE TRUE 19886.72469 25323.54794 26563.91789 27581.97345 25291.53099 23686.47699 23012.5656 23864.60563 22537.44414 0.882385978 1.123621108 1.178657071 1.223828811 1.122200496 1.050983281 1.021081426 1.058886957 1 14.4600363 2.659124464 4.347027256 1.033868444 1.117658577 0.137341639 0.089695675 0.439291139 15.43386849 0.032445823 0.028616364 456.1676296 -2.659124464 0.083790133 SDEAVKPFGLK ddPTM_MDA-MB-175_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 ;;; 165.7 1.94E-05 18989550000 23779500 19486600 16879700 17632100 19593900 16928050 30275700 32731700 29589000 FALSE TRUE 20636978.83 19358591.24 25042779.38 21635737.79 19204019.72 17579283.04 27339567.27 25732280.67 26091022.13 0.790960918 0.741963697 0.959823623 0.829240713 0.736039379 0.673767511 1.047853439 0.986250387 1 24.63705013 2.224943272 24.9958496 1.007655397 0.793747946 0.658348425 0.07556348 150.9644128 277106.3615 0.03237139 0.021956469 167.8584744 -2.224943272 -0.213907452 SDEGHPFR ddPTM_MDA-MB-175_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 ; 103.74 0.0047148 1279190000 798540 605760 344080 644290 736050 907710 531380 899270 952540 FALSE TRUE 693010.9158 601780.7227 510478.2389 790585.8919 721404.0451 942630.1911 479846.8494 706968.1086 839931.8063 0.825079977 0.716463787 0.607761529 0.941250094 0.858884066 1.122269908 0.571292628 0.841697032 1 19.67991268 3.729397894 24.97438561 0.872854862 0.716437964 0.226208784 0.148612511 1049.56592 2860750.797 0.040900906 0.061629139 5362.87771 -3.729397894 -0.156416898 SDEGIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDEGIYR 7 0 H9KV31;O15394-2;O15394 H9KV31 NCAM2 Neural cell adhesion molecule 2 0 91.093 0.061802 0 342130 340340 213610 249880 378050 445470 316850 383390 404050 FALSE TRUE 296916.6537 338104.2841 316912.5105 306619.0732 370527.5446 462607.5192 286121.9358 301405.032 356283.6693 0.833371494 0.948974969 0.88949491 0.860603782 1.03997903 1.298424708 0.803073395 0.84596926 1 18.44266683 3.251979259 24.91107544 0.979014862 0.888271803 0.143799533 0.134289132 620.6673659 1152232.39 0.042571576 0.054639629 1786.40226 -3.251979259 -0.09074306 SDEGQLS(ph)PATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SDEGQLSPATR 11 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 SDEGQLS(1)PATR;SDEGQLS(1)PATR;SDEGQLS(1)PATR;SDEGQLS(1)PATR;SDEGQLS(1)PATR;SDEGQLS(1)PATR 193.11 1.15E-06 7032480000 6868230 6513680 4344020 5061960 6476220 6821160 6301820 6815890 9041140 TRUE FALSE 5960576.004 6470891.207 6444802.602 6211355.385 6347355.893 7083574.439 5690670.466 5358364.965 7972306.729 0.747660145 0.811671129 0.808398726 0.779116459 0.796175575 0.888522567 0.713804757 0.672122279 1 22.92656579 4.753390635 21.98222307 0.794770642 0.747659964 0.023427522 0.090200387 2453.565629 3636522.561 0.021873991 0.399803346 56674.88335 -4.753390635 -0.047110679 SDES(ph)PKPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SDESPKPGK 9 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 SDES(1)PKPGK;SDES(1)PKPGK;SDES(1)PKPGK;SDES(1)PKPGK 121.08 0.00037792 2014510000 5577600 4439000 3769930 3581730 2824430 2770030 5779900 6834400 5632400 TRUE FALSE 4840506.028 4409839.917 5593080.758 4395016.54 2768229.369 2876594.847 5219366.188 5372916.745 4966544.088 0.974622583 0.887909145 1.126151436 0.884924499 0.557375374 0.579194465 1.050905035 1.081822017 1 22.24381089 2.080554223 24.99998246 1.052691118 0.838206449 0.254410944 0.168573409 43.54166224 13509.79988 0.076419462 0.051521983 120.3799679 -2.080554223 -0.21448467 SDFFELLSNHHLDSQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDFFELLSNHHLDSQSR 17 0 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 137.45 4.01E-06 50333000 45963 46268 11604 34369 55566 49492 41579 53089 68326 FALSE TRUE 39888.87309 45964.06246 17215.73321 42173.00675 54460.34531 51395.98927 37546.67498 41736.33049 60248.57812 0.66207161 0.762907008 0.285745054 0.699983436 0.903927479 0.853065597 0.623196035 0.692735527 1 15.87863957 3.483396262 24.91905548 0.788290166 0.573400544 0.32591015 0.158218063 356.0848205 1414071.311 0.045566101 0.060991335 3043.660879 -3.483396262 -0.214889622 SDGAHFQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDGAHFQK 8 0 Q9BW83-2;Q9BW83;B1AH58;F5GZ09 Q9BW83-2 IFT27 Intraflagellar transport protein 27 homolog 0 ; 84.476 0.017425 390590000 683030 664280 336730 503260 612140 624730 775450 807430 797830 FALSE TRUE 592765.8549 659916.3009 499573.7543 617532.8748 599959.6116 648763.7674 700246.9784 634767.3779 703511.4463 0.842581678 0.938032074 0.710114607 0.877786535 0.852807179 0.922179406 0.995359751 0.902284364 1 19.42421437 2.682132402 2.695037083 0.95480271 0.841678503 0.45014515 0.06190518 0.270099962 3.880851357 0.022438454 0.019948839 480.9859632 -2.682132402 -0.113124208 SDGSLEDGDDVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDGSLEDGDDVHR 13 0 Q9NRX5 Q9NRX5 SERINC1 Serine incorporator 1 0 166.48 3.36E-05 201130000 248800 201800 130460 174610 199710 225870 180020 242000 216960 FALSE TRUE 215920.4496 200474.3625 193550.8924 214257.8692 195736.1617 234559.3651 162561.6881 190250.1832 191311.236 1.12863444 1.047896437 1.011706873 1.119943992 1.023129461 1.226061626 0.849723683 0.994453788 1 17.54556208 2.228538666 24.9998553 0.953627429 1.085217976 0.462740228 0.073176236 189.1145058 471743.4278 0.02812306 0.019216563 169.2538928 -2.228538666 0.131590547 SDIDEIVLVGGSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDIDEIVLVGGSTR 14 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 221.55 9.83E-12 103841000 140550 126508 98185 113004 139841 170395 122772 127907 146571 FALSE TRUE 121975.9614 125676.9606 145667.5944 138663.2854 137058.4377 176950.2059 110865.5903 100555.0834 129243.5434 0.943768317 0.972404171 1.12707831 1.072883656 1.06046642 1.369122212 0.857803705 0.778027906 1 16.97973268 2.084322841 25 0.856492379 1.08737406 0.383506514 0.125823714 22.88168233 6780.843507 0.051282434 0.034574609 121.4291183 -2.084322841 0.23088168 SDIYVCMISFAHNVAAQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDIYVCMISFAHNVAAQGK 19 0 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 184.01 2.58E-14 235680000 205980 199410 125420 153150 159310 141070 251480 294330 267390 FALSE TRUE 178759.2211 198100.0626 186073.5315 187925.0483 156140.0427 146497.0542 227091.5083 231389.82 235779.4588 0.758162827 0.840192202 0.789184658 0.797037406 0.662229201 0.621330861 0.963152216 0.981382437 1 17.84707851 2.14741445 7.883898672 0.983380985 0.749994904 0.753729814 0.063828422 0.128400581 9.70263302 0.028782007 0.019379727 140.4153056 -2.14741445 -0.233386081 SDKGS(ph)PGEDGFVPSALGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SDKGSPGEDGFVPSALGTR 19 1 G3V238;A0A494BZY7;Q5JPI9 G3V238 METTL10 Protein-lysine N-methyltransferase METTL10 1 SDKGS(1)PGEDGFVPSALGTR;SDKGS(1)PGEDGFVPSALGTR;SDKGS(1)PGEDGFVPSALGTR;SDKGS(1)PGEDGFVPSALGTR;S(0.005)DKGS(0.995)PGEDGFVPSALGTR 223.82 1.28E-19 2284740000 2139540 2113680 1517430 1737780 2278520 1840760 2481570 2885570 2626050 TRUE FALSE 1856794.368 2099795.097 2251264.223 2132369.509 2233181.91 1911575.228 2240907.723 2268513.311 2315601.361 0.801862704 0.906803361 0.972215798 0.920870727 0.964406891 0.825519997 0.967743309 0.979664872 1 21.14295548 SDKLHELEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDKLHELEK 9 1 Q3V6T2;A0A2U3TZV9;A0A2R8Y4X4;A0A2R8YG73;A0A2R8Y7B1;A0A2R8Y4W8;Q3V6T2-5;Q3V6T2-4;Q3V6T2-2;Q3V6T2-3;A0A2R8YGU1;A0A2R8Y7D9;A0A2R8Y6B2;A0A087WXD9;A0A2R8YG52 Q3V6T2 CCDC88A Girdin 0 60.563 0.086553 133830000 292640 355410 103710 132850 355770 405290 287240 328790 33251 FALSE TRUE 253966.8825 353075.2883 153864.5029 163015.623 348690.8731 420881.7686 259383.509 258480.8171 29320.10466 8.661868213 12.04208827 5.247747396 5.559858155 11.89255213 14.35471576 8.846609247 8.815821776 1 14.83960263 4.270074891 24.9961962 8.366727645 10.35197433 0.057760616 3.74622229 761.5207894 604004.007 0.960186683 2.539901046 18624.08267 -4.270074891 1.98524668 SDKNNEFIVIHNGIITNYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDKNNEFIVIHNGIITNYK 19 1 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 199.15 4.25E-16 272920000 584000 498740 381600 380390 466020 408560 674590 758730 566130 FALSE TRUE 506822.9203 495463.7441 566143.0364 466763.3634 456747.1138 424277.5676 609168.3656 596481.4939 499202.7563 1.015264667 0.992510033 1.134094372 0.935017601 0.914953109 0.849910306 1.220282456 1.19486819 1 18.92926637 2.226076134 24.99999192 1.153563646 0.977355688 0.407219029 0.093036442 217.5150443 435567.2294 0.039333649 0.026725083 168.2969068 -2.226076134 -0.176207959 SDKQYAENYTRPS(ph)SR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDKQYAENYTRPSSR 15 2 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 SDKQYAENYT(0.012)RPS(0.609)S(0.379)R 98.292 0.0015573 442200000 559610 481250 210640 269660 484450 432500 521040 558670 137140 TRUE FALSE 485656.1206 478088.6371 312506.2085 330890.4245 474810.3928 449138.5549 470509.621 439202.7681 120927.4654 4.016094432 3.953515732 2.584245088 2.736271891 3.926406554 3.714115344 3.890841665 3.63195215 1 16.88378243 4.350121299 9.943238633 3.205544337 3.998679562 0.145527307 0.87566124 0.642517878 53.55279038 0.217855786 0.577615479 22393.46504 -4.350121299 0.793135225 SDKQYAENYTRPSS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDKQYAENYTRPSSR 15 2 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 SDKQYAENYT(0.01)RPS(0.221)S(0.769)R 147.64 1.92E-06 345870000 402270 333580 146920 188840 315790 307120 336970 406510 77564 TRUE FALSE 349109.0003 331388.691 217971.0034 231719.0082 309506.3968 318935.1051 304290.7013 319581 68394.47228 5.104345258 4.845255471 3.18696813 3.387978597 4.525313033 4.663170787 4.449054011 4.672614457 1 16.06159211 4.377198231 7.201575788 3.87991946 5.038578168 0.174747779 1.105837697 0.391529913 23.9442441 0.272170616 0.730180749 23834.07114 -4.377198231 1.158658708 SDKS(ph)PDLAPTPAPQSTPR ddPTM_MDA-MB-175_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;S(0.001)DKS(0.997)PDLAPT(0.002)PAPQSTPR;S(0.014)DKS(0.986)PDLAPTPAPQSTPR;SDKS(1)PDLAPTPAPQSTPR 264.52 3.45E-31 17305840000 11883380 9139380 7139000 7523810 10837860 7849710 12037950 13075590 11714290 TRUE FALSE 10312961.22 9079342.811 10591444.28 9232206.055 10622207.79 8151693.423 10870511.46 10279476.83 10329439.98 0.998404681 0.878977256 1.025364811 0.893776049 1.028343048 0.789170898 1.052381492 0.995163034 1 23.3002587 SDKTEEIAEEEETVFPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDKTEEIAEEEETVFPK 17 1 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 147.56 3.60E-07 64394000 176880 129450 113270 130480 122440 89340 154710 180950 145740 FALSE TRUE 153504.8598 128599.6344 168047.7509 160107.4783 120003.6835 92776.96761 139706.248 142255.2507 128510.7832 1.194490112 1.000691391 1.307654865 1.245868045 0.933802445 0.721939166 1.087116929 1.106951861 1 16.97152989 3.236158188 24.99996078 0.983471258 1.182461403 0.409080666 0.129102884 76.27459614 793724.3238 0.041883876 0.049773406 1722.495866 -3.236158188 0.198990144 SDKVPDNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDKVPDNK 8 1 Q9Y678;H0Y8X7 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ; 76.943 0.031459 533670000 1822610 1458620 1223520 1338420 1251030 1122920 1858770 2252480 2366100 FALSE TRUE 1581747.471 1449038.229 1815218.364 1642328.717 1226136.951 1166119.459 1678506.771 1770804.681 2086382.353 0.758129241 0.694521897 0.870031498 0.787165744 0.587685641 0.558919345 0.804505832 0.848744085 1 20.99257214 1.512258426 1.90680296 1.010522833 0.715556302 0.494788226 0.093030754 0.420222055 2.523144247 0.196344532 0.028462299 32.52807972 -1.512258426 -0.294966531 SDKVPENK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDKVPENK 8 1 Q9UBF2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 59.908 0.087233 104510000 253330 184620 145780 158610 148530 134870 239740 290580 281020 FALSE TRUE 219851.7986 183407.2191 216279.6956 194624.8247 145574.5436 140058.5362 216490.0517 228441.7283 247798.1357 0.887221359 0.740147695 0.872805984 0.785416824 0.587472312 0.565212227 0.873654885 0.921886388 1 17.91880581 2.012848737 24.87749316 0.938085778 0.739147434 0.439534404 0.105032768 210.3865673 407345.0696 0.046327684 0.03121328 103.0027304 -2.012848737 -0.198938344 SDLDYIRS(ph)PLPFQNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SDLDYIRSPLPFQNR 15 1 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;H7BYL6 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 1 SDLDYIRS(1)PLPFQNR;SDLDYIRS(1)PLPFQNR;SDLDYIRS(1)PLPFQNR;SDLDYIRS(1)PLPFQNR 215.51 1.41E-12 1941550000 1501290 1505440 1178810 1395160 1749180 1920280 1713570 1937250 1945150 TRUE FALSE 1302890.723 1495550.666 1748886.459 1711952.402 1714374.74 1994154.414 1547388.245 1522984.163 1715196.583 0.759615974 0.871941258 1.019641991 0.998108566 0.999520846 1.162638985 0.902163787 0.887935633 1 20.70994251 4.490447976 3.023105285 0.987088339 0.764529947 0.525322892 0.074599753 0.247178682 4.237873883 0.021002169 0.098750051 30934.84726 -4.490447976 -0.222558392 SDLEEDNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDLEEDNER 9 0 Q8WU90 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 0 99.855 0.011759 113290000 107760 92313 78454 104360 87594 100260 95101 110030 173990 FALSE TRUE 93519.24297 91706.58982 116394.6168 128056.533 85851.05077 104117.0671 85878.11966 86500.94075 153421.1004 0.609559198 0.59774431 0.758661074 0.83467354 0.559577858 0.678635903 0.559754293 0.563813846 1 17.22713739 1.230622128 24.99954326 1.000000647 0.643809527 0.599532957 0.091096725 223.7328673 704511.9707 0.253549739 0.023724402 17.00678132 -1.230622128 -0.356191119 SDLESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDLESR 6 0 P61019;P61019-2;A0A3B3ITL1;Q8WUD1;H7C125;Q8WUD1-2 P61019 RAB2A;RAB2B Ras-related protein Rab-2A;Ras-related protein Rab-2B 0 ; 117.7 0.05234 538320000 892940 815450 485740 614100 636510 952530 715670 983140 929090 FALSE TRUE 774935.7166 810093.2553 720645.4887 753540.7909 623844.6963 989174.4455 646264.4336 772903.1618 819254.0386 0.945904054 0.988818141 0.879636175 0.919788924 0.761478939 1.20740869 0.788844977 0.943423072 1 19.64395135 SDLNGLPS(ph)PVEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SDLNGLPSPVEER 13 0 E7EWN3;Q9C0A6 E7EWN3 SETD5 SET domain-containing protein 5 1 SDLNGLPS(1)PVEER;SDLNGLPS(1)PVEER;SDLNGLPS(1)PVEER 152.37 4.74E-05 528430000 780420 675038 455591 513913 822960 746730 710072 869550 751360 TRUE FALSE 677285.5197 670603.6309 675916.3315 630604.8013 806584.7061 775457.1863 641209.3267 683603.4993 662535.0768 1.022263641 1.012178305 1.020197051 0.95180591 1.217421891 1.170439443 0.967811893 1.031799709 1 19.33763731 6.257221346 12.99068659 1.044028146 1.017478631 0 0.084658205 0 0 0.01968555 0 1808095.418 -6.257221346 -0.026549514 SDLQPPNYYEVMEFDPLAPAVTTEAIYEEIDAHQHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDLQPPNYYEVMEFDPLAPAVTTEAIYEEIDAHQHK 36 0 J3KQU4;I3L4I4;O75674;O75674-3 J3KQU4 TOM1L1 TOM1-like protein 1 0 87.368 0.00051394 85303000 30319 27455 15500 21265 24591 23974 25449 31931 29635 FALSE TRUE 26312.26733 27274.6463 22995.85184 26093.54327 24101.68721 24896.29529 22980.9599 25102.80414 26131.58406 1.006914364 1.043742554 0.880002215 0.99854426 0.922320176 0.952728133 0.879432332 0.960630786 1 14.67350696 4.2587079 24.99909658 0.941974696 1.025328508 0.405602829 0.04196208 226.4256951 280948.112 0.009809214 0.025881518 18142.94985 -4.2587079 0.083353812 SDLSSS(ph)SGSLSLSHGSSSLEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDLSSSSGSLSLSHGSSSLEHR 22 0 H0YAN8;O15013-7;O15013-4;O15013-5;O15013-6;O15013 H0YAN8 ARHGEF10 Rho guanine nucleotide exchange factor 10 1 SDLS(0.005)S(0.035)S(0.903)S(0.056)GSLSLSHGSSSLEHR;SDLSS(0.002)S(0.995)S(0.002)GSLSLSHGSSSLEHR 151.91 7.55E-08 613830000 231480 311730 84608 143753 436000 430400 280300 360320 353070 TRUE FALSE 200889.3315 309682.2251 125524.7118 176394.3158 427324.453 446957.7665 253116.5491 283268.372 311330.4668 0.645260753 0.994705813 0.403188011 0.566582248 1.372575121 1.435637736 0.813015673 0.909863962 1 18.24808724 3.257136827 24.99943634 1.076154979 0.659078785 0.471989675 0.237266799 257.9156534 347094.8674 0.074290345 0.095734798 1807.743578 -3.257136827 -0.417076194 SDLYSSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDLYSSGR 8 0 P38159;P38159-2;H3BUY5 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 0 242.52 1.80E-08 858010000 586800 525290 292890 393230 529170 515340 478830 539260 482770 FALSE TRUE 509252.8932 521839.3354 434532.5837 482518.8816 518640.5523 535165.4633 432393.1403 423943.4455 425697.4806 1.196278852 1.225845487 1.020754417 1.133478359 1.21833127 1.257149708 1.015728681 0.995879621 1 18.69946903 2.153448631 7.773264341 1.000866111 1.170410711 0.610522016 0.064515311 0.171608426 13.57779296 0.028065614 0.018899111 142.3798826 -2.153448631 0.169544601 SDNKDDDIDIDAI ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SDNKDDDIDIDAI 13 1 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ;; 105.13 0.012044 1728148000 5145060 4676800 3383080 3816510 4446140 3407980 5490860 6537980 5357530 FALSE TRUE 4465127.285 4646077.793 5019148.804 4683106.927 4357670.513 3539087.196 4958357.242 5139883.856 4724168.907 0.945166732 0.983469873 1.062440591 0.991308105 0.922420557 0.749144932 1.049572388 1.087997478 1 22.17162912 2.048574083 24.99999969 1.05583723 0.94667535 0.25822818 0.081994868 151.2500513 77844.34526 0.035562169 0.023976004 111.8340579 -2.048574083 -0.10916188 SDNSDIRPSGS(ph)PPPPTLPAS(ph)PSNHVSSLPPFIAPPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDNSDIRPSGSPPPPTLPASPSNHVSSLPPFIAPPGR 37 1 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 2 S(0.003)DNS(0.004)DIRPS(0.452)GS(0.534)PPPPT(0.04)LPAS(0.883)PS(0.072)NHVS(0.005)S(0.006)LPPFIAPPGR 70.148 0.0058709 414280000 120800 160380 32243 80000 175960 155760 116020 148830 131100 TRUE FALSE 104835.9739 159326.4532 47835.82265 98165.22272 172458.7403 161752.188 104768.3983 117003.8627 115601.5073 0.906873763 1.378238544 0.413799298 0.849169055 1.491838162 1.399222136 0.906289206 1.012130943 1 16.81880068 SDPDGGDS(ph)PLPASGGPLTCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDPDGGDSPLPASGGPLTCK 20 0 Q8N1G0 Q8N1G0 ZNF687 Zinc finger protein 687 1 SDPDGGDS(1)PLPASGGPLTCK;SDPDGGDS(1)PLPASGGPLTCK 247.82 3.75E-30 228945000 231038 175111 131064 148241 181085 154496 205273 225431 255680 TRUE FALSE 200505.7429 173960.6843 194446.9888 181901.3848 177481.7628 160439.5611 185365.6561 177224.335 225453.8017 0.889342923 0.771602355 0.862469328 0.80682332 0.787220093 0.711629433 0.82218909 0.786078273 1 17.78247231 1.235759359 24.99925452 1.000000266 0.802006555 0.61407348 0.04862409 51.02989482 455317.4868 0.077141167 0.011433848 17.2091476 -1.235759359 -0.197993711 SDPDHLAELVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDPDHLAELVK 11 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0 Q9UM54-1 MYO6 Unconventional myosin-VI 0 98.353 0.0055837 163590000 300110 232390 182630 217140 275300 271150 261830 319860 418500 FALSE TRUE 260449.7031 230863.4148 270950.4789 266444.9558 269822.0686 281581.316 236437.7669 251460.4282 369025.4068 0.705777159 0.625603036 0.734232586 0.722023337 0.731174775 0.76304046 0.640708641 0.681417657 1 18.49336062 1.236516529 24.99999856 1.000000383 0.699099879 0.832448473 0.042223702 21.7256144 265643.8371 0.0676003 0.01061666 17.23917703 -1.236516529 -0.300900504 SDPEGENIHAGLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SDPEGENIHAGLLK 14 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ;; 163.99 4.19E-06 829920000 1578040 1403090 1093848 1328800 1528600 1290700 1430040 1947910 2566170 FALSE TRUE 1369498.016 1393873.009 1622836.552 1630524.349 1498183.851 1340354.064 1291354.941 1531364.605 2262800.306 0.605222658 0.615994706 0.717180631 0.720578102 0.662092827 0.592343063 0.570688866 0.676756407 1 21.10967784 1.242896613 4.651693251 1.026224299 0.643250815 0.837764716 0.049311751 0.078063123 3.754683466 0.097564256 0.01359476 17.49430175 -1.242896613 -0.382973484 SDPES(ph)PIKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDPESPIKK 9 1 Q8NDI1-3;Q8NDI1-2;Q8NDI1;H7C0Q4 Q8NDI1-3 EHBP1 EH domain-binding protein 1 1 SDPES(1)PIKK 71.555 0.030165 161440000 596740 490530 440740 512870 625040 481240 829420 965890 836310 TRUE FALSE 517879.2971 487307.6761 653883.3382 629324.9722 612602.9269 499753.6142 748982.9761 759341.9401 737442.3845 0.702264079 0.660807795 0.886690746 0.853388665 0.830712934 0.677684962 1.015649482 1.029696633 1 19.49217081 -2 0.177557706 2.545895297 0.612580166 0.550301704 0.09250737 89.5138642 1.253013457 45.0838722 0.918477804 0.01 2 -1.933315131 SDPFLEFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SDPFLEFFR 9 0 Q99829;B0QZ18;F2Z2V0;A6PVH9;E7ENH5;Q5JX45;Q5JX60;Q5JX52;Q5JX44;Q5JX61;Q5JX59;Q5JX58;Q5JX56 Q99829 CPNE1 Copine-1 0 ;;;;; 166.3 0.00014156 1721725000 891335 1100248 613249 736629 1047156 1031679 964941 1044724 1116589 FALSE TRUE 773542.8214 1093020.398 909818.2676 903891.8731 1026319.644 1071368.359 871361.1703 821317.9027 984587.1204 0.785651981 1.110130709 0.924060704 0.918041537 1.042385811 1.088139725 0.885001593 0.834174941 1 19.90915934 SDPMVQCIIEESGEHIIAGAGELHLEICLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 SDPMVQCIIEESGEHIIAGAGELHLEICLK 30 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;;;;;;; 368.07 7.40E-137 3450066000 2167600 2085598 1186798.4 1639128.6 1911687 1656562 2446187 2741879 2351315 FALSE TRUE 1881146.168 2071897.569 1760738.076 2011317.801 1873648.169 1720291.012 2208956.161 2155549.513 2073345.219 0.907300024 0.999301781 0.849225715 0.97008341 0.903683647 0.829717596 1.065406832 1.039648146 1 20.98352892 2.221666948 24.99918235 1.037249089 0.913646857 0.564921586 0.051684663 171.1712877 253296.6853 0.020352793 0.013761692 166.5969124 -2.221666948 -0.123602231 SDPPQEAAQFTSQVIILNHPGQISAGYSPVIDCHTAHIACK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDPPQEAAQFTSQVIILNHPGQISAGYSPVIDCHTAHIACK 41 0 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ; 357.75 1.07E-154 1603910000 626790 508011 273628 357147 493940 438988 579081 661260 425985 FALSE TRUE 543958.1134 504673.8423 405955.416 438242.685 484111.5604 455876.1524 522921.8137 519854.6949 375625.5386 1.448139324 1.343555724 1.080744982 1.166700983 1.288814286 1.213645255 1.392135944 1.383970581 1 18.51893563 4.472389797 24.9156956 1.240654247 1.421993487 0.270112336 0.123005547 157.5081118 829437.7398 0.031984773 0.085312393 29674.93644 -4.472389797 0.18133924 SDPYSTGHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDPYSTGHLR 10 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 0 96.171 0.0069221 113750000 85166 81552 42500 53537 86675 91028 92000 108800 87220 FALSE TRUE 73911.09732 81016.27954 63053.14215 65693.39411 84950.33708 94529.90606 83077.85416 85533.96668 76908.95096 0.961020745 1.053405079 0.819841402 0.854170981 1.10455722 1.22911449 1.080210471 1.112145799 1 16.23086389 3.22326659 24.55740276 1.110394 0.924182953 0.549005042 0.082377044 148.9641519 239188.9021 0.025791546 0.02935805 1672.11672 -3.22326659 -0.186211046 SDQDYILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDQDYILK 8 0 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7;F8VZ69 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 135.79 0.0019046 126770000 76778 73234 58303 63968 80175 63243 75123 99553 96523 FALSE TRUE 66631.59277 72752.92103 86498.52581 78492.91209 78579.67436 65675.99913 67837.58302 78264.36567 85112.1609 0.782868066 0.85478879 1.016288682 0.922229106 0.923248494 0.771640603 0.797037489 0.919543868 1 16.37707766 -1.999999754 0.007882555 1.857497356 7.05E-09 0.043473204 0.083992524 298333.8409 234.4906311 30248.09437 25229.46467 0.010000006 1.999999754 -1.857497348 SDQWKPLNLEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDQWKPLNLEEK 12 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 194.85 9.10E-07 843300000 1074800 776810 612430 676230 721040 547360 1034200 1238200 1206700 FALSE TRUE 932762.4568 771707.084 908603.1965 829778.357 706692.7147 568417.2934 933903.4432 973420.5657 1064045.301 0.876619122 0.725257734 0.853914017 0.779833675 0.664156605 0.534204035 0.877691432 0.914830003 1 20.02112814 2.015411823 24.98947407 0.934810268 0.739042185 0.471261445 0.097861772 210.9445598 342034.3954 0.041833255 0.028194017 103.6124213 -2.015411823 -0.195768083 SDRPELTGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SDRPELTGAK 10 1 H0YL12;P13804-2;P13804;H0YK49;H0YNX6;H0YKF0;H0YLU7 H0YL12 ETFA "Electron transfer flavoprotein subunit alpha, mitochondrial" 0 ;; 112.13 0.001516 616040000 675570 715770 459290 712760 788530 714420 778520 903910 937810 FALSE TRUE 586291.7128 711068.0597 681404.1802 874603.0519 772839.7957 741904.1997 703019.2502 710615.8807 826943.1702 0.708986704 0.859875364 0.824003638 1.057633805 0.934574253 0.897164674 0.850142157 0.859328557 1 19.65742866 4.773749613 1.476867821 0.915587015 0.620752851 0.490081728 0.068476276 1.202348245 2.270149734 0.019787498 0.5333199 59394.96251 -4.773749613 -0.294834164 SDS(ph)ASSEPVGIYQGFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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(0.347)DS(0.653)ASSEPVGIYQGFEK;S(0.039)DS(0.96)ASSEPVGIYQGFEK;S(0.002)DS(0.998)ASSEPVGIYQGFEK;S(0.01)DS(0.99)ASSEPVGIYQGFEK;S(0.072)DS(0.869)AS(0.06)SEPVGIYQGFEK;S(0.305)DS(0.628)AS(0.067)SEPVGIYQGFEK 400.27 6.63E-123 1266688000 1916150 1709830 1162940 1999750 1920310 1218747 2527020 2516780 3662010 TRUE FALSE 1662925.923 1698598.014 1725341.674 2453823.802 1882099.588 1265632.986 2281949.989 1978586.183 3229091.35 0.51498262 0.526029719 0.534311819 0.759911547 0.582857338 0.391947099 0.706684867 0.612737754 1 21.62269682 -0.009915949 1.300086578 9.943655081 0.567182072 0.630971927 0.101621999 20.8750599 1.964110245 520.1076294 0.02981764 0.977426368 0.009915949 -9.376473009 SDS(ph)DSSTLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SDSDSSTLPR 10 0 Q9ULE0 Q9ULE0 WWC3 Protein WWC3 1 SDS(0.999)DS(0.001)STLPR;S(0.009)DS(0.982)DS(0.009)STLPR;SDS(0.985)DS(0.015)STLPR;SDS(1)DSSTLPR 171.92 4.06E-06 1249900000 1439680 1128560 750520 859510 1234750 1170550 1108060 1230120 1235950 TRUE FALSE 1249422.64 1121146.415 1113473.982 1054674.882 1210180.891 1215581.816 1000600.512 967068.4108 1089837.399 1.146430322 1.028728153 1.021688174 0.967735997 1.110423346 1.115379062 0.918119081 0.887351096 1 20.05568147 2.225019246 24.98848969 0.924487268 1.059078673 0.515326635 0.058898067 180.8558133 333738.4096 0.024498125 0.016616183 167.8878416 -2.225019246 0.134591404 SDS(ph)DSSTLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDSDSSTLSK 10 0 H0YAU4;H3BLZ3;Q8IX03-2;H0YBE8;Q8IX03 H0YAU4;H0YBE8 WWC1 Protein KIBRA 1 S(0.003)DS(0.96)DS(0.003)S(0.01)T(0.024)LSK 97.779 0.0061115 149420000 533810 392900 312880 380240 333680 340010 486980 542710 585910 TRUE FALSE 463265.656 390319.014 464189.8145 466579.3036 327040.4208 353090.4047 439752.7546 426655.6899 516644.3873 0.896681871 0.755488734 0.898470642 0.903095659 0.633008756 0.683430254 0.851171067 0.825820817 1 18.97881207 1.038850544 1.876420339 1.171625877 0.797774063 0.307439469 0.091846711 2.103877354 4.44582763 1.68196244 0.02610472 10.93579961 -1.038850544 -0.373851814 SDS(ph)ENVYEVIQDLHVPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SDSENVYEVIQDLHVPPR 18 0 A0A0G2JRG8;A0A0G2JNY3;A0A0G2JP16 A0A0G2JRG8 1 S(0.152)DS(0.751)ENVY(0.097)EVIQDLHVPPR;S(0.104)DS(0.894)ENVY(0.001)EVIQDLHVPPR;S(0.142)DS(0.854)ENVY(0.004)EVIQDLHVPPR;S(0.096)DS(0.904)ENVYEVIQDLHVPPR;S(0.445)DS(0.553)ENVY(0.002)EVIQDLHVPPR 174.7 3.34E-12 201966000 331203 281325 232437 297345 322160 265649 315084 346928 592130 TRUE FALSE 287433.6844 279476.9576 344844.3107 364861.7269 315749.6463 275868.6889 284527.2022 272740.147 522129.066 0.550503129 0.535264125 0.660457985 0.698796046 0.604734857 0.528353442 0.544936531 0.522361548 1 18.99404695 1.233747547 24.99793497 1.000000639 0.580149256 0.833208552 0.058960226 65.53075697 340309.7685 0.128885504 0.016181161 17.12961282 -1.233747547 -0.419851383 SDS(ph)ENVYEVIQDLHVPPREESAEQVDDPPEPVYANIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDSENVYEVIQDLHVPPREESAEQVDDPPEPVYANIER 38 1 A0A0G2JRG8;A0A0G2JNY3 A0A0G2JRG8 1 S(0.187)DS(0.8)ENVY(0.012)EVIQDLHVPPREESAEQVDDPPEPVYANIER;S(0.172)DS(0.669)ENVY(0.16)EVIQDLHVPPREESAEQVDDPPEPVYANIER 84.159 0.00046045 74605000 60117.8 61386.6 34655 34127 58848 56077 74223 63457 31948.5 TRUE FALSE 52173.08041 60983.34738 51414.27391 41876.05695 57677.03993 58234.31848 67024.86488 49887.21437 28171.58473 1.851975347 2.164711285 1.825040175 1.48646437 2.047348081 2.067129664 2.379165586 1.770834508 1 14.7819531 1.272131457 3.88717719 0.921391319 1.97002879 0.627689623 0.234238576 0.154383771 3.815355905 0.434736977 0.061764816 18.71248463 -1.272131457 1.048637471 SDS(ph)FENPVLQQHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SDSFENPVLQQHFR 14 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 1 S(0.025)DS(0.975)FENPVLQQHFR;S(0.001)DS(0.999)FENPVLQQHFR;S(0.001)DS(0.999)FENPVLQQHFR;S(0.004)DS(0.996)FENPVLQQHFR;S(0.001)DS(0.999)FENPVLQQHFR;S(0.003)DS(0.997)FENPVLQQHFR 256.67 1.64E-24 1882511000 2660450 1514680 683333 1375582 1199819 668727 1535927 1780212 1164318 TRUE FALSE 2308864.792 1504729.967 1013795.124 1687928.918 1175944.949 694453.3604 1386973.036 1399527.517 1026673.652 2.248878976 1.465636099 0.987456065 1.644075421 1.145393131 0.676411008 1.35093857 1.363166878 1 19.96954624 4.691262613 2.897065085 1.192621046 2.376340255 0.62872024 0.260862853 0.234683135 2.974905437 0.065924025 0.613814679 49120.48128 -4.691262613 1.183719209 SDS(ph)KSSPQAGRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDSKSSPQAGRR 12 2 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 S(0.005)DS(0.444)KS(0.444)S(0.107)PQAGRR 66.059 0.046527 212250000 368530 321490 149930 144630 241780 280760 370620 402460 27934 TRUE FALSE 319827.8268 319378.111 222436.6495 177470.452 236969.051 291561.0189 334677.3294 316397.0609 24631.67434 12.98441277 12.96615515 9.030512761 7.20496908 9.620501138 11.83683313 13.58727486 12.84513008 1 14.58822708 4.24881424 23.98323639 9.876132323 12.97528761 0.141691399 3.545471355 287.6673819 672830.5265 0.899236744 2.317349174 17734.30774 -4.24881424 3.099155291 SDS(ph)LILDHQWELEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SDSLILDHQWELEK 14 0 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3;H7C3Y8 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 1 S(0.002)DS(0.998)LILDHQWELEK;S(0.001)DS(0.999)LILDHQWELEK;S(0.001)DS(0.999)LILDHQWELEK;SDS(1)LILDHQWELEK;S(0.001)DS(0.999)LILDHQWELEK;SDS(1)LILDHQWELEK 276.38 2.72E-33 2146074000 6382980 2563722 2448966 2409996 2368163 2998210 2973140 3094860 4060770 TRUE FALSE 5539453.021 2546880.741 3633294.149 2957222.426 2321041.19 3113553.079 2684805.34 2433048.273 3580710.397 1.547026262 0.711278059 1.014685285 0.825875901 0.648206901 0.869535018 0.74979684 0.679487589 1 21.77181441 4.742837409 24.99318193 0.80244731 1.547026557 0.774929845 0.124326995 197.452173 1153850.277 0.029527958 0.224959064 55314.29845 -4.742837409 0.744579247 SDS(ph)LLSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SDSLLSFR 8 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 S(0.001)DS(0.999)LLSFR;S(0.002)DS(0.998)LLSFR;SDS(0.934)LLS(0.066)FR;SDS(0.999)LLSFR;S(0.011)DS(0.915)LLS(0.074)FR;S(0.001)DS(0.999)LLSFR 194.94 0.00017072 706369000 1217640 1094820 619664 696415 987510 1142200 940240 1044620 1351750 TRUE FALSE 1056725.789 1087628.055 919335.5831 854546.6698 967860.483 1186141.173 849055.6695 821236.1422 1191947.655 0.886553855 0.912479714 0.771288554 0.716933052 0.81199915 0.995128577 0.712326306 0.688986751 1 20.18488945 4.244180335 24.99714923 0.800178722 0.899516822 0.087009563 0.108656431 292.8689269 1302676.716 0.0276926 0.069108493 17546.08928 -4.244180335 0.0993381 SDS(ph)PEIPFQAAAGPSDGLDASSPGNSFVGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 31 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 S(0.163)DS(0.837)PEIPFQAAAGPSDGLDASSPGNSFVGLR;S(0.264)DS(0.736)PEIPFQAAAGPSDGLDASSPGNSFVGLR 203.25 5.41E-26 863980000 475980 428683 302700 361586 488090 428547 409659 476810 644290 TRUE FALSE 413078.037 425866.9531 449086.7325 443689.6278 478377.9639 445033.4804 369930.3332 374847.892 568122.7702 0.727092908 0.74960374 0.790474799 0.780974907 0.842032724 0.783340334 0.651145056 0.659800859 1 19.1158432 4.477282714 5.49582572 0.769951679 0.731687924 0.021713489 0.09724822 0.868236346 89.77844323 0.024845169 0.08059656 30011.1553 -4.477282714 -0.038263755 SDS(ph)PENKYSDSTGHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.014)DS(0.986)PENKYSDSTGHSK;S(0.002)DS(0.998)PENKYSDSTGHSK 144.57 7.87E-07 581620000 1079190 788570 309870 377190 822320 515470 1053210 1126280 195469 TRUE FALSE 936572.3072 783389.8317 459724.1685 462836.7545 805957.4408 535300.4645 951069.8563 885433.7867 172360.8775 5.433787068 4.54505595 2.667218774 2.685277316 4.675988267 3.105695865 5.517898668 5.137092591 1 17.39507282 1.228347104 24.99602003 0.999993374 4.217680194 0.47188911 1.070862905 426.8697863 1044626.182 3.776399183 0.278870686 16.91792535 -1.228347104 3.21768682 SDS(ph)PVPTAPTSGGPKPSTASAVPELATDPELEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDSPVPTAPTSGGPKPSTASAVPELATDPELEKK 34 2 Q86U44;F5H6D8;B4DTN4;B4E349 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 1 SDS(0.999)PVPTAPTSGGPKPSTASAVPELATDPELEKK 238.83 2.70E-47 264210000 268550 150380 143060 140010 130660 86962 241270 290540 182560 TRUE FALSE 233060.4371 149392.1439 212244.2945 171801.4104 128060.1216 90307.48441 217871.6725 228410.282 160977.9648 1.447778504 0.928028529 1.318467995 1.067235573 0.79551336 0.560992832 1.353425438 1.4188916 1 17.2965037 0.951234535 19.2410916 0.000176879 1.115253139 0.014350025 0.28821067 20066492.3 162099785.9 870681709.8 0.074753488 8.937880319 -0.951234535 1.115076259 SDS(ph)VSASER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDSVSASER 9 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 SDS(1)VSASER;SDS(1)VSASER 215.84 6.55E-07 722150000 838790 759050 516970 623770 650760 722710 902440 778510 1268590 TRUE FALSE 727941.7763 754063.7506 766978.4212 765406.5122 637811.1492 750513.1214 814921.5077 612031.6949 1118618.735 0.650750567 0.674102558 0.685647752 0.684242529 0.570177424 0.670928438 0.728506936 0.547131633 1 20.09328697 1.227893081 24.99998226 1.000000734 0.651031879 0.802582768 0.054328778 198.7754765 465810.2566 0.186116097 0.013122001 16.90024812 -1.227893081 -0.348968856 SDS(ph)YSQSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SDSYSQSLK 9 0 Q9H8W4 Q9H8W4 PLEKHF2 Pleckstrin homology domain-containing family F member 2 1 SDS(0.992)YS(0.008)QSLK;SDS(1)YSQSLK;SDS(0.999)YS(0.001)QSLK;SDS(1)YSQSLK;SDS(0.996)YS(0.004)QSLK;S(0.003)DS(0.93)YS(0.067)QSLK 261.83 3.54E-15 6181950000 4013910 3552340 3273000 4482920 6001170 5091320 6802250 7740440 7175330 TRUE FALSE 3483461.624 3529004.445 4855833.748 5500835.503 5881758.458 5287186.375 6142568.842 6085207.142 6327070.662 0.550564678 0.557762768 0.767469498 0.869412687 0.92961795 0.835645223 0.970839298 0.961773223 1 22.59310628 4.067678544 1.090556175 0.948357216 0.483809384 0.920427205 0.045449655 0.180751373 0.348670643 0.015838618 0.075725225 11686.34071 -4.067678544 -0.464547833 SDSAFFWEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SDSAFFWEER 10 0 O75116;C9JFJ0;D6REE7;Q13464;A0A0U1RQV4 O75116;Q13464 ROCK2;ROCK1 Rho-associated protein kinase 2;Rho-associated protein kinase 1 0 ;; 208.25 2.73E-07 214986000 319367 250102 179726 246285 272167 291925 242798 289534 374071 FALSE TRUE 277161.8418 248459.0635 266642.0947 302207.7735 266751.4092 303155.5437 219251.4873 227619.4073 329848.7525 0.840269486 0.753251488 0.808376848 0.91620105 0.808708255 0.919074398 0.664703097 0.690072057 1 18.33144512 1.218901141 24.96927247 1.000000714 0.794992033 0.362060739 0.083153868 1728.45233 2195168.751 0.849570882 0.022090953 16.55393101 -1.218901141 -0.205008681 SDSDMWINQSSSLDSSTS(ph)SQEHLNHSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDSDMWINQSSSLDSSTSSQEHLNHSSK 28 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 SDSDMWINQSSSLDS(0.001)S(0.025)T(0.114)S(0.52)S(0.34)QEHLNHSSK 182.56 1.46E-17 62668000 131870 121950 62824 85202 123610 114490 127410 151620 147070 TRUE FALSE 114443.0454 121148.9024 93205.89653 104548.4163 121150.4028 118894.5044 115053.7978 119197.2429 129683.5521 0.882479262 0.934188649 0.718717948 0.806181004 0.934200219 0.91680481 0.887188822 0.91913925 1 16.98463599 3.231012086 24.9706955 0.925871787 0.834114797 0.376917033 0.061136366 198.2213741 655719.3603 0.019128953 0.022109243 1702.20588 -3.231012086 -0.09175699 SDSDYDLS(ph)PK ddPTM_MDA-MB-175_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 SDSDYDLS(1)PK;SDSDYDLS(1)PK 232.7 9.58E-11 761820000 1448500 1473730 1137690 1211740 1664030 1390300 1670600 2052720 1886530 TRUE FALSE 1257077.055 1464048.971 1687880.689 1486884.087 1630919.059 1443785.741 1508585.469 1613761.802 1663506.573 0.755679043 0.880098098 1.014652252 0.893825195 0.980410349 0.867917064 0.90687076 0.970096439 1 20.66579614 4.627095553 3.30358706 0.944144224 0.749376491 0.620876011 0.047548162 0.174825483 3.082158029 0.011582684 0.071861549 42373.61862 -4.627095553 -0.194767733 SDSFENPVLQQHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SDSFENPVLQQHFR 14 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;; 270.8 6.10E-33 5230980000 2410190 2150510 1159910 1729740 2249530 2176100 2149480 2478570 2201720 FALSE TRUE 2091677.285 2136383.158 1720846.356 2122503.904 2204768.754 2259815.975 1941023.76 1948547.094 1941435.17 1.07738714 1.100414369 0.88637848 1.093265404 1.135638618 1.163992499 0.99978809 1.00366323 1 20.8886921 2.104579622 21.03583796 1.001547136 1.072952853 0.18838796 0.073201289 6.475720304 1277.332341 0.031494581 0.021233677 127.2270982 -2.104579622 0.071405717 SDSILLTHDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SDSILLTHDGR 11 0 O96013;O96013-4;O96013-2;O96013-3 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ;;;;; 214.26 1.37E-11 3230000000 2698550 2767100 1532320 2076000 3077500 2996760 2754360 3038950 2854020 FALSE TRUE 2341929.78 2748922.738 2273355.077 2547387.53 3016263.771 3112047.296 2487242.591 2389094.192 2516621.007 0.930585008 1.092306998 0.903336287 1.01222533 1.198537151 1.23659752 0.988326246 0.949326174 1 21.26305654 4.75734694 22.38892983 1.042139626 0.930584593 0.108292438 0.104476487 2650.997165 3159154.137 0.027934072 0.790180017 57193.53494 -4.75734694 -0.111555033 SDSKS(ph)SPQAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDSKSSPQAGR 11 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SDS(0.035)KS(0.482)S(0.482)PQAGR 132.24 0.00011298 377040000 767500 679530 477000 547000 453290 610160 823460 952610 631940 TRUE FALSE 666072.9304 675066.1227 707678.7955 671204.7104 444270.4158 633633.25 743600.9759 748901.7647 557232.7731 1.195322606 1.211461628 1.26998775 1.204532007 0.797279768 1.137106934 1.334453054 1.343965755 1 19.08792059 -1.11808967 12.22860434 0.35907509 1.179564992 0 0.163731322 0 0 0 0.038877326 0.076192168 1.11808967 0.820489902 SDSKSS(ph)PQAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SDSKSSPQAGR 11 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SDS(0.054)KS(0.201)S(0.745)PQAGR;SDS(0.008)KS(0.047)S(0.945)PQAGR;SDS(0.001)KS(0.016)S(0.984)PQAGR 171.73 8.59E-06 1240110000 1283770 1129000 756240 881960 705470 1013920 1299450 1427650 1010460 TRUE FALSE 1114116.542 1121583.525 1121960.193 1082222.498 691432.5272 1052926.158 1173429.539 1122358.157 891004.5699 1.250404969 1.258785378 1.259208125 1.214609368 0.776014569 1.181729246 1.316973648 1.259654771 1 19.76507331 3.463840051 24.99956998 1.131821287 1.253149977 0.17220058 0.148010836 522.575234 983653.7287 0.04612993 0.059583924 2909.64531 -3.463840051 0.12132869 SDSLDSGVDSVSHT(ph)PTPSTPAGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDSLDSGVDSVSHTPTPSTPAGFR 24 0 I3L2J0 I3L2J0 CIC 1 SDSLDSGVDSVSHT(0.974)PT(0.026)PSTPAGFR 238.2 6.73E-37 241100000 181330 159200 93631 110190 160550 177230 154240 144650 151350 TRUE FALSE 157366.7811 158154.2047 138911.2648 135210.3236 157355.3691 184048.1528 139281.8285 113717.7232 133457.5754 1.179152106 1.185052285 1.040864592 1.013133374 1.179066596 1.379076101 1.043641233 0.852088934 1 17.02602167 1.999249218 24.99988314 0.925195069 1.157077894 0.474953225 0.103388365 22.5483886 750835.6461 0.044918462 0.029874806 99.82727533 -1.999249218 0.231882825 SDSLS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDSLSPPR 8 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3;D6RJ93;D6R8Y0;Q9UPQ0-7;Q6NVB9 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 SDSLS(1)PPR 112.3 0.0032187 355870000 482250 497360 319160 376730 476170 530560 495870 547890 567800 TRUE FALSE 418519.4406 494092.8094 473506.8435 462272.3045 466695.1486 550970.9865 447780.6037 430727.9872 500675.3308 0.83590985 0.986852715 0.945736317 0.923297546 0.932131303 1.10045563 0.894353239 0.860294008 1 18.93351585 4.75197953 23.75954412 0.947601497 0.835909701 0.238611382 0.065779186 1916.257878 3392807.467 0.016691755 0.299726108 56491.03483 -4.75197953 -0.111691796 SDSPES(ph)DAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDSPESDAER 10 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 SDSPES(1)DAER 154.29 1.55E-05 120300000 104780 98165 72652 93630 100290 110510 82489 101140 242890 TRUE FALSE 90933.05752 97520.14765 107786.7502 114890.1225 98294.42521 114761.3912 74489.22948 79511.99807 214175.8209 0.424572004 0.455327531 0.503262926 0.536429005 0.45894268 0.535827951 0.347794766 0.371246379 1 17.70843609 1.233392561 24.9999959 1.00000085 0.452142534 0.883339506 0.062334215 57.93399674 280218.3677 0.139915014 0.017012368 17.11561705 -1.233392561 -0.547858316 SDSQASLTVPLS(ph)PQVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDSQASLTVPLSPQVVR 17 0 Q8TEV9;Q8TEV9-2 Q8TEV9 SMCR8 Smith-Magenis syndrome chromosomal region candidate gene 8 protein 1 SDSQASLTVPLS(1)PQVVR;SDSQASLTVPLS(1)PQVVR 332.26 5.02E-72 333370000 506680 521670 303280 390610 589260 608550 470060 622840 576950 TRUE FALSE 439720.9542 518243.1154 449947.2224 479303.9706 577534.8789 631961.3123 424473.6535 489650.5129 508743.6283 0.864327197 1.018672444 0.884428222 0.942132626 1.135217911 1.242199955 0.834356697 0.962470065 1 18.95657929 3.445655187 24.99794461 1.022727063 0.928959632 0.179531261 0.112872666 423.6903438 336595.7386 0.034776119 0.044896142 2790.327551 -3.445655187 -0.09376743 SDSVLPASHGHLPQAGS(ph)LER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 159.56 4.23E-11 1726710000 1529450 1442410 630293 1088706 1555610 1717280 1403650 1600400 1493525 TRUE FALSE 1327329.307 1432934.714 935104.803 1335913.337 1524656.404 1783344.873 1267524.239 1258166.914 1316962.176 1.007872004 1.088060644 0.710046818 1.014390057 1.157707057 1.354135225 0.962460625 0.955355391 1 20.32878248 SDT(ph)SSPEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDTSSPEVR 9 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SDT(0.342)S(0.329)S(0.329)PEVR 160.16 0.00073221 269720000 894600 647710 468170 553070 672350 768930 716850 809100 845770 TRUE FALSE 776376.3434 643455.1504 694578.5779 678652.9966 658971.5504 798511.2347 647329.9973 636080.2614 745784.0341 1.041020333 0.862790193 0.931340101 0.909985955 0.88359568 1.070700361 0.867985861 0.85290142 1 19.50839839 4.756184083 23.62683562 0.917742288 1.041020552 0.230026634 0.067719464 2607.324698 3495378.616 0.016246398 0.453587026 57040.59967 -4.756184083 0.123278264 SDTALEEAVAEVLDHRPIEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SDTALEEAVAEVLDHRPIEPK 21 1 A0A3B3ITN0;Q86TP1 A0A3B3ITN0 PRUNE Protein prune homolog 0 ;;; 241.8 3.06E-30 158804000 318608 260623 202229 218208 261399 225979 315388 372445 357930 FALSE TRUE 276503.1456 258910.9504 300027.6208 267755.4615 256197.6713 234672.5584 284801.7203 292800.5351 315615.9232 0.876074764 0.820335513 0.950609899 0.848358533 0.811738739 0.743538399 0.902368035 0.927711543 1 18.26781047 1.629123789 2.104932688 0.992719789 0.845100471 0.469327907 0.054215072 0.299361111 2.663134253 0.070355143 0.015822464 42.57197411 -1.629123789 -0.147619318 SDTSGHFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SDTSGHFER 9 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;;; 160.75 6.51E-05 3977310000 4369990 3865780 1020640 3241540 4229390 4870040 2435900 4959790 5015630 FALSE TRUE 3792484.749 3840385.437 1514224.918 3977581.201 4145233.414 5057393.59 2199666.793 3899177.506 4422687.935 0.857506748 0.868337421 0.342376614 0.899358322 0.937265634 1.143511291 0.497359711 0.88163071 1 22.07649202 SDTSGHFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDTSGHFQR 9 0 P50995;P50995-2 P50995 ANXA11 Annexin A11 0 ; 95.311 0.0081309 107476000 174738 141244 82068 169970 193596 248380 120488 195971 274490 FALSE TRUE 151645.9306 140316.1589 121756.3593 208564.2863 189743.8184 257935.3393 108803.0923 154064.1267 242040.1049 0.626532246 0.579722765 0.503042086 0.861693092 0.783935449 1.065671904 0.449525058 0.636523136 1 17.88488659 3.74253977 24.98826107 0.771135363 0.570761402 0.266851446 0.175380728 554.2471995 3480546.482 0.049013351 0.081023916 5527.64024 -3.74253977 -0.200373961 SDVEDHSVHLLFSANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SDVEDHSVHLLFSANR 16 0 P23919-2;P23919;H7C312;G5E9E9;H7C3A4;H7BZ20 P23919-2 DTYMK Thymidylate kinase 0 ;;; 237.59 5.30E-20 951380000 742860 752990 326642 586470 784270 827000 740560 856140 956560 FALSE TRUE 644689.1688 748043.5591 484607.1638 719636.9771 768664.5614 858815.2251 668740.6052 673061.1235 843476.5665 0.764323746 0.886857547 0.57453542 0.853179573 0.911305177 1.018185044 0.792838393 0.797960667 1 19.68598846 3.496375226 24.89764959 0.887622601 0.749310216 0.33055963 0.103789481 967.7751823 1251444.833 0.028971549 0.042217761 3135.994022 -3.496375226 -0.138312386 SDVKFEDRFDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDVKFEDRFDK 11 2 Q9HD45;Q5TB53 Q9HD45 TM9SF3 Transmembrane 9 superfamily member 3 0 62.89 0.043932 47484000 156210 119980 80490 67944 115550 96237 144410 189460 26134 FALSE TRUE 135566.4527 119191.8435 119415.2332 83371.72366 113250.7811 99939.29966 130405.1404 148945.4534 23044.46829 5.882819729 5.172254008 5.181947863 3.61786276 4.914445395 4.336802151 5.658847875 6.463392928 1 14.49213286 4.467266698 1.848110856 4.665427429 5.916591274 0.086209821 1.457471263 1.575731891 8.249971218 0.393748651 2.845641068 29326.93644 -4.467266698 1.251163845 SDVLELTDDNFESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SDVLELTDDNFESR 14 0 H7BZJ3 H7BZJ3 PDIA3 0 ;;;;; 350.97 1.51E-81 9623330000 5542770 5485940 3414420 4266990 5610590 6880570 4957300 5023410 4382230 FALSE TRUE 4810278.901 5449902.499 5065644.933 5235875.296 5498950.236 7145269.98 4476541.809 3949192.864 3864167.762 1.244842149 1.41036902 1.310927797 1.354981362 1.423061983 1.849109671 1.158475016 1.022003471 1 21.8817263 2.013723746 24.99971841 1.035873065 1.428616741 0.555901375 0.16045191 164.8464232 300289.5951 0.066565706 0.04485495 103.2104678 -2.013723746 0.392743676 SDVS(ph)PIIQPVPSIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDVSPIIQPVPSIK 14 0 P40818;P40818-2;A0A075B720 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 S(0.002)DVS(0.998)PIIQPVPSIK 96.993 0.0033056 74075000 183120 172240 111780 142400 178430 150080 197310 221520 213290 TRUE FALSE 158920.228 171108.5441 165837.1819 174734.0964 174879.5921 155853.6747 178174.9066 174149.6719 188075.0992 0.844982822 0.909788403 0.881760438 0.929065555 0.929839159 0.828677881 0.947360429 0.925958155 1 17.52094933 0.534401208 0.906474538 1.277338214 0.892745006 0.469012148 0.036141358 6.225787053 1.584550535 3.231286777 0.012170282 3.422955141 -0.534401208 -0.384593208 SDYAQLLEDMQNAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SDYAQLLEDMQNAFR 15 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 180.28 1.48E-06 297640000 202490 212627 120189 177625 232819 199150 224252 230139 238103 FALSE TRUE 175730.4335 211230.2392 178312.8024 217957.4711 228186.3574 206811.4294 202504.0756 180925.5658 209954.7346 0.836992001 1.006075141 0.849291647 1.038116485 1.086835969 0.985028653 0.964513022 0.86173606 1 17.6797188 6.583939909 12.36699258 0.957006747 0.471828016 0 0.084073183 0 0 0.019005873 0 3836541.576 -6.583939909 -0.485178732 SDYDGIGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SDYDGIGSR 9 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y650;A0A2R8YCU0;A0A2R8YF89;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 0 ;; 127.46 0.0010347 3025210000 3381930 3557360 2103620 2331000 3458900 3958350 2660970 3078740 3106970 FALSE TRUE 2934999.382 3533991.468 3120937.668 2860289.177 3390074.657 4110630.286 2402909.539 2420375.41 2739667.546 1.071297642 1.28993442 1.139166565 1.044027835 1.237403663 1.500412082 0.877080704 0.883455883 1 21.3855694 2.191402112 24.9999723 0.910731865 1.207148869 0.528435083 0.130513198 92.64063792 49110.5536 0.053547727 0.036101973 155.3825026 -2.191402112 0.296417005 SDYDMVDYLNELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SDYDMVDYLNELR 13 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;;;; 312.64 2.85E-50 1643099000 1853620 1677450 1254214 1436085 1799190 1851910 1679410 1941560 2710670 FALSE TRUE 1608659.421 1666430.72 1860756.085 1762170.048 1763389.639 1923154.176 1516541.077 1526372.503 2390217.681 0.673017957 0.697187848 0.778488127 0.737242496 0.737752738 0.804593737 0.634478227 0.63859142 1 21.18871058 2.497580524 0.017563361 1.479483199 4.87E-06 0.087901482 0.101078971 4859.269845 69.20543032 2972.821193 2854.43489 314.4709436 -2.497580524 -1.479478333 SDYLNTFEFMDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SDYLNTFEFMDK 12 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 178.32 0.00029521 0 217650 206010 146370 159700 197710 166230 221400 285620 254980 FALSE TRUE 188887.001 204656.7067 217155.0216 195962.3259 193775.9578 172624.9757 199928.6621 224542.3857 224836.5549 0.840108056 0.910246587 0.965835034 0.871576804 0.861852548 0.767779847 0.88921778 0.998691631 1 17.77851709 1.755457703 4.503930252 1.00044513 0.872161626 0.530629355 0.049837123 0.151111235 6.752906548 0.033380356 0.014288142 56.9452761 -1.755457703 -0.128283504 SDYMFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SDYMFQR 7 0 A0A2R8Y430;P48637;A0A2R8YF34 A0A2R8Y430 GSS Glutathione synthetase 0 ;;; 170.72 0.0022433 2494390000 2088240 2276980 1182140 1439880 2222520 2183900 1752460 1916390 2151070 FALSE TRUE 1812273.793 2262022.368 1753826.858 1766826.761 2178296.2 2267916.046 1582506.699 1506584.912 1896772.955 0.955451093 1.192563592 0.924637213 0.931490907 1.148422216 1.195670805 0.834315301 0.794288482 1 20.85511557 2.215359364 24.99855323 0.857390748 1.056446445 0.362487687 0.112748633 232.918451 250959.7456 0.046439506 0.031331548 164.1947866 -2.215359364 0.199055697 SEAAAPHTDAGGGLS(ph)S(ph)DEEEGTSSQAEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEAAAPHTDAGGGLSSDEEEGTSSQAEAAR 30 0 Q01831-2;Q01831 Q01831-2 XPC DNA repair protein complementing XP-C cells 2 SEAAAPHTDAGGGLS(1)S(1)DEEEGTSSQAEAAR;SEAAAPHTDAGGGLS(1)S(1)DEEEGTSSQAEAAR 178.8 4.19E-18 314140000 236668 176562 108759 139806 183818 154899 138596 167616 177863 TRUE FALSE 205391.7242 175402.1526 161355.2162 171551.0891 180160.3814 160858.0648 125154.9813 131772.6228 156836.2388 1.309593534 1.118377704 1.02881335 1.093823025 1.148716539 1.025643474 0.797997849 0.840192444 1 17.25889942 2.441190625 4.143252551 0.868953967 1.127698024 0.648323318 0.087057178 0.129846714 4.955986735 0.03392976 0.026497292 276.1789826 -2.441190625 0.258744057 SEAEDLAEPLSSTEGVAPLSQAPS(ph)PLAIPAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEAEDLAEPLSSTEGVAPLSQAPSPLAIPAIK 32 0 Q6P4R8-3;Q6P4R8;E9PQ59;Q6P4R8-2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 1 SEAEDLAEPLSSTEGVAPLS(0.045)QAPS(0.954)PLAIPAIK 90.672 8.55E-05 60131000 44771 37615 27352 35572 33594 33214 35470 50390 52132 TRUE FALSE 38854.39891 37367.90459 40579.51869 43649.16628 32925.54513 34491.76407 32030.12486 39614.49064 45969.01435 0.845230194 0.812893318 0.882758077 0.949534527 0.71625519 0.750326379 0.696776412 0.861765065 1 15.48837411 5.287256514 7.193155329 0.828442493 2.801076569 0 0.09685142 334356.6697 76697.65731 0.02411337 10732045.33 193756.6041 -5.287256514 1.972634076 SEAEEAITSFNGHKPPGSSEPITVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEAEEAITSFNGHKPPGSSEPITVK 25 1 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 0 245.04 5.04E-39 355600000 212050 171980 76965 137700 176860 133830 204420 240790 237460 FALSE TRUE 184027.0552 170850.2521 114185.5314 168966.8896 173340.832 138978.5267 184595.3799 189298.9323 209387.7493 0.878881672 0.815951519 0.545330526 0.806956903 0.827846102 0.663737621 0.881595893 0.904059253 1 17.67581751 1.798263775 1.791012038 0.981717073 0.755758483 0.409143637 0.098067986 0.369441557 2.202499796 0.105015456 0.029096399 62.84399347 -1.798263775 -0.22595859 SEAEEGEVRT(ph)PTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SEAEEGEVRTPTK 13 1 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 SEAEEGEVRT(0.999)PT(0.001)K;SEAEEGEVRT(0.999)PT(0.001)K;SEAEEGEVRT(0.999)PT(0.001)K 185.02 1.46E-05 2838900000 1377540 1559840 1252880 2210230 2279930 1860940 2351430 3225040 2638640 TRUE FALSE 1195494.599 1549593.308 1858776.959 2712096.503 2234563.854 1932531.566 2123388.681 2535390.293 2326702.985 0.513814873 0.66600392 0.798888801 1.165639327 0.960399272 0.830587994 0.912616992 1.089692285 1 21.14985562 4.167311177 2.376166606 0.989837969 0.553931614 0.747261831 0.09718889 0.151260671 1.684272083 0.027538146 0.083608372 14699.79156 -4.167311177 -0.435906356 SEAHLTELLEEICDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SEAHLTELLEEICDR 15 0 Q9Y2B0;F8VXJ7;F8W031;F8W1K5 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;;;;; 266.2 2.78E-25 1894590000 1242090 1225820 490612 810810 1260590 1559730 1137170 1140560 1062100 FALSE TRUE 1077944.659 1217767.508 727873.6042 994916.803 1235506.725 1619733.822 1026887.428 896660.1198 936539.7479 1.150986556 1.300283848 0.777194567 1.062332704 1.319225081 1.729487537 1.09646967 0.957418115 1 19.8369807 2.002891126 24.99985656 0.991050338 1.220980144 0.156385385 0.236348586 169.9070259 1469194.413 0.104541986 0.070046826 100.6679272 -2.002891126 0.229929806 SEAHTADGISIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEAHTADGISIR 12 0 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 0 ; 100.38 0.0032682 293370000 322209 332640 191819 237360 314324 355251 275383 291282 330030 FALSE TRUE 279628.2643 330454.8659 284583.31 291256.2158 308069.5674 368917.7358 248676.399 228993.6111 291014.2294 0.960874885 1.135528206 0.977901701 1.000831528 1.058606543 1.267696554 0.854516288 0.786881149 1 18.15073017 2.154534987 24.99992034 0.859883397 1.062607779 0.42095679 0.102049502 22.02024625 6549.026868 0.040766262 0.027484613 142.7364815 -2.154534987 0.202724382 SEALKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SEALKDR 7 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 114.89 0.0052918 948250000 1597740 1551460 1002180 1040820 1211880 1404840 1868780 1870440 1341320 FALSE TRUE 1386594.611 1541268.357 1486837.6 1277154.089 1187765.959 1458885.104 1687546.003 1470460.962 1182750.678 1.17234734 1.30312194 1.257101457 1.079816831 1.004240354 1.233467992 1.426797748 1.243255227 1 20.17371456 SEALS(ph)SVLDQEEAMEIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEALSSVLDQEEAMEIK 17 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 S(0.009)EALS(0.982)S(0.009)VLDQEEAMEIK 154.82 9.63E-09 0 21781 17490 11097 14002 14160 13824 20762 23503 18402 TRUE FALSE 18902.58566 17375.10704 16463.54632 17181.36811 13878.2437 14355.81823 18748.50444 18477.06635 16226.53652 1.164918073 1.070783467 1.014606308 1.058843832 0.855280712 0.884712409 1.155422441 1.138694405 1 13.98606748 -1.857496497 19.79950682 0.044330182 1.041499631 0 0.105683435 0 0 0 0.025632656 0.013883645 1.857496497 0.997169449 SEANDAVNS(ph)STK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEANDAVNSSTK 12 0 O15234;J3KSY7;K7EQ38 O15234 CASC3 Protein CASC3 1 SEANDAVNS(0.957)S(0.032)T(0.011)K 135.47 0.00013344 121570000 295620 199530 208210 242220 210890 214280 245060 259710 655080 TRUE FALSE 256553.068 198219.2743 308901.0524 297219.7531 206693.7016 222523.4903 221294.1189 204173.0376 577637.1887 0.444142228 0.34315532 0.53476656 0.514544006 0.357826168 0.385230547 0.383102271 0.353462418 1 19.1398041 1.235079834 24.99996334 1.000000823 0.412158046 0.885823637 0.066052686 32.96051898 236693.7726 0.120949139 0.016981567 17.18224209 -1.235079834 -0.587842777 SEASLHPVLMSEAPWNTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEASLHPVLMSEAPWNTR 18 0 O96019-2;O96019;H7C5S0 O96019-2 ACTL6A Actin-like protein 6A 0 70.837 0.024517 214710000 99636 99497 61579 65325 93438 115710 91610 112620 109960 FALSE TRUE 86468.85015 98843.39766 91358.81037 80158.03968 91578.76661 120161.4386 82725.6763 88537.08941 96960.65407 0.891793181 1.019417604 0.942225599 0.826706879 0.944494109 1.239280404 0.853188101 0.913123888 1 16.56511181 SEASSS(ph)PPVVTSSSHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SEASSSPPVVTSSSHSR 17 0 P48431 P48431 SOX2 Transcription factor SOX-2 1 SEAS(0.009)S(0.057)S(0.934)PPVVTSSSHSR;SEAS(0.001)S(0.032)S(0.967)PPVVTSSSHSR;S(0.004)EAS(0.014)S(0.262)S(0.72)PPVVTSSSHSR;S(0.003)EAS(0.05)S(0.256)S(0.69)PPVVTSSSHSR 174.04 9.04E-10 2269960000 1176430 1904310 356478 925350 2357880 1878550 1386450 2099650 1434060 TRUE FALSE 1020961.795 1891800.462 528871.9531 1135464.861 2310962.801 1950819.034 1251992.292 1650656.187 1264527.06 0.807386276 1.496053759 0.41823696 0.897936387 1.827531315 1.542726206 0.990087386 1.305354578 1 20.27016648 SEAVVEYVFSGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEAVVEYVFSGSR 13 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 97.452 0.0087753 41998000 88115 88223 58265 63696 148630 120210 117070 122250 110730 FALSE TRUE 76470.3795 87643.4573 86442.14888 78159.15033 145672.5538 124834.5565 105716.5694 96107.78885 97639.62554 0.783190012 0.897621809 0.885318316 0.80048597 1.491940931 1.278523507 1.082721987 0.984311322 1 16.57517914 SECDS(ph)SPEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SECDSSPEPK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SECDS(0.619)S(0.381)PEPK 111.27 0.0024886 0 624320 461000 372270 375300 353740 369740 489100 589000 740720 TRUE FALSE 541814.5302 457971.6606 552301.0172 460517.6011 346701.2661 383964.1371 441667.1573 463046.9336 653152.9254 0.829537018 0.701170649 0.845592197 0.705068573 0.530811779 0.587862539 0.676207883 0.70894107 1 19.31706129 1.237542499 5.164188813 1.018270175 0.692457377 0.503691181 0.094170395 0.150891732 10.93106146 0.176517356 0.025188632 17.27995068 -1.237542499 -0.325812799 SECDSS(ph)PEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SECDSSPEPK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SECDS(0.382)S(0.618)PEPK;SECDS(0.04)S(0.96)PEPK;SECDS(0.052)S(0.948)PEPK 205.12 1.83E-07 1150629000 4433020 3464600 2609440 2751690 2721400 2711250 3977980 4661050 5392740 TRUE FALSE 3847185.175 3441840.814 3871373.912 3376503.271 2667249.464 2815553.542 3592196.112 3664320.73 4755216.421 0.809045233 0.72380319 0.814132012 0.710063007 0.560910215 0.592097876 0.755422213 0.770589686 1 22.18107957 1.121767188 1.813349426 1.177395724 0.703517775 0.557840686 0.080985862 1.036694366 2.483320795 0.944298469 0.024300364 13.23631787 -1.121767188 -0.473877949 SEDDSAKFDS(ph)NEEDSASVFSPSFGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SEDDSAKFDSNEEDSASVFSPSFGLK 26 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 SEDDS(0.234)AKFDS(0.765)NEEDSASVFSPSFGLK;SEDDS(0.002)AKFDS(0.998)NEEDSASVFSPSFGLK;SEDDSAKFDS(1)NEEDSASVFSPSFGLK;SEDDSAKFDS(1)NEEDSASVFSPSFGLK;SEDDS(0.03)AKFDS(0.892)NEEDS(0.066)AS(0.012)VFSPSFGLK 309.95 6.13E-82 3211471000 3551328 2269023 1804652 2197413 2356902 1547294 2534580 3613015 2157746 TRUE FALSE 3082011.007 2254117.639 2677387.743 2696369.207 2310004.261 1606819.401 2288776.822 2840399.859 1902659.726 1.619843509 1.184719268 1.407181593 1.417157871 1.214092163 0.844512226 1.202935444 1.492857509 1 20.85958614 3.1867949 6.01184245 1.18043163 1.391319491 0.293507127 0.194339498 0.328647553 25.89544356 0.062456452 0.072008914 1537.428403 -3.1867949 0.210887861 SEDEANRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEDEANRDR 9 1 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 ; 110.38 0.0020941 200120000 642320 620430 449360 510300 376570 633420 582870 660480 776190 FALSE TRUE 557435.7846 616354.3545 666671.999 626171.4144 369076.9937 657788.0773 526343.3571 519241.4919 684429.7024 0.814452942 0.900537122 0.974054745 0.914880538 0.539247482 0.961074709 0.769024715 0.75864839 1 19.38454284 SEDES(ph)ET(ph)EDEEEKSQEDQEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEDESETEDEEEKSQEDQEQK 21 1 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 2 SEDES(1)ET(1)EDEEEKSQEDQEQK;SEDES(1)ET(1)EDEEEKSQEDQEQK 228.63 5.50E-32 324790000 1710170 1226710 1472940 1106970 1181450 815000 1834010 2083390 2284510 TRUE FALSE 1484166.701 1218651.661 2185258.711 1358324.457 1157941.456 846353.5774 1656147.992 1637873.261 2014437.83 0.736764709 0.604958685 1.084798289 0.674294554 0.574821143 0.420143806 0.822139044 0.813067168 1 20.94194585 1.458053044 1.87226511 1.019252451 0.694591155 0.240292174 0.171925356 0.820892786 4.270223532 0.424488225 0.050249242 28.71131238 -1.458053044 -0.324661296 SEDES(ph)ET(ph)EDEEEKSQEDQEQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEDESETEDEEEKSQEDQEQKR 22 2 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 2 SEDES(1)ET(1)EDEEEKSQEDQEQKR 99.135 0.001992 434790000 275550 189200 226460 124820 192010 131220 258900 306800 192730 TRUE FALSE 239135.3693 187957.1327 335976.8135 153162.2888 188189.3767 136268.1183 233791.9178 241193.2075 169945.679 1.407128271 1.105983594 1.976965908 0.901242619 1.107350171 0.801833381 1.375686156 1.41923707 1 17.37471415 3.690198587 24.99999196 1.139035637 1.457625289 0.293829281 0.283042851 588.0450046 303980.4349 0.079261015 0.11756336 4900.028281 -3.690198587 0.318589652 SEDES(ph)ETEDEEEKSQEDQEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEDESETEDEEEKSQEDQEQK 21 1 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 1 S(0.005)EDES(0.994)ET(0.001)EDEEEKSQEDQEQK 110.14 0.00018008 0 140010 71657 71927 69187 68903 49179 110490 81753 127640 TRUE FALSE 121507.3238 71186.28045 106711.1378 84896.96581 67531.96511 51070.94795 99774.69681 64270.75715 112550.5446 1.079580061 0.632482772 0.948117472 0.7543008 0.600014556 0.453760114 0.886487908 0.57103906 1 16.78021351 6.576923196 1.739918202 0.716961824 199.9989716 0.262470058 0.176855085 1111.086312 7.620937436 0.044476978 880148.099 3775054.242 -6.576923196 199.2820098 SEDES(ph)ETEDEEEKSQEDQEQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEDESETEDEEEKSQEDQEQKR 22 2 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 1 SEDES(0.995)ET(0.005)EDEEEKSQEDQEQKR;S(0.011)EDES(0.895)ET(0.094)EDEEEKSQEDQEQKR 189.2 1.16E-17 434350000 426740 212195 227670 240960 218942 185019 317460 426350 228890 TRUE FALSE 370345.2278 210801.0771 337771.9735 295673.6508 214585.4826 192136.8007 286672.7781 335178.3704 201830.885 1.834928425 1.0444441 1.673539575 1.464957412 1.063194479 0.951969272 1.4203613 1.660689197 1 17.62278743 4.760443967 23.88129868 1.321043502 1.834929411 0.28373957 0.269251232 4628.574003 5051013.383 0.067669437 2.983290227 57602.84945 -4.760443967 0.513885909 SEDFGVNEDLADSDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEDFGVNEDLADSDAR 16 0 P04083 P04083 ANXA1 Annexin A1 0 ; 276.32 6.32E-35 466800000 374820 375950 243990 362320 328340 328910 243070 397720 579220 FALSE TRUE 325286.5873 373480.3597 361984.3801 444590.2937 321806.6764 341563.3805 219497.1088 312670.6731 510745.2714 0.636886146 0.731245849 0.708737604 0.870473636 0.630072747 0.668754856 0.429758475 0.612185155 1 18.96224442 SEDFSLPAYMDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEDFSLPAYMDRR 13 1 H3BN72;H3BNV9;P13073;Q86WV2;H3BNI5 H3BN72 COX4I1 "Cytochrome c oxidase subunit 4 isoform 1, mitochondrial" 0 91.62 0.0055979 0 57713 61477 25718 32758 79233 73958 47086 69498 14961 FALSE TRUE 50086.08082 61073.15354 38155.31082 40196.20457 77656.41832 76803.21212 42519.60697 54636.39353 13192.32762 3.796606805 4.629444877 2.892234935 3.046938017 5.886483457 5.821809032 3.223055717 4.141527947 1 13.68741151 5.078170986 18.80754447 3.917246965 0.23317836 0 1.447722177 6022.408226 1545543.544 0.341746386 61946.34707 119721.1793 -5.078170986 -3.684068606 SEDHLTESHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEDHLTESHQR 11 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 ; 244.27 4.19E-16 324660000 264830 298180 153799 238550 314980 334630 256590 322650 426380 FALSE TRUE 229832.0445 296221.2359 228176.7108 292716.4235 308712.5142 347503.4326 231705.9413 253653.8084 375973.8421 0.611297965 0.787877248 0.606895175 0.77855529 0.821101044 0.924275558 0.61628208 0.674658128 1 18.52027277 3.636043164 8.963177134 0.783699584 0.680756089 0.20419751 0.120013948 0.71828039 57.43385933 0.033840401 0.050231638 4325.568205 -3.636043164 -0.102943495 SEDIY(ph)ADPAAYVMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SEDIYADPAAYVMR 14 0 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 SEDIY(1)ADPAAYVMR;SEDIY(1)ADPAAYVMR;SEDIY(1)ADPAAYVMR;SEDIY(1)ADPAAYVMR 267.85 4.73E-24 475157000 941800 988700 635860 646297 975620 1082580 1059400 1142470 1071570 TRUE FALSE 817338.7438 982205.1646 943364.0228 793048.6119 956207.0708 1124227.553 956659.5511 898161.6812 944890.2153 0.865009215 1.039491307 0.998384794 0.839302386 1.0119769 1.18979701 1.012455771 0.95054607 1 19.84978719 3.022145356 24.92185822 1.030845544 0.944732384 0.252734226 0.083221464 395.039588 444565.249 0.026503423 0.030050027 1052.314019 -3.022145356 -0.08611316 SEDLLDYGPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SEDLLDYGPFR 11 0 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ;;; 213.53 5.12E-09 403084000 769590 821160 501850 830070 1108290 1056730 620750 1203760 1088400 FALSE TRUE 667886.7316 815765.7459 744546.3386 1018550.08 1086237.197 1097383.087 560549.7605 946345.2917 959730.5919 0.695910641 0.849994522 0.775786814 1.0612875 1.131814706 1.143428266 0.58406991 0.986053065 1 19.87226995 3.755815176 23.52470732 0.972351698 0.78150698 0.279024656 0.158594568 596.0108743 812590.5964 0.044035902 0.075980348 5699.216777 -3.755815176 -0.190844718 SEDMPFS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SEDMPFSPK 9 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SEDMPFS(1)PK;SEDMPFS(1)PK;SEDMPFS(1)PK;SEDMPFS(1)PK;SEDMPFS(1)PK;SEDMPFS(1)PK 163.83 6.58E-05 2447970000 8062470 6744500 4643770 5246340 7278380 5616620 8365280 9318800 8075390 TRUE FALSE 6996994.162 6700194.935 6889512.704 6437601.682 7133554.478 5832695.006 7554016.433 7326047.139 7120726.594 0.982623623 0.940942592 0.967529453 0.90406528 1.001801485 0.819115146 1.060849105 1.028834213 1 22.76359303 SEDPPTT(ph)PIR ddPTM_MDA-MB-175_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(0.001)T(0.999)PIR;SEDPPT(0.028)T(0.972)PIR;SEDPPT(0.011)T(0.989)PIR 154.15 0.00016763 3634530000 4121560 4104490 2775320 3401400 4604120 4914100 4754200 5271700 4861750 TRUE FALSE 3576885.403 4077527.335 4117474.035 4173739.857 4512507.02 5103148.607 4293138.416 4144387.979 4286999.454 0.834356394 0.951137825 0.960455927 0.973580683 1.052602658 1.190377713 1.001431995 0.966733965 1 22.0315368 4.758838488 0.918728942 1.031167527 0.732630906 0.503731816 0.062865608 2.18566686 1.427318031 0.024061031 0.662083661 57390.29905 -4.758838488 -0.298536621 SEDRRS(ph)S(ph)EER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEDRRSSEER 10 2 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 2 SEDRRS(1)S(1)EER;S(0.001)EDRRS(1)S(1)EER 103.67 0.013691 3697700000 6396800 5249400 4177600 5115900 4369600 5426500 5013600 5405100 11037800 TRUE FALSE 5551446.673 5214916.346 6197901.333 6277543.287 4282653.509 5635260.966 4527381.844 4249261.428 9732923.858 0.570378106 0.535801617 0.636797475 0.644980211 0.440017159 0.578989525 0.465161539 0.436586322 1 23.21444184 1.231108271 24.99999532 1.000000821 0.534854484 0.793437241 0.073965981 128.619593 431436.36 0.198824826 0.019481289 17.02582913 -1.231108271 -0.465146338 SEDRRS(ph)S(ph)EEREAGEI ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEDRRSSEEREAGEI 15 3 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 2 S(0.005)EDRRS(0.995)S(1)EEREAGEI;SEDRRS(1)S(1)EEREAGEI 119.43 0.00038832 35130000000 3407000 3002000 1648030 1906850 2984100 2873300 2964800 3259400 2044080 TRUE FALSE 2956756.318 2982279.664 2445022.82 2339829.437 2924722.248 2983837.71 2677274.152 2562402.675 1802431.191 1.640426737 1.654587248 1.35651382 1.298151879 1.622654037 1.655451662 1.485368299 1.421636891 1 20.78151275 1.142825966 2.063321424 0.730356104 1.528006401 0.641742988 0.123907188 0.696115052 2.350862714 1.160520345 0.035867991 13.89395749 -1.142825966 0.797650297 SEDSGIGLSASS(ph)PELSEHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SEDSGIGLSASSPELSEHLR 20 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 SEDSGIGLSAS(0.021)S(0.979)PELSEHLR;SEDSGIGLSAS(0.046)S(0.954)PELSEHLR;SEDSGIGLSAS(0.054)S(0.946)PELSEHLR;SEDSGIGLSAS(0.262)S(0.738)PELSEHLR;SEDSGIGLSAS(0.013)S(0.987)PELSEHLR;SEDSGIGLSAS(0.062)S(0.938)PELSEHLR 272.51 1.28E-44 5817410000 2044670 2375790 1478110 2358480 3014610 3283630 2786320 3167190 4923480 TRUE FALSE 1774461.679 2360183.279 2192928.94 2894008.931 2954625.159 3409953.371 2516103.115 2489911.066 4341431.803 0.408727295 0.54364168 0.505116524 0.666602416 0.680564683 0.785444417 0.579556061 0.573523017 1 22.04973949 5.344655517 0.403393385 0.733258203 3.79E-14 0.459589497 0.120573148 12.13696276 1.172154545 0.144421809 4.709747708 221133.9976 -5.344655517 -0.733258203 SEDSLLRNS(ph)DEEESASESELWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEDSLLRNSDEEESASESELWK 22 1 Q70Z53 Q70Z53 FRA10AC1 Protein FRA10AC1 1 SEDS(0.001)LLRNS(0.999)DEEESASESELWK 260.97 1.68E-37 111320000 48804 38719 31487 43543 41012 37456 47309 54223 69552 TRUE FALSE 42354.42775 38464.65234 46714.21852 53430.10366 40195.94144 38896.95656 42720.98046 42627.83341 61329.64179 0.690602888 0.627178819 0.761690712 0.87119543 0.655408058 0.634227682 0.696579651 0.695060857 1 15.9042969 1.237488884 24.92381635 1.000000365 0.704156037 0.635207783 0.070496688 17.92911879 416743.8069 0.107354348 0.01801405 17.27781756 -1.237488884 -0.295844328 SEDVWLEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEDVWLEAAR 10 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 116.52 0.0025118 64326000 131250 101540 68681 80387 109350 108870 102120 121280 109440 FALSE TRUE 113904.98 100872.9771 101895.3613 98640.09699 107174.1489 113058.2993 92216.41812 95345.2158 96502.12787 1.18033646 1.045292775 1.055887197 1.022154632 1.110588453 1.171562761 0.955589479 0.988011538 1 16.55827313 2.219217302 24.99623684 0.981552191 1.090517736 0.527524397 0.051653493 203.7173615 263250.0617 0.021408865 0.014456988 165.6598647 -2.219217302 0.108965545 SEEAHAEDSVMDHHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SEEAHAEDSVMDHHFR 16 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;; 138.21 2.72E-06 1707070000 1403810 1232430 836810 1120560 1069720 1190950 1326000 1614090 2122140 FALSE TRUE 1218292.952 1224334.086 1241494.115 1375000.275 1048434.665 1236766.617 1197404.724 1268929.414 1871263.027 0.651053825 0.654282198 0.66345249 0.734797971 0.560281826 0.660926123 0.63989119 0.678113871 1 20.83558093 1.235054993 4.47638611 1.030867118 0.653184561 0.871453384 0.041710811 0.066846589 2.783262631 0.081032402 0.010079785 17.18125933 -1.235054993 -0.377682556 SEEEIDFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEEEIDFLR 9 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ; 168.08 0.00013842 131999000 268070 253780 186451 197754 280360 280630 231190 266150 338010 FALSE TRUE 232643.8703 252112.9025 276619.3272 242657.0682 274781.3845 291426.0177 208769.2294 209235.8937 298050.8429 0.780550956 0.845872134 0.92809443 0.814146559 0.921927889 0.977772835 0.700448378 0.702014098 1 18.18519893 2.23014727 24.99999222 0.776053927 0.877960705 0.100473943 0.100193993 317.4692261 943340.2601 0.040364367 0.027713672 169.8819626 -2.23014727 0.101906778 SEEELEDYMVEIDILASCDHPNIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEEELEDYMVEIDILASCDHPNIVK 25 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 152.88 1.15E-07 70599000 61376 47432 35432 47130 46718 43329 60056 69056 70848 FALSE TRUE 53265.00609 47120.41607 52567.03371 57831.58684 45788.4032 44995.89467 54231.77836 54288.91179 62472.43015 0.852616201 0.754259374 0.841443715 0.925713738 0.732937763 0.720252031 0.868091384 0.869005923 1 15.93093203 1.21113068 1.537748621 1.084743757 0.808631617 0.469338955 0.063268824 1.145609826 2.300961571 0.49934998 0.018696907 16.26037959 -1.21113068 -0.27611214 SEEHNDKEHSSDKGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEEHNDKEHSSDKGR 15 2 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 0 82.102 0.0038697 32899000 17824 13837 7483.6 8007.3 2848 4900.5 10015 9386.4 1812.1 FALSE TRUE 15468.51324 13746.10384 11102.69399 9825.479849 2791.330372 5089.025406 9043.746841 7379.191405 1597.875602 9.680674276 8.602737169 6.948409485 6.14908935 1.746900928 3.184869585 5.659856642 4.618126339 1 10.64193938 3.817559063 1.533307428 3.623792312 9.298896717 0.729742231 1.4469059 0.236233675 1.065912165 0.473168874 1.178224407 6569.90459 -3.817559063 5.675104405 SEEHS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEEHSPPR 8 0 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 SEEHS(1)PPR 114.89 0.0016544 46808000 56633 42564 25928 31015 36344 41963 38728 43630 46047 TRUE FALSE 49148.80556 42284.39428 38466.86752 38057.42978 35620.82551 43577.34376 34972.16452 34300.06403 40603.37612 1.210461057 1.041400946 0.947381011 0.937297176 0.877287283 1.073244344 0.86131174 0.844758917 1 15.30931207 4.789543206 1.336250549 0.92103824 1.362677296 0.633608052 0.067437289 0.947071849 1.375718957 0.019660659 0.586644952 61594.68033 -4.789543206 0.441639056 SEEITTGSAWFSFLESHNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SEEITTGSAWFSFLESHNK 19 0 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 ;; 237.34 3.24E-24 688665000 975111 841942 709277 963905 871329 718480 991996 1194268 1922580 FALSE TRUE 846247.6107 836411.2276 1052285.73 1182774.363 853991.2576 746120.3905 895792.3806 938883.082 1695294.783 0.499174314 0.493372148 0.62070959 0.697680648 0.503742043 0.44011248 0.528399184 0.553817007 1 20.69310472 1.238351787 6.642664331 1.011945842 0.5425788 0.799808427 0.072015015 0.055181577 12.0745896 0.116900514 0.0191506 17.31218111 -1.238351787 -0.469367042 SEENTKEEKPDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SEENTKEEKPDSK 13 2 P50502;Q3KNR6;Q8NFI4;F6VDH7;Q8IZP2 P50502 ST13;ST13P5;ST13P4 Hsc70-interacting protein;Putative protein FAM10A5;Putative protein FAM10A4 0 ;; 106.3 0.00077889 801520000 1433910 908099 1036935 880609 738447 530848 1590260 1748190 880020 FALSE TRUE 1244415.16 902133.6379 1538400.234 1080564.733 723753.3494 551270.0661 1436036.83 1374353.173 775985.0381 1.603658704 1.162565763 1.982512753 1.392507174 0.932689825 0.710413267 1.850598606 1.771107825 1 19.56566931 3.492320611 24.70287621 1.319713924 1.565316442 0.111284925 0.400912561 1872.185898 3042780.944 0.122179054 0.174574381 3106.852325 -3.492320611 0.245602518 SEEQLKEEGIEYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEEQLKEEGIEYK 13 1 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 145.69 3.82E-05 345950000 608970 379130 391980 562020 470050 343360 575200 731640 529960 FALSE TRUE 528493.0716 376639.4701 581542.8391 689635.2309 460696.9246 356569.2814 519417.1925 575184.4796 467308.7325 1.130929158 0.805975673 1.244451042 1.475759349 0.985851307 0.763027216 1.111507567 1.230844706 1 18.83401647 3.936812062 0.009629219 1.320988085 0.855070269 0 0.211324813 332601.7458 1596.369439 37819.58557 39424.50433 8645.936904 -3.936812062 -0.465917816 SEETQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEETQER 7 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 157.58 0.0034116 267940000 121236 114307 65956 81019 65313 116687 112478 116026 128678 FALSE TRUE 105214.3554 113556.1098 97852.54221 99415.60225 64013.39908 121176.0244 101569.9009 91214.74282 113465.8334 0.927277862 1.000795626 0.86239654 0.876172141 0.564164534 1.067951653 0.895158461 0.803896116 1 16.79189842 4.223806419 23.44319144 0.859642263 0.964036696 0.082717096 0.132393554 235.0214697 373433.4306 0.032869241 0.068986875 16741.96459 -4.223806419 0.104394433 SEEVPAFGVAS(ph)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEEVPAFGVASPPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK 44 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 1 SEEVPAFGVAS(1)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK;SEEVPAFGVAS(1)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK 336.26 1.78E-133 348100000 410670 316680 230960 299390 317340 305810 395410 456020 484700 TRUE FALSE 356398.919 314599.7082 342653.0285 367371.0754 311025.5549 317574.7086 357063.1991 358503.6718 427399.3182 0.833878071 0.736079106 0.801716367 0.85954998 0.727716544 0.743039811 0.835432309 0.838802629 1 18.70522508 0.885833327 1.339167098 1.304282018 0.78555208 0.689466807 0.044177288 1.766374139 1.419384828 1.591761752 0.012921478 7.68835321 -0.885833327 -0.518729938 SEEWADNHLPLTDAELAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SEEWADNHLPLTDAELAR 18 0 O60664-4;O60664;O60664-3;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 0 ;;;;; 136.04 7.13E-06 4641360000 6378320 6211690 3688760 4709450 6625240 6716820 6142480 7336760 6552050 FALSE TRUE 5535408.851 6170884.999 5472656.674 5778802.602 6493410.686 6975220.412 5546783.235 5767850.969 5777474.113 0.958101887 1.068093925 0.947240363 1.000229943 1.123918612 1.20731314 0.960070634 0.998334368 1 22.46200746 3.438526172 24.99972235 1.05165066 0.994655903 0.147807713 0.076251307 388.7022704 251778.2264 0.023808186 0.030736284 2744.897753 -3.438526172 -0.056994757 SEFGSVDGPLPHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEFGSVDGPLPHPR 14 0 Q5JRA6-2;Q5JRA6;Q5JRA6-4 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 0 150.21 7.27E-06 115350000 130310 138190 85321 136150 174680 175460 90848 195700 158820 FALSE TRUE 113089.2033 137282.2208 126582.521 167064.9384 171204.2098 182210.0597 82037.57494 153851.0779 140044.4805 0.807523459 0.98027584 0.903873687 1.19294197 1.222498803 1.301087048 0.58579656 1.09858723 1 17.0955256 4.558894769 1.525506577 1.049443881 0.779707749 0.131952693 0.197493435 1.813977221 5.174773228 0.056818457 0.66630117 36215.5236 -4.558894769 -0.269736132 SEGEASEEGLYLDSEAVLDYVMTRPDLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEGEASEEGLYLDSEAVLDYVMTRPDLDK 29 1 Q7L211 Q7L211 ABHD13 Alpha/beta hydrolase domain-containing protein 13 0 52.329 0.07028 10472000 5803.2 3419.6 2503.3 3897.1 4697.2 4529.3 3499.5 5686.7 4458.4 FALSE TRUE 5036.292417 3397.136422 3713.904253 4781.996118 4603.73491 4703.545102 3160.119029 4470.643459 3931.333031 1.281064814 0.8641182 0.944693371 1.216380317 1.171036611 1.196424995 0.80382888 1.137182585 1 11.94080287 SEGEGKPQGEGKPASQAKPESQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEGEGKPQGEGKPASQAKPESQPR 24 3 Q969E4 Q969E4 TCEAL3 Transcription elongation factor A protein-like 3 0 102.07 0.0015233 148150000 151180 106210 90596 98912 97505 63232 149140 170150 141910 FALSE TRUE 131201.18 105512.2995 134408.5286 121371.4814 95564.84127 65664.57596 134676.4258 133764.7466 125133.5615 1.048489138 0.843197447 1.07412054 0.969935483 0.76370272 0.52475591 1.07626143 1.068975781 1 16.93310925 SEGEIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEGEIAR 7 0 P50395;P50395-2;Q5SX91 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ; 132.96 0.0077193 929710000 902810 887430 512580 650730 693240 940640 845270 882160 962880 FALSE TRUE 783501.3711 881600.4139 760465.4025 798488.1923 679445.8803 976827.0295 763295.8455 693516.949 849049.4233 0.922798308 1.038338158 0.895666826 0.940449602 0.800243027 1.150494898 0.899000488 0.816815759 1 19.69548901 7.998631571 0.121895294 0.875268574 1.167880152 0 0.103945892 1106.082197 11.99311601 3.561044379 54.88449289 99685403.58 -7.998631571 0.292611579 SEGEVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEGEVAR 7 0 P31150 P31150 GDI1 Rab GDP dissociation inhibitor alpha 0 86.872 0.045964 81643000 176530 140900 100320 139820 102200 159580 165670 161340 203180 FALSE TRUE 153201.1132 139974.4186 148835.0876 171568.268 100166.42 165719.1459 149603.3489 126838.6965 179160.2919 0.855106406 0.781280367 0.830737023 0.957624406 0.559088283 0.924976981 0.835025146 0.7079621 1 17.4508914 1.21987257 24.85074489 1.000000687 0.803862197 0.228444601 0.111680106 1763.724568 2345206.522 0.873789451 0.025597355 16.59100024 -1.21987257 -0.196138491 SEGFDTYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SEGFDTYR 8 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ;; 214.69 2.03E-05 5880400000 8111800 6838600 4183300 6149100 7874700 7223600 7127300 8197200 7656700 FALSE TRUE 7039805.077 6793676.786 6206357.872 7545347.138 7718008.877 7501496.566 6436095.543 6444292.571 6751533.649 1.042697177 1.00624201 0.919251565 1.117575285 1.143148991 1.111080379 0.953279044 0.954493143 1 22.68678382 2.219801449 24.99371535 0.965515712 1.054827462 0.290039038 0.064335316 337.9934862 450320.8224 0.029075232 0.019637992 165.882835 -2.219801449 0.08931175 SEGGFIWACK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEGGFIWACK 10 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 204.62 4.27E-07 694710000 1093550 843880 509290 628900 809150 761210 896850 995440 975130 FALSE TRUE 949034.5968 838336.4967 755584.3475 771701.3571 793049.4981 790494.2413 809873.625 782572.9025 859851.2423 1.103719516 0.974978526 0.87873845 0.897482401 0.922310115 0.919338372 0.941876438 0.91012592 1 19.71372756 4.66446959 3.09582222 0.922807951 1.117764471 0.753052013 0.0322702 0.139016712 2.117101594 0.007850379 0.059443498 46181.66535 -4.66446959 0.194956519 SEGS(ph)PVLPHEPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEGSPVLPHEPAK 13 0 Q9UKE5-6;Q9UKE5-2;Q9UKE5-4;Q9UKE5;Q9UKE5-8;Q9UKE5-5;Q9UKE5-7;Q9UKE5-3 Q9UKE5-6 TNIK TRAF2 and NCK-interacting protein kinase 1 S(0.132)EGS(0.868)PVLPHEPAK 102.65 0.0010775 142270000 1094000 791430 431450 573670 596370 458950 635710 784990 970300 TRUE FALSE 949425.1282 786231.0442 640100.6631 703930.5415 584503.4038 476606.1035 574058.942 617125.9973 855592.2394 1.109670103 0.918931949 0.748137528 0.822740681 0.683156505 0.557048184 0.670949216 0.721285174 1 19.70656387 4.706726815 1.241041521 0.722341903 1.278716921 0.525554981 0.114492366 1.103694507 1.527938961 0.034594364 0.777727081 50901.0586 -4.706726815 0.556375019 SEGSMSTDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SEGSMSTDKR 10 1 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 0 ;;; 120.45 0.00089445 692889000 449851 361033 258412 304508 304062 320202 434473 437833 418511 FALSE TRUE 390402.0506 358661.3505 383380.9075 373651.1955 298011.7611 332520.3781 392337.8753 344205.8202 369035.1063 1.057899489 0.971889515 1.038873812 1.012508537 0.80754312 0.901053511 1.063145128 0.932718363 1 18.49339854 3.436398093 24.99940923 0.943681774 1.019105691 0.249943819 0.068345071 231.8856184 142350.6759 0.020144605 0.026006591 2731.480426 -3.436398093 0.075423917 SEGTYLNSVIESHTEFIFTTIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEGTYLNSVIESHTEFIFTTIK 22 0 A0A0A0MSX9;P41252;J3KR24;Q5TCC6 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 319.19 1.60E-67 53782000 111710 82301 57877 86269 80893 75776 106241 115411 137140 FALSE TRUE 96947.24046 81760.35931 85866.51079 105857.695 79283.38756 78691.15175 95937.76417 90731.25578 120927.4654 0.801697448 0.67611075 0.710066241 0.875381739 0.65562763 0.650730183 0.793349665 0.75029486 1 16.88378243 1.023112394 2.131561871 1.241799708 0.732716932 0.566649686 0.071315456 1.143513774 3.013850152 1.422458783 0.018721654 10.54659804 -1.023112394 -0.509082776 SEGVVAVLLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEGVVAVLLTK 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 0 149.23 0.0038995 0 336150 296670 301200 244370 334120 355700 380350 418540 384010 FALSE TRUE 291726.9258 294721.1552 446861.3275 299857.9435 327471.6657 369384.0092 343463.7155 329038.4781 338612.7753 0.861535498 0.870378133 1.319682422 0.885548229 0.967097787 1.090874403 1.014325922 0.971724938 1 18.36927688 4.422283128 24.99996277 1.027738155 0.863725952 0.274618691 0.114117115 99.88873932 45537.56344 0.027036055 0.071530706 26441.31976 -4.422283128 -0.164012203 SEHPGLSIGDTAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SEHPGLSIGDTAK 13 0 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 ;;; 168.31 3.04E-05 1975970000 3721020 2742230 1297530 2464930 2831260 2107540 2839160 3556370 4527660 FALSE TRUE 3229277.779 2724216.111 1925019.848 3024630.031 2774923.465 2188618.428 2563818.7 2795867.951 3992405.193 0.80885522 0.682349606 0.48217046 0.757595956 0.69505056 0.548195467 0.642173972 0.700296642 1 21.92882672 1.226479166 3.313102349 1.061546996 0.655175804 0.56461739 0.093135804 0.258580641 3.840278952 0.276783526 0.023573296 16.84531616 -1.226479166 -0.406371192 SEHPPLCGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SEHPPLCGR 9 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ;; 82.426 0.018487 657000000 1496890 1376090 565690 1002950 1455660 1531700 1296740 1427590 1418010 FALSE TRUE 1299072.194 1367050.374 839259.5761 1230685.127 1426695.214 1590625.49 1170982.354 1122310.988 1250374.473 1.038946509 1.093312766 0.671206582 0.98425324 1.141014348 1.272119292 0.936505327 0.897579895 1 20.2539288 SEIDLFNIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SEIDLFNIR 9 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;;;; 224.51 7.14E-07 686870000 1296197 1615558 599736 671865 907276 966943 691472 1039619 2212473 FALSE TRUE 1124901.282 1604945.293 889770.3356 824422.2171 889222.9827 1004141.923 624413.1519 817304.5672 1950916.962 0.576601313 0.822662022 0.456078015 0.42258191 0.455797453 0.514702544 0.320061368 0.418933549 1 20.89572094 -0.316282783 10.66977574 1.400066825 0.532265376 0 0.20734753 0 0 0 0.046122683 0.48274437 0.316282783 -0.867801449 SEIDLFNIRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEIDLFNIRK 10 1 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 68.355 0.096564 483130000 925540 570130 327930 446620 671010 553990 624850 876710 361560 FALSE TRUE 803227.544 566384.7785 486518.0449 548031.8972 657658.2138 575302.3538 564252.1432 689232.3891 318816.7887 2.519401652 1.776521183 1.526011371 1.718955578 2.062809228 1.804492029 1.769831964 2.161844713 1 18.28236808 8 0.033612554 1.26E-09 4.546728136 0.176876012 0.362713753 6798.619753 22.59182134 1036.272329 2242.902906 99999999.98 -8 4.546728135 SEIDLLDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SEIDLLDIR 9 0 P12429;D6RA82 P12429 ANXA3 Annexin A3;Annexin 0 ;;; 98.582 0.013764 267753000 1581190 1300960 874370 1148640 1288370 1295050 1314630 1457370 1735150 FALSE TRUE 1372231.735 1292413.908 1297218.257 1409456.268 1262733.958 1344871.412 1187137.385 1145722.767 1530022.544 0.896870272 0.844702526 0.847842577 0.921199674 0.825304152 0.878987971 0.775895355 0.748827376 1 20.54512148 2.266683149 24.99732524 0.819515315 0.867444123 0.000948183 0.071523275 522.1853858 464154.268 0.026150383 0.020251521 184.7919928 -2.266683149 0.047928807 SEIPS(ph)PQSQLLEDAEANLVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SEIPSPQSQLLEDAEANLVGR 21 0 Q9ULJ8;Q9ULJ8-4;Q9ULJ8-5;Q9ULJ8-3 Q9ULJ8 PPP1R9A Neurabin-1 1 SEIPS(0.997)PQS(0.002)QLLEDAEANLVGR;SEIPS(1)PQSQLLEDAEANLVGR;S(0.001)EIPS(0.999)PQSQLLEDAEANLVGR;SEIPS(1)PQSQLLEDAEANLVGR;SEIPS(0.596)PQS(0.403)QLLEDAEANLVGR 198.77 8.79E-22 296165000 124950 101011 64885.2 76721.9 105474.8 107689 100343 129890 102065 TRUE FALSE 108437.5409 100347.4521 96263.89975 94142.78002 103376.0578 111831.8655 90611.7513 102114.0343 89998.99197 1.204875061 1.114984178 1.069610866 1.046042605 1.14863573 1.242590201 1.006808513 1.134613089 1 16.45762122 0.280873982 1.307620888 1.19E-09 1.121520776 0.2161682 0.070532998 24.82727215 4.977301106 67.43500226 0.020563781 1.909299163 -0.280873982 1.121520775 SEISQVFEIALKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEISQVFEIALKR 13 1 O95793-2;O95793-3;O95793;Q5JW30;A0A087X1A5;Q5JW28 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 ; 116.63 0.00091357 220220000 175792 160711 105597 120491 158809 150086 158413 203119 99352 FALSE TRUE 152560.6418 159655.2789 156664.0624 147850.3231 155649.0116 155859.9055 143050.1316 159683.5825 87606.71974 1.741426254 1.82240905 1.788265362 1.687659618 1.776678913 1.779086193 1.632867114 1.822732126 1 16.41875391 1.235483969 24.99999993 0.999998969 1.755964777 0.942702875 0.058603956 17.77491539 144408.3075 0.094019708 0.013638967 17.19823856 -1.235483969 0.755965809 SEIYPELMDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEIYPELMDLR 11 0 Q9NPB8;H0Y565 Q9NPB8 GPCPD1 Glycerophosphocholine phosphodiesterase GPCPD1 0 76.465 0.082073 20532000 23945 23763 11274 18306 23913 23104 23373 24800 25559 FALSE TRUE 20780.60758 23606.89929 16726.14411 22462.65709 23437.17808 23992.82583 21106.29006 19496.71299 22537.44414 0.922048102 1.047452371 0.74214911 0.996681654 1.039921738 1.064576164 0.93649883 0.865080924 1 14.4600363 SELDMLDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SELDMLDIR 9 0 P08133;P08133-2 P08133 ANXA6 Annexin A6 0 99.442 0.010792 0 78439 65087 51943 86268 85202 106580 44052 89301 115810 FALSE TRUE 68073.08741 64659.43921 77062.80854 105856.4679 83506.64689 110680.2016 39779.84382 70204.67609 102119.0737 0.666605022 0.633176907 0.754636776 1.036598395 0.817737998 1.083834758 0.38954372 0.687478583 1 16.63989283 7.343110285 12.04783427 0.773273149 0.097168254 0 0.212166661 0 0 0.048136849 0 22034859.49 -7.343110285 -0.676104894 SELGNQS(ph)PSTSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SELGNQSPSTSSR 13 0 A0A0A0MSK5;J3KN66;Q5JTV8;Q5JTV8-3;H0YD16 A0A0A0MSK5 TOR1AIP1 Torsin-1A-interacting protein 1 1 SELGNQS(0.999)PS(0.001)TSSR;SELGNQS(1)PSTSSR 177.39 1.62E-05 859870000 559990 529150 305940 492770 675120 632970 394500 751400 643520 TRUE FALSE 485985.9027 525673.9788 453893.6073 604660.96 661686.4328 657320.7655 356241.4507 590718.9574 567443.7987 0.856447641 0.926389503 0.79989174 1.065587396 1.166082763 1.158389196 0.627800412 1.041017558 1 19.11411799 3.73756013 24.98406028 1.001889518 0.867457616 0.176071298 0.150976661 183.0238767 4570471.482 0.042552125 0.067464407 5464.622048 -3.73756013 -0.134431902 SELHLMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SELHLMDR 8 0 P42704;B8ZZ38;A0A0C4DG06;C9JCA9 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ; 130.75 0.0010346 294480000 485690 546450 329320 649100 728330 757440 480850 644770 741000 FALSE TRUE 421504.8359 542860.334 488580.2535 796488.0759 713837.658 786579.2069 434217.241 506890.9531 653399.8241 0.645094811 0.83082412 0.747750819 1.218990343 1.092497475 1.20382525 0.664550594 0.775774548 1 19.31760654 3.887519258 22.64470338 0.964091886 0.750065505 0.300003477 0.177313417 17.73825848 3537.180507 0.052810579 0.091470778 7718.257408 -3.887519258 -0.214026382 SELISS(ph)TFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SELISSTFK 9 0 H0YHG7;Q92730 H0YHG7 RND1 Rho-related GTP-binding protein Rho6 1 SELIS(0.009)S(0.495)T(0.495)FK;SELIS(0.046)S(0.477)T(0.477)FK;SELIS(0.058)S(0.593)T(0.349)FK;SELIS(0.072)S(0.584)T(0.344)FK 71.501 0.05182 7874290000 2240430 2620280 1379830 1630130 2651530 3523640 1876580 2010360 2053840 TRUE FALSE 1944351.499 2603067.208 2047120.403 2000275.931 2598769.741 3659196.711 1694589.56 1580460.159 1811037.375 1.073612023 1.437334891 1.1303579 1.104491801 1.43496196 2.020497623 0.935701043 0.872682243 1 20.78838489 2.057543805 24.99999962 0.920311232 1.361130245 0.360707731 0.27006755 83.98340139 36486.17928 0.112816188 0.076060648 114.1678453 -2.057543805 0.440819013 SELNEIKENQRS(ph)PVR ddPTM_MDA-MB-175_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 190.37 1.15E-07 4393280000 4645780 3626120 1621000 1694870 3356240 2879080 4186190 4501760 751271 TRUE FALSE 4031828.402 3602299.779 2404921.022 2079716.138 3289457.39 2989840.071 3780213.938 3539093.657 662456.5982 6.086177438 5.43778987 3.630307296 3.139399839 4.965544006 4.513261818 5.706357138 5.342378152 1 19.33746641 4.407766822 5.256594068 4.269131171 5.942727614 0.214420257 1.340400998 0.308580898 15.51834895 0.338795426 0.961906336 25572.12517 -4.407766822 1.673596443 SELNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SELNLR 6 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41;A0A2R8YF08;K7ELR7;K7ENA0;K7ERK8;A0A0J9YXM3;A0A0J9YXH9;K7EIL4;A0A0J9YYI8 P06744 GPI Glucose-6-phosphate isomerase 0 ;;; 159.42 0.02122 2229120000 2213440 2086800 1139830 1591380 2150840 2270820 1957240 2142780 2198830 FALSE TRUE 1920928.296 2073091.673 1691055.601 1952727.152 2108042.492 2358179.915 1767427.166 1684563.172 1938886.822 0.990737713 1.069217475 0.872178603 1.007138286 1.087243705 1.216254548 0.911567991 0.868830069 1 20.88679716 2.097790073 21.31513467 0.913929116 1.037168704 0.251173595 0.091493307 6.26841629 1354.158706 0.038810123 0.026165809 125.2535584 -2.097790073 0.123239588 SELPIAELTGHTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SELPIAELTGHTR 13 0 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y9R3 A0A499FIZ0 WDR26 WD repeat-containing protein 26 0 165.51 3.52E-05 135560000 131460 135740 89383 112120 137150 136350 124570 147710 151920 FALSE TRUE 114087.2279 134848.315 132608.9178 137578.5596 134420.9833 141595.4727 112489.2206 116123.366 133960.1907 0.851650235 1.006629763 0.989912877 1.027010778 1.003439773 1.05699665 0.839721264 0.866849811 1 17.03144481 2.234365866 24.99999944 0.892224869 0.99245061 0.267598564 0.067106564 122.5899413 730602.7459 0.026331672 0.018465939 171.5401818 -2.234365866 0.100225741 SELTLTPDPAPPMAHS(ph)PLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SELTLTPDPAPPMAHSPLHR 20 0 M0R344;Q9NRA0-4;Q9NRA0-2;Q9NRA0;Q9NRA0-5;E9PCV4;Q9NRA0-3 M0R344 SPHK2 Sphingosine kinase 2 1 SELTLTPDPAPPMAHS(1)PLHR;SELTLTPDPAPPMAHS(1)PLHR 102.21 0.00043502 182570000 104911 120628 103312 142645 192612 202430 169269 194787 272710 TRUE FALSE 91046.74554 119835.5867 153274.0288 175034.7274 188779.398 210217.6131 152853.3184 153133.3159 240470.5345 0.378619134 0.498337923 0.637392141 0.727884303 0.785041704 0.874192813 0.635642611 0.636806984 1 17.8755006 4.275388128 1.396733582 0.760898043 0.352700764 0.637569719 0.106677536 0.422413596 1.304604298 0.032920704 0.193669333 18853.33254 -4.275388128 -0.408197279 SELVAMLEEEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SELVAMLEEEELR 13 0 B4DZG7;F8VYN9;P40616-2;P40616 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ;; 214.26 7.24E-11 59667000 127108 111122 74089 96918 114554 109913 122216 137236 163592 FALSE TRUE 110310.3557 110392.0323 109918.6882 118924.7132 112274.5995 114141.4242 110363.5111 107889.1494 144252.3401 0.764704099 0.765270305 0.761988943 0.824421379 0.778320819 0.791262202 0.765072588 0.747919578 1 17.1382352 1.234426257 24.99999964 1.000000329 0.774613481 0.919949202 0.020870564 33.73794444 203981.4086 0.040589709 0.005407941 17.15640372 -1.234426257 -0.225386848 SELVAMLEEEELRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SELVAMLEEEELRK 14 1 B4DZG7;F8VYN9;P40616-2;P40616 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ;;;;; 313.88 1.32E-55 1134951000 1313852 1063497 751271 874431 1106478 937927 1341601 1644420 1287266 FALSE TRUE 1140223.129 1056510.818 1114588.168 1072983.923 1084461.253 974009.6586 1211492.742 1292773.58 1135086.88 1.004524983 0.930775289 0.981940844 0.945287927 0.955399337 0.858092606 1.067312787 1.138920379 1 20.1143713 2.107282925 7.853030135 1.08629831 0.947592267 0.561729644 0.050585925 0.143390629 9.49908727 0.019819003 0.013333628 128.021504 -2.107282925 -0.138706043 SENFEELLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SENFEELLK 9 0 P29373;Q5SYZ4 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 ;;;;; 234.81 8.13E-10 1506194000 2351456 2054709 1490519 1725294 1890978 1759010 2525787 2618834 2526836 FALSE TRUE 2040705.132 2041211.481 2211338.974 2117048.372 1853351.237 1826680.253 2280836.565 2058816.729 2228116.327 0.915888056 0.916115311 0.992470163 0.950151636 0.83180183 0.819831636 1.023661349 0.924016715 1 21.08739312 2.216396895 24.99979634 0.972075521 0.907696075 0.29435515 0.056132543 386.4009049 435841.5415 0.024559953 0.016572584 164.5875176 -2.216396895 -0.064379446 SENSEDGAAWMQEPGRYS(ph)PPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SENSEDGAAWMQEPGRYSPPPR 22 1 P35548 P35548 MSX2 Homeobox protein MSX-2 1 SENSEDGAAWMQEPGRY(0.029)S(0.971)PPPR 54.3 0.062141 161760000 114510 78017 59473 80930 82198 97684 95060 117090 93645 TRUE FALSE 99377.21337 77504.50119 88234.34173 99306.39344 80562.42062 101441.9667 85841.09583 92051.2147 82574.39478 1.203487033 0.93860211 1.068543608 1.202629383 0.975634406 1.228491798 1.039560702 1.114767053 1 16.33340687 5.07258163 19.3781286 1.078480357 4.391046329 0.164154342 0.092585693 448.4773816 123401.1735 0.020109525 1952.358262 118190.2442 -5.07258163 3.312565973 SEPDKADPFSFEGPEIVDCDGCTIDWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEPDKADPFSFEGPEIVDCDGCTIDWK 27 1 Q99733;Q99733-2;C9JZI7;E9PP22;H0YCI4 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 108.44 0.0015211 299570000 32074 28687 26291 24180 24006 22018 34616 38263 39721 FALSE TRUE 27835.33963 28498.55321 39005.41554 29670.43857 23528.32757 22865.04671 31258.94565 30080.75521 35025.22863 0.794722568 0.813657878 1.113637714 0.8471162 0.671753718 0.652816487 0.892469425 0.858831088 1 15.09610685 1.131014015 1.819158349 1.097747606 0.825937641 0.157242704 0.125768651 2.648426597 6.524719161 1.376237967 0.037354977 13.52116195 -1.131014015 -0.271809965 SEPHS(ph)PGIPEIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEPHSPGIPEIFR 13 0 Q9UJJ2;Q8ND82 Q9UJJ2 ZNF280C Zinc finger protein 280C 1 SEPHS(1)PGIPEIFR;SEPHS(1)PGIPEIFR 146.2 2.72E-05 145043000 153239 162083 108462 150505 204911 273090 129548 202520 134148 TRUE FALSE 132988.0779 161018.2661 160914.586 184679.4606 200833.672 283595.949 116984.4549 159212.674 118289.1763 1.12426244 1.361225694 1.360349197 1.561254093 1.697819516 2.397480124 0.98897007 1.345961474 1 16.85195854 SEPIS(ph)PPRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEPISPPRDR 10 1 Q02078-8;Q02078-7;Q02078-4;Q02078-6;Q02078-3;Q02078-5;Q02078-2;Q02078 Q02078-8 MEF2A Myocyte-specific enhancer factor 2A 1 S(0.009)EPIS(0.991)PPRDR 79.804 0.015691 234210000 434790 364560 250560 289550 382570 312260 382200 462640 458760 TRUE FALSE 377331.3999 362165.1814 371731.6541 355296.753 374957.6055 324272.8443 345134.3028 363708.0363 404525.9154 0.932774355 0.895283015 0.918931618 0.878304058 0.926906265 0.80161204 0.853182181 0.899096998 1 18.6258726 1.247926337 4.477836716 1.008711925 0.885568025 0.457256109 0.038452193 0.182100847 7.559352352 0.070246907 0.009892766 17.69808746 -1.247926337 -0.123143899 SEPRPPIS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SEPRPPISSPR 11 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 SEPRPPIS(0.5)S(0.5)PR;SEPRPPIS(0.5)S(0.5)PR;S(0.003)EPRPPIS(0.619)S(0.377)PR 105.99 0.0014483 2422690000 4357300 4275600 2679270 3299190 5006100 5720200 4562700 5495000 5205200 TRUE FALSE 3781471.765 4247513.302 3974973.934 4048321.514 4906488.404 5940259.795 4120210.056 4319937.012 4589847.186 0.823877487 0.925414971 0.866036226 0.882016623 1.068987312 1.294217336 0.897679136 0.941194083 1 22.13001469 3.249205073 23.98900317 1.029997739 0.877391853 0.370974925 0.106951028 169.0780557 381040.9801 0.033585759 0.04285516 1775.027447 -3.249205073 -0.152605885 SEPRPPISS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEPRPPISSPR 11 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 S(0.001)EPRPPIS(0.141)S(0.858)PR 76.01 0.022119 581320000 1209700 1150400 776790 784050 1221400 1478600 1135400 1388200 1403100 TRUE FALSE 1049835.08 1142842.947 1152448.242 962080.536 1197096.53 1535482.699 1025289.083 1091344.233 1237227.116 0.848538693 0.923713142 0.931476709 0.777610289 0.96756409 1.24106777 0.828699169 0.882088841 1 20.23867893 3.048987156 24.99917623 0.972915175 0.877773603 0.191558983 0.114294413 240.4337648 122696.7635 0.0364575 0.041338911 1119.404778 -3.048987156 -0.095141572 SEPTQALELTEDDIKEDGIVPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SEPTQALELTEDDIKEDGIVPLR 23 1 O43396;K7ER96 O43396 TXNL1 Thioredoxin-like protein 1 0 ; 159.98 1.78E-11 82114000 133302 87587 65903 75983 74093 68790 96491 111508 104241 FALSE TRUE 115685.803 87011.63523 97773.91123 93236.10148 72618.69426 71436.39581 87133.31767 87662.88196 91917.74773 1.258579609 0.94662497 1.063710912 1.014342755 0.790039966 0.777177396 0.947948789 0.953710074 1 16.48805583 8 0.801165456 0.914337883 83.66380911 0.566066097 0.08939205 424.2313088 1.465274786 0.033906222 63718.0776 100000000 -8 82.74947123 SEPVKEESSELEQPFAQDTSS(ph)VGPDR ddPTM_MDA-MB-175_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 SEPVKEESSELEQPFAQDT(0.009)S(0.057)S(0.934)VGPDR;SEPVKEESSELEQPFAQDT(0.001)S(0.029)S(0.971)VGPDR 224.78 1.18E-34 551640000 836000 700040 548980 591980 683250 623240 801900 914320 1028840 TRUE FALSE 725520.4818 695441.3911 814468.5642 726398.1068 669654.6618 647216.4461 724131.8614 718799.7832 907211.7073 0.799725661 0.766570124 0.897771223 0.800693048 0.738145966 0.713412802 0.798195014 0.792317579 1 19.79107973 1.237355514 6.424649064 1.006354664 0.78776991 0.65519584 0.048261195 0.082811853 15.4189177 0.078934831 0.012578843 17.27251244 -1.237355514 -0.218584754 SEPVKEESSELEQPFAQDTSSVGPDRK ddPTM_MDA-MB-175_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 0 103.86 0.0012706 166200000 156120 123410 79296 97734 131220 99456 164650 183610 84286 FALSE TRUE 135488.3464 122599.3116 117643.8108 119925.9985 128608.9787 103282.1367 148682.2683 144346.4304 74321.8051 1.822995906 1.649573923 1.582897653 1.613604491 1.730434003 1.389661305 2.000520145 1.942181439 1 16.18149792 4.73947765 19.6557975 1.653107774 1.822996856 0.035837105 0.28140413 17.71254964 378137.9918 0.067417003 0.392362012 54888.03075 -4.73947765 0.169889082 SEPVS(ph)PSR ddPTM_MDA-MB-175_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(0.979)PS(0.021)R;SEPVS(0.988)PS(0.012)R;SEPVS(0.898)PS(0.102)R;SEPVS(0.999)PS(0.001)R 180.27 0.00025172 4287150000 3223350 3254860 2340130 2757600 3011860 3441470 2899370 3306000 4532010 TRUE FALSE 2797376.131 3233478.61 3471824.695 3383755.227 2951929.879 3573865.578 2618189.544 2599037.627 3996240.941 0.70000187 0.809130045 0.868772616 0.846734538 0.738676652 0.894306833 0.655163085 0.650370602 1 21.93021214 2.238774917 24.99999791 0.739175776 0.810735513 0.006979671 0.111594101 15.28503914 1783452.569 0.042848006 0.031075062 173.2905649 -2.238774917 0.071559737 SEPVS(ph)PSRER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SEPVSPSRER 10 1 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 SEPVS(0.582)PS(0.418)RER;SEPVS(1)PSRER;SEPVS(0.991)PS(0.009)RER 116.71 0.00063815 997490000 693061 718400 349540 414282 634628 683870 709351 772089 179237 TRUE FALSE 601471.2329 713680.7831 518578.7131 508351.06 622000.1444 710178.9214 640558.2492 606983.7758 158047.806 3.805628486 4.515600697 3.281150976 3.216438575 3.935519005 4.493443719 4.052939836 3.840507445 1 17.27000148 1.238632178 7.083632668 0.940832149 3.901274781 0.821666802 0.423601417 0.045854694 13.75341637 0.652809769 0.109660532 17.32336187 -1.238632178 2.960442632 SEPVSPS(ph)RER ddPTM_MDA-MB-175_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 SEPVS(0.11)PS(0.89)RER 101.39 0.0088541 438580000 501030 514440 234600 283260 451420 501410 464070 536020 117930 TRUE FALSE 434817.6161 511060.6098 348053.3447 347578.5124 442437.6252 520699.5672 419064.5628 421396.2943 103988.4497 4.181403003 4.91459014 3.347038498 3.342472296 4.25468046 5.007282717 4.029914513 4.052337498 1 16.66606377 4.238412002 24.99999997 3.710047453 4.54799661 0.11762606 1.058245354 9.168264477 1543507.82 0.266813979 0.618705787 17314.58161 -4.238412002 0.837949157 SERGS(ph)LKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SERGSLKR 8 2 A0A0C4DGT3;A0A3B3IU98;Q6DN90-2;A0A3B3IRZ4;Q6DN90-3;A0A2R8Y7T6;Q6DN90;A0A2R8Y695 A0A0C4DGT3;A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 SERGS(1)LKR 65.879 0.049718 353820000 205150 161750 95182 136050 134870 95673 277280 216210 137010 TRUE FALSE 178038.9077 160687.4536 141212.3336 166942.2319 132186.3509 99353.60222 250389.4283 169975.174 120812.8339 1.473675453 1.330052847 1.168852092 1.381825312 1.094141629 0.822376225 2.07253998 1.406929782 1 16.88241419 2.26441374 24.99999942 1.49933491 1.217620375 0.154365084 0.310098743 411.8586248 398266.5013 0.115612886 0.089521979 183.8288794 -2.26441374 -0.281714535 SERPPTILMTEEPSS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SERPPTILMTEEPSSPK 17 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SERPPTILMTEEPS(0.037)S(0.963)PK;SERPPTILMTEEPS(0.048)S(0.952)PK;SERPPTILMTEEPS(0.042)S(0.958)PK;SERPPTILMTEEPS(0.085)S(0.915)PK 141.08 3.86E-07 1027450000 669170 701695 661349 714425 1000600 809320 1002990 1126840 1502890 TRUE FALSE 580737.489 697085.5193 981179.5885 876646.1156 980690.0176 840455.0641 905720.1842 885874.0351 1325220.056 0.438219665 0.526014918 0.740389933 0.661509846 0.740020507 0.634200381 0.683448896 0.668473157 1 20.33780051 5.173641244 0.787048917 0.731712032 1.84E-12 0.49424575 0.10449713 4.204819117 1.253956286 0.0381849 3.151905742 149156.1773 -5.173641244 -0.731712032 SES(ph)ELIDELSEDFDR ddPTM_MDA-MB-175_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(0.013)ES(0.987)ELIDELSEDFDR;S(0.001)ES(0.999)ELIDELSEDFDR;S(0.139)ES(0.861)ELIDELSEDFDR;SES(1)ELIDELSEDFDR;SES(1)ELIDELSEDFDR 341.29 2.06E-69 341993000 134624 163517 168655 197531 225687 248621 245943 266976 385646 TRUE FALSE 116833.0973 162442.8461 250217.1221 242383.4326 221196.2702 258185.6107 222091.4857 209885.26 340055.3692 0.343570806 0.477695284 0.735812885 0.712776373 0.650471336 0.7592458 0.653103894 0.617209075 1 18.37541015 4.382913171 3.165112613 0.71611596 0.36036125 0.619119088 0.106756539 0.162284773 3.097690854 0.02660469 0.094095812 24149.77956 -4.382913171 -0.355754711 SES(ph)ELIDELSEDFDRSECK ddPTM_MDA-MB-175_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 S(0.014)ES(0.986)ELIDELSEDFDRSECK;S(0.144)ES(0.856)ELIDELSEDFDRSECK 161.8 1.75E-11 99506000 102818 114271 86701 84768 121307 112738 218293 200174 56372.6 TRUE FALSE 89230.34079 113520.3463 128629.8936 104015.87 118893.228 117075.1038 197122.9785 157368.3479 49708.29545 1.795079473 2.283730417 2.587694719 2.092525384 2.391818648 2.355242777 3.965595213 3.165836737 1 15.60119901 2.447127657 24.99802261 2.900894577 2.258176974 0.058552317 0.759105962 414.9459134 345832.2705 0.282005913 0.218443151 279.9804177 -2.447127657 -0.642717603 SES(ph)FSSEDLIPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SESFSSEDLIPSR 13 0 Q9P219;Q9P219-2;A0A0A0MR69;Q9P219-3 Q9P219 CCDC88C Protein Daple 1 S(0.158)ES(0.837)FS(0.002)S(0.003)EDLIPSR 96.464 0.0044321 72706000 115600 109240 69095 102200 157490 122600 123330 156650 137500 TRUE FALSE 100323.1671 108522.3952 102509.5731 125406.072 154356.2571 127316.5013 111369.4756 123151.6166 121244.9066 0.827442322 0.895067663 0.845475294 1.034320332 1.273094775 1.050077111 0.918549724 1.015726103 1 16.88756462 3.722704332 8.267950967 1.046654111 0.859786216 0.50234565 0.090349514 0.18497949 81.16304796 0.026908124 0.041424948 5280.856082 -3.722704332 -0.186867895 SES(ph)LDPDSSMDTTLILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SESLDPDSSMDTTLILK 17 0 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 S(0.014)ES(0.986)LDPDSSMDTTLILK;S(0.001)ES(0.996)LDPDS(0.003)SMDTTLILK 297.72 3.46E-46 153025000 685230 359420 232150 310470 379170 224120 643150 571230 469020 TRUE FALSE 594675.1193 357058.9464 344418.5165 380966.9587 371625.2588 232742.0414 580777.412 449076.9098 413572.9899 1.437896415 0.863351706 0.832787742 0.921160153 0.898572363 0.562759288 1.404292413 1.085846805 1 18.65778244 2.223127964 24.99989755 1.157264929 0.912066043 0.192246765 0.235299215 391.6153298 634386.4935 0.093441978 0.063253022 167.1583071 -2.223127964 -0.245198885 SES(ph)LELPQAAPPQIYHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SESLELPQAAPPQIYHEK 18 0 H0YGT9;Q15040;B0QY58;B0QY55;B0QY57;B0QY56 H0YGT9 JOSD1 Josephin-1 1 S(0.157)ES(0.843)LELPQAAPPQIYHEK;S(0.15)ES(0.85)LELPQAAPPQIYHEK 126.04 1.83E-05 382830000 509070 381360 292480 319480 365910 340060 397150 459700 528860 TRUE FALSE 441795.1097 378854.821 433924.3063 392022.8169 358629.1069 353142.3282 358634.4541 361396.7324 466338.7733 0.947369455 0.812402577 0.930491589 0.840639551 0.769031287 0.757265637 0.769042753 0.774966083 1 18.83101886 3.490672057 7.489972712 0.803029183 0.888062206 0.179031121 0.078198172 0.250314797 82.14518734 0.021490063 0.030085026 3095.08127 -3.490672057 0.085033023 SES(ph)LESPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SESLESPR 8 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;Q5VY93 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 SES(0.683)LES(0.317)PR 158.08 0.00038505 223470000 354980 344670 209730 322620 349410 304830 377000 397970 420050 TRUE FALSE 308068.4936 342405.8401 311156.1295 395875.8019 342457.4246 316557.0074 340438.598 312867.2125 370392.1675 0.831735983 0.924441363 0.840072109 1.068801764 0.924580633 0.854653622 0.919130122 0.844691762 1 18.49869407 5.553452649 1.485896716 0.917549208 0.26336212 0.132988214 0.07086529 27.29636131 8.846486654 0.019193643 47.04268082 357645.4048 -5.553452649 -0.654187088 SES(ph)LKGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SESLKGR 7 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 SES(1)LKGR;SES(1)LKGR 154.56 0.0010118 1120440000 1675540 1548980 1136720 1221240 1265920 1365280 2028790 2230820 1638060 TRUE FALSE 1454113.144 1538804.648 1686441.594 1498541.207 1240730.669 1417803.205 1832038.258 1753776.503 1444410.413 1.006717433 1.065351395 1.167563996 1.037476048 0.858987624 0.981579191 1.268364062 1.21418157 1 20.4620493 2.250620063 24.99996071 1.176439414 1.021927539 0.296725462 0.101517179 262.5960557 544377.5016 0.040421527 0.031067174 178.0820158 -2.250620063 -0.154511876 SES(ph)LSNCSIGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SESLSNCSIGK 11 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 SES(0.994)LS(0.005)NCSIGK;SES(1)LSNCSIGK;SES(1)LSNCSIGK;SES(0.958)LS(0.042)NCSIGK;SES(0.96)LS(0.04)NCSIGK;SES(0.991)LS(0.009)NCSIGK 276.78 3.55E-27 3856880000 4980360 4040240 3055750 3324350 3806870 3217380 4584870 4990870 6290200 TRUE FALSE 4322192.807 4013699.397 4533520.921 4079194.477 3731120.735 3341154.691 4140230.013 3923611.289 5546579.722 0.779253707 0.723635033 0.817354324 0.735443225 0.672688562 0.602381081 0.7464474 0.707392932 1 22.40316698 1.236807137 24.99946354 1.000000347 0.721439095 0.693502086 0.057847828 27.65057021 394097.8007 0.092373491 0.014807674 17.25071648 -1.236807137 -0.278561252 SES(ph)PIPVAEQGTLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SESPIPVAEQGTLMR 15 0 P86452 P86452 ZBED6 Zinc finger BED domain-containing protein 6 1 SES(1)PIPVAEQGTLMR;SES(1)PIPVAEQGTLMR;SES(1)PIPVAEQGTLMR 233.14 1.33E-17 414780000 628570 425375 224015 307932 450433 394915 390094 474780 394885 TRUE FALSE 545502.8819 422580.6836 332349.4033 377852.667 441470.2646 410107.6356 352262.7439 373251.9917 348202.1452 1.566627 1.213607353 0.95447259 1.085153186 1.267856246 1.177786069 1.011661613 1.071940529 1 18.40956557 4.677058988 3.214424193 1.086658217 1.605193606 0.738526864 0.090586878 0.152891691 2.56414429 0.023838197 0.180514353 47539.97932 -4.677058988 0.518535389 SES(ph)PKEPEQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 SESPKEPEQLR 11 1 F8W6I7;P09651-2;P09651;P09651-3;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 SES(1)PKEPEQLR;S(0.004)ES(0.996)PKEPEQLR;S(0.001)ES(0.999)PKEPEQLR;S(0.001)ES(0.999)PKEPEQLR;S(0.037)ES(0.963)PKEPEQLR;S(0.001)ES(0.999)PKEPEQLR;S(0.001)ES(0.999)PKEPEQLR;S(0.003)ES(0.997)PKEPEQLR;S(0.006)ES(0.994)PKEPEQLR;S(0.003)ES(0.997)PKEPEQLR;SES(1)PKEPEQLR 200.79 1.20E-07 46301910000 43841190 34469710 28948990 29718790 39745210 30197730 42995630 47319460 55050290 TRUE FALSE 38047465.66 34243276.21 42948818.39 36466895.49 38954358.08 31359456.21 38825920.42 37200561.72 48542307.43 0.783800105 0.705431571 0.884770846 0.751239433 0.802482621 0.646023188 0.79983673 0.766353387 1 25.53273935 1.2383935 24.95429806 1.000000248 0.767470188 0.577454094 0.062505487 2.732472951 406765.5527 0.080658313 0.014351159 17.31384398 -1.2383935 -0.23253006 SES(ph)PKEPEQLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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(0.177)ES(0.823)PKEPEQLRK;S(0.092)ES(0.908)PKEPEQLRK;S(0.008)ES(0.992)PKEPEQLRK;S(0.001)ES(0.999)PKEPEQLRK;S(0.001)ES(0.999)PKEPEQLRK;S(0.002)ES(0.998)PKEPEQLRK;S(0.002)ES(0.998)PKEPEQLRK;S(0.005)ES(0.995)PKEPEQLRK;S(0.28)ES(0.72)PKEPEQLRK;S(0.202)ES(0.798)PKEPEQLRK 144.18 4.95E-05 23000290000 7559080 5071910 4530570 4225340 5349160 3665760 7452930 7998300 4252390 TRUE FALSE 6560128.426 5038592.289 6721568.806 5184768.027 5242722.181 3806784.159 6730145.996 6287925.788 3749677.299 1.749518133 1.343740244 1.792572606 1.382723796 1.398179567 1.015229807 1.794860053 1.676924516 1 21.83833501 7.999990596 0.731786071 1.43876372 42.12896294 0.106291827 0.279432443 1058.506725 4.949607371 0.107648131 70814.38245 99997834.72 -7.999990596 40.69019922 SES(ph)PPAELPSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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;SES(1)PPAELPSLR 304.26 8.80E-37 1482630000 2574420 2265620 1509740 2067720 2489360 2189830 2171290 2515180 2813090 TRUE FALSE 2234203.874 2250736.993 2239855.314 2537227.429 2439826.606 2274074.177 1960718.63 1977328.33 2480529.705 0.900696279 0.907361435 0.902974598 1.022857104 0.983590965 0.916769581 0.790443519 0.797139549 1 21.2422168 2.420298566 7.389623622 0.846353866 0.944309221 0.215643198 0.068193388 0.284512184 30.94620884 0.026175972 0.020253462 263.2076854 -2.420298566 0.097955354 SES(ph)PPPLSDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SESPPPLSDPK 11 0 Q15059;Q15059-2 Q15059 BRD3 Bromodomain-containing protein 3 1 SES(1)PPPLSDPK;SES(1)PPPLSDPK;SES(1)PPPLSDPK;SES(0.999)PPPLS(0.001)DPK;SES(1)PPPLSDPK;SES(1)PPPLSDPK 232.39 3.81E-13 7930320000 4903990 4070700 2837660 3295030 3995700 3002080 4755270 5477840 4779290 TRUE FALSE 4255915.296 4043959.304 4209961.867 4043216.923 3916193.387 3117571.96 4294104.647 4306446.545 4214287.781 1.009877711 0.959583093 0.998973513 0.959406935 0.929265772 0.739762475 1.018939586 1.021868171 1 22.0068574 SES(ph)VEGFLSPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SESVEGFLSPSR 12 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 S(0.293)ES(0.707)VEGFLSPSR 107.99 0.0018397 51477000 57948 45094 25464 28924 50902 44897 54496 47373 49312 TRUE FALSE 50290.02498 44797.77454 37778.47557 35491.63628 49889.14979 46624.21664 49210.98631 37242.65261 43482.39154 1.156560695 1.030250935 0.868822395 0.816230088 1.147341442 1.072255113 1.131745163 0.856499638 1 15.40814367 2.535931352 0.009547036 1.50E-07 1.992470662 0.012855107 0.124173587 27308.77925 222.5220037 23453.98553 22980.4397 343.503647 -2.535931352 1.992470512 SES(ph)WER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SESWER 6 0 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 1 SES(1)WER;SES(1)WER;SES(1)WER 137.9 0.013148 1411350000 1381850 1225760 803840 1020460 1231430 1174870 1437550 1452810 1395230 TRUE FALSE 1199235.021 1217707.902 1192579.713 1252171.04 1206926.952 1220068.009 1298136.622 1142137.887 1230287.499 0.974759983 0.989775075 0.969350427 1.017787339 0.981012124 0.991693413 1.055148998 0.928350396 1 20.23056406 SESAPTLHPYSPLS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SESAPTLHPYSPLSPK 16 0 Q8WUF5;K7EN03 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 SESAPTLHPYSPLS(1)PK;SESAPTLHPYSPLS(1)PK;SESAPTLHPYSPLS(1)PK;SESAPTLHPYSPLS(1)PK 256.67 7.74E-27 4265080000 3116870 3819150 2347100 3525000 6045230 4235510 5945370 7669140 5998300 TRUE FALSE 2704967.732 3794061.752 3482165.411 4325405.126 5924941.75 4398452.81 5368788.932 6029154.092 5289187.807 0.511414575 0.717324075 0.658355411 0.817782481 1.120198784 0.831593237 1.015049782 1.139901685 1 22.33461477 3.946159677 0.596901255 1.074735828 0.426694329 0.761755074 0.099532261 0.806850975 0.45126504 0.071578213 0.336787315 8834.04641 -3.946159677 -0.648041499 SESELIDELS(ph)EDFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SESELIDELSEDFDR 15 0 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;D6RC54;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 1 SESELIDELS(1)EDFDR 182.1 1.55E-11 0 14876 12682 4789.7 10193 11421 12027 14247 14713 19312 TRUE FALSE 12910.09891 12598.69111 7106.014941 12507.47644 11193.74444 12489.68647 12865.32813 11566.73945 17028.95736 0.75812621 0.739839254 0.417290078 0.734482809 0.657335867 0.73343812 0.755497114 0.679239439 1 14.05570248 0.035489044 1.496392476 9.999997267 0.674950505 0.480418477 0.101688889 34.40124358 3.20591688 1005.917186 0.028678414 1.085148173 -0.035489044 -9.325046762 SESELIDELS(ph)EDFDRSECK ddPTM_MDA-MB-175_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 167.73 1.05E-11 98613000 189257 199058 107275 123474 167004 129482 196198 244630 130452 TRUE FALSE 164246.2079 197750.3749 159153.5488 151510.6589 163680.9471 134463.2563 177170.7482 192317.7782 115030.1132 1.427854006 1.71911832 1.383581607 1.317139093 1.422939982 1.168939616 1.540211891 1.671890715 1 16.81165206 4.203745334 24.79578464 1.389756037 1.573486237 0.156406247 0.197691285 299.9757904 213645.4844 0.05111371 0.106409436 15986.20339 -4.203745334 0.1837302 SESELIDELSEDFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SESELIDELSEDFDR 15 0 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;D6RC54;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ;;;;;;; 422.72 8.40E-153 4030783000 2702117 2990036 2212919 2838911 3000701 2934280 2872886 3466155 5194868 FALSE TRUE 2345025.392 2970394.257 3283094.03 3483529.133 2940992.921 3047163.65 2594273.958 2724944.727 4580736.623 0.511931941 0.648453404 0.716717485 0.76047357 0.642034931 0.665212585 0.566344274 0.594870422 1 22.12714818 1.234137642 24.99924603 1.000000534 0.640400922 0.721047202 0.070700078 78.24252203 442179.8594 0.141625932 0.018372203 17.14500604 -1.234137642 -0.359599612 SESELIDELSEDFDRSECK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 348.64 1.00E-90 983490000 629047 624012 307725 357958 564189 434949 671871 797024 249394 FALSE TRUE 545916.8451 619912.8241 456541.8393 439237.8349 552962.7427 451681.7695 606713.0538 626586.62 219910.9254 2.482445309 2.818926904 2.076030731 1.997344307 2.514485088 2.053930557 2.758903645 2.849274627 1 17.74655976 4.240972586 24.99994288 2.270614601 2.650686116 0.10448805 0.523164478 163.170038 1691151.221 0.130959373 0.314472469 17416.9693 -4.240972586 0.380071515 SESGGLGVSMVEYVLS(ph)SSPADKLDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SESGGLGVSMVEYVLSSSPADKLDSR 26 1 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;C9JW01 Q8TB72-3 PUM2 Pumilio homolog 2 1 SESGGLGVSMVEYVLS(0.322)S(0.322)S(0.322)PADKLDS(0.033)R 58.015 0.046921 46996000 35873 26084 15470 26967 29879 23937 43275 48651 29601 TRUE FALSE 31132.29216 25912.65249 22951.34374 33090.26951 29284.46636 24857.87188 39078.19716 38247.36225 26101.6035 1.192734851 0.992760942 0.879307807 1.267748532 1.121941277 0.952350375 1.497156953 1.465326153 1 14.67185082 2.241415748 24.9999998 1.358278604 1.067376809 0.312741408 0.173883549 76.38995767 668891.7292 0.066723957 0.049356591 174.3475093 -2.241415748 -0.290901795 SESGGLGVSMVEYVLSS(ph)SPADKLDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SESGGLGVSMVEYVLSSSPADKLDSR 26 1 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;C9JW01 Q8TB72-3 PUM2 Pumilio homolog 2 1 SESGGLGVSMVEYVLS(0.018)S(0.541)S(0.44)PADKLDSR 76.611 0.013893 50501000 79521 64755 49392 65442 82511 79440 94061 108620 66643 TRUE FALSE 69012.09837 64329.62014 73278.13641 80301.60632 80869.19253 82496.1082 84938.9787 85392.45828 58764.54046 1.174383358 1.094701322 1.246978804 1.366497648 1.376156299 1.403841629 1.445412115 1.453129006 1 15.84265825 3.967139217 3.037597495 1.362985018 1.135326064 0.288163045 0.130158121 0.28051544 5.204528733 0.034841773 0.07434737 9271.269753 -3.967139217 -0.227658954 SESGGLGVSMVEYVLSS(ph)SPGDSCLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SESGGLGVSMVEYVLSSSPGDSCLR 25 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2 Q5T1Z4 PUM1 Pumilio homolog 1 1 SESGGLGVSMVEYVLS(0.013)S(0.558)S(0.428)PGDS(0.001)CLR 89.365 1.33E-05 0 23700 21377 13324 10814 21178 26520 15750 23843 22834 TRUE FALSE 20567.98495 21236.57308 19767.53097 13269.48398 20756.59923 27540.24156 14222.56742 18744.36 20134.59053 1.021524869 1.054730815 0.981769703 0.659039177 1.030892543 1.367807382 0.706374803 0.930953126 1 14.29738851 SESGGLGVSMVEYVLSSS(ph)PGDSCLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SESGGLGVSMVEYVLSSSPGDSCLR 25 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2 Q5T1Z4 PUM1 Pumilio homolog 1 1 SESGGLGVSMVEYVLS(0.002)S(0.2)S(0.795)PGDS(0.002)CLR;SESGGLGVSMVEYVLSS(0.171)S(0.828)PGDSCLR;SESGGLGVSMVEYVLS(0.003)S(0.135)S(0.861)PGDS(0.001)CLR 153.83 6.04E-08 66945000 118800 116208 76813 84840 123746 128890 120134 141122 121596 TRUE FALSE 103100.279 115444.622 113960.0237 104104.2187 121283.6967 133848.4817 108483.4232 110944.1585 107221.0594 0.961567434 1.07669727 1.062851126 0.970930704 1.131155553 1.248341347 1.011773469 1.034723581 1 16.71022877 4.742141548 23.69687995 1.066473971 0.961567354 0.152579307 0.078120013 357.7639202 2367286.24 0.019827512 0.139290727 55225.74051 -4.742141548 -0.104906618 SESIRPDEFSLEIFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SESIRPDEFSLEIFER 16 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 0 200.69 3.18E-11 70524000 78351 74805 41292 59123 73693 78003 70905 81248 70721 FALSE TRUE 67996.71683 74313.60103 61260.94931 72547.78079 72226.65348 81003.82588 64028.64401 63873.74747 62360.44395 1.09038218 1.191678512 0.982368717 1.16336216 1.158212625 1.298961662 1.026750933 1.024267042 1 15.92834358 2.043971565 24.99979929 1.017358891 1.14484311 0.377711065 0.079008267 138.1779547 78559.77145 0.03217397 0.021691668 110.6551331 -2.043971565 0.127484218 SESPKEPEQLR ddPTM_MDA-MB-175_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 ;;;;;;; 167.44 1.75E-05 14607420000 8158450 6782010 4205390 5188790 6381960 5340750 7643740 8903850 6444200 FALSE TRUE 7080290.162 6737458.53 6239130.67 6366984.075 6254971.482 5546212.108 6902451.271 6999830.967 5682374.017 1.246009175 1.18567671 1.097979586 1.120479584 1.100767296 0.976037848 1.214712592 1.231849742 1 22.43806236 4.472392626 3.220317205 1.118842277 1.241287263 0.250449197 0.0799141 0.417377932 8.464123301 0.02171096 0.092298016 29675.12975 -4.472392626 0.122444985 SESPKEPEQLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 146.67 3.65E-05 6376320000 6268020 4687530 3033030 3329010 4395610 3257770 6359490 7323220 2205800 FALSE TRUE 5439685.276 4656737.307 4499813.453 4084912.601 4308145.961 3383098.52 5742747.639 5757206.392 1945032.837 2.796706139 2.394168992 2.31348971 2.100176678 2.214947676 1.739352907 2.952519634 2.959953315 1 20.89136308 4.759166574 2.200478873 2.276017805 2.949793151 0.090235659 0.565427126 2.087358719 11.09004741 0.148784703 2.807745577 57433.67078 -4.759166574 0.673775346 SESSEKPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SESSEKPAR 9 1 A0A087WVI0;E9PBL8;Q8WTW3 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 0 82.645 0.016294 51006000 149920 118250 77005 89961 94494 110940 141110 170470 133640 FALSE TRUE 130107.6922 117473.208 114244.8756 110388.02 92613.75427 115207.9336 127425.1739 134016.3171 117841.2314 1.104093114 0.996876955 0.969481345 0.936752091 0.785919776 0.97765385 1.08132928 1.137261682 1 16.84648489 -0.771652992 10.62161267 1.587223178 1.002772724 0 0.098708257 0 0 0 0.025069576 0.169179216 0.771652992 -0.584450454 SESVVSGLDS(ph)PAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SESVVSGLDSPAK 13 0 O14578-4;H7BYJ3;O14578;O14578-2 O14578-4 CIT Citron Rho-interacting kinase 1 SESVVSGLDS(1)PAK;SESVVSGLDS(1)PAK 264.08 3.40E-24 495120000 1184800 1037860 705730 833850 1057720 864590 1177000 1382370 1305390 TRUE FALSE 1028225.678 1031042.229 1047023.389 1023188.387 1036673.441 897851.3368 1062854.721 1086760.933 1151068.281 0.893279482 0.895726384 0.909610147 0.888903294 0.900618546 0.780015705 0.923363747 0.944132464 1 20.13454199 1.619529512 2.229003973 0.993692455 0.881315811 0.511899652 0.038285925 0.249975438 2.555858017 0.046347797 0.010715397 41.64180176 -1.619529512 -0.112376644 SESWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SESWER 6 0 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ; 130.05 0.037058 2875800000 2718300 2666500 1582010 1916910 2378700 2544600 2459900 2930700 2855400 FALSE TRUE 2359069.768 2648983.586 2347075.328 2352173.714 2331368.524 2642492.409 2221339.277 2303992.612 2517837.865 0.936942684 1.052086643 0.932178899 0.934203805 0.925940688 1.049508567 0.882240794 0.915067902 1 21.26375395 4.186475132 24.99997359 0.94421803 0.994516396 0.108486486 0.053848565 172.9461748 83010.1747 0.013348546 0.027787268 15362.96821 -4.186475132 0.050298366 SETEDSILHQLFIVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SETEDSILHQLFIVR 15 0 Q9UKG1 Q9UKG1 APPL1 DCC-interacting protein 13-alpha 0 ; 229.32 4.78E-13 241680000 599910 628480 312130 440560 577260 604840 619400 734260 645660 FALSE TRUE 520630.3735 624351.4735 463077.112 540595.8815 565773.6554 628108.5862 559330.6833 577244.213 569330.8103 0.914460212 1.096640937 0.813370897 0.94952859 0.993752042 1.103240111 0.982435296 1.013899481 1 19.11890765 3.128132514 4.312692203 1.021768255 0.945318902 0.207698077 0.074636251 0.364971207 11.99989684 0.022404899 0.025822527 1343.174736 -3.128132514 -0.076449353 SETELKDTYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SETELKDTYAR 11 1 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 107.37 0.002012 1357260000 3035300 2677900 1602590 2009620 2538500 2150400 2977900 3554400 1691570 FALSE TRUE 2634177.415 2660308.699 2377607.884 2465934.936 2487988.816 2233127.279 2689103.716 2794319.22 1491594.522 1.766014407 1.783533433 1.594004168 1.653220698 1.668006137 1.497140977 1.80283829 1.873377235 1 20.50842397 1.230228997 24.99849308 0.999998688 1.70701984 0.804281885 0.109254495 149.0876813 447292.4635 0.325473508 0.029241113 16.99139347 -1.230228997 0.707021152 SETITADVNHNLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SETITADVNHNLK 13 0 Q16222;Q16222-3 Q16222 UAP1 UDP-N-acetylhexosamine pyrophosphorylase;UDP-N-acetylgalactosamine pyrophosphorylase;UDP-N-acetylglucosamine pyrophosphorylase 0 128.68 0.00016255 264470000 129750 125690 69533 100710 114860 117780 125330 158330 130090 FALSE TRUE 112603.2088 124864.3341 103159.3914 123577.7448 112574.5107 122311.0728 113175.5159 124472.3616 114710.9084 0.981625988 1.088513166 0.899298879 1.077297238 0.981375811 1.066254941 0.986615113 1.08509612 1 16.80764306 2.920723151 1.28359382 1.038102266 1.005794982 0.033852196 0.059861158 1.492587626 5.207154072 0.025782611 0.025731056 833.1499079 -2.920723151 -0.032307285 SETSWES(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SETSWESPK 9 0 E5RJU9;Q86UE4 E5RJU9 MTDH Protein LYRIC 1 SETSWES(1)PK;SETSWES(1)PK 168.3 6.22E-05 162610000 658560 542260 417050 513760 741190 638730 563100 888720 765940 TRUE FALSE 571529.6274 538697.8584 618736.7749 630417.0603 726441.7691 663302.3564 508490.6487 698674.144 675391.4458 0.84621982 0.797608353 0.9161158 0.933409898 1.075586275 0.982100618 0.752882868 1.034472895 1 19.36536438 4.046946379 2.857254747 0.96224761 0.821423415 0.308619829 0.085757588 0.328360108 5.414646937 0.023641121 0.056313643 11141.56963 -4.046946379 -0.140824195 SEVELAAALSDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SEVELAAALSDKR 13 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ;;; 182.33 1.81E-05 754750000 839960 738820 488679 643070 757150 749330 785390 1062550 835980 FALSE TRUE 728957.1578 733966.6428 725005.7989 789088.8722 742084.1963 778157.21 709222.9987 835331.9513 737151.3968 0.988883913 0.995679647 0.983523605 1.070456999 1.006691705 1.055627397 0.962113077 1.133189132 1 19.49160143 5.191973993 0.258675496 1.067706727 0.89017361 0.118880141 0.047880022 34.08599988 2.123398785 0.200564385 2.071148541 155587.2458 -5.191973993 -0.177533117 SEVQQPVHPKPLS(ph)PDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 SEVQQPVHPKPLSPDSR 17 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 SEVQQPVHPKPLS(0.999)PDS(0.001)R;SEVQQPVHPKPLS(0.996)PDS(0.004)R;SEVQQPVHPKPLS(1)PDSR;SEVQQPVHPKPLS(1)PDSR;SEVQQPVHPKPLS(1)PDSR;SEVQQPVHPKPLS(0.992)PDS(0.008)R;SEVQQPVHPKPLS(1)PDSR;SEVQQPVHPKPLS(0.998)PDS(0.002)R;SEVQQPVHPKPLS(0.979)PDS(0.02)R;SEVQQPVHPKPLS(1)PDSR 218.95 2.72E-15 25276810000 12052480 11055550 7315123 9093471 12874360 10864090 13498630 15955330 12659537 TRUE FALSE 10459714.23 10982925.36 10852740.95 11158282.58 12618185.42 11282038.57 12189534.94 12543406.84 11162940.96 0.937003454 0.98387382 0.972211623 0.999582692 1.130363895 1.010669018 1.091964473 1.123665071 1 23.41221383 3.412759049 5.985240759 1.076186188 0.969242735 0.567750298 0.043252797 0.13823336 9.365052963 0.012240569 0.015936013 2586.777348 -3.412759049 -0.106943453 SEVQQPVHPKPLSPDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 131.51 1.61E-05 854610000 1136950 900840 512790 607850 876080 817390 1048010 1067650 645070 FALSE TRUE 986699.1768 894922.3227 760776.9592 745871.6329 858647.722 848835.5222 946374.1515 839341.356 568810.5595 1.734670991 1.573322274 1.337487405 1.311283028 1.509549546 1.492299164 1.663777396 1.475607901 1 19.11758872 1.242740184 5.747066643 0.979732332 1.508865281 0.61280196 0.128210734 0.09923237 11.23432569 0.206026667 0.033494913 17.48800158 -1.242740184 0.529132948 SEWLDPS(ph)QKSPLHVGETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEWLDPSQKSPLHVGETR 18 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 SEWLDPS(0.669)QKS(0.331)PLHVGETR 72.771 0.012906 510560000 192840 159840 102560 150190 167200 120440 202800 210220 186650 TRUE FALSE 167355.7054 158790.0005 152158.359 184292.935 163873.0471 125073.4047 183132.4872 165266.0889 164584.4496 1.016837896 0.964793459 0.924500215 1.119746947 0.995677584 0.75993452 1.112696173 1.004141578 1 17.32846851 SEWLDPSQKS(ph)PLHVGETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SEWLDPSQKSPLHVGETR 18 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 SEWLDPS(0.004)QKS(0.996)PLHVGETR;SEWLDPS(0.022)QKS(0.977)PLHVGET(0.001)R;SEWLDPS(0.001)QKS(0.999)PLHVGETR 160.69 2.42E-11 1523530000 763030 599820 428650 500670 661520 594320 751830 842820 624520 TRUE FALSE 662193.6522 595879.7429 635946.5737 614354.7758 648357.0462 617183.875 678917.6423 662589.5018 550689.9571 1.202479987 1.082060305 1.154817816 1.115609188 1.177354041 1.12074656 1.232849144 1.203198811 1 19.07088077 3.235703711 24.99147891 1.159023146 1.135841431 0 0.06879422 371.0171048 3245595.399 0.020126272 0.023844569 1720.694265 -3.235703711 -0.023181715 SEWMNHINK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEWMNHINK 9 0 Q9H8W4 Q9H8W4 PLEKHF2 Pleckstrin homology domain-containing family F member 2 0 75.294 0.038668 467990000 307990 284440 174210 193510 270980 266260 292270 346650 348770 FALSE TRUE 267288.3412 282571.4949 258458.5387 237449.4031 265588.0282 276503.1945 263925.7004 272521.5951 307538.8079 0.869120691 0.918815732 0.840409509 0.772095739 0.863591915 0.899083912 0.858186653 0.886137255 1 18.23040895 1.10605522 2.038184465 1.086969761 0.859366751 0.563816535 0.038361979 0.931815204 2.792995491 0.455430038 0.011044742 12.76601117 -1.10605522 -0.22760301 SEWNTVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SEWNTVER 8 0 B5MCF9;O00541-2;O00541 B5MCF9 PES1 Pescadillo homolog 0 114.39 0.0062028 107890000 101950 102900 49944 77917 99897 95279 103620 114780 122170 FALSE TRUE 88477.04919 102224.0431 74097.08545 95609.24574 97909.24515 98944.44478 93570.94835 90235.19022 107727.2018 0.821306483 0.948915793 0.687821499 0.88751257 0.90886279 0.918472244 0.868591654 0.83762679 1 16.71702306 3.511825139 24.98293556 0.896021078 0.824865102 0.217035206 0.074405073 1071.819115 771587.5959 0.019764337 0.029297452 3249.564334 -3.511825139 -0.071155975 SFAFLHCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFAFLHCK 8 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 0 81.296 0.023227 359260000 371410 453930 245230 336180 491160 438330 456760 562810 508130 FALSE TRUE 322327.2275 450948.1039 363824.0482 412514.8072 481386.8769 455192.8387 412463.4855 442457.4613 448059.4503 0.719384955 1.006447032 0.811999497 0.920669806 1.074381707 1.015920629 0.920555264 0.987497219 1 18.77333064 3.473008944 24.03995419 0.993436958 0.862717554 0.437209805 0.079037531 71.76903906 419546.1234 0.021313404 0.027650331 2971.727233 -3.473008944 -0.130719405 SFAGAVSPQEEEEFRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SFAGAVSPQEEEEFRR 16 1 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ;;; 232.78 1.57E-16 1724920000 903360 894940 453872 635540 872600 922730 786330 945960 723000 FALSE TRUE 783978.6872 889061.0802 673366.0173 779849.0706 855236.9672 958228.0202 710071.8376 743673.8155 637527.7636 1.229716935 1.394544882 1.05621442 1.223239387 1.341489761 1.503037318 1.11378967 1.16649636 1 19.28212865 1.620138129 1.790511879 1.016934734 1.279836431 0.324515597 0.126896217 0.51540549 2.997519052 0.198347575 0.037331137 41.70019915 -1.620138129 0.262901696 SFATASHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFATASHR 8 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ; 136.8 0.00077559 592590000 1270880 1324580 756830 950400 990520 1330160 1178910 1363490 1240250 FALSE TRUE 1102929.988 1315878.747 1122835.519 1166202.846 970810.5899 1381332.116 1064579.49 1071918.274 1093629.058 1.008504648 1.203222187 1.026706004 1.066360516 0.887696411 1.263071885 0.973437458 0.980147945 1 20.06069205 -1.999976793 0.275208652 0.204450067 1.092084231 0.060917011 0.107526186 202.4065951 3.274282709 83.81951828 0.257841581 0.010000534 1.999976793 0.887634164 SFDFIHLDPFGTSVNYLDSAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFDFIHLDPFGTSVNYLDSAFR 22 0 Q7Z2T5-2;Q7Z2T5 Q7Z2T5-2 TRMT1L TRMT1-like protein 0 176.84 6.59E-17 196940000 273260 285230 157170 206190 269110 300930 287520 337960 274070 FALSE TRUE 237147.9986 283356.3053 233177.9377 253008.5909 263755.2375 312506.9718 259636.3547 265689.884 241669.7568 0.981289516 1.172493857 0.964861887 1.046918714 1.091387027 1.293115762 1.074343592 1.099392359 1 17.88267742 3.134795731 4.988641792 1.118049818 1.045593723 0.131725845 0.090558261 0.457454778 18.38059876 0.027587586 0.031665027 1363.94146 -3.134795731 -0.072456095 SFEAPATINSASLHPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFEAPATINSASLHPEK 17 0 Q9Y3F4;Q9Y3F4-2 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 250.41 2.72E-21 296990000 186090 158830 53744 125450 161220 133170 193990 206120 199580 FALSE TRUE 161497.735 157786.6353 79734.77816 153935.3399 158012.0374 138293.1361 175176.8797 162042.842 175985.8798 0.917674391 0.896586905 0.453074862 0.874702789 0.897867702 0.7858195 0.99540304 0.920771838 1 17.42510015 2.440143838 1.050699757 0.978017048 0.779480425 0.227707643 0.137095777 0.858840991 1.957175487 0.120389736 0.06088004 275.514105 -2.440143838 -0.198536623 SFEEEFGTASDKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFEEEFGTASDKER 14 1 Q5JY65;Q9BZJ0-2;Q9BZJ0-3;Q9BZJ0 Q5JY65 CRNKL1 Crooked neck-like protein 1 0 ; 180.11 1.63E-06 364400000 201663 186587 129278 151870 179041 165819 191905 244257 159107 FALSE TRUE 175012.7236 185361.2977 191797.2732 186354.4047 175478.4344 172198.1642 173294.0826 192024.5414 140297.5517 1.247439613 1.321201229 1.367074984 1.328279805 1.250759063 1.227378255 1.235189642 1.368694885 1 17.09813031 3.170435289 4.85157765 1.236106835 1.320063049 0.199434971 0.094881306 0.400424752 17.95738359 0.02862467 0.033203339 1480.591625 -3.170435289 0.083956214 SFEEKVENLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFEEKVENLK 10 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 0 ; 107.18 0.0021147 981730000 927850 710870 433460 616610 696840 540080 885420 1033960 355360 FALSE TRUE 805232.2716 706200.2482 643082.7058 756620.7248 682974.2473 560857.2271 799552.1047 812855.7003 313349.7456 2.569755626 2.253712531 2.052284116 2.414620517 2.179590878 1.789876121 2.551628383 2.594084443 1 18.2574143 1.230588895 24.99705139 0.999997631 2.300790987 0.723772169 0.252528464 168.3822631 527955.6518 0.696160077 0.064867938 17.00548 -1.230588895 1.300793356 SFEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFEELR 6 0 Q9NUU7;I3L0H8;F6QDS0;H3BQK0;Q9UMR2;Q9UMR2-2;Q9UMR2-4;H3BN59;H3BTB3;H3BMQ5 Q9NUU7 DDX19A;DDX19B ATP-dependent RNA helicase DDX19A;ATP-dependent RNA helicase DDX19B 0 120.9 0.046264 288890000 678520 637940 373880 541420 688960 715820 593880 675540 640270 FALSE TRUE 588851.8628 633749.3301 554689.6186 664357.6861 675251.0439 743358.0586 536285.609 531081.0281 564578.01 1.042994684 1.122518623 0.982485341 1.176733196 1.196027886 1.316661374 0.949887526 0.940668993 1 19.10681341 2.165953153 24.99998619 0.958188579 1.135913867 0.460502621 0.089707886 39.38119543 13558.5059 0.038354946 0.025858905 146.5389763 -2.165953153 0.177725288 SFEHMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SFEHMK 6 0 Q96EK6;G3V5E4;G3V4W4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 0 ;;;; 94.151 0.044808 930270000 1963930 2143840 1060880 1645950 2063030 1977130 2120910 2562070 2405560 FALSE TRUE 1704391.675 2129756.974 1573925.116 2019688.104 2021979.739 2053191.47 1915224.475 2014191.269 2121177.437 0.803512071 1.004044705 0.742005402 0.952154246 0.953234606 0.967948949 0.902906301 0.949562839 1 21.01643388 3.583475675 20.64120831 0.951164969 0.862234821 0.33114597 0.069136131 9.790737116 1890.158764 0.017430051 0.025852898 3832.442742 -3.583475675 -0.088930148 SFELPPYT(ph)PPPILS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFELPPYTPPPILSPVR 17 0 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 2 SFELPPY(0.039)T(0.962)PPPILS(1)PVR;SFELPPY(0.269)T(0.731)PPPILS(1)PVR 93.754 0.01583 92979000 166257 142407 122077 153972 179870 199599 185709 207194 240150 TRUE FALSE 144285.7162 141471.519 181113.8455 188933.6959 176290.9389 207277.7027 167698.9698 162887.1755 211759.7406 0.681365192 0.668075616 0.85527988 0.892207817 0.832504509 0.978834325 0.79193037 0.769207476 1 17.69206881 4.229826117 8.220159854 0.863562529 0.674241191 0.560923819 0.072930463 0.090990859 46.29573972 0.018804874 0.042580552 16975.63845 -4.229826117 -0.189321338 SFELPPYTPPPILS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFELPPYTPPPILSPVR 17 0 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 SFELPPYT(0.001)PPPILS(0.999)PVR;SFELPPYTPPPILS(1)PVR 147.64 4.11E-07 171460000 246820 223690 188319 244780 299130 285440 265740 320770 353610 TRUE FALSE 214202.1116 222220.5657 279390.6983 300361.0402 293177.8982 296421.0615 239968.5757 252175.8317 311806.6286 0.686971001 0.712687112 0.896038354 0.963292671 0.940255502 0.950656703 0.769607037 0.808757122 1 18.25029207 4.256623982 5.824466963 0.893795858 0.696086853 0.59174936 0.070202985 0.127024102 13.80363716 0.019715534 0.05000008 18056.10126 -4.256623982 -0.197709005 SFEVEEVET(ph)PNSTPPRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFEVEEVETPNSTPPRR 17 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 1 S(0.075)FEVEEVET(0.421)PNS(0.252)T(0.252)PPRR 194.19 1.24E-17 0 145280 121900 58641 60884 122060 85940 182790 152400 46966 TRUE FALSE 126080.8799 121099.2309 86999.98374 74708.64275 119631.2448 89246.16741 165063.0539 119810.446 41413.73298 3.044422003 2.924132218 2.100752033 1.803958189 2.888685375 2.154989685 3.985708171 2.893012471 1 15.33782163 SFEVEEVETPNS(ph)TPPRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFEVEEVETPNSTPPRR 17 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 1 SFEVEEVET(0.099)PNS(0.451)T(0.451)PPRR 67.136 0.041991 388870000 138880 119550 74391 84109 119870 111970 148790 143420 95936 TRUE FALSE 120526.6561 118764.6682 110366.7364 103207.234 117484.8215 116277.5584 134360.3687 112750.7491 84594.55537 1.42475666 1.403928038 1.304655317 1.220022181 1.388798854 1.374527685 1.588286245 1.332836949 1 16.36827719 1.254309442 4.92603301 0.979485843 1.383402964 0.626560459 0.092840848 0.112093816 6.50481878 0.149832672 0.024353525 17.96012859 -1.254309442 0.403917121 SFEVNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFEVNLR 7 0 Q7Z4W1;J3KS22;J3QS36;J3QL34;J3QS45;J3KRZ4;J3KSZ5 Q7Z4W1 DCXR L-xylulose reductase 0 ; 135.6 0.0071227 406040000 893640 572850 372370 518190 711840 701360 571670 688180 658140 FALSE TRUE 775543.2098 569086.9106 552449.3775 635852.9595 697675.7767 728341.773 516229.5314 541018.0624 580335.439 1.336370585 0.980617196 0.951948374 1.095664536 1.20219399 1.255035836 0.889536459 0.932250602 1 19.14652751 2.221323266 24.99986317 0.936729621 1.122541638 0.376020058 0.118246205 279.4942865 405356.0632 0.049916626 0.033744719 166.4651268 -2.221323266 0.185812017 SFFDNISCDDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SFFDNISCDDNR 12 0 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;A0A0G2JQ95;A0A096LP11 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;;;; 316.19 4.23E-46 1983120000 2296530 2179530 1497340 1726330 2195540 2258490 2247350 2553920 2579180 FALSE TRUE 1993037.742 2165212.524 2221458.632 2118319.612 2151853.05 2345375.572 2029402.343 2007784.083 2274272.279 0.876340868 0.952046307 0.976777782 0.931427442 0.946172132 1.031264195 0.892330422 0.88282485 1 21.11697356 4.741759908 23.91862671 0.945929023 0.87634082 0.207380236 0.045043351 318.2543626 2379120.735 0.011529516 0.079709787 55177.23171 -4.741759908 -0.069588203 SFFDNISCDDNRER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SFFDNISCDDNRER 14 1 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;A0A0G2JQ95;A0A096LP11 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;; 182.37 1.40E-06 996820000 617990 612970 177436 186355 500240 529380 530050 571560 28529.1 FALSE TRUE 536321.0557 608943.3597 263244.6431 228669.751 490286.2027 549745.5912 478645.8326 449336.3419 25156.4223 21.31944874 24.20627832 10.46431166 9.089915422 19.48950439 21.85309122 19.02678477 17.86169498 1 14.61863914 1.238482788 24.99465989 0.999981672 17.82402954 0.55498077 4.759276746 1.546975549 493591.0739 6.918471074 1.236689935 17.31740397 -1.238482788 16.82404787 SFFSDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFFSDKR 7 1 Q9Y3B3 Q9Y3B3 TMED7 Transmembrane emp24 domain-containing protein 7 0 107.59 0.011934 435670000 286780 317090 221230 233720 333300 337460 296900 319080 451900 FALSE TRUE 248881.2964 315007.0149 328217.568 286789.6982 326667.9821 350442.3046 268106.6837 250847.2251 398476.8968 0.624581496 0.790527675 0.823680295 0.719714745 0.819791523 0.879454511 0.672828678 0.629515104 1 18.60413656 4.742080833 23.70584213 0.776006547 0.624581389 0.185274778 0.105698474 323.9940022 2181630.895 0.026047889 0.183187921 55218.02042 -4.742080833 -0.151425158 SFFTDDDKQDHLSWEWNLSIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SFFTDDDKQDHLSWEWNLSIK 21 1 P52566;H0YGX7 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ;;;; 267.56 2.27E-37 2435024000 2095296 2127293 866703 1758089 1964098.5 1517441 2470905 3177741 3174930 FALSE TRUE 1818397.325 2113318.672 1285843.47 2157289.978 1925016.783 1575817.937 2231277.013 2498205.816 2799593.392 0.649521938 0.754866288 0.459296508 0.770572607 0.687605846 0.562873859 0.797000386 0.892345947 1 21.41678588 1.788515519 1.914821022 0.984128855 0.651550155 0.639530693 0.092903026 0.207530354 1.438420236 0.089701458 0.025868764 61.44909893 -1.788515519 -0.3325787 SFGEKS(ph)YLNVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SFGEKSYLNVHR 12 1 Q6ZN11-3;Q6ZN11-2;Q6ZN11 Q6ZN11-3 ZNF793 Zinc finger protein 793 1 SFGEKS(0.566)Y(0.434)LNVHR;S(0.001)FGEKS(0.55)Y(0.449)LNVHR;S(0.002)FGEKS(0.549)Y(0.449)LNVHR 68.536 0.031648 7833600000 2888540 1291990 6524400 3039580 259140 471515 1238980 1627250 1552740 TRUE FALSE 2506812.12 1283502.833 9679621.663 3729763.096 253983.621 489654.4872 1118823.91 1279275.251 1369176.846 1.830889945 0.937426627 7.069665026 2.724091564 0.185500961 0.357626912 0.817150767 0.934338946 1 20.38487737 3.332528516 5.558852467 0.69641865 3.324161233 0.379183625 1.584516589 0.222808607 10.61347731 0.466914477 0.603230155 2150.445876 -3.332528516 2.627742584 SFGQTPSQLLIEPHPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFGQTPSQLLIEPHPPR 17 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6;A0A3B3IS13;A0A3B3ISK3 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 162.77 2.80E-09 571610000 280630 285300 156734 207698 273670 307280 265150 315420 293330 FALSE TRUE 243544.0345 283425.8455 232531.0866 254859.0054 268224.5024 319101.2604 239435.7938 247969.8876 258652.8616 0.941586468 1.095776957 0.899008367 0.985332247 1.037005741 1.233704737 0.925703247 0.958697639 1 17.98065763 5.054461273 12.59729921 1.011278679 0.603360113 0.05597706 0.094732468 588049.5617 4674017.339 0.023437961 5571028.364 113360.3748 -5.054461273 -0.407918565 SFGS(ph)PNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SFGSPNR 7 0 D6RAD4;P50613;D6REC6;D6R9G1 D6RAD4 CDK7 Cyclin-dependent kinase 7 1 S(0.001)FGS(0.999)PNR;S(0.003)FGS(0.997)PNR;S(0.001)FGS(0.999)PNR;S(0.007)FGS(0.993)PNR;S(0.004)FGS(0.996)PNR;S(0.214)FGS(0.786)PNR 100.57 0.010173 7119610000 6370790 6655790 3837430 4745090 5806130 6661970 6123060 6882760 6463990 TRUE FALSE 5528873.96 6612067.677 5693223.983 5822535.209 5690599.373 6918260.297 5529246.584 5410935.336 5699824.466 0.97000776 1.160047597 0.998841985 1.021528863 0.998381513 1.213767255 0.970073134 0.949316136 1 22.44248606 2.062349766 24.99999717 0.96762588 1.060431981 0.225191245 0.076122628 85.75483696 34383.82464 0.029511888 0.019896908 115.4382583 -2.062349766 0.092806101 SFGTEDRPTDRPAPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SFGTEDRPTDRPAPPR 16 2 Q9BX40;Q9BX40-2;Q5TBQ1;Q5TBQ0;A0A0C4DFV2 Q9BX40 LSM14B Protein LSM14 homolog B 0 ;;; 273.99 1.81E-35 1096740000 552763 515683 393043 541176 552685 575981 501313 569591 812555 FALSE TRUE 479713.969 512295.4444 583119.9094 664058.2822 541687.6498 598139.3618 452695.7424 447788.3972 716495.6736 0.669528075 0.715001448 0.813849868 0.926814085 0.756023616 0.834812245 0.631819227 0.624970134 1 19.45059847 4.432210902 4.947881165 0.778089775 0.678839562 0.113427686 0.116108122 0.46319305 25.28487244 0.030836249 0.0918104 27052.71777 -4.432210902 -0.099250213 SFGTEDRPTDRPIPPRDEVFEYIIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SFGTEDRPTDRPIPPRDEVFEYIIFR 26 3 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9;I3L4Q1 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;; 254.75 6.11E-53 817550000 237512 268507 148871 169558 237814 271913 226415 290801 185000 FALSE TRUE 206124.1874 266743.1598 220865.5135 208058.7354 233081.9667 282373.6691 204457.3081 228615.4692 163129.5108 1.263561611 1.635161894 1.353927395 1.275420581 1.428815458 1.730978459 1.253343477 1.401435388 1 17.31565827 0.767512812 1.568069004 2.04E-11 1.43393219 0.407327128 0.157373164 4.096242376 3.201181683 13.31660871 0.042763986 5.854810085 -0.767512812 1.43393219 SFGTRPLS(ph)SGFSPEEAQQQDEEFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SFGTRPLSSGFSPEEAQQQDEEFEK 25 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 SFGTRPLS(0.774)S(0.145)GFS(0.081)PEEAQQQDEEFEK;SFGT(0.009)RPLS(0.92)S(0.07)GFS(0.001)PEEAQQQDEEFEK;SFGT(0.001)RPLS(0.794)S(0.204)GFS(0.001)PEEAQQQDEEFEK 238.36 1.02E-38 3827650000 638320 617740 478880 593090 707040 656720 825630 955860 838700 TRUE FALSE 553964.3947 613682.0253 710467.9698 727760.1493 692971.2873 681984.4434 745560.5297 751456.7775 739549.8415 0.749056201 0.829804823 0.960676252 0.984058286 0.937017694 0.922161571 1.008127496 1.016100248 1 19.49628785 4.374448616 2.171815701 0.980608141 0.745791099 0.878336437 0.02964684 0.129910229 1.097300112 0.009239281 0.044223199 23683.64902 -4.374448616 -0.234817042 SFGTRPLSS(ph)GFSPEEAQQQDEEFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SFGTRPLSSGFSPEEAQQQDEEFEK 25 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 SFGTRPLS(0.371)S(0.615)GFS(0.014)PEEAQQQDEEFEK;S(0.003)FGT(0.013)RPLS(0.355)S(0.614)GFS(0.015)PEEAQQQDEEFEK;SFGTRPLS(0.298)S(0.42)GFS(0.281)PEEAQQQDEEFEK 224.06 5.30E-34 8297200000 775351 767895 557461 676507 888791 811387 1025180 1180590 1043340 TRUE FALSE 672886.4009 762850.6472 827051.0042 830118.2541 871105.798 842601.5829 925758.2014 928130.0159 919997.5338 0.731400222 0.829187709 0.898970893 0.902304869 0.946856666 0.915873741 1.006261612 1.008839678 1 19.81127047 6.390154851 0.31283791 1.025490603 1.34E-14 0.92835403 0.023071139 7.430893516 0.293894001 0.047510884 3.478863533 2455584.314 -6.390154851 -1.025490603 SFGTRPLSSGFS(ph)PEEAQQQDEEFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFGTRPLSSGFSPEEAQQQDEEFEK 25 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 SFGTRPLS(0.21)S(0.054)GFS(0.735)PEEAQQQDEEFEK 279.28 2.08E-53 391470000 149330 146080 125660 133030 170460 125420 186050 222870 198540 TRUE FALSE 129595.6621 145120.3909 186429.5963 163236.4947 167068.1795 130244.9886 168006.8996 175210.9849 175068.8274 0.740255499 0.828933357 1.064893157 0.932413252 0.954299986 0.743964477 0.959661992 1.000812009 1 17.4175627 4.447466336 8.15442863 0.948033153 0.761796653 0.429341446 0.082784507 0.17662226 42.06188239 0.021370212 0.058058261 28019.88416 -4.447466336 -0.1862365 SFGWETLDSFMQHDVQELCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFGWETLDSFMQHDVQELCR 20 0 Q93009;A0A669KBL1;Q93009-3;H3BND8;F5H2X1 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 214.19 1.28E-24 16653000 31058 29585 14356 13993 23256 25665 23607 26512 23129 FALSE TRUE 26953.60661 29390.65419 21298.60962 17170.32452 22793.2511 26652.34916 21317.59677 20842.61512 20394.71597 1.321597548 1.441091616 1.044319992 0.841900645 1.117605714 1.306826199 1.045250976 1.021961529 1 14.31590779 4.233239613 24.99897698 1.054382395 1.381344621 0.573041632 0.117476336 86.94863614 408506.7961 0.031673473 0.069186769 17109.59039 -4.233239613 0.326962226 SFIKDYPVVSIEDPFDQDDWGAWQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFIKDYPVVSIEDPFDQDDWGAWQK 25 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 285.84 1.03E-53 1099100000 2037900 2001500 655100 849430 1676500 1356400 2227200 2463000 348130 FALSE TRUE 1768586.352 1988352.015 971908.5512 1042306.064 1643140.93 1408581.586 2011206.487 1936306.617 306974.468 5.761346744 6.477255349 3.166089211 3.395416143 5.352695749 4.58859525 6.551706075 6.307712266 1 18.22775914 4.273121655 24.95361507 4.643576832 6.119302916 0.150424501 1.639409625 402.9459948 290927.0186 0.417913088 1.105579347 18755.19805 -4.273121655 1.475726084 SFKDEWTQLDMFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFKDEWTQLDMFYR 14 1 Q9NRN7;E9PLW6;E9PNF3 Q9NRN7 AASDHPPT L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase 0 81.311 0.012641 177980000 249650 167950 165230 174810 157160 197620 210080 224330 193060 FALSE TRUE 216658.12 166846.7254 245135.7807 214503.2823 154032.8235 205222.5693 189706.4739 176358.7752 170236.6667 1.272687748 0.980086891 1.439970515 1.260029854 0.904815786 1.20551332 1.114369058 1.035962338 1 17.37718228 3.273784763 24.99943388 1.062447569 1.234170311 0.320716416 0.134030301 233.0919509 165429.5033 0.037706117 0.048676422 1878.385653 -3.273784763 0.171722742 SFKLS(ph)GFSFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFKLSGFSFK 10 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 SFKLS(1)GFSFK 144.68 1.92E-05 1599500000 3065800 2405300 1713600 2285000 2491000 1652600 3546400 4066200 3179500 TRUE FALSE 2660646.762 2389499.426 2542302.692 2803844.174 2441433.974 1716176.591 3202470.674 3196674.773 2803623.132 0.949003 0.85228981 0.90679188 1.000078842 0.870813893 0.612128132 1.142261468 1.140194178 1 21.418861 2.170090832 24.99999961 1.105750077 0.872867332 0.497246784 0.108138992 41.55364702 15171.44982 0.044318168 0.02987931 147.9417773 -2.170090832 -0.232882745 SFKLSGFS(ph)FK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFKLSGFSFK 10 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 SFKLS(0.494)GFS(0.506)FK 115.91 0.00070268 1358200000 2738000 2248600 1532800 1991700 2095500 1364500 3240500 3413400 2678200 TRUE FALSE 2376166.363 2233828.799 2274067.207 2443945.926 2053803.65 1416993.198 2926236.809 2683470.973 2361586.247 1.006173865 0.945901849 0.96294057 1.034874729 0.869671244 0.600017552 1.239098006 1.13630022 1 21.17132479 2.180000563 24.99999737 1.132207865 0.912360535 0.385660329 0.131570515 82.35572647 35157.78688 0.054809628 0.036952659 151.3563211 -2.180000563 -0.21984733 SFKPDFGAESIYGGFLLGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFKPDFGAESIYGGFLLGVR 20 1 P35606;P35606-2;H0Y938 P35606 COPB2 Coatomer subunit beta 0 ; 183.54 3.95E-17 1299020000 1556530 1476710 908600 1025830 1341370 1286550 1453880 1843990 1621010 FALSE TRUE 1350830.617 1467009.395 1348001.999 1258760.38 1314679.361 1336044.411 1312882.941 1449667.088 1429376.044 0.945049151 1.026328516 0.943070233 0.880636264 0.919757517 0.934704633 0.918500731 1.014195735 1 20.44695408 1.705545199 7.260700883 1.006396448 0.938855855 0.377978697 0.036575639 0.136320971 16.2981395 0.02322087 0.010231008 50.76275676 -1.705545199 -0.067540593 SFLDDPIWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SFLDDPIWR 9 0 Q7L576;Q7L576-2;Q7L576-3;H0YL50 Q7L576 CYFIP1 Cytoplasmic FMR1-interacting protein 1 0 ;; 152.63 0.00018614 204754000 951410 815620 526133 636180 855360 888990 817010 909020 933960 FALSE TRUE 825678.7579 810262.1385 780572.6786 780634.3924 838340.0095 923190.0206 737776.496 714633.147 823548.3128 1.00258691 0.983867159 0.947816499 0.947891436 1.017960934 1.120990725 0.895850898 0.867748905 1 19.65149376 SFLEDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SFLEDIR 7 0 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;;;; 132.09 0.0079152 1757191000 6090250 6050770 4405260 5629320 6246160 6723930 5903410 6732840 11981870 FALSE TRUE 5285408.032 6011022.093 6535658.471 6907543.145 6121873.636 6982603.938 5330898.207 5293074.561 10565386.98 0.500256928 0.568935346 0.61859149 0.653789886 0.579427299 0.660894291 0.504562513 0.500982555 1 23.33284227 1.232592649 24.99292102 1.000000696 0.573508643 0.836780459 0.059206983 82.55129151 345676.6865 0.138533883 0.015683812 17.08412141 -1.232592649 -0.426492053 SFLEDIRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SFLEDIRK 8 1 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;; 111.95 0.0050275 5046830000 6687990 6415580 3630180 4493660 5838320 5358590 7427820 8080240 4557550 FALSE TRUE 5804155.176 6373435.633 5385747.19 5514014.184 5722148.854 5564738.425 6707471.16 6352343.556 4018761.631 1.444264604 1.585920295 1.340150943 1.372067988 1.423858736 1.384689846 1.669039315 1.580671893 1 21.93831958 4.244802493 24.99359478 1.42668898 1.515092407 0.051139914 0.178507805 583.6869944 2337122.134 0.045149905 0.113272398 17571.24335 -4.244802493 0.088403426 SFLEEVLASGLHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFLEEVLASGLHSR 14 0 A0A2R8YE10;Q9NRW7;A0A087WU65 A0A2R8YE10 VPS45 Vacuolar protein sorting-associated protein 45 0 ; 216.88 5.96E-12 520810000 625900 636790 282920 468710 627160 701860 547220 715260 655820 FALSE TRUE 543185.7292 632606.8846 419741.0583 575137.7693 614680.743 728861.0084 494150.6886 562307.2152 578289.7067 0.939296901 1.093927278 0.725831799 0.994549553 1.062928729 1.260373477 0.854503691 0.972362483 1 19.1414329 SFLIWVNEEDHTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SFLIWVNEEDHTR 13 0 P12532;P12532-2;F8WCN3 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ;; 228.25 7.74E-12 2599261000 3109560 3153930 1897602 2673200 3202950 3455370 2462050 3724750 3364160 FALSE TRUE 2698623.767 3133211.626 2815288.674 3280190.917 3139217.561 3588300.32 2223280.77 2928241.199 2966452.837 0.909714031 1.05621488 0.949042115 1.105762032 1.058239498 1.20962662 0.749474504 0.987118744 1 21.50030742 2.241038546 24.9999922 0.921026181 1.047047976 0.271260789 0.104663142 90.64311634 914519.4556 0.039382161 0.029045318 174.1961477 -2.241038546 0.126021795 SFLQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFLQAR 6 0 P46098-3 P46098-3 0 103.28 0.080999 187890000 273990 323540 235560 216470 319930 391440 279700 324020 304130 FALSE TRUE 237781.5273 321414.6444 349477.6039 265622.822 313564.0189 406498.9501 252574.7371 254730.8445 268176.0979 0.886661896 1.198520849 1.303164625 0.990479107 1.169246706 1.515791129 0.941824193 0.949864088 1 18.03282113 SFLSEPS(ph)SPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFLSEPSSPGR 11 0 Q69YN4-3;Q69YN4;H0YC41 Q69YN4-3 KIAA1429 Protein virilizer homolog 1 SFLS(0.001)EPS(0.561)S(0.438)PGR 77.593 0.033768 275910000 704380 585130 373900 443080 618610 609440 548320 618980 584010 TRUE FALSE 611294.3983 581286.2425 554719.2906 543688.0861 606300.8713 632885.5512 495144.0108 486615.9439 514969.0031 1.187050861 1.12877909 1.07718967 1.055768566 1.177354108 1.228977953 0.961502552 0.944942202 1 18.97412607 2.21835087 24.90769881 0.96353665 1.136566 0.709844533 0.052224144 130.0287748 160253.9844 0.022743629 0.01535533 165.3296972 -2.21835087 0.17302935 SFLSEPSS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SFLSEPSSPGR 11 0 Q69YN4-3;Q69YN4;H0YC41 Q69YN4-3 KIAA1429 Protein virilizer homolog 1 SFLSEPS(0.013)S(0.987)PGR;SFLSEPSS(1)PGR;SFLSEPSS(1)PGR;SFLSEPSS(1)PGR;SFLSEPSS(1)PGR;SFLSEPSS(1)PGR 232.98 1.93E-15 9808020000 10042600 8891100 4859140 5940640 8844300 8871000 8158300 9246500 8209500 TRUE FALSE 8715444.965 8832693.779 7209036.357 7289553.109 8668315.734 9212273.11 7367109.322 7269207.931 7238982.262 1.203959984 1.220156848 0.995863244 1.006985906 1.197449506 1.272592303 1.017699596 1.004175403 1 22.78735545 2.039948093 24.73433165 1.004951326 1.141740581 0.365937139 0.088008939 159.5764126 98802.91329 0.038878383 0.026211767 109.6347152 -2.039948093 0.136789255 SFLVASVLPGPDGNINS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFLVASVLPGPDGNINSPTR 20 0 Q7Z3K3-5;Q7Z3K3-7;Q7Z3K3-2;Q7Z3K3-3;Q7Z3K3-6;Q7Z3K3 Q7Z3K3-5 POGZ Pogo transposable element with ZNF domain 1 SFLVASVLPGPDGNINS(0.999)PT(0.001)R;SFLVASVLPGPDGNINS(0.947)PT(0.053)R 357.92 2.00E-95 180166000 342050 326160 162161 225346 345500 357920 334300 401710 337450 TRUE FALSE 296847.2259 324017.4335 240582.602 276514.2535 338625.226 371689.414 301879.6375 315807.4426 297557.0454 0.997614509 1.088925429 0.808525981 0.929281487 1.138017839 1.24913666 1.014526936 1.061334112 1 18.18280675 3.244141414 24.99764829 1.090665453 0.955035242 0.329833733 0.096667135 175.3014966 785209.9365 0.029602395 0.037137699 1754.451691 -3.244141414 -0.135630211 SFPIKPVPS(ph)PSWSGSCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFPIKPVPSPSWSGSCR 17 1 Q9P0U3-2;Q9P0U3 Q9P0U3-2 SENP1 Sentrin-specific protease 1 1 SFPIKPVPS(0.961)PS(0.039)WSGSCR 181.69 4.78E-10 740200000 864990 738680 472900 571470 773890 719320 904520 1036400 887100 TRUE FALSE 750679.3799 733827.5624 701596.0218 701230.9979 758491.1031 746992.7059 816799.7896 814773.9253 782228.0486 0.959668196 0.938124839 0.896920052 0.896453405 0.969654699 0.954955153 1.044196499 1.041606635 1 19.57722974 2.48174935 1.875110834 1.032857239 0.926086719 0.722202645 0.026956504 0.16931388 1.215569123 0.013155279 0.009381567 303.2140697 -2.48174935 -0.10677052 SFPIKPVPSPS(ph)WSGSCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFPIKPVPSPSWSGSCR 17 1 Q9P0U3-2;Q9P0U3 Q9P0U3-2 SENP1 Sentrin-specific protease 1 1 SFPIKPVPS(0.376)PS(0.607)WS(0.016)GS(0.001)CR 145.55 2.85E-07 537540000 857840 737930 470800 583400 783170 751480 849180 1017300 926330 TRUE FALSE 744474.2705 733082.4892 698480.4547 715869.8867 767586.4492 780389.9219 766826.6543 799758.3116 816820.3227 0.911429662 0.897483166 0.855121298 0.876410475 0.939724965 0.955399738 0.938794779 0.979111672 1 19.63965924 3.044075153 2.528375466 0.967536048 0.883634492 0.769702184 0.021449295 0.142217608 1.844068542 0.007745934 0.008675653 1106.815297 -3.044075153 -0.083901557 SFQQELDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFQQELDAR 9 0 C4P0D6;C4P0D8;Q99598;C4P0D4;Q5VVQ1 C4P0D6 DISC1;TSNAX Translin-associated protein X 0 83.883 0.036915 125110000 184170 175150 95818 138790 187520 180710 165320 179550 147520 FALSE TRUE 159831.4679 173999.4281 142155.9053 170304.3908 183788.7189 187662.0306 149287.2918 141154.6298 130080.3537 1.228713356 1.337630343 1.092831479 1.309224537 1.412886064 1.442662365 1.147654412 1.085134117 1 16.98904356 2.038464562 6.433256159 1.067734273 1.301473765 0.553317976 0.098628723 0.145103557 16.49638981 0.044083313 0.02902214 109.2608467 -2.038464562 0.233739492 SFQSLACS(ph)PGLPAADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SFQSLACSPGLPAADR 16 0 Q96JY6;Q96JY6-5;Q96JY6-3;Q96JY6-4;C9JS55;C9JSR2;C9K0F0;C9J0X3;A0A087WXJ0 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 S(0.001)FQS(0.018)LACS(0.981)PGLPAADR;SFQSLACS(1)PGLPAADR;SFQSLACS(1)PGLPAADR;SFQSLACS(1)PGLPAADR;SFQSLACS(1)PGLPAADR 281.58 1.67E-35 1266191000 1020325 1336883 821789 1004280 1534675 1678793 1496365 1656706 1518276 TRUE FALSE 885486.4661 1328100.928 1219208.909 1232317.123 1504137.97 1743377.253 1351247.753 1302432.314 1338787.141 0.66140945 0.992017989 0.91068167 0.920472782 1.12350793 1.302206452 1.009307388 0.972844954 1 20.35249517 5.341368722 0.851586242 1.055597853 8.95E-18 0.534929615 0.110228359 5.328477781 1.460097964 0.041687087 6.705667204 219466.745 -5.341368722 -1.055597853 SFREPAPAEALPQQYPEPAPAALCGPPPRAPS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFREPAPAEALPQQYPEPAPAALCGPPPRAPSR 33 2 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 SFREPAPAEALPQQYPEPAPAALCGPPPRAPS(1)R;SFREPAPAEALPQQYPEPAPAALCGPPPRAPS(1)R 130.87 3.33E-08 423560000 193768 172832 65982 56844 166517 186078 160415 162508 49255 TRUE FALSE 168161.0679 171696.6552 97891.1159 69751.29901 163203.6375 193236.5411 144857.978 127756.9288 43432.13001 3.871812592 3.953217472 2.253887062 1.605983842 3.757670587 4.449161048 3.33527225 2.941530356 1 15.40647509 4.260038841 24.63085919 2.864288065 3.912516468 0.180996563 0.998473854 400.8906201 459724.9041 0.261336423 0.689936856 18198.63609 -4.260038841 1.048228403 SFS(ph)ADNFIGIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SFSADNFIGIQR 12 0 Q8N7R7-3;Q8N7R7;Q8N7R7-2 Q8N7R7-3 CCNYL1 Cyclin-Y-like protein 1 1 SFS(1)ADNFIGIQR;SFS(1)ADNFIGIQR;SFS(1)ADNFIGIQR;S(0.001)FS(0.999)ADNFIGIQR;SFS(1)ADNFIGIQR;SFS(1)ADNFIGIQR 271 1.10E-27 1110346000 1170199 1116852 756631 1059003 1356301 1417143 864458 1485583 1260021 TRUE FALSE 1015554.237 1109515.326 1122540.282 1299465.817 1329313.264 1471661.408 780622.9962 1167902.636 1111062.753 0.914038595 0.998607255 1.010330226 1.169570138 1.196434009 1.324552915 0.702591275 1.051158122 1 20.08350887 2.240738099 24.99999701 0.936703301 1.100706375 0.261024178 0.145053704 90.54938731 1039628.648 0.058030415 0.042727831 174.0756795 -2.240738099 0.164003075 SFS(ph)ASQSTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SFSASQSTDR 10 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 SFS(0.978)AS(0.022)QSTDR;SFS(0.997)AS(0.003)QSTDR;SFS(0.976)AS(0.024)QSTDR;S(0.002)FS(0.986)AS(0.012)QSTDR 252.84 4.78E-17 1666500000 822320 831360 753943 1004000 1392830 1404010 1235240 1447370 1641760 TRUE FALSE 713648.3285 825898.7414 1118552.357 1231973.545 1365115.408 1458023.173 1115446.615 1137861.189 1447673.003 0.49296238 0.570500893 0.772655395 0.851002638 0.942972208 1.007149522 0.770510062 0.785993236 1 20.46530434 4.199471319 1.865408266 0.882118164 0.486195453 0.781597209 0.078618739 0.19282823 1.255103009 0.02409555 0.092499298 15829.65023 -4.199471319 -0.395922712 SFS(ph)EDTLMDGPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SFSEDTLMDGPAR 13 0 Q9BRG2;M0QZQ6 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 SFS(0.998)EDT(0.002)LMDGPAR;SFS(0.992)EDT(0.008)LMDGPAR;S(0.108)FS(0.884)EDT(0.009)LMDGPAR;S(0.006)FS(0.988)EDT(0.006)LMDGPAR;S(0.035)FS(0.964)EDT(0.001)LMDGPAR;S(0.015)FS(0.955)EDT(0.03)LMDGPAR 276.28 3.30E-32 1128708000 1764950 1835680 1145674 1302260 1717170 1737500 1649280 1808680 1844300 TRUE FALSE 1531707.386 1823621.297 1699725.778 1597958.037 1683001.677 1804342.749 1489333.079 1421907.857 1626268.955 0.941853671 1.121352831 1.045168927 0.982591491 1.034885202 1.109498367 0.915797522 0.874337454 1 20.63313444 2.21715715 24.88545991 0.917845532 1.040456809 0.414138288 0.060627859 188.0311244 218618.9929 0.023799241 0.016062959 164.8758889 -2.21715715 0.122611277 SFS(ph)KEVEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SFSKEVEER 9 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 S(0.04)FS(0.96)KEVEER;S(0.043)FS(0.957)KEVEER;S(0.319)FS(0.681)KEVEER 120.87 0.00038139 4858640000 9861400 9022300 8041500 8573200 12603200 11566400 16494000 16492300 10788600 TRUE FALSE 8558191.004 8963031.917 11930396.3 10519876.09 12352420.98 12011366.89 14894414.42 12965549.99 9513183.998 0.899613737 0.942169511 1.254090775 1.105820732 1.298452861 1.262602184 1.56566029 1.362903313 1 23.18149685 4.364358457 0.796091473 1.327136128 0.742129077 0.458626661 0.151396997 1.386067184 0.988706606 0.063082225 0.65731584 23139.73905 -4.364358457 -0.585007051 TVAISDAAQLPHDYCTT(ph)PGGTLFSTT(ph)PGGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.007)CT(0.472)T(0.521)PGGT(0.333)LFS(0.044)T(0.148)T(0.412)PGGT(0.063)R;TVAISDAAQLPHDYCT(0.386)T(0.614)PGGT(0.001)LFS(0.004)T(0.05)T(0.855)PGGT(0.09)R;TVAISDAAQLPHDYCT(0.189)T(0.724)PGGT(0.087)LFS(0.025)T(0.034)T(0.587)PGGT(0.354)R;TVAISDAAQLPHDYCT(0.043)T(0.957)PGGTLFS(0.006)T(0.056)T(0.935)PGGT(0.003)R;TVAISDAAQLPHDY(0.002)CT(0.446)T(0.552)PGGTLFS(0.031)T(0.067)T(0.902)PGGTR;TVAISDAAQLPHDYCT(0.101)T(0.899)PGGTLFS(0.108)T(0.055)T(0.836)PGGTR;TVAISDAAQLPHDY(0.006)CT(0.469)T(0.525)PGGT(0.088)LFS(0.191)T(0.163)T(0.485)PGGT(0.073)R 198.2 2.09E-25 17781950000 804848 1379827 1105927 1348060 2117171 2397396 2100883 2396562 2253278 TRUE FALSE 698485.2976 1370762.826 1640756.996 1654157.627 2075043.439 2489625.375 1897139.69 1884075.866 1986898.042 0.351545617 0.689900939 0.82578822 0.832532718 1.044363322 1.253021203 0.954824883 0.948249898 1 20.92208641 4.734236172 0.850055558 1.024807252 1.67E-18 0.829780384 0.098344482 1.024694832 0.582385146 0.039142893 0.989606035 54229.57144 -4.734236172 -1.024807252 down SFS(ph)LEGLTGGAGVGNKPSSSLEVSSANAEELRHPFSGEER ddPTM_MDA-MB-175_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 237.53 6.18E-51 211820000 39747 48935 27262 28845 58221 44594 59217 61903 24055 TRUE FALSE 34494.33324 48613.54276 40445.99439 35394.69812 57062.51601 46309.56004 53474.14445 48665.52518 21211.2453 1.626228576 2.29187594 1.906818473 1.668676101 2.690201126 2.183255126 2.521028053 2.294326641 1 14.3725417 SFS(ph)LSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SFSLSWR 7 0 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7;A0A3B3IS41 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 S(0.011)FS(0.988)LS(0.002)WR;S(0.001)FS(0.982)LS(0.017)WR;SFS(0.996)LS(0.004)WR;S(0.002)FS(0.986)LS(0.011)WR 154.12 0.0017834 408788000 998340 1333120 894900 960790 1339350 1519820 1226800 1263240 1896830 TRUE FALSE 866406.8395 1324362.647 1327676.633 1178952.054 1312699.555 1578288.459 1107825.125 993105.9565 1672588.918 0.518003456 0.791804031 0.793785382 0.704866594 0.784830953 0.943620062 0.662341543 0.593753758 1 20.67365148 4.742242847 24.0367941 0.766562713 0.518003288 0.314259508 0.121145276 288.9588265 1886117.63 0.029979568 0.213928534 55238.62342 -4.742242847 -0.248559424 SFS(ph)MQDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SFSMQDLR 8 0 Q9H6H4;E5RGS2 Q9H6H4 REEP4 Receptor expression-enhancing protein 4;Receptor expression-enhancing protein 1 SFS(1)MQDLR;S(0.001)FS(0.999)MQDLR;S(0.001)FS(0.999)MQDLR;SFS(1)MQDLR 143.97 0.00062186 918550000 2575030 2636200 1416210 2071050 2594650 2191230 2296800 2650870 2875400 TRUE FALSE 2234733.261 2618882.629 2101093.893 2541313.557 2543021.541 2275528.036 2074056.69 2084002.08 2535473.488 0.881386957 1.03289687 0.828679102 1.002303344 1.00297698 0.897476565 0.81801553 0.821938028 1 21.27382376 2.48572567 23.5053078 0.86422896 0.950453141 0.141787341 0.077603837 281.8398091 769930.0794 0.026921641 0.021966914 306.0029897 -2.48572567 0.086224181 SFS(ph)PEER ddPTM_MDA-MB-175_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 S(0.001)FS(0.999)PEER;S(0.003)FS(0.997)PEER;S(0.04)FS(0.96)PEER;S(0.029)FS(0.971)PEER 125.16 0.0042758 4724310000 2908130 2858000 1975350 2290240 2919310 3259330 3110230 3282400 3428440 TRUE FALSE 2523813.252 2839225.61 2930635.867 2810273.996 2861221.443 3384718.534 2808600.373 2580484.304 3023133.729 0.83483348 0.939166396 0.969403318 0.929589707 0.946442235 1.119605958 0.929036101 0.853579277 1 21.52761337 4.73202517 3.486162861 0.95594951 0.820852776 0.257603624 0.067417338 0.468832592 9.999599405 0.017915545 0.165939434 53954.18908 -4.73202517 -0.135096734 SFS(ph)PLQPGQAPTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SFSPLQPGQAPTGR 14 0 Q7Z3C6;H7C152;Q7Z3C6-2;H7C1G6 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 SFS(1)PLQPGQAPTGR;SFS(1)PLQPGQAPTGR;SFS(1)PLQPGQAPTGR 193.43 2.72E-07 274069000 302016 317490 204946 225768 311456 332273 273107 345323 310065 TRUE FALSE 262103.8204 315404.3873 304058.5711 277032.075 305258.635 345055.7573 246621.1252 271478.3638 273409.4689 0.958649389 1.153597162 1.112099637 1.013249746 1.116488892 1.262047575 0.902021156 0.992936948 1 18.06070368 2.208315428 24.99999438 0.968185615 1.101992587 0.375492105 0.083678039 216.9393063 179315.704 0.033345391 0.022484696 161.5531492 -2.208315428 0.133806972 SFS(ph)PTMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SFSPTMK 7 0 A3KN83-3;A3KN83-2;A3KN83;A3KN83-4 A3KN83-3 SBNO1 Protein strawberry notch homolog 1 1 S(0.014)FS(0.984)PT(0.002)MK;S(0.002)FS(0.969)PT(0.029)MK;SFS(1)PTMK;SFS(0.995)PT(0.005)MK 155.58 0.0016795 2396000000 4191680 3332480 2335380 2522800 3328900 2761520 3680670 4388320 3959570 TRUE FALSE 3637738.868 3310588.719 3464777.579 3095640.299 3262661.403 2867757.461 3323719.19 3449911.918 3491474.145 1.041891968 0.948192248 0.992353784 0.886628447 0.934465291 0.821360074 0.951952972 0.98809608 1 21.73540486 5.37284963 1.191096507 0.936632802 1.330337992 0.270418962 0.053248488 9.199164169 3.777204762 0.016547908 6.481840038 235966.1083 -5.37284963 0.39370519 SFS(ph)SQRPGMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SFSSQRPGMER 11 1 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 S(0.185)FS(0.714)S(0.101)QRPGMER;S(0.409)FS(0.573)S(0.018)QRPGMER;S(0.184)FS(0.776)S(0.04)QRPGMER 92.151 0.0061828 832880000 781890 654890 512460 488835 571940 798230 592790 740020 845510 TRUE FALSE 678561.2554 650587.9845 760287.3701 599832.4581 560559.513 828938.4246 535301.317 581772.4818 745554.771 0.910142731 0.872622656 1.019760586 0.804545127 0.75186899 1.111841084 0.7179906 0.780321587 1 19.50795482 3.71465961 24.91538955 0.849633423 0.928020094 0.066677722 0.123329987 1956.347894 2039377.413 0.033573461 0.049825569 5183.935753 -3.71465961 0.07838667 SFS(ph)SQRPVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SFSSQRPVDR 10 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;H7C5N8 E7EPN9 PRRC2C Protein PRRC2C 1 SFS(0.5)S(0.5)QRPVDR;S(0.001)FS(0.709)S(0.29)QRPVDR;S(0.345)FS(0.52)S(0.135)QRPVDR 121.68 0.001338 2999180000 4743190 4279540 3123530 3361780 4323510 4410770 4335060 5212480 5650010 TRUE FALSE 4116365.424 4251427.42 4634079.556 4125123.531 4237480.61 4580455.176 3914646.548 4097831.716 4982072.254 0.826235593 0.853345195 0.930151013 0.827993518 0.850545796 0.919387544 0.785746643 0.822515513 1 22.24831451 1.231749287 24.99985286 1.000000254 0.851299334 0.531586013 0.0436595 196.8452228 722421.1394 0.103722092 0.010832492 17.05097772 -1.231749287 -0.14870092 SFSERFPEDGPELEEILTQLATADAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SFSERFPEDGPELEEILTQLATADAR 26 1 G3V1D3;G3V180;Q9NY33-4;Q9NY33;Q9NY33-2 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ;; 208.11 2.15E-25 364957000 170636 141878 72554 77163.6 134199 147256 124314 143323 54089 FALSE TRUE 148086.0203 140945.9941 107641.3571 94684.77475 131528.7025 152921.0336 112258.0474 112674.4918 47694.66004 3.104876314 2.955173471 2.25688488 1.985228004 2.75772387 3.206250626 2.353681677 2.362413144 1 15.54154013 1.109159705 1.910679612 6.56E-16 2.656701507 0.649614473 0.380709318 0.84028142 2.194562407 4.531570904 0.110089785 12.8575939 -1.109159705 2.656701507 SFSKEELMS(ph)SDLEETAGSTSIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFSKEELMSSDLEETAGSTSIPK 23 1 O00567 O00567 NOP56 Nucleolar protein 56 1 S(0.067)FS(0.057)KEELMS(0.506)S(0.371)DLEETAGSTSIPK;S(0.001)FS(0.001)KEELMS(0.499)S(0.499)DLEETAGSTSIPK 182.44 5.98E-17 692700000 810250 634310 348920 426030 583110 403330 807060 878250 162680 TRUE FALSE 703173.4096 630143.1758 517658.8791 522766.623 571507.2518 418846.3661 728791.4454 690443.072 143448.1557 4.901934124 4.392828703 3.608682708 3.644289606 3.984068313 2.919844901 5.080521543 4.813188908 1 17.13016989 4.448829603 3.277008809 3.763567632 4.850805436 0.1274544 1.120015276 0.579442937 12.28013188 0.283403674 1.117261908 28107.97786 -4.448829603 1.087237803 SFSKEELMSS(ph)DLEETAGSTSIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFSKEELMSSDLEETAGSTSIPK 23 1 O00567 O00567 NOP56 Nucleolar protein 56 1 SFSKEELMS(0.113)S(0.887)DLEETAGSTSIPK;SFSKEELMS(0.193)S(0.806)DLEETAGSTSIPK 250.18 2.28E-38 1362320000 1288000 1065200 660230 614090 945540 715350 1279890 1504870 267300 TRUE FALSE 1117787.537 1058202.631 979519.4363 753528.5203 926725.6039 742869.9774 1155766.465 1183065.261 235700.0985 4.74241438 4.489614717 4.155787132 3.196980082 3.931799816 3.1517593 4.903546804 5.019366852 1 17.84659284 4.134911018 3.076133661 3.77016372 4.646364762 0.11831277 1.120640013 0.655156068 12.22594321 0.298772973 0.759702767 13643.03578 -4.134911018 0.876201042 SFSLASSSNS(ph)PISQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SFSLASSSNSPISQR 15 0 Q9BXB4 Q9BXB4 OSBPL11 Oxysterol-binding protein-related protein 11 1 SFSLASSSNS(1)PISQR;SFSLASSSNS(1)PISQR;SFSLASSSNS(1)PISQR;SFSLASSSNS(1)PISQR 415.37 2.13E-133 3973590000 3834010 3081760 1803680 2175310 3350500 3727430 2916720 3365140 3055180 TRUE FALSE 3327335.864 3061515.716 2675945.681 2669247.383 3283831.605 3870826.644 2633856.943 2645530.999 2694000.101 1.235091217 1.136420045 0.993298285 0.990811909 1.218942644 1.436832405 0.977675147 0.9820085 1 21.36131847 SFSS(ph)PPSPSNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFSSPPSPSNK 11 0 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 SFSS(0.635)PPS(0.365)PSNK 196.02 6.49E-08 165500000 418620 361650 321550 481370 440530 363710 490410 558600 766100 TRUE FALSE 363298.3064 359274.2973 477052.6555 590672.4158 431764.3149 377702.1591 442850.1137 439147.737 675532.5307 0.537795428 0.531838632 0.706187539 0.874380417 0.639146592 0.559117647 0.655557051 0.650076372 1 19.36566572 1.238423324 8.7484895 1.002892848 0.647663464 0.560077647 0.099044009 0.070666447 66.05896608 0.148080438 0.025857643 17.31503301 -1.238423324 -0.355229384 SFSS(ph)QRPVDR ddPTM_MDA-MB-175_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(0.011)S(0.989)QRPVDR 137.4 0.00024278 570880000 614670 636670 385690 348770 598550 684890 558420 640500 688700 TRUE FALSE 533439.8021 632487.6728 572210.9741 427963.5591 586640.026 711238.1615 504264.5143 503534.0594 607282.6706 0.878404453 1.041504564 0.942248152 0.704718873 0.966008178 1.171181389 0.830362101 0.829159276 1 19.21200868 SFSSPPS(ph)PSNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SFSSPPSPSNK 11 0 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 SFSS(0.116)PPS(0.883)PSNK;SFSS(0.028)PPS(0.968)PS(0.004)NK;SFSS(0.003)PPS(0.995)PS(0.001)NK 154.1 3.37E-05 530610000 1355140 1110430 998210 1443370 1455680 1224510 1497030 1750890 2290460 TRUE FALSE 1176054.816 1103135.512 1480947.695 1771109.219 1426714.816 1271617.692 1351848.261 1376475.799 2019684.428 0.582296323 0.546192017 0.733256975 0.876923738 0.706404821 0.629612069 0.669336379 0.681530134 1 20.94569846 -2 0.043174463 1.858922021 2.75E-11 0.27131238 0.115387584 2734.263432 11.60111194 408.30645 151.6391759 0.01 2 -1.858922021 SFSSQRPVDR ddPTM_MDA-MB-175_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 ; 107.06 0.0021292 370400000 400340 415060 209403 294740 426340 422400 380150 449560 353160 FALSE TRUE 347434.0547 412333.4435 310670.9912 361665.2218 417856.6681 438650.0013 343283.1115 353425.0925 311409.8271 1.115681088 1.324086164 0.997627448 1.161380247 1.341822357 1.408593959 1.102351569 1.134919523 1 18.24845495 1.516437996 1.805415329 0.997339543 1.217833025 0.229803267 0.123172118 0.769263952 4.038817078 0.260004886 0.036199338 32.84263514 -1.516437996 0.220493481 SFWELIGEAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SFWELIGEAAK 11 0 Q9HCY8 Q9HCY8 S100A14 Protein S100-A14 0 166.55 4.72E-05 136370000 374460 345500 248450 441120 392950 350100 327050 583290 418600 FALSE TRUE 324974.1622 343230.3878 368601.251 541283.0381 385131.0638 363568.5735 295332.7413 458557.9727 369113.5849 0.880417778 0.929877419 0.998611989 1.466440305 1.043394444 0.984977493 0.800113443 1.242322124 1 18.49370531 3.996844015 24.63793253 1.09273626 0.919921757 0.161262621 0.173834218 207.010535 1616143.032 0.045661012 0.092113883 9927.594159 -3.996844015 -0.172814503 SFYGSTLFLCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SFYGSTLFLCR 11 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 225.66 1.23E-11 4494700000 577880 1175160 724750 621540 1218800 1304250 1114300 967670 1463650 FALSE TRUE 501511.6938 1167440.297 1075241.524 762670.1566 1194548.265 1354425.341 1006235.358 760741.3009 1290618.964 0.388582306 0.904558455 0.833120816 0.590933635 0.925562306 1.049438586 0.779653318 0.589439116 1 20.2996317 4.746177147 24.52248943 0.81438287 0.388582037 0.449471436 0.153580937 747.3063686 2405982.374 0.038888798 0.397455379 55741.30687 -4.746177147 -0.425800833 SGAGSS(ph)PETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGAGSSPETK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SGAGS(0.032)S(0.968)PETK;SGAGS(0.021)S(0.979)PETK;SGAGS(0.028)S(0.972)PETK;SGAGS(0.003)S(0.997)PETK 202.69 2.30E-07 3009000000 8900470 6468300 4619490 5156120 5356700 5531520 8317580 9603930 9896680 TRUE FALSE 7724250.339 6425809.311 6853490.815 6326895.852 5250112.15 5744321.154 7510942.372 7550204.307 8726705.765 0.885127853 0.736338486 0.785346842 0.725003916 0.601614434 0.658246228 0.860684727 0.865183783 1 23.05700572 1.656164855 1.64539904 0.99207257 0.732075175 0.526166639 0.080721993 0.372177155 1.774517769 0.131917639 0.025084776 45.30695293 -1.656164855 -0.259997395 SGAHSSAS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SGAHSSASPPR 11 0 P18615;P18615-3;A0A0A0MT02;E9PD43;A0A0A0MSN9;P18615-4;A0A0G2JI50 P18615 NELFE Negative elongation factor E 1 SGAHS(0.003)S(0.096)AS(0.901)PPR;SGAHSS(0.003)AS(0.997)PPR;SGAHS(0.001)S(0.035)AS(0.964)PPR;SGAHSS(0.018)AS(0.981)PPR;SGAHS(0.002)S(0.068)AS(0.93)PPR;SGAHS(0.002)S(0.288)AS(0.71)PPR 86.413 0.0093327 2499976000 279752 239946 132291 192598 235732 304212 222744 287593 248102 TRUE FALSE 242782.0644 238369.7789 196267.3701 236330.3196 231041.3944 315915.2325 201142.3212 226093.475 218771.6642 1.10975096 1.08958251 0.897133414 1.08026019 1.056084641 1.444040907 0.919416698 1.033467821 1 17.73906636 SGAMS(ph)PMSWNSDASTSEAS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGAMSPMSWNSDASTSEAS 19 0 Q13158 Q13158 FADD FAS-associated death domain protein 1 SGAMS(1)PMSWNSDASTSEAS;S(0.001)GAMS(0.999)PMSWNSDASTSEAS 298.68 8.72E-50 239930000 421430 406410 234380 310460 466490 453840 398660 509260 461650 TRUE FALSE 365736.9577 403740.266 347726.952 380954.6881 457207.7617 471299.5185 359998.0146 400358.7121 407074.2629 0.898452668 0.991809856 0.854210113 0.935835848 1.123155658 1.157772823 0.884354643 0.983502885 1 18.63493249 3.450019323 24.88085025 1.020382383 0.917939438 0.308491107 0.081387662 293.1060082 269084.0705 0.025000638 0.032276439 2818.508329 -3.450019323 -0.102442946 SGAQASS(ph)TPLS(ph)PTR ddPTM_MDA-MB-175_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(0.004)S(0.686)T(0.309)PLS(0.986)PT(0.014)R;SGAQAS(0.038)S(0.658)T(0.304)PLS(0.999)PT(0.001)R 204.9 1.90E-08 1814730000 1710780 1751300 938760 1126730 1621630 1834250 1602300 1802020 1928010 TRUE FALSE 1484696.088 1739795.595 1392747.476 1382571.267 1589362.736 1904814.784 1446909.193 1416672.046 1700082.854 0.873308077 1.023359297 0.819223294 0.813237581 0.934873693 1.120424678 0.851081575 0.833295885 1 20.69717363 4.247547666 24.99989912 0.905171716 0.948333606 0.022095554 0.100773147 905.6100834 2519145.521 0.025939956 0.066560237 17682.66283 -4.247547666 0.04316189 SGAQASST(ph)PLS(ph)PTR ddPTM_MDA-MB-175_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 SGAQASS(0.212)T(0.788)PLS(1)PTR;SGAQAS(0.146)S(0.363)T(0.491)PLS(0.994)PT(0.006)R;SGAQASS(0.028)T(0.972)PLS(0.993)PT(0.007)R 210.31 2.88E-08 2186670000 2536710 2543810 1505800 1738220 2417420 2670910 2430520 2696860 2959320 TRUE FALSE 2201477.346 2527099.545 2234009.917 2132909.418 2369318.072 2773661.636 2194808.544 2120157.476 2609472.561 0.843648398 0.968433078 0.856115504 0.817371851 0.907968188 1.062920407 0.841092785 0.812485062 1 21.3153268 SGAQASST(ph)PLSPTR ddPTM_MDA-MB-175_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 1 SGAQAS(0.001)S(0.013)T(0.984)PLS(0.002)PTR;SGAQASS(0.001)T(0.52)PLS(0.472)PT(0.007)R 249.89 3.65E-17 870360000 1344430 1352190 691780 911910 1337390 1435260 1273010 1399250 1351420 TRUE FALSE 1166760.169 1343307.375 1026327.122 1118973.103 1310778.556 1490475.381 1149553.686 1100031.276 1191656.667 0.979107659 1.127260403 0.861260756 0.939006288 1.099963263 1.250759067 0.964668531 0.923110915 1 20.1845372 2.032056769 24.99999602 0.952410713 1.042291246 0.108558385 0.107785722 408.6522867 318692.6203 0.046324583 0.0312318 107.6605933 -2.032056769 0.089880533 SGAQASSTPLS(ph)PTR ddPTM_MDA-MB-175_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(0.989)PT(0.011)R;SGAQASSTPLS(0.999)PT(0.001)R;SGAQASSTPLS(1)PTR;SGAQASSTPLS(0.994)PT(0.006)R;SGAQASSTPLS(0.986)PT(0.014)R;SGAQASSTPLS(0.85)PT(0.15)R;SGAQASSTPLS(0.993)PT(0.007)R;SGAQASSTPLS(0.999)PT(0.001)R;SGAQAS(0.006)S(0.004)T(0.003)PLS(0.848)PT(0.139)R 233.92 3.54E-17 32148886000 5668303 5583176 2993996 4096169 6068902 5883198 5808733 6774980 5906938 TRUE FALSE 4919222.397 5546499.749 4441902.48 5026266.777 5948142.724 6109528.434 5245402.968 5326203.25 5208626.519 0.944437536 1.064868009 0.852797271 0.9649889 1.141979119 1.172963431 1.007060681 1.022573462 1 22.31247156 3.355753548 9.074843427 1.063555573 0.955913173 0.359397583 0.074295193 0.338231077 25.36788037 0.022540663 0.029102844 2268.577123 -3.355753548 -0.1076424 SGAVQGAGSLGPGS(ph)PVR ddPTM_MDA-MB-175_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 336.57 3.34E-72 2019190000 1418830 1353020 703700 963610 1370120 1451990 1399190 1535720 1400520 TRUE FALSE 1231328.021 1344131.923 1044011.674 1182412.378 1342857.293 1507848.995 1263496.769 1207318.229 1234952.121 0.997065392 1.088408125 0.845386356 0.957456049 1.087375996 1.220977696 1.023113971 0.977623511 1 20.23602368 3.245675265 24.96333045 1.056349049 0.971338718 0.204635581 0.087538309 312.4678468 1096357.182 0.027653182 0.034942266 1760.659058 -3.245675265 -0.085010331 SGAWDESGVFIYTTSNHIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGAWDESGVFIYTTSNHIK 19 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 79.97 0.0079624 247710000 102280 116380 52680 75523 99867 112680 115780 117840 91119 FALSE TRUE 88763.43886 115615.4921 78156.2242 92671.65145 97879.84209 117014.8725 104551.6734 92640.83303 80347.01562 1.104750913 1.438951917 0.972733382 1.153392578 1.218213786 1.456368623 1.301251485 1.153009011 1 16.29395682 1.356967553 3.133257189 0.988861187 1.236985444 0.210924074 0.144607466 0.474327532 6.681783079 0.248439383 0.03759211 22.74927461 -1.356967553 0.248124256 SGCDVNS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGCDVNSPR 9 0 Q9P2R3;Q9P2R3-2;Q9P2R3-4 Q9P2R3 ANKFY1 Rabankyrin-5 1 S(0.013)GCDVNS(0.987)PR;S(0.002)GCDVNS(0.998)PR 65.5 0.042758 536140000 51398 51224 31049 20735.2 20957.1 57064 52113 37702 15648.4 TRUE FALSE 44605.62407 50887.50617 46064.40025 25443.44408 20540.09471 59259.28901 47059.08928 29639.7207 13798.46398 3.232651413 3.687910933 3.338371599 1.843933072 1.488578348 4.294629395 3.410458538 2.148044938 1 13.75222006 3.87131297 6.8672573 2.452889059 3.471306359 0.21641949 0.938086585 0.433990837 22.22167265 0.263269076 0.460570331 7435.547808 -3.87131297 1.0184173 SGCSEAQPPES(ph)PETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGCSEAQPPESPETR 15 0 Q9Y6A5;A0A494BZT8;A0A494C117;H0Y8F2 Q9Y6A5 TACC3 Transforming acidic coiled-coil-containing protein 3 1 SGCSEAQPPES(0.999)PET(0.001)R 171.72 2.79E-11 0 136720 123620 74458 84289 115740 120840 120260 134570 118300 TRUE FALSE 118652.1056 122807.9321 110466.1378 103428.1057 113437.0004 125488.793 108597.2037 105793.2527 104314.7088 1.137443674 1.177282988 1.058969911 0.99150069 1.087449716 1.202982729 1.041053606 1.014173878 1 16.67058307 SGDAAIVDMVPGKPMCVESFSDYPPLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 SGDAAIVDMVPGKPMCVESFSDYPPLGR 28 1 P68104;A0A087WVQ9;Q5VTE0 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3 0 ;;;;;;;; 327.53 7.74E-96 8015982000 6169320 5396542 3268551 4168107 5527242 4968042 6193946 6979080 5933634 FALSE TRUE 5354028.731 5361091.76 4849233.196 5114539.4 5417260.698 5159165.79 5593258.07 5486658.053 5232166.548 1.02329096 1.024640885 0.926811704 0.977518463 1.035376196 0.9860477 1.069013767 1.048639794 1 22.31897703 2.637606856 1.605724737 1.03996433 0.990120399 0.190311941 0.036315896 0.55067782 2.880120438 0.01763098 0.013944973 434.1170628 -2.637606856 -0.049843931 SGDAAIVEMVPGKPMCVESFSQYPPLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGDAAIVEMVPGKPMCVESFSQYPPLGR 28 1 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ; 191.42 3.65E-18 901420000 721140 552590 305350 419100 554350 502150 631720 740210 533690 FALSE TRUE 625839.5219 548959.9999 453018.2813 514263.0605 543319.5196 521468.0354 570455.8916 581921.8518 470597.7762 1.329882021 1.166516349 0.962644331 1.092786848 1.154530572 1.108097109 1.212194193 1.236558865 1 18.84413498 2.258471929 24.98755643 1.170312812 1.128174992 0 0.109064351 1057.605317 1327230.498 0.041570091 0.032154632 181.3309466 -2.258471929 -0.042137821 SGDET(ph)PGSEVPGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGDETPGSEVPGDK 14 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 SGDET(1)PGSEVPGDK;SGDET(1)PGSEVPGDK 279.18 3.68E-32 336110000 921470 588280 484830 564280 593850 511100 654280 768970 951650 TRUE FALSE 799695.4048 584415.5499 719295.4097 692408.3985 582033.5468 530762.3477 590828.0263 604531.7496 839147.0211 0.95298605 0.696439998 0.857174478 0.825133595 0.693601398 0.632502213 0.704081658 0.720412198 1 19.67856407 4.750291893 24.16076743 0.757925041 0.952986239 0.231955052 0.10589454 1678.718409 3457245.711 0.025775743 0.389187075 56271.94064 -4.750291893 0.195061198 SGDGEGTPVEHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGDGEGTPVEHVR 13 0 Q7L576;Q7L576-2;Q7L576-3 Q7L576 CYFIP1 Cytoplasmic FMR1-interacting protein 1 0 114.87 0.00070911 321310000 264110 227500 134940 191330 236900 280090 213410 261760 262660 FALSE TRUE 229207.1943 226005.5375 200197.4353 234774.4008 232186.1535 290865.2435 192713.531 205784.661 231608.634 0.989631476 0.975807912 0.864378119 1.013668604 1.002493514 1.255848016 0.832065401 0.888501683 1 17.82132951 SGDGVVTVDDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SGDGVVTVDDLR 12 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ;;;;; 229.73 1.75E-11 2826110000 2926480 3168560 1845790 2232310 3186200 3090230 3148960 3474090 3235220 FALSE TRUE 2539738.253 3147745.521 2738420.218 2739190.104 3122800.854 3209113.148 2843574.344 2731182.889 2852755.977 0.890275324 1.103405109 0.959920947 0.960190821 1.09466105 1.124916808 0.996781487 0.957383986 1 21.44392491 4.767185401 23.57050771 1.019378197 0.890274902 0.307580573 0.062923366 6919.093821 5697182.29 0.016246064 1.441357178 58503.97846 -4.767185401 -0.129103295 SGDIVMIQSEHTGAIDVLSADLESADLLGDHRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGDIVMIQSEHTGAIDVLSADLESADLLGDHRK 33 1 Q6PL24 Q6PL24 TMED8 Protein TMED8 0 ; 93.295 9.05E-05 42771000 79999 82970 32574 54025 78189 76021 83948 105466 75705 FALSE TRUE 69426.92946 82424.96461 48326.89535 66292.20197 76633.19187 78945.57706 75806.73588 82912.91664 66755.24114 1.040022151 1.23473398 0.723941589 0.993063628 1.147972662 1.182612417 1.135592271 1.242043549 1 16.02659349 3.230609243 7.697651906 1.156088098 0.995036724 0.212773455 0.135766253 0.191681451 72.322851 0.040331227 0.048048734 1700.627678 -3.230609243 -0.161051373 SGEDGEKDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGEDGEKDTK 10 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 108.35 0.0019728 229100000 682990 434480 496150 542650 285170 311690 712810 838060 1280490 FALSE TRUE 592731.141 431625.8723 736089.7995 665866.9764 279495.6749 323680.916 643681.7959 658847.3908 1129111.931 0.524953395 0.382270225 0.651919247 0.589726278 0.247535844 0.286668582 0.570077933 0.583509369 1 20.10675708 1.056969833 1.612502741 1.437930616 0.456272066 0.629568591 0.128975007 1.20304831 1.945834739 2.165894394 0.038388755 11.40170585 -1.056969833 -0.98165855 SGEGEVSGLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGEGEVSGLMR 11 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 92.538 0.023079 252490000 122240 119720 67208 78535 115130 123180 111170 106440 106840 FALSE TRUE 106085.6743 118933.5514 99710.0136 96367.57208 112839.1382 127918.8143 100388.7505 83678.63432 94209.49691 1.126061361 1.262436966 1.058386011 1.022907193 1.197746957 1.357812307 1.065590559 0.888218673 1 16.52358488 1.997713586 24.98700755 0.948358826 1.168372187 0.476645887 0.098279362 72.60565119 793472.1777 0.042387552 0.028043435 99.47491706 -1.997713586 0.220013362 SGEIWAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGEIWAR 7 0 Q12996;E9PLP8 Q12996 CSTF3 Cleavage stimulation factor subunit 3 0 ; 94.662 0.032653 248050000 653120 446890 532390 372960 344950 321920 560020 579650 572120 FALSE TRUE 566808.5372 443954.3502 789855.5847 457646.2683 338086.1699 334304.4707 505709.3466 455696.3583 504484.6254 1.123539765 0.88001562 1.565668298 0.907156027 0.670161493 0.66266533 1.002427668 0.903290874 1 18.94445078 3.504063905 24.92419586 0.850794854 1.171709291 0.382904792 0.199622101 765.5271083 708174.5242 0.05466655 0.080813223 3192.007515 -3.504063905 0.320914437 SGELTALEFSAS(ph)PGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGELTALEFSASPGLR 16 0 A0A2R8YF49;H0Y895;Q12774-2;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 SGELTALEFS(0.046)AS(0.954)PGLR;SGELTALEFSAS(1)PGLR;SGELTALEFSAS(1)PGLR;SGELTALEFSAS(1)PGLR 375.49 1.61E-104 570996000 609536 639906 392096 514676 638204 634856 600626 678463 882922 TRUE FALSE 528984.2732 635702.4154 581714.9371 631541.0521 625504.989 659279.3211 542377.383 533378.9673 778543.967 0.679453307 0.816527315 0.747183154 0.811182257 0.803429242 0.846810648 0.696656073 0.685098068 1 19.57041899 4.748930652 23.49998672 0.787093589 0.679453165 0.14065591 0.088683961 1416.055983 3208832.891 0.021282569 0.274340605 56095.83947 -4.748930652 -0.107640424 SGELTALEFSAS(ph)PGLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGELTALEFSASPGLRR 17 1 A0A2R8YF49;H0Y895;Q12774-2;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 SGELTALEFS(0.037)AS(0.963)PGLRR;SGELTALEFS(0.043)AS(0.957)PGLRR;SGELTALEFS(0.003)AS(0.997)PGLRR;SGELTALEFS(0.001)AS(0.999)PGLRR 162.42 1.74E-09 793510000 496887 484766 199093 277352 460495 485169 452864 523423 207094 TRUE FALSE 431222.124 481581.5402 295375.0407 340329.0107 451332.0504 503833.7654 408945.319 411493.0647 182611.5832 2.361417147 2.637190542 1.617504407 1.863677017 2.471541194 2.759046039 2.239427049 2.253378769 1 17.47841875 4.281767927 24.99927406 2.096447584 2.499304332 0.126835462 0.488602932 337.5250143 195282.9614 0.123272852 0.326144707 19132.3328 -4.281767927 0.402856748 SGEQAEGS(ph)PGGPGDSQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SGEQAEGSPGGPGDSQGR 18 0 P38936 P38936 CDKN1A Cyclin-dependent kinase inhibitor 1 1 S(0.001)GEQAEGS(0.999)PGGPGDSQGR;SGEQAEGS(1)PGGPGDSQGR;SGEQAEGS(1)PGGPGDSQGR 229.41 1.99E-19 332390000 388525 328909 184647 247993 312608 289573 312368 362888 329511 TRUE FALSE 337180.4369 326748.3751 273942.9068 304303.601 306387.7124 300713.0607 282074.5994 285287.2252 290556.585 1.160463931 1.124560213 0.942821196 1.047312698 1.054485523 1.034955242 0.970807801 0.9818646 1 18.14845963 4.361488455 6.053742718 1.00544816 1.151162097 0.732737736 0.034875596 0.102301111 4.894899253 0.00923931 0.025149764 22987.32602 -4.361488455 0.145713937 SGEWTEDEVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SGEWTEDEVLR 11 0 Q13938-4;Q13938 Q13938-4 CAPS Calcyphosin 0 ;;;;;; 295.96 3.12E-35 5962430000 3982300 4265290 2814870 3484920 4367290 3870970 4402020 4726090 6266460 FALSE TRUE 3456028.965 4237271.029 4176150.547 4276224.35 4280389.473 4019888.721 3975112.778 3715452.432 5525646.238 0.625452448 0.766837189 0.755775952 0.773886739 0.77464052 0.727496576 0.719393281 0.67240143 1 22.39771177 1.231165459 24.99937419 1.000000477 0.729186917 0.765602223 0.04746092 132.2397661 446998.7841 0.119643846 0.011823714 17.02807127 -1.231165459 -0.27081356 SGEWTEDEVLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SGEWTEDEVLRR 12 1 Q13938-4;Q13938 Q13938-4 CAPS Calcyphosin 0 ;;;; 278.93 9.46E-28 8330970000 3352970 3358000 1807510 2185860 3469420 3420980 3477860 3912640 1585700 FALSE TRUE 2909866.519 3335941.077 2681627.882 2682192.922 3400385.33 3552587.314 3140577.672 3075952.384 1398240.352 2.081091791 2.385813763 1.917859027 1.918263135 2.431903302 2.540755821 2.24609286 2.199873848 1 20.41518095 1.238425437 7.259736972 0.977299219 2.221231205 0.776599652 0.204843932 0.051519936 17.46005727 0.315236048 0.053128572 17.31511726 -1.238425437 1.243931986 SGFEPASLKEEVGEEAIVELVENGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGFEPASLKEEVGEEAIVELVENGK 25 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 197.33 7.45E-25 74746000 151930 114400 100800 127000 104740 83720 163980 181110 189620 FALSE TRUE 131852.0656 113648.4989 149547.2172 155837.2911 102655.8789 86940.76257 148077.2448 142381.0359 167203.3396 0.788573158 0.679702326 0.894403291 0.932022599 0.613958305 0.519970252 0.885611766 0.851544211 1 17.35124414 1.58353495 1.905734198 0.9886396 0.749156478 0.276503966 0.128005639 0.577450543 3.826364528 0.213769348 0.038607481 38.3296585 -1.58353495 -0.239483122 SGFEPASLKEEVGEEAIVELVENGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGFEPASLKEEVGEEAIVELVENGKK 26 2 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ; 246.77 1.09E-45 840060000 1530390 1053070 862800 922220 913700 576610 1589800 1893960 922840 FALSE TRUE 1328145.084 1046152.314 1280052.966 1131624.146 895519.1576 598792.5598 1435621.441 1488951.393 813742.9065 1.632143363 1.285605448 1.573043471 1.390640873 1.100493965 0.735849806 1.764219914 1.829756525 1 19.63421354 4.753227239 22.14275046 1.376861864 1.632144257 0.05881568 0.338536922 1997.204838 3014991.77 0.088840442 1.627487364 56653.56442 -4.753227239 0.255282393 SGFGEISS(ph)PVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SGFGEISSPVIR 12 0 P57740;G3V1T4 P57740 NUP107 Nuclear pore complex protein Nup107 1 SGFGEIS(0.023)S(0.977)PVIR;SGFGEIS(0.006)S(0.994)PVIR;SGFGEIS(0.002)S(0.998)PVIR;SGFGEIS(0.001)S(0.999)PVIR;SGFGEISS(1)PVIR;SGFGEIS(0.063)S(0.937)PVIR 246.73 1.51E-16 933641000 3261040 3341810 1854970 2243770 3195900 3347130 3159240 3769120 3321550 TRUE FALSE 2830085.302 3319857.43 2752039.697 2753252.272 3132307.843 3475896.257 2852857.391 2963123.019 2928880.143 0.966268732 1.133490368 0.939621822 0.940035829 1.069455795 1.186766302 0.974043748 1.011691457 1 21.48191773 4.234467283 24.99583291 1.019692768 1.049879525 0.026211952 0.081420525 514.5898984 3142390.517 0.021176728 0.04681105 17158.02449 -4.234467283 0.030186757 SGFSLDNGELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGFSLDNGELR 11 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ;;; 142.94 8.71E-05 698940000 1610900 1601390 1013030 1176440 1693570 1760120 1576890 1774280 1550070 FALSE TRUE 1398015.483 1590870.364 1502934.696 1443568.683 1659871.27 1827832.955 1423963.451 1394864.029 1366822.49 1.022821539 1.163918779 1.099582943 1.056149348 1.214401491 1.337286274 1.041805692 1.02051586 1 20.38239446 2.025948498 24.9998717 1.017554403 1.149817753 0.332158774 0.086446269 252.4087557 243180.1859 0.036631518 0.024696101 106.156966 -2.025948498 0.13226335 SGGASHSELIHNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 208.27 4.78E-09 128200000 113140 139770 51441 69078 111220 124260 98548 110810 167630 FALSE TRUE 98188.26234 138851.8417 76318.03966 84763.21569 109006.9396 129040.3626 88990.83013 87114.14382 147812.9724 0.664273648 0.939375208 0.516314897 0.573449098 0.737465311 0.872997549 0.602050204 0.589353846 1 17.17341336 1.227695716 24.97987719 1.000000677 0.684767109 0.352243048 0.133402784 565.3629199 1299758.084 0.478896154 0.033092681 16.89256957 -1.227695716 -0.315233568 SGGDTHS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGGDTHSPPR 10 0 O43295-2;O43295 O43295-2 SRGAP3 SLIT-ROBO Rho GTPase-activating protein 3 1 SGGDTHS(1)PPR 104.87 0.0016908 94627000 290390 304020 174460 208210 264080 318700 265160 303830 298550 TRUE FALSE 252014.2257 302022.8726 258829.4395 255487.2628 258825.3247 330960.5952 239444.824 238858.3189 263255.7591 0.957298053 1.147260267 0.983186238 0.970490688 0.983170608 1.257182735 0.909552083 0.907324192 1 18.00610557 SGGGGGGGGSSWGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGGGGGGGGSSWGGR 15 0 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 151.55 6.95E-06 95985000 125330 115340 32621 56136 92728 113240 121730 132630 83866 FALSE TRUE 108767.323 114582.3239 48396.62471 68882.53679 90882.89422 117596.4161 109924.6433 104268.1066 73951.45702 1.470793509 1.549426185 0.654437744 0.931456114 1.228953396 1.590183896 1.486443239 1.409953378 1 16.17429095 2.989972983 24.19095184 1.390745973 1.136413379 0.111778009 0.290341262 661.6504541 1596289.813 0.095361371 0.101935492 977.176429 -2.989972983 -0.254332595 SGGGGYSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGGGGYSSR 9 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;; 115.71 0.0033294 193508000 258724 243158 126554 162249 153267 252020 235275 261597 260656 FALSE TRUE 224532.9679 241560.6791 187755.9377 199090.1153 150217.2866 261715.3725 212458.0667 205656.5173 229841.5446 0.976903319 1.050987886 0.816892951 0.866205958 0.653568905 1.1386774 0.924367555 0.894775214 1 17.81028007 1.230542266 23.33588551 1.000000382 0.913193274 0.03974097 0.130486221 513.6726711 1494651.354 0.321164611 0.031395239 17.00365426 -1.230542266 -0.086807107 SGGGLHSVAEGVRLS(ph)PEPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 175.42 1.19E-12 589516000 371505 344428 150387 198428 357579 396400 347057 369710 148126 TRUE FALSE 322409.673 342165.4298 223114.6562 243484.1102 350463.8775 411649.7645 313399.4656 290650.3936 130614.713 2.468402414 2.619654569 1.708189308 1.864139993 2.683188359 3.151633954 2.399419317 2.225250026 1 16.99495789 1.218056609 3.144396568 0.707743372 2.407634563 0.543778703 0.403443667 0.343758232 4.28268111 1.504896427 0.113201132 16.5217714 -1.218056609 1.699891191 SGGGPGPSGSET(ph)PPPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGGGPGPSGSETPPPPR 17 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 SGGGPGPSGSET(0.999)PPPPR 213.36 3.67E-17 0 299270 235470 139120 171900 247340 241640 220490 243880 303040 TRUE FALSE 259720.7112 233923.1821 206398.8973 210932.5223 242418.4179 250936.0472 199106.9137 191728.1599 267214.9564 0.971954245 0.87541201 0.772407728 0.789373938 0.907203778 0.939079348 0.745118898 0.717505346 1 18.02764123 4.628987274 3.368015571 0.826945908 0.976367002 0.16818271 0.089651666 0.444942626 8.160219141 0.02317167 0.141403952 42558.59421 -4.628987274 0.149421094 SGGGPGPSGSET(ph)PPPPRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SGGGPGPSGSETPPPPRR 18 1 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 SGGGPGPS(0.001)GS(0.004)ET(0.996)PPPPRR;SGGGPGPS(0.006)GS(0.154)ET(0.839)PPPPRR;SGGGPGPS(0.001)GS(0.028)ET(0.971)PPPPRR 74.505 0.010447 280780000 214031 171321 86537 99963 181292 182892 165469 199845 99014 TRUE FALSE 185746.2611 170195.5811 128386.5826 122661.127 177684.6439 189927.9736 149421.8418 157109.7019 87308.67772 2.127466203 1.949354698 1.470490517 1.404913351 2.035131542 2.175361929 1.711420282 1.799474074 1 16.41383743 1.230802539 4.919205547 0.938861419 1.826616713 0.512063639 0.255856004 0.173648801 10.25942859 0.534502846 0.067935538 17.01384761 -1.230802539 0.887755294 SGGGYGGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGGGYGGDR 9 0 Q92804-2;Q92804;A0A075B7F4;A0A075B7C1 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;;; 128.36 0.00097595 1077180000 922490 830479 454111 567012 574184 857870 835854 928750 891010 FALSE TRUE 800580.6092 825023.5288 673720.5985 695760.7408 562758.8618 890872.814 754793.0077 730144.04 785675.8128 1.01897067 1.050081363 0.857504568 0.885557032 0.716273624 1.133893649 0.960692687 0.929319737 1 19.58357462 1.23062303 23.63868158 1.000000206 0.941725278 0.023041218 0.113640117 777.0310886 2313662.98 0.282223057 0.027705182 17.00681667 -1.23062303 -0.058274928 SGGIVIS(ph)PFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SGGIVISPFR 10 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 SGGIVIS(1)PFR;SGGIVIS(1)PFR;SGGIVIS(1)PFR;SGGIVIS(1)PFR;SGGIVIS(1)PFR;SGGIVIS(1)PFR 129.34 0.00032059 3361035000 2928840 3120320 2123096 3036095 3437080 3364540 2977793 3645040 6605220 TRUE FALSE 2541786.373 3099822.412 3149832.327 3725486.774 3368688.833 3493976.031 2689007.093 2865576.562 5824358.416 0.436406243 0.532216974 0.540803313 0.639638997 0.578379384 0.599890285 0.46168297 0.491998664 1 22.47366771 1.235223522 24.99990398 1.000000643 0.536390666 0.849457471 0.061500835 37.49290865 280832.0817 0.112842002 0.016033455 17.18792784 -1.235223522 -0.463609977 SGGIVIS(ph)PFRLEELTNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SGGIVISPFRLEELTNR 17 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 SGGIVIS(1)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR;S(0.025)GGIVIS(0.975)PFRLEELTNR 311.16 2.44E-58 3644210000 1736310 1912260 841200 1113730 1887770 1958650 1895340 2136680 697676 TRUE FALSE 1506852.234 1899698.238 1248007.134 1366619.419 1850207.07 2034000.533 1711530.219 1679767.61 615197.5381 2.449379494 3.087948375 2.028628296 2.221431872 3.007500771 3.30625597 2.78208236 2.730452425 1 19.2306902 3.270043951 24.9998381 2.639220193 2.462767528 0.000709204 0.661151669 1284.812768 1020217.486 0.192851471 0.248947637 1862.275592 -3.270043951 -0.176452666 ALPNNTSSS(ph)PQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 ALPNNTSSSPQPK 13 0 P04637-7;P04637;P04637-4;A0A087WZU8;A0A0U1RQC9;A0A087X1Q1;A0A087WT22;J3KP33;A0A087WXZ1;E7ESS1;P04637-5;P04637-9;P04637-8;P04637-6;P04637-2;P04637-3 P04637-7 TP53 Cellular tumor antigen p53 1 ALPNNTS(0.005)S(0.085)S(0.911)PQPK;ALPNNTS(0.004)S(0.079)S(0.917)PQPK 231.13 3.08E-12 224680000 2044350 316610 141845 234700 284510 212812 270890 411750 320880 TRUE FALSE 1774183.968 314530.1681 210441.7164 287992.2222 278848.8076 220999.0153 244619.1295 323700.4667 282945.9319 6.270399279 1.111626401 0.743752402 1.017834822 0.985519762 0.781064473 0.864543723 1.144036475 1 18.11016687 4.738446177 5.806332085 0.94662847 6.43161469 0.995096533 0.117300527 0.008684647 1.305724155 0.029975617 0.188930772 54757.82342 -4.738446177 5.484986221 up VREEYPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VREEYPDR 8 1 Q13509;A0A0B4J269;Q13509-2;G3V2A3 Q13509 TUBB3 Tubulin beta-3 chain 0 85.807 0.01503 400650000 646300 175630 102050 136810 151440 177740 142840 191820 243070 FALSE TRUE 560889.8175 174476.275 151401.7213 167874.8015 148426.6403 184577.7728 128987.3988 150800.7857 214334.5415 2.61688953 0.81403713 0.70638041 0.783237272 0.692499861 0.861166714 0.601804067 0.703576683 1 17.70950484 4.738581475 5.645926025 0.751949863 2.679223831 0.966546528 0.10798283 0.021650899 2.866154318 0.025186478 0.161239744 54774.88507 -4.738581475 1.927273968 up SGGLQTPECLS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SGGLQTPECLSR 12 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 SGGLQTPECLS(1)R;SGGLQTPECLS(1)R;SGGLQTPECLS(1)R 156.2 7.66E-05 2195500000 1804700 1775850 1392530 1610860 2368550 2176730 2305530 2648040 2876850 TRUE FALSE 1566204.322 1764184.324 2065962.166 1976630.383 2321420.489 2260470.212 2081940.055 2081777.253 2536752.07 0.617405359 0.695450038 0.814412331 0.779197308 0.915115244 0.891088348 0.820710892 0.820646715 1 21.27455109 4.621908663 0.808948087 0.876239962 0.484930068 0.721721395 0.056891853 1.219801635 0.701715708 0.022219621 0.417451808 41870.54971 -4.621908663 -0.391309894 SGGLQTPECLS(ph)REGS(ph)PIPHDPEFGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGGLQTPECLSREGSPIPHDPEFGSK 26 1 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 S(0.006)GGLQT(0.174)PECLS(0.821)REGS(0.999)PIPHDPEFGSK 128.86 0.00011176 102810000 99431 132310 41969 56296 146460 127040 210780 206740 18407 TRUE FALSE 86290.94142 131440.8469 62265.34878 69078.86723 143545.7325 131927.311 190338.588 162530.2599 16230.94543 5.316445786 8.098163318 3.836212071 4.25599775 8.843953864 8.128134715 11.72689471 10.01360399 1 13.98645942 3.22836495 24.69874758 8.494512959 5.461059407 0.140131274 2.986033014 298.1586285 722280.193 0.906673613 1.039865373 1691.862055 -3.22836495 -3.033453552 SGGMERPFVLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGGMERPFVLAR 12 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 129.34 0.00021516 1265370000 1362820 1067140 703630 907480 1239670 1473420 1074930 1158370 779880 FALSE TRUE 1182719.884 1060129.887 1043907.822 1113537.204 1215002.992 1530103.421 970683.454 910661.5899 687683.4748 1.719860848 1.541595699 1.518006263 1.619258343 1.766805568 2.225011181 1.411526508 1.324245272 1 19.39138515 1.672476165 2.167354314 1.053838411 1.708079306 0.553448448 0.212088111 0.239433412 2.309878431 0.243753905 0.062401616 47.04095883 -1.672476165 0.654240895 SGGPPPKR ddPTM_MDA-MB-175_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 ;; 95.909 0.014937 257696000 476050 409365 198616 286851 279291 372278 457690 555960 378456 FALSE TRUE 413138.7863 406675.8544 294667.3619 351984.9038 273733.6555 386599.7756 413303.2942 437072.2805 333715.3628 1.237997504 1.218630904 0.882990101 1.054745879 0.820260875 1.158471616 1.238490463 1.309715791 1 18.34825858 2.492153348 24.50326639 1.209651147 1.038948755 0.160053893 0.148735919 815.2599262 1328927.478 0.053296239 0.045414765 310.5655989 -2.492153348 -0.170702392 SGGPS(ph)PKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGGPSPKR 8 1 Q96E39 Q96E39 RBMXL1 "RNA binding motif protein, X-linked-like-1" 1 SGGPS(1)PKR 97.456 0.005034 340720000 830780 551790 245970 307040 357970 444720 662550 727780 147590 TRUE FALSE 720990.3181 548165.2552 364921.9147 376758.1248 350847.0974 461828.6662 598296.003 572149.9106 130142.0783 5.54002462 4.212052414 2.804027102 2.894975473 2.695877474 3.548649845 4.597252561 4.396348344 1 16.98972797 4.578351519 3.075588645 3.318517627 5.5728224 0.367148702 1.007014372 0.354726161 5.614377474 0.264244706 1.557966422 37874.90209 -4.578351519 2.254304774 SGGTEGLLAEKLEALITQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGGTEGLLAEKLEALITQTR 20 1 Q9UHB9;Q9UHB9-4 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 193.63 6.08E-18 386670000 224480 235590 107480 105170 227980 196970 272240 306550 58517 FALSE TRUE 194814.3992 234042.3938 159457.6875 129050.4559 223443.644 204547.5634 245838.2067 240996.6681 51599.18692 3.775532346 4.535776777 3.090313957 2.501017237 4.330371414 3.96416253 4.764381405 4.670551659 1 15.65506071 SGGYGGSRDYYSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGGYGGSRDYYSSR 14 1 Q14011;K7EMY9;K7EPM4;K7EQR7;D6W5Y5;Q14011-2;K7EJV1;Q14011-3 Q14011 CIRBP Cold-inducible RNA-binding protein 0 ;;; 143.38 8.34E-06 506166000 86802.2 92746.8 53507.4 60398.5 92015.6 106583 81036.4 120784.6 81143.6 FALSE TRUE 75331.06934 92137.54016 79383.75761 74112.90256 90184.66959 110683.317 73177.5024 94955.75324 71550.89605 1.052831949 1.287720284 1.109472585 1.03580677 1.260426837 1.546917273 1.022733557 1.327107814 1 16.12668221 3.207096147 24.95812816 1.243517228 1.132477601 0.093883561 0.165894614 466.9556345 370395.1904 0.048432721 0.054922565 1611.00225 -3.207096147 -0.111039627 SGILPILVHCLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGILPILVHCLER 13 0 O00629 O00629 KPNA4 Importin subunit alpha-3 0 ; 161.63 4.18E-05 496830000 653470 686300 308980 378960 645820 700490 622090 712860 342670 FALSE TRUE 567112.2838 681791.6501 458403.7615 465008.66 632969.4455 727438.3036 561759.8075 560420.4365 302159.943 1.876861235 2.256393231 1.51708978 1.538948729 2.094815876 2.407461083 1.859147186 1.85471453 1 18.20495289 1.208713847 3.332639286 0.808630658 1.937078581 0.524410515 0.277772119 0.332896315 4.851656966 1.017571674 0.074812194 16.17014248 -1.208713847 1.128447924 SGISTNHADYSSS(ph)PAGS(ph)PGAQVSLYNSPSVASPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGISTNHADYSSSPAGSPGAQVSLYNSPSVASPAR 35 0 Q8WV41 Q8WV41 SNX33 Sorting nexin-33 2 SGISTNHADY(0.013)S(0.271)S(0.325)S(0.391)PAGS(1)PGAQVSLYNSPSVASPAR 203.16 3.25E-42 0 49593 37714 18107 37048 59014 60396 59306 65250 54987 TRUE FALSE 43039.1594 37466.25425 26863.60576 45460.31464 57839.73686 62719.4732 53554.51325 51296.79528 48486.4995 0.887652436 0.772715181 0.554043002 0.937587063 1.192903952 1.293545087 1.104524224 1.057960377 1 15.56529548 3.472619749 5.058081764 1.124324054 0.740109117 0.721027472 0.111393724 0.097878855 7.384248074 0.033889859 0.046636714 2969.0653 -3.472619749 -0.384214938 SGIT(ph)SPVEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGITSPVEKR 10 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 S(0.001)GIT(0.5)S(0.5)PVEKR 81.625 0.019631 0 214670 187770 107850 127270 198180 170930 235930 254620 109200 TRUE FALSE 186300.8156 186536.5265 160006.6207 156168.5987 194236.6057 177505.7877 213049.5449 200171.4945 96290.5004 1.934778767 1.937226681 1.66170723 1.621848449 2.017193855 1.843440287 2.212570752 2.078829102 1 16.55510585 3.222969441 24.92195335 1.890773497 1.790401149 0 0.339606505 1316.167139 2103841.659 0.102960705 0.117158926 1670.973034 -3.222969441 -0.100372348 SGITS(ph)PVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGITSPVEK 9 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 SGIT(0.009)S(0.991)PVEK;SGIT(0.015)S(0.985)PVEK 120.96 0.00065802 431980000 1308460 1197660 923210 1174740 1306640 1157310 1517220 1785720 2715100 TRUE FALSE 1135543.696 1189792.493 1369677.444 1441482.672 1280640.42 1201832.465 1370080.238 1403857.674 2394123.971 0.474304468 0.49696361 0.572099632 0.602091909 0.534909819 0.501992578 0.572267875 0.58637635 1 21.19106643 1.190599684 2.946319114 1.128533194 0.538531728 0.930380696 0.039491021 0.127930062 1.232484004 0.192949405 0.010869162 15.50956737 -1.190599684 -0.590001467 SGITS(ph)PVEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGITSPVEKR 10 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 S(0.001)GIT(0.104)S(0.896)PVEKR;S(0.015)GIT(0.217)S(0.768)PVEKR 63.624 0.071517 337800000 739520 665640 375760 487080 759860 713520 769130 858470 430400 TRUE FALSE 641790.5583 661267.367 557478.7928 597678.9586 744740.2726 740969.5761 694539.891 674892.8711 379518.6023 1.691064824 1.742384597 1.468910323 1.574834422 1.962328772 1.952393299 1.830054935 1.778286669 1 18.53381108 SGIYETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGIYETR 7 0 A0A087WY71;Q96CW1-2;Q96CW1;E9PFW3 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 ; 98.523 0.04872 0 425110 423940 242850 301860 399630 468160 388790 407760 431810 FALSE TRUE 368930.6364 421155.1102 360293.0723 370401.9266 391678.1449 486170.4181 351085.2056 320563.6972 380761.9137 0.968927361 1.106085181 0.946242414 0.97279143 1.028669441 1.276835735 0.922059673 0.841900636 1 18.53852965 2.031356422 24.99997586 0.901353887 1.047972459 0.260534564 0.100908735 226.0920898 180258.7433 0.041097037 0.027707355 107.4871189 -2.031356422 0.146618572 SGKNS(ph)QEDS(ph)EDS(ph)EDKDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGKNSQEDSEDSEDKDVK 18 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 S(0.553)GKNS(0.701)QEDS(0.762)EDS(0.984)EDKDVK 50.498 0.058882 0 292450 201960 220460 108660 195590 98282 277660 279380 214770 TRUE FALSE 253801.9915 200633.3115 327075.1934 133332.9138 191698.1417 102062.9721 250732.5759 219636.7611 189380.1353 1.340172195 1.059421101 1.727082901 0.7040491 1.012239966 0.538931773 1.323964499 1.159766629 1 17.53092548 3.728429337 24.99645476 0.98555797 1.343944987 0.344738562 0.269211447 894.9101692 2207972.294 0.074471557 0.111891787 5350.930831 -3.728429337 0.358387016 SGKNS(ph)QEDSEDSEDKDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGKNSQEDSEDSEDKDVK 18 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 S(0.029)GKNS(0.971)QEDSEDSEDKDVK 143.31 5.55E-08 132160000 362100 208670 290320 228760 186390 117810 376280 388450 325040 TRUE FALSE 314247.5676 207299.233 430719.7231 280703.4544 182681.2037 122342.2269 339788.4235 305382.9904 286614.1415 1.096413338 0.723269382 1.502786013 0.979377545 0.637376798 0.426853421 1.185525675 1.065484727 1 18.12875027 3.480734549 24.99615176 0.883242268 1.097736592 0.134205894 0.281119394 363.161239 2512298.329 0.085110509 0.112300432 3025.063873 -3.480734549 0.214494324 SGKYDLDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGKYDLDFK 9 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;; 103.91 0.0030515 29048950000 51237100 44465300 30784400 28098100 40220300 30636500 54271800 59676000 35921600 FALSE TRUE 44465987.42 44173204.52 45671838.81 34478203.06 39419994.72 31815105.98 49008529.19 46914751.8 31674989.37 1.403820121 1.394576775 1.441889633 1.088499278 1.244514852 1.004423572 1.547231117 1.481129204 1 24.9168408 3.836868362 24.77304385 1.265359089 1.411545225 0.168971947 0.181810171 98.82307225 24889.84435 0.0514036 0.089033632 6868.602159 -3.836868362 0.146186136 SGKYDLDFKSPDDPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGKYDLDFKSPDDPSR 16 2 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 101.96 0.00087424 360500000 2065800 1764220 707370 935900 1451500 1090600 2237600 2417300 459330 FALSE TRUE 1792799.296 1752630.723 1049456.498 1148410.399 1422617.99 1132556.088 2020597.896 1900379.206 405028.5307 4.426353109 4.327178433 2.591068082 2.835381491 3.512389578 2.7962378 4.988779168 4.691963806 1 18.62766401 SGLEPAS(ph)SPSKGSEPRPLVPPVSGHATIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SGLEPASSPSKGSEPRPLVPPVSGHATIAR 30 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 SGLEPAS(0.586)S(0.405)PS(0.008)KGSEPRPLVPPVSGHATIAR;SGLEPAS(0.499)S(0.499)PS(0.003)KGSEPRPLVPPVSGHATIAR;SGLEPAS(0.5)S(0.5)PSKGSEPRPLVPPVSGHATIAR 177.78 4.00E-18 1282060000 600730 530560 145708 270198 594330 525980 613530 715620 173652 TRUE FALSE 521342.0084 527074.7164 216172.8762 331550.5856 582503.9958 546214.791 554029.955 562590.232 153123.0584 3.404725676 3.442164243 1.411759133 2.16525577 3.804155964 3.567162234 3.618200687 3.674105245 1 17.22433203 3.245332317 24.99064938 3.258529944 2.580402778 0.057564596 0.98636271 401.0553363 1480067.627 0.29039318 0.366319252 1759.26927 -3.245332317 -0.678127166 SGLFTNTEPHS(ph)ITEDVTISAVMLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGLFTNTEPHSITEDVTISAVMLR 24 0 P57740;P57740-2;F5GY77 P57740 NUP107 Nuclear pore complex protein Nup107 1 SGLFTNTEPHS(0.986)IT(0.013)EDVTISAVMLR;SGLFTNTEPHS(1)ITEDVTISAVMLR;SGLFTNTEPHS(1)ITEDVTISAVMLR;SGLFTNTEPHS(1)ITEDVTISAVMLR 216.49 8.55E-33 318479000 285212 283324 165031 205209 305626 288276 268637 322769 309388 TRUE FALSE 247520.5116 281462.826 244840.5436 251804.8399 299544.6405 299366.1643 242584.6251 253747.3611 272812.5031 0.90729167 1.031707942 0.897468191 0.922995966 1.097987215 1.097333007 0.889199074 0.930116319 1 18.05755024 4.779441416 21.95762932 0.977353018 0.907290806 0.0857548 0.075831576 15040.38765 8077556.23 0.019552538 4.893231796 60178.50792 -4.779441416 -0.070062212 SGLIHVGDELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SGLIHVGDELR 11 0 S4R337;Q5T2T1-2;Q5T2T1 S4R337 MPP7 MAGUK p55 subfamily member 7 0 ;; 132.76 0.0001757 550040000 410740 420630 211035 309282 410910 477850 376250 445430 434820 FALSE TRUE 356459.6683 417866.8538 313092.2319 379509.2052 402733.6949 496233.1987 339761.3329 350178.2608 383416.0749 0.929694115 1.089852203 0.816586086 0.989810365 1.050382916 1.294242029 0.88614264 0.91331137 1 18.5485513 5.870166809 11.88674153 0.993426577 0.956874402 0 0.131804074 0 0 0.029956019 0 741595.0274 -5.870166809 -0.036552175 SGLS(ph)LEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGLSLEELR 9 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 S(0.151)GLS(0.849)LEELR;S(0.012)GLS(0.988)LEELR;S(0.001)GLS(0.999)LEELR;SGLS(1)LEELR 143 0.00010804 1092960000 2224110 2099480 1286540 1498740 2127480 2141420 2030990 2251750 2102900 TRUE FALSE 1930188.228 2085688.378 1908715.047 1839051.824 2085147.31 2223801.813 1834024.902 1770230.786 1854297.558 1.040926911 1.12478624 1.029346687 0.991778162 1.124494449 1.199269127 0.989067205 0.954663818 1 20.82244134 2.031130398 24.99879941 0.973425092 1.082939488 0.410581769 0.058704906 184.6171453 148253.3038 0.024895234 0.016784199 107.4311928 -2.031130398 0.109514396 SGLSLEELR ddPTM_MDA-MB-175_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 ;; 66.27 0.064204 5232390000 1700690 1921920 1353380 1166340 1545130 2472310 1252250 1289200 686400 FALSE TRUE 1475939.508 1909294.781 2007879.095 1431175.323 1514384.936 2567421.365 1130806.988 1013514.613 605254.5739 2.438543335 3.154531768 3.317412509 2.364584069 2.50206277 4.241886763 1.868316303 1.674526152 1 19.20718255 2.019250134 24.98620627 1.501236619 2.9794111 0.609984362 0.569447691 152.5667117 198027.1038 0.228184675 0.153819157 104.5322105 -2.019250134 1.478174481 SGLTVPTS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SGLTVPTSPK 10 0 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 1 SGLTVPT(0.162)S(0.838)PK;SGLTVPT(0.054)S(0.946)PK;SGLTVPT(0.112)S(0.888)PK;SGLTVPT(0.251)S(0.749)PK;SGLTVPT(0.049)S(0.951)PK;SGLTVPT(0.024)S(0.976)PK;SGLTVPT(0.002)S(0.998)PK;SGLTVPTS(1)PK 215.77 8.43E-09 22930640000 24940000 24108800 14324510 16631600 27021600 18803330 26217000 32924500 24527300 TRUE FALSE 21644115.81 23950427.71 21251890.95 20408058.98 26483923.03 19526706.27 23674479.38 25883851.89 21627710.54 1.00075853 1.107395425 0.982623238 0.943606996 1.224536595 0.90285591 1.094636408 1.196791119 1 24.36637762 2.014425006 24.99820708 1.122430614 1.030874358 0.086358376 0.100619594 416.7515737 722218.2738 0.038722085 0.026095322 103.3772573 -2.014425006 -0.091556256 SGMLQAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGMLQAEK 8 0 P12270 P12270 TPR Nucleoprotein TPR 0 ; 77.058 0.079558 619740000 793610 827170 473160 508040 764230 618000 1166710 978120 852460 FALSE TRUE 688732.4277 821736.2658 701981.7586 623398.2469 749023.3182 641774.8599 1053562.644 768956.6497 751683.1499 0.916253647 1.093195006 0.933879865 0.829336466 0.996461499 0.853783752 1.401604711 1.022979762 1 19.51976514 SGMNS(ph)PLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGMNSPLR 8 0 Q9UQR1 Q9UQR1 ZNF148 Zinc finger protein 148 1 SGMNS(1)PLR 99.174 0.007343 236490000 329190 301500 153450 245170 311510 308230 252880 342020 303980 TRUE FALSE 285686.7074 299519.4266 227658.9333 300839.5957 305311.5605 320087.8076 228355.7365 268881.6846 268043.8307 1.065820865 1.117427049 0.849334725 1.122352247 1.139035954 1.194162189 0.851934312 1.003125809 1 18.0321094 2.235356305 25 0.958246862 1.076934042 0.27436592 0.099043422 123.4388281 963049.1341 0.040097512 0.028311222 171.9318375 -2.235356305 0.11868718 SGMNVAR ddPTM_MDA-MB-175_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 ;; 133.7 0.0075516 1001000000 1438780 1214530 757650 961640 1088000 1348650 1187520 1240280 1376180 FALSE TRUE 1248641.578 1206551.672 1124052.074 1179995.06 1066350.929 1400533.438 1072354.493 975055.7739 1213489.568 1.028967706 0.99428269 0.92629727 0.97239819 0.878747504 1.154137188 0.883694859 0.803513932 1 20.21073028 2.04188798 24.99999117 0.874486015 0.986418767 0.20648808 0.085762457 176.3542492 105252.7183 0.033560176 0.022626244 110.1255219 -2.04188798 0.111932752 SGMS(ph)PEQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 SGMSPEQSR 9 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.217)GMS(0.783)PEQSR;S(0.44)GMS(0.56)PEQSR;S(0.03)GMS(0.97)PEQSR;SGMS(1)PEQSR;SGMS(1)PEQSR;SGMS(1)PEQSR;S(0.001)GMS(0.999)PEQSR;S(0.001)GMS(0.999)PEQSR;SGMS(1)PEQSR 168.05 6.24E-05 17513197000 16250683 13137175 7518017 9036840 11711555 13343909 12292918 14425179 12568343 TRUE FALSE 14103114.07 13050876.03 11153755.17 11088792.64 11478517.97 13857257.81 11100752.7 11340466.73 11082527.81 1.272553907 1.177608237 1.006426996 1.000565289 1.035731032 1.250369776 1.001644471 1.023274376 1 23.40178365 4.42830103 3.76098124 1.04682368 1.258094002 0.515161986 0.075142101 0.175771562 5.016467302 0.019710735 0.067218429 26810.26024 -4.42830103 0.211270322 SGMS(ph)PPPCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SGMSPPPCK 9 0 Q9H6T0-2;Q9H6T0 Q9H6T0-2 ESRP2 Epithelial splicing regulatory protein 2 1 SGMS(1)PPPCK;SGMS(1)PPPCK;SGMS(1)PPPCK;SGMS(1)PPPCK;SGMS(1)PPPCK 144.17 0.0001051 1759030000 3811650 2872310 2229060 2547940 2876140 2467000 3192000 3660740 4698880 TRUE FALSE 3307930.795 2853441.606 3307040.872 3126488.72 2818910.441 2561907.086 2882440.331 2877919.239 4143383.759 0.79836457 0.688674227 0.798149789 0.754573774 0.680340177 0.618312769 0.695673029 0.69458187 1 21.98237802 1.236346095 24.99817849 1.00000037 0.712857602 0.722147178 0.055313956 32.92762402 371607.5069 0.090348868 0.01401882 17.23241303 -1.236346095 -0.287142768 SGNFGGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SGNFGGSR 8 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;; 144.9 0.0013446 3512740000 2381180 2043020 1056610 1319900 1587030 2032630 1973440 2227110 1982720 FALSE TRUE 2066501.03 2029599.267 1567590.13 1619603.468 1555451.208 2110826.591 1782056.093 1750859.858 1748325.1 1.181988996 1.160882073 0.896623934 0.926374316 0.889680762 1.207342153 1.019293318 1.00144982 1 20.73754205 4.324359193 8.169439401 0.995813825 1.174833138 0.413185834 0.089081372 0.257737497 21.47885741 0.02299082 0.061180973 21103.72858 -4.324359193 0.179019313 SGNLTEDDKHNNAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGNLTEDDKHNNAK 14 1 P13797;A0A0A0MSQ0;P13797-3;P13797-2 P13797 PLS3 Plastin-3 0 ; 69.878 0.027501 159033000 77771 66626 42244 71673 72440 70057 69939 87390 77255 FALSE TRUE 67493.3653 66188.32942 62673.3397 87947.4501 70998.58573 72752.13812 63156.32654 68702.32857 68122.00191 0.990771901 0.971614567 0.920016117 1.291028561 1.042226942 1.067968293 0.927106144 1.008518931 1 16.05583321 SGPFGQIFRPDNFVFGQSGAGNNWAK ddPTM_MDA-MB-175_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 ; 292.1 2.62E-70 16419200000 5954900 4868300 2684270 3512980 5076300 3891600 5099800 6295200 5488900 FALSE TRUE 5167944.877 4836319.817 3982391.95 4310655.802 4975291.562 4041312.37 4605222.181 4949020.469 4840008.495 1.067755332 0.999237878 0.82280681 0.890629801 1.027950998 0.834980429 0.951490516 1.022523096 1 22.20657815 1.814808727 5.34811329 1.010863522 0.936274375 0.117120946 0.078337018 0.422553149 19.81519666 0.042833513 0.021143582 65.28429622 -1.814808727 -0.074589147 SGPKPFSAPKPQT(ph)SPSPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGPKPFSAPKPQTSPSPKR 19 3 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 SGPKPFS(0.002)APKPQT(0.498)S(0.498)PS(0.002)PKR 55.228 0.055521 4951200000 410380 254470 131420 124500 237490 168490 398190 413280 35222 TRUE FALSE 356147.2432 252798.3698 194975.1516 152769.6279 232764.4136 174971.9193 359573.5951 324903.2881 31058.09529 11.46713087 8.139532302 6.277756243 4.918834412 7.494484498 5.633697679 11.5774516 10.46114661 1 14.92268174 4.70294457 3.414757348 7.27042122 11.84708613 0.188939404 2.932095192 0.526936357 10.55790582 0.752233429 5.935239527 50459.68906 -4.70294457 4.576664909 SGPKPFSAPKPQTS(ph)PS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGPKPFSAPKPQTSPSPK 18 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 2 SGPKPFSAPKPQT(0.316)S(0.69)PS(0.994)PK;SGPKPFSAPKPQT(0.48)S(0.545)PS(0.975)PK 89.946 0.0015001 3022000000 4631300 3849800 2965300 2684900 3848900 2764100 4926100 6306500 3026900 TRUE FALSE 4019261.971 3824510.41 4399328.998 3294547.581 3772314.42 2870436.716 4448367.58 4957904.052 2669063.33 1.50586984 1.432903583 1.648266996 1.234345976 1.413347663 1.075447211 1.666639952 1.857544554 1 21.34790211 SGPKPFSAPKPQTS(ph)PSPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGPKPFSAPKPQTSPSPKR 19 3 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 SGPKPFSAPKPQT(0.122)S(0.877)PS(0.001)PKR 170.59 6.58E-11 6586900000 4028000 2793300 1449300 1138300 2384600 1571000 4000600 4500700 241000 TRUE FALSE 3495689.594 2774950.628 2150186.328 1396768.413 2337151.125 1631437.387 3612622.428 3538260.329 212509.2545 16.44958758 13.0580225 10.11808324 6.572741577 10.99787927 7.677018067 16.99983577 16.64991173 1 17.69716614 4.511564237 2.527302624 10 16.55584121 0.174334277 4.625784197 0.674321014 7.33530468 1.287323873 7.582636336 32476.12745 -4.511564237 6.555841209 SGPKPFSAPKPQTSPS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGPKPFSAPKPQTSPSPK 18 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 SGPKPFSAPKPQT(0.001)S(0.005)PS(0.994)PK;SGPKPFSAPKPQT(0.001)S(0.038)PS(0.961)PK 192.75 8.29E-15 70107000000 4399400 2987700 2680000 2501200 3304100 2089440 4812100 5519600 2997300 TRUE FALSE 3818008.143 2968073.602 3976056.964 3069135.688 3238354.874 2169822.109 4345423.283 4339276.494 2642962.609 1.444594082 1.123010062 1.504393952 1.161248244 1.22527457 0.820981009 1.644148604 1.641822885 1 21.33372458 2.185979651 24.99999543 1.482045234 1.220558343 0.124970367 0.255527391 163.4712348 77722.16535 0.102136528 0.068860498 153.4545078 -2.185979651 -0.261486891 SGPKPFSAPKPQTSPSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGPKPFSAPKPQTSPSPK 18 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 0 161.22 2.17E-11 408700000 442620 357640 261890 303210 467670 286460 587970 629130 429910 FALSE TRUE 384126.6455 355290.6393 388540.88 372058.4648 458364.282 297480.3016 530948.7599 494595.4454 379086.5296 1.013295424 0.937228341 1.024939822 0.981460526 1.209128382 0.784729286 1.400600439 1.304703298 1 18.53216767 2.228617842 24.99992071 1.256497449 1.000231914 0.387796674 0.143008428 190.9721198 480172.1376 0.055524804 0.037931267 169.2847523 -2.228617842 -0.256265535 SGPLFNFDVHDDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SGPLFNFDVHDDVR 14 0 Q14320;B0S8I6 Q14320 FAM50A Protein FAM50A 0 ;;;; 163.99 4.19E-06 1545850000 1749030 1672580 868107 1115470 1706970 1658150 1481780 1840210 1607100 FALSE TRUE 1517891.254 1661592.712 1287926.449 1368754.512 1673004.637 1721940.103 1338077.204 1446695.412 1417110.469 1.071117099 1.172521655 0.908839838 0.965877073 1.180574608 1.215106473 0.944229284 1.020876949 1 20.4345208 SGPPS(ph)PPSTATSFGGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGPPSPPSTATSFGGPR 17 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2;A0A087X0E3 A0A0A0MS59 SRCAP Helicase SRCAP 1 SGPPS(0.84)PPS(0.057)T(0.103)ATSFGGPR 124.68 5.19E-05 87909000 84904 59000 41688 73678 72396 65501 63091 71772 160470 TRUE FALSE 73683.72128 58612.42512 61848.45624 90407.716 70955.46124 68020.86585 56972.44453 56424.11633 141499.4194 0.520735149 0.414223785 0.437093357 0.63892641 0.50145408 0.480714805 0.402633769 0.398758642 1 17.11043661 1.233818988 24.99979448 1.000000801 0.470566268 0.842251604 0.071480562 59.08598758 311487.0167 0.148481719 0.018727727 17.13243085 -1.233818988 -0.529434533 SGPPS(ph)PPSTATSFGGPRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SGPPSPPSTATSFGGPRPR 19 1 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2;A0A087X0E3 A0A0A0MS59 SRCAP Helicase SRCAP 1 SGPPS(1)PPSTATSFGGPRPR;SGPPS(0.993)PPS(0.006)T(0.001)ATSFGGPRPR;S(0.056)GPPS(0.941)PPS(0.001)T(0.002)ATSFGGPRPR 194.7 1.53E-15 2197910000 627780 549930 437416 407550 561480 516580 525810 678310 455090 TRUE FALSE 544817.2824 546317.4736 648951.8407 500090.4565 550307.6465 536453.1669 474817.0271 533258.6851 401289.7786 1.357665486 1.36140391 1.617165139 1.246207811 1.37134728 1.336822405 1.183227315 1.328861869 1 18.61428488 -0.041404295 0.499988188 3.25E-15 1.409155454 0.518175949 0.108606588 13.63291594 1.008203763 14.84710899 0.073321662 0.909066608 0.041404295 1.409155454 SGPS(ph)PLS(ph)SPNGK ddPTM_MDA-MB-175_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(0.688)S(0.312)PNGK;SGPS(1)PLS(0.973)S(0.027)PNGK 208.68 9.37E-08 661970000 2885600 2527700 1900670 2124300 2844800 2237300 3104000 3578400 3254700 TRUE FALSE 2504260.649 2511095.372 2819840.369 2606654.783 2788194.046 2323370.379 2802974.558 2813187.007 2869933.074 0.872585034 0.874966526 0.982545689 0.908263265 0.971518838 0.809555596 0.976668963 0.98022739 1 21.45258566 2.035488951 24.99999912 0.985625597 0.907575955 0.382769767 0.049262472 179.6384618 126544.6771 0.019463638 0.01312233 108.5147943 -2.035488951 -0.078049642 SGPS(ph)PLSS(ph)PNGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGPSPLSSPNGK 12 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 2 S(0.006)GPS(0.962)PLS(0.13)S(0.902)PNGK 90.926 0.005941 0 261910 238440 157500 199910 263420 216480 289650 316050 292940 TRUE FALSE 227297.9299 236873.6719 233667.5268 245302.6209 258178.4574 224808.1257 261559.7876 248465.167 258308.9669 0.879945952 0.917016837 0.904604782 0.949648105 0.999494754 0.870307091 1.012585009 0.961891374 1 17.9787382 8 0.157966147 1.023977674 0.48280874 0.408119608 0.038963898 141.7250172 1.847137468 0.524278011 17.32964608 99999999.95 -8 -0.541168933 SGPS(ph)PLSSPNGK ddPTM_MDA-MB-175_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;S(0.003)GPS(0.774)PLS(0.193)S(0.03)PNGK;SGPS(1)PLSSPNGK;SGPS(1)PLSSPNGK 235.6 4.96E-16 360673000 887250 778284 452466 612535 753671 621437 909679 1027474 958194 TRUE FALSE 769997.6645 773171.4012 671280.071 751620.4338 738674.4216 645344.0835 821458.4706 807756.6809 844917.3969 0.911328927 0.915085195 0.794491951 0.889578598 0.874256376 0.763795474 0.972235243 0.956018522 1 19.68845078 2.193853543 24.818604 0.971744053 0.859955534 0.565464997 0.048692594 91.19932935 50627.51401 0.019607997 0.013219784 156.2620593 -2.193853543 -0.11178852 SGPTHVSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGPTHVSTR 9 0 Q13111;Q13111-2;Q13111-3 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 0 69.276 0.060902 0 20126 24690 12450 14503 25666 28825 20210 24037 20965 FALSE TRUE 17466.29811 24527.80976 18470.86164 17796.12781 25155.29681 29933.9164 18250.03731 18896.87461 18486.54158 0.944811555 1.326792773 0.999151819 0.962653168 1.360735684 1.619227494 0.987206678 1.022196311 1 14.17418773 SGQGAFGNMCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SGQGAFGNMCR 11 0 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 ;; 187.97 7.80E-06 481446000 291865 267095 161327 195532 275521 268186 284111 298702 268386 FALSE TRUE 253294.3008 265340.4354 239345.2768 239930.5291 270038.6711 278503.289 256557.9589 234826.9018 236657.7128 1.070298102 1.121199188 1.011356334 1.013829324 1.141051639 1.176818983 1.084088728 0.992263886 1 17.85244242 1.748268714 5.497180778 0.99638292 1.089509148 0.359477085 0.051159175 0.183590627 14.00524558 0.033198923 0.014581987 56.01040513 -1.748268714 0.093126228 SGQGFHGNSEVNAILS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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;SGQGFHGNSEVNAILS(1)PR 225.88 2.46E-19 2513046000 595379 639921 370330 557716 888575 927337 865742 920260 972094 TRUE FALSE 516698.1567 635717.3168 549422.8267 684353.942 870894.096 963012.2545 781782.4741 723469.5605 857174.1547 0.602792506 0.741643123 0.640969894 0.79838378 1.016006014 1.123473275 0.912046251 0.844017002 1 19.70922883 3.451400361 3.722322742 0.963536556 0.673037966 0.76544819 0.080369122 0.126001774 3.77485932 0.026424868 0.036605112 2827.485336 -3.451400361 -0.29049859 SGQKPVLDVHAELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGQKPVLDVHAELDR 15 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 ; 105.28 0.00079776 395370000 1237890 1214620 734930 980740 1339970 1202370 1379440 1632200 1545810 FALSE TRUE 1074299.7 1206641.081 1090344.606 1203432.007 1313307.219 1248625.952 1245662.121 1283166.732 1363066.103 0.788149377 0.885240326 0.799920564 0.88288602 0.963494885 0.916042112 0.913867727 0.941382615 1 20.3784241 7.999999971 0.141507239 1.049459939 0.163819694 0.696339944 0.036377859 100.3933495 1.215406377 0.755807736 17.69766113 99999993.24 -7.999999971 -0.885640245 SGS(ph)AAQAEGLCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGSAAQAEGLCK 12 0 F8WF93;H7BZZ2;F8WE30;H7C0X4;Q92685 F8WF93 ALG3 "Dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase" 1 S(0.004)GS(0.996)AAQAEGLCK;S(0.001)GS(0.999)AAQAEGLCK 155.43 7.24E-05 183272000 374420 281582 235936 325950 375250 318270 321010 492350 525240 TRUE FALSE 324939.4483 279732.2693 350035.4388 399961.9293 367783.2592 330514.0528 289878.4996 387064.784 463146.7256 0.701590728 0.603981965 0.755776559 0.863574991 0.794096641 0.713627096 0.625889127 0.83572821 1 18.82110979 1.38849291 3.2965086 1.003923042 0.727204078 0.58435078 0.07530965 0.210520853 3.462520421 0.120720046 0.021170706 24.46205339 -1.38849291 -0.276718964 SGS(ph)FGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGSFGK 6 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 SGS(1)FGK;SGS(1)FGK;SGS(1)FGK;SGS(1)FGK 95.741 0.045106 5761800000 11480100 9365800 7140500 7589600 6132200 8036800 12996200 12999000 15422900 TRUE FALSE 9962975.698 9304275.443 10593669.68 9312934.68 6010181.217 8345980.897 11735830.52 10219265.01 13599622.33 0.732592086 0.684156899 0.778967932 0.684793625 0.441937362 0.613692108 0.862952679 0.751437412 1 23.69706325 1.020614742 1.053286352 1.282206598 0.665762158 0.480219704 0.105863652 2.599381327 1.726594728 2.025920902 0.037001065 10.48611804 -1.020614742 -0.616444441 SGS(ph)FSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SGSFSK 6 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;G3V3H3;Q07866-5;Q07866-10;H0YG16 Q07866-6 KLC1 Kinesin light chain 1 1 SGS(0.997)FS(0.002)K;SGS(0.998)FS(0.002)K;SGS(0.876)FS(0.124)K 125.98 0.018555 7189500000 8688600 8913700 5652630 5936260 4527160 6432250 10177400 10437000 12206100 TRUE FALSE 7540379.496 8855145.318 8386260.775 7284178.563 4437078.373 6679702.82 9190397.314 8205128.771 10763108.76 0.700576354 0.822731193 0.77916715 0.676772736 0.412248772 0.620610919 0.853879443 0.762338182 1 23.3595915 1.074864381 1.17858148 1.233816191 0.6811453 0.400006894 0.120155066 2.598381884 2.334980577 1.96052184 0.041217942 11.88131147 -1.074864381 -0.552670891 SGS(ph)GGGSAKEPQEER ddPTM_MDA-MB-175_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(0.065)GS(0.933)GGGS(0.001)AKEPQEER;S(0.022)GS(0.978)GGGSAKEPQEER 138.75 5.24E-06 782200000 808190 631160 347420 363570 623760 514670 764560 892640 201561 TRUE FALSE 701385.6438 627013.8684 515433.4741 446124.1253 611348.3964 534469.6879 690413.0889 701755.8825 177732.6882 3.946295141 3.527847774 2.900048828 2.510084835 3.439707139 3.007154696 3.884558861 3.948378262 1 17.43934952 4.476442296 3.783538332 3.098866378 3.893178404 0.123642736 0.834326297 0.523806241 16.10102855 0.209371188 0.80454805 29953.13583 -4.476442296 0.794312026 SGS(ph)IVELIAGGGS(ph)SCSPVLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSIVELIAGGGSSCSPVLSR 21 0 P42858 P42858 HTT Huntingtin 2 S(0.42)GS(0.58)IVELIAGGGS(0.484)S(0.298)CS(0.218)PVLS(0.001)R 88.755 0.003524 54096000 96186 82735 61945 60334 96265 89039 96149 106000 101410 TRUE FALSE 83474.7764 82191.50834 91901.80919 74033.75685 94349.51484 92464.38795 86824.48478 83332.72489 89421.42533 0.933498612 0.919147822 1.027738138 0.827919669 1.055110836 1.034029458 0.970958408 0.931910049 1 16.44833292 3.206931193 24.99998615 0.989813365 0.933699539 0.26222889 0.057999403 342.2247702 270494.4301 0.017696794 0.02006792 1610.390476 -3.206931193 -0.056113826 SGS(ph)IVELIAGGGSS(ph)CSPVLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSIVELIAGGGSSCSPVLSR 21 0 P42858 P42858 HTT Huntingtin 2 S(0.414)GS(0.586)IVELIAGGGS(0.111)S(0.592)CS(0.295)PVLS(0.001)R 107.47 0.00045498 0 29412 28307 19267 21912 32430 29978 25425 27984 29521 TRUE FALSE 25525.12968 28121.04945 28584.58564 26887.4545 31784.70645 31131.27306 22959.28741 21999.83937 26031.06101 0.980564322 1.080288254 1.098095296 1.032898908 1.221030001 1.195927936 0.881995836 0.84513802 1 14.6679465 2.224348583 24.99651592 0.894603635 1.102669389 0.56415744 0.079386554 162.3220764 285494.2993 0.033408317 0.02264484 167.6287794 -2.224348583 0.208065754 SGS(ph)IVELIAGGGSSCS(ph)PVLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSIVELIAGGGSSCSPVLSR 21 0 P42858 P42858 HTT Huntingtin 2 S(0.144)GS(0.856)IVELIAGGGS(0.054)S(0.087)CS(0.844)PVLS(0.014)R 110.4 0.00039899 72484000 146400 138620 91916 82336 148690 147790 147990 160580 158520 TRUE FALSE 127052.8691 137709.3961 136366.885 101031.6472 145731.3599 153475.5769 133637.9526 126241.2166 139779.9462 0.908949191 0.985187073 0.975582612 0.722790715 1.042577021 1.09797994 0.956059551 0.903142547 1 17.09279787 SGS(ph)MDPSGAHPSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SGSMDPSGAHPSVR 14 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 1 S(0.04)GS(0.959)MDPSGAHPSVR;S(0.097)GS(0.863)MDPS(0.04)GAHPSVR;SGS(0.668)MDPS(0.332)GAHPSVR;SGS(0.932)MDPS(0.068)GAHPSVR;S(0.008)GS(0.967)MDPS(0.025)GAHPS(0.001)VR 294.18 1.52E-43 1680753000 2479080 2066780 641377 1290292 2591220 2434950 2364350 2551170 2794920 TRUE FALSE 2151463.297 2053203.186 951549.0625 1583272.519 2539659.792 2528624.102 2135055.701 2005622.149 2464507.742 0.872978916 0.83310884 0.386101064 0.642429518 1.030493737 1.026015889 0.866321361 0.813802333 1 21.23286808 3.248531565 24.99940458 0.928495188 0.673076012 0.443707308 0.145645129 214.5953479 538035.5988 0.045073136 0.057482119 1772.276852 -3.248531565 -0.255419176 SGS(ph)PAPETTNESVPFAQHSSLDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGSPAPETTNESVPFAQHSSLDSR 24 0 O15047 O15047 SETD1A Histone-lysine N-methyltransferase SETD1A 1 S(0.142)GS(0.648)PAPET(0.193)T(0.017)NESVPFAQHSSLDSR;S(0.163)GS(0.837)PAPETTNESVPFAQHSSLDSR 228.05 2.52E-33 665250000 231255 214115 55072 108663 345180 264250 232010 266360 249026 TRUE FALSE 200694.0658 212708.4645 81705.0034 133336.595 338311.5933 274415.8685 209509.7059 209400.9868 219586.43 0.913963881 0.968677639 0.37208585 0.607216917 1.540676231 1.249694111 0.954110443 0.953615334 1 17.74442938 3.279773328 24.99998774 1.107960545 0.709042286 0.441178065 0.2356531 161.5059094 97969.81538 0.073223969 0.094530745 1904.466456 -3.279773328 -0.398918259 SGS(ph)PISSEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSPISSEER 10 0 H8Y6P7;P0CAP2-3;P0CAP2;P0CAP1-11;P0CAP2-2 H8Y6P7 GCOM1;POLR2M DNA-directed RNA polymerase II subunit GRINL1A 1 S(0.014)GS(0.983)PIS(0.003)SEER 121.29 0.0028791 0 204060 211170 146590 162220 185750 168430 229610 200610 273560 TRUE FALSE 177092.954 209782.8104 217481.4143 199054.5304 182053.9384 174909.6111 207342.4575 157711.1126 241220.0484 0.734155204 0.869674025 0.901589299 0.825198949 0.754721424 0.725103955 0.859557317 0.65380599 1 17.87999029 3.408231068 6.70832344 0.781766891 0.842583011 0.011494068 0.099986329 0.57369639 44.55172158 0.027439963 0.035575504 2559.947557 -3.408231068 0.06081612 SGS(ph)PLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGSPLEK 7 0 B1AKL4;Q9NRA8;Q9NRA8-3;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 SGS(1)PLEK;S(0.004)GS(0.996)PLEK 140.11 0.0027759 554630000 2323880 1784950 1435400 1572000 1283700 1496450 2287250 2547600 2852700 TRUE FALSE 2016773.37 1773224.546 2129564.241 1928946.627 1258156.882 1554019.4 2065432.847 2002815.565 2515457.056 0.801752256 0.704931353 0.846591372 0.766837431 0.500170289 0.617788086 0.821096445 0.796203442 1 21.26238913 1.157230368 1.418780056 1.160415065 0.712759061 0.431965076 0.101326894 1.609728959 2.446254165 1.102648431 0.031787482 14.3625108 -1.157230368 -0.447656004 SGS(ph)PRPTEPTDFLMLFEGS(ph)PSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSPRPTEPTDFLMLFEGSPSGK 23 1 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 2 S(0.457)GS(0.54)PRPT(0.002)EPT(0.002)DFLMLFEGS(0.95)PS(0.05)GK 58.861 0.040674 24105000 21137 21609 16077 19648 20125 19544 22341 28818 23251 TRUE FALSE 18343.6919 21467.04906 23851.89097 24109.3787 19724.55187 20295.87033 20174.37326 22655.49496 20502.29327 0.89471415 1.047055994 1.163376734 1.175935706 0.962065639 0.989931715 0.984005691 1.10502248 1 14.32349767 3.202000761 24.99986668 1.017578706 1.075263456 0.111031653 0.084473041 444.5557756 303988.6151 0.02713922 0.030773829 1592.211515 -3.202000761 0.057684751 SGS(ph)PRPTEPTDFLMLFEGSPSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGSPRPTEPTDFLMLFEGSPSGK 23 1 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 S(0.095)GS(0.851)PRPT(0.018)EPT(0.036)DFLMLFEGSPSGK;S(0.134)GS(0.793)PRPT(0.029)EPT(0.044)DFLMLFEGSPSGK 183.49 2.20E-17 427300000 777680 645030 482680 557790 728480 569180 812380 1016550 717670 TRUE FALSE 674907.6176 640792.7555 716105.6625 684444.7448 713984.6732 591076.7229 733595.5126 799168.6933 632827.8702 1.066494776 1.01258618 1.131596278 1.081565426 1.128244673 0.934024481 1.159233888 1.262853188 1 19.27145361 2.040746768 24.99995145 1.168454721 1.062949364 0.143311854 0.085492783 194.9107002 119585.6119 0.03364343 0.022682376 109.8365208 -2.040746768 -0.105505357 SGS(ph)PSDNS(ph)GAEEMEVSLAKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSPSDNSGAEEMEVSLAKPK 21 1 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 2 S(0.021)GS(0.97)PS(0.009)DNS(1)GAEEMEVSLAKPK 185.68 2.00E-17 199440000 490220 347460 356220 309390 373430 265870 534010 633780 478390 TRUE FALSE 425436.1849 345177.5124 528489.1835 379641.7282 365999.4736 276098.1909 482221.7924 498251.0791 421835.2792 1.008536284 0.818275591 1.25283306 0.899976239 0.867635998 0.654516596 1.14315188 1.181150804 1 18.68632023 SGS(ph)PSDNSGAEEMEVSLAKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SGSPSDNSGAEEMEVSLAKPK 21 1 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 1 S(0.009)GS(0.984)PS(0.006)DNS(0.001)GAEEMEVSLAKPK;S(0.017)GS(0.616)PS(0.367)DNSGAEEMEVSLAKPK;S(0.046)GS(0.779)PS(0.176)DNSGAEEMEVSLAKPK;S(0.004)GS(0.94)PS(0.055)DNSGAEEMEVSLAKPK;S(0.003)GS(0.97)PS(0.027)DNSGAEEMEVSLAKPK;S(0.002)GS(0.9)PS(0.098)DNSGAEEMEVSLAKPK;S(0.005)GS(0.994)PS(0.001)DNSGAEEMEVSLAKPK 243.37 2.59E-30 8434260000 7746600 5340300 5085910 4609330 5392930 4095550 7792170 8833670 7402700 TRUE FALSE 6722867.183 5305219.218 7545473.087 5655948.826 5285621.244 4253108.459 7036486.553 6944658.414 6527561.239 1.029920201 0.812741393 1.155940605 0.866471967 0.809739051 0.651561633 1.077965613 1.063897857 1 22.63811266 SGS(ph)SQELDVKPSAS(ph)PQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSSQELDVKPSASPQER 18 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.291)GS(0.531)S(0.177)QELDVKPS(0.272)AS(0.728)PQER 132.66 6.43E-05 0 158090 122420 93191 114330 126520 110730 137170 154900 203250 TRUE FALSE 137198.006 121615.815 138258.4793 140290.3739 124002.4995 114989.8548 123867.2745 121775.8404 179222.0165 0.765519821 0.678576312 0.771436914 0.782774218 0.691893228 0.64160563 0.691138717 0.679469201 1 17.45138835 1.234849585 24.99954155 1.000000412 0.710294999 0.790466696 0.046453669 50.98217055 343391.8766 0.087030106 0.011991989 17.17313506 -1.234849585 -0.289705413 SGS(ph)SQELDVKPSASPQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGSSQELDVKPSASPQER 18 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.072)GS(0.499)S(0.428)QELDVKPSASPQER;S(0.073)GS(0.51)S(0.417)QELDVKPSASPQER 131.59 1.01E-05 827620000 446510 351770 253692 294367 389210 295395 403740 485340 472560 TRUE FALSE 387502.5722 349459.1997 376378.2997 361207.5265 381465.4825 306759.0368 364585.3569 381553.8179 416694.4951 0.929944064 0.838646068 0.903247593 0.866840169 0.915456016 0.736172521 0.87494642 0.915668007 1 18.66863052 1.376166723 2.327875798 1.013402786 0.864202069 0.390518993 0.053424731 0.454052777 3.372677536 0.124937063 0.014013772 23.77752915 -1.376166723 -0.149200718 SGS(ph)TESLNPRPQTTISPADLHGMWYPTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSTESLNPRPQTTISPADLHGMWYPTVR 29 1 Q96JB2 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 1 S(0.204)GS(0.768)T(0.028)ESLNPRPQTTISPADLHGMWYPTVR 216.94 1.55E-34 199170000 150760 110810 56304 74925 121020 99264 115230 139960 57085 TRUE FALSE 130836.684 110082.0818 83532.80273 91937.86641 118611.9388 103082.7503 104055.0123 110030.6432 50336.47633 2.599242012 2.186924668 1.659488483 1.826466076 2.356381444 2.047873785 2.067189043 2.185902772 1 15.61931661 1.235889968 24.99887069 0.999998536 2.101411831 0.647391904 0.258677119 48.63018618 455115.3903 0.428315645 0.064117968 17.21432383 -1.235889968 1.101413294 SGS(ph)TGSSLSVSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSTGSSLSVSVR 13 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 SGS(0.534)T(0.461)GS(0.005)SLSVSVR 269.57 4.07E-25 381190000 213490 210840 152810 175120 322690 292090 285870 313620 317270 TRUE FALSE 185276.7556 209454.9782 226709.4271 214883.6725 316269.1003 303326.8913 258146.3714 246554.8036 279762.702 0.662263962 0.748688001 0.810363302 0.768092641 1.130490584 1.084229202 0.922733336 0.881299765 1 18.09384411 3.334522158 8.2647254 0.986086236 0.749754841 0.716950709 0.079674136 0.167128171 12.77858596 0.026061371 0.033644709 2160.340255 -3.334522158 -0.236331395 SGS(ph)VSNYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGSVSNYR 8 0 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 1 S(0.001)GS(0.921)VS(0.078)NYR;S(0.001)GS(0.959)VS(0.04)NYR;S(0.001)GS(0.994)VS(0.005)NYR;S(0.004)GS(0.993)VS(0.003)NYR 163.86 0.0003498 4315830000 2987460 3340770 2395030 3105520 4150200 4443060 4836960 4873430 4858880 TRUE FALSE 2592659.592 3318824.262 3553274.519 3810675.781 4067619.14 4613987.393 4367872.364 3831284.92 4284468.742 0.605129772 0.774617452 0.829338416 0.889416171 0.94938705 1.076910037 1.019466503 0.894226368 1 22.0306849 4.601387187 0.763412261 0.985428612 0.441078794 0.860815441 0.050575068 0.911920069 0.472701025 0.023272666 0.41216826 39938.08038 -4.601387187 -0.544349819 SGS(ph)YSGRS(ph)PS(ph)PYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSYSGRSPSPYGR 14 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 3 S(0.223)GS(0.553)Y(0.058)S(0.272)GRS(0.895)PS(1)PYGR 147.37 6.56E-06 272390000 534330 388240 212740 260640 374170 362070 333540 392240 384630 TRUE FALSE 463716.9367 385689.6259 315621.7756 319822.2956 366724.7491 375999.0672 301193.3421 308362.5284 339159.4796 1.367253356 1.137192528 0.930599894 0.942984982 1.081275244 1.10862025 0.888058156 0.909196254 1 18.37160429 4.584103519 2.601173561 0.975999591 1.389591944 0.751236079 0.071726045 0.189659083 2.031628361 0.020356353 0.145327154 38379.87172 -4.584103519 0.413592353 SGS(ph)YSYLEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSYSYLEER 10 0 O14974;O14974-5;O14974-2;O14974-3;O14974-4;H0YIS3;H0YIM2;A0A0U1RQZ1 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 S(0.009)GS(0.988)YS(0.003)YLEER 167.18 5.58E-06 254640000 200070 167190 107880 147330 189810 149240 211400 191100 205530 TRUE FALSE 173630.2426 166091.7179 160051.1288 180783.5283 186033.1524 154981.3594 190898.4605 150234.7521 181232.4775 0.958052579 0.916456698 0.883126088 0.997522799 1.026489043 0.855152241 1.053334718 0.828961532 1 17.46748199 5.202630652 15.59092708 0.940362714 26.48382224 0 0.074924315 265651.9028 1438062.302 0.017075974 260532295 159452.25 -5.202630652 25.54345952 SGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFK 39 0 P28072;A0A087X2I4 P28072 PSMB6 Proteasome subunit beta type-6;Proteasome subunit beta type 0 331.31 1.07E-129 316610000 158450 129950 79225 102400 122430 104180 144720 179300 128770 FALSE TRUE 137510.431 129096.3499 117538.475 125651.4851 119993.8825 108187.872 130685.0767 140958.0903 113546.9573 1.211044614 1.136942398 1.035153013 1.106603718 1.056777613 0.952802916 1.150934202 1.241407904 1 16.79292952 -1.887974934 19.17174686 0.005550087 1.105364993 0 0.090932515 0 0 0 0.021415635 0.012942705 1.887974934 1.099814906 SGSAS(ph)PAPGDTLPWNLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGSASPAPGDTLPWNLPK 18 0 F6QMI7;E7ETB9;Q5T0V7;Q03001-11 F6QMI7 DST Dystonin 1 S(0.026)GS(0.026)AS(0.947)PAPGDTLPWNLPK;S(0.001)GS(0.003)AS(0.996)PAPGDTLPWNLPK 248.36 1.80E-24 74423000 148186 137320 81709 102147 141604 114627 144097 173714 157285 TRUE FALSE 128602.8446 136417.9359 121223.7457 125341.0376 138786.3574 119036.7749 130122.4951 136566.6129 138690.9465 0.927262002 0.983610966 0.874056662 0.903743472 1.000687939 0.858287998 0.938219101 0.984682969 1 17.08151409 1.720896179 3.573402227 0.99561021 0.925548768 0.292215822 0.043148866 0.241455844 6.84762464 0.029516855 0.011181682 52.5891534 -1.720896179 -0.070061442 SGSGSVGNGS(ph)SRYSPSQNS(ph)PIHHIPSRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSGSVGNGSSRYSPSQNSPIHHIPSRR 28 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 SGSGSVGNGS(0.254)S(0.254)RY(0.228)S(0.264)PS(0.18)QNS(0.794)PIHHIPS(0.026)RR 76.691 0.014075 56586000 23443 19428 4331.6 3115 16246 19864 18210 18512 2494.3 TRUE FALSE 20344.94815 19300.37619 6426.376248 3822.30836 15922.73638 20628.18093 16443.997 14553.35286 2199.426696 9.25011422 8.775185019 2.921841524 1.737865766 7.239494009 9.378889952 7.476492413 6.616884705 1 11.1029118 4.365011845 8.827555321 5.546823263 9.125219272 0.25328195 2.677436275 0.38940119 28.13106551 0.711043468 1.889754102 23174.57858 -4.365011845 3.578396008 SGSGSVGNGSS(ph)RYSPSQNSPIHHIPS(ph)RR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSGSVGNGSSRYSPSQNSPIHHIPSRR 28 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 SGSGSVGNGS(0.06)S(0.321)RY(0.289)S(0.321)PS(0.287)QNS(0.287)PIHHIPS(0.435)RR 76.691 0.014075 123660000 44202 35016 9756.1 9823 34289 35433 38580 37755 6463.6 TRUE FALSE 38360.59371 34785.97759 14474.18259 12053.46229 33606.71599 36796.13044 34838.51754 29681.38706 5699.480571 6.73054206 6.103359272 2.539561704 2.114835227 5.896452416 6.456049806 6.112577647 5.207735457 1 12.47661473 4.454768791 24.50795709 4.442669398 6.573747685 0.196336805 1.839634422 290.2970872 318290.8369 0.48348804 1.279399857 28495.00851 -4.454768791 2.131078287 SGSGSVGNGSSRYS(ph)PSQNS(ph)PIHHIPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGSGSVGNGSSRYSPSQNSPIHHIPSR 27 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 SGSGSVGNGS(0.004)S(0.004)RYS(0.992)PSQNS(1)PIHHIPSR;SGSGSVGNGS(0.006)S(0.005)RY(0.001)S(0.987)PS(0.003)QNS(0.997)PIHHIPSR;S(0.002)GS(0.002)GSVGNGS(0.056)S(0.046)RY(0.004)S(0.881)PS(0.008)QNS(1)PIHHIPSR;SGSGSVGNGS(0.005)S(0.014)RY(0.001)S(0.971)PS(0.008)QNS(1)PIHHIPSR 170.47 7.12E-12 3124270000 612502 553783 174321 236408 527901 571164 527523 600231 135913 TRUE FALSE 531558.3088 550145.163 258623.2187 290088.0497 517396.8029 593137.0487 476363.9007 471876.2717 119845.52 4.435362364 4.590452469 2.157971518 2.420516426 4.317197698 4.949179984 3.974816086 3.937370974 1 16.87081645 SGSGSVGNGSSRYS(ph)PSQNS(ph)PIHHIPSRR ddPTM_MDA-MB-175_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(0.06)GS(0.065)GS(0.075)VGNGS(0.095)S(0.102)RY(0.005)S(0.597)PS(0.004)QNS(0.6)PIHHIPS(0.397)RR 71.359 0.0059639 139940000 50307 42728 13917 16017 41632 42389 44764 48343 15743 TRUE FALSE 43658.80249 42447.31695 20647.30775 19653.90465 40803.60465 44019.73226 40422.79417 38005.22566 13881.88047 3.145020775 3.057749779 1.487356687 1.415795554 2.939342744 3.171020838 2.911910547 2.737757736 1 13.76091539 SGSGSVGNGSSRYS(ph)PSQNSPIHHIPSR ddPTM_MDA-MB-175_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(0.003)S(0.004)RYS(0.991)PS(0.002)QNSPIHHIPSR;SGSGSVGNGS(0.051)S(0.022)RYS(0.886)PS(0.042)QNSPIHHIPSR 202.66 2.47E-25 701960000 198351 160614 27863 84691 207313 194273 171581 204656 44236 TRUE FALSE 172138.4128 159558.9161 41337.64 103921.386 203187.8769 201746.808 154941.101 160891.907 39006.47047 4.413073285 4.090575592 1.059763662 2.664208905 5.209081325 5.17213697 3.97218972 4.124749178 1 15.25142584 1.234876799 24.94244191 0.999995856 3.826828564 0.35075625 1.213440632 133.9374271 906723.2273 2.308891311 0.319272325 17.17421119 -1.234876799 2.826832708 SGSIVELIAGGGS(ph)SCSPVLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSIVELIAGGGSSCSPVLSR 21 0 P42858 P42858 HTT Huntingtin 1 SGSIVELIAGGGS(0.38)S(0.331)CS(0.25)PVLS(0.04)R 70.335 0.019048 152630000 181330 158810 88767 120100 156650 164920 148380 195300 169590 TRUE FALSE 157366.7811 157766.7667 131695.0181 147370.5406 153532.9715 171264.5791 133990.1304 153536.6148 149541.2634 1.052330156 1.055004907 0.880660061 0.985484122 1.026693021 1.145266365 0.896007747 1.026717384 1 17.1901841 SGSIVELIAGGGSSCS(ph)PVLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSIVELIAGGGSSCSPVLSR 21 0 P42858 P42858 HTT Huntingtin 1 SGSIVELIAGGGSS(0.001)CS(0.999)PVLSR 198.61 8.88E-22 146780000 330540 251510 135490 170910 256410 278300 236660 287870 262430 TRUE FALSE 286858.3015 249857.8142 201013.4172 209717.7277 251307.9427 289006.3811 213708.7496 226311.2407 231405.8244 1.239633023 1.079738658 0.868661875 0.90627679 1.086005261 1.24891576 0.923523642 0.977984203 1 17.82006565 4.633079481 3.703731764 1.002473287 1.243275226 0.32984776 0.106858431 0.296791757 6.557676439 0.0280013 0.15604831 42961.50444 -4.633079481 0.240801939 SGSMDPS(ph)GAHPSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGSMDPSGAHPSVR 14 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 1 SGS(0.16)MDPS(0.84)GAHPSVR;S(0.002)GS(0.2)MDPS(0.798)GAHPSVR 169.46 3.49E-06 697603000 920700 762170 233051 491922 944330 946100 890400 982850 1077390 TRUE FALSE 799027.1622 757163.2551 345755.2431 603620.4087 925539.6806 982497.0792 804049.145 772675.176 950022.1816 0.841061585 0.796995344 0.36394439 0.635375068 0.974229548 1.034183305 0.84634776 0.8133233 1 19.85760167 3.244358664 24.99332862 0.917063255 0.648076294 0.478783696 0.141397295 134.6301919 580339.5762 0.043670048 0.054845714 1755.329549 -3.244358664 -0.26898696 SGSMDPSGAHPSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SGSMDPSGAHPSVR 14 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ;;;; 134.13 3.64E-05 1085004000 2072040 2010000 667029 1159661 1934600 2274840 1955945 2088400 1975550 FALSE TRUE 1798214.664 1996796.178 989606.4555 1422979.754 1896105.245 2362354.567 1766257.755 1641811.912 1742002.73 1.032268569 1.146264666 0.568085479 0.816864251 1.088462844 1.356114159 1.013923644 0.942485269 1 20.73231545 3.228416655 24.89751641 1.071808559 0.886057073 0.208157857 0.182974828 349.8577734 858695.0688 0.059354421 0.068063339 1692.063491 -3.228416655 -0.185751486 SGSPS(ph)DNS(ph)GAEEMEVSLAKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSPSDNSGAEEMEVSLAKPK 21 1 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 2 S(0.008)GS(0.244)PS(0.748)DNS(1)GAEEMEVSLAKPK 190.35 1.04E-17 151090000 450040 280070 282700 246800 294910 213290 414220 494490 404590 TRUE FALSE 390566.0737 278230.2017 419414.6656 302839.7121 289041.868 221495.4043 374049.0082 388747.1616 356759.8311 1.094759106 0.779880966 1.175621886 0.848861575 0.810186133 0.62085298 1.04846167 1.089660684 1 18.44459366 2.051935353 24.99974355 1.056587091 0.886431267 0.183182887 0.156502488 152.8572809 73579.02788 0.063598892 0.04287837 112.7029679 -2.051935353 -0.170155824 SGSPS(ph)DNSGAEEMEVSLAKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSPSDNSGAEEMEVSLAKPK 21 1 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 1 S(0.078)GS(0.341)PS(0.576)DNS(0.005)GAEEMEVSLAKPK 86.813 0.0027548 0 280120 215990 186690 183350 199190 164260 297990 331730 289620 TRUE FALSE 243101.4323 214571.1475 276973.9084 224982.4198 195226.5087 170579.1885 269090.9757 260792.121 255381.4535 0.951914984 0.84019863 1.084549816 0.880966165 0.764450613 0.667938827 1.053682528 1.021186611 1 17.96229423 SGSS(ph)PEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGSSPEVK 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SGS(0.015)S(0.985)PEVK;SGS(0.025)S(0.975)PEVK;SGS(0.139)S(0.861)PEVK;SGS(0.033)S(0.967)PEVK 146.48 0.00057967 1441850000 6327380 4523490 3000890 3592990 2875610 3466190 5314470 6414460 6204450 TRUE FALSE 5491200.701 4493774.896 4452130.441 4408833.295 2818390.987 3599536.572 4799073.517 5042777.646 5470966.989 1.00369838 0.821385855 0.813773954 0.80585997 0.515154084 0.657934252 0.877189266 0.921734249 1 22.38336442 1.879193403 2.746195932 0.963403237 0.764981361 0.278123001 0.126355545 0.374159594 5.04890361 0.092474897 0.038045531 75.71700088 -1.879193403 -0.198421876 SGSS(ph)PGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SGSSPGLR 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.014)GS(0.083)S(0.903)PGLR;S(0.021)GS(0.086)S(0.893)PGLR;S(0.121)GS(0.158)S(0.722)PGLR 107.1 0.0042673 4061430000 2653070 2437010 1267015 1645400 1895300 2125970 2010290 2604920 2107030 TRUE FALSE 2302460.077 2421001.121 1879747.692 2019013.218 1857587.238 2207757.442 1815332.385 2047878.13 1857939.314 1.239254727 1.303057157 1.011737939 1.086694922 0.999810502 1.18828286 0.977067643 1.102230904 1 20.82527195 4.24071525 24.99999999 1.05690861 1.271156005 0.666917749 0.064247518 28.719033 333203.1861 0.014530073 0.034765894 17406.65214 -4.24071525 0.214247395 SGSS(ph)QELDVKPSASPQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGSSQELDVKPSASPQER 18 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.023)GS(0.241)S(0.736)QELDVKPSASPQER;S(0.001)GS(0.024)S(0.975)QELDVKPSASPQER 218.69 4.69E-19 770910000 814210 653130 465900 596730 650160 516220 605930 844980 801430 TRUE FALSE 706610.0856 648839.546 691210.7983 732226.6669 637223.088 536079.3174 547167.0019 664287.6026 706685.8584 0.999892777 0.918144234 0.978101925 1.036141672 0.901706296 0.758582206 0.774271899 0.940004098 1 19.43070951 3.03867649 8.852534467 0.866161739 0.977202609 0.344539639 0.075175731 0.368327069 77.80906291 0.02465661 0.027903782 1093.141771 -3.03867649 0.111040869 SGSS(ph)S(ph)PDSEITELKFPSINHD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 2 S(0.029)GS(0.189)S(0.839)S(0.941)PDS(0.001)EITELKFPSINHD;S(0.029)GS(0.184)S(0.836)S(0.951)PDSEITELKFPSINHD 118.54 4.56E-05 234410000 221419 186522 95187 144547 181665 155104 199374 228700 220708 TRUE FALSE 192157.9181 185296.7247 141219.7516 177368.6056 178050.2219 161070.9512 180038.7402 179794.2847 194616.1517 0.98736881 0.952113805 0.725632227 0.911376595 0.914878957 0.827634037 0.9250966 0.92384051 1 17.57027192 1.180885605 1.379992147 1.060478207 0.885658968 0.185853861 0.071823618 2.607763792 3.902439714 0.672568931 0.021403557 15.16650822 -1.180885605 -0.174819239 SGSS(ph)SPDSEITELKFPSINHD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 1 S(0.1)GS(0.1)S(0.373)S(0.373)PDS(0.042)EIT(0.014)ELKFPSINHD 69.639 0.011487 1468500000 113850 97792 50629 85658 114250 100930 110300 140830 107050 TRUE FALSE 98804.43404 97149.59791 75113.35374 105107.9581 111976.6485 104812.8424 99603.12298 110714.6004 94394.67095 1.046716229 1.029185196 0.795737227 1.113494618 1.186260277 1.110368216 1.055177395 1.172890369 1 16.52641779 3.57916045 24.99976903 1.113626491 0.962775425 0.406047412 0.084645619 35.52436088 8695.359792 0.022481174 0.033344968 3794.55149 -3.57916045 -0.150851067 SGSSS(ph)PDSEITELKFPSINHD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 1 S(0.002)GS(0.015)S(0.126)S(0.853)PDS(0.004)EITELKFPSINHD;SGSS(0.013)S(0.824)PDS(0.162)EITELKFPSINHD;SGS(0.001)S(0.024)S(0.72)PDS(0.255)EITELKFPSINHD;S(0.001)GS(0.003)S(0.026)S(0.935)PDS(0.035)EITELKFPSINHD 285.82 1.28E-45 1610632000 1339480 1361900 541135 1112560 1648190 1334390 1881190 2141280 1421580 TRUE FALSE 1162464.324 1352953.589 802829.696 1365183.752 1615394.244 1385724.847 1698752.483 1683383.935 1253522.432 0.927358214 1.079321402 0.640458978 1.089078039 1.288683954 1.105464738 1.355183154 1.342922865 1 20.25755638 3.490218672 8.615204816 1.234419418 0.895599326 0.511212436 0.149352788 0.141859906 74.52119573 0.041070043 0.057412624 3091.851821 -3.490218672 -0.338820092 SGSSSPDS(ph)EITELKFPSINHD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 1 S(0.012)GS(0.012)S(0.075)S(0.403)PDS(0.493)EIT(0.006)ELKFPSINHD;S(0.001)GS(0.007)S(0.05)S(0.403)PDS(0.538)EIT(0.001)ELKFPSINHD 202.41 3.88E-22 1583040000 595290 574680 255000 508070 670230 538930 754970 910950 604140 TRUE FALSE 516620.9182 570904.8892 378318.8529 623435.0589 656893.7343 559662.9858 681753.1256 716150.4315 532719.2574 0.96978082 1.071680592 0.710165528 1.170288196 1.233095528 1.050577726 1.279760617 1.34432991 1 19.02301591 3.567224708 9.630281003 1.20263092 0.93292525 0.455340139 0.133905714 0.381031186 38.53395341 0.036489486 0.054129494 3691.685606 -3.567224708 -0.26970567 SGSTGS(ph)SLSVSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSTGSSLSVSVR 13 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 SGST(0.001)GS(0.956)S(0.043)LSVSVR 211.83 1.97E-08 361030000 128500 113240 83133 85485 139190 152850 147930 181890 156420 TRUE FALSE 111518.3994 112496.119 123336.3969 104895.6758 136420.3913 158730.2384 133583.7714 142994.239 137928.2058 0.808524977 0.815613589 0.894207216 0.760509246 0.989068121 1.150817829 0.968502204 1.036729494 1 17.07355799 3.119094626 5.55813897 1.035731691 0.825704706 0.774517739 0.056529095 0.093681745 4.193862652 0.01646408 0.018799639 1315.511429 -3.119094626 -0.210026985 SGSYSGRS(ph)PS(ph)PYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGSYSGRSPSPYGR 14 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 SGS(0.01)Y(0.001)S(0.209)GRS(0.78)PS(0.999)PY(0.001)GR 92.528 0.058862 685770000 1209200 897250 432360 586930 866120 872760 782190 851070 658450 TRUE FALSE 1049401.156 891355.9057 641450.7422 720201.4272 848885.9065 906335.642 706333.3342 669075.3035 580608.7911 1.807415203 1.53520911 1.104789924 1.240424599 1.462061752 1.561009161 1.216539165 1.152368538 1 19.14720689 8 0.057004984 8.45E-14 3.910098583 0.438802922 0.185454447 985.0901145 5.459474946 96.91501571 357.1011382 100000000 -8 3.910098583 YHEEFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YHEEFEK 7 0 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;;;; 169.37 0.0010144 9627010000 43587100 11178200 6701330 8649330 10208300 8930790 11580600 13794900 11856600 FALSE TRUE 37826954.3 11104769.67 9942115.603 10613292.57 10005174.8 9274363.27 10457515.19 10844967.99 10454926.26 3.618098624 1.062156671 0.950950333 1.015147531 0.956981863 0.887080697 1.000247629 1.037306981 1 23.31767955 4.738667073 5.795055249 0.98330129 3.698715128 0.997485585 0.04150776 0.00655754 0.976510722 0.011136272 0.070467542 54785.68207 -4.738667073 2.715413838 up SGT(ph)PTQDEMMDKPTSSSVDTMSLLSK ddPTM_MDA-MB-175_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(0.062)GT(0.779)PT(0.158)QDEMMDKPTSSSVDTMSLLSK;S(0.182)GT(0.8)PT(0.018)QDEMMDKPTSSSVDTMSLLSK 156.67 3.96E-08 591510000 413213 264887 259845 238598 295859 191973 380472 434920 393522 TRUE FALSE 358605.8551 263146.9399 385506.9111 292775.3226 289971.9847 199358.3255 343573.884 341915.7426 347000.2775 1.033445442 0.758347923 1.110970037 0.843732244 0.835653467 0.574519211 0.990125675 0.985347173 1 18.40457729 2.080025177 24.87225174 0.990625547 0.857639896 0.158540431 0.143717799 52.52633154 16321.58865 0.058176888 0.039222845 120.2334135 -2.080025177 -0.132985651 SGTHNMYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SGTHNMYR 8 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ;;;;; 153.08 0.00044675 3360760000 3391990 4221040 1791350 2491349 4250160 4953730 3776560 4123190 4464750 FALSE TRUE 2943729.927 4193311.71 2657652.852 3057047.868 4165590.131 5144303.199 3410309.792 3241477.905 3936932.341 0.747721747 1.065121609 0.675056776 0.776505056 1.058080193 1.306678081 0.866235306 0.823351184 1 21.90864049 3.242601359 24.99901029 0.991372168 0.82381384 0.25805777 0.162007811 184.3615269 1140588.804 0.051017446 0.063445488 1748.241234 -3.242601359 -0.167558328 SGTNS(ph)PPPPFSDWGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SGTNSPPPPFSDWGR 15 0 D6RAU6;D6REP2;D6RAJ6;Q9UKT5-2;Q9UKT5 D6RAU6 FBXO4 F-box only protein 4 1 SGTNS(0.998)PPPPFS(0.001)DWGR;SGTNS(1)PPPPFSDWGR;S(0.002)GT(0.007)NS(0.991)PPPPFSDWGR;SGTNS(1)PPPPFSDWGR;SGTNS(1)PPPPFSDWGR;SGT(0.001)NS(0.999)PPPPFSDWGR;SGT(0.003)NS(0.997)PPPPFSDWGR 177.04 8.07E-07 2638394000 2212761 2011975 1172327 1358723 2200907 1982170 1953777 2320264 2015409 TRUE FALSE 1920339.027 1998758.204 1739268.258 1667241.824 2157113.257 2058425.363 1764300.007 1824093.6 1777149.644 1.080572496 1.124698874 0.978684189 0.938155 1.213805075 1.158273514 0.992769525 1.026415308 1 20.76113374 2.187581126 24.99999216 1.009998013 1.07899653 0.166822997 0.079662226 224.0182491 109855.1412 0.034743849 0.023424339 154.0214211 -2.187581126 0.068998516 SGTS(ph)QEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGTSQEELR 9 0 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 1 SGT(0.004)S(0.996)QEELR;S(0.009)GT(0.094)S(0.897)QEELR 110.08 0.0024592 342600000 2634700 614940 486960 571650 611910 589460 562680 613360 711540 TRUE FALSE 2286517.72 610900.4186 722455.4848 701451.8696 599734.1882 612136.9076 508111.3802 482197.7372 627422.5518 3.644302732 0.973666657 1.1514656 1.117989571 0.955869671 0.975637401 0.809839204 0.768537465 1 19.25907786 4.738674092 8.01401776 0.95476526 3.665960495 0.980950974 0.117144912 0.013349911 10.62513544 0.033966353 0.195523369 54786.56747 -4.738674092 2.711195235 SGTSSPQS(ph)PVFR ddPTM_MDA-MB-175_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;SGTS(0.002)S(0.384)PQS(0.614)PVFR 275.19 8.48E-28 2269420000 3028580 2500630 1240680 1661200 2771750 2550240 2372960 2754530 2523940 TRUE FALSE 2628345.48 2484203.197 1840676.998 2038400.85 2716597.598 2648349.383 2142830.704 2165495.195 2225562.688 1.180980205 1.116213535 0.827061402 0.915903587 1.22063405 1.18996845 0.962826487 0.973010199 1 21.08573871 SGTT(ph)PKPVINSTPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGTTPKPVINSTPGR 15 1 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 1 S(0.055)GT(0.178)T(0.766)PKPVINSTPGR 73.11 0.062642 278270000 449390 363260 242860 297110 422910 332760 429550 558300 437380 TRUE FALSE 390001.9729 360873.7211 360307.9083 364573.3665 414494.9184 345561.4925 387892.3071 438911.8897 385673.4347 1.011223325 0.935697636 0.934230559 0.945290325 1.07473028 0.895995061 1.005753242 1.138040244 1 18.55702025 1.989748537 24.55423629 1.076785139 0.965966608 0.340801345 0.058473893 346.8110348 830678.7819 0.023873167 0.01498213 97.66715488 -1.989748537 -0.110818531 SGVAFYHLGDYDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGVAFYHLGDYDK 13 0 Q92623 Q92623 TTC9 Tetratricopeptide repeat protein 9A 0 94.09 0.0053148 858010000 1145000 1087900 668750 863020 1019400 953310 1327700 1385100 1345500 FALSE TRUE 993685.3489 1080753.513 992159.7368 1058981.881 999115.9344 989984.4526 1198939.858 1088907.144 1186436.523 0.837537727 0.910924009 0.83625185 0.892573569 0.842114951 0.834418389 1.010538563 0.917796378 1 20.17820348 2.244786668 24.99999648 0.965397091 0.86106026 0.707039492 0.035304895 80.28305083 322368.7264 0.012541586 0.009468777 175.7060307 -2.244786668 -0.104336831 SGVGTGPPS(ph)PIALPPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGVGTGPPSPIALPPLR 17 0 Q92630 Q92630 DYRK2 Dual specificity tyrosine-phosphorylation-regulated kinase 2 1 SGVGTGPPS(1)PIALPPLR 95.751 0.0026129 87625000 58037 55799 32716 52797 74629 52534 56281 66423 63495 TRUE FALSE 50367.2634 55432.45269 48537.56703 64785.3658 73144.02891 54555.01697 50822.87728 52218.95835 55988.69343 0.899597049 0.990065124 0.866917302 1.157115157 1.306407141 0.974393465 0.907734654 0.932669708 1 15.77284789 7.831150551 19.93197819 1.002579812 0.051994189 0 0.133351146 0 0 0.032006712 0 67787645.68 -7.831150551 -0.950585623 SGVHSHMTNTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SGVHSHMTNTR 11 0 O14841 O14841 OPLAH 5-oxoprolinase 0 ;;;; 122.51 0.00027248 69019100 74589 85769 32714 52257.8 83827 95331 74071.4 90493 73359.6 FALSE TRUE 64731.87467 85205.57779 48534.59982 64123.7322 82159.0067 98998.44526 66887.96703 71141.77617 64687.11166 1.000691993 1.317195584 0.750297835 0.9912907 1.27009855 1.530419936 1.034023089 1.099782852 1 15.98119068 3.252462134 24.88974397 1.181694253 1.0175658 0.15661289 0.19808508 480.247371 859846.0484 0.059480584 0.076383663 1788.389592 -3.252462134 -0.164128453 SGVRGT(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 90.697 0.010992 369770000 764620 795170 321102 426730 725110 726840 663600 785150 398440 TRUE FALSE 663573.5297 789946.4759 476388.0012 523625.5687 710681.7297 754802.0051 599244.1741 617251.7825 351336.8771 1.888710161 2.248401826 1.355929401 1.490380324 2.022792869 2.148371134 1.705611375 1.756865911 1 18.42249549 1.128144656 2.44297038 0.586126489 1.838856085 0.474713283 0.273967372 0.824013197 4.03109124 2.496010951 0.075086028 13.43212288 -1.128144656 1.252729596 SGVS(ph)SDNEDDDDEEDGNYLHPSLFASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGVSSDNEDDDDEEDGNYLHPSLFASK 27 0 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 S(0.022)GVS(0.524)S(0.454)DNEDDDDEEDGNYLHPSLFASK;S(0.002)GVS(0.57)S(0.428)DNEDDDDEEDGNYLHPSLFASK 326.35 2.27E-84 1447330000 716720 687320 173311 491558 777570 575490 652520 877300 880560 TRUE FALSE 622003.6361 682804.9497 257124.7793 603173.7569 762097.8783 597629.4727 589238.7108 689696.2222 776461.1999 0.801074975 0.879380644 0.331149553 0.776824079 0.981501559 0.769683627 0.758877212 0.888255874 1 19.56655431 3.480237835 24.97778538 0.867359999 0.668514156 0.263767671 0.159241052 175.0626784 1403044.72 0.045502536 0.0599406 3021.606008 -3.480237835 -0.198845843 SGVSLAALKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGVSLAALKK 10 1 P10412;P16402;P16403 P10412;P16402;P16403 HIST1H1E;HIST1H1D;HIST1H1C Histone H1.4;Histone H1.3;Histone H1.2 0 73.885 0.055767 0 824580 519490 1546700 661610 337300 402480 624870 610180 537040 FALSE TRUE 715609.6638 516077.436 2294689.293 811838.6626 330588.3899 417963.666 564270.2036 479697.7554 473551.743 1.511154112 1.089801576 4.845699181 1.714361048 0.698104051 0.882614566 1.191570323 1.012978545 1 18.85316255 3.478748811 24.5828035 0.998667153 2.499152042 0.337312907 0.978088654 56.57084573 854464.72 0.278676876 0.365329119 3011.263855 -3.478748811 1.500484889 SGVSS(ph)DNEDDDDEEDGNYLHPSLFASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SGVSSDNEDDDDEEDGNYLHPSLFASK 27 0 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 S(0.001)GVS(0.035)S(0.964)DNEDDDDEEDGNYLHPSLFASK;SGVS(0.091)S(0.909)DNEDDDDEEDGNYLHPSLFASK;S(0.003)GVS(0.185)S(0.812)DNEDDDDEEDGNYLHPSLFASK 383.48 3.23E-145 2145340000 1309620 1407510 397419 948090 1623930 1305610 1448960 1855810 1903900 TRUE FALSE 1136550.399 1398263.974 589612.1577 1163368.325 1591616.97 1355837.662 1308440.082 1458959.473 1678823.111 0.676992347 0.832883444 0.351205647 0.692966589 0.948055194 0.807611983 0.77937936 0.869037044 1 20.6790188 3.389647233 5.940111181 0.866708215 0.622931465 0.459023211 0.131972366 0.194361971 10.5091866 0.037970834 0.049273985 2452.715822 -3.389647233 -0.24377675 SGVYQHVTGEMMGGHAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGVYQHVTGEMMGGHAIR 18 0 P07858;R4GMQ5 P07858 CTSB Cathepsin B;Cathepsin B light chain;Cathepsin B heavy chain 0 ; 166.91 1.42E-11 1062410000 686310 646200 325540 510770 726020 790800 671200 739820 638740 FALSE TRUE 595612.3946 641955.0697 482972.2329 626748.1351 711573.6224 821222.5877 606107.1273 581615.2503 563228.8849 1.057496181 1.13977654 0.85750615 1.112776976 1.263382688 1.458061917 1.076129339 1.032644571 1 19.1033618 3.488481725 24.59144558 1.160031032 1.02286635 0.176003519 0.145522783 909.3462362 1968414.858 0.044904342 0.062390441 3079.510752 -3.488481725 -0.137164681 SGWSSQSDYYASYYSSQYDYGDPGHWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGWSSQSDYYASYYSSQYDYGDPGHWDR 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 0 ; 213.09 3.50E-26 862420000 578630 614350 259447 421348 541500 524920 511760 629330 527820 FALSE TRUE 502162.5794 610314.2944 384916.437 517021.5033 530725.2094 545114.0121 462129.594 494752.677 465421.7209 1.078941005 1.311314593 0.827027231 1.110866726 1.140310359 1.171225982 0.992926572 1.06302017 1 18.82817902 2.223223646 24.99215748 1.026821162 1.104935311 0.105508369 0.119889137 624.8700649 1018240.119 0.047779667 0.032349375 167.1951387 -2.223223646 0.078114148 SGYFDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGYFDER 7 0 P12532;P12532-2;F8WCN3;C9JSQ1;C9J6W7;C9JT96 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 81.784 0.061099 1310100000 2747300 3102800 1772700 2513200 3266300 3789700 2543100 3259700 3264000 FALSE TRUE 2384237.344 3082417.502 2629983.649 3083860.472 3201307.02 3935492.211 2296470.553 2562638.522 2878133.638 0.828397025 1.070977894 0.913780936 1.07147925 1.112285746 1.367376469 0.797902683 0.890382048 1 21.45670215 SGYHDDS(ph)DEDLLE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SGYHDDSDEDLLE 13 0 Q99523;Q99523-2 Q99523 SORT1 Sortilin 1 SGYHDDS(1)DEDLLE;SGYHDDS(1)DEDLLE;S(0.001)GYHDDS(0.999)DEDLLE;SGYHDDS(1)DEDLLE;SGYHDDS(1)DEDLLE;SGYHDDS(1)DEDLLE 211.38 2.35E-08 11438320000 10960450 11092080 5528960 7616750 11447300 11998270 9795410 12365830 11010900 TRUE FALSE 9511998.762 11019215.4 8202783.549 9346249.502 11219521.13 12459851.21 8845452.646 9721493.485 9709203.946 0.979688841 1.134924702 0.844846148 0.962617487 1.155555202 1.283303068 0.911037887 1.001265762 1 23.21092158 5.111059553 11.40914695 1.032687234 7.77E-05 0.018628239 0.127107006 1197276.692 2614161.54 0.031864728 30157984.08 129139.6344 -5.111059553 -1.032609567 SGYHQSASEHGLVVIAPDTSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGYHQSASEHGLVVIAPDTSPR 22 0 P10768;X6RA14;U3KQT1;H7BZT7 P10768 ESD S-formylglutathione hydrolase 0 ; 98.689 0.00064865 371640000 125477 166096 38159 82266 216529 231027 162686 184684 164709 FALSE TRUE 108894.8965 165004.9044 56612.82003 100945.7527 212220.4965 239914.7582 146908.7368 145190.7638 145237.2897 0.749772299 1.136105644 0.389795349 0.695040185 1.461198409 1.651881268 1.011508388 0.999679656 1 17.14805239 3.255706964 24.99920245 1.202057316 0.745574242 0.434404512 0.272693031 269.5387849 392982.5267 0.085093099 0.109580186 1801.80158 -3.255706964 -0.456483074 SGYIDEHELDALLKDLYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGYIDEHELDALLKDLYEK 19 1 P22676 P22676 CALB2 Calretinin 0 132.14 8.55E-06 65690000 224910 242770 105320 100380 167310 128760 267090 280220 45731 FALSE TRUE 195187.5737 241175.2279 156253.1043 123172.8132 163980.8583 133713.4805 241187.6529 220297.1337 40324.73328 4.840393421 5.980826364 3.874870125 3.054522701 4.066508195 3.315917296 5.981134488 5.463077267 1 15.29937737 4.228059962 24.84057257 4.047658178 5.410609933 0.171566649 1.38372411 344.8796535 815861.346 0.363505282 0.769843603 16906.74341 -4.228059962 1.362951756 SGYLSSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SGYLSSER 8 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;; 160.11 0.00082654 4224710000 3704700 4167160 2312470 3170000 4403160 4441970 3887120 4521360 4643900 FALSE TRUE 3215114.508 4139785.652 3430788.227 3889796.95 4315545.731 4612855.46 3510147.701 3554502.349 4094903.432 0.785150263 1.010960507 0.83781908 0.949911766 1.053882174 1.126486994 0.85719914 0.868030811 1 21.965398 4.751260867 23.84268193 0.954276473 0.785150057 0.267541255 0.091484779 1699.686974 3190778.702 0.023779037 0.39144594 56397.63168 -4.751260867 -0.169126416 SGYSS(ph)PGS(ph)PGTPGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGYSSPGSPGTPGSR 15 0 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 2 SGYSS(1)PGS(0.69)PGT(0.31)PGSR 270.99 3.20E-33 379180000 855460 926990 560600 683750 1065900 1005300 982940 1119900 974380 TRUE FALSE 742408.7935 920900.5417 831708.0351 839005.888 1044690.675 1043974.542 887614.6301 880418.1001 859189.9064 0.864079976 1.071824209 0.968014206 0.976508082 1.215901942 1.215068443 1.033083168 1.02470722 1 19.71261752 3.37361633 22.09613395 1.090243764 0.977141511 0.341435076 0.087502377 6.745336796 1418.996629 0.026935198 0.034773207 2363.830488 -3.37361633 -0.113102253 SGYSS(ph)PGSPGT(ph)PGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGYSSPGSPGTPGSR 15 0 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 2 SGYSS(1)PGS(0.239)PGT(0.761)PGSR 287.12 1.23E-33 323440000 347900 376380 214220 277210 393970 392560 376540 410700 378300 TRUE FALSE 301924.1335 373907.535 317817.5085 340154.7674 386130.7678 407662.0372 340023.2088 322875.0011 333577.805 0.90510858 1.12090052 0.952753762 1.019716427 1.157543344 1.222089813 1.01932204 0.96791512 1 18.34766377 4.757190341 23.39694543 1.052549911 0.905108267 0.235200976 0.085961976 2984.823107 3748470.966 0.022810793 0.698422423 57172.91569 -4.757190341 -0.147441644 SGYSS(ph)PGSPGTPGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SGYSSPGSPGTPGSR 15 0 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 SGYS(0.005)S(0.983)PGS(0.012)PGTPGSR;S(0.001)GYS(0.23)S(0.768)PGS(0.001)PGTPGSR;SGYS(0.001)S(0.999)PGSPGTPGSR;SGYS(0.001)S(0.999)PGSPGTPGSR 388.98 2.02E-114 1221350000 2121910 1808170 1132508 1339910 1939330 1985070 1868060 2009080 1903360 TRUE FALSE 1841494.217 1796292.012 1680192.657 1644157.045 1900741.127 2061436.927 1686895.829 1579453.877 1678346.949 1.097207117 1.070274542 1.001099718 0.979628822 1.132507869 1.228254342 1.005093631 0.941077098 1 20.67860955 2.012606398 24.99620256 0.968356412 1.080990677 0.336021661 0.069218403 257.0324367 509647.1092 0.030563524 0.020591619 102.9452702 -2.012606398 0.112634266 SGYSSPGS(ph)PGTPGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SGYSSPGSPGTPGSR 15 0 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 SGYSS(0.001)PGS(0.999)PGTPGSR 196.97 9.08E-09 31742000 55846 59011 37534 45470 72728 66820 63175 72858 66462 TRUE FALSE 48465.8096 58623.35286 55685.56794 55794.65847 71280.85509 69390.60864 57048.29822 57277.88368 58604.93807 0.826991909 1.000314219 0.950185595 0.952047051 1.21629435 1.184040303 0.973438418 0.977355929 1 15.83873461 3.443813488 24.99998575 1.059514418 0.936251627 0.361106762 0.090690905 254.32405 190888.5351 0.028790118 0.037168087 2778.519749 -3.443813488 -0.12326279 SHAEQEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHAEQEKK 8 1 A0A1C7CYX1 A0A1C7CYX1 0 81.594 0.014577 6840600 32711 32338 17840 24157 19748 23344 32302 40625 30862 FALSE TRUE 28388.15847 32125.56955 26467.48367 29642.21607 19355.05344 24242.05879 29169.35701 31937.65989 27213.52952 1.043163418 1.180499925 0.97258548 1.089245555 0.711229075 0.890809065 1.071869674 1.173594916 1 14.73203646 -0.839304917 17.5414649 0.43998957 1.021809784 0 0.138343817 0 0 0 0.033272203 0.144775503 0.839304917 0.581820215 SHAGGINVFGQITVETFASIVAHELGHNLGMNHDDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHAGGINVFGQITVETFASIVAHELGHNLGMNHDDGR 37 0 F8WC54;A0AVL1;Q13443-2;Q13443 F8WC54 ADAM9 Disintegrin and metalloproteinase domain-containing protein 9 0 74.605 0.00099729 49319000 12625 16981 11016 11813 15222 15641 14064 20223 11168 FALSE TRUE 10956.57426 16869.45069 16343.37445 14495.3222 14919.11198 16242.71939 12700.07544 15898.46883 9847.731763 1.112598772 1.713029061 1.659608003 1.471945271 1.514979524 1.649386862 1.289644738 1.614429516 1 13.26557575 1.231665798 24.99306029 0.999999116 1.513810174 0.425705622 0.183310698 219.7497627 796499.2673 0.397941535 0.041192261 17.04770015 -1.231665798 0.513811058 SHDPEEAIR ddPTM_MDA-MB-175_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 0 127.4 0.00044656 230160000 282740 266180 189540 238700 261500 279610 260880 245760 378430 FALSE TRUE 245375.1926 264431.4461 281202.178 292900.4833 256296.6616 290366.7776 235579.8978 193206.1365 333692.4365 0.735333396 0.792440634 0.842698687 0.877755835 0.768062544 0.870162898 0.705979135 0.578994653 1 18.34815946 2.223068061 24.97818515 0.721283103 0.815469079 0.005778242 0.113026672 488.1433897 787013.1124 0.045053017 0.030495886 167.1352522 -2.223068061 0.094185976 SHEAEVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SHEAEVLK 8 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 0 ;; 92.439 0.011777 1734000000 3937400 2627280 2029820 2255700 2308890 2259460 2577700 3048670 2942050 FALSE TRUE 3417062.614 2610021.225 3011447.741 2767891.161 2262947.606 2346382.888 2327715.051 2396735.645 2594244.201 1.317170763 1.006081549 1.160818916 1.066935472 0.872295525 0.904457216 0.897261349 0.923866629 1 21.30688286 3.406433419 3.987352703 0.918167539 1.142785224 0.651053235 0.081258552 0.134027749 4.220673393 0.022478099 0.030011341 2549.373218 -3.406433419 0.224617685 SHEGETAYIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SHEGETAYIR 10 0 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;;; 168.74 4.85E-06 6520570000 2165790 1784810 1029470 1331720 1480750 1802420 1773040 1879100 1575060 FALSE TRUE 1879575.364 1773085.466 1527325.135 1634107.38 1451285.972 1871760.264 1601090.854 1477269.088 1388858.201 1.353324164 1.276649743 1.099698396 1.17658331 1.044948988 1.347697168 1.152810886 1.063657245 1 20.40546788 8 0.033848216 8.04E-15 2.891245612 0.375087212 0.097767747 2890.983724 9.672785292 279.409068 608.0238622 100000000 -8 2.891245612 SHEGETSYIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SHEGETSYIR 10 0 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 ;;;;; 153.1 1.69E-05 2391788000 802051 852495 415095 557940 672396 772376 640850 746325 716057 FALSE TRUE 696057.9282 846894.9042 615836.3304 684628.8046 659016.6351 802089.8045 578700.4656 586729.2067 631405.5572 1.102394365 1.341285161 0.975341955 1.084293283 1.043729545 1.270324272 0.916527356 0.92924302 1 19.26820743 0.735081509 0.208082901 0.578683578 1.25250314 0.234283547 0.1212416 39.61403666 1.867839176 7.613291463 1.024890348 5.433522993 -0.735081509 0.673819563 SHEHAGHDSSVNSVCWAPHDYGLILACGSSDGAISLLTYTGEGQWEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHEHAGHDSSVNSVCWAPHDYGLILACGSSDGAISLLTYTGEGQWEVK 48 0 P55735;P55735-4;P55735-3;P55735-2;A8MXL6 P55735 SEC13 Protein SEC13 homolog 0 ; 105.28 3.52E-08 241430000 101626 128544 37384.7 75055 160928 115331 116113 113184 103080 FALSE TRUE 88195.86661 127699.586 55464.06596 92097.38489 157725.8477 119767.8582 104852.3791 88980.4824 90893.99983 0.970315607 1.404928667 0.610206021 1.013239433 1.735272383 1.317665175 1.153567665 0.978947814 1 16.47189744 5.044276256 14.74367604 1.143260914 0.192971207 0.034691372 0.297778116 3389712.744 33766560.08 0.074999112 86780802.42 110732.7935 -5.044276256 -0.950289708 SHELDIDENPASDFDDSGS(ph)LLGFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHELDIDENPASDFDDSGSLLGFK 24 0 Q96RS0 Q96RS0 TGS1 Trimethylguanosine synthase 1 SHELDIDENPAS(0.256)DFDDS(0.305)GS(0.439)LLGFK 82.476 0.0093793 28377000 17114 14718 16288 13693 13777 22680 15455 20233 20666 TRUE FALSE 14852.34154 14621.31649 24164.93128 16802.20493 13502.86465 23552.51428 13956.17648 15906.3304 18222.88902 0.815037699 0.802359959 1.326075753 0.922038482 0.740983751 1.292468732 0.765859709 0.872876435 1 14.15346408 0.93386507 17.26143776 1.803619752 0.942000014 0.007698275 0.206174346 15171851.28 72456667.24 475728546.5 0.048700911 8.587466784 -0.93386507 -0.861619738 SHELDIDENPASDFDDSGSLLGFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHELDIDENPASDFDDSGSLLGFK 24 0 Q96RS0 Q96RS0 TGS1 Trimethylguanosine synthase 0 124.31 6.43E-05 45812000 28838 27087 14554 20894 28350 30009 24202 27722 23431 FALSE TRUE 25026.98523 26909.06371 21592.36308 25638.30204 27785.89047 31163.46565 21854.89377 21793.86603 20661.01387 1.211314478 1.302407708 1.045077614 1.240902417 1.344846416 1.508322188 1.057784187 1.054830424 1 14.33462343 2.04188005 24.99984634 1.038823981 1.269081577 0.485397726 0.115546719 126.5016133 75513.25828 0.049509348 0.033379165 110.1235112 -2.04188005 0.230257596 SHESNAPGS(ph)AGGQASEKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SHESNAPGSAGGQASEKPR 19 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 SHESNAPGS(0.745)AGGQAS(0.255)EKPR;SHESNAPGS(0.926)AGGQAS(0.074)EKPR;SHESNAPGS(0.903)AGGQAS(0.097)EKPR 83.871 0.0019853 254956000 177802 179351 45003 117978 202075 194609 180132 211173 194052 TRUE FALSE 154305.0152 178172.8315 66766.60133 144766.7081 198054.1029 202095.7342 162662.8264 166015.2973 171111.3936 0.901781068 1.041268075 0.390193779 0.846037806 1.157457132 1.181077016 0.950625338 0.970217668 1 17.3845763 3.403532268 6.980176405 1.038875178 0.774091616 0.344824882 0.177503735 0.260200217 20.2579482 0.052556123 0.068053845 2532.399783 -3.403532268 -0.264783562 SHFASSHALICISHWILGIGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHFASSHALICISHWILGIGDR 22 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 173.55 1.26E-12 53474000 18398 24351 7450 11634 13373 18336 21150 15508 11781 FALSE TRUE 15966.65769 24191.03668 11052.84492 14275.67751 13106.90346 19041.39778 19098.87626 12191.73488 10388.2636 1.53699004 2.328689144 1.063974245 1.374212098 1.261703011 1.832972142 1.838505162 1.173606615 1 13.34266691 1.588090053 5.228681721 1.042134627 1.597940551 0.279990834 0.350079055 0.186267393 10.64570109 0.249292599 0.09138558 38.73379531 -1.588090053 0.555805924 SHFEQWGTLTDCVVMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 ;;;;;;; 290.62 1.61E-45 4797199000 2362961 2444200 1518036 1964362 2249279 2309544 2150805 2393011 3277675 FALSE TRUE 2050689.717 2428143.889 2252163.287 2410400.415 2204522.749 2398393.652 1942220.262 1881284.22 2890191.995 0.709534079 0.840132383 0.779243486 0.833993181 0.762759966 0.829838867 0.672003889 0.650920154 1 21.4627339 2.271457962 24.99866084 0.744339272 0.794665206 0 0.101475885 625.0609756 474980.868 0.036949826 0.028619312 186.834882 -2.271457962 0.050325935 SHFEQWGTLTDCVVMRDPNTKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHFEQWGTLTDCVVMRDPNTKR 22 2 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8W646 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ; 85.945 0.0018389 2014310000 1492690 1211480 432340 536500 1056940 925620 1309510 1568820 222533 FALSE TRUE 1295427.235 1203521.708 641421.0701 658320.5249 1035908.962 961229.2004 1182513.922 1233340.052 196225.4023 6.601730559 6.13336344 3.268797326 3.354919992 5.279178689 4.898597171 6.026303976 6.28532309 1 17.58215229 4.400204715 8.352671431 4.595393346 6.485705463 0.220189372 1.552921748 0.394104397 37.34206159 0.394567232 1.051680737 25130.70748 -4.400204715 1.890312117 SHFGGPDYEEGPNSLINEEEFFDAVEAALDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SHFGGPDYEEGPNSLINEEEFFDAVEAALDR 31 0 Q9Y5P4-3;Q9Y5P4;Q9Y5P4-2;A0A2R8Y7C5;A0A2R8YE18;A0A2R8Y7Q9;A0A2R8Y5S9;A0A2R8YEA4;A0A2R8YE59;A0A2R8YFA1 Q9Y5P4-3 COL4A3BP Collagen type IV alpha-3-binding protein 0 ;; 215.86 8.65E-35 95693000 63568 55891.6 29784.3 47786.3 46806.2 47620 42023.2 51357.4 45005 FALSE TRUE 55167.32774 55524.4444 44188.0871 58636.90978 45874.84819 49451.97221 37947.79653 40375.01967 39684.56017 1.390145878 1.39914476 1.113483101 1.477574894 1.155987316 1.246126252 0.956235785 1.017398694 1 15.2762902 2.494060348 1.411494307 0.983742016 1.326939569 0.626164946 0.111062928 0.256664233 1.054307872 0.061216794 0.03916651 311.9323002 -2.494060348 0.343197553 SHFTDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHFTDK 6 0 B7Z7P8;P62495-2;P62495 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 83.801 0.056575 201210000 244410 201930 118650 187250 119900 168620 169380 201430 575350 FALSE TRUE 212110.5992 200603.5085 176029.5369 229767.9744 117514.2246 175106.9205 152953.5537 158355.762 507332.7784 0.41808968 0.395408137 0.346970557 0.452894006 0.231631445 0.345151995 0.301485652 0.312133906 1 18.95257285 1.236704102 24.99998636 1.00000082 0.346993142 0.914144627 0.06254916 12.98564688 174816.1585 0.096249412 0.015308793 17.24662428 -1.236704102 -0.653007678 SHFTDKETGQEHELIESMPLLEWFANNYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHFTDKETGQEHELIESMPLLEWFANNYK 29 1 B7Z7P8;P62495-2;P62495 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 82.849 0.0015245 86382000 95513 84898 52718 71516 69822 61518 86572 89052 94884 FALSE TRUE 82890.71505 84340.29945 78212.60113 87754.80085 68432.6788 63884.63727 78176.26076 70008.9228 83666.92161 0.990722659 1.008048316 0.934809117 1.048858966 0.817917971 0.763559075 0.934374772 0.836757484 1 16.35236973 3.236116172 24.99999931 0.865742139 0.992155332 0.445580543 0.069171935 58.53360018 598640.2182 0.02007761 0.023842677 1722.329231 -3.236116172 0.126413193 SHGLEPAAPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHGLEPAAPSPR 12 0 Q9ULL5;Q9ULL5-2;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 SHGLEPAAPS(1)PR;SHGLEPAAPS(1)PR 112.5 0.00081613 381680000 396980 374340 200386 220330 322690 361980 287650 301950 290170 TRUE FALSE 344518.0872 371880.9359 297293.3399 270359.294 316269.1003 375905.6048 259753.7473 237380.3423 255866.4332 1.346476296 1.45341822 1.161908329 1.056642291 1.236071088 1.46914779 1.015192747 0.927751012 1 17.96503137 2.096830574 7.393439895 0.962655016 1.275716037 0.57486831 0.12441981 0.168440252 11.13847278 0.054676818 0.036738152 124.9771377 -2.096830574 0.313061022 SHGS(ph)VKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SHGSVKR 7 1 E7ET89;Q86UW9 E7ET89 DTX2 Probable E3 ubiquitin-protein ligase DTX2 1 SHGS(1)VKR;S(0.009)HGS(0.991)VKR;SHGS(1)VKR 78.939 0.020763 125200000 560020 530050 249963 363429 240002 254347 609520 578780 453990 TRUE FALSE 486011.9381 526568.0666 370845.9429 445951.1091 235226.4298 264131.8937 550408.8442 455012.4011 400319.8194 1.214059146 1.315368466 0.926374176 1.113987086 0.587596263 0.65980219 1.374922793 1.136622218 1 18.61079352 4.239935497 24.9968757 0.987972827 1.264713876 0.221129639 0.227247974 61.09779098 1110718.255 0.062610827 0.148285479 17375.42743 -4.239935497 0.276741049 SHHAASTTTAPTPAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHHAASTTTAPTPAAR 16 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 64.244 0.035815 20422000 17123 17493 5877.8 8975 15472 16171 12550 12200 9273.7 FALSE TRUE 14860.15217 17378.08733 8720.32374 11012.91092 15164.13747 16793.10883 11332.90293 9591.124941 8177.373751 1.817227953 2.125142847 1.066396621 1.346754014 1.854401906 2.053606616 1.385885405 1.172885725 1 12.99742187 1.861769371 2.84286736 1.07593177 1.690372762 0.394454861 0.316996427 0.290745127 4.186852632 0.228121854 0.093588381 72.73934256 -1.861769371 0.614440992 SHHANS(ph)PTAGAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SHHANSPTAGAAK 13 0 Q15555-4;Q15555-5;Q15555-3;Q15555;K7EL66;K7ERD8;Q15555-2 Q15555-4 MAPRE2 Microtubule-associated protein RP/EB family member 2 1 SHHANS(1)PTAGAAK;SHHANS(1)PTAGAAK;S(0.007)HHANS(0.961)PT(0.032)AGAAK 160.97 2.77E-05 166274000 438325 454646 201720 376649 356674 358949 343974 372417 741997 TRUE FALSE 380399.2407 451659.4005 299272.4667 462172.9122 349576.8852 372758.0003 310615.4544 292778.5227 654278.9599 0.581402221 0.690316254 0.457408055 0.706385106 0.534293331 0.569723349 0.474744678 0.447482711 1 19.31954635 1.230103353 24.99972454 1.000000832 0.553960444 0.712400227 0.088285882 182.1102427 538276.6424 0.248310736 0.022039224 16.98647845 -1.230103353 -0.446040388 SHHCTLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SHHCTLAR 8 0 Q9HCN6-3 Q9HCN6-3 0 ;;; 92.692 0.02698 2377200000 3314730 3117530 2125950 2488440 3065420 3378700 3019980 3347910 3258740 FALSE TRUE 2876680.032 3097050.74 3154066.531 3053478.335 3004424.139 3508680.775 2727102.804 2631985.5 2873495.47 1.001108254 1.077799068 1.097641031 1.062635514 1.045564251 1.221049698 0.949054151 0.915952549 1 21.45437534 2.066290414 24.99853272 0.946130705 1.08213125 0.511781405 0.059303582 38.98527625 14701.10512 0.023215715 0.01565203 116.4904745 -2.066290414 0.136000545 SHHGEHERPEFIAYPHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SHHGEHERPEFIAYPHLR 18 1 P12074;H0YIV9 P12074 COX6A1 "Cytochrome c oxidase subunit 6A1, mitochondrial" 0 ;;; 185.99 1.69E-14 5529710000 1148560 1284150 786168 1884120 1511800 1754500 556332 917860 773370 FALSE TRUE 996774.8859 1275714.334 1166361.474 2311938.243 1481718.138 1821996.75 502379.0083 721582.7818 681943.0796 1.461668746 1.870705008 1.710350188 3.390221724 2.172788583 2.671772476 0.736687596 1.058127582 1 19.3792918 2.232162767 24.99931983 0.949842135 2.226208466 0.558598179 0.536759765 114.7937886 448546.4551 0.221665971 0.153513258 170.6721923 -2.232162767 1.276366332 SHIEIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SHIEIIR 7 0 P00390-5;P00390-4;P00390-2;P00390-3;P00390 P00390-5 GSR "Glutathione reductase, mitochondrial" 0 ;;; 174.21 0.00083478 1946740000 3698020 3774760 2185870 3019920 3740690 3947500 3447480 3776780 3892780 FALSE TRUE 3209317.287 3749963.353 3242964.043 3705638.993 3666257.588 4099362.879 3113143.92 2969144.988 3432579.983 0.934957759 1.092462046 0.944759935 1.079549205 1.068076376 1.194251234 0.906939951 0.864989309 1 21.71086191 2.148587854 25 0.910973339 1.051240686 0.358094092 0.080382878 18.97960988 5268.317746 0.031937319 0.02153214 140.7952015 -2.148587854 0.140267347 SHIMAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHIMAAK 7 0 P48643;E7ENZ3;H0Y914 P48643 CCT5 T-complex protein 1 subunit epsilon 0 81.297 0.027584 568620000 1377400 1695400 950190 1254000 1364900 1345100 1600900 1802600 1774800 FALSE TRUE 1195373.1 1684262.806 1409705.062 1538739.866 1337741.16 1396846.867 1445644.964 1417128.018 1564985.166 0.763823917 1.076216467 0.900778546 0.983229682 0.854794786 0.892562369 0.923743557 0.905521694 1 20.57771755 1.233504103 24.62055732 1.000000156 0.917296647 0.102171046 0.080365749 318.8506307 1552286.893 0.143230646 0.017709748 17.12001351 -1.233504103 -0.082703508 SHISDQS(ph)PLSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SHISDQSPLSSK 12 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 SHISDQS(1)PLSSK;SHISDQS(1)PLSSK;SHIS(0.002)DQS(0.998)PLSSK 145.94 4.14E-05 752940000 1635350 1689130 537410 1069350 1614580 1582890 1620120 1809100 1935100 TRUE FALSE 1419234.354 1678033.994 797303.2735 1312162.261 1582453.017 1643784.803 1463001.012 1422238.043 1706334.682 0.831744422 0.983414339 0.467260779 0.768994661 0.927398964 0.963342549 0.857393937 0.833504739 1 20.70246922 3.263207399 9.08452621 0.903912209 0.757209512 0.241772125 0.133899998 0.416514682 139.2866882 0.039422286 0.050112532 1833.189658 -3.263207399 -0.146702698 SHKDEVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SHKDEVVK 8 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;; 120.99 0.00087272 2840020000 7246000 6499400 5066400 5664700 4907370 4439450 8292100 9380300 7814800 FALSE TRUE 6288422.741 6456705.013 7516527.986 6950956.715 4809722.938 4610238.514 7487933.418 7374395.843 6890943.247 0.912563421 0.93698421 1.090783615 1.008709035 0.697977442 0.669028658 1.086634028 1.070157681 1 22.71627004 SHLDSPEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHLDSPEAR 9 0 K7EP90;Q9BTD8-4;Q9BTD8-2;Q9BTD8-3;Q9BTD8;K7ER08 K7EP90 RBM42 RNA-binding protein 42 0 122.26 0.00059086 141930000 210850 197950 95646 135440 153670 187160 147860 176050 136090 FALSE TRUE 182985.6383 196649.6534 141900.7255 166193.7221 150612.2677 194360.1663 133520.56 138403.0775 120001.5952 1.524860048 1.638725327 1.182490326 1.384929273 1.255085546 1.619646522 1.112656542 1.153343647 1 16.87269406 0.10997368 0.359918409 2.01E-23 1.496739265 0.477230439 0.158744167 16.29894706 0.986716615 12.32336065 0.229385314 1.288171481 -0.10997368 1.496739265 SHLEPSGNPLPATPTTSAPSAPPASSQGPDT(ph)APRPSPPQEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHLEPSGNPLPATPTTSAPSAPPASSQGPDTAPRPSPPQEEAR 43 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 SHLEPSGNPLPATPTTSAPS(0.015)APPAS(0.013)S(0.009)QGPDT(0.491)APRPS(0.472)PPQEEAR;SHLEPSGNPLPATPTTSAPSAPPAS(0.091)S(0.091)QGPDT(0.56)APRPS(0.258)PPQEEAR 225.96 2.16E-44 1232980000 189425 165535 73645 113252 161460 161527 154476 157776 154244 TRUE FALSE 164392.0063 164447.5897 109259.9683 138967.5975 158247.2619 167741.0482 139494.9413 124036.8302 136009.45 1.208680766 1.209089439 0.8033263 1.021749573 1.163501961 1.233304364 1.025626832 0.911972147 1 17.05334737 2.000764249 24.9913632 0.955428687 1.098981491 0.197523244 0.126321921 42.0595007 1375345.542 0.055212872 0.036865696 100.1761297 -2.000764249 0.143552803 SHLEPSGNPLPATPTTSAPSAPPASSQGPDTAPRPS(ph)PPQEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHLEPSGNPLPATPTTSAPSAPPASSQGPDTAPRPSPPQEEAR 43 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 SHLEPSGNPLPATPTTSAPSAPPAS(0.001)S(0.007)QGPDT(0.183)APRPS(0.809)PPQEEAR;SHLEPSGNPLPATPTTSAPS(0.002)APPAS(0.105)S(0.105)QGPDT(0.086)APRPS(0.701)PPQEEAR 242.07 4.31E-55 1654260000 265871 259323 142755 190539 236606 218191 222627 234387 229891 TRUE FALSE 230735.4737 257619.4901 211791.7955 233803.7922 231898.0035 226584.949 201036.6678 184265.1641 202713.5479 1.138234105 1.270854824 1.044783626 1.153370333 1.143968945 1.117759278 0.991727834 0.908992842 1 17.62908299 2.223566021 2.88137053 0.947379785 1.150105009 0.682039856 0.057969396 0.135271905 2.31988599 0.026192039 0.01674464 167.3269985 -2.223566021 0.202725224 SHLEVPLEENVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHLEVPLEENVNR 13 0 Q96CT7;M0R2F5 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 ; 136.21 5.70E-06 102010000 156616 178804 104945 142465 155337 166370 157269 159699 250230 FALSE TRUE 135918.7988 177629.4248 155696.753 174813.8557 152246.0976 172770.3616 142017.0766 125548.6116 220648.0945 0.615998063 0.805034937 0.705633798 0.792274486 0.689995071 0.783013159 0.643636089 0.568999302 1 17.75138776 2.245137394 24.99895587 0.69851854 0.734944845 0 0.123924809 872.5847522 3316787.947 0.045416613 0.034340453 175.8479839 -2.245137394 0.036426305 DSQDGSSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 DSQDGSSYR 9 0 Q14847;Q14847-2;C9J9W2;Q14847-3;J3KSN1 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;;;; 200.56 5.33E-05 3493455000 10192690 2798940 1642855 2062072 2069585 2600727 2477341 3267205 2992985 FALSE TRUE 8845700.192 2780553.579 2437345.173 2530296.964 2028404.308 2700778.651 2237088.851 2568538.636 2639157.723 3.351713357 1.053576129 0.923531455 0.958751704 0.768580176 1.02334871 0.847652579 0.973241809 1 21.33164614 4.739361699 4.825356977 0.929430871 3.485738354 0.990563079 0.073966385 0.014269619 0.970366423 0.0172368 0.122865587 54873.37832 -4.739361699 2.556307483 up SHLLNCCPHDVLSGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHLLNCCPHDVLSGTR 16 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 164.93 4.17E-09 628320000 739810 636610 306420 416710 514570 449560 481720 604640 404040 FALSE TRUE 642042.2341 632428.067 454605.7369 511330.3745 504331.0637 466854.8641 435002.8685 475342.4413 356274.8515 1.802098103 1.77511285 1.275997267 1.435213214 1.415567396 1.310378384 1.22097551 1.3342015 1 18.44263113 8 0.311421923 1.163478512 7.575990371 0.738484115 0.123341973 39.97076782 0.633685042 0.214635196 142.1323732 100000000 -8 6.412511859 SHLVGVKPFEADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHLVGVKPFEADR 13 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 0 127.36 0.00010688 942930000 518880 488090 275710 352960 489430 385960 472310 539560 402290 FALSE TRUE 450308.6933 484883.7047 409044.2782 433104.9627 479691.3006 400808.1309 426505.4489 424179.2929 354731.7345 1.269434476 1.366902528 1.153108782 1.220936614 1.352264976 1.129890822 1.202332375 1.195774868 1 18.43636887 0.131082514 0.745862772 8.67E-26 1.25908411 0.519607733 0.07397613 10.93426705 1.323722358 16.9060677 0.029801965 1.352329476 -0.131082514 1.25908411 SHNVAAGSYEAPLPPGS(ph)FHGDFAYGTYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SHNVAAGSYEAPLPPGSFHGDFAYGTYR 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 SHNVAAGSYEAPLPPGS(1)FHGDFAYGTYR;SHNVAAGS(0.002)Y(0.003)EAPLPPGS(0.52)FHGDFAY(0.124)GT(0.187)Y(0.163)R;SHNVAAGSYEAPLPPGS(0.86)FHGDFAYGT(0.14)YR 197.58 3.46E-25 1746610000 369292 459734 259454 262705 433584 466916 297659 368751 367222 TRUE FALSE 320489.1265 456713.9771 384926.8222 322356.1854 424956.5267 484878.5607 268792.076 289896.4683 323809.4335 0.989746108 1.410440617 1.18874493 0.995512027 1.31236611 1.497419502 0.830093407 0.895268755 1 18.30478549 2.215070498 24.99905267 0.902441972 1.23135242 0.466304395 0.163313189 199.7019868 212528.6487 0.066018562 0.044538827 164.085611 -2.215070498 0.328910448 SHNVAAGSYEAPLPPGSFHGDFAYGT(ph)YR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHNVAAGSYEAPLPPGSFHGDFAYGTYR 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 SHNVAAGSYEAPLPPGS(0.293)FHGDFAY(0.002)GT(0.702)Y(0.003)R 155.79 3.16E-08 923390000 201050 236650 95896 136500 226800 251130 180090 209780 212280 TRUE FALSE 174480.7331 235095.4306 142271.6264 167494.4113 222287.1237 260791.1336 162624.8995 164920.1795 187184.5002 0.932132377 1.25595565 0.760060935 0.894809191 1.187529541 1.393230387 0.868794688 0.881056815 1 17.51410145 SHPAMS(ph)PGTPGPTMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHPAMSPGTPGPTMGR 16 0 A0A3F2YNW7;Q8NFD5;Q8NFD5-2;Q8NFD5-3;A0A1B0GUC6;A0A1B0GUG2;A0A1B0GU09;A0A6I8PTU7 A0A3F2YNW7 ARID1B AT-rich interactive domain-containing protein 1B 1 SHPAMS(1)PGTPGPTMGR;SHPAMS(1)PGTPGPTMGR 103.41 0.00092824 198378000 181806 177648 99831 124528 158805 152152 150217 176379 161836 TRUE FALSE 157779.8765 176481.0186 148109.6055 152803.9857 155645.0912 158005.3859 135648.9785 138661.7234 142703.9324 1.105644909 1.23669345 1.037880337 1.070776278 1.090685369 1.10722517 0.950562302 0.971674158 1 17.12266557 2.703201269 0.406318885 0.922734215 1.176803628 0.511222337 0.057250417 1.348758746 0.731192112 0.216171907 0.143315867 504.8952317 -2.703201269 0.254069413 SHPDLLQLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHPDLLQLPR 10 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 ; 121.83 0.00050465 419830000 28578 25951 16929.9 16608.8 29412 32390 26306 32046 25707.6 FALSE TRUE 24801.34489 25780.52617 25117.25627 20380.08189 28826.75874 33636.06426 23754.84817 25193.21228 22668.47681 1.094089607 1.137285332 1.108025761 0.899049462 1.271667213 1.483825514 1.047924321 1.111376494 1 14.46839983 1.453407656 2.046114349 0.998586868 1.154563778 0.08783409 0.150801481 1.318335488 8.465333576 0.344056221 0.043931034 28.40584129 -1.453407656 0.155976911 SHPFIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHPFIK 6 0 O14579;M0QXB4;O14579-3;O14579-2 O14579 COPE Coatomer subunit epsilon 0 ; 106.84 0.03178 957220000 5062300 4558900 2661300 3556100 4425200 4382900 4830600 5577400 4952500 FALSE TRUE 4393304.229 4528952.286 3948313.582 4363566.857 4337147.178 4551512.999 4362129.156 4384716.413 4367021.092 1.00601855 1.03708047 0.904120566 0.999209018 0.993159201 1.042246626 0.9988798 1.004052035 1 22.05821807 3.150889033 3.242742143 1.009392763 0.983973774 0.092265283 0.035404728 0.614611361 12.8924764 0.011182515 0.013193313 1415.432076 -3.150889033 -0.025418989 SHPLDLS(ph)PNVQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHPLDLSPNVQSR 13 0 H0YBF7;A0A0A0MRE5;Q9ULH1;Q9ULH1-2;H0YBM4 H0YBF7 ASAP1 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1" 1 SHPLDLS(0.999)PNVQS(0.001)R;SHPLDLS(1)PNVQSR 91.518 0.0041835 370940000 321720 325150 188906 266647 344850 367450 324070 412990 378110 TRUE FALSE 279203.8869 323014.0682 280261.5735 327193.2768 337988.1597 381586.0393 292641.7413 324675.3024 333410.2665 0.837418385 0.968818602 0.840590712 0.981353334 1.01373051 1.144493969 0.877722646 0.973801154 1 18.346939 3.617725785 6.158266844 0.996246325 0.891425321 0.35736385 0.073327654 0.292340841 13.53503997 0.020373243 0.030378096 4146.921218 -3.617725785 -0.104821004 SHPLDPIDTVDFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SHPLDPIDTVDFER 14 0 P47897;A0A1B0GVU9;P47897-2;A0A0U1RQT0;C9J165;A0A0U1RQE9;A0A0U1RQL2;A0A0U1RRI9;A0A0U1RQM8;A0A0U1RQU2 P47897 QARS Glutamine--tRNA ligase 0 ;;;;; 240.59 2.10E-17 3867430000 2359360 2387820 1385675 1734280 2422350 2572930 2310770 2587810 2392030 FALSE TRUE 2047564.598 2372134.253 2055792.065 2128074.781 2374149.974 2671912.282 2086671.881 2034426.97 2109246.938 0.970756226 1.124635627 0.974656892 1.008926334 1.125591286 1.266761247 0.989297101 0.964527639 1 21.00829658 2.037463127 24.99992904 0.97888397 1.079327136 0.206930338 0.086715719 246.7763658 164678.0699 0.036542375 0.024636802 109.0091935 -2.037463127 0.100443165 SHQGLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 166.68 0.0025927 1430214000 937565 939050 595390 667183 773708 1138350 885652 929923 987874 FALSE TRUE 813663.4098 932881.3187 883322.5955 818677.0974 758312.7245 1182143.061 799761.6054 731066.2031 871088.6611 0.934076456 1.070937277 1.014044419 0.939832113 0.870534491 1.357086958 0.918117341 0.839255791 1 19.73246004 2.031034112 24.99999109 0.899307455 1.030420268 0.127825233 0.135572006 336.4232205 271009.3601 0.054221445 0.036555749 107.4073773 -2.031034112 0.131112812 SHRPQQNVGVQGAATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHRPQQNVGVQGAATR 16 1 O75362 O75362 ZNF217 Zinc finger protein 217 0 ; 103.61 0.00085669 47325000 39205 37292 18573.1 28412 38930 35077 29761 37573 31668 FALSE TRUE 34023.95992 37047.0264 27555.11328 34863.37885 38155.36917 36426.43489 26874.7828 29538.30634 27924.24512 1.218437948 1.326697508 0.986780956 1.248498525 1.366388563 1.304473397 0.962417522 1.057801427 1 14.76923066 2.236817054 24.99999156 1.015530741 1.240099838 0.531760131 0.103896996 38.4460985 551238.8099 0.042245938 0.030146465 172.511104 -2.236817054 0.224569096 SHS(ph)DNDRPNCSWNTQYSSAYYTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHSDNDRPNCSWNTQYSSAYYTSR 24 1 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.281)HS(0.365)DNDRPNCS(0.354)WNTQYSSAYYTSR 259.32 3.46E-44 1077800000 252920 195790 132440 166620 197380 170220 156800 172760 234200 TRUE FALSE 219495.9812 194503.8426 196488.427 204453.6176 193452.5242 176768.4735 141593.5601 135816.6184 206513.1428 1.062866887 0.941847284 0.95145725 0.990027147 0.936756477 0.855967185 0.685639462 0.657665738 1 17.65587407 2.606889991 2.598335565 0.75272706 0.977113608 0.449034505 0.098024907 0.227415949 3.006776919 0.037967083 0.032068673 404.4734236 -2.606889991 0.224386549 SHS(ph)DTSIASR ddPTM_MDA-MB-175_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 SHS(0.742)DT(0.253)S(0.005)IASR;S(0.492)HS(0.508)DTSIASR 116.6 0.0025285 788880000 178037 172449 106490 114586 162098 202137 178679 183183 160076 TRUE FALSE 154508.9594 171316.1712 157988.9202 140604.5026 158872.5669 209913.3412 161350.7381 144010.741 141151.9976 1.094628216 1.213699941 1.119282212 0.996121238 1.125542462 1.487143963 1.143099218 1.020252943 1 17.10689002 1.744312272 4.474531504 1.008048394 1.17319985 0.215907762 0.12622655 0.283471157 12.87647103 0.08377611 0.035142073 55.50246504 -1.744312272 0.165151456 SHS(ph)FCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHSFCK 6 0 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 S(0.002)HS(0.998)FCK;S(0.002)HS(0.998)FCK 105.57 0.021169 354290000 501490 508000 321959 351770 434190 470280 501680 565920 550240 TRUE FALSE 435216.8259 504662.9146 477659.4493 431644.755 425550.4685 488371.9759 453027.1508 444902.412 485191.254 0.897000559 1.040131928 0.984476627 0.889638367 0.877077781 1.006555604 0.933708403 0.916962967 1 18.88819402 3.794815439 24.98664737 0.935351302 0.980495982 0.089428218 0.053353738 589.0925106 261654.5066 0.013707292 0.023741719 6234.69825 -3.794815439 0.04514468 SHS(ph)GPAGSFNKPAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHSGPAGSFNKPAIR 15 1 Q9UJM3 Q9UJM3 ERRFI1 ERBB receptor feedback inhibitor 1 1 SHS(0.963)GPAGS(0.037)FNKPAIR;S(0.008)HS(0.992)GPAGSFNKPAIR 112.16 0.00047581 488680000 287420 324280 174638 237200 321650 268020 311160 353220 336080 TRUE FALSE 249436.7188 322149.7833 259093.5209 291059.8854 315249.7943 278330.9028 280983.7511 277686.6518 296349.0053 0.841699194 1.087062138 0.874285104 0.982152395 1.063778817 0.93919972 0.948151491 0.93702576 1 18.17693769 4.789427946 23.21016935 0.972474179 0.841697501 0.319731164 0.062284959 29402.38807 13414999.67 0.014332299 13.68744868 61578.33553 -4.789427946 -0.130776678 SHS(ph)GTS(ph)PDNTAPPPPPPRPQPSHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHSGTSPDNTAPPPPPPRPQPSHSR 25 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 2 S(0.411)HS(0.491)GT(0.335)S(0.763)PDNTAPPPPPPRPQPSHSR;S(0.42)HS(0.487)GT(0.272)S(0.821)PDNTAPPPPPPRPQPSHSR 107.17 0.0049035 285050000 87465 83224 80997 59915 68144 78411 77707 83396 70765 TRUE FALSE 75906.27864 82677.29606 120167.4201 73519.61649 66788.06772 81427.52191 70170.9871 65562.41439 62399.24232 1.216461544 1.324972756 1.925783321 1.178213289 1.070334595 1.304944081 1.124548704 1.050692476 1 15.92924089 3.504625243 24.85922844 1.114482026 1.485885242 0.440894928 0.196495306 624.4886533 564436.7513 0.053745016 0.079479637 3196.135944 -3.504625243 0.371403217 LS(ph)SPVLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LSSPVLHR 8 0 Q16643;Q16643-3;Q16643-2;D6R9W4;D6RCR4 Q16643 DBN1 Drebrin 1 LS(0.626)S(0.374)PVLHR;LS(0.634)S(0.366)PVLHR 134.25 0.00056991 2527160000 2029750 711020 430028 543600 676280 666960 679370 770560 728630 TRUE FALSE 1761513.395 706349.2628 637990.9792 667032.6884 662823.3511 692618.3828 613484.802 605781.7405 642492.1915 2.74168841 1.099389646 0.992994137 1.03819579 1.031644213 1.078018367 0.954851763 0.942862417 1 19.2933194 4.739409563 4.715096563 1.003939661 2.844469923 0.994841138 0.039082228 0.013488364 0.836844394 0.011303813 0.082046248 54879.42635 -4.739409563 1.840530262 up SHS(ph)LPSSIIF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHSLPSSIIF 10 0 Q86Z20-2;Q86Z20 Q86Z20-2 CCDC125 Coiled-coil domain-containing protein 125 1 S(0.142)HS(0.857)LPSSIIF 79.148 0.029238 28212000 94001 101090 47163 60620 101420 84919 80474 107410 82269 TRUE FALSE 81578.52968 100425.9331 69971.18455 74384.69752 99401.94042 88185.88888 72669.64387 84441.20737 72543.25254 1.124550207 1.384359394 0.964544353 1.025384097 1.370243778 1.215631858 1.001742289 1.164011874 1 16.14655381 -0.078764209 0.757002168 2.70E-11 1.171757738 0.109651946 0.141322554 43.48053297 3.992322914 67.9298605 0.056637315 0.834133938 0.078764209 1.171757738 SHS(ph)LSGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SHSLSGAR 8 0 A0A0J9YYJ3;Q9Y519 A0A0J9YYJ3 TMEM184B Transmembrane protein 184B 1 S(0.001)HS(0.997)LS(0.002)GAR;S(0.001)HS(0.999)LS(0.001)GAR;SHS(0.999)LS(0.001)GAR;S(0.003)HS(0.996)LS(0.001)GAR 108.26 0.0040327 717751000 546854 463624 281145 379106 449671 465736 483354 542238 475199 TRUE FALSE 474585.8583 460578.4234 417107.6624 465187.8116 440723.4269 483653.1653 436478.4035 426284.6234 419021.5156 1.132604987 1.099176072 0.995432566 1.110176433 1.051791878 1.154244227 1.041661078 1.017333496 1 18.6766648 2.009663189 24.98463884 1.015782573 1.086781704 0.381534246 0.043681101 211.2209432 546119.133 0.017521939 0.011798737 102.24997 -2.009663189 0.070999131 SHS(ph)PLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHSPLR 6 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 S(0.015)HS(0.985)PLR 96.285 0.044458 160870000 206560 182380 117020 162670 129820 180060 158230 197940 248140 TRUE FALSE 179262.5726 181181.9338 173611.2634 199606.7098 127236.836 186987.0247 142884.879 155612.0714 218805.1719 0.819279412 0.828051422 0.79345137 0.912257732 0.581507443 0.854582289 0.653023316 0.711190097 1 17.73928731 SHS(ph)PSASQSGSQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 SHSPSASQSGSQLR 14 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 SHS(0.998)PS(0.002)ASQSGSQLR;SHS(0.997)PS(0.003)ASQSGSQLR;S(0.001)HS(0.954)PS(0.046)ASQSGSQLR;SHS(1)PSASQSGSQLR;SHS(0.975)PS(0.017)AS(0.007)QS(0.001)GSQLR;SHS(0.923)PS(0.059)AS(0.018)QS(0.001)GSQLR;S(0.037)HS(0.95)PS(0.013)ASQSGSQLR;S(0.01)HS(0.99)PSASQSGSQLR;S(0.034)HS(0.947)PS(0.018)ASQSGSQLR;S(0.172)HS(0.82)PS(0.008)ASQSGSQLR 316.33 4.25E-56 17798531000 5239844 6701389 2214063 3784492 6619871 6522662 6070185 6768378 5672528 TRUE FALSE 4547385.339 6657367.134 3284791.272 4643818.751 6488148.519 6773593.028 5481499.393 5321013.036 5001928.202 0.909126472 1.330960155 0.656705002 0.928405719 1.297129478 1.354196373 1.095877264 1.063792366 1 22.25405292 3.260979895 24.91368743 1.154524013 0.96166116 0.221855582 0.191195248 395.8111741 439846.7947 0.05642545 0.072788645 1823.811271 -3.260979895 -0.192862853 SHS(ph)QASLAGPGPVDPSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SHSQASLAGPGPVDPSNR 18 0 Q9P2M7;Q9P2M7-2;A6PVU7;A2A3M4 Q9P2M7 CGN Cingulin 1 S(0.406)HS(0.591)QAS(0.003)LAGPGPVDPSNR;S(0.238)HS(0.758)QAS(0.003)LAGPGPVDPSNR;S(0.22)HS(0.77)QAS(0.01)LAGPGPVDPSNR;S(0.185)HS(0.814)QAS(0.001)LAGPGPVDPSNR;S(0.034)HS(0.745)QAS(0.221)LAGPGPVDPSNR 188.04 4.18E-14 8149410000 2205360 2277180 1122010 1379980 2029350 1975690 2049930 2142860 2183600 TRUE FALSE 1913916.088 2262221.055 1664617.789 1693325.551 1988969.905 2051696.073 1851128.104 1684626.065 1925457.296 0.994005992 1.174900664 0.864531139 0.87944072 1.032985728 1.065563011 0.961396603 0.87492258 1 20.8767697 4.237668807 24.99989184 0.951568224 1.084453313 0.316066275 0.079637884 26.87068064 753364.4736 0.020834944 0.047864358 17284.97705 -4.237668807 0.132885089 SHSAHFFEFLTK ddPTM_MDA-MB-175_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 ; 97.734 0.0027498 1433260000 1375830 1464680 421350 963570 1480380 1332590 1428470 1524880 1445360 FALSE TRUE 1194010.58 1455058.421 625116.2693 1182363.296 1450923.334 1383855.6 1289937.199 1198796.279 1274491.187 0.936852755 1.141677899 0.490483006 0.927713983 1.138433399 1.085810254 1.012119356 0.940607743 1 20.28148997 3.471902363 24.98804262 1.025116762 0.855576332 0.198673412 0.165401538 238.9315877 1143996.266 0.047832604 0.061962631 2964.164917 -3.471902363 -0.16954043 SHSANDS(ph)EEFFREDDGGADLHNATNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHSANDSEEFFREDDGGADLHNATNLR 27 1 B0QY16;Q6ICG6-3;Q6ICG6;Q6ICG6-2 B0QY16 KIAA0930 Uncharacterized protein KIAA0930 1 S(0.304)HS(0.304)ANDS(0.392)EEFFREDDGGADLHNATNLR 63.403 0.019759 263790000 37273 36443 24351 26573 35050 37081 35381 34049 34497 TRUE FALSE 32347.27861 36203.60353 36127.22505 32606.80579 34352.57357 38507.53006 31949.75607 26767.88632 30418.80396 1.063397452 1.190171829 1.187660932 1.071929253 1.129320325 1.265912036 1.050329136 0.879978265 1 14.89267581 1.992359673 7.082517201 0.94058479 1.151084957 0.646869888 0.064730509 0.07512321 22.28781554 0.02790557 0.017011182 98.25613409 -1.992359673 0.210500167 SHSDASVGSHSSTESEHGSS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHSDASVGSHSSTESEHGSSSPR 23 0 Q6XZF7;A0A1C7CYY6;A0A1B0GTX1;Q6XZF7-2 Q6XZF7 DNMBP Dynamin-binding protein 1 SHSDASVGSHSSTESEHGS(0.233)S(0.756)S(0.011)PR 262.93 1.25E-43 463230000 129640 170360 27522 73393 243100 253580 121690 129420 131610 TRUE FALSE 112507.7455 169240.8939 40831.73126 90058.00239 238262.7856 263335.3867 109888.5225 101744.5401 116051.2157 0.969466324 1.458329349 0.35184234 0.776019465 2.053083064 2.269130789 0.94689678 0.876721019 1 16.82440211 SHSDNDRPNCS(ph)WNTQYSSAYYTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHSDNDRPNCSWNTQYSSAYYTSR 24 1 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.279)HS(0.279)DNDRPNCS(0.442)WNTQYSSAYYTSR 240.28 9.32E-38 842280000 218540 224390 119350 156360 182850 198230 159890 186210 231610 TRUE FALSE 189659.3853 222915.9673 177068.0592 191863.9278 179211.6427 205856.0364 144383.8924 146390.4406 204229.3297 0.928658903 1.091498306 0.867006025 0.93945335 0.877501988 1.007965098 0.706969428 0.716794404 1 17.63983054 2.242841832 24.99999743 0.784730181 0.950532309 0.300028441 0.101699089 112.1030821 654626.826 0.038294612 0.028597638 174.9209521 -2.242841832 0.165802128 SHSESASPSALSSS(ph)PNNLS(ph)PTGWSQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHSESASPSALSSSPNNLSPTGWSQPK 27 0 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 2 SHSESASPSALSS(0.007)S(0.993)PNNLS(0.997)PT(0.003)GWSQPK;SHSESASPSALS(0.056)S(0.045)S(0.899)PNNLS(0.997)PT(0.003)GWSQPK 237.79 2.38E-45 416680000 311530 260400 114942 186197 260130 264650 328380 339040 339700 TRUE FALSE 270360.5212 258689.4153 170528.3357 228475.8747 254953.9219 274831.2568 296533.7581 266538.9344 299541.053 0.902582529 0.863619236 0.569298712 0.762753127 0.851148513 0.917507814 0.989960325 0.889824389 1 18.19239422 2.91942473 2.482609144 0.945558976 0.767653403 0.446348893 0.091652243 0.285904869 3.476497895 0.033496563 0.034662219 830.6627403 -2.91942473 -0.177905573 MGPSGGEGMEPERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 MGPSGGEGMEPERR 14 1 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;;;;;;; 245.15 1.97E-17 6519200000 7242320 2526744 1443974 1802945 2384966 2390104 2505851 2820909 1773720 FALSE TRUE 6285229.062 2510145.652 2142284.656 2212331.219 2337509.843 2482052.847 2262833.956 2217679.563 1564032.842 4.018604273 1.604918762 1.36971846 1.414504324 1.494540127 1.586956987 1.446794399 1.41792391 1 20.57683938 4.740005388 4.200920436 1.410292556 4.229933874 0.966473782 0.152754405 0.035474968 1.42124306 0.037432547 0.302183775 54954.76919 -4.740005388 2.819641319 up SHSPSASQSGSQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHSPSASQSGSQLR 14 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 0 ; 213.52 9.18E-10 119313000 65978 85963 35214 50999 90241 111198 70496 89889 73427 FALSE TRUE 57258.84013 85398.30339 52243.60818 62579.10242 88445.38065 115475.859 63659.30877 70666.93687 64746.54371 0.884353617 1.318963121 0.806894163 0.966524216 1.366024742 1.783506152 0.98320783 1.091439524 1 15.98251556 3.254090137 24.86378875 1.232972581 1.004004415 0.184754281 0.260608891 464.8332196 744224.2167 0.079376493 0.102093494 1795.106158 -3.254090137 -0.228968166 SHSS(ph)SPQSVLWNRPQPSEDRLPSQQGLAEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHSSSPQSVLWNRPQPSEDRLPSQQGLAEAR 31 2 Q8NCE2;Q8NCE2-2 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 S(0.063)HS(0.059)S(0.448)S(0.419)PQS(0.011)VLWNRPQPSEDRLPSQQGLAEAR;SHS(0.005)S(0.429)S(0.429)PQS(0.137)VLWNRPQPSEDRLPSQQGLAEAR 230.22 7.06E-36 488600000 95032.6 121344 39109 88512.8 164296.7 169404.7 124072.9 125842.3 142770 TRUE FALSE 82473.80113 120546.8833 58022.24321 108610.9841 161027.5171 175921.8084 112040.3293 98931.90345 125891.8932 0.65511606 0.957542858 0.460889432 0.862732153 1.279093617 1.397403787 0.88997255 0.785848087 1 16.94182586 3.474633959 24.9912961 1.040716516 0.708484109 0.401650577 0.210705292 93.88176665 943274.5156 0.066776181 0.086744012 2982.867478 -3.474633959 -0.332232407 SHSSS(ph)PQSVLWNRPQPSEDRLPSQQGLAEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHSSSPQSVLWNRPQPSEDRLPSQQGLAEAR 31 2 Q8NCE2;Q8NCE2-2 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 S(0.017)HS(0.053)S(0.207)S(0.67)PQS(0.053)VLWNRPQPSEDRLPSQQGLAEAR;SHS(0.008)S(0.046)S(0.899)PQS(0.046)VLWNRPQPSEDRLPSQQGLAEAR 123.86 3.80E-06 399750000 81949 101381 35322 79236 140148 137099 115108 130929 131991 TRUE FALSE 71119.23202 100715.0215 52403.83734 97227.74485 137359.329 142373.2872 103944.8439 102930.8522 116387.1743 0.611057296 0.865344675 0.4502544 0.835381952 1.180193005 1.223272994 0.893095347 0.884383119 1 16.82857256 3.476406025 18.02465677 1.015105493 0.660911615 0.602564048 0.145848238 0.541493484 13600.38972 0.043846165 0.057659044 2995.063437 -3.476406025 -0.354193878 SHTCFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SHTCFNR 7 0 O00308-2;O00308;O00308-3;A0A590UJQ1;Q96J02-3;Q96J02-2;Q96J02;A0A590UK44;A0A590UJW8;Q9H0M0-3;Q9H0M0;Q9H0M0-6 O00308-2;A0A590UJQ1;Q9H0M0-3 WWP2;ITCH;WWP1 NEDD4-like E3 ubiquitin-protein ligase WWP2;E3 ubiquitin-protein ligase Itchy homolog;NEDD4-like E3 ubiquitin-protein ligase WWP1 0 ; 103.91 0.0082707 179844000 313690 291050 167029 186006 270790 324750 260550 296170 200646 FALSE TRUE 272235.0717 289138.0734 247804.7831 228241.5052 265401.8088 337243.3426 235281.9011 232836.3503 176925.8585 1.53869578 1.634232983 1.40061371 1.2900404 1.500073596 1.906128056 1.329833316 1.316010855 1 17.43278539 1.419194055 1.718986749 0.931682422 1.525184839 0.495664134 0.16959641 0.580314775 2.267119875 0.528592673 0.050076727 26.2539138 -1.419194055 0.593502418 SHTEEDCTEELFDFLHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SHTEEDCTEELFDFLHAR 18 0 P07919 P07919 UQCRH "Cytochrome b-c1 complex subunit 6, mitochondrial" 0 ;;;;; 414.82 7.20E-148 722996000 326417 366066 233938 382653 402221 493838 233977 333642 354224 FALSE TRUE 283280.1664 363661.2883 347071.1993 469540.2121 394217.589 512836.2674 211285.9466 262295.2547 312348.0423 0.906937544 1.164282272 1.11116816 1.503259661 1.262110005 1.641874441 0.67644396 0.839753157 1 18.25279496 2.218814599 24.99999511 0.832182972 1.264078117 0.467715111 0.214296491 211.713485 268043.763 0.088314013 0.059631872 165.5063264 -2.218814599 0.431895146 SHTFPELAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SHTFPELAYR 10 0 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 ;;; 112.13 0.0016617 1278460000 719320 808050 466008 627269 689010 791370 719930 798900 1313950 FALSE TRUE 624260.0395 802741.8663 691371.0275 769700.0137 675300.049 821814.516 650111.2994 628061.452 1158616.328 0.538797896 0.692845291 0.596721288 0.664326918 0.582850451 0.709306866 0.561110079 0.542078889 1 20.14397147 1.232295203 24.99992973 1.000000642 0.611404596 0.804638572 0.060237048 89.54463666 357261.3709 0.131269898 0.014446958 17.07242457 -1.232295203 -0.388596046 SHTPSPTS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SHTPSPTSPK 10 0 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 1 SHTPSPT(0.006)S(0.994)PK;SHTPSPT(0.013)S(0.987)PK;SHTPSPT(0.007)S(0.993)PK;SHTPSPT(0.006)S(0.994)PK 130.77 0.00017249 1051900000 2617010 1575520 1050740 1206580 1609450 1414830 1926710 2109910 1889050 TRUE FALSE 2271165.498 1565170.305 1558881.379 1480552.43 1577425.094 1469259.426 1739857.961 1658722.166 1665728.661 1.363466662 0.939631011 0.93585553 0.888831696 0.946988024 0.882052077 1.044502626 0.995793736 1 20.66772198 4.740010975 24.97886626 0.956591547 1.363466797 0.870678158 0.04956126 45.84416691 789476.9102 0.013114225 0.080179283 54955.47608 -4.740010975 0.40687525 SHVEDGDIAGAPASS(ph)PEAPPAEQDPVQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SHVEDGDIAGAPASSPEAPPAEQDPVQLK 29 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 SHVEDGDIAGAPAS(0.16)S(0.84)PEAPPAEQDPVQLK;SHVEDGDIAGAPAS(0.192)S(0.808)PEAPPAEQDPVQLK;SHVEDGDIAGAPAS(0.168)S(0.832)PEAPPAEQDPVQLK;SHVEDGDIAGAPAS(0.188)S(0.812)PEAPPAEQDPVQLK;SHVEDGDIAGAPAS(0.115)S(0.885)PEAPPAEQDPVQLK 246.89 5.70E-46 3608950000 2821790 2710880 1760350 2509910 2768760 2136510 2807390 3596520 2969560 TRUE FALSE 2448883.302 2693072.051 2611661.148 3079823.427 2713667.093 2218702.922 2535129.75 2827432.186 2618502 0.935223002 1.028478134 0.997387494 1.176177611 1.036343334 0.847317635 0.968160326 1.079789966 1 21.32031028 4.74278483 23.18979845 1.019059532 0.935222909 0.086729998 0.082785311 442.8428912 2430812.265 0.021134584 0.156473288 55307.60215 -4.74278483 -0.083836623 SHVSSEPYEPIS(ph)PPQVPVVHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SHVSSEPYEPISPPQVPVVHEK 22 0 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 SHVSSEPYEPIS(1)PPQVPVVHEK;SHVSSEPYEPIS(1)PPQVPVVHEK;SHVSSEPYEPIS(1)PPQVPVVHEK;SHVSSEPYEPIS(1)PPQVPVVHEK 189.2 3.71E-17 1401270000 1280820 1217130 386835 809460 1351470 1219120 1242810 1339040 1238460 TRUE FALSE 1111556.392 1209134.593 573909.6999 993260.2648 1324578.391 1266020.335 1122282.477 1052696.716 1092050.67 1.017861554 1.107214735 0.525533948 0.909536794 1.212927594 1.159305489 1.027683521 0.963963253 1 20.05860837 3.449851685 23.23641063 1.060220336 0.874509702 0.232249098 0.164510518 152.8149464 130212.3993 0.049325377 0.063681359 2817.420595 -3.449851685 -0.185710634 SHVTEEEEEEEEEES(ph)DS ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SHVTEEEEEEEEEESDS 17 0 O75971-2;O75971 O75971-2 SNAPC5 snRNA-activating protein complex subunit 5 1 SHVTEEEEEEEEEES(0.5)DS(0.5) 110.22 0.0011832 0 57962 54533 31290 41302 60954 48175 54779 60655 50725 TRUE FALSE 50302.17484 54174.76913 46421.94866 50680.25036 59741.13465 50028.32342 49466.54101 47684.40027 44728.34829 1.124615077 1.211195387 1.037864138 1.133067781 1.335643657 1.11849253 1.105932656 1.066089004 1 15.44890186 1.680440796 1.467297031 0.997006404 1.162489003 0.335333159 0.07635974 0.64195659 2.300458264 0.133241121 0.024021996 47.91161347 -1.680440796 0.165482599 SICEVLDLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SICEVLDLER 10 0 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;H0Y8X0;D6RDA2 H0Y993 DEK Protein DEK 0 ; 160.16 1.74E-05 200655000 445640 435900 241880 329880 426670 424730 430060 446160 440630 FALSE TRUE 386747.5449 433036.5442 358853.977 404784.2959 418180.1018 441069.6379 388352.8474 350752.156 388539.2234 0.995388681 1.114524656 0.923597813 1.041810637 1.076287995 1.135199772 0.999520316 0.90274581 1 18.56770072 1.998414962 24.99926677 0.946438232 1.047973747 0.286601659 0.063148446 64.94701344 1024351.085 0.025749595 0.017079798 99.63569675 -1.998414962 0.101535515 SIDQFANLVLHQTVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SIDQFANLVLHQTVER 16 0 O15116 O15116 LSM1 U6 snRNA-associated Sm-like protein LSm1 0 ; 185.33 1.68E-09 476380000 342060 329870 163255 225700 301510 333830 277660 332850 293190 FALSE TRUE 296855.9043 327703.0622 242205.6641 276948.6346 295510.5409 346672.6561 250732.5759 261672.6177 258529.4122 1.148248092 1.267565881 0.936859222 1.071246139 1.143044184 1.340940875 0.969841589 1.012158019 1 17.9799689 SIEAVHEDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SIEAVHEDIR 10 0 P23919-2;P23919;H7C312;H7BZ20 P23919-2 DTYMK Thymidylate kinase 0 ; 150.94 2.07E-05 1170190000 1710840 1604450 931390 1255580 1639470 1839470 1567090 1730500 1617150 FALSE TRUE 1484748.159 1593910.262 1381813.319 1540678.629 1606847.755 1910235.601 1415113.853 1360446.042 1425972.369 1.041218043 1.11777079 0.969032324 1.080440731 1.126843541 1.339602115 0.992385185 0.954047968 1 20.4435146 2.031913698 24.99998184 0.973583683 1.110449898 0.299812057 0.094047908 231.2853552 181179.2811 0.039771244 0.02681356 107.6251323 -2.031913698 0.136866215 SIEDFAHSSFQMALSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SIEDFAHSSFQMALSK 16 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 164.62 7.31E-09 79338000 257650 279570 61620 164260 389920 359730 315980 346270 305150 FALSE TRUE 223600.8997 277733.4863 91419.63811 201557.7436 382161.3549 373569.0459 285336.3082 272222.8552 269075.5146 0.83099683 1.032176735 0.339754579 0.749075009 1.420275477 1.388342772 1.060432082 1.011696867 1 18.03765159 3.309120139 10.08810877 1.157303922 0.729281572 0.495701852 0.219085323 0.370971763 50.40272328 0.067147415 0.086660026 2037.605664 -3.309120139 -0.42802235 SIEEVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SIEEVLR 7 0 A0A2R8YF87;Q96AX1;H3BMM5;A0A2R8Y5U3 A0A2R8YF87 VPS33A Vacuolar protein sorting-associated protein 33A 0 105.12 0.018609 114980000 120190 110680 62273 86728 99672 102100 91156 113780 107670 FALSE TRUE 104306.587 109952.9358 92388.43109 106420.918 97688.7222 106027.8531 82315.70515 89449.03244 94941.37526 1.098642048 1.158113999 0.97311031 1.120911907 1.028937299 1.116771827 0.867016145 0.942150166 1 16.53474933 2.24616053 24.99999884 0.93469853 1.080478905 0.569205551 0.059994823 115.1077944 378649.3792 0.021695621 0.016474009 176.2627454 -2.24616053 0.145780375 SIEIPRPVDGVEVPGCGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SIEIPRPVDGVEVPGCGK 18 1 P26368-2;P26368;K7ENG2 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 104.03 0.00047298 264020000 176570 143830 77116 115610 147900 131270 146360 177320 160130 FALSE TRUE 153235.8271 142885.1713 114409.5555 141861.0175 144957.0794 136320.0418 132166.0297 139401.4979 141199.6138 1.085242537 1.011937408 0.81026819 1.004684175 1.026611019 0.96544203 0.936022601 0.987265433 1 17.10737662 4.479049623 24.99759543 0.962734026 1.066916304 0.305669191 0.0597524 77.18504574 1000529.887 0.01483567 0.040644473 30133.50315 -4.479049623 0.104182278 SIFDHIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SIFDHIK 7 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 92.925 0.015312 372300000 768360 704850 370940 570950 622840 624730 794070 842050 774190 FALSE TRUE 666819.2792 700219.7939 550327.8247 700592.9239 610446.7026 648763.7674 717061.2136 661984.1603 682666.1402 0.976786807 1.02571338 0.806144896 1.026259957 0.894209727 0.950338283 1.050383447 0.969704108 1 19.38082067 2.410491408 14.07327159 1.00077615 0.944501591 0.15320255 0.066182353 2.51173216 527.127708 0.023266474 0.018020478 257.3305854 -2.410491408 -0.056274559 SIFEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SIFEAR 6 0 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ; 106.76 0.074087 909300000 716850 630950 441060 533210 654560 717780 641950 715320 711300 FALSE TRUE 622116.4562 626805.2479 654358.0913 654283.4801 641535.5366 745393.4611 579693.7878 562354.3846 627210.9243 0.991877584 0.999353206 1.043282357 1.0431634 1.022838589 1.188425508 0.924240579 0.896595328 1 19.25859116 SIFEMYEPSELESSHLTDQDNEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SIFEMYEPSELESSHLTDQDNEIR 24 0 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 134.34 3.57E-05 63511000 20026 21110 11193 13815 22017 23868 16322 22645 23107 FALSE TRUE 17379.51336 20971.32702 16605.97224 16951.9069 21578.90478 24786.2174 14739.09495 17802.54297 20375.31678 0.852968989 1.029251581 0.815004371 0.831982495 1.059070885 1.216482554 0.723379916 0.873730856 1 14.31453487 5.042165279 14.31394029 0.932967585 0.531999355 0.034026891 0.14204695 7872361.901 83248413.32 0.035502667 80692594.71 110195.8601 -5.042165279 -0.40096823 SIFGEDALANVSIEKPIHQGPDAAVTGHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SIFGEDALANVSIEKPIHQGPDAAVTGHIR 30 1 P53618 P53618 COPB1 Coatomer subunit beta 0 239.78 9.42E-46 628160000 300180 252150 149160 183810 295860 257620 312090 356390 255450 FALSE TRUE 260510.4524 250493.61 221294.2749 225546.8699 289972.9648 267530.8081 281823.5598 280178.7719 225250.992 1.156534096 1.112064403 0.982434186 1.001313547 1.287332687 1.18770091 1.251153468 1.243851445 1 17.78117393 3.244334935 24.99993751 1.204208764 1.06082409 0.33621805 0.090756796 153.3334599 663853.9571 0.026527896 0.03330135 1755.233645 -3.244334935 -0.143384675 SIFKPFIFVDDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SIFKPFIFVDDVK 13 1 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 ; 136.33 6.71E-05 944260000 1912790 1256110 851580 1054340 1142610 1009160 1608710 1903440 1267020 FALSE TRUE 1660009.955 1247858.531 1263406.936 1293744.012 1119874.296 1047983.038 1452697.552 1496404.169 1117234.339 1.485820742 1.116917452 1.130834322 1.157988048 1.00236294 0.93801542 1.300262175 1.339382542 1 20.09150039 4.740944662 24.52828156 1.140166841 1.485820893 0.440093647 0.127263723 189.7009709 1951580.27 0.034366034 0.223446097 55073.75172 -4.740944662 0.345654052 SIFLFLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SIFLFLDR 8 0 Q13619;A0A0A0MR50;Q13619-2;A0A087WWN2;A0A669KAX4;Q13620-1;K4DI93;Q13620;Q13620-3 Q13619;A0A669KAX4 CUL4A;CUL4B Cullin-4A;Cullin-4B 0 ; 140.5 0.0015088 216790000 279810 318670 211183 261010 314810 320950 343350 337430 439980 FALSE TRUE 242832.3996 316576.6358 313311.8052 320276.3098 308545.8969 333297.1542 310051.9698 265273.2204 387966.0656 0.625911442 0.815990531 0.807575283 0.825526607 0.79529094 0.85908842 0.799172911 0.683753668 1 18.56557094 4.739523903 23.85735364 0.811088125 0.625911338 0.378785722 0.078061341 48.44547789 1199479.181 0.01838109 0.108280008 54893.87672 -4.739523903 -0.185176787 SIFQHIQSAQSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SIFQHIQSAQSQR 13 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ; 192.51 2.65E-06 2092570000 1781400 1867990 732520 1148040 1971630 1941830 1623100 1897780 1691370 FALSE TRUE 1545983.477 1855719.051 1086769.122 1408720.029 1932398.42 2016533.457 1465692.012 1491954.516 1491418.165 1.036586192 1.24426475 0.728681699 0.944550671 1.295678479 1.352091253 0.982750543 1.000359624 1 20.50825339 SIGEAIQYLHSINIAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SIGEAIQYLHSINIAHR 17 0 P49137-2;P49137 P49137-2 MAPKAPK2 MAP kinase-activated protein kinase 2 0 177.56 5.91E-10 193150000 141170 151070 71069 99163 138920 155000 133520 170750 104580 FALSE TRUE 122514.0268 150077.6112 105438.2061 121679.4748 136155.7638 160962.9503 120571.251 134236.4413 92216.67154 1.328545314 1.627445544 1.143374667 1.319495409 1.476476667 1.745486446 1.307477801 1.455663483 1 16.49273997 1.236237601 24.99436063 0.999999444 1.427152728 0.381504305 0.170249785 67.85512572 729914.2118 0.265748598 0.040834052 17.2281086 -1.236237601 0.427153284 SIGS(ph)PESTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.006)IGS(0.989)PES(0.004)T(0.001)PK 67.08 0.067183 427100000 750360 662960 544230 602790 614390 624710 775780 968020 835460 TRUE FALSE 651198.0248 658604.9721 807421.4483 739662.6826 602164.841 648742.9979 700544.975 761016.4561 736692.8706 0.883947776 0.894002098 1.096008229 1.004031276 0.817389261 0.880615279 0.950932204 1.033017268 1 19.49070376 1.844915883 4.968304077 1.016234982 0.932444671 0.177151165 0.076205676 0.408647025 14.57573024 0.044373851 0.022044635 69.97064598 -1.844915883 -0.083790311 SIGTANRPMGAGEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SIGTANRPMGAGEALR 16 1 Q12906;Q12906-5;Q12906-2;Q12906-3;K7EQR9;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;;; 165.45 6.40E-09 1418420000 834390 722140 431387 562835 717010 752000 715230 768700 950810 FALSE TRUE 724123.2474 717396.2148 640007.1961 690635.2891 702742.9038 780929.9266 645867.1047 604319.487 838406.325 0.863690106 0.855666511 0.763361603 0.823747709 0.838188934 0.931445653 0.770350945 0.720795477 1 19.67729008 2.084745025 0.003982298 0.627497646 1.030509232 0 0.082529934 1899168.903 3904.029905 199171.5246 195920.4841 121.5472186 -2.084745025 0.403011587 SIGVSNFNHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SIGVSNFNHR 10 0 S4R3P0;P52895;B4DK69 S4R3P0 AKR1C2 Aldo-keto reductase family 1 member C2 0 ;;; 169.58 4.59E-06 1896140000 1798480 2183400 1002410 1390620 2134750 2231920 2173370 2314200 2379920 FALSE TRUE 1560806.311 2169057.102 1487178.829 1706381.525 2092272.652 2317783.407 1962596.912 1819326.339 2098568.569 0.743748064 1.033588863 0.708663444 0.813116879 0.996999899 1.104459221 0.935207427 0.866936809 1 21.00097417 3.240945025 24.99519673 0.96927113 0.831400272 0.357603644 0.103055205 81.92809744 858826.3659 0.030840984 0.037941565 1741.586399 -3.240945025 -0.137870858 SIIECVDDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SIIECVDDFR 10 0 Q9Y6Y8;Q9Y6Y8-2;H7C0V8 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 ;;; 228.05 5.29E-09 415930000 847514 907539 544684 658191 882084 970190 873925 1019990 897279 FALSE TRUE 735512.8776 901577.3166 808095.0043 807643.3264 864532.2542 1007513.837 789171.888 801873.0761 791203.6988 0.929612537 1.139500887 1.021348871 1.020777996 1.092679743 1.27339374 0.997432 1.013484994 1 19.59368965 SIIPLPHPVRPEDIE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SIIPLPHPVRPEDIE 15 1 P61599;A8MZB2 P61599 NAA20 N-alpha-acetyltransferase 20 0 83.54 0.0079113 99878000 313170 244210 224840 270710 141490 207570 190790 216100 199200 FALSE TRUE 271783.791 242605.7684 333573.376 332178.843 138674.6258 215555.3522 172287.2152 169888.6967 175650.8029 1.547296036 1.381182234 1.899071171 1.891131936 0.789490418 1.227181138 0.980850712 0.967195674 1 17.42235065 3.238247429 25 1.000529983 1.674021289 0.779107866 0.181660944 3.992164307 318679.8006 0.055256494 0.066649527 1730.802163 -3.238247429 0.673491306 SIKPSDS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SIKPSDSPR 9 1 Q92610;H0YM74 Q92610 ZNF592 Zinc finger protein 592 1 SIKPS(0.003)DS(0.997)PR;S(0.001)IKPS(0.025)DS(0.974)PR 62.924 0.048107 1178900000 1453850 1158550 819370 1176250 1198300 1114640 1321370 1663350 1830260 TRUE FALSE 1261720.039 1150939.409 1215620.073 1443335.54 1174456.174 1157520.922 1193223.741 1307655.547 1613888.748 0.781788733 0.713146684 0.753224207 0.894321583 0.727718175 0.71722473 0.739346961 0.810251356 1 20.6221097 1.241260742 2.851430571 1.048469014 0.761423559 0.675288413 0.051802849 0.259340939 2.532188116 0.174710144 0.013812559 17.42852935 -1.241260742 -0.287045454 SILCCLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SILCCLR 7 0 A0A087WYT3;Q15185-4;Q15185;Q15185-3 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 153.88 0.0039921 910600000 1077100 1031100 824370 796230 852520 945360 1408900 1497900 1006700 FALSE TRUE 934758.506 1024326.636 1223038.089 977026.1911 835556.5199 981728.6109 1272265.095 1177585.742 887689.0728 1.053024685 1.153925026 1.377777565 1.100640101 0.941271607 1.105937474 1.433232799 1.326574561 1 19.75969491 2.292417179 24.99999074 1.276041333 1.125969928 0.136021475 0.152070042 164.1453508 76194.67258 0.058958315 0.045668875 196.0727226 -2.292417179 -0.150071405 SILEYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SILEYLR 7 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 143.23 0.0056669 331190000 440820 579340 377240 396200 533580 605320 532160 528110 582510 FALSE TRUE 382564.5201 575534.2774 559674.5258 486163.2655 522962.8019 628607.0521 480551.2051 415177.7863 513646.3314 0.744801426 1.120487468 1.089610675 0.946494184 1.018137909 1.223812989 0.935568261 0.808295048 1 18.97041582 2.011149667 24.99920233 0.884897475 1.031839398 0.129776404 0.132089497 323.2603071 724794.7417 0.051813843 0.034898514 102.6005449 -2.011149667 0.146941923 SILKPSTPIPPQEGEEVGES(ph)SEEQDNAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SILKPSTPIPPQEGEEVGESSEEQDNAPK 29 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;A0A3B3ISZ5;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 SILKPSTPIPPQEGEEVGES(0.765)S(0.235)EEQDNAPK 90.336 0.00097095 152160000 117460 90346 77051 78958 93957 74542 125050 135850 132800 TRUE FALSE 101937.3634 89752.51118 114313.1213 96886.6207 92087.43952 77409.67898 112922.6702 106799.5347 117100.5353 0.870511507 0.766456882 0.976196403 0.827379828 0.786396401 0.661053161 0.964322409 0.912032848 1 16.83738815 SILPYPVS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SILPYPVSPK 10 0 Q8IWI9-3;Q8IWI9;H3BP52;H3BTF4 Q8IWI9-3 MGA MAX gene-associated protein 1 SILPYPVS(1)PK 102.87 0.0042119 0 542510 432760 260540 368390 526340 427880 479110 588690 469310 TRUE FALSE 470815.929 429917.1711 386538.0155 452038.58 515866.8638 444340.8205 432645.9859 462803.2247 413828.7064 1.137707273 1.038877111 0.934053171 1.092332583 1.246570998 1.073731265 1.04547118 1.118344903 1 18.6586742 4.762653253 22.00044677 1.073715652 1.137707652 0.063808764 0.081081861 4531.06844 4137248.698 0.020500399 0.960128654 57896.62572 -4.762653253 0.063992 SILS(ph)PGGSCGPIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SILSPGGSCGPIK 13 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;P78347-5 A0A494C1K3 GTF2I General transcription factor II-I 1 SILS(1)PGGSCGPIK;SILS(0.996)PGGS(0.004)CGPIK;SILS(1)PGGSCGPIK;SILS(1)PGGSCGPIK 250.16 1.03E-17 2583080000 3077770 2807450 1659590 2083780 2554530 2089390 3103060 3437970 3241630 TRUE FALSE 2671034.896 2789007.676 2462173.275 2556934.098 2503699.851 2169770.185 2802125.719 2702786.87 2858408.194 0.934448376 0.975720571 0.861379169 0.894530775 0.875907037 0.759083391 0.980309854 0.945556648 1 21.44678052 SILVS(ph)PTGPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SILVSPTGPSR 11 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 SILVS(0.949)PT(0.051)GPSR;SILVS(0.981)PT(0.019)GPSR 111.63 0.001714 362800000 334930 326790 193522 213591 283505 334010 273496 317770 285690 TRUE FALSE 290668.1519 324643.295 287109.8865 262090.1011 277863.8052 346859.5808 246972.4 249817.3584 251916.0537 1.153829411 1.288696335 1.139704605 1.040386658 1.10300158 1.376885577 0.98037579 0.991669069 1 17.94258354 2.131983229 22.70264116 0.990430136 1.176580534 0.485319616 0.09352965 4.530796825 949.5225619 0.038675417 0.026074959 135.5137082 -2.131983229 0.186150398 SILYDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SILYDER 7 0 A0A024RA52;P25787 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 0 ;;;;; 138.9 0.0063773 4876040000 9648160 9349570 5528490 6764600 8991470 9488160 8856930 9963400 9369450 FALSE TRUE 8373131.211 9288152.059 8202086.256 8300605.82 8812557.339 9853175.655 7997986.292 7832804.445 8261804.295 1.013474891 1.124228041 0.992771792 1.004696495 1.066662562 1.192617896 0.96806775 0.948074315 1 22.97802546 2.072124086 25 0.966636526 1.06385035 0.347395141 0.060351898 45.188623 15662.40764 0.024721643 0.016667326 118.0657923 -2.072124086 0.097213824 SINHQIES(ph)PSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SINHQIESPSER 12 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 SINHQIES(0.999)PS(0.001)ER;SINHQIES(1)PSER;SINHQIES(0.995)PS(0.005)ER;SINHQIES(1)PSER;SINHQIES(0.997)PS(0.003)ER 289.23 4.68E-36 5630990000 2552250 2662910 1063275 1626660 2507600 2767930 2324730 2395490 2469460 TRUE FALSE 2214963.696 2645417.169 1577478.346 1996018.015 2457703.666 2874414.058 2099278.042 1883233.105 2177523.252 1.01719405 1.214874361 0.72443697 0.916646017 1.12866931 1.320038285 0.964066878 0.864850974 1 21.05425669 2.011999085 24.99755161 0.920277984 1.051429515 0.093604315 0.163476608 502.215561 1046255.995 0.070219236 0.04730539 102.8014131 -2.011999085 0.131151531 SINNAEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SINNAEKR 8 1 P62244;I3L3P7;I3L246;H3BN98;H3BV27;H3BT37;I3L303 P62244 RPS15A 40S ribosomal protein S15a 0 98.009 0.01255 295600000 149750 144610 65695 69959 100530 136660 146510 175660 20305 FALSE TRUE 129960.1581 143660.0474 97465.32174 85844.26021 98529.64968 141917.3986 132301.4828 138096.476 17904.56603 7.25849249 8.023654253 5.443601457 4.794545707 5.503045955 7.926324401 7.389259394 7.712919472 1 14.12803993 1.232799891 24.99977968 0.999990736 6.76562417 0.715947566 1.139496956 115.0151395 499078.1236 2.673605429 0.30818107 17.09227576 -1.232799891 5.765633434 SINPLGGFVHYGEVTNDFVMLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SINPLGGFVHYGEVTNDFVMLK 22 0 P39023;G5E9G0 P39023 RPL3 60S ribosomal protein L3 0 ;;; 286.38 3.79E-46 3004570000 2074430 1840260 1093402 1710422 1742216 1663503 2069960 2349150 2295358 FALSE TRUE 1800288.82 1828171.211 1622174.864 2098799.457 1707549.31 1727499.037 1869215.598 1846802.554 2024003.392 0.88946927 0.903245132 0.801468451 1.036954516 0.843649431 0.853505999 0.923523945 0.912450325 1 20.94878028 0.786875122 1.354711226 1.211321597 0.891224164 0.229276504 0.06150443 5.948418386 3.968613464 3.589796266 0.017099648 6.121743399 -0.786875122 -0.320097433 SINQQSGAHVELQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SINQQSGAHVELQR 14 0 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 0 133.45 4.45E-05 122250000 55152 57855 31968 43305 62766 64737 59138 67953 63379 FALSE TRUE 47863.52346 57474.9467 47427.83173 53138.06213 61517.0794 67227.47428 53402.80586 53421.77976 55886.40682 0.856443028 1.028424441 0.848647004 0.950822662 1.100752095 1.202930696 0.955559838 0.955899347 1 15.7702098 3.424116299 8.079962562 1.033208797 0.919066001 0.332587498 0.086488909 0.353010648 47.6020352 0.02676616 0.034646718 2655.31653 -3.424116299 -0.114142796 SINTEVVACSVDSQFTHLAWINTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SINTEVVACSVDSQFTHLAWINTPR 25 0 Q13162;H7C3T4;A6NJJ0 Q13162;A6NJJ0 PRDX4 Peroxiredoxin-4 0 145.2 2.86E-07 57382000 50234 47364 21858 33074 45019 52936 37214 44382 32414 FALSE TRUE 43595.44962 47052.86277 32428.60191 40583.9572 44123.20998 54972.48217 33604.99201 34891.25468 28582.05385 1.525273511 1.646237986 1.134579134 1.419910459 1.543738257 1.923321622 1.175737482 1.220739939 1 14.80282197 2.043485795 24.99801716 1.147766544 1.517613163 0.46601545 0.201468457 127.2437088 73146.12555 0.084564705 0.057013476 110.5314315 -2.043485795 0.369846619 SIPLDEGEDEAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SIPLDEGEDEAQR 13 0 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 147.91 0.00010006 149320000 69376 78831 50141 43660 80845 80852 61440 72672 67814 FALSE TRUE 60207.78582 78313.15397 74389.35531 53573.6703 79236.34267 83962.42876 55481.55826 57131.65833 59797.10617 1.006867885 1.309647891 1.244029353 0.89592413 1.325086576 1.404121941 0.927830154 0.955425137 1 15.86778805 2.205494463 24.99994326 0.958520106 1.196896535 0.354523127 0.150435242 208.3892384 157552.9936 0.061410531 0.041406035 160.5071794 -2.205494463 0.238376429 SIPLDEGEDEAQRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SIPLDEGEDEAQRR 14 1 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 178.84 3.11E-06 1205090000 598070 578000 326770 382170 575110 647580 583230 638170 467240 FALSE TRUE 519033.5342 574203.0799 484797.065 468947.5396 563666.4362 672492.8216 526668.4444 501702.3117 412003.4195 1.259779676 1.393685229 1.176682139 1.138212737 1.368111063 1.632250583 1.278310857 1.217713951 1 18.65229679 1.319422774 2.18528408 0.94363089 1.323667929 0.363337318 0.135069705 0.665377953 3.791957463 0.46965276 0.038892662 20.86521068 -1.319422774 0.380037039 SIPLECPLSS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SIPLECPLSSPK 12 0 Q92667-2;Q92667;I3L2A2;I3L2N7 Q92667-2 AKAP1 "A-kinase anchor protein 1, mitochondrial" 1 SIPLECPLSS(1)PK 202.29 1.45E-07 187740000 228960 256380 203470 306010 460040 445530 311830 551580 472150 TRUE FALSE 198702.3559 254695.8229 301868.7726 375494.2476 450886.1041 462669.8274 281588.7746 433628.9094 416332.9649 0.47726789 0.611759924 0.725065748 0.901908519 1.082994003 1.111297607 0.676354741 1.041543538 1 18.66737827 4.017010939 1.620033058 0.974352482 0.504464634 0.693053248 0.120513174 0.240508031 1.191369747 0.036387734 0.115089706 10399.46359 -4.017010939 -0.469887848 SIQEIQELDKDDESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SIQEIQELDKDDESLR 16 1 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;;;;; 276.5 2.44E-35 16246140000 13557160 9910320 8313802 8920876 9985207 8740544 12160900 14650470 13006690 FALSE TRUE 11765546.96 9845218.455 12334384.46 10946497.24 9786520.916 9076798.384 10981537.79 11517581 11469053.93 1.025851568 0.858415918 1.075449164 0.954437682 0.853298012 0.791416488 0.957492908 1.004231131 1 23.45124305 1.997789107 24.99780414 0.995951075 0.923629869 0.123025634 0.082470369 178.2362103 2015267.951 0.035350787 0.023399554 99.49221664 -1.997789107 -0.072321206 SIQEIQELDKDDESLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SIQEIQELDKDDESLRK 17 2 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;; 231.86 1.86E-16 4857100000 1549520 1048220 938130 962530 965930 655410 1504640 1658320 1235520 FALSE TRUE 1344747.006 1041334.174 1391812.806 1181087.148 946709.8828 680624.0468 1358720.244 1303701.173 1089458.233 1.234326352 0.955827532 1.277527457 1.084105028 0.868973086 0.624736246 1.247152211 1.196650898 1 20.05517946 4.758940552 22.36438401 1.046331722 1.23432712 0.093418164 0.193603116 3247.576442 3563554.892 0.050104465 1.649296276 57403.78805 -4.758940552 0.187995399 SIQFVDWCPTGFK ddPTM_MDA-MB-175_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 ; 213.84 6.20E-09 1188090000 3975500 3328600 2017210 2750500 3191900 2771600 3523800 4071000 4031500 FALSE TRUE 3450127.602 3306734.207 2992739.503 3375043.064 3128387.435 2878225.245 3182062.418 3200448.331 3554900.663 0.970527148 0.930190326 0.841863047 0.949405731 0.880021056 0.809649979 0.895119926 0.900291916 1 21.76137782 1.234275179 4.71189537 1.008369578 0.894235073 0.316298862 0.047445683 0.244411148 12.32293115 0.093264101 0.011990091 17.15043655 -1.234275179 -0.114134505 SIRDT(ph)PAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SIRDTPAK 8 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 S(0.007)IRDT(0.993)PAK;S(0.001)IRDT(0.999)PAK;S(0.004)IRDT(0.996)PAK 89.9 0.021951 16078400000 13601800 12812900 7481500 9429200 8655500 8552300 12567300 13773300 12546600 TRUE FALSE 11804287.67 12728731.22 11099578.42 11570243.98 8483272.484 8881312.515 11348525.18 10827986.98 11063355.24 1.066971765 1.150530823 1.003274159 1.045816909 0.76679021 0.802768448 1.025776081 0.978725418 1 23.39928565 3.734487202 2.174815866 0.928030201 1.097285863 0.382335915 0.091065906 0.361539613 3.338709115 0.0289131 0.055307882 5426.09261 -3.734487202 0.169255663 SIRPDNMSEYSK ddPTM_MDA-MB-175_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 ;;; 107.39 0.0019094 1074690000 563709 451084 272488 377845 483928 425917 507753 630704 585907 FALSE TRUE 489213.4274 448120.7995 404264.1082 463640.4822 474298.7796 442302.3026 458511.1922 495832.8577 516641.7419 0.946910378 0.867372423 0.782484409 0.897411968 0.918041926 0.856110273 0.887483831 0.959722797 1 18.97880468 1.630837369 2.421108617 0.998292703 0.875240532 0.498537396 0.042899647 0.225847335 2.845137097 0.047317465 0.012083683 42.74028064 -1.630837369 -0.123052171 SIRPLLEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SIRPLLEGR 9 1 Q9NVP1 Q9NVP1 DDX18 ATP-dependent RNA helicase DDX18 0 121.9 0.0016664 0 159050 154430 101230 107550 194980 178080 145800 209880 175890 FALSE TRUE 138031.1395 153415.5392 150185.1666 131970.8713 191100.2795 184930.8528 131660.3384 164998.7953 155096.4846 0.889969492 0.989161937 0.968333789 0.85089531 1.232138046 1.192360055 0.848893118 1.063846133 1 17.24280646 3.272653253 24.99995552 1.056851783 0.932327006 0.290955565 0.109832074 287.8960402 211110.7762 0.032695722 0.0422078 1873.498084 -3.272653253 -0.124524777 SIS(ph)ADDDLQESSR ddPTM_MDA-MB-175_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 298.17 9.27E-41 753370000 1079490 540690 350530 449630 535190 490430 688330 606400 632430 TRUE FALSE 936832.6614 537138.1718 520047.4805 551725.3637 524540.7661 509297.1595 621575.8625 476726.079 557664.8459 1.679920598 0.963191737 0.932544851 0.98934937 0.940602173 0.913267464 1.114604708 0.854861271 1 19.0890388 4.738535045 8.829316481 0.959466937 1.683460542 0.917953406 0.067297908 0.01987933 28.68811628 0.015164248 0.085991862 54769.02949 -4.738535045 0.723993605 SIS(ph)CGPSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SISCGPSSR 9 0 Q5VU43-13;Q5VU43-2 Q5VU43-13 PDE4DIP Myomegalin 1 S(0.086)IS(0.913)CGPSSR;S(0.051)IS(0.949)CGPSSR;S(0.02)IS(0.98)CGPSSR 146.9 9.83E-05 707330000 638710 615930 323548 388010 480210 525330 581770 588610 593110 TRUE FALSE 554302.8552 611883.9153 480016.895 476113.6009 470654.7605 545539.785 525350.0349 462740.3321 522993.2115 1.059866253 1.169965311 0.917826244 0.91036287 0.899925181 1.043110643 1.004506413 0.884792234 1 18.99643269 4.233406797 24.99993028 0.948346762 1.114915797 0.58333046 0.057369362 77.47564395 375822.8585 0.014742291 0.032253295 17116.1781 -4.233406797 0.166569034 SIS(ph)ESSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SISESSR 7 0 Q9H307 Q9H307 PNN Pinin 1 S(0.057)IS(0.933)ES(0.009)S(0.001)R;S(0.005)IS(0.993)ES(0.002)SR 133.98 0.0033769 812840000 761940 766070 568370 790670 781100 1044520 1034570 1180820 1041220 TRUE FALSE 661247.6985 761037.6357 843235.6331 970203.7081 765557.6382 1084703.36 934237.5606 928310.8322 918128.1578 0.720212851 0.828901313 0.918429117 1.056719261 0.833824376 1.181429141 1.01754592 1.01109069 1 19.80833602 4.680630119 0.815214398 1.027404348 0.548267953 0.600532425 0.083654585 1.537922839 0.846568609 0.030289687 0.659548599 47932.50416 -4.680630119 -0.479136395 SIS(ph)LGDSEGPIVATLAQPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SISLGDSEGPIVATLAQPLR 20 0 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 S(0.05)IS(0.95)LGDSEGPIVATLAQPLR;S(0.002)IS(0.998)LGDSEGPIVATLAQPLR;S(0.001)IS(0.999)LGDSEGPIVATLAQPLR;S(0.003)IS(0.997)LGDSEGPIVATLAQPLR;SIS(1)LGDSEGPIVATLAQPLR 267.38 7.68E-37 517488000 125016 113580 68245.9 99456 127078 120523 137230 142406 120116 TRUE FALSE 108494.8188 112833.8855 101249.8455 122039.0049 124549.3964 125159.5978 123921.4557 111953.5851 105916.0233 1.024347549 1.065314595 0.955944552 1.152224197 1.175925913 1.181687094 1.169997247 1.05700329 1 16.69256134 3.725928144 24.70236196 1.123567932 1.020213466 0.397519761 0.062341038 728.4616535 1424482.585 0.018639537 0.02785565 5320.202265 -3.725928144 -0.103354467 SIS(ph)LLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 43 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 S(0.14)IS(0.86)LLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.118)IS(0.879)LLEPS(0.003)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.115)IS(0.885)LLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.17)IS(0.82)LLEPS(0.01)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 257.73 7.14E-67 1044029000 498988 577889 56251.2 287752 571702 353084 546537 500720 483389 TRUE FALSE 433045.4715 574092.8091 83454.46847 353090.4896 560326.2487 366667.37 493533.9259 393644.9246 426243.3031 1.015958417 1.346866461 0.195790685 0.8283778 1.314569038 0.860230219 1.157869044 0.923521664 1 18.70131764 SIS(ph)PEWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SISPEWK 7 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 1 S(0.003)IS(0.997)PEWK 65.305 0.074418 99354000 197720 194460 128480 171640 190430 165740 179570 232250 246180 TRUE FALSE 171590.801 193182.5795 190613.3577 210613.4854 186640.8156 172116.125 162155.329 182585.1449 217076.8808 0.790460967 0.88992701 0.878091472 0.970225316 0.859791309 0.792880957 0.746994928 0.841108202 1 17.72784656 3.000872801 24.99650596 0.83438263 0.886509332 0.039646322 0.076847281 78.15721039 2238257.605 0.023848271 0.026822262 1002.011719 -3.000872801 0.052126702 SIS(ph)PSALQDLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SISPSALQDLLR 12 0 Q92793-2;Q92793 Q92793-2 CREBBP CREB-binding protein 1 SIS(1)PSALQDLLR;S(0.006)IS(0.994)PSALQDLLR;S(0.001)IS(0.999)PSALQDLLR;SIS(1)PSALQDLLR 260.97 2.55E-21 324666000 426092 330412 245579 249443 302488 442509 366263 324556 386697 TRUE FALSE 369782.8626 328241.5018 364341.8258 306082.8456 296469.0806 459532.6076 330742.8706 255152.2251 340982.1212 1.084464081 0.962635521 1.068507124 0.897650717 0.86945638 1.347673614 0.969971298 0.748286227 1 18.37933657 1.990040742 24.99452834 0.857053092 1.033627358 0.179152563 0.143438593 685.0827747 1719335.798 0.060979067 0.038368889 97.73289017 -1.990040742 0.176574265 SIS(ph)QQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SISQQK 6 0 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 S(0.001)IS(0.999)QQK 78.149 0.074 128240000 329050 211830 154520 177050 137180 177360 268810 296990 345170 TRUE FALSE 285565.2088 210438.4748 229246.3888 217251.9085 134450.3864 184183.154 242740.8476 233480.9997 304364.3958 0.938234605 0.691403061 0.753197128 0.713788838 0.441741505 0.605140274 0.79753365 0.767110092 1 18.21544008 1.044606645 1.420107438 1.2592037 0.690744514 0.346383342 0.126703347 2.388976963 2.926943268 2.23835168 0.038296357 11.08170652 -1.044606645 -0.568459186 SIS(ph)REPS(ph)PALGPNLDGSGLLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SISREPSPALGPNLDGSGLLPR 22 1 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 2 S(0.459)IS(0.541)REPS(1)PALGPNLDGSGLLPR 133.23 5.34E-06 308710000 266020 249080 162860 171860 204150 202340 204130 218390 232300 TRUE FALSE 230864.783 247443.7771 241619.6407 210883.4397 200087.8144 210124.1507 184333.504 171688.998 204837.7586 1.127061654 1.207998851 1.179565927 1.029514486 0.976811188 1.025807703 0.899900025 0.838170653 1 17.64412215 3.323174662 0.9554688 0.905578762 1.191167698 0.754845364 0.057391882 0.262104646 0.53438124 0.029023307 0.04795171 2104.624696 -3.323174662 0.285588936 SIS(ph)S(ph)PNVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SISSPNVNR 9 0 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 2 S(0.006)IS(0.994)S(1)PNVNR 78.136 0.031254 0 706250 743800 484150 503480 624100 706590 598120 701260 711010 TRUE FALSE 612917.2731 738913.9288 718286.5594 617802.8292 611681.631 733772.9745 540114.4145 551301.0062 626955.2078 0.97760935 1.178575311 1.145674444 0.985401862 0.975638488 1.170375436 0.861488042 0.879330771 1 19.25800285 2.226611267 24.9971146 0.904293923 1.072050677 0.439723575 0.084177993 196.0503535 410118.6063 0.034371611 0.023376663 168.5044084 -2.226611267 0.167756754 SIS(ph)SPNVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SISSPNVNR 9 0 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 SIS(0.93)S(0.07)PNVNR;SIS(0.924)S(0.076)PNVNR;SIS(0.932)S(0.068)PNVNR;S(0.004)IS(0.922)S(0.074)PNVNR;S(0.002)IS(0.499)S(0.499)PNVNR;S(0.001)IS(0.983)S(0.017)PNVNR;S(0.003)IS(0.942)S(0.055)PNVNR 186.24 4.40E-05 11638495000 10435219 11367435 6660254 7087513 10267578 10825104 8837881 10011968 11300554 TRUE FALSE 9056178.37 11292761.57 9881175.112 8696841.153 10063273.29 11241552.76 7980784.661 7870986.556 9964615.38 0.908833711 1.133286247 0.991626343 0.872772387 1.009900824 1.128147182 0.800912464 0.789893664 1 23.24838269 2.220439509 24.99988059 0.845634034 1.006422106 0.315944269 0.098581146 258.7323327 356944.3785 0.039988608 0.027019715 166.1267271 -2.220439509 0.160788073 SIS(ph)SPSVSSETMDKPVDLSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SISSPSVSSETMDKPVDLSTR 21 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 SIS(0.499)S(0.499)PS(0.001)VSSETMDKPVDLSTR 180.37 3.28E-17 265310000 176980 177020 149830 220290 203210 180400 215370 293500 347770 TRUE FALSE 153591.6446 175857.144 222288.2892 270310.2114 199166.5186 187340.1047 194483.4505 230737.309 306657.0268 0.500858063 0.573465235 0.724875903 0.88147405 0.649476455 0.610910849 0.634205101 0.752427921 1 18.22626648 1.259310852 2.475573949 1.075444049 0.660790966 0.543808484 0.099852029 0.443172409 3.056530122 0.387369788 0.028362051 18.16815609 -1.259310852 -0.414653083 SISEIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SISEIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE 35 1 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;; 287.65 2.52E-75 1607690000 816361 968644 559996 726233 978500 765553 940570 1350490 997570 FALSE TRUE 708476.8255 962280.9138 830811.9387 891135.3024 959029.7644 795004.3193 849353.6662 1061698.223 879638.411 0.805418245 1.093950539 0.944492565 1.01307002 1.090254532 0.903785361 0.965571371 1.206971194 1 19.74655108 4.748274947 24.28225649 1.03348982 0.80541806 0.390244161 0.086838762 998.4465649 2495672.136 0.022143831 0.277636179 56011.20897 -4.748274947 -0.228071761 SISEPQHS(ph)DAEGDAASPLPSEWTSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SISEPQHSDAEGDAASPLPSEWTSVR 26 0 A0A2R8YFA9 A0A2R8YFA9 1 S(0.001)IS(0.001)EPQHS(0.998)DAEGDAASPLPSEWTSVR 85.337 0.008673 125180000 35023 39267 21662 30641 32243 36793 29439 29507 33089 TRUE FALSE 30394.62181 39009.05249 32137.81566 37598.50737 31601.42738 38208.45052 26584.01031 23197.15767 29177.25612 1.041723104 1.33696782 1.101468059 1.288623825 1.083084278 1.309528571 0.911120984 0.795042467 1 14.8325566 2.165692952 6.962703501 0.876223009 1.194786319 0.606278839 0.110255258 0.120943641 9.460088528 0.040631279 0.027360137 146.4512057 -2.165692952 0.31856331 SISLLEPS(ph)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 43 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 S(0.009)IS(0.064)LLEPS(0.255)LELES(0.247)T(0.247)S(0.17)ET(0.007)S(0.002)DMPEVFSSHESSHEEPLQPFPQLAR;S(0.149)IS(0.134)LLEPS(0.715)LELES(0.002)TSETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.058)IS(0.058)LLEPS(0.818)LELES(0.013)T(0.013)S(0.013)ET(0.013)S(0.013)DMPEVFSSHESSHEEPLQPFPQLAR;S(0.048)IS(0.048)LLEPS(0.904)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.031)IS(0.227)LLEPS(0.742)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 224.87 2.85E-44 2123542000 393160 459600 55244.4 244521 442302 339142 407729 395976 415076 TRUE FALSE 341202.9099 456580.8573 81960.77662 300043.2303 433501.0555 352189.0122 368187.5043 311299.6139 366006.1881 0.932232626 1.24746759 0.223932762 0.819776386 1.184409088 0.962248791 1.00595978 0.850531013 1 18.48150852 3.446355657 24.8563928 0.982324973 0.791839511 0.119414443 0.26019372 432.905634 349755.2005 0.075481747 0.09744749 2794.831679 -3.446355657 -0.190485462 SISLLEPSLELES(ph)TSETSDMPEVFSSHESSHEEPLQPFPQLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 43 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 S(0.001)IS(0.001)LLEPS(0.428)LELES(0.495)T(0.065)S(0.01)ETSDMPEVFSSHESSHEEPLQPFPQLAR 175.58 1.07E-20 1339400000 86958 101590 10316 49379 104680 63021 89485 82699 88106 TRUE FALSE 75466.27998 100922.6486 15304.8521 60591.25666 102597.0728 65445.45865 80806.75847 65014.46241 77690.20905 0.971374397 1.299039478 0.196998467 0.779908529 1.320592055 0.842390044 1.040115086 0.836842418 1 16.24544517 SISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 43 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 238.21 5.80E-55 87261000 42355 56303 7314.8 34902 64064 80847 46654 63947 62402 FALSE TRUE 36757.67944 55933.14189 10852.26175 42827.03254 62789.25174 83957.2364 42129.50226 50272.43169 55024.90665 0.668018933 1.016505893 0.197224537 0.778320858 1.141106011 1.52580425 0.76564423 0.913630477 1 15.74779717 3.399431166 5.522672999 1.047003938 0.63872509 0.35690189 0.274318197 0.246158731 12.90626339 0.081847264 0.106615542 2508.598542 -3.399431166 -0.408278848 SISS(ph)PNVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SISSPNVNR 9 0 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 SIS(0.006)S(0.994)PNVNR;SIS(0.023)S(0.977)PNVNR 177.57 5.45E-05 417180000 1040950 1200210 707120 815140 1155000 1285710 1009140 1202550 1275550 TRUE FALSE 903385.8201 1192325.741 1049085.597 1000229.996 1132017.76 1335172.096 911273.7581 945394.0408 1124755.932 0.803183868 1.060075086 0.932722884 0.889286259 1.006456359 1.187077176 0.81019689 0.840532611 1 20.10118055 SISS(ph)PSVSSETMDKPVDLSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SISSPSVSSETMDKPVDLSTR 21 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 SIS(0.033)S(0.844)PS(0.122)VSSETMDKPVDLSTR 129.9 9.54E-06 337650000 160040 193650 143940 175190 203170 167580 208920 304500 287650 TRUE FALSE 138890.3085 192377.9004 213549.8655 214969.5671 199127.3145 174026.911 188658.9706 239385.0446 253644.3447 0.547578968 0.758455311 0.841926382 0.847523596 0.785065067 0.686106017 0.743793325 0.943782306 1 17.95244747 1.662075616 3.84181026 0.987421683 0.751506628 0.555428975 0.084996727 0.137662665 4.722819065 0.064855767 0.023207119 45.92779715 -1.662075616 -0.235915055 SISSS(ph)NPDLAVAPGSVDDEVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SISSSNPDLAVAPGSVDDEVSR 22 0 K7ESB7;K7EKT0;K7EP20;Q96HP0 K7ESB7;Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 1 SIS(0.029)S(0.081)S(0.89)NPDLAVAPGSVDDEVSR;SISS(0.025)S(0.975)NPDLAVAPGSVDDEVSR;SIS(0.012)S(0.101)S(0.887)NPDLAVAPGSVDDEVSR;SISS(0.088)S(0.912)NPDLAVAPGSVDDEVSR 447.72 1.05E-198 2426540000 1098340 1126550 951420 799450 1132790 1468160 1086130 1190340 1392660 TRUE FALSE 953191.5862 1119149.619 1411529.894 980977.3413 1110249.695 1524641.065 980797.2798 935795.0542 1228021.321 0.77620117 0.911343801 1.149434354 0.798827613 0.904096432 1.241542829 0.798680986 0.762034859 1 20.22790418 SISVPPS(ph)PSDIPPPGPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SISVPPSPSDIPPPGPPR 18 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 SISVPPS(0.98)PS(0.02)DIPPPGPPR 105.46 0.00050059 81186000 29841 36993 29327 38830 45218 44425 45919 53851 44792 TRUE FALSE 25897.43624 36749.99055 43509.63529 47646.94498 44318.25027 46134.0585 41465.78245 42335.38272 39496.74079 0.655685399 0.930456281 1.101600649 1.20635131 1.122073604 1.168047226 1.049853269 1.071870283 1 15.26944599 4.618558185 2.209698913 1.104264599 0.599422278 0.859442194 0.058172914 0.17888718 1.219745727 0.0164092 0.159852642 41548.77128 -4.618558185 -0.504842321 SITHDIEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SITHDIEEK 9 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4;K7EL40;K7EK18;K7EIE4;K7EQD7;K7ER52;K7ELJ9;K7EJZ2;K7ENQ5;K7EN52;K7EKN4;K7EIR4 Q9UHD8 9-Sep Septin-9 0 ;;;;; 175.91 5.36E-05 7659640000 9773140 9211010 3847040 7561240 9922070 8481050 11161670 12870220 12109790 FALSE TRUE 8481594.787 9150502.269 5707481.412 9278135.108 9724640.219 8807321.481 10079212.96 10118023.61 10678184.42 0.794291843 0.856934279 0.534499236 0.868886951 0.910701654 0.824795783 0.943906994 0.947541568 1 23.34816304 2.757386655 0.811764891 0.978374106 0.746859081 0.43869068 0.096104638 0.636586811 1.000250921 0.087927877 0.064034975 571.9876538 -2.757386655 -0.231515024 SITS(ph)PTTLYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SITSPTTLYDR 11 0 Q08999;F5H837 Q08999 RBL2 Retinoblastoma-like protein 2 1 SIT(0.134)S(0.844)PT(0.018)T(0.004)LYDR;SITS(0.454)PT(0.423)T(0.123)LYDR;SIT(0.04)S(0.444)PT(0.444)T(0.071)LYDR 182.71 5.94E-06 657930000 1304260 1192430 672180 901180 1265610 1176040 1144270 1338890 1180630 TRUE FALSE 1131898.736 1184596.849 997248.4963 1105806.693 1240426.837 1221283.02 1033298.872 1052578.793 1041057.266 1.08725886 1.137878662 0.957918962 1.062195835 1.191506824 1.173118002 0.992547581 1.01106714 1 19.989618 2.21084889 24.99690147 1.002898751 1.099051458 0.351472249 0.064238677 269.8757848 243435.0878 0.028174762 0.019000181 162.4983253 -2.21084889 0.096152707 SITS(ph)TPLSGK ddPTM_MDA-MB-175_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 184.03 1.68E-06 164280000 445120 470970 406980 531950 600580 609290 705090 731210 739920 TRUE FALSE 386296.2642 467876.1671 603796.8893 652737.3778 588629.633 632729.7806 636710.4803 574846.4318 652447.5005 0.592072564 0.717109295 0.925433677 1.000444292 0.902186969 0.969778841 0.975880021 0.881061589 1 19.31550229 4.359748767 2.637876699 0.949014538 0.60203889 0.912696151 0.039141673 0.075324071 0.991803907 0.010215989 0.03978663 22895.42804 -4.359748767 -0.346975649 SITSPT(ph)TLYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SITSPTTLYDR 11 0 Q08999;F5H837 Q08999 RBL2 Retinoblastoma-like protein 2 1 SITS(0.278)PT(0.558)T(0.163)LYDR 202 4.64E-07 409920000 654090 650510 373370 417330 591690 604730 535520 656670 555280 TRUE FALSE 567650.3492 646236.757 553932.9808 512091.155 579916.5266 627994.3544 483585.3528 516246.2307 489635.431 1.159332665 1.319832504 1.131317192 1.04586213 1.184384319 1.282575391 0.987643708 1.054348191 1 18.90134843 2.223935811 24.99838689 1.021305632 1.184150405 0.528676577 0.076961021 203.8366636 348418.1497 0.032573183 0.022068736 167.4695336 -2.223935811 0.162844773 SIVDYKPNLDLLEQQHQLIQEALIFDNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SIVDYKPNLDLLEQQHQLIQEALIFDNK 28 1 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 250.95 1.00E-46 983250000 874790 538090 653160 851690 450420 419690 581480 873000 2292100 FALSE TRUE 759184.2851 534555.2514 969030.3607 1045079.232 441457.5232 435835.7459 525088.1591 686315.7437 2021130.549 0.375623576 0.264483287 0.479449663 0.51707656 0.218421083 0.215639582 0.259799229 0.339570219 1 20.94673108 1.238881091 8.391985203 1.006611164 0.330928074 0.80737708 0.102271371 0.039594686 29.44259665 0.152994771 0.026802693 17.33329351 -1.238881091 -0.675683091 SIVEEIEDLVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SIVEEIEDLVAR 12 0 P04844-2;P04844;F2Z3K5;Q5JYR4;Q5JYR7 P04844-2 RPN2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 0 164.43 0.00013337 30434000 28804 28715 24829 29556 34691 27308 36470 40759 30344 FALSE TRUE 24997.47842 28526.36927 36836.38745 36267.14154 34000.71697 28358.55643 32933.14501 32043.00504 26756.76689 0.93424884 1.06613663 1.376712949 1.35543811 1.270733385 1.059864839 1.230834247 1.197566401 1 14.70761618 4.459517317 9.753115111 1.214851864 0.966833982 0.392393651 0.115896293 0.228778661 120.5185498 0.029889992 0.08134852 28808.27919 -4.459517317 -0.248017883 SIVEGIIEEEEEDEEGSESISKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SIVEGIIEEEEEDEEGSESISKR 23 1 Q9Y570;Q9Y570-4;Q9Y570-2 Q9Y570 PPME1 Protein phosphatase methylesterase 1 0 220.86 2.99E-32 81362000 172840 130610 71885 92750 122240 118070 135070 188180 106810 FALSE TRUE 149998.7561 129752.0143 106648.8264 113810.3051 119807.6632 122612.2293 121970.9322 147939.1714 94183.04348 1.592630165 1.377657904 1.132356977 1.208394854 1.272072538 1.301850363 1.295041312 1.570762273 1 16.52317972 4.649165805 3.591606748 1.284176303 1.602962514 0.336467798 0.14672216 0.314581891 6.667493094 0.037557761 0.224812086 44582.64231 -4.649165805 0.318786211 SIVIRPLEPQPAPHLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SIVIRPLEPQPAPHLAR 17 1 Q15029;Q15029-3;Q15029-2;K7EP67 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ; 97.579 0.0012256 1058660000 1332320 1093690 632000 873480 1184400 1301810 964570 1267760 1121680 FALSE TRUE 1156250.536 1086505.478 937637.3139 1071816.984 1160832.757 1351891.473 871026.1499 996659.3897 989076.2682 1.169020604 1.098505255 0.947992934 1.083654536 1.173653433 1.366822273 0.880646092 1.007666872 1 19.91572225 2.177812804 24.99999961 0.968702541 1.128316419 0.367978571 0.108653356 88.2106197 36300.94357 0.046599177 0.031417169 150.5957805 -2.177812804 0.159613878 SIWDEFIS(ph)DEADEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SIWDEFISDEADEK 14 0 D6RD48;D6RAZ7;D6RCR8;D6RDI6;D6RFX6;D6RCE6;D6R9S8;D6RC11;A0A0R4J2F2;D6RA76;D6RDY1;D6RHU6;H0Y8T9;D6RDP6;D6RIU2;Q9NY35;Q9NY35-2 D6RD48 CLDND1 Claudin domain-containing protein 1 1 S(0.192)IWDEFIS(0.808)DEADEK 70.908 0.044996 1588000000 150470 141130 120280 102850 124090 90868 219820 163240 186300 TRUE FALSE 130585.0083 140202.9077 178447.8103 126203.6645 121620.8518 94363.75076 198501.8902 128332.3963 164275.8262 0.794913112 0.853460372 1.086269443 0.768242458 0.740345397 0.574422622 1.208345103 0.781200736 1 17.32576067 1.216914498 23.77102131 1.00000101 0.857145536 0.063470636 0.178565661 3019.812281 3315926.276 1.822624479 0.042400303 16.47837941 -1.216914498 -0.142855474 SIYDDISSPGLGST(ph)PLTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SIYDDISSPGLGSTPLTSR 19 0 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 SIYDDISSPGLGS(0.04)T(0.959)PLT(0.001)S(0.001)R 171.29 1.18E-10 63320000 168650 193480 105080 101850 166970 185200 130770 171810 166410 TRUE FALSE 146362.4752 192209.0171 155897.0395 124976.5992 163647.6237 192324.7638 118087.9455 135069.7685 146737.1994 0.997446291 1.309886095 1.062423435 0.851703588 1.115242927 1.310674898 0.804758071 0.920487573 1 17.16287513 2.217894168 24.99999974 0.90661126 1.103699525 0.304787252 0.141918845 307.4637961 371933.1582 0.058933808 0.039781887 165.1559287 -2.217894168 0.197088264 SIYGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 114.54 0.058621 2742100000 2443650 1869230 1578590 2073720 1532410 1492080 1787260 2207870 4729500 FALSE TRUE 2120715.461 1856950.905 2342001.404 2544589.821 1501918.039 1549481.283 1613931.8 1735734.182 4170383.898 0.508518044 0.445270975 0.561579332 0.610157214 0.360139037 0.37154404 0.386998377 0.416204893 1 21.99174876 1.236137308 24.99990003 1.000000713 0.454210326 0.81203731 0.082003927 29.86589681 308041.123 0.143018011 0.021822739 17.22413051 -1.236137308 -0.545790387 SIYGEKFEDENFILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 ;;;;;; 252.36 1.11E-24 23116569000 39051522 27544326 18492119 19874765 23735767 17840880 32524335 41841010 14497559 FALSE TRUE 33890764.42 27363385.51 27434969.6 24387634.16 23263471.67 18527230.2 29370130 32893635.62 12783674.09 2.651097344 2.140494612 2.146094261 1.907717139 1.819779784 1.449288371 2.297471743 2.57309717 1 23.6077992 5.079562225 1.12255223 1.936171867 3.51340318 0.241662721 0.433103231 5.591793463 3.526835536 0.13462612 12.4653572 120105.3145 -5.079562225 1.577231313 SIYVGNVDYGATAEELEAHFHGCGSVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SIYVGNVDYGATAEELEAHFHGCGSVNR 28 0 Q92843-2;Q86U42-2;Q86U42;B4DEH8;G3V4T2 Q92843-2 PABPN1 Polyadenylate-binding protein 2 0 ; 200 2.65E-25 388420000 216850 192566 68217 144322 177688 194583 168109 194829 181947 FALSE TRUE 188192.7231 191301.0213 101206.9694 177092.5159 174152.3564 202068.7339 151805.8151 153166.3345 160437.4329 1.172997596 1.192371492 0.630818927 1.103810455 1.085484561 1.259486207 0.946199477 0.954679539 1 17.29165126 SIYYITGESK ddPTM_MDA-MB-175_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 ; 163.94 1.47E-05 966590000 1396590 967630 629880 836510 980310 858810 1124430 1322420 1235490 FALSE TRUE 1212027.093 961273.5748 934492.0748 1026452.381 960803.7489 891848.9764 1015382.952 1039630.774 1089431.78 1.112531427 0.88236234 0.857779342 0.942190599 0.881931083 0.818636828 0.932029862 0.954287174 1 20.05514443 1.543870892 2.384397523 0.997537676 0.909963559 0.098530603 0.078257495 0.677660337 7.506446813 0.104440603 0.020895472 34.98411501 -1.543870892 -0.087574117 SKADVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKADVER 7 1 P49792;O14715;Q99666;F8W705;Q99666-2;F8WBP7;C9J1W9;C9JF75 P49792 RANBP2;RGPD8;RGPD5;RGPD6 E3 SUMO-protein ligase RanBP2;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6 0 72.485 0.046948 88172000 362300 269200 162780 219530 198990 264460 313560 347110 249300 FALSE TRUE 314421.137 267431.6075 241500.9525 269377.6418 195030.4883 274633.9473 283150.9995 272883.2277 219828.038 1.430304978 1.216549126 1.09859031 1.225401656 0.887195692 1.249312644 1.288056801 1.241348602 1 17.74601588 4.702337562 3.172120406 1.155835316 1.459943501 0.34396691 0.124024689 0.378760563 6.142052109 0.031270199 0.271858066 50389.21143 -4.702337562 0.304108185 SKAELMEISEDKTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKAELMEISEDKTK 14 2 P05455;E7ERC4;E9PGX9;E9PFL9 P05455 SSB Lupus La protein 0 136.34 1.55E-05 516640000 1683300 1021500 926890 967090 938940 620380 1498800 1766500 1105000 FALSE TRUE 1460847.64 1014789.699 1375137.104 1186682.566 920256.931 644246.42 1353446.607 1388747.722 974368.1588 1.499276867 1.041484874 1.41131162 1.217899574 0.944465316 0.661194041 1.389050529 1.42528028 1 19.89410746 4.752296077 23.36242974 1.161053309 1.499277439 0.176178797 0.2414456 1956.852712 3328232.25 0.063020658 1.133417346 56532.22475 -4.752296077 0.33822413 SKAEVACIAVYETDVFVVGTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 171.15 5.80E-12 171532000 391253 315989 194509 279378 280971 267975 353357 402967 287381 FALSE TRUE 339547.9247 313913.2475 288574.203 342815.0449 275380.2268 278284.1717 319088.4925 316795.6429 253407.1456 1.339930348 1.238770307 1.138776897 1.352823119 1.086710583 1.098170184 1.259192955 1.25014487 1 17.95109768 7.999999936 0.651215471 1.172140941 15.87103496 0.235460096 0.099809191 384.4056487 2.4931364 0.042418105 8144.685645 99999985.33 -7.999999936 14.69889402 SKCEELSGLHGQLQEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKCEELSGLHGQLQEAR 17 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 137.45 4.16E-06 195444000 433440 401030 164395 292220 468490 367890 402040 518400 208744 FALSE TRUE 376159.8058 398395.6075 243896.9719 358573.0173 459167.9656 382042.9664 363050.2227 407544.1942 184066.5221 2.043607938 2.164411013 1.325047972 1.948062109 2.494576202 2.075570082 1.972385953 2.214113623 1 17.48986773 1.232334676 24.99925287 0.999998296 2.031273188 0.548101542 0.293837915 170.7703447 685633.1449 0.667871465 0.07368195 17.07397639 -1.232334676 1.031274893 SKDAS(ph)PINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SKDASPINR 9 1 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 S(0.004)KDAS(0.996)PINR;S(0.003)KDAS(0.997)PINR;S(0.006)KDAS(0.994)PINR 98.182 0.016276 325012000 482390 414710 314731 379087 403480 403430 473400 548530 726500 TRUE FALSE 418640.9393 411985.7427 466935.9643 465164.4973 395451.5374 418950.2132 427489.7409 431231.1282 640613.9976 0.653499519 0.643110741 0.72888817 0.726122906 0.617300807 0.653982296 0.66731252 0.673152834 1 19.2890958 1.238537711 8.922948745 1.002449399 0.670780021 0.9005944 0.034412233 0.025006579 26.35151421 0.050058076 0.00878373 17.31959415 -1.238537711 -0.331669379 SKDAS(ph)PINRWS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKDASPINRWSPTR 14 2 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(0.063)KDAS(0.937)PINRWS(0.917)PT(0.083)R 82.367 0.053671 641650000 917810 783780 474610 534340 837830 702860 778240 961780 499030 TRUE FALSE 796519.0831 778631.2976 704132.9835 655670.0639 821158.8222 729899.479 702766.4046 756110.8316 440035.2419 1.810125661 1.769474859 1.600174069 1.490039891 1.866120583 1.658729596 1.597068457 1.718296081 1 18.74725955 1.236816489 24.9997206 0.999999148 1.683989829 0.792436294 0.110755777 20.26981403 290453.0531 0.167206544 0.026811537 17.25108792 -1.236816489 0.683990681 SKDDQVTVIGAGVTLHEALAAAELLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SKDDQVTVIGAGVTLHEALAAAELLK 26 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;;;; 260.97 5.03E-53 3077246000 3467386 3188973 2724478 2762869 2603796 1799788 3276952 3596818 6435888 FALSE TRUE 3009162.155 3168024.426 4042044.674 3390220.634 2551985.554 1869027.009 2959153.699 2827666.461 5675044.652 0.530244666 0.558237797 0.712248964 0.597391006 0.449685546 0.329341375 0.521432672 0.498263297 1 22.43620031 1.236682088 24.99248206 1.000000602 0.523968245 0.69993826 0.097820165 30.82600126 410002.3598 0.16524371 0.026224917 17.24575007 -1.236682088 -0.476032357 SKDDQVTVIGAGVTLHEALAAAELLKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SKDDQVTVIGAGVTLHEALAAAELLKK 27 2 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;; 257.07 3.93E-53 1263014000 2015330 1710686 1064067 939469 1240756 820625 1932679 2009330 484775 FALSE TRUE 1748999.034 1699448.391 1578653.36 1152789.795 1216067.383 852194.9748 1745248.088 1579650.416 427465.4518 4.091556469 3.975639163 3.693054851 2.696802258 2.84483197 1.993599649 4.082781616 3.695387334 1 18.7054483 3.891693145 3.534866026 2.88173987 4.007943167 0.30037341 0.849368484 0.35640445 8.152832249 0.237039059 0.453131479 7792.793084 -3.891693145 1.126203297 SKDEEEDEES(ph)DDADDTPILKPVSLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKDEEEDEESDDADDTPILKPVSLLR 26 2 A0A3B3IS53;A0A3F2YNX6;Q92794;A0A3B3ITI3 A0A3B3IS53 KAT6A Histone acetyltransferase KAT6A 1 SKDEEEDEES(1)DDADDTPILKPVSLLR;SKDEEEDEES(1)DDADDTPILKPVSLLR 237.34 2.98E-45 286090000 559260 390390 355380 365970 384780 291080 395780 585630 606180 TRUE FALSE 485352.374 387825.5024 527242.9567 449069.082 377123.6308 302278.036 357397.3165 460397.5819 534518.091 0.90801861 0.725561041 0.986389358 0.840138228 0.705539508 0.565515071 0.66863465 0.861332085 1 19.02787925 4.763281448 22.21945784 0.791037326 0.908019258 0.064304354 0.136063628 5071.912165 4558375.489 0.035268887 1.771010685 57980.43211 -4.763281448 0.116981932 SKDEYEKS(ph)R ddPTM_MDA-MB-175_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;SKDEY(0.007)EKS(0.993)R;SKDEYEKS(1)R 113.96 0.0013511 4990910000 4126030 2704508 2900247 3077419 2457877 2092465 3882330 4565480 4561450 TRUE FALSE 3580764.681 2686741.909 4302816.15 3776194.019 2408970.056 2172963.483 3505822.234 3589187.631 4022200.577 0.890250154 0.667978102 1.069766678 0.938837819 0.59891843 0.540242447 0.871617953 0.892344268 1 21.9395536 1.611196001 2.395612252 0.983665633 0.788738879 0.150680246 0.159945722 0.578881284 7.036571625 0.193853811 0.046768889 40.85037061 -1.611196001 -0.194926754 SKDFVQVMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKDFVQVMR 9 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 88.056 0.011895 939990000 996470 1047400 504510 859430 1319800 971180 1772200 1743300 1449500 FALSE TRUE 864783.9648 1040519.56 748492.7235 1054576.717 1293538.562 1008541.923 1600332.317 1370508.861 1278141.761 0.676594718 0.814087758 0.585610099 0.825085878 1.012046239 0.789068907 1.252077324 1.07226671 1 20.28561643 3.029370292 1.021983579 1.091956726 0.695142898 0.60293302 0.124200514 0.333651874 0.789047009 0.065108194 0.07225594 1069.966776 -3.029370292 -0.396813828 SKDGVCVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKDGVCVR 8 1 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ; 104.2 0.0042194 756890000 1522960 1399420 904860 1072480 1322850 1409700 1651180 1853170 1539470 FALSE TRUE 1321696.977 1390227.118 1342453.323 1316002.976 1296527.873 1463932.071 1491048.818 1456884.017 1357475.61 0.973643259 1.024126774 0.988933659 0.969448707 0.955102149 1.078422375 1.098398237 1.073230344 1 20.37249485 2.730804627 24.95577484 1.067551634 0.984237377 0.626609266 0.03065612 377.233342 1213788.004 0.010755489 0.009659373 538.0276898 -2.730804627 -0.083314257 SKDQDDQKPGPSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SKDQDDQKPGPSER 14 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 ;;;; 140.46 5.59E-06 1868320000 1313407 954438 760357 763552 811080 672357 1253252 1406000 1158244 FALSE TRUE 1139836.937 948168.2339 1128068.188 936928.1518 794941.0949 698223.0089 1131711.814 1105337.842 1021317.714 1.116045401 0.928377351 1.104522298 0.917371881 0.778348485 0.683649171 1.108089871 1.082266396 1 19.9620003 SKDVVDYSEENFAIVFAAMGVNMETAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKDVVDYSEENFAIVFAAMGVNMETAR 27 1 P21281 P21281 ATP6V1B2 "V-type proton ATPase subunit B, brain isoform" 0 162.45 1.11E-11 97525000 229780 185570 126760 150960 170370 157810 206310 254760 184620 FALSE TRUE 199413.9908 184350.9785 188061.56 185237.7753 166979.9703 163881.0528 186302.088 200281.5565 162794.4339 1.224943544 1.132415734 1.155208784 1.137863076 1.025710562 1.006674791 1.144400846 1.230272754 1 17.31269185 5.225537962 0.970413718 1.105287596 1.412537463 0.238272405 0.072180851 8.598978789 3.377180831 0.025515894 3.457103249 168088.4848 -5.225537962 0.307249867 SKDVVEPLLRPQWYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKDVVEPLLRPQWYVR 16 2 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ; 74.816 0.017565 2132900000 698930 596430 425441 453028 585030 490770 644990 745530 629280 FALSE TRUE 606564.6296 592512.0121 631185.6906 555894.9315 573389.0476 509650.2395 582438.9691 586104.2112 554887.2353 1.093131345 1.067806167 1.137502632 1.001816038 1.033343373 0.918475335 1.049652852 1.056258234 1 19.08183509 3.725871757 24.95574949 1.014399208 1.096312661 0.507180151 0.041419666 661.8735124 1301736.143 0.011777581 0.017588864 5319.511563 -3.725871757 0.081913452 SKEDS(ph)RR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKEDSRR 7 2 P62995 P62995 TRA2B Transformer-2 protein homolog beta 1 S(0.39)KEDS(0.61)RR 62.005 0.069357 2185800000 3023500 2216000 1547300 1708700 1840300 1478800 2621800 3189800 1814400 TRUE FALSE 2623936.814 2201442.95 2295579.455 2096686.451 1803681.63 1535690.393 2367538.24 2507686.093 1599903.699 1.640059221 1.375984662 1.434823519 1.310507909 1.127368873 0.959864268 1.479800466 1.567398147 1 20.60955364 5.01151958 1.03748424 1.280545149 1.984110112 0.278418427 0.195101692 4.987932398 3.009739381 0.066925952 4.4277531 102687.9728 -5.01151958 0.703564964 SKEESSGTPAHQMNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKEESSGTPAHQMNLR 16 1 A0A0U1RRM8;H0YJ34;Q96AC1-2;Q96AC1;Q96AC1-3 A0A0U1RRM8 FERMT2 Fermitin family homolog 2 0 82.259 0.0063032 77344000 71241 71512 49584 63824 67264 62376 78811 90451 93144 FALSE TRUE 61826.32135 71042.23296 73562.98825 78316.21469 65925.578 64775.64508 71167.92135 71108.75754 82132.62243 0.752762051 0.864969739 0.895661018 0.953533594 0.802672264 0.788671336 0.866500049 0.865779704 1 16.32566774 1.173480822 2.727775788 1.051271269 0.849656537 0.41574414 0.056578542 0.661765359 4.905889422 0.330681123 0.015226075 14.91010912 -1.173480822 -0.201614732 SKEEVNDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKEEVNDKR 9 2 R4GMX3;P35226;Q5T8Z2 R4GMX3 COMMD3-BMI1;BMI1 Polycomb complex protein BMI-1 0 88.681 0.0070979 58681000 166030 136420 102010 113720 96761 99674 179060 218990 175420 FALSE TRUE 144088.7148 135523.848 151342.3772 139541.8641 94835.64541 103508.5233 161694.7888 172160.6927 154682.0474 0.931515436 0.876144648 0.978409452 0.902120617 0.613100531 0.669169597 1.045336491 1.112997245 1 17.23894624 2.120526437 8.403921919 1.068607077 0.831270558 0.456698157 0.115165262 0.232795539 16.0938206 0.052038289 0.035041372 131.9855654 -2.120526437 -0.237336519 SKEGHSLEMENENLVENGADS(ph)DEDDNSFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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(0.993)DEDDNS(0.007)FLK;SKEGHSLEMENENLVENGADS(0.997)DEDDNS(0.003)FLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK 377.45 5.71E-137 7786430000 3276322 2485263 1504001 1936514 2373920 1918171 3335026 3874526 1752178 TRUE FALSE 2843347.747 2468937.144 2231340.914 2376229.101 2326683.636 1991964.28 3011595.692 3045988.766 1545037.513 1.840309845 1.597978769 1.444198536 1.537975021 1.505907538 1.289265965 1.949205548 1.971465897 1 20.55921044 2.235432474 24.99881486 1.722106749 1.533316694 0.001984622 0.298495105 222.8448833 1780847.188 0.11767731 0.083149918 171.9619946 -2.235432474 -0.188790055 SKEGLTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SKEGLTER 8 1 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 0 ;; 82.831 0.017562 575250000 1556510 1349300 808340 1006920 1353400 1204250 1550830 1672760 1268470 FALSE TRUE 1350813.26 1340436.359 1199255.928 1235556.576 1326469.988 1250578.277 1400430.745 1315053.291 1118512.922 1.207686772 1.198409364 1.072187817 1.104642201 1.185922811 1.118072266 1.252046998 1.175715779 1 20.09315049 2.549736058 0.006410493 2.09E-05 2.296091816 0.062156735 0.071841529 43402.8491 241.8901672 43605.3375 43028.19255 354.5978171 -2.549736058 2.296070954 SKEIDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKEIDEK 7 1 Q8WXA9-2;Q8WXA9 Q8WXA9-2 SREK1 Splicing regulatory glutamine/lysine-rich protein 1 0 69.423 0.054518 104360000 197090 130300 144110 140500 113260 110450 200320 201090 392890 FALSE TRUE 171044.0571 129444.0507 213802.078 172402.6724 111006.3476 114699.083 180892.9972 158088.4684 346442.9918 0.493714871 0.373637377 0.617134949 0.497636484 0.320417356 0.331076355 0.522143618 0.456318852 1 18.40225845 1.237238872 7.093376702 1.01144451 0.450602221 0.78300816 0.09074216 0.052345552 15.62202091 0.139970542 0.022970125 17.26787404 -1.237238872 -0.560842289 SKEIEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SKEIEAK 7 1 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;; 110.87 0.006116 1285190000 1907380 1534950 1058510 1245730 928740 1122540 1983420 2231350 1515960 FALSE TRUE 1655314.9 1524866.812 1570408.977 1528592.036 910259.891 1165724.84 1791068.234 1754193.167 1336744.936 1.238317689 1.140731318 1.174800767 1.143518105 0.680952564 0.872062283 1.33987284 1.312287124 1 20.35029278 0.949729985 18.46501215 0.000231869 1.117947828 0.030135477 0.199258939 126.8083993 72873.41168 13823.49497 0.052187037 8.906969903 -0.949729985 1.117715959 SKEIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKEIKR 6 2 Q15172;Q15172-2 Q15172 PPP2R5A Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform 0 66.994 0.056213 114840000 579510 488340 349590 399410 314240 375430 534000 595890 406000 FALSE TRUE 502926.2852 485132.0624 518652.8933 490102.1451 307987.2388 389873.035 482212.7622 468463.5607 358003.1425 1.404809694 1.355105598 1.448738382 1.368988388 0.860291998 1.089021265 1.346951199 1.308545946 1 18.44961273 3.443554753 24.99171392 1.1556601 1.399899807 0.471700913 0.14153732 195.4583561 145526.5894 0.0443303 0.057230479 2776.864912 -3.443554753 0.244239707 SKEITVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SKEITVR 7 1 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;; 105.57 0.0072026 579110000 1426910 1120170 600459 818322 1093220 1041550 1243840 1407510 630868 FALSE TRUE 1238340.228 1112811.53 890842.9808 1004134.517 1071467.061 1081619.102 1123212.588 1106524.94 556287.5037 2.226079536 2.00042518 1.6014075 1.805063947 1.926103056 1.944352687 2.019122451 1.989124207 1 19.08547117 1.236428061 24.98508079 0.999998797 1.932023735 0.774848511 0.159027344 27.96242164 327525.9859 0.260634129 0.040608876 17.23566568 -1.236428061 0.932024938 SKEPHELVGS(ph)SPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKEPHELVGSSPHR 14 1 Q3T8J9-3;Q3T8J9 Q3T8J9-3 GON4L GON-4-like protein 1 SKEPHELVGS(0.654)S(0.346)PHR 147.1 4.91E-06 92864000 209720 186650 95164 157110 181690 185160 204860 226070 258600 TRUE FALSE 182004.9706 185423.8839 141185.6287 192784.2268 178074.7245 192283.225 184992.7087 177726.6898 228028.6026 0.798167285 0.813160638 0.61915754 0.845438794 0.780931525 0.843241693 0.811269756 0.779405249 1 17.79885527 1.237445061 24.97173227 1.000000258 0.786258117 0.528231538 0.063454775 22.1082412 494661.3789 0.089735467 0.015057495 17.2760742 -1.237445061 -0.21374214 SKEQAELEAAR ddPTM_MDA-MB-175_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 ;;;;; 173.19 1.14E-05 2515490000 4136430 3818670 2414150 2891520 3673670 3451120 4134630 4589520 3817040 FALSE TRUE 3589790.295 3793584.905 3581641.015 3548083.81 3600571.154 3583886.82 3733654.219 3608086.864 3365793.88 1.066550842 1.127099591 1.064129636 1.054159564 1.069753907 1.064796879 1.109293781 1.071986875 1 21.6825154 1.246725809 5.143844766 0.995798898 1.079646791 0.549647972 0.022405377 0.120213502 8.4867651 0.035425044 0.005575658 17.6492319 -1.246725809 0.083847894 SKEQLLVLSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKEQLLVLSLR 11 1 O15327;D6RJC3;E7EQN9;E9PHC0;E9PG59 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 141.32 0.0014967 0 734630 697240 419460 453050 650170 640430 766590 824120 626890 FALSE TRUE 637546.7842 692659.7845 622312.259 555921.9269 637232.889 665067.7565 692246.2198 647888.3513 552779.7784 1.153346792 1.253048342 1.125786947 1.005684268 1.152778944 1.203133296 1.252300187 1.172055087 1 19.07634531 2.402594102 0.004925483 3.55E-05 2.299065053 0.022915343 0.086055622 141605.3699 499.7740239 117425.2961 115844.4107 252.6935184 -2.402594102 2.299029539 SKESSQVTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SKESSQVTSR 10 1 A0A2R8YE10;Q9NRW7;A0A087WU65 A0A2R8YE10 VPS45 Vacuolar protein sorting-associated protein 45 0 ;; 119.39 0.0006377 187887000 184855 176815 87781 111336 174553 181360 182175 228624 87981 FALSE TRUE 160425.9434 175653.4906 130232.1852 136616.5405 171079.7368 188337.0366 164507.6965 179734.5368 77579.98641 2.067877952 2.264159853 1.678682754 1.760976597 2.205204522 2.427649775 2.120491433 2.316764221 1 16.2433969 3.221218325 24.86702044 2.080531311 1.946995178 0 0.419362747 1193.209733 1710932.516 0.126143783 0.143359541 1664.249079 -3.221218325 -0.133536133 SKESVPEFPLS(ph)PPK ddPTM_MDA-MB-175_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 137.69 1.20E-05 6409800000 4603920 2997230 2519830 2859330 3752280 2778350 4678520 5824760 3901590 TRUE FALSE 3995500.307 2977540.999 3738428.216 3508584.579 3677616.969 2885234.922 4224797.85 4579180.402 3440348.475 1.161365 0.86547657 1.086642311 1.019834067 1.068966413 0.838646127 1.228014511 1.33102226 1 21.71412327 2.204405618 24.99768864 1.218223014 1.00744137 0.300427924 0.126047121 180.3054407 131962.4617 0.048469839 0.032680215 160.1052664 -2.204405618 -0.210781644 SKETQEELNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKETQEELNK 10 1 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 0 ; 81.017 0.020313 81073000 231650 177909 143554 148474 174915 148922 213235 286680 213520 FALSE TRUE 201036.8656 176740.3041 212977.1946 182187.291 171434.5337 154651.1257 192555.5025 225375.7129 188277.9088 1.067766616 0.938720348 1.131185256 0.967650916 0.910539823 0.821398148 1.022719573 1.197037477 1 17.52250421 1.990527709 24.91637024 1.111778568 0.970999894 0.22380682 0.095379922 533.5334935 1403431.157 0.041494668 0.026216724 97.8425379 -1.990527709 -0.140778673 SKEYFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SKEYFSK 7 1 Q06830;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 ;;; 92.838 0.014023 17226560000 11054070 8291020 5425410 6772540 7559910 6837490 10701640 11671860 7741110 FALSE TRUE 9593246.642 8236555.744 8049156.423 8310348.719 7409482.582 7100532.665 9663796.6 9175923.57 6825964.795 1.405405233 1.20665078 1.179196885 1.217461409 1.085485027 1.040224038 1.415740762 1.344267638 1 22.70260154 4.738131759 6.519761478 1.202043055 1.409389399 0.216693549 0.127909363 0.215411506 56.48835819 0.03308567 0.198140547 54718.19456 -4.738131759 0.207346343 SKFDNLYGCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SKFDNLYGCR 10 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;; 167.6 4.74E-06 11640690000 14286750 17099690 9303260 11956200 17355480 16512530 17705610 20053920 17744710 FALSE TRUE 12398719.79 16987361.01 13802347.65 14671037.95 17010139.9 17147777.71 15988522.67 15765545.27 15646950.6 0.792404866 1.08566592 0.882111026 0.937629211 1.087121724 1.095918186 1.021829945 1.007579411 1 23.89937818 3.259981497 21.97357661 1.039247917 0.932943283 0.361725309 0.077482062 70.96236098 72791.27046 0.021223071 0.027351533 1819.623331 -3.259981497 -0.106304634 SKFDS(ph)DEEEEDTENVEAASSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKFDSDEEEEDTENVEAASSGK 22 1 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 S(0.05)KFDS(0.95)DEEEEDTENVEAASSGK 287.79 1.07E-46 474720000 381700 329750 365280 410850 461500 326140 747000 805660 743470 TRUE FALSE 331257.3779 327583.8505 541930.6298 504139.7719 452317.0529 338686.8168 674556.055 633375.8787 655577.8236 0.505290701 0.499687205 0.826645762 0.769000649 0.689951729 0.516623358 1.028948861 0.966133777 1 19.32240753 -1.999999996 0.167948909 3.106521177 0.389668301 0.554205667 0.136028749 99.06736137 1.342883483 65.47377494 1.621941744 0.01 1.999999996 -2.716852875 SKFEDMAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKFEDMAK 8 1 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 ; 111.06 0.0030158 2848800000 5728700 4916400 3388800 4300000 4701400 3369900 6789700 7693600 6538400 FALSE TRUE 4971637.78 4884103.845 5027635.015 5276380.721 4607851.338 3499542.234 6131235.939 6048383.512 5765437.801 0.862317477 0.847134947 0.87203005 0.915174338 0.799219677 0.606986382 1.063446724 1.049076188 1 22.45899873 2.187011488 24.99999212 1.040999147 0.824642258 0.607001438 0.083425059 70.51337279 34196.57386 0.035049063 0.023630102 153.8195328 -2.187011488 -0.216356889 SKFGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKFGGR 6 1 P25391 P25391 LAMA1 Laminin subunit alpha-1 0 71.258 0.080902 401940000 849070 679690 466930 466960 470840 661190 714390 763330 731240 FALSE TRUE 736863.2482 675225.0716 692738.9098 572990.405 461471.2052 686626.4071 645108.5678 600097.8197 644793.6402 1.142789262 1.047195613 1.074357541 0.888641527 0.715688208 1.06487776 1.000488416 0.930681977 1 19.29847799 3.757999154 17.05396844 0.933714323 1.084024997 0.372580247 0.094596019 16.47605871 14451.3604 0.02592721 0.044573474 5727.949156 -3.757999154 0.150310674 SKGGVVGIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKGGVVGIK 9 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ; 118.4 0.0018379 0 3561400 3031700 1771320 2379100 2725400 2271400 3681800 4000000 2942000 FALSE TRUE 3090751.967 3011784.563 2627936.277 2919311.017 2671169.872 2358782.228 3324739.603 3144631.128 2594200.112 1.191408463 1.160968481 1.013004458 1.125322216 1.02966994 0.909252227 1.281604911 1.212177547 1 21.30685834 1.196666642 23.42257805 0.999997162 1.117159846 0.100914662 0.108165323 11600.49938 6484740.432 10.32579026 0.028057319 15.72775163 -1.196666642 0.117162684 SKGGVVGIKVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKGGVVGIKVDK 12 2 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ; 102.52 0.0013191 907810000 2423430 1823590 864780 1018170 1572190 1213720 2827030 3001030 270903 FALSE TRUE 2103167.585 1811610.717 1282990.501 1249361.06 1540906.495 1260412.594 2552865.066 2359283.089 238877.156 8.804389758 7.583859202 5.3709217 5.230140384 6.450623078 5.27640489 10.68693679 9.876553826 1 17.86590937 4.478670698 23.97383578 6.743616061 8.499258342 0.069449924 2.684539273 99.77962111 1543754.434 0.696751216 1.908598716 30107.22293 -4.478670698 1.755642281 SKGHYEVTGS(ph)DDETGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SKGHYEVTGSDDETGK 16 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 SKGHYEVT(0.024)GS(0.976)DDETGK;SKGHYEVT(0.002)GS(0.998)DDETGK;SKGHYEVT(0.005)GS(0.995)DDETGK 161.22 5.14E-09 593110000 1047860 642690 425180 726000 801130 658400 786460 1143320 1099430 TRUE FALSE 909382.6461 638468.1271 630798.4701 890849.3962 785189.0804 683729.074 710189.2302 898829.9153 969456.6379 0.938033338 0.658583481 0.650672186 0.918916186 0.809926973 0.705270403 0.732564204 0.927148137 1 19.88681684 1.604196181 3.941464921 0.985302894 0.768924096 0.405470952 0.097214901 0.164299622 5.733657514 0.07527071 0.02526915 40.197235 -1.604196181 -0.216378798 SKGQENDHVHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKGQENDHVHEK 12 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 0 ; 170.18 2.70E-05 155722000 240694 152514 102120 119034 125059 123464 198717 223610 150342 FALSE TRUE 208885.6781 151512.1255 151505.5736 146062.489 122570.5706 128213.74 179445.4559 175792.7416 132568.74 1.575678233 1.142894814 1.142845391 1.101786809 0.924581244 0.967149118 1.353603088 1.326049728 1 17.0163811 4.7386772 6.756032369 1.135725366 1.58323027 0.508916086 0.139967382 0.112347889 35.13528184 0.038517851 0.23007258 54786.95966 -4.7386772 0.447504904 SKGQESFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SKGQESFK 8 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 0 ;;; 111.61 0.0029193 9201000000 13161720 9715820 5715990 7225780 7868840 7480720 12270660 15042450 7472700 FALSE TRUE 11422365.35 9651996.139 8480261.883 8866503.788 7712265.479 7768508.139 11080653.28 11825739.13 6589285.919 1.733475447 1.464801537 1.286977373 1.345594029 1.170425077 1.178960548 1.681616706 1.794692061 1 22.6516907 4.701048146 3.565768003 1.394773945 1.76033452 0.187716281 0.237967496 0.522013907 11.836754 0.0649607 0.479010524 50239.82824 -4.701048146 0.365560576 SKHDSSAPDPAPDS(ph)ADEVMPEAVPEVASEPGLESASHPNVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKHDSSAPDPAPDSADEVMPEAVPEVASEPGLESASHPNVDR 42 1 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 SKHDSSAPDPAPDS(1)ADEVMPEAVPEVASEPGLESASHPNVDR 100.35 1.98E-05 105500000 50130 60396 22111 35424 67790 53579 56264 74530 60596 TRUE FALSE 43505.19349 59999.2547 32803.95356 43467.56062 66441.11163 55640.2188 50807.52594 58592.33949 53432.40991 0.814209832 1.12290003 0.613933633 0.813505524 1.243460883 1.041319658 0.950874685 1.096569284 1 15.70542747 3.269001532 24.99998893 1.060286513 0.845034205 0.380321799 0.142749055 226.8025639 186262.99 0.040427152 0.052184979 1857.811008 -3.269001532 -0.215252307 SKHEEEEWT(ph)DDDLVESL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SKHEEEEWTDDDLVESL 17 1 D6RHI7;P51946 D6RHI7 CCNH Cyclin-H 1 SKHEEEEWT(1)DDDLVESL;S(0.001)KHEEEEWT(0.999)DDDLVESL;S(0.001)KHEEEEWT(0.999)DDDLVESL;S(0.027)KHEEEEWT(0.973)DDDLVESL;S(0.094)KHEEEEWT(0.906)DDDLVESL;S(0.016)KHEEEEWT(0.984)DDDLVESL 215.98 8.80E-15 3001195000 5091100 4490850 2499891 3182050 4337780 4072140 4977700 5725840 5121410 TRUE FALSE 4418298.236 4461349.311 3708846.649 3904583.087 4251466.665 4228797.861 4494963.42 4501413.675 4515962.744 0.978373491 0.98790658 0.821274855 0.864618091 0.941430854 0.936411149 0.995349978 0.996778302 1 22.10660215 2.366681178 1.999043579 1.00012144 0.913794209 0.35146261 0.048778395 0.38459162 3.169427195 0.026459867 0.017135031 232.6382801 -2.366681178 -0.086327231 SKIETEIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKIETEIK 8 1 Q9HB71;B2ZWH1;Q9HB71-2 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 104.22 0.0042152 503810000 1205130 966880 712660 859950 865650 662220 1216200 1354610 1136760 FALSE TRUE 1045869.017 960528.5016 1057304.76 1055214.791 848425.2586 687696.0319 1098253.111 1064937.193 1002373.528 1.043392496 0.958254059 1.05480116 1.05271614 0.846416266 0.686067631 1.095652549 1.06241552 1 19.93498879 SKKPAGGVDFDET ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKKPAGGVDFDET 13 2 Q9BUH6 Q9BUH6 C9orf142 Protein PAXX 0 87.18 0.033715 271940000 619440 530900 336970 418510 519830 383730 630450 725950 506230 FALSE TRUE 537579.4345 527412.4829 499929.8191 513539.092 509486.4 398492.3414 569309.056 570711.2418 446384.0661 1.204297992 1.18152175 1.119954445 1.150442256 1.141363321 0.892711841 1.275379431 1.27852064 1 18.767926 -0.136422077 0.002077414 0.143971601 2.137484932 0.001276957 0.117592098 2348957.733 885.2494151 429470.784 420092.1734 0.730428857 0.136422077 1.993513331 SKLEVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKLEVGR 7 1 P41223;C9JCD9 P41223 BUD31 Protein BUD31 homolog 0 82.452 0.022299 144440000 346440 348340 195480 231390 271900 322560 297100 339270 294200 FALSE TRUE 300657.0762 346051.7316 290014.7818 283930.6361 266489.722 334969.0919 268287.2877 266719.7507 259420.0112 1.15895869 1.333943862 1.117935276 1.094482399 1.027251987 1.291223026 1.034181159 1.028138691 1 17.98493025 -1.999999996 0.103598415 0.165118769 1.419744586 0.33174882 0.092831892 314.2779496 2.987396668 57.06059701 5.50060923 0.01 1.999999996 1.254625817 SKLILFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKLILFPR 8 1 P26373 P26373 RPL13 60S ribosomal protein L13 0 74.165 0.038016 316950000 257560 326850 132120 145480 293470 288010 323900 338440 229290 FALSE TRUE 223522.7934 324702.9008 196013.6739 178513.4575 287630.5212 299089.9311 292488.2279 266067.2397 202183.5974 1.105543656 1.605980431 0.969483561 0.882927497 1.422620454 1.479298691 1.44664667 1.315968472 1 17.62530643 SKLS(ph)PS(ph)PSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKLSPSPSLR 10 1 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 S(0.153)KLS(0.846)PS(0.782)PS(0.219)LR;S(0.032)KLS(0.966)PS(0.606)PS(0.397)LR 65.043 0.039918 825770000 1850710 1429970 1034740 1183330 1645310 1368700 1647290 1915490 1887110 TRUE FALSE 1606133.984 1420576.433 1535143.725 1452023.163 1612571.55 1421354.775 1487536.069 1505877.37 1664018.006 0.965214306 0.853702561 0.922552352 0.872600632 0.969082993 0.854170309 0.893942292 0.904964589 1 20.66623961 1.238895342 6.714662256 1.002428631 0.9022962 0.358188554 0.040081294 0.116882181 26.99604808 0.053470517 0.008867788 17.33386231 -1.238895342 -0.100132432 SKLS(ph)PSPSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKLSPSPSLR 10 1 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 SKLS(1)PSPSLR;S(0.002)KLS(0.941)PS(0.057)PSLR 156.6 6.45E-06 2149000000 3797600 3198800 1845940 2573900 3514100 2760800 3467000 4163100 3555500 TRUE FALSE 3295737.538 3177786.872 2738642.758 3158343.335 3444176.285 2867009.762 3130770.874 3272853.462 3135172.84 1.051213986 1.013592243 0.873522098 1.0073905 1.098560258 0.914466254 0.998595941 1.043914843 1 21.58011355 3.50599945 24.97034176 1.013395928 0.97579083 0.049522927 0.06319848 2062.762939 1783620 0.017444312 0.025820245 3206.265262 -3.50599945 -0.037605098 SKLTFSCLGGSDNFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKLTFSCLGGSDNFK 15 1 A0A087WYT3;Q15185-4;Q15185;Q15185-3;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ; 102.99 0.001375 1097070000 983020 874840 435300 620920 877980 707190 968170 1205330 476610 FALSE TRUE 853111.4163 869093.1184 645812.536 761909.3762 860509.9157 734396.0569 874277.0224 947579.5594 420265.7088 2.029933441 2.067961055 1.536676732 1.812923016 2.047537779 1.74745653 2.08029588 2.254715385 1 18.68094222 1.227081261 24.983992 0.999997895 1.951486599 0.68281463 0.202863186 331.3842856 721186.886 0.825867228 0.0533495 16.86868628 -1.227081261 0.951488704 SKPAGS(ph)DGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SKPAGSDGER 10 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 SKPAGS(1)DGER;S(0.012)KPAGS(0.988)DGER;S(0.002)KPAGS(0.998)DGER 101.2 0.0021147 1047680000 2717610 1975630 1352050 1678260 1242260 1723580 2142320 2480320 3058760 TRUE FALSE 2358470.953 1962651.956 2005905.902 2059334.584 1217541.456 1789887.238 1934558.136 1949922.87 2697156.877 0.874428541 0.727674379 0.743711246 0.763520506 0.451416626 0.663619997 0.717258292 0.722954933 1 21.36300801 -0.485554376 11.55231155 5.073272124 0.728523674 0 0.140476376 0 0 0 0.031287699 0.326923112 0.485554376 -4.34474845 SKPAGS(ph)DGERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 SKPAGSDGERR 11 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.004)KPAGS(0.996)DGERR;SKPAGS(1)DGERR;SKPAGS(1)DGERR;S(0.027)KPAGS(0.973)DGERR;S(0.003)KPAGS(0.997)DGERR;S(0.001)KPAGS(0.999)DGERR;S(0.133)KPAGS(0.867)DGERR;S(0.001)KPAGS(0.999)DGERR;S(0.118)KPAGS(0.882)DGERR 105.14 0.0019737 2670366000 6084910 4386075 2713455 3479299 3423618 3814969 4819030 5571906 4480108 TRUE FALSE 5280773.726 4357262.585 4025690.914 4269327.016 3355494.7 3961733.326 4351681.212 4380397.263 3950474.736 1.336744082 1.10297189 1.019039782 1.080712396 0.849390244 1.002849933 1.101559054 1.108828066 1 21.9135946 4.74327044 2.325558172 1.029892188 1.414359675 0.642320309 0.073368421 0.423220186 2.697583145 0.020418256 0.332449555 55369.47939 -4.74327044 0.384467487 SKPAGSDGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SKPAGSDGER 10 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;; 114.86 0.0011849 780130000 1976260 1430730 946860 1272340 826590 1247450 1563460 1821570 2290660 FALSE TRUE 1715092.234 1421331.44 1404764.663 1561244.243 810142.4762 1295440.209 1411835.89 1432041.431 2019860.784 0.849114081 0.703677922 0.695475982 0.77294646 0.401088274 0.641351235 0.698976831 0.708980263 1 20.94582443 1.186589227 2.872837493 1.096284381 0.673958526 0.429293107 0.114621766 0.53031891 4.704013713 0.565773282 0.030189214 15.36700482 -1.186589227 -0.422325855 SKPAGSDGERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SKPAGSDGERR 11 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;; 125.97 0.00017841 343253000 1176460 856290 407294 530968 636728 782340 940700 1094280 345782 FALSE TRUE 1020987.83 850664.9746 604262.7407 651532.3997 624058.3585 812437.126 849471.0588 860276.7377 304904.0459 3.34855455 2.789943217 1.981812799 2.136844061 2.04673689 2.664566565 2.786027507 2.821467112 1 18.21799577 4.509803927 3.70058216 2.300441233 3.294862607 0.327449276 0.531291912 0.299673338 8.289177555 0.135066714 0.581711275 32344.75956 -4.509803927 0.994421374 SKPCGS(ph)PR ddPTM_MDA-MB-175_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 82.171 0.012696 828985000 2662440 2216920 1485200 1861970 1499750 2261160 2862970 3040820 3179920 TRUE FALSE 2310591.808 2202356.907 2203447.688 2284758.747 1469907.909 2348148.288 2585319.61 2390564.307 2803993.48 0.824036084 0.785435816 0.785824826 0.814823131 0.524219446 0.83743001 0.922013417 0.852557013 1 21.41905156 2.482145108 24.16913146 0.905396766 0.747537562 0.438760231 0.091390778 144.9348181 697273.4644 0.033222112 0.026508406 303.4905048 -2.482145108 -0.157859204 SKPDLESS(ph)LESLVFDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SKPDLESSLESLVFDLR 17 1 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 SKPDLES(0.127)S(0.872)LESLVFDLR;SKPDLES(0.129)S(0.871)LESLVFDLR;SKPDLES(0.025)S(0.975)LESLVFDLR 237.01 2.01E-20 122159000 249958 177498 125481 190843 177442 186416 211826 253510 240692 TRUE FALSE 216925.417 176332.004 186164.0313 234176.82 173911.2514 193587.5441 191283.1471 199298.8593 212237.666 1.022087272 0.830823328 0.877148882 1.10337069 0.81941747 0.91212624 0.901268614 0.939036238 1 17.69532119 1.272691014 3.249284616 1.00976502 0.920812141 0.072571122 0.084556555 0.848389872 12.41775222 0.183002862 0.020694587 18.73660988 -1.272691014 -0.088952879 SKPGAAMVEMADGYAVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SKPGAAMVEMADGYAVDR 18 1 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;; 198.24 1.60E-15 4521470000 7199810 6239210 3692330 4834500 6369080 5822220 6669640 7702550 7046340 FALSE TRUE 6248336.867 6198224.219 5477953.138 5932247.116 6242347.769 6046204.571 6022819.339 6055419.624 6213329.712 1.005634202 0.997568857 0.881645332 0.954761358 1.004670291 0.973102161 0.969338441 0.974585271 1 22.56693518 3.283450755 24.97795207 0.981433118 0.957003062 0.103463103 0.034707764 325.5574366 181145.6131 0.010347281 0.013358202 1920.661164 -3.283450755 -0.024430056 SKPIPIMPAS(ph)PQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKPIPIMPASPQK 13 1 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;O00429-7;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 1 SKPIPIMPAS(1)PQK;SKPIPIMPAS(1)PQK 110.12 0.0016433 1035910000 1611010 1425720 1206710 1610620 1685920 1244650 1859430 2350970 3641200 TRUE FALSE 1398110.947 1416354.351 1790278.992 1976335.888 1652373.49 1292532.491 1679102.765 1848233.361 3210741.484 0.435447997 0.441129988 0.557590513 0.615538777 0.514639219 0.402565108 0.522964173 0.575640664 1 21.61447508 1.181715628 2.569464097 1.17228241 0.500825229 0.862486152 0.062385589 0.237453144 1.530552969 0.375405496 0.017604549 15.19552216 -1.181715628 -0.671457181 SKPIPIMPAS(ph)PQKGHAVNLLDVPVPVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.144)KPIPIMPAS(0.856)PQKGHAVNLLDVPVPVAR 148.98 3.25E-08 1794700000 1248200 1202600 686560 866180 1509500 999340 1597800 1966800 351740 TRUE FALSE 1083247.207 1194700.041 1018582.712 1062859.408 1479463.903 1037785.256 1442845.602 1546215.126 310157.6979 3.49256915 3.851911623 3.284080064 3.426835493 4.770037672 3.34599226 4.651974179 4.985254714 1 18.24264241 SKPLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKPLTR 6 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ; 94.407 0.0406 855520000 1717700 1421020 812470 1144970 1045660 1341040 1578910 1725760 1870750 FALSE TRUE 1490701.593 1411685.226 1205383.21 1404952.938 1024853.412 1392630.677 1425787.551 1356719.654 1649592.066 0.90367893 0.85577838 0.730715935 0.851697197 0.62127688 0.844227312 0.864327357 0.822457674 1 20.65367787 -0.446996252 1.147522178 9.999999952 0.800635021 0.347539476 0.080891333 83.63067881 2.97659192 1904.715004 0.024564538 0.357275921 0.446996252 -9.199364931 SKPNLPS(ph)ESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKPNLPSESR 10 1 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 SKPNLPS(1)ESR 109.44 0.0012222 157710000 323560 207870 183370 234590 241360 217180 235830 295230 522190 TRUE FALSE 280800.7262 206504.4883 272048.3453 287857.245 236557.4082 225535.0551 212959.2429 232097.362 460457.2931 0.60983012 0.448476963 0.590822101 0.625155143 0.513744514 0.489806674 0.462495102 0.50405839 1 18.81270783 1.236905432 24.99996017 1.000000586 0.526593808 0.855732883 0.060557634 15.53306386 234537.6634 0.093383053 0.015063336 17.2546213 -1.236905432 -0.473406778 SKPNLPSES(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SKPNLPSESR 10 1 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 SKPNLPS(0.024)ES(0.976)R;SKPNLPS(0.011)ES(0.989)R;SKPNLPS(0.002)ES(0.998)R 102.28 0.0017977 1360150000 1525110 986280 878200 1262430 1083530 957380 1138050 1372280 3230900 TRUE FALSE 1323562.849 979801.0617 1302900.457 1549084.027 1061969.873 994211.0281 1027682.086 1078828.601 2848946.683 0.464579719 0.343916953 0.457327076 0.543739213 0.372758774 0.348974951 0.360723524 0.378676304 1 21.44199719 1.236968606 24.99219054 1.000000735 0.405872039 0.895991821 0.063291037 12.6665998 198781.0423 0.099619396 0.016144264 17.2571314 -1.236968606 -0.594128697 SKPNLPSESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKPNLPSESR 10 1 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 0 105.17 0.0023572 215880000 208010 180430 109420 152400 186740 184700 189400 198800 203390 FALSE TRUE 180520.9515 179244.7434 162335.878 187004.7493 183024.2394 191805.5285 171032.0172 156288.1671 179345.4659 1.006554309 0.999438389 0.905157413 1.042706869 1.020512219 1.069475203 0.953645615 0.871436399 1 17.45238175 2.008652225 24.93860665 0.922336856 1.005102881 0.256620159 0.052112073 205.0183185 590929.2226 0.02132096 0.014349334 102.012226 -2.008652225 0.082766025 SKPYEGSQRNS(ph)TELAPPLPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKPYEGSQRNSTELAPPLPVR 21 2 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 SKPYEGS(0.005)QRNS(0.88)T(0.114)ELAPPLPVR;SKPYEGS(0.001)QRNS(0.932)T(0.067)ELAPPLPVR 188.38 1.33E-17 523230000 239100 275590 166807 173004 335070 301460 361630 425970 118182 TRUE FALSE 207502.3292 273779.6311 247475.4231 212287.2024 328402.7626 313057.3613 326559.1783 334879.6304 104210.6586 1.99118144 2.627174944 2.374761147 2.037096831 3.151335641 3.004081977 3.133644703 3.213487324 1 16.66914332 3.244210428 24.99729646 2.812295816 2.292327099 0.084880345 0.664589775 297.2524004 1315170.288 0.190087976 0.238522527 1754.730513 -3.244210428 -0.519968717 SKRPNPCAYT(ph)PPSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKRPNPCAYTPPSLK 15 2 Q9UD71;J3KSJ8;Q9UD71-2 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 1 SKRPNPCAYT(1)PPSLK 137.14 0.00088473 1004700000 650530 579960 354250 391670 584130 387600 715760 822510 497600 TRUE FALSE 564560.8123 576150.2046 525566.4849 480604.6598 572506.9558 402511.2228 646345.7054 646622.6373 438774.2949 1.286677043 1.31309015 1.197806004 1.095334584 1.304786909 0.9173537 1.473071037 1.473702185 1 18.74311948 SKRPNPCAYTPPSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKRPNPCAYTPPSLK 15 2 Q9UD71;J3KSJ8;Q9UD71-2 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 0 93.823 0.0026482 359610000 811950 822310 449040 565070 868040 630740 931380 1156100 692390 FALSE TRUE 704648.7503 816908.1915 666197.2459 693377.7801 850767.7023 655004.9759 841054.911 908877.0118 610536.443 1.154146912 1.338017085 1.091167044 1.135686146 1.393475708 1.072835182 1.37756709 1.488653171 1 19.21971789 2.209125829 24.99795266 1.334089804 1.205196714 0.042377035 0.159320275 432.1299065 366990.0751 0.06288495 0.04240424 161.8548914 -2.209125829 -0.12889309 SKS(ph)ATT(ph)TPSGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKSATTTPSGSPR 13 1 A0A096LNZ0;A0A096LP60;A0A096LP25;Q2M2I8;Q2M2I8-2 A0A096LNZ0;A0A096LP25;Q2M2I8 AAK1 AP2-associated protein kinase 1 3 SKS(0.987)AT(0.051)T(0.945)T(0.017)PSGS(1)PR;S(0.023)KS(0.901)AT(0.44)T(0.525)T(0.1)PS(0.012)GS(0.999)PR 212.21 1.13E-07 387200000 881020 808720 525260 544940 655900 701520 696340 890310 747630 TRUE FALSE 764590.9748 803407.4651 779277.4929 668676.9559 642848.8732 728507.9283 628809.054 699924.1349 659246.0331 1.159796095 1.218676222 1.182073845 1.014305619 0.975127405 1.105062286 0.953830622 1.061703977 1 19.33045746 3.749382861 7.526794302 1.020536487 1.190530648 0.763136354 0.044232792 0.065585457 25.78468753 0.01092691 0.018051672 5615.427973 -3.749382861 0.169994161 SKS(ph)DLSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SKSDLSER 8 1 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 S(0.381)KS(0.618)DLS(0.001)ER;S(0.001)KS(0.999)DLSER;S(0.031)KS(0.969)DLSER;S(0.275)KS(0.71)DLS(0.015)ER 127.83 0.00079619 4812500000 7472530 6365880 4590750 5389490 5183790 5340680 7512270 8146030 7706030 TRUE FALSE 6485016.228 6324062.115 6810852.055 6613256.078 5080642.721 5546139.415 6783731.212 6404064.877 6795031.912 0.954376125 0.930689097 1.002328193 0.973248715 0.747699612 0.816205058 0.998336917 0.942462811 1 22.6960489 2.173195054 24.99999787 0.97314385 0.905795671 0.179799284 0.076133256 126.3553114 48324.48578 0.034143948 0.023019851 149.0030144 -2.173195054 -0.06734818 SKS(ph)DSYTLDPDTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SKSDSYTLDPDTLR 14 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.028)KS(0.936)DS(0.029)YT(0.007)LDPDTLR;S(0.026)KS(0.964)DS(0.011)YTLDPDTLR;SKS(0.5)DS(0.5)YTLDPDTLR 209.89 1.58E-08 1100840000 1494670 1650520 1353150 1739410 2217750 1988510 2572840 3124630 2914070 TRUE FALSE 1297145.572 1639677.625 2007537.866 2134369.626 2173621.114 2065009.266 2323326.373 2456452.19 2569571.964 0.50480998 0.638113136 0.78127326 0.83063236 0.845907857 0.803639398 0.904168634 0.955977192 1 21.29309663 5.234857514 0.388991915 0.969110691 3.31E-21 0.916475139 0.042154017 3.171236179 0.314863501 0.061201476 1.545197966 171734.486 -5.234857514 -0.969110691 SKS(ph)EDMDNVQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SKSEDMDNVQSK 12 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 S(0.194)KS(0.806)EDMDNVQSK;S(0.343)KS(0.657)EDMDNVQSK;S(0.001)KS(0.999)EDMDNVQSK;S(0.003)KS(0.997)EDMDNVQSK;S(0.452)KS(0.548)EDMDNVQSK 220.21 7.92E-11 1428240000 2920040 1844990 1797020 1878760 1973230 1495888 2964630 3272250 3224510 TRUE FALSE 2534149.316 1832870.139 2666064.883 2305361.173 1933966.584 1553435.779 2677120.639 2572504.802 2843312.101 0.891266673 0.644625027 0.937661709 0.810801309 0.6801809 0.546347261 0.941550046 0.904756393 1 21.43914104 2.107186985 23.44197424 0.939390643 0.753897494 0.389370276 0.116050656 6.354077202 1363.784599 0.047555168 0.032061693 127.9932259 -2.107186985 -0.185493149 SKS(ph)EEAHAEDSVMDHHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKSEEAHAEDSVMDHHFR 18 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 S(0.43)KS(0.57)EEAHAEDSVMDHHFR;S(0.417)KS(0.583)EEAHAEDSVMDHHFR 270.71 3.07E-39 1697870000 2150780 1131727 457343 1097570 967064 656162 1459690 1188420 1184220 TRUE FALSE 1866548.974 1124292.611 678515.6045 1346790.044 947821.3184 681404.9767 1318129.488 934285.6313 1044222.861 1.787500584 1.076678795 0.649780454 1.289753456 0.907681065 0.652547461 1.262306676 0.894718615 1 19.99399822 4.719923941 4.099229185 0.957376626 1.844152434 0.603359466 0.211148184 0.133886591 4.860445299 0.048611817 0.339092027 52471.55579 -4.719923941 0.886775808 SKS(ph)HESQLGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKSHESQLGNR 11 1 A8MY87;A0A2R8Y4X0;A0A0A0MQW1;A0A2R8Y5H9;Q8IVT5-4;Q8IVT5-3;Q8IVT5-2;Q8IVT5;J3QLI1 A8MY87 KSR1 Kinase suppressor of Ras 1 1 S(0.003)KS(0.996)HES(0.001)QLGNR;S(0.002)KS(0.996)HES(0.002)QLGNR 134.14 8.91E-05 163122000 231443 215443 99100 147326 180264 184154 231151 248160 226618 TRUE FALSE 200857.2211 214027.7407 147025.0915 180778.62 176677.0991 191238.5235 208734.0116 195092.9152 199827.4782 1.00515316 1.071062612 0.735760131 0.90467348 0.88414817 0.95701815 1.044571114 0.976306747 1 17.60839546 2.469884356 7.983937142 1.002115543 0.917687145 0.171057067 0.086948674 0.243598167 119.1721625 0.032868785 0.026217949 295.0423483 -2.469884356 -0.084428398 SKS(ph)LDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SKSLDSR 7 1 Q9P2M7;Q9P2M7-2;A6PVU7 Q9P2M7 CGN Cingulin 1 S(0.004)KS(0.996)LDSR;S(0.242)KS(0.758)LDSR;S(0.222)KS(0.778)LDSR;S(0.159)KS(0.841)LDSR 123.63 0.002559 7253640000 23129800 21607700 14419100 17089300 12675000 17191900 25036900 27511400 24567700 TRUE FALSE 20073138.33 21465757.6 21392224.99 20969686.76 12422792.3 17853283.52 22608825.29 21628301.2 21663334.49 0.926595042 0.990879664 0.987485329 0.967980565 0.573447837 0.824124445 1.043644749 0.99838283 1 24.36875199 2.232526695 24.99624199 1.011988531 0.878696909 0.217587592 0.12118481 250.7820196 1038881.804 0.053129161 0.036860724 170.8152715 -2.232526695 -0.133291623 SKS(ph)MSDVSAEDVQNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SKSMSDVSAEDVQNLR 16 1 E9PMS6;E9PJ10 E9PMS6 LMO7 1 S(0.047)KS(0.95)MS(0.003)DVSAEDVQNLR;S(0.241)KS(0.758)MS(0.001)DVSAEDVQNLR;S(0.01)KS(0.988)MS(0.001)DVSAEDVQNLR;S(0.002)KS(0.992)MS(0.006)DVSAEDVQNLR;S(0.001)KS(0.846)MS(0.153)DVSAEDVQNLR;SKS(0.916)MS(0.081)DVS(0.003)AEDVQNLR;S(0.07)KS(0.928)MS(0.002)DVSAEDVQNLR;SKS(0.963)MS(0.037)DVSAEDVQNLR 260.89 5.02E-27 12237650000 7500270 8715440 4030210 4536110 8273140 6502300 8643130 10116780 3392000 TRUE FALSE 6509090.316 8658187.701 5979233.036 5566103.106 8108520.7 6752447.689 7804920.583 7953385.326 2991001.624 2.176224267 2.894745235 1.999073818 1.860949543 2.710971681 2.257587436 2.609467183 2.659104315 1 21.51219726 1.232367126 24.99971641 0.999997678 2.410329882 0.639487437 0.329254148 134.950236 544666.0329 0.725167405 0.080215302 17.07525215 -1.232367126 1.410332205 SKS(ph)PASVDR ddPTM_MDA-MB-175_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(0.416)KS(0.583)PAS(0.001)VDR;S(0.003)KS(0.88)PAS(0.117)VDR 139.46 6.75E-05 1041120000 1531990 1414570 791950 1130110 1243950 1206500 1491580 1854510 1565650 TRUE FALSE 1329533.64 1405277.597 1174939.669 1386718.748 1219197.829 1252914.836 1346926.801 1457937.468 1380560.641 0.963038928 1.017903564 0.851059805 1.004460585 0.883117911 0.907540603 0.97563755 1.056047395 1 20.39682283 1.966911636 5.283608377 1.028646693 0.938139997 0.335384903 0.052200748 0.199924875 14.92068137 0.024599525 0.013580974 92.66412648 -1.966911636 -0.090506696 SKS(ph)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SKSPLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 36 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.117)KS(0.883)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.023)KS(0.977)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.04)KS(0.96)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.179)KS(0.821)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 272.11 2.46E-76 2939080000 1019320 602065 535578 575176 520640 361414 867447 1029102 886900 TRUE FALSE 884614.2794 598109.9954 794585.3122 705778.5018 510280.2826 375317.8304 783322.1235 809036.5458 782051.6924 1.131145534 0.764795986 1.016026587 0.902470398 0.652489199 0.479914351 1.001624485 1.034505204 1 19.57690444 2.040623747 24.99999842 1.019223365 0.819076932 0.195507189 0.179339118 232.4829083 143069.8706 0.075845472 0.051134936 109.8054124 -2.040623747 -0.200146433 SKS(ph)PPKVPIVIQDDSLPAGPPPQIR ddPTM_MDA-MB-175_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(0.164)KS(0.836)PPKVPIVIQDDSLPAGPPPQIR 134.67 3.76E-05 340100000 185220 142750 136640 141210 148990 124000 205240 235840 245340 TRUE FALSE 160742.7077 141812.2659 202719.561 173273.8888 146025.3905 128770.3602 185335.8564 185407.4513 216336.1847 0.743022754 0.655518013 0.937058039 0.800947327 0.674992908 0.595232649 0.856702991 0.857033933 1 17.72291547 1.531612411 1.711304233 1.00914085 0.743629076 0.42136451 0.096961443 0.537339843 2.509268191 0.210708322 0.02924697 34.01045253 -1.531612411 -0.265511773 SKS(ph)PRDPDANWDSPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKSPRDPDANWDSPSR 16 2 Q9UHB7;Q9UHB7-2;Q9UHB7-3 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 S(0.427)KS(0.572)PRDPDANWDSPSR 81.574 0.009766 206040000 220040 185030 115750 127270 202930 161450 209490 251720 117940 TRUE FALSE 190961.1565 183814.5257 171727.0872 156168.5987 198892.09 167661.086 189173.692 197891.6369 103997.2676 1.83621321 1.767493801 1.651265376 1.501660595 1.91247419 1.612168184 1.8190256 1.902854195 1 16.6661861 1.231446309 24.9982045 0.999998697 1.751167113 0.766249596 0.130250973 123.6280656 434364.8278 0.31921233 0.032371198 17.03908655 -1.231446309 0.751168416 SKS(ph)PS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SKSPSPPR 8 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 2 S(0.446)KS(0.554)PS(0.999)PPR;S(0.439)KS(0.561)PS(1)PPR;S(0.231)KS(0.769)PS(1)PPR;S(0.417)KS(0.583)PS(1)PPR 94.616 0.0058227 2675760000 3205140 2495340 1957180 2171500 2402170 2178280 2894320 3304550 3801440 TRUE FALSE 2781572.628 2478947.947 2903678.794 2664572.264 2354371.517 2262079.841 2613629.292 2597897.699 3352038.094 0.829815339 0.739534539 0.866242779 0.794911093 0.702370155 0.674837152 0.779713481 0.775020339 1 21.67660711 1.236299015 5.723718843 1.010350166 0.767933201 0.624983835 0.05591601 0.102049943 11.31995476 0.09712341 0.014489308 17.23054505 -1.236299015 -0.242416965 SKS(ph)PSGQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKSPSGQKR 9 2 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(0.018)KS(0.641)PS(0.342)GQKR 73.36 0.034764 466840000 682070 490710 288220 340800 315470 339080 631190 739670 255210 TRUE FALSE 591932.7214 487486.4937 427604.156 418183.8488 309192.7642 352124.627 569977.291 581497.3266 225039.3645 2.630351906 2.16622765 1.900130481 1.858269773 1.373949686 1.564724588 2.532789284 2.583980486 1 17.77981786 4.648878769 2.229879394 1.910283155 2.739311024 0.212727771 0.480962158 0.967549299 6.466243439 0.134975773 1.465053245 44553.18635 -4.648878769 0.829027869 SKS(ph)PSPPR ddPTM_MDA-MB-175_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(0.01)KS(0.54)PS(0.45)PPR 58.63 0.062823 273790000 205530 168100 115470 134790 148840 140800 175050 208740 186190 TRUE FALSE 178368.6898 166995.74 171311.6782 165396.1296 145878.3752 146216.6671 158073.6779 164102.5754 164178.8303 1.086429288 1.01715757 1.043445601 1.007414472 0.888533405 0.890593914 0.96281401 0.999535538 1 17.32490859 3.468949517 23.96268194 0.952455991 1.042426264 0.560307763 0.04092409 100.1374929 293639.3188 0.01328343 0.017184284 2944.07939 -3.468949517 0.089970274 SKS(ph)PTISDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKSPTISDK 9 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 SKS(0.933)PT(0.067)ISDK 110.66 0.0059208 82805000 164190 108360 88995 93573 92587 77743 139500 166160 141170 TRUE FALSE 142491.8755 107648.176 132033.2797 114820.1798 90744.69984 80733.82352 125971.3115 130627.9771 124481.0434 1.144687348 0.864775656 1.06066977 0.922390885 0.728984087 0.648563197 1.011971847 1.04938048 1 16.92556653 6.667749246 1.754482894 0.915521952 193.1376523 0.216413266 0.136033541 2449.16019 11.35821216 0.040126716 1891496.677 4653173.503 -6.667749246 192.2221303 SKS(ph)PVGNPQLIQFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKSPVGNPQLIQFSR 15 1 G8JLP4;Q9Y4F3-3;Q9Y4F3-4;Q9Y4F3-5;Q9Y4F3 G8JLP4 KIAA0430 Meiosis arrest female protein 1 1 S(0.068)KS(0.932)PVGNPQLIQFSR;S(0.002)KS(0.998)PVGNPQLIQFSR 166.21 8.36E-07 1321200000 283330 245620 142649 176542 291730 235730 235440 313030 194526 TRUE FALSE 245887.2226 244006.506 211634.5335 216628.5594 285925.1438 244798.6856 212607.065 246090.9705 171529.3579 1.433499348 1.422534947 1.233809396 1.262924097 1.666916657 1.42715328 1.239479164 1.434687179 1 17.38809599 1.234262287 24.96083277 0.999999417 1.387112515 0.480338538 0.127490176 117.6666338 683208.8121 0.239685956 0.031449784 17.14992745 -1.234262287 0.387113098 SKS(ph)YDEGLDDYREDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKSYDEGLDDYREDAK 16 2 Q5T5U3;E7ESW5;A0A1B0GV73;Q5T5U3-3 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 S(0.13)KS(0.87)YDEGLDDYREDAK 160.3 4.61E-09 94912000 305130 202610 192820 172540 182140 141400 265940 327740 270800 TRUE FALSE 264806.2974 201279.0416 286068.3969 211717.8441 178515.7704 146839.7495 240149.1797 257655.3515 238786.3325 1.108967564 0.842925303 1.198009928 0.886641383 0.747596265 0.614942019 1.005707392 1.079020515 1 17.86536074 7.999992021 0.851172684 0.920174297 58.82386362 0.100489592 0.166463821 2164.634363 5.961313415 0.06163654 242724.0657 99998162.69 -7.999992021 57.90368932 SKSDS(ph)YTLDPDTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKSDSYTLDPDTLR 14 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.031)KS(0.295)DS(0.672)YT(0.002)LDPDTLR 183.31 3.74E-06 609250000 531100 566070 496810 557470 733210 712160 907940 976940 980490 TRUE FALSE 460913.7894 562351.4489 737068.9777 684052.0839 718620.5555 739557.256 819888.1185 768028.9836 864577.5892 0.533108648 0.650434913 0.85251918 0.791198028 0.831181105 0.855397208 0.94831063 0.888328582 1 19.72163591 5.331600741 0.470158453 0.935556756 1.11E-26 0.871093746 0.04901843 3.086911385 0.366812741 0.039588906 1.791418102 214585.6819 -5.331600741 -0.935556756 SKSEEAHAEDSVMDHHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SKSEEAHAEDSVMDHHFR 18 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;; 171.25 5.20E-12 1254590000 2018210 1829480 721930 1111480 1812720 1682720 1878760 2109370 837450 FALSE TRUE 1751498.435 1817462.025 1071057.763 1363858.522 1776650.419 1747455.327 1696558.144 1658297.641 738447.615 2.371865518 2.461192898 1.450418067 1.846926572 2.405926138 2.366390373 2.297465805 2.245653729 1 19.49413606 1.236546079 24.94631195 0.99999846 2.177595392 0.589444822 0.309673061 39.9716712 494840.8933 0.506749906 0.079724921 17.24035001 -1.236546079 1.177596932 SKSLT(ph)NLVAAGDDVLEDQEILMHHPPQVDELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKSLTNLVAAGDDVLEDQEILMHHPPQVDELDR 33 1 Q7Z5Y7-2;Q7Z5Y7-3;Q7Z5Y7 Q7Z5Y7-2 KCTD20 BTB/POZ domain-containing protein KCTD20 1 S(0.309)KS(0.309)LT(0.381)NLVAAGDDVLEDQEILMHHPPQVDELDR 112.59 3.24E-06 18998000 12441 10962 6604.1 13909 10855 9312.3 12276 12541 16259 TRUE FALSE 10796.89033 10889.9899 9797.864849 17067.25104 10639.00674 9670.550207 11085.47541 9859.204744 14336.87954 0.753085098 0.75957881 0.683402886 1.190443917 0.742072688 0.674522666 0.77321396 0.687681355 1 13.80744343 SKSPS(ph)GQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKSPSGQKR 9 2 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(0.001)KS(0.053)PS(0.946)GQKR 76.728 0.027257 708430000 2033300 1415700 852470 1004900 989450 923300 1871400 2307700 774750 TRUE FALSE 1764594.253 1406400.173 1264727.343 1233077.904 969761.8808 958819.9485 1689911.916 1814216.314 683159.9376 2.582988487 2.058668982 1.851290267 1.804962259 1.419523932 1.403507284 2.473669522 2.655624567 1 19.38186385 2.22225365 24.999748 2.18864806 1.840784837 0.002745036 0.545750754 674.823216 1034544.597 0.226624948 0.153294617 166.8221255 -2.22225365 -0.347863224 SKSPS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKSPSPPR 8 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 SKS(0.054)PS(0.946)PPR 86.344 0.0097501 250120000 228550 165030 106930 142200 175420 151940 202550 242490 188860 TRUE FALSE 198346.5384 163945.9071 158641.7057 174488.6834 171929.4852 157785.2301 182906.7322 190635.4006 166533.186 1.19103311 0.984463884 0.952613167 1.047771244 1.032403747 0.947470195 1.09832002 1.144729199 1 17.34545017 2.162364211 24.99998391 1.095011853 1.022021445 0.092769296 0.076472078 64.68754545 21221.15783 0.030311047 0.020435708 145.3329907 -2.162364211 -0.072990409 SKSPT(ph)ISDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKSPTISDK 9 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 S(0.002)KS(0.308)PT(0.676)IS(0.015)DK 103.44 0.0055324 226060000 331050 220160 201600 187030 195850 188990 301210 372570 336760 TRUE FALSE 287300.9037 218713.7545 299094.4343 229498.0201 191952.9682 196260.5676 271998.7006 292898.8048 296948.6164 0.967510498 0.736537375 1.007226226 0.772854317 0.646418126 0.660924338 0.915979013 0.986361911 1 18.17985379 2.011587038 23.46691091 0.979895942 0.796431272 0.337215801 0.115064147 117.6782525 238328.7306 0.048713106 0.032802693 102.7039241 -2.011587038 -0.18346467 SKT(ph)FDWAEFRPIQQALAQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKTFDWAEFRPIQQALAQER 20 2 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 S(0.45)KT(0.55)FDWAEFRPIQQALAQER;S(0.051)KT(0.949)FDWAEFRPIQQALAQER 127.24 3.92E-05 1068100000 343430 308110 216650 211509 300520 289920 247510 322240 299590 TRUE FALSE 298044.8554 306086.0051 321422.6647 259535.3512 294540.24 301073.41 223506.5183 253331.4837 264172.8115 1.128219266 1.158658241 1.216713646 0.982445353 1.114952891 1.139683559 0.846061777 0.958961228 1 18.01112247 2.252968696 24.98569622 0.936291914 1.122490444 0.623387865 0.069039533 147.5704973 255908.4323 0.026044726 0.020080859 179.0476792 -2.252968696 0.186198529 SKT(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKTPSR 6 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.001)KT(0.998)PS(0.001)R 101.64 0.05867 131210000 248180 210350 145710 168140 213720 196410 237710 290730 297200 TRUE FALSE 215382.3842 208968.197 216175.8434 206318.7569 209467.3901 203966.0198 214656.9208 228559.652 262065.3546 0.821865159 0.797389633 0.824892873 0.787279788 0.799294476 0.778302115 0.819096905 0.872147531 1 17.99956711 1.212035051 1.63285664 1.087908834 0.801458116 0.948979539 0.014539364 0.225016028 0.517802315 0.106447996 0.004122895 16.29427536 -1.212035051 -0.286450717 SKTDLLVNDNPDPAPLS(ph)PELQDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SKTDLLVNDNPDPAPLSPELQDFK 24 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 SKTDLLVNDNPDPAPLS(1)PELQDFK;SKTDLLVNDNPDPAPLS(1)PELQDFK;SKTDLLVNDNPDPAPLS(1)PELQDFK;SKTDLLVNDNPDPAPLS(1)PELQDFK 235.14 1.36E-37 1032390000 1097660 998710 809430 1115890 982300 689080 1199670 1624120 1600850 TRUE FALSE 952601.4499 992149.4083 1200873.055 1369269.88 962754.1518 715589.3535 1083326.188 1276814.577 1411599.337 0.674838409 0.702854827 0.850718064 0.970013122 0.682030748 0.506935173 0.767445946 0.904516277 1 20.42889923 1.629853354 3.038131815 0.982741415 0.736797908 0.372731653 0.119871702 0.251762199 5.335234305 0.116315424 0.035081297 42.64355021 -1.629853354 -0.245943508 SKVDDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SKVDDLR 7 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ;;; 101.64 0.0081244 3016800000 9656100 8601500 5395400 6686000 7997700 7169300 9966400 11673500 9158500 FALSE TRUE 8380021.92 8544996.18 8004633.487 8204158.489 7838561.417 7445107.61 8999860.062 9177212.868 8075792.563 1.037671765 1.058100009 0.991188595 1.015895149 0.970624413 0.921904265 1.114424373 1.136385413 1 22.94517242 2.212324217 24.99740967 1.095883801 1.000998188 0.371596571 0.050859271 213.379663 203301.3998 0.021364351 0.014408654 163.0512815 -2.212324217 -0.094885614 SKVDEAVAVLQAHQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKVDEAVAVLQAHQAK 16 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;Q9H361;H0YB75;H0YAS6;H0YAS7;H0YC10 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 139.67 1.07E-06 892120000 1736500 1399100 1077800 1213600 1220600 1050000 1663900 1963600 2704600 FALSE TRUE 1507017.125 1389909.22 1599027.685 1489166.429 1196312.448 1090394.179 1502535.234 1543699.421 2384865.269 0.631908706 0.582804085 0.670489736 0.624423714 0.501626848 0.457214164 0.6300294 0.647289992 1 21.18547633 1.122614439 2.165890144 1.229079309 0.582191484 0.802997494 0.063943964 0.464177363 1.671060007 0.665553895 0.018412674 13.26216538 -1.122614439 -0.646887826 SKVGS(ph)TENIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SKVGSTENIK 10 1 E7EVA0;H0Y2V1;F8W9U4;H7C4C5;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 SKVGS(0.918)T(0.082)ENIK;SKVGS(0.856)T(0.144)ENIK;SKVGS(0.5)T(0.5)ENIK;SKVGS(0.65)T(0.35)ENIK;SKVGS(0.791)T(0.209)ENIK;SKVGS(0.93)T(0.07)ENIK 189.1 6.35E-07 12109586000 17763610 9432930 8503620 8420220 7890990 7836170 15046930 12930770 11476270 TRUE FALSE 15416103.93 9370964.462 12615999.07 10332159.65 7733974.737 8137632.531 13587681.04 10165625.46 10119558.43 1.523396898 0.926025036 1.246694622 1.021008942 0.7642601 0.804148974 1.342714816 1.004552277 1 23.270643 4.745334929 24.70835976 1.021555618 1.523397169 0.45397517 0.175492199 665.3793229 2426804.439 0.043517683 0.410328399 55633.31375 -4.745334929 0.501841551 SKYDEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKYDEER 7 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ; 99.136 0.0098044 344210000 953630 858280 539150 732080 713080 773550 973380 1074170 994370 FALSE TRUE 827605.3793 852641.9022 799884.7433 898309.9531 698891.1031 803308.9691 878981.7574 844467.1047 876816.7114 0.943875007 0.972428891 0.91225992 1.02451281 0.797077763 0.916165213 1.002469212 0.963105623 1 19.74191577 2.243099784 24.9982541 0.983810266 0.927510823 0.195738483 0.057838713 197.9987531 1090432.988 0.021888979 0.016368918 175.0248782 -2.243099784 -0.056299443 SKYNDDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SKYNDDIR 8 1 Q9Y3D6 Q9Y3D6 FIS1 Mitochondrial fission 1 protein 0 ; 60.436 0.084181 604970000 1657150 1463260 992870 1313520 1397900 1401780 1270900 1667790 2453400 FALSE TRUE 1438153.429 1453647.749 1473025.253 1611774.792 1370084.525 1455707.384 1147648.314 1311146.087 2163361.847 0.664777106 0.671939255 0.680896381 0.745032457 0.633312697 0.672891308 0.530492999 0.606068786 1 21.04484356 1.234439998 24.99986947 1.000000513 0.647660855 0.796063611 0.05554669 59.56393012 361325.6496 0.112346827 0.014978464 17.15694654 -1.234439998 -0.352339658 SKYTTPSGEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SKYTTPSGEVR 11 1 E9PLK3;P55786;P55786-2;A6NEC2;E9PP11 E9PLK3 NPEPPS;NPEPPSL1 Puromycin-sensitive aminopeptidase;Puromycin-sensitive aminopeptidase-like protein 0 91.62 0.009672 201930000 347610 357780 177970 239880 389140 332460 375850 380770 245680 FALSE TRUE 301672.4578 355429.7196 264036.8873 294348.4203 381396.8753 345249.9513 339400.1248 299345.2987 216635.9903 1.39253158 1.640677152 1.21880435 1.358723543 1.760542534 1.593686953 1.566683931 1.381789324 1 17.72491342 1.261445548 2.758518731 0.906661416 1.505476596 0.514896386 0.153513576 0.360879787 3.321517256 0.484731848 0.041343499 18.25767819 -1.261445548 0.598815179 SLAALDALNT(ph)DDENDEEEYEAWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLAALDALNTDDENDEEEYEAWK 23 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 SLAALDALNT(1)DDENDEEEYEAWK;SLAALDALNT(1)DDENDEEEYEAWK;SLAALDALNT(1)DDENDEEEYEAWK 234.95 1.63E-36 369606000 218253 175067 116160 144217 163706 145160 190851 229378 195553 TRUE FALSE 189410.3131 173916.9733 172335.3645 176963.6741 160448.5709 150744.3991 172342.2994 180327.2997 172434.9471 1.098445044 1.008594698 0.999422492 1.026263394 0.930487547 0.874210255 0.999462709 1.045770029 1 17.39569267 5.538151708 1.069740155 0.982230259 1.536454722 0.367897917 0.048268019 10.97268652 2.932438992 0.016632712 10.40959206 345264.3265 -5.538151708 0.554224462 SLADELALVDVLEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLADELALVDVLEDK 15 0 A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50;C9J7H8;F5H793 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 ;;; 281.25 2.20E-33 749410000 1374570 1157660 1214500 1407100 1218830 1003870 1573480 1829040 2668150 FALSE TRUE 1192917.092 1150055.255 1801836.262 1726603.561 1194577.668 1042489.528 1420884.152 1437914.03 2352724.347 0.507036489 0.488818529 0.765850987 0.733874142 0.507742299 0.443098882 0.603931418 0.611169784 1 21.16590087 1.226116715 4.025204947 1.05190001 0.582212961 0.616748308 0.103611875 0.192717249 5.416503521 0.272076294 0.028091456 16.83126335 -1.226116715 -0.469687048 SLADELALVDVLEDKLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLADELALVDVLEDKLK 17 1 A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50;C9J7H8;F5H793 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 ; 171.56 1.56E-09 1023710000 2214990 1607000 1384410 1360050 1531100 1073810 2412200 2742500 819690 FALSE TRUE 1922273.459 1596443.511 2053915.307 1668870.14 1500634.106 1115120.166 2178265.215 2156037.717 722787.182 2.659528984 2.208732461 2.841659838 2.3089371 2.076176976 1.542805674 3.013702054 2.982949575 1 19.4632114 1.225717653 24.99689128 0.999996525 2.464898962 0.50516481 0.452241069 582.5882299 1133850.613 2.129049983 0.11866254 16.81580463 -1.225717653 1.464902437 SLAES(ph)IDDALNCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLAESIDDALNCR 13 0 A0A0C4DGT3;A0A3B3IU98;Q6DN90-2;A0A3B3IRZ4;Q6DN90-3;A0A2R8Y7T6;Q6DN90;A0A2R8Y695 A0A0C4DGT3;A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 SLAES(1)IDDALNCR 186.62 3.26E-07 0 77639 89255 50801 50321 66508 71724 78541 78930 77760 TRUE FALSE 67378.80944 88668.67803 75368.53352 61747.15216 65184.62092 74483.26869 70924.10591 62051.43373 68567.30138 0.982666783 1.293162721 1.099190605 0.900533504 0.950666274 1.086279716 1.034372135 0.90497121 1 16.06523312 3.941062181 6.915149492 0.979428335 1.152096308 0.360559058 0.091957836 0.221381478 22.014101 0.023455882 0.041450168 8730.963664 -3.941062181 0.172667973 SLAGSSGPGASSGTSGDHGELVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SLAGSSGPGASSGTSGDHGELVVR 24 0 P29692;P29692-2;E9PRY8;E9PK01;E9PQ49;A0A087X1X7;E9PI39;E9PPR1;E9PL12;E9PMW7;H0YCK7;E9PIZ1 P29692 EEF1D Elongation factor 1-delta 0 ;;;; 458.68 6.70E-229 3412730000 808353 805715 237266 435851 810760 847174 833473 874260 746473 FALSE TRUE 701527.1029 800422.2051 352008.6312 534817.6311 794627.4622 879765.332 752642.9167 687306.3025 658225.8123 1.065784857 1.216029803 0.534783998 0.812513914 1.207226224 1.336570696 1.143441814 1.044180112 1 19.32822308 3.234811497 24.99844976 1.142822026 0.9027251 0.271586626 0.194388587 141.5326925 943714.1885 0.061996215 0.073009472 1717.162901 -3.234811497 -0.240096926 SLALDIDRDAEDQNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLALDIDRDAEDQNR 15 1 H7BXT7;A0A0C4DH16;B8ZZS0;Q9NYM9;E9PQJ6 H7BXT7 BET1L BET1-like protein 0 166.9 1.59E-09 0 478040 518780 269950 302280 561250 612600 437910 577530 294850 FALSE TRUE 414865.8028 515372.1 400498.7229 370917.2941 550082.2231 636167.1184 395441.5556 454029.7038 259993.1689 1.595679627 1.982252465 1.540420176 1.42664246 2.115756446 2.446860897 1.520969021 1.746313973 1 17.98811419 0.952295289 1.787461484 5.11E-08 1.822444863 0.38884336 0.313244953 2.456568546 3.7847907 9.944099423 0.088880915 8.959737572 -0.952295289 1.822444812 SLAPDRS(ph)DDEHDPLDNTSRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLAPDRSDDEHDPLDNTSRPR 21 2 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR 211.94 6.38E-23 35609600000 4834650 4448400 2772930 3547200 4505980 5067690 4633880 5333950 4664880 TRUE FALSE 4195738.753 4419178.167 4113928.223 4352645.976 4416319.814 5262647.314 4184487.031 4193326.301 4113403.201 1.020016407 1.07433625 1.000127637 1.058161761 1.073641362 1.279390095 1.017281027 1.019429921 1 21.97190106 4.748001739 21.59262839 1.064153791 1.020016251 0.029812124 0.080944842 941.4969712 2152946.016 0.020440797 0.221221674 55975.98428 -4.748001739 -0.04413754 SLAS(ph)PAGLQDGSAQHHPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLASPAGLQDGSAQHHPK 18 0 F1LLU8;Q9NQG7-2;Q9NQG7-3;Q9NQG7;Q9NQG7-4 F1LLU8 HPS4 Hermansky-Pudlak syndrome 4 protein 1 S(0.453)LAS(0.547)PAGLQDGSAQHHPK 105.67 0.00078749 64554000 193450 181550 146370 184710 204710 188720 187610 259430 255330 TRUE FALSE 167885.0924 180357.3861 217155.0216 226651.2286 200636.6715 195980.1805 169415.6111 203952.9134 225145.1783 0.745674829 0.801071502 0.964511091 1.006689241 0.891143541 0.870461371 0.752472748 0.90587289 1 17.78049606 4.407052408 5.468501586 0.904493078 0.758170087 0.39376043 0.072937753 0.204103571 10.91250068 0.019750332 0.055478457 25530.09364 -4.407052408 -0.146322991 SLASEAPSQPSLNGGS(ph)PEGVESQDGVDHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLASEAPSQPSLNGGSPEGVESQDGVDHFR 30 0 P38935 P38935 IGHMBP2 DNA-binding protein SMUBP-2 1 SLASEAPS(0.016)QPS(0.025)LNGGS(0.958)PEGVESQDGVDHFR;SLASEAPSQPSLNGGS(1)PEGVESQDGVDHFR;SLASEAPSQPSLNGGS(1)PEGVESQDGVDHFR;SLASEAPSQPS(0.001)LNGGS(0.999)PEGVESQDGVDHFR 138.29 7.12E-07 1169250000 274620 290702 194942 253194 302803 339617 294706 340411 366410 TRUE FALSE 238328.2712 288792.3594 289216.6032 310685.5675 296777.8127 352682.2858 266125.4575 267616.7567 323093.4272 0.737645062 0.893835452 0.89514852 0.961596682 0.918551068 1.091579884 0.823679577 0.828295268 1 18.30159188 4.913078981 1.816926084 0.923347968 0.607217788 0.370504372 0.078430486 1.85483157 4.284921453 0.021885113 1.158003659 81861.36489 -4.913078981 -0.31613018 SLDADEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SLDADEFR 8 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ;;;;;;; 193.96 0.00039056 19904390000 10507210 11737730 7208340 8689850 11130790 11874450 11178830 12293410 11417180 FALSE TRUE 9118655.577 11660624.08 10694317.33 10663013.26 10909309.06 12331267.78 10094708.79 9664559.939 10067453.99 0.905755873 1.158249553 1.062266324 1.05915689 1.083621447 1.224864578 1.002707219 0.959980542 1 23.26319554 2.021466019 24.99956911 0.978395308 1.086358764 0.235422788 0.081037232 284.1607372 330935.5735 0.031385121 0.021157939 105.0669242 -2.021466019 0.107963456 SLDAFPEDFCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLDAFPEDFCR 11 0 E9PS17;Q96KG9-2;Q96KG9;Q96KG9-3;E9PK59;Q96KG9-4;E9PPN3;Q96KG9-5;Q96KG9-6 E9PS17 SCYL1 N-terminal kinase-like protein 0 ; 178.55 1.74E-05 258390000 228840 255850 147934 159053 215180 234000 225540 240840 220590 FALSE TRUE 198598.2142 254169.3045 219475.3772 195168.4146 210898.339 243002.1314 203667.1655 189338.2402 194512.1015 1.021006984 1.306701756 1.128337906 1.003374151 1.084242766 1.249290556 1.047066809 0.973400826 1 17.56950039 2.007978612 24.80453603 0.992430457 1.133244861 0.308061862 0.091810401 189.7819761 590006.2738 0.037499835 0.025231301 101.8541227 -2.007978612 0.140814404 SLDFLIELLHK ddPTM_MDA-MB-175_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 ; 150.94 3.37E-05 368530000 865370 762680 585560 752530 721480 658040 916080 1026690 1306940 FALSE TRUE 751009.1619 757669.9049 868738.7746 923403.4382 707123.9596 683355.2246 827238.7026 807140.3332 1152435.042 0.651671578 0.65745129 0.753828843 0.801262895 0.613591165 0.592966371 0.717818074 0.700378159 1 20.136254 1.229027067 4.532536108 1.029067109 0.685960326 0.715480396 0.062248318 0.126052186 5.445093826 0.141135638 0.016581013 16.94443401 -1.229027067 -0.343106783 SLDFYTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLDFYTR 7 0 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 ;; 137.18 0.0067653 596540000 759820 645230 399590 476290 563000 621910 528520 625970 892850 FALSE TRUE 659407.8619 640991.4416 592833.0605 584438.9241 551797.4015 645835.2801 477264.2117 492111.1868 787298.2901 0.837557848 0.814165926 0.752996759 0.742334807 0.700874635 0.820318408 0.606205066 0.625063198 1 19.58655082 4.251220998 1.652320431 0.727460694 0.843982909 0.056534773 0.110041007 1.067648302 5.089912919 0.031418875 0.149180797 17832.8599 -4.251220998 0.116522215 SLDGAEFSRPAS(ph)VSENHDAGPDGDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLDGAEFSRPASVSENHDAGPDGDKR 26 2 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 SLDGAEFS(0.001)RPAS(0.931)VS(0.068)ENHDAGPDGDKR;SLDGAEFSRPAS(0.959)VS(0.041)ENHDAGPDGDKR;SLDGAEFS(0.001)RPAS(0.837)VS(0.162)ENHDAGPDGDKR 226.74 7.71E-35 3291020000 612770 521580 353241 802260 631940 550180 559690 811400 1358930 TRUE FALSE 531790.8919 518153.7066 524069.5291 984425.3948 619365.6304 571345.7806 505411.3499 637888.4243 1198278.843 0.443795611 0.432414967 0.4373519 0.821532818 0.516879384 0.476805364 0.421781084 0.532337217 1 20.19253224 1.240209429 6.068267911 1.017005769 0.51005686 0.637041928 0.116279696 0.087089702 12.57329536 0.183057659 0.029668573 17.38639047 -1.240209429 -0.506948909 SLDGAEFSRPAS(ph)VSENHDAGPDGDKRDEDGESGGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLDGAEFSRPASVSENHDAGPDGDKRDEDGESGGQR 36 3 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 S(0.005)LDGAEFS(0.13)RPAS(0.741)VS(0.124)ENHDAGPDGDKRDEDGESGGQR;SLDGAEFS(0.001)RPAS(0.991)VS(0.007)ENHDAGPDGDKRDEDGESGGQR 223.84 2.50E-39 1136890000 413691 354038 174056 304452 429908 370695 435482 560307 196826 TRUE FALSE 359020.6862 351712.3011 258230.0638 373582.4799 421353.6719 384955.8765 393249.0227 440489.7084 173557.4545 2.068598478 2.026489165 1.48786501 2.15250034 2.427747475 2.218031358 2.265814648 2.538005121 1 17.40505381 3.520102495 24.83534415 2.176855183 1.867975915 0.042561427 0.446944412 1072.946378 619965.0489 0.119144089 0.176703432 3312.092785 -3.520102495 -0.308879268 SLDGAEFSRPASVS(ph)ENHDAGPDGDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLDGAEFSRPASVSENHDAGPDGDKR 26 2 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 SLDGAEFSRPAS(0.286)VS(0.714)ENHDAGPDGDKR 219.93 1.63E-34 1098800000 337660 275840 201240 451000 338240 299680 292350 445040 705110 TRUE FALSE 293037.3755 274027.9889 298560.3371 553406.4431 331509.6858 311208.8835 263997.942 349871.6593 621752.6991 0.47130857 0.440734699 0.480191461 0.890074854 0.533185761 0.500534833 0.424602808 0.56271836 1 19.24598134 1.241367824 5.896002159 1.017343215 0.537178641 0.550431902 0.131446969 0.107523857 13.64431555 0.208038398 0.03373381 17.43282715 -1.241367824 -0.480164574 SLDGEGNFNWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLDGEGNFNWR 11 0 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-2;Q9NZM1-5 Q9NZM1-6 MYOF Myoferlin 0 ; 128.52 0.00061442 193167000 170164 180182 131456 176838 184863 209564 155285 205618 277800 FALSE TRUE 147676.3963 178998.3726 195028.5613 216991.7707 181184.588 217626.0627 140225.4846 161648.1908 244958.8005 0.602862179 0.730728483 0.796168829 0.885829659 0.739653312 0.888419041 0.57244518 0.659899504 1 17.9021796 4.689742538 3.011447365 0.772896103 0.584566088 0.18392075 0.121292945 0.64445819 9.084653064 0.031172724 0.273189899 48948.8551 -4.689742538 -0.188330015 SLDGIPFTVDAGGLIHCIEDFHKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLDGIPFTVDAGGLIHCIEDFHKK 24 1 Q93052;A0A087WZF1 Q93052 LPP Lipoma-preferred partner 0 116.45 0.00035915 136270000 361530 317970 187880 184380 254020 185030 373950 408260 131830 FALSE TRUE 313752.8945 315881.2341 278739.3964 226246.2971 248965.499 192148.2238 337684.3866 320956.7761 116245.2076 2.699060899 2.717369952 2.397857101 1.946284942 2.141726994 1.65295609 2.904931683 2.761032328 1 16.82681171 4.076875519 3.716777823 2.176966635 2.706315857 0.17928762 0.536371196 0.462729985 12.58765107 0.1453221 0.33002541 11936.45923 -4.076875519 0.529349222 SLDLFNCEITNLEDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLDLFNCEITNLEDYR 16 0 Q9BTT0;Q9BTT0-3;Q9BTT0-2;E9PPH5 Q9BTT0 ANP32E Acidic leucine-rich nuclear phosphoprotein 32 family member E 0 ;;; 287.04 9.88E-36 302240000 86331.6 85781.7 53100.2 84427.4 81410.6 104642 94364.1 109056.6 110841.7 FALSE TRUE 74922.66032 85218.19436 78779.63433 103597.9316 79790.68834 108667.6455 85212.68411 85735.69477 97738.1205 0.766565389 0.871903347 0.806027719 1.059954202 0.81637224 1.111824587 0.871846969 0.877198112 1 16.57663374 3.780034319 24.96411552 0.943356327 0.820539212 0.336802094 0.092233174 620.4938148 373489.678 0.023020236 0.039871718 6026.072037 -3.780034319 -0.122817115 SLDLFNCEVTNLNDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLDLFNCEVTNLNDYR 16 0 Q92688;Q92688-2;P39687;H0YN26 Q92688;P39687 ANP32B;ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member B;Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;;; 378.62 2.00E-104 1909696000 550610 480755 327215 345384 445467 495852 467985 524151 534780 FALSE TRUE 477845.4934 477596.8887 485457.2685 423808.7161 436603.0782 514927.7473 422599.8867 412065.3876 471558.9176 1.013331475 1.012804277 1.029473201 0.898739691 0.925871746 1.091969058 0.896176217 0.873836486 1 18.84707851 4.792692209 0.322377946 0.918201351 1.114930189 0.115608051 0.066297653 19.95382748 2.072697775 0.171518767 1.623450308 62042.9171 -4.792692209 0.196728839 SLDLFNCEVTNLNDYRENVFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLDLFNCEVTNLNDYRENVFK 21 1 P39687;H0YN26 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ; 328.51 4.62E-80 973310000 543660 409010 139748 138240 360530 295490 538620 531340 43188 FALSE TRUE 471813.9535 406323.1864 207330.6002 169629.5049 353356.1584 306857.6915 486384.7153 417717.0759 38082.36384 12.38930324 10.66958942 5.444268142 4.454279823 9.278734898 8.057737508 12.77191504 10.96878013 1 15.21683541 4.441082266 8.51049038 8.00896432 11.96851988 0.198237091 3.359575381 0.396859168 85.08165018 0.873513064 2.349781632 27611.00827 -4.441082266 3.959555559 SLDLLAALPT(ph)PPHNQTEDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLDLLAALPTPPHNQTEDVR 20 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 SLDLLAALPT(0.999)PPHNQT(0.001)EDVR;SLDLLAALPT(1)PPHNQTEDVR;SLDLLAALPT(1)PPHNQTEDVR;SLDLLAALPT(1)PPHNQTEDVR;SLDLLAALPT(0.997)PPHNQT(0.003)EDVR;SLDLLAALPT(1)PPHNQTEDVR 173.89 1.55E-11 1011269000 803336 732141 446537 555056 701018 790345 688917 810626 841897 TRUE FALSE 697173.1122 727331.5176 662483.7868 681089.9483 687069.1133 820750.0836 622105.9354 637279.9382 742368.8958 0.939119508 0.979744062 0.892391627 0.917454856 0.925509026 1.105582532 0.838001079 0.858441055 1 19.50177674 SLDNEWDRDYGRPLDEQESQFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLDNEWDRDYGRPLDEQESQFR 22 2 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 ; 229.86 1.39E-26 338907000 117879 116207 59896 71533 119941 118811 109911 115447 63628 FALSE TRUE 102300.9915 115443.6286 88861.90594 87775.66096 117554.4088 123381.7361 99251.84814 90759.55746 56105.97033 1.823353039 2.057599715 1.583822638 1.564462043 2.095221027 2.1990839 1.769006891 1.617645269 1 15.77586668 1.216263392 1.863501829 0.662304826 1.876829015 0.642219336 0.205576322 0.63244085 1.986014435 1.394139656 0.060330264 16.4536931 -1.216263392 1.214524189 SLDQEIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLDQEIAR 8 0 P48681 P48681 NES Nestin 0 ;;;;; 154.35 0.00099204 12582200000 8899730 9129140 6179870 6852260 8748710 9383420 7692470 9541440 9949760 FALSE TRUE 7723608.131 9069170.078 9168475.802 8408170.363 8574627.788 9744406.239 6946455.443 7501077.308 8773510.708 0.880332673 1.033699095 1.045017908 0.958358705 0.977331432 1.110662147 0.79175323 0.85496873 1 23.06472282 2.230806472 24.99999297 0.872788709 1.001391504 0.336312914 0.078202113 181.25526 584375.5863 0.030755442 0.021167726 170.140017 -2.230806472 0.128602795 SLDQIETVNGGSVASRLTFPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLDQIETVNGGSVASRLTFPDR 22 1 Q8NE63 Q8NE63 HIPK4 Homeodomain-interacting protein kinase 4 0 ; 57.496 0.071067 512040000 273250 357050 232070 263208 377690 441040 230011 247560 365170 FALSE TRUE 237139.3202 354704.515 344299.8282 322973.3993 370174.7079 458007.0942 207704.5686 194621.2205 322000.0186 0.736457474 1.101566753 1.069254063 1.003022921 1.149610828 1.422382198 0.645045207 0.604413693 1 18.29670125 2.205228801 24.99999657 0.715160862 1.080470159 0.383921541 0.195764268 174.5208218 130895.3988 0.079378448 0.053520538 160.4090256 -2.205228801 0.365309297 SLDS(ph)DES(ph)EDEEDDYQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLDSDESEDEEDDYQQK 17 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 S(0.088)LDS(0.947)DES(0.965)EDEEDDYQQK 202.6 5.51E-12 450040000 235050 200170 146960 140830 222010 166300 197170 253220 287230 TRUE FALSE 203987.547 198855.0701 218030.3476 172807.604 217592.4354 172697.6686 178048.4837 199070.8736 253273.9966 0.805402646 0.785138122 0.86084774 0.682295089 0.859118734 0.681861032 0.702987619 0.785990178 1 17.95033944 1.243587588 5.238793279 1.012170948 0.767437592 0.555735067 0.064668336 0.11408874 8.734940412 0.100512243 0.015525623 17.52215784 -1.243587588 -0.244733357 SLDS(ph)DES(ph)EDEEDDYQQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLDSDESEDEEDDYQQKR 18 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 S(0.011)LDS(0.989)DES(1)EDEEDDYQQKR;S(0.041)LDS(0.959)DES(1)EDEEDDYQQKR;SLDS(1)DES(1)EDEEDDYQQKR;SLDS(1)DES(1)EDEEDDYQQKR;S(0.012)LDS(0.988)DES(1)EDEEDDYQQKR;SLDS(1)DES(1)EDEEDDYQQKR 246.34 9.77E-24 17787700000 7615020 6158840 3860950 4046320 6504860 4869950 6513570 8148750 4165810 TRUE FALSE 6608675.813 6118382.175 5728118.334 4965098.8 6375426.013 5057300.128 5881884.984 6406203.226 3673332.688 1.799095365 1.665621574 1.559379131 1.351660528 1.735597223 1.376760712 1.601239388 1.743975777 1 21.80865813 7.999999348 0.030259148 7.91E-09 3.768163615 0.222916585 0.212002075 6482.427512 19.42489991 852.7170608 1709.290379 99999849.77 -7.999999348 3.768163607 SLDS(ph)PTS(ph)SPGAGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLDSPTSSPGAGTR 14 0 Q9P107;K7EJC2 Q9P107 GMIP GEM-interacting protein 2 SLDS(1)PT(0.024)S(0.758)S(0.219)PGAGTR 211.53 5.41E-09 296060000 1345800 1356300 876990 1026800 1414000 1499600 1391300 1486800 1414000 TRUE FALSE 1167949.12 1347390.376 1301105.297 1259950.634 1385864.166 1557290.582 1256371.94 1168859.39 1246838.531 0.936728447 1.080645443 1.043523492 1.01051628 1.111502518 1.248991384 1.007646066 0.937458509 1 20.24984321 2.008651017 24.99984092 0.966749054 1.07493949 0.229658364 0.080184955 253.9764576 733941.8663 0.033642458 0.02264337 102.0119423 -2.008651017 0.108190436 SLDS(ph)PTSS(ph)PGAGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLDSPTSSPGAGTR 14 0 Q9P107;K7EJC2 Q9P107 GMIP GEM-interacting protein 2 SLDS(1)PT(0.006)S(0.48)S(0.514)PGAGTR 142.32 1.38E-05 274650000 499880 502590 328930 380660 502610 536590 513780 537760 469420 TRUE FALSE 433819.5915 499288.4532 488001.6482 467094.671 492609.0443 557232.9645 463953.6947 422764.2089 413925.7024 1.048061497 1.20622723 1.178959522 1.128450513 1.190090496 1.34621494 1.120862251 1.021352882 1 18.65901231 1.823938769 3.582142637 1.009846687 1.184536599 0.468164651 0.074340902 0.193149929 4.297512607 0.046438207 0.020219631 66.67127637 -1.823938769 0.174689912 SLDSEPSVPSAAKPPS(ph)PEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLDSEPSVPSAAKPPSPEK 19 1 Q7Z3K3-5;Q7Z3K3-7;Q7Z3K3-2;Q7Z3K3-3;Q7Z3K3-6;Q7Z3K3 Q7Z3K3-5 POGZ Pogo transposable element with ZNF domain 1 SLDSEPSVPSAAKPPS(1)PEK;SLDSEPSVPSAAKPPS(1)PEK;SLDSEPSVPSAAKPPS(1)PEK;SLDSEPSVPSAAKPPS(1)PEK 261.74 2.18E-31 3908110000 5106590 3601670 3589220 3373450 4172830 2691070 4917940 6067840 6184600 TRUE FALSE 4431741.193 3578010.393 5324978.797 4139443.382 4089798.847 2794597.204 4440998.936 4770279.636 5453463.634 0.812647061 0.656098699 0.976439774 0.759048498 0.749945195 0.512444456 0.81434465 0.874724754 1 22.37874138 1.554496752 2.321240595 0.993320516 0.748767908 0.327131981 0.117428098 0.381781485 4.028238572 0.161844863 0.032536325 35.85062669 -1.554496752 -0.244552609 SLDTITLS(ph)GDERDFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLDTITLSGDERDFGR 16 1 Q8N9U0;Q8N9U0-2;H0YJ73 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 SLDTITLS(1)GDERDFGR;SLDTIT(0.028)LS(0.972)GDERDFGR;SLDTITLS(1)GDERDFGR;S(0.001)LDT(0.025)IT(0.05)LS(0.924)GDERDFGR 205.36 1.38E-11 441790000 521610 534559 285096 326252 577810 654440 431360 634330 323659 TRUE FALSE 452677.9169 531047.4467 422969.3792 400332.503 566312.7115 679616.7303 389526.7736 498683.4659 285396.4017 1.586137436 1.860736307 1.482041738 1.402724423 1.984302213 2.381307985 1.364862245 1.747336206 1 18.12260762 0.930725072 1.959585169 8.04E-11 1.741207574 0.350475826 0.306007035 2.809214465 4.810176536 12.20868291 0.084270378 8.525602342 -0.930725072 1.741207574 SLDVNQDSELKFNEYWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLDVNQDSELKFNEYWR 17 1 Q99584 Q99584 S100A13 Protein S100-A13 0 ; 200.67 1.11E-11 980390000 1167690 1118030 577820 646480 1035800 949900 1184960 1349610 418449 FALSE TRUE 1013376.808 1110685.587 857255.6847 793273.1648 1015189.607 986443.2677 1070042.762 1061006.404 368980.4359 2.746424226 3.010147637 2.323309317 2.149905761 2.751337219 2.673429731 2.899998638 2.875508566 1 18.4931848 4.239741033 24.99708333 2.4690682 2.878285971 0.105850014 0.556614888 78.2019347 1655855.799 0.138770288 0.327749735 17367.64899 -4.239741033 0.409217771 SLEAEILQLQEELASSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLEAEILQLQEELASSER 18 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 188.31 8.95E-14 5486400 10207 7906.4 5232.8 4356.4 7719.4 9956.9 8482.8 9691.7 7751.2 FALSE TRUE 8858.119089 7854.462338 7763.399583 5345.587203 7565.799043 10339.94839 7660.139362 7619.205376 6834.861966 1.296020188 1.149176439 1.135853163 0.782106095 1.106942478 1.512824756 1.120745291 1.114756291 1 12.73869649 7.961179708 0.007602835 0.022090849 2.347841779 0.01404522 0.185185217 584000.0766 446.3756062 62591.46577 74456.23623 91449157.25 -7.961179708 2.325750931 SLEAQVAHADQQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLEAQVAHADQQLR 14 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;; 179.79 1.83E-06 2528800000 3564100 4042760 2195040 2903910 4012470 4509390 3164760 3873470 4176020 FALSE TRUE 3093095.155 4016202.843 3256568.686 3563287.149 3932629.697 4682869.151 2857842.062 3045158.584 3682335.673 0.839981856 1.090667229 0.884375835 0.967670377 1.067971539 1.271711644 0.776094934 0.826963877 1 21.81218971 SLEATDSAFDNPDY(ph)WHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLEATDSAFDNPDYWHSR 18 0 F8VYK4;P21860-5;P21860-4;P21860;B3KWG5;F8VW56 F8VYK4 ERBB3 Receptor tyrosine-protein kinase erbB-3 1 SLEATDSAFDNPDY(1)WHSR 217.88 4.75E-18 46557000 18630 28889 23111 39895 49295 62217 27839 58304 40090 TRUE FALSE 16167.9983 28699.22626 34287.5569 48953.76951 48314.12594 64610.52825 25139.17806 45836.14332 35350.60587 0.457361279 0.811845386 0.969928409 1.384807086 1.366712812 1.82770639 0.711138535 1.296615495 1 15.10944732 4.329378041 1.664397278 1.257506633 0.453177875 0.462528658 0.288528706 0.449832954 2.065729932 0.081236863 0.456328486 21349.02477 -4.329378041 -0.804328758 SLEDQVEMLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLEDQVEMLR 10 0 K7ELL7;P14314-2;P14314 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;; 209.73 2.10E-07 712557000 640345 551988 387836 453273 564774 747357 484968 483328 446220 FALSE TRUE 555721.7858 548361.9545 575394.7868 556195.5625 553536.1024 776108.3074 437935.878 379972.0685 393468.3799 1.412367077 1.393662064 1.462366015 1.413571181 1.406812162 1.972479485 1.113014159 0.965699121 1 18.58588818 2.020989931 24.99858312 0.998086518 1.497736746 0.646854019 0.170344424 134.1716112 159795.0387 0.068356672 0.046081437 104.9518096 -2.020989931 0.499650228 SLEEIYLFSLPIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLEEIYLFSLPIK 13 0 P15880;H0YEN5;E9PQD7;E9PPT0;E9PMM9;H3BNG3;H0YE27 P15880 RPS2 40S ribosomal protein S2 0 140.3 9.14E-05 62238000 128790 126960 87281 96662 123890 114330 129650 152770 145190 FALSE TRUE 111770.0752 126125.9914 129490.3835 118610.5845 121424.8314 118728.3491 117076.563 120101.3244 128025.8036 0.873027718 0.985160709 1.011439725 0.926458426 0.948440299 0.927378276 0.914476298 0.938102484 1 16.96607509 SLELYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLELYR 6 0 D6RHI9;O00584;H0YAE9;D6REQ6;A0A087WZM2;Q07343-4;Q07343-2 D6RHI9 RNASET2 Ribonuclease T2 0 98.415 0.092966 292480000 481460 501410 264940 326820 478660 552760 430510 466310 422450 FALSE TRUE 417833.8411 498116.2047 393065.8702 401029.4761 469135.6025 574025.0349 388759.2065 366593.2353 372508.4423 1.121676166 1.337194405 1.055186475 1.076564799 1.259395894 1.540971881 1.043625224 0.98412061 1 18.5069136 2.02424215 24.99908723 0.997809885 1.228579512 0.365147717 0.139495111 238.275979 245714.8631 0.05857153 0.039486945 105.7406924 -2.02424215 0.230769627 SLENETLNKEEDCHS(ph)PTSKPPKPDQPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLENETLNKEEDCHSPTSKPPKPDQPLK 28 3 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SLENETLNKEEDCHS(0.997)PT(0.003)SKPPKPDQPLK;SLENET(0.001)LNKEEDCHS(0.991)PT(0.007)S(0.001)KPPKPDQPLK;SLENETLNKEEDCHS(0.971)PT(0.025)S(0.005)KPPKPDQPLK 200.15 3.24E-25 3616570000 5014860 3321590 3332260 2653220 2541810 1437010 5194150 5785450 3900790 TRUE FALSE 4352133.545 3299770.257 4943752.082 3255674.153 2491232.954 1492292.705 4690422.132 4548276.54 3439643.05 1.265286392 0.959335085 1.437286372 0.94651512 0.72427078 0.433851037 1.363636303 1.322310622 1 21.71382743 3.664041892 24.99964512 0.995045839 1.194520984 0.140603046 0.289224111 361.9269043 121418.2541 0.089371978 0.132560081 4613.620755 -3.664041892 0.199475146 SLENPT(ph)PPFTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLENPTPPFTPK 12 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 SLENPT(1)PPFTPK;SLENPT(1)PPFTPK 269.05 3.67E-21 247733000 790810 638580 503350 545490 741690 591990 839000 963530 814260 TRUE FALSE 686302.4548 634385.1259 746771.7436 669351.8418 726931.8201 614764.2384 757633.9091 757486.6077 717999.1104 0.955854185 0.883545838 1.040073355 0.93224606 1.012441115 0.856218663 1.055201738 1.054996582 1 19.45362253 2.190186766 24.99985311 1.041307456 0.950428922 0.367135296 0.055455088 114.1592481 58997.21038 0.02115822 0.014264905 154.9482824 -2.190186766 -0.090878534 SLENYHFVDEHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLENYHFVDEHGK 13 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 189.86 2.84E-06 1117090000 1177410 976970 642620 770960 889020 836800 919810 1154920 2299900 FALSE TRUE 1021812.285 970552.2197 953393.1814 946018.2514 871330.2413 868992.2375 830606.9678 907949.3456 2028008.442 0.503850114 0.478574053 0.470113024 0.466476486 0.429648232 0.428495375 0.409567806 0.447704914 1 20.95163223 1.238291242 24.99874951 1.00000061 0.451953285 0.974931607 0.027497509 0.990413677 91741.29721 0.041823836 0.007391189 17.30976778 -1.238291242 -0.548047325 SLENYHFVDEHGKDQGINIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLENYHFVDEHGKDQGINIR 20 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 207.22 4.44E-22 342740000 376400 291000 153520 174710 302180 292360 323230 406310 153820 FALSE TRUE 326657.7863 289088.4018 227762.7855 214380.5758 296167.2092 303607.2784 291883.2044 319423.7684 135635.5748 2.408348892 2.131361202 1.679226013 1.580563035 2.183551104 2.23840448 2.151966434 2.355014669 1 17.0493761 1.229771035 24.97313288 0.999997902 2.086215159 0.624417926 0.265904163 251.3906585 714200.63 0.826133699 0.070901309 16.97348556 -1.229771035 1.086217258 SLEPEPQQSLEDGS(ph)PAKGEPSQAWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLEPEPQQSLEDGSPAKGEPSQAWR 25 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 SLEPEPQQSLEDGS(1)PAKGEPSQAWR;SLEPEPQQS(0.042)LEDGS(0.958)PAKGEPSQAWR;SLEPEPQQSLEDGS(1)PAKGEPSQAWR;SLEPEPQQSLEDGS(1)PAKGEPSQAWR 202.81 3.34E-25 4463310000 1824770 1700690 1173800 1380780 1923690 1492140 1909420 2403050 1912450 TRUE FALSE 1583622.021 1689518.055 1741453.606 1694307.203 1885412.333 1549543.591 1724244.742 1889176.458 1686362.34 0.939075775 1.001871315 1.032668701 1.004711243 1.118035127 0.918867526 1.022463976 1.120267225 1 20.68548312 6.204526485 0.801351323 1.040239498 1.92E-13 0.193666374 0.057975411 35.71776288 2.705130521 0.020766335 55.3927333 1601498.312 -6.204526485 -1.040239498 SLEPSPS(ph)PGPQEEDGEVALVLLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLEPSPSPGPQEEDGEVALVLLGR 24 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 SLEPS(0.002)PS(0.998)PGPQEEDGEVALVLLGR 172.75 3.24E-12 34438000 54180 47081 37737 68812 54434 54379 41530 71252 93613 TRUE FALSE 47019.97573 46771.72181 55986.73942 84436.81633 53350.8699 56470.99532 37502.42699 56015.31428 82546.17778 0.569620266 0.566612811 0.678247509 1.022904011 0.646315448 0.684113993 0.454320575 0.678593677 1 16.33291379 4.15970357 4.884706663 0.724330441 0.568025008 0.15331419 0.166161622 0.421922318 17.82310001 0.044481502 0.099284165 14444.53516 -4.15970357 -0.156305432 SLEQYDQVLDGAHGAS(ph)LTDLANLSEGVSLAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 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(0.989)LT(0.011)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(1)LTDLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.998)LT(0.002)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.998)LT(0.002)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.999)LT(0.001)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.975)LT(0.025)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.997)LT(0.003)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(1)LTDLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.779)LT(0.219)DLANLS(0.002)EGVSLAER;SLEQYDQVLDGAHGAS(0.995)LT(0.005)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.991)LT(0.009)DLANLSEGVSLAER 362.16 1.06E-132 2485682000 1364353 1227056 874990 920501.9 1263048 1459995 1185045 1327722 1391400 TRUE FALSE 1184050.294 1218995.388 1298138.091 1129515.925 1237915.816 1516161.952 1070119.518 1043798.983 1226910.277 0.965066734 0.993548926 1.058054623 0.920618196 1.008970125 1.235756176 0.872206826 0.850754128 1 20.22659832 SLESINSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLESINSR 8 0 E5RI99;P62888;E5RJH3;A0A0C4DH44 E5RI99 RPL30 60S ribosomal protein L30 0 ; 179.17 0.00057169 926540000 621290 505390 353350 466680 551850 555930 568620 587080 630560 FALSE TRUE 539184.9524 502070.0598 524231.2419 572646.8268 540869.2647 577316.9868 513475.3199 461537.5107 556015.9151 0.969729351 0.902977858 0.942834958 1.029910855 0.972758603 1.038310183 0.923490328 0.830079676 1 19.08476665 2.010158825 24.71531336 0.895067365 0.974160354 0.173992055 0.056300191 223.6805031 544187.9827 0.023002865 0.015488549 102.3667287 -2.010158825 0.079092989 SLESLHSFVAAATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLESLHSFVAAATK 14 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 189.5 7.11E-07 449850000 624130 625590 245490 417410 603200 587990 634910 749810 724690 FALSE TRUE 541649.6392 621480.4581 364209.7851 512189.3202 591197.5001 610610.3558 573336.5259 589468.9665 639017.9738 0.847628175 0.972555521 0.569952333 0.801525687 0.925165683 0.955544884 0.897215023 0.922460699 1 19.28549699 3.233767776 5.814578627 0.936112123 0.793368004 0.33000306 0.100642874 0.198556317 23.2636319 0.030373551 0.03668049 1713.041071 -3.233767776 -0.142744119 SLETCMYDHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLETCMYDHK 10 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 136.48 0.00011669 391440000 364810 335510 242340 262090 358870 376920 407340 475490 487380 FALSE TRUE 316599.4342 333306.0127 359536.4346 321601.5403 351729.1891 391420.3563 367836.2295 373810.1638 429762.4916 0.736684658 0.775558638 0.836593331 0.748323892 0.818426912 0.910782965 0.855905847 0.869806396 1 18.71318005 -2 0.223356082 2.00202282 0.730059374 0.735050328 0.040403848 51.9855936 0.807112302 23.19452472 0.190706367 0.01 2 -1.271963447 SLETEHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLETEHK 7 0 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ; 91.906 0.01606 659170000 837840 648170 452560 755990 784500 814440 612080 1208950 1071430 FALSE TRUE 727117.3212 643912.1286 671419.5297 927649.0841 768889.9848 845772.0338 552720.5758 950425.4506 944766.766 0.769626269 0.68155671 0.710672257 0.981881579 0.813841058 0.895217809 0.58503389 1.005989504 1 19.84959869 1.6123734 12.52624874 1.004276126 0.784840197 0.422186621 0.109660194 0.069069861 53.00651523 0.063915258 0.027779413 40.96126875 -1.6123734 -0.21943593 SLETENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLETENR 7 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 163.34 0.0028812 28605700000 23749700 23389900 14562530 16470060 19665500 24569600 22291600 24199700 25140200 FALSE TRUE 20611116.97 23236250.21 21605018.22 20209838.85 19274195.02 25514808.41 20129764.06 19024782.48 22168154.2 0.929762433 1.048181549 0.974597074 0.911660875 0.869454211 1.150966751 0.908048721 0.858203273 1 24.40198532 SLETENRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SLETENRR 8 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;; 151.97 0.00074486 23538070000 11703780 11412750 6677880 8136930 10347390 12119420 10971070 11922920 8583460 FALSE TRUE 10157095.82 11337778.89 9907325.104 9984544.322 10141497.18 12585661.93 9907097.32 9373296.342 7568733.137 1.341980968 1.497975776 1.308980634 1.319183031 1.339920037 1.662849212 1.308950539 1.238423415 1 22.85162041 1.398719327 1.867563108 0.944624779 1.404399395 0.583839358 0.109070846 0.430153765 1.980039296 0.321407728 0.030569761 25.04490143 -1.398719327 0.459774616 SLFDYHDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLFDYHDTR 9 0 A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599;Q92599-3;C9J4G8;C9JV02 A0A087X142 8-Sep Septin-8 0 ;;;;; 170.85 5.74E-05 3086880000 4575410 4820880 2326520 4041840 5190310 5371240 4670030 5480200 6038140 FALSE TRUE 3970757.976 4789211.322 3451632.854 4959601.548 5087032.986 5577875.078 4217131.209 4308301.877 5324317.968 0.745777769 0.899497617 0.648276995 0.93149988 0.955433732 1.047622458 0.79205097 0.809174415 1 22.3441653 3.698467705 24.99640467 0.909225564 0.77801535 0.358944488 0.097976425 672.950575 419559.0233 0.028020166 0.041561243 4994.220409 -3.698467705 -0.131210214 SLFNYHDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLFNYHDTR 9 0 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2 D6RGI3 11-Sep Septin-11 0 ; 109.16 0.0024948 1045780000 2509200 2067100 985220 1680410 2351900 2302500 2313000 2445000 2607900 FALSE TRUE 2177602.862 2053521.084 1461675.687 2061972.774 2305101.791 2391078.665 2088685.616 1922155.777 2299597.033 0.946949762 0.892991709 0.635622531 0.896667001 1.002393793 1.039781592 0.908283315 0.835866349 1 21.13294964 3.48567448 24.71106317 0.943177665 0.820997773 0.273934996 0.096731008 511.4890066 1477740.294 0.028904168 0.039294425 3059.669239 -3.48567448 -0.122179892 SLFS(ph)PQNTLAAPTGHPPTSGVEK ddPTM_MDA-MB-175_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(0.665)PQNT(0.335)LAAPTGHPPTSGVEK 166.08 7.98E-12 185730000 210060 177860 85154 137930 148170 134730 191610 211130 182700 TRUE FALSE 182300.0388 176691.6259 126334.7592 169249.1146 145221.7069 139913.1503 173027.6917 165981.4925 161101.4141 1.13158559 1.096772657 0.784193981 1.050574978 0.901430367 0.868478722 1.074029627 1.030291965 1 17.29760963 4.449254883 24.96811795 0.967174097 1.122882728 0.346828035 0.088854247 203.899103 182692.321 0.022152621 0.058613051 28135.51588 -4.449254883 0.155708631 SLFSPQNT(ph)LAAPTGHPPTSGVEK ddPTM_MDA-MB-175_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(0.319)PQNT(0.681)LAAPTGHPPTSGVEK 137.5 2.68E-05 181940000 141810 137700 63061 100350 120530 108540 130950 159170 160830 TRUE FALSE 123069.4492 136795.4396 93557.51053 123136.0013 118131.6888 112715.604 118250.4892 125132.7342 141816.8606 0.867805483 0.964592214 0.659706541 0.868274764 0.832987617 0.79479692 0.83382532 0.882354423 1 17.11366954 1.24329083 2.029402257 1.053302064 0.830190159 0.331782574 0.075517842 0.883993703 3.599404679 0.371722646 0.019902747 17.51018885 -1.24329083 -0.223111905 SLGDDISSETSGDFRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLGDDISSETSGDFRK 16 1 P12429;D6RA82;D6RFG5 P12429 ANXA3 Annexin A3;Annexin 0 149.6 1.31E-06 265620000 186920 126480 97591 89518 145000 113590 161370 127340 134970 FALSE TRUE 162218.0484 125649.1446 144786.334 109844.4301 142114.7837 117959.8808 145720.3622 100109.332 119014.0004 1.363016518 1.055750955 1.216548755 0.922953852 1.194101394 0.991142895 1.224396809 0.841155928 1 16.86077177 8 0.445540112 1.00292953 7.762195444 0.355412383 0.127878358 107.7656618 1.368378944 0.093547197 657.8927235 100000000 -8 6.759265914 SLGGES(ph)SGGTT(ph)PVGSFHTEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLGGESSGGTTPVGSFHTEAAR 22 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 2 S(0.003)LGGES(0.497)S(0.493)GGT(0.054)T(0.953)PVGSFHTEAAR 80.406 0.011594 197820000 89413 124440 58095 82245 161800 154280 114770 150640 147600 TRUE FALSE 77596.84551 123622.5454 86189.93632 100919.9843 158580.4966 160215.2514 103639.6231 118426.8083 130150.8961 0.596206771 0.94984014 0.662230833 0.775407525 1.218435687 1.230996145 0.796303569 0.909919269 1 16.98982572 3.379246086 10.1334446 1.008177046 0.751092369 0.448212464 0.156301454 0.361996618 34.43422569 0.047416039 0.061218271 2394.672277 -3.379246086 -0.257084678 SLGGES(ph)SGGTTPVGSFHTEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLGGESSGGTTPVGSFHTEAAR 22 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 SLGGES(0.597)S(0.403)GGTTPVGSFHTEAAR 304.37 2.84E-56 514970000 213720 250610 72598 163580 263900 286850 222120 268120 245140 TRUE FALSE 185476.3605 248963.7264 107706.6356 200723.3392 258648.9063 297885.3051 200578.8366 210784.6245 216159.8285 0.858051942 1.151757605 0.498273136 0.928587613 1.196563247 1.37807893 0.927919114 0.975133197 1 17.72173891 3.463693891 18.10591907 1.080276127 0.841906526 0.265759605 0.199241179 13.10814192 17673.05136 0.058991489 0.076347481 2908.666244 -3.463693891 -0.238369601 SLGGESS(ph)GGTT(ph)PVGSFHTEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLGGESSGGTTPVGSFHTEAAR 22 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 2 S(0.046)LGGES(0.176)S(0.735)GGT(0.382)T(0.661)PVGSFHTEAAR;SLGGES(0.033)S(0.967)GGT(0.001)T(0.999)PVGSFHTEAAR;S(0.001)LGGES(0.179)S(0.82)GGT(0.002)T(0.998)PVGSFHTEAAR 200.97 2.81E-22 714180000 321068 391018 171944 298323 511020 543010 402860 502060 486198 TRUE FALSE 278638.0503 388449.377 255096.6935 366061.7967 500851.7018 563899.9461 363790.6992 394698.376 428720.2263 0.649929799 0.906067298 0.595019031 0.853847741 1.168248361 1.315309872 0.848550353 0.920643235 1 18.70967696 3.451992506 7.111862421 1.031339958 0.733674556 0.510140598 0.149833682 0.161304216 31.03114806 0.045876371 0.060268695 2831.343142 -3.451992506 -0.297665402 SLGGESS(ph)GGTTPVGSFHTEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLGGESSGGTTPVGSFHTEAAR 22 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 SLGGES(0.025)S(0.975)GGTTPVGSFHTEAAR;SLGGES(0.151)S(0.849)GGTTPVGSFHTEAAR;SLGGES(0.134)S(0.866)GGTTPVGSFHTEAAR 279.04 9.24E-46 1514630000 680370 723830 273658 464850 773230 814940 662560 784500 754980 TRUE FALSE 590457.3807 719075.1131 405999.9241 570401.2973 757844.2358 846291.2691 598305.0332 616740.78 665727.1245 0.886936042 1.080134918 0.609859369 0.856809459 1.138370675 1.271228463 0.898724134 0.926416781 1 19.34457143 3.264152512 23.95370016 1.031978813 0.85651506 0.270181455 0.152844449 223.1767834 208888.3936 0.046762044 0.060340975 1837.183395 -3.264152512 -0.175463753 SLGGESSGGTT(ph)PVGSFHTEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLGGESSGGTTPVGSFHTEAAR 22 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 SLGGESSGGT(0.003)T(0.997)PVGSFHTEAAR 154.92 8.45E-08 174650000 27826 31627 12541 36520 54647 58028 51885 64567 55605 TRUE FALSE 24148.7236 31419.24015 18605.86955 44812.42417 53559.63162 60260.37471 46853.20069 50759.84951 49031.44025 0.492515078 0.640797823 0.379468142 0.913952842 1.092352812 1.229014983 0.955574636 1.03525104 1 15.58141952 3.585173018 4.254922099 1.056043603 0.520678542 0.875727053 0.095934508 0.07476002 2.276343634 0.026991248 0.040640611 3847.450298 -3.585173018 -0.535365061 SLGGQQGS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLGGQQGSPK 10 0 A0A0C4DGT3;A0A3B3IU98;Q6DN90-2;A0A3B3IRZ4;Q6DN90-3;A0A2R8Y7T6;Q6DN90;A0A2R8Y695 A0A0C4DGT3;A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 SLGGQQGS(1)PK;SLGGQQGS(1)PK;SLGGQQGS(1)PK;SLGGQQGS(1)PK;SLGGQQGS(1)PK;SLGGQQGS(1)PK 153.81 1.64E-05 1758862000 2787560 2496350 1829400 1880930 2349900 2260990 3062540 3446060 3112780 TRUE FALSE 2419176.883 2479951.312 2714103.959 2308023.905 2303141.588 2347971.748 2765535.342 2709146.886 2744790.694 0.881370258 0.903511994 0.988820009 0.840874282 0.839095525 0.85542834 1.007557825 0.987014016 1 21.38826471 2.232292356 24.99405288 0.99625248 0.88634559 0.611549301 0.042562038 108.2320427 431558.9903 0.018362199 0.012724163 170.7231266 -2.232292356 -0.10990689 SLGGSSLTETEAAPSLTLPSVDYIPQDS(ph)PTPSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLGGSSLTETEAAPSLTLPSVDYIPQDSPTPSVR 34 0 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 SLGGSSLTETEAAPSLTLPSVDYIPQDS(0.699)PT(0.227)PS(0.074)VR;SLGGSSLTETEAAPSLTLPSVDYIPQDS(0.734)PT(0.206)PS(0.059)VR;SLGGSSLTETEAAPSLTLPSVDYIPQDS(0.751)PT(0.209)PS(0.04)VR;SLGGSSLTETEAAPSLTLPSVDYIPQDS(0.784)PT(0.176)PS(0.04)VR 170.89 8.26E-15 551080000 596109 637688 357388 497108 634254 685767 545270 696619 625013 TRUE FALSE 517331.6853 633498.9855 530222.0322 609983.9692 621633.5863 712148.9002 492389.7993 547652.4479 551124.6752 0.938683584 1.149465836 0.962072751 1.10679851 1.127936408 1.292173863 0.893427243 0.993699743 1 19.0720192 SLGLSLS(ph)GGDQEDAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLGLSLSGGDQEDAGR 16 0 C9JEV6;Q9UJ70;Q9UJ70-2;H7C3G9;H0YEB7;H0YE82;H7C1L7 C9JEV6 NAGK N-acetyl-D-glucosamine kinase 1 SLGLSLS(1)GGDQEDAGR;SLGLS(0.001)LS(0.999)GGDQEDAGR;SLGLSLS(1)GGDQEDAGR;SLGLSLS(1)GGDQEDAGR;SLGLSLS(1)GGDQEDAGR;SLGLSLS(1)GGDQEDAGR 299.23 8.42E-46 1683760000 2139030 1846690 1162940 1377277 1870260 2081740 1885370 2046820 1992090 TRUE FALSE 1856351.766 1834558.972 1725341.674 1690008.793 1833045.485 2161825.885 1702527.108 1609123.471 1756587.39 1.056794428 1.044388103 0.982212262 0.96209776 1.043526497 1.230696462 0.969224257 0.916050907 1 20.74434392 2.024160726 24.99840757 0.949211458 1.049637156 0.253906745 0.073625895 294.2836352 304485.5355 0.031398158 0.02116762 105.7208694 -2.024160726 0.100425699 SLGNILQAKPTS(ph)SPAKGPPQK ddPTM_MDA-MB-175_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(0.283)S(0.359)S(0.359)PAKGPPQK 92.147 0.000997 2429800000 676510 430630 397490 411350 435970 274370 621190 792410 331990 TRUE FALSE 587107.4894 427801.1632 589717.4935 504753.3046 427295.05 284925.1914 560947.0894 622959.288 292742.5204 2.005542238 1.461356425 2.014457936 1.724222719 1.459627557 0.97329623 1.916179066 2.128010947 1 18.15927278 3.458691497 13.92052803 1.581015517 1.803671768 0.117431958 0.385218225 4.859370319 3664.024449 0.117590848 0.152329728 2875.355165 -3.458691497 0.22265625 SLGNILQAKPTSS(ph)PAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLGNILQAKPTSSPAK 16 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 SLGNILQAKPT(0.013)S(0.236)S(0.751)PAK;SLGNILQAKPT(0.002)S(0.216)S(0.782)PAK 190.25 5.37E-10 1559440000 1594030 1182250 1130790 1393310 1235240 885780 1532740 1746730 2723500 TRUE FALSE 1383374.897 1174483.722 1677643.826 1709682.331 1210661.141 919856.5298 1384095.111 1373205.383 2401530.933 0.576038758 0.489056254 0.698572649 0.711913516 0.504120569 0.383029224 0.576338656 0.571804162 1 21.19552296 1.23775482 6.664570561 1.011397422 0.562999435 0.672879379 0.095587215 0.076243129 16.89483637 0.154433889 0.025089596 17.2884007 -1.23775482 -0.448397987 SLGNILQAKPTSS(ph)PAKGPPQK ddPTM_MDA-MB-175_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(0.011)S(0.048)S(0.941)PAKGPPQK 125.39 1.21E-05 3114000000 941950 639350 449800 514800 526050 391820 811640 986540 384310 TRUE FALSE 817468.9209 635150.0678 667324.7845 631693.2082 515582.6342 406893.5689 732927.2777 775576.0983 338877.3096 2.412285797 1.874277356 1.969222387 1.864076438 1.521443365 1.200710574 2.162810129 2.288663408 1 18.37040352 6.759323343 0.904446215 1.751940151 27.96166206 0.235131499 0.397513894 135.6759063 3.586055009 0.136599266 6871.938906 5745440.649 -6.759323343 26.20972191 SLGS(ph)PLLHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLGSPLLHER 10 0 E7EV32;E7EMT6;E7ENY2;E7EVA2;E7EW82;H7C3L4;E7EQA9;Q92844 E7EV32 TANK TRAF family member-associated NF-kappa-B activator 1 S(0.016)LGS(0.984)PLLHER;SLGS(1)PLLHER;S(0.094)LGS(0.906)PLLHER 128.21 0.00021613 633010000 615850 637700 296487 385005 575490 644920 487020 522650 476850 TRUE FALSE 534463.8621 633510.9067 439869.1049 472426.2697 564038.8749 669730.4897 439788.8754 410885.3648 420477.3362 1.271088394 1.506646975 1.046118463 1.123547523 1.341425153 1.592786179 1.045927658 0.977187899 1 18.68166852 2.02805393 24.9369419 0.994342401 1.304220547 0.454739879 0.15857498 183.8086936 163385.5053 0.06704272 0.045199265 106.6728577 -2.02805393 0.309878146 SLGS(ph)VQAPSYGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLGSVQAPSYGAR 13 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.002)LGS(0.933)VQAPS(0.064)YGAR;SLGS(1)VQAPSYGAR;SLGS(0.81)VQAPS(0.19)YGAR 253.82 9.01E-24 2184220000 388590 532870 344884 295274 452880 419138 417807 423045 660930 TRUE FALSE 337236.8469 529369.5419 511671.056 362320.4747 443868.574 435262.5101 377288.1414 332580.1189 582795.6083 0.57865372 0.908327953 0.877959697 0.6216939 0.761619627 0.746852763 0.647376432 0.570663392 1 19.15263048 3.74113176 24.99830973 0.706283912 0.800315201 0.02923305 0.144077426 601.9220857 5852240.156 0.03768246 0.061657925 5509.748299 -3.74113176 0.094031289 SLGSASPGPGQPPLS(ph)SPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLGSASPGPGQPPLSSPTR 19 0 Q9C0B5;Q9C0B5-2 Q9C0B5 ZDHHC5 Palmitoyltransferase ZDHHC5 1 SLGSASPGPGQPPLS(0.498)S(0.498)PT(0.005)R 143.67 1.50E-07 104500000 170870 124800 73278 141650 182910 177260 92812 213220 158490 TRUE FALSE 148289.0966 123980.1806 108715.4859 173813.7975 179270.4489 184079.3069 83811.10653 167624.5623 139753.4928 1.061076139 0.887134755 0.777908901 1.24371702 1.28276185 1.317171423 0.599706704 1.199430218 1 17.09252481 5.115453919 18.86039715 1.04092352 4.096655401 0.000827689 0.23338641 9961.919547 1604754.672 0.055334543 18246.26839 130452.9543 -5.115453919 3.05573188 SLGSVQAPS(ph)YGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLGSVQAPSYGAR 13 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 SLGS(0.002)VQAPS(0.996)Y(0.002)GAR 76.563 0.029715 449480000 138630 126330 84925 95826 106810 86423 125530 128100 217850 TRUE FALSE 120309.6943 125500.1299 125995.0141 117584.7579 104684.69 89747.74873 113356.1199 100706.8119 192096.0212 0.626299772 0.653319778 0.655896011 0.612114489 0.54496022 0.467202539 0.590101342 0.524252461 1 17.55146811 1.233719322 24.99999163 1.000000636 0.582108225 0.830426596 0.059032478 65.60907397 338758.2824 0.127704364 0.015980314 17.12849961 -1.233719322 -0.417892411 SLGSVQAPS(ph)YGARPVSSAASVYAGAGGSGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLGSVQAPSYGARPVSSAASVYAGAGGSGSR 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 SLGS(0.001)VQAPS(0.998)YGARPVS(0.001)SAASVYAGAGGSGSR 105.67 8.98E-05 156500000 36409 54400 34906 26437 40178 51448 45021 36823 28027 TRUE FALSE 31597.4584 54042.64282 51786.65835 32439.92491 39378.53641 53427.23785 40654.87035 28948.68801 24713.67999 1.278541213 2.186750126 2.09546528 1.312630289 1.593390237 2.161848736 1.645035072 1.171362906 1 14.59302223 1.718950345 3.106087429 1.037550185 1.783921503 0.436000175 0.320282459 0.195389909 4.096152168 0.243060943 0.086544106 52.35405737 -1.718950345 0.746371318 SLGSVQAPSYGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLGSVQAPSYGAR 13 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 184.44 2.21E-05 922740000 861920 752148 503050 577801 656417 729100 739040 808563 653045 FALSE TRUE 748015.0882 747207.0903 746326.6626 708999.5482 643355.586 757148.9488 667368.0145 635658.0947 575842.7641 1.298991903 1.297588746 1.296059809 1.231238096 1.117241765 1.31485363 1.158941392 1.103874416 1 19.13531541 -0.422364099 0.392204311 1.08E-15 1.294691568 0.716599435 0.056242046 13.42335521 0.620081024 10.5983712 0.063162355 0.378125443 0.422364099 1.294691568 SLGTADVHFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SLGTADVHFER 11 0 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 ;;;;;;; 212.12 7.01E-09 10407480000 9190910 9104440 5183640 6283050 9050100 8808360 8355870 8872760 8462570 FALSE TRUE 7976307.957 9044632.334 7690465.642 7709712.533 8870020.716 9147223.309 7545519.013 6975389.322 7462134.615 1.068904324 1.212070379 1.030598621 1.033177895 1.188670692 1.225818587 1.011174336 0.934771306 1 22.83115696 2.048284588 8.210671333 0.965694491 1.124494181 0.491932465 0.070271797 0.199694893 30.32795478 0.029595467 0.019854411 111.7595354 -2.048284588 0.15879969 SLGTIQQCCDAIDHLCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLGTIQQCCDAIDHLCR 17 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;; 274.23 1.10E-35 1081280000 1064190 993280 513670 665760 1000910 865160 1033440 1085420 978940 FALSE TRUE 923554.5952 986755.0783 762082.5301 816930.9835 980993.8492 898443.265 933217.1479 853311.3797 863210.8284 1.069906174 1.143121756 0.882846351 0.946386394 1.136447571 1.040815564 1.081099909 0.98853183 1 19.71935344 1.920593231 0.006230543 1.16E-07 2.047106265 0.017482632 0.08071165 117789.9793 322.2072047 53754.988 52113.92763 83.2900707 -1.920593231 2.04710615 SLGTRPPHVFAIADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLGTRPPHVFAIADK 15 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71;A0A590UJW9 Q9UM54-1 MYO6 Unconventional myosin-VI 0 87.148 0.0043759 391020000 413300 370890 217830 289370 377940 317510 436320 490650 410450 FALSE TRUE 358681.3578 368453.5992 323173.3166 355075.8812 370419.7334 329724.8152 394005.7536 385728.3157 361927.0686 0.991032141 1.018032723 0.892923864 0.981070254 1.023465128 0.911025573 1.088633009 1.065762551 1 18.46533949 2.226807049 24.99999415 1.055992467 0.971279133 0.406472343 0.04650137 207.4824198 441314.2517 0.01848649 0.012575545 168.5803881 -2.226807049 -0.084713334 SLGVLPFTLNSGS(ph)PEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLGVLPFTLNSGSPEK 16 0 P42695 P42695 NCAPD3 Condensin-2 complex subunit D3 1 SLGVLPFTLNS(0.085)GS(0.915)PEK;SLGVLPFTLNS(0.066)GS(0.934)PEK 219.97 1.25E-14 299330000 670800 590390 381970 471570 673650 463120 652980 877530 482980 TRUE FALSE 582152.0804 586511.6892 566691.9696 578647.176 660245.683 480936.5261 589654.1001 689877.0384 425882.6546 1.366930712 1.377167356 1.330629373 1.35870097 1.550299539 1.129270049 1.384545939 1.619875877 1 18.70009645 -0.710001164 6.815592616 1.378708759 1.367356537 0 0.17971764 0 0 0 0.038367181 0.194983937 0.710001164 -0.011352222 SLGYAYVNFQQPADAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLGYAYVNFQQPADAER 17 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YBN4;E5RGH3;B1ANR1;E5RJB9;E5RHG7;E5RH24;B1ANR0;Q13310-2;Q13310;Q13310-3 P11940-2;B1ANR0 PABPC1;PABPC4 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 4 0 ; 275.42 2.36E-35 105560000 93165 78901 45680 63792 74806 71246 71196 92878 78518 FALSE TRUE 80853.0092 78382.69414 67771.00079 78276.9486 73317.50696 73986.87972 64291.42288 73016.76248 69235.69149 1.16779377 1.132113978 0.978844861 1.130586651 1.058955365 1.068623395 0.928587864 1.054611587 1 16.07922833 8 0.339878099 1.005625628 2.779244442 0.421434737 0.05630654 78.3831472 1.211077563 0.078236596 87.04605888 100000000 -8 1.773618814 SLGYHGS(ph)SYSPEGVEPVS(ph)PVSSPSLTHDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLGYHGSSYSPEGVEPVSPVSSPSLTHDK 29 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 2 S(0.011)LGY(0.007)HGS(0.711)S(0.124)Y(0.004)S(0.144)PEGVEPVS(0.999)PVS(0.001)SPSLTHDK 151.49 1.68E-08 243540000 73338 90495 24938 53419 117240 106740 102940 126170 103720 TRUE FALSE 63646.19749 89900.53239 36998.10021 65548.60041 114907.1534 110846.3569 92956.89464 99189.52736 91458.33976 0.695903705 0.982967028 0.404535008 0.716704464 1.256387921 1.211987416 1.016385109 1.084532341 1 16.48082711 3.254136045 24.06728734 1.107788676 0.699130619 0.632384664 0.156745351 101.714615 157168.8309 0.045218467 0.058139392 1795.295923 -3.254136045 -0.408658057 SLGYHGSSYS(ph)PEGVEPVS(ph)PVS(ph)SPSLTHDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLGYHGSSYSPEGVEPVSPVSSPSLTHDK 29 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 3 S(0.024)LGY(0.007)HGS(0.145)S(0.145)Y(0.023)S(0.656)PEGVEPVS(0.992)PVS(0.465)S(0.422)PS(0.096)LT(0.025)HDK 72.792 0.0033189 70179000 65597 50214 26237 37313 69170 72654 65477 55252 72660 TRUE FALSE 56928.19025 49884.14093 38925.30096 45785.48694 67793.65233 75449.04639 59127.05062 43436.78977 64070.21757 0.888528124 0.778585477 0.607541264 0.714614195 1.058114907 1.177599347 0.922847664 0.677956021 1 15.96736627 3.256621356 24.97781428 0.938315743 0.739566645 0.357607915 0.143451596 342.9895911 474348.1837 0.047526215 0.061231991 1805.59921 -3.256621356 -0.198749097 SLGYHGSSYS(ph)PEGVEPVS(ph)PVSS(ph)PSLTHDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLGYHGSSYSPEGVEPVSPVSSPSLTHDK 29 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 3 S(0.001)LGYHGS(0.031)S(0.031)Y(0.002)S(0.935)PEGVEPVS(1)PVS(0.108)S(0.848)PS(0.034)LT(0.009)HDK 165.61 2.26E-12 81674000 89395 90628 31132 64250 89256 97355 87116 106120 98741 TRUE FALSE 77581.22425 90032.6587 46187.53933 78838.9445 87479.98023 101100.3098 78667.50373 83427.06383 87067.95147 0.89104226 1.034050499 0.530476927 0.905487532 1.004732267 1.161165597 0.903518486 0.958183378 1 16.40985416 3.475831175 17.17645334 0.995680777 0.819728352 0.276836367 0.138271793 1.143332718 15180.7927 0.039582492 0.052055685 2991.101665 -3.475831175 -0.175952425 SLGYHGSSYS(ph)PEGVEPVS(ph)PVSSPSLTHDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLGYHGSSYSPEGVEPVSPVSSPSLTHDK 29 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 2 SLGYHGSSYS(1)PEGVEPVS(0.999)PVS(0.001)SPSLTHDK 225.18 5.87E-35 338530000 108400 122140 34603 81649 130350 130200 135200 177830 137360 TRUE FALSE 94074.66535 121337.6543 51337.12654 100188.6534 127756.29 135208.8783 122088.3248 139802.4384 121121.4573 0.776696941 1.00178496 0.423848323 0.827175099 1.054778343 1.116308219 1.007982628 1.154233457 1 16.88609494 3.291069178 4.161696201 1.077511897 0.74237435 0.533707089 0.14520474 0.160566994 5.723379275 0.042160525 0.053734637 1954.650783 -3.291069178 -0.335137547 SLGYHGSSYSPEGVEPVS(ph)PVS(ph)SPSLTHDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLGYHGSSYSPEGVEPVSPVSSPSLTHDK 29 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 2 SLGYHGSSYSPEGVEPVS(1)PVS(0.52)S(0.451)PS(0.015)LT(0.015)HDK;SLGYHGSSYSPEGVEPVS(1)PVS(0.641)S(0.356)PS(0.002)LTHDK 128.6 8.10E-06 252943000 137497 152946 62830 96672 156820 154448 158395 168763 168370 TRUE FALSE 119326.4231 151941.2877 93214.79815 118622.8551 153699.5888 160389.7145 143033.8773 132674.3458 148465.4904 0.803731714 1.023411483 0.627854984 0.798992782 1.035254647 1.08031647 0.963414979 0.893637608 1 17.1797681 3.245909172 25 0.983870207 0.815231349 0.420387052 0.105202226 186.6146022 634864.5595 0.031491995 0.039826988 1761.607588 -3.245909172 -0.168638857 SLGYHGSSYSPEGVEPVS(ph)PVSS(ph)PSLTHDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLGYHGSSYSPEGVEPVSPVSSPSLTHDK 29 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 2 SLGYHGSSYSPEGVEPVS(0.997)PVS(0.297)S(0.7)PS(0.005)LT(0.001)HDK 153.63 1.02E-08 41993000 38893 37146 16195 27653 33036 32526 34474 45198 41802 TRUE FALSE 33753.19151 36901.98548 24026.95617 33932.0363 32378.64823 33777.29627 31130.71679 35532.75943 36860.21518 0.915707934 1.001133208 0.651839824 0.920559908 0.878417233 0.916361885 0.84456145 0.963986761 1 15.16977687 1.603930034 4.368619131 0.992192646 0.875326027 0.200039485 0.089627137 0.249895555 10.47103169 0.064488677 0.022650822 40.17260865 -1.603930034 -0.116866619 SLHDAIMIVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLHDAIMIVR 10 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;; 188.87 1.07E-06 2822570000 324918 339877 169431 291801 376011 406184 368480 371728 414883 FALSE TRUE 281979.2631 337644.3256 251368.3983 358058.8769 368529.1168 421810.1613 332744.8663 292236.86 365836.0044 0.770780513 0.922939026 0.687106778 0.978741493 1.007361529 1.153003412 0.909546524 0.798819297 1 18.48083754 3.710746947 24.67023543 0.961006256 0.806541777 0.392501374 0.104823345 770.2811554 683225.7027 0.031619031 0.046910974 5137.442175 -3.710746947 -0.154464478 SLHDALCVIR ddPTM_MDA-MB-175_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 3498790000 775390 796703 391171 538906 855290 821340 808280 839460 859130 FALSE TRUE 672920.2469 791469.4055 580342.604 661272.844 838271.4023 852937.4813 729893.13 659948.0117 757564.6301 0.888267773 1.044754961 0.766063489 0.872892975 1.106534504 1.125894013 0.963473083 0.871144171 1 19.53100945 5.047843813 13.76751347 0.9611703 0.556053462 0.045679009 0.110919568 2680987.153 24581086.76 0.0286881 27335290.46 111646.1657 -5.047843813 -0.405116837 SLHDALCVLAQTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLHDALCVLAQTVK 14 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 142.85 9.29E-06 509490000 1236070 1224650 575570 1037240 1232690 1123290 1293870 1537760 1440850 FALSE TRUE 1072720.218 1216605.194 853917.5772 1272761.195 1208161.881 1166503.693 1168390.687 1208921.991 1270514.354 0.844319636 0.957569026 0.672103841 1.00176845 0.95092344 0.918134997 0.919620217 0.95152171 1 20.27698124 SLHDALCVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLHDALCVVK 10 0 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 112.36 0.0016315 2028610000 3348700 3386500 1513750 2775200 3466800 3222800 3558500 4095000 4567100 FALSE TRUE 2906160.81 3364253.859 2245804.563 3405351.576 3397817.463 3346783.201 3213397.218 3219316.117 4027182.641 0.721636208 0.835386462 0.557661463 0.845591541 0.843720726 0.831048279 0.797926865 0.799396602 1 21.94133947 3.593580941 21.27241428 0.842666845 0.715210569 0.386461904 0.086973985 7.514051702 1352.446486 0.022869377 0.033920724 3922.662472 -3.593580941 -0.127456275 SLHDPDGLVATYISEVHEHDGHLYLGSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLHDPDGLVATYISEVHEHDGHLYLGSFR 29 0 Q9HDC9;H0Y512 Q9HDC9 APMAP Adipocyte plasma membrane-associated protein 0 ; 139.16 1.07E-07 714620000 48756 56250 21634.3 44987 64858 64350 32776.8 76812 64007 FALSE TRUE 42312.77107 55880.49005 32096.71984 55201.98593 63567.45269 66825.58614 29598.11098 60386.35155 56440.16538 0.749692542 0.99008374 0.568685787 0.978062087 1.126280412 1.184007625 0.524415738 1.069918048 1 15.78443459 3.590319406 19.67632909 0.975912118 0.788486671 0.1919263 0.202662847 8.716454858 1494.615937 0.055043066 0.081642002 3893.313773 -3.590319406 -0.187425448 SLHINNIS(ph)PGNTISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLHINNISPGNTISR 15 0 Q8IZ41 Q8IZ41 RASEF Ras and EF-hand domain-containing protein 1 SLHINNIS(1)PGNTISR;SLHINNIS(1)PGNTISR 184.6 2.95E-07 780380000 393780 361910 180382 287690 373770 499320 298730 386150 398650 TRUE FALSE 341740.9753 359532.5894 267615.3385 353014.4116 366332.7083 518529.1635 269759.2106 303574.8275 351522.0511 0.972175072 1.022788153 0.761304554 1.004245425 1.042132939 1.475097115 0.767403381 0.863601093 1 18.42325567 SLHLS(ph)PQEQSASYQDR ddPTM_MDA-MB-175_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 207.1 1.18E-11 1068960000 366093 392351 234779 341078 383350 403162 347029 442323 570630 TRUE FALSE 317712.8825 389773.6204 348318.9097 418524.973 375722.085 418671.903 313374.181 347735.6686 503170.7715 0.631421578 0.774634861 0.6922479 0.831775208 0.746708884 0.832067216 0.622798856 0.691088768 1 18.94068859 3.901850201 0.024701687 1.459413103 4.27E-06 0.135495671 0.104183563 2843.108559 36.25848202 1016.394392 1126.012223 7977.194866 -3.901850201 -1.459408835 SLHLS(ph)PQEQSASYQDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLHLSPQEQSASYQDRR 17 1 Q5JW53;Q9H410-4;Q9H410 Q5JW53 DSN1 Kinetochore-associated protein DSN1 homolog 1 SLHLS(1)PQEQSASYQDRR 146.19 2.10E-07 170220000 75197 68979 37904 51662 68392 61554 60516 76680 50151 TRUE FALSE 65259.52593 68525.87241 56234.50118 63392.6467 67031.13301 63922.02221 54647.16763 60282.57872 44222.20591 1.475718467 1.549580601 1.271634918 1.43350259 1.515779949 1.445473397 1.235740427 1.363174394 1 15.43248337 0.550659032 0.911150102 1.22E-16 1.441902738 0.662688918 0.094620547 4.290986335 1.125625866 8.342382078 0.032940036 3.553522193 -0.550659032 1.441902738 SLHPWYGITPTS(ph)SPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLHPWYGITPTSSPK 15 0 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 1 SLHPWYGITPT(0.002)S(0.728)S(0.271)PK 177.67 4.79E-07 566480000 507440 555890 250380 414710 649050 475330 634800 762960 639670 TRUE FALSE 440380.5183 552238.322 371464.6055 508876.2439 636135.1748 493616.2527 573237.1937 599806.9414 564048.9413 0.780748772 0.979061003 0.65856804 0.902184556 1.127801381 0.875130182 1.016289814 1.063395208 1 19.10546082 3.472284023 24.64304701 1.015267697 0.816245584 0.489252472 0.09859223 90.34154597 460236.9893 0.026701285 0.034603291 2966.770982 -3.472284023 -0.199022113 SLHPWYGITPTSS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLHPWYGITPTSSPK 15 0 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 1 SLHPWYGITPTS(0.253)S(0.747)PK 170.61 7.28E-07 549820000 317030 302240 154120 215050 379610 292800 408150 442800 377540 TRUE FALSE 275133.6822 300254.5655 228652.9475 263880.3893 372056.5037 304064.2055 368567.6758 348110.6659 332907.6513 0.82645647 0.901915484 0.686835964 0.792653423 1.117596734 0.913359018 1.107116867 1.045667363 1 18.3447625 3.24957675 24.98260254 1.036971132 0.800881038 0.701669875 0.07606972 114.8084451 260363.3548 0.021366467 0.027317652 1776.547199 -3.24957675 -0.236090094 SLHS(ph)AHSLASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLHSAHSLASR 11 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 S(0.002)LHS(0.998)AHS(0.001)LASR 116.63 0.00061996 244550000 159090 112960 70539 125300 146020 116620 153160 173260 119070 TRUE FALSE 138065.8534 112217.9583 104651.8963 153751.2801 143114.4877 121106.4469 138306.5668 136209.6973 104993.6802 1.314992037 1.06880679 0.996744719 1.464386044 1.363077162 1.153464157 1.317284683 1.297313295 1 16.67994297 5.071822981 19.53014456 1.222467963 3.653765484 0.036860098 0.156951372 1166.133668 340924.5075 0.037525594 9216.519347 117983.9633 -5.071822981 2.43129752 SLIEEGGDWDR ddPTM_MDA-MB-175_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 ;;; 221.68 1.92E-11 1336670000 1518920 1441500 953040 1335870 1518000 1422590 1419960 1642210 2349840 FALSE TRUE 1318190.874 1432030.692 1413933.332 1639199.701 1487794.77 1477317.958 1282252.498 1291036.171 2072044.592 0.636178815 0.69111963 0.682385571 0.791102521 0.718032216 0.712975948 0.618834412 0.623073546 1 20.98262362 1.231812645 24.99992062 1.000000537 0.683737051 0.788548262 0.05139063 117.8984951 436750.5644 0.133145463 0.013987532 17.05346544 -1.231812645 -0.316263486 SLIEEGGDWDRR ddPTM_MDA-MB-175_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 ;;;;; 221.75 4.24E-11 9975220000 4064380 3889200 2253530 2796850 3935090 4082940 3736380 4418220 3501580 FALSE TRUE 3527261.885 3863651.589 3343344.646 3431917.54 3856789.408 4240013.344 3374026.443 3473418.036 3087627.201 1.142385934 1.251333577 1.082820052 1.111506447 1.249111099 1.373227099 1.092757066 1.124947349 1 21.55806714 1.446016229 1.719746019 0.983780771 1.193482359 0.320808442 0.087606979 0.779240028 3.20207716 0.248551272 0.025959748 27.92648199 -1.446016229 0.209701587 SLIGS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SLIGSPGR 8 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.004)LIGS(0.996)PGR;SLIGS(1)PGR;S(0.003)LIGS(0.997)PGR;SLIGS(1)PGR;SLIGS(1)PGR 121.64 0.0014944 4517180000 5394220 4600700 2815750 3159850 4373370 4987270 4312350 4647420 4645880 TRUE FALSE 4681360.16 4570477.699 4177456.118 3877342.238 4286348.493 5179133.504 3894138.961 3653605.399 4096649.359 1.142729033 1.11566241 1.019725086 0.946466709 1.046305924 1.264236465 0.950566822 0.891852116 1 21.96601298 2.03496638 24.98975516 0.933103364 1.081180908 0.367917243 0.086797533 180.4967371 128996.6018 0.036701876 0.024744302 108.3843007 -2.03496638 0.148077544 SLIIDEGEDDLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLIIDEGEDDLGR 13 0 J3KNF4;O14618;E9PP76 J3KNF4 CCS Copper chaperone for superoxide dismutase;Superoxide dismutase [Cu-Zn] 0 ; 180.88 2.91E-05 206980000 336680 396820 227099 244053 305718 343890 336250 397410 313960 FALSE TRUE 292186.885 394213.2633 336924.836 299468.9638 299634.8099 357119.6708 303640.5268 312426.9641 276844.0065 1.055420663 1.42395448 1.217020517 1.08172457 1.08232363 1.289967138 1.09679285 1.128530714 1 18.07871376 -0.654377575 0.45127828 1.62E-18 1.211732627 0.204909717 0.112412328 45.62085334 1.905593798 42.19661071 0.090476007 0.221626876 0.654377575 1.211732627 SLIPDIKPLAGQEAVVDLHADDS(ph)RISEDETER ddPTM_MDA-MB-175_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(0.631)RIS(0.369)EDETER 158.01 4.91E-13 1279800000 83185 75659 58147 71090 77504 61172 72985 87154 104550 TRUE FALSE 72191.89149 75161.99105 86267.08369 87232.07104 75961.82203 63525.32642 65906.92593 68516.79533 92190.2181 0.783075395 0.815292475 0.935750945 0.946218296 0.823968351 0.68906797 0.714901508 0.743211121 1 16.49232606 2.99865692 24.98550165 0.771386562 0.872640095 0.133640256 0.096455048 86.31757482 1605828.675 0.030020463 0.033594564 996.912222 -2.99865692 0.101253533 SLIPDIKPLAGQEAVVDLHADDS(ph)RISEDETERNGDDGTHDK ddPTM_MDA-MB-175_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(0.472)RIS(0.472)EDET(0.055)ERNGDDGT(0.001)HDK 96.918 4.41E-05 256170000 255720 214860 139220 160160 202810 205220 236800 326650 134980 TRUE FALSE 221925.9541 213448.5705 206547.2577 196526.7759 198774.4778 213114.9462 213835.1724 256798.4395 119022.8182 1.864566455 1.793341594 1.735358487 1.651168901 1.670053531 1.790538566 1.796589727 2.15755637 1 16.86087866 4.534691759 2.637017062 1.73608507 1.866926709 0.022051689 0.286309867 1.868247743 21.95232814 0.071921464 0.43477521 34252.45928 -4.534691759 0.130841639 SLIPDIKPLAGQEAVVDLHADDSRIS(ph)EDETER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SLIPDIKPLAGQEAVVDLHADDSRISEDETER 32 2 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2 S4R3H4 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 SLIPDIKPLAGQEAVVDLHADDS(0.042)RIS(0.958)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.008)RIS(0.991)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.336)RIS(0.664)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.046)RIS(0.954)EDETER;SLIPDIKPLAGQEAVVDLHADDSRIS(1)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.001)RIS(0.999)EDETER;SLIPDIKPLAGQEAVVDLHADDSRIS(0.999)EDET(0.001)ER 299.35 6.09E-90 6829370000 2843790 2266860 1774690 2299310 2391390 2181080 2654360 3104840 3257790 TRUE FALSE 2467975.946 2251968.847 2632936.02 2821403.478 2343806.018 2264987.559 2396940.576 2440894.128 2872657.777 0.859126334 0.783932171 0.916550534 0.982157882 0.815901579 0.78846411 0.834398234 0.849698891 1 21.4539547 1.237719334 24.95142024 1.000000174 0.853245028 0.37683985 0.059089246 23.88451015 707944.3922 0.088814183 0.015166913 17.28698813 -1.237719334 -0.146755146 SLKDMEESIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLKDMEESIR 10 1 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;; 134.98 0.00014262 2528340000 4715680 3755650 1976810 2293500 3567030 4200120 3988370 3762120 627590 FALSE TRUE 4092490.94 3730978.888 2932801.928 2814274.229 3496053.082 4361701.334 3601578.491 2957619.915 553397.0252 7.395216732 6.741956892 5.29963443 5.085452399 6.317441047 7.881685546 6.508127669 5.344481051 1 19.07795536 4.379743861 3.847197895 5.526971247 7.274278474 0.13990485 1.762342663 0.483405079 13.11666599 0.457904429 1.432270959 23974.18551 -4.379743861 1.747307227 SLKEEGVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLKEEGVQR 9 1 P40222 P40222 TXLNA Alpha-taxilin 0 ; 70.942 0.046499 287560000 458610 405480 230280 301110 403600 384620 417990 489320 439770 FALSE TRUE 398003.5265 402816.3752 341644.1782 369481.6277 395569.1496 399416.5803 377453.3941 384682.7259 387780.8916 1.026361884 1.038773142 0.881023758 0.9528103 1.020084172 1.030005833 0.973367699 0.992010525 1 18.56488219 3.237880929 24.99978415 1.000824418 0.972621727 0.087809647 0.04484718 52.50646477 1931279.566 0.014053494 0.016925374 1729.342157 -3.237880929 -0.028202691 SLKLS(ph)PVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLKLSPVQK 9 1 H7C4H4;A0A2R8Y838;A0A2R8YFT6;A0A2R8Y414;Q92834-3;Q92834-4;Q92834-2;Q92834;Q92834-6 H7C4H4 RPGR X-linked retinitis pigmentosa GTPase regulator 1 SLKLS(1)PVQK 102.62 0.0042728 0 977050 706640 518560 601340 728230 513430 892840 1102700 832410 TRUE FALSE 847930.367 701998.0353 769337.3505 737883.4379 713739.6478 533181.9843 806252.5142 866896.1862 734003.4381 1.155213073 0.956396113 1.04813862 1.005286079 0.972392786 0.726402571 1.098431523 1.181051942 1 19.4854273 2.035589594 24.99998978 1.114344114 0.974938971 0.178427162 0.11470884 239.6726906 168357.6702 0.046535184 0.031373902 108.5399442 -2.035589594 -0.139405143 SLKPDSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLKPDSVR 8 1 O43488;H3BLU7;H7C5H7 O43488 AKR7A2 Aflatoxin B1 aldehyde reductase member 2 0 80.239 0.02368 198820000 236760 220270 135930 158560 223380 204800 235100 265620 267840 FALSE TRUE 205471.5661 218823.0319 201666.2027 194563.4714 218935.175 212678.7885 212300.0382 208819.2301 236176.2603 0.869992462 0.926524247 0.853880074 0.823806216 0.926999076 0.900508748 0.898905072 0.884166892 1 17.84950443 1.237917756 24.99999981 1.000000129 0.886271077 0.567542463 0.031379176 12.07491466 469203.6984 0.044468174 0.007670163 17.2948881 -1.237917756 -0.113729053 SLLAWQSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLLAWQSLR 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 ; 155.84 0.0001683 395680000 315500 485970 322680 354850 484090 520760 471670 484640 504880 FALSE TRUE 273805.8756 482777.6311 478729.1273 435424.116 474457.5561 540793.9742 425927.516 381003.5075 445193.6616 0.615026446 1.084421619 1.075327815 0.978055515 1.065732954 1.21473871 0.956724124 0.855815211 1 18.76407353 4.744277902 24.92098861 1.018778973 0.615026265 0.652799065 0.094593092 450.4823099 1963540.918 0.026136763 0.226171987 55498.07279 -4.744277902 -0.403752708 SLLDFLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLLDFLPR 8 0 P53992;G5EA31 P53992 SEC24C Protein transport protein Sec24C 0 84.568 0.044919 0 86185 78975 55866 61644 90340 97763 98780 98903 81123 FALSE TRUE 74795.43389 78456.20802 82882.98446 75641.21237 88542.41075 101524.0059 89200.3308 77753.36311 71532.73136 1.045611323 1.096787534 1.158672162 1.05743498 1.237788759 1.419266453 1.246986227 1.086962033 1 16.12631591 3.238943663 24.99999285 1.199008067 1.095069831 0.188313627 0.111748168 21.11183979 1377826.695 0.036757306 0.04455755 1733.579102 -3.238943663 -0.103938237 SLLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 38.22 0.078211 27004000 4335.3 3735.7 3670.6 2778.7 4439.7 4974.6 2987.9 3345.7 4183.5 FALSE TRUE 3762.379121 3711.159941 5445.714437 3409.646305 4351.358656 5165.976081 2698.133918 2630.248091 3688.931396 1.019910298 1.006025741 1.476230879 0.924291059 1.179571586 1.400399066 0.731413417 0.713010845 1 11.84898724 2.220582437 24.99930775 0.790125425 1.163882071 0.443457973 0.185663935 205.7439554 286092.221 0.073865357 0.049913678 166.1814092 -2.220582437 0.373756646 SLLENDQLLSHGGQDLSADAFHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLLENDQLLSHGGQDLSADAFHR 23 0 Q9UBB9 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 0 ; 211.71 2.52E-25 168126000 85481 74634 48931.5 63678 72056 87039 70810 83136 79023 FALSE TRUE 74184.46927 74143.72434 72594.93707 78137.06316 70622.22658 90387.44665 63942.8571 65358.01337 69680.99096 1.064629941 1.064045205 1.041818379 1.121354075 1.013507782 1.297160752 0.917651374 0.937960446 1 16.08847752 SLLGDSAPTLHLNKGT(ph)PS(ph)QSPVVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLLGDSAPTLHLNKGTPSQSPVVGR 25 1 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 2 SLLGDSAPTLHLNKGT(0.999)PS(0.959)QS(0.042)PVVGR;SLLGDSAPTLHLNKGT(1)PS(0.725)QS(0.275)PVVGR;SLLGDSAPTLHLNKGT(1)PS(0.587)QS(0.413)PVVGR 180.23 3.97E-16 7918600000 2949470 2522990 895510 1209730 2146750 1896010 2280130 2440240 606660 TRUE FALSE 2559690.066 2506416.313 1328581.631 1484417.686 2104033.875 1968950.732 2059003.344 1918413.666 534941.3459 4.784992011 4.685403983 2.483602439 2.774916722 3.93320481 3.680685269 3.849026364 3.586213107 1 19.02902119 4.2576028 23.86416801 3.180386797 4.735201286 0.387123749 0.871637535 158.9995679 199256.4 0.216874565 0.571351996 18096.84222 -4.2576028 1.554814489 SLLGDSAPTLHLNKGT(ph)PSQS(ph)PVVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLLGDSAPTLHLNKGTPSQSPVVGR 25 1 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 2 SLLGDSAPTLHLNKGT(0.986)PS(0.022)QS(0.992)PVVGR;SLLGDSAPTLHLNKGT(0.983)PS(0.045)QS(0.972)PVVGR 235.07 3.22E-37 2750500000 3492400 2827900 1105280 1202600 2405500 2195500 2791000 2949600 677340 TRUE FALSE 3030870.491 2809323.339 1639797.105 1475668.711 2357635.256 2279962.306 2520329.25 2318850.994 597265.6368 5.074577047 4.703641337 2.745507198 2.470707537 3.947381384 3.817333804 4.219779432 3.882445014 1 19.18801319 4.336901847 5.90863917 3.307109208 4.96830525 0.356846818 0.9548115 0.238286886 11.76117038 0.241845678 0.657748876 21722.10192 -4.336901847 1.661196042 SLLGLDSGELQSGPESSSS(ph)PGVHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLLGLDSGELQSGPESSSSPGVHVR 25 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7 P49815 TSC2 Tuberin 1 SLLGLDSGELQSGPES(0.016)S(0.075)S(0.227)S(0.681)PGVHVR;SLLGLDSGELQSGPESS(0.002)S(0.249)S(0.75)PGVHVR 198.02 5.05E-25 397640000 477420 363760 154211 191273 292800 282920 245610 301040 314040 TRUE FALSE 414327.7374 361370.4366 228787.9554 234704.4581 286973.8529 293804.1155 221790.78 236664.9387 276914.549 1.496229573 1.304988987 0.826204171 0.847569978 1.036326383 1.06099198 0.800935815 0.854649709 1 18.07908133 4.371331717 4.103710269 0.913499963 1.457519105 0.829700573 0.092555481 0.081692942 2.430004299 0.025066249 0.075480986 23514.2817 -4.371331717 0.544019142 SLLGLGLPSGGFHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLLGLGLPSGGFHDR 15 0 Q96P48-3;Q96P48;E7EU13;Q96P48-7;Q96P48-2;Q96P48-4;Q96P48-1;A0A0A0MSJ2;Q96P48-5;F5GWQ2 Q96P48-3 ARAP1 "Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1" 0 93.424 0.004573 0 103590 110370 56454 79925 111930 129590 110620 124110 113310 FALSE TRUE 89900.31904 109644.9722 83755.34323 98073.19283 109702.812 134575.4112 99892.08943 97570.04233 99914.62088 0.899771407 1.097386661 0.838269139 0.981569984 1.097965553 1.346904086 0.999774493 0.97653418 1 16.60840819 4.755923331 22.88489013 1.038153691 0.89977104 0.105278177 0.130082879 2910.60315 3836109.514 0.033382651 0.83944458 57006.3626 -4.755923331 -0.138382651 SLLIDFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLLIDFFR 8 0 Q9H7B2;Q5VXN0 Q9H7B2 RPF2 Ribosome production factor 2 homolog 0 75.696 0.087759 17110000 115440 100670 74305 82648 114560 109470 109300 113620 112380 FALSE TRUE 100184.3115 100008.6921 110239.1465 101414.4916 112280.4801 113681.3817 98700.10282 89323.24719 99094.56442 1.010997042 1.009224802 1.112464111 1.023411245 1.133063966 1.147200983 0.996019342 0.901394014 1 16.5965183 2.016747598 10.43197479 0.945133753 1.072153729 0.482081022 0.053714152 0.250918463 150.7754937 0.022621235 0.01505888 103.9315963 -2.016747598 0.127019976 SLLNEIESVYDEHQEQHSEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLLNEIESVYDEHQEQHSEGR 21 0 O75182-2;O75182;M0QYC5 O75182-2 SIN3B Paired amphipathic helix protein Sin3b 0 103.95 0.00024632 16253000 10879 10355 6643.5 7860.7 9912.8 11011 9969.3 11209 11463 FALSE TRUE 9441.312586 10286.97732 9856.318821 9645.592078 9715.554674 11434.6003 9002.47882 8812.042579 10107.8572 0.934056784 1.01772088 0.97511457 0.954266754 0.961188359 1.131258591 0.89064167 0.871801254 1 13.30318957 SLLS(ph)PLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLLSPLHR 8 0 Q9BY84 Q9BY84 DUSP16 Dual specificity protein phosphatase 16 1 SLLS(1)PLHR;SLLS(1)PLHR;SLLS(1)PLHR;S(0.004)LLS(0.996)PLHR 123.51 0.00086595 621090000 352202 318892 264227 345486 502460 560299 507204 563422 557066 TRUE FALSE 305657.6133 316797.1775 392008.061 423933.8767 492462.029 581854.0651 458015.4341 442938.5899 491210.2921 0.62225409 0.644931881 0.798045292 0.863039483 1.002548271 1.184531502 0.932422308 0.90172905 1 18.90598126 3.877190895 1.463214619 0.992267345 0.616933019 0.784305175 0.078017911 0.223536215 0.90656186 0.027253524 0.075768579 7536.867747 -3.877190895 -0.375334327 SLLSHEFQDET(ph)DTEEETLYSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLLSHEFQDETDTEEETLYSSK 22 0 O75976-2;O75976 O75976-2 CPD Carboxypeptidase D 1 SLLSHEFQDET(0.907)DT(0.092)EEETLYSSK;SLLSHEFQDET(0.989)DT(0.011)EEETLYSSK 146.45 3.14E-07 194684000 125684 114594 105882 141784 134339 142388 126664 200003 274040 TRUE FALSE 109074.541 113841.2245 157086.8894 173978.2242 131665.9167 147865.7585 114380.1448 157233.9149 241643.3034 0.451386566 0.471112681 0.650077561 0.719979498 0.544877159 0.611917469 0.473342912 0.650686002 1 17.88251949 1.256776759 3.382936018 1.057026534 0.56760607 0.724174307 0.084693986 0.167198194 2.734600869 0.20852263 0.022656019 18.06245422 -1.256776759 -0.489420464 SLLSHEFQDET(ph)DTEEETLYSSKH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLLSHEFQDETDTEEETLYSSKH 23 1 O75976-2;O75976 O75976-2 CPD Carboxypeptidase D 1 SLLSHEFQDET(0.999)DT(0.001)EEETLYSSKH 206.57 1.03E-24 104660000 120720 114490 32174 80284 143230 146500 103730 176820 51480 TRUE FALSE 104766.5461 113737.9077 47733.45402 98513.70926 140380.0032 152135.9498 93670.28057 139008.419 45394.09305 2.307933458 2.505566254 1.05153448 2.170187852 3.092472915 3.351448164 2.063490518 3.062257877 1 15.47021696 3.465972514 24.40495583 2.594272773 1.943532588 0.10023476 0.753384508 316.0708999 691885.6724 0.21096438 0.272624117 2923.967317 -3.465972514 -0.650740185 SLLSHEFQDETDT(ph)EEETLYSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLLSHEFQDETDTEEETLYSSK 22 0 O75976-2;O75976 O75976-2 CPD Carboxypeptidase D 1 SLLSHEFQDET(0.217)DT(0.783)EEETLYSSK 202.38 5.20E-22 166280000 74299 59111 46338 87593 74916 87201 63297 105340 161530 TRUE FALSE 64480.1989 58722.69595 68747.21179 107482.3294 73425.31817 90555.6789 57158.46668 82813.86076 142434.1074 0.452701955 0.412279734 0.482659758 0.754610896 0.515503762 0.635772432 0.401297609 0.58141875 1 17.11993513 1.24678375 4.454971425 1.037034625 0.526917349 0.665256471 0.105610252 0.121227666 4.947487314 0.193480571 0.026842324 17.65158668 -1.24678375 -0.510117276 SLLSNVS(ph)IEDEEEELVAIVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SLLSNVSIEDEEEELVAIVR 20 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 SLLS(0.001)NVS(0.999)IEDEEEELVAIVR;SLLSNVS(1)IEDEEEELVAIVR;SLLSNVS(1)IEDEEEELVAIVR;SLLSNVS(1)IEDEEEELVAIVR;SLLSNVS(1)IEDEEEELVAIVR;SLLSNVS(1)IEDEEEELVAIVR;SLLSNVS(1)IEDEEEELVAIVR;SLLSNVS(1)IEDEEEELVAIVR 207.22 1.50E-25 123455000 133680.7 108462 65962.1 87555.2 95757.7 86489.4 133945.2 127131.5 104869.3 TRUE FALSE 116014.4568 107749.506 97861.59219 107435.9464 93852.30912 89816.70318 120955.2151 99945.41806 92471.77082 1.254593221 1.165215125 1.058286127 1.161824256 1.014929294 0.971287804 1.30802313 1.080820851 1 16.4967254 4.551902696 2.864235203 1.092790001 1.257457778 0.249908225 0.095613882 0.465350645 6.507829271 0.024288553 0.142478457 35637.12794 -4.551902696 0.164667776 SLLSS(ph)PTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLLSSPTK 8 0 Q92667-2;Q92667;I3NI36 Q92667-2 AKAP1 "A-kinase anchor protein 1, mitochondrial" 1 SLLS(0.104)S(0.893)PT(0.003)K 138.25 0.0014005 0 881430 689040 666640 982910 936590 979150 706070 1125300 1703000 TRUE FALSE 764946.7922 684513.6509 989029.3338 1206094.738 917953.6914 1016818.534 637595.4401 884663.3521 1501673.28 0.509396286 0.455833942 0.658618187 0.80316721 0.611287224 0.677123678 0.424589988 0.589118395 1 20.51813953 -1.999995308 0.045310642 1.666505134 3.96E-06 0.175186726 0.15395632 3508.607391 15.59984883 480.3683075 169.935145 0.010000108 1.999995308 -1.666501178 SLLTEADAGHTEFTDEVYQNESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLLTEADAGHTEFTDEVYQNESR 23 0 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-2;H0YD14;Q9NZM1-5 Q9NZM1-6 MYOF Myoferlin 0 ;;; 352.47 1.10E-101 683810000 447236 413481 274718 356556 442919 543050 340889 515710 587140 FALSE TRUE 388132.6294 410764.8161 407572.5437 437517.4894 434105.7785 563941.4849 307829.6372 405429.4298 517728.9781 0.749683031 0.793397383 0.787231468 0.845070506 0.838480743 1.089260035 0.594576797 0.783092017 1 18.98183754 3.867102245 2.506048312 0.843260969 0.771972043 0.073726408 0.129778012 1.067292624 13.01825825 0.037429589 0.077450388 7363.80442 -3.867102245 -0.071288926 SLLVNPEGPTLMR ddPTM_MDA-MB-175_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 ; 188.6 1.39E-05 828480000 629310 704940 391330 402810 720640 811220 691030 691700 728070 FALSE TRUE 546145.089 700309.2027 580578.4969 494274.1671 706300.6739 842428.1583 624014.017 543785.3378 641998.394 0.850695413 1.090827032 0.904330139 0.769899382 1.100159565 1.312196676 0.971986882 0.847019779 1 19.29221016 3.209560532 24.99984441 1.029090733 0.917314936 0.19315567 0.140989111 493.9623971 425824.2438 0.047719866 0.054117782 1620.169797 -3.209560532 -0.111775797 SLMDQYFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLMDQYFAR 9 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 123.35 0.003503 0 148040 135940 77511 96604 136280 153170 119710 131010 130860 FALSE TRUE 128476.1389 135047.0012 114995.5789 118539.4147 133568.2946 159062.549 108100.5426 102994.531 115389.8799 1.113409071 1.170353946 0.99658288 1.027294723 1.157539073 1.378479198 0.936828626 0.892578544 1 16.81615717 2.062333428 24.99997227 0.931435548 1.133252795 0.439376597 0.104675589 59.2717937 23771.5288 0.044332935 0.029889255 115.4339158 -2.062333428 0.201817247 SLNS(ph)TPPPPPAPAPAPPPALARPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLNSTPPPPPAPAPAPPPALARPR 24 1 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 S(0.013)LNS(0.547)T(0.44)PPPPPAPAPAPPPALARPR 84.035 0.0079472 1273200000 1244900 1293000 508430 673090 1266000 1237300 1149400 1383300 247000 TRUE FALSE 1080383.311 1284506.198 754308.4486 825925.372 1240809.077 1284899.732 1037931.365 1087492.06 217799.9414 4.960438942 5.897642532 3.463308777 3.792128532 5.697012906 5.899449391 4.765526374 4.993077835 1 17.73264404 4.257124182 24.9898419 4.423252867 5.429040623 0.100269707 1.403215444 667.2818958 898264.1801 0.347850959 0.916704847 18076.90941 -4.257124182 1.005787756 SLNSIEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLNSIEFR 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 74.2 0.096766 79563000 179480 171640 91378 129110 162230 157880 176650 171880 205410 FALSE TRUE 155761.2633 170512.4855 135568.7064 158426.3988 159001.9404 163953.7458 159518.5102 135124.7996 181126.6638 0.859957667 0.94139914 0.748474596 0.874671876 0.87784944 0.905188349 0.880701421 0.746023787 1 17.46663942 SLNST(ph)PPPPPAPAPAPPPALAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLNSTPPPPPAPAPAPPPALAR 22 0 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 SLNS(0.015)T(0.985)PPPPPAPAPAPPPALAR;S(0.001)LNS(0.207)T(0.792)PPPPPAPAPAPPPALAR;SLNS(0.031)T(0.969)PPPPPAPAPAPPPALAR;S(0.001)LNS(0.054)T(0.944)PPPPPAPAPAPPPALAR 200.68 1.81E-21 2891060000 1216800 1305990 867380 1197580 1399320 1357510 1201010 1529920 1897720 TRUE FALSE 1055996.797 1297410.866 1286847.869 1469508.843 1371476.27 1409734.288 1084536.235 1202758.514 1673373.703 0.631058558 0.775326434 0.769014038 0.878171349 0.819587559 0.842450366 0.648113588 0.718762648 1 20.67432824 4.836826149 2.176768034 0.797760478 0.556716411 0.255792354 0.093860853 1.51820714 6.516161711 0.024918152 0.778256079 68679.34562 -4.836826149 -0.241044067 SLNST(ph)PPPPPAPAPAPPPALARPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLNSTPPPPPAPAPAPPPALARPR 24 1 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 S(0.007)LNS(0.197)T(0.795)PPPPPAPAPAPPPALARPR;S(0.006)LNS(0.164)T(0.83)PPPPPAPAPAPPPALARPR;S(0.01)LNS(0.188)T(0.803)PPPPPAPAPAPPPALARPR 104.54 0.0049022 3842200000 2821230 2892300 1173800 1445740 2652750 2830240 2521450 2993850 560270 TRUE FALSE 2448397.307 2873300.291 1741453.606 1774017.364 2599965.465 2939121.164 2276920.167 2353638.476 494035.5189 4.95591352 5.815979178 3.524956283 3.590870081 5.262709594 5.949210233 4.608818759 4.764107814 1 18.91425524 4.248904458 24.99985453 4.27601089 5.385946439 0.126542289 1.344031155 496.3687226 1199640.544 0.335613928 0.867070039 17737.99212 -4.248904458 1.109935549 SLPAPVAQRPDS(ph)PGGGLQAPGQK ddPTM_MDA-MB-175_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 243.75 1.26E-37 4090320000 2669740 2372580 1746920 2233110 2310680 2167020 2752330 3083550 4142340 TRUE FALSE 2316927.095 2356994.366 2591736.355 2740171.756 2264701.989 2250386.662 2485409.46 2424156.829 3652637.284 0.634316225 0.645285634 0.709552073 0.750189943 0.620018308 0.616099132 0.680442449 0.663673023 1 21.80050707 1.238305263 24.99943371 1.000000371 0.666126499 0.867509075 0.041147902 2.191067139 214086.4044 0.059405126 0.010500486 17.31032664 -1.238305263 -0.333873872 SLPEEDVAEIQHAEEFLIKPESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLPEEDVAEIQHAEEFLIKPESK 23 1 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ; 193.11 4.27E-18 102396000 150066 102616 95549 117398 103248 84740 117637 161937 200767 FALSE TRUE 130234.3979 101941.9087 141756.816 144055.0102 101193.5668 88000.00263 106228.5818 127308.0327 177032.554 0.735652257 0.575837079 0.800738694 0.813720454 0.571609936 0.497083732 0.600051117 0.719122161 1 17.43365515 1.251554238 3.313846642 1.049488645 0.655790442 0.523291602 0.102347184 0.275247604 4.217368589 0.274983258 0.028130918 17.84654856 -1.251554238 -0.393698203 SLPEHNYVVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLPEHNYVVLR 11 0 B1AHC3;B1AHC4;H0Y9T8;P85298-4;P85298-3;P85298 B1AHC3 PRR5-ARHGAP8;ARHGAP8 Rho GTPase-activating protein 8 0 147.37 3.53E-05 425080000 166720 177240 96765 130930 187980 218780 175740 191870 210880 FALSE TRUE 144687.5296 176075.6988 143560.8777 160659.6576 184239.5658 227196.6082 158696.7618 150840.0936 185950.0066 0.778099083 0.94689805 0.772040186 0.863993826 0.990801609 1.221815542 0.853437785 0.811186277 1 17.50455527 3.344273963 5.688441039 0.957710674 0.840149958 0.240042826 0.117846902 0.401766895 18.79292786 0.037456491 0.048447706 2209.398033 -3.344273963 -0.117560716 SLPLSPELESS(ph)P ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLPLSPELESSP 12 0 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 SLPLSPELES(0.01)S(0.99)P;SLPLSPELES(0.083)S(0.917)P 158.05 7.81E-05 63216000 85133 75799 46403 55985 71156 86642 69701 75411 79197 TRUE FALSE 73882.45835 75301.07138 68843.64601 68697.24993 69740.13481 89975.1738 62941.40775 59284.9445 69834.42088 1.057966221 1.078280172 0.985812514 0.983716183 0.998649863 1.288407245 0.901294905 0.848935865 1 16.09165069 SLPS(ph)LEDIDPDVLDSMHSLGCFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLPSLEDIDPDVLDSMHSLGCFR 23 0 Q8IWQ3-6;Q8IWQ3-3;Q8IWQ3-2;Q8IWQ3-4;Q8IWQ3;Q8IWQ3-5 Q8IWQ3-6 BRSK2 Serine/threonine-protein kinase BRSK2 1 S(0.052)LPS(0.948)LEDIDPDVLDSMHSLGCFR 66.282 0.018211 26356000 9473.4 9486.6 5958.9 9363.9 10419 9877.4 8817.3 11984 11608 TRUE FALSE 8221.466187 9424.2819 8840.643971 11490.11661 10211.68228 10257.38997 7962.199603 9421.31486 10235.71546 0.803213631 0.920725272 0.863705522 1.122551389 0.997652027 1.002117537 0.777884031 0.9204354 1 13.32132433 4.765061629 1.601183688 0.952168709 0.747181621 0.221104241 0.090853406 2.003062801 4.670310007 0.02627775 0.653777622 58218.58275 -4.765061629 -0.204987089 SLPS(ph)SPERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLPSSPERR 9 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 S(0.033)LPS(0.564)S(0.403)PERR 72.152 0.02913 376720000 88970 81874 69915 52286 91967 96855 96457 129480 76422 TRUE FALSE 77212.38908 81336.1643 103726.1279 64158.33544 90137.03663 100581.0745 87102.61499 101791.7096 67387.47822 1.145797277 1.206992255 1.539249288 0.952080967 1.337593259 1.492578105 1.292563801 1.510543387 1 16.04019292 3.030525599 24.99898199 1.35735762 1.223017225 0.065624891 0.198125117 481.3436646 394194.039 0.057134186 0.06478337 1072.816882 -3.030525599 -0.134340394 SLPSASTSKATIS(ph)DEEIERQLKALGVD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLPSASTSKATISDEEIERQLKALGVD 27 3 C9J0A7;Q9UQN3;Q9UQN3-2 C9J0A7 CHMP2B Charged multivesicular body protein 2b 1 SLPSAST(0.001)SKAT(0.198)IS(0.8)DEEIERQLKALGVD 117.94 0.0024506 52027000 5418.9 3133.4 2407 5869.8 7027.7 4587.4 2247.5 5204.4 5733.5 TRUE FALSE 4702.778635 3112.816489 3571.033251 7202.627804 6887.862519 4763.880246 2029.537796 4091.479561 5055.692162 0.930194815 0.615705306 0.706339139 1.424657114 1.362397531 0.942280521 0.401436189 0.809281782 1 12.30369291 2.456743256 24.98252785 0.728556583 1.00846313 0.158223981 0.286231525 460.3390116 564351.5985 0.116265137 0.090068315 286.248524 -2.456743256 0.279906547 SLPSRS(ph)PPITPNWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLPSRSPPITPNWR 14 1 J3KN34;P26045-2;P26045 J3KN34 PTPN3 Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 3 1 S(0.016)LPS(0.403)RS(0.581)PPITPNWR 53.536 0.089531 322960000 66633 62938 36080 66951 87286 118830 63359 116560 46163 TRUE FALSE 57827.28022 62524.55613 53528.40868 82153.24783 85549.17937 123401.467 57214.45393 91634.55107 40705.66273 1.42062004 1.536016169 1.315011354 2.018226515 2.101653029 3.031555285 1.405564978 2.251149961 1 15.31294189 3.73124876 23.79549953 2.012245044 1.435095879 0.187018341 0.529319693 443.6871207 1443924.989 0.140074416 0.212953018 5385.781869 -3.73124876 -0.577149165 SLPSS(ph)PERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLPSSPERR 9 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 S(0.004)LPS(0.03)S(0.966)PERR;S(0.029)LPS(0.192)S(0.778)PERR 86.014 0.0088354 812310000 151918 117370 102096 122619 158550 183064 163096 220430 150030 TRUE FALSE 131841.6514 116598.9887 151469.9671 150461.5181 155395.1652 190106.5905 147278.975 173292.7599 132293.6243 0.996583562 0.88136514 1.144952887 1.137330078 1.174623237 1.437004931 1.113273416 1.30991014 1 17.01338401 4.024257711 1.948259081 1.215853579 0.933646387 0.40480921 0.122149953 0.304997317 2.254063498 0.03297429 0.092569545 10574.44812 -4.024257711 -0.282207192 SLPTTVPES(ph)PNYR ddPTM_MDA-MB-175_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 346.06 8.52E-76 43703580000 10928990 9658800 5340630 6784810 8724360 8912940 7961080 9185580 8175440 TRUE FALSE 9484696.281 9595350.707 7923376.531 8325404.81 8550762.305 9255826.569 7189015.687 7221315.199 7208948.797 1.31568368 1.331033272 1.0991029 1.154870848 1.186131646 1.283935679 0.997234949 1.001715424 1 22.78135747 -1.10306721 0.143878766 9.69E-15 1.46023078 0.596677878 0.081951102 87.17269485 1.398758455 25.30136946 1.840456687 0.078873805 1.10306721 1.46023078 SLQALGEVIEAELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLQALGEVIEAELR 14 0 K7ER00;Q9Y285;Q9Y285-2;K7ER16;K7EK06 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ;; 164.81 9.45E-06 66155800 116598 104534 64670 77775 109010 112211 106465 123356 113691 FALSE TRUE 101189.2789 103847.3093 95944.62831 95435.00247 106840.9143 116527.8298 96140.04069 96977.27936 100250.5795 1.009363531 1.035877396 0.957048117 0.951964597 1.06573862 1.162365648 0.958997356 0.967348816 1 16.61325105 SLQDIIAILGMDELSEEDKLTVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLQDIIAILGMDELSEEDKLTVSR 24 1 P06576;F8W079 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 93.006 0.0087041 90885000 40105 53791 35587 38672 47915 51132 49839 59846 36110 FALSE TRUE 34805.02264 53437.64338 52796.99223 47453.06866 46961.58524 53099.08113 45005.62145 47048.39862 31841.11694 1.093084225 1.678259073 1.658138825 1.490307917 1.474872422 1.667626209 1.413443553 1.477598877 1 14.95860332 1.080407915 2.312601268 0.659280157 1.515128212 0.447597774 0.170922603 1.001641389 3.73594523 2.101826506 0.04265865 12.03394204 -1.080407915 0.855848055 SLQEEHVAVAQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 172.58 2.32E-05 3188630000 2159980 2083940 1173825 1445703 2070490 2531640 1924230 2186090 1998850 FALSE TRUE 1874533.17 2070250.461 1741490.696 1773971.962 2029291.3 2629033.829 1737618.471 1718611.666 1762548.23 1.063535816 1.174578049 0.98805279 1.006481373 1.151339444 1.491609582 0.985855843 0.975072135 1 20.74923131 2.073541405 24.99999982 0.984073888 1.14269599 0.22689025 0.138203575 61.99748404 21073.94721 0.058882272 0.039698415 118.4517292 -2.073541405 0.158622102 SLQELFLAHILSPWGAEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLQELFLAHILSPWGAEVK 19 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 187.06 1.92E-14 682110000 2916000 2262300 1307080 1794040 2008690 1759320 2497900 3015500 1650410 FALSE TRUE 2530643.212 2247438.802 1939188.26 2201404.202 1968720.999 1827002.179 2255654.042 2370658.792 1455300.41 1.738914656 1.544312629 1.332500319 1.51268026 1.352793544 1.255412399 1.549957677 1.628982426 1 20.47288556 4.579443858 2.89380053 1.407821179 1.748985683 0.299904068 0.176380689 0.428482402 5.919355084 0.044599477 0.28009505 37970.28508 -4.579443858 0.341164505 SLQGVAGVQDVEVHLEDQMVLVHTTLPSQEVQALLEGTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLQGVAGVQDVEVHLEDQMVLVHTTLPSQEVQALLEGTGR 40 0 J3KNF4;O14618;E9PK03 J3KNF4 CCS Copper chaperone for superoxide dismutase 0 223 2.06E-40 54422000 26501 23667 12278 16989 25199 26012 24608 28360 26460 FALSE TRUE 22998.82571 23511.52992 18215.68187 20846.61211 24697.5892 27012.69847 22221.51995 22295.4347 23331.92894 0.985723288 1.007697648 0.78071907 0.89348001 1.05853182 1.157756761 0.952408179 0.955576144 1 14.51001797 3.245672043 24.99981165 1.017406407 0.913662612 0.292524315 0.082903505 245.9903405 864759.7668 0.026176284 0.033073953 1760.645996 -3.245672043 -0.103743795 SLQLPAS(ph)PAPDPSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLQLPASPAPDPSPR 15 0 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 SLQLPAS(0.995)PAPDPS(0.005)PR;SLQLPAS(1)PAPDPSPR;S(0.001)LQLPAS(0.999)PAPDPSPR 138.66 9.66E-06 516607000 471576 522631 333457 548007 555308 534524 468112 585577 972060 TRUE FALSE 409256.0368 519197.8025 494717.9205 672440.3651 544258.4572 555087.4842 422714.5703 460355.9155 857144.1742 0.477464643 0.605729839 0.57717002 0.784512554 0.634967224 0.64760107 0.493166241 0.537081076 1 19.70917836 1.233468308 24.99941702 1.000000624 0.595888417 0.681403627 0.087090009 101.6202704 498821.6308 0.183200448 0.022415186 17.11860251 -1.233468308 -0.404112207 SLQSVAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLQSVAEER 9 0 P61313;A0A2R8YEM3;E7EQV9;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;;; 166.66 0.00014093 2271950000 2491540 2298440 1407130 1715760 2409840 2698330 2297620 2479730 2246300 FALSE TRUE 2162276.676 2283341.396 2087622.775 2105349.532 2361888.899 2802136.501 2074797.166 1949459.037 1980744.973 1.091648196 1.152768997 1.053958386 1.062907926 1.192424533 1.41468818 1.047483242 0.984204965 1 20.91761171 2.014355172 24.99999337 0.99843513 1.15955916 0.341412038 0.100844702 266.5371404 464181.3466 0.043688742 0.029441873 103.3606357 -2.014355172 0.161124031 SLQYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLQYER 6 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 152.63 0.023807 263300000 349200 348630 172040 217330 319520 366750 290180 356150 308770 FALSE TRUE 303052.3352 346339.8266 255239.1194 266678.0982 313162.1771 380859.1098 262038.3883 279990.0941 272267.5624 1.113068089 1.272056883 0.937456953 0.979470694 1.150200099 1.398841296 0.9624297 1.02836376 1 18.05466559 SLRDDYEVSCPELDQLVEAALAVPGVYGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLRDDYEVSCPELDQLVEAALAVPGVYGSR 30 1 P51570;P51570-2;K7EII7 P51570 GALK1 Galactokinase 0 ; 221.8 1.06E-34 504960000 466540 447700 281440 329910 475650 486610 474280 512710 412900 FALSE TRUE 404885.5569 444759.0292 417545.3254 404821.1079 466185.4956 505330.2016 428284.3986 403070.9564 364087.4324 1.112055844 1.221572045 1.146827076 1.111878829 1.280421828 1.387936404 1.176322939 1.107071875 1 18.47392542 1.514363819 2.403270404 1.00136479 1.210213248 0.404239062 0.082371202 0.349099865 3.736281891 0.129518433 0.023918545 32.68615371 -1.514363819 0.208848458 SLRQS(ph)FR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 122.96 0.002598 2411700000 2081760 2109310 889875 1644230 2100030 1555895 1961170 2010110 2149710 TRUE FALSE 1806650.141 2095453.804 1320221.526 2017577.552 2058243.512 1615751.287 1770976.035 1580263.619 1895573.733 0.953088825 1.105445685 0.696475955 1.064362476 1.08581559 0.852381134 0.934269137 0.8336598 1 20.85420314 2.699548382 24.99317059 0.896655219 0.976769557 0.085420681 0.1216872 1351.212337 865652.3043 0.040749664 0.035938241 500.6663253 -2.699548382 0.080114338 SLRVDIAEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLRVDIAEGR 10 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ; 142.08 3.32E-05 594850000 622480 650790 175589 212827 627070 637860 545680 593140 77443 FALSE TRUE 540217.6908 646514.9176 260504.4277 261152.6232 614592.5338 662398.887 492760.0376 466301.6268 68287.77676 7.910898794 9.467505728 3.814803176 3.824295292 9.000037239 9.700109131 7.215933231 6.828478667 1 16.05933974 4.266650982 24.99970101 6.234659695 8.689203633 0.155393907 2.608765817 467.4931658 416049.1002 0.671050624 1.774651503 18477.83063 -4.266650982 2.454543938 SLS(ph)APLHPEFEEVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSAPLHPEFEEVYR 15 0 Q53HC0-2;Q53HC0 Q53HC0-2 CCDC92 Coiled-coil domain-containing protein 92 1 S(0.017)LS(0.983)APLHPEFEEVYR 133.47 2.65E-05 67500000 110440 87059 43464 74308 75641 57401 120790 92261 91556 TRUE FALSE 95845.07418 86487.1037 64483.33578 91180.76713 74135.89209 59609.25361 109075.8044 72531.70313 80732.35398 1.187195337 1.071281827 0.798729786 1.129420395 0.918292214 0.738356442 1.351079202 0.898421755 1 16.30085934 4.476475754 24.99939954 0.981055105 1.158217024 0.137949172 0.170958526 36.12316362 1399090.561 0.040234565 0.108596044 29955.44352 -4.476475754 0.177161919 SLS(ph)ASPALGSTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSASPALGSTK 12 0 O95544;O95544-2 O95544 NADK NAD kinase 1 S(0.001)LS(0.995)AS(0.005)PALGSTK 125.29 0.00032288 330790000 970670 836490 549750 559340 735590 779070 855510 913610 1101700 TRUE FALSE 842393.5001 830995.0421 815610.9388 686346.696 720953.1982 809041.327 772542.7719 718241.6112 971458.2811 0.867143259 0.855409911 0.839573819 0.706511756 0.742135007 0.83281119 0.795240297 0.739343753 1 19.88979252 3.982997378 24.07809491 0.79270683 0.857830445 0.079567364 0.079939242 940.3313167 1331650.922 0.020469579 0.036649194 9616.064719 -3.982997378 0.065123615 SLS(ph)CLSDLDGGVALEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSCLSDLDGGVALEPR 17 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 S(0.024)LS(0.976)CLSDLDGGVALEPR;S(0.005)LS(0.995)CLSDLDGGVALEPR 153.72 1.73E-07 222890000 212190 120281 63495 130100 103441 101190 116004 116162 108335 TRUE FALSE 184148.5539 119490.8662 94201.39438 159641.1935 101382.7265 105082.8448 104753.9499 91321.66027 95527.75972 1.92769677 1.250849665 0.986115394 1.671149768 1.061290737 1.100024172 1.096581248 0.955969872 1 16.54363241 7.33789397 1.020435368 1.101167494 200 0.594099634 0.205065405 299.3260538 1.700584097 0.064290925 137595.8112 21771781.66 -7.33789397 198.8988325 SLS(ph)DPIPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSDPIPQR 9 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 S(0.026)LS(0.974)DPIPQR 99.864 0.0052956 198510000 210320 191520 121860 153110 190110 206900 175100 204730 181240 TRUE FALSE 182525.6791 190261.8925 180791.9036 187875.9656 186327.1829 214859.5769 158118.829 160950.0827 159814.0137 1.142113103 1.190520707 1.131264396 1.17559131 1.165900153 1.344435147 0.989392766 1.007108695 1 17.28603439 2.201745179 24.99980773 1.000164128 1.186943285 0.707619053 0.058368912 90.33151498 61339.72334 0.023246147 0.015672988 159.1274776 -2.201745179 0.186779157 SLS(ph)DS(ph)ESDDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 SLS(1)DS(1)ESDDSK;SLS(1)DS(1)ESDDSK;SLS(1)DS(1)ESDDSK 232.83 6.95E-12 271840000 2336360 1679550 1323100 1477830 1556950 1465890 2067950 2536380 2665280 TRUE FALSE 2027604.106 1668516.925 1962955.586 1813393.889 1525969.741 1522283.737 1867400.527 1993994.875 2350193.635 0.86273917 0.709948704 0.835231428 0.771593396 0.649295326 0.647726942 0.794573051 0.848438548 1 21.1643482 1.366529443 1.815088788 1.04604632 0.745901228 0.564676504 0.070119159 0.511762143 2.060889082 0.249038006 0.02033888 23.25570141 -1.366529443 -0.300145091 SLS(ph)DSESDDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 SLS(1)DSESDDSK;SLS(0.997)DS(0.003)ESDDSK;SLS(0.999)DS(0.001)ESDDSK;S(0.001)LS(0.996)DS(0.003)ESDDSK;SLS(0.992)DS(0.008)ESDDSK;SLS(0.718)DS(0.282)ESDDSK 315.83 9.34E-46 1182398000 3235110 2352750 1798440 2086050 2021100 1795830 2820760 3400340 3071850 TRUE FALSE 2807582.017 2337294.63 2668171.599 2559719.536 1980884.064 1864916.742 2547203.129 2673203.752 2708699.392 1.036505573 0.862884467 0.985037914 0.944999487 0.731304503 0.688491587 0.940378669 0.986895689 1 21.36916886 2.008155147 24.99807306 0.983849468 0.870865307 0.181445796 0.104901628 322.0714433 987245.5161 0.045999804 0.030951294 101.8955334 -2.008155147 -0.112984161 SLS(ph)ELESLKLPAESNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSELESLKLPAESNEK 17 1 P22059 P22059 OSBP Oxysterol-binding protein 1 1 SLS(1)ELESLKLPAESNEK;SLS(1)ELESLKLPAESNEK 232.82 1.33E-17 293540000 991090 689230 593070 625020 635720 512440 1012170 1101960 818120 TRUE FALSE 860114.9454 684702.4027 879880.6357 766940.3438 623070.4158 532153.8984 914009.9092 866314.4295 721402.7856 1.192281154 0.949126364 1.219680119 1.063123624 0.863692833 0.737665433 1.266989714 1.200874805 1 19.46044547 0.946073753 21.98973109 0.000101474 1.065184186 0.012447102 0.170130999 363.0241101 802338.523 81236.81314 0.04246173 8.832298793 -0.946073753 1.065082712 SLS(ph)ESSVIMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSESSVIMDR 11 0 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2;H3BNX5 H3BSS6 ZNF106 Zinc finger protein 106 1 S(0.001)LS(0.998)ES(0.001)S(0.001)VIMDR;S(0.001)LS(0.998)ES(0.001)SVIMDR 216.97 1.23E-11 200900000 195847 234268 180920 252690 318270 343680 309790 354240 347370 TRUE FALSE 169965.3227 232729.0781 268413.5171 310067.1266 311937.0497 356901.592 279746.6135 278488.5327 306304.3143 0.554890398 0.759796931 0.876296887 1.012284555 1.018389344 1.165186304 0.913296354 0.909189064 1 18.22460616 4.47592027 1.405860555 0.99512129 0.490167951 0.809498742 0.072042374 0.36375617 0.935445807 0.023248336 0.227774381 29917.15354 -4.47592027 -0.50495334 SLS(ph)ESYELSSDLQDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSESYELSSDLQDK 15 0 A0A3B3IRZ4;Q6DN90-3;A0A2R8Y7T6;Q6DN90;A0A2R8Y695 A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 S(0.002)LS(0.998)ESYELSSDLQDK;SLS(0.999)ES(0.001)YELSSDLQDK 364.82 1.24E-71 56463000 156570 153537 144768 164461 215820 196505 290770 340260 346430 TRUE FALSE 135878.8778 152528.4053 214778.289 201804.3837 211525.6042 204064.6745 262571.1702 267498.0469 305475.4401 0.444811137 0.49931479 0.703095113 0.660623923 0.692447171 0.668023179 0.8595492 0.875677753 1 18.22069687 -1.999999998 0.097844599 2.855829644 3.28E-13 0.884266392 0.057056949 100.1931463 0.907465399 39.31684884 4.297563191 0.01 1.999999998 -2.855829644 SLS(ph)FEMQQDELIEKPMSPMQYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 16 SLSFEMQQDELIEKPMSPMQYAR 23 1 Q9Y6Y0 Q9Y6Y0 IVNS1ABP Influenza virus NS1A-binding protein 1 S(0.039)LS(0.961)FEMQQDELIEKPMSPMQYAR;S(0.001)LS(0.999)FEMQQDELIEKPMSPMQYAR;S(0.006)LS(0.994)FEMQQDELIEKPMSPMQYAR;SLS(1)FEMQQDELIEKPMSPMQYAR;SLS(1)FEMQQDELIEKPMSPMQYAR;S(0.046)LS(0.954)FEMQQDELIEKPMSPMQYAR;S(0.009)LS(0.991)FEMQQDELIEKPMSPMQYAR;S(0.066)LS(0.934)FEMQQDELIEKPMSPMQYAR;SLS(1)FEMQQDELIEKPMSPMQYAR;S(0.158)LS(0.842)FEMQQDELIEKPMSPMQYAR;S(0.029)LS(0.971)FEMQQDELIEKPMSPMQYAR;S(0.181)LS(0.819)FEMQQDELIEKPMSPMQYAR;S(0.035)LS(0.965)FEMQQDELIEKPMSPMQYAR;S(0.11)LS(0.89)FEMQQDELIEKPMSPMQYAR;S(0.135)LS(0.865)FEMQQDELIEKPMSPMQYAR;S(0.487)LS(0.513)FEMQQDELIEKPMSPMQYAR 261.92 5.15E-44 7489962000 5405094 4738688 2708033 3462103 4529457 2983968 6111085 6509726 3993491 TRUE FALSE 4690797.133 4707559.247 4017646.817 4248226.401 4439329.667 3098763.18 5518432.917 5117671.754 3521385.043 1.332088674 1.336848765 1.140928006 1.206407805 1.260677152 0.879984194 1.567119997 1.453312174 1 21.74771156 1.212210047 24.55778372 0.99999828 1.27773731 0.177812298 0.183581775 4238.15273 3949540.868 3.708764912 0.046927431 16.30084233 -1.212210047 0.277739031 SLS(ph)FSDEMSSCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSFSDEMSSCR 12 0 Q14153-2;Q14153 Q14153-2 FAM53B Protein FAM53B 1 SLS(0.99)FS(0.01)DEMSSCR;SLS(0.5)FS(0.5)DEMSSCR 254.82 4.23E-21 287620000 269550 285830 210590 269690 353620 347420 346450 408830 353270 TRUE FALSE 233928.2845 283952.3639 312432.0284 330927.2365 346583.6538 360785.4722 312851.3323 321404.886 311506.823 0.750957177 0.911544605 1.002970097 1.062343461 1.112603732 1.158194446 1.004316147 1.031774787 1 18.24890424 4.581917531 1.461751475 1.060636016 0.682242206 0.817850382 0.047682987 0.387744068 0.960898242 0.014946866 0.196595993 38187.17499 -4.581917531 -0.37839381 LSS(ph)PVLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 LSSPVLHR 8 0 Q16643;Q16643-3;Q16643-2;D6R9W4;D6RCR4 Q16643 DBN1 Drebrin 1 LS(0.06)S(0.94)PVLHR;LS(0.019)S(0.981)PVLHR;LS(0.003)S(0.997)PVLHR;LS(0.242)S(0.758)PVLHR;LS(0.322)S(0.678)PVLHR 152.37 0.00029512 7558500000 4342370 1574444 864432 1134635 1542686 1366770 1339425 1625367 1432455 TRUE FALSE 3768514.802 1564101.374 1282474.207 1392271.219 1511989.567 1419350.526 1209527.77 1277794.916 1263111.802 2.983516421 1.238292106 1.01532913 1.102254936 1.197035421 1.123693504 0.95757776 1.011624556 1 20.26855091 4.740645254 3.836742038 1.059710322 3.178504788 0.986804337 0.069450252 0.028853062 0.83856695 0.019436456 0.173055557 55035.79629 -4.740645254 2.118794466 up SLS(ph)GSSPCPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.003)LS(0.973)GS(0.023)SPCPK;S(0.002)LS(0.825)GS(0.158)S(0.015)PCPK;SLS(0.571)GS(0.404)S(0.025)PCPK 197.94 3.21E-07 539000000 1311940 797400 575646 733680 807620 776820 1021910 1115580 1048710 TRUE FALSE 1138563.805 792161.8269 854030.331 900273.2576 791549.9421 806704.7681 922805.3255 877021.8985 924732.6985 1.231235585 0.856638711 0.923542914 0.973549718 0.855977023 0.872365354 0.997915751 0.948405847 1 19.81867688 4.74728402 24.99943099 0.930578412 1.231235738 0.75800756 0.053736743 580.7144096 1664168.884 0.013320298 0.153621576 55883.55428 -4.74728402 0.300657325 SLS(ph)LDPGQSLEPHPEGPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLSLDPGQSLEPHPEGPQR 19 0 P98174 P98174 FGD1 "FYVE, RhoGEF and PH domain-containing protein 1" 1 S(0.185)LS(0.815)LDPGQSLEPHPEGPQR;S(0.006)LS(0.994)LDPGQSLEPHPEGPQR;S(0.186)LS(0.81)LDPGQS(0.004)LEPHPEGPQR 223.68 1.38E-19 611060000 821940 680367 235434 428259 652199 472189 770660 735050 564529 TRUE FALSE 713318.5465 675897.6244 349290.6699 525501.7515 639221.5159 490354.4164 695921.5118 577865.2777 497791.0247 1.432967874 1.357793915 0.701681333 1.055667389 1.284116194 0.985060783 1.398019404 1.160859174 1 18.92518069 4.451033107 24.99973864 1.104656937 1.414175225 0.325616823 0.186137537 227.2277342 217747.5368 0.046622149 0.123357925 28250.95326 -4.451033107 0.309518288 SLS(ph)LESTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLSLESTDR 9 0 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 1 S(0.003)LS(0.988)LES(0.008)T(0.001)DR;S(0.001)LS(0.999)LESTDR;SLS(0.996)LES(0.004)TDR;SLS(0.977)LES(0.022)TDR;SLS(0.986)LES(0.013)TDR;SLS(0.999)LES(0.001)TDR 184.71 4.58E-05 4184460000 4049890 3782790 2906560 3425190 4484360 5097370 4161110 4590390 4743220 TRUE FALSE 3514686.775 3757940.603 4312182.138 4202931.74 4395130.01 5293469.122 3757566.193 3608770.821 4182481.935 0.840335196 0.898495358 1.031010344 1.004889395 1.050842557 1.265628688 0.898405839 0.862829984 1 21.99592788 6.587939657 13.90955652 0.980912837 0.471889873 0 0.123246778 0 0 0.029484587 0 3872038.412 -6.587939657 -0.509022964 TPLS(ph)PSPMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TPLSPSPMK 9 0 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 T(0.001)PLS(0.995)PS(0.004)PMK;TPLS(0.995)PS(0.005)PMK;T(0.003)PLS(0.993)PS(0.003)PMK;TPLS(0.914)PS(0.086)PMK;TPLS(0.906)PS(0.094)PMK 133.81 0.00027965 2162640000 2361560 3836760 2841360 4093930 5680130 4670220 6211470 7712890 6813300 TRUE FALSE 2049473.863 3811556.071 4215451.2 5023519.378 5567106.526 4849886.385 5609082.595 6063548.495 6007839.436 0.341133262 0.634430416 0.701658432 0.836160725 0.926640365 0.807259654 0.933627247 1.009272728 1 22.51841483 4.741987416 0.593785521 0.971635893 7.83E-17 0.924278624 0.055543421 1.014391763 0.281079256 0.032992747 0.684189468 55206.14429 -4.741987416 -0.971635893 down SLS(ph)LGDKEISR ddPTM_MDA-MB-175_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(0.002)LS(0.998)LGDKEISR;SLS(1)LGDKEISR;SLS(1)LGDKEISR;SLS(0.999)LGDKEIS(0.001)R 218.68 6.32E-12 1883930000 3033600 2552620 2030930 2562380 3570600 3282590 4285860 4736190 2758710 TRUE FALSE 2632702.074 2535851.671 3013094.541 3144207.543 3499552.046 3408873.361 3870217.957 3723392.626 2432578.447 1.082268108 1.042454222 1.238642291 1.292541068 1.438618373 1.401341595 1.5909941 1.530636198 1 21.2140549 3.850745548 1.398195357 1.425271729 1.047755493 0.388486864 0.15944412 0.427249887 1.580518455 0.051228693 0.141764078 7091.621494 -3.850745548 -0.377516236 SLS(ph)LSLADSGHLPDVHGFNSYGSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLSLSLADSGHLPDVHGFNSYGSHR 25 0 Q9Y446;Q9Y446-2;E9PKC4;E9PRW6 Q9Y446 PKP3 Plakophilin-3 1 S(0.191)LS(0.618)LS(0.191)LADSGHLPDVHGFNSYGSHR;S(0.184)LS(0.804)LS(0.013)LADSGHLPDVHGFNSYGSHR;S(0.171)LS(0.658)LS(0.171)LADSGHLPDVHGFNSYGSHR;S(0.14)LS(0.856)LS(0.003)LADSGHLPDVHGFNSYGSHR 165.4 2.57E-11 1298890000 272248 320344 128617.4 238393.9 314345 352048 283626 296605 286850 TRUE FALSE 236269.737 318239.6392 190817.2048 292524.8786 308090.1495 365591.5144 256119.9942 233178.3289 252938.9198 0.934097992 1.258167938 0.754400331 1.156504024 1.218041691 1.445374696 1.012576453 0.921876037 1 17.94842952 2.013757243 24.99874126 0.958918177 1.131034367 0.13151885 0.184658464 431.3432718 783805.073 0.076356411 0.051452761 103.2184287 -2.013757243 0.17211619 SLS(ph)MDSQVPVYSPSIDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLSMDSQVPVYSPSIDLK 18 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 S(0.047)LS(0.953)MDSQVPVYSPSIDLK;S(0.151)LS(0.844)MDS(0.005)QVPVYSPSIDLK;S(0.142)LS(0.858)MDSQVPVYSPSIDLK;S(0.022)LS(0.591)MDS(0.387)QVPVYSPSIDLK;S(0.115)LS(0.885)MDSQVPVYSPSIDLK;S(0.14)LS(0.86)MDSQVPVYSPSIDLK 321.84 1.17E-61 494345000 2454890 1631630 1150775 1578850 1820140 1427061 2157610 2538100 2685570 TRUE FALSE 2130470.067 1620911.715 1707293.639 1937352.024 1783922.775 1481960.96 1948365.314 1995347.067 2368084.974 0.899659467 0.684482074 0.720959618 0.818109166 0.753318734 0.625805652 0.822759882 0.842599437 1 21.17528942 1.301271152 1.592109985 1.073581427 0.750922262 0.507849994 0.07562672 0.752757272 1.950326394 0.373620071 0.020981154 20.01110873 -1.301271152 -0.322659166 SLS(ph)MVDLQDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLSMVDLQDAR 11 0 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 SLS(1)MVDLQDAR;SLS(1)MVDLQDAR;SLS(1)MVDLQDAR;S(0.002)LS(0.998)MVDLQDAR 245.55 6.26E-16 666620000 1332930 1377220 931180 946690 1390030 1603230 1259130 1357510 1364680 TRUE FALSE 1156779.923 1368172.951 1381501.763 1161650.434 1362371.123 1664907.296 1137019.766 1067217.051 1203349.085 0.961300372 1.136970949 1.148047379 0.965347835 1.132149548 1.383561359 0.944879404 0.886872366 1 20.19862379 2.042312802 24.99997261 0.929510471 1.12054547 0.330529708 0.118589044 146.6343861 86636.41614 0.04830214 0.03256527 110.2332983 -2.042312802 0.191034998 SLS(ph)PFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSPFR 6 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36;H0YLH1 Q12802-2 AKAP13 A-kinase anchor protein 13 1 S(0.159)LS(0.841)PFR;S(0.003)LS(0.997)PFR 98.523 0.041788 1404780000 772530 851360 425870 531990 873630 789740 854780 908250 847750 TRUE FALSE 670438.2032 845767.3601 631822.1564 652786.4605 856246.4722 820121.8088 771883.5672 714027.8055 747529.9608 0.896871347 1.131416003 0.845213155 0.873257922 1.14543432 1.097108948 1.03257877 0.95518286 1 19.51177188 3.253964202 24.99948136 1.036242475 0.94406463 0.254950378 0.091674653 429.1292279 696457.4331 0.027663043 0.035583004 1794.585697 -3.253964202 -0.092177845 SLS(ph)PFRR ddPTM_MDA-MB-175_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 S(0.001)LS(0.999)PFRR;SLS(1)PFRR 104.01 0.0050512 386070000 239140 257700 139890 153003 245550 265400 202647 249440 149914 TRUE FALSE 207537.0431 256007.1517 207541.2719 187744.6697 240664.0354 275610.1097 182994.3251 196099.1971 132191.3377 1.569974604 1.936640904 1.570006594 1.420249412 1.820573417 2.084933208 1.384314043 1.483449676 1 17.01226812 1.207568475 1.318708672 0.660541305 1.711607898 0.515974287 0.2137421 1.251540332 1.779942399 1.844428276 0.065129528 16.12755289 -1.207568475 1.051066593 SLS(ph)PGGAALGYR ddPTM_MDA-MB-175_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 S(0.001)LS(0.999)PGGAALGYR;S(0.001)LS(0.999)PGGAALGYR;SLS(1)PGGAALGYR;S(0.003)LS(0.997)PGGAALGYR;S(0.008)LS(0.992)PGGAALGYR;SLS(1)PGGAALGYR;S(0.005)LS(0.995)PGGAALGYR;S(0.006)LS(0.994)PGGAALGYR 221.52 3.22E-11 14629300000 10571280 7531300 4628050 5695280 7770230 8038510 7035160 8057760 7675890 TRUE FALSE 9174258.564 7481826.394 6866190.46 6988480.371 7615617.625 8347756.681 6352891.266 6334670.73 6768455.029 1.355443528 1.105396485 1.014439843 1.032507469 1.125163363 1.233332665 0.938602863 0.935910884 1 22.69039513 4.725944894 2.662766089 1.035120657 1.414501982 0.560586927 0.087195621 0.376285653 3.609592177 0.024920377 0.312951193 53204.07464 -4.725944894 0.379381324 SLS(ph)PGVSR ddPTM_MDA-MB-175_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(0.016)LS(0.984)PGVSR;S(0.008)LS(0.992)PGVSR 134.51 0.00091634 1202000000 1708770 1636740 1118790 1419160 1704320 1695060 1530550 1846200 2420700 TRUE FALSE 1482951.715 1625988.147 1659840.586 1741401.969 1670407.366 1760270.055 1382117.497 1451404.497 2134527.604 0.694744688 0.761755502 0.777614955 0.815825462 0.782565362 0.824664929 0.647505094 0.679965204 1 21.02548539 4.733521007 3.180959266 0.774111919 0.683559041 0.073958266 0.094458501 1.11343563 17.79439691 0.023750798 0.249451711 54140.34354 -4.733521007 -0.090552878 SLS(ph)PIIGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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;S(0.007)LS(0.993)PIIGK;S(0.015)LS(0.985)PIIGK;SLS(1)PIIGK 174.41 0.0002854 9330630000 14626540 13797480 9122340 13545660 14093690 12235880 14148440 18791000 16179750 TRUE FALSE 12693605.68 13706843.45 13533934.14 16621409.14 13813253.14 12706602.22 12776326.47 14772690.88 14266998.39 0.889718029 0.960737716 0.948618186 1.165024954 0.968196166 0.89062898 0.89551608 1.035444911 1 23.7661785 4.669704353 2.102835282 0.987601668 0.872854148 0.13628576 0.07713235 1.306152961 7.246711197 0.021188571 0.269022331 46741.68381 -4.669704353 -0.114747521 SLS(ph)PILPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSPILPGR 9 0 M0QZS0;A0A590UK10;A0A3B3IPE9;A0A087WZG4;Q6ZSZ5-2;Q6ZSZ5-1;Q6ZSZ5-6;Q6ZSZ5-5;Q6ZSZ5 M0QZS0 ARHGEF18 Rho guanine nucleotide exchange factor 18 1 SLS(1)PILPGR;S(0.078)LS(0.922)PILPGR 142.94 0.00010818 952990000 984980 904850 574190 679000 915000 943850 853870 966420 994980 TRUE FALSE 854812.3974 898905.9808 851870.2046 833177.3279 896793.2902 980160.5203 771061.8188 759758.6037 877354.5979 0.974306625 1.024564051 0.970953143 0.949647189 1.022156027 1.117177163 0.878848553 0.865965261 1 19.74280052 2.196719137 24.99999395 0.903231467 1.006533604 0.371070304 0.057444925 141.8134186 84731.55617 0.023715439 0.015989104 157.2965283 -2.196719137 0.103302137 SLS(ph)PNHNTLQTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSPNHNTLQTLK 13 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.002)LS(0.993)PNHNT(0.005)LQTLK;S(0.007)LS(0.993)PNHNTLQTLK 274.08 2.38E-32 1187200000 2532520 2390950 1075634 1898000 2605390 2257280 2651840 3292320 2835660 TRUE FALSE 2197841.065 2375243.692 1595814.2 2328969.909 2553547.836 2344119.022 2394664.965 2588282.989 2500431.505 0.878984712 0.949933516 0.638215523 0.931427197 1.021242866 0.937485797 0.957700685 1.035134529 1 21.25374565 3.487417846 24.84361888 0.989510691 0.82674812 0.466733215 0.081897497 397.266794 958524.8018 0.022572181 0.031107881 3071.976193 -3.487417846 -0.162762572 SLS(ph)PS(ph)GLKIQT(ph)GK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSPSGLKIQTGK 13 1 F6VUX8;Q9HC77-2;Q9HC77 F6VUX8 CENPJ Centromere protein J 3 S(0.002)LS(0.998)PS(1)GLKIQT(1)GK 85.864 0.065379 651370000 463360 383830 249710 410940 338680 348570 344000 463030 645180 TRUE FALSE 402125.802 381308.5955 370470.5912 504250.2078 331940.9306 361979.7135 310638.9329 364014.6378 568907.5554 0.706838568 0.670247023 0.651196469 0.886348235 0.583470772 0.636271588 0.546027083 0.639848486 1 19.11783472 1.236338266 24.99919529 1.000000436 0.661471612 0.576061688 0.090261612 44.73488578 503101.0449 0.144541451 0.022395218 17.23210238 -1.236338266 -0.338528824 SLS(ph)PSHLTEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SLSPSHLTEDR 11 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 SLS(1)PSHLTEDR;S(0.078)LS(0.922)PSHLTEDR;S(0.105)LS(0.62)PS(0.275)HLTEDR;S(0.095)LS(0.887)PS(0.018)HLTEDR;S(0.121)LS(0.868)PS(0.01)HLTEDR 280.71 2.41E-27 4514850000 2610660 2295610 1463290 1832030 2252580 2378220 2082440 2382050 2219880 TRUE FALSE 2265654.666 2280529.987 2170941.938 2248020.412 2207758.065 2469711.662 1880485.289 1872667.145 1957448.315 1.157453123 1.165052466 1.10906731 1.148444327 1.127875535 1.261699552 0.960681963 0.956687914 1 20.90054278 2.218933584 24.99870075 0.968680769 1.157237114 0.822356912 0.041395116 89.78017344 114351.0199 0.016347971 0.01103906 165.5516769 -2.218933584 0.188556345 SLS(ph)PSLLGYQQPALMAAPLSLADAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSPSLLGYQQPALMAAPLSLADAHR 26 0 Q13469-3;Q13469-4;Q13469-2;Q13469;Q13469-5 Q13469-3 NFATC2 "Nuclear factor of activated T-cells, cytoplasmic 2" 1 S(0.151)LS(0.83)PS(0.019)LLGYQQPALMAAPLSLADAHR;S(0.133)LS(0.758)PS(0.108)LLGYQQPALMAAPLSLADAHR 188.26 6.65E-18 617330000 131571 189697 85825 151134 226040 220180 173285 255270 185272 TRUE FALSE 114183.559 188450.8679 127330.2571 185451.2846 221542.2462 228650.4671 156479.8474 200682.497 163369.3552 0.698928871 1.153526423 0.779401112 1.135165676 1.356082026 1.39959215 0.95782864 1.228397436 1 17.31777786 3.598954772 5.911306833 1.19145704 0.906847155 0.390622881 0.177575752 0.249343733 11.02678649 0.047575436 0.070925542 3971.50188 -3.598954772 -0.284609885 SLS(ph)PVAAPPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSPVAAPPLR 11 0 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 S(0.016)LS(0.984)PVAAPPLR;SLS(1)PVAAPPLR 109.16 0.0020627 220750000 352820 302340 219589 292560 294870 287570 302450 319150 680640 TRUE FALSE 306193.9431 300353.9086 325782.9749 358990.2195 289002.6639 298633.004 273118.4456 250902.2561 600175.5146 0.510174 0.500443456 0.542812839 0.598142061 0.481530247 0.49757612 0.455064292 0.418048138 1 19.19502494 1.232965204 24.99972611 1.000000798 0.498173327 0.914656915 0.04794841 55.21156898 246653.1733 0.114350397 0.013386348 17.09878314 -1.232965204 -0.501827471 SLS(ph)PVAAPPLREPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLSPVAAPPLREPR 14 1 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 S(0.009)LS(0.991)PVAAPPLREPR;S(0.048)LS(0.952)PVAAPPLREPR;S(0.042)LS(0.958)PVAAPPLREPR;S(0.031)LS(0.969)PVAAPPLREPR 128.59 4.41E-05 6764100000 7078800 6459300 3656180 4589670 6032660 6249610 5758350 6355300 4639950 TRUE FALSE 6143318.645 6416868.433 5424320.877 5631824.722 5912621.869 6490036.541 5199906.103 4996268.552 4091420.397 1.501512445 1.568371815 1.3257794 1.376496223 1.445126947 1.586255117 1.27092931 1.221157463 1 21.96417035 1.543453717 1.396546729 0.950236555 1.458306311 0.741602361 0.08962749 0.361216983 1.00038863 0.236127178 0.028215494 34.95052604 -1.543453717 0.508069755 SLS(ph)S(ph)SPQAQPPRPAELSDEEVAELFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSSSPQAQPPRPAELSDEEVAELFQR 27 1 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 2 S(0.199)LS(0.775)S(0.513)S(0.513)PQAQPPRPAELSDEEVAELFQR 70.525 0.0119 47976000 30970 36810 26470 17794 21839 35552 26435 23925 25424 TRUE FALSE 26877.23603 36568.19269 39270.98054 21834.39966 21404.44663 36919.70845 23871.33777 18808.82493 22418.40368 1.198891608 1.631168445 1.751729565 0.973949795 0.95477122 1.646848231 1.064809881 0.838990376 1 14.45239593 1.828943977 0.348336536 0.558004265 1.543292777 0.266951311 0.282849742 7.16980271 1.318999662 3.261327367 0.718386212 67.44410204 -1.828943977 0.985288512 SLS(ph)SPTVTLSAPLEGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLSSPTVTLSAPLEGAK 17 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-2;Q96PU5-4;Q96PU5-5;Q96PU5-6;Q96PU5-9 Q96PU5-7;Q96PU5-5 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 S(0.021)LS(0.604)S(0.372)PT(0.003)VTLSAPLEGAK;SLS(0.943)S(0.057)PTVTLSAPLEGAK;S(0.005)LS(0.892)S(0.103)PTVTLSAPLEGAK;SLS(0.652)S(0.348)PTVTLSAPLEGAK 358.31 5.09E-88 2266677000 3230450 1451915 1227793 1473181 1678634 1847190 1620970 2391580 2501643 TRUE FALSE 2803537.848 1442377.275 1821557.802 1807689.262 1645232.468 1918252.595 1463768.579 1880159.228 2205901.614 1.27092606 0.653871988 0.82576566 0.819478643 0.745832206 0.86960025 0.663569295 0.852331408 1 21.07293702 4.749988247 24.96548062 0.802443988 1.27092634 0.679620421 0.100789059 984.794912 2151400.841 0.023376246 0.35937807 56232.61078 -4.749988247 0.468482352 SLS(ph)TEVEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSTEVEPK 9 0 A0A087WVA8;Q8IWB9;Q8IWB9-2 A0A087WVA8 TEX2 Testis-expressed sequence 2 protein 1 SLS(0.987)T(0.013)EVEPK;S(0.003)LS(0.644)T(0.353)EVEPK 136.81 0.00019132 173310000 539550 389370 242552 365922 394824 259073 557490 628780 489180 TRUE FALSE 468247.1005 386812.2028 359850.9585 449010.1829 386967.7749 269039.706 503424.7056 494320.2902 431349.6977 1.08553942 0.89674852 0.834244142 1.040942385 0.897109183 0.623715995 1.167091824 1.145985016 1 18.71849842 SLS(ph)TSGESLYHVLGLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLSTSGESLYHVLGLDK 17 0 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 S(0.001)LS(0.901)T(0.097)S(0.001)GESLYHVLGLDK;S(0.006)LS(0.753)T(0.172)S(0.064)GES(0.006)LYHVLGLDK;S(0.017)LS(0.931)T(0.041)S(0.011)GESLYHVLGLDK 282.33 3.22E-36 6047970000 5598520 4698290 2719019 5602390 5535400 4999350 4192210 7586710 10030780 TRUE FALSE 4858661.397 4667426.624 4033945.683 6874498.277 5425256.37 5191678.23 3785650.119 5964351.106 8844952.616 0.549314576 0.527693796 0.456073182 0.777222737 0.613373141 0.58696507 0.428001176 0.674322562 1 23.07642298 1.2842712 3.370209265 1.043706483 0.567591643 0.675732243 0.094971433 0.16948785 2.750911088 0.195721749 0.024670943 19.24293002 -1.2842712 -0.47611484 SLS(ph)VEHLETK ddPTM_MDA-MB-175_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(0.058)LS(0.942)VEHLETK;S(0.029)LS(0.971)VEHLETK 201.04 1.60E-07 1134710000 4310600 3557000 2459900 3316600 3447300 3384000 3314200 4596300 4325800 TRUE FALSE 3740943.288 3533633.833 3649515.868 4069684.721 3378705.475 3514184.67 2992789.394 3613417.013 3814408.852 0.980739987 0.926390948 0.956771025 1.066924097 0.885774338 0.921292081 0.784601103 0.947307212 1 21.86302806 SLS(ph)VPDSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSVPDSGR 9 0 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 S(0.008)LS(0.992)VPDSGR 92.409 0.01059 163000000 406570 285620 203960 246370 296010 208510 380900 328000 313810 TRUE FALSE 352840.7444 283743.7434 302595.7382 302312.074 290119.9801 216531.5146 343960.3766 257859.7525 276711.7393 1.275120258 1.025412742 1.093541383 1.092516258 1.048455627 0.782516547 1.243027771 0.931871388 1 18.07802432 7.99999994 0.855000112 1.013424973 90.41168973 0.295282206 0.118736366 894.4474597 2.420831886 0.037823819 155588.6779 99999986.25 -7.99999994 89.39826476 SLS(ph)VPVDLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLSVPVDLSR 10 0 Q9NYF3;D6RHW3 Q9NYF3 FAM53C Protein FAM53C 1 S(0.002)LS(0.998)VPVDLSR;SLS(1)VPVDLSR;SLS(1)VPVDLSR;SLS(1)VPVDLSR 201.09 1.37E-06 238321000 1056640 886780 505447 644330 894710 904030 762170 914280 875880 TRUE FALSE 917002.3468 880954.6838 749882.8598 790634.9745 876907.0215 938808.6191 688254.8707 718768.3369 772334.4642 1.187312478 1.140638835 0.970930205 1.023695058 1.13539802 1.215546713 0.891135774 0.930643873 1 19.55886623 2.224085217 24.996355 0.936459682 1.104146649 0.529462975 0.07599667 199.6906348 344826.4288 0.033004736 0.02236476 167.5271565 -2.224085217 0.167686967 SLS(ph)YEEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSYEEPR 8 0 Q8IZD4;Q8IZD4-2;F5GZK9 Q8IZD4 DCP1B mRNA-decapping enzyme 1B 1 S(0.048)LS(0.95)Y(0.001)EEPR;S(0.005)LS(0.994)Y(0.001)EEPR 104.22 0.0048482 1203730000 3468600 2604900 1787140 1903410 2782800 2435500 2966600 3197000 2709300 TRUE FALSE 3010215.722 2587788.24 2651406.882 2335608.332 2727427.724 2529195.261 2678899.589 2513346.429 2389009.64 1.260026611 1.083205441 1.109835154 0.977647094 1.141656224 1.058679387 1.121343147 1.052045327 1 21.18798124 4.937516377 1.967236168 1.0664809 1.407633651 0.586012562 0.050817251 1.086440492 2.806074038 0.01254275 0.802157768 86599.69799 -4.937516377 0.341152751 SLS(ph)YS(ph)PVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SLSYSPVER 9 0 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 SLS(0.968)Y(0.455)S(0.577)PVER;SLS(0.97)Y(0.089)S(0.94)PVER;S(0.005)LS(0.971)Y(0.024)S(0.999)PVER;S(0.003)LS(0.96)Y(0.19)S(0.846)PVER;S(0.002)LS(0.973)Y(0.242)S(0.783)PVER 178.53 7.43E-05 3662440000 4994140 4338960 2713660 3134770 4292750 4181600 3880450 4412640 4227700 TRUE FALSE 4334151.745 4310457.086 4025995.053 3846567.44 4207332.674 4342468.858 3504124.556 3469031.275 3727906.122 1.162623629 1.156267606 1.079961491 1.031830554 1.128604781 1.164854671 0.939971244 0.930557573 1 21.8299341 2.230604572 24.99839708 0.950663791 1.11677694 0.752022442 0.044267787 88.59648284 278372.7288 0.019092024 0.01313151 170.0609388 -2.230604572 0.166113149 SLSCLS(ph)DLDGGVALEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLSCLSDLDGGVALEPR 17 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 S(0.001)LS(0.006)CLS(0.993)DLDGGVALEPR;SLSCLS(1)DLDGGVALEPR;SLSCLS(1)DLDGGVALEPR 155.79 9.14E-08 82214000 157325 125839 63290.3 122904 126915 91504 158628 161225 145255 TRUE FALSE 136534.1026 125012.3553 93897.70077 150811.2317 124389.6398 95024.21809 143244.281 126748.2884 128083.1194 1.065980461 0.976025224 0.733099734 1.177448148 0.971163416 0.741894939 1.118369709 0.989578401 1 16.96672082 SLSFPILNPALSQPSQPSS(ph)PLPGSHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSFPILNPALSQPSQPSSPLPGSHGR 27 0 Q8ND24;E9PN76;Q8ND24-2 Q8ND24 RNF214 RING finger protein 214 1 SLSFPILNPALSQPS(0.001)QPS(0.217)S(0.729)PLPGS(0.052)HGR 147.35 8.72E-08 227930000 168700 195110 93567 195200 247490 204160 218370 299040 253310 TRUE FALSE 146405.8676 193828.3096 138816.3142 239523.1434 242565.4332 212014.1673 197192.511 235092.6231 223363.9804 0.655458715 0.867768873 0.621480303 1.072344534 1.085964858 0.949186914 0.882830395 1.052509105 1 17.76903703 3.733294397 24.99818629 1.004965735 0.730189251 0.715143126 0.086759295 231.9445977 1101016.567 0.02320851 0.035596925 5411.210101 -3.733294397 -0.274776484 SLSGS(ph)SPCPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SLSGS(0.782)S(0.218)PCPK 171.67 4.15E-06 242910000 1017400 892390 485780 637350 814440 619140 835950 1015100 860930 TRUE FALSE 882948.0122 886527.8313 720704.8328 782070.0588 798234.2374 642958.7164 754879.6977 798028.7645 759151.8362 1.163071694 1.167787245 0.949355318 1.030189247 1.051481666 0.846943504 0.994372485 1.051211005 1 19.53402894 4.247186222 24.99829241 0.993530725 1.165429574 0.604789418 0.059181588 129.7164724 375929.4884 0.015215974 0.038920574 17667.95245 -4.247186222 0.171898849 SLSGSS(ph)PCPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SLSGS(0.204)S(0.796)PCPK;SLSGS(0.014)S(0.986)PCPK;SLSGS(0.123)S(0.877)PCPK;SLSGS(0.047)S(0.953)PCPK;SLSGS(0.105)S(0.895)PCPK;SLSGSS(1)PCPK;SLSGS(0.186)S(0.814)PCPK 220.45 6.13E-09 6257990000 11295840 9566370 5523910 6536230 8234070 6671820 9261460 11044200 9141100 TRUE FALSE 9803066.124 9503527.886 8195291.352 8020380.922 8070228.117 6928489.233 8363285.035 8682483.776 8060449.572 1.216193469 1.179031988 1.016728816 0.995028981 1.001213151 0.859566104 1.037570542 1.077171155 1 22.94242888 4.26018551 3.694965945 1.000844756 1.208707082 0.696911046 0.055032135 0.133264306 3.82392141 0.0156846 0.043619758 18204.78315 -4.26018551 0.207862326 SLSKS(ph)DSDLLTCSPTEDATMGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLSKSDSDLLTCSPTEDATMGSR 23 1 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 S(0.033)LS(0.157)KS(0.759)DS(0.051)DLLTCSPTEDATMGSR;S(0.001)LS(0.016)KS(0.982)DS(0.001)DLLTCSPTEDATMGSR;S(0.005)LS(0.141)KS(0.853)DS(0.001)DLLTCSPTEDATMGSR;S(0.046)LS(0.329)KS(0.625)DSDLLTCSPTEDATMGSR;S(0.006)LS(0.034)KS(0.956)DS(0.004)DLLTCSPTEDATMGSR;SLS(0.012)KS(0.988)DSDLLTCSPTEDATMGSR 270.28 1.81E-46 3678000000 2288380 2024170 1226232 1223215 1938160 1634340 2182240 2517330 1362757 TRUE FALSE 1985964.785 2010873.094 1819241.897 1500964.661 1899594.408 1697214.117 1970606.701 1979018.569 1201653.42 1.652693491 1.673421854 1.51394892 1.249082836 1.580817211 1.412399024 1.639912697 1.646912942 1 20.19658942 -1.999999889 0.035459801 1.12E-06 2.510696456 0.17027438 0.196777079 5855.507262 20.50311312 1087.997797 481.8354075 0.010000003 1.999999889 2.510695336 SLSLESTDRGS(ph)WDP ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSLESTDRGSWDP 14 1 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 1 SLSLES(0.006)T(0.006)DRGS(0.989)WDP 89.624 0.015982 53447000 186260 218100 122850 154830 246320 266250 213240 263430 233560 TRUE FALSE 161645.2691 216667.2867 182260.6709 189986.5179 241418.7139 276492.8098 192560.0176 207097.5445 205948.8029 0.784880838 1.05204441 0.884980482 0.922493917 1.172226838 1.342531765 0.93498974 1.005577802 1 17.65192621 3.263185147 23.44594811 1.081246923 0.919301467 0.326158001 0.127864026 162.1133547 154352.1015 0.038861873 0.05013797 1833.095735 -3.263185147 -0.161945456 SLSLS(ph)TNLQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSLSTNLQER 11 0 A0A087WWS6;P01562 A0A087WWS6 IFNA13;IFNA1 Interferon alpha-1/13 1 SLS(0.02)LS(0.49)T(0.49)NLQER;SLS(0.017)LS(0.491)T(0.491)NLQER 73.951 0.044219 654460000 838520 1040990 588230 743010 1048620 1067820 958110 1140270 977790 TRUE FALSE 727707.4575 1034151.668 872699.9955 911721.7767 1027754.514 1108899.726 865192.6397 896432.1341 862196.7801 0.844015513 1.1994381 1.012181924 1.05744048 1.192018501 1.286132994 1.003474682 1.039707123 1 19.71765765 4.754752377 23.95323058 1.094482345 0.844015169 0.401998383 0.09753295 2005.282142 2966420.138 0.024747752 0.604708901 56852.8679 -4.754752377 -0.250467176 SLSLSLADSGHLPDVHGFNSYGSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSLSLADSGHLPDVHGFNSYGSHR 25 0 Q9Y446;Q9Y446-2;E9PKC4;E9PRW6 Q9Y446 PKP3 Plakophilin-3 0 214.44 6.35E-34 732550000 92061 121920 44846 89214 137600 150450 114550 143210 115600 FALSE TRUE 79894.9056 121119.0995 66533.6756 109471.4023 134862.0292 156237.9089 103440.9586 112585.656 101933.8997 0.783791318 1.188212164 0.652713923 1.073945003 1.323034139 1.532737483 1.014784669 1.104496701 1 16.6372744 3.484695374 24.44867574 1.188104314 0.899085255 0.341285928 0.201928793 328.9167197 1061718.434 0.058149819 0.078546506 3052.779059 -3.484695374 -0.289019059 SLSNS(ph)NPDISGTPTSPDDEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLSNSNPDISGTPTSPDDEVR 21 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A0U1RRC1;A0A0U1RQJ5 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 SLSNS(1)NPDISGTPTSPDDEVR;SLSNS(1)NPDISGTPTSPDDEVR;SLSNS(1)NPDISGTPTSPDDEVR 374.03 1.63E-112 1037990000 689720 687350 416240 460690 730750 796550 531920 704200 656260 TRUE FALSE 598571.7545 682834.7526 617535.0562 565296.7057 716209.5047 827193.7939 480334.4803 553612.3101 578677.6904 1.034378488 1.179991494 1.067148547 0.976876619 1.237665658 1.429455131 0.830055294 0.956685076 1 19.1424005 2.196269244 24.99999859 0.930580106 1.147193541 0.398724479 0.130248134 154.0604483 91069.74986 0.054841474 0.036974427 157.1336665 -2.196269244 0.216613435 SLSNVIAHEISHSWTGNLVTNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSNVIAHEISHSWTGNLVTNK 22 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 190.63 9.90E-18 228770000 409760 365990 159310 271480 381860 328870 391500 433610 458390 FALSE TRUE 355609.1778 363585.7876 236352.8489 333123.6833 374261.7331 341521.8417 353532.3903 340885.8759 404199.6564 0.879785948 0.899520279 0.584742825 0.824156275 0.925932833 0.844933528 0.874647924 0.843360133 1 18.62470857 3.469299286 22.69580421 0.885546354 0.78338061 0.220016557 0.094585612 94.66399965 274667.4593 0.027193439 0.03520437 2946.451425 -3.469299286 -0.102165743 SLSQS(ph)FENLLDEPAYGLIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSQSFENLLDEPAYGLIQK 20 0 Q8TC07-2;Q8TC07-3;C9JA93 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 S(0.002)LS(0.012)QS(0.985)FENLLDEPAYGLIQK 213.39 5.08E-23 165570000 251480 204420 118900 155830 195030 148690 191580 248280 196810 TRUE FALSE 218246.2808 203077.1516 176400.4377 191213.5832 191149.2846 154410.2005 173000.6011 195187.2541 173543.346 1.257589449 1.170181146 1.016463274 1.10182031 1.101449805 0.889750048 0.996872569 1.124717591 1 17.40493652 4.424009258 2.914201385 1.038601782 1.251966356 0.561429735 0.068301369 0.212925384 3.433922983 0.018467696 0.075536068 26546.62149 -4.424009258 0.213364574 SLSS(ph)PGGPSKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLSSPGGPSKPK 12 1 Q9BZE9;Q9BZE9-2;J3KRY8;Q9BZE9-3;J3QL04;J3QR12;Q9BZE9-4 Q9BZE9 ASPSCR1 Tether containing UBX domain for GLUT4 1 S(0.007)LS(0.044)S(0.948)PGGPSKPK;S(0.006)LS(0.403)S(0.591)PGGPSKPK;SLS(0.008)S(0.992)PGGPSKPK 93.478 0.0043298 1032290000 1562040 1267850 923180 1027010 1103580 906800 1379320 1711250 1509630 TRUE FALSE 1355612.456 1259521.41 1369632.936 1260208.317 1081620.917 941685.1828 1245553.759 1345312.504 1331163.261 1.018366789 0.946181018 1.028899291 0.946697039 0.812538138 0.707415244 0.935688202 1.010629232 1 20.34425609 3.476459612 24.98690355 0.899798555 0.99184323 0.21948021 0.089690358 43.96153191 1660150.863 0.029625787 0.038606799 2995.433011 -3.476459612 0.092044675 SLSS(ph)PNCFGPQPGGPEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSSPNCFGPQPGGPEMR 18 0 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 SLS(0.103)S(0.897)PNCFGPQPGGPEMR 270.11 2.13E-32 75194000 120460 111220 59165 84184 113920 117590 107580 109430 119230 TRUE FALSE 104540.9058 110489.3885 87777.3919 103299.2639 111653.2149 122113.7634 97146.90816 86029.24609 105134.7652 0.994351446 1.050931043 0.83490358 0.982541442 1.062000896 1.161497466 0.924022686 0.818275914 1 16.68188028 2.015732275 24.97973985 0.888655112 1.011440625 0.202481996 0.09206057 311.2030814 494127.0352 0.038825106 0.026167282 103.6889018 -2.015732275 0.122785513 SLSS(ph)PTDNLELSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSSPTDNLELSLR 14 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 S(0.003)LS(0.13)S(0.689)PT(0.178)DNLELSLR 85.729 0.007994 52535000 468410 449430 316280 336430 370340 420930 392630 489310 466980 TRUE FALSE 406508.4317 446477.6647 469234.0659 412821.5735 362970.9586 437123.4495 354552.803 384674.8643 411774.1564 0.987212105 1.084278015 1.139542292 1.002543669 0.881480668 1.061561156 0.861037046 0.934188944 1 18.65149376 3.480387087 24.01355977 0.944882569 1.071621781 0.415668583 0.066428257 70.10062172 515450.5574 0.0182288 0.024061264 3022.644603 -3.480387087 0.126739212 SLSS(ph)PTVTLSAPLEGAK ddPTM_MDA-MB-175_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(0.319)S(0.681)PTVTLSAPLEGAK 385.79 9.94E-122 1513500000 1762600 652660 628120 762560 819020 942940 787170 1252000 1209400 TRUE FALSE 1529667.944 648372.6335 931880.9329 935710.903 802723.1044 979215.512 710830.3746 984269.5431 1066426.11 1.434387184 0.607986458 0.873835444 0.877426851 0.752722666 0.918221622 0.666553799 0.922960845 1 20.02435258 4.752030075 24.99997963 0.830892579 1.43438758 0.713380971 0.120883194 1229.781929 2282496.324 0.027818101 0.535878163 56497.60986 -4.752030075 0.603495001 SLSSS(ph)PQAQPPRPAELSDEEVAELFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSSSPQAQPPRPAELSDEEVAELFQR 27 1 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 1 SLS(0.004)S(0.181)S(0.816)PQAQPPRPAELSDEEVAELFQR 155.49 1.95E-08 1073600000 156830 170130 130100 124120 158750 232860 144730 138430 144980 TRUE FALSE 136104.5181 169012.4048 193016.7952 152303.3431 155591.1856 241818.2749 130694.1069 108827.8218 127840.6296 1.064642114 1.32205548 1.509823566 1.1913532 1.217071491 1.891560419 1.022320582 0.851277267 1 16.96398689 2.021227346 24.99999449 0.921550343 1.364321052 0.428128016 0.224459633 197.2584663 232315.4653 0.089196631 0.060130504 105.009199 -2.021227346 0.442770708 SLSSS(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSSSPVK 8 0 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 SLS(0.001)S(0.114)S(0.885)PVK 78.816 0.031098 128030000 334910 361140 262530 341780 377950 357430 476570 555630 585570 TRUE FALSE 290650.7949 358767.6476 389490.3861 419386.3728 370429.5344 371180.5634 430352.3148 436812.8484 516344.5817 0.562900833 0.694822141 0.754322598 0.812221891 0.717407614 0.718862125 0.833459535 0.845971593 1 18.97797464 -2 0.307312791 3.483257263 0.659311356 0.728506244 0.059823591 44.28931442 0.712577178 68.00640252 0.116130205 0.01 2 -2.823945907 SLSSS(ph)PVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLSSSPVKK 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 S(0.001)LS(0.036)S(0.195)S(0.768)PVKK;S(0.001)LS(0.015)S(0.228)S(0.757)PVKK;SLSS(0.076)S(0.924)PVKK;SLSS(0.061)S(0.938)PVKK 143 6.31E-05 3527620000 8322200 6382300 4831970 7221500 6271600 4420040 10588300 11933800 9231300 TRUE FALSE 7222400.184 6340374.251 7168726.854 8861251.949 6146807.43 4590081.799 9561448.296 9381849.739 8139986.23 0.887274251 0.778917073 0.880680464 1.088607732 0.755137325 0.563893067 1.174627085 1.152563343 1 22.95659492 2.203998045 24.99998761 1.120857992 0.834857578 0.483301138 0.137697767 157.7690656 114117.3312 0.05813913 0.039199414 159.9550828 -2.203998045 -0.286000414 SLST(ph)SGESLYHVLGLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSTSGESLYHVLGLDK 17 0 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 S(0.009)LS(0.054)T(0.461)S(0.461)GES(0.013)LYHVLGLDK 142.54 6.51E-06 1959300000 371640 298210 206510 397950 353460 363400 310630 487480 691960 TRUE FALSE 322526.8324 296251.0389 306378.9267 488310.6298 346426.8375 377380.2332 280505.1504 383236.1956 610157.2771 0.528596223 0.485532255 0.502131071 0.800302886 0.56776646 0.618496652 0.459725977 0.628094116 1 19.21882164 1.249000782 4.119493879 1.039787188 0.569922524 0.669583776 0.094977471 0.134908609 4.163722545 0.186356316 0.024285181 17.74192676 -1.249000782 -0.469864664 SLSVLS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLSVLSPR 8 0 A0A087WVP4;A0A087X1R1;P53814-5;P53814;P53814-6 A0A087WVP4 SMTN Smoothelin 1 SLS(0.001)VLS(0.999)PR;SLSVLS(1)PR 91.867 0.012779 101529000 183507 218620 133213 155864 183590 205507 185470 209648 202457 TRUE FALSE 159256.085 217183.8708 197635.2524 191255.3034 179936.9182 213412.9873 167483.1479 164816.4067 178522.7641 0.892077186 1.216561215 1.10705911 1.071321657 1.007921422 1.195438511 0.938161297 0.923223475 1 17.44574852 2.205929702 24.97227512 0.946774328 1.085181875 0.297422817 0.092380972 205.7745959 157476.871 0.035225755 0.023751019 160.6681164 -2.205929702 0.138407548 SLSYS(ph)PVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLSYSPVER 9 0 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SLSYS(1)PVER;SLSYS(1)PVER;SLSYS(1)PVER;SLSYS(1)PVER;SLSYS(1)PVER;SLSYS(1)PVER 217.02 6.10E-07 3331800000 3514160 3027500 1882180 2292650 2798350 3082530 2699270 3125750 2744060 TRUE FALSE 3049754.852 3007612.153 2792408.544 2813231.223 2742668.31 3201116.924 2437495.211 2457332.687 2419660.353 1.260406176 1.242989393 1.154049799 1.16265542 1.133493098 1.322961266 1.007370811 1.015569265 1 21.20637312 2.21511098 24.9989629 1.009285597 1.205584225 0.749561474 0.055784468 115.3732061 122995.0525 0.022750126 0.015348169 164.1009063 -2.21511098 0.196298628 SLT(ph)AHSLLPLAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLTAHSLLPLAEK 13 0 F2Z2E2;Q86VI3 F2Z2E2 IQGAP3 Ras GTPase-activating-like protein IQGAP3 1 S(0.244)LT(0.673)AHS(0.083)LLPLAEK 133.23 0.00040332 108760000 513780 534730 341720 434390 538320 500470 605450 706370 484980 TRUE FALSE 445882.6712 531217.3234 506976.935 533024.8887 527608.4852 519723.4047 546733.5522 555318.2725 427646.2169 1.042643787 1.242188759 1.185505483 1.246415536 1.233749918 1.215311592 1.278471621 1.298545972 1 18.70605825 4.742298313 24.37822312 1.223300675 1.04264369 0.288202632 0.082368702 313.7223558 2046053.842 0.019112243 0.137158755 55245.67872 -4.742298313 -0.180656985 SLTDPSQESHTEAIS(ph)DAETSSSDISFSGIATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLTDPSQESHTEAISDAETSSSDISFSGIATR 32 0 Q5QJE6;J3KP30 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 SLTDPSQESHTEAIS(0.999)DAET(0.001)SSSDISFSGIATR;SLTDPS(0.003)QES(0.01)HT(0.01)EAIS(0.929)DAET(0.031)S(0.007)S(0.008)S(0.002)DISFSGIATR;SLTDPSQESHTEAIS(1)DAETSSSDISFSGIATR;SLTDPSQESHTEAIS(1)DAETSSSDISFSGIATR 284.3 4.18E-74 531140000 131529 122755 68497 77629 131343 132090 121567 154266 121169 TRUE FALSE 114147.1094 121948.6143 101622.3783 95255.85093 128729.5313 137171.5878 109777.4511 121277.4164 106844.5389 1.068347626 1.141364974 0.951123749 0.891536919 1.204830239 1.283842761 1.027450277 1.135082969 1 16.70515364 3.221163923 24.99999743 1.1308172 1.017829123 0.242605867 0.102698817 386.8423369 555912.1146 0.032472137 0.036905614 1664.040619 -3.221163923 -0.112988078 SLTEISTDFDRSS(ph)PPLQPPPVNSLTTENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLTEISTDFDRSSPPLQPPPVNSLTTENR 29 1 J3KRR7;Q9NQC7-2;Q9NQC7 J3KRR7 CYLD Ubiquitin carboxyl-terminal hydrolase CYLD 1 SLTEISTDFDRS(0.2)S(0.8)PPLQPPPVNSLTTENR;SLTEISTDFDRS(0.163)S(0.837)PPLQPPPVNSLTTENR;SLTEIS(0.001)T(0.001)DFDRS(0.27)S(0.728)PPLQPPPVNSLTTENR 149.49 2.52E-08 1114990000 276663 226964 164340.1 185355.1 273970 301776 262618 307237 234722 TRUE FALSE 240101.2836 225473.0585 243815.522 227442.8084 268518.533 313385.518 237149.3468 241536.7585 206973.4326 1.16005847 1.089381646 1.178003955 1.098898567 1.29735749 1.514134032 1.145796076 1.166994022 1 17.65908607 3.253581935 24.86456623 1.226157914 1.131886673 0.110897271 0.131199927 571.2223387 945530.414 0.040375518 0.0519141 1793.006793 -3.253581935 -0.094271241 SLTELQELEAVYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLTELQELEAVYER 14 0 A0A6I8PIQ6;A0A0A0MS45;J3KNI1;Q9H9E3;Q9H9E3-2;E9PRT5;H3BSD2;H3BMV9;J3QLW1 A0A6I8PIQ6 COG4 Conserved oligomeric Golgi complex subunit 4 0 ;; 177.42 4.88E-06 61321000 110189 99672 59038 71111 103421 97108 104648 99752 113216 FALSE TRUE 95627.24447 99017.24807 87588.97427 87257.83941 101363.1244 100843.8076 94499.25307 78420.81107 99831.73346 0.957884243 0.991841418 0.877366056 0.874049126 1.015339721 1.0101378 0.946585317 0.785529895 1 16.60721086 1.959941472 24.77675353 0.8740292 0.953965627 0.102321002 0.070179876 740.1558682 457795.1297 0.032232682 0.018604182 91.18879406 -1.959941472 0.079936427 SLTLLPHGTPNS(ph)ASPCSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLTLLPHGTPNSASPCSQR 19 0 Q9BXB5 Q9BXB5 OSBPL10 Oxysterol-binding protein-related protein 10 1 SLTLLPHGT(0.006)PNS(0.493)AS(0.493)PCS(0.007)QR 50.827 0.090474 101390000 18728 21008 7359.1 7221 17100 12709 12221 16906 9503.2 TRUE FALSE 16253.04735 20869.99706 10917.98537 8860.638416 16759.74346 13197.92345 11035.8093 13290.78346 8379.742522 1.939564051 2.490529633 1.302902249 1.057387908 2.000030838 1.574979591 1.316962815 1.586061079 1 13.0326902 4.231977557 24.99999513 1.431713108 2.215046898 0.536858509 0.311870919 104.3440462 396265.1236 0.077435965 0.167416767 17059.94226 -4.231977557 0.78333379 SLTLLPHGTPNSAS(ph)PCSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLTLLPHGTPNSASPCSQR 19 0 Q9BXB5 Q9BXB5 OSBPL10 Oxysterol-binding protein-related protein 10 1 SLTLLPHGTPNS(0.08)AS(0.92)PCSQR 177.38 2.59E-14 184380000 122220 125610 28175 58634 156780 157800 90165 124660 104900 TRUE FALSE 106068.3173 124784.8596 41800.52424 71947.74586 153660.3847 163870.6681 81420.81218 98002.42911 92498.8415 1.146698873 1.349042405 0.451903219 0.77782321 1.661214154 1.771596978 0.880236021 1.05949899 1 16.49714768 3.282417236 24.99999581 1.242919323 0.926953471 0.182028821 0.35792979 285.1576898 162549.1586 0.11203604 0.144637077 1916.095874 -3.282417236 -0.315965852 SLTNDWEDHLAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 SLTNDWEDHLAVK 13 0 P08238;P07900;P07900-2 P08238;P07900 HSP90AB1;HSP90AA1 Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha 0 ;;;;;;;;;;; 234.82 1.14E-16 66108443400 47831747 37203766.3 25337961.3 33649349.4 37975840 32415604.4 44620275 50678852 46135383 FALSE TRUE 41510660.44 36959372.31 37591484.14 41289948.48 37220195.08 33662653.68 40293007.6 39841573.88 40681310.58 1.020386508 0.908509873 0.924048011 1.014961118 0.914921239 0.827472203 0.990455003 0.97935817 1 25.27786282 SLTPAVPVESKPDKPSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLTPAVPVESKPDKPSGK 18 2 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;H0YA91;E7EQK6;P20810-5;E9PCH5;P20810-2;P20810-3;F8W7E0;E9PSG1;A0A0C4DGB5;H0Y944;E7EVY3 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ; 145.48 5.10E-08 1272900000 1200420 943940 800820 921610 888920 585270 1324000 1613730 1512440 FALSE TRUE 1041781.456 937739.196 1188099.231 1130875.636 871232.2311 607785.7156 1195598.684 1268646.398 1333641.066 0.781155801 0.703142112 0.890868811 0.847961018 0.653273398 0.455734103 0.896492103 0.951265247 1 20.346939 2.017719705 24.99977481 0.957669794 0.726828192 0.458768456 0.118241834 223.3468506 315106.841 0.051558767 0.03475362 104.1644931 -2.017719705 -0.230841602 SLTSS(ph)LENIFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SLTSSLENIFSR 12 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 SLTS(0.002)S(0.998)LENIFSR;SLTS(0.01)S(0.99)LENIFSR;SLTS(0.012)S(0.988)LENIFSR;SLTS(0.182)S(0.818)LENIFSR;SLT(0.006)S(0.169)S(0.825)LENIFSR;SLTS(0.016)S(0.984)LENIFSR 290.64 4.32E-36 2869850000 3084960 2226480 1728500 2234970 3258330 3452160 3058190 3545430 3445820 TRUE FALSE 2677274.72 2211854.106 2564408.381 2742454.098 3193495.608 3584966.829 2761607.205 2787267.385 3038459.085 0.8811291 0.727952572 0.843983187 0.902580558 1.05102472 1.179863453 0.908884118 0.917329247 1 21.53490843 3.566156409 2.797261645 0.999422731 0.806893905 0.521449796 0.084329641 0.242948084 3.695453237 0.027004046 0.042062185 3682.615776 -3.566156409 -0.192528826 SLTTECHLLDS(ph)PGLNCSNPFTQLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLTTECHLLDSPGLNCSNPFTQLER 25 0 Q15398-1;Q15398 Q15398-1 DLGAP5 Disks large-associated protein 5 1 SLTTECHLLDS(1)PGLNCSNPFTQLER;SLTTECHLLDS(1)PGLNCSNPFTQLER 333.24 4.01E-88 469120000 173790 211131 107299 170604 214798 193881 194932 254790 188924 TRUE FALSE 150823.2112 209744.0666 159189.1553 209342.2457 210523.94 201339.7275 176027.5246 200305.1413 166589.6199 0.905357796 1.259046432 0.955576676 1.256634392 1.263727837 1.208597076 1.056653618 1.202386687 1 17.34593898 4.755161437 24.09476927 1.152604724 0.905357475 0.32356668 0.111269753 2432.814477 3530939.512 0.025630175 0.669641103 56906.4425 -4.755161437 -0.247247249 SLTVSDDAESS(ph)EPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLTVSDDAESSEPER 15 0 H0Y9Y2;Q8NFC6 H0Y9Y2;Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 SLTVSDDAES(0.397)S(0.603)EPER 246.18 3.91E-18 67684000 155740 143740 81470 95110 129040 144220 125170 135800 127110 TRUE FALSE 135158.5644 142795.7625 120869.1645 116706.1792 126472.3565 149768.2367 113031.0327 106760.2268 112083.2006 1.205877096 1.274015746 1.078387875 1.041245954 1.128379238 1.336223769 1.008456504 0.952508728 1 16.77421053 2.028326687 24.12465053 0.975148243 1.16912922 0.518198895 0.086699364 112.4099494 95734.22192 0.037010409 0.024951767 106.7398742 -2.028326687 0.193980977 SLTWPPS(ph)GSPSHAGTTPPENGLSEHPCETEQINAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLTWPPSGSPSHAGTTPPENGLSEHPCETEQINAK 35 0 P23497;P23497-2;P23497-3;P23497-4;E9PHV6;P23497-7;P23497-6;P23497-5 P23497 SP100 Nuclear autoantigen Sp-100 1 S(0.065)LT(0.061)WPPS(0.43)GS(0.43)PS(0.011)HAGT(0.002)TPPENGLSEHPCETEQINAK 63.762 0.015821 69719000 35719 30750 8517.4 21546 24098 22479 31142 33250 31944 TRUE FALSE 30998.64365 30548.00123 12636.44313 26438.34861 23618.49695 23343.78168 28121.85363 26139.74625 28167.61671 1.100506442 1.084507842 0.448615985 0.938607937 0.838498237 0.828745361 0.99837533 0.928007027 1 14.78174988 2.237072206 24.99149643 0.966529364 0.86493979 0.065651579 0.178910875 121.7237991 2043750.54 0.071024385 0.050809271 172.6124856 -2.237072206 -0.101589574 SLVDTVYALKDEVQELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLVDTVYALKDEVQELR 17 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 0 ; 210.75 2.82E-12 424640000 836400 710830 492000 613000 696140 615200 760040 972110 739860 FALSE TRUE 725867.6208 706160.5109 729932.8456 752191.0191 682288.176 638867.1421 686331.4378 764231.8415 652394.5937 1.112620533 1.082413186 1.11885177 1.152969424 1.045821321 0.979264924 1.052018892 1.171425773 1 19.3153853 3.222517865 24.99874805 1.061572517 1.114416415 0.266194695 0.053235608 453.6662324 706927.2181 0.01789854 0.02035549 1669.23647 -3.222517865 0.052843898 SLVEIIEHGLVDEQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLVEIIEHGLVDEQQK 16 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;;; 240.2 7.45E-20 278123000 803508 625342 451767 551094 610158 519441 727631 870276 782743 FALSE TRUE 697322.382 621234.0872 670243.0323 676228.3156 598017.0496 539424.2314 657065.4576 684174.2499 690208.0142 1.01030757 0.900067913 0.971073964 0.979745673 0.866430174 0.781538638 0.951981785 0.991258049 1 19.3966717 2.000101085 24.99999999 0.987989213 0.915763755 0.196370511 0.064068476 5.841193113 1444351.745 0.027930861 0.01861957 100.0232784 -2.000101085 -0.072225458 SLVES(ph)VSSSPNKESNEEEQVWHFLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLVESVSSSPNKESNEEEQVWHFLGK 26 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;Q9H2U2-4 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 1 S(0.044)LVES(0.239)VS(0.239)S(0.239)S(0.239)PNKES(0.001)NEEEQVWHFLGK 77.984 0.012816 553930000 78139 55262 38915 33594 49124 46278 70116 62166 63371 TRUE FALSE 67812.73317 54898.98028 57734.42416 41222.03115 48146.52851 48058.34461 63316.16111 48872.28468 55879.35257 1.213556171 0.982455554 1.0331978 0.737697007 0.861615718 0.860037606 1.133086877 0.874603631 1 15.77002769 4.888929088 1.535734813 0.921480262 1.406075897 0.409732669 0.107969228 1.663358873 2.78240271 0.029669053 1.352404139 77433.53541 -4.888929088 0.484595635 SLVESVS(ph)SSPNKESNEEEQVWHFLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLVESVSSSPNKESNEEEQVWHFLGK 26 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;Q9H2U2-4 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 1 S(0.007)LVES(0.257)VS(0.257)S(0.222)S(0.257)PNKESNEEEQVWHFLGK 137.89 7.15E-06 1649800000 2070200 1124500 930930 1110000 1156600 975750 1489500 1624000 1527600 TRUE FALSE 1796617.825 1117113.085 1381130.862 1362042.465 1133585.923 1013287.734 1345048.519 1276720.238 1347008.868 1.333783219 0.829328679 1.025331677 1.011160726 0.841557877 0.752250232 0.998544665 0.947818732 1 20.36132792 4.747347821 24.72525354 0.928613815 1.333783462 0.663377046 0.091325962 636.5566164 1791083.881 0.022713406 0.263092519 55891.76461 -4.747347821 0.405169646 SLVESVSS(ph)SPNKESNEEEQVWHFLGK ddPTM_MDA-MB-175_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(0.003)S(0.968)S(0.028)PNKESNEEEQVWHFLGK 308.21 6.78E-82 334740000 505360 271420 224650 235380 265920 268550 391030 445630 421990 TRUE FALSE 438575.3956 269637.0241 333291.4914 288826.6266 260628.7123 278881.2923 353107.9708 350335.4924 372102.8229 1.178640334 0.724630418 0.895697294 0.776201116 0.700421217 0.749473734 0.948952679 0.94150184 1 18.50534181 2.146880908 8.076671033 0.959736951 0.826172163 0.157660707 0.135636721 0.428149708 33.16881018 0.053685998 0.03615442 140.242908 -2.146880908 -0.133564788 SLVGS(ph)WLK ddPTM_MDA-MB-175_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 132.78 0.00099402 452920000 978950 775020 738130 697600 818880 779910 981680 930090 1069320 TRUE FALSE 849579.2772 769928.8426 1095092.137 856000.7421 802585.8901 809913.6424 886476.8247 731197.4915 942906.2078 0.901022042 0.816548705 1.16140092 0.907832333 0.851183165 0.858954619 0.940153769 0.775472137 1 19.84675475 3.485131656 24.89959873 0.874735086 0.960224735 0.094058428 0.102873909 742.9155481 2309287.105 0.028437425 0.038504216 3055.847351 -3.485131656 0.085489649 SLVLQRPQTWADCVTWACHHWHTQYSNNIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLVLQRPQTWADCVTWACHHWHTQYSNNIR 30 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;; 228.9 1.41E-35 2046645000 93517.6 63590.6 53009.14 55509.05 71157.9 66828.7 68061 104909.8 49844.9 FALSE TRUE 81159.01222 63172.86916 78644.53741 68113.22821 69741.99701 69399.64333 61460.4547 82475.65568 43952.29271 1.846525112 1.437305434 1.789315928 1.549708195 1.586765848 1.578976637 1.39834468 1.876481307 1 15.4236508 1.223871105 24.99783055 0.999998361 1.626393126 0.602191528 0.16159127 533.2409297 907388.6475 0.803566962 0.036429164 16.7444584 -1.223871105 0.626394764 SLVPAAELLESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLVPAAELLESR 12 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 94.297 0.015562 20440000 47833 44983 34064 34254 43137 57446 45104 55179 41038 FALSE TRUE 41511.74786 44687.50371 50537.46434 42031.89424 42278.6581 59655.98479 40729.82102 43379.40025 36186.53439 1.147160085 1.234920792 1.396582049 1.161534116 1.168353334 1.648568613 1.125551858 1.198771891 1 15.14316533 1.336241327 1.698363242 0.943682779 1.280058149 0.231766548 0.155449952 1.192765275 3.855203274 0.633213699 0.043119122 21.6890898 -1.336241327 0.336375371 SLY(ph)S(ph)FIKGDT(ph)S(ph)GDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLYSFIKGDTSGDYR 15 1 P09525;Q6P452;P09525-2 P09525 ANXA4 Annexin A4;Annexin 4 S(0.642)LY(0.709)S(0.737)FIKGDT(0.958)S(0.954)GDYR;S(0.765)LY(0.801)S(0.816)FIKGDT(0.816)S(0.801)GDYR 48.112 0.080393 5635270000 1883780 1685620 956150 1175140 1712200 2001410 1281770 1545140 1172870 TRUE FALSE 1634833.7 1674547.051 1418547.338 1441973.498 1678130.57 2078405.538 1157464.143 1214723.835 1034214.645 1.580748937 1.619148462 1.371617918 1.394269077 1.622613428 2.009646207 1.119172068 1.174537454 1 19.98010421 2.139667614 14.36469048 1.113991541 1.581869494 0.639706719 0.177046619 0.543070031 76.18961717 0.07500402 0.050567471 137.9328196 -2.139667614 0.467877953 SLYDELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLYDELR 7 0 Q66K74-2;Q66K74;M0QXQ9;M0R1J2;M0QY41 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 0 ; 94.407 0.033089 159547000 545860 562570 346300 426320 566760 602590 528600 602420 616200 FALSE TRUE 473723.218 558874.4406 513771.8383 523122.4719 555482.5848 625772.0272 477336.4534 473597.171 543353.538 0.871850802 1.028565016 0.945557179 0.962766294 1.022322569 1.15168483 0.878500681 0.871618823 1 19.05153168 SLYQSAGVAPES(ph)FEYIEAHGTGTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SLYQSAGVAPESFEYIEAHGTGTK 24 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 SLYQSAGVAPES(1)FEYIEAHGTGTK;SLYQSAGVAPES(1)FEYIEAHGTGTK 264.31 2.02E-44 442900000 450560 410390 208001 296150 400870 370730 467760 491130 495650 TRUE FALSE 391017.3544 407694.1211 308590.9793 363395.3839 392893.4713 384992.223 422396.7072 386105.6715 437054.8216 0.894664319 0.93282147 0.706069271 0.831464077 0.898956954 0.880878562 0.966461611 0.88342618 1 18.73745473 2.728614764 1.639096896 0.936196423 0.841443129 0.303018354 0.066579043 0.516361151 2.795863638 0.030028473 0.026010977 535.3215965 -2.728614764 -0.094753294 SLYQSAGVAPESFEYIEAHGTGTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 349.02 7.37E-102 16834700000 10060400 9364490 4816970 7109580 10374100 10176300 11790300 12900500 12961000 FALSE TRUE 8730892.65 9302974.049 7146472.804 8723918.802 10167675.71 10567788.85 10646878.52 10141828.47 11428765.35 0.763940145 0.813996418 0.62530576 0.763329943 0.889656529 0.924665835 0.931586064 0.887394934 1 23.44616622 3.212666269 3.405907604 0.925933053 0.735235883 0.747576321 0.054040713 0.119284297 2.882194772 0.016649004 0.020275862 1631.797522 -3.212666269 -0.190697171 SLYVAEYHSEPVEDEKP ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SLYVAEYHSEPVEDEKP 17 1 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ;;; 274.56 1.73E-35 708740000 1728730 1322670 938073 1166320 1373790 1148910 1666590 1989360 1850330 FALSE TRUE 1500273.95 1313981.294 1391728.24 1431150.782 1346454.267 1193109.311 1504964.358 1563950.845 1631586.095 0.919518715 0.805339845 0.852990991 0.877153088 0.825242548 0.731257342 0.922393469 0.958546319 1 20.63784369 2.012266572 24.82284986 0.965559512 0.835370181 0.598099456 0.049683985 134.5596371 272296.116 0.020200381 0.013608587 102.8647493 -2.012266572 -0.13018933 SMAHS(ph)PGPVSQASPGTSSAVLFLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SMAHSPGPVSQASPGTSSAVLFLSK 25 0 Q8TDZ2-2;Q8TDZ2;Q8TDZ2-4;H0Y6Z4 Q8TDZ2-2 MICAL1 Protein-methionine sulfoxide oxidase MICAL1 1 S(0.001)MAHS(0.999)PGPVSQASPGTSSAVLFLSK;S(0.002)MAHS(0.929)PGPVS(0.069)QASPGTSSAVLFLSK 284.48 1.03E-53 655300000 821480 949410 414590 679320 906880 899110 920450 1248070 1046440 TRUE FALSE 712919.3366 943173.2632 615087.1107 833569.9888 888834.8623 933699.3435 831184.9007 981179.943 922731.0553 0.772618774 1.022154026 0.666594136 0.903372639 0.96326536 1.011886766 0.900787825 1.063343362 1 19.81555069 3.326534746 3.374937948 0.993461515 0.834060393 0.384005293 0.095844642 0.246189485 5.546145165 0.027345641 0.035671857 2120.971077 -3.326534746 -0.159401122 SMDELNHDFQALALEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SMDELNHDFQALALEGR 17 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4;E9PR38 Q5T1Z4 PUM1 Pumilio homolog 1 0 ;; 191.21 2.55E-10 249202000 295244 290130 165830 195811 265988 291314 266463 300820 301832 FALSE TRUE 256226.7573 288224.1169 246025.9427 240272.8803 260695.3592 302521.0381 240621.4593 236491.984 266149.7648 0.962716452 1.082939589 0.924389104 0.902773221 0.979506254 1.136657169 0.90408293 0.888567323 1 18.02187877 SMDFEEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SMDFEEAER 9 0 O43396;K7ER96 O43396 TXNL1 Thioredoxin-like protein 1 0 150.17 0.00019977 523260000 759060 548340 335340 368280 493680 503670 459250 556760 484640 FALSE TRUE 658748.2978 544737.9184 497511.5456 451903.6028 483856.7339 523046.5108 414712.0057 437701.2067 427346.4113 1.541485503 1.274698708 1.164187957 1.057464368 1.132235397 1.223940337 0.970435213 1.024230449 1 18.70504648 8 0.550517252 1.039448109 23.61022939 0.833754165 0.068463577 57.08903891 0.533237596 0.038569415 1521.88884 100000000 -8 22.57078128 SMEAEMIQLQEELAAAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SMEAEMIQLQEELAAAER 18 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 318.74 4.32E-61 736142000 554047 571195 361160 429854 552301 567810 543410 625340 582306 FALSE TRUE 480828.2852 567442.7824 535818.184 527458.9206 541311.2907 589654.0181 490710.1818 491615.9074 513466.448 0.936435646 1.105121444 1.043531055 1.027250997 1.054229138 1.148378868 0.955681104 0.957445047 1 18.96991048 2.167699938 24.9999944 0.96756864 1.053412005 0.325127707 0.055231295 49.12051652 17328.75998 0.021411924 0.014435919 147.1295605 -2.167699938 0.085843364 SMEMLVEHQAHDILT ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SMEMLVEHQAHDILT 15 0 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2;H0YD73 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ;; 167.61 1.30E-06 1619200000 1395740 1363010 913380 1085300 1331790 1428090 1397370 1546890 1429020 FALSE TRUE 1211289.423 1354056.298 1355093.623 1331733.953 1305289.985 1483029.546 1261853.272 1216099.611 1260082.884 0.961277578 1.074577169 1.075400389 1.056862188 1.035876292 1.176930157 1.001404978 0.965094937 1 20.2650872 2.019804618 24.99596011 0.981012909 1.065159278 0.312315423 0.052723535 243.5173506 307348.8719 0.020714704 0.013964029 104.6657567 -2.019804618 0.084146369 SMESS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SMESSPR 7 0 Q1ED39;H3BPL4 Q1ED39 KNOP1 Lysine-rich nucleolar protein 1 1 SMES(0.126)S(0.874)PR;SMES(0.1)S(0.9)PR 94.114 0.056442 110153000 615750 499570 299330 403560 413350 581880 465390 580700 547190 TRUE FALSE 534377.0774 496288.2918 444086.9892 495194.466 405125.1437 604265.3001 420256.5494 456521.824 482501.8216 1.107513078 1.028572887 0.920384068 1.0263059 0.839634434 1.252358588 0.870994742 0.946155649 1 18.88017486 4.57696399 3.559334021 0.976805044 1.105621052 0.116697524 0.112232501 0.525912356 11.22828508 0.026229394 0.135881678 37754.08852 -4.57696399 0.128816008 SMEVLSVTDGGS(ph)PVPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SMEVLSVTDGGSPVPAR 17 0 Q8IWQ3-6;Q8IWQ3-3;Q8IWQ3-2;Q8IWQ3-4;Q8IWQ3;Q8IWQ3-5 Q8IWQ3-6 BRSK2 Serine/threonine-protein kinase BRSK2 1 SMEVLSVTDGGS(1)PVPAR;SMEVLS(0.001)VT(0.121)DGGS(0.878)PVPAR 164.58 2.70E-09 140865000 181022 169499 117215 134967 168654 165474 168808 164207 235060 TRUE FALSE 157099.484 168385.5499 173900.5661 165613.3202 165298.1154 171839.8919 152437.0261 129092.6109 207271.4746 0.757940688 0.812391335 0.83899903 0.799016462 0.797495727 0.82905712 0.735446238 0.622818992 1 17.66116206 2.233881259 24.91640265 0.749963852 0.80693653 0 0.096029038 323.2091498 1720980.856 0.037435813 0.026163283 171.3488756 -2.233881259 0.056972677 SMFQDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SMFQDVR 7 0 P49902-2;P49902;Q5JUV4;Q5JUV3 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;;;;; 104.75 0.018802 3314840000 6884230 10297400 5459490 6445190 10401970 10209700 9169350 10556800 9765270 FALSE TRUE 5974461.563 10229755.7 8099717.625 7908668.898 10194991.15 10602473.77 8280107.848 8299310.473 8610830.905 0.693831017 1.188010288 0.940642978 0.918455952 1.183972982 1.231295084 0.961592202 0.963822256 1 23.03772103 4.754954244 24.12790218 1.040302688 0.693830581 0.486613496 0.114204686 1911.661336 2813479.562 0.029020842 0.726212182 56879.30015 -4.754954244 -0.346472107 SMGFIGHYLDQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SMGFIGHYLDQK 12 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 180.2 1.97E-05 5199900000 10441500 9521400 6100700 8062400 9464000 8857400 12022400 13005000 12049600 FALSE TRUE 9061629.32 9458853.296 9051018.926 9893091.146 9275684.916 9198149.91 10856469.5 10223981.96 10625110.01 0.852850399 0.890235798 0.851851784 0.93110482 0.8729966 0.865699263 1.021774785 0.962247162 1 23.34097444 2.244729408 24.99999992 0.989047599 0.879109306 0.810802742 0.026638165 57.90822644 234683.2985 0.00961619 0.007257398 175.6828662 -2.244729408 -0.109938293 SMGTGDTPGLEVPS(ph)SPLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SMGTGDTPGLEVPSSPLRK 19 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SMGTGDTPGLEVPS(0.559)S(0.441)PLRK;SMGTGDTPGLEVPS(0.5)S(0.5)PLRK 79.013 0.0021237 883390000 667525 499499 326395 418867 572505 473842 649631 738576 510308 TRUE FALSE 579309.88 496217.7582 484240.7137 513977.1543 561113.2706 492071.0084 586629.8856 580637.27 449979.9696 1.287412594 1.102755215 1.076138376 1.142222297 1.246973884 1.093539805 1.303679997 1.290362481 1 18.77950126 3.270334058 23.32294626 1.203931719 1.143176949 0.009105176 0.10539875 280.2290651 205695.4816 0.030245369 0.039041078 1863.519998 -3.270334058 -0.060754771 SMGTGDTPGLEVPSS(ph)PLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SMGTGDTPGLEVPSSPLR 18 0 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SMGTGDTPGLEVPS(0.001)S(0.999)PLR;SMGTGDTPGLEVPS(0.004)S(0.996)PLR;SMGTGDTPGLEVPS(0.001)S(0.999)PLR;SMGTGDTPGLEVPS(0.085)S(0.915)PLR;SMGTGDTPGLEVPS(0.001)S(0.999)PLR 346.37 3.09E-90 1062670000 2581170 2128030 1295010 1687440 2218790 2304940 2099960 2600870 2817450 TRUE FALSE 2240061.845 2114050.831 1921281.168 2070599.043 2174640.42 2393612.533 1896306.202 2044694.19 2484374.271 0.901660378 0.850938949 0.773346106 0.833448916 0.875327218 0.963466963 0.763293287 0.823021803 1 21.2444511 3.239363756 24.49390182 0.872064462 0.835890576 0.071127604 0.072601507 59.21121213 1805742.257 0.022084384 0.026840143 1735.256803 -3.239363756 -0.036173886 SMGTGDTPGLEVPSS(ph)PLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SMGTGDTPGLEVPSSPLRK 19 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SMGTGDTPGLEVPS(0.226)S(0.774)PLRK 110.57 0.00010006 656250000 889050 673540 378020 546220 697810 628480 830690 987770 693160 TRUE FALSE 771559.7899 669115.4714 560831.7364 670247.5994 683924.9462 652658.0323 750129.8117 776543.0723 611215.4145 1.26233693 1.094729379 0.917568051 1.096581637 1.11895893 1.06780362 1.227275677 1.270490001 1 19.2213214 2.244774561 24.99863108 1.190263327 1.086444247 0.075686883 0.108032851 264.0067146 1062099.847 0.041267276 0.031142653 175.7011325 -2.244774561 -0.10381908 SMIEISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SMIEISR 7 0 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8;Q5SZW8;E9PM09;Q5SZX9 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 137.18 0.0067653 393880000 450190 437000 257160 332120 411720 512480 416230 455100 461430 FALSE TRUE 390696.2509 434129.3182 381523.4361 407532.9221 403527.5775 532195.4372 375864.0787 357780.4066 406880.2711 0.960224122 1.066970677 0.937679861 1.001604037 0.99176 1.307990274 0.923770714 0.879326013 1 18.6342448 2.071495873 24.99999989 0.922136188 1.042852462 0.190369915 0.105922359 65.07412838 22753.05746 0.043009924 0.028997281 117.8951321 -2.071495873 0.120716274 SMIGSTAQQFLTFLSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SMIGSTAQQFLTFLSHR 17 0 O15357;A0A0A0MTP6;O15357-2 O15357 INPPL1 "Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2" 0 72.187 0.028924 88938000 14551 9454.8 13485 10449 13352 11129 23427 18053 7143.2 FALSE TRUE 12628.04848 9392.690796 20006.3911 12821.60515 13086.32132 11557.13983 21155.05315 14192.50644 6298.739034 2.004853418 1.49120177 3.176253374 2.03558285 2.077609701 1.834833888 3.358617182 2.253229791 1 12.62084732 SMMQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SMMQDR 6 0 P35579;P35579-2;Q5BKV1 P35579 MYH9 Myosin-9 0 ; 119.56 0.048646 986260000 772200 833210 558100 705820 746690 934730 812610 873850 1118830 FALSE TRUE 670151.8135 827736.5886 827999.0267 866087.2188 731832.3299 970689.668 733803.2073 686983.9778 986563.192 0.679279157 0.839010208 0.83927622 0.877883166 0.741799751 0.983910282 0.743797471 0.696340572 1 19.91205194 4.741511613 23.87868787 0.827045942 0.679279054 0.196145487 0.099262721 272.1877007 2202248.928 0.023781259 0.160430382 55145.69484 -4.741511613 -0.147766888 SMMSAYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SMMSAYER 8 0 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;H7C1M2 P18583-7 SON Protein SON 0 ; 93.162 0.026205 294804000 211388 227580 147887 164751 233550 226880 216380 251120 237610 FALSE TRUE 183452.5402 226085.012 219405.6479 202160.2326 228902.8119 235608.2204 195395.5009 197419.9422 209520.0165 0.875584793 1.079061637 1.047182277 0.964873123 1.092510471 1.124514136 0.932586319 0.9422486 1 17.67672855 2.191086896 24.99999164 0.953868186 1.033400798 0.182591359 0.071793302 182.8623734 96295.23605 0.028684231 0.019338955 155.2697652 -2.191086896 0.079532612 SMNLRPEEDDIPWEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SMNLRPEEDDIPWEDLR 17 1 Q14CX7;Q14CX7-2 Q14CX7 NAA25 "N-alpha-acetyltransferase 25, NatB auxiliary subunit" 0 ;; 174.23 1.26E-09 211130000 320920 281379 169977 228397 295014 305120 273521 299258 334889 FALSE TRUE 278509.6089 279530.6028 252178.4457 280258.0297 289143.7986 316858.1638 246994.9755 235264.0055 295298.8039 0.943145063 0.946602557 0.8539772 0.949065915 0.979156687 1.073008626 0.836423894 0.796698132 1 18.17181599 SMQHS(ph)PNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SMQHSPNLR 9 0 O76041-2;O76041 O76041-2 NEBL Nebulette 1 SMQHS(1)PNLR;SMQHS(1)PNLR;SMQHS(1)PNLR;SMQHS(1)PNLR;S(0.001)MQHS(0.999)PNLR;S(0.006)MQHS(0.994)PNLR 178.65 3.27E-05 4908220000 1791210 2120750 1165631 1832590 2654310 2946650 2515910 2662100 2788960 TRUE FALSE 1554497.06 2106818.654 1729334.05 2248707.569 2601494.424 3060009.532 2271917.435 2092830.631 2459252.326 0.63210149 0.856690723 0.703195045 0.91438668 1.05783957 1.244284492 0.923824453 0.851002807 1 21.22978834 3.575406302 3.878779449 0.998979214 0.744327962 0.556892269 0.114916989 0.213856585 5.773091412 0.035985506 0.054303961 3761.891814 -3.575406302 -0.254651252 SMQNWHQLENLSNFIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SMQNWHQLENLSNFIK 16 0 B4DDF4;B4DUT8;Q99439;A0A087X1X5;H3BVI6;Q99439-2;A0A087X271;K7ES69;H3BQH0;A0A087WV51 B4DDF4 CNN2 Calponin;Calponin-2 0 ; 270.17 1.26E-28 2194700000 2292600 2495800 1340260 1789090 2186800 2123800 2559500 2964800 2581800 FALSE TRUE 1989627.101 2479404.925 1988414.219 2195330.229 2143286.958 2205503.96 2311280.084 2330800.592 2276582.545 0.87395342 1.089090721 0.873420655 0.964309523 0.941449263 0.968778384 1.015241063 1.023815542 1 21.11843834 2.319837231 3.673361627 1.01585092 0.953120931 0.194908015 0.059354275 0.362126914 9.593229281 0.022177777 0.016193619 208.8513232 -2.319837231 -0.062729989 SMS(ph)AAFCSLLAPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SMSAAFCSLLAPER 14 0 E9PNR2;Q13671-2;Q13671 E9PNR2 RIN1 Ras and Rab interactor 1 1 S(0.004)MS(0.996)AAFCSLLAPER;S(0.002)MS(0.998)AAFCSLLAPER;S(0.001)MS(0.999)AAFCSLLAPER;SMS(1)AAFCSLLAPER 226.1 2.65E-12 285749000 185693 231638 112460 132123 194193 198989 164981 177481 163841 TRUE FALSE 161153.1996 230116.3547 166846.0322 162123.5465 190328.9392 206644.2356 148981.168 139528.0693 144471.9036 1.115463945 1.592810429 1.154868372 1.122180455 1.317411444 1.430342028 1.031212051 0.96577996 1 17.14042942 2.127792476 6.552914471 0.986542548 1.289613953 0.470711486 0.145340052 0.177903791 9.596949863 0.05877108 0.03942609 134.2123486 -2.127792476 0.303071405 SMS(ph)AEDLLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SMSAEDLLER 10 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 SMS(1)AEDLLER;SMS(1)AEDLLER;SMS(1)AEDLLER;S(0.004)MS(0.996)AEDLLER 215.72 8.45E-09 1431842000 2591880 1684750 1320290 1680303 1948570 2013310 1964240 2098530 2274950 TRUE FALSE 2249356.491 1673682.766 1958786.66 2061841.478 1909797.269 2090763.338 1773748.307 1649775.69 2006008.003 1.121309829 0.83433504 0.976460043 1.027833127 0.952038709 1.042250747 0.884217962 0.822417302 1 20.93589593 2.215117442 24.39368909 0.884838076 0.984243146 0.18756093 0.084840634 249.4979872 259611.3114 0.032816158 0.022141277 164.103348 -2.215117442 0.09940507 SMS(ph)APSDLEMIGNEDLEFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SMSAPSDLEMIGNEDLEFTR 20 0 F8VWT9;J3KPF0;Q9Y4D8-4;Q9Y4D8;Q9Y4D8-2 F8VWT9 HECTD4 Probable E3 ubiquitin-protein ligase HECTD4 1 S(0.114)MS(0.885)APS(0.001)DLEMIGNEDLEFTR;S(0.011)MS(0.986)APS(0.004)DLEMIGNEDLEFTR;S(0.02)MS(0.979)APS(0.001)DLEMIGNEDLEFTR;S(0.018)MS(0.836)APS(0.146)DLEMIGNEDLEFTR 212.69 1.55E-22 178385000 190779 131045 97630 118938 148325 129448 168605 164730 162662 TRUE FALSE 165567.0718 130184.1568 144844.1946 145944.6908 145373.6227 134427.9483 152253.7131 129503.7714 143432.2837 1.154322218 0.907634972 1.009843745 1.017516329 1.013534882 0.937222394 1.061502398 0.902891372 1 17.13001026 4.754232046 24.79409903 0.980563678 1.154322362 0.531420147 0.051065124 2093.127535 3311520.185 0.011739319 0.283124958 56784.79288 -4.754232046 0.173758684 SMS(ph)FQGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 SMSFQGIR 8 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 S(0.006)MS(0.994)FQGIR;S(0.01)MS(0.99)FQGIR;SMS(1)FQGIR;S(0.01)MS(0.99)FQGIR;SMS(1)FQGIR;S(0.031)MS(0.969)FQGIR;S(0.004)MS(0.996)FQGIR;S(0.007)MS(0.993)FQGIR;S(0.002)MS(0.998)FQGIR 150.15 0.00051793 5819480000 7362970 6208330 3612361 4430530 5686830 4392680 7653440 6892610 6720080 TRUE FALSE 6389934.859 6167547.071 5359310.862 5436549.553 5573673.209 4561669.242 6911210.567 5418678.99 5925639.798 1.078353575 1.040823824 0.904427377 0.917462036 0.94060277 0.769818855 1.166323098 0.914446233 1 22.4985395 4.373469561 5.33197081 0.946804374 1.069333336 0.195797064 0.097909365 0.307831016 13.02004217 0.023550711 0.065575603 23630.31772 -4.373469561 0.122528962 SMS(ph)GGHGLR ddPTM_MDA-MB-175_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(0.001)MS(0.999)GGHGLR;SMS(1)GGHGLR 139.32 0.00011726 191730000 327780 282530 221764 233029 347750 400980 325930 373350 414550 TRUE FALSE 284463.0425 280674.0418 329009.8122 285941.7961 340830.4554 416405.9601 294321.3588 293512.0079 365542.3713 0.778194444 0.767829023 0.900059304 0.782239813 0.932396576 1.139145535 0.805163455 0.802949346 1 18.47967912 3.233425774 24.98027137 0.919661453 0.810918287 0.275864671 0.101771724 215.4742439 1048249.207 0.032900609 0.038432046 1711.692602 -3.233425774 -0.108743167 SMS(ph)PTSTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SMSPTSTPK 9 0 E9PQ01;E9PKN0;O94913 E9PQ01 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 1 S(0.001)MS(0.683)PT(0.145)S(0.167)T(0.005)PK;SMS(0.589)PT(0.097)S(0.306)T(0.007)PK;SMS(0.577)PT(0.32)S(0.102)T(0.001)PK 117.99 0.0011148 347160000 941670 685540 434990 528500 616280 568670 730740 804420 748860 TRUE FALSE 817225.9236 681036.6426 645352.619 648504.0026 604017.2337 590547.1029 659872.9473 632401.043 660330.6239 1.237601126 1.031357047 0.977317416 0.982089849 0.914719402 0.894320332 0.999306898 0.957703641 1 19.33282903 4.954184737 1.46334455 0.956595707 1.481071931 0.871828771 0.033435537 0.681863678 0.903281496 0.009581262 0.602652944 89988.0284 -4.954184737 0.524476225 SMSPT(ph)STPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SMSPTSTPK 9 0 E9PQ01;E9PKN0;O94913 E9PQ01 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 1 SMS(0.227)PT(0.746)S(0.026)T(0.001)PK 98.04 0.070237 96160000 401010 316370 212040 262370 293760 257930 316310 365320 310690 TRUE FALSE 348015.5125 314291.7446 314583.2532 321945.1186 287914.7507 267852.734 285634.3049 287199.1609 273960.5821 1.270312356 1.147215202 1.148279255 1.175151243 1.05093495 0.977705376 1.042610958 1.048322933 1 18.06360881 3.201444024 3.881549331 1.023413449 1.181679397 0.808483643 0.039242473 0.096331245 3.070194937 0.012015171 0.014400059 1590.171715 -3.201444024 0.158265948 SMSSIPPYPASSLAS(ph)SSPPGSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SMSSIPPYPASSLASSSPPGSGR 23 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 SMSSIPPY(0.002)PAS(0.08)S(0.08)LAS(0.264)S(0.264)S(0.264)PPGS(0.046)GR 58.024 0.081399 58698000 43331 51700 25419 35022 51335 57810 43045 47850 48272 TRUE FALSE 37604.69856 51360.3793 37711.71342 42974.28038 50313.53394 60033.98811 38870.50253 37617.64987 42565.33915 0.883458215 1.206624458 0.885972347 1.009607376 1.182030613 1.410396095 0.913196119 0.883762484 1 15.37739151 SMSSIPPYPASSLASSS(ph)PPGSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SMSSIPPYPASSLASSSPPGSGR 23 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 SMSSIPPYPASSLASS(0.031)S(0.969)PPGSGR;SMSSIPPYPASSLASS(0.017)S(0.983)PPGSGR;SMSSIPPYPASSLASS(0.028)S(0.971)PPGS(0.001)GR;SMSSIPPYPASSLAS(0.001)S(0.088)S(0.911)PPGSGR;SMSSIPPYPASSLASS(0.055)S(0.944)PPGS(0.001)GR;SMSSIPPYPASSLAS(0.001)S(0.056)S(0.943)PPGSGR 309.77 4.05E-73 2278200000 1073203 1108447 707682 822912 1205060 1237090 1117883 1245370 1150207 TRUE FALSE 931376.5044 1101165.539 1049919.382 1009766.747 1181081.664 1284681.653 1009470.879 979057.317 1014230.839 0.918308208 1.085714905 1.035187792 0.995598545 1.164509714 1.266656074 0.995306828 0.965320004 1 19.95195462 4.745494778 23.89550116 1.059159187 0.918308087 0.196870201 0.091806687 871.4211261 3002815.999 0.024626792 0.232082443 55653.7942 -4.745494778 -0.1408511 SMSSLQDDRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SMSSLQDDRDR 11 1 Q14789;Q14789-2;Q14789-4;Q14789-3 Q14789 GOLGB1 Golgin subfamily B member 1 0 151.07 0.0017399 0 230100 226970 113860 120760 216860 239760 170360 216330 159420 FALSE TRUE 199691.702 225479.0191 168923.0768 148180.4037 212544.9103 248983.7223 153838.5134 170069.513 140573.5492 1.420549621 1.603993215 1.201670427 1.054112986 1.511983666 1.771198947 1.094363159 1.209825845 1 17.10096563 SMVEGLGGPLGHAGEESEVDNDVDS(ph)PGSLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SMVEGLGGPLGHAGEESEVDNDVDSPGSLRR 31 1 Q96DR7;Q96DR7-4;Q96DR7-3 Q96DR7 ARHGEF26 Rho guanine nucleotide exchange factor 26 1 SMVEGLGGPLGHAGEESEVDNDVDS(0.809)PGS(0.19)LRR 57.832 0.019176 30337000 22030 24117 12221 15957 14730 20130 21637 17501 17552 TRUE FALSE 19118.67968 23958.57384 18131.11648 19580.28074 14436.90182 20904.41413 19538.64707 13758.54734 15477.02256 1.235294425 1.548009235 1.17148608 1.265119351 0.932795812 1.35067414 1.262429321 0.888966033 1 13.91784033 -0.469142474 0.179746049 3.82E-12 1.488927129 0.328906016 0.163796645 73.93872797 1.788404891 27.10203622 1.795140191 0.339513874 0.469142474 1.488927129 SMVWPGDGLVPDTAEPHVAPS(ph)PTLPSTEDVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 SMVWPGDGLVPDT(0.111)AEPHVAPS(0.443)PT(0.443)LPS(0.001)T(0.002)EDVIR 137.57 1.13E-08 180250000 27407 25782 16271 19119 29840 27960 20009 33252 28875 TRUE FALSE 23785.09551 25612.63634 24139.71002 23460.26117 29246.24238 29035.63929 18068.53026 26141.31857 25461.43039 0.934161795 1.005938627 0.948089312 0.921403896 1.148648836 1.14037738 0.709643173 1.02670267 1 14.63602585 SMWTEHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SMWTEHK 7 0 O75400-3;O75400;O75400-2;F5H578;H0YG38 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 63.306 0.080225 290810000 1305600 1127500 693330 906750 1059500 976460 1248800 1337100 1432500 FALSE TRUE 1133061.652 1120093.378 1028626.707 1112641.446 1038418.023 1014025.048 1127691.568 1051171.57 1263151.482 0.897011695 0.886745093 0.814333611 0.880845617 0.822085108 0.802773905 0.892760357 0.832181718 1 20.26859623 1.233740484 24.99999537 1.000000224 0.852512738 0.637151289 0.034713794 95.16237624 493507.1403 0.065838844 0.008217151 17.12933424 -1.233740484 -0.147487486 SMYEEEINETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SMYEEEINETR 11 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ; 187.16 5.24E-05 424910000 513540 393730 229212 351470 387080 393770 391200 468190 560410 FALSE TRUE 445674.3879 391143.5617 340059.6899 431276.6354 379377.8653 408918.5867 353261.4842 368071.212 494158.9682 0.90188465 0.791533872 0.688158491 0.872748777 0.767724335 0.827504129 0.714874174 0.744843736 1 18.9146157 1.232331977 24.99937035 1.000000358 0.783283214 0.499549941 0.066284023 173.9087226 697934.3189 0.142715277 0.015760666 17.07387025 -1.232331977 -0.216717144 SNATNSSYS(ph)PTTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SNATNSSYSPTTGR 14 0 Q13009;Q13009-2 Q13009 TIAM1 T-lymphoma invasion and metastasis-inducing protein 1 1 SNATNS(0.001)S(0.002)YS(0.969)PT(0.027)T(0.001)GR;SNATNSSYS(0.951)PT(0.048)T(0.001)GR 153.26 6.76E-06 264740000 303260 294550 200933 228050 309280 350780 300870 328410 401360 TRUE FALSE 263183.4226 292615.0817 298104.8709 279832.238 303125.9331 364274.7336 271691.6737 258182.0772 353911.678 0.743641533 0.826802561 0.84231431 0.790683821 0.856501641 1.029281474 0.767682138 0.729509912 1 18.43302984 3.226240717 22.64693922 0.857675289 0.805674553 0.119436343 0.094335806 235.0739541 432119.9164 0.030291969 0.034660058 1683.606979 -3.226240717 -0.052000736 SNDRNS(ph)MDIQCEVDALLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SNDRNSMDIQCEVDALLER 19 1 Q02241;H7BYN4;A0A2U3TZL8;A0A2R8Y531;H0YME6;Q02241-2 Q02241;Q02241-2 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 S(0.01)NDRNS(0.99)MDIQCEVDALLER;SNDRNS(1)MDIQCEVDALLER;S(0.072)NDRNS(0.928)MDIQCEVDALLER 322.7 2.34E-62 348975000 235181 260122 162334 195659 246417 239484 227420 267202 232555 TRUE FALSE 204101.235 258413.2415 240839.2654 240086.3664 241513.7838 248697.1044 205364.8434 210062.9317 205062.6128 0.995311784 1.260167506 1.174466969 1.170795413 1.177756298 1.212786188 1.001473845 1.024384352 1 17.64570496 2.23150652 24.99998507 1.011605993 1.170774488 0.543551681 0.067500038 112.287007 397944.8707 0.025164984 0.017378488 170.4144903 -2.23150652 0.159168494 SNDS(ph)GEEAEKEFIFV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SNDSGEEAEKEFIFV 15 1 Q5VZK9;Q5VZK9-2 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SNDS(1)GEEAEKEFIFV;S(0.005)NDS(0.995)GEEAEKEFIFV;SNDS(1)GEEAEKEFIFV;SNDS(1)GEEAEKEFIFV;SNDS(1)GEEAEKEFIFV 169.28 3.17E-06 1346040000 2280960 1954530 1511970 1612420 2137640 1788730 2344500 2750390 2183430 TRUE FALSE 1979525.357 1941690.564 2243163.749 1978544.605 2095105.146 1857543.601 2117130.751 2162240.502 1925307.393 1.028160679 1.008509379 1.165093822 1.027651279 1.088192542 0.96480365 1.099632588 1.123062484 1 20.87665737 SNEDQSMGNWQIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 221.73 6.67E-12 1680380000 787760 710570 311335 432015 682670 664110 792970 824260 220633 FALSE TRUE 683655.5201 705902.2189 461897.6474 530110.6087 669086.2026 689658.7414 716067.8915 647998.4134 194550.0181 3.514034729 3.628384237 2.374184551 2.724803698 3.439147471 3.544891685 3.680636468 3.330754835 1 17.56978159 1.237776806 24.99993367 0.999997358 3.279344251 0.747120573 0.416795858 10.58567772 337414.4312 0.640752025 0.109649613 17.28927594 -1.237776806 2.279346892 SNEEGSEEKGPEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SNEEGSEEKGPEVR 14 1 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ; 211.57 3.33E-09 3221800000 4074800 3218600 2377750 2774500 3224000 2568100 4098600 4572100 3802000 FALSE TRUE 3536304.856 3197456.805 3527637.853 3404492.631 3159848.708 2666896.469 3701118.403 3594391.995 3352531.891 1.054816172 0.953743889 1.052230961 1.015498955 0.94252607 0.795487278 1.10397709 1.072142521 1 21.67681963 SNEHDHS(ph)KSKEK ddPTM_MDA-MB-175_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(0.5)KS(0.5)KEK 73.91 0.01801 72193000 200174 112578 62698 53794 61533 64790 194294 185724 35009 TRUE FALSE 173720.4987 111838.4677 93018.96251 66008.74989 60308.61369 67282.51322 175451.3978 146008.3679 30870.2759 5.627435896 3.622852872 3.013220964 2.138262389 1.95361434 2.179524195 5.683505983 4.729739649 1 14.91393076 2.270705612 24.99997064 4.075492369 3.015122396 0.03342901 1.572677913 494.2942861 384423.4148 0.602783593 0.4668766 186.5114987 -2.270705612 -1.060369973 SNFLNCYVSGFHPSDIEVDLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNFLNCYVSGFHPSDIEVDLLK 22 0 P61769 P61769 B2M Beta-2-microglobulin;Beta-2-microglobulin form pI 5.3 0 120.25 4.02E-05 105430000 161820 180770 99405 139520 171930 161860 186490 229900 217160 FALSE TRUE 140435.077 179582.51 147477.5905 171200.1484 168508.9294 168086.8589 168404.2285 180737.6741 191487.5922 0.733389957 0.937828441 0.770167867 0.894053481 0.879999208 0.877795042 0.879452431 0.94386102 1 17.54689139 -2 0.294444289 2.304919386 0.814934084 0.497939084 0.055682829 63.95057005 1.033706422 48.82181267 0.105372464 0.01 2 -1.489985302 SNFSSGPGFPEYGYPADTVWPAMEQVS(ph)SRPTSPEKFSVPHVCAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SNFSSGPGFPEYGYPADTVWPAMEQVSSRPTSPEKFSVPHVCAR 44 2 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 SNFSSGPGFPEYGYPADT(0.012)VWPAMEQVS(0.234)S(0.234)RPT(0.234)S(0.234)PEKFS(0.052)VPHVCAR;SNFSSGPGFPEYGY(0.019)PADT(0.065)VWPAMEQVS(0.213)S(0.213)RPT(0.213)S(0.213)PEKFS(0.065)VPHVCAR 135.59 4.63E-10 1087140000 746590 568330 252546 262297 713180 527420 746830 942440 99145 TRUE FALSE 647926.2399 564596.6028 374678.0903 321855.5428 698989.1133 547710.1887 674402.5415 740906.5401 87424.19105 7.411292368 6.458127848 4.285748439 3.681538702 7.995374106 6.264972911 7.714141057 8.47484582 1 16.41574492 5.903271249 13.07940637 6.147251737 6.392059573 0 2.334186257 0 0 0.515848516 0 800333.9662 -5.903271249 0.244807836 SNIHCNTIAPNAGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SNIHCNTIAPNAGSR 15 0 P51659-3;P51659;P51659-2;A0A2R8YD50;A0A2R8Y7L2;E7ET17;E7ER27;A0A2R8Y7W2 P51659-3 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 ; 183.73 4.93E-07 350640000 333710 294770 151970 256000 307810 388030 279490 321770 355100 FALSE TRUE 289609.378 292833.6365 225463.2003 314128.7127 301685.1832 402957.7652 252385.1028 252961.9895 313120.4825 0.924913553 0.935210735 0.720052545 1.003219943 0.963479555 1.286909633 0.806031917 0.807874296 1 18.25635836 4.823809274 14.96853637 0.930335293 0.924901408 0 0.153875771 41306.29646 7199362.533 0.038647691 54.29071333 66651.39963 -4.823809274 -0.005433885 SNLDEEVNVIPPHT(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SNLDEEVNVIPPHTPVR 17 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 SNLDEEVNVIPPHT(1)PVR;SNLDEEVNVIPPHT(1)PVR 126.45 0.00016029 453860000 283960 297550 170041 226050 310580 289900 262110 336430 392370 TRUE FALSE 246433.9665 295595.3745 252273.3964 277378.1075 304400.0656 301052.6406 236690.6125 264487.0626 345984.4656 0.712268876 0.85436025 0.729146599 0.801706825 0.879808477 0.870133403 0.684107629 0.764447797 1 18.40034774 SNMGHPEPASGLAALAK ddPTM_MDA-MB-175_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 ;; 142.3 5.92E-07 1927470000 1895930 1756690 946650 1327310 1967280 1825100 2180970 2351070 2335740 FALSE TRUE 1645378.047 1745150.188 1404453.106 1628696.022 1928134.977 1895312.778 1969459.865 1848311.977 2059611.478 0.798877878 0.847320092 0.681901961 0.79077828 0.936164416 0.920228304 0.956228826 0.897408077 1 20.97394078 3.254699524 5.67427431 0.936909349 0.77621757 0.738434573 0.047981907 0.086659359 8.722701216 0.013953916 0.017340833 1797.626758 -3.254699524 -0.160691779 SNMS(ph)PHGLPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SNMSPHGLPAR 11 0 E7ESY4;Q13330-3;Q13330;H0Y4T7 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 S(0.007)NMS(0.993)PHGLPAR;SNMS(1)PHGLPAR;SNMS(1)PHGLPAR;SNMS(1)PHGLPAR;S(0.001)NMS(0.999)PHGLPAR 143.46 2.39E-05 1480209000 1540810 1432130 781088 989425 1460280 1522430 1418840 1593270 1375550 TRUE FALSE 1337188.055 1422722.244 1158824.769 1214089.069 1431223.285 1580998.867 1281241.115 1252561.609 1212934.046 1.102440861 1.172959279 0.955389762 1.000952255 1.179967938 1.303449988 1.056315568 1.032670831 1 20.21006967 2.012374558 24.99804859 1.02641623 1.117271447 0.169978262 0.095677207 441.7062351 892294.1487 0.042395174 0.028561352 102.8903296 -2.012374558 0.090855217 SNNIAELS(ph)PGAINSCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SNNIAELSPGAINSCR 16 0 Q9Y2I9;F8VZ81;Q9Y2I9-2;Q9Y2I9-3 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 SNNIAELS(1)PGAINSCR;SNNIAELS(1)PGAINSCR;SNNIAELS(1)PGAINSCR 403.07 9.78E-140 699870000 762740 931080 509610 710310 1097280 957720 961960 1262860 1007420 TRUE FALSE 661941.9765 924963.6742 756059.1005 871596.7419 1075446.275 994564.1081 868669.2673 992807.2166 888323.9553 0.745158309 1.041245898 0.85110741 0.981169918 1.210646486 1.119596181 0.977874414 1.117618421 1 19.76072637 3.473206216 24.73087863 1.084067146 0.898838157 0.487923061 0.095992011 84.04844304 530919.9597 0.026069366 0.033810108 2973.077401 -3.473206216 -0.185228989 SNNWS(ph)LEDVTASDK ddPTM_MDA-MB-175_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;S(0.001)NNWS(0.999)LEDVTASDK 335.68 1.41E-68 458089000 462347 414041 325945 419011 422471 355111 469339 570631 696630 TRUE FALSE 401246.6725 411321.1374 483573.0922 514153.8517 414064.6537 368772.35 423822.576 448606.0013 614275.195 0.653203443 0.669604016 0.787225491 0.837008976 0.674070282 0.600337362 0.689955543 0.730301345 1 19.2285256 1.234254371 4.142111683 1.031753396 0.704431131 0.659270598 0.066878922 0.161133507 5.065697687 0.159958806 0.018400565 17.14961486 -1.234254371 -0.327322265 SNPKS(ph)PQKPIVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNPKSPQKPIVR 12 2 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y467;A0A2R8YES9;H7C5K3 P15056 BRAF Serine/threonine-protein kinase B-raf 1 S(0.007)NPKS(0.993)PQKPIVR 113.65 0.00059608 1591100000 2940700 2489800 2383400 2317300 3204000 2559700 4179600 4520000 3564500 TRUE FALSE 2552079.044 2473444.34 3536020.212 2843478.383 3140246.669 2658173.315 3774263.035 3553433.175 3143108.871 0.811960116 0.786941987 1.125007232 0.904670662 0.999089372 0.845714681 1.200805696 1.130547277 1 21.58376081 6.631592118 0.240245091 1.141595425 5.63E-16 0.341658757 0.115509583 51.08897578 1.468895799 0.49519549 19.85884942 4281462.235 -6.631592118 -1.141595425 SNPQHRES(ph)WPGMGSGEAPTPLQPPEEVTPHPATPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNPQHRESWPGMGSGEAPTPLQPPEEVTPHPATPAR 36 1 O43896 O43896 KIF1C Kinesin-like protein KIF1C 1 S(0.128)NPQHRES(0.871)WPGMGS(0.001)GEAPTPLQPPEEVTPHPATPAR 135.63 3.33E-09 217260000 93883 130390 53007 77664 130680 140590 126340 156960 90723 TRUE FALSE 81476.12368 129533.4595 78641.3625 95298.79822 128079.7237 145998.5883 114087.5662 123395.3255 79997.83029 1.018479169 1.619212159 0.983043693 1.191267287 1.601039968 1.825031851 1.426133257 1.542483403 1 16.28767325 3.248005764 24.96992877 1.500225285 1.217018706 0.208758702 0.264522347 307.719947 813508.0014 0.074983969 0.095495872 1770.13245 -3.248005764 -0.283206579 SNPS(ph)PAPTDHSLSGEPPAGGAQEPAHAQENWLLNSNIPLETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNPSPAPTDHSLSGEPPAGGAQEPAHAQENWLLNSNIPLETR 42 0 E9PPG4;Q6N022 E9PPG4 TENM4 Teneurin-4 1 S(0.007)NPS(0.993)PAPTDHSLSGEPPAGGAQEPAHAQENWLLNSNIPLETR 255.75 1.71E-66 108860000 35961 34087 22777 35376 39061 41943 33432 50315 39325 TRUE FALSE 31208.66274 33863.08025 33792.03338 43408.66149 38283.76252 43556.57435 30189.76979 39555.5288 34676.0433 0.900006453 0.976555484 0.974506609 1.251834332 1.104040683 1.256099895 0.870623258 1.140716329 1 15.08165167 3.971733733 23.72156337 1.100544286 0.947593402 0.293894406 0.112934787 453.8357578 380868.7554 0.028866597 0.050170625 9369.873617 -3.971733733 -0.152950884 SNRDELELELAENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNRDELELELAENR 14 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 180.62 1.58E-06 287860000 195450 209510 116870 159120 234120 223430 195020 247420 217230 FALSE TRUE 169620.7873 208133.715 173388.7229 195250.628 229461.47 232025.4967 176106.9904 194511.1584 191549.3169 0.885520189 1.086580304 0.905191027 1.019323019 1.197923719 1.211309445 0.919381981 1.015462553 1 17.54735636 4.749734199 23.36636615 1.041156021 0.885519958 0.195923321 0.100960784 1227.003182 2565801.509 0.025902182 0.355470986 56199.72604 -4.749734199 -0.155636064 SNRDELELELAENRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SNRDELELELAENRK 15 2 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 168.05 7.18E-07 572780000 484480 506610 284631 347430 469640 402750 501080 542030 338860 FALSE TRUE 420454.7405 503282.0456 422279.5036 426319.2916 460295.0828 418244.0531 452485.3387 426121.1026 298800.3568 1.407142699 1.684342184 1.413249663 1.426769687 1.540477019 1.399744155 1.514340021 1.426106405 1 18.18882235 1.229721917 3.51344571 0.924048411 1.484811293 0.757033575 0.085419987 0.144084718 2.588688584 0.220176731 0.020537869 16.97156598 -1.229721917 0.560762883 SNRNS(ph)IER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SNRNSIER 8 1 Q8TF01 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 SNRNS(1)IER;S(0.002)NRNS(0.998)IER;SNRNS(1)IER;SNRNS(1)IER 132.17 0.00058965 1041970000 595657 517276 308046 376003 452429 563217 540888 617332 547783 TRUE FALSE 516939.4182 513877.9799 457018.076 461380.228 443426.5481 584884.3224 488432.765 485320.3559 483024.7178 1.070213178 1.063875121 0.946158776 0.955189685 0.918020407 1.210878659 1.011196212 1.004752631 1 18.88173749 SNS(ph)APLIHGLSDTSPVFQAEAPSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SNSAPLIHGLSDTSPVFQAEAPSAR 25 0 Q96E09 Q96E09 FAM122A Protein FAM122A 1 S(0.179)NS(0.821)APLIHGLSDTSPVFQAEAPSAR;S(0.209)NS(0.791)APLIHGLSDTSPVFQAEAPSAR;S(0.117)NS(0.883)APLIHGLSDTSPVFQAEAPSAR;S(0.173)NS(0.827)APLIHGLSDTSPVFQAEAPSAR 268.88 4.51E-46 4471740000 1277577 1173802 594618 866974 1271384 1104791 1213789 1347208 1276346 TRUE FALSE 1108741.962 1166091.217 882177.2537 1063833.698 1246085.946 1147293.025 1096075.93 1059118.053 1125457.83 0.985147496 1.036103874 0.783838568 0.945245276 1.107181373 1.019401167 0.97389338 0.941055298 1 20.10208057 SNS(ph)AWQIYLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNSAWQIYLQR 11 0 Q8N4C8;Q8N4C8-4 Q8N4C8 MINK1 Misshapen-like kinase 1 1 S(0.001)NS(0.999)AWQIYLQR 122.1 0.00041738 211840000 142490 171950 97746 98642 140450 166430 117750 133250 151770 TRUE FALSE 123659.5855 170820.4491 145016.2925 121040.1737 137655.3198 172832.6698 106330.6231 104755.5245 133827.9235 0.92401931 1.276418588 1.08360265 0.904446326 1.028599385 1.291454468 0.794532414 0.782762832 1 17.03001964 2.210227139 24.98352094 0.840504786 1.082667783 0.369625467 0.138192381 207.7997259 183229.421 0.05570471 0.037564298 162.2658537 -2.210227139 0.242162997 SNS(ph)DNNLNASAPDWAVCSTATSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SNSDNNLNASAPDWAVCSTATSHR 24 0 Q9UPX8;Q9UPX8-3;A0A2R8Y2H5;A0A087X158 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 S(0.204)NS(0.796)DNNLNASAPDWAVCSTATSHR;S(0.222)NS(0.778)DNNLNASAPDWAVCSTATSHR;S(0.221)NS(0.779)DNNLNASAPDWAVCSTATSHR 280.71 2.02E-52 2473590000 426637 384234 199331 298764 428017 379371 325752 436218 377811 TRUE FALSE 370255.8395 381709.9416 295728.1383 366602.9325 419500.2991 393965.6479 294160.6212 342936.1754 333146.614 1.111390073 1.145771638 0.887681657 1.10042521 1.259206252 1.182559364 0.88297647 1.029385144 1 18.3457977 2.24530668 24.99955083 0.979336325 1.111553965 0.312050633 0.100262789 216.8387405 803563.1719 0.040307421 0.030492692 175.9165421 -2.24530668 0.13221764 SNS(ph)DVTISDIDAEDVLDQNAVNPNTGAALHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNSDVTISDIDAEDVLDQNAVNPNTGAALHR 31 0 Q9P2F8 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 S(0.112)NS(0.888)DVTISDIDAEDVLDQNAVNPNTGAALHR 289.33 2.39E-81 1471900000 67859 88284 58535 73272 107030 78556 83232 107430 101370 TRUE FALSE 58891.26122 87704.05659 86842.72179 89909.52749 104900.3124 81578.10015 75160.17345 84456.93052 89386.15408 0.658840978 0.981181677 0.971545567 1.005855196 1.173563327 0.91264806 0.840848051 0.94485473 1 16.44776375 4.739334361 24.37248356 0.974328471 0.658840849 0.587091309 0.084256486 36.05048575 1135270.79 0.021972679 0.128080399 54869.92432 -4.739334361 -0.315487623 SNS(ph)EDKLNSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SNSEDKLNSK 10 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 S(0.285)NS(0.715)EDKLNSK;SNS(0.873)EDKLNS(0.127)K;SNS(1)EDKLNSK 195.71 9.12E-07 574206000 2025650 1000920 938390 858410 782740 696910 1329520 1502110 1417120 TRUE FALSE 1757955.22 994344.8906 1392198.543 1053325.11 767165.0054 723720.5787 1200583.355 1180895.466 1249589.688 1.406825966 0.795737113 1.114124545 0.842936782 0.613933528 0.579166574 0.96078206 0.945026577 1 20.25302302 6.863613384 1.37267781 0.848636717 200 0.50068101 0.168958485 505.5648762 3.417354797 0.050289508 314566.1468 7304885.004 -6.863613384 199.1513633 SNS(ph)ELEDEILCLEK ddPTM_MDA-MB-175_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(0.019)NS(0.981)ELEDEILCLEK 188.04 9.22E-07 15097000 48033 24658 17560 29113 36201 21925 27693 39928 33975 TRUE FALSE 41685.31735 24496.01997 26052.07473 35723.55161 35480.67093 22768.46894 25007.33712 31389.70792 29958.5142 1.391434738 0.817664715 0.869605033 1.192434023 1.184326789 0.759999938 0.834732222 1.04777252 1 14.87067845 2.751116415 24.9208863 0.924940221 1.06922775 0.191798878 0.179951431 1590.659206 3157156.632 0.05925767 0.058871594 563.7887618 -2.751116415 0.144287529 SNS(ph)FIGVPNGEVEMPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNSFIGVPNGEVEMPLK 17 0 Q9H7E2-2;Q9H7E2;Q9H7E2-3 Q9H7E2-2 TDRD3 Tudor domain-containing protein 3 1 S(0.032)NS(0.968)FIGVPNGEVEMPLK 180.05 9.25E-10 28709000 84504 78234 56484 78176 92572 77584 106130 110230 120170 TRUE FALSE 73336.58229 77720.0757 83799.85133 95927.05565 90729.99831 80568.70668 95837.52894 86658.17231 105963.6395 0.692091954 0.733459855 0.790835911 0.905282756 0.85623709 0.760342954 0.904437875 0.817810456 1 16.69320978 6.234952215 0.431645982 0.88418226 5.35E-13 0.526007512 0.063124451 17.44637389 0.965507759 0.054776079 10.30464496 1717719.378 -6.234952215 -0.88418226 SNS(ph)FNNPLGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SNSFNNPLGNR 11 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 S(0.002)NS(0.998)FNNPLGNR;SNS(1)FNNPLGNR;SNS(1)FNNPLGNR 278.84 2.95E-27 1081130000 942700 846950 581117 689380 999670 976470 993240 1079060 1057210 TRUE FALSE 818119.8065 841386.3297 862147.1249 845914.2655 979778.5228 1014035.433 896915.7377 848311.4163 932227.8382 0.877596413 0.902554392 0.924824479 0.907411505 1.051007579 1.087754936 0.96212074 0.909982926 1 19.83032307 3.3118096 10.76309755 0.99189124 0.904396568 0.497530557 0.048866716 0.519074584 73.28154709 0.016538304 0.021347006 2050.263121 -3.3118096 -0.087494673 SNS(ph)FSDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SNSFSDER 8 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 S(0.006)NS(0.967)FS(0.028)DER;S(0.005)NS(0.987)FS(0.007)DER;S(0.035)NS(0.953)FS(0.012)DER;SNS(0.993)FS(0.007)DER;S(0.004)NS(0.969)FS(0.027)DER 198.4 0.00014291 7510754000 12338790 8630390 6127042 8871580 7990820 8257020 6570150 8896030 11381060 TRUE FALSE 10708187.64 8573696.4 9090100.005 10886007.83 7831818.316 8574672.902 5932977.864 6993683.213 10035604.05 1.067019741 0.854327887 0.905785039 1.084738674 0.78040328 0.85442519 0.5911929 0.696887121 1 23.25862412 3.132445952 7.706560489 0.760773373 0.963520653 0.363439915 0.124549577 0.248914646 16.30610001 0.038069165 0.043271558 1356.581692 -3.132445952 0.20274728 SNS(ph)GRELTDEEILASVMIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNSGRELTDEEILASVMIK 19 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 S(0.256)NS(0.736)GRELT(0.008)DEEILASVMIK 186.54 1.23E-14 315710000 586820 502770 266850 299810 467420 398530 605910 708330 150540 TRUE FALSE 509270.2502 499467.2708 395899.5526 367886.4428 458119.2565 413861.707 547148.9415 556859.1417 132743.3327 3.836503422 3.762654294 2.982443973 2.771411832 3.451165849 3.1177589 4.121856295 4.195006487 1 17.01827987 1.229389452 24.99196967 0.999995054 3.539910384 0.740550604 0.470560264 213.2005384 580940.7542 1.582717518 0.130418666 16.95857873 -1.229389452 2.539915331 SNS(ph)ISQIPSLEEMQQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SNSISQIPSLEEMQQLR 17 0 A0A1B0GV57;Q9NYJ8 A0A1B0GV57 TAB2 TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 1 SNS(0.992)IS(0.008)QIPSLEEMQQLR;S(0.003)NS(0.967)IS(0.03)QIPSLEEMQQLR;S(0.031)NS(0.967)IS(0.002)QIPSLEEMQQLR;SNS(0.994)IS(0.006)QIPSLEEMQQLR 315.44 3.04E-58 796260000 767640 810060 402705 600930 853180 673590 880540 930010 825410 TRUE FALSE 666194.429 804738.6625 597454.485 737380.3411 836203.3872 699503.4432 795145.3663 731134.5988 727830.9701 0.915314759 1.105666969 0.82086983 1.013120314 1.148897782 0.961079525 1.092486304 1.004539005 1 19.47324392 3.490106894 24.74660048 1.040644657 0.955434315 0.199566603 0.08562161 896.5756757 1708592.599 0.022392733 0.031500723 3091.056146 -3.490106894 -0.085210342 SNS(ph)LDKHQQSSTLGNSVVR ddPTM_MDA-MB-175_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(0.157)NS(0.843)LDKHQQSSTLGNSVVR;S(0.14)NS(0.86)LDKHQQSSTLGNSVVR 240.75 1.49E-24 838530000 638330 577500 309750 458610 644900 548630 728500 853970 496480 TRUE FALSE 553973.0732 573706.3645 459546.1361 562744.4099 632067.7517 569736.1511 657850.1821 671355.1611 437786.7 1.265394936 1.310470063 1.049703283 1.285430576 1.44378016 1.301401233 1.502672836 1.533521144 1 18.7398686 3.46089782 8.53029328 1.384928478 1.210222191 0.136901171 0.161045308 0.286131114 120.6378615 0.045726197 0.06009566 2889.999851 -3.46089782 -0.174706287 SNS(ph)LNNGQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNSLNNGQPK 10 0 O60333-3 O60333-3 KIF1B Kinesin-like protein KIF1B 1 S(0.004)NS(0.996)LNNGQPK 84.718 0.016083 0 71441 66695 43309 55788 60302 64923 82846 90810 82443 TRUE FALSE 61999.89084 66256.87615 64253.37726 68455.51807 59102.10818 67420.62982 74811.60767 71390.98818 72696.68246 0.852857225 0.911415403 0.883855701 0.941659451 0.812995947 0.927423749 1.029092458 0.982039149 1 16.14960191 2.420708498 5.304265256 0.999089994 0.884321873 0.712891898 0.035540047 0.101651633 5.970577748 0.012623213 0.009761937 263.4562453 -2.420708498 -0.114768122 SNS(ph)LPHSAVSNAGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SNSLPHSAVSNAGSK 15 0 A0A088AWN2;Q8TBZ3-4;Q8TBZ3-5;Q8TBZ3-6;Q8TBZ3;Q8TBZ3-2;Q8TBZ3-7 A0A088AWN2 WDR20 WD repeat-containing protein 20 1 S(0.171)NS(0.828)LPHSAVSNAGSK;S(0.193)NS(0.807)LPHSAVSNAGSK;S(0.193)NS(0.807)LPHSAVSNAGSK;S(0.211)NS(0.789)LPHSAVSNAGSK;SNS(0.998)LPHS(0.002)AVSNAGSK 256.19 6.14E-25 3023230000 2654030 2534590 1499200 2517600 3274080 2551750 3770820 4242150 3596980 TRUE FALSE 2303293.211 2517940.111 2224218.135 3089259.559 3208932.214 2649917.474 3405126.457 3334999.235 3171749.122 0.726190226 0.793864841 0.701259163 0.973992406 1.011723213 0.835475119 1.073580011 1.051470058 1 21.59684723 3.694556145 6.317059316 0.997893596 0.745801464 0.756671635 0.066924107 0.101943385 10.94127352 0.019200525 0.029054458 4949.440928 -3.694556145 -0.252092132 SNS(ph)LRRDS(ph)PPPPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNSLRRDSPPPPAR 14 2 O96013;O96013-4;O96013-2;M0R2X4 O96013 PAK4 Serine/threonine-protein kinase PAK 4 2 S(0.184)NS(0.816)LRRDS(1)PPPPAR 81.788 0.061628 643690000 546010 549790 235140 343930 519030 482960 560000 594580 220270 TRUE FALSE 473853.3951 546178.3933 348854.4905 422024.5631 508702.3185 501539.7837 505691.2862 467433.694 194229.9315 2.439651764 2.812019697 1.796090272 2.172809102 2.619072737 2.582196162 2.603570326 2.406599695 1 17.56740602 1.239029559 7.754883342 0.979966862 2.432464134 0.720870749 0.279494941 0.053073856 25.5384074 0.407182661 0.070469672 17.33922008 -1.239029559 1.452497272 SNS(ph)LSEQLAINTSPDAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNSLSEQLAINTSPDAVK 18 0 Q5T1M5;Q5T1M5-2;Q5T1M5-3 Q5T1M5 FKBP15 FK506-binding protein 15 1 S(0.035)NS(0.953)LS(0.012)EQLAINTSPDAVK 319.81 4.84E-52 0 197690 152080 159930 190840 253080 232510 340460 387970 508520 TRUE FALSE 171564.7656 151080.9765 237272.6829 234173.1388 248044.2031 241454.8102 307442.2416 305005.6347 448403.3449 0.382612591 0.336930976 0.529150118 0.522237716 0.553172063 0.538476826 0.685637708 0.680203745 1 18.77443751 -2 0.32991862 6.14829559 0.387650083 0.879554988 0.063784016 25.94858205 0.411066022 89.69094646 0.102019856 0.01 2 -5.760645507 SNS(ph)LSTPRPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNSLSTPRPTR 11 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 SNS(0.7)LS(0.125)T(0.125)PRPT(0.051)R 93.011 0.025171 215380000 157400 138800 72982 89053 133050 113120 155800 143590 129440 TRUE FALSE 136599.1912 137888.2137 108276.3393 109273.8447 130402.5653 117471.7996 140690.54 112884.3959 114137.7507 1.196792388 1.208085956 0.948646164 0.957385651 1.142501622 1.029210747 1.232638099 0.989018929 1 16.80041651 4.263251415 24.85743819 1.048171649 1.202439402 0.369515044 0.086484611 239.6793236 241292.3624 0.021604713 0.057102576 18333.75466 -4.263251415 0.154267753 SNS(ph)LVSTFTMEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SNSLVSTFTMEK 12 0 Q9HB21 Q9HB21 PLEKHA1 Pleckstrin homology domain-containing family A member 1 1 SNS(0.999)LVSTFTMEK;SNS(0.98)LVS(0.02)TFTMEK;SNS(1)LVSTFTMEK;S(0.007)NS(0.993)LVSTFTMEK 266.63 1.01E-21 879120000 2198820 2261790 1737190 1706070 2244760 2051720 2632060 2851800 3120910 TRUE FALSE 1908240.366 2246932.153 2577300.895 2093459.269 2200093.668 2130650.996 2376803.226 2241964.763 2751959.575 0.693411481 0.816484433 0.936532977 0.760715851 0.799464384 0.774230485 0.86367665 0.814679395 1 21.39202785 -0.161131233 1.434903594 9.998877226 0.806522867 0.471085909 0.06381133 59.22022541 3.159394953 1688.272596 0.017976918 0.690031262 0.161131233 -9.192354358 SNS(ph)MLELAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SNSMLELAPK 10 0 Q9P2M7;Q9P2M7-2;A6PVU7;A2A3M4 Q9P2M7 CGN Cingulin 1 SNS(1)MLELAPK;S(0.012)NS(0.988)MLELAPK;S(0.247)NS(0.753)MLELAPK 193.93 5.44E-07 1317570000 1768940 1801340 999300 1136850 1410990 1160430 1582490 1826840 1768910 TRUE FALSE 1535170.097 1789506.879 1482564.822 1394989.168 1382914.06 1205072.493 1429020.363 1436184.482 1559791.475 0.984214955 1.14727315 0.950489117 0.894343373 0.886601883 0.772585639 0.916161158 0.920754156 1 20.57292174 4.054179018 5.850371853 0.897841238 1.064819295 0.508971688 0.067095121 0.148683553 10.85040225 0.017289832 0.036568166 11328.67241 -4.054179018 0.166978057 SNS(ph)PDKFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SNSPDKFK 8 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 S(0.199)NS(0.801)PDKFK;S(0.035)NS(0.965)PDKFK;S(0.02)NS(0.98)PDKFK;S(0.124)NS(0.876)PDKFK;SNS(1)PDKFK;S(0.119)NS(0.881)PDKFK 116.84 0.0023627 6091030000 12165790 9540400 9724240 8973510 8382770 6653340 12219470 13601100 18267500 TRUE FALSE 10558050.03 9477728.484 14426914.99 11011082.6 8215969.278 6909298.295 11034427.68 10692610.61 16107936.96 0.655456379 0.588388725 0.895640145 0.683581183 0.510057203 0.428937505 0.685030473 0.663810061 1 23.9412684 1.187623314 3.042288594 1.099767841 0.634196698 0.464464044 0.121991513 0.488729281 5.122414272 0.596469081 0.033558783 15.40363836 -1.187623314 -0.465571143 SNS(ph)PDKFKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNSPDKFKR 9 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 S(0.169)NS(0.831)PDKFKR 48.948 0.089233 81365000 122590 102150 108030 116240 112220 97906 126740 148990 212940 TRUE FALSE 106389.4209 101478.9699 160273.6693 142634.0686 109987.0416 101672.5072 114448.7743 117129.6479 187766.4758 0.566604983 0.540453079 0.853579792 0.759635436 0.585765063 0.541483813 0.6095272 0.623804902 1 17.51857998 1.237324292 24.88927202 1.000000462 0.63667117 0.57103935 0.09938207 23.85162553 479959.9536 0.155076676 0.025764046 17.27127074 -1.237324292 -0.363329292 SNS(ph)PGTASSGSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SNSPGTASSGSSR 13 0 Q96GY0;H0YAP0 Q96GY0 ZC2HC1A Zinc finger C2HC domain-containing protein 1A 1 S(0.001)NS(0.977)PGT(0.021)ASSGSSR;SNS(0.994)PGT(0.006)ASSGSSR 133.91 0.00010667 402340000 347360 358470 206946 255270 249700 274330 315020 341870 341590 TRUE FALSE 301455.4959 356115.187 307025.7778 313232.9551 244731.4585 284883.6526 284469.4089 268763.7609 301207.6193 1.000822943 1.18229143 1.019316106 1.039923743 0.812500889 0.945804934 0.944429658 0.892287391 1 18.20039874 3.405045929 8.030199641 0.918969237 1.070894592 0.529884401 0.066649829 0.17994391 17.57908611 0.018205368 0.023534238 2541.241441 -3.405045929 0.151925355 SNS(ph)PLPVPPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 SNSPLPVPPSK 11 0 Q13247;Q13247-3 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 S(0.012)NS(0.988)PLPVPPSK;S(0.007)NS(0.993)PLPVPPSK;SNS(1)PLPVPPSK;SNS(1)PLPVPPSK;SNS(1)PLPVPPSK;S(0.011)NS(0.989)PLPVPPSK;SNS(1)PLPVPPSK;S(0.005)NS(0.995)PLPVPPSK;S(0.008)NS(0.992)PLPVPPSK 168.18 1.93E-05 16196029000 17107470 14614800 11173110 14737080 17114590 12819830 18741160 23288810 25258380 TRUE FALSE 14846674.49 14518794.42 16576463.37 18083359.26 16774043.14 13313017.16 16923645.19 18308679.22 22272363.09 0.666596285 0.651874898 0.744261545 0.811919201 0.753132619 0.597737074 0.759849555 0.822035773 1 24.4087513 1.304598886 1.702815423 1.080894048 0.7104618 0.702659405 0.060575264 0.50946005 1.555995434 0.303376796 0.01818115 20.16503065 -1.304598886 -0.370432248 SNS(ph)PPALGPEACPVSLPSPPEASTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNSPPALGPEACPVSLPSPPEASTLK 26 0 Q9H0F6-2;Q9H0F6 Q9H0F6-2 SHARPIN Sharpin 1 S(0.233)NS(0.767)PPALGPEACPVSLPSPPEASTLK 86.519 0.0082341 66388000 171580 163070 115790 129300 163210 117090 178690 214170 196750 TRUE FALSE 148905.2683 161998.7824 171786.4313 158659.5412 159962.4403 121594.5281 161360.6713 168371.4122 173490.4391 0.858290918 0.933762017 0.990178088 0.91451461 0.922024528 0.700871637 0.930083941 0.970493896 1 17.40449663 1.773441299 3.685576735 0.987308991 0.891454611 0.215707907 0.075624475 0.347927065 9.309468339 0.051482661 0.021312646 59.3528119 -1.773441299 -0.09585438 SNS(ph)TTQVSQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SNSTTQVSQPR 11 0 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 SNS(0.997)T(0.003)TQVSQPR;SNS(0.818)T(0.167)T(0.016)QVSQPR;SNS(0.698)T(0.277)T(0.026)QVSQPR;SNS(0.923)T(0.077)TQVSQPR;S(0.004)NS(0.938)T(0.023)T(0.036)QVSQPR;SNS(0.9)T(0.094)T(0.005)QVSQPR 236.83 1.53E-15 1407768000 916620 1001107 546566 735547 959635 816910 945145 1066710 1053730 TRUE FALSE 795486.3446 994530.6622 810887.1458 902564.1885 940540.141 848337.0563 853484.9834 838602.3676 929159.2398 0.856135644 1.070355456 0.87271063 0.971377294 1.012248601 0.913015789 0.918556203 0.90253891 1 19.82556634 1.209702271 23.90574707 1.000000571 0.941317694 0.079277828 0.064438866 5404.765968 4476785.151 1.401212245 0.014630137 16.20698654 -1.209702271 -0.058682876 SNS(ph)VEKPVSSILSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SNSVEKPVSSILSR 14 1 H0YJN0;Q9UI08-5;Q9UI08;Q9UI08-2;Q9UI08-4;Q9UI08-3 H0YJN0 EVL Ena/VASP-like protein 1 S(0.09)NS(0.91)VEKPVSSILSR;S(0.011)NS(0.989)VEKPVSSILSR;SNS(0.645)VEKPVS(0.275)S(0.008)ILS(0.073)R 170.35 8.39E-06 706720000 633920 481930 271291 372587 508940 304136 668760 675620 505660 TRUE FALSE 550145.8659 478764.1701 402488.235 457188.573 498813.0897 315836.3087 603903.7581 531143.9207 445881.4508 1.233838871 1.073747673 0.902679926 1.025359032 1.118712359 0.708341439 1.354404309 1.191222285 1 18.76630066 SNSFFEGVDWEHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SNSFFEGVDWEHIR 14 0 Q15208 Q15208 STK38 Serine/threonine-protein kinase 38 0 ;; 148.03 7.87E-06 294876000 337100 316245 190410 228547 340752 359759 313630 353593 349274 FALSE TRUE 292551.3809 314167.5658 282492.9129 280442.0895 333971.7019 373599.1615 283214.2109 277979.8886 307983.2256 0.949893879 1.02008012 0.917234737 0.910575857 1.084382765 1.213050356 0.919576741 0.902581263 1 18.23249225 4.783204682 19.94036536 0.989484585 0.949892414 0.018150931 0.096563107 12337.52506 5508858.301 0.02543201 6.241778527 60702.23499 -4.783204682 -0.03959217 SNSLS(ph)EQLAINTSPDAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNSLSEQLAINTSPDAVK 18 0 Q5T1M5;Q5T1M5-2;Q5T1M5-3 Q5T1M5 FKBP15 FK506-binding protein 15 1 S(0.031)NS(0.103)LS(0.866)EQLAINTSPDAVK 212.41 2.05E-16 261110000 232080 167360 185170 219960 291950 264310 397790 444510 595180 TRUE FALSE 201410.04 166260.6011 274718.8314 269905.2799 286140.7662 274478.1767 359212.387 349454.9957 524818.4984 0.383770848 0.316796381 0.523454932 0.514283092 0.545218522 0.522996384 0.684450697 0.665858762 1 19.00145905 -2 0.343126711 6.665582402 0.384546564 0.866171554 0.068330515 27.51441386 0.430211049 109.478109 0.098491644 0.01 2 -6.281035838 SNSLS(ph)TPRPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNSLSTPRPTR 11 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 SNS(0.018)LS(0.395)T(0.395)PRPT(0.192)R 83.137 0.044787 181460000 303040 276190 141320 206290 289050 250060 312640 322960 278860 TRUE FALSE 262992.4962 274375.6897 209662.8247 253131.2974 283298.4705 259679.97 282320.2209 253897.5173 245893.4885 1.06953827 1.115831458 0.852657083 1.029434732 1.152118636 1.056066883 1.148140289 1.032550796 1 17.90767401 3.461860295 24.88484045 1.077628986 1.009333632 0.125733409 0.080662331 457.8979745 746655.2435 0.023366454 0.030177996 2896.411711 -3.461860295 -0.068295354 SNSLVS(ph)TFTMEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNSLVSTFTMEK 12 0 Q9HB21 Q9HB21 PLEKHA1 Pleckstrin homology domain-containing family A member 1 1 S(0.001)NS(0.3)LVS(0.688)T(0.012)FTMEK 124.39 0.0012663 297330000 837830 865730 595250 563410 793920 748870 988560 1035600 1180100 TRUE FALSE 727108.6427 860042.9626 883114.891 691340.8517 778122.5453 777679.5135 892689.6034 814144.999 1040589.922 0.698746574 0.826495572 0.848667541 0.664373964 0.747770595 0.747344844 0.857868776 0.782387934 1 19.98897021 -0.385028198 1.150492792 9.999999924 0.764722568 0.574477809 0.061807954 47.33729938 1.957205563 1076.067973 0.018811677 0.412070763 0.385028198 -9.235277355 SNT(ph)PILVDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNTPILVDGK 10 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41 P06744 GPI Glucose-6-phosphate isomerase 1 S(0.001)NT(0.999)PILVDGK 129.17 0.0034678 85763000 445730 296540 301860 308550 359970 233410 395070 448330 662860 TRUE FALSE 386825.6512 294592.0092 447840.5057 378610.9934 352807.3013 242389.4337 356756.1722 352458.1184 584497.4459 0.661808967 0.504009062 0.766197541 0.647754744 0.603607943 0.414697165 0.610363954 0.603010536 1 19.1568372 1.238335423 8.206673985 1.004436881 0.599409057 0.645884047 0.092740595 0.05889671 38.20261856 0.132011611 0.022796433 17.31152883 -1.238335423 -0.405027824 SNT(ph)PTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNTPTPR 7 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9;Q04727-4;Q04727;Q04727-3;Q04727-2;H7C4E4;H7C4W5;H0Y5S0;H7C4P7;Q5JSY7 H0YKT5;Q04727-4 TLE3;TLE4 Transducin-like enhancer protein 3;Transducin-like enhancer protein 4 1 S(0.017)NT(0.982)PT(0.001)PR 106.29 0.086467 98316000 234530 155470 102890 102420 124920 159440 161920 185050 166350 TRUE FALSE 203536.2663 154448.7073 152647.9481 125676.0264 122434.3364 165573.76 146217.0233 145478.4976 146684.2925 1.387580516 1.052932831 1.040656403 0.856779034 0.834679258 1.128776348 0.996814457 0.991779659 1 17.16235486 4.857591359 1.870782902 0.975560288 1.611964651 0.702897574 0.083227941 0.696667281 1.963087006 0.022787224 0.854529967 72042.92863 -4.857591359 0.636404363 SNTENLSQHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SNTENLSQHFR 11 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;;; 265.72 5.64E-21 4113500000 3125100 3327070 975870 1849190 3719490 3808120 2987420 3322920 3470620 FALSE TRUE 2712110.117 3305214.258 1447803.996 2269076.853 3645479.426 3954620.841 2697700.468 2612339.417 3060327.257 0.886215718 1.080019874 0.473087966 0.741449088 1.19120575 1.292221553 0.881507186 0.8536144 1 21.54525451 3.258990751 24.89461134 1.020208288 0.792530352 0.279436381 0.196273976 369.3064917 450005.9074 0.061481081 0.079274722 1815.476998 -3.258990751 -0.227677935 ALS(ph)SDSILS(ph)PAPDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 2 ALS(1)SDSILS(1)PAPDAR;ALS(1)SDSILS(1)PAPDAR;ALS(0.999)S(0.001)DSILS(1)PAPDAR;ALS(0.999)S(0.001)DSILS(1)PAPDAR 310.46 5.60E-56 1796310000 1270210 2027840 1801410 2128200 2939780 3155780 2579760 3310880 3947590 TRUE FALSE 1102348.53 2014518.986 2672577.901 2611440.338 2881284.13 3277184.899 2329575.272 2602874.077 3480910.407 0.316683971 0.578733363 0.767781295 0.750217625 0.827738664 0.941473498 0.6692431 0.747756699 1 21.73103325 4.750565871 1.246854559 0.814298528 0.071774092 0.756105696 0.09408237 0.762217136 1.00077978 0.028021333 0.735331983 56307.45148 -4.750565871 -0.742524436 down MGS(ph)SPLEVPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MGSSPLEVPKPR 12 1 Q8NCE2;Q8NCE2-2 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 MGS(0.5)S(0.5)PLEVPKPR 70.889 0.069877 266610000 346840 397160 391860 509460 650730 599100 823660 854630 902490 TRUE FALSE 301004.2152 394551.0298 581364.8067 625140.6796 637781.7461 622147.7647 743781.58 671874.0252 795798.6603 0.378241671 0.495792528 0.73054258 0.785551309 0.801436064 0.781790415 0.934635376 0.844276396 1 19.60204394 4.755112819 0.594869394 0.901941772 4.94E-20 0.906650611 0.057032711 1.071580944 0.294531318 0.03156585 0.673674487 56900.07241 -4.755112819 -0.901941772 down SNTGGQAFPQCVFDHWQILPGDPFDNSSRPSQVVAETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SNTGGQAFPQCVFDHWQILPGDPFDNSSRPSQVVAETR 38 1 P13639 P13639 EEF2 Elongation factor 2 0 ; 158.99 6.51E-18 1134150000 722130 711150 336070 475390 728040 739570 676560 819170 579880 FALSE TRUE 626698.6909 706478.4088 498594.5761 583334.5654 713553.4284 768021.7365 610947.3153 643996.8703 511327.247 1.225631324 1.381656098 0.975098783 1.140824333 1.395492676 1.502016059 1.194826442 1.259461283 1 18.96388738 1.237329491 8.118280849 0.996914667 1.259621878 0.236963337 0.146263045 0.156804128 93.69120867 0.220940238 0.037334331 17.27147751 -1.237329491 0.26270721 SNVSSPATPTASS(ph)SSSTTPTRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNVSSPATPTASSSSSTTPTRK 22 1 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SNVSSPATPT(0.012)AS(0.047)S(0.189)S(0.189)S(0.139)S(0.139)T(0.139)T(0.139)PT(0.007)RK 96.052 0.00093297 261740000 76693 71299 42364 58087 88685 76498 85546 101940 77977 TRUE FALSE 66557.82573 70830.63217 62851.3721 71276.54115 86920.34201 79440.92756 77249.76209 80140.9243 68758.64789 0.967992068 1.030134163 0.914086795 1.036619296 1.264136871 1.155359071 1.123491582 1.165539561 1 16.06925355 3.466891354 24.82259001 1.144581065 0.976456602 0.566122436 0.069153924 131.7534281 319694.9463 0.019230249 0.024853667 2930.160125 -3.466891354 -0.168124463 SNVSSPATPTASSSSSTT(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNVSSPATPTASSSSSTTPTR 21 0 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SNVSSPATPTASSSSS(0.004)T(0.175)T(0.821)PTR 231.29 7.54E-35 0 36272 40728 23464 31790 48985 51716 42150 52224 49736 TRUE FALSE 31478.5633 40460.45509 34811.26888 39008.40538 48010.29434 53705.54798 38062.29949 41056.30401 43856.26674 0.717766596 0.922569523 0.793758144 0.889460236 1.094719134 1.224580932 0.867887358 0.936155926 1 15.42049539 3.430026938 5.786072151 1.011344617 0.825051974 0.461499887 0.105877001 0.201227036 15.66983383 0.032724226 0.042905064 2691.701754 -3.430026938 -0.186292643 SNVSSPATPTASSSSSTT(ph)PTRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNVSSPATPTASSSSSTTPTRK 22 1 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SNVSSPATPTASSSS(0.003)S(0.062)T(0.211)T(0.723)PT(0.001)RK 222.01 5.21E-26 216930000 94649 100200 55844 73874 103040 92473 110950 142140 106930 TRUE FALSE 82140.89484 99541.7796 82850.34519 90648.22079 100989.7056 96030.49615 100190.0861 111744.4671 94288.85722 0.871162269 1.055710956 0.878686492 0.961388477 1.071067235 1.018471312 1.062586705 1.185129086 1 16.52479967 2.976050584 1.086525145 1.10059033 0.939393717 0.409953551 0.071641299 0.4446953 1.164287895 0.036563393 0.03812528 946.3473805 -2.976050584 -0.161196613 SNVVS(ph)PTKNEDNGAPENSVEKPHEKPEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SNVVSPTKNEDNGAPENSVEKPHEKPEAR 29 3 Q71RC2-5;Q71RC2-3;Q71RC2;Q71RC2-4;X6RLN4;Q71RC2-2;Q71RC2-6 Q71RC2-5 LARP4 La-related protein 4 1 S(0.009)NVVS(0.814)PT(0.177)KNEDNGAPENSVEKPHEKPEAR;SNVVS(0.979)PT(0.021)KNEDNGAPENSVEKPHEKPEAR 186.53 4.70E-18 895250000 630190 429450 468580 402070 424720 281505 666840 742410 612840 TRUE FALSE 546908.7948 426628.9147 695186.8553 493366.1388 416268.903 292334.6795 602169.9594 583651.3989 540390.7533 1.012061719 0.789482263 1.286452166 0.912980349 0.770310928 0.540969063 1.114323211 1.080054378 1 19.04364346 SNYNFEKPFLWLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SNYNFEKPFLWLAR 14 1 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 150.59 6.54E-06 16222200000 1161690 1181380 600550 816250 1245480 1044160 1242950 1392770 1265350 FALSE TRUE 1008169.723 1173619.437 890977.9887 1001592.038 1220697.385 1084329.511 1122408.9 1094936.974 1115761.764 0.903570776 1.051854862 0.798537839 0.897675534 1.09404841 0.971828884 1.005957487 0.981335809 1 20.08959759 3.277121568 24.99998197 1.004680966 0.914664904 0.331823505 0.068599212 206.3679765 133791.9615 0.019370627 0.02500684 1892.873398 -3.277121568 -0.090016063 SPAAET(ph)PPLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPAAETPPLQR 11 0 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 SPAAET(1)PPLQR;S(0.001)PAAET(0.999)PPLQR;S(0.001)PAAET(0.999)PPLQR 107.65 0.02425 3062380000 2153300 2315380 1465190 1961910 2378150 2396550 2147790 2457990 2848710 TRUE FALSE 1868735.949 2300170.116 2173760.785 2407391.651 2330829.468 2488746.829 1939497.656 1932367.967 2511938.749 0.743941686 0.915695145 0.865371732 0.958379918 0.927900598 0.990767323 0.772111843 0.769273521 1 21.26036986 4.745496833 24.16725355 0.888195981 0.743941578 0.260023575 0.080566392 855.3245665 2980007.998 0.021258478 0.200745002 55654.05755 -4.745496833 -0.144254403 SPAAPYFLGSSFS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPAAPYFLGSSFSPVR 16 0 P30291 P30291 WEE1 Wee1-like protein kinase 1 SPAAPYFLGSS(0.002)FS(0.998)PVR;SPAAPYFLGSSFS(1)PVR;SPAAPYFLGSSFS(1)PVR 223.29 9.29E-15 162284000 263248 249104 164031 223729 236269 244745 223503 262239 255379 TRUE FALSE 228459.1098 247467.6194 243356.9403 274530.0889 231567.7092 254160.4985 201827.7135 206161.2306 225188.3855 1.014524391 1.098935981 1.08068158 1.219113003 1.02832883 1.128657226 0.896261648 0.915505611 1 17.78077289 2.239244365 24.99998615 0.931016369 1.097171939 0.594150058 0.061385141 11.27736026 412363.2813 0.023095726 0.016808807 173.4779832 -2.239244365 0.16615557 SPADPIDLGGQTS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SPADPIDLGGQTSPR 15 0 O60504-2;O60504;H0YAZ3;H0YB51 O60504-2 SORBS3 Vinexin 1 SPADPIDLGGQT(0.008)S(0.992)PR;SPADPIDLGGQT(0.005)S(0.995)PR;SPADPIDLGGQT(0.001)S(0.999)PR;SPADPIDLGGQT(0.001)S(0.999)PR;SPADPIDLGGQT(0.168)S(0.832)PR;SPADPIDLGGQT(0.462)S(0.538)PR 250.08 1.10E-18 4810570000 4295480 5279940 3546640 4244110 5672210 5595690 4908130 6020650 6169600 TRUE FALSE 3727821.435 5245255.726 5261806.967 5207800.043 5559344.118 5810959.815 4432140.308 4733180.85 5440236.916 0.685231451 0.96415943 0.967201805 0.957274494 1.021893753 1.068144624 0.814696194 0.870032119 1 22.37523805 4.740436107 24.67972198 0.950057708 0.685231344 0.5832781 0.072165602 116.066343 1527184.362 0.01934052 0.121498302 55009.29855 -4.740436107 -0.264826363 SPADPIDLGGQTS(ph)PRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPADPIDLGGQTSPRR 16 1 O60504-2;O60504;H0YAZ3;H0YB51 O60504-2 SORBS3 Vinexin 1 SPADPIDLGGQT(0.139)S(0.861)PRR;SPADPIDLGGQT(0.269)S(0.731)PRR 89.816 0.003468 764520000 678790 832180 442250 529950 851050 887640 793300 876650 365880 TRUE FALSE 589086.1817 826713.3548 656123.5792 650283.2473 834115.7701 921788.0852 716365.8881 689185.2196 322626.0832 1.825909969 2.562450458 2.033696633 2.015594154 2.585394714 2.857140613 2.220421489 2.136173284 1 18.29950355 1.181836287 2.624920201 0.556136208 2.317990332 0.634250275 0.307224913 0.404903051 2.764699751 1.704449262 0.081417476 15.19974448 -1.181836287 1.761854124 SPAGPAATPAQAQAAST(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPAGPAATPAQAQAASTPR 19 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 SPAGPAATPAQAQAAS(0.002)T(0.998)PR;SPAGPAATPAQAQAAS(0.001)T(0.999)PR;SPAGPAATPAQAQAAS(0.053)T(0.947)PR;SPAGPAATPAQAQAAS(0.002)T(0.998)PR 319.81 7.65E-61 978910000 867730 797550 559914 733380 856020 974660 730790 756660 1096110 TRUE FALSE 753057.282 792310.8415 830690.2832 899905.138 838986.8768 1012155.801 659918.0983 594854.1473 966529.1245 0.779135634 0.819748543 0.859457064 0.931068827 0.868040968 1.047206727 0.682771043 0.615453929 1 19.88245368 2.20218921 24.99997394 0.731224535 0.881467965 0.153960041 0.121502857 241.3942155 165921.2752 0.049286589 0.03323015 159.2902559 -2.20218921 0.150243429 SPAGSQQQFGYSPGQQQTHPQGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPAGSQQQFGYSPGQQQTHPQGSPR 25 0 Q8TAP9 Q8TAP9 MPLKIP M-phase-specific PLK1-interacting protein 1 SPAGSQQQFGYSPGQQQTHPQGS(1)PR 254.48 4.98E-45 255300000 109180 81198 51374 50831 68978 84035 84470 73131 72363 TRUE FALSE 94751.58637 80664.60499 76218.63824 62372.95545 67605.47275 87267.88083 76278.1124 57492.50476 63808.32858 1.484940736 1.264170474 1.194493571 0.977504925 1.059508598 1.367656586 1.195425646 0.901018817 1 15.96145712 7.99999994 0.64095439 1.070407862 36.7639337 0.489286959 0.130056047 202.9364746 1.369408514 0.062566741 10251.60103 99999986.09 -7.99999994 35.69352584 SPALKS(ph)PLQSVVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPALKSPLQSVVVR 14 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.001)PALKS(0.998)PLQS(0.001)VVVR;SPALKS(1)PLQSVVVR 117.84 0.0001697 1939440000 1512860 1431940 924190 1070170 1510790 1257200 1359240 1746610 1460460 TRUE FALSE 1312931.718 1422533.492 1371131.375 1313168.455 1480728.235 1305565.298 1227421.114 1373111.044 1287806.083 1.019510418 1.104617777 1.064703292 1.019694248 1.149806834 1.013790287 0.953110201 1.066240533 1 20.29648394 2.536778009 24.99997702 1.011935953 1.071380542 0.316004936 0.046204724 312.1785426 130822.1586 0.015171967 0.013380376 344.1739599 -2.536778009 0.059444589 SPALLLSQLLPYMENRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPALLLSQLLPYMENRR 17 1 Q13268;C9JZP6;Q13268-2;H0YJG9;H0YJP4 Q13268;H0YJP4 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 83.968 0.0086573 84416000 75310 49475 37145 67807 63259 65975 60934 75301 24559 FALSE TRUE 65357.59269 49149.99547 55108.44624 83203.61572 62000.26966 68513.10094 55024.63006 59198.46714 21655.663 3.018037023 2.269613979 2.544759135 3.842118144 2.863004918 3.163749868 2.54088873 2.733625248 1 14.40245672 1.116800113 2.364667248 2.93E-09 2.89919693 0.65421657 0.42770502 0.609443712 2.664619423 4.223127047 0.115030703 13.08579501 -1.116800113 2.899196927 SPAPPPPAVFPAARPEPGDGLS(ph)SPAGGSYETGDRDDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR 38 2 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 SPAPPPPAVFPAARPEPGDGLS(0.5)S(0.5)PAGGSYETGDRDDGR 151.18 1.01E-13 543100000 126360 126870 88528 111910 147200 134420 146480 170190 156790 TRUE FALSE 109661.2058 126036.5826 131340.4369 137320.8759 144271.008 139591.2244 132274.3921 133796.1929 138254.4648 0.793183829 0.911627576 0.949990563 0.993247315 1.043517894 1.009668835 0.956745898 0.967753143 1 17.07696655 4.737641158 1.315653892 0.991732952 0.707165443 0.873443139 0.024435942 0.520044907 0.790129685 0.008117867 0.199248149 54656.41699 -4.737641158 -0.28456751 SPAPPPPAVFPAARPEPGDGLSS(ph)PAGGSYETGDRDDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR 38 2 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 SPAPPPPAVFPAARPEPGDGLS(0.089)S(0.91)PAGGS(0.001)YETGDRDDGR 199.17 1.26E-30 820850000 174740 173880 116510 152810 160920 198460 187100 179890 199930 TRUE FALSE 151647.6663 172737.7708 172854.6257 187507.8461 157718.0068 206094.8846 168955.0708 141421.9234 176294.5032 0.860195091 0.979825053 0.980487892 1.063605743 0.894628046 1.169037496 0.958368343 0.802191338 1 17.42762797 1.988090959 24.96590344 0.884960472 0.995387098 0.122336939 0.096486324 837.7156696 1756171.061 0.040047073 0.024758497 97.29509787 -1.988090959 0.110426626 SPARPSESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPARPSESR 9 1 Q8IY33;Q8IY33-5;Q8IY33-4;Q8IY33-2 Q8IY33 MICALL2 MICAL-like protein 2 0 85.355 0.015405 0 34351 31975 18886 21112 31444 37620 31860 36384 29567 FALSE TRUE 29811.42832 31764.95412 28019.33277 25905.80228 30818.32592 39067.26574 28770.2221 28603.56474 26071.62294 1.14344352 1.218372718 1.074706121 0.993639803 1.182063962 1.498459295 1.103507141 1.097114852 1 14.67019277 1.584953584 2.509656089 1.014566356 1.177759285 0.157295948 0.131464375 0.555249348 7.375634862 0.161216828 0.037889172 38.45506805 -1.584953584 0.163192929 SPAVATSTAAPPPPS(ph)SPLPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPAVATSTAAPPPPSSPLPSK 21 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 SPAVATSTAAPPPPS(0.636)S(0.358)PLPS(0.006)K 142.57 1.52E-07 1187600000 929860 843390 586360 795760 995560 834000 979080 1302000 1023200 TRUE FALSE 806976.645 837849.7156 869925.6573 976449.4704 975750.3038 866084.5197 884128.9723 1023577.432 902238.4616 0.894416143 0.928634448 0.96418596 1.082252101 1.081477176 0.959928618 0.979928267 1.134486586 1 19.78314926 3.994204759 3.092269983 1.043999128 0.912096704 0.508199258 0.052765784 0.207646657 4.066857344 0.015053931 0.032912149 9867.44601 -3.994204759 -0.131902423 SPAVATSTAAPPPPSS(ph)PLPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(0.015)S(0.985)PLPSK;SPAVATSTAAPPPPS(0.006)S(0.994)PLPSK;SPAVATSTAAPPPPS(0.002)S(0.998)PLPSK;SPAVATSTAAPPPPS(0.007)S(0.993)PLPSK 331.54 4.35E-80 16728740000 11796400 11057070 7175340 9452030 12135370 10181010 12526980 15744200 13253850 TRUE FALSE 10237475.85 10984435.38 10645358.42 11598257.88 11893899.88 10572680.04 11312115.41 12377425.35 11686994.95 0.875971616 0.939885353 0.910872168 0.992407195 1.01770386 0.904653428 0.967923359 1.059076812 1 23.47840069 8 0.162897154 1.064599151 0.369343266 0.465817602 0.041280689 124.7072447 1.656863337 0.555018283 20.32199459 100000000 -8 -0.695255885 SPDDPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPDDPSR 7 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;; 120.65 0.010504 2342460000 7352410 8046610 5295610 4928780 4542850 7978150 6973100 7300510 9631070 FALSE TRUE 6380770.39 7993751.289 7856584.709 6047934.831 4452456.173 8285074.593 6296849.835 5739352.749 8492495.876 0.751342183 0.941272319 0.925120815 0.712150458 0.524281229 0.975575934 0.741460452 0.675814605 1 23.01775718 3.738580504 24.9999865 0.757893016 0.879447827 0.09071537 0.146057348 3.725451326 4680268.257 0.038596003 0.061767472 5477.476266 -3.738580504 0.12155481 SPDEALPGGLSGCSSGSGHS(ph)PYALER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPDEALPGGLSGCSSGSGHSPYALER 26 0 Q5JSZ5;A0A494C0D3;H0Y412;A0A494C065;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 SPDEALPGGLSGCS(0.003)S(0.003)GS(0.003)GHS(0.991)PYALER;SPDEALPGGLSGCS(0.001)S(0.015)GS(0.051)GHS(0.755)PY(0.179)ALER 110.43 1.80E-09 0 132205 147528 80140 98006 138529 145400 135001 142202 171685 TRUE FALSE 114733.7743 146558.8789 118895.9721 120259.7602 135772.5439 150993.6321 121908.6238 111793.2089 151388.5949 0.757875944 0.968097227 0.785369414 0.794377941 0.896847903 0.997391066 0.805269538 0.738451988 1 17.207897 3.227446171 24.83381908 0.868265332 0.833616294 0.069634046 0.096236718 973.3952913 2174924.234 0.030415801 0.034811486 1688.286589 -3.227446171 -0.034649038 SPDEATAADQES(ph)EDDLSASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPDEATAADQESEDDLSASR 20 0 C9JME2;Q9Y4F1;Q9Y4F1-2;M0QXT1 C9JME2 FARP1 "FERM, RhoGEF and pleckstrin domain-containing protein 1" 1 SPDEATAADQES(1)EDDLSASR;SPDEATAADQES(1)EDDLSASR 434.26 4.54E-174 506990000 373320 302160 249602 502780 392380 399480 181343 416350 646600 TRUE FALSE 323984.8161 300175.0911 370310.3621 616943.8835 384572.4057 414848.2541 163756.3838 327316.7925 570159.6846 0.568235224 0.526475475 0.64948535 1.082054554 0.674499471 0.727600119 0.28721144 0.57407916 1 19.12100651 4.125900819 5.709790415 0.692527432 0.549511314 0.087949884 0.217947645 0.62469082 28.53247082 0.059704134 0.128362826 13362.9031 -4.125900819 -0.143016118 SPDKPGGS(ph)PSASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPDKPGGSPSASR 13 1 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 SPDKPGGS(0.981)PS(0.019)ASR;SPDKPGGS(0.992)PS(0.008)ASR;SPDKPGGS(0.892)PS(0.108)ASR;SPDKPGGS(0.997)PS(0.002)ASR 124.25 0.00012959 897370000 1586650 1123150 819490 1022020 1166250 1012600 1208770 1483300 1399280 TRUE FALSE 1376970.182 1115771.954 1215798.105 1254085.262 1143043.907 1051555.377 1091543.671 1166107.838 1233858.712 1.115986919 0.904294748 0.9853625 1.016392922 0.926397727 0.852249424 0.88465856 0.945090249 1 20.23474577 3.187128434 7.146540251 0.917951596 0.996769436 0.296422515 0.063442462 0.293039182 32.832468 0.019043744 0.02179453 1538.609587 -3.187128434 0.07881784 SPDMLAHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPDMLAHFR 9 0 O43747;O43747-2;H3BNR4 O43747 AP1G1 AP-1 complex subunit gamma-1 0 93.649 0.0092562 203790000 188960 180380 111970 143600 187640 187570 198290 200470 220620 FALSE TRUE 163988.4572 179195.0719 166119.0665 176206.5748 183906.3311 194785.9393 179059.8663 157601.0506 194538.5549 0.842961218 0.921128832 0.853913336 0.905766854 0.945346444 1.001271647 0.920433825 0.810127589 1 17.56969658 3.488293035 20.3488099 0.922267886 0.877901531 0.182132039 0.056823473 111.6551192 203372.2923 0.017306414 0.024019929 3078.173078 -3.488293035 -0.044366355 SPDTNYLFMGDYVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPDTNYLFMGDYVDR 15 0 P67775;P62714;P67775-2;E7ESG8;E5RHC1;E5RFI3;E5RHP4 P67775 PPP2CA;PPP2CB Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform;Serine/threonine-protein phosphatase 0 ; 104.17 0.0032908 427990000 147211 134363 103239 111608 146652 128775 125640 145410 141191 FALSE TRUE 127756.6934 133480.3606 153165.7257 136950.3022 143733.9121 133729.0576 113455.4521 114315.2031 124499.5608 1.026161799 1.072135192 1.230251133 1.100006308 1.154493326 1.074132766 0.911291987 0.918197641 1 16.92578113 2.347369643 4.418050436 0.936940606 1.119021388 0.651491984 0.057879618 0.123888217 4.216473223 0.022799977 0.017200253 222.5203031 -2.347369643 0.182080782 SPDVGLYGVIPECGETYHSDLAEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPDVGLYGVIPECGETYHSDLAEAK 25 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;; 299.34 3.89E-63 1215170000 1320462 1516220 620695 717400 838317 826025 924022 1226974 1905720 FALSE TRUE 1145959.601 1506259.851 920865.1781 880296.6348 821636.1318 857802.7163 834410.4887 964595.1584 1680427.953 0.681945096 0.896354913 0.547994442 0.523852649 0.488944575 0.510466822 0.496546423 0.574017563 1 20.68039726 -0.5202505 13.2866833 6.174989246 0.619662345 0 0.178157923 0 0 0 0.040432737 0.301821032 0.5202505 -5.555326901 SPEDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPEDKR 6 1 A0A3B3ISG5;P14735;Q5T5N3 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 100.82 0.059688 304510000 799360 771820 550760 646960 387110 637710 874950 1025840 1030270 FALSE TRUE 693722.5507 766749.8636 817109.3782 793862.1562 379407.2684 662243.1164 790097.4837 806472.0991 908472.6543 0.763614125 0.843998837 0.899432002 0.873842655 0.417632019 0.728963181 0.869698697 0.887723032 1 19.79308356 1.7268499 1.86218935 0.979214445 0.759458363 0.258305936 0.135138477 0.55707064 3.687055058 0.168279372 0.042258887 53.31505973 -1.7268499 -0.219756081 SPEDLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SPEDLER 7 0 P06744;A0A2U3TZU2;P06744-2;Q8N196 P06744 GPI;SIX5 Glucose-6-phosphate isomerase;Homeobox protein SIX5 0 ;;;;; 158.36 0.003312 6701120000 5950840 5299160 3506570 3875890 4687520 5209460 4936410 5576480 5219350 FALSE TRUE 5164421.416 5264349.469 5202358.981 4755970.064 4594247.523 5409871.297 4457677.718 4383993.148 4602324.389 1.122133292 1.14384581 1.130376423 1.033384364 0.998245046 1.175465013 0.968570953 0.952560658 1 22.13393124 2.111539744 0.216280428 0.81709756 1.216088228 0.445184679 0.05936788 9.661086771 1.214484232 1.539523341 0.685732613 129.2825008 -2.111539744 0.398990668 SPEEGAETPVYLALLPPDAEGPHGQFVSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPEEGAETPVYLALLPPDAEGPHGQFVSEK 30 0 P16152 P16152 CBR1 Carbonyl reductase [NADPH] 1 0 137.64 1.77E-06 55278000 54831 59267 33809 51630 52816 45145 61304 70343 64121 FALSE TRUE 47584.94443 58877.67117 50159.14548 63353.38062 51765.06493 46881.75736 55358.74752 55300.69686 56540.68843 0.841605324 1.041332761 0.887133618 1.120491851 0.915536517 0.829168492 0.979095746 0.97806904 1 15.78700183 2.031077965 24.99703613 0.984802663 0.944940223 0.057110206 0.087352143 709.2878654 570500.7559 0.034825587 0.023479216 107.4182235 -2.031077965 -0.03986244 SPFEGAVT(ph)ESQSLFSDNFR ddPTM_MDA-MB-175_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(0.344)PFEGAVT(0.656)ESQSLFSDNFR 385.05 8.86E-126 752830000 61608 68120 45132 49262 63422 58077 66551 68569 70988 TRUE FALSE 53466.34671 67672.51523 66957.98616 60447.69002 62160.02628 60311.25977 60096.89426 53906.05295 62595.87951 0.854151218 1.081101756 1.069686802 0.965681615 0.99303703 0.963502075 0.96007748 0.861175742 1 15.93378007 2.42493608 1.611181282 0.921156058 1.002195825 0.091168773 0.070412244 0.6412961 3.423640545 0.038436714 0.024128228 266.0333477 -2.42493608 0.081039767 SPFNSPS(ph)PQDSPR ddPTM_MDA-MB-175_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(0.001)PS(0.999)PQDSPR 273.09 4.13E-32 238250000 432970 345700 188620 256700 275600 259620 284040 286670 509010 TRUE FALSE 375751.9175 343429.0739 279837.2629 314987.6584 270116.0992 269607.7494 256493.8445 225367.8514 448835.4177 0.837170826 0.765155913 0.623474111 0.701788776 0.601815473 0.600682876 0.571465251 0.502116906 1 18.775827 4.396556606 2.71431798 0.635514235 0.834151014 0.159650032 0.134266921 0.441324172 6.11055896 0.033948466 0.138990556 24920.49162 -4.396556606 0.198636779 SPFNSPSPQDS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPFNSPSPQDSPR 13 0 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5;P08651-4 P08651-3 NFIC Nuclear factor 1 C-type 1 SPFNSPSPQDS(1)PR;SPFNSPSPQDS(1)PR 230.55 7.67E-12 276990000 121278 130555 110343 174516 181514 191221 179665 198956 315630 TRUE FALSE 105250.805 129697.3756 163705.2439 214142.5251 177902.2265 198577.3956 162241.116 156410.8077 278316.581 0.378169366 0.466006643 0.588197955 0.769420652 0.639208149 0.713494665 0.582937299 0.561988823 1 18.08636734 4.216547037 2.306375291 0.684903808 0.392493549 0.477270407 0.12340487 0.288489781 2.989558687 0.032983683 0.110326376 16464.44276 -4.216547037 -0.292410259 SPFSVAVS(ph)PSLDLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPFSVAVSPSLDLSK 15 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 SPFSVAVS(0.569)PS(0.431)LDLSK 133.86 4.06E-05 92589000 314170 282940 190050 238830 274900 240220 301090 346700 324280 TRUE FALSE 272651.6385 281081.3485 281958.8157 293060.0018 269430.0278 249461.4188 271890.3381 272560.903 285943.9878 0.95351415 0.982994434 0.986063102 1.024886042 0.942247571 0.872413583 0.950851739 0.953196831 1 18.12537305 3.161317402 14.92059116 0.94187303 0.986527629 0.272467002 0.034938468 1.904141265 364.8898251 0.01098913 0.012461226 1449.831067 -3.161317402 0.044654599 SPGETSKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPGETSKPR 9 1 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 74.92 0.036231 96149000 92760 76643 66251 85200 70850 75412 77852 95971 177000 FALSE TRUE 80501.53098 76139.52709 98290.2052 104545.9622 69440.22362 78313.14844 70301.92502 75448.3485 156075.2616 0.515786616 0.487838536 0.629761592 0.669843261 0.444914991 0.501765287 0.450436054 0.48341004 1 17.25188236 1.235793542 24.99996134 1.00000064 0.52144254 0.809330579 0.072762242 34.73057683 313722.055 0.12861447 0.019108861 17.21050214 -1.235793542 -0.4785581 SPGETSKPRPFAGGGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPGETSKPRPFAGGGYR 17 2 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 117.2 0.00012892 1009000000 707840 721070 387000 447090 629930 635770 734500 897050 335380 FALSE TRUE 614297.1506 716333.2437 574154.4944 548608.6178 617395.6254 660228.4833 663268.3031 705222.8384 295731.7585 2.077210624 2.422239828 1.941470532 1.855088614 2.087687939 2.232524795 2.242803771 2.384670629 1 18.17392966 1.231850932 24.99998772 0.999998031 2.162853565 0.806599627 0.1777779 106.7394833 397669.6185 0.44486678 0.04691747 17.05496891 -1.231850932 1.162855534 SPGGGS(ph)EANGLALVSGFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPGGGSEANGLALVSGFK 18 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 S(0.281)PGGGS(0.719)EANGLALVSGFK 161.19 2.49E-11 99629000 257840 228390 171920 210900 221440 192390 268020 308230 303630 TRUE FALSE 223765.7907 226889.6911 255061.087 258788.0684 217033.7772 199791.3678 242027.4617 242317.4131 267735.2073 0.835772751 0.847440624 0.952661735 0.966582135 0.810628454 0.746227475 0.903980706 0.905063684 1 18.03044734 1.264701576 1.888491372 1.038617004 0.866153797 0.301635833 0.064637644 1.146281549 4.115122049 0.349251274 0.019282386 18.39507556 -1.264701576 -0.172463207 SPGGPGSHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPGGPGSHVR 10 0 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 0 ; 131.82 0.00024004 91610000 137836 125318 66156 94020 116871 133945 114341 126978 144483 FALSE TRUE 119620.6234 124494.7778 98149.26288 115368.678 114545.4958 139097.9508 103252.2274 99824.74284 127402.3843 0.938919817 0.97717777 0.770387959 0.905545674 0.899084396 1.091800217 0.810441876 0.783539047 1 16.95903275 1.921026935 0.010237158 7.29E-08 1.77642491 0 0.102054895 38469.14852 173.3023678 15420.28587 14655.81655 83.37328922 -1.921026935 1.776424838 SPGLVPPS(ph)PEFAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPGLVPPSPEFAPR 14 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 SPGLVPPS(1)PEFAPR 103.77 0.0011504 154770000 331740 269610 173200 222810 277040 231490 231830 299760 308360 TRUE FALSE 287899.7185 267838.9142 256960.0993 273402.4159 271527.446 240395.5701 209347.1623 235658.6567 271906.0321 1.058820638 0.985042193 0.945032728 1.005503312 0.998607658 0.884112678 0.769924671 0.866691537 1 18.05274863 2.705092545 5.196758381 0.866535105 0.995552076 0.472828821 0.061513709 0.166178676 12.31681194 0.021621021 0.019477294 507.0987559 -2.705092545 0.129016971 SPGS(ph)PPGPELPIETALDDR ddPTM_MDA-MB-175_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;S(0.039)PGS(0.961)PPGPELPIETALDDR 170.59 1.25E-11 88711000 31584.6 26233.1 21219.1 26839.8 34575.7 20988.6 27957.5 40178.6 45274.3 TRUE FALSE 27410.61508 26060.77304 31480.72773 32934.18681 33887.71122 21796.04502 25246.18595 31586.71906 39922.02383 0.686603846 0.652791881 0.788555407 0.824962856 0.848847527 0.545965433 0.632387428 0.791210365 1 15.28489724 1.294746304 3.268134201 1.027553861 0.715453149 0.493473293 0.091867446 0.272646559 4.07731865 0.199661329 0.025368228 19.71270869 -1.294746304 -0.312100712 SPGS(ph)PVGEGTGSPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPGSPVGEGTGSPPK 15 0 P35611;P35611-3;E7EV99;E7ENY0;P35611-2;P35611-6;P35611-4;H0Y9H2;P35611-5;A0A0A0MSR2 P35611 ADD1 Alpha-adducin 1 SPGS(1)PVGEGTGSPPK;SPGS(1)PVGEGTGSPPK 296.36 4.66E-44 358380000 675840 397110 315670 379830 412690 323920 478010 585710 601430 TRUE FALSE 586526.0316 394501.3583 468329.0679 466076.2068 404478.2764 336381.412 431652.6638 460460.4745 530329.6306 1.105965041 0.743879534 0.883090517 0.878842478 0.762692207 0.634287418 0.813932767 0.868253343 1 19.01652983 4.748555319 24.55836797 0.822043123 1.105965241 0.453429775 0.097585891 1074.424594 2639941.664 0.024698229 0.316270365 56047.38038 -4.748555319 0.283922118 SPGS(ph)TPTT(ph)PTSSQAPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658;P35658-5;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 2 SPGS(0.943)T(0.057)PT(0.003)T(0.997)PTSSQAPQK;SPGS(1)TPT(0.001)T(0.987)PT(0.011)SSQAPQK;SPGS(1)TPTT(0.995)PT(0.005)SSQAPQK;SPGS(0.996)T(0.004)PT(0.001)T(0.973)PT(0.024)S(0.001)SQAPQK;SPGS(0.951)T(0.049)PT(0.039)T(0.96)PTSSQAPQK 355.72 3.77E-87 1739660000 2173340 2053430 1636610 2179430 2663210 2050120 2684660 3375400 3485660 TRUE FALSE 1886127.612 2039940.883 2428080.07 2674302.892 2610217.331 2128989.443 2424302.086 2653596.977 3073589.246 0.613656368 0.663699903 0.789981964 0.870091179 0.849240781 0.692672076 0.788752788 0.863354458 1 21.55149295 5.694097094 0.541073983 0.854669828 1.41E-24 0.533406563 0.077507992 9.78215578 1.029062255 0.048446329 6.57965653 494421.2115 -5.694097094 -0.854669828 SPGS(ph)TPTTPTSSQAPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658;P35658-5;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 S(0.001)PGS(0.995)T(0.004)PTTPTSSQAPQK;S(0.006)PGS(0.99)T(0.004)PTTPTSSQAPQK 363.28 5.49E-89 554010000 793140 542770 358880 402710 442210 354660 451610 523340 616840 TRUE FALSE 688324.5394 539204.5081 532435.5684 494151.4605 433410.8862 368303.9997 407812.9317 411427.8136 543917.8779 1.265493501 0.991334409 0.978889627 0.908503803 0.796831477 0.677131631 0.749769309 0.756415316 1 19.05302932 5.077834878 0.691144078 0.783030363 1.762267996 0.717932408 0.090556938 2.487233704 0.660699097 0.040032051 2.116268954 119628.5609 -5.077834878 0.979237633 SPGSTPTT(ph)PTSSQAPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658;P35658-5;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 SPGS(0.001)T(0.033)PT(0.221)T(0.72)PT(0.008)S(0.014)S(0.003)QAPQK 97.904 0.0060681 0 27407 22844 16397 26199 30474 24932 33728 34669 35293 TRUE FALSE 23785.09551 22693.93626 24326.64404 32147.88338 29867.62702 25891.15017 30457.06375 27255.30414 31120.70175 0.764285321 0.729223153 0.781686873 1.033006378 0.959735011 0.831959073 0.978675353 0.875793366 1 14.92558697 3.881838422 6.031157308 0.936523073 0.74895031 0.695371008 0.058725639 0.128177243 5.823768532 0.01524551 0.026872055 7617.955341 -3.881838422 -0.187572762 SPGTGPSPFSSSLGHLNHLGGS(ph)LDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPGTGPSPFSSSLGHLNHLGGSLDR 25 0 O15049 O15049 N4BP3 NEDD4-binding protein 3 1 SPGTGPSPFSS(0.001)S(0.003)LGHLNHLGGS(0.995)LDR;SPGTGPSPFS(0.001)S(0.001)S(0.01)LGHLNHLGGS(0.989)LDR 99.319 0.011703 304795000 77510 72190 19387.7 45256 82264 74501 65015 84565 55098 TRUE FALSE 67266.85711 71715.77914 28763.65657 55532.06649 80627.10735 77367.10168 58709.85531 66481.43284 48584.37721 1.384536779 1.47610782 0.592035099 1.143002539 1.659527444 1.592427569 1.208410166 1.368370589 1 15.56820485 3.426497985 24.99971179 1.36885061 1.130763385 0.118222345 0.292529903 221.9386201 109600.8539 0.08655803 0.111745962 2669.918379 -3.426497985 -0.238087225 SPGVVISDDEPGYDLDLFCIPNHYAEDLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPGVVISDDEPGYDLDLFCIPNHYAEDLER 30 0 P00492 P00492 HPRT1 Hypoxanthine-guanine phosphoribosyltransferase 0 ; 222.71 1.07E-34 581730000 265544 272760 156534 171761 244822 244787 233690 262005 235938 FALSE TRUE 230451.6876 270968.2216 232234.366 210761.9603 239950.5212 254204.1143 211026.7798 205977.2697 208045.6784 1.107697547 1.302445807 1.116266234 1.01305618 1.153354989 1.221866833 1.014329071 0.990057911 1 17.6665408 2.147833073 7.069877672 0.997327029 1.151069955 0.476268308 0.074724013 0.198355042 13.10941242 0.03186061 0.021427722 140.5507193 -2.147833073 0.153742926 SPIIFIGTGEHIDDFEPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPIIFIGTGEHIDDFEPFK 19 0 G3V4F7;P61011-2;P61011 G3V4F7 SRP54 Signal recognition particle 54 kDa protein 0 ; 249.69 4.33E-25 845260000 1718950 1362960 1017920 1264410 1324730 1148820 1577090 1998400 1737840 FALSE TRUE 1491786.402 1354006.626 1510189.517 1551513.616 1298370.465 1193015.849 1424144.055 1571057.712 1532394.535 0.97350021 0.883588785 0.985509594 1.012476605 0.847282103 0.778530477 0.92935861 1.025230563 1 20.54735636 1.795838955 5.484194911 1.012088607 0.912347395 0.256085939 0.068765261 0.279951249 16.00143081 0.040646514 0.019637643 62.4940909 -1.795838955 -0.099741213 SPITS(ph)SPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPITSSPPK 9 0 Q52LA3;G3V5T8 Q52LA3;G3V5T8 LIN52 Protein lin-52 homolog 1 SPIT(0.054)S(0.57)S(0.376)PPK 61.353 0.09412 181000000 327260 264660 243900 301420 295250 218330 326530 351680 537350 TRUE FALSE 284011.7618 262921.431 361850.8558 369862.0179 289375.1026 226729.2964 294863.1709 276475.9688 473825.0952 0.59940211 0.554891317 0.763680226 0.780587651 0.610721352 0.478508417 0.622303829 0.583497944 1 18.85399508 1.234771352 24.99905301 1.000000537 0.624308429 0.634226864 0.089689926 79.13089393 521975.7862 0.171577871 0.023505556 17.1700418 -1.234771352 -0.375692108 SPITSS(ph)PPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPITSSPPK 9 0 Q52LA3;G3V5T8 Q52LA3;G3V5T8 LIN52 Protein lin-52 homolog 1 SPIT(0.024)S(0.126)S(0.849)PPK;SPIT(0.055)S(0.406)S(0.539)PPK 72.2 0.049744 358500000 993900 797670 727010 843330 926240 705160 897920 1094770 1541880 TRUE FALSE 862553.5968 792430.0532 1078594.468 1034820.966 907809.6362 732287.9615 810839.8566 860661.955 1359600.703 0.634416851 0.582840279 0.793317086 0.761121235 0.667703124 0.538605165 0.596380875 0.63302553 1 20.37475158 1.236840991 24.98724376 1.000000438 0.650310198 0.669272703 0.077116446 29.60747269 430083.1113 0.127383467 0.020467076 17.25206125 -1.236840991 -0.34969024 SPLAQMEEERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SPLAQMEEERR 11 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2 E7EPK1 7-Sep Septin-7 0 ;;;;; 163.51 3.83E-05 7434040000 2314370 2157160 1222784 1630190 2180570 2246620 2102240 2386010 1724530 FALSE TRUE 2008520.141 2142989.474 1814126.432 2000349.555 2137180.923 2333048.925 1898365.088 1875780.329 1520658.028 1.320823028 1.409251413 1.192987772 1.315449969 1.405431651 1.534236418 1.248383958 1.233531994 1 20.53626432 1.264834265 1.593292223 0.877984249 1.353884826 0.596566028 0.091542957 0.753274298 1.821336225 0.562783192 0.027143047 18.40069661 -1.264834265 0.475900576 (ac)SAADEVDGLGVARPHYGSVLDNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SAADEVDGLGVARPHYGSVLDNER 24 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;;;;; 187.07 5.89E-118 8599070000 93002 28549.8 14862 13700 36299.2 17916.2 20636.4 23533 15283 FALSE TRUE 80711.55006 28362.25448 22049.31291 16810.79439 35576.91694 18605.44781 18635.0851 18500.65108 13476.26115 5.989164885 2.104608553 1.636159515 1.247437565 2.639969391 1.380609028 1.38280825 1.372832633 1 13.71813267 4.756027296 2.995149335 1.532418047 6.825166096 0.912230167 0.431897076 0.112542959 1.436781449 0.109054563 1.45532028 57020.01088 -4.756027296 5.292748049 up SPLELGEKLS(ph)PLPGGPGAGDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPLELGEKLSPLPGGPGAGDPR 22 1 Q15742;Q15742-2;Q15742-3 Q15742 NAB2 NGFI-A-binding protein 2 1 S(0.055)PLELGEKLS(0.945)PLPGGPGAGDPR;SPLELGEKLS(1)PLPGGPGAGDPR 122.04 1.60E-05 269850000 705990 641660 432780 529980 655540 618910 801650 962800 777040 TRUE FALSE 612691.6327 637444.8932 642073.8556 650320.0592 642496.0365 642719.8682 723906.1064 756912.7125 685179.2164 0.894206389 0.930333084 0.937088925 0.94912403 0.937705087 0.938031763 1.056520818 1.104693041 1 19.38612187 2.234324067 5.321159956 1.065757309 0.931829161 0.796118738 0.029105539 0.065045383 5.516412332 0.011484643 0.00812924 171.5236725 -2.234324067 -0.133928149 SPLLAGGS(ph)PPQPVVPAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPLLAGGSPPQPVVPAHK 18 0 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4;C9JIY9 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 SPLLAGGS(1)PPQPVVPAHK;SPLLAGGS(1)PPQPVVPAHK 148.52 4.43E-08 386960000 695620 712180 451270 607660 769650 668500 748410 960380 832270 TRUE FALSE 603692.0545 707501.6427 669505.6814 745638.4905 754335.4708 694217.6276 675829.3134 755010.2107 733879.9887 0.822603237 0.964056322 0.912282242 1.016022377 1.027873062 0.945955249 0.920898953 1.028792476 1 19.48518463 5.736019648 0.973492871 0.986443193 2.57E-09 0.591899858 0.04094637 8.578975509 1.49343856 0.013204153 14.01049608 544527.2873 -5.736019648 -0.986443191 LCPSCPASS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 LCPSCPASSPK 11 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 LCPSCPAS(0.001)S(0.999)PK;LCPSCPAS(0.006)S(0.994)PK 192.68 1.35E-06 308410000 440650 478460 449430 535280 792180 717690 961900 1049840 1004680 TRUE FALSE 382416.986 475316.9648 666775.8513 656823.5052 776417.1679 745299.9987 868615.0861 825339.8859 885907.8749 0.431666765 0.536530917 0.75264694 0.741412876 0.876408473 0.841283862 0.98048015 0.93163173 1 19.75679716 4.767330489 0.447855049 0.98798237 2.39E-19 0.94760988 0.042267608 1.139874105 0.192576567 0.04014689 0.613929905 58523.52663 -4.767330489 -0.98798237 down SPMFPALGEASS(ph)DDDLFQSAKPKPAK ddPTM_MDA-MB-175_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(0.205)S(0.795)DDDLFQSAKPKPAK 218.16 1.85E-34 405560000 443120 279200 239060 267670 256300 164220 379640 490070 311130 TRUE FALSE 384560.5693 277365.9168 354670.2156 328448.5646 251200.1314 170537.6497 342822.5712 385272.3442 274348.5658 1.401722543 1.010998239 1.29277226 1.197194392 0.915624001 0.621609408 1.249587619 1.404316961 1 18.06565051 4.75170932 23.008596 1.109021334 1.401723131 0.159221088 0.222352173 1602.288702 2803649.803 0.059202035 0.984881759 56455.89806 -4.75170932 0.292701798 ACSMPQELPQS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 ACSMPQELPQSPR 13 0 Q8N5J2;Q8N5J2-3 Q8N5J2 FAM63A Protein FAM63A 1 ACSMPQELPQS(1)PR;ACSMPQELPQS(1)PR;ACSMPQELPQS(1)PR;ACSMPQELPQS(1)PR;ACSMPQELPQS(1)PR 166.64 3.49E-05 968014000 724929 1002078 849915 1069000 1399410 1501206 1596650 1647640 1614170 TRUE FALSE 629127.7959 995495.2836 1260936.737 1311732.789 1371564.479 1558958.366 1441807.129 1295305.008 1423344.661 0.442006643 0.69940564 0.88589698 0.921584788 0.96362077 1.095278191 1.012971185 0.910043114 1 20.44085362 4.770429366 1.009824673 0.990214486 0.120786591 0.935039234 0.047494843 0.510373526 0.403973328 0.017001184 0.489666783 58942.6104 -4.770429366 -0.869427895 down SPPHCELMAGHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPPHCELMAGHLR 13 0 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 ;; 143.31 2.36E-05 293063000 105455 73868 52769 68922 75930 82327 79103 99075 67950 FALSE TRUE 91518.85456 73382.75624 78288.2649 84571.79351 74419.14155 85494.17296 71431.60324 77888.58225 59917.02841 1.527426459 1.224739581 1.306611275 1.411481773 1.242036588 1.426876052 1.192175332 1.299940673 1 15.87067845 0.56866929 1.15592649 2.62E-13 1.338575766 0.51502342 0.101296108 5.28919996 1.863272081 12.64523224 0.02842824 3.703985602 -0.56866929 1.338575766 SPPLLES(ph)PDATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPPLLESPDATR 12 0 Q15036-2;Q15036 Q15036-2 SNX17 Sorting nexin-17 1 SPPLLES(1)PDATR;S(0.041)PPLLES(0.959)PDATR 150.29 6.38E-05 736520000 182937 199586 145748 165463 218340 250940 211490 236190 231870 TRUE FALSE 158761.4119 198274.9064 216232.2203 203033.9031 213995.4612 260593.8242 190979.7324 185682.6065 204458.5927 0.776496648 0.969755801 1.057584411 0.993031892 1.046644498 1.274555501 0.934075354 0.908167292 1 17.64144917 4.711562444 3.007432628 1.022359176 0.744120528 0.39182963 0.098779197 0.409690828 5.67311254 0.026877737 0.264508103 51470.98082 -4.711562444 -0.278238648 SPPMELQPPVS(ph)PQQSECNPVGALQELVVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPPMELQPPVSPQQSECNPVGALQELVVQK 30 0 H3BV98;F8VSA1;Q15633-2;Q15633;F8VW32;F8VZ57 H3BV98 TARBP2 RISC-loading complex subunit TARBP2 1 SPPMELQPPVS(0.997)PQQS(0.002)ECNPVGALQELVVQK 100.68 0.00030063 24163000 77805 75109 48024 61057 75195 75984 81516 105940 82266 TRUE FALSE 67522.87212 74615.60403 71248.56703 74920.92505 73698.76662 78907.15365 73610.59087 83285.55543 72540.6072 0.930828604 1.028604625 0.982188732 1.032813591 1.01596567 1.087765277 1.014750134 1.148123219 1 16.1465012 8 0.251378162 1.092138934 0.162592335 0.379061857 0.04599046 78.87431179 1.253908213 0.141218984 30.20479034 100000000 -8 -0.929546599 SPPSQKS(ph)PHDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPPSQKSPHDSK 12 1 O14647 O14647 CHD2 Chromodomain-helicase-DNA-binding protein 2 1 S(0.035)PPS(0.198)QKS(0.767)PHDSK 69.594 0.029927 15659000 142940 106680 53409 71464 77931 62520 137510 146370 69889 TRUE FALSE 124050.1168 105979.2121 79237.77104 87690.99346 76380.32557 64925.18486 124174.3014 115069.9146 61626.80204 2.012924778 1.719693519 1.285768017 1.422935972 1.239401089 1.053521888 2.014939884 1.867205676 1 15.91127031 2.227769449 24.99953917 1.693493222 1.448660611 0.035602515 0.370196652 579.1857677 1341768.561 0.154658217 0.105442531 168.9543776 -2.227769449 -0.244832611 SPPVLGSAAAS(ph)PVHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPPVLGSAAASPVHLK 16 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 SPPVLGSAAAS(1)PVHLK 143.04 9.34E-07 169680000 173740 208180 67657 89169 215440 231050 153450 190410 110210 TRUE FALSE 150779.8188 206812.4519 100376.1515 109416.1843 211153.1655 239938.643 138568.4426 149692.3033 97181.09935 1.551534401 2.128113936 1.0328773 1.125899841 2.172780169 2.468984655 1.425878525 1.540343794 1 16.56838813 3.255566329 24.99994375 1.71413136 1.476876499 0.065549748 0.489153704 918.2706967 1349933.347 0.150595087 0.193918384 1801.21821 -3.255566329 -0.237254861 SPPYT(ph)AFLGNLPYDVTEESIK ddPTM_MDA-MB-175_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(0.328)PPY(0.267)T(0.405)AFLGNLPYDVTEESIK 141.86 5.59E-07 124350000 58463 46831 46416 61560 47470 37209 59392 63390 136280 TRUE FALSE 50736.96642 46523.36408 68862.93285 75538.13889 46525.43987 38640.45431 53632.17298 49834.5418 120169.1337 0.422212967 0.387149035 0.57305009 0.628598514 0.387166309 0.321550577 0.446305731 0.414703346 1 16.87470685 1.236472261 24.99995249 1.000000705 0.447851156 0.786978478 0.090321729 27.01156035 323276.1756 0.151137111 0.023614315 17.2374199 -1.236472261 -0.55214955 SPQEEDFRCPS(ph)DEDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPQEEDFRCPSDEDFR 16 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 S(0.001)PQEEDFRCPS(0.999)DEDFR;SPQEEDFRCPS(1)DEDFR;SPQEEDFRCPS(1)DEDFR;SPQEEDFRCPS(1)DEDFR 143.95 8.26E-07 1592770000 833870 937520 558730 552522 791530 798600 774620 878300 441596 TRUE FALSE 723671.9667 931361.3694 828933.6968 677980.5649 775780.1016 829322.6588 699497.4716 690482.3799 389391.0239 1.858471105 2.39184088 2.128795082 1.74113044 1.992290664 2.12979398 1.79638828 1.773236509 1 18.5708601 0.988570822 1.308257307 7.57E-17 2.036549405 0.74801431 0.184069611 1.254059744 1.180702138 4.043738284 0.055223964 9.740266115 -0.988570822 2.036549405 SPQPVPS(ph)PRPQSQPPHSSPSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SPQPVPSPRPQSQPPHSSPSPR 22 1 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 SPQPVPS(0.931)PRPQS(0.052)QPPHSS(0.016)PSPR;S(0.125)PQPVPS(0.867)PRPQS(0.008)QPPHSSPSPR;SPQPVPS(0.998)PRPQS(0.002)QPPHSSPSPR;SPQPVPS(0.476)PRPQS(0.006)QPPHS(0.28)S(0.168)PS(0.07)PR;SPQPVPS(0.587)PRPQS(0.021)QPPHS(0.061)S(0.283)PS(0.049)PR 204.89 6.73E-23 1294753000 511180 614835 196750 314753 799869 829443 626050 644667 401917 TRUE FALSE 443626.2678 610796.1084 291898.9581 386222.4793 783953.1718 861352.2089 565335.7674 506809.9789 354402.8301 1.251757125 1.723451554 0.823636081 1.089783846 2.212039818 2.430432648 1.595178479 1.430039311 1 18.4350306 3.269953744 24.99976403 1.720068976 1.229497927 0.244358315 0.446417411 336.4675268 267942.094 0.139997098 0.180718057 1861.888818 -3.269953744 -0.490571049 SPQPVPSPRPQSQPPHSS(ph)PSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPQPVPSPRPQSQPPHSSPSPR 22 1 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 SPQPVPS(0.022)PRPQSQPPHS(0.156)S(0.731)PS(0.091)PR 97.063 0.00082927 221130000 20789 23447 5805.2 11140 30247 30099 23846 27873 14267 TRUE FALSE 18041.68098 23292.97511 8612.614137 13669.50726 29645.14388 31256.92801 21533.41859 21912.57586 12580.37151 1.434113528 1.851533167 0.684607297 1.086574212 2.356460129 2.48457909 1.71166794 1.741806737 1 13.61888691 3.258742113 24.99169366 1.864507111 1.264758837 0.267322564 0.489172364 354.6872344 439223.0657 0.148493964 0.191461187 1814.437919 -3.258742113 -0.599748273 SPQT(ph)PELVEALAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPQTPELVEALAFR 14 0 Q9NZB2;Q9NZB2-4;Q9NZB2-6;A0A0C4DG79 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 1 S(0.043)PQT(0.957)PELVEALAFR;SPQT(1)PELVEALAFR 256.28 2.93E-23 153015000 127609 125617 95582 106146 135506 138629 131361 144999 158746 TRUE FALSE 110745.1473 124791.8137 141805.7749 130248.0716 132809.6957 143962.1473 118621.6304 113992.0922 139979.2287 0.791154147 0.891502366 1.013048694 0.930481421 0.948781451 1.02845364 0.847423089 0.814350052 1 17.09485324 4.669335043 3.8207365 0.928368989 0.785861534 0.308519806 0.068782386 0.325027004 8.226293974 0.018704506 0.110689724 46701.95303 -4.669335043 -0.142507456 SPQYCQVIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPQYCQVIHR 10 0 Q13228;Q13228-4;A6PVX1;F2Z2W8;F8WCR4;C9JVL0 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 175.86 2.67E-06 1398260000 654880 697500 327140 448150 684530 716470 611920 714280 637050 FALSE TRUE 568335.9487 692918.0766 485345.9982 549909.307 670909.1923 744033.0645 552576.0926 561536.7805 561738.6747 1.011744383 1.233523892 0.864006735 0.978941511 1.194343958 1.32451814 0.983688889 0.999640591 1 19.09953961 SPRPGSSAPEHS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPRPGSSAPEHSPR 14 1 O75385 O75385 ULK1 Serine/threonine-protein kinase ULK1 1 SPRPGSS(0.001)APEHS(0.999)PR 54.964 0.08265 50682000 64807 54889 40583 47192 66381 85695 68473 67254 69115 TRUE FALSE 56242.59075 54528.43054 60209.07454 57907.66488 65060.14797 88991.7421 61832.499 52872.25547 60944.30344 0.922852302 0.894725634 0.987936052 0.950173546 1.067534524 1.460214279 1.01457389 0.867550411 1 15.89520376 3.25319003 6.22830172 1.069286004 0.93838953 0.178528806 0.151278939 0.360050599 51.33689913 0.050357131 0.062533887 1791.389523 -3.25319003 -0.130896474 SPRPQDLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPRPQDLIR 9 1 Q9UHB9;Q9UHB9-4;Q9UHB9-2;Q9UHB9-3 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 84.658 0.013993 181980000 141550 140930 76230 83605 140040 141050 158700 160780 105580 FALSE TRUE 122843.8089 140004.2216 113095.083 102588.7931 137253.478 146476.2848 143309.2984 126398.4482 93098.45268 1.319504302 1.503829736 1.214790147 1.101938755 1.474283128 1.57334822 1.539330615 1.357685811 1 16.50646957 SPS(ph)AGDVHILTGFAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSAGDVHILTGFAK 15 0 A0A3B3ITL0;A0A3B3IRJ9;Q9Y2H2-4;Q9Y2H2 A0A3B3ITL0 INPP5F Phosphatidylinositide phosphatase SAC2 1 S(0.096)PS(0.904)AGDVHILTGFAK 200.58 4.41E-09 296920000 542790 536190 394650 513900 587260 480460 581110 721020 977870 TRUE FALSE 471058.9262 532667.7326 585504.06 630588.8495 575574.675 498943.6071 524754.0416 566835.484 862267.3226 0.546302653 0.617752429 0.679028469 0.731314794 0.667513032 0.578641442 0.608574659 0.657377903 1 19.71777568 1.238227623 5.172653617 1.021273956 0.636847074 0.829036828 0.052064913 0.069866491 5.09709684 0.096498102 0.01389895 17.30723229 -1.238227623 -0.384426881 SPS(ph)DSSTASTPVAEQIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSDSSTASTPVAEQIER 18 0 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 S(0.175)PS(0.824)DS(0.002)STASTPVAEQIER 158.17 4.85E-11 155940000 35208 23420 9349.9 21782 18404 18603 18592 25875 33824 TRUE FALSE 30555.17359 23266.15248 13871.54291 26727.93602 18037.79641 19318.66945 16788.9507 20341.83261 29825.36525 1.024469385 0.780079381 0.465092139 0.896147819 0.604780403 0.647726165 0.562908469 0.682031299 1 14.86425219 4.663916572 3.815850953 0.685320826 1.036196146 0.304320252 0.155197846 0.256573523 6.376072705 0.036379867 0.212035512 46122.89635 -4.663916572 0.350875321 SPS(ph)FASEWDEIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SPSFASEWDEIEK 13 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 S(0.006)PS(0.994)FASEWDEIEK;S(0.093)PS(0.907)FASEWDEIEK;S(0.002)PS(0.998)FASEWDEIEK;S(0.061)PS(0.939)FASEWDEIEK;S(0.119)PS(0.881)FASEWDEIEK;SPS(1)FASEWDEIEK;S(0.001)PS(0.999)FASEWDEIEK;S(0.025)PS(0.975)FASEWDEIEK 420.04 5.76E-146 2379434000 3512190 2768741 2073050 2248574 2600066 2345711 3241087 3631890 3367230 TRUE FALSE 3048045.193 2750552.958 3075583.914 2759147.094 2548329.774 2435952.02 2926766.882 2855238.587 2969159.905 1.026568218 0.926374141 1.035843138 0.929268609 0.858266262 0.820417929 0.985722216 0.961631801 1 21.50162336 3.63218948 9.155874833 0.925936524 0.98918029 0.225297905 0.061074439 0.634644056 50.04684707 0.018019685 0.026744374 4287.355342 -3.63218948 0.063243766 SPS(ph)FGAGEGLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPSFGAGEGLLR 12 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 S(0.369)PS(0.631)FGAGEGLLR;S(0.004)PS(0.996)FGAGEGLLR;S(0.016)PS(0.984)FGAGEGLLR;S(0.133)PS(0.867)FGAGEGLLR 142.1 6.21E-05 661030000 722270 558532 312786 417415 588336 615404 505265 581220 517157 TRUE FALSE 626820.1895 554862.9665 464050.3558 512195.4555 576629.2647 639078.9901 456264.4781 456930.6261 456019.2886 1.374547536 1.216753283 1.017611245 1.123188138 1.264484374 1.401429733 1.000537673 1.001998463 1 18.79873532 2.195640227 24.40045741 1.001072175 1.218912707 0.493744007 0.110203793 102.6189554 58338.45184 0.047992717 0.032357014 156.9062441 -2.195640227 0.217840532 SPS(ph)FNMQLISQV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSFNMQLISQV 12 0 Q8IXS8 Q8IXS8 FAM126B Protein FAM126B 1 S(0.121)PS(0.879)FNMQLISQV 93.258 0.0076299 40444000 46159 50579 41458 43741 52590 78851 53778 54361 58177 TRUE FALSE 40058.9712 50246.74322 61507.22747 53673.06259 51543.56189 81884.44899 48562.61784 42736.32319 51299.38134 0.780886049 0.979480491 1.198985755 1.046271148 1.004759912 1.596207339 0.94665114 0.833076775 1 15.64665381 2.021625787 24.99989937 0.900189467 1.108005276 0.132019123 0.210576266 405.7824947 469091.8597 0.086524242 0.058329622 105.1055834 -2.021625787 0.207815809 SPS(ph)HTRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSHTRPR 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 S(0.267)PS(0.73)HT(0.004)RPR 96.034 0.005588 983600000 227870 154860 124560 189780 93525 167300 163040 185540 370030 TRUE FALSE 197756.4022 153842.7145 184797.6326 232872.4496 91664.03548 173736.1393 147228.4059 145863.7149 326285.4749 0.606083989 0.471497282 0.566367941 0.713707681 0.280932014 0.532466667 0.451225743 0.447043237 1 18.31577524 1.234572021 24.99943479 1.000000717 0.50376088 0.648978667 0.113510581 72.87733623 456710.5498 0.1993287 0.026875212 17.16216295 -1.234572021 -0.496239837 SPS(ph)LGSDLTFATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSLGSDLTFATR 13 0 Q13425 Q13425 SNTB2 Beta-2-syntrophin 1 S(0.002)PS(0.968)LGS(0.029)DLTFATR 63.727 0.070139 144420000 136210 137280 113410 168200 197560 213500 167590 208890 213710 TRUE FALSE 118209.5034 136378.1986 168255.4553 206392.3808 193628.9425 221713.4832 151337.1476 164220.4991 188445.4473 0.627287659 0.723701212 0.892860283 1.095236758 1.027506609 1.176539345 0.803082005 0.871448483 1 17.52378742 4.239559133 2.675216673 0.980344241 0.645885449 0.609308102 0.105217056 0.209034079 2.958426435 0.030900589 0.097101403 17360.37624 -4.239559133 -0.334458791 SPS(ph)LNLLQNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSLNLLQNK 10 0 O43353-2;O43353 O43353-2 RIPK2 Receptor-interacting serine/threonine-protein kinase 2 1 S(0.021)PS(0.979)LNLLQNK 77.22 0.024318 0 307170 305050 155260 191440 300290 226970 348190 364010 197000 TRUE FALSE 266576.7062 303046.1065 230344.2553 234909.378 294314.8165 235701.6828 314422.5874 286169.2942 173710.8844 1.534599902 1.744542994 1.326020854 1.352300858 1.69427965 1.356861912 1.810033887 1.64738839 1 17.40632863 1.233407813 24.99518339 0.999999123 1.564319547 0.513374781 0.170719485 137.0943793 664939.9742 0.342540603 0.041712868 17.11621815 -1.233407813 0.564320424 SPS(ph)MPENLNRPR ddPTM_MDA-MB-175_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(0.007)PS(0.993)MPENLNRPR;S(0.011)PS(0.989)MPENLNRPR 124.16 0.00019857 1146330000 881670 924890 473010 612820 815610 802110 719330 842860 905300 TRUE FALSE 765155.0756 918814.3367 701759.2181 751970.1474 799380.9567 832967.6907 649569.4873 662620.9481 798276.4653 0.958508874 1.150997651 0.879092957 0.941992129 1.001383595 1.043457658 0.813714942 0.830064491 1 19.60652895 2.240208646 24.99960302 0.867779746 0.995443863 0.280202986 0.085715335 50.21373899 761730.8673 0.032933353 0.024151365 173.8635913 -2.240208646 0.127664117 SPS(ph)MPSLNQTWPELNQSSEDTAIVHPVPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSMPSLNQTWPELNQSSEDTAIVHPVPIR 30 0 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2 E9PMG1 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.155)PS(0.842)MPS(0.002)LNQTWPELNQSSEDTAIVHPVPIR 192.63 8.68E-19 171840000 33128 34150 20067 31287 27805 32752 32855 34973 49611 TRUE FALSE 28750.05086 33925.6664 29771.46832 38391.19154 27251.7349 34011.99063 29668.72716 27494.29611 43746.0441 0.657203445 0.775513926 0.68055224 0.877592302 0.622953126 0.77748723 0.678203659 0.628497883 1 15.41686494 1.228143471 24.94232952 1.000000616 0.712130082 0.568870995 0.078725131 315.4838509 755326.5571 0.25366995 0.018374356 16.90999469 -1.228143471 -0.287870534 SPS(ph)PAHLPDDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SPSPAHLPDDPK 12 0 Q92615;H0Y4V9;A0A087X183;H0Y641 Q92615 LARP4B La-related protein 4B 1 S(0.426)PS(0.574)PAHLPDDPK;S(0.148)PS(0.852)PAHLPDDPK;S(0.072)PS(0.928)PAHLPDDPK;S(0.244)PS(0.756)PAHLPDDPK;S(0.041)PS(0.959)PAHLPDDPK;S(0.205)PS(0.795)PAHLPDDPK;S(0.152)PS(0.848)PAHLPDDPK;S(0.153)PS(0.847)PAHLPDDPK 177.64 2.41E-05 14349260000 20005680 17333440 13274180 14050270 16682460 14940390 19817520 21187750 19833260 TRUE FALSE 17361878.7 17219575.49 19693617.85 17240598.55 16350511.68 15515156.47 17895619.96 16656914.55 17488594.6 0.992754369 0.984617454 1.126083502 0.985819555 0.934924278 0.887158564 1.023273761 0.952444432 1 24.05991102 3.487919951 24.82049856 0.959878503 1.033907208 0.303015686 0.051869887 585.7981146 1346439.974 0.014500111 0.020029358 3075.529885 -3.487919951 0.074028705 SPS(ph)PAHLPDDPKVAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSPAHLPDDPKVAEK 16 1 Q92615;H0Y4V9;A0A087X183;H0Y641 Q92615 LARP4B La-related protein 4B 1 S(0.106)PS(0.894)PAHLPDDPKVAEK 140.95 9.97E-07 248260000 770060 578050 157510 168900 441190 344660 835330 821370 21743 TRUE FALSE 668294.6199 574252.7515 233682.3628 207251.3265 432411.1822 357919.2932 754319.8252 645726.4174 19172.56731 34.85681438 29.95179217 12.18837097 10.80978479 22.55364006 18.66830286 39.34370463 33.67970533 1 14.22675591 7.999999044 0.017210084 9.999996457 40.04680758 0.00625818 12.14926617 263114.8193 450.6285792 322518.0017 479227.8668 99999779.9 -7.999999044 30.04681112 SPS(ph)PAVPLR ddPTM_MDA-MB-175_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(0.435)PS(0.565)PAVPLR 112.75 0.0020059 474590000 532030 471780 274460 341320 454560 527250 405760 511340 422790 TRUE FALSE 461720.8875 468680.8461 407189.774 418821.9227 445515.1453 547533.6487 366409.4577 401993.9203 372808.2478 1.238494293 1.257163297 1.092223083 1.123424509 1.195024917 1.468673646 0.982836243 1.078286016 1 18.50807425 SPS(ph)PFTHTHLAQGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSPFTHTHLAQGYR 15 0 P38398-7;P38398;P38398-4;P38398-8;Q5YLB2 P38398-7 BRCA1 Breast cancer type 1 susceptibility protein 1 S(0.424)PS(0.548)PFT(0.029)HTHLAQGYR 125.96 5.62E-05 124250000 53836 58729 36019 43414 58450 49243 47253 61155 54002 TRUE FALSE 46721.4362 58343.20533 53437.90888 53271.81224 57286.95936 51137.41007 42670.41133 48077.47916 47617.94508 0.981172878 1.22523568 1.12222207 1.118733959 1.203054001 1.073910476 0.896099386 1.009650439 1 15.53921774 2.446783647 7.200251912 0.97491438 1.134814268 0.52003533 0.07064872 0.135633393 23.68961316 0.024384031 0.019023821 279.7587297 -2.446783647 0.159899887 SPS(ph)PGLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPSPGLFR 8 0 E7ESG2;Q9HAW4-2;Q9HAW4-3;Q9HAW4 E7ESG2 CLSPN Claspin 1 S(0.489)PS(0.511)PGLFR;S(0.005)PS(0.995)PGLFR;S(0.008)PS(0.992)PGLFR 117.31 0.0022063 219603000 567470 486460 296212 377967 494550 518690 459017 545800 482480 TRUE FALSE 492477.4017 483264.4122 439461.114 463790.1842 484709.4226 538644.3399 414501.602 429084.9174 425441.764 1.15756713 1.135912017 1.032952453 1.090137884 1.139308511 1.266082424 0.974285171 1.008563225 1 18.69860214 2.194877522 24.99999954 0.996424457 1.13019087 0.565745729 0.0587289 108.419443 62048.08125 0.024990566 0.016848749 156.6309285 -2.194877522 0.133766414 SPS(ph)PGPNHTSNSSNASNATVVPQNSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSPGPNHTSNSSNASNATVVPQNSSAR 28 0 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 S(0.034)PS(0.966)PGPNHTSNSSNASNATVVPQNSSAR 241.09 1.73E-45 286650000 41956 50940 16957 22673 63622 59974 51724 53513 46043 TRUE FALSE 36411.4083 50605.37179 25157.46192 27821.25119 62356.04667 62281.23859 46707.81444 42069.66139 40599.84899 0.896836052 1.246442365 0.619644224 0.685255041 1.535868931 1.534026361 1.150443058 1.03620241 1 15.30918674 3.250431376 24.97932868 1.230990996 0.872187141 0.390380377 0.24082379 278.895864 586869.8617 0.07635183 0.09777449 1780.046619 -3.250431376 -0.358803855 SPS(ph)PLTGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPSPLTGK 8 0 Q9P2F8;Q9P2F8-2 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 S(0.003)PS(0.997)PLTGK;S(0.035)PS(0.965)PLTGK;S(0.01)PS(0.99)PLTGK 118.04 0.0020592 1527640000 3502980 3222280 2210620 2591300 2666490 2482530 3409400 3665120 3629630 TRUE FALSE 3040052.318 3201112.631 3279683.226 3179694.271 2613432.066 2578034.536 3078756.913 2881362.61 3200539.276 0.949856276 1.000179143 1.024728317 0.993487033 0.816559911 0.805500046 0.961949424 0.900274098 1 21.60988358 3.324658405 12.73256692 0.897613548 0.995135344 0.381177718 0.060218671 0.721568114 103.573757 0.018018261 0.023260583 2111.827327 -3.324658405 0.097521795 SPS(ph)PLVSLQAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPSPLVSLQAVK 12 0 Q9UPZ3-2;Q9UPZ3 Q9UPZ3-2 HPS5 Hermansky-Pudlak syndrome 5 protein 1 S(0.254)PS(0.746)PLVSLQAVK;S(0.042)PS(0.958)PLVSLQAVK;S(0.006)PS(0.994)PLVSLQAVK;S(0.242)PS(0.758)PLVSLQAVK 193.06 3.45E-06 481636000 914030 755850 589420 547538 782060 775590 806920 943170 916130 TRUE FALSE 793238.6196 750884.7716 874465.4835 671864.8715 766498.5361 805427.4492 728665.0226 741480.4353 807826.1551 0.981942234 0.929512825 1.082492165 0.831694873 0.94884095 0.997030666 0.902007218 0.91787129 1 19.62368533 3.744383842 24.99481587 0.932745653 0.991135437 0.203890819 0.060111052 832.0119058 3571200.369 0.015439429 0.025883623 5551.161238 -3.744383842 0.058389784 SPS(ph)PPTQHTGQPPGQPSAPSQLSAPR ddPTM_MDA-MB-175_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(0.036)PS(0.865)PPT(0.088)QHT(0.011)GQPPGQPSAPSQLSAPR;S(0.018)PS(0.982)PPTQHTGQPPGQPSAPSQLSAPR;S(0.194)PS(0.801)PPT(0.005)QHTGQPPGQPSAPSQLSAPR;S(0.124)PS(0.795)PPT(0.081)QHTGQPPGQPSAPSQLSAPR;S(0.004)PS(0.982)PPT(0.014)QHTGQPPGQPSAPSQLSAPR;S(0.016)PS(0.973)PPT(0.011)QHTGQPPGQPSAPSQLSAPR 180.91 1.34E-17 9605110000 526729 438256 277268 339484 453651 488938 461131 521208 465645 TRUE FALSE 457120.4281 435377.0675 411355.7322 416569.0309 444624.2327 507747.7612 416410.5866 409751.7252 410596.9786 1.113306848 1.060351367 1.001847928 1.014544803 1.082872636 1.236608616 1.014158916 0.997941404 1 18.64736349 2.028165269 24.99908155 1.000991358 1.08079086 0.265136116 0.063586669 301.3577108 267479.3143 0.027632293 0.018629351 106.7002087 -2.028165269 0.079799503 SPS(ph)PQGTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPSPQGTK 8 0 Q9ULL5;Q9ULL5-2;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 S(0.007)PS(0.993)PQGTK;S(0.005)PS(0.995)PQGTK 107.03 0.0042822 324300000 1487900 1171040 744020 923610 667670 939820 1162440 1343950 1342080 TRUE FALSE 1291270.245 1163347.361 1103830.561 1133329.767 654384.6733 975975.4835 1049706.748 1056556.751 1183420.831 1.091133611 0.983037758 0.932745589 0.957672653 0.552960245 0.824707034 0.887010538 0.892798845 1 20.17453176 4.230550401 1.462426855 0.846566338 1.08379192 0.312806133 0.118561238 0.703533528 2.518516982 0.036712332 0.187321269 17003.97277 -4.230550401 0.237225582 SPS(ph)PSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSPSFR 7 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 S(0.315)PS(0.685)PSFR 128.36 0.0039495 361100000 782780 705690 446760 502130 665070 713760 688930 787040 752610 TRUE FALSE 679333.6397 701054.2759 662814.6303 616146.2911 651836.4082 741218.8091 622117.6746 618737.6208 663637.3032 1.02365198 1.05638166 0.998760358 0.928438302 0.982217855 1.116903474 0.937436265 0.93234304 1 19.34003546 8 0.176511004 0.945507672 1.334931905 0.08274952 0.056454704 283.0159345 3.940640134 0.588091191 28.4956932 100000000 -8 0.389424233 SPS(ph)PSLSSLLLPSSPGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSPSLSSLLLPSSPGPR 18 0 Q8TER5;Q8TER5-4;Q8TER5-3;Q8TER5-2 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 S(0.031)PS(0.969)PSLSSLLLPSSPGPR 115.31 0.00020235 110380000 44424 41852 24354 31809 35717 40946 45848 50097 41171 TRUE FALSE 38553.25584 41577.07146 36131.67586 39031.71962 35006.30158 42521.21912 41401.66802 39384.14641 36303.81128 1.061961664 1.145253625 0.995258475 1.075141101 0.964259684 1.171260471 1.140422081 1.084848808 1 15.14783339 2.725369621 24.96079088 1.100771817 1.052293152 0.131578421 0.064299045 1718.806011 3252425.767 0.022094813 0.01959134 531.3364638 -2.725369621 -0.048478665 SPS(ph)PSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSPSVR 7 0 O75376;O75376-2;A0A088AWL3;E7EVK1 O75376 NCOR1 Nuclear receptor corepressor 1 1 S(0.413)PS(0.583)PS(0.004)VR 72.879 0.052876 100520000 137720 129860 91950 78303 119040 119720 132820 146820 99722 TRUE FALSE 119519.9531 129006.9411 136417.3276 96082.89294 116671.3369 124325.7059 119939.1368 115423.6856 87932.97876 1.359216471 1.467105322 1.551378442 1.092683249 1.32682116 1.413868922 1.363983553 1.312632498 1 16.42411672 1.200495957 2.756070982 0.895947368 1.367702705 0.489499826 0.117071016 0.476166638 3.8915343 0.542470415 0.031148622 15.86704148 -1.200495957 0.471755337 SPS(ph)PVLR ddPTM_MDA-MB-175_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(0.316)PS(0.684)PVLR 83.783 0.023105 231700000 279870 271350 212160 217990 270500 285940 231870 269710 309500 TRUE FALSE 242884.4704 269567.484 314761.2856 267487.9613 265117.5792 296940.2968 209383.2831 212034.6154 272911.2626 0.889975987 0.987747744 1.153346632 0.980127968 0.971442427 1.08804706 0.767221115 0.776936112 1 18.05807241 2.23637686 24.99885897 0.829868532 1.013851287 0.397873833 0.094043449 51.10041034 584963.3547 0.037025361 0.026341787 172.3363381 -2.23637686 0.183982754 SPS(ph)PVQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPSPVQGK 8 0 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 S(0.04)PS(0.96)PVQGK;S(0.093)PS(0.907)PVQGK;S(0.051)PS(0.949)PVQGK 125.66 0.001314 3735080000 9189980 6510720 4174310 5154910 5004190 5277450 7147780 8504430 7417660 TRUE FALSE 7975500.859 6467950.652 6193020.278 6325411.103 4904616.41 5480476.916 6454589.396 6685823.826 6540752.685 1.219355209 0.988869472 0.946836026 0.967076942 0.749855047 0.837896979 0.986826701 1.022179579 1 22.64102523 4.837477648 1.960130095 0.931966515 1.359043938 0.554461182 0.081107628 0.942019475 3.113737597 0.02417973 0.790477175 68782.45108 -4.837477648 0.427077423 SPS(ph)PYYSR ddPTM_MDA-MB-175_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(0.293)PS(0.707)PYYSR 102.55 0.0051858 997030000 138030 122390 109250 124260 142910 130730 133880 162070 234860 TRUE FALSE 119788.9858 121586.012 162083.6654 152475.1322 140066.3706 135759.2677 120896.3382 127412.5917 207095.1184 0.578424961 0.58710226 0.78265324 0.736256525 0.67633835 0.655540646 0.583772033 0.61523706 1 17.65993402 1.234812118 24.99914355 1.000000495 0.652574359 0.727159456 0.067006908 63.95544016 426461.8827 0.129675493 0.017831727 17.17165358 -1.234812118 -0.347426136 SPS(ph)TLLPK ddPTM_MDA-MB-175_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(0.293)PS(0.707)TLLPK;S(0.361)PS(0.535)T(0.104)LLPK;S(0.182)PS(0.818)TLLPK 154.35 0.00044723 1893100000 1435040 1160500 982040 1185640 1093040 1017310 1359710 1540150 1719690 TRUE FALSE 1245395.828 1152876.599 1456957.829 1454857.683 1071290.642 1056446.574 1227845.533 1210800.908 1516390.207 0.821289812 0.760277001 0.960806672 0.959421708 0.706474255 0.696685173 0.809716079 0.798475816 1 20.53220961 SPS(ph)VAAMASPQLCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSVAAMASPQLCR 14 0 P25325-2 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 1 S(0.436)PS(0.564)VAAMASPQLCR 167.92 3.75E-06 180130000 74633 67802 42145 57821 74693 82472 65250 64506 79566 TRUE FALSE 64770.05995 67356.6042 62526.46297 70950.14179 73206.75543 85644.75121 58922.06504 50711.89389 70159.79812 0.92317911 0.960045582 0.891200725 1.011264908 1.043428821 1.220709773 0.839826605 0.722805584 1 16.09835698 2.040198539 24.99941684 0.823516493 1.004831915 0.287793991 0.1110598 158.7143289 98703.57735 0.046262915 0.031190403 109.697957 -2.040198539 0.181315422 SPSDLHIS(ph)PLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSDLHISPLAK 12 0 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785;O95785-2 M0QXA7 WIZ Protein Wiz 1 SPSDLHIS(1)PLAK 115.82 0.00058541 196190000 392590 354480 195210 287100 330280 295380 356070 446910 354780 TRUE FALSE 340708.2368 352151.3975 289614.2089 352290.443 323708.0742 306743.4597 321538.3862 351341.7744 312838.3126 1.089087312 1.125665826 0.925763237 1.126110291 1.034745622 0.980517563 1.027810128 1.123077834 1 18.25505768 SPSDVSASES(ph)PQHDVVDLGSTAPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSDVSASESPQHDVVDLGSTAPLK 25 0 Q8N9M5 Q8N9M5 TMEM102 Transmembrane protein 102 1 S(0.015)PS(0.003)DVS(0.06)AS(0.043)ES(0.879)PQHDVVDLGSTAPLK 124.03 0.00010064 159830000 73024 78785 54787 58155 68400 72980 82812 84448 84191 TRUE FALSE 63373.69338 78267.45615 81282.17645 71359.98159 67038.97382 75787.58782 74780.90499 66389.45238 74238.03589 0.853655308 1.054277032 1.094885869 0.961232079 0.90302731 1.02087275 1.007312547 0.894278136 1 16.17987092 3.534696633 24.99757676 0.959466381 1.009904151 0.044595803 0.073592266 688.9316488 299111.9307 0.020018312 0.029691839 3425.284371 -3.534696633 0.05043777 SPSFGDPQLS(ph)PEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSFGDPQLSPEAR 14 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 SPSFGDPQLS(1)PEAR 112.34 0.0006287 52185000 237110 203060 160500 196810 187250 198880 174360 205820 419370 TRUE FALSE 205775.3127 201726.0855 238118.3368 241498.7186 183524.0913 206531.0423 157450.594 161806.9947 369792.5563 0.556461479 0.545511482 0.643924094 0.653065386 0.496289307 0.558505137 0.425780864 0.437561524 1 18.49635666 1.231100853 24.99997716 1.00000082 0.535737707 0.79081654 0.074385443 137.6173903 461158.864 0.212218578 0.020789827 17.02553836 -1.231100853 -0.464263113 SPSFGDPQLS(ph)PEARPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPSFGDPQLSPEARPR 16 1 O95425-2;O95425-3 O95425-2 SVIL Supervillin 1 SPSFGDPQLS(1)PEARPR;SPSFGDPQLS(1)PEARPR;SPSFGDPQLS(1)PEARPR;SPSFGDPQLS(1)PEARPR 144.27 8.07E-07 1402390000 2467660 1919290 1085220 1238570 1770030 1929890 1723970 1900370 1204750 TRUE FALSE 2141552.479 1906682.058 1610036.022 1519806.249 1734809.866 2004134.117 1556779.655 1493990.664 1062325.827 2.015909266 1.794818509 1.515576465 1.430640402 1.633029925 1.886553132 1.465444607 1.406339398 1 20.01879489 1.010326336 1.037971089 0.339202948 1.692220524 0.615069305 0.177726011 2.067541504 1.315625005 3.505102718 0.062340303 10.24062202 -1.010326336 1.353017576 SPSGSAFGS(ph)QENLR ddPTM_MDA-MB-175_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 SPSGSAFGS(1)QENLR;SPSGS(0.008)AFGS(0.992)QENLR;SPSGSAFGS(1)QENLR;SPSGSAFGS(1)QENLR 195.66 2.72E-08 1558140000 872880 888380 551590 636380 941360 955460 712100 887410 910260 TRUE FALSE 757526.6964 882544.1733 818340.769 780879.8055 922628.7777 992217.1645 643040.6516 697644.2773 802650.0998 0.943781975 1.09953786 1.019548579 0.97287698 1.149478182 1.236176467 0.801146915 0.869176092 1 19.61441168 2.221021301 24.99999081 0.882040225 1.068438299 0.436904999 0.096238098 223.2599588 318225.2722 0.03997561 0.027019491 166.3494237 -2.221021301 0.186398074 SPSHSSSNRPFT(ph)PPTSTGGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSHSSSNRPFTPPTSTGGSK 21 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 S(0.014)PS(0.014)HS(0.007)S(0.017)S(0.01)NRPFT(0.939)PPTSTGGSK 162.07 2.80E-11 92537000 144260 119890 40063 76280 157790 119490 119520 139610 166290 TRUE FALSE 125195.6755 119102.4347 59437.6008 93600.53987 154650.2877 124086.8576 107928.9688 109755.4879 146631.3856 0.853812265 0.812257445 0.405353878 0.638339053 1.054687488 0.846250324 0.736056393 0.748512929 1 17.16183441 3.312264709 25 0.848922362 0.667634341 0.283178297 0.153919092 62.09464105 21060.21387 0.0464198 0.05992769 2052.412774 -3.312264709 -0.181288021 SPSPFHAVAECR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPSPFHAVAECR 12 0 E5RIA4;E7ETB3;Q9ULA0-2;Q9ULA0;C9JBE1;E7EPX3;B9ZVU2;F8WAN0;E5RJ35 E5RIA4 DNPEP Aspartyl aminopeptidase 0 ; 118.61 0.00060734 819920000 768810 956370 233130 373530 1000000 1114260 785380 861280 551040 FALSE TRUE 667209.8106 950087.5425 345872.4478 458345.6955 980101.9565 1157126.303 709213.9685 677101.9745 485896.6789 1.373151617 1.955328331 0.711823033 0.943298679 2.017099517 2.381424598 1.459598304 1.393510192 1 18.89029005 3.244202401 24.99898374 1.640474763 1.258425527 0.147656349 0.482088509 322.1978657 1427663.817 0.151458823 0.190064226 1754.69808 -3.244202401 -0.382049236 SPSPGGPQLS(ph)PQLPR ddPTM_MDA-MB-175_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 241.79 7.09E-18 873490000 611800 503454 343403 395875 466593 563450 420594 484067 471951 TRUE FALSE 530949.0799 500146.7775 509473.8394 485764.4693 457308.7122 585126.2861 379804.8586 380553.0391 416157.4904 1.275836894 1.201820919 1.224233256 1.167261146 1.09888377 1.406021277 0.912646936 0.914444766 1 18.66677008 2.215529808 24.99999881 0.935309047 1.218835051 0.729045173 0.08218447 113.0820599 122749.9217 0.031978447 0.021575552 164.2592397 -2.215529808 0.283526004 SPSS(ph)ESSPQHPTPPARPR ddPTM_MDA-MB-175_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(0.168)PS(0.214)S(0.274)ES(0.274)S(0.07)PQHPTPPARPR 101.53 0.00039234 148530000 48660 49504 26226 39857 56051 62309 53996 63378 56057 TRUE FALSE 42229.45771 49178.80496 38908.98132 48907.14103 54935.69476 64706.06755 48759.47623 49825.10791 49430.00532 0.854328407 0.994918059 0.787153088 0.989422127 1.111383549 1.309044317 0.986434776 1.007993173 1 15.59309944 3.481604711 5.622414923 1.076133693 0.889217208 0.445311961 0.103747013 0.171247182 19.2082383 0.031195493 0.04322086 3031.131032 -3.481604711 -0.186916485 SPSSDLDT(ph)DAEGDDFELLDQSELSQLDPASSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSSDLDTDAEGDDFELLDQSELSQLDPASSR 32 0 K7EQI9;Q86VR2-2;Q86VR2 K7EQI9 FAM134C Protein FAM134C 1 S(0.231)PS(0.231)S(0.231)DLDT(0.308)DAEGDDFELLDQSELSQLDPASSR 137.88 5.37E-08 44749000 25216 23322 17954 17173 25569 22940 20606 32795 30022 TRUE FALSE 21883.64171 23168.79625 26636.61445 21072.39212 25060.22692 23822.51664 18607.63329 25782.04446 26472.83336 0.826645241 0.875191406 1.006186761 0.796000633 0.946639394 0.899885415 0.702895419 0.973905744 1 14.69222499 1.56423473 10.61859349 0.991701832 0.87017049 0.276971937 0.082142406 0.143079732 26.00087362 0.052102542 0.01982681 36.66356821 -1.56423473 -0.121531342 SPSSESS(ph)PQHPTPPARPR ddPTM_MDA-MB-175_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(0.005)PS(0.002)S(0.009)ES(0.212)S(0.771)PQHPTPPARPR 79.293 0.0063422 170460000 40086 28892 22804 34804 52153 52536 48271 48372 35520 TRUE FALSE 34788.53354 28702.20655 33832.09067 42706.78015 51115.25734 54557.09392 43589.68585 38028.02423 31320.86606 1.110714291 0.916392493 1.080177368 1.36352488 1.631987354 1.741876926 1.391713938 1.214143445 1 14.93483649 3.767856591 3.976515155 1.399014233 1.013182107 0.397819595 0.206882321 0.245156787 8.773886586 0.063431678 0.109969127 5859.446465 -3.767856591 -0.385832125 SPSSQETHDS(ph)PFCLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPSSQETHDSPFCLR 15 0 Q8TB45;Q8TB45-2 Q8TB45 DEPTOR DEP domain-containing mTOR-interacting protein 1 SPSSQETHDS(1)PFCLR;SPSSQET(0.004)HDS(0.996)PFCLR;SPSSQETHDS(1)PFCLR 206.7 2.43E-09 1036420000 964890 673020 422962 447968 650590 595076 573600 663550 701710 TRUE FALSE 837377.3418 668598.8873 627507.8379 549685.9812 637644.5319 617968.9588 517972.3603 521654.9963 618754.6432 1.353326962 1.08055575 1.014146471 0.888374717 1.030528884 0.998730217 0.837120765 0.843072455 1 19.23900792 7.999999996 0.669205256 0.910960792 45.99365804 0.796503113 0.066544826 111.0829247 0.671330507 0.029386049 7447.421457 99999998.99 -7.999999996 45.08269725 SPSVPKS(ph)PTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSVPKSPTPK 11 1 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 1 SPSVPKS(0.5)PT(0.5)PK 74.475 0.024661 608100000 503040 404490 331160 383300 502500 356800 517310 665060 569280 TRUE FALSE 436561.9895 401832.8786 491310.0837 470334.1234 492501.2331 370526.3269 467141.3558 522842.0945 501980.3669 0.86967941 0.800495209 0.978743624 0.936957209 0.981116525 0.738129121 0.930596865 1.041558852 1 18.93727141 1.888874954 5.010400342 1.018347357 0.887438133 0.352572989 0.075219346 0.246416897 8.983823759 0.039952397 0.02037928 77.42388394 -1.888874954 -0.130909224 SPT(ph)FSEELPVLGDGQQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPTFSEELPVLGDGQQLR 18 0 Q8N0Z3 Q8N0Z3 SPICE1 Spindle and centriole-associated protein 1 1 S(0.167)PT(0.833)FSEELPVLGDGQQLR 191.96 2.22E-13 65792000 37087 36840 21944 25394 41667 36618 34904 41554 40601 TRUE FALSE 32185.85898 36597.99561 32556.1918 31160.09582 40837.90822 38026.71816 31519.01545 32668.00047 35801.19603 0.899016305 1.022256228 0.909360452 0.87036466 1.140685584 1.062163346 0.880390013 0.912483495 1 15.12772016 4.781696707 21.32415787 0.968046212 0.899014789 0.066619649 0.085880207 13466.8576 6656288.683 0.021931896 6.120092519 60491.82783 -4.781696707 -0.069031423 SPT(ph)GPSNSFLANMGGTVAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPTGPSNSFLANMGGTVAHK 20 0 H0Y6J6;Q5W012;Q96I25 H0Y6J6 RBM17 Splicing factor 45 1 S(0.412)PT(0.588)GPSNSFLANMGGTVAHK;S(0.381)PT(0.619)GPSNSFLANMGGTVAHK 333.57 2.37E-79 2528800000 1276420 1079020 810510 1076580 1103520 916720 1156590 1471880 1821200 TRUE FALSE 1107737.863 1071931.847 1202475.347 1321033.943 1081562.111 951986.8116 1044424.08 1157129.916 1605899.811 0.689792636 0.667496091 0.748786032 0.822612927 0.673492894 0.592805856 0.650366899 0.720549257 1 20.61495046 1.24023909 4.531636359 1.024900043 0.693414311 0.716510429 0.060394457 0.117623181 5.13606855 0.125283356 0.016613682 17.38757796 -1.24023909 -0.331485732 SPT(ph)PPPSSKPSSIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPTPPPSSKPSSIPR 15 1 B4E2D5;R4GND2;F6S7C4;Q8NEM7-2;Q8NEM7;Q8NEM7-3;H7C5F9 B4E2D5 SUPT20H Transcription factor SPT20 homolog 1 S(0.246)PT(0.747)PPPS(0.004)S(0.003)KPSSIPR;S(0.001)PT(0.999)PPPSSKPSSIPR 125.73 0.00014335 704810000 1651410 1313260 862180 1161310 1372280 1226540 1490780 1815420 1507410 TRUE FALSE 1433171.984 1304633.109 1279133.132 1425003.185 1344974.313 1273725.787 1346204.385 1427206.561 1329205.707 1.078216845 0.981513322 0.96232895 1.072071221 1.011863179 0.958260848 1.012788598 1.073728884 1 20.34213296 1.966586244 23.66243285 1.042469202 1.007982887 0.051937555 0.043580299 734.7469719 520318.9177 0.019546703 0.0112988 92.59472463 -1.966586244 -0.034486315 SPT(ph)PPPTLHLVPEPAAPPPPPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPTPPPTLHLVPEPAAPPPPPPR 23 0 A0A087WWH3;Q9NZM4-2;Q9NZM4 A0A087WWH3 GLTSCR1 Glioma tumor suppressor candidate region gene 1 protein 1 S(0.351)PT(0.649)PPPTLHLVPEPAAPPPPPPR 173.36 1.45E-11 84982000 108640 91439 60915 75982 110990 113300 85559 95509 103560 TRUE FALSE 94282.94874 90838.33119 90373.69775 93234.87441 108781.5161 117658.7243 77261.50135 75085.1436 91317.25478 1.032476819 0.994755388 0.989667265 1.020999532 1.191248208 1.288461032 0.846077793 0.822244863 1 16.47859987 2.190624401 24.99998842 0.873634493 1.079523165 0.442309698 0.103496784 110.2988382 57522.90003 0.045562562 0.030718355 155.104501 -2.190624401 0.205888672 SPTDWALFTYEGNSNDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPTDWALFTYEGNSNDIR 18 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;F8WBG8;F8WC20;F8WBB2;F8WFE1;Q9UJU6 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ; 189.33 7.75E-14 169745000 108852 101758 55032 70107 85688 93894 88016 96617 84546 FALSE TRUE 94466.9324 101089.545 81645.65927 86025.86587 83982.97645 97506.16294 79480.22187 75956.20642 74551.0682 1.267143915 1.35597715 1.095164177 1.153918622 1.126516071 1.307911011 1.066117814 1.018847996 1 16.1859414 -1.349211873 0.199118802 3.13E-11 1.331072576 0.504077798 0.085027367 68.01629636 1.283955767 26.01123146 0.6127562 0.044749494 1.349211873 1.331072576 SPTLYGISHDDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPTLYGISHDDLK 13 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 155.02 4.65E-05 164250000 268610 217520 146430 184990 232800 195240 252110 285590 308780 FALSE TRUE 233112.5079 216091.0968 217244.0378 226994.8069 228167.7355 202751.0091 227660.411 224518.801 272276.3802 0.856161331 0.793646135 0.797880586 0.833692613 0.838000473 0.744651479 0.836137203 0.82459889 1 18.05471231 1.212583204 3.65261519 1.031768908 0.812889871 0.774330735 0.031284717 0.14777334 2.907271447 0.092600467 0.007652134 16.31485446 -1.212583204 -0.218879037 SPTPKS(ph)PPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPTPKSPPSR 10 1 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 1 S(0.001)PT(0.071)PKS(0.928)PPSR;SPT(0.02)PKS(0.979)PPS(0.001)R;S(0.001)PT(0.027)PKS(0.972)PPS(0.001)R 83.474 0.0094343 763740000 456430 387860 129776 136564 356110 296586 445030 452970 42360 TRUE FALSE 396111.6191 385312.1221 192536.1077 167572.9435 349024.1077 307995.8553 401871.0591 356105.8905 37352.24906 10.60475953 10.31563378 5.15460548 4.486287913 9.344125629 8.245711118 10.75895212 9.533720178 1 15.18890749 4.346365463 9.250474901 7.417041739 10.5216722 0.191411338 2.88582234 0.510692083 40.1984347 0.736618194 1.955263136 22200.63837 -4.346365463 3.104630462 SPVDIVTGGIS(ph)PVRDLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPVDIVTGGISPVRDLDR 18 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6;H0Y9N9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 SPVDIVTGGIS(1)PVRDLDR;SPVDIVTGGIS(1)PVRDLDR;SPVDIVTGGIS(1)PVRDLDR;SPVDIVTGGIS(1)PVRDLDR 252.8 1.04E-30 1369010000 1161180 1232290 757521 817110 1213770 1361970 1169400 1306490 812200 TRUE FALSE 1007727.121 1224195.006 1123860.689 1002647.314 1189618.352 1414365.867 1055991.768 1027107.281 716182.6413 1.407081187 1.709333535 1.569237544 1.399988294 1.661054434 1.974867563 1.474472721 1.434141546 1 19.44996803 1.212174284 1.760248865 0.751821518 1.612351187 0.565301733 0.166185322 0.767735037 2.095397226 1.153853918 0.046881398 16.29950007 -1.212174284 0.860529669 SPVGKS(ph)PPSTGSTYGSSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPVGKSPPSTGSTYGSSQK 19 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.2)PVGKS(0.788)PPS(0.01)T(0.002)GSTYGSSQK;SPVGKS(0.999)PPS(0.001)TGSTYGSSQK 234.73 2.32E-24 399560000 417204 272193 251804 262684 281881 230972 333659 407040 427968 TRUE FALSE 362069.4343 270404.9463 373577.2566 322330.4171 276272.1196 239857.6423 301300.8015 319997.6636 377374.1106 0.959444287 0.716543448 0.989938754 0.85414025 0.732090813 0.635596443 0.798414075 0.847958709 1 18.52563593 4.777564748 21.52064265 0.820416632 0.959446546 0.126499956 0.113586725 7092.955199 3913068.816 0.028332735 5.349817249 59919.02634 -4.777564748 0.139029913 SPVPSPGSS(ph)SPQLQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPVPSPGSSSPQLQVK 16 0 Q8N3F8 Q8N3F8 MICALL1 MICAL-like protein 1 1 SPVPSPGS(0.048)S(0.707)S(0.245)PQLQVK 247.5 2.81E-20 159200000 236110 250250 188710 217980 248280 222190 308090 341690 365020 TRUE FALSE 204907.4653 248606.0913 279970.7872 267475.6906 243339.7138 230737.7931 278211.4792 268622.2525 321867.7514 0.636620054 0.772385833 0.869831743 0.831011151 0.756023903 0.716871423 0.864365809 0.834573365 1 18.29610851 -0.922444965 0.834354207 9.999836318 0.77298817 0.532584322 0.067116192 69.77017527 1.560979888 1148.245027 0.025064262 0.119551502 0.922444965 -9.226848148 SPVPSPGSSS(ph)PQLQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SPVPSPGSSSPQLQVK 16 0 Q8N3F8 Q8N3F8 MICALL1 MICAL-like protein 1 1 SPVPSPGSS(0.011)S(0.989)PQLQVK;SPVPSPGSS(0.042)S(0.958)PQLQVK;SPVPSPGS(0.03)S(0.419)S(0.55)PQLQVK 327.7 1.95E-71 815380000 1048790 1058000 807170 1103740 1253670 1031350 1365200 1475280 1539780 TRUE FALSE 910189.7442 1051049.928 1197520.112 1354361.037 1228724.42 1071026.702 1232803.114 1159802.853 1357748.963 0.670366739 0.77411212 0.88198934 0.997504748 0.904971724 0.788825277 0.907975736 0.854210082 1 20.37278533 4.433028608 2.483220618 0.900696002 0.673191546 0.625447532 0.061733772 0.218942827 2.43672446 0.016415371 0.079336013 27103.70166 -4.433028608 -0.227504456 SPWSNKYDPPLEDGAMPSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPWSNKYDPPLEDGAMPSAR 20 1 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ; 89.483 0.0018901 600720000 1875940 1608970 963500 1281450 1601240 1529230 1692760 2066200 1291630 FALSE TRUE 1628029.776 1598400.57 1429451.823 1572422.808 1569378.457 1588060.468 1528596.396 1624359.209 1138934.973 1.429431719 1.403416884 1.255077644 1.380608064 1.377935083 1.394338137 1.342127893 1.426208913 1 20.11925395 1.233755356 24.99096104 0.999999428 1.374728574 0.8495201 0.049748529 54.33852374 282566.8665 0.095805115 0.012056841 17.12992085 -1.233755356 0.374729146 SPYLYPLYGLGELPQGFAR ddPTM_MDA-MB-175_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 ; 236.92 7.76E-24 310010000 350290 300145 178727 226289 333790 305276 317252 359050 271727 FALSE TRUE 303998.289 298173.3277 265159.975 277671.3761 327148.232 317020.1653 286484.9499 282269.9516 239603.7436 1.268754337 1.244443527 1.106660401 1.158877453 1.365371956 1.323101887 1.19566141 1.178069872 1 17.87029092 1.142739968 1.759292634 0.867970784 1.238345948 0.504526733 0.074168191 1.148021773 2.695709417 0.783419265 0.022364669 13.89120653 -1.142739968 0.370375165 SPYQEFTDHLVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPYQEFTDHLVK 12 0 P15880;H0YEN5;E9PQD7 P15880 RPS2 40S ribosomal protein S2 0 ;;; 194.7 1.19E-06 7103200000 5254350 4927350 3204520 4004830 4856530 4217230 5421000 6036200 5818400 FALSE TRUE 4559974.335 4894981.913 4754236.59 4914187.861 4759894.555 4379469.567 4895272.254 4745405.604 5130555.38 0.888787665 0.954084217 0.926651452 0.957827661 0.927754249 0.853605359 0.954140808 0.924930198 1 22.29068357 0.913293111 1.970916616 1.114385507 0.923498985 0.355862703 0.032079438 2.905170849 4.772791547 1.419212652 0.008475447 8.190173668 -0.913293111 -0.190886522 SQAFIEMETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQAFIEMETR 10 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 183.07 0.00058316 556580000 782290 702420 428938 544250 759920 799350 673060 765670 748900 FALSE TRUE 678908.3944 697805.7568 636373.8515 667830.2808 744799.0788 830101.5117 607786.7448 601937.429 660365.8951 1.028079129 1.056695632 0.96366856 1.011303409 1.127858183 1.257032681 0.920378762 0.911521072 1 19.33290609 SQANGAGALSYVS(ph)PNTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQANGAGALSYVSPNTSK 18 0 A0A494C0Q6;A0A494C0K5;A0A494C0W0;O95453-2;O95453-3;O95453;F5H1Z4;A0A494C002;A0A494C156;A0A494C1G3;A0A494BZU6;A0A494BZW7;A0A494C0P9;A0A494C1K5;A0A494C1N1;A0A494C0Q2 A0A494C0Q6;A0A494C0Q2 PARN Poly(A)-specific ribonuclease PARN 1 SQANGAGALSYVS(0.999)PNT(0.001)SK;SQANGAGALSYVS(1)PNTSK 335.42 4.84E-75 63118000 255270 254620 138590 182056 245130 197909 251430 324800 266410 TRUE FALSE 221535.4227 252947.3845 205612.5876 223394.5974 240252.3926 205522.6873 227046.3573 255344.0476 234915.3133 0.94304377 1.07675988 0.875262599 0.950958004 1.022719163 0.874879906 0.96650301 1.086962123 1 17.84178124 1.759712384 24.99998776 1.046823975 0.958882976 0.236110841 0.063415921 12.89796211 15260.7368 0.032245973 0.015484848 57.50589727 -1.759712384 -0.087940999 SQAPGQPGASQWGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQAPGQPGASQWGSR 15 0 K7EQ55;K7EK33;Q96EP5;Q96EP5-2;K7EQ02 K7EQ55 DAZAP1 DAZ-associated protein 1 0 ; 180.95 3.85E-11 0 74893 66811 38235 46248 69084 69021 62325 69272 65390 FALSE TRUE 64995.7003 66372.11414 56725.57389 56749.31526 67709.36356 71676.28253 56280.73109 54458.72188 57659.66869 1.12722986 1.151101206 0.983799858 0.984211608 1.174293316 1.243092168 0.976084885 0.944485515 1 15.81527493 2.044108465 24.91904031 0.965879574 1.10432378 0.393597137 0.079888865 133.7686997 75571.9448 0.035110693 0.023671609 110.6900198 -2.044108465 0.138444206 SQAPLESSLDSLGDVFLDS(ph)GRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQAPLESSLDSLGDVFLDSGRK 22 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 SQAPLESSLDSLGDVFLDS(1)GRK;SQAPLESSLDSLGDVFLDS(1)GRK 134.04 4.99E-06 69159000 59261 60744 40474 44637 59171 56375 58026 72503 69107 TRUE FALSE 51429.5087 60344.96866 60047.36178 54772.51308 57993.61287 58543.78273 52398.64745 56998.79767 60937.24919 0.843974899 0.990280485 0.985396659 0.898834683 0.951693974 0.96072244 0.859878779 0.935368735 1 15.89503676 3.601912105 0.002366924 1.858285767 0.010109548 0.022617764 0.05312083 902099.7648 1461.897542 568800.8209 572693.6094 3998.638146 -3.601912105 -1.848176218 SQATS(ph)PGQTNGDSSLEVLATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SQATSPGQTNGDSSLEVLATR 21 0 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;Q96JY6-4;C9JS55;C9JSR2;C9K0F0;C9J0X3;Q96JY6-2;C9J760 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 SQAT(0.001)S(0.999)PGQTNGDSSLEVLATR;SQAT(0.001)S(0.999)PGQTNGDSSLEVLATR;S(0.001)QAT(0.032)S(0.966)PGQT(0.001)NGDSSLEVLATR 305.9 1.16E-55 369770000 488241 545239 322636 393095 540441 573008 501694 577107 543730 TRUE FALSE 423718.7148 541657.2891 478663.8488 482353.2278 529687.2815 595051.9885 453039.7931 453697.1591 479450.8588 0.883758381 1.129745164 0.998358518 1.006053528 1.104779086 1.241111529 0.944913926 0.946285007 1 18.87102343 SQDADS(ph)PGSSGAPENLTFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQDADSPGSSGAPENLTFK 19 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;H0Y8L4;H0Y8U8 P55196-5 MLLT4 Afadin 1 SQDADS(1)PGSSGAPENLTFK;SQDADS(1)PGSSGAPENLTFK;SQDADS(1)PGSSGAPENLTFK;SQDADS(0.997)PGS(0.003)SGAPENLTFK 279.1 1.49E-39 742700000 1635630 1444510 1009960 1285360 1425780 1249870 1544970 1862740 1873360 TRUE FALSE 1419477.351 1435020.919 1498380.034 1577220.633 1397409.767 1297953.308 1395139.047 1464407.547 1651893.515 0.859303181 0.868712726 0.907068174 0.954795584 0.845944218 0.785736669 0.844569601 0.886502389 1 20.65568926 1.245863193 3.775068732 1.015419398 0.86763342 0.478746516 0.043390517 0.256186019 5.899065131 0.105460685 0.012153621 17.61421095 -1.245863193 -0.147785977 SQDAT(ph)FSPGSEQAEKS(ph)PGPIVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQDATFSPGSEQAEKSPGPIVSR 23 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 2 SQDAT(0.555)FS(0.444)PGS(0.003)EQAEKS(0.998)PGPIVSR 90.123 0.012877 206900000 254820 194520 124300 157710 213580 178350 238670 282080 180380 TRUE FALSE 221144.8914 193242.1853 184411.8958 193520.4659 209330.1759 185211.2399 215523.8201 221759.3871 159055.6819 1.390361468 1.214934185 1.159417215 1.216683765 1.316081094 1.164442777 1.355021195 1.394224868 1 17.27917238 4.746149878 23.92984332 1.24491044 1.390361598 0.155409825 0.11301181 1094.393092 3450597.008 0.027670488 0.276131712 55737.80713 -4.746149878 0.145451158 SQDATFSPGSEQAEKS(ph)PGPIVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQDATFSPGSEQAEKSPGPIVSR 23 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SQDATFSPGSEQAEKS(1)PGPIVSR;SQDATFSPGSEQAEKS(1)PGPIVSR;SQDATFSPGSEQAEKS(1)PGPIVSR;SQDATFSPGSEQAEKS(1)PGPIVSR 303.42 2.51E-62 1586440000 1591630 1107300 716993 841379 1229050 1074140 1362440 1636120 940243 TRUE FALSE 1381292.063 1100026.073 1063733.213 1032426.962 1204594.31 1115462.861 1230310.779 1286248.47 829088.5437 1.666036847 1.32678962 1.283015211 1.24525537 1.452913948 1.345408605 1.483931708 1.551400607 1 19.66116666 4.742352875 24.34840073 1.359285541 1.666037016 0.305334738 0.152885523 358.6285746 2302454.646 0.037156122 0.269052556 55252.6198 -4.742352875 0.306751475 SQDDQHMLPFWTDLCSIFGSNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQDDQHMLPFWTDLCSIFGSNK 22 0 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8;K7EMK2 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 0 140.17 8.63E-09 0 90030 70490 45814 52011 73740 63102 72554 91089 78045 FALSE TRUE 78132.30739 70026.94655 67969.80364 63820.89249 72272.71827 65529.57477 65517.72425 71610.32621 68818.60901 1.135336917 1.017558296 0.987666049 0.927378414 1.050191501 0.952207197 0.952034997 1.040566312 1 16.07051111 4.734713852 2.733080197 0.989154658 1.162657734 0.596314687 0.038098111 0.314622811 3.201943769 0.009582068 0.122826943 54289.2512 -4.734713852 0.173503077 SQDIYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SQDIYLR 7 0 J3QQ67;Q07020;F8VYV2;G3V203;A0A075B7A0;F8VXR6 J3QQ67 RPL18 60S ribosomal protein L18 0 ;;;; 200.66 0.00081247 5013330000 2848040 2781280 1747850 2111430 2773690 2914130 2845670 3117450 3356110 FALSE TRUE 2471664.298 2763009.589 2593116.106 2590862.453 2718498.996 3026238.467 2569697.361 2450807.578 2959354.499 0.835203859 0.933652791 0.876243825 0.87548229 0.918612149 1.022600864 0.868330361 0.828156133 1 21.4968511 3.232901568 24.48865303 0.915429267 0.883688922 0.111734294 0.060967174 371.2121032 1606364.786 0.019390763 0.022607878 1709.627788 -3.232901568 -0.031740346 SQDLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SQDLAK 6 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 101.21 0.08557 1268060000 1873830 1679430 997160 1311770 914480 1294300 1802980 1945670 2085200 FALSE TRUE 1626198.618 1668397.714 1479389.911 1609627.428 896283.6371 1344092.559 1628127.277 1529603.612 1838690.031 0.88443326 0.90738389 0.804589075 0.875420762 0.487457713 0.731005518 0.885482191 0.831898572 1 20.81024686 1.010860391 1.376023797 1.196144787 0.787688781 0.216654166 0.121764492 3.842024728 4.14702892 2.570092391 0.037852239 10.25322272 -1.010860391 -0.408456006 SQDLHCGACR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQDLHCGACR 10 0 Q9Y2B0;F8VXJ7;F8W031;F8W1U5;F8VP03;Q9Y2B0-2 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;;; 90.05 0.011095 1159350000 3199450 3333190 1747890 2223850 3305820 4364860 3085210 2838810 2838240 FALSE TRUE 2776634.576 3311294.055 2593175.45 2728809.132 3240040.65 4532778.989 2786006.809 2231752.573 2502706.501 1.109452737 1.32308525 1.036148446 1.090343247 1.29461471 1.811150843 1.113197576 0.891735636 1 21.25505768 2.000939829 24.99999245 0.957434166 1.277621884 0.291368015 0.21468337 38.92598222 1035435.725 0.092732719 0.061930289 100.2166378 -2.000939829 0.320187718 SQDQDS(ph)EVNELSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQDQDSEVNELSR 13 0 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 SQDQDS(1)EVNELSR;SQDQDS(1)EVNELSR 331.4 2.02E-62 515000000 1012430 626460 508750 595520 678200 655150 644350 769050 854670 TRUE FALSE 878634.8103 622344.743 754783.2017 730741.918 664705.1469 680354.0444 581861.0362 604594.6423 753631.8862 1.16586735 0.825794071 1.001527689 0.969627123 0.882002419 0.902767063 0.772075926 0.802241324 1 19.52350048 3.128994133 1.460412958 0.846503553 0.987265368 0.246698119 0.101105199 0.536705561 2.40620236 0.03781639 0.046486658 1345.842174 -3.128994133 0.140761816 SQDS(ph)PGESEETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQDSPGESEETLR 13 0 Q8IWU2 Q8IWU2 LMTK2 Serine/threonine-protein kinase LMTK2 1 SQDS(0.999)PGES(0.001)EETLR;SQDS(1)PGESEETLR 228.49 7.71E-12 169030000 276882 271812 191521 216378 271785 302702 235937 274630 292780 TRUE FALSE 240291.3422 270026.4491 284141.1962 265509.932 266377.0102 314347.1418 213055.8661 215902.5117 258167.8819 0.930756144 1.045933549 1.100606296 1.028439053 1.031797636 1.217607471 0.825260929 0.836287264 1 17.97795 2.214257704 24.99970746 0.873999378 1.057827195 0.47480638 0.084894308 181.5588097 186762.9435 0.033935935 0.02289189 163.7788074 -2.214257704 0.183827818 SQDSYPGS(ph)PSLSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQDSYPGSPSLSPR 14 0 A0A0D9SEU5;Q6VN20;R4GMX8;Q6VN20-2;Q6VN20-3 A0A0D9SEU5 RANBP10 Ran-binding protein 10 1 SQDSYPGS(0.999)PS(0.001)LSPR;SQDSYPGS(0.968)PS(0.032)LSPR 270.79 6.40E-33 332340000 681580 651540 337150 397450 604840 599270 541170 651440 571460 TRUE FALSE 591507.4761 647259.9908 500196.8677 487697.0971 592804.8673 622324.3047 488687.4167 512134.6255 503902.6498 1.17385268 1.28449412 0.992645837 0.967839914 1.176427367 1.235008994 0.969805213 1.016336441 1 18.94278552 7.352886571 0.030280643 5.11E-07 2.565601651 0.214131527 0.104777062 4268.024031 14.72509415 459.945935 842.9709216 22536505.28 -7.352886571 2.56560114 SQDVAVS(ph)PQQQQCSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SQDVAVSPQQQQCSK 15 0 Q96F86;H3BPW9;H3BQ37;H3BTD6 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 1 SQDVAVS(1)PQQQQCSK;SQDVAVS(1)PQQQQCSK;SQDVAVS(1)PQQQQCSK;SQDVAVS(1)PQQQQCSK;SQDVAVS(1)PQQQQCSK;SQDVAVS(1)PQQQQCSK;SQDVAVS(1)PQQQQCSK 431.76 1.65E-153 6987720000 4679790 4506610 3480921 4764570 6062780 5436580 7102460 8093290 7223160 TRUE FALSE 4061343.894 4477005.782 5164306.039 5846438.44 5942142.54 5645728.751 6413664.522 6362602.916 6369246.253 0.637649061 0.702909827 0.810819025 0.917916847 0.932942817 0.886404533 1.006973866 0.998956966 1 22.60269122 5.181542285 0.424613337 1.014893376 0.155024816 0.941236998 0.030637658 1.989146579 0.229960265 0.033443954 0.932139769 151894.5828 -5.181542285 -0.85986856 SQDVELWEGEVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQDVELWEGEVVK 13 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 100.22 0.0058171 31504000 82458 74512 51785 57629 71294 63798 85882 95232 94665 FALSE TRUE 71560.96638 74022.52577 76828.39921 70714.54525 69875.38888 66252.35034 77553.17686 74867.3779 83473.81154 0.857286436 0.886775438 0.920389255 0.847146476 0.837093546 0.79369025 0.92907195 0.896896602 1 16.34903603 1.002043965 1.261623386 1.12907816 0.863483507 0.547586415 0.038441039 2.018139739 1.821472207 0.812547461 0.012086572 10.04717495 -1.002043965 -0.265594653 SQEADVQDWEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQEADVQDWEFR 12 0 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 203.51 0.00029063 0 915310 808850 484020 659790 799750 819400 730660 917100 903690 FALSE TRUE 794349.4644 803536.6111 718093.6909 809605.4038 783836.5397 850922.8482 659800.7057 720985.3019 796856.7977 0.996853471 1.008382702 0.901157765 1.015998616 0.983660479 1.067849143 0.828004113 0.904786536 1 19.60396096 2.239632352 24.99990138 0.90619504 0.992313906 0.322720121 0.057585569 32.67987697 762343.0373 0.022089599 0.01611891 173.633033 -2.239632352 0.086118866 SQEDEISS(ph)PVNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQEDEISSPVNK 12 0 Q5UIP0-2;Q5UIP0;H7C2B5 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 SQEDEIS(0.15)S(0.85)PVNK 101.36 0.001265 0 221100 193400 117020 139150 189980 137830 208880 237220 179300 TRUE FALSE 191881.0748 192129.5427 173611.2634 170746.1343 186199.7697 143132.4093 188622.8497 186492.349 158103.3583 1.213643258 1.215214811 1.098087133 1.079965259 1.177709137 0.905309102 1.193035062 1.179559695 1 17.27050849 4.238935455 24.57013617 1.100086831 1.214429078 0.251021453 0.087779004 11.28903046 739640.3307 0.021975376 0.051298746 17335.46339 -4.238935455 0.114342247 SQEEPKDTFEHDPSESIDEFNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQEEPKDTFEHDPSESIDEFNK 22 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 176.84 3.96E-17 203650000 310360 194500 148350 151250 175590 131000 249060 300170 174640 FALSE TRUE 269345.1396 193222.3167 220092.5562 185593.6242 172096.1025 136039.6548 224906.1995 235980.9814 153994.2582 1.749059627 1.254737151 1.429225731 1.205198339 1.117548827 0.883407319 1.460484321 1.53240117 1 17.23251703 7.086423073 1.244744957 1.246897327 199.4621674 0.381663062 0.203958317 753.1974758 3.885056865 0.063089632 423299.733 12201776.71 -7.086423073 198.2152701 SQEPIPDDQKVS(ph)DDDKEKGEGALPTGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQEPIPDDQKVSDDDKEKGEGALPTGK 27 3 E5RJU9;Q86UE4;H0YBJ8 E5RJU9 MTDH Protein LYRIC 1 SQEPIPDDQKVS(1)DDDKEKGEGALPTGK;SQEPIPDDQKVS(1)DDDKEKGEGALPTGK 124.95 5.47E-05 1023190000 1201530 652497 1088380 719720 676198 390762 959150 1694040 992320 TRUE FALSE 1042744.766 648210.7042 1614724.208 883143.4262 662742.9828 405794.867 866131.7806 1331782.729 875009.0601 1.191695965 0.740804563 1.845379988 1.009296322 0.757412709 0.46376076 0.989854643 1.522021645 1 19.73893843 3.518212324 24.99669299 0.987247401 1.244093462 0.125756298 0.369775588 1370.872741 833931.6245 0.110282631 0.163554742 3297.708961 -3.518212324 0.256846061 SQEPLDLVLVPDDCRPGT(ph)PPSDLIEIQVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQEPLDLVLVPDDCRPGTPPSDLIEIQVVK 30 1 Q8NCA9 Q8NCA9 ZNF784 Zinc finger protein 784 1 SQEPLDLVLVPDDCRPGT(0.974)PPS(0.026)DLIEIQVVK;SQEPLDLVLVPDDCRPGT(0.952)PPS(0.048)DLIEIQVVK;SQEPLDLVLVPDDCRPGT(0.921)PPS(0.079)DLIEIQVVK;SQEPLDLVLVPDDCRPGT(0.993)PPS(0.007)DLIEIQVVK 125.96 2.21E-05 182698000 576830 420009 263554 317383 388788 340474 443241 513624 467687 TRUE FALSE 500600.454 417249.9332 391009.5959 389449.661 381051.8795 353572.2551 400255.556 403789.5046 412397.5757 1.213878266 1.011766213 0.948137475 0.944354875 0.92399156 0.857357744 0.97055749 0.979126766 1 18.65367633 4.759359585 2.142233479 0.946041915 1.29579022 0.829981813 0.038031926 0.30583209 1.512373146 0.010820927 0.209641779 57459.20132 -4.759359585 0.349748305 SQEPLPDDDEEFELPEFVEPFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQEPLPDDDEEFELPEFVEPFLK 23 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 107.08 1.92E-05 0 40215 30460 19062 26010 26183 25888 27217 39087 38156 FALSE TRUE 34900.48586 30259.90625 28280.44696 31915.96804 25662.00953 26883.92811 24577.49953 30728.54923 33645.24115 1.037308239 0.899381464 0.840548202 0.948602743 0.762723305 0.799041029 0.730489623 0.913310417 1 15.03811484 5.232850395 1.248022362 0.849712506 1.409902668 0.319445128 0.082285101 5.464201459 3.140792932 0.02449433 5.311027814 170942.6354 -5.232850395 0.560190161 SQEPS(ph)PVGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQEPSPVGSR 10 0 M0QZ12;Q96CP6-2;Q96CP6-3;Q96CP6 M0QZ12 GRAMD1A GRAM domain-containing protein 1A 1 SQEPS(1)PVGSR 111.63 0.0024131 0 112150 113980 77218 114610 155050 175130 105260 167530 183930 TRUE FALSE 97329.09335 113231.2579 114560.8831 140633.9522 151964.8084 181867.3644 95051.9014 131705.0132 162186.0049 0.600107842 0.698156773 0.706354923 0.867115213 0.936978554 1.121350541 0.586067222 0.812061517 1 17.30728981 3.859786622 2.616687384 0.873606266 0.652027971 0.359537459 0.138541939 0.364402219 4.835481602 0.040845921 0.08274127 7240.801168 -3.859786622 -0.221578295 SQEQLAAELAEYTAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQEQLAAELAEYTAK 15 0 P15311;E7EQR4 P15311 EZR Ezrin 0 163.8 3.53E-06 47193000 91714 84173 57670 80581 84845 68045 78291 101280 94342 FALSE TRUE 79593.76253 83620.06202 85559.40489 98878.14765 83156.7505 70662.73518 70698.35087 79622.06016 83188.99623 0.956782341 1.005181764 1.028494257 1.188596475 0.99961238 0.849424063 0.849852193 0.957122501 1 16.34410509 2.990098772 24.5642215 0.915878723 1.04744058 0.418751123 0.072909256 388.2032315 963107.8057 0.023873316 0.02553658 977.4595008 -2.990098772 0.131561857 SQESGYYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQESGYYDR 9 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 148.94 0.0002066 5329830000 4676890 4244720 2301390 2891190 4174810 4256410 3822830 4122630 4078150 FALSE TRUE 4058827.137 4216836.155 3414349.902 3547678.879 4091739.449 4420156.847 3452092.535 3241037.657 3596035.753 1.128694878 1.172634658 0.949476072 0.986552727 1.137847266 1.229174889 0.959971694 0.90128071 1 21.77797593 2.035122552 23.32736681 0.939700121 1.093700176 0.396073443 0.085082274 85.27398038 56635.83568 0.036855833 0.02484799 108.4232825 -2.035122552 0.154000055 SQET(ph)PEKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQETPEKPR 9 1 J3QQY0;Q68DK7;J3KSZ8;Q68DK7-2;Q68DK7-3;J3KTC2 J3QQY0;Q68DK7 MSL1 Male-specific lethal 1 homolog 1 S(0.008)QET(0.992)PEKPR 77.185 0.028048 0 395100 341750 229300 286190 283860 271010 353070 405080 384400 TRUE FALSE 342886.5339 339505.0217 340190.247 351173.8136 278211.7414 281435.9301 318829.3257 318456.7943 338956.6699 1.011594001 1.001617764 1.003639336 1.036043379 0.820788514 0.830300611 0.940619714 0.93952066 1 18.37074133 3.264025801 24.99957792 0.909185978 1.011710071 0.504247907 0.052653601 216.7430903 212778.6522 0.016530818 0.021333278 1836.647453 -3.264025801 0.102524093 SQFFSQS(ph)VDSPSSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SQFFSQSVDSPSSEK 15 0 Q9UPQ0-4;Q9UPQ0-5 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 SQFFS(0.01)QS(0.989)VDS(0.001)PSSEK;SQFFS(0.002)QS(0.998)VDS(0.001)PSSEK;SQFFS(0.001)QS(0.95)VDS(0.05)PSSEK;SQFFS(0.021)QS(0.975)VDS(0.003)PSSEK;SQFFSQS(1)VDSPSSEK 253.73 1.17E-24 258720000 1347620 1105090 534210 580350 804903 579710 1160070 1073550 892886 TRUE FALSE 1169528.603 1097830.591 792555.7428 712127.3376 788887.0051 602011.8188 1047566.59 843979.6869 787330.0343 1.485436287 1.394371538 1.006637253 0.904483897 1.001977533 0.764624481 1.330530457 1.071951596 1 19.58660899 4.283900342 4.711333185 1.020107836 1.458872596 0.614132404 0.141617309 0.13286291 6.356733973 0.037013752 0.100492352 19226.50487 -4.283900342 0.43876476 SQGDEAGGHGEDRPEPLS(ph)PK ddPTM_MDA-MB-175_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 224.44 3.49E-25 10521000000 12440140 11573380 7590270 9410980 13974530 10754680 14853220 17039250 14743620 TRUE FALSE 10796143.98 11497353.7 11260949.96 11547886.85 13696464.19 11168419.5 13412757.01 13395538.99 13000646.04 0.830431345 0.884367874 0.866183875 0.888254846 1.053521814 0.859066501 1.031699269 1.030374871 1 23.63207998 3.518857629 0.389000746 1.049593338 0.783323274 0.539931737 0.056664342 1.757684734 0.718655628 0.134027615 0.274530164 3302.612564 -3.518857629 -0.266270065 SQGRLS(ph)VGS(ph)NRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQGRLSVGSNRDR 13 2 H3BLT5;H0Y781;Q2LD37-4;Q2LD37 H3BLT5 KIAA1109 Uncharacterized protein KIAA1109 2 S(0.315)QGRLS(0.69)VGS(0.995)NRDR 54.281 0.07429 1110700000 38459 36747 24772 24978 37356 63221 35290 41731 23145 TRUE FALSE 33376.54571 36505.60654 36751.82206 30649.63666 36612.68869 65653.15278 31867.58123 32807.1504 20408.82447 1.635397755 1.788716768 1.800780938 1.50178354 1.793963623 3.216900262 1.561460891 1.607498289 1 14.31690547 3.006937713 24.89816548 1.862743247 1.691580098 0.018838856 0.557228033 979.9857106 3516952.843 0.177478843 0.200812275 1016.102951 -3.006937713 -0.171163149 SQGS(ph)SQFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQGSSQFR 8 0 Q15172 Q15172 PPP2R5A Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform 1 S(0.002)QGS(0.914)S(0.084)QFR;S(0.01)QGS(0.898)S(0.092)QFR 104.82 0.0047266 1523300000 564980 604890 380830 456950 536260 675200 617090 699020 685040 TRUE FALSE 490316.4615 600916.4378 565000.6618 560707.4815 525589.4752 701175.3809 557244.7068 549540.0128 604055.3516 0.811707835 0.994803599 0.935345843 0.92823858 0.870101513 1.160780016 0.922506034 0.909751087 1 19.20432123 SQHHSSTSNQET(ph)SDSEMEMEAEHYPNGVLGSMSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQHHSSTSNQETSDSEMEMEAEHYPNGVLGSMSTR 35 0 A0A0D9SEU5;Q6VN20 A0A0D9SEU5 RANBP10 Ran-binding protein 10 1 S(0.008)QHHS(0.008)S(0.008)T(0.008)S(0.008)NQET(0.319)S(0.319)DS(0.319)EMEMEAEHYPNGVLGSMSTR 124.32 4.00E-08 63390000 18114 26950 11078 7865.9 39796 35142 24461 24065 27881 TRUE FALSE 15720.189 26772.96368 16435.35785 9651.972818 39004.13746 36493.93548 22088.77598 18918.88702 24584.93994 0.639423527 1.088998539 0.66851324 0.392596965 1.586505298 1.484402059 0.898467763 0.769531553 1 14.58548721 3.254061953 24.99994246 1.098632765 0.723293618 0.353317953 0.297783643 365.4680469 589408.9379 0.095867221 0.123312728 1794.989668 -3.254061953 -0.375339147 SQHSGNAQVTQTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SQHSGNAQVTQTK 13 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ;; 170.79 2.62E-05 207171000 444890 407880 155885 287177 370950 362572 428660 510740 464290 FALSE TRUE 386096.6593 405200.6094 231271.5074 352384.9271 363568.8208 376520.3795 387088.6192 401522.2256 409402.1651 0.943074298 0.989737339 0.564900548 0.860730492 0.888048114 0.91968341 0.945497245 0.98075257 1 18.64315921 2.564459113 1.388840742 0.98307674 0.835535166 0.22488923 0.110920316 0.656999195 2.61648492 0.064134289 0.044358072 366.8251579 -2.564459113 -0.147541574 SQIDVALS(ph)QDSTYQGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQIDVALSQDSTYQGER 17 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 1 SQIDVALS(0.989)QDS(0.011)TYQGER;SQIDVALS(0.962)QDS(0.037)T(0.001)YQGER;SQIDVALS(1)QDSTYQGER;SQIDVALS(0.997)QDS(0.003)TYQGER 322.71 1.03E-58 1132010000 487710 503331 325392 360232 551302 621963 511509 530306 581274 TRUE FALSE 423257.8878 500024.5855 482752.6596 442028.1814 540332.1688 645890.3191 461902.9359 416904.1887 512556.4499 0.825778093 0.975550275 0.941852667 0.862399023 1.054190556 1.260134994 0.90117476 0.813381997 1 18.96735138 4.740963196 23.09959994 0.966557728 0.825777958 0.12599869 0.122139943 198.1361568 1904606.444 0.032413994 0.209739836 55076.102 -4.740963196 -0.14077977 SQIHDIVLVGGSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SQIHDIVLVGGSTR 14 0 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;; 159.34 4.93E-06 21454180000 16475150 15864260 7298610 11673650 16625120 17619900 14763180 17225710 17311030 FALSE TRUE 14297917.18 15760046.63 10828242.21 14324330.65 16294312.64 18297748.95 13331449.08 13542125.97 15264539.75 0.936675289 1.032461305 0.709372335 0.93840567 1.067461771 1.198709509 0.873360697 0.887162416 1 23.86368076 SQIYGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQIYGSR 7 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;; 148.99 0.0047618 878350000 1064640 1091430 563460 725460 995600 1120440 1010760 1126690 955560 FALSE TRUE 923945.1265 1084260.324 835951.1407 890186.781 975789.5079 1163544.052 912736.6508 885756.1114 842594.7854 1.096547406 1.286811102 0.992115255 1.056482661 1.158076842 1.38090583 1.083245074 1.051224298 1 19.68447946 2.010518598 24.99954165 1.040660065 1.161268909 0.210083144 0.110331945 343.7469955 816979.9325 0.046426998 0.031267127 102.4515652 -2.010518598 0.120608843 SQKPVMVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQKPVMVK 8 1 P46779 P46779 RPL28 60S ribosomal protein L28 0 ; 101.65 0.0047853 960370000 1575120 1453640 951410 1120650 1397650 1264710 1847390 1971130 1930120 FALSE TRUE 1366963.901 1444090.943 1411515.058 1375110.711 1369839.499 1313364.212 1668230.402 1549619.189 1701943.412 0.803178232 0.848495275 0.82935487 0.807965001 0.804867829 0.771685006 0.980191462 0.910499831 1 20.69875164 2.234981672 24.99999951 0.953201618 0.813060069 0.849931668 0.030121599 34.27704051 239431.1822 0.011852274 0.00834652 171.7835888 -2.234981672 -0.140141549 SQLDDHPES(ph)DDEENFIDANDDEDMEKFTDADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQLDDHPESDDEENFIDANDDEDMEKFTDADK 32 1 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 1 SQLDDHPES(1)DDEENFIDANDDEDMEKFTDADK 208.55 1.95E-27 25385000 34910 24440 28480 27435 24016 20168 30692 38273 35612 TRUE FALSE 30296.55505 24279.45203 42253.02326 33664.53607 23538.12859 20943.87601 27715.49456 30088.61679 31401.98993 0.964797298 0.773181957 1.345552411 1.072051043 0.749574426 0.666960153 0.882603129 0.958175481 1 14.93856836 3.254319494 24.9906129 0.857912149 1.041820222 0.237173022 0.166772402 395.8526398 627744.1297 0.050988902 0.065600576 1796.054429 -3.254319494 0.183908073 SQLDIIIHSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQLDIIIHSLK 11 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 135.6 0.00011667 731140000 1011000 803550 586910 738840 765780 708310 908990 1006000 1314000 FALSE TRUE 877393.7885 798271.4271 870741.6391 906604.9145 750542.4762 735559.144 820836.2897 790874.7287 1158660.417 0.757248436 0.688960644 0.751507194 0.782459555 0.647767426 0.634835827 0.708435602 0.682576808 1 20.14402637 1.235940713 24.99962744 1.000000391 0.704794479 0.793659479 0.046986124 33.0124295 314946.0343 0.079368082 0.01193034 17.21633531 -1.235940713 -0.295205912 SQLDIIIHSLKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQLDIIIHSLKK 12 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 163.27 3.92E-05 820930000 2215400 1692180 956570 1309900 1503270 1164670 2159480 2372300 1072360 FALSE TRUE 1922629.277 1681063.958 1419170.452 1607332.816 1473357.868 1209475.609 1950053.962 1865002.106 945586.8224 2.033265726 1.777799688 1.50083569 1.699825735 1.558141287 1.279074094 2.062268547 1.972322437 1 19.8508504 4.61322219 3.234192391 1.634770091 2.044297019 0.168525638 0.308508362 0.573128885 9.723357603 0.078803597 0.482801873 41041.40219 -4.61322219 0.409526928 SQLEEKENK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQLEEKENK 9 1 P04080;A0A1W2PS52 P04080 CSTB Cystatin-B 0 ; 112.13 0.0018361 274800000 286718 207431 167649 151914 165153 172464 281898 372590 276792 FALSE TRUE 248827.4898 206068.3721 248724.6172 186408.3956 161866.7784 179098.8017 254559.5753 292914.528 244069.9651 1.019492463 0.844300412 1.019070974 0.763749835 0.663198269 0.733801071 1.042977882 1.200125251 1 17.89693524 2.08823854 5.665467493 1.1164198 0.8383526 0.466321219 0.121868527 0.167734387 8.471690209 0.0536838 0.035616614 122.5289014 -2.08823854 -0.278067199 SQLLGSAHEVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQLLGSAHEVQR 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 163.33 6.03E-05 1780990000 2184380 2365380 1151410 1755300 2487810 2577090 2621940 2745960 2537960 FALSE TRUE 1895708.648 2349841.663 1708235.727 2153867.693 2438307.448 2676232.32 2367664.662 2158757.823 2237925.26 0.847083092 1.050008999 0.763312233 0.962439511 1.089539267 1.195854199 1.057973072 0.964624629 1 21.09373042 3.436847603 5.752002441 1.054491849 0.89664635 0.430846347 0.091976779 0.195214149 16.33248665 0.027579632 0.03629684 2734.309067 -3.436847603 -0.157845498 SQLQALHIGLDSSS(ph)IGS(ph)GPGDAEADDGFPESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQLQALHIGLDSSSIGSGPGDAEADDGFPESR 32 0 O75116;E9PF63;Q14DU5 O75116 ROCK2 Rho-associated protein kinase 2 2 SQLQALHIGLDS(0.078)S(0.439)S(0.484)IGS(0.999)GPGDAEADDGFPESR;SQLQALHIGLDS(0.062)S(0.21)S(0.733)IGS(0.995)GPGDAEADDGFPESR;SQLQALHIGLDS(0.021)S(0.069)S(0.912)IGS(0.998)GPGDAEADDGFPESR;SQLQALHIGLDS(0.302)S(0.334)S(0.369)IGS(0.995)GPGDAEADDGFPESR 109.01 2.25E-06 272726000 125498 143172 67850.7 101763 148500 150975 129701 159389 138093 TRUE FALSE 108913.1213 142231.4937 100663.5255 124869.8445 145545.1405 156783.1059 117122.617 125304.9027 121767.8029 0.894432837 1.168055023 0.826684256 1.025475056 1.195267855 1.287557977 0.961852101 1.029047907 1 16.89377319 3.473637183 24.98745183 1.088403476 0.973977552 0.183119592 0.12654589 203.2352066 1457572.308 0.037296512 0.048391002 2976.029163 -3.473637183 -0.114425924 SQLQALHIGLDSSS(ph)IGSGPGDAEADDGFPESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQLQALHIGLDSSSIGSGPGDAEADDGFPESR 32 0 O75116;E9PF63;Q14DU5 O75116 ROCK2 Rho-associated protein kinase 2 1 SQLQALHIGLDS(0.025)S(0.164)S(0.81)IGSGPGDAEADDGFPESR;SQLQALHIGLDS(0.033)S(0.188)S(0.777)IGS(0.002)GPGDAEADDGFPESR;SQLQALHIGLDS(0.081)S(0.171)S(0.668)IGS(0.081)GPGDAEADDGFPESR;S(0.005)QLQALHIGLDS(0.118)S(0.393)S(0.467)IGS(0.016)GPGDAEADDGFPESR 177.41 1.35E-19 673870000 189714 186179 82248 140163 206721 196840 168437 208276 170731 TRUE FALSE 164642.8142 184955.9779 122023.4079 171989.1514 202607.6565 204412.5622 152102.0057 163737.7982 150547.3757 1.093627926 1.228556639 0.810531617 1.142425437 1.345806632 1.357795586 1.010326517 1.087616423 1 17.19985803 SQNKEDYAGLKEEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQNKEDYAGLKEEFR 15 2 Q5TA02;P78417-3;P78417 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 ; 122.96 5.94E-05 1281100000 1778700 1667770 1349670 1502970 1559010 1259150 1976500 2288740 2231840 FALSE TRUE 1543640.288 1656814.309 2002374.926 1844242.31 1527988.751 1307590.315 1784819.334 1799310.762 1967994.418 0.78437229 0.841879578 1.01746982 0.937117653 0.776419251 0.664427858 0.906922966 0.914286517 1 20.9082947 1.546423349 2.202239797 0.995001401 0.846249073 0.217515002 0.095817619 0.613708882 5.613155997 0.154602958 0.028827668 35.19033075 -1.546423349 -0.148752327 SQPERDWVLNEFR ddPTM_MDA-MB-175_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 ; 212.11 1.51E-08 954200000 964020 832500 270335 279497 757370 798930 738450 940320 52522 FALSE TRUE 836622.3145 827031.2527 401069.9102 342961.0657 742299.8188 829665.3541 666835.2327 739239.8856 46312.90899 18.06455981 17.85746719 8.660002555 7.405301743 16.02792472 17.91434337 14.39847436 15.96185387 1 15.49912676 1.234627112 24.99897513 0.999980548 14.44610404 0.566440947 3.721008379 95.54317938 607127.2926 7.178346088 0.971215869 17.16434014 -1.234627112 13.4461235 SQPFVDHVFTFTILDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQPFVDHVFTFTILDNR 17 0 Q8TDN6 Q8TDN6 BRIX1 Ribosome biogenesis protein BRX1 homolog 0 ; 143.39 5.51E-07 554980000 374570 334530 210790 287530 344650 364640 314230 406920 376700 FALSE TRUE 325069.6255 332332.4504 312728.7491 352818.0811 337792.1393 378667.9368 283756.023 319903.3247 332166.9551 0.978633246 1.000498229 0.941480615 1.062170922 1.01693481 1.139992798 0.85425723 0.96307992 1 18.34154903 2.222844322 24.99946376 0.940570043 1.020009872 0.281815111 0.063184956 332.7685792 529321.5866 0.025605259 0.01732752 167.0491698 -2.222844322 0.079439829 SQPPGEDS(ph)DT(ph)DVDDDSRPPGRPAEVHLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQPPGEDSDTDVDDDSRPPGRPAEVHLER 29 2 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 2 SQPPGEDS(1)DT(1)DVDDDSRPPGRPAEVHLER 143.48 1.34E-07 548850000 78492 57085 51682 57468 62465 66226 44906 70386 58759 TRUE FALSE 68119.08333 56710.00488 76675.58807 70516.98774 61222.06871 68773.75707 40551.02303 55334.50164 51812.57796 1.314720981 1.09452197 1.479864371 1.361001334 1.181606303 1.327356402 0.782648242 1.067974299 1 15.66101475 2.255822017 24.99974009 0.967760613 1.290645886 0.628678293 0.123999949 152.6261603 221048.6191 0.045240333 0.034957374 180.2278978 -2.255822017 0.322885274 SQPPGEDS(ph)DTDVDDDSRPPGRPAEVHLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQPPGEDSDTDVDDDSRPPGRPAEVHLER 29 2 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 SQPPGEDS(0.995)DT(0.005)DVDDDSRPPGRPAEVHLER 201.71 1.62E-25 569680000 12910 11765 5907.2 9696.3 11553 12064 8693.8 12854 9583.7 TRUE FALSE 11203.91079 11687.71494 8763.941678 11897.99311 11323.1179 12528.10989 7850.676614 10105.27213 8450.725904 1.325792709 1.38304272 1.037063772 1.407925573 1.339898848 1.4824892 0.92899435 1.195787468 1 13.04485956 2.235830018 24.99999955 1.069025951 1.322571333 0.506696153 0.132825335 63.7001689 583193.5705 0.051453281 0.036460631 172.1194771 -2.235830018 0.253545382 SQPVYIQYSNHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQPVYIQYSNHR 12 0 O95758-1;O95758-6;O95758;O95758-5;O95758-4;O95758-2;O95758-7;X6R242 O95758-1 PTBP3 Polypyrimidine tract-binding protein 3 0 85.554 0.011608 151240000 173330 166710 55857 116610 202350 201080 165570 197160 142480 FALSE TRUE 150424.0013 165614.871 82869.63203 143088.0828 198323.6309 208815.6777 149513.0469 154998.8683 125636.1767 1.197298463 1.318210052 0.659600079 1.138908287 1.578555127 1.662066478 1.19004773 1.233712075 1 16.93889242 3.463144007 24.88882523 1.329183042 1.053503663 0.210882529 0.248493033 358.4562345 638288.9138 0.075136194 0.097046507 2904.985757 -3.463144007 -0.275679379 GPVSGT(ph)EPEPVYSMEAADYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPVSGTEPEPVYSMEAADYR 20 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 GPVS(0.014)GT(0.986)EPEPVYSMEAADYR 258.68 3.24E-35 119550000 56656 80133 75249 81335 113310 156820 139430 146740 136950 TRUE FALSE 49168.76605 79606.60105 111639.6681 99803.35488 111055.3527 162852.9669 125908.1001 115360.7929 120759.927 0.407161277 0.659213723 0.924476114 0.826460874 0.919637461 1.348567947 1.042631469 0.95529035 1 16.88178226 4.772499624 0.777145219 1.049543821 7.02E-18 0.737312432 0.125758033 1.530245013 0.692653342 0.052490376 1.418828785 59224.25747 -4.772499624 -1.049543821 down SQQLSNDHICYFLYQILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQQLSNDHICYFLYQILR 18 0 P27361;E9PBK7;E9PQW4;P27361-3;P27361-2;E9PJF0;B3KR49;H0YDH9 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 141.22 1.21E-07 307440000 176600 177980 106900 126220 168500 159250 214610 218640 197690 FALSE TRUE 153261.8626 176810.8377 158597.1976 154880.1802 165147.1797 165376.4505 193797.1552 171885.5375 174319.3134 0.879201848 1.014292876 0.909808526 0.888485487 0.947383147 0.948698382 1.111736568 0.986038403 1 17.41137289 2.450658928 24.64575151 1.026766085 0.931309192 0.487810398 0.04916089 161.2839522 150210.9722 0.017645197 0.013668273 282.2662336 -2.450658928 -0.095456893 SQQQPTPVT(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQQQPTPVTPK 11 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 SQQQPTPVT(1)PK;SQQQPTPVT(1)PK;SQQQPTPVT(1)PK;SQQQPTPVT(1)PK 228.17 3.87E-11 2278320000 3757460 2718740 1744960 2115630 2812000 2248150 3076200 3669570 3313940 TRUE FALSE 3260902.141 2700880.418 2588828.493 2596016.127 2756046.702 2334637.785 2777870.597 2884861.012 2922169.788 1.115918094 0.924272241 0.885926787 0.888386478 0.943150775 0.798939813 0.950619163 0.987232509 1 21.47860858 1.828614651 3.975997193 0.992948759 0.920283107 0.10153082 0.078991038 0.468445643 12.3299953 0.04657578 0.021191719 67.39297849 -1.828614651 -0.072665652 SQS(ph)DLSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SQSDLSSR 8 0 Q1W6H9 Q1W6H9 FAM110C Protein FAM110C 1 SQS(0.998)DLS(0.002)SR;SQS(0.998)DLS(0.002)SR;S(0.005)QS(0.964)DLS(0.029)S(0.001)R;SQS(1)DLSSR;S(0.062)QS(0.937)DLS(0.001)SR;S(0.062)QS(0.938)DLSSR;SQS(0.997)DLS(0.003)SR;SQS(1)DLSSR 186.82 0.00014329 3896242000 13027160 12837300 7561920 8616850 8984250 12028170 12569050 12871550 13339290 TRUE FALSE 11305587.8 12752970.93 11218889.81 10573437.49 8805481.002 12490901.48 11350105.47 10119069.2 11762334.33 0.961168717 1.084221088 0.953797902 0.898923393 0.748616793 1.061940694 0.964953482 0.860294302 1 23.48767107 4.036681476 7.543572659 0.917848042 1.022532834 0.177008757 0.087950616 0.331540716 55.0058462 0.022219413 0.046254206 10881.31733 -4.036681476 0.104684791 AEDTAVYYCAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 210.6 2.84E-08 594520000 2777500 991690 171943 83863 74469 51221 47006 64478 62067 FALSE TRUE 2410446.338 985175.5231 255095.2099 102905.3759 72987.2126 53191.50501 42447.36535 50689.88147 54729.50997 44.04290006 18.00081023 4.661017613 1.880253925 1.333598869 0.971898068 0.775584605 0.926189208 1 15.74003132 4.776722162 1.416462948 0.950593721 64.86523399 0.999268711 0.37083987 0.036976436 0.062889535 0.124090719 3.446989347 59802.88865 -4.776722162 63.91464027 up SQS(ph)DRTEYNQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQSDRTEYNQK 11 1 Q9NXL2-1;Q9NXL2 Q9NXL2-1 ARHGEF38 Rho guanine nucleotide exchange factor 38 1 S(0.002)QS(0.998)DRTEYNQK;S(0.009)QS(0.991)DRTEYNQK 177.39 4.85E-06 707680000 491510 441080 295970 332220 382540 340730 476340 556440 524220 TRUE FALSE 426555.7082 438182.5164 439102.082 407655.6287 374928.2024 353838.1036 430144.6201 437449.6362 462247.3088 0.922786785 0.947939573 0.949928909 0.881899409 0.811098724 0.765473583 0.930550837 0.946354101 1 18.81830539 1.678381791 2.464927545 0.988015722 0.882496454 0.299210654 0.058779634 0.368923977 4.827192906 0.06361343 0.01829321 47.68500041 -1.678381791 -0.105519268 SQS(ph)ES(ph)SDEVTELDLSHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQSESSDEVTELDLSHGK 18 0 Q86YS7;Q86YS7-5;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 2 S(0.031)QS(0.966)ES(0.555)S(0.449)DEVTELDLSHGK 111.53 8.30E-05 0 100030 133560 123180 140250 154320 135190 180650 205860 293730 TRUE FALSE 86810.78206 132682.6356 182750.26 172095.9061 151249.3339 140390.8468 163130.5908 161838.441 259005.574 0.335169551 0.512277143 0.705584274 0.664448658 0.583961695 0.542037936 0.629834286 0.624845398 1 17.98262362 0.957221463 1.83695107 1.519527274 0.572232053 0.641095931 0.10062215 1.467839195 2.408382757 3.159621074 0.028492092 9.061945853 -0.957221463 -0.94729522 SQS(ph)ESSDEVTELDLSHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQSESSDEVTELDLSHGK 18 0 Q86YS7;Q86YS7-5;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 S(0.113)QS(0.886)ES(0.001)S(0.001)DEVTELDLSHGK;S(0.055)QS(0.942)ES(0.003)S(0.001)DEVTELDLSHGK 257.11 8.35E-31 602020000 629830 494000 338030 377580 433410 310210 505190 497190 665190 TRUE FALSE 546596.3697 490754.8815 501502.4386 463315.3099 424785.989 322143.9794 456196.7516 390869.7876 586551.996 0.931880504 0.836677541 0.855000822 0.7898964 0.724208581 0.549216406 0.777760121 0.666385572 1 19.16189948 3.629424954 2.129739934 0.727652181 0.878099484 0.209828568 0.114114265 0.461846319 4.099944802 0.033759056 0.059014201 4260.150623 -3.629424954 0.150447303 SQS(ph)ESSDEVTELDLSHGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SQSESSDEVTELDLSHGKK 19 1 Q86YS7;Q86YS7-5;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 S(0.062)QS(0.935)ES(0.002)S(0.001)DEVTELDLSHGKK;S(0.189)QS(0.807)ES(0.002)S(0.002)DEVT(0.001)ELDLSHGKK;S(0.073)QS(0.853)ES(0.073)SDEVTELDLSHGKK 226.9 6.56E-20 1270490000 2479944 1673939 911605 1034267 1264898 838624 2030036 1961816 638210 TRUE FALSE 2152213.117 1662942.784 1352460.227 1269113.13 1239729.005 870886.4079 1833163.421 1542296.915 562761.5409 3.824378464 2.954968781 2.403256315 2.255152561 2.202938393 1.547522964 3.257442608 2.740586915 1 19.10216421 4.633885811 1.639934266 2.268367853 4.196581631 0.433997051 0.608950212 0.841766444 2.593427967 0.169825329 2.419043051 43041.34269 -4.633885811 1.928213778 SQS(ph)FSHQQPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SQSFSHQQPSR 11 0 B3KNS5;Q8WVR3-2;Q8WVR3-3;Q8WVR3 B3KNS5 C7orf43 Uncharacterized protein C7orf43 1 S(0.228)QS(0.732)FS(0.04)HQQPSR;S(0.122)QS(0.861)FS(0.017)HQQPSR;S(0.001)QS(0.79)FS(0.208)HQQPS(0.002)R;S(0.049)QS(0.902)FS(0.049)HQQPSR;S(0.175)QS(0.755)FS(0.07)HQQPSR;SQS(0.99)FS(0.009)HQQPSR 171.81 9.08E-06 3347468000 1910549 1903977 1010790 1279099 1979322 2183685 1919977 2031187 2080663 TRUE FALSE 1658065.109 1891469.65 1499611.425 1569537.978 1939937.365 2267692.775 1733777.926 1596833.467 1834689.39 0.90373069 1.030948159 0.81736529 0.855478854 1.057365555 1.236009096 0.944998066 0.870356299 1 20.80710441 3.238561364 25 1.0077792 0.90506303 0.230095226 0.107203379 0.086533264 1345764.656 0.035604853 0.04304419 1732.053747 -3.238561364 -0.10271617 SQS(ph)FSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQSFSK 6 0 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2 A0A0X1KG75;REV__E7ESW5 COBLL1 Cordon-bleu protein-like 1 1 SQS(0.998)FS(0.002)K;SQS(0.996)FS(0.004)K;SQS(0.984)FS(0.016)K;SQS(0.998)FS(0.002)K 104.01 0.035868 2310050000 3259950 3326840 2375010 2948070 2497350 3214650 4412700 4819900 4860200 TRUE FALSE 2829139.348 3304985.769 3523572.78 3617474.352 2447657.621 3338319.666 3984757.033 3789201.894 4285632.693 0.660145083 0.771178028 0.822182635 0.844093419 0.571130985 0.778956085 0.929794343 0.884163942 1 22.03107678 2.292291171 4.657597071 0.927360717 0.740780047 0.561464347 0.082344687 0.160902572 7.239908329 0.032735583 0.02428189 196.0158414 -2.292291171 -0.186580671 DNLGEVPLT(ph)PTEEASLPLAVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DNLGEVPLTPTEEASLPLAVTK 22 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 DNLGEVPLT(0.856)PT(0.144)EEASLPLAVTK;DNLGEVPLT(0.489)PT(0.489)EEAS(0.023)LPLAVTK 110.4 0.0013187 74816000 137122 227540 179634 245560 323850 253190 365210 478450 401450 TRUE FALSE 119000.9803 226045.2748 266505.6032 301318.1511 317406.0186 262930.3831 329791.9904 376137.1908 353991.0383 0.336169472 0.638562139 0.752859746 0.851202767 0.89664987 0.742759999 0.931639377 1.062561337 1 18.43335331 4.77684768 0.572862248 0.976611437 1.23E-33 0.849261623 0.080291916 1.735446844 0.437605847 0.053521915 1.147611801 59820.17505 -4.77684768 -0.976611437 down SQS(ph)GEDESMNQPGPIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQSGEDESMNQPGPIK 16 0 A0A0C4DG33;O43933-2;O43933 A0A0C4DG33 PEX1 Peroxisome biogenesis factor 1 1 S(0.004)QS(0.996)GEDESMNQPGPIK;SQS(1)GEDESMNQPGPIK;S(0.033)QS(0.967)GEDESMNQPGPIK;SQS(1)GEDESMNQPGPIK 340.52 5.18E-72 655760000 1423910 1130200 866880 1005240 1212270 1076530 1333360 1514770 1730160 TRUE FALSE 1235736.686 1122775.642 1286106.068 1233495.106 1188148.199 1117944.806 1204050.952 1190848.223 1525622.456 0.809988527 0.735945933 0.843004154 0.808519238 0.778795694 0.732779464 0.789219474 0.780565479 1 20.54096655 1.237996843 24.99323633 1.000000246 0.78406798 0.808315799 0.032924254 5.691901304 252107.5805 0.045416652 0.007891347 17.29803787 -1.237996843 -0.215932266 SQS(ph)IEQESQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SQSIEQESQEK 11 0 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 SQS(1)IEQESQEK;SQS(0.997)IEQES(0.003)QEK;SQS(1)IEQESQEK;SQS(1)IEQESQEK;SQS(1)IEQESQEK 295.29 1.49E-35 1265510000 3914240 2672600 1848700 2106810 2505910 2091730 2998280 3539260 3301730 TRUE FALSE 3396963.267 2655043.515 2742737.504 2585193.411 2456047.294 2172200.207 2707507.267 2782416.792 2911403.241 1.166778693 0.911946335 0.942067202 0.887954432 0.843595713 0.746100772 0.929966426 0.955696124 1 21.47328324 4.745263448 4.455103325 0.900601308 1.186477221 0.592871925 0.068960444 0.165674209 8.172318758 0.018512386 0.150178326 55624.15781 -4.745263448 0.285875913 SQS(ph)LNIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 129.63 0.0038206 867140000 1321890 1320390 778610 922580 1161900 1207990 1253320 1290140 1354190 TRUE FALSE 1147198.887 1311716.271 1155148.4 1132065.89 1138780.463 1254462.157 1131773.219 1014253.601 1194099.201 0.960723269 1.098498575 0.967380599 0.948050119 0.953673248 1.05055104 0.947805022 0.849388058 1 20.18749126 2.506792541 0.50362108 0.901812802 1.018741411 0.101138801 0.062845545 2.471186859 1.534656839 0.180598139 0.086244066 321.2125763 -2.506792541 0.116928609 SQS(ph)LPHSATVTLGGTSDPSTLSSSALSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQSLPHSATVTLGGTSDPSTLSSSALSER 29 0 A0A0A0MRY0;Q8WUA7-3;Q8WUA7-4;Q8WUA7;F8WDP1 A0A0A0MRY0 TBC1D22A TBC1 domain family member 22A 1 S(0.227)QS(0.773)LPHS(0.001)ATVTLGGTSDPSTLSSSALSER;S(0.212)QS(0.788)LPHSATVTLGGTSDPSTLSSSALSER;S(0.243)QS(0.757)LPHSATVTLGGTSDPSTLSSSALSER;S(0.206)QS(0.794)LPHSATVTLGGTSDPSTLSSSALSER 328.01 3.01E-105 2359610000 792790 599430 299187 490739 568695 426051 720530 656800 631560 TRUE FALSE 688020.7928 595492.3049 443874.8339 602168.7904 557379.0821 442441.4577 650653.1115 516348.4312 556897.6963 1.235452754 1.06930287 0.797049147 1.081291581 1.000864406 0.794475288 1.168353031 0.927187228 1 19.0870528 4.594328771 3.927101171 0.971395501 1.229603716 0.357596583 0.114388566 0.244946202 6.027891622 0.026313723 0.130521748 39294.22892 -4.594328771 0.258208215 SQS(ph)LPNSLDYTQTSDPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SQSLPNSLDYTQTSDPGR 18 0 Q96TC7;H0YLG5;H0YNE5 Q96TC7 RMDN3 Regulator of microtubule dynamics protein 3 1 SQS(1)LPNSLDYTQTSDPGR;SQS(1)LPNSLDYTQTSDPGR;SQS(1)LPNSLDYTQTSDPGR;SQS(1)LPNSLDYTQTSDPGR;SQS(1)LPNSLDYTQTSDPGR;S(0.002)QS(0.998)LPNSLDYTQTSDPGR;S(0.02)QS(0.98)LPNSLDYTQTSDPGR 424.46 1.01E-168 13150040000 3318007 2942860 2140492 3058915 3913720 5103600 2198379 3990748 4026360 TRUE FALSE 2879523.968 2923528.159 3175641.091 3753488.403 3835844.629 5299938.794 1985180.543 3137357.596 3550368.308 0.811049367 0.823443628 0.894453988 1.057210993 1.080407523 1.492785631 0.559147776 0.883671024 1 21.75953726 3.99498863 3.795592191 0.993160152 0.820695748 0.112683808 0.226615832 0.581681748 18.64956326 0.063641452 0.132055009 9885.272137 -3.99498863 -0.172464404 SQS(ph)LPTTLLS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQSLPTTLLSPVR 13 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7 E9PHV5 SSFA2 Sperm-specific antigen 2 2 S(0.033)QS(0.965)LPT(0.18)T(0.147)LLS(0.676)PVR 66.201 0.08262 29054000 88484 87149 47852 70372 91437 86116 92920 108080 93418 TRUE FALSE 76790.61521 86576.51248 70993.38726 86351.03817 89617.58259 89428.93824 83908.6327 84967.93308 82374.23046 0.932216481 1.051014522 0.861839763 1.048277328 1.087932259 1.085642169 1.018627212 1.031486821 1 16.32990546 SQS(ph)LPTTLLSPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SQSLPTTLLSPVR 13 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7 E9PHV5 SSFA2 Sperm-specific antigen 2 1 S(0.059)QS(0.896)LPT(0.022)T(0.022)LLS(0.001)PVR;S(0.004)QS(0.483)LPT(0.169)T(0.343)LLSPVR;SQS(0.998)LPT(0.001)T(0.001)LLSPVR;SQS(0.995)LPT(0.003)T(0.002)LLSPVR;S(0.035)QS(0.943)LPT(0.009)T(0.013)LLSPVR 149.37 4.46E-05 2349970000 2213490 2458900 1013959 1240583 2127170 1873060 2030780 2295150 2164960 TRUE FALSE 1920971.688 2442747.324 1504312.964 1522276.331 2084843.479 1945117.83 1833835.268 1804350.033 1909020.895 1.006260169 1.27958124 0.788002356 0.797412084 1.092100922 1.018908612 0.960615608 0.945170395 1 20.86440146 4.242559742 24.99999977 0.947103608 1.142920656 0.351640121 0.112663516 111.5804387 697503.391 0.02826071 0.069214225 17480.73713 -4.242559742 0.195817048 SQS(ph)MDIDGVSCEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQSMDIDGVSCEK 13 0 O95155-2;O95155;O95155-4 O95155-2 UBE4B Ubiquitin conjugation factor E4 B 1 S(0.006)QS(0.994)MDIDGVSCEK;SQS(1)MDIDGVSCEK 288.42 1.55E-33 339080000 1690220 1097560 694490 917500 1067860 670720 1824650 1534000 1287370 TRUE FALSE 1466853.145 1090350.056 1030347.687 1125832.398 1046611.675 696523.0324 1647695.724 1205966.038 1135178.585 1.292178309 0.960509712 0.907652505 0.991766769 0.921979756 0.613580138 1.451485912 1.062357988 1 20.11448785 0.922104412 12.76238684 0.75855071 1.024505292 0.001233612 0.224496204 2305995.792 11006490.32 15887097.07 0.054040654 8.358039366 -0.922104412 0.265954582 SQS(ph)NPILGSPFFSHFDGQDSYAAAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQSNPILGSPFFSHFDGQDSYAAAVR 26 0 Q9NYL2 Q9NYL2 ZAK Mitogen-activated protein kinase kinase kinase MLT 1 S(0.002)QS(0.998)NPILGSPFFSHFDGQDSYAAAVR;S(0.005)QS(0.995)NPILGSPFFSHFDGQDSYAAAVR 408.27 2.82E-165 267550000 105438 88847 39892 60846 72910 73431 77243 86751 74779 TRUE FALSE 91504.10115 88263.35821 59183.90463 74662.01427 71459.23365 76255.93809 69751.98575 68199.97375 65938.71181 1.387714419 1.338566614 0.897559309 1.132294099 1.083722015 1.156466907 1.05783058 1.03429339 1 16.00883808 4.33654399 7.275507556 1.058685857 1.372809742 0.765664745 0.071677914 0.09779136 6.244960924 0.017420626 0.046604394 21704.21038 -4.33654399 0.314123884 SQS(ph)PAASDCSSSSSSASLPSSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SQSPAASDCSSSSSSASLPSSGR 23 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 SQS(1)PAASDCSSSSSSASLPSSGR;S(0.004)QS(0.996)PAASDCSSSSSSASLPSSGR;S(0.004)QS(0.996)PAASDCSSSSSSASLPSSGR;S(0.008)QS(0.992)PAASDCSSSSSSASLPSSGR;S(0.002)QS(0.998)PAASDCSSSSSSASLPSSGR;S(0.232)QS(0.768)PAASDCSSSSSSASLPSSGR 431.4 1.26E-179 7528410000 1733073 1611745 1011506 1256095 1778061 1761671 1703548 1877300 1705886 TRUE FALSE 1504043.012 1601157.341 1500673.685 1541310.568 1742681.065 1829443.623 1538338.177 1475854.004 1504218.1 0.999883602 1.064444937 0.997643682 1.024658969 1.158529514 1.216209021 1.022682932 0.981143628 1 20.52058233 2.010783605 24.99943752 0.9930314 1.077844922 0.226418715 0.067793001 322.3708798 747343.4943 0.030282258 0.020394974 102.5141003 -2.010783605 0.084813523 SQS(ph)PHYFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SQSPHYFR 8 0 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 SQS(1)PHYFR;SQS(1)PHYFR;S(0.009)QS(0.99)PHY(0.001)FR 128.88 0.00071792 1983940000 1632760 1511570 839700 1109160 1523900 1627710 1440810 1574310 1442000 TRUE FALSE 1416986.629 1501640.397 1245781.729 1361011.73 1493577.371 1690329.057 1301080.468 1237656.058 1271528.403 1.114396364 1.180972752 0.979751397 1.07037462 1.174631544 1.329367911 1.023241372 0.973360921 1 20.27813226 2.020892591 24.99984637 0.988834616 1.137784325 0.371181205 0.088416188 250.8574031 300172.0484 0.038048671 0.025649868 104.928289 -2.020892591 0.148949709 SQS(ph)PINCIRPSVLGPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQSPINCIRPSVLGPLK 17 1 Q96E09 Q96E09 FAM122A Protein FAM122A 1 S(0.004)QS(0.996)PINCIRPSVLGPLK 189.45 2.14E-10 869720000 682290 556660 402110 460310 531500 493460 653030 692190 890910 TRUE FALSE 592123.6478 553003.2638 596571.741 564830.4209 520924.1899 512443.7255 589699.2511 544170.5551 785587.6347 0.753733411 0.703935805 0.759395533 0.718990977 0.66310131 0.652306252 0.750647318 0.692692363 1 19.5834127 1.236376118 24.99991534 1.000000372 0.710848371 0.860830537 0.036409107 20.63695 236116.4849 0.057792573 0.008977683 17.23360435 -1.236376118 -0.289152001 SQS(ph)PINCIRPSVLGPLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQSPINCIRPSVLGPLKR 18 2 Q96E09 Q96E09 FAM122A Protein FAM122A 1 S(0.008)QS(0.992)PINCIRPSVLGPLKR 76.417 0.0079664 704490000 694970 484520 350000 395240 468960 444410 576290 633660 508690 TRUE FALSE 603127.9537 481337.1562 519261.1707 484985.2829 459628.6135 461506.7403 520401.4845 498156.7401 448553.2477 1.344607261 1.073088109 1.157635517 1.081221205 1.024691307 1.028878383 1.160177721 1.110585516 1 18.77491973 SQS(ph)SDLLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQSSDLLER 9 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 S(0.001)QS(0.914)S(0.086)DLLER;S(0.009)QS(0.935)S(0.056)DLLER 105.4 0.0032554 1247660000 2016500 1628100 841930 1231040 1414180 1245380 1775060 1688090 1099800 TRUE FALSE 1750014.416 1617404.904 1249090.164 1510566.447 1386040.585 1293290.574 1602914.954 1327105.09 969782.8969 1.804542461 1.667801019 1.288010098 1.557633623 1.429227706 1.333587732 1.652859583 1.368455862 1 19.88730229 7.999998419 0.046905758 1.85E-09 3.977507839 0.439653472 0.171960758 1452.286553 6.677705482 164.6604226 482.5859004 99999636.01 -7.999998419 3.977507837 SQS(ph)SSQFR ddPTM_MDA-MB-175_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(0.001)QS(0.568)S(0.341)S(0.091)QFR;S(0.003)QS(0.717)S(0.065)S(0.215)QFR 105.2 0.00465 1225060000 2209350 2153970 1255020 1499850 1818050 2403380 2250360 2064490 2557860 TRUE FALSE 1917378.8 2139820.429 1861951.87 1840413.866 1781874.362 2495839.584 2032120.434 1623014.879 2255472.705 0.850100644 0.948723709 0.825526226 0.815977007 0.790022579 1.106570511 0.900973188 0.719589679 1 21.1049984 SQS(ph)TSEQEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SQSTSEQEKR 10 1 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 SQS(0.904)T(0.094)S(0.002)EQEKR;S(0.006)QS(0.962)T(0.031)S(0.001)EQEKR;S(0.032)QS(0.937)T(0.032)SEQEKR 132.08 0.00014277 844811000 1469630 1089930 585092 775590 610262 670702 1594870 1416660 1046900 TRUE FALSE 1275414.672 1082770.178 868044.4482 951699.5637 598118.9802 696504.3399 1440199.753 1113718.283 923136.6746 1.381609795 1.172925102 0.940320618 1.030941127 0.647920288 0.754497529 1.560115411 1.206450046 1 19.81618474 0.955089245 16.77378194 0.502246024 1.08786056 0.010039386 0.270862595 1061205.151 10886379.73 19841793.79 0.070845312 9.017564233 -0.955089245 0.585614536 SQS(ph)TTFNPDDMSEPEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQSTTFNPDDMSEPEFK 17 0 F5GZP6;Q86W92-3;Q86W92-4;Q86W92;Q86W92-2 F5GZP6;Q86W92-2 PPFIBP1 Liprin-beta-1 1 S(0.001)QS(0.901)T(0.096)T(0.003)FNPDDMSEPEFK 343.13 7.89E-73 164730000 247300 226340 118230 162170 173330 104790 208750 245920 266610 TRUE FALSE 214618.6784 224853.1576 175406.4235 198993.1771 169881.0721 108821.3391 188505.4571 193331.9218 235091.6695 0.912914859 0.956448853 0.746119264 0.846449292 0.722616299 0.462888963 0.801838098 0.822368237 1 17.84286389 4.238535786 24.99999902 0.767766874 0.9346819 0.204018168 0.133612482 1.019724109 1030271.383 0.035448502 0.082343728 17319.51739 -4.238535786 0.166915026 SQS(ph)VPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQSVPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR 36 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 S(0.056)QS(0.944)VPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR;S(0.145)QS(0.848)VPAS(0.006)TGLGWGSGLVAPLQEGSIDSTLAGTQDTR;S(0.191)QS(0.809)VPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR;S(0.199)QS(0.801)VPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR 262.09 2.03E-62 645500000 142036 106242 59424 73644 113781 80670 170695 160144 131457 TRUE FALSE 123265.5827 105544.0893 88161.64516 90365.99578 111516.9807 83773.4271 154141.0252 125898.4518 115916.3032 1.063401604 0.910519801 0.760562947 0.77957969 0.962047422 0.722706166 1.329761396 1.08611514 1 16.82272396 2.245397298 24.99992116 1.135649853 0.86405286 0.500363262 0.128175601 126.4782742 462499.0766 0.047938865 0.036286109 175.9532522 -2.245397298 -0.271596993 SQS(ph)WEER ddPTM_MDA-MB-175_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;S(0.004)QS(0.996)WEER;S(0.002)QS(0.998)WEER;S(0.002)QS(0.998)WEER 140.49 0.0027495 3142600000 9095710 6831230 4752150 7063080 7683030 7162090 8320120 8775410 10300840 TRUE FALSE 7893688.878 6786355.2 7050305.635 8666860.266 7530152.735 7437620.237 7513236.043 6898856.862 9083086.43 0.869053591 0.747141982 0.776201536 0.954175691 0.829030175 0.818842834 0.827167737 0.759527823 1 23.11475118 3.084936131 0.011442047 1.66335513 7.61E-07 0.052226568 0.079045063 7130.634083 111.040325 8051.046217 8086.950528 1216.007156 -3.084936131 -1.663354369 SQSAAVT(ph)PSSTTSSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQSAAVTPSSTTSSTR 16 0 Q16186;A0A087WX59 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 1 SQSAAVT(0.545)PS(0.319)S(0.076)T(0.03)T(0.007)S(0.007)S(0.007)T(0.007)R;SQSAAVT(0.474)PS(0.474)S(0.051)TTSSTR 224.61 2.83E-13 0 384820 411400 254920 288740 411660 384540 389970 478440 401050 TRUE FALSE 333965.062 408697.4863 378200.1647 354302.8301 403468.7714 399333.5026 352150.7694 376129.3292 353638.3259 0.944368971 1.15569342 1.069454686 1.00187905 1.140907933 1.129214436 0.995793565 1.063598885 1 18.43191511 2.223374902 24.9999121 1.027922623 1.076931401 0.122975468 0.066144856 540.6212801 890005.6629 0.025800313 0.01747076 167.2533794 -2.223374902 0.049008777 SQSASVES(ph)IPEVLEECTSPADHSDSASVHDMDYVNPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SQSASVESIPEVLEECTSPADHSDSASVHDMDYVNPR 37 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 SQSAS(0.002)VES(0.997)IPEVLEECTSPADHSDSASVHDMDYVNPR;S(0.001)QSAS(0.002)VES(0.965)IPEVLEECT(0.001)S(0.031)PADHSDSASVHDMDYVNPR;S(0.001)QS(0.001)AS(0.027)VES(0.971)IPEVLEECTSPADHSDSASVHDMDYVNPR 239.57 1.39E-49 378026000 200388 232819 77146 151154 252203 268908 237586 257338 256007 TRUE FALSE 173906.2181 231289.5967 114454.0636 185475.8259 247184.6537 279253.0648 214544.9463 202308.2713 225742.1441 0.770375504 1.024574288 0.507012388 0.821626935 1.094986737 1.237044442 0.950398284 0.896191857 1 17.78431626 3.338443592 5.980170001 1.021239402 0.773531201 0.410536241 0.151952249 0.234549693 11.88796272 0.045906028 0.059322045 2179.935241 -3.338443592 -0.247708201 SQSASVESIPEVLEECT(ph)SPADHSDSASVHDMDYVNPR ddPTM_MDA-MB-175_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 SQSASVESIPEVLEECT(0.624)S(0.094)PADHS(0.186)DS(0.043)AS(0.053)VHDMDYVNPR;SQSASVES(0.001)IPEVLEECT(0.485)S(0.485)PADHS(0.027)DS(0.001)AS(0.001)VHDMDYVNPR 240.15 1.48E-49 205358000 92050 94806 43914.3 53530 115639 116762 112840 119906 112196 TRUE FALSE 79885.35928 94183.21314 65151.40236 65684.80465 113338.0101 121253.9097 101896.7942 94265.03501 98932.31669 0.807474867 0.951996438 0.658545201 0.663936789 1.145611605 1.225624889 1.029964703 0.952823487 1 16.59415424 3.235306209 24.999977 1.06073525 0.775457242 0.647103058 0.110035201 61.78306247 474610.2774 0.03654313 0.043167525 1719.120063 -3.235306209 -0.285278008 SQSASVESIPEVLEECTSPADHS(ph)DSASVHDMDYVNPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQSASVESIPEVLEECTSPADHSDSASVHDMDYVNPR 37 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 SQSASVES(0.084)IPEVLEECT(0.009)S(0.037)PADHS(0.629)DS(0.12)AS(0.12)VHDMDYVNPR 117.28 8.00E-06 93630000 39129 47741 14696 23356 50734 46526 39964 42308 42468 TRUE FALSE 33958.00351 47427.38623 21803.03476 28659.33677 49724.49266 48315.88533 36088.29743 33260.76344 37447.48142 0.906816753 1.266504033 0.58222967 0.765320809 1.327846113 1.290230571 0.963704262 0.888197608 1 15.19258107 3.273246286 24.99747524 1.068311522 0.886524912 0.190544919 0.215184345 396.3979331 285675.9152 0.066900489 0.086364328 1876.058109 -3.273246286 -0.18178661 SQSASVESIPEVLEECTSPADHSDS(ph)ASVHDMDYVNPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQSASVESIPEVLEECTSPADHSDSASVHDMDYVNPR 37 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 SQSASVESIPEVLEECT(0.001)S(0.004)PADHS(0.076)DS(0.46)AS(0.46)VHDMDYVNPR 106.44 3.40E-05 111220000 29972 36847 20077 19902 44353 41524 31461 39543 37521 TRUE FALSE 26011.12426 36604.94963 29786.30435 24421.05328 43470.46208 43121.45515 28409.91706 31087.03717 33085.31012 0.78618348 1.106380732 0.900287899 0.738123753 1.31389012 1.303341422 0.858686739 0.939602411 1 15.01390318 4.755202 23.36618359 1.011675575 0.786183038 0.137528901 0.182983282 3070.487934 4311097.478 0.046526141 1.130169648 56911.75781 -4.755202 -0.225492537 SQSDLDDQHDYDS(ph)VAS(ph)DEDTDQEPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQSDLDDQHDYDSVASDEDTDQEPLR 26 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 2 SQSDLDDQHDYDS(1)VAS(1)DEDTDQEPLR;SQSDLDDQHDYDS(1)VAS(1)DEDTDQEPLR 284.55 2.25E-61 1385940000 529990 486180 318501 374510 487620 505180 424790 494360 492410 TRUE FALSE 459950.4787 482986.2516 472529.1489 459548.2195 477917.316 524614.6015 383593.9312 388644.9611 434197.8508 1.059310814 1.112364446 1.088280718 1.058384372 1.100690193 1.208238596 0.883454238 0.895087252 1 18.72799306 2.224222914 24.99999974 0.917922431 1.101887603 0.727350223 0.051379278 114.6731875 199948.8884 0.020791634 0.014091049 167.580281 -2.224222914 0.183965172 SQSDLDDQHDYDSVAS(ph)DEDTDQEPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQSDLDDQHDYDSVASDEDTDQEPLR 26 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 SQSDLDDQHDYDSVAS(1)DEDTDQEPLR;SQSDLDDQHDYDSVAS(1)DEDTDQEPLR 264.85 3.15E-53 1463550000 1052520 813170 507510 621470 808070 727390 748800 894650 811250 TRUE FALSE 913426.8153 807828.2327 752943.5335 762584.2621 791990.988 755373.164 676181.4913 703336.0597 715344.9492 1.276903984 1.129284877 1.052560075 1.06603711 1.107145565 1.055956521 0.945252346 0.983212449 1 19.44827957 8 0.368174007 0.981258173 4.63380705 0.806179024 0.04050793 37.84561723 0.562737995 0.052359192 96.63316402 100000000 -8 3.652548877 SQSFNTDTTTSGISSMSS(ph)SPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQSFNTDTTTSGISSMSSSPSR 22 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 SQSFNTDTTTSGISSMS(0.001)S(0.455)S(0.455)PS(0.089)R 382.75 1.33E-131 165230000 163500 146910 115740 153560 186930 204050 156930 192730 269470 TRUE FALSE 141893.0607 145944.9385 171712.2511 188428.145 183210.4587 211899.9355 141710.9528 151516.1893 237613.5636 0.597158927 0.614211312 0.722653406 0.793002479 0.771043774 0.891783837 0.596392523 0.637657998 1 17.85825767 4.191000797 3.269559464 0.759266203 0.599570204 0.269847703 0.114603154 0.361996407 7.782654713 0.031002575 0.081881938 15523.89859 -4.191000797 -0.159695999 SQSFNTDTTTSGISSMSSS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQSFNTDTTTSGISSMSSSPSR 22 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 SQSFNTDTTTSGISSMSS(0.006)S(0.769)PS(0.225)R;SQSFNTDTTTSGISSMS(0.001)S(0.013)S(0.744)PS(0.242)R 423.16 1.89E-174 298340000 272870 308800 222231 313020 355310 371450 296060 381410 556550 TRUE FALSE 236809.5381 306771.4725 329702.6549 384095.9752 348240.0262 385739.9219 267348.1468 299848.4396 490755.293 0.482540976 0.62510069 0.671826997 0.782662929 0.709600143 0.786012759 0.544768748 0.610993796 1 18.9046443 4.659341234 1.676425802 0.713981787 0.424987532 0.302884232 0.121058538 1.153631212 3.613404293 0.033301093 0.512353057 45639.53743 -4.659341234 -0.288994254 GYYS(ph)PYSVSGSGSTAGS(ph)R ddPTM_MDA-MB-175_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(0.69)PY(0.215)S(0.095)VSGS(0.003)GS(0.165)T(0.197)AGS(0.635)R 230.63 1.80E-19 376810000 950490 533590 297750 170540 175550 240450 181140 175730 198910 TRUE FALSE 824880.3383 530084.8122 441742.8959 209263.7135 172056.8985 249700.2671 163573.0707 138151.507 175395.0864 4.702984304 3.022232966 2.518559128 1.193099065 0.980967609 1.423644597 0.932597794 0.787658935 1 17.42024881 4.787952625 0.755119297 0.909020187 7.215302685 0.965934749 0.230368719 0.474430223 0.199445689 0.093562828 2.589581015 61369.50568 -4.787952625 6.306282498 up SQSGGYSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SQSGGYSDR 9 0 Q14011;K7EMY9;K7EPM4;K7EQR7;D6W5Y5;Q14011-2;Q14011-3;F6WMK9 Q14011 CIRBP Cold-inducible RNA-binding protein 0 ;;; 207.29 2.77E-05 1382410000 1733200 1554820 777330 1018572 1075628 1519191 1411269 1520887 1399864 FALSE TRUE 1504153.229 1544606.285 1153249.388 1249854.34 1054225.107 1577635.261 1274404.35 1195657.151 1234373.673 1.218555825 1.251327956 0.93427899 1.012541314 0.854056701 1.278085636 1.03242995 0.968634683 1 20.23534777 4.248519397 24.9974711 1.012678467 1.234942015 0.425806538 0.107897116 192.0591928 482076.6821 0.026615755 0.068629647 17722.27196 -4.248519397 0.222263548 SQSPAAS(ph)DCSSSSSSASLPSSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQSPAASDCSSSSSSASLPSSGR 23 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 S(0.003)QS(0.442)PAAS(0.552)DCS(0.001)S(0.001)SSSSASLPSSGR 310.96 2.08E-58 0 17196 20230 11190 15716 20104 18584 19872 21035 19061 TRUE FALSE 14923.50503 20097.1078 16601.52143 19284.558 19703.96973 19298.93851 17944.8165 16536.82894 16807.63029 0.8879006 1.195713342 0.987737185 1.14736924 1.172322891 1.148224834 1.067658925 0.98388819 1 14.03682871 1.847546542 4.025624053 0.992410998 1.097087511 0.153680777 0.092228587 0.364556087 9.459540435 0.050583477 0.023519317 70.39576644 -1.847546542 0.104676513 SQSS(ph)DTEQQS(ph)PTSGGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 SQSS(1)DTEQQS(0.997)PT(0.003)SGGGK;SQS(0.03)S(0.97)DTEQQS(0.99)PT(0.01)SGGGK;SQS(0.154)S(0.845)DTEQQS(0.965)PT(0.033)S(0.002)GGGK;SQS(0.016)S(0.984)DTEQQS(0.987)PT(0.012)S(0.001)GGGK;SQS(0.01)S(0.99)DTEQQS(0.939)PT(0.061)SGGGK;SQS(0.043)S(0.957)DTEQQS(0.999)PT(0.001)SGGGK;SQS(0.024)S(0.976)DTEQQS(0.999)PT(0.001)SGGGK 344.6 3.06E-73 2824511000 5752400 5116600 3477042 4416792 5077909 4216801 6119440 7618700 6327640 TRUE FALSE 4992205.765 5082988.718 5158551.141 5419692.13 4976868.546 4379024.063 5525977.651 5989500.294 5579593.608 0.894725694 0.910996226 0.924538865 0.971341734 0.891976889 0.784828497 0.990390706 1.07346533 1 22.41172862 2.01071733 24.99257983 1.038964552 0.900387342 0.597611978 0.049323813 133.6229993 311604.8097 0.020613078 0.013881688 102.4984577 -2.01071733 -0.138577211 SQSS(ph)DTEQQSPTSGGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SQS(0.002)S(0.997)DT(0.001)EQQSPTSGGGK;SQSS(1)DTEQQSPTSGGGK;SQS(0.001)S(0.999)DTEQQSPTSGGGK;SQS(0.006)S(0.993)DT(0.001)EQQSPTSGGGK;SQSS(1)DTEQQSPTSGGGK;SQS(0.05)S(0.95)DTEQQSPTSGGGK;SQS(0.051)S(0.948)DT(0.001)EQQSPTSGGGK;SQS(0.174)S(0.824)DT(0.002)EQQSPTSGGGK 456.93 7.07E-184 3122038000 6194086 5233831 3022850 4131539 5145954 3994430 5852497 7246868 5890424 TRUE FALSE 5375521.841 5199449.62 4484710.371 5069668.077 5043559.583 4148098.307 5284922.742 5697181.673 5194064.785 1.034935463 1.001036728 0.86342981 0.97605022 0.971023619 0.798622751 1.01749265 1.096863807 1 22.30843258 2.012169527 24.99364422 1.055899024 0.940122975 0.298716772 0.071221469 233.4913735 479540.2653 0.028774824 0.019386548 102.8417662 -2.012169527 -0.115776049 SQSS(ph)SQFR ddPTM_MDA-MB-175_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 SQS(0.439)S(0.514)S(0.047)QFR;SQS(0.107)S(0.855)S(0.038)QFR 115.91 0.0024882 1393230000 2829990 2973100 1835310 2180420 2318360 3142300 2851980 2998000 3467800 TRUE FALSE 2455999.651 2953569.51 2722872.055 2675517.687 2272229.172 3263186.314 2575395.419 2356901.03 3057840.635 0.80318105 0.965900406 0.890455841 0.874969629 0.743082928 1.06715382 0.842226828 0.77077301 1 21.54408179 3.737985715 6.118998661 0.870574649 0.894598463 0 0.103215475 1.140700241 204.9576773 0.027605179 0.04461378 5469.979706 -3.737985715 0.024023815 SQSSDTEQQS(ph)PTSGGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SQSSDTEQQS(0.999)PT(0.001)SGGGK;SQSSDTEQQS(0.591)PT(0.407)S(0.001)GGGK;SQSSDTEQQS(0.782)PT(0.202)S(0.016)GGGK;SQSSDTEQQS(0.998)PT(0.002)SGGGK;SQSSDTEQQS(0.995)PT(0.005)SGGGK;SQSSDTEQQS(0.793)PT(0.206)SGGGK;SQSSDTEQQS(1)PTSGGGK;SQSSDTEQQS(0.876)PT(0.123)S(0.001)GGGK;SQSSDT(0.006)EQQS(0.991)PT(0.002)S(0.001)GGGK;SQSSDT(0.004)EQQS(0.992)PT(0.003)SGGGK;SQSSDT(0.006)EQQS(0.85)PT(0.127)S(0.017)GGGK 442.05 2.12E-182 6436672000 6146145 5351873 3838695 4722127 5118731 5080900 6671337 7901770 7073437 TRUE FALSE 5333916.366 5316716.194 5695100.742 5794358.109 5016878.268 5276365.511 6024351.765 6212037.977 6237223.336 0.855174824 0.852417159 0.913082703 0.928996413 0.804344818 0.845947824 0.965870779 0.995962088 1 22.57247249 2.133412676 4.632362124 0.992914626 0.868301524 0.73017942 0.034836788 0.11498719 4.189278619 0.015938019 0.01047641 135.9604758 -2.133412676 -0.124613102 SQSSEGVSSLSSS(ph)PSNSLETQSQSLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQSSEGVSSLSSSPSNSLETQSQSLSR 27 0 O95155-2;O95155;O95155-4 O95155-2 UBE4B Ubiquitin conjugation factor E4 B 1 SQSSEGVSSLSS(0.041)S(0.743)PS(0.173)NS(0.041)LET(0.001)QSQSLSR 77.322 5.20E-06 0 47563 45722 22124 21022 44032 46181 46131 48892 26496 TRUE FALSE 41277.42904 45421.64917 32823.2404 25795.3664 43155.84935 47957.61295 41657.22272 38436.82628 23363.67306 1.766735433 1.944114226 1.404883569 1.104080096 1.847134619 2.052657252 1.782991168 1.645153404 1 14.51197948 1.239570639 4.868500695 0.952685796 1.69578965 0.394709758 0.270665824 0.205752105 11.80409075 0.521020073 0.07288496 17.36083618 -1.239570639 0.743103854 SQSSHS(ph)YDDSTLPLIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SQSSHSYDDSTLPLIDR 17 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;H0YC95 O60716-13 CTNND1 Catenin delta-1 1 SQSSHS(1)YDDSTLPLIDR;SQSSHS(1)YDDSTLPLIDR;SQSS(0.001)HS(0.999)YDDSTLPLIDR;SQS(0.001)S(0.004)HS(0.995)YDDSTLPLIDR;SQS(0.001)S(0.01)HS(0.989)YDDSTLPLIDR;SQS(0.001)S(0.005)HS(0.995)YDDSTLPLIDR 317.81 2.39E-58 5081400000 1252200 1232730 468880 912020 1390810 1549850 1087130 1436860 1166810 TRUE FALSE 1086718.597 1224632.115 695631.9363 1119108.08 1363135.602 1609473.732 981700.2999 1129598.671 1028871.051 1.056224292 1.190267832 0.676111876 1.087704897 1.324884786 1.564310446 0.954152903 1.097901112 1 19.97263075 3.480173084 24.94453364 1.180755923 0.97682472 0.17651815 0.211098772 226.9389534 1854923.707 0.063147026 0.083143846 3021.155536 -3.480173084 -0.203931203 SQSSHSYDDSTLPLIDR ddPTM_MDA-MB-175_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 ;;; 219.01 4.47E-15 1696600000 821450 864862 252924 581226 1061640 1074520 711546 923480 802156 FALSE TRUE 712893.3012 859180.6646 375238.8924 713202.2468 1040515.441 1115857.48 642540.3784 726000.9885 707326.0315 1.007870868 1.214688314 0.530503439 1.008307647 1.471054923 1.577571629 0.908407651 1.026402191 1 19.43201583 3.466095214 24.93282323 1.178902763 0.917723906 0.195698512 0.26224967 387.6970666 876682.9822 0.080727743 0.104313869 2924.793536 -3.466095214 -0.261178858 SQSWEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 85.161 0.080016 0 484820 424960 290250 301860 440640 405260 337590 432200 512510 FALSE TRUE 420749.8086 422168.4098 430615.8708 370401.9266 431872.1261 420850.6144 304850.5738 339777.3934 451921.6517 0.931023789 0.934162832 0.952855145 0.819615359 0.955634952 0.93124685 0.674565099 0.75185022 1 18.78571315 2.278755383 24.99891206 0.791345981 0.919813062 0.2521618 0.089200847 176.0231622 109475.9634 0.033054431 0.025603535 190.0007795 -2.278755383 0.128467081 SQT(ph)PERPAKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQTPERPAKK 10 2 A8CG34-2;A8CG34;A6NF01;C9JFL1;Q96HA1-2;Q96HA1-3;Q96HA1 A8CG34-2;Q96HA1-2 POM121C;POM121B;POM121 Nuclear envelope pore membrane protein POM 121C;Putative nuclear envelope pore membrane protein POM 121B;Nuclear envelope pore membrane protein POM 121 1 S(0.039)QT(0.961)PERPAKK 79.466 0.043283 112870000 191780 129530 87685 129790 140390 91226 149460 233860 117660 TRUE FALSE 166435.7871 128679.1089 130089.7593 159260.8032 137596.5137 94735.52325 134965.3922 183850.8589 103750.3688 1.604194654 1.240276158 1.25387274 1.535038429 1.326226742 0.913110231 1.300866625 1.772050172 1 16.66275694 3.02411643 24.84702497 1.30993567 1.390972495 0.057518476 0.252737681 1224.899634 1261997.955 0.082194091 0.093195332 1057.100868 -3.02411643 0.081036824 SQT(ph)PPGVATPPIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SQTPPGVATPPIPK 14 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 S(0.021)QT(0.979)PPGVATPPIPK;S(0.001)QT(0.999)PPGVATPPIPK;S(0.144)QT(0.856)PPGVATPPIPK 189.52 7.93E-06 2193030000 2336830 1226960 826150 1091020 1281430 1038530 1559120 1783990 1532170 TRUE FALSE 2028011.995 1218900.019 1225678.903 1338752.766 1255932.05 1078482.921 1407916.782 1402497.622 1351038.608 1.50107627 0.902194809 0.907212345 0.990906372 0.929604856 0.798262103 1.042099592 1.038088485 1 20.36563747 4.74205693 24.87932617 0.956545681 1.50107649 0.847877005 0.073185415 129.5543588 921850.3555 0.019341782 0.137485118 55214.98133 -4.74205693 0.54453081 SQT(ph)PPRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SQTPPRR 7 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.024)QT(0.976)PPRR;S(0.007)QT(0.993)PPRR;S(0.018)QT(0.982)PPRR;S(0.008)QT(0.992)PPRR;S(0.386)QT(0.614)PPRR;S(0.152)QT(0.848)PPRR 78.932 0.019922 3416437000 2051761 1649746 1021416 1158004 1369357 1670230 1596368 1854746 1880367 TRUE FALSE 1780615.585 1638908.71 1515376.194 1420946.507 1342109.475 1734484.829 1441552.477 1458123.002 1658072.155 1.073907176 0.988442333 0.91393863 0.856987136 0.809439728 1.046085252 0.869414803 0.879408653 1 20.66107536 4.496139857 2.318915804 0.904559729 1.07871914 0.378977743 0.06867352 0.381948981 3.41946462 0.017686516 0.108829676 31342.9491 -4.496139857 0.174159411 SQTGDVS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQTGDVSPK 9 0 H0YBF7;A0A0A0MRE5;Q9ULH1;Q9ULH1-2;H0YBM4 H0YBF7 ASAP1 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1" 1 SQTGDVS(1)PK 112.43 0.002072 0 149630 117180 88908 109990 112560 117890 157500 176900 169310 TRUE FALSE 129856.0164 116410.2369 131904.2062 134964.9106 110320.2762 122425.3046 142225.6742 139071.3116 149294.3647 0.869798513 0.779736309 0.88351765 0.904018788 0.738944678 0.820026294 0.952652664 0.931524187 1 17.18780018 2.234626917 24.62310552 0.95480565 0.831561089 0.585127068 0.050987531 60.2429749 377084.9124 0.020408156 0.014342646 171.6433242 -2.234626917 -0.123244561 SQTTTERDS(ph)DTDVEEEELPVENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQTTTERDSDTDVEEEELPVENR 23 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 S(0.001)QT(0.024)T(0.015)T(0.045)ERDS(0.916)DTDVEEEELPVENR 156.52 1.02E-08 279200000 110650 74278 51469 57318 77126 77426 71998 91675 78226 TRUE FALSE 96027.32215 73790.06293 76359.58055 70332.92795 75591.34349 80404.62832 65015.64504 72071.01467 68978.2114 1.392139927 1.069759007 1.107010156 1.019639775 1.095872769 1.165652555 0.942553362 1.044837394 1 16.0738531 SQTTYYAQCYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQTTYYAQCYR 11 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39 B7ZC38 SH3GLB2 Endophilin-B2 0 ; 222.3 1.81E-11 586720000 205316 257474 158334 186963 254334 280169 239642 250066 264604 FALSE TRUE 178182.9704 255782.6363 234904.852 229415.8067 249273.251 290947.2827 216401.5557 196591.3319 233322.8166 0.763675722 1.096260709 1.006780457 0.983254917 1.068362086 1.246973129 0.927477042 0.842572256 1 17.83196787 2.025281421 24.99966152 0.902536086 1.034376231 0.12918577 0.124691051 348.5286325 344642.7959 0.049700637 0.033506886 105.994034 -2.025281421 0.131840145 SQVEEELFSVR ddPTM_MDA-MB-175_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 ;;; 205.52 6.86E-08 352987000 572023 520781 317923 383292 514415 630950 468828 550036 552724 FALSE TRUE 496428.7112 517359.9553 471671.6262 470324.3069 504179.1479 655223.0548 423361.1327 432415.0818 487381.5984 1.018562689 1.061509005 0.967766587 0.965002184 1.034464883 1.344373807 0.868644065 0.88722078 1 18.89469226 SQWLDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQWLDVK 7 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 125.31 0.0094482 791600000 1944750 1654180 1164380 1453750 1723480 1423370 1994660 2215400 2068700 FALSE TRUE 1687746.36 1643313.583 1727478.063 1783846.157 1689186.12 1478127.965 1801218.18 1741653.95 1824140.643 0.925228198 0.900870001 0.94700925 0.977910428 0.926017479 0.810314693 0.987433829 0.954780519 1 20.79878554 SRADLT(ph)AEMISAPLGDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRADLTAEMISAPLGDFR 18 1 Q9H3Q1;Q9H3Q1-2;J3KRZ9;J3QQS6;J3QR93 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 S(0.194)RADLT(0.806)AEMISAPLGDFR 112.23 0.00077902 147080000 48331 49464 24342 23868 48490 59226 45530 52251 57736 TRUE FALSE 41943.93589 49139.06773 36113.87262 29287.5942 47525.14387 61504.46254 41114.50761 41077.53027 50910.51585 0.823875681 0.965204671 0.709359786 0.575275927 0.933503483 1.208089557 0.807583795 0.806857475 1 15.63567606 3.075281178 24.99996849 0.935442676 0.775279532 0.272729009 0.146880917 63.38513218 21047.13023 0.047797861 0.054197677 1189.271955 -3.075281178 -0.160163144 SRAEDLNTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRAEDLNTR 9 1 Q9Y3B3;A0A0A6YYA0;Q86XR7-2;Q9Y3B3-2 Q9Y3B3 TMED7;TMED7-TICAM2 Transmembrane emp24 domain-containing protein 7 0 ; 123.96 0.00049537 368380000 280060 268660 164587 169131 283670 316960 213560 283580 144117 FALSE TRUE 243049.3614 266895.1548 244181.8237 207534.7786 278025.522 329153.6563 192848.9841 222938.6238 127079.6524 1.912574962 2.100219427 1.921486399 1.633107855 2.187805181 2.59013658 1.517544157 1.754321951 1 16.95537352 1.02808279 1.252518276 0.114525742 2.015497649 0.543044894 0.287030783 1.865924555 1.740733497 5.25711817 0.088103387 10.66799467 -1.02808279 1.900971907 SRAS(ph)PVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SRASPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.459)RAS(0.537)PVS(0.004)R;S(0.337)RAS(0.637)PVS(0.026)R;S(0.282)RAS(0.709)PVS(0.009)R;S(0.409)RAS(0.581)PVS(0.01)R 68.44 0.034217 4890600000 1145752 865403 572061 719544 777190 925138 864727 1073403 792795 TRUE FALSE 994337.9702 859718.1107 848711.613 882927.4627 761725.4395 960728.6575 780865.9086 843864.1217 699071.6783 1.422369123 1.229799658 1.21405521 1.262999904 1.089624231 1.374292061 1.117004068 1.207121026 1 19.41508086 7.008254827 0.031902383 6.07E-07 2.847412876 0.380748968 0.099010282 2550.452474 10.06928678 334.2855597 601.6103036 10191892.34 -7.008254827 2.847412268 SRDEIVEMIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRDEIVEMIR 10 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 0 178.67 2.00E-06 252150000 114590 109620 65066 84991 114100 121120 116260 123940 124340 FALSE TRUE 99446.64117 108899.899 96532.13523 104289.5056 111829.6332 125779.5648 104985.1231 97436.3955 109640.6668 0.907023316 0.993243676 0.880440971 0.951193645 1.019964913 1.147198101 0.957538166 0.888688461 1 16.74242348 3.432199936 7.307518662 0.991903915 0.930629249 0.19503372 0.069764803 0.468090336 61.89452624 0.022568333 0.029320882 2705.203469 -3.432199936 -0.061274666 SRDPFWNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRDPFWNR 8 1 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ;; 110.41 0.0031297 947020000 289257 270241 153942 197551 293319 319523 257260 317698 252281 FALSE TRUE 251030.9546 268465.7691 228388.8661 242407.9739 287482.5258 331815.2566 232310.9648 249760.755 222456.6276 1.12844898 1.206822975 1.026666944 1.089686455 1.292308208 1.491595284 1.044297791 1.122739105 1 17.76316456 SRDPGMVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRDPGMVR 8 1 P33993;P33993-2;C9J8M6 P33993 MCM7 DNA replication licensing factor MCM7 0 87.308 0.017416 0 64674 70649 40967 53139 65369 87154 61110 65080 63283 FALSE TRUE 56127.16704 70184.90207 60778.77823 65205.02213 64068.28479 90506.87078 55183.56161 51163.14845 55801.75583 1.005831559 1.257754367 1.089191143 1.168512015 1.148141019 1.621935895 0.988921599 0.916873451 1 15.7680229 2.031732787 24.99999107 0.952617872 1.214523121 0.34004994 0.162330499 197.8533532 155873.7114 0.064794143 0.043683822 107.5803088 -2.031732787 0.261905249 SRDPQLCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SRDPQLCR 8 1 Q8TAT6;Q8TAT6-2;I3L4S2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 ;;; 121.09 0.0013206 834050000 480597 477207 248611 283226 453986 548596 433101 481695 444074 FALSE TRUE 417084.8888 474072.1958 368840.1112 347536.7921 444952.5668 569700.8431 391098.9317 378688.2728 391576.0776 1.065143947 1.210677115 0.941937295 0.887533259 1.136311926 1.454891848 0.998781473 0.967087354 1 18.5789331 2.033062502 24.99997955 0.981714153 1.113317393 0.13441239 0.152715924 388.9022037 294064.1506 0.066306315 0.044703425 107.9102012 -2.033062502 0.13160324 SRDS(ph)DESGDKTTR ddPTM_MDA-MB-175_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(0.007)RDS(0.989)DES(0.003)GDKTTR;S(0.002)RDS(0.985)DES(0.014)GDKTTR 119.38 0.00018445 509930000 364560 327140 190993 303700 341860 306610 299760 542730 242262 TRUE FALSE 316382.4723 324990.9958 283357.8536 372659.7268 335057.6548 318405.4851 270689.3213 426671.413 213622.0623 1.481038376 1.52133629 1.326444706 1.744481458 1.568459976 1.490508432 1.267141223 1.997319043 1 17.70470113 1.199846842 24.59836227 0.999993272 1.554315888 0.415438853 0.204813756 6793.902848 4316425.121 15.95432617 0.04944725 15.84334365 -1.199846842 0.554322616 SRDSFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRDSFLK 7 1 P46778;M0R181 P46778 RPL21 60S ribosomal protein L21 0 83.313 0.020403 132880000 138970 140340 86077 96187 149620 144190 173910 185630 96671 FALSE TRUE 120604.7624 139418.0973 127704.1251 118027.7285 146642.8547 149737.0826 157044.235 145934.4691 85242.66451 1.414840363 1.635543634 1.498124511 1.384608625 1.720298815 1.756597866 1.84231964 1.711988591 1 16.37928807 3.230272059 24.99549257 1.644683171 1.495215676 0.04735152 0.239407551 496.2529673 1496527.647 0.072374049 0.08344515 1699.307833 -3.230272059 -0.149467495 SRDYNGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRDYNGR 7 1 P98179 P98179 RBM3 RNA-binding protein 3 0 ; 113.7 0.0055374 91416000 208140 186999 64911 81415 172533 232810 236952 260110 35912 FALSE TRUE 180633.7716 185770.5913 96302.17671 99901.5201 169099.9309 241766.3513 213972.4315 204487.5007 31666.52427 5.704250018 5.866466104 3.041135045 3.154799031 5.340021829 7.634761216 6.757054537 6.457529059 1 14.9506709 3.011467194 24.50231905 5.822345737 4.418897958 0.046164037 1.973737764 432.7129728 924582.6362 0.607992364 0.688796634 1026.75587 -3.011467194 -1.403447779 SREDVSNFDPDFIKEEPVLT(ph)PIDEGHLPMINQDEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SREDVSNFDPDFIKEEPVLTPIDEGHLPMINQDEFR 36 2 P24723-2;P24723 P24723-2 PRKCH Protein kinase C eta type 1 SREDVSNFDPDFIKEEPVLT(1)PIDEGHLPMINQDEFR;SREDVSNFDPDFIKEEPVLT(1)PIDEGHLPMINQDEFR 177.85 7.56E-23 165514000 97981 86111 62645 73703 71321 85484 87602 126411 92709 TRUE FALSE 85032.5626 85545.33117 92940.33153 90438.39263 69901.85164 88772.6248 79106.37152 99378.99138 81749.04763 1.040165789 1.04643826 1.136898034 1.10629292 0.855078483 1.085916318 0.96767331 1.215659317 1 16.3189143 1.750655362 25 1.119284267 1.036384778 0.09401758 0.093493279 6.950835301 14397.70004 0.048293655 0.023191066 56.31905539 -1.750655362 -0.082899489 SRENLS(ph)AVMLYNPGLEFER ddPTM_MDA-MB-175_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(0.244)RENLS(0.756)AVMLYNPGLEFER 167.72 1.06E-11 193930000 169300 139190 87594 103770 139300 137280 136810 139290 141530 TRUE FALSE 146926.576 138275.6517 129954.7514 127332.5645 136528.2025 142561.2504 123542.1873 109503.9175 124798.4846 1.177310578 1.107991432 1.041316742 1.020305374 1.093989265 1.142331582 0.989933392 0.87744589 1 16.92924089 2.050065337 5.346863074 0.930558167 1.090800145 0.616911933 0.053351625 0.116204669 7.388289876 0.023425052 0.015188927 112.2187267 -2.050065337 0.160241978 SRES(ph)MIQLF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRESMIQLF 9 1 P30520;G3V5D8;G3V232;Q8N142;Q8N142-2 P30520;Q8N142 ADSS;ADSSL1 Adenylosuccinate synthetase isozyme 2;Adenylosuccinate synthetase isozyme 1 1 S(0.056)RES(0.944)MIQLF;S(0.295)RES(0.705)MIQLF 89.805 0.031196 92900000 201671 222181 127564 156693 190987 220420 214810 220548 268510 TRUE FALSE 175019.6664 220721.4784 189254.3771 192272.5406 187186.7324 228899.7 193977.7593 173385.5265 236767.0537 0.739206168 0.93223054 0.799327331 0.812074727 0.790594508 0.966771755 0.819276822 0.732304279 1 17.85310882 SRES(ph)S(ph)PSHGLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRESSPSHGLLK 12 1 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 2 S(0.434)RES(0.727)S(0.716)PS(0.123)HGLLK 58.885 0.05858 300070000 821000 620030 394670 460890 541410 470380 621330 672560 618780 TRUE FALSE 712502.7699 615956.9821 585533.7321 565542.1188 530637.0003 488475.823 561073.5122 528738.2779 545628.5333 1.305838545 1.128894375 1.073136202 1.036496598 0.972524287 0.895253443 1.028306765 0.969044406 1 19.05755957 5.202579992 0.749815253 0.972860534 1.766971388 0.890994513 0.036779267 1.552060148 0.413673847 0.014560656 1.212685187 159433.6512 -5.202579992 0.794110854 SRFS(ph)GGFGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRFSGGFGAR 10 1 A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7 A0A2R8YFS5 1 S(0.003)RFS(0.997)GGFGAR;S(0.001)RFS(0.999)GGFGAR 112.42 0.00098275 783690000 152300 172988 97845 133154 182313 156491 181942 188754 158655 TRUE FALSE 132173.1691 171851.6304 145163.1693 163388.6508 178685.328 162511.31 164297.2928 148390.426 139898.9866 0.944775744 1.228397965 1.037628454 1.167904463 1.277245335 1.161633218 1.174399449 1.060696932 1 17.09402599 1.546623292 3.433801243 1.007750848 1.147836214 0.208111326 0.093230711 0.296046188 7.483905176 0.084321595 0.023478908 35.2065356 -1.546623292 0.140085365 SRGS(ph)PSSYNSSSSSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRGSPSSYNSSSSSPR 16 1 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 1 S(0.005)RGS(0.611)PS(0.352)S(0.012)YNS(0.02)S(0.001)S(0.001)SSPR;SRGS(0.69)PS(0.302)S(0.006)YNS(0.001)SSSSPR 168.16 1.60E-08 228631000 436300 387770 172527 226824 356920 359875 326247 364950 251842 TRUE FALSE 378641.8496 385222.7133 255961.6343 278327.856 349817.9903 373719.6241 294607.6162 286908.2825 222069.5257 1.705059929 1.734694178 1.152619359 1.253336563 1.575263374 1.682894684 1.326645857 1.291975032 1 17.7606519 1.34691445 1.432830461 0.865088652 1.49665934 0.411880705 0.193658573 1.11236686 2.440970753 0.983148942 0.061740888 22.22871975 -1.34691445 0.631570688 SRGSPSS(ph)YNSSSSSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRGSPSSYNSSSSSPR 16 1 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 1 SRGS(0.007)PS(0.187)S(0.573)YNS(0.057)S(0.057)S(0.057)S(0.057)S(0.007)PR 226.32 1.60E-14 50815000 94108 85836 40548 49622 77363 76934 68203 75925 56576 TRUE FALSE 81671.38936 85272.13766 60157.14842 60889.43352 75823.62766 79893.70076 61588.68356 59689.0296 49887.64973 1.637106374 1.709283523 1.205852526 1.220531211 1.519887749 1.601472533 1.234547706 1.196469064 1 15.60639508 0.490435485 0.593897748 4.28E-11 1.491060997 0.471880555 0.170799924 8.285596815 1.184483565 10.33123806 0.100374566 3.093395753 -0.490435485 1.491060997 SRGSPSSYNSSS(ph)SSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRGSPSSYNSSSSSPR 16 1 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 1 SRGS(0.029)PS(0.209)S(0.079)YNS(0.027)S(0.027)S(0.21)S(0.21)S(0.21)PR 195.57 1.27E-10 233490000 349170 302930 149760 216270 306900 299140 261390 309990 218060 TRUE FALSE 303026.2998 300940.0329 222184.4369 265377.409 300793.2904 310648.1094 236040.438 243701.0508 192281.1952 1.575953902 1.565103819 1.155518285 1.380152691 1.564340653 1.615592773 1.22757942 1.267420096 1 17.55285815 1.458732877 1.325073633 0.927065009 1.458105304 0.505260279 0.146855697 0.797863474 1.722091226 0.539606644 0.04760355 28.75629147 -1.458732877 0.531040295 SRIPS(ph)PLQPEMQGTPDDEPSEPEPSPSTLIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SRIPSPLQPEMQGTPDDEPSEPEPSPSTLIYR 32 1 Q96GY3;K7EMY4 Q96GY3 LIN37 Protein lin-37 homolog 1 SRIPS(1)PLQPEMQGTPDDEPSEPEPSPSTLIYR;SRIPS(0.999)PLQPEMQGTPDDEPSEPEPSPSTLIYR;SRIPS(1)PLQPEMQGTPDDEPSEPEPSPSTLIYR;SRIPS(1)PLQPEMQGTPDDEPSEPEPSPSTLIYR 325.24 2.42E-105 844350000 435281 365603 200229 215959 395725 429178 421425 442979 218864 TRUE FALSE 377757.513 363201.3298 297060.4141 264995.7917 387850.8467 445688.7554 380555.2684 348251.3881 192990.1473 1.957392739 1.881968251 1.53925171 1.373105288 2.009692475 2.309386058 1.971889621 1.804503458 1 17.55816767 1.239766132 5.232123372 0.952407656 1.857634536 0.526977518 0.255380764 0.144676268 11.0595634 0.474263774 0.070107182 17.36865275 -1.239766132 0.90522688 SRKS(ph)PHKDLGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRKSPHKDLGHR 12 3 O94888;C9JAT7 O94888 UBXN7 UBX domain-containing protein 7 1 S(0.062)RKS(0.938)PHKDLGHR 104.2 0.0015445 261550000 671720 452540 240840 272410 352700 318770 641540 732110 75402 TRUE FALSE 582950.5001 449567.2349 357311.0296 334264.854 345681.96 331033.2882 579323.5495 575553.9738 66488.06146 8.76774698 6.761623442 5.374062978 5.02744172 5.199158352 4.978838019 8.713196578 8.656501049 1 16.02080769 4.666462472 3.045192275 5.958669737 9.00107728 0.165661301 2.167016593 0.659889161 9.642921425 0.562264862 4.385824996 46394.06981 -4.666462472 3.042407542 SRLDS(ph)YVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRLDSYVR 8 1 Q9Y5R8 Q9Y5R8 TRAPPC1 Trafficking protein particle complex subunit 1 1 S(0.002)RLDS(0.998)YVR 77.124 0.020607 198420000 118910 105620 54178 72484 107970 108680 95919 102710 103260 TRUE FALSE 103195.7422 104926.1753 80378.66201 88942.60005 105821.6082 112860.9899 86616.79014 80746.26579 91052.72043 1.133362537 1.152367274 0.882770571 0.97682529 1.1622015 1.239512553 0.951281738 0.886807834 1 16.4744145 2.032184078 24.93618917 0.930436459 1.083586663 0.301411428 0.103370543 226.5851199 175556.9953 0.045172512 0.030455044 107.6921575 -2.032184078 0.153150204 SRLNS(ph)HGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SRLNSHGGR 9 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IU26;B1AN86 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 SRLNS(1)HGGR;SRLNS(1)HGGR;SRLNS(1)HGGR;S(0.012)RLNS(0.988)HGGR 105.03 0.001916 650311000 143565 222205 115133.2 162161 396214 491783 454216 437808 70352.5 TRUE FALSE 124592.5215 220745.3207 170812.0006 198982.1335 388330.1166 510702.2102 410166.2022 344186.1662 62035.5076 2.008406578 3.558370509 2.753455355 3.207552275 6.259803968 8.232417692 6.61179731 5.548212299 1 15.92080659 3.285677485 6.511076588 5.748090748 2.89526035 0.331074902 1.858227366 0.231659682 23.0555161 0.557371684 0.713422175 1930.534136 -3.285677485 -2.852830397 SRLS(ph)AIEIDIPVVSHTT ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRLSAIEIDIPVVSHTT 17 1 P56749 P56749 CLDN12 Claudin-12 1 S(0.494)RLS(0.506)AIEIDIPVVSHTT 120.39 0.00019408 78975000 55918 59411 35599 66880 89712 92442 44423 95975 62593 TRUE FALSE 48528.29462 59020.72523 52814.79547 82066.1262 87926.90672 95998.30356 40114.8643 75451.49313 55193.32685 0.879242064 1.06934531 0.956905454 1.486884935 1.593071332 1.739309968 0.72680642 1.367040138 1 15.75220623 3.755877387 23.87002538 1.315813732 0.978582296 0.245506598 0.289320009 721.0475341 993911.1652 0.078619761 0.135681022 5700.033228 -3.755877387 -0.337231437 SRLT(ph)PVS(ph)PESSSTEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRLTPVSPESSSTEEK 16 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 2 S(0.139)RLT(0.862)PVS(0.999)PESSSTEEK 105.92 0.016486 0 205140 160490 138150 136970 154850 148310 187200 203740 212330 TRUE FALSE 178030.2292 159435.7306 204959.8021 168071.132 151768.788 154015.5817 169045.3728 160171.7865 187228.5893 0.950870964 0.851556545 1.094703554 0.897678782 0.810606909 0.822607179 0.902882265 0.855487867 1 17.51444122 3.493376806 24.93385201 0.872667657 0.961277674 0.209762879 0.077264821 1041.626668 1597714.448 0.020841388 0.029969536 3114.417321 -3.493376806 0.088610017 SRNDQVVTDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRNDQVVTDLR 11 1 A0A5F9ZHC6;A0A5F9ZHM8;P04424-3;P04424-2;P04424;F8W943 A0A5F9ZHC6 ASL Argininosuccinate lyase 0 100.55 0.002637 0 526910 507580 249050 350380 559200 547390 538960 566180 463500 FALSE TRUE 457277.5085 504245.6736 369491.413 429939.1342 548073.0141 568448.4475 486691.7422 445106.813 408705.558 1.118843381 1.233762702 0.904052822 1.051953236 1.340997213 1.390850788 1.190812634 1.089064742 1 18.64070234 SRNS(ph)PLLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SRNSPLLER 9 1 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 S(0.001)RNS(0.999)PLLER;S(0.029)RNS(0.971)PLLER;S(0.001)RNS(0.999)PLLER;S(0.001)RNS(0.999)PLLER;S(0.242)RNS(0.758)PLLER 131.32 0.00020371 16519530000 2338750 2018210 1282670 1442160 1936240 2045970 1908510 2023170 2047190 TRUE FALSE 2029678.262 2004952.246 1902973.502 1769624.47 1897712.612 2124679.79 1723422.994 1590530.84 1805173.53 1.124367396 1.110670089 1.054177601 0.980307123 1.051263261 1.176994762 0.954713198 0.881095813 1 20.7837061 2.082597439 8.134860235 0.927866954 1.076552684 0.544417144 0.059021793 0.177318746 15.29684297 0.024826536 0.016701046 120.9476512 -2.082597439 0.14868573 SRNTDEMVELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRNTDEMVELR 11 1 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ; 154.36 2.92E-05 517660000 404370 304870 143294 175963 438340 420510 478210 462140 136667 FALSE TRUE 350931.48 302867.2889 212591.4577 215918.0886 429617.8916 436687.2918 431833.2678 363314.9574 120510.383 2.912043522 2.513204933 1.764092458 1.791696975 3.564986527 3.623648694 3.583369808 3.014802115 1 16.87879793 3.242062613 24.999303 3.0448065 2.230029391 0.152765056 0.818697866 160.8914172 1148528.607 0.246961465 0.306068685 1746.07387 -3.242062613 -0.814777108 SRPDS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRPDSPR 7 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 S(0.006)RPDS(0.994)PR 58.699 0.065395 60330000 30467 27075 16150 14028 18252 31453 23572 27849 23753 TRUE FALSE 26440.70876 26897.14254 23960.19402 17213.2718 17888.82091 32663.01726 21285.99107 21893.70807 20944.9474 1.262390793 1.284182864 1.143960573 0.821834091 0.85408765 1.559470007 1.016282861 1.04529783 1 14.35431464 4.069771918 4.906079913 1.054852368 1.267974369 0.175470332 0.198557825 0.369584698 16.86499397 0.052555226 0.113498049 11742.80687 -4.069771918 0.213122001 SRPELLEYYIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRPELLEYYIK 11 1 Q14258 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 123.84 0.00032982 480910000 402110 357960 228670 280780 376120 303040 385090 472870 414970 FALSE TRUE 348970.1447 355608.5372 339255.5769 344535.3905 368635.9479 314698.1449 347744.0311 371750.4304 365912.7193 0.953697771 0.971839781 0.927148904 0.941578066 1.00744229 0.860036091 0.950346934 1.015953835 1 18.48114004 1.773100144 6.166211647 1.007522431 0.94379894 0.335403156 0.037110686 0.188752846 17.50120178 0.020147337 0.009483981 59.30620631 -1.773100144 -0.06372349 SRPEPSYHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRPEPSYHSR 10 1 M0QZ22;Q5PRF9;A0A087WZT0;M0R0X3;M0QY61 M0QZ22 SAMD4B Protein Smaug homolog 2 0 56.087 0.075939 21015000 52571 48122 18221 37513 47323 57526 50447 56535 34335 FALSE TRUE 45623.60915 47805.88341 27032.73655 46030.9 46381.36489 59739.06244 45554.6577 44445.43021 30275.95541 1.506925497 1.579004948 0.892878067 1.520378114 1.531953798 1.973152015 1.504648064 1.468010822 1 14.88588487 SRPFTVAASFQSTSVKS(ph)PK ddPTM_MDA-MB-175_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;SRPFTVAASFQSTSVKS(1)PK 207.07 1.75E-16 4419700000 2626500 2445800 2115940 2282440 3464600 2401200 4826800 5580700 2441800 TRUE FALSE 2279401.37 2429733.379 3139215.661 2800702.887 3395661.238 2493575.718 4358697.679 4387310.734 2153133.186 1.058643927 1.128464042 1.457975606 1.300756918 1.57707905 1.158114944 2.024351168 2.037640199 1 21.03800613 3.714283296 0.570276238 1.722374634 0.974753041 0.197104562 0.333596279 2.012345593 1.269583712 0.302608063 0.95600294 5179.445836 -3.714283296 -0.747621593 SRPT(ph)SEGSDIES(ph)TEPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 2 S(0.001)RPT(0.836)S(0.161)EGS(0.002)DIES(0.922)T(0.078)EPQK;S(0.309)RPT(0.51)S(0.181)EGS(0.104)DIES(0.891)T(0.006)EPQK 246.67 2.82E-19 1786340000 8560000 5904600 4298500 4999300 6383100 5620600 6992100 8369700 8115100 TRUE FALSE 7428774.312 5865812.294 6377268.978 6134467.475 6256088.798 5836828.119 6314007.218 6579904.788 7155742.123 1.038155678 0.819735003 0.891210006 0.857279003 0.874275329 0.815684526 0.882369307 0.919527936 1 22.77066997 1.315443344 2.171686343 1.023003939 0.876933361 0.266198532 0.061171393 0.702069402 3.909846904 0.190367058 0.015381549 20.6748965 -1.315443344 -0.146070578 SRPTS(ph)EGS(ph)DIESTEPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 2 S(0.02)RPT(0.538)S(0.621)EGS(0.822)DIESTEPQK;SRPT(0.077)S(0.923)EGS(0.999)DIESTEPQK;S(0.001)RPT(0.072)S(0.926)EGS(0.99)DIES(0.008)T(0.002)EPQK 192.18 2.40E-09 1626930000 2141770 1463360 1098940 1168390 1582010 1426200 1613870 1890160 2039530 TRUE FALSE 1858729.668 1453747.092 1630391.06 1433690.807 1550531.096 1481066.837 1457357.136 1485963.993 1798419.087 1.033535332 0.808347233 0.906569037 0.797195057 0.86216339 0.823538211 0.810354576 0.826261245 1 20.77829782 4.746511441 24.60866247 0.849185528 1.033535445 0.460048382 0.060798599 686.8550985 2125829.082 0.013899295 0.146947908 55784.22973 -4.746511441 0.184349917 SRPTSEGS(ph)DIESTEPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 1 S(0.003)RPT(0.231)S(0.231)EGS(0.535)DIESTEPQK;S(0.004)RPT(0.271)S(0.271)EGS(0.455)DIESTEPQK;S(0.005)RPT(0.229)S(0.229)EGS(0.537)DIESTEPQK;SRPT(0.075)S(0.129)EGS(0.796)DIESTEPQK 205.63 4.67E-12 4933970000 5699500 4104490 2822710 3457260 4173130 3592760 4451810 5481900 5264400 TRUE FALSE 4946296.634 4077527.335 4187781.997 4242283.724 4090092.878 3730975.802 4020074.151 4309638.345 4642048.629 1.065541753 0.878389621 0.902140915 0.913881793 0.881096517 0.803734752 0.866012934 0.928391469 1 22.14633021 4.74198551 24.87235146 0.895056125 1.065541822 0.532963835 0.04964855 262.8751824 1908967.081 0.012700594 0.08995944 55205.90204 -4.74198551 0.170485697 SRPVS(ph)MDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRPVSMDAR 9 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 S(0.094)RPVS(0.906)MDAR 63.091 0.047442 182210000 100610 118080 85884 101920 125580 161810 109460 145400 163570 TRUE FALSE 87314.13359 117304.3247 127417.7897 125062.4937 123081.2037 168034.9354 98844.58605 114307.3415 144232.9409 0.605368878 0.813297739 0.883416707 0.867086901 0.853350163 1.165024677 0.685312144 0.792518968 1 17.13804117 4.755274031 2.193499975 0.880197896 0.525272703 0.338063493 0.125676842 0.861997629 4.578341451 0.032808613 0.607353169 56921.19783 -4.755274031 -0.354925193 SRQELASGLPS(ph)PAATQELPVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRQELASGLPSPAATQELPVER 22 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 SRQELAS(0.001)GLPS(0.999)PAATQELPVER 154.26 1.68E-08 141380000 31713 50859 45216 47402 82218 88370 73269 86313 59429 TRUE FALSE 27522.0467 50524.90388 67082.60884 58165.34859 80582.02266 91769.65108 66163.38366 67855.63664 52403.37132 0.525196109 0.964153691 1.280120098 1.109954324 1.537725925 1.751216549 1.262578761 1.294871588 1 15.67737201 4.774237781 1.199166646 1.34989662 0.083154277 0.617323929 0.205760458 1.150831052 1.333428485 0.064358259 1.857488807 59461.76293 -4.774237781 -1.266742343 SRQPS(ph)PLLLLPPPAGLTSDPGPSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SRQPSPLLLLPPPAGLTSDPGPSVR 25 1 I3L2J0 I3L2J0 CIC 1 S(0.077)RQPS(0.923)PLLLLPPPAGLTSDPGPSVR;S(0.066)RQPS(0.934)PLLLLPPPAGLTSDPGPSVR;S(0.03)RQPS(0.97)PLLLLPPPAGLTSDPGPSVR;S(0.02)RQPS(0.98)PLLLLPPPAGLTSDPGPSVR 103.1 0.0028787 1685830000 654527 569057 317395 396508 650660 687090 642510 722640 412203 TRUE FALSE 568029.5986 565318.8271 470888.2836 486541.2016 637713.139 713522.7969 580199.4791 568109.0596 363472.8309 1.562784204 1.555326228 1.295525397 1.338590289 1.754500157 1.963070514 1.596266432 1.56300282 1 18.471488 3.252929824 24.99957346 1.59477488 1.436252165 0.064996484 0.252862202 676.773877 1177445.883 0.076107638 0.097801204 1790.316539 -3.252929824 -0.158522715 SRS(ph)AQEPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSAQEPAR 9 1 P25685;P25685-2;M0R080;M0QZD0;M0QYT3;M0QXK0;M0R128;A0A1B0GX60;M0R1D6 P25685 DNAJB1 DnaJ homolog subfamily B member 1 1 S(0.136)RS(0.864)AQEPAR 69.451 0.056335 0 35025 34698 27315 28171 30453 40592 23916 33080 25631 TRUE FALSE 30396.35751 34470.06655 40524.62536 34567.65612 29847.04488 42153.60051 21596.63 26006.09943 22600.93238 1.344916086 1.525161262 1.793051042 1.529479206 1.32061122 1.865126615 0.955563675 1.150664893 1 14.46409467 2.223503668 24.99981414 1.056094026 1.559242705 0.668568655 0.174914755 140.0134878 232469.6691 0.06876007 0.046561998 167.3029765 -2.223503668 0.503148679 SRS(ph)DIDVNAAAGAK ddPTM_MDA-MB-175_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(0.014)RS(0.986)DIDVNAAAGAK;S(0.003)RS(0.997)DIDVNAAAGAK;S(0.043)RS(0.957)DIDVNAAAGAK;S(0.005)RS(0.995)DIDVNAAAGAK 192.85 8.59E-07 1210760000 2496140 2005920 1337930 1489520 1792790 1496760 2186840 2492960 2392750 TRUE FALSE 2166268.775 1992742.979 1984957.423 1827738.282 1757116.987 1554341.326 1974760.593 1959859.904 2109881.821 1.026725172 0.944480852 0.940790808 0.866275193 0.83280351 0.736695918 0.935957917 0.928895583 1 21.00873076 4.500397074 1.454938189 0.88517935 1.043042595 0.290990758 0.070304179 1.105541336 3.013741243 0.021935012 0.223776929 31651.70239 -4.500397074 0.157863245 SRS(ph)DIDVNAAASAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRSDIDVNAAASAK 14 1 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 S(0.009)RS(0.991)DIDVNAAASAK;S(0.002)RS(0.998)DIDVNAAASAK 224.76 7.97E-12 677490000 804580 604680 367377 451190 489590 473960 706110 661220 704560 TRUE FALSE 698252.7145 600707.8173 545041.746 553639.5855 479848.1169 492193.5479 637631.5609 519823.2486 621267.7194 1.123915975 0.966906534 0.877305756 0.891144942 0.772369305 0.79224066 1.026339436 0.836713759 1 19.24485557 4.668923738 2.08064252 0.880749459 1.171495819 0.475428298 0.079777511 0.508711315 2.748241894 0.02057792 0.263567666 46657.74419 -4.668923738 0.29074636 SRS(ph)FDYNYR ddPTM_MDA-MB-175_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(0.145)RS(0.855)FDYNYR;S(0.007)RS(0.993)FDYNYR;S(0.078)RS(0.922)FDYNYR;S(0.001)RS(0.999)FDYNYR 167.83 3.61E-05 1666390000 1173280 1052160 670810 762430 1000250 996530 979330 1021800 823060 TRUE FALSE 1018228.075 1045248.292 995215.9597 935551.3845 980346.982 1034867.154 884354.7273 803296.0217 725758.7844 1.402984156 1.440214454 1.371276492 1.289066567 1.350788999 1.425910614 1.218524317 1.106836099 1 19.4691306 1.797968847 1.654236764 1.002782159 1.378429594 0.888803449 0.048048697 0.128991074 0.642223836 0.059223021 0.015287451 62.80133083 -1.797968847 0.375647435 SRS(ph)GEGEVSGLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SRSGEGEVSGLMR 13 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 S(0.266)RS(0.734)GEGEVSGLMR;S(0.051)RS(0.697)GEGEVS(0.252)GLMR;S(0.144)RS(0.856)GEGEVSGLMR;S(0.001)RS(0.999)GEGEVSGLMR 194.58 5.44E-07 4289220000 4042730 2131830 1486140 1753710 2213730 2412870 2265110 2431420 1991210 TRUE FALSE 3508472.988 2117825.868 2204842.275 2151916.659 2169681.104 2505694.67 2045439.981 1911479.754 1755811.422 1.998206039 1.20618071 1.255739795 1.225596685 1.235714198 1.427086439 1.164954251 1.088658913 1 20.74370647 4.738673979 7.962406651 1.200364502 2.004833241 0.836910388 0.110671674 0.038949813 29.8549969 0.029192022 0.168207875 54786.5533 -4.738673979 0.804468739 SRS(ph)HSDNDRPNCSWNTQYSSAYYTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSHSDNDRPNCSWNTQYSSAYYTSR 26 2 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.227)RS(0.738)HS(0.035)DNDRPNCSWNTQYSSAYYTSR 250.29 2.73E-46 731890000 107560 90782 27051 42792 74629 74452 71687 82409 29899 TRUE FALSE 93345.67348 90185.64706 40132.95408 52508.57763 73144.02891 77316.21662 64734.80577 64786.47666 26364.37428 3.540598858 3.420739142 1.522241858 1.991648923 2.774351029 2.932601995 2.455389424 2.457349299 1 14.68630214 4.316878825 8.930203109 2.248136076 3.496484767 0.470449595 0.576220247 0.274195667 28.29613418 0.146064973 0.387738556 20743.34663 -4.316878825 1.248348691 SRS(ph)PAYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRSPAYSR 8 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 S(0.226)RS(0.774)PAYSR;S(0.039)RS(0.961)PAYSR 59.84 0.058186 256540000 148353 133181 67672 102534 125890 165348 112215 115831 125460 TRUE FALSE 128747.7752 132306.1252 100398.4055 125815.9118 123385.0353 171709.0446 101332.4066 91061.44205 110628.2617 1.163787383 1.195952311 0.90752945 1.137285445 1.115312067 1.55212639 0.915972148 0.823130009 1 16.75536047 2.039573075 24.99970791 0.890115958 1.168339996 0.371197071 0.162082033 151.2437027 95545.37255 0.066299726 0.044699194 109.5400853 -2.039573075 0.278224038 SRS(ph)PHEAGFCVYLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSPHEAGFCVYLK 14 1 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(0.253)RS(0.747)PHEAGFCVYLK 187.47 5.72E-07 780020000 513470 443680 192320 303380 420240 338510 447620 508810 359720 TRUE FALSE 445613.6385 440765.4369 285326.5953 372267.0659 411878.0462 351532.6987 404209.8813 400004.9411 317194.3114 1.404860121 1.389575478 0.899532511 1.17362466 1.298503887 1.10825663 1.274328911 1.261072241 1 18.27500737 4.425537654 24.99964153 1.165987186 1.401043415 0.406149288 0.124853393 90.01218011 43623.52907 0.030784832 0.081449047 26640.21063 -4.425537654 0.235056229 SRS(ph)PIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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(0.023)RS(0.977)PIER;S(0.041)RS(0.959)PIER;S(0.036)RS(0.964)PIER 112.11 0.0038932 1966890000 610875 585899 370840 485861 550601 621340 575057 611276 580670 TRUE FALSE 530146.321 582050.1909 550179.4644 596183.166 539645.1173 645243.3519 519288.0607 480559.3844 512023.8541 1.035393794 1.136763817 1.074519204 1.164365998 1.053945266 1.26018221 1.014187242 0.938548821 1 18.9658515 2.014521876 24.99929403 0.968329913 1.119978132 0.508454455 0.064446788 156.4635753 269349.7531 0.024123189 0.016256597 103.4003185 -2.014521876 0.151648219 SRS(ph)PIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSPIQR 7 1 Q9Y252 Q9Y252 RNF6 E3 ubiquitin-protein ligase RNF6 1 S(0.187)RS(0.813)PIQR 80.755 0.017595 93106000 28191 20922 15343 18008 21822 24465 17541 26231 25764 TRUE FALSE 24465.48792 20784.562 22762.92612 22096.99164 21387.78489 25406.18438 15839.87652 20621.70478 22718.20927 1.076910932 0.914885577 1.001968326 0.972655519 0.941437973 1.118318089 0.697232618 0.907717001 1 14.4715615 2.252997209 24.99999465 0.869396403 0.995885266 0.314266087 0.094176708 284.4749571 492627.964 0.033877241 0.026117506 179.0594345 -2.252997209 0.126488863 SRS(ph)PITTNHRPS(ph)PDPEQRPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRSPITTNHRPSPDPEQRPLR 21 3 P41212 P41212 ETV6 Transcription factor ETV6 2 S(0.417)RS(0.583)PIT(0.021)T(0.025)NHRPS(0.954)PDPEQRPLR;S(0.208)RS(0.792)PIT(0.128)T(0.046)NHRPS(0.826)PDPEQRPLR 107.91 0.00047679 805200000 199691 189943 121155 154213 198370 179429 166832 191278 206350 TRUE FALSE 173301.3284 188695.2519 179745.9632 189229.4186 194422.8251 186331.7497 150652.6583 150374.6882 181955.5381 0.952437778 1.037040444 0.987856512 1.039976143 1.068518316 1.024050995 0.827964127 0.826436446 1 17.47322644 2.247838158 24.98278413 0.870272908 1.021046934 0.544760886 0.056985652 123.1914851 331733.418 0.021297888 0.016265085 176.9449442 -2.247838158 0.150774026 SRS(ph)PITTNHRPSPDPEQRPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSPITTNHRPSPDPEQRPLR 21 3 P41212 P41212 ETV6 Transcription factor ETV6 1 S(0.459)RS(0.539)PIT(0.001)TNHRPSPDPEQRPLR 104.33 0.00029756 682940000 332440 298930 154710 231240 324410 292700 237310 339720 237960 TRUE FALSE 288507.2117 296966.3091 229528.2735 283746.5763 317954.8757 303960.3584 214295.7127 267073.5217 209828.6399 1.374965838 1.415280151 1.093884389 1.352277632 1.515307328 1.448612347 1.021289147 1.272817294 1 17.67885208 2.242173471 24.99987791 1.131250589 1.362624213 0.475792324 0.131368298 93.25113291 645276.5637 0.051813913 0.038520823 174.6519629 -2.242173471 0.231373623 SRS(ph)PLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRSPLAR 7 1 Q8N3Y1 Q8N3Y1 FBXW8 F-box/WD repeat-containing protein 8 1 S(0.077)RS(0.923)PLAR;S(0.26)RS(0.74)PLAR;S(0.429)RS(0.571)PLAR 83.647 0.0134 532158000 194163 191085 138099 138077 163190 212638 159775 179695 202559 TRUE FALSE 168503.8676 189829.7501 204884.1383 169429.4932 159942.8383 220818.3215 144280.0451 141268.6226 178612.7058 0.943403589 1.062800931 1.147086023 0.948585894 0.895472904 1.236296827 0.807781532 0.790921463 1 17.44647519 2.192520556 24.9999464 0.848108355 1.0343137 0.333137591 0.114107589 130.2154984 70706.62828 0.045412359 0.030617129 155.7831768 -2.192520556 0.186205345 SRS(ph)PLHPMSEIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSPLHPMSEIPR 13 1 Q9NVW2-2;Q9NVW2 Q9NVW2-2 RLIM E3 ubiquitin-protein ligase RLIM 1 S(0.087)RS(0.913)PLHPMSEIPR 94.639 0.003066 385650000 137120 146070 101430 108190 170360 141990 142950 179380 146560 TRUE FALSE 118999.2446 145110.4566 150481.8873 132756.1931 166970.1693 147452.4472 129086.731 141020.9829 129233.8438 0.920805581 1.122851819 1.164415473 1.027255626 1.292000334 1.140973934 0.998861655 1.091207836 1 16.97962441 2.247948447 24.95136115 1.041471571 1.118701438 0.126902813 0.097849022 408.8512291 1086664.164 0.036314071 0.027738957 176.9898851 -2.247948447 0.077229867 SRS(ph)PLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSPLLK 7 1 A0A0U1RQD2;Q6ZUS6-6;Q6ZUS6;Q6ZUS6-5;Q6ZUS6-4 A0A0U1RQD2 CCDC149 Coiled-coil domain-containing protein 149 1 S(0.207)RS(0.793)PLLK 77.192 0.023446 510630000 577180 525950 296700 380960 519680 454960 577660 700670 576230 TRUE FALSE 500904.2006 522494.9998 440185.1124 467462.7906 509339.3847 472462.6056 521638.6221 550837.1731 508108.7458 0.98582086 1.028313337 0.866320676 0.920005401 1.002421999 0.92984545 1.026627915 1.084093076 1 18.95477777 2.112669184 5.204258529 1.049998406 0.955512187 0.374974756 0.049482382 0.197940832 8.243263121 0.021138496 0.013988224 129.6191545 -2.112669184 -0.094486219 SRS(ph)PNRFDAHDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSPNRFDAHDPR 13 2 Q96T58;A0A669KB49;F6WRY4 Q96T58 SPEN Msx2-interacting protein 1 S(0.344)RS(0.656)PNRFDAHDPR 79.393 0.010765 1136100000 400230 364750 181480 204960 351360 333330 335040 367820 186120 TRUE FALSE 347338.5914 362353.9332 269244.335 251499.3006 344368.6234 346153.4208 302547.8724 289164.5554 164117.1056 2.116407002 2.207898633 1.640562292 1.53243807 2.098310363 2.109185508 1.843487741 1.76194038 1 17.32436609 1.105861668 1.999797689 0.421244252 1.933067376 0.644977407 0.216667918 0.811867254 2.329728038 2.595362405 0.062546059 12.76032301 -1.105861668 1.511823123 SRS(ph)PQWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSPQWR 7 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.168)RS(0.832)PQWR 98.044 0.006996 288170000 53429 50420 34658 39626 36722 47454 40552 47564 46299 TRUE FALSE 46368.22228 50088.7877 51418.72472 48623.68895 35991.30405 49279.58609 36619.27328 37392.80874 40825.58496 1.135763819 1.226897 1.259473067 1.19101022 0.881586977 1.207076056 0.896968735 0.915916055 1 15.31718594 3.303927249 7.893398744 0.977582445 1.210514882 0.576025285 0.09499486 0.175635702 18.49151036 0.027262879 0.035144359 2013.386949 -3.303927249 0.232932437 SRS(ph)RDDLYDQDDSRDFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSRDDLYDQDDSRDFPR 18 3 S4R3V8;Q86X29-6;Q86X29-5;Q86X29-2;Q86X29-3;Q86X29-4;Q86X29 S4R3V8 LSR Lipolysis-stimulated lipoprotein receptor 1 S(0.173)RS(0.827)RDDLYDQDDSRDFPR 146.25 4.70E-07 372650000 159680 154770 66662 111850 186800 175610 107360 208020 47870 TRUE FALSE 138577.8834 153753.3057 98899.96617 137247.252 183083.0455 182365.8303 96948.24372 163536.5418 42210.86313 3.282990992 3.642505608 2.342997959 3.251467557 4.337344273 4.320353028 2.296760514 3.874276186 1 15.36532671 1.23182166 24.98489156 0.999995868 3.412416031 0.542928875 0.697383763 185.8324972 688915.4139 1.613719832 0.169623539 17.05381941 -1.23182166 2.412420163 SRS(ph)S(ph)SSPPPKQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSSSSPPPKQK 12 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.144)RS(0.648)S(0.709)S(0.459)S(0.04)PPPKQK 82.529 0.072334 113810000 290640 197070 84121 77065 116630 134120 251480 306750 16200 TRUE FALSE 252231.1876 195775.4342 124802.197 94563.78611 114309.2912 139279.6832 227091.5083 241153.8996 14284.85446 17.65724589 13.70510528 8.736679632 6.619863465 8.002132016 9.750164667 15.89736241 16.88178906 1 13.80219872 4.501326376 3.225699474 10 17.41570335 0.261275854 4.484487872 0.416621209 8.28120819 1.242575302 5.72348256 31719.50312 -4.501326376 7.415703348 SRS(ph)SDIVSSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SRSSDIVSSVR 11 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 S(0.007)RS(0.966)S(0.027)DIVSSVR;S(0.004)RS(0.62)S(0.08)DIVS(0.291)S(0.005)VR;S(0.003)RS(0.965)S(0.032)DIVSSVR;S(0.002)RS(0.905)S(0.088)DIVS(0.004)S(0.001)VR;S(0.005)RS(0.981)S(0.014)DIVSSVR 182.7 3.44E-06 4017990000 2489140 1794490 944210 1296450 1834280 1314070 2850490 2270590 1538220 TRUE FALSE 2160193.842 1782701.877 1400833.114 1590828.787 1797781.417 1364623.123 2574049.919 1785041.998 1356373.384 1.592624765 1.314314995 1.032778386 1.172854618 1.325432538 1.006082204 1.897744345 1.316040273 1 20.37132295 SRS(ph)SHKDSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSSHKDSPR 10 2 O15042-2;O15042;E7ET15;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 S(0.148)RS(0.851)S(0.001)HKDSPR 114.74 0.00068621 33410000 21009 17954 3832 6516.9 12167 12871 21030 21682 4110.1 TRUE FALSE 18232.60742 17836.05899 5685.168017 7996.66175 11924.9005 13366.1557 18990.51384 17045.47303 3624.20866 5.030783029 4.921366473 1.568664652 2.206457326 3.29034601 3.688020462 5.239906313 4.703226174 1 11.8234503 2.478672578 24.95346944 4.009667174 3.336385277 0 1.52167492 241.7313266 3888460.788 0.584390497 0.459286331 301.0735326 -2.478672578 -0.673281897 SRS(ph)SS(ph)PVTELASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSSSPVTELASR 13 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.437)RS(0.558)S(0.428)S(0.576)PVT(0.001)ELASR 57.41 0.038019 0 84110 84664 59110 66713 89178 79388 81394 91186 105140 TRUE FALSE 72994.65039 84107.83661 87695.79371 81861.20629 87403.53227 82442.10773 73500.42241 71686.58351 92710.46898 0.787339889 0.907209699 0.945910367 0.882976941 0.942757956 0.8892427 0.792795282 0.773230729 1 16.50044464 1.209426005 24.73865113 1.000000894 0.865047739 0.316118074 0.062317665 4541.071545 3855649.7 1.884861516 0.017075986 16.19668013 -1.209426005 -0.134953155 SRS(ph)TTELDDYSTNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRSTTELDDYSTNK 14 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.145)RS(0.424)T(0.322)T(0.109)ELDDYSTNK;S(0.003)RS(0.498)T(0.498)T(0.001)ELDDYSTNK;S(0.341)RS(0.624)T(0.035)TELDDYSTNK 254.68 7.67E-24 4193420000 1830150 1901940 1149469 1475980 1991360 1613170 2372870 2788780 2161270 TRUE FALSE 1588291.04 1889446.031 1705356.053 1811123.818 1951735.832 1675229.694 2142749.433 2192421.099 1905767.123 0.833412971 0.991435946 0.894839686 0.950338473 1.024120843 0.87903169 1.124350088 1.150413958 1 20.86194041 2.230797877 24.99109874 1.105208545 0.935466987 0.566233342 0.066618753 114.0436749 367144.705 0.025593378 0.017617838 170.1366501 -2.230797877 -0.169741557 SRS(ph)VEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSVEK 6 1 Q8TF01 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 S(0.215)RS(0.785)VEK 63.216 0.068807 292830000 735070 557620 335680 425860 417840 503290 683470 783390 633000 TRUE FALSE 637928.6371 553956.9575 498015.9708 522558.0219 409525.8015 522651.892 617187.1846 615868.1448 558167.4611 1.14289829 0.992456558 0.892233972 0.936202947 0.733697018 0.936371122 1.105738381 1.103375219 1 19.0903385 2.247230633 23.41221126 1.078220671 0.929825853 0.256879978 0.103705834 106.0705688 286430.2678 0.040768468 0.031020013 176.6975929 -2.247230633 -0.148394818 SRS(ph)WEDS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SRSWEDSPER 10 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IU26;B1AN86 Q9UDY2-7 TJP2 Tight junction protein ZO-2 2 S(0.006)RS(0.994)WEDS(1)PER;S(0.005)RS(0.995)WEDS(1)PER;S(0.003)RS(0.997)WEDS(1)PER;S(0.02)RS(0.98)WEDS(1)PER;S(0.452)RS(0.548)WEDS(0.999)PER;S(0.013)RS(0.987)WEDS(1)PER 164.98 7.17E-05 9731270000 6995880 6295430 3852200 4707320 6052820 6189180 6114700 6662450 6419700 TRUE FALSE 6071356.733 6254074.906 5715136.805 5776188.953 5932380.724 6427281.76 5521697.335 5237736.915 5660770.379 1.072531886 1.104809856 1.009604068 1.020389199 1.047981163 1.135407609 0.975432135 0.925269277 1 22.43256697 2.075191511 8.480683749 0.955226572 1.06143606 0.562517196 0.04073903 0.180967021 18.23847605 0.016921812 0.011387155 118.9026437 -2.075191511 0.106209488 SRS(ph)WEDSPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SRSWEDSPER 10 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IU26;B1AN86 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 S(0.043)RS(0.955)WEDS(0.002)PER;S(0.023)RS(0.957)WEDS(0.02)PER;S(0.003)RS(0.996)WEDS(0.001)PER;SRS(0.988)WEDS(0.012)PER 167.3 1.39E-05 1760130000 1862480 1743810 1225840 1450820 1926930 1731450 1668330 1887130 1818840 TRUE FALSE 1616348.549 1732354.797 1818660.324 1780250.855 1888587.863 1798060.002 1506535.613 1483581.935 1603818.807 1.007812442 1.08014371 1.133956227 1.110007469 1.177556875 1.121111683 0.939342778 0.925030888 1 20.61307973 2.237757846 24.99314172 0.947947439 1.108792263 0.693821221 0.046953157 11.31279099 352184.4422 0.019167965 0.013780204 172.8852115 -2.237757846 0.160844823 SRS(ph)WPASPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SRSWPASPR 9 1 Q86YD1 Q86YD1 PTOV1 Prostate tumor-overexpressed gene 1 protein 1 S(0.002)RS(0.998)WPASPR;SRS(1)WPASPR;SRS(1)WPASPR;SRS(1)WPASPR 124.12 0.00032619 3654280000 411115 448992 278910 336029 452256 423752 423718 539930 383861 TRUE FALSE 356785.1111 446042.542 413791.8089 412329.5203 443256.9904 440054.0136 382625.8936 424470.1712 338481.3899 1.054076005 1.317775675 1.222495006 1.218174862 1.309546119 1.300083333 1.130419293 1.254042863 1 18.36871699 1.234939374 24.99824306 0.999999674 1.230143999 0.427151087 0.082052426 96.63056976 666959.2752 0.133873271 0.018601693 17.17668591 -1.234939374 0.230144325 SRS(ph)WTS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSWTSPK 8 1 O75494-2;O75494 O75494-2 SRSF10 Serine/arginine-rich splicing factor 10 2 S(0.411)RS(0.564)WT(0.208)S(0.816)PK 49.423 0.079754 0 89119 69134 56958 52821 68481 77448 90193 106230 86574 TRUE FALSE 77341.69835 68679.8542 84503.07931 64814.81537 67118.36208 80427.47468 81446.09674 83513.54118 76339.32035 1.01313056 0.899665518 1.10694042 0.849035793 0.879210894 1.053552407 1.066895754 1.093978055 1 16.22013872 2.631445906 7.742952816 1.062042777 0.950134065 0.317031434 0.075478429 0.323015261 20.8823962 0.025565824 0.022508502 428.0021061 -2.631445906 -0.111908713 SRSES(ph)ETSTMAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SRSESETSTMAAK 13 1 Q96B23-2;Q96B23;A0A087WVF1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 S(0.133)RS(0.133)ES(0.735)ETSTMAAK;S(0.074)RS(0.076)ES(0.835)ET(0.012)S(0.002)TMAAK;S(0.224)RS(0.224)ES(0.549)ET(0.003)STMAAK;S(0.144)RS(0.144)ES(0.71)ET(0.001)STMAAK 132.64 7.05E-05 1080934000 868270 605884 539647 691660 775710 697890 1001240 1104560 1189230 TRUE FALSE 753525.9196 601903.9081 800622.0942 848711.9744 760274.8887 724738.2799 904139.8989 868358.4397 1048640.584 0.718574058 0.573984945 0.763485704 0.809344963 0.72500998 0.691121716 0.862201895 0.828080138 1 20.00008886 -2 0.404533393 5.683311963 0.685867764 0.657879111 0.066256417 53.2450684 0.757439102 211.0132569 0.065383248 0.01 2 -4.997444198 SRSHS(ph)DNDRPNCSWNTQYSSAYYTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSHSDNDRPNCSWNTQYSSAYYTSR 26 2 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.327)RS(0.327)HS(0.341)DNDRPNCS(0.004)WNTQYSSAYYTSR 93.776 0.004488 499440000 46728 40718 12213 14215 39416 39406 37812 30554 18689 TRUE FALSE 40552.77641 40450.52078 18119.24765 17442.73301 38631.69872 40921.97432 34144.99806 24020.26487 16479.60771 2.4607853 2.454580321 1.099495083 1.05844346 2.344212277 2.483188619 2.071954543 1.45757504 1 14.00839428 4.275649455 23.43976225 1.685083044 2.457687738 0.290833546 0.524701183 127.9488786 80858.63469 0.14191703 0.37544152 18864.68054 -4.275649455 0.772604694 SRSPIS(ph)AK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSPISAK 8 1 A0A0B4J207;P21108 A0A0B4J207 PRPS1L1 Ribose-phosphate pyrophosphokinase 3 1 S(0.006)RS(0.006)PIS(0.988)AK 62.2 0.049142 299970000 359830 390960 172370 255430 401230 510950 287850 285810 293380 TRUE FALSE 312277.5538 388391.758 255728.7085 313429.2855 393246.308 530606.5771 259934.3513 224691.7557 258696.9506 1.207117258 1.501338756 0.988526181 1.211569308 1.520104149 2.051073953 1.004783206 0.868552007 1 17.98090352 2.028769575 24.99940384 0.928420335 1.404857778 0.374208048 0.278625049 213.681163 185677.9729 0.118451557 0.079858749 106.8487818 -2.028769575 0.476437444 SRSS(ph)PSTDHYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRSSPSTDHYK 11 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 S(0.007)RS(0.146)S(0.555)PS(0.146)T(0.146)DHYK;S(0.066)RS(0.066)S(0.47)PS(0.2)T(0.2)DHYK;S(0.122)RS(0.122)S(0.736)PS(0.01)T(0.01)DHYK 102.29 0.0017489 636781000 952030 822760 441914 673250 770280 774920 913650 1063320 870960 TRUE FALSE 826216.8234 817355.2354 655625.0885 826121.7025 754952.935 804731.6738 825044.3636 835937.2928 767996.101 1.075808617 1.064270033 0.853682835 1.075684761 0.983016625 1.04783302 1.074281969 1.088465543 1 19.55073946 2.558736103 5.627954934 1.06213353 1.00857793 0.083198115 0.067890793 0.488942815 25.7868705 0.023348238 0.020333005 362.0229504 -2.558736103 -0.0535556 SRSS(ph)S(ph)SPPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRSSSSPPPK 10 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.301)RS(0.398)S(0.441)S(0.637)S(0.223)PPPK 62.14 0.049518 517070000 251250 172650 132230 164020 111330 153210 196060 249040 290290 TRUE FALSE 218046.6759 171515.8508 196176.8703 201263.2479 109114.7508 159104.0878 177046.1314 195784.734 255972.2469 0.851837176 0.670056433 0.766398985 0.786269802 0.426275708 0.621567728 0.691661434 0.764867037 1 17.96562787 1.217201036 2.132864294 1.108364967 0.681520415 0.425728438 0.113674259 0.751617909 3.263670948 0.639893236 0.03145597 16.48925508 -1.217201036 -0.426844552 SRSS(ph)SS(ph)PPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRSSSSPPPK 10 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.223)RS(0.362)S(0.426)S(0.312)S(0.677)PPPK;S(0.255)RS(0.356)S(0.412)S(0.401)S(0.575)PPPK 60.401 0.055954 881410000 1135630 781260 582390 739330 518410 662470 870370 1103720 1217760 TRUE FALSE 985553.6182 776127.8516 864035.752 907206.1765 508094.6553 687955.6496 785961.6514 867698.0672 1073797.8 0.917820485 0.722787709 0.804654053 0.844857548 0.473175355 0.640675227 0.731945671 0.808064672 1 20.03429092 1.266331762 2.22339908 1.066881354 0.72724641 0.329492068 0.119440949 0.749260235 3.998822801 0.498836785 0.033132652 18.46425385 -1.266331762 -0.339634944 SRST(ph)TELDDYSTNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRSTTELDDYSTNK 14 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.014)RS(0.236)T(0.728)T(0.021)ELDDYS(0.001)TNK;S(0.02)RS(0.069)T(0.906)T(0.005)ELDDYSTNK 290.37 1.18E-42 2166420000 2136960 2321420 1553960 1933220 2638660 2083470 3020800 3615200 2902000 TRUE FALSE 1854555.322 2306170.439 2305460.254 2372187.148 2586155.828 2163622.439 2727843.281 2842117.614 2558928.866 0.724738912 0.901224911 0.900947379 0.927023482 1.010639984 0.84551879 1.066009813 1.110666909 1 21.28710861 6.706073632 0.210073897 1.128440024 1.88E-15 0.619044506 0.068846275 38.97416396 0.978495483 0.453184002 12.89651805 5082456.055 -6.706073632 -1.128440024 SRT(ph)AS(ph)LTSAASVDGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRTASLTSAASVDGNR 16 1 Q9UN36;Q9UN36-5;G3V578;H0YJT9;A0A0A0MS87;Q9UN36-2;Q9UN36-3;Q9UN36-6;Q9UN36-4 Q9UN36 NDRG2 Protein NDRG2 2 S(0.017)RT(0.982)AS(0.917)LT(0.068)S(0.017)AASVDGNR 143.23 3.59E-05 241390000 225080 192760 123310 151590 236580 156730 288770 240930 183030 TRUE FALSE 195335.1077 191493.7469 182943.1284 186010.8264 231872.5209 162759.5045 260765.1298 189408.9944 161392.4019 1.210311671 1.186510298 1.133529994 1.152537692 1.436700353 1.008470675 1.615721228 1.173593008 1 17.30021313 SRT(ph)GS(ph)ESSQTGTSTTSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 S(0.437)RT(0.57)GS(0.984)ES(0.008)S(0.001)QTGTSTTSSR 73.981 0.044242 377970000 101520 96934 76373 74303 106610 131040 111220 126270 97083 TRUE FALSE 88103.87478 96297.23417 113307.2383 91174.6318 104488.6696 136081.1936 100433.9015 99268.14313 85605.95834 1.029179236 1.124889389 1.323590559 1.065050069 1.220577067 1.589622922 1.173211579 1.159593854 1 16.38542359 4.464315076 7.664925351 1.219414596 1.052042694 0.135055419 0.158509581 0.253590951 90.12241602 0.040323754 0.114595433 29128.29581 -4.464315076 -0.167371901 SRT(ph)PSASNDDQQE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SRTPSASNDDQQE 13 1 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 SRT(0.988)PS(0.012)ASNDDQQE;SRT(0.999)PS(0.001)ASNDDQQE;S(0.013)RT(0.981)PS(0.006)ASNDDQQE;S(0.369)RT(0.613)PS(0.018)ASNDDQQE;S(0.058)RT(0.941)PS(0.001)ASNDDQQE;S(0.139)RT(0.852)PS(0.01)ASNDDQQE 208.66 2.81E-07 1639803000 1776849 1621192 924206 1099875 1497319 1502958 1479853 1632452 1510432 TRUE FALSE 1542033.903 1610542.283 1371155.113 1349618.429 1467525.281 1560777.767 1336337.084 1283364.844 1331870.45 1.157795717 1.209233438 1.029495859 1.013325605 1.101852873 1.171869056 1.003353655 0.963580838 1 20.34502233 2.208358664 0.037293561 3.31E-12 2.070461109 0.410475178 0.064726058 344.8044758 7.422633417 219.8947995 192.0026477 161.5692333 -2.208358664 2.070461109 SRT(ph)PSRHS(ph)CSGS(ph)SPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRTPSRHSCSGSSPPR 16 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(0.158)RT(0.839)PS(0.003)RHS(0.76)CS(0.386)GS(0.518)S(0.337)PPR 79.69 0.028251 54504000 80408 73992 29696 58927 83277 79553 72980 82251 60393 TRUE FALSE 69781.87907 73505.94168 44057.08493 72307.27599 81619.95063 82613.45539 65902.41083 64662.26373 53253.40834 1.310373951 1.380304923 0.827310144 1.35779621 1.532670925 1.551327097 1.23752475 1.214237093 1 15.70058624 1.305693463 1.91837276 0.928124107 1.316738455 0.203754619 0.197893238 1.272494927 5.163907577 0.858199235 0.057765072 20.21591781 -1.305693463 0.388614348 SRT(ph)S(ph)VQT(ph)EDDQLIAGQSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 3 S(0.184)RT(0.858)S(0.959)VQT(0.999)EDDQLIAGQSAR;S(0.21)RT(0.822)S(0.966)VQT(0.921)EDDQLIAGQS(0.08)AR 146.39 2.11E-07 390560000 773090 675020 515000 557500 878920 924990 457130 804890 893960 TRUE FALSE 670924.1977 670585.7492 764055.7226 684088.8959 861431.2116 960574.9638 412797.603 632770.5372 788277.0672 0.851127384 0.850698031 0.969273057 0.867827981 1.092802578 1.2185753 0.523670699 0.802726051 1 19.58834328 2.238215171 24.99999999 0.77065345 0.969614274 0.256406333 0.159974622 13.22270479 956785.328 0.064247822 0.046376935 173.067361 -2.238215171 0.198960824 SRT(ph)SPITR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRTSPITR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.103)RT(0.584)S(0.313)PITR 87.184 0.025065 1542900000 172410 196410 100230 157970 139630 200130 174880 220420 173870 TRUE FALSE 149625.5817 195119.7698 148701.5632 193839.5029 136851.6362 207829.1306 157920.1645 173284.8983 153315.2867 0.975933874 1.272670025 0.969906958 1.264319476 0.892615728 1.355566918 1.030035347 1.130251928 1 17.22614203 0.673441288 2.000356492 0.474096241 1.116206659 0.048528441 0.150151003 22.06849934 16.82549949 47.12383929 0.035543494 4.71456131 -0.673441288 0.642110418 SRT(ph)SVQTEDDQLIAGQS(ph)AR ddPTM_MDA-MB-175_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(0.001)RT(0.831)S(0.167)VQTEDDQLIAGQS(1)AR 236.19 8.77E-23 534070000 572230 485320 321860 408070 555820 605350 448740 528890 487850 TRUE FALSE 496608.3557 482131.901 477512.5726 500728.5305 544760.2694 628638.2062 405221.2639 415790.9893 430176.9288 1.154428149 1.120775822 1.110037616 1.16400601 1.266363287 1.461348027 0.94198744 0.966558087 1 18.71457063 2.161342585 25 0.967749279 1.204202974 0.562822007 0.100892873 27.59762776 8933.658856 0.043839694 0.029556722 144.9915141 -2.161342585 0.236453694 SRT(ph)SVQTEDDQLIAGQSAR ddPTM_MDA-MB-175_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(0.191)RT(0.571)S(0.236)VQT(0.003)EDDQLIAGQSAR 265.3 3.40E-31 367050000 148040 141220 69151 123260 145680 164280 126850 167540 126120 TRUE FALSE 128476.1389 140292.3165 102592.6549 151248.0669 142781.253 170599.9579 114548.1065 131712.8748 111210.2373 1.155254607 1.261505415 0.922510889 1.360019281 1.283885877 1.534031058 1.030014047 1.184359264 1 16.76293007 SRTGS(ph)ESSQTGTSTTSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SRT(0.293)GS(0.697)ES(0.009)SQTGTSTTSSR;SRT(0.277)GS(0.645)ES(0.069)S(0.008)QT(0.002)GTSTTSSR;S(0.027)RT(0.085)GS(0.804)ES(0.084)S(0.001)QTGTSTTSSR 191.07 6.42E-14 583470000 156713 168299 45858.9 59163.6 303993 309898 386214 361782 8490.11 TRUE FALSE 136002.98 167193.4328 68036.41743 72597.59964 297944.1341 321819.9766 348759.0257 284417.7347 7486.418868 18.16662711 22.33289851 9.087978996 9.697239885 39.79795137 42.98717214 46.58556139 37.99115969 1 12.87006005 1.227148813 24.99999829 0.999940635 29.08462756 0.28750637 13.4750414 793.9383594 1739178.662 58.09923778 3.775049855 16.87131031 -1.227148813 28.08468692 SRTS(ph)PAPWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRTSPAPWK 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.279)RT(0.279)S(0.442)PAPWK 69.451 0.033432 1757300000 1697500 1290800 895290 1217900 1293600 1117100 1406300 1635600 1888400 TRUE FALSE 1473171.074 1282320.65 1328255.239 1494442.809 1267859.891 1160075.56 1269917.242 1285839.668 1665155.503 0.884704805 0.77009063 0.797676395 0.897479428 0.7614063 0.696677012 0.762641831 0.772203957 1 20.66722548 1.235753861 24.99762369 1.000000283 0.789194976 0.546106669 0.059264113 62.09507418 552925.2136 0.100135511 0.014822565 17.20892974 -1.235753861 -0.210805307 S(ph)SGASSIFDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSGASSIFDLR 11 0 Q96HP0 Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 1 S(0.922)S(0.078)GASSIFDLR 185.84 4.50E-06 40715000 40456 53242 44806 48033 74943 76143 68270 74936 86574 TRUE FALSE 35109.6371 52892.2498 66474.33147 58939.62679 73451.78092 79072.27048 61649.18591 58911.51955 76339.32035 0.459915505 0.692857227 0.870774473 0.772074293 0.962174939 1.035800032 0.807567917 0.771706105 1 16.22013872 4.789373576 1.27451349 0.885642935 0.227039795 0.709781736 0.090210318 0.947529777 1.234158617 0.027918661 0.842234487 61570.62694 -4.789373576 -0.65860314 down SRTS(ph)PITR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRTSPITR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.171)RT(0.171)S(0.658)PITR;S(0.066)RT(0.04)S(0.894)PITR;S(0.193)RT(0.125)S(0.682)PITR 84.507 0.010539 4305580000 602590 593920 277213 384114 606064 470310 552390 625628 479298 TRUE FALSE 522956.2047 590018.5004 411274.134 471332.9545 594004.5121 488403.13 498819.3028 491842.3208 422635.9365 1.23736805 1.396044324 0.973116809 1.115222142 1.405475637 1.15561193 1.180257663 1.163749408 1 18.68905592 0.416473237 1.151094925 1.91E-08 1.212821071 0.215824167 0.125600681 15.42745198 3.998877754 35.98142943 0.038924799 2.608994942 -0.416473237 1.212821052 SRTS(ph)PVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRTSPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.136)RT(0.136)S(0.729)PVSR;S(0.355)RT(0.124)S(0.521)PVSR;S(0.302)RT(0.184)S(0.514)PVSR 74.962 0.023996 3226050000 1213080 787360 1798540 759529 522700 771260 734520 805850 638130 TRUE FALSE 1052768.404 782187.7803 2668319.96 931991.6681 512299.2926 800930.8713 663286.3635 633525.2486 562690.9984 1.870952988 1.390084047 4.742069746 1.656311672 0.910445154 1.423393787 1.178775501 1.125884812 1 19.10198336 3.48915566 24.94194843 1.158569093 2.649815487 0.397685397 0.864702666 562.7010752 1166227.134 0.237073932 0.331193091 3084.293229 -3.48915566 1.491246394 SRTS(ph)PVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SRTSPVTR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.311)RT(0.164)S(0.525)PVTR;S(0.301)RT(0.185)S(0.513)PVT(0.001)R;S(0.134)RT(0.095)S(0.771)PVTR;S(0.027)RT(0.204)S(0.769)PVTR 108.98 0.0022441 14258500000 1095907 989328 450838 623962 746889 835506 867872 1003670 850696 TRUE FALSE 951080.1133 982829.0392 668864.7648 765642.1088 732027.3702 867648.4565 783705.907 789042.9811 750127.688 1.267890958 1.310215654 0.891667879 1.020682373 0.975870351 1.156667685 1.044763338 1.051878225 1 19.51677667 4.254938919 24.99992234 1.027666091 1.289053509 0.73492943 0.067005972 122.5647646 187080.1827 0.016640575 0.043740539 17986.17931 -4.254938919 0.261387419 SRTS(ph)VQT(ph)EDDQLIAGQSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 2 S(0.001)RT(0.087)S(0.912)VQT(1)EDDQLIAGQSAR;S(0.355)RT(0.355)S(0.399)VQT(0.892)EDDQLIAGQSAR 203.58 1.25E-14 790490000 925680 836100 534764 764422 979380 1021080 697710 1062320 832620 TRUE FALSE 803349.0426 830607.604 793377.6591 937995.6986 959892.2541 1060361.608 630046.1916 835151.135 734188.6121 1.094199814 1.131327278 1.080618312 1.277594998 1.307419154 1.444263219 0.858153043 1.137515784 1 19.48579121 2.227137294 24.99970477 1.021656103 1.218328573 0.404792986 0.126957247 258.530129 565782.9693 0.053867504 0.036668562 168.7086283 -2.227137294 0.19667247 SRTS(ph)VQTEDDQLIAGQSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 1 S(0.007)RT(0.126)S(0.867)VQTEDDQLIAGQSAR;S(0.065)RT(0.216)S(0.719)VQTEDDQLIAGQSAR;S(0.111)RT(0.357)S(0.531)VQTEDDQLIAGQSAR 299.12 4.79E-50 3537060000 824530 700254 397319 710096 801990 866170 580921 964790 606681 TRUE FALSE 715566.2714 695653.9854 589463.7974 871334.1499 786031.9681 899492.1204 524583.3708 758477.1665 534959.8633 1.337607399 1.30038538 1.101884156 1.628784157 1.469328864 1.681419826 0.980603232 1.417820697 1 19.02907113 1.232960523 24.91968055 0.999999402 1.360404364 0.225573655 0.212248134 280.7416431 1249124.345 0.434338115 0.050904034 17.09859884 -1.232960523 0.360404962 SRTSPVT(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRTSPVTR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.002)RT(0.012)S(0.041)PVT(0.945)R 99.788 0.041813 2698500000 2287200 1803000 994350 1242200 1581400 1775900 1619400 1889100 1489400 TRUE FALSE 1984940.725 1791155.974 1475220.986 1524260.496 1549933.234 1844220.022 1462350.837 1485130.666 1313324.829 1.511385974 1.363833178 1.123271984 1.160611954 1.180159851 1.404237537 1.113472315 1.130817474 1 20.32479236 4.432587015 3.219590299 1.163617628 1.496080045 0.585771505 0.101014606 0.178992618 3.6180947 0.026780551 0.102986392 27076.15648 -4.432587015 0.332462417 SRWDETPASQMGGST(ph)PVLTPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRWDETPASQMGGSTPVLTPGK 22 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 SRWDETPASQMGGS(0.157)T(0.843)PVLTPGK;SRWDETPASQMGGS(0.009)T(0.991)PVLTPGK 181.77 7.84E-17 577010000 543300 436270 227785 344830 513930 361930 519420 628960 321410 TRUE FALSE 471501.5285 433404.1136 337942.5879 423128.9219 503703.7985 375853.6813 469046.7283 494461.7986 283413.276 1.663653641 1.529230105 1.192402109 1.492974951 1.777276653 1.326168226 1.654992085 1.744667031 1 18.11254781 1.225526911 24.87936167 0.999998603 1.548801088 0.474621153 0.181082397 577.7821723 1102826.822 0.83336199 0.045719088 16.80842074 -1.225526911 0.548802485 SRWS(ph)GSHQFEQLSGSILWMAPEVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRWSGSHQFEQLSGSILWMAPEVIR 25 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8Y492;H7C4S5 P15056 BRAF Serine/threonine-protein kinase B-raf 1 S(0.01)RWS(0.8)GS(0.184)HQFEQLS(0.007)GSILWMAPEVIR;S(0.145)RWS(0.828)GS(0.026)HQFEQLSGSILWMAPEVIR 269.55 2.25E-46 673405000 300455 221046 134586 151474 239832 254923 247411 273722 183169 TRUE FALSE 260749.1105 219593.9343 199672.2398 185868.4868 235059.8124 264730.0528 223417.1193 215188.6804 161514.9695 1.614395937 1.359588743 1.23624603 1.150781797 1.455343818 1.63904345 1.383259521 1.332314157 1 17.30130836 1.20716039 2.705454378 0.890364537 1.397017187 0.420984853 0.148145721 0.581206209 4.580769087 0.696763133 0.04122603 16.11240577 -1.20716039 0.50665265 SRWS(ph)GSQQVEQPTGSVLWMAPEVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SRWSGSQQVEQPTGSVLWMAPEVIR 25 1 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 S(0.22)RWS(0.663)GS(0.117)QQVEQPTGSVLWMAPEVIR;S(0.049)RWS(0.775)GS(0.176)QQVEQPTGSVLWMAPEVIR;S(0.155)RWS(0.69)GS(0.155)QQVEQPTGSVLWMAPEVIR 219.93 7.77E-34 941900000 138603 136199 80181 102672 166822 163049 154433 179922 137170 TRUE FALSE 120286.2624 135304.2998 118956.7998 125985.2468 163502.5686 169321.6005 139456.1114 141447.0805 120953.9189 0.994480076 1.118643373 0.983488596 1.041597065 1.351775702 1.399885197 1.152968938 1.169429497 1 16.88409799 3.327517221 11.1880483 1.213692615 1.036375284 0.382871806 0.113714541 0.514658781 61.33350321 0.034814726 0.044942796 2125.774636 -3.327517221 -0.177317331 SRWSGS(ph)HQFEQLSGSILWMAPEVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SRWSGSHQFEQLSGSILWMAPEVIR 25 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8Y492;H7C4S5 P15056 BRAF Serine/threonine-protein kinase B-raf 1 S(0.003)RWS(0.379)GS(0.617)HQFEQLSGSILWMAPEVIR 233 1.44E-38 621180000 396330 328420 280650 233130 277850 338610 386910 376800 237290 TRUE FALSE 343953.9863 326262.5874 416373.2787 286065.7297 272321.3286 351636.5458 349387.5278 296224.2523 209237.8465 1.643842125 1.559290505 1.989952036 1.367179669 1.301491738 1.680558999 1.669810379 1.415729789 1 17.6747843 1.289737822 2.545429998 0.896798048 1.596472386 0.510476383 0.186288232 0.391606855 3.062463524 0.568582665 0.05025131 19.48667859 -1.289737822 0.699674338 SRWSGS(ph)QQVEQPTGSVLWMAPEVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SRWSGSQQVEQPTGSVLWMAPEVIR 25 1 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 S(0.309)RWS(0.309)GS(0.383)QQVEQPTGSVLWMAPEVIR;S(0.31)RWS(0.31)GS(0.381)QQVEQPTGSVLWMAPEVIR 85.573 0.010485 212896000 34282 31912 18409.2 25283 28838 36592 38343 38779 34680 TRUE FALSE 29751.54684 31702.36797 27311.9507 31023.89158 28264.18022 37999.71792 34624.50176 30486.41263 30580.16991 0.972903255 1.03669692 0.893126192 1.014510111 0.924264983 1.242626121 1.132253413 0.99693405 1 14.9003088 2.839699755 22.77519926 1.081894883 0.970490517 0.374767513 0.079405291 23.72302248 5333.468483 0.026600947 0.026601014 691.3528459 -2.839699755 -0.111404365 SS(ph)DEENGPPSS(ph)PDLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSDEENGPPSSPDLDR 16 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 2 S(0.185)S(0.815)DEENGPPS(0.04)S(0.96)PDLDR;S(0.316)S(0.684)DEENGPPS(0.01)S(0.99)PDLDR;S(0.488)S(0.512)DEENGPPS(0.018)S(0.982)PDLDR 439.78 9.72E-182 1690540000 1031190 973970 717120 896660 1219410 1110760 1071510 1207040 1407630 TRUE FALSE 894915.6288 967571.9269 1063921.631 1100260.358 1195146.127 1153491.656 967595.1251 948923.8892 1241221.585 0.720995864 0.779531986 0.857156888 0.886433471 0.962878942 0.929319688 0.779550676 0.764508046 1 20.24332926 4.380737916 2.347701321 0.872745499 0.722659548 0.371448457 0.073184006 0.430049334 4.333096555 0.021426378 0.09656445 24029.12275 -4.380737916 -0.15008595 SS(ph)DGS(ph)LSHEEDLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSDGSLSHEEDLAK 14 0 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 2 S(0.122)S(0.878)DGS(0.988)LS(0.012)HEEDLAK;S(0.422)S(0.578)DGS(1)LSHEEDLAK 226.7 4.47E-09 88781000 620570 566050 434020 480680 580940 490320 671460 759880 812540 TRUE FALSE 538560.1022 562331.5803 643913.5237 589825.7407 569380.4306 509182.9277 606341.9125 597385.5754 716482.4468 0.75167243 0.784850463 0.898715002 0.823224272 0.794688597 0.710670485 0.846276019 0.833775591 1 19.45057183 0.995064218 1.725541985 1.203699213 0.801268809 0.601056127 0.050499371 1.439649293 2.310033024 1.19376949 0.014449445 9.886992811 -0.995064218 -0.402430404 SS(ph)DSWEVWGSASTNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSDSWEVWGSASTNR 15 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 S(0.245)S(0.755)DSWEVWGSASTNR 194 7.31E-08 547970000 401420 411640 318200 375960 415470 489310 453850 462520 1060100 TRUE FALSE 348371.3299 408935.9097 472082.5843 461327.4642 407202.9599 508134.0723 409835.6969 363613.6973 934776.1857 0.372678867 0.437469328 0.505022049 0.493516492 0.435615462 0.543589022 0.438431898 0.388984768 1 19.83426145 1.23446173 24.99999801 1.000000796 0.453195638 0.917959852 0.051492293 33.21853017 202578.852 0.097850372 0.013050288 17.15780509 -1.23446173 -0.546805157 SS(ph)FSHYSGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSFSHYSGLK 10 0 Q8NC51;Q8NC51-3 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 S(0.201)S(0.784)FS(0.015)HYSGLK 190.78 5.56E-07 723730000 695430 706080 217090 688660 912380 715430 1015300 905730 1769300 TRUE FALSE 603527.1635 701441.714 322075.4501 845030.7785 894225.423 742953.055 916836.3623 712046.6879 1560135.37 0.386842818 0.44960311 0.206440708 0.541639396 0.573171688 0.476210635 0.587664622 0.45640058 1 20.57323978 0.226358486 1.569207948 9.999999973 0.451510364 0.694288804 0.111384491 13.77860805 2.263936324 413.532069 0.03215853 1.684063587 -0.226358486 -9.548489609 SS(ph)FSQHAR ddPTM_MDA-MB-175_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(0.361)S(0.586)FS(0.054)QHAR;S(0.356)S(0.644)FSQHAR 136.49 0.00050808 3229000000 3846700 3692100 1722340 2281200 3719400 4045500 3743400 3823200 4060800 TRUE FALSE 3338348.849 3667846.352 2555269.385 2799181.326 3645391.217 4201133.003 3380365.644 3005638.432 3580736.85 0.932307787 1.024327256 0.713615519 0.781733326 1.018056163 1.173259354 0.944041907 0.839391041 1 21.77182507 3.224557964 24.99973911 0.980602268 0.863849589 0.238983711 0.115434485 433.3072428 773606.1181 0.03883483 0.044250803 1677.096156 -3.224557964 -0.116752679 SS(ph)GFISELPSEEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSGFISELPSEEGK 14 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 S(0.229)S(0.771)GFISELPSEEGK;S(0.209)S(0.791)GFISELPSEEGK;S(0.16)S(0.84)GFISELPSEEGK 318.7 5.31E-56 381281000 1102830 1150920 896150 994460 1324880 1118470 1525970 1691130 1571000 TRUE FALSE 957088.2213 1143359.531 1329531.137 1220267.342 1298517.48 1161498.265 1377981.664 1329495.01 1385278.17 0.690899663 0.825364577 0.959757518 0.880882533 0.937369482 0.838458506 0.994732823 0.959731438 1 20.40174427 5.497710399 0.855296759 0.946442538 5.20E-18 0.71956149 0.050219542 4.000725332 0.892313613 0.017394989 4.83859536 314564.9995 -5.497710399 -0.946442538 SS(ph)GS(ph)ETEQVVDFSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSGSETEQVVDFSDR 15 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 2 S(0.433)S(0.567)GS(0.994)ET(0.005)EQVVDFSDR 103.87 0.0037521 0 181920 141270 94979 99180 135630 129940 128660 157330 153690 TRUE FALSE 157878.8111 140341.9881 140911.1621 121700.3349 132931.2284 134938.8759 116182.573 123686.2038 135520.9433 1.164977215 1.035574168 1.039774065 0.898018652 0.980890666 0.995704963 0.857303456 0.912672247 1 17.0481563 5.988447634 0.595710855 0.928440137 2.068799341 0.673336546 0.049447938 8.419724739 0.733231852 0.024358305 9.174882418 973750.3667 -5.988447634 1.140359205 SS(ph)GSETEQVVDFSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSGSETEQVVDFSDR 15 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 S(0.098)S(0.891)GS(0.011)ETEQVVDFSDR;SS(0.763)GS(0.237)ETEQVVDFSDR;S(0.002)S(0.638)GS(0.36)ETEQVVDFSDR;S(0.263)S(0.734)GS(0.003)ETEQVVDFSDR 426.29 2.94E-153 895410000 1132020 727397 539980 588404 776780 863120 809840 897610 922910 TRUE FALSE 982420.6888 722618.6812 801116.1341 722010.1214 761323.5977 896324.7849 731301.8414 705663.0867 813804.6312 1.207194763 0.887951055 0.984408424 0.88720326 0.935511508 1.101400447 0.898620889 0.867116086 1 19.63432296 4.745616157 24.84626361 0.940965005 1.207194898 0.579779832 0.069991452 567.6797686 1999044.825 0.017222503 0.166721634 55669.35085 -4.745616157 0.266229893 SS(ph)IDSQASLSGPLSGGAPGAGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSIDSQASLSGPLSGGAPGAGAR 23 0 A6NKD9 A6NKD9 CCDC85C Coiled-coil domain-containing protein 85C 1 S(0.206)S(0.794)IDSQASLSGPLSGGAPGAGAR;S(0.246)S(0.754)IDSQASLSGPLSGGAPGAGAR;S(0.187)S(0.813)IDSQASLSGPLSGGAPGAGAR;S(0.246)S(0.754)IDSQASLSGPLSGGAPGAGAR 404.34 3.39E-157 1590580000 590302 640577 494696 633443 795349 776460 703387 827930 1002120 TRUE FALSE 512292.0951 636369.0075 733932.6403 777275.9147 779523.111 806330.9186 635172.637 650883.6125 883650.5152 0.579745144 0.720159154 0.830568904 0.87961915 0.882162232 0.9124998 0.718805258 0.736584884 1 19.75311637 4.550969947 2.144150611 0.839220412 0.558355158 0.544793786 0.081640677 0.394332864 2.725179987 0.022974694 0.182672139 35560.67098 -4.550969947 -0.280865254 SS(ph)IEDAQCPGLPDLIEENHVVNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSIEDAQCPGLPDLIEENHVVNK 23 0 Q15398-1;Q15398;Q15398-3 Q15398-1 DLGAP5 Disks large-associated protein 5 1 S(0.43)S(0.57)IEDAQCPGLPDLIEENHVVNK 245.2 8.00E-40 0 29359 26219 16831 21600 26644 20854 26509 35678 26998 TRUE FALSE 25479.13376 26046.76566 24970.5279 26504.61014 26113.83653 21656.26687 23938.16126 28048.53735 23806.3272 1.07026731 1.094111051 1.048902995 1.113343101 1.096928405 0.909685341 1.005537774 1.178196751 1 14.53905744 SS(ph)ITEPEGPNGPNIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSITEPEGPNGPNIQK 16 0 Q13625-2;Q13625;Q13625-3 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 S(0.217)S(0.783)ITEPEGPNGPNIQK 293.42 1.42E-45 153000000 283120 212360 171240 299840 219900 173130 212180 277250 544800 TRUE FALSE 245704.9747 210964.9932 254052.2368 367923.2548 215524.4202 179790.4231 191602.8163 217962.2451 480394.3646 0.511465148 0.4391496 0.528841001 0.765877541 0.448640609 0.374255895 0.398844846 0.453715241 1 18.8738597 1.236271111 24.99586169 1.000000665 0.487436676 0.686623718 0.10824527 38.5243366 420493.9372 0.183271577 0.028243204 17.22943796 -1.236271111 -0.512563989 SS(ph)LETLEDIEENAPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSLETLEDIEENAPLR 16 0 Q8TDN4-2;Q8TDN4;V9GYB4 Q8TDN4-2 CABLES1 CDK5 and ABL1 enzyme substrate 1 1 S(0.205)S(0.795)LETLEDIEENAPLR 247.9 2.53E-20 67397000 141200 123180 89048 130370 157620 135180 186170 186680 236060 TRUE FALSE 122540.0622 122370.8225 132111.9106 159972.5011 154483.6704 140380.4621 168115.2621 146759.9347 208153.2557 0.588701156 0.587888102 0.634685776 0.768532303 0.742163123 0.674409159 0.80765137 0.705057119 1 17.6672866 -2 0.198248722 2.159492419 0.547322728 0.63960172 0.073008457 76.13981249 1.127324078 36.78983015 0.495005349 0.01 2 -1.612169691 SS(ph)LETLEDIEENAPLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSLETLEDIEENAPLRR 17 1 Q8TDN4-2;Q8TDN4;V9GYB4 Q8TDN4-2 CABLES1 CDK5 and ABL1 enzyme substrate 1 1 S(0.101)S(0.898)LET(0.001)LEDIEENAPLRR;S(0.163)S(0.837)LETLEDIEENAPLRR;S(0.187)S(0.813)LETLEDIEENAPLRR;S(0.015)S(0.984)LETLEDIEENAPLRR 345.77 9.66E-88 1067060000 206262 185008 109636 139798 183838 188076 244428 253348 167842 TRUE FALSE 179003.9541 183792.6703 162656.3363 171541.2726 180179.9835 195311.4054 220723.4102 199171.5018 147999.91 1.209486912 1.241843122 1.099029968 1.159063358 1.217433061 1.319672461 1.4913753 1.345754209 1 17.17523677 2.859180043 3.744951598 1.316748122 1.177596572 0.133093552 0.126274941 0.399506276 9.999789211 0.043216432 0.043354219 723.0694999 -2.859180043 -0.13915155 SS(ph)LGSLQTPEAVTTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSLGSLQTPEAVTTR 15 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 S(0.088)S(0.912)LGSLQTPEAVTTR 207.65 3.45E-09 241660000 207740 185700 120740 140670 206320 208970 228910 234710 247780 TRUE FALSE 180286.6327 184480.1245 179130.2679 172611.2735 202214.6357 217009.2111 206710.3434 184519.093 218487.7307 0.825156782 0.844350042 0.819864197 0.790027307 0.92551941 0.99323294 0.946095887 0.844528397 1 17.73719274 3.223824775 21.41986058 0.932591597 0.821600708 0.647935061 0.044395756 31.00697803 45070.82439 0.014278329 0.016297224 1674.267223 -3.223824775 -0.110990889 SS(ph)LPNGEGLQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSLPNGEGLQLK 12 0 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 S(0.409)S(0.591)LPNGEGLQLK;S(0.045)S(0.955)LPNGEGLQLK;S(0.269)S(0.731)LPNGEGLQLK;S(0.018)S(0.982)LPNGEGLQLK 196.05 2.21E-07 1819500000 4873350 3871270 3925760 5190000 4695800 3720110 4872030 5728100 14332900 TRUE FALSE 4229324.45 3845839.372 5824270.667 6368468.824 4602362.767 3863225.039 4399541.28 4503190.391 12638480.89 0.334638671 0.304296015 0.460836292 0.503895118 0.364154744 0.305671629 0.348106811 0.356307885 1 23.59131973 1.23764751 24.99996258 1.000000734 0.37278738 0.905522369 0.063725115 6.933084361 189714.6685 0.099245387 0.016840816 17.28412945 -1.23764751 -0.627213355 SS(ph)LQVDWHEEEWEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSLQVDWHEEEWEK 14 0 Q96PE3-2;Q96PE3-4;Q96PE3-3;Q96PE3 Q96PE3-2 INPP4A "Type I inositol 3,4-bisphosphate 4-phosphatase" 1 S(0.142)S(0.858)LQVDWHEEEWEK 293.44 9.86E-44 140080000 252690 222240 248500 229260 290120 266370 326530 380030 418380 TRUE FALSE 219296.3763 220780.0908 368675.4312 281316.987 284347.1796 276617.4263 294863.1709 298763.5419 368919.593 0.594428652 0.598450435 0.999338171 0.762542821 0.770756514 0.749804108 0.799261347 0.809833762 1 18.49294689 4.273914037 23.86908951 0.8278996 0.596438432 0.555443046 0.090553912 83.11434876 56113.1526 0.021980464 0.058147764 18789.44869 -4.273914037 -0.231461169 SS(ph)LS(ph)GDEEDELFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSLSGDEEDELFK 13 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 2 S(0.097)S(0.903)LS(1)GDEEDELFK;S(0.494)S(0.506)LS(1)GDEEDELFK;S(0.432)S(0.568)LS(1)GDEEDELFK;S(0.036)S(0.964)LS(1)GDEEDELFK 236.12 1.53E-16 733417000 2544920 2126180 1824840 1708870 2552040 1879400 2744800 3278700 3039820 TRUE FALSE 2208602.374 2112212.984 2707338.728 2096895.052 2501259.397 1951701.734 2478609.718 2577575.52 2680455.943 0.823965184 0.788005111 1.010029184 0.782290437 0.933146991 0.728123042 0.924697056 0.961618312 1 21.35404699 2.009997775 24.98017809 0.967594653 0.848457143 0.338557061 0.079914086 224.0030892 559686.0454 0.030736778 0.020696004 102.3287749 -2.009997775 -0.11913751 SS(ph)LSGDEEDELFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSLSGDEEDELFK 13 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 S(0.225)S(0.775)LSGDEEDELFK;S(0.134)S(0.864)LS(0.001)GDEEDELFK 232.5 6.74E-13 80560000 357500 318530 247740 310410 349760 276920 422560 478270 438540 TRUE FALSE 310255.4692 316437.5555 367547.8926 380893.3348 342800.4603 287573.2916 381580.1962 375995.6824 386696.3008 0.802323344 0.818310273 0.95048205 0.984993479 0.886484974 0.743667035 0.986769709 0.972328108 1 18.56084144 -1.999999438 0.393774764 3.339774665 0.861582862 0.267431166 0.077158253 120.2331216 1.745337071 227.8567169 0.084868707 0.010000013 1.999999438 -2.478191803 SS(ph)LSLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSLSLAK 7 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8;REV__J3KQ37 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 S(0.088)S(0.912)LSLAK 164.46 0.0012557 277610000 568390 515480 225610 436160 451070 284130 821810 684800 766750 TRUE FALSE 493275.8214 512093.7779 334715.7506 535196.7943 442094.5895 295060.665 742110.9927 538360.8491 676105.6885 0.729583895 0.757416757 0.495064243 0.791587474 0.653883848 0.436412043 1.097625719 0.796267297 1 19.36688926 2.232339258 24.99999206 0.935096658 0.64953623 0.562997406 0.132257651 115.6974916 464914.7533 0.051008441 0.035358384 170.741565 -2.232339258 -0.285560428 SS(ph)LSLEEADSEVEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSLSLEEADSEVEGR 15 0 Q5JTZ5 Q5JTZ5 C9orf152 Uncharacterized protein C9orf152 1 S(0.026)S(0.974)LSLEEADSEVEGR 219.95 5.73E-12 0 35307 40652 24103 33720 40547 37036 40478 45856 50721 TRUE FALSE 30641.09049 40384.95434 35759.29142 41376.64138 39740.19403 38460.79889 36552.44979 36050.05125 44724.82116 0.685102583 0.902965139 0.799540177 0.925138219 0.888548976 0.859943045 0.817274364 0.806041261 1 15.44878809 4.745826285 24.7635557 0.866016834 0.685102486 0.481937658 0.061236009 699.543184 2384184.146 0.014484504 0.143487051 55696.29234 -4.745826285 -0.180914348 SS(ph)LVTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SSLVTSK 7 0 A6NMQ3;Q5T5H1;O43768-2;O43768;O43768-9;O43768-3;O43768-4;A0A1W2PRU0;O43768-6;O43768-5;O43768-7 A6NMQ3 ENSA Alpha-endosulfine 1 S(0.118)S(0.882)LVTSK;SS(1)LVTSK;S(0.001)S(0.999)LVTSK;S(0.116)S(0.884)LVTSK;S(0.145)S(0.855)LVTSK 215.14 4.23E-05 9585840000 41081500 35959920 20631830 27901430 27590710 25535690 50481200 44950300 40343700 TRUE FALSE 35652475.69 35723696.92 30609452 34236876.13 27041708.85 26518064.52 45585540.99 35338028.15 35574313.75 1.002197145 1.004199186 0.860436893 0.962404401 0.760147028 0.745427296 1.281417298 0.993357972 1 25.08433259 2.249461827 24.99991465 1.079035817 0.890528362 0.396451879 0.117408129 230.122689 527743.9533 0.04518076 0.034649697 177.6077151 -2.249461827 -0.188507455 SS(ph)LYGIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSLYGIAK 8 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.426)S(0.574)LYGIAK;S(0.021)S(0.979)LYGIAK;S(0.009)S(0.991)LYGIAK;S(0.001)S(0.999)LYGIAK 213.24 1.73E-05 903740000 3780680 3967790 2493200 3336450 4644940 3768890 5363130 5607450 5767560 TRUE FALSE 3281053.559 3941725.326 3698919.859 4094041.967 4552514.782 3913881.637 4843014.478 4408340.455 5085725.627 0.645149542 0.775056622 0.727314081 0.805006457 0.895155405 0.769581752 0.952276004 0.866806583 1 22.2780222 6.216413593 0.116421318 1.179774545 1.06E-13 0.725481964 0.05559562 69.38152115 1.224564215 2.607028645 14.00075259 1645938.458 -6.216413593 -1.179774545 SS(ph)PAELSSSSQHLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPAELSSSSQHLLR 15 0 Q9UQC2;Q9UQC2-2;E9PJE2 Q9UQC2 GAB2 GRB2-associated-binding protein 2 1 S(0.159)S(0.841)PAELSSSSQHLLR 184.22 4.96E-07 176150000 80373 105290 52386 84346 151920 145620 122860 150270 151250 TRUE FALSE 69751.50441 104598.3431 77720.04482 103498.0484 148897.0892 151222.0956 110945.0561 118135.9299 133369.3973 0.522994824 0.784275442 0.582742716 0.776025464 1.116426198 1.133859031 0.831862919 0.885779889 1 17.02506814 3.444440185 5.71197346 0.974297942 0.649700398 0.688306366 0.112245319 0.114521481 10.34831451 0.034271929 0.045349106 2782.532109 -3.444440185 -0.324597544 SS(ph)PELTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPELTR 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.183)S(0.817)PELTR;S(0.256)S(0.744)PELTR 185.55 0.00064179 1125470000 902250 818080 494954 620100 705520 673350 654260 813640 967030 TRUE FALSE 783015.3765 812705.9786 734315.4099 760903.1826 691481.5323 699254.2102 590809.9659 639649.4178 852708.815 0.918268186 0.953087343 0.861156114 0.89233648 0.810923401 0.820038679 0.692862505 0.750138156 1 19.70169365 3.450721761 1.309135483 0.793952345 0.926509759 0.224948918 0.081181421 0.566850347 2.006329783 0.030033505 0.052819669 2823.070743 -3.450721761 0.132557414 SS(ph)PEQPRPSTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(0.118)S(0.882)PEQPRPSTSK;S(0.039)S(0.961)PEQPRPSTSK;S(0.123)S(0.876)PEQPRPSTSK;S(0.125)S(0.875)PEQPRPSTSK;S(0.021)S(0.979)PEQPRPSTSK 200.63 9.55E-08 6336670000 7080480 5489640 3835170 4244300 5427370 4369790 6573580 7294490 6498250 TRUE FALSE 6144776.628 5453578.193 5689871.04 5208033.185 5319375.955 4537898.649 5936075.223 5734620.079 5730034.288 1.072380429 0.951753152 0.992990749 0.908900876 0.928332308 0.79194965 1.035958063 1.000800308 1 22.45011234 -0.97707507 8.949214652 9.217853308 0.963307256 0 0.077809254 0 0 0 0.017675217 0.105420466 0.97707507 -8.254546051 SS(ph)PGAVAGLSNAPGTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPGAVAGLSNAPGTPR 17 0 V9GYB2;Q9BWG4-2;Q9BWG4;U3KPY3 V9GYB2 SSBP4 Single-stranded DNA-binding protein 4 1 S(0.347)S(0.653)PGAVAGLSNAPGTPR;S(0.15)S(0.85)PGAVAGLSNAPGTPR 325.49 2.65E-59 1393150000 1106690 1180280 727440 805890 1220810 1097260 1044640 1273130 1144550 TRUE FALSE 960438.1125 1172526.663 1079232.417 988879.6418 1196518.269 1139472.302 943330.9736 1000881.057 1009242.603 0.951642459 1.161788711 1.06934885 0.979823522 1.185560604 1.129037061 0.934691987 0.991715029 1 19.94484158 2.237419647 24.99985624 0.977154548 1.083096606 0.303657857 0.07414204 35.96478319 787989.8752 0.028300142 0.020302738 172.7506329 -2.237419647 0.105942059 SS(ph)PGGQDEGGFMAQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSPGGQDEGGFMAQGK 16 0 F5GZ78;A0A1B0GTU4;P49023;A0A1B0GV30 F5GZ78 PXN Paxillin 1 S(0.313)S(0.687)PGGQDEGGFMAQGK;S(0.006)S(0.994)PGGQDEGGFMAQGK;S(0.001)S(0.999)PGGQDEGGFMAQGK;S(0.027)S(0.973)PGGQDEGGFMAQGK 403.4 9.59E-140 1246640000 2624410 2267180 1555100 1991770 2334260 1795990 2614740 3126790 2850300 TRUE FALSE 2277587.569 2252286.745 2307151.561 2444031.821 2287812.793 1865082.897 2361162.917 2458150.291 2513340.781 0.906199265 0.896132654 0.917962092 0.972423572 0.910267645 0.742073224 0.939451958 0.978040984 1 21.26117487 2.003151544 24.99782139 0.978840359 0.892228612 0.325136134 0.058332648 116.2574122 922140.5635 0.025114663 0.016834402 100.7283092 -2.003151544 -0.086611747 SS(ph)PGQTPEEGAQALAEFAALHGPALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSPGQTPEEGAQALAEFAALHGPALR 26 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 1 S(0.018)S(0.982)PGQTPEEGAQALAEFAALHGPALR;S(0.028)S(0.972)PGQTPEEGAQALAEFAALHGPALR;S(0.126)S(0.873)PGQT(0.001)PEEGAQALAEFAALHGPALR 351.8 3.70E-110 13742400000 2234030 1953980 1342720 1496570 2048590 2056740 1997200 2307750 2095130 TRUE FALSE 1938797.275 1941144.177 1992063.883 1836389.092 2007827.067 2135864.119 1803511.851 1814255.621 1847446.118 1.049447265 1.050717614 1.078279828 0.994014967 1.086812247 1.156117138 0.976218918 0.98203439 1 20.81710086 2.146775535 24.99726811 0.984827323 1.066214276 0.483636527 0.040412888 15.77903771 4291.445032 0.01676445 0.01130259 140.2088847 -2.146775535 0.081386953 SS(ph)PIMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPIMR 6 0 A0A087WZV0;O43314-2;O43314;A0A087WWN8;K7ENU7;H0Y9S9 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 S(0.297)S(0.703)PIMR 158.08 0.01 867100000 358300 360350 204720 222750 271650 327620 329970 349930 335480 TRUE FALSE 310949.7472 357982.8371 303723.2767 273328.792 266244.6965 340223.7534 297969.5602 275100.1927 295819.9366 1.051145338 1.210137631 1.026716726 0.923970153 0.90002283 1.150104206 1.007266662 0.929958257 1 18.17435976 4.053031413 7.293479534 0.983465206 1.129246326 0.367172001 0.077915719 0.224278527 25.2905191 0.020015954 0.041951157 11298.77637 -4.053031413 0.145781119 SS(ph)PKT(ph)PPRRPVPVADCEPPPVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPKTPPRRPVPVADCEPPPVDR 23 3 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 2 S(0.465)S(0.535)PKT(1)PPRRPVPVADCEPPPVDR;S(0.152)S(0.852)PKT(0.996)PPRRPVPVADCEPPPVDR 90.974 0.010131 194777000 46280 39985 28979 34276 62366 46392 60934 73871 43177 TRUE FALSE 40163.98074 39722.3359 42993.34133 42058.88968 61125.03862 48176.73026 55024.63006 58074.26151 38072.66425 1.054929607 1.043329556 1.129244359 1.104700459 1.605483615 1.265388993 1.445252943 1.525353233 1 15.21646791 3.35054054 8.775642811 1.388209224 1.080278213 0.428008337 0.163157953 0.229529158 16.84436851 0.045133499 0.058273535 2241.509272 -3.35054054 -0.30793101 SS(ph)PLLNYNTGVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPLLNYNTGVYR 13 0 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 S(0.122)S(0.878)PLLNYNTGVYR 75.669 0.032267 125540000 210250 223050 145750 195810 229310 211450 209970 261360 217700 TRUE FALSE 182464.9298 221584.7699 216235.1875 240271.6533 224747.1796 219584.6183 189607.1417 205470.1979 191963.754 0.950517616 1.154305254 1.126437585 1.251651149 1.170779248 1.143885831 0.98772366 1.070359345 1 17.55047441 2.250929953 24.63971868 1.028667437 1.140722903 0.317848488 0.077475088 220.111544 438462.017 0.028993417 0.022289544 178.2091313 -2.250929953 0.112055466 SS(ph)PLPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSPLPAK 7 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 S(0.483)S(0.517)PLPAK;S(0.077)S(0.923)PLPAK;S(0.116)S(0.884)PLPAK 97.635 0.012433 1769460000 5119900 3752900 3083700 4113600 3355400 3201010 4819900 5518200 9409700 TRUE FALSE 4443292.243 3728246.953 4574987.634 5047655.752 3288634.105 3324154.926 4352466.84 4338175.873 8297295.986 0.535510876 0.449332766 0.551382962 0.608349487 0.396350101 0.400631113 0.52456449 0.522842126 1 22.98420982 1.230192423 4.446304642 1.04827947 0.494864055 0.85033063 0.066182202 0.082911485 3.3451746 0.147435792 0.01729557 16.98996261 -1.230192423 -0.553415415 SS(ph)PLSFPSVPQEETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPLSFPSVPQEETLR 16 0 Q9ULD5 Q9ULD5 ZNF777 Zinc finger protein 777 1 S(0.271)S(0.728)PLSFPSVPQEETLR 66.331 0.044342 0 58283 60729 35111 41534 58530 50291 60152 56031 46840 TRUE FALSE 50580.75388 60330.0672 52090.79704 50964.92951 57365.36751 52225.72731 54318.4683 44049.20668 41302.62856 1.224637648 1.46068348 1.261198109 1.233939129 1.388903552 1.264464978 1.315133448 1.06649887 1 15.33394598 1.668183581 3.386339133 1.010442254 1.311282549 0.713970593 0.072458467 0.094472629 2.511796499 0.053445953 0.018282252 46.57829435 -1.668183581 0.300840295 SS(ph)PNPFITGLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSPNPFITGLTR 12 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 S(0.103)S(0.897)PNPFITGLTR;S(0.006)S(0.994)PNPFITGLTR;S(0.167)S(0.833)PNPFITGLTR 195.78 2.25E-07 694430000 653170 652080 414907 463670 643130 692370 633640 789400 703420 TRUE FALSE 566851.9296 647796.4435 615557.413 568953.3603 630332.9713 719005.9219 572189.6903 620592.9531 620262.4889 0.913890393 1.04439081 0.992414379 0.917278363 1.01623584 1.159196203 0.922496041 1.000532781 1 19.24251935 3.068072697 24.99978882 1.017067764 0.97338987 0.125045936 0.068150791 138.4105553 50829.04792 0.020792266 0.023576213 1169.695172 -3.068072697 -0.043677893 SS(ph)PNVANQPPS(ph)PGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.109)S(0.891)PNVANQPPS(1)PGGK;S(0.362)S(0.638)PNVANQPPS(1)PGGK 243.18 8.47E-18 476550000 770200 716530 576730 689510 800150 637070 881490 1034020 1153140 TRUE FALSE 668416.1186 711823.0673 855638.557 846073.784 784228.5805 661578.4951 796003.2355 812902.8698 1016817.103 0.657361208 0.70005025 0.841487181 0.832080599 0.771258251 0.650636671 0.782838166 0.799458297 1 19.95562877 1.115919881 1.951412923 1.14917782 0.750073196 0.597856688 0.064635278 0.89134976 2.480558566 0.730063376 0.018612276 13.05929947 -1.115919881 -0.399104623 SS(ph)PPAPPLPPGS(ph)GSPGTPQALPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPPAPPLPPGSGSPGTPQALPR 23 0 Q9Y3L3;A0A2R8Y5V0 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 2 S(0.407)S(0.593)PPAPPLPPGS(0.888)GS(0.109)PGT(0.002)PQALPR;S(0.416)S(0.584)PPAPPLPPGS(0.974)GS(0.022)PGT(0.004)PQALPR 197 4.45E-24 270691000 171373 180009 108908 132690 207730 191492 162858 202909 180419 TRUE FALSE 148725.6238 178826.509 161576.2731 162819.2925 203596.5794 198858.8212 147064.0562 159518.4894 159090.0714 0.934851701 1.124058261 1.015627636 1.023440942 1.279756667 1.249976315 0.924407507 1.002692928 1 17.27948428 2.207946562 24.99998756 0.979186439 1.105728261 0.250158 0.105147561 307.3306739 250969.6048 0.045070668 0.030390649 161.415993 -2.207946562 0.126541822 SS(ph)PPLPPPAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPPLPPPAEER 12 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 S(0.039)S(0.961)PPLPPPAEER;S(0.313)S(0.687)PPLPPPAEER 106.54 0.00077133 0 201384 177498 112904 134305 182406 193512 181365 181604 185189 TRUE FALSE 174770.5942 176332.004 167504.752 164801.003 178776.4775 200956.5319 163776.2502 142769.3978 163296.1674 1.070267582 1.079829409 1.025772709 1.009215376 1.09479898 1.230626138 1.002939952 0.874297298 1 17.31713141 2.001774453 24.99968132 0.931304488 1.082279719 0.470759918 0.065670914 44.48115333 626672.8173 0.027734992 0.018551982 100.4094188 -2.001774453 0.150975231 SS(ph)PPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPPLR 6 0 E9PJN1;O75676-2;O75676;A0A0A6YYC0 E9PJN1 RPS6KA4 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-4 1 S(0.197)S(0.803)PPLR 85.212 0.057662 133400000 183860 163410 81175 107310 123170 143160 138420 156240 95226 TRUE FALSE 159562.4352 162336.549 120431.5015 131676.3756 120719.158 148667.4578 124996.0497 122829.2919 83968.49076 1.900265608 1.933303165 1.434246351 1.568164134 1.437672118 1.770514826 1.488606602 1.462802186 1 16.35756044 0.789515431 1.009698781 1.72E-25 1.664540202 0.590735062 0.173008451 3.363515299 1.45859154 7.59416738 0.060165953 6.159074133 -0.789515431 1.664540202 SS(ph)PPMLSADDAEYPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPPMLSADDAEYPR 15 0 A0A087X165;Q9C0H9;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 S(0.212)S(0.788)PPMLSADDAEYPR 143.64 1.09E-05 0 62638 53571 41163 44571 49460 52769 43031 54026 67182 TRUE FALSE 54360.2296 53219.08857 61069.56448 54691.52678 48475.84277 54799.05758 38857.86024 42472.96033 59239.82049 0.917629884 0.89836681 1.030887062 0.923222358 0.818298272 0.925037536 0.65594156 0.716966391 1 15.85427965 2.928104623 1.483662874 0.782567429 0.945852549 0.218612278 0.103456734 0.493693335 2.241013917 0.044176892 0.045098366 847.4315396 -2.928104623 0.16328512 SS(ph)PPSAGNSPSSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPPSAGNSPSSLK 14 0 P57682;P57682-2 P57682 KLF3 Krueppel-like factor 3 1 S(0.003)S(0.997)PPSAGNSPSSLK;S(0.008)S(0.992)PPSAGNSPSSLK 330.35 2.20E-68 613030000 995270 896930 682640 887010 952670 658770 937170 1077600 1187730 TRUE FALSE 863742.5478 891038.0078 1012766.987 1088419.178 933713.7309 684113.3082 846283.3976 847163.6259 1047317.912 0.824718586 0.850780835 0.967010089 1.039244306 0.891528465 0.653205011 0.808048242 0.808888701 1 19.99826801 2.984412033 24.94555499 0.81052519 0.924614076 0.190081728 0.100569006 1073.83453 1718469.602 0.032736567 0.033745336 964.7438819 -2.984412033 0.114088886 SS(ph)PQLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSPQLAK 7 0 Q13370-2;Q13370 Q13370-2 PDE3B "cGMP-inhibited 3,5-cyclic phosphodiesterase B" 1 S(0.104)S(0.896)PQLAK;S(0.258)S(0.742)PQLAK;S(0.445)S(0.555)PQLAK;S(0.218)S(0.782)PQLAK 96.367 0.01341 6402590000 13940300 9683700 7531700 8823300 8559300 10010400 13357400 17118700 19039200 TRUE FALSE 12098054.03 9620087.137 11174055.31 10826765.12 8388986.676 10395506.57 12062001.4 13457999.22 16788407.47 0.720619514 0.573019636 0.665581612 0.644895303 0.499689246 0.619207426 0.718472043 0.801624529 1 24.00096205 1.35240216 1.269996996 1.122615261 0.617268595 0.805787717 0.060162263 0.479375173 0.794612702 0.309984735 0.018661666 22.51138214 -1.35240216 -0.505346666 SS(ph)PQLDPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSPQLDPLR 9 0 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.224)S(0.776)PQLDPLR;S(0.025)S(0.975)PQLDPLR;S(0.025)S(0.975)PQLDPLR 179.94 5.16E-05 7574000000 2399800 2244780 1869370 2274550 2437350 2276950 2261830 2524390 6138000 TRUE FALSE 2082660.35 2230033.892 2773403.585 2791021.342 2388851.504 2364545.74 2042478.075 1984568.843 5412372.632 0.384796187 0.412025196 0.512419187 0.515674277 0.441368632 0.436877854 0.377372035 0.366672618 1 22.36782974 1.234650095 24.99999734 1.000000819 0.430501545 0.924676804 0.051045666 32.84448979 209944.7782 0.10495736 0.014235464 17.1652485 -1.234650095 -0.569499274 SS(ph)PQLDPLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SSPQLDPLRK 10 1 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.208)S(0.792)PQLDPLRK;S(0.114)S(0.886)PQLDPLRK;S(0.125)S(0.875)PQLDPLRK;S(0.132)S(0.868)PQLDPLRK;S(0.132)S(0.868)PQLDPLRK;S(0.1)S(0.9)PQLDPLRK;S(0.108)S(0.892)PQLDPLRK 124.3 0.00026899 31460680000 14969030 12372530 10350860 13458090 13199310 10700770 14478640 16826080 23444350 TRUE FALSE 12990834.76 12291254.04 15356570.52 16513955.03 12936669.56 11112435.55 13074503.72 13227953.73 20672785.65 0.628402721 0.594562061 0.742839924 0.798825824 0.6257826 0.53753934 0.632450021 0.639872824 1 24.30122947 1.237526404 24.99324561 1.000000415 0.650276853 0.694215866 0.072993985 16.11722317 389300.995 0.114261587 0.01921038 17.27931032 -1.237526404 -0.349723562 SS(ph)PQLDPLRKS(ph)PTMEQAVQTASAHLPAPAAVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SSPQLDPLRKSPTMEQAVQTASAHLPAPAAVGR 33 2 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 2 S(0.389)S(0.611)PQLDPLRKS(0.964)PT(0.036)MEQAVQTASAHLPAPAAVGR;S(0.165)S(0.835)PQLDPLRKS(0.993)PT(0.007)MEQAVQTASAHLPAPAAVGR;S(0.464)S(0.536)PQLDPLRKS(0.831)PT(0.169)MEQAVQTASAHLPAPAAVGR;S(0.472)S(0.528)PQLDPLRKS(0.5)PT(0.5)MEQAVQTASAHLPAPAAVGR;S(0.46)S(0.54)PQLDPLRKS(0.823)PT(0.177)MEQAVQTASAHLPAPAAVGR 197.82 3.68E-27 5749880000 2335090 2026710 601111 1018230 2279290 1814600 2496350 2755620 551328 TRUE FALSE 2026501.94 2013396.409 891810.2902 1249434.684 2233936.588 1884408.836 2254254.361 2166352.107 486150.6319 4.168465095 4.141507336 1.834432029 2.570056691 4.59515311 3.876183044 4.636946274 4.45613348 1 18.89104387 3.244828395 24.989672 3.883259191 3.151380353 0.034025308 1.238429148 438.4614954 1748138.298 0.364111795 0.458262476 1757.229133 -3.244828395 -0.731878838 SS(ph)PSARPPDVPGQQPQAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPSARPPDVPGQQPQAAK 19 1 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 S(0.134)S(0.866)PSARPPDVPGQQPQAAK;S(0.179)S(0.82)PS(0.002)ARPPDVPGQQPQAAK 176.1 7.84E-13 1461370000 665430 486090 408420 488320 549730 446900 524780 671220 1172370 TRUE FALSE 577491.7395 482896.8428 605933.2781 599200.5195 538791.4485 464092.5322 473886.9164 527684.8264 1033773.754 0.55862488 0.467120432 0.586137224 0.579624427 0.521188941 0.448930465 0.458404863 0.510445177 1 19.97948905 1.238307054 24.99374448 1.000000541 0.513990774 0.90791144 0.048406777 1.776013443 174714.2366 0.070834517 0.012525399 17.31039801 -1.238307054 -0.486009768 SS(ph)PSIICMPK ddPTM_MDA-MB-175_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(0.352)S(0.646)PS(0.003)IICMPK;S(0.075)S(0.925)PSIICMPK 179.2 8.34E-06 391880000 1008830 934720 706980 823230 871960 760020 986720 1123260 1503790 TRUE FALSE 875510.5595 928579.7628 1048877.893 1010156.954 854609.702 789258.4612 891028.0463 883059.5902 1326013.659 0.660257572 0.700279184 0.791000821 0.76179981 0.644495399 0.595211411 0.67195993 0.665950599 1 20.33866421 1.23626316 24.9998961 1.000000406 0.686641129 0.756119962 0.055977342 33.93417857 369170.2236 0.098236511 0.015119876 17.22912254 -1.23626316 -0.313359277 SS(ph)PSPALEQPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPSPALEQPFR 12 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 S(0.019)S(0.98)PSPALEQPFR 166.87 0.00017014 0 179940 167030 142980 168740 176920 161530 184950 220140 296200 TRUE FALSE 156160.4731 165932.7689 212125.6062 207054.996 173399.6381 167744.1636 167013.5775 173064.7741 261183.5734 0.597895461 0.635310892 0.812170549 0.792756578 0.663899478 0.642246223 0.63944901 0.662617376 1 17.99470464 1.236387145 24.99709775 1.000000409 0.682453735 0.680214507 0.06877461 37.7545132 434107.7212 0.117026014 0.018175343 17.23404192 -1.236387145 -0.317546674 SS(ph)PSPQKR ddPTM_MDA-MB-175_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(0.182)S(0.817)PS(0.001)PQKR;S(0.073)S(0.927)PSPQKR;S(0.141)S(0.859)PSPQKR 118.18 0.0011863 697070000 597370 518200 335147 386089 306568 467340 566460 639580 487670 TRUE FALSE 518426.041 514795.9101 497225.2102 473756.4085 300467.8966 485318.8722 511524.7964 502810.7942 430018.2082 1.205590906 1.197149098 1.156288736 1.101712438 0.698732963 1.12860075 1.189542179 1.169277916 1 18.71403822 3.748745365 3.814507478 1.057268115 1.191786445 0.18834928 0.136991953 0.456923236 15.1308593 0.040995886 0.069902653 5607.191192 -3.748745365 0.13451833 SS(ph)PSTENMHFPSSISSQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPSTENMHFPSSISSQTR 19 0 A0A0U1RR27;Q7Z401;Q7Z401-2 A0A0U1RR27 DENND4A C-myc promoter-binding protein 1 S(0.172)S(0.607)PS(0.206)T(0.015)ENMHFPSSISSQTR 92.41 0.0012374 310060000 86627 99442 52356 69941 114430 119610 112100 123890 110250 TRUE FALSE 75179.02247 98788.75895 77675.53672 85822.17303 112153.0669 124211.4741 101228.5593 97397.08761 97216.3706 0.77331649 1.016174111 0.798996468 0.882795485 1.153643838 1.277680635 1.04127071 1.001858915 1 16.56891165 3.251602875 24.10889923 1.088379801 0.873501174 0.549544366 0.102002289 129.500946 239383.0935 0.031213134 0.040013158 1784.854731 -3.251602875 -0.214878627 SS(ph)PVCSTAPVETEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPVCSTAPVETEPK 15 0 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 1 S(0.004)S(0.996)PVCSTAPVETEPK;S(0.183)S(0.817)PVCSTAPVETEPK 365.28 1.18E-71 287850000 494650 390120 311380 375620 393820 273710 434840 522250 775550 TRUE FALSE 429280.7492 387557.276 461964.4095 460910.262 385983.7525 284239.8008 392669.2837 410570.9017 683865.3625 0.627726995 0.566715756 0.675519532 0.673978077 0.56441483 0.415637078 0.574190923 0.600368032 1 19.38335279 1.237698103 5.748093853 1.017893059 0.584730373 0.761385899 0.072649224 0.074526501 8.445414875 0.127289502 0.019400849 17.28614307 -1.237698103 -0.433162687 SS(ph)PVESLKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPVESLKK 9 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 S(0.014)S(0.986)PVESLKK;S(0.386)S(0.614)PVESLKK 155.97 4.41E-05 2824050000 5529030 3980370 3323060 4137830 4153550 3193130 5781490 7045250 6173220 TRUE FALSE 4798354.677 3954222.687 4930102.931 5077387.544 4070902.481 3315971.777 5220801.99 5538678.114 5443428.964 0.881494864 0.726421289 0.905698038 0.93275536 0.74785627 0.609169661 0.959101703 1.017498005 1 22.3760843 2.021763649 24.99172023 1.003489216 0.803799483 0.482981875 0.09443147 193.632612 222352.0787 0.039896225 0.026895574 105.1389533 -2.021763649 -0.199689733 SS(ph)PVKVGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSPVKVGEK 9 1 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 1 S(0.108)S(0.892)PVKVGEK;S(0.381)S(0.619)PVKVGEK;S(0.098)S(0.902)PVKVGEK 146.36 5.75E-05 1647930000 4643670 3265110 2520410 2588020 3008560 2412010 4768900 5451500 1662160 TRUE FALSE 4029997.244 3243661.277 3739288.706 3175669.496 2948695.542 2504801.585 4306412.812 4285739.149 1465661.338 2.749610117 2.213104209 2.551263794 2.166714379 2.01185326 1.708990692 2.938204549 2.924099201 1 20.48312036 4.743480995 21.8087933 2.271845829 2.749611385 0.07042207 0.573879579 284.0935637 1258913.625 0.140573491 1.070960119 55396.33021 -4.743480995 0.477765556 SS(ph)PVNRPSSATNK ddPTM_MDA-MB-175_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(0.206)S(0.792)PVNRPS(0.002)SATNK 103.6 0.0042024 20737000 77316 58496 31082 40156 53034 39189 59756 62909 56800 TRUE FALSE 67098.49471 58111.73592 46113.35916 49274.03355 51978.72716 40696.62619 53960.87232 49456.39991 50085.16871 1.339687904 1.160258364 0.920698889 0.983804883 1.03780677 0.81254845 1.077382261 0.987446008 1 15.61209583 4.493384298 3.048798379 0.978051872 1.331846332 0.739565625 0.071967041 0.129887213 2.26725768 0.017617891 0.082943397 31144.71049 -4.493384298 0.353794459 SS(ph)PVPPVPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SSPVPPVPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 S(0.276)S(0.724)PVPPVPER;S(0.157)S(0.843)PVPPVPER;S(0.224)S(0.776)PVPPVPER;S(0.051)S(0.949)PVPPVPER;S(0.107)S(0.893)PVPPVPER;S(0.138)S(0.862)PVPPVPER 189.17 1.09E-06 5859260000 4524140 4072630 2551420 3259110 3892860 4115260 3890330 4455650 4632130 TRUE FALSE 3926263.436 4045876.625 3785295.246 3999140.738 3815399.702 4273576.715 3513046.395 3502843.921 4084524.868 0.961253405 0.990537885 0.926740654 0.979095701 0.934111023 1.046284905 0.860086916 0.857589079 1 21.96173684 2.216888935 24.99999684 0.893920345 0.970207121 0.268262855 0.050848561 267.4029832 308468.1407 0.020002564 0.013499105 164.7740952 -2.216888935 0.076286776 SS(ph)QSASSLEVAGPGREPLELEVAVEALAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSQSASSLEVAGPGREPLELEVAVEALAR 29 1 A0A2R8Y5E4;A0A2R8YFK2;A0A2R8Y6M6;A0A2R8Y4C2;A0A2R8YFS8;A0A2R8Y8C4;A0A2R8Y5C9;A0A2R8Y596;P56945-4;P56945-5;P56945-8;P56945;P56945-7;P56945-3;P56945-2;P56945-6 A0A2R8Y5E4 BCAR1 Breast cancer anti-estrogen resistance protein 1 1 S(0.222)S(0.692)QS(0.074)AS(0.006)S(0.006)LEVAGPGREPLELEVAVEALAR 44.347 0.077602 26377000 1691.2 3076.5 1435.3 1661.7 2565.3 2234.8 2552.6 2966.1 1846.8 TRUE FALSE 1467.703635 3056.290269 2129.415881 2039.014382 2514.255549 2320.774202 2305.049245 2331.822597 1628.473408 0.901275776 1.876782423 1.30761477 1.252101737 1.543934053 1.425122566 1.41546631 1.431907077 1 10.66930445 1.236752584 24.9507858 0.999999472 1.410600952 0.203976824 0.242883531 67.57418778 932243.0285 0.331265265 0.052908671 17.2485497 -1.236752584 0.41060148 SS(ph)REKEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSREKEQR 8 2 H7C1L9 H7C1L9 TRIP12 1 S(0.065)S(0.935)REKEQR;S(0.102)S(0.898)REKEQR;S(0.444)S(0.556)REKEQR 105.86 0.0022468 109668000 168616 137665 47279.2 64775 81486 114500 146903 172568 20824.1 TRUE FALSE 146332.9684 136760.6696 70143.57926 79483.15377 79864.58802 118904.8891 132656.3697 135665.6761 18362.29862 7.969207527 7.447905754 3.819978136 4.32860588 4.349378565 6.475490435 7.224387992 7.388273055 1 14.16445905 4.368464907 7.168209453 5.297600811 7.83359179 0.257978573 1.885552143 0.322367432 18.7888862 0.487624041 1.307873633 23359.57341 -4.368464907 2.535990979 SS(ph)RSS(ph)PELTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSRSSPELTR 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.413)S(0.586)RS(0.032)S(0.97)PELTR;S(0.192)S(0.806)RS(0.346)S(0.613)PELT(0.044)R;S(0.407)S(0.557)RS(0.073)S(0.963)PELTR;S(0.093)S(0.896)RS(0.46)S(0.546)PELT(0.004)R 109.47 0.0012076 1809970000 1980920 1584090 1029470 1163480 1628150 1704980 1550650 1754210 1746650 TRUE FALSE 1719136.403 1573684.008 1527325.135 1427665.917 1595753 1770571.684 1400268.202 1379085.843 1540163.027 1.116204176 1.021764567 0.991664589 0.926957661 1.036093565 1.149600174 0.90916882 0.895415497 1 20.55465164 6.316460589 0.023160263 2.37E-06 2.190813429 0.158762313 0.07613161 6137.52824 21.28870041 842.9436923 1200.148995 2072337.994 -6.316460589 2.190811062 SS(ph)S(ph)AS(ph)T(ph)AAT(ph)WLWQAR ddPTM_MDA-MB-175_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 467400000 15801 17161 0 12213 22555 13027 14255 15672 20824 TRUE FALSE 13712.85782 17048.26826 0 14986.14831 22106.19963 13528.15712 12872.55229 12320.66476 18362.21044 0.74679777 0.928443137 0 0.816140756 1.203896432 0.736739031 0.701035005 0.67097939 1 14.16445212 3.520031213 24.99957969 0.83744269 0.564192249 0.198956025 0.279186898 851.1442031 495879.1626 0.07730854 0.114656582 3311.549206 -3.520031213 -0.273250441 SS(ph)S(ph)AS(ph)T(ph)AATWLWQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSASTAATWLWQAR 15 0 J3QKM6 J3QKM6 LLGL2 4 S(0.629)S(0.685)S(0.685)AS(0.725)T(0.725)AAT(0.551)WLWQAR 53.001 0.070884 457240000 0 7013.7 0 0 0 9359.4 0 10986 8791.6 TRUE FALSE 0 6967.626543 0 0 0 9719.462174 0 8636.729393 7752.267063 0 0.89878567 0 0 0 1.253757397 0 1.114090797 1 12.92040256 1.612333748 0.771184829 1.361738323 0.243066024 0.289910337 0.452766924 2.148411607 1.446444761 1.960102168 0.198635884 40.95752905 -1.612333748 -1.118672299 SS(ph)SESLIFSGNQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSSESLIFSGNQGR 14 0 Q8IZW8 Q8IZW8 TNS4 Tensin-4 1 S(0.013)S(0.98)S(0.007)ESLIFSGNQGR;S(0.019)S(0.981)SESLIFSGNQGR;S(0.01)S(0.989)S(0.001)ESLIFSGNQGR;S(0.023)S(0.965)S(0.012)ESLIFSGNQGR 273.72 5.37E-33 885560000 912580 1322050 836360 1192770 1534100 1588440 1101700 1575810 1648260 TRUE FALSE 791980.2408 1313365.367 1240826.493 1463606.659 1503574.411 1649548.315 994857.3036 1238835.294 1453404.581 0.544913819 0.903647466 0.853737844 1.007019435 1.034518834 1.134954669 0.684501285 0.85236782 1 20.47100493 4.927551417 2.058015905 0.930885899 0.267301116 0.495885028 0.123184509 1.403749136 4.110449451 0.034219572 2.074724326 84635.27648 -4.927551417 -0.663584783 SS(ph)SKESLVR ddPTM_MDA-MB-175_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(0.104)S(0.547)S(0.329)KES(0.02)LVR 79.492 0.022016 0 432180 345570 241890 301180 380820 294460 429650 477800 358240 TRUE FALSE 375066.318 343299.9279 358868.8131 369567.5222 373242.4271 305788.0667 387982.6091 375626.1882 315889.2753 1.187334764 1.086772976 1.13605887 1.169927412 1.181560934 0.968022946 1.22822343 1.189107126 1 18.26905943 4.777456948 21.42945478 1.129677952 1.187335739 0.049942375 0.083256743 11264.07616 6204993.163 0.019718863 3.665863589 59904.15523 -4.777456948 0.057657787 SS(ph)SPATEQSWMENDFDELREEGFRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSPATEQSWMENDFDELREEGFRR 25 2 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.025)S(0.551)S(0.424)PATEQSWMENDFDELREEGFRR 227.36 2.85E-34 462820000 52977 53563 29999 22370 50534 66476 54515 71008 13826 TRUE FALSE 45975.95522 53211.14113 44506.61674 27449.4504 49528.47227 69033.37474 49228.14369 55823.49178 12191.50603 3.771146494 4.364607702 3.650625003 2.251522522 4.062539291 5.662415666 4.037905044 4.578883991 1 13.57358873 7.124822894 14.93092163 3.823186524 2.074554291 0 1.283370939 0 0 0.281333401 0 13329777.31 -7.124822894 -1.748632233 SS(ph)SPVTELASRS(ph)PIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSSPVTELASRSPIR 15 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.263)S(0.368)S(0.368)PVTELAS(0.03)RS(0.97)PIR;S(0.383)S(0.533)S(0.083)PVTELAS(0.037)RS(0.963)PIR;S(0.269)S(0.365)S(0.365)PVTELAS(0.005)RS(0.995)PIR 194.08 3.79E-08 1689370000 1766150 1689330 926370 1098780 1609650 1585870 1524090 1708010 984050 TRUE FALSE 1532748.803 1678232.68 1374365.631 1348274.793 1577621.114 1646879.445 1376283.986 1342765.353 867716.73 1.766416101 1.934078971 1.58388744 1.553819059 1.818129189 1.89794594 1.586098249 1.547469706 1 19.72686462 0.902711049 1.318281142 4.00E-17 1.747077379 0.769457644 0.127216048 1.480061153 1.197954347 4.367616741 0.039262066 7.993022741 -0.902711049 1.747077379 SS(ph)SSSTTPTSANSLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSSSTTPTSANSLYR 16 0 Q0VF96 Q0VF96 CGNL1 Cingulin-like protein 1 1 S(0.028)S(0.866)S(0.104)S(0.001)STTPTSANSLYR;S(0.029)S(0.969)S(0.001)SSTTPTSANSLYR 294.06 1.35E-45 261830000 422550 383490 264852 301576 384240 365040 356170 426690 558220 TRUE FALSE 366708.9469 380970.8289 392935.3131 370053.4401 376594.3758 379083.325 321628.6882 335445.664 492227.8675 0.744998345 0.773972491 0.798279291 0.751792949 0.765081379 0.770137877 0.65341422 0.681484504 1 18.90896681 1.230609845 24.99999534 1.000000472 0.739971724 0.774361404 0.043683587 161.0738682 506430.7043 0.133256378 0.012414453 17.00630036 -1.230609845 -0.260028748 SS(ph)SVPHPFQVTLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSVPHPFQVTLLR 14 0 Q5VV41;Q5VV41-2 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 S(0.027)S(0.971)S(0.002)VPHPFQVTLLR;S(0.015)S(0.974)S(0.011)VPHPFQVTLLR 201.3 1.89E-08 1094950000 373170 415020 247126 288020 394660 405630 428030 433690 442100 TRUE FALSE 323854.639 412293.7063 366636.9602 353419.3431 386807.0381 421234.8486 386519.7165 340948.7685 389835.4416 0.830747039 1.057609602 0.940491605 0.906585973 0.992231585 1.080545285 0.991494552 0.874596643 1 18.57250573 3.211620904 24.84667611 0.978544147 0.943171658 0.103787362 0.073866071 745.8948443 687941.5406 0.023334297 0.026465461 1627.874439 -3.211620904 -0.035372489 SS(ph)TDFSELEQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSTDFSELEQPR 12 0 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 S(0.361)S(0.638)TDFSELEQPR 208.28 0.00011604 0 179520 223700 149480 197650 255830 229970 246360 256620 233020 TRUE FALSE 155795.9772 222230.5 221769.028 242529.4534 250739.4835 238817.0947 222468.0451 201743.81 205472.6411 0.758232222 1.081557617 1.079311712 1.180349131 1.220305936 1.16228172 1.082713708 0.981852421 1 17.64858678 4.740762875 4.759316223 1.097707265 0.738339336 0.675535867 0.074211503 0.13118562 8.427275807 0.021466711 0.157113373 55050.70376 -4.740762875 -0.359367929 SS(ph)TDSLPGPISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SSTDSLPGPISR 12 0 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 S(0.004)S(0.996)TDSLPGPISR;S(0.041)S(0.959)T(0.001)DSLPGPISR;S(0.149)S(0.841)T(0.01)DSLPGPISR;SS(0.986)T(0.014)DSLPGPISR;S(0.024)S(0.975)TDSLPGPISR 281.19 4.80E-28 1839070000 2855430 2330780 1753780 2238780 2865050 2803210 2983710 3135240 2881980 TRUE FALSE 2478077.691 2315468.953 2601913.874 2747129.217 2808041.11 2911051.303 2694350.263 2464793.324 2541275.608 0.97513142 0.911144366 1.02386135 1.081004047 1.10497307 1.145507907 1.060235362 0.969903979 1 21.27712142 4.087096066 4.96857668 1.056064235 0.944420024 0.462360477 0.051364384 0.21176486 8.93259118 0.015551725 0.033744608 12220.69951 -4.087096066 -0.111644212 SS(ph)TPGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSTPGLK 7 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 S(0.077)S(0.462)T(0.462)PGLK;S(0.005)S(0.497)T(0.497)PGLK 122.44 0.0045536 1392600000 8716800 5883000 3999700 4723000 4513200 5124700 7082200 8471400 7665100 TRUE FALSE 7564852.794 5844354.186 5933968.298 5795429.337 4423396.15 5321850.525 6395369.334 6659857.035 6758940.61 1.119236465 0.864684944 0.877943548 0.857446406 0.654451105 0.787379389 0.946208837 0.985340369 1 22.68836571 2.063907475 5.891559454 0.98443756 0.851996612 0.19591264 0.113425358 0.312427038 20.72936268 0.049526308 0.032760796 115.853051 -2.063907475 -0.132440948 SS(ph)TPLHS(ph)PSPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSTPLHSPSPIR 12 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 2 S(0.257)S(0.371)T(0.371)PLHS(1)PSPIR;S(0.263)S(0.369)T(0.369)PLHS(0.981)PS(0.019)PIR 127.66 0.00014035 1719270000 1703000 1929560 950190 1261800 1915850 1839900 1788720 2004060 1919670 TRUE FALSE 1477944.235 1916884.593 1409705.062 1548310.975 1877728.333 1910682.144 1615250.21 1575507.365 1692728.799 0.873113422 1.132422745 0.832800306 0.914683425 1.109290711 1.128758573 0.954228587 0.93075002 1 20.69091942 SS(ph)TPLPTISSSAENTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSTPLPTISSSAENTR 16 0 P42166;P42167;G5E972;H0YJH7;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 S(0.043)S(0.954)T(0.003)PLPTISSSAENTR;SS(0.5)T(0.5)PLPTISSSAENTR 254.13 1.50E-26 2614949000 1745930 1396006 779860 1213610 1887010 1622960 1254612 1885330 1771670 TRUE FALSE 1515200.927 1386835.545 1157002.904 1489178.699 1849462.193 1685396.321 1132939.921 1482166.851 1562225.191 0.969899177 0.887730881 0.740612116 0.953242022 1.183864019 1.07884339 0.725209098 0.948753649 1 20.575171 5.107061652 16.8103557 0.936136848 3.099715223 0.004068971 0.137972524 24312441.81 34250707.63 0.035468881 1986304275 127956.2938 -5.107061652 2.163578375 SS(ph)TPTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSTPTPR 7 0 Q04724;A0A669KBK8;A0A669KAE5;F6T2C8 Q04724 TLE1 Transducin-like enhancer protein 1 1 S(0.218)S(0.301)T(0.301)PT(0.18)PR 66.429 0.071221 60004000 126620 115740 56756 93372 83605 116720 112240 136910 132770 TRUE FALSE 109886.8462 114979.6963 84203.39144 114573.5397 81941.42407 121210.2939 101354.9821 107632.8619 117074.0819 0.938609506 0.982110596 0.719231704 0.978641369 0.699910884 1.03532987 0.865733734 0.919356874 1 16.8370622 SS(ph)TSSEPTPTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSTSSEPTPTVK 12 0 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 S(0.322)S(0.677)T(0.001)SSEPTPTVK 248.91 8.32E-17 198670000 425090 387450 354530 467740 435320 347810 498610 528710 1366600 TRUE FALSE 368913.2795 384904.8154 525981.8938 573947.516 426657.9837 361190.4758 450254.8789 415649.4809 1205042.105 0.306141402 0.319411923 0.436484245 0.47628835 0.354060644 0.29973266 0.373642445 0.344925276 1 20.20065213 1.237433761 24.99999503 1.000000755 0.365496534 0.928006779 0.05568376 7.369242996 163416.4316 0.086685784 0.014493378 17.27562471 -1.237433761 -0.634504221 SS(ph)VEKENQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSVEKENQK 9 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 S(0.011)S(0.989)VEKENQK;S(0.122)S(0.878)VEKENQK 162.49 3.86E-05 788170000 1141460 767340 644490 670820 426270 537790 980210 1211870 1174630 TRUE FALSE 990613.1689 762299.293 956167.5197 823139.9338 417788.061 558479.1293 885149.3851 952721.0313 1035766.58 0.956405805 0.735975951 0.923149616 0.794715673 0.40336121 0.539194004 0.854583844 0.91982214 1 19.98226748 2.009190893 24.43927362 0.934089794 0.721224432 0.262158598 0.163442975 218.5670222 581183.1531 0.072649544 0.048898763 102.1388334 -2.009190893 -0.212865362 SSAIPDFRDPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSAIPDFRDPQK 12 1 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 0 72.496 0.038064 241120000 444310 372410 229000 250260 350550 315970 390050 502890 327400 FALSE TRUE 385593.3078 369963.6142 339745.166 307085.358 343574.7408 328125.5704 352223.011 395350.887 288695.145 1.335641816 1.281502722 1.176830203 1.063701151 1.19009532 1.136581533 1.22005173 1.369440719 1 18.13918732 4.367037217 3.646790397 1.182662662 1.325336511 0.264544715 0.097910169 0.354675745 8.723653894 0.02641657 0.083741211 23282.90772 -4.367037217 0.142673849 SSAQLLEDWGMEDIDHVFSEEDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 SSAQLLEDWGMEDIDHVFSEEDYR 24 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YFD8;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3;F5H6N4 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ;;;;;;;;; 274.65 5.42E-52 1134108000 579358 554609 308398.3 390043 523049 510066 470229 576819 580182 FALSE TRUE 502794.3724 550965.737 457540.7494 478608.2246 512641.3482 529688.5691 424626.264 453470.7457 511593.5449 0.982800462 1.076959908 0.894344258 0.935524362 1.002048117 1.035369923 0.830007079 0.886388717 1 18.96463854 2.246171264 24.99948961 0.89834689 0.985909893 0.265430465 0.064183923 218.2267512 716833.8338 0.024661385 0.018726574 176.267102 -2.246171264 0.087563003 SSASS(ph)SPKRPSVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSASSSPKRPSVER 14 2 S4R3M9;O75764;S4R419;O75764-2 S4R3M9 TCEA3 Transcription elongation factor A protein 3 1 S(0.003)S(0.037)AS(0.184)S(0.62)S(0.149)PKRPS(0.007)VER 73.168 0.028815 162870000 209290 213170 88404 102070 214560 169750 226610 262440 29809 TRUE FALSE 181631.7962 211769.6722 131156.4701 125246.5535 210290.6758 176280.3923 204633.3971 206319.2483 26285.01398 6.910089391 8.056669569 4.989781257 4.764941485 8.0004019 6.706497949 7.785173607 7.84931096 1 14.68195288 4.258396547 24.98115743 6.216471119 7.483379359 0.07420763 2.108979088 782.4705571 985417.9691 0.518280671 1.367202165 18129.94754 -4.258396547 1.26690824 SSATSGDIWPGLSAYDNS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 SSATSGDIWPGLSAYDNSPR 20 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR 432.39 6.45E-174 15947524000 3204671 2319007 1748752 2531844 2637883 2714574 2357538 2819085 4825440 TRUE FALSE 2781165.608 2303773.29 2594454.316 3106737.877 2585394.289 2819005.418 2128904.328 2216245.611 4254981.98 0.653625708 0.541429623 0.609745077 0.730141254 0.607615802 0.662518768 0.500332161 0.520858989 1 22.02072159 1.23172247 24.99970072 1.000000685 0.598813725 0.762290106 0.069582179 124.1417831 453810.5902 0.175890239 0.018307816 17.04992487 -1.23172247 -0.40118696 SSAWAEGGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSAWAEGGSPR 11 0 Q8N9B5-2;Q8N9B5 Q8N9B5-2 JMY Junction-mediating and -regulatory protein 1 SSAWAEGGS(1)PR;SSAWAEGGS(1)PR 202.69 4.11E-08 1078760000 660210 659540 316500 451810 628870 663460 554090 634070 685480 TRUE FALSE 572961.5757 655207.4383 469560.4586 554400.366 616356.7174 688983.7355 500354.4371 498479.0648 604443.3353 0.947916111 1.083984883 0.776847772 0.917208171 1.019709676 1.139864889 0.827793786 0.824691143 1 19.20524757 SSCS(ph)TPLSQANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSCSTPLSQANR 12 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 SS(0.002)CS(0.499)T(0.499)PLSQANR;SSCS(0.5)T(0.5)PLSQANR 190.57 6.79E-06 963400000 821170 988050 534780 591540 983010 1055440 808040 927410 902420 TRUE FALSE 712650.3039 981559.4345 793401.3967 725858.1981 963450.0242 1096043.46 729676.4052 729090.5886 795736.9356 0.895585302 1.233522526 0.997064936 0.91218362 1.210764489 1.377394225 0.916981948 0.916245754 1 19.60193204 SSCST(ph)PLSQANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSCSTPLSQANR 12 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 SSCS(0.11)T(0.89)PLSQANR;SSCS(0.07)T(0.93)PLSQANR 293.76 3.77E-35 742420000 1142930 1316950 685250 763780 1326250 1481760 1076220 1203450 1165790 TRUE FALSE 991888.9047 1308298.869 1016639.192 937207.9226 1299860.22 1538764.266 971848.35 946101.5828 1027971.634 0.9648991 1.272699387 0.988975919 0.911706015 1.264490358 1.496893703 0.945403859 0.920357674 1 19.97136902 SSDEENGPPSS(ph)PDLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSDEENGPPSSPDLDR 16 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 SSDEENGPPS(0.001)S(0.999)PDLDR;SSDEENGPPS(0.001)S(0.999)PDLDR;SSDEENGPPSS(1)PDLDR 300.54 7.12E-46 2278780000 1948210 1930750 1218970 1582380 2201540 2203720 2091380 2380130 2247100 TRUE FALSE 1690749.112 1918066.776 1808467.969 1941683.564 2157733.661 2288498.534 1888558.289 1871157.722 1981450.398 0.853288639 0.968011502 0.912699087 0.979930442 1.088966781 1.154961304 0.953119135 0.944337402 1 20.91812542 3.584284155 4.032176641 1.0195871 0.917571559 0.380836596 0.067112348 0.314211076 8.860821437 0.021336974 0.032223421 3839.583842 -3.584284155 -0.102015542 SSDKPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSDKPIR 7 1 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 0 ; 74.127 0.042886 761470000 2090840 2008480 1281860 1618520 1325450 1882120 2244700 2538100 2392400 FALSE TRUE 1814530.196 1995286.163 1901771.784 1986029.704 1299076.138 1954526.374 2027009.339 1995347.067 2109573.197 0.860140904 0.94582457 0.901495993 0.941436735 0.615800457 0.926503227 0.960862293 0.94585344 1 21.00851972 2.489536083 24.97909824 0.96089842 0.856257855 0.250975938 0.092444729 922.4200166 1855947.827 0.033253488 0.027866149 308.6996117 -2.489536083 -0.104640564 SSDQPLTVPVS(ph)PK ddPTM_MDA-MB-175_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 279.91 2.36E-32 3731720000 6379050 5644730 3655540 4517710 6649950 4921010 6726080 8018800 6652530 TRUE FALSE 5536042.38 5607649.397 5423371.371 5543525.104 6517629.005 5110324.439 6073785.797 6304042.022 5866075.482 0.943738688 0.95594566 0.924531467 0.945014281 1.111071452 0.871165817 1.035408735 1.074660911 1 22.4839642 2.703639963 0.442448389 1.062450322 0.92691184 0.182451028 0.065658388 2.350669483 1.432777597 0.201354871 0.131703829 505.4054996 -2.703639963 -0.135538483 SSDYQFPS(ph)SPFTDTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSDYQFPSSPFTDTLK 16 0 Q9UK61-3;Q9UK61 Q9UK61-3 FAM208A Protein FAM208A 1 SSDYQFPS(0.761)S(0.239)PFTDTLK 120.77 0.00099787 0 86217 70060 56146 65142 75907 70254 79982 95858 93649 TRUE FALSE 74823.205 69599.77125 83298.3934 79933.48673 74396.59921 72956.71684 72225.35795 75359.51267 82577.92191 0.906092128 0.842837524 1.008724747 0.967976487 0.900926028 0.883489378 0.874632787 0.912586693 1 16.33346849 0.902585756 0.004969636 1.58302635 0.270354593 0.02120679 0.05368242 428623.5233 507.1063437 68572.95377 65404.34776 7.990717121 -0.902585756 -1.312671757 SSDYQFPSS(ph)PFTDTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSDYQFPSSPFTDTLK 16 0 Q9UK61-3;Q9UK61 Q9UK61-3 FAM208A Protein FAM208A 1 SSDYQFPS(0.087)S(0.913)PFTDTLK;SSDYQFPS(0.301)S(0.699)PFTDTLK 224.06 8.54E-15 318990000 682490 567530 451180 527680 561170 554530 679620 770380 833590 TRUE FALSE 592297.2173 563801.8581 669372.1571 647497.8091 550003.8149 575863.1279 613710.557 605640.2321 735043.9398 0.805798382 0.767031503 0.910655977 0.880896738 0.748259778 0.783440413 0.834930436 0.823951058 1 19.48747097 1.236206129 5.958807404 1.007091661 0.819617886 0.572798862 0.049034831 0.109122529 14.40707336 0.083182425 0.012632905 17.22686019 -1.236206129 -0.187473775 SSEAS(ph)PTAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSEASPTAQR 10 0 J3KNN7;Q7Z569 J3KNN7 BRAP BRCA1-associated protein 1 SSEAS(0.987)PT(0.013)AQR 110.08 0.0027327 0 70075 72676 58094 70037 76510 78596 72232 85840 169670 TRUE FALSE 60814.4112 72198.58657 86188.45271 85939.9713 74987.60069 81619.63898 65226.95176 67483.78401 149611.8059 0.406481366 0.48257279 0.576080559 0.574419718 0.501214461 0.54554277 0.43597463 0.451059217 1 17.1908645 1.235315571 24.99998993 1.000000693 0.49782553 0.886369227 0.056635291 31.085606 239444.2031 0.103961051 0.014881272 17.19157122 -1.235315571 -0.502175162 SSEAVIWEVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSEAVIWEVLR 11 0 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 0 ; 146.48 8.32E-05 80793000 205247 200393 107254 161978 203844 186843 185047 218300 206201 FALSE TRUE 178123.0889 199076.6052 159122.3931 198757.5806 199787.9032 194030.9711 167101.1704 171618.2438 181824.1527 0.979644818 1.094885373 0.875144423 1.093130795 1.098797383 1.067135297 0.919026257 0.943869345 1 17.47218433 2.238691396 24.99999999 0.950656104 1.035826013 0.226177806 0.070058507 4.940091335 944674.9629 0.027065882 0.019614208 173.2572416 -2.238691396 0.085169909 SSEEIESAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSEEIESAFR 10 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3;A0A0D9SFH4 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 228.4 4.91E-09 1107580000 843790 765450 476430 594120 790830 834550 728260 846660 838110 FALSE TRUE 732281.0136 760421.7085 706833.1416 729024.0266 775094.0302 866655.6785 657633.4573 665608.3477 739029.5906 0.990868326 1.028946227 0.956434154 0.986461213 1.048799723 1.172694151 0.889860793 0.900651823 1 19.49527261 SSEIEQAVQSLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSEIEQAVQSLDR 13 0 Q9BPX5 Q9BPX5 ARPC5L Actin-related protein 2/3 complex subunit 5-like protein 0 ;; 193.49 4.24E-06 175662000 229120 215605 131034 158512 224223 228720 214181 236249 250759 FALSE TRUE 198841.2115 214188.6766 194402.4807 194504.5723 219761.401 237519.0064 193409.7596 185728.9898 221114.5567 0.899267848 0.968677412 0.879193499 0.879655212 0.993880296 1.074189823 0.874703875 0.839967267 1 17.75443448 5.07161014 12.56494307 0.930519778 0.651205583 0.017419734 0.072629889 33040537.14 172219544.5 0.018897647 230089761 117926.1553 -5.07161014 -0.279314196 SSEMS(ph)PVPMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSEMSPVPMR 10 0 E9PCH4;Q8TEU7-2;Q8TEU7-5;Q8TEU7-3;Q8TEU7;Q8TEU7-4;D6RE77;B7Z7Y1;A0A5F9ZHG7 E9PCH4 RAPGEF6 Rap guanine nucleotide exchange factor 6 1 SSEMS(1)PVPMR;SSEMS(1)PVPMR;SSEMS(1)PVPMR 132.17 0.0019364 426770000 893460 940000 583410 637600 1054180 1056750 869120 1043840 928530 TRUE FALSE 775386.9973 933825.0781 865549.0274 782376.8251 1033203.88 1097403.856 784832.8762 820622.9392 818760.2412 0.947025708 1.140535448 1.057145894 0.955562796 1.261912619 1.340323823 0.958562515 1.002275023 1 19.64308152 SSEPVKETVQTTQS(ph)PTPVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSEPVKETVQTTQSPTPVEK 20 1 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 1 SSEPVKETVQT(0.001)T(0.007)QS(0.992)PTPVEK;SSEPVKETVQTTQS(1)PTPVEK;SSEPVKETVQTTQS(1)PTPVEK 279.69 6.81E-45 4021500000 3667090 2822770 1910310 2135400 2686580 1964910 3535610 4043700 2392960 TRUE FALSE 3182474.765 2804227.038 2834142.306 2620275.208 2633122.314 2040501.359 3192727.086 3178986.223 2110066.995 1.508233991 1.328975357 1.343152759 1.241797163 1.247885646 0.967031551 1.513092757 1.506580706 1 21.00885737 5.028270401 1.380148289 1.281669143 1.754690329 0.154986726 0.178908482 5.884811344 5.991940973 0.052857058 4.678510357 106726.0414 -5.028270401 0.473021186 SSEPVQADESQS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SSEPVQADESQSPR 14 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 SSEPVQADESQS(1)PR;SSEPVQADESQS(1)PR;SSEPVQADESQS(1)PR;SSEPVQADESQS(1)PR;SSEPVQADES(0.056)QS(0.944)PR;SSEPVQADES(0.009)QS(0.991)PR;SSEPVQADESQS(1)PR;SSEPVQADESQS(1)PR 395.36 2.73E-114 8576898000 6256110 6526770 3770536 4788501 7091960 7262000 6355310 6929190 6985280 TRUE FALSE 5429349.213 6483895.218 5593979.821 5875803.34 6950843.871 7541373.839 5738973.014 5447436.642 6159488.156 0.881461101 1.05266786 0.90818907 0.953943443 1.128477512 1.224350733 0.931728882 0.884397616 1 22.55437904 4.755601876 22.59261667 1.002337917 0.881460729 0.127245031 0.104265177 2274.723824 3015545.846 0.028005809 0.668469054 56964.18345 -4.755601876 -0.120877188 SSEPVQHEESIRKPS(ph)PEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SSEPVQHEESIRKPSPEPR 19 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 SSEPVQHEES(0.002)IRKPS(0.998)PEPR;SSEPVQHEES(0.016)IRKPS(0.984)PEPR;SSEPVQHEESIRKPS(1)PEPR;SSEPVQHEES(0.003)IRKPS(0.997)PEPR;SSEPVQHEES(0.078)IRKPS(0.922)PEPR 213.71 1.17E-17 5523870000 2947632 2779298 1098195 1450443 2691259 2365194 3171696 3499686 692753 TRUE FALSE 2558094.963 2761040.608 1629285.775 1779788.252 2637708.211 2456184.544 2864105.41 2751305.383 610856.5295 4.187718129 4.519949407 2.667215126 2.913594544 4.318048648 4.020886125 4.688671188 4.5040124 1 19.22047405 SSERPLS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSERPLSPK 9 1 Q15052-2;Q15052 Q15052-2 ARHGEF6 Rho guanine nucleotide exchange factor 6 1 SSERPLS(1)PK 58.172 0.066964 132950000 130780 114980 96522 101260 142320 110080 144590 179560 152970 TRUE FALSE 113497.0916 114224.6888 143200.362 124252.6307 139488.1104 114314.8488 130567.6841 141162.4913 134886.0609 0.841429358 0.84682352 1.061639439 0.921167316 1.034118052 0.847491936 0.967985003 1.04653135 1 17.04138174 4.263022418 24.187595 0.982424358 0.844126117 0.456620041 0.062847353 142.4475863 140847.1263 0.015525766 0.041027297 18324.09006 -4.263022418 -0.138298241 SSESPS(ph)SSPSS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSESPSSSPSSPAR 14 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 2 SSESPS(0.583)S(0.393)S(0.024)PS(0.04)S(0.96)PAR 188.44 1.22E-06 48317000 100180 121550 74950 87403 133310 137920 129610 146940 174530 TRUE FALSE 86940.95918 120751.53 111196.0707 107249.187 130657.3918 143225.8716 117040.4421 115518.0245 153897.2622 0.564928563 0.78462429 0.72253443 0.696888206 0.848991008 0.930658997 0.760510229 0.750617801 1 17.23160804 5.997160385 0.428137764 0.849101352 3.05E-12 0.474677185 0.088244984 18.37116036 1.2025149 0.083449623 9.863717546 993482.8741 -5.997160385 -0.849101352 SSESPSS(ph)SPS(ph)SPARK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSESPSSSPSSPARK 15 1 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 2 SSES(0.001)PS(0.025)S(0.964)S(0.013)PS(0.553)S(0.445)PARK;SSESPS(0.015)S(0.981)S(0.004)PS(0.783)S(0.216)PARK 117.26 0.001344 988930000 1108230 1168270 665600 768880 1187200 1042010 1427840 1593980 875080 TRUE FALSE 961774.5976 1160595.557 987486.3863 943465.9556 1163577.043 1082096.799 1289368.297 1253119.781 771629.0393 1.246420947 1.504084862 1.279742384 1.222693688 1.507948747 1.402353649 1.67096912 1.623992511 1 19.55754791 3.220645637 24.86181987 1.479229064 1.324475189 0.076371316 0.19574033 481.7071168 668495.3503 0.059180061 0.067242149 1662.05594 -3.220645637 -0.154753875 SSESPSS(ph)SPSS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSESPSSSPSSPAR 14 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 2 SSESPS(0.032)S(0.967)SPSS(1)PAR;SSESPS(0.021)S(0.979)SPS(0.02)S(0.98)PAR 272.12 8.27E-33 769780000 1022130 1205190 855250 923430 1390720 1455740 1255240 1532450 1891350 TRUE FALSE 887052.9308 1197273.028 1268851.761 1133108.895 1363047.393 1511743.26 1133507.018 1204747.493 1667756.758 0.531883877 0.717894274 0.760813443 0.679420959 0.817293881 0.906453086 0.679659676 0.722376022 1 20.66947746 5.439320553 0.797311976 0.796533353 2.96E-22 0.433341065 0.097324178 7.500881841 1.653114227 0.035751095 6.867733104 274992.3125 -5.439320553 -0.796533353 SSESPSSSPSS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSESPSSSPSSPAR 14 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 SSESPSSSPS(0.001)S(0.999)PAR;SSESPSSSPSS(1)PAR 317.91 5.84E-56 604410000 525940 623290 389920 528430 792970 737410 770840 865050 939340 TRUE FALSE 456435.6964 619195.5669 578486.6162 648418.108 777191.4484 765778.6399 696084.0554 680065.7893 828292.2953 0.551056311 0.747556835 0.698408786 0.782837305 0.93830578 0.924527059 0.840384559 0.821045654 1 19.65978044 4.833123929 0.597492582 0.897915367 0.325625641 0.748305509 0.064949915 2.340552324 0.605732107 0.037758967 0.952105919 68096.36492 -4.833123929 -0.572289726 SSESPSSSPSS(ph)PARK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSESPSSSPSSPARK 15 1 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 SSESPSSS(0.001)PS(0.131)S(0.868)PARK;SSESPSSSPS(0.021)S(0.979)PARK;SSESPSSSPS(0.012)S(0.988)PARK 192.16 8.91E-08 501031000 219231 228390 133781 184925 287289 209245 338858 382373 200326 TRUE FALSE 190259.0679 226889.6911 198477.9391 226915.0477 281572.511 217294.7905 305995.6033 300605.5096 176643.6885 1.07707821 1.284448332 1.123606174 1.284591879 1.594013992 1.23013051 1.732275894 1.70176196 1 17.43048268 3.416712749 4.804169791 1.491926646 1.177342039 0.252260703 0.223072651 0.25351046 11.84646897 0.064982522 0.085776586 2610.434187 -3.416712749 -0.314584607 SSFASSSASDASKPS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSFASSSASDASKPSSPR 18 1 Q96IF1 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 SSFASSSASDASKPS(0.925)S(0.074)PR 103.95 0.00031547 195480000 304110 121730 86395 108820 135820 115980 157960 168890 178050 TRUE FALSE 263921.093 120930.3476 128175.911 133529.2442 133117.4477 120441.8256 142641.0635 132774.1878 157001.1318 1.681013951 0.770251438 0.816401191 0.850498609 0.84787572 0.767139856 0.908535256 0.845689367 1 17.26041543 4.741873534 24.99987815 0.849316116 1.68101426 0.93825654 0.066930105 69.06912688 521184.762 0.015722016 0.110221597 55191.66981 -4.741873534 0.831698144 SSFASSSASDASKPSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSFASSSASDASKPSSPR 18 1 Q96IF1 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 SSFASSSASDASKPS(0.089)S(0.911)PR 114.72 0.00012716 231330000 408910 160930 111980 141940 163240 172350 209270 234450 229330 TRUE FALSE 354871.5075 159872.8402 166133.9026 174169.6464 159991.8434 178980.416 188975.0276 184314.692 202218.8687 1.754888205 0.79059309 0.821554901 0.861292755 0.791181577 0.885082669 0.934507392 0.911461394 1 17.62555809 4.741940266 24.99890427 0.87582961 1.754888533 0.947986474 0.064811063 71.4383129 528398.0264 0.016791323 0.118643803 55200.15099 -4.741940266 0.879058923 SSFATCVLVSEEDKHAIIVEPEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSFATCVLVSEEDKHAIIVEPEKR 24 2 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;;; 257.2 4.10E-44 2623890000 2080850 1581730 1251110 1394330 1521120 1155650 2250560 2354140 1776170 FALSE TRUE 1805860.4 1571339.511 1856150.981 1710933.937 1490852.688 1200108.603 2032301.038 1850725.481 1566193.206 1.153025306 1.003285869 1.18513538 1.09241563 0.95189577 0.766258338 1.297605576 1.181671248 1 20.57883076 -0.874358818 9.282232114 0.414154341 1.077596214 0 0.149437702 0 0 0 0.034621018 0.133549167 0.874358818 0.663441874 SSFDWLTGSSTDPLVDHTS(ph)PSSDSLLFAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSFDWLTGSSTDPLVDHTSPSSDSLLFAHK 30 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 1 SSFDWLTGSSTDPLVDHT(0.455)S(0.517)PS(0.012)S(0.016)DS(0.001)LLFAHK;SSFDWLTGSSTDPLVDHT(0.215)S(0.757)PS(0.014)S(0.014)DS(0.001)LLFAHK;SSFDWLTGSSTDPLVDHT(0.199)S(0.581)PS(0.167)S(0.035)DS(0.019)LLFAHK;SSFDWLTGSSTDPLVDHT(0.048)S(0.842)PS(0.031)S(0.031)DS(0.048)LLFAHK 202.61 3.13E-25 975670000 773573 634145 301210 554029 787218 539680 797069 917187 904720 TRUE FALSE 671343.3681 629979.2597 446876.1635 679829.7523 771553.902 560441.8388 719769.3711 721053.6976 797765.0323 0.841530201 0.789680212 0.560160129 0.8521679 0.967144298 0.702514921 0.902232289 0.903842195 1 19.60560436 -2 0.338286772 3.503871464 0.74883556 0.317469482 0.10645142 93.64674691 1.47175697 160.2634299 0.157083631 0.01 2 -2.755035904 SSFFSDR ddPTM_MDA-MB-175_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 ;;;;; 139.68 0.0062246 4366880000 5843910 5902310 3368830 4050690 6243110 6621370 5644510 6247000 5700690 FALSE TRUE 5071622.487 5863537.337 4998007.456 4970461.075 6118884.325 6876098.388 5097106.289 4911127.664 5026760.922 1.008924547 1.166464335 0.994279922 0.988799975 1.217261855 1.367898433 1.013994174 0.976996468 1 22.26119764 2.026083374 24.99495398 0.989446884 1.124149406 0.215912961 0.114795843 334.916423 320939.4822 0.049679913 0.033493086 106.1899395 -2.026083374 0.134702522 SSFFSDRGS(ph)GSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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(0.823)GS(0.177)R;SSFFSDRGS(0.996)GS(0.004)R;SSFFSDRGS(0.559)GS(0.441)R;SSFFSDRGS(0.995)GS(0.005)R;SSFFSDRGS(0.999)GS(0.001)R;SSFFSDRGS(0.966)GS(0.034)R 184.59 8.55E-06 6021090000 4336960 3663750 796374 2431420 3377770 1220720 5955910 4304840 1854380 TRUE FALSE 3763819.748 3639682.585 1181503.13 2983511.073 3310558.985 1267681.888 5378306.765 3384283.466 1635157.309 2.301808962 2.225891396 0.722562364 1.824601863 2.024611924 0.775266013 3.289167798 2.069699012 1 20.640998 2.257618429 24.99998188 2.157953776 1.655541136 0.078936387 0.758755142 606.7708317 795958.8712 0.280093011 0.21660128 180.9749347 -2.257618429 -0.50241264 SSFFSDRGSGS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.283)GS(0.717)R 159.41 4.29E-05 577360000 548410 442170 95188 294120 416000 128510 730940 492390 222800 TRUE FALSE 475936.229 439265.3562 141221.2352 360904.4413 407722.4139 133453.8629 660053.5513 387096.2303 196460.8378 2.422550134 2.235892716 0.718826392 1.837029941 2.075336838 0.6792899 3.359720739 1.970348058 1 17.58388223 2.258020658 24.9997593 2.132996103 1.67153981 0.064749651 0.801399042 695.1311445 893013.5362 0.295292648 0.22839583 181.1426256 -2.258020658 -0.461456293 SSFS(ph)QHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSFSQHAR 8 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 S(0.216)S(0.216)FS(0.568)QHAR 61.353 0.055718 443210000 200960 156710 90943 120710 150110 165800 152680 164620 162810 TRUE FALSE 174402.6268 155680.5617 134923.339 148119.0504 147123.1047 172178.4333 137873.1171 129417.2941 143562.7873 1.214817782 1.084407489 0.939821116 1.031737077 1.024799723 1.199324954 0.960368071 0.901468246 1 17.13132231 SSFSQHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SSFSQHAR 8 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;; 203.02 9.90E-05 5519678000 2859180 3923710 1037554 2167958 3950670 4676640 3628730 3924480 3826550 FALSE TRUE 2481332.119 3897934.891 1539318.585 2660225.999 3872059.396 4856553.367 3276816.323 3085260.492 3374179.618 0.735388272 1.155224479 0.456205288 0.788406754 1.147555802 1.439328642 0.971144602 0.914373519 1 21.68610534 3.246956127 24.85327057 1.079959355 0.786935925 0.333196574 0.21782943 228.997675 677898.7907 0.065822582 0.083540217 1765.859421 -3.246956127 -0.293023429 SSFTPSS(ph)PENVIGDFLLQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSFTPSSPENVIGDFLLQDR 20 0 F5H212;P15822 F5H212 HIVEP1 Zinc finger protein 40 1 SSFTPS(0.173)S(0.827)PENVIGDFLLQDR;SSFTPS(0.165)S(0.835)PENVIGDFLLQDR;SSFTPS(0.115)S(0.885)PENVIGDFLLQDR;SSFT(0.004)PS(0.109)S(0.887)PENVIGDFLLQDR 157.47 6.90E-09 185357000 317459 270429 152703 207887 284856 269765 264649 307466 276796 TRUE FALSE 275505.9888 268652.5341 226550.6816 255090.9207 279187.9229 280143.0341 238983.3807 241716.7886 244073.4922 1.128782918 1.100703447 0.928206826 1.045139799 1.143868268 1.14778148 0.979145169 0.990344287 1 17.89695609 2.209483031 24.99956944 0.989491742 1.077334865 0.320145601 0.063312559 284.5974197 244681.7483 0.027949394 0.018846661 161.9880698 -2.209483031 0.087843122 SSGEIVYCGQVFEKS(ph)PLR ddPTM_MDA-MB-175_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 236.48 4.87E-24 3244410000 2793310 2240410 1704590 1979080 2585900 2219550 2805360 3303270 2908690 TRUE FALSE 2424167.006 2225692.599 2528935.426 2428460.362 2534445.649 2304937.525 2533296.619 2596891.417 2564827.982 0.945157735 0.867774609 0.986005862 0.94683167 0.988154242 0.898671389 0.987706247 1.012501203 1 21.29043064 -1.999999999 0.176680118 1.410275718 0.894414564 0.323562091 0.03803483 129.1625409 1.803026389 17.25121086 0.357759583 0.01 1.999999999 -0.515861154 SSGFGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSGFGSPR 8 0 A1L390-3;A1L390;A1L390-2;G3V311;A0A0U1RR71 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 SSGFGS(1)PR;SSGFGS(1)PR;SSGFGS(1)PR;SSGFGS(1)PR 114.97 0.0026792 2109850000 2974950 3004610 1646920 2094980 2575870 3264490 2611350 3023160 2801680 TRUE FALSE 2581802.82 2984872.519 2443376.021 2570677.229 2524615.227 3390077.043 2358101.679 2376680.76 2470468.582 1.045066041 1.208221202 0.989033432 1.040562607 1.02191756 1.3722405 0.954515955 0.962036424 1 21.23635328 SSGGGYGGGPAGGHGGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSGGGYGGGPAGGHGGNR 18 0 Q9H2U1-2;Q9H2U1;Q9H2U1-3 Q9H2U1-2 DHX36 ATP-dependent RNA helicase DHX36 0 ;;; 158.29 4.59E-11 91482000 59515.9 60492.1 30820.8 40536.9 61798.7 70441 55593.3 59952 55007.7 FALSE TRUE 51650.72302 60094.72341 45725.84197 49741.42271 60569.02678 73150.91085 50201.87032 47131.73135 48504.75237 1.064859019 1.238945062 0.942708492 1.025495859 1.248723554 1.508118427 1.034988694 0.971693062 1 15.56583849 2.018997567 24.99787739 0.989679284 1.170230456 0.219499664 0.152497232 363.4157258 478197.3992 0.066070039 0.044537468 104.4714366 -2.018997567 0.180551172 SSGGGYSGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SSGGGYSGDR 10 0 Q92804-2;Q92804;A0A075B7F4 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;;;; 195.57 8.13E-07 981510000 740221 657531 359519 442168 495625 690105 650130 693487 670485 FALSE TRUE 642398.9194 653211.6356 533383.5909 542569.0025 485763.0322 716653.7859 587080.4927 545190.2018 591221.0271 1.086563045 1.104851833 0.902172904 0.917709245 0.821626786 1.212158826 0.992996639 0.92214278 1 19.17333806 4.254276202 24.97562784 0.966170297 1.095707539 0.219191433 0.101004455 371.3502942 590149.3628 0.025416123 0.066749732 17958.75401 -4.254276202 0.129537242 SSGGSGGGPLSHFYSGS(ph)PTSYFTSGLQAGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSGGSGGGPLSHFYSGSPTSYFTSGLQAGLK 31 0 A0A087WZ13;Q8IY67-2;E9PAU2;K7EQG2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 SSGGSGGGPLSHFYS(0.021)GS(0.915)PT(0.026)S(0.037)YFT(0.001)SGLQAGLK 195.08 5.41E-20 162510000 180230 152680 52270 94679 126270 123050 141410 174040 166360 TRUE FALSE 156412.1489 151677.035 77547.94683 116177.314 123757.474 127783.8131 127696.08 136822.9004 146693.1103 1.066254226 1.033975179 0.528640688 0.791975259 0.843648852 0.871096215 0.870498142 0.932715245 1 17.16244159 1.424317729 1.284750667 1.041071052 0.844640722 0.09689394 0.144551007 2.475827284 4.704005272 0.612413373 0.047341215 26.56548377 -1.424317729 -0.196430331 SSGHSSSELS(ph)PDAVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSGHSSSELSPDAVEK 16 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SSGHSSSELS(1)PDAVEK;SSGHS(0.001)S(0.001)S(0.012)ELS(0.986)PDAVEK 140.8 1.07E-06 3751000000 1962180 2113830 786700 1427260 2405440 1871440 2312170 2897510 2497270 TRUE FALSE 1702872.941 2099944.112 1167150.751 1751341.197 2357576.45 1943435.508 2087936.109 2277900.035 2202045.585 0.773314119 0.953633351 0.530030241 0.795324678 1.070630175 0.882559163 0.948180239 1.034447266 1 21.0704129 3.342951908 6.330471781 0.984282418 0.755548327 0.49958318 0.111896169 0.178667517 9.486385097 0.031891542 0.041211631 2202.682534 -3.342951908 -0.228734091 SSGNS(ph)PTPVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSGNSPTPVSR 11 0 H0YBT1;O95429-2;O95429 H0YBT1 BAG4 BAG family molecular chaperone regulator 4 1 SSGNS(0.999)PT(0.001)PVSR;SSGNS(1)PTPVSR;SS(0.02)GNS(0.96)PT(0.02)PVSR;SSGNS(0.98)PT(0.02)PVSR 225.36 5.80E-12 1264890000 1412210 1353520 826960 977260 1275720 1516700 1379730 1505770 1514230 TRUE FALSE 1225582.87 1344628.638 1226880.622 1199161.819 1250335.668 1575048.43 1245923.997 1183772.803 1335219.454 0.917888716 1.007046919 0.918860655 0.898100919 0.93642709 1.179617647 0.93312301 0.886575461 1 20.34864545 SSGNSS(ph)SSGSGSGSTSAGSSSPGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSGNSSSSGSGSGSTSAGSSSPGAR 25 0 Q12797;E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2 Q12797 ASPH Aspartyl/asparaginyl beta-hydroxylase 1 SSGNS(0.042)S(0.44)S(0.44)S(0.077)GSGSGSTSAGSSSPGAR;SSGNS(0.003)S(0.886)S(0.099)S(0.011)GSGSGSTSAGSSSPGAR 301.77 2.90E-63 475760000 326290 401560 193850 328310 558450 430480 298810 574960 499290 TRUE FALSE 283169.9498 398922.1259 287596.5084 402857.8034 547337.9376 447040.8442 269831.4522 452009.2783 440264.505 0.643181421 0.906096497 0.653235737 0.915035845 1.24320251 1.015391518 0.612884866 1.02667663 1 18.74801101 3.562259908 6.746290308 0.970093525 0.754237596 0.305586607 0.168024787 0.356384981 23.87038504 0.04755461 0.070578405 3649.723028 -3.562259908 -0.215855929 SSGNSSSSGSGSGSTSAGSS(ph)SPGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSGNSSSSGSGSGSTSAGSSSPGAR 25 0 Q12797;E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2 Q12797 ASPH Aspartyl/asparaginyl beta-hydroxylase 1 SSGNSSSSGSGSGSTSAGS(0.109)S(0.445)S(0.445)PGAR 255.58 7.54E-45 278440000 102540 109360 58733 107510 156980 152100 78530 164880 137670 TRUE FALSE 88989.0792 108641.607 87136.47525 131921.7887 153856.4051 157951.3854 70914.17269 129621.6951 121394.8094 0.733055059 0.894944417 0.717794077 1.086716881 1.267405137 1.301137884 0.584161489 1.067769666 1 16.88934721 3.734080341 24.86215157 1.043157613 0.793232504 0.290932674 0.19763647 501.593014 2783464.327 0.056121134 0.086542077 5421.01166 -3.734080341 -0.249925109 SSGNSSSSGSGSGSTSAGSSS(ph)PGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SSGNSSSSGSGSGSTSAGSSSPGAR 25 0 Q12797;E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2 Q12797 ASPH Aspartyl/asparaginyl beta-hydroxylase 1 SSGNSSSSGSGSGSTSAGSSS(1)PGAR;SSGNSSSSGSGSGSTSAGS(0.001)S(0.316)S(0.684)PGAR;SSGNSSSSGSGSGSTSAGSS(0.024)S(0.976)PGAR;SSGNSSSSGSGSGSTSAGS(0.064)S(0.018)S(0.918)PGAR;SSGNSSSSGSGS(0.001)GS(0.001)T(0.001)S(0.001)AGS(0.018)S(0.21)S(0.767)PGAR;SSGNSSSSGSGSGSTSAGS(0.028)S(0.15)S(0.822)PGAR 455.34 2.65E-205 769719000 440555.7 459086.8 282289.79 448085.4 681413.2 645065.4 369879.5 731371.2 620863.6 TRUE FALSE 382335.148 456071.0286 418806.0766 549830.0386 667854.4105 669881.4834 334008.643 574973.1604 547465.8125 0.698372646 0.833058464 0.764990374 1.004318491 1.219901581 1.223604229 0.610099545 1.050244869 1 19.06240935 3.731952067 8.906294533 1.012984799 0.772063614 0.328398621 0.170071439 0.185274668 177.5431249 0.047905471 0.075218535 5394.510805 -3.731952067 -0.240921186 SSGNSSSSGSGSGSTSAGSSS(ph)PGARR ddPTM_MDA-MB-175_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 SSGNSSSSGSGSGSTSAGS(0.091)S(0.061)S(0.848)PGARR 164.39 8.47E-12 111800000 22307 23577 6459.8 10557 25684 29100 16052 36555 1464.4 TRUE FALSE 19359.07343 23422.12113 9583.780887 12954.1282 25172.93865 30219.49583 14495.27951 28737.99772 1291.2803 14.99215424 18.13868076 7.421921395 10.03200328 19.49455796 23.40273899 11.22550968 22.25542953 1 10.33458649 2.289850921 0.000597698 9.728231472 19.98158256 0 7.021819917 50683334.16 30797.30309 264128454.8 264191691.3 194.9175397 -2.289850921 10.25335109 SSGPYGGGGQYFAKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSGPYGGGGQYFAKPR 16 1 F8W6I7;P09651-2;P09651;P09651-3;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 ; 336.06 8.83E-72 16380800000 2951400 3266000 1497570 2061010 4271500 4289400 4727000 5526800 3348200 FALSE TRUE 2561365.012 3244545.431 2221799.861 2528993.821 4186505.507 4454415.994 4268576.268 4344936.83 2952379.61 0.867559511 1.098959436 0.752545456 0.856595071 1.418010574 1.50875449 1.445808748 1.471672821 1 21.4934468 3.237276296 24.99999875 1.394469532 0.898463037 0.672907669 0.163983833 19.17547042 373262.4884 0.048144049 0.057650753 1726.936211 -3.237276296 -0.496006495 SSGRNS(ph)PSAASTSSNDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSGRNSPSAASTSSNDSK 18 1 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 S(0.281)S(0.281)GRNS(0.428)PS(0.01)AASTSSNDSK 126.03 1.72E-05 175170000 197660 144470 90690 116860 148640 123190 166200 198750 108460 TRUE FALSE 171538.7302 143520.9671 134547.9873 143394.8491 145682.3548 127929.199 150081.9496 156248.8592 95637.98236 1.793625566 1.500669122 1.406846778 1.499350421 1.523268802 1.337640087 1.569271391 1.633753194 1 16.54529607 7.999982552 0.02821364 7.86E-09 3.553184822 0.248541629 0.180063395 7268.960911 20.32867298 924.0995945 1767.584963 99995982.46 -7.999982552 3.553184815 SSGS(ph)ETEQVVDFSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSGSETEQVVDFSDR 15 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 SS(0.053)GS(0.947)ETEQVVDFSDR;S(0.005)S(0.366)GS(0.628)ETEQVVDFSDR 432.39 1.50E-153 1644630000 1899290 1120610 848330 1005370 1231480 1336070 1299540 1432480 1487280 TRUE FALSE 1648294.014 1113248.639 1258585.225 1233654.625 1206975.957 1387469.477 1173510.811 1126155.3 1311455.453 1.256843312 0.848865005 0.959685838 0.940675966 0.920333172 1.057961576 0.89481561 0.858706483 1 20.32273737 4.747601372 24.98286836 0.931586785 1.256843482 0.723298586 0.062500071 647.9254632 1790413.542 0.015221794 0.183391872 55924.40494 -4.747601372 0.325256697 SSGS(ph)PYGGGYGSGGGSGGYGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 29 SSGSPYGGGYGSGGGSGGYGSR 22 0 P51991;H7C1J8;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 1 SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;S(0.002)S(0.006)GS(0.992)PYGGGYGSGGGSGGYGSR;S(0.001)S(0.006)GS(0.992)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SS(0.001)GS(0.999)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;S(0.041)S(0.041)GS(0.918)PYGGGYGSGGGSGGYGSR;SS(0.002)GS(0.998)PYGGGYGSGGGSGGYGSR;S(0.145)S(0.145)GS(0.71)PY(0.001)GGGYGSGGGSGGYGSR;S(0.003)S(0.007)GS(0.99)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SS(0.001)GS(0.999)PYGGGYGSGGGSGGYGSR;SS(0.001)GS(0.999)PYGGGYGSGGGSGGYGSR;SS(0.003)GS(0.996)PYGGGYGSGGGSGGYGSR;S(0.041)S(0.16)GS(0.799)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR 608 0 42572507000 6095832 5791586 3237495 4127940 5788008 5581689 5571450 6304764 5909129 TRUE FALSE 5290252.356 5753540.69 4803158.411 5065251.869 5672837.965 5796420.188 5031131.637 4956539.282 5210558.501 1.015294686 1.104208059 0.921812587 0.972113041 1.088719753 1.112437407 0.965564754 0.951249138 1 22.31300659 SSGS(ph)PYGGGYGSGGGSGGYGSRRF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSGSPYGGGYGSGGGSGGYGSRRF 24 2 P51991;H7C1J8;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 1 S(0.014)S(0.026)GS(0.959)PY(0.001)GGGYGSGGGSGGYGSRRF;SS(0.002)GS(0.998)PYGGGYGSGGGSGGYGSRRF;S(0.001)S(0.012)GS(0.987)PYGGGYGSGGGSGGYGSRRF 148.84 1.22E-07 1426680000 52992 34511.9 22499 22368.3 45979.3 46573.7 70194 105898 36382.8 TRUE FALSE 45988.97294 34285.18906 33379.59165 27447.36439 45064.40189 48365.42038 63386.59668 83252.5368 32081.66683 1.433496993 1.06868478 1.040456901 0.855546706 1.404677697 1.50757193 1.975788759 2.595019057 1 14.96946148 2.550451403 2.018002097 2.010831981 1.113210049 0.346701612 0.422487499 0.288912518 2.367739407 0.183778264 0.142802004 355.182372 -2.550451403 -0.897621932 SSGSPYGGGYGSGGGSGGYGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSGSPYGGGYGSGGGSGGYGSR 22 0 P51991;H7C1J8;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 252.3 1.25E-36 238820000 21444 19472 9260.4 12273 18874.3 18711.5 18821.4 19872.4 15501 FALSE TRUE 18610.12107 19344.08715 13738.76041 15059.77223 18498.73836 19431.34351 16996.10352 15622.84191 13668.48944 1.361534583 1.415232256 1.005141093 1.101787604 1.353385715 1.421616017 1.243451488 1.14298233 1 13.73856619 1.466091986 2.28060401 0.989608276 1.269611371 0.313598114 0.132770934 0.528520395 4.525100622 0.259771424 0.03893738 29.24771798 -1.466091986 0.280003095 SSHKDS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SSHKDSPR 8 1 O15042-2;O15042;E7ET15;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 S(0.003)S(0.003)HKDS(0.994)PR;S(0.001)S(0.001)HKDS(0.998)PR;S(0.005)S(0.005)HKDS(0.99)PR;S(0.005)S(0.005)HKDS(0.99)PR;S(0.051)S(0.051)HKDS(0.897)PR;S(0.003)S(0.003)HKDS(0.994)PR;S(0.005)S(0.005)HKDS(0.99)PR 93.096 0.0068503 1952655000 6064012 5527277 2441141 4101365 5236808 5224275 6373941 7220164 7307523 TRUE FALSE 5262637.45 5490967.953 3621684.953 5032642.609 5132605.766 5425256.24 5755797.183 5676188.116 6443635.956 0.816718618 0.852153658 0.562056109 0.781025285 0.796538756 0.841955734 0.893253005 0.880898324 1 22.61944356 2.045192656 0.787871762 0.987715066 0.748548311 0.488831519 0.079537825 0.968715525 0.974098257 0.175728433 0.040621982 110.9666962 -2.045192656 -0.239166754 SSHPEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSHPEDLR 8 0 B0QYR6;Q9UJY5-4;Q9UJY5-3;Q9UJY5;Q9UJY5-6;Q9UJY5-2 B0QYR6 GGA1 ADP-ribosylation factor-binding protein GGA1 0 91.069 0.012749 476060000 751620 838520 354010 547760 730660 926040 708420 805690 877020 FALSE TRUE 652291.5126 833011.7069 525210.4201 672137.28 716121.2955 961665.358 639717.5374 633399.4634 773339.6947 0.843473466 1.07716145 0.679145819 0.869135885 0.926011299 1.243522561 0.827214149 0.819044293 1 19.56074274 SSHYDELLAAEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSHYDELLAAEAR 13 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 176.08 1.72E-05 4476430000 3108000 3176720 1469810 2250460 3133280 3442890 2924280 3204060 3277670 FALSE TRUE 2697269.925 3155851.917 2180615.032 2761461.339 3070933.858 3575340.206 2640683.776 2518896.703 2890187.587 0.933250817 1.091919408 0.7544891 0.955460937 1.062537903 1.237061644 0.913672105 0.871533984 1 21.4627317 5.085554571 15.44541948 0.977767318 0.000215067 0.012447679 0.130677315 10942168.8 28584802.93 0.033182629 357839764.2 121773.9998 -5.085554571 -0.977552251 SSHYGGS(ph)LPNVNQIGS(ph)GLAEFQSPLHSPLDSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSHYGGSLPNVNQIGSGLAEFQSPLHSPLDSSR 33 0 Q53ET0 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 2 S(0.117)S(0.131)HY(0.008)GGS(0.745)LPNVNQIGS(0.376)GLAEFQS(0.241)PLHS(0.187)PLDS(0.1)S(0.095)R 45.464 0.046879 36570000 9958.9 11069 7222.2 7873.5 11460 9213.5 11585 10992 14795 TRUE FALSE 8642.806132 10996.28701 10714.88008 9661.298514 11231.96842 9567.949307 10461.48848 8641.44634 13045.95195 0.662489496 0.842888817 0.821318376 0.740559106 0.860954299 0.73340369 0.801895371 0.662385265 1 13.6713146 2.439122766 0.010409565 1.577590507 4.98E-08 0.056826247 0.097772086 21584.51082 168.802626 12961.578 12617.59735 274.8671037 -2.439122766 -1.577590458 SSHYGGS(ph)LPNVNQIGSGLAEFQSPLHSPLDSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSHYGGSLPNVNQIGSGLAEFQSPLHSPLDSSR 33 0 Q53ET0 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 S(0.001)S(0.001)HYGGS(0.998)LPNVNQIGSGLAEFQSPLHSPLDSSR;SSHYGGS(1)LPNVNQIGSGLAEFQSPLHSPLDSSR;SSHYGGS(1)LPNVNQIGSGLAEFQSPLHSPLDSSR;SSHYGGS(0.994)LPNVNQIGS(0.006)GLAEFQSPLHSPLDSSR 384.19 2.21E-166 3075180000 990677 968459 270936 593207 1027218 1057938 792240 1011394 843558 TRUE FALSE 859756.5244 962097.1291 401961.5558 727903.716 1006778.372 1098637.559 715408.6867 795115.2638 743833.5342 1.15584534 1.2934307 0.540391818 0.978584162 1.353499574 1.476993855 0.96178601 1.068942481 1 19.50462026 SSIIVAADESTISWGPSPTFGELGYGDHKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSIIVAADESTISWGPSPTFGELGYGDHKPK 31 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 159.7 1.28E-12 117360000 333750 176740 130540 175490 172920 141040 267430 302190 240330 FALSE TRUE 289644.0919 175578.9833 193669.5806 215337.6867 169479.2303 146465.9001 241494.6798 237569.0201 211918.4612 1.3667714 0.828521415 0.913887254 1.016134628 0.799737925 0.691142712 1.139564144 1.121039757 1 17.69314975 SSILLDVKPWDDETDMAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSILLDVKPWDDETDMAK 18 1 P24534 P24534 EEF1B2 Elongation factor 1-beta 0 ; 237.31 6.92E-24 2092080000 4464200 3139350 3074860 3290390 2996130 2020790 4422900 5292900 4778100 FALSE TRUE 3874244.659 3118727.403 4561872.581 4037523.34 2936512.875 2098531.099 3993967.839 4161054.524 4213238.461 0.919540799 0.740220956 1.082747303 0.958294523 0.696972863 0.498080305 0.94795675 0.987614293 1 22.00649814 2.021736894 24.99919365 0.985381629 0.817160138 0.194986524 0.157526892 397.7897052 457488.5312 0.068810069 0.04638802 105.1324764 -2.021736894 -0.168221491 SSILLDVKPWDDETDMAQLEACVR ddPTM_MDA-MB-175_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 87.102 0.012039 68122000 79452 74563 41553 49189 69561 59829 83813 86177 73928 FALSE TRUE 68952.21689 74073.19074 61648.16979 60358.11426 68176.87219 62130.66034 75684.82816 67748.71918 65188.31606 1.057738887 1.136295508 0.945693546 0.925903872 1.045844966 0.953095035 1.161018304 1.039277025 1 15.99232579 1.233235302 23.09386489 0.999999851 1.034433669 0.017676905 0.077003473 399.1141483 1730272.75 0.153739458 0.019112317 17.10942057 -1.233235302 0.034433818 SSINSVDGES(ph)PNGSSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSINSVDGESPNGSSDR 17 0 Q9NUY8-2;Q9NUY8;E9PGE5 Q9NUY8-2 TBC1D23 TBC1 domain family member 23 1 SSINSVDGES(1)PNGSSDR 107.28 0.0014175 0 160550 175670 114570 128680 226220 222540 181320 211590 232780 TRUE FALSE 139332.9107 174516.0122 169976.4352 157898.7608 221718.6646 231101.2578 163735.6143 166343.1251 205261.0136 0.678808451 0.850215095 0.828098976 0.769258409 1.080179137 1.125889684 0.797694659 0.81039805 1 17.64710011 3.276916816 24.99969587 0.939545739 0.789818198 0.382935361 0.111960573 231.3008677 150755.1328 0.035881315 0.04632168 1891.981197 -3.276916816 -0.149727541 SSISSIS(ph)GRDDLMDYHRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSISSISGRDDLMDYHRR 18 2 E9PDY7;G5E9V3;A0A1W2PQ63;E9PFQ4;Q86SQ0-2;Q86SQ0-3;Q86SQ0 E9PDY7 PHLDB2 Pleckstrin homology-like domain family B member 2 1 SSIS(0.003)S(0.205)IS(0.792)GRDDLMDYHRR 61.942 0.043717 2629500000 1705600 1239900 829760 1079500 1470700 1386000 1420000 1782100 1666600 TRUE FALSE 1480200.639 1231755.015 1231034.711 1324616.974 1441435.947 1439320.317 1282288.619 1401011.783 1469576.447 1.007229424 0.838170085 0.837679941 0.901359693 0.980851286 0.979411667 0.872556594 0.953343929 1 20.48696898 3.387115716 6.398480574 0.951230518 0.885700493 0.211038345 0.0573448 0.3195039 18.6819531 0.016464132 0.021325832 2438.460449 -3.387115716 -0.065530025 SSKAS(ph)LGS(ph)LEGEAEAEASSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSKASLGSLEGEAEAEASSPK 21 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 S(0.103)S(0.387)KAS(0.852)LGS(0.657)LEGEAEAEASSPK 118.05 5.22E-05 133020000 319230 137030 105100 126830 151760 137420 185700 237930 141970 TRUE FALSE 277042.9467 136129.8409 155926.7115 155628.69 148740.2729 142706.6363 167690.8426 187050.5211 125186.4683 2.213042275 1.087416577 1.245555639 1.243175018 1.188149765 1.13995257 1.339528503 1.494175238 1 16.9337191 4.744181123 24.9988945 1.242981987 2.213042689 0.838067079 0.137148938 254.5675079 1132232.751 0.035020145 0.298789182 55485.70681 -4.744181123 0.970060702 SSLDVLPSQVYSLVGS(ph)SPLR ddPTM_MDA-MB-175_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 231.42 1.05E-25 54089000 160000 131310 70138 80025 107320 129590 106680 127720 103750 TRUE FALSE 138855.5946 130447.416 104056.9714 98195.89936 105184.542 134575.4112 96334.19002 100408.0719 91484.79319 1.517799732 1.425891795 1.137423694 1.073357614 1.149748918 1.471013995 1.053007682 1.097538382 1 16.48124433 4.303371003 3.952097357 1.140523854 1.496283325 0.546738333 0.126610806 0.166786084 5.076024934 0.033488533 0.096500698 20108.09845 -4.303371003 0.35575947 SSLFPFEDAFLDDSHGDQALSSGLSS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSLFPFEDAFLDDSHGDQALSSGLSSPTR 29 0 Q8NE35-2 Q8NE35-2 1 SSLFPFEDAFLDDSHGDQALSSGLS(0.032)S(0.964)PT(0.003)R;SSLFPFEDAFLDDSHGDQALSSGLS(0.028)S(0.944)PT(0.028)R;SSLFPFEDAFLDDSHGDQALSSGLS(0.332)S(0.665)PT(0.003)R;SSLFPFEDAFLDDSHGDQALSSGLS(0.112)S(0.884)PT(0.004)R 352.67 3.28E-120 702710000 427516 462480 266168 348377 510798 519840 458150 562719 501789 TRUE FALSE 371018.6774 459441.9384 394887.7351 427481.3225 500634.1192 539838.5812 413718.6835 442385.9209 442468.0761 0.838520783 1.038361779 0.892466048 0.966129187 1.131458169 1.220062216 0.935024934 0.999814325 1 18.75521384 3.453925842 17.5975593 1.049038118 0.933750113 0.313702556 0.091642804 11.73958966 8904.885517 0.027622628 0.035681223 2843.975443 -3.453925842 -0.115288005 SSLFPIDDGLLDDGHSDQVGVLNS(ph)PTCYSAHQNGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSLFPIDDGLLDDGHSDQVGVLNSPTCYSAHQNGER 36 0 A0A5K1VW61;A0A5K1VW79;A0A5K1VW71;A0A5K1VW93;Q7Z5Q1-7;Q7Z5Q1-5;Q7Z5Q1-4;Q7Z5Q1-6;Q7Z5Q1-3;Q7Z5Q1;Q7Z5Q1-8;Q7Z5Q1-9 A0A5K1VW61 CPEB2 Cytoplasmic polyadenylation element-binding protein 2 1 SSLFPIDDGLLDDGHSDQVGVLNS(0.965)PT(0.033)CYS(0.001)AHQNGER 124.59 3.68E-08 37160000 14132 22242 10519 17297 25293 29956 25316 30836 27011 TRUE FALSE 12264.42039 22095.89084 15606.02358 21224.54822 24789.71878 31108.4267 22860.85822 24241.96137 23817.79035 0.514926877 0.927705321 0.6552255 0.891121632 1.040806826 1.30610045 0.9598228 1.017808999 1 14.53975196 3.445574277 2.933497029 1.063351485 0.722791117 0.59865907 0.136230807 0.186628998 3.274936243 0.039867208 0.05659438 2789.807754 -3.445574277 -0.340560369 SSLFS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSLFSPR 7 0 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 S(0.074)S(0.291)LFS(0.636)PR;S(0.003)S(0.01)LFS(0.987)PR;S(0.017)S(0.052)LFS(0.931)PR;S(0.001)S(0.005)LFS(0.993)PR 90.761 0.017728 378711000 971070 999130 575410 762600 1018540 1030830 995040 1159900 1129180 TRUE FALSE 842740.6391 992566.6492 853680.2006 935759.9856 998273.0467 1070486.697 898541.174 911864.4114 995689.6268 0.846388891 0.996863503 0.85737581 0.939810921 1.002594604 1.075120869 0.902430988 0.915811902 1 19.92533657 3.477811122 24.97184906 0.970389903 0.907994569 0.24402363 0.062124296 44.51950093 1611550.061 0.01837919 0.024026516 3004.769221 -3.477811122 -0.062395334 SSLGQSAS(ph)ETEEDTVSVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSLGQSASETEEDTVSVSK 19 0 Q13435;E9PPJ0;H0YCG1;E9PJ04 Q13435 SF3B2 Splicing factor 3B subunit 2 1 SSLGQSAS(1)ETEEDTVSVSK 342.85 4.91E-76 142500000 226900 176110 118430 149970 170110 151440 173270 232260 337380 TRUE FALSE 196914.5901 174953.1218 175703.1441 184022.9806 166725.1438 157265.9948 156466.3021 182593.0064 297495.3207 0.661908193 0.58808697 0.590608093 0.61857437 0.560429466 0.528633507 0.525945422 0.613767659 1 18.18250745 1.239677548 4.703998839 1.031197727 0.58045695 0.914511627 0.03989102 0.051378659 2.582108787 0.076723482 0.010449131 17.36511037 -1.239677548 -0.450740777 SSLGQSAS(ph)ETEEDTVSVSKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSLGQSASETEEDTVSVSKK 20 1 Q13435;E9PPJ0;H0YCG1;E9PJ04 Q13435 SF3B2 Splicing factor 3B subunit 2 1 SSLGQSAS(0.896)ET(0.104)EEDTVSVSKK;SSLGQS(0.007)AS(0.949)ET(0.043)EEDTVSVSKK 250.82 4.53E-31 831770000 1078750 820580 400580 433810 672500 521440 903070 1101050 338360 TRUE FALSE 936190.4543 815189.5559 594301.8279 532313.1909 659118.5657 541500.1342 815490.4104 865599.0259 298359.4663 3.137793702 2.732239624 1.991898683 1.784133742 2.209142462 1.814925268 2.733247986 2.901195114 1 18.18669203 4.423573458 3.823350445 2.161138784 3.072894887 0.319232746 0.530106205 0.282750423 8.277720647 0.139232914 0.465579028 26519.99624 -4.423573458 0.911756103 SSLGSHQLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSLGSHQLPR 10 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 0 ; 117.02 0.0010127 205280000 704930 754360 309560 410950 818340 885880 704530 767610 412580 FALSE TRUE 611771.7144 749404.5595 459264.2514 504262.4785 802056.6351 919960.3768 636204.789 603462.575 363805.2624 1.681591163 2.059905771 1.262390347 1.386078022 2.204631757 2.528716519 1.748750925 1.658751638 1 18.47280689 1.21119853 2.268649633 0.724004292 1.844730069 0.335276616 0.369595565 0.893402638 4.462818971 2.095468141 0.105966609 16.26292018 -1.21119853 1.120725778 SSLLDDLLTESEDMAQR ddPTM_MDA-MB-175_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 ; 266.85 4.39E-26 16009000 41340 42234 25467 33363 42057 38824 39815 47561 44058 FALSE TRUE 35876.81426 41956.56207 37782.92638 40938.57907 41220.14798 40317.5844 35953.74743 37390.45027 38849.51343 0.923481688 1.079976514 0.972545678 1.053773277 1.061020959 1.037788658 0.925461975 0.962443206 1 15.24560891 2.25156987 24.99806619 0.961046209 1.02513986 0.243845148 0.048488832 273.2179006 525004.3426 0.017062195 0.013133343 178.4719093 -2.25156987 0.064093651 SSLPLDHGSPAQENPESEKS(ph)SPAVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSLPLDHGSPAQENPESEKSSPAVSR 26 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5;A0A0A0MRX3 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 SSLPLDHGSPAQENPES(0.218)EKS(0.467)S(0.312)PAVS(0.002)R 117.22 0.00050329 221780000 47854 61526 7358.3 30079 70491 58996 43089 80586 56974 TRUE FALSE 41529.97265 61121.83165 10916.79849 36908.89668 69088.36701 61265.6143 38910.23541 63353.31102 50238.59862 0.82665468 1.216630904 0.217299025 0.734672099 1.3752049 1.219492899 0.774508774 1.261048532 1 15.6165086 3.26591331 24.52526198 1.121232124 0.744263952 0.300314674 0.286030923 228.2950588 204694.4698 0.082105238 0.105968312 1844.647169 -3.26591331 -0.376968172 SSLSTSS(ph)PESAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSLSTSSPESAR 12 0 D6REJ6;D6R9F1;D6REQ4;D6RDH3;D6RBZ2;D6RF08;D6RF67;D6RF51;D6RB63;D6R9D1;D6RC23;D6RAM4;D6RGK2;D6R9N9;D6RC13;Q8N7B6-2;Q8N7B6-3;Q8N7B6-4;Q8N7B6 D6REJ6 PACRGL PACRG-like protein 1 SSLS(0.007)T(0.037)S(0.037)S(0.919)PESAR 104.59 0.0022251 325520000 242850 245360 154780 174350 259540 259650 237770 228350 258290 TRUE FALSE 210756.7572 243748.214 229632.1257 213938.8323 254375.6618 269638.9035 214711.102 179519.1295 227755.2504 0.925365087 1.070219956 1.008240755 0.939336555 1.116881658 1.18389764 0.942727343 0.788210718 1 17.79712479 2.006519528 24.98055418 0.87492498 1.041380383 0.317107789 0.091273206 153.9922886 590041.9299 0.037254501 0.025049181 101.5125011 -2.006519528 0.166455403 SSMIT(ph)SLEGLGTDNVFSLHEDNHYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSMITSLEGLGTDNVFSLHEDNHYR 25 0 Q8IZQ1-2;Q8IZQ1 Q8IZQ1-2 WDFY3 WD repeat and FYVE domain-containing protein 3 1 S(0.015)S(0.015)MIT(0.525)S(0.445)LEGLGTDNVFSLHEDNHYR;S(0.012)S(0.012)MIT(0.488)S(0.488)LEGLGTDNVFSLHEDNHYR 134.76 8.76E-05 98186000 45476 36920 10144.8 21328.6 27080.5 21993 20258.9 32435.3 22625.6 TRUE FALSE 39466.23138 36677.47009 15050.85921 26171.58462 26541.65103 22839.08494 18294.195 25499.26351 19950.82734 1.978175175 1.838393439 0.754397748 1.311804476 1.330353402 1.144768813 0.916964228 1.278105568 1 14.28416095 4.335543035 6.884871819 1.128560031 1.936056196 0.767963343 0.183596717 0.093369645 5.613607051 0.044034956 0.118174522 21654.24446 -4.335543035 0.807496165 SSMITS(ph)LEGLGTDNVFSLHEDNHYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSMITSLEGLGTDNVFSLHEDNHYR 25 0 Q8IZQ1-2;Q8IZQ1 Q8IZQ1-2 WDFY3 WD repeat and FYVE domain-containing protein 3 1 S(0.003)S(0.003)MIT(0.167)S(0.827)LEGLGTDNVFSLHEDNHYR 146.34 4.36E-07 67776000 39955 29156 9074.7 12536 22908 21630 22605 25546 17661 TRUE FALSE 34674.84552 28964.47232 13463.25527 15382.4904 22452.17562 22462.1201 20412.77058 20083.1867 15573.1367 2.226580694 1.859899703 0.86451789 0.987758003 1.441724686 1.442363252 1.310768086 1.28960447 1 13.92677194 4.41065743 5.20533686 1.218933284 2.146434884 0.770619631 0.197576505 0.086702296 4.387945591 0.05290509 0.150955423 25742.89766 -4.41065743 0.927501601 SSNADAEEKLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSNADAEEKLDR 12 1 O60828-2;O60828;A0A5H1ZRR1;O60828-3;O60828-6 O60828-2 PQBP1 Polyglutamine-binding protein 1 0 72.891 0.037093 204180000 192350 144750 81878 105560 141700 120390 155420 193920 113120 FALSE TRUE 166930.4601 143799.1277 121474.4747 129529.0114 138880.4472 125021.4812 140347.3923 152451.7171 99747.08247 1.673537271 1.441637431 1.217824839 1.298574436 1.392325909 1.253384842 1.407032555 1.528382719 1 16.60598702 4.634344173 3.214771271 1.327352489 1.688883289 0.409451733 0.140641907 0.297309473 4.943872692 0.034871821 0.227726632 43086.79323 -4.634344173 0.3615308 SSPAAKPGSTPSRPS(ph)SAKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPAAKPGSTPSRPSSAKR 19 3 Q15555-4;Q15555-5;Q15555-3;Q15555;K7EL66;K7ERD8;Q15555-2 Q15555-4 MAPRE2 Microtubule-associated protein RP/EB family member 2 1 SSPAAKPGS(0.01)T(0.01)PS(0.041)RPS(0.47)S(0.47)AKR 83.727 0.018293 540380000 412560 349700 226700 275870 347160 210040 496060 542430 349830 TRUE FALSE 358039.1507 347402.7977 336332.8783 338510.4999 340252.1952 218120.3747 447952.1776 426435.5657 308473.4959 1.160680433 1.126199827 1.090313699 1.097373046 1.103019221 0.707095999 1.452157749 1.382405851 1 18.23478701 2.197881412 24.99999906 1.30714859 1.057769057 0.281329338 0.171254432 177.9871532 109383.3806 0.069119301 0.046600807 157.7180549 -2.197881412 -0.249379533 SSPAFGDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSPAFGDRR 9 1 P13716;P13716-2 P13716 ALAD Delta-aminolevulinic acid dehydratase 0 ;;; 102.07 0.005844 351318000 347803 377415 198420 249031 393610 451052 407937 401214 234083 FALSE TRUE 301839.9523 374935.736 294376.5757 305577.2948 385777.9311 468404.2623 368375.3325 315417.5084 206409.9744 1.462332202 1.816461327 1.426174178 1.480438606 1.868988803 2.269290831 1.784677962 1.528111756 1 17.65515316 3.261596239 24.97508266 1.705989868 1.557061057 0.043263958 0.329881342 942.79207 1022162.617 0.101683127 0.13118541 1826.401432 -3.261596239 -0.148928811 SSPCIHYFTGTPDPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSPCIHYFTGTPDPSR 16 0 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 ;;; 164.7 7.29E-09 3070060000 2213740 1859620 745120 1228010 1914570 1996040 1934990 2149060 1948720 FALSE TRUE 1921188.65 1847404.034 1105462.524 1506848.439 1876473.803 2072828.95 1747334.968 1689500.243 1718344.542 1.118046238 1.075106877 0.643329959 0.876918687 1.092024188 1.20629414 1.016871137 0.983213903 1 20.71258791 3.23759458 24.9983764 1.054242292 0.91847443 0.176989897 0.13973193 48.68810775 1259925.063 0.044351626 0.053249146 1728.202306 -3.23759458 -0.135767862 SSPGAVAGLSNAPGT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSPGAVAGLSNAPGTPR 17 0 V9GYB2;Q9BWG4-2;Q9BWG4;U3KPY3 V9GYB2 SSBP4 Single-stranded DNA-binding protein 4 1 SSPGAVAGLSNAPGT(1)PR;SSPGAVAGLSNAPGT(1)PR;SSPGAVAGLS(0.001)NAPGT(0.999)PR;SSPGAVAGLSNAPGT(1)PR 212.34 1.86E-11 1181720000 649189 702109 381346 491337 717433 698506 652767 725758 645528 TRUE FALSE 563397.0288 697496.7997 565766.2011 602902.5755 703157.4869 725377.9778 589461.7568 570560.2996 569214.4152 0.989779973 1.225367421 0.993942153 1.059183603 1.235312157 1.274349276 1.035570676 1.002364459 1 19.11861267 2.020853517 24.97472111 1.006635993 1.131563731 0.249946867 0.096778141 311.4175286 372960.3121 0.0401031 0.027034764 104.9188489 -2.020853517 0.124927738 SSPLIQFHLLHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPLIQFHLLHSK 13 0 O94973-3;O94973;O94973-2;A0A0G2JQM1;A0A0G2JS82 O94973-3 AP2A2 AP-2 complex subunit alpha-2 0 175.66 1.03E-05 208320000 339190 320280 160930 262710 334050 277840 360460 427530 334200 FALSE TRUE 294365.1821 318176.0596 238756.2863 322362.3208 327403.0586 288528.6846 325502.6447 336106.0365 294691.2567 0.998893504 1.079692907 0.810191279 1.09389849 1.111003639 0.979088039 1.104554809 1.140536168 1 18.16884473 SSPNVANQPPS(ph)PGGK ddPTM_MDA-MB-175_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 287.93 1.39E-34 2630940000 2452330 2446060 1621670 2327800 2950670 2133870 3384830 3768980 3042630 TRUE FALSE 2128248.377 2429991.671 2405915.036 2856362.568 2891957.44 2215961.36 3056569.708 2963012.957 2682933.748 0.793254168 0.905721833 0.896747837 1.064641485 1.07790863 0.825947104 1.139263953 1.104392891 1 21.35538 6.109310984 0.424149725 1.067852192 1.17E-12 0.451742208 0.088656685 17.10349952 1.024078445 0.083208662 11.65673396 1286207.341 -6.109310984 -1.067852192 SSPPAPPLPPGS(ph)GSPGTPQALPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPPAPPLPPGSGSPGTPQALPR 23 0 Q9Y3L3;A0A2R8Y5V0 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 SSPPAPPLPPGS(0.596)GS(0.387)PGT(0.016)PQALPR;S(0.148)S(0.148)PPAPPLPPGS(0.603)GS(0.086)PGT(0.014)PQALPR 191.97 1.11E-17 1150700000 224671 232364 129733 148472 232740 250834 199891 244370 229670 TRUE FALSE 194980.1581 230837.5856 192472.3127 182184.8369 228108.9293 260483.7463 180505.6016 192113.3772 202518.6742 0.962776193 1.139833581 0.950392913 0.899595247 1.126359977 1.286220875 0.891303492 0.948620555 1 17.62769542 SSPPAPPLPPGSGSPGT(ph)PQALPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSPPAPPLPPGSGSPGTPQALPR 23 0 Q9Y3L3;A0A2R8Y5V0 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 S(0.122)S(0.122)PPAPPLPPGS(0.039)GS(0.148)PGT(0.57)PQALPR 135.29 0.00017672 716580000 68955 72049 40299 42193 75104 84351 66493 80919 81532 TRUE FALSE 59842.42204 71575.70537 59787.73119 51773.56553 73609.57734 87596.03755 60044.51909 63615.10156 71893.37984 0.832377365 0.995581311 0.831616643 0.720143713 1.023871426 1.218415906 0.835188431 0.8848534 1 16.13357131 3.206957827 24.99998324 0.978515995 0.854739403 0.268053432 0.119430763 341.4153259 270081.935 0.038916289 0.044130713 1610.489238 -3.206957827 -0.123776591 SSPS(ph)PALEQPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSPSPALEQPFR 12 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 SS(0.003)PS(0.997)PALEQPFR;SS(0.005)PS(0.994)PALEQPFR;S(0.009)S(0.005)PS(0.986)PALEQPFR;S(0.004)S(0.045)PS(0.95)PALEQPFR 228.93 9.86E-12 824610000 1162750 1108050 738510 951180 1325420 1282210 1140280 1402150 1314100 TRUE FALSE 1009089.641 1100771.147 1095655.906 1167159.957 1299046.735 1331537.448 1029695.821 1102311.134 1158748.595 0.870844328 0.949965464 0.945551012 1.007259005 1.12107729 1.149116775 0.88862746 0.951294473 1 20.14413616 4.299313389 1.539937097 1.011864494 0.87740838 0.280530478 0.076062275 0.874048139 3.386473629 0.024827059 0.140405275 19921.10335 -4.299313389 -0.134456113 SSPS(ph)TENMHFPSSISSQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPSTENMHFPSSISSQTR 19 0 A0A0U1RR27;Q7Z401;Q7Z401-2 A0A0U1RR27 DENND4A C-myc promoter-binding protein 1 S(0.172)S(0.172)PS(0.614)T(0.041)ENMHFPSSISSQTR;S(0.033)S(0.142)PS(0.806)T(0.019)ENMHFPSSISSQTR 179.33 2.32E-14 511570000 296191 342432 150119 263840 452716 459410 408319 452286 441052 TRUE FALSE 257048.6089 340182.5416 222717.0505 323748.9045 443707.8373 477083.8 368720.2862 355568.1586 388911.335 0.660943988 0.87470462 0.572667933 0.832449135 1.140897159 1.22671611 0.948083157 0.914265352 1 18.56908176 3.430396302 5.717772689 1.029627821 0.716683704 0.649929055 0.116048654 0.131445357 10.01159888 0.035938408 0.047159988 2693.992001 -3.430396302 -0.312944118 SSPSGASS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPSGASSPR 10 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 SSPSGAS(0.003)S(0.997)PR;SSPSGAS(0.001)S(0.999)PR 160.67 7.66E-06 952710000 1905830 1873450 1029070 1207270 1253520 1950670 1744360 1942090 2004940 TRUE FALSE 1653969.737 1861143.184 1526731.694 1481399.105 1228577.404 2025713.537 1575192.236 1526789.167 1767918.277 0.935546489 1.052731457 0.863575943 0.837934154 0.694928844 1.145818539 0.890987019 0.863608452 1 20.75362016 4.228829221 24.98090604 0.895169356 0.994138982 0.09855845 0.118351882 402.0494056 1032086.202 0.02982356 0.063336885 16936.71661 -4.228829221 0.098969627 SSPSGNTQSS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSPSGNTQSSPK 12 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 SSPSGNTQS(0.008)S(0.992)PK;SSPSGNTQS(0.007)S(0.993)PK 145.49 0.00030121 0 395750 334960 236690 254170 283170 300760 415280 485500 444770 TRUE FALSE 343450.6348 332759.6257 351154.0757 311883.1832 277535.471 312330.4318 375006.2095 381679.6032 392189.7973 0.875725573 0.848465789 0.895367697 0.795235331 0.70765602 0.796375719 0.956185531 0.973201256 1 18.58119248 2.181804685 5.521412447 0.977776307 0.81833301 0.671296361 0.051792804 0.12778329 7.989549318 0.023971176 0.016162385 151.9863849 -2.181804685 -0.159443297 SSQCHTGS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSQCHTGSSPR 11 0 O15226;O15226-2 O15226 NKRF NF-kappa-B-repressing factor 1 SSQCHT(0.002)GS(0.499)S(0.499)PR 74.769 0.025713 88972000 143480 132210 48248 83277 88996 146520 132800 150860 148080 TRUE FALSE 124518.7545 131341.5038 71580.89418 102186.3157 87225.15372 152156.7192 119921.0764 118599.763 130574.1511 0.953624844 1.005876758 0.548201107 0.782592227 0.668012413 1.165289745 0.918413602 0.908294345 1 16.9945098 2.751641189 24.99819444 0.976521844 0.789532903 0.326854213 0.145679789 1060.847881 2027378.224 0.048333029 0.048054984 564.4704201 -2.751641189 -0.18698894 SSQQPST(ph)PQQAPPGQPQQGTFVAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSQQPSTPQQAPPGQPQQGTFVAHK 25 0 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 SSQQPS(0.005)T(0.995)PQQAPPGQPQQGTFVAHK;SSQQPST(1)PQQAPPGQPQQGTFVAHK;SSQQPS(0.006)T(0.994)PQQAPPGQPQQGTFVAHK;SSQQPS(0.146)T(0.854)PQQAPPGQPQQGTFVAHK 222.47 3.79E-33 2138370000 2246820 1705880 1120760 1386370 1767570 1869490 2137550 2282210 2346490 TRUE FALSE 1949897.044 1694673.962 1662763.285 1701166.498 1732398.815 1941410.49 1930250.73 1794177.152 2069090.625 0.942393253 0.819042888 0.803620327 0.822180758 0.837275465 0.938291666 0.932898108 0.867133189 1 20.98056541 2.743565395 24.49164621 0.923884315 0.839910109 0.441403234 0.049305808 314.0898279 1537048.542 0.015973964 0.015490425 554.0709678 -2.743565395 -0.083974207 SSQRHS(ph)PPFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSQRHSPPFSK 11 1 Q8WV28-3;Q8WV28;Q8WV28-2 Q8WV28-3 BLNK B-cell linker protein 1 S(0.258)S(0.258)QRHS(0.484)PPFSK;S(0.218)S(0.218)QRHS(0.563)PPFSK 88.561 0.0077823 217206000 515750 418580 151124 294770 499720 423410 439070 528270 489680 TRUE FALSE 447592.3308 415830.3204 224208.0719 361702.0338 489776.5497 439698.8567 396489.059 415303.5715 431790.5882 1.036595847 0.963037018 0.519251873 0.837679291 1.13429186 1.018315055 0.918243866 0.9618171 1 18.71997227 3.372702716 10.25781246 0.994741824 0.823203878 0.247750825 0.143169726 0.485073827 43.97016786 0.04277885 0.05522969 2358.862985 -3.372702716 -0.171537946 SSQTQNKASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSQTQNKASR 10 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ; 122.18 0.00045183 60851000 1341.8 861.07 0 0 0 2153.48 0 9865 903.32 FALSE TRUE 1164.47773 855.4135745 0 0 0 2236.325769 0 7755.44652 796.5305387 1.461937332 1.073924392 0 0 0 2.807583213 0 9.736533809 1 9.637585865 1.763399166 25 5.851675684 0.765836338 0.415606126 2.254011687 10.99925328 11080.36421 1.09530958 0.526018825 57.99615017 -1.763399166 -5.085839345 SSRPAS(ph)PCNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSRPASPCNKR 11 2 O95644-6;O95644;K7ER53;O95644-8;O95644-11;O95644-3;O95644-10;O95644-2;O95644-5;O95644-4 O95644-6 NFATC1 "Nuclear factor of activated T-cells, cytoplasmic 1" 1 S(0.007)S(0.007)RPAS(0.987)PCNKR 47.774 0.090737 38404000 35580 31470 17310 24379 29702 28637 32659 43328 18757 TRUE FALSE 30878.01285 31263.2715 25681.1739 29914.62456 29110.98831 29738.68392 29491.73521 34062.64438 16539.56883 1.866917643 1.890210792 1.552711208 1.808670158 1.760081452 1.798032599 1.783101816 2.059463867 1 14.013634 1.227905409 24.99999966 0.999998283 1.8165976 0.806854724 0.125297353 207.8966865 487748.8092 0.4562791 0.032140905 16.90072788 -1.227905409 0.816599317 SSS(ph)ADFGTFNTSQSHQTASAVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSSADFGTFNTSQSHQTASAVSK 23 0 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 1 S(0.123)S(0.123)S(0.753)ADFGTFNTSQSHQTASAVSK;S(0.027)S(0.136)S(0.837)ADFGTFNTSQSHQTASAVSK;S(0.001)S(0.001)S(0.999)ADFGTFNTSQSHQTASAVSK 351.84 7.47E-102 967690000 577630 634640 254534 565940 929570 892830 1062680 1162880 1090260 TRUE FALSE 501294.732 630471.0081 377627.4938 694445.3269 911073.3757 927177.7478 959621.4572 914207.1615 961370.7048 0.521437495 0.655804265 0.392801124 0.722349166 0.94768165 0.964433119 0.998180465 0.950941356 1 19.87473332 3.387667115 3.058113949 0.973391986 0.536333912 0.905433136 0.066502304 0.06548206 1.230317 0.018695611 0.025409355 2441.558389 -3.387667115 -0.437058074 SSS(ph)APLIHGLSDLSQVFQPYTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSAPLIHGLSDLSQVFQPYTLR 23 0 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 S(0.089)S(0.089)S(0.822)APLIHGLSDLSQVFQPYTLR;S(0.137)S(0.137)S(0.726)APLIHGLSDLSQVFQPYTLR 329.48 1.10E-86 2501600000 476350 491410 212360 316630 427190 428250 442040 486900 404750 TRUE FALSE 413399.1406 488181.8954 315058.0063 388525.6809 418689.7548 444725.0546 399171.0288 382780.2241 356900.9161 1.158302268 1.367835927 0.88276043 1.088609369 1.17312603 1.246074287 1.118436549 1.072511184 1 18.44516408 SSS(ph)APNVHINTIEPVNIDDLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSAPNVHINTIEPVNIDDLIR 22 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 S(0.134)S(0.134)S(0.731)APNVHINTIEPVNIDDLIR;S(0.004)S(0.022)S(0.973)APNVHINTIEPVNIDDLIR 259.84 2.01E-37 2210000000 406460 356770 201364 273561 342980 358930 356320 372350 440590 TRUE FALSE 352745.2812 354426.3544 298744.3039 335677.2062 336155.369 372738.2694 321764.1412 292725.8501 388503.9521 0.907958025 0.912285068 0.768960785 0.864025203 0.865255983 0.959419505 0.828213303 0.753469427 1 18.56756975 SSS(ph)ASSPEMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SSSASSPEMK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.01)S(0.038)S(0.952)ASSPEMK;SSS(1)ASSPEMK;SSS(0.978)AS(0.021)SPEMK;SS(0.012)S(0.988)ASSPEMK;SSS(1)ASSPEMK 261.83 2.32E-17 1312550000 3459880 2489770 2012480 2422970 2537700 2631350 3734130 4201790 4065470 TRUE FALSE 3002648.092 2473414.537 2985722.059 2973142.371 2487204.735 2732579.737 3371994.647 3303269.907 3584854.768 0.837592674 0.689962271 0.832871135 0.829362014 0.693809065 0.762256748 0.940622387 0.921451529 1 21.77348324 2.23514761 23.0514136 0.946680273 0.771980252 0.698835488 0.055531541 17.82033088 120352.537 0.021498179 0.015186058 171.8492375 -2.23514761 -0.174700021 SSS(ph)EDAESLAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSEDAESLAPR 12 0 Q4G0J3;Q4G0J3-3;H0YA82 Q4G0J3 LARP7 La-related protein 7 1 S(0.113)S(0.02)S(0.867)EDAESLAPR;S(0.084)S(0.011)S(0.904)EDAESLAPR 268.95 3.73E-22 2831300000 1165890 852850 645520 796440 1112930 1130710 1046120 1240250 1372120 TRUE FALSE 1011814.683 847247.5722 957695.6311 977283.8748 1090784.87 1174209.145 944667.4434 975032.1891 1209909.537 0.836273004 0.700256958 0.791543171 0.807733012 0.901542502 0.970493338 0.780775269 0.805871976 1 20.20646775 3.448328425 3.343540846 0.876301124 0.770481722 0.339176439 0.07365573 0.31603507 7.367691723 0.022611735 0.031632747 2807.555983 -3.448328425 -0.105819402 SSS(ph)EITLSECDAEDAGEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSSEITLSECDAEDAGEPR 19 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 SS(0.004)S(0.996)EITLSECDAEDAGEPR;SS(0.002)S(0.998)EITLSECDAEDAGEPR;S(0.001)S(0.001)S(0.999)EITLSECDAEDAGEPR;S(0.004)S(0.093)S(0.903)EITLSECDAEDAGEPR 533.03 0 1062080000 728946 650620 361750 413395 603438 610667 572442 656209 628020 TRUE FALSE 632613.9392 646346.0344 536693.51 507262.6531 591430.7644 634159.7546 516926.6629 515883.812 553776.191 1.142363918 1.167161111 0.969152374 0.916006613 1.067996014 1.145155326 0.933457724 0.931574561 1 19.0789435 4.240570245 24.9973676 0.99101102 1.154762572 0.480055798 0.069140723 45.75476112 569095.0563 0.019040134 0.045482978 17400.84126 -4.240570245 0.163751552 SSS(ph)ENDVELLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSENDVELLTK 12 0 Q9C0D6 Q9C0D6 FHDC1 FH2 domain-containing protein 1 1 SS(0.003)S(0.997)ENDVELLTK 233.02 5.76E-16 90834000 324070 277450 198690 241890 280790 242180 311020 396770 368340 TRUE FALSE 281243.3284 275627.4127 294777.1486 296814.8216 275202.8284 251496.8213 280857.3283 311923.8232 324795.2648 0.865909571 0.848618938 0.907578344 0.913852059 0.847311701 0.774324162 0.86472113 0.960370599 1 18.30917107 1.653439381 3.46553745 0.991569942 0.859598409 0.639308635 0.037974256 0.128242157 3.583727019 0.032734008 0.011067705 45.02351329 -1.653439381 -0.131971533 SSS(ph)ESYTQSFQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSESYTQSFQSR 13 0 Q9BTU6;E9PAM4 Q9BTU6 PI4K2A Phosphatidylinositol 4-kinase type 2-alpha 1 S(0.001)S(0.014)S(0.985)ESYTQSFQSR 130.03 2.83E-05 0 173760 195980 167100 202440 274510 317390 249100 312730 323970 TRUE FALSE 150797.1757 194692.5945 247910.1189 248407.0961 269047.7881 329600.1987 224942.3203 245855.1232 285670.6357 0.527870761 0.681528201 0.867817997 0.869557683 0.941811144 1.153776964 0.787418419 0.860624413 1 18.12399322 4.46498982 1.380147698 0.930956869 0.457553735 0.680825129 0.096006937 0.490330964 1.218234176 0.029316068 0.283071705 29173.58631 -4.46498982 -0.473403133 SSS(ph)ETILSSLAGSDIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSETILSSLAGSDIVK 17 0 Q01850 Q01850 CDR2 Cerebellar degeneration-related protein 2 1 SS(0.023)S(0.976)ETILSSLAGSDIVK;S(0.008)S(0.013)S(0.978)ET(0.001)ILSSLAGSDIVK 405.77 2.87E-140 197969000 612150 515430 316870 425570 515330 375930 610250 685400 581260 TRUE FALSE 531252.8265 512044.1064 470109.3919 522202.1729 505075.9412 390392.2704 551068.0489 538832.5438 512544.105 1.036501681 0.999024477 0.917207685 1.018843389 0.985429227 0.761675467 1.075162203 1.051290101 1 18.96731663 FDPFGPIGTS(ph)PPGPNPDHLPPPGYDDMYL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 FDPFGPIGTSPPGPNPDHLPPPGYDDMYL 29 0 Q92530 Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 FDPFGPIGT(0.206)S(0.794)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.238)S(0.762)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.231)S(0.769)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.153)S(0.847)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.053)S(0.947)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.15)S(0.85)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.161)S(0.839)PPGPNPDHLPPPGYDDMYL 244.72 4.33E-45 2051331000 286206 414245 330674 421135 607480 649748 617911 693187 646125 TRUE FALSE 248383.1519 411523.7973 490589.0524 516760.1384 595392.3365 674744.226 557986.0863 544954.3544 569740.8386 0.435958132 0.722299982 0.861074052 0.907009123 1.045023099 1.184300265 0.979368247 0.95649516 1 19.1199463 4.791578929 0.899918045 1.023006065 0.070534856 0.888738448 0.067615344 0.819061545 0.492444869 0.026148684 0.787119993 61884.07859 -4.791578929 -0.952471209 down SSS(ph)FSLPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SSSFSLPSR 9 0 Q14153-2;Q14153 Q14153-2 FAM53B Protein FAM53B 1 S(0.001)S(0.01)S(0.99)FSLPSR;S(0.001)S(0.059)S(0.939)FSLPSR;SS(0.013)S(0.987)FSLPSR;SS(0.01)S(0.99)FSLPSR;S(0.002)S(0.047)S(0.951)FSLPSR 235.01 3.62E-10 1982420000 2498810 2811550 1594792 2098520 3057020 3026920 2838130 3319910 2988910 TRUE FALSE 2168585.927 2793080.743 2366038.745 2575021.04 2996191.283 3143367.571 2562888.589 2609973.082 2635564.465 0.8228165 1.059765671 0.897735106 0.977028289 1.136830961 1.192673377 0.97242493 0.99028998 1 21.32968055 3.464985893 24.30409927 1.050797878 0.939623397 0.318739012 0.088032156 227.1180652 454858.2256 0.026377602 0.034080717 2917.332252 -3.464985893 -0.11117448 SSS(ph)FTLLQSLAIEDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSSFTLLQSLAIEDSR 16 0 F8VWT9;J3KPF0;Q9Y4D8-4;Q9Y4D8;Q9Y4D8-2 F8VWT9 HECTD4 Probable E3 ubiquitin-protein ligase HECTD4 1 S(0.001)S(0.035)S(0.963)FT(0.001)LLQSLAIEDSR;S(0.015)S(0.152)S(0.833)FT(0.001)LLQSLAIEDSR;S(0.066)S(0.066)S(0.868)FTLLQSLAIEDSR 199.96 3.86E-11 132494000 186239 114156 88574 99547 138735 142871 154460 163486 164827 TRUE FALSE 161627.0443 113406.1017 131408.6827 122150.6678 135974.4449 148367.3398 139480.493 128525.7911 145341.3398 1.112051426 0.780274228 0.904138374 0.840439946 0.935552439 1.020819954 0.959675294 0.884303057 1 17.14908559 3.010982357 24.58728887 0.955613221 0.898194797 0.069604415 0.090881248 466.6106116 1044637.818 0.026186422 0.029664157 1025.610261 -3.010982357 -0.057418424 SSS(ph)FVLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSSFVLPK 8 0 Q8WYP3-2;Q8WYP3 Q8WYP3-2 RIN2 Ras and Rab interactor 2 1 S(0.014)S(0.076)S(0.91)FVLPK;S(0.004)S(0.097)S(0.899)FVLPK;S(0.011)S(0.015)S(0.974)FVLPK 96.331 0.0094581 232380000 1162180 1142310 795820 971920 1275580 999280 1499040 1572490 1481660 TRUE FALSE 1008594.968 1134806.09 1180681.214 1192609.291 1250198.454 1037722.948 1353663.332 1236225.251 1306499.843 0.771982464 0.868584942 0.903697938 0.912827734 0.9569067 0.794277132 1.036099116 0.946211557 1 20.31727552 7.63404193 0.236465544 0.998674606 3.66E-21 0.464410967 0.060602911 70.22045694 1.291983614 0.23576536 25.65883194 43056817.87 -7.63404193 -0.998674606 SSS(ph)ISGVDMAGLQTSFLSQDESHDHSFGPMPISANGSNLYDAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSISGVDMAGLQTSFLSQDESHDHSFGPMPISANGSNLYDAVR 44 0 A0A2R8Y7M0;P82094;P82094-2 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 S(0.134)S(0.134)S(0.732)ISGVDMAGLQTSFLSQDESHDHSFGPMPISANGSNLYDAVR 397.05 7.75E-195 507280000 5454.2 7249 2393 5055.3 8771.9 8497 7961.7 6208.7 8265.5 TRUE FALSE 4733.413651 7201.380842 3550.262804 6203.18313 8597.356352 8823.885088 7189.575559 4881.017821 7288.362006 0.649448209 0.988065746 0.48711395 0.851107989 1.179600621 1.210681506 0.986446002 0.669700245 1 12.8313789 3.476896317 24.99999577 0.978845237 0.725014272 0.340834307 0.189041316 11.13615419 1237560.313 0.059123689 0.077101108 2998.446586 -3.476896317 -0.253830964 SSS(ph)KDSRPSQAAGDNQGDEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSKDSRPSQAAGDNQGDEAK 21 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.302)S(0.302)S(0.392)KDS(0.003)RPSQAAGDNQGDEAK 198.67 4.40E-22 198590000 236560 193640 211670 182000 199040 126210 292750 341270 267560 TRUE FALSE 205297.9966 192367.9661 314034.32 223325.8817 195079.4934 131065.3804 264359.1501 268292.0663 235929.3616 0.87016722 0.815362551 1.331052303 0.946579435 0.826855513 0.555528059 1.120501273 1.137171162 1 17.84799545 SSS(ph)KESLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SSSKESLVR 9 1 Q13439-5;Q13439-3;Q13439-4;Q13439;E7EVX2;Q86W71 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 S(0.042)S(0.297)S(0.625)KES(0.036)LVR;S(0.006)S(0.06)S(0.934)KESLVR;S(0.002)S(0.091)S(0.907)KESLVR;S(0.044)S(0.087)S(0.869)KESLVR;S(0.003)S(0.005)S(0.992)KESLVR;S(0.047)S(0.314)S(0.62)KES(0.019)LVR 161.99 3.88E-05 7012630000 6052130 4747630 3528890 3668360 4936580 3670420 5957900 6850130 5329680 TRUE FALSE 5252325.686 4716442.506 5235473.007 4501317.205 4838351.716 3811623.432 5380103.775 5385283.007 4699611.302 1.117608532 1.003581403 1.114022559 0.957806277 1.029521679 0.811050784 1.144797608 1.145899663 1 22.16411001 SSS(ph)LDALGPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSSLDALGPTR 11 0 Q9H425;Q9H425-3;Q9H425-2;E5RI90 Q9H425 C1orf198 Uncharacterized protein C1orf198 1 SSS(1)LDALGPTR;SS(0.009)S(0.991)LDALGPTR;SS(0.001)S(0.999)LDALGPTR;SSS(1)LDALGPTR 283.19 1.69E-27 1804040000 2302810 1578680 924790 1136270 1575860 1457430 1614360 1684300 1691770 TRUE FALSE 1998487.824 1568309.547 1372021.537 1394277.47 1544503.469 1513498.275 1457799.616 1324125.552 1491770.878 1.339674781 1.051307255 0.91972672 0.934645857 1.035348988 1.014564835 0.97722756 0.887619923 1 20.50859454 4.706334106 2.860694481 0.96378074 1.392143898 0.8699795 0.045050877 0.131593643 1.588797822 0.01232817 0.126145792 50855.05239 -4.706334106 0.428363158 SSS(ph)LDGEHHDGYHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSLDGEHHDGYHR 14 0 Q9C0J8 Q9C0J8 WDR33 pre-mRNA 3 end processing protein WDR33 1 S(0.132)S(0.132)S(0.735)LDGEHHDGYHR 151.38 4.48E-06 182300000 132090 104410 63836 92265 99837 106740 102910 130610 146770 TRUE FALSE 114633.9718 103724.1238 94707.30312 113215.1784 97850.43903 110846.3569 92929.80404 102680.0679 129419.0178 0.88575832 0.801459674 0.731788146 0.874795531 0.756074653 0.856492027 0.718053696 0.793392421 1 16.98169011 1.237738043 24.96332794 1.000000239 0.798163195 0.539402089 0.05732551 14.59862871 442756.3397 0.076073714 0.013004676 17.28773287 -1.237738043 -0.201837044 SSS(ph)LDMNR ddPTM_MDA-MB-175_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(0.032)S(0.967)LDMNR;S(0.005)S(0.202)S(0.793)LDMNR;S(0.001)S(0.001)S(0.998)LDMNR;SSS(1)LDMNR;S(0.002)S(0.005)S(0.993)LDMNR;S(0.002)S(0.007)S(0.992)LDMNR 160.53 0.00048977 3185210000 4985800 5088460 3327040 4205390 5785890 6269210 5744240 6260980 5842070 TRUE FALSE 4326913.898 5055033.571 4936007.672 5160288.075 5670762.109 6510390.565 5187164.489 4922118.15 5151427.14 0.839944695 0.981287988 0.958182565 1.001720093 1.100813805 1.26380329 1.006937369 0.955486318 1 22.29654074 4.748875828 0.988937489 1.050416628 0.743196366 0.375908147 0.086621477 2.608064477 2.02521673 0.03199652 0.861408638 56088.75854 -4.748875828 -0.307220262 SSS(ph)LESLQTAVAEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSSLESLQTAVAEVR 15 0 R4GN62;A0A087WZG6;A0A087X1S9;Q8TEW8-5;Q8TEW8-2;Q8TEW8 R4GN62 PARD3B Partitioning defective 3 homolog B 1 SS(0.005)S(0.995)LESLQTAVAEVR;SSS(1)LESLQTAVAEVR;SS(0.007)S(0.993)LESLQTAVAEVR;SSS(1)LESLQTAVAEVR 319.53 1.74E-56 376258000 893960 770320 512205 642066 813990 810340 745659 889580 1035330 TRUE FALSE 775820.921 765259.7172 759909.0512 787856.8987 797793.1915 841514.3042 673345.1049 699350.2397 912934.4669 0.84981009 0.838241676 0.832380723 0.862993925 0.873877831 0.921768577 0.73756127 0.766046485 1 19.80015178 1.224025884 24.95120205 1.000000446 0.832272381 0.496313553 0.052050921 743.2867808 1275895.15 0.307586291 0.0141816 16.75042705 -1.224025884 -0.167728064 SSS(ph)LESLQTAVAEVTLNGDIPFHRPR ddPTM_MDA-MB-175_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(0.167)S(0.167)S(0.658)LES(0.003)LQT(0.003)AVAEVT(0.001)LNGDIPFHRPR 46.783 0.08835 40946000 11888 7571.4 6820.2 9740.3 8841.2 10204 11759 12412 12561 TRUE FALSE 10316.97068 7521.662975 10118.47153 11951.98399 8665.277418 10596.55448 10618.61399 9757.79039 11076.05289 0.931466361 0.679092367 0.913544891 1.079083326 0.782343449 0.956708548 0.958700188 0.880980841 1 13.43515623 4.027706227 24.72212843 0.936370462 0.803038999 0.251313908 0.096595732 236.4937365 211018.6264 0.022745621 0.047347364 10658.74879 -4.027706227 -0.133331463 SSS(ph)LESQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSSLESQGK 9 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 SS(0.001)S(0.999)LESQGK;SSS(1)LESQGK;SS(0.001)S(0.998)LESQGK;SSS(1)LESQGK 219.89 3.40E-05 952740000 3807820 2942110 2205430 2710330 2463670 2718940 3757990 4543780 4323980 TRUE FALSE 3304606.939 2922783.086 3271983.325 3325751.851 2414647.787 2823539.381 3393540.708 3572128.007 3812804.01 0.866713036 0.766570502 0.858156705 0.8722588 0.63329974 0.740541442 0.890038066 0.936876901 1 21.86242094 1.89234132 2.409873867 0.973766758 0.789475398 0.507189938 0.073096713 0.251084839 2.654374337 0.055788692 0.021807355 78.04432343 -1.89234132 -0.18429136 SSS(ph)LGNLKK ddPTM_MDA-MB-175_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(0.025)S(0.04)S(0.935)LGNLKK;S(0.008)S(0.016)S(0.976)LGNLKK;SS(0.012)S(0.987)LGNLKK 127.87 0.00059388 453080000 2662380 2351720 1514870 1911000 2391430 1713360 2775490 3405220 2047420 TRUE FALSE 2310539.737 2336271.396 2247466.199 2344921.758 2343845.222 1779274.068 2506323.407 2677040.202 1805376.34 1.279810578 1.294063373 1.244874074 1.298854818 1.298258524 0.985541922 1.388255374 1.482815601 1 20.78386818 SSS(ph)LIQLTSQNSSPNQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSLIQLTSQNSSPNQQR 18 0 O95639;H7C419 O95639 CPSF4 Cleavage and polyadenylation specificity factor subunit 4 1 S(0.059)S(0.059)S(0.881)LIQLTSQNSSPNQQR 195.57 2.15E-15 132380000 313440 150900 82548 105440 159080 131820 182620 185090 164090 TRUE FALSE 272018.1098 149908.728 122468.4889 129381.7635 155914.6192 136891.2007 164909.5405 145509.9439 144691.4671 1.879987225 1.036057834 0.846411273 0.894190695 1.077566095 0.946090349 1.139732313 1.005656704 1 17.14262032 4.736753841 5.32915622 0.992082419 1.914940994 0.918291945 0.083239162 0.04023635 4.143127317 0.021074224 0.136175254 54544.86123 -4.736753841 0.922858575 SSS(ph)LKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SSSLKER 7 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 SS(0.025)S(0.974)LKER;SS(0.017)S(0.982)LKER;S(0.003)S(0.002)S(0.995)LKER;SSS(1)LKER;S(0.013)S(0.015)S(0.972)LKER 109.44 0.018488 2261920000 5893300 4535860 2134760 3887230 2389580 2241810 5300600 5365720 4152870 TRUE FALSE 5114485.473 4506063.637 3167137.076 4769884.984 2342032.033 2328053.881 4786548.628 4218302.534 3661922.44 1.396666794 1.23051859 0.864883713 1.302563083 0.639563528 0.635746365 1.307113601 1.151936614 1 21.8041698 4.436326082 4.919734703 1.004911786 1.363329173 0.263541226 0.234006429 0.255082259 14.19341026 0.061517213 0.184868284 27310.27556 -4.436326082 0.358417387 SSS(ph)LPAYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSLPAYGR 9 0 Q08495;Q08495-2;Q08495-3;Q08495-4 Q08495 DMTN Dematin 1 S(0.01)S(0.088)S(0.902)LPAYGR;SS(0.129)S(0.87)LPAYGR 133.99 0.00027417 374060000 430160 445370 285690 309260 492810 448310 394970 460110 439050 TRUE FALSE 373313.2661 442444.3351 423850.6396 379482.2097 483004.0452 465556.7758 356665.8702 361719.0571 387146.0092 0.964269958 1.142835841 1.094808237 0.980204369 1.247601767 1.202535387 0.921269655 0.934322061 1 18.56251824 2.222445726 24.99797631 0.946934546 1.107373501 0.400452757 0.088455617 234.7467104 364144.344 0.036419242 0.024639525 166.8959223 -2.222445726 0.160438955 SSS(ph)LSDLTHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSLSDLTHR 10 0 Q5T9C2-3;Q5T9C2;Q5T9C2-2 Q5T9C2-3 FAM102A Protein FAM102A 1 SS(0.01)S(0.966)LS(0.023)DLTHR;S(0.29)S(0.29)S(0.421)LSDLTHR 136.81 0.00058081 244640000 370950 419940 261921 327460 450920 513870 503530 458740 598420 TRUE FALSE 321928.0176 417181.3865 388586.8717 401814.7979 441947.5742 533638.9114 454697.7381 360642.0209 527675.4693 0.610087139 0.790602199 0.736412614 0.761480913 0.837536706 1.011301344 0.861699595 0.68345421 1 19.00929139 3.321415738 2.955896158 0.860818885 0.723047759 0.367682133 0.100645552 0.362739925 6.394597007 0.0327166 0.042957848 2096.11805 -3.321415738 -0.137771127 SSS(ph)MAAGLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSSMAAGLER 10 0 Q9UQB8;Q9UQB8-2;Q9UQB8-4;Q9UQB8-5;Q9UQB8-3;I3L4C2;Q9UQB8-6;B4DWA1;I3L3C6;I3L0Y9 Q9UQB8 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 1 S(0.092)S(0.049)S(0.859)MAAGLER;S(0.002)S(0.08)S(0.918)MAAGLER;SS(0.016)S(0.984)MAAGLER;SS(0.017)S(0.983)MAAGLER 208.17 1.24E-07 1778610000 2486520 2597990 1387110 1582400 2268080 2378860 1764920 2102310 2464670 TRUE FALSE 2157920.082 2580923.633 2057921.036 1941708.105 2222949.645 2470376.284 1593758.33 1652747.367 2173299.52 0.992923461 1.187560025 0.946910914 0.893437875 1.022845505 1.136693889 0.733335794 0.760478411 1 21.05145559 2.23355533 24.99999564 0.812442202 1.026903154 0.420473586 0.109231423 112.3301171 561049.3737 0.044414009 0.031000298 171.2203301 -2.23355533 0.214460952 SSS(ph)MADGDNSYCLEAIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SSSMADGDNSYCLEAIIR 18 0 Q9ULV0;A0A0A0MR36;Q9ULV0-2;Q9ULV0-3 Q9ULV0 MYO5B Unconventional myosin-Vb 1 S(0.11)S(0.11)S(0.779)MADGDNSYCLEAIIR;S(0.124)S(0.124)S(0.752)MADGDNSYCLEAIIR;S(0.207)S(0.207)S(0.587)MADGDNSYCLEAIIR;S(0.115)S(0.115)S(0.77)MADGDNSYCLEAIIR;SS(0.007)S(0.993)MADGDNSYCLEAIIR;SS(0.004)S(0.996)MADGDNSYCLEAIIR 282.47 2.30E-39 621627000 761860 652907 511805 596399 827020 879040 850630 941200 983790 TRUE FALSE 661178.2707 648618.0109 759315.6099 731820.5083 810563.92 912857.2376 768136.0335 739931.7044 867487.4669 0.762176165 0.74769727 0.875304415 0.843609316 0.93438113 1.052300203 0.885472197 0.852959533 1 19.72648339 3.980569104 1.270325197 0.930957647 0.741193428 0.579756517 0.061275479 0.43856362 1.266157101 0.021179763 0.076732958 9562.448385 -3.980569104 -0.189764219 SSS(ph)MELHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSMELHR 8 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.185)S(0.185)S(0.63)MELHR 84.817 0.011068 236450000 109240 148960 90360 112420 133980 112080 118770 139330 202240 TRUE FALSE 94803.65722 147981.472 134058.3982 137946.6792 131314.0601 116391.7901 107251.7037 109535.3638 178331.4176 0.531615004 0.829811561 0.751737411 0.77354109 0.736348434 0.652671255 0.601417883 0.614223591 1 17.44420137 1.23006845 24.99807991 1.000000583 0.688802206 0.546490288 0.089750941 271.9653636 800511.682 0.258495392 0.022807858 16.98511336 -1.23006845 -0.311198377 SSS(ph)MSSLTGAYASGIPSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSMSSLTGAYASGIPSSSR 20 0 Q96HA1-2;Q96HA1-3;Q96HA1 Q96HA1-2 POM121 Nuclear envelope pore membrane protein POM 121 1 S(0.047)S(0.047)S(0.906)MSSLTGAYASGIPSSSR;S(0.001)S(0.039)S(0.96)MS(0.001)SLTGAYASGIPSSSR 266.29 1.05E-36 288460000 169062 197882 149152 221778 348860 319090 261599 402340 356550 TRUE FALSE 146720.0284 196582.1001 221282.4061 272136.0846 341918.3685 331365.5988 236229.1692 316302.722 314399.0652 0.466668144 0.625262992 0.70382654 0.865575362 1.087529851 1.053964962 0.751367276 1.006054906 1 18.2622374 3.979447736 1.492209815 0.969880018 0.503282728 0.780464504 0.095356526 0.212231995 0.881935549 0.030198417 0.096026908 9537.789571 -3.979447736 -0.46659729 SSS(ph)MSSLTGAYTSGIPSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSMSSLTGAYTSGIPSSSR 20 0 A8CG34-2;A8CG34 A8CG34-2 POM121C Nuclear envelope pore membrane protein POM 121C 1 SSS(0.781)MS(0.216)S(0.003)LTGAYTSGIPSSSR 327.27 1.04E-79 123980000 89782 107680 64333 131660 174760 142590 126470 204160 161080 TRUE FALSE 77917.08122 106972.643 95444.65398 161555.4153 171282.6179 148075.5296 114204.9589 160501.9728 142037.3059 0.548567721 0.753130611 0.671968912 1.137415373 1.205898808 1.042511533 0.804049036 1.129998712 1 17.11591038 3.747055986 24.49801668 1.051629211 0.667413181 0.71778871 0.116827172 267.9610326 772713.7716 0.031891877 0.054073415 5585.421936 -3.747055986 -0.38421603 SSS(ph)MSYVDGFIGTWPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSMSYVDGFIGTWPK 16 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 S(0.298)S(0.298)S(0.404)MSYVDGFIGTWPK;S(0.231)S(0.231)S(0.537)MSYVDGFIGTWPK 294 1.36E-45 201180000 926470 807150 473460 636670 729800 592420 948390 1024790 948850 TRUE FALSE 804034.6421 801847.7785 702426.8396 781235.6544 715278.4078 615210.7807 856415.2838 805646.6334 836678.0339 0.960984524 0.958370778 0.839542585 0.933735108 0.854902817 0.7353017 1.023590018 0.962911181 1 19.67431303 S(ph)QGGEEEGPLSDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQGGEEEGPLSDK 13 0 E9PR76;E9PSH4;Q9H063 E9PR76 MAF1 Repressor of RNA polymerase III transcription MAF1 homolog 1 S(1)QGGEEEGPLSDK;S(1)QGGEEEGPLSDK 252.25 7.08E-17 749060000 403500 387870 489310 546330 661290 664160 885670 882580 1109720 TRUE FALSE 350176.4527 385322.0564 725941.9526 670382.5766 648131.6228 689710.665 799777.8597 693847.1352 978530.1658 0.35785964 0.39377637 0.741869774 0.685091375 0.662352215 0.704843539 0.817325707 0.709070767 1 19.9002568 4.79406544 0.56143389 0.805541246 1.47E-31 0.718612324 0.098818517 2.445840404 0.586694906 0.060605124 1.314599905 62239.40605 -4.79406544 -0.805541246 down SSS(ph)PAELDLKDDLQQTQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSSPAELDLKDDLQQTQGK 19 1 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 S(0.022)S(0.1)S(0.878)PAELDLKDDLQQTQGK;S(0.013)S(0.013)S(0.975)PAELDLKDDLQQTQGK;S(0.019)S(0.131)S(0.85)PAELDLKDDLQQTQGK;S(0.13)S(0.13)S(0.74)PAELDLKDDLQQTQGK 251.02 7.90E-26 2963980000 3080190 2651430 2579580 2494140 2906410 2004400 3948230 4737290 4903910 TRUE FALSE 2673135.087 2634012.582 3827073.516 3060472.608 2848578.127 2081510.565 3565331.262 3724257.399 4324175.346 0.618183786 0.609136395 0.885041241 0.707758674 0.658756387 0.481365902 0.82451126 0.861264195 1 22.0439936 1.748546112 2.149268953 0.966784469 0.671719428 0.519880042 0.10758258 0.254817367 2.326075981 0.106471403 0.031479785 56.04619226 -1.748546112 -0.295065041 SSS(ph)PAGETEGDREPQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SSSPAGETEGDREPQAR 17 1 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 SS(0.019)S(0.981)PAGETEGDREPQAR;S(0.244)S(0.244)S(0.495)PAGET(0.016)EGDREPQAR;S(0.001)S(0.055)S(0.944)PAGETEGDREPQAR;S(0.002)S(0.081)S(0.917)PAGETEGDREPQAR;S(0.014)S(0.088)S(0.898)PAGETEGDREPQAR;S(0.021)S(0.108)S(0.871)PAGETEGDREPQAR 278.46 4.77E-36 3537790000 1298684 1105194 928042 1137140 1194194 1193548 1093108 1259722 2345490 TRUE FALSE 1127059.619 1097933.908 1376846.215 1395345.017 1170431.876 1239464.564 987098.5544 990340.2535 2068208.844 0.544944783 0.530862205 0.665719141 0.6746635 0.56591571 0.599293716 0.477272185 0.47883958 1 20.97995044 1.231576695 24.99930379 1.000000749 0.565098568 0.806150813 0.066692824 119.1683339 426530.6818 0.180407471 0.018525834 17.04420289 -1.231576695 -0.43490218 SSS(ph)PAGETEGDREPQARPGEGTAPLPPPGQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSSPAGETEGDREPQARPGEGTAPLPPPGQK 31 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 S(0.005)S(0.005)S(0.99)PAGETEGDREPQARPGEGTAPLPPPGQK;S(0.027)S(0.147)S(0.825)PAGET(0.001)EGDREPQARPGEGTAPLPPPGQK;S(0.003)S(0.15)S(0.844)PAGET(0.002)EGDREPQARPGEGTAPLPPPGQK 298 1.02E-81 1771410000 1655822 1165934 732358 854891 1269952 1057306 1500685 1615340 723789 TRUE FALSE 1437000.927 1158274.903 1086528.778 1049007.068 1244682.44 1097981.246 1355148.8 1269912.112 638223.489 2.251563837 1.814842172 1.70242681 1.643635946 1.950229757 1.7203711 2.123313891 1.98976085 1 19.28370218 1.23479696 24.98268559 0.999998713 1.8934235 0.686298573 0.191083983 65.92378153 437527.9794 0.345196023 0.047400401 17.17105425 -1.23479696 0.893424786 SSS(ph)PAPADIAQTVQEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 SSSPAPADIAQTVQEDLR 18 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 1 SSS(0.999)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;S(0.192)S(0.192)S(0.615)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;SS(0.001)S(0.999)PAPADIAQTVQEDLR;S(0.188)S(0.188)S(0.623)PAPADIAQTVQEDLR;SS(0.001)S(0.998)PAPADIAQTVQEDLR;SS(0.001)S(0.999)PAPADIAQTVQEDLR;S(0.142)S(0.142)S(0.716)PAPADIAQTVQEDLR 444.45 1.14E-190 1.71421E+11 16996888 15197596 9664899.9 11599104 15949439 16099433 15477310 17883923 15621084 TRUE FALSE 14750706.19 15097761.99 14338877.82 14232857.84 15632076.37 16718788.61 13976322.86 14059585.24 13774377.25 1.070880079 1.096075831 1.040981931 1.033285033 1.134866288 1.213760035 1.014660961 1.020705691 1 23.71548376 2.073400459 24.99999678 1.013568777 1.095966019 0.3915011 0.050777499 45.10718415 15362.09219 0.022118797 0.014912486 118.413293 -2.073400459 0.082397242 SSS(ph)PAPPSQQSLYK ddPTM_MDA-MB-175_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 SS(0.004)S(0.996)PAPPSQQSLYK 267.88 4.76E-25 151980000 475210 366260 249530 306980 413020 361140 399310 476300 477410 TRUE FALSE 412409.7945 363854.0139 370203.5426 376684.5009 404801.7101 375033.2895 360584.9777 374446.9516 420971.1337 0.979662883 0.864320579 0.879403629 0.894798885 0.961590184 0.890876498 0.856555115 0.889483676 1 18.68336178 1.235345223 24.80346825 1.000000155 0.898753818 0.375933643 0.0394393 87.16909936 672291.9023 0.065532892 0.009415137 17.19274503 -1.235345223 -0.101246337 SSS(ph)PATEQSWMENDFDELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSPATEQSWMENDFDELR 19 0 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.238)S(0.238)S(0.523)PATEQSWMENDFDELR;S(0.094)S(0.094)S(0.812)PATEQSWMENDFDELR 439.59 6.67E-191 612010000 386050 365300 310007 401730 423720 412670 361620 448980 903170 TRUE FALSE 335032.5144 362900.3202 459927.4221 492948.9366 415288.801 428545.6819 326550.1481 352969.121 796398.2715 0.420684633 0.455676931 0.577509317 0.618972886 0.521458692 0.538104736 0.410033723 0.443206789 1 19.60313056 1.234722678 24.99987651 1.000000718 0.498391434 0.843190314 0.068006638 47.19576837 307382.483 0.135139134 0.018448478 17.16811753 -1.234722678 -0.501609284 SSS(ph)PATEQSWMENDFDELREEGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SSSPATEQSWMENDFDELREEGFR 24 1 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.047)S(0.047)S(0.905)PATEQSWMENDFDELREEGFR;SSS(1)PATEQSWMENDFDELREEGFR;SSS(1)PATEQSWMENDFDELREEGFR;SS(0.013)S(0.986)PATEQSWMENDFDELREEGFR;S(0.005)S(0.05)S(0.937)PAT(0.009)EQSWMENDFDELREEGFR;S(0.003)S(0.003)S(0.993)PATEQSWMENDFDELREEGFR;S(0.004)S(0.004)S(0.992)PATEQSWMENDFDELREEGFR 346.35 5.26E-102 2585081000 77446.7 80559.2 53339.9 68484.1 61228.4 79250 82792.1 92211.1 92265.9 TRUE FALSE 67211.92237 80030.00131 79135.25405 84034.46162 60010.07463 82298.79878 74762.93489 72492.47385 81358.33041 0.826122193 0.983673103 0.972675492 1.032893143 0.737602091 1.011559583 0.918933986 0.891027059 1 16.31200245 1.221539272 24.03854176 1.000000367 0.924275158 0.070596982 0.088758068 1915.994254 2705635.186 0.536876823 0.020363178 16.65479426 -1.221539272 -0.075725209 SSS(ph)PATEQSWMENDFDELREEGFRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSSPATEQSWMENDFDELREEGFRR 25 2 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.117)S(0.117)S(0.767)PATEQSWMENDFDELREEGFRR;S(0.303)S(0.303)S(0.394)PATEQSWMENDFDELREEGFRR;S(0.307)S(0.307)S(0.385)PATEQSWMENDFDELREEGFRR 278.17 2.00E-53 1568340000 124769 112597 60713 63891 122350 132641 124725 147270 47342.8 TRUE FALSE 108280.4605 111857.3429 90074.00987 78398.42806 119915.4744 137743.7851 112629.1887 115777.4566 41745.98812 2.59379321 2.679475273 2.157668651 1.877987122 2.872502959 3.299569403 2.697964374 2.773379234 1 15.34934994 3.205451973 24.99827052 2.610510376 2.340277974 0.015333194 0.632257459 747.7520911 564578.6852 0.193805757 0.219768899 1604.914768 -3.205451973 -0.270232402 SSS(ph)PELVTHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSSPELVTHLK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.229)S(0.284)S(0.488)PELVTHLK;S(0.007)S(0.244)S(0.749)PELVTHLK;S(0.049)S(0.371)S(0.58)PELVTHLK 220.37 5.92E-12 20191000000 13670900 13300200 9471700 12159200 15205100 13157200 16198200 20053500 18428800 TRUE FALSE 11864255.93 13212830.11 14052245.8 14920132.2 14902548.26 13663366 14627301.06 15765215.08 16250168.26 0.730100497 0.813088819 0.864744634 0.918152475 0.917070397 0.840813817 0.900132283 0.970157037 1 23.95395132 6.801833257 0.298076346 0.970658859 3.05E-29 0.755595177 0.038417266 22.36206462 0.685419833 0.092847653 9.819090972 6336263.895 -6.801833257 -0.970658859 SSS(ph)PGKPQAVSSLNSSHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSPGKPQAVSSLNSSHSR 19 1 Q9UHB7;Q9UHB7-2;Q9UHB7-3 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 S(0.384)S(0.096)S(0.52)PGKPQAVSSLNSSHSR 149.9 4.90E-08 585150000 125210 118290 32387 69573 145290 101010 126010 152180 120240 TRUE FALSE 108663.1813 117512.9452 48049.46153 85370.61301 142399.0133 104895.9201 113789.5696 119637.4913 106025.3642 1.024879114 1.10834748 0.453188366 0.805190472 1.343065542 0.989347416 1.073229698 1.128385573 1 16.69404991 3.276217155 24.99990432 1.101112275 0.838310605 0.303938711 0.194342686 212.7916956 141269.4848 0.056679106 0.073170815 1888.935616 -3.276217155 -0.26280167 SSS(ph)PIPLTPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSSPIPLTPSK 11 0 Q8N5Y2;Q8N5Y2-3;Q8N5Y2-2;A0A3B3IT59;Q8N5Y2-6;Q8N5Y2-4;A0A3B3ITL5;A0A3B3ITF3;A0A3F2YNX2;A0A3B3IRN2 Q8N5Y2 MSL3 Male-specific lethal 3 homolog 1 S(0.021)S(0.021)S(0.959)PIPLTPSK;S(0.029)S(0.029)S(0.942)PIPLTPSK;SS(0.012)S(0.988)PIPLTPSK;SS(0.006)S(0.994)PIPLTPSK 171.92 1.46E-05 1811410000 6298270 5361210 3341210 4614880 5818580 4835300 5849720 7196000 6337800 TRUE FALSE 5465937.662 5325991.859 4957030.332 5662759.038 5702801.642 5021317.12 5282415.055 5657191.399 5588552.504 0.978059642 0.95301813 0.886997184 1.01327831 1.020443422 0.898500482 0.945220619 1.012282053 1 22.41404323 1.72122077 7.505205402 1.005430491 0.956128243 0.190401659 0.042436634 0.195538129 29.55723199 0.025055691 0.011179907 52.62847307 -1.72122077 -0.049302247 SSS(ph)PPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SSSPPPR 7 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.001)S(0.013)S(0.987)PPPR;S(0.005)S(0.222)S(0.773)PPPR;SS(0.006)S(0.994)PPPR;S(0.003)S(0.076)S(0.921)PPPR;S(0.002)S(0.022)S(0.976)PPPR;S(0.005)S(0.014)S(0.981)PPPR 118.89 0.0051439 2125615000 2001412 1752226 1010101 1276764 1194822 1907164 1839488 2006326 1859774 TRUE FALSE 1736920.333 1740715.512 1498589.222 1566672.78 1171047.38 1980533.833 1661094.737 1577288.798 1639913.636 1.05915354 1.061467795 0.913822039 0.95533859 0.714090885 1.20770618 1.012915985 0.961812112 1 20.64518841 4.261833957 24.20957657 0.967789194 1.060310853 0.09642609 0.119304855 412.0160982 428579.4392 0.029274865 0.077331581 18274.01417 -4.261833957 0.092521659 SSS(ph)PPPRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSSPPPRK 8 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.3)S(0.3)S(0.4)PPPRK;S(0.308)S(0.308)S(0.384)PPPRK;S(0.3)S(0.3)S(0.401)PPPRK 78.934 0.017971 4828900000 2684840 2071450 1143110 1466690 1230910 1627340 2286570 2582680 2107150 TRUE FALSE 2330031.591 2057842.509 1695921.819 1799724.381 1206417.299 1689944.823 2064818.793 2030393.98 1858045.127 1.254023143 1.107530963 0.912745226 0.968611771 0.649293863 0.909528406 1.111285599 1.092758163 1 20.82535411 4.492954499 3.074739578 0.959498926 1.247020424 0.389209335 0.126784259 0.329735195 5.878684484 0.036737531 0.171560106 31113.90338 -4.492954499 0.287521498 SSS(ph)PQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSPQPK 7 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.001)S(0.083)S(0.915)PQPK;S(0.001)S(0.113)S(0.885)PQPK 80.438 0.041465 0 1177550 965280 638670 826210 2302340 1018650 1149720 1438280 1236340 TRUE FALSE 1021933.784 958939.0121 947532.9482 1013813.608 2256527.938 1057838.125 1038220.331 1130715.015 1090181.294 0.937398018 0.87961426 0.869151722 0.929949554 2.069864849 0.970332302 0.95233732 1.037180716 1 20.05613664 3.442690492 24.999993 1.185488364 0.894764292 0.176134075 0.323501256 349.0393129 253434.523 0.09623414 0.124238183 2771.344351 -3.442690492 -0.290724072 SSS(ph)PTLTPSQEGSPVFAGFEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSPTLTPSQEGSPVFAGFEGR 22 0 P0C860 P0C860 MSL3P1 Putative male-specific lethal-3 protein-like 2 1 S(0.13)S(0.13)S(0.656)PT(0.083)LTPSQEGSPVFAGFEGR 103.41 0.00061303 71513000 43450 48780 27245 37370 50923 51649 47452 53926 49028 TRUE FALSE 37707.97241 48459.56097 40420.77313 45855.42966 49909.73193 53635.97045 42850.11234 42394.34455 43231.96569 0.872224332 1.120919676 0.934974214 1.06068343 1.154463627 1.240655371 0.991167338 0.980624958 1 15.39981081 4.751995032 24.07965737 1.05561112 0.872224129 0.292462112 0.09172781 2020.122789 3620733.117 0.023971637 0.436336982 56493.05122 -4.751995032 -0.183386991 SSS(ph)PTQYGLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSSPTQYGLTK 11 0 Q9NYL2 Q9NYL2 ZAK Mitogen-activated protein kinase kinase kinase MLT 1 SS(0.001)S(0.999)PTQYGLTK;S(0.001)S(0.021)S(0.975)PT(0.003)QYGLTK;SS(0.002)S(0.998)PTQYGLTK 250.53 1.11E-16 2137100000 5440660 5352540 3352360 4393580 5579660 4822020 5880290 7458890 6427190 TRUE FALSE 4721662.996 5317378.812 4973572.509 5391209.491 5468635.682 5007526.23 5310020.381 5863864.419 5667374.92 0.833130517 0.9382437 0.877579581 0.951271015 0.964932753 0.883570665 0.936945315 1.034670284 1 22.43424922 -2 0.190758148 1.656030457 0.848580531 0.525581839 0.040846006 85.91626994 1.248901627 19.78568422 0.309057803 0.01 2 -0.807449926 SSS(ph)PTSYWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SSSPTSYWK 9 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 SS(0.002)S(0.997)PT(0.001)SYWK;S(0.003)S(0.122)S(0.875)PTSYWK;SS(0.008)S(0.992)PTSYWK;SS(0.011)S(0.988)PTSYWK;S(0.001)S(0.016)S(0.982)PT(0.001)SYWK 198.93 2.68E-05 4654600000 6827090 5617950 4732410 6206820 6190150 5493920 6965010 7895500 11915400 TRUE FALSE 5924872.759 5581045.317 7021019.305 7616173.346 6066978.126 5705274.657 6289544.402 6207108.768 10506774.99 0.563909741 0.531185385 0.668237334 0.724882122 0.577434858 0.543009122 0.598617978 0.590772028 1 23.32481657 1.237694903 24.99871832 1.000000466 0.600718087 0.825299342 0.057870529 9.172578114 264714.7614 0.088226911 0.015014514 17.28601569 -1.237694903 -0.399282379 SSS(ph)PVGLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSPVGLAK 9 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 S(0.001)S(0.03)S(0.969)PVGLAK;SS(0.034)S(0.966)PVGLAK 112.83 0.0019913 10643100000 1122140 961930 662320 811190 936700 805490 1084880 1241990 1171750 TRUE FALSE 973846.3559 955611.0185 982620.1673 995383.0878 918061.5026 836477.7215 979668.5046 976400.1037 1033227.05 0.942528901 0.924879985 0.95102056 0.963373044 0.888538006 0.809577838 0.948163818 0.945000524 1 19.97872589 1.390232975 2.004332318 1.00891951 0.91633533 0.262210772 0.043810289 0.827527632 4.441129483 0.130016716 0.012906141 24.56026087 -1.390232975 -0.092584179 SSS(ph)PVTELASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SSSPVTELASR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.001)S(0.113)S(0.885)PVTELASR;SS(0.002)S(0.997)PVTELASR;SS(0.001)S(0.999)PVTELASR;SSS(1)PVTELASR;SS(0.002)S(0.997)PVTELASR;S(0.03)S(0.224)S(0.746)PVTELASR 309.86 1.46E-45 10192020000 7081690 6027290 4638280 5867960 6629150 6324190 5713140 6915150 10134880 TRUE FALSE 6145826.724 5987696.335 6881367.722 7200370.004 6497242.885 6567485.682 5159080.562 5436398.986 8936746.032 0.687702963 0.670008559 0.7700082 0.805703774 0.727025571 0.734885568 0.577288483 0.608319736 1 23.0913182 SSS(ph)PVTELASRS(ph)PIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSPVTELASRSPIR 15 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.022)S(0.117)S(0.86)PVTELAS(0.004)RS(0.996)PIR 181.83 3.25E-07 325440000 487330 450920 279170 348830 465850 460580 401880 500360 294770 TRUE FALSE 422928.1058 447957.8768 414177.5458 428037.183 456580.4964 478298.8106 362905.7395 393361.9078 259922.6264 1.62713078 1.723427787 1.593464761 1.646786926 1.756601581 1.840158424 1.396206804 1.513380783 1 17.9877227 0.821512073 1.082093801 1.79E-13 1.682828333 0.786168763 0.108911025 1.75023676 0.889143549 4.235836447 0.03416824 6.629977777 -0.821512073 1.682828333 SSS(ph)PVTELASRS(ph)PIRQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSPVTELASRSPIRQDR 18 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.059)S(0.069)S(0.871)PVT(0.004)ELAS(0.177)RS(0.82)PIRQDR;S(0.14)S(0.166)S(0.695)PVTELAS(0.063)RS(0.937)PIRQDR 88.504 0.015074 1397860000 1397010 1291510 499420 530150 1172910 1221330 1176410 1334940 244180 TRUE FALSE 1212391.589 1283025.986 740941.1825 650528.6603 1149571.386 1268315.355 1062321.939 1049473.47 215313.3186 5.630824869 5.958878876 3.441223178 3.021311755 5.339063061 5.890556905 4.933842209 4.874168846 1 17.71607804 4.254489019 24.97819467 4.262057668 5.794852947 0.199246269 1.396263946 437.5832115 686186.1018 0.352785896 0.926733212 17967.5565 -4.254489019 1.532795279 SSS(ph)QGPLSSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSQGPLSSIR 11 0 A0A0U1RQE4 A0A0U1RQE4 1 S(0.022)S(0.052)S(0.926)QGPLSSIR 139.28 4.21E-05 144600000 174410 187230 116960 103290 207390 202720 183290 202900 212110 TRUE FALSE 151361.2766 186000.0738 173522.2472 126743.5732 203263.3448 210518.7696 165514.564 159511.414 187034.5974 0.809268866 0.994468811 0.927754809 0.677647745 1.086768692 1.125560578 0.884940895 0.852844426 1 17.51294564 3.206791022 24.99986789 0.97177124 0.867831078 0.24999638 0.114786228 389.4453404 306457.8679 0.037458528 0.0424776 1609.870795 -3.206791022 -0.103940162 SSS(ph)QIPEGFGLTSGGSNYSLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSQIPEGFGLTSGGSNYSLAR 22 0 Q9Y4E6-2;Q9Y4E6;A2RRE0 Q9Y4E6-2 WDR7 WD repeat-containing protein 7 1 S(0.014)S(0.014)S(0.973)QIPEGFGLTSGGSNYSLAR;S(0.022)S(0.022)S(0.957)QIPEGFGLTSGGSNYSLAR 282.34 1.01E-45 348240000 145088 157419 137057 139096 214035 274300 215412 223534 267930 TRUE FALSE 125914.2532 156384.9042 203338.2236 170679.8727 209776.1223 284852.4985 194521.3774 175732.9936 236255.6206 0.532957704 0.661930937 0.860670417 0.7224373 0.887920134 1.205696177 0.823351321 0.743825663 1 17.84998913 4.651899435 0.907982219 0.901420196 0.35297814 0.483651817 0.133309163 1.920657903 1.381233887 0.049993023 1.019915925 44864.14909 -4.651899435 -0.548442056 SSS(ph)QPSSCCSDPSKPGGNVEGATQSLAEQMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSQPSSCCSDPSKPGGNVEGATQSLAEQMR 31 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 S(0.001)S(0.019)S(0.979)QPS(0.001)SCCSDPSKPGGNVEGATQSLAEQMR;S(0.001)S(0.031)S(0.947)QPS(0.005)S(0.005)CCS(0.01)DPSKPGGNVEGATQSLAEQMR 278.9 5.08E-72 452160000 629340 460470 371180 439170 505400 415500 607160 664530 604150 TRUE FALSE 546171.1245 457445.1423 550683.8895 538890.2608 495343.5288 431484.5539 548277.7167 522425.4309 532728.0752 1.025234355 0.858684127 1.033705403 1.011567225 0.929824336 0.809952721 1.029188703 0.980660594 1 19.02303979 SSS(ph)SPELQTLQDILGDPGDKADVGRLS(ph)PEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSSPELQTLQDILGDPGDKADVGRLSPEVK 31 2 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;H3BQK4;A0A2R8Y670 P49815 TSC2 Tuberin 2 S(0.301)S(0.322)S(0.345)S(0.022)PELQT(0.01)LQDILGDPGDKADVGRLS(1)PEVK 60.659 0.014047 67800000 46714 44386 34702 32278 49132 38106 56933 62521 39434 TRUE FALSE 40540.62654 44094.42544 51484.00327 39607.21324 48154.36933 39571.96248 51411.64642 49151.37069 34772.15744 1.165893333 1.268095761 1.480609978 1.139049635 1.38485423 1.138035871 1.478529093 1.413526635 1 15.08564496 2.247805977 24.99946704 1.329104045 1.272828501 0 0.163642837 928.8604188 2511643.106 0.059803643 0.045691633 176.9318333 -2.247805977 -0.056275544 SSS(ph)SSASPSSPSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSSSASPSSPSSR 14 0 E9PK91;Q9NYF8-3;H0YF63;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 S(0.001)S(0.026)S(0.972)S(0.002)SASPSSPSSR 105.03 0.0022555 0 78084 77866 43967 51106 70132 80562 70490 89854 77552 TRUE FALSE 67765.00156 77354.49312 65229.58826 62710.39841 68736.51041 83661.27227 63653.89065 70639.42134 68383.89091 0.990949779 1.13118005 0.953873601 0.917034664 1.00515647 1.223406144 0.930831659 1.032983359 1 16.06136889 1.597653432 0.00655236 0.912324107 1.128066248 0 0.093282524 1329464.251 3043.49296 51158.25037 49064.32005 39.59619294 -1.597653432 0.21574214 SSS(ph)TEPPPPVR ddPTM_MDA-MB-175_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 S(0.002)S(0.015)S(0.97)T(0.013)EPPPPVR 112.59 0.0015791 240870000 336950 254480 180550 210550 274680 281050 229370 300110 321500 TRUE FALSE 292421.2038 252808.3041 267864.5839 258358.5956 269214.4054 291862.1754 207125.7327 235933.812 283492.6363 1.031494883 0.891763213 0.944873163 0.911341469 0.949634562 1.029522951 0.730621209 0.832239649 1 18.11295174 2.251132725 24.99999894 0.844540997 0.953341037 0.283672565 0.078066592 269.8719801 536648.2776 0.028828046 0.02217522 178.2923566 -2.251132725 0.10880004 SSS(ph)TGNLLDKDDLAIPPPDYGAASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSTGNLLDKDDLAIPPPDYGAASR 25 1 Q9UQB8;Q9UQB8-2;Q9UQB8-4;Q9UQB8-5;Q9UQB8-3;I3L4C2;Q9UQB8-6;B4DWA1;I3L3C6 Q9UQB8 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 1 S(0.097)S(0.097)S(0.804)T(0.003)GNLLDKDDLAIPPPDYGAASR 180.35 1.56E-17 703680000 1413100 953360 611780 720770 784640 665170 724300 1018700 886620 TRUE FALSE 1226355.255 947097.3154 907638.8543 884431.8448 769027.1991 690759.5203 654057.4975 800858.9325 781804.7936 1.568620792 1.211424288 1.160953299 1.131269406 0.983656285 0.883544749 0.836599497 1.02437199 1 19.5764489 7.999999999 0.495034096 0.933490701 20.41942666 0.883970057 0.070094455 38.3564969 0.426116162 0.04821 773.3456454 99999999.66 -7.999999999 19.48593596 SSS(ph)TSDILEPFTVER ddPTM_MDA-MB-175_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 S(0.018)S(0.018)S(0.945)T(0.018)SDILEPFTVER;SSS(0.999)T(0.001)SDILEPFTVER;SSS(0.995)T(0.005)SDILEPFTVER;SSS(0.961)T(0.039)SDILEPFTVER;SSS(0.957)T(0.042)SDILEPFTVER;SS(0.001)S(0.949)T(0.049)S(0.001)DILEPFTVER;SS(0.029)S(0.955)T(0.014)S(0.002)DILEPFTVER 412.68 3.37E-133 5962210000 6334060 6526710 4367710 4644570 7216430 7663200 6795130 7437980 7018130 TRUE FALSE 5496997.923 6483835.612 6479949.165 5699190.606 7072837.162 7958008.263 6136139.338 5847425.859 6188454.666 0.888266654 1.04773097 1.047102955 0.920939219 1.142908455 1.285944342 0.991546302 0.944892736 1 22.56114776 4.739607862 22.98507222 1.043426293 0.888266518 0.186226015 0.104367447 57.85224905 1269162.464 0.027453656 0.16234294 54904.49002 -4.739607862 -0.155159776 SSS(ph)VEEKPLSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSVEEKPLSHR 12 1 Q06190 Q06190 PPP2R3A Serine/threonine-protein phosphatase 2A regulatory subunit B subunit alpha 1 S(0.001)S(0.021)S(0.978)VEEKPLSHR;S(0.162)S(0.162)S(0.676)VEEKPLSHR 123.02 0.00021083 260528000 334291 244932 184641 235975 225578 186800 339785 326172 387941 TRUE FALSE 290113.5974 243323.0256 273934.0052 289556.7304 221089.4391 193986.3169 306832.703 256422.6561 342079.0569 0.848089328 0.711306409 0.800791512 0.846461438 0.646310947 0.567080366 0.896964303 0.74960057 1 18.38397026 -0.122143581 1.38814308 9.999999915 0.74960737 0.358878142 0.099927462 58.71516835 3.722342347 1606.982897 0.028810738 0.75484263 0.122143581 -9.250392545 SSS(ph)VGS(ph)SSSYPISPAVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSSVGSSSSYPISPAVSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 2 S(0.01)S(0.017)S(0.973)VGS(0.999)S(0.001)SSYPISPAVSR;S(0.009)S(0.042)S(0.949)VGS(0.982)S(0.018)SSYPISPAVSR;SS(0.016)S(0.983)VGS(1)SSSYPISPAVSR;S(0.001)S(0.006)S(0.993)VGS(0.999)S(0.001)SSYPISPAVSR 309.45 5.99E-61 1191510000 975640 1060390 718870 931630 1451690 1183400 1409020 1571410 1582230 TRUE FALSE 846706.702 1053424.228 1066517.936 1143170.831 1422804.209 1228926.164 1272373.457 1235376.2 1395180.572 0.606879654 0.755045081 0.764430037 0.819371237 1.019799328 0.880836638 0.91197762 0.885459721 1 20.41202042 4.292089606 0.841438355 0.930344699 0.557034562 0.789431233 0.05594239 0.628087486 0.543746117 0.022061214 0.194301382 19592.48876 -4.292089606 -0.373310137 SSS(ph)VGSS(ph)SSYPISPAVSR ddPTM_MDA-MB-175_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 SSS(1)VGS(0.106)S(0.887)S(0.007)SYPISPAVSR;SSS(1)VGS(0.034)S(0.955)S(0.01)S(0.002)YPISPAVSR 312.28 4.99E-61 1640320000 1037740 1196130 747050 1053280 1590530 1288330 1619020 1785780 1749410 TRUE FALSE 900600.0297 1188272.543 1108325.879 1292443.322 1558881.565 1337892.889 1462007.69 1403904.844 1542596.743 0.583820777 0.770306659 0.718480629 0.837836154 1.010556759 0.867299179 0.947757537 0.910091928 1 20.55692954 4.305887349 0.704301274 0.949640362 0.51172225 0.806562284 0.057976997 0.790015475 0.453283211 0.027344631 0.254467494 20224.94497 -4.305887349 -0.437918112 SSS(ph)VGSSSSYPIS(ph)PAVSR ddPTM_MDA-MB-175_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(0.027)S(0.046)S(0.926)VGSSSSYPIS(1)PAVSR;S(0.233)S(0.321)S(0.446)VGS(0.247)S(0.061)S(0.004)S(0.017)Y(0.001)PIS(0.672)PAVSR 254.3 2.30E-30 940810000 1022440 1074320 741090 994260 1472190 1522230 1370770 1524450 1476000 TRUE FALSE 887321.9635 1067262.721 1099483.603 1220021.929 1442896.299 1580791.173 1237832.936 1198458.231 1301508.961 0.681764006 0.820019495 0.844776053 0.937390341 1.108633396 1.214583395 0.951075231 0.920822112 1 20.31175381 3.952923246 1.528101831 1.024070973 0.726495981 0.647532706 0.088067041 0.323713381 1.424401339 0.030784759 0.092392156 8972.702026 -3.952923246 -0.297574992 SSS(ph)VGSSSSYPISPAVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 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(1)VGSSSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(0.996)VGS(0.004)SSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(0.998)VGS(0.001)SSSYPISPAVSR 488.14 6.42E-240 1.08021E+11 10123680 11209930 8471260 10520430 16239940 17280520 15565490 16670990 15909630 TRUE FALSE 8785810.038 11136291.23 12567989.67 12909254.43 15916796.97 17945312.79 14055951.18 13106028.52 14028811.67 0.626269013 0.79381572 0.895869869 0.920195861 1.134579132 1.279175543 1.001934555 0.934222287 1 23.74188947 4.272233914 1.157632425 1.050695215 0.594931733 0.677948846 0.10022921 0.551807375 1.06170614 0.03672806 0.253949895 18716.89973 -4.272233914 -0.455763482 SSSASS(ph)PEMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSSASSPEMK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SSSAS(0.002)S(0.998)PEMK;SSSAS(0.003)S(0.997)PEMK;SSSAS(0.003)S(0.997)PEMK 213.72 1.79E-08 695120000 2760580 2438370 1593600 1994190 2008910 1867900 2672530 3290030 2896820 TRUE FALSE 2395762.359 2422352.187 2364270.29 2447001.319 1968936.621 1939759.322 2413348.452 2586482.688 2554361.24 0.937910551 0.948320132 0.925581806 0.957969954 0.770813693 0.759391151 0.944795284 1.012575139 1 21.28453114 2.002220791 24.98134088 0.998635638 0.883618077 0.353589343 0.068941613 80.77093862 908573.2492 0.031434848 0.021039148 100.5126656 -2.002220791 -0.115017561 SSSDPGIPGGPQAIPAT(ph)NSPDHSDHTLSVSSDSGHSTASAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSDPGIPGGPQAIPATNSPDHSDHTLSVSSDSGHSTASAR 41 0 Q68CZ2;E9PCX8;C9JHU5 Q68CZ2 TNS3 Tensin-3 1 SSSDPGIPGGPQAIPAT(0.376)NS(0.376)PDHS(0.096)DHT(0.025)LS(0.029)VS(0.032)S(0.029)DS(0.009)GHS(0.009)T(0.009)AS(0.009)AR 65.722 0.0060972 177160000 40529 50525 9404.9 27090 57147 56345 43283 49755 44429 TRUE FALSE 35172.98996 50193.09795 13953.1411 33241.19854 56009.88651 58512.62861 39085.42132 39115.28044 39176.65423 0.897804845 1.281199197 0.35615959 0.848495085 1.429675086 1.493558594 0.997671243 0.998433409 1 15.25770657 3.331422835 12.15390491 1.162133564 0.841250522 0.26601182 0.27761685 0.815495881 101.9014154 0.084108332 0.108579136 2144.977965 -3.331422835 -0.320883042 SSSFS(ph)DTLEESSPIAAIFDTENLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSFSDTLEESSPIAAIFDTENLEK 25 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 S(0.212)S(0.212)S(0.212)FS(0.301)DT(0.064)LEESSPIAAIFDTENLEK;S(0.226)S(0.226)S(0.226)FS(0.291)DT(0.031)LEESSPIAAIFDTENLEK 232.82 4.36E-36 299510000 396280 269170 214316 244926 325640 255754 411050 493380 436630 TRUE FALSE 343910.594 267401.8045 317959.9344 300540.1918 319160.4011 265593.0219 371186.4343 387874.5265 385012.0988 0.893246199 0.694528316 0.825844007 0.780599344 0.828962004 0.689830327 0.964090311 1.007434643 1 18.55454426 2.123020514 6.318053331 0.998383405 0.785455361 0.720378503 0.060473845 0.096771678 4.976556796 0.022735723 0.015231031 132.745716 -2.123020514 -0.212928044 SSSFSDT(ph)LEESSPIAAIFDTENLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSFSDTLEESSPIAAIFDTENLEK 25 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 S(0.167)S(0.167)S(0.167)FS(0.167)DT(0.241)LEES(0.044)S(0.044)PIAAIFDTENLEK 144.77 1.09E-06 175350000 41373 38012 27967 35222 44833 37554 50246 52546 45679 TRUE FALSE 35905.45322 37762.29667 41491.93474 43219.69343 43940.91101 38998.72668 45373.15065 41309.44681 40278.88066 0.891421326 0.937521005 1.03011638 1.073011284 1.090916885 0.968217737 1.126474964 1.025585769 1 15.29773597 4.304383808 2.741764818 1.049037963 0.897249633 0.606855494 0.044619608 0.171940046 2.509088722 0.011183304 0.038386484 20155.04665 -4.304383808 -0.151788329 SSSHSS(ph)PGSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSHSSPGSPK 11 0 Q6NZY4;Q6NZY4-2;F5GX80 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 SSSHS(0.036)S(0.89)PGS(0.074)PK 55.232 0.08157 131800000 371080 225980 139170 242650 67080 151650 203010 263950 251330 TRUE FALSE 322040.8378 224495.5225 206473.0775 297747.3912 65745.23924 157484.0736 183322.1214 207506.3466 221618.0537 1.453134492 1.01298391 0.931661812 1.343515955 0.296660124 0.710610309 0.827198499 0.936324199 1 17.75771589 6.892713685 0.713622441 0.826498097 15.21086933 0.358005797 0.255348969 64.36347299 1.814602735 0.100591078 1355.175372 7811126.751 -6.892713685 14.38437123 SSSHSSPGS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSHSSPGSPK 11 0 Q6NZY4;Q6NZY4-2;F5GX80 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 SSSHS(0.008)S(0.003)PGS(0.989)PK;SSSHSS(0.001)PGS(0.998)PK 70.563 0.042856 159620000 289016 258793 59513.9 158777 270652 329890 333606 372693 408391 TRUE FALSE 250821.8033 257092.9717 88295.0211 194829.7446 265266.5547 342581.0818 301252.9415 292995.5023 360111.4812 0.696511543 0.713926062 0.24518802 0.541026195 0.736623431 0.951319521 0.83655467 0.81362444 1 18.45808407 3.064263819 3.401176072 0.879410084 0.539890325 0.591225903 0.136839255 0.179398947 4.218901287 0.045407833 0.051267402 1159.481487 -3.064263819 -0.33951976 SSSISEEKGDS(ph)DDEKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SSSISEEKGDSDDEKPR 17 2 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR 252.31 2.88E-27 6746650000 5479057 3511971 3348822 2876122 3749455 2478133 5187038 5798317 5147873 TRUE FALSE 4754985.735 3488900.631 4968323.52 3529189.459 3674848.181 2573468.38 4683999.853 4558392.032 4539297.318 1.047515816 0.768599276 1.094513792 0.777474841 0.809563226 0.566931003 1.031877739 1.004206535 1 22.11403756 SSSLEMTPYNTPQLS(ph)PATTPANKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSLEMTPYNTPQLSPATTPANKK 24 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7;B4DGD8;B0QZ65;A0A0A0MQV8 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 SSSLEMTPYNTPQLS(1)PATTPANKK;SSSLEMTPYNTPQLS(0.993)PAT(0.006)T(0.001)PANKK 144.18 1.90E-10 0 348820 318359 166868 153911 272420 232084 337490 391820 150128 TRUE FALSE 302722.5532 316267.6788 247565.9229 188858.8449 266999.375 241012.4217 304760.2717 308032.3421 132380.0389 2.28676888 2.38908888 1.870115201 1.426641407 2.016915671 1.820609993 2.302161824 2.326879073 1 17.01432607 4.23587076 24.85845652 1.886591994 2.337928973 0.216300582 0.393134841 104.2456991 963435.6975 0.101891729 0.228677698 17213.56247 -4.23587076 0.451336978 SSSPAPEFLASS(ph)PPDNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSPAPEFLASSPPDNK 17 0 C9JME2;Q9Y4F1;Q9Y4F1-2;M0QXT1 C9JME2 FARP1 "FERM, RhoGEF and pleckstrin domain-containing protein 1" 1 SSSPAPEFLAS(0.004)S(0.996)PPDNK 235.35 3.89E-20 126040000 109650 167720 194880 482410 347790 331710 202080 463990 795980 TRUE FALSE 95159.47468 166618.2363 289124.6198 591948.5637 340869.6594 344471.0983 182482.3127 364769.3493 701880.1512 0.135577954 0.237388443 0.411928759 0.843375557 0.485652228 0.490783359 0.259990701 0.519703184 1 19.42086518 4.158502197 3.198788712 0.564351015 0.171925332 0.39898722 0.205799385 0.265050599 5.354333523 0.055316683 0.141894217 14404.63297 -4.158502197 -0.392425683 SSSPELVTHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSPELVTHLK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 180.07 6.83E-06 1523680000 2235900 2071690 1168050 1575200 2258300 1986540 2218700 2799700 2518600 FALSE TRUE 1940420.15 2058080.932 1732922.887 1932873.235 2213364.248 2062963.479 2003530.815 2201005.942 2220853.977 0.87372703 0.926707002 0.780295735 0.870328826 0.996627546 0.928905502 0.902144326 0.991062882 1 21.08268311 3.300413884 7.640228185 0.960701168 0.860747217 0.540267335 0.04625188 0.195359488 20.65124612 0.01360218 0.017522926 1997.164715 -3.300413884 -0.099953951 SSSPT(ph)SSLTQPIEMPTLSS(ph)SPTEERPTVGPGQQDNPLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSPTSSLTQPIEMPTLSSSPTEERPTVGPGQQDNPLLK 39 1 Q7LBC6;Q7LBC6-2 Q7LBC6 KDM3B Lysine-specific demethylase 3B 2 S(0.155)S(0.155)S(0.155)PT(0.177)S(0.177)S(0.177)LT(0.004)QPIEMPT(0.003)LS(0.108)S(0.674)S(0.108)PT(0.108)EERPTVGPGQQDNPLLK 146.01 4.72E-12 68907000 118330 86094 64749 77058 85294 77803 104360 118470 109880 TRUE FALSE 102692.3907 85528.44285 96061.83297 94555.19666 83596.81627 80796.13176 94239.18326 93136.11243 96890.11158 1.059885153 0.88273655 0.991451361 0.975901412 0.862800289 0.833894506 0.972639847 0.961255085 1 16.56406181 4.75560069 23.80571272 0.936505696 1.059885345 0.320087933 0.057128949 2402.614578 3356448.865 0.01454137 0.381846879 56964.02779 -4.75560069 0.123379649 SSSQRS(ph)PS(ph)PGPNHTSNSSNASNATVVPQNSSAR ddPTM_MDA-MB-175_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(0.294)S(0.324)S(0.343)QRS(0.337)PS(0.627)PGPNHT(0.03)S(0.029)NS(0.008)S(0.008)NASNATVVPQNSSAR 120.15 6.21E-07 90189000 59510 61863 17712 26753 91271 80826 56747 73684 20998 TRUE FALSE 51645.60272 61456.61788 26277.58244 32827.67754 89454.88567 83935.42852 51243.68467 57927.25001 18515.64036 2.789296061 3.319173233 1.419210026 1.772970143 4.831314711 4.533217695 2.767589113 3.128557743 1 14.17645683 SSSQRSPS(ph)PGPNHTSNSSNASNATVVPQNSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSQRSPSPGPNHTSNSSNASNATVVPQNSSAR 33 1 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 S(0.17)S(0.17)S(0.17)QRS(0.135)PS(0.181)PGPNHT(0.043)S(0.043)NS(0.043)S(0.043)NASNATVVPQNSSAR 99.515 4.31E-05 80240000 18502 22574 5446.7 5447.9 27521 32685 21759 23199 4241 TRUE FALSE 16056.91382 22425.70991 8080.742338 6684.928961 26973.38594 33942.4131 19648.81553 18238.07438 3739.633811 4.293712869 5.996766271 2.160837864 1.787589186 7.212841499 9.076400207 5.254208439 4.876967988 1 11.86868129 1.236039688 4.782798082 0.692167592 5.130290014 0.264261172 2.14392796 0.292153665 15.62548954 4.377346941 0.580761174 17.22025934 -1.236039688 4.438122423 SSSQSGSGPS(ph)SPDSVLRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSQSGSGPSSPDSVLRPR 19 1 O75427;H7C5D9 O75427 LRCH4 Leucine-rich repeat and calponin homology domain-containing protein 4 1 S(0.008)S(0.008)S(0.008)QS(0.032)GS(0.094)GPS(0.392)S(0.392)PDS(0.067)VLRPR 68.41 0.06413 51557000 53251 74135 46557 80348 128800 135430 81390 135110 132700 TRUE FALSE 46213.74543 73648.0023 69072.12092 98592.24144 126237.132 140640.0797 73496.81033 106217.7779 117012.3572 0.394947564 0.62940363 0.590297663 0.84257974 1.078835903 1.20192502 0.628111527 0.907748382 1 16.83630137 3.730574363 2.57596926 0.944668986 0.525986327 0.609781184 0.155654451 0.213912874 2.80449788 0.047006787 0.084956173 5377.425008 -3.730574363 -0.418682659 S(ph)LPVSVPVWGFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SLPVSVPVWGFK 12 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 S(1)LPVSVPVWGFK;S(1)LPVSVPVWGFK;S(1)LPVSVPVWGFK 227.93 1.23E-11 7753462000 1303846 2445997 2109931 2431910 3277510 3178086 3493376 3903076 4439759 TRUE FALSE 1131539.448 2429929.085 3130300.689 2984112.335 3212293.963 3300349.025 3154588.933 3068433.571 3914895.749 0.289034375 0.62068807 0.799587241 0.76224567 0.820531163 0.843023477 0.8057913 0.783784235 1 21.90054246 4.805524863 1.357356192 0.831185155 6.69E-17 0.885436175 0.063033389 0.461230052 0.676894752 0.017335919 0.549625122 63903.53202 -4.805524863 -0.831185155 down SSSSESSHSSSSHSHGKT(ph)TPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSSESSHSSSSHSHGKTTPTK 22 1 O75582-3;O75582 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 1 SSSSESSHS(0.001)S(0.003)S(0.003)S(0.003)HS(0.079)HGKT(0.414)T(0.414)PT(0.081)K;SSSSESSHS(0.001)S(0.001)S(0.001)S(0.001)HS(0.005)HGKT(0.465)T(0.435)PT(0.093)K 85.231 0.0017573 99711000 37134 63746 2567.4 11482.8 101470 72911 73125 87792 6118.3 TRUE FALSE 32226.64781 63327.24833 3809.003227 14090.14524 99450.94552 75715.93335 66033.34876 69018.364 5395.001544 5.973426986 11.73813349 0.706024493 2.611703654 18.43390492 14.03446 12.2397275 12.79302025 1 12.39740766 SSSSLLAS(ph)PGHISVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSSLLASPGHISVK 15 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5 A0A499FIX8 ESYT2 Extended synaptotagmin-2 1 S(0.008)S(0.008)S(0.008)S(0.008)LLAS(0.968)PGHISVK 84.035 0.0054646 202370000 192370 200090 54756 127210 224680 203570 156960 270650 249360 TRUE FALSE 166947.8171 198775.5956 81236.18475 156094.9748 220209.3076 211401.4696 141738.0434 212773.6037 219880.9449 0.759264597 0.904014651 0.36945532 0.709906786 1.001493366 0.961436061 0.644612672 0.967676412 1 17.74636306 3.340124686 6.831733829 0.903066222 0.674946803 0.320984499 0.165568057 0.278944254 16.37221436 0.048358597 0.062460534 2188.389819 -3.340124686 -0.228119419 SSSSSASPSS(ph)PSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SSSSSASPSSPSSR 14 0 E9PK91;Q9NYF8-3;H0YF63;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 SSSSSASPS(0.004)S(0.984)PS(0.011)S(0.001)R;SSSSSASPS(0.029)S(0.969)PS(0.002)SR;SSSSSASPS(0.002)S(0.997)PSSR;SSSSSASPS(0.009)S(0.991)PSSR;SSSSSASPS(0.005)S(0.994)PSSR 333.86 1.68E-68 4089721000 2194971 1703207 923967 1254106 1500610 1895276 1713671 1894686 1809027 TRUE FALSE 1904900.021 1692018.521 1370800.532 1538869.935 1470750.797 1968188.494 1547479.45 1489522.143 1595165.889 1.194170484 1.060716339 0.859346693 0.964708402 0.922004919 1.233845651 0.970105655 0.933772565 1 20.60527503 4.598069328 3.813744593 0.983165577 1.19108464 0.318597073 0.097797994 0.291119148 6.790169757 0.024564443 0.12524662 39634.12986 -4.598069328 0.207919063 SSSSSASPSSPS(ph)SR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSSSASPSSPSSR 14 0 E9PK91;Q9NYF8-3;H0YF63;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 SSSSSASPSS(0.028)PS(0.699)S(0.274)R 226.15 2.63E-12 383210000 470470 349970 229480 268840 323960 408910 379470 443880 407970 TRUE FALSE 408296.1975 347671.024 340457.2956 329884.231 317513.8298 424641.0323 342669.0578 348959.7163 359740.2514 1.134975016 0.966450162 0.946397558 0.917006728 0.882619692 1.180410117 0.952545779 0.970032447 1 18.45659607 4.740707044 23.87481793 0.975835038 1.134975115 0.283399649 0.078962355 140.7412498 1565263.042 0.019015668 0.121419593 55043.62711 -4.740707044 0.159140076 SSSSSGVPYS(ph)PAIPNK ddPTM_MDA-MB-175_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;SSSSSGVPYS(1)PAIPNK;SSSSSGVPYS(1)PAIPNK;SSSSSGVPYS(1)PAIPNK 306.07 1.65E-46 2596580000 2595840 2473340 1357890 1600260 2395660 2122970 2359420 2697090 2433370 TRUE FALSE 2252793.167 2457092.467 2014570.146 1963623.491 2347991.053 2204642.03 2130603.812 2120338.292 2145699.771 1.049910709 1.145124076 0.938887245 0.915143637 1.094277534 1.027469947 0.992964552 0.988180323 1 21.0330168 4.241550046 24.99988875 0.995269945 1.097517392 0.400070435 0.052756615 76.75288424 641834.9934 0.013453563 0.032539053 17440.14319 -4.241550046 0.102247447 SSSSSGVPYS(ph)PAIPNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSSSSGVPYSPAIPNKR 17 1 A0A0A0MRE1;B4DJ07;A0A0A0MSB8;Q9UPT5-2;Q9UPT5-5;Q9UPT5-1;Q9UPT5-6;Q9UPT5;Q9UPT5-4 A0A0A0MRE1 EXOC7 Exocyst complex component 7 1 SSSSSGVPYS(1)PAIPNKR;SSSSSGVPYS(1)PAIPNKR;SSSSSGVPYS(1)PAIPNKR;SSSSSGVPYS(1)PAIPNKR 236.95 2.05E-20 2132920000 2179110 2189970 1298240 1643830 2196260 2005320 2171470 2464750 2094910 TRUE FALSE 1891135.092 2175583.943 1926073.206 2017086.726 2152558.723 2082465.958 1960881.174 1937682.393 1847252.126 1.023755808 1.177740662 1.042669368 1.091939047 1.165276083 1.127331742 1.061512473 1.048953938 1 20.81694936 1.657063881 1.673207951 1.001650833 1.106266222 0.328212756 0.048435716 0.491367397 2.449135648 0.070735839 0.013704285 45.40083927 -1.657063881 0.104615389 SSSSSSQPEHSAMLVSTAAS(ph)PSLIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSSSSQPEHSAMLVSTAASPSLIK 25 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 SSSSSSQPEHSAMLVSTAAS(0.893)PS(0.107)LIK;SSSSSSQPEHSAMLVSTAAS(1)PSLIK 256.12 4.46E-45 834840000 833010 782450 296020 548660 763270 753450 876870 1061640 983010 TRUE FALSE 722925.6179 777310.0344 439176.2621 673241.6387 748082.4203 782435.709 791831.2824 834616.5477 866799.6776 0.834016944 0.896758564 0.506664081 0.776698072 0.863039569 0.902671897 0.913511279 0.962871318 1 19.72533909 2.935690365 1.823873222 0.951726983 0.746987764 0.441251251 0.102099353 0.336609784 2.255256481 0.040070911 0.041677061 862.3634964 -2.935690365 -0.204739219 SSSSVGS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSSVGSPTR 10 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 SSSSVGS(0.998)PT(0.002)R;SSSSVGS(0.989)PT(0.011)R 193.32 6.15E-07 302540000 289430 341510 238700 274300 356650 507160 407340 486940 443740 TRUE FALSE 251181.0922 339266.5983 354136.1184 336584.0074 349553.3628 526670.7734 367836.2295 382811.6704 391281.5627 0.641944615 0.867065128 0.905067226 0.860209219 0.893355057 1.346014797 0.940080659 0.978353459 1 18.57784761 2.982835646 24.5737567 1.049373405 0.834284647 0.447769077 0.129603708 616.3797897 882456.2106 0.041435942 0.042417321 961.2484357 -2.982835646 -0.215088758 SSSVAVGNDFGFSS(ph)PVPGTGDANPAVSEDALFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSVAVGNDFGFSSPVPGTGDANPAVSEDALFR 33 0 Q9NWM3;J3QLQ8;Q9NWM3-2 Q9NWM3 CUEDC1 CUE domain-containing protein 1 1 SSSVAVGNDFGFS(0.035)S(0.917)PVPGT(0.048)GDANPAVSEDALFR 154.42 6.42E-11 25731000 5949.6 5569 4099.2 4306.4 6267.2 6788.8 4424.9 6598.3 6458.4 TRUE FALSE 5163.345286 5532.416872 6081.586831 5284.233939 6142.494982 7049.969529 3995.773879 5187.304893 5694.895309 0.90666202 0.97146946 1.067901428 0.927889566 1.078596646 1.237945414 0.701641323 0.910869228 1 12.47545361 2.229587069 24.99998087 0.872127189 1.028056861 0.295773513 0.116945079 253.1587164 705284.4275 0.04747063 0.03253226 169.6629714 -2.229587069 0.155929672 SSSVGSSSSYPIS(ph)PAVSR ddPTM_MDA-MB-175_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 407.49 3.15E-147 4316880000 3993300 3540510 1574600 1821960 2499890 2690900 2291710 2792560 2581630 TRUE FALSE 3465575.287 3517252.157 2336081.827 2235663.865 2450147.08 2794420.664 2069460.317 2195392.776 2276432.642 1.522371109 1.545071921 1.026202921 0.982090936 1.07630994 1.227543751 0.909080409 0.964400499 1 21.11834334 4.237507244 24.98839895 1.022051808 1.533721676 0.862794893 0.08407348 8.908864114 211362.462 0.022784271 0.052189825 17278.548 -4.237507244 0.511669869 SSSVLS(ph)LEGSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSVLSLEGSEK 12 0 A1L390-3;A1L390;A1L390-2;G3V311;A0A0U1RR71 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 SSSVLS(1)LEGSEK 294.52 3.34E-36 170740000 470830 395760 302470 376630 437050 415890 473750 603440 512430 TRUE FALSE 408608.6226 393160.2265 448745.5037 462149.5979 428353.5601 431889.5574 427805.7979 474399.052 451851.1092 0.904299258 0.870110128 0.993126927 1.022791775 0.947997142 0.955822723 0.946784879 1.049901267 1 18.78548794 4.233801602 24.9996891 0.990029163 0.887204678 0.6086048 0.033596235 74.14846557 389519.0011 0.009283072 0.020384852 17131.74502 -4.233801602 -0.102824484 SSSVS(ph)PSASFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSVSPSASFR 11 0 Q04727-4;Q04727;Q04727-3;Q04727-2;H7C4W5;H7C4P7;Q5JSY7 Q04727-4 TLE4 Transducin-like enhancer protein 4 1 SSS(0.001)VS(0.648)PS(0.351)ASFR 166.11 2.18E-05 308460000 301880 378860 209990 311540 348340 407230 286890 356940 291650 TRUE FALSE 261985.7931 376371.2437 311541.8664 382279.9186 341408.7155 422896.4016 259067.452 280611.1587 257171.4692 1.018720288 1.463503105 1.211416909 1.486478728 1.327552844 1.644414145 1.007372446 1.091144206 1 17.97237107 2.202441854 24.99997428 1.043924377 1.361146093 0.456115375 0.167572245 149.4862814 103467.4834 0.063946405 0.043114144 159.3829477 -2.202441854 0.317221716 SSSVS(ph)PSSWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSSVSPSSWK 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 SSSVS(0.993)PS(0.003)S(0.003)WK;SSSVS(0.999)PS(0.001)SWK 177.44 2.44E-06 640000000 925860 794370 578520 815630 927690 807350 1009290 1194000 1414060 TRUE FALSE 803505.2552 789151.7312 858294.207 1000831.258 909230.784 838409.2769 911409.2111 938672.3917 1246891.438 0.644406747 0.632895301 0.688347182 0.802661104 0.729198033 0.672399578 0.73094512 0.752810039 1 20.24990443 0.967147388 1.707399435 1.346196038 0.699546023 0.790376729 0.048196538 1.048844692 1.541624085 1.418769226 0.014508327 9.271444187 -0.967147388 -0.646650015 SSSVSPS(ph)ASFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSSVSPSASFR 11 0 Q04727-4;Q04727;Q04727-3;Q04727-2;H7C4W5;H7C4P7;Q5JSY7 Q04727-4 TLE4 Transducin-like enhancer protein 4 1 SSSVS(0.057)PS(0.942)ASFR 138.63 5.62E-05 465790000 233120 267480 144080 164660 258490 283150 204550 243250 191780 TRUE FALSE 202312.6013 265722.9063 213757.5699 202048.5697 253346.5547 294042.9637 184712.7725 191232.8805 169107.9869 1.196351545 1.571320853 1.264030007 1.194790225 1.498134768 1.73878815 1.092277047 1.130832931 1 17.36758527 2.067339286 24.99991924 1.085794949 1.406234138 0.460159469 0.171484356 48.05218781 17838.86034 0.07046713 0.047508934 116.7721527 -2.067339286 0.320439189 SST(ph)PLHS(ph)PSPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSTPLHSPSPIR 12 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 2 S(0.222)S(0.318)T(0.459)PLHS(0.999)PS(0.001)PIR;S(0.002)S(0.357)T(0.641)PLHS(0.999)PS(0.001)PIR 187.74 5.35E-05 1417020000 1657190 1679410 948640 1176360 1936820 1824120 1653520 1946050 1831670 TRUE FALSE 1438188.143 1668377.845 1407405.477 1443470.518 1898281.071 1894295.077 1493161.885 1529902.352 1615132.059 0.890446162 1.032966831 0.871387246 0.893716715 1.17531013 1.172842224 0.924482847 0.947230502 1 20.6232207 SST(ph)PLPTISSSAENTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SSTPLPTISSSAENTR 16 0 P42166;P42167;G5E972;H0YJH7;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 S(0.001)S(0.023)T(0.976)PLPTISSSAENTR;SST(1)PLPTISSSAENTR;SS(0.002)T(0.998)PLPTISSSAENTR;SS(0.001)T(0.999)PLPTISSSAENTR;S(0.005)S(0.018)T(0.977)PLPTISSSAENTR;SST(1)PLPTISSSAENTR;S(0.001)S(0.003)T(0.996)PLPTISSSAENTR 399.67 3.19E-121 34836290000 5987700 4753420 3082440 4281080 6003490 5293390 4494580 6579100 6162400 TRUE FALSE 5196410.274 4722194.471 4573118.294 5253164.646 5884032.295 5497030.139 4058696.323 5172210.664 5433888.092 0.956296888 0.869026817 0.841592285 0.966741412 1.082840168 1.011620049 0.74692306 0.951843427 1 22.37355342 5.102882724 19.2581879 0.93058448 3.420081403 0.004444259 0.095316323 3476.519374 662411.92 0.023443861 6803.697254 126730.9599 -5.102882724 2.489496923 SST(ph)PPGESYFGVSSLQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SSTPPGESYFGVSSLQLK 18 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.126)S(0.126)T(0.748)PPGESYFGVSSLQLK;S(0.014)S(0.014)T(0.971)PPGESYFGVSSLQLK;S(0.076)S(0.076)T(0.849)PPGESYFGVSSLQLK;S(0.103)S(0.103)T(0.794)PPGESYFGVSSLQLK;S(0.026)S(0.026)T(0.948)PPGESYFGVSSLQLK;S(0.113)S(0.113)T(0.774)PPGESYFGVSSLQLK 258.14 1.34E-29 8202860000 8139170 5788380 3891090 4711500 6323370 4959850 6778240 8284710 7005240 TRUE FALSE 7063558.062 5750355.751 5772834.139 5781318.086 6197547.308 5150658.639 6120887.328 6513089.238 6177088.508 1.143509285 0.930916846 0.93455584 0.935929294 1.003312046 0.833832741 0.990901672 1.054394676 1 22.55849557 1.998014224 24.99816341 1.028552337 0.957317364 0.096887957 0.078306365 143.0147423 1800364.72 0.031214332 0.020685258 99.54380191 -1.998014224 -0.071234973 SST(ph)PPRQS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSTPPRQSPSR 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.278)S(0.061)T(0.661)PPRQS(0.872)PS(0.128)R 125.29 0.0083086 64080000 115670 89667 61725 71282 96187 96775 97170 105000 115730 TRUE FALSE 100383.9164 89077.97157 91575.41646 87467.66758 94273.06689 100497.9969 87746.46836 82546.56711 102048.5312 0.983688008 0.872898125 0.897371234 0.857118339 0.92380621 0.984805912 0.85985038 0.8088952 1 16.63889589 4.747150765 23.39185022 0.893417233 0.983688125 0.157357898 0.058366899 814.0128082 2216513.622 0.01452472 0.15713565 55866.41006 -4.747150765 0.090270891 SST(ph)PSHGQTTATEPTPAQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSTPSHGQTTATEPTPAQK 19 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 S(0.148)S(0.148)T(0.699)PS(0.005)HGQTTATEPTPAQK;S(0.121)S(0.121)T(0.731)PS(0.027)HGQTTATEPTPAQK 206.92 1.26E-15 911390000 951070 857830 455947 663901 941400 765000 1041790 1225940 1066010 TRUE FALSE 825383.6898 852194.8582 676444.4943 814649.8691 922667.9818 794430.045 940757.3661 963782.2713 939987.5122 0.87807942 0.906602319 0.719631363 0.86666031 0.981574723 0.845149573 1.000819004 1.02531391 1 19.84228207 2.384171338 0.891403739 1.034599588 0.844330337 0.489934264 0.066485556 0.576107751 0.927259608 0.078039076 0.03327794 242.1984381 -2.384171338 -0.190269251 SSTAISSIAADGEFLHELEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSTAISSIAADGEFLHELEEK 21 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ; 154.34 3.47E-08 54566000 115201 93092 56834 81694 96676 83964 110649 128307 124606 FALSE TRUE 99976.89597 92480.47252 84319.1125 100243.8713 94752.33674 87194.14941 99918.27701 100869.5465 109875.2206 0.909913039 0.841686342 0.767407902 0.912342844 0.862363108 0.793574283 0.909379535 0.91803726 1 16.74550654 1.424438832 1.333286723 1.032419793 0.848461375 0.510580934 0.04697192 0.75527629 1.574923544 0.179677262 0.01421983 26.5728926 -1.424438832 -0.183958418 SSTEESS(ph)PQDQPPVMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSTEESSPQDQPPVMR 16 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 1 SSTEES(0.048)S(0.952)PQDQPPVMR 206.43 2.10E-11 390370000 323440 327090 219370 249620 333520 390570 381220 409100 403220 TRUE FALSE 280696.5845 324941.3243 325458.0657 306300.0362 326883.6045 405595.4806 344249.3431 321617.1486 355551.7909 0.789467503 0.913907151 0.915360502 0.861477973 0.919369872 1.140749367 0.968211529 0.904557808 1 18.4397002 2.990627035 24.77237987 0.989688175 0.878172161 0.456486392 0.067857218 446.8156756 1180920.768 0.022143123 0.023774884 978.6491774 -2.990627035 -0.111516015 SSTFPQTDVLSSS(ph)LEAEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSTFPQTDVLSSSLEAEHR 19 0 D4PHA4;Q86WP2-3;Q86WP2;Q86WP2-2;Q86WP2-4 D4PHA4 GPBP1 Vasculin 1 SSTFPQTDVLSS(0.011)S(0.988)LEAEHR;SSTFPQTDVLS(0.002)S(0.248)S(0.75)LEAEHR;SSTFPQTDVLSS(0.079)S(0.921)LEAEHR 159.76 2.11E-11 1356530000 769540 991540 674560 937920 1453890 1611050 1337750 1613490 1391470 TRUE FALSE 667843.3392 985026.5085 1000779.472 1150889.071 1424960.433 1673028.136 1208015.211 1268457.72 1226972.002 0.54430202 0.802810909 0.815649804 0.937991307 1.161363447 1.363542227 0.98454994 1.033811463 1 20.2266709 4.062111727 1.169430912 1.097544275 0.580600487 0.696542927 0.12039254 0.400247224 0.915871694 0.043007608 0.192287117 11537.50034 -4.062111727 -0.516943788 SSTLSSSSMSLS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SSTLSSSSMSLSPK 14 0 O15119;O15119-2;O15119-3 O15119 TBX3 T-box transcription factor TBX3 1 SSTLSSSSMS(0.002)LS(0.998)PK;SSTLSSSSMSLS(1)PK;SSTLSSSSMSLS(1)PK;SSTLSSSSMSLS(1)PK;SSTLSSSSMS(0.002)LS(0.998)PK;SSTLSSSSMS(0.047)LS(0.953)PK 212.14 2.99E-09 1470280000 2570840 2030583 1373925 1515137 2391961 1782037 2386003 2800960 2372901 TRUE FALSE 2231096.98 2017243.967 2038359.726 1859172.013 2344365.656 1850593.117 2154608.796 2201996.501 2092379.347 1.066296598 0.964090938 0.974182683 0.88854443 1.120430509 0.884444362 1.029740998 1.052388757 1 20.996713 2.045380386 24.9999918 1.033275951 0.981475102 0.076332008 0.071788534 274.3070225 151114.2285 0.027265359 0.018382296 111.0146734 -2.045380386 -0.051800849 SSTPLHSPS(ph)PIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSTPLHSPSPIR 12 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 S(0.005)S(0.017)T(0.017)PLHS(0.404)PS(0.558)PIR 105.65 0.0021055 174560000 74567 94777 58726 78774 124250 115150 113220 138660 115380 TRUE FALSE 64712.78202 94154.40365 87126.09003 96660.84069 121777.6681 119579.895 102239.9418 109008.6381 101739.9078 0.636060946 0.925442195 0.856361008 0.950077927 1.196950839 1.175348961 1.004914826 1.071444238 1 16.63452617 4.868143701 0.758640861 1.079469281 0.3467061 0.714327592 0.085825393 1.882443628 0.735203067 0.036085077 1.2280113 73814.84308 -4.868143701 -0.732763181 SSTS(ph)PCGTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSTSPCGTSK 10 0 H0Y459;O75376;O75376-2;A0A088AWL3;O75376-3 H0Y459;O75376 NCOR1 Nuclear receptor corepressor 1 1 SST(0.003)S(0.997)PCGT(0.001)SK;SST(0.003)S(0.997)PCGTSK;SST(0.001)S(0.995)PCGT(0.003)SK;SST(0.003)S(0.997)PCGTSK 190.68 9.18E-07 654935000 2940600 2087810 1626300 2149560 1402670 1871690 2514540 3004000 4841800 TRUE FALSE 2551992.259 2074095.039 2412784.12 2637650.452 1374759.611 1943695.125 2270680.298 2361617.977 4269407.92 0.59773915 0.485803905 0.565133191 0.617802398 0.322002403 0.455261048 0.531848992 0.553148826 1 22.02560458 1.215133466 3.447730189 1.090210829 0.508348747 0.771088689 0.083095355 0.168333669 2.770036158 0.26901982 0.021647436 16.41094032 -1.215133466 -0.581862082 SSTSPSIINEDVIINGHS(ph)HEDDNPFAEYMWMENEEEFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSTSPSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNR 39 0 Q9BPZ3;D6RA77;D6R9Y1 Q9BPZ3 PAIP2 Polyadenylate-binding protein-interacting protein 2 1 S(0.173)S(0.173)T(0.173)S(0.173)PS(0.086)IINEDVIINGHS(0.221)HEDDNPFAEYMWMENEEEFNR 130.26 1.60E-08 48012000 12896 8722.6 7043.8 7331.6 10408 11017 10420 11034 11789 TRUE FALSE 11191.76093 8665.300666 10450.20524 8996.351836 10200.90116 11440.83112 9409.470004 8674.464967 10395.31785 1.076615558 0.833577269 1.005280011 0.86542345 0.981297668 1.100575402 0.905164242 0.834458849 1 13.34364625 2.03172108 24.99983591 0.894726725 0.969984423 0.085797133 0.090708666 379.5782028 299149.4803 0.035709408 0.024075071 107.5774089 -2.03172108 0.075257698 SSTVATLQGTPDHGDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSTVATLQGTPDHGDPR 17 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 ; 115.31 0.00032095 655600000 1085480 1144630 665490 1063850 1268660 1398850 1023010 1406570 1728350 FALSE TRUE 942031.0677 1137110.85 987323.1899 1305413.402 1243416.148 1452664.665 923798.6477 1105785.951 1524026.432 0.618119901 0.746122788 0.647838626 0.856555618 0.815875711 0.953175506 0.606156579 0.725568749 1 20.53945649 3.743848307 24.85752645 0.806841852 0.678236669 0.281481557 0.114165169 666.8464152 3134846.632 0.031276399 0.052195146 5544.320241 -3.743848307 -0.128605183 SSVASGPIS(ph)PTNYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSVASGPISPTNYR 14 0 Q9BYK8 Q9BYK8 HELZ2 Helicase with zinc finger domain 2 1 SSVASGPIS(0.98)PT(0.02)NYR 130.01 6.77E-05 185230000 112500 137570 70936 91040 146700 118800 117320 153770 119310 TRUE FALSE 97632.83996 136666.2936 105240.8869 111712.0235 143780.957 123370.3129 105942.3245 120887.4821 105205.3077 0.928021999 1.299043713 1.000338188 1.06184779 1.366670182 1.17266244 1.007005509 1.149062578 1 16.68284797 0.246090433 1.204011463 7.66E-11 1.133826991 0.066395204 0.135592148 42.36998654 7.742419662 105.8696909 0.039540266 1.762342979 -0.246090433 1.13382699 SSVKT(ph)PETVVPTALELQPSTSTDRPVTSEPTSQATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSVKTPETVVPTALELQPSTSTDRPVTSEPTSQATR 36 2 Q14676;Q14676-2;H0Y6Z8 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 S(0.136)S(0.136)VKT(0.727)PETVVPTALELQPSTSTDRPVTSEPTSQATR 94.849 0.021312 81200000 8667.7 4606.1 2082 3277.9 5477.6 2431.3 4680.6 5255.2 4860.1 TRUE FALSE 7522.241484 4575.842226 3088.862164 4022.197295 5368.606477 2524.833684 4226.676132 4131.416376 4285.544515 1.755259211 1.067738816 0.720763057 0.938549881 1.252724469 0.589151198 0.9862635 0.964035343 1 12.06526281 4.716171949 3.63751246 0.927616325 1.829136647 0.68818999 0.174859367 0.137489429 3.362441868 0.041362647 0.32482824 52020.19184 -4.716171949 0.901520322 SSVLDQALPNDILFS(ph)TTPPYHSTLPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SSVLDQALPNDILFSTTPPYHSTLPPR 27 0 Q9P2F8;Q9P2F8-2 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 SSVLDQALPNDILFS(0.312)T(0.312)T(0.312)PPY(0.047)HS(0.009)T(0.009)LPPR 53.55 0.058325 27151000 7250.1 8953.7 5065.9 9048.4 13827 17758 14110 15763 12633 TRUE FALSE 6291.980916 8894.882555 7515.786184 11102.97752 13551.86975 18441.16175 12741.61437 12392.20512 11139.54113 0.564833043 0.798496316 0.674694415 0.996717673 1.216555475 1.655468707 1.143818603 1.112452028 1 13.44340218 3.533167104 2.652552395 1.225641364 0.68722695 0.662037252 0.177891325 0.184809629 2.568044718 0.056699945 0.087080258 3413.242179 -3.533167104 -0.538414414 SSVQGAS(ph)SREGS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSVQGASSREGSPAR 15 1 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 2 S(0.001)S(0.001)VQGAS(0.552)S(0.446)REGS(1)PAR;S(0.001)S(0.001)VQGAS(0.541)S(0.457)REGS(1)PAR 87.062 0.0041631 832980000 1228390 1325830 462530 427280 1186200 1251590 1174900 1186720 159104 TRUE FALSE 1066055.149 1317120.535 686211.0551 524300.4546 1162596.941 1299739.477 1060958.379 932949.1631 140294.9064 7.598673229 9.388227766 4.891204341 3.737131077 8.286807916 9.26433832 7.562344252 6.64991472 1 17.09810311 4.244794284 24.98819077 6.19399292 8.493450646 0.158132213 2.408305073 308.789004 1237773.42 0.621446617 1.559419474 17570.91118 -4.244794284 2.299457726 SSVQGASS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SSVQGASSR 9 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 SSVQGAS(0.021)S(0.979)R;SSVQGAS(0.013)S(0.987)R;SSVQGAS(0.048)S(0.952)R;SSVQGAS(0.069)S(0.931)R 83.652 0.016809 708704000 7322740 6482040 4161090 5550950 4193510 6798100 6567470 7480350 9672800 TRUE FALSE 6355021.356 6439459.052 6173407.042 6811378.038 4110067.355 7059627.306 5930557.77 5880735.365 8529292.603 0.745081879 0.754981609 0.723788868 0.798586513 0.481876698 0.827692006 0.695316487 0.689475158 1 23.02399466 1.235711769 24.99406266 1.000000387 0.712953451 0.482367745 0.09289943 66.17713342 580486.5124 0.143121571 0.021160946 17.20726191 -1.235711769 -0.287046937 SSVQGASS(ph)REGS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSVQGASSREGSPAR 15 1 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 2 SSVQGAS(0.074)S(0.926)REGS(1)PAR;SSVQGAS(0.065)S(0.935)REGS(1)PAR;SSVQGAS(0.02)S(0.98)REGS(1)PAR 215.59 2.77E-11 1511940000 2690470 2946580 905740 881310 2468550 2707020 2741070 2747130 163418 TRUE FALSE 2334917.573 2927223.722 1343758.894 1081424.905 2419430.685 2811160.811 2475241.453 2159677.628 144098.9102 16.20357551 20.31398931 9.325253686 7.504740348 16.79006927 19.50855011 17.17737802 14.98746677 1 17.1366999 1.23908734 7.922655324 0.818716636 15.23539951 0.552303484 4.025949852 0.078078524 42.22320744 6.08226118 1.058533753 17.34152713 -1.23908734 14.41668287 SSVSHS(ph)VLSEMQVIEQETPVSAK ddPTM_MDA-MB-175_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(0.059)S(0.059)VS(0.072)HS(0.405)VLS(0.405)EMQVIEQETPVSAK 155.8 1.59E-08 32628000 100640 88420 46209 56488 84762 66265 106500 94036 91990 TRUE FALSE 87340.16901 87839.1632 68555.82696 69314.46377 83075.40203 68814.25743 96171.64639 73927.13319 81115.047 1.076744356 1.08289604 0.845167814 0.854520417 1.024167588 0.848353789 1.1856203 0.911386185 1 16.30768194 0.960444739 15.63059449 1.097612225 0.976428578 0.003060077 0.115548653 5282478.799 65085927.48 17988728.02 0.027368872 9.129452616 -0.960444739 -0.121183647 SSVSHSVLS(ph)EMQVIEQETPVSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSVSHSVLSEMQVIEQETPVSAK 23 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;Q8N6H7-3 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 S(0.075)S(0.075)VS(0.075)HS(0.335)VLS(0.442)EMQVIEQETPVSAK;S(0.193)S(0.193)VS(0.193)HS(0.193)VLS(0.227)EMQVIEQETPVSAK 139.4 1.33E-07 110876000 163882 147455 54644 96214 122155 89529 174059 145762 137759 TRUE FALSE 142224.5785 146486.3584 81070.02117 118060.8592 119724.3545 92973.23856 157178.785 114591.9306 121473.288 1.170830072 1.205914163 0.6673897 0.971907991 0.985602321 0.765380111 1.293937026 0.94335086 1 16.89027957 SSVVGGFVSHYLLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSVVGGFVSHYLLEK 15 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ; 153.09 2.72E-06 1106450000 1032670 862430 504820 738510 847200 806450 1054830 1166950 1096020 FALSE TRUE 896200.043 856764.6405 748952.6405 906199.9829 830342.3775 837474.6533 952532.749 917406.8237 966449.7642 0.927311565 0.886507165 0.774952479 0.937658652 0.859167655 0.866547527 0.985599857 0.949254537 1 19.88233522 2.240740621 24.98621 0.972541632 0.873396403 0.530874486 0.045479808 43.7810853 501808.4815 0.017059391 0.012558891 174.0766905 -2.240740621 -0.099145229 SSWSSSDEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSWSSSDEKR 10 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;Q9ULU4-2 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 0 ; 148.9 3.90E-05 133351000 154369 126400 97606 103688 126218 121261 146110 167769 124372 FALSE TRUE 133968.7455 125569.6701 144808.5881 127231.9452 123706.5087 125925.9891 131940.2747 131892.9049 109668.8838 1.221574806 1.14498904 1.320416357 1.160146258 1.128000071 1.148238085 1.203078486 1.202646551 1 16.74279472 1.236352043 24.99723519 0.999999754 1.190551457 0.547525482 0.054603693 46.4567502 525683.0486 0.085067734 0.013196017 17.23264902 -1.236352043 0.190551703 SSWYWGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSWYWGR 7 0 P46108-2;P46108;I3L297 P46108-2 CRK Adapter molecule crk 0 ; 139.27 0.0062933 2396100000 1483260 1649020 983860 1007570 1779800 1668170 1618720 1742060 1818070 FALSE TRUE 1287243.433 1638187.479 1459657.987 1236354.168 1744385.462 1732345.579 1461736.784 1369534.026 1603139.836 0.802951436 1.021861875 0.91049948 0.771207939 1.088105618 1.080595429 0.911796183 0.854282325 1 20.61246884 3.238766375 25 0.969416693 0.889423135 0.229610129 0.096260998 12.33244886 1498252.865 0.030759157 0.037250455 1732.871565 -3.238766375 -0.079993557 SSYSS(ph)PTSLS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SSYSSPTSLSPR 12 0 Q96JY6;Q96JY6-5;Q96JY6-3;Q96JY6-4;C9JS55;C9JSR2;C9K0F0;C9J0X3;Q96JY6-2;C9J760;A0A087WXJ0 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 2 SSYS(0.043)S(0.957)PTS(0.001)LS(0.999)PR;SSYSS(0.999)PT(0.001)SLS(1)PR 246.77 2.09E-16 1156390000 1453670 1319320 761030 882300 1194520 1278340 1183890 1281760 1227160 TRUE FALSE 1261563.826 1310653.3 1129066.653 1082639.7 1170751.389 1327518.567 1069076.53 1007665.599 1082086.543 1.165862227 1.211227798 1.043416223 1.000511195 1.081938775 1.226813674 0.98797692 0.931224591 1 20.04538446 -2 0.127237493 0.17516032 1.283712135 0.347491504 0.080889987 224.104589 2.511359215 44.06224165 2.552783944 0.01 2 1.108551816 SSYSSPTSLS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SSYSSPTSLSPR 12 0 Q96JY6;Q96JY6-5;Q96JY6-3;Q96JY6-4;C9JS55;C9JSR2;C9K0F0;C9J0X3;Q96JY6-2;C9J760;A0A087WXJ0 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 SSYSSPTSLS(1)PR;SSYSSPTSLS(1)PR;SSYSSPTSLS(1)PR 237.48 4.38E-16 1214590000 1150550 1166380 661890 810020 1136930 1202200 1129140 1289280 1167180 TRUE FALSE 998501.9024 1158717.973 981982.2179 993947.4214 1114307.317 1248449.412 1019636.177 1013577.505 1029197.31 0.970175391 1.12584629 0.954124353 0.965750116 1.082695521 1.213032137 0.990710106 0.984823314 1 19.97308816 2.074915086 24.99999267 0.990197906 1.052792658 0.113756979 0.07900086 83.4478325 27844.64071 0.033224189 0.02239974 118.8269874 -2.074915086 0.062594752 ST(ph)PDSTYSESFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STPDSTYSESFK 12 0 Q6ISB3;Q6ISB3-2 Q6ISB3 GRHL2 Grainyhead-like protein 2 homolog 1 S(0.206)T(0.794)PDSTYSESFK;S(0.36)T(0.64)PDSTYSESFK 327.17 5.21E-57 1788900000 3055300 2163500 1819220 2024330 2261300 1782270 2606600 3197400 3270900 TRUE FALSE 2651534.364 2149287.826 2699000.877 2483985.066 2216304.554 1850835.08 2353812.333 2513660.892 2884217.928 0.919325249 0.745189122 0.935782574 0.861233488 0.768424789 0.641711246 0.816100722 0.871522525 1 21.45974875 1.32061827 2.384731523 1.02862355 0.809184906 0.328322561 0.084869572 0.587796165 4.142010941 0.250964779 0.023330211 20.92272613 -1.32061827 -0.219438645 ST(ph)PLSQPSANGVQTEGLDYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STPLSQPSANGVQTEGLDYDR 21 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 1 S(0.206)T(0.793)PLS(0.001)QPSANGVQTEGLDYDR 373.04 1.94E-111 530430000 82569 96300 49237 70926 96661 94668 89790 114220 121150 TRUE FALSE 71657.29745 95667.39896 73048.17789 87030.83234 94737.63521 98309.93922 81082.17962 89794.94186 106827.785 0.67077397 0.895529182 0.683793808 0.814683486 0.886825794 0.920265633 0.758998978 0.84055793 1 16.7049274 3.468371711 6.21516678 0.867847266 0.761911273 0.323077247 0.085277213 0.207572831 33.42395377 0.023627821 0.031895704 2940.165051 -3.468371711 -0.105935993 ST(ph)PVRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STPVRDR 7 1 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 S(0.206)T(0.794)PVRDR 81.95 0.041729 365710000 765920 618670 403060 476690 478180 589210 623380 718230 546490 TRUE FALSE 664701.7314 614605.916 597981.1642 584929.7503 468665.1535 611877.29 562924.7035 564642.1038 481884.5748 1.379379557 1.275421435 1.240921987 1.213837879 0.972567246 1.269759029 1.16817332 1.171737244 1 18.8783281 4.265787797 1.101372869 1.13488107 1.397740867 0.478862483 0.089012806 0.793039848 1.353364316 0.028723513 0.203802941 18441.14135 -4.265787797 0.262859797 ST(ph)TPPPAEPVSLPQEPPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STTPPPAEPVSLPQEPPKPR 20 1 Q9UN86-2 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 S(0.073)T(0.463)T(0.463)PPPAEPVSLPQEPPKPR 185.5 5.86E-17 3515000000 1979600 1429900 1000800 1207200 1491900 1230000 1660800 1923200 1658400 TRUE FALSE 1717990.844 1420506.893 1484790.227 1481313.211 1462214.109 1277318.896 1499735.872 1511938.646 1462345.841 1.174818429 0.971389156 1.015348207 1.012970509 0.999909917 0.873472512 1.025568528 1.033913185 1 20.47985311 4.74305138 24.87111255 0.994454778 1.174818507 0.616403994 0.045379438 312.2084099 1729034.557 0.011458119 0.088815399 55341.55778 -4.74305138 0.180363729 ST(ph)TPTSSPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STTPTSSPFR 10 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;H7C5N8;A0A2R8YET2;A0A2R8Y7F4;A0A2R8Y424 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.04)T(0.48)T(0.48)PTSSPFR 118.23 0.0095258 1433900000 1216300 1198500 666310 827990 1202000 1233800 1113300 1226200 1110700 TRUE FALSE 1055562.873 1190626.975 988539.7447 1015997.785 1178082.552 1281265.084 1005332.337 963986.6723 979394.3113 1.077771089 1.215676833 1.009337846 1.037373582 1.202868485 1.308221898 1.026483742 0.984268196 1 19.90153029 2.022417239 24.99829137 0.995319986 1.139738009 0.359024823 0.087942914 250.4601756 279296.129 0.037534994 0.025304329 105.2973008 -2.022417239 0.144418023 STAGDTHLGGEDFDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 STAGDTHLGGEDFDNR 16 0 P11142;E9PKE3;P11142-2;E9PN89;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 ;;;;;;;;;;; 229.54 3.09E-15 1.27067E+11 41966660 38788660 20581760 29131140 40981640 43508580 37156810 43557440 41818300 FALSE TRUE 36420659.55 38533854.74 30535167.98 35745810.58 40166185.54 45182383.23 33553348.29 34243020.42 36874588.21 0.987689933 1.044997561 0.828081599 0.969388739 1.089264653 1.225298652 0.909931471 0.928634653 1 25.1361236 5.114624921 12.95686811 0.994646591 0.775980932 0 0.107823371 3349686.182 5151716.401 0.027796264 20872193.16 130204.1782 -5.114624921 -0.218665658 STAPSAAASASASAAAS(ph)SPAGGGAEALELLEHCGVCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 STAPSAAASASASAAASSPAGGGAEALELLEHCGVCR 37 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 STAPSAAASAS(0.001)AS(0.003)AAAS(0.498)S(0.498)PAGGGAEALELLEHCGVCR;STAPSAAASASAS(0.001)AAAS(0.499)S(0.499)PAGGGAEALELLEHCGVCR;S(0.001)T(0.001)APS(0.001)AAAS(0.003)AS(0.008)AS(0.019)AAAS(0.484)S(0.484)PAGGGAEALELLEHCGVCR;STAPSAAASASAS(0.004)AAAS(0.498)S(0.498)PAGGGAEALELLEHCGVCR;STAPSAAASAS(0.001)AS(0.001)AAAS(0.499)S(0.499)PAGGGAEALELLEHCGVCR 127.95 9.85E-09 164299400 58168.4 55313.7 31464.2 37108.7 49662 50904.4 51621.8 62859.4 55944.8 TRUE FALSE 50481.29856 54950.34066 46680.39236 45534.79751 48673.82336 52862.72521 46615.52578 49417.40648 49331.06948 1.023316524 1.113909373 0.946267593 0.92304501 0.986676832 1.071590901 0.944952669 1.001750155 1 15.59020894 4.235099464 24.99999827 0.983070236 1.06861295 0.380140299 0.045944932 85.00642539 614023.8619 0.011694203 0.025998162 17183.01874 -4.235099464 0.085542715 STAPSAAASASASAAASS(ph)PAGGGAEALELLEHCGVCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 STAPSAAASASASAAASSPAGGGAEALELLEHCGVCR 37 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 STAPSAAASASASAAAS(0.034)S(0.966)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.003)S(0.997)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.004)S(0.996)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.199)S(0.801)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.176)S(0.824)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.002)S(0.998)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.027)S(0.973)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.004)S(0.996)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.006)S(0.994)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.149)S(0.851)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.047)S(0.953)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAASS(1)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.008)S(0.992)PAGGGAEALELLEHCGVCR 421.91 1.78E-220 41431979000 2539714.6 2212524.8 1082613.4 1247436.3 1918007.2 2074664.6 1907153.9 2145563.3 1958525.5 TRUE FALSE 2204084.881 2197990.579 1606168.861 1530685.778 1879842.609 2154478.29 1722198.408 1686751.285 1726990.847 1.276257419 1.272728563 0.930039012 0.886331147 1.08850757 1.247533126 0.997224978 0.976699609 1 20.71982901 4.251520834 24.98344274 1.019248743 1.274493199 0.545550696 0.097301505 185.9158353 358383.7619 0.026282956 0.068610343 17845.17594 -4.251520834 0.255244455 VVSS(ph)TSEEEEAFTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVSSTSEEEEAFTEK 15 0 Q8N573-2;Q8N573-3;Q8N573-5;Q8N573-8;Q8N573 Q8N573-2 OXR1 Oxidation resistance protein 1 1 VVSS(0.957)T(0.039)S(0.004)EEEEAFTEK;VVSS(0.999)TSEEEEAFTEK 415.32 2.16E-133 624250000 508270 693540 641490 852390 998620 926510 1179470 1407970 1398350 TRUE FALSE 441100.8317 688984.0901 951716.7097 1045938.177 978749.4158 962153.4392 1065085.181 1106886.572 1233038.656 0.357734796 0.558769254 0.771846612 0.848260655 0.793770261 0.780310848 0.863788962 0.897690082 1 20.2337866 4.80743813 0.848821959 0.878914582 3.54E-17 0.899523 0.057776998 0.817944925 0.427301666 0.022477317 0.693416768 64185.6776 -4.80743813 -0.878914582 down STAQQELDGKPAS(ph)PTPVIVASHTANKEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 STAQQELDGKPASPTPVIVASHTANKEEK 29 2 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 1 STAQQELDGKPAS(0.492)PT(0.492)PVIVAS(0.015)HT(0.002)ANKEEK;STAQQELDGKPAS(0.992)PT(0.008)PVIVASHTANKEEK;STAQQELDGKPAS(0.862)PT(0.138)PVIVASHTANKEEK 202.88 1.34E-25 1400630000 1052220 702224 771133 629162 669886 434366 1068510 1295360 928427 TRUE FALSE 913166.461 697611.0443 1144055.498 772022.8482 656556.5792 451076.3411 964886.0647 1018357.345 818669.4177 1.115427597 0.852127891 1.397457232 0.943021483 0.801980097 0.550987164 1.178602796 1.243917658 1 19.64292148 0.927678473 21.61353215 0.272684442 1.019818707 0 0.242317364 8092.074942 3177919.95 91988.55017 0.060403001 8.466004072 -0.927678473 0.747134265 STAS(ph)PASTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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(1)PASTK;STAS(0.989)PAS(0.011)TK;STAS(0.998)PAS(0.002)TK;STAS(0.994)PAS(0.006)TK;STAS(0.999)PASTK;STAS(0.998)PAS(0.002)TK 177.57 5.45E-05 3454539000 9384790 7539280 5138600 6302280 4742090 6465950 8754320 9564850 10336830 TRUE FALSE 8144566.223 7489753.973 7623644.148 7733308.998 4647731.687 6714699.281 7905327.394 7519481.261 9114821.733 0.893551894 0.821711515 0.836400795 0.848432281 0.509909225 0.736679167 0.867304663 0.824972938 1 23.11978301 0.943326174 1.346609993 1.257122892 0.778313791 0.277876437 0.107513379 3.859563607 3.509139048 3.103228524 0.03337774 8.776597337 -0.943326174 -0.478809102 STAYEDYYYHPPPR ddPTM_MDA-MB-175_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 ;;;;; 170.95 3.09E-06 4027000000 2540640 2297670 1345680 1607250 2205120 2315650 2197150 2582050 2339670 FALSE TRUE 2204887.987 2282576.454 1996455.349 1972200.678 2161242.426 2404734.554 1984070.731 2029898.701 2063076.878 1.068737675 1.106394279 0.967707685 0.955951132 1.047582109 1.165605887 0.961704701 0.983918109 1 20.97636615 2.385190531 0.013457489 1.71E-05 2.034393706 0.07383411 0.066574178 6186.751793 58.51568888 4506.355233 4337.912525 242.7674915 -2.385190531 2.034376656 STDEPSEKDALQPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 STDEPSEKDALQPGR 15 1 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;;; 193.06 9.89E-08 3212290000 2605540 2123800 1332980 1500060 2060590 1891930 2622010 2729970 1181470 FALSE TRUE 2261211.287 2109848.618 1977613.587 1840671.55 2019588.29 1964713.771 2367727.874 2146187.16 1041797.963 2.170489259 2.025199409 1.898269778 1.766821991 1.938560415 1.885887516 2.272732294 2.060080013 1 19.99064409 1.236548257 24.98922191 0.99999872 2.002127537 0.82517713 0.144979375 22.89878866 284278.7819 0.2422176 0.038074324 17.2404365 -1.236548257 1.002128817 STDEYS(ph)EADEEEEEEEGKPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STDEYSEADEEEEEEEGKPSR 21 1 Q96T23-2;Q96T23;Q96T23-3 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 S(0.001)T(0.001)DEYS(0.998)EADEEEEEEEGKPSR 99.711 0.00048239 172990000 84748 84931 60762 57991 73519 62174 73647 90974 85981 TRUE FALSE 73548.33708 84373.08267 90146.70644 71158.74289 72056.11574 64565.87401 66504.72528 71519.91806 75816.42413 0.970084489 1.112860223 1.189012902 0.938566329 0.950402457 0.851608009 0.877180981 0.943330141 1 16.21022279 3.627115617 6.917818849 0.922041349 1.092302571 0.57858184 0.065922836 0.173081261 9.47631623 0.018461096 0.027471684 4237.557627 -3.627115617 0.170261221 STDSEVSQS(ph)PAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 STDSEVSQSPAK 12 0 O75175;H7C3F5;A0A2H2FJL5;B7Z6J7;A0A0G2JNJ7;H7C148 O75175 CNOT3 CCR4-NOT transcription complex subunit 3 1 STDSEVSQS(1)PAK;STDSEVSQS(1)PAK;STDSEVSQS(1)PAK;STDSEVSQS(1)PAK 246.47 1.59E-16 2071110000 3891010 3457940 2655240 2657050 3221240 2859240 4293340 4184920 4220290 TRUE FALSE 3376803.17 3435224.564 3939322.945 3260373.813 3157143.626 2969236.813 3876972.548 3290007.425 3721372.124 0.90740809 0.923106975 1.058567328 0.876121416 0.848381597 0.797887638 1.041812648 0.884084503 1 21.82740323 1.222264916 24.47325099 1.000000302 0.918906918 0.095660393 0.079877269 2019.251058 3032334.716 0.497171148 0.019432526 16.6826453 -1.222264916 -0.081093384 STEDGAELEEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 STEDGAELEEQK 12 0 Q8IVF2;Q8IVF2-3;Q8IVF2-2 Q8IVF2 AHNAK2 Protein AHNAK2 0 ;;; 84.658 0.012113 3128660000 3791290 3584240 2225210 3336900 3164320 3443230 3541370 4405980 4709310 FALSE TRUE 3290261.421 3560694.891 3301328.999 4094594.146 3101356.223 3575693.286 3197928.482 3463795.464 4152580.737 0.792341348 0.857465542 0.795006577 0.986036011 0.746850313 0.861077367 0.770106275 0.834130793 1 21.98557679 1.23979749 8.491799846 1.001550962 0.830570168 0.394797763 0.066012207 0.083237752 67.25048981 0.083620555 0.014942549 17.36990687 -1.23979749 -0.170980794 STELDSNWNWFQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 270.67 1.43E-32 683790000 383180 448080 288280 325540 440120 443420 458680 496590 441600 FALSE TRUE 332541.7921 445136.533 427693.1722 399458.8326 431362.4731 460478.6543 414197.2842 390398.093 389394.5511 0.853997035 1.14315039 1.098354281 1.025845974 1.107777374 1.182550329 1.063695635 1.002577185 1 18.57087317 4.749843585 24.72097887 1.074636495 0.853996884 0.587403442 0.05893855 1174.930991 2574216.531 0.015623545 0.231077196 56213.88292 -4.749843585 -0.220639612 STESLQANVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STESLQANVQR 11 0 P26373;J3QSB4 P26373 RPL13 60S ribosomal protein L13 0 150.1 7.92E-05 151190000 48620 48595 36028 32119 41104 53930 46850 53628 51461 FALSE TRUE 42194.74381 48275.77625 53451.26131 39412.10986 40286.11082 56004.722 42306.49421 42160.06953 45377.3392 0.929863772 1.063874107 1.177928504 0.868541667 0.887802404 1.234200219 0.932326464 0.92909964 1 15.4696844 3.732794971 24.965593 0.974964698 1.057887324 0.099398878 0.116194444 1143.122022 4949791.583 0.032159889 0.049190102 5404.990946 -3.732794971 0.082922626 STETSDFENIES(ph)PLNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STETSDFENIESPLNER 17 0 Q96K76-2;Q96K76-4;Q96K76 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 1 STETSDFENIES(1)PLNER;STETSDFENIES(1)PLNER 363.87 7.08E-91 630840000 558270 535820 318590 398620 497110 548780 512210 532680 537910 TRUE FALSE 484493.205 532300.1631 472661.1896 489132.7635 487218.4836 569891.9217 462535.953 418770.5273 474318.8926 1.021450363 1.122241116 0.996505088 1.03123188 1.02719603 1.201495303 0.975158191 0.882888145 1 18.85549781 2.012637259 24.99386606 0.931862183 1.064757803 0.410561979 0.06507392 182.825601 361589.6684 0.025600432 0.017247915 102.9525858 -2.012637259 0.132895621 STFAGS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STFAGSPER 9 0 H0YE03;H7C3G7;Q2TBE0-3;Q2TBE0-2;Q2TBE0 H0YE03 CWF19L2 CWF19-like protein 2 1 STFAGS(1)PER 92.445 0.010565 311030000 323230 251030 200680 251140 291350 275740 271900 319710 413350 TRUE FALSE 280514.3365 249380.9674 297729.5192 308165.1754 285552.705 286347.8962 245531.1798 251342.5045 364484.2339 0.769619946 0.684202345 0.816851571 0.845482868 0.783443229 0.785624918 0.673640056 0.689584023 1 18.47549689 4.391041809 0.008762876 1.521496767 1.20E-07 0.028809312 0.094508924 83611.74211 255.1818897 21537.48877 22780.3572 24606.04469 -4.391041809 -1.521496647 STFDAHIYEGR ddPTM_MDA-MB-175_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 ;;; 116.84 0.00093537 2039290000 3287880 3562070 2017230 2353850 3643740 4115310 3279720 3713380 3178570 FALSE TRUE 2853378.328 3538670.528 2992769.175 2888327.619 3571236.703 4273628.639 2961653.259 2919302.585 2802803.076 1.018044526 1.262546969 1.067777184 1.030513932 1.274166114 1.524769498 1.056675471 1.041565356 1 21.41843895 2.029860761 24.99940717 1.03136163 1.197912641 0.217050487 0.147281048 314.5011116 263298.8335 0.062529187 0.04215659 107.1175821 -2.029860761 0.166551011 STFREES(ph)PLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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;S(0.002)T(0.002)FREES(0.997)PLR;STFREES(1)PLR;STFREES(1)PLR 153.81 9.45E-06 24470950000 15414000 13938060 6066560 6865050 12534900 13685960 12941940 13430800 3316865 TRUE FALSE 13377000.85 13846499.97 9000368.707 8423864.528 12285480.01 14212467.74 11686832.65 10558727.94 2924748.998 4.573726106 4.734252401 3.077313203 2.880200842 4.200524565 4.859380325 3.995841235 3.610131312 1 21.47988139 4.248996365 24.84301304 3.493906081 4.653989986 0.206286373 1.022628066 342.5779405 815512.3848 0.260427711 0.673017086 17741.74632 -4.248996365 1.160083905 STFS(ph)PAPRPEMPGTVEVESTFLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STFSPAPRPEMPGTVEVESTFLAR 24 1 Q92576-2;Q92576;E7EVH3;E7ER40 Q92576-2 PHF3 PHD finger protein 3 1 ST(0.001)FS(0.999)PAPRPEMPGTVEVESTFLAR;ST(0.005)FS(0.994)PAPRPEMPGTVEVESTFLAR 196.8 1.17E-24 261410000 125624 102368 76252 75525 96235 111070 100683 117410 120159 TRUE FALSE 109022.4701 101695.5379 113127.7222 92674.10558 94320.11178 115342.9348 90918.77816 92302.78519 105953.9399 1.028960983 0.959808932 1.067706612 0.874664082 0.890199193 1.088613929 0.858097191 0.871159537 1 16.69307771 3.736677525 24.99372295 0.924669148 1.01292385 0.235843159 0.074248799 245.3581909 3256577.251 0.020266852 0.031903368 5453.527715 -3.736677525 0.088254702 STFS(ph)TNYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 STFSTNYR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.001)T(0.076)FS(0.904)T(0.019)NYR;S(0.004)T(0.267)FS(0.462)T(0.267)NYR;S(0.002)T(0.051)FS(0.721)T(0.226)NYR;S(0.009)T(0.323)FS(0.634)T(0.033)NYR 156.26 0.00041511 1718090000 1163420 1645790 840240 786070 1418070 1347860 1256760 1257410 1459410 TRUE FALSE 1009671.099 1634978.697 1246582.874 964559.2078 1389853.181 1399713.046 1134879.609 988522.6567 1286880.212 0.784588254 1.27049797 0.968686023 0.749533017 1.080017525 1.08767936 0.881884419 0.768154368 1 20.29544634 2.077794915 8.281375415 0.854891142 0.994768989 0.085110605 0.158295527 0.496577318 46.71622046 0.063514761 0.042731097 119.6175532 -2.077794915 0.139877847 STFSTNYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 STFSTNYR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;; 199.07 0.00030447 32206400000 12977020 12124080 7048450 8967800 13189970 13729020 12420500 13475100 13398230 FALSE TRUE 11262073.93 12044436.12 10457104 11004076.05 12927515.4 14257184.28 11215961.82 10593554.73 11814306.51 0.9532573 1.019478893 0.885122117 0.93141955 1.094225496 1.206772845 0.949354227 0.896671736 1 23.49403161 4.780209812 19.16170123 0.991637016 0.953254987 0.017176904 0.096281266 6223.89984 2862182.151 0.025668045 4.064430848 60285.07585 -4.780209812 -0.038382029 STGS(ph)PTQETQAPFIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 STGSPTQETQAPFIAK 16 0 O15231-3;H0Y704;O15231-2 O15231-3 ZNF185 Zinc finger protein 185 1 STGS(1)PTQETQAPFIAK;STGS(1)PTQETQAPFIAK;STGS(0.999)PTQETQAPFIAK;STGS(1)PTQETQAPFIAK;S(0.059)T(0.059)GS(0.881)PTQETQAPFIAK 454.11 1.32E-182 2547540000 2880660 2350350 1611150 2085960 2257880 2085690 2750020 2928390 3140790 TRUE FALSE 2499973.482 2334910.396 2390307.529 2559609.1 2212952.605 2165927.844 2483323.484 2302176.587 2769489.384 0.902683901 0.843083353 0.863086005 0.924216975 0.799047152 0.782067574 0.896671963 0.831263915 1 21.40118858 1.233087695 24.98889927 1.000000232 0.854055228 0.507857046 0.044762462 148.0103296 675728.3824 0.09134136 0.01078279 17.10360646 -1.233087695 -0.145945004 STGSVDYLALDFQPS(ph)SPSPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STGSVDYLALDFQPSSPSPHR 21 0 Q9UQC2;Q9UQC2-2 Q9UQC2 GAB2 GRB2-associated-binding protein 2 1 STGSVDYLALDFQPS(0.621)S(0.36)PS(0.019)PHR 102.07 0.00030301 96402000 103480 100810 57954 84107 96520 111430 86162 106320 178790 TRUE FALSE 89804.85582 100147.7725 85980.74824 103204.7798 94599.44084 115716.7842 77806.0225 83584.29538 157653.6499 0.569633852 0.635239162 0.545377467 0.654629816 0.600045993 0.73399369 0.493525031 0.530176723 1 17.26639905 1.233101633 24.99992568 1.000000641 0.593521989 0.775425422 0.068434838 84.15752921 385365.1841 0.143955584 0.017066291 17.10415537 -1.233101633 -0.406478652 STHALSEVEVESDSFMNAVLWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 STHALSEVEVESDSFMNAVLWLR 23 0 C9JIF9;P13798 C9JIF9 APEH Acylamino-acid-releasing enzyme 0 ;;;;; 263.31 7.09E-44 1262157000 710174 730146 316074 500765 682757 722343 613264 761820 679753 FALSE TRUE 616322.7065 725349.6229 468928.4436 614471.347 669171.4715 750132.0026 553789.7517 598910.7215 599393.3747 1.028244109 1.21013954 0.782338383 1.025155387 1.116414528 1.251485309 0.923917039 0.999194764 1 19.19314361 STHDHWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 STHDHWK 7 0 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ;; 110.63 0.0067597 350110000 998960 985400 344563 662140 891540 897420 946730 1085350 990070 FALSE TRUE 866944.905 978926.8425 511194.8193 812489.0072 873800.0983 931944.3281 854916.2703 853256.3487 873025.0525 0.993035541 1.121304411 0.585544273 0.930659441 1.00088777 1.067488642 0.979257431 0.977356086 1 19.73566353 3.312981381 5.177270306 1.002702198 0.897459738 0.115998595 0.134311036 0.465066552 22.41344886 0.039706432 0.051110502 2055.802456 -3.312981381 -0.10524246 STHHLASHGFYEFLNWFDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STHHLASHGFYEFLNWFDER 20 0 Q8TCJ2 Q8TCJ2 STT3B Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B 0 142.78 6.10E-08 293840000 216460 235150 100880 217410 348950 311770 205070 360650 327770 FALSE TRUE 187854.2626 233605.2842 149665.9054 266776.2634 342006.5777 323763.9936 185182.343 283527.8041 289021.404 0.649966611 0.808262921 0.517836753 0.923032896 1.183326124 1.12020767 0.640721899 0.980992411 1 18.14081681 3.600952637 6.522852566 0.972849715 0.675440539 0.476777516 0.15656043 0.232601243 11.39348911 0.04465256 0.066449799 3989.813881 -3.600952637 -0.297409176 STIGVMVTAS(ph)HNPEEDNGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 19 STIGVMVTASHNPEEDNGVK 20 0 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A494C099;A0A494C163;D6RCQ8;D6RF77;D6RC77 O95394-4 PGM3 Phosphoacetylglucosamine mutase 1 STIGVMVT(0.022)AS(0.978)HNPEEDNGVK;STIGVMVT(0.002)AS(0.998)HNPEEDNGVK;STIGVMVT(0.001)AS(0.999)HNPEEDNGVK;STIGVMVT(0.001)AS(0.999)HNPEEDNGVK;STIGVMVT(0.001)AS(0.999)HNPEEDNGVK;STIGVMVT(0.013)AS(0.987)HNPEEDNGVK;STIGVMVT(0.001)AS(0.999)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK;STIGVMVT(0.002)AS(0.998)HNPEEDNGVK;STIGVMVT(0.007)AS(0.993)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK;STIGVMVT(0.001)AS(0.999)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK;STIGVMVT(0.025)AS(0.975)HNPEEDNGVK;STIGVMVT(0.001)AS(0.999)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK;STIGVMVT(0.001)AS(0.999)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK 325.28 1.39E-67 42486860000 30818340 26946690 17726410 20937030 25605500 20048760 30094000 33944970 33738280 TRUE FALSE 26745618.29 26769675.42 26298961.17 25691102.66 25096000.65 20820048.77 27175488.51 26686102.33 29749778.97 0.899019059 0.899827708 0.884005262 0.863572892 0.843569314 0.699838772 0.913468585 0.897018507 1 24.82637561 1.293574294 1.773210685 1.03755195 0.853815015 0.363551029 0.059814259 0.964106767 3.167838151 0.294434462 0.017434202 19.65958264 -1.293574294 -0.183736935 STKPGAAPTEHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STKPGAAPTEHK 12 1 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 116.01 0.00053342 132600000 238620 199290 119530 136950 177430 154220 227170 275680 244340 FALSE TRUE 207085.7624 197980.8509 177335.1078 168046.5906 173899.4901 160152.9432 205139.0884 216727.9773 215454.4036 0.96115818 0.918899069 0.823074882 0.779963593 0.807128967 0.743326386 0.952122978 1.005911106 1 17.71702306 2.057060611 7.116513454 0.996345846 0.83789565 0.559269247 0.062678101 0.161472566 16.42265517 0.028215235 0.018865603 114.0408933 -2.057060611 -0.158450196 STLDIVLANKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STLDIVLANKDR 12 1 P23921 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ; 82.85 0.011028 536050000 1462490 1400550 1471090 921900 1096460 962330 1373950 1567420 588010 FALSE TRUE 1269218.241 1391349.695 2182514.045 1131231.485 1074642.591 999351.4578 1240704.54 1232239.431 518496.1277 2.447883742 2.683433146 4.209315997 2.181754935 2.072614498 1.927403898 2.392890659 2.376564385 1 18.98397369 3.510317503 24.92430518 2.046406231 3.091367173 0.442486956 0.59340458 600.1789766 450622.9868 0.160374317 0.237680556 3238.303157 -3.510317503 1.044960941 STLEPVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STLEPVEK 8 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;P17066;P48741 A0A0G2JIW1;P17066 HSPA1B;HSPA1A;HSPA6;HSPA7 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 6;Putative heat shock 70 kDa protein 7 0 ; 124.08 0.0030711 322320000 656880 633920 387990 498040 637830 555280 668510 824870 774140 FALSE TRUE 570071.6437 629755.7378 575623.2617 611127.5941 625138.4309 576641.9809 603678.0031 648477.9696 682622.0511 0.835120463 0.92255405 0.843253248 0.895264947 0.915789975 0.84474561 0.884351747 0.949980987 1 19.38072749 1.562009012 2.461987699 0.998889287 0.878083436 0.668324308 0.029738227 0.162512505 2.000978216 0.034896772 0.007579017 36.4761516 -1.562009012 -0.120805851 STLESEKPGS(ph)PEAAET(ph)SPPSNIIDHCEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.536)S(0.464)PPSNIIDHCEK;S(0.001)T(0.001)LES(0.037)EKPGS(0.962)PEAAET(0.529)S(0.47)PPS(0.001)NIIDHCEK 159.62 1.57E-10 577030000 591640 498020 427290 423480 456180 362520 712490 778250 694090 TRUE FALSE 513453.275 494748.4738 633928.8732 519637.6065 447102.9105 376466.379 643392.8295 611827.2938 612035.4709 0.838927316 0.808365687 1.03577146 0.849031847 0.730517971 0.615105491 1.051234544 0.999659861 1 19.22325574 2.191952281 24.99999764 1.014787826 0.820764991 0.453813735 0.105265217 123.9887452 66504.74626 0.045979094 0.030999206 155.5794676 -2.191952281 -0.194022835 STLESEKPGS(ph)PEAAETS(ph)PPSNIIDHCEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STLESEKPGSPEAAETSPPSNIIDHCEK 28 1 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 2 S(0.001)T(0.001)LES(0.007)EKPGS(0.99)PEAAET(0.204)S(0.794)PPS(0.001)NIIDHCEK 106.78 0.0011489 416860000 506390 393910 353670 326860 384510 298100 547740 630950 554620 TRUE FALSE 439469.2785 391322.3793 524705.995 401078.5587 376859.0033 309568.0999 494620.2591 496026.2526 489053.4554 0.898611948 0.800162794 1.07290111 0.8201119 0.770588571 0.632994403 1.011382812 1.01425774 1 18.89963264 2.101384403 24.58968444 1.009944839 0.837255547 0.365574228 0.109164393 11.28256454 2714.912071 0.046222378 0.031163109 126.2944899 -2.101384403 -0.172689292 STLINSLFLTDLYPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STLINSLFLTDLYPER 16 0 Q15019-2;Q15019-3;Q15019;B5MCX3;C9J2Q4;C9J938;C9JB25;C9IY94;C9IZU3;C9JQJ4;A0A1B0GXJ2;C9JZI2;B5MD47;F8WB65;C9JFT1 Q15019-2 2-Sep Septin-2 0 ; 236.55 6.82E-14 0 146987 140258 85126 114343 144712 158763 144063 159774 129263 FALSE TRUE 127562.2955 139336.636 126293.2183 140306.3258 141832.5143 164870.7153 130091.7924 125607.5735 113981.6754 1.119147399 1.222447692 1.108013353 1.23095511 1.244344881 1.446466853 1.141339535 1.101997957 1 16.79844238 1.655688271 2.421832387 1.018831194 1.225299069 0.377570411 0.09423521 0.288961283 3.652731883 0.09930504 0.026848586 45.25726145 -1.655688271 0.206467876 STLINSLFLTDLYS(ph)PEYPGPSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STLINSLFLTDLYSPEYPGPSHR 23 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1;A0A5F9ZGZ7 E7EPK1 7-Sep Septin-7 1 STLINSLFLTDLYS(1)PEYPGPSHR;STLINSLFLTDLYS(1)PEYPGPSHR 165.3 8.56E-12 232010000 184030 168454 104216 137996 158628 157250 190314 206395 154952 TRUE FALSE 159709.9692 167347.4146 154615.2062 169330.1009 155471.6132 163299.5093 171857.3776 162259.0354 136633.7511 1.168891053 1.224788262 1.131603319 1.239299219 1.137871221 1.195162308 1.257795941 1.18754725 1 17.05995437 1.240789285 7.020460726 0.99605389 1.194858847 0.691393955 0.040503042 0.056579042 16.36341245 0.05399884 0.009364343 17.40961973 -1.240789285 0.198804957 STLINSLFLTDLYSPEYPGPSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STLINSLFLTDLYSPEYPGPSHR 23 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1;A0A5F9ZGZ7 E7EPK1 7-Sep Septin-7 0 ; 210.74 6.09E-25 2512300000 715900 714520 356510 530310 700110 678730 724750 780320 745040 FALSE TRUE 621292.0011 709826.2711 528919.4285 650724.9908 686179.1807 704841.1823 654463.8566 613454.6405 656962.22 0.945704307 1.080467414 0.805098699 0.990505955 1.044472817 1.072879324 0.996197097 0.93377461 1 19.32545088 STLPDADRER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STLPDADRER 10 1 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ; 136.02 0.00011736 2601300000 876920 823290 576250 759880 726640 903850 592660 738010 1292910 FALSE TRUE 761032.8002 817881.7538 854926.4274 932422.368 712181.2856 938621.6944 535183.9244 580192.3047 1140063.653 0.667535359 0.717400078 0.749893592 0.817868692 0.624685546 0.823306394 0.469433372 0.508912203 1 20.12068295 2.259209672 24.99405684 0.620169351 0.732359827 0.029026893 0.153217756 538.9303448 652331.5209 0.056272622 0.043539832 181.6392383 -2.259209672 0.112190476 STLTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 STLTSR 6 0 H0YDZ5;M0R104;Q9Y2N7-4;Q9Y2N7-6;Q9Y2N7-7;Q9Y2N7-5;Q9Y2N7-3;Q9Y2N7-2;Q9Y2N7 H0YDZ5 HIF3A Hypoxia-inducible factor 3-alpha 0 ;;;;;;; 132.96 0.034132 6832490000 4831670 4271086 2172674 3234919 2761024 4722640 3414361 4599470 4263460 FALSE TRUE 4193152.568 4243028.955 3223386.414 3969456.802 2706085.024 4904323.017 3083236.796 3615909.134 3759438.616 1.11536668 1.128633657 0.857411636 1.055864241 0.719810935 1.304536001 0.820132235 0.961821565 1 21.84208581 4.262237888 24.86535543 0.959774761 1.122000393 0.158215931 0.155407946 378.5681319 397556.5211 0.035154184 0.092893785 18291.01846 -4.262237888 0.162225631 STMGKPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 STMGKPQR 8 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;; 83.168 0.016766 2614381000 4822770 4399890 2475593 3379259 4348320 3904860 5088300 5298170 4661870 FALSE TRUE 4185428.725 4370986.833 3672798.055 4146571.405 4261796.939 4055082.491 4594837.449 4165197.576 4110749.039 1.018166929 1.06330666 0.893461999 1.008714316 1.036744617 0.986458296 1.117761606 1.013245405 1 21.97096987 3.471034367 18.99946362 1.03201405 0.990857753 0.099936429 0.054065884 18.46389975 57625.58159 0.015379232 0.019995612 2958.24655 -3.471034367 -0.041156297 STMKPVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STMKPVQK 8 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 68.735 0.050834 630330000 479170 434820 266130 444700 493070 544660 574850 687870 628260 FALSE TRUE 415846.4704 431963.6388 394831.3582 545675.9318 483258.8717 565613.4226 519101.1355 540774.3535 553987.8185 0.750641903 0.779734905 0.712707653 0.984996264 0.872327614 1.020985306 0.937026263 0.976148456 1 19.07949473 3.735892 24.999999 0.963069803 0.750898823 0.850928916 0.042911323 78.23956429 732961.0864 0.011009237 0.017212789 5443.672631 -3.735892 -0.212170981 STNGDTFLGGEDFDQALLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 STNGDTFLGGEDFDQALLR 19 0 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;; 283.05 1.99E-39 385851000 387068 366176 236802 406189 469494 509592 343148 450994 413956 FALSE TRUE 335915.9831 363770.5657 351320.2393 498420.4207 460151.9879 529196.334 309869.5598 354552.4427 365018.5933 0.920270883 0.996580921 0.962472175 1.365465842 1.260626161 1.449779117 0.848914454 0.971327076 1 18.47761043 2.181180579 24.99999995 0.942791513 1.156858208 0.260499608 0.173985018 123.8496316 53958.98566 0.076527698 0.051594989 151.7681286 -2.181180579 0.214066695 STPDGTEHGEFLALDLGGTNFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STPDGTEHGEFLALDLGGTNFR 22 0 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 ; 181.29 5.02E-17 485545000 315320 317490 170949 224946 334970 350570 283665 328060 360870 FALSE TRUE 273649.6631 315404.3873 253620.5082 276023.4274 328304.7524 364056.6547 256155.212 257906.922 318208.3597 0.859970063 0.99118825 0.797026541 0.867429843 1.031728873 1.144082623 0.804992088 0.810497003 1 18.27961221 5.042253984 15.2228687 0.919588415 0.597814967 0.028563166 0.114183515 2195525.683 22957661.9 0.029505875 19589620.98 110218.37 -5.042253984 -0.321773448 STPESGDS(ph)DKESVGSSSTSNEGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STPESGDSDKESVGSSSTSNEGGR 24 1 Q6GQQ9;Q6GQQ9-2 Q6GQQ9 OTUD7B OTU domain-containing protein 7B 1 STPES(0.003)GDS(0.997)DKESVGSSSTSNEGGR 229.7 1.56E-33 245060000 113660 117810 71247 74146 124830 88992 129820 167140 147110 TRUE FALSE 98639.54302 117036.0984 105702.2875 90981.98255 122346.1272 92415.57983 117230.0764 131398.4117 129718.8234 0.760410405 0.902229108 0.814856971 0.701378414 0.943164022 0.712429988 0.903724481 1.012947915 1 16.98502832 1.961132561 4.161937856 0.99971233 0.811280272 0.547963368 0.0751643 0.153735387 5.672117966 0.036886153 0.019255314 91.43923026 -1.961132561 -0.188432058 STPFIVPS(ph)SPTEQEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 STPFIVPSSPTEQEGR 16 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 STPFIVPS(0.716)S(0.284)PTEQEGR;STPFIVPS(0.819)S(0.16)PT(0.021)EQEGR;STPFIVPS(0.836)S(0.162)PT(0.002)EQEGR;STPFIVPS(0.714)S(0.286)PTEQEGR 383.26 6.07E-88 5447730000 3058200 2986240 1672988 1988040 2988580 3116380 2864530 3245230 2411390 TRUE FALSE 2654051.122 2966623.193 2482050.593 2439454.867 2929113.105 3236269.155 2586728.321 2551262.819 2126318.221 1.248190932 1.39519248 1.167299686 1.147267066 1.377551618 1.52200603 1.216529255 1.199849953 1 21.01992609 1.312141093 1.807815834 0.928581341 1.301748048 0.415014834 0.1125259 0.814772039 2.910477167 0.506153531 0.033014668 20.51828668 -1.312141093 0.373166707 STPFIVPSS(ph)PTEQEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 STPFIVPSSPTEQEGR 16 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 STPFIVPS(0.001)S(0.998)PTEQEGR;STPFIVPS(0.027)S(0.972)PTEQEGR;STPFIVPSS(1)PTEQEGR;STPFIVPS(0.065)S(0.934)PTEQEGR;STPFIVPS(0.002)S(0.998)PTEQEGR 403.51 4.83E-105 11765240000 7598600 7404570 3823310 4819520 7532370 7657300 7211170 8135100 6153480 TRUE FALSE 6594425.758 7355928.892 5672275.504 5913865.678 7382490.574 7951881.286 6511831.843 6395472.172 5426022.604 1.215333263 1.35567605 1.045383685 1.089908043 1.36057129 1.465508323 1.200111448 1.178666703 1 22.37146363 1.2603661 2.030891187 0.931051982 1.249696326 0.280939482 0.125092297 1.050573842 4.443060439 0.622548906 0.036253636 18.21235472 -1.2603661 0.318644344 STPLEENVVDREQIDFLAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STPLEENVVDREQIDFLAAR 20 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 ; 249.2 2.08E-30 574550000 377100 409170 181736 237310 409290 454390 330140 438400 126853 FALSE TRUE 327265.2796 406482.1353 269624.1375 291194.8626 401145.9298 471870.6773 298123.0736 344651.5716 111856.5829 2.925757888 3.6339581 2.41044497 2.603287667 3.58625232 4.218532922 2.665226006 3.081191673 1 16.77129064 1.194423778 3.462772338 0.533131527 3.161053591 0.598003045 0.550080149 0.29531712 4.649245806 2.194792144 0.144326604 15.64673681 -1.194423778 2.627922064 STPSHGSVSSLNSTGSLS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 STPSHGSVSSLNSTGSLSPK 20 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4;M0R2S2 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 STPSHGSVSSLNSTGS(0.002)LS(0.998)PK;STPSHGSVSSLNSTGSLS(1)PK;STPSHGSVSSLNSTGSLS(1)PK;STPSHGSVSSLNSTGSLS(1)PK;STPSHGSVSSLNSTGSLS(1)PK;STPSHGSVSSLNSTGSLS(1)PK 332.26 7.51E-80 4237140000 2208270 2080284 532418 1172169 3131570 2706194 2820970 3053140 2864930 TRUE FALSE 1916441.524 2066618.477 789897.1256 1438327.887 3069257.884 2810303.034 2547392.764 2400249.771 2526241.239 0.758613823 0.818060621 0.312676839 0.569354923 1.214950432 1.112444445 1.008372726 0.950126905 1 21.26856098 3.249595246 24.99979831 1.042900217 0.607632471 0.682757353 0.149672481 135.2882107 306504.0894 0.045980386 0.058784556 1776.622859 -3.249595246 -0.435267747 STPTAEAEEAGIGDTPS(ph)LEDEAAGHVTQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STPTAEAEEAGIGDTPSLEDEAAGHVTQAR 30 0 P10636-7;P10636-4 P10636-7 MAPT Microtubule-associated protein tau 1 STPTAEAEEAGIGDT(0.001)PS(0.999)LEDEAAGHVTQAR 246.3 4.22E-46 125160000 81313 49235 35204 44445 66477 73699 61313 67182 69024 TRUE FALSE 70567.28103 48911.57204 52228.77215 54536.91655 65154.23776 76534.24822 55366.8747 52815.65211 60864.06135 1.159424453 0.803619919 0.858121706 0.89604465 1.070487843 1.257462064 0.90968091 0.867764177 1 15.89330299 4.776036864 22.69346463 0.956424761 1.159426116 0.19160533 0.130058496 11236.97378 6804015.29 0.034188812 6.879959604 59708.59668 -4.776036864 0.203001356 STPTDLILCVPHLYSCLEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STPTDLILCVPHLYSCLEDR 20 0 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 135.04 7.88E-06 228280000 137700 133760 61237 89563 150530 152830 130510 145380 86465 FALSE TRUE 119502.5961 132881.3218 90851.41803 109899.648 147534.7475 158709.469 117853.1603 114291.6183 76243.2062 1.567386815 1.742861146 1.191600177 1.44143529 1.935054346 2.081621129 1.545752942 1.499040033 1 16.21832117 1.19031788 2.052763707 0.740364695 1.648528252 0.401121354 0.246535611 0.975466728 3.635900328 1.762789415 0.072057279 15.49950683 -1.19031788 0.908163557 STQIENQHQGAQDTSDLMS(ph)PSKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STQIENQHQGAQDTSDLMSPSKR 23 1 Q9NVR2;H0YBW3 Q9NVR2 INTS10 Integrator complex subunit 10 1 STQIENQHQGAQDTS(0.001)DLMS(0.958)PS(0.041)KR;STQIENQHQGAQDT(0.032)S(0.039)DLMS(0.917)PS(0.011)KR 145.33 6.60E-08 446200000 212340 163227 117617 140400 203600 147193 187035 255130 195055 TRUE FALSE 184278.731 162154.7511 174496.9746 172279.9659 199548.7583 152855.61 168896.3745 200572.4349 171995.8201 1.071414008 0.942783092 1.014541949 1.00165205 1.160195394 0.888717004 0.981979529 1.166147147 1 17.39201398 1.761086801 25 1.092328845 1.007374472 0.12216669 0.081927965 19.90100487 22108.2198 0.041697984 0.020025151 57.68817507 -1.761086801 -0.084954373 STQKS(ph)PATAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STQKSPATAPK 11 1 Q07960;H0YE29 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 STQKS(0.999)PAT(0.001)APK;STQKS(0.995)PAT(0.005)APK 137.75 0.00018915 119964000 401630 314380 219890 212210 236330 207873 375810 436530 275370 TRUE FALSE 348553.5779 312314.8171 326229.5395 260395.5239 231627.4954 215870.0088 339364.004 343181.4566 242816.0723 1.435463372 1.286219706 1.343525313 1.072398221 0.953921597 0.889026854 1.39761755 1.413339131 1 17.88950439 3.756702317 22.04803715 1.152151381 1.34818467 0.271463588 0.175749761 331.169215 402471.8243 0.053809382 0.092820629 5710.870567 -3.756702317 0.196033289 STQVPHFLLEDLLLNEWEASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STQVPHFLLEDLLLNEWEASK 21 0 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 0 123.77 2.59E-05 45238000 114040 81785 38664 65226 84692 58283 88614 69342 84329 FALSE TRUE 98969.32506 81247.74895 57362.03972 80036.56022 83006.7949 60525.18472 80020.22792 54513.75292 74359.72169 1.330953409 1.09263116 0.771412781 1.076342923 1.116287057 0.8139512 1.076123284 0.73310862 1 16.18223375 4.577157973 3.512428103 0.935613866 1.326320328 0.462628097 0.13413592 0.219524487 4.567416553 0.032792807 0.171711719 37770.95562 -4.577157973 0.390706462 STS(ph)FRGGMGSGGLATGIAGGLAGMGGIQNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 STSFRGGMGSGGLATGIAGGLAGMGGIQNEK 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 ST(0.001)S(0.998)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.051)T(0.17)S(0.779)FRGGMGS(0.001)GGLATGIAGGLAGMGGIQNEK;S(0.024)T(0.024)S(0.952)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.156)T(0.156)S(0.688)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.01)T(0.16)S(0.83)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.137)T(0.137)S(0.725)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.218)T(0.368)S(0.414)FRGGMGSGGLATGIAGGLAGMGGIQNEK 298.45 1.13E-81 11571260000 10051100 9519140 2090394 2963175 6151538 3714393 11813710 10423860 622363 TRUE FALSE 8722821.669 9456608.143 3101315.53 3636009.173 6029134.429 3857288.102 10668018.22 8194798.658 548787.9551 15.8947032 17.23180703 5.651209181 6.625526561 10.98627325 7.028740456 19.43923536 14.93254103 1 19.06588929 4.260614762 24.9652264 10 16.5632617 0.247827066 5.114503035 382.7849157 433303.7515 1.347581471 3.558976993 18222.78544 -4.260614762 6.563261701 STS(ph)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STSFRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR 40 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.164)T(0.164)S(0.671)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR 233.2 8.09E-51 715400000 179260 178110 15789 26191 85973 53417 184210 185050 5898.5 TRUE FALSE 155570.3368 176939.9837 23424.61321 32138.06685 84262.3055 55471.98656 166345.3426 145478.4976 5201.18605 29.91055027 34.01916063 4.503706075 6.178988128 16.20059438 10.66525712 31.98219425 27.97025451 1 12.34462493 8 0.092292348 10 44.10244412 0.052788031 11.96952099 2161.257875 18.61409052 1188.059949 9624.584677 100000000 -8 34.10244412 STS(ph)GPRPGCQPSSPCVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STSGPRPGCQPSSPCVPK 18 1 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 ST(0.003)S(0.997)GPRPGCQPSSPCVPK;S(0.155)T(0.155)S(0.691)GPRPGCQPSSPCVPK 178.35 5.40E-14 460260000 351390 196003 104444 189843 178732 92426 343030 264649 240952 TRUE FALSE 304952.9212 194715.4434 154953.4677 232949.7547 175175.5829 95981.68803 309763.0034 208055.8709 212466.9291 1.435295943 0.916450594 0.72930629 1.096404771 0.824483997 0.451748837 1.457935147 0.979238848 1 17.69687877 2.217047802 24.99999541 1.124048555 0.905804988 0.135073925 0.280589245 527.0521014 612481.5591 0.112731493 0.076080922 164.8343812 -2.217047802 -0.218243567 STS(ph)GSPRPAGAKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STSGSPRPAGAKPK 14 2 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3-2 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 S(0.011)T(0.075)S(0.457)GS(0.457)PRPAGAKPK;S(0.033)T(0.137)S(0.491)GS(0.339)PRPAGAKPK 75.463 0.015749 512210000 1487760 1052860 674640 772980 914430 714380 1267750 1531040 900650 TRUE FALSE 1291148.746 1045943.693 1000898.161 948496.9233 896234.6321 741862.6609 1144803.8 1203639.011 794176.183 1.625771175 1.317017201 1.260297377 1.194315498 1.128508574 0.934128568 1.44149853 1.515581852 1 19.59909957 4.792361944 2.117440544 1.236338357 1.768227691 0.346351668 0.176727796 1.127363063 5.029766531 0.050540291 1.199656546 61995.75368 -4.792361944 0.531889335 S(ph)PSLSLAPLS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SPSLSLAPLSPR 12 0 G3V160;Q969H4-2;Q969H4 G3V160 CNKSR1 Connector enhancer of kinase suppressor of ras 1 2 S(0.996)PS(0.004)LSLAPLS(1)PR;S(1)PSLSLAPLS(1)PR;S(0.994)PS(0.006)LSLAPLS(1)PR;S(0.994)PS(0.006)LSLAPLS(1)PR 270.75 1.56E-27 885350000 479464 790340 634934 830260 1083550 1174530 1011770 1211580 1261010 TRUE FALSE 416101.6176 785148.2045 941990.2061 1018783.223 1061989.475 1219714.929 913648.7011 952493.0455 1111934.834 0.374214032 0.706109909 0.84716314 0.916225656 0.955082476 1.096930226 0.821674682 0.856608693 1 20.08464081 4.812310549 1.257080759 0.932860059 0.052751672 0.852930866 0.07521386 0.653874441 0.796422261 0.023538164 0.777539885 64909.8416 -4.812310549 -0.880108387 down STS(ph)LSALVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 STSLSALVR 9 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5;A0A0A0MRX3 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.006)T(0.281)S(0.713)LSALVR;S(0.02)T(0.02)S(0.961)LSALVR;S(0.001)T(0.001)S(0.998)LSALVR;ST(0.001)S(0.999)LSALVR;S(0.045)T(0.011)S(0.943)LSALVR;S(0.03)T(0.055)S(0.914)LS(0.001)ALVR 233.09 4.04E-10 2208120000 4444690 4292470 2515330 2963790 4348900 4575180 4683150 5054950 5151830 TRUE FALSE 3857312.955 4264272.482 3731752.001 3636763.818 4262365.398 4751190.135 4228978.834 3973988.28 4542786.526 0.849107246 0.938690924 0.821467612 0.800557939 0.938271119 1.045875721 0.930921761 0.874790893 1 22.11514608 3.117075573 7.645240454 0.951056077 0.856717624 0.460318649 0.056573987 0.256195257 16.10534182 0.018371197 0.020877205 1309.409757 -3.117075573 -0.094338453 STS(ph)PAGQHHS(ph)PISSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 STSPAGQHHSPISSR 15 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 S(0.271)T(0.329)S(0.4)PAGQHHS(0.722)PIS(0.275)S(0.003)R;S(0.282)T(0.33)S(0.387)PAGQHHS(0.987)PIS(0.011)S(0.002)R;S(0.245)T(0.3)S(0.454)PAGQHHS(0.996)PIS(0.003)S(0.001)R 108.08 0.00058469 2313240000 1224640 1206050 617348 871195 1202650 1262950 1127970 1216990 1185360 TRUE FALSE 1062800.721 1198127.378 915899.5577 1069013.14 1178719.618 1311536.504 1018579.643 956746.1591 1045228.091 1.016812244 1.146283178 0.876267645 1.022755846 1.127715212 1.254784975 0.974504658 0.915346772 1 19.99538637 2.023781599 24.99726044 0.949616277 1.072340376 0.215579206 0.099732629 325.6760838 342322.433 0.04222979 0.028469661 105.6286183 -2.023781599 0.122724099 STS(ph)PIIGS(ph)PPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 STSPIIGSPPVR 12 0 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 2 S(0.052)T(0.198)S(0.757)PIIGS(0.993)PPVR;ST(0.001)S(0.999)PIIGS(1)PPVR;ST(0.005)S(0.995)PIIGS(1)PPVR;S(0.02)T(0.028)S(0.952)PIIGS(1)PPVR;S(0.003)T(0.066)S(0.931)PIIGS(1)PPVR 204.31 1.68E-07 1279580000 1323590 1265370 1111970 1412210 1906710 2098990 1846790 2010800 2624130 TRUE FALSE 1148674.228 1257057.701 1649722.411 1732873.865 1868770.201 2179739.504 1667688.59 1580806.068 2313908.341 0.496421664 0.543261666 0.712959274 0.748894774 0.80762499 0.942016356 0.720723704 0.683175751 1 21.14190029 4.176600772 1.470712563 0.806676161 0.473264146 0.626597816 0.094540647 0.364262898 1.365569607 0.029180438 0.132558032 15017.60827 -4.176600772 -0.333412015 STS(ph)PIIGSPPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 STSPIIGSPPVR 12 0 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 ST(0.003)S(0.997)PIIGSPPVR;STS(1)PIIGSPPVR;ST(0.007)S(0.993)PIIGSPPVR;S(0.01)T(0.184)S(0.807)PIIGSPPVR 249.69 5.91E-17 4711490000 9212600 7055300 3596590 3408030 3987300 3668500 3102740 3985510 5736600 TRUE FALSE 7995131.568 7008953.27 5335912.954 4181875.3 3907960.531 3809629.569 2801836.752 3133239.702 5058425.683 1.580557286 1.385599732 1.054856449 0.826714785 0.772564583 0.753125539 0.553895012 0.619410049 1 22.27025702 4.205489171 1.094661345 0.701627661 1.699401242 0.872079963 0.116352218 0.259509672 0.458413547 0.039425364 0.246747486 16050.52237 -4.205489171 0.997773581 STS(ph)PPPSPEVWADSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 STSPPPSPEVWADSR 15 0 Q08495;Q08495-2;Q08495-3;E5RGQ0;E5RFK4;E5RJ61;E5RGQ7;E5RJC0 Q08495 DMTN Dematin 1 S(0.001)T(0.003)S(0.995)PPPSPEVWADSR;S(0.252)T(0.151)S(0.598)PPPSPEVWADSR;S(0.008)T(0.022)S(0.969)PPPSPEVWADSR 138.73 9.23E-06 336910000 645240 500910 288482 255271 384066 409950 378256 402312 365551 TRUE FALSE 559969.8992 497619.4892 427992.8601 313234.1821 376423.838 425721.0418 341572.7913 316280.7096 322335.9772 1.737224321 1.543791337 1.327784952 0.971763018 1.16779964 1.32073697 1.059679389 0.981214422 1 18.2982057 4.202825946 1.839635416 1.083322378 1.725545378 0.821472162 0.107973213 0.166792799 1.050184906 0.033125224 0.129493934 15952.39687 -4.202825946 0.642223 STS(ph)PSTSSEAEPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STSPSTSSEAEPVK 14 0 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;H0Y6V3 Q5VT25-2 CDC42BPA Serine/threonine-protein kinase MRCK alpha 1 ST(0.003)S(0.748)PS(0.249)TSSEAEPVK;S(0.037)T(0.037)S(0.926)PS(0.001)TSSEAEPVK 260.15 1.99E-24 943960000 2620800 2425600 1959390 2012520 2418000 2306100 2672200 3046200 4019800 TRUE FALSE 2274454.64 2409666.074 2906957.558 2469493.425 2369886.531 2394817.159 2413050.455 2394793.836 3544583.823 0.641670434 0.67981636 0.820112516 0.696694887 0.668593733 0.675627176 0.680771164 0.675620596 1 21.75718482 1.236529946 24.98754265 1.000000392 0.693504763 0.805304217 0.047534825 23.73769228 292017.0425 0.07617485 0.011979334 17.23970962 -1.236529946 -0.306495629 STS(ph)PTFNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 STSPTFNK 8 0 Q9BX63 Q9BX63 BRIP1 Fanconi anemia group J protein 1 ST(0.004)S(0.995)PT(0.001)FNK;S(0.001)T(0.009)S(0.99)PTFNK;S(0.001)T(0.001)S(0.996)PT(0.001)FNK;S(0.001)T(0.002)S(0.997)PTFNK;ST(0.002)S(0.998)PTFNK 133.75 0.00095031 1605047000 4615710 4539240 2614440 3528010 4193160 3787890 4770650 6110830 4758490 TRUE FALSE 4005732.229 4509421.434 3878791.929 4329098.593 4109724.32 3933612.579 4307993.097 4804076.559 4195946.733 0.954667083 1.074708932 0.924414006 1.031733449 0.979451023 0.937479151 1.026703476 1.144932685 1 22.00056493 1.993695907 24.48417571 1.083718509 0.986743784 0.298631749 0.055689622 203.4084321 790008.7803 0.021785464 0.014092003 98.55891355 -1.993695907 -0.096974725 STS(ph)PVTDPSIPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 STSPVTDPSIPIR 13 0 A0A087WU18;Q99607 A0A087WU18 ELF4 ETS-related transcription factor Elf-4 1 S(0.099)T(0.099)S(0.802)PVTDPSIPIR;S(0.154)T(0.154)S(0.691)PVT(0.002)DPSIPIR;S(0.159)T(0.159)S(0.681)PVTDPSIPIR;ST(0.002)S(0.998)PVTDPSIPIR 193.15 2.21E-06 1345440000 2017600 2018890 1249360 1612840 2234730 2115080 1938160 2243080 2177760 TRUE FALSE 1750969.048 2005627.779 1853554.675 1979059.973 2190263.245 2196448.496 1750197.542 1763414.798 1920307.694 0.911816921 1.044430424 0.965238373 1.030595242 1.140579321 1.14380029 0.911415159 0.918298043 1 20.87290606 2.20458331 24.99653787 0.936715961 1.04046489 0.276682836 0.073035632 238.0054009 175094.9179 0.031336794 0.021128529 160.1707872 -2.20458331 0.103748929 STS(ph)QGSINSPVYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 STSQGSINSPVYSR 14 0 O14639-3;F8W8M4;O14639-5;O14639-2;O14639;J3QSX6;A0A0A0MRL6;A0A3B3IS55;O14639-4;O14639-6;A0A494C1P1;A0A494C1G0;H0Y7N6;F6XFR5 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 ST(0.001)S(0.999)QGSINSPVYSR;STS(1)QGSINSPVYSR;STS(1)QGSINSPVYSR;STS(1)QGSINSPVYSR;STS(1)QGSINSPVYSR;ST(0.006)S(0.994)QGSINSPVYSR 243.63 1.60E-17 3719760000 5144200 5083630 2963342 3547124 4917032 4794085 5293900 5539630 5384950 TRUE FALSE 4464380.936 5050235.3 4396424.103 4352552.719 4819192.683 4978516.552 4780498.393 4355023.234 4748347.346 0.940196791 1.063577479 0.92588511 0.916645814 1.014919999 1.04847354 1.006770997 0.917166104 1 22.17899404 4.220105221 24.99984975 0.974024869 1.001887247 0.039588799 0.053141479 802.9549926 1087693.404 0.014065782 0.029376013 16599.89043 -4.220105221 0.027862378 STS(ph)QSIVSLLTGTAGEDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STSQSIVSLLTGTAGEDEK 19 0 V9GZ20;V9GXZ5;Q70EL4-2;Q70EL4-3;Q70EL4-4;Q70EL4 V9GZ20 USP43 Ubiquitin carboxyl-terminal hydrolase 43 1 S(0.117)T(0.117)S(0.766)QSIVSLLTGTAGEDEK;S(0.145)T(0.145)S(0.71)QSIVSLLTGTAGEDEK 236.96 3.49E-24 53673000 105209 89343 95672 99193 129310 127747 142449 167726 150044 TRUE FALSE 91305.36408 88756.09995 141939.2992 121716.2867 126736.984 132661.5098 128634.3179 131859.1001 132305.9693 0.690107669 0.670839724 1.072811 0.919960659 0.957908284 1.00268726 0.972248785 0.996622457 1 17.01351863 4.247589976 24.99998182 0.985614318 0.680473515 0.915415317 0.038966097 45.32475343 125489.8979 0.009136786 0.02343941 17684.38561 -4.247589976 -0.305140803 STS(ph)TPNVHMVSTTLPVDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 STSTPNVHMVSTTLPVDSR 19 0 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 S(0.146)T(0.146)S(0.702)T(0.007)PNVHMVSTTLPVDSR;S(0.281)T(0.281)S(0.437)T(0.001)PNVHMVSTTLPVDSR;S(0.069)T(0.31)S(0.617)T(0.005)PNVHMVSTTLPVDSR;S(0.042)T(0.15)S(0.798)T(0.011)PNVHMVSTTLPVDSR 260.99 2.52E-31 4385150000 1392260 1281430 701111 866121 1312240 1438090 1243070 1353940 1246540 TRUE FALSE 1208269.313 1273012.202 1040170.625 1062787.011 1286128.991 1493414.253 1122517.263 1064410.467 1099175.461 1.099250626 1.158151948 0.946319001 0.966894776 1.170085247 1.358667752 1.021235737 0.968371752 1 20.06799027 2.016586957 24.99278529 0.985789704 1.113310924 0.204375311 0.113265183 389.5951198 587029.1494 0.049981048 0.03368719 103.8931604 -2.016586957 0.127521219 STS(ph)TPTS(ph)PGPR ddPTM_MDA-MB-175_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 ST(0.002)S(0.986)T(0.012)PT(0.032)S(0.967)PGPR 133.18 0.00024437 512510000 816880 657520 350280 354670 475640 516650 485800 521550 461120 TRUE FALSE 708927.2383 653200.7078 519676.5796 435203.2443 466175.6946 536525.8598 438687.1908 410020.5912 406606.9189 1.74351986 1.606467272 1.278081005 1.070329166 1.14650212 1.31951975 1.078897506 1.00839551 1 18.63327524 4.214310295 2.01202951 1.10150735 1.746988235 0.874175796 0.089221056 0.126175165 0.969605933 0.027601316 0.102182702 16379.86412 -4.214310295 0.645480884 STS(ph)YGYS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STSYGYSR 8 0 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 2 S(0.003)T(0.004)S(0.993)YGYS(1)R;S(0.046)T(0.056)S(0.882)Y(0.016)GY(0.002)S(0.998)R 95.094 0.014465 801780000 2210980 1908520 1408240 1655830 1876630 2094220 1956070 2169940 2675800 TRUE FALSE 1918793.391 1895982.806 2089269.574 2031811.509 1839288.735 2174785.999 1766370.632 1705915.217 2359469.972 0.813230689 0.803563016 0.885482587 0.86113048 0.779534707 0.9217265 0.748630266 0.72300781 1 21.17003138 2.209905122 24.99986508 0.79972914 0.84198716 0 0.083948423 718.6136918 626933.6357 0.033575326 0.022640858 162.1455827 -2.209905122 0.042258021 STSAPQMS(ph)PGSSDNQSSSPQPAQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 STSAPQMSPGSSDNQSSSPQPAQQK 25 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 STSAPQMS(0.726)PGS(0.272)S(0.002)DNQSSSPQPAQQK;STSAPQMS(0.957)PGS(0.036)S(0.007)DNQSSSPQPAQQK;STSAPQMS(0.993)PGS(0.006)S(0.001)DNQSSSPQPAQQK;STSAPQMS(0.999)PGS(0.001)SDNQSSSPQPAQQK 285.93 3.66E-53 2252030000 2610580 2070950 1315100 1698980 2140370 1935280 2476630 2702320 2415010 TRUE FALSE 2265585.239 2057345.793 1951086.759 2084759.376 2097780.825 2009731.474 2236446.804 2124449.897 2129510.269 1.063899654 0.966112173 0.91621383 0.97898536 0.985100121 0.943752892 1.050216492 0.997623692 1 21.02209026 2.244896398 24.9994063 1.013557336 0.973118348 0.181718157 0.039930986 251.5093921 992398.0227 0.015006639 0.011329111 175.7504307 -2.244896398 -0.040438988 STSESFIQHIVSLVHHVK ddPTM_MDA-MB-175_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 ; 249.69 3.52E-25 298940000 511590 410640 121839 319610 415240 381690 453800 541330 471690 FALSE TRUE 443982.0853 407942.4788 180760.7479 392182.3354 406977.5364 396373.8613 409790.5458 425570.7921 415927.3456 1.067451059 0.980802256 0.434596931 0.942910678 0.978482278 0.952988221 0.985245501 1.023185411 1 18.66597201 3.495070578 24.94901116 0.987723549 0.817238406 0.167831633 0.162781497 1245.226231 1730823.677 0.045451996 0.065907761 3126.587431 -3.495070578 -0.170485143 STSGPRPGCQPSS(ph)PCVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 STSGPRPGCQPSSPCVPK 18 1 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 S(0.002)T(0.002)S(0.002)GPRPGCQPS(0.183)S(0.812)PCVPK;STSGPRPGCQPS(0.109)S(0.891)PCVPK;STSGPRPGCQPS(0.019)S(0.981)PCVPK;STSGPRPGCQPS(0.02)S(0.98)PCVPK 194.24 5.01E-15 841820000 942193 886960 586618 719254 988655 791521 1168571 1308441 1077849 TRUE FALSE 817679.8078 881133.5014 870308.4269 882571.6138 968982.6998 821971.3251 1055243.164 1028641.074 950426.9191 0.860328965 0.927092324 0.915702627 0.928605447 1.019523627 0.864844323 1.11028333 1.082293708 1 19.85821617 2.23392891 24.99997889 1.069883935 0.924509814 0.639799839 0.051074777 69.78275028 376652.1083 0.01992271 0.013935003 171.3676773 -2.23392891 -0.145374121 STSMDSGSSES(ph)PASLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STSMDSGSSESPASLKR 17 1 F8W7U0;Q15811-6;Q15811-12;Q15811-11;Q15811-3;Q15811-10;Q15811-7;Q15811-2;Q15811-4;Q15811-9;Q15811-8;Q15811;H0Y7J7 F8W7U0 ITSN1 Intersectin-1 1 STSMDSGSS(0.003)ES(0.982)PAS(0.015)LKR 126.91 2.57E-05 184760000 72770 66727 33609 39449 59275 56073 70920 73263 59876 TRUE FALSE 63153.26012 66288.66594 49862.42482 48406.49839 58095.54347 58230.16459 64042.18932 57596.27758 52797.52749 1.196140485 1.255525952 0.944408331 0.916832676 1.100345911 1.102895673 1.212977053 1.090889675 1 15.68818275 4.259975742 24.99994922 1.063278983 1.225833339 0.404775695 0.086576652 277.6882101 324166.7341 0.023703221 0.062583483 18195.99221 -4.259975742 0.162554356 STSQGSINS(ph)PVYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 STSQGSINSPVYSR 14 0 O14639-3;F8W8M4;O14639-5;O14639-2;O14639;J3QSX6;A0A0A0MRL6;A0A3B3IS55;O14639-4;O14639-6;A0A494C1P1;A0A494C1G0;H0Y7N6;F6XFR5 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 STSQGS(0.002)INS(0.998)PVYSR;STSQGSINS(1)PVYSR;STSQGS(0.028)INS(0.972)PVYSR 276.14 4.52E-33 1213820000 1133580 1103290 538200 772640 1061240 1082680 971980 1154180 1090580 TRUE FALSE 983774.5309 1096042.415 798475.3202 948079.7211 1040123.4 1124331.4 877717.5292 907367.5888 961652.8748 1.023003785 1.139748494 0.830315534 0.9858856 1.081599637 1.169165537 0.912717626 0.94355002 1 19.8751567 STSSFPCPAGHFNGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STSSFPCPAGHFNGFR 16 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 ; 211.13 7.90E-12 2715500000 2639200 3069700 1251690 2368000 3219800 3350300 2580700 3290000 2767200 FALSE TRUE 2290423.033 3049534.939 1857011.471 2905690.593 3155732.279 3479188.209 2330424.111 2586459.103 2440064.768 0.938673048 1.249776226 0.761050073 1.19082519 1.293298572 1.425858958 0.955066497 1.059996085 1 21.21848801 4.782881065 21.64619295 1.111288645 0.938669755 0.080541538 0.188466173 15078.03941 7363181.463 0.046680629 15.27551738 60657.01926 -4.782881065 -0.17261889 STSSVDSDILSS(ph)SHSSDTLCNADNAQIPLANGLDSHSITSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STSSVDSDILSSSHSSDTLCNADNAQIPLANGLDSHSITSSR 42 0 Q96K76-2;Q96K76-4;Q96K76 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 1 STSSVDSDILS(0.065)S(0.347)S(0.347)HS(0.197)S(0.043)DT(0.001)LCNADNAQIPLANGLDSHSITSSR 181.17 2.24E-27 164640000 10473 14705 1528.9 11042 19472 20457 15497 21169 15669 TRUE FALSE 9088.966515 14608.40189 2268.281154 13549.25487 19084.5453 21243.99403 13994.10333 16642.17409 13816.62867 0.657828095 1.057305819 0.164170378 0.980648405 1.381273663 1.537567125 1.012845004 1.204503246 1 13.75411801 3.482969483 23.2548148 1.219935691 0.653336418 0.520785249 0.262659678 82.79309193 329218.3756 0.072988111 0.097668909 3040.671358 -3.482969483 -0.566599274 STSTLEIQPSRAS(ph)PT(ph)SDIESVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STSTLEIQPSRASPTSDIESVER 23 1 Q96JK2-2;Q96JK2-3;Q96JK2 Q96JK2-2 DCAF5 DDB1- and CUL4-associated factor 5 2 S(0.017)T(0.019)S(0.022)T(0.024)LEIQPS(0.156)RAS(0.761)PT(0.531)S(0.469)DIESVER;STSTLEIQPS(0.003)RAS(0.997)PT(0.533)S(0.467)DIESVER 88.595 0.013988 181700000 169582 166202 111646 116575 152771 169710 158809 183400 137206 TRUE FALSE 147171.309 165110.2081 165638.379 143045.1355 149731.156 176238.8535 143407.7276 144181.3372 120985.663 1.216435943 1.364708876 1.369074442 1.182331294 1.23759421 1.456692051 1.185328278 1.191722504 1 16.88447657 1.225793518 1.342248235 0.863647485 1.298766028 0.534824263 0.086797464 1.102218267 1.682615906 0.675704329 0.025757105 16.81874238 -1.225793518 0.435118544 STSTLEIQPSRAS(ph)PTSDIESVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 STSTLEIQPSRASPTSDIESVER 23 1 Q96JK2-2;Q96JK2-3;Q96JK2 Q96JK2-2 DCAF5 DDB1- and CUL4-associated factor 5 1 STSTLEIQPS(0.003)RAS(0.643)PT(0.177)S(0.177)DIESVER;STSTLEIQPS(0.003)RAS(0.775)PT(0.111)S(0.111)DIESVER;STSTLEIQPS(0.014)RAS(0.688)PT(0.149)S(0.149)DIESVER 245.55 9.71E-38 3727670000 2300300 2064460 1042310 1191470 1897630 2277080 1741360 1902310 947570 TRUE FALSE 1996309.527 2050898.426 1546374.602 1462011.474 1859870.876 2364680.741 1572483.175 1495515.81 835549.3541 2.389217964 2.454550909 1.850728021 1.749760761 2.225925813 2.830091041 1.881975215 1.789859334 1 19.67236552 1.26415919 1.603393966 0.579853196 2.210199225 0.597606206 0.31631861 0.769094254 1.884334884 1.978196793 0.095518159 18.37211646 -1.26415919 1.630346029 STSTPTS(ph)PGPR ddPTM_MDA-MB-175_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 STSTPT(0.001)S(0.999)PGPR;ST(0.002)S(0.057)T(0.319)PT(0.036)S(0.586)PGPR;STST(0.016)PT(0.002)S(0.982)PGPR;STS(0.001)T(0.006)PT(0.004)S(0.989)PGPR;STST(0.006)PT(0.004)S(0.99)PGPR;STST(0.306)PT(0.059)S(0.634)PGPR;STS(0.007)T(0.014)PT(0.01)S(0.968)PGPR 199.12 5.38E-08 18464136000 12867970 13507640 8068030 9963390 14495890 16925410 13175900 14864750 14025410 TRUE FALSE 11167435.16 13418907.42 11969756.29 12225729.98 14207450.15 17576541.47 11898103.25 11686038.89 12367342.01 0.902977791 1.085027601 0.967851967 0.988549518 1.148787681 1.421206065 0.962058237 0.944911112 1 23.56003213 4.744906867 23.06785452 1.058966779 0.902977585 0.113823398 0.141068072 650.6455668 2364813.472 0.036912165 0.323000766 55578.50583 -4.744906867 -0.155989194 STSYGYS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 STSYGYSR 8 0 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 STSYGYS(1)R;STSYGYS(1)R;STSYGYS(1)R;STSYGYS(1)R;STSYGYS(1)R;STSYGYS(1)R;STSYGYS(1)R 132.39 0.0010115 47272371000 25256094 22971132 12760253 16747720 22957248 23717304 21741225 24215506 25017930 TRUE FALSE 21918437.19 22820233.12 18931154.03 20550545.8 22500443.68 24629724.03 19632764.35 19037208.49 22060338.82 0.993567568 1.034446176 0.858153367 0.931560751 1.01995005 1.116470796 0.889957517 0.862960839 1 24.39495161 STSYGYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 STSYGYSR 8 0 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 ;; 168.08 0.00071867 365568000 383839 411152 208890 257397 408214 476613 390722 403638 370309 FALSE TRUE 333113.7036 408451.1154 309909.9027 315842.9229 400091.3401 494948.6105 352829.8406 317323.1548 326531.4919 1.020157969 1.250878171 0.94909652 0.967266346 1.225276428 1.515776036 1.080538476 0.971799544 1 18.31686261 1.998431313 24.9991823 0.996570478 1.157257742 0.15273888 0.163563181 112.8774798 1798869.892 0.07201396 0.047759888 99.63944799 -1.998431313 0.160687263 STT(ph)PANLDSESEHFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STTPANLDSESEHFFR 16 0 Q13315 Q13315 ATM Serine-protein kinase ATM 1 S(0.134)T(0.134)T(0.733)PANLDSESEHFFR 125.23 0.00028767 68855000 36906 33285 21562 25046 33221 35885 38895 47298 33620 TRUE FALSE 32028.77859 33066.34864 31989.45532 30733.0771 32559.9671 37265.51917 35122.96889 37183.69077 29645.4819 1.080393252 1.115392516 1.079066801 1.03668671 1.098311277 1.257038739 1.184766333 1.254278507 1 14.85552463 2.903201941 7.19276416 1.187246711 1.079059957 0.279413013 0.072697207 0.297437709 19.26046171 0.022657594 0.022715168 800.206254 -2.903201941 -0.108186754 STT(ph)PPPAEPVSLPQEPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 STTPPPAEPVSLPQEPPK 18 0 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 S(0.086)T(0.086)T(0.828)PPPAEPVSLPQEPPK;S(0.157)T(0.157)T(0.686)PPPAEPVSLPQEPPK;S(0.002)T(0.002)T(0.995)PPPAEPVSLPQEPPK;S(0.037)T(0.037)T(0.926)PPPAEPVSLPQEPPK 278.79 3.83E-38 1422660000 1117460 760205 594905 688021 791408 678609 940170 1118630 1093790 TRUE FALSE 969784.8297 755211.1633 882603.0478 844246.6838 775660.5292 704715.5273 848992.4581 879419.6797 964483.3922 1.00549666 0.783021428 0.915104454 0.875335636 0.804223832 0.730666316 0.880256171 0.91180386 1 19.87939687 1.42555814 2.106205207 1.011744301 0.849560271 0.273937828 0.075061805 0.606492635 3.944935337 0.168656049 0.02014147 26.64146728 -1.42555814 -0.16218403 STT(ph)PPPAEPVSLPQEPPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 STTPPPAEPVSLPQEPPKPR 20 1 Q9UN86-2 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 S(0.163)T(0.163)T(0.674)PPPAEPVSLPQEPPKPR;S(0.129)T(0.129)T(0.742)PPPAEPVSLPQEPPKPR;S(0.116)T(0.116)T(0.769)PPPAEPVSLPQEPPKPR;S(0.02)T(0.105)T(0.875)PPPAEPVSLPQEPPKPR;S(0.265)T(0.265)T(0.471)PPPAEPVSLPQEPPKPR 204.18 1.60E-21 33825980000 20735160 13195590 9485170 11862250 14705160 12057960 15564550 18742830 17385830 TRUE FALSE 17994956.07 13108907.3 14072229.94 14555755.17 14412556.09 12521837.52 14055102.34 14734821.66 15330496.98 1.17380122 0.85508691 0.917923923 0.949464012 0.940123213 0.816792667 0.916806699 0.961144422 1 23.86990113 4.74788242 24.90607789 0.921075014 1.17380136 0.702877912 0.051919672 718.6110264 1919948.846 0.013027487 0.161729421 55960.60738 -4.74788242 0.252726346 STT(ph)PTSSPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.003)T(0.297)T(0.699)PT(0.001)SSPFR;S(0.034)T(0.015)T(0.933)PT(0.018)S(0.001)SPFR;S(0.375)T(0.158)T(0.467)PTSSPFR;S(0.001)T(0.019)T(0.979)PT(0.001)SSPFR 222.34 5.53E-08 6646680000 7889060 8045870 4410860 5514810 7809160 8087480 6954500 8145330 7036420 TRUE FALSE 6846500.733 7993016.15 6543966.649 6767031.899 7653772.994 8398610.589 6280053.66 6403514.567 6204582.444 1.103458741 1.288244007 1.05469896 1.090650654 1.233567781 1.35361415 1.012163787 1.032062129 1 22.56490269 2.149116409 24.99999967 1.018238136 1.183647806 0.443663094 0.091036315 19.50278098 5445.993667 0.037768153 0.025463291 140.9666598 -2.149116409 0.16540967 STTTGHLIYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 ;;;;;; 99.815 0.0044381 53692238000 143296328 121937664 50985005 97381982 129641690 117188957 144424503 156237402 147822309 FALSE TRUE 124359355.2 121136647.5 75641523.95 119494049.4 127062074 121697292 130418236.9 122827249.4 130346924 0.954064364 0.929340284 0.580309236 0.916738544 0.974799175 0.933641457 1.000547101 0.942310303 1 26.9577813 3.489482789 24.91645595 0.965257733 0.818127481 0.312037856 0.100815684 679.6603152 1369952.238 0.028052599 0.03927988 3086.617322 -3.489482789 -0.147130252 STTTIGLVQALGAHLYQNVFACVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STTTIGLVQALGAHLYQNVFACVR 24 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ; 230.99 1.53E-33 387890000 439096 454110 230660 335663 437990 428340 485800 596100 361484 FALSE TRUE 381068.3511 451126.9215 342207.9475 411880.4144 429274.8559 444818.517 438687.1908 468628.6539 318749.7733 1.195509403 1.415301152 1.073594324 1.292174768 1.346745604 1.395510065 1.376274518 1.470208587 1 18.28206479 3.479194908 21.16661488 1.342753827 1.236190609 0.056261704 0.148256832 26.15280411 266962.7726 0.040914644 0.053978345 3014.35854 -3.479194908 -0.106563218 STVDGLQVTQLNVDHTTENEDELFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STVDGLQVTQLNVDHTTENEDELFR 25 0 Q15750;Q15750-2 Q15750 TAB1 TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 0 ; 287.32 6.02E-54 275970000 113810 100797 50592 62305 111817 118414 101302 119691 109721 FALSE TRUE 98769.72014 100134.8579 75058.46042 76452.30252 109592.0605 122969.4632 91477.74763 94096.01109 96749.90837 1.020876627 1.034986591 0.775798775 0.790205426 1.132735548 1.271003407 0.945507331 0.972569511 1 16.56197267 3.229783983 24.99997176 1.054306773 0.905456251 0.292066827 0.122370058 290.75628 828208.9836 0.040691802 0.046828726 1697.39916 -3.229783983 -0.148850522 STVLSLDWHPNNVLLAAGSCDFK ddPTM_MDA-MB-175_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 ; 227.38 8.53E-33 670280000 1090640 882040 495740 746190 897420 777470 1139380 1230490 1087510 FALSE TRUE 946509.1607 876245.8212 735481.5222 915623.8443 879563.0978 807379.774 1028883.103 967359.2892 958945.8067 0.987030919 0.913759479 0.766968808 0.954823347 0.917218775 0.841945153 1.072931438 1.008773679 1 19.87108976 2.237013777 24.998042 1.025292945 0.895364082 0.490190696 0.062605674 34.18370417 552412.9573 0.024444861 0.01748096 172.5892641 -2.237013777 -0.129928863 STVPGHAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 STVPGHAGR 9 0 P00491;G3V5M2;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 ;; 140.14 0.00010981 1363940000 2743310 2916010 1298370 2073980 2735310 3095820 2891480 3156830 2996060 FALSE TRUE 2380774.633 2896854.538 1926266.075 2544908.858 2680882.683 3214918.199 2611064.715 2481766.471 2641869.2 0.901170517 1.096517018 0.729129994 0.963298583 1.014767379 1.216910436 0.98833989 0.939397935 1 21.33312761 3.360632112 4.49982226 1.025924884 0.916324315 0.196460863 0.112740134 0.401303685 13.91994461 0.033865531 0.044146986 2294.204418 -3.360632112 -0.109600569 STVTGERQS(ph)GDGQESTEPVENK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 STVTGERQSGDGQESTEPVENK 22 1 O15234;J3KSY7 O15234 CASC3 Protein CASC3 1 STVTGERQS(1)GDGQESTEPVENK;STVTGERQS(0.992)GDGQES(0.008)TEPVENK 323.94 3.34E-68 1286660000 1125150 741330 512640 569200 817370 692390 942700 1058980 540150 TRUE FALSE 976458.5767 736460.1544 760554.4187 698445.5597 801105.9362 719026.6913 851277.0991 832525.368 476294.0823 2.050116961 1.546229907 1.596816855 1.466416623 1.681956518 1.509627598 1.787293042 1.747922972 1 18.8614931 7.999973984 0.03002559 5.94E-06 3.900659219 0.21421102 0.239171924 7276.700105 21.63894807 993.6369898 1981.151048 99994009.81 -7.999973984 3.900653276 STYNHLSSWLTDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 STYNHLSSWLTDAR 14 0 P61106;X6RFL8 P61106 RAB14 Ras-related protein Rab-14 0 132.44 5.04E-05 918330000 909850 964420 300240 614140 1290700 1438600 828530 1112100 1245100 FALSE TRUE 789611.0172 958084.6615 445437.0682 753589.8735 1265017.595 1493943.873 748179.2881 874286.0694 1097905.696 0.719197486 0.8726475 0.405715236 0.686388527 1.152209702 1.360721488 0.68146043 0.796321644 1 20.06632271 3.328838619 8.662482655 0.966936816 0.664191782 0.359866174 0.214629697 0.36031023 30.93062689 0.067209998 0.086757862 2132.252432 -3.328838619 -0.302745035 SVAAEGALLPQT(ph)PPS(ph)PR ddPTM_MDA-MB-175_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 145.88 2.43E-06 263460000 278980 282610 165231 205292 279060 276680 256460 306890 305280 TRUE FALSE 242112.0862 280753.5163 245137.2643 251906.6863 273507.252 287324.0586 231588.5487 241263.9617 269190.1462 0.899409171 1.042956142 0.910647242 0.935794604 1.016037384 1.067364696 0.860315847 0.896258519 1 18.03826607 2.216255759 24.99977442 0.911710642 0.97827565 0.159900372 0.063961594 392.8694683 440333.3646 0.025890836 0.017470118 164.5340389 -2.216255759 0.066565008 SVAAEGALLPQTPPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SVAAEGALLPQTPPSPR 17 0 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 SVAAEGALLPQTPPS(1)PR;SVAAEGALLPQTPPS(1)PR;SVAAEGALLPQTPPS(1)PR;SVAAEGALLPQTPPS(1)PR;SVAAEGALLPQTPPS(1)PR;SVAAEGALLPQTPPS(1)PR 378.05 3.60E-105 4055050000 3274740 3465200 2062880 2587320 3414390 3589520 3283610 3660720 3612510 TRUE FALSE 2841974.812 3442436.873 3060495.668 3174810.551 3346450.319 3727611.157 2965166.008 2877903.516 3185443.183 0.89217564 1.080677531 0.960775469 0.996662118 1.050544658 1.17020174 0.930848814 0.903454669 1 21.60306267 SVAHLPWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVAHLPWR 8 0 K7ERL5;O96005-3;O96005-4;O96005 K7ERL5 CLPTM1 Cleft lip and palate transmembrane protein 1 0 ; 60.436 0.092303 833840000 298680 285750 290690 295330 343180 391830 254260 371190 367750 FALSE TRUE 259208.6812 283872.8894 431268.6563 362389.1903 336351.3894 406903.9536 229601.9043 291813.9071 324275.0139 0.7993483 0.87540784 1.329947229 1.117536581 1.037241153 1.254811306 0.708046857 0.899896367 1 18.30685834 2.234964836 24.99999857 0.868966202 1.072864085 0.234423094 0.170059706 137.908552 958804.3636 0.069346928 0.04884101 171.7769296 -2.234964836 0.203897883 SVAHVTEADLFHTIETLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVAHVTEADLFHTIETLMR 19 0 A5YKK6-3;A5YKK6-2;A5YKK6;H3BMZ2 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 ; 258.82 2.79E-31 227830000 185780 184380 78451 131455 200728 205858 181022 212730 218790 FALSE TRUE 161228.7023 183168.7956 116390.166 161303.8669 196733.9055 213777.4905 163466.5143 167239.345 192924.8954 0.835707087 0.949430581 0.603292622 0.836096692 1.019743487 1.108086595 0.847306481 0.866862437 1 17.5576798 3.389080697 6.554006143 0.952798201 0.796851041 0.343261202 0.111405743 0.277803593 17.022512 0.033821704 0.043796461 2449.518346 -3.389080697 -0.15594716 SVAVS(ph)DEEEVEEEAER ddPTM_MDA-MB-175_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 338.89 7.00E-72 2050010000 590476 568893 385883 449740 525232 547676 556250 617134 536967 TRUE FALSE 512443.1005 565155.9044 572497.3095 551860.3408 514780.9108 568745.4501 502304.9606 485164.6966 473487.373 1.082274058 1.193602906 1.209107871 1.165522826 1.087211487 1.201183986 1.060862421 1.024662376 1 18.85296643 2.075843865 4.448603094 1.020997699 1.157571894 0.663861621 0.043713298 0.12145785 4.573677048 0.019155385 0.012203921 119.0813816 -2.075843865 0.136574195 SVAVS(ph)DEEEVEEEAERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVAVSDEEEVEEEAERR 17 1 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 SVAVS(1)DEEEVEEEAERR 138.04 3.05E-06 216860000 55829 54265 33251 41396 45185 44144 45233 47105 46078 TRUE FALSE 48451.0562 53908.52964 49331.29482 50795.5945 44285.9069 45842.24824 40846.31062 37031.96232 40630.71133 1.192473737 1.326792662 1.214138104 1.250177337 1.089961397 1.128265953 1.005306313 0.911427861 1 15.310283 2.631139571 0.876900257 0.932059752 1.2618991 0.826953419 0.052926071 0.219443575 0.378135852 0.045863572 0.02830608 427.7003161 -2.631139571 0.329839348 SVCGHLENTS(ph)VGNS(ph)PNPSSAENSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVCGHLENTSVGNSPNPSSAENSFR 25 0 D6REP5;B7Z4W8;E9PD09;Q96HH9-5;Q96HH9-4;Q96HH9;Q96HH9-2;Q96HH9-3 D6REP5 GRAMD3 GRAM domain-containing protein 3 2 S(0.001)VCGHLENT(0.038)S(0.961)VGNS(0.998)PNPS(0.002)SAENSFR 92.49 0.0064041 78850000 43715 33115 23005 36524 48034 49382 28657 55371 49306 TRUE FALSE 37937.95199 32897.46538 34130.29495 44817.33243 47078.21738 51281.75749 25877.84855 43530.34255 43477.10085 0.872596177 0.756661892 0.785017728 1.030826149 1.08282789 1.179511892 0.595206397 1.001224592 1 15.40796812 3.747977087 24.08996022 0.9719584 0.799948905 0.227880829 0.152678006 665.5506731 1702655.708 0.041551254 0.070662409 5597.280706 -3.747977087 -0.172009495 SVCPGGS(ph)SPGSSSGGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVCPGGSSPGSSSGGGR 17 0 Q53LP3 Q53LP3 SOWAHC Ankyrin repeat domain-containing protein SOWAHC 1 SVCPGGS(0.5)S(0.5)PGSSSGGGR 101.9 0.0010219 106730000 135850 122060 71256 84774 118080 122370 115360 136760 120080 TRUE FALSE 117897.0783 121258.1798 105715.6399 104023.2324 115730.439 127077.6531 104172.405 107514.9383 105884.2792 1.11345215 1.145195309 0.998407325 0.982423767 1.092989818 1.200156001 0.983832593 1.015400389 1 16.69212888 SVDALDDLT(ph)PPSTAESGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVDALDDLTPPSTAESGSR 19 0 S4R3V8;Q86X29-6;Q86X29-5;Q86X29-2;Q86X29-3;Q86X29-4;Q86X29 S4R3V8 LSR Lipolysis-stimulated lipoprotein receptor 1 SVDALDDLT(0.998)PPS(0.001)T(0.001)AESGSR;SVDALDDLT(1)PPSTAESGSR 271.64 2.78E-38 180095000 341330 291290 228680 455740 434970 433900 240520 520790 460260 TRUE FALSE 296222.3757 289376.4968 339270.4129 559222.7325 426314.948 450592.4138 217194.4074 409423.1113 405848.5871 0.729883964 0.713015903 0.83595317 1.377909768 1.050428563 1.110247585 0.535161177 1.008807531 1 18.63058207 3.991647096 24.43613344 0.997960129 0.734708449 0.266490676 0.203993921 437.5433782 1280037.142 0.055173312 0.106708031 9809.505066 -3.991647096 -0.26325168 SVDEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVDEALR 7 0 P32119 P32119 PRDX2 Peroxiredoxin-2 0 ; 178.24 0.0016715 2862800000 6567900 5672000 3543000 4106400 5512300 6239000 5397100 6000000 5983200 FALSE TRUE 5699935.374 5634740.259 5256406.651 5038820.882 5402616.015 6479018.367 4873690.073 4716946.692 5275872.912 1.080377687 1.068020468 0.996310324 0.955068662 1.024023153 1.228046709 0.923769422 0.894059954 1 22.33097838 SVDETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SVDETLR 7 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5;Q13162;H7C3T4 Q06830;Q13162 PRDX1;PRDX4 Peroxiredoxin-1;Peroxiredoxin-4 0 ;;;;;; 199.65 0.00086569 7617770000 8114920 7183580 4572330 5484530 6641600 7634460 7012260 7343520 7245030 FALSE TRUE 7042512.761 7136390.59 6783524.082 6729876.362 6509445.154 7928162.616 6332212.104 5773165.395 6388530.807 1.10236813 1.117062875 1.0618285 1.053430995 1.018926785 1.240999356 0.991184405 0.903676537 1 22.60705276 2.014246898 24.99995113 0.945699728 1.094470138 0.511142909 0.062551824 162.2751584 284753.6203 0.024620002 0.016591244 103.3348701 -2.014246898 0.14877041 SVDFEMPPPS(ph)PPLNLHELSGPAEGASLTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SVDFEMPPPSPPLNLHELSGPAEGASLTPK 30 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;Q9C0H9-4 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(0.967)PPLNLHELS(0.021)GPAEGAS(0.008)LT(0.003)PK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK 298.4 2.66E-81 1553345000 2761986 1549692 1051944 1453097 1598220 1529700 1824405 2390090 2225951 TRUE FALSE 2396982.552 1539511.971 1560667.637 1783044.883 1566418.549 1588548.549 1647474.484 1878987.853 1962801.609 1.221204701 0.784344156 0.795122457 0.908418291 0.798052407 0.809327108 0.839348448 0.957298916 1 20.90448293 1.593768826 4.213319302 0.990970784 0.868038887 0.092445646 0.128275526 0.346931597 13.56038117 0.093223045 0.03185475 39.24359874 -1.593768826 -0.122931897 SVDIS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SVDISPTR 8 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 SVDIS(0.98)PT(0.02)R;SVDIS(0.992)PT(0.008)R;SVDIS(0.896)PT(0.104)R 132.22 0.0010191 1471180000 3165970 2856300 1829900 2254610 3035760 3212120 2665580 3112570 3053200 TRUE FALSE 2747579.043 2837536.777 2714845.761 2766553.66 2975354.315 3335692.335 2407072.462 2446971.128 2692254.174 1.020549645 1.053963182 1.008391327 1.0275975 1.105153571 1.238996068 0.894073258 0.908893057 1 21.36038319 2.178455511 24.99999374 0.927346915 1.07086965 0.470203264 0.070523687 64.54389136 26845.51272 0.029861694 0.020132756 150.8188105 -2.178455511 0.143522735 SVDISLGDS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SVDISLGDSPR 11 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 SVDISLGDS(1)PR;SVDISLGDS(1)PR;SVDISLGDS(1)PR;SVDISLGDS(1)PR;SVDISLGDS(1)PR;SVDISLGDS(1)PR;SVDISLGDS(1)PR 199.13 5.38E-08 3520403000 2989183 2863137 1757479 2296556 2752592 2839460 2749738 3232135 3318540 TRUE FALSE 2594154.893 2844328.865 2607401.723 2818024.14 2697820.805 2948695.864 2483068.832 2540968.083 2926225.982 0.886518987 0.972012716 0.89104592 0.963023416 0.921945476 1.007678792 0.848556758 0.86834308 1 21.48060976 2.220656713 24.99994257 0.895486332 0.939759274 0.075937939 0.053314246 489.4736697 683466.6161 0.020828041 0.014074783 166.209833 -2.220656713 0.044272942 SVDTGETDIDPVMDDDDVFPPYVLRPDDGGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVDTGETDIDPVMDDDDVFPPYVLRPDDGGPR 32 1 Q9UPY3-2;Q9UPY3 Q9UPY3-2 DICER1 Endoribonuclease Dicer 0 ; 115.18 1.91E-06 53445000 36877 37261 27622 27379 42000 39242 38820 38512 37909 FALSE TRUE 32003.61102 37016.23004 40980.09159 33595.82041 41164.28217 40751.66513 35055.24238 30276.5085 33427.44121 0.957405349 1.107360561 1.225941625 1.005037155 1.231451786 1.219108124 1.048696553 0.905738142 1 15.0287453 1.983425177 6.272794989 0.954017336 1.128429071 0.366262025 0.092947993 0.158678134 25.2748756 0.042487166 0.024907615 96.25541627 -1.983425177 0.174411735 SVDVILDDDLVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVDVILDDDLVDK 13 0 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 0 135.6 0.00019096 22576000 25129 23093 14899 17684 18475 16872 24080 29717 20817 FALSE TRUE 21808.13898 22941.30056 22104.20623 21699.42248 18107.38365 17521.07676 21744.72531 23362.25081 18356.03797 1.188063514 1.249795876 1.204192662 1.182140858 0.986453813 0.954512994 1.184608865 1.272728398 1 14.16396708 3.461075468 24.86567937 1.10348881 1.213523826 0.284922739 0.096536913 384.1867367 595360.793 0.031859489 0.041142941 2891.182242 -3.461075468 0.110035016 SVDVTNTTFLLMAASIYLHDQNPDAALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVDVTNTTFLLMAASIYLHDQNPDAALR 28 0 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 0 158.73 1.08E-11 104240000 57194 60700 37040 56420 56988 65448 77745 75030 73141 FALSE TRUE 49635.66799 60301.2577 54952.66789 69231.02333 55854.0503 67965.82691 70205.30187 58985.41838 64494.3543 0.769612604 0.93498506 0.852053928 1.073443158 0.866030072 1.053825992 1.088549573 0.914582664 1 15.97688526 5.883629653 0.638862171 0.996399026 1.80E-17 0.448205358 0.077662944 12.19899607 1.255510992 0.033411168 12.34257399 764944.0182 -5.883629653 -0.996399026 SVEDEMDS(ph)PGEEPFYTGQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 324.91 2.98E-67 829035000 1396710 929380 633172 827883 878900 832285 861260 995210 1068680 TRUE FALSE 1212131.235 923274.8416 939376.097 1015866.489 861411.6095 864303.5425 777735.1378 782392.0862 942341.8678 1.2862967 0.979766339 0.996852766 1.078023298 0.914117943 0.917186821 0.825321642 0.830263531 1 19.84589102 8 0.453254819 0.877884128 9.299148434 0.672325919 0.076021649 59.85756665 0.745499108 0.058135425 465.6118504 100000000 -8 8.421264306 SVEDRFDQQKNDYDQLQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVEDRFDQQKNDYDQLQK 18 2 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 84.035 0.0021899 112150000 145230 86637 51259 39572 80400 66144 119600 128610 31998 FALSE TRUE 126037.4875 86067.87584 76048.02385 48557.42742 78800.1973 68688.60248 108001.2104 101107.7523 28215.23289 4.467001496 3.050404587 2.695282514 1.72096497 2.792824628 2.43445102 3.827762501 3.583445607 1 14.78418664 SVEEEEQVWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SVEEEEQVWR 10 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;; 204.79 4.20E-07 1522650000 786430 823230 515260 676780 836930 861770 675340 935270 760930 FALSE TRUE 682501.2829 817822.1479 764441.4594 830453.2429 820276.7304 894922.8495 609845.6307 735269.7888 670973.7223 1.017180346 1.218858684 1.139301636 1.237683706 1.222516923 1.333767359 0.908896445 1.095825014 1 19.35589674 2.2329579 24.99999959 1.017347944 1.196649405 0.495333255 0.091510087 117.8635996 525914.9979 0.035512025 0.024705513 170.9849555 -2.2329579 0.179301461 SVEEGKIDGIIDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVEEGKIDGIIDK 13 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 ; 144.12 3.75E-05 386270000 650290 568810 402860 446650 535290 440360 808930 981330 457170 FALSE TRUE 564352.5289 565073.4497 597684.4435 548068.7091 524638.7763 457300.9342 730480.0931 771480.2162 403123.8834 1.399948135 1.401736471 1.482632184 1.359554052 1.301433127 1.134393056 1.812048661 1.913754674 1 18.62086373 2.231194401 24.99998456 1.655651737 1.35383849 0.125213211 0.256666666 250.1246889 848881.715 0.102941959 0.070977457 170.2920608 -2.231194401 -0.301813247 SVEETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVEETLR 7 0 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 164.89 0.0027471 254220000 280400 278300 201040 333100 324460 380670 288600 309180 341530 FALSE TRUE 243344.4296 276471.829 298263.6164 408735.4461 318003.8808 395314.6212 260611.6164 243064.263 301154.7125 0.808037927 0.918039192 0.990399964 1.357227462 1.055948546 1.31266291 0.865374526 0.807107619 1 18.20014531 SVEGWILFVTGVHEEATEEDIHDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVEGWILFVTGVHEEATEEDIHDK 24 0 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ; 333.36 3.81E-87 324450000 248615 202986 216995 217806 221933 151364 266373 318890 379200 FALSE TRUE 215759.8978 201652.5716 321934.5078 267262.1813 217516.9675 157187.071 240540.1875 250697.8551 334371.408 0.645270178 0.60307959 0.962805133 0.799297353 0.650525022 0.470097225 0.719380251 0.749758649 1 18.35109196 1.197237538 2.466999864 1.099495625 0.694909794 0.360231301 0.127714359 0.782487303 4.699988962 0.712069824 0.035887976 15.74843991 -1.197237538 -0.404585831 SVESTS(ph)PEPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SVESTSPEPSK 11 0 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;P18583-8 P18583-7 SON Protein SON 1 SVEST(0.294)S(0.706)PEPSK;SVEST(0.214)S(0.786)PEPSK;SVEST(0.305)S(0.695)PEPSK;SVEST(0.001)S(0.999)PEPSK;SVEST(0.019)S(0.981)PEPSK 345.43 1.12E-70 5751800000 12577040 10835750 7142210 9086110 9973400 9251920 11858990 14252020 12520380 TRUE FALSE 10914952.3 10764569.24 10596206.65 11149250.15 9774948.853 9607847.349 10708906.98 11204336.43 11040234.94 0.988652176 0.975030813 0.959780902 1.009874356 0.885393192 0.870257508 0.969989048 1.014863949 1 23.39626754 1.993066646 24.99358115 1.003673539 0.947387197 0.242935956 0.042760551 460.1678997 1658828.622 0.019579066 0.012642343 98.41621228 -1.993066646 -0.056286342 SVETLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVETLK 6 0 P14618;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34;H3BU13 P14618;P14618-2;H3BU13 PKM Pyruvate kinase PKM;Pyruvate kinase 0 100.67 0.087001 157450000 594760 485690 292110 356280 436930 463470 526870 594170 554190 FALSE TRUE 516160.9591 482499.4704 433375.373 437178.8194 428235.9478 481299.9908 475774.2285 467111.3693 488674.2895 1.056247423 0.987364142 0.886838907 0.894622101 0.87632183 0.984909583 0.973601924 0.955874658 1 18.89851368 SVFALTNGIYPHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVFALTNGIYPHK 13 0 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ; 180.09 1.32E-05 5360000000 4638900 4220300 1975640 2849600 4157500 3670100 4508800 5052700 3545900 FALSE TRUE 4025857.612 4192576.571 2931066.112 3496645.233 4074773.884 3811291.122 4071537.27 3972219.425 3126707.742 1.287570807 1.340891736 0.937428872 1.118315341 1.303215465 1.218947032 1.302180314 1.270415963 1 21.57621294 2.477120172 0.002729302 6.82E-05 2.406917239 0.007227672 0.136736779 1061841.868 2315.28936 1024128.86 1017600.393 299.9992521 -2.477120172 2.406849007 SVFGT(ph)PTLETANK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVFGTPTLETANK 13 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 SVFGT(0.901)PT(0.099)LET(0.001)ANK 88.087 0.090208 135850000 255760 200970 139250 192000 192850 184140 233050 298870 288910 TRUE FALSE 221960.668 199649.8148 206591.7658 235596.5345 189012.6623 191223.985 210448.8469 234958.9763 254755.3889 0.871269766 0.783692214 0.810941691 0.924795097 0.741937837 0.750618017 0.826082022 0.922292468 1 17.95875314 1.569139368 2.509147928 0.996448422 0.812253541 0.579590317 0.053722101 0.200086639 2.604484433 0.065932406 0.014859063 37.0799695 -1.569139368 -0.184194881 SVFKPIVQIAVIENSESLDCQLLAVTHAGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVFKPIVQIAVIENSESLDCQLLAVTHAGVR 31 1 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 252.33 1.50E-58 792920000 659250 598780 386330 456100 570690 557200 695830 769870 788620 FALSE TRUE 572128.4422 594846.5748 573160.4802 559664.4761 559334.3855 578635.8446 628348.5137 605239.2916 695390.242 0.822744421 0.855414038 0.824228535 0.804820721 0.804346037 0.832102336 0.903591215 0.870359196 1 19.4074633 -1.410526339 0.716351925 10 0.82384255 0.827609293 0.024430925 50.09537876 0.651407768 713.7145243 0.010378106 0.038857393 1.410526339 -9.17615745 SVFPEQANNNEWAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SVFPEQANNNEWAR 14 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;;; 205.02 2.98E-08 558460000 208857 199609 118635 140213 189637 219477 201247 202365 192346 FALSE TRUE 181256.0183 198297.7553 176007.2828 172050.5047 185863.5947 227920.4222 181730.0969 159090.8196 169607.075 1.068681942 1.169159691 1.0377355 1.014406414 1.095848123 1.343814356 1.0714771 0.937996363 1 17.37183683 1.91253841 5.803827038 0.972652734 1.12099762 0.314263754 0.091803571 0.277308059 14.43556442 0.048093119 0.025554727 81.75953455 -1.91253841 0.148344886 SVFWASS(ph)PYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SVFWASSPYR 10 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 SVFWAS(0.015)S(0.985)PYR;SVFWAS(0.226)S(0.774)PYR;SVFWAS(0.022)S(0.978)PYR;SVFWAS(0.158)S(0.842)PYR;SVFWASS(1)PYR;SVFWAS(0.04)S(0.96)PYR;SVFWAS(0.003)S(0.997)PYR 209.19 1.05E-07 1971164000 1829889 3331180 1702785 1897255 2882300 3209330 2542470 2812080 3418080 TRUE FALSE 1588064.532 3309297.259 2526257.521 2328055.745 2824947.869 3332795.002 2295901.651 2210738.576 3013998.476 0.526896262 1.097975757 0.838174784 0.772414374 0.937275812 1.10577196 0.761746122 0.733490276 1 21.52324726 4.762744236 24.21463352 0.886579026 0.526895609 0.434057121 0.134397659 5139.112564 5145575.252 0.033685041 2.008756246 57908.75613 -4.762744236 -0.359683417 SVFWASS(ph)PYRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SVFWASSPYRR 11 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 SVFWAS(0.318)S(0.682)PYRR;SVFWAS(0.072)S(0.928)PYRR;SVFWAS(0.199)S(0.801)PYRR;SVFWAS(0.005)S(0.995)PYRR 114.7 0.00037489 1186540000 689284 761150 350752 434483 611967 708087 562223 672424 396066 TRUE FALSE 598193.373 756149.9555 520376.8404 533139.0058 599790.054 735327.5651 507698.7 528631.3604 349243.5287 1.712825933 2.165107993 1.490011404 1.526553714 1.71739776 2.105486587 1.453709685 1.513646831 1 18.41387386 1.04849164 1.167135901 0.358476 1.76612564 0.514828686 0.232031773 1.994976546 1.683877035 3.853075741 0.07319665 11.181283 -1.04849164 1.407649639 SVGATNMNEHSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVGATNMNEHSSR 13 0 J3KPF9;A0A087X011;E9PES4;Q9Y496;O15066 J3KPF9;O15066 KIF3A;KIF3B "Kinesin-like protein;Kinesin-like protein KIF3A;Kinesin-like protein KIF3B;Kinesin-like protein KIF3B, N-terminally processed" 0 83.633 0.0076714 35899000 24778 25285 10142 11247 25902 26529 25950 24155 14056 FALSE TRUE 21503.52452 25118.90117 15046.70512 13800.80325 25386.60088 27549.5878 23433.37299 18989.64122 12394.31569 1.734950525 2.026646875 1.214000474 1.113478436 2.048245462 2.222759891 1.890654843 1.532125024 1 13.597391 3.215554317 24.99952405 1.748520328 1.536276304 0.064004657 0.4088745 817.1006127 887889.8503 0.134016744 0.152056958 1642.685098 -3.215554317 -0.212244023 SVGGS(ph)GGGSFGDNLVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVGGSGGGSFGDNLVTR 17 0 P02545;P02545-3;P02545-5;P02545-4;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 SVGGS(0.939)GGGS(0.061)FGDNLVTR 115.53 0.00032565 282570000 415250 386040 292730 284010 349610 425740 402490 427060 450770 TRUE FALSE 360373.6604 383504.0778 434295.2071 348498.8113 342653.445 442118.4933 363456.5817 335736.5424 397480.4841 0.906644917 0.964837503 1.092620203 0.876769616 0.86206357 1.112302392 0.914401074 0.844661702 1 18.6005245 2.025531923 24.99995245 0.901723918 0.969529528 0.053422651 0.08980195 492.0953338 481840.2579 0.036292988 0.024467877 106.0551891 -2.025531923 0.06780561 SVGGSGGGS(ph)FGDNLVTR ddPTM_MDA-MB-175_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(0.014)VGGS(0.118)GGGS(0.867)FGDNLVTR;S(0.007)VGGS(0.002)GGGS(0.991)FGDNLVTR 233.55 4.32E-20 566120000 1194710 1015960 599450 707610 1008010 1019600 1031020 1064190 1044460 TRUE FALSE 1036826.046 1009286.092 889346.025 868283.6656 987952.5731 1058824.672 931031.8391 836621.25 920985.1287 1.125779358 1.095876644 0.965646455 0.942777075 1.07271284 1.14966533 1.010908657 0.908398218 1 19.81281834 -1.99990151 0.027624405 1.11E-06 1.771891842 0.166364057 0.072952803 6873.297267 18.82310523 828.0612781 438.7631286 0.010002268 1.99990151 1.771890727 SVGRPS(ph)PLASGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SVGRPSPLASGR 12 1 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 SVGRPS(1)PLASGR;SVGRPS(1)PLASGR;S(0.001)VGRPS(0.995)PLAS(0.004)GR 111.78 0.00081472 1234840000 753680 694810 466280 624110 726830 854960 506290 807990 731340 TRUE FALSE 654079.2784 690245.7474 691774.5676 765823.7144 712367.505 887850.8644 457190.0737 635207.6263 644881.8183 1.014262241 1.070344562 1.07271526 1.187541178 1.104648146 1.376765229 0.708951719 0.984998504 1 19.29867527 2.231488289 24.99999998 0.908235296 1.132458139 0.451733225 0.124239281 155.8574326 550934.8044 0.049057406 0.033868687 170.4073368 -2.231488289 0.224222843 SVGYKPDFVGFEIPDKFVVGYALDYNEYFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVGYKPDFVGFEIPDKFVVGYALDYNEYFR 30 2 P00492 P00492 HPRT1 Hypoxanthine-guanine phosphoribosyltransferase 0 201.49 1.16E-25 58237000 57358 59360 31853 40665 44909 38769 62039 78034 25507 FALSE TRUE 49777.99497 58970.06025 47257.21734 49898.60978 44015.39876 40260.46852 56022.46733 61347.03636 22491.59152 2.213182421 2.621871387 2.101105976 2.218545083 1.956971285 1.790023106 2.490818281 2.727554265 1 14.45709813 4.212704825 24.49549852 2.120560839 2.417526968 0.081331903 0.470306965 474.2778211 449326.1436 0.120874782 0.251768213 16319.42396 -4.212704825 0.29696613 SVHELEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SVHELEK 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;; 135.84 0.0030379 15639360000 26083020 25687900 9323610 18837940 23916320 22801880 28659180 31269380 29679450 FALSE TRUE 22636082.82 25519154.49 13832538.98 23115382.2 23440432.02 23679083.08 25879817.13 24582666.43 26170779.23 0.864937288 0.975101057 0.528548992 0.883251583 0.895671918 0.904790907 0.988882177 0.939317328 1 24.64145355 3.031049653 1.804498486 0.961020791 0.802903429 0.274099965 0.114669181 0.474437947 3.154369457 0.042167271 0.047175377 1074.11221 -3.031049653 -0.158117361 SVHELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVHELER 7 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;A1L2Z2 Q7Z406 MYH14 Myosin-14 0 89.296 0.017977 120150000 253510 272190 123110 207060 246860 299220 255980 299910 292020 FALSE TRUE 220008.0112 270401.966 182646.4078 254076.1377 241947.969 310731.187 231155.099 235776.5804 257497.7283 0.854407581 1.050113987 0.709312696 0.986712152 0.939612052 1.206733703 0.897697625 0.915645283 1 17.97420018 SVHFPGQAVGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVHFPGQAVGTR 12 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 110.92 0.0014375 705240000 386460 370750 157956 263584 442530 450740 344740 423870 422000 FALSE TRUE 335388.3318 368314.5188 234344.0499 323434.7758 433724.5188 468080.2595 311307.1679 333228.6991 372111.6407 0.901311045 0.989795745 0.629768124 0.869187471 1.165576325 1.257902759 0.836596155 0.895507322 1 18.505376 3.450147724 24.24282848 1.011503597 0.837614646 0.269921345 0.14871581 242.3203785 217787.5198 0.046518119 0.060056537 2819.34176 -3.450147724 -0.173888952 SVIDLRPEDVVHES(ph)GSLGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVIDLRPEDVVHESGSLGDR 20 1 Q96C24-2;Q96C24 Q96C24-2 SYTL4 Synaptotagmin-like protein 4 1 SVIDLRPEDVVHES(0.633)GS(0.367)LGDR;SVIDLRPEDVVHES(0.743)GS(0.257)LGDR 127.38 1.31E-05 350580000 402220 426210 164219 359940 509900 635560 428870 570920 538530 TRUE FALSE 349065.6079 423410.1984 243635.8577 441669.8783 499753.9876 660010.4045 387278.2534 448833.2009 474865.5969 0.735082959 0.891642185 0.513062768 0.930094497 1.052411442 1.389888863 0.815553403 0.945179444 1 18.85715971 3.511433981 9.199546723 1.025946143 0.729157205 0.435940985 0.169231841 0.439177038 113.2659153 0.047869242 0.069909785 3246.638846 -3.511433981 -0.296788939 SVIDYQTHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SVIDYQTHFR 10 0 Q9Y3B3;A0A0A6YYA0;Q86XR7-2;Q9Y3B3-2 Q9Y3B3 TMED7;TMED7-TICAM2 Transmembrane emp24 domain-containing protein 7 0 ;;; 209.97 8.58E-08 2316950000 3216740 3667130 2207960 2443860 3845670 4360630 2581240 3516490 4132290 FALSE TRUE 2791639.659 3643040.382 3275736.841 2998775.765 3769148.691 4528386.258 2330911.742 2764515.979 3643775.384 0.766139338 0.999798286 0.898995272 0.8229859 1.034407529 1.242773163 0.639696879 0.758695498 1 21.7970026 2.198539044 24.99999977 0.78431393 0.956887102 0.192417496 0.154682026 241.8444135 151069.6228 0.063606237 0.042883935 157.9570607 -2.198539044 0.172573172 SVIEDVINDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 120.09 0.0011599 18964000 41773 45625 28700 31574 41614 44955 40753 47611 46922 FALSE TRUE 36252.59221 45325.28637 42579.416 38743.35928 40785.96282 46684.44794 36800.78033 37429.75816 41374.93461 0.876196967 1.095476931 1.029111379 0.93639687 0.98576501 1.128326809 0.889446247 0.904648153 1 15.33646941 2.156539051 24.99844492 0.924051902 1.009159597 0.181715106 0.076676269 42.475453 12941.86656 0.030154274 0.020330012 143.3966649 -2.156539051 0.085107695 SVISHSVTSDMQTIEQES(ph)PIMAKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVISHSVTSDMQTIEQESPIMAKPR 25 1 Q9NP61;Q9NP61-2;H0Y6A0 Q9NP61;H0Y6A0 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 1 SVISHSVTSDMQTIEQES(1)PIMAKPR;SVISHSVTSDMQTIEQES(1)PIMAKPR 373.39 4.24E-120 683760000 370960 388670 132586 228070 333260 345250 287750 361830 288100 TRUE FALSE 321936.6961 386116.8012 196705.0331 279856.7793 326628.778 358531.9909 259844.0493 284455.4703 254041.1462 1.26726202 1.519898674 0.774303832 1.101619889 1.285731791 1.411314648 1.022842375 1.119722039 1 17.95470266 3.687720641 0.033042148 1.22E-06 2.400322087 0.082405409 0.206381794 1155.717205 24.70507214 849.871442 943.3554952 4872.149896 -3.687720641 2.400320868 SVKHDSIPAADTFEDLS(ph)DVEGGGSEPTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVKHDSIPAADTFEDLSDVEGGGSEPTQR 29 1 O95671;O95671-2;O95671-3 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 1 SVKHDSIPAADT(0.007)FEDLS(0.992)DVEGGGSEPTQR 81.18 0.0018757 52128000 118770 146800 19582 33563 175650 133850 162970 191530 22601 TRUE FALSE 103074.2436 145835.6611 29051.9207 41183.99213 172154.9087 138999.2961 147165.1945 150572.8 19929.13553 5.172037866 7.317711345 1.457761209 2.066521755 8.638353049 6.974677648 7.384424391 7.555410509 1 14.28259151 SVLIMDGASAFGTIAIQLAHHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVLIMDGASAFGTIAIQLAHHR 22 0 H7C3S0;H7C338;C9K0F7;C9JAL0;F8WF64;C9JZK8;H7C3I5;A6NND8;A6NHJ8;A6NMA8;O95825-2;O95825 H7C3S0 CRYZL1 Quinone oxidoreductase-like protein 1 0 74.662 0.0074278 4121100 10027 8166.2 3555.3 5544.5 6570.2 7527.5 8965.7 9085.3 3399 FALSE TRUE 8701.906545 8112.555695 5274.654972 6803.463467 6439.465874 7817.087796 8096.207794 7142.479297 2997.174092 2.903370401 2.706734893 1.759876073 2.269959388 2.148512458 2.608152732 2.701280455 2.383071212 1 11.54938717 4.412345771 8.198395541 2.20224084 2.855058741 0.24887153 0.482772343 0.34022451 37.81702525 0.120035246 0.320583859 25843.16919 -4.412345771 0.652817901 SVLLLAYKPMEGNFEEIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVLLLAYKPMEGNFEEIAR 19 1 Q16531;F5GY55;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 ; 187.33 1.70E-14 724700000 1366480 1120990 626460 900660 1024370 878290 1106330 1343570 1221410 FALSE TRUE 1185896.206 1113626.143 929418.1514 1105168.619 1003987.041 912078.3846 999038.2869 1056258.011 1077016.301 1.101094017 1.03399191 0.862956438 1.026139175 0.932192985 0.84685662 0.927598111 0.980726113 1 20.03860866 4.441352181 6.624082796 0.942087143 1.085490273 0.496508472 0.055600384 0.129946628 16.57416687 0.01403127 0.038979015 27628.17391 -4.441352181 0.14340313 SVLSEGHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SVLSEGHQR 9 0 O76071 O76071 CIAO1 Probable cytosolic iron-sulfur protein assembly protein CIAO1 0 ;; 136.57 0.0014443 423330000 745590 666000 471845 599312 674330 722520 754470 868490 879150 FALSE TRUE 647058.3924 661625.0021 700030.8202 735394.9495 660912.1523 750315.8119 681301.6155 682770.1721 775217.8885 0.834679388 0.85346973 0.903011696 0.948630005 0.852550182 0.967877319 0.878851773 0.880746152 1 19.56424234 4.26184058 3.319028722 0.91444054 0.838854065 0.333532052 0.044247668 0.277922038 6.226561447 0.01094385 0.031776092 18274.29284 -4.26184058 -0.075586475 SVLSGGPLPQGHEFELYEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVLSGGPLPQGHEFELYEVR 20 0 P35219 P35219 CA8 Carbonic anhydrase-related protein 0 ; 281.36 9.23E-45 963320000 675440 777630 396920 525560 821690 809510 756330 874380 835630 FALSE TRUE 586178.8927 772521.6973 588871.8396 644896.4307 805339.9766 840652.3735 682981.233 687400.6414 736842.7734 0.795527776 1.048421353 0.799182486 0.875215791 1.092960406 1.14088433 0.926902262 0.932900025 1 19.49099729 3.263812132 24.86181084 1.007221454 0.88590322 0.346882729 0.093961292 293.8299702 289293.1388 0.028125119 0.036294454 1835.744063 -3.263812132 -0.121318233 SVMSGDQLREDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVMSGDQLREDR 12 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7;B4DGD8;B0QZ65;A0A0A0MQV8 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 0 62.298 0.071829 134470000 111960 123280 57908 73591 119620 120210 106030 129960 61339 FALSE TRUE 97164.20233 122470.1656 85912.50249 90300.96132 117239.796 124834.5565 95747.22692 102169.0653 54087.5733 1.79642377 2.264293961 1.588396322 1.669532497 2.16759209 2.308008085 1.77022597 1.888956356 1 15.72300955 1.173692665 3.005931049 0.710938183 1.945583149 0.585580951 0.245813144 0.401698539 3.902296435 1.312910307 0.06442396 14.91738384 -1.173692665 1.234644965 SVNEILGLAES(ph)SPNEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVNEILGLAESSPNEPK 17 0 Q9H8G2;Q9H8G2-2 Q9H8G2 CAAP1 Caspase activity and apoptosis inhibitor 1 1 SVNEILGLAES(0.5)S(0.5)PNEPK 118.24 0.00018717 40960000 103470 99392 63925 79609 92897 76500 97855 121020 108050 TRUE FALSE 89796.17734 98739.08741 94839.34382 97685.4402 91048.53145 79443.0045 88365.03716 95140.81478 95276.45209 0.942480281 1.036343034 0.995412211 1.025284192 0.955624705 0.833815731 0.927459359 0.998576382 1 16.53983207 3.110549811 6.503406023 0.942338442 1.001783926 0.234552873 0.051442371 0.346977947 18.61971318 0.016881531 0.01921434 1289.881491 -3.110549811 0.059445484 SVNEILGLAESS(ph)PNEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SVNEILGLAESSPNEPK 17 0 Q9H8G2;Q9H8G2-2 Q9H8G2 CAAP1 Caspase activity and apoptosis inhibitor 1 1 SVNEILGLAES(0.015)S(0.985)PNEPK;SVNEILGLAESS(1)PNEPK;SVNEILGLAES(0.014)S(0.986)PNEPK;SVNEILGLAES(0.003)S(0.997)PNEPK 325.19 3.47E-59 610250000 1683000 1380750 1005510 1166870 1398000 1208750 1671250 2062540 1752740 TRUE FALSE 1460587.286 1371679.762 1491777.999 1431825.668 1370182.535 1255251.395 1509172.432 1621481.872 1545533.074 0.945037871 0.887512397 0.965219072 0.926428358 0.886543652 0.812180222 0.976473721 1.049140843 1 20.5596731 2.007249994 24.96884446 1.023498534 0.905130077 0.592106224 0.042376826 109.0552348 375582.7763 0.017675638 0.011889016 101.6833847 -2.007249994 -0.118368457 SVNELIYKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVNELIYKR 9 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 113.93 0.0027598 657410000 1388570 1218500 409600 486530 1110320 1033830 1348780 1553650 126464 FALSE TRUE 1205066.956 1210495.593 607683.93 597004.0726 1088226.804 1073602.109 1217975.523 1221414.038 111513.57 10.8064602 10.85514161 5.449416874 5.353645056 9.758693982 9.627546757 10.92221802 10.95305296 1 16.76685976 4.323090716 24.99608875 8.132094671 10.83092548 0.142021923 3.098553726 58.36841352 17252.64069 0.787845401 2.084442642 21042.17927 -4.323090716 2.698830806 SVNESLNNLFITEEDYQALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVNESLNNLFITEEDYQALR 20 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 386.06 2.02E-130 192890000 202371 180754 113058 139151 166055 202086 181673 185549 183461 FALSE TRUE 175627.1596 179566.6151 167733.227 170747.3613 162750.8304 209860.3792 164054.3804 145870.7903 161772.4496 1.085643199 1.10999503 1.036846678 1.055478617 1.006047883 1.297256608 1.014105806 0.901703539 1 17.30360641 2.003641541 24.99979864 0.948052789 1.095563942 0.370437747 0.080898462 99.95136212 686178.0643 0.032471545 0.021778492 100.8420211 -2.003641541 0.147511153 SVPAFLQDES(ph)DDRETDTASESSYQLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SVPAFLQDESDDRETDTASESSYQLSR 27 1 A0A0U1RR07;Q9HCH5-7;Q9HCH5-13;Q9HCH5-8;A0A0U1RQP0;Q9HCH5;Q9HCH5-14;E9PRW5;E9PS29;Q9HCH5-2;E9PK22;E9PS39;Q9HCH5-12 A0A0U1RR07;Q9HCH5-12 SYTL2 Synaptotagmin-like protein 2 1 SVPAFLQDES(1)DDRETDTASESSYQLSR;SVPAFLQDES(1)DDRETDTASESSYQLSR;SVPAFLQDES(1)DDRETDTASESSYQLSR;SVPAFLQDES(1)DDRETDTASESSYQLSR 238.37 2.62E-45 1076980000 239828 197632 122441 177936 202394 211505 205849 272163 202796 TRUE FALSE 208134.1222 196333.7424 181653.8771 218339.0884 198366.7554 219641.7342 185885.7957 213963.0604 178821.6879 1.163919906 1.09793026 1.015838063 1.220987739 1.1092992 1.228272347 1.039503641 1.196516278 1 17.44816219 4.761349675 21.59740096 1.120312071 1.163920192 0.030458049 0.081744954 4065.271868 3852297.723 0.018331311 0.7112339 57723.10374 -4.761349675 0.043608121 SVPGALDKDS(ph)LEETEESIDALVSSQLSTNTHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVPGALDKDSLEETEESIDALVSSQLSTNTHR 32 1 Q8TDW5;Q8TDW5-2 Q8TDW5 SYTL5 Synaptotagmin-like protein 5 1 S(0.003)VPGALDKDS(0.761)LEET(0.212)EES(0.024)IDALVSSQLSTNTHR 78.784 0.0008006 23422000 14038 13065 8895.4 8611.6 12387 12272 15296 12665 10882 TRUE FALSE 12182.84273 12979.17515 13197.24519 10566.9954 12140.52293 12744.11178 13812.59627 9956.688309 9595.542357 1.269635658 1.352625487 1.375351669 1.101240035 1.265225298 1.328128344 1.439480517 1.037636846 1 13.22814864 1.628305598 6.357524658 1.009370921 1.300044604 0.642361271 0.088673759 0.078481819 6.601228432 0.058518116 0.023474584 42.49184595 -1.628305598 0.290673683 SVPHEEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVPHEEYR 8 0 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WUT0;H0YN19 A0A0A0MQW0 MYEF2 Myelin expression factor 2 0 ; 135.83 0.00081697 763620000 651290 556220 386440 548560 395920 557910 569270 593330 1066690 FALSE TRUE 565220.3763 552566.1542 573323.6766 673118.9322 388041.9666 579373.1587 514062.283 466450.9968 940587.1234 0.600922937 0.587469401 0.609538088 0.715636984 0.412552922 0.61596969 0.546533405 0.495914717 1 19.84320206 1.232454231 24.98526006 1.000000709 0.57057667 0.739854262 0.079548248 102.4386928 419102.1867 0.170712668 0.019071256 17.07867723 -1.232454231 -0.429424039 SVPIWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVPIWER 7 0 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 ; 88.942 0.042427 1142220000 1844710 1836370 875140 1182490 1677430 1403150 2488500 1968280 1821390 FALSE TRUE 1600926.9 1824306.765 1298360.631 1450992.428 1644052.425 1457130.088 2247165.653 1547378.639 1606067.349 0.996799356 1.135884349 0.808409829 0.903444322 1.023650986 0.907265869 1.39917274 0.963458126 1 20.61510096 SVPTWLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVPTWLK 7 0 P62277;J3KMX5;E9PS50 P62277 RPS13 40S ribosomal protein S13 0 82.671 0.055501 365330000 731130 758110 501470 610100 793540 642190 763500 1011200 897970 FALSE TRUE 634509.3181 753129.9255 743982.5693 748632.5298 777750.1065 666895.4649 689455.8875 794962.7492 791813.0096 0.801337324 0.951146188 0.939593768 0.945466317 0.982239616 0.84223858 0.870730689 1.003977883 1 19.59480025 -1.999999942 0.017026309 2.057818787 1.26E-12 0.197914566 0.060834479 19388.47778 32.85002511 2413.383673 1631.012154 0.010000001 1.999999942 -2.057818787 SVPVTVDDDDDDNDPENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 232.5 4.88E-20 256400000 268866 216556 172318 205751 221278 223024 271540 311030 371670 FALSE TRUE 233334.6769 215133.4294 255651.5612 252469.9093 216875.0007 231603.8776 245206.0926 244518.6549 327731.596 0.711968818 0.656431763 0.780063821 0.770355719 0.66174578 0.706687669 0.7481918 0.746094237 1 18.32215524 1.169849475 2.771282148 1.09659814 0.719059923 0.821849131 0.040677659 0.252075872 1.931476266 0.239538355 0.010812855 14.78595822 -1.169849475 -0.377538217 SVQNHNNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SVQNHNNK 8 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 118.06 0.0019595 1661422000 2219640 1901460 959519 1380013 1495561 1792650 2234610 2506200 2740310 FALSE TRUE 1926308.95 1888969.184 1423545.598 1693366.044 1465802.262 1861614.405 2017897.866 1970268.633 2416353.674 0.797196607 0.781743668 0.589129652 0.700793953 0.606617433 0.770422983 0.835100378 0.815389177 1 21.2044002 0.945893658 0.797495212 1.295472728 0.698911647 0.61603891 0.072776653 2.692198671 0.973290737 1.601159235 0.030124297 8.828636937 -0.945893658 -0.596561081 SVRPTDSNVS(ph)PAISIHEIGAVGATK ddPTM_MDA-MB-175_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 SVRPTDS(0.015)NVS(0.985)PAISIHEIGAVGATK;S(0.17)VRPT(0.123)DS(0.066)NVS(0.641)PAISIHEIGAVGATK 181.21 1.47E-17 407770000 508570 414130 144031 321070 446120 519360 499090 537680 555480 TRUE FALSE 441361.1859 411409.5528 213684.8734 393973.8507 437243.0848 539340.1153 450688.3286 422701.3162 489811.7872 0.901083227 0.839933957 0.436259149 0.804337219 0.89267571 1.10111706 0.920125527 0.862987227 1 18.90186797 3.267955279 3.536786202 0.951674298 0.723128284 0.382419257 0.135391676 0.252323192 6.601217023 0.042345837 0.053376448 1853.340768 -3.267955279 -0.228546014 SVS(ph)ANPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SVSANPK 7 0 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 SVS(1)ANPK;SVS(1)ANPK;S(0.003)VS(0.997)ANPK 103.88 0.0086823 1226550000 3256570 2802050 1644010 2015030 1414330 1994580 3243240 3157270 4059710 TRUE FALSE 2826206.023 2783643.149 2439058.735 2472573.359 1386187.6 2071312.783 2928711.084 2482112.38 3579775.709 0.789492486 0.77760267 0.68134401 0.690706223 0.387227501 0.578615241 0.818126978 0.693370921 1 21.77143777 -0.169447911 1.198993475 9.528804737 0.660981361 0.403955974 0.123289196 44.41766268 2.981661607 981.2149245 0.03978611 0.67694298 0.169447911 -8.867823376 SVS(ph)EAALAQPQGPLGTDSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SVSEAALAQPQGPLGTDSLK 20 0 M0R201;M0QY29;Q05469-2;Q05469 M0R201 LIPE Hormone-sensitive lipase 1 S(0.055)VS(0.945)EAALAQPQGPLGTDSLK;S(0.147)VS(0.853)EAALAQPQGPLGTDSLK;S(0.044)VS(0.956)EAALAQPQGPLGTDSLK 284.98 5.11E-45 395930000 1267020 1191990 771860 825130 1044410 1024870 1196300 1355260 1375830 TRUE FALSE 1099580.097 1184159.739 1145134.078 1012488.378 1023628.284 1064297.412 1080283.01 1065448.196 1213180.945 0.906361167 0.97607842 0.943910373 0.834573261 0.843755656 0.877278379 0.890454977 0.878226946 1 20.21036331 3.844061287 10.35121795 0.884399374 0.945809328 0.226949605 0.047254724 0.632255749 58.37261408 0.012430368 0.02155825 6983.309449 -3.844061287 0.061409955 SVS(ph)EESANSLVSVGVEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVSEESANSLVSVGVEAK 18 0 Q8NEZ4;Q8NEZ4-3;H0YMU7;C9J4Z5 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 S(0.063)VS(0.937)EESANSLVSVGVEAK 205.23 1.03E-15 53915000 79151 56903 39220 41957 56369 50140 72237 80339 65762 TRUE FALSE 68690.99481 56529.20045 58186.92318 51483.97812 55247.36718 52068.91824 65231.46686 63159.13005 57987.69128 1.184578887 0.974848269 1.003435762 0.887843213 0.952743004 0.897930528 1.124919193 1.089181664 1 15.82345908 0.927278841 21.41880027 0.496895159 1.013928674 0.002233182 0.095357562 7969.97636 1582484.45 64440.57021 0.023600544 8.45821735 -0.927278841 0.517033516 SVS(ph)HGSNHTQKPDEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVSHGSNHTQKPDEQR 16 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.446)VS(0.548)HGS(0.006)NHTQKPDEQR 112.56 0.00044052 1013100000 21401 20573 4815.2 16126 33672 29332 30536 28897 34415 TRUE FALSE 18572.80363 20437.85461 7143.846826 19787.65477 33001.99308 30460.42102 27574.62342 22717.60143 30346.49791 0.612024613 0.673483137 0.235409267 0.652057276 1.08750582 1.003754078 0.908659164 0.748607022 1 14.88924241 3.426478532 6.390043616 0.921849759 0.510544301 0.673698574 0.142743055 0.123345419 11.30964285 0.042904062 0.055906159 2669.798792 -3.426478532 -0.411305457 SVS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVSPER 6 0 Q14966;Q14966-3;Q14966-4;A0A096LPI0;Q14966-2;Q14966-6;A0A096LPB4;A0A096LNR2;A0A096LNX0;A0A096LNQ0 Q14966 ZNF638 Zinc finger protein 638 1 S(0.003)VS(0.997)PER;S(0.101)VS(0.899)PER 88.358 0.05391 893250000 740910 609960 353300 433990 398180 569870 555330 638400 557100 TRUE FALSE 642996.8663 605953.1326 524157.0617 532534.0626 390256.997 591793.2677 501474.1821 501883.128 491240.2727 1.308925392 1.233516807 1.067007513 1.08406027 0.79443201 1.204692084 1.020832798 1.021665275 1 18.90606931 4.289788452 1.925577019 1.019651594 1.316269963 0.521169723 0.099620724 0.301567548 2.024940607 0.026203343 0.116793017 19488.95047 -4.289788452 0.296618368 SVS(ph)PESNDSISEELNHFKPIVCSPCTPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVSPESNDSISEELNHFKPIVCSPCTPPK 29 1 Q8NCN4 Q8NCN4 RNF169 E3 ubiquitin-protein ligase RNF169 1 S(0.003)VS(0.996)PESNDSISEELNHFKPIVCSPCTPPK 135.08 4.12E-06 115460000 92243 68446 45395 57149 68763 51019 81067 100170 78919 TRUE FALSE 80052.85384 67996.37372 67348.17384 70125.55392 67394.75083 52981.73394 73205.13482 78749.42502 69589.28572 1.150361769 0.97710981 0.967795159 1.007706189 0.968464472 0.761349012 1.051959854 1.13163146 1 16.08657758 2.018927111 24.99878852 1.080191401 0.968030997 0.151498445 0.098146989 355.7300408 469843.8641 0.040076666 0.027015269 104.4544895 -2.018927111 -0.112160404 SVS(ph)PLVWCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SVSPLVWCR 9 0 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 S(0.001)VS(0.999)PLVWCR;S(0.021)VS(0.979)PLVWCR;S(0.001)VS(0.999)PLVWCR 131.82 0.00033822 465500000 383390 423460 226217 268684 377240 429380 329390 397720 329367 TRUE FALSE 332724.0401 420678.2634 335616.2979 329692.8088 369733.6621 445898.5264 297445.8085 312670.6731 290429.6085 1.145627134 1.448468927 1.155585684 1.135190074 1.273057744 1.535306709 1.024158005 1.07657988 1 18.14782901 2.134739732 24.10477603 1.042126481 1.277204512 0.448559169 0.129754734 7.766262104 1785.219587 0.052362115 0.035302541 136.3765602 -2.134739732 0.235078031 SVS(ph)PPPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVSPPPKR 8 1 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 S(0.251)VS(0.749)PPPKR 54.191 0.080742 384590000 524920 403580 259740 332520 356170 337180 431420 453500 402490 TRUE FALSE 455550.492 400928.8564 385351.1328 408023.7482 349082.9138 350151.5328 389580.9548 356522.5541 354908.0907 1.283573139 1.129669531 1.085777256 1.149660317 0.983586802 0.986597775 1.097695333 1.004548962 1 18.43708594 8 0.488371865 1.016020036 8.701648368 0.743965808 0.047472937 56.34922654 0.638174231 0.030641555 440.4505647 100000000 -8 7.685628332 SVS(ph)PSPS(ph)VLSEGRDEPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVSPSPSVLSEGRDEPQR 18 1 C9IYE1;A0A087X1P3;Q86UW7-3;Q86UW7-2;Q86UW7 C9IYE1 CADPS2 Calcium-dependent secretion activator 2 2 S(0.014)VS(0.911)PS(0.097)PS(0.541)VLS(0.437)EGRDEPQR 143.39 2.45E-05 0 221020 234130 120900 136680 221940 208100 187420 226960 161080 TRUE FALSE 191811.647 232591.9846 179367.6444 167715.283 217523.8282 216105.7417 169244.0372 178426.3702 142037.3059 1.350431464 1.637541512 1.26282066 1.18078333 1.531455605 1.521471703 1.191546377 1.25619371 1 17.11591038 1.20389311 1.056882468 0.784774161 1.406078711 0.4361675 0.144302079 1.924640182 1.684308356 1.400751377 0.049128372 15.99164387 -1.20389311 0.62130455 SVS(ph)PSPSVLS(ph)EGRDEPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SVSPSPSVLSEGRDEPQR 18 1 C9IYE1;A0A087X1P3;Q86UW7-3;Q86UW7-2;Q86UW7 C9IYE1 CADPS2 Calcium-dependent secretion activator 2 2 S(0.116)VS(0.883)PS(0.001)PS(0.001)VLS(0.999)EGRDEPQR;S(0.392)VS(0.608)PS(0.001)PS(0.032)VLS(0.967)EGRDEPQR;S(0.095)VS(0.905)PS(0.029)PS(0.463)VLS(0.508)EGRDEPQR 126.9 1.51E-05 835210000 531120 589010 324181 331111 539080 511170 460880 562940 390860 TRUE FALSE 460931.1463 585140.7545 480956.0159 406294.8133 528353.3627 530835.0407 416183.9285 442559.6618 344652.9761 1.337377531 1.697767886 1.395479074 1.178851893 1.533001017 1.540201529 1.207544857 1.284073235 1 18.39478495 0.495709244 0.736302869 7.63E-14 1.449623813 0.46002042 0.14883308 7.022184346 1.323903995 10.89505586 0.062295933 3.131188724 -0.495709244 1.449623813 SVS(ph)PSPSVLSEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SVSPSPSVLSEGR 13 0 C9IYE1;A0A087X1P3;Q86UW7-3;Q86UW7-2;Q86UW7 C9IYE1 CADPS2 Calcium-dependent secretion activator 2 1 SVS(1)PSPSVLSEGR;SVS(1)PSPSVLSEGR;SVS(1)PSPSVLSEGR;SVS(1)PSPSVLSEGR 361.26 1.25E-76 4097350000 2866490 3045490 1828870 2266140 2940350 2837300 2480960 2977310 2947550 TRUE FALSE 2487676.084 3025483.976 2713317.649 2780701.723 2881842.788 2946452.767 2240356.881 2340635.426 2599093.997 0.957132019 1.164053312 1.043947488 1.069873474 1.108787443 1.133646098 0.86197609 0.900558206 1 21.30957738 2.23881318 24.99989671 0.914165528 1.08268097 0.571717953 0.064638993 4.245602263 420325.1309 0.023834329 0.017284414 173.3058329 -2.23881318 0.168515442 SVS(ph)PSPSVLSEGRDEPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVSPSPSVLSEGRDEPQR 18 1 C9IYE1;A0A087X1P3;Q86UW7-3;Q86UW7-2;Q86UW7 C9IYE1 CADPS2 Calcium-dependent secretion activator 2 1 S(0.008)VS(0.855)PS(0.135)PS(0.001)VLS(0.002)EGRDEPQR;S(0.001)VS(0.998)PSPSVLSEGRDEPQR 242.16 3.04E-24 736690000 612480 738650 275240 293250 617420 552680 574140 680630 85523 TRUE FALSE 531539.2162 733797.7595 408346.9846 359836.8945 605134.55 573941.9572 518459.9912 535082.5712 75412.56837 7.048416831 9.730443816 5.414839906 4.771577236 8.024319594 7.610693677 6.874981218 7.095403097 1 16.20251736 4.228331587 24.99121545 6.101178981 8.38943056 0.197238411 2.092896168 315.9033346 771810.1345 0.526358001 1.115665867 16917.32089 -4.228331587 2.288251579 SVS(ph)PSPVPLLFQPDQNAPPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SVSPSPVPLLFQPDQNAPPIR 21 0 Q02241-2;Q02241-3 Q02241-2 KIF23 Kinesin-like protein KIF23 1 S(0.138)VS(0.862)PS(0.001)PVPLLFQPDQNAPPIR;S(0.127)VS(0.872)PS(0.001)PVPLLFQPDQNAPPIR;S(0.007)VS(0.993)PSPVPLLFQPDQNAPPIR;S(0.395)VS(0.463)PS(0.141)PVPLLFQPDQNAPPIR;S(0.13)VS(0.87)PSPVPLLFQPDQNAPPIR 363.51 6.78E-97 1226578000 189656 200316.8 107454.5 170889.9 207648.7 184321.5 163591.5 220762.9 172695.1 TRUE FALSE 164592.4791 199000.9058 159419.8556 209693.0637 203516.8971 191412.4674 147726.4215 173554.4718 152279.282 1.080859306 1.306815367 1.046891301 1.377029501 1.336471347 1.256982991 0.970101905 1.13971165 1 17.21636015 2.252048132 24.99937639 1.055314228 1.240107167 0.404861437 0.112004251 230.4326967 427111.3826 0.040784418 0.031410487 178.668558 -2.252048132 0.184792938 SVS(ph)PTFLNPSDENLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVSPTFLNPSDENLK 15 0 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 S(0.002)VS(0.998)PTFLNPSDENLK 335.23 5.29E-69 568220000 909430 796860 547060 651040 803870 733480 889640 1079500 991130 TRUE FALSE 789246.5213 791625.3742 811620.0458 798868.5825 787874.5597 761697.4502 803362.8497 848657.3257 873959.7405 0.903069655 0.90579158 0.928669832 0.914079385 0.901499833 0.871547527 0.919221805 0.971048535 1 19.7372073 1.666188046 2.687637425 0.99599449 0.904987079 0.845719707 0.014437577 0.090811037 1.459320453 0.014205444 0.004240478 46.36476323 -1.666188046 -0.091007411 SVS(ph)SDSLGPPRPAPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SVSSDSLGPPRPAPAR 16 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 S(0.005)VS(0.976)S(0.018)DSLGPPRPAPAR;SVS(0.825)S(0.174)DSLGPPRPAPAR;SVS(0.986)S(0.013)DSLGPPRPAPAR;S(0.002)VS(0.969)S(0.029)DSLGPPRPAPAR 180.62 1.48E-09 3231050000 2409080 1760000 1057434 1157398 1658340 1307680 1881180 1793060 1514310 TRUE FALSE 2090713.974 1748438.444 1568812.619 1420202.906 1625342.278 1357987.296 1698743.453 1409628.073 1335289.997 1.565737764 1.309407281 1.174885323 1.063591361 1.217220441 1.01699803 1.272190653 1.055671858 1 20.34872167 4.730880108 1.334221501 1.108161045 1.764058048 0.755285147 0.084577726 0.617614872 0.980346806 0.02309775 0.549393523 53812.12071 -4.730880108 0.655897003 SVS(ph)TMNLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVSTMNLSK 9 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 SVS(0.978)T(0.022)MNLSK;S(0.006)VS(0.796)T(0.198)MNLSK 110.98 0.0023698 0 640370 631800 354080 366170 387650 497940 529380 496160 664210 TRUE FALSE 555743.482 627649.6642 525314.2723 449314.4951 379936.5234 517096.074 478040.8091 390060.0451 585687.8505 0.948873161 1.071645355 0.896918507 0.767156933 0.648701391 0.882886803 0.816204073 0.665986233 1 19.15977244 3.976828788 3.720527142 0.782928174 1.009053986 0.410626748 0.104517411 0.191495025 5.716079865 0.027092973 0.055194036 9480.446407 -3.976828788 0.226125812 SVS(ph)TTNIAGHFNDES(ph)PLGLR ddPTM_MDA-MB-175_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 2 S(0.452)VS(0.506)T(0.02)T(0.022)NIAGHFNDES(1)PLGLR;S(0.135)VS(0.829)T(0.024)T(0.011)NIAGHFNDES(1)PLGLR 138.29 1.09E-06 141349000 139076 137627 82630 103521 107433 116856 102405 114298 142822 TRUE FALSE 120696.7542 136722.9192 122590.1444 127027.0253 105295.2935 121351.5259 92473.77886 89856.26217 125937.7459 0.958384267 1.085638926 0.973418601 1.008649348 0.836090028 0.963583436 0.734281674 0.713497463 1 16.94235122 3.02422663 1.160518041 0.803891606 1.020637442 0.362699527 0.096714032 0.424886671 1.249117543 0.045907776 0.050934195 1057.369138 -3.02422663 0.216745837 SVS(ph)TTNIAGHFNDESPLGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SVSTTNIAGHFNDESPLGLR 20 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 S(0.002)VS(0.986)T(0.012)TNIAGHFNDESPLGLR;S(0.011)VS(0.956)T(0.017)T(0.017)NIAGHFNDESPLGLR;S(0.002)VS(0.858)T(0.135)T(0.005)NIAGHFNDESPLGLR;S(0.005)VS(0.939)T(0.052)T(0.003)NIAGHFNDESPLGLR;S(0.008)VS(0.962)T(0.028)T(0.002)NIAGHFNDESPLGLR;S(0.034)VS(0.951)T(0.006)T(0.009)NIAGHFNDESPLGLR 347.71 3.33E-95 12264510000 1753922 2136422 1223452 1515510 1762181 2195120 1383729 1649566 1984733 TRUE FALSE 1522136.764 2122387.703 1815117.479 1859629.709 1727117.046 2279567.687 1249535.175 1296819.148 1750100.126 0.869742674 1.212723588 1.037150648 1.062584752 0.986867563 1.302535583 0.71397925 0.740997117 1 20.73900603 2.219358853 24.99999708 0.797867576 1.077915547 0.43650363 0.138756011 197.5890043 257251.71 0.0532865 0.035987443 165.7138672 -2.219358853 0.280047971 SVS(ph)VDESRPELIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SVSVDESRPELIFR 14 1 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 1 S(0.116)VS(0.884)VDESRPELIFR;S(0.029)VS(0.971)VDESRPELIFR;S(0.004)VS(0.996)VDESRPELIFR;SVS(1)VDESRPELIFR;S(0.026)VS(0.974)VDESRPELIFR 250.26 1.54E-18 861854000 1108020 971874 774367 953905 1022580 1018636 1394930 1294040 1306210 TRUE FALSE 961592.3496 965489.6957 1148853.471 1170503.71 1002232.659 1057823.586 1259649.903 1017319.616 1151791.342 0.834866798 0.838250524 0.997449303 1.016246318 0.870151235 0.918415991 1.093644185 0.883249925 1 20.13544795 4.248559516 24.62742859 0.963959838 0.836558553 0.406103614 0.066136609 169.1624179 416638.8742 0.016073019 0.04142539 17723.90918 -4.248559516 -0.127401286 SVSDNDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SVSDNDIR 8 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 116.25 0.0053682 2562270000 7572360 5208080 3121970 3850890 4692550 5626530 5144110 5610840 5767560 FALSE TRUE 6571653.44 5173867.78 4631765.134 4725293.432 4599177.436 5842986.25 4645235.004 4411005.53 5085725.627 1.292176166 1.017331283 0.910738304 0.929128659 0.904330625 1.148899229 0.913386868 0.867330614 1 22.2780222 4.718653177 2.995412673 0.948179031 1.340538604 0.647405133 0.077939455 0.225367598 3.063192685 0.02003631 0.206649505 52318.24622 -4.718653177 0.392359573 SVSDQFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SVSDQFYR 8 0 P55010;H0YLZ1;H0YN40;H0YMJ8;H0YM54;H0YK11;H0YK29 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ;;;; 142.79 0.0014234 2112390000 1574640 1699720 1077795 1223952 1607480 1664220 1537920 1687120 1606110 FALSE TRUE 1366547.334 1688554.427 1599020.267 1501869.009 1575494.293 1728243.62 1388772.755 1326342.517 1416237.505 0.964913956 1.192281959 1.129062224 1.060464084 1.112450621 1.220306349 0.980607243 0.936525485 1 20.4336318 2.108094578 8.275766704 0.962313384 1.114907887 0.469212623 0.070615627 0.188548214 13.16668755 0.027467637 0.018490797 128.2609873 -2.108094578 0.152594503 SVSDYDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVSDYDGK 8 0 P07237;H7BZ94;I3L398;I3L312;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ; 113.71 0.0065069 546240000 912580 746180 631880 832550 624680 755950 759470 840650 1040850 FALSE TRUE 791980.2408 741278.2944 937459.2815 1021593.202 612250.0902 785031.8857 685816.7163 660883.5394 917801.8987 0.862909787 0.807666987 1.021417893 1.113086826 0.66708305 0.855339139 0.747238284 0.720072099 1 19.80782327 3.227988468 24.99959921 0.787278751 0.946023548 0.283840337 0.120228724 271.7200053 642525.539 0.036668524 0.042008586 1690.396044 -3.227988468 0.158744797 SVSEINS(ph)DDELSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SVSEINSDDELSGK 14 0 A0A2R8Y7M0;P82094;P82094-2;F8WF45 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 S(0.045)VS(0.129)EINS(0.826)DDELSGK;SVSEINS(1)DDELSGK;SVSEINS(1)DDELSGK;SVSEINS(0.996)DDELS(0.004)GK;SVSEINS(1)DDELSGK 355.43 4.45E-82 6104193000 8906590 7672750 6130560 6547990 7389220 6158890 8841750 10271950 8972520 TRUE FALSE 7729561.565 7622347.2 9095319.321 8034811.209 7242188.979 6395826.484 7984278.446 8075373.429 7911798.907 0.976966383 0.963415184 1.149589294 1.015547956 0.915365654 0.808390931 1.009160943 1.020674757 1 22.91557433 SVSGS(ph)PEPAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SVSGSPEPAAK 11 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 SVSGS(1)PEPAAK;SVSGS(1)PEPAAK;SVSGS(1)PEPAAK;SVS(0.01)GS(0.99)PEPAAK;SVSGS(1)PEPAAK 204.32 3.52E-08 877260000 2422100 1864790 1206589 1643844 1835587 1557391 2169410 2594660 1977690 TRUE FALSE 2102013.348 1852540.072 1790099.476 2017103.905 1799062.41 1617304.84 1959020.952 2039812.151 1743889.741 1.205359088 1.06230344 1.026498083 1.156669402 1.031637705 0.927412325 1.123362851 1.169691009 1 20.7338774 4.740707752 23.42763737 1.070131676 1.205359198 0.26565153 0.073762849 125.9650907 1374169.562 0.018856889 0.119270845 55043.71688 -4.740707752 0.135227522 SVSHGSNHTQKPDEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVSHGSNHTQKPDEQR 16 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 106.19 0.00079047 63609000 33274 35288 12484 19452 44106 40805 31636 40754 33676 FALSE TRUE 28876.75659 35056.1908 18521.30416 23868.87391 43228.37689 42374.79475 28567.94559 32039.07425 29694.86164 0.972449609 1.18054737 0.623720844 0.803804853 1.455752763 1.427007651 0.962050133 1.078943375 1 14.85792569 3.270499887 24.99925397 1.166935514 0.89613109 0.317050662 0.21031458 278.9454126 218332.155 0.064998533 0.083905539 1864.231695 -3.270499887 -0.270804424 SVSMLSLNT(ph)PNSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVSMLSLNTPNSNR 14 0 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C3G1 Q9H8V3-2 ECT2 Protein ECT2 1 SVSMLS(0.004)LNT(0.995)PNSNR 190.82 6.25E-06 201880000 299440 349360 176270 262950 299620 309610 341460 360910 355790 TRUE FALSE 259868.2453 347065.0312 261514.7616 322656.8164 293658.1482 321520.897 308345.2618 283732.2051 313728.9115 0.828320999 1.106257723 0.833569212 1.028457387 0.93602514 1.024836683 0.982839804 0.904386541 1 18.25915896 SVSPS(ph)PVPLSSNYIAQISNGQQLMSQPQLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVSPSPVPLSSNYIAQISNGQQLMSQPQLHR 31 0 Q02241;H7BYN4 Q02241 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 S(0.003)VS(0.018)PS(0.97)PVPLS(0.004)S(0.004)NYIAQISNGQQLMSQPQLHR 185.55 1.43E-18 529970000 114040 119630 60981 115640 139110 116810 109110 146920 119290 TRUE FALSE 98969.32506 118844.1427 90471.61557 141897.8294 136341.9832 121303.7563 98528.52899 115502.3013 105187.6721 0.94088331 1.129829573 0.860097137 1.348996766 1.296178349 1.153212671 0.936692742 1.098059298 1 16.68260611 7.41942211 9.756422434 1.089731983 0.013361584 0 0.157023076 0 0 0.035435081 0 26267703.79 -7.41942211 -1.076370399 SVSSDSLGPPRPAPART(ph)PTQPPPEPGDLPTIEEALQIIHSAEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVSSDSLGPPRPAPARTPTQPPPEPGDLPTIEEALQIIHSAEPR 44 2 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 S(0.043)VS(0.043)S(0.039)DS(0.189)LGPPRPAPART(0.677)PT(0.009)QPPPEPGDLPTIEEALQIIHSAEPR 132.39 1.82E-09 64081000 16647 13945 9111 12527 15992 21114 15435 18515 10694 TRUE FALSE 14447.05677 13853.39438 13517.11007 15371.44681 15673.79049 21926.26924 13938.11608 14555.71133 9429.767503 1.532069244 1.469113037 1.433451044 1.630098177 1.662160863 2.325218436 1.478097532 1.543591751 1 13.20300649 3.728058496 21.84512596 1.624208585 1.477301318 0.032810305 0.318915382 494.8285445 1029281.522 0.090696886 0.136678414 5346.363658 -3.728058496 -0.146907268 SVSSNVASVS(ph)PIPAGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVSSNVASVSPIPAGSK 17 0 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 SVSSNVASVS(1)PIPAGSK;SVSSNVAS(0.001)VS(0.999)PIPAGSK 334.98 3.96E-72 521530000 1122250 1070760 704690 833880 943750 799610 1105490 1359160 1608820 TRUE FALSE 973941.8191 1063726.107 1045480.441 1023225.199 924971.2214 830371.5141 998279.75 1068514.211 1418627.132 0.686538271 0.749827832 0.736966337 0.721278464 0.652018561 0.585334578 0.703694246 0.753202999 1 20.43606401 1.192437168 2.33492417 1.110043344 0.691045609 0.811672198 0.046539336 0.324702244 1.672410681 0.296114123 0.013733723 15.57532679 -1.192437168 -0.418997735 SVSSVLSSLT(ph)PAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVSSVLSSLTPAK 13 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;F8W9Y9 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 SVSSVLSS(0.002)LT(0.998)PAK 180.85 0.00014028 227920000 550420 485540 310680 355160 445510 440830 428480 652890 535280 TRUE FALSE 477680.6024 482350.4558 460925.8872 435804.5063 436645.2226 457789.0154 386926.0755 513274.5543 471999.8082 1.012035586 1.021929347 0.976538293 0.923315007 0.925096187 0.969892376 0.819758968 1.087446532 1 18.84842675 SVSTTNIAGHFNDES(ph)PLGLR ddPTM_MDA-MB-175_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 SVSTTNIAGHFNDES(1)PLGLR;SVSTTNIAGHFNDES(1)PLGLR;SVSTTNIAGHFNDES(1)PLGLR;SVSTTNIAGHFNDES(1)PLGLR;SVSTTNIAGHFNDES(1)PLGLR 324.66 2.13E-67 2661507000 2019449 1841411 1000297 1406569 1711359 1945353 1701052 1926502 2213014 TRUE FALSE 1752573.698 1829314.65 1484043.975 1725951.99 1677306.304 2020191.989 1536084.239 1514534.539 1951394.006 0.898113704 0.937439925 0.760504527 0.884471298 0.859542614 1.035255813 0.787172777 0.776129544 1 20.89607367 SVSVATSGSGFS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVSVATSGSGFSR 13 0 Q1W6H9 Q1W6H9 FAM110C Protein FAM110C 1 SVSVATS(0.003)GS(0.015)GFS(0.982)R;SVSVAT(0.062)S(0.093)GS(0.233)GFS(0.612)R 125.93 0.00020399 552420000 966390 851080 646640 770090 918520 973390 913450 1037280 1256040 TRUE FALSE 838679.113 845489.1994 959357.2669 944950.7046 900243.2491 1010836.943 824863.7596 815465.7441 1107552.382 0.757236521 0.763385293 0.866195841 0.853188273 0.812822277 0.91267642 0.744762752 0.73627736 1 20.0789435 4.2614473 21.15587892 0.83265328 0.760310169 0.160662222 0.077014179 87.67297042 81033.07248 0.019398464 0.051156454 18257.75185 -4.2614473 -0.072343111 AHS(ph)NPMADHTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 AHSNPMADHTLR 12 0 Q9UBP6;F8VSD9;H0YHX0;Q9UBP6-2 Q9UBP6 METTL1 tRNA (guanine-N(7)-)-methyltransferase 1 AHS(1)NPMADHTLR 118.47 0.00040072 247280000 53562 82083 57882 87557 115440 100720 97797 132900 115740 TRUE FALSE 46483.64599 81543.79137 85873.9288 107438.1551 113142.9699 104594.7636 88312.66199 104480.3692 102057.3491 0.455465936 0.798999701 0.841428173 1.052723357 1.108621485 1.024862634 0.865323887 1.023741751 1 16.63902055 4.817290013 1.173458462 1.005926164 0.134983669 0.858955812 0.070775258 0.679194714 0.703452445 0.022364621 0.756496493 65658.35738 -4.817290013 -0.870942495 down SVT(ph)PPPPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVTPPPPPR 9 0 O95835;O95835-2;H0YG09 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 S(0.001)VT(0.999)PPPPPR 107.95 0.030072 188510000 423470 382920 290210 362430 436320 449820 369680 478080 601760 TRUE FALSE 367507.3666 380404.5733 430556.5267 444725.2709 427638.0856 467124.8665 333828.4905 375846.3124 530620.6183 0.692599107 0.716904998 0.811420649 0.838122861 0.805920597 0.880336818 0.629128381 0.708314565 1 19.01732121 4.324457847 4.996805248 0.794873645 0.699320878 0.154402002 0.098176993 0.438240982 18.38094926 0.025434522 0.070566813 21108.52303 -4.324457847 -0.095552767 SVTDSIRDEYAFLQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVTDSIRDEYAFLQK 15 1 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;O00429-7;F8VZ52;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 0 ; 158.35 1.67E-06 168063000 237810 200968 135245 162461 187123 183471 203662 235870 181087 FALSE TRUE 206382.806 199647.828 200649.9344 199350.2531 183399.6184 190529.2481 183910.8906 185431.036 159679.1012 1.292484768 1.250306562 1.256582314 1.248442981 1.14855117 1.193200906 1.151753043 1.161273045 1 17.28481598 -1.471761405 0.262918819 4.39E-16 1.294111618 0.817996849 0.035437296 27.50573208 0.571509722 14.74754246 0.10590717 0.033747266 1.471761405 1.294111618 SVTDYDFAPFLNNS(ph)PQQNPAAQIPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SVTDYDFAPFLNNSPQQNPAAQIPAR 26 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2 Q9UM54-1 MYO6 Unconventional myosin-VI 1 SVTDYDFAPFLNNS(1)PQQNPAAQIPAR;SVTDYDFAPFLNNS(1)PQQNPAAQIPAR;SVTDYDFAPFLNNS(1)PQQNPAAQIPAR 288.98 2.82E-63 340822000 240464 273659 190858 222735 286094 340838 291522 293094 328279 TRUE FALSE 208686.0731 271861.316 283157.5672 273310.386 280401.2891 353950.2584 263250.2413 230418.129 289470.2306 0.720924127 0.939168478 0.978192357 0.944174416 0.968670556 1.222751845 0.909420775 0.795999397 1 18.14305546 4.73757881 3.942426906 0.962340646 0.698667587 0.354646336 0.105585191 0.316291229 10.13120544 0.028497853 0.239709193 54648.57093 -4.73757881 -0.263673059 SVTEQGAELSNEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SVTEQGAELSNEER 14 0 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;E5RGE1 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;;;;;; 452.74 9.14E-175 10383290000 3097899 2873301 1611248 1958409 2771992 2967082 2508875 2911999 2657568 FALSE TRUE 2688503.798 2854426.097 2390452.922 2403095.696 2716834.783 3081227.564 2265564.689 2289290.675 2343393.339 1.14726954 1.218073829 1.020081812 1.025476883 1.159359267 1.314857183 0.966788055 0.976912684 1 21.1601677 2.139150472 22.61199189 0.979715536 1.140073224 0.457476132 0.085099244 6.344161785 1432.655981 0.03645872 0.024580453 137.7686721 -2.139150472 0.160357688 SVTLGYLFSQGHLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVTLGYLFSQGHLTR 15 0 A0A3B3IRQ9;P55265-3;P55265-2;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 207.55 3.34E-09 951080000 996900 948080 395240 711080 1101050 1064820 956620 1124850 1278600 FALSE TRUE 865157.1392 941852.0001 586379.386 872541.5822 1079141.259 1105784.314 863847.1396 884309.5811 1127445.365 0.767360589 0.835385935 0.520095611 0.773910302 0.957156145 0.980787495 0.766198671 0.784348057 1 20.10462609 3.465767939 17.10583861 0.876706648 0.708160405 0.385668025 0.109700441 5.912207788 8905.552135 0.032714125 0.042414892 2922.590304 -3.465767939 -0.168546243 SVTLLEVCGS(ph)WPEGFGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SVTLLEVCGSWPEGFGLR 18 0 K7ESE9;Q9H6U6-6;Q9H6U6-2;Q9H6U6;K7EIE2;Q9H6U6-7;Q9H6U6-3;Q9H6U6-8 K7ESE9;Q9H6U6-7 BCAS3 Breast carcinoma-amplified sequence 3 1 SVTLLEVCGS(1)WPEGFGLR;SVTLLEVCGS(1)WPEGFGLR;SVTLLEVCGS(1)WPEGFGLR;SVTLLEVCGS(1)WPEGFGLR 200.58 1.57E-15 431942000 270730 295445 202827 262775 379436 440259 392784 431142 436592 TRUE FALSE 234952.3446 293504.2023 300914.8156 322442.08 371885.966 457196.0486 354691.8681 338945.6385 384978.5911 0.610299767 0.762390972 0.781640389 0.837558471 0.96599129 1.187588243 0.921328812 0.88042724 1 18.55441869 3.810961051 1.25306072 0.979920911 0.663610936 0.676001844 0.08819708 0.348195791 1.030768155 0.032618574 0.092206614 6470.845804 -3.810961051 -0.316309975 SVTPDSLGHT(ph)PPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVTPDSLGHTPPAR 14 0 P35568 P35568 IRS1 Insulin receptor substrate 1 1 SVTPDSLGHT(1)PPAR;SVTPDSLGHT(1)PPAR 155.1 2.18E-05 193220000 128960 150156 122306 219470 243009 262690 214791 249261 434760 TRUE FALSE 111917.6093 149169.6153 181453.5907 269304.0179 238173.5963 272795.8543 193960.6019 195958.4749 383363.1681 0.291936259 0.389107843 0.473320355 0.702477547 0.621274072 0.711585976 0.505944801 0.511156238 1 18.54835221 4.069816058 2.09238474 0.64730503 0.319036451 0.498655993 0.139914491 0.30109106 2.587044608 0.039236265 0.112205543 11744.00043 -4.069816058 -0.32826858 SVTQATQTS(ph)PGVPWPSQSANFPEFSFDFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVTQATQTSPGVPWPSQSANFPEFSFDFTR 30 0 A0A0C4DGH6;A0JNW5;H0YHT7 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 S(0.001)VT(0.001)QAT(0.003)QT(0.17)S(0.825)PGVPWPSQSANFPEFSFDFTR 147.17 2.19E-08 200870000 314160 282820 160370 251430 279760 314510 268700 327250 313590 TRUE FALSE 272642.96 280962.1368 237925.4684 308521.0244 274193.3233 326609.4032 242641.5154 257270.1342 276517.7474 0.985987202 1.016072709 0.860434712 1.115736792 0.991593942 1.181151685 0.877489845 0.930392847 1 18.07701255 SVTVVEDDEDEDGDDLLHHHHGSHCSSSGDPAEYNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 SVTVVEDDEDEDGDDLLHHHHGSHCSSSGDPAEYNLR 37 0 P02545;P02545-6;P02545-5;P02545-4 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;;;; 139.59 1.74E-13 14165830000 2326176 2916579 677301.4 1519088.5 4463083 4479842 2977191 3852100 3584688 FALSE TRUE 2018765.948 2897419.801 1004846.622 1864020.762 4374276.38 4652184.421 2688463.475 3028358.392 3160910.268 0.63866601 0.916640953 0.317897864 0.589710116 1.383866041 1.471786298 0.850534576 0.958065283 1 21.59190865 3.258171423 24.98874904 1.106775392 0.61594862 0.546836411 0.233248099 212.1876403 270374.9509 0.072564859 0.093545647 1812.055198 -3.258171423 -0.490826772 SVTVVEDDEDEDGDDLLHHHHVSGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 SVTVVEDDEDEDGDDLLHHHHVSGSR 26 0 P02545-2;Q3BDU5;Q5TCI8 P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;;;;; 266.94 1.75E-53 8506650000 3294758.8 3032012.4 1346891.9 2035734.7 3121256.5 2950640 3404313.3 3821161 3012394.9 FALSE TRUE 2859348.077 3012094.911 1998253.328 2497979.378 3059149.602 3064153.03 3074163.52 3004035.456 2656273.007 1.076451129 1.133955321 0.75227709 0.940407621 1.151669875 1.153553502 1.157322125 1.1309212 1 21.340972 3.23768095 24.9997689 1.124862001 0.97110755 0.301198214 0.107841807 29.2284947 830669.9609 0.033148855 0.039805912 1728.546033 -3.23768095 -0.153754451 SVVLFGVETHVCIQQTALELVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVVLFGVETHVCIQQTALELVGR 23 0 Q96CN7 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 ; 243.23 2.22E-37 180018000 118282 106384 71212 83803 98473 110091 110788 128088 110133 FALSE TRUE 102650.734 105685.1565 105650.3614 102831.752 96513.57996 114326.272 100043.7968 100697.378 97113.2022 1.057021411 1.088267652 1.087909357 1.0588854 0.993825533 1.177247474 1.030177098 1.036907194 1 16.56737982 2.037320864 24.99989433 1.024825077 1.076074286 0.243299769 0.045595261 238.0427299 159455.2258 0.017898052 0.012066835 108.9734911 -2.037320864 0.051249209 SVVLMSHLGRPDGVPMPDKYSLEPVAVELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVVLMSHLGRPDGVPMPDKYSLEPVAVELK 30 2 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 142.31 1.64E-06 635090000 379680 278660 155203 163920 233321 199712 310320 385650 260680 FALSE TRUE 329504.326 276829.4641 230259.6899 201140.5414 228678.3686 207395.0499 280225.2142 303181.7486 229862.7074 1.433483186 1.204325257 1.001727042 0.87504643 0.994847625 0.902256187 1.219098206 1.318968841 1 17.8104129 4.60002262 2.954353618 1.066282276 1.44688995 0.454950197 0.135768734 0.353889216 5.002532512 0.040774731 0.265682603 39812.7906 -4.60002262 0.380607674 SVVLYVILAPFDNEQSDLVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVVLYVILAPFDNEQSDLVHR 21 0 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 ; 157.79 2.31E-09 585800000 844330 809030 505130 751300 622360 650010 782140 1007630 982120 FALSE TRUE 732749.6512 803715.4287 749412.5576 921894.1479 609976.2536 675016.3053 706288.1832 792156.1659 866014.8924 0.846116686 0.928061902 0.865357587 1.06452459 0.704348457 0.779451152 0.815561244 0.914714254 1 19.72403231 1.386464473 3.232661733 1.002583447 0.859910947 0.191601527 0.094033464 0.494321362 7.777934011 0.145671651 0.024900388 24.34806615 -1.386464473 -0.1426725 SVVS(ph)DLEADDVK ddPTM_MDA-MB-175_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 270.85 1.11E-27 850370000 1833830 1722520 1426200 1928800 1877130 1286690 1847400 2439490 2617010 TRUE FALSE 1591484.719 1711204.653 2115915.09 2366763.52 1839778.786 1336189.797 1668239.432 1917824.048 2307630.059 0.689661982 0.741542019 0.916921273 1.025625191 0.797258979 0.579031198 0.722923254 0.831079505 1 21.13798053 SVVS(ph)FDK ddPTM_MDA-MB-175_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 123.63 0.0044323 2012960000 4934850 3774180 3765630 4149440 4274870 4017710 5069230 5684880 13647300 TRUE FALSE 4282697.069 3749387.163 5586701.263 5091633.772 4189808.451 4172273.904 4577616.855 4469212.652 12033931.74 0.355885106 0.311567927 0.464245716 0.42310642 0.348166214 0.346709122 0.380392456 0.371384245 1 23.52060474 1.238314393 24.99998905 1.000000692 0.375807211 0.955310481 0.042470221 1.144305118 115948.6203 0.060155976 0.010649346 17.31069057 -1.238314393 -0.624193481 SVVS(ph)FDKVKEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVVSFDKVKEPR 12 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 S(0.111)VVS(0.889)FDKVKEPR;S(0.008)VVS(0.992)FDKVKEPR 126.16 0.00015258 1053590000 5319100 3579600 1801080 1541290 3810100 3020600 5735900 5984000 315130 TRUE FALSE 4616167.458 3556085.372 2672088.312 1891263.452 3734286.464 3136804.437 5179633.301 4704368.168 277875.6904 16.61234724 12.79739644 9.616128379 6.806149357 13.43869433 11.28851693 18.64010952 16.92975791 1 18.0840801 -1.449459913 0.008228277 0.002860343 23.77225028 0.003231674 5.224487225 1094806.302 1009.133576 1585454.23 1339635.578 0.035525491 1.449459913 23.76938994 SVWGSLAVQNS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SVWGSLAVQNSPK 13 0 P18615;P18615-3;P18615-4 P18615 NELFE Negative elongation factor E 1 SVWGSLAVQNS(1)PK 262.42 4.31E-24 284680000 513480 351300 227390 244120 364080 279620 384170 427880 399780 TRUE FALSE 445622.317 348992.2872 337356.5646 299551.1771 356835.5203 290377.1623 346913.2525 336381.1918 352518.4638 1.264110572 0.989997186 0.956989773 0.849746064 1.012246327 0.823721853 0.984099524 0.954222903 1 18.4273393 4.770712856 2.576660421 0.939246959 1.348197935 0.736179923 0.060491876 0.272994099 2.17582239 0.014405668 0.250842385 58981.09835 -4.770712856 0.408950976 SVWVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SVWVAR 6 0 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;;;; 138.61 0.028449 5324900000 4685340 4481440 2942360 3079660 4120530 4514880 4143300 4673100 4323360 FALSE TRUE 4066160.448 4452001.126 4365295.138 3778943.873 4038539.515 4688570.355 3741483.404 3673793.931 3812257.306 1.066601785 1.16781234 1.145068338 0.991261494 1.059356489 1.229867236 0.981435172 0.963679426 1 21.86221407 2.095690113 15.41553687 0.977240076 1.106513213 0.461581303 0.065202148 0.926560775 145.4120185 0.026863575 0.018111373 124.6493771 -2.095690113 0.129273137 SVYAHFPINVVIQENGSLVEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SVYAHFPINVVIQENGSLVEIR 22 0 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ;;; 265.63 1.39E-37 2781695000 1732953 1728672 815324.5 1248585 1743541 1831138 1579283 1876029 1949163 FALSE TRUE 1503938.87 1717316.24 1209618.155 1532095.308 1708847.945 1901583.064 1426124.378 1474854.798 1718735.171 0.875026529 0.999174433 0.703783908 0.891408597 0.994247383 1.106385147 0.829752252 0.858104741 1 20.71291584 3.467795717 24.20134456 0.943063655 0.860693473 0.155862235 0.103599628 310.488635 805764.9123 0.031281753 0.040445187 2936.268169 -3.467795717 -0.082370182 SVYATMGDHENRS(ph)PVKEPVEQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SVYATMGDHENRSPVKEPVEQPR 23 2 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 SVYATMGDHENRS(1)PVKEPVEQPR;SVYATMGDHENRS(1)PVKEPVEQPR 149.2 5.10E-08 548750000 189344 145293 112552 138601 183303 141413 202741 220748 201998 TRUE FALSE 164321.7107 144338.5607 166982.5237 170072.4754 179655.6289 146853.2496 183079.209 173542.7581 178118.0266 0.922543966 0.810353469 0.937482449 0.954830225 1.008632492 0.824471573 1.027853343 0.974313277 1 17.44247401 8 0.088007255 1.145040669 0.379117977 0.243986701 0.063427134 497.7145323 4.112019084 6.490664503 47.8377103 99999999.95 -8 -0.765922692 SVYRGS(ph)LTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(1)LTQR;SVYRGS(1)LTQR;SVYRGS(0.985)LT(0.015)QR 186.16 8.30E-07 5818769000 2379730 3037020 1002594 987423 2611230 3082670 2653960 2691180 829411 TRUE FALSE 2065242.651 3017069.616 1487451.812 1211632.484 2559271.632 3201262.31 2396579.368 2115692.1 731358.9764 2.823842624 4.125292384 2.033819041 1.656686419 3.499337144 4.377142296 3.276885148 2.892823043 1 19.48022018 4.243471209 24.99863761 2.781808248 3.474567113 0.090593413 1.009096371 355.3986578 1809190.286 0.264033861 0.653720977 17517.46302 -4.243471209 0.692758865 SWAS(ph)PVYTEADGTFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SWASPVYTEADGTFSR 16 0 E9PMS6;E9PJ10;E9PK58;E9PLU6;Q8WWI1-3;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.036)WAS(0.964)PVYTEADGTFSR 349.86 3.67E-87 3094700000 586570 726140 460430 487810 734820 681590 623760 795830 766170 TRUE FALSE 509053.2883 721369.9385 683095.488 598574.7162 720198.5197 707811.2083 563267.8512 625647.9477 675594.2554 0.753489664 1.067756176 1.011103162 0.885997344 1.066022267 1.047686837 0.833736887 0.926070556 1 19.36579754 4.75543877 24.35020305 0.971615967 0.753489415 0.451190155 0.077976306 2497.942425 3603710.541 0.01967451 0.531149079 56942.79363 -4.75543877 -0.218126551 SWASLFHDSKPSSSSPVAYVETKYS(ph)PPAISPLVSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SWASLFHDSKPSSSSPVAYVETKYSPPAISPLVSEK 36 2 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 S(0.006)WAS(0.006)LFHDS(0.006)KPS(0.001)S(0.001)S(0.001)S(0.001)PVAYVET(0.154)KY(0.024)S(0.793)PPAIS(0.008)PLVSEK 74.946 0.0016802 396340000 301260 314450 59437 200400 512740 352270 464230 592230 358530 TRUE FALSE 261447.7277 312384.3572 88180.932 245903.8829 502537.4772 365822.0548 419209.0461 465586.2232 316144.9918 0.826986776 0.988104716 0.278925601 0.777819954 1.589579118 1.157133797 1.326002489 1.472698399 1 18.27022684 3.330841287 6.882860998 1.32191045 0.697126347 0.606887668 0.2366416 0.141394479 8.920372441 0.066783187 0.086218451 2142.107625 -3.330841287 -0.624784103 SWDIFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SWDIFFR 7 0 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;Q02218-3;C9J4G7 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 ; 132.29 0.007872 226210000 569160 585290 398090 661600 685270 745010 523260 721700 674460 FALSE TRUE 493944.0639 581445.1915 590607.6555 811826.3919 671634.4677 773671.0168 472514.3257 567370.0713 594726.1071 0.830540408 0.977668854 0.993075045 1.365042466 1.129317277 1.300886252 0.794507455 0.954002295 1 19.18186588 2.223723839 24.99996807 0.918982437 1.102486155 0.222946294 0.161178773 382.0385138 643729.816 0.068644422 0.046493587 167.3878146 -2.223723839 0.183503718 SWDSSS(ph)PVDRPEPEAASPTTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SWDSSSPVDRPEPEAASPTTR 21 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SWDS(0.179)S(0.152)S(0.667)PVDRPEPEAAS(0.002)PTTR 118.57 4.81E-05 565510000 88835 93054 61730 78903 108810 95955 103650 118810 98677 TRUE FALSE 77095.22967 92442.72215 91582.83447 96819.13211 106644.8939 99646.45094 93598.03895 93403.40608 87011.51747 0.886034768 1.062419377 1.052536918 1.112716281 1.225641122 1.145209897 1.075697122 1.073460259 1 16.40891876 5.095943797 1.377008569 1.10353479 0.590972731 0.560793151 0.058802415 2.484479756 2.202033757 0.017886732 2.240165702 124722.2098 -5.095943797 -0.512562059 SWDSSSPVDRPEPEAAS(ph)PTTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SWDSSSPVDRPEPEAASPTTR 21 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SWDSSSPVDRPEPEAAS(0.995)PT(0.005)TR;SWDSSSPVDRPEPEAAS(0.979)PT(0.021)TR;SWDSSSPVDRPEPEAAS(0.846)PT(0.124)T(0.03)R 200.63 4.46E-22 1960160000 873280 950800 508640 666040 939680 1018120 818310 1003010 939550 TRUE FALSE 757873.8354 944554.1322 754620.0053 817274.5618 920982.2065 1057287.735 738950.4222 788524.1169 828477.4693 0.914779054 1.140108412 0.910851572 0.986477716 1.11165631 1.27618164 0.891937861 0.951774968 1 19.66010294 SWEDS(ph)PER ddPTM_MDA-MB-175_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 220.87 6.05E-06 5451000000 6574620 6799490 4673880 6138320 6620180 7411300 6654470 7387700 8427400 TRUE FALSE 5705767.309 6754823.702 6934184.001 7532119.374 6488451.37 7696417.507 6009120.524 5807897.846 7431122.373 0.767820394 0.908991047 0.933127414 1.013591083 0.873145542 1.035700547 0.808642386 0.781564016 1 22.8251487 0.944490455 16.22632283 1.866112999 0.891151287 0.128751523 0.089640052 1488641.052 11018354.87 46952449.46 0.022912029 8.800157699 -0.944490455 -0.974961712 SWEEQMIEVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SWEEQMIEVGR 11 0 Q00059;Q00059-2 Q00059 TFAM "Transcription factor A, mitochondrial" 0 121.29 0.00096487 81397000 57284 51648 44381 68922 74927 71964 48817 62549 82032 FALSE TRUE 49713.77426 51308.72089 65843.80005 84571.79351 73436.09929 74732.50165 44082.73485 49173.38311 72334.27041 0.687278298 0.709327966 0.910271157 1.169180155 1.01523246 1.033154841 0.609430836 0.679807549 1 16.14239171 2.242855049 24.99986806 0.739329123 0.92624301 0.149976365 0.173571911 186.6139159 1086373.282 0.071769294 0.053597821 174.9262755 -2.242855049 0.186913888 SWFLTEWSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SWFLTEWSER 10 0 Q6ZMP0-4;Q6ZMP0 Q6ZMP0-4 THSD4 Thrombospondin type-1 domain-containing protein 4 0 74.92 0.062923 0 125790 114210 93185 97781 135040 123930 101690 151710 111700 FALSE TRUE 109166.5328 113459.747 138249.5777 119983.6705 132352.9682 128697.6673 91828.11945 119267.9971 98494.95325 1.10834646 1.151934625 1.403620928 1.218170745 1.343753805 1.30664225 0.93231294 1.210904652 1 16.58776218 2.259283295 24.99998302 1.076922513 1.259767596 0.42953433 0.111061344 241.1896916 290972.2379 0.040923632 0.03166426 181.6700328 -2.259283295 0.182845083 SWGHES(ph)PEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SWGHESPEER 10 0 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 S(0.038)WGHES(0.962)PEER;S(0.001)WGHES(0.999)PEER 87.719 0.0081702 174110000 911220 619730 451970 626250 637920 549840 793310 962040 855280 TRUE FALSE 790799.9683 615658.9528 670544.2037 768449.6341 625226.6401 570992.7006 716374.9183 756315.2326 754169.7727 1.048570225 0.816340001 0.889115724 1.018934545 0.829026385 0.757114275 0.949885482 1.002844797 1 19.5245298 2.005558682 24.99658154 0.994047483 0.889071661 0.2088687 0.087384889 211.2833214 950105.5258 0.035594893 0.023915729 101.28816 -2.005558682 -0.104975822 SWHDIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SWHDIEK 7 0 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;; 109.86 0.0069328 1694050000 2566570 2669940 1138200 2298860 2869130 2502540 2704490 3237450 4740400 FALSE TRUE 2227391.272 2652400.988 1688637.327 2820851.299 2812039.926 2598814.333 2442208.976 2545146.511 4179995.312 0.532869323 0.634546403 0.403980675 0.674845565 0.672737579 0.621726614 0.584261176 0.608887408 1 21.99506989 1.237328407 5.551951037 1.01966357 0.592262429 0.729636919 0.07817368 0.07868589 7.683797331 0.12857763 0.019136608 17.27143436 -1.237328407 -0.427401141 SWHDIEKDNAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SWHDIEKDNAR 11 1 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 91.858 0.0062657 505090000 362950 346500 167720 235090 317750 292140 362780 396610 295630 FALSE TRUE 314985.2379 344223.8187 248829.953 288470.7776 311427.3967 303378.8148 327597.6514 311798.0379 260680.9582 1.208317017 1.320479336 0.954538278 1.106604716 1.194668758 1.163793539 1.256699583 1.196090578 1 17.99192568 7.752190596 0.006558285 0.046771985 2.361025493 0.028530709 0.109191294 509028.3233 350.2519128 57514.54095 66388.05588 56518495.98 -7.752190596 2.314253508 SWHDVQVSSAYVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SWHDVQVSSAYVK 13 0 O43399;O43399-7;O43399-5;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 0 ; 138.87 4.41E-05 1485900000 1624470 1624270 747050 1186610 1726200 1491010 1630900 1870800 1801370 FALSE TRUE 1409792.174 1613600.063 1108325.879 1456047.937 1691851.997 1548370.12 1472735.569 1470743.979 1588414.091 0.887547008 1.01585605 0.697756262 0.916667729 1.06512024 0.974789967 0.927173574 0.925919751 1 20.59915563 3.4749778 24.99857754 0.9700522 0.869479833 0.263972785 0.084973789 99.44271322 1159761.652 0.024287638 0.031567244 2985.230021 -3.4749778 -0.100572367 SWLSYSYQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SWLSYSYQSR 10 0 Q15393 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ; 130.66 0.00063011 960410000 636430 716230 567470 540400 500870 538260 752790 664500 629420 FALSE TRUE 552324.163 711525.038 841900.3901 663106.0795 490903.6669 558967.2105 679784.5417 522401.8461 555010.6846 0.995159514 1.282002415 1.516908437 1.194762728 0.884494084 1.007128738 1.224813432 0.941246467 1 19.08215602 3.440181509 8.684604428 1.019963561 1.281218571 0.381088411 0.150728429 0.270559954 58.17992034 0.043610635 0.05654886 2755.380045 -3.440181509 0.261255011 SWMGYELPFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SWMGYELPFDR 11 0 P53701 P53701 HCCS Cytochrome c-type heme lyase 0 85.377 0.025627 0 53790 49212 38319 46251 65188 75665 52832 64592 58663 FALSE TRUE 46681.51521 48888.72313 56850.19657 56752.99645 63890.88634 78575.88151 47708.36077 50779.50346 51727.92697 0.902443186 0.945112747 1.099023292 1.097144227 1.235133323 1.519022434 0.922294079 0.981665155 1 15.65865576 4.268363553 3.071420556 1.118371813 0.907838819 0.202051277 0.16527368 0.462618417 8.720321528 0.047448202 0.144189993 18550.83887 -4.268363553 -0.210532994 SWPEGHFATITLTFIDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SWPEGHFATITLTFIDK 17 0 O95433;G3V438 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ; 191.86 1.19E-17 152070000 671390 561090 427710 594480 474540 499320 624740 753660 1049120 FALSE TRUE 582664.1104 557404.1628 634551.9866 729465.7701 465097.5824 518529.1635 564152.811 592495.674 925094.2288 0.629842985 0.602537715 0.685932272 0.788531316 0.502756982 0.56051497 0.609832808 0.64047062 1 19.8192408 1.23808671 5.824534345 1.01535177 0.626260967 0.710511286 0.074769997 0.080258333 9.638081301 0.124619886 0.019225163 17.30161763 -1.23808671 -0.389090803 SWQGDGS(ph)PMANGAGAVVHHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 SWQGDGSPMANGAGAVVHHQR 21 0 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 1 SWQGDGS(1)PMANGAGAVVHHQR;S(0.004)WQGDGS(0.996)PMANGAGAVVHHQR;S(0.004)WQGDGS(0.996)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR;S(0.006)WQGDGS(0.994)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR 222.46 2.53E-25 8174089000 2714723 2314036 1586335 1938841 2323011 2368910 2510654 2720995 1966458 TRUE FALSE 2355965.477 2298834.945 2353491.912 2379084.482 2276787.626 2460043.501 2267171.162 2139131.394 1733985.575 1.358699582 1.325752058 1.357273062 1.372032453 1.313037235 1.41872201 1.307491362 1.233650051 1 20.72566047 1.148788927 1.504628329 0.790466268 1.354751095 0.931611267 0.030357627 0.325981885 0.552311955 0.297029773 0.00831766 14.08604031 -1.148788927 0.564284827 RLSS(ph)LR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 RLSSLR 6 1 P62753;A2A3R5;Q9Y253-2;Q9Y253 P62753 RPS6;POLH 40S ribosomal protein S6;DNA polymerase eta 1 RLS(0.006)S(0.994)LR;RLS(0.107)S(0.893)LR;RLS(0.012)S(0.988)LR 90.135 0.052301 7992500000 3442640 6437900 5103510 6565110 9427120 9594000 8200900 9632900 8768500 TRUE FALSE 2987686.401 6395609.011 7571584.506 8055818.567 9239538.756 9963087.388 7405577.98 7572979.298 7731897.919 0.386410482 0.827171941 0.979265969 1.041894067 1.194989749 1.288569442 0.957795622 0.979446363 1 22.88239116 4.822985489 1.374703642 1.071581188 8.70E-21 0.824409178 0.100613177 0.69838097 1.025011499 0.032216024 1.095462814 66525.09274 -4.822985489 -1.071581188 down SWS(ph)LATFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.001)WS(0.999)LATFR 132.01 0.0010286 87542000 134860 125740 95112 104430 139010 110860 142630 131770 141510 TRUE FALSE 117037.9093 124914.0057 141108.4813 128142.4276 136243.973 115124.8559 128797.7646 103592.0109 124780.849 0.937947692 1.001067124 1.130850467 1.02693986 1.091866052 0.922616386 1.032191763 0.830191586 1 16.92903701 2.332872034 1.629955305 0.917772202 1.037564359 0.211977149 0.075973138 0.470812521 2.560953124 0.044677587 0.025108948 215.2147508 -2.332872034 0.119792156 SWS(ph)PPPEVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 SWSPPPEVSR 10 0 Q9NR19;Q9NR19-2;F8WCJ4;C9IYL0;B4DEH9;C9JY31;C9JXD9 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 1 S(0.001)WS(0.999)PPPEVSR;SWS(1)PPPEVSR;SWS(1)PPPEVSR;SWS(1)PPPEVSR;SWS(1)PPPEVSR;SWS(1)PPPEVSR;SWS(1)PPPEVSR;S(0.002)WS(0.998)PPPEVSR;SWS(1)PPPEVSR;S(0.008)WS(0.992)PPPEVSR 208.17 1.24E-07 40383030000 8346830 6243710 4046719 4472700 6308280 6818550 5997720 6330880 6377680 TRUE FALSE 7243775.267 6202694.658 6003725.844 5488294.896 6182757.57 7080864.031 5416062.038 4977070.579 5623717.936 1.288075851 1.10295266 1.067572363 0.975919304 1.099407481 1.259107251 0.96307498 0.885014262 1 22.42309281 7.999988951 0.039683883 2.44E-08 2.739560645 0.342732066 0.102785575 2115.608771 8.270743575 180.483884 448.7482925 99997455.84 -7.999988951 2.73956062 SWSHYTVPAGMTVIQWVSDFSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SWSHYTVPAGMTVIQWVSDFSER 23 0 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 225.05 1.21E-32 1227750000 518140 512600 253002 357903 580540 593110 605860 677150 603770 FALSE TRUE 449666.4862 509232.6968 375354.6134 439170.3464 568988.3898 615927.3255 547103.7905 532346.7421 532392.9984 0.844613824 0.956497734 0.705032964 0.824898802 1.068737552 1.156903504 1.027631453 0.999913116 1 19.02213207 3.240704765 24.99894398 1.047884533 0.832475726 0.682074695 0.073901007 35.0166923 408260.7809 0.02278988 0.027983615 1740.623189 -3.240704765 -0.215408807 SWSLATFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 104.44 0.010656 486960000 205250 338320 245930 225800 343770 377510 327250 303200 418680 FALSE TRUE 178125.6925 336097.5536 364862.5706 277071.3411 336929.6496 392033.054 295513.3454 238363.0395 369184.1274 0.482484699 0.910379208 0.988294305 0.750496353 0.912633086 1.061890328 0.800449758 0.645648125 1 18.493981 4.74257494 24.63976696 0.866796332 0.482484516 0.498956882 0.125344507 319.0651355 1958316.187 0.032660017 0.241712169 55280.87895 -4.74257494 -0.384311816 SWSTAT(ph)SPLGGERPFR ddPTM_MDA-MB-175_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 SWS(0.001)T(0.001)AT(0.565)S(0.433)PLGGERPFR 135.09 4.00E-05 811110000 212420 243340 147250 191480 318780 292070 299030 348410 360820 TRUE FALSE 184348.1588 241741.4835 218460.5925 234958.4606 312436.9017 303306.1219 270030.1166 273905.2328 318164.2706 0.579411882 0.759800851 0.686628301 0.738481603 0.981998705 0.953300386 0.848712887 0.860892495 1 18.27941231 3.362567015 5.074647042 0.915047445 0.688224102 0.769865191 0.064906479 0.107561427 4.339649849 0.019247652 0.025000905 2304.448542 -3.362567015 -0.226823344 SWSTATS(ph)PLGGERPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 SWSTAT(0.031)S(0.969)PLGGERPFR;SWSTAT(0.222)S(0.777)PLGGERPFR;SWSTAT(0.147)S(0.853)PLGGERPFR 173.49 2.54E-09 1892310000 420350 445501 310925 387095 535370 573740 533430 636040 616880 TRUE FALSE 364799.6825 442574.4746 461289.37 474990.8361 524717.1844 595812.1491 481698.0407 500027.7957 543953.1492 0.67064541 0.813626091 0.848031436 0.873220124 0.964636725 1.095337255 0.885550606 0.91924791 1 19.05312287 4.64954766 0.781270828 0.963885714 0.537204415 0.723497947 0.059774148 1.3884567 0.720666549 0.025424003 0.507566207 44621.8591 -4.64954766 -0.426681299 SWTS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SWTSPK 6 0 O75494-2;O75494 O75494-2 SRSF10 Serine/arginine-rich splicing factor 10 1 SWT(0.017)S(0.983)PK;S(0.001)WT(0.031)S(0.967)PK;SWT(0.074)S(0.926)PK;SWT(0.021)S(0.979)PK 130.28 0.016606 1644530000 7742800 5990400 4231630 4806400 6048300 5012660 6917900 8189700 7000700 TRUE FALSE 6719569.362 5951048.668 6278060.422 5897766.581 5927950.663 5205500.274 6247003.123 6438396.387 6173085.221 1.088526907 0.96403151 1.017005306 0.955400156 0.960289782 0.843257478 1.011974223 1.042978698 1 22.55756028 SWVIGS(ph)PEILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SWVIGSPEILR 11 0 Q6P0Q8;Q6P0Q8-2;A0A669KBJ4;E7ERL6 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 SWVIGS(1)PEILR;SWVIGS(1)PEILR;SWVIGS(1)PEILR 168.76 1.86E-05 149688000 399276 306052 201936 246024 320271 335762 280490 332224 355583 TRUE FALSE 346510.665 304041.5243 299592.925 301887.5094 313898.2337 348678.9814 253288.123 261180.483 313546.3828 1.105133671 0.969685957 0.955497947 0.962816113 1.001122165 1.112049127 0.807817079 0.832988346 1 18.25831935 2.227701137 24.99997343 0.867399638 1.00945624 0.430755409 0.073586327 193.8364955 446233.6504 0.029908375 0.020389416 168.9278041 -2.227701137 0.142056602 SWVNQMESQTGEASKLPYDVTPEQALAHEEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SWVNQMESQTGEASKLPYDVTPEQALAHEEVK 32 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 180.33 1.05E-19 95230000 98017 81286 54573 55831 71804 65909 111320 127780 29572 FALSE TRUE 85063.80511 80752.02691 80964.68534 68508.28187 70375.24088 68444.56188 100524.2035 100455.2414 26076.03185 3.262145314 3.096791237 3.104946558 2.627251043 2.698847788 2.62480742 3.855042213 3.852397557 1 14.67043672 3.97895183 22.63763713 2.940171128 3.159819026 0.02196877 0.796064176 1453.721687 1563517.841 0.215995502 0.380571872 9526.904903 -3.97895183 0.219647898 SWWDAVCTLIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SWWDAVCTLIHR 12 0 P49792;J3KNE0;A6NKT7;Q7Z3J3;O14715;Q99666;J3KQ37;F8W705;Q99666-2;F8VYC4;A0A286YES2;P0DJD0;A0A1W2PNU4;P0DJD1 P49792;F8VYC4 RANBP2;RGPD3;RGPD4;RGPD8;RGPD5;RGPD1;RGPD2 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6;RANBP2-like and GRIP domain-containing protein 1;RANBP2-like and GRIP domain-containing protein 2 0 ; 103.14 0.0022788 333240000 620530 714590 391600 509160 637280 642420 649790 733230 584080 FALSE TRUE 538525.3883 709895.8112 580979.0698 624772.56 624599.3748 667134.3131 586773.4658 576434.4705 515030.7278 1.045617978 1.378356228 1.128047393 1.213078223 1.212741961 1.295329147 1.139297976 1.119223455 1 18.97429898 1.422446912 1.492162262 0.961532776 1.214251757 0.351555376 0.090012376 0.807751365 2.227768297 0.285641206 0.024301458 26.45129335 -1.422446912 0.252718981 SYCAEIAHNVSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SYCAEIAHNVSSK 13 0 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ;;; 182.07 1.15E-05 5510760000 5405700 4805950 2551500 3992640 4961000 4332760 5115500 5906000 6169800 FALSE TRUE 4691323.049 4774379.398 3785413.934 4899229.936 4862285.806 4499444.081 4619399.597 4643047.861 5440413.273 0.862310051 0.877576603 0.695795291 0.900525326 0.893734642 0.827040862 0.849089833 0.85343661 1 22.37528482 1.229918394 4.289234849 1.016301535 0.843425273 0.421529205 0.057177393 0.230357026 8.154044457 0.12465358 0.014154611 16.97924575 -1.229918394 -0.172876263 SYDPPCPGHWT(ph)PEAPGSGTTCPGLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYDPPCPGHWTPEAPGSGTTCPGLPR 26 0 H3BM67;H3BUP2;H3BUN4;O60936;O60936-3;J3QLT7 H3BM67 NOL3 Nucleolar protein 3 1 SYDPPCPGHWT(1)PEAPGSGTTCPGLPR 89.684 0.040325 452840000 80978 66836 29726 34450 62306 58286 44138 61940 46842 TRUE FALSE 70276.55213 66396.94992 44101.59303 42272.39904 61066.2325 60528.30014 39857.50355 48694.61302 41304.39212 1.70143049 1.607503379 1.067721633 1.023435932 1.478444043 1.465420432 0.964970104 1.178920946 1 15.33400758 4.300148643 6.110951946 1.175239949 1.669067289 0.5604801 0.179157634 0.152352247 10.87824451 0.046828608 0.125634742 19959.45338 -4.300148643 0.493827339 SYDQVHSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SYDQVHSGK 9 0 Q15067-2;Q15067;Q15067-3 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ;;; 140.49 0.00010899 1089030000 3425260 2541330 1735760 2892610 2384750 3231130 2656480 3654990 3189820 FALSE TRUE 2972603.212 2524635.836 2575179.342 3549421.311 2337298.141 3355433.662 2398854.978 2873398.832 2812723.113 1.056841748 0.897577093 0.915546692 1.261916359 0.830973418 1.192948444 0.852858558 1.021571877 1 21.42353611 5.106634372 19.00484123 0.997329347 7.384957477 0.018133486 0.13906552 1786.937884 316962.2526 0.02976454 2351.59531 127830.466 -5.106634372 6.38762813 SYDTDQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYDTDQGR 8 0 Q9HA64;I3L3W5;I3L139;I3L407 Q9HA64 FN3KRP Ketosamine-3-kinase 0 133.58 0.0037433 0 433760 416790 223950 271900 331490 430100 358440 435820 378730 FALSE TRUE 376437.517 414052.079 332252.9691 333639.0507 324893.9975 446646.2253 323678.544 342623.2846 333956.9709 1.127203652 1.239836611 0.994897541 0.999048021 0.972861853 1.337436449 0.969222302 1.02595039 1 18.3493027 4.236714475 24.99970092 1.043796619 1.183520141 0.219117108 0.110448949 69.04321022 935009.6096 0.027794386 0.06296155 17247.03621 -4.236714475 0.139723522 SYDVPPPPMEPDHPFYSNISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SYDVPPPPMEPDHPFYSNISK 21 0 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 0 ;;;;; 254.39 2.18E-36 2905200000 3080620 2741730 1714920 2332290 2658480 2416910 2892570 3344560 3748440 FALSE TRUE 2673508.262 2723719.395 2544261.048 2861872.091 2605581.449 2509890.092 2612049.007 2629351.871 3305303.693 0.808854045 0.824045125 0.769751068 0.865842403 0.788303191 0.759352339 0.790259912 0.795494791 1 21.6563514 1.237824207 24.99976931 1.000000231 0.799738575 0.819495038 0.029462857 7.304063877 247787.8446 0.041375111 0.007085876 17.29116307 -1.237824207 -0.200261656 SYEALVQHVIEDHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SYEALVQHVIEDHER 15 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 ;;; 247.46 1.65E-18 1164760000 841210 794713 393057 545163 744621 800938 701181 811340 734696 FALSE TRUE 730041.9671 789492.478 583140.6799 668950.5914 729804.4989 831750.6031 633180.5745 637841.2549 647841.0758 1.126884346 1.218651468 0.900129216 1.032584404 1.126517793 1.283880622 0.97737022 0.984564392 1 19.30528042 SYEDMIGEEVPSDQYYWAPLAQHER ddPTM_MDA-MB-175_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 ;;; 184.14 1.93E-17 444056000 328506 279523 181358 259731 269556 315888 227556 307873 291225 FALSE TRUE 285093.0998 277686.795 269063.3354 318706.8933 264192.363 328040.4158 205487.6541 242036.7548 256796.7123 1.110189836 1.081348716 1.047767836 1.241086346 1.028799632 1.277432304 0.800195814 0.942522794 1 17.97026721 2.232401915 24.99998118 0.915380072 1.12540348 0.555217805 0.091403841 105.2671655 427304.9785 0.03445558 0.023896163 170.7662001 -2.232401915 0.210023408 SYEFFNELYHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SYEFFNELYHR 11 0 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 ;; 164.04 2.32E-05 435120000 750420 703230 575370 582350 750090 772940 735080 819570 807070 FALSE TRUE 651250.0957 698610.4358 853620.8565 714581.4682 735164.6765 802675.502 663792.0547 644311.3334 711659.104 0.915115245 0.98166444 1.199479992 1.00410641 1.033029258 1.127893253 0.932738794 0.905365125 1 19.44082681 2.207059445 24.98456987 0.937007719 1.045552093 0.242926381 0.080575257 254.4797087 201834.0778 0.032989623 0.022243839 161.0866111 -2.207059445 0.108544374 SYELPDGQVITIGNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 15 SYELPDGQVITIGNER 16 0 P60709;A0A2R8Y793;P63267-2;A0A2R8YEA7;Q562R1;Q9BYX7;P63261;P68133;P68032;P63267;P62736;Q6S8J3;A5A3E0 P60709;P63261;P68133;Q6S8J3 ACTB;ACTG2;ACTBL2;POTEKP;ACTG1;ACTA1;ACTC1;ACTA2;POTEE;POTEF "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Beta-actin-like protein 2;Putative beta-actin-like protein 3;Putative beta-actin-like protein 3, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F" 0 ;;;;;;;;;;;;;; 379.08 1.77E-104 47261390000 5047410 4680310 2632851 3467493 4440990 4755230 4010970 4813230 4455430 FALSE TRUE 4380381.98 4649564.735 3906106.55 4254840.283 4352622.988 4938166.775 3621986.747 3783958.221 3928714.141 1.114965819 1.183482577 0.994245549 1.083010912 1.10790015 1.256942246 0.921926772 0.963154377 1 21.90562577 2.212200043 24.9999057 0.960341004 1.117740106 0.54609037 0.06937605 171.6426037 162781.5842 0.028506139 0.019225142 163.0046685 -2.212200043 0.157399102 SYELQESNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYELQESNVR 10 0 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;D6R9Y6;D6RDP1 D6RGI3 11-Sep Septin-11 0 79.16 0.064761 124940000 151630 136440 84505 107590 119830 145370 122190 120740 173570 FALSE TRUE 131591.7113 135543.7167 125371.9007 132019.9539 117445.6174 150962.478 110340.0326 94920.6906 153050.7523 0.859791339 0.885612874 0.819152462 0.862589382 0.767363869 0.986355674 0.720937538 0.620190944 1 17.22365061 2.182908357 24.99996834 0.74452734 0.858061192 0.082851074 0.109678522 141.1924065 63424.77264 0.043196645 0.029123189 152.3731189 -2.182908357 0.113533852 SYESANGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYESANGR 8 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 106.91 0.014629 0 327920 226390 204220 253390 231310 296510 265700 342410 554130 FALSE TRUE 284584.5412 224902.8292 302981.4751 310926.0723 226707.3836 307916.9316 239932.4549 269188.2861 488621.3827 0.582423429 0.460280367 0.620074122 0.636333332 0.463973521 0.630174901 0.491039614 0.550913848 1 18.89835747 1.238438889 25 1.000000491 0.552481403 0.820349078 0.065527733 1.100900687 225167.2484 0.083756155 0.014940032 17.3156536 -1.238438889 -0.447519089 SYETLVDFDNHLDDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SYETLVDFDNHLDDIR 16 0 M0R1B0;O43402 M0R1B0 EMC8 ER membrane protein complex subunit 8 0 ;;; 258.16 1.07E-26 1293160000 2227360 1971180 1232760 1793660 1965220 2370150 1645200 2341740 2364550 FALSE TRUE 1933008.733 1958231.189 1828926.859 2200937.917 1926115.967 2461331.204 1485648.757 1840977.124 2085015.593 0.927095576 0.939192587 0.877176586 1.055597821 0.923789718 1.180485754 0.712536042 0.882956046 1 20.99162674 2.221258926 24.99991265 0.862511314 0.977535116 0.208419298 0.108561951 388.8287899 561830.3255 0.04295885 0.029039516 166.440467 -2.221258926 0.115023803 SYGSLVQSACS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYGSLVQSACSPVR 14 0 Q96S90 Q96S90 LYSMD1 LysM and putative peptidoglycan-binding domain-containing protein 1 1 SYGSLVQS(0.016)ACS(0.984)PVR 75.968 0.0131 0 94634 95605 54080 70369 99473 105060 92678 101320 127240 TRUE FALSE 82127.87713 94976.96446 80233.26889 86347.35697 97493.68192 109101.7262 83690.10182 79653.50647 112197.8322 0.731991658 0.846513365 0.71510534 0.769599156 0.868944435 0.972404939 0.745915498 0.709938017 1 16.77568528 3.257620604 23.10986464 0.837886581 0.767946142 0.175696908 0.094534223 246.6794447 299089.3858 0.028756719 0.037041011 1809.758413 -3.257620604 -0.069940439 SYHEEFNPPKEPMKDDITGEPLIR ddPTM_MDA-MB-175_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" 0 107.74 0.081855 99708000 82178 67700 28637 64363 67629 60732 76489 100180 88760 FALSE TRUE 71317.96909 67255.27424 42485.94899 78977.60288 66283.31521 63068.39934 69071.10855 78757.2866 78266.89392 0.911215017 0.859306801 0.542834229 1.009080582 0.846888281 0.805811962 0.882507342 1.006265646 1 16.25611457 1.859686281 2.892082849 1.006452566 0.826764243 0.267928956 0.117018797 0.337621465 5.016231287 0.077821873 0.032109333 72.39128417 -1.859686281 -0.179688322 SYIEGYVPSQADVAVFEAVS(ph)SPPPADLCHALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYIEGYVPSQADVAVFEAVSSPPPADLCHALR 32 0 P24534;C9JZW3;F2Z2G2 P24534 EEF1B2 Elongation factor 1-beta 1 SYIEGYVPSQADVAVFEAVS(0.585)S(0.415)PPPADLCHALR 124.06 9.54E-08 302850000 154980 161400 96636 112870 151860 174190 149040 177250 138340 TRUE FALSE 134499.0003 160339.7528 143369.4928 138498.8586 148838.2831 180891.202 134586.1237 139346.4669 121985.6028 1.102580938 1.314415383 1.175298474 1.135370531 1.220129914 1.482889766 1.103295148 1.142318959 1 16.89635136 1.534672288 1.853348411 1.001828905 1.231008115 0.285643433 0.112262019 0.58742434 3.39537359 0.208414279 0.031572455 34.25092367 -1.534672288 0.229179211 SYIEGYVPSQADVAVFEAVSS(ph)PPPADLCHALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SYIEGYVPSQADVAVFEAVSSPPPADLCHALR 32 0 P24534;C9JZW3;F2Z2G2 P24534 EEF1B2 Elongation factor 1-beta 1 SYIEGYVPSQADVAVFEAVS(0.217)S(0.783)PPPADLCHALR;SYIEGYVPSQADVAVFEAVS(0.218)S(0.782)PPPADLCHALR;SYIEGYVPSQADVAVFEAVS(0.08)S(0.92)PPPADLCHALR 198.94 5.63E-27 1350570000 977458 982227 573767 703567 986574 1055793 876263 1133100 898163 TRUE FALSE 848284.4487 975774.6862 851242.6403 863322.6407 966943.1076 1096410.04 791283.1491 890795.3828 791983.1933 1.071088952 1.23206489 1.074824122 1.090076971 1.220913671 1.384385488 0.999116087 1.124765513 1 19.59511029 SYIEGYVPSQADVAVFEAVSSPPPADLCHALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SYIEGYVPSQADVAVFEAVSSPPPADLCHALR 32 0 P24534;C9JZW3;F2Z2G2 P24534 EEF1B2 Elongation factor 1-beta 0 ;; 116.13 1.76E-06 390921000 572065 523625 298913 336386 511984 529434 485876 569791 354857 FALSE TRUE 496465.1608 520185.2729 443468.3266 412767.5826 501796.5201 549801.6686 438755.8203 447945.6288 312906.2097 1.586626105 1.662431926 1.417256395 1.31914155 1.603664307 1.75708136 1.402195951 1.431565162 1 18.25537076 0.93178436 1.494466191 0.31548984 1.541465305 0.629888202 0.128759303 1.806978568 1.925850941 4.172152555 0.03855909 8.546422516 -0.93178436 1.225975465 SYIYSGSHDGHINYWDSETGENDSFAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYIYSGSHDGHINYWDSETGENDSFAGK 28 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 208.12 1.13E-25 149240000 164130 129340 43321 100270 152830 135630 155040 189880 173810 FALSE TRUE 142439.8046 128490.357 64271.1805 123037.836 149788.982 140847.7739 140004.2447 149275.6396 153262.3798 0.929385312 0.838368536 0.419353925 0.802792154 0.977336919 0.918997696 0.913493871 0.973987484 1 17.22564409 3.375148295 4.948834666 0.952673392 0.720979736 0.392289033 0.131296633 0.213496512 8.536840101 0.039030376 0.050843062 2372.183577 -3.375148295 -0.231693656 SYLFLLSSDYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYLFLLSSDYER 12 0 B7Z683;A0A0G2JQ41;A0A1C7CYZ0;Q12979-4;Q12979-2;Q12979;I3L0R7;A0A0G2JSE0;A0A0D9SGD7 B7Z683 ABR Active breakpoint cluster region-related protein 0 116.55 0.00046308 0 131620 161750 98102 122470 169460 193670 181940 195560 168530 FALSE TRUE 114226.0835 160687.4536 145544.4553 150278.6853 166088.0775 201120.6102 164295.4868 153741.0158 148606.5754 0.768647573 1.081294372 0.979394451 1.011251924 1.117636128 1.353376253 1.105573467 1.03455056 1 17.18113843 5.435965153 0.960770083 1.10368823 8.51E-13 0.462539627 0.106256617 6.904160907 1.945816651 0.036515459 10.89317675 272875.8823 -5.435965153 -1.10368823 SYLLGNSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SYLLGNSSPR 10 0 P02545;P02545-3;P02545-5;P02545-4;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 SYLLGNS(0.186)S(0.814)PR;SYLLGNS(0.081)S(0.919)PR;SYLLGNS(0.017)S(0.983)PR 117.03 0.0010614 508800000 1237500 1227640 685820 878360 1159960 1288220 1105700 1312790 1215510 TRUE FALSE 1073961.24 1219575.552 1017484.846 1077805.063 1136879.065 1337778.657 998469.3842 1032060.075 1071813.793 1.002003564 1.137861409 0.949311208 1.005589843 1.060705762 1.248144656 0.931569822 0.962909865 1 20.03162286 SYLMTNYESAPPS(ph)PQYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYLMTNYESAPPSPQYK 17 0 O75223;M0QZK8;B8ZZK2;H7BZK5 O75223 GGCT Gamma-glutamylcyclotransferase 1 SYLMTNYESAPPS(1)PQYK 209.23 4.68E-12 65039000 129630 108500 78753 101810 128800 106210 129920 160310 161870 TRUE FALSE 112499.0671 107787.2564 116838.2142 124927.5166 126237.132 110295.9674 117320.3784 126028.954 142733.913 0.788173355 0.755162204 0.818573608 0.875247612 0.884422835 0.772738343 0.821951672 0.882964331 1 17.12296863 1.287689032 1.958916666 1.047712844 0.817223763 0.678867341 0.040373719 0.462817277 1.901413747 0.189886913 0.012072998 19.39496644 -1.287689032 -0.230489081 SYLTPVRDEESESQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYLTPVRDEESESQR 15 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8;H0YIS4;A0A3B3ISH4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 0 134.14 3.37E-05 157300000 246810 185370 171780 183960 185860 182380 204920 244380 232900 FALSE TRUE 214193.4332 184152.2923 254853.3826 225730.9297 182161.7496 189396.2766 185046.8899 192121.2388 205366.8273 1.042979706 0.89669931 1.240966644 1.099159648 0.887006689 0.922234029 0.901055406 0.935502784 1 17.64784364 3.241282266 24.99996857 0.927498536 1.069791578 0.391198118 0.08726097 76.27338201 700611.4127 0.026007811 0.032066886 1742.939316 -3.241282266 0.142293042 SYMNPGDQS(ph)PADSNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SYMNPGDQSPADSNK 15 0 Q92754;Q92754-2 Q92754 TFAP2C Transcription factor AP-2 gamma 1 SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK 391.64 1.59E-114 534420000 1054280 566140 402590 572970 649250 557930 668960 817450 766140 TRUE FALSE 914954.2268 562420.9891 597283.8706 703071.5958 636331.1952 579393.9281 604084.3622 642644.6789 675567.802 1.354348482 0.832515978 0.884121281 1.040712115 0.941920549 0.857639938 0.894187616 0.951265997 1 19.36574104 4.746331776 24.9898618 0.926591584 1.354348689 0.820830821 0.062994182 405.9785046 1305482.158 0.015684945 0.165583991 55761.15689 -4.746331776 0.427757105 SYNPFDDDGEDEGARPAPWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SYNPFDDDGEDEGARPAPWR 20 1 O95721 O95721 SNAP29 Synaptosomal-associated protein 29 0 ;;; 229.46 2.14E-25 1504600000 888993 699096 524898 658938 973399 848659 790429 953951 776302 FALSE TRUE 771510.3226 694503.5923 778740.4285 808559.9441 954030.2643 881307.4609 713773.3172 749956.0023 684528.4619 1.127068289 1.014572265 1.137630459 1.181192586 1.393704305 1.287466497 1.042722629 1.095580453 1 19.384751 2.212031323 24.99916159 1.056268388 1.188727418 0.306195304 0.101903849 335.0879327 315758.5513 0.046990737 0.031691364 162.9413548 -2.212031323 0.13245903 SYQEHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYQEHVK 7 0 P32456;H3BNS1;Q9H0R5-4;Q9H0R5;Q5T8M0 P32456 GBP2;GBP3 Interferon-induced guanylate-binding protein 2;Guanylate-binding protein 3 0 62.2 0.086891 123080000 70001 67684 35776 56143 64575 65376 70815 77846 79141 FALSE TRUE 60750.19049 67239.37935 53077.39326 68891.12624 63290.08384 67891.05702 63947.3722 61199.2387 69785.04114 0.870533133 0.963521383 0.760584108 0.987190451 0.90692909 0.972859741 0.916347847 0.876967867 1 16.0906302 SYQNS(ph)PS(ph)SDDGIRPLPEYSTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYQNSPSSDDGIRPLPEYSTEK 22 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 2 SYQNS(1)PS(0.883)S(0.117)DDGIRPLPEYSTEK 200 9.67E-23 263410000 652670 333470 287080 334580 337980 413260 441450 496280 501430 TRUE FALSE 566418.0058 331279.4136 425912.8482 410551.5027 331254.8592 429158.3796 398638.2469 390154.3841 442151.5166 1.28104956 0.749244097 0.963273521 0.928531255 0.749188563 0.970613836 0.901587424 0.882399742 1 18.75418131 4.752233106 24.94208027 0.89389072 1.281049826 0.67227745 0.085122273 1326.191891 2419266.118 0.019221207 0.38094457 56524.02846 -4.752233106 0.387159106 SYQNS(ph)PSS(ph)DDGIRPLPEYSTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYQNSPSSDDGIRPLPEYSTEK 22 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 2 SYQNS(1)PS(0.132)S(0.868)DDGIRPLPEYSTEK 228.55 2.02E-26 199100000 529190 322470 253820 259010 345010 338910 388580 415300 450390 TRUE FALSE 459256.2007 320351.6733 376568.201 317822.1792 338144.976 351948.087 350895.5714 326491.3269 397145.4073 1.15639308 0.806635724 0.948187223 0.800266536 0.851438717 0.886194529 0.883544327 0.822095184 1 18.59930779 4.746509056 24.91800828 0.870679005 1.156393225 0.668235471 0.062296542 529.348335 1659443.688 0.01384474 0.148197101 55783.92347 -4.746509056 0.285714221 SYQSELEALRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SYQSELEALRR 11 1 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 ;; 173.19 2.00E-05 746490000 723830 708300 391076 562799 724240 833490 646850 764730 521080 FALSE TRUE 628174.0315 703647.1307 580201.6617 690591.1148 709829.041 865554.8996 584118.5866 601198.4406 459478.516 1.3671456 1.531403768 1.262739478 1.502988912 1.544857956 1.88377665 1.271264197 1.308436455 1 18.80963788 1.44243568 1.688589597 0.948905957 1.498861478 0.452368489 0.172175485 0.597207872 2.328434444 0.49457048 0.050144917 27.6971881 -1.44243568 0.549955521 SYS(ph)FDEIRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYSFDEIRK 9 1 P43490 P43490 NAMPT Nicotinamide phosphoribosyltransferase 1 S(0.121)YS(0.879)FDEIRK 93.258 0.0031011 0 143120 109060 42756 88439 82688 61421 96434 148620 95964 TRUE FALSE 124206.3294 108343.5777 63432.94461 108520.4267 81042.67058 63783.90561 87081.84552 116838.7696 84619.24524 1.467826013 1.280365682 0.74962787 1.28245562 0.957733319 0.753775402 1.02910213 1.380758824 1 16.3686982 4.468460236 24.90515149 1.049328887 1.420961039 0.363985989 0.198548895 181.9599596 523235.4898 0.051994152 0.138037376 29407.64428 -4.468460236 0.371632151 SYS(ph)HDVLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYSHDVLPK 9 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 S(0.438)YS(0.562)HDVLPK 88.441 0.0082332 500490000 1406700 1299900 980110 1396900 1646000 1462300 2094100 2114300 2244700 TRUE FALSE 1220801.031 1291360.871 1454094.474 1714087.495 1613247.82 1518555.627 1891014.504 1662173.399 1979334.123 0.616773599 0.652421871 0.734638209 0.86599199 0.815045727 0.767205299 0.955379126 0.839763928 1 20.91658374 5.893567546 0.261316672 0.969371727 4.03E-12 0.759542851 0.059105635 14.16430238 0.618866996 0.211440626 4.855551407 782649.9223 -5.893567546 -0.969371727 SYS(ph)LSELSVLQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SYSLSELSVLQAK 13 0 Q9P0V3;Q9P0V3-2 Q9P0V3 SH3BP4 SH3 domain-binding protein 4 1 SYS(1)LSELSVLQAK;SYS(1)LSELSVLQAK;SYS(0.772)LS(0.228)ELSVLQAK;SYS(0.943)LS(0.057)ELSVLQAK;SYS(0.875)LS(0.125)ELSVLQAK;S(0.003)YS(0.969)LS(0.028)ELSVLQAK 310.81 1.46E-50 1808927000 2474830 1928290 1321185 1907630 1972480 1752730 1957640 2505510 2285100 TRUE FALSE 2147774.945 1915622.936 1960114.485 2340786.548 1933231.507 1820158.657 1767788.374 1969726.184 2014958.081 1.065915448 0.950701136 0.972781768 1.161704836 0.959440062 0.903323337 0.877332581 0.977551942 1 20.94231839 3.021574098 24.99994303 0.93873694 1.031121097 0.340952155 0.065335028 292.2753613 338684.759 0.020147658 0.02284332 1050.930746 -3.021574098 0.092384157 SYS(ph)PAHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SYSPAHNR 8 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 SYS(1)PAHNR;S(0.101)YS(0.899)PAHNR;S(0.048)YS(0.952)PAHNR;S(0.419)YS(0.58)PAHNR 90.827 0.0083223 766179000 1404192 1140607 657648 867208 1083584 1252137 1113376 1165953 1016490 TRUE FALSE 1218624.469 1133114.278 975688.7725 1064120.831 1062022.798 1300307.521 1005400.967 916623.0244 896321.7102 1.359583792 1.264182564 1.088547517 1.187208587 1.184867873 1.450715191 1.121696547 1.022649584 1 19.77365712 2.005414514 24.98803935 1.030711721 1.245938964 0.513650482 0.098961547 118.3827513 546335.1485 0.041817692 0.028092354 101.254542 -2.005414514 0.215227243 SYS(ph)PDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SYSPDGK 7 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 SYS(1)PDGK;SYS(1)PDGK;SYS(1)PDGK;SYS(1)PDGK;SYS(1)PDGK 131.22 0.0036575 12323420000 33070950 24628390 19212720 22488490 19372610 21107010 28322430 32381760 38357830 TRUE FALSE 28700540.17 24466604.48 28504055.65 27594845.37 18987132.96 21919010.33 25575725.1 25457172.62 33823211.03 0.848545697 0.723367289 0.842736535 0.815855282 0.561363998 0.648046405 0.75615899 0.752653927 1 25.01151029 1.23054485 4.521361337 1.02388501 0.738980314 0.458195103 0.087607748 0.208729401 8.962067974 0.193410799 0.0230812 17.00375545 -1.23054485 -0.284904696 SYS(ph)PDGKES(ph)PSDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 SYSPDGKESPSDKK 14 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 2 S(0.347)Y(0.005)S(0.648)PDGKES(0.58)PS(0.42)DKK;S(0.028)YS(0.972)PDGKES(0.994)PS(0.006)DKK;S(0.126)Y(0.014)S(0.86)PDGKES(0.923)PS(0.077)DKK;S(0.01)Y(0.015)S(0.974)PDGKES(0.941)PS(0.059)DKK;S(0.014)YS(0.986)PDGKES(0.864)PS(0.136)DKK;S(0.102)Y(0.003)S(0.895)PDGKES(0.955)PS(0.045)DKK;S(0.091)Y(0.007)S(0.903)PDGKES(0.6)PS(0.4)DKK;S(0.084)Y(0.001)S(0.915)PDGKES(0.998)PS(0.002)DKK 201.8 8.53E-08 9306870000 17155440 9743650 12331290 8814270 8892860 6026620 16228320 18335870 15129690 TRUE FALSE 14888305.14 9679643.322 18294743.09 10815684.72 8715909.485 6258467.971 14654500.02 14414886.89 13341075.28 1.115974899 0.72555196 1.371309486 0.810705621 0.653313867 0.469112709 1.098449691 1.080489135 1 23.66937162 SYS(ph)PDGKESPSDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SYSPDGKESPSDKK 14 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 S(0.026)YS(0.948)PDGKES(0.025)PS(0.001)DKK;S(0.002)YS(0.998)PDGKESPSDKK;S(0.001)YS(0.964)PDGKES(0.035)PSDKK;SYS(1)PDGKESPSDKK;SYS(1)PDGKESPSDKK;S(0.001)YS(0.999)PDGKESPSDKK 158.45 3.99E-06 9776130000 17882190 9525260 6341490 5517710 7331920 4802300 15326010 16095120 2351940 TRUE FALSE 15519013.28 9462687.94 9408255.775 6770590.388 7186029.137 4987047.589 13839695.91 12653303.84 2073896.333 7.483022676 4.562758413 4.536512085 3.264671566 3.464989558 2.404675446 6.673282407 6.101222921 1 20.98391235 4.793509517 2.582881975 4.171965959 8.466245592 0.302637074 1.654207182 0.915102882 6.92080678 0.440028694 9.046242754 62159.78687 -4.793509517 4.294279634 SYS(ph)PDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SYSPDHR 7 0 A0A024RAC6;Q14241 A0A024RAC6 TCEB3 Transcription elongation factor B polypeptide 3 1 S(0.13)YS(0.87)PDHR;S(0.018)YS(0.982)PDHR;S(0.022)YS(0.977)PDHR 105.36 0.0083336 1428963000 3414690 3265320 1886400 2430410 2718230 2694880 3142670 3237500 2960480 TRUE FALSE 2963430.065 3243869.898 2798669.35 2982271.737 2664142.541 2798553.777 2837894.347 2545185.819 2610495.427 1.135198336 1.242626156 1.072083606 1.142415997 1.020550549 1.072039333 1.087109488 0.974981911 1 21.3158922 3.893124353 0.159196878 0.845579847 1.408944261 0.580165796 0.050397674 12.89991477 1.133807276 1.39926673 2.608523397 7818.516423 -3.893124353 0.563364414 SYS(ph)PER ddPTM_MDA-MB-175_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(0.005)YS(0.995)PER;S(0.001)YS(0.999)PER 88.358 0.05391 1300040000 1115040 961330 599920 787510 772750 990910 907790 1019710 959890 TRUE FALSE 967684.6388 955014.9599 890043.3186 966326.1818 757373.7869 1029030.949 819752.6655 801652.9519 846412.8977 1.143277284 1.12830861 1.051547443 1.141672326 0.894804166 1.215755279 0.968502096 0.947118072 1 19.69100209 -0.178517542 0.041943343 1.81E-07 1.826238089 0.251117218 0.088599795 1243.799242 8.133989427 239.6152297 129.9540555 0.662952569 0.178517542 1.826237908 SYS(ph)SER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYSSER 6 0 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 1 S(0.004)YS(0.856)S(0.14)ER 69.825 0.097012 205280000 188640 194600 126630 134750 136340 158340 167090 172680 168160 TRUE FALSE 163710.746 193321.6598 187868.6916 165347.047 133627.1007 164431.4423 150885.6375 135753.7258 148280.3164 1.104062562 1.303758075 1.266983347 1.115097749 0.901178956 1.108922926 1.017570243 0.91552088 1 17.17796757 3.477036315 4.531240639 0.987923757 1.229177356 0.672029095 0.075635853 0.109633632 5.786923489 0.02169132 0.030235754 2999.413316 -3.477036315 0.241253599 SYS(ph)SERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SYSSERR 7 1 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 1 S(0.035)YS(0.816)S(0.15)ERR;SYS(0.911)S(0.089)ERR 98.233 0.0069908 1010980000 720660 656300 523440 461600 528190 656390 677280 719210 398930 TRUE FALSE 625422.9551 651988.7221 776577.3348 566413.3351 517680.0524 681641.748 611597.4898 565412.5384 351768.9499 1.777936783 1.853457283 2.207634685 1.610185707 1.471647946 1.937754166 1.738634095 1.607340667 1 18.42426862 0.994654829 1.562688451 0.167265714 1.807954068 0.628203084 0.193154453 1.452393911 1.927159741 4.462996343 0.056696083 9.877677192 -0.994654829 1.640688354 SYS(ph)SPDITQAIQEEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SYSSPDITQAIQEEEK 16 0 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 SYS(0.998)S(0.002)PDITQAIQEEEK;SYS(0.974)S(0.026)PDITQAIQEEEK;SYS(0.99)S(0.01)PDITQAIQEEEK 422.41 5.60E-160 396530000 544840 437652 392513 383941 465454 386097 533390 628840 894210 TRUE FALSE 472838.0136 434777.0352 582333.5997 471120.6722 456192.376 400950.4014 481661.9199 494367.4596 788497.5125 0.599669633 0.551399375 0.738535747 0.59749164 0.578559055 0.50849926 0.610860418 0.626974026 1 19.58874668 1.228866386 4.137813462 1.045717835 0.598805191 0.822584221 0.058293047 0.100949045 3.139360917 0.137784279 0.014998733 16.93816604 -1.228866386 -0.446912644 SYS(ph)SPDITQAIQEEEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 SYSSPDITQAIQEEEKR 17 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 SYS(0.913)S(0.087)PDITQAIQEEEKR;SYS(0.869)S(0.131)PDITQAIQEEEKR;S(0.001)YS(0.499)S(0.499)PDITQAIQEEEKR;SYS(0.5)S(0.5)PDITQAIQEEEKR;SYS(0.922)S(0.078)PDITQAIQEEEKR;SYS(0.978)S(0.022)PDITQAIQEEEKR;S(0.003)YS(0.96)S(0.037)PDITQAIQEEEKR 310.08 4.57E-58 5388358000 4023694 3446412 2764078 2760524 3324082 3079948 4235498 4705068 4268510 TRUE FALSE 3491952.643 3423772.293 4100795.366 3387343.166 3257939.272 3198435.593 3824740.056 3698925.823 3763891.611 0.927750585 0.909636261 1.08950942 0.899957681 0.865577336 0.849768251 1.016166365 0.982739729 1 21.84379365 2.197753565 24.99960882 0.996804288 0.926876129 0.232649734 0.064771634 255.2192152 156353.0856 0.027907401 0.01881541 157.6716328 -2.197753565 -0.069928159 SYSFDEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYSFDEIR 8 0 P43490 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 110.12 0.0081123 138830000 362400 517920 250130 270190 407380 501930 361870 371760 650010 FALSE TRUE 314507.9218 514517.7494 371093.7046 331540.7691 399273.935 521239.5719 326775.9031 292262.017 573166.5583 0.548719944 0.897675801 0.647444795 0.578437043 0.696610661 0.909403322 0.570123812 0.509907657 1 19.12859491 5.440532454 0.003728462 1.370327698 5.39E-05 0.001881547 0.171751345 3684506.994 2771.662432 498692.7694 520138.2329 275760.7518 -5.440532454 -1.370273844 SYSFDEIRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SYSFDEIRK 9 1 P43490 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;; 172.59 8.99E-05 1803080000 2269670 1858830 987180 1413910 1787600 1740280 2032640 2398540 1488020 FALSE TRUE 1969727.359 1846619.223 1464583.55 1734959.876 1752030.257 1807229.698 1835514.886 1885630.886 1312107.971 1.501193044 1.407368345 1.116206579 1.322269138 1.335279029 1.377348311 1.398905369 1.437100398 1 20.32345501 -1.999827827 0.015522312 6.87E-06 2.448819584 0.094312172 0.14461953 50193.49085 77.55416108 7310.543546 5114.263419 0.010003965 1.999827827 2.448812715 SYSMIVNNLLKPISVEGSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SYSMIVNNLLKPISVEGSSK 20 1 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 210.38 3.43E-22 354950000 1152020 827450 612690 816910 867990 674670 1009940 1338840 1337990 FALSE TRUE 999777.6382 822014.4265 908988.9333 1002401.901 850718.6972 700624.9915 911996.1742 1052539.485 1179814.346 0.84740251 0.696732015 0.770450822 0.849626811 0.721061496 0.593843424 0.772999733 0.892122975 1 20.17012843 1.577601076 2.596854063 0.99131922 0.7448061 0.572378796 0.07354844 0.193642026 2.765158243 0.086464107 0.020550129 37.80951235 -1.577601076 -0.24651312 SYSS(ph)ER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SYSSER 6 0 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 1 S(0.002)YS(0.343)S(0.655)ER 96.19 0.04457 212050000 360180 323810 205140 239250 271340 341170 311030 390820 457920 TRUE FALSE 312581.3004 321682.8708 304346.3902 293575.3692 265940.8649 354295.0307 280866.3585 307246.1844 403785.2193 0.774127644 0.796668267 0.75373336 0.727058236 0.658619613 0.877434373 0.695583555 0.760914887 1 18.62322858 1.239930153 7.258017752 1.004446734 0.753751081 0.633819734 0.058411293 0.063520805 21.71283798 0.078993053 0.013653387 17.37521363 -1.239930153 -0.250695653 SYSSGGEDGYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SYSSGGEDGYVR 12 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ;; 141.27 0.00014045 958240000 868650 820050 442000 587160 863200 874670 726260 931370 766170 FALSE TRUE 753855.7016 814663.0376 655752.6784 720483.6522 846024.0088 908319.1209 655827.417 732203.7734 675594.2554 1.115840899 1.205846602 0.970630927 1.066444314 1.252266434 1.344474311 0.970741553 1.083792184 1 19.36579754 SYTVGVMMMHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 SYTVGVMMMHR 11 0 P50454;E9PKH2;E9PR70;E9PPV6;E9PK86;E9PMI5 P50454 SERPINH1 Serpin H1 0 ;; 103.31 0.0027512 1800770000 2614280 3227300 2082860 2276930 2965560 2823290 4021780 3233430 3369870 FALSE TRUE 2268796.274 3206099.654 3090138.063 2793941.757 2906551.158 2931903.793 3631748.395 2541986.157 2971487.808 0.763521987 1.078954336 1.039929578 0.940250116 0.978146756 0.986678722 1.222198653 0.855459057 1 21.50275403 2.467309223 24.97251395 1.013685477 0.971318357 0.051635713 0.11980764 996.6872833 2536635.275 0.043718508 0.033904624 293.2980822 -2.467309223 -0.04236712 SYVAWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 SYVAWDR 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 110.81 0.015635 3689120000 3729580 3638660 1975710 2498750 3839780 3659300 3968470 3943690 3540360 FALSE TRUE 3236706.553 3614757.403 2931169.964 3066129.379 3763375.89 3800075.639 3583608.39 3100362.583 3121822.674 1.036800258 1.157899657 0.938929039 0.982160007 1.205505976 1.217261849 1.147921828 0.993125782 1 21.57395716 7.882245062 12.13694449 1.076258708 1.030138087 0 0.100213681 0 0 0.023840413 0 76250915.45 -7.882245062 -0.04612062 SYVS(ph)EPELATLSGDMAQPSLGLVGPESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.036)YVS(0.964)EPELATLSGDMAQPSLGLVGPESR;S(0.17)YVS(0.83)EPELATLSGDMAQPSLGLVGPESR;S(0.144)YVS(0.856)EPELATLSGDMAQPSLGLVGPESR;S(0.044)YVS(0.956)EPELATLSGDMAQPSLGLVGPESR 275.58 9.82E-62 317371000 211804 181783 102103 113351 179641 195867 159404 183141 179223 TRUE FALSE 183813.5648 180588.8555 151480.3523 139089.077 176066.4956 203402.1302 143945.0246 143977.7224 158035.4611 1.163115945 1.142710973 0.958521279 0.880113084 1.114094864 1.287066389 0.910840033 0.911046934 1 17.26988879 -1.999999955 0.040573731 8.18E-07 1.684104775 0.10789879 0.125677352 3980.193109 15.89747615 523.8677754 206.436222 0.010000001 1.999999955 1.684103957 SYYVDHNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SYYVDHNSR 9 0 P46934-4;H0Y8X6;P46934-3;P46934-2;P46934 P46934-4 NEDD4 E3 ubiquitin-protein ligase NEDD4 0 ; 105.86 0.0030289 146381000 191084 213370 70499 126160 242610 280170 179960 212900 228590 FALSE TRUE 165831.7653 211968.3584 104592.5522 154806.5562 237782.5357 290948.3212 162507.5069 167372.9918 201566.3506 0.822715521 1.051605875 0.518898873 0.768017855 1.179673765 1.443436964 0.806223392 0.830361771 1 17.62089529 3.260716754 24.97076911 1.025388219 0.789586974 0.257353551 0.218268597 405.5491301 457065.6036 0.068641195 0.088544046 1822.706547 -3.260716754 -0.235801245 T(ph)AMRVSPHHPAPTPNPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TAMRVSPHHPAPTPNPR 17 1 A8MZI9;Q01196-7;Q01196-3;Q01196-4;Q01196;Q01196-9;Q01196-10;Q01196-2;Q01196-8;Q01196-11 A8MZI9 RUNX1 Runt-related transcription factor 1 1 T(0.5)AMRVS(0.5)PHHPAPTPNPR;T(0.592)AMRVS(0.408)PHHPAPTPNPR 110.67 0.0010918 132829000 72551 64617 29275 36354 72206 73495 66607 70043 35593 TRUE FALSE 62963.20153 64192.52667 43432.48792 44608.73134 70769.24187 76322.40021 60147.46339 55064.84953 31385.23609 2.006140765 2.045309664 1.383850923 1.421328526 2.254857719 2.431793089 1.916425393 1.754482565 1 14.93779844 1.219403689 2.748200753 0.771385876 1.916936399 0.443977023 0.322252836 0.520527494 4.399696593 1.404621664 0.092048692 16.57309764 -1.219403689 1.145550523 T(ph)AS(ph)PPPPPK ddPTM_MDA-MB-175_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 150.04 0.00045722 2881920000 5471100 4058710 2929500 3425580 3824310 3083810 4607480 5355780 5899700 TRUE FALSE 4748080.273 4032048.067 4346215.999 4203410.296 3748213.713 3202446.166 4160647.299 4210488.126 5202244.187 0.912698463 0.775059363 0.83545021 0.807999422 0.72049938 0.615589359 0.799779316 0.809359956 1 22.31070269 1.180228947 2.521355386 1.079179333 0.776050051 0.441631467 0.076532836 0.651294889 3.977633422 0.459560036 0.020988887 15.14359364 -1.180228947 -0.303129281 T(ph)AS(ph)PPPPPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TASPPPPPKR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 T(1)AS(1)PPPPPKR;T(1)AS(1)PPPPPKR;T(1)AS(1)PPPPPKR;T(1)AS(1)PPPPPKR 90.005 0.0096303 2818660000 4393230 3434150 2173120 2705180 3088960 2713560 3756950 4400470 3569800 TRUE FALSE 3812653.524 3411590.843 3224048.101 3319432.465 3027495.739 2817952.409 3392601.567 3459463.735 3147782.311 1.211218931 1.083807743 1.024228419 1.054530504 0.961786884 0.895218325 1.077775155 1.099016194 1 21.58590434 4.77361883 1.677467954 1.020544604 1.29102248 0.535871045 0.057911189 0.9886779 2.544342221 0.017627031 0.443684762 59377.07918 -4.77361883 0.270477877 T(ph)ASFGNILDVPEIVISGNGQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TASFGNILDVPEIVISGNGQPR 22 0 O43318;O43318-3 O43318 MAP3K7 Mitogen-activated protein kinase kinase kinase 7 1 T(0.5)AS(0.5)FGNILDVPEIVISGNGQPR 161.68 1.91E-10 42235000 73244 66556 47422 64027 78013 74528 64039 83603 105990 TRUE FALSE 63564.61982 66118.78925 70355.43782 78565.30894 76460.69393 77395.14039 57828.50764 65725.14905 93459.98294 0.680126593 0.70745561 0.752786761 0.840630465 0.818111576 0.828109935 0.618751532 0.703243752 1 16.51206115 4.20987829 3.031722674 0.782344315 0.687909029 0.151912275 0.098593519 0.570751004 10.54985719 0.027019678 0.075850851 16213.55653 -4.20987829 -0.094435287 T(ph)ASISSSPSEGTPTVGSYGCTPQSLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TASISSSPSEGTPTVGSYGCTPQSLPK 27 0 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 T(0.305)AS(0.305)IS(0.305)S(0.05)S(0.03)PS(0.005)EGTPTVGSYGCTPQSLPK 98.3 4.47E-08 0 40444 31781 18824 22065 29640 19969 27831 33921 23107 TRUE FALSE 35099.22293 31572.22852 27927.34936 27075.19549 29050.22199 20737.22035 25131.9539 26667.25812 20375.31678 1.722634465 1.549533136 1.370646143 1.32882329 1.425755599 1.017761862 1.233450953 1.308802136 1 14.31453487 7.999999999 0.327453035 1.133730788 7.341660694 0.730104698 0.113467027 42.70650566 0.668433885 0.177496084 157.6444844 99999999.84 -7.999999999 6.207929905 T(ph)CNSPQNSTDSVSDIVPDSPFPGALGSDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TCNSPQNSTDSVSDIVPDSPFPGALGSDTR 30 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 T(0.59)CNS(0.333)PQNS(0.075)T(0.003)DSVSDIVPDSPFPGALGSDTR;T(0.535)CNS(0.366)PQNS(0.097)T(0.002)DSVSDIVPDSPFPGALGSDTR;T(0.471)CNS(0.35)PQNS(0.074)T(0.104)DS(0.001)VSDIVPDSPFPGALGSDTR 176.94 3.24E-17 565850000 314370 286887 151061 195588 280873 284267 248098 327810 252612 TRUE FALSE 272825.208 285002.4204 224114.6049 239999.2448 275284.1768 295202.9354 224037.4941 257710.3825 222748.4971 1.224812789 1.279480778 1.00613296 1.077444956 1.235852005 1.325274645 1.005786782 1.156956773 1 17.76505617 0.351977227 0.907503 0.371511882 1.174025626 0.194895454 0.107672796 17.53733031 3.381759228 20.53005401 0.038530035 2.248936674 -0.351977227 0.802513744 T(ph)DGSIS(ph)GDRQPVTVADYISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TDGSISGDRQPVTVADYISR 20 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 2 T(0.628)DGS(0.382)IS(0.953)GDRQPVT(0.031)VADY(0.001)IS(0.005)R 87.228 0.060014 150400000 226500 166330 121040 139530 201320 194310 191490 230140 219710 TRUE FALSE 196567.4511 165237.3673 179575.3489 171212.4191 197314.1259 201785.2314 172919.3293 180926.352 193736.1341 1.014614295 0.852899063 0.926906845 0.883740247 1.018468376 1.041546702 0.892550737 0.933880263 1 17.56373353 3.250879011 24.99821993 0.968720591 0.915306239 0.1852706 0.058366964 429.9771793 872564.9488 0.017089675 0.021902501 1781.882288 -3.250879011 -0.053414352 T(ph)EAT(ph)DKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TEATDKK 7 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 2 T(1)EAT(1)DKK 54.525 0.045525 0 76255 67458 49524 61403 241250 152270 103600 119690 117230 TRUE FALSE 66177.70854 67014.86396 73473.97205 75345.48964 236449.597 158127.9254 93552.88795 94095.22493 103371.2029 0.640194819 0.648293355 0.710777953 0.728882779 2.287383626 1.529709638 0.905018857 0.910265357 1 16.65747481 3.437240185 24.99996896 1.276195574 0.673808553 0.388368531 0.39970536 188.7928298 118346.6487 0.12738606 0.164454919 2736.781877 -3.437240185 -0.602387021 T(ph)ES(ph)KIRR ddPTM_MDA-MB-175_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 68.915 0.067494 1904560000 2420100 2411400 1079240 1329400 2282230 2228600 2321100 2564800 535840 TRUE FALSE 2100277.653 2395559.355 1601164.074 1631260.589 2236818.088 2314335.684 2096000.079 2016337.479 472493.6056 4.445092226 5.070035501 3.388752895 3.452450084 4.734070602 4.898131227 4.436039037 4.26743866 1 18.84993528 4.246279194 24.98990226 3.890641225 4.757563941 0.115141692 1.113594428 432.1262237 1399031.646 0.27727091 0.704698082 17631.0913 -4.246279194 0.866922716 T(ph)FSLTEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TFSLTEVR 8 0 O95239;O95239-2 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 T(0.64)FS(0.36)LTEVR;T(0.606)FS(0.394)LTEVR 236.89 1.40E-07 328940000 340390 308750 275680 396890 605230 631320 565260 685550 705080 TRUE FALSE 295406.5991 306721.8009 408999.7701 487009.9406 593187.1071 655607.2889 510441.1722 538950.4675 621726.2456 0.475139342 0.493338995 0.657845431 0.783318935 0.954096938 1.054495115 0.821006312 0.866861374 1 19.24591996 3.832601825 1.559368761 0.926300056 0.470052597 0.879127797 0.068805954 0.142135427 0.662986512 0.022994714 0.057744723 6801.45494 -3.832601825 -0.456247459 T(ph)FVY(ph)S(ph)LLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TFVYSLLNR 9 0 P31213 P31213 SRD5A2 3-oxo-5-alpha-steroid 4-dehydrogenase 2 3 T(1)FVY(1)S(1)LLNR;T(1)FVY(1)S(1)LLNR 60.972 0.059009 582220000 146991 115582 78932 98352 112602 132367 123656 108776 117981 TRUE FALSE 127565.7669 114822.7342 117103.7792 120684.3248 110361.4405 137459.2441 111663.8602 85515.0989 104033.4206 1.226199871 1.103710073 1.125636152 1.160053415 1.060826799 1.3212989 1.073346041 0.821996416 1 16.66668754 1.947162487 6.283937455 0.909845628 1.159849567 0.618291969 0.08204204 0.12876308 11.60087414 0.037529417 0.020575296 88.54468282 -1.947162487 0.250003939 T(ph)HTDSSEKELEPEAAEEALENGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 THTDSSEKELEPEAAEEALENGPK 24 1 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 1 T(0.271)HT(0.271)DS(0.229)S(0.229)EKELEPEAAEEALENGPK;T(0.271)HT(0.271)DS(0.229)S(0.229)EKELEPEAAEEALENGPK 126.31 0.00013579 209875000 244440 208180 164749 162272 184083 131727 239877 288020 205887 TRUE FALSE 212136.6347 206812.4519 244422.1675 199118.3378 180420.1085 136794.6229 216613.7655 226429.1644 181547.2734 1.16849254 1.139165838 1.346327945 1.096785063 0.993791342 0.753493128 1.193153504 1.247218755 1 17.46998574 3.498375065 23.20180208 1.059764389 1.212019876 0.245538825 0.141381715 556.4648604 607464.6572 0.043364867 0.063459082 3150.467942 -3.498375065 0.152255487 T(ph)ISEPDEQRSELPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TISEPDEQRSELPR 14 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 T(0.552)IS(0.448)EPDEQRSELPR 97.579 0.0047184 226220000 79179 88924 29707 27105 73882 90536 80282 81299 18856 TRUE FALSE 68715.29454 88339.85239 44073.40456 33259.60452 72411.89275 94018.9785 72496.264 63913.84152 16626.86516 4.132787141 5.313079257 2.650734467 2.000353296 4.355113971 5.654642507 4.360188364 3.844010335 1 14.02122857 4.248456896 24.99919446 3.562698064 4.722933065 0.134197058 1.3439515 483.8765186 1222305.142 0.350591087 0.90376515 17719.72166 -4.248456896 1.160235002 T(ph)KFASDDEHDEHDENGATGPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TKFASDDEHDEHDENGATGPVK 22 1 P05455 P05455 SSB Lupus La protein 1 T(0.631)KFAS(0.369)DDEHDEHDENGATGPVK;T(0.5)KFAS(0.5)DDEHDEHDENGATGPVK;T(0.639)KFAS(0.361)DDEHDEHDENGATGPVK 276.9 2.55E-45 1609570000 2183770 1547700 1313640 1317276 1631150 1204718 2240360 2453490 1819640 TRUE FALSE 1895179.262 1537533.057 1948920.698 1616383.649 1598693.306 1251064.281 2023090.232 1928830.257 1604524.232 1.181147173 0.958248574 1.214640863 1.007391236 0.996365947 0.779710431 1.260866113 1.202119742 1 20.61371415 0.942856185 19.38060801 8.66E-05 1.078071424 0.02491993 0.146487002 9852899.163 61061365.49 431619759.4 0.036704906 8.767104534 -0.942856185 1.077984817 T(ph)KSDES(ph)GEEKNGDEDCQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TKSDESGEEKNGDEDCQR 18 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBM7;E5RHK4 Q6PKG0 LARP1 La-related protein 1 2 T(0.824)KS(0.179)DES(0.997)GEEKNGDEDCQR 63.63 0.046203 153710000 239930 163140 170830 117890 166940 125990 224800 261580 235330 TRUE FALSE 208222.6426 162068.3226 253443.9594 144658.7263 163618.2206 130836.9168 202998.9306 205643.1526 207509.5555 1.003436406 0.781016191 1.221360427 0.697118386 0.788485235 0.630510323 0.97826305 0.991005702 1 17.66281825 2.038707206 24.99994242 0.991793502 0.852605574 0.133494532 0.163821404 312.7740751 202011.1269 0.06670811 0.044974519 109.3219087 -2.038707206 -0.139187928 T(ph)KSPTDDEVTPSAVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKSPTDDEVTPSAVVR 16 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 T(0.724)KS(0.269)PT(0.007)DDEVTPSAVVR;T(0.777)KS(0.222)PT(0.001)DDEVTPSAVVR 200.99 5.51E-11 6185000000 921380 737170 579160 693220 815650 658590 970210 1093260 993480 TRUE FALSE 799617.2985 732327.4817 859243.7132 850626.1962 799420.1608 683926.3835 876119.1835 859474.8568 876031.9262 0.912771869 0.835959809 0.980836072 0.970999082 0.912546834 0.780709427 1.000099605 0.981099925 1 19.74062392 T(ph)KSSDDLLAGMAGGVTVTNGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TKSSDDLLAGMAGGVTVTNGVK 22 1 Q69YQ0-2;Q69YQ0;F8WAN1;C9J8U1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 T(0.333)KS(0.333)S(0.333)DDLLAGMAGGVTVTNGVK 102.21 0.0010079 31780000 40784 30405 24009 23191 28520 19047 46629 46616 33367 TRUE FALSE 35394.29107 30205.26755 35619.83271 28456.871 27952.5078 19779.75042 42106.92676 36647.53117 29422.39127 1.202971259 1.02660818 1.210636905 0.967184167 0.950042012 0.672268621 1.431118442 1.245566033 1 14.84462688 0.960348632 18.25562334 0.500780772 1.094309585 0.017118363 0.205840873 14134116.13 168221436.1 288946691.8 0.052653685 9.127432553 -0.960348632 0.593528813 T(ph)KTLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TKTLLR 6 1 E7ENT7;A0A0A0MTJ2;Q9BQ16-9;Q9BQ16-7;Q9BQ16-2;Q9BQ16-5;Q9BQ16-6;Q9BQ16-4;Q9BQ16-1;Q9BQ16 E7ENT7 SPOCK3 Testican-3 1 T(0.964)KT(0.036)LLR;T(0.964)KT(0.036)LLR;T(0.956)KT(0.044)LLR;T(0.964)KT(0.036)LLR 94.669 0.071489 5170810000 2105920 4147720 2994870 1379490 3048660 4533330 2437390 1600590 1742300 TRUE FALSE 1827617.336 4120473.354 4443199.149 1692724.289 2987997.631 4707730.139 2201012.293 1258316.284 1536327.279 1.189601566 2.682028374 2.892091555 1.101799279 1.944896554 3.064275564 1.432645455 0.819041816 1 20.55105415 2.007653949 24.7869123 0.965369682 2.155909121 0.392904564 0.646007473 151.5772695 490872.8006 0.261942991 0.176214222 101.7780085 -2.007653949 1.190539439 T(ph)LSALRSPDVGLYGVIPECGETYHSDLAEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLSALRSPDVGLYGVIPECGETYHSDLAEAK 31 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 1 T(0.378)LS(0.331)ALRS(0.29)PDVGLYGVIPECGETYHSDLAEAK 126.62 8.78E-06 69259000 46058 41265 18064 30436 33697 33197 41552 43476 48814 TRUE FALSE 39971.3186 40993.9275 26799.81082 37346.95899 33026.49563 34474.11007 37522.29344 34178.99573 43043.26453 0.928631205 0.952388903 0.622624959 0.867660931 0.767286032 0.800917645 0.871734378 0.794061419 1 15.39349988 1.232901742 24.98286628 1.000000286 0.822671514 0.259562903 0.092414057 256.0478275 1130281.883 0.187249119 0.021815023 17.09628473 -1.232901742 -0.177328771 T(ph)LTPPLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLTPPLRR 8 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 T(0.512)LT(0.488)PPLRR;T(0.863)LT(0.137)PPLRR 91.867 0.0071392 294044000 373240 320510 187076 214370 397590 359250 323550 391190 303370 TRUE FALSE 323915.3883 318404.5487 277546.5793 263045.9849 389678.7369 373070.58 292172.1708 307537.0627 267505.9442 1.210871741 1.190270929 1.037534251 0.983327626 1.456710572 1.394625383 1.092208144 1.149645716 1 18.02921142 1.257804839 1.676365025 0.937631415 1.198735328 0.154700977 0.14455253 2.123879403 5.693023373 0.906552721 0.043892853 18.10526304 -1.257804839 0.261103914 T(ph)MIISPERLDPFADGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TMIISPERLDPFADGGK 17 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 T(0.788)MIIS(0.212)PERLDPFADGGK 71.148 0.086006 20394000 125690 108120 72534 105090 110330 98265 134800 153380 122660 TRUE FALSE 109079.748 107409.7526 107611.685 128952.2907 108134.6489 102045.3181 121727.1167 120580.8806 108159.2745 1.008510352 0.993070202 0.994937193 1.192244412 0.99977232 0.943472657 1.12544317 1.114845501 1 16.72279785 T(ph)NRTSQDYDQLPSCSDGSQAPARPPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TNRTSQDYDQLPSCSDGSQAPARPPKPR 28 3 Q13191 Q13191 CBLB E3 ubiquitin-protein ligase CBL-B 1 T(0.41)NRT(0.295)S(0.295)QDYDQLPSCSDGSQAPARPPKPR 119.65 0.00011093 139880000 56279 76097 49760 74821 106960 81967 106360 135700 103790 TRUE FALSE 48841.58756 75597.1138 73824.10244 91810.25162 104831.7053 85120.32353 96045.22357 106681.611 91520.06444 0.533670817 0.826016833 0.806643908 1.003170749 1.145450519 0.93007281 1.049444449 1.165663635 1 16.48180045 5.049869929 0.638677415 1.081662219 1.17E-23 0.814810776 0.079696869 1.975597396 0.471667513 0.03845322 1.703460179 112168.2462 -5.049869929 -1.081662219 T(ph)NSDSALHQSTMTPTQPESFSSGSQDVHQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TNSDSALHQSTMTPTQPESFSSGSQDVHQK 30 0 M0QXN6;M0QX46;Q6UUV9;Q6UUV9-2;Q6UUV9-3 M0QXN6 CRTC1 CREB-regulated transcription coactivator 1 1 T(0.615)NS(0.384)DS(0.001)ALHQSTMTPTQPESFSSGSQDVHQK;T(0.605)NS(0.395)DSALHQSTMTPTQPESFSSGSQDVHQK 262.95 3.77E-58 709400000 519020 533370 77300 351770 735090 563610 614490 713690 731170 TRUE FALSE 450430.192 529866.2574 114682.5386 431644.755 720463.1472 585292.4414 554896.8544 561072.9474 644731.9156 0.698631759 0.821839659 0.177876317 0.66949494 1.117461583 0.907807458 0.860662922 0.870242242 1 19.29833988 3.420599454 7.634858779 0.930131787 0.564203503 0.508487615 0.177237221 0.194863826 22.50596283 0.051054913 0.066118678 2633.901042 -3.420599454 -0.365928284 T(ph)NSIGHNPPHWGAERPFYNHLGGNQVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TNSIGHNPPHWGAERPFYNHLGGNQVSK 28 1 O95622;C9JRT8;B3KWA8;O95622-2 O95622 ADCY5 Adenylate cyclase type 5 1 T(0.5)NS(0.5)IGHNPPHWGAERPFYNHLGGNQVSK 128.42 1.65E-05 280260000 110880 80477 68792 93085 115520 98632 92947 164930 134860 TRUE FALSE 96226.92707 79948.34129 102060.0413 114221.372 113221.378 102426.4369 83933.01425 129661.003 118917.0044 0.809194005 0.672303693 0.858245982 0.960513364 0.952104189 0.861327086 0.70581171 1.090348715 1 16.8595955 -1.99990498 0.04493008 2.350081185 2.80E-05 0.29040258 0.108616533 1772.600215 7.817340617 340.8736751 121.6382796 0.010002188 1.99990498 -2.350053234 T(ph)NSSDSERSPDLGHSTQIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TNSSDSERSPDLGHSTQIPR 20 1 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 T(0.328)NS(0.328)S(0.328)DS(0.014)ERS(0.003)PDLGHSTQIPR 99.387 0.00097425 256050000 103040 97084 50613 61577 111420 101430 103170 108420 64167 TRUE FALSE 89423.00293 96446.24881 75089.61609 75558.999 109202.96 105332.0777 93164.58928 85235.22673 56581.25036 1.580435257 1.704561992 1.327111289 1.335407021 1.930020268 1.861607459 1.646562928 1.50642176 1 15.78803644 1.226926558 2.746934579 0.851494454 1.625920648 0.509989716 0.191763287 0.434436879 3.723047815 0.785075316 0.054079384 16.86267843 -1.226926558 0.774426194 T(ph)PDIAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPDIAQR 7 0 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 1 T(1)PDIAQR 106.42 0.086135 734790000 798470 752690 452110 524770 671820 654760 633610 839380 662230 TRUE FALSE 692950.1664 747745.5298 670751.9082 643927.0491 658452.0964 679949.0409 572162.5997 659885.1191 583941.9238 1.186676514 1.280513523 1.148662017 1.102724471 1.127598601 1.164412098 0.979827918 1.130052651 1 19.15546537 4.056501652 0.305580465 1.013131094 1.346024623 0.524646801 0.059632651 5.17483087 0.87038859 0.21397214 0.754742961 11389.42114 -4.056501652 0.332893529 T(ph)PDSTFSETFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TPDSTFSETFK 11 0 Q9NZI5-3;Q9NZI5;B7Z1S6 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 T(0.946)PDS(0.054)T(0.001)FSETFK;T(0.986)PDS(0.014)TFSETFK;T(0.953)PDS(0.047)TFSETFK;T(0.973)PDS(0.027)TFSETFK 295.83 1.52E-34 2033520000 4223370 3222330 2260100 2816350 3019680 2569020 3362930 4117310 4027640 TRUE FALSE 3665240.954 3201162.302 3353091.92 3455845.313 2959594.276 2667851.862 3036793.566 3236855.297 3551496.988 1.032027049 0.90135577 0.944134806 0.973067223 0.833337121 0.7511908 0.855074234 0.911405897 1 21.75999583 3.246044846 24.99483618 0.868267051 0.956946093 0.302401016 0.069495797 244.7774587 817471.0391 0.021479657 0.027172187 1762.158001 -3.246044846 0.088679042 T(ph)PDTIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPDTIRR 7 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 1 T(1)PDTIRR;T(1)PDTIRR 71.708 0.0314 480960000 757100 705030 409650 376200 592340 716990 690560 779980 120362 TRUE FALSE 657047.3168 700398.6115 607758.1102 461621.9599 580553.5929 744573.0693 623589.5975 613187.3468 106132.9415 6.190795314 6.599257514 5.726385246 4.349469198 5.47006033 7.015475675 5.87555182 5.777540303 1 16.69551298 4.01995459 5.699005279 5.164110378 6.358934217 0.120408779 1.581065043 0.417587627 43.77829206 0.409490153 0.840920946 10470.19065 -4.01995459 1.194823839 T(ph)PDVDNPEQPFDALNIEECSLTQQNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPDVDNPEQPFDALNIEECSLTQQNK 26 0 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 T(1)PDVDNPEQPFDALNIEECSLTQQNK 86.791 0.046458 28804000 23594 15802 15785 18822 15338 16867 18958 20943 39114 TRUE FALSE 20475.99312 15698.19562 23418.6788 23095.82278 15032.80381 17515.8844 17119.45608 16464.50243 34489.98748 0.593679343 0.455152256 0.678999342 0.66963848 0.435859938 0.507854183 0.496360171 0.477370496 1 15.07388998 1.234144592 24.99981885 1.000000689 0.536026324 0.746557905 0.084326685 70.01530028 396316.1006 0.163769259 0.021279688 17.14528039 -1.234144592 -0.463974365 T(ph)PELPEPSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TPELPEPSVK 10 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(1)PELPEPSVK;T(1)PELPEPSVK;T(1)PELPEPSVK;T(1)PELPEPSVK 163.9 7.07E-05 911170000 1831990 1438410 1002470 1178470 1286300 1071770 1570580 1781630 1920340 TRUE FALSE 1589887.88 1428960.99 1487267.845 1446059.625 1260705.147 1113001.685 1418265.393 1400642.289 1693319.593 0.938917784 0.843881448 0.87831491 0.853979149 0.744516955 0.657289793 0.8375651 0.82715767 1 20.69142286 4.795200681 1.028292749 0.815001306 0.998870265 0.136440984 0.087439035 4.384805964 3.498169548 0.029251029 0.9128091 62402.31203 -4.795200681 0.183868959 T(ph)PESFLGPNAALVDLDSLVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TPESFLGPNAALVDLDSLVSR 21 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 T(0.962)PES(0.038)FLGPNAALVDLDSLVSR;T(0.974)PES(0.026)FLGPNAALVDLDSLVSR;T(0.967)PES(0.033)FLGPNAALVDLDSLVSR;T(0.99)PES(0.01)FLGPNAALVDLDSLVSR 313.81 1.43E-65 2819550000 242291.8 199330.1 211360.8 198992.7 193797 191193.8 189564.4 207155 488352 TRUE FALSE 210272.3247 198020.6874 313575.5898 244177.0339 189940.8189 198549.1492 171180.4737 162856.5153 430619.5829 0.488301817 0.459850632 0.728196307 0.56703653 0.441087276 0.461077845 0.39752134 0.37819115 1 18.7160544 1.231076079 24.99993012 1.000000907 0.487018932 0.724243446 0.098851822 161.3860713 539017.1776 0.274165664 0.026808904 17.02456714 -1.231076079 -0.512981975 T(ph)PESFLGPNAALVDLDSLVSRPGPTPPGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TPESFLGPNAALVDLDSLVSRPGPTPPGAK 30 1 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 T(0.985)PES(0.015)FLGPNAALVDLDSLVSRPGPTPPGAK;T(0.982)PES(0.018)FLGPNAALVDLDSLVSRPGPTPPGAK;T(0.997)PES(0.003)FLGPNAALVDLDSLVSRPGPTPPGAK 233.34 3.65E-45 1584635000 444856 352983 239013 266425 312446 274575 347607 431932 278311 TRUE FALSE 386067.1525 350664.2314 354600.4863 326920.8683 306228.9359 285138.0779 313896.1266 339566.7031 245409.3906 1.573155581 1.428894919 1.444934464 1.332144901 1.247828924 1.161887396 1.279071375 1.383674448 1 17.90483093 3.915865063 0.989074118 1.23251167 1.556461661 0.599316626 0.101180368 0.58099705 0.978121151 0.039040084 0.153453947 8238.820924 -3.915865063 0.323949992 T(ph)PIQAGGYGAFPVH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TPIQAGGYGAFPVH 14 0 P15056;A0A2U3TZI2 P15056 BRAF Serine/threonine-protein kinase B-raf 1 T(1)PIQAGGYGAFPVH;T(1)PIQAGGYGAFPVH;T(1)PIQAGGYGAFPVH 142.35 0.00010536 475150000 84789 104053 125524 141003 157845 174395 149491 152728 315450 TRUE FALSE 73583.91882 103369.469 186227.8263 173019.8862 154704.1933 181104.0885 134993.3858 120068.3057 278157.8604 0.264540138 0.3716216 0.669504094 0.622020482 0.556174084 0.651083842 0.485312138 0.431655268 1 18.08554435 4.371705667 4.442480595 0.602493546 0.287727298 0.415682734 0.15342527 0.205640772 6.857965675 0.038062446 0.111233301 23534.53746 -4.371705667 -0.314766248 T(ph)PLSEAEFEEIMNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TPLSEAEFEEIMNR 14 0 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 1 T(0.939)PLS(0.061)EAEFEEIMNR;T(0.994)PLS(0.006)EAEFEEIMNR;T(1)PLSEAEFEEIMNR 284.91 1.54E-32 135222000 20539.4 20486.1 19147.1 18722.1 18447.8 21101.9 17366.5 22812.9 29751.3 TRUE FALSE 17825.06625 20351.52546 28406.7016 22973.23895 18080.72487 21913.70375 15682.2995 17934.53887 26234.13521 0.679460791 0.77576506 1.082814485 0.875700257 0.689206057 0.835312602 0.597782217 0.683633698 1 14.67915761 3.251364288 24.69207229 0.742943695 0.86427156 0.080369845 0.146046905 414.6391461 799632.7636 0.042883421 0.054981496 1783.87446 -3.251364288 0.121327866 T(ph)PLTQDPASITDNLLQLPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPLTQDPASITDNLLQLPAR 20 0 Q96DF8 Q96DF8 DGCR14 Protein DGCR14 1 T(0.96)PLT(0.04)QDPASITDNLLQLPAR;T(0.958)PLT(0.042)QDPASITDNLLQLPAR 82.01 0.049292 51540000 38237 39650 32103 33575 47507 46452 42216 46623 81217 TRUE FALSE 33183.88357 39389.53654 47628.11818 41198.71691 46561.70365 48239.0385 38121.89882 36653.03427 71615.61878 0.463360984 0.550013212 0.665052107 0.575275584 0.650161298 0.673582653 0.532312636 0.511802242 1 16.12798664 1.232915069 24.99997361 1.00000067 0.579529344 0.789145426 0.068596929 88.27154091 390848.0751 0.151874929 0.017693558 17.09680935 -1.232915069 -0.420471326 T(ph)PNGPNIDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPNGPNIDKK 10 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;Q5TBM3 Q92598-2 HSPH1 Heat shock protein 105 kDa 1 T(1)PNGPNIDKK;T(1)PNGPNIDKK 126.63 0.00022117 775090000 1306980 994200 955960 1061940 887320 661980 1330760 1624250 1449680 TRUE FALSE 1134259.282 987669.0347 1418265.453 1303069.708 869664.068 687446.799 1201703.1 1276916.777 1278300.482 0.887318199 0.772642308 1.109493013 1.019376685 0.680328358 0.537781851 0.940078735 0.998917544 1 20.28579557 2.012504557 24.99657558 0.990416558 0.836688443 0.162467887 0.159311136 438.8924671 877341.5086 0.07108372 0.047891291 102.9211326 -2.012504557 -0.153728115 T(ph)PPFSESEEQLHLHDAGMKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPPFSESEEQLHLHDAGMKPR 21 1 Q8IVM0-2 Q8IVM0-2 CCDC50 Coiled-coil domain-containing protein 50 1 T(0.641)PPFS(0.344)ES(0.015)EEQLHLHDAGMKPR;T(1)PPFSESEEQLHLHDAGMKPR 169.28 5.38E-12 1162550000 413900 278090 243479 302140 273520 263380 305690 338960 502680 TRUE FALSE 359202.0663 276263.2085 361226.2588 370745.5049 268077.4871 273512.399 276044.2309 266476.0418 443253.7431 0.810375709 0.623261987 0.814942377 0.836418216 0.604794638 0.617056039 0.622767963 0.601181707 1 18.75777329 3.235664987 24.99997672 0.669578171 0.763799941 0.07748707 0.130304151 175.9982218 1519517.534 0.038307493 0.045368475 1720.540844 -3.235664987 0.09422177 T(ph)PPGLQHEYAAPADYFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPPGLQHEYAAPADYFR 17 0 Q5JRG1;H7BYF2;Q9BVL2-2;Q9BVL2-3;Q9BVL2 Q5JRG1 NUPL1 Nucleoporin p58/p45 1 T(1)PPGLQHEYAAPADYFR;T(1)PPGLQHEYAAPADYFR 151.01 9.79E-07 406310000 74288 58178 52629 67039 74541 70765 65734 76342 94053 TRUE FALSE 64470.65258 57795.82489 78080.56043 82261.22958 73057.77994 73487.37534 59359.1268 60016.85739 82934.16149 0.777371489 0.696888036 0.941476456 0.99188595 0.880912987 0.886092944 0.715737951 0.723668707 1 16.33967887 1.215324581 24.68452478 1.000000855 0.824952195 0.230129397 0.099535055 3102.768838 3295985.06 1.535834872 0.027182127 16.41816367 -1.215324581 -0.17504866 T(ph)PPKSYSTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPPKSYSTAR 10 1 Q05519-2;Q05519;Q5T757;Q5T760 Q05519-2;Q5T760 SRSF11 Serine/arginine-rich splicing factor 11 1 T(1)PPKSYSTAR 76.868 0.056113 480720000 891180 603600 394830 510360 626160 495250 652630 710220 490190 TRUE FALSE 773408.305 599634.9119 585771.1086 626245.0384 613700.6411 514302.588 589338.043 558344.9799 432240.2966 1.789301717 1.387272118 1.355197822 1.448835389 1.419813576 1.189853403 1.363450025 1.291746707 1 18.72147405 8 0.306902009 1.193749874 5.574136189 0.628952182 0.121785612 57.96375776 0.921499268 0.226446457 137.9593289 100000000 -8 4.380386316 T(ph)PPRDLPTIPGVTSPSSDEPPMEAS(ph)QSHLRNSPEDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPPRDLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 37 3 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 T(0.998)PPRDLPT(0.002)IPGVTSPSSDEPPMEAS(0.508)QS(0.316)HLRNS(0.177)PEDKR 138.46 7.20E-10 419360000 93985 82999 31135 48077 89070 71970 106900 100040 44760 TRUE FALSE 81564.64412 82453.7741 46191.99014 58993.61766 87297.68126 74738.73247 96532.85445 78647.22451 39468.52379 2.066574482 2.089102054 1.170350084 1.494700384 2.211830413 1.893628778 2.445818723 1.992656856 1 15.26841494 3.245682975 24.94416944 1.958790169 1.694402422 0.041359094 0.451504842 482.1873843 1688722.64 0.134164605 0.169516111 1760.690312 -3.245682975 -0.264387747 T(ph)PPRDLPTIPGVTSPSSDEPPMEASQS(ph)HLRNSPEDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPPRDLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 37 3 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 T(0.997)PPRDLPT(0.003)IPGVTSPSSDEPPMEAS(0.281)QS(0.489)HLRNS(0.23)PEDKR 147.26 2.05E-13 333080000 93176 78886 57860 47984 91569 86394 112590 135430 54097 TRUE FALSE 80862.55552 78367.79267 85841.28953 58879.50059 89746.95605 89717.63308 101671.0391 106469.3484 47701.71429 1.695170849 1.642871621 1.799543073 1.234326721 1.881419932 1.880805217 2.131391726 2.231981597 1 15.54175349 3.043541743 24.99770235 1.903989891 1.604618301 0.070872075 0.359289423 273.5052173 157020.0466 0.107354138 0.121728072 1105.456717 -3.043541743 -0.29937159 T(ph)PPRDLPTIPGVTSPSSDEPPMEASQSHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 17 TPPRDLPTIPGVTSPSSDEPPMEASQSHLR 30 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 T(0.99)PPRDLPT(0.01)IPGVTSPSSDEPPMEASQSHLR;T(0.992)PPRDLPT(0.007)IPGVTSPSSDEPPMEASQSHLR;T(0.999)PPRDLPT(0.001)IPGVTSPSSDEPPMEASQSHLR;T(0.982)PPRDLPT(0.018)IPGVTSPSSDEPPMEASQSHLR;T(0.998)PPRDLPT(0.002)IPGVTSPSSDEPPMEASQSHLR;T(0.989)PPRDLPT(0.011)IPGVTSPSSDEPPMEASQSHLR;T(0.993)PPRDLPT(0.007)IPGVTSPSSDEPPMEASQSHLR;T(0.615)PPRDLPT(0.214)IPGVT(0.018)S(0.018)PS(0.062)S(0.074)DEPPMEASQSHLR;T(0.991)PPRDLPT(0.009)IPGVTSPSSDEPPMEASQSHLR;T(0.99)PPRDLPT(0.01)IPGVTSPSSDEPPMEASQSHLR;T(0.775)PPRDLPT(0.223)IPGVTSPS(0.001)S(0.001)DEPPMEASQSHLR;T(0.95)PPRDLPT(0.05)IPGVTSPSSDEPPMEASQSHLR;T(0.999)PPRDLPT(0.001)IPGVTSPSSDEPPMEASQSHLR;T(0.997)PPRDLPT(0.003)IPGVTSPSSDEPPMEASQSHLR;T(0.992)PPRDLPT(0.008)IPGVTSPSSDEPPMEASQSHLR;T(0.5)PPRDLPT(0.5)IPGVT(0.001)SPSSDEPPMEASQSHLR;T(0.943)PPRDLPT(0.057)IPGVTSPSSDEPPMEASQSHLR 185.55 9.42E-18 22742788000 1013980.4 703588 451294.1 640789.5 823632.3 876775 783257.5 904171 834203 TRUE FALSE 879980.321 698966.0841 669541.4362 786290.5498 807243.6286 910505.1016 707297.3082 710821.0679 735584.4717 1.19630084 0.950218651 0.910216926 1.068933046 1.097417985 1.237798155 0.961544643 0.966335065 1 19.4885315 T(ph)PPRDLPTIPGVTSPSSDEPPMEASQSHLRNS(ph)PEDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPPRDLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 37 3 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 T(0.997)PPRDLPT(0.003)IPGVTSPSSDEPPMEAS(0.226)QS(0.193)HLRNS(0.58)PEDKR 92.332 0.0004215 160540000 45951 33317 18116 26392 37658 40003 44986 54897 21735 TRUE FALSE 39878.45892 33098.13843 26876.95819 32384.70698 36908.67948 41541.9413 40623.26464 43157.70376 19165.51306 2.080740484 1.726963339 1.402360485 1.689738588 1.925786143 2.167536093 2.119602252 2.251841817 1 14.226225 3.190681944 5.303758263 1.971472249 1.701633701 0.023030114 0.382617832 0.474478696 29.56787392 0.115726491 0.134688019 1551.250532 -3.190681944 -0.269838548 T(ph)PPSEEDSAEAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPPSEEDSAEAER 13 0 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 T(0.998)PPS(0.002)EEDSAEAER;T(0.998)PPS(0.002)EEDSAEAER 127.7 0.0019442 525210000 25661.9 28554 17962.5 25572 25217 28976.9 26418 35790 57966 TRUE FALSE 22270.6149 28366.42689 26649.22508 31378.51344 24715.23104 30091.66009 23855.98643 28136.58702 51113.32552 0.435710545 0.554971264 0.521375293 0.61390084 0.483537919 0.588724365 0.466727339 0.550474592 1 15.64141184 1.239543282 5.724706103 1.020039134 0.527627571 0.884388671 0.053822628 0.040456155 4.51341153 0.078220231 0.01219073 17.35974261 -1.239543282 -0.492411562 T(ph)PPTANHPVEPVTSVTQPSELLQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPPTANHPVEPVTSVTQPSELLQQK 25 0 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 1 T(0.925)PPT(0.075)ANHPVEPVTSVTQPSELLQQK 179.47 1.01E-16 372750000 155070 141960 118050 150700 162800 130970 158800 197200 281370 TRUE FALSE 134577.1066 141027.4554 175139.3749 184918.7383 159560.5985 136008.5006 143399.6004 155030.3146 248106.7591 0.542416124 0.568414403 0.705903279 0.745319228 0.643112663 0.548185391 0.577975388 0.624853249 1 17.92060151 1.23883341 9.055781266 1.002600978 0.621189499 0.7662382 0.066041923 0.042329573 49.219986 0.099864062 0.017665038 17.33139059 -1.23883341 -0.381411479 T(ph)PPVPDSGSANGSFFAPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TPPVPDSGSANGSFFAPSR 19 0 Q9NPA3 Q9NPA3 MID1IP1 Mid1-interacting protein 1 1 T(1)PPVPDSGSANGSFFAPSR;T(1)PPVPDSGSANGSFFAPSR;T(1)PPVPDSGSANGSFFAPSR;T(1)PPVPDSGSANGSFFAPSR;T(1)PPVPDSGSANGSFFAPSR;T(1)PPVPDSGSANGSFFAPSR 237.83 3.49E-23 4119930000 77608 74607.5 63710.3 60246.5 82357.8 81867 76155.7 85014.7 119095 TRUE FALSE 67351.90617 74117.39842 94520.81418 73926.38864 80719.04091 85016.47647 68770.13194 66834.96799 105015.7248 0.641350677 0.705774288 0.900063437 0.70395542 0.76863766 0.809559489 0.654855566 0.636428193 1 16.68024584 4.474264607 24.99856198 0.762728113 0.657456529 0.138697518 0.109893294 160.8948795 1408008.639 0.027274428 0.073050229 29803.31734 -4.474264607 -0.105271584 T(ph)PRT(ph)PQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPRTPQLK 8 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 2 T(1)PRT(1)PQLK 90.697 0.064071 216350000 520530 538160 263270 339710 566680 576170 795300 754000 86071 TRUE FALSE 451740.6416 534624.7915 390588.2526 416846.3476 555404.1767 598335.6327 718171.9284 592762.9676 75895.78443 5.952117697 7.044196137 5.14637612 5.492351792 7.317984534 7.883647784 9.462606307 7.810222558 1 16.21173213 3.231667874 24.77406748 7.101324956 5.935406962 0.011696786 2.261068677 476.8839673 1714025.537 0.686291026 0.795356871 1704.778163 -3.231667874 -1.165917995 T(ph)PRTPQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPRTPQLK 8 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 1 T(0.774)PRT(0.226)PQLK 72.434 0.074633 314650000 705510 751670 523880 453290 738960 701390 1029400 1079300 169980 TRUE FALSE 612275.066 746732.2303 777230.1203 556216.4226 724256.1418 728372.9272 929568.9464 848500.0941 149885.158 4.084961273 4.982029175 5.185504225 3.710950636 4.832073777 4.859540042 6.201874546 5.661001431 1 17.19349801 T(ph)PRTPRT(ph)PQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPRTPRTPQLK 11 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 2 T(0.514)PRT(0.486)PRT(0.999)PQLK 96.489 0.011189 487390000 633970 595700 321860 346120 784200 722140 1086700 1173400 137050 TRUE FALSE 550189.2582 591786.8075 477512.5726 424711.8361 768595.9543 749921.1931 981312.0013 922477.5414 120848.1051 4.552733844 4.896947344 3.951345137 3.514426938 6.360016596 6.20548574 8.120210079 7.633363721 1 16.88283533 3.226739765 24.73209209 6.271322385 4.256760935 0.129872406 1.949768165 317.4327313 664144.733 0.590011296 0.674443604 1685.542722 -3.226739765 -2.01456145 T(ph)PS(ph)PES(ph)HRSPAEGSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPSPESHRSPAEGSER 16 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 3 T(0.999)PS(0.963)PES(0.634)HRS(0.39)PAEGS(0.014)ER 65.454 0.047972 225360000 128110 120910 88754 91421 115720 125930 117830 121720 112910 TRUE FALSE 111179.9389 120115.7342 131675.7313 112179.5353 113417.3984 130774.6086 106402.8647 95691.12523 99561.90843 1.116691521 1.206442666 1.322551298 1.126731469 1.139164568 1.313500421 1.068710578 0.961121846 1 16.60330626 2.032868014 6.152818919 0.987845576 1.203085254 0.642177938 0.070563749 0.100614386 11.20455356 0.029594954 0.019285494 107.861887 -2.032868014 0.215239678 T(ph)PS(ph)PESHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPSPESHR 8 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 2 T(1)PS(0.997)PES(0.004)HR;T(1)PS(1)PESHR 125.23 0.0022555 985510000 236910 216663 145500 168305 202132 216215 207757 238290 222184 TRUE FALSE 205601.7432 215239.7265 215864.2867 206521.2226 198109.9687 224532.931 187608.7581 187333.5379 195917.6606 1.04942935 1.0986234 1.101811271 1.054122543 1.011189946 1.146057636 0.957589824 0.956185049 1 17.57988793 2.21610616 24.98936958 0.967548456 1.074974987 0.635315618 0.037667447 139.2415532 154959.5684 0.014904615 0.010057229 164.4773725 -2.21610616 0.107426531 T(ph)PS(ph)PESHRS(ph)PAEGSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPSPESHRSPAEGSER 16 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 3 T(0.998)PS(0.713)PES(0.305)HRS(0.982)PAEGS(0.002)ER 130.83 4.00E-05 287250000 135920 132830 101200 103280 141140 130460 120060 137890 146430 TRUE FALSE 117957.8276 131957.431 150140.6585 126731.3025 138331.5901 135478.8806 108416.5997 108403.2966 129119.2122 0.913557523 1.021981382 1.162806494 0.981506163 1.071347848 1.049254238 0.839662803 0.839559774 1 16.97834416 2.244975043 24.99686 0.879699874 1.038136513 0.420104025 0.077059458 124.2450075 484181.6767 0.028929587 0.021856218 175.7822596 -2.244975043 0.158436639 T(ph)PS(ph)PPPPIPEDIALGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPSPPPPIPEDIALGK 16 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 T(1)PS(1)PPPPIPEDIALGK;T(1)PS(1)PPPPIPEDIALGK 106.3 0.0064535 207980000 326950 256320 209520 293770 252340 179825 272520 349280 563510 TRUE FALSE 283742.7291 254636.217 310844.5728 360474.9685 247318.9277 186742.9841 246091.0523 274589.1901 496892.4898 0.571034449 0.512457367 0.62557712 0.725458678 0.497731265 0.375821708 0.495260157 0.552612881 1 18.92257421 1.239006499 7.224561357 1.008573361 0.542405541 0.713418164 0.090745983 0.062316885 20.69673495 0.142767316 0.02426856 17.33829943 -1.239006499 -0.46616782 T(ph)PS(ph)PSYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPSPSYQR 8 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 T(0.999)PS(0.703)PS(0.287)Y(0.011)QR 84.817 0.091157 621780000 1351700 1124400 665000 911810 1085400 1070600 1085100 1191800 1202000 TRUE FALSE 1173069.42 1117013.742 986596.2243 1118850.397 1063802.664 1111786.675 979867.169 936942.8446 1059900.929 1.106772707 1.053885049 0.930838154 1.055617903 1.003681225 1.048953392 0.924489395 0.883990964 1 20.01549799 7.999999997 0.126244903 0.839463134 1.635912307 0.352100277 0.056116113 215.3343785 2.39774583 1.781459245 30.16199533 99999999.36 -7.999999997 0.796449173 T(ph)PSFELPDASERPPTYCELVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPSFELPDASERPPTYCELVPR 22 1 Q9BRG2;Q9BRG2-2 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 T(0.5)PS(0.5)FELPDASERPPTYCELVPR;T(0.613)PS(0.387)FELPDASERPPTYCELVPR 145.19 1.53E-07 1586200000 112620 81351 83107 111201 108730 98621 137859 94634 102830 TRUE FALSE 97736.98166 80816.59992 123297.8232 136450.8867 106566.4857 102415.0137 124489.4554 74397.25554 90673.55454 1.077899528 0.891291847 1.359799159 1.504858692 1.175276367 1.12949155 1.372941163 0.820495633 1 16.46839422 1.71619235 9.756710029 0.915237697 1.215055851 0.341801724 0.176064832 0.121455638 30.04593739 0.102530087 0.047430232 52.02263551 -1.71619235 0.299818154 T(ph)PSNTPSAEADWS(ph)PGLELHPDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TPSNTPSAEADWSPGLELHPDYK 23 0 Q9Y3Z3-4;Q9Y3Z3;A0A2R8YCS7;Q9Y3Z3-3;A0A2R8YF51;A0A2R8Y5D2;A0A2R8Y586;A0A2R8Y7R5;A0A2R8Y755 Q9Y3Z3-4 SAMHD1 Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 2 T(0.989)PS(0.005)NT(0.007)PS(0.002)AEADWS(0.997)PGLELHPDYK;T(0.991)PS(0.004)NT(0.006)PS(0.002)AEADWS(0.998)PGLELHPDYK;T(0.998)PS(0.002)NTPSAEADWS(1)PGLELHPDYK 168.5 1.70E-11 284430000 189473 169632 182448 224675 170598 155555 215122 243554 442016 TRUE FALSE 164433.663 168517.6762 270680.4631 275690.8927 167203.4336 161539.3015 194259.5016 191471.8724 389761.372 0.421882913 0.432361153 0.694477397 0.707332518 0.428989237 0.41445693 0.498406244 0.491254101 1 18.57223159 1.236975094 24.97873816 1.000000606 0.513424638 0.673472849 0.106964477 26.42870582 416225.5778 0.172321625 0.027903566 17.25738922 -1.236975094 -0.486575969 T(ph)PSSEEISPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPSSEEISPTK 11 0 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 T(0.684)PS(0.316)SEEISPTK 195.29 1.57E-06 447580000 905920 695140 688480 686030 811180 664670 821740 956080 1808500 TRUE FALSE 786200.3767 690573.5796 1021431.231 841803.5968 795039.105 690240.285 742047.7813 751629.7322 1594701.19 0.493007958 0.433042619 0.640515751 0.527875443 0.498550518 0.432833617 0.465320893 0.471329511 1 20.60485469 1.236964144 24.99952514 1.000000623 0.494538176 0.878132493 0.059086319 13.86011115 216967.3614 0.092231282 0.014926039 17.2569541 -1.236964144 -0.505462447 T(ph)PTAPAVNLAGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPTAPAVNLAGAR 13 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.996)PT(0.004)APAVNLAGAR;T(0.989)PT(0.011)APAVNLAGAR 94.023 0.059753 467890000 59126 50778 31439 43111 36493 39487 39422 54009 81601 TRUE FALSE 51312.34929 50444.43597 46643.00556 52900.01146 35766.8607 41006.09044 35598.86051 42459.59565 71954.22274 0.713124919 0.701062899 0.648231664 0.735189812 0.497077994 0.569891368 0.494743174 0.590091784 1 16.13479174 1.236467827 24.98731208 1.000000498 0.613342075 0.66937963 0.08414756 35.95515847 429184.6194 0.141230552 0.022105178 17.23724392 -1.236467827 -0.386658422 T(ph)PTPEPAEVETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPTPEPAEVETR 12 0 F8W6G1;Q9UHY1 F8W6G1 NRBP1 Nuclear receptor-binding protein 1 T(0.901)PT(0.099)PEPAEVETR;T(0.545)PT(0.455)PEPAEVETR 195.77 2.40E-06 3812600000 1169550 1076050 791973 906677 1072670 1044160 1070285 1190710 1174880 TRUE FALSE 1014991.004 1068981.357 1174973.792 1112551.871 1051325.966 1084329.511 966488.9254 936085.9326 1035987.025 0.979733317 1.03184821 1.134158791 1.073905217 1.014806113 1.046663216 0.932916052 0.903569167 1 19.9825745 2.243576265 10.28246296 0.936185259 1.049956855 0.511549345 0.046326961 0.097893841 148.9815024 0.018562402 0.013637395 175.2170099 -2.243576265 0.113771596 T(ph)PTQPPPEPGDLPTIEEALQIIHSAEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPTQPPPEPGDLPTIEEALQIIHSAEPR 28 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 T(0.967)PT(0.033)QPPPEPGDLPTIEEALQIIHSAEPR 93.29 0.0093662 54710000 19241 16428 20249 21315 13525 18030 16097 19044 52588 TRUE FALSE 16698.2531 16320.08339 30041.48413 26154.89653 13255.87896 18723.62577 14535.91542 14971.5888 46371.10655 0.36010038 0.351945093 0.647849197 0.564034341 0.285865056 0.403777851 0.313469238 0.322864601 1 15.50093853 1.233738522 24.99997035 1.000000905 0.404927782 0.725746318 0.114706746 86.50985325 448452.7852 0.240600437 0.0301631 17.12925688 -1.233738522 -0.595073122 T(ph)PVS(ph)PVKFSPGDFWGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPVSPVKFSPGDFWGR 16 1 P23443-5;P23443;P23443-3;P23443-2 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 2 T(1)PVS(1)PVKFSPGDFWGR;T(1)PVS(1)PVKFSPGDFWGR 159.74 2.07E-08 189810000 361120 252070 213030 272360 393390 337490 404540 494410 309970 TRUE FALSE 313397.077 250414.1356 316052.0205 334203.5008 385562.3087 350473.4587 365307.7731 388684.269 273325.6997 1.146606694 0.916174863 1.156320174 1.222729883 1.410633208 1.282255781 1.336529179 1.422055333 1 18.06026159 3.809432591 2.411231446 1.30823386 1.033527189 0.370265106 0.130648504 0.26515332 3.009668522 0.035668083 0.070806957 6448.112276 -3.809432591 -0.274706671 T(ph)QLASWSDPTEETGPVAGILDTETLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TQLASWSDPTEETGPVAGILDTETLEK 27 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 T(0.366)QLAS(0.26)WS(0.366)DPT(0.007)EETGPVAGILDTETLEK 151.66 2.97E-07 25255000 19312 14661 14174 17446 25719 21420 29178 33706 34655 TRUE FALSE 16759.87027 14564.69093 21028.59381 21407.38095 25207.24222 22244.04126 26348.32205 26498.2342 30558.12538 0.548458718 0.476622527 0.688150649 0.700546276 0.824894914 0.727925584 0.862236205 0.867142008 1 14.89926842 4.428996022 0.1864899 1.155686235 2.44E-19 0.857608415 0.05848782 7.804724608 0.530321886 0.865735992 2.731065368 26853.19846 -4.428996022 -1.155686235 T(ph)QTPPVS(ph)PAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 3 T(0.501)QT(0.501)PPVS(0.997)PAPQPT(0.005)EERLPS(0.422)S(0.288)PVY(0.285)EDAASFK 157.96 2.39E-10 147150000 55223 59074 54698 62890 94644 77455 109040 148880 69720 TRUE FALSE 47925.14063 58685.939 81150.13575 77170.13571 92760.76957 80434.74397 98465.31758 117043.1706 61477.78103 0.779552219 0.954587788 1.319991294 1.255252457 1.50885032 1.308354704 1.601640722 1.903828808 1 15.90777747 4.8081152 0.580243157 1.55971663 0.149020287 0.483368195 0.237345554 3.326458119 0.835313785 0.139510084 3.232710787 64285.82179 -4.8081152 -1.410696343 T(ph)RSLDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TRSLDFR 7 1 Q9H1K0 Q9H1K0 RBSN Rabenosyn-5 1 T(0.897)RS(0.103)LDFR;T(0.8)RS(0.2)LDFR 122.26 0.0070461 402670000 373550 350730 181486 251180 409060 349570 426230 456550 287660 TRUE FALSE 324184.421 348426.0315 269253.2366 308214.258 400920.5063 363018.1841 384894.2802 358920.3354 253653.1625 1.278061814 1.373631726 1.061501595 1.215101184 1.580585483 1.431159701 1.51740383 1.415004378 1 17.95249762 3.296334086 24.99995 1.403863064 1.230000972 0.17073468 0.169853129 134.1093693 58030.98917 0.049030565 0.063298158 1978.49103 -3.296334086 -0.173862092 T(ph)RSPDVISSASTALSQDIPEIASEALSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 TRSPDVISSASTALSQDIPEIASEALSR 28 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 T(0.583)RS(0.417)PDVISSASTALSQDIPEIASEALSR;T(0.492)RS(0.492)PDVIS(0.004)S(0.004)AS(0.004)T(0.004)ALSQDIPEIASEALSR;T(0.566)RS(0.431)PDVIS(0.001)S(0.001)ASTALSQDIPEIASEALSR;T(0.495)RS(0.495)PDVIS(0.002)S(0.002)AS(0.003)T(0.002)ALSQDIPEIASEALSR;T(0.5)RS(0.5)PDVISSASTALSQDIPEIASEALSR;T(0.5)RS(0.5)PDVISSASTALSQDIPEIASEALSR;T(0.434)RS(0.434)PDVIS(0.033)S(0.033)AS(0.033)T(0.033)ALSQDIPEIASEALSR;T(0.5)RS(0.5)PDVISSASTALSQDIPEIASEALSR;T(0.499)RS(0.499)PDVIS(0.001)S(0.001)ASTALSQDIPEIASEALSR;T(0.5)RS(0.5)PDVISSASTALSQDIPEIASEALSR 186.31 1.46E-17 31633210000 683879 554938 336250 419731 603270 584874 563496 633505 612144 TRUE FALSE 593502.6574 551292.5757 498861.6247 515037.3387 591266.1073 607374.4812 508848.2447 498034.8857 539777.0337 1.099532993 1.021333887 0.924199426 0.954166826 1.095389523 1.125232167 0.942700806 0.922667795 1 19.04200407 T(ph)RSYDNLTTACDNTVPLASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TRSYDNLTTACDNTVPLASR 20 1 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 T(0.432)RS(0.432)Y(0.135)DNLTTACDNTVPLASR;T(0.691)RS(0.309)YDNLTTACDNTVPLASR 251.52 1.22E-31 781520000 328942 296224 152274 187128 358704 309337 318615 364050 115330 TRUE FALSE 285471.4813 294278.085 225914.2157 229618.2725 351566.4922 321237.3946 287715.7663 286200.7405 101695.8188 2.807111292 2.893708793 2.221470051 2.257892952 3.457039792 3.158806315 2.829179899 2.814282278 1 16.63390084 1.238389357 24.96965254 0.999998025 2.805393408 0.707240126 0.364952711 2.39744159 348506.1164 0.531556277 0.094458255 17.31367881 -1.238389357 1.805395383 T(ph)RTPASINATPANINLADLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TRTPASINATPANINLADLTR 21 1 Q7KZ85;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 1 T(0.644)RT(0.355)PASINATPANINLADLTR;T(0.5)RT(0.5)PASINATPANINLADLTR;T(0.5)RT(0.5)PASINATPANINLADLTR 205.65 7.50E-22 1694420000 579010 464734 323449 413511 663360 592270 514140 661120 587447 TRUE FALSE 502492.3615 461681.1318 479870.0183 507404.9927 650160.4338 615055.0101 464278.7819 519744.6328 517999.6849 0.970063064 0.891276858 0.92639056 0.979546914 1.255136736 1.187365607 0.89629163 1.003368627 1 18.98259169 3.468871491 24.99789127 1.059154363 0.930033781 0.289333615 0.100609524 282.6317032 856408.0114 0.032065966 0.041468693 2943.550497 -3.468871491 -0.129120582 T(ph)RWSGAQPLEQPSGSVLWMAAEVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TRWSGAQPLEQPSGSVLWMAAEVIR 25 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 T(0.576)RWS(0.424)GAQPLEQPSGSVLWMAAEVIR 122.77 0.00027326 684430000 83574 71633 36540 52397 80687 89726 84654 89622 57949 TRUE FALSE 72529.48415 71162.43811 54210.86622 64294.53969 79081.48656 93177.81728 76444.26811 70457.03274 51098.33524 1.419409924 1.392656684 1.060912571 1.258251162 1.547633327 1.823500058 1.496022674 1.378851824 1 15.64098867 3.251975729 24.72972825 1.462634363 1.274804247 0.120542058 0.221218195 438.1340412 807661.2428 0.067794402 0.086991162 1786.387737 -3.251975729 -0.187830116 T(ph)SAQTTPSKIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSAQTTPSKIPR 12 1 O95684 O95684 FGFR1OP FGFR1 oncogene partner 1 T(0.33)S(0.33)AQT(0.197)T(0.143)PS(0.001)KIPR 68.034 0.086908 200100000 216860 222760 165680 174410 234030 181760 262600 293340 167700 TRUE FALSE 188201.4015 221296.6749 245803.4022 214012.4562 229373.2609 188752.4248 237133.0924 230611.5238 147874.697 1.27270862 1.496514815 1.662241121 1.447255416 1.551132584 1.276434905 1.603608306 1.559506314 1 17.17401569 1.233867302 24.97788596 0.999999246 1.493326796 0.586204159 0.127480962 99.92066857 531712.7459 0.238221226 0.030253423 17.1343369 -1.233867302 0.49332755 T(ph)SMGGTQQQFVEGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSMGGTQQQFVEGVR 15 0 A0A2R8Y804;A0A2R8Y543;A0A2R8Y5C3;A0A2R8Y750;A0A2R8Y5Z1;B4DGU4;A0A2R8YCH5;A0A2R8Y5A3;P35222;A0A2R8Y6G0 A0A2R8Y804 CTNNB1 Catenin beta-1 1 T(0.763)S(0.237)MGGTQQQFVEGVR 125.98 0.00090875 167850000 332720 258490 223320 325860 338970 311910 276170 411590 569960 TRUE FALSE 288750.209 256791.9622 331318.299 399851.4935 332225.1602 323909.3795 249387.0759 323574.6815 502579.9781 0.574535838 0.510947458 0.659234974 0.795597737 0.661039386 0.644493202 0.496213711 0.643827243 1 18.93899367 1.242355298 6.110164478 1.012358046 0.62204196 0.664083597 0.084345015 0.082233599 12.23044627 0.133675699 0.022366134 17.47251003 -1.242355298 -0.390316087 T(ph)SNRYSPESQAQSVHHQRPGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSNRYSPESQAQSVHHQRPGSR 22 2 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 T(0.257)S(0.257)NRY(0.229)S(0.257)PESQAQSVHHQRPGSR 57.989 0.074475 180620000 16442 15005 6041.6 8624.6 18387 14048 13122 18201 11273 TRUE FALSE 14269.14804 14906.43117 8963.337968 10582.94725 18021.13467 14588.43565 11849.43046 14308.85779 9940.318782 1.435481935 1.49959287 0.901715344 1.064648678 1.812933274 1.467602395 1.19205739 1.439476752 1 13.2790764 1.229052308 24.60884641 0.999999154 1.34794749 0.160786912 0.252377231 650.1634127 1682564.762 0.781068682 0.063196525 16.94541887 -1.229052308 0.347948336 T(ph)SPADGKPR ddPTM_MDA-MB-175_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(0.696)S(0.304)PADGKPR 140.07 0.00017778 187950000 267030 262990 166080 202720 174440 223390 299970 346620 335230 TRUE FALSE 231741.3089 261262.4014 246396.8435 248750.6744 170968.9853 231983.9579 270878.9556 272498.0104 295599.4913 0.783970595 0.883839144 0.83354962 0.841512525 0.578380513 0.784791465 0.916371521 0.921848712 1 18.17328426 2.180859765 4.236826252 0.944727388 0.783959788 0.462213536 0.082788378 0.211817699 7.72535008 0.037699264 0.025066724 151.6560587 -2.180859765 -0.1607676 T(ph)SPADHGGSVGSESGGSAVDSVAGEHSVSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TSPADHGGSVGSESGGSAVDSVAGEHSVSGR 31 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 T(0.5)S(0.5)PADHGGSVGSESGGSAVDSVAGEHSVSGR;T(0.5)S(0.5)PADHGGSVGSESGGSAVDSVAGEHSVSGR;T(0.5)S(0.5)PADHGGSVGSESGGSAVDSVAGEHSVSGR;T(0.5)S(0.5)PADHGGSVGSESGGSAVDSVAGEHSVSGR 288.7 5.07E-73 1310100000 121251 130195 71765 101181 149869 149471 128644 147552 162288 TRUE FALSE 105227.3731 129339.7405 106470.794 124155.6925 146886.9001 155221.2461 116168.1247 115999.1531 143102.4975 0.735328698 0.903825878 0.744017721 0.86759976 1.026445399 1.084685794 0.81178265 0.810601877 1 17.12668933 3.477530546 24.98659017 0.92833895 0.805413344 0.330013572 0.097192943 21.98731622 1342344.371 0.030423321 0.039738602 3002.828616 -3.477530546 -0.122925606 T(ph)SPDTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TSPDTLR 7 0 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 T(0.558)S(0.442)PDTLR;T(0.717)S(0.283)PDTLR;T(0.907)S(0.093)PDTLR;T(0.719)S(0.281)PDTLR;T(0.871)S(0.129)PDTLR 201.39 0.0037181 14995290000 20383040 17940250 13216770 15501680 18046630 17745660 18073580 21903030 29496300 TRUE FALSE 17689369.62 17822399.32 19608444.18 19021573.37 17687537.37 18428347.02 16320806.99 17219237.48 26009281.02 0.680117594 0.685232295 0.753901816 0.731337916 0.680047148 0.70852966 0.627499352 0.662042041 1 24.63252318 1.235420591 24.99997757 1.000000425 0.689983875 0.884793531 0.035029104 30.84636817 245546.7527 0.065655606 0.009479939 17.19572895 -1.235420591 -0.31001655 T(ph)SPDTLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TSPDTLRR 8 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 T(0.993)S(0.007)PDTLRR;T(0.5)S(0.5)PDTLRR;T(0.992)S(0.007)PDTLRR;T(0.803)S(0.197)PDTLRR;T(0.9)S(0.1)PDTLRR;T(0.953)S(0.047)PDTLRR 169.76 0.0001753 18556190000 12019200 10457580 5615340 6769500 11519900 10405950 10995230 12436030 5584970 TRUE FALSE 10430832.27 10388883.47 8330937.206 8306618.44 11290676.53 10806273.63 9928914.287 9776681.762 4924721.209 2.118055383 2.109537378 1.691656614 1.686718514 2.292652934 2.194291447 2.016137334 1.985225426 1 22.23161062 1.238018422 6.488459509 0.971122169 2.010179437 0.727347219 0.194744548 0.06917671 13.52726354 0.316959757 0.051218765 17.29889736 -1.238018422 1.039057268 T(ph)SPENVQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSPENVQDR 9 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 T(0.844)S(0.156)PENVQDR 160.88 0.00072616 391740000 523960 447750 317270 368740 479090 449670 483670 598140 624900 TRUE FALSE 454717.3585 444808.7008 470702.8332 452468.0528 469557.0463 466969.0959 436763.7578 470232.4157 551025.0339 0.825220871 0.807238643 0.854231304 0.821138832 0.85215193 0.847455319 0.792638684 0.853377591 1 19.07175834 1.247444977 3.935532936 1.01782532 0.829687362 0.882648549 0.019480772 0.072209094 1.909427342 0.038811141 0.004748895 17.67848224 -1.247444977 -0.188137958 T(ph)SPGGRTS(ph)PEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSPGGRTSPEAR 12 1 Q8TD16;Q8TD16-2 Q8TD16 BICD2 Protein bicaudal D homolog 2 2 T(0.992)S(0.008)PGGRT(0.001)S(0.999)PEAR;T(0.991)S(0.009)PGGRT(0.002)S(0.998)PEAR 167.37 0.0012389 315040000 574590 500210 288270 332120 549950 535220 558880 594360 277320 TRUE FALSE 498656.4757 496924.0876 427678.3362 407532.9221 539007.071 555810.2597 504679.9036 467260.7393 244535.5455 2.039198328 2.032113926 1.748941387 1.666559032 2.204207449 2.272922158 2.063830445 1.910809074 1 17.89968466 1.235487211 4.196412106 0.897111588 1.999150114 0.748039806 0.181740781 0.126618802 4.173167047 0.426417729 0.050263132 17.19836696 -1.235487211 1.102038527 T(ph)SPINEDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TSPINEDIR 9 0 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 T(0.954)S(0.046)PINEDIR;T(0.896)S(0.104)PINEDIR;T(0.5)S(0.5)PINEDIR 150.46 0.00095237 923840000 1150900 923380 664430 779630 1088630 971590 958500 1091840 1599860 TRUE FALSE 998805.649 917314.256 985750.5704 956656.9074 1066968.393 1008967.696 865544.8175 858358.5127 1410726.373 0.708008064 0.650242509 0.698753911 0.678130731 0.756325545 0.715211479 0.6135455 0.608451454 1 20.42800676 1.23126984 24.99983038 1.000000568 0.675552095 0.830826225 0.045562534 114.6764914 393187.5187 0.125522695 0.012507448 17.03216439 -1.23126984 -0.324448472 T(ph)SPINLGLNVNDLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSPINLGLNVNDLLK 15 0 P50616 P50616 TOB1 Protein Tob1 1 T(0.5)S(0.5)PINLGLNVNDLLK 209.67 2.54E-08 468160000 1375000 927590 715310 868050 1159300 927610 1456400 1516400 1356300 TRUE FALSE 1193290.266 921496.6002 1061236.309 1065154.02 1136232.198 963295.7569 1315158.552 1192129.661 1195959.759 0.997767907 0.770508032 0.887351184 0.890626973 0.950058887 0.805458336 1.099667896 0.996797469 1 20.18973742 2.237493875 24.99999972 1.027601976 0.881993593 0.504069813 0.069386856 21.91112831 513479.4256 0.025422903 0.018241411 172.7801614 -2.237493875 -0.145608383 T(ph)SPKPAVVETVTTAKPQQIQALMDEVTK ddPTM_MDA-MB-175_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 223.71 9.05E-33 3013300000 2098180 1293660 1381380 1059850 1405390 838310 2000820 2261410 1913550 TRUE FALSE 1820900.197 1285161.862 2049419.988 1300505.141 1377425.489 870560.3282 1806780.784 1777825.07 1687332.299 1.079159214 0.761653092 1.214591808 0.770746309 0.816333267 0.515938875 1.070791323 1.053630675 1 20.68631269 T(ph)SPLNSSGSSQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSPLNSSGSSQGR 13 0 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 T(0.639)S(0.361)PLNSSGSSQGR;T(0.584)S(0.416)PLNSSGSSQGR 165.87 0.00038664 457400000 399160 366830 323130 425440 430260 400240 404880 456390 1012210 TRUE FALSE 346409.9947 364420.2696 479396.7488 522042.6544 421698.6678 415637.4918 365614.7999 358794.5501 892547.6869 0.388113711 0.408292212 0.537110516 0.584890491 0.47246626 0.46567539 0.40963055 0.401989222 1 19.76756973 1.23488025 24.99960039 1.000000767 0.45907403 0.880234907 0.062769377 38.41479544 260900.1367 0.123261099 0.017047465 17.17434768 -1.23488025 -0.540926738 T(ph)SPPCS(ph)PANLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSPPCSPANLSR 12 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 T(0.5)S(0.5)PPCS(1)PANLSR 99.991 0.018489 757000000 487350 495730 342390 312870 526850 511140 448610 523050 521340 TRUE FALSE 422945.4627 492473.517 507970.9492 383911.9154 516366.7158 530803.8866 405103.8712 411199.8279 459707.7791 0.92003112 1.071275143 1.104986629 0.835121642 1.123249897 1.154655002 0.881220396 0.8944809 1 18.81035755 2.207334723 24.99998507 0.916992983 1.03466337 0.209136207 0.100091901 292.6118972 234268.0169 0.040548028 0.027340455 161.1887482 -2.207334723 0.117670386 T(ph)SPPCSPANLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSPPCSPANLSR 12 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 T(0.891)S(0.109)PPCSPANLSR;T(0.602)S(0.398)PPCSPANLSR 150.49 0.00067786 2978160000 2008780 1787660 1077130 1429220 2092820 1670740 1709310 2049450 2374470 TRUE FALSE 1743314.633 1775916.744 1598033.671 1753746.245 2051176.977 1735014.449 1543541.379 1611191.066 2093762.862 0.83262277 0.848193831 0.763235274 0.837605002 0.979660598 0.828658527 0.737209265 0.769519364 1 20.99766662 3.49352866 24.88726845 0.846394524 0.815099143 0.045696937 0.084058486 3443.426514 5223089.737 0.024870614 0.035767779 3115.506486 -3.49352866 -0.031295381 T(ph)SPPLLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 TSPPLLDR 8 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.603)S(0.397)PPLLDR;T(0.715)S(0.285)PPLLDR;T(0.802)S(0.198)PPLLDR;T(0.772)S(0.228)PPLLDR;T(0.656)S(0.344)PPLLDR;T(0.656)S(0.344)PPLLDR;T(0.665)S(0.335)PPLLDR 185.6 0.0023689 58834740000 20057540 15631320 9829870 12111540 17110370 14523930 15461730 18559480 17931570 TRUE FALSE 17406885.27 15528636.83 14583628.01 14861650.27 16769907.11 15082674.99 13962253.8 14590679.63 15811720.22 1.100884978 0.98209661 0.922330259 0.939913562 1.060599788 0.953892099 0.883031929 0.922776234 1 23.914491 4.707485751 3.244196809 0.95116241 1.116977084 0.471642375 0.04814029 0.27603358 4.770184701 0.012720691 0.110320852 50990.08672 -4.707485751 0.165814673 T(ph)SPQPESGIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSPQPESGIK 10 0 A0A1B0GVV3;Q5EBL4-2;Q5EBL4;Q5EBL4-3 A0A1B0GVV3 RILPL1 RILP-like protein 1 1 T(0.647)S(0.353)PQPESGIK;T(0.595)S(0.405)PQPESGIK 122.7 0.0064542 0 707100 658400 482130 571050 749000 621000 785840 947940 959280 TRUE FALSE 613654.9434 654074.927 715289.6806 700715.6305 734096.3654 644890.2718 709629.3578 745230.4079 845875.0112 0.725467634 0.773252453 0.845621009 0.828391454 0.867854418 0.762394282 0.838929332 0.881017169 1 19.69008498 -1.136497798 0.773158817 10 0.800725027 0.696816521 0.04172006 57.77616757 1.014877925 883.389127 0.016707376 0.073030152 1.136497798 -9.199274973 T(ph)SPQVLGSILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSPQVLGSILK 11 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 T(0.576)S(0.424)PQVLGSILK 113.76 0.015078 145810000 492250 490470 343900 420010 533690 437140 590130 683660 753590 TRUE FALSE 427197.9153 487248.0703 510211.1903 515379.69 523070.6131 453957.0587 532899.2834 537464.6292 664501.4487 0.642884852 0.733253586 0.767810501 0.775588512 0.787162487 0.683154355 0.801953531 0.808823864 1 19.34191282 -0.640034833 0.935586689 9.999999998 0.736963596 0.759517986 0.046308096 31.46990215 1.008263061 577.869875 0.015608107 0.229068392 0.640034833 -9.263036402 T(ph)SPSSPAPLPHQEATPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSPSSPAPLPHQEATPR 17 0 P04920-2;P04920-3;P04920 P04920-2 SLC4A2 Anion exchange protein 2 1 T(0.499)S(0.499)PS(0.001)S(0.001)PAPLPHQEATPR;T(0.5)S(0.5)PS(0.001)SPAPLPHQEATPR 107.06 0.0026597 427320000 198489 140858 139410 142869 164593 164879 151995 211622 241460 TRUE FALSE 172258.1757 139932.6945 206829.1423 175309.5901 161317.9213 171222.0018 137254.5483 166368.2821 212914.8739 0.809047168 0.657223669 0.971417067 0.823378785 0.757663936 0.804180557 0.644645185 0.78138403 1 17.69991721 1.239539087 10.23017604 1.000782956 0.778061944 0.365189558 0.090619062 0.074271343 194.4766942 0.120379955 0.021901085 17.35957494 -1.239539087 -0.222721011 T(ph)SPYILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSPYILR 7 0 P49454 P49454 CENPF Centromere protein F 1 T(0.5)S(0.5)PYILR 149.91 0.02218 374470000 524740 551180 311240 421290 551650 501140 521410 604970 595150 TRUE FALSE 455394.2795 547559.2623 461756.705 516950.3335 540673.2443 520419.1801 470843.7385 475601.8734 524792.045 0.8677614 1.043383313 0.879885108 0.985057488 1.03026189 0.991667433 0.897200602 0.906267307 1 19.00138633 7.685267861 20.08510729 0.954060161 0.104324471 0 0.063890114 0 0 0.013903265 0 48447108.4 -7.685267861 -0.849735689 T(ph)SSDSALHTSVMNPSPQDTYPGPTPPSILPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TSSDSALHTSVMNPSPQDTYPGPTPPSILPSR 32 0 Q53ET0;H0YDQ8 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 T(0.332)S(0.332)S(0.332)DS(0.003)ALHTSVMNPSPQDTYPGPTPPSILPSR;T(0.358)S(0.358)S(0.283)DSALHTSVMNPSPQDTYPGPTPPSILPSR;T(0.332)S(0.332)S(0.332)DS(0.003)ALHTSVMNPSPQDTYPGPTPPSILPSR;T(0.332)S(0.332)S(0.332)DS(0.005)ALHTSVMNPSPQDTYPGPTPPSILPSR 323.63 3.44E-104 1800670000 212384 240824 58543.8 140904 330185 314964 263696 301782 275856 TRUE FALSE 184316.9163 239242.0113 86855.7775 172898.4068 323614.9645 327080.8689 238122.8025 237248.2678 243244.6179 0.75774304 0.983544932 0.357071734 0.710800544 1.330409557 1.344658195 0.978943767 0.975348478 1 17.89204836 3.263233675 23.21098098 1.106976124 0.697720555 0.529174352 0.198070774 90.03179396 84695.33131 0.060663928 0.078263569 1833.300575 -3.263233675 -0.409255568 T(ph)SSEEEDSRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSSEEEDSRR 10 1 A0A087WZV0;O43314-2;O43314;D6RBU4 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 T(0.444)S(0.444)S(0.113)EEEDSRR 75.788 0.022236 78270000 9309.6 5997.4 6013.8 5722.6 6969.9 8996.3 8645.2 7777 8994.3 TRUE FALSE 8079.312772 5958.002685 8922.093795 7022.003794 6831.212626 9342.393482 7806.789835 6113.949071 7931.0041 1.018699861 0.751229303 1.124963962 0.885386479 0.861330109 1.177958473 0.984338141 0.770892184 1 12.95328781 1.782289646 25 0.870153939 0.969714928 0.063862019 0.134737782 181.7329139 103941.987 0.068641372 0.03314206 60.57447324 -1.782289646 0.09956099 T(ph)SSEEEDSRREEPSLLLVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSSEEEDSRREEPSLLLVLK 20 2 A0A087WZV0;O43314-2;O43314;D6RBU4 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 T(0.333)S(0.333)S(0.333)EEEDSRREEPSLLLVLK 122.39 0.0014565 76035000 155830 150480 82066 84443 137640 102040 159160 201890 55337 TRUE FALSE 135236.6707 149491.487 121753.3921 103617.0738 134901.2333 105965.5448 143724.6877 158717.3946 48795.1229 2.771520239 3.063656326 2.495195931 2.123512917 2.764645835 2.171642134 2.945472399 3.252730707 1 15.57444934 4.22562793 24.20737568 2.495336892 2.91758823 0.095216714 0.611966804 379.6610713 710654.805 0.154853607 0.325894402 16812.33094 -4.22562793 0.422251337 T(ph)SSGTSLSAMHSSGSSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TSSGTSLSAMHSSGSSGK 18 0 Q12888;Q12888-2;A6NNK5;Q12888-3;M0R142 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 T(0.309)S(0.309)S(0.268)GT(0.05)S(0.05)LS(0.013)AMHSSGSSGK;T(0.329)S(0.329)S(0.329)GT(0.006)S(0.006)LS(0.001)AMHSSGSSGK;T(0.326)S(0.326)S(0.281)GT(0.025)S(0.039)LS(0.002)AMHSSGSSGK 80.156 0.025715 201881000 232893 240833 70085 151861 405490 337531 351831 388685 384528 TRUE FALSE 202115.6 239250.9522 103978.3404 186343.3611 397421.5423 350516.036 317710.4838 305567.7375 339069.5379 0.596088936 0.705610282 0.306657865 0.549572699 1.172094505 1.033758556 0.937006862 0.901194898 1 18.37122165 3.254488482 24.99636078 0.991221002 0.534718196 0.78851013 0.120576527 113.5969443 178272.0887 0.036152841 0.046518021 1796.753429 -3.254488482 -0.456502806 T(ph)SSISGPLSPAYTGQVPYNYNQLEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSSISGPLSPAYTGQVPYNYNQLEGR 26 0 Q01082-3 Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 T(0.262)S(0.262)S(0.206)IS(0.262)GPLS(0.009)PAYTGQVPYNYNQLEGR 167.51 3.80E-11 154310000 134140 149490 92625 114110 172700 176100 179650 169450 142490 TRUE FALSE 116413.0591 148507.9903 137418.7598 140020.4196 169263.6079 182874.681 162227.5707 133214.4362 125644.9945 0.926523652 1.181965035 1.0937066 1.114413034 1.347157589 1.455487197 1.291158245 1.060244673 1 16.93899367 5.551687667 0.988290662 1.208990019 3.73E-18 0.270104219 0.138479278 13.34282704 3.221675523 0.048753522 25.16977041 356194.8754 -5.551687667 -1.208990019 T(ph)SSLDNEGPHPDLLSFE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSSLDNEGPHPDLLSFE 17 0 A1L170;A1L170-2 A1L170 C1orf226 Uncharacterized protein C1orf226 1 T(0.333)S(0.333)S(0.333)LDNEGPHPDLLSFE 130.06 0.00035266 50403000 42780 35179 30509 37345 42741 45649 44877 51239 55569 TRUE FALSE 37126.51461 34947.90683 45263.25445 45824.75303 41890.53772 47405.14657 40524.83545 40281.93859 48999.69612 0.75768867 0.713227012 0.923745615 0.935204841 0.854914235 0.967457971 0.827042587 0.822085478 1 15.58048518 4.240104609 24.99998757 0.894453821 0.735457795 0.582421691 0.05899296 28.77377063 465858.2061 0.015099817 0.03584518 17382.19466 -4.240104609 -0.158996026 T(ph)SSLDTLAAPYLAGHWPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSSLDTLAAPYLAGHWPR 18 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 T(0.372)S(0.372)S(0.257)LDTLAAPYLAGHWPR 231.21 3.36E-19 120400000 107760 91302 48832 61126 93825 78981 77179 98311 96171 TRUE FALSE 93519.24297 90702.23115 72447.31853 75005.59255 91958.06607 82019.45018 69694.19246 77287.95771 84801.77394 1.102798192 1.069579408 0.854313715 0.88448141 1.084388472 0.967190265 0.821848285 0.91139553 1 16.37180682 4.3478343 6.539442484 0.929508667 1.093503868 0.426180156 0.074689563 0.197004894 10.44792881 0.019486382 0.0525486 22275.8508 -4.3478343 0.163995201 T(ph)SSPHKEESPKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSSPHKEESPKK 12 2 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 T(0.479)S(0.479)S(0.042)PHKEESPKK 119.32 0.025295 370270000 657870 454520 348500 363470 359150 244790 716420 780420 474290 TRUE FALSE 570930.8127 451534.2282 517035.7657 446001.4188 352003.6177 254207.2297 646941.6987 613533.2562 418219.9765 1.365144768 1.079657246 1.236277066 1.066427822 0.84167098 0.60783139 1.546893346 1.467010881 1 18.67390245 0.965925967 18.60019048 0.310030043 1.160367022 0.026897331 0.2815297 87269694.86 1247593225 2511391806 0.075234035 9.245405563 -0.965925967 0.850336979 T(ph)SSPIPAQHAPRPYASSLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSSPIPAQHAPRPYASSLEK 20 1 H0YKX0;Q96EP0-3;Q96EP0 H0YKX0 RNF31 E3 ubiquitin-protein ligase RNF31 1 T(0.358)S(0.358)S(0.284)PIPAQHAPRPYASSLEK 155.87 3.66E-08 300970000 350610 333030 199240 235320 357790 277870 364120 424250 224760 TRUE FALSE 304276.0002 330842.304 295593.1304 288753.0026 350670.679 288559.8387 328807.6984 333527.439 198189.1288 1.535280981 1.669326193 1.491469952 1.456956819 1.769373936 1.455982174 1.659060214 1.68287454 1 17.5965183 1.23334218 24.99998306 0.999999077 1.594280816 0.75501012 0.105604167 79.09482306 378876.9186 0.205434322 0.024861507 17.11363164 -1.23334218 0.594281739 T(ph)SSPPRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSSPPRK 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(0.333)S(0.333)S(0.333)PPRK;T(0.367)S(0.367)S(0.265)PPRK 70.919 0.032654 3315000000 1024400 841220 506000 656180 502960 597920 927040 1051920 1021620 TRUE FALSE 889022.9445 835693.9704 750703.2925 805175.6981 492952.08 620922.3693 837135.8035 826975.0941 900845.2474 0.986876433 0.927677615 0.833332134 0.89380024 0.547210613 0.68926641 0.929278148 0.917999064 1 19.78091977 2.038495622 23.32157717 0.944291263 0.810627077 0.209576058 0.12477061 134.9880018 81777.9666 0.055502037 0.037419323 109.2686613 -2.038495622 -0.133664186 T(ph)SSPRSPPSSSEIFTPAHEENVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSSPRSPPSSSEIFTPAHEENVR 23 1 I3L3A7;I3L2L5;I3L317;I3L4Q0;C9JLW8 I3L3A7 FAM195B Protein FAM195B 1 T(0.383)S(0.383)S(0.116)PRS(0.116)PPS(0.002)S(0.002)SEIFTPAHEENVR 74.13 0.016333 601960000 45360 44031 22725 26410 63188 52492 45142 56485 19464 TRUE FALSE 39365.56107 43741.75746 33714.88601 32406.79415 61930.68243 54511.40121 40764.13579 44406.12232 17162.98809 2.293630973 2.548609672 1.964394884 1.888179027 3.608385794 3.176102023 2.375118806 2.587318833 1 14.06701313 T(ph)SSVPEYVYNLHLVENDFVGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSSVPEYVYNLHLVENDFVGGR 22 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 1 T(0.333)S(0.333)S(0.333)VPEYVYNLHLVENDFVGGR 177.6 2.33E-16 94071000 32025 24379 15014 18678 24498 23594 18403 23385 19884 TRUE FALSE 27792.81511 24218.85274 22274.82062 22919.12538 24010.53773 24501.67645 16618.27989 18384.29973 17533.33617 1.58514129 1.381303165 1.270426826 1.307174239 1.369422082 1.397433792 0.947810487 1.048534036 1 14.09781291 2.24208781 24.99999377 1.007022793 1.375501427 0.819733866 0.085302374 36.99335902 262203.6708 0.033507367 0.024903002 174.6175176 -2.24208781 0.368478634 T(ph)TGIVMDSGDGVTHTVPIYEGYALPHAILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTGIVMDSGDGVTHTVPIYEGYALPHAILR 30 0 P60709;A0A2R8Y793;A0A2R8YEA7;P63261;I3L3I0;I3L1U9;I3L4N8 P60709;P63261 ACTB;ACTG1 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 1 T(0.866)T(0.134)GIVMDSGDGVTHTVPIYEGYALPHAILR 245.43 1.42E-45 63505000 33178 33540 17426 24038 37393 30879 26001 34545 24699 TRUE FALSE 28793.44324 33319.67353 25853.27189 29496.1953 36648.95246 32066.93511 23479.42702 27157.82058 21779.11236 1.322066885 1.529891255 1.18706729 1.354334135 1.68275694 1.472371077 1.078070889 1.246966365 1 14.41065754 2.24008503 24.99986592 1.135963565 1.427250584 0.515381864 0.143790835 35.18441126 577029.3759 0.05685844 0.041651434 173.8141106 -2.24008503 0.291287018 T(ph)TPDQELAPASEPVWERPWSVEEIR ddPTM_MDA-MB-175_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 129.01 0.00017051 101370000 6433.6 8226.8 3187.3 2724.1 4305.2 3245.2 3460.8 3006.2 4463.7 TRUE FALSE 5583.383459 8172.757609 4728.688941 3342.64854 4219.534943 3370.044944 3125.172149 2363.347524 3936.006471 1.418540213 2.07640858 1.201392573 0.849248741 1.072034554 0.856209198 0.793995684 0.600442998 1 11.94251688 4.023171836 4.16394831 0.8464971 1.744721292 0.763930211 0.201067692 0.087997329 3.531576053 0.052637073 0.111431056 10548.04166 -4.023171836 0.898224192 T(ph)TPDQELAPASEPVWERPWSVEEIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TTPDQELAPASEPVWERPWSVEEIRR 26 2 Q641Q2;Q641Q2-2;E7ESD2;A0A087WYF6;Q5T1D7 Q641Q2 FAM21A WASH complex subunit FAM21A 1 T(0.5)T(0.5)PDQELAPASEPVWERPWSVEEIRR;T(0.5)T(0.5)PDQELAPASEPVWERPWSVEEIRR 149.4 7.39E-06 271790000 57750.1 44255.3 22208 29557.1 53229.5 57453.6 50482.9 59281.2 33317.8 TRUE FALSE 50118.27796 43964.58402 32947.86308 36268.49131 52170.33709 59663.87717 45587.07613 46604.37671 29379.00764 1.705921404 1.496462527 1.121476378 1.234503621 1.775769207 2.030833645 1.551688767 1.586315552 1 14.84249805 3.242247943 24.99987328 1.607898855 1.378073638 0.098340528 0.295930823 218.7718975 1483251.46 0.090358338 0.112143719 1746.819146 -3.242247943 -0.229825217 T(ph)TPDQELVPASEPVWERPWSVEEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 159.54 3.77E-11 578540000 32365.4 27215.1 22489.1 27362.6 31640.5 31496.6 30978.6 33806 52749 TRUE FALSE 28088.23039 27036.32222 33364.90398 33575.69654 31010.91595 32708.29458 27974.30014 26576.84998 46513.07331 0.603878187 0.581262864 0.717323144 0.721855043 0.666713974 0.703206481 0.601428763 0.571384518 1 15.50534865 1.231208318 24.99994408 1.000000623 0.645335632 0.798864026 0.055841191 128.8325435 438029.9412 0.153381658 0.015164663 17.02975178 -1.231208318 -0.354664991 T(ph)TPDQELVPASEPVWERPWSVEEIRR ddPTM_MDA-MB-175_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 144.28 1.18E-05 318840000 87796 82127 44226 54478 91851 79295 101370 101400 51994 TRUE FALSE 76193.53615 81587.50233 65613.84153 66848.06254 90023.3448 82345.52996 91539.153 79716.3991 45847.32855 1.661896965 1.779547575 1.431137726 1.458057964 1.963546136 1.796081311 1.996608219 1.738735966 1 15.48455005 3.270087207 24.99903529 1.731137922 1.585900556 0.032220379 0.288077195 680.0888725 539272.5468 0.084074973 0.108530807 1862.461083 -3.270087207 -0.145237367 T(ph)TPPEAAQNGQSPMAALILVADNAGGSHASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TTPPEAAQNGQSPMAALILVADNAGGSHASK 31 0 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 T(0.5)T(0.5)PPEAAQNGQSPMAALILVADNAGGSHASK;T(0.5)T(0.5)PPEAAQNGQSPMAALILVADNAGGSHASK;T(0.5)T(0.5)PPEAAQNGQSPMAALILVADNAGGSHASK;T(0.5)T(0.5)PPEAAQNGQSPMAALILVADNAGGSHASK 236.98 3.28E-45 1215751000 326271 326994 104703 290551 465725 314411 427544 515004 834660 TRUE FALSE 283153.4607 324845.9549 155337.721 356525.0453 456457.9837 326506.5946 386080.8487 404874.4024 735987.4456 0.384725938 0.441374315 0.211060286 0.484417292 0.620198057 0.443630658 0.524575318 0.550110474 1 19.48932163 -0.205785385 1.00111192 10 0.427724285 0.745467894 0.102065332 16.21923392 1.166213602 309.6006237 0.034877548 0.622607883 0.205785385 -9.572275715 T(ph)TPPPGRPPAPSSEEEDGEAVAH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 TTPPPGRPPAPSSEEEDGEAVAH 23 1 Q96KN1 Q96KN1 FAM84B Protein FAM84B 1 T(0.815)T(0.185)PPPGRPPAPSSEEEDGEAVAH;T(0.833)T(0.167)PPPGRPPAPSSEEEDGEAVAH;T(0.843)T(0.157)PPPGRPPAPSSEEEDGEAVAH;T(0.815)T(0.185)PPPGRPPAPSSEEEDGEAVAH;T(0.8)T(0.2)PPPGRPPAPSSEEEDGEAVAH;T(0.5)T(0.5)PPPGRPPAPSSEEEDGEAVAH;T(0.5)T(0.5)PPPGRPPAPSSEEEDGEAVAH 132.28 4.44E-05 14773590000 3686376 3156092 2113154 2156846 3930842 3294072 3131691 3821417 3531675 TRUE FALSE 3199212.072 3135359.424 3135082.342 2646590.85 3852625.935 3420797.081 2827980.089 3004236.713 3114164.405 1.027309948 1.006806005 1.006717031 0.849855854 1.237129912 1.098463869 0.908102374 0.964700742 1 21.57041368 2.23223271 24.99665002 0.957017709 1.035425303 0.130774 0.097241369 335.228604 1324212.746 0.040089724 0.027774227 170.6996811 -2.23223271 0.078407594 T(ph)TPTMSEEPPLDLTGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TTPTMSEEPPLDLTGK 16 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 T(0.5)T(0.5)PTMSEEPPLDLTGK;T(0.5)T(0.5)PT(0.001)MSEEPPLDLTGK 196.18 3.83E-12 80079000 267886 198782 128887 142778 201105 141318 200700 256370 215241 TRUE FALSE 232484.1864 197476.188 191217.1843 175197.9271 197103.404 146754.5949 181236.1449 201547.2706 189795.4542 1.224919677 1.040468481 1.007490854 0.92308811 1.038504346 0.773225026 0.954902454 1.061918324 1 17.53408591 4.918940454 1.401544697 0.96507158 1.425003119 0.524766853 0.078569698 1.654598425 2.139749235 0.023049272 1.203764344 82973.69956 -4.918940454 0.459931539 T(ph)TPVDLCLLEESVGSLEGSR ddPTM_MDA-MB-175_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 102.58 0.0033303 54709000 24871 22718.5 13426.1 13206.9 26629 25721 22830.7 28243 25777 TRUE FALSE 21584.23433 22569.26068 19919.00687 16205.7285 26099.135 26710.50351 20616.58223 22203.45424 22729.67243 0.949606045 0.992942628 0.876343772 0.712976773 1.148240701 1.175138076 0.907033847 0.976848844 1 14.47228927 3.222865527 24.99993282 1.029979732 0.890349504 0.355536132 0.105191894 328.3527479 523015.5254 0.034366893 0.039097128 1670.573264 -3.222865527 -0.139630228 T(ph)TSPPLSIPTTHLIHQPAGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTSPPLSIPTTHLIHQPAGSR 21 0 Q5T5U3;E7ESW5;A0A1B0GV73;Q5T5U3-3;A0A087WW76;A0A452Q6Z5 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 T(0.333)T(0.333)S(0.333)PPLSIPTTHLIHQPAGSR 61.522 0.090062 162700000 154370 96542 50390 58137 84624 67017 111120 134170 44401 TRUE FALSE 133969.6134 95907.80925 74758.77254 71337.89442 82940.14796 69595.18736 100343.5995 105478.7896 39151.96436 3.42178523 2.44962956 1.909451384 1.822077017 2.118416006 1.77756566 2.562926309 2.69408678 1 15.25679707 4.680388288 2.749114712 2.071489476 3.587640977 0.48078326 0.467168911 0.356419553 3.961682486 0.120443249 1.144615821 47905.82111 -4.680388288 1.516151501 T(ph)TTPPDSGVLFEGLGISTRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTTPPDSGVLFEGLGISTRPR 21 1 Q9NS56-2;Q9NS56 Q9NS56-2 TOPORS E3 ubiquitin-protein ligase Topors 1 T(0.528)T(0.392)T(0.08)PPDSGVLFEGLGISTRPR 74.222 0.022058 144280000 58817 55995 33824 36908 67795 58716 57209 75159 65263 TRUE FALSE 51044.18443 55627.16516 50181.39953 45288.5255 66446.01214 60974.84251 51660.87999 59086.83274 57547.68249 0.886989401 0.966627373 0.871996879 0.786973924 1.154625334 1.059553398 0.897705655 1.026745651 1 15.81247021 3.248614489 24.99999944 1.019443317 0.884027667 0.48862856 0.075667509 203.5997031 506269.0663 0.022616885 0.028845795 1772.61528 -3.248614489 -0.13541565 T(ph)VHRDSEEEDDYLFDDPLPIPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVHRDSEEEDDYLFDDPLPIPLR 23 1 B3KSJ7;Q96SD1-2;Q96SD1-3;Q96SD1 B3KSJ7 DCLRE1C Protein artemis 1 T(0.35)VHRDS(0.35)EEEDDY(0.3)LFDDPLPIPLR;T(0.496)VHRDS(0.496)EEEDDY(0.008)LFDDPLPIPLR 137.09 1.30E-05 93823000 85071 84304 51141 68378 85192 88865 63927 92026 82625 TRUE FALSE 73828.65181 83750.20147 75872.95866 83904.26999 83496.84588 92283.69405 57727.36938 72346.95605 72857.16663 1.013334106 1.149512194 1.04139321 1.151626859 1.146034766 1.266638525 0.792336184 0.992997112 1 16.15278327 2.239335695 24.99999792 0.936221745 1.127008445 0.534659656 0.087697174 16.07754081 518606.4924 0.033270625 0.024229918 173.5144687 -2.239335695 0.1907867 T(ph)VLSLFDEEEDKMEDQNIIQAPQK ddPTM_MDA-MB-175_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(0.5)VLS(0.5)LFDEEEDKMEDQNIIQAPQK 81.683 0.025315 49759000 34604 22447 41015 28383 41947 37624 49432 70164 81244 TRUE FALSE 30030.99372 22299.54418 60849.99119 34827.79396 41112.33677 39071.41963 44638.09225 55159.97462 71639.42687 0.419196454 0.311274743 0.84939249 0.486154 0.573878639 0.545389897 0.623093933 0.769966721 1 16.12846618 -1.193530436 0.576901613 10 0.509642548 0.570732226 0.134762721 42.55477249 0.999778438 466.9243988 0.071360435 0.06404269 1.193530436 -9.490357452 T(ph)VSFLHVFT(ph)LLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVSFLHVFTLLR 12 0 E7EWU0 E7EWU0 POR 2 T(0.995)VS(0.005)FLHVFT(1)LLR 65.574 0.06198 145890000 114640 125650 101020 52845 98758 202710 65533 54294 61066 TRUE FALSE 99490.03354 124824.5969 149873.6099 64844.26494 96792.90902 210508.3849 59177.61975 42683.65062 53846.84705 1.847648265 2.318141242 2.783331209 1.204235132 1.797559455 3.909391105 1.09899879 0.792686164 1 15.71657425 2.030990673 24.99960357 0.900825454 2.278857819 0.447093778 0.707782829 168.5860076 135994.5451 0.285144478 0.192242372 107.3966346 -2.030990673 1.378032365 T(ph)VSPPIRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.577)VS(0.423)PPIRK 54.066 0.07771 3489300000 1786000 1685300 988460 1304300 1643000 1430600 1751800 2053600 1469700 TRUE FALSE 1549975.575 1674229.153 1466482.562 1600461.25 1610307.514 1485636.108 1581910.706 1614453.621 1295953.74 1.196011498 1.291889596 1.131585578 1.234967885 1.242565583 1.146365076 1.220653683 1.245764853 1 20.30558279 1.233533207 24.99850616 0.999999669 1.214887905 0.669084655 0.047230093 91.40640484 454459.9023 0.088559382 0.010876503 17.12116082 -1.233533207 0.214888236 T(ph)YSDTDSCSDIPLEDPDRPVHCSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TYSDTDSCSDIPLEDPDRPVHCSK 24 1 Q9HB20 Q9HB20 PLEKHA3 Pleckstrin homology domain-containing family A member 3 1 T(0.486)YS(0.401)DT(0.112)DSCSDIPLEDPDRPVHCSK 137.5 1.95E-05 215820000 196600 239620 90669 188250 387490 337440 427490 453420 434350 TRUE FALSE 170618.8119 238045.9204 134516.8317 230995.0397 379779.7071 350421.5352 386032.0856 356459.6615 383001.6378 0.445478022 0.621527161 0.35121738 0.603117629 0.991587684 0.914934822 1.007912362 0.930700097 1 18.54699104 3.3275721 4.062933604 0.965369993 0.486279611 0.910522219 0.072970221 0.055084401 1.703179744 0.019867353 0.02573624 2126.043273 -3.3275721 -0.479090382 T(ph)YSFTSAMSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TYSFTSAMSR 10 0 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 T(0.706)YS(0.294)FTSAMSR 110.84 0.02049 558050000 282210 311740 183100 185860 334200 344550 360610 325620 380280 TRUE FALSE 244915.2335 309692.1594 271647.7724 228062.3537 327550.0739 357805.0615 325638.0977 255988.697 335323.7316 0.730384433 0.923561711 0.810106016 0.680125897 0.976817454 1.067043659 0.971115573 0.763407635 1 18.35519506 3.216511472 24.99943783 0.938369475 0.797585796 0.413391292 0.09880236 302.2062813 342642.0938 0.03250045 0.03688138 1646.309453 -3.216511472 -0.140783678 T(ph)YTHEVVTLWYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TYTHEVVTLWYR 12 0 G3V5T9;P24941;Q00526;K7EJ83 G3V5T9 CDK2;CDK3 Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 1 T(0.593)YT(0.407)HEVVTLWYR 124.42 0.0011898 138540000 129770 126260 75524 100680 125360 112060 125850 121820 147680 TRUE FALSE 112620.5657 125430.5897 112047.659 123540.9328 122865.5813 116371.0207 113645.0864 95769.741 130221.4386 0.8648389 0.963209983 0.860439419 0.948698879 0.943512701 0.893639495 0.872706427 0.73543759 1 16.99060746 2.201074936 3.515120087 0.838479824 0.916477153 0.034437512 0.072426274 0.378138778 9.745501734 0.030476946 0.020050601 158.882087 -2.201074936 0.077997329 TAAAAAEHSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 TAAAAAEHSQR 11 0 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;;;;;;; 199.21 5.10E-08 2069598000 2709038 2572563 1329925 1635707 2473627 2648421 2463399 2763958 2591051 FALSE TRUE 2351031.764 2555663.664 1973081.178 2007119.275 2424406.662 2750307.47 2224498.944 2172907.091 2284739.903 1.029015059 1.118579695 0.863591158 0.878489176 1.061130267 1.203772677 0.973633341 0.951052279 1 21.12359851 1.814370884 0.003877144 0.13594513 1.866759608 0 0.103261454 915454.1117 1408.677831 317842.5683 311028.7376 65.21851174 -1.814370884 1.730814478 TAAAVAIQSAVGTALVFEGPAEQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TAAAVAIQSAVGTALVFEGPAEQEK 25 0 Q499Z4 Q499Z4 ZNF672 Zinc finger protein 672 0 52.061 0.073357 232970000 703830 620410 119960 194870 662690 622980 576500 644530 29361 FALSE TRUE 610817.0822 616334.4859 177973.0572 239118.2119 649503.7655 646946.4437 520591.1187 506702.2752 25889.97603 23.59280215 23.8059118 6.874207108 9.235937941 25.08707481 24.98829829 20.10782544 19.57136904 1 14.66010601 1.237532204 24.85026794 0.999977107 19.04064177 0.448025259 6.332796965 24.77288686 598280.8282 9.785450772 1.647456323 17.2795411 -1.237532204 18.04066466 TAADKDRGEEDADGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 214.82 9.38E-15 961560000 2224890 1500035 1367540 1241075 1322784 1022206 2278820 2433410 1214313 FALSE TRUE 1930865.149 1490181.171 2028886.918 1522880.047 1296463.186 1061530.926 2057820.387 1913044.208 1070758.3 1.803268906 1.391706392 1.894813159 1.422244447 1.210789761 0.991382393 1.921834635 1.786625616 1 20.03020143 7.999996344 0.738186995 1.467741281 50.26520887 0.094965616 0.335207686 1194.941901 5.434545872 0.133338452 96798.32244 99999158.21 -7.999996344 48.79746759 TAADLPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TAADLPLR 8 0 Q7Z4T9-8 Q7Z4T9-8 0 ;; 78.77 0.029765 379060000 420376 502382 273748 295733 508238 720531 320958 349196 422666 FALSE TRUE 364822.2465 499081.8196 406133.4484 362883.6976 498125.0582 748250.2938 289831.5426 274523.1528 372698.907 0.978865888 1.339101914 1.089709255 0.973664507 1.336534797 2.007653577 0.777656004 0.736581588 1 18.50765106 TAAGSSWEDPSLLEWDADDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TAAGSSWEDPSLLEWDADDFR 21 0 K7EP90;Q9BTD8-4;Q9BTD8-2;Q9BTD8-3;Q9BTD8;K7EQ03 K7EP90 RBM42 RNA-binding protein 42 0 ;; 211.13 3.87E-22 256419000 559642 489199 289412 341276 503000 502247 479197 546858 473020 FALSE TRUE 485683.8917 485985.4196 429372.6112 418767.9319 492991.2841 521568.7671 432724.5487 429916.6724 417100.1145 1.164430013 1.165152928 1.029423384 1.003998602 1.18194953 1.250464215 1.037459674 1.030727774 1 18.67003418 2.031159736 24.99936951 1.022519093 1.127279385 0.342995273 0.071745183 245.4763148 196943.9407 0.031736815 0.021396727 107.4384505 -2.031159736 0.104760292 TAALESNLPGS(ph)PNTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TAALESNLPGSPNTSR 16 0 A0A2U3TZV8;Q4KWH8-2;Q4KWH8 A0A2U3TZV8 PLCH1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-1" 1 TAALESNLPGS(0.474)PNT(0.263)S(0.263)R;TAALESNLPGS(1)PNTSR;TAALESNLPGS(1)PNTSR;TAALESNLPGS(1)PNTSR 464.4 9.17E-206 1981800000 1602420 1751270 929560 1199790 1868960 1799710 1703840 2042890 1651890 TRUE FALSE 1390656.137 1739765.792 1379098.325 1472220.657 1831771.353 1868946.008 1538601.859 1606033.871 1456605.446 0.954723972 1.194397424 0.946789214 1.010720275 1.25756179 1.283083222 1.05629281 1.102586754 1 20.47417871 4.763796071 23.00098426 1.106042338 0.954723415 0.15645863 0.110698808 5318.65524 4847484.121 0.027903413 1.632183078 58049.17752 -4.763796071 -0.151318923 TAAPS(ph)PSLLYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TAAPSPSLLYK 11 0 Q9BTC0;Q9BTC0-1;Q9BTC0-2;Q9BTC0-3 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 TAAPS(0.972)PS(0.028)LLYK;TAAPS(0.992)PS(0.008)LLYK;TAAPS(0.992)PS(0.008)LLYK 228.93 3.05E-12 438123000 1498550 1148350 772794 889520 1097560 1027140 1334560 1467820 1447950 TRUE FALSE 1300512.821 1140806.413 1146519.763 1091499.111 1075720.703 1066654.74 1205134.577 1153938.116 1276775.001 1.018592015 0.893506227 0.897981056 0.854887597 0.842529579 0.835428905 0.943889547 0.903791283 1 20.28407288 0.613445209 1.31649278 1.349251222 0.890953956 0.25638175 0.053503436 8.628649314 3.814484921 8.088021316 0.015949279 4.106248314 -0.613445209 -0.458297266 TAATLATHELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TAATLATHELR 11 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 155.26 3.16E-05 547250000 326980 322450 182261 261370 292070 354610 284300 310280 284760 FALSE TRUE 283768.7645 320331.8047 270403.0292 320718.0533 286258.3784 368252.0762 256728.6298 243929.0366 251095.9972 1.130120622 1.275734413 1.076891039 1.277272664 1.14003561 1.466578839 1.022432188 0.971457289 1 17.9378795 2.030469461 24.99906474 0.987666179 1.223285279 0.509775857 0.106621653 141.5228232 116113.6553 0.040398197 0.027236143 107.2678216 -2.030469461 0.2356191 TADEDRGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TADEDRGPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 128.27 0.00038494 1006714000 1977340 2051010 1012250 1145962 1654985 2251540 1879270 2149150 980802 FALSE TRUE 1716029.509 2037536.78 1501777.486 1406170.187 1622054.036 2338158.201 1697018.685 1689570.997 864852.7049 1.984187017 2.355935027 1.736454632 1.625907139 1.875526349 2.703533431 1.962205443 1.953593933 1 19.72209492 4.233319841 24.99950352 1.878711528 2.170061026 0.090225631 0.424041332 334.4646341 1595491.24 0.109808382 0.239942615 17112.75137 -4.233319841 0.291349498 TADGIVSHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TADGIVSHLK 10 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 130.94 0.00026331 3874590000 6697900 6199390 4550370 5689590 6709730 7138300 6684100 6875400 7998400 FALSE TRUE 5812755.545 6158665.799 6750944.152 6981498.369 6576219.5 7412915.02 6035877.011 5405149.214 7052838.264 0.824172528 0.873218067 0.957195373 0.989884938 0.932421708 1.051054163 0.855808227 0.766379295 1 22.74977253 2.045937711 24.99989753 0.849879238 0.93930936 0.093405601 0.083363443 195.8913923 106605.7856 0.034285883 0.023115529 111.1572287 -2.045937711 0.089430122 TADGRVS(ph)PAGGTLDDKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TADGRVSPAGGTLDDKPK 18 2 C9JA69;Q8WY36-2;Q8WY36 C9JA69 BBX HMG box transcription factor BBX 1 TADGRVS(1)PAGGTLDDKPK 142.79 5.75E-08 395330000 1610300 837050 809470 700290 825770 566590 1322700 1424600 1114800 TRUE FALSE 1397494.775 831551.3634 1200932.4 859301.5478 809338.7926 588387.0839 1194424.758 1119960.376 983009.614 1.421649143 0.845923938 1.221689374 0.874153758 0.823327444 0.598556795 1.215069253 1.139317826 1 19.906846 4.74972945 24.24002332 0.979460658 1.421649538 0.351906064 0.193949965 1394.957914 3027425.997 0.049754587 0.716608223 56199.11156 -4.74972945 0.442188881 TADSVS(ph)PLEPPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TADSVSPLEPPTK 13 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 TADSVS(1)PLEPPTK;TADS(0.033)VS(0.967)PLEPPTK 186.16 8.44E-06 225008000 554230 463890 365830 504160 552580 461970 657260 727720 1090190 TRUE FALSE 480987.1013 460842.676 542746.6116 618637.2336 541584.7391 479742.2848 593519.0264 572102.7411 961308.9801 0.500345998 0.479390795 0.564591222 0.64353631 0.563382586 0.49905108 0.617407138 0.595128885 1 19.87464069 1.073496147 2.209849624 1.313268165 0.5514929 0.875593517 0.052453838 0.417827027 1.377978371 0.757376696 0.0146333 11.84393859 -1.073496147 -0.761775265 TAEALDKDGWLHTGDIGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TAEALDKDGWLHTGDIGK 18 1 E7EPM6;P33121-2;P33121;P33121-3;B7Z3Z9;H0Y9U7 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 ; 151.23 2.96E-08 935210000 2208450 1325390 1195910 1170570 1355610 1272230 1788390 2095080 1656930 FALSE TRUE 1916597.737 1316683.426 1774256.076 1436365.81 1328636.013 1321173.511 1614952.213 1647063.446 1461049.623 1.3117951 0.901190079 1.214370852 0.983105424 0.909370902 0.904263271 1.105337004 1.127315199 1 20.47857375 4.755983222 24.22855573 1.028820696 1.311795456 0.433520562 0.104869063 2515.862671 3498569.26 0.026232145 0.737740619 57014.22462 -4.755983222 0.28297476 TAELSLGRNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TAELSLGRNER 11 1 Q9H611-2;Q9H611;Q9H611-3 Q9H611-2 PIF1 ATP-dependent DNA helicase PIF1 0 ;; 85.958 0.0089094 223076000 279888 327649 148063 154919 312313 459255 222136 268528 58212 FALSE TRUE 242900.0917 325496.6521 219666.762 190095.7267 306098.5823 476922.837 200593.2849 211105.3769 51330.24368 4.732104784 6.34122554 4.279480211 3.703386408 5.963318317 9.291263841 3.907896603 4.112689942 1 15.64752149 4.221577484 24.95143024 4.709844503 5.536665964 0.030875479 2.103332509 1060.923805 1558702.188 0.564118091 1.179131164 16656.25971 -4.221577484 0.826821461 TAENATSGETLEENEAGD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TAENATSGETLEENEAGD 18 0 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 291.2 8.26E-49 854880000 2502500 2345100 1429850 1681830 2206440 2231770 2359600 2662700 2329450 FALSE TRUE 2171788.284 2329694.884 2121330.243 2063715.207 2162536.161 2317627.636 2130766.355 2093302.326 2054065.075 1.057312308 1.134187477 1.03274734 1.004698065 1.052808009 1.128312664 1.037341213 1.019102244 1 20.97005046 1.843425665 3.187276008 1.009080017 1.066824833 0.268256401 0.039526942 0.350682505 6.228022546 0.026800659 0.011348897 69.73096334 -1.843425665 0.057744816 TAENFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 160.77 0.020256 14115000000 9129400 7300500 4151750 5521110 6527560 7154340 7000290 8201610 8849100 FALSE TRUE 7922926.659 7252542.535 6159550.187 6774762.41 6397674.327 7429572.089 6321402.953 6447759.527 7802969.479 1.015373273 0.929459298 0.7893854 0.868228747 0.819902518 0.952146758 0.810127858 0.826321254 1 22.89559183 4.512377298 4.377238246 0.861008851 1.003299571 0.346549803 0.065551682 0.212231875 9.071622293 0.015545355 0.062264433 32536.98431 -4.512377298 0.142290719 TAESQT(ph)PTPSATSFFSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TAESQTPTPSATSFFSGK 18 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 1 TAESQT(0.999)PTPS(0.001)ATSFFSGK;TAESQT(0.919)PT(0.08)PS(0.001)ATSFFSGK 195.97 2.24E-14 419607000 912430 713670 467380 520470 688340 593570 749190 898980 939090 TRUE FALSE 791850.0637 708981.8548 693406.5313 638650.6684 674643.3807 616405.022 676533.6691 706740.1229 828071.85 0.956257677 0.856183983 0.837374838 0.771250307 0.814715994 0.744385915 0.816998753 0.853476812 1 19.65939643 1.22750082 2.970141478 1.037089968 0.824121184 0.478671966 0.055767613 0.378299589 4.053110347 0.197488322 0.014966446 16.88499047 -1.22750082 -0.212968785 TAESQTPT(ph)PSATSFFSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TAESQTPTPSATSFFSGK 18 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 1 TAES(0.001)QT(0.089)PT(0.519)PS(0.269)AT(0.051)S(0.07)FFS(0.002)GK;TAESQT(0.329)PT(0.601)PS(0.045)AT(0.018)S(0.007)FFSGK 141.64 4.86E-06 326650000 640382 497224 338476 358293 503621 439904 555846 693331 676760 TRUE FALSE 555753.8962 493957.7028 502164.1257 439648.9018 493599.9274 456827.3915 501940.1405 545067.5612 596754.2038 0.93129448 0.827740634 0.841492398 0.736733649 0.827141098 0.76552019 0.841117058 0.913387049 1 19.1867773 1.502179234 2.048830359 1.009051573 0.818391983 0.570706191 0.050813226 0.29777569 2.107640709 0.093757132 0.014140633 31.78185445 -1.502179234 -0.19065959 TAESQTPTPSATSFFSGKS(ph)PVTTLLECMHK ddPTM_MDA-MB-175_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(0.002)GKS(0.997)PVTTLLECMHK 230.51 1.51E-35 444340000 366440 283140 190040 214590 330560 236150 394360 426290 246290 TRUE FALSE 318014.0256 281280.0347 281943.9796 263315.9393 323982.5027 245234.8433 356115.0279 335131.2009 217173.8768 1.464329091 1.295183559 1.298240764 1.212465989 1.491811573 1.129209677 1.639769171 1.543146928 1 17.72849105 2.24343932 24.99998146 1.435541667 1.316882943 0.021148738 0.195012066 332.5519398 1704109.739 0.072324783 0.05421869 175.1617679 -2.24343932 -0.118658724 TAFDDAIAELDTLNEDSYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TAFDDAIAELDTLNEDSYK 19 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;; 299.76 1.70E-49 165380000 388041 272688 266214 330657 280259 234464 353485 429345 671050 FALSE TRUE 336760.3987 270896.6946 394955.9808 405737.7256 274682.3942 243483.9818 319204.0791 337532.9129 591719.2335 0.569121941 0.457812894 0.667471933 0.685692982 0.464210691 0.411485664 0.539451924 0.570427483 1 19.17455326 1.234481201 4.648440744 1.037373156 0.542448038 0.732167774 0.086504382 0.110240735 5.281192957 0.180441874 0.023007823 17.15857434 -1.234481201 -0.494925118 TAFDEAIAELDTLNEDSYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TAFDEAIAELDTLNEDSYK 19 0 P27348 P27348 YWHAQ 14-3-3 protein theta 0 ; 178.12 3.87E-14 23748000 56874 35702 37449 46619 44888 31812 44979 57519 76247 FALSE TRUE 49357.9568 35467.47121 55559.46166 57204.55648 43994.81662 33035.82823 40616.9435 45219.00946 67233.16652 0.734131075 0.527529388 0.826369849 0.85083835 0.654361811 0.491362075 0.604120639 0.67256998 1 16.03688548 1.239237512 8.233533294 1.00356207 0.666915577 0.450008116 0.114563669 0.08868762 59.53404899 0.168321914 0.029595207 17.34752459 -1.239237512 -0.336646493 TAFDEAIAELDTLNEESYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TAFDEAIAELDTLNEESYK 19 0 P31946-2;P31946 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 ;; 235.95 3.55E-24 70493000 166754 119201 111812 132349 118110 97341 152366 162283 244202 FALSE TRUE 144717.0364 118417.9608 165884.6572 162400.8633 115759.8421 101085.7713 137589.5688 127580.0433 215332.7178 0.672062462 0.549930183 0.770364387 0.754185732 0.537585943 0.469439908 0.638962672 0.592478675 1 17.71620801 1.235904554 24.99820454 1.000000503 0.621365548 0.615782605 0.093547134 52.22048303 491385.5433 0.159284803 0.023862951 17.21490198 -1.235904554 -0.378634956 TAFDEAIAELDTLS(ph)EESYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TAFDEAIAELDTLSEESYK 19 0 B7Z2E6;H0YB80;P63104-2;P63104;E7EX29;B0AZS6 B7Z2E6;P63104 YWHAZ 14-3-3 protein zeta/delta 1 TAFDEAIAELDT(0.002)LS(0.952)EES(0.045)Y(0.002)K;TAFDEAIAELDTLS(0.998)EES(0.002)YK;TAFDEAIAELDT(0.004)LS(0.996)EESYK 186.9 1.26E-14 34970000 101949 74399 76610 92754 76390 67229 90868 100676 243724 TRUE FALSE 88476.18134 73910.26807 113658.8522 113815.2134 74869.98845 69815.34313 82055.63535 79147.22086 214911.2264 0.411687108 0.34391069 0.528864193 0.529591754 0.348376349 0.32485666 0.381811768 0.368278671 1 17.71338132 1.236505014 24.99999915 1.00000076 0.403527061 0.872181453 0.071621752 19.49732784 237062.9729 0.119617399 0.01874629 17.23871995 -1.236505014 -0.596473699 TAFDEAIAELDTLSEESYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TAFDEAIAELDTLSEESYK 19 0 B7Z2E6;H0YB80;P63104-2;P63104;E7EX29;B0AZS6 B7Z2E6;P63104 YWHAZ 14-3-3 protein zeta/delta 0 ; 300.4 1.57E-49 384900000 1066122 808807 721526 940561 789877 651048 999762 1210438 1675740 FALSE TRUE 925231.2765 803493.8936 1070458.387 1154129.751 774159.9931 676094.2378 902805.2351 951595.2533 1477635.926 0.626156457 0.543769869 0.724439876 0.781065031 0.523917955 0.457551299 0.610979484 0.643998455 1 20.49485942 1.228435028 3.887507046 1.050816571 0.610206878 0.631782565 0.092942684 0.191696798 4.801179218 0.247000158 0.025271299 16.92135077 -1.228435028 -0.440609693 TAFPSLPDTDDHKTDNTGTLPEDVAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TAFPSLPDTDDHKTDNTGTLPEDVAFR 27 1 A8MXV4 A8MXV4 NUDT19 "Nucleoside diphosphate-linked moiety X motif 19, mitochondrial" 0 143.54 1.10E-07 202870000 99134 88825 58905 71757 115990 115130 109290 126010 89993 FALSE TRUE 86033.19073 88241.50273 87391.65503 88050.52359 113682.0259 119559.1256 98691.07262 99063.74211 79354.13006 1.084167776 1.111996347 1.101286788 1.109589678 1.432591169 1.506652842 1.243679095 1.248375378 1 16.27601769 3.336650335 10.24219071 1.289243338 1.101496773 0.327038949 0.131510664 0.434885036 41.94162116 0.040255532 0.051967268 2170.952569 -3.336650335 -0.187746564 TAFQEALDAAGDKLVVVDFSATWCGPCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TAFQEALDAAGDKLVVVDFSATWCGPCK 28 1 P10599;P10599-2 P10599 TXN Thioredoxin 0 ;; 292.26 3.10E-71 333731000 858972 736319 503660 543432 540664 423769 862764 1038677 882247 FALSE TRUE 745456.6738 731482.072 747231.6606 666826.5414 529905.8442 440071.6676 779093.2801 816564.0065 777948.7647 0.958233637 0.94027024 0.960515261 0.857159972 0.681157768 0.56568207 1.001471196 1.049637256 1 19.56931562 2.032838622 24.99853774 1.027521611 0.82897133 0.341577572 0.124548617 220.7080502 168014.0751 0.056468023 0.038070529 107.8545875 -2.032838622 -0.198550281 TAFYNEDDS(ph)EEEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TAFYNEDDSEEEQR 14 0 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 TAFYNEDDS(1)EEEQR;TAFYNEDDS(1)EEEQR 299.65 9.07E-44 756810000 881170 685500 553700 733730 945820 1148920 664580 957270 977600 TRUE FALSE 764721.1519 680996.9054 821471.172 900334.6109 927000.0325 1193119.696 600129.1339 752565.26 862029.2417 0.887117414 0.789992813 0.952950471 1.044436276 1.07536959 1.384082625 0.696181875 0.87301593 1 19.71737728 4.089221517 5.243932988 0.996282304 0.840490475 0.139826974 0.172924137 0.4627486 20.82397829 0.047730602 0.10294983 12280.6546 -4.089221517 -0.15579183 TAGAPDPAWDWQHVGPGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TAGAPDPAWDWQHVGPGYR 19 0 H3BM67;H3BUP2;H3BUN4;O60936;O60936-3 H3BM67 NOL3 Nucleolar protein 3 0 ;;; 146.81 1.12E-07 1199900000 750603 527403 475961 495362 571352 602653 552582 718472 1173536 FALSE TRUE 651408.9118 523938.455 706137.3316 607841.5132 559983.213 625837.4509 498992.6827 564832.354 1034801.911 0.629501072 0.506317634 0.682388894 0.587398909 0.541150154 0.604789616 0.482210825 0.545836211 1 19.98092319 1.236705059 24.99960305 1.000000542 0.568840469 0.840047319 0.058613119 17.97423609 242094.9274 0.088037193 0.013996652 17.24666228 -1.236705059 -0.431160073 TAGTICLETFKDFPQMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TAGTICLETFKDFPQMGR 18 1 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 131.45 1.54E-05 329610000 580910 453230 553380 281760 447020 393090 522510 660590 222400 FALSE TRUE 504141.2717 450252.7023 820996.4189 345737.9144 438125.1766 408212.4267 471837.0606 519327.9692 196108.1254 2.570731176 2.295941086 4.186447744 1.762996377 2.23410007 2.081568145 2.406004645 2.648171606 1 17.58128979 TAHETDKSEGGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TAHETDKSEGGKR 13 2 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 0 ;;; 214.23 1.87E-11 1459800000 1950280 1510260 664020 1045300 1072020 1058490 1950110 2274660 1063420 FALSE TRUE 1692545.557 1500339.003 985142.293 1282651.341 1050688.899 1099210.795 1760988.632 1788241.66 937703.6991 1.804989741 1.600013953 1.050590175 1.367864223 1.120491367 1.172236812 1.877979829 1.907043411 1 19.8387726 2.242568636 24.9999326 1.671805679 1.340341756 0.090441529 0.332298735 178.5762516 1113875.315 0.129515467 0.096551477 174.8109512 -2.242568636 -0.331463923 TAHNSEAADLEESFNEHELEPSS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TAHNSEAADLEESFNEHELEPSSPK 25 0 A0A0D9SGE8;Q5JRC6;Q8IWS0-2 A0A0D9SGE8 PHF6 PHD finger protein 6 1 TAHNSEAADLEESFNEHELEPS(0.037)S(0.963)PK 249.97 3.48E-39 96740000 44687 57801 16674 31113 79393 59906 67611 70717 70061 TRUE FALSE 38781.49973 57421.30143 24737.60217 38177.68218 77813.23463 62210.62258 61054.09563 55594.71987 61778.46839 0.627751071 0.929471107 0.400424336 0.617977156 1.259552667 1.006995223 0.988274673 0.89990447 1 15.91481648 3.263018604 24.9999228 1.010167497 0.646911698 0.604075067 0.155185893 169.6943318 173453.1927 0.045085246 0.058177173 1832.392916 -3.263018604 -0.363255799 TAHNSEADLEESFNEHELEPSS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TAHNSEADLEESFNEHELEPSSPK 24 0 Q8IWS0-5;Q8IWS0 Q8IWS0-5 PHF6 PHD finger protein 6 1 TAHNSEADLEESFNEHELEPS(0.013)S(0.987)PK;TAHNSEADLEESFNEHELEPS(0.011)S(0.989)PK 175.23 1.23E-12 366430000 218653 226740 50315 154024 292820 219432 277960 303840 291180 TRUE FALSE 189757.4521 225250.53 74647.50229 188997.5033 286993.4549 227873.691 251003.482 238866.1805 256757.0321 0.739054547 0.877290597 0.290732066 0.73609475 1.117762783 0.887507108 0.97759146 0.930319916 1 17.97004426 3.41595253 6.940532619 0.968932976 0.636147971 0.51861562 0.156202347 0.170351474 15.55868731 0.044218988 0.057341109 2605.868706 -3.41595253 -0.332785005 TAHSLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TAHSLFK 7 0 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 ; 97.602 0.011877 1234230000 2584800 2060780 1171810 1459060 2164200 1740470 2239700 2528000 2383300 FALSE TRUE 2243212.131 2047242.6 1738501.235 1790361.873 2121136.654 1807427.007 2022494.239 1987406.873 2101548.989 1.067408917 0.974158876 0.827247542 0.851924881 1.009320585 0.860045146 0.962382628 0.945686674 1 21.00302166 1.046156151 1.419210322 1.058274962 0.929632937 0.063892777 0.074274913 6.012299718 7.379645539 1.272689906 0.021943085 11.12131524 -1.046156151 -0.128642025 TALAEAELEYNPEHVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TALAEAELEYNPEHVSR 17 0 Q9NSE4 Q9NSE4 IARS2 "Isoleucine--tRNA ligase, mitochondrial" 0 ;; 244.08 1.71E-20 668980000 358792 444318 133231 389254 601142 642506 421141 536877 492275 FALSE TRUE 311376.7281 441399.2458 197661.9572 477640.0701 589180.4503 667223.6216 380298.8106 422070.0315 434078.8103 0.717327639 1.016864301 0.455359609 1.100353343 1.357312166 1.537102493 0.876105448 0.972335027 1 18.72759747 3.587969978 9.237968971 1.13478498 0.759279416 0.409836273 0.2317487 0.410275071 31.54209108 0.067906139 0.100759618 3872.308755 -3.587969978 -0.375505564 TALHWACSAGHTEIVEFLLQLGVPVNDKDDAGWSPLHIAASAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TALHWACSAGHTEIVEFLLQLGVPVNDKDDAGWSPLHIAASAGR 44 1 O75832;O75832-2 O75832 PSMD10 26S proteasome non-ATPase regulatory subunit 10 0 124.11 1.34E-09 258700000 193520 169190 56965 144740 113950 95189 240710 211770 161390 FALSE TRUE 167945.8417 168078.5797 84513.46454 177605.4292 111682.6179 98850.98243 217365.9812 166484.6335 142310.6581 1.180135374 1.181068109 0.593866023 1.248012142 0.78478042 0.694614049 1.527404793 1.169867639 1 17.11868419 2.243788687 24.99999998 1.231682388 0.947961632 0.225455281 0.249314676 190.0508989 908805.5974 0.093367557 0.070111465 175.302733 -2.243788687 -0.283720756 TALIHDGLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 TALIHDGLAR 10 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 ;;;;;;;; 188.99 1.06E-06 15323630000 10904800 10783540 5533301 7147310 11304720 11370960 10615720 11886580 10628760 FALSE TRUE 9463703.051 10712702.22 8209223.871 8770215.975 11079778.19 11808408.19 9586209.108 9344727.368 9372240.101 1.009758921 1.14302473 0.875908404 0.935765183 1.182191031 1.259934451 1.022830082 0.997064444 1 23.15996248 TALPTSGS(ph)SAGELELLAGEVPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TALPTSGSSAGELELLAGEVPAR 23 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 TALPT(0.031)S(0.073)GS(0.448)S(0.448)AGELELLAGEVPAR;TALPTS(0.006)GS(0.971)S(0.023)AGELELLAGEVPAR 218.74 3.63E-34 54354000 58902 53641 43498 44759 59022 64764 62920 74367 69544 TRUE FALSE 51117.95146 53288.62874 64533.77829 54922.21505 57847.57767 67255.51299 56818.02808 58464.19577 61322.58754 0.833590908 0.868988588 1.052365545 0.895627814 0.943332302 1.096749431 0.926543226 0.95338762 1 15.90413095 4.389046707 6.949342036 0.975247282 0.842328482 0.455694491 0.059299419 0.175243063 11.27324581 0.014377917 0.038720117 24493.26643 -4.389046707 -0.1329188 TALPTSGSS(ph)AGELELLAGEVPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TALPTSGSSAGELELLAGEVPAR 23 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 TALPTSGS(0.273)S(0.727)AGELELLAGEVPAR;TALPTSGS(0.052)S(0.948)AGELELLAGEVPAR;TALPTSGS(0.031)S(0.969)AGELELLAGEVPAR 238.72 3.58E-37 270272000 208981 206069 118279 152328 208727 223321 196600 247028 231625 TRUE FALSE 181363.6314 204715.3192 175479.12 186916.4006 204573.7411 231912.3034 177533.7623 194202.9846 204242.5564 0.887981597 1.002314713 0.85917021 0.915168728 1.001621526 1.135474935 0.869230024 0.950844858 1 17.63992397 3.246146862 24.87459713 0.984397308 0.918242174 0.200232088 0.073964464 319.6905551 1048229.039 0.022063639 0.027931673 1762.571981 -3.246146862 -0.066155134 TALPTSGSSAGELELLAGEVPARS(ph)PGAFDMSGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 TALPTSGSSAGELELLAGEVPARSPGAFDMSGVR 34 1 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR 312.62 1.31E-104 1632807000 307470.5 421323.2 187792.9 174975.1 547641 561803 540142 608509 89746.2 TRUE FALSE 266837.4944 418555.5002 278610.1746 214705.8708 536744.0155 583415.9249 487759.112 478384.0858 79136.50648 3.371863458 5.289031811 3.520627672 2.713107772 6.782508345 7.372272936 6.16351585 6.045049334 1 16.27205576 3.238256627 24.99999772 5.691010435 3.820968023 0.178340855 1.827161396 13.7635896 1131935.894 0.544789775 0.657189997 1730.838819 -3.238256627 -1.870042412 TAMLLALQRPELVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TAMLLALQRPELVER 15 1 Q8NFV4;Q8NFV4-4 Q8NFV4 ABHD11 Alpha/beta hydrolase domain-containing protein 11 0 150.39 2.91E-06 342080000 186790 208780 108810 197210 239890 258430 192240 255370 176220 FALSE TRUE 162105.2282 207408.5104 161430.8799 241989.5447 235116.6583 268371.9693 173596.5944 200761.1128 155387.4724 1.043232288 1.334782703 1.038892502 1.557329822 1.513099189 1.727114582 1.117185264 1.292003208 1 17.24551067 3.751293719 24.95255758 1.365258168 1.15855053 0.187479144 0.223279271 1525.47213 2989400.026 0.061649611 0.105848461 5640.1898 -3.751293719 -0.206707638 TAMPS(ph)PGVSQNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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(0.999)PGVS(0.001)QNK;TAMPS(1)PGVSQNK;TAMPS(1)PGVSQNK;T(0.095)AMPS(0.903)PGVS(0.002)QNK;TAMPS(0.999)PGVSQNK 247.66 1.22E-16 931690000 2731710 2466588 1790181 2097397 2388453 1986504 2576408 3090070 3462460 TRUE FALSE 2370707.602 2450384.821 2655918.519 2573643.046 2340927.458 2062926.094 2326548.349 2429282.577 3053131.923 0.776483841 0.802580721 0.869899692 0.842951798 0.766729875 0.675675387 0.762020249 0.79566905 1 21.5418585 1.239237065 5.768620094 1.008908202 0.785882416 0.630821014 0.051387131 0.103282244 11.90885044 0.091100549 0.014200645 17.34750674 -1.239237065 -0.223025786 TANKDHLVTAYNHLFETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TANKDHLVTAYNHLFETK 18 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 207.82 4.52E-16 999890000 1757200 1391800 820770 936580 1346700 1107300 1764600 2069300 1016800 FALSE TRUE 1524981.568 1382657.174 1217697.117 1149244.804 1319903.305 1149898.548 1593469.364 1626796.298 896595.0623 1.700858762 1.542119996 1.35813498 1.281788013 1.472128679 1.282517154 1.777245303 1.814415857 1 19.77409703 2.243848154 24.99984474 1.599970474 1.434855226 0.003401462 0.25244433 339.941663 1607275.835 0.096246107 0.072285579 175.3267386 -2.243848154 -0.165115248 TANQASDTFS(ph)GIGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TANQASDTFSGIGKK 15 1 Q15847 Q15847 ADIRF Adipogenesis regulatory factor 1 TANQASDT(0.135)FS(0.865)GIGKK;TANQASDT(0.021)FS(0.979)GIGKK 162.33 9.81E-07 526610000 388050 423640 313870 252610 396120 245330 459510 508150 363650 TRUE FALSE 336768.2093 420857.0809 465658.5818 309968.9614 388237.987 254768.0038 414946.7909 399486.0769 320659.7113 1.050235491 1.312472587 1.452189238 0.96666014 1.210747635 0.794512048 1.29404093 1.245825599 1 18.29068357 3.731151529 24.82365039 1.108176846 1.275716455 0.192748759 0.175582704 929.2843708 3113505.922 0.04820863 0.073172976 5384.576223 -3.731151529 0.167539609 TANQASDTFSGIGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TANQASDTFSGIGK 14 0 Q15847 Q15847 ADIRF Adipogenesis regulatory factor 0 ; 289.86 4.45E-43 399040000 324170 324820 245880 336560 344030 278410 350720 440920 647190 FALSE TRUE 281330.1132 322686.236 364788.3904 412981.092 337184.4761 289120.6129 316707.2284 346632.6892 570679.9355 0.492973549 0.565441706 0.63921713 0.723664994 0.590846909 0.506624808 0.554964716 0.607402973 1 19.12232231 1.238347135 5.365785677 1.021769656 0.586205921 0.800808792 0.0651168 0.073013398 6.189024188 0.11792794 0.017423226 17.31199566 -1.238347135 -0.435563735 TANQASDTFSGIGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TANQASDTFSGIGKK 15 1 Q15847 Q15847 ADIRF Adipogenesis regulatory factor 0 ; 173.03 1.59E-06 2182400000 1796570 1692750 800910 972550 1494500 1232160 2074640 2299370 349100 FALSE TRUE 1559148.723 1681630.214 1188232.755 1193382.342 1464762.374 1279561.993 1873441.732 1807667.619 307829.7957 5.064970137 5.462857194 3.860031652 3.876760335 4.758351512 4.156719104 6.085966201 5.872295809 1 18.23177336 4.259615968 24.71948528 4.47971035 5.263914102 0.065015354 1.399857518 748.8358827 879133.9749 0.349179623 0.921699366 18180.92468 -4.259615968 0.784203751 TAPAAPAEDAVAAAAAAPS(ph)EPSEPSRPSPQPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPKPR 34 2 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 TAPAAPAEDAVAAAAAAPS(0.415)EPS(0.229)EPS(0.185)RPS(0.171)PQPKPR 112.9 4.32E-06 1032100000 604520 503370 325760 395700 533160 500840 652940 731630 445140 TRUE FALSE 524631.1503 500063.3293 483298.6256 485549.7329 522551.1591 520107.6389 589617.9793 575176.6181 392516.0563 1.336585197 1.273994583 1.231283709 1.237018779 1.331286073 1.325060798 1.502149963 1.465358191 1 18.58239214 3.004076598 3.035770534 1.361215425 1.267745985 0.003691251 0.13739152 0.687551443 13.00961397 0.045959104 0.050020692 1009.430906 -3.004076598 -0.09346944 TAPAAPAEDAVAAAAAAPSEPSEPSRPS(ph)PQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPK 32 1 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 TAPAAPAEDAVAAAAAAPSEPS(0.002)EPS(0.009)RPS(0.989)PQPK;TAPAAPAEDAVAAAAAAPSEPS(0.001)EPS(0.039)RPS(0.96)PQPK 232.24 2.06E-37 590860000 319070 288350 288440 251384 244537 207917 415610 365200 532450 TRUE FALSE 276904.0911 286455.8099 427930.5488 308464.5794 239671.1921 215915.7015 375304.2062 287104.822 469504.3676 0.589779585 0.610123845 0.911451689 0.657000447 0.510477024 0.45988007 0.799362545 0.611506179 1 18.84077905 1.235019352 24.98739815 1.0000005 0.647311872 0.424551154 0.130304156 106.4353335 750895.8476 0.231945403 0.032431095 17.17984938 -1.235019352 -0.352688628 TAPAAPAEDAVAAAAAAPSEPSEPSRPS(ph)PQPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPKPR 34 2 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 TAPAAPAEDAVAAAAAAPSEPS(0.038)EPS(0.203)RPS(0.759)PQPKPR;TAPAAPAEDAVAAAAAAPS(0.015)EPS(0.052)EPS(0.27)RPS(0.664)PQPKPR;TAPAAPAEDAVAAAAAAPSEPS(0.002)EPS(0.187)RPS(0.811)PQPKPR;TAPAAPAEDAVAAAAAAPS(0.113)EPS(0.202)EPS(0.157)RPS(0.528)PQPKPR;TAPAAPAEDAVAAAAAAPSEPS(0.014)EPS(0.251)RPS(0.735)PQPKPR 198.52 2.21E-27 7560070000 2362850 2139320 1439259 1644298 2382680 2112740 2809850 3067650 1744890 TRUE FALSE 2050593.386 2125266.666 2135289.466 2017660.992 2335269.33 2194018.475 2537351.179 2411656.92 1538611.092 1.332756144 1.381289058 1.387803245 1.311352169 1.517777521 1.42597339 1.649117956 1.567424629 1 20.55319718 3.24064118 24.99956097 1.46495462 1.357763867 0.029894298 0.172930328 152.019613 1826613.195 0.050622479 0.062145351 1740.368363 -3.24064118 -0.107190753 TAPFDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TAPFDSR 7 0 P14854;A0A494C160;K7EQD3 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 0 ; 124.89 0.0095448 405850000 1041000 875570 572300 773010 930040 1255450 708450 1029260 977810 FALSE TRUE 903429.2124 869818.323 849066.1942 948533.7352 911534.0236 1303747.974 639744.628 809160.7587 862214.4157 1.047801099 1.008819044 0.984750636 1.100113519 1.057201094 1.512092526 0.74197858 0.93846814 1 19.71768716 TAPPALPTGYDS(ph)EEEEESRPMSYDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TAPPALPTGYDSEEEEESRPMSYDEK 26 1 H0Y6K2;A0A140T9E9;A0A0G2JK44;P25440-4;P25440-3;P25440;P25440-2;A0A0G2JHN8;A0A140T9I1 H0Y6K2 BRD2 Bromodomain-containing protein 2 1 TAPPALPTGYDS(1)EEEEESRPMSYDEK;TAPPALPTGYDS(1)EEEEESRPMSYDEK;TAPPALPT(0.006)GY(0.004)DS(0.991)EEEEESRPMSYDEK 325.19 4.68E-83 657450000 320488 236790 190345 261557 246831 228437 303790 328744 434110 TRUE FALSE 278134.6988 235234.5109 282396.4787 320947.5145 241919.546 237225.1192 274328.4926 258444.6539 382790.0103 0.726598634 0.614526253 0.737732101 0.838442765 0.631990228 0.619726515 0.716655307 0.675160393 1 18.54619365 1.236400833 24.99512216 1.000000394 0.694144923 0.671707167 0.066984684 35.30717914 408507.7303 0.106178395 0.016502405 17.23458509 -1.236400833 -0.305855471 TAPPALPTGYDS(ph)EEEEESRPMSYDEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TAPPALPTGYDSEEEEESRPMSYDEKR 27 2 H0Y6K2;A0A140T9E9;A0A0G2JK44;P25440-4;P25440-3;P25440;P25440-2;A0A0G2JHN8;A0A140T9I1 H0Y6K2 BRD2 Bromodomain-containing protein 2 1 TAPPALPTGYDS(1)EEEEESRPMSYDEKR;TAPPALPTGYDS(1)EEEEESRPMSYDEKR 249 4.43E-46 938060000 733160 557290 285880 355580 574260 492620 633830 769090 257738 TRUE FALSE 636271.0484 553629.1253 424132.5242 436319.8737 562833.3495 511571.4102 572361.2642 604626.0886 227268.5073 2.799644597 2.436013383 1.866217759 1.919843092 2.476512722 2.250956001 2.518436325 2.660404188 1 17.79403826 4.548338871 4.050102854 2.181755395 2.766528058 0.17649055 0.472098163 0.44746745 13.39231358 0.11591297 0.524422951 35345.88589 -4.548338871 0.584772662 TAPPAS(ph)PEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TAPPASPEAR 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 TAPPAS(1)PEAR;TAPPAS(1)PEAR;TAPPAS(1)PEAR;TAPPAS(1)PEAR 175.12 3.04E-06 6694200000 4428680 4390490 2424150 3082630 4770120 4516660 4007770 4788000 3996230 TRUE FALSE 3843418.717 4361648.582 3596477.048 3782588.257 4675203.945 4690418.833 3619097.082 3764123.46 3523800.242 1.090702779 1.237768399 1.020624553 1.073440035 1.32675056 1.33106831 1.027043769 1.068200012 1 21.74870071 2.135334874 24.25965092 1.039136223 1.177441568 0.315515748 0.102734562 11.97529379 2789.05956 0.044466339 0.029979205 136.5635738 -2.135334874 0.138305346 TAPS(ph)PLVEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TAPSPLVEAK 10 0 Q8TEH3;Q8TEH3-7;Q8TEH3-6;A0A0A0MS48;Q8TEH3-4;Q8TEH3-3;Q8TEH3-5;Q8TEH3-2 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 TAPS(1)PLVEAK;TAPS(1)PLVEAK;TAPS(1)PLVEAK;TAPS(1)PLVEAK 173.72 3.49E-06 1190920000 2978120 2551250 1970080 2129880 2747920 2266070 3067410 3514070 3510010 TRUE FALSE 2584553.896 2534490.671 2922817.278 2613501.807 2693241.768 2353247.179 2769933.05 2762613.477 3095060.616 0.835057602 0.818882402 0.944348961 0.84441054 0.870174159 0.760323454 0.894952763 0.892587842 1 21.56153623 1.154397009 1.582451966 1.081802175 0.851039308 0.492819709 0.047461948 1.18242759 2.257876751 0.457400691 0.013320737 14.26911405 -1.154397009 -0.230762867 TAPTALGITLSSS(ph)PTSTPELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TAPTALGITLSSSPTSTPELR 21 0 F5H1U9;O75970-5;O75970-3;O75970-2;O75970 F5H1U9 MPDZ Multiple PDZ domain protein 1 TAPTALGITLS(0.006)S(0.061)S(0.881)PT(0.023)S(0.023)T(0.006)PELR;TAPTALGITLSS(0.004)S(0.995)PT(0.001)STPELR;TAPTALGIT(0.01)LS(0.024)S(0.195)S(0.767)PT(0.004)S(0.001)TPELR;TAPTALGITLS(0.002)S(0.014)S(0.902)PT(0.035)S(0.035)T(0.011)PELR 253.52 2.41E-36 581435000 509742 514046 307022 464789 603998 666543 481472 682620 589189 TRUE FALSE 442378.3032 510669.198 455498.8661 570326.4463 591979.6215 692185.3405 434778.9195 536647.0252 519535.7476 0.851487708 0.982933706 0.876742107 1.097761702 1.139439633 1.332315137 0.83686045 1.032935708 1 18.98686349 3.737460601 24.99999851 1.06780511 0.911642424 0.282427699 0.12695685 146.7248098 3334612.451 0.035776317 0.056587738 5463.369836 -3.737460601 -0.156162687 TAPTLS(ph)PEHWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TAPTLSPEHWK 11 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 TAPT(0.001)LS(0.999)PEHWK;TAPT(0.001)LS(0.999)PEHWK;TAPT(0.002)LS(0.998)PEHWK;TAPTLS(1)PEHWK;TAPT(0.003)LS(0.997)PEHWK;TAPT(0.003)LS(0.997)PEHWK 224.43 4.00E-12 4439910000 2438790 2101290 1348520 1800350 2247200 1889860 2400070 2883970 2945150 TRUE FALSE 2116497.722 2087486.488 2000668.783 2209146.984 2202485.117 1962564.137 2167311.581 2267255.459 2596977.722 0.814984936 0.803813783 0.770383498 0.850660737 0.848095499 0.75571081 0.834551472 0.87303616 1 21.30840221 1.1880443 1.611309859 1.093351363 0.809013565 0.801202114 0.030012202 0.525934467 1.119008899 0.248446168 0.008549457 15.41857721 -1.1880443 -0.284337798 THLPGFVEQAEALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 THLPGFVEQAEALK 14 0 P30044-2;P30044 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 ; 171.21 3.05E-06 979600000 1901980 935340 577940 781210 769210 658410 905710 1088710 866390 FALSE TRUE 1650628.524 929195.69 857433.7171 958595.6705 753904.2259 683739.4587 817874.3836 855897.8389 763966.3612 2.16060367 1.216278278 1.122344858 1.254761622 0.986829086 0.894986342 1.070563346 1.120334458 1 19.54314959 4.843764019 2.181866074 1.064421318 2.669211692 0.926322328 0.096331212 0.251650795 1.066556246 0.026430463 0.866114178 69785.31104 -4.843764019 1.604790375 up TAQVPS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TAQVPSPPR 9 0 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 TAQVPS(1)PPR;TAQVPS(1)PPR;TAQVPS(1)PPR;TAQVPS(1)PPR;TAQVPS(1)PPR 105.94 0.0031648 15261100000 2552470 2093450 1293190 1598780 2321480 2256360 2038800 2354080 2638890 TRUE FALSE 2215154.622 2079697.989 1918581.009 1961807.435 2275287.09 2343163.629 1841077.49 1850678.311 2326923.43 0.951967131 0.893754372 0.824514028 0.84309067 0.977809179 1.006979258 0.791206735 0.795332707 1 21.14999231 1.582863744 0.006909052 3.89E-05 1.75777774 0 0.083955239 138366.1606 327.3181628 42581.10767 40705.48716 38.27046543 -1.582863744 1.757738792 TAQVPS(ph)PPRGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 88.706 0.0077387 3301100000 1742920 1226620 368930 502280 1312110 1127360 1565760 1765160 124589 TRUE FALSE 1512588.706 1218562.252 547345.782 616330.3509 1286001.578 1170730.269 1413912.836 1387694.27 109860.2304 13.76830088 11.09193244 4.982201296 5.610131609 11.70579721 10.656543 12.87010624 12.6314524 1 16.7453097 4.477341833 24.99940176 9.109969696 13.09921032 0.157805328 3.817740839 13.97339455 1583365.242 0.983575966 2.665614695 30015.24087 -4.477341833 3.989240619 MGSS(ph)PLEVPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 MGSSPLEVPKPR 12 1 Q8NCE2;Q8NCE2-2 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 MGS(0.183)S(0.817)PLEVPKPR 61.409 0.051513 468620000 84570 100250 98231 108850 141010 155610 202830 181140 210650 TRUE FALSE 73393.86023 99591.45115 145735.8402 133566.0562 138204.1769 161596.4174 183159.5778 142404.6206 185747.197 0.395127687 0.536166644 0.784592406 0.719074411 0.744044482 0.869980382 0.986069135 0.766658248 1 17.50298091 4.878976176 0.553245744 0.896084529 4.42E-15 0.804436167 0.081602626 2.145859305 0.467390095 0.050982592 1.286033061 75679.13785 -4.878976176 -0.896084529 down TAS(ph)ELLLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TASELLLDR 9 0 Q92508 Q92508 PIEZO1 Piezo-type mechanosensitive ion channel component 1 1 T(0.002)AS(0.998)ELLLDR 160.18 6.87E-05 38407000 60988 56898 37793 64554 71702 79374 42975 80195 100480 TRUE FALSE 52928.28128 56524.23329 56069.82121 79211.97235 70275.27048 82427.56914 38807.29111 63045.92333 88601.36887 0.597375435 0.637961174 0.632832449 0.894026507 0.793162356 0.930319364 0.437998776 0.711568276 1 16.43504137 3.886670792 9.756099191 0.769143846 0.622094258 0.208925115 0.15249159 0.718189689 57.04149946 0.041708507 0.072384502 7703.193222 -3.886670792 -0.147049588 TAS(ph)FGNILDVPEIVISGNGQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TASFGNILDVPEIVISGNGQPR 22 0 O43318;O43318-3 O43318 MAP3K7 Mitogen-activated protein kinase kinase kinase 7 1 T(0.016)AS(0.984)FGNILDVPEIVISGNGQPR;T(0.086)AS(0.914)FGNILDVPEIVISGNGQPR;T(0.126)AS(0.874)FGNILDVPEIVISGNGQPR;T(0.13)AS(0.87)FGNILDVPEIVISGNGQPR 335.39 6.78E-81 777570000 951330 960170 644270 714260 1071870 1041120 963470 1093480 1386490 TRUE FALSE 825609.3301 953862.58 955841.127 876443.6498 1050541.884 1081172.56 870032.8277 859647.8115 1222580.732 0.67530046 0.780204166 0.781822502 0.716879979 0.859282219 0.884336332 0.711636299 0.70314196 1 20.2214983 5.886062158 0.86431909 0.800294114 1.42E-11 0.170923136 0.091129078 30.97330102 3.92793319 0.031277646 37.15052003 769240.5293 -5.886062158 -0.800294114 SQS(ph)FTHSPSGDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SQSFTHSPSGDPK 13 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 S(0.223)QS(0.766)FT(0.011)HSPSGDPK 126.25 0.00012287 664180000 943500 986780 821790 1120600 1494100 1329400 1825200 2034900 1961200 TRUE FALSE 818814.0845 980297.7772 1219210.393 1375049.357 1464370.333 1380542.878 1648192.385 1599752.471 1729349.17 0.473481064 0.566859368 0.705011118 0.795125346 0.846775399 0.798301987 0.953070909 0.925060421 1 20.72179776 4.907284079 0.371084255 0.993781004 2.46E-19 0.949970287 0.037220135 1.804958252 0.209730147 0.059671278 0.838043711 80776.32289 -4.907284079 -0.993781004 down TAS(ph)FSESRADEVAPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TASFSESRADEVAPAK 16 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 T(0.002)AS(0.995)FS(0.003)ESRADEVAPAK 245.03 2.60E-20 709380000 643620 793210 508350 530670 1063900 1006000 1685000 1658000 104970 TRUE FALSE 558563.9863 787999.3513 754189.7603 651166.7343 1042730.471 1044701.471 1521588.959 1303449.603 92560.56618 6.034578323 8.513337632 8.148067708 7.035034045 11.26538562 11.28667978 16.43884672 14.08212651 1 16.49811007 3.249653721 24.50634943 10 7.561032292 0.130930979 4.030956503 520.1260812 1149029.078 1.256178313 1.605572779 1776.862086 -3.249653721 -2.438967708 TAS(ph)FSESRADEVAPAKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TASFSESRADEVAPAKK 17 2 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 T(0.003)AS(0.793)FS(0.175)ES(0.029)RADEVAPAKK;T(0.002)AS(0.965)FS(0.033)ESRADEVAPAKK;T(0.152)AS(0.828)FS(0.02)ESRADEVAPAKK;T(0.047)AS(0.905)FS(0.047)ESRADEVAPAKK 194.24 4.46E-11 2168960000 1189110 1269190 614742 656180 1650060 1254040 2855440 2689900 182057.8 TRUE FALSE 1031966.101 1260852.607 912033.2874 805175.6981 1617227.034 1302283.73 2578519.868 2114685.818 160535.1343 6.428288146 7.85406019 5.681206743 5.015573081 10.07397565 8.112141533 16.06202829 13.17272899 1 17.29252955 3.226138809 24.29986582 10 6.319475238 0.159422051 3.88527457 296.5057143 580030.4541 1.217569571 1.390852326 1683.211962 -3.226138809 -3.680524762 TAS(ph)GSSVTSLDGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 TAS(0.969)GS(0.015)S(0.015)VT(0.001)SLDGTR;TAS(0.999)GS(0.001)SVTSLDGTR;TAS(0.966)GS(0.033)S(0.002)VTSLDGTR;TAS(1)GSSVTSLDGTR 294.95 1.43E-43 1926120000 6025200 633510 379985 626480 671150 732590 733830 802180 978230 TRUE FALSE 5228954.554 629348.4311 563747.017 768731.8591 657795.4281 760773.2113 662663.2795 630640.0496 862584.7638 6.061960254 0.729607637 0.6535555 0.891195731 0.762586421 0.88196922 0.768229752 0.731105018 1 19.71830671 4.738988716 25 0.794504969 6.061961844 0.996392287 0.099462249 1.76539598 103062.656 0.023182589 0.1325177 54826.27196 -4.738988716 5.267456875 TAS(ph)LPGYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 TASLPGYGR 9 0 O14639-3;F8W8M4;O14639-5;O14639-2;O14639;J3QSX6;A0A0A0MRL6;A0A3B3IS55;O14639-4;O14639-6 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 TAS(1)LPGYGR;TAS(1)LPGYGR;TAS(1)LPGYGR;TAS(1)LPGYGR;TAS(1)LPGYGR;TAS(1)LPGYGR;TAS(1)LPGYGR 200.68 2.38E-05 5202740000 3715960 3748480 2179020 2419000 3939680 3629040 3425530 3948390 3609350 TRUE FALSE 3224886.471 3723855.988 3232801.36 2968270.922 3861288.076 3768651.517 3093322.628 3104057.525 3182656.755 1.0132687 1.170046372 1.015755581 0.932639348 1.213227933 1.184121257 0.971930958 0.975303894 1 21.60180014 2.197490902 24.9712671 0.980493975 1.087220398 0.249965668 0.086332666 213.5927617 129867.5463 0.036384031 0.024530397 157.5763012 -2.197490902 0.106726423 TAS(ph)LTSAASVDGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TASLTSAASVDGNR 14 0 Q9UN36;Q9UN36-5;G3V578;H0YJT9;A0A0A0MS87;Q9UN36-2;Q9UN36-3;Q9UN36-6;Q9UN36-4 Q9UN36 NDRG2 Protein NDRG2 1 TAS(0.999)LT(0.001)SAASVDGNR;TAS(0.996)LT(0.004)SAASVDGNR;TAS(1)LTSAASVDGNR;TAS(0.97)LT(0.028)S(0.002)AASVDGNR;TAS(1)LTSAASVDGNR 370.76 4.18E-97 6941130000 1805740 1937180 1404560 1663440 2659610 2328650 2308780 2758080 2692780 TRUE FALSE 1567106.884 1924454.537 2083809.914 2041149.476 2606688.964 2418234.672 2084874.871 2168286.055 2374442.616 0.659989369 0.810486859 0.87759961 0.859633104 1.097810891 1.018443089 0.878048118 0.913176861 1 21.17915746 4.626993843 1.023959171 0.961102238 0.548573973 0.684103668 0.067947678 1.02227402 0.996947737 0.023825653 0.444921628 42363.69605 -4.626993843 -0.412528265 TAS(ph)NPKVENEDEPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TASNPKVENEDEPVR 15 1 Q9UBF8-2 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 T(0.029)AS(0.971)NPKVENEDEPVR;T(0.116)AS(0.884)NPKVENEDEPVR 216.3 1.35E-12 1813030000 2135080 1872310 1422570 1545360 2064440 1379350 2300420 2608660 1728580 TRUE FALSE 1852923.768 1860010.672 2110529.61 1896257.607 2023361.683 1432414.487 2077325.622 2050818.36 1524229.242 1.215646386 1.220295886 1.384653668 1.244076387 1.327465468 0.939763159 1.362869551 1.34547895 1 20.53964847 TAS(ph)PLPLRPDAPVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TASPLPLRPDAPVEK 15 1 Q9HCK8-2;Q9HCK8;H0YJG4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 TAS(1)PLPLRPDAPVEK;T(0.011)AS(0.989)PLPLRPDAPVEK;TAS(1)PLPLRPDAPVEK;T(0.03)AS(0.97)PLPLRPDAPVEK 193.71 4.95E-08 3042020000 6728790 4882370 3560000 4053560 5106850 4206360 6143170 7147330 6524240 TRUE FALSE 5839563.353 4850297.39 5281627.907 4973982.753 5005233.676 4368181.391 5547406.319 5618929.1 5752951.78 1.015055154 0.843097174 0.918072689 0.864596635 0.87002879 0.759293934 0.964271305 0.976703667 1 22.45587095 2.028007572 24.99951341 0.981827794 0.876241369 0.367097898 0.063530437 206.800319 184588.7385 0.024981201 0.016842023 106.6614718 -2.028007572 -0.105586425 TAS(ph)PPGPPPYGK ddPTM_MDA-MB-175_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 202.29 1.45E-07 1196410000 1925900 1527160 1068800 1269970 1676000 1376050 1814810 2115750 1857880 TRUE FALSE 1671387.435 1517127.985 1585675.255 1558336.099 1642650.879 1428987.534 1638810.006 1663313.327 1638243.543 1.020231359 0.92606987 0.967911799 0.951223709 1.002690281 0.87226807 1.000345774 1.015302843 1 20.64371841 2.029521234 24.99999336 1.008468558 0.955903944 0.246071675 0.04013384 243.2664525 206008.7892 0.015149054 0.01021336 107.0338714 -2.029521234 -0.052564614 TAS(ph)PPPPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TASPPPPPK 9 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(0.002)AS(0.998)PPPPPK;T(0.012)AS(0.988)PPPPPK;T(0.001)AS(0.999)PPPPPK;TAS(1)PPPPPK;T(0.004)AS(0.996)PPPPPK;T(0.001)AS(0.999)PPPPPK 121.6 0.00063906 6763570000 4037860 3092190 1958470 2559340 3119440 2467140 3568800 4121800 4141680 TRUE FALSE 3504246.57 3071877.2 2905592.643 3140477.264 3057369.247 2562052.472 3222698.325 3240385.146 3652055.309 0.959527245 0.841136549 0.795604775 0.85992051 0.837164005 0.70153715 0.882434151 0.887277128 1 21.80027718 1.292354047 1.783874115 1.0445227 0.833110535 0.381936329 0.064627836 0.859747916 2.857951777 0.303541533 0.017975205 19.60442221 -1.292354047 -0.211412164 TAS(ph)PPPPPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 TASPPPPPKR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(0.02)AS(0.98)PPPPPKR;T(0.01)AS(0.99)PPPPPKR;T(0.002)AS(0.998)PPPPPKR;T(0.001)AS(0.999)PPPPPKR;TAS(1)PPPPPKR;T(0.005)AS(0.995)PPPPPKR;T(0.009)AS(0.991)PPPPPKR 133.05 0.00012705 3282768000 3426618 2663800 1758344 2071798 2711210 2259955 2953293 3428533 2701986 TRUE FALSE 2973781.749 2646301.322 2608685.04 2542231.401 2657262.225 2346896.931 2666883.099 2695367.899 2382560.293 1.248145433 1.110696476 1.0949083 1.067016608 1.115296949 0.985031497 1.119334989 1.131290531 1 21.18408129 4.962424811 1.636802121 1.07794698 1.397726195 0.561345868 0.048313387 1.483243276 2.439804817 0.012904043 0.891010708 91711.71417 -4.962424811 0.319779214 TAS(ph)PWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TASPWK 6 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3;A0A1B0GTD1 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 TAS(1)PWK;TAS(1)PWK;TAS(1)PWK;TAS(1)PWK;TAS(1)PWK;TAS(1)PWK 107.29 0.032926 5455360000 11065900 8969600 6647450 7247720 8908810 8187310 10415000 11734600 10789200 TRUE FALSE 9603513.278 8910678.107 9862179.054 8893425.6 8731542.111 8502281.114 9404954.903 9225247.109 9513713.067 1.009439029 0.936614132 1.036627759 0.934800696 0.917784891 0.893686939 0.988568274 0.96967893 1 23.18157708 4.758157464 22.95030778 0.960101092 1.009439169 0.122417377 0.041824525 3362.013684 3937129.323 0.01040601 0.333877574 57300.375 -4.758157464 0.049338077 DGQSS(ph)PQPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 DGQSSPQPSPR 11 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 2 DGQS(0.094)S(0.906)PQPS(1)PR;DGQS(0.449)S(0.551)PQPS(1)PR 94.023 0.0048951 276920000 197394 301460 237930 304800 369930 431240 415240 505210 468270 TRUE FALSE 171307.8828 299479.6894 352993.7438 374009.4986 362569.1168 447830.0818 374970.0887 397174.773 412911.6541 0.41487781 0.725287568 0.854889273 0.905785765 0.878079156 1.084566341 0.908112147 0.961888019 1 18.65547361 4.907380916 0.944660236 0.965713514 2.38E-21 0.911481565 0.054450835 0.714713878 0.412609964 0.017441942 0.760643911 80794.33603 -4.907380916 -0.965713514 down TAS(ph)TPTPPQTGGGLEPQANGETPQVAVIVRPDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TASTPTPPQTGGGLEPQANGETPQVAVIVRPDDR 34 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JWW9;C9JSU8;C9J556;C9JWH7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 T(0.08)AS(0.42)T(0.42)PT(0.08)PPQT(0.001)GGGLEPQANGETPQVAVIVRPDDR 65.69 0.0033295 141220000 89541 84489 56035 61175 93051 92430 86724 105400 81398 TRUE FALSE 77707.92998 83933.9862 83133.71343 75065.71875 91199.46715 95985.84191 78313.51983 82861.03022 71775.22117 1.082656782 1.169400593 1.158250885 1.045844478 1.270626069 1.337311684 1.091094093 1.154451758 1 16.13119825 0.917630194 1.677403155 0.766078852 1.170682269 0.258859326 0.086696213 3.759500945 4.739902914 3.268384262 0.024774202 8.272374629 -0.917630194 0.404603417 TASDTDSSYCIPTAGMS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TASDTDSSYCIPTAGMSPSR 20 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 TASDTDSSYCIPTAGMS(0.816)PS(0.184)R 342.85 1.35E-80 260020000 116080 118670 87956 105580 123660 144250 148160 140430 145790 TRUE FALSE 100739.7339 117890.449 130491.8158 129553.5527 121199.4079 149799.3908 133791.466 110400.1373 128554.8723 0.783632173 0.917043803 1.015067056 1.007768515 0.942783465 1.165256425 1.040734308 0.858778321 1 16.97202476 4.625062389 2.421963436 0.996925651 0.760791122 0.458808095 0.076818248 0.434844988 3.71560013 0.021451898 0.191809326 42175.70875 -4.625062389 -0.236134529 TASESISNLSEAGS(ph)IK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TASESISNLSEAGSIK 16 0 J3KP58;P30622-2;P30622-1;P30622;F5H6A0;F5H1T5 J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 1 TASESISNLSEAGS(1)IK;TASESISNLSEAGS(1)IK;TASESISNLSEAGS(1)IK;TASESISNLSEAGS(1)IK;TASESISNLSEAGS(1)IK;TASESISNLSEAGS(1)IK 348.45 4.04E-87 1495950000 2337060 1821280 1412730 1546580 2198110 1767800 2367530 2641210 2466280 TRUE FALSE 2028211.6 1809315.892 2095930.953 1897754.627 2154371.912 1835808.41 2137927.305 2076407.795 2174719.188 0.932631491 0.831976791 0.963770847 0.872643529 0.990643722 0.844158832 0.983082007 0.954793523 1 21.05239769 -2 0.352682654 2.166295115 0.895302065 0.250124585 0.052771063 99.3098195 1.53553089 83.0448249 0.063128368 0.01 2 -1.27099305 TASFSESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TASFSESR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;; 113.91 0.0065106 281430000 619830 563300 356607 375998 517600 551240 499520 575230 528980 FALSE TRUE 537917.8951 559599.6452 529063.338 461374.0927 507300.7727 572446.5595 451076.6273 452221.5409 466444.587 1.153230009 1.199713022 1.134246924 0.989129482 1.087590652 1.227255231 0.967052979 0.969507533 1 18.83134618 -1.999999971 0.138454637 0.163996305 1.274613307 0.386354098 0.075676959 175.5683798 2.094314253 37.89020719 1.731046676 0.010000001 1.999999971 1.110617002 TASLT(ph)SAASVDGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TASLTSAASVDGNR 14 0 Q9UN36;Q9UN36-5;G3V578;H0YJT9;A0A0A0MS87;Q9UN36-2;Q9UN36-3;Q9UN36-6;Q9UN36-4 Q9UN36 NDRG2 Protein NDRG2 1 TAS(0.288)LT(0.669)S(0.043)AASVDGNR 316.32 7.39E-55 754980000 206530 238190 154980 179040 284890 294850 271040 301400 314410 TRUE FALSE 179236.5372 236625.3142 229928.8464 219693.7685 279221.2464 306193.0703 244754.5825 236947.9555 277240.808 0.64650128 0.853501027 0.829347051 0.792429405 1.007143387 1.104430017 0.882823075 0.854664785 1 18.0807801 3.250617918 24.6271295 0.955625514 0.789155957 0.534081465 0.087162634 180.6509141 368978.3032 0.027055065 0.034647534 1780.811362 -3.250617918 -0.166469557 TASLTSAAS(ph)VDGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TASLTSAASVDGNR 14 0 Q9UN36;Q9UN36-5;G3V578;H0YJT9;A0A0A0MS87;Q9UN36-2;Q9UN36-3;Q9UN36-6;Q9UN36-4 Q9UN36 NDRG2 Protein NDRG2 1 TASLTSAAS(1)VDGNR;TASLTSAAS(1)VDGNR;TASLTS(0.001)AAS(0.999)VDGNR;TASLTS(0.02)AAS(0.98)VDGNR 289.2 2.08E-43 1030600000 1274902 1513380 613100 893097 1299580 848469 1139813 1303230 1053573 TRUE FALSE 1106420.471 1503438.507 909597.2107 1095888.324 1273720.901 881110.1515 1029274.111 1024544.406 929020.8002 1.190953389 1.618304463 0.979092406 1.179616564 1.371035934 0.948428874 1.10791288 1.102821816 1 19.82535137 3.868353554 0.416131136 1.022778825 1.458087566 0.234035466 0.176158011 4.31989054 1.369471573 0.290549006 1.014400761 7385.051938 -3.868353554 0.435308741 TASQGQWGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TASQGQWGR 9 0 Q9UBM7;E9PRL8;E9PQ71;E9PIP9;E9PJ54;E9PM00 Q9UBM7 DHCR7 7-dehydrocholesterol reductase 0 ; 134.26 0.00059066 242650000 199646 162207 110694 144262 334160 219452 165569 256000 177019 FALSE TRUE 173262.2753 161141.4515 164225.9886 177018.892 327510.8698 227894.4604 149512.1439 201256.3922 156092.0155 1.110000885 1.032349099 1.052110117 1.134067566 2.098191049 1.460000755 0.9578462 1.289344568 1 17.25203722 3.456606861 24.99954399 1.35311525 1.066825075 0.17088057 0.308189414 461.2295463 562068.3196 0.094306498 0.121761742 2861.586387 -3.456606861 -0.286290175 TASRPDDIPDSPS(ph)SPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TASRPDDIPDSPSSPK 16 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 TASRPDDIPDSPS(0.5)S(0.5)PK;TASRPDDIPDSPS(0.5)S(0.5)PK 153.36 2.78E-07 828570000 407590 479690 508030 484230 785290 612470 851880 979540 796370 TRUE FALSE 353725.9488 476538.8848 753715.0073 594181.8225 769664.2654 636032.1172 769264.8087 770072.9938 702224.0458 0.503722353 0.678613738 1.073325546 0.846142803 1.096038038 0.905739587 1.095469193 1.096620086 1 19.42157187 4.376383818 3.40146448 1.02119448 0.528782529 0.811696415 0.086796066 0.090357807 1.973779419 0.021941794 0.073250739 23789.41803 -4.376383818 -0.492411951 TAST(ph)PT(ph)PPQTGGGLEPQANGETPQVAVIVRPDDR ddPTM_MDA-MB-175_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(0.042)AS(0.182)T(0.776)PT(0.856)PPQT(0.143)GGGLEPQANGET(0.001)PQVAVIVRPDDR 68.503 0.023345 117500000 63145 63284 43068 40149 50986 60614 43139 52309 69280 TRUE FALSE 54800.22826 62868.28324 63895.82885 49265.44409 49971.47835 62945.8598 38955.38642 41123.12742 61089.79732 0.897043871 1.02911265 1.0459329 0.806443076 0.818000395 1.030382528 0.63767418 0.673158681 1 15.89864383 3.226015218 0.889801802 0.773507477 0.992702578 0.172030503 0.134895455 0.846170593 1.56194778 0.077713012 0.113098182 1682.733022 -3.226015218 0.2191951 TAST(ph)PTPPQTGGGLEPQANGETPQVAVIVRPDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TASTPTPPQTGGGLEPQANGETPQVAVIVRPDDR 34 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JWW9;C9JSU8;C9J556;C9JWH7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 TAS(0.021)T(0.975)PT(0.004)PPQTGGGLEPQANGETPQVAVIVRPDDR;T(0.001)AS(0.022)T(0.532)PT(0.445)PPQTGGGLEPQANGETPQVAVIVRPDDR;T(0.031)AS(0.136)T(0.698)PT(0.136)PPQTGGGLEPQANGETPQVAVIVRPDDR;T(0.018)AS(0.115)T(0.752)PT(0.115)PPQTGGGLEPQANGETPQVAVIVRPDDR;TAS(0.034)T(0.96)PT(0.006)PPQTGGGLEPQANGETPQVAVIVRPDDR;TAS(0.011)T(0.975)PT(0.014)PPQTGGGLEPQANGETPQVAVIVRPDDR 227.49 2.17E-36 3578930000 310378 274444 160394.5 212370.9 283985.9 281987 276357.6 328218 278451 TRUE FALSE 269360.7609 272641.1593 237961.8167 260592.9587 278335.1362 292835.2224 249556.4825 258031.1349 245532.84 1.097045759 1.110406084 0.969164926 1.061336474 1.13359637 1.192651958 1.01638739 1.050902742 1 17.90555647 TASTPT(ph)PPQTGGGLEPQANGETPQVAVIVRPDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TASTPTPPQTGGGLEPQANGETPQVAVIVRPDDR 34 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JWW9;C9JSU8;C9J556;C9JWH7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 TAS(0.002)T(0.059)PT(0.939)PPQTGGGLEPQANGETPQVAVIVRPDDR 208.81 2.35E-27 512370000 59892 50849 30836 35036 54637 63403 61054 61598 57572 TRUE FALSE 51977.12045 50514.96957 45748.39274 42991.45929 53549.8306 65842.15444 55132.99248 48425.74706 50765.90375 1.023858862 0.995057033 0.901163761 0.846856967 1.054838516 1.296975915 1.086024052 0.953902984 1 15.63157223 3.079474895 9.372052914 1.076361513 0.943119757 0.318068054 0.099911492 0.457205165 49.69201367 0.03375768 0.0383039 1200.811656 -3.079474895 -0.133241756 TAT(ph)PPGYKPGS(ph)PPSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TATPPGYKPGSPPSFR 16 1 P54259 P54259 ATN1 Atrophin-1 2 T(0.108)AT(0.892)PPGYKPGS(0.963)PPS(0.037)FR 90.464 0.029257 0 395870 305750 225180 207650 320330 253370 324440 387370 354670 TRUE FALSE 343554.7765 303741.5081 334077.8012 254800.1062 313956.0597 263117.3079 292975.8587 304533.94 312741.3166 1.098526988 0.971222835 1.068224067 0.814731194 1.003884178 0.841325702 0.936799339 0.97375666 1 18.2546103 4.601344637 1.167192529 0.937309033 1.130757944 0.310161731 0.073221299 1.563276797 2.152513667 0.021256421 0.348695674 39934.16762 -4.601344637 0.193448911 TATAVAHCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TATAVAHCK 9 0 P62249;M0R210;M0R3H0;M0R1M5;Q6IPX4 P62249 RPS16 40S ribosomal protein S16 0 ; 76.221 0.036044 564610000 1805180 1748920 844720 1138780 1424310 1393600 1917550 1915250 1416980 FALSE TRUE 1566620.889 1737431.229 1253229.417 1397357.404 1395969.018 1447212.694 1731586.296 1505688.692 1249466.239 1.253832109 1.390538756 1.003011829 1.118363475 1.117252291 1.158264745 1.385860812 1.205065528 1 20.25288049 4.259352783 24.9994418 1.158885371 1.322185443 0.296232471 0.113486051 346.7222685 416873.9539 0.029521963 0.077929043 18169.91031 -4.259352783 0.163300073 TATESFAS(ph)DPILYRPVAVALDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TATESFASDPILYRPVAVALDTK 23 1 P14618;P14618-3;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 1 T(0.002)AT(0.005)ES(0.034)FAS(0.956)DPILY(0.003)RPVAVALDTK;TATES(0.001)FAS(0.999)DPILYRPVAVALDTK 133.46 1.39E-05 135499000 304070 208719 149992 196780 195183 184630 281948 281120 293950 TRUE FALSE 263886.3791 207347.9111 222528.6329 241461.9066 191299.2402 191732.8356 254604.7264 221004.6757 259199.5659 1.018081871 0.799954701 0.858522398 0.931567558 0.738038428 0.739711253 0.982272966 0.852642924 1 17.98370378 -0.579548238 1.142889816 9.999993928 0.854951773 0.161503379 0.093600371 183.9562088 4.734079887 4211.732157 0.028083522 0.263300547 0.579548238 -9.145042155 TATESFASDPILYRPVAVALDTK ddPTM_MDA-MB-175_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 ;;; 223.89 1.27E-32 6725580000 9662520 6888290 5102910 6339550 6950490 6431480 8952480 9528200 9705430 FALSE TRUE 8385593.5 6843040.369 7570694.344 7779041.721 6812188.847 6678903.197 8084269.868 7490668.579 8558065.122 0.979846891 0.799601344 0.884626868 0.908972018 0.795996379 0.780422105 0.944637573 0.87527595 1 23.02885323 0.162037537 1.163084319 2.286214905 0.862078729 0.276402097 0.065028445 21.74269966 3.276228112 67.36687402 0.019167429 1.452237132 -0.162037537 -1.424136176 TATESFASDPILYRPVAVALDTKGPEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TATESFASDPILYRPVAVALDTKGPEIR 28 2 P14618;P14618-3;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 125.54 2.12E-05 852220000 736270 569700 144840 161260 486650 467900 717590 739940 8226.5 FALSE TRUE 638970.054 565957.6032 214885.1085 197876.5477 476966.6171 485900.4158 647998.2322 581709.5892 7253.972542 88.08553525 78.02036745 29.62309372 27.2783701 65.75247072 66.98404398 89.33011926 80.19186534 1 12.82455557 7.999990363 0.024739322 0.000663026 141.4996081 0.032050404 29.17976887 45618.69316 112.0117864 240720.8125 425230.7728 99997780.92 -7.999990363 141.498945 TATNDEESPLSVS(ph)SPEGTGTWLHYTSGVGTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TATNDEESPLSVSSPEGTGTWLHYTSGVGTGR 32 0 A0A087WZV0;O43314-2;O43314;A0A087WWN8 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 TATNDEES(0.002)PLS(0.074)VS(0.462)S(0.462)PEGTGTWLHYTSGVGTGR;TATNDEESPLS(0.003)VS(0.88)S(0.116)PEGTGTWLHYTSGVGTGR;TATNDEESPLS(0.001)VS(0.894)S(0.105)PEGTGTWLHYTSGVGTGR;TATNDEESPLS(0.137)VS(0.668)S(0.195)PEGTGTWLHYTSGVGTGR 313.19 2.83E-104 939398000 228729 418958 244282 387124 763489 780136 603673 717162 829406 TRUE FALSE 198501.8831 416205.8373 362417.5923 475026.421 748297.0626 810148.3367 545128.8854 563802.4873 731354.5675 0.271416755 0.569088997 0.49554294 0.649515901 1.023165911 1.107736757 0.745368812 0.770901711 1 19.48021148 3.490339617 3.143194887 0.903802063 0.460006876 0.732059167 0.133722965 0.149958899 3.035590003 0.042489791 0.061806099 3092.712983 -3.490339617 -0.443795187 TATPPGYKPGS(ph)PPSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TATPPGYKPGSPPSFR 16 1 P54259 P54259 ATN1 Atrophin-1 1 TAT(0.007)PPGYKPGS(0.989)PPS(0.003)FR 81.356 0.0078781 295970000 569660 526640 328440 422560 521920 464780 606960 706100 594900 TRUE FALSE 494377.9877 523180.4672 487274.6826 518508.7064 511534.8131 482660.3874 548097.1126 555106.0099 524571.5997 0.94244139 0.99734806 0.928900236 0.988442201 0.975147746 0.920103924 1.044847096 1.058208279 1 19.00078018 2.221332077 24.99909991 1.039759231 0.961226769 0.60858932 0.028431711 145.036225 210450.0975 0.010967499 0.007414522 166.4685043 -2.221332077 -0.078532462 TATPQQAQEVHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TATPQQAQEVHEK 13 0 P60174;P60174-3;P60174-4;U3KPZ0 P60174 TPI1 Triosephosphate isomerase 0 ;; 223.58 1.56E-11 1725410000 2670970 2494250 1326390 1496810 2103790 1845320 2488020 2593330 2869400 FALSE TRUE 2317994.547 2477865.108 1967836.641 1836683.588 2061928.695 1916310.654 2246732.203 2038766.561 2530182.801 0.916137184 0.979322564 0.777744849 0.725909443 0.814932697 0.757380318 0.887972285 0.805778365 1 21.27081019 4.241401901 24.99974458 0.819777878 0.947729901 0.304660423 0.077328795 83.0666886 730845.3846 0.019157904 0.046282321 17434.19507 -4.241401901 0.127952023 TATYNGPPAS(ph)PSLSHEATPLSQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TATYNGPPASPSLSHEATPLSQTR 24 0 H0YIY6;P27448-6;P27448-7;A2SY06;J3KNR0;P27448-8;P27448-3;P27448-4;P27448-2;P27448 H0YIY6;J3KNR0 MARK3 MAP/microtubule affinity-regulating kinase 3 1 TATYNGPPAS(0.999)PS(0.001)LSHEATPLSQTR;TATYNGPPAS(1)PSLSHEATPLSQTR;TATYNGPPAS(0.999)PS(0.001)LSHEATPLSQTR 323.27 2.43E-74 1373390000 425100 401730 167038 306510 478410 360370 371080 397780 374810 TRUE FALSE 368921.9579 399091.0092 247818.1355 376107.7802 468890.577 374233.6671 335092.7187 312717.8425 330500.3888 1.11625272 1.207535672 0.749827062 1.137994971 1.418729275 1.132324438 1.013895082 0.946195082 1 18.33429244 2.138394558 4.25188035 0.972697111 1.127210132 0.146082631 0.161854235 0.436938331 14.2515013 0.073951193 0.048159916 137.5290864 -2.138394558 0.154513021 TAVAHRPGAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TAVAHRPGAFK 11 1 Q969H8 Q969H8 MYDGF Myeloid-derived growth factor 0 ; 107.03 0.0013534 3172100000 2775500 2850800 1490380 2068700 2841700 2828300 2885900 3001100 2967200 FALSE TRUE 2408710.643 2832072.907 2211132.753 2538429.953 2785155.73 2937106.531 2606025.862 2359338.12 2616420.996 0.920612794 1.082422481 0.84509823 0.970191707 1.064490666 1.122566489 0.996026964 0.901742542 1 21.31916327 7.23736753 12.8388658 0.987295586 0.968755087 0 0.085519726 0 0 0.019613249 0 17272990.33 -7.23736753 -0.018540498 TAVEHATDEDILAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TAVEHATDEDILAK 14 0 A0A494C1L5;P50851-2;E9PEM5;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 98.676 0.0024832 446000000 176960 161340 114740 120210 142390 179110 166410 171780 170500 FALSE TRUE 153574.2876 160280.1469 170228.6478 147505.5178 139556.7176 186000.4776 150271.5838 135046.1838 150343.6842 1.021488122 1.066091653 1.132263378 0.981122144 0.928251282 1.237168548 0.999520429 0.898249797 1 17.19790474 2.001517959 24.99998504 0.94396543 1.060148862 0.227724142 0.08624154 63.41465604 1044396.207 0.034906085 0.023337082 100.3501346 -2.001517959 0.116183431 TAVIPINGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 TAVIPINGSPR 11 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 TAVIPINGS(1)PR;TAVIPINGS(1)PR;TAVIPINGS(1)PR;TAVIPINGS(1)PR;TAVIPINGS(1)PR;TAVIPINGS(1)PR;TAVIPINGS(1)PR;TAVIPINGS(1)PR 217.96 1.15E-11 6606070000 4506940 4542430 2314142 3260050 4890160 4274470 4284020 5284120 4607050 TRUE FALSE 3911336.46 4512590.478 3433268.812 4000294.179 4792855.383 4438911.627 3868556.4 4154152.059 4062409.797 0.962811891 1.110816167 0.845131088 0.984709662 1.179805983 1.092679431 0.952281181 1.022583212 1 21.95390435 3.445929897 24.99795195 1.044732915 0.974744281 0.152043322 0.086307002 418.5925931 335474.8859 0.025458485 0.032867001 2792.093111 -3.445929897 -0.069988634 TAVPS(ph)PVEAAAASDPAAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TAVPSPVEAAAASDPAAAR 19 0 Q147X3;Q147X3-2;J3KNC2 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 TAVPS(1)PVEAAAASDPAAAR;TAVPS(1)PVEAAAASDPAAAR 231.62 3.09E-20 452040000 227522 201764 125994 143052 192022 233257 205852 220178 219085 TRUE FALSE 197454.3912 200438.599 186925.1198 175534.143 188201.1379 242230.5477 185888.5047 173094.6481 193185.0209 1.022099904 1.037547311 0.967596343 0.908632265 0.974201504 1.253878518 0.962230425 0.8960045 1 17.55962371 2.015879733 24.99998381 0.937136925 1.024831387 0.123993098 0.092866007 447.4062028 704363.6547 0.039340792 0.026514889 103.7241137 -2.015879733 0.087694462 TAVTATNVSAHGSQANS(ph)PSTPNSAGGYPSPCYQPDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TAVTATNVSAHGSQANSPSTPNSAGGYPSPCYQPDRR 37 1 A0A087X0P4;P40424-2 A0A087X0P4 PBX1 Pre-B-cell leukemia transcription factor 1 1 TAVTATNVSAHGSQANS(0.93)PS(0.031)T(0.031)PNS(0.008)AGGYPSPCYQPDRR 117.65 2.01E-06 104050000 7673.3 13217 3662.4 5113.5 16147 14335 10228 12993 9262.4 TRUE FALSE 6659.253963 13130.17666 5433.54889 6274.59833 15825.70629 14886.47673 9236.090134 10214.54806 8167.409624 0.815344677 1.60763048 0.665271994 0.768248272 1.937665309 1.822668069 1.130846934 1.25064721 1 12.99566287 3.272844378 24.99981011 1.403553133 0.98874212 0.26879447 0.378282464 299.9206303 218700.966 0.114080806 0.14727033 1874.322756 -3.272844378 -0.414811014 TAVVVGTITDDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TAVVVGTITDDVR 13 0 J3QQ67;Q07020;F8VYV2;G3V203;H0YHA7;Q07020-2;F8VUA6;A0A075B7A0 J3QQ67 RPL18 60S ribosomal protein L18 0 ; 117.94 0.0010851 231130000 268386 228246 153508 168286 224733 223974 225948 259052 265033 FALSE TRUE 232918.1101 226746.637 227744.9823 206497.9084 220261.253 232590.4247 204035.5977 203655.7457 233701.1007 0.996649607 0.970242059 0.974513948 0.883598356 0.942491295 0.995247451 0.873062203 0.871436827 1 17.834305 3.868054098 7.225592955 0.921882842 0.980668263 0.224758077 0.045551177 0.371472054 20.06403115 0.012553573 0.021917591 7379.961538 -3.868054098 0.058785421 TAWVFDDKYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TAWVFDDKYK 10 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ; 147.72 2.41E-05 2500500000 3718300 3287100 2379600 2786700 3200000 2324790 4222100 5152600 3232500 FALSE TRUE 3226917.234 3265506.824 3530382.519 3419462.827 3136326.261 2414226.176 3812641.392 4050756.588 2850357.532 1.132109638 1.145648146 1.238575329 1.199661021 1.100327319 0.846990649 1.337601107 1.421139819 1 21.44271146 TCAYTNHTVLPEALER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TCAYTNHTVLPEALER 16 0 P11216;P11217;P11217-2 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form" 0 ;;; 132.47 3.89E-05 2319620000 926510 814170 460120 578720 890460 909500 820250 922280 819810 FALSE TRUE 804069.356 808821.6637 682635.571 710127.2212 872741.5882 944489.0535 740702.2812 725057.5992 722892.9957 1.112293743 1.118867756 0.944310673 0.982340713 1.207290143 1.306540607 1.02463613 1.002994362 1 19.46342259 2.025492863 24.9874912 1.005342078 1.108288195 0.188355033 0.101115348 404.3858512 396367.3547 0.045454556 0.030644267 106.0456511 -2.025492863 0.102946117 TCDISFSDPDDLLNFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TCDISFSDPDDLLNFK 16 0 P61081 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ; 280.21 4.39E-35 128369000 403310 345280 210668 251910 321360 309680 363430 420750 423090 FALSE TRUE 350011.5616 343011.8329 312547.7494 309110.0157 314965.5647 321593.59 328184.6145 330775.8868 373072.7822 0.938185733 0.919423365 0.837766153 0.828551506 0.844246967 0.862013005 0.879679865 0.88662562 1 18.50909759 1.161537366 2.543110172 1.05115414 0.870183192 0.567629533 0.03449338 0.569599458 3.38955488 0.246733184 0.009856158 14.50565573 -1.161537366 -0.180970948 TCEERPAEDGS(ph)DEEDPDSMEAPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 TCEERPAEDGSDEEDPDSMEAPTR 24 1 Q9H6Y2;D6RGJ8 Q9H6Y2 WDR55 WD repeat-containing protein 55 1 TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(0.999)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR 291.12 4.98E-62 8625230000 4561291 4382772 2617464 3412158 4277245 4188856 3911387 4582233 4647079 TRUE FALSE 3958504.838 4353981.282 3883278.345 4186940.625 4192136.193 4350004.001 3532061.291 3602358.132 4097706.615 0.966029345 1.062541 0.947671151 1.021776574 1.023044495 1.061570388 0.861960512 0.879115679 1 21.96638526 2.236835917 24.99984321 0.904333164 1.013769641 0.461740849 0.050602333 35.67252777 517063.2173 0.019317252 0.013793122 172.5185969 -2.236835917 0.109436477 LMLPDS(ph)PLVEEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 LMLPDSPLVEEGR 13 0 Q9P2F8;Q9P2F8-2 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 LMLPDS(1)PLVEEGR;LMLPDS(1)PLVEEGR;LMLPDS(1)PLVEEGR;LMLPDS(1)PLVEEGR;LMLPDS(1)PLVEEGR;LMLPDS(1)PLVEEGR;LMLPDS(1)PLVEEGR;LMLPDS(1)PLVEEGR 227.63 9.22E-12 1471055000 952821 1439476 1133739 1435792 1917340 2093800 1820300 2241250 2110830 TRUE FALSE 826903.2907 1430019.987 1682018.973 1761810.518 1879188.685 2174349.841 1643767.586 1761976.129 1861290.082 0.444263524 0.768295066 0.903684487 0.946553434 1.009616235 1.168195039 0.883133479 0.94664241 1 20.82787149 4.909324042 1.130312091 0.991084648 0.013822593 0.854807012 0.072245125 0.859965576 0.716366169 0.023016054 1.090542159 81156.63689 -4.909324042 -0.977262055 down TCFETFPDKVAIQLNDTHPALSIPELMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TCFETFPDKVAIQLNDTHPALSIPELMR 28 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 190.28 3.09E-18 251160000 361640 269760 114230 176430 293680 276020 364510 402980 97222 FALSE TRUE 313848.3577 267987.9288 169472.0101 216491.1281 287836.3426 286638.668 329159.8763 316805.863 85728.52592 3.660955958 3.126006495 1.976845026 2.525310283 3.357532857 3.343562308 3.839560669 3.695454455 1 16.38748772 3.229800266 24.9467262 3.202493522 2.783586044 0 0.891213149 670.1233114 1908296.504 0.271021298 0.311956198 1697.462802 -3.229800266 -0.418907479 TCFS(ph)PNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TCFSPNR 7 0 O00303 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 1 TCFS(1)PNR;TCFS(1)PNR;TCFS(1)PNR;TCFS(1)PNR 112.11 0.0067433 1518530000 2072910 2175560 1534460 1821140 2281850 2309760 2021940 2392930 2644660 TRUE FALSE 1798969.691 2161268.603 2276529.988 2234657.671 2236445.649 2398617.962 1825852.57 1881220.541 2332011.308 0.771424086 0.926783072 0.976208812 0.95825336 0.959020071 1.028561892 0.782951851 0.806694434 1 21.15314335 0.919975591 9.960154377 1.613891452 0.902021169 0.111768819 0.08747134 15300.19151 83709.74098 205949.5413 0.023195453 8.317170244 -0.919975591 -0.711870282 TCFVDCLIEQTHPEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TCFVDCLIEQTHPEIR 16 0 Q15029;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;; 183.23 2.02E-09 1206250000 216170 209733 125681 162093 233477 248800 214356 257282 272163 FALSE TRUE 187602.5868 208355.2501 186460.752 198898.6931 228831.2645 258371.497 193567.7881 202264.2465 239988.2002 0.781715879 0.868189561 0.776958 0.828785302 0.953510482 1.076600836 0.806572106 0.842809131 1 17.87260395 3.318213958 6.247068251 0.921399707 0.81352988 0.364313542 0.078948699 0.287369782 17.76021224 0.024533019 0.031636392 2080.721518 -3.318213958 -0.107869827 TCHSFIINEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TCHSFIINEK 10 0 Q99613-2;Q99613;B5ME19 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 ; 126.19 0.00038905 951050000 2223500 2029120 1180440 1536340 1939530 1753180 2239000 2433700 2048120 FALSE TRUE 1929658.841 2015790.577 1751304.732 1885189.478 1900937.148 1820625.969 2021862.125 1913272.194 1805993.587 1.068474913 1.116167074 0.969718135 1.043851701 1.052571372 1.008102123 1.119528961 1.059401433 1 20.78436134 TCNS(ph)PQNSTDSVSDIVPDSPFPGALGSDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TCNSPQNSTDSVSDIVPDSPFPGALGSDTR 30 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 T(0.167)CNS(0.658)PQNS(0.168)T(0.007)DSVSDIVPDSPFPGALGSDTR 135.44 2.58E-06 219640000 183130 152510 86995 109230 163390 135570 139730 180130 135180 TRUE FALSE 158928.9065 151508.1518 129066.073 134032.341 160138.8587 140785.4656 126179.0061 141610.6013 119199.1744 1.33330543 1.271050345 1.082776568 1.124440179 1.343456106 1.181094302 1.058556041 1.188016628 1 16.86301472 -1.999999998 0.043930595 2.64E-07 1.891623586 0.340621904 0.093022542 1986.378486 8.571060457 304.2547837 111.0667203 0.01 1.999999998 1.891623322 TCNSPQNSTDS(ph)VSDIVPDSPFPGALGSDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TCNSPQNSTDSVSDIVPDSPFPGALGSDTR 30 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 T(0.175)CNS(0.175)PQNS(0.214)T(0.214)DS(0.22)VS(0.002)DIVPDSPFPGALGSDTR 56.156 0.03395 30066000 34021 24838 12743 17152 26538 29535 23445 29599 26211 TRUE FALSE 29525.03865 24674.83754 18905.55742 21046.62375 26009.94572 30671.23056 21171.30751 23269.48419 23112.36544 1.277456378 1.067603297 0.817984532 0.910621797 1.125369266 1.327048529 0.916016475 1.006798038 1 14.4963773 3.634621889 0.013408683 4.20E-07 2.106031789 0.028317682 0.157601221 14714.27532 135.5191076 10432.57795 10849.15735 4311.435455 -3.634621889 2.106031369 TCNVLVALEQQS(ph)PDIAQGVHLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TCNVLVALEQQSPDIAQGVHLDR 23 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 1 TCNVLVALEQQS(1)PDIAQGVHLDR;TCNVLVALEQQS(1)PDIAQGVHLDR;TCNVLVALEQQS(1)PDIAQGVHLDR;TCNVLVALEQQS(1)PDIAQGVHLDR 165.31 8.56E-12 254342000 222201 198923 133709 170121 217899 232623 223986 239885 239190 TRUE FALSE 192836.5749 197616.2617 198371.1196 208749.5732 213563.2362 241572.1573 202263.8722 188587.4595 210913.2307 0.9142934 0.936955264 0.940534261 0.98974148 1.012564435 1.145362747 0.958990916 0.894147128 1 17.68629007 3.805256658 3.135215376 0.993500697 0.92772642 0.215471848 0.062181596 0.530225269 10.26783881 0.019857853 0.036721664 6386.407962 -3.805256658 -0.065774277 TCNVLVALEQQSPDIAQGVHLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TCNVLVALEQQSPDIAQGVHLDR 23 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ;; 223.97 1.38E-32 815269000 823020 711680 443279 606100 811280 886930 751900 935450 908150 FALSE TRUE 714255.8217 707004.9272 657650.2071 743724.2687 795137.1152 921050.771 678980.8537 735411.2972 800789.5416 0.891939498 0.882884816 0.821252243 0.928738739 0.992941433 1.150178322 0.847889262 0.918357769 1 19.61106361 3.503393942 5.308754803 0.971700681 0.867481224 0.315054978 0.077664638 0.264687476 21.35520826 0.023326991 0.033392309 3187.087167 -3.503393942 -0.104219457 TCS(ph)FGGFDLTNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TCSFGGFDLTNR 12 0 O94885;A0A1B0GWB9 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 T(0.175)CS(0.825)FGGFDLTNR;TCS(1)FGGFDLTNR;TCS(1)FGGFDLTNR;TCS(1)FGGFDLTNR;T(0.001)CS(0.999)FGGFDLTNR 278.84 6.24E-28 1104796000 1528190 1711000 1019431 1097685 1801070 1560560 1631210 1913820 1854730 TRUE FALSE 1326235.82 1699760.328 1512431.241 1346931.156 1765232.231 1620595.753 1473015.505 1504564.486 1635465.932 0.810922315 1.039312587 0.924770863 0.823576407 1.079345155 0.99090768 0.900670247 0.919960763 1 20.64127028 3.256492398 24.99999299 0.965723381 0.91141649 0.18260162 0.078454456 609.9060582 850308.5728 0.022829356 0.029412279 1805.063139 -3.256492398 -0.054306891 TCVQEITAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TCVQEITAHR 10 0 F5GYK2;Q9NRL3;Q9NRL3-3;M0R317;Q13033-2;Q13033 F5GYK2;Q13033-2 STRN4;STRN3 Striatin-4;Striatin-3 0 69.554 0.05663 297910000 232540 227150 266630 198360 226800 244680 195540 189970 208410 FALSE TRUE 201809.2498 225657.8367 395573.1598 243400.6697 222287.1237 254092.9979 176576.5609 149346.3938 183772.0072 1.098150109 1.227922795 2.1525213 1.324470867 1.209580975 1.38265344 0.960845798 0.812672159 1 17.4875575 2.304504988 1.54969679 0.864079914 1.446497471 0.362421642 0.291504828 0.419442791 2.047320634 0.196409297 0.103166902 201.6067124 -2.304504988 0.582417557 TCVQTLEGHAQNVSCASFHPELPIIITGSEDGTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TCVQTLEGHAQNVSCASFHPELPIIITGSEDGTVR 35 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 247.81 4.14E-48 116860000 26393 25540 7238.8 18022 28769 31188 33862 24408 25879 FALSE TRUE 22905.09818 25372.22606 10739.50789 22114.17055 28196.55319 32387.82254 30578.06845 19188.53914 22819.6141 1.003746079 1.111860435 0.470626183 0.969086088 1.235627958 1.419297557 1.339990603 0.840879213 1 14.47798677 3.440157416 7.376553773 1.148575433 0.85980551 0.275627342 0.228544556 0.30121672 47.92490574 0.071333941 0.092901718 2755.22719 -3.440157416 -0.288769923 TDALTSS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TDALTSSPGR 10 0 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 TDALTS(0.001)S(0.999)PGR 160.91 7.59E-06 479780000 1456300 1115800 921760 1137900 1312900 1339000 1223500 1589800 2724600 TRUE FALSE 1263846.265 1108470.236 1367526.219 1396277.587 1286775.859 1390512.196 1104845.158 1249833.642 2402500.892 0.526054442 0.461381821 0.569209453 0.581176719 0.535598494 0.578776974 0.459872944 0.520221926 1 21.19610554 1.237994623 24.99980159 1.000000538 0.527911348 0.923605128 0.042566448 3.526933768 155644.3315 0.061177075 0.010620409 17.29794943 -1.237994623 -0.47208919 TDCDIEDDRLAAMFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TDCDIEDDRLAAMFR 15 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;; 268.01 1.42E-25 682064000 803416 641646 427801 430701 735471 700852 666092 865514 550753 FALSE TRUE 697242.54 637430.9852 634686.9945 528498.2449 720836.566 727814.23 601494.5004 680430.5665 485643.6078 1.435708262 1.312548904 1.306898689 1.088242976 1.484291267 1.498659137 1.238551256 1.401090338 1 18.88953845 1.232507367 24.97903957 0.999999434 1.342127377 0.441570562 0.122132922 197.4031328 814510.8451 0.264471449 0.029614825 17.08076693 -1.232507367 0.342127943 TDDEVVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TDDEVVQR 8 0 P14625;Q96GW1;A0A1W2PRR1;F8VPC7 P14625 HSP90B1 Endoplasmin 0 ; 183.74 0.00051576 191979000 268340 266440 219263 279520 296110 328390 233067 261150 321200 FALSE TRUE 232878.1891 264689.7381 325299.3202 342989.2882 290217.9903 341023.3758 210464.1982 205305.1048 283228.1019 0.8222284 0.934546171 1.148541822 1.2110002 1.02467936 1.204059108 0.743090805 0.724875475 1 18.11160489 2.226651161 24.99979742 0.798969361 1.061542404 0.384138158 0.139044917 212.8822253 446869.087 0.05835055 0.039686684 168.5198878 -2.226651161 0.262573043 TDDEVVQREEEAIQLDGLNASQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TDDEVVQREEEAIQLDGLNASQIR 24 1 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 ;;;; 335.2 5.07E-87 1121130000 853705 879080 408296 458950 864192 1013670 834044 813984 160162 FALSE TRUE 740885.7212 873305.2656 605749.3113 563161.6121 846996.27 1052666.541 753158.5413 639919.856 141227.8308 5.24603201 6.183662671 4.289163883 3.98761072 5.997375057 7.453676338 5.332932871 4.531117219 1 17.10766489 1.243487946 2.51949572 1.26E-15 5.50003351 0.679487737 0.966522501 0.334936748 2.346200506 3.992674582 0.274069213 17.5181381 -1.243487946 5.50003351 TDDIPVWDQEFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TDDIPVWDQEFLK 13 0 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2;E5RGM3 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ;;; 206.58 1.41E-07 141600000 403866 334355 248676 281622 330481 263494 366745 433820 475007 FALSE TRUE 350494.0848 332158.6 368936.5454 345568.5794 323905.0747 273630.7847 331178.1263 341050.969 418852.2136 0.836796544 0.793020997 0.880827493 0.825037014 0.773315896 0.653287188 0.790680139 0.814251323 1 18.67608177 1.226754099 3.591402438 1.032038641 0.792331542 0.549819035 0.058313719 0.258455417 4.961230532 0.172060671 0.016012868 16.85598354 -1.226754099 -0.239707099 TDDVHAK ddPTM_MDA-MB-175_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 399530000 1719410 1394000 955560 1127360 817140 1143550 1675630 1910720 1991860 FALSE TRUE 1492185.612 1384842.722 1417672.012 1383344.319 800880.5127 1187543.108 1513127.661 1502127.397 1756384.58 0.849577951 0.788462127 0.807153529 0.787609009 0.455982432 0.676129318 0.861501335 0.85523832 1 20.74417734 1.635895784 1.644593344 0.991622429 0.729656776 0.361612422 0.113547213 0.555342381 2.610147685 0.200607573 0.036214279 43.24100543 -1.635895784 -0.261965653 TDDYLDQPCYETINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TDDYLDQPCYETINR 15 0 P50395;P50395-2;Q5SX87;Q5SX91 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;; 408.15 1.21E-132 2497360000 2252290 2044290 1289090 1466750 2091440 1920070 2135830 2423820 2228410 FALSE TRUE 1954644.17 2030860.924 1912498.236 1799798.005 2049824.436 1993936.335 1928697.535 1905504.955 1964969.908 0.994745091 1.033532837 0.97329645 0.915941765 1.043183627 1.01474141 0.981540494 0.969737474 1 20.90607579 2.797469949 0.002773887 1.17E-06 1.980244026 0.001506742 0.035986689 218826.7269 734.8953649 262640.7163 261984.1679 627.292289 -2.797469949 1.980242859 TDEAAFQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TDEAAFQK 8 0 P26447 P26447 S100A4 Protein S100-A4 0 143.61 0.0013928 346240000 499060 496760 431760 379330 378540 451370 484670 445150 546770 FALSE TRUE 433107.9565 493496.7509 640560.5802 465462.6742 371007.7946 468734.496 437666.778 349958.1367 482131.4735 0.898319194 1.023572984 1.328601461 0.965426859 0.769515817 0.97221302 0.90777475 0.725856236 1 18.87906709 3.480592657 24.8821335 0.864069881 1.089090186 0.338344761 0.132571683 137.9898626 989080.3518 0.037741267 0.04979162 3024.075689 -3.480592657 0.225020306 TDEFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TDEFPR 6 0 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 ;; 121.68 0.045473 903300000 1290710 1174860 682030 869100 1132910 1154450 1120740 1312780 1139590 FALSE TRUE 1120139.403 1167142.267 1011861.989 1066442.438 1110367.308 1198862.439 1012050.807 1032052.213 1004868.968 1.114711906 1.161487024 1.006959137 1.061275123 1.10498716 1.193053499 1.00714704 1.027051532 1 19.93857596 2.178723769 24.99987524 1.014482756 1.102824796 0.440654218 0.050625681 75.88336944 31703.27694 0.021369195 0.014407115 150.911998 -2.178723769 0.08834204 TDEGIAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TDEGIAYR 8 0 P32119 P32119 PRDX2 Peroxiredoxin-2 0 ;;;;; 157.21 0.00088539 12250750000 19905780 16853450 9429970 13164010 18054440 18363240 16683870 19010610 16946340 FALSE TRUE 17275180.74 16742738.58 13990335.03 16153099.67 17695191.97 19069685.73 15065870.86 14945338.99 14942962.99 1.156074652 1.12044302 0.936249059 1.080983717 1.184182279 1.276164957 1.008225133 1.000159005 1 23.83296291 2.048273158 24.99999831 1.001319945 1.119522655 0.3154696 0.085069987 149.4246527 77384.23983 0.037613727 0.025359159 111.756594 -2.048273158 0.11820271 TDFEEFFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TDFEEFFLR 9 0 B1AKV2;B1AKV6;B1AKV3;Q9NVA1-5;Q9NVA1-2;Q9NVA1 B1AKV2 UQCC1 Ubiquinol-cytochrome-c reductase complex assembly factor 1 0 ;;; 176.75 0.00012311 107110000 157115 143587 99278 175185 165488 174887 127261 156209 211867 FALSE TRUE 136351.8547 142643.7675 147289.1729 214963.4318 162195.1126 181615.0161 114919.2478 122804.921 186820.3246 0.729855571 0.763534524 0.788400155 1.150642641 0.868187725 0.972137354 0.61513247 0.657342402 1 17.51129189 2.244321141 24.99785388 0.730695571 0.881319944 0.111211035 0.155515052 252.5193219 1095815.371 0.060733744 0.045734465 175.5177897 -2.244321141 0.150624373 TDFEMVHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TDFEMVHLR 9 0 Q15042-4;Q15042;Q15042-3 Q15042-4 RAB3GAP1 Rab3 GTPase-activating protein catalytic subunit 0 ; 158.87 0.00023969 271780000 481210 525670 321780 358860 587530 572410 502400 528660 646640 FALSE TRUE 417616.8793 522216.8392 477393.8843 440344.6478 575839.3025 594430.9831 453677.3253 415610.173 570194.9559 0.732410687 0.915856645 0.837246769 0.772270332 1.009898977 1.042504808 0.795652997 0.728891353 1 19.12109575 4.749748505 23.25387296 0.874518574 0.732410461 0.162589634 0.10712019 1373.163631 2853951.356 0.027837668 0.385117533 56201.57745 -4.749748505 -0.142108113 TDFKEEPEPGFKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TDFKEEPEPGFKR 13 2 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A0U1RQX5;A0A0U1RRC8 P47897 QARS Glutamine--tRNA ligase 0 108.17 0.00069594 115220000 631090 508990 346860 310480 430300 317390 704460 743610 255280 FALSE TRUE 547689.8575 505646.4112 514602.6562 380979.2294 421737.8719 329600.1987 636141.5776 584594.7883 225101.0892 2.433083995 2.24630815 2.286095807 1.692480613 1.873548784 1.464231914 2.826026208 2.59703225 1 17.78021351 3.962449698 23.56667944 2.015689767 2.321322949 0.099688994 0.524205395 862.9131122 541568.0174 0.146525042 0.253905704 9171.696982 -3.962449698 0.305633182 TDGALLVNAMFFKPHWDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TDGALLVNAMFFKPHWDEK 19 1 P50454;E9PR70;E9PPV6;E9PK86;E9PMI5 P50454 SERPINH1 Serpin H1 0 ;; 227.95 6.91E-20 3081200000 5370760 4474280 3343470 3612917 4749280 4573580 5854400 5998030 3183530 FALSE TRUE 4661000.458 4444888.16 4960383.275 4433285.025 4654778.62 4749528.582 5286641.189 4715397.961 2807176.71 1.660387264 1.583401623 1.767036346 1.579268241 1.65817086 1.69192362 1.883259137 1.679765276 1 21.42068845 1.239480162 8.5378457 0.993776917 1.692128875 0.859251594 0.087493842 0.029949136 24.86655325 0.123101961 0.02188245 17.35721975 -1.239480162 0.698351958 TDGCHAYLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TDGCHAYLSK 10 0 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 0 ;;;;; 129.89 0.00029116 5684770000 20194500 19869500 10605400 14832900 20913400 17275200 22256400 25180000 23953000 FALSE TRUE 17525745.66 19738975.95 15734206.91 18200936.65 20497264.26 17939788.12 20097977.75 19795452.95 21121303.63 0.829766286 0.934552918 0.744944876 0.861733583 0.970454505 0.849369359 0.951550061 0.937226854 1 24.33219555 0.617219456 0.33970063 1.196123067 0.834026792 0.401868018 0.0594373 14.84048348 1.146028117 2.401451433 0.107534418 4.142089287 -0.617219456 -0.362096274 AEELSPAALS(ph)PSLEPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 AEELSPAALSPSLEPIR 17 0 A0A2R8YF49;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 AEELSPAALS(0.989)PS(0.011)LEPIR;AEELSPAALS(0.963)PS(0.037)LEPIR;AEELSPAALS(0.993)PS(0.007)LEPIR;AEELSPAALS(0.997)PS(0.003)LEPIR;AEELSPAALS(0.999)PS(0.001)LEPIR;AEELSPAALS(0.771)PS(0.229)LEPIR 397.84 2.22E-122 1193259000 775553 1208007 927979 1224137 1601066 1616050 1607024 1905150 1762470 TRUE FALSE 673061.706 1200071.522 1376752.748 1502096.016 1569207.919 1678220.489 1451175.06 1497748.498 1554112.804 0.433084204 0.772190744 0.885876974 0.966529593 1.009713011 1.079857578 0.933764303 0.963732165 1 20.56765979 4.909457081 1.116001125 0.991942325 2.18E-20 0.953317394 0.039330035 0.47673054 0.38662032 0.012853239 0.606677157 81181.50184 -4.909457081 -0.991942325 down TDGS(ph)IS(ph)GDRQPVTVADYISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TDGSISGDRQPVTVADYISR 20 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 2 T(0.009)DGS(0.991)IS(1)GDRQPVTVADYISR;T(0.018)DGS(0.982)IS(1)GDRQPVTVADYISR;T(0.01)DGS(0.99)IS(0.918)GDRQPVT(0.08)VADYIS(0.002)R 130.78 8.83E-06 1254745000 1554590 1058140 777215 868520 1336770 1292660 1194430 1343470 1441350 TRUE FALSE 1349146.993 1051189.009 1153078.774 1065730.74 1310170.892 1342389.467 1078594.362 1056179.395 1270955.245 1.061522031 0.827085779 0.907253641 0.838527355 1.030855254 1.056205143 0.848648579 0.831012264 1 20.2774818 1.206237397 0.006610897 8.32E-05 1.821477026 0 0.097054541 207301.508 376.3013107 53260.4024 50445.12775 16.07819889 -1.206237397 1.821393862 TDGS(ph)ISGDRQPVTVADYISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TDGSISGDRQPVTVADYISR 20 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 1 TDGS(1)ISGDRQPVTVADYISR;T(0.001)DGS(0.999)IS(0.001)GDRQPVTVADYISR;TDGS(0.999)IS(0.001)GDRQPVTVADYISR 248.47 1.80E-30 1001690000 897560 646910 421254 432221 760960 733740 682140 775210 696330 TRUE FALSE 778945.1719 642660.4056 624973.8434 530363.3841 745818.3848 761967.4526 615986.1678 609437.3742 614010.6607 1.268618319 1.046660012 1.017855036 0.863769016 1.214666833 1.24096779 1.003217382 0.99255178 1 19.22790418 2.045617561 24.9983722 0.996385051 1.097697858 0.156389967 0.118861274 258.8078356 141825.3103 0.050792364 0.034244189 111.075317 -2.045617561 0.101312807 TDHGAEIVYKS(ph)PVVS(ph)GDT(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TDHGAEIVYKSPVVSGDTSPR 21 1 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 3 TDHGAEIVY(0.008)KS(0.992)PVVS(0.969)GDT(0.547)S(0.485)PR 89.954 0.002199 168750000 75186 52252 34166 37581 52653 44349 55384 58845 65746 TRUE FALSE 65249.9796 51908.75317 50688.79188 46114.34044 51605.30831 46055.13473 50012.8682 46261.45468 57973.58278 1.125512285 0.895386324 0.874342924 0.795437132 0.890152132 0.794415879 0.862683757 0.797974741 1 15.82310803 4.814311014 2.199272151 0.850240527 1.234269743 0.646667673 0.061089548 0.482564396 2.252947223 0.014596678 0.388761669 65209.52157 -4.814311014 0.384029216 TDIELEIYGMEGIPEKDMDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 170.53 7.38E-12 177632000 314911 255711 194240 262805 223713 176917 269361 337324 371870 FALSE TRUE 273294.7135 254031.2176 288175.1137 322478.892 219261.549 183723.1115 243238.4117 265189.8877 327907.9522 0.833449484 0.774702827 0.878829293 0.983443341 0.668667983 0.560288673 0.741788694 0.808732712 1 18.32293136 4.767948921 19.23248715 0.796097046 0.833450631 0.003710231 0.132886837 3660.122992 2394362.68 0.034170748 1.858791723 58606.92313 -4.767948921 0.037353585 TDIIDRLEQELLCASNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TDIIDRLEQELLCASNR 17 1 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;A0A0A0MRE9;A0A6I8PUA5;A0A6I8PUD8;A0A2R8Y590 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 0 ; 174.23 1.26E-09 28876000 23328 21907.8 12892.7 11956.8 21782 21678 22915 28325 10677.6 FALSE TRUE 20245.14569 21763.88622 19127.65284 14671.77419 21348.58082 22511.96669 20692.70683 22267.91918 9415.306292 2.15023761 2.311543092 2.031548656 1.558289633 2.267433491 2.390996744 2.197773093 2.365076449 1 13.20079231 4.222035117 22.71472082 2.030693609 2.230890239 0.047033026 0.424800201 292.0487975 401433.5104 0.107890181 0.226009956 16673.8203 -4.222035117 0.20019663 TDKVDFDSAEDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TDKVDFDSAEDTR 13 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 0 93.478 0.0051031 298580000 394100 379340 226960 269940 381940 298180 418160 486460 414980 FALSE TRUE 342018.6865 376848.0906 336718.6151 331234.0028 374340.1413 309651.1775 377606.9076 382434.3146 365921.5371 0.934677661 1.029860373 0.920193487 0.905204994 1.023006583 0.846222881 1.031934088 1.045126553 1 18.48117481 TDKVFEVMLATDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 87.932 0.0074243 216080000 378050 350550 169900 166910 261310 270730 393610 413100 218010 FALSE TRUE 328089.7346 348247.214 252064.2083 204809.4666 256110.4422 281145.1583 355437.7628 324761.7797 192237.1062 1.706693058 1.811550439 1.311215162 1.065400279 1.332263304 1.462491628 1.848955022 1.689381339 1 17.55252731 4.245410424 24.99987621 1.428077184 1.75912187 0.256581135 0.25597779 264.9222796 966867.3868 0.070824206 0.178745716 17595.857 -4.245410424 0.331044686 TDLADKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TDLADKR 7 1 P20340-2;P20340;P20340-4;J3KR73;Q9NRW1-2;Q9NRW1;C9JU14;Q53S08;Q9H0N0 P20340-2 RAB6A;RAB6B;RAB6C Ras-related protein Rab-6A;Ras-related protein Rab-6B;Ras-related protein Rab-6C 0 ; 103.92 0.013257 652310000 1524430 1142780 813940 1003140 1209540 1242630 1339430 1876410 1699660 FALSE TRUE 1322972.713 1135273.003 1207564.106 1230918.269 1185472.52 1290434.78 1209532.285 1475154.324 1498728.131 0.882730287 0.757490955 0.805725923 0.821308577 0.7909857 0.861019923 0.807039155 0.984270791 1 20.51530727 1.700422008 4.542833155 0.996955437 0.815590991 0.811005197 0.034894364 0.059017804 2.869442015 0.021748136 0.008596976 50.1674479 -1.700422008 -0.181364447 TDLCDHALHISHDEL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TDLCDHALHISHDEL 15 0 Q9Y2B0;H0YI18 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;;; 249.75 7.35E-19 938150000 748300 697600 187202 499920 879460 1059590 752350 676480 698570 FALSE TRUE 649410.259 693017.4197 277733.5134 613434.4768 861960.4666 1100353.113 679387.2128 531820.0164 615985.8504 1.05426165 1.125054121 0.45087645 0.995858065 1.399318614 1.786328553 1.102926654 0.863364014 1 19.23253769 3.4677253 23.55520744 1.202278253 0.871863803 0.226170511 0.301881952 175.0986649 438959.8824 0.096572915 0.124890312 2935.792119 -3.4677253 -0.33041445 TDLEKDIISDTSGDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TDLEKDIISDTSGDFR 16 1 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;A6NMY6;H0YL33;H0YNP5;H0YN28;H0YKS4;H0YNA0;H0YN52 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 ; 185.25 1.54E-09 409810000 1794710 1297340 970690 1458640 1525420 1221900 978140 2070600 1221770 FALSE TRUE 1557534.526 1288817.688 1440118.931 1789846.506 1495067.126 1268907.284 883280.1334 1627818.303 1077333.742 1.445730756 1.196303093 1.336743549 1.661366794 1.387747425 1.177821908 0.81987605 1.510969386 1 20.03903381 2.73658512 5.931360331 1.157370658 1.405132204 0.308069744 0.205372744 0.230047449 35.74706694 0.069929208 0.065374726 545.2367498 -2.73658512 0.247761546 TDLEKDIISDTSGDFRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 132.13 1.39E-05 258800000 521370 345020 252040 348320 401030 287280 272260 617540 159220 FALSE TRUE 452469.6335 342753.5409 373927.387 427411.3797 393050.2876 298331.8475 245856.2671 485483.8767 140397.193 3.222782621 2.441313345 2.663353726 3.044301461 2.799559445 2.124913192 1.751148024 3.457931504 1 17.09915457 2.750335127 21.7924336 2.267095594 2.81460582 0.232085437 0.640473653 262.5960885 486014.3777 0.203474872 0.201298437 562.7754276 -2.750335127 0.547510226 TDLFYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TDLFYER 7 0 Q7RTV0 Q7RTV0 PHF5A PHD finger-like domain-containing protein 5A 0 ;; 172.03 0.0021301 1321890000 1488200 1541670 860360 987730 1524410 1523600 1426740 1657530 1533550 FALSE TRUE 1291530.599 1531542.668 1276432.974 1212009.193 1494077.223 1582213.878 1288374.974 1303080.108 1352255.466 0.955093643 1.132583825 0.94392887 0.896287147 1.104877932 1.17005545 0.952760042 0.963634565 1 20.3669363 TDLLVNDNPDPAPLS(ph)PELQDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TDLLVNDNPDPAPLSPELQDFK 22 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 TDLLVNDNPDPAPLS(1)PELQDFK;TDLLVNDNPDPAPLS(1)PELQDFK 189.78 1.30E-17 120108000 136627 132944 114328 163176 145248 103781 146988 193464 479190 TRUE FALSE 118571.3958 132070.6821 169617.4032 200227.6048 142357.849 107773.5222 132733.1264 152093.2291 422540.7041 0.280615322 0.312563218 0.401422636 0.473865838 0.336909196 0.255060687 0.314130982 0.359949296 1 18.6887308 1.238433038 6.523108798 1.018315733 0.342250983 0.919090597 0.061396885 0.033653787 6.758960219 0.100951544 0.016450168 17.31542031 -1.238433038 -0.67606475 TDLQGSAS(ph)PSKVEGVHTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TDLQGSASPSKVEGVHTPR 19 1 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 TDLQGSAS(0.996)PS(0.004)KVEGVHTPR;TDLQGS(0.001)AS(0.996)PS(0.003)KVEGVHTPR 209.64 1.29E-16 835060000 653020 586920 361770 438370 627280 497080 687750 809740 695040 TRUE FALSE 566721.7525 583064.4839 536723.182 537908.6086 614798.3553 516202.9893 621052.1109 636583.4024 612873.163 0.924696637 0.951362401 0.8757492 0.877683412 1.003141257 0.842267243 1.013345254 1.038687025 1 19.22522901 2.125563414 8.443905251 1.023104854 0.915252871 0.546242752 0.044982947 0.172615832 12.11146027 0.017381931 0.011705662 133.5252543 -2.125563414 -0.107851983 TDMDNQIVVSDYAQMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TDMDNQIVVSDYAQMDR 17 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ; 297.97 7.47E-46 166537000 155253 140031 78110 108851 144469 141222 151373 150971 138208 FALSE TRUE 134735.9227 139111.1271 115884.2573 133567.2832 141594.3495 146654.9017 136692.8698 118687.0265 121869.2077 1.105578064 1.141478884 0.95089038 1.095988772 1.16185501 1.203379463 1.121635829 0.973888554 1 16.89497413 1.736632448 7.045386866 0.988543526 1.111435152 0.3845712 0.065395827 0.135212357 20.16896991 0.040587872 0.018123772 54.52961714 -1.736632448 0.122891626 TDNAGDQHGGGGGGGGGAGAAGGGGGGENYDDPHKTPASPVVHIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TDNAGDQHGGGGGGGGGAGAAGGGGGGENYDDPHKTPASPVVHIR 45 1 P14866 P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ; 143.39 1.37E-14 749780000 776140 555370 264260 496830 638900 502960 683830 799440 697510 FALSE TRUE 673571.1325 551721.7379 392057.0199 609642.8451 626187.14 522309.1967 617512.2719 628485.9772 615051.1624 1.095146508 0.897033892 0.63743806 0.99120672 1.018105774 0.8492126 1.004001471 1.02184341 1 19.2303469 2.16162205 0.982543214 1.030674536 0.900519971 0.087091048 0.122729717 1.604321977 2.828437459 0.16769685 0.052767248 145.0848448 -2.16162205 -0.130154565 TDPTTLTDEEINR ddPTM_MDA-MB-175_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 81.017 0.023709 0 89087 87670 68534 58671 72192 72980 99996 93088 104050 FALSE TRUE 77313.92723 87094.09 101677.2716 71993.14728 70755.52044 75787.58782 90298.40331 73181.85561 91749.32753 0.842664784 0.949261344 1.108207268 0.784672206 0.771182987 0.82602881 0.984185996 0.797628251 1 16.48540996 3.711135189 24.99883872 0.85661068 0.964966242 0.200324674 0.099691456 1116.771358 1017959.895 0.02712101 0.040238291 5142.036904 -3.711135189 0.108355563 TDPVPEEGEDVAATISATETLSEEEQEELRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TDPVPEEGEDVAATISATETLSEEEQEELRR 31 1 H0YC42;P55327-8;H0YC44;P55327-2;P55327-4;P55327-3;E5RFR7 H0YC42;P55327-2 TPD52 0 ; 182.89 4.50E-18 170312000 11167.1 7710.3 2387.6 4762.4 8123.2 8364.5 9035.6 6033.6 5080.1 FALSE TRUE 9691.339441 7659.650532 3542.251346 5843.775709 7961.564213 8686.287728 8159.328903 4743.361594 4479.536365 2.163469308 1.709920382 0.79076294 1.304549228 1.777318803 1.939104188 1.821467276 1.058895655 1 12.1291337 1.651345908 5.91459353 1.014220479 1.61572164 0.315265363 0.374420162 0.177790684 12.93048405 0.258359128 0.104389611 44.80700425 -1.651345908 0.601501161 TDQDEEHCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TDQDEEHCR 9 0 Q16186;A0A087WX59;A0A087WUX6 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 0 ;;; 157.49 6.84E-05 818678000 1172999 1061824 659345 699112 783294 962716 1009556 1101501 1243090 FALSE TRUE 1017984.21 1054848.808 978206.4474 857856.0649 767707.9819 999752.3075 911649.4145 865953.583 1096133.316 0.928704743 0.962336235 0.892415578 0.782620191 0.700378294 0.912071819 0.831695744 0.790007538 1 20.06399184 3.985728634 4.813152498 0.828719682 0.943109427 0.24285991 0.079601121 0.23811628 15.15586971 0.020767069 0.040731117 9676.730238 -3.985728634 0.114389745 TDQVIQSLIALVNDPQPEHPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TDQVIQSLIALVNDPQPEHPLR 22 0 P68036-2;P68036;P68036-3;A0A1B0GUS4 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 ; 227.6 4.31E-26 2652400000 538980 513220 304701 379798 523187 473368 498400 556290 705730 FALSE TRUE 467752.4274 509848.624 452055.4228 466036.9407 512776.6023 491578.7733 450065.2447 437331.7126 622299.4034 0.751651737 0.819297948 0.726427537 0.748895047 0.824003043 0.789939329 0.723229433 0.702767366 1 19.24724934 1.230194441 24.99999028 1.000000446 0.759568512 0.778576655 0.040088292 160.0605886 478258.7492 0.118427655 0.010603241 16.99004154 -1.230194441 -0.240431935 TDRDKYNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TDRDKYNR 8 2 P61077-3;P61077-2;P61077;A0A087WY85;H9KV45;D6RAH7 P61077-3 UBE2D3 Ubiquitin-conjugating enzyme E2 D3 0 ; 115.86 0.00134 152671000 380440 342360 136512 159070 309190 305780 393370 418630 135880 FALSE TRUE 330163.8901 340111.0146 202529.6598 195189.2747 303037.7239 317543.5545 355221.0379 329109.2323 119816.4212 2.755581303 2.838601013 1.690333076 1.629069478 2.52918357 2.650250703 2.9647108 2.746779022 1 16.87046612 TDS(ph)IGEK ddPTM_MDA-MB-175_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 124.95 0.0042969 746350000 2082510 1583700 1266630 1259860 1301660 1274130 2685900 2663900 2451940 TRUE FALSE 1807301.027 1573296.57 1879176.505 1545930.469 1275759.513 1323146.606 2425421.831 2094245.715 2162074.446 0.835910637 0.727679185 0.869154394 0.715021849 0.590062713 0.611980132 1.121803107 0.968627939 1 21.04398477 2.237101796 24.99996638 1.021147063 0.725061123 0.70588662 0.092800408 22.46538787 384976.768 0.038748146 0.027722297 172.6242466 -2.237101796 -0.296085939 TDS(ph)PDMHEDT ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 TDSPDMHEDT 10 0 Q9BW61 Q9BW61 DDA1 DET1- and DDB1-associated protein 1 1 TDS(1)PDMHEDT;TDS(1)PDMHEDT;TDS(1)PDMHEDT;T(0.018)DS(0.982)PDMHEDT;T(0.019)DS(0.981)PDMHEDT;TDS(1)PDMHEDT;T(0.044)DS(0.956)PDMHEDT;T(0.001)DS(0.999)PDMHEDT;TDS(1)PDMHEDT;TDS(1)PDMHEDT 223.87 4.44E-09 6506949000 7375825 6507840 4332616 4762310 7015132 6810986 7166764 7448734 7467944 TRUE FALSE 6401091.038 6465089.571 6427883.589 5843665.273 6875544.598 7073009.039 6471732.33 5855880.2 6585092.168 0.972057926 0.981776626 0.976126594 0.887408274 1.044107573 1.07409416 0.982785383 0.88926321 1 22.6507722 1.965135091 23.66119979 0.936512528 0.989708828 0.095041465 0.055143872 618.0581497 419445.2616 0.026230591 0.015147909 92.28584462 -1.965135091 0.053196301 TDS(ph)REDEIS(ph)PPPPNPVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TDSREDEISPPPPNPVVK 18 1 P10644;P10644-2;K7EPB2;K7EIE5;K7EID3;K7EJ40;K7EK41;K7EMU2;K7EMZ6 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 2 T(0.027)DS(0.973)REDEIS(1)PPPPNPVVK 128.07 1.37E-05 103270000 180250 113540 87255 105020 125780 102530 136380 166860 154160 TRUE FALSE 156429.5058 112794.1483 129451.8099 128866.3961 123277.2241 106474.3954 123153.8886 131178.2875 135935.3804 1.150763733 0.829762994 0.952304025 0.947997466 0.906881076 0.783272134 0.905973766 0.965004748 1 17.05256148 4.75155425 24.7001857 0.913609871 1.150763913 0.579637494 0.064036665 1445.38432 2747538.352 0.01617841 0.294466324 56435.74336 -4.75155425 0.237154042 TDS(ph)TSDGRPAWMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 TDSTSDGRPAWMR 13 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 1 T(0.001)DS(0.978)T(0.021)SDGRPAWMR;TDS(0.972)T(0.027)S(0.001)DGRPAWMR;TDS(0.972)T(0.019)S(0.009)DGRPAWMR;TDS(0.898)T(0.097)S(0.005)DGRPAWMR;T(0.001)DS(0.981)T(0.018)S(0.001)DGRPAWMR;T(0.001)DS(0.904)T(0.086)S(0.009)DGRPAWMR;T(0.004)DS(0.971)T(0.022)S(0.003)DGRPAWMR;T(0.001)DS(0.47)T(0.47)S(0.059)DGRPAWMR 185.74 5.09E-06 17382610000 5356840 5014800 3585790 3755170 6429460 5659670 6057600 6517950 6661360 TRUE FALSE 4648920.021 4981857.449 5319890.038 4607838.743 6301526.325 5877401.167 5470134.884 5124137.115 5873861.609 0.791458895 0.848140079 0.905688692 0.784464982 1.072808102 1.000602595 0.931267239 0.872362588 1 22.48587784 3.256581516 24.99910617 0.960476606 0.838791909 0.563750989 0.061610131 227.9334427 316193.9345 0.019154757 0.024677473 1805.43358 -3.256581516 -0.121684696 TDSEKPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TDSEKPFR 8 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 86.136 0.014818 577980000 1177600 959560 578950 698000 1063000 920890 1053200 1322600 1129300 FALSE TRUE 1021977.176 953256.5872 858932.1565 856491.5683 1041848.38 956317.2342 951060.8261 1039772.282 995795.4405 1.026292283 0.957281534 0.862558836 0.860107943 1.046247389 0.960355104 0.955076502 1.044162526 1 19.92548988 3.229851925 24.99999737 1.001045032 0.924183007 0.313024746 0.054870785 238.5637891 684842.7014 0.017399309 0.020028687 1697.664726 -3.229851925 -0.076862025 TDSHFDWWEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TDSHFDWWEGK 11 0 H7C499;Q96HL8-4;Q96HL8-3;Q96HL8-2;Q96HL8 H7C499 SH3YL1 SH3 domain-containing YSC84-like protein 1 0 117.23 0.00088222 159370000 464330 401800 252340 324760 413600 352680 460270 539410 490590 FALSE TRUE 402967.614 399160.5493 374372.468 398501.7216 405370.1692 366247.8278 415633.0862 424061.3692 432593.0091 0.931516704 0.922716135 0.865414975 0.921193161 0.937070551 0.846633718 0.960794737 0.980277906 1 18.72265083 2.016435955 23.87566593 0.983272069 0.905310762 0.615100884 0.029009752 87.04582622 126446.1946 0.011555964 0.007788091 103.8570433 -2.016435955 -0.077961308 TDSREDEIS(ph)PPPPNPVVK ddPTM_MDA-MB-175_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 TDS(0.005)REDEIS(0.995)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDS(0.001)REDEIS(0.999)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDS(0.01)REDEIS(0.99)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK 204.65 6.36E-16 24857120000 10141970 7395580 5041280 5951730 7682610 6637820 9319080 10560600 7435800 TRUE FALSE 8801682.968 7346997.948 7479259.87 7303161.263 7529741.092 6893181.231 8415317.056 8302297.873 6556748.195 1.342385388 1.120524646 1.140696523 1.11383891 1.148395648 1.051310959 1.283458935 1.266221857 1 22.64454906 4.744896625 24.34953425 1.153697734 1.342385509 0.343738281 0.085953489 655.5051371 2519030.376 0.021829363 0.196078475 55577.19507 -4.744896625 0.188687775 TDSS(ph)PNQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TDSSPNQAR 9 0 A6NLN1;P26599;P26599-2;P26599-3;K7ES59;A0A087WU68 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 1 TDS(0.016)S(0.984)PNQAR;TDS(0.025)S(0.975)PNQAR;TDS(0.017)S(0.983)PNQAR;TDS(0.084)S(0.916)PNQAR;TDS(0.002)S(0.998)PNQAR 219.93 4.98E-07 5507531000 3298408 3136459 1954595 2302557 1923505 3026547 2984195 3390984 3688844 TRUE FALSE 2862515.026 3115855.394 2899843.68 2825387.759 1885231.014 3142980.222 2694788.228 2665848.46 3252753.065 0.880028385 0.957913291 0.891504403 0.868614279 0.579580121 0.966252328 0.82846382 0.819566812 1 21.63322987 3.720387243 4.009851715 0.833491089 0.916563032 0.070425734 0.112671383 0.525447752 19.7519436 0.030578022 0.050092463 5252.756191 -3.720387243 0.083071944 TDST(ph)SDGRPAWMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TDSTSDGRPAWMR 13 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 1 T(0.001)DS(0.097)T(0.805)S(0.097)DGRPAWMR 116.63 0.0036288 929130000 1592700 1625600 1154000 1256200 2129700 1786100 1920400 2243300 2279000 TRUE FALSE 1382220.66 1614921.327 1712078.26 1541439.41 2087323.137 1854812.423 1734159.904 1763587.752 2009579.216 0.687815961 0.803611678 0.851958582 0.767045856 1.038686666 0.922985473 0.862946775 0.877590561 1 20.93846202 5.413097829 0.576170051 0.9231732 0.301762825 0.549093109 0.069625793 6.60077595 0.964033185 0.038040624 3.232179759 258879.6003 -5.413097829 -0.621410375 TDSTSDGRPAWMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TDSTSDGRPAWMR 13 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 184.31 8.76E-06 1436520000 1948510 1772970 1026850 1151630 1940630 1917250 1716370 1949730 1791840 FALSE TRUE 1691009.467 1761323.243 1523438.095 1413125.193 1902015.26 1991007.848 1549916.702 1532795.412 1580010.716 1.070251897 1.114753986 0.964194786 0.894376967 1.203798962 1.260123003 0.980953284 0.970117099 1 20.59150291 TDT(ph)SPVLETAGTVAAMAATPSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TDTSPVLETAGTVAAMAATPSAR 23 0 Q8WWH5 Q8WWH5 TRUB1 Probable tRNA pseudouridine synthase 1 1 T(0.011)DT(0.803)S(0.186)PVLETAGTVAAMAATPSAR 92.098 0.055805 76679000 51775 50531 39953 41605 60776 51094 52023 61567 58712 TRUE FALSE 44932.80257 50199.05853 59274.40443 51052.05114 59566.67651 53059.61924 46977.81747 48401.37616 51771.13424 0.867912269 0.969634127 1.14493154 0.986110347 1.150577003 1.024888097 0.907413333 0.934910484 1 15.65986031 2.290327543 9.187548966 0.943237125 1.031235841 0.150215121 0.084514922 0.544041754 90.8523317 0.031876782 0.024599599 195.1315719 -2.290327543 0.087998716 TDTAVQATGS(ph)VPSTPIAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TDTAVQATGSVPSTPIAHR 19 0 Q9NXR1;Q9NXR1-1;I3L533;I3L2R9;I3L2R3;I3L522 Q9NXR1 NDE1 Nuclear distribution protein nudE homolog 1 1 T(0.003)DT(0.003)AVQAT(0.189)GS(0.783)VPS(0.01)T(0.012)PIAHR 57.655 0.022107 0 150090 139520 112690 128830 149650 106670 164800 177830 177400 TRUE FALSE 130255.2262 138603.4839 167187.2609 158082.8205 146672.2578 110773.6639 148817.7214 139802.4384 156427.9741 0.832684991 0.886053052 1.068781092 1.010578967 0.937634452 0.708144848 0.951349797 0.893717631 1 17.25513901 2.982449582 24.96257825 0.887040835 0.956083884 0.082589317 0.097037077 1815.546007 2582318.44 0.031682967 0.03235901 960.3943179 -2.982449582 0.069043049 TDTGEPMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TDTGEPMGR 9 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;; 151.04 0.00019499 2250690000 3034090 2824870 1608710 2192710 2761580 3004070 2740290 3204190 2998120 FALSE TRUE 2633127.319 2806313.243 2386687.537 2690598.319 2706629.961 3119638.517 2474537.098 2518998.904 2643685.669 0.996006201 1.061515473 0.902787939 1.017745169 1.023809295 1.180033827 0.936017896 0.95283601 1 21.33411922 TDTS(ph)PVLETAGTVAAMAATPSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TDTSPVLETAGTVAAMAATPSAR 23 0 Q8WWH5 Q8WWH5 TRUB1 Probable tRNA pseudouridine synthase 1 1 T(0.024)DT(0.12)S(0.856)PVLETAGTVAAMAATPSAR 167.05 1.18E-11 45564000 138300 127530 85956 111220 150320 141520 139750 153530 143940 TRUE FALSE 120023.3046 126692.247 127524.6091 136474.2009 147328.9261 146964.366 126197.0665 120698.8043 126923.5772 0.94563443 0.998177406 1.004735384 1.075247042 1.160768782 1.157896502 0.994275999 0.950956528 1 16.95360056 6.844108317 13.22830207 1.031352609 0.404757309 0 0.076497271 0 0 0.019361771 0 6984065.718 -6.844108317 -0.6265953 TDVKDDLSDPPVAS(ph)SCISEKSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TDVKDDLSDPPVASSCISEKSPR 23 2 Q8IX90-3;Q8IX90 Q8IX90-3 SKA3 Spindle and kinetochore-associated protein 3 1 TDVKDDLSDPPVAS(0.25)S(0.25)CIS(0.25)EKS(0.25)PR 73.805 0.010002 51428000 87922 74424 59213 62733 67049 51708 98911 117670 81764 TRUE FALSE 76302.88493 73935.10384 87848.60486 76977.48646 65714.85608 53697.24022 89318.62644 92507.18621 72097.95307 1.058322486 1.025481317 1.218461844 1.067679222 0.911466322 0.744781758 1.238851072 1.283076457 1 16.13767068 TDVSNFDEEFTGEAPT(ph)LSPPRDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TDVSNFDEEFTGEAPTLSPPRDAR 24 1 Q16512;Q16512-2 Q16512 PKN1 Serine/threonine-protein kinase N1 1 TDVSNFDEEFTGEAPT(0.575)LS(0.425)PPRDAR 80.067 0.02893 156920000 81402 73011 21617 19877 66824 71497 70628 79106 9816.4 TRUE FALSE 70644.51945 72531.38593 32071.0535 24390.37665 65494.33314 74247.53585 63778.50743 62189.7975 8655.916375 8.161414274 8.37940003 3.70510205 2.817769442 7.56642397 8.577663258 7.368198197 7.184657847 1 13.07947085 4.277790522 24.95504305 5.80840091 8.270415029 0.181434097 2.394408708 311.4531939 198117.6701 0.620230361 1.640916478 18957.91281 -4.277790522 2.46201412 TDVSNFDEEFTGEAPTLS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TDVSNFDEEFTGEAPTLSPPR 21 0 Q16512;Q16512-2 Q16512 PKN1 Serine/threonine-protein kinase N1 1 TDVSNFDEEFTGEAPTLS(1)PPR;TDVSNFDEEFTGEAPTLS(1)PPR 191.09 1.01E-17 157987000 202332 160122 104729 131549 164777 161902 159032 184564 192032 TRUE FALSE 175593.3136 159070.148 155376.2947 161419.2111 161498.2601 168130.4747 143609.1011 145096.4249 169330.1957 1.036987602 0.939408044 0.917593546 0.953280721 0.953747555 0.992914902 0.848100957 0.856884528 1 17.36947974 2.243611272 24.9998452 0.89010152 0.961173954 0.240709239 0.051844598 155.0421699 767435.3248 0.019635612 0.014726981 175.2311343 -2.243611272 0.071072433 TDVSNFDEEFTGEAPTLS(ph)PPRDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TDVSNFDEEFTGEAPTLSPPRDAR 24 1 Q16512;Q16512-2 Q16512 PKN1 Serine/threonine-protein kinase N1 1 TDVSNFDEEFT(0.001)GEAPT(0.16)LS(0.839)PPRDAR;TDVSNFDEEFTGEAPT(0.043)LS(0.957)PPRDAR 112.33 0.00098475 301132000 221474 190995 58428 56864 175778 194143 190889 200807 35028 TRUE FALSE 192205.6498 189740.3413 86683.97623 69775.84031 172280.3617 201611.8068 172376.6142 157865.9857 30887.02974 6.222859606 6.143042657 2.806484694 2.259066051 5.577757497 6.527393812 5.580873771 5.111076948 1 14.91471352 4.343077272 11.55137188 4.361157837 6.19995158 0.190560682 1.711307052 0.776395414 80.56107889 0.446478678 1.182168098 22033.18456 -4.343077272 1.838793743 TDWDAGFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TDWDAGFK 8 0 P52298-2;P52298;C9JQX9;B3KSB0;P52298-3 P52298-2 NCBP2 Nuclear cap-binding protein subunit 2 0 105.57 0.01015 71042000 238880 206250 135990 165720 204770 167020 232840 254630 260590 FALSE TRUE 207311.4028 204895.1302 201755.2189 203349.2589 200695.4776 173445.3675 210259.2126 200179.356 229783.3471 0.902203773 0.891688335 0.878023675 0.884960818 0.87341176 0.754821312 0.915032422 0.871165638 1 17.80991472 1.043053158 2.331463782 1.105309075 0.868963425 0.453149812 0.043945829 1.28686679 4.352818177 0.78644415 0.011587005 11.04213768 -1.043053158 -0.236345651 TDWHMAFTGMSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TDWHMAFTGMSR 12 0 Q96M27;Q96M27-3;Q96M27-2 Q96M27 PRRC1 Protein PRRC1 0 ; 113.69 0.0011381 1058700000 1565030 1672280 862540 1260120 1745340 1630310 1520420 1928130 2323100 FALSE TRUE 1358207.32 1661294.683 1279667.229 1546249.506 1710611.149 1693029.081 1372969.902 1515814.404 2048465.764 0.663036378 0.810994605 0.624695443 0.754832974 0.835069435 0.826486393 0.670243031 0.739975464 1 20.96611235 1.238290179 24.97282587 1.00000029 0.741981476 0.565761203 0.071393428 4.827312865 444924.9212 0.096973396 0.017137517 17.30972544 -1.238290179 -0.258018814 TDYMVGSYGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TDYMVGSYGPR 11 0 P52565;J3KTF8;J3QQX2;J3KRE2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 170.5 3.64E-05 148540000 189350 161900 140330 158080 172240 115670 238990 264400 225600 FALSE TRUE 164326.9177 160836.4682 208194.0574 193974.4801 168812.761 120119.8997 215812.7866 207860.1176 198929.825 0.826054704 0.808508569 1.046570354 0.975089985 0.848604582 0.60383052 1.084868931 1.044891673 1 17.60190007 TDYNASVSVPDSSGPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TDYNASVSVPDSSGPER 17 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ; 255.28 1.07E-26 474900000 513640 405550 240850 296360 410880 377430 416690 477750 448980 FALSE TRUE 445761.1726 402885.9153 357325.8656 363653.0676 402704.2919 391949.9763 376279.4679 375586.8804 395902.0959 1.125937895 1.017640269 0.902561187 0.918542921 1.01718151 0.990017432 0.950435655 0.948686264 1 18.59478418 4.621971092 3.322222002 0.96080778 1.130558669 0.682561327 0.035602315 0.157365054 2.809194332 0.00920381 0.056009316 41876.56899 -4.621971092 0.169750889 TDYYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TDYYAR 6 0 P46777;A0A2R8Y4A2;R4GNJ2 P46777 RPL5 60S ribosomal protein L5 0 ;;;; 166.66 0.016052 8330700000 2594130 2421720 1439100 1736540 2412110 2483760 2391950 2661450 2562870 FALSE TRUE 2251309.148 2405811.562 2135053.574 2130847.948 2364113.73 2579311.854 2159979.057 2092319.629 2259890.428 0.996202789 1.064570004 0.944759775 0.942898789 1.046118741 1.141343767 0.955789285 0.925850034 1 21.10782139 2.052249079 24.99999817 0.952583454 1.020965103 0.187821184 0.060095197 151.8137921 72638.66386 0.025684881 0.01731674 112.7844119 -2.052249079 0.068381649 TEAEIAHIALETLEGHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TEAEIAHIALETLEGHQR 18 0 O75955;A0A140T9R1;A0A140T9X0;A2AB09;A0A140T9C3;A0A140T959;A2AB13;A2AB11;A0A0G2JJQ6;A0A140T910;A2AB12;A0A140T957;A2AB10;A0A140T9B1 O75955 FLOT1 Flotillin-1 0 ; 185.33 3.10E-14 71980000 97877 69585 40199 62258 80162 84273 64079 94541 74439 FALSE TRUE 84942.30646 69127.89155 59639.37086 76394.63045 78566.93303 87515.03684 57864.62844 74324.14287 65638.90622 1.294084733 1.053154227 0.908597877 1.163862027 1.196956768 1.333279938 0.881559913 1.132318424 1 16.00226358 2.22477775 24.99987235 1.026101007 1.144199022 0.220343845 0.132514159 472.7015998 857396.7473 0.05548303 0.037621414 167.7945111 -2.22477775 0.118098015 TEAPQASPLAKPLQS(ph)SSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TEAPQASPLAKPLQSSSPR 19 1 Q8IY33;Q8IY33-5;Q8IY33-4;Q8IY33-2 Q8IY33 MICALL2 MICAL-like protein 2 1 TEAPQASPLAKPLQS(0.36)S(0.36)S(0.281)PR 86.006 0.0017839 215310000 154040 146820 85713 88816 139670 134530 136190 185250 76567 TRUE FALSE 133683.2237 145855.5298 127164.0935 108983.0303 136890.8403 139705.4562 122982.3148 145635.7291 67515.33649 1.980042323 2.16033182 1.883484555 1.614196654 2.027551774 2.069240315 1.82154635 2.157076254 1 16.04292764 1.231527834 24.99999915 0.999998337 1.964473425 0.774690726 0.163413301 118.2687884 420381.9229 0.394729871 0.040342039 17.04228541 -1.231527834 0.964475087 TEAQDLCRAS(ph)PEPPGPESSSR ddPTM_MDA-MB-175_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 202.33 3.90E-22 2736960000 2357920 2596530 604540 552835 2023800 2028980 2341790 2462950 124608 TRUE FALSE 2046314.898 2579473.223 896897.5661 678364.6363 1983530.339 2107036.174 2114683.566 1936267.309 109876.9842 18.62369005 23.4760104 8.162742841 6.173855619 18.05228232 19.17631967 19.24591926 17.62213737 1 16.74552969 1.235575515 24.98511652 0.999979044 16.3106934 0.457358431 5.243161883 84.25703275 705095.8929 9.355544417 1.367239626 17.20186421 -1.235575515 15.31071435 TEAQGEEDDAEGQDQDKKS(ph)PKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TEAQGEEDDAEGQDQDKKSPKPK 23 3 O14617-5;O14617-2;A0A2R8Y611 O14617-5 AP3D1 AP-3 complex subunit delta-1 1 TEAQGEEDDAEGQDQDKKS(1)PKPK 180.85 3.16E-17 230140000 152530 107090 170190 115920 91461 54457 159270 157880 234550 TRUE FALSE 132372.774 106386.5187 252494.4533 142241.4077 89641.10504 56551.99603 143824.0199 124118.5906 206821.7662 0.64003309 0.514387439 1.220831143 0.687748733 0.433422007 0.273433484 0.695400791 0.600123444 1 17.6580285 3.478571466 24.99058961 0.588416039 0.79572685 0.1036599 0.255675008 119.3436171 2056601.491 0.07443321 0.097496289 3010.034446 -3.478571466 0.207310811 TEARSS(ph)DEENGPPS(ph)SPDLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TEARSSDEENGPPSSPDLDR 20 1 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 2 T(0.004)EARS(0.435)S(0.561)DEENGPPS(0.68)S(0.32)PDLDR 128.25 1.14E-05 288640000 282510 295260 159570 136600 321730 322530 263860 287860 99658 TRUE FALSE 245175.5877 293320.4176 236738.5857 167617.1178 315328.2025 334937.9378 238270.8978 226303.3791 87876.54477 2.790000316 3.337869262 2.693990602 1.907415889 3.588309068 3.811460028 2.711427702 2.575242116 1 16.42319052 4.136443192 9.16620142 2.665437827 3.06247994 0.04989286 0.793997913 1.020602205 82.25116396 0.209974344 0.438952822 13691.25288 -4.136443192 0.397042113 TEAVS(ph)PTVSQLSAVFENTDSPSAIISEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TEAVSPTVSQLSAVFENTDSPSAIISEK 28 0 Q9ULJ8;Q9ULJ8-4;Q9ULJ8-5;Q9ULJ8-3 Q9ULJ8 PPP1R9A Neurabin-1 1 TEAVS(0.929)PT(0.07)VSQLSAVFENTDSPSAIISEK;TEAVS(0.871)PT(0.128)VSQLSAVFENTDSPSAIISEK 265.81 3.10E-54 133096000 227110 205470 143391 180549 205843 167498 250570 320380 292070 TRUE FALSE 197096.8381 204120.254 212735.3672 221545.41 201747.127 173941.7564 226269.76 251869.2302 257541.8173 0.765300331 0.792571304 0.826022622 0.860230825 0.783356773 0.675392285 0.878574836 0.977974112 1 17.97444718 1.890726703 3.320044099 0.987164043 0.788865892 0.746504297 0.048890408 0.125628591 2.394710998 0.031312292 0.014109633 77.75470948 -1.890726703 -0.19829815 TEDEEFLIQHLLQAPS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 TEDEEFLIQHLLQAPSPPR 19 0 Q9ULL5;Q9ULL5-2 Q9ULL5 PRR12 Proline-rich protein 12 1 TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR 311.89 9.66E-62 3661654000 1945160 1638463 1133463 1312695 1718461 1587391 1697937 2036710 1847925 TRUE FALSE 1688102.178 1627699.829 1681609.498 1610762.463 1684266.988 1648458.959 1533271.331 1601175.416 1629465.412 1.035985278 0.998916465 1.032000732 0.988522034 1.033631629 1.011656306 0.940965865 0.982638481 1 20.6359673 2.391311425 10.24413593 0.974876503 1.016590456 0.483051512 0.020671762 0.296481932 33.0949434 0.007249336 0.005611256 246.2132522 -2.391311425 0.041713952 TEDGDWEWS(ph)DDEMDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 TEDGDWEWSDDEMDEK 16 0 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 1 TEDGDWEWS(1)DDEMDEK;TEDGDWEWS(1)DDEMDEK;TEDGDWEWS(1)DDEMDEK;TEDGDWEWS(1)DDEMDEK;TEDGDWEWS(1)DDEMDEK;TEDGDWEWS(1)DDEMDEK;TEDGDWEWS(1)DDEMDEK 371.8 2.45E-104 2546591000 3506791 2820324 2893805 3210543 3109261 2272614 3651516 4308833 6287330 TRUE FALSE 3043359.684 2801797.106 4293258.777 3939545.858 3047392.789 2360042.931 3297392.54 3387422.594 5544049.01 0.548941699 0.505370191 0.774390481 0.710590013 0.549669165 0.425689406 0.594762516 0.61100156 1 22.40250858 1.234712937 4.865208858 1.029754534 0.589541339 0.635155083 0.097782766 0.131046559 7.475865774 0.197742102 0.026167942 17.16773246 -1.234712937 -0.440213195 TEDGDWEWS(ph)DDEMDEKSEEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TEDGDWEWSDDEMDEKSEEGK 21 1 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 1 TEDGDWEWS(1)DDEMDEKSEEGK;TEDGDWEWS(1)DDEMDEKSEEGK;TEDGDWEWS(1)DDEMDEKSEEGK;TEDGDWEWS(1)DDEMDEKSEEGK 297.99 3.56E-55 1343590000 1345950 1029550 908350 585540 861120 568470 1521400 1718560 363880 TRUE FALSE 1168079.297 1022786.818 1347631.098 718495.8064 843985.3968 590339.4087 1373854.862 1351059.318 320862.5209 3.640435455 3.187616975 4.200026523 2.239263733 2.630364538 1.839851557 4.281755495 4.210710911 1 18.29159576 3.743796603 24.88125925 2.917727726 3.627185323 0.146001029 1.023952496 1120.289845 5323568.706 0.289786983 0.483268751 5543.660213 -3.743796603 0.709457597 TEDGGWEWS(ph)DDEFDEESEEGKAAISQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TEDGGWEWSDDEFDEESEEGKAAISQLR 28 1 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 T(0.005)EDGGWEWS(0.995)DDEFDEESEEGKAAISQLR;TEDGGWEWS(1)DDEFDEESEEGKAAISQLR;T(0.001)EDGGWEWS(0.999)DDEFDEESEEGKAAISQLR 150.68 3.37E-08 101790000 106489 85041 51289.4 58198.4 71376.1 65019.2 80232.8 98264 27852 TRUE FALSE 92416.20884 84482.36007 76093.12539 71413.23623 69955.85525 67520.5307 72451.83541 77251.00829 24559.36829 3.762971741 3.439923987 3.098333984 2.907779849 2.848438707 2.74927799 2.950069177 3.145480266 1 14.58398583 1.237645449 24.99864984 0.999997549 3.09043468 0.831100154 0.29917604 9.721772714 265410.4693 0.463315001 0.078563905 17.28404742 -1.237645449 2.09043713 TEDGKVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TEDGKVEK 8 1 O75436;S4R3Q6;O75436-2;S4R2Y3 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ; 78.934 0.026759 488660000 847240 647600 527560 512770 417070 545260 776890 937770 624900 FALSE TRUE 735275.0874 643345.873 782689.7806 629202.2657 408771.123 566236.505 701547.3274 737235.1832 551025.0339 1.33437692 1.16754382 1.420425085 1.141876007 0.741837662 1.027605771 1.273167795 1.337934101 1 19.07175834 3.502399041 24.00041013 1.104888334 1.291406944 0.2653925 0.171672306 826.0626521 784315.9523 0.053287593 0.078607423 3179.794404 -3.502399041 0.18651861 TEDPDLPAFYFDPLINPISHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TEDPDLPAFYFDPLINPISHR 21 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;; 246.13 2.85E-30 724922000 616229 525698 329679 417914 557033 561176 493848 682597 639667 FALSE TRUE 534792.7763 522244.6552 489112.8671 512807.7611 545949.1331 582764.8038 445954.697 536628.9435 564046.296 0.948136315 0.925889699 0.867150216 0.909158991 0.967915465 1.03318612 0.790634918 0.951391663 1 19.10545406 3.279774748 24.2998317 0.941350125 0.910288907 0.062622095 0.065771758 407.6485274 240345.6715 0.01922327 0.024816827 1904.472686 -3.279774748 -0.031061217 TEDSLMPEEEFLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TEDSLMPEEEFLRR 14 1 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 ; 150.11 1.17E-05 89807000 236950 221189 140452 161056 208360 196796 212366 236814 209350 FALSE TRUE 205636.4571 219735.9949 208375.057 197626.2264 204214.0436 204366.8695 191770.778 186173.169 184600.8815 1.113951653 1.19033015 1.128786901 1.070559495 1.106246308 1.10707418 1.038839991 1.008517226 1 17.49404992 1.463101057 0.350186342 0.870012473 1.164310851 0.763473535 0.028173425 3.423886447 0.47841155 0.449725365 0.060580854 29.04698479 -1.463101057 0.294298378 TEDTEHVIIPVCLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TEDTEHVIIPVCLR 14 0 Q9Y4E8;Q9Y4E8-2;Q9Y4E8-3 Q9Y4E8;Q9Y4E8-2 USP15 Ubiquitin carboxyl-terminal hydrolase 15 0 103.97 0.0010846 207340000 308400 266070 158920 218370 280810 276940 266950 339870 317620 FALSE TRUE 267644.1586 264322.1687 235774.2436 267954.2461 275222.4304 287594.061 241061.2301 267191.4454 280071.3254 0.955628564 0.943767336 0.841836426 0.956735737 0.982686928 1.026860071 0.860713712 0.954012143 1 18.09543476 3.523067426 24.99746424 0.959781995 0.913836362 0.167085172 0.051978468 856.8973066 466200.8699 0.014533097 0.021555345 3334.781823 -3.523067426 -0.045945633 TEEARPSPAPGPGT(ph)PTGTPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TEEARPSPAPGPGTPTGTPTR 21 1 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 TEEARPSPAPGPGT(0.998)PT(0.002)GTPTR;TEEARPSPAPGPGT(0.914)PT(0.085)GT(0.001)PTR;TEEARPSPAPGPGT(0.999)PT(0.001)GTPTR;TEEARPSPAPGPGT(0.97)PT(0.03)GTPTR 262.68 1.69E-36 3651230000 664110 564130 354161 498780 663390 655310 522530 692050 642870 TRUE FALSE 576346.1809 560424.1929 525434.4442 612035.6224 650189.8369 680520.1997 471855.121 544060.493 566870.641 1.016715524 0.988628009 0.926903611 1.079674229 1.146980969 1.200485879 0.832385887 0.959761282 1 19.11266003 2.22529638 24.99994182 0.932669847 1.055470545 0.328982739 0.086803097 310.3968441 585019.7304 0.038346532 0.026025898 167.9950092 -2.22529638 0.122800698 TEEDSEEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TEEDSEEVR 9 0 Q16543;K7EKQ2 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ; 204.27 3.92E-05 711040000 1336830 1206310 1025810 1278470 1144210 1145110 1178640 1480940 2577600 FALSE TRUE 1160164.528 1198385.67 1521895.147 1568766.154 1121442.46 1189163.123 1064335.674 1164252.506 2272879.064 0.510438301 0.52725448 0.669589144 0.69021101 0.493401729 0.523196831 0.468276421 0.512236891 1 21.11608949 1.235747709 24.99984078 1.000000606 0.548694905 0.789728552 0.07308239 38.48923842 342008.6382 0.132238201 0.019593861 17.20868596 -1.235747709 -0.451305701 TEEEEIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TEEEEIDR 8 0 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ; 188.98 0.00045163 569490000 619980 447090 435120 565930 454760 457490 492950 579270 1036630 FALSE TRUE 538048.0722 444153.0364 645545.4874 694433.0562 445711.1657 475089.9363 445143.7849 455397.6184 914080.7823 0.588622015 0.485901296 0.706223673 0.759706439 0.487605882 0.519746116 0.48698517 0.498202814 1 19.80196214 1.233312224 24.9995259 1.000000681 0.563623289 0.667015374 0.096209409 110.1767661 524742.7541 0.209190818 0.025287499 17.11245125 -1.233312224 -0.436377392 TEEEFKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TEEEFKK 7 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;; 119.17 0.0077625 5144340000 4488890 3680820 3728210 4419270 4739330 5564610 9167520 10499800 12022910 FALSE TRUE 3895671.813 3656640.451 5531184.826 5422732.798 4645026.605 5778684.147 8278455.321 8254499.48 10601575.28 0.3674616 0.344914822 0.521732354 0.511502551 0.438144944 0.545077877 0.780870305 0.778610656 1 23.33777531 -2 0.28832746 5.818401434 0.328159192 0.912146215 0.061347337 20.98071869 0.339499873 57.32445641 0.138402211 0.01 2 -5.490242242 TEEGSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TEEGSVR 7 0 O43896 O43896 KIF1C Kinesin-like protein KIF1C 0 83.614 0.084764 0 1716800 1346600 973230 1191400 1152800 1112800 1297700 1569900 2290000 FALSE TRUE 1489920.53 1337754.096 1443887.283 1461925.579 1129861.535 1155610.136 1171849.254 1234189.102 2019278.809 0.737847851 0.662491029 0.715050976 0.723984015 0.559537163 0.572288547 0.580330586 0.611202919 1 20.94540869 1.235680561 24.99989135 1.000000484 0.640901586 0.745353739 0.065101885 44.06842856 382457.0843 0.117787367 0.017372126 17.20602544 -1.235680561 -0.359098897 TEELIES(ph)PKLESSEGEIIQTVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TEELIESPKLESSEGEIIQTVDR 23 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 TEELIES(0.999)PKLESS(0.001)EGEIIQTVDR;TEELIES(1)PKLESSEGEIIQTVDR;TEELIES(1)PKLESSEGEIIQTVDR;TEELIES(0.987)PKLES(0.005)S(0.008)EGEIIQTVDR 211.78 1.30E-24 689200000 454820 312837 255017 236361 357290 264014 373458 455324 376542 TRUE FALSE 394714.3846 310781.9531 378344.0742 290030.3776 350180.628 274170.7894 337240.1006 357956.5059 332027.6337 1.1887998 0.936012312 1.13949574 0.873512769 1.054673143 0.8257469 1.015698895 1.078092513 1 18.34094379 4.750159102 24.27431149 0.996309532 1.188799974 0.30579727 0.093566994 1520.364648 3181860.674 0.021742958 0.329732806 56254.73745 -4.750159102 0.192490442 TEEPDRDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TEEPDRDER 9 1 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 ;;; 140.16 0.00010009 899710000 2217880 1696230 1184440 1486390 1670910 1761470 1762180 1965270 2400470 FALSE TRUE 1924781.539 1685087.353 1757239.146 1823897.568 1637662.16 1829234.891 1591284.055 1545012.304 2116689.171 0.909335941 0.796095797 0.830182896 0.861674729 0.773690432 0.864196272 0.751779749 0.729919312 1 21.013378 3.25748482 24.98383814 0.808771062 0.844153339 0.003132728 0.079859039 916.3256905 1209731.698 0.022646591 0.029187349 1809.192673 -3.25748482 0.035382277 TEES(ph)PAS(ph)DEAGEK ddPTM_MDA-MB-175_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 305.98 2.37E-41 847880000 2548500 1701740 2024710 2144450 1580420 1581290 2085830 2471500 6471300 TRUE FALSE 2211709.268 1690561.158 3003866.528 2631380.148 1548972.734 1642123.25 1883546.528 1942988.958 5706270.286 0.387592798 0.296263772 0.526415045 0.461138365 0.271450993 0.287775231 0.330083651 0.340500688 1 22.44411665 1.237444586 24.9998495 1.00000076 0.361018136 0.863563091 0.07961314 10.23488401 229162.6692 0.122384825 0.020486908 17.27605533 -1.237444586 -0.638982624 TEES(ph)PASDEAGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TEESPASDEAGEK 13 0 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 TEES(1)PASDEAGEK;TEES(1)PASDEAGEK;TEES(1)PASDEAGEK;TEES(1)PASDEAGEK 349.01 7.11E-76 1027450000 1999890 1456910 1637440 1893470 1452750 1217370 1767500 2012790 4885930 TRUE FALSE 1735599.469 1447339.462 2429311.461 2323411.303 1423843.117 1264203.012 1596088.122 1582370.522 4308320.921 0.402848233 0.335940495 0.56386502 0.539284641 0.330486782 0.293432879 0.370466395 0.367282417 1 22.03869429 1.236701408 24.99849193 1.000000755 0.399389145 0.823453095 0.08724323 21.17485952 284631.366 0.144297757 0.022937936 17.24651728 -1.236701408 -0.60061161 TEESPASDEAGEKEAKS(ph)D ddPTM_MDA-MB-175_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 159.46 3.39E-11 974430000 945050 671900 651300 539030 707070 473790 975800 1075260 463070 TRUE FALSE 820159.248 667486.2447 966270.8585 661425.0001 693000.6904 492017.0079 881167.0662 845324.0167 408326.3921 2.008587404 1.634687979 2.366417839 1.619843862 1.697173398 1.204960094 2.157996846 2.070216457 1 18.63936329 TEFLDLDNSPLSPPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TEFLDLDNSPLSPPSPR 17 0 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 TEFLDLDNSPLS(0.002)PPS(0.998)PR;TEFLDLDNSPLS(0.014)PPS(0.986)PR;TEFLDLDNSPLS(0.001)PPS(0.999)PR;TEFLDLDNSPLS(0.006)PPS(0.994)PR 171.98 1.74E-09 311722000 189395 163251 125121 169505 172548 156167 160989 187027 356180 TRUE FALSE 164365.9709 162178.5934 185629.9341 207993.701 169114.6324 162174.8455 145376.3116 147032.7315 314072.8062 0.523337162 0.516372606 0.591041091 0.662246769 0.538456782 0.516360673 0.462874559 0.468148559 1 18.26073951 1.233700272 24.99999559 1.000000711 0.533047712 0.865542236 0.057611649 59.56734534 306357.7688 0.129079958 0.016128451 17.12774827 -1.233700272 -0.466952999 TEGAQVDEPVVIT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TEGAQVDEPVVITPR 15 0 A0A0J9YWL0;A0A494C1M5 A0A0J9YWL0 1 TEGAQVDEPVVIT(1)PR;TEGAQVDEPVVIT(1)PR 260.44 7.45E-24 498860000 274020 255670 196325 276080 399500 428270 391310 464740 444730 TRUE FALSE 237807.5627 253990.4869 291268.4267 338768.1836 391550.7316 444745.824 353360.8164 365358.9676 392154.526 0.606412898 0.647679601 0.742738914 0.863864016 0.998460315 1.134108609 0.901075451 0.931670919 1 18.58106273 3.771206133 1.651908071 0.984851679 0.621318707 0.85344326 0.062912733 0.151951611 0.802556474 0.021264272 0.047895543 5904.812791 -3.771206133 -0.363532972 TEGT(ph)PPPPGQPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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;T(0.009)EGT(0.991)PPPPGQPAK;T(0.021)EGT(0.979)PPPPGQPAK;T(0.044)EGT(0.956)PPPPGQPAK 185.2 9.90E-05 807950000 3045660 2363440 1722100 1799610 2646020 2203520 3030510 3440790 3256780 TRUE FALSE 2643168.314 2347914.407 2554913.32 2208238.956 2593369.379 2288290.84 2736611.607 2705003.835 2871767.179 0.920397842 0.817585222 0.889665896 0.768947766 0.903056974 0.796823244 0.952936445 0.941930061 1 21.45350736 2.177616773 8.873836594 0.960189424 0.848646117 0.550421856 0.049166942 0.215420793 28.87995873 0.018255175 0.012314561 150.5278204 -2.177616773 -0.111543308 TEHAEFLHCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TEHAEFLHCK 10 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 129.16 0.0001796 69508000 226410 162290 124180 153140 177820 177340 216450 240860 223920 FALSE TRUE 196489.3449 161223.9063 184233.8634 187912.7776 174281.7299 184162.3846 195458.7123 189353.9634 197448.4327 0.995142591 0.816536774 0.933073314 0.951705592 0.882669604 0.932711301 0.989922835 0.959004641 1 17.59111639 2.376640534 4.603470648 0.977961276 0.912755801 0.295378535 0.047039149 0.256528217 9.384623707 0.016971537 0.012931748 238.0348437 -2.376640534 -0.065205475 TEIEDFPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TEIEDFPR 8 0 H3BS10;H3BP20;P06865;H3BU85;H3BTD4 H3BS10 HEXA Beta-hexosaminidase;Beta-hexosaminidase subunit alpha 0 78.377 0.071616 183310000 133520 114530 64074 85388 120640 132980 103580 122450 105380 FALSE TRUE 115874.9937 113777.6449 95060.40071 104776.6505 118239.5 138095.8266 93534.82754 96265.02041 92922.09645 1.247012262 1.224441217 1.023011795 1.127575189 1.272458377 1.486146266 1.00659403 1.035975555 1 16.50373408 TEIIILATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TEIIILATR 9 0 P23396;P23396-2;E9PPU1;E9PL09;F2Z2S8;H0YCJ7;H0YEU2;H0YF32;E9PQ96;E9PJH4;E9PK82 P23396 RPS3 40S ribosomal protein S3 0 107.9 0.0062799 251240000 177760 178600 134770 135960 183040 169970 165260 197340 193710 FALSE TRUE 154268.5656 177426.7648 199945.2228 166831.796 179397.8621 176508.8559 149233.1106 155140.3767 170809.8245 0.903159792 1.03873864 1.170572146 0.976710775 1.050278359 1.033364775 0.873679902 0.908263779 1 17.38203143 2.25466057 24.63585728 0.921110881 1.034307917 0.297253597 0.07302893 218.2749492 333999.9244 0.027112134 0.020930085 179.7465527 -2.25466057 0.113197036 TEIKEEEDQPSTSATQS(ph)SPAPGQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TEIKEEEDQPSTSATQSSPAPGQSK 25 1 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 TEIKEEEDQPSTSAT(0.007)QS(0.822)S(0.17)PAPGQSK 214.44 1.11E-33 710650000 441230 327150 335650 333130 320870 227820 449310 549550 585060 TRUE FALSE 382920.3376 325000.9301 497971.4627 408772.2581 314485.3148 236584.3828 405735.9854 432033.0091 515894.8733 0.742244898 0.629975111 0.96525763 0.792355728 0.609591859 0.458590296 0.78647028 0.837443889 1 18.97671758 1.486237588 2.114291442 1.008295592 0.707055832 0.33794887 0.132352787 0.518991642 3.854175234 0.263421076 0.038939937 30.6363899 -1.486237588 -0.30123976 TEKHESQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TEKHESQR 8 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;; 128.6 0.00067684 459346000 1095140 1224880 284844 617900 983370 1217420 1439510 1602170 626720 FALSE TRUE 950414.4743 1216833.683 422595.5111 758203.639 963802.8609 1264254.935 1299906.542 1259558.414 552629.8756 1.719802921 2.201896308 0.764698996 1.371991766 1.7440296 2.287706458 2.352219088 2.279207964 1 19.07595403 2.975548364 5.420813136 2.059592996 1.513312828 0.144509311 0.517108342 0.309074254 27.19228893 0.167640879 0.175579337 945.2536521 -2.975548364 -0.546280168 TELDAHFENLLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TELDAHFENLLAR 13 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39;F8WFB9 B7ZC38 SH3GLB2 Endophilin-B2 0 ;;; 174.72 1.95E-05 2188030000 4275440 4445640 2693320 3525630 4638400 4595850 4519740 5189600 5115500 FALSE TRUE 3710429.771 4416436.298 3995818.561 4326178.177 4546104.915 4772655.323 4081416.31 4079844.426 4510751.418 0.822574651 0.97909104 0.88584322 0.959081487 1.007837607 1.058062146 0.904819604 0.904471129 1 22.10493635 4.744399586 24.55128268 0.957089075 0.822574575 0.400493026 0.053413583 590.1507416 2481331.27 0.013811487 0.119669225 55513.6248 -4.744399586 -0.134514501 TELDWFLQDLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TELDWFLQDLER 12 0 P53804-3;P53804-2;P53804 P53804-3 TTC3 E3 ubiquitin-protein ligase TTC3 0 105.86 0.0046157 4629900 8392.8 7380.3 4647 6653.1 8170 8163.3 7311.7 8368.9 6664.3 FALSE TRUE 7283.670215 7331.818323 6894.304743 8163.788041 8007.432984 8477.347433 6602.612459 6579.275862 5876.454046 1.239466889 1.247660284 1.173208314 1.389237111 1.362630069 1.442595716 1.123570849 1.119599645 1 12.52073016 2.092465892 7.171013548 1.084101897 1.30587606 0.627002234 0.083467031 0.157462474 10.39900942 0.036917729 0.024783994 123.7274016 -2.092465892 0.221774163 QVVSVVQDEEVGLPFEASPESPPPAS(ph)PDGVTEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 QVVSVVQDEEVGLPFEASPESPPPASPDGVTEIR 34 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 QVVSVVQDEEVGLPFEASPES(0.126)PPPAS(0.871)PDGVT(0.003)EIR 161.43 2.16E-14 1066000000 58020 92743 66604 93687 122990 117410 116550 146400 132700 TRUE FALSE 50352.51 92133.76513 98813.91718 114960.0653 120542.7396 121926.8387 105246.9989 115093.4993 117012.3572 0.430317884 0.787384917 0.844474204 0.982460896 1.030171022 1.04199968 0.899452002 0.983601237 1 16.83630137 4.919319127 1.088316377 0.987105522 1.49E-17 0.935495622 0.04607117 0.57157506 0.433676247 0.014663894 0.711097625 83046.07795 -4.919319127 -0.987105522 down TELFIAAEGIHTGQFVYCGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TELFIAAEGIHTGQFVYCGK 20 0 P62917;E9PKZ0;G3V1A1;E9PKU4 P62917 RPL8 60S ribosomal protein L8 0 212.55 1.61E-22 112540000 166210 162770 117970 140070 171750 149180 184480 208330 264320 FALSE TRUE 144244.9274 161700.7532 175020.6866 171875.0343 168332.511 154919.0511 166589.158 163780.2507 233072.3907 0.61888466 0.693779099 0.750928439 0.737431979 0.722232739 0.664682122 0.714752861 0.702701209 1 17.83041859 1.238469115 24.99164674 1.000000323 0.703481693 0.862940011 0.037474838 0.769265226 208949.5367 0.051685092 0.009231344 17.31685875 -1.238469115 -0.296518631 TELFVHAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TELFVHAFK 9 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 ; 104.17 0.0033041 1007070000 2015260 1846030 1188280 1446200 2047670 1747410 2158910 2394630 2350190 FALSE TRUE 1748938.285 1833903.307 1762936.183 1774581.814 2006925.373 1814633.993 1949539.24 1882557.01 2072353.216 0.843938317 0.884937613 0.850692908 0.856312428 0.968428238 0.875639336 0.940736949 0.908415127 1 20.98283849 -2 0.171611147 1.436910158 0.819540649 0.545981686 0.035243102 101.7434469 1.396842479 15.68837528 0.360648664 0.01 2 -0.617369509 TELSQSDMFDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TELSQSDMFDQR 12 0 B7Z7P8;P62495-2;P62495 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 133.05 0.00039573 160630000 167760 157570 95038 124080 163270 166900 172290 176830 179390 FALSE TRUE 145590.091 156534.9123 140998.6947 152254.2604 160021.2464 173320.751 155581.3423 139016.2806 158182.7186 0.920391888 0.989582893 0.891365985 0.962521455 1.011622811 1.09569966 0.983554612 0.878833553 1 17.27123247 3.479835758 24.58335555 0.984154169 0.937291053 0.176068231 0.057416543 213.107079 1929974.213 0.0186114 0.024492741 3018.809849 -3.479835758 -0.046863116 TEMDKS(ph)PFNSPS(ph)PQDSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TEMDKSPFNSPSPQDSPR 18 1 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5;P08651-4 P08651-3 NFIC Nuclear factor 1 C-type 2 TEMDKS(1)PFNS(0.067)PS(0.933)PQDSPR 130.83 1.04E-05 148910000 342360 246630 149200 171180 242520 180950 279310 340880 295310 TRUE FALSE 297116.2586 245009.8713 221353.619 210049.0353 237694.3265 187911.2636 252222.5592 267985.4647 260398.7882 1.141004767 0.940902502 0.850056256 0.806643674 0.912808881 0.721628794 0.968601125 1.029134838 1 17.99036321 2.011000968 24.90895415 1.011314371 0.888323992 0.179114285 0.107279775 315.0181507 713277.3784 0.044504424 0.029974985 102.5654212 -2.011000968 -0.122990379 TEMDKS(ph)PFNSPSPQDSPR ddPTM_MDA-MB-175_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 245.36 2.01E-24 836820000 1108690 813890 577270 641800 904170 710550 937280 1184510 972850 TRUE FALSE 962173.8074 808543.503 856439.7029 787530.4993 886178.786 737885.3183 846382.7299 931211.7544 857840.7813 1.121622833 0.942533301 0.998366738 0.918038075 1.033034108 0.860165819 0.986643149 1.085529826 1 19.71035038 1.898289299 7.60172218 1.04606497 0.973503852 0.113161348 0.072013293 0.479188057 31.77326185 0.032548122 0.017962914 79.12055019 -1.898289299 -0.072561118 TEMDKSPFNSPS(ph)PQDSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TEMDKSPFNSPSPQDSPR 18 1 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5;P08651-4 P08651-3 NFIC Nuclear factor 1 C-type 1 TEMDKSPFNS(0.021)PS(0.979)PQDSPR 210.64 2.36E-16 378310000 296640 218990 116310 132550 183710 144330 210970 244530 91752 TRUE FALSE 257438.2724 217551.4403 172557.905 162647.5034 180054.5304 149882.4685 190510.1619 192239.1624 80905.18308 3.18197503 2.6889679 2.132841166 2.01034714 2.225500562 1.852569425 2.354733709 2.376104411 1 16.30394451 4.467779239 1.854298367 2.036744919 3.275728523 0.522599932 0.389502649 0.416168679 2.196196429 0.103409088 0.745753925 29361.56762 -4.467779239 1.238983604 TEMDWVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TEMDWVLK 8 0 P52597;A0A1B0GW42 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 141.47 0.0028122 0 293280 268520 186120 218500 243470 213270 263150 321790 470600 FALSE TRUE 254522.3049 266756.0744 276128.2545 268113.7646 238625.4233 221474.6349 237629.7535 252977.7127 414966.2041 0.613356708 0.642838072 0.665423477 0.646109881 0.57504785 0.533717283 0.57264845 0.609634496 1 18.66263432 1.238740377 9.278171583 1.002396442 0.60649157 0.908268186 0.039216592 0.024714906 33.23354478 0.061885219 0.010954863 17.32767834 -1.238740377 -0.395904872 TENDHINLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TENDHINLK 9 0 A8MUA9;A8MU27;P55854;P55854-2 A8MUA9 SUMO3 Small ubiquitin-related modifier 3 0 ;;;;; 157.24 6.90E-05 3688890000 8710230 7470040 5236200 6080000 7572630 6437980 8848410 9846650 10182830 FALSE TRUE 7559151.037 7420968.815 7768443.834 7460556.927 7421949.479 6685653.257 7990292.56 7741020.524 8979027.438 0.841867462 0.82647802 0.865176534 0.830886973 0.826587237 0.744585458 0.889883967 0.862122382 1 23.09812776 0.817719425 1.333364008 1.29839978 0.828244391 0.676966474 0.036420494 2.152796137 1.496328994 1.834564134 0.010560329 6.572330966 -0.817719425 -0.47015539 TENNDHINLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 TENNDHINLK 10 0 P61956;P61956-2 P61956 SUMO2 Small ubiquitin-related modifier 2 0 ;;;;;; 165.63 5.79E-06 12361583200 13452047 11479591 7589364 9203359 11788114 9949866 13855399 15466587 14430627 FALSE TRUE 11674324.91 11404180.81 11259605.82 11293122.33 11553553.59 10332643.78 12511704.54 12159177.73 12724654.72 0.917457107 0.896227133 0.884865332 0.887499314 0.90796598 0.812017616 0.983264758 0.955560524 1 23.60112317 2.205532944 24.99774203 0.97475088 0.886120661 0.689494347 0.030063556 106.8006257 80833.76209 0.011703549 0.007891095 160.5214018 -2.205532944 -0.088630219 TENSWGEPS(ph)SPSTLVDNGTAAWGKPPSSGSGWGDHPAEPPVAFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TENSWGEPSSPSTLVDNGTAAWGKPPSSGSGWGDHPAEPPVAFGR 45 1 A0A1B0GU24;Q9HCJ0-2;Q9HCJ0;K7ELY5 A0A1B0GU24 TNRC6C Trinucleotide repeat-containing gene 6C protein 1 TENS(0.001)WGEPS(0.373)S(0.282)PS(0.282)T(0.062)LVDNGTAAWGKPPSSGSGWGDHPAEPPVAFGR 147.59 1.75E-14 185560000 69419 75740 41457 65209 97612 83222 100790 119540 96419 TRUE FALSE 60245.10326 75242.45895 61505.74387 80015.70011 95669.71217 86423.60419 91015.40131 93977.30126 85020.45566 0.708595394 0.884992422 0.723422891 0.941134689 1.125255227 1.016503658 1.070511803 1.105349301 1 16.37552237 3.505637487 3.989505719 1.066112969 0.785785568 0.830237736 0.059887141 0.078618441 2.755728635 0.015913593 0.022992934 3203.594111 -3.505637487 -0.280327401 TENVFVDEPLIHATTYIPLMDNADS(ph)SPVVDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TENVFVDEPLIHATTYIPLMDNADSSPVVDKR 32 1 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 1 TENVFVDEPLIHATTYIPLMDNADS(0.5)S(0.5)PVVDKR 130.77 3.92E-08 52736000 16716 13148 8693.1 12471 20522 11507 13086 28037 27510 TRUE FALSE 14506.93825 13061.62992 12897.11224 15302.73116 20113.65235 11949.68174 11816.92173 22041.50573 24257.79914 0.598031922 0.538450741 0.531668688 0.630837574 0.829162293 0.49261195 0.487139071 0.908635842 1 14.56616104 1.627913864 4.908470282 0.976833662 0.590966495 0.709413425 0.098290246 0.08048328 4.194586979 0.07095318 0.026604613 42.45353553 -1.627913864 -0.385867167 TEPS(ph)SPLSDPSDIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TEPSSPLSDPSDIIR 15 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 TEPS(0.58)S(0.419)PLS(0.001)DPSDIIR 127.02 8.47E-05 97220000 186790 140070 98109 138310 168710 140700 140890 172930 253450 TRUE FALSE 162105.2282 139149.8709 145554.8406 169715.3994 165353.0011 146112.82 127226.5095 135950.2652 223487.4297 0.72534383 0.622629519 0.651288713 0.759395728 0.739876069 0.653785406 0.569278145 0.608312805 1 17.76983416 1.232998274 24.99992343 1.000000537 0.661971633 0.751030614 0.060347984 99.45331244 446944.4314 0.139357696 0.016368377 17.10008519 -1.232998274 -0.338028904 TEPSS(ph)PLSDPSDIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TEPSSPLSDPSDIIR 15 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 TEPS(0.001)S(0.999)PLSDPSDIIR;TEPS(0.002)S(0.998)PLSDPSDIIR;TEPS(0.026)S(0.974)PLSDPSDIIR;TEPS(0.006)S(0.994)PLSDPSDIIR 255.37 1.06E-24 771860000 1313070 1053190 813719 1078080 1194650 1054210 1095070 1283400 1960820 TRUE FALSE 1139544.473 1046271.526 1207236.23 1322874.541 1170878.802 1094766.141 988870.2799 1008954.897 1729014.093 0.659071824 0.605126083 0.698222319 0.765103388 0.677194481 0.633173636 0.571927252 0.583543478 1 20.7215182 1.232290809 24.99995685 1.000000584 0.646628537 0.788962347 0.057009599 108.8829653 434112.7198 0.1450753 0.015946759 17.07225185 -1.232290809 -0.353372047 TEPTS(ph)PTPSAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TEPTSPTPSAFK 12 0 Q86XN7-2;Q86XN7 Q86XN7-2 PROSER1 Proline and serine-rich protein 1 1 TEPT(0.023)S(0.966)PT(0.009)PS(0.003)AFK;TEPT(0.036)S(0.959)PT(0.005)PS(0.001)AFK;TEPT(0.035)S(0.952)PT(0.013)PSAFK;TEPT(0.002)S(0.934)PT(0.063)PSAFK 259.47 2.96E-21 1283590000 3239160 3013670 2529710 3210610 3919840 3014610 3977770 5209400 5404600 TRUE FALSE 2811096.799 2993873.003 3753086.217 3939628.072 3841842.853 3130583.997 3592006.478 4095410.35 4765674.345 0.589863385 0.628216027 0.787524691 0.826667495 0.806148842 0.656902627 0.753724702 0.859355897 1 22.18424894 -1.243367467 0.663551857 10 0.71076897 0.591972265 0.077143422 62.41023797 1.181138627 806.7546571 0.037900416 0.05709953 1.243367467 -9.28923103 TEQELPRPQS(ph)PSDLDS(ph)LDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TEQELPRPQSPSDLDSLDGR 20 1 P54259 P54259 ATN1 Atrophin-1 2 TEQELPRPQS(0.981)PS(0.031)DLDS(0.988)LDGR;TEQELPRPQS(0.999)PS(0.001)DLDS(1)LDGR 162.91 1.16E-11 345240000 366214 355527 214939 251143 329459 355006 366971 379527 363546 TRUE FALSE 317817.892 353191.5197 318884.2193 308168.8566 322903.4105 368663.3105 331382.2089 298368.1045 320568.006 0.991421121 1.10176784 0.99474749 0.961321314 1.007285208 1.150031518 1.033734505 0.930748231 1 18.29027092 1.756556885 24.99935092 0.963152344 1.036003131 0.198043243 0.057573209 10.717766 14907.85829 0.031300122 0.015031008 57.08958484 -1.756556885 0.072850786 TEQELPRPQS(ph)PSDLDSLDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TEQELPRPQSPSDLDSLDGR 20 1 P54259 P54259 ATN1 Atrophin-1 1 TEQELPRPQS(0.983)PS(0.017)DLDSLDGR;TEQELPRPQS(0.995)PS(0.005)DLDSLDGR 271.44 1.28E-44 503410000 472400 391100 264570 314490 455780 453160 413690 485140 458690 TRUE FALSE 409971.1431 388530.8383 392516.9369 385899.7612 446710.8697 470593.3584 373570.4075 381396.5864 404464.1907 1.013615426 0.960606272 0.970461529 0.954101179 1.104450975 1.163498201 0.923618001 0.942967499 1 18.62565245 TEQFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TEQFYR 6 0 O76021;J3QSV6;I3L3U9;I3L3C4;I3L234 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 ; 144.29 0.026267 633635000 317250 325964 213432 262846 332820 315160 289720 315210 468630 FALSE TRUE 275324.6087 323822.721 316648.4291 322529.2016 326197.5332 327284.4091 261622.999 247804.7945 413229.0953 0.666275952 0.783639692 0.766278156 0.78050942 0.789386655 0.792016857 0.633118534 0.599678961 1 18.65658231 2.288238852 24.99895267 0.709511003 0.76609701 0 0.112534827 358.4104032 180356.6688 0.041387812 0.032058801 194.1953614 -2.288238852 0.056586007 TES(ph)PATAAETASEELDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 TESPATAAETASEELDNR 18 0 Q9NTJ3;Q9NTJ3-2;C9JR83;C9JWF0;C9IYK2;C9JJ64 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4 1 TES(1)PATAAETASEELDNR;TES(0.999)PAT(0.001)AAETASEELDNR;T(0.021)ES(0.979)PATAAETASEELDNR;TES(1)PATAAETASEELDNR;TES(1)PATAAETASEELDNR;TES(1)PATAAETASEELDNR;TES(1)PATAAETASEELDNR;TES(1)PATAAETASEELDNR 363.39 8.60E-92 3860750000 1312475 1153223 714192 899368 1307671 1160154 1157183 1396420 1240345 TRUE FALSE 1139028.103 1145647.402 1059577.64 1103583.25 1281650.906 1204785.875 1044959.571 1097806.45 1093712.827 1.041432518 1.047484654 0.968789625 1.009024694 1.17183494 1.101555953 0.955424079 1.003742868 1 20.06080255 2.231733848 24.99820399 0.988714174 1.055340958 0.266997756 0.054832718 249.2253701 912601.2005 0.024090009 0.016655743 170.5037159 -2.231733848 0.066626785 TESDDLHTFLLEIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TESDDLHTFLLEIK 14 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 0 128.9 7.10E-05 45384000 85759 72139 44469 53135 64691 54894 74010 93995 78536 FALSE TRUE 74425.73086 71665.11416 65974.35714 65200.11387 63403.77567 57005.8077 66832.52159 73894.90072 69251.56355 1.074715531 1.034851929 0.952676788 0.941496632 0.915557316 0.823169973 0.965068775 1.067050286 1 16.07955902 4.361923681 3.339168673 0.956576177 1.068418568 0.331745561 0.061493867 0.341096521 7.183092443 0.018637851 0.061676407 23010.37416 -4.361923681 0.111842391 TESEVPPRPAS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TESEVPPRPASPK 13 1 Q9Y3L3;Q6ZT62-2;Q6ZT62;A0A2R8Y5V0;A0A3B3IU28 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 TESEVPPRPAS(1)PK;TESEVPPRPAS(1)PK 103.5 0.00097239 628300000 732480 624770 498120 473710 700140 516550 784920 872150 820680 TRUE FALSE 635680.9121 620665.8447 739012.4981 581273.0957 686208.5838 536422.0128 708798.5792 685647.5096 723660.1453 0.878424653 0.85767587 1.021214866 0.803240443 0.94824703 0.74126234 0.979463335 0.947471702 1 19.46495279 TESSTEGKEQEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TESSTEGKEQEEK 13 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 141.65 3.64E-05 362690000 466690 325230 240921 235097 256360 213494 437720 487980 177454 FALSE TRUE 405015.7341 323093.5427 357431.2014 288479.3671 251258.9376 221707.2523 395269.9818 383629.2745 156475.5903 2.588363676 2.064817536 2.284261723 1.843606192 1.60573887 1.416880754 2.526080784 2.451687664 1 17.25557809 5.009541344 1.035819869 1.913075463 3.219004309 0.197415748 0.465180528 6.129271084 3.697563176 0.153567569 10.0737256 102221.2868 -5.009541344 1.305928847 TET(ph)PPPLASLNVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TETPPPLASLNVSK 14 0 K7ELG9;Q3MHD2;Q3MHD2-2 K7ELG9 LSM12 Protein LSM12 homolog 1 T(0.004)ET(0.996)PPPLASLNVSK;T(0.003)ET(0.997)PPPLASLNVSK;T(0.006)ET(0.994)PPPLASLNVSK;TET(1)PPPLASLNVSK;T(0.004)ET(0.996)PPPLASLNVSK;TET(1)PPPLASLNVSK 149.22 8.44E-05 1436672000 1486200 1165100 1302701 1366169 1408980 1113333 1533240 1656190 3322210 TRUE FALSE 1289794.904 1157446.381 1932691.561 1676378.552 1380944.055 1156163.641 1384546.621 1302026.657 2929462.118 0.440283865 0.395105427 0.659742807 0.572247902 0.471398502 0.394667551 0.472628273 0.444459291 1 21.48220436 1.236046276 24.999324 1.000000681 0.481887301 0.804090989 0.080459431 31.16495471 309797.1901 0.136868798 0.020728741 17.22052056 -1.236046276 -0.51811338 TET(ph)QEKNPLPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TETQEKNPLPSK 12 1 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 1 T(0.011)ET(0.989)QEKNPLPSK;T(0.004)ET(0.996)QEKNPLPSK;T(0.003)ET(0.997)QEKNPLPSK 116.96 0.001362 789538000 938720 481610 341768 574810 544858 294267 1098430 726263 815133 TRUE FALSE 814665.7736 478446.2722 507048.1479 705329.3959 534016.3918 305587.6419 991904.4277 570957.3092 718768.9053 1.13341822 0.66564687 0.705439738 0.981302044 0.742959786 0.425154232 1.380004644 0.794354493 1 19.45516847 2.240471353 24.99996792 1.016580431 0.775323289 0.23849806 0.23404046 81.21617912 1062651.53 0.086875919 0.063824519 173.9687941 -2.240471353 -0.241257142 TETGQELECLQDHLDDLVVECR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TETGQELECLQDHLDDLVVECR 22 0 Q92896;Q92896-3;Q92896-2;H3BM42 Q92896 GLG1 Golgi apparatus protein 1 0 ;;;; 320.51 1.31E-67 453954000 464912 486755 302243 293070 438901 538982 370913 477110 497228 FALSE TRUE 403472.7013 483557.4744 448408.7257 359616.0228 430167.7288 559716.9863 334941.9143 375083.7394 438446.2723 0.920232938 1.10288878 1.022722176 0.820205452 0.981118454 1.27659196 0.76392921 0.855483928 1 18.74204054 TETQEKNPLPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TETQEKNPLPSK 12 1 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 ;;; 189.3 7.39E-06 2900930000 4831790 3045340 2080050 2270640 3008270 2055130 3869180 4354740 2331330 FALSE TRUE 4193256.709 3025334.961 3085969.137 2786223.517 2948411.313 2134192.181 3493947.519 3423512.74 2055722.823 2.039796738 1.471664821 1.501160128 1.3553498 1.434245551 1.038171176 1.699619949 1.665357168 1 20.97121433 4.845602062 2.342901707 1.414331053 2.316251325 0.439120685 0.228561852 0.943038996 4.748723046 0.059275212 1.927056524 70081.28593 -4.845602062 0.901920273 TETQEKNPLPSKETIEQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TETQEKNPLPSKETIEQEK 19 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 ;;; 249.14 3.14E-25 3246070000 3250820 1765000 813310 673366 1431210 911220 2645160 2912720 156536 FALSE TRUE 2821215.9 1753405.599 1206629.436 826264.0421 1402731.721 946275.223 2388632.79 2289857.495 138030.4924 20.43907727 12.70303082 8.741759993 5.98609791 10.16247712 6.855552034 17.30510954 16.58950464 1 17.07462748 4.688606417 2.867346502 10 21.68664181 0.33801984 4.783115465 0.469871275 5.803922454 1.289494651 12.02278506 48820.9715 -4.688606417 11.68664181 TEVLS(ph)PNSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TEVLSPNSK 9 0 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 TEVLS(0.999)PNS(0.001)K;TEVLS(0.999)PNS(0.001)K 118.87 0.00096503 371690000 858830 674220 518430 647540 721520 595020 769160 976650 1086930 TRUE FALSE 745333.4395 669791.0044 769144.482 794573.854 707163.1636 617910.8044 694566.9816 767800.9978 958434.3736 0.77765725 0.698838672 0.802500936 0.829033136 0.737831596 0.644708518 0.72468914 0.801099187 1 19.87032012 1.247122417 2.776936397 1.051592067 0.745199478 0.70276586 0.051877053 0.26069526 2.387911768 0.183077564 0.01450836 17.66535693 -1.247122417 -0.306392589 TEVNYTQLVDLHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TEVNYTQLVDLHAR 14 0 A0A087X2I2;A0A087WT12;P36969-2;P36969;K7ERP4;K7EKX7;K7ENB4;K7EJ20;A0A087X247;R4GNE4 A0A087X2I2 GPX4 "Glutathione peroxidase;Phospholipid hydroperoxide glutathione peroxidase, mitochondrial" 0 90.853 0.0055876 151200000 212560 169420 104590 131690 168070 177570 193380 234240 214670 FALSE TRUE 184469.6574 168307.0689 155170.0738 161592.2273 164725.7358 184401.2328 174626.0374 184149.5989 189291.9572 0.97452454 0.889140096 0.819739392 0.853666631 0.870220469 0.974163063 0.922522224 0.97283372 1 17.53025359 2.73993943 24.91830964 0.964026543 0.876912192 0.492855949 0.043112992 104.4233704 1887180.329 0.014789573 0.014030356 549.4642359 -2.73993943 -0.087114351 TEVS(ph)PVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TEVSPVPR 8 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 1 TEVS(1)PVPR;TEVS(1)PVPR 142 0.00065516 806660000 903030 906890 593840 735290 895450 939940 831430 1020180 996770 TRUE FALSE 783692.2975 900932.5799 881023.0103 902248.8327 877632.2969 976100.1 750798.0466 802022.446 878932.9861 0.891640557 1.025029887 1.002377911 1.026527445 0.99852015 1.11055122 0.854215348 0.912495558 1 19.74539365 2.223585489 24.99999248 0.917373297 1.009836243 0.296431657 0.062934516 274.9150675 458949.1836 0.02482842 0.016812338 167.3344994 -2.223585489 0.092462946 TEVSETARPS(ph)SPDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TEVSETARPSSPDTR 15 1 O75132 O75132 ZBED4 Zinc finger BED domain-containing protein 4 1 TEVSET(0.029)ARPS(0.486)S(0.486)PDTR 88.264 0.0041499 333630000 327930 276200 183980 261140 327230 311580 243460 349700 360910 TRUE FALSE 284593.2196 274385.624 272953.3434 320435.8283 320718.7632 323566.6842 219849.2867 274919.3764 318243.631 0.894262106 0.862187322 0.857686743 1.006888425 1.007777476 1.016726347 0.690820696 0.863864504 1 18.27977212 2.283746204 24.99999195 0.847424759 0.939596511 0.169479396 0.093069252 227.4710309 125852.7751 0.036312586 0.028127471 192.1968228 -2.283746204 0.092171751 TEVSLTLTNKFDVPGDENAEMDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TEVSLTLTNKFDVPGDENAEMDAR 24 1 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 112.13 0.0017451 658450000 476980 457860 240110 291860 461820 403190 582130 632350 258910 FALSE TRUE 413945.8845 454852.2875 356227.9991 358131.2738 452630.6855 418700.9802 525675.1222 497126.8735 228301.9548 1.813150855 1.992327608 1.560337052 1.568673708 1.982596627 1.833978954 2.302543238 2.177497227 1 17.80058369 3.213094166 24.98546443 1.931069287 1.739723617 0.007577636 0.366413443 721.8472416 708211.5587 0.111824442 0.126844062 1633.406074 -3.213094166 -0.19134567 TEWLDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 TEWLDGK 7 0 P62937;P0DN26;A0A0H2UH34;A0A0B4J2A2;A0A075B767;A0A075B759;Q9Y536;F5H284;P0DN37;P62937-2 P62937;P62937-2 PPIA;PPIAL4C;PPIAL4E;PPIAL4A;PPIAL4D "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase A-like 4A/B/C;Peptidyl-prolyl cis-trans isomerase A-like 4D" 0 ;;;;;;;; 170.73 0.0022429 32342039000 48043980 34689140 23204950 28767220 32596980 26122760 38688980 43811380 49353560 FALSE TRUE 41694846.32 34461264.76 34426941.44 35299256.98 31948363.87 27127719.48 34936928.67 34442657.33 43519038.36 0.958082896 0.791866412 0.791077715 0.811122173 0.734123847 0.623352916 0.802796431 0.791438842 1 25.37514334 4.739123672 5.595806908 0.786485156 0.964043611 0.238998842 0.091809714 0.214797127 27.28457511 0.022550217 0.146078514 54843.31168 -4.739123672 0.177558455 TEWLDGKHVVFGK ddPTM_MDA-MB-175_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 ; 148.68 2.61E-05 3894100000 15870400 10780600 5253200 6175600 11397000 8711700 15411900 17810600 2269400 FALSE TRUE 13773086.43 10709781.53 7793665.091 7577864.368 11170222 9046844.736 13917256.31 14001941.79 2001114.117 6.882709142 5.351909437 3.89466299 3.786822702 5.582001497 4.520903959 6.954753949 6.997073116 1 20.93237201 4.702085921 4.072574526 4.982307969 6.986144034 0.120908314 1.732784093 0.503933784 16.97071157 0.433737445 2.727810486 50360.02313 -4.702085921 2.003836065 TEYGDLELCIEVVDNVQDAIDHIHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TEYGDLELCIEVVDNVQDAIDHIHK 25 0 P54886-2;P54886 P54886-2 ALDH18A1 Delta-1-pyrroline-5-carboxylate synthase;Glutamate 5-kinase;Gamma-glutamyl phosphate reductase 0 ; 207.17 1.96E-25 139195000 194295 195091 142292 220665 203393 168595 219401 251421 255207 FALSE TRUE 168618.4235 193809.4344 211104.8871 270770.3609 199345.8772 175080.9587 198123.5248 197656.5757 225036.7192 0.749292934 0.861234713 0.93809085 1.203227464 0.885837111 0.778010626 0.88040532 0.878330329 1 17.7798009 4.584642363 2.872916426 0.930456394 0.744127381 0.230485824 0.110548683 0.536720356 7.248625855 0.029928935 0.192214946 38427.52053 -4.584642363 -0.186329013 TEYLSNADER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TEYLSNADER 10 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0;H0YJ21 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 188.91 2.49E-06 865732000 760486 731343 442683 462696 811928 790765 748286 794925 819956 FALSE TRUE 659985.8483 726538.7597 656765.9795 567758.1987 795772.2213 821186.2412 675717.3389 624936.4749 723021.7358 0.912816055 1.00486434 0.908362705 0.785257442 1.100620053 1.135769785 0.934574032 0.864339817 1 19.46367949 TEYNLR ddPTM_MDA-MB-175_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 ; 141.55 0.027076 600970000 743360 653760 401120 511930 719570 707780 684310 762580 650030 FALSE TRUE 645123.0926 649465.4075 595102.9737 628171.5309 705251.9648 735008.7546 617945.7215 599508.2014 573184.1939 1.125507471 1.133083247 1.038240377 1.095933101 1.230410699 1.282325581 1.078092746 1.045925913 1 19.1286393 2.009453457 24.99362193 1.036973137 1.148941137 0.380380528 0.068102035 235.0677195 621483.9875 0.030893222 0.020798394 102.2006027 -2.009453457 0.111968 TFCPAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 TFCPAHK 7 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;; 110.63 0.0067597 22081990000 20723970 19844630 13017120 14357210 20087980 20885260 24434550 24661490 25974190 FALSE TRUE 17985244.86 19714269.32 19312242.77 17617233.97 19688268.5 21688729.47 22064891.1 19387822.28 22903550.85 0.78526011 0.860751656 0.843198633 0.769192257 0.859616425 0.946959256 0.963382981 0.846498537 1 24.44906795 2.928281224 4.528452776 0.926188846 0.819149674 0.607395305 0.046761707 0.170082549 6.605919458 0.015192909 0.015516729 847.7762071 -2.928281224 -0.107039172 TFDAQIVIIEHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TFDAQIVIIEHK 12 0 P15170-2;P15170-3;P15170 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 87.498 0.010514 330730000 107050 92706 61901 89236 97492 97951 114860 137240 141510 FALSE TRUE 92903.07127 92097.00818 91836.53065 109498.3977 95552.09994 101719.2384 103720.8949 107892.294 124780.849 0.744529886 0.738070056 0.735982576 0.877525666 0.765759335 0.815183092 0.831224468 0.864654271 1 16.92903701 -2 0.486430598 7.273223822 0.761526555 0.762672986 0.039861418 53.65580762 0.627185699 352.9443155 0.027819452 0.01 2 -6.511697267 TFDGDVFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TFDGDVFR 8 0 P98088;A0A0G2JM87;A0A0G2JR65;Q02817;Q9HC84 P98088;Q9HC84 MUC5AC;MUC2;MUC5B Mucin-5AC;Mucin-2;Mucin-5B 0 ; 192.11 0.00041331 536140000 708230 882340 435490 669020 920030 933190 670750 932640 867740 FALSE TRUE 614635.6111 876543.8504 646094.4206 820931.2163 901723.203 969090.4232 605700.7682 733202.1938 765156.7657 0.803280633 1.145574201 0.844394835 1.072892841 1.178481644 1.266525327 0.791603493 0.958237876 1 19.54539583 4.762295385 23.25336141 1.022450781 0.803279975 0.193296723 0.145771332 4798.295194 4700776.61 0.036621838 1.845981146 57848.93725 -4.762295385 -0.219170806 TFDHYCEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TFDHYCEYR 9 0 Q14204;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;;;; 200.11 2.36E-05 4475390000 4867050 5353190 3132899 3433695 5579840 5671400 5126790 5664150 5853720 FALSE TRUE 4223857.011 5318024.542 4647979.435 4213367.93 5468812.101 5889582.428 4629594.695 4452915.601 5161699.89 0.81830736 1.030285498 0.90047456 0.816275262 1.059498269 1.141016052 0.896912799 0.862683941 1 22.29941483 3.237478899 24.9999996 0.976171403 0.901913448 0.197433885 0.096983169 70.50495969 1629478.611 0.031501675 0.037783703 1727.742033 -3.237478899 -0.074257954 FNWYVDGVEVHNAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 FNWYVDGVEVHNAK 14 0 A0A0A0MS08;P01857 A0A0A0MS08 IGHG1 Ig gamma-1 chain C region 0 ; 179.41 1.87E-06 4172700000 9014700 3111740 751290 403340 284662 270943 286867 409330 182810 FALSE TRUE 7823384.555 3091298.775 1114616.357 494924.5117 278997.7831 281366.3525 259046.6825 321797.9649 161198.4101 48.53264094 19.17698055 6.914561729 3.070281596 1.730772549 1.745466053 1.607005196 1.996284981 1 17.29847799 4.920583765 1.236785985 1.63957888 86.21154266 0.998951498 0.479863821 0.067620743 0.066848185 0.158870451 8.096964672 83288.25534 -4.920583765 84.57196378 up TFDQLTPEESKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 182.02 1.05E-05 1012560000 1356330 1088110 623257 687940 1078000 1105400 1215270 1256600 365788 FALSE TRUE 1177087.554 1080962.134 924666.1699 844147.2915 1056549.909 1147925.453 1097413.302 987885.8689 322544.9593 3.649375133 3.351353362 2.866782267 2.617146128 3.275667092 3.558962619 3.402357627 3.062785017 1 18.29914075 4.409111119 3.274008172 2.913055911 3.610763156 0.131645912 0.712296343 0.559444031 11.57001791 0.182654722 0.660464868 25651.40273 -4.409111119 0.697707245 TFEGIDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TFEGIDPK 8 0 P50395;P50395-2;Q5SX87;Q5SX86 P50395;Q5SX86 GDI2 Rab GDP dissociation inhibitor beta 0 ; 106.04 0.0099378 349580000 1343450 1154580 771910 909990 1051540 918320 1284570 1454090 1403360 FALSE TRUE 1165909.679 1146995.488 1145208.258 1116617.138 1030616.411 953648.3646 1159992.599 1143144.169 1237456.38 0.942182446 0.926897713 0.925453436 0.902348686 0.8328507 0.770652106 0.937400799 0.923785426 1 20.23894624 1.368323992 1.810450163 1.017279128 0.887067239 0.30183301 0.052801266 0.931553807 3.741789832 0.196192853 0.016095776 23.35199516 -1.368323992 -0.13021189 TFEHVTSEIGAEEAEEVGVEHLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TFEHVTSEIGAEEAEEVGVEHLLR 24 0 P51665;H3BNT7;H3BTM8 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ;;;; 348.48 4.41E-102 1201420000 348949 364636 191254 241390 335723 338829 327919 402174 350079 FALSE TRUE 302834.5055 362240.6821 283745.0741 296201.2889 329042.7691 351863.9709 296117.4659 316172.2198 308693.0594 0.981021427 1.173465587 0.919181904 0.959533361 1.065922148 1.139850606 0.959261819 1.02422847 1 18.23581352 TFEINPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TFEINPR 7 0 P14625;H0YIV0;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ;;; 170.73 0.0022429 1576370000 2042340 2085830 1328320 1690610 2261970 2814300 1947390 1978310 1875210 FALSE TRUE 1772439.594 2072128.045 1970699.995 2074488.84 2216961.222 2922567.942 1758532.418 1555263.802 1653524.81 1.071915936 1.253158122 1.191817615 1.254585856 1.34074869 1.767477527 1.063505311 0.940574821 1 20.65711326 2.018363938 24.99995859 0.976841754 1.31293354 0.409383394 0.179186935 223.797007 304667.4122 0.075362079 0.050799686 104.3191255 -2.018363938 0.336091786 TFEMSDFIVDTR ddPTM_MDA-MB-175_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 81.865 0.038376 10167000 20656 19295 12133 12452 18430 24284 17145 18174 18241 FALSE TRUE 17926.25726 19168.24987 18000.55938 15279.41692 18063.27906 25218.22119 15482.28054 14287.63153 16084.56976 1.114500265 1.191716668 1.119119731 0.949942532 1.1230191 1.567851772 0.962554844 0.888281859 1 13.97338973 2.033923291 24.99998807 0.932937234 1.171360642 0.317826334 0.156856693 206.5309155 152203.4509 0.06534658 0.044056413 108.1242957 -2.033923291 0.238423409 TFFILHDINSDGVLDEQELEALFTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TFFILHDINSDGVLDEQELEALFTK 25 0 Q02818;H7BZI1 Q02818 NUCB1 Nucleobindin-1 0 204.31 4.78E-25 268210000 136670 110980 76005 81566 103840 120910 133990 171060 153010 FALSE TRUE 118608.7132 110250.9651 112761.2722 100086.807 101773.7872 125561.4859 120995.6704 134480.1502 134921.3321 0.879095332 0.817149989 0.835755699 0.74181603 0.754319466 0.930627381 0.896786806 0.99673008 1 17.04175894 2.255122716 1.520017908 0.993493613 0.807185594 0.700877942 0.048631936 0.227610804 1.055407243 0.035260255 0.017076756 179.9379285 -2.255122716 -0.186308019 TFGETHPFTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TFGETHPFTK 10 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ; 117.7 0.00092313 950920000 2539700 2380600 1460240 1767710 2373000 2215400 2634600 2952400 2738200 FALSE TRUE 2204072.21 2364961.682 2166416.948 2169095.573 2325781.943 2300627.872 2379096.898 2321052.236 2414493.115 0.912850899 0.979485784 0.897255384 0.898364779 0.963258884 0.952840932 0.985340104 0.961300002 1 21.20328892 3.096978049 6.448895897 0.972055191 0.924465688 0.486758419 0.025894526 0.201400382 11.36565784 0.007870042 0.008952611 1250.195838 -3.096978049 -0.047589502 TFGHNTMDAVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TFGHNTMDAVPR 12 0 G3XAL9;P55011-3;P55011 G3XAL9 SLC12A2 Solute carrier family 12 member 2 0 152.47 6.98E-05 134530000 113750 114860 56605 109560 169950 162190 84557 161110 136460 FALSE TRUE 98717.64929 114105.4771 83979.36733 134437.2725 166568.3275 168429.5543 76356.67515 126657.8803 120327.8543 0.820405632 0.94828814 0.697921257 1.117258122 1.384287358 1.399755321 0.6345719 1.05260649 1 16.87661112 3.722310783 24.39098457 1.088868947 0.834813321 0.25922785 0.219127148 919.4627943 1380112.712 0.064501008 0.096025653 5276.072842 -3.722310783 -0.254055626 TFHHVYSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TFHHVYSGK 9 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 104.2 0.0019076 552430000 1059100 1016900 477140 776670 932520 883590 992260 1163500 954050 FALSE TRUE 919137.2516 1010219.917 707886.4999 953024.7942 913964.6764 917582.2791 896030.7779 914694.5794 841263.2959 1.092567875 1.200836791 0.841456537 1.132849607 1.086419295 1.090719497 1.065101476 1.087286922 1 19.68219788 1.232045836 23.88367121 0.999999776 1.074143074 0.062201193 0.091080093 399.7530128 1465273.102 0.189681368 0.020913069 17.06262459 -1.232045836 0.074143298 TFHIFYYLLSGAGEHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TFHIFYYLLSGAGEHLK 17 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 252.3 3.20E-27 1060316000 2400697 2432100 1291653 2052150 1614995 1436492 3307743 2973182 3104644 FALSE TRUE 2083438.809 2416123.375 1916300.711 2518122.023 1582859.759 1491754.777 2986958.593 2337390.167 2737616.523 0.761041143 0.882564579 0.699988729 0.919822773 0.578189 0.544910057 1.091079984 0.853804814 1 21.38448894 2.228604516 24.99977205 0.959558842 0.738186984 0.453952224 0.128621137 210.3187106 528105.3922 0.052817484 0.036083826 169.2795579 -2.228604516 -0.221371857 TFHVETPEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TFHVETPEER 10 0 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 0 120.09 0.00060585 85728000 90984 76190 63647 72335 74991 104260 78559 84155 125180 FALSE TRUE 78960.23388 75689.50287 94426.90209 88759.76732 73498.82582 108270.9497 70940.36027 66159.10814 110381.363 0.715340269 0.68570908 0.855460555 0.804119146 0.66586264 0.98088071 0.642684221 0.599368465 1 16.75213708 TFIAIKPDGVQR ddPTM_MDA-MB-175_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 ; 132.86 0.00015825 25704000000 11288000 10954000 6080700 7643700 11137000 9871200 12905600 14515900 13123600 FALSE TRUE 9796262.2 10882042.45 9021346.859 9379318.912 10915395.49 10250951.45 11654016.9 11411787.75 11572142.96 0.846538298 0.940365366 0.779574439 0.810508386 0.94324755 0.885830005 1.007075089 0.986142998 1 23.46415272 2.518049138 1.315894786 1.001323418 0.852068599 0.598935452 0.050337316 0.304805293 1.093061335 0.030950045 0.019701116 329.647008 -2.518049138 -0.149254819 TFIGPGGNMPGYLRPETAQGIFLNFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TFIGPGGNMPGYLRPETAQGIFLNFK 26 1 P41250 P41250 GARS Glycine--tRNA ligase 0 142.32 2.57E-07 370710000 106610 89662 53161 78006 88837 82341 107420 120710 87261 FALSE TRUE 92521.21838 89073.00442 78869.83741 95718.45455 87069.31751 85508.71155 97002.42493 94897.10587 76945.10399 1.202431521 1.157617572 1.025014372 1.243983692 1.131577098 1.111295029 1.260670529 1.233309216 1 16.23154191 TFLDKDAQRLS(ph)PIPEEVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TFLDKDAQRLSPIPEEVPK 19 2 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 TFLDKDAQRLS(1)PIPEEVPK;TFLDKDAQRLS(1)PIPEEVPK 139.47 9.64E-08 3271100000 3862500 3155700 1706400 1594710 2771800 2233600 4289400 4823700 736860 TRUE FALSE 3352060.839 3134969.999 2531620.748 1956813.279 2716646.603 2319528.037 3873414.648 3792189.293 649749.2502 5.159006859 4.824892061 3.896304223 3.011643766 4.181069239 3.569881822 5.961399181 5.836388871 1 19.30952354 4.391118888 4.908283542 4.169040148 5.084532719 0.072722103 1.407139948 0.639601478 25.97066073 0.365410424 1.046647043 24610.41223 -4.391118888 0.915492572 TFLEGDWTS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TFLEGDWTSPSK 12 0 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 TFLEGDWTS(0.999)PS(0.001)K;TFLEGDWTS(0.992)PS(0.008)K;TFLEGDWTS(1)PSK;TFLEGDWTS(0.934)PS(0.066)K;TFLEGDWTS(0.999)PS(0.001)K;TFLEGDWT(0.001)S(0.995)PS(0.004)K 290.64 4.32E-36 2137625000 7311140 6266330 4135450 5200180 6928190 5630070 7503160 9298210 7832940 TRUE FALSE 6344954.325 6225166.066 6135367.452 6380960.349 6790332.574 5846662.436 6775504.698 7309860.15 6906938.757 0.918634803 0.901291626 0.888290409 0.923847825 0.983117531 0.846491136 0.980970722 1.058335741 1 22.719615 2.018087491 7.950253873 1.029424374 0.912715323 0.654974399 0.036413877 0.088135394 28.74461265 0.014568544 0.009567548 104.252743 -2.018087491 -0.11670905 TFLVGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TFLVGER 7 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;;;; 126.67 0.0091423 1854810000 1747564 1762747 969364 1367002 1687883 1854400 1750408 1917458 2088181 FALSE TRUE 1516618.99 1751167.399 1438151.673 1677400.697 1654297.431 1925739.968 1580653.702 1507424.528 1841318.621 0.823659182 0.951039857 0.781044441 0.910977969 0.898430837 1.04584831 0.858435734 0.818665771 1 20.81230786 3.554900288 24.99980638 0.911535333 0.85919095 0.144732718 0.076947045 302.5078609 97229.82611 0.0216042 0.032044199 3588.395373 -3.554900288 -0.052344383 TFLVIPELAQELHVWTDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TFLVIPELAQELHVWTDK 18 0 P49902-2;P49902;Q5JUV6 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ; 159.06 4.40E-11 872430000 669250 729290 456090 675540 872660 594600 884200 1000170 978340 FALSE TRUE 580806.9168 724499.246 676656.6495 828931.682 855295.7733 617474.6468 798450.4201 786291.4288 862681.7597 0.673257444 0.839822145 0.784364155 0.96087772 0.991438342 0.715761797 0.925544572 0.911450161 1 19.71846893 5.623999485 0.752459464 0.91167185 1.29E-08 0.434852908 0.085113742 9.09034418 1.48220349 0.032163973 9.511595206 420726.1299 -5.623999485 -0.911671837 TFNIKNDFTEEEEAQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TFNIKNDFTEEEEAQVR 17 1 E5RJR5;P63208 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 117.29 0.0002047 111860000 145110 142030 59538 82334 133360 169610 140440 152300 84452 FALSE TRUE 125933.3458 141096.9956 88330.77594 101029.1931 130706.3969 176135.0065 126820.1504 119731.8302 74468.18077 1.691102757 1.89472865 1.18615461 1.356675993 1.755197932 2.365238477 1.703011261 1.607825369 1 16.18433649 1.222692927 3.132714833 0.858050118 1.705639439 0.335746574 0.310128863 0.510136437 6.342075055 1.103947657 0.085782424 16.69909466 -1.222692927 0.847589322 TFNQVEIKPEMIGHYLGEFSITYKPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TFNQVEIKPEMIGHYLGEFSITYKPVK 27 2 K7EM56;A0A0B4J2B4;S4R417;K7ELC2;P62841 K7EM56 RPS15 40S ribosomal protein S15 0 ; 230.85 2.73E-35 1249360000 2522500 1853510 1312370 1624060 1555690 1277280 2614860 3189600 2521850 FALSE TRUE 2189145.234 1841334.171 1947036.522 1992827.645 1524734.813 1326417.788 2361271.28 2507528.861 2223719.766 0.984451938 0.828042364 0.875576388 0.896168517 0.685668597 0.596486036 1.061856496 1.127628085 1 21.08454356 2.115760808 10.16968336 1.079328459 0.81309311 0.530104338 0.111654055 0.238137966 20.09774699 0.047746848 0.032180745 130.54517 -2.115760808 -0.266235349 TFNTSTGGLLLPSDTKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TFNTSTGGLLLPSDTKR 17 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 161.1 4.82E-09 1741810000 934060 783950 371560 539400 742920 668730 921010 989590 546020 FALSE TRUE 810621.6044 778800.1808 551247.6588 661879.0142 728137.3455 694456.4758 831690.592 777973.8795 481470.1376 1.683638384 1.617546178 1.144925958 1.374704187 1.512320887 1.442366663 1.727398081 1.615829973 1 18.87708679 1.231589179 24.87375255 0.999999052 1.514465535 0.479109228 0.168706106 224.5914447 801253.8543 0.428735221 0.044188779 17.04469283 -1.231589179 0.514466483 TFNVDMYEEIHR ddPTM_MDA-MB-175_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 ;; 126.51 0.00028628 767070000 446370 428790 254960 351800 435980 447280 428050 461320 546590 FALSE TRUE 387381.0735 425973.2503 378259.5088 431681.5669 427304.851 464487.151 386537.7769 362670.308 481972.7529 0.803740608 0.883811891 0.78481513 0.895655541 0.886574705 0.963720767 0.801990931 0.752470562 1 18.87859206 4.756211273 22.11537976 0.860063981 0.803740385 0.054080272 0.077079738 2681.426538 3359415.366 0.019078261 0.468295584 57044.17098 -4.756211273 -0.056323596 TFPAHDYFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TFPAHDYFK 9 0 Q9Y3P9;Q9Y3P9-2;A0A0U1RQX4;Q5R372-4;Q5R372;Q5R372-3 Q9Y3P9;Q5R372-4 RABGAP1;RABGAP1L Rab GTPase-activating protein 1;Rab GTPase-activating protein 1-like 0 ; 115.78 0.0014203 831600000 1322040 1728790 887450 1168090 1778380 1533030 1755460 2051800 1930720 FALSE TRUE 1147329.064 1717433.465 1316623.788 1433322.688 1742993.717 1592006.656 1585215.759 1613038.537 1702472.481 0.673919301 1.008787798 0.773359806 0.841906523 1.023801405 0.935114473 0.931125629 0.9474682 1 20.69920005 3.30492738 8.854856128 0.960549999 0.833427593 0.40091841 0.086344416 0.325782568 39.86766624 0.022914653 0.029558512 2018.028894 -3.30492738 -0.127122405 TFQARPLS(ph)ADLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TFQARPLSADLTK 13 1 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 TFQARPLS(0.999)ADLT(0.001)K 106.67 0.00082119 443910000 234000 234460 139910 180960 263890 258360 323670 377990 221820 TRUE FALSE 203076.3071 232919.8168 207570.944 222049.7338 258639.1053 268299.2764 292280.5332 297159.78 195596.6923 1.038239986 1.190816747 1.061219091 1.135242786 1.322308175 1.371696388 1.494302024 1.519247471 1 17.57752245 3.187186676 2.831041101 1.385203103 1.103274137 0.380717518 0.146133115 0.247538422 4.04772449 0.046481212 0.056440953 1538.81594 -3.187186676 -0.281928966 TFQQIQEEEDDDYPGSYS(ph)PQDPSAGPLLTEELIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TFQQIQEEEDDDYPGSYSPQDPSAGPLLTEELIK 34 0 Q9NQG5;A2A2M0 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 1 TFQQIQEEEDDDYPGS(0.018)Y(0.001)S(0.965)PQDPS(0.015)AGPLLTEELIK 175.15 5.84E-15 43263000 41453 40938 23704 29960 41124 32635 39999 51459 47533 TRUE FALSE 35974.88102 40669.07558 35167.33369 36762.87591 40305.71286 33890.48957 36119.90314 40454.8933 41913.70289 0.858308346 0.970305002 0.839041441 0.877108759 0.961635696 0.808577797 0.861768363 0.965194925 1 15.35513436 1.607002324 4.294001781 0.99215856 0.884320864 0.414956205 0.050088234 0.153417388 6.247863037 0.0362127 0.012676488 40.45780569 -1.607002324 -0.107837695 TFS(ph)ATVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 TFSATVR 7 0 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 T(0.001)FS(0.996)AT(0.004)VR;TFS(0.996)AT(0.004)VR;T(0.108)FS(0.581)AT(0.311)VR;TFS(0.93)AT(0.07)VR;TFS(0.999)AT(0.001)VR;TFS(0.897)AT(0.103)VR;TFS(0.994)AT(0.006)VR;T(0.002)FS(0.995)AT(0.003)VR;T(0.002)FS(0.932)AT(0.066)VR;TFS(0.799)AT(0.201)VR;TFS(0.844)AT(0.156)VR 178.27 0.00075329 1.16158E+11 8859440 11321050 9325730 11337390 17166590 15548690 16342990 17739680 16930070 TRUE FALSE 7688642.557 11246681.28 13835684.22 13911717.68 16825008.44 16146858.17 14758049.35 13946187.48 14928616.41 0.515027136 0.75336394 0.926789452 0.931882587 1.127030663 1.081604465 0.988574489 0.934191562 1 23.83157713 4.612474913 1.257855378 1.011033965 0.360292247 0.890419883 0.057567722 0.39527759 0.644450808 0.019347935 0.31481779 40970.84421 -4.612474913 -0.650741718 TFS(ph)EPGDHPGMLTSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TFSEPGDHPGMLTSGK 16 0 Q9HA47-3;Q9HA47;Q9HA47-4 Q9HA47-3 UCK1 Uridine-cytidine kinase 1 1 T(0.099)FS(0.901)EPGDHPGMLTSGK 117.29 0.00023266 164680000 247050 136200 116550 155400 197260 181050 219340 225270 316510 TRUE FALSE 214401.7166 135305.2932 172913.9698 190685.9451 193334.9119 188015.1107 198068.4406 177097.7636 279092.5484 0.768210107 0.484804392 0.619557816 0.68323553 0.692726886 0.673665821 0.709687312 0.63454852 1 18.09038408 1.236466064 24.9977848 1.000000441 0.65530165 0.679123287 0.073787951 32.03978817 382286.7386 0.111543986 0.017450597 17.23717393 -1.236466064 -0.344698791 TFS(ph)LTEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TFSLTEVR 8 0 O95239;O95239-2 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 T(0.15)FS(0.79)LT(0.06)EVR;T(0.14)FS(0.859)LTEVR;T(0.142)FS(0.843)LT(0.015)EVR 205.73 8.09E-05 762376000 785940 714210 659822 868860 1381530 1373920 1345880 1573920 1529600 TRUE FALSE 682076.0377 709518.3075 978914.1262 1066147.943 1354040.256 1426775.591 1215356.765 1237349.456 1348772.431 0.505701349 0.526047457 0.725781536 0.790457989 1.003905644 1.057832707 0.901083635 0.917389345 1 20.36321552 3.875921726 1.356222926 0.966145404 0.489316012 0.913187819 0.056719902 0.135722573 0.467797564 0.019557104 0.057314769 7514.8744 -3.875921726 -0.476829392 TFSAT(ph)VR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TFSATVR 7 0 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 TFS(0.443)AT(0.557)VR;T(0.001)FS(0.388)AT(0.61)VR 144.9 0.025966 6032300000 2268190 2973180 2441970 2805710 4064580 3738840 4164990 4063440 4383980 TRUE FALSE 1968442.945 2953648.985 3622914.86 3442789.338 3983702.81 3882675.594 3761069.911 3194504.978 3865710.879 0.509205941 0.764063604 0.937192401 0.890596696 1.0305227 1.004388511 0.97293099 0.826369348 1 21.88230231 4.676608672 1.654787964 0.948160872 0.383004857 0.854414293 0.059428349 0.337219412 0.993706681 0.017605681 0.293467816 47490.71108 -4.676608672 -0.565156015 TFSATVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TFSATVR 7 0 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 0 ; 117.18 0.030951 0 176284 210143 182900 186686 285840 291050 274010 282510 316660 FALSE TRUE 152987.6228 208762.5568 271351.0518 229075.9096 280152.3432 302246.8818 247436.5524 222097.435 279224.8155 0.54790124 0.747650442 0.971801347 0.820399538 1.003321795 1.082449929 0.886155308 0.795407223 1 18.09106764 4.545981365 2.461151772 0.925663073 0.528825239 0.677690259 0.088176111 0.237507226 2.329204662 0.024524669 0.164817662 35154.5356 -4.545981365 -0.396837835 TFSHELSDFGLESTAGEIPVVAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TFSHELSDFGLESTAGEIPVVAIR 24 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 282.2 2.57E-52 4582680000 2998660 2964490 1920422 2632280 3236130 4151850 2728020 2783730 3086730 FALSE TRUE 2602379.483 2945016.07 2849144.503 3229979.406 3171737.344 4311574.356 2463457.04 2188451.003 2721820.296 0.956117304 1.082002392 1.046779064 1.186698259 1.165300056 1.584077524 0.905077034 0.80403949 1 21.37614039 2.039473061 24.99993573 0.877981701 1.168035868 0.351766811 0.170234085 154.9005757 98104.36524 0.070559971 0.047571443 109.5148623 -2.039473061 0.290054167 TFTAWCNSHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TFTAWCNSHLR 11 0 O43707;F5GXS2;O43707-3;K7EP19;P12814-3;P12814;P12814-2;P12814-4;P35609-2;P35609;G3V2N5;A0A494C1A0;Q08043;A0A494C166;A0A494C033;A0A494C0Q3 O43707;P12814-3 ACTN4;ACTN1;ACTN2;ACTN3 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2;Alpha-actinin-3 0 ; 176.62 8.44E-06 5033600000 3932900 5092000 2926900 3745200 5003600 5346600 4413400 4744300 7124400 FALSE TRUE 3413157.3 5058550.317 4342358.63 4595604.902 4904038.149 5552287.162 3985389.147 3729768.365 6282161.548 0.543309381 0.805224488 0.691220466 0.73153243 0.780629105 0.883817953 0.634397749 0.593707808 1 22.58282961 4.749410895 23.87196939 0.746395502 0.543309159 0.243767446 0.11876924 1362.269572 2997051.735 0.028964507 0.397736638 56157.90464 -4.749410895 -0.203086343 TFTEMDSHEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TFTEMDSHEEK 11 0 B0YIW6;P48444;P48444-2;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 ;; 207.29 2.35E-08 1337890000 3611040 3145890 2130510 2399310 3147100 2836120 3692650 4139190 3695480 FALSE TRUE 3133831.915 3125224.441 3160831.762 2944110.007 3084478.867 2945227.372 3334537.371 3254056.43 3258604.564 0.961709791 0.959068331 0.9699955 0.903487965 0.946564336 0.903830862 1.023302247 0.998604269 1 21.63582286 2.227134489 24.99976829 1.006156788 0.941503929 0.647846125 0.023112182 137.6069039 301074.0553 0.009449337 0.006432561 168.7075385 -2.227134489 -0.064652859 TFVDFFSQCLHEEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TFVDFFSQCLHEEYR 15 0 Q53GQ0;A0A1B0GV93 Q53GQ0 HSD17B12 Very-long-chain 3-oxoacyl-CoA reductase 0 ; 191.78 1.61E-07 520460000 417050 384770 286160 413950 531910 493990 375640 658630 556470 FALSE TRUE 361935.7858 382242.4205 424547.9331 507943.6743 521326.0317 512994.115 339210.4906 517787.1 490684.7505 0.737613683 0.778997962 0.865215258 1.035173141 1.062445962 1.045465779 0.69130025 1.055233731 1 18.90443691 4.05540949 2.880114093 0.976682565 0.754830448 0.423662562 0.108084576 0.261072578 4.368416999 0.029672167 0.071142039 11360.81505 -4.05540949 -0.221852117 TFYEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TFYEKR 6 1 P62753;A2A3R7 P62753 RPS6 40S ribosomal protein S6 0 ; 98.133 0.064588 463300000 782230 740650 276200 289120 679310 672070 857220 891300 184584 FALSE TRUE 678856.3236 735784.6214 409771.2438 354769.1149 665793.06 697924.9678 774086.9363 700702.4311 162762.6898 4.170835002 4.520597579 2.517599361 2.179671001 4.090575431 4.287991115 4.755923715 4.305055612 1 17.3124105 TGADTTAAGPLFQQRPYPS(ph)PGAVLR ddPTM_MDA-MB-175_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 185.44 1.04E-17 381390000 254010 271790 130544 198722 292400 294470 280760 308540 218080 TRUE FALSE 220441.9349 270004.5936 193675.515 243844.8674 286581.8121 305798.4514 253531.9384 242561.1221 192298.8308 1.146350885 1.404088587 1.007159088 1.268051742 1.490294095 1.590225225 1.318426832 1.261375958 1 17.55299047 1.226468949 2.699128426 0.921562357 1.323026341 0.268840716 0.163338429 0.721352525 5.883315366 0.668573202 0.044982314 16.84491986 -1.226468949 0.401463984 TGCTFPEKPDFH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TGCTFPEKPDFH 12 1 P55263-3;P55263-2;P55263;P55263-4;A0A5F9ZHJ1 P55263-3 ADK Adenosine kinase 0 ; 126.76 0.0002569 419540000 1354180 1184770 715990 1038110 1293950 1068940 1400040 1556870 1575960 FALSE TRUE 1175221.682 1176987.168 1062245.159 1273828.742 1268202.927 1110062.813 1264264.336 1223945.466 1389651.804 0.845695072 0.846965524 0.764396632 0.916653178 0.912604814 0.798806442 0.909770586 0.880756937 1 20.40629201 -1.158185072 0.831992109 9.999999999 0.849094734 0.469309388 0.048382891 115.5933733 1.69537763 1922.976356 0.017520389 0.06947282 1.158185072 -9.150905265 TGDLGIPPNPEDRS(ph)PS(ph)PEPIYNSEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 TGDLGIPPNPEDRSPSPEPIYNSEGK 26 1 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 2 TGDLGIPPNPEDRS(1)PS(0.999)PEPIY(0.001)NSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(0.992)PS(0.994)PEPIY(0.008)NS(0.007)EGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(0.995)PEPIY(0.005)NSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK 224.27 1.18E-34 11015030000 7077730 4963470 3755430 4422010 5230370 4371900 5989070 6951310 7198340 TRUE FALSE 6142390.048 4930864.639 5571568.509 5426094.957 5126295.87 4540089.822 5408250.913 5464826.452 6347360.446 0.967707774 0.77683703 0.877777236 0.854858489 0.807626401 0.715272098 0.852047234 0.860960473 1 22.59772534 1.170955816 2.276433929 1.069140158 0.830889629 0.375438561 0.065663684 0.824874544 3.786205094 0.429719885 0.016973779 14.82367264 -1.170955816 -0.238250529 TGDLGIPPNPEDRS(ph)PS(ph)PEPIYNSEGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TGDLGIPPNPEDRSPSPEPIYNSEGKR 27 2 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 2 TGDLGIPPNPEDRS(0.998)PS(0.946)PEPIY(0.019)NS(0.037)EGKR;TGDLGIPPNPEDRS(0.956)PS(0.893)PEPIY(0.028)NS(0.122)EGKR 89.266 0.035043 375900000 428040 315740 144926 148230 315320 281620 413170 452290 81852 TRUE FALSE 371473.4295 313665.8832 215012.6983 181887.8871 309045.7489 292454.1036 373100.837 355571.3032 72175.54981 5.146804292 4.345874524 2.979024045 2.520076224 4.281862067 4.051983039 5.169352197 4.926478623 1 16.13922257 TGENFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TGENFR 6 0 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ;;; 132.96 0.034132 2211420000 2942360 2713500 1605590 2003430 2498120 2765570 2787010 3024430 2888100 FALSE TRUE 2553519.671 2695674.84 2382058.694 2458339.402 2448412.299 2871963.267 2516726.199 2377679.181 2546672.108 1.002688828 1.058508801 0.935361363 0.965314457 0.961416388 1.127731858 0.98824116 0.933641662 1 21.28018179 1.994806585 24.97182453 0.961739078 1.00790162 0.08490337 0.056211447 484.1790891 2328106.806 0.024018662 0.015670556 98.81129353 -1.994806585 0.046162542 TGENVEDAFLEAAKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TGENVEDAFLEAAKK 15 1 P61106;X6RFL8 P61106 RAB14 Ras-related protein Rab-14 0 133.86 6.21E-05 54632000 174340 117690 102720 94815 118130 107910 151020 208200 88408 FALSE TRUE 151300.5273 116916.8866 152395.7356 116344.1949 115779.4441 112061.3675 136374.1036 163678.0502 77956.50695 1.940832564 1.499770721 1.95488153 1.492424423 1.485179989 1.437485746 1.749361394 2.099607289 1 16.25038183 4.757028644 23.02843485 1.637473923 1.940833353 0.098469456 0.304849128 3617.383063 4510424.11 0.073592563 2.110888791 57151.63303 -4.757028644 0.30335943 TGFINLDKPSNPSSHEVVAWIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TGFINLDKPSNPSSHEVVAWIR 22 1 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 212.65 1.11E-23 576520000 510410 421480 142930 324220 514000 440140 449710 604090 577730 FALSE TRUE 442958.0253 418711.2701 212051.4261 397839.1064 503772.4056 457072.4706 406097.1934 474910.0545 509431.4176 0.869514541 0.821918821 0.416251175 0.780947332 0.988891514 0.897220813 0.797157732 0.932235504 1 18.95852841 3.460680006 11.32772888 0.910987587 0.695217631 0.38094625 0.129891427 0.50149536 339.6976326 0.037783951 0.049193541 2888.550775 -3.460680006 -0.215769956 TGFLEIDEHMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TGFLEIDEHMR 11 0 P35813;P35813-3;P35813-2;E9PL75;E9PJN3;E9PKB5 P35813 PPM1A Protein phosphatase 1A 0 132.32 0.0001849 232510000 452420 391830 247570 295700 384710 435050 397820 438800 602780 FALSE TRUE 392631.5507 389256.0429 367295.6801 362843.2045 377055.0237 451786.655 359239.4776 344966.0347 531520.0351 0.738695674 0.732345005 0.691028853 0.68265198 0.709390049 0.849989888 0.675871941 0.649017933 1 19.01976455 1.230566609 24.99910968 1.000000522 0.713741078 0.72866272 0.054423307 165.6343732 517934.6246 0.150294783 0.013964849 17.00460736 -1.230566609 -0.286259444 TGFSTSPESPYTHWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TGFSTSPESPYTHWK 15 0 E9PKG1;Q99873-2;Q99873-3;Q99873;Q99873-5 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ; 205.27 4.48E-09 2384600000 1683480 1381300 619480 1026200 1601980 1260410 1631150 1694320 1766510 FALSE TRUE 1461003.853 1372226.149 919062.6 1259214.394 1570103.732 1308898.788 1472961.324 1332002.853 1557675.2 0.9379387 0.880944981 0.590021976 0.808393428 1.007978898 0.840289932 0.945615186 0.855122334 1 20.57096301 3.380551523 9.061845587 0.916938797 0.792357099 0.261205011 0.103116732 0.398083385 33.65338246 0.029790771 0.0384696 2401.881201 -3.380551523 -0.124581698 TGGIGDSRPPS(ph)FHPHAGGGSQENLDNDTETDSLVSAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TGGIGDSRPPSFHPHAGGGSQENLDNDTETDSLVSAQR 38 1 Q92997-2;Q92997 Q92997-2 DVL3 Segment polarity protein dishevelled homolog DVL-3 1 T(0.009)GGIGDS(0.075)RPPS(0.63)FHPHAGGGS(0.285)QENLDNDTETDSLVSAQR 266.94 3.45E-63 649260000 246040 256470 68048 160430 345360 323830 276480 320120 221140 TRUE FALSE 213525.1906 254785.2317 100956.2404 196858.0835 338488.0117 336287.9496 249667.0122 251664.8292 194997.0811 1.095017368 1.30661049 0.51773206 1.009543745 1.735861941 1.724579402 1.280362817 1.290608186 1 17.573093 3.37525232 9.644443494 1.397805857 0.966338226 0.351429149 0.286407717 0.358125508 30.96102611 0.086578837 0.111785615 2372.751848 -3.37525232 -0.431467631 TGGIGDSRPPSFHPHAGGGS(ph)QENLDNDTETDSLVSAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TGGIGDSRPPSFHPHAGGGSQENLDNDTETDSLVSAQR 38 1 Q92997-2;Q92997 Q92997-2 DVL3 Segment polarity protein dishevelled homolog DVL-3 1 TGGIGDSRPPSFHPHAGGGS(1)QENLDNDTETDSLVSAQR;TGGIGDSRPPSFHPHAGGGS(1)QENLDNDTETDSLVSAQR;TGGIGDSRPPSFHPHAGGGS(1)QENLDNDTETDSLVSAQR 337.13 1.11E-129 2520100000 402406 403222 95896 233553 502170 487487 395008 494920 349378 TRUE FALSE 349227.0275 400573.2081 142271.6264 286584.7783 492177.7995 506240.9403 356700.185 389085.2095 308074.9309 1.133578206 1.300246038 0.461808515 0.930243748 1.597591203 1.643239646 1.157835803 1.262956413 1 18.23292176 3.266956331 24.96734808 1.32611269 0.945691439 0.306650102 0.280538615 277.4022705 243908.1649 0.084514958 0.109086946 1849.082683 -3.266956331 -0.38042125 TGGMAFHSYFMEAIAPPLLQELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TGGMAFHSYFMEAIAPPLLQELK 23 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;; 134.9 1.31E-05 1978750000 2276340 1892680 1506420 1666710 2046800 1928160 2602700 2981610 3717730 FALSE TRUE 1975515.901 1880246.86 2234929.751 2045161.98 2006072.684 2002337.563 2350290.555 2344015.904 3278224.195 0.602617693 0.57355652 0.681750124 0.623862756 0.611938832 0.610799458 0.716940153 0.715026113 1 21.64448309 -0.492139811 0.923801237 10 0.618755665 0.913941962 0.035909375 12.08933367 0.52640118 216.2591131 0.012010843 0.322003201 0.492139811 -9.381244335 TGGMAFHSYFMEAIAPPLLQELKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 148.89 9.97E-08 488979000 964000 813230 517240 524160 755030 671310 1240770 1235140 415712 FALSE TRUE 836604.9575 807887.8386 767378.9941 643178.5393 740006.3802 697135.7301 1120440.316 971014.9229 366567.0009 2.282270241 2.203929531 2.093420826 1.754600217 2.018747946 1.901796202 3.056577143 2.648942541 1 18.48371739 TGGQVPDTNYIFMGDFVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TGGQVPDTNYIFMGDFVDR 19 0 O00743;O00743-3;Q5T1S7 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed;Serine/threonine-protein phosphatase" 0 ;; 107.61 0.00067725 96831000 67991 63888 38797 53248 66532 73896 70387 75761 72556 FALSE TRUE 59005.81708 63468.31552 57559.35897 65338.77224 65208.14337 76738.82694 63560.87957 59560.09972 63978.51234 0.922275541 0.992025497 0.899667042 1.021261199 1.019219438 1.199446879 0.993472296 0.930939116 1 15.96529983 3.713442232 22.18000554 1.022051677 0.943392997 0.25558104 0.071340567 310.3113536 274010.3543 0.021563592 0.032011166 5169.424917 -3.713442232 -0.07865868 TGGS(ph)PSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TGGSPSVR 8 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 T(0.327)GGS(0.666)PS(0.008)VR 70.929 0.052511 52732000 176850 165080 89419 107640 135900 168740 153250 179670 171500 TRUE FALSE 153478.8244 163995.5786 132662.3275 132081.3072 133195.8559 175231.537 138387.8386 141248.9687 151225.4654 1.014900659 1.084444199 0.877248598 0.873406518 0.880776631 1.158743579 0.915109358 0.93402899 1 17.20634157 4.251310321 24.99826966 0.94780729 1.049672446 0.194643335 0.085571596 382.9299687 750794.5949 0.021548002 0.056205524 17836.52803 -4.251310321 0.101865155 TGHSGTLDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TGHSGTLDPK 10 0 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 102.52 0.0029357 62460000 217570 153200 116180 114110 155820 137670 186030 219590 218290 FALSE TRUE 188817.5732 152193.6191 172365.0366 140020.4196 152719.4869 142966.254 167988.8392 172632.3874 192484.0049 0.980952019 0.790681902 0.895477194 0.727439247 0.79341391 0.742743555 0.872741812 0.896866145 1 17.55437904 1.42051659 1.688835861 1.02590958 0.819520857 0.35815821 0.074293049 0.706806341 2.648866465 0.221346354 0.02073381 26.33398535 -1.42051659 -0.206388722 TGHYLTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TGHYLTVK 8 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 114.89 0.0025684 396750000 1016700 953510 563350 819170 964940 783470 1039300 1127700 1216800 FALSE TRUE 882340.519 947246.33 835787.9443 1005175.069 945739.5819 813610.5979 938508.846 886550.1308 1072951.29 0.822349092 0.882841876 0.778961684 0.936831968 0.881437574 0.758292203 0.874698464 0.826272487 1 20.03315315 1.234061698 24.99829792 1.00000023 0.846089926 0.461700401 0.052518497 123.314212 685109.0042 0.09412559 0.012124452 17.14200818 -1.234061698 -0.153910304 TGIIVTTSEAVLLQLVADKDHPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TGIIVTTSEAVLLQLVADKDHPK 23 1 Q96CN7 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 155.76 1.51E-08 218660000 325800 241850 179770 229890 232140 179980 294680 362130 337390 FALSE TRUE 282744.7045 240261.2714 266707.3733 282090.0381 227520.8682 186903.9471 266101.979 284691.3176 297504.1386 0.950389147 0.807589678 0.896482901 0.948188619 0.764765389 0.628239822 0.894447991 0.956932293 1 18.18255021 1.791437038 3.421777014 0.981762314 0.832584922 0.279237998 0.094587733 0.301154063 6.616082588 0.065647109 0.027035829 61.86386342 -1.791437038 -0.149177391 TGKPEEASLDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TGKPEEASLDSR 12 1 Q9BY42;A2A2L5;A0A0A0MQR2 Q9BY42 RTFDC1 Protein RTF2 homolog 0 ; 90.861 0.0078638 444530000 1578580 950510 611900 834480 1059210 902220 1092350 1306810 1197400 FALSE TRUE 1369966.653 944266.0372 907816.8867 1023961.438 1038133.793 936928.9872 986414.0651 1027358.851 1055844.736 1.297507679 0.894322816 0.859801499 0.969803043 0.983225808 0.88737383 0.93424159 0.973020763 1 20.00996627 4.742885598 24.98829079 0.938733951 1.297507823 0.859967872 0.045624871 163.509884 944670.8566 0.011637196 0.089009839 55320.43646 -4.742885598 0.358773872 TGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPR 39 2 P38606;P38606-2;C9JVW8;C9JA17 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 223.71 6.22E-40 522390000 64057.1 57053.2 21484 33344 56115.4 50017.5 63190.3 71863.6 52903.3 FALSE TRUE 55591.79193 56678.41377 31873.73426 40915.26483 54998.81333 51941.70559 57062.11443 56496.12838 46649.13214 1.191700454 1.21499396 0.683265321 0.877085231 1.178988993 1.113454918 1.223219207 1.211086376 1 15.50956262 3.218962668 24.80712593 1.157812454 0.985671 0.181190039 0.160801542 365.6879578 462887.075 0.051406753 0.05837271 1655.62764 -3.218962668 -0.172141454 TGLFEWDNDFEDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TGLFEWDNDFEDIR 14 0 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 0 ;;; 198.14 5.23E-08 187004000 253906 213143 151438 202901 246875 222680 213889 262455 317359 FALSE TRUE 220351.6788 211742.8496 224673.9233 248972.7732 241962.6705 231246.6437 193146.0777 206331.0407 279841.1806 0.787416914 0.756653646 0.802862262 0.889693121 0.864642831 0.826349586 0.69019891 0.737314788 1 18.09424876 4.031685923 9.107841368 0.818699365 0.773769399 0.067083169 0.084126163 1.117296629 295.4601217 0.022843038 0.047415419 10756.87007 -4.031685923 -0.044929966 TGLVEFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TGLVEFAR 8 0 P31939-2;P31939;F8WEF0 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 95.741 0.02195 85916000 423480 479240 331460 376750 418000 462020 391840 482040 530690 FALSE TRUE 367516.045 476091.8409 491755.1647 462296.8458 409682.6178 479794.2084 353839.4171 378959.4972 467952.4328 0.785370519 1.017393666 1.050865708 0.987914184 0.875479192 1.025305511 0.756143985 0.809824826 1 18.83600236 2.245006143 24.99994138 0.841711705 0.961756319 0.185764504 0.098718599 210.323744 815775.4957 0.036882332 0.027864892 175.7948478 -2.245006143 0.120044614 TGLVSSTWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TGLVSSTWDR 10 0 Q9UKG1 Q9UKG1 APPL1 DCC-interacting protein 13-alpha 0 89.029 0.025865 0 61003 66468 39737 45894 78845 74534 57798 66901 75732 FALSE TRUE 52941.29899 66031.36733 58953.94611 56314.93415 77276.13876 77401.37121 52192.75886 52594.74177 66779.04923 0.79278306 0.988803646 0.882820986 0.843302425 1.157191359 1.159066685 0.781573854 0.78759345 1 16.02710793 TGLWVGDCFIYTSSVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TGLWVGDCFIYTSSVNR 17 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 110.29 0.002683 0 53210 56803 30207 50970 62917 51590 56997 59327 62688 FALSE TRUE 46178.16368 56429.85735 44815.20624 62543.51753 61665.0748 53574.70068 51469.43971 46640.38273 55277.09605 0.835394168 1.02085423 0.810737348 1.131454472 1.11556285 0.969202518 0.931116925 0.843756023 1 15.75439421 7.935562429 20.26421466 0.959114235 0.004813059 0 0.111143698 0 0 0.025469085 0 86210949.55 -7.935562429 -0.954301176 TGLYNYYDDEKEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TGLYNYYDDEKEK 13 1 P50454;E9PKH2;E9PR70;E9PPV6 P50454 SERPINH1 Serpin H1 0 ;; 210.36 2.78E-08 2064370000 1346430 991900 1108670 1067210 1004900 1020820 1455800 1492200 1235650 FALSE TRUE 1168495.864 985384.1436 1644826.52 1309536.342 984904.4561 1060091.606 1314616.74 1173104.642 1089572.865 1.072434806 0.904376546 1.509606722 1.201880466 0.903936293 0.972942371 1.206543209 1.076664701 1 20.05533125 3.293702702 24.99905392 1.047732384 1.177063067 0.144038813 0.167037443 202.8829103 91976.57232 0.04970687 0.064171248 1966.539627 -3.293702702 0.129330683 TGMGSGS(ph)AGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TGMGSGSAGK 10 0 Q86YS7;H0YFE9;Q86YS7-3 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 TGMGS(0.013)GS(0.987)AGK;TGMGS(0.003)GS(0.997)AGK;TGMGS(0.44)GS(0.56)AGK;TGMGS(0.082)GS(0.918)AGK 147.39 2.83E-05 565242000 684555 780495 571009 781704 692916 840690 1152850 1391060 1483710 TRUE FALSE 594089.3223 775367.877 847150.8623 959201.8408 679128.3273 873031.8883 1041046.784 1093592.644 1308307.494 0.454089979 0.592649572 0.647516632 0.733162384 0.519089228 0.667298699 0.795720264 0.835883498 1 20.31927023 -2 0.342354535 5.7410181 0.54342785 0.785993401 0.073460089 35.61046975 0.557267897 116.886649 0.106602521 0.01 2 -5.19759025 TGNAWHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TGNAWHSK 8 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;; 90.15 0.0134 537440000 1769480 1525560 767364 1037210 1414740 1435780 1751310 1910990 1454340 FALSE TRUE 1535638.735 1515538.496 1138463.797 1272724.383 1386589.442 1491015.386 1581468.226 1502339.66 1282409.582 1.197463553 1.181789747 0.887753658 0.992447656 1.081237587 1.162667066 1.233200569 1.171497532 1 20.29042568 2.825344188 4.632990771 1.154933018 1.058396909 0.102611492 0.104695752 0.453587063 17.08034067 0.036426829 0.036284508 668.8738053 -2.825344188 -0.096536109 TGPFAEHSNQLWNISAVPSWSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TGPFAEHSNQLWNISAVPSWSK 22 0 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;Q15257-4;A6PVN9;H0Y6E5;Q68CR8;B7ZBQ0;B4DDQ6;B7ZBP7;B7ZBP9 Q15257 PPP2R4;DKFZp781M17165 Serine/threonine-protein phosphatase 2A activator 0 209.01 6.20E-23 621870000 631880 553330 314430 419830 537370 465590 590030 669730 695010 FALSE TRUE 548375.457 549695.1388 466489.3997 515158.8182 526677.3883 483501.5486 532808.9814 526513.4513 612846.7096 0.894800361 0.896953725 0.761184473 0.840599795 0.859394984 0.788943697 0.869400085 0.859127483 1 19.22516673 1.048600981 2.059287546 1.127507676 0.841443445 0.562554434 0.042609377 1.06999011 2.82004739 0.704496647 0.011433229 11.18409843 -1.048600981 -0.28606423 TGPPPIS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TGPPPISPSK 10 0 Q14135-4;G5E9M7;Q14135;Q14135-2;A0A0A6YYI5;A0A075B6E4;E7ERW0;E7EWF5;F8W708;E7EQU6;F8WBN7;E7EUJ2;A0A096LP98 Q14135-4 VGLL4 Transcription cofactor vestigial-like protein 4 1 TGPPPIS(1)PSK;TGPPPIS(0.997)PS(0.003)K 229.68 1.58E-09 1072070000 1051300 831010 510630 629120 974380 686440 945630 1157010 997750 TRUE FALSE 912368.0413 825551.0406 757572.376 771971.3115 954991.7443 712847.791 853922.9481 909592.4154 879797.1316 1.037020932 0.938342501 0.861076206 0.877442405 1.085468127 0.810241095 0.970590739 1.033866084 1 19.74681137 1.997795295 24.99085193 1.014214972 0.932163958 0.149850954 0.080302664 142.3662438 1613762.296 0.032212764 0.021331153 99.49363434 -1.997795295 -0.082051015 TGPPPIS(ph)PSKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TGPPPISPSKR 11 1 Q14135-4;G5E9M7;Q14135;Q14135-2;A0A0A6YYI5;A0A075B6E4;E7ERW0;E7EWF5;F8W708;E7EQU6;F8WBN7;E7EUJ2;A0A096LP98 Q14135-4 VGLL4 Transcription cofactor vestigial-like protein 4 1 TGPPPIS(0.98)PS(0.02)KR 109.83 0.00054935 0 291980 216130 133800 173090 248360 209880 328450 347890 251960 TRUE FALSE 253394.1032 214710.2278 198506.1275 212392.73 243418.1219 217954.2194 296596.9696 273496.4308 222173.5758 1.140523135 0.96640758 0.893473163 0.955976557 1.09562139 0.981008739 1.334978601 1.231003416 1 17.76132771 2.260102605 24.99770581 1.203578673 1.000477689 0.391298004 0.107029364 211.4406965 245358.9038 0.040205056 0.031114005 182.0130824 -2.260102605 -0.203100984 TGQAGSLSGS(ph)PKPFSPQLSAPITTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TGQAGSLSGSPKPFSPQLSAPITTK 25 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 TGQAGSLS(0.005)GS(0.995)PKPFSPQLSAPITTK;TGQAGS(0.005)LS(0.078)GS(0.916)PKPFS(0.001)PQLSAPITTK 199.8 4.22E-25 2652500000 1502580 1175220 824730 914590 1273900 851020 1729000 1920510 1518010 TRUE FALSE 1304010.246 1167499.902 1223572.187 1122261.638 1248551.882 883759.2901 1561321.846 1509823.882 1338552.587 0.974194259 0.87221071 0.914100946 0.838414306 0.932762668 0.660235017 1.166425482 1.127952608 1 20.35224239 2.212656658 24.99999978 1.107185798 0.869692743 0.583370081 0.092590644 144.7835412 139729.9951 0.03597069 0.024260523 163.1761408 -2.212656658 -0.237493055 HLMEQSS(ph)PGFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 HLMEQSSPGFR 11 0 Q5SXH7-4;Q5SXH7-3;Q5SXH7-2;Q5SXH7-1;Q5SXH7 Q5SXH7-4 PLEKHS1 Pleckstrin homology domain-containing family S member 1 1 HLMEQS(0.045)S(0.955)PGFR;HLMEQS(0.054)S(0.946)PGFR;HLMEQS(0.007)S(0.993)PGFR;HLMEQS(0.007)S(0.993)PGFR;HLMEQS(0.003)S(0.997)PGFR;HLMEQS(0.02)S(0.98)PGFR;HLMEQS(0.052)S(0.948)PGFR;HLMEQS(0.003)S(0.997)PGFR;HLMEQS(0.009)S(0.991)PGFR;HLMEQSS(1)PGFR;HLMEQS(0.007)S(0.993)PGFR;HLMEQS(0.001)S(0.999)PGFR;HLMEQS(0.018)S(0.982)PGFR;HLMEQS(0.016)S(0.984)PGFR 209.79 9.63E-09 21047490000 5996050 10197720 6147830 8808500 13728500 14064960 12274910 14934400 13385320 TRUE FALSE 5203656.8 10130730.51 9120941.151 10808604.55 13455329.71 14606048.11 11084491.12 11740794.78 11802922.72 0.440878664 0.858323887 0.772769709 0.915756615 1.139999815 1.237494175 0.939131043 0.994736224 1 23.49264082 4.939299903 0.809838194 1.044826614 2.48E-12 0.743349388 0.108991744 1.855435067 0.761130407 0.043298937 1.876253109 86956.06992 -4.939299903 -1.044826614 down TGQLEGAPAPGPAAS(ph)PQTLDHSGATATGGASELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TGQLEGAPAPGPAASPQTLDHSGATATGGASELK 34 0 P55317-2;P55317 P55317-2 FOXA1 Hepatocyte nuclear factor 3-alpha 1 TGQLEGAPAPGPAAS(0.999)PQT(0.001)LDHSGATATGGASELK;TGQLEGAPAPGPAAS(1)PQTLDHSGATATGGASELK;TGQLEGAPAPGPAAS(1)PQTLDHSGATATGGASELK;TGQLEGAPAPGPAAS(0.999)PQT(0.001)LDHSGATATGGASELK;TGQLEGAPAPGPAAS(0.993)PQT(0.007)LDHSGATATGGASELK;TGQLEGAPAPGPAAS(1)PQTLDHSGATATGGASELK 310.94 1.56E-104 19079860000 7578540 6075760 4031670 5097950 6360070 4842550 6926890 8833500 8712130 TRUE FALSE 6577016.737 6035847.933 5981399.097 6255517.465 6233517.05 5028846.032 6255121.274 6944524.767 7682191.916 0.856138041 0.785693458 0.778605789 0.814288101 0.811424281 0.654610831 0.814236528 0.903976996 1 22.87308658 1.564722535 2.425406654 0.995476349 0.78323546 0.655378482 0.052130946 0.178030612 2.122534081 0.066656978 0.014382956 36.70477233 -1.564722535 -0.212240889 TGQPAQPAPSAQQPPRPPAS(ph)PDEPSVAASSVGSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TGQPAQPAPSAQQPPRPPASPDEPSVAASSVGSSR 35 1 O94964-2 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 TGQPAQPAPSAQQPPRPPAS(1)PDEPSVAASSVGSSR;TGQPAQPAPSAQQPPRPPAS(1)PDEPSVAASSVGSSR;TGQPAQPAPSAQQPPRPPAS(1)PDEPSVAASSVGSSR;TGQPAQPAPS(0.262)AQQPPRPPAS(0.734)PDEPS(0.003)VAASSVGSSR 307.74 3.41E-94 3267950000 504170 535021 279633 353712 600110 564844 554876 681401 568587 TRUE FALSE 437542.6571 531506.4118 414864.4541 434027.7157 588168.9851 586573.9142 501064.2109 535688.6988 501369.2926 0.872695364 1.060109623 0.827462831 0.86568468 1.173125267 1.169943837 0.999391503 1.068451353 1 18.93551411 3.248930375 24.99102158 1.078644773 0.911816407 0.522223404 0.083398052 182.7932481 440527.4865 0.024649653 0.031471192 1773.905069 -3.248930375 -0.166828366 TGQPMIHIYLDK ddPTM_MDA-MB-175_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 ; 115.78 0.0009127 1076450000 2788300 2483500 1702720 2379000 2627100 2248000 2661900 3326800 5348600 FALSE TRUE 2419819.09 2467185.725 2526161.087 2919188.311 2574825.85 2334482.015 2403749.348 2615389.709 4716294.601 0.513076323 0.523119511 0.535624108 0.618958008 0.545942539 0.494982229 0.509669041 0.554543329 1 22.16922241 1.238293161 5.803022727 1.019217796 0.536138905 0.949972302 0.033421093 0.029823293 3.525283581 0.057301765 0.008848007 17.30984429 -1.238293161 -0.483078892 TGRDT(ph)PENGETAIGAENSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TGRDTPENGETAIGAENSEK 20 1 Q8N3X1-2;Q8N3X1 Q8N3X1-2 FNBP4 Formin-binding protein 4 1 T(0.062)GRDT(0.938)PENGETAIGAENSEK 193.09 1.39E-17 382310000 622450 383010 359450 420670 417320 407460 521990 605180 772670 TRUE FALSE 540191.6554 380493.9821 533281.2223 516189.553 409016.1485 423135.2499 471367.4901 475766.9665 681325.8328 0.792853624 0.558461112 0.782710998 0.757625101 0.600323852 0.621046832 0.69183857 0.698295799 1 19.37798538 1.234666065 4.975932399 1.021646612 0.683264042 0.616639671 0.077352307 0.116926686 7.282007499 0.13811139 0.018558976 17.16587972 -1.234666065 -0.33838257 TGS(ph)EPALSPAVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TGSEPALSPAVVR 13 0 O75815;O75815-3;O75815-2 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 T(0.004)GS(0.995)EPALSPAVVR;T(0.001)GS(0.998)EPALSPAVVR 166.05 3.60E-05 207460000 306460 240110 181338 168035 272230 232400 235530 253880 251860 TRUE FALSE 265960.5345 238532.7016 269033.6633 206189.915 266813.1556 241340.5784 212688.3369 199589.7377 222085.3977 1.197559755 1.074058466 1.211397355 0.928426259 1.201398914 1.086701696 0.957687174 0.898707163 1 17.76075501 2.255348519 4.064078357 0.938424055 1.116418798 0.454819064 0.085299682 0.169609472 6.282451055 0.032699994 0.023121679 180.0315078 -2.255348519 0.177994744 TGS(ph)ESSQTGTSTTSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 TGSESSQTGTSTTSSR 16 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 T(0.011)GS(0.839)ES(0.148)S(0.002)QTGTSTTSSR;TGS(0.699)ES(0.301)S(0.001)QTGTSTTSSR;T(0.006)GS(0.974)ES(0.02)SQTGTSTTSSR;T(0.008)GS(0.856)ES(0.135)S(0.001)QTGTSTTSSR;T(0.01)GS(0.966)ES(0.024)SQTGTSTTSSR;T(0.021)GS(0.979)ESSQTGTSTTSSR;TGS(0.729)ES(0.271)SQTGTSTTSSR;TGS(0.972)ES(0.028)SQTGTSTTSSR 385.27 2.95E-121 2560631000 1029965 981663 1066050 1177778 1784693 1648651 1925420 2011680 1953801 TRUE FALSE 893852.5157 975214.3911 1581595.346 1445210.496 1749181.101 1712075.671 1738693.065 1581497.887 1722824.872 0.518829586 0.56605544 0.918024445 0.838860943 1.015298264 0.993760712 1.009210567 0.917967875 1 20.71634463 4.238570673 2.691285574 0.962238929 0.510307566 0.911249087 0.053815553 0.072116301 1.033926705 0.014493613 0.04530862 17320.90871 -4.238570673 -0.451931363 TGS(ph)IVLPYIMSSTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TGSIVLPYIMSSTLR 15 0 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 T(0.006)GS(0.994)IVLPYIMSSTLR;T(0.002)GS(0.998)IVLPYIMSSTLR 138.77 8.96E-06 308090000 416070 418310 292780 289750 486580 429690 543320 456810 387020 TRUE FALSE 361085.2953 415562.0941 434369.3873 355542.1661 476898.01 446220.4523 490628.91 359124.7364 341266.9365 1.058072895 1.217703943 1.272814155 1.041830098 1.39743397 1.307540827 1.437669043 1.052327952 1 18.38054112 1.585084165 7.832183789 1.015354452 1.248102542 0.351929651 0.125746973 0.120570706 15.56314323 0.082432796 0.031935689 38.46663221 -1.585084165 0.23274809 TGS(ph)NAAQYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TGSNAAQYK 9 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 T(0.005)GS(0.995)NAAQYK;T(0.004)GS(0.996)NAAQYK 104.04 0.0034872 225379000 435150 364170 310430 284800 385270 299920 442250 531840 491760 TRUE FALSE 377643.825 361777.7433 460554.9863 349468.1929 377603.8808 311458.1165 399360.6631 418110.1548 433624.693 0.870900184 0.834310751 1.062105073 0.805923183 0.870808067 0.71826656 0.920982291 0.964221276 1 18.72608739 1.830076328 3.36553978 0.982930974 0.864103374 0.247927763 0.085961473 0.341521402 6.755902019 0.055045662 0.023523125 67.62018086 -1.830076328 -0.1188276 TGS(ph)PGDAPERPPLCDFSEGLSAPMDFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TGSPGDAPERPPLCDFSEGLSAPMDFYR 28 1 A0A2R8Y575;Q5VVD7;Q8IWE5 A0A2R8Y575 PLEKHM2 Pleckstrin homology domain-containing family M member 2 1 T(0.45)GS(0.55)PGDAPERPPLCDFSEGLSAPMDFYR;T(0.174)GS(0.826)PGDAPERPPLCDFSEGLSAPMDFYR;T(0.026)GS(0.974)PGDAPERPPLCDFSEGLSAPMDFYR;T(0.138)GS(0.862)PGDAPERPPLCDFSEGLSAPMDFYR 189.39 3.64E-18 310869000 104149 99335 72908.3 75637.8 120339 106933 109050 132127 116879 TRUE FALSE 90385.44577 98682.46184 108166.9977 92812.51854 117944.4893 111046.7817 98474.34778 103872.6693 103061.6978 0.877003268 0.957508599 1.049536347 0.900552975 1.144406621 1.077478676 0.955489284 1.007868796 1 16.65314874 4.589111808 2.571213697 1.017423373 0.86734413 0.328506329 0.065825849 0.442804998 4.584993418 0.016753179 0.123145208 38825.03071 -4.589111808 -0.150079243 TGS(ph)PGPELLFHEGQQK ddPTM_MDA-MB-175_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(0.014)GS(0.986)PGPELLFHEGQQK;T(0.069)GS(0.931)PGPELLFHEGQQK;T(0.015)GS(0.985)PGPELLFHEGQQK 234.11 7.37E-20 734380000 1683540 1413990 1203930 1136940 1799050 1164810 1804070 2033510 1745600 TRUE FALSE 1461055.923 1404701.407 1786154.575 1395099.604 1763252.425 1209620.994 1629111.569 1598659.711 1539237.157 0.949207805 0.912595827 1.160415448 0.906357801 1.145536552 0.785857455 1.058388931 1.038605198 1 20.5537841 TGS(ph)QEGTSMEGSRPAAPAEPGTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TGSQEGTSMEGSRPAAPAEPGTLK 24 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 T(0.02)GS(0.98)QEGTSMEGSRPAAPAEPGTLK;T(0.127)GS(0.871)QEGT(0.001)S(0.001)MEGSRPAAPAEPGTLK;T(0.006)GS(0.994)QEGTSMEGSRPAAPAEPGTLK;T(0.169)GS(0.735)QEGT(0.048)S(0.048)MEGSRPAAPAEPGTLK;T(0.002)GS(0.905)QEGT(0.047)S(0.047)MEGSRPAAPAEPGTLK 190.31 7.35E-18 2645790000 3511710 2346820 1734770 2027870 2814000 1626530 3818960 3905050 2481900 TRUE FALSE 3047628.626 2331403.585 2573710.574 2488328.878 2758006.905 1689103.662 3448597.847 3069985.447 2188492.609 1.392569759 1.0653011 1.17601977 1.13700584 1.260231309 0.771811453 1.575786837 1.402785385 1 21.06150608 2.21037828 24.99999859 1.352547544 1.138516559 0.153064319 0.210092406 351.3577164 311679.9519 0.082361667 0.055540319 162.3223346 -2.21037828 -0.214030986 TGS(ph)TSSKEDDYESDAATIVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TGSTSSKEDDYESDAATIVQK 21 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 T(0.021)GS(0.86)T(0.116)S(0.003)SKEDDYESDAATIVQK;T(0.007)GS(0.96)T(0.032)S(0.001)SKEDDYESDAATIVQK;T(0.018)GS(0.965)T(0.011)S(0.002)S(0.005)KEDDYESDAATIVQK 280.92 3.25E-45 555230000 436810 374756 512860 352034 543160 342954 815280 857390 667080 TRUE FALSE 379084.4518 372294.2032 760880.8114 431968.7002 532352.1787 356147.6623 736214.2711 674043.8207 588218.5623 0.644461899 0.632918148 1.293534173 0.734367679 0.905024446 0.605468248 1.251599861 1.145907089 1 19.16599279 2.227146223 24.99877238 1.140257399 0.818780359 0.360787497 0.206152559 242.3398545 530746.2122 0.082891894 0.056433476 168.7120968 -2.227146223 -0.321477039 TGS(ph)YGALAEITASK ddPTM_MDA-MB-175_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(0.002)GS(0.998)YGALAEITASK;T(0.002)GS(0.998)YGALAEITASK 201.72 1.83E-08 553560000 886130 620690 468570 500150 592350 472060 640050 703390 947270 TRUE FALSE 769025.6753 616612.6465 695172.0193 613716.7018 580563.3939 490220.4537 577978.0495 552975.5223 835284.8197 0.920674789 0.738206456 0.832257456 0.734739441 0.69504842 0.586890175 0.691953255 0.662020318 1 19.67190869 7.999998077 0.76654167 0.716267234 39.8028602 0.188184079 0.111615949 663.1262084 2.6706257 0.040159348 44844.16199 99999557.11 -7.999998077 39.08659297 TGSEPALS(ph)PAVVR ddPTM_MDA-MB-175_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 201.3 1.08E-07 412530000 515770 522250 289310 377160 588290 598010 462930 597630 584630 TRUE FALSE 447609.6877 518819.3054 429221.2837 462799.9425 576584.18 621015.8317 418035.1199 469831.4753 515515.7074 0.868275556 1.006408336 0.832605636 0.89774169 1.118460935 1.204649679 0.810906659 0.911381493 1 18.97565686 3.367200693 18.80749556 0.993286864 0.9037727 0.173128699 0.114146045 4.244096432 702.9433905 0.035778469 0.046189697 2329.167345 -3.367200693 -0.089514164 TGSES(ph)SQTGTSTTSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TGSESSQTGTSTTSSR 16 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 T(0.001)GS(0.197)ES(0.801)S(0.001)QTGTSTTSSR;TGS(0.161)ES(0.827)S(0.012)QTGTSTTSSR 358.68 1.36E-87 10705100000 3424000 3359300 4049300 4063700 6282700 5821100 6597500 7299100 6496300 TRUE FALSE 2971509.725 3337232.537 6007555.024 4986425.195 6157686.562 6045041.484 5957675.465 5738244.267 5728314.815 0.518740646 0.582585393 1.048747357 0.870487282 1.074956032 1.055291422 1.040039812 1.001733398 1 22.44967935 4.264280468 6.478644148 1.012468878 0.543355327 0.917336914 0.057728827 0.04040721 5.608070095 0.014260504 0.03662067 18377.24765 -4.264280468 -0.469113551 TGSGS(ph)PFAGNS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TGSGSPFAGNSPAR 14 0 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 2 TGSGS(1)PFAGNS(1)PAR;TGSGS(1)PFAGNS(1)PAR;TGS(0.001)GS(0.999)PFAGNS(1)PAR;TGSGS(1)PFAGNS(1)PAR 283.88 2.52E-33 2072660000 4193720 2983160 1855580 2017760 2639700 2506550 2353560 2534490 3348900 TRUE FALSE 3639509.276 2963563.426 2752944.695 2475923.248 2587175.134 2602978.6 2125312.113 1992509.037 2952996.857 1.232479902 1.003578253 0.932254529 0.838444254 0.876118486 0.881470156 0.719713639 0.674741333 1 21.49374839 8 0.504621866 0.785603899 15.60535159 0.667620652 0.090112211 67.54950837 0.729494704 0.056530336 1061.233935 100000000 -8 14.81974769 TGSGS(ph)PFAGNSPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TGSGSPFAGNSPAR 14 0 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 TGS(0.009)GS(0.991)PFAGNSPAR;TGS(0.007)GS(0.992)PFAGNSPAR;TGS(0.011)GS(0.989)PFAGNSPAR 193.43 2.72E-07 950220000 1485100 1243710 632280 806290 1109600 1026580 1027200 1181280 946790 TRUE FALSE 1288840.272 1235539.987 938052.7228 989370.4679 1087521.131 1066073.197 927582.3021 928672.4647 834861.5648 1.543777228 1.479933967 1.123602717 1.185071286 1.302636481 1.276946073 1.111061212 1.112367013 1 19.67117747 8 0.362116634 1.092625124 7.111298898 0.68662251 0.095540673 49.83203239 0.747813588 0.123655312 204.9467534 100000000 -8 6.018673774 TGSGSPFAGNS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TGSGSPFAGNSPAR 14 0 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 TGSGSPFAGNS(1)PAR;TGSGSPFAGNS(1)PAR;TGSGSPFAGNS(1)PAR;TGSGSPFAGNS(1)PAR;TGSGSPFAGNS(1)PAR;TGSGSPFAGNS(1)PAR 328.81 2.43E-68 4293820000 1686890 1760610 1369150 2049170 3026870 2892750 2822000 3165320 3667540 TRUE FALSE 1463963.212 1749044.437 2031275.52 2514465.368 2966641.209 3004035.964 2548322.874 2488440.951 3233967.599 0.452683327 0.540835486 0.62810633 0.77751718 0.91733795 0.92890107 0.78798652 0.76946997 1 21.62487379 3.904799051 1.603379095 0.862755562 0.475865902 0.837500784 0.070051023 0.170611344 0.837599484 0.022883542 0.062029585 8031.544153 -3.904799051 -0.38688966 TGSNIS(ph)GASSDISLDEQYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TGSNISGASSDISLDEQYK 19 0 P22059 P22059 OSBP Oxysterol-binding protein 1 1 TGSNIS(0.95)GAS(0.049)SDISLDEQYK 214.18 4.57E-19 147880000 237810 239630 215250 270620 252990 233770 346570 360720 473150 TRUE FALSE 206382.806 238055.8548 319345.62 332068.4072 247955.994 242763.2832 312959.6947 283582.8351 417214.746 0.494668053 0.570583511 0.765422658 0.795917235 0.594312632 0.581866498 0.750116571 0.679704727 1 18.67043062 -0.069427609 1.316605101 9.999999998 0.648556978 0.562487503 0.096089397 31.16478888 2.46113016 798.5771762 0.029458906 0.852260559 0.069427609 -9.351443021 TGSQEGT(ph)SMEGSRPAAPAEPGTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TGSQEGTSMEGSRPAAPAEPGTLK 24 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 T(0.01)GS(0.075)QEGT(0.457)S(0.457)MEGSRPAAPAEPGTLK 164.2 2.56E-11 1139400000 799420 618170 447750 495750 687300 381550 943210 883450 654330 TRUE FALSE 693774.6215 614109.2006 664283.3976 608317.6146 673624.0747 396228.4754 851737.6394 694531.0925 576975.8528 1.202432681 1.064358582 1.151319235 1.054320751 1.167508261 0.686733203 1.476210201 1.203743777 1 19.13815142 1.214926948 23.56670917 0.999998867 1.130126583 0.039465013 0.19406119 3878.116721 3866707.717 2.386632742 0.04620164 16.40313835 -1.214926948 0.130127717 TGSQEGTS(ph)MEGSRPAAPAEPGTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TGSQEGTSMEGSRPAAPAEPGTLK 24 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 TGS(0.058)QEGT(0.371)S(0.57)MEGS(0.001)RPAAPAEPGTLK 166.28 7.99E-12 545130000 421270 284380 214380 278360 349410 206360 461810 505640 271370 TRUE FALSE 365598.1021 282511.8891 318054.8851 341565.8925 342457.4246 214298.8027 417023.7373 397512.8209 239288.9477 1.52785202 1.180630747 1.329166633 1.427420262 1.431146018 0.895564984 1.742762218 1.661225162 1 17.86839424 2.190637357 24.999997 1.519699807 1.306526634 0.074971545 0.259113404 241.4286799 125943.5961 0.103172201 0.069558856 155.1091281 -2.190637357 -0.213173173 TGSQGQCTQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TGSQGQCTQVR 11 0 P62857 P62857 RPS28 40S ribosomal protein S28 0 ;;; 175.54 2.26E-05 135174000 82419 82628 41178.5 48761.1 113025 111800 86905 95395 91581 FALSE TRUE 71527.12033 82085.21123 61092.56033 59833.05302 110776.0236 116101.0183 78476.96648 74995.52161 80754.39851 0.885736525 1.016479755 0.756523006 0.740926242 1.371764581 1.437705196 0.971798044 0.928686524 1 16.30125322 3.259291291 24.99968167 1.11734918 0.855142808 0.393248323 0.17877418 320.7440697 386791.6277 0.058727287 0.075730885 1816.733779 -3.259291291 -0.262206372 TGSS(ph)PTQGIVNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TGSSPTQGIVNK 12 0 E9PFH7;A0A087WYG2;A0A669KB35;Q9UPT6 E9PFH7 MAPK8IP3 C-Jun-amino-terminal kinase-interacting protein 3 1 TGSS(0.999)PT(0.001)QGIVNK;TGS(0.124)S(0.876)PTQGIVNK;TGS(0.002)S(0.998)PTQGIVNK;TGS(0.001)S(0.999)PTQGIVNK;TGS(0.002)S(0.998)PTQGIVNK;TGS(0.003)S(0.997)PTQGIVNK 313.8 2.35E-46 3171320000 9080370 8317840 5403810 5753770 8858920 6931550 9623020 10692190 9674480 TRUE FALSE 7880376.098 8263199.561 8017110.591 7060251.419 8682644.824 7198211.214 8689781.002 8405748.375 8530773.996 0.92375863 0.968634214 0.939787011 0.827621435 1.017802702 0.843793449 1.018639224 0.985344164 1 23.02424521 2.200782844 24.99990981 0.998719235 0.923547023 0.323531034 0.05509637 195.7922212 129566.6147 0.020869086 0.014070287 158.7752641 -2.200782844 -0.075172211 TGSS(ph)SPPGGPPKPGSQLDSMLGSLQSDLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TGSSSPPGGPPKPGSQLDSMLGSLQSDLNK 30 1 F5GZ78;A0A1B0GTU4;P49023;P49023-2;P49023-3;P49023-4 F5GZ78;P49023-3;P49023-4 PXN Paxillin 1 T(0.107)GS(0.107)S(0.392)S(0.392)PPGGPPKPGSQLDSMLGSLQSDLNK 54.745 0.091328 403550000 217510 155440 148560 138400 167560 140650 246270 290180 241340 TRUE FALSE 188765.5024 154418.9044 220404.1129 169825.8353 164225.8838 146060.8965 222386.7733 228127.2652 212809.0601 0.887018167 0.725621852 1.035689518 0.798019761 0.77170532 0.686347172 1.045006134 1.071980982 1 17.69920005 2.214501821 24.87582182 1.04611825 0.820192827 0.540260624 0.096264963 161.1508355 166622.1006 0.039041739 0.026337138 163.8708933 -2.214501821 -0.225925423 TGSSS(ph)PPGGPPKPGSQLDSMLGSLQSDLNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TGSSSPPGGPPKPGSQLDSMLGSLQSDLNK 30 1 F5GZ78;A0A1B0GTU4;P49023;P49023-2;P49023-3;P49023-4 F5GZ78;P49023-3;P49023-4 PXN Paxillin 1 T(0.002)GS(0.012)S(0.102)S(0.884)PPGGPPKPGSQLDSMLGSLQSDLNK;TGSS(0.02)S(0.979)PPGGPPKPGSQLDSMLGSLQSDLNK;T(0.008)GS(0.008)S(0.148)S(0.835)PPGGPPKPGSQLDSMLGSLQSDLNK 335.82 9.85E-106 5672000000 3696290 2837380 2500020 2426380 2981870 2002670 4350680 4767550 3983910 TRUE FALSE 3207815.911 2818741.064 3709038.034 2977326.664 2922536.621 2079714.011 3928751.723 3748046.534 3512936.698 0.913143671 0.802388801 1.055822622 0.847532113 0.831935464 0.592015795 1.118366786 1.066926864 1 21.74424615 2.178954504 24.99999864 1.065199067 0.84845839 0.443386948 0.116630792 69.91012019 29320.92351 0.047860873 0.032267806 150.9921969 -2.178954504 -0.216740677 TGSVQTS(ph)PSSTPVAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TGSVQTSPSSTPVAGR 16 0 A0A590UJL1;F8W6W8;Q9UQ26-3;A0A590UK62;Q9UQ26;Q9UQ26-1;Q9UQ26-8;A0A0J9YWD4;D6RA03 A0A590UJL1;D6RA03 RIMS2 Regulating synaptic membrane exocytosis protein 2 1 TGSVQT(0.044)S(0.393)PS(0.393)S(0.169)T(0.001)PVAGR 165.66 3.60E-09 0 219970 141970 97392 123770 186730 168970 167460 199460 174240 TRUE FALSE 190900.4072 141037.3897 144491.097 151873.8702 183014.4383 175470.3852 151219.755 156807.0312 153641.5457 1.24250512 0.917963882 0.940442875 0.988494808 1.19117806 1.142076412 0.984237397 1.020603057 1 17.22920886 1.673647429 0.005921537 0.000111425 2.065255668 0.018630422 0.107671622 220787.9162 473.6283985 84098.59894 81095.71066 47.1679964 -1.673647429 2.065144243 TGTITTFEHAHNMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 TGTITTFEHAHNMR 14 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;;;; 224.05 1.90E-12 14459490000 5245786 5087227 2309570 3352198 5708216 5544605 5332941 6088018 3351574 FALSE TRUE 4552542.089 5053808.671 3426485.777 4113365.791 5594633.67 5757909.542 4815753.203 4786142.728 2955354.74 1.540438455 1.710051454 1.15941607 1.391834874 1.89304979 1.94829726 1.629500898 1.619481636 1 21.49489988 TGTIVVEGHELHDEDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TGTIVVEGHELHDEDIR 17 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 136.34 6.15E-06 594050000 460970 401730 219840 284650 449210 432030 399140 452880 437650 FALSE TRUE 400051.6466 399091.0092 326155.3593 349284.1331 440271.5999 448650.4737 360431.4642 356035.1363 385911.5156 1.036640863 1.034151595 0.845155809 0.905088651 1.140861524 1.162573428 0.933974369 0.922582307 1 18.55791057 TGTLQDLIQHGS(ph)PINNECHPSLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TGTLQDLIQHGSPINNECHPSLER 24 0 A0A2R8YH03;Q5VWN6 A0A2R8YH03 FAM208B Protein FAM208B 1 TGTLQDLIQHGS(1)PINNECHPSLER;TGTLQDLIQHGS(1)PINNECHPSLER 242.63 2.05E-37 312690000 192178 169534 65911 134683 239280 251740 160564 195674 177658 TRUE FALSE 166781.1904 168420.32 97785.78006 165264.8337 234518.7961 261424.6007 144992.528 153830.6378 156655.4736 1.064636853 1.07510013 0.62420915 1.054957288 1.497035442 1.66878689 0.925550347 0.981967845 1 17.25723565 3.476446744 24.9996959 1.194729384 0.92050873 0.210972966 0.259107161 42.0255106 1557561.316 0.082436272 0.107410533 2995.344264 -3.476446744 -0.274220654 TGTRFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TGTRFER 7 1 Q16401-2;Q16401;Q4VXH0 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ; 94.302 0.013042 142921000 186407 177979 64424 75501 177677 198635 177281 187904 40013 FALSE TRUE 161772.8427 176809.8442 95579.66189 92644.65601 174141.5753 206276.617 160088.3159 147722.1919 35282.70872 4.585046004 5.011232148 2.708966101 2.625780711 4.93560675 5.846394011 4.537302313 4.186815503 1 15.1066737 TGTVSLEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TGTVSLEVR 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 ; 120.15 0.0016539 737570000 722050 769510 441600 528460 865250 983300 826420 866700 875160 FALSE TRUE 626629.2631 764455.0381 655159.2371 648454.92 848033.2178 1021128.187 746273.9156 681362.9497 771699.5818 0.812011925 0.990612223 0.848982237 0.840294507 1.098916259 1.323219827 0.967052378 0.882938083 1 19.5576798 3.242848203 24.99870757 1.039876166 0.879664066 0.348152338 0.122324711 160.7696387 937359.0939 0.040224109 0.050115425 1749.23518 -3.242848203 -0.1602121 TGVIHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TGVIHEK 7 0 Q96M27;Q96M27-3;Q96M27-2;Q96M27-5 Q96M27 PRRC1 Protein PRRC1 0 ; 84.568 0.02145 708130000 2716400 2261800 1338150 1819440 2025580 2071240 2497700 2960400 3618300 FALSE TRUE 2357420.858 2246942.087 1985283.816 2232571.66 1985274.921 2150921.943 2255473.438 2327341.498 3190548.696 0.738876313 0.704249426 0.622238996 0.699745365 0.622236208 0.674154244 0.706923371 0.729448668 1 21.60537312 1.026131911 1.864487836 1.292832932 0.676759641 0.879229885 0.036788312 0.527190071 1.064729361 0.699177871 0.009994089 10.62018082 -1.026131911 -0.616073291 TGVKVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TGVKVDK 7 1 P52566;F5H3P3;H0YGX7 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ; 60.019 0.091228 1353840000 2019330 1792660 934740 1143080 1596080 1218800 2413000 2631100 546840 FALSE TRUE 1752470.424 1780883.898 1386783.391 1402633.785 1564321.131 1265688.025 2178987.631 2068459.74 482193.1982 3.634374004 3.693299502 2.875991192 2.908862651 3.244179173 2.624856654 4.51890993 4.28969083 1 18.87925177 1.227147833 24.98832154 0.999994498 3.497830669 0.623171515 0.60428931 389.5531827 852871.9013 2.549853849 0.16574598 16.87127223 -1.227147833 2.497836171 THAPSALS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THAPSALSPPR 11 0 H9KVB4;O15417;O15417-2 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 THAPSALS(1)PPR 108.36 0.0013358 183540000 108300 115990 56244 80007 114460 113080 109570 112200 96491 TRUE FALSE 93987.8806 115228.0541 83443.78652 98173.81218 112182.4699 117430.2608 98943.91826 88206.90314 85083.9439 1.104648848 1.354286705 0.980723068 1.153846515 1.318491654 1.380169458 1.162897648 1.036704449 1 16.37659929 1.761661583 3.433908609 1.011596409 1.216222326 0.308875942 0.119863991 0.260914493 6.213892672 0.083516132 0.033103383 57.76457511 -1.761661583 0.204625917 THAVS(ph)VSETDDYAEIIDEEDTYTMPSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 THAVSVSETDDYAEIIDEEDTYTMPSTR 28 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;Q05397-2;Q05397-4;Q05397-3;H0YB99;H0YB33 E7ESA6 PTK2 Focal adhesion kinase 1 1 T(0.002)HAVS(0.994)VS(0.002)ET(0.003)DDYAEIIDEEDTYTMPSTR;T(0.001)HAVS(0.996)VS(0.003)ETDDYAEIIDEEDTYTMPSTR 293.43 2.02E-71 211120000 67288 63272 51825 52553 70320 87901 68856 84632 85368 TRUE FALSE 58395.72031 62856.36207 76887.74334 64485.96187 68920.76958 91282.60835 62178.35572 66534.10541 75275.89229 0.775755936 0.835013178 1.02141258 0.856661541 0.915575591 1.212640668 0.826006226 0.883870033 1 16.19990028 4.408123562 5.733476618 0.949047835 0.789309894 0.26082056 0.108856701 0.256480642 15.00460717 0.027323681 0.075986015 25593.13937 -4.408123562 -0.159737941 THAVSVSETDDYAEIIDEEDTYTMPSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THAVSVSETDDYAEIIDEEDTYTMPSTR 28 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;Q05397-2;Q05397-4;Q05397-3;H0YB99;H0YB33 E7ESA6 PTK2 Focal adhesion kinase 1 0 84.524 0.0039638 41903000 32219 24644 17353 20762 30110 31423 28095 24767 26292 FALSE TRUE 27961.17752 24482.11194 25744.96884 25476.32943 29510.86991 32631.86314 25370.35122 19470.76979 23183.78971 1.20606587 1.056001294 1.110472842 1.09888546 1.272909661 1.407529293 1.09431424 0.839844134 1 14.50082879 1.945001257 6.290512218 0.922368508 1.187057625 0.526528541 0.105516823 0.180817936 15.81712661 0.055302028 0.030263774 88.10514234 -1.945001257 0.264689117 THEAQIQEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 THEAQIQEMR 10 0 P35579 P35579 MYH9 Myosin-9 0 ;;;;;; 194.49 4.58E-07 9589600000 3410870 3162780 1975850 2179920 2972580 3165760 3070400 2927970 2924430 FALSE TRUE 2960114.887 3142003.49 2931377.669 2674904.154 2913431.474 3287548.836 2772633.081 2301846.401 2578707.217 1.147906543 1.218441345 1.136762502 1.037304327 1.129803126 1.274882551 1.075202746 0.892635808 1 21.29821655 1.950239095 5.54507783 0.94840335 1.15452727 0.632227238 0.066023377 0.128330738 9.103501833 0.033656198 0.018225964 89.17417404 -1.950239095 0.20612392 THETLSHAGQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THETLSHAGQK 11 0 Q16890-5;E9PPQ1;J3KNE7;Q16890;E9PNK6;E9PNQ9;Q16890-4;Q16890-3;Q16890-2 Q16890-5 TPD52L1 Tumor protein D53 0 227.94 2.10E-12 122090000 213650 189030 58925 119810 145320 146790 180580 177480 159760 FALSE TRUE 185415.6112 187788.2495 87421.32709 147014.6917 142428.4163 152437.1063 163067.3794 139527.2832 140873.3548 1.316186524 1.333028874 0.620566801 1.043594737 1.01103872 1.082086151 1.157545936 0.99044481 1 17.10403924 THFELEPS(ph)PPSGLGFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 THFELEPSPPSGLGFTR 17 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 THFELEPS(0.998)PPS(0.002)GLGFTR;THFELEPS(1)PPSGLGFTR;THFELEPS(0.999)PPS(0.001)GLGFTR 96.633 0.0014643 316702000 506531 532779 359638 410890 498071 571690 507826 577670 505550 TRUE FALSE 439591.645 529279.1397 533560.1397 504188.8546 488160.3616 593683.2842 458577.1127 454139.7659 445784.4549 0.986108062 1.187298332 1.196901628 1.131014886 1.095059184 1.331772065 1.028696958 1.018742939 1 18.76598678 2.03830426 24.99999176 1.014612734 1.156466972 0.366468379 0.086274036 156.6375921 102231.8025 0.033600681 0.022653534 109.2205251 -2.03830426 0.141854239 THFEYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THFEYEK 7 0 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 0 112.17 0.0064142 427870000 367000 321690 208940 271440 319790 295010 345990 410540 381280 FALSE TRUE 318500.0201 319576.7972 309984.0829 333074.6007 313426.8047 306359.2256 312435.9431 322749.2158 336205.5128 0.947337292 0.950540027 0.922007734 0.990687505 0.932247666 0.911226063 0.929300476 0.959975978 1 18.35898386 1.325362183 2.870999492 1.005777479 0.940804872 0.439751324 0.021299725 0.337783721 3.748045828 0.046492686 0.005639302 21.15252337 -1.325362183 -0.064972607 THFGGGK ddPTM_MDA-MB-175_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 5056780000 24870800 23221500 13834100 17312060 15222010 20063100 25460600 27315200 25683300 FALSE TRUE 21584060.77 23068956.44 20524317.03 21243027.82 14919121.78 20834940.44 22991434.93 21474057.05 22647049.53 0.953062814 1.018629663 0.906268916 0.938004211 0.658766687 0.91998476 1.015206634 0.948205505 1 24.43281977 2.452418808 14.00139219 0.978841583 0.893298479 0.168117617 0.093784834 3.598059461 2034.39644 0.036732673 0.028493238 283.4123741 -2.452418808 -0.085543104 THILLFLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 THILLFLPK 9 0 P07237;H7BZ94;I3L398;I3L312;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ; 108.98 0.0025238 1989490000 3164500 3256500 2158000 2875500 2353900 2676200 2753600 2593200 3530400 FALSE TRUE 2746303.307 3235107.837 3201616.018 3528426.224 2307061.995 2779155.146 2486556.296 2038664.36 3113040.134 0.882193351 1.039211735 1.028453178 1.133434223 0.74109613 0.892746327 0.798754975 0.65487892 1 21.56989275 3.230255184 24.98572031 0.799525241 1.022681604 0.460964297 0.108283137 147.6874062 444295.8202 0.032311543 0.037247273 1699.241806 -3.230255184 0.223156364 THINIVVIGHVDSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 194.58 2.65E-08 6717253000 15775071 12679351 7519012 11063135 9390236 8156138 13989663 15598834 14010004 FALSE TRUE 13690355.4 12596059.51 11155231.35 13575188.89 9203388.675 8469909.907 12632947.64 12263144.74 12353757.29 1.108193652 1.019613646 0.902982882 1.098871264 0.744987008 0.685614078 1.02259963 0.992665183 1 23.55844656 4.733527748 1.171014291 0.918852173 1.201665126 0.20129248 0.124867776 2.927096999 3.403409729 0.040349157 1.014555343 54141.18391 -4.733527748 0.282812953 THKHS(ph)PEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 THKHSPEKR 9 2 Q86X95 Q86X95 CIR1 Corepressor interacting with RBPJ 1 1 THKHS(1)PEKR;THKHS(1)PEKR;T(0.003)HKHS(0.997)PEKR 113.99 0.00081262 316120000 340758 222567 160970 183253 141484 163517 278445 297999 239226 TRUE FALSE 295725.9669 221104.9427 238815.6304 224863.3945 138668.7452 169807.6048 251441.4468 234274.2329 210944.9748 1.401910461 1.048164067 1.132122871 1.065981281 0.657369275 0.804985305 1.191976472 1.110594045 1 17.68650719 5.829757847 1.062351906 0.991104268 4.508979999 0.401630046 0.157099587 18.37849534 2.797448994 0.052923154 124.382394 675706.1115 -5.829757847 3.517875731 THKPDPGT(ph)PQHTSSRPPEPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 THKPDPGTPQHTSSRPPEPQK 21 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 THKPDPGT(1)PQHTSSRPPEPQK;THKPDPGT(1)PQHTSSRPPEPQK 153.24 4.53E-08 274300000 334660 425220 85961 244136 506320 395700 449230 490690 612270 TRUE FALSE 290433.8331 422426.7018 127532.0271 299570.8102 496245.2226 410922.8351 405663.7437 385759.7621 539888.1381 0.537951869 0.782433752 0.236219354 0.554875703 0.919163041 0.761125882 0.751384806 0.714517943 1 19.04230099 3.317531835 7.192707763 0.805196009 0.522227884 0.481945882 0.154302158 0.211643566 16.15303289 0.043974869 0.056728417 2077.456005 -3.317531835 -0.282968125 THLENNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 THLENNR 7 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;;; 157.21 0.0014914 672363000 1434380 1432070 765347 951675 999251 1399097 1261223 1269573 1183997 FALSE TRUE 1244823.049 1422662.638 1135471.369 1167767.354 979367.8601 1452921.167 1138909.788 998084.6938 1044026.223 1.192329293 1.362669448 1.087588936 1.11852301 0.938068257 1.391651986 1.090882357 0.955995809 1 19.99372652 -1.83991333 0.165947232 4.31E-18 1.317200789 0.226584793 0.135559944 181.9455976 2.576778193 56.9703658 1.656183493 0.014457283 1.83991333 1.317200789 THLGTGMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 THLGTGMER 9 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E5RFW9;E5RJP0;E5RGA6;E5RH08;E5RG54;E5RH48;E5RH01;E5RG66;E5RI72;E5RIK4 E7ESA6 PTK2 Focal adhesion kinase 1 0 ; 118.71 0.00094499 221350000 186916 184473 94186 123508 130273 177051 162462 164479 172268 FALSE TRUE 162214.577 183261.1847 139734.6646 151552.3791 127680.8222 183862.2665 146706.4602 129306.4458 151902.6733 1.067884939 1.20643818 0.91989602 0.997693956 0.840543615 1.210395199 0.965792485 0.85124536 1 17.21278773 4.233412021 24.99861688 0.963647663 1.137161572 0.297922209 0.106807835 136.7510131 663996.6146 0.027108304 0.059300177 17116.38398 -4.233412021 0.173513909 THLMSESEWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 THLMSESEWR 10 0 P61024;Q5T179;Q9BZU3 P61024 CKS1B Cyclin-dependent kinases regulatory subunit 1;Cyclin-dependent kinases regulatory subunit 0 ;;;; 208.6 1.11E-07 2479419000 1710349 1880260 844503 1294600 1784711 1674436 1404905 1686710 1359081 FALSE TRUE 1484322.046 1867908.448 1252907.475 1588558.717 1749198.743 1738852.636 1268657.529 1326020.192 1198411.992 1.238574093 1.558653001 1.045473079 1.325553088 1.459597162 1.450963982 1.058615516 1.106481077 1 20.19269254 2.225932983 24.80321741 1.065899906 1.346623611 0.48855388 0.140419784 177.9028765 349433.8929 0.056207149 0.038185971 168.2414425 -2.225932983 0.280723705 THLPGCGARARLCGTGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 THLPGCGARARLCGTGAR 18 2 Q9NYQ6;Q9NYQ6-2 Q9NYQ6 CELSR1 Cadherin EGF LAG seven-pass G-type receptor 1 0 ; 52.52 0.07906 1306560000 954820 1148740 746270 424750 1017680 2125740 568770 507960 378050 FALSE TRUE 828638.1178 1141193.851 1107168.668 521195.9794 997430.1591 2207518.593 513610.7729 399336.7069 333357.3597 2.485735184 3.423334803 3.321266611 1.563475244 2.992074811 6.622078467 1.540721265 1.197923776 1 18.34671005 FDPFGPIGTS(ph)PPGPRPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 FDPFGPIGTSPPGPRPDR 18 1 Q5QPM7 Q5QPM7 PSMF1 1 FDPFGPIGT(0.031)S(0.969)PPGPRPDR;FDPFGPIGT(0.034)S(0.966)PPGPRPDR;FDPFGPIGT(0.006)S(0.994)PPGPRPDR;FDPFGPIGT(0.073)S(0.927)PPGPRPDR 163.95 1.93E-11 1217110000 370336 504880 413319 512300 657060 795320 684030 749030 924380 TRUE FALSE 321395.1593 501563.41 613201.4509 628625.545 643985.7915 825916.475 617692.8759 588855.7635 815100.8495 0.394301097 0.615339084 0.752301327 0.771224255 0.790068851 1.013269064 0.757811596 0.722433014 1 19.63661904 4.946332054 0.903669757 0.838222348 1.18E-12 0.71169808 0.094512713 1.762628302 0.887041885 0.033084581 1.588260693 88375.53464 -4.946332054 -0.838222348 down THLSLSHNPEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THLSLSHNPEQK 12 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 150.49 3.94E-05 112210000 151180 211560 30001 85107 205690 153400 153590 183930 158600 FALSE TRUE 131201.18 210170.2484 44509.58395 104431.8451 201597.1714 159301.3973 138694.8654 144598.0008 139850.4887 0.938153175 1.50282098 0.318265487 0.746739222 1.441519249 1.139083594 0.991736724 1.033947055 1 17.09352577 3.296599942 24.99999981 1.101532438 0.881359025 0.131133185 0.310657372 194.833141 83920.99714 0.091190286 0.117726108 1979.702548 -3.296599942 -0.220173412 THMNEGGYNTPVHHPVIKS(ph)ENSVIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THMNEGGYNTPVHHPVIKSENSVIK 25 1 H0YKC7;Q8IYA7 H0YKC7 MKX Homeobox protein Mohawk 1 THMNEGGYNTPVHHPVIKS(0.5)ENS(0.5)VIK 60.991 0.035289 304710000 331790 371810 198470 244710 353360 354940 287330 305620 193710 TRUE FALSE 287943.1109 369367.5556 294450.7558 300275.1457 346328.8273 368594.7715 259464.7808 240265.5413 170809.8245 1.68575263 2.162449126 1.723851405 1.757950086 2.027569716 2.157924889 1.519027267 1.406626007 1 17.38203143 1.659820256 1.604784344 0.999306211 1.913047706 0.71761747 0.189257516 0.241265747 1.079664185 0.295440581 0.055316061 45.6899051 -1.659820256 0.913741495 THMNEGGYNTPVHHPVIKSENS(ph)VIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THMNEGGYNTPVHHPVIKSENSVIK 25 1 H0YKC7;Q8IYA7 H0YKC7 MKX Homeobox protein Mohawk 1 THMNEGGYNTPVHHPVIKS(0.141)ENS(0.859)VIK 56.72 0.048908 3815700000 720170 983540 282450 539990 945140 1137900 677790 721530 504670 TRUE FALSE 624997.7098 977079.061 419043.7647 662602.9827 926333.5631 1181675.749 612058.0301 567236.4245 445008.4875 1.404462448 2.195641405 0.941653421 1.488967068 2.081608754 2.655400475 1.375385071 1.274664282 1 18.76347333 2.015842067 24.98726047 1.207372782 1.793410714 0.257691744 0.471977257 337.4087894 532183.6893 0.19994333 0.134756765 103.7151184 -2.015842067 0.586037931 THMQDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 133.55 0.0032609 2765590000 5514540 4850690 3054040 3884040 4303840 3803800 5149930 5701870 5294280 FALSE TRUE 4785779.567 4818825.498 4530983.959 4765970.646 4218202.004 3950134.647 4650490.581 4482569.473 4668396.25 1.025144249 1.032222896 0.970565418 1.020901053 0.903565546 0.846143822 0.996164493 0.960194729 1 22.15449559 3.254565133 24.99455308 0.942954155 1.010663529 0.362034955 0.046778055 304.514607 475563.3856 0.01434991 0.018466701 1797.070573 -3.254565133 0.067709374 THNDIIHNENMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 THNDIIHNENMR 12 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;;;;;;;; 214.42 2.54E-11 10133690000 4123225 3980984 2326413 3148883 3428778 3672770 2978687 3344269 2814408 FALSE TRUE 3578330.369 3954832.654 3451474.108 3863885.013 3360552.026 3814063.838 2689814.393 2629123.099 2481691.892 1.441891469 1.593603407 1.390774624 1.556955972 1.354137488 1.536880485 1.083863151 1.059407539 1 21.24289258 2.21026381 7.530603669 1.049530332 1.478197037 0.879631566 0.075219043 0.054428262 10.94207806 0.027988918 0.019189094 162.2795556 -2.21026381 0.428666705 THNGESVSYLFSHVPL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THNGESVSYLFSHVPL 16 0 B1ALA9;P60891;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 0 182.1 2.20E-09 559720000 453580 468390 156660 313580 450240 472630 381370 411730 438150 FALSE TRUE 393638.2538 465313.1152 232421.3 384783.1318 441281.1049 490812.3819 344384.7961 323684.7436 386352.4061 1.018858036 1.204374835 0.601578498 0.995938231 1.142172529 1.270374855 0.891374793 0.837796629 1 18.55955786 THNSSLEYNIFEGMECR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THNSSLEYNIFEGMECR 17 0 A0A1C7CYX9;Q16555-2;Q16555 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 0 65.175 0.043801 108230000 407200 325310 253330 258460 314680 242300 429130 465320 413060 FALSE TRUE 353387.4883 323173.0172 375841.2353 317147.2933 308418.4837 251621.4378 387513.0386 365814.9391 364228.5174 0.970235639 0.887280929 1.031883055 0.870737128 0.846771927 0.690833984 1.063928331 1.004355567 1 18.47448436 THPQWYPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 THPQWYPAR 9 0 Q9NZ01;M0R2N5;M0R3C3 Q9NZ01 TECR Very-long-chain enoyl-CoA reductase 0 ; 129.85 0.00037767 713370000 256100 501340 249120 418550 769260 711330 381390 705180 722050 FALSE TRUE 222255.7361 498046.6645 369595.2653 513588.1746 753953.231 738695.3254 344402.8565 554382.7447 636690.0716 0.349079947 0.782243491 0.580494784 0.806653343 1.184176202 1.160211787 0.54092701 0.870726228 1 19.28023174 3.608674189 4.008246105 0.925852202 0.59227921 0.412477578 0.204514811 0.272660458 7.4767565 0.060163368 0.09164985 4061.38527 -3.608674189 -0.333572992 THPQYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 THPQYSR 7 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;;; 109.71 0.0069661 1254625000 3670786 3634389 1613554 2531964 3390278 4400025 2843359 3673093 3760584 FALSE TRUE 3185682.33 3610514.459 2393874.111 3106885.125 3322818.101 4569296.809 2567610.482 2887630.646 3316012.044 0.960696851 1.088812227 0.721913576 0.93693421 1.002052483 1.377949401 0.774306742 0.870814282 1 21.66101782 THPVEIFYTPEPERDYLEAAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 THPVEIFYTPEPERDYLEAAIR 22 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ;;; 178.77 3.55E-17 516093000 159656 147096 94968.4 110839.3 155762 161467 150536 164954 123956 FALSE TRUE 138557.0551 146129.7167 140895.4359 136007.0571 152662.6409 167678.74 135937.0419 129679.8708 109302.0629 1.267652699 1.336934664 1.289046448 1.244322875 1.396704114 1.534085776 1.243682308 1.186435712 1 16.7379611 1.469017447 1.876184118 0.974847808 1.33885128 0.622789676 0.084745142 0.352703938 1.882633857 0.204039453 0.025149934 29.4453992 -1.469017447 0.364003472 THPYS(ph)PK ddPTM_MDA-MB-175_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;THPY(0.002)S(0.998)PK 123.21 0.0044748 1189381000 5699590 4049340 2975240 3372350 3798730 3715390 5054400 4949590 4900570 TRUE FALSE 4946374.741 4022739.619 4414076.016 4138093.611 3723142.705 3858323.457 4564225.066 3891158.696 4321230.197 1.144668188 0.930924629 1.021485969 0.95761934 0.861593235 0.892876167 1.056232799 0.900474753 1 22.04301066 EVVQGSSASAASSPT(ph)WK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVVQGSSASAASSPTWK 17 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 EVVQGSSASAAS(0.017)S(0.265)PT(0.718)WK 205.3 8.95E-11 398130000 468820 661670 516980 684010 905410 727380 973680 1201600 1089300 TRUE FALSE 406864.2492 657323.4462 766993.2572 839324.9249 887394.1124 755362.7793 879252.6635 944647.1909 960524.1949 0.423585633 0.68433825 0.798515291 0.873819659 0.923864404 0.786406822 0.915388356 0.98347048 1 19.87346243 4.955419205 0.780698072 0.932829401 7.92E-24 0.89286425 0.055529645 1.159648019 0.435876228 0.023158957 1.017191529 90244.18035 -4.955419205 -0.932829401 down THS(ph)FENVSCHLPDSR ddPTM_MDA-MB-175_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(0.016)HS(0.984)FENVSCHLPDSR;T(0.014)HS(0.986)FENVSCHLPDSR;T(0.004)HS(0.996)FENVSCHLPDSR;T(0.007)HS(0.993)FENVSCHLPDSR 236.95 1.69E-17 1446750000 724750 819760 240295 450217 871210 667360 787960 851340 694220 TRUE FALSE 628972.4512 814374.9426 356502.4657 552445.651 853874.6255 693033.771 711543.7605 669287.5661 612150.1025 1.027480758 1.330351721 0.582377532 0.902467628 1.394877861 1.13213045 1.162368115 1.093338976 1 19.22352593 THSAGT(ph)SPTITHQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THSAGTSPTITHQK 14 0 P35568 P35568 IRS1 Insulin receptor substrate 1 1 THS(0.001)AGT(0.611)S(0.385)PT(0.003)ITHQK 164.79 1.50E-05 294930000 454590 385030 186110 245470 304770 250740 300910 334820 305430 TRUE FALSE 394514.7797 382500.7126 276113.4185 301207.7153 298705.6733 260386.1301 271727.7945 263221.3486 269322.4133 1.464841989 1.420233496 1.02521515 1.118390822 1.109100686 0.966819385 1.008931233 0.977346613 1 18.03897477 4.252841145 5.646735752 1.026470753 1.450612942 0.921012123 0.050336346 0.042894222 4.319799749 0.014340292 0.036133239 17899.51012 -4.252841145 0.424142189 THSAGTS(ph)PTITHQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 THSAGTSPTITHQK 14 0 P35568 P35568 IRS1 Insulin receptor substrate 1 1 T(0.001)HS(0.01)AGT(0.354)S(0.635)PTITHQK;THSAGT(0.046)S(0.953)PTITHQK 180.02 1.16E-06 441970000 629790 568100 291150 384380 418620 369660 433330 460100 404110 TRUE FALSE 546561.6558 564368.1137 431951.1138 471659.3539 410290.281 383881.0594 391305.7233 361711.1955 356336.5762 1.533835403 1.583806298 1.212199765 1.32363441 1.1514122 1.077299062 1.098135161 1.015082985 1 18.44288105 4.477071077 0.418825631 0.977378334 1.952422683 0.877327156 0.071200788 1.538518658 0.292089713 0.087014239 0.763455772 29996.53407 -4.477071077 0.975044349 THSDQFLVAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 THSDQFLVAFK 11 0 P36542-2;P36542 P36542-2 ATP5C1 "ATP synthase subunit gamma, mitochondrial" 0 ; 75.78 0.022238 0 1098300 1041920 746650 1316750 1275820 1167620 1037210 1372810 1342530 FALSE TRUE 953156.8723 1035075.559 1107732.437 1615738.213 1250433.678 1212539.097 936621.5338 1079245.265 1183817.633 0.805155157 0.874353896 0.935728956 1.364853984 1.056272219 1.02426173 0.791187348 0.911665137 1 20.17501542 6.983788866 8.966455057 0.9725514 0.045018245 0 0.163285053 0 0 0.038955233 0 9633605.691 -6.983788866 -0.927533155 THSLCNGDS(ph)PGPVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 THSLCNGDSPGPVQK 15 0 A0A1B0GWK2;Q674X7-4;Q674X7-3;Q674X7-2;Q674X7 A0A1B0GWK2 KAZN Kazrin 1 THSLCNGDS(1)PGPVQK;THSLCNGDS(1)PGPVQK;THSLCNGDS(1)PGPVQK 268.37 8.43E-26 525290000 895260 698240 360908 474690 531880 440371 604360 630930 576020 TRUE FALSE 776949.1227 693653.2155 535444.316 582475.6197 521296.6286 457312.3573 545749.2602 496010.5294 507923.5718 1.529657543 1.365664549 1.054182845 1.146778082 1.026328876 0.900356634 1.074471221 0.9765456 1 18.9542519 4.662403389 0.946807661 0.997555268 1.80567657 0.886349874 0.064287517 0.536681668 0.419142601 0.020803807 0.435782552 45962.47309 -4.662403389 0.808121302 THSQGGYGSQGYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THSQGGYGSQGYK 13 0 K7ER00;Q9Y285;Q9Y285-2;K7EPH2;K7ERS0 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 162.88 3.97E-05 93734000 163480 136860 70797 97817 133030 134880 146860 155540 161170 FALSE TRUE 141875.7038 135960.9576 105034.666 120027.8449 130382.9633 140068.9209 132617.5398 122278.9814 142116.6662 0.998304475 0.956685527 0.739073529 0.844572618 0.917436123 0.985591097 0.933159659 0.860412678 1 17.11671623 3.023142432 16.8443418 0.932849148 0.879603116 0.109223507 0.077133002 15.81752076 11508.14967 0.024752954 0.02804775 1054.732751 -3.023142432 -0.053246032 THSTSSS(ph)LGSGESPFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 1 T(0.006)HS(0.03)T(0.161)S(0.074)S(0.268)S(0.462)LGSGESPFSR;T(0.007)HS(0.038)T(0.029)S(0.029)S(0.017)S(0.879)LGSGESPFSR;THS(0.001)T(0.002)S(0.014)S(0.047)S(0.935)LGSGESPFSR 140.32 4.29E-07 1109080000 325993 352004 153663 252768 342923 279345 336249 359485 320600 TRUE FALSE 282912.1991 349691.6625 227974.9408 310162.8377 336099.5032 290091.5829 303639.6237 282611.9303 282699.0332 1.000754038 1.236975092 0.806422782 1.097148562 1.188895128 1.026149894 1.074073796 0.999691888 1 18.10890742 1.696345384 5.717166211 0.999353958 1.06332088 0.047052691 0.114752478 0.468581216 35.25728182 0.068500126 0.028485135 49.69874065 -1.696345384 0.063966921 THTDS(ph)SEKELEPEAAEEALENGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THTDSSEKELEPEAAEEALENGPK 24 1 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 1 T(0.031)HT(0.031)DS(0.469)S(0.469)EKELEPEAAEEALENGPK 92.231 0.0052756 54155000 42629 35817 28580 26170 34119 26411 39327 45774 36305 TRUE FALSE 36995.46964 35581.71577 42401.38359 32112.29848 33440.09865 27427.04826 35513.07359 35985.58631 32013.06426 1.155636628 1.111474849 1.324502498 1.003099804 1.044576626 0.856745485 1.109330657 1.124090653 1 14.96637316 3.709674052 24.99511416 1.032878088 1.188631717 0.451427206 0.089934999 710.0555014 614400.191 0.02567859 0.038093573 5124.76614 -3.709674052 0.155753629 THTDSS(ph)EKELEPEAAEEALENGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THTDSSEKELEPEAAEEALENGPK 24 1 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 1 T(0.024)HT(0.024)DS(0.125)S(0.827)EKELEPEAAEEALENGPK 142.65 1.56E-07 97256000 164420 158740 114440 109730 129650 80447 162760 195970 134900 TRUE FALSE 142691.4804 157697.2265 169783.5668 134645.8736 127070.2187 83541.84815 146975.5603 154063.3405 118952.2757 1.199569152 1.32571845 1.427325083 1.131931885 1.068245378 0.702313997 1.235584266 1.295169341 1 16.86002335 3.588560352 5.685872139 1.086140941 1.317004899 0.328588827 0.165787524 0.322120369 14.09111132 0.050311917 0.075006146 3877.576302 -3.588560352 0.230863958 THTDSSEKELEPEAAEEALENGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 THTDSSEKELEPEAAEEALENGPK 24 1 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 ; 129.84 4.06E-05 179038000 474950 386740 238280 256980 324430 213601 434460 483630 190035 FALSE TRUE 412184.1541 384199.4795 353513.005 315331.2367 317974.4777 221818.3687 392326.1361 380209.4881 167569.2788 2.459783542 2.292779931 2.109652841 1.881796228 1.897570247 1.323741263 2.341277225 2.268968935 1 17.35439815 4.135584882 1.530358093 1.850493138 2.458249358 0.274224787 0.39753769 0.743496137 3.126756958 0.120670237 0.488887372 13664.22113 -4.135584882 0.60775622 THTGEKPYVCDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THTGEKPYVCDK 12 1 Q49AA0 Q49AA0 ZFP69 Zinc finger protein ZFP69 0 52.344 0.089716 334770000 859280 419420 3233100 744650 128140 147520 616780 526600 451270 FALSE TRUE 745723.9709 416664.8024 4796637.974 913734.1638 125590.2647 153195.1899 556964.7705 413990.688 397921.3747 1.874048539 1.047103345 12.05423553 2.296268112 0.315615779 0.384988592 1.399685481 1.040383137 1 18.60212387 3.488973933 24.95901399 0.914516614 5.026980573 0.299190934 2.907085906 691.1321505 1455364.309 0.808638259 1.128030947 3083.002901 -3.488973933 4.112463959 THTLCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THTLCR 6 0 P61927;D6RG19;D6R9X9 P61927 RPL37 60S ribosomal protein L37;Ribosomal protein L37 0 105.22 0.077156 44369000 27063 27730 17186 18644 22984 31561 28473 25634 29204 FALSE TRUE 23486.55598 27547.8398 25497.20708 22877.40516 22526.66337 32775.17209 25711.69284 20152.36858 25751.53639 0.912044844 1.069755194 0.990123723 0.888389912 0.874769685 1.272746278 0.99845277 0.782569563 1 14.65237089 1.776428907 24.99999998 0.877603577 1.004408973 0.115701562 0.124420804 85.59669997 56538.49563 0.066028065 0.031754409 59.76252072 -1.776428907 0.126805396 THTMEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 THTMEGK 7 0 P33176;O60282;Q12840 P33176;Q12840 KIF5B;KIF5C;KIF5A Kinesin-1 heavy chain;Kinesin heavy chain isoform 5C;Kinesin heavy chain isoform 5A 0 ;; 101.64 0.0089085 239050000 757920 717550 416829 544682 414669 559448 711720 760050 722090 FALSE TRUE 657758.9517 712836.3668 618408.8986 668360.373 406417.8982 580970.3266 642697.5039 597519.2222 636725.3428 1.033034038 1.119535094 0.971233367 1.04968395 0.638293894 0.912434746 1.009379493 0.938425381 1 19.28031166 THTRVS(ph)VQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 THTRVSVQR 9 1 P15880;H0YEN5;E9PQD7 P15880 RPS2 40S ribosomal protein S2 1 THT(0.002)RVS(0.998)VQR;THTRVS(1)VQR;THT(0.001)RVS(0.999)VQR;THTRVS(1)VQR;THTRVS(1)VQR;THTRVS(1)VQR;THT(0.001)RVS(0.999)VQR;THTRVS(1)VQR 142.08 6.37E-05 5105400000 2469833 2664880 1277269 1520789 2352580 2637276 2246500 2295844 1349162 TRUE FALSE 2143438.311 2647374.228 1894960.561 1866107.386 2305768.261 2738733.714 2028634.776 1804895.627 1189665.605 1.801714954 2.225309546 1.59285143 1.56859825 1.938165019 2.302103803 1.705214278 1.517145338 1 20.18212468 1.387886314 1.8003076 0.855275668 1.891155671 0.591310969 0.237681867 0.476661915 1.963877685 0.788955139 0.06943265 24.42791013 -1.387886314 1.035880003 THTTALAGRS(ph)PS(ph)PASGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 THTTALAGRSPSPASGR 17 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 THTTALAGRS(0.999)PS(0.998)PAS(0.003)GR;THTTALAGRS(1)PS(0.998)PAS(0.002)GR;T(0.012)HT(0.014)T(0.015)ALAGRS(0.937)PS(0.983)PAS(0.039)GR;THTTALAGRS(1)PS(0.999)PAS(0.001)GR;THTTALAGRS(0.999)PS(1)PAS(0.001)GR;THTTALAGRS(1)PS(1)PASGR 126.26 2.51E-05 14137970000 7349790 7490950 1976910 3407040 7329500 6821950 5783020 6015340 2457340 TRUE FALSE 6378496.63 7441741.456 2932950.288 4180660.505 7183657.29 7084394.831 5222183.61 4729006.352 2166836.065 2.943691373 3.43438139 1.353563537 1.929384771 3.315274933 3.269465072 2.410050163 2.182447685 1 21.04715858 1.19773568 1.787918463 0.27965779 2.667048711 0.399048882 0.647395987 1.165507237 3.197118258 4.969793948 0.19015819 15.76651399 -1.19773568 2.387390921 THTTALAGRS(ph)PS(ph)PASGRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 THTTALAGRSPSPASGRR 18 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 THTTALAGRS(1)PS(0.985)PAS(0.016)GRR;THTTALAGRS(1)PS(0.975)PAS(0.026)GRR;THTTALAGRS(0.997)PS(0.895)PAS(0.108)GRR;THTTALAGRS(0.988)PS(0.897)PAS(0.115)GRR 145.13 5.00E-08 994251000 680754 596793 165175 228009 560510 584948 524149 543248 81457.4 TRUE FALSE 590790.6341 592872.6275 245054.1825 279781.9283 549356.9476 607451.3281 473317.1107 427078.6428 71827.59897 8.225120185 8.254106165 3.411699486 3.895186981 7.648271076 8.457074116 6.58962735 5.945884993 1 16.13225067 4.277477425 24.16668944 5.556890078 8.239626402 0.237158731 2.163628018 186.6964208 115931.357 0.558096619 1.476512506 18944.25039 -4.277477425 2.682736324 THTYECR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THTYECR 7 0 P30876;C9J2Y9;C9J4M6 P30876 POLR2B DNA-directed RNA polymerase II subunit RPB2;DNA-directed RNA polymerase 0 90.777 0.01689 46999000 46247 46689 25655 25138 32824 50772 32714 36887 35953 FALSE TRUE 40135.34178 46382.29688 38061.84381 30845.96711 32170.86662 52725.23169 29541.40132 28999.0021 31702.6773 1.265992187 1.463040375 1.200587681 0.972976724 1.014768132 1.663116058 0.931826705 0.914717764 1 14.95231706 -0.365269027 0.232906471 4.10E-15 1.374310096 0.19506762 0.222135149 68.18341132 2.159276871 30.21049598 1.107798358 0.431251852 0.365269027 1.374310096 THVADFAPEVAWVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 THVADFAPEVAWVTR 15 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;;; 158.17 1.84E-06 2515380000 1723290 1749760 937830 1175070 1742320 1807460 1516290 1758220 1765160 FALSE TRUE 1495552.86 1738265.711 1391367.725 1441887.603 1707651.241 1876994.156 1369240.429 1382238.335 1556484.796 0.960852855 1.116789394 0.893916682 0.926374358 1.097120412 1.205918722 0.879700485 0.888051293 1 20.56986005 THVEKEDGEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THVEKEDGEAR 11 1 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 0 119.39 0.00035637 149970000 239740 194880 152700 113220 168280 221640 169250 175740 66543 FALSE TRUE 208057.7516 193599.8204 226546.2308 138928.3315 164931.5572 230166.6342 152836.1611 138159.3686 58676.36235 3.545852934 3.299451648 3.860945391 2.367705255 2.810868817 3.922646616 2.604731359 2.354600099 1 15.84049181 1.240195668 1.281976073 3.13E-16 3.258280599 0.687717093 0.486439849 0.849343528 1.199995584 3.734802285 0.149294989 17.3858396 -1.240195668 3.258280599 THVSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 THVSEK 6 0 A0A0C4DGB5;H0Y944;E7EN75;D6RGF7;D6RBR1 A0A0C4DGB5 CAST 0 ; 122.15 0.019343 366430000 1094280 1316590 259660 772740 885870 1146910 1355890 1632290 1609950 FALSE TRUE 949668.1254 1307941.234 385232.4445 948202.4276 868242.9202 1191032.37 1224395.996 1283237.486 1419623.545 0.668957717 0.921329629 0.271362395 0.667925262 0.611600817 0.838977611 0.862479353 0.90392801 1 20.43707698 2.561518486 2.025850842 0.922798569 0.623401322 0.426682919 0.159160822 0.326307956 2.689523646 0.068859472 0.054066553 364.3497582 -2.561518486 -0.299397247 THYDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THYDAK 6 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 71.852 0.08714 160440000 402590 386410 273930 345010 219320 306690 384700 439270 818050 FALSE TRUE 349386.7115 383871.6473 406403.4642 423349.7936 214955.9611 318488.5628 347391.8532 345335.5289 721341.0609 0.484357165 0.532163865 0.563399876 0.586892687 0.297994905 0.441522852 0.48159168 0.478740983 1 19.46032202 1.2382607 24.99999914 1.000000571 0.483202005 0.81004386 0.078629493 3.169689535 263770.8375 0.113359363 0.019990884 17.30855052 -1.2382607 -0.516798566 THYDPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 THYDPPR 7 0 P31943;G8JLB6;E9PCY7;H0YB39;D6RBM0;H0YBD7;E7EN40;E5RGV0;P55795 P31943;P55795 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 ;;;;; 105.39 0.0079373 3262130000 3244450 2738480 1480460 1836670 2639070 2725370 2546390 2870630 2984040 FALSE TRUE 2815687.712 2720490.745 2196415.408 2253713.995 2586557.67 2830216.747 2299441.49 2256768.114 2631270.191 1.070086881 1.033907789 0.834735792 0.856511811 0.983007249 1.075608563 0.873890298 0.857672512 1 21.32732797 4.393562462 7.425360318 0.922133711 1.061145555 0.326775063 0.075909149 0.242905857 17.91231476 0.020119634 0.053937072 24749.27393 -4.393562462 0.139011844 THYDPPRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 THYDPPRK 8 1 P31943;G8JLB6;E9PCY7;H0YB39;D6RBM0;H0YBD7;E7EN40;E5RGV0;P55795 P31943;P55795 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 ;;; 111.74 0.0020614 1688600000 2268930 2007830 1123090 1511060 1631880 2017530 1897970 2262630 1964780 FALSE TRUE 1969085.152 1994640.433 1666220.081 1854169.268 1599408.781 2095145.685 1713905.162 1778784.182 1732505.947 1.136553185 1.151303657 0.961739891 1.070223898 0.923176503 1.209315148 0.989263653 1.026711733 1 20.72442887 4.258264393 24.98082275 1.02838153 1.143928535 0.292367907 0.076335714 291.8915938 370059.3348 0.017626618 0.04649252 18124.43149 -4.258264393 0.115547005 THYPAQQGEYQTHQPVYHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 THYPAQQGEYQTHQPVYHK 19 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 0 ; 249.14 1.94E-25 281600000 364600 339980 203587 271010 316290 296430 341170 353810 334820 FALSE TRUE 316417.1862 337746.649 302042.3542 332546.9626 309996.4478 307833.8539 308083.3859 278150.4849 295237.961 1.071736118 1.143981105 1.023047148 1.126369256 1.049988446 1.042663528 1.043508717 0.942123038 1 18.17151871 2.19557362 1.044945226 0.961585424 1.089497254 0.552304498 0.03868986 0.410285235 0.841080003 0.042262357 0.014601007 156.8821818 -2.19557362 0.127911831 THYQADIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THYQADIER 9 0 O95573 O95573 ACSL3 Long-chain-fatty-acid--CoA ligase 3 0 113.44 0.0017992 563750000 321720 356100 284990 339810 359130 533980 263810 437740 539770 FALSE TRUE 279203.8869 353760.7557 422812.1172 416969.0542 351984.0156 554522.5561 238225.7468 344132.7075 475959.0055 0.586613308 0.743258876 0.888337257 0.876060857 0.739525908 1.165063692 0.500517364 0.723030142 1 18.86047779 4.631601456 3.154503701 0.821922564 0.575770455 0.171615581 0.175552236 0.55917482 8.927900256 0.043587717 0.288748432 42815.54293 -4.631601456 -0.24615211 THYSNIEANESEEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 THYSNIEANESEEVR 15 0 A0A0C4DGQ5;K7ELJ7;P04632;U3KQE2;K7EIV0;A0A075B7C0;K7EM73 A0A0C4DGQ5 CAPNS1 Calpain small subunit 1 0 174.39 9.15E-07 470380000 521130 462860 213940 313030 445470 479180 456310 465930 478140 FALSE TRUE 452261.3501 459819.4422 317402.0996 384108.2459 436606.0185 497614.3647 412057.1264 366294.4954 421614.8339 1.07268842 1.090614953 0.752824792 0.911040635 1.035556587 1.180258199 0.977330713 0.868789392 1 18.6855661 2.307653114 0.008814143 1.15E-07 1.947801289 0.002982031 0.121211249 46988.52888 265.4856316 29745.25826 28920.04234 203.0734346 -2.307653114 1.947801174 TIADHCPDSACK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TIADHCPDSACK 12 0 P35221-2;P35221;G3XAM7;P35221-3 P35221-2 CTNNA1 Catenin alpha-1 0 ;; 167.18 4.99E-05 820470000 1602540 1317650 964630 1455800 1401150 1376030 1289290 1893980 1931520 FALSE TRUE 1390760.279 1308994.27 1431128.294 1786361.641 1373269.856 1428966.765 1164254.854 1488967.116 1703177.906 0.816567825 0.768559917 0.84026941 1.048840309 0.806298538 0.839000294 0.683577946 0.874228764 1 20.69979771 4.012249608 20.40751768 0.865430093 0.795525955 0.098412715 0.100144889 70.92094789 118131.8809 0.026464032 0.054933222 10286.07313 -4.012249608 -0.069904138 TIADLELHYQEFIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TIADLELHYQEFIR 14 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;; 169.4 3.34E-06 467566000 552890 463880 281650 353100 436050 430400 423140 521500 470330 FALSE TRUE 479824.1857 460832.7417 417856.8821 433276.7518 427373.4581 446957.7665 382103.9479 409981.2833 414728.1232 1.156960811 1.111168295 1.00754412 1.044724791 1.030490662 1.077712703 0.921335995 0.988554333 1 18.66180636 8 0.349857826 0.977434223 3.13354517 0.631000236 0.040298762 51.22526149 0.781896995 0.054057968 71.97705088 100000000 -8 2.156110946 TIAEIFGNPNYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TIAEIFGNPNYLR 13 0 Q16401-2;Q16401 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 151.07 0.00010366 76964000 174370 198460 109410 106430 190390 177990 195340 228570 211180 FALSE TRUE 151326.5627 197156.3032 162321.042 130596.5582 186601.6115 184837.3905 176395.9569 179692.0842 186214.541 0.812646327 1.058758903 0.871688328 0.701323095 1.002078627 0.992604495 0.947272731 0.96497343 1 17.50660621 TIAPTGHLHTVEFHQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TIAPTGHLHTVEFHQQR 17 0 Q96FX7;H0Y2Q1 Q96FX7 TRMT61A tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 0 84.41 0.001839 78631000 40901 36251 14990 30457 38713 39680 31852 33502 37228 FALSE TRUE 35495.82922 36012.86479 22239.21414 37372.72736 37942.68704 41206.51528 28762.99794 26337.85801 32826.94825 1.081301525 1.097051865 0.677468218 1.138477055 1.155839609 1.255264881 0.876200789 0.802324292 1 15.00259302 2.06863385 24.99955618 0.872704507 1.059022141 0.210471894 0.157367744 73.82173892 26888.04909 0.066549251 0.044867491 117.1207515 -2.06863385 0.186317634 TIAQDYGVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TIAQDYGVLK 10 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 158.79 1.83E-05 187150000 311700 270160 147030 179940 245040 233140 270210 301370 300960 FALSE TRUE 270508.0553 268385.3012 218134.1998 220798.1272 240164.1834 242109.0467 244005.0758 236924.3708 265380.8517 1.019320172 1.011321275 0.821966613 0.832004743 0.904979323 0.912307897 0.919452456 0.89277116 1 18.01770475 4.3060277 10.62746463 0.89684841 1.01594959 0.502639272 0.048664777 0.387106931 58.49142125 0.012388739 0.03280672 20231.48213 -4.3060277 0.11910118 TICSHVQNMIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TICSHVQNMIK 11 0 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9R4 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 191.53 1.79E-06 674380000 1301000 1534300 845950 1149000 1467900 1338800 1590900 1966900 1700600 FALSE TRUE 1129069.554 1524221.082 1255054.25 1409898.011 1438691.662 1390304.502 1436614.763 1546293.741 1499557.005 0.7529354 1.016447575 0.836950009 0.940209679 0.959411117 0.927143481 0.958026109 1.031167029 1 20.51610494 8 0.160004262 1.070545806 0.173196583 0.435455859 0.063398564 134.9293539 1.772853697 0.805515107 27.7772929 100000000 -8 -0.897349224 TIDDLEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TIDDLEDK 8 0 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 102.95 0.011323 207710000 191730 183180 167940 194640 190880 150720 201230 237430 477660 FALSE TRUE 166392.3947 181976.6785 249156.3457 238835.9869 187081.8615 156518.2959 181714.7456 186657.4422 421191.579 0.39505157 0.432052034 0.591551109 0.567048343 0.444172844 0.371608322 0.431430149 0.443165181 1 18.68411707 1.237421857 24.99988174 1.000000643 0.460830104 0.858095788 0.069072993 11.13174894 244271.2272 0.110141236 0.018403051 17.27515117 -1.237421857 -0.539170539 TIDDLEDKLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TIDDLEDKLK 10 1 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ; 156.51 9.87E-06 2313200000 3180300 2475600 2004140 1974020 2193680 1359300 3198400 3797100 1834720 FALSE TRUE 2760015.297 2459337.621 2973348.807 2422251.412 2150030.06 1411593.151 2888219.66 2985119.714 1617821.492 1.706007314 1.520153882 1.837871992 1.497230334 1.328966187 0.872527135 1.785252375 1.845147768 1 20.625621 3.500007413 18.29957935 1.431143105 1.670614756 0.167290016 0.308587396 62.83649716 50240.52607 0.091955656 0.13427901 3162.331635 -3.500007413 0.239471651 TIDDLEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TIDDLEEK 8 0 P67936;A0A2R8YE05;K7ENT6;A0A5F9UN72;K7EPB9;P67936-2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;;; 148.99 0.0011922 1133060000 2548910 2309240 1698470 1906810 2203400 1940900 2686650 3004510 2654660 FALSE TRUE 2212065.085 2294070.45 2519855.773 2339780.354 2159556.651 2015567.679 2426099.097 2362018.918 2340829.119 0.944992126 0.980024741 1.076480018 0.999551969 0.922560572 0.861048618 1.036427254 1.009052262 1 21.15858819 TIDLGAAAHYTGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TIDLGAAAHYTGDK 14 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 193.06 3.02E-07 575020000 1217160 1046320 575790 835030 1046120 909340 1197380 1397370 1253900 FALSE TRUE 1056309.222 1039446.655 854243.9699 1024636.324 1025304.259 944322.8982 1081258.272 1098553.3 1105665.37 0.955360682 0.940109623 0.772606245 0.926714675 0.927318777 0.85407658 0.97792542 0.99356761 1 20.07648339 2.129450474 6.24484748 0.992976988 0.895460871 0.423602118 0.052161097 0.201066095 10.33869862 0.021661659 0.014512166 134.7257079 -2.129450474 -0.097516116 TIDLGAAAHYTGDKAS(ph)PDQNASTHT(ph)PQSSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TIDLGAAAHYTGDKASPDQNASTHTPQSSVK 31 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 2 TIDLGAAAHYT(0.106)GDKAS(0.894)PDQNAS(0.012)T(0.05)HT(0.933)PQS(0.005)S(0.001)VK;TIDLGAAAHYTGDKAS(1)PDQNAS(0.013)T(0.049)HT(0.922)PQS(0.012)S(0.003)VK 169.7 1.41E-12 496430000 385670 303130 140345 257394 332190 314210 511030 539690 488910 TRUE FALSE 334702.7323 301138.7191 208216.3114 315839.2417 325580.0689 326297.862 461470.3893 424281.4934 431111.6168 0.776371407 0.698516828 0.482975414 0.732615939 0.755210614 0.756875596 1.07041975 0.984156949 1 18.71770191 2.352755299 3.994036314 1.013294768 0.686207683 0.766223867 0.083192352 0.107110354 3.151518711 0.034434595 0.025793879 225.296943 -2.352755299 -0.327087085 TIDLGAAAHYTGDKAS(ph)PDQNASTHTPQSSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TIDLGAAAHYTGDKASPDQNASTHTPQSSVK 31 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 1 TIDLGAAAHYTGDKAS(1)PDQNASTHTPQSSVK;TIDLGAAAHYTGDKAS(1)PDQNASTHTPQSSVK;TIDLGAAAHYT(0.002)GDKAS(0.247)PDQNAS(0.247)T(0.247)HT(0.247)PQS(0.008)S(0.002)VK;TIDLGAAAHYTGDKAS(1)PDQNASTHTPQSSVK;TIDLGAAAHYTGDKAS(1)PDQNASTHTPQSSVK 302.11 6.86E-82 5585520000 3009986 2341147 1077563 1994985 2502530 2026756 3463846 3725405 3322275 TRUE FALSE 2612208.724 2325767.851 1598676.071 2447976.836 2452734.549 2104726.615 3127922.748 2928756.132 2929519.434 0.891685064 0.793907637 0.545712738 0.83562403 0.837248089 0.718454566 1.06772555 0.999739445 1 21.48223259 2.238458168 24.99999994 1.019633892 0.767290388 0.612525788 0.094470343 1.802051942 439484.5976 0.037356949 0.027016842 173.1642226 -2.238458168 -0.252343505 TIDQIHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TIDQIHK 7 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C044 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;; 104.75 0.008082 1457820000 3026790 2675980 1720220 2165880 2569070 2561740 3067180 3490950 3301690 FALSE TRUE 2626792.033 2658401.311 2552124.146 2657676.157 2517950.533 2660291.795 2769725.356 2744437.509 2911367.969 0.902253532 0.913110723 0.876606521 0.912861646 0.864868529 0.913760069 0.951348433 0.942662535 1 21.47326576 1.404165294 0.84196092 1.035169708 0.894541783 0.75897787 0.018851622 0.90887549 0.611542832 0.116850217 0.007436471 25.36093691 -1.404165294 -0.140627926 TIEAEAAHGTVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TIEAEAAHGTVTR 13 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;;; 267.21 1.62E-24 2871490000 1880270 2010630 880520 2154970 2694360 2792670 1744330 2214630 2381560 FALSE TRUE 1631787.556 1997422.039 1306342.417 2644288.875 2640747.507 2900105.822 1575165.145 1741048.609 2100014.69 0.777036258 0.951146699 0.622063466 1.25917637 1.257490017 1.380993112 0.750073394 0.829064967 1 21.00196799 3.74246928 24.97904948 1.052777049 0.800188609 0.302842546 0.208632819 556.1378891 3554091.159 0.063435551 0.104831608 5526.743135 -3.74246928 -0.25258844 TIEDAIAVLSVAEEAADRHPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TIEDAIAVLSVAEEAADRHPER 22 1 Q96CT7 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 ;;;;; 231.06 8.96E-27 725083000 387389 375526 220902 265076 385359 371490 395608 431535 285748 FALSE TRUE 336194.5621 373059.145 327730.9461 325265.5572 377691.1098 385781.4607 357241.9971 339254.5985 251967.197 1.334279089 1.480586162 1.300688939 1.290904376 1.498969367 1.531078114 1.41781153 1.346423672 1 17.9428764 1.219145056 2.962011132 0.907766031 1.409232296 0.709048712 0.081413727 0.25120732 2.627567358 0.311612634 0.022157859 16.5632309 -1.219145056 0.501466265 TIEDLDENQLKDEFFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TIEDLDENQLKDEFFK 16 1 Q9H993;F5GZY1 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 79.771 0.01589 25833000 36236 23493 24527 27019 23776 23586 36524 39299 48470 FALSE TRUE 31447.32079 23338.67294 36388.33924 33154.07691 23302.90412 24493.36868 32981.9081 30895.21468 42739.93182 0.73578313 0.546062475 0.851389735 0.775716654 0.54522558 0.573079264 0.771688365 0.722865324 1 15.38329699 0.763208059 1.4833135 1.724705385 0.678538465 0.470001869 0.10406223 3.846217676 2.761283646 8.573394299 0.030092169 5.797063515 -0.763208059 -1.04616692 TIEELSNAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TIEELSNAR 9 0 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 ; 69.812 0.054182 1833860000 4223640 2458350 1161873 1323071 2380614 2723440 1536855 1912031 1247697 FALSE TRUE 3665475.273 2442200.937 1723758.669 1623494.492 2333244.439 2828212.499 1387811.039 1503158.05 1100195.682 3.33165757 2.219787786 1.566774618 1.475641578 2.120754041 2.570644973 1.261422001 1.36626427 1 20.06932872 4.663724506 2.199243038 1.625558086 3.625967274 0.601320917 0.443502663 0.400352237 2.52302243 0.125181279 1.469901067 46102.50308 -4.663724506 2.000409188 TIEGQS(ph)PEPVFGDADVDVSAVQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TIEGQSPEPVFGDADVDVSAVQAK 24 0 Q9Y2I9;F8VZ81;Q9Y2I9-2 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 T(0.045)IEGQS(0.955)PEPVFGDADVDVSAVQAK;T(0.012)IEGQS(0.988)PEPVFGDADVDVSAVQAK;T(0.08)IEGQS(0.92)PEPVFGDADVDVSAVQAK 245.02 5.78E-38 471650000 300510 270840 179893 244876 268128 239975 293498 394834 338451 TRUE FALSE 260796.8421 269060.8342 266889.8565 300478.8385 262792.7774 249206.9935 265034.6091 310401.8217 298439.7083 0.873867769 0.901558428 0.894284001 1.006832637 0.88055567 0.835032962 0.888067512 1.040082177 1 18.18707998 1.74566682 8.123311627 1.018177475 0.898381324 0.569531862 0.044339483 0.08405592 20.37858258 0.026093751 0.011946098 55.67584535 -1.74566682 -0.119796151 TIEKFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TIEKFEK 7 1 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;A0A2R8YDN5;P68104;A0A087WVQ9;Q5VTE0;A0A087WV01;A6PW80;Q5JR01 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;; 103.56 0.0076133 18773080000 20504710 18463710 6850170 9381770 16425580 13995040 27791390 28884380 3081060 FALSE TRUE 17794960.62 18342420.67 10162935.12 11512044.27 16098743.09 14533438.24 25096185.28 22707680.12 2716820.597 6.549921126 6.751428745 3.740745759 4.237322215 5.925581952 5.349428763 9.23733621 8.358181671 1 21.37348787 TIELDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TIELDGK 7 0 Q9H0U4;E9PLD0;H0YMN7;H0YNE9;Q92930;P61006-2;P61006;P62820;P62820-3 Q9H0U4;P62820 RAB1B;RAB8B;RAB8A;RAB1A Ras-related protein Rab-1B;Ras-related protein Rab-8B;Ras-related protein Rab-8A;Ras-related protein Rab-1A 0 ; 101.99 0.020244 215790000 729740 637050 440630 599500 646810 595000 672100 877890 925950 FALSE TRUE 633303.0101 632865.1766 653720.1418 735625.6378 633939.7465 617890.035 606919.8454 690160.0552 816485.2458 0.775645382 0.77510914 0.800651506 0.900966235 0.776425232 0.756768157 0.743332287 0.845281723 1 19.63906729 1.282683571 3.100111486 1.025786761 0.792298793 0.703043937 0.042878664 0.193253239 2.498980477 0.105026715 0.011736598 19.172713 -1.282683571 -0.233487968 TIET(ph)SPSLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TIETSPSLSR 10 0 F8W7R3;Q9NVI1-2;Q9NVI1-1;Q9NVI1;H3BP78 F8W7R3 FANCI Fanconi anemia group I protein 1 TIET(0.843)S(0.148)PS(0.01)LSR 174.77 3.36E-05 398360000 571010 615390 324130 454540 614340 534630 545830 670990 577520 TRUE FALSE 495549.5817 611347.4626 480880.3521 557750.2542 602115.8359 555197.5621 492895.4906 527504.0102 509246.2435 0.973104049 1.200494791 0.944298281 1.095246674 1.18236677 1.090233986 0.967892246 1.035852531 1 18.95800391 2.25496976 24.90878348 1.007067651 1.085438207 0.177874648 0.080072918 377.9676159 573747.3211 0.028494723 0.022002245 179.8745663 -2.25496976 0.078370557 TIETS(ph)PSLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TIETSPSLSR 10 0 F8W7R3;Q9NVI1-2;Q9NVI1-1;Q9NVI1;H3BP78 F8W7R3 FANCI Fanconi anemia group I protein 1 TIET(0.059)S(0.82)PS(0.122)LSR;TIET(0.058)S(0.929)PS(0.014)LSR;TIET(0.038)S(0.961)PSLSR 227.36 2.72E-09 1164910000 2128640 2433160 1353410 1695040 2409240 2164960 2176590 2526670 2184920 TRUE FALSE 1847334.831 2417176.412 2007923.603 2079924.739 2361300.838 2248247.412 1965504.637 1986361.283 1926621.247 0.958846911 1.25461941 1.04219945 1.079571163 1.225617563 1.166937931 1.020182166 1.03100767 1 20.87764155 2.224367725 24.44246063 1.020098254 1.126608399 0.246506849 0.085518264 239.9290195 413192.4538 0.032972493 0.022359361 167.636168 -2.224367725 0.106510145 TIFTGHTAVVEDVSWHLLHESLFGSVADDQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TIFTGHTAVVEDVSWHLLHESLFGSVADDQK 31 0 Q09028-3;Q09028;Q09028-2;Q09028-4 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 ;; 158.8 6.92E-13 1148070000 1496410 1178050 460437 903400 950259 841233 1379290 1554190 1143310 FALSE TRUE 1298655.627 1170311.312 683105.8733 1108530.778 931350.7051 873595.7779 1245526.668 1221838.563 1008149.194 1.288158176 1.160851309 0.677584109 1.099570167 0.923822298 0.866534222 1.235458675 1.211962049 1 19.94327773 0.945104961 21.68674403 0.086508839 1.058919952 0.009238473 0.188520874 142.3317559 814894.2984 100585.4916 0.046268917 8.812618325 -0.945104961 0.972411113 TIGGGDDS(ph)FNTFFSETGAGK ddPTM_MDA-MB-175_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 1 TIGGGDDS(1)FNTFFSETGAGK;TIGGGDDS(1)FNTFFSETGAGK;TIGGGDDS(1)FNTFFSETGAGK;TIGGGDDS(1)FNTFFSETGAGK 353.12 3.61E-95 1115855000 1432400 1316995 990565 1069619 1328696 1172370 1542180 1830510 1673630 TRUE FALSE 1243104.711 1308343.573 1469605.547 1312492.342 1302257.549 1217471.833 1392619.621 1439069.682 1475775.368 0.842340059 0.886546558 0.995819268 0.889357805 0.882422608 0.824970967 0.943652843 0.975127863 1 20.49304171 2.007543775 24.67112103 0.977868263 0.891130899 0.46296297 0.04511055 143.8055127 470298.5363 0.019380748 0.01303675 101.7521923 -2.007543775 -0.086737364 TIGGGDDSFNTFFSETGAGK ddPTM_MDA-MB-175_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 0 ;;;; 465.11 5.75E-223 997654000 1355000 1238854 783743 831725 1122665 982682 1511510 1562410 1219440 FALSE TRUE 1175933.317 1230715.887 1162763.736 1020580.873 1100326.163 1020486.412 1364923.993 1228300.78 1075279.192 1.093607433 1.144554731 1.081359841 0.949131054 1.023293458 0.949043206 1.269367065 1.142308704 1 20.03627987 1.207828538 23.03859407 0.999998616 1.085090373 0.066501514 0.095258092 4569.562419 3425104.872 2.608546822 0.025024469 16.13721326 -1.207828538 0.085091758 TIHLSSIRPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TIHLSSIRPPR 11 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 172.92 7.68E-06 614340000 965960 1177870 496980 643190 1617020 1604390 1031170 1193720 1194280 FALSE TRUE 838305.9386 1170132.494 737321.1903 789236.12 1584844.466 1666111.921 931167.2921 938452.2675 1053093.579 0.796041259 1.111138191 0.700147836 0.749445382 1.504941723 1.582111937 0.884220843 0.891138533 1 20.00620221 3.297985386 24.99997563 1.136186492 0.848685597 0.292425241 0.253963833 127.0546453 53450.50098 0.082132194 0.106032165 1986.028088 -3.297985386 -0.287500895 TIISYIDEQFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TIISYIDEQFER 12 0 Q15019-2;Q15019-3;Q15019;B5MCX3;C9J2Q4;C9J938;C9JB25;C9IY94;H7C310;C9IZU3;C9JQJ4 Q15019-2 2-Sep Septin-2 0 ;;;; 248.88 1.87E-16 990281000 1038879 967418 595925 750451 986149 990529 919389 1101324 1003793 FALSE TRUE 901588.508 961062.9675 884116.3232 920852.3695 966526.5643 1028635.292 830226.7963 865814.4331 885125.7351 1.018599361 1.085792594 0.998859584 1.040363344 1.091965272 1.162134656 0.937976113 0.97818242 1 19.75552288 2.208742881 24.99998939 0.971909956 1.064096693 0.473343107 0.046818696 186.5688254 156423.0504 0.019561593 0.013190267 161.7122355 -2.208742881 0.092186737 TILHYMGTSTFSEYTVVADISVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TILHYMGTSTFSEYTVVADISVAK 24 0 P11766;H0YAG8 P11766 ADH5 Alcohol dehydrogenase class-3 0 ; 192.98 5.84E-18 131672000 155727 108539 66677 105592 107993 108958 141615 156331 177971 FALSE TRUE 135147.2824 107826.0002 98922.22022 129568.2775 105844.1506 113149.6848 127881.1991 122900.8322 156931.4711 0.861186615 0.687089718 0.630352978 0.825636034 0.674460959 0.721013344 0.81488562 0.783149685 1 17.25977517 -0.545012467 0.99118346 9.999998825 0.731217699 0.553363609 0.07180316 44.32364822 1.589403944 862.7890446 0.02249626 0.285093643 0.545012467 -9.268781126 TILMMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TILMMGR 7 0 P13639 P13639 EEF2 Elongation factor 2 0 ; 139.92 0.0061873 834430000 1880180 2192500 1133730 1368530 2143210 2363500 1718460 2094920 2029400 FALSE TRUE 1631709.449 2178097.323 1682005.62 1679275.653 2100564.314 2454425.374 1551804.014 1646937.661 1789486.644 0.91183103 1.217163219 0.93993751 0.938411951 1.173836263 1.371580717 0.867178316 0.920340851 1 20.77111435 TILSLMTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TILSLMTR 8 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 89.401 0.033159 0 83590 113800 55777 82396 113460 117720 99117 114090 92854 FALSE TRUE 72543.36971 113052.4403 82750.94376 101105.2711 111202.368 122248.7646 89504.6486 89692.74135 81876.9059 0.886005265 1.380761022 1.010675023 1.234844796 1.358165245 1.493079926 1.093161101 1.095458364 1 16.32116896 2.029129196 24.99825242 1.066475896 1.235886726 0.162115545 0.176536556 355.7284862 305279.5562 0.070740513 0.047692561 106.9372955 -2.029129196 0.16941083 TIPWLEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TIPWLEDR 8 0 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ;;; 188.98 0.00045163 630280000 992172 785218 799123 1206110 783552 895067 662559 846495 4394200 FALSE TRUE 861053.9564 780059.8513 1185581.556 1479975.71 767960.8482 929500.8067 598304.1302 665478.6317 3874722.682 0.222223376 0.201320176 0.305978428 0.381956551 0.198197629 0.239888344 0.154412116 0.171748712 1 21.88566163 1.235798906 24.99998983 1.000001026 0.232617416 0.928967021 0.066525109 20.20325588 182851.0485 0.120138849 0.017854584 17.21071471 -1.235798906 -0.76738361 TIPWLEDRVPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TIPWLEDRVPQK 12 1 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ; 204.49 1.03E-07 3212300000 1053250 841560 665580 922720 823280 790360 837760 1043720 1219780 FALSE TRUE 914060.3439 836031.7369 987456.7142 1132237.679 806898.3387 820765.6606 756514.1641 820528.6002 1075578.998 0.849830971 0.777285293 0.91806991 1.052677378 0.750199047 0.763091937 0.703355277 0.762871534 1 20.03668206 TIQAPTQVPVVVS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TIQAPTQVPVVVSPR 15 0 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 TIQAPTQVPVVVS(1)PR 131.82 5.37E-05 89805000 82908 71044 35727 52186 74032 66272 65942 81938 70459 TRUE FALSE 71951.49774 70577.30729 53004.6967 64035.62891 72558.90804 68821.52672 59546.95499 64416.19634 62129.41729 1.158090658 1.135972465 0.853133653 1.030681305 1.167867191 1.107712413 0.958434146 1.036806704 1 15.9229889 TIQEVLEEQS(ph)EDEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 425.24 3.19E-153 2007180000 1380534 1272225 1070270 1364108 1326092 1349587 1104429 1474948 2691182 TRUE FALSE 1198092.934 1263867.67 1587856.152 1673849.57 1299705.364 1401506.485 997321.6456 1159541.848 2373033.53 0.504878216 0.532595791 0.669125038 0.705362798 0.547697851 0.590597001 0.420272884 0.488632728 1 21.17830105 1.233264524 24.99967059 1.000000695 0.555819483 0.73586082 0.083332086 98.36006277 464246.7395 0.188713514 0.022706004 17.11057186 -1.233264524 -0.444181211 TIQEVLEEQS(ph)EDEDREAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TIQEVLEEQSEDEDREAK 18 1 P18858;P18858-3;P18858-2;M0R0Q7 P18858 LIG1 DNA ligase 1;DNA ligase 1 TIQEVLEEQS(1)EDEDREAK;TIQEVLEEQS(1)EDEDREAK;TIQEVLEEQS(1)EDEDREAK;TIQEVLEEQS(1)EDEDREAK 274.48 2.95E-39 2106740000 1547020 1241740 918900 957430 1195230 1056460 1404620 1656650 1312120 TRUE FALSE 1342577.387 1233582.928 1363283.114 1174829.115 1171447.261 1097102.7 1268400.169 1302388.29 1157002.668 1.160392646 1.06618849 1.178288651 1.015407438 1.012484494 0.948228323 1.096281109 1.125657118 1 20.14196076 3.728837723 24.9677543 1.042227196 1.128079786 0.405650776 0.057252673 834.5342199 2143029.714 0.01716997 0.02582248 5355.964912 -3.728837723 0.085852591 TIQGDEEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TIQGDEEDLR 10 0 P54920;M0R0Y2;M0R213 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;; 189.72 2.28E-06 1496240000 2098710 1918030 1265240 1523770 1949580 1941850 1827720 2160740 2156550 FALSE TRUE 1821360.156 1905430.335 1877114.296 1869765.268 1910787.172 2016554.226 1650467.996 1698682.566 1901605.116 0.95780146 1.002011574 0.987120975 0.98325633 1.004828582 1.060448465 0.867934137 0.893288807 1 20.85878626 2.231385862 24.99857185 0.912571498 0.998346348 0.434721825 0.042055269 141.2593343 492176.1607 0.016856449 0.011630648 170.3671515 -2.231385862 0.08577485 TIS(ph)AQDTLAYATALLNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TISAQDTLAYATALLNEK 18 0 Q9UPU5;A0A0U1RQI9 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 TIS(1)AQDTLAYATALLNEK;TIS(1)AQDTLAYATALLNEK;T(0.002)IS(0.998)AQDTLAYATALLNEK;T(0.039)IS(0.961)AQDTLAYATALLNEK 364.64 2.02E-107 1855171000 536554 529637 498582 618356 785658 670076 919637 1067210 1048430 TRUE FALSE 465647.0294 526157.7797 739697.9229 758763.1808 770024.9429 695854.2573 830450.7453 838995.4465 924485.7998 0.503682187 0.569135599 0.80011821 0.820740763 0.832922413 0.752693289 0.898283938 0.907526591 1 19.81829163 5.165133765 0.457127567 0.925095889 1.21E-14 0.838265492 0.060637739 3.29102529 0.426229165 0.056604804 1.781884484 146262.7601 -5.165133765 -0.925095889 TIS(ph)DGTISASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TISDGTISASK 11 0 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 TIS(0.997)DGT(0.003)ISASK;T(0.001)IS(0.938)DGT(0.062)ISASK;TIS(1)DGTISASK 214.4 1.42E-11 536300000 5585700 1182250 833100 1359590 1320550 1133070 1524460 1690640 1665300 TRUE FALSE 4847535.593 1174483.722 1235989.947 1668305.69 1294273.639 1176659.936 1376618.104 1329109.793 1468430.131 3.301168704 0.799822679 0.84170838 1.13611513 0.881399538 0.80130468 0.937476067 0.905122937 1 20.48584319 4.740219095 24.9999981 0.913699885 3.301169496 0.98267648 0.099656106 16.78554108 253004.9407 0.024051269 0.149204892 54981.81784 -4.740219095 2.387469611 TIS(ph)EPDEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(0.023)IS(0.977)EPDEQR;TIS(1)EPDEQR;TIS(1)EPDEQR 203.52 1.90E-05 9897820000 6155430 5905740 4115370 4697310 5720940 6047130 5987780 6317590 6734950 TRUE FALSE 5341974.33 5866944.805 6105576.697 5763906.029 5607104.487 6279767.004 5407086.017 4966622.542 5938751.883 0.899511284 0.987908726 1.028090888 0.970558485 0.944155371 1.057422019 0.910475151 0.836307467 1 22.50172833 2.029080214 24.37079628 0.896540362 0.981731342 0.201990841 0.058257349 173.7039867 145572.4884 0.022895675 0.015435976 106.9252352 -2.029080214 0.08519098 TIS(ph)EPDEQRSELPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TISEPDEQRSELPR 14 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 T(0.171)IS(0.829)EPDEQRSELPR;T(0.004)IS(0.996)EPDEQRSELPR;T(0.016)IS(0.984)EPDEQRSELPR 204.05 8.59E-09 2422980000 1610670 1580750 471868 442208 1383890 1550710 1601060 1614310 80458.8 TRUE FALSE 1397815.879 1570365.949 700064.9431 542618.0851 1356353.297 1610366.817 1445789.448 1269102.369 70947.05232 19.70224037 22.13433677 9.867428176 7.648211833 19.11782452 22.69814974 20.37842871 17.8880211 1 16.11445512 1.237551661 24.99989467 0.999980704 17.41154936 0.522031319 4.940506533 22.84034922 565650.4933 7.747939766 1.306680908 17.28031526 -1.237551661 16.41156866 TIS(ph)NPEVVMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 TIS(1)NPEVVMK;T(0.002)IS(0.998)NPEVVMK;TIS(1)NPEVVMK;TIS(1)NPEVVMK;T(0.002)IS(0.998)NPEVVMK 158.58 8.34E-06 1721090000 4868720 4386080 2674720 3767900 4484040 3177080 6264730 5806010 5016720 TRUE FALSE 4225306.316 4357267.552 3968223.538 4623459.284 4394816.377 3299304.323 5657177.449 4564439.944 4423649.077 0.955163089 0.984993944 0.897047544 1.045168639 0.993482146 0.745833195 1.278848605 1.031826862 1 22.07680551 2.234858059 24.99989543 1.095918097 0.944807191 0.348411795 0.106878535 113.2393217 764584.6808 0.041173341 0.028971839 171.7347014 -2.234858059 -0.151110906 TIS(ph)PSTSNNIPLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TISPSTSNNIPLMR 14 0 F8WBA3;Q15139;O94806;O94806-2 F8WBA3;O94806 PRKD1;PRKD3 Serine/threonine-protein kinase;Serine/threonine-protein kinase D1;Serine/threonine-protein kinase D3 1 TIS(0.998)PS(0.002)TSNNIPLMR;TIS(1)PSTSNNIPLMR;T(0.005)IS(0.97)PS(0.018)T(0.004)S(0.004)NNIPLMR 330.25 2.21E-68 1046483000 613759 647524 351671 463836 612917 599824 573866 700046 614786 TRUE FALSE 532649.1931 643270.3722 521740.2719 569157.0531 600721.1509 622899.6174 518212.5636 550346.6107 542106.6994 0.982554161 1.186612106 0.962430961 1.049898578 1.108123459 1.149035085 0.955923556 1.015199796 1 19.04821731 2.221044208 24.99904341 0.994110947 1.073774026 0.241734752 0.068962665 350.8470188 500717.3219 0.026901681 0.018182144 166.3581984 -2.221044208 0.079663078 SQS(ph)DLSSSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SQSDLSSSSSR 11 0 J3KP75 J3KP75 PHACTR2 Phosphatase and actin regulator 1 SQS(0.968)DLS(0.032)SSSSR;SQS(0.993)DLS(0.006)SSSSR 209.7 1.60E-08 681210000 453062 748980 542430 645180 847950 1010420 905260 1134120 1077640 TRUE FALSE 393188.7088 744059.9011 804750.9623 791677.98 831077.454 1049291.511 817468.0245 891597.2637 950242.6269 0.413777174 0.783020968 0.846889983 0.833132463 0.874595004 1.104235362 0.860272947 0.938283801 1 19.8579364 4.967313143 1.019128287 0.940781638 2.99E-30 0.81656942 0.076973946 1.178766763 0.731430389 0.0241717 1.346457233 92749.83434 -4.967313143 -0.940781638 down TISINS(ph)PK ddPTM_MDA-MB-175_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(0.002)INS(0.998)PK;TIS(0.001)INS(0.999)PK;TISINS(1)PK;TIS(0.002)INS(0.998)PK;TIS(0.001)INS(0.999)PK 145.41 0.00059779 2489400000 5574330 4815900 3342700 3655770 5259960 4286110 5624590 6602350 5749600 TRUE FALSE 4837668.167 4784264.036 4959240.901 4485868.453 5155297.087 4450999.425 5079118.128 5190488.832 5069888.838 0.954196102 0.943662512 0.978175471 0.884806077 1.016846178 0.877928406 1.001820413 1.023787503 1 22.27352268 2.027827823 24.99639442 1.013356215 0.944586778 0.371964353 0.040479193 188.5724796 169384.8847 0.014784458 0.00996742 106.617335 -2.027827823 -0.068769437 TISLCCWDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TISLCCWDSR 10 0 Q05048 Q05048 CSTF1 Cleavage stimulation factor subunit 1 0 108.57 0.0069342 0 91200 90458 61133 77334 90296 97194 92028 119750 164020 FALSE TRUE 79147.68893 89863.77544 90697.12328 94893.86668 88499.28626 100933.1161 83103.13872 94142.3944 144629.7425 0.547243517 0.621336759 0.627098699 0.656115852 0.611902398 0.697872473 0.574592316 0.650920017 1 17.14200474 1.239607492 4.857262703 1.025768198 0.623268757 0.894551981 0.040757989 0.050415545 2.866461893 0.069013838 0.009640546 17.36230942 -1.239607492 -0.402499441 TITEYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TITEYAR 7 0 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ; 139.27 0.0062933 417340000 599540 601750 357470 414470 602620 613480 514670 605810 610390 FALSE TRUE 520309.27 597797.0646 530343.6877 508581.7483 590629.041 637080.9726 464757.3826 476262.2459 538230.3896 0.966703627 1.110671334 0.985346978 0.944914591 1.097353573 1.183658494 0.86349153 0.884866881 1 19.03786433 2.209713676 24.99998718 0.907415642 1.045647025 0.377689968 0.079563942 214.7569451 186116.04 0.032993484 0.022248595 162.0741214 -2.209713676 0.138231383 TITGFQTHTTPVLLAHGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TITGFQTHTTPVLLAHGER 19 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 267.7 6.33E-32 2359300000 1407490 1539290 507450 972980 1551320 1747590 1400500 1537650 1249550 FALSE TRUE 1221486.63 1529178.303 752854.5173 1193909.98 1520451.767 1814820.918 1264679.726 1208835.514 1101829.622 1.108598467 1.387853686 0.683276708 1.083570414 1.379933645 1.647097592 1.147799714 1.097116549 1 20.07146972 3.38101449 8.97100025 1.245940813 1.058188322 0.131299689 0.241051898 0.645526014 54.17260744 0.073669125 0.095133562 2404.443021 -3.38101449 -0.187752491 TITLVKS(ph)PISVPGGSALISNLGK ddPTM_MDA-MB-175_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(0.918)PIS(0.082)VPGGSALISNLGK;T(0.004)IT(0.023)LVKS(0.972)PIS(0.001)VPGGSALISNLGK 233.19 2.96E-37 430960000 1004990 821800 469770 501320 826190 623040 1073590 1274210 349520 TRUE FALSE 872178.0252 816401.5417 696952.3433 615152.3682 809750.4354 647008.752 969473.407 1001730.107 308200.1438 2.829907911 2.648933033 2.26136281 1.995950945 2.627352556 2.099313595 3.145596868 3.250258404 1 18.23350801 2.270383968 24.9977768 2.657169622 2.405548529 0 0.658903229 849.514435 667304.7715 0.244123339 0.189080312 186.373417 -2.270383968 -0.251621093 TITSSYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TITSSYYR 8 0 Q9H0U4;P62820;E7END7 Q9H0U4;P62820 RAB1B;RAB1A Ras-related protein Rab-1B;Ras-related protein Rab-1A 0 ;;;; 197.6 0.00033205 2933380000 981819 1446160 787406 874324 1548770 1509200 1231680 1400780 1476380 FALSE TRUE 852069.1315 1436660.08 1168198.175 1072852.627 1517952.507 1567259.901 1112231.863 1101234.098 1301844.038 0.654509378 1.103557752 0.897341111 0.82410227 1.166001812 1.20387685 0.854351082 0.845903246 1 20.31212519 4.753907923 24.30221359 0.974156533 0.654509032 0.368302676 0.135895284 2462.718118 3899578.102 0.035292635 0.796719323 56742.42902 -4.753907923 -0.3196475 TITVALADGGRPDNTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TITVALADGGRPDNTGR 17 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;; 176.49 1.00E-09 2806490000 1680190 1141630 674100 902130 1236000 1206700 1131810 1322070 1235550 FALSE TRUE 1458148.634 1134130.557 1000097.015 1106972.405 1211406.018 1253122.53 1022047.24 1039355.619 1089484.687 1.338383781 1.040978888 0.917954173 1.016051367 1.111907339 1.15019747 0.93810152 0.953988277 1 20.05521449 4.730915859 4.554424327 1.010138726 1.357585772 0.66373288 0.072301815 0.120920261 6.549882202 0.019453797 0.133287628 53816.55071 -4.730915859 0.347447046 TIVAVGS(ph)MEEAVILPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TIVAVGSMEEAVILPFR 17 0 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;A0A590UJF3 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 TIVAVGS(1)MEEAVILPFR;TIVAVGS(1)MEEAVILPFR 126.63 4.51E-05 55534000 75710 45934 24077.8 33095 48744 35764 66831 55415 46716 TRUE FALSE 65704.73168 45632.25653 35721.90462 40609.72558 47774.08977 37139.86422 60349.73991 43564.93349 41193.2877 1.595034904 1.107759518 0.8671778 0.985833563 1.159754233 0.901599904 1.465038196 1.057573598 1 15.33012165 4.73348048 5.302574862 1.073139598 1.614905783 0.501338405 0.165434765 0.127334577 12.81151594 0.040205569 0.250879894 54135.2915 -4.73348048 0.541766185 TIVEELLADSEFRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TIVEELLADSEFRR 14 1 Q5QJE6 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 0 121.76 0.00018068 17636000 26673 24650 13783 19043 24664 23538 19747 29725 13406 FALSE TRUE 23148.09547 24488.07253 20448.5049 23367.0042 24173.23465 24443.52209 17831.93898 23368.54007 11821.15795 1.958191876 2.071546005 1.729822492 1.97671026 2.044912584 2.067777302 1.5084765 1.976840185 1 13.52908374 0.985694609 2.35915592 3.79E-12 1.921771084 0.709058156 0.181661923 0.998695245 2.855813583 5.408849804 0.046593249 9.675972129 -0.985694609 1.921771084 TIVHESER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TIVHESER 8 0 D6RFN0;Q9BT78;D6RAX7;Q9BT78-2;D6RD63 D6RFN0 COPS4 COP9 signalosome complex subunit 4 0 ;; 110.41 0.0034316 429000000 1040200 1092080 637980 796291 1056830 1392560 971710 1135550 1194360 FALSE TRUE 902734.9345 1084906.055 946509.2619 977101.0421 1035801.151 1446132.684 877473.7138 892721.4694 1053164.121 0.857164535 1.030139588 0.898729118 0.927776614 0.983513519 1.373131362 0.83317851 0.847656553 1 20.00629885 4.757765075 22.17302216 0.976076102 0.857164046 0.063580326 0.151448603 3086.764905 3563628.689 0.038206821 1.095640785 57248.62697 -4.757765075 -0.118912056 TIVLVPS(ph)PLGQQQDMIFEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TIVLVPSPLGQQQDMIFEAR 20 0 Q96R06;F5GZT2 Q96R06 SPAG5 Sperm-associated antigen 5 1 TIVLVPS(1)PLGQQQDMIFEAR;TIVLVPS(1)PLGQQQDMIFEAR;TIVLVPS(1)PLGQQQDMIFEAR 175.8 1.46E-12 169133000 200542 227210 125899 181668 212635 241817 226199 288573 253102 TRUE FALSE 174039.8666 225717.4425 186784.1775 222918.496 208403.9795 251119.8565 204262.2558 226863.9096 223180.5699 0.779816391 1.011366906 0.836919529 0.998825732 0.933790874 1.125186913 0.915233149 1.016503855 1 17.76785191 6.232953765 0.540120941 1.002837443 5.99E-14 0.382272963 0.077041426 20.86792633 1.337152944 0.040417797 18.68241609 1709833.276 -6.232953765 -1.002837443 TIVMGAS(ph)FR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TIVMGASFR 9 0 P37837;F2Z393 P37837 TALDO1 Transaldolase 1 TIVMGAS(1)FR;TIVMGAS(1)FR 94.363 0.0057758 0 188462 187518 118592 137026 178788 180168 168894 193856 230100 TRUE FALSE 163556.2692 186286.1819 175943.4879 168139.8476 175230.4686 187099.1795 152514.6859 152401.403 202897.8401 0.806101578 0.918127969 0.867153084 0.828692151 0.863638906 0.9221349 0.751682156 0.751123831 1 17.63039398 2.243474053 24.99972582 0.813505722 0.867961712 0.017203044 0.076980002 290.0851615 1475973.489 0.028891192 0.021657397 175.1757772 -2.243474053 0.054455991 TIYENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TIYENR 6 0 I3L0A0;Q13404;Q13404-7;Q13404-2;Q13404-1;G3V2F7;Q13404-6 I3L0A0 TMEM189-UBE2V1;UBE2V1 Ubiquitin-conjugating enzyme E2 variant 1 0 114.19 0.059325 674490000 1057400 992240 709130 796770 821720 1030900 1002700 1139700 1169700 FALSE TRUE 917661.9109 985721.9101 1052067.64 977688.8064 805369.3797 1070559.39 905458.3083 895984.0242 1031419.399 0.889707826 0.955694562 1.020019249 0.947906165 0.780835983 1.037947698 0.877875973 0.868690298 1 19.97619965 3.455885322 24.99689916 0.906876352 0.959990497 0.060366055 0.07644798 554.7160932 652956.2706 0.021200686 0.027372363 2856.836077 -3.455885322 0.053114145 TIYLSS(ph)PDSAVGVQWPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TIYLSSPDSAVGVQWPR 17 0 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 TIYLS(0.02)S(0.978)PDS(0.002)AVGVQWPR;TIYLS(0.165)S(0.835)PDSAVGVQWPR 185.02 2.05E-14 0 92249 96858 54438 77695 99209 106326 95365 107930 91264 TRUE FALSE 80058.06092 96221.73342 80764.39888 95336.83724 97234.935 110416.43 86116.51698 84850.00941 80474.87389 0.994820583 1.195674237 1.003597707 1.184678306 1.208264522 1.372060926 1.070104404 1.054366479 1 16.29625079 2.019813571 24.99997674 1.040417096 1.162986202 0.219038956 0.106882031 358.7884345 452703.2496 0.0443722 0.029912074 104.6679144 -2.019813571 0.122569106 TKADFFEDENGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TKADFFEDENGQR 13 1 O95573 O95573 ACSL3 Long-chain-fatty-acid--CoA ligase 3 0 107.35 0.00076916 0 179420 162820 127840 132950 205620 175970 186770 249830 117910 FALSE TRUE 155709.1924 161750.4247 189663.8516 163138.3295 201528.5643 182739.6798 168657.0741 196405.7987 103970.8141 1.497624057 1.555729135 1.824202813 1.56907812 1.938318614 1.757605548 1.622157868 1.889047425 1 16.66581908 1.229915286 24.99818286 0.99999865 1.714782281 0.693038742 0.147726573 189.7347541 548580.2035 0.409024159 0.035579485 16.97912424 -1.229915286 0.714783631 TKADVT(ph)PPPDGSTTHNLEVSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKADVTPPPDGSTTHNLEVSPK 22 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 T(0.015)KADVT(0.985)PPPDGSTTHNLEVSPK;T(0.002)KADVT(0.997)PPPDGSTTHNLEVSPK 165.42 1.88E-11 1207350000 1313310 963630 494720 686000 1053380 742610 1423860 1549270 769410 TRUE FALSE 1139752.756 957299.8511 733968.2467 841766.7849 1032419.799 771178.6872 1285774.276 1217970.667 678451.2263 1.679933224 1.411007621 1.081829052 1.240718201 1.521730316 1.136675206 1.895160958 1.795222147 1 19.37188558 2.246813458 24.99990713 1.625565448 1.339589395 0.098391541 0.29141369 313.6805241 950218.3339 0.109708863 0.083503899 176.5279421 -2.246813458 -0.285976053 TKDEPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TKDEPQR 7 1 A6NNI4;A0A2R8Y478;G8JLH6;P21926;A0A087WU13 A6NNI4 CD9 Tetraspanin;CD9 antigen 0 ;;;; 101.64 0.0081244 1205210000 1974160 1945900 1172200 1544600 1301090 1731190 1812190 2630430 2057400 FALSE TRUE 1713269.754 1933117.255 1739079.841 1895325.038 1275200.855 1797790 1636444.093 2067933.015 1814176.516 0.944378752 1.065561834 0.95860564 1.044730224 0.70290892 0.990967518 0.902031351 1.139874205 1 20.7908834 1.745099293 25 1.072565408 0.945781647 0.202053291 0.103839497 1.997337585 7668.221488 0.054154162 0.026005571 55.60313687 -1.745099293 -0.126783761 TKDGVVEITGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TKDGVVEITGK 11 1 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;; 166.62 1.84E-05 52569000000 45177400 35121800 26995800 31574000 33883600 27012000 52497500 54699300 45793200 FALSE TRUE 39207092.13 34891082.58 40051059.18 38743359.28 33209382.65 28051169.12 47406300.53 43002280.37 40379580.06 0.970963345 0.864077401 0.991864183 0.959479004 0.822430114 0.694686995 1.17401668 1.064951153 1 25.26712257 2.218397698 24.99999924 1.080524133 0.888561469 0.487189494 0.094586007 214.5841982 266060.9242 0.03985215 0.026905935 165.3475248 -2.218397698 -0.191962664 TKDGVVEITGKHEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TKDGVVEITGKHEER 15 2 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;; 169.61 7.13E-07 475417000 1633700 1323890 291640 264932 1124250 914980 2043240 2027030 74255.5 FALSE TRUE 1417802.406 1315193.279 432678.0795 325088.8598 1101879.625 950179.8727 1845086.899 1593565.409 65477.09938 21.65340889 20.08630944 6.608082575 4.964924575 16.82847339 14.51163661 28.17911784 24.33775204 1 15.99870279 7.971212597 1.10E-19 1.514839685 30.7419158 0 8.857111777 0 0.100675866 8.818839868 8.818840042 93586368.8 -7.971212597 29.22707611 TKDIEDVFYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKDIEDVFYK 10 1 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ; 128.67 0.00029488 3793000000 14978400 10657300 6709300 7993400 10395400 7833700 13490500 15811400 8491000 FALSE TRUE 12998966.49 10587291.49 9953939.921 9808423.641 10188551.88 8135067.508 12182193.39 12430255.15 7487203.653 1.736157729 1.414051492 1.329460288 1.310024957 1.360795345 1.086529482 1.627068523 1.660199953 1 22.83599557 4.733081416 3.907114005 1.373710948 1.768709948 0.257679415 0.204028404 0.381851146 11.88527969 0.052389102 0.427839088 54085.57064 -4.733081416 0.394999 TKDQILLLIDIEQSYINTNHEDFIGFANAQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TKDQILLLIDIEQSYINTNHEDFIGFANAQQR 32 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 273.66 1.27E-73 56122000 114480 86268 51625 76787 76298 66311 105060 119630 92542 FALSE TRUE 99351.17794 85701.29983 76591.02268 94222.66197 74779.81907 68862.02708 94871.29737 94048.05546 81601.79018 1.217512235 1.050237987 0.938594883 1.154664153 0.916399247 0.843878877 1.162612942 1.152524415 1 16.31631318 0.927894782 17.5715504 0.000290647 1.054067162 0.019234592 0.122379257 8270677.363 31437738.27 329318658.1 0.030810671 8.470221775 -0.927894782 1.053776515 TKDQPDGSSLS(ph)PAQS(ph)PSQSQPPAASSLR ddPTM_MDA-MB-175_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(0.045)S(0.036)LS(0.919)PAQS(0.991)PS(0.006)QS(0.003)QPPAASSLR 217.65 1.79E-34 603520000 286170 213230 208820 256420 274050 227330 288570 317600 437700 TRUE FALSE 248351.9094 211829.2781 309806.0505 314644.0801 268596.9412 236075.5322 260584.5258 249683.7116 385955.6046 0.643472737 0.548843638 0.80269867 0.815233867 0.695927039 0.611664993 0.675167099 0.646923399 1 18.55807538 1.23488995 24.99360976 1.000000455 0.68054056 0.611120137 0.080223706 78.77891305 536324.295 0.149988726 0.020744309 17.17473124 -1.23488995 -0.319459895 TKDSGS(ph)ISLQETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TKDSGSISLQETR 13 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 TKDS(0.011)GS(0.978)IS(0.011)LQETR 121.51 0.00014885 405490000 202890 186750 137160 148590 200590 196880 223110 276220 143580 TRUE FALSE 176077.5724 185523.227 203491.0348 182329.6306 196598.6514 204454.101 201472.8265 217152.5025 126606.136 1.390750702 1.465357311 1.607276245 1.440132654 1.552836677 1.614883034 1.591335404 1.715181503 1 16.9499878 1.228276892 24.99995914 0.999998857 1.555422556 0.765081901 0.095198115 224.807329 546473.6589 0.341542776 0.025059404 16.91519044 -1.228276892 0.555423699 TKECS(ph)VEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TKECSVEK 8 1 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 TKECS(1)VEK;T(0.002)KECS(0.998)VEK;TKECS(1)VEK;TKECS(1)VEK 108.72 0.0022753 1680980000 6799700 3954320 3617560 3579450 3245520 3098350 5978820 6609500 6884500 TRUE FALSE 5901102.417 3928343.812 5367024.116 4392218.831 3180940.502 3217545.529 5398994.957 5196109.86 6070622.253 0.972075377 0.647107273 0.884097856 0.723520365 0.523989201 0.530019065 0.889364341 0.855943533 1 22.53341297 2.050237189 21.55866506 0.904173701 0.710020501 0.308685146 0.142061409 34.84712707 14953.52041 0.059464343 0.040090784 112.263141 -2.050237189 -0.1941532 TKEGVMYVGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKEGVMYVGAK 11 1 O76070;F8W754 O76070 SNCG Gamma-synuclein 0 ; 133.71 0.00014226 2497700000 5151700 5142800 2702700 3342700 5272800 3907000 6597100 7436700 2400400 FALSE TRUE 4470889.792 5109016.608 4009734.76 4101711.125 5167881.596 4057304.818 5957314.257 5846419.577 2116627.447 2.112270537 2.413753359 1.89439798 1.937852186 2.441564104 1.91687244 2.814531328 2.76213917 1 21.01333593 TKENILEEFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKENILEEFSK 11 1 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ; 147.26 3.23E-05 1144980000 2683200 2047660 1473800 1707950 1965080 1508460 2516100 2957400 2269400 FALSE TRUE 2328608.322 2034208.787 2186534.61 2095766.152 1925978.753 1566491.432 2272089.009 2324983.025 2001114.117 1.163655936 1.016538122 1.09265863 1.047299669 0.962453233 0.782809645 1.135412014 1.161844297 1 20.93237201 -1.740575669 19.60435118 0.039519651 1.044375075 0 0.11378646 0 0 0 0.026888763 0.018172904 1.740575669 1.004855424 TKENVVQSVTSVAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKENVVQSVTSVAEK 15 1 O76070 O76070 SNCG Gamma-synuclein 0 ; 185.99 3.65E-07 4599100000 4209000 3925100 2570500 3253200 3919500 2922900 5246200 6064100 4464600 FALSE TRUE 3652769.986 3899315.76 3813602.398 3991888.782 3841509.618 3035345.854 4737424.331 4767339.406 3936800.074 0.92785255 0.990478482 0.968706138 1.01399327 0.975794947 0.771018542 1.203369295 1.210968125 1 21.90859202 2.212442115 24.99998484 1.156009852 0.949659227 0.524990146 0.087458868 162.9705758 155990.1908 0.035329695 0.023827732 163.0955511 -2.212442115 -0.206350625 TKEPSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKEPSTR 7 1 Q641Q2;F8W7U3;A0A0A0MR88;A0A096LPC5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A 0 ; 76.221 0.037707 63527000 132108 113188 64733 80624 81901 100353 129805 141842 125478 FALSE TRUE 114649.5931 112444.4606 96038.09532 98930.91146 80271.33034 104213.6448 117216.5311 111510.1921 110644.1338 1.03620128 1.016271326 0.867990846 0.894136075 0.725491064 0.941881339 1.059401227 1.007827422 1 16.75556744 2.420690484 6.936671012 1.019115196 0.903566936 0.271661522 0.085319785 0.29604551 29.03931388 0.034201373 0.026461228 263.4453179 -2.420690484 -0.11554826 TKEQILEEFSK ddPTM_MDA-MB-175_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 ; 164.53 2.07E-05 1185300000 3644100 2460830 1677340 2017860 2375100 1890610 3105100 3699600 2244990 FALSE TRUE 3162522.952 2444664.646 2488507.234 2476045.954 2327840.157 1963342.99 2803967.88 2908469.33 1979589.84 1.597564752 1.234934933 1.257082242 1.250787362 1.175920441 0.99179282 1.416438812 1.469228257 1 20.91677011 4.739679644 23.69131703 1.245683314 1.597564965 0.364866675 0.152420775 58.15019034 1230769.543 0.039118549 0.233183623 54913.56565 -4.739679644 0.351881652 TKEQLGYIVFSGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKEQLGYIVFSGPR 14 1 A0A3B3ISG5;P14735;P14735-2 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 86.367 0.0067196 1164880000 1239470 1109850 1051400 1107670 989070 952900 1402690 1553440 1995380 FALSE TRUE 1075670.899 1102559.322 1559860.557 1359183.403 969389.4421 989558.6796 1266657.34 1221248.945 1759488.45 0.61135434 0.626636295 0.886542084 0.772487824 0.550949591 0.562412717 0.719900912 0.694093187 1 20.74672461 1.223720658 4.205389177 1.037299198 0.678659087 0.503514914 0.100516326 0.232403281 7.570524034 0.259092067 0.027041327 16.73865884 -1.223720658 -0.358640111 TKEVYELLDSPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKEVYELLDSPGK 13 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 111.74 0.00087167 1006860000 1953390 1446130 1325180 1323880 1449010 1066280 1842790 2234230 1365770 FALSE TRUE 1695244.562 1436630.277 1966041.48 1624487.188 1420177.536 1107300.482 1664076.509 1756457.301 1204310.226 1.407647735 1.192907147 1.632504181 1.34889429 1.1792456 0.919447877 1.381767316 1.458475784 1 20.19977564 3.38472588 5.629769448 1.223874683 1.404793952 0.221925827 0.189104851 0.400108182 19.55703955 0.058037337 0.075382421 2425.078939 -3.38472588 0.180919268 TKEYVSNDAAQS(ph)DDEEKLQSQPTDTDGGR ddPTM_MDA-MB-175_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 420.46 1.33E-196 2261940000 1245007 864454 716435 695226 1046489 730742 1474095 1487469 632485 TRUE FALSE 1080476.171 858775.3448 1062905.362 853087.6892 1025665.916 758854.1176 1331137.494 1169385.33 557713.3438 1.937332471 1.53981495 1.905827383 1.52961678 1.839055722 1.360652611 2.386777201 2.096749778 1 19.08916426 TKFAS(ph)DDEHDEHDENGATGPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKFASDDEHDEHDENGATGPVK 22 1 P05455 P05455 SSB Lupus La protein 1 T(0.18)KFAS(0.82)DDEHDEHDENGATGPVK;T(0.131)KFAS(0.869)DDEHDEHDENGATGPVK 280.56 7.34E-46 2167110000 3699590 2482670 2166000 2129900 2568460 1942920 3473640 4026830 2919620 TRUE FALSE 3210679.808 2466361.177 3213484.845 2613526.348 2517352.671 2017665.39 3136766.927 3165723.741 2574465.85 1.247124645 0.958008892 1.248214205 1.015172273 0.977815523 0.783721948 1.218414658 1.229662356 1 21.2958417 -1.350035743 10.91960812 0.076766567 1.081086506 0 0.156912049 0 0 0 0.035724208 0.044664683 1.350035743 1.004319939 TKFAS(ph)DDEHDEHDENGATGPVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TKFASDDEHDEHDENGATGPVKR 23 2 P05455 P05455 SSB Lupus La protein 1 T(0.023)KFAS(0.977)DDEHDEHDENGATGPVKR;T(0.192)KFAS(0.808)DDEHDEHDENGATGPVKR;T(0.162)KFAS(0.838)DDEHDEHDENGATGPVKR 241.22 1.31E-37 1845230000 1663299 1249600 486376 416265 1048747 751241 1611758 1701387 165138 TRUE FALSE 1443489.823 1241391.295 721589.0604 510784.3305 1027878.987 780141.7274 1455449.957 1337558.63 145615.5738 9.913018131 8.525127246 4.955438775 3.507758939 7.05885339 5.357543202 9.995153125 9.185546543 1 17.15180514 4.422629199 5.42489501 6.330159202 9.608740713 0.214690798 2.613412242 0.30428972 18.64547547 0.684443754 1.950655876 26462.39809 -4.422629199 3.278581512 TKFEECR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TKFEECR 7 1 P43487;F6WQW2;P43487-2;C9JXG8;C9JGV6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;;;;; 106.42 0.0070274 7453640000 12202100 12016470 7272160 9323440 11622220 9744960 12897950 14850300 15135950 FALSE TRUE 10589561.57 11937533.02 10789000.9 11440469.55 11390960.56 10119854.92 11647108.79 11674678.91 13346595.23 0.79342794 0.894425343 0.808371027 0.857182626 0.853473141 0.758234946 0.87266517 0.874730874 1 23.66996842 1.055112552 1.548363453 1.135828388 0.833278174 0.640404055 0.039262857 1.11267506 1.652049338 0.595975423 0.010522789 11.35305004 -1.055112552 -0.302550215 TKFENLCK ddPTM_MDA-MB-175_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 ; 143.03 0.00055443 6028000000 9472400 9540200 5691700 7652900 9835600 7704200 12773100 15288000 12547200 FALSE TRUE 8220598.34 9477529.798 8444225.158 9390607.912 9639890.803 8000585.559 11534366.73 12018780.17 11063884.31 0.743011958 0.856618664 0.763224282 0.848762302 0.871293529 0.723126285 1.042524163 1.08630747 1 23.39935464 2.224539757 24.92488012 1.051960587 0.807182275 0.821309406 0.053090404 80.78435946 143609.1375 0.02031903 0.013775672 167.702585 -2.224539757 -0.244778312 TKFPAEQYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKFPAEQYYR 10 1 E9PGT1;Q15631;H7C1D4;Q15631-2 E9PGT1 TSN Translin 0 ; 124.6 0.00039334 1137840000 1749610 1275530 1000460 1027900 1338780 1058600 1605600 1893840 1823910 FALSE TRUE 1518394.606 1267150.959 1484285.802 1261300.405 1312140.897 1099325.027 1449889.159 1488857.054 1608289.438 0.944105315 0.787887385 0.92289719 0.784249636 0.815861167 0.683536807 0.901510092 0.925739496 1 20.61709564 1.733063432 2.395684936 0.980353576 0.82388079 0.367123333 0.07529691 0.280052603 3.287390617 0.065654677 0.020497253 54.08333105 -1.733063432 -0.156472786 TKGDFILVGDLMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKGDFILVGDLMR 13 1 Q16531;F5GY55;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 ; 114.31 0.00068686 569060000 967430 884220 431160 623550 883950 751180 931770 1046320 595260 FALSE TRUE 839581.6743 878411.5006 639670.4181 765136.5579 866361.1244 780078.3807 841407.0888 822572.6105 524889.0409 1.599541253 1.673518462 1.218677412 1.457711056 1.650560513 1.486177687 1.603018968 1.567136188 1 19.00165295 1.236233156 24.99155965 0.999999307 1.531590727 0.625394561 0.129406924 42.60832132 457409.3427 0.207367958 0.031871121 17.22793227 -1.236233156 0.531591421 TKGGQQVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TKGGQQVDR 9 1 Q8TE77;Q8TE77-3;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ;;; 126.19 0.00043809 596680000 1141210 1069060 532460 691310 790220 1023040 1282500 1431180 635420 FALSE TRUE 990396.207 1062037.274 789959.437 848282.5015 774496.168 1062397.011 1158123.347 1125133.294 560301.3715 1.767613391 1.895475058 1.409883104 1.513975415 1.382284976 1.896117099 2.066965041 2.008085919 1 19.0958435 2.714015953 24.77245538 1.814635411 1.595946034 0.028455931 0.329568822 1805.856321 1822613.567 0.114855229 0.101341896 517.6258459 -2.714015953 -0.218689377 TKGS(ph)PRTS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TKGSPRTSPK 10 2 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 2 T(0.373)KGS(0.627)PRT(0.306)S(0.694)PK 58.831 0.058213 55592000 326520 203770 76267 64889 139840 152860 283270 290470 32913 TRUE FALSE 283369.5547 202431.4215 113149.9763 79623.03922 137057.4576 158740.6231 255798.519 228355.2509 29022.06263 9.763935743 6.975087333 3.898757222 2.743534814 4.722526421 5.469653384 8.813933118 7.868332924 1 14.82486244 4.599433584 3.339688227 5.336303617 9.811448389 0.308027094 2.280189364 0.389704297 7.128009103 0.618304412 3.547731457 39758.82897 -4.599433584 4.475144772 TKGTSSFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKGTSSFGK 9 1 P61927;D6RG19;D6R9X9 P61927 RPL37 60S ribosomal protein L37;Ribosomal protein L37 0 ; 103.91 0.0030515 361340000 1128010 926510 412740 458900 847780 816140 1268880 1410910 186544 FALSE TRUE 978940.6205 920423.6948 612342.4445 563100.2588 830910.8367 847537.4339 1145824.213 1109197.876 164490.9808 5.95133311 5.595587613 3.722650576 3.423289569 5.051406663 5.152485745 6.965878659 6.743213948 1 17.32764896 4.459745187 24.62034079 4.880968199 5.862398079 0.058270671 1.714446208 628.0317234 889865.1911 0.444140222 1.175651013 28823.39857 -4.459745187 0.98142988 TKIDCDNLEQYFIQQGGGPDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TKIDCDNLEQYFIQQGGGPDKK 22 2 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 225.34 3.47E-26 190640000 491920 311570 245130 222540 254960 214980 467110 558830 237700 FALSE TRUE 426911.5256 309523.2762 363675.6879 273071.1083 249886.7948 223250.4197 421809.7441 439328.5533 209599.3768 2.036797686 1.476737579 1.73509909 1.302824047 1.192211535 1.065129215 2.012457053 2.096039406 1 17.6772749 2.217762673 24.99678492 1.797651274 1.460602985 0.05468156 0.398937701 501.5429337 602793.5291 0.164858672 0.111281091 165.1059303 -2.217762673 -0.33704829 TKIDWNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKIDWNK 7 1 P47755;P52907 P47755;P52907 CAPZA2;CAPZA1 F-actin-capping protein subunit alpha-2;F-actin-capping protein subunit alpha-1 0 ; 112.84 0.0057124 4262000000 9442800 8039900 5168400 6545400 8114300 6632800 10970000 12446600 7270400 FALSE TRUE 8194910.055 7987085.368 7667855.527 8031633.11 7952841.305 6887968.108 9906131.088 9784991.45 6410901.594 1.278277312 1.245859923 1.19606508 1.252808672 1.240518387 1.074414886 1.545200927 1.526305045 1 22.61209583 2.238796356 25 1.400240064 1.218140231 0.134898407 0.15787832 9.361968104 993020.1221 0.060895852 0.044162849 173.2991195 -2.238796356 -0.182099834 TKKDDSHS(ph)AEDS(ph)EDEKEDHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKKDDSHSAEDSEDEKEDHK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 TKKDDS(0.11)HS(0.89)AEDS(1)EDEKEDHK;TKKDDS(0.012)HS(0.988)AEDS(1)EDEKEDHK 145.34 7.00E-08 126588000 181391 93440 112042 49276 72527 40097 170089 178616 31919 TRUE FALSE 157419.7198 92826.18649 166225.886 60464.86894 71083.8546 41639.55754 153593.795 140420.3584 28145.57218 5.593054522 3.298074237 5.905933796 2.148290628 2.525578593 1.47943546 5.457121069 4.989074569 1 14.78062036 3.737258886 24.99849453 3.22757848 4.768926154 0.252509644 1.559376155 220.1071731 4226971.351 0.44779234 0.708102853 5460.832888 -3.737258886 1.541347674 TKKDDSHSAEDS(ph)EDEKEDHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TKKDDSHSAEDSEDEKEDHK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 T(0.003)KKDDS(0.041)HS(0.041)AEDS(0.915)EDEKEDHK 50.029 0.057995 37350000 34981 18734 17850 9971.9 18087 10778 31543 30042 7948.8 TRUE FALSE 30358.17222 18610.93512 26482.3197 12236.17231 17727.10409 11192.63663 28483.96471 23617.75209 7009.101919 4.331249933 2.655252461 3.778275735 1.745754655 2.529154846 1.59687172 4.063853692 3.369583202 1 12.77501389 7.012228928 1.029648172 2.63133064 199.8976351 0.243593677 0.966515375 333.9278516 3.921070009 0.297227807 151498.3565 10285583.35 -7.012228928 197.2663045 TKLDELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TKLDELK 7 1 P80303-2;P80303;E9PKG6;Q2L696;E9PLR0;E9PLE9;A0A2R8Y6G7;Q02818;H7BZI1;C9JKZ2;C9JBD3;C9J3C1 P80303-2;Q02818 NUCB2;Nucb2;NUCB1 Nucleobindin-2;Nesfatin-1;Nucleobindin-1 0 76.064 0.049147 0 292960 360560 241460 319020 432440 400870 489430 644650 704830 FALSE TRUE 254244.5937 358191.4576 358230.8636 391458.3669 423835.2901 416291.7283 441965.1539 506796.6142 621505.8003 0.409078392 0.576328423 0.576391827 0.629854728 0.68194905 0.669811493 0.711119918 0.815433442 1 19.24540833 -2 0.231744085 3.402028021 0.443903952 0.894393075 0.050685435 27.86435116 0.437600943 30.38379146 0.212447556 0.01 2 -2.958124069 TKMIMVEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TKMIMVEER 9 1 Q5JYW6;H0Y5P0;H0YE38;B1AJZ9-4;B1AJZ9;B1AJZ9-3 Q5JYW6 FHAD1 Forkhead-associated domain-containing protein 1 0 ;; 78.934 0.038152 703050000 548680 657670 205646 319195 484549 742800 404976 410611 211624 FALSE TRUE 476170.5478 653349.7225 305097.0934 391673.1033 474907.4229 771375.9967 365701.4899 322805.033 186606.0518 2.551742257 3.501224725 1.63497963 2.098930338 2.544973318 4.13371372 1.9597515 1.729874406 1 17.50963625 4.241952457 24.99867244 2.191021414 3.026483399 0.155183374 0.840134466 176.2084274 1298641.531 0.223315981 0.543167754 17456.31044 -4.241952457 0.835461985 TKNETDEDGWTTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TKNETDEDGWTTVR 14 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 144.33 8.10E-06 1026390000 803900 670370 444400 523330 646720 565770 792350 890950 569070 FALSE TRUE 697662.5782 665966.2953 659313.3264 642160.0751 633851.5373 587535.538 715508.019 700427.2759 501795.1929 1.390333323 1.327167547 1.313909212 1.279725442 1.263167815 1.170867211 1.425896519 1.395842937 1 18.93673912 4.657432209 1.180942631 1.278302482 1.429783752 0.10935045 0.117958264 3.910686148 5.14824433 0.036276706 0.705884714 45439.36031 -4.657432209 0.15148127 TKNT(ph)IERALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TKNTIERALK 10 2 Q8IZU1 Q8IZU1 FAM9A Protein FAM9A 1 T(0.015)KNT(0.985)IERALK 72.643 0.076167 839440000 1101500 1305300 718360 707050 1156100 1233000 1150900 973070 938640 TRUE FALSE 955933.9842 1296725.398 1065761.299 867596.5091 1133095.872 1280434.308 1039285.895 764986.5529 827675.0485 1.154962912 1.566708336 1.287656672 1.048233254 1.369010548 1.547025382 1.255668994 0.924259532 1 19.65870494 1.815839284 4.562458067 0.963135138 1.331578011 0.474937407 0.156805272 0.175122388 6.102836722 0.090176789 0.042450873 65.4393962 -1.815839284 0.368442873 TKPFPWGDGNHTLFHNPHVNPLPTGYEDE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TKPFPWGDGNHTLFHNPHVNPLPTGYEDE 29 1 P12074 P12074 COX6A1 "Cytochrome c oxidase subunit 6A1, mitochondrial" 0 168.57 2.21E-12 585990000 446660 484820 356520 671040 751000 747330 442600 694970 615630 FALSE TRUE 387632.7493 481635.1855 528934.2645 823409.8882 736056.5693 776080.2687 399676.7201 546356.0738 542850.9227 0.71406851 0.887232876 0.974363757 1.516825069 1.355909216 1.429637929 0.736255026 1.006456931 1 19.05019654 4.187298058 2.903834802 1.15115512 0.774557754 0.302664806 0.232936583 0.371845249 6.257089184 0.068548805 0.190709266 15392.10644 -4.187298058 -0.376597366 TKPIVKPQTS(ph)PEYGQGINPISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKPIVKPQTSPEYGQGINPISR 22 2 O95793-2;O95793-3;O95793;A0A087X1A5 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 1 T(0.002)KPIVKPQT(0.23)S(0.769)PEYGQGINPISR;TKPIVKPQT(0.068)S(0.932)PEYGQGINPISR 211.4 2.62E-23 6018640000 1495980 1270610 788600 1101710 1401310 1089930 1581240 1812280 1590810 TRUE FALSE 1298282.453 1262263.279 1169969.598 1351870.094 1373426.673 1131860.312 1427891.588 1424738.025 1402746.254 0.925529082 0.89985147 0.834056476 0.963731031 0.979098443 0.80688885 1.01792579 1.015677654 1 20.41982263 2.193955627 24.99988276 1.012414174 0.904736439 0.497509577 0.051887948 108.7637358 60958.32129 0.020837691 0.014048845 156.298794 -2.193955627 -0.107677735 TKPIVKPQTSPEYGQGINPISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKPIVKPQTSPEYGQGINPISR 22 2 O95793-2;O95793-3;O95793;A0A087X1A5 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 ; 187.79 1.53E-17 1228420000 559610 431400 293955 377000 502300 439960 546280 645770 628530 FALSE TRUE 485656.1206 428566.105 436112.6212 462603.6121 492305.2127 456885.5459 493301.8497 507677.1109 554225.8994 0.876278285 0.773269718 0.786886036 0.834684219 0.888275364 0.824367007 0.890073615 0.916011163 1 19.08011461 -2 0.437046631 4.741100182 0.811860633 0.727765626 0.034438183 46.00482223 0.610512317 158.8950786 0.02840813 0.01 2 -3.929239548 TKPIWTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKPIWTR 7 1 P08238;P07900;P07900-2;Q58FG0;Q14568;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AA1;HSP90AA5P;HSP90AA2P;HSP90AB2P Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5;Heat shock protein HSP 90-alpha A2;Putative heat shock protein HSP 90-beta 2 0 ; 128.38 0.0034318 51695000000 9285900 8306600 4082200 6209200 8654700 7515600 8553800 9994600 8718100 FALSE TRUE 8058744.788 8252033.398 6056365.574 7619093.762 8482488.403 7804729.995 7724253.793 7857332.568 7687456.15 1.048297984 1.073441362 0.787824406 0.991107281 1.10341942 1.015255221 1.004786713 1.022097872 1 22.87407485 3.471196556 24.95020236 1.027676563 0.965088692 0.105065281 0.079790729 336.4110036 1416693.233 0.02322589 0.030068353 2959.35153 -3.471196556 -0.062587871 TKPPRPDS(ph)PATTPNISVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TKPPRPDSPATTPNISVK 18 2 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 TKPPRPDS(1)PATTPNISVK;T(0.008)KPPRPDS(0.991)PAT(0.001)TPNISVK;T(0.005)KPPRPDS(0.995)PATTPNISVK 220.13 5.47E-19 763270000 1609800 1055560 794870 994550 1119050 863570 1394370 1619140 1924830 TRUE FALSE 1397060.851 1048625.957 1179271.791 1220377.778 1096783.094 896792.0967 1259144.212 1272899.511 1697278.79 0.823118075 0.617827762 0.694801465 0.719020225 0.646200907 0.528370532 0.741860571 0.749964896 1 20.69479213 1.091503103 1.680761789 1.22781324 0.673094393 0.62369274 0.07745004 0.961135465 1.826679649 0.986190347 0.02108754 12.34534137 -1.091503103 -0.554718848 TKPQMQEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TKPQMQEER 9 1 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;;; 136.02 0.00018642 1061460000 1384450 1449180 779870 989600 1489690 1353280 1646840 1804370 1631110 FALSE TRUE 1201491.425 1439660.241 1157017.741 1214303.805 1460048.084 1405341.557 1487129.71 1418519.517 1438282.034 0.835365663 1.000958232 0.80444427 0.844273777 1.015133367 0.977097345 1.033962516 0.986259637 1 20.45591517 3.233583761 24.99893717 1.001552455 0.875752017 0.600036078 0.053179492 86.27530455 433363.5576 0.015455131 0.018077117 1712.315394 -3.233583761 -0.125800438 QVVSVVQDEEVGLPFEASPES(ph)PPPASPDGVTEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 QVVSVVQDEEVGLPFEASPESPPPASPDGVTEIR 34 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 QVVSVVQDEEVGLPFEASPES(0.959)PPPAS(0.041)PDGVTEIR;QVVSVVQDEEVGLPFEAS(0.017)PES(0.982)PPPAS(0.001)PDGVTEIR;QVVSVVQDEEVGLPFEAS(0.002)PES(0.998)PPPASPDGVTEIR 250.31 3.36E-48 1927710000 485548 738785 538901 711317 917029 918852 976036 1095815 1006552 TRUE FALSE 421381.6016 733931.8727 799515.3261 872832.3966 898781.917 954200.831 881380.1789 861483.4899 887558.5692 0.474764839 0.82691092 0.900802892 0.983408224 1.012645191 1.075084917 0.993038893 0.970621568 1 19.7594828 4.973301472 1.128063357 1.005147003 6.03E-23 0.964482892 0.031909683 0.469678137 0.353551607 0.010443407 0.632492836 94037.58606 -4.973301472 -1.005147003 down TKPTQAAGPSS(ph)PQKPPT(ph)PEETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKPTQAAGPSSPQKPPTPEETK 22 2 F5H8D7;P18887 F5H8D7 XRCC1 DNA repair protein XRCC1 2 TKPTQAAGPS(0.02)S(0.98)PQKPPT(0.997)PEET(0.003)K;TKPTQAAGPS(0.158)S(0.842)PQKPPT(0.997)PEET(0.003)K 136 9.79E-06 1972670000 1834590 988160 1202460 968960 1159010 741120 1726760 1917480 1974200 TRUE FALSE 1592144.283 981668.7119 1783973.678 1188977.178 1135947.969 769631.366 1559299.081 1507441.824 1740812.325 0.914598467 0.563914155 1.0247938 0.683001355 0.65253902 0.442110476 0.895730722 0.865941608 1 20.73132925 2.043564398 24.99996941 0.910628934 0.712706605 0.25675427 0.166000965 186.5879534 107075.0355 0.066480369 0.044821025 110.5514385 -2.043564398 -0.19792233 TKPTQAAGPSS(ph)PQKPPTPEETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TKPTQAAGPSSPQKPPTPEETK 22 2 F5H8D7;P18887 F5H8D7 XRCC1 DNA repair protein XRCC1 1 TKPTQAAGPS(0.174)S(0.825)PQKPPT(0.001)PEETK 110.61 0.00018351 161190000 183100 126570 128400 132210 138540 91989 225010 272100 210410 TRUE FALSE 158902.8711 125738.5533 190494.6695 162230.3012 135783.325 95527.87635 203188.5648 213913.5325 185535.5695 0.856455026 0.677705917 1.026728567 0.874389216 0.731845249 0.514876347 1.095146151 1.152951604 1 17.50133627 2.149515215 14.24858199 1.098234909 0.788960176 0.513985842 0.138161489 0.732934013 114.8074757 0.057670708 0.038881462 141.0961666 -2.149515215 -0.309274733 TKPTQNSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TKPTQNSVR 9 1 Q9NRF8;P17812;B4E1E0;A0A3B3IRI2;A0A3B3IRQ8;A0A3B3ITF6;A0A3B3ITB8 Q9NRF8;P17812 CTPS2;CTPS1 CTP synthase 2;CTP synthase 1;CTP synthase 0 62.466 0.07518 22483000 40441 48050 19512 25144 54297 48100 49541 46229 28670 FALSE TRUE 35096.61939 47734.35639 28948.06846 30853.3295 53216.59593 49950.43812 44736.52145 36343.2881 25280.66526 1.388279107 1.888176434 1.145067512 1.220431867 2.105031469 1.975835589 1.769594312 1.437592236 1 14.62574681 TKQGVTEAAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TKQGVTEAAEK 11 1 O76070;F8W754;G4Y816;Q16143 O76070 SNCG;SNCB Gamma-synuclein;Beta-synuclein 0 ;; 154.1 2.93E-05 1561740000 2521290 2367650 1388330 1488890 2407000 1828690 3148280 3658670 1174600 FALSE TRUE 2188095.138 2352096.751 2059731.032 1826965.231 2359105.409 1899040.888 2842960.29 2876291.892 1035740.126 2.112590874 2.270933308 1.988656208 1.763922421 2.27770012 1.833510974 2.744858694 2.777040128 1 19.98223064 2.27252404 24.99806969 2.323395721 2.047416213 0 0.513335139 566.9645879 417300.6287 0.189254956 0.146587842 187.2940755 -2.27252404 -0.275979509 TKS(ph)PTDDEVTPSAVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TKSPTDDEVTPSAVVR 16 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 T(0.002)KS(0.899)PT(0.099)DDEVTPSAVVR;T(0.091)KS(0.717)PT(0.192)DDEVTPSAVVR;T(0.001)KS(0.986)PT(0.013)DDEVTPSAVVR;T(0.003)KS(0.869)PT(0.128)DDEVTPSAVVR 218.72 7.92E-15 5798810000 1321000 1227440 850150 1023600 1325050 1063100 1478320 1699700 1545280 TRUE FALSE 1146426.503 1219376.866 1261285.384 1256024.025 1298684.097 1103998.145 1334952.754 1336232.382 1362598.759 0.841352963 0.894890633 0.925646949 0.921785681 0.953093557 0.810215141 0.979710825 0.980649933 1 20.37792937 2.043934236 24.99500407 0.986314158 0.896928968 0.540262807 0.041403919 101.1950141 57571.30372 0.016527359 0.011142736 110.6456223 -2.043934236 -0.08938519 TKTEMYQNMDDEMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TKTEMYQNMDDEMK 14 1 Q5TEZ5 Q5TEZ5 C6orf163 Uncharacterized protein C6orf163 0 87.18 0.0073934 858820000 399830 320140 193450 251940 274890 250230 352700 407780 343480 FALSE TRUE 346991.4525 318036.9793 287003.0671 309146.8277 269420.2268 259856.51 318495.2083 320579.4203 302874.1857 1.145662024 1.050063011 0.947598312 1.020710388 0.889545031 0.857968497 1.051575946 1.058457391 1 18.2083591 4.573871801 2.851135382 0.981141085 1.150602445 0.419013922 0.064924657 0.362234189 4.871682661 0.01854926 0.116393587 37486.23307 -4.573871801 0.169461359 TKVEAFQTTISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TKVEAFQTTISK 12 1 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ; 148.72 6.06E-05 1045820000 2062770 1719020 1163210 1320940 1787460 1362970 2231700 2599000 2049440 FALSE TRUE 1790169.718 1707727.644 1725742.247 1620879.616 1751893.043 1415404.338 2015270.077 2043224.075 1807157.538 0.990599702 0.944979953 0.954948426 0.896922146 0.969419105 0.783221334 1.115160154 1.130628643 1 20.78529085 2.206304963 24.9999999 1.093459979 0.926660911 0.560342317 0.06591134 127.9720626 99184.87907 0.025821592 0.017410468 160.8070047 -2.206304963 -0.166799068 TKVENGEGTIPVESSDIVPTWDGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TKVENGEGTIPVESSDIVPTWDGIR 25 1 A0A3B3IRQ9;P55265-3;P55265-2;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 138.92 4.14E-06 83830000 138730 117300 53998 76595 109160 100800 141360 163860 59013 FALSE TRUE 120396.479 116529.4486 80111.61341 93987.06543 106987.9296 104677.8412 127650.929 128819.8142 52036.55037 2.31369063 2.239376895 1.53952583 1.806174021 2.056015028 2.011621456 2.453101292 2.475564065 1 15.6672377 3.015812744 23.35480762 2.097614473 1.958587094 0 0.457669534 637.2076844 941115.9089 0.140839322 0.159629389 1037.081158 -3.015812744 -0.13902738 TKVQDHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TKVQDHSK 8 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 78.934 0.017629 23271000 161390 156310 89724 103480 102700 121630 189400 207820 86598 FALSE TRUE 140061.9026 155283.1893 133114.8265 126976.7156 100656.4709 126309.1848 171032.0172 163379.3103 76360.48309 1.834219703 2.033554308 1.743242331 1.662858987 1.318174884 1.654117152 2.239797474 2.139579317 1 16.22053861 4.213475027 20.86450654 1.736324708 1.933885897 0.062788028 0.359813652 115.331907 95926.40003 0.098049072 0.204442766 16348.3914 -4.213475027 0.197561189 TLADLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLADLIR 7 0 Q16878 Q16878 CDO1 Cysteine dioxygenase type 1 0 ;; 97.068 0.028543 193403000 465890 471528 319900 369680 470891 540470 457265 542030 508051 FALSE TRUE 404321.4561 468430.5015 474604.71 453621.4942 461521.1904 561262.2306 412919.5107 426121.1026 447989.7896 0.90252382 1.045627629 1.059409659 1.012571056 1.030204708 1.252846033 0.921716343 0.951184854 1 18.77310633 TLAEEQHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLAEEQHK 8 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 ; 91.069 0.012749 200785000 364280 307970 213250 253680 273000 258760 349770 371270 419290 FALSE TRUE 316139.475 305946.9248 316378.4133 311281.9213 267567.8341 268714.6646 315849.3592 291876.7997 369722.0139 0.855073442 0.827505297 0.855719707 0.841935047 0.723700034 0.726801907 0.854288756 0.78944934 1 18.49608142 1.235136363 24.98253351 1.00000027 0.808271547 0.592695581 0.049672731 73.59345536 536832.7805 0.090091307 0.012745407 17.18447875 -1.235136363 -0.191728724 TLAGDVHIVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TLAGDVHIVR 10 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ;;;;; 143.5 3.39E-05 3623620000 4375860 4258660 2353197 3050443 4282210 4341670 3882320 4637950 4413070 FALSE TRUE 3797579.014 4230684.582 3491210.94 3743092.706 4197002.399 4508696.854 3505813.204 3646160.485 3891361.892 0.975899729 1.087198955 0.897169432 0.961897868 1.078543326 1.158642393 0.900921914 0.93698828 1 21.89184372 TLAGHEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLAGHEGK 8 0 O43172-2;O43172 O43172-2 PRPF4 U4/U6 small nuclear ribonucleoprotein Prp4 0 ; 87.639 0.015181 148085000 765970 589140 333380 516900 471770 556640 669050 794570 721990 FALSE TRUE 664745.1238 585269.9005 494603.6831 634270.0453 462382.7 578054.301 604165.634 624657.3889 636637.1647 1.044150673 0.919314694 0.776900424 0.996281839 0.726289205 0.907980767 0.948995232 0.981182726 1 19.28011185 2.090872659 2.702005138 0.986145971 0.887575769 0.157771057 0.09193258 0.481684651 6.978691918 0.048694456 0.026172675 123.2743325 -2.090872659 -0.098570202 TLAYLLPAIVHINHQPYLER ddPTM_MDA-MB-175_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 ; 187.06 1.77E-17 2786500000 905390 967980 431390 595380 822780 931300 809530 995470 779270 FALSE TRUE 785740.4175 961621.2756 640011.6469 730570.1288 806408.2877 967127.7136 731021.9052 782596.4873 687145.5883 1.143484628 1.399443279 0.931406179 1.063195546 1.17356249 1.407456775 1.063853014 1.13890928 1 19.39025628 1.169013657 1.557804712 0.914434481 1.174092632 0.118795953 0.144878441 3.152632814 5.993340986 1.341417863 0.041661997 14.7575294 -1.169013657 0.259658151 TLCGCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLCGCR 6 0 P84103;P84103-2 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 154.91 0.023134 334240000 193600 180910 109970 136710 148720 176980 179880 191000 170380 FALSE TRUE 168015.2695 179721.5903 163151.8598 167752.095 145760.763 183788.5351 162435.2653 150156.1364 150237.8705 1.118328348 1.196246923 1.085956951 1.116576629 0.970199874 1.223316961 1.081187218 0.999455969 1 17.19688899 -1.048918695 0.399538085 1.36E-10 1.133182321 0.281634583 0.069935308 49.17102796 1.468676374 38.49486356 0.071395267 0.089347274 1.048918695 1.133182321 TLCTLGPNETAPFKPEGELHELSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLCTLGPNETAPFKPEGELHELSTR 25 1 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 0 143.29 1.97E-07 76666000 146340 147480 106420 129420 133080 124380 163160 191820 176070 FALSE TRUE 127000.7982 146511.1942 157885.068 158806.7891 130431.9684 129164.9791 147336.7683 150800.7857 155255.2052 0.818013142 0.943679756 1.016938967 1.02287578 0.840113336 0.831952648 0.948997286 0.971309049 1 17.24428211 1.74155371 2.947360159 0.990614055 0.918991073 0.147189073 0.071206556 0.519689445 9.375377046 0.058399918 0.02098007 55.15104049 -1.74155371 -0.071622982 TLDDSANRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLDDSANRR 9 1 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A1B0GTG9;A0A1B0GWF8;P30566-2 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 0 ;; 125.57 0.00079833 517180000 1075980 1132730 588130 732250 1096130 1250480 1071070 1177100 756480 FALSE TRUE 933786.5168 1125289.022 872551.6352 898518.5542 1074319.158 1298586.775 967197.7963 925386.3252 667049.7962 1.399875275 1.686964044 1.308075709 1.347003716 1.610553161 1.94676137 1.449963409 1.387282225 1 19.34743494 1.249191533 1.999679837 0.836626603 1.542779209 0.453243377 0.185688202 0.739939658 2.944888344 0.970428152 0.052688917 17.74972107 -1.249191533 0.706152606 TLDGFKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLDGFKK 7 1 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ; 87.754 0.030641 3565800000 6526200 5836200 3550500 5043700 6539800 6329800 8028600 8006300 3625900 FALSE TRUE 5663746.135 5797861.618 5267533.676 6188949.173 6409670.775 6573311.502 7249987.608 6294215.05 3197250.233 1.771442872 1.813390006 1.647519991 1.935709977 2.004744799 2.055926507 2.267569655 1.968633855 1 21.60840023 3.716833936 23.03186861 1.920056898 1.751044854 0.018276798 0.335083334 987.3532499 1046665.936 0.092900758 0.137990604 5209.95457 -3.716833936 -0.169012044 TLDHFSSLGS(ph)VDSLDHPSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLDHFSSLGSVDSLDHPSSR 20 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 TLDHFSSLGS(0.999)VDSLDHPSSR 151.23 1.31E-07 123710000 56347 69571 37344 47430 81456 105630 46896 55610 65500 TRUE FALSE 48900.60118 69113.98352 55403.68331 58199.70642 79835.18497 109693.6545 42348.03314 43718.23426 57756.66462 0.846665948 1.196640838 0.959260436 1.007670834 1.382267925 1.899238039 0.733214659 0.756938347 1 15.81769981 TLDPNQVSLHPQVLPLPHS(ph)SSPEHNRPTDHPTSILSSPEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLDPNQVSLHPQVLPLPHSSSPEHNRPTDHPTSILSSPEDR 41 1 F5H527;Q76I76;A0A3B3IS79 F5H527 SSH2 Protein phosphatase Slingshot homolog 2 1 TLDPNQVSLHPQVLPLPHS(0.332)S(0.332)S(0.332)PEHNRPT(0.003)DHPTSILSSPEDR 98.153 3.01E-05 115370000 38423 43898 10861 22196 56819 60113 42794 44273 31138 TRUE FALSE 33345.3032 43609.63115 16113.41593 27235.94104 55688.41306 62425.58601 38643.84447 34805.56348 27456.90111 1.214459821 1.588293995 0.586862147 0.991952476 2.028211881 2.273584544 1.407436488 1.267643546 1 14.74488119 3.271029885 24.99914192 1.574224291 1.094275557 0.248499443 0.431172894 324.6243479 249936.7117 0.135959068 0.175509202 1866.508127 -3.271029885 -0.479948734 KVTSPLQS(ph)PTK ddPTM_MDA-MB-175_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 1 KVTSPLQS(0.999)PT(0.001)K;KVTSPLQS(1)PTK 122.12 0.00024347 885350000 279520 379100 320620 403550 478310 437690 573430 738040 620160 TRUE FALSE 242580.7238 376609.6671 475672.9044 495182.1954 468792.5668 454528.2175 517818.8469 580215.8894 546845.3913 0.443600198 0.688694964 0.869848977 0.905525041 0.857267107 0.831182314 0.946920016 1.061023643 1 19.06077347 4.974298257 0.748379332 0.964442377 5.56E-31 0.868030608 0.063067186 1.5075665 0.51324246 0.02977162 1.321696842 94253.66738 -4.974298257 -0.964442377 down TLDS(ph)DEERPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLDSDEERPR 10 1 Q9BW71;Q9BW71-2 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 TLDS(1)DEERPR 124.48 0.00026302 315030000 242180 167600 151650 187970 198430 195990 182220 207110 465220 TRUE FALSE 210175.2994 166499.0246 224988.4472 230651.4614 194481.6312 203529.8621 164548.3324 162821.1382 410222.2216 0.512344988 0.405875196 0.548455046 0.562259793 0.474088484 0.496145385 0.401119988 0.396909601 1 18.64604612 1.233653987 25 1.000000808 0.471108227 0.886853271 0.058960017 51.93247073 264572.0474 0.126441079 0.015741683 17.12592301 -1.233653987 -0.528892581 TLDS(ph)DEERPRPAPPDWSHMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 TLDSDEERPRPAPPDWSHMR 20 2 Q9BW71;Q9BW71-2 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 TLDS(1)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR;T(0.068)LDS(0.932)DEERPRPAPPDWSHMR;T(0.042)LDS(0.958)DEERPRPAPPDWSHMR;T(0.043)LDS(0.957)DEERPRPAPPDWSHMR 273.88 9.52E-45 9147650000 3945670 3241160 1858080 2338420 3265220 3226730 3007650 3385790 2407370 TRUE FALSE 3424239.712 3219868.607 2756653.703 2869394.002 3200248.51 3350864.391 2715968.566 2661765.157 2122773.461 1.613097099 1.516821585 1.298609462 1.351719368 1.507578915 1.578531319 1.279443434 1.253909193 1 21.01751899 1.374757658 1.237274196 0.866193788 1.463940317 0.678594541 0.1046273 0.726533564 1.169818465 0.540782264 0.034742929 23.70050816 -1.374757658 0.597746529 TLDSGTSEIVKS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLDSGTSEIVKSPR 14 1 Q9H501 Q9H501 ESF1 ESF1 homolog 1 TLDSGTSEIVKS(1)PR 116.29 0.00022402 403120000 613710 547030 314680 418870 575930 456940 609440 733770 462500 TRUE FALSE 532606.6686 543436.5239 466860.3005 513980.8355 564470.1198 474518.7775 550336.6026 576858.9957 407823.7769 1.305972576 1.332527809 1.144759887 1.260301298 1.384103017 1.163538774 1.349447074 1.414481029 1 18.63758636 1.223978241 24.99800879 0.99999923 1.296766161 0.531709095 0.086800289 664.4774138 1139022.352 0.475174928 0.021921824 16.74858959 -1.223978241 0.296766931 TLDSWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLDSWR 6 0 P51149;C9J592 P51149 RAB7A Ras-related protein Rab-7a 0 ;; 128.82 0.0383 625940000 988850 959340 780910 1089790 1156430 1261870 860810 1234310 2371310 FALSE TRUE 858170.9671 953038.0324 1158560.688 1337243.476 1133419.306 1310414.955 777328.7787 970362.4119 2090976.433 0.410416375 0.455786119 0.554076397 0.63953063 0.542052645 0.626700012 0.371753964 0.464071424 1 20.99574537 1.23542824 24.99999836 1.000000674 0.508282686 0.761397736 0.086547759 46.02668773 367281.8518 0.155756777 0.022499306 17.19603183 -1.23542824 -0.491717988 TLEAEFNSPSPPT(ph)PEPGEGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLEAEFNSPSPPTPEPGEGPR 21 0 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-7 A0MZ66 KIAA1598 Shootin-1 1 TLEAEFNSPS(0.001)PPT(0.999)PEPGEGPR;TLEAEFNS(0.001)PS(0.035)PPT(0.964)PEPGEGPR 282.38 4.91E-44 220810000 203866 236130 130447 187859 259590 241000 227230 293160 255030 TRUE FALSE 176924.5916 234578.8465 193531.6055 230515.2572 254424.6669 250271.4259 205193.2696 230470.0154 224880.6439 0.786748866 1.043126 0.860596991 1.025056017 1.13137646 1.112907814 0.912454118 1.024854836 1 17.77879996 4.743489878 24.28331474 1.012246011 0.786748725 0.438265872 0.08076532 353.770884 1742714.51 0.020206358 0.160432317 55397.46321 -4.743489878 -0.225497286 TLEDEEEQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLEDEEEQER 10 0 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 0 209.73 2.10E-07 196260000 296960 233330 189970 221890 239410 278020 246460 269670 383600 FALSE TRUE 257715.9836 231797.2399 281840.1274 272273.5159 234646.2094 288715.6093 222558.3471 212003.1691 338251.245 0.761906977 0.685281261 0.833227169 0.804944608 0.693703905 0.853553722 0.657967562 0.626762421 1 18.36773572 2.226268153 24.99594907 0.729173363 0.7688641 0 0.112647749 1090.909693 2218277.403 0.044951263 0.030546643 168.3713341 -2.226268153 0.039690736 TLEDEEEQERER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLEDEEEQERER 12 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 0 ; 220.9 2.60E-11 1054330000 1071660 1195890 719710 751350 1106230 1307010 1048480 1340140 639720 FALSE TRUE 930037.4158 1188034.12 1067764.163 921955.5012 1084218.187 1357291.52 946798.571 1053561.49 564093.0304 1.648730556 2.10609608 1.892886644 1.634403284 1.922055634 2.406148361 1.678444015 1.867708752 1 19.10557359 1.065276842 2.311537503 0.344450555 1.915245983 0.587993427 0.233802674 0.862227024 3.068749463 3.381061632 0.0605293 11.62189219 -1.065276842 1.570795428 TLEDPDLNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLEDPDLNVR 10 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 163.32 1.51E-05 383080000 270230 223840 154826 201506 243387 290680 251210 288560 311720 FALSE TRUE 234518.4208 222369.5803 229700.3715 247261.0171 238544.0749 301862.6477 226847.6929 226853.6896 274868.8167 0.85320126 0.809002574 0.835672719 0.899560089 0.867846989 1.098206233 0.825294392 0.825316208 1 18.06838372 3.678482673 2.499380266 0.911440308 0.827941875 0.196765118 0.081960132 0.569026361 6.962506577 0.02491853 0.043333688 4769.607841 -3.678482673 -0.083498432 TLEDPDLNVRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLEDPDLNVRR 11 1 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 68.069 0.094119 0 469650 443280 105570 122050 397860 422890 432540 441980 48599 FALSE TRUE 407584.5626 440368.0645 156624.0051 149763.3179 389943.3644 439158.8519 390592.3374 347466.0165 42853.68158 9.511074603 10.27608477 3.654855296 3.494759665 9.099413399 10.24786753 9.114557325 8.108195227 1 15.38713153 4.290618998 24.99962527 6.819392198 9.893596241 0.183774152 2.964741122 200.6921368 96373.41304 0.772485327 2.043801869 19526.25686 -4.290618998 3.074204043 TLEEDEEELFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TLEEDEEELFK 11 0 P43487;F6WQW2;P43487-2;C9JJ34;C9JDM3 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;;;;; 271.01 1.16E-26 1423493000 1538142 1350986 1104063 1123102 1393331 1014471 1663466 1981706 1609206 FALSE TRUE 1334872.638 1342111.284 1637991.56 1378119.475 1365606.439 1053498.356 1502143.323 1557933.594 1418967.5 0.940735174 0.945836521 1.154354529 0.971212854 0.962394445 0.742440088 1.058617145 1.097934656 1 20.43641012 2.05568414 24.99999992 1.062664195 0.95774071 0.175156622 0.100452429 142.9598662 64182.52647 0.042445921 0.028617028 113.6800198 -2.05568414 -0.104923485 TLEFVPINLHLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLEFVPINLHLQR 13 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3;E9PG59 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 ; 180.09 1.32E-05 1604750000 1817180 1764970 1107280 1353070 1785270 2070440 1867510 2045850 1946020 FALSE TRUE 1577035.059 1753375.796 1642764.312 1660305.224 1749746.62 2150091.167 1686399.168 1608360.898 1715963.733 0.919037523 1.021802363 0.957342093 0.967564286 1.019687413 1.252993362 0.982770868 0.93729306 1 20.71058763 3.192947766 5.908124586 1.03296616 0.969675814 0.146455134 0.086087509 0.488231158 39.9865173 0.028513918 0.033004665 1559.36494 -3.192947766 -0.063290346 TLEGELHDLR ddPTM_MDA-MB-175_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 ;;;;;;;; 280.09 4.95E-24 32091350000 9790640 8876000 5430179 6723508 8300750 8875590 8146392 9324490 10014220 FALSE TRUE 8496782.118 8817692.972 8056231.727 8250183.254 8135581.315 9217039.691 7356356.158 7330520.377 8830350.32 0.962224805 0.998566609 0.912334328 0.934298522 0.921320335 1.043790943 0.833076366 0.830150573 1 23.07403924 2.218038561 24.99962854 0.87346629 0.958369414 0.241628589 0.060108415 293.1542837 357112.9898 0.02419817 0.016335491 165.2108483 -2.218038561 0.084903125 TLENPVNVYNPSHSDSLASQQSVASHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLENPVNVYNPSHSDSLASQQSVASHPR 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 0 ; 269.57 4.55E-55 970800000 281820 284480 100247 187323 321650 303790 270321 344600 267579 FALSE TRUE 244576.773 282611.2321 148726.7845 229857.5502 315249.7943 315476.9979 244105.311 270909.9717 235946.1154 1.036578935 1.197778703 0.630342162 0.974195103 1.336109279 1.337072226 1.034580758 1.148185768 1 17.84809789 3.383328798 9.862185952 1.166070763 0.949884185 0.265956463 0.174621012 0.455918396 43.92859225 0.051537456 0.066542459 2417.290236 -3.383328798 -0.216186578 TLEPVKPPTVPNDYMT(ph)SPAR ddPTM_MDA-MB-175_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 TLEPVKPPTVPNDY(0.008)MT(0.496)S(0.496)PAR;TLEPVKPPTVPNDYMT(0.524)S(0.476)PAR;TLEPVKPPTVPNDYMT(0.579)S(0.421)PAR 91.114 0.0029758 849920000 515610 451107 276940 354109 449846 403415 483570 575400 516040 TRUE FALSE 447470.8321 448143.6484 410869.1103 434514.8607 440894.9447 418934.6361 436673.4558 452355.1878 455034.3391 0.983378162 0.984856768 0.902940888 0.954905649 0.968926753 0.920665981 0.959649456 0.9941122 1 18.7956159 1.743905319 3.749760578 0.998435234 0.951832516 0.340158285 0.025314255 0.219836085 6.622321014 0.017183661 0.006853532 55.45048122 -1.743905319 -0.046602718 TLEPVKPPTVPNDYMTS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLEPVKPPTVPNDYMTSPAR 20 1 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7;Q8IZP0-11 A0A0A0MRT6 ABI1 Abl interactor 1 1 TLEPVKPPTVPNDYMT(0.059)S(0.941)PAR 130.14 1.01E-05 248990000 266770 238310 155780 184620 210860 205770 261420 319330 281630 TRUE FALSE 231515.6686 236744.5259 231115.7291 226540.7927 206664.2985 213686.1051 236067.5286 251043.7645 248336.0222 0.932267766 0.953323339 0.930657288 0.912234925 0.832196218 0.860471643 0.950597205 1.010903542 1 17.92193402 1.956566518 4.074860425 1.002483171 0.903999364 0.584186129 0.035395428 0.172525082 5.920294241 0.021480713 0.011077977 90.4829013 -1.956566518 -0.098483807 TLEPVRPPVVPNDYVPS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLEPVRPPVVPNDYVPSPTR 20 1 H7C3Q7;B7Z836;E7EW77;E7EP65;A0A0C4DG21;F8WAL6;Q9NYB9-3;Q9NYB9-2;Q9NYB9-4;Q9NYB9;H0Y6B5 H7C3Q7 ABI2 Abl interactor 2 1 TLEPVRPPVVPNDYVPS(0.953)PT(0.047)R 89.272 0.0012733 164970000 97993 113550 58139 70986 92502 114280 93439 113150 105100 TRUE FALSE 85042.97677 112804.0826 86255.21486 87104.45625 90661.39118 118676.4255 84377.30016 88953.75303 92675.19773 0.917645485 1.217198186 0.930725987 0.939889619 0.978270275 1.28056296 0.910462586 0.959844222 1 16.49989567 TLEQHDNIVTHYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TLEQHDNIVTHYK 13 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;;; 167.32 1.86E-05 1849100000 3608810 2249340 1384170 1754030 2239400 1972670 2500640 2831340 2636210 FALSE TRUE 3131896.615 2234563.937 2053559.242 2152309.32 2194840.321 2048559.891 2258128.318 2225879.975 2324560.257 1.347307133 0.961284583 0.883418374 0.92589956 0.944195925 0.881267709 0.971421718 0.957548839 1 21.14852639 4.736743795 5.027885051 0.938036278 1.366652269 0.926239812 0.036123721 0.040647127 3.27414921 0.009034181 0.060660057 54543.59946 -4.736743795 0.42861599 TLETVPLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLETVPLER 9 0 P22626;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 109.11 0.0058216 180570000 202670 152950 83466 114670 161150 168760 142380 156560 157160 FALSE TRUE 175886.646 151945.2614 123830.4368 140707.5761 157943.4303 175252.3064 128572.0095 123080.8624 138580.7238 1.269199937 1.096438647 0.893561769 1.015347389 1.139721499 1.264622536 0.927777009 0.888152832 1 17.08036707 2.156275604 21.31370203 0.927658656 1.099169935 0.342383771 0.112561875 10.47548496 2710.365357 0.048614269 0.032775726 143.3097058 -2.156275604 0.171511279 TLFGLHLSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLFGLHLSQK 10 0 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 205.53 1.67E-07 690190000 1417600 2005600 398000 1017900 2371700 2230100 2085300 2325700 2380300 FALSE TRUE 1230260.568 1992425.082 590474.1312 1249029.753 2324507.81 2315893.39 1883067.927 1828367.154 2098903.646 0.586144376 0.949269437 0.28132503 0.595086752 1.10748667 1.103382423 0.8971674 0.871105807 1 21.00120451 3.250098518 24.99365129 0.978216243 0.604719264 0.554217718 0.174683855 179.1609685 388100.1772 0.051360527 0.065726794 1778.682851 -3.250098518 -0.373496979 TLFLGIPDENFEDHSAPPS(ph)PEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TLFLGIPDENFEDHSAPPSPEEK 23 0 Q99683-2;Q99683 Q99683-2 MAP3K5 Mitogen-activated protein kinase kinase kinase 5 1 TLFLGIPDENFEDHSAPPS(1)PEEK;TLFLGIPDENFEDHS(0.001)APPS(0.999)PEEK;TLFLGIPDENFEDHSAPPS(1)PEEK;TLFLGIPDENFEDHSAPPS(1)PEEK;TLFLGIPDENFEDHSAPPS(1)PEEK 191.99 6.78E-18 604290000 806372 739431 545163 595998 873273 626462 1119305 1144303 1045209 TRUE FALSE 699807.8971 734573.6291 808805.6503 731328.4552 855896.5758 650562.3985 1010754.973 899602.7084 921645.5827 0.759302611 0.797023978 0.877566893 0.793502914 0.92866129 0.705870468 1.096685095 0.976083134 1 19.81385255 2.232936651 24.9999924 1.017237929 0.817388158 0.689073825 0.067578201 75.71955429 336588.7981 0.025306674 0.017596806 170.9765901 -2.232936651 -0.19984977 TLFYSSPLLGPSSTSEAVGSSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLFYSSPLLGPSSTSEAVGSSSPR 24 0 Q5SXH7-4;Q5SXH7-3;Q5SXH7-2;Q5SXH7-1;Q5SXH7 Q5SXH7-4 PLEKHS1 Pleckstrin homology domain-containing family S member 1 1 TLFYSSPLLGPSSTSEAVGS(0.002)S(0.075)S(0.923)PR 163.39 1.08E-11 88726000 76359 95153 52389 60148 91004 97378 91098 108740 101990 TRUE FALSE 66267.96468 94527.93368 77724.49563 73805.5227 89193.19845 101124.1947 82263.32998 85486.79722 89932.85839 0.73686043 1.05109451 0.864250253 0.820673601 0.991775421 1.124441016 0.914719397 0.950562439 1 16.4565607 3.216956268 24.33461202 0.990871108 0.880998667 0.311031749 0.093676158 245.8739768 276945.2705 0.02786635 0.031628689 1647.996437 -3.216956268 -0.109872441 TLGEDDPWLDDTAAWIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TLGEDDPWLDDTAAWIER 18 0 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 ;;; 154.07 6.68E-08 189921000 415530 360988 229902 278696 362521 353051 344851 410663 387519 FALSE TRUE 360616.6577 358616.6461 341083.3762 341978.1864 355307.5414 366633.1004 311407.4031 322845.9132 341706.9453 1.055338976 1.049485973 0.998175135 1.000793783 1.03980193 1.072946001 0.911328866 0.944803486 1 18.38240005 2.237782952 24.99999875 0.948839182 1.033540101 0.618111849 0.031064902 13.7450587 441838.7466 0.012634335 0.00908409 172.8952061 -2.237782952 0.084700919 TLGEIPTYGLAGNREEQEELMDFERDEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLGEIPTYGLAGNREEQEELMDFERDEER 29 2 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 44.555 0.070822 33387000 27465 20953 15801 13190 24538 23869 22771 29305 10255 FALSE TRUE 23835.43066 20815.35836 23442.41645 16184.9911 24049.74181 24787.25588 20562.67192 23038.3538 9042.665583 2.635885453 2.301905138 2.592423245 1.789847357 2.659585449 2.741144815 2.273961338 2.547739225 1 13.1425324 1.235845514 24.99735315 0.999998085 2.435779216 0.730709846 0.275234817 37.98158117 349618.0594 0.429765758 0.064189875 17.21256186 -1.235845514 1.435781131 TLGT(ph)PTQPGSTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLGTPTQPGSTPR 13 0 Q8NFH5-2;Q8NFH5;Q8NFH5-3 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 TLGT(0.997)PT(0.003)QPGSTPR;T(0.006)LGT(0.992)PT(0.002)QPGSTPR;TLGT(0.984)PT(0.016)QPGSTPR 191.43 3.99E-05 905770000 1092590 999600 614360 741510 1104300 1039670 953670 1128450 1048740 TRUE FALSE 948201.4632 993033.5618 911466.5509 909881.1788 1082326.591 1079666.778 861183.2302 887139.7491 924759.1519 1.02534964 1.073829396 0.985625878 0.983911516 1.170387542 1.167511319 0.931251373 0.959319783 1 19.81871815 2.20869398 24.99961868 0.961303179 1.065163726 0.359998919 0.06543874 243.4352104 203763.6716 0.028804878 0.019423164 161.694028 -2.20869398 0.103860548 TLGTMIAGDTSGDYRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLGTMIAGDTSGDYRR 16 1 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 134.14 4.79E-05 196710000 156660 145080 81340 114850 159560 152200 139060 171310 153690 FALSE TRUE 135956.9841 144126.9599 120676.2961 140928.4479 156385.0682 158055.2325 125573.9826 134676.6896 135520.9433 1.003217516 1.063503223 0.890462338 1.039901616 1.153954986 1.166279017 0.926602041 0.993770309 1 17.0481563 5.081703356 13.04414539 1.026325924 0.734614309 0.00783663 0.086666145 3569655.563 13797285.05 0.022338084 28103296.03 120698.9122 -5.081703356 -0.291711615 TLHCEGTEINS(ph)DDEQESK ddPTM_MDA-MB-175_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 415.81 6.50E-148 3892210000 1999790 1574920 1402890 1547330 1560500 1269280 1805040 2209340 2999770 TRUE FALSE 1735512.685 1564574.247 2081332.296 1898674.926 1529449.103 1318110.023 1629987.499 1736889.834 2645140.608 0.656113584 0.591490011 0.786851289 0.717797353 0.578210889 0.498313783 0.616219604 0.656634218 1 21.33491298 1.237184367 4.971886778 1.024182234 0.635204711 0.682275809 0.077832262 0.112221274 6.986072612 0.151881271 0.021016312 17.265707 -1.237184367 -0.388977523 TLHCEGTEINS(ph)DDEQESKEVEETATAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLHCEGTEINSDDEQESKEVEETATAK 27 1 Q9BPX3;H0Y9Z8 Q9BPX3 NCAPG Condensin complex subunit 3 1 TLHCEGTEINS(0.999)DDEQES(0.001)KEVEETATAK 150.23 5.97E-08 111790000 101530 83146 59259 54793 67349 44229 96508 114270 29598 TRUE FALSE 88112.55326 82599.80845 87916.85061 67234.58811 66008.88667 45930.51825 87148.66901 89834.24975 26098.95816 3.376094659 3.164869952 3.368596174 2.576140691 2.529177075 1.75986022 3.339162755 3.442062676 1 14.6717046 3.734326615 22.70289707 2.5767561 3.289355271 0.233503657 0.708289155 179.0347686 960001.5389 0.198383564 0.307270216 5424.086603 -3.734326615 0.712599171 TLHEWCDGCEAVLLGIEQQVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLHEWCDGCEAVLLGIEQQVLR 22 0 J3QT73;A0A087X1P5;J3KQ34;Q9H9Q2-2;Q9H9Q2;J3QT95;J3KQ41;Q9H9Q2-3 J3QT73 COPS7B COP9 signalosome complex subunit 7b 0 ; 166.25 1.19E-11 76249000 94872 89681 52650 67057 81471 93761 87422 104758 101626 FALSE TRUE 82334.42482 89091.87961 78111.7161 82283.31675 79849.8865 97368.04634 78943.8279 82356.31693 89611.89005 0.918789067 0.994197082 0.871666874 0.91821874 0.891063523 1.086552759 0.880952604 0.919033366 1 16.45140255 TLHGQETYTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLHGQETYTPR 11 0 Q9BUK6-2;Q9BUK6;A0A3B3IUD2;Q9BUK6-7;Q9BUK6-3;Q9BUK6-4 Q9BUK6-2 MSTO1 Protein misato homolog 1 0 ; 122.55 0.0003885 280270000 169633 146291 80619 101320 160369 163505 153125 170513 168052 FALSE TRUE 147215.5693 145330.0048 119606.6181 124326.2546 157177.9707 169795.1432 138274.9611 134050.1219 148185.084 0.993457407 0.980733019 0.807143437 0.838993043 1.060686855 1.145831541 0.933123344 0.904612787 1 17.17704071 3.238263168 25 0.996990601 0.903489803 0.259242511 0.085852422 14.12349065 1187095.943 0.028622115 0.034537199 1730.864887 -3.238263168 -0.093500798 TLHNLVIQYASQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLHNLVIQYASQGR 14 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;G5E9S8;E9PQ02;Q9H0B6;Q9H0B6-2;A8MZ87;A8MX29 Q07866-6;Q9H0B6 KLC1;KLC2 Kinesin light chain 1;Kinesin light chain 2 0 ; 135.45 3.28E-05 2216570000 1150350 1096660 697190 828390 1088410 1266530 1117370 1264060 1119580 FALSE TRUE 998328.3329 1089455.968 1034353.416 1016488.611 1066752.77 1315254.229 1009007.629 993750.6059 987224.5278 1.011247497 1.103554397 1.047738774 1.029642783 1.080557401 1.332274667 1.022064992 1.006610531 1 19.91301871 2.028767394 24.99999663 1.006945086 1.101286615 0.194319517 0.088157638 336.5988182 292516.2793 0.036931234 0.024898597 106.8482452 -2.028767394 0.094341528 TLHPDLGTDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TLHPDLGTDK 10 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;; 157.38 9.28E-06 2840140000 4358190 3436320 2983980 3626270 3409750 2874710 3821080 4394850 10426100 FALSE TRUE 3782244.149 3413746.588 4427042.709 4449670.028 3341902.646 2985301.954 3450512.25 3455045.528 9193538.335 0.411402445 0.37132021 0.481538505 0.483999725 0.363505598 0.32471741 0.375319287 0.375812381 1 23.13218879 1.23731945 24.99996749 1.000000724 0.397332017 0.933694 0.05037791 7.953040844 160125.9933 0.080703052 0.013405562 17.27107817 -1.23731945 -0.602668707 FDPFGPIGT(ph)SPPGPNPDHLPPPGYDDMYL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 FDPFGPIGTSPPGPNPDHLPPPGYDDMYL 29 0 Q92530 Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 FDPFGPIGT(0.536)S(0.464)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.548)S(0.452)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.646)S(0.354)PPGPNPDHLPPPGYDDMYL 197.81 1.50E-24 463542000 89309 141178 93571 122965 179142 201004 181500 209702 190468 TRUE FALSE 77506.58937 140250.5924 138822.2486 150886.0827 175577.4247 208736.7539 163898.1579 164858.8592 167951.09 0.461483098 0.835068069 0.826563546 0.898392994 1.045408069 1.242842508 0.975868379 0.981588504 1 17.35768163 4.97621058 0.790504015 1.037112963 7.19E-12 0.788172977 0.092036444 1.761413557 0.662410941 0.037207908 1.750598982 94669.6082 -4.97621058 -1.037112963 down TLHPDLGTDKDKEQWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLHPDLGTDKDKEQWK 16 2 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 246.27 1.96E-20 2283800000 2366750 1294630 1357790 1232610 1126620 709860 2082940 2178940 1380260 FALSE TRUE 2053977.991 1286125.49 2014421.786 1512492.94 1104202.466 737168.7735 1880936.799 1712990.638 1217087.235 1.687617725 1.056724163 1.65511701 1.242715309 0.907250059 0.605682775 1.545441235 1.407450993 1 20.21500115 7.999982294 0.817345761 1.174623294 127.7983551 0.195173332 0.313350402 1166.948333 3.754749606 0.115418821 274026.379 99995923.08 -7.999982294 126.6237318 TLHS(ph)PPLQLQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(0.038)LHS(0.962)PPLQLQQR;TLHS(1)PPLQLQQR;TLHS(1)PPLQLQQR;TLHS(1)PPLQLQQR;TLHS(1)PPLQLQQR 206.27 5.93E-08 5169420000 1358611 1490764 871974 1035445 1653756 1600636 1492052 1646118 1496908 TRUE FALSE 1179067.114 1480971.073 1293663.543 1270558.613 1620849.491 1662213.503 1347353.027 1294108.476 1319945.242 0.893269718 1.121994327 0.980088796 0.962584335 1.227967222 1.259304894 1.020764335 0.980425881 1 20.33204665 4.751033613 24.18175642 1.064735806 0.893269548 0.217058139 0.10467547 2314.226982 4486528.955 0.027715263 0.45551819 56368.12816 -4.751033613 -0.171466258 TLHSCSVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TLHSCSVR 8 0 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ;;; 189.14 0.00019329 1545920000 1321610 1592940 752730 1018590 1560720 1634930 1602260 1615500 1632290 FALSE TRUE 1146955.89 1582475.872 1116752.746 1249876.428 1529664.725 1697826.815 1446873.072 1270037.897 1439322.536 0.796872043 1.099458831 0.775887765 0.86837828 1.062767161 1.179601356 1.005245896 0.88238589 1 20.45695849 3.245615485 24.97810201 1.014171794 0.892652652 0.275434705 0.112320231 271.3712249 960797.1493 0.034304436 0.043336299 1760.416722 -3.245615485 -0.121519142 TLHSDDEGTVLDDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TLHSDDEGTVLDDSR 15 0 O00170;E9PMH2 O00170 AIP AH receptor-interacting protein 0 ;;; 284.68 5.28E-34 2670030000 1254140 1154610 674783 864220 1117790 1259890 1141100 1259950 1234010 FALSE TRUE 1088402.221 1147025.291 1001110.316 1060454.36 1095548.166 1308358.784 1030436.298 990519.4974 1088126.744 1.000253167 1.054128389 0.920030981 0.974568786 1.006820366 1.202395577 0.946981869 0.910297907 1 20.05341518 2.050177517 24.99990432 0.942707573 1.024146536 0.172123413 0.075405226 169.1423183 84270.83714 0.031510239 0.021244226 112.247717 -2.050177517 0.081438964 TLIPS(ph)PPPRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLIPSPPPRPK 11 1 J3KSG3;J3KSS7;Q9NZ52-3;Q9NZ52-4;Q9NZ52-2;Q9NZ52 J3KSG3 GGA3 ADP-ribosylation factor-binding protein GGA3 1 TLIPS(1)PPPRPK 90.759 0.0068117 870850000 1479900 1420800 932790 1189300 1339700 1186100 1731800 1942800 1799000 TRUE FALSE 1284327.465 1411466.671 1383890.364 1459348.742 1313042.591 1231730.035 1563850.303 1527347.339 1586324.269 0.809624798 0.889771845 0.872388068 0.919956134 0.827726472 0.776468001 0.985832678 0.962821643 1 20.59725628 2.216028856 24.99099005 0.978827857 0.854438566 0.697029565 0.041389659 140.3514768 155668.9689 0.017369324 0.011719914 164.4480983 -2.216028856 -0.124389291 TLKPEEQR ddPTM_MDA-MB-175_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 ; 96.331 0.0082232 631170000 1670900 1334430 1022640 1255110 1436610 1364900 1647180 1841670 1751410 FALSE TRUE 1450086.331 1325664.041 1517192.125 1540101.909 1408024.272 1417408.586 1487436.737 1447843.202 1544360.305 0.938955972 0.858390388 0.982408133 0.997242615 0.911720061 0.917796567 0.963141006 0.937503507 1 20.55857795 3.139033049 0.009913606 1.882760924 1.16E-05 0.123727562 0.040592603 5269.56552 68.07168971 6442.243717 6483.172957 1377.314277 -3.139033049 -1.882749328 TLLEGSGLESIISIIHSS(ph)LAEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLLEGSGLESIISIIHSSLAEPR 23 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 TLLEGSGLESIISIIHS(0.204)S(0.796)LAEPR 87.881 0.0040777 51415000 61848 82880 32981 46299 77195 68689 65594 70428 52351 TRUE FALSE 53674.6301 82335.55582 48930.72191 56811.89559 75658.97053 71331.51028 59232.70398 55367.52027 46162.12442 1.162741767 1.783617129 1.059975522 1.230703662 1.638983723 1.545238898 1.283145105 1.199414476 1 15.494422 1.545138486 1.835841793 0.986611173 1.405065848 0.257700043 0.219840999 0.618508705 3.54076922 0.397115249 0.061592438 35.0863738 -1.545138486 0.418454676 TLLEGSGLESIISIIHSSLAEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 401.02 1.18E-138 3022200000 1102420 1481579.5 327684.39 787761.5 1861802 2488039.7 1607786.7 1642257.6 1837673.61 FALSE TRUE 956732.4038 1471846.907 486153.657 966634.7888 1824755.783 2583756.197 1451863.793 1291073.592 1620425.929 0.590420325 0.908308661 0.30001597 0.596531302 1.126096386 1.59449201 0.895976649 0.796749527 1 20.62794164 3.243564034 24.57305796 1.058513749 0.599582261 0.473444085 0.252839004 103.3244292 507448.3493 0.080091868 0.100105739 1752.120754 -3.243564034 -0.458931488 TLLEQLDDDQ ddPTM_MDA-MB-175_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 0.006322 0 228250 185457 117499 141030 192702 200431 173678 210501 194635 FALSE TRUE 198086.1842 184238.7208 174321.9094 173053.017 188867.6072 208141.7103 156834.7343 165486.9993 171625.472 1.154177069 1.073492871 1.015711172 1.008317792 1.100463731 1.212767008 0.913819682 0.964233323 1 17.38890416 2.212016795 24.9999963 0.958470989 1.086035283 0.500971117 0.063075688 199.2118233 187623.9022 0.02691833 0.018154256 162.9359043 -2.212016795 0.127564294 TLLISSLS(ph)PALPAEHLEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLLISSLSPALPAEHLEDR 19 0 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 TLLIS(0.026)S(0.004)LS(0.97)PALPAEHLEDR;TLLIS(0.002)S(0.003)LS(0.995)PALPAEHLEDR;TLLIS(0.003)S(0.001)LS(0.996)PALPAEHLEDR 195.13 1.03E-15 174411000 138251 128013 79169 95212 128250 140129 135558 144963 135108 TRUE FALSE 119980.7801 127172.0742 117455.3932 116831.3398 125698.0759 145519.8533 122411.606 113963.7906 119135.6862 1.007093541 1.067455758 0.985895973 0.980657799 1.055083325 1.221463174 1.027497385 0.956588191 1 16.8622461 1.989676007 24.65484908 0.980248093 1.053791741 0.168492449 0.067816044 724.2634147 1729621.038 0.031130587 0.019521232 97.65084531 -1.989676007 0.073543648 TLLIVSHDQGFLDDVCTDIIHLDAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLLIVSHDQGFLDDVCTDIIHLDAQR 26 0 Q8NE71;Q8NE71-2;H0YGW7 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 ;; 226.18 9.33E-35 219424000 114836 110888 66935 86862 92540 91931 112066 102854 98742 FALSE TRUE 99660.13164 110159.5694 99304.98988 106585.3447 90698.63505 95467.64506 101197.8566 80859.47251 87068.83325 1.144613152 1.265200937 1.14053429 1.224150373 1.041688876 1.096461748 1.162274178 0.928684461 1 16.40986877 1.456541364 0.397468467 0.791995276 1.217550595 0.54684612 0.067981016 4.089132553 0.686728573 0.856338524 0.097834896 28.61154853 -1.456541364 0.425555319 TLLLSS(ph)DDEF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLLLSSDDEF 10 0 A0A0J9YYJ3;Q9Y519 A0A0J9YYJ3 TMEM184B Transmembrane protein 184B 1 TLLLS(0.077)S(0.923)DDEF 98.392 0.0056729 28391000 159220 141170 81135 124620 168470 149760 144210 181700 131700 TRUE FALSE 138178.6736 140242.645 120372.1574 152916.8757 165117.7766 155521.3641 130224.5364 142844.869 116130.576 1.189856094 1.207628945 1.036524243 1.316766703 1.42182862 1.339193944 1.121363045 1.230036687 1 16.82538834 0.563519544 1.428536485 5.35E-11 1.240951731 0.304473785 0.109709064 10.1229227 4.289992023 29.40561515 0.033778859 3.660324127 -0.563519544 1.240951731 TLLPWDS(ph)DESPEASPGPPGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLLPWDSDESPEASPGPPGPR 21 0 A0A669KBI7;Q9UMN6 A0A669KBI7 KMT2B Histone-lysine N-methyltransferase 2B 1 TLLPWDS(1)DESPEASPGPPGPR 226 2.72E-25 18792000 9518.3 10835 6981.3 9164.5 13041 10740 11768 13985 12610 TRUE FALSE 8260.432539 10763.82417 10357.48003 11245.4398 12781.50961 11153.17475 10626.74117 10994.41658 11119.26017 0.742894079 0.968034205 0.931490034 1.011347844 1.14949281 1.003050076 0.955705777 0.988772312 1 13.44077318 5.37945831 1.177488252 1.011101592 4.93E-09 0.687876605 0.055710207 3.806803325 1.521679653 0.017371137 6.819894038 239584.2751 -5.37945831 -1.011101587 TLLS(ph)PSSIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLLSPSSIK 9 0 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 TLLS(0.721)PS(0.258)S(0.021)IK 83.775 0.016513 0 244440 169390 142520 192380 189490 167210 209440 248080 321980 TRUE FALSE 212136.6347 168277.2659 211443.1487 236062.8193 185719.5197 173642.6769 189128.541 195030.0226 283915.8912 0.747181265 0.592701117 0.744738689 0.831453352 0.654135698 0.611599006 0.66614285 0.686928871 1 18.11510408 1.238255382 24.97331186 1.000000348 0.689652417 0.65842257 0.069733634 4.597286562 375505.0656 0.09838895 0.017342299 17.30833857 -1.238255382 -0.31034793 TLLSESSSQSSKS(ph)PSLSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLLSESSSQSSKSPSLSSK 19 1 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 TLLSESSSQSS(0.037)KS(0.925)PS(0.037)LSSK;TLLSESSSQSS(0.051)KS(0.946)PS(0.002)LSSK 198.39 4.50E-16 797490000 437440 353450 226458 233150 280470 284590 377630 432740 250460 TRUE FALSE 379631.1957 351128.1637 335973.8463 286090.271 274889.1957 295538.3615 341007.5007 340201.9186 220850.9041 1.71894789 1.589887825 1.521269961 1.295400044 1.244682229 1.338180446 1.544062054 1.540414425 1 17.75271321 4.140681161 2.077189856 1.361190496 1.685617611 0.426302997 0.157208801 0.375258476 3.150759713 0.045660784 0.145771331 13825.51001 -4.140681161 0.324427115 TLLWTELFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLLWTELFR 9 0 O00217;E9PPW7;E9PN51;F8W9K7;E9PKH6 O00217 NDUFS8 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial" 0 123.98 0.0012619 122690000 72101 97972 61313 94059 116960 123380 82715 112810 124830 FALSE TRUE 62572.67017 97328.41548 90964.17188 115416.5336 114632.7248 128126.5084 74693.31203 88686.45939 110072.7396 0.568466547 0.88421907 0.826400544 1.048547842 1.041427017 1.164016712 0.678581384 0.80570775 1 16.74809769 5.063273998 1.561030028 0.929911305 0.112903341 0.406302729 0.139383897 3.14478196 3.749750466 0.041419298 5.012134058 115684.1868 -5.063273998 -0.817007964 TLMAGDSTLSTVTHVIVDEVHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLMAGDSTLSTVTHVIVDEVHER 23 0 Q9H6S0;D6RA70 Q9H6S0 YTHDC2 Probable ATP-dependent RNA helicase YTHDC2 0 178.53 2.97E-17 25232000 28495 28512 17547 19213 28489 28209 25411 28478 29527 FALSE TRUE 24729.31355 28324.70279 26032.78789 23575.6053 27922.12464 29294.21848 22946.64513 22388.20132 26036.3517 0.94979949 1.08789062 0.999863122 0.905488049 1.072428463 1.125127622 0.881331048 0.859882428 1 14.66823969 2.209291119 24.99995893 0.901167592 1.022157425 0.326427078 0.073530926 222.599082 190126.9975 0.030233231 0.02038668 161.9165044 -2.209291119 0.120989833 TLMELLNQMDGFDTLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLMELLNQMDGFDTLHR 17 0 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ;; 164.2 2.62E-09 3152500000 948970 882490 559070 693780 919380 872310 817250 980200 865780 FALSE TRUE 823561.2101 876692.8651 829438.122 851313.3528 901086.1367 905868.3302 737993.2208 770591.8579 763428.4747 1.078766692 1.148362806 1.086464744 1.11511868 1.180315074 1.186579176 0.966682859 1.009383175 1 19.54213347 2.231914156 24.99991371 0.994583101 1.132594676 0.770036423 0.036205987 74.31402883 279520.5862 0.015054798 0.010409369 170.5745194 -2.231914156 0.138011575 TLMLPLTEGS(ph)LR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLMLPLTEGSLR 12 0 Q7L4E1;Q7L4E1-3 Q7L4E1 FAM73B Protein FAM73B 1 TLMLPLT(0.001)EGS(0.999)LR;TLMLPLT(0.001)EGS(0.999)LR;TLMLPLTEGS(1)LR 137.09 0.00010315 55209000 161076 149453 96141 132494 179578 231986 111311 174729 172261 TRUE FALSE 139789.3985 148471.2334 142635.1092 162578.7877 176004.7491 240910.6515 100516.0764 137364.5631 151896.5008 0.920293738 0.977449991 0.939028275 1.07032609 1.158714968 1.586018442 0.661740566 0.904330003 1 17.21272911 TLNAET(ph)PKSS(ph)PLPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLNAETPKSSPLPAK 15 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 2 TLNAET(1)PKS(0.041)S(0.959)PLPAK 135.49 6.57E-05 373240000 1659100 981880 687700 567850 763850 505930 884180 1173700 884110 TRUE FALSE 1439845.731 975429.9656 1020274.02 696789.0215 748650.8794 525393.4545 798432.3597 922713.3887 779591.523 1.846923278 1.25120648 1.308728982 0.893787325 0.960311724 0.673934284 1.024167575 1.183585713 1 19.57235888 5.088156683 0.990258275 0.978524592 2.868906291 0.769883485 0.150349057 1.851646013 0.917738469 0.052228447 4.37860493 122505.8091 -5.088156683 1.890381698 TLNAETPKS(ph)SPLPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLNAETPKSSPLPAK 15 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 TLNAETPKS(0.771)S(0.229)PLPAK 175.33 5.22E-07 758700000 1071500 713380 445060 521640 711160 477060 1092500 1266100 320580 TRUE FALSE 929898.5602 708693.7598 660292.5046 640086.3348 697009.3074 495412.8069 986549.5182 995354.3678 282681.3976 3.289564039 2.507040668 2.335818735 2.264338369 2.465706316 1.752548314 3.48996972 3.521117329 1 18.10881742 2.233366528 24.99988958 2.881753045 2.428088815 0 0.786071881 384.9828289 1852953.186 0.311334333 0.2170386 171.1459112 -2.233366528 -0.45366423 TLNAETPKSS(ph)PLPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLNAETPKSSPLPAK 15 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 TLNAETPKS(0.113)S(0.887)PLPAK 203.89 3.14E-09 623360000 731380 500980 306140 289770 488110 326630 686360 813620 170720 TRUE FALSE 634726.2799 497689.0294 454190.328 355566.7074 478397.566 339195.6675 619796.9128 639633.6946 150537.6761 4.216394835 3.306076209 3.017120629 2.361978188 3.177925808 2.253227739 4.11722121 4.248994081 1 17.19976508 4.716262421 2.711815709 3.042701629 4.410840556 0.153789528 0.936302729 0.933346218 9.571635987 0.241362678 2.800908165 52031.02978 -4.716262421 1.368138927 TLNDELEIIEGMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLNDELEIIEGMK 13 0 P10809;E7EXB4;E7ESH4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 164.68 1.96E-06 11116000 72228 63632 44092 74594 68334 64554 63063 85326 75163 FALSE TRUE 62682.8868 63213.9972 65415.03868 91531.7078 66974.28709 67037.43415 56947.15997 67079.69891 66277.31577 0.945766829 0.953780286 0.986989861 1.381041262 1.010515986 1.011468756 0.859225503 1.012106452 1 16.01622755 -0.349934436 9.462848292 0.51634133 1.017930948 0 0.136532056 0 0 0 0.031472193 0.446751031 0.349934436 0.501589618 TLNDELEIIEGMKFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLNDELEIIEGMKFDR 16 1 P10809;E7EXB4;E7ESH4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 151.62 5.71E-07 89866000 176330 145460 42331 91644 171370 139610 149060 182650 12052 FALSE TRUE 153027.5437 144504.4637 62802.41319 112453.1709 167960.0723 144980.887 134604.1841 143591.7189 10627.22629 14.39957516 13.59757097 5.909577107 10.58161065 15.8046952 13.64240142 12.66597515 13.51168357 1 13.37547748 1.235406628 24.99644032 0.999984146 12.47317581 0.64372075 2.691879293 60.89190114 482504.664 4.784325082 0.689830505 17.19517608 -1.235406628 11.47319166 TLNEWDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLNEWDSR 8 0 O15371-2;O15371;O15371-3 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 123.86 0.0030931 134640000 187460 180830 111820 137780 186540 186070 172560 206950 184300 FALSE TRUE 162686.686 179642.1158 165896.526 169065.0548 182828.219 193228.2333 155825.1578 162695.353 162512.264 1.001073286 1.105406518 1.020824656 1.040321824 1.125011827 1.189007085 0.958851683 1.001126617 1 17.31018907 2.189307553 24.9999982 0.988514683 1.078932676 0.392981965 0.054813745 120.106686 60963.16038 0.022872861 0.015420905 154.6349124 -2.189307553 0.090417993 TLNMTT(ph)SPEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLNMTTSPEEK 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 1 TLNMT(0.003)T(0.499)S(0.499)PEEK;TLNMT(0.002)T(0.517)S(0.481)PEEK 211.82 4.70E-06 428710000 2635800 2141150 1410760 1735740 2242010 1933300 2467200 3042300 2576100 TRUE FALSE 2287472.352 2127084.645 2093008.255 2129866.296 2197398.387 2007675.302 2227931.324 2391727.82 2271556.393 1.007006632 0.936399665 0.921398325 0.937624222 0.967353659 0.883832472 0.980795076 1.052902683 1 21.11524969 1.997622815 24.97123368 1.026215746 0.94117701 0.518096519 0.033554685 60.8398207 639097.4016 0.013262658 0.008771208 99.45412822 -1.997622815 -0.085038736 TLNMTTS(ph)PEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLNMTTSPEEK 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 1 TLNMT(0.034)T(0.258)S(0.708)PEEK;TLNMT(0.004)T(0.205)S(0.792)PEEK;TLNMTT(0.339)S(0.66)PEEK 214.72 1.40E-11 943080000 3063250 2463490 1636870 2000140 2633350 2196480 2978220 3476360 3125090 TRUE FALSE 2658433.751 2447307.172 2428465.807 2454302.357 2580951.487 2280980.007 2689392.683 2732967.467 2755645.42 0.964722722 0.888106704 0.881269335 0.890645197 0.936605076 0.827748008 0.975957452 0.991770366 1 21.39395883 2.074333591 9.245944209 0.991885901 0.898419277 0.596406253 0.035555874 0.193287043 22.15772729 0.013708366 0.009232483 118.6679913 -2.074333591 -0.093466624 TLNPS(ph)PAGWFVQQHPELELMSSFR ddPTM_MDA-MB-175_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(0.008)LNPS(0.992)PAGWFVQQHPELELMSSFR 269.35 3.23E-45 2179066000 390629 525869 435493 602193 843667 885957 854979 968186 732055 TRUE FALSE 339006.3879 522414.5319 646098.8714 738930.1246 826879.6773 920040.3391 772063.2682 761146.9583 645512.2919 0.525174179 0.809302222 1.000908704 1.144718906 1.280966587 1.425287095 1.196047353 1.179136274 1 19.30008504 4.404478151 1.231250969 1.218733406 0.424004842 0.823099994 0.106593918 0.360380139 0.714948717 0.034989166 0.316453367 25379.21301 -4.404478151 -0.794728564 TLPAHSDPVSAVHFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLPAHSDPVSAVHFNR 16 0 P61964 P61964 WDR5 WD repeat-containing protein 5 0 ; 186.08 9.01E-10 410390000 327660 408180 265694 293060 474520 488990 387710 390840 363330 FALSE TRUE 284358.9008 405498.6387 394184.5071 359603.7521 465077.9804 507801.7617 350109.9439 307261.9075 320377.5413 0.88757439 1.265689964 1.230374968 1.122437455 1.451656001 1.585010484 1.092804266 0.959061944 1 18.28941349 2.00926834 24.99707048 0.991404649 1.265675134 0.288925758 0.183305206 238.0160082 641935.7329 0.077305806 0.052043245 102.1570493 -2.00926834 0.274270486 TLPGWNTDISNAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLPGWNTDISNAR 13 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 99.732 0.0030304 0 59253 63647 33160 43327 44983 60419 46232 62839 56709 FALSE TRUE 51422.56592 63228.89867 49196.28691 53165.05756 44087.92631 62743.35803 41748.42776 49401.36886 50004.92662 1.028349993 1.264453384 0.983828799 1.063196392 0.881671653 1.254743528 0.834886292 0.987930034 1 15.60978262 4.208281317 24.89254452 0.997876237 1.146401813 0.191824518 0.124047465 250.4690303 205910.08 0.029347532 0.061103745 16154.04606 -4.208281317 0.148525575 TLPLTGSTFHDQIAMLSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLPLTGSTFHDQIAMLSHR 19 0 P55265-5;P55265;P55265-4 P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 202.39 3.21E-16 1714880000 506860 511970 262012 345980 566620 571290 447350 537110 522710 FALSE TRUE 439877.1668 508606.8354 388721.8796 424540.047 555345.3706 593267.896 403966.0659 422253.2063 460915.8193 0.954354675 1.103470122 0.843368492 0.921079358 1.204873748 1.287150215 0.876442181 0.916117843 1 18.81414376 TLPQQES(ph)LEIELAEEKPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLPQQESLEIELAEEKPVK 19 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 TLPQQES(1)LEIELAEEKPVK 116.65 6.92E-05 125170000 106270 77556 75465 94758 70032 33953 134910 110450 232370 TRUE FALSE 92226.15025 77046.52953 111960.1264 116274.2522 68638.50022 35259.19388 121826.449 86831.12702 204899.4833 0.450104357 0.376021102 0.546414879 0.567469719 0.334986204 0.172080443 0.594566892 0.423774261 1 17.64455682 1.237867723 24.96139925 1.00000066 0.435023017 0.673578125 0.124000854 10.27802992 369987.5987 0.177772604 0.030612112 17.29289572 -1.237867723 -0.564977644 TLPQQES(ph)LEIELAEEKPVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TLPQQESLEIELAEEKPVKR 20 2 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 TLPQQES(1)LEIELAEEKPVKR;TLPQQES(1)LEIELAEEKPVKR;TLPQQES(1)LEIELAEEKPVKR;TLPQQES(1)LEIELAEEKPVKR 220.23 4.52E-25 1400250000 1771390 1229740 664288 1093550 1097330 560261 2171380 1725230 969540 TRUE FALSE 1537296.323 1221661.757 985539.8987 1341857.241 1075495.28 581814.6032 1960799.902 1356302.99 854922.0857 1.798171259 1.42897438 1.152783295 1.569566705 1.258003855 0.680546933 2.293542224 1.586463858 1 19.70543342 2.239255306 24.99999999 1.646078923 1.321521353 0.108756597 0.419497657 41.2565968 1484815.478 0.162085708 0.117955934 173.4823538 -2.239255306 -0.324557571 TLPS(ph)GSPRPGQLERPTSLALDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLPSGSPRPGQLERPTSLALDSR 23 2 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 T(0.031)LPS(0.484)GS(0.484)PRPGQLERPTSLALDSR;T(0.085)LPS(0.483)GS(0.431)PRPGQLERPTSLALDSR 81.341 0.0052448 581550000 378840 401500 217425 259456 392380 414110 346300 402750 280640 TRUE FALSE 328775.3341 398862.5201 322572.4572 318369.4503 384572.4057 430041.0797 312715.8793 316625.0467 247463.0589 1.328583489 1.611806311 1.303517619 1.286533238 1.554059856 1.737799094 1.263687116 1.27948409 1 17.91685365 1.418620678 1.601537758 0.933432775 1.458312942 0.469850999 0.152919628 0.659349295 2.157016208 0.508095492 0.045127348 26.21927495 -1.418620678 0.524880167 TLPSGS(ph)PRPGQLERPTSLALDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLPSGSPRPGQLERPTSLALDSR 23 2 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 T(0.009)LPS(0.153)GS(0.838)PRPGQLERPTSLALDSR;TLPS(0.006)GS(0.994)PRPGQLERPTSLALDSR;T(0.037)LPS(0.2)GS(0.763)PRPGQLERPTSLALDSR 214.19 1.51E-32 2379540000 2142830 2284490 1291360 1495070 2403790 2523660 2017810 2439820 1667350 TRUE FALSE 1859649.586 2269483.035 1915866.015 1834548.494 2355959.282 2620746.833 1822123.097 1918083.48 1470237.782 1.264863146 1.54361632 1.303099429 1.247790334 1.602434184 1.782532638 1.23933905 1.304607665 1 20.48761807 1.304913451 1.585221074 0.879955003 1.443090802 0.37712709 0.175072193 1.056566795 2.728822067 0.910801763 0.051759775 20.17964169 -1.304913451 0.563135799 TLQALEFHTVPFQLLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLQALEFHTVPFQLLAR 17 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 ; 178.14 9.89E-10 1828500000 1554590 1893040 946230 1524760 1994190 2201300 1709610 2145820 1644640 FALSE TRUE 1349146.993 1880604.496 1403829.993 1870980.062 1954509.521 2285985.435 1543812.285 1686953.092 1450212.533 0.930309842 1.296778543 0.968016729 1.290141976 1.347740056 1.576310633 1.064542093 1.163245423 1 20.46783292 4.749796183 23.72184759 1.2127332 0.930309499 0.195497906 0.180438467 1472.365328 3108506.627 0.044931592 0.637351345 56207.74768 -4.749796183 -0.282423701 TLQEQMDELLQQCFLHALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLQEQMDELLQQCFLHALK 19 0 Q5SY38;P41214 Q5SY38 EIF2D Eukaryotic translation initiation factor 2D 0 188.6 1.58E-14 112420000 107330 102120 80896 99095 91600 93830 95987 126980 95177 FALSE TRUE 93146.06856 101449.167 120017.5762 121596.0343 89777.33921 97439.70082 86678.19551 99826.31516 83925.28349 1.109868977 1.208803388 1.430052675 1.448860573 1.069729353 1.161029153 1.032801939 1.189466523 1 16.35681788 3.21603231 24.99968742 1.102148912 1.302258105 0.464319772 0.111033951 226.7321972 251604.2315 0.034855409 0.039550257 1644.494063 -3.21603231 0.200109193 TLQLEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLQLEYR 7 0 Q99829;B0QZ18;F2Z2V0;A6PVH9;E7ENH5;Q5JX45;Q5JX60;Q5JX52;Q5JX44;Q5JX61;Q5JX59;Q5JX58;Q5JX56;Q5JX54;Q5JX55;E7EV27;Q5JX57 Q99829 CPNE1 Copine-1 0 94.302 0.033268 214530000 258800 245780 147250 184220 273780 281040 258530 289280 263410 FALSE TRUE 224598.9243 244165.455 218460.5925 226049.9666 268332.3136 291851.7907 233457.8004 227419.7232 232269.9699 0.96697358 1.051214047 0.940546006 0.973220803 1.155260466 1.25651969 1.005114008 0.979118064 1 17.82544311 4.743019935 22.1809946 1.042624764 0.96697344 0.062267161 0.094871626 349.568592 1738437.495 0.025266194 0.185868442 55337.55095 -4.743019935 -0.075651324 TLQRLS(ph)SGFDDIDLPSAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLQRLSSGFDDIDLPSAVK 19 1 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 T(0.019)LQRLS(0.856)S(0.125)GFDDIDLPSAVK;TLQRLS(0.961)S(0.039)GFDDIDLPSAVK;T(0.047)LQRLS(0.934)S(0.018)GFDDIDLPSAVK 275.29 1.19E-39 2835680000 4668530 5290030 2546470 2897950 5629100 5123130 6807790 8033260 1047210 TRUE FALSE 4051571.932 5255279.445 3777951.409 3555973.84 5517091.923 5320220.126 6147571.574 6315409.864 923410.0268 4.3876196 5.691165671 4.091304296 3.850915343 5.974693541 5.761492698 6.657466776 6.839226 1 19.81661187 7.047138761 16.02248147 5.144863869 4.834933518 0 1.734093762 0 0 0.383274016 0 11146506.17 -7.047138761 -0.309930351 TLQRLSS(ph)GFDDIDLPSAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLQRLSSGFDDIDLPSAVK 19 1 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 TLQRLS(0.248)S(0.752)GFDDIDLPSAVK 197.44 4.77E-16 568780000 578500 632580 322380 353250 715380 671240 826940 891790 168990 TRUE FALSE 502049.7593 628424.5403 478284.0463 433460.8116 701145.3376 697063.0372 746743.4861 701087.6484 149012.1947 3.369185725 4.217269208 3.209697349 2.908894889 4.705288309 4.677892561 5.011291106 4.704901164 1 17.18507088 3.23548148 24.99033895 4.212760031 3.467293463 0.044715607 1.183726196 215.6775605 1750445.27 0.35240259 0.416766393 1719.814001 -3.23548148 -0.745466567 TLQTDSIDSFETQRT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TLQTDSIDSFETQRTPR 17 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFET(0.004)QRT(0.996)PR;TLQTDSIDSFET(0.004)QRT(0.996)PR;TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFETQRT(1)PR 278.98 1.21E-35 8385680000 6928370 7286290 3733660 4597760 7436240 7833060 7198030 8129420 4155480 TRUE FALSE 6012768.35 7238425.881 5539270.464 5641751.68 7288273.373 8134402.887 6499966.158 6391006.796 3664223.888 1.640939127 1.975432207 1.511717251 1.539685306 1.98903604 2.219952474 1.773899837 1.744163837 1 21.80507623 1.221960763 3.704622441 0.876515732 1.81164002 0.575909271 0.216074101 0.235987769 4.970657547 0.630043198 0.057850005 16.67096589 -1.221960763 0.935124288 TLQVVPPSDPDPLLASWHGGTGTS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TLQVVPPSDPDPLLASWHGGTGTSPPR 27 0 C9J069 C9J069 C9orf172 Uncharacterized protein C9orf172 1 TLQVVPPSDPDPLLASWHGGT(0.001)GT(0.252)S(0.748)PPR;TLQVVPPSDPDPLLASWHGGT(0.005)GT(0.253)S(0.742)PPR;TLQVVPPSDPDPLLASWHGGT(0.012)GT(0.05)S(0.938)PPR;TLQVVPPSDPDPLLASWHGGT(0.008)GT(0.06)S(0.931)PPR 187.79 5.97E-18 527800000 554250 563000 185438 413958 686520 764480 648430 708510 700320 TRUE FALSE 481004.4582 559301.6159 275116.4371 507953.4909 672859.5952 793890.0403 585545.3584 557000.6501 617528.9674 0.778918049 0.905709117 0.445511792 0.822558159 1.089600052 1.285591579 0.948207111 0.901983032 1 19.23614729 3.391301059 5.087421166 1.030174497 0.715259187 0.511315193 0.151647452 0.184989265 8.167617792 0.046679065 0.060924342 2462.073758 -3.391301059 -0.314915311 TLRDPSLPLLELQDIMTSVSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLRDPSLPLLELQDIMTSVSGR 22 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 142.41 1.05E-07 85835000 98964 109480 68425 107890 101460 153110 112950 152490 160710 FALSE TRUE 85885.65666 108760.8187 101515.5589 132388.0735 99441.1445 159000.2408 101996.1264 119881.2002 141711.0469 0.606061832 0.767482995 0.716356001 0.934211386 0.701717662 1.122003148 0.71974718 0.845955222 1 17.1125927 5.665445942 0.541666913 0.88867685 7.38E-11 0.346531733 0.126533347 12.85090431 1.38817448 0.069901804 8.936186599 462856.0467 -5.665445942 -0.888676849 TLRDS(ph)PNVEAAHLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TLRDSPNVEAAHLAR 15 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 T(0.256)LRDS(0.744)PNVEAAHLAR;T(0.026)LRDS(0.974)PNVEAAHLAR;T(0.077)LRDS(0.923)PNVEAAHLAR;TLRDS(1)PNVEAAHLAR;T(0.351)LRDS(0.649)PNVEAAHLAR 216.04 1.36E-12 4432810000 1734850 1629290 1030260 1294600 1626030 1775210 1812370 1927600 1521260 TRUE FALSE 1505585.177 1618587.087 1528497.182 1588558.717 1593675.184 1843503.477 1636606.636 1515397.741 1341418.376 1.122382997 1.206623613 1.139463429 1.184238076 1.188052298 1.374294188 1.220056819 1.129698063 1 20.35532784 1.366988525 2.61072449 0.983341662 1.206738761 0.485225349 0.067518016 0.34399591 3.271304564 0.150068467 0.018779439 23.28029748 -1.366988525 0.223397099 TLS(ph)DESICSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLSDESICSNR 11 0 Q9P2F8;Q9P2F8-2 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 TLS(1)DESICSNR;TLS(1)DESICSNR;TLS(0.999)DES(0.001)ICSNR 293.41 1.71E-35 1331930000 1031180 1017580 695849 801580 1177130 1105700 1136160 1196150 1296000 TRUE FALSE 894906.9503 1010895.45 1032363.904 983590.9904 1153707.416 1148236.994 1025975.378 940362.6309 1142788.356 0.783090714 0.88458676 0.903372788 0.86069392 1.009554752 1.004767845 0.897782492 0.822866829 1 20.12412681 5.445807773 0.998863209 0.924300688 0.390684872 0.362195016 0.061804141 9.048422653 2.633367093 0.021173311 7.265130603 279130.8082 -5.445807773 -0.533615816 TLS(ph)DESIYNSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TLSDESIYNSQR 12 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 TLS(1)DESIYNSQR;TLS(1)DESIYNSQR;TLS(1)DESIYNSQR;TLS(1)DESIYNSQR;T(0.001)LS(0.999)DESIYNSQR 340.11 1.37E-58 3140170000 1638371 1503850 986583 1204114 1642570 1527276 1556862 1774120 1560940 TRUE FALSE 1421856.121 1493971.11 1463697.839 1477526.487 1609886.071 1586031.296 1405877.763 1394738.244 1376407.451 1.033019779 1.085413414 1.063419002 1.073465917 1.169629 1.152297813 1.021411037 1.013317853 1 20.39247618 2.110775161 7.828773439 1.010594022 1.096396182 0.500937475 0.039960366 0.207288956 13.49309696 0.017775824 0.011959336 129.0550969 -2.110775161 0.085802161 TLS(ph)DESLCSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TLSDESLCSGR 11 0 O60292;M0R2Q7 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 TLS(1)DESLCSGR;TLS(0.999)DESLCSGR;TLS(1)DESLCSGR;T(0.001)LS(0.999)DESLCSGR;TLS(1)DESLCSGR 293.41 1.71E-35 2730800000 1842560 1434520 980560 1089310 1638330 1416840 1509530 1735130 1491800 TRUE FALSE 1599061.028 1425096.544 1454762.096 1336654.485 1605730.438 1471346.752 1363136.013 1364085.952 1315441.103 1.215608227 1.083360205 1.105911996 1.016126439 1.220678322 1.118519672 1.036257731 1.036979876 1 20.32711523 2.223218943 4.953289886 1.026117346 1.12345075 0.394449949 0.059806492 0.198954997 12.89437673 0.024047668 0.016728272 167.1933282 -2.223218943 0.097333404 TLS(ph)FGSDLNYATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLSFGSDLNYATR 13 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 T(0.002)LS(0.997)FGSDLNYATR 99.927 0.0027652 52746000 53426 44709 34537 36164 43167 47833 43296 52771 55054 TRUE FALSE 46365.61874 44415.30364 51239.20872 44375.58893 42308.06115 49673.16646 39097.16058 41486.33231 48545.57884 0.95509457 0.914919642 1.055486616 0.914101551 0.871512137 1.023227401 0.80537016 0.854585182 1 15.56705229 3.503080015 24.52404598 0.900792895 0.971750868 0.137654452 0.072609433 1045.580183 987788.8981 0.019886629 0.02936914 3184.784235 -3.503080015 0.070957973 TLS(ph)INEEEPEGGFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLSINEEEPEGGFSK 15 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2 E9PP16 PPFIBP2 Liprin-beta-2 1 T(0.001)LS(0.999)INEEEPEGGFSK;TLS(1)INEEEPEGGFSK;T(0.001)LS(0.999)INEEEPEGGFSK 307.02 2.93E-45 944840000 1489750 885570 544030 779810 1045900 701330 1429490 1325880 1173640 TRUE FALSE 1292875.763 879752.6324 807124.7277 956877.7791 1025088.636 728310.6189 1290858.28 1042350.88 1034893.616 1.249283736 0.850089921 0.779910819 0.924614631 0.990525616 0.703754094 1.247334276 1.007205826 1 19.98105104 2.231001364 24.99997681 1.075441768 0.910894425 0.200442272 0.158005797 278.5872519 921334.9138 0.061350803 0.042266184 170.2163854 -2.231001364 -0.164547343 TLS(ph)MDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLSMDK 6 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 1 T(0.001)LS(0.999)MDK 109.11 0.031299 289720000 440280 291300 212330 368500 275020 164490 495340 415210 840240 TRUE FALSE 382095.8825 289386.4311 315013.4982 452173.5572 269547.6401 170818.0367 447302.003 326420.5727 740907.7844 0.515713143 0.390583602 0.425172342 0.610296675 0.363807272 0.230552358 0.603721559 0.440568421 1 19.49893447 1.238108414 24.99143079 1.000000626 0.447752882 0.705182184 0.112258667 6.036253339 333225.4522 0.153701159 0.026883408 17.3024823 -1.238108414 -0.552247744 TLS(ph)MDKGF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 TLSMDKGF 8 1 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 1 TLS(1)MDKGF;TLS(1)MDKGF;TLS(1)MDKGF;TLS(1)MDKGF;T(0.002)LS(0.998)MDKGF;TLS(1)MDKGF;TLS(1)MDKGF 113.93 0.0072465 2537700000 8114130 5362460 2544810 4523620 5762160 2821390 9544170 7711990 4186520 TRUE FALSE 7041827.162 5327233.647 3775488.628 5550777.06 5647504.289 2929930.699 8618577.862 6062840.953 3691594.375 1.907530039 1.443071233 1.022725751 1.503625939 1.529827959 0.793676228 2.334649202 1.642336708 1 21.81581261 2.247149445 24.99940091 1.683677061 1.368210278 0.091230578 0.432469083 427.2928653 1243718.955 0.160396571 0.12222778 176.6645636 -2.247149445 -0.315466783 TLS(ph)MIEEEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 122.33 0.00051558 33888000 118410 119800 77977 89402 143260 130830 126000 149880 125160 TRUE FALSE 102761.8185 119013.0259 115686.938 109702.0905 140409.4063 135863.1148 113780.5394 117829.3284 110363.7274 0.931119498 1.078370845 1.048233335 0.994004943 1.272242336 1.231048624 1.030959556 1.067645423 1 16.75190656 5.778848957 0.973601194 1.099848389 2.85E-13 0.23361216 0.091729822 21.23111729 3.428935316 0.030899009 39.31653621 600964.6925 -5.778848957 -1.099848389 TLS(ph)PEFNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLSPEFNER 9 0 Q9BSJ8-2;Q9BSJ8 Q9BSJ8-2 ESYT1 Extended synaptotagmin-1 1 T(0.004)LS(0.996)PEFNER;TLS(1)PEFNER 120.57 0.00067445 422200000 550790 435150 352620 429810 571090 544900 482630 651540 622270 TRUE FALSE 478001.706 432291.471 523148.2114 527404.9297 559726.4263 565862.6556 435824.6169 512213.2413 548705.9495 0.871143654 0.787838133 0.953421795 0.961179536 1.020084486 1.031267578 0.794277185 0.933493143 1 19.06567369 4.226888938 24.76673818 0.950673285 0.8294909 0.370532373 0.068385529 197.3188105 418703.8281 0.018319048 0.038649393 16861.21779 -4.226888938 -0.121182385 TLS(ph)PGRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLSPGRR 7 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 T(0.002)LS(0.998)PGRR;T(0.003)LS(0.997)PGRR;T(0.007)LS(0.993)PGRR 75.387 0.02671 1184590000 1216170 1043710 640906 815150 969030 1130260 1028290 1182300 907690 TRUE FALSE 1055450.053 1036853.8 950850.2853 1000242.266 949748.1989 1173741.834 928566.5941 929474.3457 800383.9222 1.318679728 1.295445562 1.187992736 1.249703097 1.186615788 1.466473527 1.160151483 1.161285628 1 19.61033266 1.433378791 1.625620925 0.96406936 1.272115284 0.516254225 0.084990809 0.556724988 1.940836525 0.252915019 0.023997111 27.1255649 -1.433378791 0.308045924 TLS(ph)PTPSAEGYQDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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(0.999)PT(0.001)PSAEGYQDVR;TLS(1)PTPSAEGYQDVR;TLS(1)PTPSAEGYQDVR;TLS(1)PTPSAEGYQDVR;TLS(1)PTPSAEGYQDVR;TLS(1)PTPSAEGYQDVR;TLS(1)PTPSAEGYQDVR;TLS(1)PTPSAEGYQDVR 351.8 2.27E-82 22570070000 2411153 2738066 1648811 2190718 2933510 2929597 2589135 3094849 2792469 TRUE FALSE 2092513.022 2720079.464 2446181.515 2688154.005 2875138.89 3042300.492 2338041.086 2433039.625 2462346.496 0.849804455 1.104669659 0.993435131 1.091704197 1.167641879 1.235528995 0.949517499 0.988097991 1 21.23160236 4.745888168 24.37078261 1.061706797 0.849804311 0.370029406 0.088603674 793.8265679 2640102.255 0.023548935 0.234380463 55704.22908 -4.745888168 -0.211902487 TLS(ph)SSAQEDIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLSSSAQEDIIR 12 0 Q9H788-2;Q9H788 Q9H788-2 SH2D4A SH2 domain-containing protein 4A 1 TLS(0.333)S(0.333)S(0.333)AQEDIIR;TLS(0.69)S(0.283)S(0.028)AQEDIIR;TLS(0.85)S(0.138)S(0.012)AQEDIIR 231.36 3.80E-12 1762620000 1027070 985680 448767 859160 1048930 612150 1231530 1229860 1131360 TRUE FALSE 891340.0972 979205.0032 665792.2222 1054245.409 1028058.345 635699.8066 1112096.41 966864.0098 997611.9096 0.893473793 0.981549031 0.667386 1.056769069 1.030519318 0.637221549 1.114758554 0.969178496 1 19.92811916 TLSALRS(ph)PDVGLYGVIPECGETYHSDLAEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLSALRSPDVGLYGVIPECGETYHSDLAEAK 31 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 1 T(0.001)LS(0.001)ALRS(0.998)PDVGLYGVIPECGETYHSDLAEAK;TLS(0.003)ALRS(0.996)PDVGLYGVIPECGETYHSDLAEAK 289.21 2.26E-81 294450000 222110 188198 106669 121594 163815 150782 215900 258290 132308 TRUE FALSE 192757.6007 186961.7149 158254.4852 149203.7761 160555.402 156582.6811 194962.0512 203056.6935 116666.699 1.652207549 1.602528542 1.35646664 1.278889156 1.376188779 1.342136895 1.671102834 1.740485463 1 16.8320333 4.35245544 5.90640383 1.434377501 1.638875477 0.162442644 0.205759001 0.434200179 20.31450029 0.054710111 0.149175092 22514.14403 -4.35245544 0.204497976 TLSASTQDLS(ph)PH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLSASTQDLSPH 12 0 Q6P597;Q6P597-3;Q6P597-2 Q6P597 KLC3 Kinesin light chain 3 1 TLSASTQDLS(1)PH;TLSASTQDLS(1)PH;TLSASTQDLS(1)PH 239.98 3.60E-16 804740000 1595940 1849030 1084910 1487950 2119790 2117600 1957850 2121400 2085600 TRUE FALSE 1385032.485 1836883.6 1609576.105 1825811.789 2077610.326 2199065.442 1767978.008 1667755.119 1839042.744 0.753126859 0.998825942 0.875224956 0.992805521 1.129723783 1.195766357 0.961357758 0.906860444 1 20.81052358 5.504632216 0.977743725 1.016464455 1.40E-18 0.42751566 0.0937025 8.955675854 2.310308008 0.033314346 13.71937307 319618.7259 -5.504632216 -1.016464455 TLSDDLDEAAKEFQEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLSDDLDEAAKEFQEK 16 1 Q9H0A0;Q9H0A0-2;A0A087WV29 Q9H0A0 NAT10 N-acetyltransferase 10 0 126.88 6.32E-05 18534000 46803 33755 25408 29285 32730 26487 46997 61881 10606 FALSE TRUE 40617.86497 33533.26118 37695.39378 35934.60684 32078.73704 27505.97203 42439.23817 48648.22971 9352.170762 4.343148345 3.585612585 4.030657132 3.842381385 3.430084614 2.941132356 4.537902403 5.201811531 1 13.19108556 3.47066801 23.07343985 3.69808064 3.944742238 0.02185199 1.114850354 500.8825692 1790868.655 0.326886611 0.423490916 2955.752125 -3.47066801 0.246661598 TLSDPPS(ph)PLPHGPPNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLSDPPSPLPHGPPNK 16 0 H0YBF7;A0A0A0MRE5;Q9ULH1;Q9ULH1-2 H0YBF7 ASAP1 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1" 1 T(0.002)LS(0.002)DPPS(0.996)PLPHGPPNK 96.143 0.0022629 348980000 831260 776880 513570 639630 810510 669820 878330 1072000 981190 TRUE FALSE 721406.8849 771776.6241 761934.1698 784867.7676 794382.4367 695588.4088 793149.6918 842761.1423 865194.836 0.833808588 0.892026388 0.88065039 0.907157249 0.91815439 0.803967361 0.916729572 0.974070934 1 19.72266553 1.786830463 2.929672267 0.992011378 0.876780272 0.647772023 0.034327998 0.14639743 2.408409052 0.024252843 0.00925622 61.21113931 -1.786830463 -0.115231106 TLSDVEDQKELASPVS(ph)PELR ddPTM_MDA-MB-175_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 TLSDVEDQKELASPVS(1)PELR;TLSDVEDQKELAS(0.001)PVS(0.999)PELR 252.04 2.76E-36 384800000 440840 392430 287650 257350 424870 358560 477700 542550 320660 TRUE FALSE 382581.8771 389852.1015 426758.5021 315785.2508 416415.9182 372354.0352 431372.7275 426529.9046 282751.9401 1.353065436 1.378777813 1.509303533 1.116827884 1.472725238 1.316892945 1.52562252 1.508495059 1 18.1091774 TLSFSHDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLSFSHDGK 9 0 Q96J01;D6REC9;Q96J01-2;H7C0C5 Q96J01 THOC3 THO complex subunit 3 0 ;; 155.84 7.23E-05 518790000 1546450 1337060 471370 933770 1416800 1217180 1501350 1808840 1549790 FALSE TRUE 1342082.714 1328276.765 699326.1086 1145796.75 1388608.452 1264005.702 1355749.308 1422033.642 1366575.592 0.982077188 0.971974601 0.511736133 0.83844374 1.016122679 0.92494386 0.992077801 1.040581766 1 20.38213383 3.281462498 6.155460164 0.996867609 0.812169869 0.291467615 0.130186198 0.240887997 22.47820823 0.039123619 0.049904957 1911.888224 -3.281462498 -0.184697739 TLSKEEETKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLSKEEETKK 10 2 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ; 95.401 0.0041887 1915320000 2932400 1842850 1369940 1161760 1350300 947240 2883200 3120000 713730 FALSE TRUE 2544875.91 1830744.197 2032447.566 1425555.364 1323431.672 983680.9357 2603587.708 2452812.28 629353.6525 4.043634132 2.90892758 3.229420467 2.265110179 2.102842601 1.56300187 4.136923171 3.897351307 1 19.26351141 5.115618172 1.388468582 2.719588814 5.946843539 0.171941779 0.972367081 7.007939202 6.053913643 0.289586344 40.70144986 130502.302 -5.115618172 3.227254725 TLSNAEDYLDDEDS(ph)D ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLSNAEDYLDDEDSD 15 0 Q92882 Q92882 OSTF1 Osteoclast-stimulating factor 1 1 TLSNAEDYLDDEDS(1)D;TLSNAEDYLDDEDS(1)D;TLSNAEDYLDDEDS(1)D 380.61 2.51E-98 209236000 1240910 1094610 542200 572100 702880 781640 667090 771950 729080 TRUE FALSE 1076920.599 1087419.435 804409.7336 702004.049 688894.0632 811710.1966 602395.7145 606874.4998 642888.993 1.675126828 1.69145754 1.251242038 1.091952198 1.071559897 1.262597751 0.937013576 0.943980231 1 19.29421012 4.103526382 2.133021208 1.039344698 1.717364253 0.881831444 0.09413918 0.107654944 0.961407843 0.028847013 0.085517861 12691.89241 -4.103526382 0.678019555 TLSS(ph)PSNRPSGETSVPPPPAVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLSSPSNRPSGETSVPPPPAVGR 23 1 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3 Q8WWM7 ATXN2L Ataxin-2-like protein 1 TLS(0.018)S(0.967)PS(0.015)NRPSGETSVPPPPAVGR;TLS(0.042)S(0.94)PS(0.018)NRPSGETSVPPPPAVGR;TLS(0.031)S(0.966)PS(0.003)NRPSGETSVPPPPAVGR 203.78 1.12E-24 2234420000 727060 665360 406070 468370 628870 674340 597130 668910 637440 TRUE FALSE 630977.1789 660989.2063 602446.8102 574720.5671 616356.7174 700282.2962 539220.4245 525868.802 562082.5694 1.122570265 1.175964604 1.071811942 1.022484237 1.096559031 1.245870864 0.959326003 0.935572157 1 19.10042255 2.196411835 23.76961746 0.958606751 1.116936441 0.593816886 0.061243904 59.99667931 33834.13659 0.025763827 0.017370212 157.1852662 -2.196411835 0.15832969 TLSS(ph)SAQEDIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLSSSAQEDIIR 12 0 Q9H788-2;Q9H788 Q9H788-2 SH2D4A SH2 domain-containing protein 4A 1 TLS(0.274)S(0.684)S(0.042)AQEDIIR 286.78 1.38E-28 721880000 443130 411250 169460 388050 416170 239390 536300 504730 452400 TRUE FALSE 384569.2478 408548.4717 251411.4228 476162.6835 407889.0312 248599.4882 484289.7085 396797.4173 398917.7874 0.964031337 1.024142028 0.630233674 1.193636129 1.022488954 0.623184767 1.214008811 0.994684694 1 18.60573193 TLSSFFT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TLSSFFTPR 9 0 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135 P18858 LIG1 DNA ligase 1;DNA ligase 1 TLSSFFT(1)PR;TLSSFFT(1)PR;TLSSFFT(1)PR;TLSSFFT(1)PR 143.22 0.0011455 504928000 707758 936320 425824 527092 723430 804970 588067 766120 830830 TRUE FALSE 614225.9871 930169.2523 631753.9107 646776.2947 709035.1584 835937.7168 531036.3529 602291.2 732610.2239 0.83840761 1.26966458 0.862332916 0.882838205 0.967820452 1.141040201 0.724855231 0.822116837 1 19.48268631 2.230942249 24.99998416 0.838219689 0.994044006 0.178206905 0.145862663 274.4531901 900620.1256 0.057108993 0.039331702 170.1932178 -2.230942249 0.155824317 TLSSS(ph)SMDLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 TLSSSSMDLSR 11 0 Q9H0B6;Q9H0B6-2 Q9H0B6 KLC2 Kinesin light chain 2 1 TLSS(0.062)S(0.909)S(0.029)MDLSR;TLSS(0.046)S(0.908)S(0.046)MDLSR;TLSS(0.261)S(0.738)SMDLSR;TLS(0.003)S(0.159)S(0.838)SMDLSR;TLSS(0.029)S(0.971)SMDLSR;TLS(0.081)S(0.235)S(0.682)S(0.002)MDLSR;TLS(0.003)S(0.031)S(0.962)S(0.004)MDLSR;TLSS(0.005)S(0.955)S(0.039)MDLSR;TLSS(0.026)S(0.934)S(0.04)MDLSR;TLSS(0.01)S(0.949)S(0.042)MDLSR 287.96 3.10E-28 7565460000 6972860 8151660 3966620 3800650 5870560 6621750 6714450 6106390 7923590 TRUE FALSE 6051378.884 8098111.209 5884890.7 4663645.672 5753747.342 6876493.007 6063283.672 4800586.018 6986872.217 0.866106993 1.159046703 0.842278278 0.667486899 0.823508311 0.984201914 0.867810872 0.687086563 1 22.73621532 4.103985435 9.610022655 0.824184887 1.011917784 0.240064575 0.126795284 0.360190276 30.53231036 0.031763604 0.066322589 12705.31496 -4.103985435 0.187732897 TLSVAAAFNEDEDS(ph)EPEEMPPEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 TLSVAAAFNEDEDSEPEEMPPEAK 24 0 Q8WW12 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 1 TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK 184.75 8.45E-17 911996000 1213044 950791 698263 779453 953517 832515 1141838 1355750 1208020 TRUE FALSE 1052737.162 944545.1913 1035945.322 956439.7168 934543.8772 864542.3908 1031102.727 1065833.413 1065209.252 0.988291418 0.88672267 0.97252753 0.897889044 0.877333609 0.811617426 0.967981385 1.000585952 1 20.02270543 2.014403657 24.99870656 0.995519502 0.90488402 0.406846908 0.048779127 218.0505469 378442.8226 0.020129084 0.013565157 103.3721757 -2.014403657 -0.090635482 EVVQGSSAS(ph)AASSPTWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 EVVQGSSASAASSPTWK 17 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 EVVQGS(0.001)SAS(0.658)AAS(0.066)S(0.273)PT(0.002)WK 226.72 2.08E-15 180570000 98583 134970 101860 144570 179710 150500 200130 241030 215290 TRUE FALSE 85555.00677 134083.3732 151119.8367 177396.8281 176134.1226 156289.8324 180721.4234 189487.6102 189838.6615 0.450672198 0.70630172 0.796043522 0.934461014 0.927809548 0.823277151 0.951973755 0.998150792 1 17.53441431 4.977483013 0.772114895 0.955929332 7.77E-13 0.913219856 0.049230317 1.066091065 0.383195532 0.020691717 0.955372492 94947.38616 -4.977483013 -0.955929332 down TLT(ph)PPLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TLTPPLRR 8 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 T(0.368)LT(0.632)PPLRR;T(0.32)LT(0.68)PPLRR;T(0.174)LT(0.826)PPLRR;T(0.018)LT(0.982)PPLRR;T(0.018)LT(0.982)PPLRR 121.5 0.00083827 3341720000 2313770 2002010 1205200 1334730 2480150 2133760 2019820 2369960 1717080 TRUE FALSE 2007999.432 1988858.664 1788038.751 1637800.847 2430799.867 2215847.128 1823938.167 1863162.497 1514088.759 1.326209855 1.313568081 1.180933906 1.081707289 1.605454009 1.463485622 1.204644151 1.23055038 1 20.53001835 1.164689438 1.554594515 0.834359842 1.316038769 0.316629066 0.145046571 1.824539299 3.423183406 1.441943293 0.043856498 14.61131952 -1.164689438 0.481678927 TLTAVHDAILEDLVFPSEIVGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLTAVHDAILEDLVFPSEIVGK 22 0 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ; 169.39 8.34E-12 3432800000 2169090 1944560 1285940 1703540 2018550 1843980 2322400 2740000 2531200 FALSE TRUE 1882439.261 1931786.057 1907824.885 2090354.794 1978384.804 1914919.104 2097174.005 2154072.323 2231964.42 0.84340021 0.865509343 0.854773879 0.936553816 0.88638725 0.857952343 0.939609067 0.965101551 1 21.0898826 -2 0.329135478 2.468174476 0.853124212 0.746131016 0.026695928 38.6097693 0.612057931 37.29216583 0.043015112 0.01 2 -1.615050263 TLTDEELADWKR ddPTM_MDA-MB-175_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 ; 91.123 0.013589 334950000 290940 332720 159872 329190 255730 259160 315590 375360 256710 FALSE TRUE 252491.5419 330534.3404 237186.6339 403937.6209 250641.4733 269130.0529 284984.1304 295092.1851 226362.0362 1.115432367 1.460202187 1.047819846 1.784475999 1.107259316 1.188936349 1.258974937 1.30362931 1 17.78827249 TLTDEVNS(ph)PDSDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TLTDEVNSPDSDRR 14 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 TLTDEVNS(0.596)PDS(0.404)DRR;TLTDEVNS(1)PDSDRR;TLTDEVNS(1)PDSDRR;TLTDEVNS(1)PDSDRR;TLTDEVNS(0.967)PDS(0.033)DRR 221.79 2.53E-12 3785670000 2586610 2351200 1381670 1743880 2372800 2320360 2195830 2482950 2192920 TRUE FALSE 2244782.935 2335754.812 2049850.233 2139854.608 2325585.922 2409625.751 1982878.745 1951990.465 1933675.496 1.160889167 1.20793526 1.060079749 1.106625498 1.20267642 1.246137605 1.025445453 1.009471584 1 20.88291428 2.133088944 7.546874834 1.00938341 1.160222028 0.654949499 0.052198065 0.149130789 9.577722764 0.022793961 0.015335218 135.8591659 -2.133088944 0.150838618 TLTDEVNSPDS(ph)DRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLTDEVNSPDSDRR 14 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 TLTDEVNS(0.037)PDS(0.963)DRR 235.64 3.23E-17 681880000 885360 865710 450600 579890 822850 847340 803400 882110 767360 TRUE FALSE 768357.4328 860023.094 668511.6672 711562.8876 806476.8949 879937.7181 725486.3917 693477.6411 676643.575 1.135542346 1.271013464 0.987981992 1.051606657 1.191878449 1.300444947 1.072183966 1.024878779 1 19.36803656 2.009355074 24.9431775 1.024510894 1.153771383 0.302844004 0.09163209 251.5896924 670804.3676 0.03933226 0.026478325 102.1774532 -2.009355074 0.12926049 TLTDEVNSPDSDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLTDEVNSPDSDRR 14 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 0 123.76 0.00016199 476920000 216120 179180 86878 145010 181120 171060 200900 204240 202410 FALSE TRUE 187559.1944 178002.9548 128892.4914 177936.7368 177516.0664 177640.7889 181416.7489 160564.8654 178481.3204 1.05086176 0.9973198 0.722162359 0.996948792 0.994591848 0.995290647 1.016446699 0.899617198 1 17.44541357 TLTGDVKTS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLTGDVKTSPPR 12 1 Q9H8T0;Q9H8T0-2;H3BSX7;H3BNB8;H3BVH0;H3BRV2;H3BM79 Q9H8T0 AKTIP AKT-interacting protein 1 TLTGDVKT(0.026)S(0.974)PPR;TLTGDVKT(0.355)S(0.645)PPR 124.78 0.00019197 705340000 2429400 1881050 1032370 1067220 1950500 1630250 2275200 2507100 530270 TRUE FALSE 2108348.635 1868693.259 1531627.585 1309548.612 1911688.866 1692966.772 2054551.454 1970976.175 467582.0847 4.509044944 3.996503117 3.275633595 2.800681753 4.088456185 3.620683572 4.393990962 4.215251696 1 18.83486013 4.487208015 3.603974748 3.495616961 4.454589423 0.127964475 0.96985992 0.540731564 14.48654832 0.241991867 0.990424469 30704.92318 -4.487208015 0.958972462 TLTPDQWAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TLTPDQWAR 9 0 Q9H3K6;A0A087WZT3 Q9H3K6 BOLA2 BolA-like protein 2 0 ;;;;; 160.26 0.00015221 2013090000 3669720 4134080 2424850 2864190 4016030 4358350 3824550 4364780 4086480 FALSE TRUE 3184757.204 4106922.956 3597515.571 3514548.116 3936118.86 4526018.545 3453645.73 3431405.764 3603380.99 0.883824723 1.139741528 0.998372246 0.975347355 1.092340463 1.256047739 0.958445898 0.952273926 1 21.78091977 TLTPGGHAEHDGKPFCHKPCYATLFGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLTPGGHAEHDGKPFCHKPCYATLFGPK 28 2 P52943;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 75.71 0.0027562 631080000 601800 379810 105260 310750 381750 274680 516630 653830 599200 FALSE TRUE 522270.6052 377315.0031 156164.0881 381310.537 374153.9219 285247.1173 466527.3021 514013.5426 528363.2586 0.988468817 0.714120441 0.295561975 0.721682537 0.708137661 0.539869328 0.882966964 0.972841193 1 19.01117062 2.082871949 4.9989106 0.969522122 0.652765153 0.395551398 0.172023342 0.202613463 8.869719375 0.074527622 0.04869667 121.0241244 -2.082871949 -0.316756969 TLTPGGHAEHDGQPYCHKPCYGILFGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLTPGGHAEHDGQPYCHKPCYGILFGPK 28 1 P52943;H0YFA4;H0YHD8;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 ; 86.732 0.0012126 1414670000 1926690 1560030 555050 1127100 1672220 1363930 1910800 2216980 1976620 FALSE TRUE 1672073.035 1549782.06 823474.0365 1383025.282 1638946.094 1416401.27 1725490.91 1742896.08 1742946.235 0.959337128 0.889173762 0.472460951 0.793498533 0.940330838 0.812647712 0.989985161 0.999971224 1 20.73309664 2.456885106 1.149507171 1.013239404 0.77909807 0.29268624 0.13403051 0.645032253 1.762435373 0.106224347 0.057866196 286.3420342 -2.456885106 -0.234141333 TLTPIIQEYFEHGDTNEVAEMLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLTPIIQEYFEHGDTNEVAEMLR 23 0 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 0 ; 322.08 1.01E-73 294340000 191258 217040 96429 137012 205470 181997 162436 240170 160864 FALSE TRUE 165982.7707 215614.2499 143062.3869 168122.6687 201381.549 188998.5424 146682.9817 188811.5145 141846.8412 1.170154861 1.520049711 1.008569424 1.185240837 1.419711199 1.332412769 1.034094101 1.331094249 1 17.1139745 1.226825014 24.66514943 0.999999334 1.250554618 0.194368484 0.160059354 769.0509098 1616219.303 0.583442355 0.037221392 16.85873617 -1.226825014 0.250555284 TLTSGGHAEHEGKPYCNHPCYAAMFGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLTSGGHAEHEGKPYCNHPCYAAMFGPK 28 1 P50238;K4DIB9;H3BRQ4 P50238 CRIP1 Cysteine-rich protein 1 0 ; 120.57 3.43E-05 2533710000 1590970 1159800 407760 861160 1183970 984880 1194660 1645570 1611670 FALSE TRUE 1380719.283 1152181.197 604954.0999 1056699.54 1160411.313 1022768.971 1078802.057 1293677.661 1421140.209 0.971557398 0.810744211 0.425682207 0.743557556 0.816535417 0.71968196 0.75911022 0.910309661 1 20.43861747 1.60443867 2.224414933 1.002556178 0.737739704 0.295883205 0.135074271 0.396059875 3.985945095 0.174466649 0.038709966 40.21968547 -1.60443867 -0.264816473 TLTTGSSAYLWKPPS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLTTGSSAYLWKPPSR 16 1 Q9BQS8;Q9BQS8-4;Q9BQS8-3;Q9BQS8-2 Q9BQS8 FYCO1 FYVE and coiled-coil domain-containing protein 1 1 TLTTGSSAYLWKPPS(1)R 184.6 1.09E-09 1774800000 1148000 902100 648540 636280 1012400 877180 997060 1131900 1136200 TRUE FALSE 996288.8913 896174.0457 962176.1132 780757.0989 992255.2207 910925.6822 900365.2747 889851.9935 1001879.73 0.994419651 0.894492641 0.960370875 0.77929224 0.990393548 0.9092166 0.898676006 0.88818245 1 19.9342779 4.746194392 23.75215359 0.911550515 0.994419731 0.13597599 0.062292726 892.8873242 2778042.573 0.013967358 0.140136204 55743.52029 -4.746194392 0.082869216 TLTVLGAQPDLLSYEDLELAVGHLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLTVLGAQPDLLSYEDLELAVGHLYR 26 0 Q96T76-5;Q96T76;Q96T76-8;Q96T76-9;H0Y746 Q96T76-5 MMS19 MMS19 nucleotide excision repair protein homolog 0 127.38 9.60E-05 102530000 65340 57794 27761 42833 52322 59731 55838 62499 65626 FALSE TRUE 56705.15345 57414.34741 41186.31245 52558.88731 51280.89457 62028.89022 50422.83935 49134.07522 57867.76904 0.979909099 0.992164522 0.711731472 0.9082584 0.886173692 1.071907406 0.871345832 0.849074987 1 15.8204724 TLVGICSEHQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLVGICSEHQSR 12 0 Q9H3U1;A0A1W2PNX8;Q9H3U1-2 Q9H3U1;Q9H3U1-2 UNC45A Protein unc-45 homolog A 0 ; 113.99 0.0011064 385160000 1282920 1253770 403960 550650 1259210 1083330 1435110 1584670 553350 FALSE TRUE 1113378.871 1245533.902 599316.4072 675683.4987 1234154.185 1125006.406 1295933.253 1245800.652 487933.5934 2.28182459 2.552670936 1.228274534 1.384785774 2.529348668 2.305654748 2.65596235 2.553217629 1 18.89632529 3.216029806 24.99545276 2.290259578 1.865971947 0.068064304 0.597005845 567.3402833 629399.7023 0.185194162 0.210137766 1644.484583 -3.216029806 -0.424287631 TLVLLGAHGVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLVLLGAHGVGR 12 0 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8YEK3;O14936-6;O14936-2;A0A2U3TZN6;A0A2R8Y3B3;Q5JS79;A0A2R8Y6F8;O14936-3;A0A2U3TZM4;A0A2R8YFN5;O14936-4;Q5JS72;O14936-5 A0A2U3TZM1;A0A2R8Y6F8 CASK Peripheral plasma membrane protein CASK 0 96.604 0.0053906 321090000 160080 174690 113020 172530 186860 204400 149180 212370 224430 FALSE TRUE 138925.0224 173542.4499 167676.85 211705.5735 183141.8516 212263.4003 134712.5466 166956.3282 197898.1411 0.702002665 0.876928146 0.847288656 1.0697704 0.925434926 1.072589157 0.680716584 0.843647784 1 17.59439854 4.874089004 1.817264486 0.911430492 0.57881841 0.256414278 0.115795175 2.088960867 5.292361736 0.031871875 1.326674161 74832.28457 -4.874089004 -0.332612082 TLVLLMGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLVLLMGK 8 0 P07737;K7EJ44;CON__P02584 P07737 PFN1 Profilin-1 0 148.98 0.0011923 69195000 364320 399100 206950 305690 358970 307240 400850 449220 441270 FALSE TRUE 316174.1889 396478.2858 307031.7122 375101.5867 351827.1993 319059.7216 361975.6287 353157.7988 389103.5633 0.812570788 1.01895311 0.789074532 0.964014782 0.904199376 0.819986635 0.93028094 0.90761903 1 18.56979467 0.847042892 1.524752132 1.184019683 0.892522541 0.18734941 0.070694174 5.466183711 4.974062807 3.280170693 0.018154174 7.031417603 -0.847042892 -0.291497142 TLVRPSEHALVDNDGLYDPDCDPEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TLVRPSEHALVDNDGLYDPDCDPEGR 26 1 P09758 P09758 TACSTD2 Tumor-associated calcium signal transducer 2 0 ; 129.27 4.86E-05 350720000 262639 317161 126095 233322 338507 403847 264063 444012 282771 FALSE TRUE 227930.5907 315077.5485 187074.9638 286301.3262 331771.373 419383.2554 238454.2109 349063.4891 249342.1345 0.914127855 1.263635403 0.750274173 1.14822682 1.330586881 1.681959033 0.956333399 1.39993784 1 17.92776717 3.482205596 9.486472867 1.282090876 0.995458605 0.247844453 0.235815634 0.180953239 219.8102683 0.063441938 0.08661762 3035.327776 -3.482205596 -0.286632271 TLVTQNSGVEALIHAILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLVTQNSGVEALIHAILR 18 0 P14923 P14923 JUP Junction plakoglobin 0 228.46 2.41E-19 190020000 123240 110710 53275 114680 121780 126110 105360 141850 95086 FALSE TRUE 106953.5217 109982.7387 79038.96819 140719.8468 119356.8163 130961.5333 95142.20342 111516.4814 83845.0414 1.275609386 1.311738141 0.9426791 1.678332367 1.423540549 1.561947267 1.134738582 1.330030727 1 16.35543784 0.650514468 1.364075971 2.82E-16 1.34534409 0.203738052 0.204664626 9.592273553 4.785990375 26.93063703 0.059386393 4.472130496 -0.650514468 1.34534409 TLVVHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 TLVVHEK 7 0 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;;;;; 100.45 0.0097841 16819560000 28531700 23509260 14113010 18807000 22627220 20870050 26166700 29903100 27456030 FALSE TRUE 24761163.55 23354826.12 20938108.84 23077416.8 22176982.59 21672934.33 23629057.46 23508554.77 24210209.41 1.022757099 0.964668489 0.864846251 0.953210127 0.916017793 0.895198136 0.975995584 0.971018233 1 24.52911222 2.092874941 10.48271967 0.980460645 0.934055644 0.207378519 0.042515987 0.578545548 60.51318388 0.017653691 0.011898524 123.8439916 -2.092874941 -0.046405002 TLVYGGIFLYPANKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLVYGGIFLYPANKK 15 1 P09467;A0A3B3IUC7 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 116.19 0.00075099 661760000 439760 450640 239360 377370 390120 300760 555480 597280 376790 FALSE TRUE 381644.6018 447679.7162 355115.2966 463057.6262 382357.3753 312330.4318 501609.6351 469556.32 332246.3154 1.148679712 1.3474332 1.068831406 1.393717867 1.150825028 0.940056871 1.509752289 1.413277735 1 18.34189367 2.219651193 24.99893207 1.33809658 1.186792601 0.096648992 0.181227442 498.9507012 659625.4434 0.072760567 0.049145252 165.8254534 -2.219651193 -0.151303979 TLWEDPGIQECYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLWEDPGIQECYDR 14 0 P29992 P29992 GNA11 Guanine nucleotide-binding protein subunit alpha-11 0 92.866 0.011141 59592000 315900 274850 243260 310520 305260 312660 317060 449410 432520 FALSE TRUE 274153.0146 273044.4923 360901.3497 381028.312 299185.9232 324688.2325 286311.57 353307.1688 381387.9783 0.718829722 0.715923175 0.946284021 0.999056954 0.784466056 0.851333159 0.750709478 0.926372064 1 18.54089984 4.250804392 24.84482308 0.887554131 0.717376311 0.442855459 0.082126455 206.6747669 419371.5785 0.021307597 0.055466515 17815.76159 -4.250804392 -0.17017782 TLYHSVHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TLYHSVHEK 9 0 M0QXB5;O95571 M0QXB5 ETHE1 "Persulfide dioxygenase ETHE1, mitochondrial" 0 135.55 0.0001259 176410000 123810 172590 50880 135040 192810 177150 162550 197020 204250 FALSE TRUE 107448.1948 171456.2449 75485.73818 165702.896 188973.4582 183965.0751 146785.926 154888.8062 180103.7977 0.596590389 0.951985728 0.419123523 0.920041099 1.049247493 1.021439178 0.81500739 0.859997447 1 17.45846908 3.524101702 24.73143323 0.936377676 0.68285392 0.458154706 0.146823624 353.7260875 186207.3148 0.038856537 0.057631414 3342.733103 -3.524101702 -0.253523757 TMELS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TMELSPR 7 0 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 T(0.003)MELS(0.997)PR 66.692 0.070474 248170000 270410 256740 180140 164190 260950 249210 236960 234200 231710 TRUE FALSE 234674.6334 255053.458 267256.3065 201471.849 255757.6055 258797.27 213979.6557 184118.1525 204317.5078 1.148578191 1.248319152 1.30804408 0.986072369 1.251765492 1.266642652 1.047289868 0.901137424 1 17.64045331 2.046009767 4.593421436 0.95024475 1.200142854 0.575651236 0.09118857 0.130619202 6.090586973 0.040193471 0.02512898 111.175673 -2.046009767 0.249898105 TMFAQVES(ph)DDEEAKNEPEWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TMFAQVESDDEEAKNEPEWK 20 1 Q9NW82 Q9NW82 WDR70 WD repeat-containing protein 70 1 TMFAQVES(1)DDEEAKNEPEWK;TMFAQVES(1)DDEEAKNEPEWK;T(0.015)MFAQVES(0.985)DDEEAKNEPEWK;TMFAQVES(1)DDEEAKNEPEWK 262.78 1.14E-36 1152320000 766013 484134 434241 432256 437205 339458 622784 721058 653225 TRUE FALSE 664782.4412 480953.6919 644241.4 530406.3314 428505.4759 352517.1689 562386.5035 566865.358 576001.4847 1.154133208 0.834986896 1.11847177 0.920841952 0.7439312 0.612007396 0.976362941 0.98413871 1 19.135713 7.999990646 0.941295843 0.891112355 158.3808219 0.220445776 0.144336924 2207.370478 3.967605075 0.04990093 748259.1422 99997846.15 -7.999990646 157.4897096 TMGYSVTAPEDTRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TMGYSVTAPEDTRR 14 1 O15305;H3BRM0;H3BV55 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 ; 200.16 3.15E-08 584330000 530420 518630 256657 335450 583830 563600 527040 562090 403000 FALSE TRUE 460323.6531 515223.0854 380777.1837 411619.0495 572212.9252 585282.0567 475927.7419 441891.4277 355357.7991 1.295380752 1.449871332 1.071531804 1.158322824 1.610244454 1.647021842 1.339291675 1.243511269 1 18.43891284 1.330155904 2.247977332 0.942401979 1.369897013 0.304582554 0.176832679 0.719923419 4.486384234 0.575897604 0.051663404 21.3872972 -1.330155904 0.427495034 TMHHLLLEVEVIEGTLQCPESGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 TMHHLLLEVEVIEGTLQCPESGR 23 0 F5GYQ2;Q9UI30;Q9UI30-2 F5GYQ2 TRMT112 Multifunctional methyltransferase subunit TRM112-like protein 0 ;;;;;;;; 297.26 5.83E-62 1478533000 422932.1 376143.4 211422.8 270985.3 347720.3 320799.1 381652.2 435510.1 307109 FALSE TRUE 367040.5514 373672.4892 313667.5732 332516.6541 340801.3463 333140.449 344639.6284 342379.6543 270802.9239 1.355378835 1.37986874 1.158287247 1.227891669 1.258484737 1.23019517 1.272658446 1.26431299 1 18.04688379 -1.999999999 0.035138756 6.38E-07 2.079961636 0.37048374 0.083372566 3075.200715 10.67215774 471.7359837 210.4522341 0.01 1.999999999 2.079960998 TMIIS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TMIISPER 8 0 O75533;B4DGZ4;A0A494C1M2;O75533-2 O75533 SF3B1 Splicing factor 3B subunit 1 1 TMIIS(1)PER;TMIIS(1)PER;TMIIS(1)PER;TMIIS(1)PER;TMIIS(1)PER 149.17 0.00053452 2948620000 1974800 1861300 1452230 1786020 1997590 2037930 1671420 1942440 3978950 TRUE FALSE 1713825.176 1849072.998 2154533.285 2191563.139 1957841.867 2116330.486 1509325.946 1527064.322 3508563.064 0.488469252 0.527017176 0.61407854 0.624632677 0.558018149 0.603190094 0.430183502 0.43523924 1 21.74244886 1.23114305 24.99595732 1.000000824 0.53336114 0.818278381 0.068846825 125.5976815 423206.5834 0.195755794 0.019268856 17.02719267 -1.23114305 -0.466639684 TMIIS(ph)PERLDPFADGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 TMIISPERLDPFADGGK 17 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 T(0.022)MIIS(0.978)PERLDPFADGGK;TMIIS(1)PERLDPFADGGK;TMIIS(1)PERLDPFADGGK;TMIIS(1)PERLDPFADGGK;T(0.003)MIIS(0.997)PERLDPFADGGK;T(0.002)MIIS(0.998)PERLDPFADGGK;T(0.035)MIIS(0.965)PERLDPFADGGK;TMIIS(1)PERLDPFADGGK;T(0.034)MIIS(0.966)PERLDPFADGGK 239.57 1.66E-20 1788946000 5072569 3919160 2850757 3795207 4237573 3402111 4829121 5794600 4360341 TRUE FALSE 4402216.154 3893414.78 4229392.62 4656966.755 4153253.588 3532992.412 4360793.589 4555469.884 3844866.454 1.144959443 1.012626791 1.100010279 1.211216777 1.080207502 0.918885598 1.13418597 1.184818755 1 21.87450206 3.037696783 24.99964407 1.076449138 1.113156287 0.076303464 0.086058477 705.314575 467744.1448 0.027980595 0.031726984 1090.678578 -3.037696783 0.036707149 TMIIS(ph)PERLDPFADGGKT(ph)PDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TMIISPERLDPFADGGKTPDPK 22 2 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 T(0.117)MIIS(0.883)PERLDPFADGGKT(1)PDPK 105.54 0.00097479 49909000 139350 119960 95813 65296 111920 96432 145110 165480 74628 TRUE FALSE 120934.5444 119171.9749 142148.4873 80122.45479 109693.011 100141.8014 131037.2545 130093.3898 65805.56286 1.837755642 1.810971135 2.160128735 1.217563551 1.666926111 1.521783222 1.991279291 1.976936054 1 16.00592193 3.764170388 24.99846293 1.635059614 1.923753706 0.213547225 0.318191342 1538.390839 1501664.097 0.085964671 0.148829753 5809.923154 -3.764170388 0.288694092 TMLELLNQLDGFDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TMLELLNQLDGFDSR 15 0 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 172.99 2.32E-06 331010000 412770 391840 223137 278780 355210 390290 395160 439980 387450 FALSE TRUE 358221.3987 389265.9772 331046.7995 342081.2599 348142.016 405304.7089 356837.444 345893.7009 341646.1024 1.048515982 1.139383633 0.968975783 1.001273708 1.019013574 1.186329087 1.04446514 1.012432744 1 18.38214314 1.746852386 4.125734744 1.005122003 1.059570887 0.107790794 0.063223466 0.450081775 16.7379257 0.042128389 0.017379277 55.82804064 -1.746852386 0.054448884 TMLITHMQDLQEVTQDLHYENFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TMLITHMQDLQEVTQDLHYENFR 23 0 Q15019-2;Q15019-3;Q15019;B5MCX3 Q15019-2 2-Sep Septin-2 0 ;; 297.95 5.45E-62 4497015000 1008815 932951 501561 630921 915877 928780 862332 1034076 810905 FALSE TRUE 875497.5417 926822.3835 744117.5772 774181.2561 897652.8396 964510.7676 778703.1754 812946.8946 715040.7347 1.22440233 1.296181236 1.040664596 1.082709304 1.255386996 1.34888926 1.089033306 1.136923891 1 19.44766591 1.305200364 1.470870325 0.944380292 1.196162604 0.288041707 0.096911696 1.507732436 3.268781133 0.551158725 0.029919857 20.19297762 -1.305200364 0.251782312 TMLTHSSKLQSGLMMSEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TMLTHSSKLQSGLMMSEQK 19 1 F5GX61 F5GX61 RAB6A 0 48.547 0.095492 2914500000 279860 281580 501290 234670 192340 342830 169230 138500 111580 FALSE TRUE 242875.7919 279730.2824 743715.5207 287955.4102 188512.8103 356018.8919 152818.1006 108882.8528 98389.13951 2.468522371 2.843101219 7.558918844 2.926699142 1.915992062 3.618477544 1.553200906 1.106655199 1 16.58621145 2.371073218 0.865105442 0.727006095 4.015906164 0.349966926 1.517504333 0.819932162 1.235156708 1.919728829 0.791003846 235.0028981 -2.371073218 3.28890007 TMPGGNDHEIFTDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TMPGGNDHEIFTDPR 15 0 O15305;H3BRM0;H3BV55 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 ;; 69.729 0.048794 1434210000 2329960 2224700 1265300 1497010 2302610 2289340 2093110 2424710 2126770 FALSE TRUE 2022049.883 2210085.799 1877203.312 1836929.001 2256792.566 2377412.391 1890120.514 1906204.636 1875345.673 1.078227823 1.17849516 1.000990558 0.979514885 1.203400844 1.26771956 1.007878463 1.01645508 1 20.83872511 2.09753497 21.27410252 1.009700723 1.115131914 0.26172969 0.086934497 7.123052005 1540.152011 0.037804886 0.025488054 125.1800066 -2.09753497 0.105431191 TMVGFGPEDDHFVAELTYNYGVGDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TMVGFGPEDDHFVAELTYNYGVGDYK 26 0 Q9HC38-2;F6TLX2;Q9HC38;I3L3Q4;Q9HC38-3 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 201.63 4.88E-25 128150000 228380 183490 140610 180750 172550 155970 200400 258210 342010 FALSE TRUE 198199.0044 182284.6421 208609.4663 221792.0501 169116.5926 161970.2668 180965.2388 202993.8009 301577.9674 0.657206513 0.604436205 0.691726482 0.735438507 0.560772374 0.537075928 0.600061206 0.673105541 1 18.20217151 1.233288213 3.583837273 1.054480218 0.627080905 0.799156962 0.05834022 0.139732539 2.689432348 0.164029919 0.01610963 17.11150518 -1.233288213 -0.427399313 TMYLEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TMYLEDR 7 0 P20340-2;P20340;P20340-4;J3KR73;Q9NRW1-2;Q9NRW1;P20340-3;C9JB90;F5GX61 P20340-2;F5GX61 RAB6A;RAB6B Ras-related protein Rab-6A;Ras-related protein Rab-6B 0 ;;; 116.3 0.012765 1385170000 1851470 1564890 1013467 1217090 1752940 1973180 1461390 1902700 1918950 FALSE TRUE 1606793.548 1554610.135 1503583.031 1493448.887 1718059.924 2049089.511 1319664.623 1495822.412 1692093.917 0.949588869 0.918749319 0.888593131 0.882604016 1.015345488 1.210978593 0.779900341 0.884006731 1 20.69037821 3.25668407 24.96808383 0.963076986 0.908996323 0.078365491 0.109651991 898.4597945 1237770.854 0.034013497 0.043820889 1805.859967 -3.25668407 -0.054080663 TNAVS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TNAVSPK 7 0 Q6XZF7 Q6XZF7 DNMBP Dynamin-binding protein 1 TNAVS(1)PK;TNAVS(1)PK 95.483 0.014091 235870000 1209670 1076480 742160 780660 778780 1013950 1390190 1489150 1466510 TRUE FALSE 1049809.045 1069408.532 1101071.058 957920.7846 763283.8017 1052957.313 1255369.588 1170706.861 1293140.858 0.811828841 0.82698534 0.851470318 0.740770643 0.59025573 0.814263431 0.970791062 0.905320448 1 20.302448 2.341536539 4.885748713 0.947562174 0.765372036 0.58398114 0.074691235 0.164091041 6.428163845 0.030860182 0.02341974 219.5515661 -2.341536539 -0.182190138 TNDAS(ph)SESIASFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TNDASSESIASFSK 14 0 A0A1W2PPI1;J3KSA2;A0A1W2PR65;J3QQS3;A0A1W2PRQ6;J3QS66;A0A1W2PS04;A0A1W2PP78;A0A1W2PNV7;A0A1W2PPG2;A0A1W2PPJ9;A0A1W2PQF1;Q7RTN6-6;Q7RTN6 A0A1W2PPI1 STRADA STE20-related kinase adapter protein alpha 1 TNDAS(0.84)S(0.053)ES(0.107)IASFSK;TNDAS(0.949)S(0.046)ES(0.005)IASFSK 158.92 5.24E-06 158327000 451170 319070 241550 284650 314430 305760 389370 407550 402110 TRUE FALSE 391546.7414 316974.0082 358364.3879 349284.1331 308173.4582 317522.7851 351608.9573 320398.6041 354573.0139 1.104276767 0.893959765 1.010692788 0.985083803 0.86913963 0.895507477 0.99164049 0.903618131 1 18.43572321 4.749473982 24.54691267 0.942370501 1.104276887 0.492039083 0.051256766 1075.919029 2419952.897 0.012162346 0.173610688 56166.06294 -4.749473982 0.161906386 TNEGVIEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TNEGVIEFR 9 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;; 141.25 0.00024931 943090000 2331920 2202980 1267660 1562920 2476030 2370510 2164170 2606540 2298560 FALSE TRUE 2023750.864 2188508.479 1880704.616 1917804.874 2426761.847 2461705.054 1954289.126 2049151.705 2026826.855 0.998482361 1.079770812 0.927905909 0.946210511 1.197320748 1.214561099 0.964211186 1.01101468 1 20.95079142 4.829689098 17.82114429 1.040088556 0.998448566 0.019091821 0.097948459 39928.41527 7787332.528 0.025338402 180.0346797 67559.91562 -4.829689098 -0.04163999 TNHIGHTGYLNTVTVSPDGSLCASGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TNHIGHTGYLNTVTVSPDGSLCASGGK 27 0 P63244;J3KPE3;D6RHH4;D6R9L0;H0Y8W2;D6RAC2;D6R9Z1;D6RFX4;D6REE5;H0YAM7;H0Y8R5 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 ; 178.39 1.19E-17 1675430000 685880 536890 339430 431560 551680 472000 632440 633900 549140 FALSE TRUE 595239.2202 533363.1342 503579.4833 529552.294 540702.6473 490158.1454 571106.0661 498345.418 484221.2948 1.229271052 1.101486325 1.039977979 1.093616286 1.116643678 1.012260615 1.17943195 1.029168736 1 18.885307 4.712451395 3.283263695 1.070543796 1.246685473 0.472848039 0.053347191 0.258905234 4.629895249 0.012706324 0.111588569 51576.44391 -4.712451395 0.176141676 TNHRLS(ph)LPMPASGTSLSAAIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TNHRLSLPMPASGTSLSAAIHR 22 1 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 1 T(0.321)NHRLS(0.679)LPMPASGTSLSAAIHR;T(0.112)NHRLS(0.888)LPMPASGTSLSAAIHR 236.18 1.05E-30 2953000000 835430 780990 375080 612980 901560 1002220 810580 898130 962850 TRUE FALSE 725025.8088 775859.6253 556469.9426 752166.4778 883620.7199 1040776.052 731970.0764 706071.8888 849022.9699 0.853953114 0.913826425 0.655423896 0.885920057 1.040750075 1.225851466 0.862132242 0.831628724 1 19.69544406 3.474354717 22.34573403 0.972994612 0.810398397 0.313520384 0.123891946 32.42821545 261917.427 0.038968382 0.050716862 2980.950176 -3.474354717 -0.162596214 TNHSNIMDDPFIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TNHSNIMDDPFIR 13 0 P61201;P61201-2;B4DIH5;H0YMC2 P61201 COPS2 COP9 signalosome complex subunit 2 0 ;; 146 4.21E-05 393643000 383790 362000 204706 267289 397480 395750 354180 394550 333026 FALSE TRUE 333071.1791 359621.9982 303702.5063 327981.0527 389570.9257 410974.7586 319831.6781 310178.5529 293656.0457 1.134222108 1.224636794 1.034211659 1.116888474 1.326623209 1.399510634 1.089137046 1.056264829 1 18.16376781 2.016441221 24.88907948 1.044316143 1.20413695 0.34697151 0.103856568 273.2306447 413620.9998 0.046063359 0.031046555 103.8583027 -2.016441221 0.159820807 TNIIPVLEDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TNIIPVLEDAR 11 0 A6NHQ2 A6NHQ2 FBLL1 rRNA/tRNA 2-O-methyltransferase fibrillarin-like protein 1 0 ; 117.23 0.0020524 91104000 203090 189356 114180 142733 217950 228260 193277 207487 193607 FALSE TRUE 176251.1419 188112.108 169397.8299 175142.7092 213613.2214 237041.3099 174533.0263 163117.5197 170719.001 1.032404951 1.101881494 0.992261136 1.025912219 1.251256276 1.38848815 1.022340954 0.955473724 1 17.38126411 2.0160133 24.99281263 0.978861583 1.131614698 0.246929401 0.116719497 338.5409234 528376.8984 0.052113197 0.035123306 103.7560189 -2.0160133 0.152753115 TNILQYASTRPPTLS(ph)PIPHIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TNILQYASTRPPTLSPIPHIPR 22 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 TNILQYAST(0.001)RPPT(0.027)LS(0.971)PIPHIPR;TNILQYASTRPPT(0.061)LS(0.939)PIPHIPR 240.41 7.63E-31 3336200000 1342720 1458100 737150 1112020 1553680 1440850 1388040 1741100 1678290 TRUE FALSE 1165276.15 1448521.645 1093638.206 1364521.137 1522764.808 1496280.432 1253428.094 1368779.314 1479884.468 0.787410217 0.978807249 0.739002422 0.922045718 1.028975464 1.011079219 0.846976991 0.924923089 1 20.49705312 3.492490994 24.68342777 0.953669908 0.846292911 0.346997445 0.078783432 753.3096456 1209795.251 0.021619549 0.030931053 3108.071449 -3.492490994 -0.107376998 TNKLPGS(ph)PGLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TNKLPGSPGLSK 12 1 Q8N9U0;Q8N9U0-2 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 T(0.003)NKLPGS(0.997)PGLSK;T(0.042)NKLPGS(0.958)PGLSK 88.385 0.0060655 2608000000 4390000 3563200 2222360 2794600 4897300 3642000 4231600 7200100 2325360 TRUE FALSE 3809850.377 3539793.105 3297100.729 3429156.643 4799853.311 3782110.097 3821220.083 5660414.646 2050458.59 1.858047949 1.726342157 1.60798211 1.672385221 2.340868201 1.844519131 1.863592907 2.760560332 1 20.96751518 3.272737476 24.91349721 2.048496732 1.709185172 0.050831546 0.447425766 388.5941004 283266.2471 0.125092335 0.161484718 1873.861445 -3.272737476 -0.33931156 TNLEFLQEQFNSIAAHVLHCTDSGFGAR ddPTM_MDA-MB-175_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 ; 188.17 4.18E-18 573420000 290530 257630 102068 184343 274000 290280 308540 316360 209610 FALSE TRUE 252135.7244 255937.6116 151428.4262 226200.8957 268547.9361 301447.2594 278617.8383 248708.8759 184830.1446 1.364148283 1.38471791 0.819284249 1.223831189 1.452944468 1.630942074 1.507426394 1.345607755 1 17.49584054 3.322082273 5.979930327 1.4028693 1.180308399 0.152038383 0.220514722 0.37536663 21.07695429 0.066619561 0.08594227 2099.337546 -3.322082273 -0.222560901 TNLSVHEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TNLSVHEDK 9 0 P33176;Q12840;J3KNA1 P33176;Q12840 KIF5B;KIF5A Kinesin-1 heavy chain;Kinesin heavy chain isoform 5A;Kinesin-like protein 0 ; 99.343 0.0054013 811670000 1821430 1576720 760450 1279310 1716790 1546330 1772370 2156100 2533300 FALSE TRUE 1580723.411 1566362.423 1128206.164 1569796.889 1682629.238 1605818.316 1600485.83 1695034.794 2233816.16 0.707633618 0.701204714 0.50505775 0.702742203 0.75325323 0.718867714 0.71648055 0.758806756 1 21.09107903 -0.609199824 0.902104238 10 0.673363214 0.693148541 0.065866221 33.30022578 1.189875716 585.7692599 0.02381894 0.245923582 0.609199824 -9.326636786 TNNVSEHEDTDKYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 TNNVSEHEDTDKYR 14 1 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ;;;;;; 201.3 1.08E-08 3996263000 4473023 3761104 1720820 2946095 4662081 3726409 4625470 5451370 5036640 FALSE TRUE 3881901.677 3736397.06 2553014.308 3615050.898 4569314.709 3869766.366 4176892.631 4285636.948 4441214.157 0.874063159 0.841300808 0.574846026 0.813978063 1.028843588 0.871330728 0.9404844 0.964969667 1 22.08252271 3.394780551 6.110661725 0.954533259 0.759087224 0.529472576 0.0875186 0.162270617 9.494588938 0.025411291 0.032970043 2481.878694 -3.394780551 -0.195446035 TNPPTQKPPS(ph)PPMSGR ddPTM_MDA-MB-175_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(0.995)PPMS(0.005)GR;TNPPT(0.009)QKPPS(0.986)PPMS(0.005)GR;TNPPT(0.001)QKPPS(0.984)PPMS(0.015)GR;TNPPTQKPPS(0.999)PPMS(0.001)GR;TNPPTQKPPS(0.989)PPMS(0.011)GR;TNPPTQKPPS(0.851)PPMS(0.149)GR;TNPPTQKPPS(0.985)PPMS(0.015)GR;TNPPT(0.002)QKPPS(0.982)PPMS(0.016)GR;TNPPTQKPPS(1)PPMSGR;TNPPT(0.001)QKPPS(0.983)PPMS(0.015)GR;TNPPT(0.005)QKPPS(0.746)PPMS(0.249)GR;TNPPTQKPPS(0.996)PPMS(0.004)GR 159.77 5.46E-09 15152340000 5277280 4266930 3019433 3230834 5389010 3969860 5303870 6207060 5180260 TRUE FALSE 4579874.077 4238900.256 4479640.898 3964444.24 5281779.244 4122583.083 4789501.504 4879728.522 4567855.564 1.002631106 0.92798474 0.980687948 0.867900524 1.156292963 0.902520455 1.048522975 1.068275573 1 22.1230856 3.257989923 24.99996981 1.033641548 0.946163303 0.284148928 0.071200013 316.804077 407633.8489 0.019178743 0.024722291 1811.298063 -3.257989923 -0.087478245 TNPPTQKPPSPPMS(ph)GR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.301)PPMS(0.699)GR 100.43 0.0054151 194390000 83452 67467 49701 56864 86053 66017 83681 104480 89137 TRUE FALSE 72423.60676 67023.80483 73736.56984 69775.84031 84340.71366 68556.71671 75565.6295 82137.76506 78599.32541 0.921427842 0.852727482 0.93813235 0.887740956 1.073046279 0.872230345 0.961403029 1.045018703 1 16.26222931 -1.995285167 0.102294355 1.559665629 0.758839547 0.295003526 0.060768242 319.5537918 3.00890522 36.60594431 3.638472512 0.010109154 1.995285167 -0.800826081 TNPS(ph)PTNPFSSDLQK ddPTM_MDA-MB-175_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(0.997)PT(0.003)NPFSSDLQK;TNPS(0.926)PT(0.074)NPFSSDLQK;TNPS(1)PTNPFSSDLQK;TNPS(0.999)PT(0.001)NPFSSDLQK 337.85 3.90E-69 649700000 702830 561580 382097 512180 592790 513040 692720 767580 723000 TRUE FALSE 609949.2348 557890.944 566880.3872 628478.2972 580994.6388 532776.9808 625540.121 603438.9903 637527.7636 0.956741446 0.875084939 0.889185412 0.985805377 0.91132445 0.835692202 0.981196674 0.946529743 1 19.28212865 TNQIGTVNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TNQIGTVNDR 10 0 P53990-2;P53990;P53990-4;P53990-5;J3KR23;H3BQF7;H3BMU1;H3BUI0;P53990-3 P53990-2 IST1 IST1 homolog 0 97.734 0.013626 58313000 78235 70388 45566 47843 75912 71494 89709 81912 79674 FALSE TRUE 67896.04653 69925.61659 67601.87001 58706.48438 74401.49972 74244.42044 81009.03499 64395.75624 70255.03048 0.966422562 0.99531117 0.962235295 0.835619656 1.059020247 1.056784403 1.153070953 0.916599933 1 16.10031391 3.172995404 24.99996709 1.03171601 0.945442861 0.312354657 0.071203095 83.83624594 31965.75084 0.022667282 0.02570229 1489.345316 -3.172995404 -0.086273149 TNRGS(ph)QLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TNRGSQLHK 9 1 P42356;P42356-2 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 1 TNRGS(1)QLHK;TNRGS(1)QLHK;T(0.007)NRGS(0.993)QLHK 117.03 0.00073755 421489000 328561 294993 196971 180196 291502 292280 363748 359254 324030 TRUE FALSE 285140.8314 293055.1716 292226.8344 221112.2559 285701.6805 303524.2007 328471.7749 282430.3278 285723.5425 0.997960577 1.02565987 1.022760784 0.773867823 0.999923485 1.062300285 1.149613966 0.988474122 1 18.12426039 2.998850462 24.99970233 1.047721965 0.955184961 0.229405809 0.08207115 70.0451982 1523374.661 0.025949661 0.029070129 997.3565915 -2.998850462 -0.092537003 TNRPPLSLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TNRPPLSLSR 10 1 J3QQ67;Q07020;F8VYV2;G3V203;H0YHA7;Q07020-2;F8VUA6;A0A075B7A0 J3QQ67 RPL18 60S ribosomal protein L18 0 ; 113.63 0.0013341 2298200000 978740 1094440 688330 718500 1381980 1329120 1190130 1168690 1334950 FALSE TRUE 849397.0292 1087250.552 1021208.69 881646.4066 1354481.302 1380252.106 1074711.376 918774.7383 1177133.732 0.72158074 0.923642338 0.86753838 0.748977268 1.150660511 1.172553355 0.912990042 0.780518571 1 20.1668468 3.26467044 24.99312206 0.977175264 0.826885509 0.347767228 0.12461396 360.3943229 344978.0489 0.040929918 0.052823348 1839.375682 -3.26467044 -0.150289755 TNRTS(ph)QDYDQLPSCSDGSQAPARPPKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TNRTSQDYDQLPSCSDGSQAPARPPKPR 28 3 Q13191 Q13191 CBLB E3 ubiquitin-protein ligase CBL-B 1 T(0.04)NRT(0.15)S(0.81)QDYDQLPSCSDGSQAPARPPKPR;T(0.019)NRT(0.185)S(0.796)QDYDQLPSCSDGSQAPARPPKPR 181.93 7.41E-17 354690000 183171 225295 161503 203971 302330 256950 306430 399210 305070 TRUE FALSE 158964.4883 223815.0223 239606.391 250285.7331 296314.2245 266835.0328 276712.4658 313842.0482 269004.9721 0.59093513 0.832010727 0.890713614 0.930413037 1.101519508 0.99193346 1.028651863 1.166677499 1 18.03727331 5.226879019 0.558456737 1.083299731 4.49E-20 0.862200902 0.058962881 2.280008807 0.37539517 0.034104532 1.796546492 168608.3268 -5.226879019 -1.083299731 TNS(ph)DSALHQSTMTPTQPESFSSGSQDVHQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TNSDSALHQSTMTPTQPESFSSGSQDVHQK 30 0 M0QXN6;M0QX46;Q6UUV9;Q6UUV9-2;Q6UUV9-3 M0QXN6 CRTC1 CREB-regulated transcription coactivator 1 1 T(0.158)NS(0.571)DS(0.27)ALHQSTMTPTQPESFSSGSQDVHQK 238.91 2.62E-45 318430000 143870 177610 22500 106580 215830 154110 169440 227830 225360 TRUE FALSE 124857.215 176443.2682 33381.07526 130780.618 211535.4053 160038.7114 153007.7349 179110.3275 198718.1975 0.62831294 0.887906948 0.167981975 0.658120995 1.064499416 0.805355088 0.769973444 0.901328261 1 17.60036447 3.42708551 8.396936155 0.889953528 0.564240886 0.417446582 0.191541994 0.267269687 40.53309701 0.054348871 0.070337169 2673.532757 -3.42708551 -0.325712643 HSPAPPPDPGFPAPS(ph)PPPADSPSEGFSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HSPAPPPDPGFPAPSPPPADSPSEGFSLK 29 0 M0QZS0;A0A590UK10;A0A3B3IPE9;A0A087WZG4;Q6ZSZ5-2;Q6ZSZ5-1;Q6ZSZ5-6;Q6ZSZ5-5;Q6ZSZ5 M0QZS0 ARHGEF18 Rho guanine nucleotide exchange factor 18 1 HSPAPPPDPGFPAPS(1)PPPADSPSEGFSLK;HSPAPPPDPGFPAPS(1)PPPADSPSEGFSLK 166.56 2.75E-12 402220000 176138 207894 144370 207818 305830 248270 317700 413230 350230 TRUE FALSE 152860.917 206528.3306 214187.8149 255006.2532 299744.5813 257821.1076 286889.5029 324863.9803 308826.2084 0.494973914 0.668752603 0.693554527 0.825727371 0.970593082 0.834842059 0.928967475 1.051931382 1 18.23643567 4.980012951 0.365213949 1.047750293 4.12E-22 0.902070967 0.053659069 2.851542981 0.308761632 0.091070748 1.382090569 95502.10647 -4.980012951 -1.047750293 down TNS(ph)MQQLEQWIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TNSMQQLEQWIK 12 0 Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;A0JP02;B4DJX4;Q9HAU0-5;Q9HAU0-8;Q9HAU0-3 Q9HAU0 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 T(0.004)NS(0.996)MQQLEQWIK;T(0.001)NS(0.999)MQQLEQWIK 215.48 4.34E-11 129511000 222969 191218 104909 107208 176054 151984 195535 210497 187153 TRUE FALSE 193503.0817 189961.8764 155643.3433 131551.215 172550.8698 157830.9228 176572.0458 165483.8546 165027.9855 1.172547075 1.151088864 0.943133025 0.797144887 1.045585506 0.956388835 1.069952137 1.002762374 1 17.33235117 4.247671317 23.46402648 0.976994773 1.161818276 0.53064645 0.073549986 73.82591824 190124.5442 0.019153028 0.048979997 17687.6981 -4.247671317 0.184823502 TNS(ph)PGFQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TNSPGFQK 8 0 A0A087X0H9;Q5T8P6-3;Q5T8P6-2;Q5T8P6;Q5T8P6-5;Q5T8P6-4 A0A087X0H9 RBM26 RNA-binding protein 26 1 T(0.005)NS(0.995)PGFQK;T(0.002)NS(0.998)PGFQK;T(0.002)NS(0.998)PGFQK;T(0.001)NS(0.999)PGFQK 91.313 0.013191 859860000 3022110 2277030 1636190 1762750 2253100 1989240 2840510 3005510 2936450 TRUE FALSE 2622730.506 2262072.04 2427456.957 2163009.329 2208267.718 2065767.35 2565037.777 2362805.075 2589306.226 1.012908585 0.873620902 0.937493191 0.835362503 0.852841466 0.797807277 0.990627432 0.912524386 1 21.30413417 2.208344834 24.9913257 0.957173346 0.883155349 0.274008716 0.062639756 297.012088 245655.1366 0.025344528 0.017089745 161.5640881 -2.208344834 -0.074017997 TNS(ph)SSSSPVVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TNSSSSSPVVLK 12 0 Q7Z589-4;E9PMC9;Q7Z589-6;Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-4;Q7Z589-7 EMSY;C11orf30 Protein EMSY 1 T(0.001)NS(0.866)S(0.114)S(0.014)S(0.004)S(0.001)PVVLK;TNS(0.477)S(0.477)S(0.046)SSPVVLK;TNS(0.967)S(0.033)SSSPVVLK 212.69 1.81E-08 1366180000 1620330 1533620 1338840 1631710 2316190 1731980 2720390 2994020 2926670 TRUE FALSE 1406199.285 1523545.549 1986307.502 2002214.695 2270102.351 1798610.391 2456566.997 2353772.122 2580682.407 0.544894359 0.59036538 0.769683049 0.775846997 0.879651965 0.696951468 0.951905973 0.912073534 1 21.29932118 5.272699502 0.251583436 1.032950069 2.83E-15 0.781683723 0.070076188 9.997787264 0.577504168 0.322820156 3.447933428 187369.7609 -5.272699502 -1.032950069 TNS(ph)TGGSSGSSVGGGSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TNSTGGSSGSSVGGGSGK 18 0 G8JLD3;X6RLX0;Q8IUD2-3;Q8IUD2;Q8IUD2-2;X6RM00;Q8IUD2-4;Q8IUD2-5;K7EKH8;K7EIZ7 G8JLD3 ERC1 ELKS/Rab6-interacting/CAST family member 1 1 TNS(0.619)T(0.38)GGSSGSSVGGGSGK;TNS(0.5)T(0.5)GGSSGSSVGGGSGK;TNS(0.5)T(0.5)GGSSGSSVGGGSGK 371.03 1.30E-107 673190000 715600 640650 473480 590120 631060 577840 908550 1045810 1131310 TRUE FALSE 621031.6469 636441.528 702456.5117 724115.7654 618503.1406 600069.8787 820438.9608 822171.67 997567.8206 0.62254579 0.637993242 0.704169177 0.725881239 0.620011119 0.601532915 0.822439281 0.824176214 1 19.9280554 1.488205354 1.141252768 1.068825675 0.656472861 0.815057541 0.053559385 0.442962915 0.67956333 0.206772305 0.018115727 30.77551678 -1.488205354 -0.412352814 TNSGISSASGGSTEPTT(ph)PDSERPAQALLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TNSGISSASGGSTEPTTPDSERPAQALLR 29 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4;A0A0J9YW54 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 TNSGISSASGGST(0.001)EPT(0.174)T(0.825)PDSERPAQALLR;TNSGISSASGGS(0.002)T(0.006)EPT(0.109)T(0.883)PDSERPAQALLR;TNSGISSASGGST(0.001)EPT(0.103)T(0.892)PDS(0.004)ERPAQALLR;TNSGISSASGGST(0.004)EPT(0.206)T(0.79)PDSERPAQALLR 194.26 1.43E-18 2770610000 337531 399128 275318 306483 556366 583015 521947 634503 556377 TRUE FALSE 292925.4232 396506.1019 408462.7057 376074.6494 545295.4051 605443.9643 471328.6603 498819.4712 490602.7449 0.597072532 0.808201964 0.832573217 0.76655635 1.111480543 1.234081893 0.960713459 1.016748227 1 18.90419578 3.245372622 24.99295981 1.059304758 0.760999022 0.725173418 0.095784187 91.82644648 336905.3902 0.029081665 0.03669766 1759.432548 -3.245372622 -0.298305736 TNSMSSSGLGS(ph)PNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 TNSMSSSGLGSPNR 14 0 Q9NZN8;Q9NZN8-5;F8VP97;F8VV52;F8VUB4;Q9NZN8-4;F8VX63;F8VVY1;F8VQD8;A0A087X050 Q9NZN8 CNOT2 CCR4-NOT transcription complex subunit 2 1 TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR;TNSMS(0.003)S(0.008)S(0.006)GLGS(0.983)PNR;TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR 288.22 2.81E-34 7007210000 7506180 7625680 5224220 6651400 9924320 8677470 9802240 11547810 8956620 TRUE FALSE 6514219.295 7575586.406 7750670.266 8161702.03 9726845.449 9011297.886 8851620.274 9078400.697 7897778.587 0.824816652 0.959204708 0.981373456 1.033417427 1.231592573 1.140991456 1.120773414 1.149487871 1 22.91301549 4.104647914 1.179300491 1.12902468 0.836097191 0.696630953 0.064282425 0.361642021 0.823858131 0.020963474 0.100761668 12724.7106 -4.104647914 -0.292927489 TNSMSSSGLGS(ph)PNRS(ph)SPSIICMPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TNSMSSSGLGSPNRSSPSIICMPK 24 1 Q9NZN8;Q9NZN8-5;F8VP97;F8VV52;F8VUB4;Q9NZN8-4;F8VX63;F8VVY1;F8VQD8;A0A087X050 Q9NZN8 CNOT2 CCR4-NOT transcription complex subunit 2 2 T(0.037)NS(0.036)MS(0.163)S(0.166)S(0.183)GLGS(0.418)PNRS(0.426)S(0.385)PS(0.186)IICMPK 51.066 0.074468 208550000 226160 190410 98733 115290 161290 143680 212480 191120 167510 TRUE FALSE 196272.383 189159.1842 146480.609 141468.3566 158080.6446 149207.4626 191873.7223 150250.4753 147707.1586 1.328793979 1.280636537 0.991696072 0.957762358 1.070230082 1.010157287 1.299014375 1.017218642 1 17.17238022 4.304390566 6.254589865 1.056197975 1.312243711 0.556960055 0.094656603 0.154300165 10.9252415 0.024177497 0.064894406 20155.36032 -4.304390566 0.256045736 TNSMSSSGLGS(ph)PNRSS(ph)PSIICMPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TNSMSSSGLGSPNRSSPSIICMPK 24 1 Q9NZN8;Q9NZN8-5;F8VP97;F8VV52;F8VUB4;Q9NZN8-4;F8VX63;F8VVY1;F8VQD8;A0A087X050 Q9NZN8 CNOT2 CCR4-NOT transcription complex subunit 2 2 TNS(0.001)MS(0.016)S(0.072)S(0.132)GLGS(0.78)PNRS(0.19)S(0.809)PS(0.001)IICMPK;TNSMSSS(0.004)GLGS(0.995)PNRS(0.116)S(0.864)PS(0.02)IICMPK;T(0.002)NS(0.007)MS(0.125)S(0.108)S(0.125)GLGS(0.632)PNRS(0.234)S(0.762)PS(0.004)IICMPK 149.29 8.35E-08 712270000 862650 697180 394456 459590 683080 589110 747830 812250 731440 TRUE FALSE 748648.6168 692600.1787 585216.241 563946.9339 669488.0444 611773.4429 675305.5617 638556.6584 644969.9965 1.160749525 1.073848679 0.907354209 0.874377005 1.038014246 0.948530081 1.047034072 0.990056378 1 19.29887252 4.45638432 4.929319472 0.975950801 1.143853795 0.58146947 0.053646263 0.12095055 7.816885316 0.013968733 0.043914077 28601.20432 -4.45638432 0.167902994 TNSS(ph)DSERS(ph)PDLGHSTQIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TNSSDSERSPDLGHSTQIPR 20 1 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 2 T(0.053)NS(0.318)S(0.627)DS(0.003)ERS(0.999)PDLGHSTQIPR 148.15 6.47E-08 1045100000 917260 822240 481600 497010 928320 742210 838310 1041900 872390 TRUE FALSE 796041.767 816838.6513 714503.3709 609863.7168 909848.2482 770763.299 757010.8252 819097.7931 769257.048 1.034818945 1.061853971 0.928822651 0.792795748 1.182762317 1.001958059 0.984080454 1.064790755 1 19.55310623 3.226680547 24.99998931 1.042041465 0.960396429 0.205564298 0.089425842 417.0268621 877573.9409 0.02754875 0.031482043 1685.312907 -3.226680547 -0.081645036 TNST(ph)GGSSGSSVGGGSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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(0.192)T(0.808)GGSSGSSVGGGSGK 374.08 1.02E-106 293260000 519510 442280 322340 422090 493470 411720 621160 725590 815590 TRUE FALSE 450855.4372 439374.6336 478224.7022 517931.9857 483650.9125 427559.1348 560919.9988 570428.225 719171.8793 0.626909158 0.610945236 0.664965797 0.720178306 0.672510879 0.594515925 0.77995263 0.793173706 1 19.45597708 -1.124298577 0.661503285 9.998725621 0.644999828 0.859040473 0.04493275 23.22905873 0.521170223 297.085082 0.020471098 0.075110633 1.124298577 -9.353725793 TNSTFNQVVLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TNSTFNQVVLKR 12 1 J3QQ67;Q07020;F8VYV2;G3V203;H0YHA7;Q07020-2;A0A075B7A0 J3QQ67 RPL18 60S ribosomal protein L18 0 96.866 0.002894 0 201400 170150 69748 87957 159010 152530 211470 217020 48906 FALSE TRUE 174784.4797 169032.2734 103478.3661 107928.9812 155846.0121 158397.9278 190961.6719 170611.9619 43124.38839 4.053030923 3.919644539 2.399532375 2.502736507 3.613871823 3.673047519 4.428159542 3.956275514 1 15.39621638 TNT(ph)PVKEDWNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TNTPVKEDWNVR 12 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 1 TNT(1)PVKEDWNVR;T(0.01)NT(0.99)PVKEDWNVR;T(0.001)NT(0.999)PVKEDWNVR 147.7 0.00010638 2120850000 3855030 3078680 2541240 2450160 3200190 2393650 3485510 3937210 3071270 TRUE FALSE 3345578.018 3058455.948 3770192.164 3006506.276 3136512.48 2485735.264 3147485.777 3095268.281 2708187.959 1.235356655 1.129336661 1.392145678 1.110154214 1.158159082 0.917859211 1.162210978 1.142929637 1 21.36889644 3.509732836 23.58049737 1.087740403 1.241846215 0.404625684 0.097410328 349.4853145 252701.4557 0.026042993 0.038581939 3233.946541 -3.509732836 0.154105813 TNTMNGSKS(ph)PVISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 TNTMNGSKSPVISR 14 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 1 TNTMNGS(0.178)KS(0.822)PVISR;TNTMNGS(0.13)KS(0.87)PVISR;TNTMNGS(0.159)KS(0.841)PVISR;TNTMNGS(0.007)KS(0.993)PVISR;TNTMNGS(0.032)KS(0.968)PVISR;TNTMNGS(0.067)KS(0.933)PVISR;TNT(0.001)MNGS(0.074)KS(0.925)PVISR;TNT(0.001)MNGS(0.379)KS(0.62)PVISR;TNTMNGS(0.008)KS(0.992)PVISR;TNTMNGS(0.015)KS(0.973)PVIS(0.012)R;TNTMNGS(0.01)KS(0.982)PVIS(0.008)R 236.03 1.80E-17 14336110000 8516880 7071480 4096839 5033181 8243910 6706930 8540710 9727180 6000050 TRUE FALSE 7391352.729 7025026.982 6078084.044 6176041.673 8079872.32 6964949.937 7712433.259 7647098.254 5290730.924 1.39703811 1.327798953 1.148817457 1.167332409 1.527175061 1.316443803 1.457725477 1.44537652 1 22.33503562 3.264218598 24.99993935 1.36783196 1.257112717 0.066864184 0.156981758 541.0618514 527181.704 0.044800398 0.057816277 1837.462981 -3.264218598 -0.110719244 TNTNVNCPIECFMPLDVQADREDS(ph)RE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TNTNVNCPIECFMPLDVQADREDSRE 26 2 H0Y7Z1;P02751-12;P02751-10;P02751-6;P02751-5;P02751-9;P02751-14;P02751-13;P02751-8;P02751-17;P02751-3;P02751-11;P02751-1;P02751-7;P02751 H0Y7Z1 FN1 Fibronectin;Anastellin;Ugl-Y1;Ugl-Y2;Ugl-Y3 1 TNTNVNCPIECFMPLDVQADREDS(1)RE;TNTNVNCPIECFMPLDVQADREDS(1)RE;TNTNVNCPIECFMPLDVQADREDS(1)RE;TNTNVNCPIECFMPLDVQADREDS(1)RE 246.89 1.48E-45 480408000 119084 156207 84288 89804 139054 111371 202121 144834 104237 TRUE FALSE 103346.7477 155180.8659 125049.9587 110195.3708 136287.0975 115655.5144 182519.3365 113862.3762 91914.22061 1.124382571 1.688322709 1.360507198 1.198893599 1.482764001 1.258298375 1.985757322 1.238789552 1 16.48800047 1.482555051 11.32333789 1.059214407 1.446352614 0.250185285 0.24988318 0.094949149 55.45274478 0.156468376 0.059026394 30.37771133 -1.482555051 0.387138207 TNTPVKEDWNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TNTPVKEDWNVR 12 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 162.93 5.60E-05 462110000 1039100 879920 481700 569100 1014800 921990 1092200 1246800 578820 FALSE TRUE 901780.3023 874139.7476 714651.7312 698322.8531 994607.4654 957459.5519 986278.6121 980181.5226 510392.559 1.766836695 1.712681214 1.400200137 1.368207355 1.948710748 1.875927725 1.932392224 1.920446341 1 18.96124777 3.234633294 24.9999859 1.78040313 1.561189835 0.064979047 0.301403126 235.5331317 1499322.61 0.090345437 0.10627377 1716.458448 -3.234633294 -0.219213295 TNVLGHLQQGGAPTPFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TNVLGHLQQGGAPTPFDR 18 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ; 184.7 5.69E-14 2329600000 853140 831480 416280 565360 883160 920880 897720 890260 881570 FALSE TRUE 740395.3874 826017.9531 617594.4004 693733.629 865586.8439 956306.8495 810659.2526 699884.827 777351.7989 0.952458576 1.062605058 0.794485073 0.892432011 1.113507224 1.230211149 1.042847336 0.900345028 1 19.56820813 3.248964848 24.99091528 1.04530385 0.925930866 0.275564417 0.105249805 357.1703262 857916.6461 0.034381645 0.043907661 1774.045882 -3.248964848 -0.119372984 TNYNDRYDEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 TNYNDRYDEIR 11 1 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 ;;;;;; 222.25 7.12E-12 13746190000 10464000 10486070 6055260 7123070 11610280 10902490 11210080 11686150 9910270 FALSE TRUE 9081155.888 10417186.32 8983603.99 8740471.913 11379258.14 11321915.85 10122928.17 9187157.764 8738689.17 1.039189713 1.192076536 1.028026494 1.000204006 1.302169916 1.295608028 1.158403505 1.051319893 1 23.05898546 1.604811698 3.697041491 1.010337776 1.148467361 0.194138555 0.103281905 0.313422044 9.723199075 0.089348665 0.029043506 40.25424614 -1.604811698 0.138129585 TNYNDRYDEIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TNYNDRYDEIRR 12 2 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 ;;;; 197.19 1.11E-07 6732580000 3983720 3853200 1481010 1480356 3756470 3640220 3962950 4204110 730728 FALSE TRUE 3457261.309 3827888.075 2197231.39 1816493.456 3681723.596 3780261.619 3578623.719 3305093.793 644342.1683 5.365567363 5.94076915 3.410038172 2.819144152 5.713926199 5.866854297 5.553918236 5.129407876 1 19.29746749 4.262574416 24.98449079 4.429792184 5.65316911 0.121071058 1.528625426 582.570048 606108.0968 0.388839747 1.027618943 18305.19737 -4.262574416 1.223376927 TPAAAAAMNLAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TPAAAAAMNLASPR 14 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR 180.93 1.78E-06 2833039000 942020 859926 522375 608224 822947 862206 772333 993048 775830 TRUE FALSE 817529.6702 854277.0895 774997.2972 746330.5553 806571.9648 895375.6227 697432.2645 780692.4131 684112.2612 1.195022683 1.248738165 1.132851056 1.090947492 1.179005275 1.30881388 1.019470493 1.141175882 1 19.38387356 -0.137013072 0.673052892 9.73E-10 1.183432982 0.344020414 0.076887629 21.005163 1.711079989 28.84101521 0.034239858 0.729435555 0.137013072 1.183432981 TPAAPAS(ph)PAAVPSEGSGGSTTGWR ddPTM_MDA-MB-175_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 385.91 3.50E-137 4110440000 1800200 1648150 946487 1290000 1706920 1824480 1509400 1760970 1628290 TRUE FALSE 1562299.009 1637323.194 1404211.279 1582914.216 1672955.632 1894668.926 1363018.62 1384400.269 1435795.411 1.08810698 1.140359679 0.978002345 1.10246502 1.16517689 1.319595335 0.949312562 0.964204411 1 20.45341876 TPADTGFAFPDWAYKPES(ph)SPGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TPADTGFAFPDWAYKPESSPGSR 23 1 P50548 P50548 ERF ETS domain-containing transcription factor ERF 1 TPADTGFAFPDWAYKPES(0.499)S(0.499)PGS(0.001)R;TPADTGFAFPDWAYKPES(0.499)S(0.499)PGS(0.002)R;TPADTGFAFPDWAYKPES(0.5)S(0.5)PGSR 189.88 1.02E-17 508435000 215343 264585 227024 290534 331076 270033 358878 442923 417998 TRUE FALSE 186884.8769 262846.9237 336813.5657 356504.1852 324488.2353 280421.3442 324074.0668 348207.3633 368582.7526 0.507036413 0.713128658 0.91380718 0.9672297 0.880367388 0.760809729 0.87924371 0.944719634 1 18.49162904 4.522196104 2.392749805 0.905178955 0.491413649 0.805259303 0.064889847 0.169486019 1.594072522 0.018455145 0.118761224 33280.97982 -4.522196104 -0.413765306 TPADTGFAFPDWAYKPESS(ph)PGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TPADTGFAFPDWAYKPESSPGSR 23 1 P50548 P50548 ERF ETS domain-containing transcription factor ERF 1 TPADTGFAFPDWAYKPES(0.059)S(0.939)PGS(0.002)R;TPADTGFAFPDWAYKPES(0.015)S(0.982)PGS(0.003)R;TPADTGFAFPDWAYKPES(0.059)S(0.94)PGS(0.001)R 259.84 6.43E-44 1823090000 1717290 1895640 1686190 2504080 2627120 2114130 3059560 3493500 3369060 TRUE FALSE 1490345.775 1883187.416 2501637.124 3072669.636 2574845.452 2195461.949 2762844.342 2746442.211 2970773.565 0.50166926 0.633904731 0.842082733 1.034299508 0.866725584 0.739020293 0.930008391 0.924487226 1 21.50240722 4.307844 2.58103394 0.910220545 0.517918065 0.768892898 0.079413449 0.13830927 1.774017455 0.021849501 0.07870467 20316.2711 -4.307844 -0.39230248 TPAEGRDS(ph)PTREPGALPCACGQLPDLEDELSLLDPLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPAEGRDSPTREPGALPCACGQLPDLEDELSLLDPLPR 38 2 Q96RY5 Q96RY5 CRAMP1L Protein cramped-like 1 T(0.001)PAEGRDS(0.997)PT(0.002)REPGALPCACGQLPDLEDELSLLDPLPR 259.53 1.15E-62 115770000 13165 12638 8708.4 10583 13739 12568 11961 17193 7423.3 TRUE FALSE 11425.21189 12554.98015 12919.81137 12986.0319 13465.62078 13051.49909 10801.02406 13516.41075 6545.725931 1.745446115 1.918042442 1.973778234 1.98389484 2.057162326 1.993896358 1.650088038 2.064921582 1 12.67633748 1.233348484 24.99997378 0.999998558 1.9269056 0.829670197 0.131479645 63.26560742 303418.8233 0.256621134 0.031105629 17.11388008 -1.233348484 0.926907041 TPAGNFVTLEEGKGDLEEYGQDLLHTVFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPAGNFVTLEEGKGDLEEYGQDLLHTVFK 29 1 P43490 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 238.21 1.51E-45 475860000 556290 409790 338310 314700 387650 298480 547270 584950 418100 FALSE TRUE 482774.867 407098.0625 501917.8476 386157.4449 379936.5234 309962.7187 494195.8396 459862.9946 368672.6943 1.309494504 1.104226239 1.361418557 1.047426215 1.030552382 0.840753122 1.340473128 1.247347584 1 18.49198104 3.721899144 24.69997971 1.105001727 1.24296443 0.21992582 0.150231448 1369.024111 2029524.538 0.044191713 0.065762436 5271.074375 -3.721899144 0.137962703 TPALIVYGDQDPMGQTSFEHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPALIVYGDQDPMGQTSFEHLK 22 0 F8W9U3;Q96IU4;Q96IU4-2 F8W9U3 ABHD14B Alpha/beta hydrolase domain-containing protein 14B 0 195.34 4.35E-19 248380000 374300 375930 199730 260850 368620 305540 392960 439540 375800 FALSE TRUE 324835.3066 373460.4911 296320.0961 320079.9793 361285.1832 317294.3215 354850.7997 345547.7915 331373.3521 0.980269851 1.127008218 0.894218241 0.96591949 1.090266254 0.957513088 1.07084893 1.042774832 1 18.33809807 3.272876089 24.99665162 1.0327468 0.994533874 0.082180315 0.066856585 535.6512704 390184.4851 0.018814872 0.024288726 1874.45962 -3.272876089 -0.038212926 TPALVFEHVNNTDFK ddPTM_MDA-MB-175_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 ; 167.61 1.30E-06 1580050000 2033760 1450070 1008150 1393420 1495450 1203530 1666690 1880020 1739840 FALSE TRUE 1764993.463 1440544.395 1495694.712 1709817.308 1465693.471 1249830.578 1505054.66 1477992.353 1534158.097 1.150463871 0.938980407 0.974928669 1.114498767 0.955373161 0.814668697 0.981029702 0.963389859 1 20.54901573 3.02912847 24.45112355 0.940406983 1.032524841 0.294490987 0.07762952 232.6335633 195276.1766 0.023332914 0.026456593 1069.371166 -3.02912847 0.092117859 TPAPPEPGS(ph)PAPGEGPSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TPAPPEPGSPAPGEGPSGR 19 0 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 TPAPPEPGS(1)PAPGEGPSGR;TPAPPEPGS(1)PAPGEGPSGR;TPAPPEPGS(1)PAPGEGPSGR 184.37 2.63E-14 1008660000 1034280 850840 600780 744580 919910 821480 880040 1124130 1230860 TRUE FALSE 897597.2775 845250.776 891319.2175 913648.2692 901605.5908 853082.8672 794693.8563 883743.5475 1085349.133 0.827012479 0.778782375 0.82122811 0.841801261 0.830705589 0.785998571 0.732201125 0.814248172 1 20.04972777 1.242968312 5.964624373 1.006962405 0.801707444 0.790121753 0.031790142 0.060012323 7.998042554 0.050051509 0.008333518 17.49719019 -1.242968312 -0.205254961 TPAPSYPHAASAGTPAS(ph)PPPLHRPEAYPPSSHNGGLGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPAPSYPHAASAGTPASPPPLHRPEAYPPSSHNGGLGAR 39 1 A0A087WWH3;Q9NZM4-2;Q9NZM4 A0A087WWH3 GLTSCR1 Glioma tumor suppressor candidate region gene 1 protein 1 TPAPSYPHAASAGT(0.001)PAS(0.999)PPPLHRPEAYPPSSHNGGLGAR 184.4 7.37E-24 328400000 32598 38052 12649 16503 30581 37826 31067 37694 24531 TRUE FALSE 28290.09171 37802.03391 18766.09871 20250.25838 29972.49793 39281.1907 28054.12712 29633.43144 21630.97313 1.307851087 1.747588224 0.867556841 0.93616955 1.385628735 1.81596965 1.296942443 1.369953689 1 14.40081095 3.062663448 24.99991867 1.390037088 1.219652274 0.061594084 0.304310968 205.7556518 82084.92968 0.095923347 0.108766846 1155.216673 -3.062663448 -0.170384814 TPARPFGS(ph)VGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TPARPFGSVGR 11 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 TPARPFGS(1)VGR;TPARPFGS(1)VGR;TPARPFGS(1)VGR;TPARPFGS(1)VGR;TPARPFGS(1)VGR 134.24 8.78E-05 3328720000 966210 957060 624867 700208 950320 1075850 918150 1005450 1319020 TRUE FALSE 838522.9004 950773.0098 927054.7713 859200.9284 931410.4913 1117238.646 829107.9543 790442.3419 1163086.958 0.720946009 0.817456514 0.797064024 0.738724583 0.800808989 0.960580495 0.712851218 0.679607261 1 20.14952753 3.018907989 23.77449139 0.810488965 0.773539201 0.066672371 0.100865862 664.9280524 836055.8661 0.03179164 0.036040691 1044.498905 -3.018907989 -0.036949764 TPASTPVSGT(ph)PQAS(ph)PMIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TPASTPVSGTPQASPMIER 19 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 2 TPASTPVSGT(1)PQAS(1)PMIER;TPASTPVSGT(1)PQAS(1)PMIER;TPASTPVS(0.005)GT(0.995)PQAS(1)PMIER;TPASTPVS(0.001)GT(0.999)PQAS(1)PMIER;TPASTPVS(0.064)GT(0.936)PQAS(1)PMIER;TPASTPVS(0.012)GT(0.988)PQAS(1)PMIER 272.21 1.28E-38 2910230000 1797270 1989710 1424549 1793630 2297810 2371350 2108070 2604520 2345020 TRUE FALSE 1559756.216 1976639.464 2113465.661 2200901.105 2252088.077 2462577.369 1903629.696 2047563.666 2067794.407 0.754309138 0.955916825 1.022086942 1.064371341 1.089125722 1.190919833 0.920608785 0.990216271 1 20.97966132 4.750169026 1.924115785 1.037667824 0.66136263 0.623297973 0.070192698 0.600813637 2.286182282 0.020083102 0.407745532 56256.02293 -4.750169026 -0.376305193 TPASTPVSGTPQAS(ph)PMIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TPASTPVSGTPQASPMIER 19 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 TPASTPVS(0.001)GT(0.042)PQAS(0.957)PMIER;TPASTPVSGTPQAS(1)PMIER;TPASTPVSGTPQAS(1)PMIER;TPASTPVSGTPQAS(1)PMIER;TPASTPVSGTPQAS(1)PMIER;TPASTPVSGTPQAS(1)PMIER 354.88 6.79E-91 1806730000 704463 664867 500794 642154 773192 823738 763296 881826 774657 TRUE FALSE 611366.4297 660499.4449 742979.6535 787964.8804 757806.9919 855427.7339 689271.6714 693254.3723 683077.932 0.8950171 0.966945957 1.087693832 1.153550486 1.109400489 1.252313527 1.009067398 1.01489792 1 19.38169066 4.378834848 3.111394132 1.087775952 0.904691669 0.446044364 0.075560809 0.257696565 4.75233725 0.021449491 0.076263325 23924.05806 -4.378834848 -0.183084283 TPAVEGLTEAEEEELRAELTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TPAVEGLTEAEEEELRAELTK 21 1 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;O43399-6;A0A087WZ51;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 0 ;; 176.84 6.09E-17 174295000 142151 114260 103431 116927 104418 99586 122701 134132 253484 FALSE TRUE 123365.3852 113509.4185 153450.5776 143477.0625 102340.2861 103417.1379 110801.4759 105448.9156 223517.4103 0.551927409 0.507832559 0.686526286 0.641905533 0.457862705 0.462680458 0.495717429 0.471770479 1 17.77002769 1.234030198 24.9988262 1.000000699 0.53239711 0.786822567 0.076135531 68.72189863 379158.7374 0.158429154 0.020405335 17.14076489 -1.234030198 -0.467603589 TPDGTENGDFLALDLGGTNFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPDGTENGDFLALDLGGTNFR 21 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 102.38 0.0014187 0 17647 12707 6504.5 9437.6 14171 14365 13824 17148 14882 FALSE TRUE 15314.90424 12623.52688 9650.097956 11580.55132 13889.02483 14917.63085 12483.35061 13481.03365 13122.66691 1.167057302 0.961963522 0.735376278 0.88248459 1.058399555 1.136783471 0.951281526 1.027308986 1 13.67977333 3.233412537 24.93369067 1.03266495 0.924141774 0.150311068 0.114031219 228.8113044 1108200.373 0.035549928 0.041521297 1711.640434 -3.233412537 -0.108523176 TPDS(ph)PPTPAPLLLDLGIPVGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TPDSPPTPAPLLLDLGIPVGQR 22 0 Q16584;Q16584-2;E9PID4 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 T(0.006)PDS(0.994)PPT(0.001)PAPLLLDLGIPVGQR;T(0.011)PDS(0.988)PPTPAPLLLDLGIPVGQR;T(0.008)PDS(0.992)PPTPAPLLLDLGIPVGQR 180.32 5.63E-17 280679000 66707 61836 32095.5 54472 66047 62506 56873 67930 57196 TRUE FALSE 57891.50094 61429.79524 47616.99115 66840.70015 64732.79392 64910.64627 51357.46521 53403.69813 50434.35404 1.147858479 1.218014911 0.94413802 1.325301006 1.283505958 1.287032371 1.018303222 1.058875426 1 15.62211916 2.222078125 24.88002432 1.032322942 1.199477824 0.378293932 0.105783312 259.5674003 391809.2867 0.044291877 0.029958777 166.7547161 -2.222078125 0.167154882 TPDSEDKLFS(ph)PVIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPDSEDKLFSPVIAR 15 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 TPDSEDKLFS(1)PVIAR 92.993 0.0030453 89741000 152560 151150 106460 146030 176600 163250 179690 210170 217180 TRUE FALSE 132398.8095 150157.0857 157944.4121 179188.3434 173086.0055 169530.3331 162263.6915 165226.781 191505.2278 0.691358722 0.784088703 0.824752483 0.935683822 0.903818697 0.885251724 0.847306851 0.862779481 1 17.54702425 4.382000984 1.531355814 0.896367672 0.67969987 0.719806892 0.044461381 0.333671901 1.184538957 0.012926768 0.090018289 24099.1089 -4.382000984 -0.216667802 TPDTIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPDTIRR 7 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 104.75 0.012959 408610000 997880 872500 348990 347450 790580 912120 925930 944940 70885 FALSE TRUE 866007.6297 866768.4901 517762.7313 426343.8329 774849.0047 947209.8466 836133.4511 742871.9345 62505.05605 13.85500125 13.86717403 8.283533589 6.820949534 12.39658123 15.15413162 13.37705306 11.88498949 1 15.93168527 4.255678806 24.14904446 10 13.86109355 0.149894419 3.962589629 343.1907405 484134.5315 1.022852953 2.689564175 18016.84766 -4.255678806 3.861093547 TPEEIRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPEEIRK 7 1 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ; 97.033 0.019714 977720000 1283120 1168740 676430 873160 977730 983610 1242460 1348240 954690 FALSE TRUE 1113552.441 1161062.47 1003553.811 1071424.323 958275.0859 1021450.113 1121966.42 1059929.368 841827.6358 1.322779621 1.379216387 1.192113169 1.272735983 1.138326951 1.213372037 1.332774517 1.259081222 1 19.68316535 7.991102087 0.022870553 2.08E-06 2.861928723 0.291858256 0.091730668 8702.574409 19.80676215 952.1193374 1609.661896 97972025.6 -7.991102087 2.86192664 TPEELDDS(ph)DFETEDFDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 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(0.964)DFET(0.036)EDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(0.999)DFET(0.001)EDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR 392.64 1.04E-126 37670276000 4330133 3605319 2657156.8 3654248 3876492 4488268.6 2926133.7 4569802 4104475 TRUE FALSE 3757894.953 3581635.422 3942166.716 4484000.86 3799357.393 4660935.197 2642357.704 3592585.405 3619248.641 1.038308037 0.989607451 1.089222407 1.23893142 1.049764128 1.287818456 0.730084602 0.992632936 1 21.78725879 2.240591074 24.99987614 0.917898128 1.111294575 0.418930628 0.115209903 54.2921374 668482.4393 0.043871827 0.032263529 174.0167584 -2.240591074 0.193396447 TPEEREWR ddPTM_MDA-MB-175_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 ;;; 78.77 0.027146 3001850000 2717100 2169960 1338380 1788880 2129250 2518620 1861450 2005080 1805650 FALSE TRUE 2358028.351 2155705.39 1985625.045 2195072.545 2086882.091 2615512.941 1680926.866 1576309.246 1592188.114 1.480998589 1.353926317 1.247104552 1.378651509 1.31070071 1.642716032 1.055733836 0.990027015 1 20.60257937 2.103744182 7.893619639 1.003055449 1.387259593 0.74813442 0.106008328 0.111696484 7.586739301 0.042531086 0.028613642 126.9825902 -2.103744182 0.384204144 TPEEVIEYSAVFWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPEEVIEYSAVFWER 15 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 134.08 8.70E-05 28905000 6374.2 8708.8 7540 5144.4 8100.6 4310.3 9878.2 12698 9165.7 FALSE TRUE 5531.83332 8651.591319 11186.36922 6312.514647 7939.413909 4476.12003 8920.213684 9982.631516 8082.141388 0.684451441 1.070457804 1.384084821 0.781044818 0.982340388 0.553828474 1.103694338 1.235146855 1 12.98052187 2.025311706 24.99963392 1.144885317 0.926836413 0.142119365 0.231195778 404.4445832 399456.3646 0.095584654 0.06444089 106.0014255 -2.025311706 -0.218048904 TPEFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPEFLR 6 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 110.54 0.066582 1683600000 605710 524560 329070 381550 542980 623950 525400 581640 541030 FALSE TRUE 525663.8888 521114.1308 488209.3527 468186.7591 532175.7603 647953.7602 474446.7889 457260.8123 477070.0497 1.101858918 1.092322042 1.023349407 0.981379484 1.115508636 1.35819417 0.994501309 0.958477298 1 18.86384159 2.031774749 24.99603937 0.976337124 1.107628865 0.2729351 0.098338131 257.303128 202410.004 0.042378679 0.028571455 107.5907039 -2.031774749 0.131291741 TPEKLDNTPAS(ph)PPRS(ph)PAEPNDIPIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.004)PAS(0.996)PPRS(1)PAEPNDIPIAK;TPEKLDNT(0.011)PAS(0.989)PPRS(1)PAEPNDIPIAK 162.38 8.63E-12 574730000 1087480 1054560 854810 943220 1248410 989720 1787970 2052310 699690 TRUE FALSE 943766.7627 1047632.526 1268198.975 1157392.517 1223569.083 1027795.169 1614572.945 1613439.478 616973.4453 1.529671609 1.698018827 2.055516303 1.8759195 1.983179491 1.665866135 2.616924532 2.615087391 1 19.23484887 5.653401665 0.528353747 2.113294618 0.209424879 0.058020414 0.468753522 23.64362846 2.509243528 0.29410489 34.10285497 450196.0345 -5.653401665 -1.903869739 TPELNLDQFHDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPELNLDQFHDK 12 0 P27824;P27824-2;P27824-3;H0Y9Q7;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 ; 159.52 6.90E-05 817980000 766110 574230 557870 854220 800160 668200 534380 1010380 1530780 FALSE TRUE 664866.6224 570457.8453 827657.798 1048183.707 784238.3815 693906.0864 482555.9098 794318.0998 1349812.932 0.492562048 0.422619929 0.613164816 0.77653998 0.580997828 0.514075743 0.35749836 0.58846532 1 20.36432805 1.248289991 5.023251215 1.025424879 0.539948893 0.623257376 0.112194567 0.115720445 7.404207839 0.192648974 0.030202934 17.71291306 -1.248289991 -0.485475985 TPELRDDDFLGGAECSLGQIVSSQVLTLPLMLKPGKPAGR ddPTM_MDA-MB-175_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 0 151.13 7.06E-14 193340000 100870 113720 69828 73765 102080 78238 143210 160070 102160 FALSE TRUE 87539.77393 112972.9658 103597.0544 90514.47068 100048.8077 81247.86649 129321.5162 125840.2762 90082.76118 0.971770545 1.254101943 1.150020859 1.004792365 1.110632117 0.90192469 1.435585616 1.396940708 1 16.45896343 2.231147858 24.99989835 1.308976947 1.077239761 0.296683925 0.150567228 190.931382 643918.9107 0.060048329 0.041392194 170.2738115 -2.231147858 -0.231737185 TPELTWER ddPTM_MDA-MB-175_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 ;;; 126.52 0.0028279 1200850000 649900 656606 460914 509749 649695 708881 625025 702371 695354 FALSE TRUE 564014.0684 652292.712 683813.5521 625495.3015 636767.3406 736152.1108 564410.1717 552174.4275 613150.0423 0.919863051 1.063838648 1.115246685 1.020134157 1.038517976 1.200606801 0.920509064 0.900553518 1 19.22588063 2.13859907 22.10199687 0.931220151 1.059792309 0.35945429 0.07476933 5.496971151 1205.092565 0.029720412 0.020037514 137.5938651 -2.13859907 0.128572158 TPEPVVPTAPELRPSTSTDRPVT(ph)PKPTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TPEPVVPTAPELRPSTSTDRPVTPKPTSR 29 3 Q14676;Q14676-2 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 TPEPVVPTAPELRPS(0.057)T(0.057)S(0.217)T(0.217)DRPVT(0.451)PKPT(0.001)S(0.001)R;TPEPVVPT(0.001)APELRPS(0.07)T(0.07)S(0.07)T(0.07)DRPVT(0.581)PKPT(0.07)S(0.07)R;TPEPVVPT(0.004)APELRPS(0.076)T(0.076)S(0.076)T(0.076)DRPVT(0.541)PKPT(0.076)S(0.076)R 113.41 0.00026253 1220940000 1026770 615719 434981 502391 625938 551011 648489 807212 644028 TRUE FALSE 891079.743 611674.3013 645339.2665 616466.5551 613483.0584 572208.7497 585598.6366 634595.9955 567891.7435 1.569101423 1.077096662 1.136377265 1.085535337 1.080281701 1.007601812 1.03118005 1.11745945 1 19.11525641 4.739184563 6.612663045 1.069935658 1.578529545 0.928320904 0.043849897 0.028949127 8.083387995 0.010849155 0.065750231 54851.00165 -4.739184563 0.508593887 TPESQPDT(ph)PPGTPLVSQDEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(0.993)PPGT(0.007)PLVSQDEKR;TPESQPDT(0.998)PPGT(0.002)PLVSQDEKR;TPESQPDT(1)PPGTPLVSQDEKR;TPESQPDT(0.971)PPGT(0.029)PLVSQDEKR 175.11 1.25E-12 9847130000 3322630 2740060 1832710 2207140 2768660 2280530 3260460 3805200 1893960 TRUE FALSE 2883536.027 2722060.365 2719014.686 2708304.871 2713569.083 2368263.465 2944261.091 2991487.592 1670058.206 1.7266081 1.629919457 1.628095761 1.621682921 1.624835034 1.41807241 1.762969147 1.791247503 1 20.67146696 1.231024782 24.99988039 0.999998844 1.652006931 0.798808614 0.102582666 128.2575633 425453.8862 0.27592775 0.026857705 17.0225564 -1.231024782 0.652008086 TPEYLHIDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPEYLHIDQR 10 0 O00178;B0QY59 O00178 GTPBP1 GTP-binding protein 1 0 66.758 0.065012 304490000 70538 87448 53591 68362 79774 99696 61980 64356 81893 FALSE TRUE 61216.22458 86873.54833 79507.78685 83884.63695 78186.65348 103531.3696 55969.18914 50593.97022 72211.70283 0.847732738 1.203039742 1.101037418 1.161648786 1.082742137 1.433720098 0.775070895 0.700633945 1 16.13994504 2.200170817 24.99875531 0.797185749 1.138101552 0.45514513 0.160505915 126.3384172 82268.47226 0.062323943 0.042019713 158.5516686 -2.200170817 0.340915802 TPGHPPPPEIPSELGACDFEKPES(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TPGHPPPPEIPSELGACDFEKPESPR 26 1 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 TPGHPPPPEIPSELGACDFEKPES(1)PR;TPGHPPPPEIPSELGACDFEKPES(1)PR;TPGHPPPPEIPSELGACDFEKPES(1)PR;TPGHPPPPEIPSELGACDFEKPES(1)PR 182.56 1.12E-17 5543800000 2209390 2700330 2016850 2122230 3628050 2697580 3697230 4471160 3932310 TRUE FALSE 1917413.514 2682591.354 2992205.406 2604114.758 3555858.903 2801357.648 3338673.204 3515037.229 3467436.792 0.552977207 0.773652561 0.86294447 0.751020109 1.025500713 0.80790446 0.962864907 1.013727846 1 21.72543815 5.520854458 0.387292696 1.003508128 1.54E-16 0.711083431 0.079626759 7.211489926 0.589457833 0.095937772 3.760596573 331783.2506 -5.520854458 -1.003508128 TPGNERPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPGNERPPR 9 1 P82673;H0YG82;P82673-2 P82673 MRPS35 "28S ribosomal protein S35, mitochondrial" 0 ; 101.65 0.0035039 47670000 69347 82143 58428 61713 69950 108443 71551 79537 85272 FALSE TRUE 60182.61825 81603.39722 86683.97623 75725.87987 68558.13185 112614.8724 64611.99503 62528.63151 75191.2413 0.800393998 1.085277963 1.152846724 1.007110384 0.911783483 1.497712638 0.859302146 0.831594617 1 16.198277 TPGRQS(ph)PGPGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TPGRQSPGPGHR 12 1 O15169-2;O15169 O15169-2 AXIN1 Axin-1 1 T(0.007)PGRQS(0.993)PGPGHR;T(0.218)PGRQS(0.782)PGPGHR;T(0.026)PGRQS(0.974)PGPGHR 71.344 0.027155 157564000 187149 165116 92094 116428 156028 161401 163598 179639 103060 TRUE FALSE 162416.7855 164031.3421 136630.9664 142864.7569 152923.3481 167610.2009 147732.2911 141224.5978 90876.36421 1.787228031 1.80499455 1.503481875 1.572078264 1.682762613 1.844376174 1.625640423 1.554030017 1 16.4716175 1.118821611 2.000960038 0.598714348 1.687856517 0.806734579 0.105309145 0.505552066 1.499822149 1.150017571 0.030121542 13.14684706 -1.118821611 1.089142168 TPHDILEDINAS(ph)PEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TPHDILEDINASPEMR 16 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 TPHDILEDINAS(1)PEMR;TPHDILEDINAS(1)PEMR;TPHDILEDINAS(1)PEMR 218.38 8.62E-15 368706000 346573 234915 148215 170308 224295 246425 222762 255354 232847 TRUE FALSE 300772.4999 233371.8279 219892.2697 208979.0344 219831.9683 255905.1292 201158.5755 200748.5343 205320.0929 1.464895596 1.136624402 1.07097297 1.017820669 1.070679275 1.246371583 0.979731563 0.97773448 1 17.64751529 4.827120038 1.931725097 1.046509949 1.660904095 0.738578857 0.07684857 0.569081124 1.858826369 0.021791433 0.673268185 67161.44596 -4.827120038 0.614394146 TPHPS(ph)PAHSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPHPSPAHSSR 11 0 A0A0A0MTL6;Q6ZS17-2;Q6ZS17;Q6ZS17-3;Q6ZS17-4 A0A0A0MTL6 FAM65A Protein FAM65A 1 T(0.011)PHPS(0.988)PAHS(0.001)SR;T(0.001)PHPS(0.989)PAHS(0.008)S(0.002)R 63.185 0.049107 277508000 242115 251086 129231 180002 316700 383540 231961 275851 276460 TRUE FALSE 210118.8893 249436.5995 191727.5439 220874.2053 310398.2896 398295.032 209465.4579 216862.4103 243777.2137 0.861929981 1.023215401 0.786486731 0.906049429 1.273286723 1.633848488 0.859249537 0.88959262 1 17.89520376 3.350514201 10.15309347 1.105593424 0.894404056 0.210652754 0.224840751 0.644902813 55.197366 0.072267632 0.09329681 2241.373337 -3.350514201 -0.211189368 TPHS(ph)PPLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPHSPPLAK 9 0 Q8IZW8 Q8IZW8 TNS4 Tensin-4 1 T(0.065)PHS(0.935)PPLAK;T(0.205)PHS(0.795)PPLAK 64.64 0.044327 952080000 1975680 1807060 1120640 1174630 1721950 1395730 2121600 2442810 1015170 TRUE FALSE 1714588.882 1795189.304 1662585.252 1441347.695 1687686.564 1449424.636 1915847.559 1920434.091 895157.7591 1.915404145 2.005444611 1.857309771 1.610160533 1.885350986 1.619183458 2.140234544 2.145358259 1 19.77178243 4.037929989 7.174498294 1.798080696 1.954995211 0.055575183 0.325523237 0.791134395 115.1042705 0.083646234 0.174344071 10912.64405 -4.037929989 0.156914514 TPHTATLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPHTATLR 8 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 103.83 0.0046967 456480000 69349 58053 48282 63642 47987 63586 65742 64857 77749 FALSE TRUE 60184.35394 57671.64602 71631.33669 78092.88881 47032.15258 66032.19457 59366.35096 50987.83527 68557.60179 0.877865508 0.841214461 1.044834341 1.139084314 0.686023889 0.963163717 0.865933892 0.743722562 1 16.06502902 3.236039806 24.99772332 0.844895185 0.971074598 0.202580957 0.121647491 109.7836393 1088674.528 0.03646743 0.04329268 1722.026403 -3.236039806 0.126179412 TPHYGSQTPLHDGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPHYGSQTPLHDGSR 15 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 0 129.05 3.95E-05 207260000 71217 72012 33847 46792 81296 72879 63748 75957 59518 FALSE TRUE 61805.49301 71538.94843 50215.52241 57416.83877 79678.36865 75682.70229 57565.72877 59714.18665 52481.84984 1.177654621 1.36311789 0.956816929 1.094032298 1.518208083 1.442073832 1.096869279 1.137806438 1 15.67953095 2.055325196 24.99864521 1.090322098 1.255284849 0.207311147 0.16572115 156.8697937 70880.59936 0.072234031 0.048700167 113.586102 -2.055325196 0.164962751 TPIHAAATNGHSECLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPIHAAATNGHSECLR 16 0 O15084-2;O15084;O15084-4;O15084-1;B4DIW9 O15084-2 ANKRD28 Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit A 0 97.291 0.0018061 48192000 128870 80379 93743 87422 68680 66443 67822 75901 81858 FALSE TRUE 111839.503 79850.98506 139077.4284 107272.5013 67313.40237 68999.1052 61244.63288 59670.16181 72180.84049 1.549434756 1.106262888 1.926791478 1.486163094 0.932566065 0.955919947 0.848488774 0.826675907 1 16.13932832 3.237253697 5.48573393 0.896093443 1.521266184 0.693623205 0.199734727 0.091982346 8.707885439 0.058578843 0.071193723 1726.846349 -3.237253697 0.625172741 TPIS(ph)PLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TPISPLK 7 0 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 TPIS(1)PLK;TPIS(1)PLK;TPIS(1)PLK;TPIS(1)PLK;T(0.001)PIS(0.999)PLK 111.61 0.0068612 7549460000 12345900 10401800 8150900 9708800 11314300 9279300 12168100 14844700 14991200 TRUE FALSE 10714358.03 10333469.89 12092702.5 11913331.43 11089167.57 9636280.676 10988039.53 11670276.43 13218957.41 0.810529734 0.781715953 0.91480002 0.90123079 0.838883674 0.728974334 0.831233447 0.882843939 1 23.65610506 1.291131921 2.34982625 1.032584532 0.830873763 0.508172132 0.053084557 0.476479509 3.061799261 0.190420498 0.015248785 19.54933195 -1.291131921 -0.201710769 TPKDS(ph)PGIPPSANAHQLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TPKDSPGIPPSANAHQLFR 19 1 B4DG22;B1AXG1;B7ZB17;P51812 B4DG22 RPS6KA3 Ribosomal protein S6 kinase alpha-3 1 T(0.006)PKDS(0.994)PGIPPSANAHQLFR;T(0.028)PKDS(0.972)PGIPPSANAHQLFR;T(0.074)PKDS(0.926)PGIPPSANAHQLFR 116.74 6.79E-05 510504000 504843 421382 181541 300540 404197 319000 395987 488288 301997 TRUE FALSE 438126.7184 418613.9139 269334.8348 368782.2005 396154.2705 331272.1364 357584.2417 383871.4111 266295.2587 1.645266689 1.571991615 1.011414308 1.38486206 1.487650484 1.244003134 1.342811147 1.441525519 1 18.02266722 4.449110024 24.69029728 1.301824942 1.626948098 0.415220798 0.163889522 152.8604987 134737.6297 0.039326432 0.104052302 28126.13289 -4.449110024 0.325123157 TPLALAGS(ph)PTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPLALAGSPTPK 12 0 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 1 TPLALAGS(0.996)PT(0.004)PK;TPLALAGS(0.999)PT(0.001)PK 159.75 7.33E-05 566380000 1013190 794020 577070 681490 885990 691200 927390 1085890 1043940 TRUE FALSE 879294.3744 788804.0303 856142.9822 836232.7204 868360.5324 717790.9113 837451.8605 853680.8739 920526.6025 0.955207999 0.856905198 0.930057839 0.90842863 0.943330187 0.779761182 0.909753024 0.927383165 1 19.81209989 1.298841951 2.224777464 1.020304423 0.895489439 0.296293507 0.049781482 0.702632743 4.010814433 0.167243198 0.012944644 19.89949023 -1.298841951 -0.124814984 TPLAVELEVLDGHDPDPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TPLAVELEVLDGHDPDPGR 19 0 Q86TX2;G3V4F2;A0A087X0W7;A0A087WT95;P49753 Q86TX2 ACOT1;ACOT2 "Acyl-coenzyme A thioesterase 1;Acyl-coenzyme A thioesterase 2, mitochondrial" 0 ;;; 183.23 2.75E-14 721260000 1312440 1050900 681580 920860 1067200 1215020 1023160 1168600 1082240 FALSE TRUE 1138997.729 1043996.569 1011194.368 1129955.337 1045964.808 1261762.606 923934.1007 918703.9841 954298.8201 1.193544102 1.093993356 1.059620264 1.184068673 1.096055854 1.322188165 0.96818112 0.962700534 1 19.86408156 2.173336863 24.99995838 0.973622633 1.149189575 0.576747714 0.072915188 41.02287307 15723.25788 0.028725083 0.019366452 149.0516757 -2.173336863 0.175566942 TPLCATAPCLPS(ph)PTATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPLCATAPCLPSPTATR 17 0 Q6PI47-3;Q6PI47 Q6PI47-3 KCTD18 BTB/POZ domain-containing protein KCTD18 1 TPLCATAPCLPS(0.995)PT(0.002)AT(0.003)R 143.67 5.67E-07 69916000 76371 61684 35518 47742 57850 56773 60036 60566 69318 TRUE FALSE 66278.37885 61278.79374 52694.6236 58582.55079 56698.89818 58957.09405 54213.71796 47614.43223 61123.30501 1.084338925 1.002543854 0.862103638 0.958432316 0.927615059 0.964559983 0.886956586 0.778989818 1 15.89943493 7.999999999 0.628966068 0.892011017 16.15460431 0.409317252 0.064934055 194.4876506 1.373874154 0.030218663 4110.002082 99999999.83 -7.999999999 15.26259329 TPLDLFAHFGPEPGDHSDPLPPSAPS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TPLDLFAHFGPEPGDHSDPLPPSAPSPTR 29 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 TPLDLFAHFGPEPGDHSDPLPPS(0.331)APS(0.527)PT(0.142)R;TPLDLFAHFGPEPGDHSDPLPPS(0.009)APS(0.949)PT(0.042)R;TPLDLFAHFGPEPGDHSDPLPPS(0.008)APS(0.973)PT(0.018)R;TPLDLFAHFGPEPGDHSDPLPPS(0.037)APS(0.93)PT(0.033)R;TPLDLFAHFGPEPGDHS(0.031)DPLPPS(0.007)APS(0.897)PT(0.065)R;TPLDLFAHFGPEPGDHSDPLPPS(0.005)APS(0.966)PT(0.029)R 219.77 3.53E-34 824745000 451013 335054.3 247603.7 304353 330727 346216.3 341648 380581 416322 TRUE FALSE 391410.4893 332853.3062 367345.6775 373461.0004 324146.1798 359535.4651 308515.0295 299196.7148 367104.8874 1.066208876 0.906698106 1.000655916 1.017314161 0.882979745 0.979380764 0.840400224 0.815016975 1 18.4858328 2.844881562 1.283942586 0.875721914 0.990312766 0.248684817 0.070993064 0.533245967 1.851094813 0.034001601 0.031304804 699.6511663 -2.844881562 0.114590852 TPLGAS(ph)LDEQSSSTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TPLGASLDEQSSSTLK 16 0 E9PHV5;P28290-3;P28290 E9PHV5 SSFA2 Sperm-specific antigen 2 1 TPLGAS(1)LDEQSSSTLK;TPLGAS(1)LDEQSSSTLK;TPLGAS(0.998)LDEQS(0.002)SSTLK;TPLGAS(1)LDEQSSSTLK;TPLGAS(1)LDEQSSSTLK;TPLGAS(1)LDEQSSSTLK 270.15 1.47E-28 1296220000 2092210 1700730 1044248 1325562 1749330 1154574 2515070 2489770 2017380 TRUE FALSE 1815719.148 1689557.793 1549249.826 1626551.112 1714521.756 1198991.209 2271158.899 1957352.061 1778887.635 1.0207048 0.949783314 0.870909323 0.914364168 0.963816782 0.674011773 1.276729825 1.100323608 1 20.76254395 2.225597754 24.99999908 1.126694472 0.903620153 0.476946126 0.111866315 195.6489671 377322.8374 0.044188448 0.030000325 168.1116279 -2.225597754 -0.22307432 TPLHNDNSWIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPLHNDNSWIR 11 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 0 ; 178.71 7.42E-06 707820000 501710 577880 304800 413970 562260 564250 495520 596730 586930 FALSE TRUE 435407.7523 574083.8682 452202.2995 507968.2156 551072.126 585957.0626 447464.5467 469123.9333 517543.804 0.841296425 1.109246915 0.87374691 0.981498014 1.064783544 1.132188344 0.864592607 0.906442951 1 18.98132145 TPLRPLDPTR ddPTM_MDA-MB-175_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 ;;; 138.22 6.43E-05 2213380000 2744250 2812990 1751150 2241590 2912560 3033320 2731410 3165350 3175660 FALSE TRUE 2381590.409 2794511.283 2598011.997 2750577.27 2854605.754 3150013.783 2466518.279 2488464.535 2800237.093 0.850495987 0.997955241 0.927782867 0.982265851 1.019415735 1.12490967 0.880824801 0.888662086 1 21.41711755 4.746888785 24.05400022 0.970709853 0.850495883 0.239100186 0.070346364 1082.719265 3127062.249 0.018545044 0.197616767 55832.71988 -4.746888785 -0.12021397 KAGS(ph)FSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 KAGSFSR 7 1 O14523;O14523-2 O14523 C2CD2L C2 domain-containing protein 2-like 1 KAGS(0.98)FS(0.02)R 59.542 0.063031 66383000 85035 102830 77662 125900 138490 138820 127050 218370 198090 TRUE FALSE 73797.4093 102154.503 115219.603 154487.5193 135734.32 144160.4952 114728.7106 171673.2749 174672.0259 0.422491289 0.58483608 0.659633976 0.884443393 0.777081042 0.825321024 0.65682361 0.982832105 1 17.41428905 4.984975838 0.500737884 0.898424191 6.32E-29 0.707501191 0.097478383 3.676240704 0.625164381 0.076749087 2.050916068 96599.71352 -4.984975838 -0.898424191 down TPLSDTLHLPVWVDNDGNCAALAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPLSDTLHLPVWVDNDGNCAALAER 25 0 Q9Y223-5;Q9Y223-3;Q9Y223;Q9Y223-2 Q9Y223-5 GNE Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase;UDP-N-acetylglucosamine 2-epimerase (hydrolyzing);N-acetylmannosamine kinase 0 69.528 0.040279 103510000 26895 27902 18052 21070 26619 30903 28737 25589 29445 FALSE TRUE 23340.75761 27718.70992 26782.00758 25854.26553 26089.33398 32091.85841 25950.09016 20116.99148 25964.04564 0.898964588 1.067580542 1.03150364 0.995771841 1.004825455 1.236011477 0.999462507 0.774801884 1 14.66422758 1.981707899 24.57396329 0.876060369 1.043296993 0.279533638 0.098912139 626.6834835 841897.2653 0.043218829 0.025568742 95.87555676 -1.981707899 0.167236624 TPLSFTNPLHS(ph)DDS(ph)DSDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPLSFTNPLHSDDSDSDER 19 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 2 TPLSFTNPLHS(0.999)DDS(0.956)DS(0.044)DER;TPLSFTNPLHS(0.999)DDS(0.985)DS(0.016)DER 98.267 0.00051961 72680000 62761 67865 45985 59559 64838 65193 65933 77052 121420 TRUE FALSE 54466.97483 67419.19035 68223.49981 73082.78125 63547.85065 67701.0169 59538.82781 60575.02942 107065.8659 0.508723993 0.629698268 0.637210555 0.682596462 0.593539781 0.632330541 0.556095328 0.565773497 1 16.70813908 1.235353067 24.99994286 1.000000547 0.602377613 0.867582083 0.049015915 31.95574184 249023.2771 0.085479118 0.012284396 17.19305558 -1.235353067 -0.397622934 TPLSFTNPLHSDDS(ph)DSDERNSDGAVTQNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPLSFTNPLHSDDSDSDERNSDGAVTQNK 29 1 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 TPLSFTNPLHSDDS(0.987)DS(0.012)DERNSDGAVTQNK 175.75 2.53E-13 53938000 85693 59012 38311 49809 72802 65557 74107 92642 53642 TRUE FALSE 74368.45293 58624.34629 56838.32774 61118.89473 71353.38263 68079.02021 66920.11455 72831.22924 47300.50387 1.572254984 1.239402152 1.201643177 1.292140458 1.508512104 1.439287421 1.414786505 1.539755886 1 15.52956793 3.286705558 24.99918702 1.40589466 1.31124041 0.008352916 0.176402177 359.3422851 186585.1392 0.049322202 0.06367455 1935.109557 -3.286705558 -0.094654249 TPLYLQPDAYGS(ph)LDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPLYLQPDAYGSLDR 15 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 TPLYLQPDAYGS(1)LDR;TPLYLQPDAYGS(1)LDR 174.65 9.45E-07 365190000 475070 418500 213162 254150 371850 402220 387590 367740 339660 TRUE FALSE 412288.2958 415750.8459 316247.8562 311858.6419 364450.9125 417693.6637 350001.5815 289101.6628 299505.7817 1.37656206 1.388122939 1.055899002 1.041244146 1.216840992 1.394609684 1.168597078 0.965262377 1 18.19222433 1.834136808 4.1597425 0.983643977 1.235803331 0.420801917 0.124961877 0.230920359 6.462700666 0.078766521 0.036610997 68.25536723 -1.834136808 0.252159354 TPMAGVS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPMAGVSPK 9 0 A0A087WWD1;B7Z6K7;Q9H707 A0A087WWD1 ZNF814;ZNF552 Putative uncharacterized zinc finger protein 814;Zinc finger protein 552 1 TPMAGVS(1)PK 69.815 0.056824 135920000 148540 134660 91596 111010 148700 127310 145610 168070 162790 TRUE FALSE 128910.0626 133775.4096 135892.132 136216.5172 145741.1609 132207.6981 131488.7646 132129.5384 143545.1517 0.898045397 0.931939589 0.946685628 0.948945441 1.015298387 0.921018206 0.916009793 0.920473711 1 17.13114508 4.686155397 2.020111999 0.948883385 0.886747027 0.216709547 0.032815213 1.16287846 5.649114562 0.008976145 0.128118632 48546.21748 -4.686155397 -0.062136358 TPMYGSQT(ph)PLQDGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPMYGSQTPLQDGSR 15 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 1 TPMYGS(0.006)QT(0.994)PLQDGSR 195.38 1.41E-07 290640000 117000 105830 66249 96320 133700 128960 96665 134770 144360 TRUE FALSE 101538.1536 105134.7958 98287.23799 118190.9282 131039.6316 133921.1746 87290.44318 105950.4843 127293.9253 0.797666922 0.825921548 0.772128268 0.928488362 1.029425649 1.052062574 0.685739268 0.832329462 1 16.95780405 3.735927084 24.88977867 0.907294032 0.801307174 0.222544257 0.10598448 423.9768422 4007057.984 0.031814152 0.049709334 5444.112406 -3.735927084 -0.105986857 TPNNVVST(ph)PAPS(ph)PDASQLASSLSSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPNNVVSTPAPSPDASQLASSLSSQK 26 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 2 TPNNVVS(0.148)T(0.852)PAPS(1)PDASQLASSLSSQK 204.47 6.70E-25 144980000 153950 179390 105420 105090 150580 137760 175180 183720 182860 TRUE FALSE 133605.1174 178211.5753 156401.4646 128952.2907 147583.7526 143059.7163 158191.0706 144432.9077 161242.4991 0.828597412 1.105239476 0.969976684 0.79974133 0.915290655 0.887233311 0.981075532 0.895749622 1 17.29887252 3.976141931 24.98183152 0.912326948 0.984590868 0.07647692 0.084912884 1405.861205 1472084.702 0.021004912 0.036663974 9465.464497 -3.976141931 0.07226392 TPNTEQQTPLFQVIS(ph)PQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPNTEQQTPLFQVISPQR 18 0 Q8IZD4;Q8IZD4-2 Q8IZD4 DCP1B mRNA-decapping enzyme 1B 1 TPNTEQQTPLFQVIS(1)PQR 138.07 2.94E-06 43798000 64050 44919 36786 41421 44573 47507 39110 49517 79809 TRUE FALSE 55585.63022 44623.92413 54575.83264 50826.27113 43686.08451 49334.62503 35317.11822 38928.17489 70374.07094 0.789859525 0.634096103 0.775510524 0.722230084 0.620769609 0.701034122 0.501848447 0.553160765 1 16.10275635 3.258422771 19.01628138 0.648357607 0.726764851 0.017285346 0.138516265 46.49001968 44504.54252 0.039615299 0.050939185 1813.104231 -3.258422771 0.078407244 TPPGLQHEYAAPADYFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPPGLQHEYAAPADYFR 17 0 Q5JRG1;H7BYF2;Q9BVL2-2;Q9BVL2-3;Q9BVL2 Q5JRG1 NUPL1 Nucleoporin p58/p45 0 99.021 0.0016838 220670000 146530 143970 83441 124050 141360 140610 106180 150640 162480 FALSE TRUE 127165.6892 143024.2516 123793.3467 152217.4485 138547.2126 146019.3577 95882.67994 118426.8083 143271.7995 0.887583528 0.99827218 0.864045452 1.06243831 0.967023609 1.019177244 0.669236237 0.826588405 1 17.12839514 2.270031504 24.99975175 0.824046603 0.967609134 0.298228721 0.096984739 217.482057 172762.0615 0.035289826 0.027332686 186.2222218 -2.270031504 0.143562531 TPPGPCCS(ph)PGVGWAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPPGPCCSPGVGWAQR 16 0 H3BSW6;Q2VPK5-3;Q2VPK5;Q2VPK5-5 H3BSW6 CTU2 Cytoplasmic tRNA 2-thiolation protein 2 1 TPPGPCCS(1)PGVGWAQR 184.01 1.33E-12 0 68878 56145 33324 45508 68202 55661 63787 59497 59650 TRUE FALSE 59775.59779 55776.1798 49439.59786 55841.28695 66844.91363 57802.31469 57600.94656 46774.02956 52598.24495 1.136456128 1.060419028 0.939947671 1.061656848 1.270858252 1.098939988 1.095111569 0.889269777 1 15.68272704 1.75128471 24.99990903 0.943649817 1.093153506 0.349720394 0.085087902 4.16705013 8203.521088 0.047862382 0.02298424 56.40072799 -1.75128471 0.14950369 TPPKS(ph)PSSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPPKSPSSAK 10 1 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 T(0.065)PPKS(0.934)PS(0.001)SAK;TPPKS(0.995)PS(0.004)S(0.001)AK 92.039 0.0058983 378880000 1117890 909560 660720 753820 736630 558110 1029210 1229950 1283730 TRUE FALSE 970158.0041 903585.0405 980246.402 924986.3524 721972.5042 579580.8528 929397.3726 966934.764 1131968.902 0.857053584 0.79824193 0.865965841 0.817148202 0.637802419 0.512011286 0.82104497 0.85420612 1 20.11040289 1.451678191 2.113627545 1.012320076 0.752016005 0.343919743 0.108127312 0.559917297 3.876993037 0.248003023 0.03259359 28.29294735 -1.451678191 -0.260304071 TPPSTTVGSHS(ph)PPETPVLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 262.78 1.21E-36 2319490000 1060340 786250 374900 549470 768550 856420 693550 809070 788540 TRUE FALSE 920213.3824 781085.072 556202.894 674235.5616 753257.3586 889367.0316 626289.6277 636056.6767 695319.6995 1.323439251 1.123346674 0.799923969 0.969677059 1.083325209 1.279076419 0.900721824 0.91476867 1 19.40731694 4.564013598 4.026884475 0.991521727 1.308558932 0.410371694 0.126809232 0.243672416 6.779927283 0.033325651 0.155510758 36644.90483 -4.564013598 0.317037205 TPPTAALSAPPPLISTLGGRPVS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPPTAALSAPPPLISTLGGRPVSPR 25 1 A0A2R8Y8C6;Q8WXX7-2;Q8WXX7;A0A087WVB5;Q75MD7;A0A2R8Y568;A0A024RDL5;A0A2R8Y522;Q8WXX7-5 A0A2R8Y8C6 AUTS2 Autism susceptibility gene 2 protein 1 TPPTAALSAPPPLISTLGGRPVS(0.999)PR 110.38 0.0017308 1899700000 529630 502840 280500 323230 465470 527000 438290 469780 437390 TRUE FALSE 459638.0536 499536.8109 416150.7382 396624.3118 456208.0577 547274.031 395784.7033 369321.2028 385682.2525 1.191753187 1.295203001 1.078998931 1.028370658 1.182859867 1.418976444 1.026193714 0.957578941 1 18.55705323 2.022485671 24.98784995 0.98059738 1.192462084 0.453134329 0.10680374 205.9824173 228903.0153 0.045504578 0.030677042 105.3138939 -2.022485671 0.211864703 TPQEAIMDGTEIAVS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TPQEAIMDGTEIAVSPR 17 0 Q06587 Q06587 RING1 E3 ubiquitin-protein ligase RING1 1 TPQEAIMDGTEIAVS(1)PR;TPQEAIMDGTEIAVS(1)PR;TPQEAIMDGTEIAVS(1)PR;TPQEAIMDGTEIAVS(1)PR;TPQEAIMDGTEIAVS(1)PR 268.25 6.63E-28 544730000 454457 406019 256204 309472 398124 399570 378024 434183 422540 TRUE FALSE 394399.356 403351.8345 380105.1114 379742.3476 390202.1113 414941.7165 341363.2907 341336.3443 372587.8026 1.058540707 1.082568543 1.020175939 1.019202306 1.047275592 1.113674988 0.916195561 0.916123238 1 18.50722092 2.226699548 24.99996466 0.937113497 1.054251666 0.684866087 0.03593595 120.7440775 254494.1734 0.014816934 0.010077705 168.5386642 -2.226699548 0.117138169 TPQEAITDGLEIVVS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TPQEAITDGLEIVVSPR 17 0 X6RFN3;Q99496-2;Q99496 X6RFN3 RNF2 E3 ubiquitin-protein ligase RING2 1 TPQEAITDGLEIVVS(1)PR;TPQEAITDGLEIVVS(1)PR;TPQEAITDGLEIVVS(1)PR;TPQEAITDGLEIVVS(1)PR 155.86 8.87E-08 124288000 131279 141839 89979 111433 143207 148886 128117 147341 143578 TRUE FALSE 113930.1475 140907.2503 133493.1454 136735.5658 140357.4609 154613.7408 115692.2331 115833.2738 126604.3724 0.899891097 1.112973017 1.054411809 1.080022461 1.108630438 1.221235395 0.913809143 0.91492317 1 16.9499677 2.199292557 24.99999707 0.935867281 1.081251566 0.382458836 0.081651783 150.7794482 95992.64209 0.0325916 0.021973652 158.2313587 -2.199292557 0.145384285 TPQPCS(ph)RPAS(ph)PEPELLPEADSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPQPCSRPASPEPELLPEADSK 22 1 A0A3B3ITW6;Q12756-3;Q12756-2;A0A3F2YNW9;A0A3B3IUA1;A0A3B3IU40;A0A3B3IT28;A0A3B3ITE5;A0A3B3ITF7;Q12756;A0A3B3ITK3;H7C3Y8 A0A3B3ITW6 KIF1A Kinesin-like protein KIF1A 2 T(0.002)PQPCS(0.998)RPAS(1)PEPELLPEADSK 123.22 1.40E-05 91953000 577530 108040 84845 94749 94739 121700 101840 127090 184280 TRUE FALSE 501207.9472 107330.2781 125876.3258 116263.2086 92853.87925 126381.8778 91963.57247 99912.79252 162494.6283 3.084458559 0.660515854 0.77464915 0.715489551 0.571427377 0.777760342 0.565948385 0.614868279 1 17.3100325 4.739074721 24.99988668 0.695856101 3.084459285 0.971686724 0.127354345 6.000094751 291696.1668 0.02967268 0.17037367 54837.13053 -4.739074721 2.388603185 TPQS(ph)PAPCVLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TPQSPAPCVLLR 12 0 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 T(0.009)PQS(0.991)PAPCVLLR;T(0.003)PQS(0.997)PAPCVLLR;T(0.001)PQS(0.999)PAPCVLLR;T(0.108)PQS(0.892)PAPCVLLR 117.67 0.00074364 1515440000 861130 1220450 824290 1017710 1692320 1546100 1439570 1724870 1469460 TRUE FALSE 747329.4887 1212432.784 1222919.401 1248796.61 1658646.143 1605579.467 1299960.723 1356019.973 1295742.113 0.576757891 0.935705316 0.943798453 0.963769409 1.280074273 1.239119615 1.003255748 1.046519952 1 20.30534718 5.083787062 0.974791436 1.090995582 1.28E-12 0.697884462 0.10453317 2.205033527 1.068779953 0.03643343 2.955779686 121279.4063 -5.083787062 -1.090995582 TPRPAS(ph)PGPSLPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TPRPASPGPSLPAR 14 1 Q8IY33;Q8IY33-5;Q8IY33-3 Q8IY33 MICALL2 MICAL-like protein 2 1 T(0.001)PRPAS(0.996)PGPS(0.003)LPAR;T(0.005)PRPAS(0.993)PGPS(0.002)LPAR;T(0.001)PRPAS(0.999)PGPSLPAR;TPRPAS(0.998)PGPS(0.002)LPAR 113.54 0.00032066 1839670000 1015550 886330 565090 716470 867110 955670 904350 1021160 971110 TRUE FALSE 881342.4944 880507.6399 838369.4141 879155.4641 849856.2075 992435.2433 816646.2762 802792.8807 856306.4821 1.02923721 1.028262262 0.979052981 1.026683182 0.992467329 1.158972008 0.953684567 0.937506486 1 19.70776772 TPRPAS(ph)PGPSLPARS(ph)PS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPRPASPGPSLPARSPSPPR 20 2 Q8IY33;Q8IY33-5;Q8IY33-3 Q8IY33 MICALL2 MICAL-like protein 2 3 T(0.348)PRPAS(0.643)PGPS(0.089)LPARS(0.949)PS(0.971)PPR 79.663 0.0048153 203620000 122500 121800 63789 71621 128160 125100 121530 129160 65501 TRUE FALSE 106311.3146 120999.8878 94637.57376 87883.64271 125609.8667 129912.678 109744.0393 101540.1391 57757.5464 1.840648041 2.094962396 1.638531753 1.521595847 2.174778441 2.24927626 1.900081395 1.758041078 1 15.81772184 1.203415497 2.598879959 0.726830137 1.918497998 0.620829721 0.223556368 0.409828504 2.869094697 1.129995231 0.062514339 15.97406684 -1.203415497 1.191667861 TPRT(ph)PRT(ph)PQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPRTPRTPQLK 11 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 2 T(0.223)PRT(0.777)PRT(1)PQLK;T(0.374)PRT(0.628)PRT(0.999)PQLK 112.24 0.0017992 891280000 666240 669740 340372 384620 865510 800130 1113220 1116670 173271 TRUE FALSE 578194.696 665340.4338 504977.0377 471953.8495 848288.0443 830911.5189 1005260.096 877878.8104 152787.0998 3.784316194 4.354689858 3.30510258 3.088963991 5.552092065 5.438361747 6.579482805 5.745765263 1 17.22116321 3.234971839 24.99896755 5.130955315 3.661357831 0.126227617 1.518890442 163.2660369 1137289.862 0.455293342 0.536707182 1717.796996 -3.234971839 -1.469597484 TPS(ph)ASNDDQQE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPSASNDDQQE 11 0 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 T(0.005)PS(0.927)AS(0.068)NDDQQE 118.76 0.00086256 0 63165 66375 45383 59466 82653 92948 80481 77516 112640 TRUE FALSE 54817.58521 65938.97825 67330.3706 72968.66418 81008.36701 96523.76971 72675.96501 60939.80663 99323.82752 0.5519077 0.663878748 0.677887394 0.734654171 0.815598523 0.971808801 0.731707253 0.6135467 1 16.59985224 4.130486048 1.169087736 0.797167594 0.559223618 0.38665556 0.112899954 0.881045957 1.93331491 0.039458296 0.200839437 13504.73444 -4.130486048 -0.237943976 TPS(ph)FELPDASERPPTYCELVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TPSFELPDASERPPTYCELVPR 22 1 Q9BRG2;Q9BRG2-2 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 T(0.471)PS(0.529)FELPDASERPPTYCELVPR;T(0.008)PS(0.992)FELPDASERPPTYCELVPR;T(0.067)PS(0.933)FELPDASERPPTYCELVPR;T(0.015)PS(0.985)FELPDASERPPTYCELVPR 181.24 3.05E-17 1783160000 51286 70290 38467.6 40033 68267 79162 55737 61235 77968 TRUE FALSE 44508.42516 69828.26036 57070.66003 49123.10452 66908.62026 82207.41336 50331.63432 48140.37178 68750.71186 0.647388572 1.01567327 0.830110096 0.714510486 0.973206218 1.195731813 0.732088919 0.700216339 1 16.06908703 4.7651904 23.00217416 0.876463872 0.647387661 0.186254509 0.15854072 5703.473294 4926285.673 0.040585499 2.701571935 58235.84748 -4.7651904 -0.229076212 TPS(ph)FLKK ddPTM_MDA-MB-175_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(0.007)PS(0.993)FLKK 54.608 0.08124 427880000 1325400 742880 543790 708790 743820 475990 1042900 1111800 1137100 TRUE FALSE 1150245.032 737999.9724 806768.6629 869731.6027 729019.4373 494301.6433 941759.7185 874050.222 1002673.333 1.147178242 0.736032313 0.804617652 0.867412719 0.727075721 0.492983733 0.939248793 0.871719824 1 19.93542023 4.745989206 24.3971177 0.806172963 1.147178471 0.376305026 0.138480165 748.13124 2456942.477 0.03484008 0.347041677 55717.19002 -4.745989206 0.341005508 TPS(ph)PAAEDAREPEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TPSPAAEDAREPEAK 15 1 Q92797 Q92797 SYMPK Symplekin 1 T(0.45)PS(0.55)PAAEDAREPEAK;T(0.027)PS(0.973)PAAEDAREPEAK;T(0.104)PS(0.896)PAAEDAREPEAK 145.05 2.50E-06 2137680000 1591030 1339250 1007450 921060 1248740 1021230 1302350 1437970 1481610 TRUE FALSE 1380771.354 1330452.379 1494656.19 1130200.751 1223892.517 1060517.379 1176048.297 1130471.306 1306455.754 1.056883366 1.018367729 1.144054198 0.865089191 0.936803649 0.81175147 0.900182263 0.865296282 1 20.31722683 3.728437447 24.99928912 0.891643236 1.067628362 0.67423512 0.057752847 367.0127152 906342.2414 0.014990963 0.022525215 5351.030753 -3.728437447 0.175985126 TPS(ph)PAPK ddPTM_MDA-MB-175_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(0.402)PS(0.598)PAPK;T(0.029)PS(0.971)PAPK;T(0.129)PS(0.871)PAPK 108.74 0.0075361 1407150000 5808800 3960770 2971490 3391080 2978890 3489320 4741890 5357100 4989040 TRUE FALSE 5041152.362 3934751.441 4408512.503 4161076.543 2919615.917 3623556.398 4282022.238 4211525.854 4399241.375 1.145914019 0.894415902 1.002107438 0.945862295 0.663663497 0.823677559 0.973354693 0.957330025 1 22.06882333 TPS(ph)PSQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TPSPSQPK 8 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 T(0.003)PS(0.985)PS(0.012)QPK;T(0.297)PS(0.702)PS(0.001)QPK;T(0.005)PS(0.995)PSQPK;T(0.369)PS(0.631)PSQPK;T(0.056)PS(0.861)PS(0.083)QPK;T(0.006)PS(0.964)PS(0.03)QPK 134.23 0.00092897 4202850000 8581180 7019880 4702370 5861340 6563020 5197190 8124440 8974410 8305380 TRUE FALSE 7447155.321 6973765.946 6976451.86 7192246.832 6432428.742 5397129.262 7336533.059 7055302.26 7323527.438 1.01688092 0.95224139 0.952608141 0.982074129 0.87832384 0.736957608 1.001775868 0.963374865 1 22.80410727 5.015813539 1.014967822 0.927137482 1.102961954 0.115444759 0.077376914 7.930531912 4.560034406 0.026135498 1.726011711 103708.3056 -5.015813539 0.175824473 TPS(ph)PSQPKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPSPSQPKK 9 1 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 T(0.432)PS(0.567)PS(0.001)QPKK 81.431 0.013047 141770000 570970 387720 260250 305120 308660 282330 476990 568410 256620 TRUE FALSE 495514.8678 385173.0418 386107.7705 374402.1595 302518.2699 293191.4178 430731.5832 446859.9449 226282.6759 2.189804702 1.702176449 1.70630725 1.654577214 1.336904244 1.295686541 1.90351109 1.974786373 1 17.78776661 5.39966203 1.18681161 1.58707677 3.993143104 0.320014044 0.289893981 9.046014688 3.509060175 0.088891412 39.3875735 250993.2429 -5.39966203 2.406066334 TPS(ph)QDSDYINANFIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPSQDSDYINANFIK 15 0 Q05209;H0YC15 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 T(0.004)PS(0.995)QDSDYINANFIK 117 0.00042462 50536000 64781 48392 19050 47046 52849 25857 51497 68601 44995 TRUE FALSE 56220.02672 48074.10977 28262.64372 57728.51335 51797.4083 26851.73552 46502.82887 53931.21 39675.74236 1.416987393 1.211675117 0.71234064 1.455007769 1.305518315 0.676779662 1.172072055 1.35929933 1 15.2759696 TPS(ph)SEEISPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPSSEEISPTK 11 0 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 T(0.007)PS(0.991)S(0.002)EEISPTK 148.96 3.63E-05 445790000 789830 698560 605800 751040 753530 713390 777670 880210 1670300 TRUE FALSE 685451.9643 693971.1134 898766.9063 921575.1109 738536.2273 740834.5749 702251.6831 691983.9413 1472839.037 0.465395028 0.471179196 0.610227516 0.625713393 0.501437162 0.50299765 0.476801379 0.469829984 1 20.49016834 1.235260344 24.99998642 1.00000067 0.515695165 0.876034271 0.057283942 34.01335681 257612.302 0.107949011 0.015391486 17.18938521 -1.235260344 -0.484305505 TPS(ph)SEEISPTKFPGLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TPSSEEISPTKFPGLYR 17 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 T(0.003)PS(0.989)S(0.008)EEISPTKFPGLYR;T(0.024)PS(0.967)S(0.01)EEISPTKFPGLYR;T(0.002)PS(0.998)S(0.001)EEISPTKFPGLYR;T(0.004)PS(0.984)S(0.012)EEISPTKFPGLYR 338.97 1.39E-72 6940400000 4113050 3314680 2285530 2456260 3675340 3085930 3936810 4567940 2442980 TRUE FALSE 3569500.021 3292905.649 3390819.953 3013991.375 3602207.925 3204647.724 3555018.772 3591121.579 2154173.687 1.657015886 1.528616596 1.574069896 1.399140372 1.672199389 1.487645932 1.650293471 1.66705294 1 21.03870315 1.233274786 24.9997845 0.999999094 1.579556116 0.808150419 0.088734684 70.86451974 335122.0991 0.17761065 0.021349018 17.11097613 -1.233274786 0.579557022 TPS(ph)SQNLLALLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPSSQNLLALLAR 13 0 O75385 O75385 ULK1 Serine/threonine-protein kinase ULK1 1 T(0.087)PS(0.913)SQNLLALLAR 188.75 6.13E-06 44345000 78085 56717 34026 46523 75485 59725 84564 86116 76345 TRUE FALSE 67765.86941 56344.42229 50481.08741 57086.75821 73982.99618 62022.6594 76362.9963 67700.76356 67319.58107 1.006629399 0.836969295 0.749872275 0.847996338 1.098981827 0.921316776 1.134335584 1.005662282 1 16.03873858 3.251774578 24.96242112 1.030893259 0.850803045 0.505950716 0.084065125 176.9429293 334259.976 0.023580439 0.030256393 1785.560532 -3.251774578 -0.180090214 TPSNEHAAVWVPDSEATVCMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPSNEHAAVWVPDSEATVCMR 21 0 Q9H8W4 Q9H8W4 PLEKHF2 Pleckstrin homology domain-containing family F member 2 0 154.6 3.22E-08 184400000 105940 99382 44090 64550 100140 93174 89529 107580 93326 FALSE TRUE 91939.76058 98729.1531 65412.07147 79207.06408 98147.40992 96758.46407 80846.49136 84574.85419 82293.1066 1.117223111 1.199725678 0.79486696 0.96249938 1.192656517 1.175778483 0.982421186 1.02772708 1 16.32848397 2.208574412 0.009309665 1.37E-07 2.080262172 0.017092754 0.125152209 41886.36484 224.198944 25473.53135 24622.72201 161.6495171 -2.208574412 2.080262035 TPSNELYKPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPSNELYKPLR 11 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 123.84 0.00032982 2138750000 1842130 1757490 955620 1531590 1776120 1595900 1918220 2340360 1947640 FALSE TRUE 1598687.853 1745944.932 1417761.028 1879360.918 1740778.687 1657295.306 1732191.32 1839892.227 1717392.218 0.93088104 1.016625622 0.825531299 1.094310839 1.01361743 0.96500688 1.008617194 1.071329081 1 20.71178813 3.722538062 24.99977916 1.026188208 0.933573935 0.401147911 0.057881287 822.7625034 1283745.322 0.015434875 0.02297358 5278.834688 -3.722538062 -0.092614273 TPSNTPSAEADWS(ph)PGLELHPDYK ddPTM_MDA-MB-175_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 229.95 2.93E-33 5082180000 2804560 2678540 1880600 2238880 2661490 2325080 3020620 3664970 3153840 TRUE FALSE 2433930.29 2660944.494 2790064.45 2747251.923 2608531.556 2414527.332 2727680.737 2881244.686 2780996.628 0.875200734 0.956831255 1.003260638 0.987865967 0.937984437 0.868223754 0.980828495 1.03604753 1 21.40717056 2.000971404 24.9999052 1.016950426 0.942628952 0.37218448 0.043051107 34.80576779 895740.1216 0.018636072 0.012454799 100.2239245 -2.000971404 -0.074321473 TPSPKEEDEEPES(ph)PPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TPSPKEEDEEPESPPEK 17 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 TPSPKEEDEEPES(1)PPEK;TPSPKEEDEEPES(1)PPEK;TPSPKEEDEEPES(1)PPEK 171.42 1.05E-09 1217100000 1626840 1159210 1026210 870940 1105500 805260 1647140 1849400 1152110 TRUE FALSE 1411848.972 1151595.073 1522488.588 1068700.238 1083502.713 836238.8733 1487400.616 1453920.202 1015908.868 1.389739785 1.133561394 1.498646814 1.051964671 1.066535343 0.82314359 1.46410831 1.43115219 1 19.95433956 7.954807976 0.904806381 1.196831395 82.88951719 0.072614984 0.221038536 3232.534999 7.590703889 0.076722048 545032.2529 90117259.4 -7.954807976 81.6926858 TPSPKEEDEEPES(ph)PPEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 TPSPKEEDEEPESPPEKK 18 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK 202.73 9.93E-16 20583870000 13311130 8636430 9243240 7174670 7498040 4715550 14197560 15318320 7120550 TRUE FALSE 11552030.44 8579696.723 13713301.78 8803788.481 7348843.674 4896960.26 12820682.82 12042616.48 6278766.691 1.839856617 1.366462101 2.184075704 1.402152511 1.170427894 0.779923909 2.041911007 1.917990757 1 22.58204977 TPSRHS(ph)CSGS(ph)SPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPSRHSCSGSSPPR 14 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 TPSRHS(0.995)CS(0.079)GS(0.78)S(0.146)PPR 113.86 0.00029091 376160000 566440 462860 165040 288980 582220 526660 462740 489300 298740 TRUE FALSE 491583.5188 459819.4422 244853.896 354597.3258 570634.9611 546920.951 417863.546 384667.0027 263423.2975 1.866135317 1.745553436 0.929507368 1.346112243 2.166228145 2.076205697 1.586281661 1.460261892 1 18.00702342 TPSRHS(ph)CSGSS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPSRHSCSGSSPPR 14 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 T(0.025)PS(0.029)RHS(0.917)CS(0.142)GS(0.299)S(0.588)PPR 56.799 0.069353 369510000 481750 373500 117000 220980 448290 448070 345990 415510 246970 TRUE FALSE 418085.5169 371046.4539 173581.5913 271156.8865 439369.9061 465307.5428 312435.9431 326656.42 217773.4879 1.919818252 1.703818299 0.797074029 1.245132679 2.017554617 2.136658356 1.434683101 1.499982496 1 17.7324688 TPSS(ph)PCPASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPSSPCPASK 10 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 T(0.021)PS(0.055)S(0.919)PCPAS(0.005)K;T(0.038)PS(0.379)S(0.583)PCPASK 88.187 0.012971 769260000 1230150 971480 653320 915670 880270 824090 986220 1260680 1205090 TRUE FALSE 1067582.561 965098.2839 969267.7372 1123586.869 862754.3492 855793.2756 890576.5362 991093.3926 1062625.633 1.004664792 0.908220406 0.912144133 1.057368497 0.811908091 0.805357267 0.838090583 0.932683498 1 20.01920199 3.225876495 24.99980132 0.877916026 0.961968452 0.294098985 0.071030005 342.3894549 674831.8148 0.022734503 0.025944755 1682.195608 -3.225876495 0.084052426 TPSS(ph)PLQSCTPSLSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPSSPLQSCTPSLSPR 16 0 R4GNJ5;A0A590TQL1;Q96AP0-2;Q96AP0 R4GNJ5 ACD Adrenocortical dysplasia protein homolog 1 TPS(0.001)S(0.999)PLQSCTPSLSPR;TPS(0.029)S(0.971)PLQSCTPSLSPR 237.34 9.78E-20 430110000 239180 224030 123984 163948 229470 230130 204011 251940 219113 TRUE FALSE 207571.757 222558.3322 183943.0771 201174.8992 224903.996 238983.25 184226.0446 198064.5916 193209.7108 1.074333977 1.151900343 0.952038468 1.041225611 1.16404085 1.236911173 0.95350303 1.02512752 1 17.55980808 2.180803978 24.99996711 0.997955113 1.098665044 0.308356938 0.077695565 113.0080481 48914.39491 0.033356219 0.022488767 151.6365791 -2.180803978 0.10070993 EVVQGSSASAASS(ph)PTWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 EVVQGSSASAASSPTWK 17 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 EVVQGSSAS(0.001)AAS(0.08)S(0.834)PT(0.085)WK;EVVQGS(0.088)S(0.01)AS(0.002)AAS(0.147)S(0.751)PT(0.003)WK 272.3 1.31E-35 614010000 762710 1027460 776600 1110340 1351510 1191630 1544720 1947690 1701340 TRUE FALSE 661915.941 1020710.548 1152166.358 1362459.667 1324617.595 1237472.777 1394913.292 1531191.65 1500209.523 0.441215664 0.680378662 0.768003629 0.908179588 0.882955064 0.824866632 0.929812316 1.020651867 1 20.51673257 4.986740866 0.592666228 0.967427226 6.94E-15 0.908673523 0.051514019 1.545240385 0.34453881 0.031497165 1.090886441 96993.10572 -4.986740866 -0.967427226 down TPSSPLQSCTPSLS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPSSPLQSCTPSLSPR 16 0 R4GNJ5;A0A590TQL1;Q96AP0-2;Q96AP0 R4GNJ5 ACD Adrenocortical dysplasia protein homolog 1 TPSSPLQS(0.001)CT(0.002)PS(0.149)LS(0.848)PR;TPSSPLQSCT(0.001)PSLS(0.999)PR 163.79 7.98E-09 205009000 76155 71110 38904 48614 68705 81381 62430 80833 65620 TRUE FALSE 66090.9238 70642.87373 57718.10453 59652.55172 67337.90492 84511.77973 56375.54821 63547.49199 57862.47835 1.142206931 1.220875354 0.99750488 1.030936687 1.163757703 1.460562737 0.974302343 1.098250434 1 15.8203405 TPT(ph)PEPAEVETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TPTPEPAEVETR 12 0 F8W6G1;Q9UHY1 F8W6G1 NRBP1 Nuclear receptor-binding protein 1 T(0.086)PT(0.914)PEPAEVETR;T(0.034)PT(0.966)PEPAEVETR;T(0.002)PT(0.998)PEPAEVETR;T(0.015)PT(0.985)PEPAEVETR 262.15 2.37E-20 6803700000 2172910 2050610 1251970 1773820 2175940 1907180 2046600 2208670 2031950 TRUE FALSE 1885754.438 2037139.408 1857426.88 2176592.942 2132643.051 1980550.449 1848121.047 1736363.108 1791735.186 1.052473855 1.13696456 1.036663729 1.214796115 1.190266881 1.105381233 1.031469975 0.969095836 1 20.772926 2.155899349 2.84871432 0.985471629 1.128271877 0.546048404 0.05402974 0.193491077 3.173817276 0.027342924 0.016241427 143.1856019 -2.155899349 0.142800248 TPTHQPPKPGS(ph)PGRPACPLSNLLLQSYEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TPTHQPPKPGSPGRPACPLSNLLLQSYEER 30 2 Q96F63 Q96F63 CCDC97 Coiled-coil domain-containing protein 97 1 T(0.003)PT(0.003)HQPPKPGS(0.988)PGRPACPLS(0.006)NLLLQSYEER;TPTHQPPKPGS(1)PGRPACPLSNLLLQSYEER;TPTHQPPKPGS(1)PGRPACPLSNLLLQSYEER 207.62 5.54E-26 1628290000 937420 746030 542270 643770 834650 727420 949740 1059220 898850 TRUE FALSE 813537.5719 741129.2798 804513.5858 789947.8179 818042.098 755404.3181 857634.361 832714.0459 792588.977 1.026430591 0.935073918 1.015045136 0.996667681 1.032113897 0.953084562 1.08206698 1.050625318 1 19.59621338 2.235086815 24.99987689 1.047139468 0.993370364 0.310813935 0.035824185 98.81193262 711108.6474 0.013558035 0.009557468 171.8251829 -2.235086815 -0.053769104 TPTS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPTSPK 6 0 A0A087X0K9;G5E9E7;Q07157-2;H0Y3R8;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 TPT(0.002)S(0.998)PK 81.642 0.064342 661780000 2486700 2217700 1630200 1923900 1732600 2023400 2830000 3392200 3326800 TRUE FALSE 2158076.295 2203131.783 2418570.173 2360750.9 1698124.65 2101241.507 2555547.036 2666804.428 2933509.494 0.735663648 0.751022551 0.824463046 0.804753114 0.578871367 0.716289315 0.8711569 0.909083278 1 21.48419623 1.914497518 2.042298944 0.965668021 0.73715826 0.639298534 0.069354815 0.228691276 1.75359697 0.05995602 0.021826885 82.12918594 -1.914497518 -0.228509762 TPTS(ph)PLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TPTSPLK 7 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 1 T(0.027)PT(0.151)S(0.822)PLK;T(0.062)PT(0.019)S(0.919)PLK;TPT(0.009)S(0.991)PLK;T(0.003)PT(0.002)S(0.996)PLK;TPT(0.002)S(0.998)PLK 152.79 0.0018773 17988600000 28134700 21629500 16466000 20163600 23128600 20509300 26175600 31253100 27750500 TRUE FALSE 24416628.11 21487414.39 24429012.68 24742053.56 22668386.11 21298306.04 23637094.34 24569867.78 24469867.5 0.997824288 0.878117317 0.998330403 1.011123316 0.926379602 0.870389104 0.965967402 1.00408667 1 24.54450295 1.860509367 4.500651468 1.000923312 0.946211064 0.178389921 0.047716846 0.379901573 11.49738714 0.026841514 0.013077565 72.52861213 -1.860509367 -0.054712248 TPTSS(ph)PASSPLVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPTSSPASSPLVAK 14 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 TPTS(0.001)S(0.999)PASSPLVAK;TPTS(0.002)S(0.996)PASSPLVAK 212.69 2.19E-09 277690000 903320 784740 605720 801650 1005890 842690 923910 1254880 1069360 TRUE FALSE 783943.9733 779584.9913 898648.218 983676.885 985874.757 875108.8296 834309.3504 986533.6775 942941.479 0.831381364 0.826758615 0.953026501 1.043200354 1.045531222 0.928062716 0.884794411 1.046230015 1 19.84680871 4.169297347 3.966267146 0.990439026 0.826795825 0.617896816 0.05194901 0.143259152 4.381199498 0.014392232 0.034349583 14767.17248 -4.169297347 -0.163643202 CSPTVAFVEFPSS(ph)PQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 CSPTVAFVEFPSSPQLK 17 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 CSPTVAFVEFPS(0.027)S(0.973)PQLK;CSPTVAFVEFPSS(1)PQLK;CSPTVAFVEFPS(0.229)S(0.771)PQLK 332.56 4.91E-72 225754000 321829 376790 246963 343730 523250 463150 574280 670930 653530 TRUE FALSE 279298.4822 374314.8417 366395.1328 421779.1501 512838.3487 480967.6802 518586.414 527456.8407 576270.4279 0.484665651 0.649547198 0.635804156 0.731911841 0.889926541 0.834621485 0.899901138 0.915293958 1 19.13638646 4.990219805 0.296015226 1.023029506 9.94E-14 0.935761743 0.03993532 3.183774746 0.261659418 0.119401709 1.253016805 97773.19448 -4.990219805 -1.023029506 down TPVCHQCHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPVCHQCHK 9 0 Q9NR12-2;Q9NR12 Q9NR12-2 PDLIM7 PDZ and LIM domain protein 7 0 ; 101.54 0.0022626 67584000 131691 128101 77015 88367 92296 142808 102440 126035 145282 FALSE TRUE 114287.7007 127259.4961 114259.7116 108432.078 90459.49017 148301.9162 92505.38457 99083.39606 128106.9275 0.892127404 0.993384968 0.891908922 0.846418536 0.706124891 1.15764166 0.7220951 0.77344292 1 16.96698897 4.018353164 6.369136588 0.855052422 0.943453511 0.043839059 0.135114126 0.445346062 69.53358352 0.034075043 0.06962485 10431.65377 -4.018353164 0.088401089 TPVEPEVAIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TPVEPEVAIHR 11 0 P60866;P60866-2;E5RJX2;E5RIP1 P60866 RPS20 40S ribosomal protein S20 0 ;;;;; 203.02 3.80E-08 13381800000 5162980 4963170 3331210 4310290 5075650 4927800 4615030 5225680 6702440 FALSE TRUE 4480679.112 4930566.609 4942194.298 5289007.223 4974654.495 5117375.655 4167465.101 4108208.998 5910085.179 0.758141207 0.834263206 0.836230638 0.894912182 0.841722978 0.865871726 0.705144676 0.695118408 1 22.49474749 1.217443361 24.88985609 1.000000777 0.802112834 0.465379642 0.066019946 1692.178306 1994374.298 0.842751433 0.0186489 16.49845819 -1.217443361 -0.197887943 TPVIDADKPVSSQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPVIDADKPVSSQLR 15 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 112.96 0.00065873 140290000 182770 156110 117490 131620 139670 130490 185580 225330 191750 FALSE TRUE 158616.4814 155084.5031 174308.557 161506.3327 136890.8403 135510.0347 167582.4802 177144.933 169081.5334 0.938106476 0.917217274 1.030914219 0.955197941 0.809614376 0.801447869 0.99113414 1.047689416 1 17.36735958 2.015061457 24.93557956 1.024899322 0.910959161 0.355911639 0.067102972 254.4531824 421268.179 0.030194362 0.020348362 103.5288661 -2.015061457 -0.113940161 TPVLLHDHDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TPVLLHDHDER 11 0 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-3;Q03154-4;C9JMV9 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 ;;; 117.95 0.00045461 2927260000 784581 809327 527653 564880 735424 852482 718994 787425 798035 FALSE TRUE 680896.633 804010.4776 782827.7557 693144.6377 720790.5012 885277.5342 649266.0725 619040.2915 703692.2114 0.967605754 1.142559864 1.11245761 0.985011098 1.024297967 1.258046515 0.922656329 0.879703202 1 19.42458502 2.09019315 24.99999993 0.922160791 1.079792462 0.383413945 0.087744579 17.33873225 4800.116752 0.034729291 0.023414479 123.0816049 -2.09019315 0.15763167 TPVLPAGPPTTDPWALNS(ph)PHHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPVLPAGPPTTDPWALNSPHHK 22 0 Q9H201 Q9H201 EPN3 Epsin-3 1 TPVLPAGPPTTDPWALNS(1)PHHK;TPVLPAGPPT(0.001)T(0.004)DPWALNS(0.996)PHHK 251.19 2.96E-32 876130000 658980 659360 644980 982850 1025920 939630 1145380 1358100 2165350 TRUE FALSE 571894.1234 655028.6207 956894.4853 1206021.114 1005506.199 975778.1741 1034301.224 1067680.884 1909364.79 0.299520619 0.343061014 0.501158548 0.631634731 0.526618174 0.511048585 0.541699119 0.559181194 1 20.86466133 -0.015763564 1.215149534 10 0.474948129 0.745919926 0.094926153 15.69768656 1.530741133 364.9030836 0.031362642 0.964353889 0.015763564 -9.525051871 TPVQYSQQQNS(ph)PQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TPVQYSQQQNSPQK 14 0 P46013 P46013 MKI67 Antigen KI-67 1 TPVQYSQQQNS(1)PQK;TPVQYSQQQNS(1)PQK;TPVQYSQQQNS(1)PQK;TPVQYSQQQNS(1)PQK 315.03 7.81E-56 443523000 334816 318559 216384 318545 331910 275535 346281 395456 347327 TRUE FALSE 290569.2173 316466.365 321028.0262 390875.5109 325305.6404 286135.0097 312698.7219 310890.8118 306266.3977 0.948746645 1.033304232 1.048198655 1.276259863 1.062165627 0.934268375 1.021002383 1.015099319 1 18.22442756 2.981119814 24.84101387 0.998710885 1.083716017 0.18414233 0.084335761 1244.252613 1637088.124 0.02800447 0.028475616 957.4581809 -2.981119814 0.085005132 TPVS(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TPVSPVK 7 0 P23443-5;P23443;P23443-3;P23443-2 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 1 T(0.04)PVS(0.96)PVK;T(0.054)PVS(0.946)PVK;T(0.054)PVS(0.946)PVK 90.15 0.018199 1757550000 3425600 2084900 1735560 2164040 2251380 1796450 2455060 2994740 4577420 TRUE FALSE 2972898.281 2071204.155 2574882.621 2655418.357 2206581.943 1865560.594 2216968.659 2354338.156 4036282.622 0.736543637 0.513146464 0.637934174 0.657887122 0.546686679 0.462197712 0.549260016 0.583293683 1 21.94459577 1.23869936 9.497377789 1.002267647 0.580396248 0.73707826 0.077672433 0.038761916 60.18558057 0.105790055 0.01875377 17.32604189 -1.23869936 -0.421871399 TPVS(ph)PVKFSPGDFWGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPVSPVKFSPGDFWGR 16 1 P23443-5;P23443;P23443-3;P23443-2 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 1 TPVS(1)PVKFSPGDFWGR;T(0.009)PVS(0.991)PVKFSPGDFWGR 162.65 4.85E-09 2127740000 4360900 2463100 1282590 1662100 3015100 2474100 3014100 3889400 1021500 TRUE FALSE 3784596.016 2446919.734 1902854.814 2039505.209 2955105.409 2569280.228 2721793.046 3057682.077 900739.4337 4.201654634 2.716567791 2.112547472 2.264256601 3.280755009 2.852412287 3.021731862 3.394635522 1 19.7807503 4.736915286 6.470580005 2.668472893 4.231909814 0.345238859 0.69260892 0.14182063 36.0116749 0.166379989 0.981022123 54565.14151 -4.736915286 1.563436921 TPVSGSLKS(ph)PVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TPVSGSLKSPVPR 13 1 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477 Q8NI27 THOC2 THO complex subunit 2 1 TPVS(0.006)GS(0.015)LKS(0.979)PVPR 70.335 0.027414 200690000 478310 347120 198560 283360 368420 310190 435210 469420 369630 TRUE FALSE 415100.1216 344839.7459 294584.2801 347701.2189 361089.1628 322123.21 393003.4012 369038.186 325932.7625 1.273575932 1.058008846 0.903819174 1.066788181 1.107863966 0.988311846 1.205780598 1.132252503 1 18.31421485 2.246153466 24.99873278 1.120635074 1.060526563 0.037644123 0.105085229 513.5585749 1690846.666 0.039807586 0.030228861 176.2598783 -2.246153466 -0.060108512 TPVSHPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPVSHPQR 8 0 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 0 ; 92.439 0.011777 54365000 41989 56502 30007.3 33819 47936 55992 47864 56046 52220 FALSE TRUE 36440.04726 56130.83464 44518.93065 41498.12084 46982.16739 58146.04847 43222.15665 44060.99905 46046.61109 0.791373054 1.219000341 0.966823173 0.90121987 1.020317593 1.262764992 0.93866097 0.956878216 1 15.49080736 4.784835991 23.12283438 1.023384615 0.791370597 0.289240887 0.11825084 22350.05966 11167120.35 0.028893723 16.51418329 60930.67522 -4.784835991 -0.232014018 TPYHVNLLLAGYDEHEGPALYYMDYLAALAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TPYHVNLLLAGYDEHEGPALYYMDYLAALAK 31 0 P49721 P49721 PSMB2 Proteasome subunit beta type-2 0 ; 135.35 1.09E-06 1302720000 934210 715570 436030 697360 585990 480730 933740 1031880 827020 FALSE TRUE 810751.7815 710869.3736 646895.5664 855706.2465 574329.9455 499223.9942 843186.0385 811220.4921 729250.6377 1.111760127 0.974794312 0.887068907 1.173404865 0.787561801 0.684571214 1.156236272 1.112402856 1 19.47605522 TQATGLTKPTLPPS(ph)PLMAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TQATGLTKPTLPPSPLMAAR 20 1 B1AHC3;B1AHC4;H0Y9T8;P85298-4;P85298-3;P85298 B1AHC3 PRR5-ARHGAP8;ARHGAP8 Rho GTPase-activating protein 8 1 TQATGLTKPTLPPS(1)PLMAAR;TQATGLTKPTLPPS(1)PLMAAR;TQATGLTKPT(0.005)LPPS(0.995)PLMAAR 182.89 2.77E-17 3350630000 3283250 3670440 2004640 2472510 3793270 3469350 3885120 4549370 3936810 TRUE FALSE 2849360.194 3646328.638 2974090.609 3033931.185 3717791.348 3602818.139 3508341.66 3576522.629 3471404.807 0.820808967 1.050389926 0.856739785 0.87397793 1.070976033 1.037855952 1.010640319 1.030281061 1 21.72708818 3.24084965 24.99978814 1.028938963 0.908062815 0.516239474 0.062081332 50.61104234 552746.0839 0.017318897 0.021294604 1741.203976 -3.24084965 -0.120876147 TQDECILHFLR ddPTM_MDA-MB-175_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 ;;; 178.1 7.69E-06 763510000 1656870 1322020 663500 892530 1246290 1226910 1141020 1350370 1358120 FALSE TRUE 1437910.432 1313335.564 984370.8193 1095192.578 1221491.267 1274110.022 1030364.056 1061603.884 1197564.601 1.200695504 1.096671998 0.821977218 0.914516492 1.019979437 1.063917571 0.86038286 0.886468992 1 20.19167205 4.428172004 5.822860135 0.936304281 1.177339567 0.596063819 0.074436758 0.115109054 8.761508638 0.019689752 0.05538856 26802.29629 -4.428172004 0.241035286 TQDHDENVALEACEFWLTLAEQPICK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TQDHDENVALEACEFWLTLAEQPICK 26 0 O14787-2;O14787;A0A075B780 O14787-2 TNPO2 Transportin-2 0 ; 154.71 5.97E-08 126836000 177213 128945 83824 103963 123431 110016 159456 170709 167628 FALSE TRUE 153793.853 128097.9518 124361.5668 127569.3881 120974.9646 114248.3867 143991.9817 134204.2088 147811.2088 1.040474902 0.866632191 0.841354102 0.863056254 0.818442428 0.772934527 0.974161451 0.907943382 1 17.17339615 2.203158209 24.99979448 0.95027119 0.86355297 0.267247939 0.072177198 257.7611853 182019.1479 0.029542109 0.019918125 159.6460615 -2.203158209 -0.08671822 TQDPSS(ph)PGTTPPQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TQDPSSPGTTPPQAR 15 0 Q13112 Q13112 CHAF1B Chromatin assembly factor 1 subunit B 1 TQDPS(0.248)S(0.462)PGT(0.248)T(0.043)PPQAR;TQDPS(0.218)S(0.771)PGT(0.011)TPPQAR;TQDPS(0.018)S(0.975)PGT(0.006)T(0.001)PPQAR 142.91 4.73E-06 2167950000 1047420 1173300 629610 861890 1296140 1213570 1196600 1441360 1324370 TRUE FALSE 909000.7932 1165592.515 934091.5019 1057595.298 1270349.35 1260256.823 1080553.916 1133136.381 1167804.487 0.778384398 0.998105871 0.799869766 0.90562702 1.087809958 1.079167649 0.925286662 0.970313433 1 20.15536733 3.424779633 8.434898833 1.003704446 0.869400994 0.479036092 0.074338923 0.256931721 37.49988093 0.021264816 0.027511531 2659.375313 -3.424779633 -0.134303453 TQEDEEEISTS(ph)PGVSEFVSDAFDACNLNQEDLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TQEDEEEISTSPGVSEFVSDAFDACNLNQEDLRK 34 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 1 TQEDEEEIST(0.004)S(0.996)PGVSEFVSDAFDACNLNQEDLRK;TQEDEEEIST(0.014)S(0.986)PGVSEFVSDAFDACNLNQEDLRK 238.74 2.45E-47 448440000 445520 432900 293090 291020 486560 367650 636100 731790 245240 TRUE FALSE 386643.4032 430056.2514 434829.3043 357100.539 476878.4079 381793.7334 574411.1199 575302.4033 216248.0066 1.787962855 1.988717761 2.010789885 1.651347194 2.2052384 1.765536429 2.656260878 2.660382458 1 17.72232731 2.276678203 24.9999161 2.244086788 1.912948656 0.011702948 0.482755607 391.0279303 256459.3904 0.177053636 0.137142107 189.0941976 -2.276678203 -0.331138132 TQEEGEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TQEEGEER 8 0 Q9NR28-2;Q9NR28;Q9NR28-3 Q9NR28-2 DIABLO "Diablo homolog, mitochondrial" 0 103.19 0.011213 103010000 169360 149210 112970 145010 94020 174800 119620 151210 260990 FALSE TRUE 146978.6469 148229.8297 167602.6699 177936.7368 92149.18595 181524.6691 108019.2708 118874.9182 230136.0595 0.638659788 0.644096497 0.728276439 0.773180601 0.400411766 0.788771084 0.469371341 0.516541903 1 17.81212753 1.229406609 24.93623196 1.000000772 0.615360453 0.466991418 0.12753126 321.2980259 875173.5366 0.371523627 0.030787111 16.9592487 -1.229406609 -0.384640319 TQGLVPEHVETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TQGLVPEHVETR 12 0 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-2;H0YD14;Q9NZM1-5 Q9NZM1-6 MYOF Myoferlin 0 ; 94.728 0.0064465 483320000 312420 317670 172197 230388 381720 412450 308790 422030 427830 FALSE TRUE 271132.9054 315583.2049 255472.0452 282701.1167 374124.5188 428317.2184 278843.5933 331782.1687 377252.4248 0.718704209 0.83653062 0.677191261 0.749368587 0.991708719 1.135359749 0.739143277 0.879469944 1 18.52517065 3.250198313 24.83984335 0.933989725 0.747078927 0.469488078 0.106912498 210.2170355 448690.6982 0.032353926 0.041407001 1779.091617 -3.250198313 -0.186910797 TQHEILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TQHEILR 7 0 P49257 P49257 LMAN1 Protein ERGIC-53 0 ;; 131.03 0.0035056 403040000 618201 537425 334854 395350 539046 618742 402285 562076 562883 FALSE TRUE 536504.1715 533894.6198 496790.5144 485120.26 528320.0392 642545.4051 363271.4626 441880.4215 496339.613 1.080921525 1.075663932 1.000908453 0.977395814 1.064432549 1.29456805 0.731901007 0.89027837 1 18.92096808 2.223483532 24.99999361 0.871515432 1.072730579 0.46296452 0.105386199 220.3767545 365413.8354 0.043264685 0.029297185 167.29522 -2.223483532 0.201215147 TQHIQQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TQHIQQPR 8 0 P51397 P51397 DAP Death-associated protein 1 0 ;;;; 145.16 0.0011608 0 1533840 1610070 666386 924304 1651440 1712800 1459210 1662840 1313460 FALSE TRUE 1331139.158 1599493.344 988652.4985 1134181.35 1618579.575 1778692.524 1317696.039 1307254.606 1158184.255 1.149332804 1.381035303 0.85362281 0.979275401 1.397514746 1.535759545 1.13772574 1.128710393 1 20.14343336 1.456233685 2.277056729 0.996051982 1.208972748 0.098184364 0.199826423 1.068390405 8.926166256 0.400212783 0.057951215 28.59128568 -1.456233685 0.212920765 TQIAICPNNHEVHIYEK ddPTM_MDA-MB-175_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 ; 190.96 1.56E-10 1344430000 1832860 1606260 887430 1088680 1643520 1520100 1721430 2044130 1426430 FALSE TRUE 1590642.907 1595708.372 1316594.116 1335881.433 1610817.167 1578579.231 1554485.984 1607008.707 1257799.07 1.264624012 1.268651257 1.046744386 1.062078566 1.280663347 1.255032912 1.235877828 1.27763547 1 20.26247004 3.212252003 24.99765825 1.222528317 1.160120567 0.043011537 0.106633538 648.0737502 615778.3081 0.033044274 0.037481015 1630.24172 -3.212252003 -0.06240775 TQILAASYELHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TQILAASYELHK 12 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 166.48 5.18E-05 1225400000 672810 685960 384120 499150 761470 647600 778530 848730 828970 FALSE TRUE 583896.4538 681453.8836 569881.7168 612489.6365 746318.2368 672513.5911 703028.2804 667235.6943 730970.111 0.79879662 0.932259573 0.779623829 0.83791338 1.020996927 0.920028851 0.961774319 0.91280845 1 19.47945289 3.260673814 24.97911416 0.95457685 0.839833052 0.599248337 0.050903339 168.9579986 190854.0525 0.01384588 0.017860367 1822.526341 -3.260673814 -0.114743797 TQLAS(ph)WSDPTEETGPVAGILDTETLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TQLASWSDPTEETGPVAGILDTETLEK 27 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 T(0.027)QLAS(0.458)WS(0.458)DPT(0.038)EET(0.018)GPVAGILDTETLEK;T(0.004)QLAS(0.992)WS(0.004)DPTEETGPVAGILDTETLEK 302.55 3.39E-71 49449000 58829 52388 50262 56284 71959 70914 93659 106249 99750 TRUE FALSE 51054.5986 52043.85978 74568.87132 69064.14245 70527.15669 73642.10747 84575.9646 83528.47818 87957.66864 0.580445109 0.591692124 0.847781353 0.785197511 0.801830674 0.837244877 0.961553051 0.949644067 1 16.42452174 5.330748809 0.244301986 1.067286015 1.04E-18 0.858320705 0.053423184 8.525334853 0.462171993 0.276074498 2.959409556 214165.1535 -5.330748809 -1.067286015 TQLAVCQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TQLAVCQQR 9 0 Q02790;H0YFG2 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 129.38 0.0009091 177533000 204893 150278 130426 128748 186715 158032 194558 242070 160613 FALSE TRUE 177815.8709 149290.8139 193500.4498 157982.2012 182999.7368 164111.5933 175689.7951 190305.2143 141625.5141 1.255535572 1.054123721 1.366282418 1.115492517 1.292138199 1.158771386 1.240523618 1.34372126 1 17.11172167 4.259986489 24.99980533 1.226331465 1.154829842 0.0403342 0.118442472 720.5514523 840728.3623 0.027056787 0.071436282 18196.4425 -4.259986489 -0.071501624 TQLEELEDELQATEDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 302.63 3.91E-46 339073000 432446 346747 283063 338668 336899 284421 427388 514640 587130 FALSE TRUE 375297.1654 344469.1961 419953.2136 415567.7456 330195.369 295362.8599 385939.9775 404588.2409 517720.1603 0.724903518 0.665357895 0.811158703 0.802687972 0.63778735 0.570506777 0.745460593 0.78148056 1 18.98181297 1.187644258 1.93795067 1.125238602 0.706391712 0.617919088 0.072149839 0.686466173 2.219177508 0.549782779 0.021156118 15.40438124 -1.187644258 -0.41884689 TQLEWTEAILEDEQTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TQLEWTEAILEDEQTQR 17 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 148.03 8.78E-07 20249000 20375 22440 12227 16939 22464 22947 16968 23598 19934 FALSE TRUE 17682.39213 22292.59016 18140.0181 20785.25885 22017.01035 23829.78594 15322.44597 18551.75134 17577.42523 1.005971688 1.268251173 1.032006557 1.182497355 1.252573119 1.355704014 0.871711629 1.055430537 1 14.10143614 2.228215969 24.99999998 0.987988245 1.183015464 0.427513197 0.112687529 205.8628204 497505.9743 0.04465197 0.030472917 169.1281776 -2.228215969 0.195027219 TQLHEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TQLHEER 7 0 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 ; 109.71 0.0069661 184218000 270380 225842 134349 167374 211877 247300 233247 254460 223880 FALSE TRUE 234648.5979 224358.429 199320.6258 205378.8249 207661.0622 256813.791 210626.7418 200045.7092 197413.1614 1.188616788 1.136491749 1.009662296 1.040350214 1.05191093 1.300894982 1.066933635 1.013335219 1 17.59085865 1.999914782 24.99999944 1.017374391 1.116251018 0.245226497 0.082542786 4.644794456 1362823.033 0.035665507 0.02376411 99.98037976 -1.999914782 0.098876627 TQLS(ph)PSIKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TQLSPSIKR 9 1 H0Y9Y2;Q8NFC6 H0Y9Y2;Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 TQLS(0.944)PS(0.056)IKR 113.24 0.0011224 275240000 492400 430540 262880 336090 452620 363890 458640 535350 424680 TRUE FALSE 427328.0924 427711.7544 390009.6473 412404.3713 443613.7475 377889.0838 414161.1634 420869.5686 374474.8142 1.141139741 1.142164274 1.04148432 1.101287338 1.184629061 1.009117488 1.105978687 1.123892856 1 18.51450917 1.232384761 24.94586197 0.999999821 1.105392849 0.307020522 0.050134322 257.7455644 1040993.576 0.106423496 0.011819453 17.07594554 -1.232384761 0.105393027 TQLS(ph)QGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TQLSQGR 7 0 Q8ND56-2;Q8ND56 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 TQLS(1)QGR;TQLS(1)QGR 95.775 0.013866 424360000 488810 376260 251170 333940 309270 339870 513590 427740 522080 TRUE FALSE 424212.52 373788.3233 372636.6521 409766.181 303116.1321 352945.0188 463782.1208 336271.1297 460360.2972 0.921479377 0.81194735 0.809445676 0.890098871 0.658432393 0.766671281 1.007432925 0.730452065 1 18.81240389 1.218243933 24.73422958 1.000000719 0.822853223 0.238509319 0.098514561 1976.706961 2406364.774 0.939324392 0.023037166 16.52889926 -1.218243933 -0.177147496 TQLS(ph)QGRSS(ph)PQLDPLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TQLSQGRSSPQLDPLRK 17 2 Q8ND56-2;Q8ND56 Q8ND56-2 LSM14A Protein LSM14 homolog A 2 T(0.08)QLS(0.818)QGRS(0.197)S(0.905)PQLDPLRK 68.552 0.019649 125090000 270620 152160 78204 95283 162290 114480 261380 217890 65954 TRUE FALSE 234856.8813 151160.4509 116023.716 116918.4615 159060.7465 118884.1197 236031.4078 171295.9191 58156.99326 4.038325714 2.599179264 1.995008846 2.010393848 2.735023556 2.04419302 4.058521506 2.945405351 1 15.82766506 TQLWASEPGT(ph)PPLPTSLPSQNPILK ddPTM_MDA-MB-175_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 220.26 4.60E-33 2172700000 2058220 1622580 1007580 1446280 1740460 1491620 2010440 2160500 2137920 TRUE FALSE 1786221.012 1611921.165 1494849.058 1774679.979 1705828.251 1549003.587 1815467.838 1698493.888 1885177.533 0.947508116 0.855050061 0.792948692 0.941386128 0.904863452 0.821675179 0.963022212 0.90097291 1 20.84626896 -1.753923698 0.688422669 10 0.877627813 0.298051455 0.054079779 233.3670176 1.948706404 3227.648039 0.022587055 0.017622856 1.753923698 -9.122372187 TQLYEYLQNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TQLYEYLQNR 10 0 Q9Y2X3;H7BZ72 Q9Y2X3 NOP58 Nucleolar protein 58 0 169.37 1.08E-05 138100000 136940 131230 95717 111270 169130 153320 120390 172030 142110 FALSE TRUE 118843.032 130367.9415 142006.0614 136535.5542 165764.6439 159218.3196 108714.5963 135242.7232 125309.9177 0.948392866 1.040364114 1.133238805 1.089582985 1.322837386 1.270596315 0.867565779 1.079265917 1 16.93514108 2.237546756 24.99994461 0.99770359 1.136411839 0.269374429 0.116967651 42.16417677 1039636.219 0.048736997 0.034981072 172.8012007 -2.237546756 0.138708249 TQMAEVLPS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 204.17 3.58E-08 4373480000 2833510 2926500 1463590 2123500 2785750 2719690 2546910 2954340 2421650 TRUE FALSE 2459054.474 2907275.629 2171387.019 2605673.131 2730319.025 2824318.234 2299911.06 2322577.382 2135365.296 1.15158492 1.361488657 1.016869115 1.220247016 1.278619181 1.322639382 1.077057431 1.087672159 1 21.02605146 2.128821984 7.695758242 1.060027661 1.223910011 0.408473996 0.096733982 0.237238071 15.25972925 0.039022058 0.026256863 134.5308802 -2.128821984 0.16388235 TQPDGTSVPGEPAS(ph)PISQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 TQPDGTSVPGEPASPISQR 19 0 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(0.999)PIS(0.001)QR;TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(1)PISQR 439.26 6.79E-191 36014267000 7148892 7510652 4343300 5478757 8096510 8184477 7738922 8656112 7827836 TRUE FALSE 6204147.809 7461314.032 6443734.407 6722792.514 7935405.292 8499339.126 6988402.536 6805069.811 6902438.146 0.898834249 1.080967895 0.93354468 0.973973598 1.149652503 1.231353175 1.012454206 0.985893632 1 22.71867462 3.285126632 24.98418217 1.067641514 0.976890796 0.261623838 0.08605122 216.1296745 115959.0841 0.027020844 0.034883632 1928.087023 -3.285126632 -0.090750718 TQPNLDNCPFHDQPHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TQPNLDNCPFHDQPHLK 17 0 P01034 P01034 CST3 Cystatin-C 0 ;; 239.18 1.64E-20 786390000 765290 710790 478140 588680 739370 715040 802690 920870 861590 FALSE TRUE 664154.9875 706120.7737 709370.1033 722348.7914 724657.9836 742548.0515 724845.2473 723949.1167 759733.8117 0.874194326 0.929431813 0.933708744 0.950791949 0.953831424 0.977379235 0.95407791 0.952898378 1 19.5351345 7.010177823 0.494089222 0.968882653 5.50E-13 0.815151218 0.014087487 17.43451198 0.523428411 0.008966391 15.51142763 10237120.69 -7.010177823 -0.968882653 TQQHYYDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TQQHYYDK 8 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ; 66.435 0.061692 270060000 614220 600630 372160 465050 611750 531720 725930 739600 854520 FALSE TRUE 533049.2708 596684.422 552137.8208 570646.7103 599577.3719 552175.6125 655529.4203 581442.2956 753499.6191 0.707431374 0.791884172 0.732764565 0.757328466 0.795723524 0.73281472 0.869979763 0.771655726 1 19.52324726 -0.4467222 1.104515449 9.999999916 0.761975484 0.713227696 0.045519327 33.78971968 1.282863764 737.8777746 0.013033608 0.357501443 0.4467222 -9.238024432 TQQHYYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TQQHYYER 8 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;;; 136.63 0.00078253 1883750000 1700370 1539900 1028163 1214469 1693170 1815610 1640890 1723580 2302200 FALSE TRUE 1475661.796 1529784.296 1525386.066 1490232.748 1659479.23 1885457.692 1481756.74 1355005.83 2030036.539 0.726913909 0.753574759 0.751408182 0.734091589 0.817462739 0.928780175 0.729916291 0.667478542 1 20.95307426 3.239840919 24.99283449 0.806163214 0.743067725 0.154910484 0.09327606 90.74388004 1771397.491 0.028828111 0.035160494 1737.164392 -3.239840919 -0.063095489 TQQHYYERDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TQQHYYERDPK 11 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 82.85 0.010701 118040000 165430 122500 58089 65098 152930 117910 164830 169400 31837 FALSE TRUE 143568.0064 121695.2894 86181.0347 79879.49586 149886.9922 122446.074 148844.812 133175.1283 28073.26613 5.11404714 4.334917386 3.069861351 2.845393746 5.339136227 4.361661142 5.302012644 4.74384162 1 14.7769093 1.23487511 24.99983957 0.999995201 4.386011529 0.610439461 0.850786766 79.89144993 541843.8927 1.602166935 0.221364358 17.17414439 -1.23487511 3.386016328 TQQLHPVLQKPSVFGNDS(ph)DDDDETSVSESLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TQQLHPVLQKPSVFGNDSDDDDETSVSESLQR 32 1 Q9H0G5 Q9H0G5 NSRP1 Nuclear speckle splicing regulatory protein 1 1 TQQLHPVLQKPSVFGNDS(1)DDDDETSVSESLQR;TQQLHPVLQKPSVFGNDS(1)DDDDETSVSESLQR 303.67 3.42E-90 1626690000 552140 428980 273460 374340 476570 404840 499610 587830 683860 TRUE FALSE 479173.3001 426162.0021 405706.1707 459339.6184 467087.1894 420414.4568 451157.8991 462127.129 603014.8499 0.794629353 0.706718918 0.672796318 0.761738485 0.774586545 0.697187568 0.748170462 0.766361109 1 19.201834 1.192398847 2.858967659 1.075832914 0.734452498 0.831542636 0.036922372 0.200276854 1.779106448 0.170907283 0.009528959 15.57395255 -1.192398847 -0.341380416 TQRPLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TQRPLER 7 1 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 63.419 0.072548 89987000 176630 157100 100690 108110 119400 130740 164370 158480 112500 FALSE TRUE 153287.898 156067.9998 149384.0208 132658.0279 117024.1736 135769.6524 148429.4227 124590.2853 99200.37816 1.545235016 1.573260129 1.505881566 1.337273409 1.179674672 1.368640472 1.496258638 1.255945669 1 16.598058 2.57533205 0.061546974 1.46E-17 2.666634945 0.543788174 0.121894846 72.48208125 4.045146188 92.33453488 81.93016211 376.1248691 -2.57533205 2.666634945 TQS(ph)APLPQNAQALQHLVIQQQHQQFLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TQSAPLPQNAQALQHLVIQQQHQQFLEK 28 0 P56524-2;P56524 P56524-2 HDAC4 Histone deacetylase 4 1 T(0.115)QS(0.885)APLPQNAQALQHLVIQQQHQQFLEK 310.75 1.92E-82 459730000 366180 326890 177480 177510 330370 222270 428280 404040 327230 TRUE FALSE 317788.3852 324742.6381 263309.9216 217816.3586 323796.2834 230820.8707 386745.4715 317639.1902 288545.2422 1.101346821 1.125447904 0.912542933 0.754877665 1.12216816 0.799946896 1.340328708 1.100829762 1 18.13843802 2.243313312 24.99964294 1.145476168 0.971092201 0.236069848 0.150631125 174.4119145 917429.8818 0.057104787 0.042773625 175.1109533 -2.243313312 -0.174383968 TQS(ph)GNFYTDTLGMAEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 TQSGNFYTDTLGMAEFR 17 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2 E9PP16 PPFIBP2 Liprin-beta-2 1 TQS(1)GNFYTDTLGMAEFR;T(0.037)QS(0.963)GNFYTDTLGMAEFR;TQS(1)GNFYTDTLGMAEFR;T(0.008)QS(0.992)GNFYTDTLGMAEFR;T(0.001)QS(0.999)GNFYTDTLGMAEFR;TQS(1)GNFYTDTLGMAEFR;T(0.214)QS(0.786)GNFYTDTLGMAEFR;T(0.038)QS(0.962)GNFYTDTLGMAEFR 429.35 1.12E-160 2216724000 1832890 1448032 782660 1065258 1496670 1161804 1627176 1801635 1727895 TRUE FALSE 1590668.943 1438519.782 1161156.994 1307141.11 1466889.195 1206499.352 1469372.722 1416369.376 1523625.222 1.044002764 0.9441428 0.762101452 0.857915117 0.962762479 0.791860974 0.96439249 0.929604837 1 20.53907664 1.485706203 1.488815859 1.00772119 0.893678207 0.116578125 0.083715105 1.532219864 4.643767904 0.239229359 0.02521171 30.59892742 -1.485706203 -0.114042983 TQS(ph)LSALPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TQSLSALPK 9 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 TQS(1)LSALPK;TQS(0.995)LS(0.004)ALPK;TQS(0.998)LS(0.001)ALPK 168.05 6.24E-05 1029100000 1320970 1323420 988610 1218100 1663590 1396940 1932480 2232700 2435930 TRUE FALSE 1146400.468 1314726.367 1466705.103 1494688.222 1630487.814 1450681.186 1745068.387 1755254.48 2147957.13 0.533716642 0.612082219 0.682837233 0.695865016 0.759087689 0.67537716 0.812431665 0.817173888 1 21.03453377 -2 0.209011846 2.680844249 0.525188535 0.85229604 0.049101643 37.07643073 0.561666576 25.66795126 0.279230375 0.01 2 -2.155655714 TQS(ph)PEFEAQSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TQSPEFEAQSSK 12 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 TQS(1)PEFEAQSSK;TQS(1)PEFEAQSSK;TQS(1)PEFEAQSSK;TQS(1)PEFEAQSSK 290.39 4.39E-36 654887000 1937780 1377240 1096180 1210890 1451960 1046380 1675070 1828090 1867910 TRUE FALSE 1681697.463 1368192.82 1626296.315 1485841.082 1423068.837 1086634.916 1512621.969 1437167.18 1647087.808 1.021012635 0.83067388 0.987376816 0.902101925 0.863990875 0.659731018 0.918361463 0.872550433 1 20.65148604 3.396900575 4.029262192 0.858520323 0.936172994 0.129890091 0.096833654 0.491253303 15.382055 0.028523128 0.037878472 2494.023693 -3.396900575 0.07765267 TQS(ph)PGGCSAEAVLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TQSPGGCSAEAVLAR 15 0 Q96MH2;K7ESM2;K7ELS4;K7EJA3;K7ERG7 Q96MH2 HEXIM2 Protein HEXIM2 1 TQS(1)PGGCSAEAVLAR;TQS(1)PGGCSAEAVLAR;TQS(1)PGGCSAEAVLAR;T(0.002)QS(0.998)PGGCSAEAVLAR;TQS(1)PGGCSAEAVLAR;TQS(1)PGGCSAEAVLAR 310.49 4.01E-56 3075330000 1722400 1439800 934259 1029440 1553701 1488149 1446097 1648500 1494817 TRUE FALSE 1494780.476 1430341.859 1386069.777 1263190.086 1522785.39 1545399.055 1305854.736 1295981.104 1318101.437 1.134040548 1.085153099 1.051565333 0.958340573 1.155286951 1.172443191 0.990708832 0.983218034 1 20.33002997 2.148636749 13.52196234 0.989439299 1.087301204 0.388563511 0.059739468 0.847426295 123.9371578 0.025798468 0.017393161 140.8110538 -2.148636749 0.097861905 TQS(ph)VEITK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TQSVEITK 8 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 TQS(1)VEITK;TQS(1)VEITK;TQS(1)VEITK 130.16 0.0011115 547300000 1811130 1037710 509168 1038850 925410 502594 1711310 1327640 1352280 TRUE FALSE 1571784.582 1030893.215 755403.3479 1274736.77 906996.1515 521929.1164 1545347.42 1043734.518 1192414.999 1.318152307 0.864542308 0.633507083 1.069037853 0.760637993 0.437707608 1.295981199 0.875311463 1 20.185455 1.229264523 23.0303954 1.000000514 0.89959392 0.010821045 0.272089329 957.0560341 2370539.727 0.729698424 0.064035914 16.95370112 -1.229264523 -0.100406594 TQSAS(ph)PPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TQSASPPPK 9 0 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 TQS(0.002)AS(0.998)PPPK;TQSAS(1)PPPK;TQS(0.001)AS(0.999)PPPK 140.63 0.00011396 1163160000 1265750 1129570 969790 1199200 996550 1022170 1293270 1530200 3390680 TRUE FALSE 1098477.93 1122149.78 1438783.688 1471496.689 976720.6047 1061493.541 1167848.874 1202978.638 2989837.673 0.36740387 0.375321306 0.481224683 0.49216608 0.326680145 0.355033837 0.390606114 0.402355837 1 21.51163573 1.238567122 9.814779566 1.002735018 0.399577215 0.929832357 0.051898468 0.018978148 36.06201544 0.076056956 0.013480569 17.32076711 -1.238567122 -0.603157803 TQSAS(ph)PPPKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TQSASPPPKER 11 1 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 TQS(0.219)AS(0.781)PPPKER;TQS(0.064)AS(0.935)PPPKER;TQS(0.245)AS(0.754)PPPKER 95.067 0.0048659 3210550000 2486210 2254310 1311450 1511820 2225520 2125060 2707670 3061350 1563470 TRUE FALSE 2157651.049 2239501.289 1945671.607 1855101.838 2181236.506 2206812.433 2445080.58 2406704.126 1378638.358 1.565059493 1.624429842 1.411299487 1.345604398 1.582167284 1.600718869 1.773547476 1.745710985 1 20.39481263 3.051326451 24.99953621 1.587079783 1.487667411 0 0.224966716 396.921703 193325.6468 0.068630405 0.07781955 1125.450637 -3.051326451 -0.099412371 TQSEESRPQSLQQPATSTTETPAS(ph)PAHTTPQTQSTSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TQSEESRPQSLQQPATSTTETPASPAHTTPQTQSTSGR 38 1 B8ZZU6;E9PBF9;P15336-5;P15336;P15336-4;F5H629;P15336-2 B8ZZU6 ATF2 Cyclic AMP-dependent transcription factor ATF-2 1 TQSEESRPQSLQQPATSTTETPAS(1)PAHTTPQTQSTSGR;TQSEESRPQSLQQPATSTTETPAS(1)PAHTTPQTQSTSGR;TQSEESRPQSLQQPATSTTET(0.008)PAS(0.991)PAHTTPQTQSTSGR 194.2 1.74E-24 589125000 105133 114582 44746.4 76567 115242 130752 107354 123772 117380 TRUE FALSE 91239.40768 113829.3033 66385.90871 93952.7076 112948.9097 135782.114 96942.8256 97304.32099 103503.4701 0.881510616 1.099763159 0.641388242 0.907725195 1.091257226 1.3118605 0.936614255 0.940106847 1 16.65931961 3.324602671 6.216198227 1.044941253 0.878077472 0.246640501 0.150418425 0.346856438 20.14496125 0.045637973 0.058894197 2111.556325 -3.324602671 -0.166863781 TQSPCFGDDDPAKKEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TQSPCFGDDDPAKKEPR 17 2 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 170.61 1.03E-09 430130000 778130 502510 388940 379330 423080 345890 770300 810050 296160 FALSE TRUE 675298.149 499208.9787 577032.6849 465462.6742 414661.5357 359196.6121 695596.4246 636827.1113 261148.3022 2.585879913 1.911591898 2.209597689 1.782369138 1.587839294 1.375450689 2.663606919 2.438565007 1 17.9945098 6.870460342 1.316070097 1.921404071 194.6481024 0.163396052 0.492843234 964.9575575 7.500831373 0.145246801 555696.2803 7420964.288 -6.870460342 192.7266983 TQSSS(ph)CEDLPSTTQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TQSSSCEDLPSTTQPK 16 0 A0A2R8Y6F8;O14936-3;A0A2U3TZM4;A0A2R8YFN5;O14936-4;Q5JS72;O14936-5 A0A2R8Y6F8 CASK Peripheral plasma membrane protein CASK 1 TQSS(0.002)S(0.998)CEDLPSTTQPK;TQSS(0.024)S(0.976)CEDLPSTTQPK;TQSS(0.001)S(0.999)CEDLPSTTQPK;TQSSS(1)CEDLPSTTQPK 358.18 1.49E-87 6614400000 6134620 5455480 3470810 4765070 5460580 4468930 5669460 7329900 6310340 TRUE FALSE 5323914.424 5419642.593 5149305.325 5847051.973 5351925.141 4640852.629 5119636.642 5762457.926 5564338.794 0.956791925 0.973995796 0.925411898 1.050808046 0.961825895 0.834034878 0.920079965 1.035605153 1 22.40777883 1.725103126 9.408333775 1.016568143 0.946753783 0.231511184 0.054189827 0.154905727 43.47404522 0.031912126 0.014718459 53.10105217 -1.725103126 -0.06981436 TQSSSCERDS(ph)PSTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TQSSSCERDSPSTSR 15 1 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8YEK3;O14936-6;O14936-2;Q5JS79 A0A2U3TZM1 CASK Peripheral plasma membrane protein CASK 1 TQSSSCERDS(0.986)PS(0.012)T(0.002)SR;TQSSSCERDS(0.992)PS(0.007)TSR;TQSSSCERDS(0.943)PS(0.047)T(0.009)S(0.001)R;TQSSSCERDS(1)PSTSR 184.5 2.80E-07 3441813000 1243415 1103337 576911 921862 1191615 1171634 1017998 1228216 1068446 TRUE FALSE 1079094.557 1096089.107 855907.0893 1131184.857 1167904.193 1216707.518 919272.7106 965571.5664 942135.5311 1.145370832 1.16340916 0.908475544 1.200660435 1.239635015 1.291435763 0.975732981 1.024875439 1 19.84557509 2.205348559 24.99998517 1.004323255 1.152688314 0.355182309 0.100099296 234.8486456 176777.9593 0.043237412 0.029152684 160.453265 -2.205348559 0.148365058 TQT(ph)PPLGQTPQLGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TQTPPLGQTPQLGLK 15 0 D3DQV9;P78344;H0Y3P2;P78344-2;E9PKF8 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 T(0.001)QT(0.999)PPLGQTPQLGLK;T(0.014)QT(0.986)PPLGQTPQLGLK;TQT(1)PPLGQTPQLGLK;T(0.035)QT(0.965)PPLGQTPQLGLK;T(0.002)QT(0.998)PPLGQTPQLGLK;T(0.003)QT(0.997)PPLGQTPQLGLK 204.61 6.83E-11 4220100000 4954800 3854840 2375250 2543450 4034220 3108300 4227720 4953530 4152030 TRUE FALSE 4300010.626 3829517.302 3523928.845 3120979.197 3953946.915 3227878.312 3817716.365 3894256.158 3661181.743 1.174487072 1.045978477 0.962511312 0.852451316 1.079964665 0.881649298 1.042755217 1.063660979 1 21.80387796 4.6537027 2.918363016 0.989236632 1.189535369 0.405999146 0.073038929 0.348246973 4.601565526 0.018684416 0.146828477 45050.81997 -4.6537027 0.200298737 TQT(ph)PPVS(ph)PAPQPTEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 TQTPPVSPAPQPTEER 16 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 TQT(1)PPVS(1)PAPQPTEER;TQT(1)PPVS(0.999)PAPQPT(0.001)EER;TQT(1)PPVS(1)PAPQPTEER;T(0.001)QT(0.999)PPVS(1)PAPQPTEER;TQT(1)PPVS(1)PAPQPTEER;TQT(1)PPVS(1)PAPQPTEER;TQT(1)PPVS(1)PAPQPTEER;T(0.007)QT(0.993)PPVS(1)PAPQPTEER;TQT(1)PPVS(1)PAPQPTEER 321.67 1.91E-57 24450790000 2187624 2618650 2497080 3382054 4244149 3567805 3338610 4046700 8949130 TRUE FALSE 1898523.946 2601447.916 3704676.24 4150001.052 4159698.738 3705060.767 3014832.116 3181344.696 7891174.046 0.240588274 0.32966551 0.469470857 0.525904134 0.527133062 0.469519585 0.38205115 0.403152266 1 22.91180853 1.237353377 24.99965081 1.000000691 0.423185992 0.81142405 0.088082384 13.94695264 288691.2389 0.139337285 0.023188202 17.27242743 -1.237353377 -0.576814699 TQT(ph)PPVS(ph)PAPQPTEERLPSSPVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 T(0.001)QT(0.999)PPVS(0.508)PAPQPT(0.492)EERLPSSPVYEDAASFK 235.31 4.61E-45 2700500000 572710 641170 448940 436370 847060 593460 999400 1250600 345910 TRUE FALSE 497024.9224 636958.1121 666048.8856 535454.478 830205.1632 616290.7902 902478.3418 983168.9222 305016.9139 1.629499545 2.088271447 2.183645743 1.755491101 2.721833202 2.020513494 2.958781303 3.223325912 1 18.21852972 3.239593763 24.99977901 2.514518114 1.945902878 0.103706929 0.623050042 51.84840297 1254593.245 0.183059454 0.223020911 1736.17606 -3.239593763 -0.568615236 TQT(ph)PPVSPAPQPT(ph)EERLPSSPVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 T(0.136)QT(0.863)PPVS(0.279)PAPQPT(0.719)EERLPS(0.001)S(0.001)PVYEDAASFK 107.98 0.0013467 2432500000 389040 436370 296930 288780 529250 423320 569020 725230 213900 TRUE FALSE 337627.3783 433503.4567 440526.3412 354351.9127 518718.9605 439605.3943 513836.528 570145.2082 188612.9857 1.790053729 2.298375455 2.335609818 1.8787249 2.750176286 2.330727085 2.724290303 3.022831149 1 17.52506948 3.242972953 24.99976231 2.472915739 2.110162672 0.041497384 0.565140295 291.9751188 1654284.517 0.16115302 0.200906865 1749.737716 -3.242972953 -0.362753067 TQT(ph)PPVSPAPQPTEER ddPTM_MDA-MB-175_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;T(0.039)QT(0.959)PPVS(0.002)PAPQPTEER;T(0.193)QT(0.807)PPVSPAPQPTEER;TQT(1)PPVSPAPQPTEER;TQT(1)PPVSPAPQPTEER 283.78 1.25E-34 9732710000 667660 577200 493644 573865 714141 632753 592750 650059 1393420 TRUE FALSE 579427.0394 573408.3352 732371.8895 704169.8192 699930.9913 657095.4174 535265.1962 511048.9416 1228691.475 0.471580581 0.466682114 0.596058412 0.573105481 0.56965561 0.534792851 0.435638406 0.415929427 1 20.22869127 1.232111144 24.99996956 1.000000824 0.506499206 0.866088342 0.060805176 87.30113371 338371.2627 0.159250757 0.017182811 17.06519065 -1.232111144 -0.493501618 TQT(ph)PPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 T(0.01)QT(0.99)PPVSPAPQPTEERLPS(0.619)S(0.38)PVYEDAASFK;T(0.156)QT(0.739)PPVS(0.106)PAPQPT(0.076)EERLPS(0.366)S(0.366)PVY(0.192)EDAASFK 158.61 1.12E-11 571040000 391290 408150 308654 321707 579660 459460 617930 785390 272156 TRUE FALSE 339580.0351 405468.8358 457920.1068 394755.4913 568125.9001 477135.7235 558003.2437 617440.4604 239982.0277 1.415022776 1.689580006 1.908143335 1.644937728 2.36736853 1.988214401 2.325187636 2.572861252 1 17.87256684 4.251262765 0.860716763 2.118347918 1.324944835 0.13607751 0.439294893 2.050147544 1.941010696 0.169045169 1.355195928 17834.57501 -4.251262765 -0.793403084 TQTGDSS(ph)SISSFSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TQTGDSSSISSFSYR 15 0 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6;Q4V328-2;Q4V328-3 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 1 TQTGDS(0.075)S(0.708)S(0.215)IS(0.002)SFSYR;TQTGDS(0.027)S(0.68)S(0.292)IS(0.001)SFSYR 260.38 7.04E-25 285990000 456350 377680 262230 252290 429670 535740 420550 359910 434740 TRUE FALSE 396042.1913 375198.9952 389045.3051 309576.3005 421120.4076 556350.2645 379765.1257 282946.0473 383345.5325 1.033120665 0.97874884 1.014868499 0.807564649 1.098540017 1.45130233 0.990660106 0.738096634 1 18.54828584 1.988771814 24.8478799 0.854552125 1.062254952 0.178817487 0.170725946 773.2296656 1711149.403 0.077939744 0.048508888 97.44774947 -1.988771814 0.207702826 TQTPNRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TQTPNRK 7 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 74.127 0.075399 259430000 328740 265250 135419 187359 164710 237350 310360 325650 213690 FALSE TRUE 285296.1761 263507.5553 200908.0813 229901.7246 161432.5932 246481.0081 280261.335 256012.2817 188427.8116 1.514087404 1.39845362 1.066233692 1.22010505 0.856734427 1.308092505 1.487367138 1.358675662 1 17.52365239 4.427639169 6.342948993 1.211180293 1.487283243 0.277930155 0.182459505 0.25106427 22.81430858 0.048884842 0.134985712 26769.4328 -4.427639169 0.27610295 TQTPPVS(ph)PAPQPTEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TQTPPVSPAPQPTEER 16 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 TQTPPVS(1)PAPQPTEER;TQTPPVS(1)PAPQPTEER 278.88 2.28E-35 823490000 286390 427920 286370 548830 618560 453340 516450 571610 933950 TRUE FALSE 248542.8359 425108.9653 424859.4899 673450.2398 606251.8662 470780.2832 466364.7585 449375.6498 823539.495 0.30179832 0.516197423 0.515894493 0.817750993 0.736153967 0.571654773 0.56629313 0.545663751 1 19.65147831 4.504970336 1.47915944 0.672713874 0.257820689 0.441420902 0.143243094 0.78101119 2.208650547 0.041317879 0.420781522 31986.76624 -4.504970336 -0.414893186 TQTPPVS(ph)PAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 T(0.072)QT(0.387)PPVS(0.541)PAPQPT(0.028)EERLPS(0.859)S(0.112)PVYEDAASFK 148.04 4.15E-08 240570000 143870 154570 105260 127550 197850 159360 223740 274600 98479 TRUE FALSE 124857.215 153554.6195 156164.0881 156512.177 193913.1721 165490.6823 202041.7292 215878.9269 86836.92481 1.437835521 1.768310196 1.798360414 1.80236895 2.233072768 1.905763967 2.32667992 2.486026853 1 16.40602102 4.418052291 0.842401936 2.06666221 1.312926713 0.114948692 0.406978484 2.79666909 2.158429176 0.155500132 1.801989842 26184.98266 -4.418052291 -0.753735497 TQTPPVS(ph)PAPQPTEERLPSS(ph)PVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 TQT(0.112)PPVS(0.887)PAPQPTEERLPS(0.243)S(0.757)PVYEDAASFK 232.98 1.31E-45 161290000 77525 117080 67612 115050 163860 119730 196210 218220 87198 TRUE FALSE 67279.87483 116310.8938 100309.3893 141173.8609 160599.5066 124336.0906 177181.5844 171555.3512 76889.55178 0.87501973 1.512700895 1.304590637 1.836060397 2.088703899 1.617073942 2.304364901 2.231191979 1 16.23049995 4.469062584 0.860951985 1.933344275 0.648752727 0.361711887 0.390911379 1.664947084 1.285510366 0.145152261 1.882404547 29448.45973 -4.469062584 -1.284591548 TQTPPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 TQTPPVSPAPQPTEERLPS(0.722)S(0.278)PVYEDAASFK;TQTPPVSPAPQPTEERLPS(0.613)S(0.387)PVYEDAASFK;TQTPPVSPAPQPTEERLPS(0.5)S(0.5)PVYEDAASFK 340.73 4.67E-106 25085400000 5699500 5613500 3976800 4852800 7292900 6287900 8859400 9713000 3625600 TRUE FALSE 4946296.634 5576624.549 5899993.782 5954702.41 7147785.558 6529799.582 8000216.752 7635950.537 3196985.698 1.54717509 1.744338285 1.845486448 1.862599014 2.235789032 2.042486329 2.502424942 2.388484422 1 21.60828086 3.934974502 1.208997774 2.108629187 1.58972625 0.104124836 0.411019712 1.046149743 2.746627782 0.137265223 0.480377801 8609.432039 -3.934974502 -0.518902937 TQTPPVSPAPQPTEERLPSS(ph)PVYEDAASFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 TQTPPVSPAPQPTEERLPS(0.042)S(0.958)PVYEDAASFK;TQTPPVSPAPQPTEERLPS(0.05)S(0.95)PVYEDAASFK;TQTPPVSPAPQPTEERLPS(0.091)S(0.684)PVY(0.224)EDAASFK;TQTPPVSPAPQPT(0.001)EERLPS(0.172)S(0.802)PVY(0.025)EDAASFK;TQTPPVSPAPQPTEERLPS(0.051)S(0.949)PVYEDAASFK;TQTPPVSPAPQPTEERLPS(0.25)S(0.75)PVYEDAASFK 305.62 5.69E-82 4023200000 2101210 2045360 1259181 1547870 2451020 2193550 2910210 3216830 1221749 TRUE FALSE 1823529.775 2031923.895 1868125.143 1899337.541 2402249.497 2277937.288 2627978.282 2528935.938 1077315.225 1.692661286 1.886099675 1.734056198 1.763028589 2.229848276 2.114457528 2.439377279 2.347442865 1 20.03900902 3.251712086 24.55638326 2.101775412 1.774835096 0.076677074 0.398013791 386.4596113 721590.9443 0.113835603 0.146010653 1785.303621 -3.251712086 -0.326940316 TQTVCNFTDGALVQHQEWDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TQTVCNFTDGALVQHQEWDGK 21 0 Q01469;I6L8B7;A8MUU1 Q01469 FABP5;FABP5P3 "Fatty acid-binding protein, epidermal;Putative fatty acid-binding protein 5-like protein 3" 0 ; 375.52 1.28E-112 886000000 981460 1047990 673950 841740 1017130 807620 1057310 1342310 1655600 FALSE TRUE 851757.5743 1041105.685 999874.4742 1032869.932 996891.103 838689.664 954772.2389 1055267.452 1459876.854 0.58344481 0.713146237 0.6849033 0.707504835 0.682859722 0.574493432 0.654008752 0.722846896 1 20.47741525 1.215922948 2.687236673 1.089382644 0.660850712 0.839903088 0.04671226 0.198570898 1.565698761 0.198365212 0.012382793 16.44080008 -1.215922948 -0.428531932 TQTYLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TQTYLK 6 0 Q8TAM1 Q8TAM1 BBS10 Bardet-Biedl syndrome 10 protein 0 ;;; 77.748 0.071601 1044460000 2135170 2522530 1317270 1839980 2435900 4595840 1772210 1612920 1605930 FALSE TRUE 1853001.875 2505959.334 1954306.178 2257775.581 2387430.356 4772644.939 1600341.347 1268009.61 1416078.785 1.308544337 1.769646831 1.380082944 1.594385571 1.685944582 3.370324441 1.130121688 0.895437191 1 20.4334701 4.778308719 19.91581374 1.576323098 1.308534377 0.016327779 0.691336703 8869.033599 4442539.023 0.179596043 27.54073893 60021.75899 -4.778308719 -0.267788721 TQVCGILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TQVCGILR 8 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 128.69 0.0026123 630240000 285210 370160 290830 329730 488690 515950 420150 428400 716010 FALSE TRUE 247518.7759 367728.3946 431476.3608 404600.2361 478966.0251 535798.9304 379403.9177 336789.9938 631364.1135 0.392038082 0.582434742 0.683403367 0.640835023 0.758620921 0.848636973 0.600927277 0.533432272 1 19.26811274 4.947721239 1.158524561 0.709587228 0.1133138 0.406924682 0.130398746 2.739833344 2.264666445 0.039862419 2.212835517 88658.67556 -4.947721239 -0.596273428 TQVLS(ph)PDSLFTAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TQVLSPDSLFTAK 13 0 P55196-5;P55196;J3KN01;A8MQ02;H0Y8L4;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 TQVLS(0.995)PDS(0.005)LFTAK;TQVLS(1)PDSLFTAK 250.52 7.69E-18 159115000 484850 494250 310360 397350 500510 419570 577480 686000 627780 TRUE FALSE 420775.844 491003.2392 460451.1341 487574.3906 490550.8302 435711.1294 521476.0785 539304.2385 553564.5636 0.760120629 0.886984593 0.831793009 0.880790467 0.886167328 0.787100834 0.942032985 0.974239093 1 19.07839207 2.075880948 5.447661542 0.977854008 0.845052846 0.693436662 0.042266721 0.108905664 5.676785768 0.017017993 0.011213075 119.0915502 -2.075880948 -0.132801162 TQVTVQYMQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TQVTVQYMQDR 11 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 106.49 0.003764 0 57284 53520 34012 45323 60246 58779 51908 59661 46824 FALSE TRUE 49713.77426 53168.4236 50460.31696 55614.27987 59047.22247 61040.26617 46873.97015 46902.95943 41288.52006 1.204058033 1.287728974 1.222139154 1.346967142 1.43011235 1.478383485 1.135278525 1.13598064 1 15.33345309 2.089141285 7.545239654 1.094886718 1.326741515 0.612868854 0.089678226 0.168802695 12.25737942 0.039886446 0.026803686 122.7838608 -2.089141285 0.231854797 TRAS(ph)LPVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TRASLPVVR 9 1 Q5T5P2;Q5T5P2-7;Q5T5P2-9;Q5T5P2-2;Q5T5P2-10;Q5T5P1;Q5T5P0 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 T(0.003)RAS(0.997)LPVVR;T(0.041)RAS(0.959)LPVVR 149.41 5.31E-05 1204430000 391880 462130 183981 221020 384210 339210 371390 400130 419420 TRUE FALSE 340092.0651 459094.2376 272954.827 271205.9691 376564.9727 352259.6282 335372.655 314565.3133 369836.6454 0.919573734 1.241343288 0.738041593 0.733312862 1.0181927 0.952473565 0.906812938 0.85055204 1 18.49652866 4.236132844 24.99998229 0.885312001 1.080458483 0.306580871 0.121815937 69.88413516 719664.9475 0.030251523 0.068081976 17223.95347 -4.236132844 0.195146482 TRDDGDEEGLLT(ph)HS(ph)EEELEHSQDT(ph)DADDGALQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 3 TRDDGDEEGLLT(1)HS(1)EEELEHS(0.248)QDT(0.752)DADDGALQ 151.18 1.70E-10 315100000 37233 30756 27334 30242 36833 37477 29105 40956 39597 TRUE FALSE 32312.56471 30553.96181 40552.81383 37108.90832 36100.09536 38918.76444 26282.40158 32197.87812 34915.88777 0.925440159 0.875073319 1.161443011 1.062808672 1.03391601 1.114643417 0.752734737 0.922155505 1 15.09159603 2.253135085 24.99997734 0.892202192 1.029691568 0.289561049 0.101343104 301.1644393 516594.924 0.038904488 0.029998291 179.11629 -2.253135085 0.137489376 TRDDGDEEGLLT(ph)HS(ph)EEELEHSQDTDADDGALQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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)EEELEHS(0.001)QDTDADDGALQ;TRDDGDEEGLLT(1)HS(1)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(0.914)HS(0.701)EEELEHS(0.384)QDT(0.001)DADDGALQ 258.79 4.44E-58 7641950000 2793520 2371260 1749550 2160500 2665820 3161000 2197220 3273770 2773910 TRUE FALSE 2424349.254 2355683.037 2595638.232 2651074.546 2612775.398 3282605.715 1984133.943 2573699.762 2445981.52 0.991155998 0.963082925 1.061184727 1.083848968 1.06819098 1.342040277 0.811181085 1.052215538 1 21.22198207 4.234149778 24.50545637 1.057049131 0.977119453 0.067498881 0.127454804 240.2054391 1334559.465 0.032068695 0.070700471 17145.48515 -4.234149778 -0.079929678 TRDDGDEEGLLT(ph)HSEEELEHSQDTDADDGALQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 TRDDGDEEGLLT(0.75)HS(0.25)EEELEHSQDTDADDGALQ;T(0.053)RDDGDEEGLLT(0.462)HS(0.462)EEELEHS(0.017)QDT(0.006)DADDGALQ;TRDDGDEEGLLT(0.75)HS(0.25)EEELEHSQDTDADDGALQ 305.29 5.00E-90 31295300000 2607720 2271470 1803500 1966100 2562550 3159300 2006580 2988480 2644520 TRUE FALSE 2263103.195 2256548.564 2675678.632 2412533.055 2511560.269 3280840.315 1811982.18 2349416.808 2331887.858 0.970502585 0.967691716 1.147430235 1.034583651 1.077050193 1.406946009 0.777045163 1.007517064 1 21.15306698 2.16263154 24.99967831 0.938419268 1.092798277 0.256490981 0.137651274 56.87618871 18724.18717 0.055708028 0.037558354 145.4224777 -2.16263154 0.154379009 TRDDGDEEGLLTHS(ph)EEELEHSQDTDADDGALQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 TRDDGDEEGLLT(0.127)HS(0.873)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(0.03)HS(0.969)EEELEHS(0.001)QDTDADDGALQ;T(0.001)RDDGDEEGLLT(0.187)HS(0.812)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(0.044)HS(0.956)EEELEHSQDTDADDGALQ;T(0.001)RDDGDEEGLLT(0.121)HS(0.878)EEELEHSQDTDADDGALQ 237.91 7.10E-47 26418860000 3832690 3452990 2505780 2845410 3880300 4630020 2973070 4377110 4047800 TRUE FALSE 3326190.306 3430307.081 3717583.589 3491503.83 3803089.622 4808139.865 2684742.129 3441099.089 3569273.695 0.931895559 0.961065857 1.041551841 0.978211291 1.065507985 1.347091951 0.752181636 0.964089443 1 21.7671991 TRDDGDEEGLLTHSEEELEHS(ph)QDTDADDGALQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 T(0.156)RDDGDEEGLLT(0.239)HS(0.239)EEELEHS(0.272)QDT(0.094)DADDGALQ;T(0.002)RDDGDEEGLLT(0.045)HS(0.045)EEELEHS(0.454)QDT(0.454)DADDGALQ 57.078 0.033759 890521000 273094 245038 176140 179838 294067 320219 219440 329576 294882 TRUE FALSE 237003.936 243428.3292 261321.8932 220672.9666 288215.642 332538.0321 198158.7426 259098.7372 260021.3859 0.911478628 0.9361858 1.00500154 0.848672373 1.108430528 1.278887238 0.762086326 0.996451643 1 17.98827076 3.241716818 24.99926423 1.017535646 0.931800187 0.129580878 0.131349334 222.5415535 1762665.291 0.039799238 0.0492102 1744.684158 -3.241716818 -0.085735459 TRDDGDEEGLLTHSEEELEHSQDT(ph)DADDGALQ ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 TRDDGDEEGLLTHSEEELEHS(0.412)QDT(0.588)DADDGALQ;TRDDGDEEGLLTHSEEELEHS(0.043)QDT(0.957)DADDGALQ 166.5 6.97E-14 805910000 679329 688097 542274 554176 689374 861885 646030 857705 804373 TRUE FALSE 589553.9514 683576.8455 804519.5202 680010.1308 675656.8061 895042.2737 583378.11 674291.4604 709280.9403 0.831199484 0.963760348 1.134274833 0.958731713 0.952594054 1.261900924 0.822492297 0.950669082 1 19.43599765 7.93449962 19.6390089 0.986348367 0.010125158 0 0.130214809 0 0 0.028269206 0 86000231.53 -7.93449962 -0.976223208 TRDDWLVSWVQSYCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TRDDWLVSWVQSYCR 15 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 141.1 4.40E-06 1330500000 552420 471470 357589 394720 399310 381560 520870 541860 416080 FALSE TRUE 479416.2973 468372.8825 530520.2365 484347.2089 391364.5122 396238.8601 470356.1076 425987.4558 366891.4964 1.306697762 1.276597815 1.445986734 1.320137462 1.066703688 1.079989217 1.282003296 1.161072033 1 18.48499394 3.303081994 7.072529518 1.133988092 1.342663721 0.62045206 0.084783835 0.161747818 14.492798 0.025383964 0.032691539 2009.472162 -3.303081994 0.20867563 TRDELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TRDELER 7 1 A0A5K1VW66;P35240-4;P35240-6;P35240-5;P35240-3;P35240;P35240-2;F8VVF8;F8VW54;F8VWE0;Q12999 A0A5K1VW66 NF2;TSPAN31 Merlin;Tetraspanin-31 0 113.71 0.0055352 147420000 138780 141800 112320 99068 113670 189900 121270 161520 130310 FALSE TRUE 120439.8714 140868.5065 166638.3277 121562.9036 111408.1894 197205.5759 109509.2541 126980.205 114904.9002 1.048170018 1.225957345 1.450228209 1.057943598 0.969568653 1.716250355 0.953042506 1.105089554 1 16.8100808 TRDELEVIHLIEEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 TRDELEVIHLIEEHR 15 1 P10155-3;P10155-5;P10155-4;P10155 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 ;;;;;;; 213.51 2.18E-10 2000097000 1054303 998938 572490 730379 935223 956555 993746 1067575 963120 FALSE TRUE 914974.1873 992375.9105 849348.0789 896222.7151 916613.892 993354.2898 897372.6659 839282.3941 849261.0508 1.07737684 1.168516924 1.000102475 1.055297089 1.079307583 1.16966896 1.05665115 0.988250189 1 19.69584856 1.876045679 4.224154192 0.995721384 1.090377908 0.387652321 0.049839841 0.233098743 6.478491312 0.028234813 0.013629032 75.17019528 -1.876045679 0.094656524 TREEIQEVR ddPTM_MDA-MB-175_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 ; 156.48 0.0013221 0 386480 371920 268295 432210 452100 471370 329890 446420 393410 FALSE TRUE 335405.6888 369476.833 398043.3594 530349.8864 443104.0945 489503.9089 297897.3186 350956.557 346901.518 0.966861404 1.065077014 1.147424669 1.528819734 1.277319561 1.411074566 0.858737432 1.011689309 1 18.40416663 2.229582609 24.99968711 0.964156007 1.236744181 0.385574094 0.164075635 216.8042107 603695.6695 0.071005176 0.048655891 169.6612291 -2.229582609 0.272588174 TREFEDRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TREFEDRDR 9 2 Q13951-2;A0A494C0A9;Q13951;J3KS23 Q13951-2 CBFB Core-binding factor subunit beta 0 103.08 0.0019572 93511000 65877 60386 29508 31409 67026 66433 65469 73676 27357 FALSE TRUE 57171.18754 59989.32039 43778.1675 38540.89351 65692.31373 68988.7205 59119.82646 57920.96075 24122.88663 2.369997771 2.486821802 1.814798045 1.597689949 2.723236019 2.859886612 2.450777445 2.401079176 1 14.55811493 1.236969427 24.99162121 0.999998342 2.339783753 0.553747133 0.377486688 34.54864695 542450.0138 0.613308563 0.09943982 17.25716401 -1.236969427 1.33978541 TRESEEQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TRESEEQKR 9 2 P00367 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 91.095 0.0061784 30756000 48496 42785 22240 33402 41020 42681 41369 54852 17261 FALSE TRUE 42087.13073 42503.94252 32995.33839 40986.43462 40203.78225 44322.96569 37357.04075 43122.32666 15220.42424 2.765174614 2.792559645 2.167833029 2.692857568 2.641436376 2.912071633 2.454402068 2.833188219 1 13.89372095 1.234773427 24.99999601 0.999997643 2.653647344 0.856783597 0.212956515 38.22906388 252320.1782 0.365540463 0.050114022 17.17012381 -1.234773427 1.653649701 TRETVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TRETVQK 7 1 P53675;P53675-2;A0A087WX41 P53675 CLTCL1 Clathrin heavy chain 2 0 81.296 0.025158 141050000 351760 347710 182400 201100 190620 256900 343570 252900 335510 FALSE TRUE 305274.0248 345425.8701 270609.2501 246762.8286 186827.0349 266783.1092 310250.6343 198819.3031 295846.39 1.031866655 1.167585212 0.914695123 0.834091059 0.631500134 0.90176226 1.048688254 0.672035589 1 18.17448877 4.082021345 4.418411703 0.837591727 1.097585318 0.37705977 0.131165077 0.201597367 7.277371192 0.033498721 0.073789078 12078.73198 -4.082021345 0.259993592 TRHS(ph)PT(ph)PQQSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TRHSPTPQQSNR 12 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 T(0.039)RHS(0.963)PT(0.996)PQQS(0.002)NR;T(0.003)RHS(0.997)PT(0.999)PQQS(0.001)NR 110.9 0.0032987 2212240000 605766 501757 299142 333717 450538 520962 499925 448296 455360 TRUE FALSE 525712.4883 498460.9252 443808.0718 409492.5454 441573.1753 541003.7452 451442.3504 352431.389 401527.8595 1.30928023 1.241410561 1.105298328 1.019835948 1.099732347 1.34736291 1.124311401 0.877725868 1 18.61514057 1.859651949 5.255013319 0.938918673 1.178568556 0.491900887 0.10242118 0.189278067 7.061797421 0.056757823 0.028909089 72.38556174 -1.859651949 0.239649883 TRHS(ph)PTPQQSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TRHSPTPQQSNR 12 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(0.001)RHS(0.887)PT(0.111)PQQSNR;TRHS(0.976)PT(0.024)PQQSNR;T(0.015)RHS(0.963)PT(0.022)PQQSNR;T(0.005)RHS(0.986)PT(0.009)PQQSNR;T(0.121)RHS(0.871)PT(0.008)PQQSNR;T(0.008)RHS(0.991)PT(0.001)PQQSNR 122.46 0.00021684 9068095000 2427302.3 2054110.9 1170851.3 1417872.9 2175140.3 2291216.1 2040761.9 2279002.7 1965254.7 TRUE FALSE 2106528.151 2040617.31 1737078.905 1739822.613 2131859.264 2379360.666 1842849.125 1791655.708 1732924.528 1.215591399 1.177556943 1.002397321 1.003980603 1.23020895 1.373031905 1.063432997 1.033891366 1 20.72477739 2.017648069 24.97941065 1.028155097 1.160787918 0.264256844 0.107317359 357.4143335 505889.0673 0.047898237 0.032286242 104.1473128 -2.017648069 0.132632821 TRIEGLLAAFPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TRIEGLLAAFPK 12 1 B0YIW6;P48444;Q6P1Q5;E9PK34 B0YIW6 ARCN1 Coatomer subunit delta 0 83.769 0.011503 191590000 819280 756250 356870 451330 779740 714590 896180 967170 300100 FALSE TRUE 711010.0722 751282.144 529453.5257 553811.3746 764224.6995 742080.7397 809268.6015 760348.222 264622.5199 2.686884217 2.839071082 2.000787862 2.09283539 2.887980584 2.804299271 3.058200043 2.8733315 1 18.01357632 3.230588891 24.99856701 2.622318042 2.407042457 0 0.625152405 880.8450247 2762237.177 0.189704493 0.218957421 1700.547985 -3.230588891 -0.215275585 TRLDSSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TRLDSSIR 8 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 95.358 0.0088526 203137000 357550 373360 180809 257110 423640 457660 450990 435720 299680 FALSE TRUE 310298.8616 370907.3736 268248.8372 315490.7552 415210.3928 475266.4763 407253.0592 342544.6688 264252.1718 1.174252834 1.403611448 1.015124437 1.19390033 1.571265772 1.798533852 1.541153121 1.296279484 1 18.0115558 3.25672655 24.49923667 1.448632931 1.19852865 0.229139022 0.222815163 316.7484603 427175.1892 0.069151875 0.08909633 1806.03661 -3.25672655 -0.250104281 TRLEEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TRLEEIR 7 1 G3V158;E9PPM8;Q9Y315;E9PPK3;E9PMH9;E9PML7 G3V158 DERA Deoxyribose-phosphate aldolase 0 82.279 0.022728 92465000 114140 93465 59288 77201 88654 100660 92343 105440 99213 FALSE TRUE 99056.10981 92851.02226 87959.87511 94730.66699 86889.95885 104532.4553 83387.59007 82892.47653 87484.15216 1.132274902 1.061346769 1.005437819 1.082832315 0.993207989 1.194873046 0.953173666 0.947514201 1 16.41673407 TRLQQELDDLLVDLDHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TRLQQELDDLLVDLDHQR 18 1 P35579 P35579 MYH9 Myosin-9 0 ;;; 232.95 5.95E-24 377128000 464688 451787 81301 98299 494810 477344 606600 605540 2253.71 FALSE TRUE 403278.3034 448819.1814 120618.4355 120619.2904 484964.2491 495707.7326 547772.0254 476049.9833 1987.278971 202.9298902 225.846088 60.69527091 60.69570106 244.0343083 249.4404358 275.6392199 239.5486443 1 10.95657869 1.230796814 24.99996402 0.999700403 196.5619479 0.395742883 75.25389962 340.1100988 1095085.97 214.8837106 20.45196918 17.01362334 -1.230796814 195.5622475 TRLS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 TRLSPPR 7 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 1 T(0.006)RLS(0.994)PPR;T(0.052)RLS(0.948)PPR;T(0.061)RLS(0.939)PPR;T(0.002)RLS(0.998)PPR;T(0.027)RLS(0.973)PPR;T(0.017)RLS(0.983)PPR;T(0.004)RLS(0.996)PPR;T(0.003)RLS(0.997)PPR;T(0.045)RLS(0.955)PPR;T(0.003)RLS(0.997)PPR;T(0.022)RLS(0.978)PPR;T(0.01)RLS(0.99)PPR 86.898 0.011954 29616055500 3390072.7 3037965.4 1654877.8 2344747.3 3307690.6 3536298.2 3190336.2 3549955.4 3353427.7 TRUE FALSE 2942066.003 3018008.805 2455182.239 2877158.012 3241874.028 3672341.88 2880937.886 2790825.063 2956989.298 0.994953213 1.020635688 0.83029798 0.973002511 1.096342835 1.241919233 0.974280796 0.943806278 1 21.49569759 3.431294474 9.404459965 1.041113743 0.946856943 0.204337787 0.094482691 0.661035751 128.8435459 0.03014799 0.03898487 2699.569261 -3.431294474 -0.094256801 TRNS(ph)GIWESPELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TRNSGIWESPELDR 14 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 T(0.006)RNS(0.994)GIWESPELDR;TRNS(1)GIWESPELDR;TRNS(1)GIWESPELDR;TRNS(1)GIWESPELDR;T(0.001)RNS(0.999)GIWESPELDR 235.21 1.89E-17 4983250000 1296580 1386840 940700 1098000 1570900 1623440 1505500 1624040 1456370 TRUE FALSE 1125233.668 1377729.757 1395625.666 1347317.682 1539642.163 1685894.787 1359496.842 1276751.684 1284199.598 0.876214001 1.072831481 1.086766939 1.049149746 1.198911887 1.312798096 1.058633599 0.994200346 1 20.29243802 4.76909234 2.926551414 1.097542359 0.82884998 0.351324613 0.094757624 0.617620762 7.125806351 0.026683455 0.40487898 58761.42784 -4.76909234 -0.268692378 TRPAS(ph)QPTPFALHHAASCEVDPSSGDSISLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TRPASQPTPFALHHAASCEVDPSSGDSISLAR 32 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 T(0.133)RPAS(0.83)QPT(0.037)PFALHHAASCEVDPSSGDSISLAR;T(0.154)RPAS(0.691)QPT(0.154)PFALHHAASCEVDPSSGDSISLAR;T(0.186)RPAS(0.783)QPT(0.031)PFALHHAASCEVDPSSGDSISLAR;T(0.037)RPAS(0.925)QPT(0.037)PFALHHAASCEVDPSSGDSISLAR 250.07 7.94E-48 1730540000 563550 697038 303277 481819 832410 839900 800120 867870 529375 TRUE FALSE 489075.4396 692459.1115 449942.7716 591223.3681 815846.6696 872211.4965 722524.4856 682282.7543 466792.8906 1.047735408 1.483439713 0.963902366 1.266564637 1.747770127 1.868519239 1.547848093 1.46163913 1 18.83242306 3.408541101 7.749482922 1.535031072 1.183476294 0.29660215 0.259275437 0.314029734 30.63799083 0.076703676 0.099208969 2561.775693 -3.408541101 -0.351554778 TRPDGNCFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TRPDGNCFYR 10 1 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ;;; 214.67 7.80E-09 2974030000 861390 635880 399943 463394 698360 683240 618600 650860 827900 FALSE TRUE 747555.129 631702.8624 593356.7725 568614.6902 684464.0023 709524.6849 558608.2672 511678.654 730026.6051 1.024010801 0.86531485 0.812787874 0.778895846 0.93758775 0.971916201 0.765188917 0.700904118 1 19.47758952 4.727290292 3.602173467 0.838872996 1.042974089 0.229494623 0.095562377 0.395788987 9.40555442 0.025001403 0.214671445 53369.15073 -4.727290292 0.204101094 TRPEDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TRPEDYR 7 1 P83436 P83436 COG7 Conserved oligomeric Golgi complex subunit 7 0 69.905 0.053328 153770000 411090 415630 254590 343060 506830 544700 388750 529450 480350 FALSE TRUE 356763.4149 412899.6992 377710.5756 420957.0163 496745.0746 565654.9615 351049.0848 416231.2377 423563.5702 0.842290131 0.974823446 0.891744716 0.993846133 1.172775728 1.335466507 0.828799051 0.982688944 1 18.69221899 3.525682173 5.464438134 1.052572705 0.913426434 0.227288793 0.134021509 0.383630025 26.78121582 0.040493862 0.05926196 3354.920036 -3.525682173 -0.139146271 TRPGS(ph)PQALGGPHGPAPATAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TRPGSPQALGGPHGPAPATAK 21 1 Q8WXD9 Q8WXD9 CASKIN1 Caskin-1 1 T(0.283)RPGS(0.717)PQALGGPHGPAPATAK;T(0.29)RPGS(0.71)PQALGGPHGPAPATAK 113.79 0.00011642 519150000 402040 356760 209870 268930 339760 320770 390090 432390 357300 TRUE FALSE 348909.3954 354416.4201 311363.834 329994.6668 332999.4407 333110.2295 352259.1318 339926.7634 315060.401 1.107436524 1.12491579 0.988267116 1.047401278 1.056938414 1.057290057 1.118068569 1.078925699 1 18.26526891 TRQDAELDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TRQDAELDSK 10 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 73.624 0.040523 127510000 182560 179940 105690 131240 172490 146400 192060 236750 183060 FALSE TRUE 158434.2335 178757.9623 156802.0375 161040.0479 169057.7865 152032.1027 173434.0508 186122.8549 161418.8553 0.981510079 1.107416862 0.971398522 0.997653264 1.047323661 0.941848475 1.074434894 1.153042837 1 17.30044958 2.019422923 24.56071961 1.095338804 1.011730319 0.217025248 0.058179412 218.1629158 275870.6578 0.0225555 0.015204579 104.5738079 -2.019422923 -0.083608485 TRS(ph)LDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TRSLDFR 7 1 Q9H1K0 Q9H1K0 RBSN Rabenosyn-5 1 T(0.138)RS(0.862)LDFR;T(0.311)RS(0.689)LDFR 112.13 0.0038902 413220000 416090 381830 215280 270950 457580 399540 480440 499080 310870 TRUE FALSE 361102.6523 379321.7336 319390.1281 332473.3387 448475.0532 414910.5623 433847.0027 392355.6258 274119.3027 1.317319316 1.383783374 1.165150082 1.212878245 1.636057909 1.513613081 1.582694099 1.431331621 1 18.0644444 3.271303313 24.99919325 1.447853921 1.270451839 0.167204083 0.178952798 336.5637252 256965.694 0.052464659 0.06772665 1867.683634 -3.271303313 -0.177402082 TRS(ph)LSSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TRSLSSLR 8 1 O94915;H0Y9X0;A0A286YEZ9;A0A2C9F2R7 O94915 FRYL Protein furry homolog-like 1 T(0.032)RS(0.968)LSSLR;T(0.022)RS(0.976)LS(0.001)SLR;T(0.004)RS(0.996)LSSLR;T(0.006)RS(0.993)LS(0.001)SLR;T(0.036)RS(0.964)LSSLR 145.28 0.00034639 1055970000 419808 411787 224030 222124 445644 476551 469513 470685 161406 TRUE FALSE 364329.3091 409081.9441 332371.6573 272560.6492 436776.5563 494884.2253 423979.7015 370032.6756 142324.7666 2.559844769 2.874285017 2.335304427 1.915061277 3.068872459 3.477147634 2.978959402 2.599917671 1 17.11882721 4.252954574 24.85145713 2.555539356 2.717064636 0.011276046 0.68491536 1900.449954 3281103.012 0.175639068 0.459922469 17904.18572 -4.252954574 0.16152528 TRS(ph)NPEGAEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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(0.048)RS(0.952)NPEGAEDR;T(0.018)RS(0.982)NPEGAEDR;T(0.154)RS(0.846)NPEGAEDR;T(0.357)RS(0.643)NPEGAEDR;T(0.253)RS(0.747)NPEGAEDR;T(0.155)RS(0.845)NPEGAEDR;T(0.005)RS(0.995)NPEGAEDR;T(0.021)RS(0.979)NPEGAEDR 180.7 3.97E-06 3551155000 1434016 1467924 1246614 1414301 1957614 2014804 2141162 2258998 2025006 TRUE FALSE 1244507.152 1458281.111 1849480.7 1735439.658 1918661.311 2092314.814 1933512.439 1775928.857 1785612.098 0.696963889 0.816684157 1.035768464 0.971901826 1.074511824 1.17176335 1.082828931 0.994577075 1 20.76798728 4.424826626 1.672414646 1.054240146 0.657918075 0.823726305 0.057153668 0.233849747 0.994665165 0.017363694 0.123825401 26596.63091 -4.424826626 -0.396322071 TRS(ph)PDVISSASTALS(ph)QDIPEIASEALSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TRSPDVISSASTALSQDIPEIASEALSR 28 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 2 T(0.458)RS(0.525)PDVIS(0.121)S(0.114)AS(0.101)T(0.095)ALS(0.585)QDIPEIAS(0.001)EALS(0.001)R 42.446 0.088089 34711000 12414 14810 7238.3 9008.8 12488 12727 11603 13212 14029 TRUE FALSE 10773.45845 14712.71213 10738.76609 11054.38573 12239.51323 13216.61593 10477.74285 10386.71662 12370.5076 0.870898656 1.189337787 0.868094215 0.893608095 0.989410752 1.068397219 0.846993768 0.839635442 1 13.59461708 2.217977309 24.98639291 0.881872749 0.980895073 0.11977716 0.105711547 433.4114968 526120.889 0.042005952 0.02835571 165.1875487 -2.217977309 0.099022324 TRS(ph)PDVISSASTALSQDIPEIASEALSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TRSPDVISSASTALSQDIPEIASEALSR 28 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 T(0.345)RS(0.655)PDVISSASTALSQDIPEIASEALSR;T(0.153)RS(0.807)PDVIS(0.016)S(0.022)AS(0.001)TALSQDIPEIASEALSR 223.56 1.17E-34 860140000 663770 564940 380370 449680 671250 676530 548530 775760 629330 TRUE FALSE 576051.1127 561228.8719 564318.2043 551786.7169 657893.4383 702556.5469 495333.645 609869.761 554931.3243 1.038058382 1.011348337 1.01691539 0.99433334 1.185540281 1.26602431 0.892603505 1.099000424 1 19.08194972 TRS(ph)PS(ph)PDDILER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TRSPSPDDILER 12 1 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 T(0.004)RS(0.996)PS(1)PDDILER;T(0.001)RS(0.999)PS(1)PDDILER 149.37 0.0008036 564980000 678270 558150 408290 581250 708730 638760 643900 755260 677890 TRUE FALSE 588634.901 554483.4759 605740.4096 713231.6964 694627.6596 663333.5105 581454.6771 593753.5264 597750.6165 0.984749969 0.927616736 1.013366432 1.193192741 1.162069332 1.109716146 0.972737896 0.993313114 1 19.18918419 7.397879948 7.57024062 1.039406614 0.118426935 0 0.086874349 0 0 0.021797231 0 24996542.9 -7.397879948 -0.92097968 TRS(ph)YDNLTTACDNTVPLASR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TRSYDNLTTACDNTVPLASR 20 1 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 T(0.238)RS(0.761)YDNLTTACDNTVPLASR;T(0.285)RS(0.715)YDNLTTACDNTVPLASR;T(0.219)RS(0.781)YDNLTTACDNTVPLASR 264.37 8.97E-37 2131750000 813780 842460 422200 436710 876890 857350 804780 999500 350011 TRUE FALSE 706236.9111 836925.8248 626377.3322 535871.6802 859441.6046 890332.8093 726732.5595 785764.7031 308633.0983 2.288273406 2.711717665 2.029520928 1.736274182 2.78467089 2.884761272 2.354681217 2.545950863 1 18.23553326 1.235525015 24.99525334 0.999998059 2.422045194 0.620451014 0.348274575 59.96307075 493648.5422 0.605675958 0.088195876 17.19986407 -1.235525015 1.422047135 TRSDIVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TRSDIVSR 8 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ; 122.13 0.0017663 92514000 80410 73665 47497 41740 85976 117723 70783 76709 40162 FALSE TRUE 69783.61477 73181.08976 70466.70807 51217.70496 84265.24581 122251.88 63918.47555 60305.3773 35414.09411 1.970504019 2.066439693 1.98979276 1.446252015 2.379426833 3.452068535 1.804888058 1.702863756 1 15.11203602 5.704259037 17.93224074 1.992645945 1.995341951 0 0.640188923 0 0 0.148627278 0 506126.4538 -5.704259037 0.002696006 TRT(ph)PAS(ph)INATPANINLADLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TRTPASINATPANINLADLTR 21 1 Q7KZ85;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 2 T(0.148)RT(0.852)PAS(1)INATPANINLADLTR 148.35 2.08E-07 104550000 139480 131340 78724 93038 124200 115460 123250 126880 136200 TRUE FALSE 121047.3646 130477.2189 116795.1897 114163.6999 121728.663 119901.8209 111297.234 99747.69938 120098.5912 1.007899955 1.086417564 0.972494253 0.950583173 1.013572781 0.998361594 0.926715567 0.830548455 1 16.8738597 2.176351945 3.999549738 0.897088299 1.005580154 0.351423915 0.053649243 0.197490169 6.345365435 0.023219552 0.015295612 150.0900647 -2.176351945 0.108491855 TRTDS(ph)TSDGRPAWMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TRTDSTSDGRPAWMR 15 2 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 1 TRT(0.002)DS(0.529)T(0.11)S(0.359)DGRPAWMR;T(0.005)RT(0.015)DS(0.795)T(0.153)S(0.032)DGRPAWMR 99.059 0.0021173 1443370000 431110 474000 228484 227379 520470 481850 476920 557110 158869 TRUE FALSE 374137.7212 470886.2628 338979.6266 279008.8772 510113.6653 500387.0813 430668.3718 437976.3619 140087.6878 2.670739499 3.361367942 2.419767447 1.991673084 3.641388285 3.571956174 3.074277109 3.126444364 1 17.09597064 4.242338632 24.99944917 2.789609431 3.01605347 0.016375345 0.799079936 650.461463 4303984.701 0.201908624 0.493292589 17471.8395 -4.242338632 0.226444039 TRTDST(ph)SDGRPAWMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TRTDSTSDGRPAWMR 15 2 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 1 TRT(0.022)DS(0.381)T(0.523)S(0.073)DGRPAWMR 93.684 0.0076565 375800000 141950 145490 68826 78143 173420 159820 156910 209590 65755 TRUE FALSE 123190.9478 144534.2666 102110.4838 95886.56249 169969.2813 165968.3788 141692.8924 164770.8095 57981.51881 2.124658863 2.492764412 1.761086738 1.653743546 2.931438927 2.862435863 2.443759585 2.841781535 1 15.8233055 3.243533825 24.99688991 2.49353883 2.025043784 0.097862439 0.588640098 263.256109 1323198.792 0.169427436 0.211884755 1751.998883 -3.243533825 -0.468495046 TRTFS(ph)ATVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TRTFSATVR 9 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 TRTFS(0.929)AT(0.071)VR;TRTFS(0.994)AT(0.006)VR;T(0.113)RT(0.007)FS(0.877)AT(0.003)VR;TRT(0.001)FS(0.977)AT(0.022)VR 112.59 0.0015879 2855770000 876800 798670 421133 426889 1851160 1644840 2043280 2047670 278390 TRUE FALSE 760928.6585 793423.4842 624794.3274 523820.672 1814325.538 1708118.059 1845123.02 1609791.705 245479.0513 3.099770242 3.232143353 2.545204261 2.133871176 7.390958731 6.958304791 7.51641743 6.557755933 1 17.90524039 3.244892846 24.99168294 6.144881644 2.772164872 0.405083441 1.871232411 144.0690819 568600.248 0.546661602 0.688280347 1757.489934 -3.244892846 -3.372716773 TRWDVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TRWDVSR 7 1 REV__O15399 0 ; 63.48 0.072214 57438000 71629 97545 70720 56435 63334 75488 77723 65271 84423 FALSE TRUE 62163.04617 96904.22047 104920.4285 69249.4293 62073.77731 78392.07221 70185.43542 51313.30459 74442.60911 0.83504658 1.301730576 1.409413638 0.930239148 0.833847417 1.053053797 0.942812675 0.68930019 1 16.183841 3.581527668 7.662315211 0.886924678 1.193094602 0.353240165 0.173928661 0.281594208 18.39136267 0.048138357 0.07147587 3815.290996 -3.581527668 0.306169924 TRWS(ph)GAQPLEQPSGSVLWMAAEVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TRWSGAQPLEQPSGSVLWMAAEVIR 25 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 T(0.239)RWS(0.761)GAQPLEQPSGSVLWMAAEVIR;T(0.251)RWS(0.749)GAQPLEQPSGSVLWMAAEVIR 171.48 4.33E-12 586910000 84068 82195 47835 56500 89929 80963 88218 94826 67338 TRUE FALSE 72958.2008 81655.05563 70968.166 69329.18855 88139.58884 84077.699 79662.63194 74548.19784 59377.37835 1.228720479 1.375187957 1.195205446 1.167602721 1.484396773 1.415988737 1.341632692 1.255498304 1 15.85762578 1.238291364 2.892263322 0.935654915 1.317178103 0.501171387 0.098271096 0.373112754 3.773662453 0.338340556 0.026716413 17.30977266 -1.238291364 0.381523188 TS(ph)FSFQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSFSFQK 7 0 H0Y7F8;Q9BPZ7-4;Q9BPZ7-3;Q9BPZ7-2;Q9BPZ7 H0Y7F8 MAPKAP1 Target of rapamycin complex 2 subunit MAPKAP1 1 T(0.081)S(0.919)FSFQK 104.48 0.0085395 216210000 683270 655650 461170 596870 678670 546310 721840 800460 909810 TRUE FALSE 592974.1383 651342.992 684193.3545 732398.4561 665165.7948 567326.8992 651836.0679 629287.8582 802253.2983 0.739135806 0.811891947 0.852839566 0.9129267 0.82912192 0.707166802 0.81250656 0.784400462 1 19.61369829 1.234247134 24.99942784 1.000000283 0.808102393 0.535062892 0.056736526 112.5292973 652093.7348 0.110808573 0.014555402 17.14932908 -1.234247134 -0.19189789 TS(ph)FSVGS(ph)DDELGPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSFSVGSDDELGPIR 15 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 2 T(0.404)S(0.596)FS(0.001)VGS(0.999)DDELGPIR 197.14 1.25E-08 41375000 108660 112430 67510 79243 118270 113610 131480 136000 134540 TRUE FALSE 94300.30569 111691.4399 100158.0618 97236.3343 115916.6584 117980.6502 118729.0898 106917.4584 118634.8345 0.794878723 0.941472548 0.844255081 0.819627176 0.977087876 0.994485732 1.0007945 0.901231572 1 16.85616816 3.229731177 24.99530871 0.96847779 0.856173442 0.633016151 0.046929363 133.9767375 379274.8637 0.014137429 0.016269264 1697.192786 -3.229731177 -0.112304348 TS(ph)LGSTLSLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSLGSTLSLTR 11 0 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 T(0.226)S(0.774)LGSTLSLTR 71.888 0.036382 0 136540 132770 70763 101880 144540 127240 128000 148830 153960 TRUE FALSE 118495.8931 131897.8251 104984.2235 125013.4111 141663.9368 132135.0051 115586.5797 117003.8627 135759.0242 0.8728399 0.971558435 0.773313038 0.920847891 1.043495544 0.973305502 0.851409918 0.861849615 1 17.05068857 TS(ph)PADGKPR ddPTM_MDA-MB-175_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(0.117)S(0.883)PADGKPR 104.79 0.0019393 227430000 213120 176510 145070 121060 118820 154640 185530 268910 218600 TRUE FALSE 184955.652 175350.4942 215226.3372 148548.5233 116455.7145 160589.1009 167537.3292 211405.6892 192757.357 0.959525773 0.909695468 1.116566136 0.770650343 0.604157041 0.833115287 0.869161788 1.096745112 1 17.5564264 1.765634913 10.06171351 1.047464457 0.86234824 0.247218966 0.132068206 0.304526927 104.2617155 0.077297367 0.036781364 58.29548407 -1.765634913 -0.185116216 TS(ph)PADHGGSVGSESGGSAVDSVAGEHSVSGR ddPTM_MDA-MB-175_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(0.429)S(0.571)PADHGGSVGSESGGSAVDSVAGEHSVSGR 219.01 1.18E-34 448020000 33073 39753 14275 18740 37515 32280 32918 32466 26048 TRUE FALSE 28702.31925 39491.85993 21178.43775 22995.20342 36768.5249 33521.83249 29725.61743 25523.39855 22968.63511 1.249631034 1.719382093 0.922059045 1.001156721 1.600814533 1.459461231 1.294183014 1.111228352 1 14.48737751 1.633409537 2.835364911 1.015750608 1.326488211 0.180772184 0.241202596 0.408802541 7.449504345 0.231248439 0.067040733 42.99416684 -1.633409537 0.310737603 TS(ph)PAPWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TSPAPWK 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.013)S(0.987)PAPWK;T(0.007)S(0.993)PAPWK;T(0.025)S(0.975)PAPWK;T(0.013)S(0.987)PAPWK 129.29 0.0038548 1620130000 4880360 3459020 2943750 3989720 3932290 3063960 4064070 5188820 10655900 TRUE FALSE 4235408.061 3436297.47 4367357.346 4895646.905 3854045.122 3181832.524 3669937.117 4079231.222 9396171.641 0.450758907 0.365712505 0.464801784 0.5210257 0.410171852 0.338630737 0.390577914 0.434137581 1 23.16364164 1.238561694 6.728052537 1.014405313 0.419738623 0.926159286 0.051306769 0.029845349 6.949650343 0.08115231 0.013397458 17.32055061 -1.238561694 -0.59466669 LKS(ph)IEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 LKSIEER 7 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 LKS(1)IEER;LKS(1)IEER;LKS(1)IEER 117.14 0.0032091 606060000 1304340 1250850 1249430 1489320 1976630 1859780 2468290 2601360 2595910 TRUE FALSE 1131968.164 1242633.084 1853658.527 1827492.869 1937298.93 1931326.94 2228915.616 2045079.408 2289024.477 0.494519904 0.542865791 0.809802842 0.798371921 0.846342601 0.843733634 0.973740403 0.89342837 1 21.12630146 4.991479723 0.495569498 0.950648172 2.22E-18 0.897707747 0.052500554 1.750866937 0.291509356 0.038528529 1.024526289 98057.25299 -4.991479723 -0.950648172 down TS(ph)PCQS(ph)PTISEGPVPSLPIRPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSPCQSPTISEGPVPSLPIRPSR 23 1 A0A0D9SGJ6;J3KQV8;O43426;J3KPK1;C9JFZ1;O43426-4;O43426-2 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 2 T(0.379)S(0.621)PCQS(0.977)PT(0.023)ISEGPVPSLPIRPSR;T(0.45)S(0.55)PCQS(0.825)PT(0.175)IS(0.001)EGPVPSLPIRPSR 165.48 7.45E-12 380270000 154340 153159 130271 165492 162961 168651 163064 213710 345670 TRUE FALSE 133943.578 152152.8884 193270.4913 203069.488 159718.3949 175139.1131 147250.0784 168009.7796 304805.2864 0.439439813 0.499180609 0.634078541 0.666226923 0.524001394 0.574593424 0.483095553 0.551203628 1 18.2175284 1.23875392 10.60117275 1.001326907 0.548818318 0.816491533 0.067562691 0.029125824 93.86803632 0.096241313 0.017225632 17.3282187 -1.23875392 -0.452508589 TS(ph)PCQSPTISEGPVPSLPIRPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSPCQSPTISEGPVPSLPIRPSR 23 1 A0A0D9SGJ6;J3KQV8;O43426;J3KPK1;C9JFZ1;O43426-4;O43426-2 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 T(0.219)S(0.698)PCQS(0.061)PT(0.02)IS(0.002)EGPVPSLPIRPSR 71.418 0.013358 165920000 30951 24233 68547 33673 21211 15314 27786 21834 21843 TRUE FALSE 26860.74693 24073.81183 101696.5585 41318.96931 20788.9426 15903.13949 25091.318 17164.96901 19260.74542 1.394585014 1.249889934 5.279990792 2.145242482 1.079342577 0.825676221 1.302717909 0.891189237 1 14.23337592 3.317976127 4.497811303 1.012639641 2.673536079 0.323270687 1.088596938 0.250014318 9.345563741 0.325415817 0.419506319 2079.58237 -3.317976127 1.660896438 TS(ph)PDPSPVSAAPSK ddPTM_MDA-MB-175_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(0.265)S(0.735)PDPSPVSAAPSK;T(0.057)S(0.943)PDPSPVSAAPSK 301.95 1.34E-32 276960000 837140 943900 625350 732300 1060880 792200 1133770 1367700 1127390 TRUE FALSE 726509.828 937699.4587 927771.3517 898579.9075 1039770.564 822676.4466 1023817.16 1075227.998 994111.2385 0.730813414 0.943254057 0.933267139 0.903902775 1.045929795 0.827549689 1.029881889 1.081597267 1 19.92304777 6.596613438 0.33036404 1.037744584 5.33E-30 0.486788733 0.075727713 29.12457575 1.064256474 0.127067839 15.19010849 3950148.644 -6.596613438 -1.037744584 TS(ph)PDTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TSPDTLR 7 0 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 T(0.367)S(0.633)PDTLR;T(0.318)S(0.682)PDTLR;T(0.385)S(0.615)PDTLR;T(0.202)S(0.798)PDTLR 193.29 0.00052317 10144722000 15726490 13582740 9549160 11933180 13639870 13667510 13781030 16481490 21572780 TRUE FALSE 13648194.5 13493514.09 14167165.72 14642790.91 13368463.27 14193307.95 12444547.83 12957051.62 19022470.52 0.717477495 0.709346037 0.744759504 0.769762839 0.70277219 0.746133786 0.654202503 0.681144524 1 24.18120129 1.234531837 24.99999662 1.000000414 0.714143476 0.878869133 0.033165476 42.14745423 261502.9905 0.065903095 0.00885201 17.16057504 -1.234531837 -0.285856938 TS(ph)PDTLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSPDTLRR 8 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 T(0.401)S(0.599)PDTLRR 81.972 0.013156 188000000 175190 166100 101780 114760 155450 165040 174950 186800 103850 TRUE FALSE 152038.1976 165008.8782 151001.1484 140818.012 152356.8491 171389.1956 157983.3759 146854.2737 91572.97131 1.660295559 1.80193867 1.64897072 1.537768295 1.663775314 1.87161335 1.72521841 1.603685799 1 16.48263421 1.22425243 3.193446181 0.864668569 1.700504385 0.855394799 0.089880606 0.141624709 1.871307032 0.305369577 0.024534205 16.75916704 -1.22425243 0.835835816 TS(ph)PENVQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSPENVQDR 9 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 T(0.018)S(0.982)PENVQDR;T(0.045)S(0.955)PENVQDR 142.71 0.00010877 725550000 671050 595420 431350 476800 673210 639720 641310 752760 838440 TRUE FALSE 582369.0423 591508.6468 639952.3028 585064.7274 659814.4381 664330.4424 579115.8549 591788.132 739320.5784 0.787708417 0.800070584 0.865595144 0.791354582 0.892460534 0.898568851 0.783308178 0.800448614 1 19.49584054 -1.477322891 0.01706259 1.840607687 7.47E-07 0.204627796 0.062014804 19366.35395 36.71534785 2359.641988 1660.038417 0.033317861 1.477322891 -1.84060694 TS(ph)PHWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSPHWK 6 0 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 T(0.335)S(0.665)PHWK 107.43 0.020145 184600000 471230 351980 261910 372770 359110 313390 434970 481790 619700 TRUE FALSE 408955.7616 349667.8202 388570.552 457413.1259 351964.4136 325446.3161 392786.6763 378762.9578 546439.772 0.748400432 0.639901849 0.711094931 0.837078759 0.644104678 0.595575822 0.718810556 0.693146761 1 19.05970297 1.238096893 24.99999916 1.000000337 0.697188524 0.672752797 0.066075693 6.841127213 368411.5542 0.092884643 0.016218174 17.30202331 -1.238096893 -0.302811813 TS(ph)PINLGLNVNDLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TSPINLGLNVNDLLK 15 0 P50616 P50616 TOB1 Protein Tob1 1 T(0.174)S(0.826)PINLGLNVNDLLK;T(0.123)S(0.877)PINLGLNVNDLLK;T(0.163)S(0.837)PINLGLNVNDLLK 254.05 1.15E-24 543638000 822318 562204 432186 520986 692027 498556 813202 835182 745935 TRUE FALSE 713646.5928 558510.8449 641192.5952 639283.8341 678257.0166 517735.7719 734337.7952 656584.8287 657751.4141 1.084979184 0.849121466 0.974825111 0.971923162 1.031175307 0.78712985 1.116436665 0.998226404 1 19.32718292 TS(ph)PITR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSPITR 6 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.262)S(0.738)PITR 90.308 0.051584 913690000 1545900 1404800 904090 1227500 1115500 1572000 1371200 1502000 1884400 TRUE FALSE 1341605.398 1395571.776 1341310.948 1506222.636 1093303.732 1632475.857 1238221.235 1180808.989 1661628.379 0.807403999 0.839882006 0.807226793 0.906473827 0.657971269 0.98245545 0.745185416 0.710633619 1 20.66416633 TS(ph)PLNSSGSSQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSPLNSSGSSQGR 13 0 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 T(0.211)S(0.787)PLNS(0.001)S(0.001)GSSQGR;T(0.082)S(0.918)PLNSSGSSQGR 115.3 0.00029048 0 336189 327434 309936 348621 403440 392682 310674 385940 828920 TRUE FALSE 291760.7719 325283.0645 459822.0863 427780.7264 395412.3333 407788.7306 280544.8833 303409.7344 730926.0219 0.399165939 0.44502871 0.629095247 0.585258581 0.540974492 0.557906982 0.383821173 0.415103205 1 19.47936587 1.233051012 24.98824442 1.000000805 0.494553537 0.783850719 0.083415305 90.19964282 409046.5649 0.19169753 0.022604955 17.10216186 -1.233051012 -0.505447268 TS(ph)PPCS(ph)PANLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TSPPCSPANLSR 12 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 T(0.191)S(0.809)PPCS(1)PANLSR;T(0.245)S(0.755)PPCS(1)PANLSR;T(0.461)S(0.539)PPCS(1)PANLSR;T(0.175)S(0.825)PPCS(1)PANLSR;T(0.042)S(0.958)PPCS(1)PANLSR 236.05 6.72E-16 3356300000 6075340 6524250 5238370 5866270 7866830 8778870 7503570 7703800 10665690 TRUE FALSE 5272468.426 6481391.772 7771663.253 7198296.264 7710295.474 9116598.81 6775874.936 6056402.321 9404804.279 0.56061437 0.689157539 0.826350344 0.765385015 0.819825192 0.969355506 0.720469532 0.643968991 1 23.16496649 4.544864012 2.422544846 0.80327087 0.547846885 0.39045431 0.106212194 0.440061272 4.156828843 0.028638555 0.195075272 35064.2062 -4.544864012 -0.255423984 TS(ph)PPCSPANLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TSPPCSPANLSR 12 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 T(0.019)S(0.981)PPCSPANLSR;T(0.257)S(0.743)PPCSPANLSR;T(0.106)S(0.891)PPCS(0.002)PANLSR 134.99 0.0001423 3763170000 2342120 1978970 1269400 1588760 2461630 2002930 2142510 2380920 2921510 TRUE FALSE 2032602.908 1965970.016 1883286.086 1949512.241 2412648.379 2079984.013 1934729.71 1871778.786 2576132.416 0.789013366 0.763147889 0.73105174 0.75675933 0.936538962 0.807405706 0.751021065 0.72658485 1 21.29677532 TS(ph)PPLLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSPPLLDR 8 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.008)S(0.992)PPLLDR 126.55 0.001274 205060000 652130 501240 341860 409250 630600 558920 500250 630250 620970 TRUE FALSE 565949.3682 497947.3214 507184.6395 502176.4675 618052.2937 580422.0141 451735.832 495475.9421 547559.634 1.033584898 0.909393773 0.926263749 0.917117399 1.128739694 1.060016075 0.824998418 0.90488033 1 19.06265657 2.243270147 24.99997687 0.90536136 0.991220963 0.202762116 0.079763729 198.644469 1054486.812 0.032323772 0.02419814 175.0935495 -2.243270147 0.085859603 TS(ph)PQVLGSILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSPQVLGSILK 11 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 T(0.081)S(0.919)PQVLGSILK;T(0.262)S(0.738)PQVLGSILK 134.04 0.00015638 755520000 2765630 2394140 1829620 2121240 2794260 2193240 2915160 3546620 3720890 TRUE FALSE 2400144.988 2378412.737 2714430.352 2602899.963 2738659.693 2277615.362 2632448.232 2788202.913 3281010.623 0.731526125 0.72490248 0.827315319 0.793322626 0.834700038 0.694181039 0.80232847 0.849800026 1 21.64570883 1.226688413 1.692908857 1.091408191 0.772055087 0.725232004 0.044762867 0.559971967 1.440929353 0.300415218 0.012726838 16.85343434 -1.226688413 -0.319353104 TS(ph)PRPAS(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSPRPASPAR 10 1 O15047 O15047 SETD1A Histone-lysine N-methyltransferase SETD1A 2 T(0.456)S(0.544)PRPAS(1)PAR;T(0.457)S(0.543)PRPAS(1)PAR 68.034 0.021714 154690000 334930 252720 238500 269980 285820 289000 274070 324850 566480 TRUE FALSE 290668.1519 251059.8657 353839.3977 331283.0854 280132.7412 300118.017 247490.7336 255383.3555 499511.3797 0.581904965 0.502610903 0.708371044 0.663214291 0.560813532 0.600823183 0.495465656 0.511266341 1 18.93015802 1.233252502 24.99985775 1.000000664 0.575604386 0.789872825 0.068383419 82.06072745 386441.768 0.150089672 0.018025939 17.11009821 -1.233252502 -0.424396278 TS(ph)PSGGTWSSVVSGVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(0.183)S(0.816)PS(0.001)GGTWSSVVSGVPR;T(0.002)S(0.998)PSGGTWSSVVSGVPR;T(0.116)S(0.767)PS(0.116)GGTWSSVVSGVPR;T(0.023)S(0.977)PSGGTWSSVVSGVPR;T(0.007)S(0.985)PS(0.008)GGTWSSVVSGVPR 284.53 3.51E-36 2104830000 2396490 2265300 1508760 1734050 2427620 2395990 2428380 2769690 2933290 TRUE FALSE 2079787.775 2250419.095 2238401.382 2127792.556 2379315.112 2488165.286 2192876.081 2177413.347 2586519.798 0.804087321 0.870056783 0.865410497 0.822646924 0.919890547 0.961974189 0.84780951 0.841831309 1 21.3025808 3.235847878 24.99979342 0.902639172 0.844433702 0.328442321 0.050772193 110.7005234 1020184.472 0.015775662 0.018710483 1721.265554 -3.235847878 -0.058205471 TS(ph)PTFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TSPTFR 6 0 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3 P62750 RPL23A 60S ribosomal protein L23a 1 T(0.187)S(0.813)PTFR;T(0.129)S(0.871)PTFR;T(0.101)S(0.899)PTFR;T(0.318)S(0.682)PTFR 141.78 0.012178 2792700000 5073000 4711100 3219050 3728930 4798200 5160400 4902290 5514200 5750500 TRUE FALSE 4402590.197 4680152.474 4775793.347 4575640.55 4702725.208 5358923.927 4426866.67 4335031.242 5070682.441 0.868244117 0.92298276 0.941844299 0.902371742 0.927434376 1.056844713 0.873031731 0.854920672 1 22.2737485 4.731883122 4.336407641 0.928886515 0.864127445 0.106766135 0.058591524 0.54627812 24.64421636 0.01493665 0.108178559 53936.5448 -4.731883122 -0.06475907 TS(ph)PTGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSPTGPK 7 0 C9JB30;Q9UPY8;Q9UPY8-2 C9JB30;Q9UPY8-2 MAPRE3 Microtubule-associated protein RP/EB family member 3 1 T(0.014)S(0.982)PT(0.004)GPK;T(0.161)S(0.839)PTGPK 103.8 0.0087008 1086170000 2280540 1853880 1664900 1846770 1288810 1663770 2579400 2827100 4120800 TRUE FALSE 1979160.861 1841701.74 2470051.209 2266107.355 1263165.203 1727776.309 2329250.185 2222546.666 3633643.718 0.544676643 0.506847089 0.679772537 0.623645996 0.34763045 0.475494144 0.641023272 0.611657839 1 21.79298554 0.713689416 1.42868227 2.191734913 0.538301805 0.697927256 0.093338127 2.847163589 1.733792584 9.95077581 0.02821472 5.172367992 -0.713689416 -1.653433108 TS(ph)PTPPESATTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TSPTPPESATTVK 13 0 Q5M775-4;Q5M775;J3KSG2 Q5M775-4 SPECC1 Cytospin-B 1 T(0.055)S(0.945)PTPPESATTVK;T(0.112)S(0.887)PTPPESATTVK;T(0.007)S(0.993)PTPPESATTVK;T(0.435)S(0.564)PTPPESATTVK 235.6 1.14E-16 1325160000 3132830 2816600 1950750 2361510 3086040 2396870 3286870 3938510 3517840 TRUE FALSE 2718818.578 2798097.569 2894139.225 2897726.939 3024633.842 2489079.14 2968109.853 3096290.286 3101964.963 0.876482685 0.902040353 0.933001907 0.934158501 0.975070279 0.802420134 0.956848285 0.998170619 1 21.56475096 2.005738722 24.99996589 0.9925211 0.907210875 0.440578125 0.044766253 135.2079636 589011.9875 0.018091831 0.012157297 101.3301584 -2.005738722 -0.085310225 TS(ph)PTVATQTGASATSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TSPTVATQTGASATSTR 17 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 T(0.239)S(0.729)PT(0.032)VATQTGASATSTR;T(0.178)S(0.797)PT(0.025)VATQTGASATSTR;T(0.138)S(0.862)PTVATQTGASATSTR 131.18 2.92E-05 369057000 354994 291105 161520 205323 320618 257054 301710 347701 313915 TRUE FALSE 308080.6435 289192.7121 239631.6123 251944.7253 314238.3291 266943.0337 272450.2106 273347.847 276804.3263 1.112990709 1.044755029 0.865707612 0.910190706 1.135236336 0.9643745 0.984270059 0.987512914 1 18.07850697 4.4730987 24.99815629 0.980244261 1.095931831 0.292259934 0.069162347 123.6203956 768244.8297 0.017401384 0.046466974 29723.41466 -4.4730987 0.11568757 TS(ph)PYILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TSPYILR 7 0 P49454 P49454 CENPF Centromere protein F 1 T(0.064)S(0.936)PYILR;T(0.064)S(0.936)PYILR;T(0.217)S(0.783)PYILR;T(0.057)S(0.943)PYILR;T(0.225)S(0.775)PYILR 170.3 0.001028 1481144000 3256480 3259940 2070680 2597880 3648960 3391780 3271080 4133740 3726840 TRUE FALSE 2826127.917 3238525.239 3072067.774 3187768.36 3576352.835 3522263.971 2953851.165 3249771.87 3286257.221 0.859983783 0.985475275 0.934822677 0.970030082 1.088275383 1.071816274 0.898849654 0.988897597 1 21.64801398 5.840659737 0.971321202 0.997329758 3.75E-10 0.365522483 0.055529533 17.74189869 2.564422223 0.018552236 30.39536291 692882.7312 -5.840659737 -0.997329757 TS(ph)SESIYSRPGSSIPGS(ph)PGHTIYAK ddPTM_MDA-MB-175_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 2 T(0.404)S(0.462)S(0.013)ES(0.015)IY(0.012)S(0.023)RPGS(0.038)S(0.044)IPGS(0.989)PGHTIYAK 127.23 0.0001641 138370000 123030 147360 78201 124990 169300 133390 175540 210490 185760 TRUE FALSE 106771.2738 146391.9825 116019.2652 153370.8899 165931.2612 138521.5996 158516.1578 165478.3515 163799.6644 0.651840614 0.893725778 0.708299773 0.936332137 1.013013438 0.845676944 0.967744094 1.010248416 1 17.32157288 6.089747146 0.317189032 1.020719125 4.68E-18 0.613960049 0.077924122 16.75989936 0.791945684 0.149898756 7.648353287 1229552.694 -6.089747146 -1.020719125 TS(ph)SKES(ph)SPIPS(ph)PTSDRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSSKESSPIPSPTSDRK 17 2 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 3 T(0.292)S(0.355)S(0.355)KES(0.499)S(0.499)PIPS(0.948)PT(0.027)S(0.025)DRK 58.015 0.07235 201110000 245360 181600 189860 169660 222540 148000 235720 315580 229070 TRUE FALSE 212935.0543 180407.0576 281676.931 208183.8961 218111.8894 153693.6558 212859.9107 248095.6728 201989.6056 1.054188178 0.893150205 1.394512011 1.030666383 1.079817394 0.760898836 1.053816161 1.228259604 1 17.62392153 1.973336898 23.99105217 1.133615246 1.035523356 0.032443494 0.167897492 1371.241006 1233817.514 0.076949523 0.044635534 94.04525714 -1.973336898 -0.098091889 TS(ph)SKSEAGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSSKSEAGAR 10 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 T(0.023)S(0.387)S(0.387)KS(0.203)EAGAR 75.483 0.023533 279110000 382790 230660 183840 221850 171720 268490 341410 450620 343350 TRUE FALSE 332203.3316 229144.7793 272745.6389 272224.4333 168303.108 278818.984 308300.1107 354258.4197 302759.5541 1.097251357 0.756853999 0.900865506 0.899143989 0.555896934 0.920925468 1.018300187 1.170098234 1 18.20781296 2.236819094 3.228453178 1.092957432 0.836710144 0.33307051 0.141409355 0.239656922 5.229059671 0.060519089 0.040398934 172.511914 -2.236819094 -0.256247288 TS(ph)SLDTLAAPYLAGHWPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSSLDTLAAPYLAGHWPR 18 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 T(0.257)S(0.371)S(0.371)LDTLAAPYLAGHWPR 223.5 3.30E-19 133150000 122950 94864 53106 64055 93273 73292 90687 106270 97994 TRUE FALSE 106701.846 94240.83214 78788.23923 78599.66677 91417.04979 76111.59067 81892.1887 83544.98749 86409.26096 1.23484271 1.09063347 0.911803184 0.909620866 1.057954307 0.880826775 0.947724674 0.96685224 1 16.39889832 4.506618618 3.022381637 0.954302819 1.230224866 0.768477416 0.050898033 0.123593224 2.082509466 0.012607882 0.062059947 32108.39652 -4.506618618 0.275922046 TS(ph)SPHKEESPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSSPHKEESPK 11 1 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 T(0.02)S(0.49)S(0.49)PHKEESPK 150.22 2.06E-05 414210000 343860 240590 204750 216900 196590 170040 361420 419220 466110 TRUE FALSE 298418.0298 239009.5484 303767.7848 266150.4601 192678.2436 176581.5488 326369.544 329573.0654 411007.0068 0.726065553 0.581521834 0.739081767 0.64755699 0.46879552 0.429631481 0.794072944 0.801867267 1 18.64880346 1.653882067 1.772273162 0.982964088 0.605570332 0.575580837 0.109314169 0.303824944 1.756546196 0.163438111 0.033231225 45.06943017 -1.653882067 -0.377393756 TS(ph)STLDSEGTFNSYR ddPTM_MDA-MB-175_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(0.016)S(0.865)S(0.118)TLDSEGTFNSYR 278.85 1.30E-33 267190000 544850 446400 399960 456220 546550 481210 507990 555020 1038500 TRUE FALSE 472846.692 443467.569 593381.9938 559811.7239 535674.7243 499722.4601 458725.208 436333.2922 915729.7131 0.516360543 0.484277798 0.64798814 0.611328557 0.584970343 0.545709561 0.500939526 0.476486987 1 19.80456231 1.233274709 24.99427551 1.000000713 0.545143693 0.868474781 0.055522596 63.74740192 301394.0428 0.125688295 0.015140059 17.11097312 -1.233274709 -0.45485702 TS(ph)VQT(ph)EDDQLIAGQSAR ddPTM_MDA-MB-175_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 2 T(0.148)S(0.852)VQT(1)EDDQLIAGQSAR 233.29 1.55E-18 0 247740 202320 135500 193800 268890 286210 188110 243140 324730 TRUE FALSE 215000.5313 200990.9466 201028.2532 237805.252 263539.6151 297220.6839 169867.1212 191146.4031 286340.7893 0.750855412 0.701929149 0.702059437 0.830497299 0.920370499 1.037996314 0.593234102 0.667548635 1 18.12737367 3.737338838 24.26663893 0.819417924 0.716646109 0.141542722 0.13602435 185.3244714 3680895.493 0.040433129 0.063998411 5461.838291 -3.737338838 -0.102771814 TS(ph)VQTEDDQLIAGQSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(0.004)S(0.996)VQTEDDQLIAGQSAR;T(0.123)S(0.877)VQTEDDQLIAGQSAR;T(0.009)S(0.991)VQTEDDQLIAGQSAR;T(0.012)S(0.988)VQTEDDQLIAGQSAR;T(0.151)S(0.849)VQTEDDQLIAGQSAR 493.78 1.42E-232 2288700000 2459870 1832701 1332848 2276310 2432770 2451530 1672916 2788160 3414130 TRUE FALSE 2134791.947 1820661.866 1977417.751 2793180.977 2384362.637 2545841.945 1510676.864 2191933.681 3010515.441 0.709111775 0.60476749 0.65683694 0.927808221 0.792011429 0.845649855 0.501800072 0.728092489 1 21.52157909 3.949240025 24.98772531 0.776204806 0.650404849 0.187607801 0.133866589 652.2056645 321062.8649 0.036675277 0.06352458 8896.926964 -3.949240025 -0.125799957 TSADAQEPAS(ph)PVVSPQQS(ph)PPTS(ph)PHTWR ddPTM_MDA-MB-175_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 3 TSADAQEPAS(1)PVVS(0.01)PQQS(0.99)PPT(0.284)S(0.692)PHT(0.024)WR;TSADAQEPAS(1)PVVSPQQS(0.998)PPT(0.096)S(0.867)PHT(0.038)WR;TSADAQEPAS(1)PVVSPQQS(0.997)PPT(0.321)S(0.65)PHT(0.032)WR 185.37 5.75E-18 1184010000 457410 405900 251777 301107 462800 439830 404850 442180 439950 TRUE FALSE 396962.1096 403233.6162 373537.1993 369477.9465 453591.1855 456750.5447 365587.7093 347623.248 387939.6122 1.023257479 1.039423672 0.962874601 0.952410981 1.169231425 1.177375371 0.942383035 0.89607567 1 18.56547257 2.044869373 24.99926421 0.934198722 1.050725936 0.297033375 0.077554819 155.8051471 86807.19473 0.034218251 0.023069928 110.8841248 -2.044869373 0.116527214 TSADAQEPASPVVSPQQS(ph)PPT(ph)SPHTWR ddPTM_MDA-MB-175_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 2 TSADAQEPASPVVSPQQS(0.996)PPT(0.738)S(0.265)PHT(0.001)WR 184.55 2.34E-17 574790000 329390 331520 223250 275400 435030 440070 373890 484650 398730 TRUE FALSE 285860.2769 329342.2233 331214.4467 337933.7792 426373.7541 456999.7777 337630.2053 381011.3691 351592.5936 0.81304408 0.936715475 0.942040455 0.961151587 1.21269265 1.299799216 0.960288162 1.08367291 1 18.42354515 3.409962991 6.201636895 1.105655076 0.908973731 0.490195395 0.101716173 0.194082483 13.5355715 0.03115272 0.040485282 2570.176753 -3.409962991 -0.196681345 TSADAQEPASPVVSPQQS(ph)PPTS(ph)PHTWR ddPTM_MDA-MB-175_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(0.999)PPT(0.398)S(0.602)PHT(0.001)WR;TSADAQEPASPVVSPQQS(0.999)PPT(0.292)S(0.708)PHT(0.001)WR;TSADAQEPASPVVSPQQS(0.987)PPT(0.303)S(0.71)PHT(0.001)WR 204.47 1.82E-25 2149140000 459680 480470 312429 385810 623580 617160 579480 693020 626860 TRUE FALSE 398932.1233 477313.7609 463520.7094 473414.0572 611171.978 640902.5446 523282.1188 544823.0661 552753.3249 0.721718179 0.86352038 0.838567022 0.856465327 1.105686661 1.159472979 0.946682897 0.985653168 1 19.07627627 3.348856741 5.678694811 1.031246647 0.81927906 0.708165006 0.070222979 0.131210496 6.058264186 0.022042325 0.02852348 2232.835566 -3.348856741 -0.211967587 TSADAQEPASPVVSPQQS(ph)PPTSPHTWR ddPTM_MDA-MB-175_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 1 TSADAQEPASPVVSPQQS(0.999)PPTSPHTWR 162.38 7.91E-12 84082000 50718 50098 25869 41205 59972 55306 57601 70347 59759 TRUE FALSE 44015.4878 49768.90294 38379.33493 50561.22503 58778.67453 57433.65761 52014.86389 55303.84149 52694.3591 0.835297906 0.944482555 0.728338585 0.95951874 1.115464265 1.08993939 0.987104972 1.049521096 1 15.68536091 3.490519539 8.829731837 1.04537093 0.846194206 0.700450553 0.063282632 0.107867894 59.43827805 0.017051452 0.023855791 3093.994512 -3.490519539 -0.199176724 TSAEAPSHHLQQQQQQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TSAEAPSHHLQQQQQQQR 18 0 Q92609;Q92609-2;C9J3F6 Q92609 TBC1D5 TBC1 domain family member 5 0 ;;; 204.13 6.40E-16 150077000 219554 206691 67750 125324 231614 232444 207782 245866 215325 FALSE TRUE 190539.3826 205333.2332 100514.1266 153780.7297 227005.3345 241386.2711 187631.3336 193289.4692 189869.5238 1.003527995 1.081443873 0.529385257 0.809928453 1.195585948 1.2713271 0.988211957 1.018012082 1 17.53464883 3.249258993 24.99956392 1.085904329 0.84883466 0.335291716 0.166514306 272.4429726 636631.019 0.051164318 0.065366262 1775.247841 -3.249258993 -0.237069669 TSALS(ph)PNAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSALSPNAK 9 0 P50616 P50616 TOB1 Protein Tob1 1 TSALS(1)PNAK 130.56 0.0011959 0 197370 146540 122430 141140 197590 189990 244300 253230 251450 TRUE FALSE 171287.0544 145577.3691 181637.5575 173187.9942 193658.3456 197299.0382 220607.8236 199078.7351 221723.8675 0.772524205 0.656570584 0.819206158 0.781097661 0.873421287 0.889841227 0.994966515 0.897867863 1 17.75840455 3.207555103 0.82186303 0.961218433 0.715169017 0.778795827 0.048805927 0.272882015 0.443819099 0.028546728 0.040639731 1612.705633 -3.207555103 -0.246049416 TSASEGNPYVSSTLSVPAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSASEGNPYVSSTLSVPASPR 21 0 E9PDY7;G5E9V3;A0A1W2PQ63;E9PFQ4;Q86SQ0-2;Q86SQ0-3;Q86SQ0 E9PDY7 PHLDB2 Pleckstrin homology-like domain family B member 2 1 TSASEGNPYVSSTLSVPAS(1)PR;TSASEGNPYVSSTLSVPAS(1)PR 372.12 1.99E-112 262600000 125689 123953 66433 88905 114375 129239 131527 131950 114636 TRUE FALSE 109078.8802 123138.7446 98560.22101 109092.2391 112099.1613 134210.908 118771.5318 103733.5193 101083.8627 1.079092917 1.218184004 0.975034179 1.079225073 1.10897188 1.327718435 1.174980147 1.02621246 1 16.62519317 1.636942718 5.274162423 1.007156914 1.138121797 0.236643958 0.093270897 0.213279798 12.67427436 0.065323805 0.025229732 43.34537036 -1.636942718 0.130964883 TSAVSS(ph)PLLDQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TSAVSSPLLDQQR 13 0 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 TSAVS(0.001)S(0.999)PLLDQQR;TSAVS(0.002)S(0.998)PLLDQQR;TSAVS(0.032)S(0.968)PLLDQQR;TSAVS(0.062)S(0.938)PLLDQQR 361.58 1.10E-76 3107650000 3742730 3175870 1942760 2486260 3720630 3715970 3422450 3945830 4706680 TRUE FALSE 3248118.748 3155007.501 2882285.234 3050803.333 3646596.742 3858925.77 3090541.326 3102044.961 4150261.652 0.782629872 0.760194842 0.694482776 0.735086987 0.878642613 0.929803009 0.744661803 0.747433589 1 21.98477086 3.250107257 24.97428288 0.840850136 0.74084719 0.333915349 0.079548295 313.05165 677096.9802 0.024250186 0.031032232 1778.718642 -3.250107257 -0.100002946 TSCSGSGERES(ph)PERK ddPTM_MDA-MB-175_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 149.94 1.71E-06 646500000 681990 491670 318650 353590 484630 383870 623350 643680 501340 TRUE FALSE 591863.2936 488440.1874 472750.2058 433878.0138 474986.8112 398637.7273 562897.6129 506034.0411 442072.1563 1.33883866 1.104887925 1.069396023 0.981464242 1.07445539 0.901748101 1.273316143 1.144686527 1 18.75392234 4.741036366 3.474671741 1.074130858 1.372215412 0.425537503 0.099155386 0.3226628 6.737996515 0.025495603 0.254546624 55085.38201 -4.741036366 0.298084555 TSDANETEDHLESLICK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSDANETEDHLESLICK 17 0 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 177.56 9.44E-14 0 134420 111690 62809 83243 97532 82468 121750 134410 146020 FALSE TRUE 116656.0564 110956.301 93183.64248 102144.5954 95591.30402 85640.59732 109942.7037 105667.4675 128757.6819 0.9060124 0.861745096 0.723713266 0.793308748 0.742412434 0.665130003 0.853872966 0.820669228 1 16.97429898 0.947177655 1.580995365 1.259913261 0.785046284 0.45485298 0.070758206 2.293940196 2.795567703 2.146092224 0.020628795 8.854777551 -0.947177655 -0.474866977 TSDDEVGS(ph)PKEESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSDDEVGSPKEESR 14 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9 Q6ULP2-7 AFTPH Aftiphilin 1 TSDDEVGS(1)PKEESR 165.8 2.37E-06 447850000 386890 300040 253180 242650 331200 262920 418980 455890 319570 TRUE FALSE 335761.5062 298069.0175 375618.6948 297747.3912 324609.768 273034.7025 378347.3841 358401.4712 281790.7987 1.191527572 1.057767035 1.33297005 1.056625669 1.151953043 0.968926962 1.342653436 1.271870739 1 18.10426498 2.220947469 24.99989926 1.224547918 1.130846608 0.068679027 0.128521117 563.9524645 800461.3592 0.05084887 0.034364257 166.3211462 -2.220947469 -0.09370131 TSDIFGS(ph)PVTATSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 TSDIFGSPVTATSR 14 0 A6NGP5;Q9H910;Q9H910-3;H3BMV3;H3BTV5;Q9H910-2;H3BU16;H3BMT0 A6NGP5;Q9H910-2 HN1L Hematological and neurological expressed 1-like protein 1 TSDIFGS(1)PVTATSR;TSDIFGS(1)PVTATSR;TSDIFGS(1)PVTATSR;TSDIFGS(1)PVTATSR;TSDIFGS(1)PVTATSR;TSDIFGS(0.999)PVT(0.001)ATSR;TSDIFGS(1)PVTATSR 396.88 2.03E-114 8528160000 7529540 6827830 3893460 4968170 7537090 8013030 7532880 8423400 8185370 TRUE FALSE 6534492.212 6782977.535 5776350.279 6096268.932 7387116.655 8321296.449 6802342.457 6622121.461 7217704.883 0.905342116 0.93976931 0.800302918 0.844627071 1.023471696 1.152900622 0.942452285 0.91748299 1 22.78310873 3.23786772 24.99993351 0.998460474 0.87215688 0.466146695 0.071311179 20.03980911 723050.7383 0.023542823 0.028313217 1729.289562 -3.23786772 -0.126303594 TSDS(ph)PWFLSGSETLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSDSPWFLSGSETLGR 16 0 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 TSDS(0.999)PWFLSGSETLGR 70.529 0.045287 35289000 25028 23652 15861 18789 24907 29178 30148 28616 34667 TRUE FALSE 21720.48639 23496.62845 23531.43265 23055.32962 24411.39943 30300.49654 27224.2516 22496.69109 30568.70675 0.710546461 0.768649739 0.769788295 0.754213445 0.798574818 0.991225988 0.890592194 0.735938595 1 14.8997679 2.986641801 20.82846085 0.878822592 0.75630107 0.473351875 0.07476265 76.83977287 119812.2946 0.024593181 0.025743689 969.7098373 -2.986641801 -0.122521522 TSEEFVHINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TSEEFVHINR 10 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6;A0A3B3IS13;A0A3B3ISK3;A0A3B3IU76 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ;;;; 185.61 1.43E-06 4581270000 3499340 3522650 2019764 2275180 3587150 3644220 3562980 3754930 3695710 FALSE TRUE 3036893.353 3499509.48 2996528.626 2791794.393 3515772.733 3784415.502 3217442.748 2951967.44 3258807.374 0.931903302 1.073862023 0.919516953 0.856692057 1.078852577 1.161288492 0.987306821 0.905842875 1 21.63591265 4.227046729 24.9898075 0.984675018 1.002882706 0.004495123 0.092627916 2019.428308 4383006.477 0.025533691 0.053890933 16867.34506 -4.227046729 0.018207688 TSEIVLRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSEIVLRPR 9 1 Q92466-4;Q92466;A0A087WTQ7;A0A087WV56;A0A087WW71;A0A087X0X5;Q92466-3;Q92466-2;Q92466-5 Q92466-4 DDB2 DNA damage-binding protein 2 0 110.76 0.0025065 0 67928 75205 35489 54994 82307 74872 82242 85704 99418 FALSE TRUE 58951.14269 74710.9734 52651.5991 67481.22823 80669.25173 77752.37429 74266.1835 67376.86655 87664.9173 0.672459913 0.852233433 0.600600568 0.769763211 0.920199941 0.886926911 0.847159682 0.76857275 1 16.41971198 3.426071257 6.240764648 0.86639282 0.716722211 0.473183803 0.084969059 0.188241419 16.35026241 0.02398853 0.031285188 2667.296268 -3.426071257 -0.14967061 TSES(ph)PSKPGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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(0.031)S(0.031)ES(0.915)PS(0.022)KPGEK;TSES(0.996)PS(0.003)KPGEK;TSES(0.5)PS(0.5)KPGEK;TSES(0.861)PS(0.138)KPGEK;TSES(1)PSKPGEK 190.41 1.38E-06 2015650000 4175120 2999020 2593340 2190240 2336710 2005680 3855030 4394750 3905110 TRUE FALSE 3623367.314 2979319.24 3847487.898 2687567.468 2290214.043 2082839.807 3481169.784 3454966.912 3443452.345 1.052248427 0.865212857 1.11733444 0.780486326 0.665092417 0.604869648 1.010953379 1.003343902 1 21.71542428 3.726652396 24.93709583 0.853707872 0.99696001 0.210203662 0.151393625 1471.025085 3080483.926 0.047106101 0.070492592 5329.081917 -3.726652396 0.143252138 TSESPS(ph)KPGEK ddPTM_MDA-MB-175_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 1 TSES(0.02)PS(0.98)KPGEK 132.5 0.00047659 125880000 279950 199330 171870 157260 161700 121470 275520 305180 271980 TRUE FALSE 242953.8982 198020.5881 254986.9069 192968.2866 158482.4864 126143.0295 248800.1128 239919.6319 239826.8342 1.013038841 0.825681533 1.063212579 0.804615076 0.660820491 0.52597546 1.037415657 1.000386936 1 17.87163357 TSESPSKPGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 136.27 9.36E-05 447250000 663690 623400 444600 484600 549350 442200 775400 936600 762460 FALSE TRUE 575981.6849 619304.8444 659610.0471 594635.8366 538419.0098 459211.7201 700201.8273 736315.3786 672322.8474 0.856704018 0.921142048 0.981091227 0.884449843 0.800834022 0.683022631 1.041466656 1.095181253 1 19.35879465 2.052055709 19.59896475 1.058569716 0.86223548 0.551908542 0.080814567 9.225203249 3472.822234 0.035451766 0.023901562 112.7342056 -2.052055709 -0.196334236 TSEVNCYR ddPTM_MDA-MB-175_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 ;;; 183.74 0.00051576 2726260000 1345840 1202700 746350 967490 1277130 1223620 1184650 1380650 1563090 FALSE TRUE 1167983.834 1194799.385 1107287.356 1187173.392 1251717.612 1270693.453 1069762.825 1085408.742 1378303.281 0.84740699 0.866862469 0.803369891 0.861329584 0.908158334 0.921925871 0.776144728 0.787496306 1 20.39446194 TSFDDRLEDDDFDLIEENLGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSFDDRLEDDDFDLIEENLGVK 22 1 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 108.71 0.0001361 0 21757 18204 11898 14365 18506 15307 23950 26105 15122 FALSE TRUE 18881.75732 18084.41673 17651.9126 17626.79281 18137.76681 15895.87019 21627.33269 20522.6489 13334.29439 1.416029733 1.356233498 1.323798027 1.321914178 1.360234466 1.192104339 1.621933044 1.539087732 1 13.70285386 2.260620899 24.99991612 1.428479284 1.330596571 0.006399673 0.170420846 685.9608619 777365.9851 0.063027859 0.048780958 182.2304296 -2.260620899 -0.097882713 SLS(ph)FSEPQQPAPAMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SLSFSEPQQPAPAMK 15 0 Q9H8N7 Q9H8N7 ZNF395 Zinc finger protein 395 1 S(0.018)LS(0.982)FSEPQQPAPAMK 195.2 2.13E-08 74798000 165120 219280 167890 223040 311460 248660 315480 413790 373980 TRUE FALSE 143298.9736 217839.5352 249082.1656 273684.641 305262.5554 258226.1111 284884.7982 325304.2286 329768.5104 0.43454414 0.660583192 0.755324289 0.829929579 0.925687401 0.783052666 0.863893274 0.986462377 1 18.33109412 5.008686154 0.575629042 0.938058448 2.42E-14 0.875689146 0.058839094 1.886807583 0.39319381 0.036253099 1.262087519 102020.1961 -5.008686154 -0.938058448 down TSFNYAMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSFNYAMK 8 0 P15559-2;P15559;B4DLR8;P15559-3;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ; 132.08 0.0022738 895270000 526920 659980 423440 469230 732550 652880 747460 784350 772850 FALSE TRUE 457286.187 655644.5479 628217.0003 575775.8432 717973.6882 677996.7161 674971.4442 616622.8563 681484.5534 0.67101475 0.962082772 0.921836008 0.844884657 1.053543598 0.994882001 0.990442763 0.904822939 1 19.37832143 4.739367067 24.39773554 0.955636005 0.671014624 0.708280243 0.058059022 27.5636443 833682.3116 0.014276642 0.083498688 54874.05656 -4.739367067 -0.284621381 TSFSLSRPSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSFSLSRPSSPR 12 1 Q8N1G1;A0A2R8Y7I5;K7ESH4 Q8N1G1 REXO1 RNA exonuclease 1 homolog 1 TSFSLSRPS(0.012)S(0.988)PR;TSFSLSRPS(0.03)S(0.97)PR 68.262 0.032184 521830000 791990 780150 445440 555720 891330 931650 907580 943390 610700 TRUE FALSE 687326.5149 775025.1433 660856.2739 681904.7196 873594.2769 967491.1784 819563.0313 741653.39 538503.7417 1.276363489 1.439219607 1.227208323 1.26629523 1.622262223 1.796628516 1.521926345 1.37724835 1 19.03859684 3.265301384 24.97276398 1.473841842 1.306691938 0.128333731 0.207851811 495.3711684 462615.6171 0.063883293 0.082450254 1842.04987 -3.265301384 -0.167149905 TSFSQEQSCDS(ph)AGEGSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TSFSQEQSCDSAGEGSER 18 0 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 TSFSQEQS(0.163)CDS(0.837)AGEGSER;TSFSQEQSCDS(1)AGEGSER;TSFSQEQSCDS(1)AGEGSER 276.4 4.43E-39 420280000 412922 406121 233434 262329 419690 395398 403013 421220 404392 TRUE FALSE 358353.3115 403453.1644 346323.4632 321894.8089 411338.9901 410609.2169 363928.8613 331145.3809 356585.2384 1.004958346 1.131435407 0.971222097 0.902714903 1.153550248 1.151503687 1.020594299 0.928657009 1 18.44388746 1.989954185 23.93090951 0.963850472 1.053215606 0.163696635 0.08171322 465.6420531 1109239.833 0.036845026 0.023159133 97.71341337 -1.989954185 0.089365135 TSFSVGS(ph)DDELGPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 TSFSVGSDDELGPIR 15 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 TSFSVGS(1)DDELGPIR;TSFSVGS(1)DDELGPIR;TSFSVGS(1)DDELGPIR;TSFSVGS(1)DDELGPIR;TSFSVGS(1)DDELGPIR;TSFSVGS(1)DDELGPIR;TSFSVGS(1)DDELGPIR;TSFS(0.001)VGS(0.999)DDELGPIR 425.98 3.02E-153 6142430000 4847840 4302440 2771600 3233740 4804570 4804550 4476540 5028640 4777220 TRUE FALSE 4207185.661 4274176.988 4111955.03 3968010.092 4708968.457 4989384.147 4042405.84 3953304.469 4212462.494 0.998747328 1.014650456 0.976140449 0.941969239 1.117865966 1.184434082 0.959630108 0.938478259 1 22.00623241 TSFSVGS(ph)DDELGPIRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSFSVGSDDELGPIRK 16 1 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 TSFSVGS(1)DDELGPIRK;TSFSVGS(1)DDELGPIRK 195.96 2.89E-11 321110000 345660 265880 175532 219670 303620 272080 308870 366290 272690 TRUE FALSE 299980.1552 264133.4168 260419.8623 269549.4309 297578.556 282547.0937 278915.8349 287961.734 240452.8988 1.247563064 1.09848298 1.08303898 1.1210072 1.237575248 1.175062122 1.159960376 1.19758063 1 17.87539479 1.231033157 24.96203715 0.999999706 1.162884059 0.478110042 0.054146332 251.8341313 835042.5217 0.137997352 0.013533773 17.02288469 -1.231033157 0.162884354 TSGAPGS(ph)PQTPPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TSGAPGSPQTPPER 14 0 Q96MH2;K7ESM2;K7ELS4;K7EJA3;K7ERG7;K7EIM4 Q96MH2 HEXIM2 Protein HEXIM2 1 TSGAPGS(1)PQTPPER;TSGAPGS(0.998)PQT(0.002)PPER;TSGAPGS(0.997)PQT(0.003)PPER;T(0.001)S(0.001)GAPGS(0.996)PQT(0.001)PPER 272.96 5.64E-33 996853000 961550 869110 503910 628405 997080 944990 925760 1002690 1020350 TRUE FALSE 834478.7312 863400.7592 747602.5615 771093.9598 977240.0588 981344.3768 835979.9377 788272.5464 899725.3854 0.92748159 0.959626985 0.83092305 0.857032571 1.086153703 1.090715448 0.929150107 0.876125715 1 19.7791252 3.275103224 24.99997201 0.981059748 0.893981605 0.317051111 0.072958774 283.0776955 193660.7267 0.024147635 0.031173493 1884.096852 -3.275103224 -0.087078143 TSGHDHPDVATMLNILALVYR ddPTM_MDA-MB-175_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 ; 201.12 4.11E-22 795960000 933090 964830 309817 617060 951590 986550 983280 1101400 1003710 FALSE TRUE 809779.7924 958491.9682 459645.5375 757172.9042 932655.2208 1024503.217 887921.6569 865874.1811 885052.5472 0.914951089 1.08297747 0.519342652 0.855511807 1.053785138 1.157562023 1.003241739 0.978330816 1 19.75540359 3.264725374 7.367224306 1.034437153 0.836289294 0.309746633 0.144769734 0.235466177 47.28119722 0.043039338 0.054461332 1839.608357 -3.264725374 -0.198147859 TSGHVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSGHVDK 7 0 P41250 P41250 GARS Glycine--tRNA ligase 0 66.258 0.096804 0 357160 283470 118220 236500 262590 286600 379240 437450 520500 FALSE TRUE 309960.4011 281607.8669 175391.5874 290200.9397 257364.9727 297625.6875 342461.3632 343904.7217 458967.083 0.675343423 0.613568766 0.382144154 0.632291401 0.560748216 0.648468482 0.746156698 0.749301496 1 18.80803116 -1.476005906 0.535450394 9.999999985 0.559669342 0.723486779 0.082369447 37.15936764 0.676947397 380.8777436 0.048623989 0.03341905 1.476005906 -9.440330643 TSGNVEDDLIIFPDDCEFKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSGNVEDDLIIFPDDCEFKR 20 1 Q16186 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 0 169.84 1.63E-11 57784000 148690 135750 79684 81784 120300 98522 139140 152720 124400 FALSE TRUE 129040.2398 134858.2493 118219.4489 100354.3072 117906.2654 102312.2051 125646.2242 120062.0165 109693.5737 1.176370095 1.229408841 1.077724473 0.914860404 1.074869396 0.932709197 1.145429217 1.094521879 1 16.74311948 4.133858136 4.983622683 1.036731719 1.201752463 0.500658373 0.071012267 0.171083734 6.751874963 0.018665777 0.041024828 13610.00034 -4.133858136 0.165020745 TSHLDLPEDFQEMGLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSHLDLPEDFQEMGLLR 17 0 E9PMS5;E9PRT1;E9PJJ5;Q4G0X4 E9PMS5 KCTD21 BTB/POZ domain-containing protein KCTD21 0 ; 189.81 3.34E-10 77612000 78025 83585 47661 62455 78856 81363 74474 89254 85658 FALSE TRUE 67713.79856 83035.92463 70710.01902 76636.36231 77286.91988 84493.08726 67251.52294 70167.72668 75531.60882 0.896496177 1.099353316 0.936164609 1.014626373 1.023239424 1.118645407 0.890375884 0.928984935 1 16.2047929 2.206494672 24.99979866 0.935477748 1.015407424 0.20108511 0.070258065 281.2998503 219309.9306 0.027044141 0.018234723 160.8772643 -2.206494672 0.079929676 TSHSDSSIYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSHSDSSIYLR 11 0 Q96JQ2 Q96JQ2 CLMN Calmin 0 112.13 0.00089889 0 54458 61200 30561 46919 56350 66191 49334 67597 64761 FALSE TRUE 47261.23732 60797.97317 45340.40182 57572.67606 55228.74525 68737.4106 44549.59627 53141.90759 57105.02836 0.82761954 1.064669346 0.793982651 1.008189256 0.967143294 1.20370154 0.780134387 0.930599443 1 15.80133017 4.782136704 21.50445315 0.959843002 0.827616825 0.112036962 0.122528375 10572.05847 5216504.705 0.028659819 8.576603115 60553.14502 -4.782136704 -0.132226177 TSIDAYDNFDNISLAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TSIDAYDNFDNISLAQR 17 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 367.23 2.70E-104 553656000 396818 349667 214207 244594 386049 391502 387326 423642 415049 FALSE TRUE 344377.4959 347370.0145 317798.2217 300132.8061 378367.3802 406563.3353 349763.1841 333049.4551 365982.38 0.94096742 0.949144094 0.868342956 0.820074469 1.033840427 1.110882265 0.955683124 0.910014999 1 18.48141467 3.225153605 24.99999413 0.992535345 0.896648119 0.416248655 0.062645633 289.3830645 539610.0541 0.021524882 0.024540571 1679.397898 -3.225153605 -0.095887226 TSIFWNDVKDPVSIEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSIFWNDVKDPVSIEER 17 1 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ; 215.49 5.11E-15 845650000 702890 561480 350170 421340 600510 458460 644730 787910 634050 FALSE TRUE 610001.3056 557791.6009 519513.3832 517011.6868 588561.0259 476097.2529 582204.1838 619421.578 559093.3313 1.091054519 0.997671712 0.929206904 0.924732344 1.052706217 0.851552373 1.041336305 1.107903714 1 19.09272961 2.018183132 24.98588982 1.065547536 0.972415744 0.194954997 0.071491082 300.0697809 412331.7814 0.028175224 0.018991621 104.2757044 -2.018183132 -0.093131791 TSKEPPSS(ph)PLQPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TSKEPPSSPLQPQK 14 1 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 TSKEPPS(0.024)S(0.976)PLQPQK;TSKEPPS(0.022)S(0.978)PLQPQK;TSKEPPS(0.044)S(0.956)PLQPQK;TSKEPPS(0.058)S(0.942)PLQPQK 160.43 2.88E-06 2013940000 2808190 2778190 1729040 1972220 3380060 2343840 4327030 5067370 1615420 TRUE FALSE 2437080.576 2759939.887 2565209.527 2420042.694 3312803.419 2434009.041 3907395.297 3983752.36 1424446.888 1.710896066 1.937551979 1.800846033 1.698935015 2.325677038 1.708739766 2.743096517 2.796701227 1 20.4419704 3.238473885 24.99999999 2.226889088 1.798791771 0.06781495 0.517644926 4.885551031 1408271.027 0.154884332 0.187123914 1731.704896 -3.238473885 -0.428097317 TSKEPVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSKEPVSR 8 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 ; 93.111 0.010306 428950000 422300 404940 185910 270220 368410 365730 447710 495680 238710 FALSE TRUE 366491.985 402279.9225 275816.6978 331577.5811 361079.3618 379799.8698 404291.1531 389682.6894 210489.9757 1.741137476 1.911159527 1.310355502 1.575265425 1.715423077 1.804360842 1.920714522 1.851312339 1 17.683392 3.210358028 23.1336681 1.709457363 1.631090599 0 0.293193304 588.6632076 482856.9336 0.089547711 0.101570114 1623.147654 -3.210358028 -0.078366764 TSLDIEEYS(ph)DTEVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSLDIEEYSDTEVQK 15 0 P51580 P51580 TPMT Thiopurine S-methyltransferase 1 TSLDIEEY(0.011)S(0.986)DT(0.003)EVQK 106.36 0.0013036 66022000 39949 34097 20648 22691 33117 33807 36588 43594 39641 TRUE FALSE 34669.63843 33873.01456 30633.44186 27843.33836 32458.03649 35107.57717 33039.70139 34271.76235 34954.68614 0.991845222 0.969055034 0.876375824 0.796555239 0.92857468 1.004373978 0.945215221 0.980462597 1 15.09319826 2.987626241 24.77774247 0.977337974 0.904503431 0.294127164 0.054288959 740.9544305 1483721.883 0.018365571 0.019323752 971.9104252 -2.987626241 -0.072834543 TSLMSAES(ph)PTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSLMSAESPTPR 12 0 E5RHT1;B1AP22;P49810-2;P49810-3;P49810 E5RHT1 PSEN2 Presenilin;Presenilin-2;Presenilin-2 NTF subunit;Presenilin-2 CTF subunit 1 TSLMS(0.004)AES(0.987)PT(0.009)PR 121.66 0.00039064 193490000 202090 164150 114960 151940 178940 199230 154650 202930 187800 TRUE FALSE 175383.2945 163071.6878 170555.0405 186440.2993 175379.4441 206894.507 139652.0668 159534.9987 165598.4979 1.059087471 0.984741346 1.029931084 1.12585743 1.05906422 1.249374297 0.843317231 0.963384334 1 17.33733006 2.217301751 24.99946711 0.937518724 1.078352887 0.437696771 0.079444585 236.089626 277628.6396 0.032518895 0.021947703 164.9307944 -2.217301751 0.140834163 TSLPLS(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSLPLSPVK 9 0 Q86XL3;Q86XL3-2 Q86XL3 ANKLE2 Ankyrin repeat and LEM domain-containing protein 2 1 TSLPLS(1)PVK 98.737 0.0060958 117690000 187820 185240 130840 195710 274420 204960 211760 369350 323130 TRUE FALSE 162999.1111 184023.1462 194114.6616 240148.9467 268959.5789 212844.9438 191223.5478 290367.3768 284929.9395 0.572067335 0.645854018 0.68127155 0.842835074 0.943949868 0.747007999 0.671124797 1.019083418 1 18.1202477 5.239606626 0.157890217 1.15596882 2.10E-31 0.560235761 0.103475097 42.52236508 1.513126104 2.426535287 11.48015443 173622.7482 -5.239606626 -1.15596882 TSLS(ph)PTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSLSPTSK 8 0 Q8NDI1-3;Q8NDI1-2;Q8NDI1;H7C0Q4 Q8NDI1-3 EHBP1 EH domain-binding protein 1 1 TS(0.001)LS(0.966)PT(0.029)S(0.004)K 65.5 0.067248 195770000 259770 259850 176440 230730 324530 262490 343330 464700 330110 TRUE FALSE 225440.7363 258143.0282 261766.9742 283120.773 318072.4879 272588.1602 310033.9094 365327.5213 291084.7719 0.774484817 0.886831099 0.899280895 0.972640276 1.092714284 0.936456272 1.065098347 1.255055422 1 18.15107984 5.921812954 0.237601831 1.205801225 0.098817821 0.612014184 0.081730068 21.45712039 0.843461306 0.410568511 7.622205721 835243.2098 -5.921812954 -1.106983404 TSMTEEYRVPDGMVGLIIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSMTEEYRVPDGMVGLIIGR 20 1 A0A087WTP3;Q92945 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ; 120.31 3.48E-05 804900000 501280 452650 219830 290850 454380 451640 464320 560420 247131 FALSE TRUE 435034.5779 449676.5123 326140.5233 356891.9379 445338.727 469014.883 419290.3179 440578.5442 217915.4547 1.996345686 2.063536581 1.496637876 1.637754139 2.043630763 2.15227912 1.92409629 2.02178659 1 17.73340899 1.234541997 24.99998804 0.999998672 1.916277029 0.671973857 0.201350419 78.01802623 485284.5838 0.391716001 0.05262491 17.1609765 -1.234541997 0.916278357 TSNKPLMIIHHLDECPHSQALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSNKPLMIIHHLDECPHSQALK 22 1 O95994;B5MC07;C9J3E2 O95994 AGR2 Anterior gradient protein 2 homolog 0 ; 239.32 4.66E-31 6850400000 5439500 5157400 3485090 4748900 5456700 4668900 5775500 6270900 8098200 FALSE TRUE 4720656.293 5123520.7 5170491.181 5827210.327 5348122.346 4848515.604 5215392.899 4929916.835 7140840.021 0.661078568 0.717495517 0.724073241 0.816039893 0.748948629 0.678983928 0.730361258 0.690383319 1 22.76766237 1.23452657 24.99788509 1.000000403 0.722460964 0.809997036 0.042472637 52.82287336 327282.7518 0.080113023 0.010743255 17.16036692 -1.23452657 -0.27753944 TSNKPLMIIHHLDECPHSQALKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSNKPLMIIHHLDECPHSQALKK 23 2 O95994;B5MC07;C9J3E2 O95994 AGR2 Anterior gradient protein 2 homolog 0 ; 217.84 7.50E-33 1301160000 4756900 4295600 2764600 3381000 4369700 3496600 5444700 5904400 3016800 FALSE TRUE 4128263.613 4267381.921 4101569.807 4148707.725 4282751.519 3631116.465 4916673.832 4641790.008 2660157.341 1.551887007 1.604184029 1.541852335 1.559572309 1.609961732 1.365000637 1.848264295 1.744930624 1 21.34308015 1.230806343 24.99301719 0.999998899 1.610853828 0.689118235 0.127234513 174.3592641 561935.1788 0.34574905 0.032936722 17.01399665 -1.230806343 0.610854929 TSNRYS(ph)PESQAQSVHHQRPGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TSNRYSPESQAQSVHHQRPGSR 22 2 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 T(0.016)S(0.016)NRY(0.001)S(0.963)PES(0.003)QAQSVHHQRPGSR;T(0.003)S(0.003)NRYS(0.993)PESQAQSVHHQRPGSR;T(0.01)S(0.01)NRYS(0.98)PESQAQSVHHQRPGSR;T(0.062)S(0.062)NRY(0.011)S(0.865)PESQAQSVHHQRPGSR;T(0.004)S(0.004)NRYS(0.991)PES(0.001)QAQSVHHQRPGSR 199.46 8.38E-23 1206861000 357092 372915 97757 196642 485369 451476 360875 425035 247889 TRUE FALSE 309901.3874 370465.2968 145032.6122 241292.5716 475711.1065 468844.5739 325877.398 334144.5729 218583.8448 1.417768947 1.694842989 0.663510207 1.103890234 2.176332413 2.144918689 1.490857654 1.528679181 1 17.73782725 3.290671308 24.99999873 1.66126812 1.214170049 0.221098417 0.417797564 169.3339739 81236.253 0.127421028 0.164499657 1952.86089 -3.290671308 -0.447098071 TSPDAFVQLALQLAHYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSPDAFVQLALQLAHYK 17 0 P50416;P50416-2 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 140.46 6.60E-07 272080000 154410 189390 138500 182540 246510 229320 130280 299260 268500 FALSE TRUE 134004.3273 188145.8846 205479.0633 223988.4969 241604.9333 238142.0888 117645.4657 235265.5778 236758.2359 0.565996476 0.794675142 0.867885599 0.946064225 1.020471083 1.005845004 0.49690126 0.993695434 1 17.85305509 4.733790346 1.804591987 0.901211089 0.457469183 0.333357401 0.152567945 1.081413864 3.600448352 0.041241898 0.816585247 54173.93052 -4.733790346 -0.443741906 TSPDTLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TSPDTLRR 8 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ;;;;; 180.03 0.0003868 2212380000 4679850 4063170 1666250 2169780 4323270 4442820 4279710 4800570 863074 FALSE TRUE 4061395.965 4036478.769 2472054.073 2662461.712 4237245.385 4613738.16 3864664.383 3774005.464 761042.3749 5.336622636 5.303881757 3.248247607 3.498440822 5.567686537 6.062393255 5.07811984 4.958995173 1 19.53761726 4.414638916 24.99996481 4.397897107 5.328525571 0.082735761 1.437319058 173.3875288 69373.17021 0.362849051 0.960000453 25979.9862 -4.414638916 0.930628464 TSPGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSPGSPR 7 0 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 TSPGS(1)PR;TSPGS(1)PR 121.85 0.0046134 1603330000 2344300 1631250 841120 1199890 1020730 1841850 1484610 1798230 1773360 TRUE FALSE 2034494.815 1620534.211 1247888.445 1472343.364 1000419.47 1912707.161 1340632.751 1413692.508 1563715.401 1.30106464 1.036335775 0.798027854 0.941567348 0.639770811 1.223181124 0.857338074 0.904059976 1 20.57654653 4.639980362 3.109806235 0.908685918 1.32311059 0.411455072 0.148095794 0.274404421 4.235226241 0.034782783 0.240477236 43649.60946 -4.639980362 0.414424672 TSPTFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSPTFR 6 0 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3 P62750 RPL23A 60S ribosomal protein L23a 0 99.511 0.090068 70412000 111660 120710 59686 73827 118710 128050 110190 116850 112490 FALSE TRUE 96903.84809 119917.0481 88550.34924 90590.54873 116347.9033 132976.1664 99503.79076 91862.53683 99191.56035 0.976936422 1.208944064 0.8927206 0.913288877 1.17296172 1.340599602 1.003147752 0.926112428 1 16.59792975 2.011129249 24.99337672 0.959833923 1.085334002 0.125480677 0.137161109 428.2847813 961811.5856 0.058925667 0.039690783 102.5957213 -2.011129249 0.125500079 TSPYDHMLPGAEHFAEYAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSPYDHMLPGAEHFAEYAGR 20 0 P25325-2;P25325;B1AH49 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase 0 ; 162.76 1.19E-11 481260000 289620 295250 125190 205632 311260 312370 313130 337590 317620 FALSE TRUE 251345.9832 293310.4833 185732.3027 252323.8885 305066.535 324387.076 282762.7008 265399.0056 280071.3254 0.897435619 1.047270665 0.663160723 0.900927248 1.089245872 1.158230231 1.009609607 0.947612203 1 18.09543476 3.343032145 6.289346053 1.032293924 0.870806065 0.366945816 0.106993336 0.25592613 13.48418124 0.032304364 0.041746903 2203.089522 -3.343032145 -0.161487859 TSQLLETLNQLSTHTHVVDITR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSQLLETLNQLSTHTHVVDITR 22 0 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;E7EWF7 E7EX90 DCTN1 Dynactin subunit 1 0 ; 162.81 9.14E-12 325230000 177985 174641 78704 128853 204470 219691 186430 218883 261821 FALSE TRUE 154463.8313 173493.7718 116765.5176 158111.043 200401.447 228142.6549 168350.0473 172076.5738 230868.8196 0.669054537 0.751482041 0.505765646 0.684852304 0.86803167 0.988191715 0.729202183 0.745343499 1 17.81671382 3.309434009 5.148993381 0.846814754 0.645161615 0.500781642 0.105320844 0.194715932 9.520671076 0.03200025 0.041149213 2039.0788 -3.309434009 -0.201653139 TSQTWHGGIATIFQSPGDEVWGVVWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSQTWHGGIATIFQSPGDEVWGVVWK 26 0 O75223;B8ZZK2;H7BZK5;O75223-2;O75223-4 O75223 GGCT Gamma-glutamylcyclotransferase 0 ; 250.22 5.51E-46 941600000 904400 706250 285630 632790 623240 542620 745910 891900 1058800 FALSE TRUE 784881.2485 701610.5972 423761.6234 776474.6411 610838.7433 563494.9425 673571.763 701174.1258 933629.8702 0.840677097 0.751486879 0.453886103 0.831672878 0.654262211 0.603552822 0.721454813 0.751019379 1 19.83249119 1.109861836 1.916199587 1.194079924 0.686807577 0.42194511 0.111702405 1.170866356 3.082843266 1.20775374 0.029492182 12.87839781 -1.109861836 -0.507272347 TSQVGAASAPAKES(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 279.15 1.28E-35 23425620000 13441370 10640090 6646360 8402950 11781890 9499220 13014870 15344710 12724860 TRUE FALSE 11665058.9 10570194.55 9860561.927 10310968.23 11547453.44 9864661.14 11752689.91 12063363.18 11220541.55 1.03961639 0.942039607 0.878795545 0.918936772 1.029135126 0.879160876 1.047426264 1.075114167 1 23.41963897 2.209433577 24.5398263 1.048260112 0.946907285 0.375329178 0.056215954 161.9307839 136426.9057 0.022510744 0.015179731 161.9696251 -2.209433577 -0.101352827 TSQVGAASAPAKES(ph)PRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 161.53 1.54E-09 227430000 343240 252580 185890 205060 247110 181350 361450 390760 275790 TRUE FALSE 297879.9643 250920.7853 275787.0258 251622.0071 242192.9945 188326.6518 326396.6346 307199.0149 243186.4204 1.224903775 1.031804263 1.134056027 1.034687738 0.995914961 0.774412698 1.342166368 1.263224379 1 17.89170314 0.950677536 19.90520254 2.03E-05 1.104285285 0.037081294 0.159144075 28942195.15 221065909.1 1301388949 0.041372836 8.926424501 -0.950677536 1.104264948 TSRPENAIIYNNNEDFQVGQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TSRPENAIIYNNNEDFQVGQAK 22 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;;; 336.41 5.28E-81 5083100000 2343640 2368200 1345490 1544860 2390620 1613700 2101280 2333210 3017230 FALSE TRUE 2033922.036 2352643.138 1996173.464 1895644.075 2343051.339 1675780.083 1897498.189 1834271.199 2660536.507 0.764478154 0.884273955 0.750289823 0.71250444 0.880668742 0.629865472 0.713201335 0.689436583 1 21.34328577 4.200576283 24.80658348 0.755154646 0.824376193 0.034370254 0.108779894 381.0448877 248850.0805 0.026753156 0.055693301 15869.97646 -4.200576283 0.069221547 TSS(ph)DDES(ph)EEDEDDLLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSSDDESEEDEDDLLQR 17 0 Q9Y5J1 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 2 TS(0.02)S(0.98)DDES(1)EEDEDDLLQR 424.5 2.37E-160 67843000 100450 86423 61811 70318 99604 87013 99850 102340 158870 TRUE FALSE 87175.27799 85855.28162 91703.00635 86284.77664 97622.07527 90360.44641 90166.56237 80455.38741 140088.5696 0.622286874 0.612864289 0.654607343 0.615930171 0.696859676 0.645023692 0.643639682 0.574318002 1 17.09597972 1.232979776 24.98830939 1.000000587 0.632775332 0.929587604 0.031726271 45.12176448 202011.6645 0.068936525 0.008077879 17.09935684 -1.232979776 -0.367225256 TSS(ph)DPVLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 TSSDPVLLK 9 0 Q9BRG2;Q9BRG2-2 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 TS(0.001)S(0.999)DPVLLK;TS(0.002)S(0.998)DPVLLK;TSS(1)DPVLLK;TSS(1)DPVLLK;TS(0.001)S(0.999)DPVLLK;TSS(1)DPVLLK;TS(0.001)S(0.999)DPVLLK;TS(0.002)S(0.998)DPVLLK 223.87 3.47E-07 8489100000 21263290 19253860 13108230 15687480 19821250 15810930 23003000 26592000 22633990 TRUE FALSE 18453292.35 19127380.13 19447413.87 19249562.1 19426845.9 16419186.71 20772172.6 20905507.74 19958225.49 0.924595845 0.95837078 0.97440596 0.964492666 0.973375409 0.822677683 1.040782539 1.04746325 1 24.25048012 TSS(ph)DSALHTSVMNPSPQDTYPGPTPPSILPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSSDSALHTSVMNPSPQDTYPGPTPPSILPSR 32 0 Q53ET0;H0YDQ8 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 T(0.133)S(0.133)S(0.733)DS(0.001)ALHTSVMNPSPQDTYPGPTPPSILPSR;T(0.228)S(0.127)S(0.638)DS(0.007)ALHTSVMNPSPQDTYPGPTPPSILPSR 293.64 1.26E-89 1392090000 222264 246986 74710 119329 242674 268389 220937 257009 247352 TRUE FALSE 192891.2493 245363.5327 110840.0059 146424.4733 237845.2622 278714.0985 199510.5637 202049.6254 218110.3283 0.884374668 1.124951462 0.508183206 0.671332139 1.090481427 1.277858323 0.914723137 0.926364317 1 17.73469856 3.227980604 24.99858437 1.029706791 0.79997564 0.302839012 0.183932562 303.8570148 717955.4347 0.059317373 0.067950127 1690.365435 -3.227980604 -0.229731151 TSS(ph)EDNLYLAVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TSSEDNLYLAVLR 13 0 Q15149-4 Q15149-4 PLEC Plectin 1 TSS(1)EDNLYLAVLR;TSS(1)EDNLYLAVLR;TS(0.001)S(0.999)EDNLYLAVLR;TSS(1)EDNLYLAVLR;TS(0.001)S(0.999)EDNLYLAVLR 401.28 6.22E-111 2347120000 5170470 2902090 2216840 2423130 3116830 3095360 3212130 3424340 3479500 TRUE FALSE 4487179.289 2883025.98 3288911.239 2973338.702 3054811.181 3214440.502 2900618.127 2692071.539 3068157.474 1.462499669 0.939660368 1.071949946 0.969095859 0.995650063 1.04767781 0.94539415 0.877422871 1 21.5489411 4.741174232 24.97595133 0.976142972 1.462499844 0.882929836 0.05509355 82.29639378 786387.2679 0.014632804 0.097340984 55102.87159 -4.741174232 0.486356872 ALSSGGSITS(ph)PPLS(ph)PALPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.001)S(0.999)PPLS(1)PALPK;ALSSGGSIT(0.017)S(0.983)PPLS(1)PALPK 280.63 1.76E-39 410870000 377700 441440 350350 518240 610410 535850 723610 877590 790280 TRUE FALSE 327785.988 438540.1516 519780.4319 635914.3128 598264.0352 556464.4962 653434.4136 689924.2079 696853.9987 0.470379719 0.62931425 0.745895744 0.912550282 0.858521349 0.79853814 0.937691991 0.990055606 1 19.4104969 5.010145697 0.509120083 0.967589592 4.76E-13 0.897061683 0.05343211 2.008858976 0.343622253 0.042762155 1.23168159 102363.6343 -5.010145697 -0.967589592 down TSS(ph)FTEQLDEGTPNR ddPTM_MDA-MB-175_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 TSS(1)FTEQLDEGTPNR;TSS(0.995)FT(0.005)EQLDEGTPNR;TS(0.006)S(0.991)FT(0.004)EQLDEGTPNR;TS(0.001)S(0.999)FTEQLDEGTPNR;TS(0.001)S(0.999)FTEQLDEGTPNR;TS(0.002)S(0.988)FT(0.01)EQLDEGTPNR 415.37 2.13E-133 4610500000 2693680 2841210 2396600 3159230 4392110 4162370 4038500 4724710 5196970 TRUE FALSE 2337703.363 2822545.904 3555603.776 3876581.457 4304715.604 4322499.067 3646846.892 3714367.534 4582590.127 0.510127089 0.615928073 0.775893911 0.845936763 0.939362999 0.943243656 0.795804728 0.810538894 1 22.12773182 4.264150257 1.554798382 0.881515742 0.49240061 0.828429244 0.061826959 0.217121338 0.884267015 0.019207416 0.099411502 18371.73858 -4.264150257 -0.389115132 TSS(ph)FTEQLDEGTPNRENASTHASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSSFTEQLDEGTPNRENASTHASK 24 1 Q13439-5;E7EVX2;C9JHJ5 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 T(0.039)S(0.039)S(0.922)FTEQLDEGTPNRENASTHASK;T(0.11)S(0.11)S(0.779)FT(0.001)EQLDEGTPNRENASTHASK 241.04 8.70E-38 893550000 373490 483900 65037 153290 704760 559430 756080 801950 65072 TRUE FALSE 324132.3502 480721.229 96489.11074 188096.8374 690736.6548 580951.6341 682755.478 630459.2333 57379.26229 5.64894593 8.377961128 1.681602497 3.278132724 12.0380888 10.12476653 11.89899366 10.98757997 1 15.8082418 3.244658989 24.98663154 9.679524772 4.787106116 0.275861368 3.547933155 182.0069504 745725.7658 1.034272883 1.300799657 1756.543821 -3.244658989 -4.892418655 TSS(ph)GTSLSAMHSSGSSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TSSGTSLSAMHSSGSSGK 18 0 Q12888;Q12888-2;A6NNK5;Q12888-3;M0R142 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 T(0.109)S(0.109)S(0.751)GT(0.015)S(0.015)LS(0.002)AMHSSGSSGK;T(0.003)S(0.098)S(0.898)GTSLSAMHSSGSSGK;T(0.156)S(0.156)S(0.667)GT(0.017)S(0.004)LSAMHSSGSSGK;T(0.004)S(0.134)S(0.848)GT(0.005)S(0.008)LS(0.001)AMHSSGSSGK 252.41 1.13E-30 1240380000 1290269 1326866 351751 910414 2354370 1979756 2121831 2364375 2401820 TRUE FALSE 1119756.683 1318149.73 521858.9601 1117137.414 2307522.643 2055918.494 1916056.156 1858771.806 2117879.576 0.528715936 0.622391256 0.246406343 0.527479195 1.089543839 0.970743813 0.90470496 0.877656986 1 21.01418913 3.304820904 6.622757755 0.951918018 0.46922219 0.830028016 0.109517534 0.084815962 6.655394956 0.032156293 0.041400482 2017.534193 -3.304820904 -0.482695828 SNTEPQS(ph)PPIASPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SNTEPQSPPIASPK 14 0 A0A2R8Y7M0;P82094;P82094-2;F8WF45 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 SNTEPQS(1)PPIASPK 149.22 7.92E-06 150590000 67395 97898 63549 96444 124660 105470 143800 167880 144980 TRUE FALSE 58488.57999 97254.90159 94281.50896 118343.0843 122179.5099 109527.4991 129854.2981 131980.1684 127840.6296 0.457511671 0.760751116 0.737492527 0.925707928 0.955717367 0.856750311 1.015751397 1.032380464 1 16.96398689 5.031175718 0.554380323 1.007942176 3.39E-13 0.887804901 0.058435418 1.742897017 0.335192957 0.035226991 1.213729633 107442.4041 -5.031175718 -1.007942176 down TSS(ph)KESS(ph)PIPSPTSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSSKESSPIPSPTSDR 16 1 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 2 T(0.111)S(0.135)S(0.754)KES(0.004)S(0.993)PIPS(0.003)PT(0.001)S(0.001)DR 90.729 0.0030453 166370000 189980 121840 175870 118870 143070 103320 155220 168490 166050 TRUE FALSE 164873.6617 121039.625 260921.3202 145861.2503 140223.1869 107294.7873 140166.7883 132459.7247 146419.7582 1.126034244 0.826661829 1.782008955 0.99618557 0.957679405 0.732788994 0.957294221 0.904657448 1 17.15975072 3.494992668 24.95018541 0.910977175 1.234080943 0.287631948 0.240816188 932.5069181 1301865.899 0.064632969 0.093691259 3126.026594 -3.494992668 0.323103768 TSS(ph)KSEAGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TSSKSEAGAR 10 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 T(0.018)S(0.444)S(0.534)KS(0.004)EAGAR;T(0.056)S(0.185)S(0.621)KS(0.139)EAGAR;T(0.055)S(0.194)S(0.688)KS(0.063)EAGAR 95.98 0.004271 1080850000 1778710 1219560 894160 1048010 949610 1199820 1754700 1979940 1712350 TRUE FALSE 1543648.967 1211548.63 1326578.767 1285976.688 930714.6189 1245977.852 1584529.464 1556545.239 1509917.934 1.022339647 0.802393695 0.878576734 0.851686479 0.616400798 0.825195743 1.049414295 1.030880688 1 20.52603871 2.242249731 24.95773722 1.028566172 0.824492563 0.460038616 0.09880123 77.9486413 527346.2479 0.038317508 0.028509553 174.6826335 -2.242249731 -0.204073608 TSS(ph)LDTITGPYLTGQWPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSSLDTITGPYLTGQWPR 18 0 Q86VQ1;H7C2L5;H7C0Q2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 TS(0.005)S(0.995)LDTITGPYLTGQWPR;T(0.003)S(0.003)S(0.994)LDTITGPYLTGQWPR 357.46 1.13E-90 442550000 520720 416910 270980 359300 466790 433600 496140 511790 559430 TRUE FALSE 451905.5327 414171.2908 402026.8344 440884.5566 457501.7923 450280.8726 448024.4192 402347.6913 493294.8227 0.916096241 0.839601941 0.814982878 0.89375468 0.927440896 0.912802754 0.908228505 0.815633314 1 18.91209062 3.508755408 22.52319507 0.901260945 0.85503184 0.180759567 0.051120233 386.5377578 275208.5521 0.014158996 0.020963593 3226.676368 -3.508755408 -0.046229104 SAS(ph)FSQGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SASFSQGTR 9 0 Q9UQC2;Q9UQC2-2 Q9UQC2 GAB2 GRB2-associated-binding protein 2 1 S(0.001)AS(0.993)FS(0.006)QGTR;S(0.002)AS(0.994)FS(0.004)QGTR 125.24 0.00053192 474690000 199955 295280 195879 271890 372510 402520 350160 404720 420640 TRUE FALSE 173530.4401 293340.2862 290606.7396 333626.7801 365097.7798 418005.2049 316201.5371 318173.7775 370912.4184 0.46784748 0.790861324 0.783491534 0.899475897 0.984323419 1.126964707 0.852496496 0.857813763 1 18.50071905 5.0325883 0.933274222 0.946060806 3.07E-14 0.759306489 0.085336957 1.831510437 0.878253032 0.030607275 1.992062976 107792.4394 -5.0325883 -0.946060806 down TSS(ph)PHKEESPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSSPHKEESPK 11 1 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 T(0.065)S(0.152)S(0.783)PHKEESPK 191.63 1.06E-06 365920000 701920 489270 399510 442670 417100 362040 750230 779190 1017500 TRUE FALSE 609159.4936 486055.9532 592714.3723 543184.9893 408800.526 375967.9131 677472.8101 612566.2822 897212.3091 0.678946875 0.541740175 0.660617745 0.605414107 0.455634103 0.419040075 0.755086397 0.682743957 1 19.77508989 0.930359258 1.192548029 1.500498441 0.570936034 0.645293795 0.097278445 1.932975777 1.387624647 2.690285132 0.030537697 8.518424101 -0.930359258 -0.929562407 TSS(ph)PLFNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TSSPLFNK 8 0 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 T(0.021)S(0.406)S(0.572)PLFNK;TS(0.002)S(0.998)PLFNK;TS(0.004)S(0.996)PLFNK;TS(0.004)S(0.996)PLFNK 164.85 0.00034373 1898410000 8189000 7263800 4378140 5453200 7554500 6054600 8058800 9772700 8153600 TRUE FALSE 7106802.902 7216083.62 6495423.148 6691432.407 7404180.23 6287524.38 7277258.816 7682884.156 7189690.697 0.988471299 1.00367094 0.903435686 0.93069823 1.029832929 0.874519454 1.012179678 1.068597313 1 22.77749828 2.012464638 24.99012402 1.039555488 0.956092596 0.332636243 0.048567915 215.758739 432569.0041 0.019048656 0.012832903 102.9116728 -2.012464638 -0.083462892 TSS(ph)PPRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSSPPRK 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 TS(0.01)S(0.99)PPRK;T(0.061)S(0.06)S(0.878)PPRK 89.542 0.018851 757830000 3076000 2309900 1499730 1827960 1497680 1909680 2685100 3191300 3007900 TRUE FALSE 2669498.806 2294726.115 2225004.444 2243026.257 1467879.098 1983146.625 2424699.415 2508865.33 2652309.489 1.006480887 0.865180374 0.838893219 0.845687981 0.55343432 0.747705588 0.914184195 0.945917262 1 21.3388177 2.071550498 4.812251033 0.959014834 0.803833089 0.270329024 0.113390608 0.287763975 12.63703081 0.052618594 0.033980938 117.9099617 -2.071550498 -0.155181744 TSS(ph)TLDSEGTFNSYR ddPTM_MDA-MB-175_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 TSS(0.884)T(0.116)LDSEGTFNSYR 375.49 8.99E-98 164870000 251290 229180 215050 217780 354870 414600 327590 423120 499450 TRUE FALSE 218081.3898 227674.5015 319048.8993 267230.2776 347808.7813 430549.9303 295820.3722 332639.0807 440405.59 0.495183065 0.516965512 0.724443346 0.606782211 0.789746518 0.977621402 0.671699858 0.755301677 1 18.74847326 4.153418124 0.666345123 0.834060416 0.3887251 0.580525021 0.109540462 1.377091571 0.803071423 0.061529139 0.426074138 14236.98817 -4.153418124 -0.445335316 TSS(ph)VPEYVYNLHLVENDFVGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TSSVPEYVYNLHLVENDFVGGR 22 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 1 T(0.108)S(0.108)S(0.784)VPEYVYNLHLVENDFVGGR;TS(0.021)S(0.978)VPEYVYNLHLVENDFVGGR;T(0.002)S(0.081)S(0.917)VPEYVYNLHLVENDFVGGR;T(0.042)S(0.042)S(0.915)VPEYVYNLHLVENDFVGGR;T(0.02)S(0.085)S(0.895)VPEYVYNLHLVENDFVGGR 423.24 1.15E-174 2140870000 374784 307068 162625 211263 266793 253675 224402 263503 242313 TRUE FALSE 325255.3448 305050.8501 241270.9939 259233.4931 261484.3413 263434.0414 202639.5286 207154.934 213667.0332 1.522253293 1.427692637 1.129191482 1.213259197 1.22379357 1.232918516 0.948389303 0.969522209 1 17.70500481 8 0.177790011 0.805282621 3.820235713 0.785333923 0.086953233 56.44648548 0.789071735 0.892638404 44.3984095 100000000 -8 3.014953092 TSS(ph)VSSISQVSPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TSSVSSISQVSPER 14 0 P42356 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 1 T(0.005)S(0.008)S(0.986)VS(0.001)SISQVSPER;TS(0.081)S(0.91)VS(0.009)S(0.001)ISQVSPER;T(0.01)S(0.186)S(0.804)VSSISQVSPER 319.82 4.54E-56 631610000 669120 715220 556270 593790 938910 967490 831420 884440 1206130 TRUE FALSE 580694.0967 710521.6727 825284.0326 728619.095 920227.5279 1004709.966 750789.0164 695309.3887 1063542.685 0.545999803 0.668070668 0.775976408 0.685086838 0.865247386 0.944682315 0.705932189 0.653767261 1 20.02044651 4.883711022 0.966138446 0.798520625 0.350180137 0.393913711 0.10920977 3.070508391 1.912955458 0.037518503 1.532917302 76508.73514 -4.883711022 -0.448340488 TSS(ph)VVTLEVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSSVVTLEVAK 11 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 T(0.001)S(0.002)S(0.992)VVT(0.004)LEVAK;TSS(1)VVTLEVAK 219.92 9.99E-12 654260000 2543600 2213900 1538780 1654960 2187300 1730210 2598000 2732300 3045100 TRUE FALSE 2207456.815 2199356.745 2282939.155 2030743.962 2143777.009 1796772.298 2346046.36 2148018.908 2685111.747 0.82210985 0.81909319 0.850221283 0.756297746 0.798393963 0.669161088 0.873723919 0.799973748 1 21.3565507 0.619200331 1.634994936 1.869941171 0.793940117 0.553422104 0.056297599 5.065365759 2.779939961 14.60415887 0.015292476 4.161025055 -0.619200331 -1.076001055 TSSAQVEGGVHSLHSYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSSAQVEGGVHSLHSYEK 18 0 P12268;H0Y4R1 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 259.77 5.99E-31 1239090000 903050 892710 285310 671010 1091900 886610 1055160 1248460 1215560 FALSE TRUE 783709.6545 886845.7292 423286.8703 823373.0762 1070173.326 920718.4604 952830.7456 981486.5445 1071857.882 0.731169372 0.827391154 0.39490951 0.768173739 0.998428378 0.85899304 0.888952502 0.915687202 1 20.0316822 3.456324335 7.638526174 0.920457564 0.654385611 0.555716402 0.115662648 0.127178975 33.64024051 0.0325236 0.042745337 2859.725416 -3.456324335 -0.266071953 TSSAVST(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSSAVSTPSK 10 0 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 1 TSSAVS(0.052)T(0.947)PSK 172.74 4.05E-05 80801000 378950 347630 258740 289390 310550 307830 396130 453690 540970 TRUE FALSE 328870.7974 345346.3956 383867.5294 355100.4225 304370.6626 319672.4193 357713.3736 356671.9241 477017.1429 0.689431821 0.723970618 0.80472481 0.744418577 0.638070701 0.670148702 0.749896265 0.747713011 1 18.86368159 1.148063705 2.536754986 1.120823434 0.717416173 0.78523483 0.046018287 0.370859788 2.112380125 0.363244415 0.013024635 14.06253787 -1.148063705 -0.403407261 TSSESIYSRPGSSIPGS(ph)PGHTIYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSSESIYSRPGSSIPGSPGHTIYAK 25 1 O14639-3;F8W8M4;O14639-5;O14639-2;O14639;A0A0A0MRL6;A0A3B3IS55;O14639-6;A0A494C1P1;A0A494C1G0;H0Y7N6;F6XFR5 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 TSSESIYSRPGSSIPGS(1)PGHTIYAK;TSSESIYSRPGSSIPGS(1)PGHTIYAK 213.78 1.16E-26 922630000 670540 908140 441680 682540 1201060 922430 1137560 1420520 882010 TRUE FALSE 581926.4401 902174.3685 655277.9253 837521.139 1177161.256 957916.479 1027239.606 1116752.852 777739.7826 0.748227689 1.159995141 0.842541349 1.076865499 1.513566982 1.23166707 1.320801159 1.435895241 1 19.56892801 3.441464679 7.061945502 1.314821637 0.94377214 0.521038477 0.168516518 0.141077044 20.9803028 0.04529335 0.059119923 2763.533152 -3.441464679 -0.371049497 TSSFT(ph)EQLDEGTPNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSSFTEQLDEGTPNR 15 0 Q13439-5;Q13439-3;Q13439-4;Q13439;E7EVX2;Q86W71;C9JHJ5;C9J0Y3 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 TSS(0.324)FT(0.676)EQLDEGTPNR;TSS(0.324)FT(0.676)EQLDEGTPNR 379.24 4.52E-97 3472300000 1670100 1797810 1550580 1942770 2765200 2648600 2596300 2967200 3346400 TRUE FALSE 1449392.054 1786000.068 2300445.674 2383905.622 2710177.93 2750493.356 2344511.226 2332687.371 2950792.404 0.491187402 0.605261172 0.779602683 0.807886593 0.918457675 0.932120251 0.794536146 0.790529136 1 21.492671 4.336671356 1.384798986 0.868178292 0.449630672 0.815386094 0.064792212 0.286814537 0.822375164 0.020170707 0.138250338 21710.5765 -4.336671356 -0.41854762 TSSISGPLS(ph)PAYTGQVPYNYNQLEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSSISGPLSPAYTGQVPYNYNQLEGR 26 0 Q01082-3 Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 TSSIS(0.001)GPLS(0.999)PAYTGQVPYNYNQLEGR 183.59 1.10E-17 179830000 30814 47698 28259 40126 78010 83186 56874 89853 60564 TRUE FALSE 26741.85183 47384.6687 41925.14692 49237.22159 76457.75362 86386.21925 51358.36823 70638.63519 53404.19291 0.500744424 0.887283678 0.785053469 0.921972956 1.431680725 1.61759245 0.961691684 1.322717025 1 15.7046654 3.418923555 4.395159173 1.267053641 0.753843191 0.583238014 0.211632894 0.153054137 6.072639125 0.061865169 0.082363074 2623.756666 -3.418923555 -0.51321045 TSSKDDKGS(ph)TSSTSGSSGSSTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSSKDDKGSTSSTSGSSGSSTK 22 2 Q9NWH9;H7BXE3 Q9NWH9 SLTM SAFB-like transcription modulator 1 T(0.001)S(0.001)S(0.001)KDDKGS(0.513)T(0.115)S(0.115)S(0.115)T(0.115)S(0.023)GS(0.001)SGSSTK;TSSKDDKGS(0.641)T(0.103)S(0.103)S(0.103)T(0.022)S(0.028)GSSGSSTK 103.73 0.00029964 109370000 330620 193664 160665 134766 145047 108933 343470 370550 111612 TRUE FALSE 286927.7293 192391.8084 238363.1314 165366.6801 142160.8485 113123.723 310160.3323 291310.7661 98417.35651 2.915417966 1.954856493 2.421962343 1.680259315 1.444469284 1.149428587 3.151480016 2.959953167 1 16.58662515 2.230219814 24.99974547 2.525826615 1.918214944 0.059658929 0.747563826 401.1559953 1202365.638 0.306046053 0.210195377 169.910342 -2.230219814 -0.60761167 TSSPRS(ph)PPSSSEIFTPAHEENVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSSPRSPPSSSEIFTPAHEENVR 23 1 I3L3A7;I3L2L5;I3L317;I3L4Q0;C9JLW8 I3L3A7 FAM195B Protein FAM195B 1 T(0.113)S(0.113)S(0.113)PRS(0.642)PPS(0.006)S(0.006)S(0.006)EIFTPAHEENVR 114.98 0.00037251 459210000 80210 84981 43821 36265 84591 95316 84897 98460 35503 TRUE FALSE 69610.04527 84422.75422 65012.98217 44499.52253 82907.8046 98982.8682 76663.70201 77405.09522 31305.87579 2.223545693 2.696706356 2.076702234 1.421443145 2.648314494 3.161798407 2.448859841 2.47254208 1 14.93414584 TSSVSNPQDSVGS(ph)PCSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TSSVSNPQDSVGSPCSR 17 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 TSSVSNPQDSVGS(1)PCSR;TSSVSNPQDSVGS(1)PCSR;TSSVSNPQDSVGS(1)PCSR;TSSVSNPQDSVGS(1)PCSR;TSSVSNPQDSVGS(0.999)PCS(0.001)R;TSSVSNPQDSVGS(1)PCSR 428.65 1.21E-160 4288230000 1625060 2153840 1439050 1891820 3166130 3237560 3195960 3445830 3184390 TRUE FALSE 1410304.204 2139691.283 2134979.393 2321386.646 3103130.207 3362111.028 2886016.291 2708966.07 2807935.042 0.502256706 0.762015948 0.760337886 0.826723771 1.105128915 1.197360686 1.027807356 0.964753824 1 21.42107813 3.894958918 1.125435386 1.049127526 0.570996978 0.791979489 0.091585732 0.298981376 0.679725501 0.03493601 0.121125958 7851.613597 -3.894958918 -0.478130548 TSTDRHS(ph)LSLDDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSTDRHSLSLDDIR 14 1 Q96NE9-3;Q96NE9-2;Q96NE9 Q96NE9-3 FRMD6 FERM domain-containing protein 6 1 T(0.002)S(0.002)T(0.002)DRHS(0.99)LS(0.006)LDDIR;T(0.05)S(0.05)T(0.05)DRHS(0.846)LS(0.004)LDDIR 109.03 0.00047937 526130000 648890 839820 361750 609960 1109070 1087620 891320 1129770 939110 TRUE FALSE 563137.5424 834303.1671 536693.51 748460.7407 1087001.677 1129461.445 804879.9236 888177.4774 828089.4856 0.680044309 1.007503635 0.648110523 0.903840411 1.312662092 1.363936464 0.971972157 1.072562196 1 19.65942715 3.430493534 7.339396584 1.132291615 0.797091218 0.547852732 0.153921579 0.175142149 22.59294391 0.045580095 0.059184311 2694.595212 -3.430493534 -0.335200397 TLT(ph)EPSVDFNHSDDFTPISTVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TLTEPSVDFNHSDDFTPISTVQK 23 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 T(0.129)LT(0.839)EPS(0.031)VDFNHS(0.001)DDFTPISTVQK;T(0.006)LT(0.837)EPS(0.118)VDFNHS(0.039)DDFTPISTVQK;T(0.001)LT(0.417)EPS(0.417)VDFNHS(0.165)DDFTPISTVQK 286.31 7.32E-52 521570000 252654 276607 220643 293928 379403 397514 444900 497680 567420 TRUE FALSE 219265.1338 274789.9504 327346.6928 360668.8448 371853.6226 412806.6208 401753.6665 391255.005 500340.254 0.438232047 0.549206162 0.654248164 0.720847147 0.743201491 0.825051787 0.802960912 0.781977868 1 18.93255 5.040080909 0.359905373 0.897389788 4.59E-16 0.881016328 0.05312076 3.559840912 0.363320029 0.090890818 1.46391896 109668.2488 -5.040080909 -0.897389788 down TSTTGVATTQS(ph)PTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 TSTTGVATTQSPTPR 15 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 TSTTGVATTQS(1)PTPR;TSTTGVATTQS(0.999)PT(0.001)PR;TSTTGVATTQS(0.922)PT(0.078)PR;TSTTGVATTQS(0.992)PT(0.007)PR;TSTTGVATTQS(0.964)PT(0.036)PR;TSTTGVATTQS(1)PTPR;TSTTGVAT(0.005)T(0.033)QS(0.96)PT(0.002)PR 310.51 4.01E-56 5506276000 6567018 7198174 3838418 5042006 7004704 6890695 7475881 8275840 7807930 TRUE FALSE 5699169.933 7150888.721 5694689.784 6186870.525 6865324.095 7155784.496 6750871.211 6506116.019 6884885.41 0.827779926 1.038635837 0.827129203 0.898616339 0.997158803 1.039346927 0.980535014 0.944985375 1 22.71500121 3.240537693 24.97796641 0.987934568 0.903017769 0.361465617 0.062007814 62.68546949 791947.7764 0.017586898 0.021569884 1739.953705 -3.240537693 -0.084916799 TSTTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSTTVR 6 0 P29373;Q5SYZ4;P29762;B5MCB5 P29373;P29762 CRABP2;CRABP1 Cellular retinoic acid-binding protein 2;Cellular retinoic acid-binding protein 1 0 99.511 0.090068 27064000 52413 53513 27637 35259 31429 55804 53304 53132 64558 FALSE TRUE 45486.48925 53161.46958 41002.34564 43265.09485 30803.62439 57950.81599 48134.58628 41770.13527 56926.02678 0.799045565 0.933869314 0.720274151 0.760023091 0.541116711 1.018002121 0.845563778 0.733761649 1 15.79680079 2.712407649 24.9999922 0.868420741 0.759841748 0.242813462 0.124531143 1514.6686 1447891.667 0.043954066 0.038776454 515.7124891 -2.712407649 -0.108578993 TSTVDLPIENQLLWQIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSTVDLPIENQLLWQIDR 18 0 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 187.16 1.03E-13 89925000 72350 69165 43742 58475 70513 85417 70171 82558 82693 FALSE TRUE 62788.76419 68710.65056 64895.77751 71752.64248 69109.92926 88703.04726 63365.82722 64903.61417 72917.12774 0.861097607 0.942311535 0.889993607 0.984030017 0.947787322 1.216491242 0.869011564 0.89010108 1 16.15397011 3.736719261 24.87524359 0.975638014 0.902251975 0.151082917 0.095209918 364.6789209 4926534.648 0.027039901 0.042550377 5454.051838 -3.736719261 -0.073386038 TSVDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSVDFK 6 0 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 118.01 0.05172 133190000 391770 413920 260950 283650 422760 328750 456680 544310 452380 FALSE TRUE 339996.6019 411200.9323 387146.2928 348057.0678 414347.9031 341397.2252 412391.2439 427913.5423 398900.1518 0.852335103 1.030836741 0.970534333 0.872541829 1.03872586 0.855846316 1.033820725 1.072733466 1 18.60566815 2.063952528 14.08311714 1.045076015 0.944336111 0.31498092 0.067761008 1.425391265 312.2588356 0.025533543 0.017214194 115.8650699 -2.063952528 -0.100739904 TSVDTGQVSRPENPSQPAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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;TSVDTGQVSRPENPSQPAS(1)PR 277.38 4.66E-45 2100400000 1907530 2049990 1327740 1555720 2129370 2075560 2113190 2373470 2121630 TRUE FALSE 1655445.077 2036523.481 1969839.505 1908970.004 2086999.703 2155408.136 1908253.159 1865921.911 1870813.318 0.884879887 1.088576536 1.052932158 1.020395774 1.115557433 1.152123579 1.020012601 0.997385411 1 20.83523417 6.153434007 14.49745796 1.04024173 0.658407652 0 0.073849507 0 0 0.016502326 0 1423750.886 -6.153434007 -0.381834078 TSVLGGGEDGIEPVS(ph)PPEGMTEPGHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TSVLGGGEDGIEPVSPPEGMTEPGHSR 27 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 TSVLGGGEDGIEPVS(1)PPEGMTEPGHSR;TSVLGGGEDGIEPVS(1)PPEGMTEPGHSR;TSVLGGGEDGIEPVS(1)PPEGMTEPGHSR;TSVLGGGEDGIEPVS(1)PPEGMTEPGHSR;TSVLGGGEDGIEPVS(0.999)PPEGMT(0.001)EPGHSR 196.45 4.06E-25 1525020000 934220 762161 517170 661413 863320 899910 797874 912700 1071200 TRUE FALSE 810760.46 757154.3142 767275.1418 811596.9307 846141.6211 934530.12 720496.3023 717526.2076 944563.9563 0.858343635 0.801591368 0.812306183 0.859229198 0.895801301 0.989377282 0.762781914 0.759637506 1 19.84928896 5.127386876 18.30237067 0.85006148 2.635515048 0 0.084087034 7500.567438 1022293.317 0.020366024 28855.04002 134087.0622 -5.127386876 1.785453568 TSVLPEHKDPPPEVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TSVLPEHKDPPPEVGR 16 1 O15327;D6RJC3;E7EQN9;E9PG59 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 ;;; 88.992 0.00357 779139000 2813650 2447640 1448640 1781950 2530100 2263740 3005780 3287340 2355650 FALSE TRUE 2441819.024 2431561.292 2149207.149 2186568.983 2479755.96 2350827.543 2714279.918 2584367.923 2077167.741 1.17555216 1.170613834 1.034681556 1.052668468 1.193815941 1.131746607 1.306721583 1.244178731 1 20.98618629 3.212401579 24.43779776 1.191583271 1.10756025 0.10530954 0.090207012 319.335376 298321.9768 0.028132612 0.031910138 1630.803291 -3.212401579 -0.084023021 TSVPENHAQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TSVPENHAQSR 11 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ;;; 172.51 1.33E-05 515497000 712900 569596 238924 384270 638941 655760 554404 637172 598666 FALSE TRUE 618688.4587 565854.2864 354468.4456 471524.3767 626227.3242 680987.5115 500637.9854 500917.7263 527892.3875 1.171997311 1.071912192 0.671478608 0.893220641 1.186278376 1.290011994 0.948371292 0.948901212 1 19.00988434 TSVPS(ph)PEQPQPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TSVPSPEQPQPYR 13 0 Q8TEH3 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 TSVPS(1)PEQPQPYR;TSVPS(1)PEQPQPYR 248.67 2.09E-17 519910000 586110 445480 230760 311100 486390 478830 392120 500920 515790 TRUE FALSE 508654.0785 442553.6125 342356.3078 381740.0099 476711.7906 497250.8999 354092.2628 393802.1562 454813.8938 1.118378496 0.973043301 0.752739335 0.83933234 1.048146939 1.09330631 0.778543197 0.8658534 1 18.7949168 4.642359323 3.910210129 0.906698887 1.121159203 0.253551517 0.110966641 0.322229278 7.973771381 0.028799649 0.155126338 43889.36763 -4.642359323 0.214460315 TSVS(ph)PAPDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TSVSPAPDK 9 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 TSVS(1)PAPDK;TSVS(1)PAPDK;TSVS(1)PAPDK;TSVS(1)PAPDK 197.73 2.89E-05 1488510000 3071780 2580890 1869110 2355310 2438670 2058600 3017610 3688190 4589390 TRUE FALSE 2665836.49 2563935.964 2773017.848 2890119.134 2390145.238 2137795.674 2724962.647 2899499.27 4046837.542 0.658745616 0.63356533 0.68523083 0.714167323 0.590620506 0.52826328 0.673356076 0.716485216 1 21.9483635 1.146314025 2.002088948 1.184651592 0.638598584 0.825627993 0.051683865 0.435621979 1.382473985 0.484019777 0.015033063 14.00599687 -1.146314025 -0.546053008 TSVS(ph)PAPDKTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TSVSPAPDKTK 11 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 T(0.01)S(0.077)VS(0.914)PAPDKTK;T(0.084)S(0.084)VS(0.832)PAPDKTK;TSVS(1)PAPDKTK;TSVS(0.999)PAPDKTK 169.4 1.03E-05 1205790000 1560360 1161401 799075 817314 1089390 797435 1613170 1854880 601027 TRUE FALSE 1354154.473 1153771.68 1185510.343 1002897.636 1067713.27 828112.8405 1456725.022 1458228.347 529974.2728 2.55513247 2.177033376 2.236920552 1.892351548 2.014651135 1.562552907 2.748671203 2.751507803 1 19.0155628 4.941950295 1.692509864 2.108985142 2.911228818 0.078025438 0.518677976 5.808372754 10.74100574 0.143004879 8.868995693 87488.36392 -4.941950295 0.802243675 TSYAQHQQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TSYAQHQQVR 10 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;H0Y9Y4;D6RB09;D6RAS7;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ;;;; 271.62 9.63E-24 3781048000 2838903 3836653 1597679 2428990 4381047 4265584 3548611 3956535 5406848 FALSE TRUE 2463734.776 3811449.774 2370321.908 2980529.304 4293872.736 4429683.777 3204467.251 3110460.78 4767656.589 0.516760117 0.799438823 0.497167081 0.625156038 0.900625424 0.929111335 0.672126272 0.65240873 1 22.18484889 3.302339465 9.555222621 0.801446952 0.614546106 0.391623662 0.134210495 0.457440698 64.63028918 0.039848173 0.051409089 2006.03943 -3.302339465 -0.186900846 TSYGWIEIVGCADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TSYGWIEIVGCADR 14 0 P41250 P41250 GARS Glycine--tRNA ligase 0 121.02 0.00027218 68582000 43852 37953 21065 24500 35388 35107 34495 39764 40869 FALSE TRUE 38056.84709 37703.68424 31252.10446 30063.09946 34683.84804 36457.58901 31149.68021 31260.77804 36037.51338 1.056034213 1.046234346 0.867210346 0.83421681 0.962437327 1.011656621 0.86436819 0.867451028 1 15.13721185 4.251115299 24.74659965 0.910553989 1.051134414 0.466232163 0.060239581 176.6619498 348211.7802 0.015603476 0.040655075 17828.52028 -4.251115299 0.140580426 TT(ph)DEELSELEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTDEELSELEDR 12 0 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;H7C2D8;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 1 T(0.189)T(0.811)DEELSELEDR 122.34 0.0040262 244360000 134660 85410 154250 95222 63009 66590 73934 84067 99642 TRUE FALSE 116864.3398 84848.93609 228845.8159 116843.6105 61755.24418 69151.76039 66763.89206 66089.92626 87862.43627 1.33008308 0.965702064 2.604592197 1.32984715 0.702862871 0.787045788 0.759868436 0.752197743 1 16.42295888 3.37889332 4.903562721 0.794735119 1.625566674 0.462550524 0.414540382 0.18291481 7.304381915 0.119934096 0.156400832 2392.727938 -3.37889332 0.830831554 TT(ph)PDQELAPASEPVWERPWSVEEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTPDQELAPASEPVWERPWSVEEIR 25 1 Q641Q2;Q641Q2-2;E7ESD2;A0A087WYF6;Q5T1D7 Q641Q2 FAM21A WASH complex subunit FAM21A 1 T(0.192)T(0.808)PDQELAPASEPVWERPWSVEEIR 124.82 0.00023957 109240000 4302.4 4804.3 907.26 2499.5 5354.3 3984.2 4833 5606.4 5191.2 TRUE FALSE 3733.826939 4772.740237 1346.013971 3067.049677 5247.759906 4137.474752 4364.296404 4407.514989 4577.50225 0.815690902 1.042651642 0.294049876 0.670026908 1.14642432 0.903871703 0.953423104 0.962864625 1 12.16034488 3.256554704 24.99526711 0.982045965 0.700282726 0.356204079 0.191809266 287.2007587 398943.0994 0.05597839 0.07211725 1805.322123 -3.256554704 -0.281763239 TT(ph)PDQELVPASEPVWERPWSVEEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTPDQELVPASEPVWERPWSVEEIR 25 1 A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;A0A0A0MT65 A0A0A0MR88 FAM21C WASH complex subunit FAM21C 1 T(0.18)T(0.82)PDQELVPASEPVWERPWSVEEIR 155.8 8.07E-08 140690000 12294 9232.6 10072 11748 11154 14366 9066.5 15034 20367 TRUE FALSE 10669.31675 9171.950443 14942.85289 14415.56296 10932.05722 14918.66932 8187.232225 11819.09609 17959.23646 0.594085209 0.510709376 0.832042772 0.802682396 0.608715033 0.830696191 0.455878636 0.658106825 1 14.13243839 -1.99999989 0.030490323 1.660376144 1.18E-08 0.097392479 0.158907672 11025.84474 33.28247826 1284.124817 637.1599843 0.010000003 1.99999989 -1.660376132 TT(ph)PDQELVPASEPVWERPWSVEEIRR ddPTM_MDA-MB-175_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(0.45)T(0.55)PDQELVPASEPVWERPWSVEEIRR 154.26 3.23E-06 405030000 179470 167690 92730 107790 197990 177270 179060 194430 92700 TRUE FALSE 155752.5848 166588.4333 137574.5382 132265.367 194050.3864 184089.6916 161694.7888 152852.6576 81741.1116 1.905437567 2.038000586 1.683051961 1.618100909 2.373963145 2.252106535 1.978132981 1.869960593 1 16.31877424 1.221574679 3.402693344 0.826131434 1.978474795 0.646227728 0.2256263 0.236637576 3.786402341 0.736000286 0.061914372 16.65615213 -1.221574679 1.15234336 TT(ph)PPEAAQNGQS(ph)PMAALILVADNAGGSHASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTPPEAAQNGQSPMAALILVADNAGGSHASK 31 0 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 2 T(0.459)T(0.541)PPEAAQNGQS(1)PMAALILVADNAGGSHASK 173.94 6.25E-13 65713000 73899 68209 25973 67210 92367 70122 94472 112350 175420 TRUE FALSE 64133.05991 67760.93059 38533.62967 82471.05774 90529.07741 72819.63871 85310.11998 88324.82681 154682.0474 0.414612174 0.438065902 0.249115074 0.533165025 0.58525911 0.470769814 0.551519206 0.571008907 1 17.23894624 -0.322944147 0.925131173 10 0.443155774 0.781915605 0.089432066 16.20353918 0.973401601 286.2561909 0.031971674 0.475396361 0.322944147 -9.556844226 TT(ph)PPPGRPPAPS(ph)SEEEDGEAVAH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TTPPPGRPPAPSSEEEDGEAVAH 23 1 Q96KN1 Q96KN1 FAM84B Protein FAM84B 2 T(0.47)T(0.53)PPPGRPPAPS(0.53)S(0.47)EEEDGEAVAH;T(0.466)T(0.534)PPPGRPPAPS(0.534)S(0.466)EEEDGEAVAH 94.606 0.00038995 255200000 106378 107483 59667 81762 121877 105979 104896 111990 119633 TRUE FALSE 92319.87777 106776.9371 88522.16077 100327.3118 119451.8861 110056.0807 94723.20207 88041.81001 105490.123 0.875151864 1.012198432 0.839151176 0.951058818 1.132351378 1.043283272 0.897934322 0.834597662 1 16.6867484 2.130009761 10.36515906 0.89381721 0.976970342 0.091363427 0.09104275 0.652657433 58.20600023 0.038711463 0.02609306 134.8993201 -2.130009761 0.083153132 TT(ph)PPPGRPPAPSS(ph)EEEDGEAVAH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTPPPGRPPAPSSEEEDGEAVAH 23 1 Q96KN1 Q96KN1 FAM84B Protein FAM84B 2 T(0.458)T(0.542)PPPGRPPAPS(0.2)S(0.8)EEEDGEAVAH 97.128 0.0077819 254280000 36370 43942 22295 31769 54422 30928 46748 46620 57854 TRUE FALSE 31563.61235 43653.34211 33076.93657 38982.63701 53339.10867 32117.82017 42214.38616 36650.6758 51014.56603 0.618717649 0.855703488 0.6483822 0.764147185 1.045566253 0.629581366 0.827496722 0.718435511 1 15.63862161 5.734283514 0.845938282 0.810363199 2.47E-24 0.148310697 0.136209387 24.96295762 3.927685293 0.044762803 27.95348967 542354.8325 -5.734283514 -0.810363199 TT(ph)PPPGRPPAPSSEEEDGEAVAH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTPPPGRPPAPSSEEEDGEAVAH 23 1 Q96KN1 Q96KN1 FAM84B Protein FAM84B 1 T(0.46)T(0.54)PPPGRPPAPSSEEEDGEAVAH 77.241 0.02427 698630000 65603 59507 41740 49471 72232 62447 59479 69256 71323 TRUE FALSE 56933.39733 59116.0946 61925.60361 60704.14667 70794.72452 64849.3765 53710.73573 54446.14335 62891.27619 0.905267007 0.939972889 0.984645365 0.965223642 1.125668436 1.031134689 0.854025216 0.865718533 1 15.94057229 2.240282429 24.99996695 0.895878346 0.994147567 0.244488095 0.069864914 59.16665076 859096.5941 0.028619631 0.020992737 173.8931319 -2.240282429 0.098269221 TT(ph)PTMSEEPPLDLTGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TTPTMSEEPPLDLTGK 16 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 T(0.029)T(0.969)PT(0.002)MSEEPPLDLTGK;T(0.154)T(0.845)PT(0.001)MSEEPPLDLTGK 140.22 1.92E-05 137151000 241792 174789 121959 134576 184680 145656 197802 233770 200890 TRUE FALSE 209838.5746 173640.7996 180938.7803 165133.5377 181005.2293 151259.4806 178619.1925 183780.1047 177141.0131 1.18458493 0.980240525 1.021439232 0.932215159 1.021814351 0.853893054 1.008344648 1.037479133 1 17.43453875 4.739300957 24.56902918 0.984432962 1.184585007 0.582033163 0.053933883 36.41396425 1208153.153 0.013152158 0.076134234 54865.70412 -4.739300957 0.200152045 TT(ph)SPLEEEER ddPTM_MDA-MB-175_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(0.256)T(0.372)S(0.372)PLEEEER 179.72 2.32E-05 435760000 585730 539430 378620 422870 485430 518340 457970 592400 677580 TRUE FALSE 508324.2964 535886.4488 561721.8984 518889.0967 475770.8927 538280.8752 413556.1399 465719.8701 597477.2643 0.850784334 0.896915215 0.940156106 0.868466681 0.796299577 0.900922775 0.692170505 0.779477141 1 19.18852429 3.426467828 5.491243099 0.820154717 0.897458377 0.094295304 0.082664067 0.362590078 24.16473936 0.024097168 0.031644898 2669.732991 -3.426467828 0.07730366 TTAAHGLELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TTAAHGLELR 10 0 P08243-2;P08243;P08243-3 P08243-2 ASNS Asparagine synthetase [glutamine-hydrolyzing] 0 ;;; 129.16 0.00031058 591030000 1070300 882508 412308 558610 992000 921660 752599 899073 823348 FALSE TRUE 928857.1432 876710.7468 611701.5279 685450.9383 972261.1408 957116.8566 679612.0648 706813.2355 726012.7374 1.279395106 1.207569374 0.842549306 0.944130734 1.339179178 1.318319648 0.936088349 0.973554869 1 19.46963533 2.197580808 24.99918119 0.96923822 1.142130289 0.231958639 0.157766149 258.2714169 157553.2447 0.070229097 0.047348996 157.6089254 -2.197580808 0.172892069 TTAGS(ph)VDWTDQLGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TTAGSVDWTDQLGLR 15 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 TTAGS(1)VDWTDQLGLR;TTAGS(1)VDWTDQLGLR;TTAGS(1)VDWTDQLGLR;TTAGS(1)VDWTDQLGLR;TT(0.001)AGS(0.999)VDWTDQLGLR 330.99 7.55E-69 1069225000 1803220 1423650 910774 1068976 1370240 1281350 1418810 1454730 1382070 TRUE FALSE 1564919.908 1414297.949 1351227.353 1311703.339 1342974.905 1330644.364 1281214.025 1143647.31 1218683.259 1.284107168 1.160513151 1.108760084 1.076328348 1.101988474 1.091870553 1.051310105 0.93842867 1 20.21689178 8 0.179558704 0.902091843 2.407182279 0.828880795 0.037989561 50.32879309 0.707340957 0.387993187 20.00787515 100000000 -8 1.505090436 TTCGQGLEGPWERPPPLDESER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TTCGQGLEGPWERPPPLDESER 22 1 Q9UD71;Q9UD71-2;J3KT77 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 0 ; 167.61 9.45E-12 1190220000 497990 515380 341470 482620 612560 604330 580720 644120 919310 FALSE TRUE 432179.3598 511994.4348 506606.0341 592206.2474 600371.2545 627578.9662 524401.8638 506379.9505 810630.2191 0.533139957 0.631600479 0.624953305 0.73055042 0.740622839 0.774186493 0.646906384 0.624674406 1 19.62868443 5.902743491 0.45564025 0.7504147 3.83E-14 0.36250217 0.101249828 20.16157646 1.499103419 0.083008201 10.13677597 799361.986 -5.902743491 -0.7504147 TTDEELS(ph)ELEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TTDEELSELEDR 12 0 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;H7C2D8;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 1 TTDEELS(1)ELEDR;TTDEELS(1)ELEDR;TTDEELS(1)ELEDR;TTDEELS(1)ELEDR 245.72 1.82E-16 1422520000 1132520 1023331 697305 728888 1103460 1151670 997934 1126078 1122340 TRUE FALSE 982854.6126 1016608.671 1034524.03 894393.1608 1081503.305 1195975.49 901154.5143 885274.9828 989658.2438 0.993125272 1.027232055 1.045334626 0.903739413 1.092804826 1.208473226 0.910571422 0.894525952 1 19.91657088 TTDEELSELEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TTDEELSELEDR 12 0 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;H7C2D8;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 0 ; 215.87 9.40E-11 325630000 354430 292450 207747 228360 275360 270090 293540 314500 320250 FALSE TRUE 307591.1775 290528.8767 308214.1441 280212.6283 269880.8747 280480.5371 265072.536 247246.6224 282390.4098 1.089240876 1.028819912 1.091446924 0.992288047 0.955701275 0.993236765 0.938674002 0.875548935 1 18.10733157 3.372408138 0.915509893 0.929751174 1.077925259 0.626488905 0.039887831 0.369348072 0.68828917 0.020026517 0.03579207 2357.263536 -3.372408138 0.148174085 TTDGVYEGVAIGGDRYPGSTFMDHVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TTDGVYEGVAIGGDRYPGSTFMDHVLR 27 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 273.53 4.88E-61 1534520000 584660 576070 295060 373260 620000 581250 599970 631260 387710 FALSE TRUE 507395.6997 572285.7582 437752.0029 458014.3879 607663.213 603611.0636 541785.0017 496269.9615 341875.3655 1.484154025 1.673960209 1.280443247 1.339711585 1.77744077 1.765588061 1.584744198 1.451610767 1 18.38311094 1.230902402 2.80142204 0.874663723 1.558429495 0.536515457 0.161933809 0.388113485 3.540462524 0.624008105 0.045161638 17.01776027 -1.230902402 0.683765772 TTDGYLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TTDGYLLR 8 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;H0Y9Y4;D6RB09;D6RAS7;D6R9B6;D6RED7 P61247 RPS3A 40S ribosomal protein S3a 0 ;;; 143.11 0.0014116 1893590000 1275660 1323050 916370 987790 1400320 1553830 1107720 1261110 1532180 FALSE TRUE 1107078.299 1314358.797 1359529.597 1212082.817 1372456.372 1613606.846 1000293.485 991431.4405 1351047.426 0.819422233 0.972844308 1.006278219 0.897143056 1.015846184 1.194337678 0.740383695 0.733824307 1 20.36564689 2.196792873 24.99999366 0.802281283 0.982261036 0.278206427 0.119323159 167.1981822 100074.9533 0.048577756 0.032751435 157.3232367 -2.196792873 0.179979753 TTEINFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TTEINFK 7 0 P29373;Q5SYZ4;P29762;B5MCB5 P29373;P29762 CRABP2;CRABP1 Cellular retinoic acid-binding protein 2;Cellular retinoic acid-binding protein 1 0 ; 108.09 0.017056 462620000 627910 601510 400180 461740 614580 579430 695240 807280 814170 FALSE TRUE 544930.1026 597558.6412 593708.3865 566585.1243 602351.0604 601721.047 627815.7318 634649.4543 717919.7501 0.759040412 0.832347405 0.826984334 0.78920398 0.83902283 0.838145276 0.874492911 0.884011694 1 19.45346306 -2 0.523052101 7.767492369 0.804691055 0.865086594 0.023653709 41.20129057 0.432091533 317.617652 0.013790633 0.01 2 -6.962801313 TTEYHDRDEQFYWIIEALGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TTEYHDRDEQFYWIIEALGIR 21 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;; 167.22 7.44E-12 3311361000 3433960 3274225 1734546 2211612 3136920 3222296 3343970 3813440 2287904 FALSE TRUE 2980153.485 3252716.4 2573378.247 2713792.307 3074501.429 3346259.812 3019672.304 2997965.532 2017430.596 1.477202483 1.612306469 1.275572133 1.345172574 1.523968872 1.658674068 1.496791171 1.486031559 1 20.94408761 1.238480171 24.99999778 0.99999948 1.484908976 0.651699625 0.111305445 1.279748178 395219.8706 0.159045785 0.028435444 17.3172996 -1.238480171 0.484909496 TTFDEAMADLHTLSEDSYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 TTFDEAMADLHTLSEDSYK 19 0 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ;;;;;;; 306.26 1.36E-50 2228057000 3730281 3118558 2249412 2857496 3104210 2652822 3901789 4672039 4696397 FALSE TRUE 3237314.915 3098071.987 3337235.167 3506334.141 3042442.294 2754877.779 3523394.103 3672959.818 4141194.297 0.781734611 0.748110754 0.805862978 0.846696361 0.734677505 0.665237509 0.850815936 0.886932502 1 21.98161546 1.569993097 1.790628497 1.004833946 0.768848076 0.683222743 0.051790765 0.269617754 1.492909334 0.09532976 0.015564456 37.15293234 -1.569993097 -0.23598587 TTFFHHEYPWILSASDDQTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TTFFHHEYPWILSASDDQTIR 21 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 209.73 1.40E-22 1432740000 594280 567980 289557 403680 615250 622660 599080 684660 696380 FALSE TRUE 515744.3923 564248.902 429587.7337 495341.7139 603007.7287 646614.1331 540981.3138 538250.787 614054.7497 0.839899687 0.918890217 0.699591908 0.806673532 0.982009713 1.053023584 0.880998501 0.876551785 1 19.22800777 3.245571623 24.97535621 0.94718258 0.815260554 0.47304634 0.074066896 166.1229464 591777.5165 0.022945342 0.028974949 1760.238936 -3.245571623 -0.131922026 TTFVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTFVKR 6 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 98.807 0.063359 623560000 2385300 1973200 756860 985110 2019500 1910900 2373300 2458100 450180 FALSE TRUE 2070076.561 1960237.919 1122880.028 1208794.282 1979315.901 1984413.56 2143137.731 1932454.444 396960.2332 5.214821002 4.938121643 2.828696513 3.045126894 4.986181827 4.999023563 5.398872612 4.868131067 1 18.59863496 4.452453559 24.96048233 4.081462629 5.145648131 0.109183865 1.339919679 487.8848478 493675.4043 0.341545351 0.903719772 28343.50525 -4.452453559 1.064185502 TTGFGMIYDSLDYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTGFGMIYDSLDYAK 15 0 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4;A0A2R8Y8A0 E7ETK0 RPS24 40S ribosomal protein S24 0 208.95 3.82E-11 0 144100 113240 87881 98133 143400 100370 148830 187070 134700 FALSE TRUE 125056.8199 112496.119 130380.5455 120415.5975 140546.6206 104231.2988 134396.4895 147066.5363 118775.9195 1.052880251 0.94712901 1.097701842 1.013804802 1.183292213 0.877545712 1.131512937 1.238184785 1 16.85788285 2.028567412 24.99989149 1.150728731 1.032001973 0.150995744 0.099666174 278.1924045 243450.4653 0.038196685 0.025751674 106.7990555 -2.028567412 -0.118726758 TTGIVMDSGDGVTHTVPIYEGYALPHAILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 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 ;;;;;;;; 353.43 1.75E-120 95099940000 13392419 13106573 5157198 8271633 13914714 14100106 13100196 14685333 6400113 FALSE TRUE 11622576.9 13020475.06 7651236.203 10149833.7 13637838.42 14642546.2 11829741.01 11544988.82 5643498.932 2.059462939 2.307163555 1.355761079 1.798500154 2.416557277 2.594586511 2.096171391 2.045714717 1 22.42815847 1.237112006 5.56487455 0.94771238 2.088451363 0.503137964 0.338875108 0.13836959 13.64059936 0.604732453 0.089864613 17.26283049 -1.237112006 1.140738983 TTGT(ph)PPDSSLVTYELHSRPEQDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TTGTPPDSSLVTYELHSRPEQDK 23 1 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18 Q13561 DCTN2 Dynactin subunit 2 1 T(0.005)T(0.021)GT(0.974)PPDSSLVTYELHSRPEQDK;T(0.118)T(0.118)GT(0.762)PPDS(0.001)SLVTYELHSRPEQDK 271.97 1.83E-51 329550000 536750 436600 369390 393520 448560 379190 525330 631410 689060 TRUE FALSE 465817.1275 433731.9459 548028.2395 482874.7306 439634.5336 393777.6847 474383.5775 496387.8851 607600.1118 0.766650826 0.713844414 0.901955462 0.794724558 0.723559007 0.648086919 0.780749655 0.816964769 1 19.21276261 1.19794933 2.139630621 1.089423324 0.760891384 0.571080324 0.064840819 0.621417119 2.60549435 0.415533194 0.018390829 15.77427217 -1.19794933 -0.32853194 TTGT(ph)PPDSSLVTYELHSRPEQDKFSQAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTGTPPDSSLVTYELHSRPEQDKFSQAAK 29 2 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18 Q13561 DCTN2 Dynactin subunit 2 1 T(0.027)T(0.027)GT(0.947)PPDSSLVTYELHSRPEQDKFSQAAK 214.46 2.98E-34 589070000 725100 569110 309420 337400 533050 441710 766310 824340 238070 TRUE FALSE 629276.1978 565371.4789 459056.5469 414011.8268 522443.3479 458702.8695 691993.3741 648061.306 209925.6358 2.997614824 2.69319884 2.186757921 1.97218327 2.488706755 2.185073146 3.29637384 3.087099408 1 17.67951883 -0.056458839 16.83649994 2.529878751 2.497482859 0 0.665576827 0 0 0 0.148302757 0.878094306 0.056458839 -0.032395892 TTGTPPDS(ph)SLVTYELHSRPEQDKFSQAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTGTPPDSSLVTYELHSRPEQDKFSQAAK 29 2 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18 Q13561 DCTN2 Dynactin subunit 2 1 T(0.041)T(0.041)GT(0.166)PPDS(0.71)S(0.041)LVTYELHSRPEQDKFSQAAK 100.59 0.00034559 557720000 300350 211180 131060 152830 215830 160430 288880 331950 97008 TRUE FALSE 260657.9865 209792.7447 194441.0544 187532.3874 211535.4053 166601.8459 260864.4621 260965.0757 85539.82475 3.047212071 2.452573936 2.273105597 2.192340093 2.472946442 1.947652411 3.049625865 3.050802085 1 16.38430863 4.732035652 4.139647966 2.383488483 3.098218648 0.127296012 0.58214552 0.514157447 19.59988418 0.142739281 1.085174362 53955.49141 -4.732035652 0.714730165 TTGYSDRPTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTGYSDRPTAR 11 1 Q9NP61;Q9NP61-2 Q9NP61 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 0 101.93 0.0024232 0 148810 142250 82512 114030 131350 145430 132030 173860 153000 FALSE TRUE 129144.3815 141315.5504 122415.0792 139922.2543 128736.392 151024.7862 119225.7509 136681.392 134912.5143 0.957245383 1.047460653 0.907366376 1.037133249 0.954221279 1.119427556 0.883726403 1.013111294 1 17.04166465 TTHFVEGGDAGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTHFVEGGDAGNR 13 0 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 170.66 2.64E-05 735430000 519970 520920 358290 512960 558250 541290 490180 556090 1456200 FALSE TRUE 451254.6471 517498.0422 531560.2424 629435.4081 547141.9172 562113.7766 442642.419 437174.481 1284049.695 0.351430828 0.40302026 0.413971706 0.49019552 0.426106497 0.437766372 0.344723745 0.340465391 1 20.29226961 1.235057751 24.99999991 1.00000084 0.400683884 0.942668711 0.046427374 24.36924848 173895.964 0.090584982 0.012704868 17.18136843 -1.235057751 -0.599316956 TTHFVEGGDAGNREDQINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 TTHFVEGGDAGNREDQINR 19 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ;;;;;;; 220.1 1.79E-19 23903750000 3810401 3465941 1959385 2451043 3750213 3636165 3474785 4009598 3044281 FALSE TRUE 3306846.854 3443173.005 2906950.14 3007589.775 3675591.098 3776050.62 3137800.886 3152176.67 2684389.568 1.231880385 1.282665171 1.082909193 1.120399889 1.369246529 1.406670129 1.168906675 1.174262003 1 21.35616263 1.213779203 1.748127207 0.904145038 1.24051307 0.361652614 0.099908395 1.262436792 3.403040415 0.737017449 0.030032607 16.35984568 -1.213779203 0.336368032 TTHLAGALS(ph)PGEAWPFESV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 215.48 4.25E-19 335243000 334889 331391 178027 235586 367498 384712 331798 399035 354332 TRUE FALSE 290632.5701 329214.0707 264121.4527 289079.402 360185.5088 399512.1196 299620.281 313704.4705 312443.2746 0.930193074 1.053676291 0.845342096 0.925222034 1.152802886 1.278670889 0.958958971 1.00403656 1 18.25323476 3.258439047 24.97150554 1.070530439 0.940165586 0.315427757 0.102271061 347.3552701 436348.8764 0.031865951 0.041084707 1813.172182 -3.258439047 -0.130364853 TTHLAGALS(ph)PGGGQSAPAFPESGPSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TTHLAGALSPGGGQSAPAFPESGPSLR 27 0 A0A2R8Y4Z8 A0A2R8Y4Z8 1 TTHLAGALS(1)PGGGQSAPAFPESGPSLR;TTHLAGALS(1)PGGGQSAPAFPESGPSLR;TTHLAGALS(1)PGGGQSAPAFPESGPSLR;TTHLAGALS(1)PGGGQSAPAFPESGPSLR;TTHLAGALS(1)PGGGQSAPAFPESGPSLR;TTHLAGALS(1)PGGGQSAPAFPESGPSLR 263.09 2.30E-53 3205910000 1024424 1209897 660033 979960 1655510 1488489 1497337 1764470 1517638 TRUE FALSE 889043.7728 1201949.107 979227.1665 1202474.896 1622568.59 1545752.135 1352125.488 1387151.822 1338224.565 0.664345728 0.898166973 0.731736057 0.898559874 1.212478558 1.155076791 1.010387587 1.03656132 1 20.3518888 3.448614538 5.868903109 1.074947444 0.782972696 0.741987264 0.086134739 0.09119119 9.395749245 0.025208843 0.03340233 2809.40621 -3.448614538 -0.291974749 TTHS(ph)PYEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TTHSPYEER 9 0 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 TTHS(1)PYEER;TTHS(1)PYEER;T(0.223)T(0.3)HS(0.477)PYEER;T(0.011)T(0.002)HS(0.987)PYEER;TTHS(1)PYEER;T(0.001)THS(0.999)PYEER 232.46 1.68E-08 3640630000 2618740 2354590 1343430 1707090 2209600 2367040 2283710 2385050 2271570 TRUE FALSE 2272666.874 2339122.543 1993117.242 2094710.876 2165633.283 2458101.56 2062236.156 1875025.618 2003027.582 1.134615865 1.167793476 0.995052319 1.045772357 1.081179961 1.227193066 1.02955954 0.936095755 1 20.93375086 2.003719805 24.99821986 0.96928658 1.104223834 0.451108743 0.064976207 94.01618109 631813.754 0.027562355 0.018487288 100.8601954 -2.003719805 0.134937255 TTIESHTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTIESHTK 8 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 0 69.423 0.053956 35599000 51726 44472 22743 30129 46490 55211 48660 50377 42839 FALSE TRUE 44890.27804 44179.8605 33741.59087 36970.24994 45564.93996 57335.0029 43940.96069 39604.27058 37774.62222 1.18837133 1.169564589 0.89323437 0.978706014 1.206231519 1.517818036 1.163240242 1.048435914 1 15.20512971 3.223481455 24.94658885 1.184547288 1.053744841 0.140788502 0.158993557 524.1031279 867060.9338 0.053139761 0.060485779 1672.944198 -3.223481455 -0.130802446 TTIPEEEEEEEEAAGVVVEEELFHQQGT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 TTIPEEEEEEEEAAGVVVEEELFHQQGTPR 30 0 P20700 P20700 LMNB1 Lamin-B1 1 TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR 233.11 8.40E-45 888165000 380770 358501 207225.7 287003 336478 344389 324252 454631 383130 TRUE FALSE 330450.2798 356145.9833 307440.7416 352171.4177 329782.7461 357637.8677 292806.0909 357411.6986 337836.8079 0.97813581 1.054195325 0.91002737 1.042430575 0.976159905 1.058611316 0.866708672 1.057941853 1 18.365967 1.611680115 25 1.028970257 0.986603444 0.08197667 0.062333846 0.855235134 5582.788663 0.032018322 0.014443747 40.89593251 -1.611680115 -0.042366814 TTIPEEEEEEEEAAGVVVEEELFHQQGTPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TTIPEEEEEEEEAAGVVVEEELFHQQGTPR 30 0 P20700 P20700 LMNB1 Lamin-B1 0 ;;;;; 360.57 9.61E-121 1544376000 398743 328546 168466.1 256540.6 344969 314964 308343.8 427753 295296 FALSE TRUE 346048.1023 326387.7597 249936.8694 314792.0642 338104.7918 327080.8689 278440.6657 336281.3497 260386.4433 1.328978951 1.253474473 0.959868979 1.208941834 1.298473099 1.256136321 1.069336261 1.291470268 1 17.99029481 1.222489447 24.91806122 0.999999402 1.203692027 0.250134295 0.113108948 1385.577621 2148187.948 0.694816347 0.027397176 16.69127247 -1.222489447 0.203692625 TTIPHALLTWRPNSGETAPPPPS(ph)PVSEKPLDTISQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TTIPHALLTWRPNSGETAPPPPSPVSEKPLDTISQK 36 2 Q9Y6D6;E5RIF2;E5RHL7 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 TTIPHALLTWRPNSGETAPPPPS(0.96)PVS(0.038)EKPLDT(0.001)ISQK;TTIPHALLTWRPNSGETAPPPPS(0.959)PVS(0.04)EKPLDT(0.001)ISQK 140.24 2.81E-13 2751500000 2912300 2894400 2124760 2593600 3727800 2629400 5040200 6126300 3896500 TRUE FALSE 2527432.176 2875386.496 3152301.043 3182516.521 3653624.073 2730554.719 4551402.18 4816238.42 3435860.209 0.735603902 0.836875286 0.917470692 0.926264844 1.063379722 0.794722298 1.324676181 1.40175622 1 21.71223991 2.234179832 24.99962383 1.278835558 0.889406385 0.6140932 0.134475484 66.6439425 380308.024 0.053615289 0.037557461 171.4667168 -2.234179832 -0.389429173 TTISVAHLLAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTISVAHLLAAR 12 0 Q8NCA5;E9PH82 Q8NCA5 FAM98A Protein FAM98A 0 100.38 0.0032682 242950000 863230 889860 1585600 919500 337630 980180 512680 524580 674480 FALSE TRUE 749151.9684 884014.4511 2352401.464 1128286.529 330911.8236 1017888.159 462960.3725 412402.6493 594743.7428 1.259621438 1.486378733 3.9553194 1.89709693 0.556393956 1.711473506 0.778419913 0.693412338 1 19.18190866 3.381301407 5.784820572 0.948763633 2.277873619 0.380581483 0.769240654 0.213040264 10.58086099 0.226125147 0.293379245 2406.032042 -3.381301407 1.329109986 TTLIPGGSESLVYTTLSGGIGILVPFTSHEDHDFFQHVEMHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTLIPGGSESLVYTTLSGGIGILVPFTSHEDHDFFQHVEMHLR 43 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 144.97 4.46E-14 563820000 774210 666340 256040 525770 547400 570230 690300 885330 531280 FALSE TRUE 671896.1869 661962.7687 379861.8004 645154.1144 536507.811 592167.1171 623354.8122 696009.0691 468472.6836 1.434227033 1.413023196 0.810851547 1.377143507 1.145227523 1.264037665 1.3306108 1.485698299 1 18.8376054 2.416581956 5.194788813 1.317777403 1.227807561 0 0.213257459 0.826506214 44.96496931 0.079616628 0.061478485 260.9648146 -2.416581956 -0.089969842 TTLLHMLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TTLLHMLK 8 0 Q9Y6B6;D6RD69;D6RDB2;D6RAA2;Q9NR31;Q5SQT8;X1WI22 Q9Y6B6;Q9NR31 SAR1B;SAR1A GTP-binding protein SAR1b;GTP-binding protein SAR1a 0 ; 101.54 0.005321 2126430000 3580900 4918000 3018200 4059000 5625900 4565100 5458600 6390400 8693200 FALSE TRUE 3107674.992 4885693.334 4477811.615 4980657.988 5513955.597 4740722.351 4929225.812 5023862.69 7665499.799 0.405410616 0.637361354 0.584151292 0.649749934 0.71932108 0.618449217 0.643040368 0.655386188 1 22.86994843 1.18683464 2.904858058 1.111918973 0.615482076 0.694664955 0.080762611 0.300956046 2.756499569 0.38012606 0.02050381 15.3756909 -1.18683464 -0.496436897 TTLLHMLKDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TTLLHMLKDDR 11 1 Q9Y6B6;D6RD69;D6RDB2;D6RAA2;Q9NR31;Q5SQT8;X1WI22 Q9Y6B6;Q9NR31 SAR1B;SAR1A GTP-binding protein SAR1b;GTP-binding protein SAR1a 0 ; 206.36 1.60E-08 2340500000 4008400 4543700 1698230 2138050 4635200 3934400 5374700 6465200 659100 FALSE TRUE 3478679.784 4513852.136 2519499.708 2623526.931 4542968.589 4085758.914 4853462.421 5082667.292 581181.9488 5.985526204 7.766676416 4.335130699 4.51412322 7.816775104 7.030085711 8.35102059 8.745397723 1 19.14863037 7.503776263 18.79284946 6.457972871 1.118253082 0 2.380475857 0 0 0.525859513 0 31898940.85 -7.503776263 -5.339719788 TTMRPQSFYDGSHSCAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTMRPQSFYDGSHSCAR 17 1 B4DUC8;Q13126-4;Q13126;Q13126-3;Q13126-2;J3QSB7;Q13126-7;Q13126-6;Q13126-5 B4DUC8 MTAP S-methyl-5-thioadenosine phosphorylase;Purine nucleoside phosphorylase 0 71.697 0.0403 54300000 80233 71287 27778 48209 84245 78048 74411 86009 68105 FALSE TRUE 69630.00577 70818.711 41211.53371 59155.59028 82568.68932 81050.55706 67194.63267 67616.64467 60053.70449 1.159462291 1.179256327 0.686244655 0.985044816 1.374914171 1.349634594 1.118909037 1.125936281 1 15.87396562 3.29429489 24.99980197 1.187551534 0.992536828 0.235921967 0.170508675 137.3563317 61610.41887 0.051934338 0.067046901 1969.222954 -3.29429489 -0.195014706 TTNSS(ph)LEEIMDK ddPTM_MDA-MB-175_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(0.018)S(0.982)LEEIMDK 195.95 2.23E-07 100920000 272630 190980 118060 163930 203770 173930 249930 272670 257970 TRUE FALSE 236601.2547 189725.4398 175154.2109 201152.812 199715.3757 180621.1996 225691.8271 214361.6424 227473.0805 1.040128591 0.834056669 0.769999731 0.884292821 0.877973672 0.794033295 0.992169388 0.942360485 1 17.7953363 2.222447531 24.99892506 0.971297989 0.862171687 0.336516753 0.0733587 277.1662417 430011.0131 0.029268316 0.019800665 166.8966159 -2.222447531 -0.109126302 TTPATGEQS(ph)PGAR ddPTM_MDA-MB-175_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 199.84 1.20E-07 730300000 584290 468020 232400 321590 494370 477410 470290 466510 422640 TRUE FALSE 507074.5961 464945.5458 344789.4173 394611.9247 484533.0042 495776.2716 424681.3482 366750.4669 372675.9807 1.360631279 1.247586563 0.925172094 1.058860633 1.300145513 1.330314529 1.139545799 0.984100092 1 18.50756231 1.824204033 4.059545662 0.99239283 1.193557293 0.30271196 0.129940222 0.300388885 8.281639212 0.083369317 0.038048406 66.71201103 -1.824204033 0.201164463 TTPDVIFVFGFR ddPTM_MDA-MB-175_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 ; 132.88 0.00040294 329930000 392990 393310 252510 307740 374970 340850 441550 440060 419080 FALSE TRUE 341055.3758 390726.3207 374624.6806 377617.0705 367508.8306 353962.7201 398728.549 345956.5936 369536.8398 0.922926591 1.057340645 1.013768156 1.021865833 0.994512024 0.957855028 1.078995396 0.936189728 1 18.49535867 1.646541457 24.99999805 0.968092676 1.00723917 0.105657968 0.046739332 1.101131926 704.5455935 0.022874764 0.010983995 44.31405141 -1.646541457 0.039146493 TTPES(ph)PPYSSGSYDSIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TTPESPPYSSGSYDSIK 17 0 A0A087WTU5;A0A087X0N3;Q96MY1-2;Q96MY1 A0A087WTU5 NOL4L Nucleolar protein 4-like 1 TTPES(1)PPYSSGSYDSIK;TTPES(1)PPYSSGSYDSIK;TTPES(0.949)PPYS(0.051)SGSYDSIK;TTPES(0.997)PPYS(0.002)S(0.001)GSYDSIK;TTPES(0.999)PPYS(0.001)SGSYDSIK 364.82 2.99E-88 1797162000 1378250 1222395 824790 1053228 1252100 1058736 1538910 1688960 1574280 TRUE FALSE 1196110.77 1214365.007 1223661.203 1292379.515 1227185.66 1099466.259 1389666.745 1327789.048 1388170.412 0.861645487 0.87479534 0.881492065 0.930994858 0.884030987 0.792025424 1.001077918 0.956502916 1 20.40475325 2.215101274 24.99999246 0.980378271 0.87483024 0.691967685 0.036051688 139.6718722 148843.4107 0.014792957 0.009979896 164.0972392 -2.215101274 -0.105548032 TTPPPGAQCEVPAS(ph)PQRPSRPGALPEQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TTPPPGAQCEVPASPQRPSRPGALPEQTR 29 2 Q9H074;D6R9H8 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 1 TTPPPGAQCEVPAS(0.997)PQRPS(0.003)RPGALPEQTR;TTPPPGAQCEVPAS(0.999)PQRPS(0.001)RPGALPEQTR 147.97 2.56E-08 261380000 8820.7 5851.2 5846 10921.1 12482.3 11777.3 8883.3 15411.8 15554 TRUE FALSE 7655.022146 5812.763082 8673.145154 13400.90267 12233.92665 12230.38035 8021.798933 12116.1065 13715.22384 0.558140519 0.423818317 0.632373577 0.977082316 0.891996135 0.891737568 0.58488283 0.88340567 1 13.74349055 3.953028025 4.645474968 0.855400304 0.495703897 0.656384774 0.116494181 0.126043569 6.03492432 0.031913188 0.060140244 8974.86708 -3.953028025 -0.359696407 TTPPPGAQCEVPAS(ph)PQRPSRPGALPEQTRPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TTPPPGAQCEVPASPQRPSRPGALPEQTRPLR 32 3 Q9H074;D6R9H8 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 1 TTPPPGAQCEVPAS(0.999)PQRPS(0.001)RPGALPEQTRPLR;TTPPPGAQCEVPAS(0.982)PQRPS(0.012)RPGALPEQT(0.006)RPLR;TTPPPGAQCEVPAS(0.995)PQRPS(0.004)RPGALPEQT(0.001)RPLR;TTPPPGAQCEVPAS(1)PQRPSRPGALPEQTRPLR;TTPPPGAQCEVPAS(1)PQRPSRPGALPEQTRPLR 231.61 4.79E-37 6396420000 169160.5 167587.8 66174.1 103604.6 193505.7 163111.1 154844.7 191412.4 170544.2 TRUE FALSE 146805.5113 166486.9047 98176.1161 127129.6079 189655.3152 169386.0896 139827.8848 150480.3478 150382.659 0.976213031 1.107088449 0.652842002 0.84537412 1.261151495 1.126367167 0.929813888 1.000649602 1 17.19827869 TTPQQGASGPGRS(ph)PVGQAR ddPTM_MDA-MB-175_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;TTPQQGASGPGRS(1)PVGQAR;TTPQQGASGPGRS(1)PVGQAR 281.42 6.59E-40 985460000 142175 149001 64718 86732 149190 158217 138718 168967 87499 TRUE FALSE 123386.2135 148022.2026 96015.84127 106425.8262 146221.4109 164303.7104 125265.1497 132834.722 77154.9679 1.599199856 1.918505142 1.244454426 1.379377493 1.895165209 2.129528595 1.623552613 1.721661295 1 16.23547143 3.246123435 24.99775808 1.698936698 1.541969364 0.038701875 0.329752869 638.4057096 2110141.364 0.098120988 0.12418494 1762.476905 -3.246123435 -0.156967335 TTPS(ph)YVAFTDTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 TTPS(1)YVAFTDTER;TTPS(1)YVAFTDTER 160.46 4.60E-05 297240000 212463 275460 161834 169045 302930 275870 272480 319640 323090 TRUE FALSE 184385.4762 273650.4851 240097.4637 207429.2509 296902.2857 286482.8974 246054.9315 251287.4734 284894.6683 0.647205781 0.960532139 0.842758712 0.728091025 1.042147568 1.005574794 0.863669836 0.882036421 1 18.1200691 3.242712364 24.9998724 0.944322821 0.809932425 0.408489796 0.096460585 130.9206224 788337.2986 0.028320346 0.035241311 1748.688136 -3.242712364 -0.134390396 TTPSYVAFTDTER ddPTM_MDA-MB-175_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 ;;;;;;; 260.08 1.24E-23 10530490000 2642110 2512540 1365609 1781876 2649010 2695080 2503555 2856670 2630420 FALSE TRUE 2292948.469 2496034.959 2026022.08 2186478.18 2596299.884 2798761.472 2260760.621 2245793.351 2319454.744 0.988572196 1.076130054 0.873490671 0.942669041 1.119357853 1.206646294 0.974694862 0.968241936 1 21.14535427 5.066243664 14.54818479 1.016859104 0.728421077 0.009834148 0.094588331 5435380.325 28937225.45 0.024563956 46220036.05 116477.9354 -5.066243664 -0.288438027 TTQAAAIIDHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTQAAAIIDHER 12 0 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;H0Y6V3;H0Y6R0;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 0 62.357 0.078341 144970000 67031 51142 43480 53138 56712 78356 70462 77091 50960 FALSE TRUE 58172.68352 50806.04483 64507.07343 65203.79506 55583.54216 81370.40602 63628.60609 60605.68957 44935.56685 1.294579942 1.130642126 1.435546004 1.451050908 1.236960965 1.810824069 1.415996515 1.348724269 1 15.45557018 1.232088243 3.508124662 0.938816996 1.398610129 0.326784239 0.1773825 0.389783084 6.992695328 0.486180524 0.046173291 17.06429076 -1.232088243 0.459793133 TTQETIDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTQETIDK 8 0 Q15847;Q5TBU2 Q15847 ADIRF Adipogenesis regulatory factor 0 239.66 2.37E-08 543290000 508360 425440 312390 380510 390600 371140 468990 560870 665230 FALSE TRUE 441178.938 422645.2566 463462.8489 466910.6112 382827.8242 385417.996 423507.422 440932.3152 586587.2672 0.752111344 0.720515566 0.790100425 0.795978088 0.652635755 0.657051418 0.721985365 0.751690907 1 19.16198623 1.23033698 3.920119129 1.034330423 0.727122596 0.766143007 0.047013097 0.136691573 3.532460185 0.123178544 0.012938758 16.99561875 -1.23033698 -0.307207827 TTQSMQDFPVVDS(ph)EEEAEEEFQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TTQSMQDFPVVDSEEEAEEEFQK 23 0 Q9UBB9 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 TTQSMQDFPVVDS(1)EEEAEEEFQK;TTQSMQDFPVVDS(1)EEEAEEEFQK;TTQSMQDFPVVDS(1)EEEAEEEFQK 189.78 1.11E-17 372808000 765041 598165 443204 515992 658762 551217 750320 886130 848820 TRUE FALSE 663938.8935 594235.6147 657538.9368 633155.87 645653.925 572422.6747 677554.0819 696637.9954 748473.4666 0.887057355 0.793930101 0.878506676 0.845929613 0.862627673 0.764786863 0.905247964 0.930745078 1 19.51359165 1.668694305 1.886392337 0.994305487 0.840703023 0.635137346 0.04002605 0.215862702 1.473100371 0.048365108 0.010822946 46.63310197 -1.668694305 -0.153602464 TTQVPQFILDDFIQNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TTQVPQFILDDFIQNDR 17 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;; 175.15 2.94E-09 170346000 202516 190555 100911 126733 185858 204718 200499 228827 204712 FALSE TRUE 175752.9975 189303.2317 149711.8971 155509.6646 182159.7894 212593.6339 181054.6378 179894.1268 180511.1806 0.973640508 1.048706407 0.829377419 0.861496026 1.009133001 1.177731115 1.003010657 0.996581631 1 17.46172867 3.031706924 12.99630963 1.039706161 0.930492185 0.332963199 0.07792791 1.600344394 653.2306573 0.025050566 0.028382848 1075.739025 -3.031706924 -0.109213976 SSS(ph)FGSVSTSSNSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 SSSFGSVSTSSNSSK 15 0 A0A0C4DGW2;P57768-2;P57768;E5RGS8;E5RH07;E5RGQ6;E5RG30;E5RJ65;E5RHF1 A0A0C4DGW2 SNX16 Sorting nexin-16 1 SSS(1)FGSVSTSSNSSK;SS(0.01)S(0.989)FGSVSTSSNSSK;SSS(1)FGSVSTSSNSSK;SSS(0.762)FGS(0.23)VS(0.006)T(0.002)SSNSSK;SS(0.019)S(0.981)FGSVSTSSNSSK;S(0.001)S(0.033)S(0.966)FGSVSTSSNSSK 397.04 7.00E-115 2451570000 3424930 4231560 3413130 4464800 5725110 5120170 6653460 7848330 7487430 TRUE FALSE 2972316.823 4203762.604 5063731.084 5478601.08 5611191.512 5317146.253 6008208.473 6170025.705 6602274.555 0.450195883 0.636714297 0.766967663 0.829805097 0.849887636 0.805350673 0.910020997 0.934530313 1 22.6545317 5.052715613 0.520881437 0.935954517 2.01E-23 0.926896676 0.042626056 1.670693935 0.286135661 0.031421647 1.021072321 112905.6337 -5.052715613 -0.935954517 down TTS(ph)GDDACNLTSFRPATLTVTNFFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTSGDDACNLTSFRPATLTVTNFFK 25 1 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GUE9;Q96N67-7;A0A0U1RQT6 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 T(0.122)T(0.122)S(0.756)GDDACNLTSFRPATLTVTNFFK 97.691 0.0049798 99028000 214180 161570 67754 108480 152540 107050 208670 216310 111070 TRUE FALSE 185875.5703 160508.636 100520.061 133112.042 149504.7524 111168.2828 188433.2155 170053.7898 97939.43113 1.897862467 1.638856119 1.026349243 1.35912615 1.526502153 1.135071763 1.923977027 1.736315883 1 16.5796022 2.244126721 24.99998429 1.606971395 1.42282449 0.020499543 0.335454687 426.1100162 1913870.923 0.128842995 0.096927168 175.4392332 -2.244126721 -0.184146904 TTS(ph)PEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TTSPEPR 7 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 T(0.064)T(0.219)S(0.717)PEPR;T(0.07)T(0.031)S(0.899)PEPR;T(0.109)T(0.062)S(0.83)PEPR 104.44 0.0085507 2727210000 3271790 3023510 1650150 2116230 2003900 2896550 2836820 3289170 3174750 TRUE FALSE 2839414.662 3003648.364 2448168.059 2596752.366 1964026.311 3007982.153 2561705.633 2585806.592 2799434.672 1.014281451 1.07294819 0.874522304 0.927598844 0.701579619 1.074496284 0.915079626 0.92368885 1 21.41670408 4.241753024 24.99921787 0.915586172 1.04361485 0.234405791 0.095332337 112.0888684 877709.5691 0.023097519 0.0560069 17448.29615 -4.241753024 0.128028678 TTS(ph)PGGRPSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTSPGGRPSAR 11 1 A1L390-3;A1L390;A1L390-2;G3V311 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 T(0.275)T(0.2)S(0.465)PGGRPS(0.06)AR 89.189 0.032669 120010000 254170 270290 147330 205100 287980 325770 292650 329790 282480 TRUE FALSE 220580.7905 268514.4472 218579.2808 251671.0898 282249.7614 338302.5827 264268.848 259266.9749 249085.5362 0.885562421 1.07800096 0.87752699 1.010380183 1.133143922 1.358178351 1.060956216 1.040875271 1 17.92628172 3.378003458 4.4828402 1.115946811 0.957826697 0.343615614 0.109274408 0.276868087 9.772034342 0.033792122 0.044248788 2387.830296 -3.378003458 -0.158120115 TTS(ph)PLEEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TTSPLEEEER 10 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 TT(0.001)S(0.999)PLEEEER;T(0.002)T(0.001)S(0.997)PLEEEER;TTS(1)PLEEEER 342.74 7.61E-54 3188070000 2778000 2215890 1525560 1953030 2341080 2256600 2316490 2399750 2861460 TRUE FALSE 2410880.261 2201333.673 2263325.919 2396495.312 2294497.088 2343412.862 2091837.156 1886582.137 2523181.459 0.955492223 0.872443662 0.897012742 0.949791107 0.909366657 0.928753203 0.829047451 0.747699747 1 21.26681253 2.235760208 24.99406193 0.834501208 0.916690593 0.117896993 0.066749495 100.8663874 900227.7154 0.025754294 0.018241572 172.0918124 -2.235760208 0.082189385 TTS(ph)PSS(ph)DTDLLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTSPSSDTDLLDR 13 0 K7ENU0;K7ERZ4;K7EJ43;Q96QT6;C9J9G2;Q96QT6-2;Q96QT6-5;Q96QT6-3 K7ENU0;Q96QT6 PHF12 PHD finger protein 12 2 T(0.007)T(0.009)S(0.984)PS(0.209)S(0.791)DTDLLDR 161.76 1.35E-06 0 200630 156020 130690 117730 178330 156230 158500 168140 161410 TRUE FALSE 174116.2372 154995.0943 193892.1211 144462.3959 174781.5819 162240.2692 143128.6944 132184.5695 142328.2937 1.223342406 1.088997067 1.362287962 1.014994223 1.228017124 1.139901737 1.005623623 0.928730093 1 17.11886296 2.228093089 3.032653276 0.960578926 1.179485701 0.516217142 0.09175979 0.18091525 3.452984379 0.038345787 0.024993409 169.0803307 -2.228093089 0.218906775 TTS(ph)PSSDTDLLDR ddPTM_MDA-MB-175_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 TTS(1)PSSDTDLLDR;T(0.003)T(0.028)S(0.969)PSSDTDLLDR;T(0.002)T(0.026)S(0.954)PS(0.017)S(0.002)DTDLLDR;TT(0.039)S(0.95)PS(0.01)S(0.001)DTDLLDR 313.83 1.18E-50 1261130000 1394000 1319360 731752 845570 1351310 1273380 1191890 1396030 1277080 TRUE FALSE 1209779.368 1310693.037 1085629.715 1037569.592 1324421.575 1322367.753 1076300.691 1097499.848 1126105.057 1.074304178 1.163917193 0.964057223 0.921379036 1.176108362 1.174284534 0.955772896 0.974598099 1 20.10291 2.200238186 24.99997837 0.975457795 1.074891668 0.242645417 0.084912143 257.3970829 167913.5608 0.036927248 0.024896911 158.5762654 -2.200238186 0.099433873 TTSIS(ph)PALAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 TTSIS(1)PALAR;TTSIS(1)PALAR;TTSIS(1)PALAR;TT(0.001)S(0.001)IS(0.999)PALAR;TTS(0.001)IS(0.999)PALAR;TTS(0.002)IS(0.998)PALAR 241.35 2.71E-12 3449380000 3798690 4211480 2229380 2821810 4660860 4552940 3698780 4542510 4314820 TRUE FALSE 3296683.492 4183814.511 3307515.625 3462545.089 4568118.005 4728094.548 3340072.885 3571129.586 3804726.895 0.866470468 1.09963596 0.869317487 0.910064029 1.200642814 1.242689601 0.877874543 0.938603396 1 21.85936147 4.766779704 22.83333669 1.009453667 0.866469869 0.115582223 0.129539265 8035.047354 6501169.34 0.03345028 2.649909312 58449.35242 -4.766779704 -0.142983798 TTSRS(ph)PVLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TTSRSPVLSR 10 1 O95819-3;O95819-6;E7EN19;O95819;H7C360;O95819-2;A0A0D9SEY1;H7C0P6;A0A0D9SG62;G5E948;E7ENQ1;G3XAA2;C9J840;E7EX83;O95819-4;O95819-5;H7C3Z6 O95819-3 MAP4K4 Mitogen-activated protein kinase kinase kinase kinase 4 1 T(0.03)T(0.03)S(0.03)RS(0.91)PVLSR;T(0.047)T(0.047)S(0.038)RS(0.868)PVLSR 79.639 0.01599 481470000 526570 425590 215197 307130 473920 525000 396100 464560 281180 TRUE FALSE 456982.4403 422794.2713 319266.989 376868.5607 464489.9192 545197.0897 357686.283 365217.4592 247939.2207 1.843122839 1.705233525 1.287682473 1.520003812 1.873402352 2.198914267 1.442636957 1.473012048 1 17.91962698 1.298227077 1.646242094 0.804323387 1.703902083 0.446967116 0.248890707 0.940098813 2.618725902 1.333391676 0.07575667 19.87133648 -1.298227077 0.899578696 TTSSANNPNLMYQDECDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 TTSSANNPNLMYQDECDRR 19 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;;;; 293.22 2.13E-49 5138080000 1524273 1476573 711104 894669 1475703 1569527 1354356 1626232 1312310 FALSE TRUE 1322836.461 1466873.295 1054996.273 1097817.271 1446339.397 1629907.719 1223010.764 1278474.942 1157170.207 1.143164984 1.267638318 0.911703626 0.948708551 1.249893394 1.408528935 1.056897902 1.104828775 1 20.14216965 1.372083751 1.950137104 0.983925275 1.143520827 0.083771945 0.147524736 1.79679522 8.697148896 0.483576446 0.043455424 23.55503487 -1.372083751 0.159595552 TTSSYQNLVWSDHSQELHS(ph)PTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TTSSYQNLVWSDHSQELHSPTLK 23 0 Q8WVV4-1;Q8WVV4;Q8WVV4-3 Q8WVV4-1 POF1B Protein POF1B 1 TTSSYQNLVWSDHSQELHS(1)PTLK;TTSSYQNLVWSDHSQELHS(0.995)PT(0.005)LK 303.42 6.94E-62 1519460000 1245500 719650 327000 697200 1230660 1084690 1173470 1380330 1377790 TRUE FALSE 1080904.019 714922.5718 485138.2937 855509.916 1206172.274 1126418.726 1059667.06 1085157.171 1214909.236 0.889699401 0.588457599 0.399320607 0.704175992 0.992808548 0.927162864 0.872219116 0.893200199 1 20.21241711 3.375021813 5.030822996 0.924988229 0.611673446 0.580967605 0.123816596 0.146300908 5.970471448 0.036261094 0.047205601 2371.492816 -3.375021813 -0.313314783 TTTELFHSNEESGFFNELEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TTTELFHSNEESGFFNELEALR 22 0 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;A0A0A0MRE9;H7BYL6 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 0 ;; 243.23 9.45E-31 296422000 105501 99461 52528 69181.2 94607 111136 105684 132238 118464 FALSE TRUE 91558.77554 98807.63414 77930.7165 84889.84883 92724.5058 115411.4738 95434.78195 103959.9328 104459.3209 0.876501731 0.945895812 0.746038897 0.812659398 0.887661388 1.104846105 0.913607145 0.995219306 1 16.6725817 2.979795217 20.12588181 0.993999338 0.845971297 0.554866336 0.06733052 48.25960513 48071.35941 0.021317794 0.021696565 954.5423838 -2.979795217 -0.148028041 TTTGSYIANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTTGSYIANR 10 0 P28072;A0A087X2I4;I3L3X7 P28072 PSMB6 Proteasome subunit beta type-6;Proteasome subunit beta type 0 76.345 0.084391 80302000 87848 85218 50638 58760 86819 89114 89124 100760 103780 FALSE TRUE 76238.66422 84658.19735 75126.70617 72102.35609 85091.47176 92542.27324 80480.7682 79213.25812 91511.24663 0.833107045 0.925112491 0.820955991 0.787907047 0.929847149 1.011266666 0.879463139 0.865612272 1 16.48166144 3.208995637 24.88340976 0.927653035 0.846236872 0.40605172 0.056604584 240.6128744 202511.3842 0.018045129 0.020464091 1618.063781 -3.208995637 -0.081416163 TTTPPPSQIPDPPFS(ph)SPITPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTTPPPSQIPDPPFSSPITPHR 22 0 Q6ZS30-1;Q6ZS30 Q6ZS30-1 NBEAL1 Neurobeachin-like protein 1 1 TTTPPPSQIPDPPFS(0.553)S(0.424)PIT(0.022)PHR 80.711 0.0039929 193910000 40379 41763 18734 25623 36592 33611 27083 36445 36556 TRUE FALSE 35042.81284 41488.6561 27793.82506 31441.09377 35863.89079 34904.03692 24456.49483 28651.52037 32234.39132 1.087125005 1.287092897 0.862241349 0.975389715 1.112597115 1.082819792 0.758708132 0.88884943 1 14.97631312 5.697298155 0.256044603 0.854859516 1.6147686 0.232389181 0.130402344 36.37898624 1.717701107 0.539365704 9.469373977 498078.9121 -5.697298155 0.759909084 TTTS(ph)PFFSEDTFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TTTSPFFSEDTFR 13 0 A0A494C0H4;H0Y9M2;Q17R98-2;Q17R98;H0Y9K9;G5E9Z1;A0A590UJE4;Q17R98-3;A0A5F9ZGT0;A0A5F9ZHK5 A0A494C0H4 ZNF827 Zinc finger protein 827 1 T(0.034)T(0.042)T(0.154)S(0.77)PFFSEDTFR;T(0.017)T(0.017)T(0.117)S(0.849)PFFSEDTFR;TT(0.004)T(0.099)S(0.897)PFFSEDTFR 157.22 4.99E-05 379548000 776430 770650 453812 538632 789310 791010 760690 884600 808080 TRUE FALSE 673822.8083 765587.5494 673277.0011 660936.6281 773604.2753 821440.6666 686918.4009 695435.174 712549.703 0.945650255 1.07443389 0.944884263 0.92756565 1.085684651 1.152818762 0.964028752 0.975981284 1 19.44263113 3.242845914 24.99995799 1.02871777 0.978351465 0.171098826 0.067030063 270.2600692 1576652.856 0.021279631 0.026509692 1749.225959 -3.242845914 -0.050366305 TTVSHNTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTVSHNTK 8 0 Q9UHQ9 Q9UHQ9 CYB5R1 NADH-cytochrome b5 reductase 1 0 87.639 0.015181 34518000 78604 75997 39605 70497 54355 102080 67683 108610 131280 FALSE TRUE 68216.28224 75497.7707 58758.11047 86504.42133 53273.44184 106007.0837 61119.11308 85384.5967 115760.228 0.58928946 0.65219093 0.507584613 0.747272382 0.460205053 0.915747019 0.527980241 0.737598726 1 16.82078014 1.292523998 2.98637112 1.045667723 0.633555623 0.446459843 0.130273217 0.295807148 3.493256044 0.274411708 0.030547622 19.61209545 -1.292523998 -0.4121121 TTWAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTWAEER 7 0 Q9BX40;Q9BX40-2 Q9BX40 LSM14B Protein LSM14 homolog B 0 81.119 0.065295 141670000 126450 153550 91058 106440 146110 145670 138410 149510 157960 FALSE TRUE 109739.3121 152541.3199 135093.9534 130608.8288 143202.6969 151274.0192 124987.0195 117538.45 139286.1487 0.787869527 1.095165035 0.969902281 0.937701487 1.028118719 1.086066493 0.897339905 0.843863163 1 17.08769227 2.111319815 22.08090865 0.898444166 0.988709351 0.103201874 0.093660824 6.321265138 1220.119726 0.036265396 0.024450126 129.2170479 -2.111319815 0.090265185 TTWGDGGENS(ph)PCNVVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TTWGDGGENSPCNVVSK 17 0 H3BV99;H3BP15;H3BQY9;H3BM38;O00161 H3BV99;H3BM38 SNAP23 Synaptosomal-associated protein;Synaptosomal-associated protein 23 1 TTWGDGGENS(1)PCNVVSK;TTWGDGGENS(1)PCNVVSK;TTWGDGGENS(1)PCNVVSK 252.83 5.63E-27 1178950000 1393620 1265530 785960 1389860 1662110 1309820 978670 2389980 1704990 TRUE FALSE 1209449.586 1257216.65 1166052.885 1705448.956 1629037.263 1360209.623 883758.734 1878901.376 1503428.025 0.804461249 0.836233348 0.775596082 1.13437353 1.083548555 0.904738771 0.587829094 1.249744813 1 20.51982437 3.761541938 24.61782438 0.994795729 0.808510509 0.208523672 0.172557745 1125.714895 1205872.571 0.047172231 0.08163125 5774.866358 -3.761541938 -0.186285221 TTYLVLDEADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TTYLVLDEADR 11 0 P17844;P17844-2;J3KTA4;J3QSF1;J3KRZ1 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;; 218.6 2.44E-11 433308000 1126940 948180 504870 740249 1000400 1015320 967260 1106630 1038730 FALSE TRUE 978012.0237 941951.3431 749026.8207 908333.8494 980493.9972 1054380.017 873455.2741 869985.7863 915932.5227 1.067777374 1.028406918 0.817775111 0.991703894 1.070487152 1.151154688 0.953624042 0.949836112 1 19.80488179 4.472082947 24.99927352 0.988943248 1.057934836 0.08148162 0.085156101 318.5604669 1580653.903 0.022631954 0.060304579 29653.97706 -4.472082947 0.068991588 TTYPIDETMIHNGPPHNSNFGYSYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TTYPIDETMIHNGPPHNSNFGYSYAK 26 0 Q13630;E9PP14;A0A0J9YX13;E9PKL9 Q13630 TSTA3 GDP-L-fucose synthase 0 243.47 1.88E-45 318800000 98445 99140 31294 82423 178080 153230 115530 166370 235330 FALSE TRUE 85435.24382 98488.74281 46427.88307 101138.4019 174536.5564 159124.8573 104325.9184 130793.0702 207509.5555 0.411717155 0.474622687 0.223738531 0.48739154 0.841101298 0.766831469 0.502752358 0.630299024 1 17.66281825 3.41564623 5.724710988 0.714400449 0.376198648 0.594907875 0.144100751 0.151358006 9.769105447 0.042883222 0.055975433 2604.031481 -3.41564623 -0.338201801 TVAEGHGDTLYVGTTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVAEGHGDTLYVGTTR 16 0 O95834;O95834-2;O95834-3;K7EIK7;A0A0C4DGQ7;C9JRL6;K7ELI8;K7EKG3;K7EII6 O95834 EML2 Echinoderm microtubule-associated protein-like 2 0 ; 136.01 1.97E-05 583430000 390470 382080 232027 251951 396780 420040 360080 397980 373910 FALSE TRUE 338868.4002 379570.0913 344236.0333 309160.3254 388884.8543 436199.2106 325159.497 312875.0741 329706.7858 1.027787158 1.151235303 1.044067178 0.937682628 1.17948696 1.322991305 0.986208083 0.948949453 1 18.33082405 2.034989513 24.99972799 0.969852846 1.108809321 0.270983211 0.10222823 229.6560578 164086.5132 0.043675454 0.029445872 108.390074 -2.034989513 0.138956475 DYNPYNYSDSIS(ph)PFNK ddPTM_MDA-MB-175_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 DYNPYNYSDSIS(1)PFNK;DYNPYNYSDSIS(1)PFNK 309.33 1.36E-57 201163000 156207 177315 150877 194164 263820 207878 277610 333230 331680 TRUE FALSE 135563.8492 176150.2061 223841.6219 238251.9038 258570.4982 215875.2012 250687.4249 261971.3577 292469.1683 0.463515009 0.602286412 0.765351176 0.814622291 0.884094893 0.738112679 0.857141375 0.895722989 1 18.15792502 5.06397949 0.606204908 0.892141953 3.82E-19 0.843838255 0.060863347 2.058198161 0.444709992 0.032897399 1.395382342 115872.2633 -5.06397949 -0.892141953 down GYYS(ph)PYSVSGSGSTAGSR ddPTM_MDA-MB-175_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(0.639)PYS(0.359)VS(0.002)GSGSTAGSR;GYYS(0.5)PYS(0.5)VSGSGSTAGSR;GYYS(0.952)PYS(0.04)VS(0.007)GSGSTAGSR 342.9 1.12E-75 3352740000 3261280 1955920 1103330 852480 838890 1146630 939070 944310 952580 TRUE FALSE 2830293.585 1943071.433 1636904.078 1046048.613 822197.7303 1190741.598 847999.1359 742376.6551 839967.0776 3.369529188 2.313270942 1.94877171 1.245344778 0.978845186 1.417605082 1.009562349 0.883816372 1 19.67997326 5.163380538 0.641308574 0.96804113 6.387286662 0.958704105 0.159177063 1.000105994 0.215817344 0.076661739 4.476136885 145673.4944 -5.163380538 5.419245533 up KAAS(ph)LTEDRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KAASLTEDRDR 11 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 KAAS(0.5)LT(0.5)EDRDR;KAAS(0.5)LT(0.5)EDRDR;KAAS(0.823)LT(0.177)EDRDR;KAAS(0.5)LT(0.5)EDRDR 129.01 0.00020003 7459350000 14161200 7425300 3171100 3181280 3168090 2320030 4168930 3792590 2283280 TRUE FALSE 12289761.54 7376522.715 4704654.567 3903638.247 3105051.207 2409283.055 3764627.81 2981574.142 2013353.24 6.104125843 3.663799561 2.336725853 1.938873999 1.542228729 1.196651938 1.869829763 1.480899667 1 20.94116888 5.221293695 0.834136344 1.418631802 13.34097888 0.976996212 0.230461907 0.651379233 0.201718842 0.082425839 8.616444061 166453.7926 -5.221293695 11.92234708 up GYYS(ph)PYSVS(ph)GSGSTAGSR ddPTM_MDA-MB-175_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 GYYS(0.999)PYS(0.021)VS(0.969)GS(0.011)GSTAGSR;GYYS(0.959)PY(0.004)S(0.036)VS(1)GSGSTAGSR 307.02 2.25E-50 304370000 1390110 712080 353200 216038 182678 218661 194758 169108 170059 TRUE FALSE 1206403.441 707402.2996 524008.7014 265092.7298 179043.0652 227073.0302 175870.3991 132945.5702 149954.8188 8.045112864 4.717436262 3.494443898 1.767817347 1.193980071 1.514276314 1.172822591 0.886570844 1 17.19416836 5.279904497 0.66568573 0.960832998 18.82173719 0.989964052 0.227212641 0.532180615 0.108492793 0.10138601 8.450163096 190504.1747 -5.279904497 17.86090419 up TVAISDAAQLPHDYCTT(ph)PGGTLFSTTPGGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 TVAISDAAQLPHDYCT(0.115)T(0.883)PGGT(0.002)LFSTTPGGTR 195.17 2.42E-19 338310000 295130 420580 219800 286240 491000 425810 422900 538440 427870 TRUE FALSE 256127.8227 417817.1823 326096.0152 351235.1669 481230.0606 442191.1862 381887.2231 423298.7961 377287.696 0.678866089 1.107423292 0.864316591 0.930947843 1.275498951 1.172026522 1.012191034 1.121952294 1 18.52530553 3.390211813 9.686482165 1.111839436 0.90456665 0.425720837 0.127658424 0.324355485 33.23356652 0.035011846 0.04520836 2455.906413 -3.390211813 -0.207272785 TVAISDAAQLPHDYCTTPGGTLFSTT(ph)PGGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 TVAISDAAQLPHDYCTTPGGTLFS(0.012)T(0.065)T(0.923)PGGTR;TVAISDAAQLPHDYCTTPGGTLFS(0.04)T(0.193)T(0.766)PGGTR;TVAISDAAQLPHDYCTTPGGTLFST(0.007)T(0.993)PGGTR;TVAISDAAQLPHDYCTTPGGTLFS(0.007)T(0.026)T(0.967)PGGTR 316.46 3.31E-92 14615700000 2102160 3026240 1731290 2922070 4209200 3575250 4003150 4711200 3868790 TRUE FALSE 1824354.23 3006360.43 2568547.635 3585570.655 4125445.155 3712792.181 3614925.129 3703746.543 3411426.054 0.534777598 0.881262083 0.752924904 1.05104745 1.209302236 1.08834022 1.059652202 1.085688649 1 21.70194351 4.369992069 0.980728141 1.090491394 0.482844156 0.778301174 0.092063498 0.544069018 0.631867046 0.031830209 0.310352667 23441.86007 -4.369992069 -0.607647238 TVALWDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 157.86 0.00086109 3060526000 3553340 4459470 2624530 3473430 4877370 4592270 4375060 4900400 4930960 FALSE TRUE 3083757.116 4430175.448 3893761.487 4262125.37 4780319.879 4768937.598 3950767.355 3852487.595 4348027.526 0.709231277 1.018893147 0.895523651 0.980243419 1.099422635 1.096804832 0.908634394 0.886031096 1 22.05192964 4.74388354 24.78320494 0.978333858 0.709231149 0.569395042 0.075315144 440.0611844 2048825.69 0.020374471 0.169162852 55447.70048 -4.74388354 -0.269102709 TVAMHEVFLCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVAMHEVFLCR 11 0 G3V5X9;Q9UNH7;A0A0A0MRI2;Q9UNH7-2 G3V5X9;Q9UNH7-2 SNX6 "Sorting nexin-6;Sorting nexin-6, N-terminally processed" 0 115.18 0.0011584 297680000 209680 216200 129520 146020 192240 216440 177390 233650 231030 FALSE TRUE 181970.2567 214779.768 192156.3052 179176.0728 188414.8001 224766.5869 160186.7451 183685.7658 203717.8966 0.893246297 1.054299949 0.943247051 0.879530349 0.924880942 1.103322735 0.786316508 0.9016673 1 17.6362132 2.220729487 24.99995602 0.892606582 0.963524618 0.132136802 0.084718713 498.6509195 699123.187 0.033992137 0.022972158 166.2376866 -2.220729487 0.070918036 TVANLLSGKS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVANLLSGKSPR 12 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 TVANLLS(0.001)GKS(0.999)PR;TVANLLS(0.169)GKS(0.831)PR 121.32 0.00022912 4987800000 15024900 13440600 5787000 9445800 12462600 10969400 13400700 15905200 6720800 TRUE FALSE 13039321.4 13352307.81 8585612.556 11590613.26 12214618.64 11391399.92 12101102.18 12503996.75 5926274.68 2.200255996 2.253069345 1.448736857 1.955800884 2.061095596 1.922185611 2.041940819 2.109925278 1 22.49869407 1.234536409 24.98324216 0.999998545 1.99524124 0.671648591 0.21952888 73.12958192 453941.4193 0.401447012 0.053916833 17.16075571 -1.234536409 0.995242695 TVAQQHDEDGIEEEDDDDDEIDDDDTISDWNLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVAQQHDEDGIEEEDDDDDEIDDDDTISDWNLRK 34 1 Q92973-2;Q92973;Q92973-3 Q92973-2 TNPO1 Transportin-1 0 224.78 1.31E-36 42254000 14467 13876 9530.3 11229 17857 13372 13025 17018 11474 FALSE TRUE 12555.1493 13784.84764 14139.18496 13778.71607 17501.68064 13886.42949 11761.8375 13378.83313 10117.55679 1.24092699 1.362468027 1.397490051 1.361861995 1.729832705 1.372508183 1.162517567 1.322338328 1 13.30457333 0.517915612 0.878385051 9.16E-07 1.406269956 0.418763664 0.142220785 7.420751031 1.777767378 13.65540583 0.052665786 3.295456716 -0.517915612 1.406269041 TVART(ph)PLGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVARTPLGQR 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.015)VART(0.985)PLGQR 97.631 0.0063182 0 1193600 1070400 458030 498940 822110 1019600 913170 987160 312350 TRUE FALSE 1035862.736 1063368.472 679534.84 612231.9528 805751.6194 1058824.672 824610.914 776063.5161 275424.3388 3.760970219 3.860836978 2.467228724 2.222868013 2.925491708 3.844339524 2.993965303 2.817701295 1 18.07129653 4.243996073 24.97456781 2.690810123 3.810904132 0.321982595 0.716976255 165.1775271 758926.5546 0.183509627 0.456898366 17538.64642 -4.243996073 1.120094009 TVAS(ph)DLQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TVASDLQK 8 0 Q7L8J4;Q7L8J4-2 Q7L8J4 SH3BP5L SH3 domain-binding protein 5-like 1 TVAS(1)DLQK;TVAS(1)DLQK;TVAS(1)DLQK;TVAS(1)DLQK;TVAS(1)DLQK;TVAS(1)DLQK 155 0.00043633 2759430000 5868760 4788040 3756380 3773590 5070740 4242230 5966720 6538770 6048530 TRUE FALSE 5093188.496 4756587.05 5572977.932 4630441.285 4969842.195 4405431.333 5388068.413 5140504.92 5333479.674 0.95494664 0.891835601 1.044904691 0.868183919 0.931819843 0.825995711 1.010235108 0.963818226 1 22.34664565 TVATPLNQVANPNSAIFGGARPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVATPLNQVANPNSAIFGGARPR 23 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ; 204.5 1.56E-24 1669170000 231340 238280 109301 161532 251800 221250 184800 226910 160069 FALSE TRUE 200767.8329 236714.723 162159.3292 198210.3095 246789.6726 229761.6307 166878.1244 178387.0623 141145.8252 1.422414249 1.677093337 1.148877971 1.404294525 1.748473059 1.627831573 1.182310028 1.263849371 1 17.10682693 2.223158791 24.19834894 1.174104481 1.502986024 0.467888537 0.178332359 160.2851577 251826.711 0.075041952 0.050822541 167.1701725 -2.223158791 0.328881543 TVDGPSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 TVDGPSGK 8 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;; 136.75 0.0018088 8562910000 25425700 24065120 15101270 18642560 13970020 18969260 27033600 29864500 28935500 FALSE TRUE 22065629.32 23907034.64 22404294.68 22875638.18 13692043.93 19699019.71 24411885.63 23478209.08 25514778.15 0.864817605 0.936987753 0.878090907 0.89656426 0.536631902 0.772063139 0.956774364 0.920180804 1 24.60482976 2.229206425 24.82172376 0.950808768 0.813806433 0.273722921 0.110914783 276.4618362 733595.0641 0.048533107 0.033223548 169.5143331 -2.229206425 -0.137002335 TVDGPSGKLWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVDGPSGKLWR 11 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 98.353 0.0050924 375590000 182420 140220 201370 279750 181760 133210 198850 261170 129130 FALSE TRUE 158312.7348 139298.8856 298753.2055 343271.5132 178143.3316 138334.6749 179565.5576 205320.8279 113864.3985 1.390362017 1.223375238 2.623763085 3.014739618 1.564521782 1.214907177 1.577012306 1.803204782 1 16.79695721 3.029040652 24.99932265 1.468795488 2.073945068 0.241510369 0.556368982 351.3888716 302486.8581 0.181292841 0.205564126 1069.154953 -3.029040652 0.60514958 TVDLKPDWGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVDLKPDWGK 10 1 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 101.35 0.0030937 3985300000 5854680 3790930 2422060 3114290 3647950 3043830 4178360 4913830 4273710 FALSE TRUE 5080969.204 3766027.131 3593376.317 3821437.143 3575362.932 3160928.11 3773143.29 3863045.694 3768476.872 1.348281912 0.999349939 0.953535457 1.014053495 0.94875544 0.838781348 1.001238277 1.025094707 1 21.84555011 4.738441495 4.358641729 0.971925386 1.375534069 0.835420215 0.05255736 0.085321793 3.921041935 0.013910263 0.106800857 54757.23307 -4.738441495 0.403608682 TVDSTPLSVHT(ph)PTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TVDSTPLSVHTPTLR 15 0 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;H0Y6V3 Q5VT25-2 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 1 TVDSTPLSVHT(0.781)PT(0.219)LR;TVDSTPLSVHT(0.996)PT(0.004)LR;TVDSTPLSVHT(1)PTLR;TVDSTPLSVHT(0.994)PT(0.006)LR;TVDSTPLSVHT(0.969)PT(0.031)LR 301.7 8.68E-44 3362110000 3055670 3501490 1390497 2514470 4113910 5023580 3047370 3484810 4485310 TRUE FALSE 2651855.467 3478488.482 2062946 3085418.845 4032051.24 5216840.373 2751836.526 2739610.5 3955061.761 0.670496601 0.879502949 0.521596406 0.780119005 1.019466062 1.319028801 0.695775867 0.692684632 1 21.91526879 3.456694868 10.77775484 0.912593898 0.699675638 0.259087864 0.195653681 0.746778128 385.1270146 0.061303194 0.079681649 2862.166328 -3.456694868 -0.21291826 TVDVPASLPT(ph)PPHNNQEELR ddPTM_MDA-MB-175_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 205.38 3.20E-21 332830000 176645 162859 99720 121904 159354 169178 160706 157821 177352 TRUE FALSE 153300.9157 161789.1685 147944.9255 149584.1664 156183.1672 175686.3871 145120.7569 124072.2073 156385.6486 0.980274834 1.034552531 0.94602623 0.956508271 0.998705243 1.123417582 0.927967228 0.793373359 1 17.2547486 2.006561164 24.96715876 0.875550418 1.004401308 0.309077997 0.069626513 148.2067422 563967.6421 0.027848301 0.018724522 101.5222336 -2.006561164 0.128850889 TVEAEAAHGTVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TVEAEAAHGTVTR 13 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;;;;; 270.21 5.54E-26 6506840000 5244160 4438000 1913480 3252310 4862630 4833630 4390840 4886910 4724640 FALSE TRUE 4551130.969 4408846.486 2838845.328 3990796.694 4765873.177 5019582.874 3965017.013 3841882.326 4166098.442 1.09242041 1.058267477 0.681415806 0.957921842 1.14396557 1.204864202 0.951733875 0.922177519 1 21.9902655 3.458230676 24.94108134 1.032182731 0.932826327 0.106998249 0.13594778 586.9593741 774955.1738 0.042321601 0.054645307 2872.305807 -3.458230676 -0.099356404 TVEEAENIAVTSGVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TVEEAENIAVTSGVVR 16 0 O76070 O76070 SNCG Gamma-synuclein 0 ;;; 216.34 3.55E-14 463770000 313623 346253 226834 283193 377876 348888 347488 400910 409861 FALSE TRUE 272176.9259 343978.4412 336531.6811 347496.299 370357.0069 362309.9471 313788.6672 315178.5164 361407.6995 0.753102179 0.951773971 0.931169097 0.961507736 1.02476236 1.002496481 0.868240128 0.872085782 1 18.46326772 4.739826413 24.39162429 0.944956785 0.753102091 0.586612843 0.052085016 65.34780087 1259032.047 0.014256746 0.085818367 54932.12671 -4.739826413 -0.191854694 TVEIVHIDIADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TVEIVHIDIADR 12 0 A0A0A0MSW4;P48739;P48739-3;P48739-2;B3KYB7;B3KYB6 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 ;;; 147.87 6.58E-05 2369990000 1925190 1920600 1187600 1423140 1919440 1900740 1842180 2066000 2013460 FALSE TRUE 1670771.264 1907983.452 1761927.332 1746285.688 1881246.899 1973862.698 1663525.667 1624201.978 1775431.053 0.941051054 1.074659277 0.992394117 0.983584063 1.059600088 1.111765334 0.936970019 0.914821207 1 20.7597379 2.180448514 24.9996005 0.9425756 1.027245866 0.314972739 0.05279755 84.22612702 36232.85045 0.021207646 0.014298199 151.5125174 -2.180448514 0.084670266 TVEMHNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TVEMHNK 7 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;;;; 104.11 0.0082248 1413015000 3604470 2916908 1771023 2623069 2244807 2758887 2802540 3624950 3338930 FALSE TRUE 3128130.157 2897746.639 2627495.647 3218676.908 2200139.733 2865023.168 2530750.102 2849782.652 2944205.499 1.062470048 0.984220239 0.892429434 1.09322427 0.74727791 0.973105705 0.85956979 0.967929261 1 21.48944694 5.292056518 1.05730296 0.929626259 1.341175272 0.16648087 0.091386383 8.802801393 3.557054382 0.026172152 5.392247613 195909.9609 -5.292056518 0.411549013 TVENIKDPLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVENIKDPLFR 11 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 102.66 0.0025887 1594590000 4881800 4376300 2685300 3213000 4598300 4109100 4791500 5535800 5340100 FALSE TRUE 4236657.761 4347551.797 3983920.062 3942560.758 4506802.826 4267179.736 4326821.067 4352012.25 4708799.461 0.899732043 0.923282427 0.846058554 0.837275146 0.957102307 0.906213945 0.918879876 0.924229686 1 22.16692785 -1.999999979 0.610790917 7.935063317 0.889138707 0.482176828 0.034104871 171.8820951 1.334635361 1618.601644 0.01738478 0.01 1.999999979 -7.04592461 TVEVPFKGDVEHTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVEVPFKGDVEHTIR 15 1 A0A087WWM4;Q9P2T1;Q9P2T1-3;F8WAN9;H0YNJ6;Q9P2T1-2;H0YMB3;H0YLV5;H0YK13;H0YK71;H0YMW6;H0YN22 A0A087WWM4 GMPR2 GMP reductase;GMP reductase 2 0 ; 136.01 1.53E-05 412530000 722250 651070 349570 394210 645100 566520 714250 839490 330940 FALSE TRUE 626802.8326 646793.0783 518623.2212 483721.4056 632263.7721 588314.391 644982.1449 659971.5964 291816.6502 2.147933753 2.216436512 1.777222859 1.657620993 2.166647351 2.016041205 2.210230789 2.26159678 1 18.15470268 1.231845842 24.98552894 0.999998188 2.059465672 0.738983099 0.197362503 130.4701638 485431.2064 0.49855512 0.05251356 17.05476903 -1.231845842 1.059467485 TVFAEHISDECK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TVFAEHISDECK 12 0 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ;;;; 213.38 9.33E-09 6522960000 11290330 10931650 3220660 7551730 11595260 10131680 12639250 14425490 14750500 FALSE TRUE 9798284.284 10859839.27 4778181.948 9266465.717 11364537.01 10521452.29 11413497.48 11340711.22 13006712.69 0.753325188 0.834941121 0.367362766 0.71243718 0.873743987 0.808924786 0.877508234 0.87191218 1 23.63275305 3.300652227 4.385137013 0.880912043 0.651731704 0.428398465 0.126968945 0.208583022 7.977095615 0.037845749 0.048464886 1998.261068 -3.300652227 -0.229180339 TVFAEHISDECKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVFAEHISDECKR 13 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ; 191.06 2.52E-06 863070000 1692710 1645080 427920 1047820 1827850 1687520 1913170 2181990 1538130 FALSE TRUE 1469014.085 1634273.361 634863.5433 1285743.546 1791479.361 1752439.986 1727631.068 1715388.419 1356294.024 1.083108868 1.204955071 0.468086958 0.947982903 1.320863566 1.292079708 1.273788012 1.264761467 1 20.37123854 3.289358346 7.213238699 1.240748616 0.910891372 0.348945772 0.205983387 0.238959373 27.48129938 0.060362277 0.077522019 1946.965902 -3.289358346 -0.329857243 TVFDEAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TVFDEAIR 8 0 P63000;J3KSC4;J3QLK0;P60763;P63000-2;B1AH77;B1AH80;P15153 P63000 RAC1;RAC3;RAC2 Ras-related C3 botulinum toxin substrate 1;Ras-related C3 botulinum toxin substrate 3;Ras-related C3 botulinum toxin substrate 2 0 ;; 159.2 0.00083884 391540000 1061830 995760 648460 939320 1110070 1224620 823710 1226680 1221720 FALSE TRUE 921506.4752 989218.787 962057.425 1152606.963 1087981.779 1271731.924 743826.731 964364.028 1077289.653 0.855393415 0.918247738 0.893035055 1.069913703 1.009925024 1.180492099 0.690461222 0.895176172 1 20.03897477 2.231664497 24.99989079 0.861673677 0.985097392 0.201796235 0.118005263 273.9158479 992992.0094 0.048365463 0.033415473 170.4764909 -2.231664497 0.123423715 TVFPGAVPVLPAS(ph)PPPK ddPTM_MDA-MB-175_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 157.12 3.93E-08 621400000 569920 497920 446780 641250 574300 568460 640010 770510 1650740 TRUE FALSE 494603.628 494649.1307 662844.3024 786855.6134 562872.5536 590329.024 577941.9287 605742.4326 1455591.398 0.339795652 0.339826913 0.455378002 0.540574515 0.386696812 0.405559572 0.397049563 0.416148676 1 20.473174 1.238583925 9.055243447 1.00406388 0.411944118 0.912279863 0.057482974 0.023234281 26.77901571 0.084391415 0.014848453 17.32143726 -1.238583925 -0.592119762 TVFPGAVPVLPAS(ph)PPPKDSLR ddPTM_MDA-MB-175_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(0.999)PPPKDS(0.001)LR;TVFPGAVPVLPAS(0.999)PPPKDS(0.001)LR 103.75 0.00026083 7905347000 2636060 2473050 1544241 1875692 2442130 2407480 2904810 3435310 2867160 TRUE FALSE 2287697.992 2456804.372 2291041.113 2301596.537 2393536.391 2500097.313 2623101.973 2700695.69 2528207.611 0.904869514 0.971757367 0.906191842 0.910366904 0.946732531 0.988881333 1.037534244 1.068225441 1 21.26968351 2.552120629 1.99638352 1.043221867 0.926113045 0.789720954 0.025521276 0.134023092 1.075370521 0.011081969 0.008600762 356.5501543 -2.552120629 -0.117108822 TVFS(ph)PTLPAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TVFSPTLPAAR 11 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 TVFS(0.997)PT(0.003)LPAAR;TVFS(0.996)PT(0.004)LPAAR;TVFS(0.998)PT(0.002)LPAAR;T(0.001)VFS(0.999)PTLPAAR 208.79 1.93E-08 1217720000 2338200 2238970 1331410 1484650 2154320 2176680 2016820 2337170 2283300 TRUE FALSE 2029200.946 2224262.059 1975284.329 1821762.474 2111453.247 2260418.288 1821229.107 1837384.383 2013370.875 1.007862471 1.104745323 0.981083194 0.904832039 1.048715501 1.122703381 0.904567126 0.912591121 1 20.94118152 2.20426948 24.99393001 0.932102965 1.024963849 0.287984786 0.065727422 234.4224209 170862.9659 0.027908132 0.018816711 160.0550863 -2.20426948 0.092860884 TVGQLYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVGQLYK 7 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4;P35749;P35749-2;P35749-4;P35749-3;Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 P35579;P35580;P35749;Q7Z406 MYH9;MYH10;MYH11;MYH14 Myosin-9;Myosin-10;Myosin-11;Myosin-14 0 114.6 0.033074 0 236810 246030 179300 168210 267060 235110 266630 303310 299730 FALSE TRUE 205514.9585 244413.8127 266010.0797 206404.6514 261746.0285 244154.8338 240772.2636 238449.5169 264296.2609 0.777593137 0.924772117 1.006484461 0.780959408 0.990350857 0.923792236 0.910993833 0.902205412 1 18.01179649 4.73803866 8.555115705 0.926376191 0.776741357 0.351356616 0.06489707 0.093314511 112.5258965 0.014603451 0.082274312 54706.46592 -4.73803866 -0.149634834 TVHNLYLFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVHNLYLFDR 10 0 Q9Y5R8;I3L1R8;I3L3V5;I3L3S0 Q9Y5R8 TRAPPC1 Trafficking protein particle complex subunit 1 0 137.16 9.86E-05 165930000 122820 184650 79623 102360 200860 187810 158530 179610 187380 FALSE TRUE 106589.0258 183437.022 118128.9491 125602.4025 196863.279 195035.1722 143155.785 141201.7992 165228.1499 0.645102096 1.110204418 0.714944452 0.760175567 1.191463314 1.180399178 0.866412806 0.85458682 1 17.33409997 3.274878867 24.99881643 0.994754014 0.822601985 0.284777974 0.162963279 292.405963 201268.9202 0.04900087 0.063257877 1883.123776 -3.274878867 -0.172152029 TVHTEWTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TVHTEWTQR 9 0 C9JIF9;P13798;H7C393 C9JIF9 APEH Acylamino-acid-releasing enzyme 0 ;;;;; 220.39 4.58E-07 5075010000 851041 894878 469838 641230 855769 833506 723505 840121 831070 FALSE TRUE 738573.7756 888999.4875 697053.2283 786831.0721 838740.8712 865571.5152 653339.5965 660467.662 732821.8514 1.007849008 1.213118148 0.951190562 1.073700342 1.144535837 1.181148616 0.891539458 0.901266332 1 19.483103 2.227228124 24.99415463 0.923112708 1.095326022 0.473087847 0.081610775 175.4730374 387007.8038 0.032318761 0.022004962 168.7439161 -2.227228124 0.172213315 TVIDSQTHYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TVIDSQTHYR 10 0 Q9Y3Q3 Q9Y3Q3 TMED3 Transmembrane emp24 domain-containing protein 3 0 ;;;; 220.82 5.67E-09 2754310000 3566410 3968360 1877490 2732040 4609930 5505160 3300510 3952580 4498330 FALSE TRUE 3095099.882 3942291.582 2785450.444 3352391.439 4518201.412 5716947.068 2980427.048 3107351.526 3966542.552 0.780301696 0.993886119 0.70223637 0.845167144 1.139078014 1.441292257 0.751391674 0.783390443 1 21.9194506 3.401937027 13.54369923 0.993570472 0.830886516 0.174636591 0.20280629 2.232035705 396.9681289 0.064626179 0.083431604 2523.114893 -3.401937027 -0.162683956 TVIDYNGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TVIDYNGER 9 0 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ;;; 203.64 4.16E-05 3894220000 3828870 3470780 2379870 2814950 3851330 4725930 3434200 3289020 2939090 FALSE TRUE 3322875.128 3447980.218 3530783.092 3454127.421 3774696.068 4907739.585 3101151.813 2585688.668 2591634.128 1.282154411 1.330427077 1.36237714 1.332799018 1.456492653 1.893685351 1.196600932 0.997705903 1 21.30543063 2.006362967 24.99084909 1.028228311 1.439424562 0.541976297 0.170714936 120.925956 474940.2476 0.073035042 0.049100891 101.475913 -2.006362967 0.411196251 TVIIHDRPDITHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVIIHDRPDITHPR 14 1 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 0 ; 136.17 1.85E-05 266540000 265300 221087 140314 154515 222099 236519 216566 246743 231343 FALSE TRUE 230239.9328 219634.6649 208170.3197 189599.9924 217679.6644 245618.039 195563.4627 193978.9296 203993.8941 1.128660904 1.07667274 1.020473287 0.929439546 1.067089118 1.204046033 0.958673119 0.950905567 1 17.63816644 TVIQIHMCEEEEGDLLLFLTGQEEIDEACKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVIQIHMCEEEEGDLLLFLTGQEEIDEACKR 31 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 185.02 1.51E-18 32411000 25574 21317 12539 21528 15980 15798 25964 31692 21000 FALSE TRUE 22194.3311 21176.96722 18602.90234 26416.26143 15662.02926 16405.75928 23446.01528 24914.91243 18517.40392 1.198566019 1.143625063 1.004617192 1.42656398 0.845800487 0.885964326 1.266161033 1.345486253 1 14.17659423 AASLT(ph)EDRDR ddPTM_MDA-MB-175_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(0.028)LT(0.972)EDRDR;AAS(0.012)LT(0.988)EDRDR 142.89 0.00022252 780940000 3449300 2020320 956100 955440 879790 784920 1057950 950120 874230 TRUE FALSE 2993466.266 2007048.385 1418473.158 1172387.255 862283.9003 815116.3803 955350.1718 746944.2318 770879.5253 3.883182997 2.603582426 1.840071128 1.520843681 1.118571543 1.057384914 1.239298931 0.968950669 1 19.55614588 5.384217285 0.659007307 1.016610605 9.046089551 0.991891254 0.082866668 0.54250529 0.098010011 0.036993416 3.954643278 242224.0631 -5.384217285 8.029478946 up TVLEGSTAST(ph)SPADHSALPNQSLTVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVLEGSTASTSPADHSALPNQSLTVR 26 0 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 TVLEGS(0.004)T(0.023)AS(0.126)T(0.721)S(0.126)PADHSALPNQSLTVR 119.89 0.0010845 89791000 70593 58687 27204 50421 87957 72821 57727 86274 49829 TRUE FALSE 61263.95619 58301.48123 40359.94539 61869.85869 86206.82778 75622.47099 52128.64443 67824.97649 43938.27239 1.394318731 1.326895166 0.918560134 1.408108588 1.961998574 1.721107064 1.186406329 1.543642315 1 15.42319052 3.490382179 24.92033242 1.498608723 1.214407141 0.153809442 0.287690395 1102.408142 2071676.552 0.082188457 0.115920946 3093.016087 -3.490382179 -0.284201581 TVLELQYVLDKLGDDEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVLELQYVLDKLGDDEVR 18 1 Q14444-2;Q14444;G3V153;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ; 225.11 3.87E-19 1846670000 2269600 2113700 985110 1099300 1938900 1777310 2273900 2467700 392200 FALSE TRUE 1969666.61 2099814.966 1461512.491 1348912.867 1900319.683 1845684.266 2053377.528 1940001.559 345834.5628 5.695401274 6.071732532 4.226045191 3.900457074 5.494880755 5.336899386 5.937456081 5.609623119 1 18.39972253 4.247960808 24.9372582 4.720662989 5.883567377 0.127233282 1.417412658 454.497511 1205685.45 0.351005005 0.90218202 17699.49224 -4.247960808 1.162904387 TVLPTVPES(ph)PEEEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TVLPTVPESPEEEVK 15 0 O75152;E9PBY7;E9PQ61;A0A1W2PPR9 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 TVLPTVPES(1)PEEEVK;TVLPTVPES(1)PEEEVK;TVLPT(0.012)VPES(0.988)PEEEVK;TVLPTVPES(1)PEEEVK 314.51 3.00E-56 453745000 1105330 880010 698180 821320 877160 714400 1035850 1228510 1207340 TRUE FALSE 959257.84 874229.1564 1035822.183 1007813.259 859706.2321 741883.4303 935393.4264 965802.6968 1064609.641 0.90104185 0.821173436 0.972959612 0.94665051 0.807531887 0.696859583 0.878625734 0.907189509 1 20.02189311 1.347105101 2.295170435 1.017930525 0.859191936 0.249742475 0.076881165 0.759637129 5.145644186 0.225261127 0.022212995 22.23848004 -1.347105101 -0.158738588 TVLS(ph)LFDEEEDKMEDQNIIQAPQK ddPTM_MDA-MB-175_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(0.02)VLS(0.98)LFDEEEDKMEDQNIIQAPQK 156.73 1.33E-08 37223000 52634 33419 50277 32573 48041 46199 74250 87142 112600 TRUE FALSE 45678.28354 33199.46839 74591.12537 39969.1975 47085.07809 47976.30542 67049.24643 68507.36144 99288.55627 0.460055874 0.334373564 0.751256017 0.402555934 0.474224622 0.483200756 0.675296821 0.689982451 1 16.59933983 -0.925147652 0.644047107 10 0.474942404 0.679781776 0.112130513 27.26374273 0.820513868 333.8685132 0.050220693 0.118809823 0.925147652 -9.525057596 TVLS(ph)SAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVLSSAR 7 0 Q6GYQ0-2;A0A1B0GUI1;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5;Q6GYQ0-6 Q6GYQ0-2 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 1 T(0.012)VLS(0.98)S(0.008)AR 91.516 0.017147 620410000 1273900 1826900 1176000 945650 1296900 1340300 2055900 1662800 1771800 TRUE FALSE 1105550.887 1814898.974 1744717.533 1160374.286 1271094.227 1391862.208 1856519.134 1307223.16 1562339.822 0.707625109 1.161654429 1.116733702 0.742715681 0.813583709 0.890883141 1.188294062 0.836708596 1 20.57527686 0.942813467 20.67301218 1.906379313 0.940422873 0.013251051 0.171286303 24.94801647 395444.095 48272.07191 0.03973041 8.766242221 -0.942813467 -0.96595644 TVLSANADHMAQIEGLMDDVDFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVLSANADHMAQIEGLMDDVDFK 23 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 74.062 0.018858 156630000 55017 60851 45294 50717 70585 72847 71940 88744 71218 FALSE TRUE 47746.36405 60451.26577 67198.3299 62233.07001 69180.4966 75649.47123 64963.26987 69766.78621 62798.68917 0.760308291 0.962619866 1.070059436 0.990993137 1.101623259 1.204634559 1.034468565 1.110959275 1 15.93844682 5.379424924 0.9569949 1.086323016 1.56E-10 0.73264021 0.060538613 3.010592832 0.920799211 0.019124891 4.532742193 239565.8582 -5.379424924 -1.086323016 TVLSSAR ddPTM_MDA-MB-175_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 ;;; 128.75 0.0086702 4259980000 1725970 1935280 1362080 1304990 1479790 1666830 2135420 1710330 2003900 FALSE TRUE 1497878.691 1922567.018 2020786.444 1601307.925 1450345.074 1730954.029 1928327.297 1344589.239 1767001.225 0.847695333 1.088039437 1.143624812 0.906229097 0.820794606 0.97959979 1.091299355 0.760944147 1 20.75287161 3.692598208 24.93419285 0.917346 1.032611949 0.134704756 0.117598428 698.4017024 378876.2992 0.032193346 0.047750642 4927.177504 -3.692598208 0.115265949 TVMDGGLES(ph)DGPNMTENGLEDESRPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVMDGGLESDGPNMTENGLEDESRPQR 27 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 1 TVMDGGLES(1)DGPNMTENGLEDESRPQR 183.49 8.76E-18 258030000 265690 221470 147160 163200 234260 232850 219930 265110 264560 TRUE FALSE 230578.3933 220015.149 218327.0682 200257.0544 229598.6843 241807.8902 198601.2225 208418.2896 233284.0182 0.988402014 0.943121396 0.935885235 0.858425948 0.984202373 1.036538602 0.851328025 0.893410064 1 17.83172795 TVNSTRET(ph)PPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVNSTRETPPK 11 1 Q5SSJ5;Q5SSJ5-2;Q5SWC8;B0QZK9;B0QZK8;Q5SSJ5-5;B0QZK7;B0QZK5;B0QZK6 Q5SSJ5 HP1BP3 Heterochromatin protein 1-binding protein 3 1 TVNS(0.003)T(0.003)RET(0.993)PPK 73.91 0.068333 555090000 260090 248780 209960 214100 240400 222070 280470 286750 231040 TRUE FALSE 225718.4475 247145.7478 311497.3583 262714.6773 235616.5103 230613.1766 253270.0626 225430.744 203726.7144 1.107947223 1.213123907 1.528996132 1.289544565 1.156532225 1.131973179 1.243185329 1.10653502 1 17.63627565 3.209220923 4.693724874 1.131946034 1.298187294 0.300839287 0.118894613 0.255146375 13.28486215 0.037584025 0.04469523 1618.903355 -3.209220923 0.16624126 TVPFCSTFAAFFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVPFCSTFAAFFTR 14 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 192.68 8.04E-07 483790000 63638 80535 45533 34700 49443 32011 59511 39831 46549 FALSE TRUE 55228.07706 80005.96028 67552.9111 42579.16536 48459.18103 33242.48388 53739.63238 31313.45062 41046.03025 1.345515674 1.949176566 1.645784274 1.037351605 1.180605792 0.809883043 1.309252857 0.762886214 1 15.32495508 3.738319639 4.860986479 1.003488792 1.684249318 0.661403928 0.212189725 0.098336849 7.005497034 0.054488847 0.089424457 5474.187123 -3.738319639 0.680760526 S(ph)PSLSLAPLSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSLSLAPLSPR 12 0 G3V160;Q969H4-2;Q969H4 G3V160 CNKSR1 Connector enhancer of kinase suppressor of ras 1 1 S(0.997)PS(0.003)LSLAPLSPR 149.83 7.09E-05 128340000 100390 65968 41225 38075 45421 44887 38530 54891 46772 TRUE FALSE 87123.20714 65534.65186 61161.54789 46720.51069 44517.21096 46613.83194 34793.36653 43152.98681 41242.66744 2.112453256 1.589001292 1.482967802 1.13281981 1.079396987 1.130233198 0.843625514 1.046319006 1 15.33185002 5.578217597 0.540264289 0.963274763 4.416698386 0.952660249 0.080638508 1.805696185 0.209884131 0.045476451 4.761632827 378632.2459 -5.578217597 3.453423622 up TVPLFPHPPVPSLSTSESKPPPQPS(ph)PPTSPVR ddPTM_MDA-MB-175_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(0.986)PPT(0.008)S(0.005)PVR;TVPLFPHPPVPSLSTSESKPPPQPS(0.996)PPT(0.002)S(0.002)PVR 150.99 1.60E-10 1910830000 2371160 1688280 968810 1154430 1286020 1214060 1427020 1643250 1568000 TRUE FALSE 2057805.198 1677189.578 1437329.756 1416560.976 1260430.718 1260765.674 1288627.82 1291853.775 1382632.826 1.488323696 1.213040473 1.039559982 1.024538799 0.91161637 0.911858629 0.932010144 0.934343342 1 20.39898665 4.925817996 0.936868779 0.936973889 1.959392373 0.96865923 0.0316409 0.434306197 0.240872855 0.010629737 0.489420208 84298.14071 -4.925817996 1.022418483 TVPS(ph)TPTLVVPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVPSTPTLVVPHR 13 0 P12270 P12270 TPR Nucleoprotein TPR 1 T(0.008)VPS(0.591)T(0.401)PTLVVPHR 173.44 1.40E-05 804200000 236000 319710 271450 258730 509100 513730 472840 529830 772620 TRUE FALSE 204812.0021 317609.804 402724.1279 317478.6009 498969.906 533493.5255 426984.0496 416529.9776 681281.7438 0.300627463 0.466194503 0.591127139 0.46600192 0.732398762 0.783073274 0.626736374 0.611391662 1 19.37789202 4.761571185 0.386382466 0.783095542 1.05E-12 0.624126982 0.118097177 5.841983908 0.795022705 0.181555729 2.197466392 57752.55263 -4.761571185 -0.783095542 TVPST(ph)PTLVVPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TVPSTPTLVVPHR 13 0 P12270 P12270 TPR Nucleoprotein TPR 1 T(0.004)VPS(0.123)T(0.872)PT(0.002)LVVPHR;T(0.001)VPS(0.027)T(0.972)PTLVVPHR;T(0.001)VPS(0.031)T(0.968)PTLVVPHR;T(0.001)VPS(0.024)T(0.975)PTLVVPHR;T(0.002)VPS(0.076)T(0.922)PTLVVPHR 175.66 6.58E-05 3283650000 914940 1326460 1153875 1149550 2076530 2233360 1984440 2291890 3180110 TRUE FALSE 794028.3608 1317746.397 1711892.809 1410572.897 2035211.116 2319278.804 1791989.314 1801787.159 2804161.019 0.283160758 0.469925367 0.610483064 0.503028495 0.725782543 0.827084746 0.639046511 0.642540549 1 21.41913776 4.729362308 0.477034683 0.778801593 2.67E-16 0.66850114 0.113130602 3.610757535 0.69410439 0.10295537 1.612454669 53624.38302 -4.729362308 -0.778801593 TVQGS(ph)GHQEHINIHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVQGSGHQEHINIHK 15 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 1 T(0.002)VQGS(0.998)GHQEHINIHK;T(0.11)VQGS(0.89)GHQEHINIHK 158.5 3.04E-06 558550000 281140 298640 199986 307830 364160 362960 486250 449950 461420 TRUE FALSE 243986.6367 296678.2142 296699.8985 377727.5064 356913.9285 376923.3061 439093.5498 353731.694 406871.4533 0.599665164 0.729169402 0.729222697 0.928370628 0.877215459 0.926394081 1.079194783 0.869394231 1 18.63421354 4.128884447 0.800347401 0.965298638 0.549280568 0.805042328 0.062288126 0.522002172 0.46385918 0.026037314 0.168336353 13455.02307 -4.128884447 -0.41601807 TVQGSGHQEHINIHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TVQGSGHQEHINIHK 15 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;; 142.91 1.57E-06 5746800000 5371990 5361390 1929510 4011810 5822300 4876190 5928800 6905300 6255100 FALSE TRUE 4662067.911 5326170.676 2862627.49 4922752.777 5706447.621 5063780.185 5353825.889 5428655.332 5515629.204 0.845246796 0.965650605 0.519002889 0.892509738 1.034595947 0.918078427 0.970664577 0.984231378 1 22.39509404 3.482116665 24.90289649 0.97656686 0.780572011 0.407702697 0.112687515 201.9332574 1006671.067 0.031153931 0.041399445 3034.706292 -3.482116665 -0.195994849 TVQPKPDYGAAVAFFEETAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVQPKPDYGAAVAFFEETAR 20 1 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-3;A0A1B0GV31;C9JYZ0;A0A1B0GVA5;F8WC59;A0A1B0GTG3 A0A1B0GW23 ACY1 Aminoacylase-1 0 91.238 0.0016626 463710000 491970 493450 365740 425170 518710 464970 526480 654640 661600 FALSE TRUE 426954.918 490208.4945 542613.0873 521711.3468 508388.6858 482857.6968 475422.0506 514650.3304 583386.4017 0.731856136 0.840280975 0.930109248 0.894280952 0.871444182 0.827680754 0.814935091 0.882177454 1 19.15409223 7.999990296 0.025851018 1.505696042 4.97E-06 0.272175005 0.060918139 7893.603976 20.24717013 437.4643448 792.6602489 99997765.59 -7.999990296 -1.505691073 TVQS(ph)LEIDLDSMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 18 TVQSLEIDLDSMR 13 0 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;T(0.124)VQS(0.876)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;T(0.001)VQS(0.999)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;T(0.008)VQS(0.992)LEIDLDSMR;TVQS(1)LEIDLDSMR;T(0.001)VQS(0.999)LEIDLDSMR 375.26 1.90E-91 6384750000 6174432 6336284 3948079 4841281 6520633 6597732 6176402 7364916 6763250 TRUE FALSE 5358465.167 6294660.533 5857383.21 5940567.845 6390885.161 6851551.019 5577415.485 5789986.027 5963706.29 0.898512587 1.055494725 0.982171644 0.996120123 1.071629763 1.148874657 0.935226387 0.970870419 1 22.50777778 4.75135902 23.79060664 1.015936717 0.898512439 0.284558708 0.060250344 1606.982181 2987067.498 0.015598386 0.263732068 56410.37938 -4.75135902 -0.117424278 TVQS(ph)PNSSVPSPGLAGPVTMTSVHPPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TVQSPNSSVPSPGLAGPVTMTSVHPPIR 28 0 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 T(0.191)VQS(0.808)PNSSVPSPGLAGPVTMTSVHPPIR;T(0.028)VQS(0.469)PNS(0.082)S(0.408)VPS(0.013)PGLAGPVTMTSVHPPIR;T(0.041)VQS(0.943)PNS(0.008)S(0.008)VPSPGLAGPVTMTSVHPPIR 176.6 5.64E-14 1050580000 297842 275611 82534 214140 317074 359586 310837 344731 345565 TRUE FALSE 258481.4251 273800.4932 122447.7185 262763.7599 310764.8477 373419.5061 280692.0756 271012.9583 304712.6994 0.848279135 0.898552944 0.401846456 0.862332815 1.019861819 1.225480615 0.921169601 0.889404869 1 18.2170901 3.479869535 14.06696776 0.994595342 0.717399954 0.425707724 0.156330066 0.426323056 2153.575015 0.045850591 0.061472651 3019.044641 -3.479869535 -0.277195388 TVQSLEIDLDSMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 15 TVQSLEIDLDSMR 13 0 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;;;; 289.71 3.88E-40 11958640000 13060496 12817474 7418047 9661597 12817551 14337821 12555443 14223304 13527003 FALSE TRUE 11334518.36 12733275.17 11005439.34 11855410.27 12562506.81 14889406.25 11337818.07 11181761.13 11927856.12 0.950256128 1.067524209 0.92266701 0.993926331 1.053207441 1.248288553 0.950532766 0.937449364 1 23.50783142 4.782064226 21.19752566 1.015884324 0.950254772 0.051913463 0.093046119 14855.94467 7237521.138 0.023897891 6.864249886 60543.04028 -4.782064226 -0.065629552 TVQSNS(ph)PISALAPTGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVQSNSPISALAPTGK 16 0 O95292 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 1 T(0.009)VQS(0.265)NS(0.704)PIS(0.023)ALAPTGK 88.385 0.0064489 26994000 59135 38067 28742 51775 61108 43081 49964 81365 78174 TRUE FALSE 51320.15992 37816.93537 42641.72734 63531.30508 59892.07036 44738.35395 45118.49897 63965.72793 68932.35878 0.744500273 0.548609333 0.618602469 0.92164705 0.868852763 0.649018179 0.654532933 0.927949211 1 16.07289376 1.621667803 4.576962306 0.982681123 0.71675595 0.463721177 0.11217338 0.146548903 6.73330791 0.086816609 0.031630158 41.84733471 -1.621667803 -0.265925173 TVQTDHNAVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TVQTDHNAVQR 11 0 O43747;O43747-2 O43747 AP1G1 AP-1 complex subunit gamma-1 0 ;;; 170.04 1.62E-05 1320250000 1519160 1189910 694410 822820 1174700 1283950 1102440 1282240 1222880 FALSE TRUE 1318399.157 1182093.403 1030228.999 1009653.857 1151325.768 1333344.387 995525.5385 1008042.954 1078312.52 1.222650329 1.09624379 0.955408548 0.936327678 1.067710657 1.236510161 0.923225429 0.934833767 1 20.04034393 4.561099078 3.134915917 1.004768673 1.222801206 0.358571346 0.092513768 0.332339075 5.622700642 0.025178208 0.139522964 36399.80673 -4.561099078 0.218032534 TVS(ph)ASS(ph)TGDLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVSASSTGDLPK 12 0 P78362;P78362-2 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 2 T(0.001)VS(0.999)ASS(0.794)T(0.206)GDLPK 188.92 1.26E-05 151320000 471550 382970 347010 410960 507600 438600 642330 666720 668850 TRUE FALSE 409233.4727 380454.2449 514825.1967 504274.7491 497499.7531 455473.2258 580036.9355 524147.1164 589779.315 0.693875594 0.64507899 0.872911585 0.855022779 0.843535439 0.772277383 0.983481314 0.888717361 1 19.1698157 6.420594641 0.211151252 1.015145453 1.49E-14 0.637343611 0.067720434 33.28889751 0.943191894 0.442656087 9.81090427 2633871.851 -6.420594641 -1.015145453 TVS(ph)DLALQNAFGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TVSDLALQNAFGDR 14 0 A0A1X7SBR1;Q7Z3G6 A0A1X7SBR1 PRICKLE2 Prickle-like protein 2 1 T(0.009)VS(0.991)DLALQNAFGDR;TVS(1)DLALQNAFGDR;TVS(1)DLALQNAFGDR 257.46 2.52E-24 311463000 270343 269983 163191 213793 278928 276203 249922 313973 288281 TRUE FALSE 234616.4876 268209.4639 242110.7134 262337.9683 273377.8785 286828.7081 225684.6029 246832.3173 254200.7486 0.922957501 1.055108867 0.952439026 1.032010998 1.075440887 1.128355088 0.887820371 0.971013338 1 17.95560875 2.221119014 24.99999522 0.953995426 1.027906256 0.233964406 0.063771369 367.443643 526673.0183 0.026068011 0.01762011 166.3868555 -2.221119014 0.07391083 TVS(ph)DNS(ph)LSNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVSDNSLSNSR 11 0 Q96RU3-5;Q96RU3-2;Q96RU3;H0Y7W6;Q96RU3-3;B7ZL14;Q96RU3-4 Q96RU3-5 FNBP1 Formin-binding protein 1 2 T(0.002)VS(0.998)DNS(0.999)LS(0.001)NSR 82.109 0.029003 184630000 566030 532550 449310 536150 575920 635970 520820 604810 885680 TRUE FALSE 491227.7014 529051.644 666597.8189 657891.052 564460.3188 660436.1774 470310.9566 475476.0881 780975.9194 0.628992123 0.67742376 0.853544651 0.842396079 0.72276277 0.845654982 0.602209293 0.608822982 1 19.57491854 4.462432767 24.20193518 0.759777557 0.641099989 0.152652234 0.120107165 293.0863363 482912.9881 0.031073017 0.082295093 29002.32181 -4.462432767 -0.118677568 TVS(ph)DNSLSNSR ddPTM_MDA-MB-175_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 TVS(0.998)DNS(0.001)LSNSR;T(0.003)VS(0.97)DNS(0.027)LSNSR;T(0.059)VS(0.941)DNSLSNSR;TVS(0.93)DNS(0.07)LSNSR;T(0.052)VS(0.939)DNS(0.009)LSNSR 251.85 2.38E-20 4464400000 3253960 2435650 1524491 1875580 2687660 2556300 2544380 3025350 2613540 TRUE FALSE 2823940.942 2419650.055 2261739.947 2301459.105 2634180.824 2654642.515 2297626.419 2378402.446 2304570.279 1.225365513 1.04993546 0.981415046 0.998649999 1.143024732 1.151903476 0.996986918 1.032037282 1 21.13606633 TVS(ph)FEALPIMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.004)VS(0.996)FEALPIMR;TVS(1)FEALPIMR 197.07 6.12E-08 592080000 578617 465748 200914 253057 441008 344187 710810 652949 280087 TRUE FALSE 502151.2974 462688.4707 298076.6824 310517.4596 432232.8036 357428.0966 641875.7556 513320.9376 246975.4339 2.033203422 1.873419001 1.206908224 1.257280753 1.75010444 1.447221252 2.598945755 2.078429135 1 17.91400802 TVS(ph)PGSVS(ph)PIHGQGQVVENLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TVSPGSVSPIHGQGQVVENLK 21 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 2 T(0.007)VS(0.993)PGS(0.02)VS(0.98)PIHGQGQVVENLK;T(0.008)VS(0.992)PGS(0.171)VS(0.829)PIHGQGQVVENLK;T(0.017)VS(0.983)PGS(0.439)VS(0.561)PIHGQGQVVENLK 283.08 2.08E-45 1427310000 2309860 1892090 1260830 1515160 1709210 1624390 1912740 2351530 2302690 TRUE FALSE 2004606.149 1879660.736 1870571.605 1859200.236 1675200.065 1686881.334 1727242.769 1848673.609 2030468.611 0.987262811 0.925727552 0.92125118 0.915650813 0.825031254 0.830784246 0.850662138 0.91046648 1 20.95338129 4.598084304 1.13489103 0.884488181 1.014927841 0.271106949 0.050453982 1.870184824 2.415078311 0.016696687 0.275129025 39635.49661 -4.598084304 0.13043966 TVS(ph)PPIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TVSPPIR 7 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 TVS(1)PPIR;TVS(1)PPIR;TVS(1)PPIR 139.74 0.0028023 6436800000 393968 352119 259422 327256 395800 405890 340480 408580 484540 TRUE FALSE 341904.1306 349805.9071 384879.3469 401564.4766 387924.3544 421504.8509 307460.302 321208.3466 427258.2332 0.800228302 0.818722449 0.900812008 0.939863636 0.907938863 0.986534181 0.719612352 0.751789718 1 18.70474877 1.209618816 24.20945824 1.000001256 0.851171224 0.233718956 0.083472405 4006.810392 3351371.963 2.309304337 0.022750908 16.20387247 -1.209618816 -0.148830032 TVS(ph)PPIRK ddPTM_MDA-MB-175_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(0.022)VS(0.978)PPIRK;T(0.014)VS(0.986)PPIRK;T(0.008)VS(0.992)PPIRK;T(0.004)VS(0.996)PPIRK;T(0.001)VS(0.999)PPIRK;T(0.221)VS(0.779)PPIRK;T(0.12)VS(0.88)PPIRK 101.97 0.0030958 11633150000 8513440 7919360 4889730 6292900 7605430 6957820 8636720 9814550 7378400 TRUE FALSE 7388367.334 7867337.203 7254419.783 7721799.126 7454096.823 7225491.838 7799132.224 7715784.859 6506133.958 1.135600248 1.209218447 1.115012361 1.186849084 1.145702943 1.110566103 1.198735267 1.185924684 1 22.6333691 1.233567223 24.97144396 0.999999746 1.16272395 0.684517856 0.034320551 87.73199197 438686.1131 0.065554359 0.008076137 17.12250192 -1.233567223 0.162724204 TVS(ph)PSTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TVSPSTIR 8 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 1 T(0.003)VS(0.994)PS(0.004)TIR;T(0.013)VS(0.943)PS(0.044)TIR;T(0.007)VS(0.991)PS(0.003)TIR;T(0.002)VS(0.838)PS(0.152)T(0.007)IR;T(0.007)VS(0.993)PSTIR;T(0.016)VS(0.969)PS(0.015)TIR 150.62 0.00051008 3183350000 8989140 8954500 5021140 6248520 8635160 9060100 8095990 9395890 8562230 TRUE FALSE 7801202.373 8895677.3 7449380.099 7667341.969 8463337.21 9408647.91 7310842.136 7386652.042 7550012.924 1.033270069 1.178233387 0.986671172 1.015540244 1.120969897 1.246176398 0.968321804 0.978362834 1 22.84804768 TVS(ph)QQS(ph)FDGVSLDSSGPEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVSQQSFDGVSLDSSGPEDR 20 0 H7C1J4;Q6BDS2 H7C1J4 UHRF1BP1 UHRF1-binding protein 1 2 T(0.009)VS(0.991)QQS(1)FDGVSLDSSGPEDR 206.28 2.19E-25 0 156910 134570 69388 79901 143200 103240 187160 166070 135610 TRUE FALSE 136173.9459 133686.0008 102944.2689 98043.74326 140350.6002 107211.7096 169009.252 130557.2229 119578.3403 1.138784379 1.117978394 0.860893943 0.819912227 1.173712562 0.896581349 1.413376801 1.091813305 1 16.86759657 TVS(ph)SPIPYTPS(ph)PSSSRPIS(ph)PGLS(ph)YASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 4 T(0.087)VS(0.456)S(0.456)PIPY(0.04)T(0.04)PS(0.579)PS(0.161)S(0.16)S(0.169)RPIS(0.797)PGLS(0.549)Y(0.192)AS(0.113)HT(0.088)VGFT(0.097)PPT(0.005)S(0.005)LT(0.005)R 89.979 0.00025313 59101000 16642 17249 12569 15898 22992 31210 22172 25193 24355 TRUE FALSE 14442.71753 17135.69018 18647.41044 19507.88389 22534.50418 32410.6689 20021.76285 19805.673 21475.77965 0.672511908 0.797907711 0.86829958 0.908366737 1.049298538 1.509173098 0.93229504 0.922233015 1 14.39042289 3.806403168 1.473920216 1.066122573 0.726353329 0.41463384 0.167877792 0.496616576 2.06786775 0.058015282 0.146051718 6403.289955 -3.806403168 -0.339769244 TVS(ph)SPIPYTPSPSSSRPIS(ph)PGLSY(ph)ASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 T(0.151)VS(0.633)S(0.191)PIPY(0.016)T(0.017)PS(0.014)PS(0.003)S(0.005)S(0.005)RPIS(0.907)PGLS(0.339)Y(0.424)AS(0.272)HT(0.022)VGFT(0.001)PPTSLTR 73.993 0.0026531 396840000 27007 37933 28371 29185 61028 77622 65374 63589 59790 TRUE FALSE 23437.95652 37683.81563 42091.3105 35811.90031 59813.6622 80608.16857 59034.03954 49990.9872 52721.69431 0.444560002 0.714768676 0.79836794 0.679263077 1.134517071 1.528937369 1.119729559 0.948205247 1 15.68610911 3.239129002 8.300259583 1.139135224 0.672428302 0.654561702 0.175662731 0.081306274 50.24300697 0.057065412 0.069176701 1734.319079 -3.239129002 -0.466706921 TVS(ph)SPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 TVS(0.5)S(0.5)PIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR;T(0.009)VS(0.837)S(0.155)PIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 288.22 4.18E-78 1381480000 161963 348790 222345 268530 565110 646970 495110 585190 500310 TRUE FALSE 140559.1792 346498.7755 329871.7857 329503.8407 553865.4166 671859.3545 447094.3084 460051.6725 441163.9218 0.318609869 0.785419565 0.747730649 0.746896617 1.255463988 1.522924522 1.013442592 1.042813453 1 18.75095529 3.335681558 4.779055257 1.156944801 0.652033208 0.636727121 0.195105595 0.152689774 5.892244806 0.060523777 0.078344949 2166.115238 -3.335681558 -0.504911592 TVSASS(ph)TGDLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TVSASSTGDLPK 12 0 P78362;P78362-2 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 1 TVSASS(0.996)T(0.004)GDLPK;TVSASS(0.997)T(0.003)GDLPK;TVSAS(0.002)S(0.995)T(0.004)GDLPK;TVSAS(0.001)S(0.995)T(0.004)GDLPK 293.43 3.62E-36 1319200000 4227780 3693020 2519760 3199710 3943250 2933280 4321020 5448600 4381350 TRUE FALSE 3669068.161 3668760.308 3738324.364 3926253.06 3864787.04 3046125.18 3901968.145 4283459.291 3863391.794 0.949701288 0.949621603 0.967627557 1.016271005 1.000361145 0.78845878 1.009985099 1.108730235 1 21.88143656 2.003323204 24.99998569 1.061299415 0.947852058 0.325467457 0.066038285 99.96029679 751982.6239 0.027042145 0.018129418 100.768131 -2.003323204 -0.113447358 TVSLGAGAKDELHIVEAEAMNYEGS(ph)PIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TVSLGAGAKDELHIVEAEAMNYEGSPIK 28 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNY(0.029)EGS(0.971)PIK 220.42 1.56E-34 718517000 817887 568297 440524 486330 569756 459071 742446 909454 501702 TRUE FALSE 709801.1607 564563.8196 653562.8799 596758.6596 558418.9703 476731.7584 670443.7012 714974.3395 442391.3611 1.604464334 1.276163753 1.477340964 1.34893832 1.262273678 1.077624475 1.515499081 1.616158005 1 18.75496369 4.749552848 23.62576703 1.350056749 1.604464653 0.166183854 0.189827025 1568.322596 3370675.181 0.047441551 0.650173124 56176.26336 -4.749552848 0.254407903 TVSLGAGAKDELHIVEAEAMNYEGS(ph)PIKVTLATLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TVSLGAGAKDELHIVEAEAMNYEGSPIKVTLATLK 35 2 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 T(0.002)VS(0.002)LGAGAKDELHIVEAEAMNY(0.465)EGS(0.522)PIKVT(0.008)LATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNY(0.029)EGS(0.927)PIKVT(0.044)LATLK;TVSLGAGAKDELHIVEAEAMNY(0.12)EGS(0.878)PIKVT(0.002)LATLK;TVSLGAGAKDELHIVEAEAMNYEGS(0.999)PIKVT(0.001)LATLK;TVSLGAGAKDELHIVEAEAMNY(0.003)EGS(0.996)PIKVTLATLK 347.98 1.75E-132 4410663000 3785945 2546877 1381028 1447157 2209731 1509196 3661371 4149059 801907 TRUE FALSE 3285622.776 2530146.397 2048897.76 1775756.115 2165761.676 1567255.747 3306291.804 3261815.021 707106.468 4.646574349 3.578168935 2.897580284 2.511299494 3.062850892 2.216435314 4.675804781 4.612905084 1 19.43156793 2.240727932 24.99955369 3.728024384 3.12675595 0 1.197270893 196.7946971 2270031.829 0.464583002 0.341885385 174.0716044 -2.240727932 -0.601268434 TVSLGAGAKDELHIVEAEAMNYEGSPIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TVSLGAGAKDELHIVEAEAMNYEGSPIK 28 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;; 178.53 1.01E-17 995890000 1172940 878576 469362 530301 760932 623274 1029773 1303610 302273 FALSE TRUE 1017933.007 872804.5764 696347.0331 650713.9472 745790.9419 647251.7541 929905.773 1024843.146 266538.6303 3.819082457 3.274589411 2.612555757 2.441349483 2.798059483 2.428360022 3.488821759 3.845007927 1 18.02398512 4.519166943 3.17778922 2.800159513 3.796791737 0.192394306 0.754472358 0.511325243 9.558790989 0.194364838 0.952212012 33049.65594 -4.519166943 0.996632224 TVSLPLS(ph)SPNIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVSLPLSSPNIK 12 0 Q8IWZ3-6;Q8IWZ3;Q8IWZ3-4;H0Y785;H0Y472;H0Y4P6;H0Y7Y3;A0A0A0MQZ8 Q8IWZ3-6;A0A0A0MQZ8 ANKHD1 Ankyrin repeat and KH domain-containing protein 1 1 TVSLPLS(0.741)S(0.259)PNIK 137.16 0.00010191 142130000 262940 258920 172970 194350 266610 241390 286350 325330 292510 TRUE FALSE 228191.8128 257219.1375 256618.8705 238480.138 261304.9826 250676.4295 258579.8211 255760.7112 257929.801 0.884705109 0.99724474 0.994917491 0.924593192 1.01308566 0.971878505 1.002520143 0.991590387 1 17.97661895 4.742192456 24.78742503 0.986710044 0.884705065 0.632456337 0.024501459 201.1381216 1372710.476 0.005697827 0.040794421 55232.2144 -4.742192456 -0.102004979 TVSLPLSS(ph)PNIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVSLPLSSPNIK 12 0 Q8IWZ3-6;Q8IWZ3;Q8IWZ3-4;H0Y785;H0Y472;H0Y4P6;H0Y7Y3;A0A0A0MQZ8 Q8IWZ3-6;A0A0A0MQZ8 ANKHD1 Ankyrin repeat and KH domain-containing protein 1 1 TVSLPLS(0.368)S(0.632)PNIK;TVSLPLS(0.281)S(0.719)PNIK 203.87 1.26E-07 407680000 1598700 1666840 1049310 1299820 1677010 1569870 1771510 2168800 1885810 TRUE FALSE 1387427.744 1655890.418 1556759.826 1594963.998 1643640.782 1630263.915 1599709.233 1705018.998 1662871.69 0.834356465 0.995801677 0.936187581 0.959162398 0.988435122 0.980390685 0.962016037 1.025346097 1 20.66524542 5.454106327 1.650234481 0.983587978 2.66E-16 0.745428602 0.026346979 5.30932291 2.400624767 0.007460428 14.85358574 284515.7593 -5.454106327 -0.983587978 TVSLT(ph)PS(ph)PTTQVETPDLVDHDNT(ph)SPLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 3 T(0.006)VS(0.033)LT(0.96)PS(0.962)PT(0.018)T(0.018)QVET(0.003)PDLVDHDNT(0.629)S(0.37)PLFR 97.099 0.0020625 75340000 53097 54168 45556 49356 59342 70505 62436 66366 81491 TRUE FALSE 46080.09692 53812.16684 67587.03398 60563.03416 58161.2103 73217.37297 56380.96633 52174.14736 71857.22681 0.641272965 0.748876198 0.940573927 0.84282454 0.809399595 1.018928453 0.784624857 0.726080725 1 16.13284564 4.470862058 4.674847179 0.858229603 0.660466446 0.403799143 0.093604676 0.189370312 10.90428216 0.023952269 0.08071512 29570.73084 -4.470862058 -0.197763157 TVSLT(ph)PS(ph)PTTQVETPDLVDHDNTSPLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 2 TVS(0.01)LT(0.99)PS(0.963)PT(0.035)T(0.002)QVETPDLVDHDNTSPLFR 144.51 1.82E-07 115190000 103100 89405 52025 63492 78996 88903 80230 88689 96679 TRUE FALSE 89475.07378 88817.69267 77184.46401 77908.82901 77424.13415 92323.15594 72449.30695 69723.54753 85249.71876 1.049564445 1.041853204 0.905392594 0.913889572 0.908203983 1.082973144 0.849848046 0.817874223 1 16.37940745 4.242722108 24.0854355 0.916395314 1.045708935 0.30866381 0.073859499 76.16618229 440799.159 0.019561369 0.047949606 17487.27372 -4.242722108 0.129313621 TVSLT(ph)PSPTT(ph)QVETPDLVDHDNTSPLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 2 TVS(0.017)LT(0.981)PS(0.07)PT(0.203)T(0.729)QVETPDLVDHDNTSPLFR 168.01 8.89E-12 130240000 117130 100760 75226 82413 85635 114590 99952 102480 125840 TRUE FALSE 101650.9737 100098.1009 111605.5452 101126.1313 83931.03104 118998.3514 90258.67042 80565.4495 110963.3386 0.916077103 0.902082636 1.005787557 0.91134723 0.756385236 1.07241142 0.813409831 0.726054664 1 16.75972357 TVSLTPS(ph)PTTQVETPDLVDHDNT(ph)SPLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 2 T(0.003)VS(0.01)LT(0.146)PS(0.817)PT(0.011)T(0.012)QVET(0.003)PDLVDHDNT(0.521)S(0.477)PLFR 77.804 0.013021 724920000 33051 31694 25782 34749 43226 43305 42630 51489 58347 TRUE FALSE 28683.22661 31485.80003 38250.26144 42639.29156 42365.88717 44970.97137 38495.74916 40478.47804 51449.28413 0.557504873 0.611977417 0.743455659 0.828763554 0.823449498 0.87408352 0.74822711 0.78676465 1 15.65086338 4.180138663 1.763551255 0.833725147 0.551471199 0.724103657 0.065840549 0.220720436 1.271733768 0.018798452 0.073069621 15140.44579 -4.180138663 -0.282253948 TVSLTPS(ph)PTTQVETPDLVDHDNTS(ph)PLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 2 TVSLT(0.004)PS(0.975)PT(0.009)T(0.011)QVETPDLVDHDNT(0.137)S(0.862)PLFR;T(0.005)VS(0.015)LT(0.168)PS(0.73)PT(0.038)T(0.043)QVET(0.001)PDLVDHDNT(0.305)S(0.694)PLFR;TVSLTPS(0.985)PT(0.006)T(0.008)QVETPDLVDHDNT(0.295)S(0.705)PLFR;TVSLT(0.002)PS(0.983)PT(0.003)T(0.012)QVETPDLVDHDNT(0.148)S(0.852)PLFR 251.21 5.23E-47 2001236000 634663 725092 495909 733641 936935 926963 773676 1002867 1279733 TRUE FALSE 550790.6765 720328.8229 735732.2511 900225.4021 918291.8266 962623.8664 698645.0206 788411.6964 1128444.423 0.488097301 0.638337882 0.651988026 0.797757855 0.813767881 0.853053856 0.619122224 0.698671269 1 20.10590393 4.44954616 1.203632669 0.778350587 0.445537666 0.494914774 0.10214696 0.91207494 1.62650022 0.032415723 0.336436149 28154.39246 -4.44954616 -0.332812921 TVSLTPSPTTQVETPDLVDHDNT(ph)SPLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 TVSLTPSPTTQVETPDLVDHDNT(0.5)S(0.5)PLFR 136.03 3.35E-05 2491000000 473990 614920 312350 432920 674840 565220 606410 688150 897390 TRUE FALSE 411351.0206 610880.55 463403.5047 531221.1028 661412.0043 586964.3791 547600.4515 540994.4777 791301.5765 0.519841022 0.771994608 0.585621865 0.671325723 0.835853262 0.741770769 0.692024972 0.683676734 1 19.59386811 1.237501018 24.93894975 1.000000373 0.693013909 0.54868663 0.088881136 19.88701138 467830.0405 0.124149872 0.02083727 17.27830032 -1.237501018 -0.306986465 TVSLTPSPTTQVETPDLVDHDNTS(ph)PLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 TVSLTPSPTTQVETPDLVDHDNT(0.362)S(0.638)PLFR;TVSLTPSPTTQVETPDLVDHDNT(0.253)S(0.747)PLFR;TVSLTPSPTTQVETPDLVDHDNT(0.048)S(0.952)PLFR;TVSLTPSPTTQVETPDLVDHDNT(0.036)S(0.964)PLFR;TVSLTPSPTTQVETPDLVDHDNT(0.208)S(0.792)PLFR 319.95 3.07E-83 6055610000 1071405 1268299 787350 1032425 1449121 1375703 1241859 1510904 1873180 TRUE FALSE 929816.1147 1259967.46 1168115.094 1266852.876 1420286.327 1428627.185 1121423.705 1187808.937 1651734.794 0.562933056 0.762814627 0.707204993 0.766983223 0.859875527 0.864925283 0.678936903 0.71912812 1 20.65555063 5.452251384 0.927431425 0.797975305 1.96E-13 0.399229724 0.092342752 8.106956831 2.132627038 0.030748182 8.932308052 283303.1374 -5.452251384 -0.797975305 TVSPDRLELEAAQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TVSPDRLELEAAQK 14 1 Q14974;J3QR48 Q14974 KPNB1 Importin subunit beta-1 0 ;;; 269.87 7.44E-26 1893780000 1578975 1442026 1049517 1088928 1491282 1320024 1985407 2086030 1566775 FALSE TRUE 1370309.453 1432553.236 1557066.932 1336185.746 1461608.406 1370806.177 1792862.535 1639948.718 1381552.644 0.991861916 1.036915417 1.127041331 0.967162381 1.057946226 0.992221457 1.297715684 1.1870331 1 20.39785911 2.26301735 24.99998949 1.172557339 1.032205049 0.356630219 0.083523632 224.7568397 229748.7339 0.030703969 0.023771818 183.2387626 -2.26301735 -0.14035229 TVSPGS(ph)VSPIHGQGQVVENLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVSPGSVSPIHGQGQVVENLK 21 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 1 TVSPGS(0.788)VS(0.212)PIHGQGQVVENLK;TVSPGS(0.5)VS(0.5)PIHGQGQVVENLK 404.02 1.08E-151 2897800000 3284800 3072500 1984470 2502890 3188300 2826700 3584700 4217300 3922700 TRUE FALSE 2850705.357 3052316.545 2944166.33 3071209.429 3124859.068 2935444.978 3237056.346 3315463.214 3458962.875 0.824150319 0.88243692 0.85117026 0.887898928 0.903409253 0.848648882 0.935845935 0.958513674 1 21.7219081 -1.999999998 0.351585448 2.771339181 0.848126442 0.801725561 0.023906739 31.38669662 0.485958528 39.54466263 0.030646118 0.01 1.999999998 -1.923212738 TVSPGSVS(ph)PIHGQGQVVENLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TVSPGSVSPIHGQGQVVENLK 21 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 1 TVSPGS(0.019)VS(0.981)PIHGQGQVVENLK;TVSPGS(0.428)VS(0.572)PIHGQGQVVENLK;TVSPGS(0.111)VS(0.889)PIHGQGQVVENLK;TVSPGS(0.015)VS(0.985)PIHGQGQVVENLK 393.98 1.48E-131 4136190000 1794320 1806030 1087592 1411620 1880970 1659120 2130640 2327570 2182010 TRUE FALSE 1557196.066 1794166.07 1613555.129 1732149.896 1843542.377 1722947.42 1924010.861 1829837.269 1924055.264 0.809330218 0.932491963 0.838622029 0.90025995 0.958154587 0.895477096 0.999976922 0.951031555 1 20.87571881 7.999999986 0.081294071 1.190091976 0.241768366 0.611569627 0.038992969 286.6839942 2.207181437 5.04176324 32.02209702 99999996.74 -7.999999986 -0.948323611 TVSS(ph)PIPYT(ph)PSPSSSRPIS(ph)PGLSYASHTVGFT(ph)PPTSLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 4 T(0.03)VS(0.153)S(0.818)PIPY(0.081)T(0.377)PS(0.524)PS(0.013)S(0.013)S(0.019)RPIS(0.969)PGLS(0.034)Y(0.024)AS(0.079)HT(0.213)VGFT(0.641)PPT(0.006)S(0.004)LT(0.003)R 145.9 4.14E-10 152310000 44034 55756 36997 61026 87192 103030 94511 83206 86717 TRUE FALSE 38214.79533 55389.73516 54888.87295 74882.88602 85457.04979 106993.6308 85345.33777 65413.04441 76465.41505 0.499765748 0.72437631 0.71782613 0.97930399 1.117590871 1.399242137 1.116129922 0.855459221 1 16.22251975 3.804392475 1.866930207 1.083731806 0.603533903 0.679029568 0.143217569 0.247592703 1.673510595 0.049263685 0.108062566 6373.712572 -3.804392475 -0.480197903 TVSS(ph)PIPYTPS(ph)PSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 T(0.002)VS(0.122)S(0.876)PIPY(0.005)T(0.037)PS(0.957)PS(0.003)S(0.012)S(0.05)RPIS(0.935)PGLSYASHTVGFTPPTSLTR;T(0.074)VS(0.435)S(0.491)PIPY(0.002)T(0.012)PS(0.955)PS(0.061)S(0.055)S(0.05)RPIS(0.725)PGLS(0.069)Y(0.014)AS(0.049)HT(0.008)VGFTPPTSLTR 218.93 8.71E-31 667340000 139127 145707 79646 102089 136993 143964 120942 147765 118347 TRUE FALSE 120741.0144 144749.8411 118163.072 125269.8678 134267.1073 149502.3882 109213.0635 116166.6047 104356.1525 1.157009065 1.387075296 1.132305755 1.200407114 1.28662378 1.432616905 1.046541683 1.113174469 1 16.67115613 2.203995478 24.99999012 1.06544608 1.263387613 0.517798235 0.096529295 151.3150215 109440.8624 0.038594103 0.026021464 159.9541375 -2.203995478 0.197941533 TVSS(ph)PIPYTPS(ph)PSSSRPISPGLSYASHT(ph)VGFTPPTSLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 T(0.024)VS(0.136)S(0.84)PIPY(0.13)T(0.109)PS(0.721)PS(0.053)S(0.049)S(0.045)RPIS(0.074)PGLS(0.108)Y(0.011)AS(0.078)HT(0.311)VGFT(0.279)PPT(0.012)S(0.011)LT(0.009)R 122.15 2.33E-06 374680000 39487 40553 27912 36852 65233 66176 64970 69933 61693 TRUE FALSE 34268.6929 40286.60467 41410.33656 45219.80985 63934.99093 68721.83354 58669.2194 54978.37217 54399.72382 0.629942406 0.740566346 0.761223287 0.831250725 1.175281535 1.263275412 1.078483773 1.010636972 1 15.73131171 3.390775786 3.921316616 1.09881712 0.722743033 0.828378512 0.083681658 0.102118107 3.013724672 0.028327358 0.037607409 2459.097714 -3.390775786 -0.376074087 TVSS(ph)PIPYTPSPSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 TVSSPIPYTPSPSSSR 16 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 TVS(0.002)S(0.998)PIPYTPSPSSSR;TVSS(1)PIPYTPSPSSSR;TVSS(1)PIPYTPSPSSSR;TVSS(1)PIPYTPSPSSSR;TVSS(1)PIPYTPSPSSSR;T(0.026)VS(0.144)S(0.83)PIPYTPSPSSSR;TVS(0.427)S(0.573)PIPYTPSPSSSR 317.17 7.35E-58 6815700000 2858058 2879566 2267725 3185370 3308100 3190980 2976910 3546520 8706130 TRUE FALSE 2480358.394 2860649.941 3364404.395 3908656.944 3242275.282 3313739.065 2688209.726 2788124.297 7676901.229 0.323093696 0.372630812 0.438250317 0.509145139 0.42234167 0.431650606 0.350168596 0.363183557 1 22.87209266 1.236279947 24.99999551 1.000000773 0.40235747 0.92623198 0.053097497 16.52151437 181061.249 0.091824601 0.014157427 17.22978854 -1.236279947 -0.597643303 TVSS(ph)PIPYTPSPSSSRPIS(ph)PGLSYASHTVGFT(ph)PPTSLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 T(0.029)VS(0.152)S(0.819)PIPY(0.038)T(0.038)PS(0.031)PS(0.027)S(0.027)S(0.027)RPIS(0.502)PGLS(0.16)Y(0.145)AS(0.047)HT(0.119)VGFT(0.833)PPT(0.002)S(0.002)LT(0.002)R;T(0.055)VS(0.175)S(0.355)PIPY(0.132)T(0.121)PS(0.115)PS(0.095)S(0.095)S(0.095)RPIS(0.446)PGLS(0.167)Y(0.159)AS(0.089)HT(0.177)VGFT(0.557)PPT(0.058)S(0.056)LT(0.053)R 124.21 1.39E-06 8416300000 104231 126981 92802 166147 222357 255346 228327 268792 206636 TRUE FALSE 90456.60926 126146.8535 137681.3576 203873.2157 217932.5307 265169.3259 206183.8827 211312.9225 182207.7275 0.496447711 0.692324388 0.755628532 1.11890543 1.196066346 1.455313282 1.131586928 1.159736338 1 17.47522462 3.865810975 1.822064922 1.196420611 0.572449001 0.821184184 0.118826663 0.148978862 0.956796271 0.036719086 0.087547275 7341.942429 -3.865810975 -0.62397161 TVSS(ph)PIPYTPSPSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 T(0.031)VS(0.155)S(0.814)PIPY(0.001)T(0.066)PS(0.053)PS(0.166)S(0.15)S(0.135)RPIS(0.423)PGLS(0.005)YAS(0.001)HTVGFTPPTSLTR;T(0.006)VS(0.167)S(0.827)PIPYT(0.017)PS(0.046)PS(0.03)S(0.026)S(0.023)RPIS(0.851)PGLS(0.008)YAS(0.001)HTVGFTPPTSLTR;T(0.008)VS(0.149)S(0.843)PIPYT(0.004)PS(0.01)PS(0.117)S(0.102)S(0.088)RPIS(0.677)PGLS(0.001)YASHTVGFTPPTSLTR 153.4 1.58E-13 12671900000 2136230 2041010 898398 1504901 2087390 1888750 1937290 2453250 1727290 TRUE FALSE 1853921.793 2027602.471 1332866.278 1846611.773 2045855.023 1961411.435 1749411.914 1928641.579 1523091.744 1.217209535 1.331241193 0.875105707 1.212410073 1.343225076 1.287782855 1.148592605 1.266267503 1 20.53857141 1.228998038 24.99181505 0.999999583 1.20992371 0.199483938 0.132349594 681.897815 1782011.602 0.408522546 0.032171074 16.94330145 -1.228998038 0.209924127 TVSS(ph)PIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 T(0.005)VS(0.136)S(0.83)PIPY(0.011)T(0.003)PS(0.003)PS(0.003)S(0.003)S(0.003)RPIS(0.001)PGLS(0.001)Y(0.001)ASHTVGFTPPTSLTR;TVS(0.005)S(0.994)PIPYT(0.001)PSPSSSRPISPGLSYASHTVGFTPPTSLTR 242.84 1.49E-50 4081100000 820640 689390 237373 352550 646150 613690 538480 599800 414910 TRUE FALSE 712190.3448 684861.3517 352167.3768 432601.8659 633292.8792 637299.0514 486258.2925 471537.4376 365859.8125 1.946620865 1.871922874 0.962574639 1.182425211 1.73097142 1.74192144 1.329083643 1.288847317 1 18.48093143 4.348610056 8.243569548 1.342690371 1.925364523 0.472491933 0.258613913 0.223040568 15.25120304 0.068740017 0.183007722 22315.67642 -4.348610056 0.582674153 TVSS(ph)PPT(ph)SPRPGSAATVSASTSNIIPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 2 T(0.057)VS(0.445)S(0.499)PPT(0.528)S(0.471)PRPGSAATVSASTSNIIPPR;T(0.001)VS(0.144)S(0.854)PPT(0.546)S(0.455)PRPGSAATVSASTSNIIPPR;T(0.007)VS(0.163)S(0.828)PPT(0.501)S(0.501)PRPGSAATVSASTSNIIPPR;TVS(0.126)S(0.873)PPT(0.532)S(0.468)PRPGSAATVSASTSNIIPPR;T(0.024)VS(0.146)S(0.828)PPT(0.537)S(0.465)PRPGSAATVSASTSNIIPPR;T(0.069)VS(0.441)S(0.481)PPT(0.525)S(0.483)PRPGSAATVSASTSNIIPPR 157.5 9.23E-09 7427550000 1543930 1395976 883391 1007447 1597128 1540849 1510757 1625172 1509225 TRUE FALSE 1339895.739 1386805.742 1310601.842 1236203.239 1565348.278 1600126.458 1364244.019 1277641.615 1330806.14 1.006830145 1.042079459 0.984818001 0.928913087 1.176240649 1.202373817 1.025126033 0.960050887 1 20.343869 3.271113293 24.99999298 1.061578497 0.993915754 0.205894327 0.078311334 441.79675 339290.7533 0.026132001 0.033733677 1866.866632 -3.271113293 -0.067662743 TVSS(ph)PPTS(ph)PRPGSAATVSASTSNIIPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 2 T(0.001)VS(0.025)S(0.973)PPT(0.191)S(0.81)PRPGSAATVSASTSNIIPPR;T(0.001)VS(0.049)S(0.95)PPT(0.07)S(0.93)PRPGSAATVSASTSNIIPPR 153.37 2.01E-08 5798200000 1019250 980150 592610 684460 987760 1011140 964300 1075880 963690 TRUE FALSE 884553.53 973711.3301 879198.1782 839877.1043 968105.5085 1050039.21 870782.3344 845811.4345 849763.666 1.040940635 1.145861337 1.034638469 0.988365516 1.139264418 1.235683817 1.024734722 0.995349023 1 19.69670213 2.01940087 24.99999095 1.0011521 1.09678379 0.286040433 0.06853746 304.2424027 392045.5092 0.029310969 0.019758544 104.5684979 -2.01940087 0.09563169 TVSS(ph)PPTSPRPGSAATVSASTSNIIPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 1 T(0.006)VS(0.088)S(0.32)PPT(0.264)S(0.264)PRPGS(0.03)AAT(0.01)VS(0.003)AS(0.004)T(0.005)S(0.006)NIIPPR;T(0.001)VS(0.176)S(0.822)PPT(0.001)SPRPGSAATVSASTSNIIPPR;TVS(0.125)S(0.871)PPT(0.003)S(0.001)PRPGSAATVSASTSNIIPPR 192.09 2.02E-18 1730600000 331411 285191 141462 173182 298008 299386 244377 295964 220260 TRUE FALSE 287614.1967 283317.5615 209873.4964 212505.62 292078.2238 310903.5731 220677.3562 232674.4018 194221.1137 1.480859579 1.458737189 1.080590531 1.094142732 1.503843832 1.600771241 1.136217129 1.197987167 1 17.56734052 1.741210957 1.993405233 1.05226562 1.349347192 0.285779565 0.17933726 0.487497758 3.770739077 0.201540869 0.05527359 55.10753138 -1.741210957 0.297081572 TVSSDGCS(ph)TPSREEGGCSLASTPATTLHLLQLSGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVSSDGCSTPSREEGGCSLASTPATTLHLLQLSGQR 36 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 TVSSDGCS(0.5)T(0.5)PS(0.001)REEGGCSLASTPATTLHLLQLSGQR;TVSSDGCS(0.496)T(0.496)PS(0.008)REEGGCSLASTPATTLHLLQLSGQR 262.6 1.78E-62 2772800000 715350 621760 243880 332100 601530 578930 520800 590910 389040 TRUE FALSE 620814.685 617675.6176 361821.1837 407508.3808 589560.7299 601201.8117 470292.8962 464548.495 343048.1344 1.809701388 1.800550872 1.054724243 1.187904378 1.718594771 1.752529023 1.370923929 1.354178753 1 18.3880515 1.215479438 1.516224903 0.767072599 1.52738888 0.30247053 0.257993333 1.778721075 3.491641905 2.106389803 0.079912767 16.42401897 -1.215479438 0.760316281 TVSSHEVFLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVSSHEVFLQR 11 0 Q9Y5X3;Q5QPE5;Q5QPE4 Q9Y5X3 SNX5 Sorting nexin-5 0 ; 127.83 0.00027846 332260000 429870 433790 176412 374280 435510 466580 476300 457570 505380 FALSE TRUE 373061.5903 430940.4049 261725.4333 459265.9945 426844.2031 484529.6345 430108.4993 359722.2163 445634.5521 0.837146915 0.967026463 0.587309561 1.030588836 0.957834623 1.087280221 0.965159675 0.807213477 1 18.76550157 TVSSPIPYT(ph)PSPSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 TVSSPIPY(0.002)T(0.665)PS(0.333)PSSSRPIS(0.999)PGLS(0.001)YASHTVGFTPPTSLTR;TVSSPIPY(0.056)T(0.831)PS(0.112)PSSSRPIS(0.999)PGLS(0.001)YASHTVGFTPPTSLTR 265.72 8.34E-62 4671000000 1138980 1022190 434280 553490 790300 929790 703770 811600 636650 TRUE FALSE 988460.9072 1015475.167 644299.2606 679168.3641 774574.5762 965559.623 635518.4937 638045.6559 561385.9623 1.760751023 1.808871676 1.147693929 1.209806461 1.379754088 1.719956835 1.132052699 1.136554347 1 19.09863346 8 0.330033633 1.140693782 8.191597593 0.441282031 0.221572151 79.34701311 1.238851292 0.361296521 336.3151046 100000000 -8 7.050903811 TVSSPIPYTPS(ph)PSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVSSPIPYTPSPSSSR 16 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 TVSSPIPYTPS(0.991)PS(0.002)S(0.003)S(0.003)R 156.96 1.18E-07 196170000 152820 132820 96861 100170 120830 130030 118090 130270 303470 TRUE FALSE 132624.4498 131947.4967 143703.3036 122915.1295 118425.7194 135032.3382 106637.65 102412.7743 267594.1223 0.495617948 0.493088172 0.537019656 0.45933419 0.442557252 0.504616234 0.398505203 0.38271683 1 18.0296869 1.233486037 24.99999894 1.000000832 0.460900455 0.926321896 0.047482625 44.57117446 219555.2003 0.107452719 0.013190461 17.11930136 -1.233486037 -0.539100377 TVSSPIPYTPSPSS(ph)SRPISPGLSY(ph)ASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 T(0.018)VS(0.021)S(0.021)PIPY(0.012)T(0.089)PS(0.088)PS(0.089)S(0.262)S(0.273)RPIS(0.137)PGLS(0.212)Y(0.384)AS(0.173)HT(0.152)VGFT(0.05)PPT(0.007)S(0.007)LT(0.007)R 50.31 0.08986 987280000 183280 197970 91307 146450 246900 254540 284870 275980 121980 TRUE FALSE 159059.0836 196669.522 135463.3706 179703.7108 241987.1731 264332.3185 257243.3512 216963.8247 107559.6634 1.478798638 1.828469111 1.259425387 1.670735155 2.249794816 2.457541333 2.391634031 2.017148603 1 16.71477762 3.374862788 5.633917298 2.069675955 1.539639284 0.231026324 0.421784559 0.297573555 13.92302595 0.125666556 0.16303948 2370.624604 -3.374862788 -0.530036671 TVSSPIPYTPSPSSSRPIS(ph)PGLSYASHTVGFT(ph)PPTSLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 TVSSPIPYTPS(0.002)PS(0.085)S(0.098)S(0.113)RPIS(0.658)PGLS(0.037)YAS(0.006)HTVGFT(0.998)PPT(0.001)SLTR 142.47 6.11E-12 944290000 64653 124240 50970 129030 233290 268580 233120 280230 176840 TRUE FALSE 56108.94224 123423.8593 75619.26248 158328.2336 228647.9854 278912.4464 210512.0583 220304.9953 155934.1767 0.359824533 0.791512559 0.484943481 1.015352997 1.466310916 1.788655011 1.350005899 1.412807634 1 17.25057764 3.492770469 3.037515539 1.418336092 0.571960009 0.762432759 0.218057948 0.122624791 2.300203913 0.064915089 0.094974385 3110.072183 -3.492770469 -0.846376083 TVSSPIPYTPSPSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 TVSSPIPYTPSPS(0.012)S(0.012)S(0.012)RPIS(0.963)PGLSYASHTVGFTPPTSLTR 257.3 9.35E-63 13294000000 957050 926530 312730 697160 1039900 1005600 871460 1045100 777260 TRUE FALSE 830573.4176 920443.5634 463967.274 855460.8334 1019208.025 1044286.083 786945.9433 821613.498 685373.2083 1.211855683 1.342981535 0.676955662 1.248167893 1.487084719 1.523675087 1.148200621 1.198782631 1 19.38653027 TVSTLHHVLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TVSTLHHVLQR 11 0 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;; 199.03 2.99E-08 3728776000 1844342 1817581 605361 1179063 1965167 2027370 1635678 1894190 2100025 FALSE TRUE 1600607.532 1805641.191 898115.6044 1446787.275 1926064.021 2105364.236 1477050.199 1489132.209 1851762.437 0.864369802 0.975093324 0.485005844 0.781302853 1.040124793 1.136951584 0.797645621 0.804170222 1 20.8204676 3.335074489 8.793322352 0.93382313 0.768495143 0.234798273 0.15797029 0.476346966 39.01581546 0.048511465 0.062626035 2163.089498 -3.335074489 -0.165327987 TVT(ph)PASSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 TVTPASSAK 9 0 A0A1C7CYX9;Q16555-2;Q16555 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 1 T(0.001)VT(0.998)PAS(0.001)SAK;T(0.042)VT(0.957)PAS(0.001)SAK;T(0.402)VT(0.598)PASSAK;T(0.005)VT(0.994)PASSAK;TVT(0.994)PAS(0.005)S(0.001)AK;TVT(0.993)PAS(0.005)S(0.001)AK 181.44 0.00053076 1990970000 10075930 8325390 4525370 5183130 4729140 4933430 6630610 7866210 7194660 TRUE FALSE 8744370.321 8270699.965 6713854.068 6360038.886 4635039.366 5123222.244 5987574.463 6184082.206 6344115.491 1.378343495 1.303680549 1.058280556 1.002509947 0.730604506 0.807555009 0.943799726 0.974774532 1 22.5969876 4.14014441 1.728636537 0.904174395 1.389878041 0.821090441 0.083143412 0.178374648 0.994991743 0.026684763 0.098155062 13808.43341 -4.14014441 0.485703646 TVTAMDVVYALKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVTAMDVVYALKR 13 1 P62805 P62805 HIST1H4A Histone H4 0 ; 180.28 2.09E-05 1598850000 893410 683170 512040 1557150 629430 2594700 911690 1496110 596650 FALSE TRUE 775343.6049 678682.2113 759664.2567 1910724.707 616905.5745 2694519.788 823274.4441 1176178.519 526114.7167 1.473715865 1.289989027 1.443913718 3.631764416 1.172568558 5.121544223 1.564819265 2.235593269 1 19.00501788 3.952661518 24.94473516 2.441726156 1.378125478 0.144447172 1.207169015 712.5774981 375488.8553 0.304216439 0.526938022 8967.296266 -3.952661518 -1.063600678 TVTCVTVVEPEAPPS(ph)PDVLQAATHR ddPTM_MDA-MB-175_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 205.87 2.59E-25 8695486000 3235939 3435190 1923588 2305490 3416216 3595543 3263533 3761809 3302497 TRUE FALSE 2808301.462 3412624.011 2853841.591 2828986.742 3348239.985 3733865.866 2947036.072 2957375.42 2912079.567 0.964362888 1.171885566 0.980001241 0.971466156 1.149776271 1.282199123 1.012003966 1.01555447 1 21.47361834 2.065190802 25 1.010332264 1.088600095 0.118228647 0.099578319 128.2197528 49169.50019 0.041923625 0.028264901 116.1958994 -2.065190802 0.078267832 TVTEGGAAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVTEGGAAHR 10 0 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 0 ; 155.06 0.00045382 51878000 235890 162564 96923 117409 152206 173283 172922 195527 148478 FALSE TRUE 204716.5388 161496.1064 143795.287 144068.5079 149177.3984 179949.3091 156152.0511 153715.0726 130925.1 1.563615677 1.233499966 1.098301907 1.100388756 1.139410231 1.374444695 1.192682313 1.174068782 1 16.99838218 4.719029151 3.371228871 1.163355107 1.607594297 0.642909465 0.095066691 0.192381046 3.71938323 0.024322653 0.214772976 52363.55828 -4.719029151 0.44423919 TVTEIDEKEYISLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVTEIDEKEYISLR 14 1 K7ESG5;K9J957;P61289;P61289-2;A0A087WTV2;B3KQ25;P61289-3 K7ESG5 PSME3 Proteasome activator complex subunit 3 0 71.344 0.034311 0 191060 181280 87267 111650 184650 133830 207040 206810 121200 FALSE TRUE 165810.9369 180089.1597 129469.6131 137001.839 180975.8263 138978.5267 186961.2927 162585.2909 106871.8741 1.551492742 1.685094056 1.211447017 1.281926046 1.693390593 1.300421911 1.749396596 1.521310376 1 16.7055227 1.237216348 24.95915661 0.999999382 1.501930593 0.418643095 0.184892061 33.71040659 625658.2639 0.26904922 0.044387183 17.2669785 -1.237216348 0.501931212 TVTLPHEAERPDGSEDAEDDDDDDALSDWNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TVTLPHEAERPDGSEDAEDDDDDDALSDWNLR 32 1 O14787-2;O14787;A0A075B780 O14787-2 TNPO2 Transportin-2 0 ;;;; 401.88 3.73E-186 1770640000 1153523 853042 642314 742730 942176 1046647 824690 993890 1316170 FALSE TRUE 1001082.013 847438.3109 952939.1988 911378.1984 923428.5409 1086912.187 744711.6907 781354.358 1160573.882 0.862574997 0.730189025 0.821093093 0.785282361 0.795665451 0.936529939 0.641675383 0.67324827 1 20.14640694 2.229486511 24.99998417 0.745727497 0.814828849 0.025099997 0.108663009 526.1751082 1449646.776 0.043319493 0.029674357 169.6236919 -2.229486511 0.069101352 TVTLPHEAERPDGSEDAEDDDDDDALSDWNLRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVTLPHEAERPDGSEDAEDDDDDDALSDWNLRK 33 2 O14787-2;O14787;A0A075B780 O14787-2 TNPO2 Transportin-2 0 223.27 2.23E-36 115390000 198770 154900 80149 89959 139510 124920 166230 185880 91515 FALSE TRUE 172502.0409 153882.4517 118909.3245 110385.5659 136734.0239 129725.7532 150109.0402 146131.0085 80696.20095 2.137672392 1.906935517 1.47354303 1.367915275 1.694429506 1.607581915 1.860174809 1.810878415 1 16.30021313 4.427960911 4.006599074 1.58787302 2.098914949 0.3997346 0.246478033 0.219732246 7.21575553 0.063302006 0.207473011 26789.27195 -4.427960911 0.511041929 TVTSATIVYHLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVTSATIVYHLAR 13 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 ; 188.29 6.24E-06 1067250000 805910 879850 549550 594620 750920 791250 801650 817960 832930 FALSE TRUE 699406.9516 874070.2074 815314.2181 729637.5592 735978.1612 821689.8995 723906.1064 643045.6194 734461.9643 0.952271167 1.190082332 1.11008365 0.993431375 1.002064364 1.118764401 0.985627768 0.875532908 1 19.48632825 2.022087506 6.678761868 0.929079696 1.062941089 0.327118899 0.074687217 0.156698457 26.95225581 0.031163225 0.020241928 105.2173855 -2.022087506 0.133861394 TVVLHIDGLDDTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVVLHIDGLDDTSR 14 0 Q9NVT9;E5RJ86 Q9NVT9 ARMC1 Armadillo repeat-containing protein 1 0 118.52 0.00024053 57563000 123410 103540 65215 85827 110640 109300 99559 122650 160970 FALSE TRUE 107101.0558 102859.8389 96753.19213 105315.3321 108438.4805 113504.8417 89903.7835 96422.25196 141940.31 0.754549964 0.724669679 0.68164704 0.741969157 0.763972408 0.799666013 0.633391483 0.679315495 1 17.11492484 1.233573403 25 1.000000431 0.719329008 0.768302905 0.047882925 79.55513733 398748.5237 0.101466582 0.012542674 17.12274553 -1.233573403 -0.280671423 TVVLHIDGLDDTSRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TVVLHIDGLDDTSRR 15 1 Q9NVT9;E5RJ86 Q9NVT9 ARMC1 Armadillo repeat-containing protein 1 0 ;; 135.47 1.87E-05 463030000 327369 294394 147061 185431 298142 295818 301951 312727 186737 FALSE TRUE 284106.3572 292460.1064 218180.1915 227535.9427 292209.5575 307198.3099 272667.8385 245852.7647 164661.1646 1.725399902 1.776132867 1.325025194 1.381843395 1.774611264 1.865639118 1.655932892 1.493082873 1 17.32914081 1.234017623 2.524710001 0.838030004 1.638293443 0.582707028 0.170582062 0.427668593 2.956511005 0.750516296 0.048887714 17.14026859 -1.234017623 0.800263439 TVVLT(ph)PTYSGEADALLPSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVVLTPTYSGEADALLPSLR 20 0 Q96Q42;Q96Q42-3 Q96Q42 ALS2 Alsin 1 TVVLT(0.966)PT(0.033)YS(0.001)GEADALLPSLR 101.28 0.0044256 31877000 7057.9 10111 5375.4 5391.5 10964 9497.3 9628.6 12047 11428 TRUE FALSE 6125.180633 10044.58018 7974.96142 6615.722479 10745.83785 9862.667277 8694.819854 9470.8428 10076.99486 0.607838023 0.996783299 0.791402748 0.656517401 1.066373259 0.978731002 0.862838572 0.939847934 1 13.29877784 3.235152923 24.99998081 0.958299042 0.781843608 0.44498868 0.113316055 94.30586112 691859.0019 0.033088956 0.03905303 1718.5134 -3.235152923 -0.176455434 TVWDWELMNDIKPIWQRPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVWDWELMNDIKPIWQRPSK 20 2 P14625 P14625 HSP90B1 Endoplasmin 0 ; 298.87 5.47E-55 3558600000 4238300 3517500 3027500 3427200 3523800 3221000 4243600 4386200 3122500 FALSE TRUE 3678197.917 3494393.311 4491609.126 4205398.141 3453683.274 3344913.954 3832056.325 3448245.263 2753361.607 1.335893515 1.26913708 1.631318282 1.527368628 1.254351504 1.214847314 1.39177372 1.25237646 1 21.39276267 3.174371362 8.065276031 1.237812891 1.441975235 0.387710046 0.135594086 0.302087137 33.49331264 0.042805297 0.048718323 1494.071433 -3.174371362 0.204162344 TVWIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TVWIAR 6 0 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ;;;; 138.53 0.028531 3350677000 2758298 2683743 1784036 2311754 2860780 2995150 2449906 2927923 2792155 FALSE TRUE 2393781.931 2666113.316 2646801.777 2836673.079 2803856.075 3110375.359 2212314.493 2301809.452 2462069.617 0.972264112 1.08287487 1.07503125 1.152149825 1.138820794 1.263317389 0.89855887 0.934908353 1 21.23144012 2.213301963 24.9950188 0.940579269 1.113738761 0.523691464 0.076210956 177.5716309 175716.9158 0.031850714 0.021483077 163.4187796 -2.213301963 0.173159492 TVWQYHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVWQYHFR 8 0 Q06124;Q06124-1;Q06124-3;A0A0U1RRI0 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ; 128.12 0.0011471 1233510000 699430 963610 539310 565470 986250 988780 971250 916790 800630 FALSE TRUE 606998.5534 957279.9825 800122.1199 693868.6062 966625.5546 1026819.006 877058.3245 720741.593 705980.4335 0.859795151 1.355958235 1.133348861 0.982843962 1.369195956 1.454458166 1.242326675 1.020908737 1 19.42926867 1.678955513 5.329175942 1.006063747 1.210946722 0.159708967 0.17889107 0.25004182 15.89461374 0.115522401 0.046525136 47.74803609 -1.678955513 0.204882975 TVYCNVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TVYCNVHK 8 0 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;; 110.87 0.0033424 2122190000 2987420 2670620 1919910 2347170 2746870 2444090 2970680 3268230 4429980 FALSE TRUE 2592624.878 2653076.521 2848384.898 2880130.823 2692212.661 2538115.724 2682583.911 2569344.448 3906272.811 0.663708093 0.679183623 0.729182276 0.737309185 0.689202417 0.649753831 0.686737471 0.657748338 1 21.89736128 1.235319993 24.99995621 1.000000432 0.686869855 0.924192632 0.028207858 25.13514941 193873.296 0.052521358 0.007524731 17.19174627 -1.235319993 -0.313130577 TVYFAEEVQCEGNSFHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVYFAEEVQCEGNSFHK 17 0 P21291;E9PS42 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ; 323.98 6.51E-59 811430000 653940 779020 240330 527630 746380 643520 773750 930050 1152570 FALSE TRUE 567520.1721 773902.5663 356554.3919 647436.4558 731528.4983 668276.6308 698711.8441 731166.0452 1016314.488 0.558409999 0.76147942 0.350830768 0.637043419 0.719785566 0.657549055 0.687495704 0.719428931 1 19.95491547 -0.87085038 0.739006228 10 0.603774113 0.548446437 0.109190627 44.55318599 1.27963439 637.6175452 0.04313463 0.13463241 0.87085038 -9.396225887 TVYGGGCSEMLMAHAVTQLANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVYGGGCSEMLMAHAVTQLANR 22 0 P78371;P78371-2;F5GWF6 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 247.35 4.79E-31 1345700000 437710 514930 263770 362830 511980 435440 466080 550700 340830 FALSE TRUE 379865.5145 511547.3909 391330.0543 445216.097 501792.5997 452191.6586 420879.6333 432937.0906 300537.4657 1.263953942 1.702108553 1.302100733 1.481399652 1.669650732 1.504609941 1.40042318 1.440542827 1 18.19718533 0.81908505 1.691933113 1.79E-12 1.488926168 0.530420132 0.138616983 2.621269618 2.601352357 9.253484667 0.035894082 6.593029969 -0.81908505 1.488926168 TVYGNHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TVYGNHER 8 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ;; 120.31 0.0015271 511880000 1126220 839600 503770 610160 690190 910310 853850 954360 1008170 FALSE TRUE 977387.1735 834084.6123 747394.857 748706.1537 676456.5693 945330.2147 771043.7584 750277.5408 888985.2911 1.099441333 0.938243434 0.840728035 0.842203084 0.760931116 1.063381165 0.867330164 0.843970703 1 19.76180002 4.68586249 3.079301327 0.883447361 1.120755524 0.369467242 0.086021748 0.32690353 4.899850601 0.021039836 0.175591191 48513.48688 -4.68586249 0.237308162 TVYLDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TVYLDER 7 0 H0YJ88 H0YJ88 LRP1 0 79.597 0.074894 298390000 692510 654830 438300 525960 662940 646500 712130 743720 658010 FALSE TRUE 600993.0489 650528.3786 650263.346 645387.2568 649748.791 671371.2733 643067.7422 584681.2656 580220.8074 1.03580058 1.121173819 1.12071704 1.112313189 1.119830214 1.157096169 1.108315548 1.007687519 1 19.14624251 1.72530346 4.393763554 1.001547178 1.114199349 0.685906733 0.030048486 0.091122091 4.096672876 0.019349471 0.007845397 53.12555248 -1.72530346 0.112652172 TVYSHLFDHVVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TVYSHLFDHVVNR 13 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ; 243.11 3.33E-17 1083040000 543590 523060 286089 365110 576980 570940 519910 600670 632460 FALSE TRUE 471753.2042 519623.9844 424442.5973 448013.8059 565499.2268 592904.4312 469489.2082 472221.3949 557691.2993 0.845903827 0.931741243 0.761070861 0.803336553 1.014000447 1.063140902 0.84184424 0.846743343 1 19.08910724 3.254685417 24.97189672 0.936997634 0.837069245 0.332983895 0.080942622 365.926436 566693.6707 0.025732127 0.033116068 1797.568367 -3.254685417 -0.099928389 TWDHFWLNEGHTVYLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TWDHFWLNEGHTVYLER 17 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ;;;; 216.19 3.11E-15 1251941000 787705 799129 509207 640529 758474 883769 771475 820403 753104 FALSE TRUE 683607.7885 793879.469 755461.2084 785970.8993 743381.8513 917768.1653 696657.4732 644966.2028 664072.9031 1.029416778 1.195470355 1.13761788 1.183561166 1.119428075 1.382029234 1.049067761 0.971228008 1 19.34098211 2.01366478 24.99994034 0.991535519 1.175406056 0.458811544 0.087889205 181.1025619 331328.96 0.034244617 0.023075204 103.1964554 -2.01366478 0.183870536 TWELSLYELHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TWELSLYELHR 11 0 Q06587 Q06587 RING1 E3 ubiquitin-protein ligase RING1 0 155.15 3.17E-05 40449000 76849 74487 41016 50739 76914 83575 71255 75490 71473 FALSE TRUE 66693.20994 73997.68999 60851.47479 62260.06545 75383.56188 86790.18433 64344.70107 59347.05096 63023.54336 1.058226916 1.174127731 0.965535601 0.98788583 1.19611748 1.377107343 1.020962923 0.941664778 1 15.94360325 2.012754355 24.99792817 0.97105999 1.124947478 0.249100108 0.116151119 314.4921471 616387.3188 0.050651357 0.034127094 102.9803479 -2.012754355 0.153887488 TWEQQQEVVSR ddPTM_MDA-MB-175_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 ;;; 275.11 8.95E-27 1123180000 421088 402406 231518 288089 420226 428996 362257 401336 420660 FALSE TRUE 365440.1539 399762.5685 343480.8792 353504.0106 411864.3248 445499.7537 327125.3719 315513.4196 370930.054 0.985199635 1.077730327 0.925999054 0.953020675 1.110355767 1.201034397 0.881905816 0.850600851 1 18.50078764 TWESVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TWESVKR 7 1 A6NFX8;Q9UKK9;A6NCQ0;A6NJU6;C9JYY9 A6NFX8 NUDT5 ADP-sugar pyrophosphatase 0 ; 89.369 0.028739 1291010000 1814280 1720890 982660 1068960 1520840 1476730 2088100 2108600 775260 FALSE TRUE 1574518.301 1709585.36 1457877.663 1311683.706 1490578.259 1533540.759 1885596.383 1657692.299 683609.646 2.303241785 2.500821003 2.132617162 1.918761261 2.180452351 2.243298888 2.758293998 2.424910633 1 19.38281323 1.235701711 24.9977567 0.999998226 2.316810957 0.768798867 0.225340608 41.75221089 365004.1924 0.412431066 0.06084488 17.20686342 -1.235701711 1.316812731 TWHAWMDNIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TWHAWMDNIR 10 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ; 104.52 0.0026705 806230000 468630 726110 402980 437860 738130 728870 624590 675890 765190 FALSE TRUE 406699.3581 721340.1356 597862.4759 537282.8053 723442.6571 756910.1005 564017.3579 531356.1833 674730.1099 0.602758573 1.06907951 0.886076473 0.796292914 1.072195603 1.121796833 0.835915501 0.787509221 1 19.36395102 4.754512056 24.30020747 0.931425193 0.602758206 0.442482522 0.120120333 2259.04685 3441317.317 0.031085915 0.7469184 56821.41643 -4.754512056 -0.328666987 TWKPTLVILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TWKPTLVILR 10 1 A0A1W2PNV4;C9JEY1;C9K057;O15143;F8VXW2;C9JBJ7 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 104.87 0.0039463 0 919750 1297200 722260 941200 1311200 1209200 1377800 1455000 1594100 FALSE TRUE 798202.7072 1288678.608 1071547.352 1154913.845 1285109.685 1255718.706 1244181.168 1143859.573 1405647.314 0.567854183 0.91678659 0.762315939 0.821624197 0.914247601 0.893338389 0.885130399 0.81376001 1 20.42280323 4.744264251 24.98936505 0.867975974 0.567854053 0.681735255 0.0659489 370.9018925 1624987.411 0.015529219 0.133663687 55496.32838 -4.744264251 -0.300121921 TWPDHGVPSDPGGVLDFLEEVHHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TWPDHGVPSDPGGVLDFLEEVHHK 24 0 Q06124;Q06124-1;Q06124-3;A0A0U1RRI0 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 65.753 0.013105 349600000 207090 195940 95513 148510 178160 175220 183010 227730 217010 FALSE TRUE 179722.5318 194652.8572 141703.4063 182231.4653 174614.9646 181960.8268 165261.7184 179031.7117 191355.325 0.939208417 1.017232508 0.740525022 0.952319803 0.912516882 0.950905478 0.863637938 0.935598273 1 17.54589452 1.304292639 3.734513029 1.005168952 0.910987256 0.130726228 0.07208334 0.485762095 10.16779054 0.111923099 0.01752804 20.15081606 -1.304292639 -0.094181696 TWPLEVPETEPTLGHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TWPLEVPETEPTLGHLR 17 0 F8WBR0;F8WDR9;Q9Y3I1 F8WBR0 FBXO7 F-box only protein 7 0 72.583 0.028083 54822000 62518 50067 34963 32991 52731 58026 50854 55888 55619 FALSE TRUE 54256.0879 49738.10658 51871.22374 40482.11079 51681.75627 60258.29777 45922.18691 43936.78612 49043.78518 1.106278557 1.014157174 1.057651312 0.825427944 1.053788081 1.228663276 0.936350788 0.895868579 1 15.58178271 2.060341345 24.99992997 0.933170847 1.040580798 0.182869171 0.101654975 115.9479211 48037.32236 0.042519104 0.028666391 114.9056397 -2.060341345 0.107409951 TWS(ph)PTACGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TWSPTACGGK 10 0 Q15464;Q15464-2 Q15464 SHB SH2 domain-containing adapter protein B 1 T(0.001)WS(0.89)PT(0.108)ACGGK;TWS(0.988)PT(0.012)ACGGK;TWS(0.937)PT(0.063)ACGGK;TWS(0.884)PT(0.115)ACGGK 169.52 4.83E-06 756360000 1685710 1455760 1098340 1326390 1432760 1283210 1515400 1792370 2406130 TRUE FALSE 1462939.152 1446197.017 1629500.898 1627567.122 1404250.879 1332575.919 1368436.741 1409085.624 2121680.052 0.689519209 0.681628229 0.768023857 0.767112421 0.661857983 0.628075811 0.644977898 0.664136717 1 21.01677568 1.236006247 24.96998394 1.000000419 0.687073942 0.816606977 0.046439343 31.88766377 311647.8717 0.084422394 0.01276561 17.21893343 -1.236006247 -0.312926477 TWYVQATCATQGTGLYDGLDWLSHELSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TWYVQATCATQGTGLYDGLDWLSHELSK 28 0 P84085 P84085 ARF5 ADP-ribosylation factor 5 0 ;; 355.71 4.63E-111 1130740000 1380906 1094358 699777 940640 1034038 954323 1250155 1465277 1386225 FALSE TRUE 1198415.773 1087169.09 1038191.498 1154226.689 1013462.667 991036.4233 1128915.161 1151938.916 1222347.06 0.980421856 0.889411139 0.849342656 0.944270843 0.829112042 0.810765171 0.923563526 0.942399221 1 20.22122254 1.583925732 2.039318045 0.99762803 0.883277621 0.339652585 0.051332572 0.410472929 3.245451552 0.075352686 0.014553122 38.36416338 -1.583925732 -0.114350409 TYAHYFDLTIINNEIDETIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TYAHYFDLTIINNEIDETIR 20 0 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8YEK3;O14936-6;O14936-2;A0A2U3TZN6;Q5JS79;A0A2R8Y7X6;A0A2R8Y6F8;O14936-3;A0A2U3TZM4;A0A2R8YFN5;O14936-4;Q5JS72;O14936-5 A0A2U3TZM1;A0A2R8Y6F8 CASK Peripheral plasma membrane protein CASK 0 ; 268.3 5.01E-37 173053000 211863 184535 138398 222255 194551 219342 195183 265350 294910 FALSE TRUE 183864.7678 183322.7774 205327.7357 272721.3947 190679.8157 227780.2287 176254.1827 208606.9675 260046.0758 0.707046885 0.704962676 0.789582135 1.048742589 0.733253963 0.875922576 0.67778059 0.80219233 1 17.98840774 4.10883769 4.756085905 0.840734406 0.707825044 0.229235367 0.11053025 0.330273633 12.26345518 0.028426551 0.062495069 12848.06396 -4.10883769 -0.132909362 TYDATTHFETTCDDIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TYDATTHFETTCDDIK 16 0 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;; 266.28 3.55E-27 5957330000 7662880 6422050 4422740 5339470 6088320 5053420 7473750 8510280 8213440 FALSE TRUE 6650210.993 6379863.131 6561591.857 6551878.272 5967174.344 5247828.337 6748946.875 6690422.849 7242456.48 0.918225882 0.880897683 0.905989822 0.904648622 0.823915803 0.724592319 0.93185881 0.923778122 1 22.78804768 1.602114225 2.060833258 0.991474536 0.863964993 0.342638051 0.059252859 0.419480826 3.46942114 0.085607131 0.017573521 40.00499546 -1.602114225 -0.127509543 TYEDIKENLESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TYEDIKENLESR 12 1 P25325-2;P25325;B1AH49 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase 0 ;;;; 150.22 5.59E-05 1911680000 2542140 2178940 1433220 1707990 2206740 1944290 2640250 2869970 1613170 FALSE TRUE 2206189.758 2164626.4 2126329.986 2095815.234 2162830.191 2019088.094 2384198.961 2256249.25 1422462.88 1.550964731 1.521745439 1.494822828 1.473370774 1.520482693 1.419431131 1.676106276 1.586156856 1 20.43995957 1.235076022 24.99992185 0.999999254 1.532890325 0.856699948 0.068164608 37.8936016 271820.8871 0.125902611 0.017685251 17.18209128 -1.235076022 0.532891071 TYEDLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TYEDLKR 7 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ; 97.602 0.019044 520910000 1853900 1548570 1013800 1265330 1515650 1291300 1739300 2020940 2087870 FALSE TRUE 1608902.418 1538397.342 1504077.071 1552642.516 1485491.53 1340977.147 1570622.954 1588777.708 1841044.387 0.873907457 0.835611217 0.816969477 0.843348768 0.80687437 0.728378499 0.853115202 0.862976319 1 20.81209298 1.14213347 1.803126042 1.099035939 0.819373953 0.677258495 0.038414732 0.721501111 1.786936704 0.379387132 0.010910855 13.8718208 -1.14213347 -0.279661986 TYEDMTLEELEDHEDEFNEEDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TYEDMTLEELEDHEDEFNEEDER 23 0 Q9H2J4 Q9H2J4 PDCL3 Phosducin-like protein 3 0 ; 287.37 1.21E-52 191405000 63460 58777 39465 48304 60385 59764 56688 69210 65991 FALSE TRUE 55073.60021 58390.89002 58550.406 59272.16148 59183.45664 62063.15975 51190.40649 54409.98009 58189.61916 0.946450604 1.003458879 1.006200193 1.018603702 1.017079292 1.066567554 0.87971716 0.935046163 1 15.82847418 2.238041572 24.99999968 0.935147003 1.010019212 0.40936057 0.040412115 12.98886535 625546.4874 0.015803107 0.011391823 172.998195 -2.238041572 0.074872209 TYEIWHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TYEIWHR 7 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y4X2;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ;; 117.17 0.0052914 666430000 644310 579470 363759 463833 643040 590960 580860 665790 662620 FALSE TRUE 559162.801 575663.4234 539674.0691 569153.3719 630244.7621 613694.6136 524528.2866 523415.9897 584285.8185 0.957002178 0.985242847 0.923647386 0.974100952 1.078658325 1.050332892 0.897725514 0.895821828 1 19.15631475 2.222091942 24.99988134 0.922421605 0.99402743 0.243329299 0.052139783 330.8735824 502271.0158 0.022819065 0.015435164 166.7600215 -2.222091942 0.071605825 TYEVSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TYEVSLR 7 0 Q16531;F5GY55;F5H2L3 Q16531 DDB1 DNA damage-binding protein 1 0 141.83 0.020014 0 303210 306020 177060 216030 310200 313570 300320 325970 290460 FALSE TRUE 263140.0303 304009.7345 262686.8082 265082.9133 304027.6269 325633.2408 271195.0126 256263.8522 256122.1497 1.027400522 1.186971665 1.025630968 1.034986289 1.187041524 1.271398203 1.058850291 1.000553261 1 17.9664725 2.004574943 24.99942513 1.009131814 1.123548601 0.28936772 0.079404675 160.3798608 876380.0157 0.03382582 0.022710508 101.0589876 -2.004574943 0.114416788 TYFTDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TYFTDKK 7 1 P27824;P27824-2;P27824-3;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 ; 94.302 0.022929 1816980000 2077410 1761760 1103030 1958360 2430380 1886940 1991980 4074700 2877820 FALSE TRUE 1802875.005 1750186.883 1636458.997 2403035.57 2382020.193 1959531.803 1798798.086 3203357.114 2537607.398 0.710462543 0.68969963 0.644882655 0.946969012 0.93868744 0.772196599 0.708855943 1.262353316 1 21.27503745 -2 0.207867733 3.291060167 0.60364576 0.417645021 0.144558323 89.73983633 1.356409713 76.89464356 0.8555307 0.01 2 -2.687414407 TYGADLASVDFQHASEDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TYGADLASVDFQHASEDAR 19 0 P30740 P30740 SERPINB1 Leukocyte elastase inhibitor 0 ;; 275.23 1.97E-39 998380000 977150 1096340 255671 561241 1219760 1309920 1044150 1168190 1200490 FALSE TRUE 848017.1517 1089138.07 379314.3508 688679.3471 1195489.162 1360313.47 942888.4937 918381.6594 1058569.44 0.80109733 1.028877303 0.35832732 0.650575504 1.129344111 1.285048877 0.890719549 0.86756865 1 20.01368448 3.245077122 24.99994064 1.015404676 0.707416885 0.39215893 0.200149046 184.7295887 708692.833 0.062318423 0.078527236 1758.235814 -3.245077122 -0.307987791 TYGGDTGS(ph)PEISFTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TYGGDTGSPEISFTK 15 0 O94915;H0Y9X0;A0A286YEZ9;A0A2C9F2R7 O94915 FRYL Protein furry homolog-like 1 TYGGDT(0.05)GS(0.95)PEISFTK 152.77 2.91E-06 155640000 384160 398240 209810 287720 417290 334350 399660 521630 395480 TRUE FALSE 333392.2827 395623.9352 311274.8178 353051.2235 408986.7454 347212.6609 360901.0347 410083.4838 348726.8049 0.956027119 1.134481002 0.892603647 1.012400591 1.172799853 0.995658079 1.034910508 1.175944831 1 18.41173774 3.448317793 24.98547518 1.082319403 0.999068328 0.1681309 0.084990569 343.9805798 298383.7598 0.023618465 0.030491832 2807.48725 -3.448317793 -0.083251075 TYGNVLVLDGVIQCTERDEFSYQEMIANLPLCSHPNPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TYGNVLVLDGVIQCTERDEFSYQEMIANLPLCSHPNPR 38 1 P19623;K7ESL0 P19623 SRM Spermidine synthase 0 113.97 4.80E-06 41402000 23875 23102 9621.8 13517 18001 20525 20012 21856 10482 FALSE TRUE 20719.85826 22950.24144 14274.93466 16586.24144 17642.81532 21314.61003 18071.23932 17182.26448 9242.829901 2.241722338 2.483031895 1.544433341 1.794498181 1.908810993 2.306069706 1.955163031 1.858983089 1 13.17411892 1.158766681 2.326160049 0.556472931 2.027336071 0.593406287 0.26665781 0.602747356 2.833564866 1.995416852 0.073696687 14.41340802 -1.158766681 1.470863141 TYGQSTYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TYGQSTYSR 9 0 P35998;C9JLS9 P35998 PSMC2 26S protease regulatory subunit 7 0 ; 218.04 1.27E-06 204999000 93740 99826 43940 52430 94533 85192 87405 95611 79307 FALSE TRUE 81352.02149 99170.23643 65189.53097 64335.03284 92651.97825 88469.39137 78928.47655 75165.3317 69931.41681 1.163311502 1.418107068 0.932192339 0.919973251 1.324897771 1.265087931 1.128655476 1.074843541 1 16.09365311 1.590812824 2.328691628 1.005540113 1.167330867 0.11641332 0.154510776 0.719760387 8.019099335 0.19954018 0.04452252 38.97739623 -1.590812824 0.161790754 TYHSVGDSVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TYHSVGDSVLR 11 0 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 0 86.014 0.014786 213500000 417640 376240 214010 264340 360230 331160 384840 390020 376000 FALSE TRUE 362447.8158 373768.4547 317505.9518 324362.4372 353062.1278 343899.9395 347518.276 306617.2581 331549.7083 1.093192987 1.127337607 0.957642078 0.978322191 1.064884447 1.037250014 1.04816342 0.924800265 1 18.33886566 4.246641562 24.999303 0.99992463 1.11026534 0.527815054 0.042714867 147.1161745 455109.6897 0.011575842 0.029495837 17645.8085 -4.246641562 0.11034071 TYHTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TYHTEK 6 0 Q99805 Q99805 TM9SF2 Transmembrane 9 superfamily member 2 0 ;;;; 131.65 0.015236 1219770000 1742880 1567850 1068234 1331090 920369 1530770 1433490 1843720 2483720 FALSE TRUE 1512553.992 1557550.69 1584835.535 1633334.329 902055.4576 1589659.712 1294470.36 1449454.826 2190097.451 0.690633191 0.711178715 0.723636994 0.745781576 0.411879141 0.725839716 0.591056055 0.661822069 1 21.06256364 1.239294726 8.034282659 1.004107656 0.655430081 0.548865951 0.097516976 0.069545897 40.72718946 0.133289483 0.023352107 17.3498101 -1.239294726 -0.348677575 TYIPPKGETK ddPTM_MDA-MB-175_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 ; 100.55 0.0035882 1470280000 2173300 1601810 1070200 1196450 1557400 1000640 1885750 2204200 1705380 FALSE TRUE 1886092.899 1591287.605 1587752.3 1468122.259 1526410.787 1039135.268 1702870.255 1732848.983 1503771.919 1.254241334 1.058197446 1.055846488 0.976293173 1.015054722 0.6910192 1.132399291 1.152334979 1 20.52015434 5.005191963 1.499105356 1.009903761 1.50416067 0.2852561 0.124647118 3.468791335 4.349666835 0.036760409 3.069095988 101202.6683 -5.005191963 0.49425691 TYLPDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 TYLPDFR 7 0 Q13630;H0YCP7 Q13630 TSTA3 GDP-L-fucose synthase 0 ;;;; 111.04 0.015516 5271350000 7731750 9338690 4842780 6216000 9356620 9605180 8470340 9740650 9277280 FALSE TRUE 6709979.648 9277343.53 7184764.606 7627437.806 9170441.568 9974697.49 7648887.731 7657687.799 8180530.527 0.820237713 1.134076024 0.878276119 0.932389138 1.121008171 1.21932159 0.935011208 0.936086941 1 22.96376298 3.29399808 24.99989959 1.029818133 0.950520493 0.153307423 0.1150384 228.2996522 102951.2156 0.034685472 0.044778724 1967.877589 -3.29399808 -0.079297641 TYPAHQNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TYPAHQNR 8 0 Q8IWB7;A0A494C0A6 Q8IWB7 WDFY1 WD repeat and FYVE domain-containing protein 1 0 ; 121.96 0.0014111 34120000 247091 218133 122754 163625 184390 249930 234608 326046 224814 FALSE TRUE 214437.2983 216700.07 182118.245 200778.5571 180720.9998 259544.9688 211855.7523 256323.6002 198236.745 1.081723261 1.093137753 0.918690654 1.012822104 0.911642288 1.309267708 1.068700721 1.2930176 1 17.59686488 2.746397772 24.98726471 1.178034574 1.004372152 0.363780473 0.107479988 591.5944264 1886185.927 0.032887917 0.032300138 557.696311 -2.746397772 -0.173662423 TYQEHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TYQEHK 6 0 P09960-4;P09960 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ; 96.51 0.042126 612130000 1158730 1083730 651410 760160 604470 995540 1240260 1382680 1393620 FALSE TRUE 1005600.895 1076610.906 966434.0548 932765.9463 592442.2296 1033839.068 1119979.776 1087004.642 1228867.831 0.818314931 0.876099837 0.786442635 0.75904497 0.482104108 0.841293947 0.911391565 0.884557814 1 20.22889833 2.481931147 23.80989871 0.914830377 0.745550267 0.392336439 0.106342307 131.2985582 649965.541 0.040995247 0.032691267 303.3410227 -2.481931147 -0.16928011 TYS(ph)APAINAIQVPKPFSGPVR ddPTM_MDA-MB-175_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(0.028)YS(0.972)APAINAIQVPKPFSGPVR;T(0.007)YS(0.993)APAINAIQVPKPFSGPVR 170.53 4.90E-12 959440000 559050 477590 257580 266480 444110 437730 473220 600310 241860 TRUE FALSE 485170.126 474452.6798 382146.5496 326988.3569 435273.0799 454569.7563 427327.1972 471938.3781 213267.5863 2.274936076 2.22468256 1.791864184 1.533230448 2.040971567 2.131452623 2.00371376 2.212893137 1 17.70230519 4.252230068 17.92708538 1.870923206 2.249823701 0.196292737 0.351413888 14.55842487 19078.39675 0.086643886 0.223241437 17874.34218 -4.252230068 0.378900495 TYS(ph)FEQPWPNAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 TYSFEQPWPNAR 12 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q8TEW0-5;Q8TEW0-3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 TYS(1)FEQPWPNAR;TYS(1)FEQPWPNAR;T(0.077)YS(0.923)FEQPWPNAR;T(0.004)YS(0.996)FEQPWPNAR 247.3 1.33E-16 1107350000 1117300 1072050 868270 1185940 1719960 1645240 1513960 1756640 1654700 TRUE FALSE 969645.9741 1065007.633 1288168.276 1455225.803 1685736.161 1708533.447 1367136.392 1380996.206 1459083.251 0.664558361 0.729915604 0.882861396 0.997356252 1.155339258 1.170963649 0.936983131 0.946482118 1 20.47663077 4.091400329 1.939973522 1.030784288 0.671552797 0.768922414 0.076822321 0.194201787 1.415742547 0.025416897 0.078919973 12342.42023 -4.091400329 -0.359231491 TYS(ph)FTSAMSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TYSFTSAMSR 10 0 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 T(0.002)YS(0.997)FTSAMSR;T(0.07)YS(0.827)FT(0.101)S(0.002)AMSR 173.04 3.71E-06 916050000 634210 654530 432470 460570 731620 717880 760410 707060 797200 TRUE FALSE 550397.5416 650230.3493 641613.9385 565149.4579 717062.1934 745497.3081 686665.5552 555860.7213 702955.9242 0.782975892 0.92499448 0.912737081 0.803961441 1.020067075 1.060517854 0.976825903 0.790747616 1 19.42307471 3.241174051 24.99996078 0.952355052 0.865124168 0.303099123 0.082738291 124.295011 1188990.837 0.026987733 0.033253023 1742.505073 -3.241174051 -0.087230883 TYS(ph)IDGPNASRPQSARPSINEIPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TYSIDGPNASRPQSARPSINEIPER 25 2 Q96RT1-7;Q96RT1-6;Q96RT1-4;Q96RT1-5;Q96RT1-3;Q96RT1-9;Q96RT1-2;Q96RT1;Q96RT1-8;H0YA04 Q96RT1-7 ERBB2IP Protein LAP2 1 T(0.017)YS(0.983)IDGPNAS(0.001)RPQSARPSINEIPER 93.411 0.0059657 189970000 87623 81561 55224 80008 140290 139680 100670 128580 63066 TRUE FALSE 76043.39854 81025.22042 81930.51111 98175.03925 137498.5035 145053.58 90907.03889 101084.1676 55610.40933 1.367431016 1.457015357 1.473294516 1.7654076 2.472531764 2.608389 1.634712637 1.817720258 1 15.76306734 3.667764549 3.928482564 1.923941493 1.430517494 0.193060259 0.438609744 0.39539964 11.89319658 0.131138103 0.205601519 4653.337459 -3.667764549 -0.493423999 TYS(ph)LPEDDDFIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TYSLPEDDDFIK 12 0 F8W9X7;Q567U6 F8W9X7 CCDC93 Coiled-coil domain-containing protein 93 1 T(0.026)YS(0.974)LPEDDDFIK 112.43 0.0013371 27341000 58554 38711 20872 37707 34031 18612 46304 51343 40798 TRUE FALSE 50815.94054 38456.70489 30965.76901 46268.95067 33353.84968 19328.01568 41813.44521 40363.699 35974.90692 1.412538486 1.068986919 0.860760226 1.286145111 0.92714207 0.537263814 1.162294743 1.121995926 1 15.13470333 4.713619765 3.759514599 0.997736708 1.445665127 0.305005048 0.200593231 0.31541856 8.535197556 0.050722474 0.375871848 51715.38539 -4.713619765 0.447928419 TYS(ph)LTTPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TYSLTTPAR 9 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 TYS(0.997)LT(0.003)TPAR;T(0.001)YS(0.98)LT(0.02)TPAR;T(0.002)YS(0.643)LT(0.355)TPAR 131.52 0.00034712 1162210000 706870 732920 603540 716730 1056620 1190510 1076520 1128530 1299530 TRUE FALSE 613455.3385 728105.4003 895413.9627 879474.501 1035595.329 1236309.69 972119.2561 887202.6417 1145901.044 0.535347569 0.635399893 0.78140601 0.767496029 0.903738883 1.078897429 0.848344856 0.77424019 1 20.12805103 4.24707651 1.023580644 0.900535883 0.482660004 0.695656114 0.087874261 0.60909404 0.879995255 0.032868329 0.236430285 17663.48974 -4.24707651 -0.417875879 TYSEFCSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TYSEFCSR 8 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 0 118.32 0.0090471 0 88330 102040 59525 71134 90997 95382 99886 94723 95156 FALSE TRUE 76656.9667 101369.6925 88311.4891 87286.06192 89186.33773 99051.40726 90199.07109 74467.22359 83906.76608 0.913596963 1.208122983 1.052495445 1.040274414 1.062921882 1.180493682 1.074991628 0.887499627 1 16.35649953 1.754753168 25 0.941399737 1.082423108 0.298556176 0.083909659 5.944023485 9190.696234 0.041426419 0.019893578 56.85297139 -1.754753168 0.141023372 TYSSS(ph)LKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TYSSSLKR 8 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 TYSS(0.011)S(0.989)LKR 81.099 0.01454 391020000 705430 598810 477840 564820 442960 352150 903100 1064400 988360 TRUE FALSE 612205.6382 594876.3777 708925.0223 693071.0137 434145.9626 365697.4384 815517.501 836786.3432 871517.2067 0.702459611 0.682575597 0.81343778 0.795246506 0.498149617 0.419610118 0.935744578 0.960148964 1 19.73316962 2.099368407 9.400199858 0.968388854 0.660412956 0.603752683 0.119851915 0.213559348 18.30355373 0.053582165 0.0361009 125.7095892 -2.099368407 -0.307975898 TYSTSFTPMYHAVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TYSTSFTPMYHAVTK 15 0 P00390-5;P00390-4;P00390-2;P00390-3;P00390 P00390-5 GSR "Glutathione reductase, mitochondrial" 0 156.24 2.16E-06 404420000 253350 279280 141360 229070 288410 235130 320330 305820 340730 FALSE TRUE 219869.1556 277445.3913 209722.1688 281083.8446 282671.2053 244175.6032 289264.4459 240422.7729 300449.2876 0.731801221 0.923435011 0.698028511 0.935545053 0.940828343 0.812701555 0.962772947 0.800210827 1 18.19676198 3.712770371 24.96375992 0.898099691 0.798322887 0.313738566 0.084857014 981.5401999 950085.3069 0.021552012 0.031979316 5161.433915 -3.712770371 -0.099776805 TYSYLTPDLWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 TYSYLTPDLWK 11 0 P15880;H0YEN5;E9PQD7 P15880 RPS2 40S ribosomal protein S2 0 ; 170.72 3.58E-05 1080290000 2263950 2246260 1500830 1627120 2336840 2037050 2564800 2937200 2695700 FALSE TRUE 1964763.271 2231504.17 2226636.408 1996582.465 2290341.456 2115416.632 2316066.091 2309102.637 2377017.417 0.826566628 0.938783264 0.93673542 0.839952813 0.963535833 0.889945785 0.974358065 0.971428573 1 21.18072104 -2 0.233928985 1.679679223 0.866665233 0.460217992 0.042524422 78.75217766 1.24006319 23.90284899 0.160256126 0.01 2 -0.81301399 TYT(ph)HEVVTLWYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TYTHEVVTLWYR 12 0 G3V5T9;P24941;Q00526;K7EJ83 G3V5T9 CDK2;CDK3 Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 1 T(0.168)YT(0.832)HEVVTLWYR;T(0.323)YT(0.676)HEVVT(0.001)LWYR;T(0.048)YT(0.952)HEVVTLWYR 248.36 1.07E-15 700590000 499139 519873 340071 375087 540540 445255 513077 507447 610879 TRUE FALSE 433176.5165 516457.92 504530.4731 460256.2362 529784.3115 462384.248 463318.8715 398933.408 538661.5805 0.804171918 0.958779944 0.936637197 0.85444415 0.983519766 0.858394704 0.860129789 0.740601191 1 19.03901964 2.499604325 23.46671521 0.843020344 0.910221742 0.039005935 0.080423192 684.1979904 714132.5503 0.02667145 0.023311969 315.9397898 -2.499604325 0.067201398 TYYVDHNTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 TYYVDHNTR 9 0 Q9H0M0-3;Q9H0M0;Q9H0M0-6 Q9H0M0-3 WWP1 NEDD4-like E3 ubiquitin-protein ligase WWP1 0 119.16 0.00087304 315760000 123330 137050 86117 101440 146670 178350 130800 154830 138030 FALSE TRUE 107031.628 136149.7095 127763.4692 124473.5024 143751.554 185211.2399 118115.0361 121720.8094 121712.2506 0.879382539 1.118619603 1.049717416 1.02268672 1.181077116 1.521714034 0.970444927 1.000070319 1 16.89311486 4.741031303 23.10190006 1.103875909 0.879382316 0.167887905 0.159743046 161.5651225 1510408.238 0.041019264 0.265276238 55084.73993 -4.741031303 -0.224493593 TYYYNNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 TYYYNNR 7 0 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 ;; 154.92 0.0038296 810650000 531110 535760 302239 370620 529770 581440 499530 584390 550960 FALSE TRUE 460922.4678 532240.5573 448402.7913 454774.9356 519228.6135 603808.373 451085.6575 459422.7462 485826.1365 0.948739545 1.095537101 0.922969675 0.936085775 1.068753973 1.242848681 0.928491951 0.945652594 1 18.89008058 VAAAAGSGPS(ph)PPGS(ph)PGHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VAAAAGSGPSPPGSPGHDR 19 0 Q9BTU6 Q9BTU6 PI4K2A Phosphatidylinositol 4-kinase type 2-alpha 2 VAAAAGSGPS(1)PPGS(1)PGHDR;VAAAAGS(0.007)GPS(0.993)PPGS(1)PGHDR;VAAAAGS(0.002)GPS(0.998)PPGS(1)PGHDR 255.82 8.89E-31 1181560000 958560 888580 719790 930460 1106500 1156210 1016770 1271490 1222990 TRUE FALSE 831883.8673 882742.8595 1067882.852 1141735.164 1084482.815 1200690.147 918163.8019 999591.7582 1078409.515 0.771398857 0.818559969 0.990238714 1.058721337 1.005631719 1.113389793 0.851405509 0.926912962 1 20.0404737 4.29165632 4.392097504 0.986561808 0.784238471 0.58071816 0.06998619 0.157720299 6.196683469 0.019317194 0.053569746 19572.95151 -4.29165632 -0.202323337 VAAAAGSGPS(ph)PPGSPGHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VAAAAGSGPSPPGSPGHDR 19 0 Q9BTU6 Q9BTU6 PI4K2A Phosphatidylinositol 4-kinase type 2-alpha 1 VAAAAGSGPS(1)PPGSPGHDR;VAAAAGSGPS(1)PPGSPGHDR;VAAAAGSGPS(1)PPGSPGHDR;VAAAAGSGPS(1)PPGSPGHDR 202.65 3.49E-16 1006780000 572760 500463 158988 352876 451314 514407 364293 444302 432071 TRUE FALSE 497068.3148 497175.4256 235875.1286 433001.8892 442333.7344 534196.5702 328963.9209 349291.4749 380992.0586 1.30466844 1.304949577 0.61910773 1.136511587 1.16100513 1.402119961 0.863440362 0.916794634 1 18.5394014 7.980713627 0.03690247 8.55E-06 2.701129777 0.083546484 0.227201196 5621.929968 20.55352041 491.9041317 1144.078118 95656310.64 -7.980713627 2.701121226 VAAAPDEDLDGDDEDDAEDENNIDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VAAAPDEDLDGDDEDDAEDENNIDNR 26 0 Q9BXV9 Q9BXV9 C14orf142 Uncharacterized protein C14orf142 0 ; 332.66 5.05E-95 617780000 277530 248825 189306 209225 226361 253301 269347 293650 279750 FALSE TRUE 240853.7073 247190.4522 280855.0148 256732.7341 221856.859 263045.6534 243225.7694 230855.2327 246678.2737 0.976388004 1.002076302 1.138547836 1.040759408 0.899377378 1.06635112 0.98600402 0.935855555 1 17.91227113 3.427173213 24.99966385 0.976722498 1.04436871 0.210714702 0.059248427 158.5120609 79336.81413 0.017116065 0.022096754 2674.072717 -3.427173213 0.067646212 VAAASGHCGAFSGSDSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VAAASGHCGAFSGSDSSR 18 0 Q9NZB2;Q9NZB2-6;A0A494C0Y9 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 0 ;;; 155.2 2.05E-08 811800000 456855 455465 184765 298446 508220 486810 478881 485850 440089 FALSE TRUE 396480.4542 452473.0204 274117.972 366212.7258 498107.4163 505537.8957 432439.1943 381954.7584 388062.1798 1.021693107 1.165980722 0.706376417 0.943695997 1.283576299 1.30272395 1.114355423 0.984261745 1 18.56592831 3.285036603 24.99979876 1.124483451 0.956113669 0.254099531 0.150262307 204.8497013 110188.7956 0.047059044 0.060752765 1927.687373 -3.285036603 -0.168369782 VAAETQS(ph)PSLFGSTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VAAETQSPSLFGSTK 15 0 Q9UKX7-2;Q9UKX7 Q9UKX7-2 NUP50 Nuclear pore complex protein Nup50 1 VAAETQS(0.83)PS(0.17)LFGSTK;VAAETQS(0.994)PS(0.006)LFGSTK 322.37 1.03E-56 292260000 502920 505070 369450 501980 481900 404990 547350 704440 900900 TRUE FALSE 436457.8478 501752.1619 548117.2557 615962.2313 472311.1328 420570.2274 494268.0812 553800.988 794396.6283 0.549420569 0.631614164 0.689979333 0.775383743 0.594553295 0.529420962 0.622193075 0.697134112 1 19.59949997 1.219067644 2.759960663 1.091759626 0.631527769 0.739092715 0.069056162 0.270921048 2.315807379 0.294647432 0.019357122 16.56027879 -1.219067644 -0.460231857 VAAHPILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VAAHPILR 8 0 G3V5X9;Q9UNH7;A0A0A0MRI2;Q9UNH7-2 G3V5X9;Q9UNH7-2 SNX6 "Sorting nexin-6;Sorting nexin-6, N-terminally processed" 0 79.116 0.028419 0 132300 109170 88865 109270 126180 125790 120100 139760 132140 FALSE TRUE 114816.2198 108452.8551 131840.4112 134081.4236 123669.2649 130629.2227 108452.7205 109873.4116 116518.5597 0.985389968 0.930777512 1.13149709 1.150730183 1.061369666 1.121102278 0.930776356 0.942969188 1 16.83020025 2.227605233 24.99609405 0.953670628 1.064407936 0.34574251 0.068363401 249.4864291 569229.8367 0.029938359 0.020404199 168.8905044 -2.227605233 0.110737308 VAALAAS(ph)PASVAVDSGSELNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VAALAASPASVAVDSGSELNSR 22 0 O15119;O15119-2 O15119 TBX3 T-box transcription factor TBX3 1 VAALAAS(1)PASVAVDSGSELNSR 320.88 1.29E-67 138090000 41213 41035 19695 26171 36646 34135 32248 43679 32827 TRUE FALSE 35766.59763 40765.43838 29219.56788 32113.52555 35916.8163 35448.19554 29120.59392 34338.58576 28946.22946 1.235621989 1.40831601 1.009442971 1.109419988 1.240811566 1.224622212 1.006023737 1.186288729 1 14.82108781 8 0.315567803 1.08913469 3.134450178 0.223821339 0.1149708 120.3701959 1.902823937 0.194576312 139.0578306 99999999.99 -8 2.045315488 VAAQSPPS(ph)PASAEALLPALPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VAAQSPPSPASAEALLPALPLR 22 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 VAAQSPPS(0.985)PAS(0.015)AEALLPALPLR;VAAQS(0.001)PPS(0.996)PAS(0.003)AEALLPALPLR;VAAQSPPS(0.987)PAS(0.013)AEALLPALPLR;VAAQSPPS(1)PASAEALLPALPLR;VAAQSPPS(1)PASAEALLPALPLR 234.23 1.26E-32 355618000 266086 266477 181970.4 238820 296294 340653 314342 338617 315456 TRUE FALSE 230922.0609 264726.495 269971.8941 293047.7311 290398.3291 353758.1413 283857.1612 266206.3897 278163.151 0.830167691 0.951695054 0.970552329 1.053510251 1.043985618 1.271764934 1.020470038 0.957015294 1 18.08557179 4.541322004 1.204513028 1.052699919 0.781627207 0.434667454 0.083828438 1.207383586 1.937021031 0.028017652 0.376567049 34779.3935 -4.541322004 -0.271072712 VAAYDKLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VAAYDKLEK 9 1 P35579 P35579 MYH9 Myosin-9 0 ; 118.4 0.00090745 5043900000 7098800 6037100 4854800 5154000 5503700 4397100 8329000 9489900 5908900 FALSE TRUE 6160675.594 5997441.893 7202597.518 6324294.474 5394187.138 4566259.282 7521254.862 7460558.735 5210356.573 1.1823904 1.1510617 1.382361728 1.213793026 1.035281763 0.876381341 1.443520181 1.43187105 1 22.31295068 1.173713813 23.29731915 0.99998338 1.222560874 0.126192447 0.176347666 49507.9265 17780542.67 195.0701944 0.047139638 14.91811026 -1.173713813 0.222577495 VADAKGDS(ph)ES(ph)EEDEDLEVPVPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 VADAKGDSESEEDEDLEVPVPSR 23 1 P13861-2;P13861 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 2 VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR 255.88 8.33E-44 6570110000 6900930 5581830 4033006 4121186 6002180 4563980 6468300 8086540 5359680 TRUE FALSE 5988954.616 5545162.591 5983381.191 5056964.27 5882748.361 4739559.264 5841005.262 6357296.351 4726064.736 1.267218066 1.173314988 1.266038771 1.07001587 1.244745616 1.002855341 1.235913088 1.345156426 1 22.17220796 7.399436593 1.068834532 1.178298572 33.03863357 0.06309179 0.114301608 2256.409897 9.340656742 0.034416905 174889.0263 25086298.93 -7.399436593 31.860335 VADEDDVDNEEAALLHEEATMTIEELLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 VADEDDVDNEEAALLHEEATMTIEELLTR 29 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 ;;;;;;;;;; 281.63 2.08E-71 877276000 563424 447747 393495 463972 421890 421613 442864 562825 793575 FALSE TRUE 488966.0909 444805.7205 583790.4982 569323.934 413495.2144 437832.7249 399915.1174 442469.2537 699759.4675 0.698763094 0.635655166 0.834273097 0.813599473 0.590910497 0.62569032 0.571503689 0.632316209 1 19.41649958 1.234291465 24.95778082 1.000000493 0.672312272 0.576411046 0.087431691 102.0774122 596670.3097 0.177107019 0.023316774 17.15107968 -1.234291465 -0.327688222 VADIGLAAWGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VADIGLAAWGR 11 0 P23526 P23526 AHCY Adenosylhomocysteinase 0 ;; 111.46 0.0038569 1064605000 620298 669885 392229 436195 610801 580776 615605 727916 637831 FALSE TRUE 538324.0477 665484.4813 581912.2563 535239.7416 598647.2551 603118.8285 555903.7219 572256.828 562427.3458 0.957144157 1.183236353 1.034644316 0.951660238 1.064399268 1.072349759 0.988400948 1.017476892 1 19.10130722 1.437351698 0.315012689 0.956120946 1.06225018 0.040869603 0.065868744 28.16970128 3.33250061 1.230676042 0.183714357 27.37484683 -1.437351698 0.106129234 VADMALHYANK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VADMALHYANK 11 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 140.49 3.86E-05 3310800000 8430100 7496800 5857300 6936800 7029700 5889200 8561100 9074600 9648200 FALSE TRUE 7316040.926 7447553.027 8689909.871 8511906.462 6889822.723 6115761.335 7730845.84 7134067.409 8507600.787 0.859941728 0.875399917 1.021428966 1.000506097 0.809843209 0.718858523 0.908698708 0.838552206 1 23.02032091 3.230969759 24.99994522 0.850307252 0.940618504 0.191782451 0.085473095 284.9583446 938488.1827 0.026554442 0.030687839 1702.039988 -3.230969759 0.090311252 VADNS(ph)FDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 163.93 6.57E-05 879050000 1750580 1606390 1201780 1447480 1482410 1257840 1818700 2122810 2657720 TRUE FALSE 1519236.418 1595837.518 1782964.828 1776152.457 1452912.941 1306229.919 1642322.754 1668863.601 2343527.369 0.648269117 0.680955358 0.760803928 0.75789704 0.619968412 0.55737771 0.700790943 0.712116113 1 21.16025021 1.193483908 2.923332239 1.08918122 0.676203569 0.737659981 0.060328542 0.283569495 2.691496919 0.296723084 0.017014495 15.61291186 -1.193483908 -0.412977651 METVSNASSSS(ph)NPSS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 METVSNASSSSNPSSPGR 18 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 METVSNASSS(0.005)S(0.995)NPS(0.001)S(0.999)PGR 239.13 9.68E-24 378060000 1283900 798860 353320 338640 397090 376130 338510 366210 339650 TRUE FALSE 1114229.362 793612.2361 524186.7338 415533.3878 389188.6859 390599.9645 305681.3523 287898.8413 299496.9639 3.720336084 2.649817299 1.750223865 1.38743773 1.299474562 1.304186725 1.020649252 0.961274657 1 18.19218185 5.601650101 0.606809603 1.004359303 10.16917157 0.989106053 0.091347738 0.921356475 0.120376507 0.049065877 7.432152409 399622.6551 -5.601650101 9.164812271 up VADPDHDHTGFLTEYVATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VADPDHDHTGFLTEYVATR 19 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 ;;; 172.56 4.70E-12 3012490000 3828230 3580440 2282230 2521570 3215530 3466800 3069730 3486440 3391480 FALSE TRUE 3322319.706 3556919.854 3385924.062 3094131.008 3151547.244 3600170.039 2772028.057 2740891.938 2990543.098 1.110941925 1.189389264 1.132210422 1.034638494 1.053837762 1.203851582 0.926931319 0.916519792 1 21.51197608 2.223357668 24.99507947 0.940426474 1.117485649 0.679628778 0.055883041 135.7212043 223136.7129 0.023488358 0.01590365 167.2467428 -2.223357668 0.177059175 VADWTGATYQDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VADWTGATYQDKR 13 1 O15371-2;O15371;O15371-3;B0QYA5;B0QYA6;B0QYA8 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ;; 188.4 9.85E-06 1418590000 1012360 908610 518420 607430 852300 753970 978860 1111950 602950 FALSE TRUE 878574.061 902641.2811 769129.646 745356.2655 835340.8975 782975.7138 883930.3079 874168.1457 531669.9379 1.65248023 1.69774745 1.446629932 1.401915385 1.571164435 1.472672532 1.662554613 1.644193293 1 19.02017137 1.233920855 24.99977146 0.999999144 1.568697679 0.761306044 0.100069934 75.11418693 404676.7241 0.206273876 0.026262786 17.13644988 -1.233920855 0.568698535 VADYCENNYIQATDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VADYCENNYIQATDKR 16 1 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7;Q8IZP0-11 A0A0A0MRT6 ABI1 Abl interactor 1 0 ; 147.12 1.06E-05 0 90340 70990 52699 60212 76524 64721 80549 98594 85232 FALSE TRUE 78401.34011 70523.66202 78184.41267 73884.05488 75001.32212 67210.85875 72737.37038 77510.44036 75155.97006 1.0431818 0.938364071 1.040295436 0.983076326 0.997942307 0.894285028 0.967818928 1.031327788 1 16.19760009 1.743884193 21.02943786 1.01562336 0.978802115 0.095790623 0.044347763 0.761707914 3042.146832 0.023184326 0.01112413 55.44778387 -1.743884193 -0.036821246 VAEAHVPNFIFDEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VAEAHVPNFIFDEFR 15 0 Q12768;E7EQI7 Q12768 KIAA0196 WASH complex subunit strumpellin 0 ; 164.62 1.47E-06 153911000 298400 276560 187295 231950 269690 294560 283840 306930 393590 FALSE TRUE 258965.684 274743.2592 277871.4885 284617.7926 264323.6966 305891.9138 256313.2405 241295.408 347060.2386 0.746169267 0.791629892 0.800643397 0.820081822 0.761607546 0.881379887 0.738526665 0.695255121 1 18.40482656 2.919362161 0.010192743 1.589150161 7.92E-06 0.060042414 0.08307467 11154.39232 154.9721106 12101.33146 12055.28933 830.5430748 -2.919362161 -1.589142244 VAEEHAPSIVFIDEIDAIGTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VAEEHAPSIVFIDEIDAIGTK 21 0 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 221.85 4.15E-25 206815000 266080 210504 166877 212700 211436 165199 259210 328630 326870 FALSE TRUE 230916.8538 209121.1854 247579.2754 260996.7859 207228.8373 171554.3124 234071.8541 258355.0319 288227.801 0.801160933 0.725541341 0.858970837 0.905522594 0.718975881 0.595203904 0.812107136 0.896357086 1 18.13684997 1.574435574 2.485912477 0.9918505 0.770470761 0.452261287 0.084259414 0.276875417 3.549547017 0.109012087 0.024708412 37.53492686 -1.574435574 -0.221379739 VAEFHTELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VAEFHTELER 10 0 K7EJR3;R4GMR5;P48556;K7EJC1;K7ERW6 K7EJR3 PSMD8 26S proteasome non-ATPase regulatory subunit 8 0 ;;;; 182.28 1.79E-06 2578850000 3196430 3033610 2009130 2423200 2951930 3041850 2920160 3273110 3391110 FALSE TRUE 2774013.677 3013682.016 2980751.988 2973424.596 2893192.368 3158871.938 2636963.333 2573180.898 2990216.839 0.927696494 1.007847316 0.996834728 0.994384273 0.967552697 1.056402297 0.881863582 0.860533211 1 21.51181868 2.219572642 24.99999088 0.901621241 0.991762393 0.356550511 0.048209244 218.1934284 287276.1308 0.018940822 0.012792792 165.7954631 -2.219572642 0.090141151 VAEIEHAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VAEIEHAEK 9 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;;; 166.34 6.08E-05 4002240000 10943750 8573140 6727040 8136790 8244440 7108010 10501060 12106690 11179950 FALSE TRUE 9497505.71 8516822.479 9980259.045 9984372.533 8080391.774 7381459.744 9482668.817 9517768.558 9858269.047 0.963405002 0.863926764 1.012374383 1.012791646 0.819656243 0.748758196 0.961899982 0.965460418 1 23.23290292 2.025607891 24.9999864 0.975288429 0.903422677 0.149203019 0.082080598 460.1166767 449191.9374 0.036028021 0.024289179 106.0737423 -2.025607891 -0.071865752 VAEKLDEIYVAGLVAHSDLDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VAEKLDEIYVAGLVAHSDLDER 22 1 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ; 208.65 3.98E-23 392200000 1442790 952350 599640 710690 918490 732290 1133560 1340620 598990 FALSE TRUE 1252121.646 946093.9501 889627.9097 872063.0267 900213.846 760461.6702 1023627.526 1053938.846 528178.0846 2.370642938 1.79124045 1.68433325 1.651077643 1.704375612 1.439782703 1.938034833 1.99542328 1 19.01066492 4.761616338 2.627970476 1.676354531 2.536050001 0.406075196 0.27596031 0.571026483 4.915771976 0.06913766 1.107469489 57758.5575 -4.761616338 0.85969547 VAELALSLSST(ph)SDDEPPSSVSHGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VAELALSLSSTSDDEPPSSVSHGAK 25 0 Q8N1G2;Q5T7F5 Q8N1G2 CMTR1 Cap-specific mRNA (nucleoside-2-O-)-methyltransferase 1 1 VAELALSLS(0.002)S(0.073)T(0.525)S(0.401)DDEPPSSVSHGAK;VAELALSLSS(0.002)T(0.726)S(0.272)DDEPPSSVSHGAK 258.87 2.06E-44 389948000 316098 230965 85970 170565 247600 207246 261607 329640 264437 TRUE FALSE 274324.8484 229447.7757 127545.3796 209294.3902 242673.2444 215218.8877 236236.3934 259149.0513 233175.5591 1.176473424 0.984012975 0.546992918 0.897582881 1.040731908 0.922990765 1.013126737 1.111390286 1 17.83105705 2.455539478 1.24837024 1.063781687 0.89900595 0.09423077 0.16076925 1.002212937 3.22269587 0.116862665 0.066562693 285.4561985 -2.455539478 -0.164775737 VAELALSLSSTS(ph)DDEPPSSVSHGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VAELALSLSSTSDDEPPSSVSHGAK 25 0 Q8N1G2;Q5T7F5 Q8N1G2 CMTR1 Cap-specific mRNA (nucleoside-2-O-)-methyltransferase 1 1 VAELALSLS(0.001)S(0.004)T(0.261)S(0.735)DDEPPSSVSHGAK;VAELALSLSS(0.004)T(0.137)S(0.86)DDEPPSSVSHGAK 250.82 6.43E-40 559630000 498140 386380 129688 256280 374540 320260 429570 520060 445250 TRUE FALSE 432309.5369 383841.8443 192405.5506 314472.291 367087.3868 332580.6094 387910.3675 408849.2161 392613.0522 1.101108418 0.977659408 0.490064071 0.800972584 0.934985184 0.847095143 0.988022088 1.041354111 1 18.58274861 2.18129877 3.355849774 1.022676568 0.846620021 0.170727901 0.156363289 0.414065832 9.50703147 0.074479472 0.047710569 151.809437 -2.18129877 -0.176056546 VAELSSDDFHLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VAELSSDDFHLDR 13 0 Q92896;Q92896-3;Q92896-2;H3BM42 Q92896 GLG1 Golgi apparatus protein 1 0 ;; 272.5 4.08E-32 814390000 800833 764414 447487 516138 745909 848890 525463 776120 846890 FALSE TRUE 695000.89 759392.5141 663893.21 633335.0216 731066.8702 881547.3476 474503.6791 610152.7778 746771.629 0.930673934 1.016900595 0.889017719 0.848097326 0.978969797 1.180477824 0.635406677 0.817054042 1 19.51030759 2.22962421 24.99999963 0.809810126 0.966608967 0.262276635 0.123116942 265.7287691 743381.1167 0.050204124 0.034401673 169.6774819 -2.22962421 0.156798841 VAFISLS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VAFISLSPVR 10 0 Q6ZU65;Q6ZU65-2 Q6ZU65 UBN2 Ubinuclein-2 1 VAFIS(0.002)LS(0.998)PVR;VAFIS(0.376)LS(0.624)PVR;VAFISLS(1)PVR;VAFIS(0.001)LS(0.999)PVR 128.97 0.00033087 289006000 296638 413481 236072 315294 438493 403692 394628 440105 505659 TRUE FALSE 257436.5367 410764.8161 350237.2088 386886.3217 429767.8472 419222.2925 356357.0373 345991.9707 445880.5691 0.577366574 0.921244038 0.785495563 0.867690473 0.963863144 0.940212069 0.799220827 0.775974543 1 18.7662978 4.744756996 24.49237571 0.87053534 0.5773664 0.60025995 0.07757775 400.7465671 1583968.398 0.019535082 0.173790542 55559.32952 -4.744756996 -0.293168941 VAFRGS(ph)DEIFCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VAFRGSDEIFCR 12 1 F5GYJ3;F5H2D5;A0A087WVW6;Q9UHV5-2;Q9UHV5-3;Q9UHV5 F5GYJ3 RAPGEFL1 Rap guanine nucleotide exchange factor-like 1 1 VAFRGS(1)DEIFCR;VAFRGS(1)DEIFCR 156 4.41E-05 438470000 209619 238654 148253 168744 214735 234467 224293 247197 219866 TRUE FALSE 181917.318 237086.2662 219948.6467 207059.9043 210462.1936 243487.0972 202541.0994 194335.8452 193873.692 0.938329054 1.222890346 1.134494549 1.068014449 1.085563449 1.255905816 1.044706465 1.002383785 1 17.56475752 2.01293721 24.99779712 1.008017019 1.121965344 0.247278425 0.085853219 280.0165188 541057.2357 0.033231971 0.022390195 103.0237158 -2.01293721 0.113948325 VAGGAAPSKPAS(ph)AK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VAGGAAPSKPASAK 14 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 VAGGAAPSKPAS(1)AK 94.544 0.0038369 0 120590 91095 85833 77914 98773 68392 122460 132030 173600 TRUE FALSE 104653.726 90496.59095 127342.1259 95605.56454 96807.61055 71023.0845 110583.848 103796.412 153077.2058 0.683666294 0.591182668 0.831881698 0.624557811 0.632410358 0.463969042 0.722405713 0.678065761 1 17.22389995 1.073823308 2.206674505 1.246104983 0.646315791 0.573306256 0.093875866 0.89783211 2.954258106 1.279351969 0.024785814 11.85286418 -1.073823308 -0.599789192 VAGHPLAQNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VAGHPLAQNER 11 0 O60493-4;O60493;O60493-2 O60493-4 SNX3 Sorting nexin-3 0 ;; 121.36 0.00041322 1585740000 785870 872160 542611 623061 828180 953530 800400 917680 968990 FALSE TRUE 682015.2884 866430.7235 805019.4945 764536.5229 811700.8383 990212.9161 722777.3312 721441.2734 854437.1061 0.798204202 1.014036864 0.942163547 0.89478385 0.949983132 1.158906734 0.845910514 0.844346843 1 19.70461478 4.756860546 23.55050571 0.94612389 0.798203918 0.219908546 0.091808386 3185.654613 4099527.072 0.023316034 0.69075271 57129.51613 -4.756860546 -0.147919972 VAHALAEGLGVIACIGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VAHALAEGLGVIACIGEK 18 0 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3 P60174 TPI1 Triosephosphate isomerase 0 ; 220.59 6.70E-19 726910000 949480 947180 545250 533180 636860 605460 881270 1018560 797910 FALSE TRUE 824003.8123 940957.9122 808934.7238 654246.6681 624187.732 628752.438 795804.571 800748.8704 703581.9888 1.171155353 1.337382035 1.14973768 0.929879785 0.887157065 0.893644874 1.131075815 1.13810314 1 19.42435903 3.972833955 5.264933764 1.011949412 1.253745479 0.565713567 0.09461318 0.151235483 11.98641289 0.028867936 0.054640236 9393.640927 -3.972833955 0.241796067 VAHFLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VAHFLEK 7 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ; 111.28 0.0066147 2548600000 6352500 5899200 3970500 4616200 5784100 4785300 6508500 7346200 6865300 FALSE TRUE 5513001.03 5860447.767 5890647.081 5664378.764 5669007.726 4969393.588 5877306.672 5775272.298 6053692.055 0.910684088 0.968078276 0.973066854 0.935689941 0.936454592 0.820886418 0.970863172 0.954008272 1 22.52938386 1.503275097 1.988574366 0.99930948 0.929676493 0.206450666 0.043740347 0.755488749 4.970328437 0.085491959 0.01255227 31.86215141 -1.503275097 -0.069632987 VAHLALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VAHLALK 7 0 Q5VWC4;P55036-2;P55036;A6PVX3 Q5VWC4 PSMD4 26S proteasome non-ATPase regulatory subunit 4 0 ; 90.285 0.017251 1126770000 2019830 2281350 1397940 1735490 2077940 1943410 2346120 2825610 2660910 FALSE TRUE 1752904.348 2266363.662 2073988.46 2129559.53 2036593.059 2018174.24 2118593.644 2221375.29 2346340.251 0.747080202 0.965914326 0.883924852 0.907609 0.867987095 0.860137075 0.902935387 0.946740478 1 21.16198081 1.529176014 1.706961549 1.010463128 0.878315168 0.382693546 0.054192856 0.544574156 2.517280434 0.106198704 0.014591252 33.82018772 -1.529176014 -0.13214796 VAHSDKPGSTSTASFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VAHSDKPGSTSTASFR 16 1 Q9P0L0-2;Q9P0L0 Q9P0L0-2 VAPA Vesicle-associated membrane protein-associated protein A 0 161.91 4.97E-09 141230000 200220 127280 87926 156590 176490 167650 140530 208560 191710 FALSE TRUE 173760.4197 126443.8893 130447.3077 192146.1528 172978.1943 174099.604 126901.4222 163961.067 169046.2622 1.027886789 0.74798394 0.771666324 1.136648337 1.023259503 1.029893248 0.750690495 0.969918322 1 17.36705859 5.0633215 21.32721493 0.928774997 3.24920652 0.052320667 0.132586221 2172.126961 800340.7378 0.032113142 22266.61603 115696.8407 -5.0633215 2.320431524 VAHSFNCTPIEGMLSHQLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VAHSFNCTPIEGMLSHQLK 19 0 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 296.57 5.92E-50 1906310000 1470830 1306890 729820 1063170 1197670 1009780 1366540 1647600 1260190 FALSE TRUE 1276456.089 1298304.954 1082763.393 1304578.998 1173838.71 1048626.89 1234013.161 1295273.562 1111211.774 1.148706411 1.168368608 0.974398777 1.174014737 1.056359137 0.943678707 1.110511237 1.165640603 1 20.08370236 VAIEHLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VAIEHLDK 8 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;;;; 147.19 0.00054134 6229680000 15883070 13275490 9152340 11266840 12678260 10858350 15588570 17757890 15682420 FALSE TRUE 13784082.06 13188282.43 13578442.24 13825148.22 12425987.43 11276077.75 14076792.88 13960503.42 13828462.17 0.996790669 0.953705645 0.981919903 0.999760353 0.898580571 0.815425288 1.017957941 1.009548512 1 23.72113739 VAILVDDMADTCGTICHAADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 327.42 5.40E-80 311870000 452670 350890 260570 324200 357160 287890 419990 515950 440710 FALSE TRUE 392848.5126 348584.9805 386582.5236 397814.5651 350053.2148 298965.3146 379259.4344 405618.1076 388609.7659 1.010907463 0.897005199 0.994783347 1.023686485 0.900783371 0.769320127 0.975939021 1.04376715 1 18.56796263 2.000048331 24.99999997 1.020462805 0.931290655 0.203136433 0.073188953 2.562315852 1324645.545 0.031624343 0.021080277 100.0111293 -2.000048331 -0.08917215 VAIQLNDTHPALSIPELMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VAIQLNDTHPALSIPELMR 19 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 162.33 2.78E-11 1097210000 511380 506990 354200 431380 465070 490900 453740 499600 713020 FALSE TRUE 443799.8373 503659.5493 525492.3047 529331.4222 455816.0169 509785.2407 409736.3646 392764.4279 628727.5879 0.705869833 0.80107754 0.835802842 0.841909012 0.724981734 0.810820537 0.651691404 0.624697302 1 19.26207554 3.220809631 24.96230468 0.739333683 0.799347014 0 0.108508823 727.247086 1022687.152 0.033078217 0.037584596 1662.683667 -3.220809631 0.060013331 VAKPVVEMDGDEMTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VAKPVVEMDGDEMTR 15 1 P48735;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;;; 184.99 4.03E-07 3058560000 1389220 1274050 1008010 1563250 1469590 1374780 1426390 1749480 1500370 FALSE TRUE 1205631.057 1265680.682 1495487.008 1918209.805 1440348.034 1427668.676 1288058.917 1375367.316 1322997.968 0.911287157 0.95667621 1.130377403 1.44989626 1.088700111 1.079116303 0.973591002 1.039583847 1 20.33537941 -1.132902018 11.64953309 0.300388148 1.073661036 0 0.149695084 0 0 0 0.035608834 0.073637321 1.132902018 0.773272887 VALAAGS(ph)PARPPPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VALAAGSPARPPPAR 15 1 C9J069 C9J069 C9orf172 Uncharacterized protein C9orf172 1 VALAAGS(1)PARPPPAR;VALAAGS(1)PARPPPAR 116.06 0.00028971 504580000 327940 267120 192388 216732 317960 329670 285160 321320 315220 TRUE FALSE 284601.8981 265365.2711 285427.4803 265944.3131 311633.2181 342352.6182 257505.2271 252608.2185 277955.0507 1.02391339 0.9547057 1.02688359 0.956788921 1.121164078 1.231683387 0.926427588 0.9088096 1 18.08449207 VALS(ph)DDETKETENMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 VALSDDETKETENMR 15 1 Q15054;H0YD46;Q15054-3;Q15054-2 Q15054 POLD3 DNA polymerase delta subunit 3 1 VALS(1)DDETKETENMR;VALS(1)DDETKETENMR;VALS(1)DDETKETENMR;VALS(1)DDETKETENMR;VALS(0.589)DDET(0.235)KET(0.176)ENMR;VALS(1)DDETKETENMR;VALS(1)DDETKETENMR;VALS(1)DDETKETENMR 275.91 9.65E-34 7762750000 5042680 4136440 3461390 3687330 4320980 3484560 4827960 5990240 5416430 TRUE FALSE 4376277.061 4109267.453 5135329.782 4524594.634 4235000.952 3618613.278 4359745.182 4709273.792 4776105.816 0.916285616 0.860380321 1.075212732 0.947339696 0.886705847 0.75764931 0.912824244 0.986007005 1 22.18740337 1.70685021 4.545552786 0.995260495 0.907381912 0.170744281 0.078128898 0.311247707 15.19810515 0.054882987 0.021871715 50.91552314 -1.70685021 -0.087878583 AAS(ph)LTEDRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 AASLTEDRDR 10 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 AAS(0.998)LT(0.002)EDRDR;AAS(0.999)LT(0.001)EDRDR;AAS(1)LTEDRDR;AAS(0.991)LT(0.009)EDRDR 194.24 2.94E-07 4641850000 8118850 4746750 2126340 2252430 2191030 1862660 2379570 2083660 2281160 TRUE FALSE 7045923.402 4715568.287 3154645.136 2763878.658 2147432.79 1934317.736 2148799.668 1638085.524 2011483.864 3.502848583 2.3443232 1.568317397 1.37404963 1.067586387 0.961637213 1.068265924 0.814366724 1 20.93982873 5.628915391 0.638401761 0.911756406 10.11426462 0.990796704 0.079132385 0.749514947 0.101065719 0.034757944 6.499644269 425515.506 -5.628915391 9.20250821 up VANDNAPEHALRPGFLSTFALATDQGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VANDNAPEHALRPGFLSTFALATDQGSK 28 1 Q9UHA4 Q9UHA4 LAMTOR3 Ragulator complex protein LAMTOR3 0 157.31 3.30E-09 207740000 135870 108490 73749 102740 92023 99734 109620 142420 110410 FALSE TRUE 117914.4352 107777.322 109414.2631 126068.6873 90191.92234 103570.8315 98989.06927 111964.5913 97357.45558 1.211149516 1.107026898 1.123840618 1.294905321 0.926399748 1.063820237 1.016759001 1.150036129 1 16.57100384 3.238520377 25 1.046754733 1.174402452 0.494311028 0.075642925 1.098773296 682412.9 0.022356344 0.027013187 1731.890287 -3.238520377 0.12764772 VANILHDDCAFLSAFGDVSKPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VANILHDDCAFLSAFGDVSKPER 23 1 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 155.17 1.90E-08 363030000 295900 248590 198190 201160 233100 238410 226830 332110 304430 FALSE TRUE 256796.0653 246956.9959 294035.3469 246836.4525 228461.7661 247581.787 204832.0615 261090.861 268440.6322 0.956621444 0.919968761 1.095345904 0.919519711 0.85106999 0.922296245 0.763044178 0.972620497 1 18.03424353 3.499170034 24.41470116 0.899822544 0.987553569 0.216791598 0.077509107 889.7799371 985254.3113 0.021384404 0.031381044 3156.240109 -3.499170034 0.087731025 VANPSGNLTETYVQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VANPSGNLTETYVQDR 16 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ; 77.912 0.015626 0 84622 94166 60031 69339 100014 94059 80486 98454 95720 FALSE TRUE 73438.9883 93547.41735 89062.19239 85083.47973 98023.91707 97677.51059 72680.48011 77400.37827 84404.09064 0.870088022 1.108328004 1.055188104 1.008049244 1.16136453 1.157260387 0.861101394 0.917021648 1 16.3650253 2.230475904 24.99983332 0.92145616 1.064262038 0.335503272 0.088692167 193.4650602 598232.9732 0.035422594 0.024352013 170.0105622 -2.230475904 0.142805878 VANS(ph)PTMVNLLLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VANSPTMVNLLLGK 14 0 Q6UB99;A0A087WTN8;A0A2R8Y438 Q6UB99 ANKRD11 Ankyrin repeat domain-containing protein 11 1 VANS(0.997)PT(0.003)MVNLLLGK;VANS(0.952)PT(0.048)MVNLLLGK 146.2 8.78E-06 178102000 470530 415060 253340 320090 417350 469360 444530 498230 416700 TRUE FALSE 408348.2683 412333.4435 375856.0714 392771.3268 409045.5515 487416.5829 401419.549 391687.3917 367438.2007 1.111338635 1.122184473 1.022909623 1.06894527 1.113236323 1.326526697 1.092481806 1.065995291 1 18.4871421 1.532932422 2.582992173 1.005369914 1.123914291 0.208325145 0.078563912 0.495758972 6.517606296 0.107283402 0.022478722 34.11398244 -1.532932422 0.118544377 VANVELYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VANVELYYR 9 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 158.87 0.00015466 1318260000 790010 867260 540850 593200 864660 901730 858170 909650 969940 FALSE TRUE 685608.1769 861562.912 802406.869 727895.1265 847454.9577 936420.1366 774944.8055 715128.4264 855274.7982 0.801623266 1.007352156 0.938186032 0.851065796 0.990856926 1.094876335 0.906076979 0.83613878 1 19.7060285 4.756334546 23.57012594 0.943690826 0.801623003 0.26751219 0.077385855 2693.604584 3571878.601 0.020090751 0.556712057 57060.36506 -4.756334546 -0.142067823 VAPEEHPVLLTEAPLNPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 VAPEEHPVLLTEAPLNPK 18 0 P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65 P60709;P63261 ACTB;ACTG1 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 ;;;;;;; 252.3 1.77E-30 46349560000 26617032 20964845 14228259 19329244 19388319 17300529 23084889 28771606 24439476 FALSE TRUE 23099523.78 20827125.55 21109092.64 23718244.28 19002529.38 17966091.55 20846120.02 22619021.96 21550268.99 1.071890276 0.966443879 0.979528035 1.100600846 0.8817769 0.833682937 0.967325282 1.049593486 1 24.36120254 4.742023272 22.84865049 0.975231699 1.071890395 0.14679771 0.075121099 231.3899977 1526594.948 0.019651378 0.13707405 55210.70233 -4.742023272 0.096658696 VAPLWHSS(ph)SEVISMADR ddPTM_MDA-MB-175_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(0.005)S(0.829)S(0.165)EVISMADR;VAPLWHS(0.005)S(0.995)SEVISMADR;VAPLWHS(0.007)S(0.99)S(0.003)EVISMADR 198.49 9.11E-12 987457000 307493 322781 195190 214799 307110 324229 294698 300111 316533 TRUE FALSE 266857.021 320660.6304 289584.5369 263572.3959 300999.1119 336702.2994 266118.2333 235934.5981 279112.8293 0.956090129 1.148856651 1.037517829 0.944322038 1.078413746 1.20633043 0.953443215 0.845301876 1 18.09048891 2.015091845 24.96611151 0.907932488 1.06181154 0.334199447 0.086093101 218.7026995 361793.7728 0.034594125 0.023314247 103.5361103 -2.015091845 0.153879052 VAPSGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VAPSGSK 7 0 A0A0U1RQK4 A0A0U1RQK4 0 77.748 0.086555 79915000 348880 332450 229870 271140 179140 261100 368830 386090 432990 FALSE TRUE 302774.6241 330266.1141 341035.9009 332706.4811 175575.4645 271144.686 333060.9234 303527.6581 381802.4155 0.793013904 0.865018399 0.893226148 0.8714101 0.459859491 0.710170169 0.87233844 0.794986217 1 18.5424667 0.610894384 1.427477059 1.805800671 0.775519359 0.225397864 0.126758729 10.81941093 5.151340497 25.27686065 0.038860935 4.082200994 -0.610894384 -1.030281312 VAPVINNGS(ph)PTILGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VAPVINNGSPTILGK 15 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;F8W9Y9 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 VAPVINNGS(1)PTILGK;VAPVINNGS(0.997)PT(0.003)ILGK;VAPVINNGS(0.551)PT(0.449)ILGK 260.18 7.18E-25 1295440000 1787810 1539360 894860 1206500 1504790 1187550 1545850 1968420 1670950 TRUE FALSE 1551546.379 1529247.843 1327617.289 1480454.265 1474847.623 1233235.817 1395933.705 1547488.701 1473412.195 1.053029413 1.03789547 0.901049478 1.00477943 1.000974221 0.836993084 0.947415604 1.050275481 1 20.49072966 4.408417639 11.45345967 0.968371523 1.049252925 0.244431428 0.059947462 0.773401885 125.2802778 0.015869684 0.042030835 25610.47535 -4.408417639 0.080881401 VAPVINNGSPT(ph)ILGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VAPVINNGSPTILGK 15 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;F8W9Y9 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 VAPVINNGS(0.194)PT(0.806)ILGK 182.35 6.15E-06 309390000 296740 288100 195670 248000 285620 236380 304570 390270 364940 TRUE FALSE 257525.0572 286207.4521 290296.6665 304312.1904 279936.7208 245473.6916 275032.8483 306813.7976 321797.2089 0.800271258 0.889403153 0.902110579 0.945664481 0.869916559 0.762821071 0.854677544 0.953438343 1 18.29579229 1.606415856 3.600226645 0.991077458 0.863346 0.481481079 0.0509939 0.172541375 5.095899295 0.044978382 0.014441962 40.40320865 -1.606415856 -0.127731458 VAQGATEKS(ph)PEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VAQGATEKSPEDK 13 1 P49321;P49321-3;P49321-4 P49321 NASP Nuclear autoantigenic sperm protein 1 VAQGAT(0.004)EKS(0.996)PEDK;VAQGAT(0.047)EKS(0.953)PEDK 108.56 0.00073085 678470000 1070670 607160 661220 587820 592980 476380 909030 952690 1434040 TRUE FALSE 929178.2468 603171.526 980988.2036 721293.5153 581180.8581 494706.6469 820872.4105 748964.6573 1264509.425 0.734813224 0.477000419 0.775785601 0.570413712 0.459609748 0.391224167 0.649162746 0.592296619 1 20.27014636 1.216654648 3.987256046 1.059146879 0.574278589 0.547080068 0.119526805 0.22201236 5.904593467 0.325109997 0.030083197 16.4685229 -1.216654648 -0.484868291 VAQLEQVYIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VAQLEQVYIR 10 0 P62318;P62318-2 P62318 SNRPD3 Small nuclear ribonucleoprotein Sm D3 0 ; 102.06 0.0069722 148995000 286500 255480 158816 180269 250290 252680 235510 268560 268650 FALSE TRUE 248638.2991 253801.7351 235619.9488 221201.8317 245309.7187 262400.7631 212670.2764 211130.5339 236890.503 1.049591672 1.071388392 0.994636534 0.933772476 1.035540537 1.107687981 0.897757714 0.891257907 1 17.85386084 2.217934392 24.9830086 0.920339173 1.02787232 0.437965235 0.05421729 219.3828514 265720.0994 0.023109275 0.015599768 165.171226 -2.217934392 0.107533147 VAQRS(ph)PVDSGTILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VAQRSPVDSGTILR 14 1 P49454 P49454 CENPF Centromere protein F 1 VAQRS(0.999)PVDS(0.001)GTILR 66.152 0.034019 204640000 120120 90744 81420 80259 63805 67196 92118 83965 62618 TRUE FALSE 104245.8377 90147.89669 120794.9843 98483.03263 62535.40533 69781.0736 83184.41054 66009.73817 55215.37137 1.88798581 1.632659429 2.18770573 1.783616232 1.132572394 1.263797958 1.506544436 1.195495684 1 15.75278233 3.308101269 5.468472162 1.240781324 1.889844492 0.759021932 0.183250102 0.100370008 5.494392759 0.053418657 0.068698574 2032.830972 -3.308101269 0.649063168 VAQSIEDHHQEVIGFCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VAQSIEDHHQEVIGFCR 17 0 Q9NZB2;Q9NZB2-4;Q9NZB2-6;Q9NZB2-2;Q9NZB2-5;A0A0C4DH52 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 0 64.454 0.026274 129280000 80481 70956 37160 58941 62788 72377 58899 85263 73773 FALSE TRUE 69845.23194 70489.88536 55130.70029 72324.45491 61538.64164 75161.39002 53186.98405 67030.17097 65051.63998 1.073689025 1.083598897 0.847491321 1.111800639 0.945996775 1.155411148 0.817611732 1.030414775 1 15.98929781 2.247337629 24.9999691 0.960743514 1.029220465 0.132542415 0.102475803 453.4443181 1291568.134 0.036334115 0.027701649 176.7411305 -2.247337629 0.068476951 VAQTEFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VAQTEFDR 8 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39 B7ZC38 SH3GLB2 Endophilin-B2 0 100.98 0.0133 204110000 330260 346470 202320 240860 310590 311730 327550 354760 309610 FALSE TRUE 286615.3042 344194.0158 300162.6287 295550.9443 304409.8667 323722.4548 295784.2514 278897.3347 273008.2585 1.049841151 1.260745802 1.099463549 1.082571443 1.115020726 1.185760667 1.083426022 1.021571055 1 18.05858507 1.839623709 2.774873083 1.007087745 1.133623724 0.419171724 0.05829945 0.238150156 3.321529874 0.039504229 0.015631301 69.12317995 -1.839623709 0.126535979 VAQWMIQQPHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VAQWMIQQPHK 11 0 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZGZ8 P55263-3 ADK Adenosine kinase 0 156.12 3.12E-05 970770000 426270 458110 319450 404200 482500 416480 505140 581880 582950 FALSE TRUE 369937.3395 455100.6452 473937.0885 495979.7878 472899.194 432502.2551 456151.6005 457449.4902 514034.3151 0.719674404 0.885350709 0.921995039 0.964876805 0.919975924 0.841387904 0.887395232 0.889920141 1 18.97150515 4.736601409 3.287806862 0.912590787 0.693504126 0.671391892 0.043145469 0.204930426 3.61246473 0.011054726 0.113925895 54525.71999 -4.736601409 -0.219086661 VARPTSSEVDRFS(ph)PSGSVVPLTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VARPTSSEVDRFSPSGSVVPLTER 24 2 Q5TC79;Q5TC79-2 Q5TC79 ZBTB37 Zinc finger and BTB domain-containing protein 37 1 VARPTSSEVDRFS(0.939)PS(0.061)GSVVPLTER;VARPTSSEVDRFS(0.998)PS(0.002)GSVVPLTER 180.86 1.79E-17 426910000 220281 193564 124226 147810 196283 184886 209577 218917 170507 TRUE FALSE 191170.3077 192292.4653 184302.1091 181372.5196 192377.3523 191998.6841 189252.2548 172103.3032 150349.8567 1.271503092 1.278966735 1.225821648 1.206336498 1.279531331 1.277012751 1.258745828 1.144685515 1 17.19796397 1.37789328 2.050087107 0.962406734 1.256889784 0.919560714 0.024754665 0.149926315 0.827809033 0.076307627 0.00741105 23.87224595 -1.37789328 0.294483051 VAS(ph)DTEEADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VASDTEEADR 10 0 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 VAS(0.976)DT(0.024)EEADR;VAS(0.996)DT(0.004)EEADR 147.58 0.0026176 0 638520 532820 401660 395830 525720 524330 462580 513000 572290 TRUE FALSE 554137.9642 529319.8703 595904.1195 485709.2514 515259.2006 544501.3144 417719.0628 403298.9422 504634.5282 1.0980976 1.048917267 1.180862756 0.962497063 1.021054192 1.079001305 0.82776552 0.799190146 1 18.9448794 2.240917215 24.99997406 0.857727072 1.062937376 0.576412312 0.076015773 39.20509574 415914.4229 0.029095035 0.021442643 174.1474881 -2.240917215 0.205210304 VAS(ph)FRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VASFRK 6 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 1 VAS(1)FRK;VAS(1)FRK 61.962 0.073889 474470000 668280 609550 432980 486000 485000 498600 666520 744280 739150 TRUE FALSE 579965.1048 605545.8259 642370.5762 596353.728 475349.4489 517781.4646 601880.993 585121.514 651768.529 0.889832938 0.929081106 0.985580843 0.91497779 0.729322494 0.794425385 0.923458201 0.897744349 1 19.31400017 6.641722797 15.39343535 0.893783475 0.476027004 0 0.08112758 0 0 0.019301475 0 4382508.8 -6.641722797 -0.417756471 VAS(ph)FSIPGSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VASFSIPGSSSR 12 0 Q14573 Q14573 ITPR3 "Inositol 1,4,5-trisphosphate receptor type 3" 1 VAS(0.999)FS(0.001)IPGSSSR;VAS(0.999)FS(0.001)IPGSSSR 168.31 4.92E-05 293360000 527740 449520 329290 426720 540170 534070 393010 592550 625830 TRUE FALSE 457997.8219 446567.0735 488535.7454 523613.298 529421.6738 554616.0185 354895.9507 465837.7937 551845.0903 0.829939108 0.809225417 0.885276963 0.948841092 0.959366465 1.005021206 0.643107924 0.844145942 1 19.07390382 4.231406304 22.48279499 0.887340543 0.819582267 0.082698227 0.103947143 134.1196099 421500.9588 0.028198778 0.061022104 17037.51707 -4.231406304 -0.067758276 VAS(ph)GSDLHLTDIDSDSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VASGSDLHLTDIDSDSNR 18 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VAS(0.672)GS(0.328)DLHLTDIDSDSNR 246.31 1.81E-24 608150000 224290 213660 123060 145550 187970 223830 223540 206200 218050 TRUE FALSE 194649.5082 212256.4534 182572.2276 178599.3521 184229.7648 232440.8849 201861.1252 162105.7347 192272.3774 1.012363351 1.103936282 0.949549957 0.928887209 0.958170733 1.208914604 1.049870647 0.843104646 1 17.55279199 1.75548099 25 0.914862157 1.030174628 0.201569321 0.089712859 9.43376989 13958.045 0.049334862 0.023691211 56.94832966 -1.75548099 0.115312471 VAS(ph)PTSGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VASPTSGVK 9 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 VAS(0.981)PT(0.016)S(0.003)GVK;VAS(0.907)PT(0.08)S(0.013)GVK 129.89 0.00039505 742920000 956050 774250 746670 832160 890040 802930 1257380 1341560 1676210 TRUE FALSE 829705.5702 769163.9008 1107762.109 1021114.647 872329.9453 833819.2367 1135439.481 1054677.834 1478050.363 0.561351352 0.520390861 0.749475212 0.690852404 0.590189595 0.564134523 0.768200806 0.713560147 1 20.495264 -0.650396357 0.839351502 9.999999742 0.619223566 0.695343552 0.077434087 30.14898077 1.08558272 490.1656664 0.028819902 0.223667891 0.650396357 -9.380776176 VAS(ph)SPAPPEGPSHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VASSPAPPEGPSHPR 15 0 O14578-4;H7BYJ3;O14578;O14578-3 O14578-4 CIT Citron Rho-interacting kinase 1 VAS(0.5)S(0.5)PAPPEGPSHPR 105.9 0.00082374 197460000 88846 97810 55075 65182 78140 99607 75307 96950 118480 TRUE FALSE 77104.77599 97167.47967 81709.45421 79982.56934 76585.16688 103438.9457 68003.73873 76217.99697 104473.4294 0.738032402 0.930068825 0.782107515 0.765578098 0.733058801 0.990098117 0.650918986 0.72954432 1 16.67277654 VASEAPLEHKPQVEAS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VASEAPLEHKPQVEASSPR 19 1 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 VASEAPLEHKPQVEAS(0.5)S(0.5)PR;VASEAPLEHKPQVEAS(0.5)S(0.5)PR;VASEAPLEHKPQVEAS(0.597)S(0.403)PR;VASEAPLEHKPQVEAS(0.5)S(0.5)PR;VASEAPLEHKPQVEAS(0.5)S(0.5)PR;VASEAPLEHKPQVEAS(0.5)S(0.5)PR 189.33 8.60E-15 4738770000 2990370 2851240 1913960 2165420 2926090 2530280 3220670 3859110 3738210 TRUE FALSE 2595185.028 2832510.017 2839557.458 2657111.707 2867866.534 2627621.509 2908329.919 3033869.358 3296283.072 0.787306482 0.859304239 0.861442235 0.806093302 0.870030416 0.797146802 0.882305875 0.920391026 1 21.65240871 1.452519936 1.374149085 1.033449845 0.83347747 0.777468125 0.029740915 0.365350902 0.857460811 0.095654253 0.008485497 28.34783761 -1.452519936 -0.199972374 VASEAPLEHKPQVEASS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VASEAPLEHKPQVEASSPR 19 1 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 VASEAPLEHKPQVEAS(0.159)S(0.841)PR 218.93 1.96E-19 1448000000 1496800 1352200 983500 1160300 1507200 1294900 1645600 1995100 1856500 TRUE FALSE 1298994.088 1343317.309 1459123.89 1423763.849 1477209.669 1344715.641 1486009.965 1568463.391 1637026.685 0.793508194 0.820583636 0.89132566 0.869725498 0.902373604 0.821437826 0.907749384 0.95811718 1 20.64264641 -2 0.345703195 2.898353023 0.827321369 0.725630293 0.03323121 42.19002443 0.657782366 55.92613724 0.04807478 0.01 2 -2.071031654 VASGPSPGEGIS(ph)PQSAQAPQAPGDNHVVPVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VASGPSPGEGISPQSAQAPQAPGDNHVVPVLR 32 0 Q14764 Q14764 MVP Major vault protein 1 VASGPSPGEGIS(1)PQSAQAPQAPGDNHVVPVLR;VASGPSPGEGIS(0.992)PQS(0.008)AQAPQAPGDNHVVPVLR 298.01 8.71E-90 1444460000 184228 193564 127487 153905 175290 192428 158895 180622 223610 TRUE FALSE 159881.803 192292.4653 189140.1396 188851.4825 171802.0719 199830.8297 143485.3874 141997.3909 197175.0805 0.810862116 0.975237159 0.959249714 0.957785751 0.871317367 1.01346899 0.727705484 0.720158909 1 17.58911771 2.2346455 24.99948729 0.792320267 0.933061513 0.235749345 0.094750865 113.8374112 726882.4831 0.03660601 0.025721471 171.6506689 -2.2346455 0.140741246 VASGS(ph)DLHLTDIDSDSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VASGSDLHLTDIDSDSNR 18 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VAS(0.397)GS(0.603)DLHLTDIDSDSNR 174.91 3.00E-12 688250000 278380 250310 132900 175850 206900 238800 249400 247900 245990 TRUE FALSE 241591.3777 248665.6971 197170.8845 215779.4302 202783.0948 247986.7905 225213.2264 194888.5142 216909.3424 1.113789637 1.146403812 0.909001347 0.994790855 0.934874877 1.143273903 1.03828274 0.898479116 1 17.72673267 4.254536434 24.99940846 0.986881072 1.130096824 0.412589404 0.070278957 242.8958911 380083.7287 0.018135683 0.047648346 17969.51824 -4.254536434 0.143215752 VASGSDLHLTDIDS(ph)DSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VASGSDLHLTDIDSDSNR 18 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VASGSDLHLTDIDS(0.999)DS(0.001)NR;VASGSDLHLTDIDS(1)DSNR 151.42 3.08E-08 422640000 572170 535510 239423 397820 495330 543880 538820 568640 559100 TRUE FALSE 496556.2848 531992.1995 355208.7636 488151.1113 485473.9021 564803.4155 486565.3193 447040.7612 493003.8349 1.007205725 1.079083289 0.720498987 0.990156824 0.984726421 1.145636962 0.986940232 0.906769338 1 18.91123934 VASGSDLHLTDIDSDSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VASGSDLHLTDIDSDSNR 18 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 155.1 2.13E-08 440430000 538050 531500 243784 411210 609560 615300 578520 658420 609740 FALSE TRUE 466945.3293 528008.5415 361678.7578 504581.5155 597430.9486 638970.9892 522415.2194 517622.0068 537657.2318 0.868481444 0.982054198 0.672693933 0.938481779 1.111174394 1.188435589 0.97165106 0.962736063 1 19.03632719 3.475814428 22.82511948 1.036563712 0.846909888 0.472900161 0.099282658 13.65181135 238429.7624 0.029758845 0.038811706 2990.986327 -3.475814428 -0.189653824 VASNPYTWFTMEALEETWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VASNPYTWFTMEALEETWR 19 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 145.1 2.99E-07 158170000 21763 24703 8029.1 19155 29561 23869 29809 34815 30917 FALSE TRUE 18886.96441 24540.72437 11911.99962 23504.43552 28972.79394 24787.25588 26918.12777 27370.08318 27262.02748 0.692793829 0.900179724 0.436944744 0.862167553 1.062752723 0.90922276 0.987385395 1.003963597 1 14.73460524 3.483312522 22.21443605 0.987050301 0.690753858 0.607613358 0.115722019 41.35183747 148372.1099 0.030830421 0.041391959 3043.074058 -3.483312522 -0.296296442 VASPLS(ph)PTSLTHTSRPPAALTPVPLSQGDLSHPPR ddPTM_MDA-MB-175_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(0.004)PLS(0.944)PT(0.024)S(0.024)LT(0.004)HTSRPPAALTPVPLSQGDLSHPPR;VAS(0.006)PLS(0.984)PT(0.004)S(0.004)LT(0.001)HT(0.001)SRPPAALTPVPLSQGDLSHPPR 272.24 3.08E-74 1012910000 227180 231440 68399 136781 328670 304600 221630 326030 266600 TRUE FALSE 197157.5874 229919.6554 101476.9852 167839.2166 322130.11 316318.1591 200136.3567 256311.0217 235082.8517 0.838672774 0.978036695 0.43166477 0.713957719 1.370283318 1.345560328 0.851343921 1.090300802 1 17.84280978 3.263282611 24.99288568 1.116039675 0.735478165 0.481858458 0.201041925 215.9167869 218281.2178 0.060561675 0.078150251 1833.507162 -3.263282611 -0.38056151 VASPSQGQVGSS(ph)SPKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VASPSQGQVGSSSPKR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 VASPSQGQVGS(0.004)S(0.498)S(0.498)PKR 171.29 5.27E-09 30848000 82345 65455 45522 65429 64184 59068 58892 99830 63192 TRUE FALSE 71462.89961 65025.0218 67536.59146 80285.65447 62906.86397 61340.38418 53180.6629 78482.13138 55721.51375 1.282501045 1.166964381 1.212037989 1.440837642 1.128951095 1.100838438 0.954400901 1.408470914 1 15.76594683 VASPSQGQVGSSS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VASPSQGQVGSSSPK 15 0 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 VASPSQGQVGSSS(1)PK 227.41 7.10E-13 0 192150 147990 111450 169670 178750 131440 148960 226630 278300 TRUE FALSE 166756.8907 147017.8439 165347.5928 208196.1667 175193.2247 136496.5819 134513.8821 178166.9381 245399.691 0.679531787 0.599095473 0.67378892 0.848396206 0.71390972 0.55622149 0.548142019 0.726027557 1 17.90477391 1.264599634 3.79841214 1.031762051 0.66199172 0.604413902 0.085851714 0.179363014 4.174143953 0.178696999 0.02361347 18.39075817 -1.264599634 -0.369770331 VASPSQGQVGSSS(ph)PKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VASPSQGQVGSSSPKR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 VASPSQGQVGS(0.002)S(0.038)S(0.96)PKR;VASPSQGQVGSS(0.03)S(0.97)PKR;VASPSQGQVGS(0.033)S(0.197)S(0.77)PKR 212.34 2.92E-12 1249719000 638367 519432 351718 594307 600139 465822 491591 753890 560083 TRUE FALSE 554005.1835 516019.817 521810.0012 729253.4878 588197.4081 483742.4738 443916.5805 592676.4903 493870.6258 1.121761762 1.044848165 1.056572256 1.476608346 1.190994923 0.979492297 0.898851961 1.200064266 1 18.91377364 2.750620928 24.13321833 1.036479013 1.180576964 0.237836547 0.139555392 827.6613957 1656186.353 0.04783197 0.047450489 563.1459013 -2.750620928 0.14409795 VASS(ph)PVMVSNPATR ddPTM_MDA-MB-175_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(0.015)S(0.985)PVMVSNPATR;VAS(0.002)S(0.998)PVMVSNPATR;VAS(0.002)S(0.998)PVMVSNPATR;VASS(1)PVMVSNPATR 358.81 2.67E-82 1296660000 1398420 1435160 886860 1002790 1283230 1350610 1279060 1569560 1464400 TRUE FALSE 1213615.254 1425732.339 1315748.462 1230488.796 1257696.234 1402568.841 1155016.958 1233921.808 1291280.3 0.939854231 1.104123047 1.018948761 0.952921528 0.973991653 1.08618465 0.894474234 0.955580139 1 20.30037077 2.227792451 24.99981122 0.94886257 1.012638943 0.208463156 0.057536265 329.8033322 765678.009 0.022885579 0.015604982 168.9633263 -2.227792451 0.063776373 VASSTLLDDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VASSTLLDDRR 11 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ; 149.23 5.52E-05 1467490000 1136930 954950 493670 599500 799150 849890 792970 878920 688590 FALSE TRUE 986681.8199 948676.8706 732410.4632 735625.6378 783248.4785 882585.8183 716067.8915 690969.7978 607185.6746 1.625008397 1.562416424 1.206238048 1.211533257 1.289965345 1.45356825 1.17932277 1.137987648 1 19.21177823 8 0.31818317 1.118595985 6.159445412 0.62553721 0.11989272 56.68139552 0.894258146 0.217725193 163.2477678 100000000 -8 5.040849427 VATLNS(ph)EEESDPPTYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VATLNSEEESDPPTYK 16 0 Q00341;A0A024R4E5;Q00341-2;C9JIZ1;C9JZI8;C9J5E5;C9JHZ8;C9JES8;C9JK79;C9JHS7;C9JT62;C9JQ82;C9JHN6;C9JEJ8;C9JBS3;C9JMQ6 Q00341 HDLBP Vigilin 1 VATLNS(1)EEESDPPTYK;VATLNS(1)EEESDPPTYK;VATLNS(1)EEESDPPTYK;VATLNS(1)EEESDPPTYK;VATLNS(1)EEESDPPTYK 365.02 3.99E-104 1633150000 3920350 3405430 2304990 3127090 3540580 2619840 3754600 4936320 4436420 TRUE FALSE 3402265.815 3383059.506 3419690.874 3837143.579 3470129.385 2720626.94 3390479.47 3880726.382 3911951.482 0.869710637 0.864800988 0.874164951 0.980877088 0.887058391 0.69546541 0.86669773 0.992018025 1 21.89945705 1.7220909 4.955746494 0.997504008 0.861960794 0.393145785 0.068903502 0.16905629 10.06422231 0.046401213 0.019225629 52.73402245 -1.7220909 -0.135543214 VATTAGLYGSNLMEHTEIDHWLEFSATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VATTAGLYGSNLMEHTEIDHWLEFSATK 28 0 P07814;V9GYZ6;V9GZ76 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 100.93 0.00075757 79533000 27475 21025 16645 17156 25102 19070 32571 28733 27534 FALSE TRUE 23844.10914 20886.88539 24694.57767 21051.53201 24602.51931 19803.63524 29412.26943 22588.67155 24278.96189 0.982089319 0.860287416 1.017118351 0.867068869 1.013326658 0.815670593 1.211430273 0.930380453 1 14.56741912 2.267375768 24.99999981 1.029758725 0.928385753 0.255918063 0.095940182 305.3519434 264922.1053 0.03277841 0.025385434 185.086937 -2.267375768 -0.101372972 VATTPGS(ph)PSLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VATTPGSPSLGR 12 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 VAT(0.005)T(0.242)PGS(0.751)PS(0.002)LGR;VATT(0.056)PGS(0.906)PS(0.038)LGR;VATTPGS(1)PSLGR;VAT(0.003)T(0.106)PGS(0.88)PS(0.011)LGR 207.25 8.47E-08 1944940000 1625660 1575250 1044300 1200770 1556190 1557870 1478050 1684510 1564570 TRUE FALSE 1410824.912 1564902.079 1549326.973 1473423.181 1525224.864 1617802.267 1334708.938 1324290.645 1379608.317 1.022627143 1.134308963 1.12301945 1.068001086 1.105549195 1.172653315 0.967454981 0.95990335 1 20.3958273 2.220631186 24.97896955 0.972130007 1.104970731 0.689596975 0.040638064 124.1379968 172945.6089 0.015990583 0.010806306 166.2000636 -2.220631186 0.132840723 VATWFNQPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VATWFNQPAR 10 0 P26373;P26373-2;J3QSB4;H3BTH3 P26373 RPL13 60S ribosomal protein L13 0 ; 124.74 0.00099449 1057350000 157920 230066 168251 142717 210241 240229 169989 238480 283810 FALSE TRUE 137050.4719 228554.6813 249617.7464 175123.0761 206057.6154 249470.7651 153503.4929 187482.9079 250258.3051 0.547636059 0.913275111 0.99744041 0.699769289 0.823379729 0.996853091 0.613380215 0.749157586 1 17.93305842 4.748693912 24.3366713 0.834067909 0.547635828 0.329061305 0.133774278 1290.184427 3098485.782 0.032875994 0.427953377 56065.26923 -4.748693912 -0.286432081 VAVAT(ph)PAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VAVATPAK 8 0 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 VAVAT(1)PAK 121.6 0.0095495 0 749430 748460 536700 664920 596760 477860 719340 781410 1256400 TRUE FALSE 650390.9267 743543.317 796249.9152 815900.2487 584885.6435 496243.5834 649578.5175 614311.5524 1107869.823 0.587064394 0.671146827 0.718721549 0.736458591 0.527937156 0.447925896 0.586331087 0.554497956 1 20.07935694 1.234270468 24.99910806 1.000000585 0.603240111 0.671053101 0.087184917 87.67070556 510797.2847 0.180016511 0.023628184 17.1502505 -1.234270468 -0.396760474 VAVAT(ph)PAKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VAVATPAKK 9 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 VAVAT(1)PAKK;VAVAT(1)PAKK;VAVAT(1)PAKK;VAVAT(1)PAKK 97.911 0.0037331 6721900000 14497800 12872000 8704400 10133900 9133800 7375800 13481500 15036900 13258000 TRUE FALSE 12581879 12787442.98 12913876.95 12434956.88 8952055.25 7659551.799 12174066.21 11821375.95 11690654.34 1.076233941 1.093817558 1.104632519 1.063666457 0.765744584 0.655185892 1.041350283 1.011181719 1 23.47885235 3.398415155 9.707484902 0.908404575 1.09051801 0.396284024 0.116199161 0.418733421 48.03981912 0.037830769 0.048851051 2502.736659 -3.398415155 0.182113435 VAVEEVDEEGKFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 VAVEEVDEEGKFVR 14 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;; 239.61 2.09E-17 6402760000 6640450 5096280 3635527 3850520 4715980 4112310 6331700 6982130 3107365 FALSE TRUE 5762897.708 5062802.201 5393680.017 4724839.418 4622141.225 4270513.227 5717652.709 5489055.834 2740015.85 2.103235172 1.847727341 1.96848497 1.724383973 1.686903098 1.558572454 2.086722494 2.003293461 1 21.38575281 8 0.369474386 1.69499906 6.746249821 0.183165894 0.294797687 185.8818184 2.758298437 0.349231652 659.5496587 100000000 -8 5.051250761 VAVNDAHLLQYNHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VAVNDAHLLQYNHR 14 0 P17931 P17931 LGALS3 Galectin-3 0 ;;;;; 292.76 9.27E-44 7262940000 5373090 4756790 2808420 3549610 4150100 4537990 3699690 5040570 6536370 FALSE TRUE 4663022.543 4725542.333 4166581.306 4355603.203 4067521.13 4712569.412 3340894.633 3962683.331 5763647.785 0.809040163 0.819887424 0.722906996 0.755702528 0.705719933 0.817636606 0.57964934 0.687530446 1 22.45855074 4.243228788 24.73501075 0.738385596 0.81446383 0.041285369 0.107585423 271.9182895 1440741.768 0.026519918 0.065459196 17507.68758 -4.243228788 0.076078234 VAVTASEVQQAESEVS(ph)DIESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VAVTASEVQQAESEVSDIESR 21 0 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 1 VAVTASEVQQAESEVS(0.995)DIES(0.005)R;VAVTASEVQQAES(0.002)EVS(0.986)DIES(0.013)R 184.35 4.18E-17 100436000 86935 65858 42149 43809 61316 64681 60377 74091 70531 TRUE FALSE 75446.31948 65425.37446 62532.39738 53756.50303 60095.93156 67169.31992 54521.64783 58247.21623 62192.90553 1.213101701 1.051974882 1.005458691 0.864351047 0.966282746 1.080015789 0.876653814 0.936557244 1 15.9244624 4.67228554 1.627717191 0.95331277 1.284124264 0.636085932 0.061427655 0.560668789 1.595448638 0.016941896 0.281576372 47020.31564 -4.67228554 0.330811494 VAWHIDPFGHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VAWHIDPFGHSR 12 0 O00754;O00754-2 O00754 MAN2B1 Lysosomal alpha-mannosidase;Lysosomal alpha-mannosidase A peptide;Lysosomal alpha-mannosidase B peptide;Lysosomal alpha-mannosidase C peptide;Lysosomal alpha-mannosidase D peptide;Lysosomal alpha-mannosidase E peptide 0 ; 170.04 2.44E-05 484420000 379380 346410 208553 255665 368830 394990 306018 360820 312010 FALSE TRUE 329243.9718 344134.4099 309409.9284 313717.6458 361491.0046 410185.5209 276340.4215 283661.4509 275124.5332 1.196708879 1.250831417 1.124617731 1.140275068 1.313917739 1.490908557 1.00441941 1.031029285 1 18.06972527 VAYTEADYYHTELWMEQALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VAYTEADYYHTELWMEQALR 20 0 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 160.97 2.33E-11 41620000 44595 39274 31802 33097 37690 50677 39194 38595 40088 FALSE TRUE 38701.65776 39016.00651 47181.55357 40612.17971 36940.04274 52626.57698 35392.97191 30341.7596 35348.84231 1.094849371 1.10374213 1.334741126 1.148897023 1.045014216 1.48877795 1.001248403 0.858352286 1 15.10937535 2.015927184 24.99888934 0.922280947 1.198770299 0.446005787 0.132781281 187.1379377 293725.6941 0.051959368 0.035019429 103.7354473 -2.015927184 0.276489353 VAYVSFGPHAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VAYVSFGPHAGK 12 0 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ; 176.8 2.41E-05 2762100000 5698000 6480500 3095800 4308200 6508200 5194500 8382100 7694500 7393500 FALSE TRUE 4944994.863 6437929.169 4592939.235 5286442.657 6378699.553 5394335.776 7569205.232 6049091.054 6519448.853 0.758498912 0.987495924 0.704498085 0.810872633 0.978410859 0.827422056 1.161019191 0.927853135 1 22.63631858 2.810576537 1.426425807 1.004600651 0.824344664 0.349685558 0.108797452 0.459119865 1.923272388 0.047526483 0.043168904 646.5119206 -2.810576537 -0.180255986 VCDGAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VCDGAIR 7 0 P42345 P42345 MTOR Serine/threonine-protein kinase mTOR 0 ; 91.26 0.038468 76299000 3863.7 5550.2 3411.4 1633.42 4075.2 4705 3101.6 4175.6 5024.7 FALSE TRUE 3353.102256 5513.740371 5061.16445 2004.312976 3994.111493 4886.004395 2800.807309 3282.680435 4430.68569 0.75679082 1.244444033 1.142298237 0.452370833 0.901465771 1.10276484 0.632138568 0.740896706 1 12.11331427 VCDSCYDSIKDEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VCDSCYDSIKDEDR 14 1 Q8IWB7 Q8IWB7 WDFY1 WD repeat and FYVE domain-containing protein 1 0 115.82 0.00036257 297900000 282830 198820 156060 166070 198090 155370 268380 267510 257890 FALSE TRUE 245453.2989 197513.9383 231531.138 203778.7317 194148.3966 161347.1844 242352.5489 210305.0683 227402.538 1.07937801 0.868565233 1.01815547 0.896114588 0.853765302 0.709522356 1.065742498 0.924814077 1 17.79488883 4.750302737 23.87321895 0.918695164 1.079378194 0.207839741 0.09952958 1639.785279 3333772.652 0.024141381 0.365114075 56273.3458 -4.750302737 0.160683029 VCEEIAIIPSKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VCEEIAIIPSKK 12 1 H3BNC9;P08708;H0YN88;A0A075B716;H0YN73 H3BNC9 RPS17 40S ribosomal protein S17 0 ; 133.71 0.00025391 1992490000 2836900 2438390 1735000 2165710 2357200 1938810 2796400 3475900 3012700 FALSE TRUE 2461996.477 2422372.056 2574051.803 2657467.556 2310296.332 2013397.275 2525205.558 2732605.834 2656542.038 0.92676737 0.91185158 0.968948267 1.000348392 0.869663005 0.75790153 0.950561114 1.028632634 1 21.34111811 1.995132854 24.99731316 1.008332135 0.90690477 0.324682605 0.064179046 254.8690534 1308989.333 0.029205053 0.019089095 98.88555472 -1.995132854 -0.101427365 VCEIHFHEINNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VCEIHFHEINNK 12 0 H0YHB7;O43347;B4DM51;Q96DH6-3;B4DHE8;Q96DH6-2;Q96DH6 H0YHB7;B4DHE8 MSI1;MSI2 RNA-binding protein Musashi homolog 1;RNA-binding protein Musashi homolog 2 0 ; 136.53 6.26E-05 492860000 929280 777750 583750 643020 743080 650200 904750 1015470 950610 FALSE TRUE 806473.2935 772640.909 866053.4525 789027.5189 728294.1618 675213.6147 817007.4843 798319.6429 838229.9687 0.962114603 0.921752905 1.033193139 0.941301968 0.868847678 0.805523114 0.974681787 0.952387379 1 19.67698658 1.630779439 2.23296959 0.990153166 0.925755075 0.119251464 0.060668848 0.722574829 7.462816153 0.076231554 0.018158748 42.73457985 -1.630779439 -0.064398091 VCEKAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VCEKAFR 7 1 A6NHJ4 A6NHJ4 ZNF860 Zinc finger protein 860 0 58.981 0.096932 6051000000 580270 768170 426130 424540 817950 1114300 561200 612070 549360 FALSE TRUE 503585.8493 763123.8407 632207.8933 520938.2957 801674.3953 1157167.842 506774.9104 481183.5936 484415.2866 1.039574644 1.575350452 1.305094845 1.07539607 1.654932075 2.388792992 1.046157965 0.993328673 1 18.88588487 2.041218691 24.99999195 1.003249189 1.506797878 0.280969386 0.372641731 187.5051688 113725.0097 0.156943912 0.105811485 109.9559388 -2.041218691 0.503548689 VCEPCYEQLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VCEPCYEQLNR 11 0 O14964-2;O14964;I3L1P5 O14964-2 HGS Hepatocyte growth factor-regulated tyrosine kinase substrate 0 117.01 0.0021208 86857000 92411 88434 50738 52355 94408 92249 87872 87582 75639 FALSE TRUE 80198.65221 87853.07123 75275.06651 64243.00295 92529.46551 95797.87872 79350.18696 68853.27086 66697.04359 1.20243189 1.317195883 1.128611741 0.963206156 1.38730985 1.436313719 1.189710708 1.032328678 1 16.02533519 1.752017056 3.753114869 1.010103538 1.237069921 0.320505377 0.132287143 0.252256738 7.458915373 0.093986565 0.037958026 56.49591624 -1.752017056 0.226966383 VCEVCSAYLGLHDNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 200.71 3.48E-11 1586100000 471490 438580 257530 362210 359950 430190 375120 490000 683150 FALSE TRUE 409181.4019 435698.9391 382072.3694 444455.3165 352787.6992 446739.6877 338740.9201 385217.3132 602388.7852 0.679264641 0.723285277 0.634262089 0.737821366 0.585647854 0.741613554 0.562329393 0.639482877 1 19.20033539 1.236405288 24.99896648 1.000000436 0.660514662 0.75234478 0.060756346 26.92946116 312268.9778 0.089774808 0.013996701 17.2347619 -1.236405288 -0.339485774 VCEVCSAYLGLHDNDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VCEVCSAYLGLHDNDRR 17 1 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2;Q9NQ29-3;Q9NQ29;Q9NQ29-2;A8MYV2;B8ZZ10 Q9Y383;Q9NQ29-3 LUC7L2;LUC7L Putative RNA-binding protein Luc7-like 2;Putative RNA-binding protein Luc7-like 1 0 ;;; 186.85 3.25E-10 3600590000 2493330 2185510 1066640 1440800 2075960 2081710 1983520 2529490 1436430 FALSE TRUE 2163830.123 2171153.241 1582470.672 1767955.661 2034652.458 2161794.731 1791158.536 1988578.248 1266616.882 1.708354084 1.71413572 1.249368056 1.39580933 1.606367708 1.706747132 1.414128109 1.569991903 1 20.27254878 1.236549339 24.98392051 0.99999931 1.538853592 0.553705025 0.153836222 42.83986413 532011.9564 0.244292451 0.03846687 17.24047945 -1.236549339 0.538854283 VCGS(ph)SQAAGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VCGSSQAAGSR 11 0 H9KV82;Q8N7U6-2;Q8N7U6 H9KV82 EFHB EF-hand domain-containing family member B 1 VCGS(0.5)S(0.5)QAAGSR 70.438 0.033344 431250000 102070 104060 57319 74715 87824 96695 93712 106280 124310 TRUE FALSE 88581.19089 103376.423 85038.66012 91680.1827 86076.47422 100414.9192 84623.82466 83552.84907 109614.2134 0.808117744 0.943093234 0.775799574 0.836389551 0.785267453 0.916075718 0.77201507 0.762244662 1 16.74207536 4.226234878 24.99484802 0.826597978 0.875605526 0.032515989 0.080752668 598.9413868 1214575.043 0.019664592 0.041410632 16835.84342 -4.226234878 0.049007548 VCGTLLEYLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VCGTLLEYLGK 11 0 F8VWW7;Q8NCJ5 F8VWW7 SPRYD3 SPRY domain-containing protein 3 0 70.1 0.05269 697210000 2601700 3096900 1326200 1595700 3181100 3698300 2348000 2609500 1435900 FALSE TRUE 2257878.753 3076556.26 1967554.756 1958028.074 3117802.334 3840575.994 2120291.321 2051478.732 1266149.538 1.783263892 2.429852216 1.553967124 1.546442987 2.462428205 3.033272042 1.674597872 1.620249955 1 20.27201637 1.520773146 1.961663613 0.986628407 2.105222265 0.361586507 0.467327172 0.499565219 3.271401133 0.897120431 0.137547885 33.17211374 -1.520773146 1.118593859 VCHANPSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 VCHANPSER 9 0 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ;;;;;; 152.86 7.95E-05 1841142000 574475 540388 318481 373605 499528 581582 534913 572788 513513 FALSE TRUE 498556.6732 536838.1556 472499.4769 458437.7254 489588.3701 603955.8359 483037.2196 450301.7436 452806.0781 1.101037944 1.185580719 1.043491905 1.012437217 1.081231887 1.333806822 1.066763992 0.9944693 1 18.7885338 1.999493044 24.99999977 1.006972687 1.124836324 0.268505563 0.087738049 24.90945121 1228394.326 0.037865224 0.025195401 99.88333723 -1.999493044 0.117863637 VCIESEHSMDTLLATLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VCIESEHSMDTLLATLK 17 0 O00244;E5RGN3;E5RIM7 O00244 ATOX1 Copper transport protein ATOX1 0 ; 241.93 2.20E-20 643990000 912640 914690 440030 744790 817860 731290 967000 1155300 1430170 FALSE TRUE 792032.3117 908681.3412 652829.9798 913905.9529 801586.1861 759423.1995 873220.4888 908248.0856 1261096.932 0.628050304 0.720548372 0.517668359 0.724691282 0.635626149 0.602192568 0.692429318 0.720204817 1 20.26624774 0.841395039 1.429263395 1.609114559 0.641741452 0.774532256 0.05990528 1.45824764 1.185086535 2.715252211 0.015994057 6.940568409 -0.841395039 -0.967373107 VCIESEHSMDTLLATLKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VCIESEHSMDTLLATLKK 18 1 O00244;E5RGN3;E5RIM7 O00244 ATOX1 Copper transport protein ATOX1 0 73.464 0.013089 407490000 285560 244880 134760 201260 228730 186890 264090 338990 181640 FALSE TRUE 247822.5225 243271.3672 199930.3867 246959.1591 224178.7205 194079.7792 238478.5924 266499.6265 160166.7261 1.547278442 1.518863331 1.248264178 1.541888038 1.399658505 1.211735945 1.488939671 1.66388883 1 17.28921494 4.447037606 24.90400847 1.399222192 1.540174982 0.102580403 0.187326104 433.5965213 358941.6245 0.046132057 0.122056535 27992.23695 -4.447037606 0.14095279 VCSTLLGLEEHLNALDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 151.04 2.65E-07 173628000 110336 81756 52320 55852 78916 75936 76808 90866 82833 FALSE TRUE 95754.81804 81218.93945 77622.127 68534.05024 77345.726 78857.30706 69359.17198 71435.01302 73040.5771 1.310981126 1.111970122 1.062726091 0.938301051 1.058941879 1.079636966 0.949597809 0.97801819 1 16.15641054 4.926073216 1.212168236 0.999929551 1.563583989 0.822795035 0.045062091 0.905095508 0.850196658 0.013736533 0.711556404 84347.69451 -4.926073216 0.563654438 VCTFSPQRVS(ph)PTTSPRPAS(ph)PVPGSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VCTFSPQRVSPTTSPRPASPVPGSER 26 2 A0A5E8;Q99501;Q99501-4;Q99501-2 A0A5E8 GAS2L1 GAS2-like protein 1 2 VCT(0.108)FS(0.1)PQRVS(0.778)PT(0.057)T(0.038)S(0.035)PRPAS(0.84)PVPGS(0.044)ER 46.034 0.080686 438270000 121990 126720 66450 68608 120010 146490 145780 150050 60369 TRUE FALSE 105868.7124 125887.568 98585.44226 84186.49501 117622.0358 152125.5651 131642.278 117962.9752 53232.24559 1.988807935 2.364874271 1.85198729 1.581494338 2.209601239 2.857770951 2.472979987 2.216005992 1 15.70001281 3.055351193 24.99988178 2.219845055 1.960590127 0.029284864 0.503191321 297.5706503 134398.0801 0.156895967 0.177903285 1135.929016 -3.055351193 -0.259254927 VCTIS(ph)PAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VCTISPAPR 9 0 O43439-2;O43439-5;O43439;O43439-4 O43439-2 CBFA2T2 Protein CBFA2T2 1 VCT(0.001)IS(0.999)PAPR;VCTIS(1)PAPR 168.9 6.18E-05 519320000 635760 682920 418380 483440 647680 711040 633260 721380 713320 TRUE FALSE 551742.7052 678433.8536 620709.9674 593212.4409 634792.4352 738394.1689 571846.5427 567118.5008 628992.1222 0.877185398 1.078604691 0.986832657 0.943115851 1.009221599 1.1739323 0.909147384 0.90163053 1 19.26268242 VCTLAIIDPGDSDIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VCTLAIIDPGDSDIIR 16 0 E5RI99;P62888;A0A0C4DH44;A0A0B4J213 E5RI99 RPL30 60S ribosomal protein L30 0 ; 131.13 0.00011927 104650000 453050 444810 265350 373040 431210 422140 422070 486970 463730 FALSE TRUE 393178.2946 441888.0138 393674.1475 457744.4336 422629.7646 438379.999 381137.7164 382835.2551 408908.3677 0.961531545 1.080652901 0.962744171 1.119430341 1.033556166 1.072073926 0.932085882 0.936237273 1 18.64141806 2.23350595 24.99988626 0.95096712 1.040288672 0.35726437 0.05179215 117.8774632 583001.8147 0.019264898 0.013448184 171.2008634 -2.23350595 0.089321552 VCYYYDGDIGNYYYGQGHPMKPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VCYYYDGDIGNYYYGQGHPMKPHR 24 1 Q92769;H3BM24 Q92769 HDAC2 Histone deacetylase 2 0 ; 191.95 5.33E-18 881230000 326630 240417 175619 228629 242066 220594 273890 296540 372260 FALSE TRUE 283465.0179 238837.6849 260548.9358 280542.7088 237249.3602 229080.3939 247328.19 233127.2287 328251.8469 0.863559552 0.727605 0.793747052 0.854656909 0.722766261 0.697879985 0.753470825 0.71020843 1 18.3244436 1.230994049 24.99972278 1.000000424 0.761370502 0.62272856 0.057285463 185.9370083 614278.2142 0.14597666 0.014105158 17.02135186 -1.230994049 -0.238629922 VCYYYDGDVGNYYYGQGHPMKPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VCYYYDGDVGNYYYGQGHPMKPHR 24 1 Q13547;Q5TEE2 Q13547 HDAC1 Histone deacetylase 1 0 147.53 1.14E-07 461270000 143600 161310 87665 133660 121760 123840 139550 175510 217920 FALSE TRUE 124622.8962 160250.344 130060.0872 164009.5459 119337.2142 128604.2049 126016.4625 137978.5523 192157.7459 0.648544744 0.833952039 0.6768402 0.853515143 0.62103775 0.669263705 0.655796944 0.71804835 1 17.55193161 1.239593714 7.284696644 1.005187018 0.710442017 0.584260801 0.077002807 0.071938634 25.01823436 0.105425785 0.018139977 17.36175863 -1.239593714 -0.294745001 VDASGELEDVEWEDWE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDASGELEDVEWEDWE 16 0 Q9NW68-9;Q9NW68-8;Q9NW68;Q9NW68-7 Q9NW68-9 BSDC1 BSD domain-containing protein 1 0 201.48 7.64E-11 12663000 121540 95318 59749 76364 94375 89691 97180 104880 99838 FALSE TRUE 105478.1811 94691.84978 88643.81625 93703.61335 92497.12214 93141.47081 87755.49856 82452.22818 88035.26538 1.19813555 1.075612703 1.006912581 1.064387242 1.050682607 1.058001818 0.996822105 0.93658181 1 16.42579394 8 0.36286516 0.979605118 3.444002309 0.69236244 0.038106055 51.55717474 0.772845774 0.051838513 87.06887773 100000000 -8 2.464397191 VDAYGNLLVCAHGFNFIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VDAYGNLLVCAHGFNFIR 18 0 P49902-2;P49902;Q5JUV4;Q5JUV3;H0YHR8 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;;; 238.81 6.79E-24 1739522000 1336494 1436441 916320 1088027 1363965 1319195 1477480 1648360 1381138 FALSE TRUE 1159872.932 1427004.924 1359455.417 1335080.16 1336824.765 1369945.285 1334194.217 1295871.042 1217861.439 0.952384971 1.171730115 1.11626444 1.096249636 1.097682152 1.124877791 1.095522179 1.06405458 1 20.21591857 1.294344322 2.015810242 0.976195404 1.098939633 0.217178185 0.055568631 0.936633584 4.177521565 0.207369332 0.014008277 19.69447109 -1.294344322 0.122744229 VDCDQHSDIAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VDCDQHSDIAQR 12 0 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 ;;; 175.21 2.83E-05 3143760000 2667730 2403800 1645680 1813580 2429680 2704230 2360820 2542100 2298730 FALSE TRUE 2315182.721 2388009.28 2441536.352 2225381.058 2381334.122 2808263.478 2131868.04 1998491.698 2026976.758 1.142185135 1.178113794 1.204521139 1.097881882 1.174820635 1.385444341 1.051747649 0.985947022 1 20.95089812 2.017516043 24.981876 1.000032961 1.193392959 0.586564662 0.074183688 155.5572999 221859.3653 0.030298863 0.020423078 104.1156567 -2.017516043 0.193359998 VDCGYPHVTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VDCGYPHVTPK 11 0 X6R3S7;Q07654 X6R3S7 TFF3 Trefoil factor 3 0 ;;;;; 158.05 3.03E-05 5135080000 7142030 7614340 4031010 5320540 7193450 5618000 6860660 8327360 7367930 FALSE TRUE 6198192.64 7564320.899 5980419.919 6528649.926 7050314.419 5834128.095 6195314.249 6546618.868 6496901.709 0.954022843 1.164296651 0.92050337 1.00488667 1.085181019 0.897986203 0.953579803 1.007652441 1 22.63132045 2.747266763 24.98821368 0.970447258 1.026464348 0.147022495 0.072402577 1328.782417 3813847.309 0.022682287 0.022352587 558.813337 -2.747266763 0.05601709 VDCTAHSDVCSAQGVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDCTAHSDVCSAQGVR 16 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 160.48 8.77E-09 610130000 443550 371730 294090 283240 390740 429860 354130 383140 570160 FALSE TRUE 384933.7437 369288.0812 436312.9077 347553.9711 382965.0385 446396.9924 319786.5271 301208.4926 502756.3343 0.765646731 0.734526959 0.867841692 0.691297051 0.761730907 0.88789929 0.63606663 0.599114267 1 18.93949983 2.221139325 24.99850586 0.710113522 0.781010243 0 0.120931494 710.5510743 1019590.482 0.048440868 0.032743609 166.394637 -2.221139325 0.070896721 VDCTQHYELCSGNQVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDCTQHYELCSGNQVR 16 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ; 197.15 4.40E-11 815750000 654540 548420 376470 516190 578120 627300 547120 543240 467130 FALSE TRUE 568040.8806 544817.3929 558532.1512 633398.829 566616.5431 651432.6369 494060.3866 427072.3535 411906.4236 1.379053222 1.322672728 1.355968539 1.537725058 1.375595307 1.58150638 1.199448123 1.036818872 1 18.6519571 1.999387341 3.94283873 1.037384728 1.420547622 0.809102586 0.08236916 0.088945209 3.100498008 0.042264288 0.023284166 99.85902952 -1.999387341 0.383162894 VDDDS(ph)LGEFPVTNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDDDSLGEFPVTNSR 15 0 Q92785;J3KMZ8;Q92785-2 Q92785 DPF2 Zinc finger protein ubi-d4 1 VDDDS(1)LGEFPVTNSR 213.94 1.18E-11 0 208720 95693 74471 103900 97372 103340 109400 113580 168250 TRUE FALSE 181137.1232 95064.38638 110485.4247 127492.083 95434.48771 107315.5567 98790.40484 89291.80088 148359.6767 1.220932313 0.640769706 0.744713302 0.859344573 0.643264328 0.7233472 0.665884471 0.601860309 1 17.1787395 4.744302055 24.93854685 0.722240577 1.220932535 0.621692951 0.118788439 392.6656092 1705533.868 0.02779614 0.241047785 55501.15931 -4.744302055 0.498691958 VDDFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDDFLR 6 0 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 0 99.919 0.088987 72684000 113580 102940 65836 90020 91293 87322 87434 110300 150880 FALSE TRUE 98570.11522 102263.7804 97674.50981 110460.4169 89476.44791 90681.33384 78954.66414 86713.20336 133043.1383 0.74088838 0.768651294 0.734156688 0.830260157 0.672537111 0.681593467 0.593451606 0.651767573 1 17.02153458 3.216740199 24.99582505 0.699961953 0.766048437 0.02853477 0.110834989 664.2322265 760892.1053 0.033485191 0.037999811 1647.176733 -3.216740199 0.066086484 VDDHLMGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDDHLMGK 8 0 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 111.04 0.0046544 0 344970 318450 199110 252350 276200 258220 335470 340100 332110 FALSE TRUE 299381.3405 316358.081 295400.262 309649.9244 270704.1604 268153.8905 302936.171 267372.2617 292848.3341 1.022308497 1.080279599 1.008714162 1.05737301 0.924383474 0.915674973 1.034447308 0.913005916 1 18.15979416 3.245185816 24.9926929 0.955619785 1.04250141 0.502262025 0.041857317 122.0742163 460506.4629 0.011474877 0.014468614 1758.675915 -3.245185816 0.086881625 VDDKPS(ph)SPGDSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDDKPSSPGDSSK 13 1 Q9HC52;C9JM54;C9J6K3 Q9HC52 CBX8 Chromobox protein homolog 8 1 VDDKPS(0.767)S(0.233)PGDSSK 146.3 2.56E-05 219210000 521150 382060 362850 347730 369170 308440 517910 604670 501190 TRUE FALSE 452278.7071 379550.2227 538325.4737 426687.4112 361824.2393 320305.8864 467683.1679 475366.026 441939.8892 1.023394172 0.858827709 1.218096594 0.965487438 0.81871822 0.724772518 1.058250634 1.07563503 1 18.75349063 VDDKPSS(ph)PGDSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VDDKPSSPGDSSK 13 1 Q9HC52;C9JM54;C9J6K3 Q9HC52 CBX8 Chromobox protein homolog 8 1 VDDKPS(0.287)S(0.712)PGDSSK;VDDKPS(0.151)S(0.849)PGDSSK;VDDKPS(0.008)S(0.992)PGDSSK 176.94 5.57E-07 626530000 2931350 1908910 1902160 1842990 1693600 1182110 2770770 3100090 2699960 TRUE FALSE 2543964.67 1896370.245 2822050.938 2261469.048 1659900.673 1227586.537 2502061.152 2437159.878 2380773.805 1.068545305 0.796535244 1.185350298 0.949888244 0.697210575 0.515625018 1.050944507 1.023683927 1 21.18299913 3.471465721 24.96369311 0.870942841 1.006922209 0.132959288 0.185207544 377.1607917 1664788.338 0.057951916 0.075045164 2961.186231 -3.471465721 0.135979368 VDDKWEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDDKWEK 7 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 109.71 0.0063531 574890000 1699850 1212980 1078220 1142700 1077290 755830 1516290 1734240 1615950 FALSE TRUE 1475210.516 1205011.855 1599650.798 1402167.5 1055854.037 784907.2692 1369240.429 1363386.272 1424914.232 1.035297762 0.845673254 1.122629533 0.98403642 0.7409948 0.550845273 0.960928313 0.956819885 1 20.44244365 3.361916417 9.269579433 0.850821348 0.996758467 0.220499923 0.1444654 0.511728735 39.33207612 0.045160738 0.058308543 2300.998933 -3.361916417 0.14593712 VDDQIYSEFRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDDQIYSEFRK 11 1 Q9BVG4;A6NDF3 Q9BVG4;A6NDF3 PBDC1 Protein PBDC1 0 82.362 0.0307 207350000 136780 101810 52549 65693 96244 90639 97034 118110 43547 FALSE TRUE 118704.1764 101141.2034 77961.87217 80609.5997 94328.9327 94125.94098 87623.65762 92853.09563 38398.92327 3.091341276 2.633959361 2.030314017 2.099267189 2.456551504 2.451265113 2.281930069 2.418117169 1 15.22877824 1.238352267 24.95476057 0.999998465 2.409677126 0.701270955 0.293552299 2.884019859 344574.871 0.413904098 0.073390336 17.31220025 -1.238352267 1.409678661 VDDSTGTVIS(ph)DVEEDAGELSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDDSTGTVISDVEEDAGELSR 21 0 S4R403;Q9Y2D8-2;Q9Y2D8-3;Q9Y2D8 S4R403 SSX2IP Afadin- and alpha-actinin-binding protein 1 VDDSTGTVIS(1)DVEEDAGELSR 272.48 1.15E-44 16748000 51094 46276 33433 36618 46061 41857 38331 47837 49352 TRUE FALSE 44341.79844 45972.00991 49601.31063 44932.67657 45144.47622 43467.26588 34613.66552 37607.42982 43517.66278 1.018937958 1.056398873 1.13979721 1.03251585 1.037382831 0.998841921 0.795393486 0.864187721 1 15.40931345 2.426866576 5.182879566 0.878394076 1.056830242 0.633069611 0.059038363 0.117201139 6.933548629 0.022834235 0.017700836 267.2185333 -2.426866576 0.178436167 VDEDSAEDTQS(ph)NDGKEVVEVGQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDEDSAEDTQSNDGKEVVEVGQK 23 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 VDEDS(0.001)AEDT(0.176)QS(0.823)NDGKEVVEVGQK 104.48 0.00098865 143900000 130580 101270 98589 119760 110680 90246 125220 154950 196410 TRUE FALSE 113323.5222 100604.7507 146266.9702 146953.3384 108477.6845 93717.82202 113076.1837 121815.1483 173190.6336 0.654328238 0.580890252 0.84454319 0.84850627 0.626348448 0.541125233 0.65290011 0.703358755 1 17.40200138 1.237938061 4.708841487 1.024231241 0.680266353 0.505080205 0.099365739 0.17550467 8.85298516 0.200730912 0.026861473 17.29569671 -1.237938061 -0.343964888 VDEFPLCGHMVSDEYEQLSSEALEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 VDEFPLCGHMVSDEYEQLSSEALEAAR 27 0 P27635;X1WI28;A6QRI9;B8A6G2 P27635 RPL10 60S ribosomal protein L10 0 ;;;;;;;;;;;; 374.19 5.16E-127 4436516000 2503753 2280727 1453630.9 1603223.1 2152866.1 2136707 2327294 2753700 1997219 FALSE TRUE 2172875.697 2265744.754 2156611.665 1967259.409 2110028.277 2218907.501 2101593.386 2164842.684 1761110.045 1.233810291 1.286543541 1.224575188 1.117056492 1.198124037 1.25994824 1.193334506 1.229248956 1 20.74805363 1.236618641 24.99838908 0.999999725 1.217126462 0.700001211 0.04481366 30.61981134 394050.5565 0.07238291 0.011416434 17.24323081 -1.236618641 0.217126737 VDFGS(ph)SER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDFGSSER 8 0 A0A0G2JRG8;A0A0G2JNY3;E9PIR1;Q6ZUM4-3;Q6ZUM4;A0A0C4DGE6;E9PNT2;Q6ZUM4-2 A0A0G2JRG8 ARHGAP27 Rho GTPase-activating protein 27 1 VDFGS(0.5)S(0.5)ER;VDFGS(0.5)S(0.5)ER 136.96 0.0008063 1278760000 1812150 1647850 1133370 1462300 1636900 1515340 1501190 1900270 2290700 TRUE FALSE 1572669.786 1637025.165 1681471.523 1794337.565 1604328.893 1573636.11 1355604.825 1493912.048 2019896.056 0.778589463 0.810450201 0.832454481 0.888331635 0.794263095 0.779067866 0.671126032 0.739598478 1 20.94584962 3.0126524 24.83517973 0.777688509 0.828436052 0.007654605 0.087332389 638.9984315 1254268.207 0.026828268 0.030403249 1029.561751 -3.0126524 0.050747543 VDGAEWGVDLPSVEAQLGSHR ddPTM_MDA-MB-175_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 ;;; 264.69 7.69E-37 1176930000 1294550 1166410 780190 947510 1116430 1206710 1158990 1373630 1334690 FALSE TRUE 1123471.938 1158747.776 1157492.494 1162656.627 1094215.227 1253132.915 1046591.328 1079889.914 1176904.469 0.954599092 0.984572501 0.983505904 0.9878938 0.929740057 1.064770292 0.889274666 0.917568029 1 20.16656579 2.199052264 24.99999946 0.92992385 0.981862061 0.211581405 0.04358378 216.7719773 137166.8854 0.016880441 0.011380998 158.1438341 -2.199052264 0.051938211 VDGETAS(ph)DSESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VDGETASDSESR 12 0 O95674 O95674 CDS2 Phosphatidate cytidylyltransferase 2 1 VDGET(0.228)AS(0.763)DS(0.009)ESR;VDGET(0.056)AS(0.944)DSESR;VDGET(0.372)AS(0.628)DS(0.001)ESR 264.98 1.45E-21 930190000 932072 827217 1013880 1600589 1215143 1166050 670046 1547059 3597800 TRUE FALSE 808896.3236 821782.9571 1504195.759 1964027.196 1190964.032 1210908.698 605065.0421 1216232.472 3172472.183 0.254973496 0.259035512 0.474139937 0.619084135 0.375405666 0.381692456 0.190723514 0.383370571 1 21.59717608 1.239859984 7.789248965 1.008523921 0.367678515 0.731532633 0.120489392 0.052616122 26.12895259 0.180224506 0.031688527 17.37240656 -1.239859984 -0.640845406 VDGPRS(ph)PSYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDGPRSPSYGR 11 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 1 VDGPRS(0.965)PS(0.035)YGR;VDGPRS(0.992)PS(0.007)Y(0.001)GR 103.14 0.0016804 772800000 1934990 1704910 420020 402330 1307850 1378400 1588340 1618440 108875 TRUE FALSE 1679276.169 1693710.334 623143.0769 493685.1757 1281826.344 1431427.94 1434303.031 1272349.201 96003.92153 17.49174557 17.64209531 6.490808573 5.142343853 13.35181234 14.91009864 14.94004629 13.25309613 1 16.55080572 4.25570945 24.79235039 10 17.5669286 0.329552347 4.561347079 279.9970264 404788.5523 1.207497756 3.177018233 18018.11895 -4.25570945 7.566928596 VDHQTGPIVWGEPGTNGQHAFYQLIHQGTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDHQTGPIVWGEPGTNGQHAFYQLIHQGTK 30 0 P06744;A0A2U3TZU2;P06744-2;K7EQ48;K7ESF4 P06744;K7ESF4 GPI Glucose-6-phosphate isomerase 0 ; 301.8 9.15E-82 6569600000 2186550 1662560 841750 1238180 1827850 1533860 1889550 2428020 2043290 FALSE TRUE 1897591.877 1651638.534 1248823.115 1519327.693 1791479.361 1592868.587 1706301.732 1908806.818 1801734.584 1.053202783 0.916693584 0.693122687 0.843258328 0.994308139 0.884075047 0.947032791 1.059427307 1 20.78095507 1.963936586 3.440092886 1.030834735 0.891330416 0.243078301 0.094919376 0.332360181 7.715421254 0.055925707 0.027765623 92.03151817 -1.963936586 -0.139504319 VDHSQNQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDHSQNQK 8 0 E7EQ69;Q9GZZ1 E7EQ69 NAA50 N-alpha-acetyltransferase 50 0 91.069 0.012749 77042000 117470 122590 86218 89639 93425 177910 125590 129420 149340 FALSE TRUE 101946.0419 121784.6982 127913.3132 109992.905 91566.02528 184754.3128 113410.3011 101744.5401 131685.1953 0.774164792 0.924816931 0.971356825 0.835271609 0.695340316 1.402999877 0.861222864 0.772634615 1 17.00673363 VDIAPHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VDIAPHVR 8 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ;;; 104.06 0.0046536 978870000 1416310 1382990 947400 937720 1505160 1615930 1500620 1561730 1474180 FALSE TRUE 1229141.045 1373905.048 1405565.809 1150643.658 1475210.261 1678095.873 1355090.103 1227766.193 1299904.12 0.945562851 1.056927989 1.081284217 0.885175792 1.134860824 1.290938191 1.042453888 0.944505194 1 20.30997378 4.740773683 22.83374528 1.050801288 0.945562747 0.088849596 0.109076731 183.0682574 1888369.565 0.028410226 0.181363381 55052.07375 -4.740773683 -0.105238541 VDIDAPDVDVHGPDWHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VDIDAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;;;; 249.69 5.86E-25 5486050000 7335680 4548170 3300397 5169090 5216330 4481400 4499020 7195080 6174250 FALSE TRUE 6366251.302 4518292.772 4896480.028 6342810.889 5112535.239 4653802.358 4062705.733 5656468.134 5444337.199 1.169334497 0.829906857 0.899371191 1.165029031 0.939055582 0.854796863 0.746225956 1.038963592 1 22.37632499 3.015140099 24.86924781 0.912808827 1.001517948 0.128764779 0.128847525 571.451141 938663.4395 0.039759191 0.045065787 1035.476147 -3.015140099 0.088709121 VDIDAPDVEVHDPDWHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VDIDAPDVEVHDPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 249.69 5.86E-25 1113730000 1080670 654041 517950 733170 816880 735950 697152 1025830 934270 FALSE TRUE 937856.7214 649744.5616 768432.3524 899647.4543 800625.6862 764262.4727 629542.3063 806464.2375 823821.6649 1.138422017 0.788695648 0.932765409 1.092041509 0.971843447 0.92770378 0.76417304 0.978930601 1 19.65197254 2.703327325 5.226285828 0.912208687 0.97708016 0.08036938 0.11101701 0.587784433 43.49968385 0.038258866 0.03440823 505.0418013 -2.703327325 0.064871473 VDIDT(ph)PDIDIHGPEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDIDTPDIDIHGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VDIDT(1)PDIDIHGPEGK 169.39 2.08E-08 172420000 205780 161160 134640 173650 164670 169410 172220 228530 245780 TRUE FALSE 178585.6516 160101.3293 199752.3543 213079.8866 161393.3892 175927.3123 155518.1309 179660.6379 216724.1684 0.824022779 0.738733158 0.921689334 0.9831847 0.744694929 0.811756776 0.717585547 0.828982938 1 17.72550052 1.242858728 6.979528046 1.003589497 0.819439186 0.321877673 0.081548292 0.132967762 37.24738509 0.116632857 0.020817481 17.49277573 -1.242858728 -0.184150311 VDIDT(ph)PDINIEGSEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDIDTPDINIEGSEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VDIDT(1)PDINIEGSEGK 99.055 0.0083321 0 83436 48667 32984 57559 50330 50615 62437 69105 75811 TRUE FALSE 72409.7212 48347.30327 48935.17272 70628.65068 49328.53147 52562.1918 56381.86935 54327.43353 66848.70994 1.083188012 0.723234649 0.732028677 1.056544707 0.737912991 0.786285806 0.843424943 0.812692325 1 16.0286121 1.232757124 24.61150761 1.00000032 0.838941217 0.122546957 0.127154538 318.1267379 1348942.429 0.249230696 0.028904032 17.09059268 -1.232757124 -0.161059103 VDIDTPDIDIHGPEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDIDTPDIDIHGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 179.81 2.57E-09 202720000 355610 239850 197480 284410 251280 214380 233280 398090 424730 FALSE TRUE 308615.2375 238274.4096 292981.9885 348989.6374 246280.0196 222627.3373 210656.5415 312961.5514 374518.9033 0.824031137 0.636214641 0.78228892 0.931834507 0.657590358 0.594435516 0.562472387 0.835636195 1 18.51467901 1.42282814 3.938510586 0.988592198 0.713266671 0.410690783 0.111438482 0.23461463 6.010815698 0.135509265 0.030149 26.47452273 -1.42282814 -0.275325527 VDIDVPDVDVQGPDWHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDIDVPDVDVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 266.7 3.54E-31 680460000 3143940 1948850 1430390 2271130 2165130 1826150 1882020 3171020 2722630 FALSE TRUE 2728460.363 1936047.876 2122131.388 2786824.779 2122048.149 1896403.172 1699501.99 2492922.05 2400763.783 1.136496803 0.806429974 0.883940104 1.160807572 0.883905432 0.789916603 0.707900545 1.038387061 1 21.19506203 VDIDVPDVNVQGPDWHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDIDVPDVNVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 117.67 0.00012495 133050000 169410 124910 98613 122300 128870 127830 131040 183340 132330 FALSE TRUE 147022.0393 124089.458 146302.5766 150070.0842 126305.7391 132747.7028 118331.761 144134.1678 116686.0982 1.259979051 1.063446803 1.253813256 1.2861008 1.082440335 1.137647971 1.014103332 1.235229989 1 16.83227316 3.217974334 24.9999417 1.107757126 1.207662869 0.312557128 0.088181638 345.2384951 419255.9153 0.025961328 0.029471443 1651.864175 -3.217974334 0.099905744 VDIGDTIIYLVH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDIGDTIIYLVH 12 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 76.1 0.07451 10899000 21277 22786 26695 17172 22846 35490 19618 22397 22917 FALSE TRUE 18465.19054 22636.31727 39604.79129 21071.16506 22391.4093 36855.32327 17715.44938 17607.57584 20207.77837 0.913766482 1.120178421 1.959878546 1.042725463 1.108058931 1.82381866 0.876664869 0.871326651 1 14.3026231 VDIIENQVMDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VDIIENQVMDFR 12 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;;;; 201.6 3.41E-07 884154000 640512 563409 501755 606767 587687 645000 638383 705023 873486 FALSE TRUE 555866.7163 559707.9292 744405.3963 744542.7212 575993.1785 669813.5674 576472.7149 554259.3179 770223.4802 0.721695366 0.726682507 0.96647975 0.966658042 0.747826044 0.869635352 0.748448638 0.719608441 1 19.55491758 4.41761239 24.99469037 0.841831728 0.722939632 0.227696142 0.09966975 109.7262721 46086.19147 0.026007356 0.068809013 26158.4731 -4.41761239 -0.118892096 VDIIPGFEFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VDIIPGFEFDR 11 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ;;; 160.36 6.41E-05 515090000 607246 560284 363790 390823 552376 506672 544208 622338 613610 FALSE TRUE 526996.9025 556603.4575 539720.0608 479565.3355 541384.7983 526163.9997 491430.7919 489255.8617 541069.7248 0.973990742 1.028709299 0.997505564 0.886328163 1.000582316 0.972451378 0.908257789 0.904238103 1 19.04545499 3.959946543 22.76525066 0.942131596 1.004289374 0.28470431 0.040683388 201.1386312 114321.7228 0.01082963 0.018764133 9118.985874 -3.959946543 0.062157778 VDIKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDIKDR 6 1 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 81.297 0.056772 911890000 4979400 3785800 2274400 2477800 3196300 3051700 4606700 5161400 1567180 FALSE TRUE 4321359.674 3760930.831 3374307.447 3040422.361 3132699.883 3169100.874 4159942.943 4057674.776 1381909.766 3.127092507 2.721545881 2.441771186 2.200159834 2.266935194 2.29327627 3.010285509 2.936280557 1 20.39823198 4.555737733 2.116198418 2.392785153 3.190737888 0.188742399 0.545840642 0.906835889 6.0251397 0.145165293 1.190056599 35953.21506 -4.555737733 0.797952734 VDILDPALLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDILDPALLR 10 0 P17980;E9PM69;E9PKD5;R4GNH3 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 76.064 0.086351 23954000 134140 139220 97703 120840 139720 133470 118120 150120 174910 FALSE TRUE 116413.0591 138305.4547 144952.4976 148278.5689 136939.8454 138604.6773 106664.7406 118018.0062 154232.3391 0.754790207 0.896734469 0.939832064 0.961397395 0.887880234 0.898674546 0.691584795 0.765196242 1 17.23474577 2.3647257 19.12882129 0.801340137 0.895681602 0.1016066 0.093696858 3.198836195 528.7921322 0.035054094 0.027152598 231.593145 -2.3647257 0.094341465 VDINAPDVDVHGPDWHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDINAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 220.34 3.95E-19 504360000 1346320 830920 541650 978650 929850 810590 782440 1291820 1136770 FALSE TRUE 1168400.401 825461.6318 803593.7517 1200867.44 911347.8042 841773.9218 706559.0892 1015574.346 1002382.346 1.165623483 0.823499771 0.801683864 1.198013358 0.909181819 0.839773292 0.704879822 1.013160647 1 19.93500148 3.02261046 24.99605235 0.889589752 0.981177475 0.103056469 0.149880683 662.8092683 732736.2319 0.046045893 0.052208394 1053.441588 -3.02261046 0.091587723 VDINAPDVDVQGPDWHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VDINAPDVDVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 195.46 2.06E-15 1091610000 1659530 1055185 694469 1124610 1194915 974807 1014747 1583450 1340665 FALSE TRUE 1440218.906 1048253.42 1030316.531 1379969.889 1171138.529 1012308.456 916336.9921 1244841.54 1182173.111 1.218280887 0.88671736 0.871544549 1.167316255 0.99066585 0.856311522 0.77512928 1.053011212 1 20.17300988 2.987478449 24.58820146 0.927530844 1.021738811 0.145563449 0.129059081 1174.992078 2307303.611 0.041345658 0.043426847 971.579737 -2.987478449 0.094207967 VDINT(ph)PDVDVHGPDWHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDINTPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VDINT(1)PDVDVHGPDWHLK 201.29 2.65E-15 284670000 394070 194220 129000 201900 234070 237430 244240 296350 282320 TRUE FALSE 341992.6511 192944.156 191384.8315 247744.4808 229412.465 246564.0857 220553.6424 232977.8587 248944.4512 1.373770933 0.775049032 0.768785287 0.995179767 0.921540785 0.990438166 0.885955245 0.93586283 1 17.92546433 4.749192362 24.81524602 0.911342728 1.373771223 0.757607223 0.082592189 719.006018 1678174.824 0.020698213 0.290671018 56129.65358 -4.749192362 0.462428494 VDISAPDVDVHGPDWHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDISAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 233.49 5.56E-24 563560000 1110220 752930 509000 805430 796200 684270 684390 1121900 993360 FALSE TRUE 963501.6141 747983.9533 755154.1025 988315.1917 780357.1777 710594.3097 618017.9631 881990.4156 875926.1124 1.099980467 0.853934987 0.862120779 1.128308858 0.89089384 0.811249145 0.705559469 1.006923305 1 19.74044965 3.035901449 24.99902127 0.880498954 0.973018373 0.148273621 0.121278657 400.8671986 279130.8338 0.037957517 0.043039648 1086.179117 -3.035901449 0.092519419 VDIVAINDPFIDLNYMVYMFQYDSTHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 VDIVAINDPFIDLNYMVYMFQYDSTHGK 28 0 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;; 288.79 2.01E-63 29421670000 16443102 15780012 8790868 14029365 11852747 9684479 19562403 21166613 15777578 FALSE TRUE 14270104.41 15676352.06 13042161.17 17214946.75 11616900.52 10057047.17 17665244.17 16640297.53 13912370.7 1.025713354 1.126792291 0.937450665 1.237384132 0.835005102 0.722885221 1.269750824 1.196079222 1 23.72986494 2.179864091 24.99999361 1.168546819 0.990551627 0.214487628 0.15591784 119.8741744 51055.48225 0.064954441 0.043792293 151.3087666 -2.179864091 -0.177995192 VDKETNTETPAPS(ph)PTVVRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDKETNTETPAPSPTVVRPK 20 2 H0YAU4;H3BLZ3;Q8IX03-2;H0YBE8;Q8IX03 H0YAU4;H0YBE8 WWC1 Protein KIBRA 1 VDKETNTETPAPS(0.996)PT(0.004)VVRPK 80.83 0.003057 117310000 105970 77037 68809 80880 82860 67670 122180 138240 134750 TRUE FALSE 91965.79601 76530.93887 102085.2626 99245.04017 81211.24811 70273.30869 110331.0024 108678.4518 118820.0085 0.773992505 0.644091343 0.859158856 0.835255286 0.683481251 0.591426558 0.928555752 0.914647736 1 16.85841827 2.136032597 9.059980196 0.941995042 0.735828585 0.598872666 0.083483437 0.202876076 16.3045889 0.035438552 0.023877804 136.7831487 -2.136032597 -0.206166458 VDKGVVPLAGTNGETTTQGLDGLSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VDKGVVPLAGTNGETTTQGLDGLSER 26 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;; 324.56 1.06E-82 2466380000 1503530 1346820 648037 772667 1252600 1001020 1408220 1616040 425286 FALSE TRUE 1304834.701 1337972.651 961429.8608 948112.8518 1227675.711 1039529.887 1271651.041 1270462.422 375009.1736 3.479474085 3.567839789 2.563750245 2.52823909 3.273721811 2.772011888 3.39098649 3.387816916 1 18.51656636 4.249203089 24.90901186 2.817127652 3.52365737 0.181396423 0.692742383 381.2972521 892418.5254 0.169036238 0.437307078 17750.1934 -4.249203089 0.706529718 VDKITEYLCEPLRK ddPTM_MDA-MB-175_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 ; 139.49 5.74E-06 887240000 1567520 1296540 869490 1044960 1226790 980240 1714360 1991210 765340 FALSE TRUE 1360368.26 1288022.943 1289978.272 1282234.139 1202379.279 1017950.467 1548101.631 1565405.237 674862.3771 2.015771373 1.908571269 1.911468643 1.899993514 1.781665892 1.508382304 2.293951602 2.319591802 1 19.3642338 5.009036402 1.306429435 1.875644805 2.15744344 0.011338769 0.377702484 19.10532708 18.1262429 0.109490585 8.469442701 102102.5062 -5.009036402 0.281798636 VDKLDASESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VDKLDASESLR 11 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 145.29 3.31E-05 10860390000 15940250 11842400 8297240 10146240 12336360 10262270 13856060 16456940 16661890 FALSE TRUE 13833705.58 11764606.49 12309813.02 12450098.87 12090890.57 10657066.17 12512301.43 12937751.45 14692140.35 0.941571837 0.8007415 0.83785022 0.84739858 0.822949569 0.725358315 0.851632311 0.880589972 1 23.80854125 1.260261564 1.975237348 1.049904636 0.827777113 0.499155393 0.052905506 0.618825153 2.448258349 0.251026655 0.014193118 18.20797147 -1.260261564 -0.222127522 VDKWWGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDKWWGNR 8 1 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9R4 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 70.056 0.047714 1111200000 1565900 1455600 975280 1333400 1600700 1223300 1605900 1798300 2114900 FALSE TRUE 1358962.348 1446038.068 1446928.67 1636168.85 1568849.202 1270361.143 1450160.065 1413747.539 1864878.931 0.728713443 0.775405869 0.775883434 0.877359287 0.841260618 0.681203011 0.777616198 0.758090788 1 20.83065054 1.235407975 24.99990549 1.000000304 0.778164699 0.628957252 0.053834874 61.92942583 491004.5078 0.093825239 0.013576073 17.19522943 -1.235407975 -0.221835605 VDKWWGNRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDKWWGNRK 9 2 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9R4 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 88.681 0.0070979 4515400000 3455000 3280900 1901180 2442200 3199100 2584400 3745400 4383300 1506670 FALSE TRUE 2998412.996 3259347.552 2820597.007 2996738.837 3135444.169 2683823.54 3382171.684 3445965.406 1328553.189 2.256900981 2.453306032 2.123059152 2.255640844 2.36004414 2.020109968 2.545755573 2.593773011 1 20.34142456 1.231766969 24.99961184 0.999997726 2.335850711 0.846820518 0.177201922 92.82264422 341542.1047 0.440397136 0.04612278 17.05167197 -1.231766969 1.335852985 VDLENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDLENR 6 0 P20700;E9PBF6;A0A0D9SFE5;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 0 ; 100.74 0.086812 903290000 2064200 1900830 1062730 1465610 1768960 1881500 1638870 2149300 1792490 FALSE TRUE 1791410.74 1888343.323 1576669.783 1798399.151 1733761.157 1953882.522 1479932.64 1689688.921 1580583.874 1.133385434 1.194712507 0.997523642 1.137806845 1.096911834 1.23617769 0.936320219 1.069028318 1 20.59202616 2.228820429 24.99989734 1.01306473 1.128023129 0.437414055 0.06949002 204.6706038 525317.9816 0.027049241 0.018487607 169.3637373 -2.228820429 0.114958399 VDLHLLNHDGNIIDAASIAAIVALCHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDLHLLNHDGNIIDAASIAAIVALCHFR 28 0 D6RIY6;Q06265-3;Q06265-4;Q06265;Q06265-2;D6RA17 D6RIY6 EXOSC9 Exosome complex component RRP45 0 ; 180.88 5.02E-18 337310000 256020 233210 131569 186472 207921 178961 242280 280900 242320 FALSE TRUE 222186.3083 231678.0282 195196.2085 228813.3176 203783.7789 185845.7455 218783.7229 220831.721 213673.2057 1.039841695 1.084263361 0.913526841 1.07085639 0.953717048 0.869766262 1.023917445 1.033502167 1 17.70504648 4.266247672 24.99997506 0.986065313 1.062052577 0.24025449 0.059523211 342.0900072 308883.7329 0.015063028 0.039834277 18460.67903 -4.266247672 0.075987264 VDLNSNGFICDYELHELFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDLNSNGFICDYELHELFK 19 0 P13797;U3KQI3 P13797 PLS3 Plastin-3 0 ; 181.26 3.18E-14 277780000 505210 378410 288060 368040 370200 303420 437020 538680 484560 FALSE TRUE 438445.2185 375924.1998 427366.7795 451609.1071 362833.7443 315092.7637 394637.8677 423487.474 427275.8688 1.026140839 0.879816126 1.000212768 1.056949714 0.849179115 0.737445727 0.92361375 0.991133609 1 18.70480831 4.762602005 22.51282852 0.931940456 1.026141268 0.097671725 0.09182609 4847.917093 4539399.576 0.024075928 1.168442298 57889.79414 -4.762602005 0.094200812 VDLTLLS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDLTLLSPK 9 0 E7EVA0;P27816-4;B5MEG9 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 VDLTLLS(1)PK 101.93 0.0038467 17260000 89979 83094 60953 77807 99952 86155 109500 121890 113280 TRUE FALSE 78088.04717 82548.15004 90430.07468 95474.26856 97963.15075 89469.4386 98880.70685 95824.77205 99888.16745 0.781754728 0.826405691 0.905313182 0.955811594 0.980728281 0.895696066 0.989914115 0.959320553 1 16.60802617 4.223751027 1.541656416 0.96417771 0.773012615 0.849325642 0.027888637 0.17286836 0.70774777 0.007906822 0.037839143 16739.82937 -4.223751027 -0.191165094 VDLVDENFTELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VDLVDENFTELR 12 0 D6RDM7;P61086;P61086-3 D6RDM7 UBE2K Ubiquitin-conjugating enzyme E2 K 0 ;;;;; 215.04 9.86E-11 395724000 511545 437370 348341 418460 441881 438969 436385 523403 723673 FALSE TRUE 443943.0322 434496.8877 516799.8727 513477.7388 433088.4326 455856.4215 394064.4499 411477.3416 638121.2024 0.695703309 0.680900252 0.809877294 0.804671177 0.678693062 0.714372787 0.617538562 0.644826312 1 19.28347094 1.231548384 24.99974549 1.000000511 0.703806563 0.695413433 0.061172096 159.080445 567096.6101 0.163510388 0.016747041 17.04309183 -1.231548384 -0.296193948 VDLVDENFTELRGEIAGPPDTPYEGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDLVDENFTELRGEIAGPPDTPYEGGR 27 1 D6RDM7;P61086;P61086-3 D6RDM7 UBE2K Ubiquitin-conjugating enzyme E2 K 0 ; 161.39 1.20E-11 280650000 202509 188088 108108 104559 181580 180944 211154 218389 31545 FALSE TRUE 175746.9226 186852.4375 160389.3904 128300.719 177966.9133 187905.0328 190676.3176 171688.2119 27815.78604 6.318243976 6.71749622 5.766128277 4.612514594 6.398054437 6.755337869 6.854967799 6.172330044 1 14.76361625 4.144147293 5.527337702 5.566221603 6.510900289 0.065203417 1.699179172 0.680255749 31.63544289 0.435907458 0.944895457 13936.29378 -4.144147293 0.944678687 VDNDENEHQLSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 VDNDENEHQLSLR 13 0 P06748;P06748-3;P06748-2;E5RGW4 P06748 NPM1 Nucleophosmin 0 ;;;;;;; 310.9 1.38E-50 81713300000 42725700 33632500 22038030 27085400 33252200 29664200 32157300 39139200 37668100 FALSE TRUE 37079390.49 33411565.89 32695695.02 33235554.04 32590546.28 30805400.97 29038690 30769586.66 33215020.13 1.116344062 1.005917376 0.984364751 1.000618212 0.981199052 0.92745393 0.874263808 0.926375674 1 24.98533245 8 0.44336963 0.928300484 4.839782409 0.678320559 0.036327527 58.013549 0.740586527 0.030038169 203.639683 99999999.99 -8 3.911481925 VDNEFDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDNEFDQR 8 0 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 95.608 0.02217 477150000 1054900 986760 613320 609360 911340 928880 1013800 1036300 1049800 FALSE TRUE 915492.2922 980277.9086 909923.6034 747724.5015 893206.117 964614.6147 915481.832 814695.3095 925693.8399 0.988979566 1.058965574 0.982963874 0.807744925 0.964904462 1.042044975 0.988968266 0.880091532 1 19.8201756 4.000372771 24.9996536 0.943561615 1.023220636 0.182080024 0.066938048 21.51167109 1442204.625 0.017623271 0.036136759 10008.58706 -4.000372771 0.079659021 VDNIQAGELTEGIWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDNIQAGELTEGIWR 15 0 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 0 ; 237.48 2.26E-17 105618000 101828 63631 47434 54543 71315 68911 74760 84465 89285 FALSE TRUE 88371.1718 63213.00377 70373.24106 66927.82179 69895.97103 71562.05076 67509.78671 66402.81706 78729.82901 1.122461117 0.802910467 0.89385741 0.850094845 0.887795285 0.908957274 0.857486769 0.84342641 1 16.26462272 4.749514595 24.77713106 0.87715895 1.122461276 0.68151025 0.051922181 795.2000197 1798647.88 0.011808729 0.1710787 56171.31552 -4.749514595 0.245302326 VDNLTYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDNLTYR 7 0 Q01130;Q01130-2;J3KP15;J3QL05;Q9BRL6-2;Q9BRL6 Q01130;Q9BRL6-2 SRSF2;SRSF8 Serine/arginine-rich splicing factor 2;Serine/arginine-rich splicing factor 8 0 166.78 0.0025837 843610000 824610 799720 483490 584600 741220 660320 668040 821730 848620 FALSE TRUE 715635.6992 794466.5867 717307.3812 717342.3651 726471.1722 685722.9377 603253.5836 646009.4342 748297.1104 0.956352349 1.061699391 0.958586331 0.958633082 0.970832524 0.916377904 0.806168533 0.863306066 1 19.51325168 2.670913308 3.093676636 0.879118269 0.984662251 0.35661957 0.056439005 0.253461391 4.788943738 0.020872669 0.018510235 468.7198093 -2.670913308 0.105543982 VDNLTYRT(ph)SPDTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDNLTYRTSPDTLR 14 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 VDNLTYRT(0.657)S(0.343)PDTLR 215.51 1.05E-11 1851200000 1010800 796440 228400 230960 722230 768810 819490 903560 49412 TRUE FALSE 877220.219 791208.1332 338855.004 283402.998 707859.036 798386.6182 740015.9859 710340.7255 43570.56965 20.13331995 18.15923316 7.777153401 6.504459324 16.24626535 18.32398852 16.98430826 16.30322328 1 15.41106636 7.999998677 0.047372832 5.07E-08 37.83870209 0.095412855 5.968796812 5348.998068 24.83127677 5736.404294 16991.66101 99999695.41 -7.999998677 37.83870203 VDNLTYRTS(ph)PDTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VDNLTYRTSPDTLR 14 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 VDNLTYRT(0.296)S(0.704)PDTLR;VDNLTYRT(0.103)S(0.897)PDTLR;VDNLTYRT(0.072)S(0.928)PDTLR;VDNLTYRT(0.376)S(0.624)PDTLR;VDNLTYRT(0.148)S(0.852)PDTLR 205.06 7.73E-09 8859580000 5117020 4552170 1180612 1101639 4078100 4438680 4511810 5180960 179986 TRUE FALSE 4440792.842 4522266.496 1751559.912 1351782.972 3996953.789 4609438.892 4074255.361 4073052.022 158708.2601 27.98085518 28.49421002 11.03635003 8.517407799 25.18428332 29.04347189 25.67135042 25.66376835 1 17.27601769 1.233634064 24.92446325 0.999965774 22.62667224 0.474905765 7.170254984 148.5317876 751360.6216 15.30344805 1.904820629 17.12513739 -1.233634064 21.62670646 VDNLTYRTS(ph)PDTLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDNLTYRTSPDTLRR 15 2 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 VDNLT(0.059)Y(0.004)RT(0.227)S(0.701)PDT(0.009)LRR;VDNLT(0.018)YRT(0.214)S(0.763)PDT(0.005)LRR 73.688 0.023711 305130000 375750 305832 51424 70258 297865 309902 351550 388680 26672 TRUE FALSE 326093.6855 303822.9695 76292.8184 86211.15273 291938.0693 321824.1305 317456.7351 305563.8067 23518.86654 13.86519562 12.9182658 3.243898606 3.665616817 12.41293107 13.68365818 13.49796065 12.99228456 1 14.52153091 4.449006225 24.98602292 9.338035204 13.62848108 0.139542614 4.689132089 416.5309983 370173.6736 1.242777748 3.28820842 28119.41136 -4.449006225 4.29044588 VDPAFDKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDPAFDKDR 9 1 O43615;M0QXM9 O43615 TIMM44 Mitochondrial import inner membrane translocase subunit TIM44 0 59.757 0.09137 123200000 300050 286990 213190 343630 353180 312240 292220 382830 411780 FALSE TRUE 260397.6323 285104.7438 316289.3971 421656.4436 346152.409 324252.0748 263880.5494 300964.7837 363099.8375 0.717151608 0.785196561 0.871081076 1.16126861 0.953325706 0.893010796 0.726743783 0.828876118 1 18.47000676 4.289187969 3.336598695 0.910930491 0.735178758 0.28639196 0.11288519 0.361209371 7.993951436 0.032449007 0.097728312 19462.02246 -4.289187969 -0.175751733 VDPSLMEDS(ph)DDGPSLPTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDPSLMEDSDDGPSLPTK 18 0 O15258;Q5T092;A0A0A0MR06;Q5T091 O15258 RER1 Protein RER1 1 VDPSLMEDS(1)DDGPSLPTK 291.7 3.61E-49 81856000 105170 76567 51364 68087 77364 64690 73178 97092 123660 TRUE FALSE 91271.51803 76064.02634 76203.8022 83547.19399 75824.60776 67178.66616 66081.20882 76329.63137 109041.0557 0.8370381 0.697572358 0.698854223 0.766199423 0.695376684 0.616085985 0.60602136 0.700008184 1 16.73451191 1.239207428 9.528512392 1.001592145 0.696284175 0.666696055 0.066074335 0.046131501 74.61938439 0.093273269 0.016728427 17.34632297 -1.239207428 -0.305307971 VDQDSALHNDLQILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDQDSALHNDLQILK 15 0 Q7Z7E8;Q7Z7E8-2 Q7Z7E8 UBE2Q1 Ubiquitin-conjugating enzyme E2 Q1 0 ; 142.1 4.65E-06 172990000 287830 281310 184933 229030 271240 251480 299210 335850 362540 FALSE TRUE 249792.5362 279462.0561 274367.2174 281034.762 265842.8547 261154.5983 270192.6603 264031.0911 319680.9342 0.781380775 0.874190564 0.858253302 0.879110175 0.831588081 0.816922658 0.845194791 0.825920669 1 18.28627318 1.23531268 24.99998469 1.00000022 0.84076315 0.75874476 0.028504487 44.64554146 343586.7001 0.04735947 0.006768423 17.19145678 -1.23531268 -0.159237069 VDQICHK ddPTM_MDA-MB-175_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 ;; 95.531 0.013398 1564650000 2395990 1792020 1390300 1775760 1696510 1781310 2278520 2362230 2653450 FALSE TRUE 2079353.851 1780248.103 2062653.73 2178973.449 1662752.77 1849838.148 2057549.481 1857085.497 2339762.164 0.888703084 0.760867122 0.881565555 0.931279889 0.710650337 0.79060948 0.87938403 0.793706953 1 21.15793046 1.231547184 24.99708815 1.000000297 0.827965879 0.387796107 0.067258958 260.5090848 928415.7953 0.155837568 0.015927465 17.04304473 -1.231547184 -0.172034418 VDRDYVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDRDYVLK 8 1 Q9BUP3-3;Q9BUP3 Q9BUP3-3 HTATIP2 Oxidoreductase HTATIP2 0 ; 136.57 0.00071634 837200000 588090 563660 451260 540570 576020 580170 640820 724960 565330 FALSE TRUE 510372.4165 559957.2803 669490.8454 663314.6806 564558.329 602489.5153 578673.375 569932.9456 498497.3314 1.023821763 1.123290427 1.343017912 1.330628348 1.132520263 1.208611315 1.160835452 1.143301899 1 18.92722626 0.318923623 1.022595454 1.10E-08 1.200782752 0.283773978 0.094165854 14.65677328 2.915188485 30.34566835 0.032293892 2.084124329 -0.318923623 1.200782741 VDS(ph)EGDFS(ph)ENDDAAGDFR ddPTM_MDA-MB-175_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 348.62 3.75E-90 1030830000 1048760 775950 702040 735730 907150 844010 870800 967180 1338950 TRUE FALSE 910163.7088 770852.7334 1041548.892 902788.7414 889099.4898 876479.6108 786349.95 760356.0836 1180660.856 0.77089344 0.652899373 0.882174493 0.764646966 0.753052399 0.742363572 0.666025257 0.644008887 1 20.17116318 2.927869502 3.110975681 0.73564129 0.767001897 0 0.110290192 1.630051062 30.83619917 0.037054474 0.038436083 846.972875 -2.927869502 0.031360607 VDS(ph)LVSLSEEDLESDQR ddPTM_MDA-MB-175_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 VDS(1)LVSLSEEDLESDQR;VDS(1)LVSLSEEDLESDQR 285.94 2.41E-36 51188000 54418 53968 39973 39353 59916 54476 59366 60963 66541 TRUE FALSE 47226.52342 53613.48065 59304.0765 48288.70012 58723.78882 56571.72697 53608.69446 47926.53686 58674.59878 0.804888732 0.913742604 1.010728283 0.822991569 1.000838353 0.96416044 0.913661032 0.816819166 1 15.84044845 4.729927649 5.450445345 0.923469983 0.801001737 0.242677104 0.068883384 0.21913153 24.57516912 0.01681723 0.099161854 53694.23372 -4.729927649 -0.122468245 VDS(ph)PSHGLVTSSLCIPSPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDSPSHGLVTSSLCIPSPAR 20 0 Q9UER7-3;Q9UER7 Q9UER7-3 DAXX Death domain-associated protein 6 1 VDS(0.972)PS(0.028)HGLVTSSLCIPSPAR;VDS(0.991)PS(0.009)HGLVTSSLCIPSPAR 284.9 3.20E-45 560400000 562930 387860 289480 332200 391640 415010 409260 492740 480060 TRUE FALSE 488537.3742 385312.1221 429473.4963 407631.0874 383847.1302 430975.7032 369570.0282 387371.3855 423307.8537 1.154094756 0.910240901 1.014565387 0.96296604 0.906780082 1.018114121 0.873052614 0.915105595 1 18.69134773 4.744826907 24.82248605 0.946945085 1.154094858 0.625023319 0.049602095 423.3256018 1676857.893 0.011795927 0.107171406 55568.27398 -4.744826907 0.207149773 VDS(ph)PTVNTTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDSPTVNTTLR 11 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 VDS(0.99)PT(0.01)VNTTLR;VDS(0.999)PT(0.001)VNTTLR 162.13 3.95E-05 228770000 589990 509160 400790 455150 525950 469540 500780 571760 754560 TRUE FALSE 512021.3267 505815.2944 594613.3846 558498.764 515484.624 487603.5076 452214.4327 449493.5734 665356.7764 0.769544017 0.760216642 0.893676003 0.839397424 0.774749191 0.732845182 0.679657063 0.67556774 1 19.34376862 3.042927968 5.076327944 0.748676746 0.816921348 0.022156397 0.097411835 0.487956223 29.31272377 0.03038484 0.034116983 1103.895513 -3.042927968 0.068244602 VDS(ph)PTVTTTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VDSPTVTTTLK 11 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;H0YG16;G5E9S8;H0YJU9;H0YJT3;H0YJL0 Q07866-6 KLC1 Kinesin light chain 1 1 VDS(0.996)PT(0.004)VTTTLK;VDS(0.995)PT(0.005)VTTTLK;VDS(0.972)PT(0.028)VTTTLK 237.67 1.44E-15 519280000 1489470 1337340 1234810 1355690 1447720 1096320 1586290 1905510 2529840 TRUE FALSE 1292632.766 1328554.925 1831968.246 1663520.135 1418913.204 1138496.14 1432451.84 1498031.515 2230765.197 0.579457115 0.595560181 0.82122863 0.745717271 0.63606569 0.510361261 0.642134745 0.671532583 1 21.08910724 1.235797839 4.800046431 1.025872692 0.650695687 0.622391623 0.085777786 0.136917271 7.423371547 0.173972237 0.023081747 17.21067245 -1.235797839 -0.375177005 VDS(ph)TTCLFPVEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 VDSTTCLFPVEEK 13 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 1 VDS(0.99)T(0.01)TCLFPVEEK;VDS(0.969)T(0.03)T(0.001)CLFPVEEK;VDS(0.88)T(0.12)T(0.001)CLFPVEEK;VDS(0.5)T(0.5)TCLFPVEEK;VDS(0.5)T(0.5)TCLFPVEEK;VDS(0.499)T(0.499)T(0.002)CLFPVEEK;VDS(0.49)T(0.49)T(0.019)CLFPVEEK;VDS(0.986)T(0.014)TCLFPVEEK;VDS(0.987)T(0.013)TCLFPVEEK 315.29 1.04E-50 6069503000 12321560 10051020 6977925 6347412 9139430 6463807 12238260 12455220 12407520 TRUE FALSE 10693234.63 9984994.188 10352472.87 7788688.909 8957573.224 6712473.838 11051395.43 9791768.13 10940717.12 0.977379683 0.912645312 0.946233483 0.711899305 0.818737303 0.613531432 1.010116184 0.894984124 1 23.38320397 VDSEGDFS(ph)ENDDAAGDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDSEGDFSENDDAAGDFR 18 0 O43823;M0QYL4 O43823 AKAP8 A-kinase anchor protein 8 1 VDSEGDFS(1)ENDDAAGDFR;VDSEGDFS(1)ENDDAAGDFR 299.53 7.11E-36 223390000 357420 263770 234895 273910 271260 297750 287330 340890 436180 TRUE FALSE 310186.0414 262037.2775 348491.0077 336105.452 265862.4567 309204.6352 259464.7808 267993.3263 384615.2973 0.806483891 0.681297076 0.906076826 0.873874373 0.691242544 0.803932234 0.674608583 0.696782807 1 18.55305662 3.242548973 24.99886117 0.757875035 0.813612155 0.027558435 0.108315677 339.740534 2129467.726 0.031554246 0.039232937 1748.030365 -3.242548973 0.05573712 VDSLVS(ph)LSEEDLESDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDSLVSLSEEDLESDQR 17 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36;H0YLH1 Q12802-2 AKAP13 A-kinase anchor protein 13 1 VDSLVS(0.68)LS(0.312)EEDLES(0.008)DQR 70.98 0.020673 0 16860 15862 7193.6 13018 12604 14628 14678 16572 14424 TRUE FALSE 14631.90828 15757.80148 10672.44902 15973.93587 12353.20506 15190.74863 13254.52982 13028.20676 12718.81115 1.150414776 1.238936665 0.839107437 1.255929951 0.971254696 1.194352872 1.042120184 1.024325828 1 13.63467621 7.095111674 0.021159071 1.49E-07 2.397250565 0.083725918 0.125633704 13026.63975 33.46421308 1551.737054 2311.758713 12448346.65 -7.095111674 2.397250417 VDSPS(ph)HGLVTSSLCIPSPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDSPSHGLVTSSLCIPSPAR 20 0 Q9UER7-3;Q9UER7 Q9UER7-3 DAXX Death domain-associated protein 6 1 VDS(0.365)PS(0.635)HGLVTSSLCIPSPAR 365.02 6.09E-112 160880000 68831 46537 27154 37570 49072 45484 40654 56619 56593 TRUE FALSE 59734.80895 46231.29538 40285.76522 46100.84272 48095.56321 47233.79891 36711.38134 44511.46746 49902.64001 1.19702703 0.926429852 0.807287254 0.923815708 0.963787952 0.94651904 0.735660104 0.891966186 1 15.60682852 4.727444986 4.201098649 0.890594583 1.21848899 0.60090023 0.076474798 0.14136759 5.660916302 0.019053708 0.137140755 53388.16401 -4.727444986 0.327894407 VDSSTNSS(ph)PSPQQSESLS(ph)PAHTSDFR ddPTM_MDA-MB-175_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(0.009)NS(0.083)S(0.641)PS(0.255)PQQS(0.068)ES(0.136)LS(0.782)PAHT(0.011)S(0.004)DFR 76.446 0.012227 109070000 102330 86988 37457 44079 72672 67051 61246 66958 64296 TRUE FALSE 88806.83123 86416.5701 55571.33049 54087.81066 71225.96938 69630.49536 55306.37235 52639.55277 56695.00013 1.566396173 1.524236174 0.980180446 0.954013767 1.256300718 1.228159365 0.97550705 0.928469048 1 15.79093389 4.244454123 24.68359233 1.042528493 1.545316526 0.775697704 0.111593696 58.40981144 244627.7046 0.031444288 0.078587431 17557.15419 -4.244454123 0.502788033 VDSSTNSSPSPQQSESLS(ph)PAHTSDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDSSTNSSPSPQQSESLSPAHTSDFR 26 0 F2Z3H6;Q9BQE9-2;Q9BQE9-3;Q9BQE9 F2Z3H6 BCL7B B-cell CLL/lymphoma 7 protein family member B 1 VDSSTNSSPSPQQSES(0.006)LS(0.994)PAHTSDFR 219.52 2.07E-34 256880000 49395 44911 21980 38891 56312 59832 56070 57432 52539 TRUE FALSE 42867.3256 44615.97668 32609.60152 47721.79596 55191.50137 62133.77576 50632.34003 45150.61374 46327.89927 0.925302599 0.963047697 0.703886903 1.03008763 1.191323203 1.341174038 1.092912496 0.974587979 1 15.49959364 3.490271888 22.01387126 1.110837189 0.872811027 0.48424912 0.120248109 126.0547257 211012.0685 0.037175973 0.052301232 3092.230704 -3.490271888 -0.238026162 VDST(ph)TCLFPVEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VDSTTCLFPVEEK 13 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 1 VDS(0.016)T(0.937)T(0.046)CLFPVEEK;VDS(0.025)T(0.84)T(0.135)CLFPVEEK;VDS(0.296)T(0.704)TCLFPVEEK 368.67 3.84E-90 6330900000 5432000 4179100 3415960 2973140 3829300 2676630 5404100 5350400 5641500 TRUE FALSE 4714147.437 4151647.217 5067929.682 3648236.879 3753104.422 2779601.688 4880011.214 4206258.597 4974568.297 0.947649556 0.834574373 1.018767736 0.733377584 0.754458316 0.558762393 0.980991902 0.845552487 1 22.2461399 3.73376732 24.98243968 0.813250746 0.923754935 0.157537242 0.131743836 845.8496414 4408532.317 0.037000921 0.056949433 5417.105834 -3.73376732 0.110504189 VDTFPQPLAAPQCHTLLAPEMEDNEMSCS(ph)P ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VDTFPQPLAAPQCHTLLAPEMEDNEMSCSP 30 0 B7Z4K4;Q9UET6-2;Q9UET6 B7Z4K4 FTSJ1 Putative tRNA (cytidine(32)/guanosine(34)-2-O)-methyltransferase 1 VDTFPQPLAAPQCHTLLAPEMEDNEMS(0.029)CS(0.971)P;VDTFPQPLAAPQCHTLLAPEMEDNEMS(0.037)CS(0.963)P 131.94 4.88E-06 102132000 89023 112983 64743 66792 97971 107438 114173 129176 77091 TRUE FALSE 77258.38499 112240.8072 96052.93135 81958.14445 96021.56878 111571.2094 103100.52 101552.7176 67977.3898 1.13653062 1.651149118 1.413012939 1.205667718 1.412551571 1.641298816 1.516688421 1.493919051 1 16.05276735 3.004900169 24.98742244 1.445522204 1.368841425 0.007141478 0.212516176 649.1947711 3310392.978 0.063801697 0.072106055 1011.346951 -3.004900169 -0.076680778 VDTPHYPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VDTPHYPR 8 0 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 0 ;;; 160.63 0.00035223 773630000 1811000 1975570 1322780 1426250 1991840 2231110 1893010 2223470 2187400 FALSE TRUE 1571671.762 1962592.351 1962480.832 1750101.861 1952206.281 2316942.245 1709426.182 1747998.244 1928808.064 0.814840933 1.017515629 1.017457812 0.907348893 1.01213092 1.20123007 0.886260387 0.906258262 1 20.87927816 4.745055304 24.14140173 0.986806559 0.814840805 0.281302641 0.089185489 693.0338117 2575962.604 0.022690361 0.206343185 55597.50515 -4.745055304 -0.171965755 VDVADQAQDKDRDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VDVADQAQDKDRDDR 15 2 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;;; 223.15 7.34E-13 7893080000 11970960 9125570 8811330 10340750 9446980 7491420 11066710 13877360 18743060 FALSE TRUE 10388967.31 9065623.53 13072518.66 12688775.34 9259003.581 7779619.775 9993462.168 10909794.56 16527276.8 0.628595227 0.548524941 0.790966281 0.767747493 0.560225601 0.470713952 0.604664779 0.660108419 1 23.9783457 1.234508798 4.081508197 1.041428311 0.625670348 0.600194602 0.095589285 0.184208951 5.500264566 0.229720051 0.026117313 17.15966474 -1.234508798 -0.415757963 VDVFREDLCTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VDVFREDLCTK 11 1 Q06323;Q06323-3;Q06323-2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;;; 196.38 5.53E-08 2281640000 6391300 5654220 2407950 2564460 4811840 4129020 6342830 7096200 1155500 FALSE TRUE 5546673.512 5617077.057 3572442.674 3146759.838 4716093.798 4287866.071 5727703.323 5578732.853 1018898.106 5.443796074 5.512893803 3.506182465 3.088395021 4.628621615 4.208336481 5.621468219 5.475260792 1 19.95857835 4.25686285 24.55844375 4.165375084 5.478346574 0.175595924 1.319463681 400.2514488 537056.985 0.333234303 0.877745485 18066.0351 -4.25686285 1.31297149 VDVNAPDVQAPDWHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDVNAPDVQAPDWHLK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 188.04 1.24E-09 184740000 306140 198780 135930 193390 235760 188580 176560 305610 238520 FALSE TRUE 265682.8233 197474.2011 201666.2027 237302.1553 231068.8373 195834.7946 159437.2384 240257.6798 210322.4373 1.263216739 0.938911719 0.958843028 1.128277888 1.098640926 0.931116989 0.758061006 1.142330237 1 17.68224324 2.740089904 24.90792785 0.967965112 1.066094641 0.171844018 0.128369474 300.0444906 4886940.558 0.043294235 0.041114543 549.6546475 -2.740089904 0.098129528 VDVRPLPAS(ph)PARPCPSPGPAAASSPARPPGLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDVRPLPASPARPCPSPGPAAASSPARPPGLQR 33 3 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 VDVRPLPAS(0.916)PARPCPS(0.084)PGPAAASSPARPPGLQR 130.17 3.81E-07 676350000 35111 30101 22816 32351 38151 31709 35037 32493 51770 TRUE FALSE 30470.99239 29903.26455 33849.89391 39696.789 37391.86974 32928.86575 31639.11713 25544.62481 45649.80958 0.667494403 0.655057816 0.74151227 0.869593748 0.819102425 0.721336322 0.693083223 0.559577905 1 15.47832122 4.207068551 6.199916321 0.752571246 0.660934478 0.119677141 0.11606955 0.415799669 47.10975668 0.031208878 0.069334982 16108.99887 -4.207068551 -0.091636768 VDVSAPDVEAHGPEWNLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VDVSAPDVEAHGPEWNLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 181.41 7.36E-14 163740000 406280 264060 182310 299010 262320 237080 273130 393220 341230 FALSE TRUE 352589.0686 262325.3725 270475.7258 366904.7906 257100.3452 246200.621 246641.8946 309132.963 300890.1781 1.171819801 0.871830959 0.898918428 1.219397698 0.854465728 0.818240803 0.819707364 1.027394663 1 18.19887749 VEADIPGHGQEVLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VEADIPGHGQEVLIR 15 0 B0QYF8;P02144;F2Z2F1;F2Z337 B0QYF8 MB Myoglobin 0 ;;; 206.06 4.09E-09 3276570000 4895120 5423800 3497360 4544070 5285200 5350200 4059700 6251100 6149600 FALSE TRUE 4248217.489 5388170.701 5188694.994 5575870.545 5180034.86 5556025.656 3665990.919 4914350.911 5422601.294 0.783427964 0.993650539 0.956864559 1.028264894 0.955267515 1.024605232 0.676057619 0.906271851 1 22.37055367 VEADRPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VEADRPGK 8 1 P38159;P38159-2;H3BT71;H3BR27;P38159-3;H3BNC1;O75526;Q96E39;A0A1B0GUK8 P38159;Q96E39 RBMX;RBMXL2;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA-binding motif protein, X-linked-like-2;RNA binding motif protein, X-linked-like-1" 0 ;;; 114.28 0.0028596 943370000 2046220 1655420 1140340 1422360 1483480 1411800 1996160 2233390 2065010 FALSE TRUE 1775806.843 1644545.437 1691812.238 1745328.577 1453961.65 1466112.86 1802572.71 1755796.929 1820886.87 0.975242818 0.903156294 0.929114414 0.958504675 0.79849093 0.805164167 0.989942176 0.964253715 1 20.79620986 2.175414779 24.99997326 0.98068321 0.895375339 0.350252275 0.057558184 80.09670471 31709.89406 0.024975713 0.016838626 149.7665339 -2.175414779 -0.085307871 VEAEAGGSGART(ph)PPLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VEAEAGGSGARTPPLSR 17 1 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 VEAEAGGS(0.013)GART(0.987)PPLSR;VEAEAGGSGART(1)PPLSR;VEAEAGGSGART(1)PPLSR;VEAEAGGSGART(1)PPLSR;VEAEAGGS(0.008)GART(0.992)PPLSR;VEAEAGGSGART(1)PPLSR 170.06 3.07E-09 7081870000 1234810 1144045 508594 595788 1118593 1006030 1027340 1240852 323373 TRUE FALSE 1071626.73 1136529.693 754551.7595 731070.7714 1096335.188 1044732.625 927708.7249 975505.4561 285144.2123 3.758192113 3.985806634 2.646211029 2.563863266 3.84484461 3.663874559 3.25347205 3.42109506 1 18.12133222 4.249814008 24.91635635 3.024486061 3.871999811 0.188790537 0.800781094 383.3443016 848752.7472 0.197463877 0.512223812 17775.18004 -4.249814008 0.847513749 VEAFEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VEAFEHR 7 0 P42285 P42285 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 ; 133.9 0.0032266 197890000 550520 514760 341110 396230 447220 569160 450640 548600 562740 FALSE TRUE 477767.3872 511378.5077 506071.9369 486200.0775 438321.197 591055.9535 406937.0022 431286.1592 496213.5183 0.962826222 1.030561419 1.019867292 0.979820298 0.883331834 1.191132308 0.820084474 0.869154393 1 18.92060151 VEAKEES(ph)EES(ph)DEDMGFGLFD ddPTM_MDA-MB-175_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 40.962 0.091962 0 19317 16922 9447.6 10579 19077 13399 21960 25710 7621.7 TRUE FALSE 16764.20951 16810.83827 14016.49096 12981.12364 18697.40502 13914.4682 19830.32258 20212.11658 6720.671309 2.494424848 2.501362959 2.085579002 1.931521874 2.782074017 2.07039856 2.950646099 3.007455007 1 12.71438963 3.235669075 24.99307315 2.47233625 2.258972046 0 0.595527615 356.5816148 3082119.907 0.176613381 0.209161811 1720.557038 -3.235669075 -0.213364204 VEAKPEVQSQPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VEAKPEVQSQPPR 13 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ; 159.18 4.07E-05 841100000 625950 438380 285480 354810 442980 312350 471560 555000 443760 FALSE TRUE 543229.1215 435500.2529 423539.0829 435375.0334 434165.5647 324366.3066 425828.1838 436317.569 391299.1983 1.388270469 1.112959737 1.0823919 1.112639728 1.109548822 0.828947026 1.088241902 1.115048461 1 18.57791263 7.883309998 0.958544986 1.044249065 199.9999999 0.615806338 0.084492808 733.032503 1.565769752 0.02761806 319378.1971 76438120.2 -7.883309998 198.9557509 VEAMNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VEAMNKR 7 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;; 88.942 0.029242 1288660000 642640 592870 405680 420821 441960 425380 583790 683950 401781 FALSE TRUE 557713.4958 588975.3979 601868.2049 516374.8399 433165.8607 441744.6439 527174.1357 537692.615 354282.9079 1.574203788 1.662443727 1.698835003 1.457521174 1.222655259 1.246869759 1.488003299 1.51769279 1 18.43454234 3.539956902 4.262336589 1.334587115 1.643593066 0.527995462 0.148474094 0.201891011 7.262448127 0.043933253 0.064948942 3467.024429 -3.539956902 0.309005951 VEAQHILASAPTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEAQHILASAPTDR 14 0 A0A0A0MQS1;Q53H96-2;Q53H96 A0A0A0MQS1 PYCRL Pyrroline-5-carboxylate reductase;Pyrroline-5-carboxylate reductase 3 0 126.88 8.28E-05 577520000 317120 289010 196720 251450 313340 307270 280060 366240 372170 FALSE TRUE 275211.7885 287111.4743 291854.45 308545.5657 307105.147 319090.8757 252899.8243 287922.4261 328172.4866 0.838619323 0.874879784 0.889332476 0.940193277 0.935804065 0.972326715 0.770630795 0.877350899 1 18.32409477 4.48491115 1.999853174 0.906041092 0.835917842 0.132505537 0.062007706 1.140018377 7.144389436 0.017379844 0.121391915 30542.96185 -4.48491115 -0.07012325 VEAVNMAEGIIHDTETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VEAVNMAEGIIHDTETK 17 0 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;; 201.96 1.10E-11 271248000 439574 412057 277186 602128 477184 426576 419396 618234 750180 FALSE TRUE 381483.1822 409350.1704 411234.0767 738850.3654 467688.972 442986.6548 378723.0405 486029.4702 661494.575 0.576698882 0.618826194 0.621674149 1.116940929 0.707018606 0.669675416 0.572526298 0.734744454 1 19.3353698 3.962791092 24.99977402 0.777449103 0.60338395 0.243594428 0.158509314 894.3180489 600872.0074 0.043347212 0.075106711 9178.909578 -3.962791092 -0.174065153 VECQSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VECQSHR 7 0 O14818;H0Y586;O14818-2;O14818-4 O14818 PSMA7 Proteasome subunit alpha type-7 0 ;;; 125.5 0.0040428 383695000 776132 724978 488952 586052 438780 763211 697812 779972 1102717 FALSE TRUE 673564.1897 720215.5718 725410.8226 719124.0638 430049.1365 792572.221 630138.2996 613181.0575 972355.0525 0.692714239 0.740691962 0.746034919 0.739569422 0.442275829 0.815105777 0.64805371 0.630614358 1 19.89112368 1.233127622 24.99903311 1.000000504 0.680214388 0.499883408 0.099985603 146.2255596 672759.3704 0.197498191 0.023525811 17.10517896 -1.233127622 -0.319786116 VECVGDDIAWMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VECVGDDIAWMR 12 0 Q16822;Q16822-3;H0YML5;H0YM31;Q16822-2 Q16822 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 0 ; 205.59 2.33E-07 206921000 178543 180471 116091 186923 190526 199921 155614 206390 181479 FALSE TRUE 154948.0902 179285.4741 172232.9959 229366.7241 186734.9054 207612.0902 140522.5782 162255.1046 160024.7594 0.968275727 1.120360842 1.076289673 1.433320225 1.166912583 1.2973748 0.878130227 1.013937501 1 17.28793561 2.234653133 24.99999816 0.970842669 1.18111295 0.378639588 0.128499203 107.8735474 690161.1579 0.051853467 0.036438197 171.6536857 -2.234653133 0.210270281 VECYDYDNDGSHDLIGTFQTTMTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VECYDYDNDGSHDLIGTFQTTMTK 24 0 O75131;H0YB26 O75131 CPNE3 Copine-3 0 96.903 0.0061966 107480000 48679 46296 31720 53852 44337 43650 37342 61633 72803 FALSE TRUE 42245.94681 45991.87853 47059.8981 66079.91968 43454.78044 45329.24375 33720.57859 48453.26258 64196.31228 0.658074355 0.716425553 0.733062328 1.029341365 0.676904621 0.706103546 0.525272829 0.754767071 1 15.9702028 3.292513533 0.012511082 1.488327975 7.80E-07 0.027609769 0.149878922 15148.82657 205.2137089 12100.15891 12305.46632 1961.162287 -3.292513533 -1.488327196 VEDLAWHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VEDLAWHR 8 0 Q9NZU5;B4DEY6;Q9NZU5-2 Q9NZU5 LMCD1 LIM and cysteine-rich domains protein 1 0 ;;; 116.25 0.0023075 1433790000 2102690 2135030 1377570 1609950 2142790 2169750 2122520 2406440 2335340 FALSE TRUE 1824814.189 2121004.847 2043767.46 1975513.754 2100152.671 2253221.687 1916678.337 1891841.533 2059258.766 0.886150988 1.029984615 0.992477242 0.959332449 1.019858556 1.09419065 0.930761286 0.918700245 1 20.9736937 VEDMAELTCLNEASVLHNLK ddPTM_MDA-MB-175_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 ;;; 357.67 1.98E-95 2107980000 3520460 3131660 1807610 2751920 3082880 2615220 3923950 4237410 4335320 FALSE TRUE 3055222.291 3111087.919 2681776.242 3376785.496 3021536.72 2715829.206 3543405.933 3331272.847 3822803.408 0.79920989 0.813823675 0.701520836 0.883327008 0.790398144 0.710428687 0.926912937 0.871421439 1 21.86619958 1.414207152 1.022522332 1.056262701 0.787483809 0.530674345 0.063099763 1.090864924 1.167652665 0.311916462 0.021039496 25.95417045 -1.414207152 -0.268778892 VEDVEALDRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VEDVEALDRK 10 1 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;;; 113.63 0.0023454 1247900000 2138480 1682820 1117550 1255920 1481970 1332350 1857440 2024360 1309620 FALSE TRUE 1855874.45 1671765.445 1658000.918 1541095.832 1452481.696 1383606.367 1677305.755 1591466.368 1154798.216 1.607098474 1.447668885 1.435749463 1.334515252 1.257779651 1.198136911 1.452466528 1.378133726 1 20.13920935 7.999999968 0.419002056 1.262269989 7.746489517 0.488106944 0.118868336 88.82970927 1.199982952 0.107145757 479.6402175 99999992.63 -7.999999968 6.484219528 VEDVVVSDECR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEDVVVSDECR 11 0 Q96EK6;G3V5E4;G3V4W4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 0 119.53 0.0019994 0 90177 96250 55126 65363 95450 91379 89416 95624 93489 FALSE TRUE 78259.88097 95617.72741 81785.11799 80204.66816 93550.73174 94894.40926 80744.45008 75175.55175 82436.83692 0.949331438 1.159890784 0.992094324 0.972922678 1.134817094 1.151116574 0.979470502 0.911916985 1 16.33100153 2.017331278 24.32125573 0.948474904 1.061284645 0.264017722 0.076245176 197.655342 277371.3859 0.030707654 0.02069744 104.0713716 -2.017331278 0.112809741 VEEAS(ph)PGRPSSVDTLLSPTALIDSILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEEASPGRPSSVDTLLSPTALIDSILR 27 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 1 VEEAS(0.981)PGRPS(0.009)S(0.009)VDT(0.002)LLSPTALIDSILR 98.009 0.002381 761220000 83929 87517 48179 49982 78537 62840 81351 106830 89273 TRUE FALSE 72837.57 86942.09506 71478.52555 61331.17703 76974.26736 65257.49546 73461.59254 83985.23585 78719.24764 0.925282852 1.104457902 0.908018403 0.779112846 0.977832864 0.828990335 0.933210044 1.066895815 1 16.26442881 1.78783982 8.033349518 1.03417265 0.921682001 0.22006581 0.086939889 0.36453084 52.38159171 0.046126621 0.02335587 61.35356739 -1.78783982 -0.112490649 VEECQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 114.94 0.057818 497050000 676060 610350 472360 573980 411230 657400 675450 742530 809950 FALSE TRUE 586716.9581 606340.5707 700794.8759 704310.9317 403047.3276 682690.6034 609944.963 583745.7379 714198.6337 0.821503893 0.848980301 0.981232451 0.986155529 0.564335058 0.955883379 0.854027065 0.817343678 1 19.44596585 1.229485568 24.66589769 1.000000336 0.85412584 0.127371405 0.12035357 669.4680457 1819444.523 0.337294853 0.028459225 16.96233233 -1.229485568 -0.145874496 VEEEDDAEHVLALTMLCLTEGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VEEEDDAEHVLALTMLCLTEGAK 23 0 O75607 O75607 NPM3 Nucleoplasmin-3 0 ;;; 207.82 1.13E-24 93767000 74567 63947 67433 81384 54574 46705 64796.7 85061 206124 FALSE TRUE 64712.78202 63526.92795 100043.8243 99863.48108 53488.08417 48501.77157 58512.72601 66871.3671 181756.2555 0.356041567 0.349517147 0.550428507 0.549436281 0.294284695 0.266850632 0.321929641 0.36791783 1 17.47164549 1.237785814 25 1.000000716 0.381703318 0.803721668 0.095970549 9.016229733 290729.3469 0.149807124 0.025649983 17.28963456 -1.237785814 -0.618297398 VEEEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VEEEEER 7 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ;;;;; 197.65 0.00097132 17917780000 11797940 11790690 7726110 8743320 8680210 10640950 11827090 12943740 11942050 FALSE TRUE 10238812.34 11713236.18 11462482.64 10728624.44 8507490.804 11050314.23 10680100.63 10175821.93 10530274.45 0.972321508 1.112339116 1.088526485 1.018836165 0.807907794 1.049385207 1.014228136 0.966339669 1 23.3280397 3.47460654 24.99998633 0.969404688 1.061605276 0.248573505 0.07203626 104.5327007 1039196.497 0.020321447 0.026401339 2982.679164 -3.47460654 0.092200589 VEEESTGDPFGFDS(ph)DDESLPVSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEEESTGDPFGFDSDDESLPVSSK 24 0 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 1 VEEESTGDPFGFDS(1)DDESLPVSSK 192.18 4.98E-18 119110000 343300 279660 210240 243270 279640 233670 329910 394490 332680 TRUE FALSE 297932.0352 277822.895 311912.7672 298508.1716 274075.7111 242659.4361 297915.379 310131.3834 293350.9494 1.0156164 0.94706663 1.063275124 1.017580384 0.934292906 0.8271984 1.015559621 1.05720259 1 18.16226814 2.016833131 24.99889205 1.033795439 0.967502619 0.149807865 0.064023352 417.7750107 620435.4929 0.027715126 0.018680507 103.9520673 -2.016833131 -0.06629282 VEEFLYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEEFLYEK 8 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39;F8WFB9;H7C1Z6 B7ZC38 SH3GLB2 Endophilin-B2 0 120.07 0.0083669 0 48822 56927 32721 39195 46321 46310 52652 61764 52937 FALSE TRUE 42370.049 56553.04279 48544.98505 48094.82381 45399.30273 48091.57567 47545.81714 48556.24925 46678.84817 0.907692684 1.211534667 1.039978212 1.030334417 0.972588324 1.030264832 1.018573059 1.040219525 1 15.51048134 4.008948302 24.9930888 1.018365934 1.076149331 0.04776729 0.074462652 441.9970336 1234497.887 0.017223318 0.035765206 10208.1796 -4.008948302 0.057783397 VEEGGRHPS(ph)PCQFTIATPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VEEGGRHPSPCQFTIATPK 19 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 VEEGGRHPS(1)PCQFTIATPK;VEEGGRHPS(0.793)PCQFT(0.207)IATPK 154.65 2.03E-08 1540500000 1881200 1607260 1017220 1137540 1540120 1342260 1813670 2128100 1237030 TRUE FALSE 1632594.654 1596701.803 1509150.994 1395835.843 1509474.625 1393897.611 1637780.563 1673022.376 1090789.723 1.49670887 1.46380349 1.3835398 1.279656211 1.383836494 1.277879303 1.50146314 1.533771671 1 20.05694158 4.2507959 3.39888634 1.359711385 1.488360256 0.130924018 0.146701531 0.555435612 13.20935264 0.038269003 0.108241713 17815.41322 -4.2507959 0.128648871 VEELARSLRADIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEELARSLRADIER 14 2 Q9BX97 Q9BX97 PLVAP Plasmalemma vesicle-associated protein 0 58.32 0.065934 245630000 458780 311880 382190 358090 192890 194540 321260 389370 308070 FALSE TRUE 398151.0606 309831.2397 567018.3623 439399.8076 189051.8664 202024.0797 290104.2546 306106.2556 271650.3156 1.465674942 1.140551739 2.087309787 1.61751996 0.695938328 0.743691681 1.067932699 1.126839315 1 18.0513912 3.251414739 24.98745021 0.95329476 1.582930959 0.601764076 0.262604424 171.8162355 333996.0447 0.079843576 0.102403745 1784.081701 -3.251414739 0.629636199 VEELEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEELEHR 7 0 Q08379;Q08379-2;A0A087WYC0 Q08379 GOLGA2 Golgin subfamily A member 2 0 155.51 0.0016062 222440000 582870 476270 301340 388510 425630 497720 467690 538470 503660 FALSE TRUE 505842.2527 473141.351 447069.0319 476727.1335 417160.7957 516867.6105 422333.4958 423322.3809 444117.8886 1.138981936 1.065350807 1.006644955 1.07342475 0.939301943 1.163807232 0.950949076 0.953175704 1 18.76058316 8 0.25425006 0.966728013 1.956587337 0.273184865 0.066456043 111.8194624 1.780725654 0.204919599 46.31735358 100000000 -8 0.989859324 VEELGDLAQAHIQQLSEAAGEDDHFLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEELGDLAQAHIQQLSEAAGEDDHFLIR 28 0 A6NDU8;A0A0C4DGW6 A6NDU8 C5orf51 UPF0600 protein C5orf51 0 147.25 4.72E-08 14844000 15463 14072 9892.8 10595 9335.9 14799 16193 14987 29625 FALSE TRUE 13419.52537 13979.56011 14676.99117 13000.75668 9150.133855 15368.32711 14622.60535 11782.14668 26122.76625 0.513709966 0.535148536 0.561846744 0.497679172 0.350274307 0.588311627 0.559764813 0.451029825 1 14.67302006 1.23460005 24.98668445 1.000000717 0.506960837 0.840295301 0.067514537 44.38582156 279983.9197 0.122289388 0.016506469 17.16327063 -1.23460005 -0.49303988 VEELKFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEELKFDR 8 1 Q9BUP3-3;Q9BUP3;E9PI87 Q9BUP3-3 HTATIP2 Oxidoreductase HTATIP2 0 91.584 0.011294 169370000 215680 161710 133040 170480 178990 162840 220370 249560 184000 FALSE TRUE 187177.3415 160647.7164 197378.589 209190.0896 175428.4492 169104.5602 198998.5513 196193.5361 162247.7296 1.15365153 0.990138455 1.216526046 1.28932522 1.081238237 1.042261488 1.226510545 1.209222074 1 17.30783876 4.228425146 24.99993664 1.159674879 1.071894971 0.100895427 0.097619309 391.2643394 965092.356 0.025040244 0.053120295 16920.96574 -4.228425146 -0.087779907 VEERDPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VEERDPPR 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 76.221 0.033162 1736080000 2109200 1950180 1443470 1772360 1937300 2464200 1875970 2278400 2421600 FALSE TRUE 1830463.876 1937369.139 2141536.92 2174801.427 1898751.52 2558999.369 1694038.718 1791181.891 2135321.207 0.85723116 0.907296351 1.002910903 1.018489125 0.889211194 1.198414253 0.793341401 0.838834872 1 21.02602167 VEESGEHVILGTGELYLDCVMHDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 VEESGEHVILGTGELYLDCVMHDLR 25 0 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;;;;;; 288 2.09E-54 774823000 594287.6 474286.6 301087.5 423392.7 466326.5 490082.6 462452.3 581174 592174.5 FALSE TRUE 515750.9879 471170.9801 446694.4221 519530.4837 457047.515 508936.3947 417603.7471 456894.4628 522168.3052 0.987710251 0.902335464 0.85546062 0.994948331 0.875287739 0.974659683 0.79974932 0.87499463 1 18.99415537 2.284050971 24.99999862 0.884297825 0.927238035 0.069224866 0.066318598 318.2234588 174883.6811 0.023937099 0.018541531 192.3317448 -2.284050971 0.04294021 VEFATLQEALAHALTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VEFATLQEALAHALTEK 17 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 320.73 1.51E-58 2122570000 2791200 2825900 1861460 2225580 2563800 1977640 2949300 3628600 2625100 FALSE TRUE 2422335.848 2807336.477 2761668.282 2730931.955 2512785.396 2053721.091 2663277.34 2852652.128 2314763.669 1.046472208 1.212796155 1.193067059 1.179788672 1.085547276 0.887227115 1.150561233 1.232372949 1 21.14243347 3.232402307 23.9226347 1.088056332 1.164445398 0.144153776 0.100075985 206.8382838 803484.1109 0.032443959 0.037748691 1707.663543 -3.232402307 0.076389065 VEFEELCADLFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VEFEELCADLFER 13 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;;; 257.92 1.50E-23 273005000 292404 274373 235205 266694 286588 329087 265147 278700 265382 FALSE TRUE 253762.0705 272570.6257 348950.9247 327250.9489 280885.4595 341747.1898 239433.0848 219102.1738 234008.8423 1.084412316 1.164787719 1.49118692 1.398455484 1.200319854 1.460402891 1.023179647 0.936298696 1 17.83620352 2.118579874 6.474849815 0.96895 1.301634739 0.570113853 0.128779458 0.14928601 7.862026675 0.054506901 0.036534328 131.3953131 -2.118579874 0.33268474 VEFMDDTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VEFMDDTSR 9 0 P62857 P62857 RPS28 40S ribosomal protein S28 0 ;;;;; 219.51 1.14E-06 7642160000 5576260 5379350 3281420 4042800 5163620 5070100 5073120 5973190 5398690 FALSE TRUE 4839343.113 5344012.696 4868325.688 4960779.53 5060874.064 5265150.028 4581129.603 4695869.802 4760463.018 1.016569837 1.122582546 1.022658021 1.042079208 1.063105426 1.10601637 0.962328577 0.986431316 1 22.18267047 2.228062481 24.9999816 0.98279351 1.062248158 0.548353253 0.033904155 149.5286177 356080.2506 0.01309215 0.008930518 169.0684151 -2.228062481 0.079454647 VEFNIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VEFNIR 6 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;; 151.14 0.024247 1457850000 2572090 2696260 1962910 2157740 2733110 2703990 2999640 2991600 3056410 FALSE TRUE 2232181.79 2678548.091 2912179.842 2647687.846 2678726.458 2808014.245 2708735.374 2351869.621 2695084.692 0.828241798 0.993864163 1.080552255 0.982413597 0.993930345 1.041902043 1.005065029 0.872651471 1 21.36189918 -0.500973467 14.89553538 4.934245173 0.977159742 0 0.074437436 0 0 0 0.017015008 0.315519738 0.500973467 -3.957085431 VEGFLEEDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VEGFLEEDRR 10 1 A0A0G2JM25;A0A0G2JNK1;K7ERG0;A0A0G2JMB6;A0A0G2JPH3;A0A0G2JNK3;Q8WX94;Q8WX94-2;Q8WX94-3;Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8 A0A0G2JM25;Q9NX02 NLRP7;NLRP2 "NACHT, LRR and PYD domains-containing protein 7;NACHT, LRR and PYD domains-containing protein 2" 0 ;;; 199.68 4.40E-07 1688840000 616520 549710 346825 435249 569370 539930 569910 669780 580180 FALSE TRUE 535045.3199 546098.9188 514550.7301 534078.9378 558040.651 560701.4565 514640.2159 526552.7592 511591.7813 1.045844244 1.067450531 1.005783808 1.043955273 1.090792838 1.09599387 1.005958725 1.029243976 1 18.96463356 2.208030045 24.99999824 1.015141427 1.057156578 0.409239654 0.026245795 234.9240263 192366.3521 0.011436258 0.007711266 161.4470245 -2.208030045 0.042015151 VEGHVFPEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEGHVFPEFK 10 0 O14964-2;O14964;I3L1P5 O14964-2 HGS Hepatocyte growth factor-regulated tyrosine kinase substrate 0 79.693 0.02624 131430000 252470 205770 148270 174250 201360 186260 195690 285060 309570 FALSE TRUE 219105.4498 204418.2833 219973.8679 213816.1257 197353.33 193425.5427 176712.0139 224102.1373 272972.9873 0.802663487 0.748859019 0.805844821 0.783286756 0.722977508 0.708588585 0.647360809 0.820968183 1 18.05839867 1.312049812 3.398101789 1.017885709 0.746705807 0.739289044 0.047576156 0.143299515 2.364969664 0.090131602 0.012938341 20.51397455 -1.312049812 -0.271179902 VEGNAVACPVSSAQS(ph)PPHSAGAPAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEGNAVACPVSSAQSPPHSAGAPAAK 26 0 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37;H0Y765 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 VEGNAVACPVS(0.011)S(0.052)AQS(0.937)PPHSAGAPAAK 131.1 4.26E-05 224920000 40056 37121 23205 29878 35406 30047 36012 52197 48538 TRUE FALSE 34762.49811 36877.14971 34427.01562 36662.25656 34701.48987 31202.92753 32519.56178 41035.07775 42799.89293 0.812209932 0.861617803 0.804371536 0.856596922 0.810784502 0.729042187 0.759804746 0.958765897 1 15.38531957 1.63279135 4.941230335 0.989351426 0.806710893 0.771010539 0.039705955 0.07148504 3.781387113 0.029799152 0.011250638 42.93301121 -1.63279135 -0.182640533 VEGQKEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VEGQKEEK 8 1 A0A1W2PNT1 A0A1W2PNT1 0 ; 81.548 0.013565 489820000 1017690 1092650 469290 782120 1198890 1315740 870220 900500 993990 FALSE TRUE 883199.688 1085472.31 696240.2137 959712.3 1175034.435 1366357.369 785826.1983 707935.0827 876481.6346 1.007664797 1.238442732 0.794358018 1.094959965 1.340626418 1.558911579 0.896568927 0.807700989 1 19.74136434 2.047253554 24.99999346 0.878717882 1.167865151 0.27808587 0.204934843 148.299621 78458.81877 0.087995412 0.059326474 111.4945281 -2.047253554 0.289147268 VEGS(ph)PTEEANLPTELQDNSLSPAASEAGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEGSPTEEANLPTELQDNSLSPAASEAGEK 30 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 VEGS(0.5)PT(0.5)EEANLPTELQDNSLSPAASEAGEK 143.82 2.87E-08 312750000 322700 231260 346300 380390 262600 213120 319410 401320 1281100 TRUE FALSE 280054.3774 229740.8378 513771.8383 466763.3634 257374.7738 221318.8643 288433.6674 315500.8411 1129649.817 0.247912559 0.203373501 0.454806286 0.41319297 0.227835892 0.195918116 0.255330159 0.279290835 1 20.10744419 1.238267791 24.99999983 1.000000795 0.285313679 0.874235879 0.08526068 2.48656244 211925.9503 0.125841572 0.022220426 17.30883313 -1.238267791 -0.714687116 VEHES(ph)FEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 86.866 0.0165 9266970000 3968355 3793909 2696088 2644826 2794797 2213543 5596230 4197890 3755490 TRUE FALSE 3443926.832 3768986.562 3999925.175 3245374.167 2739186.008 2298699.432 5053508.476 3300203.892 3311520.25 1.039983624 1.138143897 1.20788184 0.980025463 0.827168732 0.69415231 1.526038826 0.99658273 1 21.65906225 3.724307166 23.99193865 1.01557251 1.129617206 0.0679303 0.214859578 1534.397744 2582756.475 0.061227247 0.091345148 5300.381945 -3.724307166 0.114044696 VEHHDHAVVSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VEHHDHAVVSGR 12 0 O95831-3;O95831;E9PMA0;O95831-5;O95831-2 O95831-3 AIFM1 "Apoptosis-inducing factor 1, mitochondrial" 0 ;;; 103.44 0.0012988 97449000 87699 82029 56875 85512 81367 107493 60143 81453 141615 FALSE TRUE 76109.35495 81490.1461 84379.94024 104928.8066 79747.95589 111628.3253 54310.34112 64034.90982 124873.436 0.609491957 0.652581916 0.6757237 0.840281247 0.638630268 0.893931719 0.434923094 0.512798493 1 16.93010708 4.482263053 2.755411733 0.688887228 0.611727551 0.027151979 0.169949858 1.676877958 23.12139788 0.044786355 0.223244513 30357.29374 -4.482263053 -0.077159677 VEHTNTGTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEHTNTGTK 9 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 73.841 0.04278 55733000 102770 119690 61505 74290 93760 123090 131310 127980 94201 FALSE TRUE 89188.68411 118903.7485 91249.02372 91158.67995 91894.35944 127825.3519 118575.5764 100612.4729 83064.66509 1.073725922 1.431460036 1.098529966 1.097442334 1.106299042 1.538865555 1.427509234 1.211254784 1 16.34194728 VEHTPDGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VEHTPDGVK 9 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;; 101.65 0.003842 1825630000 2475280 1903380 1332350 1509820 1741450 1473790 2122350 2386390 2203040 FALSE TRUE 2148165.476 1890876.571 1976678.916 1852647.707 1706798.552 1530487.655 1916524.824 1876079.069 1942599.121 1.105820266 0.973374564 1.017543401 0.953695329 0.87861594 0.78785563 0.986577623 0.965757191 1 20.88955678 5.105275321 0.923343429 0.93135233 1.304539535 0.408195266 0.0645138 4.358468893 1.861576026 0.023232452 1.910487108 127431.0674 -5.105275321 0.373187205 VEIKNVT(ph)PDT(ph)AY(ph)RDFCLAFIGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEIKNVTPDTAYRDFCLAFIGK 22 2 A0A0G2JM25;A0A0G2JNK1;K7ERG0;A0A0G2JMB6;A0A0G2JPH3;A0A0G2JNK3;Q8WX94;Q8WX94-2;Q8WX94-3 A0A0G2JM25 NLRP7 "NACHT, LRR and PYD domains-containing protein 7" 3 VEIKNVT(1)PDT(1)AY(1)RDFCLAFIGK 54.259 0.046027 108000000 86200 67115 37123 52003 60182 68579 59680 81450 62224 TRUE FALSE 74808.4516 66674.11715 55075.80697 63811.07597 58984.49594 71217.27851 53892.24279 64032.55134 54867.94961 1.36342714 1.215174207 1.00378832 1.162993632 1.075026429 1.297975941 0.982217181 1.167030148 1 15.74367604 4.550142263 3.656903769 1.106616666 1.354794578 0.443042666 0.096041014 0.215161155 5.175400161 0.021930032 0.105482177 35492.96352 -4.550142263 0.248177911 VEILANDQGNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 VEILANDQGNR 11 0 P17066;P48741 P17066 HSPA6;HSPA7 Heat shock 70 kDa protein 6;Putative heat shock 70 kDa protein 7 0 ;;;;;;; 223.31 1.64E-11 8746270000 6021240 5493070 3676400 4378460 5301980 5529720 5315900 5903440 5776140 FALSE TRUE 5225517.878 5456985.661 5454319.337 5372656.264 5196480.971 5742451.907 4800364.836 4641035.297 5093291.309 1.025960928 1.071406548 1.070883051 1.054849593 1.020259918 1.127454048 0.942487783 0.911205548 1 22.2801668 2.216160932 24.98862722 0.942528067 1.060447328 0.671625364 0.036268617 119.4579465 133263.8076 0.014018327 0.009459136 164.4981175 -2.216160932 0.117919261 VEKIPGGIIEDSCVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VEKIPGGIIEDSCVLR 16 1 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8;E9PQ35 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 130.01 4.77E-05 851330000 830420 679730 376690 449200 606870 574450 740380 897370 237310 FALSE TRUE 720677.893 675264.8089 558858.544 551197.7256 594794.4743 596549.4632 668578.0616 705474.4088 209255.4821 3.444009617 3.226987422 2.670699655 2.634089774 2.842431979 2.850818803 3.195032478 3.371354488 1 17.67490589 1.232546663 24.99996789 0.999996704 3.024402563 0.838075076 0.28033639 85.84478697 356820.1407 0.677332358 0.07623862 17.08231253 -1.232546663 2.024405859 VEKPDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VEKPDTK 7 1 Q02878;F8VZ45;U3KQR5;F8VZA3;F8VWR1;F8VU16 Q02878 RPL6 60S ribosomal protein L6 0 ;; 86.011 0.018596 1430100000 3537350 2875180 2438520 2731010 2069380 2070600 3800370 4438600 4334200 FALSE TRUE 3069880.235 2856292.753 3617796.428 3351127.561 2028203.387 2150257.322 3431810.702 3489439.931 3821815.814 0.803251749 0.747365361 0.946617159 0.876841723 0.530691034 0.562627146 0.897952929 0.913031946 1 21.86582682 2.023499741 24.86951588 0.93686058 0.748511523 0.341927468 0.127045681 271.3437847 287158.8608 0.057015373 0.038437476 105.5600875 -2.023499741 -0.188349057 VELAQLQEEWNEHNAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VELAQLQEEWNEHNAK 16 0 Q9H307 Q9H307 PNN Pinin 0 215.23 1.63E-14 136050000 104940 100490 70268 75655 96145 79683 110420 121620 95712 FALSE TRUE 91071.91312 99829.87457 104249.8398 92833.62406 94231.9026 82748.45657 99711.4854 95612.50945 84397.0364 1.079088994 1.182859954 1.235231049 1.09996308 1.116530943 0.980466378 1.181457189 1.132889418 1 16.36490472 3.548742061 13.34840702 1.0925158 1.167502274 0.224354335 0.069818444 2.864344699 531.3993054 0.019219489 0.028505069 3537.871553 -3.548742061 0.074986474 VELDNMPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VELDNMPLR 9 0 Q15233;Q15233-2;C9JYS8;C9IZL7;C9J4X2 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 138.4 0.00032053 100660000 272160 236200 149220 193510 268430 249430 225110 257740 245570 FALSE TRUE 236193.3664 234648.3866 221383.2911 237449.4031 263088.7682 259025.7335 203278.8668 202624.3067 216538.9944 1.090765971 1.083631091 1.022371475 1.096566481 1.214971784 1.196208259 0.938763327 0.935740499 1 17.72426732 2.22325405 24.99990232 0.952686974 1.115049364 0.629356444 0.057540761 165.5147831 270329.7771 0.026144544 0.017700849 167.206844 -2.22325405 0.16236239 VELS(ph)PGPPKPAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VELSPGPPKPAGR 13 1 A0A087WXE2;Q8IZ73-2;Q8IZ73 A0A087WXE2 RPUSD2 RNA pseudouridylate synthase domain-containing protein 2 1 VELS(1)PGPPKPAGR;VELS(1)PGPPKPAGR 151.8 2.58E-05 976600000 2360100 2019690 1488360 1733980 1918370 1584310 2318500 2798800 2583000 TRUE FALSE 2048206.805 2006422.523 2208135.874 2127706.661 1880198.19 1645259.431 2093652.227 2200298.4 2277640.683 0.899266869 0.880921446 0.969483857 0.934171346 0.825502549 0.722352495 0.919219718 0.966042808 1 21.11910874 1.776902477 3.353971966 0.986539911 0.874539926 0.312217763 0.06667232 0.293240345 6.412387167 0.049365812 0.019788976 59.82772342 -1.776902477 -0.111999985 VELSQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VELSQLR 7 0 P42766;F2Z388 P42766 RPL35 60S ribosomal protein L35 0 ; 127.12 0.0090405 212425000 234230 247610 193020 233613 251060 267910 239279 280950 430900 FALSE TRUE 203275.912 245983.4336 286365.1176 286658.4022 246064.3972 278216.6711 216073.7594 220871.0289 379959.4929 0.53499364 0.647393836 0.753672755 0.754444638 0.647606921 0.732227188 0.568675776 0.581301515 1 18.5354861 -1.999999891 0.024792807 1.581270232 2.80E-09 0.120803757 0.125119425 16824.85951 41.40150881 1753.690674 991.5580861 0.010000003 1.999999891 -1.581270229 VEMLETER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VEMLETER 8 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 106.93 0.009542 348360000 439690 390680 260690 338900 429480 443910 381240 459110 406010 FALSE TRUE 381583.8525 388113.5974 386760.556 415852.4248 420934.1883 460987.5049 344267.4035 360932.8993 358011.9603 1.065841074 1.084079976 1.080300657 1.161560146 1.175754541 1.287631577 0.961608666 1.008158775 1 18.44964826 2.200539848 24.99999963 0.992541834 1.139418374 0.5568429 0.064122329 132.7192716 87266.73623 0.027865063 0.018787051 158.6864511 -2.200539848 0.14687654 VENFEAAVHFYGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VENFEAAVHFYGK 13 0 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 0 ; 157.38 3.92E-05 1564500000 2870200 2516600 1677370 2242700 2568100 2107490 2725800 3309300 3442100 FALSE TRUE 2490895.798 2500068.289 2488551.742 2751939.313 2516999.834 2188566.504 2461452.336 2601631.948 3035178.859 0.820675128 0.823697187 0.819902832 0.906681102 0.829275621 0.721066733 0.810974394 0.857159353 1 21.5333501 1.239196055 2.754484854 1.039068032 0.819675086 0.62203004 0.044138851 0.324738619 2.869187668 0.164069096 0.012263424 17.34586873 -1.239196055 -0.219392946 VENMSSNQDGNDS(ph)DEFM ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VENMSSNQDGNDSDEFM 17 0 Q86WR0;Q86WR0-2 Q86WR0 CCDC25 Coiled-coil domain-containing protein 25 1 VENMSSNQDGNDS(1)DEFM;VENMSSNQDGNDS(1)DEFM;VENMSSNQDGNDS(1)DEFM;VENMSSNQDGNDS(1)DEFM;VENMSSNQDGNDS(1)DEFM 348 3.62E-72 610489000 735307 670465 425134 562780 655222 620014 672470 772028 731801 TRUE FALSE 638134.3169 666060.6713 630730.2244 690567.8006 642184.3641 643866.3398 607253.9629 606935.8201 645288.3195 0.988913479 1.032190807 0.977439395 1.07016938 0.995189816 0.997796365 0.941058353 0.940565328 1 19.29958439 2.42035218 3.315433872 0.955731301 1.014262917 0.374021601 0.030379915 0.218233972 4.928273298 0.011582803 0.008830029 263.2401806 -2.42035218 0.058531616 VENSPQVDGS(ph)PPGLEGLLGGIGEK ddPTM_MDA-MB-175_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;VENS(0.002)PQVDGS(0.998)PPGLEGLLGGIGEK;VENS(0.003)PQVDGS(0.997)PPGLEGLLGGIGEK;VENSPQVDGS(1)PPGLEGLLGGIGEK 216.52 8.53E-33 164001000 336165 279664 199432 221547 262920 207197 309984 376966 320581 TRUE FALSE 291739.9435 277826.8688 295877.9823 271852.6325 257688.4064 215168.0027 279921.7994 296354.7545 282682.2794 1.032041853 0.982823789 1.046680333 0.961689686 0.911583163 0.761165515 0.99023469 1.048366934 1 18.10882192 3.60279199 5.958897501 0.948987218 1.016304572 0.174793589 0.076863897 0.538788463 23.8757069 0.024279134 0.036198149 4006.747642 -3.60279199 0.067317353 VEPSSQSPGRS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VEPSSQSPGRSPR 13 1 G8JLD3;X6RLX0;Q8IUD2-3;Q8IUD2;Q8IUD2-2;X6RM00;Q8IUD2-4;Q8IUD2-5;K7EKH8;K7EIZ7 G8JLD3 ERC1 ELKS/Rab6-interacting/CAST family member 1 1 VEPSSQSPGRS(1)PR;VEPSSQSPGRS(1)PR;VEPSSQSPGRS(1)PR;VEPSSQSPGRS(1)PR;VEPSS(0.001)QS(0.057)PGRS(0.942)PR;VEPSSQSPGRS(1)PR 156.72 2.44E-05 3716805000 3277210 3230964 1931577 2390471 3199833 3049395 2901954 3631893 2485257 TRUE FALSE 2844118.395 3209739.585 2865694.098 2933263.977 3136162.584 3166707.199 2620522.948 2855240.945 2191452.749 1.29782328 1.464662921 1.307668668 1.338502041 1.431088389 1.445026456 1.195792585 1.302898704 1 21.06345614 0.541597134 0.995487633 1.17E-11 1.373846633 0.677528298 0.077347111 3.932186233 1.125138897 8.139428058 0.024495571 3.480143355 -0.541597134 1.373846633 HHNHGS(ph)PHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 HHNHGSPHLK 10 0 Q9UK58 Q9UK58 CCNL1 Cyclin-L1 1 HHNHGS(1)PHLK;HHNHGS(1)PHLK 102.52 0.0049076 102341000 282450 281730 110961 144470 168471 155367 156275 166174 130601 TRUE FALSE 245123.5169 279879.2971 164622.1107 177274.1216 165118.7567 161344.069 141119.4746 130638.9833 115161.4986 2.128519687 2.430320034 1.429489133 1.539352334 1.433801737 1.401024397 1.225404986 1.134398084 1 16.81329894 5.717972865 0.316258259 0.976520135 4.587349898 0.796840959 0.197889342 7.999273198 0.46440186 0.402204191 12.3435557 522363.5509 -5.717972865 3.610829762 up VEPYVDFAEFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEPYVDFAEFYR 12 0 Q15750 Q15750 TAB1 TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 0 81.017 0.043694 15563000 76636 76546 51782 62353 74807 70700 69991 92800 104170 FALSE TRUE 66508.35843 76043.16429 76823.9484 76511.20166 73318.48706 73419.87475 63203.28359 72955.44217 91855.14127 0.724057004 0.827859641 0.836359809 0.832955027 0.798196879 0.799300657 0.688075623 0.794244515 1 16.48707285 1.240567289 8.07652589 1.002399626 0.787983967 0.664351028 0.047453842 0.056168834 34.22930508 0.067272746 0.012075314 17.40072281 -1.240567289 -0.21441566 VEQALSEVAS(ph)SLQSSAPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEQALSEVASSLQSSAPK 18 0 Q86TV6;Q86TV6-2;H0YK02;H0YJS2;A0A0C4DGK5 Q86TV6 TTC7B Tetratricopeptide repeat protein 7B 1 VEQALSEVAS(0.682)S(0.318)LQSSAPK 260.53 1.01E-30 89207000 383210 335550 226130 291260 313490 259150 369700 452020 380420 TRUE FALSE 332567.8276 333345.75 335487.2244 357395.0346 307252.1623 269119.6682 333846.5509 355359.0406 335447.181 0.991416373 0.993735434 1.000119373 1.065428642 0.915947964 0.802271366 0.995228369 1.05935915 1 18.35572609 1.998456121 24.99780496 1.031931805 0.96164537 0.142432842 0.069464241 109.2310149 1768629.509 0.031127214 0.02063953 99.6451399 -1.998456121 -0.070286436 VEQATKPS(ph)FESGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VEQATKPSFESGR 13 1 P38159;P38159-2;H3BT71;H0Y6E7 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 1 VEQATKPS(1)FESGR;VEQATKPS(0.692)FES(0.308)GR 190.24 1.20E-05 1701250000 1422670 1273070 1129730 1261190 1322540 1182070 1475950 1762060 2643200 TRUE FALSE 1234660.555 1264707.119 1676071.207 1547562.466 1296224.042 1227544.998 1332812.596 1385257.181 2330723.907 0.529732651 0.542624167 0.719120442 0.663983606 0.556146542 0.526679713 0.571844907 0.594346322 1 21.15234669 1.238631924 8.145618786 1.004671883 0.589406611 0.818340543 0.060997603 0.040282747 25.21235528 0.09239196 0.016026521 17.32335176 -1.238631924 -0.415265272 VEQATKPS(ph)FESGRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VEQATKPSFESGRR 14 2 P38159;P38159-2;H3BT71;H0Y6E7 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 1 VEQAT(0.004)KPS(0.996)FESGRR;VEQAT(0.003)KPS(0.984)FES(0.013)GRR 111.65 0.00033371 522960000 830880 600150 511330 563020 623020 506550 774500 888280 799160 TRUE FALSE 721077.1028 596207.5751 758610.8983 690862.2962 610623.1209 526037.3063 699389.1092 698328.2346 704684.2152 1.023262743 0.846063474 1.076526027 0.980385655 0.86652022 0.746486575 0.992485846 0.990980385 1 19.42661737 2.066086575 24.9999956 0.993935041 0.921925217 0.116183466 0.092638659 124.7875179 47204.5203 0.038984789 0.026283537 116.4358118 -2.066086575 -0.072009824 VEQATKPSFESGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VEQATKPSFESGR 13 1 P38159;P38159-2;H3BT71;H0Y6E7 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 0 ;;; 184.76 8.42E-06 6080500000 4742460 3680300 2798340 3534060 3610190 3012610 3982370 4612100 6664300 FALSE TRUE 4115731.895 3656123.867 4151626.584 4336522.338 3538354.282 3128507.056 3596160.37 3625838.306 5876454.046 0.700376769 0.622164972 0.706484991 0.737948821 0.602124045 0.532380077 0.611960945 0.617011258 1 22.48651444 1.236479988 24.99554114 1.000000463 0.638622384 0.779402574 0.059956438 27.36064775 328611.831 0.100642554 0.015755202 17.2377266 -1.236479988 -0.361378079 VEQHVVDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEQHVVDGK 9 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 85.958 0.014463 888200000 1817100 1431100 1004800 1352700 1562100 1360400 1568900 1971900 1806100 FALSE TRUE 1576965.631 1421699.01 1490724.641 1659851.21 1531017.266 1412735.468 1416748.319 1550224.53 1592584.916 0.990192495 0.89269903 0.936040915 1.042237179 0.961341057 0.887070733 0.889590442 0.97340149 1 20.60293887 2.957744986 24.93565701 0.937027177 0.963489248 0.066456169 0.050236688 1599.848102 944106.4281 0.017166646 0.017168353 907.2876216 -2.957744986 0.026462071 VEQIAAIAQELNELDYYDSHNVNTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VEQIAAIAQELNELDYYDSHNVNTR 25 0 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 ;;;;; 360.19 1.71E-103 3597570000 931038 691039 748155 1087655 664593 711256 541264 750203 3102840 FALSE TRUE 807998.9694 686499.5193 1109965.26 1334623.692 651368.8996 738618.4786 488772.3006 589777.9265 2736025.79 0.295318477 0.250911202 0.405685233 0.487796459 0.238071184 0.26996035 0.178643163 0.215560076 1 21.3836504 1.234922247 24.9999956 1.000001005 0.289673965 0.855452397 0.09135877 41.79864783 287162.951 0.178028044 0.024688175 17.17600852 -1.234922247 -0.710327039 VEQSAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VEQSAER 7 0 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1;K7EJ01;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7;H7C034 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 ; 114.65 0.013627 479260000 467550 429010 293050 350850 292842 428330 426730 423930 544730 FALSE TRUE 405762.0829 426191.8051 434769.9602 430515.8549 287015.0171 444808.1323 385345.7903 333275.8685 480332.64 0.844752259 0.887284706 0.905143486 0.896286904 0.597533861 0.926041862 0.802247772 0.693843892 1 18.87367432 VEQVLSLEPQHELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEQVLSLEPQHELK 14 0 O95292;E5RK64;O95292-2 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 0 133.71 4.30E-05 167350000 305900 193910 192080 260880 212340 248320 189360 300020 278330 FALSE TRUE 265474.5399 192636.1924 284970.5305 320116.7913 208114.8494 257873.0311 170995.8963 235863.0578 245426.1445 1.0816881 0.784904937 1.161125401 1.304330441 0.84797343 1.050715406 0.696730565 0.961034768 1 17.90492942 VERLS(ph)SGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK ddPTM_MDA-MB-175_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(0.956)S(0.044)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK;VERLS(0.968)S(0.032)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK;VERLS(0.958)S(0.042)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK;VERLS(0.829)S(0.162)GPEQIT(0.008)LEASSTEGHPGAPSPQHTDQTEAFQK;VERLS(0.972)S(0.028)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 347.88 2.08E-145 2762060000 654624 675152 223671 503345 729484 645294 777624 959177 815759 TRUE FALSE 568113.7798 670716.8821 331839.0437 617637.1754 714968.6956 670118.8777 702210.1442 754064.4629 719320.9003 0.789791843 0.932430688 0.461322678 0.858639274 0.993949564 0.931599342 0.976212625 1.048300505 1 19.456276 3.437447916 5.086928251 0.990424044 0.73473437 0.507941773 0.117769329 0.152535197 9.445900486 0.03371764 0.04479571 2738.091241 -3.437447916 -0.255689674 VES(ph)EES(ph)GDEEGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VESEESGDEEGKK 13 1 Q15435;B5MBZ8;C9JD73;Q15435-3;H7C003;H7C118;C9JRC4 Q15435 PPP1R7 Protein phosphatase 1 regulatory subunit 7 2 VES(1)EES(1)GDEEGKK;VES(1)EES(1)GDEEGKK 124.29 0.00020008 421840000 1039390 574050 714080 583980 578360 516210 902490 924340 1493850 TRUE FALSE 902031.978 570279.0278 1059411.476 716581.5846 566851.7675 536068.9327 814966.6587 726677.0842 1317248.755 0.68478484 0.432931916 0.804260754 0.543998681 0.430330084 0.406961047 0.618688502 0.55166276 1 20.32909639 1.238214106 25 1.000000497 0.556089507 0.560334601 0.122682246 6.253735877 450539.7678 0.166194898 0.029262199 17.30669365 -1.238214106 -0.44391099 VES(ph)LESLYFTPIPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VESLESLYFTPIPAR 15 0 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 VES(0.999)LES(0.001)LYFTPIPAR;VES(1)LESLYFTPIPAR 290.26 7.16E-44 105619000 63991 48027 42725 53722 57692 42998 46144 64047 124308 TRUE FALSE 55534.42722 47711.50747 63386.95291 65920.40119 56544.04207 44652.16088 41668.96198 50351.04746 109612.4499 0.506643427 0.435274529 0.578282421 0.6013952 0.515854195 0.407363953 0.380148077 0.459355188 1 16.74205214 1.236982837 24.99972056 1.000000637 0.482824227 0.842776342 0.069823678 17.04778968 270030.6533 0.117266709 0.019027499 17.25769688 -1.236982837 -0.517176409 VES(ph)MEALPILSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VESMEALPILSR 12 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 VES(1)MEALPILSR;VES(1)MEALPILSR;VES(1)MEALPILSR 121.04 0.00040208 68483000 182905 147238 107784 144666 139752 145093 130096 125094 186058 TRUE FALSE 158733.6408 146270.7839 159908.7029 177514.6264 136971.2086 150674.8216 117479.3099 98343.62158 164062.4352 0.967519717 0.891555606 0.974682003 1.081994341 0.834872458 0.918399275 0.716064648 0.599428025 1 17.32388542 2.299310893 4.548848532 0.733109771 0.948101324 0.309059403 0.117750369 0.199497369 8.253298423 0.045861833 0.034063411 199.2098889 -2.299310893 0.214991553 VESEQHGDRLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VESEQHGDRLPR 12 1 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 174.73 1.78E-05 72687000 77970 73460 44123 55708 77056 71264 82668 80193 43004 FALSE TRUE 67666.06695 72977.43642 65461.03038 68357.35284 75522.73636 74005.57219 74650.87008 63044.35101 37920.11611 1.78443723 1.924504561 1.726287709 1.802667287 1.991627244 1.951617763 1.968635061 1.662556909 1 15.21067576 1.253776621 2.653874339 0.817555418 1.877309848 0.908996228 0.087172527 0.132109313 1.082379843 0.309695283 0.024059926 17.93810746 -1.253776621 1.05975443 VESGDPSLHPPPS(ph)PGTPSATPAS(ph)PPASATPSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VESGDPSLHPPPSPGTPSATPASPPASATPSQR 33 0 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 2 VESGDPS(0.293)LHPPPS(0.704)PGT(0.011)PS(0.028)AT(0.074)PAS(0.881)PPAS(0.007)ATPSQR;VESGDPS(0.087)LHPPPS(0.906)PGT(0.016)PS(0.022)AT(0.01)PAS(0.959)PPASATPSQR 119.59 4.58E-07 595020000 1575370 1258910 843320 1118750 1538740 1428590 1529850 1888430 1807500 TRUE FALSE 1367180.863 1250640.137 1251152.373 1372779.287 1508122.084 1483548.782 1381485.382 1484603.94 1593819.409 0.857801615 0.784681207 0.785002595 0.861314198 0.946231471 0.9308136 0.866776609 0.931475631 1 20.60405674 3.445395333 3.729565095 0.928947925 0.807711702 0.69895838 0.037893855 0.129452172 3.864655366 0.01135722 0.015655802 2788.658494 -3.445395333 -0.121236222 VESGDPSLHPPPS(ph)PGTPSATPASPPASATPSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VESGDPSLHPPPSPGTPSATPASPPASATPSQR 33 0 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 1 VESGDPS(0.001)LHPPPS(0.999)PGTPSATPASPPASATPSQR;VESGDPSLHPPPS(0.999)PGT(0.001)PSATPASPPASATPSQR 177.1 4.39E-28 390210000 97215 174061 70126 134893 223411 213732 191585 235532 215469 TRUE FALSE 84367.79144 172917.5818 104039.1682 165522.5174 218965.5582 221954.4083 173005.1162 185165.3147 189996.5003 0.444049187 0.9101093 0.547584656 0.871187191 1.152471534 1.168202614 0.910570015 0.974572239 1 17.53561332 3.50453397 5.087165994 1.029105475 0.665175132 0.636070507 0.139714412 0.127600599 8.931967219 0.038346944 0.054985396 3195.464298 -3.50453397 -0.363930343 VESGDPSLHPPPSPGTPSAT(ph)PASPPASATPSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VESGDPSLHPPPSPGTPSATPASPPASATPSQR 33 0 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 1 VESGDPSLHPPPSPGTPS(0.005)AT(0.598)PAS(0.397)PPASATPSQR;VESGDPSLHPPPSPGTPS(0.001)AT(0.668)PAS(0.331)PPASATPSQR 191.25 1.31E-19 647760000 246059 259423 106931 186801 275710 264881 249882 294583 268351 TRUE FALSE 213541.6797 257718.8332 158643.1893 229217.0221 270223.9104 275071.1435 225648.4821 231588.7179 236626.8505 0.902440612 1.08913605 0.670436127 0.968685598 1.141983295 1.162468008 0.953604723 0.978708534 1 17.85225426 3.478403316 24.99932131 1.039118602 0.892858013 0.274801339 0.118498418 69.02762956 1346010.821 0.034508487 0.045169725 3008.869248 -3.478403316 -0.146260589 VESGDPSLHPPPSPGTPSATPAS(ph)PPASATPSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VESGDPSLHPPPSPGTPSATPASPPASATPSQR 33 0 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 1 VESGDPSLHPPPSPGTPS(0.017)AT(0.171)PAS(0.812)PPASATPSQR 139.56 3.28E-10 305500000 130260 136990 50939 92019 160720 132180 122480 140100 118870 TRUE FALSE 113045.811 136090.1037 75573.27078 112913.3204 157521.9864 137265.0501 110601.9085 110140.7053 104817.324 1.07850312 1.298355066 0.720999811 1.077239106 1.502823965 1.309564534 1.055187294 1.050787227 1 16.67751766 2.03040596 24.89205896 1.036210917 1.163609487 0.08432693 0.20184033 542.5474344 444158.0602 0.087566991 0.059036894 107.2521385 -2.03040596 0.12739857 VESTDVSDLLHQYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VESTDVSDLLHQYR 14 0 Q5JNW7;A0A140T998;X5D2R7;P28062-2;P28062 Q5JNW7 PSMB8;PSM8 Proteasome subunit beta type;Proteasome subunit beta type-8 0 ; 194.86 9.89E-08 182280000 470660 499530 281110 338670 491460 494860 465570 524240 541680 FALSE TRUE 408461.0885 496248.5545 417055.7363 415570.1997 481680.9075 513897.5844 420419.0931 412135.3556 477643.2075 0.85515942 1.038952395 0.873153286 0.870043148 1.008453381 1.075902633 0.880194854 0.862851914 1 18.86557382 5.044487504 14.23310323 0.941993504 0.482053332 0.120075126 0.078253608 6658189.986 66293083.52 0.019797753 78882946.84 110786.6689 -5.044487504 -0.459940172 VETGILRPGMVVTFAPVNITTEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VETGILRPGMVVTFAPVNITTEVK 24 1 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 74.905 0.022834 206180000 436500 392490 167350 269860 441600 341970 411660 544010 498700 FALSE TRUE 378815.419 389911.7073 248281.0198 331135.8376 432813.024 355125.8072 371737.2766 427677.695 439744.2541 0.861444841 0.886678345 0.564603215 0.753019134 0.984238043 0.807573502 0.845348798 0.972560053 1 18.7463052 1.382171047 0.61265911 1.139975892 0.781991831 0.320289032 0.106301771 3.86886207 1.302837984 0.977879631 0.06529313 24.10854759 -1.382171047 -0.357984061 VETGVLKPGMVVTFAPVNVTTEVK ddPTM_MDA-MB-175_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 ; 243.47 1.01E-37 846950000 2020580 1482770 1251050 1382040 1427820 1105500 1911730 2377700 2127800 FALSE TRUE 1753555.234 1473029.586 1856061.965 1695853.305 1399409.175 1148029.3 1726330.719 1869247.358 1876253.908 0.93460444 0.785090749 0.98923816 0.903850645 0.745852771 0.611873103 0.920094403 0.996265671 1 20.83942365 2.00585857 24.99666936 0.985960317 0.827813729 0.313403689 0.104732588 185.6603932 792150.541 0.045524059 0.03059476 101.3581256 -2.00585857 -0.158146588 VETLKEEEEELKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VETLKEEEEELKR 13 2 Q9Y3L3;Q6ZT62-2;Q6ZT62;Q9Y3L3-2 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 0 98.943 0.0017366 38208000 128560 112160 117190 115480 120910 100370 132310 149160 171700 FALSE TRUE 111570.4703 111423.2136 173863.476 141701.499 118504.1276 104231.2988 119478.5966 117263.2948 151401.8216 0.736916301 0.735943679 1.148357887 0.935929948 0.782712693 0.688441511 0.789149003 0.774517067 1 17.20802304 3.229307272 24.82454888 0.795645911 0.89683893 0.076979894 0.137502209 427.6762913 1147352.37 0.042945728 0.049362545 1695.537002 -3.229307272 0.101193019 VETPSHPGGVSEEFWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VETPSHPGGVSEEFWER 17 0 Q92620;H3BQT9 Q92620 DHX38 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 0 76.713 0.019321 180700000 60111 58653 33816 45784 62246 60997 53756 77639 74193 FALSE TRUE 52167.17905 58267.70458 50169.53071 56179.95696 61007.42638 63343.59406 48542.75139 61036.50404 65421.98806 0.797395197 0.890644053 0.766860381 0.858732035 0.932521744 0.968230956 0.74199444 0.932966207 1 15.99748798 3.450546962 6.374944181 0.906408685 0.823376089 0.261257845 0.074092077 0.264483296 35.91144349 0.021323027 0.028147398 2821.934714 -3.450546962 -0.083032596 VETQFQNGHYDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VETQFQNGHYDK 12 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 163.27 6.04E-05 277390000 404170 314190 256070 228830 312910 276640 376270 389730 436320 FALSE TRUE 350757.9105 312126.0652 379906.3085 280789.3489 306683.7032 287282.5198 339779.3933 306389.2724 384738.7467 0.911678154 0.811267563 0.987439689 0.729818224 0.797121958 0.746695056 0.883143162 0.796356684 1 18.5535196 3.737891903 24.99999827 0.821617866 0.894242372 0.150233743 0.086125812 119.8404077 4480268.18 0.022386237 0.035518068 5468.798262 -3.737891903 0.072624506 VETSDEEIHDLHQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VETSDEEIHDLHQR 14 0 P07099;B1AQP8;B1AQP9 P07099 EPHX1 Epoxide hydrolase 1 0 182.33 8.88E-07 661040000 355360 355880 210350 321980 327020 405860 329550 381570 360390 FALSE TRUE 308398.2756 353542.2008 312075.9636 395090.4802 320512.9418 421473.6968 297590.2917 299974.2249 317785.1048 0.970461708 1.112519736 0.982034585 1.243263055 1.008583905 1.326285249 0.936451354 0.943953069 1 18.27769198 VEVGKDQEFTVDTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 158.93 4.55E-06 4667700000 9247800 8116100 6019400 6820600 7668800 6551800 9689800 10806100 7756400 FALSE TRUE 8025679.799 8062784.805 8930401.974 8369321.476 7516205.884 6803851.986 8750084.687 8495299.608 6839447.228 1.173439831 1.178864978 1.305719845 1.223683903 1.09894932 0.994795597 1.279355538 1.242103247 1 22.7054483 3.261079632 23.83660856 1.143234917 1.223550831 0.184313646 0.096652392 306.2162413 324129.4048 0.029735976 0.038352981 1824.230163 -3.261079632 0.080315914 VEVNNLNNLNNHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VEVNNLNNLNNHDR 14 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 0 ;; 212.7 2.07E-09 786420000 507960 459083 402420 542110 503661 514761 518580 581650 1386240 FALSE TRUE 440831.799 456067.2535 597031.658 665204.3611 493639.1315 534564.1888 468288.1914 457268.6739 1222360.286 0.360639824 0.373103788 0.488425274 0.54419664 0.403840944 0.437321299 0.383101608 0.374086658 1 20.22123815 1.235729456 24.99999678 1.000000777 0.421150552 0.909038419 0.057600314 23.50616899 207526.504 0.102939067 0.015227101 17.20796269 -1.235729456 -0.578850225 VEVT(ph)PTVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEVTPTVPR 9 0 Q8IXS8 Q8IXS8 FAM126B Protein FAM126B 1 VEVT(0.943)PT(0.057)VPR 113.63 0.019778 153050000 120990 102350 79027 90890 99902 120530 93143 129780 144290 TRUE FALSE 105000.865 101677.6561 117244.7215 111527.9637 97914.14565 125166.8671 84110.0062 102027.5569 127232.2006 0.825269582 0.799150338 0.921501955 0.876570264 0.76957048 0.983767211 0.661074837 0.801900435 1 16.95710432 2.257737497 24.99999142 0.81035103 0.858830953 0.032408125 0.100459251 820.3097073 1069397.552 0.036642643 0.028340407 181.0245584 -2.257737497 0.048479924 VEVTEFEDIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VEVTEFEDIK 10 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;;;; 220.45 1.36E-08 1178445000 3517180 2396340 1787211 2036375 2098463 1753888 2783790 3012960 2796470 FALSE TRUE 3052375.752 2380598.285 2651512.217 2498765.068 2056707.692 1821361.206 2513818.474 2368661.951 2465874.502 1.237847161 0.965417454 1.07528271 1.013338297 0.834068275 0.738626887 1.019442989 0.960576846 1 21.23366795 7.999999973 0.761538863 0.929570832 57.51111929 0.481748719 0.09559876 395.2142256 1.62729856 0.037287097 38413.45561 99999993.88 -7.999999973 56.58154846 VEWSAFLEAADNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VEWSAFLEAADNLR 14 0 F5GYQ2;Q9UI30;F5GX77 F5GYQ2 TRMT112 Multifunctional methyltransferase subunit TRM112-like protein 0 ; 240.8 4.80E-17 82169000 164935 134338 88352 118542 124491 107538 129007 167393 123232 FALSE TRUE 143138.4219 133455.5248 131079.3227 145458.7729 122013.8727 111675.0564 116495.921 131597.3096 108663.6533 1.317261269 1.228152383 1.206284886 1.338614784 1.122858186 1.027713067 1.072078081 1.211051769 1 16.72950993 3.126431596 6.472011323 1.095834687 1.264023155 0.652264768 0.067365133 0.151444504 8.049062236 0.020901402 0.023808962 1337.924467 -3.126431596 0.168188468 VEWTSDTVDNEHMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VEWTSDTVDNEHMGR 15 0 O60927 O60927 PPP1R11 Protein phosphatase 1 regulatory subunit 11 0 203.11 5.57E-09 110890000 94483 104580 81184 79105 98345 105590 94823 111200 118440 FALSE TRUE 81996.83216 103893.0071 120444.8539 97066.99929 96388.12691 109652.1156 85627.08005 87420.74536 104438.1581 0.785123308 0.994780155 1.153264823 0.929420827 0.922920594 1.049923874 0.819883092 0.837057517 1 16.67228939 2.232037373 24.99828748 0.872783935 0.977576689 0.127487449 0.104880782 269.8490391 1034099.869 0.042129594 0.029158487 170.622921 -2.232037373 0.104792754 VEYFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VEYFLK 6 0 Q13185;S4R2Y4;C9JMM0;B8ZZ43 Q13185 CBX3 Chromobox protein homolog 3 0 ; 116.35 0.055015 909440000 1838610 1644460 1160170 1341740 1483850 1399450 1578510 1913410 2107500 FALSE TRUE 1595633.03 1633657.434 1721232.093 1646402.574 1454324.288 1453287.747 1425426.343 1504242.162 1858353.751 0.858627174 0.879088512 0.926213371 0.885946808 0.782587431 0.782029657 0.767037138 0.809448772 1 20.82559372 3.297308487 9.87979658 0.819008871 0.889820483 0.153168837 0.067222817 0.658944991 105.8956747 0.019587676 0.025266673 1982.93504 -3.297308487 0.070811613 VEYQEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VEYQEDR 7 0 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 0 ; 60.682 0.096037 130593000 189505 186187 121626 115316 207089 269140 133328 165911 181321 FALSE TRUE 164461.4341 184963.9253 180444.7404 141500.2603 202968.3341 279493.99 120397.8711 130432.2238 159885.4379 1.028620469 1.156852855 1.128587711 0.885010306 1.269461038 1.748089092 0.75302587 0.815785511 1 17.28667902 VEYSEEELKTHISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VEYSEEELKTHISK 14 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;; 240.04 1.33E-17 1734750000 3409430 2650890 795707 1625440 2678530 1973090 3580160 4157840 1037586 FALSE TRUE 2958865.187 2633476.129 1180513.567 1994520.995 2625232.493 2048996.049 3232956.634 3268718.272 914923.7651 3.234001892 2.878355804 1.290286264 2.179985996 2.869345615 2.239526535 3.533580346 3.57266736 1 19.80329201 2.285238786 24.99888162 2.918107287 2.422385293 0 0.877283786 364.4108089 195161.6249 0.330241822 0.255803403 192.8585004 -2.285238786 -0.495721994 VFAENK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VFAENK 6 0 O95994;B5MC07;C9J3E2;H7C3Z9 O95994 AGR2 Anterior gradient protein 2 homolog 0 ;; 103.29 0.080996 684970000 1817650 1899630 1348640 1632580 1529740 1716690 1875860 2000760 1772630 FALSE TRUE 1577442.947 1887151.205 2000846.815 2003282.241 1499301.167 1782732.175 1693939.386 1572913.044 1563071.701 1.009194234 1.207335021 1.280073597 1.2816317 0.959201786 1.140531285 1.083724685 1.006296156 1 20.57595253 3.239282146 24.99995522 1.042556022 1.201579448 0.432962726 0.088808584 18.81473228 651885.4541 0.026646568 0.032397163 1734.930754 -3.239282146 0.159023425 VFDAIMNFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFDAIMNFK 9 0 P13639 P13639 EEF2 Elongation factor 2 0 122.52 0.0013577 134040000 404490 387560 259840 384290 405060 312220 553030 506040 536930 FALSE TRUE 351035.6217 385014.0928 385499.4931 471548.918 397000.0985 324231.3054 499397.2357 397827.284 473454.7471 0.741434369 0.813201463 0.814226693 0.995974633 0.838517516 0.684820054 1.05479402 0.840264643 1 18.85286701 7.99990474 0.054690244 1.324160192 1.64E-06 0.213738158 0.104795879 1646.20812 8.770944916 56.44639705 197.3753554 99978068.02 -7.99990474 -1.324158553 VFDDES(ph)DEKEDEEYADEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VFDDESDEKEDEEYADEK 18 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 VFDDES(1)DEKEDEEYADEK;VFDDES(1)DEKEDEEYADEK;VFDDES(1)DEKEDEEYADEK;VFDDES(1)DEKEDEEYADEK 261.74 5.10E-31 1711540000 3853820 2186240 3186460 2690630 2377310 1772260 3390940 3956280 6046900 TRUE FALSE 3344527.923 2171878.445 4727442.714 3301578.665 2330006.182 1840439.989 3062087.161 3110260.31 5332042.371 0.627250815 0.407325804 0.886610118 0.619195879 0.436981933 0.345166047 0.57428035 0.583315003 1 22.34625681 1.229703999 4.286551983 1.046477004 0.555183699 0.463731077 0.148906097 0.221101031 7.806021436 0.339952592 0.038492866 16.97086578 -1.229703999 -0.491293306 VFDFAGEEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VFDFAGEEVR 10 0 Q9UEE9;Q9UEE9-2 Q9UEE9 CFDP1 Craniofacial development protein 1 0 ; 103.7 0.0092133 40614000 123893 110332 71254 88520 113336 113778 111407 134136 131286 FALSE TRUE 107520.2261 109607.2218 105712.6727 108619.8189 111080.8353 118155.1133 100602.7663 105452.0602 115765.5186 0.928775921 0.946803704 0.913162002 0.938274369 0.959532999 1.020641679 0.86902186 0.910910792 1 16.82084608 3.481322408 24.1710396 0.944526399 0.930372079 0.039968031 0.042811903 644.4865484 3708055.445 0.012912026 0.017083288 3029.161355 -3.481322408 -0.01415432 VFDGIPPPYDKK ddPTM_MDA-MB-175_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 ; 90.926 0.013767 842440000 1582600 1206370 927930 998330 1127170 993990 1512740 1776530 1055230 FALSE TRUE 1373455.4 1198445.276 1376680.052 1225016.085 1104741.522 1032229.438 1366034.708 1396632.884 930481.9115 1.476068888 1.287983421 1.479534459 1.316539387 1.187278881 1.10934928 1.468093781 1.500978006 1 19.82761858 3.499069398 22.44072611 1.289311529 1.401234882 0.154945522 0.159101949 551.6593082 564036.7399 0.04656372 0.068203597 3155.508816 -3.499069398 0.111923353 VFDKDGNGYIS(ph)AAELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFDKDGNGYISAAELR 16 1 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2 P0DP25 CALM2;CALM1 1 VFDKDGNGYIS(1)AAELR 124.08 5.11E-05 73756000 182870 175950 113790 129150 149990 144880 137860 216130 161220 TRUE FALSE 158703.2662 174794.1729 168819.2246 158475.4814 147005.4925 150453.6273 124490.3584 169912.2814 142160.7553 1.116364821 1.229552928 1.187523408 1.114762518 1.034079287 1.058334468 0.875701302 1.195212287 1 17.11716373 3.472646059 2.865593716 1.042396161 1.182411573 0.396283015 0.081704246 0.282836779 4.713390086 0.024224652 0.035185506 2969.245175 -3.472646059 0.140015412 VFDKDGNGYISAAELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VFDKDGNGYISAAELR 16 1 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2 P0DP25 CALM2;CALM1 0 ;;;;; 276.38 2.46E-35 50081000000 16251600 13333440 11367600 17541300 14252800 12574320 9452500 18043600 25222100 FALSE TRUE 14103909.88 13245851.75 16865009.38 21524320.27 13969197.17 13058062.23 8535798.005 14185116.56 22240372.07 0.634158001 0.595576896 0.758306081 0.967803965 0.628100875 0.587133263 0.383797446 0.637809319 1 24.40667759 3.052872686 24.99998903 0.622867606 0.738582648 0.052082052 0.17800442 262.3794604 124059.8929 0.056043694 0.063547567 1129.464762 -3.052872686 0.115715042 VFDKEGNGTVMGAELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VFDKEGNGTVMGAELR 16 1 P08590;P05976-2;P05976 P08590 MYL3;MYL1 "Myosin light chain 3;Myosin light chain 1/3, skeletal muscle isoform" 0 ;;;;; 237.3 8.53E-20 4428430000 5867900 5351650 3023270 3532400 5243750 4779910 6122990 6880840 2161141 FALSE TRUE 5092442.148 5316494.659 4485333.484 4334485.409 5139409.634 4963796.231 5529183.372 5409425.913 1905653.373 2.672281444 2.789853986 2.353698499 2.274540308 2.69692784 2.604773933 2.901463325 2.838620071 1 20.86185429 1.234516623 24.99994949 0.99999761 2.647699989 0.871978583 0.197655679 44.63386717 275887.5701 0.400729552 0.0536839 17.15997392 -1.234516623 1.647702379 VFDLQFSTDS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VFDLQFSTDSPR 12 0 C9J470;E9PHA2;Q15003;C9JZP1 C9J470 NCAPH Condensin complex subunit 2 1 VFDLQFSTDS(1)PR;VFDLQFSTDS(1)PR 188.59 9.45E-06 70842000 98703 119819 67448 84420 111751 102087 106940 121787 128683 TRUE FALSE 85659.14847 119031.9011 100066.0784 103588.8513 109527.3737 106014.3529 96568.97526 95743.7978 113470.2423 0.754904076 1.049014249 0.881870668 0.912916454 0.965251959 0.934292117 0.851051106 0.843778914 1 16.79195447 1.214158616 24.36842516 1.000000596 0.902025916 0.140737901 0.078034916 3437.392947 3432411.515 1.119675813 0.01809401 16.37414439 -1.214158616 -0.09797468 VFDMLNRR ddPTM_MDA-MB-175_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 ; 133.68 0.0014576 4070400000 5865000 5961200 2260500 2325600 5550600 5865800 5547900 5966500 740570 FALSE TRUE 5089925.39 5922040.485 3353685.361 2853663.025 5440153.92 6091461.122 5009865.512 4690610.406 653020.6583 7.79443242 9.068687812 5.13564972 4.369942954 8.330753171 9.328129278 7.671833117 7.182943368 1 19.31676911 4.250891129 24.99017869 6.448274504 8.431560502 0.129317395 2.366716812 538.6701742 1091699.156 0.601152501 1.565876986 17819.32006 -4.250891129 1.983285997 VFEEDALSWEDKLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VFEEDALSWEDKLNR 15 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 290.39 6.18E-44 989660000 1040530 896450 593589 646726 916060 782560 1084690 1204120 713925 FALSE TRUE 903021.3241 890561.1609 880650.6258 793575.0229 897832.1982 812665.5896 979496.9308 946628.3085 629525.5998 1.434447343 1.414654402 1.398911539 1.26059214 1.426204428 1.290917462 1.555928672 1.50371694 1 19.26390552 1.230872718 24.99997839 0.99999926 1.413652103 0.68894071 0.086701138 175.6068943 571001.1612 0.236228895 0.022584005 17.01659716 -1.230872718 0.413652843 VFEHDSVELNCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFEHDSVELNCK 12 0 P10768;U3KQT1 P10768 ESD S-formylglutathione hydrolase 0 231.17 4.08E-12 756600000 705690 872160 185350 567690 897290 750270 951240 1022700 1017000 FALSE TRUE 612431.2785 866430.7235 274985.88 696592.6911 879435.6845 779133.3724 858988.8912 804003.5637 896771.4186 0.682929079 0.966166746 0.30663988 0.776778426 0.980668726 0.868820478 0.957868274 0.896553511 1 19.77438077 3.460497596 8.562880832 0.928486849 0.659957739 0.405045531 0.160704045 0.184138908 76.99177766 0.044379127 0.05829014 2887.337798 -3.460497596 -0.26852911 VFELMTSLHTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VFELMTSLHTK 11 0 Q06323;Q06323-3;Q06323-2;H0YLU2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ; 251.43 1.66E-17 3831200000 5736000 6047900 2048450 4466900 6426800 5397800 6524200 7857400 7258000 FALSE TRUE 4977973.067 6008170.947 3039087.272 5481177.917 6298919.254 5605456.859 5891484.088 6177156.156 6399967.508 0.777812241 0.938781476 0.474859797 0.856438398 0.98421113 0.875857081 0.920549062 0.96518555 1 22.60963315 3.482758642 24.7059949 0.943077418 0.73703669 0.423937159 0.116212143 205.225254 899406.6847 0.032027648 0.042723095 3039.19553 -3.482758642 -0.206040729 VFEVSLADLQNDEVAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VFEVSLADLQNDEVAFR 17 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;D6RB09;D6RAS7;D6RI02;D6RED7;D6RGE0 P61247 RPS3A 40S ribosomal protein S3a 0 ; 267.67 1.89E-27 166905000 139104 145000 97135 115721 147239 145860 131025 150078 177357 FALSE TRUE 120721.054 144047.4855 144109.8109 141997.2217 144309.232 151471.3286 118318.2157 117984.9876 156390.0575 0.771922818 0.921078282 0.921476807 0.907968345 0.922751959 0.968548327 0.756558425 0.754427676 1 17.25478927 1.196717877 24.02078129 1.000002539 0.865078164 0.226325816 0.078093048 10728.84251 6158415.663 8.592359844 0.021158822 15.72960717 -1.196717877 -0.134924375 VFEVSLADLQNDEVAFRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFEVSLADLQNDEVAFRK 18 1 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;D6RB09;D6RAS7;D6RI02;D6RED7;D6RGE0 P61247 RPS3A 40S ribosomal protein S3a 0 117.18 0.00022304 28695000 56504 50859 23727 26791 41304 38946 52956 67255 15677 FALSE TRUE 49036.85324 50524.90388 35201.45656 32874.30602 40482.13121 40444.27782 47820.33527 52873.04163 13823.68292 3.547307438 3.654952459 2.546460069 2.378114878 2.928462078 2.925723778 3.459304988 3.824815857 1 13.75485441 4.251589407 24.85155986 2.863283679 3.60113046 0.172248524 0.752869971 435.7865047 831217.3543 0.18926558 0.493976202 17847.99384 -4.251589407 0.737846781 VFFQS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFFQSPR 7 0 Q8TAE6 Q8TAE6 PPP1R14C Protein phosphatase 1 regulatory subunit 14C 1 VFFQS(1)PR 66.962 0.069706 70014000 109360 124360 79929 92312 109450 134850 110950 126760 138790 TRUE FALSE 94907.79892 123543.071 118582.9317 113272.8505 107272.1591 140037.7668 100190.0861 99653.36045 122382.4043 0.775501997 1.009483934 0.968954094 0.92556484 0.876532535 1.144263896 0.818664142 0.814278499 1 16.90103662 VFGALGPIGPSS(ph)PGLTLGGLAVSEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFGALGPIGPSSPGLTLGGLAVSEHR 26 0 Q86YD1;M0QZB9;M0QYQ4;M0QYH7;A0A0C4DGR2;M0QY25;Q86YD1-2 Q86YD1 PTOV1 Prostate tumor-overexpressed gene 1 protein 1 VFGALGPIGPS(0.005)S(0.995)PGLTLGGLAVSEHR 171.08 4.09E-12 182730000 174190 263860 126390 222750 419280 345180 323270 430330 361940 TRUE FALSE 151170.3502 262126.6863 187512.6267 273328.792 410937.1483 358459.298 291919.3252 338307.2783 319151.8655 0.47366275 0.821322745 0.587534171 0.856422354 1.287591246 1.123162158 0.914672157 1.060019743 1 18.28388356 3.482275008 5.633152209 1.066782049 0.655921269 0.722158571 0.127098582 0.089331564 10.08357402 0.035750958 0.049580268 3035.81294 -3.482275008 -0.41086078 VFGS(ph)LER ddPTM_MDA-MB-175_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 154.28 0.001772 1508910000 1293630 1337600 848480 995330 1420520 1348880 1331480 1502090 1315430 TRUE FALSE 1122673.518 1328813.218 1258807.766 1221334.889 1392254.431 1400772.286 1202353.275 1180879.743 1159921.364 0.967887611 1.145606296 1.085252678 1.052946283 1.200300705 1.207644182 1.036581713 1.018068793 1 20.14559557 2.022275045 24.98833861 1.015425063 1.112801905 0.284246228 0.06937335 282.6442787 317071.6613 0.028586961 0.019271767 105.2628307 -2.022275045 0.097376841 VFGWVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VFGWVHR 7 0 O43776;K7EIU7;O43776-2;K7EPK2;K7EMQ6;K7EQ35 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 149.94 0.0019825 1716880000 2218900 1778990 1221450 1604600 1853870 1904680 1682360 1924610 2467700 FALSE TRUE 1925666.743 1767303.698 1812147.306 1968948.955 1816981.614 1977954.272 1519204.986 1513047.129 2175971.317 0.884968808 0.812190714 0.832799261 0.904859793 0.83502094 0.90899832 0.698173259 0.695343324 1 21.05322811 2.248840746 24.9974112 0.772332881 0.860062914 0.083094985 0.089407479 352.5621382 857299.1799 0.033173047 0.025405435 177.353901 -2.248840746 0.087730033 VFHGNESLWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VFHGNESLWK 10 0 Q13268;H0YJG9 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ;; 127.42 0.00035647 1823260000 3593700 2779860 2036000 3217010 2991910 2830210 2825140 3670900 3137970 FALSE TRUE 3118783.44 2761598.917 3020616.41 3947481.289 2932376.845 2939090.01 2551158.358 2885906.602 2767002.761 1.127134199 0.99804704 1.091656449 1.426627159 1.059766505 1.062192655 0.921993427 1.042972072 1 21.39989265 2.820218314 3.325661062 1.002306355 1.151345674 0.272258107 0.114690896 0.35776534 7.661942275 0.040516586 0.039860076 661.0256525 -2.820218314 0.149039319 VFHTEDDQYCWQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFHTEDDQYCWQHR 14 0 Q8IWR0;Q8IWR0-2 Q8IWR0 ZC3H7A Zinc finger CCCH domain-containing protein 7A 0 167.98 2.06E-06 422400000 122830 98984 69819 87949 101970 108780 105220 106510 114450 FALSE TRUE 106597.7043 98333.76759 103583.7019 107919.1647 99940.9965 112964.837 95015.7806 83733.66536 100919.8514 1.056261011 0.974374875 1.026395704 1.069355168 0.990300671 1.119351995 0.941497429 0.829704604 1 16.62285046 2.033208047 9.910550741 0.897551786 1.034668537 0.472000873 0.057361285 0.258832073 74.63008885 0.022072444 0.014819385 107.946371 -2.033208047 0.137116751 VFIDQNLS(ph)PGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VFIDQNLSPGK 11 0 F5H452;Q5JSB6;Q5JSB5;Q14186 F5H452 TFDP1 Transcription factor Dp-1 1 VFIDQNLS(1)PGK;VFIDQNLS(1)PGK 150.9 3.53E-05 260440000 588650 553400 448310 592110 595450 479470 596510 698440 1250650 TRUE FALSE 510858.4111 549764.679 665114.2155 726557.6253 583601.71 497915.5212 538660.552 549084.0413 1102799.582 0.463237763 0.498517308 0.603114316 0.65883016 0.529200155 0.451501369 0.488448274 0.497900117 1 20.07273919 1.236592949 24.99510937 1.000000603 0.524779173 0.848385184 0.063258479 21.11841045 268192.7726 0.107883877 0.017007401 17.24221073 -1.236592949 -0.47522143 VFIDQNLS(ph)PGKGVVSLVAVHPSTVNPLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFIDQNLSPGKGVVSLVAVHPSTVNPLGK 29 1 F5H452;Q5JSB6;Q5JSB5;Q14186 F5H452 TFDP1 Transcription factor Dp-1 1 VFIDQNLS(1)PGKGVVSLVAVHPSTVNPLGK 163.55 3.34E-12 219370000 199500 205340 43960 109890 224490 150450 242200 309800 126210 TRUE FALSE 173135.5695 203991.108 65219.20304 134842.2041 220023.0882 156237.9089 218711.4813 243551.6809 111289.5976 1.555721049 1.83297552 0.586031439 1.211633495 1.977031933 1.403886008 1.965246403 2.18844965 1 16.76395922 3.248332758 24.93147811 1.771336091 1.284149298 0.160052245 0.453561638 316.970623 808676.5631 0.132838371 0.169309652 1771.465742 -3.248332758 -0.487186794 VFIGEFAYTYAAMYDKGPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VFIGEFAYTYAAMYDKGPFR 20 1 P15559-2;P15559;H3BNV2 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ;;;; 286.28 3.02E-45 2195807000 2458789 2477321 1481411.6 1680354.6 1764715 1928018 2526832 2968894 1039031.5 FALSE TRUE 2133853.804 2461047.315 2197827.205 2061904.795 1729600.624 2002190.1 2281780.222 2334019.122 916198.3797 2.329030318 2.686151132 2.398855153 2.250500372 1.887801444 2.185323773 2.490487074 2.547504093 1 19.80530049 3.730992306 2.957683572 2.128974199 2.508473985 0.158410975 0.436530226 0.574288746 10.16781768 0.124357818 0.217406184 5382.602462 -3.730992306 0.379499787 VFIPHGLIMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VFIPHGLIMDR 11 0 P00492 P00492 HPRT1 Hypoxanthine-guanine phosphoribosyltransferase 0 ; 155.26 3.16E-05 2460100000 2080500 2593400 1552600 1705510 2315700 2374600 2237600 2608600 2152800 FALSE TRUE 1805556.654 2576363.785 2303442.553 2092772.113 2269622.101 2465952.399 2020597.896 2050771.19 1898298.436 0.951144783 1.35719639 1.21342488 1.102446313 1.195608687 1.299033045 1.064425834 1.08032075 1 20.85627539 2.116431165 9.478674168 1.053905111 1.191954793 0.258931775 0.109980344 0.371441042 29.1121286 0.042512361 0.028646258 130.7468291 -2.116431165 0.138049682 VFITDDFHDMMPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VFITDDFHDMMPK 13 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;; 156.8 4.74E-05 2856290000 6261820 5382490 4851190 5820940 5490810 6255600 6104350 6183950 6580110 FALSE TRUE 5434304.622 5347132.069 7197241.71 7142673.394 5381553.624 6496256.98 5512351.077 4861560.416 5802216.892 0.936591086 0.921567078 1.240429623 1.231024887 0.927499562 1.119616364 0.95004223 0.837879815 1 22.4681728 2.084973293 5.476937014 0.903500106 1.065310382 0.213589019 0.12068358 0.280800782 13.8323208 0.052667751 0.034812737 121.6111213 -2.084973293 0.161810276 VFLATNSDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VFLATNSDYK 10 0 P49902-2;P49902;Q5JUV4 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ; 173.37 7.98E-06 158610000 440530 462720 333810 401570 431380 329590 479290 527990 608240 FALSE TRUE 382312.8443 459680.3619 495241.6325 492752.6061 422796.382 342269.5406 432808.5296 415083.4473 536334.5601 0.712825301 0.857077645 0.923381914 0.918741104 0.788307175 0.638164247 0.806974903 0.773926348 1 19.03277369 4.747641269 23.39446557 0.829174771 0.712825148 0.130831472 0.09919529 1187.182857 3058367.747 0.025182612 0.283719218 55929.5428 -4.747641269 -0.116349623 VFLENVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VFLENVIR 8 0 P62805 P62805 HIST1H4A Histone H4 0 ; 104.44 0.010656 509920000 528620 421610 389490 1058600 380070 1217620 468440 749220 719130 FALSE TRUE 458761.5276 418840.4161 577848.6668 1298971.31 372507.3506 1264462.629 423010.7609 589005.1334 634115.2706 0.723467087 0.66051148 0.911267546 2.048478202 0.58744422 1.994058002 0.667088116 0.928861298 1 19.27438559 3.994725979 24.42469848 1.174685471 0.71546408 0.161837023 0.486646212 326.8025702 1513505.77 0.120193363 0.238933698 9879.295569 -3.994725979 -0.459221391 VFLKNEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFLKNEK 7 1 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 91.065 0.01521 816260000 1501500 1396000 605140 797200 1260600 1124000 1494800 1687800 574050 FALSE TRUE 1303072.971 1386829.584 897787.7281 978216.4444 1235516.526 1167241.007 1349834.526 1326877.104 506186.463 2.574294388 2.739760317 1.773630458 1.932521938 2.440832809 2.305950658 2.666674486 2.621320801 1 18.9493094 4.271000857 24.99917758 2.194835932 2.657028021 0.161553834 0.49045643 407.739839 314207.0807 0.122471056 0.323976977 18663.83374 -4.271000857 0.462192089 VFLLDR ddPTM_MDA-MB-175_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 ; 121.68 0.045473 968860000 1231380 1118180 768580 777610 1024430 1120720 1070680 1209410 1181200 FALSE TRUE 1068650.013 1110834.602 1140267.859 954178.2355 1004045.847 1163834.824 966845.6184 950787.0831 1041559.882 1.026009192 1.06651055 1.094769373 0.916105019 0.963982835 1.117395979 0.928266954 0.912849179 1 19.99031435 3.282003793 0.372868283 0.929678557 1.08531085 0.163616508 0.067387811 3.264038502 1.609746876 0.220449642 0.322497161 1914.272644 -3.282003793 0.155632293 VFLWGSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFLWGSFR 8 0 P18754-2;C9JW69;P18754;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4 P18754-2 RCC1 Regulator of chromosome condensation 0 181.49 0.00054335 140040000 108210 146820 95209 76551 140300 150070 132280 118730 159350 FALSE TRUE 93909.77433 145855.5298 141252.3909 93933.07456 137508.3045 155843.29 119451.506 93340.51346 140511.8245 0.668340723 1.038030288 1.005270491 0.668506546 0.978624432 1.109111568 0.850117108 0.664289385 1 17.10033202 2.00318864 24.99425513 0.792876708 0.918888019 0.02953968 0.165432039 213.4264804 1672939.271 0.066393074 0.044500506 100.7369134 -2.00318864 0.126011311 VFNAGDDPSVPLHVLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VFNAGDDPSVPLHVLSR 17 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 0 ; 119.85 1.00E-04 233200000 94422 88275 50530 70280 78954 115005 85603 96677 90499 FALSE TRUE 81943.89347 87695.11571 74966.47701 86238.14816 77382.96987 119429.3168 77301.23424 76003.37589 79800.31132 1.026861827 1.098932 0.939425872 1.080674332 0.969707619 1.496602141 0.968683367 0.952419541 1 16.28410675 VFNDMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFNDMK 6 0 P23528;E9PP50;E9PK25;E9PS23;Q9Y281;G3V2U0;F8WDN3 P23528;Q9Y281 CFL1;CFL2 Cofilin-1;Cofilin-2 0 100.74 0.086812 2118100000 5500800 4146900 2908700 3449200 4076400 3848200 5010800 5723700 5665700 FALSE TRUE 4773855.343 4119658.741 4315357.049 4232393.578 3995287.615 3996242.744 4524853.387 4499731.297 4995907.4 0.955553208 0.824606705 0.86377843 0.847172143 0.799712103 0.799903286 0.905712021 0.900683487 1 22.25231531 1.231853138 1.359236629 1.066082343 0.848442561 0.495572519 0.046398046 1.133809741 1.798987831 0.35003262 0.01371334 17.05505554 -1.231853138 -0.217639782 VFNFLWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFNFLWR 7 0 Q96CW5-2;Q96CW5 Q96CW5-2 TUBGCP3 Gamma-tubulin complex component 3 0 92.191 0.058434 0 53161 57062 38405 35438 66363 57876 60196 66279 73478 FALSE TRUE 46135.63916 56687.15596 56977.78646 43484.73954 65042.50614 60102.52717 54358.20119 52105.75163 64791.51455 0.712062984 0.874916358 0.879401984 0.671148681 1.003873834 0.927629607 0.838970991 0.804206415 1 15.98351726 3.231896406 24.99990987 0.896032209 0.797636312 0.33229409 0.088885238 245.3019195 920216.4516 0.027289268 0.031650268 1705.67548 -3.231896406 -0.098395897 VFNGSGKPIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VFNGSGKPIDR 11 1 P21281;H0YC04 P21281 ATP6V1B2 "V-type proton ATPase subunit B, brain isoform" 0 ; 115.92 0.0009653 933560000 1580870 1305000 820550 1128980 1466600 1274240 1459790 1781220 1414890 FALSE TRUE 1371954.024 1296427.369 1217370.725 1385332.164 1437417.529 1323260.837 1318219.79 1400319.964 1247623.316 1.099654043 1.039117619 0.975751823 1.110376944 1.152124612 1.060625287 1.056584767 1.122390025 1 20.25075099 5.080418363 14.85555553 1.06998258 1.564193003 0.031908045 0.053874609 3123552.504 10491636.38 0.013401777 48730878.45 120342.3155 -5.080418363 0.494210424 VFNIMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFNIMR 6 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 99.511 0.090068 230660000 233780 343660 213970 218630 323260 366570 305580 304310 338030 FALSE TRUE 202885.3807 341402.4748 317446.6077 268273.2831 316827.7584 380672.1851 275944.8986 239235.6746 298068.4785 0.680667012 1.145382687 1.06501234 0.900039093 1.062936142 1.277129964 0.925776855 0.80261984 1 18.18528429 2.014751675 24.99991097 0.880307356 1.032074113 0.092779053 0.162004962 415.7400865 704558.9679 0.064105656 0.043202302 103.4550453 -2.014751675 0.151766757 VFNTTPDDLDLHVIYDVSHNIAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VFNTTPDDLDLHVIYDVSHNIAK 23 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ; 203.84 1.06E-24 1430420000 1353950 1044390 700070 1032490 1029510 953210 1212410 1432590 1318190 FALSE TRUE 1175022.077 1037529.333 1038626.194 1266932.635 1009024.765 989880.6055 1094830.665 1126241.777 1162355.08 1.0108977 0.892609626 0.89355328 1.089970403 0.86808651 0.851616363 0.94190724 0.96893092 1 20.14861942 1.568779542 2.81571197 0.996199617 0.932380816 0.084079548 0.070599351 0.632512664 10.75804653 0.075834947 0.018913184 37.04926033 -1.568779542 -0.063818801 VFNVFCLYGNVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFNVFCLYGNVEK 13 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0;M0R076 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 199.43 1.03E-06 0 104370 101220 73241 100690 97710 105870 128540 143110 92279 FALSE TRUE 90577.24006 100555.0792 108660.5926 123553.2035 95765.76217 109942.8874 116074.2106 112507.0402 81369.88174 1.113154377 1.235777624 1.335390813 1.51841444 1.176919028 1.351149652 1.426500913 1.38266196 1 16.31220727 4.547707154 2.732469521 1.328583866 1.109229376 0.16373742 0.141587132 0.53350821 6.717589961 0.035172493 0.213330521 35294.50977 -4.547707154 -0.21935449 VFNYNTLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VFNYNTLER 9 0 P35606;P35606-2;D6R997;D6RBT6;D6RBZ7;D6RCL6;D6RBG7 P35606 COPB2 Coatomer subunit beta 0 ;; 156.01 0.0001674 622260000 716650 620370 455269 487084 673410 653680 666180 758690 681390 FALSE TRUE 621942.8867 616294.7486 675438.6112 597683.8668 660010.4585 678827.4926 601573.9661 596450.0476 600836.8504 1.035127733 1.02572728 1.124163091 0.994752346 1.098485318 1.12980336 1.001226815 0.992698845 1 19.19661377 2.090181556 12.3469053 0.996170256 1.066682847 0.377661475 0.042391721 0.559221474 73.33787462 0.017019843 0.011474008 123.0783189 -2.090181556 0.070512591 VFPEPTES(ph)GDEGEELGLPLLSTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VFPEPTESGDEGEELGLPLLSTR 23 0 Q9BUR4;E9PMG4 Q9BUR4 WRAP53 Telomerase Cajal body protein 1 1 VFPEPT(0.144)ES(0.856)GDEGEELGLPLLSTR;VFPEPT(0.166)ES(0.834)GDEGEELGLPLLSTR;VFPEPT(0.138)ES(0.862)GDEGEELGLPLLSTR 109.26 0.00075368 58456000 59239 52633 40349 44022 51523 52143 47940 63731 60025 TRUE FALSE 51410.41606 52287.25036 59861.91136 54017.86793 50497.7931 54148.97495 43290.78618 50102.62161 52928.91288 0.971310636 0.9878769 1.13098698 1.020573917 0.954068209 1.023050957 0.817904314 0.946602129 1 15.6917684 2.83163217 1.661086027 0.928440911 1.029292517 0.246373021 0.067728378 0.479178911 2.664298482 0.028376116 0.026949005 678.6286182 -2.83163217 0.100851606 VFPLS(ph)PASNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VFPLSPASNLR 11 0 A0A2R8YH03;Q5VWN6;J3KPH3 A0A2R8YH03 FAM208B Protein FAM208B 1 VFPLS(0.985)PAS(0.015)NLR;VFPLS(0.98)PAS(0.02)NLR;VFPLS(0.998)PAS(0.002)NLR 123.75 0.00038133 172141000 225657 238409 134467 160255 228923 230911 232162 232561 182214 TRUE FALSE 195835.8557 236842.8756 199495.691 196643.3471 224367.8802 239794.2956 209646.965 182829.6399 160672.8685 1.218848319 1.474068882 1.241626498 1.223874005 1.396426679 1.492438007 1.304806262 1.137899893 1 17.29376681 1.590370891 2.526063472 1.009962178 1.343565001 0.589982666 0.096360891 0.186469013 2.530634119 0.110747484 0.026544482 38.93775345 -1.590370891 0.333602823 VFQGTDEQLNDLYHNHQR ddPTM_MDA-MB-175_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 ; 175.51 1.83E-12 1047430000 259692 226029 158119 170195 211427 236526 198182 276860 209479 FALSE TRUE 225373.0442 224544.2006 234585.8773 208840.376 207220.0163 245625.3083 178962.3401 217655.6435 184714.6313 1.22011474 1.215627582 1.269990773 1.130610903 1.12183867 1.329755562 0.968858498 1.178334613 1 17.49493862 -1.354507287 0.306802938 2.87E-10 1.237554303 0.318281432 0.092275654 64.34960111 1.494655754 40.06807793 0.167062975 0.04420717 1.354507287 1.237554303 VFQSLEDHHLEVVAFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFQSLEDHHLEVVAFFR 17 0 Q9NX05;F8W881 Q9NX05 FAM120C Constitutive coactivator of PPAR-gamma-like protein 2 0 131.18 1.61E-05 17016000 9859.3 10411 4147.7 7496.1 12595 12337 10787 14385 14656 FALSE TRUE 8556.368525 10342.60946 6153.541593 9198.204076 12344.38414 12811.61237 9740.8784 11308.87969 12923.38438 0.662084194 0.80030193 0.476155581 0.711748858 0.955197476 0.991351182 0.753740515 0.875071062 1 13.65769631 3.349388248 5.228154063 0.901060641 0.651807018 0.596158372 0.103793424 0.15410026 6.462920684 0.03039182 0.039377206 2235.569873 -3.349388248 -0.249253624 VFQSWWDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFQSWWDR 8 0 Q92934 Q92934 BAD Bcl2-associated agonist of cell death 0 93.267 0.026033 335590000 308670 202890 125270 134050 185550 209530 191330 191160 184920 FALSE TRUE 267878.4774 201557.2022 185850.991 164488.1013 181857.918 217590.7547 172774.846 150281.9216 163058.9683 1.642831917 1.236100071 1.139777793 1.008764517 1.115289272 1.334429851 1.059585056 0.921641558 1 17.31503427 VFS(ph)LSEADSHGGHWV ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VFSLSEADSHGGHWV 15 0 H7BXG1 H7BXG1 CLEC16A 1 VFS(0.981)LS(0.019)EADSHGGHWV;VFS(0.966)LS(0.034)EADSHGGHWV;VFS(0.994)LS(0.006)EADSHGGHWV;VFS(0.983)LS(0.017)EADSHGGHWV 275.76 1.04E-33 454372000 386963 330788 233124 333614 521077 542200 495927 524420 578540 TRUE FALSE 335824.8591 328615.0318 345863.5462 409366.1577 510708.5872 563058.7849 447832.0759 412276.864 510145.6603 0.658292102 0.644159222 0.677970182 0.802449554 1.001103463 1.103721601 0.877851388 0.808155192 1 18.96054971 3.539414245 2.929448755 0.939835688 0.657608058 0.742385516 0.079816332 0.160333362 2.706137969 0.027061386 0.041111185 3462.695044 -3.539414245 -0.28222763 VFS(ph)PVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFSPVIR 7 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 VFS(1)PVIR 85.744 0.021594 45568000 82022 73926 50351 39035 76120 99784 58397 76064 59922 TRUE FALSE 71182.58488 73440.37524 74700.91201 47898.49336 74605.36093 103622.755 52733.66793 59798.30553 52838.08942 1.347183171 1.389913527 1.41377012 0.906514484 1.411961745 1.961137433 0.998023746 1.131727248 1 15.68929068 VFS(ph)QENVCDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFSQENVCDR 10 0 Q6NV74;C9JFM2;C9JXD6;C9JK00 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 VFS(1)QENVCDR 146.96 0.0054653 0 225470 156580 102840 115310 135880 112920 168280 193560 166320 TRUE FALSE 195673.5682 155551.4157 152573.768 141492.8979 133176.2538 117264.1055 151960.2315 152168.7003 146657.8391 1.334218269 1.060641672 1.040338307 0.964782372 0.908074568 0.799576117 1.036154852 1.037576315 1 17.16209466 5.132340327 1.207204402 0.964906669 1.867390995 0.728593845 0.070737972 2.064966366 1.355725315 0.023077491 2.927802637 135625.1797 -5.132340327 0.902484326 VFSWGFGGYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VFSWGFGGYGR 11 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 200.54 1.08E-07 981870000 439860 374830 225777 279110 377710 389820 343720 427300 319910 FALSE TRUE 381731.3865 372367.717 334963.5124 342486.1914 370194.31 404816.6276 310386.0873 335925.2203 282090.6042 1.35322262 1.320028783 1.187432362 1.21409996 1.312324141 1.435058884 1.100306365 1.190841578 1 18.10579909 1.383664582 1.177514415 0.930190857 1.289177352 0.519836634 0.088022726 1.032292735 1.493226895 0.443359321 0.028705222 24.19159941 -1.383664582 0.358986495 VFSWLQQEGHLSEEEMAR ddPTM_MDA-MB-175_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 ; 280.39 2.89E-39 311890000 207098 223657 76291 141491 217574 237265 200485 244455 244337 FALSE TRUE 179729.4746 222187.7824 113185.5828 173618.6941 213244.7031 246392.7381 181041.9956 192180.2006 215451.7582 0.834198226 1.031264652 0.525340725 0.805835587 0.989756152 1.143609781 0.840290175 0.891987154 1 17.71700535 3.248004412 21.43818359 0.961547136 0.796179859 0.264432433 0.143418716 52.91807529 120123.4514 0.042522443 0.053927384 1770.126943 -3.248004412 -0.165367277 VFTTNNGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFTTNNGR 8 0 O00422;O00422-2;H7BZW6;U3KQ12;U3KPY7 O00422 SAP18 Histone deacetylase complex subunit SAP18 0 79.474 0.065008 89899000 41341 37772 12332 20773 39115 35997 28946 31096 10122 FALSE TRUE 35877.68211 37523.87324 18295.79645 25489.82715 38336.68803 37381.82788 26138.82138 24446.36239 8925.388691 4.019733296 4.204172451 2.049859909 2.855878666 4.295240169 4.188257697 2.928591939 2.738968939 1 13.12369928 4.268963538 24.95609832 2.955359792 4.111954909 0.227139498 0.94475907 339.0524494 278304.1175 0.246530948 0.652088827 18576.48486 -4.268963538 1.156595116 VFTTQELVQAFTHAPATLEADR ddPTM_MDA-MB-175_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 ; 195.03 1.54E-18 2374800000 1946090 1980030 1175090 1513170 1773710 2053130 1683010 2199910 2014370 FALSE TRUE 1688909.276 1967023.053 1743367.454 1856758.376 1738416.641 2132115.24 1519791.949 1729476.366 1776233.473 0.950837433 1.107412444 0.981496791 1.045334639 0.978709537 1.200357538 0.855626229 0.973676261 1 20.7603898 2.206754579 24.99999984 0.945826048 1.041154808 0.261878327 0.079732438 265.1818757 208434.9654 0.030232182 0.020384403 160.9735711 -2.206754579 0.095328759 VFTTVGSAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 140.83 8.98E-05 428040000 447660 503540 417080 449810 433290 495650 564060 575190 866990 FALSE TRUE 388500.5968 500232.2126 618781.283 551946.2354 424668.3767 514717.9762 509357.548 452190.0946 764495.4299 0.508179096 0.654329893 0.809398276 0.721974539 0.555488444 0.673278029 0.666266309 0.59148829 1 19.54414835 1.2325388 24.99961883 1.000000569 0.651322171 0.633014013 0.084293412 137.4817078 570698.8658 0.186503226 0.020985662 17.08200324 -1.2325388 -0.348678397 VFTTVGSAEKR ddPTM_MDA-MB-175_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 ; 218.55 1.69E-11 3060800000 3026200 2829100 1784770 1969600 2837100 2363000 3327000 3533200 1880040 FALSE TRUE 2626280.003 2810515.456 2647890.742 2416827.783 2780647.261 2453906.139 3004348.052 2777652.675 1657783.813 1.584211392 1.695344974 1.597247314 1.45786668 1.677328032 1.480232899 1.812267697 1.675521653 1 20.66082445 1.235896045 25 0.999999167 1.62749271 0.780556296 0.103699683 33.57843309 314981.3531 0.168777512 0.025250665 17.21456468 -1.235896045 0.627493543 VFVDGHQLFDFYHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VFVDGHQLFDFYHR 14 0 Q3ZCW2 Q3ZCW2 LGALSL Galectin-related protein 0 108.71 0.00046824 107090000 78425 67822 41318 55147 59704 70815 66133 70169 71086 FALSE TRUE 68060.93755 67376.47282 61299.523 67668.96922 58516.00721 73539.29887 59719.43184 55163.90541 62682.29406 1.085808019 1.074888433 0.977940006 1.079554765 0.933533274 1.173206884 0.952732071 0.880055624 1 15.93577036 2.022820862 24.98733507 0.926940359 1.048610429 0.348700387 0.070181489 208.3638626 228143.7384 0.026547491 0.017897144 105.3952073 -2.022820862 0.12167007 VFVGGLS(ph)PDTSEEQIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VFVGGLSPDTSEEQIK 16 0 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 1 VFVGGLS(0.966)PDT(0.029)S(0.005)EEQIK;VFVGGLS(0.882)PDT(0.093)S(0.025)EEQIK;VFVGGLS(1)PDTSEEQIK 203.06 3.02E-11 167062000 339953 216294 205814 256174 201640 178601 253968 294233 624296 TRUE FALSE 295027.3497 214873.1505 305346.3388 314342.2221 197627.7585 185471.896 229338.2224 231313.5627 550492.4381 0.535933519 0.390328977 0.554678534 0.571020055 0.359001768 0.336919971 0.416605582 0.420193897 1 19.07036322 1.237045115 24.99992639 1.000000681 0.444412327 0.819289442 0.081444347 16.57166538 273274.3054 0.127537524 0.020758058 17.26017184 -1.237045115 -0.555588354 VFVHYTGWLLDGTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 276.41 4.22E-33 4113374000 10203150 9794940 4681065 9317220 8856490 8495770 10762980 13132230 16530050 FALSE TRUE 8854777.876 9730596.394 6944843.691 11432837.21 8680263.176 8822607.769 9719187.856 10324004.81 14575886.32 0.607494987 0.667581798 0.476461159 0.784366518 0.595522151 0.60528791 0.666799098 0.70829345 1 23.79708028 0.888343523 1.485372197 1.554486012 0.625482446 0.699727149 0.076152355 1.548270985 1.484097796 2.784870377 0.020298999 7.732920103 -0.888343523 -0.929003566 VFVHYTGWLLDGTKFDSSLDRK ddPTM_MDA-MB-175_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" 0 102.33 0.00037208 43666000 27146 18369 4484.3 9591.5 16174 14865 30818 30399 1721.5 FALSE TRUE 23558.58732 18248.33283 6652.922479 11769.39667 15852.16904 15436.86617 27829.2751 23898.41042 1517.986231 15.51963176 12.02140866 4.382729133 7.753296065 10.44289383 10.16930579 18.33302209 15.74349617 1 10.56794299 7.908465395 1.12E-17 9.991353964 12.10449365 0 5.30663209 0 0.819620291 5.13012521 5.13012521 80996340.05 -7.908465395 2.113139686 VFVLDEADVMIATQGHQDQSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VFVLDEADVMIATQGHQDQSIR 22 0 Q9NUU7;I3L0H8;F6QDS0;H3BQK0;Q9UMR2;Q9UMR2-2;Q9UMR2-4;I3L352;Q9UMR2-3;Q9NUU7-2;H3BN59 Q9NUU7 DDX19A;DDX19B ATP-dependent RNA helicase DDX19A;ATP-dependent RNA helicase DDX19B 0 ; 266.78 1.05E-37 154161000 184991 165713 106821 121437 156880 151195 151301 191601 159127 FALSE TRUE 160543.9706 164624.4204 158479.9929 149011.1269 153758.3949 157011.5695 136627.8523 150628.6172 140315.1873 1.144166741 1.173247341 1.129457159 1.061974329 1.095807217 1.118991981 0.973721055 1.073501879 1 17.09831165 3.584902147 0.264783134 0.973386825 1.243973473 0.606401086 0.03901373 3.577395687 0.802487119 0.264012988 0.493580849 3845.051377 -3.584902147 0.270586648 VGAEDADGIDMAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VGAEDADGIDMAYR 14 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 166.14 4.13E-07 0 379580 275512 180669 208846 281020 259129 273786 327440 274947 FALSE TRUE 329417.5413 273702.1435 268041.1327 256267.6763 275428.2518 269097.8603 247234.2759 257419.5041 242443.0789 1.358741783 1.128933623 1.105583768 1.057022034 1.136053267 1.109942431 1.019762152 1.061772954 1 17.88728654 7.999999968 0.918285318 1.062286702 168.9059543 0.841227804 0.039465452 400.8660125 0.810527136 0.013228104 141126.0704 99999992.69 -7.999999968 167.8436676 VGCYDANDAS(ph)DEEEFDREGDCISLPGALPGPIRPLSEDDPR ddPTM_MDA-MB-175_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 62.19 0.0041347 124100000 65302 73648 47195 53148 64250 74662 72833 77873 70861 TRUE FALSE 56672.17525 73164.20144 70018.65986 65216.06572 62971.5507 77534.29545 65769.66687 61220.46496 62483.89331 0.906988541 1.17092898 1.120587341 1.043726027 1.00780453 1.240868508 1.052585929 0.979779936 1 15.93119673 1.897275799 5.223274435 0.992990085 1.087177223 0.144414353 0.089971227 0.389147261 15.59448899 0.044769462 0.023149067 78.93612424 -1.897275799 0.094187138 VGDDVEFEVSSDRR ddPTM_MDA-MB-175_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 ; 169.04 2.68E-07 269240000 209441 187173 141478 160451 203339 201145 202040 231080 170557 FALSE TRUE 181762.8412 185943.4482 209897.234 196883.8519 199292.9517 208883.1783 182446.1919 181665.3403 150393.9458 1.20857818 1.236375888 1.395649492 1.309120862 1.325139458 1.388906829 1.213121918 1.207929876 1 17.19838697 1.056461699 1.2526981 0.746556296 1.308336876 0.695261374 0.062953802 1.262209421 1.238530046 1.033710521 0.019585557 11.38837341 -1.056461699 0.56178058 VGDLYSDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VGDLYSDLR 9 0 O15020;O15020-2;A4QPE4;E9PJZ2;A0A494C1G7 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 75.213 0.090495 99236000 215790 226050 175130 200490 227840 292900 200590 241380 284260 FALSE TRUE 187272.8048 224565.0627 259823.4538 246014.3188 223306.4298 304168.0525 181136.8127 189762.7654 250655.1066 0.747133411 0.895912578 1.03657754 0.981485365 0.890891204 1.213492343 0.72265359 0.757067223 1 17.9353441 VGDNDFLEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VGDNDFLEVR 10 0 O00178;F5H716;F5H257 O00178 GTPBP1 GTP-binding protein 1 0 ; 112.13 0.0038658 64558000 166302 164272 122345 148767 163993 142963 159217 183030 216862 FALSE TRUE 144324.7693 163192.8864 181511.4512 182546.8211 160729.8601 148462.8791 143776.1598 143890.4588 191224.8214 0.75473868 0.853408492 0.949204449 0.95461886 0.840528227 0.776378705 0.751869756 0.752467477 1 17.54491027 3.002666197 24.92644872 0.803779332 0.883354472 0.072202565 0.08909076 159.53057 1491432.041 0.02755006 0.031063816 1006.158028 -3.002666197 0.079575141 VGDPPQPLPEEPMEVQGAERAS(ph)PEPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 VGDPPQPLPEEPMEVQGAERASPEPQR 27 1 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 VGDPPQPLPEEPMEVQGAERAS(1)PEPQR;VGDPPQPLPEEPMEVQGAERAS(1)PEPQR;VGDPPQPLPEEPMEVQGAERAS(1)PEPQR;VGDPPQPLPEEPMEVQGAERAS(1)PEPQR;VGDPPQPLPEEPMEVQGAERAS(1)PEPQR;VGDPPQPLPEEPMEVQGAERAS(1)PEPQR;VGDPPQPLPEEPMEVQGAERAS(1)PEPQR 197.89 3.51E-25 4489490000 375318 319372 237120 270566 314306 322293 314782 379120 290199 TRUE FALSE 325718.7754 317274.0243 351792.0251 332002.1456 308051.9255 334691.8203 284254.4901 298048.1383 255892.0048 1.272875937 1.239874706 1.374767552 1.297430711 1.20383568 1.307941686 1.110837716 1.164741894 1 17.96517555 0.267656542 0.523217994 0.336813621 1.298564585 0.72023342 0.056994114 5.92322938 0.595973979 4.342463003 0.035856059 1.852066353 -0.267656542 0.961750964 VGDPPQPLPEEPMEVQGAERAS(ph)PEPQRENAS(ph)PAPGTTAEEAMSR ddPTM_MDA-MB-175_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 2 VGDPPQPLPEEPMEVQGAERAS(0.999)PEPQRENAS(0.889)PAPGT(0.051)T(0.049)AEEAMS(0.013)R 59.183 0.0055417 161690000 15942 14619 9873.8 13138 17471 13853 15223 18935 8251.2 TRUE FALSE 13835.22431 14522.96683 14648.80271 16121.1837 17123.36128 14385.93387 13746.6758 14885.8976 7275.752536 1.901552347 1.996077623 2.013372862 2.215741069 2.353483189 1.977243426 1.88938199 2.045959855 1 12.82888076 1.237540745 7.714449723 0.984478622 2.052193796 0.846728153 0.140266565 0.040183049 18.41773901 0.221201895 0.037203362 17.27988092 -1.237540745 1.067715174 VGDPPQPLPEEPMEVQGAERAS(ph)PEPQRENASPAPGTTAEEAMSR ddPTM_MDA-MB-175_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(1)PEPQRENASPAPGTTAEEAMSR 142.08 5.73E-14 150690000 4689.4 4223.7 0 2899.3 3358.7 6073.3 6667.8 5576.2 0 TRUE FALSE 4069.683909 4195.954237 0 3557.630378 3291.868441 6306.943781 6021.157782 4383.773024 0 0 VGDPQELNGITR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VGDPQELNGITR 12 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 196.67 4.74E-07 2874750000 1046110 1064850 720150 796850 1110680 1177490 1168750 1219560 1229420 FALSE TRUE 907863.913 1057854.93 1068416.949 977786.9716 1088579.641 1222788.802 1055404.805 958766.5846 1084079.368 0.837451518 0.975809485 0.985552331 0.901951463 1.004151239 1.127951364 0.973549388 0.884406265 1 20.04803895 3.228564868 24.97924889 0.988473297 0.933118299 0.195517976 0.071165566 482.271835 1205187.776 0.023620819 0.027097867 1692.641046 -3.228564868 -0.055354998 VGDQVWLFIDEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VGDQVWLFIDEPR 13 0 P49588;P49588-2;H3BPK7 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;; 177.1 3.66E-05 508542000 719398 518540 327884 432324 497283 463862 528808 606642 578194 FALSE TRUE 624327.7316 515133.6766 486449.7991 530489.7719 487388.0412 481707.0713 477524.2816 476916.3292 509840.564 1.224554843 1.010381898 0.954121413 1.040501304 0.955961678 0.944819038 0.936614925 0.935422489 1 18.95968664 4.7577738 2.597900123 0.963657414 1.286362931 0.86167805 0.032196863 0.188170973 1.58163934 0.008573313 0.135426428 57249.77709 -4.7577738 0.322705517 VGDSTPVSEKPVSAAVDANASES(ph)P ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VGDSTPVSEKPVSAAVDANASESP 24 1 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 1 VGDSTPVSEKPVSAAVDANASES(1)P;VGDSTPVSEKPVSAAVDANAS(0.001)ES(0.999)P;VGDSTPVSEKPVSAAVDANAS(0.093)ES(0.907)P;VGDSTPVSEKPVSAAVDANASES(1)P;VGDSTPVSEKPVSAAVDANAS(0.018)ES(0.982)P;VGDSTPVSEKPVSAAVDANASES(1)P 256.75 4.28E-44 3004970000 6325830 5753640 4157320 4851370 5865680 4703210 6934590 8045120 7223110 TRUE FALSE 5489855.538 5715843.96 6167813.857 5952947.707 5748964.444 4884145.532 6262074.529 6324733.695 6369202.164 0.861937712 0.897419145 0.968380921 0.934645746 0.902619244 0.766837887 0.983180368 0.993018204 1 22.60268123 2.037291045 24.99994981 0.993637366 0.89369184 0.465661762 0.052164685 150.5623742 100936.5501 0.022059557 0.014872512 108.966009 -2.037291045 -0.099945526 VGDTEKPEPERS(ph)PPNR ddPTM_MDA-MB-175_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;VGDTEKPEPERS(1)PPNR;VGDTEKPEPERS(1)PPNR;VGDTEKPEPERS(1)PPNR;VGDTEKPEPERS(1)PPNR 157.88 1.94E-08 6836070000 7828190 6362630 5034000 5757160 5889370 5215530 7873900 9101430 8214140 TRUE FALSE 6793674.857 6320833.465 7468459.238 7064411.171 5772183.059 5416174.814 7110290.39 7155160.022 7243073.727 0.937954674 0.872672805 1.031117385 0.975333324 0.796924521 0.747772978 0.981667543 0.987862376 1 22.78817063 2.039425306 24.99993882 0.990575066 0.895450624 0.240270992 0.080777064 240.3295732 152394.1324 0.035831324 0.024157431 109.5028205 -2.039425306 -0.095124442 VGDTEKPEPERS(ph)PPNRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VGDTEKPEPERSPPNRK 17 3 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 1 VGDTEKPEPERS(1)PPNRK 102.98 0.0050918 77759000 116570 81597 79261 71579 81301 68998 95272 127320 100090 TRUE FALSE 101164.9791 81060.98393 117591.8847 87832.10597 79683.26916 71652.39771 86032.5361 100093.6088 88257.47422 1.146248293 0.918460274 1.332373102 0.995180371 0.902850097 0.811856427 0.974790372 1.134109147 1 16.42943084 4.779237928 21.48788196 1.017143078 1.146250555 0.082549997 0.141643067 11049.19268 5835993.459 0.035798902 8.183098301 60150.31801 -4.779237928 0.129107477 VGDVT(ph)PQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 131.17 0.0038071 267620000 1080710 917550 623190 744950 784760 765350 953430 1093870 1071970 TRUE FALSE 937891.4353 911522.5536 924566.7684 914102.2833 769144.8114 794793.5097 860966.5053 859954.413 945242.9278 0.992222642 0.964326235 0.978126089 0.967055406 0.813700678 0.840835183 0.91084152 0.909770798 1 19.85032562 3.441089755 24.9931949 0.894896538 0.976127773 0.402555624 0.048807941 182.3911581 126514.7825 0.014760877 0.01905627 2761.148442 -3.441089755 0.081231235 VGDVVEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VGDVVEFR 8 0 Q9UHQ9;H7C0R7 Q9UHQ9 CYB5R1 NADH-cytochrome b5 reductase 1 0 85.064 0.039567 146140000 278240 257810 175740 239200 282620 323650 197730 304210 283650 FALSE TRUE 241469.879 256116.4291 260728.4518 293514.0159 276996.4149 336101.0249 178554.175 239157.0589 250117.2201 0.965426846 1.02398559 1.042425034 1.17350583 1.10746639 1.34377403 0.713881975 0.956179901 1 17.93224486 2.229035845 24.99999971 0.896464765 1.105324288 0.40816884 0.124399584 208.7085415 547799.3528 0.050645292 0.034646569 169.4477649 -2.229035845 0.208859523 VGDVYIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 VGDVYIPR 8 0 Q01130;Q01130-2;J3KP15;J3QL05;Q9BRL6-2;Q9BRL6 Q01130;Q9BRL6-2 SRSF2;SRSF8 Serine/arginine-rich splicing factor 2;Serine/arginine-rich splicing factor 8 0 ;;;;;; 150.84 0.0011231 5157515000 4626780 3992340 2392100 2921530 3885720 3686310 3715010 4453600 3976170 FALSE TRUE 4015339.3 3966114.056 3548927.561 3584908.039 3808401.774 3828124.731 3354728.902 3501232.298 3506111.712 1.145239978 1.131200139 1.012211775 1.022473992 1.086218035 1.091843342 0.956823164 0.998608312 1 21.74144053 8 0.273411442 0.984365398 2.186893697 0.531540286 0.042518783 68.08411227 1.09118913 0.116305001 37.88003278 100000000 -8 1.202528299 VGDYGSLSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VGDYGSLSGR 10 0 Q9UBR2 Q9UBR2 CTSZ Cathepsin Z 0 120.31 0.0013429 155200000 294640 246090 175160 200120 278330 298650 268430 248460 302160 FALSE TRUE 255702.5775 244473.4186 259867.9619 245560.3046 272791.7775 310139.2588 242397.6999 195328.7625 266438.989 0.959704052 0.917558723 0.975337592 0.921638029 1.023843314 1.164016047 0.909768127 0.733108781 1 18.02344569 2.002690581 24.99709619 0.83967503 0.991602298 0.24062842 0.0939775 89.54902317 831957.4419 0.038732876 0.02594739 100.6214523 -2.002690581 0.151927268 VGEAWQDRPGAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VGEAWQDRPGAPR 13 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;H7BZT5;O15231-9;H7C1R1;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 0 ;;; 155.66 4.12E-05 1288090000 861650 762590 519030 638070 809010 774890 798170 943560 780450 FALSE TRUE 747780.7694 757580.4961 770034.6441 782953.5458 792912.2838 804700.5197 720763.5963 741787.0368 688186.0901 1.086596751 1.100836688 1.118933752 1.137706148 1.152177144 1.169306575 1.047338222 1.077887286 1 19.39243921 1.549874665 1.323958773 0.993224465 1.125003142 0.593787208 0.032036384 0.546306495 1.324148297 0.089050271 0.010362541 35.47110064 -1.549874665 0.131778677 VGEAWQERPGAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VGEAWQERPGAPR 13 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;H7BZT5;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 0 124.3 0.00019459 258820000 132100 123380 85186 92595 117800 110230 127030 145520 127740 FALSE TRUE 114642.6503 122569.5087 126382.2345 113620.11 115456.0105 114470.6194 114710.6502 114401.6804 112638.7227 1.017790752 1.088164937 1.122014095 1.008712699 1.025011716 1.016263472 1.018394451 1.015651436 1 16.78134335 3.713369884 24.95276406 1.015004027 1.077207433 0.559710606 0.025898097 512.3290223 507489.1204 0.006977594 0.010352465 5168.563835 -3.713369884 0.062203406 VGEDEDGS(ph)DEEVVHNEDIHFEPIVSLPEVEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VGEDEDGSDEEVVHNEDIHFEPIVSLPEVEVK 32 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK 269.11 5.06E-60 552190000 527070 399255 351076 331762 361760 298649 482820 536310 488070 TRUE FALSE 457416.3641 396632.2676 520857.5279 407093.6328 354561.6838 310138.2203 435996.1907 421624.2801 430370.9206 1.062842172 0.92160564 1.210252605 0.945913428 0.823851396 0.720630055 1.013070749 0.979676507 1 18.71522108 3.497894234 24.6493014 0.912312646 1.055156095 0.29904469 0.109998229 916.5865467 1087623.051 0.031856812 0.04662597 3146.981818 -3.497894234 0.142843449 VGEEEHVY(ph)SFPNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VGEEEHVYSFPNK 13 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 VGEEEHVY(0.983)S(0.017)FPNK;VGEEEHVY(0.982)S(0.018)FPNK;VGEEEHVY(1)SFPNK;VGEEEHVY(1)SFPNK 189.24 3.15E-05 1302930000 3185310 2932740 2484950 2294130 2918460 2765000 3631900 4244880 3955510 TRUE FALSE 2764363.213 2913474.638 3686680.132 2815047.28 2860388.356 2871371.339 3279678.897 3337145.446 3487894.114 0.792559385 0.835310518 1.056993134 0.807090808 0.820090365 0.823239251 0.940303458 0.95677946 1 21.73392481 2.086048343 4.774885805 0.968305264 0.860494581 0.325849769 0.075264411 0.26873488 10.83431645 0.033347372 0.021664662 121.9125297 -2.086048343 -0.107810682 VGEEFEEQTVDGRPCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VGEEFEEQTVDGRPCK 16 1 P29373 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 ;;;;; 275.83 2.57E-35 16323630000 4144720 3371780 3259900 2897070 2878730 2449520 4620070 4734000 3562920 FALSE TRUE 3596984.751 3349630.555 4836398.544 3554894.022 2821448.905 2543754.619 4172016.323 3721670.94 3141715.656 1.14491098 1.066178777 1.539413197 1.131513609 0.898059918 0.809670542 1.327942048 1.184598273 1 21.58312118 3.487333311 24.89848909 1.066066592 1.2490512 0.199858524 0.185459215 886.6239801 2161718.697 0.055446257 0.076336887 3071.378299 -3.487333311 0.182984609 VGEFCHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VGEFCHNR 8 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;;; 208.35 5.60E-05 8735420000 11281980 9581860 6598210 7179380 9083780 9083950 9806590 10461940 10003580 FALSE TRUE 9791037.758 9518916.131 9789126.426 8809567.959 8903030.55 9433415.435 8855548.411 8224735.546 8820968.169 1.109973143 1.079123737 1.109756462 0.998707601 1.009303104 1.069430844 1.003920232 0.932407349 1 23.07250558 5.500863812 0.134441746 0.852319424 1.412216085 0.603073226 0.03578445 51.21545698 1.371607498 1.304854244 5.825309044 316857.3692 -5.500863812 0.559896661 VGEGFEEETVDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VGEGFEEETVDGR 13 0 P29762;B5MCB5 P29762 CRABP1 Cellular retinoic acid-binding protein 1 0 ;;; 226.4 2.52E-11 2228500000 1678970 1787470 1248920 1443360 1753880 1693220 1807500 2157510 2050740 FALSE TRUE 1457089.861 1775727.992 1852901.889 1771096.948 1718981.219 1758359.269 1632208.928 1696143.276 1808303.853 0.805777114 0.981985405 1.02466291 0.979424418 0.95060419 0.972380425 0.90261873 0.937974707 1 20.78620569 4.742341779 24.85616485 0.964840288 0.805777048 0.697651185 0.033622755 223.7313842 1470673.926 0.009017022 0.065544431 55251.2081 -4.742341779 -0.15906324 VGELKDDDFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VGELKDDDFER 11 1 P36507;A0A1B0GUL7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 0 ;;; 148.62 3.17E-05 2019750000 3976760 3241940 2957620 2962360 2909260 2339090 4189560 4742930 3784570 FALSE TRUE 3451221.09 3220643.483 4387934.925 3635009.115 2851371.418 2429076.306 3783257.116 3728691.329 3337162.446 1.034178331 0.96508442 1.314870042 1.089251474 0.854429913 0.727886744 1.133674844 1.117323891 1 21.67019048 5.164257933 16.36956079 1.031973277 2.11764655 0 0.160009022 21779.11587 2344469.414 0.040165557 71302.82871 145968.0925 -5.164257933 1.085673274 VGEVCHITCKPEYAYGSAGSPPK ddPTM_MDA-MB-175_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 ; 229.15 3.48E-33 2949100000 2462300 1850770 1280940 1962750 1864290 1430790 2537400 3028200 3433100 FALSE TRUE 2136900.816 1838612.17 1900406.868 2408422.386 1827194.276 1485833.417 2291323.339 2380642.995 3027242.829 0.705890124 0.607355364 0.627768229 0.79558282 0.60358365 0.490820691 0.756901071 0.786406354 1 21.52957297 1.346881851 1.542852008 1.087854479 0.645180305 0.645944717 0.083235907 0.571495109 1.497849874 0.372697434 0.024556964 22.22705124 -1.346881851 -0.442674174 VGFAEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VGFAEAAR 8 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;H7C1V0 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ;;;; 192.56 0.00040777 10477500000 5137630 7383800 5079820 5729680 7450400 8607700 6684500 7431100 7990100 FALSE TRUE 4458679.178 7335295.332 7536437.943 7030691.417 7302151.616 8938843.789 6036238.219 5842017.094 7045519.48 0.632838954 1.041129097 1.069678107 0.997895391 1.036424871 1.268727425 0.856748496 0.829181881 1 22.74827465 4.742424346 24.63869247 1.000942474 0.63283878 0.49500066 0.120005147 315.6750138 2012933.729 0.032390881 0.236763364 55261.71342 -4.742424346 -0.368103694 VGFQYEGTYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VGFQYEGTYK 10 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 157.99 1.90E-05 596980000 631810 612620 427220 491940 576090 568440 706270 719070 808550 FALSE TRUE 548314.7077 608595.6589 633825.021 603642.4958 564626.9361 590308.2546 637776.0441 565302.4763 712964.1401 0.769063515 0.853613281 0.88899986 0.846665999 0.791942966 0.827963458 0.894541546 0.792890476 1 19.44346999 1.229318855 24.94539834 1.00000033 0.835543028 0.622238049 0.040805641 243.225275 656464.626 0.118728241 0.009719139 16.95582223 -1.229318855 -0.164457302 VGGS(ph)DEEASGIPSR ddPTM_MDA-MB-175_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(1)DEEASGIPSR;VGGS(1)DEEASGIPSR;VGGS(1)DEEASGIPSR;VGGS(1)DEEASGIPSR 278.64 3.64E-33 7031910000 4494970 4240210 2899550 3031310 4440360 3663890 4069080 4526390 4305500 TRUE FALSE 3900948.326 4212355.781 4301782.078 3719615.266 4352005.523 3804842.219 3674461.248 3558456.723 3796508.695 1.027509388 1.10953408 1.133088957 0.979746279 1.146317808 1.002195049 0.967852715 0.937297135 1 21.85624188 2.522565299 5.630794706 0.964471765 1.078562582 0.511981057 0.050493138 0.148814307 11.64268794 0.016957696 0.014534823 333.0928415 -2.522565299 0.114090818 VGGS(ph)SVDLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VGGSSVDLHR 10 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 VGGS(0.962)S(0.038)VDLHR;VGGS(0.968)S(0.032)VDLHR;VGGS(0.98)S(0.02)VDLHR 136.7 7.14E-05 1828620000 726630 785190 592960 434240 774590 1138840 537313 608360 751940 TRUE FALSE 630604.0045 780032.0352 879717.4393 532840.8289 759177.1745 1182651.912 485204.468 478266.9483 663046.5098 0.951070544 1.176436379 1.326780891 0.803625117 1.14498329 1.78366358 0.731780442 0.721317345 1 19.33875055 VGGSS(ph)VDLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VGGSSVDLHR 10 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 VGGS(0.009)S(0.991)VDLHR;VGGS(0.046)S(0.954)VDLHR 126.76 0.00024085 526340000 282110 272820 150679 175202 272920 297380 231150 282990 259680 TRUE FALSE 244828.4487 271027.8275 223547.8684 214984.2919 267489.426 308820.401 208733.1086 222474.7907 228980.9262 1.06920892 1.183626217 0.97627288 0.938874235 1.168173395 1.348673036 0.911574217 0.971586561 1 17.8048679 VGGSSVDLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VGGSSVDLHR 10 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 0 ;;; 166.34 5.58E-06 1127090000 1998150 1806920 797560 1459430 1907470 2242920 1457750 1873420 1812320 FALSE TRUE 1734089.415 1795050.224 1183262.684 1790815.887 1869515.079 2329206.584 1316377.629 1472803.712 1598069.594 1.08511508 1.123261609 0.740432512 1.120611952 1.169858363 1.457512609 0.823729851 0.921614251 1 20.60789881 VGGTNPNGGS(ph)FEEVLSSTAHASAQSLAGGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VGGTNPNGGSFEEVLSSTAHASAQSLAGGSR 31 0 Q16890-5;E9PPQ1;J3KNE7;Q16890 Q16890-5 TPD52L1 Tumor protein D53 1 VGGTNPNGGS(1)FEEVLSSTAHASAQSLAGGSR;VGGTNPNGGS(1)FEEVLSSTAHASAQSLAGGSR 292.54 1.97E-81 337160000 148845 85481 21627.7 47408 95219 72501 105830 90604 86849 TRUE FALSE 129174.7561 84919.46968 32086.92806 58172.71099 93324.32819 75290.16038 95566.62289 71229.03968 76581.81016 1.686755064 1.108872584 0.418988896 0.759615252 1.218622647 0.983133726 1.247902376 0.930103892 1 16.22471414 3.221241709 24.9930745 1.065976667 0.960753928 0.010501185 0.328135822 1321.852219 1907572.332 0.103588267 0.117726605 1664.338689 -3.221241709 -0.10522274 VGGVS(ph)PEEHPAPEVSTPFPPLPPEPEGGGEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VGGVSPEEHPAPEVSTPFPPLPPEPEGGGEEK 32 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 VGGVS(1)PEEHPAPEVSTPFPPLPPEPEGGGEEK;VGGVS(1)PEEHPAPEVSTPFPPLPPEPEGGGEEK 97.003 3.97E-05 2751791000 114035 92221 94745 101900 111618 80862 129941 144426 170181 TRUE FALSE 98964.98582 91615.19418 140563.9989 125037.9524 109397.0202 83972.81346 117339.3418 113541.6238 150062.3961 0.659492241 0.610514003 0.936703682 0.833239744 0.729010219 0.559585983 0.781937014 0.756629421 1 17.19520297 1.132369419 2.4733396 1.127990742 0.731571914 0.377177091 0.107879621 0.985967866 5.035125745 0.9491241 0.029663203 13.56342651 -1.132369419 -0.396418827 VGHFDPVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VGHFDPVTR 9 0 Q9UNE7;Q9UNE7-2;H3BTA3 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ; 155.42 7.34E-05 1326660000 550930 499960 348810 370540 491270 497090 477750 527630 522810 FALSE TRUE 478123.2046 496675.7298 517495.6827 454676.7703 481494.6882 516213.374 431417.8785 414800.4305 461003.9974 1.037134618 1.077378358 1.122540554 0.986275115 1.044447968 1.119758998 0.935822424 0.899776212 1 18.81441973 2.221952883 24.99940434 0.935345575 1.063329487 0.593578026 0.046324073 151.9247921 228688.7603 0.018728407 0.012666473 166.7066343 -2.221952883 0.127983911 VGHSELVGEIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VGHSELVGEIIR 12 0 P38606;P38606-2;C9JVW8;C9JA17 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ;;; 207.88 7.34E-08 1428800000 1288660 1152280 796480 963120 1149550 1155110 1203590 1325950 1308950 FALSE TRUE 1118360.316 1144710.597 1181660.392 1181811.116 1126676.204 1199547.829 1086866.027 1042405.911 1154207.422 0.968942232 0.991771994 1.023785127 1.023915714 0.976147079 1.03928272 0.941655725 0.903135685 1 20.13847108 2.18012251 10.31666743 0.93842418 1.003938678 0.390577483 0.032030592 0.375841954 64.00240056 0.012723014 0.008581733 151.3988269 -2.18012251 0.065514497 VGIDT(ph)PDIDIHGPEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VGIDTPDIDIHGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VGIDT(1)PDIDIHGPEGK 107.5 0.0041334 285390000 487090 624970 255330 304080 483190 518360 364700 400120 480590 TRUE FALSE 422719.8224 620864.5309 378808.442 373126.0116 473575.4643 538301.6446 329331.4501 314557.4517 423775.1977 0.997509587 1.465079916 0.893890072 0.880481004 1.117515765 1.270252831 0.777137152 0.742274332 1 18.69293963 2.221533504 24.96331456 0.816873974 1.101416113 0.312120199 0.183899645 272.0397092 398832.113 0.075724014 0.051198838 166.5457304 -2.221533504 0.284542139 VGIGAFPTEQDNEIGELLQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VGIGAFPTEQDNEIGELLQTR 21 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 140.27 3.88E-07 23633000 30283 29185 21164 27040 27003 30585 29940 34049 31726 FALSE TRUE 26281.02482 28993.28181 31398.98119 33179.84528 26465.69313 31761.62474 27036.42341 26767.88632 27975.38842 0.939433777 1.036385318 1.122378739 1.186036983 0.946034876 1.135341689 0.966436033 0.956836985 1 14.77187054 2.205416009 24.72990519 0.970427345 1.063075923 0.214208432 0.077911732 244.5004677 182425.2113 0.031537509 0.021264145 160.4781869 -2.205416009 0.092648578 VGIIAWHPTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VGIIAWHPTAR 11 0 Q9BR76;A0A087WW53;F5H390 Q9BR76 CORO1B Coronin-1B;Coronin 0 ; 150.15 3.40E-05 4024200000 3737100 3744500 1682890 2679900 3945300 3618600 3208400 4128100 4443300 FALSE TRUE 3243232.766 3719902.133 2496741.233 3288412.255 3866796.249 3757809.884 2897249.862 3245337.94 3918018.136 0.827773801 0.949434639 0.637245961 0.839305011 0.986926582 0.959109875 0.739468211 0.828311107 1 21.90169264 3.471116052 24.99227834 0.886671314 0.805779063 0.144294952 0.106843926 366.3782579 1524774.592 0.031782642 0.041150201 2958.803013 -3.471116052 -0.080892251 VGKPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VGKPYR 6 1 Q9NUY8-2;Q9NUY8;E9PGE5 Q9NUY8-2 TBC1D23 TBC1 domain family member 23 0 81.672 0.055869 223480000 323070 301320 181730 248990 309090 367680 300330 344740 311000 FALSE TRUE 280375.4809 299340.6091 269615.2359 305526.9851 302939.7137 381824.8875 271204.0428 271020.0338 274233.9343 1.022395283 1.091552035 0.983157816 1.11411079 1.104676248 1.392332749 0.988951435 0.988280442 1 18.06504758 VGLSPDSPAGDRNS(ph)VGSEGSVGSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VGLSPDSPAGDRNSVGSEGSVGSIR 25 1 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 VGLSPDSPAGDRNS(0.999)VGSEGSVGSIR 226.4 3.89E-34 280230000 268060 246310 160280 191910 235360 248090 247350 263780 255410 TRUE FALSE 232635.1918 244691.9734 237791.9441 235486.0987 230676.7965 257634.1828 223362.0351 207372.6997 225215.7208 1.032943842 1.086478211 1.055840788 1.045602402 1.024248199 1.143944046 0.991769288 0.920773643 1 17.78094801 2.011732257 24.73637501 0.955190888 1.063127328 0.583100992 0.038081572 110.8947629 233810.3816 0.01457284 0.009816166 102.7382719 -2.011732257 0.107936439 VGLVEDSPSTAGDGDDSPVVSLTVPS(ph)TSPPSSSGLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VGLVEDSPSTAGDGDDSPVVSLTVPSTSPPSSSGLSR 37 0 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 VGLVEDSPSTAGDGDDSPVVSLT(0.007)VPS(0.28)T(0.28)S(0.209)PPS(0.056)S(0.056)S(0.056)GLS(0.056)R 96.707 0.00018525 77713000 41423 39145 31288 40762 48748 56797 51885 68035 59543 TRUE FALSE 35948.8456 38887.85392 46418.98145 50017.63511 47778.01017 58982.01734 46853.20069 53486.2447 52503.89437 0.684689127 0.740666085 0.884105494 0.952646193 0.909989835 1.123383666 0.892375723 1.018710047 1 15.68013682 4.235749314 1.064675644 0.994670822 0.62990036 0.769044238 0.061556338 0.381882676 0.614220946 0.019357404 0.13202346 17208.74954 -4.235749314 -0.364770462 VGLVEDSPSTAGDGDDSPVVSLTVPSTS(ph)PPSSSGLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VGLVEDSPSTAGDGDDSPVVSLTVPSTSPPSSSGLSR 37 0 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 VGLVEDSPSTAGDGDDSPVVSLT(0.003)VPS(0.313)T(0.313)S(0.355)PPS(0.012)S(0.002)S(0.001)GLS(0.001)R;VGLVEDSPSTAGDGDDSPVVSLT(0.006)VPS(0.132)T(0.132)S(0.658)PPS(0.027)S(0.037)S(0.008)GLS(0.002)R 144.45 2.69E-13 226860000 111338 103278 78085 99184 139783 146636 143095 162672 168384 TRUE FALSE 96624.40121 102599.56 115847.1672 121705.2431 137001.5918 152277.1818 129217.6689 127885.8587 148477.8353 0.6507665 0.691009266 0.780232059 0.819686271 0.922707362 1.025588644 0.870282548 0.861312791 1 17.17988806 3.859699863 1.246306167 0.926152282 0.651259077 0.801669362 0.053487751 0.248326423 0.716038879 0.019239646 0.058589347 7239.354812 -3.859699863 -0.274893205 VGMVETNSQDRPVDDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VGMVETNSQDRPVDDVK 17 1 Q9Y3C6 Q9Y3C6 PPIL1 Peptidyl-prolyl cis-trans isomerase-like 1 0 209.25 4.05E-12 227880000 240350 197670 134790 168040 179510 145290 216500 267640 237220 FALSE TRUE 208587.1385 196371.4928 199974.8948 206196.0503 175938.1022 150879.4003 195503.8633 210407.2688 209176.1218 0.997184271 0.938785417 0.956012059 0.98575329 0.841100316 0.721303173 0.934637575 1.005885695 1 17.67435865 1.819414152 4.732273339 1.001824188 0.905251311 0.192008767 0.079557241 0.364943077 13.35116855 0.048596188 0.023240955 65.98027973 -1.819414152 -0.096572877 VGNES(ph)PVQELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VGNESPVQELK 11 0 Q5JSH3-2;Q5JSH3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 VGNES(1)PVQELK;VGNES(1)PVQELK;VGNES(1)PVQELK;VGNES(1)PVQELK;VGNES(1)PVQELK;VGNES(1)PVQELK 313.8 1.11E-45 3227250000 6725060 5572020 4634620 4918870 5304730 4168370 6852160 7459160 7316670 TRUE FALSE 5836326.282 5535417.034 6875937.734 6035774.614 5199176.252 4328729.891 6187638.578 5864076.681 6451701.608 0.904618136 0.857977844 1.065755695 0.935532202 0.805861239 0.670943908 0.959070793 0.908919389 1 22.62124828 5.135270669 17.68224773 0.898934636 2.307631376 0 0.108227536 10117.93523 1332831.968 0.026597726 4474.147885 136543.3862 -5.135270669 1.40869674 VGNPWDPNVLYGPLHTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VGNPWDPNVLYGPLHTK 17 0 P49419;P49419-2;A0A1B0GW77;A0A1B0GW82;A0A1B0GTG2;A0A1B0GUA1;A0A1B0GV49;A0A1B0GTJ4 P49419 ALDH7A1 Alpha-aminoadipic semialdehyde dehydrogenase 0 197.45 1.51E-11 466880000 1254400 1068500 855480 929660 1076600 1030100 1189800 1387100 1379700 FALSE TRUE 1088627.862 1061480.953 1269192.989 1140753.512 1055177.766 1069728.614 1074413.379 1090479.459 1216593.438 0.894816483 0.872502613 1.04323511 0.937662062 0.867321599 0.87928192 0.883132644 0.896338436 1 20.2144157 3.376356314 11.43316231 0.901180675 0.940398569 0.068533148 0.056768075 1.032041368 109.3834668 0.016614225 0.021448852 2378.791148 -3.376356314 0.039217895 VGPAT(ph)PSAQVGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VGPATPSAQVGK 12 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 VGPAT(0.994)PS(0.006)AQVGK 151.44 0.0007709 262030000 798340 727130 527760 567690 591310 543760 704990 865710 1034500 TRUE FALSE 692837.3463 722353.4352 782986.5013 696592.6911 579544.0879 564678.7991 636620.1783 680584.6535 912202.5885 0.759521355 0.7918783 0.85834716 0.763638143 0.63532388 0.619027841 0.697893414 0.746089369 1 19.79899474 1.239540215 5.509811705 1.012811728 0.731769597 0.585879824 0.070382592 0.122547854 11.6095652 0.130603433 0.019907001 17.35962004 -1.239540215 -0.281042131 VGPATPS(ph)AQVGK ddPTM_MDA-MB-175_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(0.123)PS(0.877)AQVGK;VGPAT(0.241)PS(0.759)AQVGK 130.47 0.00022651 285095000 980030 806280 644500 725960 699080 635020 879250 993630 1242650 TRUE FALSE 850516.5524 800983.4936 956182.3557 890800.3136 685169.6757 659449.6303 793980.4703 781149.9569 1095745.333 0.77619911 0.73099421 0.872631922 0.812962909 0.625300109 0.60182746 0.724603105 0.712893711 1 20.0634811 1.23630353 24.99558865 1.000000349 0.73038122 0.527615623 0.079625492 53.92085833 596991.8857 0.136827061 0.02115388 17.23072415 -1.23630353 -0.269619129 VGPCSS(ph)PPAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VGPCSSPPAAR 11 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1 Q8TDM6-4 DLG5 Disks large homolog 5 1 VGPCS(0.212)S(0.788)PPAAR;VGPCS(0.265)S(0.735)PPAAR 121.68 0.00042648 860410000 751410 685980 488510 623510 732400 738530 758780 866280 772460 TRUE FALSE 652109.2647 681473.7522 724755.07 765087.4753 717826.6729 766941.727 685193.6324 681032.7634 681140.6588 0.957378269 1.000489023 1.064031431 1.123244466 1.053859674 1.12596674 1.005950274 0.999841596 1 19.37759323 4.451500055 3.529725057 1.050885714 0.962798828 0.337748948 0.045191162 0.299604707 7.612105939 0.012842414 0.048238249 28281.34467 -4.451500055 -0.088086886 VGPDTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VGPDTER 7 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 88.643 0.042939 69518000 204050 195580 106700 126400 143450 150520 171930 187430 171360 FALSE TRUE 177084.2755 194295.2221 158300.4769 155101.0519 140595.6257 156310.6018 155256.2551 147349.5531 151102.016 1.171951773 1.285854598 1.047639741 1.026465801 0.930468232 1.034470657 1.027492943 0.97516603 1 17.20516338 4.12234484 4.766697447 0.999665042 1.227459849 0.838970366 0.040993615 0.068814227 2.537971461 0.010184739 0.022481481 13253.93511 -4.12234484 0.227794806 VGPGNHGTEGSGGERHS(ph)DTDSDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VGPGNHGTEGSGGERHSDTDSDRR 24 2 Q99442 Q99442 SEC62 Translocation protein SEC62 1 VGPGNHGTEGSGGERHS(1)DTDSDRR;VGPGNHGTEGSGGERHS(1)DTDSDRR;VGPGNHGTEGS(0.007)GGERHS(0.993)DTDSDRR;VGPGNHGT(0.015)EGS(0.185)GGERHS(0.799)DT(0.001)DSDRR 292.26 3.64E-62 1315970000 306030 310472 187898 366695 460394 402736 253965 538512 514406 TRUE FALSE 265587.3601 308432.489 278766.1013 449958.7043 451233.0601 418229.5145 229335.5134 423355.3995 453593.5087 0.585518432 0.679975536 0.61457251 0.991986648 0.994796115 0.922035934 0.505596992 0.933336548 1 18.79104047 3.753366406 24.66166121 0.8771594 0.632017462 0.421907336 0.145338067 752.5839622 1253557.375 0.040351889 0.069498012 5667.172163 -3.753366406 -0.245141938 VGPPVSLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VGPPVSLER 9 0 P08151-3;P08151-2;P08151 P08151-3 GLI1 Zinc finger protein GLI1 0 67.993 0.05933 401350000 433850 477180 378720 364640 445740 486790 478640 497390 561960 FALSE TRUE 376515.6233 474045.3732 561870.2587 447437.0852 436870.6461 505517.1263 432221.5665 391027.0192 495525.729 0.759830623 0.956651381 1.133887154 0.902954295 0.881630601 1.020163226 0.872248485 0.789115471 1 18.91860044 2.078758342 12.81938401 0.864858654 0.947264959 0.041472691 0.108337615 1.634843127 260.4602004 0.044141147 0.029758368 119.8832041 -2.078758342 0.082406305 VGQEIEVRPGIVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VGQEIEVRPGIVSK 14 1 P41091 P41091 EIF2S3 Eukaryotic translation initiation factor 2 subunit 3 0 ; 79.346 0.011763 487920000 556560 540220 385277 463070 535780 439440 557010 673080 586850 FALSE TRUE 483009.1859 536671.2592 571598.2459 568217.1211 525119.0262 456345.5412 502991.2559 529147.0799 517473.2615 0.933399311 1.037099497 1.104594746 1.098060834 1.014775188 0.881872698 0.972014002 1.022559269 1 18.98112479 2.996835898 24.98665799 0.974466942 1.048374596 0.262294383 0.058233621 188.1563961 1485876.766 0.018856169 0.020973239 992.7408624 -2.996835898 0.073907654 VGQGYPHDPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VGQGYPHDPPK 11 0 P61081;M0QYI6 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 89.403 0.012258 147380000 622370 472630 384250 401810 477870 424110 553900 613570 583180 FALSE TRUE 540122.2276 469525.2624 570074.5852 493047.1018 468361.3219 440425.7861 500182.8633 482362.8303 514237.1248 1.0503369 0.913052053 1.108583099 0.958793284 0.910788621 0.856464391 0.972669687 0.938016349 1 18.97207424 3.492667937 24.35870939 0.934723121 1.016362055 0.307856872 0.06031502 625.0026617 979259.6045 0.016128823 0.023090943 3109.338018 -3.492667937 0.081638935 VGQTIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VGQTIER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 93.561 0.034535 691570000 818730 655490 469270 572140 629930 592480 721680 873190 779510 FALSE TRUE 710532.7561 651184.043 696210.5416 702053.1316 617395.6254 615273.089 651691.5847 686465.1137 687357.2158 1.033716879 0.947373546 1.01288024 1.021380318 0.898216548 0.895128581 0.948111942 0.998702127 1 19.39070053 4.748972989 23.54565954 0.965997151 1.033716967 0.189849149 0.044440239 1288.437224 2913428.988 0.011745715 0.15286425 56101.30826 -4.748972989 0.067719816 VGRLS(ph)PCVPAKPPLAEFEEGLLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VGRLSPCVPAKPPLAEFEEGLLDR 24 2 Q15742 Q15742 NAB2 NGFI-A-binding protein 2 1 VGRLS(1)PCVPAKPPLAEFEEGLLDR 104.9 0.0015483 48071000 55449 45544 26109 35772 36009 34697 42271 53152 46971 TRUE FALSE 48121.27416 45244.81847 38735.39973 43894.57934 35292.49135 36031.81604 38171.56493 41785.85843 41418.14189 1.161840487 1.092391315 0.935227849 1.059791129 0.852102237 0.869952499 0.921614616 1.008878152 1 15.33797521 4.470782334 1.564703894 0.946642321 1.197513455 0.576118184 0.063804301 0.496778888 1.692511953 0.018908986 0.164544801 29565.30302 -4.470782334 0.250871135 VGRPSNIGQAQPIIDQLAEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 133.1 8.74E-06 219660000 141200 119530 80419 88904 122940 117820 112030 157060 142600 FALSE TRUE 122540.0622 118744.7996 119309.8974 109091.012 120493.7345 122352.6116 101165.3478 123473.9412 125741.9905 0.974535728 0.94435279 0.948846896 0.867578218 0.958261708 0.973044972 0.804547053 0.981962675 1 16.94010698 1.538153587 11.27866489 0.995119022 0.924863753 0.221742565 0.052326219 0.156658394 25.5212013 0.033239512 0.012594259 34.52658201 -1.538153587 -0.070255269 VGRPTASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VGRPTASK 8 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ;; 102.62 0.004496 7132330000 6461720 6043050 4127340 5016220 5230850 4804350 6686350 7545380 7673550 FALSE TRUE 5607787.33 6003352.807 6123335.429 6155229.419 5126766.319 4989176.453 6037908.806 5931859.205 6766391.661 0.828770726 0.887231054 0.904963197 0.909676786 0.757680988 0.737346684 0.89233806 0.876665068 1 22.68995526 1.104556475 1.731632715 1.100794753 0.84433687 0.404707728 0.058821878 1.598927726 3.332737136 0.769694684 0.017763128 12.72203175 -1.104556475 -0.256457883 VGS(ph)LDNVGHLPAGGAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VGSLDNVGHLPAGGAVK 17 0 E7EVA0;P27816-4;H0Y2V1;F8W9U4;H7C4C5;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 VGS(1)LDNVGHLPAGGAVK;VGS(1)LDNVGHLPAGGAVK;VGS(1)LDNVGHLPAGGAVK;VGS(1)LDNVGHLPAGGAVK;VGS(1)LDNVGHLPAGGAVK;VGS(1)LDNVGHLPAGGAVK 175.28 8.04E-10 5406870000 11418850 5999720 6734300 5432650 6555920 5726090 9270010 8140230 8721690 TRUE FALSE 9909820.041 5960307.444 9991030.005 6666216.215 6425470.018 5946376.388 8371005.857 6399505.162 7690621.744 1.288559023 0.775009829 1.299118633 0.866798087 0.83549422 0.773198395 1.088469325 0.832118049 1 22.87466881 3.668878813 24.99996008 0.89624674 1.086312451 0.270723371 0.168201396 222.3547228 79774.34698 0.0423494 0.062814319 4665.291801 -3.668878813 0.190065711 VGS(ph)PLTLTDAQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VGSPLTLTDAQTR 13 0 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 VGS(1)PLTLTDAQTR;VGS(1)PLTLTDAQTR 165.49 3.70E-05 206010000 328680 293910 208960 263240 394250 357090 247090 362910 279190 TRUE FALSE 285244.1052 291979.2859 310013.7549 323012.6654 386405.1963 370827.4834 223127.2498 285304.5207 246184.4763 1.15866 1.186018267 1.259274182 1.312075685 1.5695758 1.506299215 0.906341672 1.158905407 1 17.90938027 2.234270722 24.99996479 1.045514637 1.331938791 0.517118869 0.140698374 101.4685913 591313.3325 0.061239597 0.042932925 171.5026052 -2.234270722 0.286424153 VGS(ph)TENIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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(0.988)T(0.012)ENIK;VGS(0.5)T(0.5)ENIK;VGS(0.5)T(0.5)ENIK;VGS(0.5)T(0.5)ENIK 158.47 0.00038265 2515810000 4309930 2324400 2819880 2389650 2389310 2303430 3228370 2897730 4492000 TRUE FALSE 3740361.831 2309130.863 4183583.4 2932256.556 2341767.406 2392044.443 2915283.174 2278072.99 3960960.877 0.944306684 0.582972399 1.056204171 0.740289199 0.59121195 0.603905092 0.736004031 0.575131404 1 21.91741902 4.7678511 22.75465411 0.724706254 0.944307827 0.126265417 0.170268667 6486.597557 5038903.554 0.040436432 3.478318124 58593.72382 -4.7678511 0.219601573 VGSEIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VGSEIER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;; 143.56 0.0056153 3295180000 4987020 4115860 2785080 3199230 3965400 3987960 3994800 4829510 4507230 FALSE TRUE 4327972.672 4088822.645 4131954.004 3925664.069 3886496.298 4141379.402 3607384.911 3796756.87 3974390.404 1.088965157 1.028792401 1.039644721 0.987739922 0.977884884 1.042016254 0.907657413 0.955305464 1 21.92230216 7.91015018 0.297828228 0.950719943 2.049654337 0.537675049 0.034490672 55.71663821 0.935597542 0.069192823 31.59381944 81311164.33 -7.91015018 1.098934394 VGSGS(ph)LDNLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VGSGSLDNLGR 11 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 VGS(0.004)GS(0.996)LDNLGR;VGS(0.059)GS(0.941)LDNLGR 118.73 0.00086194 1441600000 1931170 1792910 1154910 1400330 1763650 1633950 1662750 1746170 1785970 TRUE FALSE 1675960.992 1781132.256 1713428.339 1718296.329 1728556.816 1696809.114 1501496.761 1372765.134 1574834.661 1.064213935 1.130996352 1.088005224 1.091096336 1.097611615 1.077452228 0.953431365 0.871688418 1 20.58676894 2.218197186 3.748771069 0.92295658 1.095164 0.803757193 0.034913585 0.077670959 2.354523703 0.014157049 0.009556554 165.271202 -2.218197186 0.17220742 VGSLT(ph)PPSS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VGSLTPPSSPK 11 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 2 VGS(0.001)LT(0.999)PPS(0.26)S(0.74)PK;VGS(0.002)LT(0.998)PPS(0.388)S(0.612)PK;VGSLT(1)PPS(0.115)S(0.885)PK;VGSLT(1)PPS(0.429)S(0.571)PK;VGSLT(1)PPS(0.394)S(0.606)PK;VGS(0.001)LT(0.999)PPS(0.291)S(0.709)PK 187.45 1.90E-05 3380650000 4678160 3883800 3030030 3290930 4643230 3479550 5091420 5594350 5051950 TRUE FALSE 4059929.303 3858287.062 4495362.643 4038185.955 4550838.807 3613410.54 4597654.872 4398041.788 4454714.226 0.911378171 0.86611326 1.009124809 0.906497196 1.02157817 0.811143063 1.032087501 0.987278098 1 22.08690145 -2 0.221143294 1.514467387 0.897996793 0.150219018 0.067982216 166.0787876 2.569813413 35.43772124 0.304158235 0.01 2 -0.616470593 VGSLYPEMSAHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VGSLYPEMSAHER 13 0 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 66.215 0.056474 200860000 159720 136190 77798 123900 165770 157380 156860 177760 165630 FALSE TRUE 138612.5973 135295.3589 115421.373 152033.3887 162471.5013 163434.5104 141647.7413 139747.4073 146049.4101 0.949080159 0.926367035 0.790289895 1.040972289 1.112442024 1.119035745 0.969861783 0.956850201 1 17.15609701 3.711012427 24.8441129 1.028161767 0.892357818 0.512541718 0.066327958 622.5611741 561451.6848 0.020449359 0.030339469 5140.583603 -3.711012427 -0.135803949 VGTEGLVDS(ph)FSQGLER ddPTM_MDA-MB-175_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(0.993)FS(0.007)QGLER;VGTEGLVDS(0.995)FS(0.005)QGLER;VGTEGLVDS(0.999)FS(0.001)QGLER;VGTEGLVDS(0.999)FS(0.001)QGLER 267.39 2.70E-27 255976000 314213 273591 188595 195652 218839 206457 225599 275045 283146 TRUE FALSE 272688.9559 271793.7627 279800.1728 240077.777 214484.5321 214399.5344 203720.4437 216228.7672 249672.8024 1.092185265 1.0885998 1.12066741 0.961569601 0.859062461 0.858722025 0.815949682 0.866048544 1 17.92967915 3.541314159 3.051765576 0.872896222 1.099364452 0.810919569 0.048376014 0.104635222 1.912717768 0.014449189 0.021864126 3477.876523 -3.541314159 0.22646823 VGVAYFFS(ph)DDEEDLDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VGVAYFFSDDEEDLDER 17 0 Q96KN4;Q96KN4-2 Q96KN4 FAM84A Protein FAM84A 1 VGVAYFFS(1)DDEEDLDER;VGVAYFFS(1)DDEEDLDER 131.56 2.28E-05 0 16884.8 18840.6 15827.1 16107.6 18790.8 23521 23186.6 27628 18845.9 TRUE FALSE 14653.4309 18716.83486 23481.1385 19765.07677 18416.89984 24425.86809 20937.9671 21719.9672 16617.95917 0.88178282 1.126301651 1.412997725 1.189380511 1.108252804 1.469847641 1.259960196 1.307017726 1 14.0204556 4.619468943 3.412611038 1.256719033 0.873831937 0.419937589 0.136298732 0.237931117 4.483180484 0.032559597 0.191413888 41635.99457 -4.619468943 -0.382887096 VGVEASEETPQTSSSSARPGT(ph)PSDHQSQEASQFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VGVEASEETPQTSSSSARPGTPSDHQSQEASQFER 35 1 Q6Y7W6;I1E4Y6;Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 VGVEASEETPQTSSSSARPGT(0.976)PS(0.024)DHQSQEASQFER;VGVEASEETPQTSSSSARPGT(0.982)PS(0.018)DHQSQEASQFER;VGVEASEETPQTSSSSARPGT(0.864)PS(0.135)DHQSQEASQFER 303.67 1.84E-90 5072260000 1530893 1717388 482681 1104258 1759380 2017340 1740090 1865560 1573355 TRUE FALSE 1328581.611 1706106.365 716107.1461 1354996.656 1724371.78 2094948.375 1571336.34 1466624.512 1387354.764 0.957636536 1.229754933 0.516167288 0.9766764 1.242920574 1.510030764 1.132613215 1.05713733 1 20.40390532 3.350357575 5.561527984 1.182945284 0.905667695 0.278391107 0.216777443 0.297813089 13.39559818 0.065475302 0.084762346 2240.565143 -3.350357575 -0.277277588 VGVEASEETPQTSSSSARPGTPS(ph)DHQSQEASQFER ddPTM_MDA-MB-175_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(0.214)PS(0.786)DHQSQEASQFER 296.42 2.11E-90 637240000 356610 419640 146270 272860 485880 493650 455090 485610 440380 TRUE FALSE 309483.085 416883.3572 217006.6612 334817.0334 476211.9386 512641.0349 410955.4418 381766.0805 388318.7781 0.796982022 1.073559613 0.558836383 0.862222103 1.226342803 1.320155151 1.058294023 0.983125468 1 18.56688195 3.34206335 6.610405136 1.105683228 0.816799218 0.465419507 0.157199323 0.214333862 11.99764112 0.047684915 0.061603872 2198.180494 -3.34206335 -0.288884009 VGVNGFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VGVNGFGR 8 0 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;; 170.44 0.00068668 41135290000 8051530 7544470 4542370 5620230 7108160 7114210 7249960 7608780 6949120 FALSE TRUE 6987499.911 7494909.88 6739075.325 6896389.121 6966721.523 7387898.262 6546859.995 5981701.609 6127602.95 1.140331704 1.223138957 1.099789817 1.125462791 1.136940755 1.205675094 1.068421053 0.976189492 1 22.54689139 1.993705999 4.011917879 0.99237129 1.153433338 0.77903798 0.036965055 0.092704807 3.377204744 0.0187272 0.010262656 98.56120368 -1.993705999 0.161062048 VGWEQLLTTIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VGWEQLLTTIAR 12 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144;P12814-3;P12814;P12814-2;P12814-4;H9KV75;H7C5W8;H0YJ11;H0YJW3 O43707;P12814-3 ACTN4;ACTN1 Alpha-actinin-4;Alpha-actinin-1 0 ; 155.97 0.00016933 453290000 226043 191941 148884 219420 184605 185507 171106 211906 386690 FALSE TRUE 196170.8448 190680.1269 220884.8004 269242.6646 180931.7217 192643.5743 154512.1665 166591.551 340975.9487 0.575321648 0.5592187 0.647801703 0.789623625 0.530628985 0.564977017 0.453146819 0.488572732 1 18.37931045 1.231609603 24.9995119 1.000000734 0.572896964 0.677197859 0.09193849 161.7937455 581843.0481 0.241485397 0.024853158 17.04549444 -1.231609603 -0.42710377 VGWSVDFSRPQLGEDEFSYGFDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VGWSVDFSRPQLGEDEFSYGFDGR 24 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;; 219.07 1.02E-32 1285510000 1222990 924023 650017 749633 943259 1049289 951643 1044824 906932 FALSE TRUE 1061368.773 917953.0321 964367.3954 919848.6301 924489.9914 1089655.827 859352.8083 821396.5184 799715.5321 1.327182892 1.147849448 1.20588804 1.150219788 1.156023554 1.362554287 1.074573112 1.027110873 1 19.60912738 2.0190173 24.19602138 1.026096925 1.214427666 0.61130408 0.072553881 104.2136226 132591.9935 0.028631825 0.019299594 104.4761836 -2.0190173 0.188330742 VGYELKDEIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VGYELKDEIER 11 1 Q8WWY3-4;Q8WWY3;Q8WWY3-3;Q8WWY3-2 Q8WWY3-4 PRPF31 U4/U6 small nuclear ribonucleoprotein Prp31 0 72.496 0.042076 192650000 501810 440550 306210 363120 408720 388350 452710 558210 430590 FALSE TRUE 435494.5371 437655.998 454294.1802 445571.9459 400587.2716 403290.0758 408806.2539 438841.1355 379686.1407 1.146985603 1.15267836 1.196499244 1.173527022 1.055048443 1.062166965 1.076695223 1.155799721 1 18.53444781 3.246907933 24.99952482 1.080792007 1.168446327 0.582636623 0.040417114 150.7982517 451625.8375 0.012131951 0.01539239 1765.663474 -3.246907933 0.08765432 VGYTPDWIFLLR ddPTM_MDA-MB-175_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 ; 137.95 0.00019319 4017900000 1491890 1249640 1082570 1154360 1285680 1361850 1338990 1558840 1947730 FALSE TRUE 1294732.957 1241431.033 1606104.473 1416475.081 1260097.483 1414241.251 1209134.956 1225494.197 1717471.578 0.753859902 0.72282479 0.935156362 0.824744409 0.733693354 0.823443758 0.704020358 0.713545547 1 20.71185479 1.228821861 24.99622247 1.000000451 0.775002406 0.501467395 0.070048778 365.5782831 938253.7106 0.231751806 0.018001599 16.93642961 -1.228821861 -0.224998045 VHAELADVLTEAVVDSILAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VHAELADVLTEAVVDSILAIK 21 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 89.261 0.0023359 660820000 118710 101410 83385 113170 97796 88150 132860 134640 168570 FALSE TRUE 103022.1727 100743.831 123710.2649 138866.9782 95850.05093 91541.18754 119975.2576 105848.2838 148641.8466 0.693089968 0.677762241 0.832270775 0.934238785 0.644838941 0.615850715 0.807143213 0.712102858 1 17.1814808 1.234550811 24.96976651 1.00000038 0.741741337 0.423076244 0.095513529 124.1868787 773222.4572 0.178719678 0.024051605 17.16132478 -1.234550811 -0.258259044 VHATSTYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VHATSTYR 8 0 Q9H074;Q9H074-3;Q9H074-2;D6REB4 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 0 ; 91.853 0.012192 348560000 168336 158089 61258 106421 153799 187893 127149 163445 255740 FALSE TRUE 146089.9711 157050.5029 90882.5737 130585.5146 150738.7008 195121.3653 114818.1096 128493.5587 225506.7085 0.647829823 0.69643384 0.403014945 0.579075964 0.668444419 0.865257475 0.50915607 0.569799273 1 17.78281083 3.184717466 4.999345802 0.696192687 0.576788755 0.156474377 0.156929794 0.467693448 24.39586824 0.049006459 0.057083973 1530.091724 -3.184717466 -0.119403931 VHCCLYFIPATGHSLRPLDIEFMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VHCCLYFIPATGHSLRPLDIEFMK 24 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4;K7EL40;K7EK18 Q9UHD8 9-Sep Septin-9 0 ; 165.66 9.01E-12 1033020000 664580 630310 281260 367570 497580 472810 603870 774530 367090 FALSE TRUE 576754.0692 626169.4521 417278.2768 451032.3865 487679.1315 490999.3066 545306.7803 608902.7869 323693.0384 1.781793245 1.934454492 1.289117242 1.393395387 1.506609885 1.516867057 1.684641669 1.881111778 1 18.30426681 4.255070893 24.98273693 1.516494386 1.858124026 0.303370281 0.237250528 341.103473 516136.1428 0.060893828 0.160119335 17991.64582 -4.255070893 0.341629641 VHCLNTLFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VHCLNTLFSR 10 0 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ; 190.57 8.87E-07 1352830000 335180 382780 265890 292270 367210 345790 316920 351150 414470 FALSE TRUE 290885.1138 380265.493 394475.2933 358634.3706 359903.2394 359092.7651 286185.1472 276059.3052 365471.8288 0.79591665 1.040478261 1.079358961 0.981291422 0.984763287 0.982545676 0.783056653 0.755350436 1 18.47940068 2.248490249 24.7938074 0.824593809 0.985407066 0.277509501 0.097227838 185.268431 462606.5933 0.03598843 0.027529584 177.2108257 -2.248490249 0.160813257 VHDAES(ph)S(ph)DEDGYDWGPATDL ddPTM_MDA-MB-175_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 179.14 8.67E-17 218923000 337195 339102 215151 239172 326068 337996 310358 348703 329486 TRUE FALSE 292633.8264 336874.4166 319198.7432 293479.6581 319579.8847 350998.9248 280259.5289 274135.5771 290534.5404 1.007225599 1.159498682 1.098660224 1.010136893 1.099972087 1.208114272 0.964634114 0.943555891 1 18.14835016 2.176262983 17.52029074 0.963796621 1.096320746 0.492507003 0.061096203 3.599458985 1011.309667 0.024497959 0.016516673 150.059323 -2.176262983 0.132524125 VHDRS(ph)EEEEEEEEEEEEEQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VHDRSEEEEEEEEEEEEEQPR 21 1 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2;V9GYQ9 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 VHDRS(1)EEEEEEEEEEEEEQPR;VHDRS(1)EEEEEEEEEEEEEQPR;VHDRS(1)EEEEEEEEEEEEEQPR;VHDRS(1)EEEEEEEEEEEEEQPR;VHDRS(1)EEEEEEEEEEEEEQPR;VHDRS(1)EEEEEEEEEEEEEQPR 412.72 4.61E-152 17005540000 2152508 2111394 1392388 1605846 1864139 1906290 2074540 2081979 2053101 TRUE FALSE 1868048.614 2097524.114 2065751.494 1970477.878 1827046.281 1979626.21 1873351.43 1636763.993 1810385.739 1.031851154 1.158606185 1.141055992 1.08842985 1.009202758 1.0934831 1.034780263 0.904096822 1 20.78786569 2.164778105 0.9218635 0.931925386 1.105520441 0.499192042 0.052457657 0.564310912 0.867252608 0.076854751 0.023425541 146.143029 -2.164778105 0.173595055 VHDRS(ph)EEEEEEEEEEEEEQPRR ddPTM_MDA-MB-175_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 406.83 1.56E-152 1302700000 218170 184781 119641 141606 189521 194915 176885 207780 110316 TRUE FALSE 189338.2817 183567.1614 177499.7878 173759.8066 185749.9029 202413.5062 159730.7199 163347.8639 97274.56815 1.946431481 1.88710333 1.824729641 1.786281964 1.909542303 2.080847132 1.642060437 1.679245326 1 16.56977505 0.947962601 1.345373686 1.75E-18 1.884916206 0.867308911 0.107124074 0.894987247 0.819835665 2.821235116 0.031068579 8.870796188 -0.947962601 1.884916206 VHDYDMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VHDYDMR 7 0 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 0 ; 111.01 0.0066756 272270000 597490 491930 307170 349670 448300 503210 483170 529140 464030 FALSE TRUE 518530.1827 488698.4794 455718.4394 429067.9179 439379.7071 522568.8143 436312.2478 415987.5288 409172.902 1.26726423 1.194356901 1.113755181 1.048622516 1.07382406 1.277134463 1.066327329 1.016654638 1 18.64235108 8 0.031053206 2.32E-14 2.710148017 0.409895396 0.075561762 3176.252913 9.763801198 297.6384804 607.5679098 100000000 -8 2.710148017 VHEIFQVDPETEQEITR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VHEIFQVDPETEQEITR 17 0 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 ;; 173.37 1.49E-09 671340000 357190 348840 201322 259958 301438 324060 301948 332710 314628 FALSE TRUE 309986.4365 346548.4471 298681.9926 318985.4371 295439.9736 336526.7979 272665.1294 261562.5557 277433.0363 1.117337865 1.24912466 1.076591298 1.149774524 1.064905527 1.213001892 0.982814207 0.942795275 1 18.08178007 2.172322006 7.67093472 0.967276411 1.14312799 0.663513923 0.056972524 0.129846029 12.90467364 0.022020474 0.014846695 148.7037793 -2.172322006 0.17585158 VHELNEEIGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VHELNEEIGK 10 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2;B8ZZ09;Q9NQ29-3;Q9NQ29;Q9NQ29-2;A8MYV2;B8ZZ10 Q9Y383;Q9NQ29-3 LUC7L2;LUC7L Putative RNA-binding protein Luc7-like 2;Putative RNA-binding protein Luc7-like 1 0 ;;; 155.11 1.33E-05 3633710000 8442100 6139550 4346170 5246780 5793550 4607450 7034950 8080200 6990710 FALSE TRUE 7326455.095 6099218.892 6447992.349 6438141.591 5678269.69 4784701.583 6352701.632 6352312.11 6164276.228 1.188534521 0.989446071 1.046025861 1.044427821 0.921157567 0.776198439 1.03056732 1.03050413 1 22.55550008 7.99999684 0.896231386 0.971165224 102.9155618 0.402708445 0.080579227 1068.052221 2.388883392 0.028822195 222644.627 99999272.41 -7.99999684 101.9443966 VHEMEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VHEMEK 6 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 164.78 0.0074774 652380000 1618530 1428460 1220400 1344940 1054470 1169500 1678490 1856430 1982560 FALSE TRUE 1404637.16 1419076.352 1810589.522 1650329.183 1033488.11 1214491.422 1515710.298 1459446.891 1748184.015 0.803483585 0.811743123 1.035697333 0.944024867 0.591178103 0.694716009 0.867019882 0.834835966 1 20.73742562 4.447611865 24.97336011 0.845579799 0.805547111 0.017616065 0.132388812 1215.087507 1028310.261 0.035079537 0.092814514 28029.275 -4.447611865 -0.040032688 VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGS(ph)SPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGSSPR 40 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 VHEPPREDAAPTKPAPPAPPPPQNLQPES(0.006)DAPQQPGS(0.507)S(0.487)PR 44.614 0.028203 347760000 141880 116040 77129 93928 109210 97481 128740 133200 105560 TRUE FALSE 123130.1985 115277.7256 114428.8424 115255.788 107036.9347 101231.1571 116254.8146 104716.2166 93080.81705 1.322831088 1.238469206 1.229349355 1.238233523 1.149935487 1.087561974 1.248966418 1.125003195 1 16.50619625 -1.999999991 0.054573606 1.76E-10 1.821797421 0.632261269 0.056897342 685.6772028 3.645205549 112.9647105 32.38626194 0.01 1.999999991 1.821797421 VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGSS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGSSPR 40 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGS(0.035)S(0.965)PR;VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGS(0.168)S(0.832)PR;VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGS(0.08)S(0.92)PR 191.61 7.27E-25 1393960000 789720 638600 429389 504800 618320 570280 673930 798580 650110 TRUE FALSE 685356.5011 634404.9946 637042.9566 619422.5554 606016.6417 592219.0406 608572.3723 627809.8816 573254.7364 1.195553142 1.10667205 1.111273778 1.080536306 1.057150693 1.03308181 1.061608974 1.095167369 1 19.12881684 8 0.524692412 1.052439696 6.352901825 0.755228692 0.025910352 66.66956466 0.676975414 0.015112415 393.3670694 100000000 -8 5.300462128 VHFEESSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VHFEESSK 8 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;;;; 144.09 0.000591 4215220000 4294150 3267930 2938030 4227550 3409420 3006940 3628040 4724130 9577520 FALSE TRUE 3726667.198 3246462.753 4358871.135 5187479.842 3341579.212 3122618.928 3276193.239 3713911.563 8445276.496 0.441272373 0.384411659 0.516131252 0.6142463 0.395674341 0.369747388 0.387932028 0.439761986 1 23.00971323 1.238371679 24.9999631 1.000000312 0.442790104 0.849454756 0.073605716 1.768794689 233421.094 0.108131544 0.019193426 17.31297407 -1.238371679 -0.557210208 VHFEESSKLEDLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VHFEESSKLEDLLR 14 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;;; 225.86 1.57E-12 2863962000 5033220 3980870 2365667 3207200 3919310 3148750 4411740 5159940 2272274 FALSE TRUE 4368067.224 3954719.403 3509711.474 3935443.779 3841323.399 3269884.45 3983890.134 4056526.986 2003648.356 2.1800568 1.973759213 1.751660396 1.96413895 1.91716445 1.63196523 1.988318021 2.024570316 1 20.9341979 1.23474403 24.99985136 0.999998679 1.92352881 0.793981764 0.148688584 50.52711625 330919.8224 0.267703362 0.036595035 17.16896164 -1.23474403 0.92353013 VHFTAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VHFTAER 7 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;; 150.02 0.0019771 5355750000 810653 919608 434922 616087 912064 902987 931957 947031 934180 FALSE TRUE 703523.1521 913567.0345 645251.7339 755978.9697 893915.7108 937725.4942 841575.9536 744515.7905 823742.3046 0.854057329 1.109044697 0.783317465 0.917737216 1.085188542 1.138372388 1.021649548 0.903821239 1 19.65183356 3.266045568 24.31264461 1.018874745 0.920345066 0.235749497 0.100589075 291.4314486 257791.9754 0.030203595 0.038981288 1845.209016 -3.266045568 -0.098529679 VHGEPT(ph)SDLS(ph)DID ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VHGEPTSDLSDID 13 0 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 2 VHGEPT(0.5)S(0.5)DLS(1)DID 141.38 0.00021125 660340000 1134700 1066200 681520 796500 1026600 996310 907430 1065500 976180 TRUE FALSE 984746.52 1059196.062 1011105.352 977357.4987 1006172.669 1034638.69 819427.5783 837651.1167 860777.1125 1.144020334 1.230511414 1.174642468 1.135436206 1.168911968 1.201982111 0.951962554 0.973133584 1 19.71528019 2.23785936 25 0.973675274 1.176182539 0.914638992 0.028928833 4.65288938 165863.3074 0.011339568 0.008160307 172.9256275 -2.23785936 0.202507266 VHGEPTS(ph)DLS(ph)DID ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VHGEPTSDLSDID 13 0 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 2 VHGEPT(0.113)S(0.887)DLS(1)DID 123.75 0.00032138 450420000 173540 153050 117370 121570 144030 140590 139870 155100 143100 TRUE FALSE 150606.2493 152044.6045 174130.5246 149174.3266 141164.0848 145998.5883 126305.4289 121933.072 126182.881 1.193555323 1.204954295 1.379985329 1.182207328 1.118726119 1.157039585 1.000971193 0.966320241 1 16.94515667 2.560425201 0.983283205 0.962542267 1.250345469 0.744990051 0.062064291 0.278750533 0.578506701 0.05271937 0.030736698 363.4337048 -2.560425201 0.287803202 VHGEPTSDLS(ph)DID ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VHGEPTSDLSDID 13 0 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 1 VHGEPT(0.001)S(0.001)DLS(0.997)DID 96.745 0.0042971 57720000 133410 119200 72324 96515 115870 102810 98533 133580 111450 TRUE FALSE 115779.5305 118416.9674 107300.1283 118430.2059 113564.4137 106765.1672 88977.28483 105014.9565 98274.50796 1.178123736 1.204961183 1.091840911 1.205095893 1.155583641 1.086397372 0.905395373 1.068587965 1 16.58452962 2.529469039 3.814499225 1.00244807 1.165969241 0.71024599 0.050865085 0.123259073 3.651793461 0.018100253 0.015122012 338.4301441 -2.529469039 0.163521172 VHHEPQLSDK ddPTM_MDA-MB-175_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 ; 118.4 0.00047974 709280000 575780 445310 364610 475000 451610 476450 531940 490700 458640 FALSE TRUE 499689.2142 442384.7293 540936.6155 582856.0099 442623.8446 494779.3398 480352.5407 385767.6236 404420.1017 1.235569676 1.093874235 1.337561148 1.441214241 1.09446549 1.223429146 1.187756342 0.95387846 1 18.62549518 1.824867781 3.616773437 0.974536875 1.236723742 0.517530987 0.102518288 0.182311815 4.117232839 0.065711668 0.028746924 66.81404745 -1.824867781 0.262186867 VHIDIGADGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VHIDIGADGR 10 0 P31942;P31942-3;P31942-2;P31942-4;P31942-5;P31942-6 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;;;; 157.75 8.62E-06 2025130000 2039180 1686300 973546 1158284 1377770 1483960 1371017 1593000 1728000 FALSE TRUE 1769697.196 1675222.584 1444356.102 1421290.085 1350355.073 1541048.901 1238055.982 1252349.347 1523717.809 1.16143369 1.099430994 0.947915745 0.932777761 0.886223857 1.011374214 0.812523143 0.821903728 1 20.53916431 4.389108176 1.151700856 0.892109567 1.223496316 0.652632552 0.065536448 0.560630341 0.953631542 0.021306979 0.195431056 24496.73344 -4.389108176 0.331386749 VHIEIGPDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 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 ;;;;;;;; 183.78 1.63E-06 29058950000 13116385 12435663 7906998 9725771 11028202 11105360 9833985 11719816 16129869 FALSE TRUE 11383021.49 12353972.31 11730848.68 11934155.95 10808762.36 11532590.39 8880286.648 9213624.552 14223014.26 0.800324128 0.868590306 0.824779366 0.839073612 0.759948781 0.810840106 0.624360384 0.6477969 1 23.76172391 2.990380709 1.741704496 0.735410585 0.836095594 0.044501115 0.104325625 0.706826356 4.36669529 0.039993392 0.043352652 978.0942581 -2.990380709 0.100685009 VHIEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VHIEVK 6 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 85.061 0.055142 117220000 425040 322930 252460 342310 318710 284760 331170 433250 510950 FALSE TRUE 368869.8871 320808.6516 374550.5004 420036.7174 312368.2945 295714.9015 299053.1844 340602.8591 450546.0731 0.81871735 0.712044052 0.831325635 0.932283605 0.693310436 0.65634775 0.663757165 0.755977866 1 18.78131512 1.238879658 11.79038847 1.000373857 0.754544294 0.44415632 0.085014146 0.059580775 424.8674447 0.122961506 0.022193154 17.33323632 -1.238879658 -0.245829564 VHIGQVIMSIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VHIGQVIMSIR 11 0 P27635;X1WI28;A0A087WV22;H7C123;H7C2C5;Q96L21;F8W7C6 P27635;F8W7C6 RPL10;RPL10L 60S ribosomal protein L10;60S ribosomal protein L10-like 0 ; 169.21 1.72E-05 3567400000 1289360 1732760 1151900 1321410 1662530 1794630 1808380 1848360 1835690 FALSE TRUE 1118967.809 1721377.385 1708962.693 1621456.337 1629448.906 1863670.577 1633003.586 1453102.598 1618676.819 0.691285497 1.063447233 1.055777579 1.001717154 1.006654872 1.151354338 1.008850912 0.897710142 1 20.62638354 4.743614347 24.95479842 1.016549763 0.691285358 0.726749047 0.063843917 325.4235563 1606855.843 0.017410519 0.142668246 55413.34243 -4.743614347 -0.325264405 VHLENMGSHDIVDGNHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VHLENMGSHDIVDGNHR 17 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;P11277-3;P11277;P11277-2;Q01082-3;O15020;O15020-2;A4QPE4 Q01082;Q01082-3;O15020 SPTBN1;SPTB;SPTBN2 "Spectrin beta chain, non-erythrocytic 1;Spectrin beta chain, erythrocytic;Spectrin beta chain, non-erythrocytic 2" 0 ;; 254.05 1.74E-27 1540930000 442472 456026 297332 411410 455822 536628 370373 414561 438047 FALSE TRUE 383998.2041 453030.3352 441122.7497 504826.9285 446752.034 557272.4264 334454.2835 325910.3563 386261.5827 0.994140296 1.172858901 1.142031125 1.306956092 1.156604887 1.442733244 0.865875092 0.843755556 1 18.55921867 2.208427398 24.98884001 0.889267928 1.201110258 0.572146441 0.121824599 134.955764 111915.0008 0.04845184 0.032670943 161.5948063 -2.208427398 0.311842331 VHLFDIITQYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VHLFDIITQYR 11 0 B4DYU2;Q96MW5;H3BQV3 B4DYU2 COG8 Conserved oligomeric Golgi complex subunit 8 0 134.13 0.0013342 0 162390 149500 75554 107110 139850 147990 144470 164550 172380 FALSE TRUE 140929.7501 148517.9247 112092.1671 131430.9626 137067.2586 153683.2711 130459.3216 129362.263 152001.4328 0.927160669 0.977082399 0.737441517 0.864669235 0.90174978 1.011064621 0.858276921 0.851059498 1 17.2137254 3.071771893 6.466600333 0.91581518 0.87446503 0.080341591 0.078780519 0.724101856 51.35859456 0.024967869 0.028350061 1179.700853 -3.071771893 -0.04135015 VHLFSYPCCQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VHLFSYPCCQPR 12 0 O95834;O95834-2;O95834-3;K7EIK7 O95834 EML2 Echinoderm microtubule-associated protein-like 2 0 105.03 0.0020739 616700000 1988100 2240300 1203600 1644600 1868100 1575100 2620900 2415200 1733300 FALSE TRUE 1725367.548 2225583.322 1785664.986 2018031.566 1830928.465 1635695.116 2366725.521 1898728.275 1528391.249 1.128878191 1.456160734 1.168329763 1.320363204 1.197944876 1.070207068 1.548507637 1.242305121 1 20.54358247 1.253426439 5.969431201 0.992026804 1.275929214 0.248671992 0.145606718 0.165882795 20.74162413 0.182030154 0.033935101 17.92364934 -1.253426439 0.28390241 VHLSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VHLSQK 6 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;D6RBK5;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 153.67 0.010102 590340000 1875400 2163300 603340 1272420 2170100 2382500 2251500 2569200 2470800 FALSE TRUE 1627561.138 2149089.14 895117.2421 1561342.409 2126919.256 2474156.317 2033149.877 2019796.574 2178704.839 0.747031498 0.986406741 0.410848329 0.716637876 0.976231024 1.135608768 0.933191977 0.927062968 1 21.05503933 3.23420671 7.079180931 0.989113087 0.712150318 0.469306252 0.147506121 0.125312723 33.88753743 0.044380019 0.053357743 1714.773289 -3.23420671 -0.276962769 VHLVGIDIFTGK ddPTM_MDA-MB-175_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 ;; 212.89 1.50E-08 11041410000 15785963 12592583 7865350 10675090 11073295 10234405 14002969 15162742 13801647 FALSE TRUE 13699807.99 12509861.49 11669059.57 13099032.34 10852958.09 10628129.18 12644963.22 11920307.62 12170032.01 1.125700243 1.027923466 0.958835569 1.076335077 0.891777284 0.873303305 1.039024647 0.979480383 1 23.53682963 5.320581695 1.041736275 0.971459329 1.464662709 0.39168706 0.060260328 5.806839076 2.191704856 0.018882144 4.254054077 209209.6415 -5.320581695 0.49320338 VHMFEAHSDYIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VHMFEAHSDYIR 12 0 P35606;P35606-2;D6R997;D6RBT6;D6RBZ7;D6RCL6;D6RBG7 P35606 COPB2 Coatomer subunit beta 0 ;;; 226.04 9.41E-12 1939920000 1236880 1225320 692669 861200 1105960 1073180 988690 1129660 1065570 FALSE TRUE 1073423.174 1217270.792 1027646.045 1056748.623 1083953.56 1114465.929 892806.996 888091 939599.5285 1.142426259 1.295520863 1.093706429 1.124679814 1.153633571 1.186107374 0.950199493 0.945180338 1 19.84168646 2.236907338 24.99987158 0.960349136 1.166171087 0.751066832 0.054495454 20.25614267 306290.5956 0.02149008 0.015355753 172.5469704 -2.236907338 0.205821951 VHMTWVQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VHMTWVQPR 9 0 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ; 176.79 5.29E-05 1577370000 481920 690310 262881 323840 690630 690770 556220 582750 592320 FALSE TRUE 418233.051 685775.3082 390011.1309 397372.8216 676887.8142 717344.3689 502277.87 458133.4475 522296.6044 0.800757745 1.312999745 0.746723466 0.760818313 1.295983563 1.373442528 0.961671713 0.877151878 1 18.9945098 3.252104654 24.9999726 1.076678988 0.923115863 0.162282023 0.21590028 605.6055518 1117837.625 0.067139824 0.086183965 1786.918125 -3.252104654 -0.153563125 VHNDAQSFDYDHDAFLGAEEAK ddPTM_MDA-MB-175_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 ;; 173.43 2.18E-12 1301310000 745960 573500 428860 620610 595210 527960 622270 620730 583400 FALSE TRUE 647379.496 569732.6407 636258.1305 761528.9859 583366.4855 548270.9628 561922.3512 487991.72 514431.1166 1.25843767 1.107500348 1.236818905 1.480332276 1.134003109 1.065781103 1.092317966 0.948604593 1 18.97261838 2.870156575 3.176767462 1.018466216 1.260017913 0.564330258 0.099345112 0.19935147 3.800599082 0.035316164 0.035569361 741.5775525 -2.870156575 0.241551697 VHNGMDDLILDGHNILDGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VHNGMDDLILDGHNILDGLR 20 0 O14653-3;O14653-2;E7EQ34;A0A1W2PS81;A0A1W2PQM3;A0A1W2PQP2;A0A1W2PRC2;I3L4Z6;A0A1W2PPG1;A0A1W2PPP5;A0A1W2PPG5;I3L0K1;A0A1W2PRV0;A0A1W2PRL0;A0A1W2PS12;A0A1W2PNV3;A0A1X7SBU8;A0A1W2PPJ0;O14653;I3NI02;A0A1W2PRE6;A0A1W2PQQ4;A0A1W2PQS3;A0A1W2PP28 O14653-3 GOSR2 Golgi SNAP receptor complex member 2 0 ; 203.77 5.95E-22 105368000 58851 60945 35335 46913 61680 56234 47827 63885 52517 FALSE TRUE 51073.69124 60544.64828 52423.12419 57565.31367 60452.68867 58397.35837 43188.7449 50223.6899 46308.50009 1.102901004 1.307419765 1.132041074 1.243083096 1.305433961 1.261050525 0.932631047 1.084545814 1 15.49898941 2.24781318 24.99999998 1.019100882 1.229262123 0.654155044 0.075023193 112.5737428 304169.3697 0.026853141 0.020507513 176.9347678 -2.24781318 0.210161242 VHNNS(ph)PDTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VHNNSPDTSR 10 0 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 1 VHNNS(0.981)PDT(0.013)S(0.005)R;VHNNS(0.921)PDT(0.058)S(0.021)R 145.06 3.26E-05 375720000 436590 374160 237810 295230 262550 362030 308990 382210 502260 TRUE FALSE 378893.5253 371702.1183 352815.7114 362266.4838 257325.7687 375957.5284 279024.1974 300477.3659 442883.395 0.855515311 0.839277612 0.796633415 0.817972604 0.581023745 0.848886033 0.630017292 0.67845706 1 18.75656738 3.438634571 24.99991049 0.73200922 0.827347385 0.095069313 0.11710639 317.7962287 206430.8202 0.03246715 0.041914982 2745.58296 -3.438634571 0.095338166 VHNNS(ph)PDTSRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VHNNSPDTSRR 11 1 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 1 VHNNS(1)PDTSRR;VHNNS(1)PDTSRR 140.31 2.37E-05 376027000 245902 240383 135273 147062 200674 197575 183853 245867 156263 TRUE FALSE 213405.4277 238803.9082 200691.4753 180454.6748 196680.98 205175.8381 166022.9644 193290.2554 137789.7662 1.548775599 1.733103371 1.456504941 1.309637717 1.427399041 1.489049904 1.204900545 1.402791084 1 17.07210922 -0.59780673 0.128487295 2.92E-12 1.912882845 0.582595232 0.127609474 97.71718134 1.666577576 33.74250196 4.280543202 0.252460402 0.59780673 1.912882845 VHPAVVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VHPAVVIR 8 0 J3KTJ3;P62829;J3KT29;J3QQT9;C9JD32 J3KTJ3 RPL23 60S ribosomal protein L23 0 ;;; 132.09 0.00097697 1581080000 2892580 3055930 2198180 2582140 3025660 2847490 2825690 3052540 4390090 FALSE TRUE 2510318.224 3035855.395 3261227.2 3168454.353 2965455.286 2957034.783 2551655.019 2399778.076 3871098.561 0.648476959 0.78423614 0.842455223 0.818489714 0.76605006 0.763874837 0.65915527 0.619921719 1 21.88431161 2.458580032 24.63044887 0.724260207 0.777711532 0 0.112493134 741.185717 984594.7279 0.041644523 0.032263057 287.461728 -2.458580032 0.053451325 VHPEEQGWICDPCHLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VHPEEQGWICDPCHLAR 17 0 Q9BV36-2;Q9BV36-5;C9JKV5;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 0 ;;; 211.99 1.14E-12 1794060000 1107200 1055430 653038 801080 1016290 1042090 952400 1146190 1066480 FALSE TRUE 960880.7147 1048496.811 968849.3611 982977.4577 996067.8173 1082179.877 860036.3946 901086.1882 940401.9493 1.021776609 1.114945382 1.030250269 1.045273735 1.059193697 1.150763115 0.914541272 0.958192599 1 19.842918 2.225541607 24.99999791 0.955912805 1.06892144 0.601408422 0.043267532 148.8950012 285916.1614 0.017001053 0.011540511 168.0898955 -2.225541607 0.113008635 VHPEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VHPEGK 6 0 P62195-2;P62195;J3QSA9;J3KRP2;J3QLH6;J3QRW1 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ;; 95.957 0.042755 442840000 1591840 1392460 917960 1130260 695760 1081110 1564810 1809650 1875210 FALSE TRUE 1381474.311 1383312.839 1361888.526 1386902.808 681915.7372 1122701.001 1413054.967 1422670.43 1653524.81 0.835472381 0.836584265 0.823627513 0.838755366 0.412401273 0.678974391 0.854571373 0.860386504 1 20.65711326 0.065475434 12.76634697 3.333984264 0.79015241 0 0.154871905 0 0 0 0.036597447 1.162720779 -0.065475434 -2.543831855 VHPEIINENGNPSYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VHPEIINENGNPSYK 15 0 O95881 O95881 TXNDC12 Thioredoxin domain-containing protein 12 0 188.47 2.98E-07 204340000 147810 124120 88402 111240 134180 140120 138620 158750 129470 FALSE TRUE 128276.534 123304.6475 131153.5029 136498.7422 131510.0805 145510.5071 125176.6537 124802.5479 114164.2041 1.123614315 1.080064005 1.148814586 1.195635211 1.151937961 1.27457208 1.096461494 1.093184583 1 16.80075084 1.45663413 1.771064127 0.986398113 1.157887588 0.470554535 0.053113829 0.53128486 2.397040217 0.140576946 0.015677019 28.61766068 -1.45663413 0.171489475 VHPVSTMIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VHPVSTMIK 9 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 113.66 0.0017646 3689400000 2290100 2945100 1836370 2125800 2719300 2436800 2954000 3464500 3851500 FALSE TRUE 1987457.483 2925753.444 2724444.674 2608495.381 2665191.25 2530545.273 2667521.535 2723643.636 3396180.058 0.585203802 0.861483606 0.802208548 0.768067457 0.784761469 0.745115168 0.785447617 0.801972684 1 21.69548152 1.12733061 2.2444667 1.12207539 0.767518256 0.52593908 0.070336384 0.743104719 2.948622919 0.597471846 0.017325683 13.40696914 -1.12733061 -0.354557133 VHQFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VHQFEK 6 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 110.61 0.028555 140120000 603950 360740 258230 345010 338340 314910 401430 471820 472830 FALSE TRUE 524136.4773 358370.2752 383110.8917 423349.7936 331607.696 327024.7915 362499.3804 370924.9647 416932.576 1.25712527 0.859540117 0.918879727 1.0153915 0.795350891 0.784358935 0.869443649 0.889652155 1 18.66945457 4.741338536 24.84929972 0.88875399 1.257125415 0.702933277 0.074662137 138.8602582 1242073.641 0.018701006 0.126026039 55123.72228 -4.741338536 0.368371424 VHQLYETIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VHQLYETIQR 10 0 Q13561;Q13561-3;Q13561-2;H0YI98 Q13561 DCTN2 Dynactin subunit 2 0 ;;; 157.38 9.28E-06 2287980000 885660 1084630 805907 957101 1167370 1364040 866474 1000290 1168240 FALSE TRUE 768617.787 1077504.994 1195646.321 1174425.41 1144141.621 1416515.501 782443.4848 786385.7678 1030131.998 0.746135241 1.045987307 1.160672926 1.140072741 1.110674771 1.375081547 0.759556529 0.763383498 1 19.97439778 2.203341851 24.99980941 0.821421223 1.099694931 0.342451251 0.166093111 186.1788316 132156.5725 0.068052572 0.045883039 159.7135824 -2.203341851 0.278273707 VHS(ph)PSGAVEECHVSELEPDKYAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VHSPSGAVEECHVSELEPDKYAVR 24 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 1 VHS(0.946)PS(0.054)GAVEECHVSELEPDKYAVR 123.35 6.87E-05 176900000 40615 37538 12060 28884 42690 33514 42245 44667 28973 TRUE FALSE 35247.62484 37291.41041 17892.25634 35442.55366 41840.55252 34803.30527 38148.0864 35115.30965 25547.84495 1.379671159 1.459669514 0.700343077 1.38730111 1.637733148 1.362279493 1.493201735 1.374492045 1 14.64091398 3.536764009 24.99996643 1.393933726 1.18053051 0.115372615 0.252545177 515.2305448 215963.2205 0.068890543 0.102180959 3441.628657 -3.536764009 -0.213403216 VHSAVITVPAYFNDSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VHSAVITVPAYFNDSQR 17 0 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 ; 146.76 4.25E-07 3121000000 1632560 1646280 1052060 1162850 1626850 1809490 1534570 1811100 1837970 FALSE TRUE 1416813.06 1635465.478 1560839.735 1426892.866 1594478.868 1879102.251 1385747.638 1423810.359 1620687.28 0.874205084 1.009118476 0.963072737 0.880424548 0.983828828 1.159447769 0.855037029 0.878522573 1 20.62817431 VHSDFTAAATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VHSDFTAAATR 11 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 80.245 0.024938 110400000 74277 69337 57616 41397 66904 82241 64736 68345 67962 FALSE TRUE 64461.10626 68881.52068 85479.29031 50796.82156 65572.7413 85404.86449 58457.91268 53729.95361 59927.60978 1.075649546 1.149412115 1.426375766 0.847636369 1.094199177 1.425133837 0.975475459 0.896580955 1 15.87093321 2.028941463 24.95390561 0.939440623 1.165560621 0.261501498 0.168463727 251.9151781 217205.2441 0.067885995 0.045767961 106.8910794 -2.028941463 0.226119998 VHSFPTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VHSFPTLK 8 0 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ; 170.66 0.00029388 4626400000 6506400 5888600 3717100 5116800 5693800 5980100 6083500 5855800 5006900 FALSE TRUE 5646562.755 5849917.399 5514701.993 6278647.645 5580504.52 6210158.317 5493523.106 4603582.74 4414989.986 1.278952562 1.325012609 1.249085957 1.422120473 1.263990301 1.406607566 1.244288917 1.042716462 1 22.07397873 1.778296882 2.873414067 1.006713561 1.323055672 0.827563324 0.056443318 0.08315596 1.336269094 0.038269188 0.014300338 60.02012306 -1.778296882 0.316342111 VHSPSGALEECYVTEIDQDKYAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VHSPSGALEECYVTEIDQDKYAVR 24 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ; 292.64 4.49E-62 374610000 498230 415490 311100 340560 367510 305440 428460 515610 438670 FALSE TRUE 432387.6431 412760.6188 461549.0006 417889.3531 360197.27 317190.4744 386908.0151 405350.814 386810.9323 1.117826843 1.067086228 1.193216018 1.080345249 0.931197233 0.820014245 1.000250983 1.047930087 1 18.56126904 3.37067086 5.038580582 0.967505973 1.122533316 0.57557573 0.066653889 0.17769809 7.191074392 0.02175836 0.028303694 2347.852772 -3.37067086 0.155027343 VHSPSGAVEECHVSELEPDKYAVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VHSPSGAVEECHVSELEPDKYAVR 24 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;; 312.74 1.05E-73 1810450000 1508270 1535800 412955 1126940 1663740 1564540 1788250 1956680 1682770 FALSE TRUE 1308948.298 1525711.229 612661.4193 1382828.951 1630634.829 1624728.866 1614825.79 1538259.209 1483834.848 0.882138804 1.028221726 0.412890572 0.931929152 1.09893283 1.094952628 1.088278654 1.03667818 1 20.5008991 3.480545672 23.46329268 1.05938441 0.778566255 0.423129407 0.154373273 59.68227782 408932.0563 0.043303376 0.057235514 3023.748546 -3.480545672 -0.280818155 VHSYLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VHSYLER 7 0 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 ; 170.06 0.00098884 562770000 282050 265770 177801 236890 268930 266510 266780 283310 278400 FALSE TRUE 244776.3779 264024.1394 263786.1583 290679.4951 263578.8192 276762.8122 240907.7167 222726.3612 245487.8692 0.997101725 1.075507887 1.074538466 1.184089039 1.073693865 1.127399138 0.981342652 0.907280519 1 17.90529221 2.11635362 5.074819374 0.946441237 1.090745514 0.568280514 0.051862328 0.134099166 5.40607737 0.021810338 0.014410295 130.7234858 -2.11635362 0.144304277 VHTGFDQHEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VHTGFDQHEQK 11 0 O96013;O96013-4;O96013-2;O96013-3;M0R2X4;M0R0L9;M0R3G6 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ;;; 153.34 1.88E-05 742640000 642813 604860 380113 452795 568443 494188 587520 663332 585035 FALSE TRUE 557863.6334 600886.6348 563936.9182 555609.0253 557132.0964 513199.7321 530542.4008 521483.6139 515872.8288 1.081397589 1.164796053 1.093170423 1.077027117 1.079979532 0.994818303 1.028436412 1.010876295 1 18.97665594 3.124634732 1.129101049 1.007519718 1.120337819 0.755806144 0.025770892 0.213348147 0.598516584 0.011243385 0.014040959 1332.400331 -3.124634732 0.112818101 VHTVEDYQAIVDAEWNILYDKLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VHTVEDYQAIVDAEWNILYDKLEK 24 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 245.09 5.34E-38 1334800000 2856600 2168600 1566200 1896300 1923300 1544200 2855600 3126100 1538500 FALSE TRUE 2479093.072 2154354.324 2323619.559 2326883.898 1885030.093 1603606.373 2578664.352 2457607.842 1356620.283 1.827403809 1.588030454 1.712800249 1.715206479 1.389504578 1.182059854 1.900800382 1.811566489 1 20.37158554 3.265978035 24.62792782 1.520698508 1.7022254 0.15658019 0.271024197 495.7926433 445346.1061 0.082097652 0.10596036 1844.922107 -3.265978035 0.181526892 VHTVMTLEQQDMVCYTAQTLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VHTVMTLEQQDMVCYTAQTLVR 22 0 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ; 181.26 5.03E-17 122076000 32143 23645 14855.1 22213 25095 25671 27397 28592 25992 FALSE TRUE 27895.22111 23489.67444 22039.07605 27256.80115 24595.6586 26658.57998 24740.04316 22477.8233 22919.25537 1.217108526 1.024888202 0.961596513 1.189253347 1.073143878 1.163152099 1.079443584 0.980739685 1 14.48427255 1.799513978 4.693731598 0.990549702 1.098648855 0.272081927 0.07572641 0.271311261 10.84148057 0.042931992 0.019972876 63.02516301 -1.799513978 0.108099153 VHVCAECGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VHVCAECGK 9 0 P25490;O15391 P25490 YY1;YY2 Transcriptional repressor protein YY1;Transcription factor YY2 0 116.52 0.0013002 197570000 188700 175110 118510 148200 172570 143320 211400 216020 202660 FALSE TRUE 163762.8169 173959.6909 175821.8324 181851.0751 169136.1946 148833.6131 190898.4605 169825.8041 178701.7657 0.916402903 0.97346375 0.983884136 1.01762327 0.946471872 0.832860339 1.068251675 0.950330868 1 17.44719436 VHVGDEDFVHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VHVGDEDFVHLR 12 0 P04080 P04080 CSTB Cystatin-B 0 ;;;;; 197.56 1.12E-07 6667570000 2563330 2279950 1340460 1458828 1835260 2193650 1596984 2072010 4590900 FALSE TRUE 2224579.446 2264972.858 1988710.94 1790077.194 1798741.917 2278041.135 1442108.737 1628926.786 4048169.032 0.549527312 0.559505505 0.491261833 0.442194281 0.444334686 0.562733699 0.356237283 0.40238606 1 21.9488381 1.234050979 24.99997825 1.00000079 0.470703328 0.852251893 0.068531537 53.68355415 297566.2796 0.140620954 0.018125332 17.14158508 -1.234050979 -0.529297462 VHVIFNYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VHVIFNYK 8 0 P27797;K7EJB9 P27797 CALR Calreticulin 0 ; 158.08 0.00036704 3702300000 6059300 9017100 5972600 7528500 8842500 9941300 8575300 8422600 10278300 FALSE TRUE 5258548.153 8957866.076 8860969.337 9237960.991 8666551.55 10323748.24 7743668.726 6621492.535 9063211.083 0.580208064 0.988376635 0.97768542 1.019281236 0.956234106 1.139082843 0.85440675 0.730590127 1 23.11159086 7.318538055 9.994060277 0.91462059 0.004546177 0 0.159548065 0 0 0.03609788 0 20822748.55 -7.318538055 -0.910074412 VHVQFFDDS(ph)PTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VHVQFFDDSPTR 12 0 P52701;P52701-2;A0A087WWJ1;A0A494C0M1;F8WAX8;C9J7Y7;C9J8Y8;C9JH55 P52701 MSH6 DNA mismatch repair protein Msh6 1 VHVQFFDDS(0.964)PT(0.036)R;VHVQFFDDS(0.991)PT(0.009)R;VHVQFFDDS(0.993)PT(0.007)R;VHVQFFDDS(0.944)PT(0.056)R 172.9 2.22E-05 959070000 669478 662874 398846 475285 636170 613852 568174 649321 620159 TRUE FALSE 581004.7861 658519.537 591729.2597 583205.7235 623511.4616 637467.2837 513072.5729 510468.7572 546844.5095 1.062467989 1.204217151 1.082079548 1.066492784 1.140198815 1.165719455 0.938242158 0.93348063 1 19.06077115 2.231973081 24.99999915 0.951499212 1.120750709 0.725499776 0.047206501 74.29314504 281942.7424 0.018582753 0.012857249 170.5976643 -2.231973081 0.169251497 VHVTQEDFEMAVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VHVTQEDFEMAVAK 14 0 P62195-2;P62195 P62195-2 PSMC5 26S protease regulatory subunit 8 0 92.935 0.0047616 95334000 112980 82756 60627 103780 90896 82326 95652 121840 166980 FALSE TRUE 98049.40675 82212.37039 89946.41999 127344.8352 89087.34744 85493.13449 86375.68376 95785.46416 147239.8146 0.665916396 0.558356927 0.610883817 0.864880437 0.605049305 0.5806387 0.586632658 0.65054051 1 17.16780831 1.239509874 6.506845756 1.009975266 0.638129508 0.634287335 0.08586195 0.079203025 15.77232111 0.130646516 0.021617444 17.3584073 -1.239509874 -0.371845757 VIAHTQMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 VIAHTQMR 8 0 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ;;;;;;; 206.09 7.42E-05 4122320000 1096655 1437432 968858 1038788 1372059 1567970 1325790 1379420 1426191 FALSE TRUE 951729.2632 1427989.415 1437400.969 1274660.692 1344757.71 1628290.821 1197215.09 1084441.768 1257588.325 0.756789201 1.135498308 1.14298212 1.013575482 1.069314722 1.294772533 0.951992847 0.862318571 1 20.2622283 2.022148876 24.99907483 0.917074007 1.076955563 0.163958436 0.138117416 330.4315424 372951.1248 0.054577332 0.036793108 105.2322547 -2.022148876 0.159881556 VIAIDSDAES(ph)PAKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VIAIDSDAESPAKR 14 1 P28749 P28749 RBL1 Retinoblastoma-like protein 1 1 VIAIDSDAES(1)PAKR;VIAIDSDAES(1)PAKR 157.47 3.24E-06 700490000 631900 656940 416340 502500 656740 578660 626810 818390 653270 TRUE FALSE 548392.814 652624.5179 617683.4166 616600.3052 643672.1589 600921.4246 566022.0627 643383.6672 576041.1648 0.952002821 1.132947709 1.07229041 1.070410142 1.11740653 1.043191809 0.982606968 1.116905712 1 19.13581239 1.195346263 23.61818295 0.999998462 1.06402505 0.09685072 0.057847764 13003.27493 7105717.752 6.083068514 0.013178776 15.68000739 -1.195346263 0.064026588 VIAINVDDPDAANYNDINDVKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VIAINVDDPDAANYNDINDVKR 22 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;; 289.22 3.88E-55 7790710000 5289370 4417400 2858360 3520240 4159590 3580870 4928840 5733080 3832370 FALSE TRUE 4590366.353 4388381.809 4240672.457 4319564.295 4076822.297 3718628.386 4450841.855 4507105.457 3379311.584 1.358373218 1.298602304 1.254892409 1.278237945 1.206406156 1.100410037 1.317085372 1.333734799 1 21.68829795 4.818520781 0.750495543 1.216544509 1.458154544 0.224375786 0.09827021 5.830152733 2.346729589 0.041101767 1.223518575 65844.69363 -4.818520781 0.241610035 VIATLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VIATLLR 7 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 94.407 0.033089 23157000 40849 39193 39894 28105 27597 42019 35423 37057 33778 FALSE TRUE 35450.70115 38935.5386 59186.87184 34486.66981 27047.87369 43635.49812 31987.68291 29132.64893 29784.80332 1.190227807 1.307228327 1.987149997 1.157861257 0.908109864 1.465025559 1.07395985 0.978104459 1 14.86228881 3.503597198 24.91666654 1.084672531 1.49217155 0.362153427 0.250524214 758.6090062 713929.6342 0.068531143 0.101266035 3188.579118 -3.503597198 0.407499018 VIDFDENTALDDAEEESFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VIDFDENTALDDAEEESFR 19 0 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 ; 268.56 1.71E-31 133618000 136446 125810 92371 106397 117017 158010 107387 126228 113544 FALSE TRUE 118414.3154 124983.5458 137041.9246 130556.065 114688.5906 164088.7469 96972.62527 99235.12451 100120.9577 1.182712572 1.248325513 1.368763621 1.303983382 1.145500336 1.638905088 0.968554711 0.99115237 1 16.61138447 2.154893706 25 0.986766974 1.305988431 0.573834258 0.133159978 17.82174883 5323.209562 0.051110489 0.034458688 142.8544278 -2.154893706 0.319221457 VIDFDENTALDDAEEESFRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VIDFDENTALDDAEEESFRK 20 1 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 ; 287.84 2.28E-45 220850000 322020 277970 207046 259210 264080 301080 307500 303670 206141 FALSE TRUE 279464.2411 276143.9968 307174.1381 318067.5923 258825.3247 312662.7424 277678.6973 238732.5337 181771.2458 1.537450216 1.519184157 1.689894002 1.749823471 1.423906864 1.720089121 1.527627189 1.313367978 1 17.47176447 1.396652563 1.648621147 0.879575545 1.607279354 0.797868505 0.09941128 0.30498413 1.030108075 0.334644839 0.02809009 24.92599842 -1.396652563 0.727703809 VIDGPHSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VIDGPHSGR 9 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 0 103.26 0.003452 157910000 361980 317680 188110 224180 296760 338490 295570 330740 334410 FALSE TRUE 314143.4259 315593.1392 279080.6252 275083.4954 290855.0566 351511.9293 266905.6669 260013.8248 294876.4308 1.065339217 1.070255559 0.946432458 0.932877187 0.986362511 1.192065193 0.905144118 0.881772152 1 18.16975099 1.329556678 0.02406904 1.10E-05 1.89645887 0.082260019 0.088372372 3705.398074 26.12373281 1127.599503 937.1711433 21.35780802 -1.329556678 1.896447882 VIDPATATSVDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VIDPATATSVDLR 13 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 134.57 1.27E-05 0 75842 75765 41414 58836 70415 78735 65785 83545 72977 FALSE TRUE 65819.28754 75267.29473 61441.94892 72195.61305 69013.87926 81763.9864 59405.18083 65679.5519 64349.7422 1.022836849 1.169659616 0.954812666 1.121925443 1.072481053 1.27061871 0.923161132 1.020665346 1 15.97364675 2.164067141 24.99999982 0.987060486 1.098026958 0.299766764 0.086722889 50.78251007 17040.8658 0.0335503 0.022619612 145.9039806 -2.164067141 0.110966473 VIDTLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VIDTLHR 7 0 Q9H993 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 ;;;; 155.51 0.0016062 2456190000 5640840 5079610 3209890 3641590 4947570 5765200 5058370 5618810 5594970 FALSE TRUE 4895388.702 5046241.707 4762203.54 4468468.668 4849123.037 5986990.975 4567810.056 4417271.207 4933539.02 0.99226715 1.022844187 0.965271283 0.905732913 0.982889365 1.213528656 0.925868841 0.895355482 1 22.23419149 VIEEEWQQVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VIEEEWQQVDR 11 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 0 ;;; 241.13 2.41E-15 1088150000 577300 513000 341458 383157 510296 529197 568027 607820 511090 FALSE TRUE 501008.3423 509630.0692 506588.2309 470158.653 500142.108 549555.551 512939.829 477842.4231 450669.5224 1.111697857 1.130828787 1.124079188 1.043244838 1.109775752 1.219420271 1.138172882 1.060294516 1 18.78171036 1.504857784 3.078300136 1.004317019 1.125020448 0.489336828 0.04269228 0.224561262 4.150472349 0.052914293 0.012103494 31.97847759 -1.504857784 0.120703429 VIEETEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VIEETEER 8 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 198.92 0.00030729 1949180000 2923330 2919920 1952550 2093960 2517270 2880970 2499900 2743070 3207950 FALSE TRUE 2537004.534 2900738.853 2896809.711 2569425.622 2467181.252 2991802.78 2257460.083 2156485.827 2828709.806 0.896876919 1.025463569 1.024074546 0.908338359 0.872193127 1.057656312 0.798052907 0.762356684 1 21.43171275 2.221115736 24.99993599 0.832178884 0.962903564 0.258173357 0.085895721 275.6272007 394993.2618 0.034654269 0.023424047 166.3855994 -2.221115736 0.130724679 VIEHIMEDLDTNADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VIEHIMEDLDTNADK 15 0 P06702 P06702 S100A9 Protein S100-A9 0 68.972 0.051042 17082000 19459 17186 13432 18335 17369 18627 12557 23161 30938 FALSE TRUE 16887.44385 17073.10403 19927.76013 22498.24198 17023.39088 19343.59274 11339.22407 18208.20039 27280.54488 0.619028832 0.625834422 0.73047515 0.824699143 0.624012129 0.709061818 0.415652404 0.667442695 1 14.73558484 1.242963349 7.260602768 1.005943228 0.649096169 0.524365016 0.10421929 0.08240087 28.18994799 0.145951764 0.026453918 17.49699023 -1.242963349 -0.356847059 VIEPFSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VIEPFSR 7 0 O00231;O00231-2 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 ; 117.17 0.01231 158190000 389200 399580 268203 293940 358620 409490 438780 408410 318120 FALSE TRUE 337766.2339 396955.1327 397906.8679 360683.5696 351484.1636 425243.3453 396227.1831 321074.6998 280512.216 1.204105257 1.415108184 1.418501032 1.28580343 1.253008402 1.515953035 1.412513112 1.144601488 1 18.09770407 1.559057625 3.458396871 1.020613872 1.361117252 0.638428542 0.092300578 0.122697259 3.201153612 0.085131327 0.024469669 36.22910665 -1.559057625 0.34050338 VIEPLKDFHKDEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VIEPLKDFHKDEVR 14 2 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ; 158.17 3.07E-06 1507870000 3301500 2417300 1852700 2049530 2404800 1954320 3004000 3678400 1943040 FALSE TRUE 2865198.41 2401420.597 2748671.917 2514907.112 2356949.185 2029503.955 2712672.542 2891802.785 1713336.025 1.672292165 1.401605151 1.6042807 1.467842312 1.375649114 1.184533522 1.583269425 1.687819986 1 20.70837669 7.999995948 0.695792254 1.424156584 27.95523722 0.134724569 0.20287713 761.8332951 4.134478962 0.082446322 31414.07295 99999066.92 -7.999995948 26.53108063 VIFGLFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VIFGLFGK 8 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 101.52 0.012411 73221000 142270 134260 91372 130940 117780 131050 117570 141390 163620 FALSE TRUE 123468.659 133378.0372 135559.8048 160671.9283 115436.4084 136091.5783 106168.0795 111154.8488 144277.03 0.855774887 0.92445788 0.939579951 1.113634847 0.800102473 0.943265732 0.735862663 0.770426511 1 17.1384821 VIFHPEFLSSTSPLLPVDYEEFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VIFHPEFLSSTSPLLPVDYEEFVR 24 0 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 0 81.949 0.01529 291110000 106360 90835 49304 70081 114100 102610 97082 107940 115850 FALSE TRUE 92304.25652 90238.2989 73147.57931 85993.96217 111829.6332 106557.4731 87667.00258 84857.87099 102154.345 0.903576412 0.883352528 0.716049614 0.841804254 1.09471245 1.0431027 0.858181829 0.830682934 1 16.64039104 3.440352099 24.98570521 0.946529114 0.829178232 0.315075627 0.092278264 247.1063492 167915.116 0.029628764 0.038250678 2756.462568 -3.440352099 -0.117350882 VIFLEDDDVAAVVDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VIFLEDDDVAAVVDGR 16 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ;;;;; 248.19 5.18E-20 339735000 211921 203680 142186 146096 192262 197658 189859 197094 199421 FALSE TRUE 183915.1029 202342.0127 210947.6252 179269.3297 188436.3624 205262.0312 171446.5034 154946.9819 175845.6766 1.045889251 1.150679486 1.199617922 1.019469647 1.07160077 1.16728506 0.974982762 0.881153207 1 17.42395034 2.102526758 5.410631224 0.931053121 1.108743232 0.592256629 0.061660566 0.127294414 5.671142332 0.025737783 0.017056742 126.6271285 -2.102526758 0.17769011 VIFLENYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VIFLENYR 8 0 P11216;H0Y4Z6;P11217;P11217-2;E9PK47;P06737-2;P06737 P11216;E9PK47 PYGB;PYGM;PYGL "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, muscle form;Glycogen phosphorylase, liver form" 0 84.498 0.040502 677670000 218230 199270 145060 197850 204420 211160 228000 249710 265240 FALSE TRUE 189390.3526 197960.9822 215211.5012 242774.8664 200352.4419 219283.4618 205888.5951 196311.4597 233883.6294 0.809763185 0.846408031 0.920164878 1.038015645 0.856633029 0.937575077 0.880303575 0.839355282 1 17.83543136 4.357274947 3.825417181 0.916641463 0.817532451 0.305440878 0.060697744 0.295344141 7.841914993 0.015800805 0.048442543 22765.38225 -4.357274947 -0.099109012 VIFWSALAGAIPLNGDS(ph)EEEANRDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VIFWSALAGAIPLNGDSEEEANRDDR 26 1 Q9H089 Q9H089 LSG1 Large subunit GTPase 1 homolog 1 VIFWSALAGAIPLNGDS(1)EEEANRDDR 53.705 0.05379 0 280120 196570 133390 118420 175400 112470 252890 322320 121890 TRUE FALSE 243101.4323 195278.7187 197897.8502 145309.0709 171909.8832 116796.7937 228364.7667 253394.3763 107480.3031 2.2618231 1.816879123 1.841247601 1.351960004 1.599454768 1.086680911 2.124712717 2.357588964 1 16.71371277 VIGHYAGEDATDAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VIGHYAGEDATDAFR 15 0 O95864-3;O95864 O95864-3 FADS2 Fatty acid desaturase 2 0 121.18 0.0001166 263800000 219770 198560 78725 166510 226770 165730 216570 260400 135380 FALSE TRUE 190726.8377 197255.6463 116796.6733 204318.6404 222257.7207 172105.7403 195567.0747 204715.4864 119375.5306 1.597704627 1.652395975 0.978397103 1.711562155 1.861836505 1.441717071 1.638250936 1.714886504 1 16.86514762 1.230092868 24.98266101 0.999998912 1.577058365 0.367622005 0.236818188 367.4277811 1083947.842 0.65307199 0.057910684 16.98606837 -1.230092868 0.577059453 VIGQDSSEIHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VIGQDSSEIHFK 12 0 B8ZZN6;P63165;B8ZZJ0;B9A032;G2XKQ0 B8ZZN6;G2XKQ0 SUMO1 Small ubiquitin-related modifier 1;Small ubiquitin-related modifier 0 ; 170.66 4.06E-05 1014980000 3039280 2574190 1332840 2044000 2548730 2329100 2849940 3190490 3035350 FALSE TRUE 2637631.447 2557279.976 1977405.882 2508121.441 2498015.26 2418701.984 2573553.257 2508228.542 2676514.381 0.985472548 0.955451611 0.738798901 0.937084986 0.933309112 0.903676065 0.961531638 0.937125001 1 21.35192397 0.854164912 0.651195185 1.100145626 0.902654162 0.148438377 0.06664907 10.3960571 2.412323454 1.719153728 0.033489326 7.14767689 -0.854164912 -0.197491464 VIGSGCNLDSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VIGSGCNLDSAR 12 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5;Q6ZMR3;A0A087WUM2;F5H5G7;F5H155;P07864;G3XAP5;F5H245;A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50 P00338;A0A5F9ZHM4 LDHA;LDHAL6A;LDHC;LDHB L-lactate dehydrogenase A chain;L-lactate dehydrogenase A-like 6A;L-lactate dehydrogenase;L-lactate dehydrogenase C chain;L-lactate dehydrogenase B chain 0 ; 168.59 0.00010727 804740000 480720 490230 296210 313160 495540 478350 449820 553840 530100 FALSE TRUE 417191.634 487009.6469 439458.1468 384267.7644 485679.7235 496752.434 406196.5256 435405.626 467432.1819 0.892517995 1.041883006 0.94015381 0.822082388 1.039037838 1.062726216 0.868995635 0.931484059 1 18.83439754 VIGTLEEVHMPQNGINHPGITALAQAFAVNPLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VIGTLEEVHMPQNGINHPGITALAQAFAVNPLLR 34 0 P46060;H0Y4Q3 P46060 RANGAP1 Ran GTPase-activating protein 1 0 115.27 3.34E-06 223280000 75292 78751 58814 58305 57578 68308 76733 103210 70685 FALSE TRUE 65341.97143 78233.6795 87256.64712 71544.04139 56432.31045 70935.85296 69291.44547 81139.34468 62328.69982 1.048344849 1.25517907 1.399943323 1.147850695 0.905398486 1.138092936 1.111710106 1.301797485 1 15.927609 3.494581878 24.871797 1.112927188 1.242781244 0.188153216 0.131143108 1298.255843 1849298.238 0.037908324 0.054873744 3123.071149 -3.494581878 0.129854056 VIHCSGYLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VIHCSGYLK 9 0 H7BZX8;Q14190-2;Q14190;P81133 H7BZX8 SIM2;SIM1 Single-minded homolog 2;Single-minded homolog 1 0 65.06 0.067627 1340000000 235830 386520 179660 209160 363200 392200 309650 242380 240210 FALSE TRUE 204664.468 383980.9247 266544.1769 256652.9748 355973.0306 407288.1878 279620.1907 190548.9232 211812.6474 0.966252348 1.812832847 1.258395946 1.211698064 1.680603283 1.922870011 1.320129813 0.899610696 1 17.69242921 1.863516474 4.381978045 0.956469247 1.487517084 0.35422698 0.2875106 0.230204814 6.702185372 0.157828428 0.076410693 73.03255156 -1.863516474 0.531047837 VIHDNFGIVEGLMTTVHAIT(ph)ATQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VIHDNFGIVEGLMTTVHAITATQK 24 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 VIHDNFGIVEGLMTTVHAIT(0.652)AT(0.348)QK 212.44 7.11E-25 2734600000 400380 339700 265280 454040 468580 387220 721490 768090 532290 TRUE FALSE 347468.7686 337468.4883 393570.2953 557136.7216 459256.1748 402116.604 651520.0108 603839.9308 469363.2826 0.740298147 0.718992092 0.838519565 1.187005337 0.978466343 0.856727867 1.388093264 1.286508666 1 18.84034546 4.030499273 0.491843108 1.230495683 0.516064592 0.499125658 0.160200361 2.136522316 0.772795267 0.176422893 0.879479724 10727.51853 -4.030499273 -0.714431091 VIHDNFGIVEGLMTTVHAITAT(ph)QK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 VIHDNFGIVEGLMTTVHAITATQK 24 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 VIHDNFGIVEGLMTTVHAITAT(1)QK;VIHDNFGIVEGLMTTVHAIT(0.017)AT(0.983)QK;VIHDNFGIVEGLMTTVHAIT(0.002)AT(0.998)QK;VIHDNFGIVEGLMTTVHAITAT(1)QK;VIHDNFGIVEGLMTTVHAIT(0.001)AT(0.999)QK;VIHDNFGIVEGLMTTVHAIT(0.031)AT(0.969)QK;VIHDNFGIVEGLMTTVHAITAT(1)QK;VIHDNFGIVEGLMTTVHAITAT(1)QK;VIHDNFGIVEGLMTTVHAITAT(1)QK;VIHDNFGIVEGLMTTVHAITAT(1)QK 290.45 1.60E-61 28796712000 3651175 2863656 2571443.8 4121134 3883115 3179901 6171928 6925344 4287602 TRUE FALSE 3168662.973 2844844.455 3815002.623 5056900.462 3805848.609 3302233.849 5573375.373 5444413.079 3780726.576 0.83810953 0.752459719 1.009065995 1.337547257 1.006644763 0.87343895 1.474154573 1.440044121 1 21.85023209 4.757398177 0.392725123 1.317470807 0.32776847 0.333276263 0.206671804 8.047096496 1.124515273 0.314320354 3.877685196 57200.28288 -4.757398177 -0.989702337 VIHDNFGIVEGLMTTVHAITATQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 29 VIHDNFGIVEGLMTTVHAITATQK 24 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;; 382.69 2.33E-137 1.81955E+11 28856069.3 27062613.4 17468027.2 21617393.2 24240685.2 21516215.3 31149794.9 34155611.1 25234329.6 FALSE TRUE 25042666.63 26884837.31 25915623.58 26525952.73 23758342.99 22343958.03 28128892.59 26851699.47 22251155.9 1.125454639 1.208244526 1.164686621 1.192115719 1.067735227 1.004170665 1.264154218 1.206755262 1 24.40737695 3.287663293 24.99997171 1.127286277 1.174602577 0.103167853 0.084265518 363.4530993 185044.5313 0.025854615 0.033378117 1939.381698 -3.287663293 0.0473163 VIHDNFGIVEGLMTTVHAITATQKTVDGPSGKLWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VIHDNFGIVEGLMTTVHAITATQKTVDGPSGKLWR 35 2 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 206.47 3.12E-28 250130000 91296 193890 86043 227040 141050 95339 104350 174170 77673 FALSE TRUE 79231.00229 192616.3238 127653.6826 278592.9021 138243.381 99006.75302 94230.15306 136925.1009 68490.58643 1.156815942 2.812303615 1.863813544 4.067608654 2.018428928 1.445552713 1.375811743 1.999181319 1 16.06361809 3.001676659 24.99925452 1.554849316 2.528986163 0.276298952 0.768998091 72.81914155 1085711.112 0.223788227 0.251970229 1003.868112 -3.001676659 0.974136847 VIHECQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VIHECQQR 8 0 A0A0A0MTN0;Q13617;Q13617-2;Q5T2B5 A0A0A0MTN0 CUL2 Cullin-2 0 ; 105.57 0.0043629 395530000 234510 261030 159914 166600 227780 281880 223381 239220 226240 FALSE TRUE 203518.9093 259315.2767 237248.9453 204429.0763 223247.6236 292724.106 201717.545 188064.6646 199494.1649 1.020174747 1.299863968 1.189252555 1.024737121 1.119068439 1.467331669 1.011145088 0.942707596 1 17.60598702 2.025238407 24.99905981 0.970160726 1.186361885 0.352901122 0.12984961 222.307084 220197.8798 0.052044578 0.035087092 105.9835364 -2.025238407 0.216201159 VIHELANER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VIHELANER 9 0 Q02880;Q02880-2;E9PCY5 Q02880 TOP2B DNA topoisomerase 2-beta;DNA topoisomerase 2 0 ;;; 114.97 0.0015521 758170000 1390080 1251570 798660 1089810 1353940 1332540 1238770 1494230 1227450 FALSE TRUE 1206377.406 1243348.354 1184894.647 1337268.017 1326999.243 1383803.676 1118634.276 1174700.543 1082342.259 1.114598821 1.148757099 1.094750424 1.235531557 1.226044009 1.278526884 1.033530999 1.085331865 1 20.04572535 2.213810892 24.99919819 1.048890238 1.181804991 0.565975187 0.059010609 187.7015523 189592.1073 0.025572421 0.017249642 163.6103945 -2.213810892 0.132914754 VIHLVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 148.33 0.0020914 585710000 717640 672410 428040 496355 649340 716560 620260 703620 680810 FALSE TRUE 622802.0557 667992.8944 635041.5757 609059.9891 636419.4044 744126.5269 560107.2807 553156.3386 600325.4174 1.037440757 1.112717994 1.0578289 1.014549728 1.060124036 1.239538599 0.933006107 0.921427483 1 19.19538523 VIHVVTSEMDNYEPGVYTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VIHVVTSEMDNYEPGVYTEK 20 0 P35221-2;P35221;G3XAM7;P35221-3 P35221-2 CTNNA1 Catenin alpha-1 0 83.936 0.0035985 0 365360 267690 198990 274690 295000 250940 251830 351940 307860 FALSE TRUE 317076.7503 265931.5268 295222.2296 337062.5629 289130.0772 260593.8242 227407.5654 276680.3698 271465.1415 1.168020132 0.979615745 1.087514323 1.241642153 1.065072574 0.959953174 0.837704481 1.019211411 1 18.05040743 2.819103653 4.121653685 0.953153992 1.111043188 0.481224852 0.080686382 0.212792076 6.774141398 0.027508971 0.027256645 659.3312383 -2.819103653 0.157889196 VIISAPSADAPMFVMGVNHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 VIISAPSADAPMFVMGVNHEK 21 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;; 348.4 2.72E-95 1.10221E+11 44063460 40896070 28178108 33443329 36611150 32102640 42364445 48150200 51300250 FALSE TRUE 38240362.12 40627421.02 41805135.28 41037148 35882659.74 33337649.33 38255947.64 37853654.44 45235592.89 0.845360029 0.898129513 0.924164637 0.907187137 0.793239515 0.736978278 0.84570457 0.836811281 1 25.43095504 5.089138013 13.25401793 0.861538031 0.599952935 0.002836735 0.072693051 41723734.87 127702298.6 0.018459833 306076214.8 122782.9356 -5.089138013 -0.261585096 VIISAPSADAPMFVMGVNHEKYDNSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VIISAPSADAPMFVMGVNHEKYDNSLK 27 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;; 276.03 4.10E-61 13114189000 7579420 5917365 2433654 3328970 5601109 4309431 9565860 11085620 973741 FALSE TRUE 6577780.443 5878493.44 3610577.214 4084863.519 5489657.889 4475217.599 8638164.37 8715046.431 858626.4483 7.66081741 6.846392225 4.205061726 4.757439661 6.393534581 5.212065862 10.06044525 10.149986 1 19.71167109 7.12215194 3.78598538 6.576037641 38.32741606 0 2.750329049 41805811.78 97273771.06 0.699738118 2485817308 13248049.43 -7.12215194 31.75137842 VIKDFMIQGGDFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VIKDFMIQGGDFTR 14 1 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ; 159.18 4.52E-06 2486600000 2654300 2300800 1214620 1585780 1972630 2007640 1730660 2271100 1203430 FALSE TRUE 2303527.53 2285685.893 1802014.295 1945855.586 1933378.522 2084875.21 1562820.86 1785442.939 1061161.876 2.170759788 2.153946485 1.698152124 1.833702877 1.821944951 1.964709868 1.472745011 1.682535887 1 20.01721332 0.7089957 0.570119099 4.65E-32 1.982993571 0.708738996 0.18388461 4.151275319 0.684864532 6.228490579 0.109495567 5.116767699 -0.7089957 1.982993571 VILGSEAAQQHPEEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VILGSEAAQQHPEEVR 16 0 G3V1D3;G3V180;Q9NY33-4;Q9NY33;Q9NY33-2;E9PKK8;E9PPK9;E9PQ14;E9PNX5 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ;;; 327 1.93E-71 3201840000 1807640 1479150 913824 1121670 1540000 1525480 1374390 1523730 1439560 FALSE TRUE 1568755.794 1469433.366 1355752.343 1376362.317 1509357.013 1584166.203 1241101.869 1197892.197 1269376.857 1.235847168 1.15760214 1.068045581 1.084281874 1.189053515 1.247987305 0.977725301 0.943685235 1 20.27568901 2.185115245 10.06375852 0.96721838 1.156635859 0.701861237 0.058200915 0.245715773 44.51074129 0.025367648 0.017118357 153.1493809 -2.185115245 0.18941748 VILHLK ddPTM_MDA-MB-175_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 ; 105.82 0.032648 20844200000 23181000 20126000 16149300 20640000 18274100 17266200 21817000 25256000 33291000 FALSE TRUE 20117572.12 19993790.98 23959155.5 25326627.46 17910481.16 17930441.89 19701190.7 19855200.94 29355375.91 0.685311344 0.681094701 0.816176075 0.862759433 0.610126105 0.610806073 0.671127182 0.676373588 1 24.8071214 1.235645748 24.99072162 1.000000406 0.70136052 0.577056362 0.080251509 65.28114279 559584.4747 0.144172541 0.021178916 17.20464627 -1.235645748 -0.298639885 VILHLKEDQTEYLEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 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 ;;;;;;;;;;;;; 321.62 2.19E-58 6918612100 6246291.1 4891632.1 2514049.59 2852099.89 4451985.2 4109800.2 5773293.8 6456400.6 1013356.54 FALSE TRUE 5420827.905 4859498.647 3729852.381 3499712.762 4363399.405 4267906.873 5213400.656 5075749.575 893558.6843 6.066560597 5.438365417 4.174154923 3.916600916 4.883170497 4.776302831 5.834424473 5.680376303 1 19.76920296 4.42670584 4.299125357 4.55037277 5.951661437 0.1549636 1.34437927 0.400305039 15.30276986 0.336368524 1.0578908 26711.96521 -4.42670584 1.401288666 VILSNMVSISSEPFGHLVDDDDIS(ph)DQEDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VILSNMVSISSEPFGHLVDDDDISDQEDHR 30 0 A8MUM1;Q53HC9;C9JVR6 A8MUM1 TSSC1 Protein TSSC1 1 VILSNMVSIS(0.008)S(0.008)EPFGHLVDDDDIS(0.984)DQEDHR 73.138 0.0087695 186390000 31650 29630 24939 17364 38076 29027 33873 44725 41174 TRUE FALSE 27467.37231 29435.35858 36999.58382 21306.76159 37318.36209 30143.68747 30588.00167 35160.9068 36306.45663 0.756542358 0.810747215 1.019091017 0.586858746 1.027871226 0.830256937 0.842494821 0.968447766 1 15.14793851 -1.999999534 0.415835054 4.392032319 0.817823739 0.187455564 0.124836542 142.8856458 1.986863144 420.2279488 0.10744209 0.010000011 1.999999534 -3.57420858 VILSNMVSISSEPFGHLVDDDDIS(ph)DQEDHRSEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VILSNMVSISSEPFGHLVDDDDISDQEDHRSEEK 34 1 A8MUM1;Q53HC9 A8MUM1 TSSC1 Protein TSSC1 1 VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHRSEEK;VILSNMVSISSEPFGHLVDDDDIS(0.994)DQEDHRS(0.006)EEK;VILSNMVSISSEPFGHLVDDDDIS(0.997)DQEDHRS(0.003)EEK;VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHRSEEK;VILSNMVSISSEPFGHLVDDDDIS(0.989)DQEDHRS(0.011)EEK 284.79 1.38E-74 826170000 324613 282281 96157.4 210309 293466 275560 350755 411981 292569 TRUE FALSE 281714.5696 280426.6775 142659.4403 258062.8728 287626.6008 286160.9715 316738.8341 323882.0692 257981.8261 1.091993858 1.087001677 0.55298252 1.000314157 1.114910322 1.109229188 1.227756384 1.255445293 1 17.97690991 3.275348532 3.454007496 1.164362946 0.90896785 0.293812642 0.162526072 0.273991111 6.763447412 0.050534943 0.064046168 1885.161372 -3.275348532 -0.255395096 VIMELFDNDQVGKDEFLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VIMELFDNDQVGKDEFLGR 19 1 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-2;H0YD14 Q9NZM1-6 MYOF Myoferlin 0 ; 223.06 2.09E-19 440900000 493370 364830 297110 355960 431470 358130 381840 562270 466140 FALSE TRUE 428169.9045 362433.4077 440793.3898 436786.1585 422884.5912 371907.4928 344809.2156 442032.9361 411033.4602 1.041691117 0.881761323 1.072402693 1.062653533 1.028832521 0.904810749 0.838883568 1.075418376 1 18.64889632 2.781786523 24.95730496 0.962763016 1.015491183 0.129236351 0.07957786 1234.478117 712747.5058 0.027018825 0.02701867 605.0433927 -2.781786523 0.052728167 VINAAHSFYNGTTTLPISDEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VINAAHSFYNGTTTLPISDEDR 22 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;;; 207.17 8.40E-23 2170170000 1046794 900884 625079 811390 889719 848007 949173 1098176 1065455 FALSE TRUE 908457.5207 894966.0337 927369.2952 995628.5008 872015.3326 880630.378 857122.3486 863339.6084 939498.1237 0.966960442 0.952600129 0.987090098 1.059745066 0.928171447 0.937341284 0.912319383 0.918937023 1 19.84153075 VINAAHSFYNGTTTLPISDEDRT(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VINAAHSFYNGTTTLPISDEDRTPR 25 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 1 VINAAHSFYNGT(0.002)T(0.001)T(0.001)LPIS(0.007)DEDRT(0.989)PR;VINAAHSFYNGTT(0.001)T(0.001)LPIS(0.003)DEDRT(0.994)PR 251.5 1.79E-40 769220000 342852 377123 211009 259719 345726 350763 319825 424610 323885 TRUE FALSE 297543.2395 374645.6542 313053.6582 318692.1685 338846.729 364257.0796 288808.4207 333810.4558 285595.6843 1.041833809 1.311804326 1.096142818 1.1158858 1.186456055 1.275429216 1.011249247 1.168821779 1 18.12361465 0.15767247 0.989827228 1.62E-16 1.162833995 0.190319818 0.094307477 23.62592841 3.443894977 48.3726355 0.029068839 1.437713896 -0.15767247 1.162833995 VINDKHDDVMAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VINDKHDDVMAK 12 1 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 133.71 0.00021297 258440000 534900 382140 294750 295900 345940 282430 509380 526780 294200 FALSE TRUE 464211.6097 379629.6972 437292.0859 363088.6175 339056.4708 293295.2649 459980.406 414132.1964 259420.0112 1.789420977 1.463378617 1.685652868 1.399616845 1.306978861 1.130580727 1.773110732 1.596377221 1 17.98493025 6.896154162 0.676510493 1.41244174 8.597112289 0.224635501 0.231721802 93.94204242 2.762528086 0.098537336 922.9851239 7873252.171 -6.896154162 7.184670549 VINDPIHGHIELHPLLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VINDPIHGHIELHPLLVR 18 0 Q9Y3Z3-4;Q9Y3Z3;A0A2R8YCS7;Q9Y3Z3-3;A0A2R8YF51;A0A2R8Y5D2;A0A2R8Y586;A0A2R8YD90;A0A2R8Y6J9 Q9Y3Z3-4 SAMHD1 Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 0 175.39 1.21E-12 223900000 40591 50458 31578 34519 46942 37625 34602 50721 42861 FALSE TRUE 35226.79651 50126.53808 46849.22642 42357.06654 46007.94604 39072.4581 31246.30337 39874.70886 37794.02141 0.932073254 1.326308665 1.239593583 1.120734576 1.217333968 1.033826427 0.826752545 1.055053349 1 15.20587041 2.589182645 4.689824074 0.969358563 1.17649157 0.404352051 0.115543439 0.214737333 7.417501747 0.039151183 0.034029877 388.3136392 -2.589182645 0.207133007 VINSVDIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VINSVDIK 8 0 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 60.828 0.089823 153610000 746940 839400 305850 426850 843530 1028700 615810 638770 414720 FALSE TRUE 648229.9865 833885.9261 453760.083 523772.8165 826745.4033 1068274.755 556088.841 502174.0064 365692.2741 1.772610559 2.280294076 1.24082491 1.432277501 2.260768034 2.921239606 1.520646949 1.3732147 1 18.48027062 1.787343526 2.824445769 1.142305271 1.959304269 0.313437497 0.480883064 0.321679321 4.92751311 0.375005512 0.140555299 61.28349505 -1.787343526 0.816998998 VIPAKS(ph)PPPPTHSTQLGAPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VIPAKSPPPPTHSTQLGAPSR 21 1 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 VIPAKS(1)PPPPTHSTQLGAPSR;VIPAKS(1)PPPPTHSTQLGAPSR;VIPAKS(1)PPPPTHSTQLGAPSR;VIPAKS(1)PPPPTHSTQLGAPSR 274.88 5.65E-45 6380070000 2534060 2741750 944600 1703950 2953620 2594310 2867570 3198960 2368690 TRUE FALSE 2199177.551 2723739.264 1401411.719 2090857.891 2894848.741 2694114.784 2589473.503 2514887.298 2088666.167 1.052910027 1.304056774 0.670960128 1.001049342 1.38597962 1.28987333 1.239773758 1.204063789 1 20.99415049 3.269738671 24.56177644 1.225938237 1.004424448 0.268074148 0.17787611 228.2230658 179790.2361 0.051639916 0.066659062 1860.966994 -3.269738671 -0.221513789 VIPDSDAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VIPDSDAHR 9 0 Q5EBL8;Q5EBL8-2 Q5EBL8 PDZD11 PDZ domain-containing protein 11 0 113.62 0.0017705 168420000 164510 189680 110460 124210 162070 210860 157500 161000 156150 FALSE TRUE 142769.5867 188433.9796 163878.8255 152413.7789 158845.1241 218971.9206 142225.6742 126571.4029 137690.1249 1.036890531 1.368536631 1.190200282 1.106933261 1.153642095 1.590324076 1.032940266 0.919248225 1 17.07106557 2.018331058 24.99597415 0.960527429 1.240923248 0.390961215 0.153261453 215.8675799 294352.8691 0.060682677 0.040904581 104.311228 -2.018331058 0.280395819 VIPELNGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VIPELNGK 8 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 119.41 0.0039554 7798200000 8612500 8051500 5209200 6538300 7356900 6186600 8676900 9968400 8996000 FALSE TRUE 7474336.304 7998609.166 7728386.544 8022920.947 7210512.084 6424602.505 7835415.574 7836735.234 7932503.128 0.942241835 1.008333566 0.974268326 1.011398397 0.908983201 0.8099086 0.987760792 0.987927153 1 22.91934475 2.042408916 24.99997654 0.991525363 0.944418994 0.144150035 0.0566672 307.4891719 181263.0161 0.025064278 0.016898316 110.2576966 -2.042408916 -0.047106369 VIPEYCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VIPEYCR 7 0 B0YIW6;P48444;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 ; 131.3 0.0080945 1226250000 1018040 1016170 664580 713150 971320 911200 919230 1068880 1008300 FALSE TRUE 883503.4346 1009494.712 985973.1109 875081.6073 951992.6324 946254.4536 830083.2161 840308.33 889099.9227 0.993705445 1.13541199 1.108956469 0.984233138 1.070737504 1.064283586 0.933621964 0.945122487 1 19.76198604 2.245118492 24.97921647 0.955487542 1.062332902 0.48687801 0.048264266 116.9760052 445567.8027 0.018149278 0.013721087 175.840331 -2.245118492 0.10684536 VIPNLPSEGQPALVEVHSMEALLQHTSEQEEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VIPNLPSEGQPALVEVHSMEALLQHTSEQEEMR 33 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 ;; 154.35 5.89E-11 313186000 181567 202414 49690.3 104429 223316 249215 208163 238021 159796 FALSE TRUE 157572.4609 201084.3291 73720.69528 128141.2005 218872.4485 258802.4623 187975.3843 187122.0614 140905.0989 1.118287856 1.427090507 0.52319395 0.909414929 1.553332351 1.83671467 1.33405665 1.328000639 1 17.10436429 3.243120399 24.99246864 1.41570572 0.99173182 0.320355122 0.300964605 146.6241781 803651.2464 0.092179157 0.114987865 1750.331864 -3.243120399 -0.4239739 VIQIVINRDDVQGYAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VIQIVINRDDVQGYAAK 17 1 O94973-3;O94973;O94973-2;A0A0G2JQM1;A0A0G2JS82 O94973-3 AP2A2 AP-2 complex subunit alpha-2 0 101.05 0.0019874 0 139610 109390 78630 91204 110040 94155 109100 148090 72505 FALSE TRUE 121160.1848 108671.4099 116655.731 111913.2622 107850.4193 97777.20378 98519.49879 116422.1059 63933.5415 1.895095781 1.69975583 1.824640529 1.750462426 1.686914517 1.529356915 1.540967331 1.820986343 1 15.96428539 1.233190463 24.99997618 0.999998883 1.711831259 0.788528086 0.116893669 81.36621181 378746.7491 0.247310886 0.0295294 17.10765419 -1.233190463 0.711832376 VIQLMPS(ph)PIMHPLILNPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VIQLMPSPIMHPLILNPR 18 0 P41212 P41212 ETV6 Transcription factor ETV6 1 VIQLMPS(1)PIMHPLILNPR;VIQLMPS(1)PIMHPLILNPR 187.83 2.64E-14 1244820000 704870 706070 483870 545340 687960 750740 586030 737840 640780 TRUE FALSE 611719.6436 701431.7797 717871.1504 669167.782 674270.942 779621.4536 529196.9008 580058.6579 565027.7184 1.082636522 1.241411274 1.270506078 1.184309655 1.193341353 1.379793288 0.936585735 1.026602128 1 19.10796212 2.222856173 24.9999902 0.993696768 1.224798328 0.677841465 0.077180701 134.8872944 214726.2047 0.030230702 0.020459366 167.0537283 -2.222856173 0.23110156 VIQPMGMS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VIQPMGMSPR 10 0 Q9NPQ8-4;Q9NPQ8;Q9NPQ8-3;Q9NPQ8-2;H0YE35 Q9NPQ8-4 RIC8A Synembryn-A 1 VIQPMGMS(1)PR;VIQPMGMS(1)PR;VIQPMGMS(1)PR;VIQPMGMS(1)PR;VIQPMGMS(1)PR;VIQPMGMS(1)PR 126.34 0.00040392 2208090000 1834120 1928880 1272350 1475140 2058210 2107910 2292620 2287290 2225790 TRUE FALSE 1591736.395 1916209.06 1887662.716 1810093.083 2017255.648 2189002.662 2070282.065 1798170.833 1962659.642 0.811009897 0.976332839 0.961788114 0.922265402 1.027817358 1.115324642 1.054834991 0.916190864 1 20.90437858 3.241765355 24.9583177 1.016527898 0.925164962 0.383587449 0.065570631 108.979198 848718.4176 0.020788359 0.025706366 1744.879157 -3.241765355 -0.091362935 VIQYLAYVASSHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VIQYLAYVASSHK 13 0 P35579;P35579-2;Q5BKV1 P35579 MYH9 Myosin-9 0 ; 257.91 6.46E-24 2978700000 4304400 4644600 1543330 3326300 4473700 4416900 5343800 5811200 5142300 FALSE TRUE 3735562.634 4614089.317 2289689.55 4081587.254 4384682.123 4586821.001 4825559.098 4568520.103 4534383.152 0.823830389 1.017578171 0.504961639 0.900141677 0.96698536 1.011564494 1.064215117 1.007528466 1 22.11247487 3.330946743 3.428619188 1.01596137 0.793504059 0.401799847 0.125467222 0.236021711 5.454840307 0.036793026 0.048055874 2142.627839 -3.330946743 -0.222457311 VIREPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VIREPK 6 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;; 110.61 0.026042 4348900000 7004180 6395420 6166290 6760950 5934900 5598240 7010190 7431680 10586180 FALSE TRUE 6078559.867 6353408.065 9148328.469 8296127.032 5816807.101 5813607.915 6330342.853 5842473.065 9334693.86 0.651179349 0.680623078 0.98003519 0.888741201 0.623138497 0.622795777 0.678152165 0.625888021 1 23.15417128 3.233965914 24.99970053 0.692733379 0.804456764 0.081628002 0.143600078 257.2426867 1399651.768 0.043810248 0.051334269 1713.822792 -3.233965914 0.111723385 VIREPKPR ddPTM_MDA-MB-175_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 ;;;;; 152.79 0.00025387 17415820000 3311700 3248180 1916855 2063890 3173040 3215490 3976950 4239250 1531473 FALSE TRUE 2874050.454 3226842.492 2843852.489 2532527.769 3109902.712 3339191.981 3591266.001 3332719.377 1350424.007 2.128257821 2.389503205 2.105895982 1.875357485 2.302908343 2.472698919 2.659361788 2.467905903 1 20.36498103 VIS(ph)HDRDSPPPPPPPPPPPQPQPSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VISHDRDSPPPPPPPPPPPQPQPSLK 26 1 Q69YN4-3;Q69YN4;Q69YN4-4;Q69YN4-2 Q69YN4-3 KIAA1429 Protein virilizer homolog 1 VIS(0.573)HDRDS(0.427)PPPPPPPPPPPQPQPSLK 122.5 8.16E-05 547470000 379150 260990 185870 257340 275310 214170 267090 375880 383740 TRUE FALSE 329044.3669 259275.5395 275757.3537 315772.9802 269831.8696 222409.2585 241187.6529 295500.9871 338374.6944 0.972426048 0.766237972 0.814946739 0.93320507 0.797435134 0.657286914 0.712782773 0.873295173 1 18.36826215 4.750803354 23.5652242 0.816276728 0.972426267 0.188070162 0.099736875 1579.460795 3040071.724 0.025483658 0.39570689 56338.25017 -4.750803354 0.156149539 VISAFVEIIFDNSDNRLPIDKEEVSLRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VISAFVEIIFDNSDNRLPIDKEEVSLRR 28 3 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 86.791 0.0015758 108350000 122120 113600 58342 65658 87422 70984 121020 134580 30519 FALSE TRUE 105981.5326 112853.7541 86556.38634 80566.65242 85682.47324 73714.80041 109283.499 105801.1143 26911.07859 3.938211999 4.193579746 3.216384883 2.99380986 3.183910781 2.739199032 4.060911148 3.93150776 1 14.71591259 4.215380797 8.589133579 3.149418481 4.066360125 0.201445837 0.836198181 0.335102931 109.0682666 0.212274738 0.458957272 16420.289 -4.215380797 0.916941644 VISFIENTST(ph)PVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VISFIENTSTPVDR 14 0 Q9NUY8-2;Q9NUY8;E9PGE5 Q9NUY8-2 TBC1D23 TBC1 domain family member 23 1 VISFIENTS(0.034)T(0.966)PVDR;VISFIENT(0.032)S(0.195)T(0.772)PVDR 114.64 0.0052062 137524000 327600 328570 207790 259380 296170 319390 300050 342440 475810 TRUE FALSE 284306.83 326411.602 308277.939 318276.1934 290276.7964 331677.14 270951.1972 269211.8709 419560.2838 0.677630464 0.777984987 0.734764349 0.758594666 0.691859567 0.790535122 0.645798012 0.641652419 1 18.67851859 1.22961028 24.99994567 1.000000548 0.713792908 0.750118522 0.051718647 189.0396453 527982.8504 0.159497628 0.013459884 16.96720396 -1.22961028 -0.28620764 VISGTTLGYLS(ph)PK ddPTM_MDA-MB-175_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 236.03 1.11E-16 432360000 531740 547280 474410 641770 814150 627990 842110 1071430 1224080 TRUE FALSE 461469.2117 543684.8816 703836.2628 787493.6873 797950.0079 652149.1817 760442.3018 842313.0324 1079370.657 0.427535443 0.503705449 0.652080227 0.72958597 0.739273393 0.604193914 0.704523786 0.780374218 1 20.04175894 -2 0.083441652 2.424285792 9.73E-13 0.71580125 0.083413988 263.652762 2.077622053 76.8397064 11.53565252 0.01 2 -2.424285792 VISSVSYYTHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VISSVSYYTHR 11 0 Q93008;Q93008-3;O00507;O00507-2 Q93008 USP9X;USP9Y Probable ubiquitin carboxyl-terminal hydrolase FAF-X;Probable ubiquitin carboxyl-terminal hydrolase FAF-Y 0 139.86 3.89E-05 465060000 310570 336610 203860 231350 317780 306470 343710 345390 357800 FALSE TRUE 269527.3876 334398.7867 302447.3779 283881.5535 311456.7997 318260.0992 310377.0571 271531.0363 315501.2916 0.854282993 1.059896728 0.958624849 0.89977937 0.987180744 1.008744204 0.983758436 0.860633676 1 18.26728639 1.797002508 25 0.920594392 0.968116468 0.038995549 0.065235477 404.7581842 173198.5709 0.030585347 0.01602473 62.66174834 -1.797002508 0.047522076 VIY(ph)DFIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VIYDFIEK 8 0 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 1 VIY(1)DFIEK;VIY(1)DFIEK 168.72 0.0031455 98232000 259450 226440 184538 180745 229040 258490 257150 303120 306660 TRUE FALSE 225163.0251 224952.5007 273781.194 221785.9148 224482.5521 268434.2776 232211.6326 238300.1469 270407.0041 0.832681926 0.83190338 1.01247819 0.820192936 0.830165449 0.992704602 0.858748586 0.881264698 1 18.044773 1.23782583 24.57361594 1.000000158 0.883683861 0.228959278 0.067723995 22.56959238 754141.4259 0.092182112 0.015842459 17.29122772 -1.23782583 -0.116316297 VKADRDESSPYAAMLAAQDVAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VKADRDESSPYAAMLAAQDVAQR 23 2 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ;; 117.6 0.00020483 1581253000 866451 803295 423701 488496 663917 610711 907782 956830 171881 FALSE TRUE 751947.305 798018.1023 628604.2208 599416.483 650706.3506 634205.4474 819745.4414 752219.3506 151561.424 4.961337029 5.265311458 4.147521211 3.954940955 4.293350732 4.18447802 5.408668115 4.963131982 1 17.20954307 4.233785384 24.82813011 4.17178114 5.113324384 0.122995304 1.170235982 236.0921925 1227554.662 0.29439936 0.64651085 17131.10526 -4.233785384 0.941543244 VKAEAEAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKAEAEAAR 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 118.28 0.00092591 576560000 808550 817640 503870 579280 726140 735030 924970 995660 750170 FALSE TRUE 701698.0689 812268.869 747543.2173 710814.3777 711691.2347 763307.0797 835266.5518 782745.8572 661485.7572 1.060790896 1.22794612 1.130097223 1.074572461 1.075898048 1.153928216 1.262712829 1.183314756 1 19.33535057 2.494151783 24.53544309 1.167454781 1.118517811 0.030094743 0.079271272 1625.21071 2341399.583 0.028031824 0.024150947 311.9979804 -2.494151783 -0.04893697 VKANLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKANLEK 7 1 P35579 P35579 MYH9 Myosin-9 0 95.099 0.012508 789290000 1323600 1213900 630740 677950 1098600 960320 1718500 1708800 369380 FALSE TRUE 1148682.906 1205925.811 935767.9737 831888.9093 1076740.009 997264.1318 1551840.135 1343386.418 325712.3172 3.52667936 3.702426182 2.872989213 2.554060333 3.30580071 3.061794348 4.76445026 4.124456912 1 18.31323875 VKAPVHFVEPLS(ph)PTGVAGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKAPVHFVEPLSPTGVAGHR 20 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 VKAPVHFVEPLS(1)PTGVAGHR 204.31 5.89E-22 801060000 550670 774770 567450 664430 1017300 963570 1127300 1265700 551410 TRUE FALSE 477897.5643 769680.4849 841870.718 815298.9867 997057.7203 1000639.161 1017974.62 995039.9047 486222.938 0.982877456 1.582978557 1.731450025 1.676800749 2.050618435 2.057984277 2.093637589 2.046468455 1 18.89125843 5.05185875 1.065794049 1.882071555 1.75E-18 0.386142154 0.324610821 3.132367637 1.874053559 0.098908088 7.794269144 112683.0906 -5.05185875 -1.882071555 VKAQT(ph)PPGPSLSGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKAQTPPGPSLSGSK 15 1 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VKAQT(0.997)PPGPS(0.003)LSGSK;VKAQT(1)PPGPSLSGSK 101.49 0.0028286 1232090000 2404200 1483440 1157430 1370790 1589390 1079520 2130120 2319350 1604020 TRUE FALSE 2086478.879 1473695.185 1717167.019 1682048.821 1557764.249 1121049.833 1923541.29 1823375.052 1414394.583 1.47517454 1.041926491 1.214065042 1.189235904 1.101364688 0.792600485 1.359975012 1.289155851 1 20.43175322 4.74958277 24.22072263 1.141409023 1.47517484 0.317911334 0.159975961 1453.990792 3194988.823 0.040067077 0.57343901 56180.1339 -4.74958277 0.333765816 VKAS(ph)PITNDGEDEFVPSDGLDKDEYTFSPGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKASPITNDGEDEFVPSDGLDKDEYTFSPGK 31 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 VKAS(0.928)PIT(0.072)NDGEDEFVPSDGLDKDEYTFSPGK 359.94 2.72E-121 647510000 1847200 1062500 983180 1193800 1002400 657170 1275300 1782300 1387400 TRUE FALSE 1603087.84 1055520.368 1458649.137 1464870.536 982454.2012 682451.7551 1151621.602 1401169.015 1223383.153 1.310372663 0.862788052 1.192307687 1.197393092 0.803063373 0.557839753 0.941341721 1.145323125 1 20.22244488 7.999999971 0.7248456 0.950115773 45.49218719 0.20844254 0.198929024 683.2376349 3.287631182 0.083490301 49510.72222 99999993.29 -7.999999971 44.54207142 VKDDIESLHDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VKDDIESLHDK 11 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 136.99 5.27E-05 1166370000 2097270 1663700 1177010 1594140 1687140 1283940 2195840 2549360 3477020 FALSE TRUE 1820110.456 1652771.045 1746215.973 1956113.852 1653569.215 1333334.003 1982887.775 2004199.203 3065970.657 0.593649013 0.539069427 0.569547516 0.638008015 0.539329759 0.434881528 0.646740624 0.65369158 1 21.54791246 0.949933335 1.521214463 1.527031716 0.559218506 0.845781309 0.058101322 0.901593425 1.031796694 1.649508712 0.01661517 8.911141404 -0.949933335 -0.96781321 VKDEPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VKDEPQR 7 1 P05204;O00479 P05204 HMGN2;HMGN4 Non-histone chromosomal protein HMG-17;High mobility group nucleosome-binding domain-containing protein 4 0 ;;;;; 111.95 0.0058957 3844970000 3439300 3308320 2298530 2845130 2850170 2559650 3795550 4221220 5924370 FALSE TRUE 2984787.791 3286587.428 3410106.796 3491160.252 2793457.193 2658121.392 3427458.145 3318544.953 5223997.728 0.571360852 0.62913263 0.652777236 0.668292835 0.53473553 0.508828972 0.656098705 0.635250076 1 22.31672284 1.181094933 2.976331112 1.116473774 0.60356598 0.844239727 0.053101138 0.208129951 2.010205002 0.27808281 0.014520969 15.17382019 -1.181094933 -0.512907794 VKDEPQRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 VKDEPQRR 8 2 P05204;O00479 P05204 HMGN2;HMGN4 Non-histone chromosomal protein HMG-17;High mobility group nucleosome-binding domain-containing protein 4 0 ;;;;;;; 123.35 0.00075995 11212120000 16427000 14680000 8201470 10036990 12005920 9941460 15141900 17360800 7835900 FALSE TRUE 14256130.33 14583566.11 12167728.32 12316041.99 11767025.68 10323914.4 13673440.87 13648328.02 6909548.829 2.063250537 2.110639417 1.761001858 1.782466886 1.703009266 1.494151739 1.978919494 1.97528498 1 22.72016008 4.188773506 4.459583832 1.709259518 2.090919513 0.271240958 0.278971243 0.279948353 11.59648579 0.071494787 0.167686898 15444.48767 -4.188773506 0.381659995 VKDGPGGK ddPTM_MDA-MB-175_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 ; 73.233 0.040216 1223620000 4147200 3310600 2419500 3046900 1654530 2196400 4275300 4779200 4466500 FALSE TRUE 3599137.012 3288852.451 3589578.293 3738745.214 1621608.09 2280896.929 3860682.064 3757205.272 3938475.458 0.913840152 0.835057241 0.911413142 0.949287422 0.411734974 0.579131939 0.980247841 0.953974529 1 21.90920586 0.063003058 13.20569055 3.364759326 0.837388737 0 0.192114629 0 0 0 0.046283644 1.156120384 -0.063003058 -2.527370589 VKDLDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKDLDNR 7 1 P46977;P46977-2 P46977 STT3A Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A 0 78.496 0.032082 169700000 287590 276140 189860 240150 296720 314080 226250 408980 273860 FALSE TRUE 249584.2528 274326.0182 281676.931 294679.728 290815.8525 326162.8608 204308.3098 321522.8097 241484.5828 1.033541148 1.135998062 1.166438568 1.220283815 1.204283309 1.350657077 0.846051154 1.331442389 1 17.88157156 4.723592187 2.429111217 1.16874302 1.00526679 0.06423955 0.147612423 1.429022077 10.65639955 0.034738536 0.482003394 52916.63106 -4.723592187 -0.163476229 VKDLESLFHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKDLESLFHR 10 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 183 1.03E-06 1553550000 3621800 3381800 1321300 2671200 3800300 3601100 3551900 4818300 2041440 FALSE TRUE 3143169.954 3359584.733 1960285.099 3277736.787 3724681.465 3739636.647 3207437.285 3787944.041 1800103.289 1.746105334 1.866328868 1.088984789 1.820860396 2.069148747 2.077456705 1.781807358 2.104292606 1 20.77964826 3.507676619 24.96379538 1.863592137 1.573369247 0.07462795 0.372484126 1455.63509 1189253.479 0.099077305 0.146735146 3218.671235 -3.507676619 -0.29022289 VKDSS(ph)PGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VKDSSPGEK 9 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 VKDS(0.079)S(0.921)PGEK;VKDS(0.132)S(0.868)PGEK;VKDS(0.028)S(0.972)PGEK 112.44 0.0011886 1546140000 4956480 3587870 3426350 3795110 2550970 2684250 6046630 7398780 6421160 TRUE FALSE 4301468.61 3564301.046 5083344.32 4656847.73 2500210.688 2787514.834 5460228.753 5816608.474 5662057.78 0.759700585 0.6295063 0.897790965 0.822465597 0.441572797 0.492314798 0.964354121 1.027295853 1 22.43289504 2.11896133 7.188024465 1.00916868 0.678905843 0.553705079 0.137190715 0.175726749 10.32410942 0.061046426 0.041023778 131.5107729 -2.11896133 -0.330262836 VKEDPDGEHAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VKEDPDGEHAR 11 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;; 172.92 7.68E-06 5917800000 18599100 14766200 10143800 12178000 13194100 11878900 15835000 19494300 19016800 FALSE TRUE 16141181.81 14669199.86 15049375.61 14943201.03 12931563.22 12335888.97 14299324.14 15325595.65 16768655.57 0.962580557 0.874798805 0.897470614 0.891138885 0.771174718 0.73565164 0.85274124 0.913943016 1 23.99926369 1.417693983 2.516291699 1.00703752 0.851530784 0.349332336 0.063744254 0.449480063 4.356659044 0.130145944 0.018543823 26.16338807 -1.417693983 -0.155506736 VKEDPDGEHARR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKEDPDGEHARR 12 2 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 67.519 0.033118 96883000 259410 207960 80334 85502 189670 155850 240590 258720 25637 FALSE TRUE 225128.3112 206593.8971 119183.7911 104916.5359 185895.9381 161845.6503 217257.6188 203394.7414 22606.22307 9.958687508 9.138806446 5.272167348 4.641046654 8.223219666 7.159340589 9.610522651 8.997289851 1 14.46443235 4.389460462 6.633749901 6.84983941 9.757480839 0.20294024 2.491498065 0.345056016 20.95366566 0.631363381 1.707820059 24516.61243 -4.389460462 2.907641429 VKEEIIEAFVQELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKEEIIEAFVQELR 14 1 P50552 P50552 VASP Vasodilator-stimulated phosphoprotein 0 ; 193.69 2.10E-07 1957040000 1690370 1693000 1119970 1414420 1410360 1181050 1714380 2064210 2201650 FALSE TRUE 1466983.322 1681878.572 1661591.238 1735585.679 1382296.595 1226485.758 1548119.691 1622794.755 1941373.445 0.755642005 0.866334386 0.855884396 0.893998877 0.712019936 0.63176189 0.797435288 0.835900357 1 20.88864623 1.229855054 2.470035974 1.056102732 0.789307822 0.427220249 0.077016206 0.621419609 4.021056719 0.360117023 0.022304856 16.97676956 -1.229855054 -0.266794911 VKEEPPS(ph)PPQS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VKEEPPSPPQSPR 13 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 2 VKEEPPS(1)PPQS(1)PR;VKEEPPS(1)PPQS(1)PR;VKEEPPS(1)PPQS(1)PR 63.488 0.039076 2900120000 2672250 2119160 1572110 1849840 2272510 1944140 2386640 2984450 2815530 TRUE FALSE 2319105.392 2105239.098 2332387.654 2269874.445 2227291.497 2018932.324 2155184.02 2346248.593 2482681.251 0.934113226 0.847969951 0.939463193 0.914283476 0.897131477 0.813206417 0.868087282 0.945046245 1 21.24346762 1.496859234 3.22350664 0.995756767 0.887022449 0.484846525 0.038451443 0.20600531 4.141632704 0.044399878 0.010355831 31.39490938 -1.496859234 -0.108734317 VKEEPPS(ph)PPQSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VKEEPPSPPQSPR 13 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 1 VKEEPPS(0.999)PPQS(0.001)PR;VKEEPPS(1)PPQSPR;VKEEPPS(1)PPQSPR;VKEEPPS(1)PPQSPR 107.98 0.00075858 2694470000 3497230 2776510 1761150 2205000 2630530 2140290 2978270 3334650 3052180 TRUE FALSE 3035062.195 2758270.923 2612848.031 2705678.951 2578187.6 2222628.341 2689437.834 2621561.048 2691354.757 1.127707964 1.024863376 0.970830034 1.005322299 0.957951601 0.825839973 0.999287748 0.974067443 1 21.35990114 5.13880062 1.013356586 0.956863568 1.365802065 0.529671042 0.050671392 3.18915395 1.529746534 0.01646396 1.712463657 137657.7353 -5.13880062 0.408938498 VKEFCENLSADCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKEFCENLSADCR 13 1 P30153;B3KQV6;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 150.59 4.04E-05 474630000 728520 746030 330010 350510 703140 650180 840940 915060 171420 FALSE TRUE 632244.2362 741129.2798 489603.9398 430098.6527 689148.8897 675192.8453 759385.7682 719381.54 151154.9229 4.1827565 4.903110436 3.239086961 2.84541611 4.559222264 4.466892857 5.023890415 4.759233284 1 17.20566844 4.255428888 24.99402557 3.892381147 4.542933271 0.061310345 1.199756503 890.9865007 1320167.681 0.301012617 0.791816731 18006.48269 -4.255428888 0.650552124 VKEFLHNQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKEFLHNQGK 10 1 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ; 154.24 8.91E-06 1238680000 1480020 1151590 924260 1014570 1210100 1059530 1649090 1763070 1326020 FALSE TRUE 1284431.607 1144025.129 1371235.227 1244943.625 1186021.378 1100290.805 1489161.506 1386051.201 1169259.426 1.098500109 0.978418565 1.172738228 1.064728321 1.014335528 0.941015125 1.273593757 1.185409473 1 20.15716363 2.239324781 24.99999983 1.164777505 1.04724675 0.233423522 0.091411515 27.48512265 899250.582 0.035490573 0.025833768 173.5101082 -2.239324781 -0.117530755 VKEGMNIVEAMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 20 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 ;;;;;;;;;;;;;;;;;;; 199.33 1.08E-07 61640180000 47339333 38456505 24449347 29981039 35887284 31609698 39328837 48811177 34347437 FALSE TRUE 41083320.2 38203881.69 36273132.99 36788692.14 35173197.26 32825743.54 35514732.44 38373286.65 30286922.13 1.356470625 1.261398617 1.197650023 1.214672524 1.161332839 1.083825666 1.172609494 1.266991954 1 24.85219164 5.893283387 0.612957939 1.152180071 2.081891691 0.504445791 0.069569382 12.27413693 1.207048641 0.033682161 11.0258869 782138.0012 -5.893283387 0.92971162 VKELEEQLENETLHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VKELEEQLENETLHK 15 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 ;; 206.63 2.28E-09 369478000 498840 427145 329161 371921 402232 311232 536740 649850 442400 FALSE TRUE 432917.0301 424339.0564 488344.3606 456371.3475 394228.3702 323205.2964 484687.0374 510884.6346 390099.976 1.109759182 1.087770014 1.251844119 1.169883044 1.010582913 0.82851914 1.24246877 1.309624881 1 18.57348438 VKELLTLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKELLTLIR 9 1 Q15067-2;Q15067;Q15067-3;K7ENF1;K7ESC7 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 127.42 0.0013953 0 326150 312310 227240 289500 374860 416210 319890 429950 201780 FALSE TRUE 283048.4511 310258.415 337134.0241 355235.3997 367401.0194 432221.868 288867.117 338008.5384 177925.7983 1.590822994 1.74375171 1.894801245 1.996536776 2.064911457 2.429225397 1.623525761 1.899716296 1 17.44091618 0.985850385 2.087453863 4.29E-15 1.929230256 0.574717961 0.242210543 1.389915583 3.145923614 6.706837929 0.066581979 9.679443403 -0.985850385 1.929230256 VKELLVDCYKPTEAFISGLLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKELLVDCYKPTEAFISGLLDK 22 2 B5MC51;P53671-3;F5GXC4;F5H2U0;Q96C90 B5MC51;Q96C90 LIMK2;PPP1R14B LIM domain kinase 2;Protein phosphatase 1 regulatory subunit 14B 0 72.145 0.0087795 231260000 279700 148670 396530 239580 78649 52480 187520 242540 161080 FALSE TRUE 242736.9363 147693.377 588293.2343 293980.3008 77084.03877 54498.93956 169334.3393 190674.7084 142037.3059 1.708966069 1.039821025 4.141821971 2.069740051 0.542702766 0.383694546 1.19218214 1.342426958 1 17.11591038 3.329504829 6.182159711 0.948866214 2.314577939 0.400287889 0.819994578 0.226953233 12.61651345 0.244089794 0.315139518 2135.525829 -3.329504829 1.365711725 VKELVEFAQDDDRLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKELVEFAQDDDRLR 15 2 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 150.59 1.77E-06 263890000 238323 192538 97519 99974 195642 171852 203927 244883 69100 FALSE TRUE 206828.0117 191273.2052 144679.5146 122674.6247 191749.107 178463.2576 184150.1909 192516.6761 60931.07672 3.394458507 3.139173235 2.37447822 2.013334267 3.146983728 2.92893655 3.022270422 3.159581063 1 15.89489061 4.394525763 5.186785722 2.625289577 3.336705889 0.173150598 0.6576927 0.360338189 16.15446926 0.163609274 0.462388557 24804.23077 -4.394525763 0.711416312 VKENDQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKENDQK 7 1 P46778;M0R181 P46778 RPL21 60S ribosomal protein L21 0 ; 87.308 0.017727 240541000 1133880 568820 597740 577060 363330 407170 1039780 1079790 674610 FALSE TRUE 984034.8851 565083.384 886809.0633 708090.2928 356100.4438 422834.0934 938942.2956 848885.3114 594858.3743 1.654233894 0.949946085 1.490790248 1.190351054 0.598630631 0.710814728 1.578429986 1.427037675 1 19.1821867 4.753703219 23.86543122 1.148869602 1.654234584 0.209202662 0.322648383 2833.593447 4465729.611 0.084991668 1.829378324 56715.68982 -4.753703219 0.505364982 VKESSIIAPAPAEDVDT(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 98.839 0.0012006 1045950000 2692630 2274800 1477470 1890480 2213630 2053820 2574400 3081500 1718020 TRUE FALSE 2336792.123 2259856.689 2191979.434 2319742.378 2169583.094 2132831.784 2324735.084 2422545.205 1514917.633 1.542520909 1.491735683 1.446929778 1.531266339 1.432145911 1.407886302 1.534562034 1.59912668 1 20.53080792 1.231495899 24.99979076 0.999999137 1.499031819 0.881167832 0.057504494 88.15561666 311926.8359 0.151841948 0.015438493 17.04103227 -1.231495899 0.499032682 VKEVHDELEDLPS(ph)PPPPLS(ph)PPPTTSPHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKEVHDELEDLPSPPPPLSPPPTTSPHK 28 1 F5H039;Q9NQX3;Q9NQX3-2;H0YJ30;G3V582 F5H039 GPHN Gephyrin;Molybdopterin adenylyltransferase;Molybdopterin molybdenumtransferase 2 VKEVHDELEDLPS(0.999)PPPPLS(0.618)PPPT(0.136)T(0.127)S(0.12)PHK 54.389 0.036269 226460000 270620 272440 171560 218130 277180 210020 385080 438750 333470 TRUE FALSE 234856.8813 270650.3237 254526.9898 267659.7504 271664.6603 218099.6053 347735.0009 344926.7269 294047.5565 0.798703734 0.920430446 0.865598044 0.910260074 0.923880013 0.741715415 1.182580821 1.173030414 1 18.16568998 2.22820347 24.99999977 1.132558398 0.868269621 0.725563819 0.074648086 99.73343172 240733.6376 0.029263037 0.019971671 169.1233099 -2.22820347 -0.264288777 VKEYQVETIVDTLCTNMLSDKEQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKEYQVETIVDTLCTNMLSDKEQLR 25 2 Q86VP6;Q86VP6-2 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 175.11 1.25E-12 289920000 410480 348380 189810 191250 268930 228750 355050 514720 109160 FALSE TRUE 356234.028 346091.4688 281602.7509 234676.2356 263578.8192 237550.1605 320617.3056 404651.1336 96255.22916 3.700931691 3.595560178 2.925583923 2.438062198 2.738332467 2.467919536 3.330907925 4.203939226 1 16.5545773 4.245592994 4.845152686 2.870235821 3.669451717 0.167906686 0.806659222 0.369102553 22.80020453 0.211053447 0.534562435 17603.25558 -4.245592994 0.799215896 VKFEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKFEER 6 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ; 94.407 0.0406 4677400000 8406100 7684100 4728800 5807800 6477900 5744100 8574300 9293900 7849900 FALSE TRUE 7295212.587 7633622.641 7015663.497 7126549.757 6349002.464 5965079.244 7742765.706 7306471.81 6921893.765 1.053933047 1.102822855 1.013546832 1.029566474 0.91723489 0.861769834 1.118590659 1.055559657 1 22.72273537 4.147800442 5.882117988 1.003380841 1.077910583 0.175086051 0.071030318 0.393532925 20.23381131 0.019994606 0.043016303 14054.01594 -4.147800442 0.074529743 VKFQGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKFQGGR 7 1 Q9UK45;K7ENY5;K7EML7 Q9UK45 LSM7 U6 snRNA-associated Sm-like protein LSm7 0 92.467 0.014271 555570000 775130 853350 424850 677910 902830 904020 1149800 1290300 731050 FALSE TRUE 672694.6066 847744.2877 630308.881 831839.8267 884865.4494 938798.2344 1038292.573 1014379.386 644626.1018 1.043542303 1.315094572 0.977789884 1.290422191 1.372680143 1.456345363 1.610689623 1.573593411 1 19.29810308 3.349617246 2.446693412 1.448695024 1.131643614 0.315909745 0.187114091 0.311206536 3.790453281 0.058033086 0.079209905 2236.748969 -3.349617246 -0.317051409 VKGDVDVSLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKGDVDVSLPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 113.65 0.00079391 0 2870400 1716600 1221300 2021900 1779900 1327500 1839600 2848300 2271900 FALSE TRUE 2491069.367 1705323.542 1811924.765 2481003.298 1744483.472 1378569.784 1661195.875 2239213.21 2003318.57 1.24347141 0.851249306 0.904461623 1.238446713 0.870796836 0.688143066 0.829222022 1.117751936 1 20.93396043 VKGPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKGPVR 6 1 P60866;P60866-2;E5RJX2 P60866 RPS20 40S ribosomal protein S20 0 ; 98.03 0.036843 2217200000 5485800 6890100 4210400 5049400 5787800 6066700 7313400 8104500 7211400 FALSE TRUE 4760837.631 6844838.479 6246563.523 6195943.445 5672634.104 6300089.875 6604147.594 6371415.744 6358876.507 0.748691632 1.076422615 0.982337606 0.974377068 0.892081187 0.990755186 1.03857145 1.001971926 1 22.60034046 4.750966594 24.96338064 0.992871535 0.748691478 0.730472193 0.046926758 1081.820098 2176805.088 0.011790201 0.199672305 56359.43028 -4.750966594 -0.244180057 VKKDDEEEDPLDQLISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKKDDEEEDPLDQLISR 17 2 Q9NYJ1;Q9NYJ1-2 Q9NYJ1 COA4 "Cytochrome c oxidase assembly factor 4 homolog, mitochondrial" 0 149.47 1.82E-07 117020000 214160 141760 132260 113680 134900 98276 183510 232870 121890 FALSE TRUE 185858.2134 140828.7692 196221.3784 139492.7815 132215.7539 102056.7413 165713.2284 183072.5627 107480.3031 1.729230455 1.310275141 1.825649657 1.29784507 1.230139385 0.949539017 1.541800904 1.703312677 1 16.71371277 3.701807838 24.63164967 1.32994048 1.590574234 0.258663072 0.258607734 848.2349298 568485.2629 0.075312859 0.111711355 5032.778742 -3.701807838 0.260633753 VKLDGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VKLDGSR 7 1 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ;;;;; 117.04 0.0048531 4613660000 9708710 8747670 5918570 6940660 7745500 7458590 10110600 11623940 8028390 FALSE TRUE 8425679.375 8690205.98 8780810.248 8516642.934 7591379.704 7745526.784 9130075.568 9138250.889 7079282.88 1.19018826 1.22755456 1.240353069 1.203037522 1.072337387 1.094111779 1.289689326 1.29084415 1 22.75517179 3.466760798 24.98675954 1.171458143 1.220436091 0.09013328 0.091164808 727.1207983 1753621.944 0.02845433 0.036779709 2929.279407 -3.466760798 0.048977948 VKLEAEIATYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VKLEAEIATYR 11 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 217.09 1.06E-11 36416360000 19965110 17335260 11942600 14465620 16804250 15257050 19975880 22737050 19046010 FALSE TRUE 17326670.13 17221383.54 17718081.31 17750260.11 16469878.3 15843998.59 18038622.23 17874908.8 16794412.4 1.031692549 1.025423405 1.054998585 1.056914627 0.980676067 0.943408928 1.07408475 1.06433666 1 24.00147798 VKLNFDMTAS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKLNFDMTASPK 12 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 VKLNFDMT(0.001)AS(0.999)PK 92.935 0.0045151 516270000 609210 436770 342030 340820 454470 348110 580590 643590 385020 TRUE FALSE 528701.355 433900.8291 507436.852 418208.3901 445426.9362 361502.017 524284.4712 505963.2869 339503.3742 1.557278646 1.278045705 1.494644503 1.231823958 1.311995609 1.064796536 1.544268808 1.490304148 1 18.37306639 7.213236138 1.327062528 1.319450917 199.9973818 0.15383056 0.179386217 2912.639024 7.912848607 0.050665296 1758529.637 16339401.24 -7.213236138 198.6779309 VKNFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKNFLK 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 ; 91.584 0.097207 0 1427830 1255010 724000 839480 1215800 1167890 1490220 1656980 737270 FALSE TRUE 1239138.648 1246765.757 1074128.822 1030096.765 1191607.959 1212819.484 1345698.694 1302647.722 650110.7805 1.906042301 1.917774315 1.652224288 1.584494206 1.832930624 1.865558179 2.069952897 2.003731919 1 19.31032605 1.232610151 24.99996535 0.999998605 1.858176112 0.773448272 0.145254175 106.5116259 447446.6126 0.359234571 0.040723857 17.0848099 -1.232610151 0.858177507 VKPAPDETSFSEALLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKPAPDETSFSEALLKR 17 2 Q12905;B4DY09;A0A0A0MRL0;X6R6Z1 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ; 93.152 0.0017618 841770000 1126910 853280 442440 501610 742790 793420 917730 1087230 259380 FALSE TRUE 977985.9883 847674.7475 656405.4639 615508.2171 728009.9322 823943.3808 828728.6859 854734.3253 228716.3919 4.275976812 3.706226478 2.869953738 2.691141689 3.183024733 3.602467554 3.623389994 3.737092555 1 17.80320024 4.469924641 3.474336587 3.08680964 4.215467329 0.232633063 0.786256106 0.376684874 9.252573218 0.197518596 0.788284784 29506.97173 -4.469924641 1.128657689 VKPAPLEIKPLPEWEELQAPVRS(ph)PITR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKPAPLEIKPLPEWEELQAPVRSPITR 27 3 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 VKPAPLEIKPLPEWEELQAPVRS(0.956)PIT(0.044)R 97.437 0.0029546 822040000 116120 126390 104920 160900 129890 135840 194520 248310 179430 TRUE FALSE 100774.4478 125559.7358 155659.6629 197434.8042 127305.4431 141065.8527 175655.4803 195210.8389 158217.9898 0.636934194 0.793586974 0.983830367 1.24786571 0.804620532 0.891591739 1.110211807 1.233809373 1 17.27155412 4.340688581 2.455756447 1.058154003 0.65173736 0.512268729 0.136342445 0.260578631 2.961390474 0.039060766 0.155505734 21912.33106 -4.340688581 -0.406416643 VKPAS(ph)PVAQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VKPASPVAQPK 11 1 Q96EV2;H0Y3K4 Q96EV2 RBM33 RNA-binding protein 33 1 VKPAS(1)PVAQPK;VKPAS(1)PVAQPK;VKPAS(1)PVAQPK 162.7 1.50E-05 2245670000 6567930 4565860 3705920 4069740 4172560 3104930 6025470 6844330 5956880 TRUE FALSE 5699961.409 4535866.565 5498115.308 4993836.669 4089534.219 3224378.666 5441120.847 5380723.292 5252664.433 1.085156206 0.86353633 1.046728832 0.950724481 0.778563769 0.613855826 1.035878251 1.024379791 1 22.32461799 VKPET(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VKPETPPR 8 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VKPET(1)PPR;VKPET(1)PPR;VKPET(1)PPR;VKPET(1)PPR;VKPET(1)PPR 104.43 0.0074061 24090400000 11498000 8143200 6416230 7945410 9050000 7291450 9964800 11375500 13214400 TRUE FALSE 9978510.168 8089706.783 9519140.289 9749536.778 8869922.706 7571956.8 8998415.23 8942937.849 11652208.69 0.856362123 0.694263809 0.816938706 0.83671148 0.761222438 0.649830174 0.772249749 0.767488644 1 23.47410011 1.238489097 9.815151129 1.001065121 0.766610554 0.578255389 0.06185555 0.054351412 102.8042426 0.084269738 0.014909046 17.31765552 -1.238489097 -0.234454566 VKPET(ph)PPRQSHSGSIS(ph)PYPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKPETPPRQSHSGSISPYPK 20 2 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 VKPET(0.999)PPRQSHS(0.002)GS(0.012)IS(0.986)PYPK;VKPET(0.998)PPRQS(0.003)HS(0.112)GS(0.035)IS(0.852)PYPK 133.4 2.05E-05 1306210000 1504080 1025840 370060 374870 993190 695120 1413420 1552230 155449 TRUE FALSE 1305312.017 1019101.189 549022.2538 459989.963 973427.4621 721861.7162 1276346.746 1220297.694 137071.9963 9.522820505 7.434787681 4.005356809 3.355827415 7.101577918 5.266296075 9.311506218 8.902603937 1 17.06457433 4.547581937 4.235287713 6.008998388 9.304594086 0.193555619 2.525497771 0.436389409 14.36327891 0.654073733 2.893700243 35284.33502 -4.547581937 3.295595698 VKPFMTGAAEQIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKPFMTGAAEQIK 13 1 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;E9PJF7;P13693-2;Q56UQ5 Q5W0H4 TPT1 Translationally-controlled tumor protein;TPT1-like protein 0 ; 166.6 3.04E-05 973110000 1560970 1349120 1119730 1291780 1322850 995200 1711400 1879410 1570240 FALSE TRUE 1354683.86 1340257.542 1661235.173 1585098.393 1296527.873 1033485.988 1545428.691 1477512.797 1384608.016 0.978387994 0.967968932 1.199787343 1.144799376 0.936386225 0.746410519 1.116148884 1.067098255 1 20.40104617 VKPLLQVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKPLLQVSR 9 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 152.54 0.0015501 0 2454300 3523100 2283100 2727600 3621700 3449500 3298800 4138500 4710800 FALSE TRUE 2129958.037 3499956.524 3387214.797 3346943.269 3549635.256 3582204.497 2978882.884 3253513.981 4153894.591 0.512761696 0.842572301 0.815431091 0.805736206 0.854531856 0.862372508 0.71713011 0.783244233 1 21.98603318 4.740474202 24.85484807 0.82546664 0.512761581 0.661097989 0.072242545 99.65637231 1294293.606 0.017332257 0.109393679 55014.12403 -4.740474202 -0.312705059 VKPPGGHS(ph)PQVNHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKPPGGHSPQVNHLK 15 1 Q92610 Q92610 ZNF592 Zinc finger protein 592 1 VKPPGGHS(1)PQVNHLK;VKPPGGHS(1)PQVNHLK 195.97 5.53E-09 700260000 1370300 972160 786350 891190 899750 729100 1240290 1338080 1299210 TRUE FALSE 1189211.383 965773.8169 1166631.49 1093548.31 881846.7353 757148.9488 1120006.867 1051942.005 1145618.874 1.038051494 0.843014932 1.018341716 0.954548092 0.769755767 0.660908236 0.977643518 0.918230337 1 20.12769574 4.752170129 23.28851377 0.893528837 1.038051748 0.145272835 0.110708292 1938.264082 3316591.535 0.028233628 0.50014066 56515.8324 -4.752170129 0.144522911 VKQIESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKQIESK 7 1 P10599;P10599-2 P10599 TXN Thioredoxin 0 99.442 0.0095993 1727400000 2415000 2116000 1202400 1555900 1477000 1389500 2542200 2939800 1501100 FALSE TRUE 2095851.631 2102099.857 1783884.662 1909190.875 1447610.59 1442954.964 2295657.835 2311146.648 1323641.668 1.583398046 1.588118527 1.34770966 1.442377436 1.093657464 1.090140178 1.734349931 1.746051596 1 20.33608118 4.246245263 24.31476157 1.39127456 1.585758449 0.113667176 0.253955739 343.0543629 1085410.927 0.069472036 0.176202259 17629.71384 -4.246245263 0.194483889 VKS(ph)PGGPGSHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VKSPGGPGSHVR 12 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 VKS(1)PGGPGSHVR;VKS(1)PGGPGSHVR;VKS(0.999)PGGPGS(0.001)HVR;VKS(1)PGGPGSHVR;VKS(1)PGGPGSHVR;VKS(1)PGGPGSHVR 146.1 3.89E-05 5798250000 3737100 3098800 2280630 2610030 3002290 2807850 3753980 3849870 3379590 TRUE FALSE 3243232.766 3078443.779 3383550.296 3202677.203 2942550.303 2915869.806 3389919.597 3026605.26 2980058.72 1.088311698 1.03301447 1.13539719 1.074702717 0.987413531 0.97846052 1.137534497 1.015619337 1 21.50690933 3.410028222 10.1297905 1.029134094 1.084423445 0.256047444 0.049829919 0.623137983 89.8157623 0.014477502 0.018695463 2570.562822 -3.410028222 0.055289351 VKS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKSPSK 6 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5;A0A3B3ISF7;A0A3B3ISJ7;A0A3B3IRN6;A0A3B3ITZ5;N0DVX5;Q9HCK1 Q5T4S7-3;A0A3B3ITZ5 UBR4;ZDBF2 E3 ubiquitin-protein ligase UBR4;DBF4-type zinc finger-containing protein 2 1 VKS(0.856)PS(0.144)K 71.223 0.053777 226990000 661710 569780 532980 472260 496600 442380 862970 1009900 1006500 TRUE FALSE 574263.3469 566037.0777 790730.9107 579493.851 486718.6316 459398.6449 779279.3022 793940.7441 887512.7166 0.647048021 0.637779118 0.89095164 0.652941462 0.548407502 0.517624859 0.878048604 0.894568302 1 19.75940827 2.108319711 6.504603563 0.923834049 0.655800955 0.621028254 0.101809261 0.153478818 8.260207901 0.045261198 0.030323677 128.3274932 -2.108319711 -0.268033094 VKS(ph)ST(ph)PPRQS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKSSTPPRQSPSR 13 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 VKS(0.882)S(0.326)T(0.791)PPRQS(0.873)PS(0.127)R 66.068 0.015541 0 423040 339260 240320 259450 407180 322070 354390 416700 422360 TRUE FALSE 367134.1922 337031.3787 356539.5558 318362.0879 399077.9146 334460.2413 320021.3123 327591.9478 372429.082 0.985782824 0.904954514 0.957335431 0.854826069 1.071554113 0.898050817 0.85928121 0.879608934 1 18.50660621 VKSGT(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKSGTPPR 8 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VKS(0.057)GT(0.943)PPR;VKS(0.031)GT(0.969)PPR 93.345 0.018001 1473260000 2282300 1558110 890650 1095500 1430840 1405970 1840770 2025800 464220 TRUE FALSE 1980688.272 1547874.673 1321371.319 1344250.019 1402369.083 1460058.576 1662252.409 1592598.435 409340.4404 4.838730985 3.781387129 3.228049781 3.283941399 3.42592362 3.566856414 4.060806714 3.890645237 1 18.64294168 1.236548267 24.99696818 0.999996526 3.732573889 0.777448935 0.463801057 25.81845214 320626.6007 0.74123095 0.116562131 17.24043689 -1.236548267 2.732577363 VKT(ph)PEMIIQKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKTPEMIIQKPK 12 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VKT(1)PEMIIQKPK 126.88 0.013328 1276500000 1718500 1343100 1094900 1333300 1390600 869540 1603400 2259700 1710600 TRUE FALSE 1491395.871 1334277.088 1624397.302 1636046.143 1362929.781 902991.7665 1447902.515 1776480.74 1508374.817 0.98874355 0.884579266 1.076918869 1.084641645 0.903575004 0.59865211 0.959908969 1.177744895 1 20.52456354 1.915059105 7.718825403 1.093599569 0.922060193 0.18891312 0.140279332 0.476230014 38.64936979 0.071553233 0.039628727 82.23545599 -1.915059105 -0.171539376 VKT(ph)PTSQSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKTPTSQSYR 10 1 Q9Y2X9-2;Q9Y2X9 Q9Y2X9-2 ZNF281 Zinc finger protein 281 1 VKT(0.478)PT(0.478)S(0.027)QS(0.018)YR;VKT(0.432)PT(0.432)S(0.131)QS(0.004)YR 75.589 0.06231 812220000 458060 414490 1348120 291540 192296 277990 260320 288070 234700 TRUE FALSE 397526.2104 411767.1879 2000075.341 357738.6129 188469.6858 288684.4552 235074.2065 226468.4723 206954.0334 1.92084302 1.989655293 9.66434579 1.728589712 0.910683801 1.394920652 1.13587642 1.094293591 1 17.65895084 3.504120506 24.97507268 1.140047638 4.508927086 0.359147212 2.10191827 776.5083004 718290.3391 0.567591346 0.839095813 3192.423549 -3.504120506 3.368879448 VKTDDIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKTDDIAR 8 1 Q52LJ0;Q52LJ0-1 Q52LJ0 FAM98B Protein FAM98B 0 82.749 0.017753 158340000 342950 306550 189740 205140 292950 257590 334110 380810 268490 FALSE TRUE 297628.2886 304536.2529 281498.8986 251720.1724 287120.8681 267499.654 301708.0636 299376.745 236749.4181 1.257144752 1.286323132 1.189016222 1.063234598 1.21276272 1.129885159 1.274377213 1.264530014 1 17.85300135 4.180510852 5.89236323 1.173630559 1.271628189 0.21675223 0.084807535 0.310953602 21.68678498 0.022171465 0.048318719 15153.42669 -4.180510852 0.097997631 VKTSEDADELHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKTSEDADELHK 12 1 Q9UKX7-2;Q9UKX7 Q9UKX7-2 NUP50 Nuclear pore complex protein Nup50 0 109.22 0.00097417 72969000 384580 287660 208550 243200 304320 216820 415130 490320 224040 FALSE TRUE 333756.7786 285770.3425 309405.4776 298422.2771 298264.6274 225161.2057 374870.7565 385468.8837 197554.2464 1.689443708 1.446541128 1.566179837 1.510583966 1.509785959 1.13974369 1.897558586 1.951205254 1 17.59188933 2.210656604 24.9990235 1.697756791 1.482723446 0.023898381 0.290817433 498.8946798 446952.8948 0.116854226 0.078802296 162.4263945 -2.210656604 -0.215033345 VKVDGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VKVDGPR 7 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;;; 98.458 0.010258 2803530000 6458200 5413500 4384850 5133970 4929240 4714290 5942990 7069000 7676900 FALSE TRUE 5604732.507 5377938.362 6505378.126 6299716.356 4831157.768 4895651.787 5366639.745 5557349.361 6769345.628 0.827957799 0.794454687 0.961005463 0.930624126 0.713681652 0.723209015 0.792785601 0.820958135 1 22.69058495 VKVDGPRS(ph)PSYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VKVDGPRSPSYGR 13 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 1 VKVDGPRS(0.989)PS(0.011)YGR;VKVDGPRS(0.906)PS(0.094)YGR;VKVDGPRS(0.947)PS(0.053)YGR;VKVDGPRS(0.85)PS(0.146)Y(0.005)GR;VKVDGPRS(0.98)PS(0.02)YGR 126.77 9.64E-05 5433120000 4320180 3366320 890747 1036295 2692320 2297800 3847280 4047120 256395.6 TRUE FALSE 3749257.267 3344206.422 1321515.229 1271601.619 2638748.099 2386197.853 3474171.378 3181674.883 226084.8043 16.58341116 14.79182307 5.845219155 5.624445317 11.67149693 10.55443713 15.36667353 14.07292672 1 17.7865045 4.40703955 7.917570286 9.952105065 16.14337401 0.276410938 4.289228941 0.319748196 30.99654658 1.117828719 2.989110559 25529.33778 -4.40703955 6.191268942 VKVDPSHDASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 117.98 0.00047017 882400000 1836580 1458600 1183860 1411350 1001230 909550 1504180 1877540 2798480 FALSE TRUE 1593871.3 1449018.361 1756378.656 1731818.589 981307.4819 944540.9771 1358304.855 1476042.682 2467646.882 0.645907367 0.587206529 0.711762557 0.701809729 0.39766933 0.382769911 0.550445392 0.598157983 1 21.23470453 1.235116906 4.464223598 1.038785617 0.566684876 0.600827754 0.109892529 0.161855244 6.67213106 0.244721236 0.030390475 17.18370885 -1.235116906 -0.472100741 VKVEPAVDTSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 136.01 9.85E-05 1958900000 3785850 3248900 2005000 2266770 2647130 2575080 2744860 3408550 5183030 FALSE TRUE 3285540.33 3227557.762 2974624.706 2781474.774 2594457.292 2674144.994 2478663.9 2679658.108 4570298.098 0.718889722 0.706202898 0.650860106 0.608598108 0.567677914 0.585113911 0.542341844 0.586320203 1 22.12385684 1.235877604 24.99992824 1.000000511 0.615920612 0.811808554 0.057343378 34.55910559 321951.6667 0.105527821 0.015797715 17.21383372 -1.235877604 -0.384079899 VKVETYNDESR ddPTM_MDA-MB-175_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 ;;; 168.76 1.61E-05 1506680000 2455800 1927410 1330870 1807070 1996390 1700260 2243840 2667430 2015240 FALSE TRUE 2131259.808 1914748.717 1974483.183 2217392.863 1956665.745 1765670.102 2026232.742 2097020.852 1777000.623 1.199357941 1.077517189 1.111132522 1.247828973 1.101105829 0.993623795 1.140254379 1.180090105 1 20.76101276 3.035201477 24.9994633 1.094291033 1.152818412 0.204078262 0.072341569 386.9360161 274792.7085 0.022707283 0.025747517 1084.429883 -3.035201477 0.058527379 VKVFGPGVER ddPTM_MDA-MB-175_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 79.82 0.022273 0 200110 174020 110050 129440 150610 167920 169670 197940 150150 FALSE TRUE 173664.9565 172876.8512 163270.5481 158831.3304 147613.1557 174379.9911 153215.4295 155612.0714 132399.4381 1.311674423 1.30572194 1.233166473 1.199637496 1.11490772 1.317075009 1.157221147 1.175322748 1 17.01453747 0.169660142 0.778925001 3.59E-31 1.246060161 0.579514547 0.064160586 9.425081637 1.238197085 15.06087516 0.025514113 1.477951361 -0.169660142 1.246060161 VKVGVNGFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKVGVNGFGR 10 1 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 205.83 1.47E-07 9224700000 6170500 6938000 3043400 4203900 6987000 5803300 8244000 9174100 2036710 FALSE TRUE 5355052.791 6892423.821 4515198.42 5158459.748 6847972.37 6026556.706 7444498.149 7212290.108 1795932.464 2.981767354 3.837796776 2.51412484 2.872301632 3.813045594 3.355670008 4.145199387 4.015902743 1 20.77630167 3.258389671 24.9613374 3.430134115 3.069278147 0 0.934370597 1044.120376 1314358.006 0.266191554 0.343174624 1812.966049 -3.258389671 -0.360855969 VKVNKDDIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKVNKDDIQK 10 2 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 61.815 0.050133 1416900000 5349300 4123600 2333400 3125000 3903400 3268900 6055700 6211400 3349200 FALSE TRUE 4642376.452 4096511.8 3461840.045 3834579.013 3825729.977 3394656.698 5468419.146 4883140.447 2953261.391 1.571949054 1.387114534 1.172209157 1.298421814 1.295425453 1.149460291 1.851654297 1.653473838 1 21.49387762 2.262924785 24.99948118 1.547908417 1.308041494 0.110679736 0.241145299 386.6289153 396709.3409 0.090081169 0.069742768 183.1997112 -2.262924785 -0.239866923 VKVPEVDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKVPEVDVR 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 79.974 0.023188 207110000 767430 532800 344880 584630 599770 554270 489260 758850 625720 FALSE TRUE 666012.1811 529300.0017 511665.1216 717379.177 587835.7504 575593.1256 441811.6405 596575.8329 551748.0944 1.207094665 0.959314599 0.927352766 1.300193302 1.065406037 1.043217242 0.800748829 1.081246748 1 19.07365022 2.467012557 24.91230238 0.970960298 1.083678425 0.179738305 0.126634453 398.946646 983171.9781 0.046948356 0.036406279 293.0977987 -2.467012557 0.112718127 VKVPLQDLMVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKVPLQDLMVR 11 1 E5RIA4;E7ETB3;Q9ULA0-2;Q9ULA0;E7EMB6 E5RIA4 DNPEP Aspartyl aminopeptidase 0 ; 144.57 3.34E-05 724890000 601390 589940 364340 442710 569020 554920 594010 713760 550540 FALSE TRUE 521914.7878 586064.6453 540536.0426 543234.0719 557697.6153 576268.1315 536403.0016 561127.9785 485455.7884 1.075102615 1.207246178 1.113460907 1.119018631 1.148812371 1.187066145 1.104947174 1.155878644 1 18.88898039 1.234789427 24.99951152 0.999999799 1.140670035 0.556309351 0.038968526 77.03538461 510597.4741 0.062914785 0.008613527 17.1707564 -1.234789427 0.140670236 VKYEETVFYGLQYILNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VKYEETVFYGLQYILNK 17 1 P43490;A0A0C4DFS8;C9JG65 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 164.62 2.34E-09 151000000 904480 630070 518920 661270 525900 418410 911730 997200 707480 FALSE TRUE 784950.6763 625931.0287 769871.4477 811421.4604 515435.6189 434506.5034 823310.5649 783956.5402 623842.5204 1.258251323 1.003347813 1.234079792 1.300683159 0.826227136 0.696500301 1.319741021 1.256657754 1 19.25082236 4.764326523 22.16098419 1.096576801 1.258252296 0.063069221 0.207408224 5916.754438 5088549.356 0.053752892 2.971821062 58120.12279 -4.764326523 0.161675496 VKYTPHHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VKYTPHHR 8 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A1B0GTT3 P47897 QARS Glutamine--tRNA ligase 0 ; 132.9 0.0005663 264710000 601240 789320 324230 397340 734080 736300 850890 930990 131718 FALSE TRUE 521784.6107 784134.9049 481028.7125 487562.12 719473.2442 764625.9374 768370.8188 731905.0335 116146.4481 4.492471524 6.751260308 4.141570581 4.197822042 6.194535055 6.583291612 6.615534365 6.301570521 1 16.82558551 5.009220305 20.68748643 5.39396882 3.093831864 0.008390865 1.780131982 2600.451136 399691.6076 0.410247636 185120.632 102145.7509 -5.009220305 -2.300136957 VLAALQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLAALQER 8 0 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;A8MXH2;E9PKT8;E9PS34;E9PNW0;E9PJJ2;E9PP22;E9PKI2;C9J1B1 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 80.684 0.057726 104780000 115310 110810 66499 82062 124160 114640 113840 125810 127630 FALSE TRUE 100071.4913 110082.0818 98658.13883 100695.4313 121689.4589 119050.275 102799.8143 98906.51055 112541.7268 0.889194561 0.978144595 0.876636085 0.894738638 1.081283026 1.057832311 0.913437329 0.878843016 1 16.78010048 VLAEDEELYGDFEDLETGDVHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLAEDEELYGDFEDLETGDVHK 22 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 0 191.65 1.35E-17 31814000 58056 44760 30161 43888 47078 40695 48802 62690 56479 FALSE TRUE 50383.7525 44465.96861 44746.96048 53853.44119 46141.23991 42260.56298 44069.18955 49284.23135 49802.11696 1.011678932 0.892852981 0.898495149 1.081348434 0.926491537 0.84856961 0.884885869 0.989601133 1 15.60391945 1.598465022 8.163650739 0.99691766 0.933838016 0.1217489 0.067068228 0.229293451 35.74897645 0.044094151 0.017530425 39.67025768 -1.598465022 -0.063079644 VLAGDKNFITAEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VLAGDKNFITAEELR 15 1 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;;; 216.99 1.94E-12 8160660000 6504040 5555210 3593320 4762970 4618190 4529010 5031150 6337540 4604700 FALSE TRUE 5644514.635 5518717.46 5331061.571 5844475.136 4526297.054 4703243.945 4543229.847 4982306.39 4060337.612 1.390158941 1.359176992 1.312960172 1.439406201 1.114758793 1.158338147 1.118929085 1.227067024 1 21.95316826 3.231527253 24.99999781 1.138083893 1.369803156 0.790817146 0.064039384 73.31425606 260593.9568 0.018491369 0.021410636 1704.226262 -3.231527253 0.231719263 VLAGDKNFITAEELRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLAGDKNFITAEELRR 16 2 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ; 199.49 2.14E-11 2723700000 3079600 2733200 1303880 1385780 2373200 2178200 2880500 3366800 559680 FALSE TRUE 2672623.057 2715245.429 1934440.729 1700442.529 2325977.963 2261996.763 2601149.553 2646836.02 493515.268 5.415482014 5.501846863 3.919718101 3.445572284 4.713082075 4.583438265 5.270656699 5.363230263 1 18.91273519 4.247039484 24.58182794 4.247973079 5.458665299 0.168652918 1.243793546 300.3264664 870678.4236 0.308092673 0.786670518 17661.98388 -4.247039484 1.21069222 VLAGQTLDINMAGEPKPDRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLAGQTLDINMAGEPKPDRPK 21 2 Q9UKM9;Q9UKM9-2;Q5QPM1;Q5QPL9 Q9UKM9 RALY RNA-binding protein Raly 0 124.2 1.41E-05 395960000 372440 339310 277240 293920 333260 283410 404170 458230 491390 FALSE TRUE 323221.1104 337081.0503 411314.1913 360659.0283 326628.778 294312.9661 364973.6556 360241.0804 433298.434 0.745954947 0.777942 0.949263046 0.832357101 0.753819429 0.679238472 0.842314735 0.831392528 1 18.7250015 1.076697199 1.897337727 1.145110605 0.797683248 0.443614873 0.070858961 1.431196232 3.402245353 1.034929046 0.020507499 11.93155915 -1.076697199 -0.347427358 VLAMSGDPNYLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VLAMSGDPNYLHR 13 0 P30153;B3KQV6;E9PH38 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ;;; 199.4 1.18E-07 2839100000 3014140 2932640 1613320 1902720 2856640 2971570 2983630 2899350 2423480 FALSE TRUE 2615813.762 2913375.295 2393526.948 2334761.657 2799798.453 3085888.221 2694278.022 2279346.565 2136978.955 1.224070904 1.363314921 1.120051717 1.09255248 1.3101666 1.444042401 1.26078828 1.06662097 1 21.02714127 1.658291567 3.801187466 1.015895412 1.260928104 0.456404799 0.103578675 0.169719947 5.698228169 0.083059061 0.029450007 45.52936227 -1.658291567 0.245032692 VLAPILPDNFS(ph)TPTGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLAPILPDNFSTPTGSR 17 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 VLAPILPDNFS(0.657)T(0.34)PT(0.001)GS(0.001)R 139.49 7.31E-07 42753000 55435 50002 35744 37722 51731 55796 49638 49735 50383 TRUE FALSE 48109.1243 49673.53357 53029.91796 46287.35664 50701.65431 57942.50822 44824.1144 39099.55729 44426.77914 1.082885711 1.118098915 1.193647592 1.04187964 1.14124083 1.304224825 1.008943598 0.880089848 1 15.43914193 2.010676511 24.6936063 0.935390935 1.143915365 0.584935315 0.074695314 111.3847366 257619.6163 0.029948449 0.020168726 102.4888243 -2.010676511 0.20852443 VLAPILPDNFST(ph)PTGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VLAPILPDNFSTPTGSR 17 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 VLAPILPDNFS(0.019)T(0.978)PT(0.002)GS(0.002)R;VLAPILPDNFS(0.004)T(0.996)PTGSR;VLAPILPDNFS(0.001)T(0.996)PT(0.002)GSR 288.42 5.00E-36 311631000 343968 336301 204705 242361 308486 337689 282255 338710 332738 TRUE FALSE 298511.7573 334091.8166 303701.0227 297392.7693 302347.7321 350680.1143 254881.9535 266279.5023 293402.0927 1.017415229 1.13868246 1.035101761 1.013601391 1.030489351 1.195220222 0.868712119 0.907558293 1 18.16251964 2.219054996 24.99998604 0.919338566 1.068609404 0.526425441 0.065295313 180.8296786 231764.2903 0.02602298 0.017573479 165.5979653 -2.219054996 0.149270839 VLATVTKPVGGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLATVTKPVGGDK 13 1 Q02878;F8VZ45;U3KQR5;F8VZA3;F8VWR1;F8VU16 Q02878 RPL6 60S ribosomal protein L6 0 130.61 1.87E-05 0 1190800 904840 657630 841650 816790 667650 1067600 1217700 1197500 FALSE TRUE 1033432.763 898896.0465 975662.0676 1032759.496 800537.477 693334.9275 964064.3163 957304.3312 1055932.914 0.978691685 0.851281397 0.923981111 0.978054081 0.758132895 0.656608879 0.912997695 0.906595787 1 20.01008675 7.999986929 0.931241495 0.867394474 63.49195697 0.086194618 0.102178162 3377.494361 6.353989502 0.03497632 450216.9264 99996990.24 -7.999986929 62.62456249 VLAVNQENEHLMEDYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VLAVNQENEHLMEDYEK 17 0 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ;;;;; 334.68 3.89E-72 5701350000 6385360 5044570 4795000 6365010 4397540 4262010 4500680 6507820 12791420 FALSE TRUE 5541518.498 5011431.888 7113878.038 7810282.804 4310037.558 4425972.283 4064204.746 5116173.337 11279232.9 0.491302782 0.444306092 0.630705838 0.692448048 0.382121514 0.392400115 0.360326343 0.453592313 1 23.42716562 1.236916292 24.9989483 1.000000646 0.47826462 0.702173333 0.106233724 26.29209772 399596.0056 0.175252558 0.02831295 17.25505278 -1.236916292 -0.521736025 VLDAPGGGSVLVMEHMDMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLDAPGGGSVLVMEHMDMR 19 0 Q9HA64;I3L3W5;I3L139;I3L2G3 Q9HA64 FN3KRP Ketosamine-3-kinase 0 149.52 8.47E-08 84480000 141560 127300 78958 98994 120750 118990 141820 162450 143630 FALSE TRUE 122852.4873 126463.7579 117142.3529 121472.1007 118347.3112 123567.6223 128066.3182 127711.3317 126650.225 0.970013968 0.9985277 0.924928107 0.959114764 0.934442171 0.975660503 1.011181135 1.008378245 1 16.95049011 2.387320268 4.126443258 1.006911422 0.957692284 0.559806226 0.019812593 0.160955666 5.143596486 0.007829465 0.005951612 243.9609232 -2.387320268 -0.049219138 VLDEEGS(ph)ER ddPTM_MDA-MB-175_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 209.95 7.95E-06 11033340000 4029460 3011760 3387510 4739750 3304430 3343540 3165800 3885770 11219350 TRUE FALSE 3496956.652 2991975.55 5025721.167 5815982.68 3238678.308 3472168.147 2858781.203 3054828.325 9893011.224 0.353477477 0.302433251 0.508007224 0.58788801 0.327370326 0.350971819 0.288969773 0.308786501 1 23.23797828 1.234754576 24.99875428 1.000000892 0.376781796 0.804753011 0.096205092 52.30332679 343486.7798 0.187663461 0.02566974 17.16937856 -1.234754576 -0.623219095 VLDEEGS(ph)EREFDEDS(ph)DEKEEEEDTYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLDEEGSEREFDEDSDEKEEEEDTYEK 27 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 2 VLDEEGS(1)EREFDEDS(1)DEKEEEEDTYEK 238.65 2.27E-45 204040000 242160 149570 182540 164970 175640 134930 216810 270430 243980 TRUE FALSE 210157.9424 148587.4648 270816.9546 202428.9599 172145.1076 140120.8444 195783.7996 212600.649 215136.9623 0.976856511 0.690664511 1.258811836 0.940930641 0.800165187 0.651309951 0.910042595 0.988210704 1 17.71489589 1.759998686 4.527413195 0.994777654 0.884972741 0.063765356 0.167071056 0.564729594 25.15349087 0.105103559 0.045396536 57.54381959 -1.759998686 -0.109804912 VLDFEHFLPMLQTVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLDFEHFLPMLQTVAK 16 0 F8VPF3;P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;G3V1Y7;P60660-2;G8JLA2;F8VZU9;F8W180 F8VPF3;P60660;P60660-2 MYL6 Myosin light polypeptide 6 0 ; 235.88 1.03E-19 5066000000 2284840 2196720 1394810 1901390 2083610 1879630 2450030 2826510 2513660 FALSE TRUE 1982892.605 2182289.602 2069344.781 2333129.66 2042150.238 1951940.582 2212426.468 2222082.832 2216497.978 0.894606097 0.984566475 0.933610047 1.052619801 0.921340898 0.880641716 0.998163088 1.002519675 1 21.07985062 2.048908383 24.99998951 1.001110859 0.948878997 0.22794187 0.047879863 171.208997 87514.31547 0.019499168 0.013146333 111.9201757 -2.048908383 -0.052231862 VLDGLHNELQTIGFQIETIGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLDGLHNELQTIGFQIETIGK 21 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 159.04 5.31E-13 0 149890 153330 106270 146360 128980 131180 160570 158090 192880 FALSE TRUE 130081.6567 152322.7651 157662.5275 179593.275 126413.5503 136226.5795 144997.9461 124283.6838 170077.9461 0.764835534 0.895605624 0.927001596 1.055946871 0.743268326 0.800965572 0.8525382 0.730745441 1 17.37583655 3.203494716 24.99993338 0.8144595 0.910913179 0.146146819 0.100554188 305.0565782 217486.5499 0.029799952 0.033791272 1597.69809 -3.203494716 0.096453679 VLDLDLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VLDLDLFR 8 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ;;; 151.56 0.0010961 493533000 1086401 894355 642958 616256 838193 862394 770524 905298 877138 FALSE TRUE 942830.3553 888479.9231 953894.6394 756186.3437 821514.5992 895570.8552 695798.7011 711707.0677 773443.7449 1.219003142 1.148732444 1.233308364 0.977687581 1.062151714 1.157900444 0.899611259 0.920179486 1 19.56093684 3.405384929 0.371439398 0.889732473 1.294356325 0.558896024 0.079126058 1.663041941 0.719626519 0.237089068 0.40903446 2543.225846 -3.405384929 0.404623852 VLDNYLTSPLPEEVDETSAEDEGVSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLDNYLTSPLPEEVDETSAEDEGVSQR 27 0 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ; 168.09 7.40E-12 64547000 112984 112925 68945 81030 110630 113864 112080 117193 100940 FALSE TRUE 98052.87814 112183.1882 102287.0326 99429.09997 108428.6794 118244.4218 101210.4989 92132.18895 89006.98819 1.101631233 1.260386297 1.149202267 1.117093185 1.218204117 1.328484697 1.137107332 1.035111858 1 16.44163099 1.78459681 3.2059436 1.011657591 1.195975859 0.5367281 0.067296452 0.172205764 3.386206747 0.046557979 0.018488031 60.89712786 -1.78459681 0.184318268 VLDPFTIKPLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VLDPFTIKPLDR 12 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;; 184.34 1.32E-05 24290889000 41837230 44611790 29370848 29640773 38324670 31302653 37717550 39304850 53798230 FALSE TRUE 36308334.05 44318732.21 43574688.33 36371163.54 37562084.05 32506886.32 34059707.81 30899813.7 47438264.54 0.765380741 0.934240168 0.918555701 0.766705188 0.791809827 0.685246112 0.717979634 0.651368974 1 25.4995479 3.639744898 5.181885033 0.749373668 0.878377741 0.166504324 0.103794166 0.314438185 13.01023434 0.028255223 0.042529687 4362.595004 -3.639744898 0.129004072 VLDPFTIKPLDRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLDPFTIKPLDRK 13 2 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 164.68 2.06E-05 1980210000 2183700 2116600 1086370 1040680 1544690 1224220 2094400 2305000 705870 FALSE TRUE 1895118.512 2102695.915 1611742.166 1276982.3 1513953.691 1271316.536 1891285.41 1812093.688 622422.8527 3.044744427 3.378243434 2.589464957 2.05163145 2.432355567 2.042528693 3.038586071 2.911354684 1 19.24753551 4.111157748 4.746682042 2.361325424 3.204003779 0.314326454 0.565683845 0.269380148 9.943969308 0.146945371 0.323407774 12916.88367 -4.111157748 0.842678355 VLDQDTDAIAVHVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLDQDTDAIAVHVVR 15 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 0 182.35 5.50E-07 128160000 85148 94866 59677 68285 83964 87584 85932 100330 89568 FALSE TRUE 73895.47606 94242.819 88536.99681 83790.15292 82293.28067 90953.41315 77598.32787 78875.21027 78979.37308 0.935630066 1.193258636 1.121014176 1.060911852 1.041959153 1.151609713 0.982513849 0.998681139 1 16.2691883 2.216703604 24.99882388 0.994295352 1.087740671 0.276612747 0.068689628 288.5592836 330035.3293 0.02651534 0.017893469 164.7037943 -2.216703604 0.093445319 VLDTSSLTQS(ph)APAS(ph)PTNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VLDTSSLTQSAPASPTNK 18 0 Q8N122;Q8N122-3;I3L436 Q8N122 RPTOR Regulatory-associated protein of mTOR 2 VLDTSSLT(0.002)QS(0.998)APAS(1)PTNK;VLDTSSLT(0.002)QS(0.998)APAS(1)PTNK;VLDTSSLT(0.037)QS(0.963)APAS(1)PTNK;VLDTSSLT(0.001)QS(0.999)APAS(0.999)PT(0.001)NK;VLDTSSLT(0.007)QS(0.993)APAS(0.998)PT(0.002)NK 389.84 1.91E-126 496741000 1975479 1819527 1336013 1317078 1925153 1718988 2255614 2505276 2723616 TRUE FALSE 1714414.445 1807574.407 1982113.355 1616140.69 1886846.222 1785118.581 2036864.901 1969542.223 2401633.219 0.713853569 0.752643823 0.825318929 0.672934017 0.785651284 0.743293591 0.848116559 0.820084519 1 21.19558441 -1.185344744 0.719703714 10 0.748709779 0.735596377 0.046128559 43.06805066 0.788079401 609.6393863 0.017832561 0.06526123 1.185344744 -9.251290221 VLDTSSLTQSAPAS(ph)PTNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VLDTSSLTQSAPASPTNK 18 0 Q8N122;Q8N122-3;I3L436 Q8N122 RPTOR Regulatory-associated protein of mTOR 1 VLDTSSLTQSAPAS(1)PTNK;VLDTSSLTQSAPAS(1)PTNK;VLDTSSLTQSAPAS(0.995)PT(0.005)NK;VLDTSSLTQSAPAS(0.994)PT(0.006)NK;VLDTSSLTQSAPAS(1)PTNK 429.95 6.19E-169 1817480000 2291870 2376440 1845502 2347150 3153670 2626590 3607700 4146570 3551910 TRUE FALSE 1988993.573 2360829.009 2737992.94 2880106.281 3090918.137 2727636.617 3257825.809 3259858.274 3132007.246 0.63505395 0.753775079 0.874197511 0.919572036 0.986880902 0.870890902 1.040171862 1.040820796 1 21.57865612 5.4736897 0.46017031 1.026058124 2.07E-22 0.884364544 0.043966422 3.277682301 0.340479599 0.037392716 2.093740356 297638.9064 -5.4736897 -1.026058124 VLDVVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLDVVER 7 0 P49961-3;P49961-4;P49961-5;P49961;P49961-2;P49961-6 P49961-3 ENTPD1 Ectonucleoside triphosphate diphosphohydrolase 1 0 88.942 0.042427 48650000 61681 58904 35993 47893 56773 58008 54506 58871 61921 FALSE TRUE 53529.69957 58517.05575 53399.33519 58767.83765 55643.32837 60239.6053 49220.01651 46281.89478 54600.76992 0.980383604 1.071725835 0.977996011 1.076318846 1.019094208 1.103273917 0.901452792 0.847641798 1 15.73663367 2.220371806 24.99611393 0.90142615 1.037796001 0.520005726 0.054522317 159.3118084 218933.8876 0.020903652 0.014123057 166.1008313 -2.220371806 0.136369851 VLEALLPLKGLEER ddPTM_MDA-MB-175_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 ; 134.14 3.69E-05 2076300000 1038470 1022980 335780 293660 931610 944140 1331900 1400320 101417 FALSE TRUE 901233.5584 1016259.977 498164.3311 360339.9913 913072.7837 980461.6767 1202732.543 1100872.465 89427.59779 10.07780127 11.36405318 5.570588313 4.029404794 10.21019021 10.96374834 13.44923237 12.31020952 1 16.4484325 VLEDFVDGDHVILQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLEDFVDGDHVILQK 15 0 Q96DU7 Q96DU7 ITPKC Inositol-trisphosphate 3-kinase C 0 151.44 3.00E-06 28098000 66917 53447 37512 56100 58023 50870 64585 70320 70414 FALSE TRUE 58073.7489 53095.90314 55652.92867 68838.36243 56868.45582 52827.00182 58321.55664 55282.61523 62089.73714 0.935319613 0.855147816 0.896330557 1.108691478 0.915907498 0.850816967 0.939310735 0.890366392 1 15.9220672 3.964227269 24.99916589 0.943150287 0.890359816 0.110371544 0.07146525 1374.28673 960399.0639 0.019339107 0.033514712 9209.313749 -3.964227269 -0.052790471 VLEDSDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLEDSDLK 8 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 117.4 0.0048542 460690000 987000 734390 576420 729450 728020 728260 783100 879040 751480 FALSE TRUE 856565.4493 729565.7437 855178.64 895082.7714 713533.8263 756276.6334 707155.0825 691064.1367 662640.8905 1.292654078 1.100997168 1.290561226 1.350781071 1.076803192 1.141306919 1.067176947 1.042893891 1 19.33786771 2.741576121 1.347599091 1.036308737 1.243944945 0.574956783 0.078073484 0.319210261 1.202825383 0.039220961 0.032725604 551.5388648 -2.741576121 0.207636209 VLEEMESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLEEMESR 8 0 Q9NUP9;G3V1D4 Q9NUP9 LIN7C Protein lin-7 homolog C 0 ; 103.56 0.011047 561060000 677960 591620 402320 518610 606130 664510 572200 677660 595400 FALSE TRUE 588365.8683 587733.6093 596883.2977 636368.327 594069.1989 690074.1297 516708.1321 532747.6826 525012.4903 1.12067023 1.119465956 1.136893519 1.212101309 1.131533458 1.314395643 0.984182551 1.014733349 1 19.00199222 2.203118327 24.99999565 1.002139184 1.168417116 0.659961942 0.058436906 105.6969039 74554.90626 0.02322916 0.015661759 159.6314017 -2.203118327 0.166277932 VLEENQEHYHIVQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLEENQEHYHIVQK 14 0 P57740;P57740-2;P57740-3 P57740 NUP107 Nuclear pore complex protein Nup107 0 132.86 2.77E-05 124540000 137010 110070 84272 91742 109990 107160 126710 137040 152000 FALSE TRUE 118903.7814 109346.9429 125026.2211 112573.4233 107801.4142 111282.5145 114421.6837 107735.0624 134030.7332 0.887138185 0.815834849 0.932817557 0.839907539 0.804303697 0.830276101 0.853697365 0.803808648 1 17.03220432 1.229357356 24.99718592 1.000000303 0.844148456 0.600215223 0.039480669 255.581061 694138.0901 0.115768422 0.009512034 16.95732548 -1.229357356 -0.155851848 VLEESSIENQDVSQERPHS(ph)NGELQDSGPLAQQLAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLEESSIENQDVSQERPHSNGELQDSGPLAQQLAGK 36 1 H7C1J4;Q6BDS2 H7C1J4 UHRF1BP1 UHRF1-binding protein 1 1 VLEES(0.002)S(0.002)IENQDVS(0.163)QERPHS(0.833)NGELQDSGPLAQQLAGK 184.5 2.83E-23 72147000 34652 21948 19868 21510 34687 28258 28108 37797 36945 TRUE FALSE 30072.6504 21803.82214 29476.23125 26394.17426 33996.79656 29345.10355 25382.09049 29714.40569 32577.40419 0.92311377 0.669292802 0.904806015 0.810198815 1.043569843 0.900780902 0.779131767 0.912117046 1 14.99158403 3.759616935 2.148753713 0.909872068 0.803854859 0.149110489 0.099386523 0.574557179 5.173625792 0.028282116 0.055697089 5749.326002 -3.759616935 -0.106017209 VLEFNCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VLEFNCR 7 0 P22102;P22102-2;F8WD69 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ;;; 148.98 0.010575 305890000 570660 563240 397428 424945 552050 600850 542620 634850 604770 FALSE TRUE 495245.8351 559540.0394 589625.5101 521435.2571 541065.2851 623965.0883 489996.7959 499092.2679 533274.7796 0.9286879 1.049252769 1.105669221 0.977798458 1.014608802 1.170063 0.918844871 0.935900753 1 19.02451957 VLEGMEVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLEGMEVVR 9 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ; 94.302 0.020505 188076000 210960 202376 140162 179169 173761 210820 154789 176059 224840 FALSE TRUE 183081.1015 201046.5787 207944.812 219852.0599 170303.4961 218930.3818 139777.5866 138410.1529 198259.6713 0.923440961 1.014056855 1.048850785 1.108909635 0.858992123 1.104260793 0.70502279 0.698125605 1 17.59703172 2.234936262 24.99978451 0.775605864 1.009379225 0.43233963 0.111469147 75.23181433 518918.7517 0.043010745 0.0302833 171.7656281 -2.234936262 0.233773362 VLELEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLELEER 7 0 A0A1B0GUE0;Q96N16-5;Q96N16-2 A0A1B0GUE0 0 ; 94.401 0.033099 295350000 770810 825180 502160 515830 825170 1113860 590160 629120 643660 FALSE TRUE 668945.5055 819759.3382 745006.2556 632957.0855 808750.7314 1156710.915 532926.374 494587.5838 567567.2481 1.178618935 1.444338695 1.312630808 1.115210731 1.424942567 2.038015617 0.938966045 0.87141671 1 19.11443181 2.055814058 24.99993511 0.920113393 1.408974755 0.455470457 0.248237003 73.65958271 32992.76794 0.102412346 0.069046379 113.7140319 -2.055814058 0.488861363 VLEQLEDLDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VLEQLEDLDSR 11 0 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 ;;; 181.4 1.45E-05 231851000 344388 318256 219164 254791 303701 298746 297804 330075 311381 FALSE TRUE 298876.2532 316165.3554 325152.4435 312645.1908 297657.9443 310238.9519 268923.0139 259491.0299 274569.8929 1.088525221 1.151493166 1.18422468 1.138672516 1.084088066 1.12990885 0.979433728 0.945081878 1 18.06681391 2.226076871 5.369604139 0.967079587 1.131938759 0.84231328 0.031511705 0.061284436 5.225162787 0.013307072 0.00931843 168.2971924 -2.226076871 0.164859172 VLETAEDIQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLETAEDIQER 11 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3;A0A0D9SFF6;A0A1B0GTB7 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 182.28 1.36E-05 153025000 194200 196641 135720 144395 183854 195438 165774 195874 198089 FALSE TRUE 168535.978 195349.2523 201354.646 177182.0917 180195.6651 202956.6263 149697.263 153987.8694 174671.1441 0.964875903 1.118383081 1.152764225 1.014375286 1.031628126 1.161935633 0.85702343 0.881587341 1 17.41428177 2.230281701 24.99999001 0.904026012 1.074956252 0.534032515 0.070784679 130.1450153 392997.0845 0.028078448 0.01928809 169.9345559 -2.230281701 0.170930241 VLEVHENLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLEVHENLDR 10 0 A6NKD9;G3V5D5;G3V2D7;H0YJE0 A6NKD9 CCDC85C Coiled-coil domain-containing protein 85C 0 ; 87.568 0.012787 86050000 71263 77407 53113 61765 85274 83344 67058 84473 76161 FALSE TRUE 61845.41399 76898.50832 78798.62445 75789.68727 83577.21424 86550.29761 60554.72548 66409.10632 67157.33334 0.920903361 1.145050056 1.173343558 1.12853926 1.244498703 1.288769123 0.901684484 0.988858595 1 16.03525732 2.224993527 24.99988491 0.966218147 1.154306548 0.442568529 0.098670259 216.7711541 399437.8898 0.040774235 0.027657908 167.8778995 -2.224993527 0.188088401 VLGAHILGPGAGEMVNEAALALEYGASCEDIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLGAHILGPGAGEMVNEAALALEYGASCEDIAR 33 0 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 232.2 2.65E-37 57077000 30528 34520 23520 30187 36256 40583 29545 41812 29784 FALSE TRUE 26493.64745 34293.23585 34894.35067 37041.41973 35534.57653 42144.25427 26679.73045 32870.82918 26262.96945 1.008783394 1.30576384 1.328652144 1.410404859 1.353029656 1.604702559 1.015868769 1.251603679 1 14.68074242 2.204974087 24.99967889 1.119946752 1.337812276 0.340797602 0.15939331 235.7118709 175447.3658 0.064364424 0.043397261 160.3149734 -2.204974087 0.217865524 VLGDHLLLDPTHELPPYTPPPMLS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLGDHLLLDPTHELPPYTPPPMLSPVR 27 0 Q05GC8;Q96PN7-2;Q96PN7-3;Q96PN7-4;Q96PN7-5;Q96PN7 Q05GC8;Q96PN7 BCAR2;TRERF1 Transcriptional-regulating factor 1 1 VLGDHLLLDPTHELPPYT(0.001)PPPMLS(0.999)PVR;VLGDHLLLDPTHELPPYTPPPMLS(1)PVR 99.515 0.0056518 139933000 149865 133981 88653 105184 137117 145410 121261 152265 145000 TRUE FALSE 130059.9605 133100.87 131525.8873 129067.6348 134388.64 151004.0168 109501.1269 119704.3147 127858.2652 1.017219813 1.041003253 1.028685061 1.009458674 1.051075109 1.181026636 0.856425877 0.936226645 1 16.9641859 2.220621519 24.99999938 0.928894782 1.05071039 0.49858653 0.058449066 203.9245541 284187.9494 0.023843179 0.016112651 166.1963644 -2.220621519 0.121815608 VLGIVVGVLLQDHDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLGIVVGVLLQDHDVR 16 0 A5YKK6-3;A5YKK6-2;A5YKK6;H3BMZ2 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 120.53 0.0011354 0 73223 63286 41994 66084 95035 80278 61017 87988 90332 FALSE TRUE 63546.39503 62870.2701 62302.43886 81089.38223 93143.98943 83366.34661 55099.58073 69172.45092 79653.05387 0.797789814 0.78930144 0.782172633 1.018032308 1.169371228 1.046618335 0.691744736 0.868421832 1 16.28144205 3.752765494 24.08527809 0.950301105 0.789709279 0.304743787 0.123829679 778.0000673 1319142.587 0.037492018 0.064504517 5659.336188 -3.752765494 -0.160591825 VLGQPHHELDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLGQPHHELDSK 12 0 B4DHE8;Q96DH6-2;Q96DH6;J3QKT5;J3KTC1 B4DHE8 MSI2 RNA-binding protein Musashi homolog 2 0 113.61 0.00066344 127730000 293140 239400 167220 216320 253320 231000 285700 327390 270960 FALSE TRUE 254400.8063 237827.3656 248088.1513 265438.7622 248279.4276 239886.7195 257992.858 257380.1963 238927.4175 1.06476188 0.995395874 1.038341074 1.110959826 1.039141637 1.004015035 1.079795951 1.077231734 1 17.86621289 3.993293037 24.91460035 1.055333206 1.026776275 0.051015634 0.037353288 741.1357208 2753168.038 0.009526409 0.018734364 9846.752836 -3.993293037 -0.028556932 VLGS(ph)EGEEEDEALS(ph)PAK ddPTM_MDA-MB-175_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 230.99 8.91E-16 284450000 786210 642830 483070 559930 667630 546870 732760 962710 832770 TRUE FALSE 682310.3565 638607.2074 716684.2678 687070.6645 654345.4692 567908.4428 661697.048 756841.9583 734320.8793 0.929171941 0.869656884 0.975982419 0.93565454 0.891089288 0.77337913 0.901100686 1.030669261 1 19.4860511 1.761875753 6.664046356 1.014206313 0.894911927 0.463282997 0.053086433 0.139443239 17.5110304 0.031711987 0.014654914 57.79306842 -1.761875753 -0.119294386 VLGS(ph)EGEEEDEALSPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 232.01 2.97E-16 557470000 396980 310860 196816 235850 301240 278070 351170 406290 364280 TRUE FALSE 344518.0872 308817.9402 291996.8759 289403.3472 295245.9134 288767.5328 317113.5875 319408.0453 321215.2334 1.072545917 0.961405027 0.90903807 0.900963956 0.9191529 0.898984552 0.987230849 0.994373903 1 18.29318079 2.089723951 8.803092949 0.994990992 0.939908703 0.180981138 0.050174396 0.447410833 39.234222 0.021340444 0.014370649 122.9487029 -2.089723951 -0.055082289 VLGTEDLYDYIDKYNIELDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLGTEDLYDYIDKYNIELDPR 21 1 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2 P68400 CSNK2A1 Casein kinase II subunit alpha 0 ; 191.8 1.20E-17 1124900000 4918000 4011500 2621100 3542300 3732700 3301400 4346400 5365100 3886500 FALSE TRUE 4268073.839 3985148.192 3888672.727 4346633.356 3658426.573 3428406.994 3924886.797 4217815.116 3427042.398 1.245410282 1.162853484 1.134702252 1.268333698 1.067517162 1.000398185 1.145269402 1.230744948 1 21.70853261 3.22434794 24.99114975 1.106347687 1.195103936 0.33591008 0.077182554 368.8647442 648599.3231 0.025093954 0.028581792 1676.285313 -3.22434794 0.088756249 VLGTPVETIELTEDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VLGTPVETIELTEDRR 16 1 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 ;; 225.31 1.12E-14 698910000 296870 275431 179824 192915 302297 309184 309581 347890 217307 FALSE TRUE 257637.8773 273621.6756 266787.4879 236719.2993 296281.8811 321078.5085 279557.8823 273496.4308 191617.214 1.344544532 1.427959784 1.39229395 1.235375958 1.546217456 1.675624553 1.458939291 1.427306164 1 17.54786765 1.238060433 5.946791904 0.982979772 1.442871198 0.586431105 0.115766768 0.104976628 13.8096916 0.19634806 0.030592649 17.30057083 -1.238060433 0.459891426 VLGVNVMLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLGVNVMLR 9 0 P29373;Q5SYZ4 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 101.28 0.0095085 199420000 237980 268480 164030 185640 241420 259840 278860 254090 212610 FALSE TRUE 206530.34 266716.3372 243355.4566 227792.3993 236616.2143 269836.2129 251816.2001 199754.8308 187475.488 1.101639165 1.422673119 1.298065466 1.215051641 1.262118141 1.439314632 1.343195331 1.065498391 1 17.51634245 1.648405355 4.469789865 1.01663532 1.302989026 0.562424925 0.097470583 0.107699222 4.846445531 0.066586896 0.024750546 44.50464645 -1.648405355 0.286353706 VLHDAQQQCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VLHDAQQQCR 10 0 A1L0T0;M0R026 A1L0T0 ILVBL Acetolactate synthase-like protein 0 ;;; 150.35 2.17E-05 766790000 574290 529132 344610 450812 646473 740530 411929 665128 622611 FALSE TRUE 498396.1214 525656.0971 511264.5487 553175.7548 633609.4521 769018.6683 371980.189 522895.5532 549006.6369 0.907814383 0.957467655 0.931253858 1.00759393 1.154101626 1.400745668 0.677551352 0.952439403 1 19.06646406 3.697387425 5.3581682 1.022626489 0.934452075 0.063860912 0.178306035 0.753450332 56.09162694 0.052514343 0.080770343 4981.813039 -3.697387425 -0.088174414 VLHDSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLHDSSK 7 0 A0A499FI31;Q15020-4;Q15020 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 92.925 0.015312 66719000 242300 249880 63594 158200 190800 286460 284970 297500 294010 FALSE TRUE 210279.4411 248238.5218 94348.27111 194121.7279 187003.4533 297480.3016 257333.6533 233881.9401 259252.4727 0.811099076 0.957516506 0.363924286 0.748774837 0.721317916 1.147454057 0.992598645 0.90213967 1 17.98399822 2.764087212 22.73485665 0.991926479 0.715450609 0.452001762 0.158035283 239.8549331 213621.9966 0.051447505 0.051416872 580.8810548 -2.764087212 -0.27647587 VLHEAEGHIVTCETNTGEVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLHEAEGHIVTCETNTGEVYR 21 0 P62318;P62318-2;H3BT13 P62318 SNRPD3 Small nuclear ribonucleoprotein Sm D3 0 ; 188.1 1.53E-17 2284200000 475220 509140 326170 327520 456520 441650 405360 480400 554700 FALSE TRUE 412418.4729 505795.4258 483906.903 401888.4218 447436.1452 458640.5613 366048.2496 377670.1985 489123.9979 0.843177752 1.034084257 0.989333799 0.821649364 0.914770379 0.937677487 0.748375159 0.7721359 1 18.89984072 3.1557993 1.015597364 0.835417394 0.953574294 0.090776509 0.093284137 0.897925157 2.092862865 0.047724224 0.062404184 1431.526197 -3.1557993 0.1181569 VLHEEHVELLMEEFAFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VLHEEHVELLMEEFAFLK 18 0 P53004 P53004 BLVRA Biliverdin reductase A 0 ;;; 139.65 7.68E-08 873571000 723940 542608 479776 587844 455659 415839 599934 716818 1253055 FALSE TRUE 628269.4948 539043.5723 711797.2784 721322.9648 446592.2774 431836.5954 541752.493 563532.049 1104920.265 0.568610708 0.48785744 0.644206918 0.65282807 0.404185072 0.39083055 0.490309129 0.510020557 1 20.07551083 1.238096791 24.96816212 1.000000552 0.516467092 0.75297425 0.086645411 5.902189183 317368.641 0.129871194 0.022684811 17.30201927 -1.238096791 -0.483533461 VLHEEHVELLMEEFAFLKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLHEEHVELLMEEFAFLKK 19 1 P53004 P53004 BLVRA Biliverdin reductase A 0 ; 169.61 5.61E-12 1465620000 4098140 2842330 1908190 2245100 2407330 1999910 3864660 4340620 1642760 FALSE TRUE 3556560.416 2823658.547 2830997.067 2754884.269 2359428.843 2076847.832 3489865.868 3412412.192 1448554.784 2.455247433 1.949293584 1.954359681 1.901815726 1.628815747 1.433737857 2.409205303 2.355735681 1 20.46618282 5.043452799 1.636973652 1.87162936 3.150473621 0.180720573 0.413864596 5.070793039 6.913986391 0.11543559 13.04874447 110523.0343 -5.043452799 1.27884426 VLHFFNVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLHFFNVK 8 0 O94855;O94855-2;E9PDM8;E9PC44 O94855 SEC24D Protein transport protein Sec24D 0 ; 132.29 0.00096878 1132430000 624280 985340 854860 723550 912550 807700 978010 1064360 1130130 FALSE TRUE 541779.8163 978867.2367 1268273.155 887843.0863 894392.0404 838772.7417 883162.7407 836754.8969 996527.3188 0.543667801 0.982278376 1.272692812 0.890937026 0.897508802 0.841695682 0.886240371 0.839670806 1 19.92654983 3.518181348 24.99976113 0.884273549 0.961818675 0.0011781 0.179284198 2037.546385 1240571.422 0.049296581 0.07310777 3297.473756 -3.518181348 0.077545126 VLHGEQYLELYKPLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLHGEQYLELYKPLPR 16 1 P51659-3;P51659;P51659-2;A0A2R8YD50;A0A2R8Y7L2;E7ET17;E7EPL9;E7ER27 P51659-3 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 126.16 4.39E-05 565180000 378440 410350 262980 291710 392620 414990 358400 442580 380730 FALSE TRUE 328428.1952 407654.3838 390158.0076 357947.214 384807.6301 430954.9338 323642.4232 347937.7112 335720.5331 0.978278546 1.214267057 1.162151162 1.066205902 1.146214164 1.283671659 0.964023321 1.036390917 1 18.35690125 2.206827841 24.9999947 1.00618592 1.142782134 0.396153702 0.082327677 197.9893612 155980.3529 0.032272939 0.021760548 161.0007284 -2.206827841 0.136596213 VLHNAQEVEKEPGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLHNAQEVEKEPGQR 15 1 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5 P49916-3 LIG3 DNA ligase 3 0 74.789 0.020283 60437000 183100 153410 115690 136400 159110 143470 183170 215470 176950 FALSE TRUE 158902.8711 152402.2396 171638.071 167371.7047 155944.0223 148989.3837 165406.2016 169393.4173 156031.1726 1.018404646 0.976742257 1.100024233 1.072681196 0.999441456 0.954869346 1.060084334 1.085638302 1 17.25147476 VLIAAHGNSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VLIAAHGNSLR 11 0 P18669;P15259 P18669 PGAM1;PGAM2 Phosphoglycerate mutase 1;Phosphoglycerate mutase 2 0 ;;; 196.48 6.03E-08 17755420000 4713255 5168403 2493962 3574952 4765385 5121283 4822919 5164678 4908651 FALSE TRUE 4090386.41 5134451.42 3700050.365 4386699.491 4670563.162 5318302.071 4355193.058 4060251.801 4328355.871 0.945020819 1.186235969 0.854839684 1.013479395 1.079061727 1.228711832 1.006200319 0.938058682 1 22.04538769 2.003302857 24.99242049 0.966862296 1.053774039 0.092849055 0.107363565 210.7432308 1594665.906 0.043873444 0.029411995 100.7634101 -2.003302857 0.086911743 VLIFDDSFEHEVWQDASSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLIFDDSFEHEVWQDASSFR 20 0 Q12797;Q12797-10 Q12797 ASPH Aspartyl/asparaginyl beta-hydroxylase 0 235.7 1.51E-29 179090000 180840 183120 105770 144480 198330 186060 197950 247530 228050 FALSE TRUE 156941.5358 181917.0727 156920.7258 177286.3922 194383.621 193217.8486 178752.8395 194597.6358 201090.1888 0.780453471 0.904654144 0.780349985 0.881626266 0.966648956 0.960851694 0.888918751 0.967713228 1 17.61748317 3.422107051 4.09503675 0.952830354 0.829659231 0.66315772 0.043993149 0.131564064 4.574348924 0.01234444 0.016577129 2643.060175 -3.422107051 -0.123171123 VLIGGDETPEGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLIGGDETPEGQR 13 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ; 100.88 0.0051171 159628000 158810 167291 110628 107352 161403 153009 159508 146069 193746 FALSE TRUE 137822.8561 166192.0544 164128.0708 131727.9124 158191.3961 158895.3552 144038.9387 114833.2811 170841.5686 0.806729049 0.972784644 0.960703371 0.771053049 0.925953779 0.930074317 0.84311412 0.672162413 1 17.38229952 2.00235188 22.18454825 0.796156474 0.896065814 0.03268993 0.101461334 30.41078574 286847.439 0.040233066 0.026859553 100.5430094 -2.00235188 0.09990934 VLKDSLHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLKDSLHEK 9 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 93.058 0.005802 526150000 1059240 911730 459930 673980 863160 650700 1209020 1270500 392550 FALSE TRUE 919258.7502 905740.7856 682353.6864 827017.4601 845984.8047 675732.8501 1091769.426 998813.462 346143.1862 2.655718174 2.616665073 1.97130469 2.389235129 2.444031368 1.952177241 3.154097697 2.885549974 1 18.40100942 4.439163891 24.96580586 2.356920681 2.645957857 0.047764229 0.584752423 549.8896778 361679.6695 0.145438503 0.384796055 27489.3133 -4.439163891 0.289037176 VLLALFCHEPCRPLHQLATDSTFSLDQPGGTLDLTLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLLALFCHEPCRPLHQLATDSTFSLDQPGGTLDLTLIR 38 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 274.76 1.37E-76 2173610000 649970 587480 326120 457770 445130 515270 575840 656110 562880 FALSE TRUE 564074.8177 583620.8052 483832.7228 561713.6751 436272.7839 535092.7703 519995.1254 515805.9824 496336.9676 1.136475529 1.175856008 0.974806944 1.131718392 0.878985069 1.078083651 1.047665516 1.039225397 1 18.92096039 4.24691216 24.99995771 1.025350134 1.156165822 0.411593662 0.066817275 168.7413776 505108.0808 0.01534847 0.039182802 17656.80662 -4.24691216 0.130815688 VLLESEQFLTELTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLLESEQFLTELTR 14 0 P37108;H0YLA2 P37108 SRP14 Signal recognition particle 14 kDa protein 0 213.73 1.45E-09 103460000 148560 173370 112690 153340 190590 162710 169130 231950 161400 FALSE TRUE 128927.4196 172231.1211 167187.2609 188158.1907 186797.6319 168969.559 152727.7986 182349.2975 142319.4759 0.90590145 1.210172536 1.174732129 1.322083218 1.312523326 1.187255349 1.07313351 1.281267349 1 17.11877358 4.739442653 24.09818001 1.202905161 0.905901294 0.446845588 0.100809404 41.07023924 1121773.991 0.02385028 0.14018229 54883.6079 -4.739442653 -0.297003868 VLLGFSSDES(ph)DVEASPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VLLGFSSDESDVEASPR 17 0 Q9Y2U8 Q9Y2U8 LEMD3 Inner nuclear membrane protein Man1 1 VLLGFSSDES(1)DVEASPR;VLLGFSS(0.003)DES(0.996)DVEASPR;VLLGFSSDES(1)DVEASPR 254.59 5.07E-27 53549000 53354 46415 31289.1 48778 66012 57457 41843 69559 52980 TRUE FALSE 46303.13372 46110.09681 46420.61342 59853.79043 64698.49035 59667.40797 37785.0723 54684.34916 46716.76476 0.991145983 0.987013914 0.993660705 1.28120581 1.384909479 1.277216183 0.808811837 1.17055086 1 15.51165275 7.419743162 10.57227354 1.10408737 0.149413328 0 0.17679266 0 0 0.041320994 0 26287129.34 -7.419743162 -0.954674042 VLLLSSPGLEELYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLLLSSPGLEELYR 14 0 Q8N163-2;Q8N163;E5RHJ4 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ; 140.39 2.32E-05 117945000 393230 270430 196155 186918 256414 234735 302330 354590 219342 FALSE TRUE 341263.6592 268653.5275 291016.2141 229360.5888 251311.8631 243765.4073 273010.0831 278763.6879 193411.6386 1.76444221 1.389024618 1.504646857 1.185867564 1.299362669 1.260345081 1.411549403 1.441297379 1 17.56131509 VLLMELEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VLLMELEEAR 10 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ;; 131.62 0.00057092 57425000 104429 109111 65480 70505 89950 102624 90651 99280 105642 FALSE TRUE 90628.44306 108394.2427 97146.34702 86514.23785 88160.17098 106572.0117 81859.67997 78049.7446 93153.12311 0.972897527 1.163613619 1.042867311 0.92873148 0.946400593 1.144051945 0.87876474 0.837865033 1 16.50731652 2.589675282 0.551989564 0.877285482 1.065264665 0.162373163 0.095615608 1.768046082 1.365045834 0.211438326 0.113556748 388.7543685 -2.589675282 0.187979183 VLLSLEHGLWAPNLHFHS(ph)PNPEIPALLDGR ddPTM_MDA-MB-175_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 1 VLLSLEHGLWAPNLHFHS(1)PNPEIPALLDGR;VLLS(0.001)LEHGLWAPNLHFHS(0.999)PNPEIPALLDGR 182.26 1.05E-17 3432300000 1207220 1299320 650480 897920 1247870 1507640 1319660 1442980 1400850 TRUE FALSE 1047682.818 1290784.681 965054.3037 1101806.46 1223039.828 1565639.886 1191679.576 1134409.956 1235243.109 0.848159209 1.044964082 0.781266697 0.891975395 0.990120746 1.267475103 0.964732827 0.918369791 1 20.23636358 3.170153951 5.123205552 1.023563762 0.894645885 0.271868192 0.111839266 0.322644985 15.90944708 0.035855174 0.041450071 1479.632802 -3.170153951 -0.128917876 VLLSLEHGLWAPNLHFHSPNPEIPALLDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VLLSLEHGLWAPNLHFHSPNPEIPALLDGR 30 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 193.11 3.89E-19 37809500000 5217547 5736253 2620068 3624431 5332794 6961562 5940517 6440538 5820659 FALSE TRUE 4528034.944 5698571.176 3887141.648 4447413.455 5226681.833 7229377.795 5364406.576 5063279.069 5132547.324 0.882219814 1.110281273 0.757351351 0.866511924 1.0183407 1.408536023 1.045174304 0.986504118 1 22.29124359 3.006993252 16.8498289 1.098973823 0.912594636 0.309953466 0.144297196 4.585944442 11040.7634 0.045871638 0.051591636 1016.232903 -3.006993252 -0.186379186 VLMATNRPDTLDPALMRPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLMATNRPDTLDPALMRPGR 20 2 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ; 132.13 7.37E-06 1928530000 1528710 1502990 854830 1060210 1377380 1474320 1375320 1515210 1368990 FALSE TRUE 1326687.1 1493116.76 1268228.647 1300946.885 1349972.833 1531038.044 1241941.678 1191194.133 1207149.562 1.09902463 1.236894588 1.050597778 1.077701493 1.118314479 1.268308495 1.028821711 0.986782558 1 20.203173 2.021633664 24.94421343 0.997053634 1.138881827 0.487581379 0.06668388 181.0907381 208801.7742 0.027081245 0.018256562 105.1074898 -2.021633664 0.141828193 VLMSVQYFLEDVDCKQS(ph)MR ddPTM_MDA-MB-175_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 85.062 0.0035318 0 56958 49578 21410 44944 36602 24727 60819 54788 45049 TRUE FALSE 49430.85599 49252.31885 31763.94761 55149.22213 35873.69181 25678.26369 54920.78274 43072.01256 39723.35854 1.24437756 1.239883048 0.799628953 1.38833231 0.903088085 0.646427307 1.382581553 1.084299368 1 15.27769998 4.407397094 24.99996437 1.045834526 1.243297363 0.12624495 0.229686906 92.41957581 33135.78776 0.055798047 0.147627796 25550.36412 -4.407397094 0.197462837 VLNEAVGALMYHTITLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLNEAVGALMYHTITLTR 18 0 Q13363-2;Q13363;E9PGB1;E7ESU7;D6RAX2;E7EPF8 Q13363-2 CTBP1 C-terminal-binding protein 1 0 115.57 0.00018546 110530000 105090 76712 62347 54273 53649 100620 73788 89472 86936 FALSE TRUE 91202.09024 76208.07382 92498.21774 66596.51416 52581.48986 104490.9165 66632.05112 70339.10907 76658.52512 1.189718822 0.994123924 1.206626629 0.86874244 0.68591836 1.363069748 0.869206015 0.91756408 1 16.22615862 3.736392848 24.97955328 0.948342053 1.116553204 0.182593658 0.178118272 347.2025775 4000883.946 0.047293498 0.074155837 5449.95414 -3.736392848 0.168211151 VLNSYWVGEDSTYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLNSYWVGEDSTYK 14 0 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 228.62 6.50E-09 0 283810 238160 169050 211550 235920 207590 279540 320670 295640 FALSE TRUE 246303.7894 236595.5113 250803.1454 259585.6608 231225.6536 215576.1216 252430.2538 252097.216 260689.776 0.944815686 0.907574953 0.962075112 0.99576464 0.886976302 0.826945057 0.968316662 0.967039137 1 17.99197448 2.028965711 24.9999705 0.977119173 0.921671164 0.26533514 0.045532165 305.8812838 264001.2399 0.019823811 0.013365049 106.8970476 -2.028965711 -0.055448009 VLNTGS(ph)DVEEAVADALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLNTGSDVEEAVADALK 17 0 E3W994;J3KR49;O75122 E3W994 CLASP2 CLIP-associating protein 2 1 VLNT(0.103)GS(0.897)DVEEAVADALK 202.95 1.06E-11 24279000 28317 28680 21704 27883 32028 25596 33631 41395 40475 TRUE FALSE 24574.8367 28491.59919 32200.127 34214.26131 31390.70546 26580.69468 30369.4708 32543.00139 35690.09161 0.688561884 0.798305577 0.902214748 0.958648739 0.879535581 0.74476398 0.850921626 0.911821739 1 15.12323598 4.540119618 2.663458128 0.888450517 0.684011305 0.496694886 0.067193928 0.306626032 3.666521945 0.018486556 0.112450205 34683.23655 -4.540119618 -0.204439212 VLNTNIDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLNTNIDGR 9 0 P62269;A0A0G2JQH2;Q5GGW2 P62269 RPS18 40S ribosomal protein S18 0 120.99 0.0014575 225200000 234260 255950 167470 191620 262680 280020 225240 243680 280100 FALSE TRUE 203301.9475 254268.6476 248459.0522 235130.2497 257453.1819 290792.5506 203396.2595 191570.9283 246986.8971 0.823128473 1.029482335 1.005960458 0.951994833 1.042375871 1.177360233 0.823510323 0.775631949 1 17.91407498 2.179205042 24.99998277 0.845687855 1.005489296 0.277452689 0.103711888 83.61541671 35217.06903 0.041776171 0.028165498 151.0793273 -2.179205042 0.159801441 VLPAFRES(ph)PSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLPAFRESPSGR 12 1 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 VLPAFRES(0.756)PS(0.244)GR 88.78 0.006237 0 84965 74001 46611 53546 74998 81826 81980 86114 57422 TRUE FALSE 73736.65998 73514.88256 69152.2355 65704.4377 73505.68653 84973.89917 74029.59222 67699.19124 50633.63658 1.456278177 1.451898136 1.365737091 1.297644059 1.451716517 1.678210473 1.462063506 1.337039877 1 15.62780848 1.251494924 2.497501936 0.896757949 1.449967339 0.685684734 0.096075794 0.33023409 2.29588756 0.390408705 0.027717565 17.84411133 -1.251494924 0.55320939 VLPAQATEYAFAFIQVPQDDDARTDAVDSVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLPAQATEYAFAFIQVPQDDDARTDAVDSVVR 32 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 189.2 6.61E-20 274330000 35933 34063 7738.2 17704 26781 30942 28244 30559 12886 FALSE TRUE 31184.36301 33839.23791 11480.4194 21723.96379 26248.1105 32132.35876 25504.90123 24024.19566 11362.63176 2.74446657 2.978116217 1.010366229 1.911877833 2.310037943 2.827897572 2.244629745 2.114316135 1 13.4720094 4.333618668 24.9771518 1.998042547 2.861345713 0.318703244 0.564376915 20.33051716 5331.43239 0.143442947 0.379514307 21558.50632 -4.333618668 0.863303166 VLPCLHTFCER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLPCLHTFCER 11 0 O75382;O75382-3;O75382-2;E9PMK8;E9PMW5;Q9C040;Q9C040-2;A0A0J9YX34;A0A0J9YW70;C9JVI3 O75382 TRIM3;TRIM2 Tripartite motif-containing protein 3;Tripartite motif-containing protein 2 0 150.46 3.39E-05 532340000 337820 418510 231090 297970 339820 412710 350500 365810 384480 FALSE TRUE 293176.2311 415760.7803 342845.8969 365628.6427 333058.2468 428587.2208 316508.5639 287584.3782 339027.2124 0.864757224 1.226334539 1.011263652 1.078463997 0.982393845 1.26416761 0.93357864 0.848263407 1 18.37104155 2.028656249 24.99971944 0.906581523 1.074097757 0.242402481 0.11908487 228.5866759 199418.1655 0.044427107 0.029952233 106.8209039 -2.028656249 0.167516234 VLPEFDTPGHTLSWGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLPEFDTPGHTLSWGK 16 0 P07686;Q5URX0 P07686 HEXB Beta-hexosaminidase subunit beta;Beta-hexosaminidase subunit beta chain B;Beta-hexosaminidase subunit beta chain A 0 ; 242.41 6.01E-20 1815420000 1886660 1752570 1028810 1559750 1662550 1731490 1662990 2096180 1972220 FALSE TRUE 1637333.101 1741057.252 1526345.957 1913915.077 1629468.508 1798101.541 1501713.486 1647928.219 1739066.398 0.9415012 1.001144783 0.877681242 1.100541692 0.936978892 1.033946457 0.86351705 0.947593617 1 20.72988159 1.22429984 23.63082097 1.000000193 0.961739811 0.026907641 0.069895865 1729.907006 2866201.241 0.308070297 0.01598884 16.76099667 -1.22429984 -0.038260382 VLPFFERPDFQLFTGNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLPFFERPDFQLFTGNK 17 1 Q96HE7 Q96HE7 ERO1L ERO1-like protein alpha 0 ; 156.5 5.54E-08 333950000 421890 332930 207193 305920 373380 367030 459580 438250 389810 FALSE TRUE 366136.1676 330742.9609 307392.2278 375383.8117 365950.4685 381149.8816 415010.0023 344533.648 343727.1059 1.06519434 0.962225426 0.894291496 1.092098369 1.064654088 1.108873508 1.207382238 1.002346461 1 18.3909041 3.712970542 24.49869949 1.079855473 0.972735911 0.331711895 0.070461337 672.3961932 643719.4133 0.020066089 0.029776663 5163.813418 -3.712970542 -0.107119563 VLPPPAGYVPIRT(ph)PAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VLPPPAGYVPIRTPAR 16 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 VLPPPAGYVPIRT(1)PAR;VLPPPAGYVPIRT(1)PAR;VLPPPAGYVPIRT(1)PAR 164.57 1.19E-08 1014430000 1838770 1719300 1174140 1286370 1689520 1536970 1856850 2194030 2072220 TRUE FALSE 1595771.886 1708005.805 1741958.031 1578459.969 1655901.857 1596098.23 1676772.973 1724853.758 1827244.512 0.873321482 0.934743978 0.953325086 0.863847153 0.90622894 0.873500082 0.91765112 0.943964394 1 20.80123827 1.362478615 1.780698695 1.019114477 0.903232175 0.563235118 0.02784054 0.53834083 2.053494626 0.100163224 0.007903921 23.03979526 -1.362478615 -0.115882302 VLPSDLDLLLHMNNAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLPSDLDLLLHMNNAR 16 0 Q8WUY1 Q8WUY1 THEM6 Protein THEM6 0 ; 246.5 3.33E-20 1085480000 647080 623970 489730 659930 849140 919830 531110 988990 799530 FALSE TRUE 561566.7385 619871.1 726565.066 809777.1929 832243.7753 955216.4553 479603.0339 777502.1848 705010.4742 0.796536731 0.879236724 1.030573435 1.148603067 1.180470086 1.354896828 0.680277884 1.102823594 1 19.42728517 4.293865987 2.794924481 1.07266524 0.809568595 0.257023882 0.169244349 0.387242204 5.909347452 0.044841392 0.149443156 19672.7914 -4.293865987 -0.263096645 VLPYIFEDPDWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VLPYIFEDPDWR 12 0 Q8IV36-2;Q8IV36;J3KSF1;E9PIM7 Q8IV36-2 HID1 Protein HID1 0 ;; 147.2 0.00014953 718050000 1168050 1269000 1102610 825630 1173890 1310020 1155490 1359660 905500 FALSE TRUE 1013689.233 1260663.855 1635835.884 1013101.91 1150531.886 1360417.317 1043430.758 1068907.29 798452.8215 1.269566849 1.578883337 2.048757096 1.268831274 1.440951619 1.703816782 1.306815794 1.338723167 1 19.60684764 0.649087653 0.772365475 2.63E-09 1.564975865 0.354941011 0.230208955 6.736203486 1.626015024 11.29105958 0.0918725 4.45746204 -0.649087653 1.564975863 VLQCHKPVHAEYLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLQCHKPVHAEYLEK 15 1 Q9NZJ9;F8VRL4;F8VRR0;A0A0C4DGJ4;A0A024RBG1;Q9NZJ9-2;Q9NZJ9-3;Q96G61;Q8NFP7 Q9NZJ9 NUDT4;NUDT11;NUDT10 Diphosphoinositol polyphosphate phosphohydrolase 2;Diphosphoinositol polyphosphate phosphohydrolase 3-beta;Diphosphoinositol polyphosphate phosphohydrolase 3-alpha 0 ; 171.08 7.12E-07 2391900000 3712700 3268900 2413100 2813200 3173900 2555400 3950700 4619000 4213100 FALSE TRUE 3222057.288 3247426.381 3580083.231 3451980.057 3110745.6 2653707.892 3567561.722 3631262.795 3715032.118 0.867302674 0.874131442 0.963674907 0.92919252 0.837340163 0.714316272 0.960304409 0.977451252 1 21.82494325 2.025403106 24.99945955 0.981643979 0.868201385 0.414157119 0.064857665 230.6034653 226938.2462 0.028424968 0.019163348 106.0237367 -2.025403106 -0.113442594 VLQGDLVMNVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VLQGDLVMNVYR 12 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 196.88 4.69E-07 2621782000 593314 686258 457811 489879 684407 756453 734923 728160 702033 FALSE TRUE 514906.0516 681749.926 679209.9309 601113.5143 670788.6397 785554.2364 663650.2806 572448.6505 619039.4585 0.831782279 1.10130286 1.097199737 0.971042324 1.083595933 1.268988956 1.072064586 0.924736933 1 19.23967185 4.745193611 24.45643649 1.059298756 0.831782138 0.383184178 0.092698171 707.9022533 2610003.843 0.024813951 0.230644215 55615.21373 -4.745193611 -0.227516618 VLQLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLQLLR 6 0 P18124;A8MUD9;C9JZ88;C9JIJ5;H0Y4W2;F2Z2U4;Q9Y4A5-2;Q9Y4A5;A0A2R8YFJ4 P18124;H0Y4W2 RPL7;TRRAP 60S ribosomal protein L7;Transformation/transcription domain-associated protein 0 ; 174.26 0.010614 508580000 285860 355160 213496 235070 351760 364340 303250 339850 393450 FALSE TRUE 248082.8767 352826.9306 316743.3797 288446.2363 344760.6642 378356.3956 273840.8617 267175.7222 346936.7892 0.715066503 1.016977563 0.912971439 0.831408618 0.993727604 1.090562913 0.789310532 0.770099138 1 18.40431331 VLQLYPNNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLQLYPNNK 9 0 Q02790;H0YFG2 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 151.27 0.0035659 0 330090 252440 239870 260440 301600 257770 322910 382130 354980 FALSE TRUE 286467.7702 250781.705 355871.9343 319576.8826 295598.7501 267686.5787 291594.2379 300414.4732 313014.6688 0.915189602 0.801181957 1.136917754 1.020964557 0.944360695 0.855188607 0.931567326 0.959745671 1 18.25587074 4.313810503 24.99999999 0.970148289 0.858185798 0.292311876 0.07692914 53.83555625 17882.99818 0.019833546 0.052474621 20597.3099 -4.313810503 -0.111962492 VLQNFHPDEAES(ph)DEDNDVVIEGTLEPARPPQTPGAPAGSLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLQNFHPDEAESDEDNDVVIEGTLEPARPPQTPGAPAGSLSR 42 1 Q9BYG4 Q9BYG4 PARD6G Partitioning defective 6 homolog gamma 1 VLQNFHPDEAES(1)DEDNDVVIEGTLEPARPPQTPGAPAGSLSR 217.25 2.83E-44 269060000 79547 44793 31328 38219 48955 51364 47343 58100 46461 TRUE FALSE 69034.6624 44498.75183 46478.32559 46897.20809 47980.89128 53340.00632 42751.68315 45675.76713 40968.43351 1.685069613 1.08617167 1.134491158 1.144715677 1.17116734 1.301978176 1.043527406 1.11490148 1 15.32222511 4.741174263 24.99569654 1.127992364 1.685069811 0.82821194 0.080203749 98.22284161 939305.2094 0.019681148 0.131294604 55102.87547 -4.741174263 0.557077447 VLS(ph)AMIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLSAMIR 7 0 O43598;H0Y8X4 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 1 VLS(1)AMIR;VLS(1)AMIR 108.98 0.0074808 134580000 169715 186211 111730 143707 181878 159713 191410 200856 199797 TRUE FALSE 147286.7327 184987.7677 165763.0017 176337.8708 178258.9836 165857.2625 172847.0877 157904.5075 176177.2263 0.836014597 1.050009536 0.940887794 1.000911835 1.011816268 0.941422827 0.981097792 0.896282175 1 17.42666792 4.762721724 24.05128511 0.971083607 0.836014329 0.505888787 0.043590803 3953.205971 3935129.918 0.010581963 0.629913316 57905.75438 -4.762721724 -0.135069279 VLS(ph)LQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLSLQGR 7 0 Q8N5J2;Q8N5J2-3;Q8N5J2-2;Q8N5J2-4 Q8N5J2 FAM63A Protein FAM63A 1 VLS(1)LQGR;VLS(1)LQGR 123.5 0.0044447 606830000 292830 284390 276710 346890 445940 454710 494490 440030 505100 TRUE FALSE 254131.7736 282521.8234 410527.8815 425656.6764 437066.6665 472202.9879 446534.4359 345933.0088 445387.6534 0.570585582 0.634327919 0.921731616 0.955699317 0.981317428 1.060206731 1.002574796 0.776700939 1 18.76470204 4.258186813 3.693561999 0.950566359 0.583206073 0.802656063 0.073499135 0.102734002 2.951532066 0.021407172 0.059363457 18121.19412 -4.258186813 -0.367360286 VLS(ph)PLIIK ddPTM_MDA-MB-175_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 157.66 0.00039157 2306709000 4726160 4196217 2660782 3310103 4426810 3591170 4586520 5676300 4635690 TRUE FALSE 4101585.981 4168651.774 3947545.075 4061712.478 4338725.142 3729324.634 4141719.996 4462467.418 4087664.009 1.00340585 1.019812726 0.965721514 0.993651256 1.061419219 0.912336392 1.013224176 1.091691344 1 21.96284519 1.988290207 24.78108063 1.052413875 0.993133593 0.197338192 0.043525259 628.6067298 1330299.026 0.018060565 0.011180438 97.3397456 -1.988290207 -0.059280282 VLS(ph)PLMSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLSPLMSR 8 0 A0A087WXR4;Q8NG45;Q8NG42;P06401-5;P06401;Q8NG44 A0A087WXR4 PGR;PR Progesterone receptor 1 VLS(1)PLMSR 116.52 0.0023665 54185000 365950 25031 14666 23789 23081 28782 25871 31786 37027 TRUE FALSE 317588.7803 24866.56971 21758.52665 29190.65604 22621.73326 29889.26216 23362.0344 24988.81126 32649.71024 9.727154635 0.761616858 0.66642327 0.894055593 0.692861685 0.915452601 0.715535735 0.765360889 1 14.99478257 4.738684319 24.99996871 0.79341918 9.727157263 0.998564542 0.106353655 0.306475153 61871.38283 0.024033246 0.134941618 54787.85764 -4.738684319 8.933738083 GPREPGPAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 GPREPGPAGR 10 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 67.334 0.057717 21460000 34726 14813 11507 16809 12799 15474 16845 17715 10372 FALSE TRUE 30136.87112 14715.69243 17071.82369 20625.74036 12544.32494 16069.29479 15211.37449 13926.78511 9145.833976 3.295147408 1.609004982 1.86662296 2.255206077 1.371588963 1.757007052 1.663202561 1.522746329 1 13.15889901 6.555418478 1.331224715 1.612185502 199.9999892 0.703963724 0.334535295 102.3448325 1.966797096 0.094089599 60388.87085 3592679.514 -6.555418478 198.3878037 up VLS(ph)PPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VLSPPK 6 0 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7ESQ0;K7EL01;Q5XUX1;Q5XUX1-2 Q9H6Z4 RANBP3;FBXW9 Ran-binding protein 3;F-box/WD repeat-containing protein 9 1 VLS(1)PPK;VLS(1)PPK;VLS(1)PPK;VLS(1)PPK 95.909 0.044905 741158000 2170770 1905830 1760510 2053720 2199650 1729730 2269670 2720460 5197080 TRUE FALSE 1883897.244 1893310.477 2611898.525 2520048.515 2155881.269 1796273.832 2049557.753 2138710.8 4582687.123 0.411090086 0.413144172 0.569949127 0.549906299 0.470440423 0.391969555 0.447239294 0.466693611 1 22.12776236 1.238569354 15.09590051 1.000133406 0.466479273 0.896022264 0.057267643 0.015183323 818.7874698 0.083653456 0.015023927 17.32085611 -1.238569354 -0.533654133 VLS(ph)PPKLNEVSSDANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VLSPPKLNEVSSDANR 16 1 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7ESQ0 Q9H6Z4 RANBP3 Ran-binding protein 3 1 VLS(0.991)PPKLNEVS(0.004)S(0.005)DANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(0.995)PPKLNEVS(0.002)S(0.003)DANR 162.43 4.89E-09 6517528000 3053590 2780500 2046720 2201880 3032120 2303360 3381190 3989160 2622210 TRUE FALSE 2650050.345 2762234.712 3036520.638 2701850.508 2971786.744 2391971.75 3053282.714 3136109.178 2312215.321 1.146108808 1.194626939 1.313251673 1.168511636 1.285255191 1.034493513 1.320501031 1.356322289 1 21.14084432 4.479287205 24.95935924 1.226756739 1.15823831 0.014779063 0.119444106 256.8510458 2959763.527 0.02901255 0.079624171 30149.99225 -4.479287205 -0.068518428 VLS(ph)PTAAKPSPFEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLSPTAAKPSPFEGK 15 1 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 1 VLS(0.84)PT(0.16)AAKPSPFEGK;VLS(0.879)PT(0.121)AAKPSPFEGK 119.38 0.00013154 3602500000 4120900 2759400 2123300 2570800 2619400 1993290 3431400 3934200 3508500 TRUE FALSE 3576312.624 2741273.32 3150134.982 3154539.432 2567279.065 2069973.156 3098623.356 3092901.946 3093729.127 1.155987637 0.886074122 1.018232319 1.019655989 0.829833175 0.669086747 1.001581984 0.999732627 1 21.56091546 4.746017076 23.9634677 0.931596988 1.155987832 0.293740768 0.110965082 739.2985157 2375840.759 0.028908261 0.285919312 55720.76579 -4.746017076 0.224390844 VLS(ph)SPQLAQQGQGLMGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLSSPQLAQQGQGLMGHR 18 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 VLS(0.5)S(0.5)PQLAQQGQGLMGHR;VLS(0.5)S(0.5)PQLAQQGQGLMGHR 162.32 4.38E-10 156980000 134350 130094 64437 101144 128612 126760 119054 125746 113230 TRUE FALSE 116595.3071 129239.4039 95598.94873 124110.2911 126052.8728 131636.5392 107508.1614 98856.19646 99844.07839 1.167773883 1.294412308 0.957482409 1.243041081 1.262497234 1.318421096 1.076760516 0.990105753 1 16.60738925 2.034501635 6.789987035 1.005382635 1.204102196 0.450243075 0.099221153 0.161767555 22.56417131 0.041863476 0.027617091 108.268379 -2.034501635 0.198719561 VLSAPPHFHFGQTNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLSAPPHFHFGQTNR 15 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 118.21 0.00017876 3646700000 3175400 3006600 2993700 2520900 2910900 2643900 4675200 4125100 3208500 FALSE TRUE 2755762.845 2986849.447 4441463.333 3093308.875 2852978.785 2745612.544 4221799.824 3242979.467 2829194.785 0.974044933 1.055724216 1.569868344 1.093353095 1.008406632 0.970457233 1.492226638 1.146255282 1 21.43196008 4.463734005 24.999287 1.188116293 0.994464413 0.113511011 0.201225651 416.7653853 778266.0037 0.050178044 0.1329064 29089.3492 -4.463734005 -0.19365188 VLSAPPHFHFGQTNRT(ph)PEFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLSAPPHFHFGQTNRTPEFLR 21 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 1 VLSAPPHFHFGQT(0.012)NRT(0.988)PEFLR;VLSAPPHFHFGQT(0.181)NRT(0.819)PEFLR 227.25 3.11E-25 1981250000 908800 840830 406060 584200 909080 856890 833790 1011170 487880 TRUE FALSE 788699.7774 835306.5324 602431.9742 716851.5389 890991.0866 889855.1128 752929.1741 794939.1644 430203.3822 1.833318402 1.941654964 1.400342255 1.666308469 2.071092705 2.068452155 1.750170281 1.847821745 1 18.71465934 1.237433118 24.86390714 0.999998949 1.821322597 0.635306932 0.195817556 18.36820634 404861.4373 0.299456267 0.050110345 17.27559914 -1.237433118 0.821323648 VLSEDEEDVDFDIIHNANDTFTVK ddPTM_MDA-MB-175_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 ;;;;; 389.97 2.46E-137 2068227000 1473678 1345506 1022215 1191405 1032244 962311 1300333 1601936 1969574 FALSE TRUE 1278927.718 1336667.282 1516561.593 1461931.715 1011704.364 999331.7269 1174226.906 1259374.453 1736733.205 0.736398495 0.769644571 0.873226578 0.841771039 0.582532977 0.575408891 0.676112429 0.725139848 1 20.72794472 1.239069836 8.534032288 1.002535884 0.72123511 0.452674378 0.095884813 0.090651892 74.52839489 0.148959403 0.02626339 17.34082822 -1.239069836 -0.281300774 VLSEDEEDVDFDIIHNANDTFTVKYVPPAAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLSEDEEDVDFDIIHNANDTFTVKYVPPAAGR 32 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ; 222.95 3.14E-36 196645000 159155 146660 93802 102970 183775 145478 173002 192691 149421 FALSE TRUE 138122.2635 145696.5808 139164.9609 126350.9123 180118.237 151074.6328 156224.2927 151485.5292 131756.6196 1.048313655 1.105800841 1.05622747 0.958972025 1.367052658 1.146618919 1.185703558 1.149737521 1 17.00751592 3.29523279 24.99999129 1.167349363 1.047855271 0.309374768 0.094453309 111.448635 49162.67057 0.026793129 0.034589761 1973.480274 -3.29523279 -0.119494093 VLSFTHPISFHSAETFESLLACLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLSFTHPISFHSAETFESLLACLK 24 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 0 53.059 0.067821 110430000 154910 165950 71660 136970 148820 149400 189310 185270 149160 FALSE TRUE 134438.251 164859.8635 106315.0157 168071.132 145858.7732 155147.5147 170950.7453 145651.4523 131526.4747 1.022138328 1.253434823 0.808316469 1.277850199 1.108968924 1.179591523 1.299743992 1.107392657 1 17.0049937 VLSNLVPAGHS(ph)PPASHLPRPTAGGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLSNLVPAGHSPPASHLPRPTAGGPR 26 1 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 VLSNLVPAGHS(0.938)PPAS(0.026)HLPRPT(0.036)AGGPR 78.662 0.012303 370120000 135850 174890 108190 150720 186230 214430 189470 205830 155030 TRUE FALSE 117897.0783 173741.1361 160511.0459 184943.2796 182524.3874 222679.2609 171095.2286 161814.8563 136702.53 0.862435233 1.270943091 1.17416295 1.352888492 1.335193923 1.628932989 1.251587871 1.183700523 1 17.06068042 5.186662058 1.640921858 1.286378829 9.95E-10 0.389770457 0.160665677 4.509206872 4.31295973 0.045601205 13.26638577 153695.8204 -5.186662058 -1.286378828 VLSNRPIMFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLSNRPIMFR 10 1 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ; 128.51 0.00029877 1612160000 720040 792250 507890 556850 822840 871550 807130 918730 811330 FALSE TRUE 624884.8897 787045.6576 753507.3028 683291.3034 806467.0939 905079.0925 728854.6568 722266.7391 715415.4917 0.873457308 1.100123868 1.05324432 0.955097159 1.12727094 1.26510972 1.018785119 1.009576599 1 19.44842183 4.74549791 24.2178507 1.063764516 0.873457169 0.330259289 0.086177867 706.9596356 2467872.266 0.022183849 0.212356266 55654.19558 -4.74549791 -0.190307347 VLSQSTPGT(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLSQSTPGTPSK 12 0 Q6MZP7-3;Q6MZP7 Q6MZP7-3 LIN54 Protein lin-54 homolog 1 VLSQSTPGT(0.998)PS(0.002)K;VLSQSTPGT(1)PSK 258.68 3.38E-20 521870000 829380 780410 495640 650540 745480 628740 809990 959670 812760 TRUE FALSE 719775.3316 775283.4353 735333.1618 798255.0499 730646.4065 652928.0346 731437.2945 754452.0387 716676.4387 1.004323978 1.08177609 1.026032282 1.113829068 1.019492713 0.911049951 1.020596262 1.052709421 1 19.4509624 3.014117954 24.84166924 1.002570968 1.057438411 0.275965504 0.045705821 322.3287054 567158.6146 0.014230068 0.016128838 1033.04194 -3.014117954 0.054867443 VLSSAAS(ph)LPGSELPSSRPEGSQGGELSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLSSAASLPGSELPSSRPEGSQGGELSR 28 1 O15027;O15027-5;A0A0C4DH09;Q8N9G1 O15027 SEC16A Protein transport protein Sec16A 1 VLSSAAS(0.993)LPGS(0.006)ELPSSRPEGSQGGELSR;VLS(0.002)S(0.008)AAS(0.989)LPGS(0.001)ELPSSRPEGSQGGELSR 140.94 7.83E-08 1081610000 705860 514960 374683 407168 599960 597750 615320 654710 590920 TRUE FALSE 612578.8126 511577.1939 555880.952 499621.7176 588021.9698 620745.8293 555646.3611 514705.3615 521062.1108 1.175634919 0.981796955 1.066822823 0.958852519 1.128506483 1.191308707 1.066372606 0.9878004 1 18.99109583 1.776549119 5.33564929 0.994302582 1.078732944 0.196756341 0.073494329 0.312713559 19.34114767 0.042863387 0.019822257 59.77906515 -1.776549119 0.084430362 VLSSIEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLSSIEQK 8 0 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ; 157.58 0.00087158 208420000 744630 542270 382330 472690 544070 477550 574500 668160 656840 FALSE TRUE 646225.2588 538707.7927 567226.0668 580021.4891 533244.0715 495921.6575 518785.0784 525279.1836 579189.1235 1.115741357 0.930106887 0.979345163 1.001437122 0.92067349 0.85623441 0.89570929 0.906921699 1 19.14367498 3.208647738 5.303264726 0.90952595 0.999601044 0.374709258 0.057734945 0.199147165 14.51657458 0.017013288 0.020055171 1616.768124 -3.208647738 0.090075094 VLST(ph)STDLEAAVADALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLSTSTDLEAAVADALK 17 0 Q7Z460 Q7Z460 CLASP1 CLIP-associating protein 1 1 VLS(0.058)T(0.443)S(0.443)T(0.056)DLEAAVADALK 104.41 0.0095185 31387000 125040 80233 72304 72180 69122 53360 82219 93541 136820 TRUE FALSE 108515.6472 79705.94414 107270.4562 88569.5722 67746.60743 55412.79373 74245.41403 73537.98509 120645.2955 0.899460246 0.660663508 0.889139156 0.734132001 0.561535426 0.459303394 0.61540248 0.609538771 1 16.88041213 3.449761385 6.74750554 0.632963252 0.802827017 0.197023252 0.151972754 0.267603659 42.23288518 0.043471166 0.05716158 2816.83485 -3.449761385 0.169863765 VLSTS(ph)PTISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLSTSPTISK 10 0 A0A087WX19;A0A087WX45;Q6IPM2-2;Q6IPM2-3;Q6IPM2-4;Q6IPM2;H7C427 A0A087WX19 IQCE IQ domain-containing protein E 1 VLSTS(1)PTISK;VLST(0.014)S(0.982)PT(0.004)ISK 207.44 1.39E-07 503360000 1170300 1203100 807450 1057770 1199280 1152690 1413510 1615950 1516920 TRUE FALSE 1015641.89 1195196.757 1197935.521 1297952.846 1175416.674 1197034.73 1276428.018 1270391.668 1337591.446 0.759306508 0.89354396 0.895591494 0.97036569 0.878756124 0.894918051 0.954273461 0.94976061 1 20.3512061 5.723589196 0.880243381 0.940929875 8.51E-14 0.708756756 0.035829672 6.247435202 1.031674797 0.012303184 8.510798482 529162.666 -5.723589196 -0.940929875 VLSTS(ph)TDLEAAVADALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VLSTSTDLEAAVADALK 17 0 Q7Z460 Q7Z460 CLASP1 CLIP-associating protein 1 1 VLS(0.016)T(0.113)S(0.785)T(0.085)DLEAAVADALK;VLST(0.003)S(0.997)TDLEAAVADALK;VLST(0.035)S(0.964)T(0.001)DLEAAVADALK 377.19 4.28E-105 207657000 389210 251067 199851 229957 203082 172327 279322 298656 406235 TRUE FALSE 337774.9124 249417.7243 296499.6121 282172.2515 199041.0655 178956.5312 252233.3954 234790.7385 358210.3611 0.942951263 0.696288414 0.827724835 0.787727777 0.555654127 0.499585022 0.704148799 0.655454906 1 18.45044754 7.999976127 0.811318266 0.689290495 65.45461787 0.191376135 0.140873588 908.2489618 3.000948267 0.050044543 108225.3723 99994503.26 -7.999976127 64.76532738 VLT(ph)PEEQLADK ddPTM_MDA-MB-175_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 152.11 0.00037002 194441000 692470 484520 608020 669580 632220 508460 610590 750320 1646890 TRUE FALSE 600958.335 481337.1562 902060.5057 821618.3729 619640.0589 528020.7852 551375.0758 589869.907 1452196.54 0.413827136 0.331454554 0.621169711 0.565776291 0.426691596 0.363601462 0.379683507 0.406191511 1 20.46980529 1.236598679 24.99846766 1.000000712 0.437896642 0.795816257 0.089374883 24.49809285 312063.4064 0.148308522 0.0233967 17.24243823 -1.236598679 -0.56210407 VLT(ph)PEEQLADKLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLTPEEQLADKLR 13 1 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 VLT(1)PEEQLADKLR;VLT(1)PEEQLADKLR 114.96 0.0011342 257096000 425030 331080 275716 295496 396350 342180 411820 502670 328942 TRUE FALSE 368861.2086 328905.1137 409053.1798 362592.8832 388463.4104 355343.886 371881.7598 395177.9323 290054.8515 1.27169467 1.133941087 1.410261465 1.250083842 1.339275687 1.225092027 1.282108394 1.362424832 1 18.14596622 1.229034536 24.99728477 0.999999433 1.285940623 0.578012004 0.076347098 276.5222634 725566.2353 0.225351948 0.017882528 16.94472543 -1.229034536 0.28594119 VLT(ph)PPHDVDSLPHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLTPPHDVDSLPHLR 15 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 VLT(1)PPHDVDSLPHLR 76.586 0.053041 61705000 46986 39615 25603 29709 44063 41161 38614 46081 43435 TRUE FALSE 40776.68105 39354.76646 37984.69644 36454.88252 43186.23251 42744.4903 34869.22022 36226.93675 38300.16378 1.064660749 1.0275352 0.99176329 0.951820539 1.12757305 1.116039361 0.910419611 0.945868977 1 15.22506294 2.22497417 24.99682156 0.949062333 1.042584947 0.385538295 0.056027286 260.5711688 479404.0913 0.024343883 0.016511631 167.8704174 -2.22497417 0.093522614 VLTANSNPSS(ph)PSAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VLTANSNPSSPSAAK 15 0 Q9NV56 Q9NV56 MRGBP MRG/MORF4L-binding protein 1 VLTANSNPS(0.001)S(0.999)PSAAK;VLTANSNPS(0.004)S(0.993)PS(0.004)AAK;VLTANSNPSS(0.998)PS(0.002)AAK;VLTANSNPS(0.022)S(0.957)PS(0.022)AAK;VLTANS(0.001)NPS(0.101)S(0.886)PS(0.012)AAK 317.03 2.37E-56 1676260000 3181614 2658247 2148060 2792677 2978427 2534519 3438843 4112995 4440303 TRUE FALSE 2761155.649 2640784.8 3186869.001 3426796.996 2919162.13 2632023.586 3105344.535 3233463.027 3915375.438 0.7052084 0.674465282 0.813937016 0.87521543 0.745563785 0.672227639 0.793115395 0.825837286 1 21.90071922 1.150603267 1.648155696 1.137224643 0.753630532 0.610137461 0.062303291 0.977764019 2.023480166 0.651580011 0.018881167 14.14501026 -1.150603267 -0.383594111 VLTEDEMGHPEIGDAIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 VLTEDEMGHPEIGDAIAR 18 0 P14324-2;P14324;A0A087WVN4;A0A087X1D8;A0A087WTP2 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 ;;;;;;; 241.08 5.59E-24 9249510000 5331140 5322220 3393980 3933380 5086900 5142020 4995950 5691270 5438660 FALSE TRUE 4626616.342 5287257.986 5035320.08 4826514.047 4985680.642 5339836.837 4511443.538 4474236.2 4795707.811 0.964741082 1.102497941 1.049963901 1.00642371 1.039613096 1.113461672 0.940725273 0.932966806 1 22.19331233 2.215274916 24.996299 0.951987942 1.046754684 0.45168609 0.04566189 187.8688005 201668.3558 0.017853574 0.012045529 164.1628624 -2.215274916 0.094766742 VLTFYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLTFYR 6 0 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 162.47 0.013082 0 693320 791770 566150 513060 790000 859300 836740 875100 876620 FALSE TRUE 601696.0054 786568.8107 839942.0337 629558.1146 774280.5456 892357.827 755593.0836 687966.675 772986.9822 0.778403801 1.017570579 1.086618602 0.814448534 1.001673461 1.154428014 0.977497812 0.890010687 1 19.56008459 VLTGEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLTGEEK 7 0 Q96ST2;Q96ST2-3;Q96ST2-2;A0A1B0GW95 Q96ST2 IWS1 Protein IWS1 homolog 0 90.986 0.030348 0 242390 251770 109800 199840 178560 268950 215980 254030 252680 FALSE TRUE 210357.5474 250116.1063 162899.6473 245216.7264 175007.0053 279296.6805 195034.2928 199707.6614 222808.4583 0.94411832 1.122561092 0.731119674 1.100571892 0.785459433 1.253528177 0.875345103 0.896319928 1 17.76544448 VLTLSDDLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VLTLSDDLER 10 0 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ;;;;; 241.96 5.66E-12 939613000 947915 1103544 683327 836843 1084854 1156656 992529 1205293 1148865 FALSE TRUE 822645.631 1096294.747 1013786.223 1026860.993 1063267.528 1201153.305 896273.6903 947550.4716 1013047.488 0.812050413 1.08217508 1.00072922 1.013635595 1.049573233 1.185683118 0.884730183 0.935346548 1 19.95027037 VLTLSERPLDFLDLERPPT(ph)TPQNEEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VLTLSERPLDFLDLERPPTTPQNEEIR 27 2 Q9GZY8-5;Q9GZY8-2;Q9GZY8;C9JHF5;A0A0A0MS29;Q9GZY8-4;Q9GZY8-3 Q9GZY8-5 MFF Mitochondrial fission factor 1 VLTLSERPLDFLDLERPPT(0.577)T(0.423)PQNEEIR;VLTLSERPLDFLDLERPPT(0.5)T(0.5)PQNEEIR;VLTLSERPLDFLDLERPPT(0.867)T(0.133)PQNEEIR;VLTLSERPLDFLDLERPPT(0.656)T(0.344)PQNEEIR 169.73 2.86E-10 952178000 187359 236398 199530 304905 384483 566757 237047 454333 406771 TRUE FALSE 162599.0334 234845.086 296023.3754 374138.3404 376832.5405 588560.5085 214058.2184 357177.4236 358682.9958 0.453322392 0.654742736 0.825306409 1.043089148 1.050600516 1.640893255 0.596789424 0.995802499 1 18.45234983 4.222913072 1.603719712 1.045371249 0.455018561 0.41337648 0.250872223 0.491041852 2.21415951 0.073283742 0.337378048 16707.56163 -4.222913072 -0.590352688 VLTPEEQLADKLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VLTPEEQLADKLR 13 1 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 0 ;; 160.48 3.86E-05 990710000 1525040 1201390 577648 907080 1183950 1233310 1237620 1566480 725319 FALSE TRUE 1323502.1 1193497.99 857000.5049 1113046.378 1160391.711 1280756.234 1117595.803 1231500.442 639572.6141 2.069353926 1.866086764 1.3399581 1.740297119 1.814323637 2.002518878 1.747410346 1.925505275 1 19.28674864 1.233362685 24.98402677 0.999998737 1.805903773 0.626017817 0.197453828 114.2452553 549060.4641 0.407048519 0.049354916 17.11443967 -1.233362685 0.805905036 VLVALYEEPEKPNSALDFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLVALYEEPEKPNSALDFLK 20 1 A0A087WV05;Q99417 A0A087WV05 MYCBP C-Myc-binding protein 0 99.451 0.0010475 0 95967 69625 54522 62158 90939 54368 110650 120930 82116 FALSE TRUE 83284.7178 69167.62879 80889.02157 76271.92393 89129.49182 56459.57214 99919.18003 95070.06058 72408.34003 1.150208909 0.955243951 1.117122993 1.053358272 1.230928534 0.779738523 1.379940211 1.312971138 1 16.14386826 2.204503085 24.99998977 1.25426091 1.055292918 0.233819583 0.154025549 235.7238106 173031.8689 0.059588791 0.040177051 160.1412024 -2.204503085 -0.198967992 VLVAQHDVYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLVAQHDVYK 10 0 H0YL12;P13804-2;P13804;H0YKF0;H0YLU7 H0YL12 ETFA "Electron transfer flavoprotein subunit alpha, mitochondrial" 0 96.015 0.0070288 447430000 854910 957530 724060 1055800 1009800 902540 891680 1107800 1030600 FALSE TRUE 741931.4774 951239.9224 1074217.838 1295535.527 989706.9556 937261.2978 805205.0108 870905.5909 908763.6421 0.816418531 1.046740735 1.182065158 1.425602287 1.089069709 1.03135871 0.886044482 0.958341147 1 19.79354559 2.585634916 3.134096034 0.948712419 1.129567671 0.192176531 0.150611925 0.414249614 7.75848791 0.060058751 0.050898219 385.1544465 -2.585634916 0.180855252 VLVDVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VLVDVER 7 0 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;; 114.43 0.013741 347883000 810270 707230 450911 522836 669007 741910 650097 728090 764060 FALSE TRUE 703190.7665 702584.1596 668973.0678 641553.9048 655695.0696 770451.7578 587050.693 572393.6195 673733.6972 1.043722126 1.042821759 0.99293396 0.952236629 0.973225879 1.143555326 0.871339367 0.849584371 1 19.36181893 2.198020451 24.99993721 0.893533339 1.018486824 0.416854161 0.064739675 136.2181492 84000.83848 0.02637552 0.017782598 157.7685563 -2.198020451 0.124953485 VLVPEHEKDVLEWIACVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLVPEHEKDVLEWIACVR 18 1 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 187.35 2.60E-14 209040000 228240 196070 134410 149690 171080 168900 226140 239940 149150 FALSE TRUE 198077.5057 194782.0033 199411.1256 183679.4024 167675.8427 175397.6923 204208.9776 188630.6982 131517.6569 1.506090592 1.481033101 1.516230826 1.396614011 1.274930277 1.333643683 1.552711494 1.434261396 1 17.00489698 1.238826443 11.41631127 0.999181604 1.436599409 0.723166651 0.084960415 0.035407254 196.2493682 0.124159063 0.0223475 17.33111258 -1.238826443 0.437417805 VLVQNAAGS(ph)QEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLVQNAAGSQEK 12 0 Q9Y490 Q9Y490 TLN1 Talin-1 1 VLVQNAAGS(1)QEK 121.13 0.00020722 0 90021 76450 69956 63793 77891 75551 91510 92764 115620 TRUE FALSE 78124.49677 75947.79492 103786.9556 78278.17566 76341.12149 78457.49586 82635.37428 72927.14049 101951.5353 0.766290537 0.744940179 1.01800287 0.767797909 0.748798154 0.769556786 0.81053585 0.715311842 1 16.63752398 1.224934302 24.93083166 1.000000531 0.792549061 0.377079454 0.083752327 763.3204459 1396492.119 0.400168583 0.020528343 16.78550075 -1.224934302 -0.20745147 VLVTVEEDDTIMEELVDNHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 VLVTVEEDDTIMEELVDNHGK 21 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;;;;;;;;;;;; 385.41 4.98E-131 2497595000 1710805.1 1578118.1 1287623.6 1621868.6 1438353.3 1334341.7 1773337.8 2119762 2875357.7 FALSE TRUE 1484717.871 1567751.338 1910322.68 1990138.654 1409732.883 1385674.689 1601359.773 1666467.392 2535436.188 0.585586763 0.618335948 0.753449323 0.784929498 0.556011975 0.546523196 0.631591432 0.657270493 1 21.27380253 1.237545142 5.55042013 1.017211337 0.642264196 0.682340747 0.076900854 0.096417454 9.407304038 0.138174701 0.020620316 17.28005587 -1.237545142 -0.374947141 VLVTVEEDDTIMEELVDNHGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VLVTVEEDDTIMEELVDNHGKK 22 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;; 299.97 6.59E-56 807980000 935568 784433 517504 537743 657649 497595 1040332 1229862 426243 FALSE TRUE 811930.3184 779280.008 767770.6653 659845.767 644563.0716 516737.8016 939440.7628 966865.5821 375853.0381 2.160233485 2.073363599 2.042741677 1.75559514 1.71493378 1.374840028 2.499489608 2.572456476 1 18.51980914 2.219958055 24.99277414 2.158060093 1.861443296 0.001811356 0.479109001 688.5466095 925063.8471 0.197072177 0.133128446 165.942663 -2.219958055 -0.296616797 VLVWDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLVWDLR 7 0 O43684;O43684-2;J3QT28 O43684 BUB3 Mitotic checkpoint protein BUB3 0 ; 105.39 0.018466 897750000 2275000 2306400 1420170 1752360 2255400 2250340 2045460 2463900 2523200 FALSE TRUE 1974352.986 2291249.107 2106968.962 2150260.121 2210521.953 2336912.036 1847091.604 1937014.159 2224910.17 0.887385483 1.029816456 0.946990575 0.966448061 0.993533124 1.050339949 0.830187047 0.87060331 1 21.08531566 2.234891876 24.9999684 0.891164416 0.98001496 0.26680774 0.060964136 109.5709776 746638.9582 0.02350013 0.016540401 171.7480743 -2.234891876 0.088850544 VLWLADCDVSDSSCSSLAATLLANHSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VLWLADCDVSDSSCSSLAATLLANHSLR 28 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 ;; 322.32 3.02E-83 1068170000 678810 719010 431600 512580 629510 697880 687630 726090 668880 FALSE TRUE 589103.5386 714286.776 640323.2036 628969.1233 616983.9826 724727.8952 620943.7484 570821.3039 589805.7684 0.998809388 1.211054239 1.085650968 1.066400427 1.04607994 1.228756879 1.052793617 0.967812345 1 19.16988041 1.997940039 24.99846204 0.990215815 1.10837465 0.341942328 0.069758316 78.67237913 954725.8159 0.027492802 0.018205442 99.52679957 -1.997940039 0.118158835 VLYEIPDTYAQTEGDAEPPRPDAGGPNSDFNTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VLYEIPDTYAQTEGDAEPPRPDAGGPNSDFNTR 33 1 Q9BU68 Q9BU68 PRR15L Proline-rich protein 15-like protein 0 69.201 0.0037858 116360000 14502 13730 10745 12861 15644 14234 15338 19494 16653 FALSE TRUE 12585.52396 13639.80673 15941.31794 15781.28662 15332.71501 14781.59119 13850.52312 15325.3598 14684.30131 0.857073394 0.928869984 1.085602754 1.074704631 1.044156932 1.006625435 0.943219757 1.043656043 1 13.841987 4.435786242 4.981413474 1.026282885 0.871684331 0.674422908 0.040566543 0.104070926 5.94752968 0.010911487 0.032595371 27276.34922 -4.435786242 -0.154598554 VLYQVEGFVDKNNDLLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VLYQVEGFVDKNNDLLYR 18 1 E9PDF6;O43795;O43795-2;A0A0U1RRI3 E9PDF6 MYO1B Unconventional myosin-Ib 0 ; 130.85 1.66E-05 184560000 434730 336110 208249 267910 340380 304290 349070 471470 195042 FALSE TRUE 377279.329 333902.0713 308958.913 328743.0602 333607.1039 315996.2332 315217.2451 370649.8095 171984.357 2.193683982 1.941467685 1.796436132 1.911470706 1.939752602 1.837354506 1.832825094 2.155136758 1 17.39191782 1.230692822 24.99999716 0.999998292 1.944775221 0.839685893 0.130567014 112.8396812 358519.613 0.341431264 0.032169999 17.00954991 -1.230692822 0.944776929 VMDDLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VMDDLDR 7 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;; 143.85 0.0055686 1652190000 5995950 4325330 2511810 3136430 4008210 4147500 4382260 4955480 4038550 FALSE TRUE 5203570.016 4296916.622 3726529.718 3848604.369 3928454.463 4307057.009 3957269.1 3895789.166 3561117.22 1.461218403 1.206620383 1.046449608 1.080729482 1.103152247 1.209467912 1.111243707 1.09397948 1 21.76389849 4.668802821 2.731964908 1.097876375 1.502418665 0.824009469 0.053851404 0.152166685 1.682329224 0.014065124 0.128117711 46644.75551 -4.668802821 0.40454229 VMDQHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 VMDQHK 6 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;;; 102.98 0.027632 4048380000 4694000 4936940 3213320 4306890 2631051 4031910 5166410 6199680 6271150 FALSE TRUE 4073676.007 4904508.916 4767292.3 5284835.201 2578698.233 4187020.187 4665372.353 4873926.678 5529781.791 0.736679341 0.886926302 0.862112192 0.955704113 0.466329112 0.757176385 0.843681094 0.881395842 1 22.39879112 1.459936995 1.72155885 1.022436578 0.783749258 0.228728149 0.130050354 0.969395808 4.094820623 0.35059943 0.038504241 28.83613132 -1.459936995 -0.23868732 VMDS(ph)DEDDDY ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VMDSDEDDDY 10 0 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 1 VMDS(1)DEDDDY;VMDS(1)DEDDDY 185.08 5.82E-06 884730000 700400 668160 443250 538060 627080 631180 603380 720850 848740 TRUE FALSE 607840.3654 663770.813 657607.1826 660234.7467 614602.3349 655461.903 544864.3005 566701.8372 748402.9241 0.812183312 0.886916381 0.87868067 0.882191565 0.821218511 0.875814193 0.728036039 0.757214889 1 19.51345567 VMEGLDAFDDLMQHTHIQPWYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VMEGLDAFDDLMQHTHIQPWYLR 23 0 Q9H7Z7;A6NHH0 Q9H7Z7 PTGES2 Prostaglandin E synthase 2;Prostaglandin E synthase 2 truncated form 0 ; 220.63 1.10E-32 1962020000 995810 867350 571350 659720 745540 984410 686450 912150 730200 FALSE TRUE 864211.1854 861652.3207 847656.7711 809519.5092 730705.2126 1022280.89 619878.1847 717093.8209 643876.5878 1.342200045 1.338225891 1.316489506 1.257258805 1.134852899 1.587696942 0.962728256 1.113713147 1 19.29642467 2.208694523 24.9998628 1.041247494 1.317136546 0.595877938 0.117476781 144.2393697 120736.7472 0.045324177 0.030562194 161.6942302 -2.208694523 0.275889052 VMEHFIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VMEHFIK 7 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 114.02 0.0059982 5049800000 12160200 9822100 7192400 9579400 9952800 10788000 9380900 10796800 9098600 FALSE TRUE 10553198.76 9757577.978 10670668.7 11754549.18 9754758.752 11203021.34 8471141.762 8487988.341 8022973.873 1.315372445 1.216204631 1.33001414 1.465111238 1.215853237 1.396367671 1.055860569 1.057960362 1 22.93570567 2.226818808 24.66660079 1.042857696 1.320179689 0.761705266 0.075172666 87.15955809 183098.5278 0.029877354 0.02033512 168.5849525 -2.226818808 0.277321993 VMEWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VMEWLR 6 0 F5GZP6;Q86W92-3;Q86W92-4;Q86W92;H0YFE4;Q86W92-2;E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30 F5GZP6;Q86W92-2;E9PP16 PPFIBP1;PPFIBP2 Liprin-beta-1;Liprin-beta-2 0 106.76 0.074087 170620000 187450 292530 177050 216760 298310 252450 260000 274110 258000 FALSE TRUE 162678.0076 290608.3512 262671.9722 265978.671 292374.2146 262161.9149 234785.24 215493.7096 227499.5339 0.71506963 1.277401963 1.154604441 1.16913941 1.285164016 1.152362426 1.032025147 0.947227038 1 17.79550406 2.093927139 3.761814292 0.974037308 1.142842256 0.136456456 0.157730847 0.375631699 10.23293777 0.069318589 0.042784575 124.1444014 -2.093927139 0.168804948 VMEYINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VMEYINR 7 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 185.22 0.0014344 1778070000 1513890 1360140 906420 997180 1330850 1415000 1301790 1474380 1369610 FALSE TRUE 1313825.601 1351205.151 1344767.744 1223604.96 1304368.689 1469435.966 1175542.606 1159095.311 1207696.266 1.087877505 1.118828623 1.113498304 1.013172761 1.080046967 1.216726429 0.973376038 0.959757303 1 20.20382623 2.18519376 24.91569186 0.973789597 1.100727208 0.582850265 0.050650453 64.2272445 29985.55917 0.020748429 0.013988599 153.1770707 -2.18519376 0.126937611 VMFEVWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VMFEVWR 7 0 Q09161 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 ; 97.602 0.048711 303680000 599810 712350 495080 593150 748180 743720 756420 845730 901250 FALSE TRUE 520543.5888 707670.5259 734502.3439 727833.7732 733292.6818 772331.3897 683062.5048 664877.221 794705.2517 0.655014658 0.890481753 0.924244986 0.915853735 0.922722834 0.971846339 0.859516787 0.836633733 1 19.60006035 4.738103184 4.295885355 0.910074461 0.635910019 0.748678264 0.047435985 0.112612471 4.905468761 0.01220442 0.094648656 54714.59443 -4.738103184 -0.274164443 VMLGETNPADSKPGTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 210.57 2.97E-12 3400840000 1150328 1166446 593929 721981 982582 876939 1205238 1230762 1120202 FALSE TRUE 998309.2402 1158783.539 881155.051 885917.8208 963030.5406 910675.4108 1088354.204 967573.1241 987772.9957 1.010666666 1.173127373 0.892062301 0.896884026 0.974951274 0.921948074 1.101826238 0.979550087 1 19.91382 4.237993226 24.99999949 0.971323716 1.091897006 0.347903715 0.071018344 16.42749327 723963.0025 0.018109311 0.041752243 17297.89377 -4.237993226 0.12057329 VMQEQGTHPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 VMQEQGTHPK 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;;;; 143.97 3.30E-05 6915060000 11714790 10889620 7015050 8874960 10143910 9896930 12613060 13323860 12591770 FALSE TRUE 10166650.82 10818085.37 10407551.64 10890155.31 9942066.037 10277671.3 11389847.38 10474656.23 11103185.3 0.91565173 0.97432269 0.93734828 0.980813616 0.895424671 0.925650705 1.025818004 0.943392004 1 23.40447028 2.27009171 24.99989875 0.981585007 0.939797463 0.351911693 0.03229515 245.481248 194632.5484 0.011608461 0.008990958 186.2480397 -2.27009171 -0.041787544 VMSS(ph)SNPDLAGTHSAADEEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VMSSSNPDLAGTHSAADEEVK 21 0 Q8NF50-3;Q8NF50;A2A369;Q8NF50-4;Q8NF50-2;A2A370 Q8NF50-3 DOCK8 Dedicator of cytokinesis protein 8 1 VMS(0.068)S(0.466)S(0.466)NPDLAGTHSAADEEVK 160.52 1.36E-11 187390000 98017 94505 60320 71795 95479 97306 104890 112640 103090 TRUE FALSE 85063.80511 93884.19043 89490.95376 88097.15207 93579.1547 101049.4248 94717.78394 88552.81257 90902.81764 0.93576643 1.032797364 0.984468426 0.969135549 1.029441739 1.111620381 1.041967525 0.97414816 1 16.47203739 3.225857053 24.06307647 1.029073791 0.984554938 0.2640196 0.041883237 250.350863 474212.918 0.013784022 0.015743435 1682.120305 -3.225857053 -0.044518854 VMSSS(ph)NPDLAGTHSAADEEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VMSSSNPDLAGTHSAADEEVK 21 0 Q8NF50-3;Q8NF50;A2A369;Q8NF50-4;Q8NF50-2;A2A370 Q8NF50-3 DOCK8 Dedicator of cytokinesis protein 8 1 VMS(0.02)S(0.109)S(0.872)NPDLAGTHSAADEEVK;VMS(0.003)S(0.106)S(0.891)NPDLAGTHSAADEEVK 256.73 1.20E-36 508940000 602920 520140 486050 508670 543990 509630 646310 748530 910640 TRUE FALSE 523242.5944 516723.1661 721105.4057 624171.298 533165.6633 529235.7959 583630.9557 588462.6846 802985.1766 0.651621736 0.643502746 0.898030782 0.7773136 0.663979459 0.659085387 0.726826563 0.732843771 1 19.61501383 1.235303368 5.11807289 1.017558261 0.720315545 0.572614095 0.076324792 0.135975159 9.477200004 0.144304417 0.019916459 17.19108818 -1.235303368 -0.297242716 VMTIPYQPMPASS(ph)PVICAGGQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VMTIPYQPMPASSPVICAGGQDR 23 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 VMTIPYQPMPAS(0.151)S(0.849)PVICAGGQDR;VMTIPYQPMPAS(0.281)S(0.719)PVICAGGQDR;VMTIPYQPMPAS(0.092)S(0.908)PVICAGGQDR;VMTIPYQPMPAS(0.357)S(0.643)PVICAGGQDR;VMTIPYQPMPAS(0.274)S(0.726)PVICAGGQDR 214.47 1.84E-32 1088390000 1611700 1404760 865460 1019770 1271120 1448520 1280540 1483910 1396680 TRUE FALSE 1398709.761 1395532.039 1283999.351 1251324.365 1245827.199 1504245.502 1156353.428 1166587.394 1231566.082 1.135716372 1.133136143 1.042574467 1.016043218 1.011579661 1.22140868 0.938929259 0.947238976 1 20.23206261 -1.999999922 0.084053691 0.304392827 1.331738911 0.273921682 0.076065714 527.8549578 4.18677162 65.57178303 9.711417189 0.010000002 1.999999922 1.027346084 VMYAFCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VMYAFCR 7 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;F8WBG8;Q9UJU6 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ; 126.05 0.0092828 462760000 433740 612450 362820 335600 563930 623000 555380 606810 336760 FALSE TRUE 376420.16 608426.7756 538280.9656 411803.1093 552708.8963 646967.2131 501519.3331 477048.4037 296948.6164 1.267627257 2.048929485 1.812707437 1.386782381 1.861294735 2.178717722 1.688909479 1.60650152 1 18.17985379 1.179321672 2.158716348 0.685688857 1.768399357 0.426026647 0.270957307 0.786854199 3.230706595 1.776964089 0.070975992 15.1119905 -1.179321672 1.0827105 VNAVPRPIPEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VNAVPRPIPEKK 12 2 Q9HD45 Q9HD45 TM9SF3 Transmembrane 9 superfamily member 3 0 ; 104.87 0.0011765 795240000 1249350 902880 776500 741260 908570 797240 992490 1519570 772420 FALSE TRUE 1084245.232 896948.9218 1152017.997 909574.4124 890491.2346 827910.3387 896238.4726 1194621.781 681105.3875 1.591890553 1.316901816 1.691394633 1.335438581 1.30742063 1.21553926 1.315858733 1.753945575 1 19.37751852 VNCLDKFWHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VNCLDKFWHK 10 1 Q14847;Q14847-2;F6S2S5;K7ESD6 Q14847 LASP1 LIM and SH3 domain protein 1 0 ; 114.83 0.00078292 2100380000 11038300 2872600 1233910 1338340 2581600 2009670 3025700 3801900 610010 FALSE TRUE 9579560.688 2853729.701 1830633.003 1642230.552 2530231.211 2086983.305 2732268.08 2988893.271 537895.3127 17.80934033 5.305362649 3.403325814 3.05306723 4.703947313 3.879906101 5.079553614 5.556644947 1 19.03696589 4.738568616 3.973234238 4.051033392 19.06727898 0.921733918 1.270510332 0.060336343 1.98416812 0.31150341 2.622376398 54773.26329 -4.738568616 15.01624559 VNDAEPGS(ph)PEAPQGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VNDAEPGSPEAPQGK 15 0 Q8N8A6 Q8N8A6 DDX51 ATP-dependent RNA helicase DDX51 1 VNDAEPGS(1)PEAPQGK;VNDAEPGS(1)PEAPQGK;VNDAEPGS(1)PEAPQGK;VNDAEPGS(1)PEAPQGK;VNDAEPGS(1)PEAPQGK;VNDAEPGS(1)PEAPQGK 338.42 3.59E-69 2149820000 5485040 3930540 3026978 3742900 3867520 3311160 4725800 5668900 6263360 TRUE FALSE 4760178.067 3904720.024 4490834.685 4592782.652 3790563.919 3438542.468 4267492.643 4456649.85 5522912.716 0.861896306 0.707003754 0.813127948 0.831587043 0.686334207 0.622595837 0.772688772 0.806938309 1 22.3969979 1.197512793 2.218499818 1.089698136 0.752424206 0.53273359 0.071247411 0.609604781 2.79221371 0.429499774 0.019601031 15.75842441 -1.197512793 -0.337273931 VNDDIIVNWVNETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VNDDIIVNWVNETLR 15 0 P13796;P13796-2 P13796 LCP1 Plastin-2 0 153.09 3.00E-08 0 106060 84577 59875 82106 112090 86738 190250 150000 74874 FALSE TRUE 92043.90228 84021.40812 88830.75027 100749.4222 109859.6283 90074.86699 171799.5843 117923.6673 66022.48102 1.394129709 1.272618157 1.345462165 1.525986613 1.663973038 1.364306 2.60213766 1.786113843 1 16.01066973 3.226081444 1.327276739 1.788029203 1.327453617 0.119619519 0.402523768 0.761739664 2.855086351 0.16163012 0.221686488 1682.989647 -3.226081444 -0.460575585 VNDGGGSHPSRPNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VNDGGGSHPSRPNSR 15 1 F8VRJ4;A0A5K1VW50;P11473;P11473-2 F8VRJ4 VDR Vitamin D3 receptor 0 86.497 0.0045269 9829900 10954 10835 4758.5 7671.2 8733.8 11002 9763.9 10479 11257 FALSE TRUE 9506.401146 10763.82417 7059.726516 9413.063207 8560.014467 11425.25406 8816.998481 8238.147398 9926.210284 0.957707007 1.084384056 0.711220729 0.948303828 0.862364812 1.151018741 0.888254251 0.829938835 1 13.2770273 2.463844589 0.006742316 9.60E-05 1.852574494 0 0.126253612 87517.31847 457.90195 63425.75541 62377.65507 290.9675714 -2.463844589 1.85247845 VNFAMNVGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VNFAMNVGK 9 0 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 87.181 0.031721 422190000 406800 375310 210430 236330 336080 298460 402890 448860 259460 FALSE TRUE 353040.3493 372844.5639 312194.6518 289992.3386 329392.6655 309941.9493 363817.7898 352874.782 228786.9344 1.543096638 1.629658463 1.364565038 1.267521414 1.439735475 1.354718748 1.590203526 1.542372964 1 17.80364514 4.2357488 24.99867102 1.392163017 1.586377581 0.228540731 0.163055477 111.1735524 988435.7202 0.041799189 0.093658513 17208.72919 -4.2357488 0.194214565 VNFDDYTVNLGGLKDHIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VNFDDYTVNLGGLKDHIK 18 1 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 242.34 2.96E-24 948780000 1569830 1210080 948990 938130 1169280 902850 1589720 1823910 893160 FALSE TRUE 1362372.988 1202130.905 1407924.738 1151146.755 1146013.616 937583.2237 1435549.199 1433881.04 787571.6423 1.729840074 1.526376574 1.787678305 1.461640685 1.455123006 1.190473569 1.822753794 1.82063569 1 19.58705164 3.719894435 24.31156751 1.507633195 1.665806166 0.123138035 0.257944798 1636.58892 2131557.295 0.073959305 0.109943715 5246.79909 -3.719894435 0.158172972 VNFEDDSR ddPTM_MDA-MB-175_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 ;;;; 229.33 4.00E-06 2901610000 6549430 6230120 3949370 4357870 6058530 6137560 6236980 6912700 6254390 FALSE TRUE 5683906.231 6189193.932 5859298.542 5347390.989 5937977.106 6373675.905 5632118.64 5434472.9 5515003.139 1.03062611 1.122246674 1.062428868 0.969607968 1.076695145 1.155697602 1.021235799 0.98539797 1 22.39493028 2.010579732 24.97311534 0.995154236 1.069159136 0.304516746 0.049354923 248.1757393 585808.5352 0.020757781 0.01397961 102.4659879 -2.010579732 0.0740049 VNFNDCS(ph)FDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VNFNDCSFDLK 11 0 A0A087WVX1;P0C875 A0A087WVX1 FAM228B Protein FAM228B 1 VNFNDCS(1)FDLK 69.01 0.03586 51172000 32875 64988 34630 13197 40539 51974 66331 41647 18900 TRUE FALSE 28530.48546 64561.08955 51377.18383 16193.58055 39732.35321 53973.47341 59898.22983 32741.11315 16665.66353 1.711932165 3.873898536 3.082816579 0.971673316 2.384084686 3.23860333 3.594110113 1.964585034 1 14.02459114 VNFPENGFLS(ph)PDKLSLLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VNFPENGFLSPDKLSLLEK 19 1 P31689 P31689 DNAJA1 DnaJ homolog subfamily A member 1 1 VNFPENGFLS(1)PDKLSLLEK 78.202 0.006342 230650000 97689 89690 76297 76215 97280 71089 131780 156210 118420 TRUE FALSE 84779.15114 89100.82048 113194.4844 93520.78062 95344.31833 73823.83983 118999.9959 122805.7071 104420.5225 0.811901235 0.853288399 1.084025263 0.895616861 0.913080265 0.706985926 1.139622682 1.17606869 1 16.67204576 2.208491473 24.99984485 1.121421631 0.88821381 0.513294902 0.103796312 159.9751383 133004.1379 0.042714306 0.028802186 161.6186494 -2.208491473 -0.233207821 VNFSEEGET(ph)EEDDQDSSHSSVTTVK ddPTM_MDA-MB-175_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 251.44 7.40E-40 524710000 248020 262770 58575 259280 423830 314610 235140 487190 430190 TRUE FALSE 215243.5286 261043.8466 86902.06592 318153.4868 415396.6122 326713.2503 212336.159 383008.2098 379333.4283 0.56742568 0.688164625 0.229091505 0.838717242 1.095069881 0.861282518 0.559761263 1.009687471 1 18.53310699 3.565255905 8.647298406 0.897004823 0.51547715 0.523345664 0.180161946 0.294833735 26.72350468 0.049676302 0.073697673 3674.987829 -3.565255905 -0.381527674 VNFTVDQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VNFTVDQIR 9 0 P13639 P13639 EEF2 Elongation factor 2 0 ; 145.72 0.00022448 954680000 1020280 1362970 887100 960410 1399620 1363980 1295620 1451280 1443540 FALSE TRUE 885447.4129 1354016.56 1316104.527 1178485.769 1371770.3 1416453.193 1169970.972 1140935.066 1272886.346 0.695621739 1.063737202 1.033952899 0.925837388 1.077684826 1.112788426 0.919148026 0.896336951 1 20.27967218 4.746704198 24.66991646 0.99557141 0.695621559 0.639915923 0.072397531 635.024572 1923671.268 0.019438925 0.209493863 55808.9945 -4.746704198 -0.299949851 VNGDAS(ph)PAAAESGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VNGDASPAAAESGAK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 VNGDAS(1)PAAAESGAK;VNGDAS(1)PAAAESGAK;VNGDAS(1)PAAAESGAK;VNGDAS(1)PAAAESGAK;VNGDAS(1)PAAAESGAK 301.56 2.53E-44 2290460000 5243170 4246840 3106512 3999220 4487020 3069459 4876540 6824980 5711560 TRUE FALSE 4550271.8 4218942.228 4608831.594 4907304.025 4397737.081 3187543.074 4403613.901 5365511.139 5036345.883 0.903486755 0.837699063 0.915114192 0.97437788 0.873199971 0.632907895 0.874366853 1.065357953 1 22.26394594 1.781154375 6.714182915 1.031865977 0.855890358 0.393456021 0.08979773 0.193774547 20.68252927 0.051325126 0.024962436 60.41633487 -1.781154375 -0.175975619 VNGDDHHEEDMDMS(ph)D ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 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 320.99 5.12E-56 9253510000 6394524 5105055 3361069 3935205 4970779 4683367 5154918 5643707 5244256 TRUE FALSE 5549471.452 5071519.558 4986493.211 4828753.441 4871870.223 4863539.159 4654994.846 4436844.177 4624286.03 1.200070977 1.096714071 1.078327158 1.044215996 1.053539982 1.051738393 1.006640769 0.959465775 1 22.14079921 8 0.259866628 0.96316694 2.445787535 0.878463728 0.022637151 28.72888699 0.458781133 0.072975778 18.36876929 100000000 -8 1.482620595 VNGEDPYPHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VNGEDPYPHK 10 0 Q15046;Q15046-2;H3BVA8 Q15046 KARS Lysine--tRNA ligase 0 91.855 0.009865 318440000 726250 553010 422180 560870 610540 507990 670950 838910 812000 FALSE TRUE 630274.2224 549377.2409 626347.6601 688224.1059 598391.4485 527532.704 605881.3723 659515.6249 716006.285 0.880263533 0.767279914 0.874779556 0.961198414 0.83573491 0.736771052 0.846195606 0.921103123 1 19.44961273 1.497493976 2.593812667 0.999349759 0.841758934 0.420004241 0.061133998 0.314729275 3.892750638 0.091148556 0.017287586 31.44082809 -1.497493976 -0.157590825 VNGRPLEMIEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 VNGRPLEMIEPR 12 1 P62249;M0R3H0;M0R1M5;Q6IPX4 P62249 RPS16 40S ribosomal protein S16 0 ;;;;;;;; 141.58 5.53E-05 7634940000 7659940 7609470 4165540 5509380 8027700 7520140 7537810 8205710 6338340 FALSE TRUE 6647659.521 7559482.891 6180009.077 6760368.935 7867964.476 7809444.652 6806794.346 6450982.773 5589028.666 1.189412314 1.352557545 1.105739377 1.209578504 1.407751677 1.397281195 1.21788503 1.154222524 1 22.41416614 1.432455657 1.911053553 0.971626367 1.27515551 0.461294627 0.094991923 0.510610823 2.659596701 0.251840205 0.027781906 27.06796813 -1.432455657 0.303529143 VNGTSS(ph)PQSPLSTSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VNGTSSPQSPLSTSGR 16 0 Q96KQ4;A0A3B3ISJ2 Q96KQ4 PPP1R13B Apoptosis-stimulating of p53 protein 1 1 VNGT(0.004)S(0.044)S(0.945)PQS(0.007)PLSTSGR;VNGTS(0.001)S(0.999)PQSPLSTSGR 278.88 2.28E-35 731330000 852590 844870 492010 517950 701490 706450 659900 784210 761050 TRUE FALSE 739918.0713 839319.9933 729947.6817 635558.4639 687531.7214 733627.5886 595902.9996 616512.7942 671079.536 1.102578803 1.250701218 1.087721563 0.94706876 1.024515999 1.093205126 0.887976712 0.918688115 1 19.35612424 3.950913655 4.014868674 0.974221094 1.177152389 0.605189001 0.066718436 0.142123914 4.76158811 0.018727754 0.036353541 8931.278977 -3.950913655 0.202931295 VNHLYSDLSDALVIFQLYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VNHLYSDLSDALVIFQLYEK 20 0 P13796 P13796 LCP1 Plastin-2 0 ; 145.75 1.41E-07 838530000 826610 781350 493440 729900 673640 627640 824410 919290 1188170 FALSE TRUE 717371.3941 776217.2604 732069.2345 895634.9508 660235.882 651785.7169 744458.8451 722706.9874 1047705.896 0.684706841 0.740873239 0.698735434 0.854853403 0.630172918 0.62210752 0.710560901 0.689799485 1 19.99880236 1.236835237 24.9928092 1.000000369 0.704459745 0.678431166 0.064048347 26.99184011 390868.4713 0.09749986 0.015675339 17.25183268 -1.236835237 -0.295540625 VNHPGSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VNHPGSK 7 0 P80303-2;P80303;E9PKG6;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 ; 89.142 0.01809 325090000 874610 957460 488530 707520 555290 874170 927700 1142650 1112000 FALSE TRUE 759028.0725 951170.3822 724784.742 868173.2298 544240.8154 907799.8856 837731.7968 898303.1896 980540.6268 0.774091406 0.970046887 0.739168498 0.88540261 0.555041577 0.925815678 0.854357049 0.916130515 1 19.90321788 1.563971545 1.200376644 1.027323528 0.80458372 0.2524162 0.112826452 1.241303976 2.364507039 0.317463555 0.035533186 36.64135663 -1.563971545 -0.222739808 VNIAFNYDMPEDSDTYLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 VNIAFNYDMPEDSDTYLHR 19 0 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;H0Y400 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ;;;;;; 187.47 1.83E-14 5020370000 5186360 4460280 2622199 3439730 4670340 4863720 4180750 4897580 4718230 FALSE TRUE 4500969.385 4430980.127 3890303.207 4220773.269 4577409.371 5050830.456 3775301.508 3850270.63 4160446.224 1.08184775 1.065025213 0.93506874 1.014500138 1.100220775 1.214011715 0.907427065 0.925446556 1 21.98830684 VNIDFEPFKPINTSLYLCDNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VNIDFEPFKPINTSLYLCDNK 21 1 B7Z7P8;P62495-2;P62495;I3L492;D6RJE8 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 120.52 1.93E-05 0 133080 100270 107520 119850 91730 61200 115410 158480 216790 FALSE TRUE 115493.1408 99611.31977 159517.0316 147063.7743 89904.75247 63554.4036 104217.556 124590.2853 191161.3332 0.604165805 0.521085086 0.834462854 0.76931758 0.470308252 0.332464744 0.545181153 0.651754637 1 17.54443121 1.2394665 3.251424386 1.068783073 0.58385073 0.459884514 0.141144205 0.349690503 4.996709124 0.433103623 0.039824703 17.35667375 -1.2394665 -0.484932343 VNIEGGAIALGHPLGASGCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VNIEGGAIALGHPLGASGCR 20 0 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 104.06 0.00027626 616820000 167960 160570 75779 124510 162990 146570 115360 170450 177490 FALSE TRUE 145763.6604 159515.2051 112425.9779 152781.8985 159746.8179 152208.6427 104172.405 134000.5939 156507.3344 0.931353543 1.01921872 0.71834319 0.976196413 1.020698605 0.972533609 0.665607177 0.856193701 1 17.25587074 VNIGQGSHPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VNIGQGSHPQK 11 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 79.036 0.028246 119900000 380380 354290 208090 283000 271650 263040 342880 404750 478310 FALSE TRUE 330111.8192 351962.6457 308723.02 347259.4754 266244.6965 273159.319 309627.5504 318197.3623 421764.7367 0.782691843 0.834499936 0.731979213 0.823348766 0.63126353 0.647658031 0.734123845 0.754442784 1 18.68607895 1.236105327 4.926342465 1.017920279 0.739938078 0.607628464 0.065112469 0.132629151 7.956208094 0.127472862 0.017302722 17.22286221 -1.236105327 -0.277982201 VNIGQGSHPQKVKVFGPGVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VNIGQGSHPQKVKVFGPGVER 21 2 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 227.2 1.28E-25 1048800000 846460 766870 550790 430990 969390 756830 1038600 975970 620720 FALSE TRUE 734598.1663 761832.3805 817153.8863 528852.8668 950101.0356 785945.7398 937876.7319 767266.4105 547339.1887 1.342126019 1.39188349 1.492957024 0.966225108 1.735854211 1.435939096 1.713520156 1.401811576 1 19.06207563 3.216041885 24.9995151 1.468605987 1.318886335 0.094479246 0.239690614 623.7056696 692414.5709 0.071658723 0.08131126 1644.530319 -3.216041885 -0.149719652 VNIKPQVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VNIKPQVDR 9 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;;; 139.43 0.00010168 15777570000 20822390 19338730 13288660 16401820 20250400 17617070 22127600 24560000 23624500 FALSE TRUE 18070658.4 19211692.61 19715100.42 20126103.92 19847456.66 18294810.08 19981668.76 19308035.13 20831638.52 0.867462172 0.92223627 0.946401811 0.966131584 0.952755427 0.878222328 0.959198132 0.926861087 1 24.31227298 4.900475858 0.011547883 1.822926725 1.49E-07 0.252821583 0.034379757 14687.96205 43.87384938 3291.489765 3641.345968 79519.90608 -4.900475858 -1.822926576 VNILSDMHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VNILSDMHLR 10 0 B4DXZ6;P51114;P51114-3;C9JZE0;C9JY20;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 ; 145.91 2.96E-05 665610000 564030 706740 366640 516340 805360 872730 650690 735740 773180 FALSE TRUE 489492.0064 702097.3784 543948.3303 633582.8888 789334.9117 906304.4878 587586.184 578407.7265 681775.5412 0.717966511 1.029807225 0.797840781 0.929313022 1.15776361 1.329329718 0.861846969 0.84838439 1 19.37893732 3.470968955 24.89656286 1.019186915 0.866150367 0.23011839 0.157444092 293.2764113 1186797.364 0.049682911 0.064320724 2957.801023 -3.470968955 -0.153036548 VNIVDLQQVINVDLIHIENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VNIVDLQQVINVDLIHIENR 20 0 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 0 ; 160.77 2.36E-11 610515000 849803 811326 513453 651770 701583 651652 918190 1024985 747976 FALSE TRUE 737499.3804 805996.3461 761760.5882 799764.3402 687622.8709 676721.4741 829144.0751 805799.9342 659551.1294 1.118183788 1.222037701 1.154968211 1.212588842 1.042561888 1.026033379 1.257133887 1.221739905 1 19.33112498 5.078901007 19.443223 1.150812234 0.000732081 0 0.091453661 2525.091195 543850.0771 0.021974872 15915.10953 119922.5922 -5.078901007 -1.150080154 VNIVFNYDMPEDSDTYLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VNIVFNYDMPEDSDTYLHR 19 0 O00148 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ;;; 133.16 5.34E-07 1541770000 1271143 946078 589757 826040 1095411 1199043 960061 1187359 1153451 FALSE TRUE 1103158.232 939863.1513 874965.4578 1013605.007 1073614.464 1245170.96 866954.432 933451.5179 1017091.337 1.084620616 0.924069567 0.860262423 0.996572255 1.055573305 1.224246943 0.852386016 0.917765676 1 19.95601781 VNKDDIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VNKDDIQK 8 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ;;; 117.31 0.0019182 7735600000 20184600 16924900 12867100 16361900 15746400 13102400 25380100 29117300 25433900 FALSE TRUE 17517153.97 16813719.22 19089672.6 20077119.47 15433077.45 13606457.81 22918741.81 22890791.99 22427133.32 0.781069686 0.749704342 0.851186477 0.895215594 0.688143118 0.606696256 1.021920255 1.020674005 1 24.41874189 2.212935927 24.99869229 1.015869181 0.768195276 0.692679358 0.079113992 134.0536748 130777.7939 0.034556139 0.02330689 163.2811034 -2.212935927 -0.247673904 VNLEESSGVENS(ph)PAGARPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VNLEESSGVENSPAGARPK 19 1 Q8WVM8;Q8WVM8-2;Q8WVM8-3 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 1 VNLEES(0.005)S(0.004)GVENS(0.991)PAGARPK;VNLEESSGVENS(1)PAGARPK 293.89 7.69E-50 1224820000 566080 482100 343335 469740 525760 452260 520580 680000 622660 TRUE FALSE 491271.0937 478933.0534 509372.9544 576401.6465 515298.4046 469658.7349 470094.2317 534587.2918 549049.8441 0.894765929 0.872294307 0.927735359 1.049816611 0.938527549 0.855402729 0.856195911 0.973658945 1 19.0665776 0.87639274 0.00970384 1.90256003 2.50E-06 0.065997207 0.06181753 51281.92661 115.4008001 11860.95455 10786.10089 7.523029076 -0.87639274 -1.902557527 VNLEVIKPWITK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VNLEVIKPWITK 12 1 A9Z1X7;Q8IYB3-2;E9PCT1;M0R1E7;M0QXG5;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 0 76.728 0.027665 264390000 655160 613430 357340 471660 590280 492320 654410 750120 677350 FALSE TRUE 568578.946 609400.3379 530150.8192 578757.6119 578534.5829 511259.869 590945.4189 589712.6754 597274.4546 0.951955908 1.020302029 0.887616765 0.968997765 0.968624354 0.855988173 0.989403472 0.987339523 1 19.18803449 2.053811683 24.99999847 0.991449509 0.943807805 0.215772275 0.044879935 142.6877844 66289.56236 0.017869719 0.01204776 113.1909442 -2.053811683 -0.047641704 VNLFPGLS(ph)PSALK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VNLFPGLSPSALK 13 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 VNLFPGLS(0.997)PS(0.003)ALK;VNLFPGLS(0.972)PS(0.028)ALK 168.1 3.23E-05 644310000 4081500 3747500 2230140 2636200 3375200 2826200 3549000 4494000 3874100 TRUE FALSE 3542119.434 3722882.426 3308643.163 3234789.502 3308040.123 2934925.743 3204818.526 3532993.072 3416108.311 1.036887332 1.089802221 0.968541645 0.946922406 0.968365117 0.859143058 0.93814898 1.034215766 1 21.70392229 4.207129872 9.858661247 0.961107655 1.063301621 0.463053913 0.046534868 0.318550088 96.93782477 0.013212107 0.027930826 16111.27355 -4.207129872 0.102193965 VNLLHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VNLLHER 7 0 Q9BZQ8 Q9BZQ8 FAM129A Protein Niban 0 95.605 0.025214 0 99413 123900 71912 91488 135290 122430 107720 142150 127030 FALSE TRUE 86275.32017 123086.0927 106688.8837 112261.7487 132597.9937 127139.9613 97273.33098 111752.3287 112012.6581 0.770228308 1.098858779 0.952471672 1.002223772 1.183776869 1.135049944 0.868413737 0.997675893 1 16.77330225 4.749264317 24.41985727 1.024554518 0.770228107 0.444811508 0.090971336 1174.160569 2678705.201 0.023160281 0.322067788 56138.95412 -4.749264317 -0.254326411 VNLS(ph)PNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VNLSPNR 7 0 P35568 P35568 IRS1 Insulin receptor substrate 1 1 VNLS(1)PNR 61.56 0.095191 286090000 344820 444540 266640 321010 424460 450150 411900 449450 485830 TRUE FALSE 299251.1633 441619.7875 395587.9959 393900.2268 416014.0764 467467.5618 371954.0014 353338.6151 428395.7309 0.698539088 1.030868787 0.923417222 0.919477479 0.971097624 1.091204996 0.868248618 0.824794903 1 18.70858458 6.139185876 12.76397017 0.924542944 0.583463945 0 0.111138513 0 0 0.024111119 0 1377799.036 -6.139185876 -0.341078999 VNLS(ph)PNRNQSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VNLSPNRNQSAK 12 1 P35568 P35568 IRS1 Insulin receptor substrate 1 1 VNLS(1)PNRNQSAK;VNLS(1)PNRNQSAK 81.526 0.010543 335930000 379080 309700 145930 209677 275270 254170 370380 442540 232572 TRUE FALSE 328983.6175 307665.5603 216502.2361 257287.3676 269792.6656 263948.0844 334460.6046 347906.2649 205077.6031 1.604190865 1.500239693 1.055708828 1.254585404 1.315563774 1.287064411 1.630897765 1.696461533 1 17.64581042 2.257722175 24.89520897 1.503223422 1.326279819 0.021564622 0.234372354 519.2267112 674591.7346 0.088765873 0.068647169 181.0181722 -2.257722175 -0.176943604 VNMEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VNMEDLR 7 0 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;H0Y961;B1AMS2;Q14141-2;Q14141-4;Q14141;A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599;Q92599-3 D6RGI3;B1AMS2;A0A087X142 SEPT11;SEPT6;SEPT8 Septin-11;Septin-6;Septin-8 0 ;;;;; 108.7 0.016738 1562360000 4236110 4124430 2743130 3415160 4212120 4293420 4185720 4631420 4558910 FALSE TRUE 3676297.331 4097336.348 4069716.843 4190624.275 4128307.053 4458590.646 3779789.519 3641026.875 4019960.853 0.914510729 1.019247823 1.012377232 1.042454001 1.026952053 1.109112951 0.940255305 0.905736898 1 21.93875002 2.075074034 24.99996745 0.939190086 1.021849013 0.292417344 0.052175506 39.71288209 13223.1629 0.021031075 0.014179146 118.8704848 -2.075074034 0.082658928 VNNVVWDLDRPLEEDCTLELLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VNNVVWDLDRPLEEDCTLELLK 22 1 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 174.7 2.12E-12 97168000 121270 84393 62349 73703 75632 56617 83635 108310 133460 FALSE TRUE 105243.8622 83838.61683 92501.18494 90438.39263 74127.07117 58795.09263 75524.09057 85148.74937 117682.5108 0.894303338 0.712413563 0.78602321 0.768494758 0.629890292 0.499607734 0.64176138 0.723546335 1 16.84454041 7.999984887 0.905451467 0.70098483 97.57408074 0.142984563 0.129065141 1882.196539 4.034144196 0.043780436 376871.1472 99996520.07 -7.999984887 96.87309591 VNPALAELNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VNPALAELNLR 11 0 P13489;E9PMJ3;E9PLZ3;E9PIM9;E9PMN0;E9PIK5;E9PMA9 P13489 RNH1 Ribonuclease inhibitor 0 110.38 0.0024358 0 54882 47724 31694 44838 54237 63559 54899 57241 51720 FALSE TRUE 47629.20465 47410.4979 47021.32441 55019.15321 53157.78981 66004.15586 49574.90343 45000.4576 45605.72052 1.044369086 1.039573487 1.031040051 1.206409033 1.165594781 1.447277997 1.087032567 0.986728355 1 15.47692718 3.76189005 23.67804763 1.141223781 1.038452096 0.142111204 0.127084023 1009.900125 1024984.586 0.037810701 0.065425806 5779.497098 -3.76189005 -0.102771685 VNPCIGGVILFHETLYQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VNPCIGGVILFHETLYQK 18 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;; 256.96 1.31E-30 10097112000 7757451 7039622 3876033 6098137 6206180.5 5442781 8072946 9291254 8272502 FALSE TRUE 6732284.195 6993378.26 5750495.523 7482812.21 6082689.65 5652168.307 7290032.939 7304391.637 7294536.238 0.922921482 0.958714582 0.788329146 1.025810547 0.833869276 0.774849575 0.999382648 1.001351066 1 22.79838483 2.077919786 24.97341971 1.000650782 0.887267402 0.346216963 0.075165696 36.07290149 11559.5396 0.029996193 0.020223428 119.6519514 -2.077919786 -0.11338338 VNPFRPGDSEPPPAPGAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VNPFRPGDSEPPPAPGAQR 19 1 Q15942;H0Y2Y8;C9IZ41 Q15942 ZYX Zyxin 0 ; 157.98 4.98E-10 1302990000 688670 734980 417810 497190 640790 696360 656450 802000 652880 FALSE TRUE 597660.5146 730151.868 619864.3135 610084.5886 628039.5327 723149.4198 592787.58 630498.5412 575697.2702 1.038150684 1.26829135 1.076719216 1.059731599 1.090919768 1.256127929 1.029686279 1.095191125 1 19.13495085 1.244735099 1.240877524 0.950537415 1.126295675 0.169911438 0.082453674 2.639442417 3.493630538 0.608950632 0.024635163 17.56851684 -1.244735099 0.17575826 VNPHKVS(ph)PASSVDSNIPSSQGYKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VNPHKVSPASSVDSNIPSSQGYKK 24 2 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 VNPHKVS(0.999)PASS(0.001)VDSNIPSSQGYKK 148.22 8.60E-08 231120000 148190 103760 65201 68427 96864 63660 132340 178260 37452 TRUE FALSE 128606.316 103078.3937 96732.42168 83964.39619 94936.59591 66109.04139 119505.6872 140140.4862 33024.46723 3.894273756 3.12127348 2.92911377 2.542490561 2.874735125 2.001820073 3.618701442 4.243535112 1 15.01124767 4.740489891 2.389873707 2.897068817 4.131498765 0.131846906 0.873141344 1.391152146 9.607456678 0.229149293 3.563456524 55016.11146 -4.740489891 1.234429948 VNPSQTHNNLYAWGQETGAPILTDDVSLQVFMDHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VNPSQTHNNLYAWGQETGAPILTDDVSLQVFMDHLK 36 0 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 256.71 3.01E-62 106470000 46924 53404 32667 51868 52783 52833 73521 76412 94712 FALSE TRUE 40722.87451 53053.18561 48464.87046 63645.42215 51732.72157 54865.5197 66390.94474 60071.88844 83515.25526 0.487610011 0.635251433 0.580311589 0.762081394 0.619440381 0.656952069 0.794955898 0.719292401 1 16.34975213 -2 0.419390207 7.150437162 0.593710236 0.703656518 0.075908723 50.69249138 0.69964346 276.6179089 0.066590982 0.01 2 -6.556726926 VNPTVFFDIAVDGEPLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VNPTVFFDIAVDGEPLGR 18 0 P62937;F8WE65;C9J5S7;E5RIZ5 P62937 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ;;; 189.1 8.02E-14 1889383000 800875 645066 422596 530142.8 612957 570026 600216 731727 850391 FALSE TRUE 695037.3396 640828.519 626964.8391 650519.8255 600760.3549 591955.2691 542007.1447 575252.8754 749858.7447 0.926891024 0.854598981 0.836110592 0.867523157 0.801164698 0.789422372 0.722812328 0.767148319 1 19.51625933 3.238879351 22.45062067 0.801657748 0.867577195 0.098971952 0.075699561 4.643518557 326937.4848 0.022466121 0.027216199 1733.322407 -3.238879351 0.065919447 VNQSALEAVTPS(ph)PSFQQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 VNQSALEAVTPSPSFQQR 18 0 Q9UKG1 Q9UKG1 APPL1 DCC-interacting protein 13-alpha 1 VNQSALEAVTPS(1)PSFQQR;VNQSALEAVTPS(1)PSFQQR;VNQSALEAVTPS(1)PSFQQR;VNQSALEAVT(0.028)PS(0.805)PS(0.167)FQQR;VNQSALEAVTPS(1)PSFQQR;VNQSALEAVT(0.136)PS(0.676)PS(0.188)FQQR;VNQSALEAVTPS(0.999)PS(0.001)FQQR;VNQSALEAVT(0.003)PS(0.993)PS(0.004)FQQR;VNQSALEAVT(0.008)PS(0.981)PS(0.011)FQQR 462.41 3.20E-214 11482047000 4729473 4609785 2693015 3057518 4263180 4270916 4548708 4715030 4475059 TRUE FALSE 4104461.16 4579503.019 3995366.062 3751774.193 4178351.059 4435220.902 4107574.998 3706757.527 3946022.623 1.040151452 1.160536433 1.012504601 0.950773615 1.05887661 1.123972497 1.04094056 0.939365503 1 21.9119678 1.854710476 5.866787864 0.968779089 1.057505425 0.274547786 0.058365888 0.290566653 12.57670033 0.031118463 0.016255332 71.56661501 -1.854710476 0.088726336 VNS(ph)GDTEVGSSLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VNSGDTEVGSSLLR 14 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 VNS(0.998)GDT(0.002)EVGSSLLR;VNS(0.999)GDT(0.001)EVGSSLLR;VNS(0.983)GDT(0.017)EVGSSLLR;VNS(0.998)GDT(0.002)EVGSSLLR 263.59 1.32E-24 532260000 594297 523704 589669 605463 847800 754606 829703 897948 1099880 TRUE FALSE 515759.1457 520263.7539 874834.9007 742942.6281 830930.4387 783636.1811 749238.5308 705928.808 969853.4394 0.53179081 0.536435437 0.902027941 0.766035978 0.856758769 0.807994434 0.77252758 0.727871634 1 19.88740722 4.24944324 24.99990293 0.818175307 0.534112918 0.715806707 0.07792561 111.7174085 256635.6703 0.018823668 0.048757067 17760.01139 -4.24944324 -0.284062388 VNS(ph)KEDTEAQGIFIDLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VNSKEDTEAQGIFIDLSK 18 1 Q9H2U2-2;A0A0C4DGB9 Q9H2U2-2;A0A0C4DGB9 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 1 VNS(0.5)KEDT(0.5)EAQGIFIDLSK 48.053 0.084107 183810000 249510 237370 74744 96557 251500 315770 174130 195860 29922 TRUE FALSE 216536.6213 235810.7008 110890.4484 118481.7426 246495.6421 327917.8762 157242.8994 153976.8632 26384.65525 8.206914939 8.937418307 4.202838633 4.49055489 9.342386313 12.42835554 5.959634414 5.835848971 1 14.68741151 4.282798395 24.98963846 6.413182043 8.572172965 0.092647598 3.045088252 392.5283016 221730.4902 0.799382618 2.114943868 19177.78279 -4.282798395 2.158990922 VNSNS(ph)LDLPSSSDTTHASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.017)NS(0.983)LDLPSSSDTTHASK;VNS(0.01)NS(0.99)LDLPSSSDTTHASK 240.8 1.58E-24 763740000 575500 507620 109811 407580 585370 354180 808640 694530 948870 TRUE FALSE 499446.2169 504285.4108 162915.9669 500127.2685 573722.2823 367805.5338 730218.2173 546010.1643 836695.6696 0.596926977 0.602710674 0.194713529 0.597740955 0.685700074 0.439592969 0.872740524 0.652579169 1 19.67434344 -2 0.41585194 9.152138459 0.484181379 0.460973948 0.160097899 78.63982716 1.093469033 560.9179564 0.143372054 0.01 2 -8.66795708 VNTLIRPDGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VNTLIRPDGEK 11 1 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3;K7EMA7 P62750 RPL23A 60S ribosomal protein L23a 0 ; 117.27 0.00080021 828370000 815570 704400 524780 647520 781860 694270 929120 997200 1553680 FALSE TRUE 707790.3581 699772.75 778565.3633 794549.3127 766302.5157 720979.0162 839014.0854 783956.5402 1370005.72 0.516633141 0.510780896 0.568293513 0.57996058 0.559342566 0.526259858 0.612416483 0.572228662 1 20.38575049 1.229878751 4.753004062 1.036275003 0.555703755 0.953500776 0.030840899 0.040934334 2.115769626 0.066474615 0.008163094 16.97769594 -1.229878751 -0.480571248 VNTLIRPDGEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VNTLIRPDGEKK 12 2 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3;K7EMA7 P62750 RPL23A 60S ribosomal protein L23a 0 108.59 0.00094994 1136300000 759650 613080 476140 519920 540100 455830 878090 962650 628550 FALSE TRUE 659260.3278 609052.6371 706402.8966 637975.7825 529353.0667 473366.0751 792932.967 756794.7889 554243.535 1.189477704 1.098889926 1.274535203 1.151074829 0.955091098 0.854075952 1.430658035 1.36545533 1 19.08016051 0.954748884 16.88884106 2.24E-05 1.172091222 0.081139996 0.172905375 5666786.865 57384710.89 214386584.5 0.046468467 9.010499858 -0.954748884 1.172068803 VNVEHMTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VNVEHMTEK 9 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ;; 146.11 9.56E-05 1033158000 2183870 2058180 1024376 1656220 2120740 1793840 2347220 2828440 2544160 FALSE TRUE 1895266.046 2044659.68 1519767.66 2032290.065 2078541.423 1862850.186 2119586.966 2223600.117 2243392.303 0.844821498 0.911414235 0.677441773 0.905900436 0.926517141 0.830372014 0.944813336 0.991177563 1 21.0972505 1.923471863 0.717278809 1.050144022 0.832246399 0.438718436 0.06979374 1.281480184 0.953889535 0.205234168 0.03731758 83.84397571 -1.923471863 -0.217897623 VNVPVIGGHAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VNVPVIGGHAGK 12 0 P40926;G3XAL0;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 ; 117.79 0.00069532 1706770000 2381200 1949730 1731430 2486300 2262600 2146720 2170400 2881300 2553200 FALSE TRUE 2066518.387 1936922.095 2568755.339 3050852.416 2217578.687 2229305.708 1959914.942 2265156.417 2251363.605 0.917896329 0.860332863 1.140977554 1.355113145 0.984993576 0.990202428 0.870545716 1.006126426 1 21.10236765 3.027049334 24.99900439 0.966497194 1.072773478 0.115307152 0.13578863 512.1430107 473319.1771 0.044452616 0.050403523 1064.263906 -3.027049334 0.106276285 VNVTVDYIRPAS(ph)PATETVPAFSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VNVTVDYIRPASPATETVPAFSER 24 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 1 VNVTVDYIRPAS(0.996)PAT(0.004)ETVPAFSER;VNVTVDYIRPAS(0.999)PAT(0.001)ETVPAFSER;VNVTVDYIRPAS(0.987)PAT(0.012)ET(0.002)VPAFSER;VNVTVDYIRPAS(0.911)PAT(0.088)ET(0.001)VPAFSER 301.1 1.99E-62 3210020000 1971885 1721502 1288291 1495611 1861871 1833094 1887211 2057353 2412501 TRUE FALSE 1711295.401 1710193.34 1911312.837 1835212.337 1824823.41 1903614.312 1704189.568 1617404.071 2127297.88 0.804445591 0.803927535 0.89846977 0.862696453 0.857812828 0.894850848 0.801105282 0.760309163 1 21.02059063 4.283856114 23.80065054 0.855125855 0.804186144 0.124360258 0.063612005 199.9773809 105073.5077 0.016117955 0.042643642 19224.54695 -4.283856114 -0.050939712 VNYEEFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VNYEEFAR 8 0 Q9NZT1 Q9NZT1 CALML5 Calmodulin-like protein 5 0 ;;;; 209.84 0.00010224 4356350000 3643143 2776618 1796126 2267706 2796855 2724394 2462698 3138379 3284173 FALSE TRUE 3161692.422 2758378.214 2664738.541 2782623.307 2741203.057 2829203.2 2223865.927 2467261.074 2895921.809 1.091774098 0.952504382 0.920169368 0.960876533 0.946573574 0.976961184 0.767930239 0.851977794 1 21.46559122 8 0.490636091 0.888373691 6.402880842 0.375304232 0.067877147 121.2893531 1.364732727 0.045857543 684.2548834 100000000 -8 5.514507151 VPAFLSAAEVEEHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VPAFLSAAEVEEHLR 15 0 Q14894;I3NI53;I3L2W5;I3L3J9 Q14894 CRYM Ketimine reductase mu-crystallin 0 ;;; 180.11 4.44E-09 682740000 840162 891197 531398 615963 843368 784352 939791 1029783 832851 FALSE TRUE 729132.463 885342.6682 788383.8502 755826.8136 826586.6268 814526.529 848650.2135 809571.9192 734392.3036 0.992837833 1.20554459 1.073518672 1.02918673 1.125538248 1.109116374 1.155581573 1.102369831 1 19.48619141 VPAHPDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VPAHPDSR 8 0 O76071 O76071 CIAO1 Probable cytosolic iron-sulfur protein assembly protein CIAO1 0 ; 66.621 0.061208 515070000 505820 450480 295910 354110 369640 476050 486730 530650 562130 FALSE TRUE 438974.6054 447520.7672 439013.0658 434516.0877 362284.8872 494363.9515 439526.9995 417174.627 495675.6318 0.885608606 0.902850047 0.885686198 0.876613777 0.730891059 0.997353753 0.886723033 0.841628275 1 18.91903681 2.686579117 24.99999555 0.913204313 0.861671094 0.21406525 0.067174065 762.5325513 366731.3073 0.023342457 0.020586116 485.936048 -2.686579117 -0.051533219 VPAKLS(ph)PMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPAKLSPMK 9 1 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 VPAKLS(1)PMK 67.456 0.036849 660760000 1285100 1326000 1078600 1080700 1351200 1024600 1755100 1890700 1484700 TRUE FALSE 1115270.779 1317289.419 1600214.568 1326089.452 1324313.764 1064017.025 1584890.672 1486388.518 1309180.457 0.851884683 1.006193922 1.222302517 1.01291571 1.011559374 0.812735188 1.210597564 1.13535801 1 20.32023254 4.668578319 3.971270691 1.06352923 0.845225367 0.227148898 0.117843974 0.32076403 8.841930443 0.029834552 0.16875961 46620.64946 -4.668578319 -0.218303863 VPAS(ph)PLPGLER ddPTM_MDA-MB-175_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 142.76 3.93E-05 10748740000 3014060 2577390 1844236 2029115 2673610 3066640 2291080 2699400 2456010 TRUE FALSE 2615744.334 2560458.955 2736114.698 2489856.574 2620410.392 3184615.625 2068891.414 2122154.317 2165663.296 1.207825953 1.182297802 1.263407245 1.149696991 1.209980516 1.470503578 0.955315362 0.979909629 1 21.04637753 2.200322712 24.99988205 0.977758544 1.23893283 0.678850493 0.087052717 92.94751335 60768.31213 0.034940062 0.023557066 158.607132 -2.200322712 0.261174286 VPCNTVFGSQHQMDVAFLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPCNTVFGSQHQMDVAFLEK 20 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q86XE2;J3KNK7;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 178.07 6.32E-17 575340000 447670 277160 138510 212230 350530 241060 278320 391410 337830 FALSE TRUE 388509.2752 275339.3177 205493.8993 260420.0652 343555.1388 250333.7342 251328.5692 307710.0175 297892.1223 1.304194526 0.924292041 0.689826564 0.874209305 1.15328709 0.8403503 0.843689881 1.032957888 1 18.18443045 4.738177393 9.106610858 0.921193471 1.305771737 0.482480688 0.125100868 0.073002334 131.0861437 0.031448546 0.176448246 54723.94442 -4.738177393 0.384578265 VPCNVEGIS(ph)PELEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VPCNVEGISPELEK 14 0 Q86VQ1;H7C2L5;H7C0B2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 VPCNVEGIS(1)PELEK;VPCNVEGIS(1)PELEK 106.6 0.00097811 493410000 675970 653350 473260 550220 652040 562010 691880 811590 790550 TRUE FALSE 586638.8518 649058.1008 702130.119 675155.8606 639065.6797 583630.8884 624781.5841 638037.7943 697092.0796 0.841551452 0.931093782 1.007227222 0.96853182 0.916759347 0.837236436 0.896268373 0.915284814 1 19.41098971 3.018488137 23.08723557 0.907387738 0.941801596 0.037211324 0.056611744 291.2996542 363756.7775 0.017799125 0.020176848 1043.489629 -3.018488137 0.034413858 VPDEEENEES(ph)DNEKETEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VPDEEENEESDNEKETEK 18 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 VPDEEENEES(1)DNEKETEK;VPDEEENEES(1)DNEKETEK;VPDEEENEES(1)DNEKETEK;VPDEEENEES(0.999)DNEKET(0.001)EK;VPDEEENEES(1)DNEKETEK 226.56 2.09E-19 1668700000 1432460 918460 1391590 1556910 995510 677666 1383700 1636960 2468330 TRUE FALSE 1243156.782 912426.5758 2064567.579 1910430.211 975701.2987 703736.2495 1249508.987 1286908.843 2176526.839 0.571165381 0.419212187 0.948560588 0.877742547 0.448283605 0.32332992 0.574083886 0.59126716 1 21.05359638 1.238277927 24.99836789 1.000000452 0.594565325 0.305853573 0.19212138 9.468106087 835779.1132 0.282259992 0.049822812 17.3092371 -1.238277927 -0.405435127 VPDGKPENEFAFNAEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VPDGKPENEFAFNAEFK 17 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 198.42 1.30E-11 860490000 1049920 811370 786480 854880 721590 506630 1046940 1295150 1661180 FALSE TRUE 911170.4118 806040.057 1166824.359 1048993.57 707231.7708 526120.3839 945407.9199 1018192.251 1464797.193 0.622045438 0.550274168 0.796577413 0.716135705 0.482818901 0.359176264 0.645418987 0.695108003 1 20.4822695 1.205028276 2.052575133 1.151186996 0.594069219 0.529641663 0.119585631 0.722711151 2.783252936 0.790501685 0.035060701 16.03349777 -1.205028276 -0.557117778 VPDHHPC ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VPDHHPC 7 0 P78371;P78371-2 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 106.76 0.0076295 216321000 613530 665820 400970 444540 506050 557790 553290 633480 777450 FALSE TRUE 532450.456 661446.1846 594880.4332 545479.6014 495980.5951 579248.5422 499632.021 498015.2317 685540.7467 0.776686811 0.964853202 0.867753574 0.795692457 0.723488133 0.844951296 0.728814477 0.726456063 1 19.38688289 3.752822644 4.939804606 0.788670819 0.880530418 0.086854364 0.092794533 0.330644136 24.0993179 0.024293761 0.040730743 5660.08097 -3.752822644 0.091859599 VPDNYGDEIAIELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPDNYGDEIAIELR 14 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 103.23 0.0026238 56122000 64153 78681 66009 44521 68837 127470 38619 51888 44786 FALSE TRUE 55675.01851 78164.13933 97931.17319 54630.17351 67467.27838 132373.8534 34873.73532 40792.15499 39491.4501 1.409799295 1.979267389 2.479806969 1.383341796 1.708402153 3.351962337 0.883070519 1.032936367 1 15.26925272 VPDS(ph)PENELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VPDSPENELK 10 0 A0A2R8Y549;Q8NI35-3;Q8NI35;A0A0X1KG69;A0A087WUZ6;Q8NI35-4;Q8NI35-2;A0A0U1RR46 A0A2R8Y549 INADL InaD-like protein 1 VPDS(1)PENELK;VPDS(1)PENELK 124.12 0.0030909 0 229975 206472 164742 208621 201932 226610 174808 275175 322750 TRUE FALSE 199583.2211 205115.6718 244411.7822 255991.5866 197913.9483 235327.8333 157855.1471 216330.9677 284594.8627 0.70128891 0.720728652 0.858806023 0.899494756 0.695423475 0.826887144 0.554666186 0.760136587 1 18.11855009 VPEALQIGS(ph)TCLFYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPEALQIGSTCLFYK 15 0 E9PFT6 E9PFT6 HBD 1 VPEALQIGS(0.5)T(0.5)CLFYK 57.679 0.07738 47473000 96955 110390 73311 79741 90001 132530 71740 85477 122200 TRUE FALSE 84142.1511 109664.8408 108764.4448 97847.41281 88210.15618 137628.5149 64782.66584 67198.40873 107753.6552 0.780875145 1.01773662 1.00938056 0.908065834 0.818627971 1.277251473 0.601210843 0.62362997 1 16.71737728 2.19941085 24.9999854 0.71118353 0.963165669 0.274926393 0.171300851 180.1114949 115013.1165 0.067234743 0.045330476 158.2744636 -2.19941085 0.251982139 VPEASSEPFDTSS(ph)PQAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VPEASSEPFDTSSPQAGR 18 0 H0Y6F5;Q9H4I2 H0Y6F5 ZHX3 Zinc fingers and homeoboxes protein 3 1 VPEASSEPFDTS(0.016)S(0.984)PQAGR;VPEASSEPFDTS(0.008)S(0.992)PQAGR 233.79 9.92E-24 1358250000 827540 776600 482400 567430 756530 770690 786930 827850 815460 TRUE FALSE 718178.4923 771498.4635 715690.2535 696273.6541 741476.5331 800338.943 710613.6497 650820.7198 719057.2478 0.998777906 1.072930515 0.995317488 0.968314632 1.031178721 1.113039254 0.988257405 0.905102788 1 19.45574711 1.999591188 24.99999558 0.946045135 1.029488067 0.325932054 0.04632163 14.26998304 872667.7788 0.019175049 0.012761278 99.90591188 -1.999591188 0.083442932 VPEEDLKR ddPTM_MDA-MB-175_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 4335210000 4245690 3621300 2554310 2561220 3187470 3164870 3682840 4034960 2411480 FALSE TRUE 3684611.309 3597511.442 3789582.86 3142784.147 3124045.583 3286624.597 3325678.744 3172115.204 2126397.582 1.7327951 1.691833866 1.782161009 1.477985196 1.469172844 1.545630331 1.563996673 1.491778975 1 21.01997994 0.85347717 1.468646841 4.18E-14 1.613208276 0.775542329 0.102473038 1.680729072 1.463677233 5.328311323 0.032319677 7.136366892 -0.85347717 1.613208276 VPEPCHPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VPEPCHPK 8 0 P35321;P22528 P35321 SPRR1A;SPRR1B Cornifin-A;Cornifin-B 0 ; 71.379 0.048894 450050000 407350 400620 287280 303850 355140 325610 421290 466460 465860 FALSE TRUE 353517.6654 397988.3008 426209.5689 372843.7866 348073.4088 338136.4274 380433.3606 366711.159 410786.5615 0.860587221 0.9688445 1.037545063 0.907633846 0.847333972 0.823143839 0.926109557 0.892704858 1 18.64802946 4.785546286 21.15035064 0.920204053 0.860585526 0.084373898 0.065134071 13988.9136 6295913.983 0.016917454 6.581519287 61030.40984 -4.785546286 -0.059618528 VPFLDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPFLDHR 7 0 P08243-2;P08243;P08243-3 P08243-2 ASNS Asparagine synthetase [glutamine-hydrolyzing] 0 135.35 0.0030858 273270000 200590 167800 97083 128400 160840 159140 151130 178090 155070 FALSE TRUE 174081.5233 166697.7108 144032.6635 157555.1825 157639.5987 165262.2188 136473.4359 140006.8394 136737.8013 1.273104596 1.219104807 1.053349273 1.15224306 1.152860418 1.208606671 0.998066625 1.023907348 1 17.06105261 -2 0.137194602 0.085586297 1.341901216 0.572388136 0.063988127 132.8612699 1.574459505 32.10925519 1.506411044 0.01 2 1.256314918 VPFS(ph)LLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VPFSLLR 7 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 VPFS(1)LLR;VPFS(1)LLR 86.67 0.02088 37971000 18743.4 25187 19240.9 18851.4 23263 26492 20093.5 21900 47431 TRUE FALSE 16266.4122 25021.54494 28545.8636 23131.8985 22800.11181 27511.16438 18144.83546 17216.85543 41823.76121 0.388927531 0.598261472 0.682527414 0.553080302 0.545147331 0.657787908 0.433840356 0.41165249 1 15.35203519 1.229122599 24.99994521 1.000000915 0.534959941 0.686802315 0.098914957 241.144592 638710.6033 0.321065624 0.025725937 16.9481617 -1.229122599 -0.465040974 VPFS(ph)PGPAPPPHMGELDQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VPFSPGPAPPPHMGELDQER 20 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 VPFS(1)PGPAPPPHMGELDQER;VPFS(1)PGPAPPPHMGELDQER;VPFS(1)PGPAPPPHMGELDQER 141.53 1.22E-07 430465000 125033 154690 107913 149434 186381 181835 175814 224018 210352 TRUE FALSE 108509.5723 153673.8312 160100.0877 183365.2737 182672.3827 188830.3101 158763.5853 176113.494 185484.4262 0.585006378 0.828499914 0.863145715 0.988575038 0.984839463 1.018038625 0.855940246 0.949478604 1 17.50093853 4.954701185 1.136180035 0.959301735 0.258302081 0.857491392 0.048569359 0.910763121 0.715762153 0.015081852 0.852552561 90095.10283 -4.954701185 -0.700999654 VPFSLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VPFSLLR 7 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ; 133.47 0.0076042 1041000000 774260 1198290 614590 576500 844130 867680 1062430 1098690 699330 FALSE TRUE 671939.5793 1190418.354 911807.7797 707403.1363 827333.4645 901060.2111 959395.7021 863743.6935 616656.0041 1.089650591 1.93044152 1.478632777 1.147160056 1.341645032 1.461203986 1.555803715 1.400689668 1 19.23410639 1.244182621 4.938098321 0.972916705 1.440352796 0.253220756 0.229543119 0.23505089 14.19966785 0.375451362 0.055756188 17.54618164 -1.244182621 0.467436091 VPGGGEQPAQPNGWQYHS(ph)PSRPGSTAFPSQDGETGGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VPGGGEQPAQPNGWQYHSPSRPGSTAFPSQDGETGGHR 38 1 A0A1B0GUN5;A0A5F9ZH45;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 VPGGGEQPAQPNGWQYHS(0.932)PS(0.064)RPGS(0.003)T(0.001)AFPSQDGETGGHR;VPGGGEQPAQPNGWQY(0.1)HS(0.784)PS(0.116)RPGSTAFPSQDGETGGHR;VPGGGEQPAQPNGWQY(0.045)HS(0.748)PS(0.201)RPGS(0.004)T(0.001)AFPSQDGETGGHR;VPGGGEQPAQPNGWQY(0.402)HS(0.475)PS(0.119)RPGS(0.002)T(0.002)AFPSQDGETGGHR 236.23 4.49E-50 2180330000 311327 266082 202788 289715 267776 332059 287791 315879 512752 TRUE FALSE 270184.3481 264334.0898 300856.9551 355499.2188 262447.7815 344833.5246 259881.0731 248330.734 452135.0427 0.597574447 0.584635264 0.665413929 0.786267786 0.580463261 0.762678165 0.574786399 0.549240184 1 18.78639421 1.230050095 24.99577765 1.000000682 0.636521141 0.668193571 0.080246223 205.2542387 602793.5497 0.227601219 0.020081205 16.98439551 -1.230050095 -0.363479541 VPGGGEQPAQPNGWQYHS(ph)PSRPGSTAFPSQDGETGGHRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VPGGGEQPAQPNGWQYHSPSRPGSTAFPSQDGETGGHRR 39 2 A0A1B0GUN5;A0A5F9ZH45;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 VPGGGEQPAQPNGWQY(0.053)HS(0.904)PS(0.042)RPGS(0.001)T(0.001)AFPSQDGETGGHRR;VPGGGEQPAQPNGWQYHS(0.826)PS(0.173)RPGSTAFPSQDGETGGHRR;VPGGGEQPAQPNGWQYHS(0.83)PS(0.17)RPGSTAFPSQDGETGGHRR;VPGGGEQPAQPNGWQY(0.002)HS(0.955)PS(0.039)RPGS(0.002)T(0.002)AFPSQDGETGGHRR 184.45 6.95E-24 3737750000 55172 41118.6 20914.5 31961.8 48048.9 50924 50433.9 61835 29474.3 TRUE FALSE 47880.88041 40848.48921 31028.82215 39219.2152 47092.8209 52883.07923 45542.82814 48612.06645 25989.88183 1.842289269 1.571707385 1.193880848 1.509018604 1.811967488 2.034756432 1.752329173 1.870422758 1 14.66566245 3.250885227 24.05310247 1.73738672 1.508305344 0.053366799 0.310927012 332.4241505 648763.4628 0.089618522 0.114750076 1781.907794 -3.250885227 -0.229081375 VPGGS(ph)PLGVSLVYSDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPGGSPLGVSLVYSDKK 17 1 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 VPGGS(0.997)PLGVS(0.002)LVYS(0.001)DKK 58.712 0.05648 279520000 332180 301340 211130 214030 240990 207850 335960 356400 301960 TRUE FALSE 288281.5714 299360.4777 313233.1742 262628.7827 236194.7705 215846.124 303378.6509 280186.6335 266262.6328 1.082696315 1.124305257 1.176406809 0.986352384 0.88707442 0.810651205 1.139396271 1.052294235 1 18.02249045 3.725466203 24.12030793 0.986035869 1.127453037 0.374977672 0.09010326 581.4973887 1071136.504 0.027507411 0.041098549 5314.546402 -3.725466203 0.141417167 VPGGS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VPGGSPR 7 0 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 VPGGS(1)PR;VPGGS(1)PR;VPGGS(1)PR 86.332 0.021141 4204100000 5218490 4564240 2447660 2897620 2755150 3484480 3384980 4127720 3775310 TRUE FALSE 4528853.325 4534257.207 3631356.563 3555568.908 2700327.905 3618530.2 3056705.161 3245039.2 3328997.153 1.360425713 1.362048989 1.090825974 1.068060063 0.811153564 1.086973054 0.918206 0.974779806 1 21.66665621 4.09859251 1.849402827 0.967098058 1.388594357 0.807267696 0.076624848 0.138767779 0.909974374 0.020186979 0.065641247 12548.52009 -4.09859251 0.421496299 VPHDPVALEEHFRDDDEGPVSNQGYMPYLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPHDPVALEEHFRDDDEGPVSNQGYMPYLNR 31 1 Q9UH65;E7EMB1;E9PJK8 Q9UH65 SWAP70 Switch-associated protein 70 0 75.661 0.0019889 234010000 135450 103100 56574 79928 91083 75772 95322 119490 70884 FALSE TRUE 117549.9393 102422.7293 83933.37563 98076.87402 89270.6265 78686.99787 86077.68711 93937.99337 62504.17427 1.880673422 1.638654226 1.342844324 1.569125185 1.428234635 1.258907886 1.377151016 1.502907517 1 15.93166492 8 0.487686483 1.322426582 17.66688302 0.601500515 0.147902558 80.90745442 0.918105728 0.09445579 1342.490289 100000000 -8 16.34445643 VPHNAAVQVYDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VPHNAAVQVYDYR 13 0 Q14764 Q14764 MVP Major vault protein 0 ; 155.08 4.65E-05 473070000 153545 133158 100970 108300 131498 163778 145083 163680 136306 FALSE TRUE 133253.6392 132283.2763 149799.4297 132891.1703 128881.4471 170078.6456 131012.873 128678.3058 120192.06 1.108672563 1.100599128 1.246333824 1.105656815 1.07229585 1.415057248 1.09002935 1.070605711 1 16.87498207 1.780322855 3.039308043 1.028521097 1.170510839 0.234757308 0.101802162 0.342678779 6.124235116 0.071285015 0.027466459 60.30076961 -1.780322855 0.141989742 VPISLSIDRLEFDLLYPAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPISLSIDRLEFDLLYPAIK 20 1 Q8TDL5 Q8TDL5 BPIFB1 BPI fold-containing family B member 1 0 54.857 0.09444 96992000 92460 104770 57113 68703 87803 76995 88199 122060 71077 FALSE TRUE 80241.17674 104081.759 84733.03783 84303.06621 86055.89208 79957.04747 79645.47456 95958.41887 62674.35803 1.280287174 1.66067531 1.351957012 1.345096605 1.373063798 1.275753753 1.270782455 1.531063451 1 15.93558769 4.027436959 24.98134312 1.325653162 1.479440097 0.147862851 0.159470659 387.1718608 352514.6772 0.03801729 0.079136428 10652.1423 -4.027436959 0.153786934 VPKPEPIPEPKEPS(ph)PEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPKPEPIPEPKEPSPEK 17 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 VPKPEPIPEPKEPS(1)PEK 85.945 0.0025627 305390000 131870 89510 88111 59395 99547 83640 141310 164110 42930 TRUE FALSE 114443.0454 88922.00292 130721.7743 72881.54255 97566.20946 86857.68492 127605.7779 129016.3536 37854.86431 3.023205801 2.349024479 3.453235845 1.925288702 2.577375755 2.294492043 3.370921552 3.408184284 1 15.20819108 4.788938288 20.54139542 2.655087746 3.023220918 0.020348367 0.761451694 20171.40909 8222700.878 0.180193341 84.16694251 61508.94644 -4.788938288 0.368133172 VPLAPITDPQQLQLS(ph)PLK ddPTM_MDA-MB-175_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 238.19 7.47E-24 3661138000 2169330 2299950 1530649 1923860 2353220 1924610 1983340 3047780 2592740 TRUE FALSE 1882647.544 2284841.477 2270875.976 2360701.817 2306395.526 1998650.992 1790995.992 2396035.965 2286229.231 0.823472782 0.999392994 0.993284464 1.032574418 1.008820767 0.874212859 0.783384259 1.048029626 1 21.12453863 4.430193435 0.003864784 1.897850699 5.41E-05 0.010535231 0.091525984 791799.2176 1039.982916 252110.6144 258597.3308 26927.33882 -4.430193435 -1.89779662 VPLAPITDPQQLQLS(ph)PLKGLSLVDKENTPPALSGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPLAPITDPQQLQLSPLKGLSLVDKENTPPALSGTR 36 2 P31350;P31350-2;A0A286YFD6 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 VPLAPITDPQQLQLS(1)PLKGLSLVDKENTPPALSGTR 207.16 1.10E-30 281060000 118100 117350 31078 30545 97423 93720 137230 194100 0 TRUE FALSE 102492.7858 116579.1201 46107.42475 37480.7091 95484.4729 97325.46904 123921.4557 152593.2255 0 0 VPLDLS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VPLDLSPR 8 0 R4GNG2;Q9UKV5 R4GNG2 AMFR E3 ubiquitin-protein ligase AMFR 1 VPLDLS(1)PR;VPLDLS(1)PR;VPLDLS(1)PR 79.489 0.029271 187292000 197415 276031 187225 291667 430897 383238 246237 490155 391291 TRUE FALSE 171326.1076 274217.7342 277767.6362 357894.4502 422322.9927 397981.4138 222356.9736 385339.1676 345033.0237 0.496549883 0.794757937 0.805046523 1.037275929 1.224007453 1.153458905 0.64445128 1.116818221 1 18.39637493 4.515541898 1.24943992 1.023102085 0.404094538 0.528349389 0.160236952 0.827163124 1.501321293 0.049240184 0.597859087 32774.93943 -4.515541898 -0.619007547 VPLS(ph)PLSLLAGPADAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VPLSPLSLLAGPADAR 16 0 Q53ET0;H0YDQ8;Q5T4K5 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 VPLS(1)PLSLLAGPADAR;VPLS(0.996)PLS(0.004)LLAGPADAR;VPLS(0.996)PLS(0.004)LLAGPADAR;VPLS(0.992)PLS(0.008)LLAGPADAR;VPLS(0.988)PLS(0.012)LLAGPADAR;VPLS(0.993)PLS(0.007)LLAGPADAR 170.11 5.65E-09 2027575000 230467.4 282087 241627 309818.6 365290.6 387793.8 311377.3 386509.3 502515 TRUE FALSE 200010.5492 280233.9519 358478.6254 380167.6484 358022.0317 402712.4784 281179.9774 303857.294 443108.2492 0.451380785 0.632427748 0.809009144 0.857956603 0.80797871 0.908835435 0.634562723 0.685740549 1 18.75729966 4.522768451 2.450058187 0.798682182 0.439720772 0.571399143 0.103862241 0.288799927 2.877018412 0.02820619 0.177355456 33324.86901 -4.522768451 -0.35896141 VPLVAEKPLKEPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VPLVAEKPLKEPK 13 2 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 142.85 2.28E-05 1071220000 3272400 2081400 2146070 2387580 1896740 1377170 3086100 3779400 4226400 FALSE TRUE 2839944.049 2067727.146 3183916.63 2929716.531 1858998.585 1430150.621 2786810.497 2971204.721 3726759.807 0.762041075 0.554832416 0.854339103 0.78612969 0.498824363 0.383751756 0.74778377 0.7972622 1 21.82949041 1.459350909 1.985192977 1.021921221 0.646115172 0.382779817 0.142858475 0.538722952 3.249824322 0.332832109 0.042027249 28.79724285 -1.459350909 -0.375806049 VPMDIPVFTGTHADLLIVVFHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPMDIPVFTGTHADLLIVVFHK 22 0 Q8IV36-2;Q8IV36;Q8IV36-3;X6R4D2 Q8IV36-2 HID1 Protein HID1 0 111.4 0.00018862 101570000 119560 143040 82811 105560 81517 67093 128990 126310 144110 FALSE TRUE 103759.8431 142100.3608 122858.6766 129529.0114 79894.97119 69674.11112 116480.5697 99299.58945 127073.48 0.816534206 1.118253477 0.966831762 1.019323713 0.628730489 0.548297813 0.916639488 0.781434407 1 16.95530345 3.259706358 24.98305441 0.775107463 0.989136843 0.327651536 0.145826549 280.5999052 331518.204 0.042428815 0.054719938 1818.47091 -3.259706358 0.21402938 VPPELLGGS(ph)PPWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VPPELLGGSPPWK 13 0 E7EVA0 E7EVA0 MAP4 Microtubule-associated protein 1 VPPELLGGS(1)PPWK;VPPELLGGS(1)PPWK 83.729 0.010563 366220000 1266150 984500 854920 1066240 1134870 1037150 1521160 1638140 1500270 TRUE FALSE 1098825.069 978032.7547 1268362.172 1308346.088 1112288.307 1077049.832 1373638.137 1287836.509 1322909.79 0.830612244 0.739304193 0.95876694 0.988991161 0.840789233 0.814152136 1.038346037 0.973487776 1 20.33528326 7.906951854 0.073699795 1.3083044 2.02E-09 0.354526197 0.078824782 589.5653478 4.240513347 16.33279391 84.88695581 80714554.58 -7.906951854 -1.308304398 VPPS(ph)PDDLPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VPPSPDDLPSR 11 0 A0A087X1N4;Q8IYJ3-2;Q8IYJ3 A0A087X1N4 SYTL1 Synaptotagmin-like protein 1 1 VPPS(1)PDDLPSR;VPPS(1)PDDLPSR;VPPS(1)PDDLPSR;VPPS(1)PDDLPSR;VPPS(1)PDDLPSR 158.02 0.00044103 925670000 735963 690896 474672 563573 646439 627772 621458 830493 717184 TRUE FALSE 638703.6249 686357.4587 704224.9669 691540.8633 633576.1286 651922.7951 561189.0988 652898.5349 632399.3245 1.00996886 1.085322884 1.113576406 1.093519295 1.001860856 1.030872061 0.88739674 1.032414978 1 19.2704763 3.16105881 4.73122855 0.988508764 1.078979243 0.441641164 0.047580068 0.19123695 7.82797673 0.014484937 0.016773066 1448.968053 -3.16105881 0.09047048 VPPVPDYVAHPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPPVPDYVAHPER 13 0 Q9Y5U2-2;Q9Y5U2;A6NCC9;E9PME3;C9JHT9;C9JJV1 Q9Y5U2-2 TSSC4 Protein TSSC4 0 64.394 0.078286 0 114580 128680 62838 112590 135450 141300 113210 132690 155480 FALSE TRUE 99437.96269 127834.6926 93226.66698 138155.2803 132754.81 146735.9024 102230.9116 104315.2761 137099.3315 0.725298669 0.932423894 0.679993593 1.007702071 0.96831114 1.070288971 0.745670387 0.760873703 1 17.06486201 4.750725722 23.42812626 0.882586776 0.725298432 0.140779414 0.128715187 1825.963758 3516366.908 0.032320716 0.49691074 56328.18033 -4.750725722 -0.157288344 VPS(ph)EGAYDIILPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VPSEGAYDIILPR 13 0 A8MXZ4;J9JIE0;A0A0C4DFY5;Q9NQ84;Q9NQ84-2 A8MXZ4 GPRC5C G-protein coupled receptor family C group 5 member C 1 VPS(1)EGAYDIILPR;VPS(0.999)EGAY(0.001)DIILPR;VPS(1)EGAYDIILPR 117.93 0.00049031 129336000 75386 74209 49006 75329 78952 79750 60107 87078 92982 TRUE FALSE 65423.5491 73721.51619 72705.46552 92433.60078 77381.00967 82818.03411 54277.83239 68457.04734 81989.77389 0.797947671 0.899155013 0.886762606 1.127379628 0.943788548 1.010101994 0.662007343 0.834946166 1 16.32315636 1.215821598 23.7810142 1.00000079 0.893715165 0.066306339 0.123398172 3412.721344 3568756.617 1.540038084 0.031908123 16.43696377 -1.215821598 -0.106285625 VPS(ph)GIFDVNSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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;VPS(1)GIFDVNSR 182.03 6.26E-06 655050000 260044 300699 223118 215534 333737 372199 327922 357576 347785 TRUE FALSE 225678.5265 298723.6885 331018.6111 264474.2889 327096.2866 386517.7364 296120.1749 281111.1551 306670.2535 0.735899631 0.974087591 1.07939589 0.862406073 1.066605851 1.260369181 0.965597972 0.916656089 1 18.22632871 4.72364562 3.774145953 1.014398186 0.711280679 0.408520079 0.106895353 0.265852779 7.353376529 0.027793772 0.219450974 52923.14196 -4.72364562 -0.303117508 VPS(ph)PDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPSPDHR 7 0 Q8NAV1;Q8NAV1-2 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 1 VPS(1)PDHR 61.78 0.0576 125710000 43426 35435 21098 25405 28836 36273 42335 42420 38894 TRUE FALSE 37687.14407 35202.22515 31301.06337 31173.59354 28262.22002 37668.44578 38229.35822 33348.81311 34295.99563 1.098878845 1.026423771 0.912673996 0.90895724 0.824067635 1.098333642 1.114688683 0.972382125 1 15.06575252 2.698141544 24.99772561 1.041200094 0.953392002 0.232432579 0.082969514 886.8494675 548483.0634 0.030625411 0.027009408 499.0471091 -2.698141544 -0.087808091 VPS(ph)PGMEEAGCSR ddPTM_MDA-MB-175_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 191.84 3.38E-06 2614630000 427825 268320 208572 193046 295695 264278 286743 289848 314817 TRUE FALSE 371286.8423 266557.3883 309438.1168 236880.0448 289811.248 274444.9457 258934.708 227866.2608 277599.6929 1.337490105 0.960222201 1.114691856 0.853315226 1.043989801 0.988635624 0.932762948 0.820844787 1 18.08264645 7.999999984 0.892349457 0.936228243 182.0339479 0.635644318 0.087364833 558.3840744 1.269103777 0.028315942 205841.3123 99999996.32 -7.999999984 181.0977196 VPS(ph)PGPPTLTSYSVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPSPGPPTLTSYSVLR 16 0 F8W1U0;F8W130;Q12815 F8W1U0 TROAP Tastin 1 VPS(1)PGPPTLTSYSVLR 82.725 0.0096436 95011000 93172 87044 70327 74679 89082 90790 124210 129490 106340 TRUE FALSE 80859.08413 86472.20223 104337.3724 91636.00835 87309.44249 94282.75005 112164.1333 101799.5712 93768.60634 0.862325754 0.922187133 1.112711135 0.977256802 0.931115923 1.005483111 1.196180019 1.085646627 1 16.51681737 2.460824046 24.01256739 1.097096481 0.96827721 0.373502282 0.078208505 163.9442363 241555.1494 0.029769343 0.023066957 288.9508961 -2.460824046 -0.128819271 VPS(ph)PPPTGDDGGGGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPSPPPTGDDGGGGGR 16 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 VPS(0.997)PPPT(0.003)GDDGGGGGR 90.444 0.0057154 226420000 51452 60985 43724 40636 59080 47651 53799 64251 103750 TRUE FALSE 44652.48784 60584.38552 64869.07265 49863.02488 57904.42359 49484.1648 48581.58126 50511.42365 91484.79319 0.488086449 0.662234492 0.709069457 0.545041675 0.632940422 0.540900439 0.531034498 0.552129178 1 16.48124433 1.235861724 24.99982252 1.000000553 0.584351289 0.792355635 0.067133722 33.8807439 313773.9033 0.111560774 0.016667136 17.21320432 -1.235861724 -0.415649264 VPS(ph)PTEEPYAPEL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VPSPTEEPYAPEL 13 0 Q6N075;Q6N075-2 Q6N075 MFSD5 Molybdate-anion transporter 1 VPS(0.5)PT(0.5)EEPYAPEL;VPS(0.5)PT(0.5)EEPYAPEL 67.563 0.055395 42856000 85571 71435 70644 90635 86414 94872 72607 109011 172820 TRUE FALSE 74262.57554 70965.73878 104807.6747 111215.062 84694.53047 98521.78723 65565.58432 85699.84597 152389.4165 0.487321083 0.465686794 0.687762163 0.729808307 0.555776985 0.646513318 0.430250249 0.562374002 1 17.21740318 1.237864489 24.99682594 1.000000495 0.570967556 0.664368601 0.095896512 11.04585862 396348.3633 0.141983094 0.024412415 17.29276698 -1.237864489 -0.429032938 VPS(ph)PYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VPSPYVR 7 0 A0A2R8Y8C6;Q8WXX7-2;Q8WXX7;A0A087WVB5;Q75MD7;A0A2R8Y568;A0A024RDL5;A0A2R8Y522;Q8WXX7-5 A0A2R8Y8C6 AUTS2 Autism susceptibility gene 2 protein 1 VPS(1)PYVR;VPS(1)PYVR;VPS(1)PYVR;VPS(1)PYVR;VPS(1)PYVR;VPS(1)PYVR 101.25 0.0096456 3718880000 5076920 5074080 3094780 3729920 4996820 4719190 4183160 5133230 4527160 TRUE FALSE 4405992.159 5040748.034 4591425.959 4576855.344 4897393.058 4900740.293 3777477.787 4035528.711 3991964.302 1.10371532 1.262723725 1.150167089 1.146517102 1.226812839 1.227651332 0.946270433 1.010913026 1 21.92866739 2.239180138 24.999998 0.98933066 1.188135602 0.790070065 0.048711342 6.68707116 269869.8203 0.018084068 0.013152032 173.4523298 -2.239180138 0.198804942 VPS(ph)S(ph)DEEVVEEPQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 248.42 3.20E-18 6386560000 1637100 1378300 940510 1067100 1442420 1320920 1389010 1669420 1477480 TRUE FALSE 1420753.087 1369245.857 1395343.782 1309401.365 1413718.664 1371736.647 1254304.024 1312427.524 1302813.998 1.090526422 1.050991054 1.07102302 1.005056261 1.085127015 1.052902908 0.962765235 1.007379048 1 20.31319969 2.310196455 7.960434653 0.992646067 1.058434989 0.615051639 0.025797347 0.160336917 15.5706973 0.009214962 0.00710688 204.2661742 -2.310196455 0.065788923 VPS(ph)S(ph)QSMEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPSSQSMEDR 10 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 VPS(0.999)S(0.869)QS(0.132)MEDR 82.85 0.037449 412330000 526430 567140 487200 550990 611760 647550 500270 625710 1032900 TRUE FALSE 456860.9417 563414.42 722811.5496 676100.7009 599587.1729 672461.6675 451753.8924 491906.7858 910791.7387 0.50160857 0.618598518 0.793607934 0.742321951 0.658314242 0.73832649 0.496001307 0.540087009 1 19.79676168 4.604020736 3.812674861 0.684604922 0.503568357 0.172444812 0.139612666 0.480855167 11.14259737 0.035269747 0.181585297 40180.99949 -4.604020736 -0.181036565 VPS(ph)SQS(ph)MEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VPSSQSMEDR 10 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 VPS(0.985)S(0.339)QS(0.676)MEDR;VPS(0.961)S(0.049)QS(0.99)MEDR;VPS(0.996)S(0.064)QS(0.94)MEDR;VPS(0.995)S(0.194)QS(0.811)MEDR 105.19 0.0057634 893022000 1355620 1306810 967980 1203350 1430460 1554960 1302650 1408870 2101560 TRUE FALSE 1176471.382 1298225.479 1436098.366 1476589.01 1401996.645 1614780.317 1176319.203 1107594.114 1853115.971 0.634861175 0.700563537 0.774964108 0.79681414 0.756561741 0.871386542 0.634779054 0.597692822 1 20.82152174 4.529417213 3.02958543 0.755786132 0.635899303 0.131192736 0.112981982 0.695381439 11.43416045 0.029535237 0.154711386 33838.97606 -4.529417213 -0.119886829 VPS(ph)SQSMEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPSSQSMEDR 10 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 VPS(0.616)S(0.303)QS(0.081)MEDR 123.95 0.00047049 1633900000 329970 321250 204460 272000 264180 292360 276140 360670 350010 TRUE FALSE 286363.6285 319139.6876 303337.5399 333761.7573 258923.3349 303607.2784 249359.9853 283543.5272 308632.2165 0.927847493 1.034045283 0.982844705 1.081422286 0.838938131 0.983718686 0.807951899 0.918710076 1 18.23552914 3.236284158 24.99999497 0.907018911 1.006812087 0.3292301 0.068501816 66.85522444 734201.3101 0.019282092 0.022924608 1722.995558 -3.236284158 0.099793177 VPS(ph)VESLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 VPSVESLFR 9 0 Q13439-5;Q13439-3;Q13439-4;Q13439;E7EVX2;Q86W71 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR 188.99 4.06E-05 6795914000 1156552 1061907 664134 826393 1063630 921245 1079823 1182580 1113485 TRUE FALSE 1003710.723 1054931.263 985311.4238 1014038.161 1042465.844 956685.8913 975101.9317 929694.4698 981850.0718 1.022264755 1.074432129 1.003525337 1.0327831 1.061736281 0.974370649 0.993127118 0.946880279 1 19.90514322 2.725487402 24.55797369 0.975001588 1.038609187 0.612187176 0.023792548 380.2601233 714315.198 0.007839574 0.006957536 531.4805825 -2.725487402 0.063607599 VPS(ph)WGLEDNVVCSQPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VPSWGLEDNVVCSQPAR 17 0 B8ZZD4;Q86VP1-2;Q86VP1;Q86VP1-4;Q86VP1-3;H7C3L5 B8ZZD4 TAX1BP1 Tax1-binding protein 1 1 VPS(1)WGLEDNVVCSQPAR;VPS(1)WGLEDNVVCSQPAR;VPS(1)WGLEDNVVCSQPAR;VPS(1)WGLEDNVVCSQPAR 297.55 3.52E-46 716930000 56518.5 52719 42924.8 41750.2 54720.9 56527 50716.3 61462.9 70219.1 TRUE FALSE 49049.43703 52372.68542 63683.37685 51230.22102 53632.06115 58701.63027 45797.84103 48319.53714 61917.87799 0.792169219 0.84584109 1.028513556 0.827389805 0.866180543 0.948056235 0.739654564 0.780381026 1 15.91806841 2.251131455 24.99821821 0.823407194 0.886017089 0.03865703 0.093367301 565.4415727 1124430.375 0.03478127 0.026747828 178.2918351 -2.251131455 0.062609895 VPSS(ph)DEEVVEEPQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VPSSDEEVVEEPQSR 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 VPS(0.183)S(0.817)DEEVVEEPQSR;VPS(0.006)S(0.994)DEEVVEEPQSR;VPS(0.057)S(0.943)DEEVVEEPQSR 288.45 7.31E-35 737930000 516870 390820 272602 322666 387100 372860 363900 444730 419300 TRUE FALSE 448564.3199 388252.6777 404433.239 395932.2469 379397.4673 387204.1655 328609.034 349627.9504 369730.8317 1.213218594 1.050095487 1.093858571 1.07086619 1.026145062 1.047259607 0.888779095 0.945628334 1 18.49611583 8 0.197222167 0.888892127 2.263277376 0.686518085 0.048493213 60.49860395 0.890839611 0.335644224 24.75145593 100000000 -8 1.374385248 VPSS(ph)QSMEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPSSQSMEDR 10 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 VPS(0.027)S(0.683)QS(0.289)MEDR 89.133 0.045818 533560000 406910 395970 293660 339060 429260 472060 452700 465980 490930 TRUE FALSE 353135.8125 393368.847 435674.9582 416048.7552 420718.5658 490220.4537 408797.2237 366333.8033 432892.8147 0.815758083 0.908698028 1.006426865 0.961089538 0.97187699 1.132429177 0.944338205 0.846245978 1 18.72365033 4.584322907 2.98298455 0.970744211 0.811768004 0.357951476 0.070635238 0.395600526 5.813300769 0.019802752 0.122251429 38399.26455 -4.584322907 -0.158976208 VPSSQS(ph)MEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPSSQSMEDR 10 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 VPS(0.012)S(0.053)QS(0.934)MEDR 134.99 0.00016368 1749000000 292440 279760 167500 196150 254480 313370 249550 275520 271210 TRUE FALSE 253793.3131 277922.2381 248503.5603 240688.8555 249416.3459 325425.5467 225348.6794 216602.1921 239147.8628 1.061240147 1.162135571 1.039120975 1.006443682 1.0429378 1.360771294 0.942298529 0.905724975 1 17.86754337 2.069665742 25 0.939464283 1.107152735 0.360689833 0.101735267 48.63799912 17453.199 0.041247415 0.027808998 117.3993634 -2.069665742 0.167688452 VPT(ph)ANVSVVDLTCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VPTANVSVVDLTCR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 VPT(1)ANVSVVDLTCR;VPT(1)ANVSVVDLTCR 204.07 1.58E-07 446510000 133894 227750 127038 80634 160089 137408 112431 134238 172913 TRUE FALSE 116199.5687 226253.8953 188474.0017 98943.18211 156903.5421 142694.1747 101527.4589 105532.2483 152471.4221 0.7621072 1.483910179 1.236126738 0.648929358 1.029068529 0.935874885 0.665878612 0.692144448 1 17.21817934 3.750641859 24.8587758 0.817075414 1.193034288 0.334245753 0.218942167 712.4317247 1465919.499 0.056310971 0.096587343 5631.730442 -3.750641859 0.375958874 VPTANVS(ph)VVDLTCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VPTANVSVVDLTCR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 VPT(0.012)ANVS(0.988)VVDLTCR;VPTANVS(1)VVDLTCR;VPTANVS(1)VVDLTCR;VPTANVS(1)VVDLTCR;VPTANVS(1)VVDLTCR 237.8 2.76E-17 2139180000 527543 995250 469856 322784 681851 632384 493214 566278 819553 TRUE FALSE 457826.8559 988712.1372 697079.9332 396077.0406 668283.4991 656712.2217 445382.1822 445183.8565 722666.378 0.6335245 1.368144648 0.964594389 0.548077305 0.924746909 0.908734987 0.616304004 0.616029568 1 19.46297025 3.98247531 24.51167259 0.755860045 1.042218259 0.166109059 0.22778122 754.8113636 1055755.973 0.057004442 0.101700056 9604.512139 -3.98247531 0.286358214 VPTANVSVVDLTCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VPTANVSVVDLTCR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;; 265.22 2.21E-24 10280750000 1057250 1205970 647438 729186 1123510 1023780 1048480 1082260 967276 FALSE TRUE 917531.7338 1198047.904 960541.1824 894758.8262 1101154.349 1063165.479 946798.571 850827.1212 852925.7332 1.075746338 1.404633319 1.126172121 1.049046583 1.291031923 1.246492441 1.110059803 0.997539514 1 19.7020606 1.934600111 3.099811615 1.00030686 1.201856194 0.385252675 0.103682128 0.255467614 4.500399797 0.061898619 0.028511362 86.02013317 -1.934600111 0.201549334 VPVAS(ph)PSAHNISSSGGAPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VPVASPSAHNISSSGGAPDR 20 0 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 VPVAS(0.953)PS(0.047)AHNISSSGGAPDR;VPVAS(0.967)PS(0.033)AHNISSSGGAPDR;VPVAS(0.975)PS(0.025)AHNISSSGGAPDR 157.96 5.68E-10 558580000 327213 304615 173445 234885 318953 291357 330001 366640 347484 TRUE FALSE 283970.973 302613.964 257323.5821 288219.2292 312606.4593 302565.6923 297997.5538 288236.8892 306404.8374 0.926783583 0.987627893 0.839815665 0.94064843 1.020239961 0.987470351 0.972561518 0.940706066 1 18.22507955 3.46724575 24.77310008 0.978268187 0.919231118 0.360078112 0.040557275 220.2968888 552621.0464 0.01170234 0.015125772 2932.552194 -3.46724575 -0.059037069 VPVDVAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 113.5 0.0065997 1514680000 1004060 980270 706510 808230 973110 955070 1047660 1032740 1035250 FALSE TRUE 871370.927 973830.5418 1048180.599 991750.9745 953747.0149 991812.1609 946058.0945 811896.5878 912863.9244 0.95454635 1.066786096 1.148233128 1.086417097 1.044785525 1.086484124 1.03636267 0.889394976 1 19.8000403 1.911572745 5.666506958 0.941509944 1.06805468 0.444749906 0.054487374 0.182794122 9.093749144 0.027375833 0.014477608 81.57794207 -1.911572745 0.126544736 VPVHDVTDASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VPVHDVTDASK 11 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;;; 160.36 2.76E-05 1291190000 2514890 1992990 1388020 1715830 1712590 1611900 2083710 2344470 2470010 FALSE TRUE 2182540.915 1979897.917 2059271.115 2105435.426 1678512.81 1673910.836 1881632.125 1843123.335 2178008.232 1.002081114 0.909040604 0.945483623 0.966679279 0.770664126 0.768551198 0.86392333 0.846242594 1 21.05457798 3.26143541 24.99978693 0.846409308 0.951741334 0.381014059 0.066929359 260.1971451 284366.7189 0.019597308 0.025282693 1825.725201 -3.26143541 0.105332026 VPVLIS(ph)PTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPVLISPTLK 10 0 P42684-2;P42684-6;P42684-3;P42684;P42684-4;P42684-7;P42684-10;P42684-5 P42684-2 ABL2 Abelson tyrosine-protein kinase 2 1 VPVLIS(0.998)PT(0.002)LK 136.96 0.00010903 134320000 287690 303920 218670 297600 346480 263230 432200 504960 558360 TRUE FALSE 249671.0376 301923.5295 324419.5434 365174.6285 339585.7259 273356.6284 390285.3105 396978.2336 492351.3169 0.50709936 0.61322783 0.658918809 0.741695241 0.689722388 0.555206453 0.792696794 0.80629059 1 18.90932859 -1.759308736 0.500215326 9.999999994 0.614279865 0.738283427 0.072078883 46.35823665 0.670677141 445.6234185 0.048514816 0.017405691 1.759308736 -9.38572013 VPVPGPGS(ph)GGNGPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VPVPGPGSGGNGPER 15 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 VPVPGPGS(1)GGNGPER;VPVPGPGS(1)GGNGPER;VPVPGPGS(1)GGNGPER;VPVPGPGS(1)GGNGPER 132.23 5.11E-05 2786420000 710290 595351 467080 554732 650930 644470 557568 663063 1006380 TRUE FALSE 616423.3769 591440.1001 692961.4503 680692.3791 637977.7665 669263.1779 503495.1412 521272.1374 887406.9029 0.694634417 0.666481293 0.780883547 0.767057792 0.718923601 0.754178467 0.567377986 0.587410506 1 19.75923625 VPWSHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VPWSHVR 7 0 Q8NDH3-3;Q8NDH3-2;Q8NDH3 Q8NDH3-3 NPEPL1 Probable aminopeptidase NPEPL1 0 104.45 0.0081492 220460000 237700 232410 140480 159520 215320 274020 197160 229990 203160 FALSE TRUE 206287.3427 230883.2834 208416.5979 195741.4541 211035.5533 284561.7267 178039.4535 180808.4283 179142.6562 1.151525533 1.288823602 1.163411341 1.09265687 1.178030725 1.588464371 0.993841764 1.009298578 1 17.45074938 VQAERPDTMLGVVCGALHVADVSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VQAERPDTMLGVVCGALHVADVSLR 25 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 131.57 4.77E-05 590760000 138500 123350 85246 78574 120410 134710 115830 156260 133480 FALSE TRUE 120196.8741 122539.7057 126471.2507 96415.42763 118014.0766 139892.3809 104596.8244 122845.015 117700.1465 1.021212613 1.0411177 1.074520759 0.819161492 1.002667202 1.188548911 0.888671999 1.043711658 1 16.84475659 VQAGPGS(ph)PR ddPTM_MDA-MB-175_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 126.21 0.00050333 1208680000 1556980 1521900 1023060 1139880 1358080 1538150 1508510 1562770 1726280 TRUE FALSE 1351221.148 1511902.539 1517815.238 1398707.176 1331056.865 1597323.626 1362214.932 1228583.797 1522201.145 0.887675819 0.993234399 0.997118707 0.918871452 0.874429026 1.049351218 0.894898113 0.80711002 1 20.53772758 2.021826223 24.99926411 0.87814518 0.95374771 0.088932967 0.07019668 355.7157828 407427.2104 0.027703086 0.018675811 105.154103 -2.021826223 0.07560253 VQAMQISS(ph)EKEEDDNEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VQAMQISSEKEEDDNEKR 18 2 Q9UKY7;Q9UKY7-2;H0Y8K3 Q9UKY7 CDV3 Protein CDV3 homolog 1 VQAMQIS(0.278)S(0.722)EKEEDDNEKR 126.45 1.44E-05 156320000 284940 201590 232430 228350 210260 212200 338170 340200 479580 TRUE FALSE 247284.4571 200265.742 344833.9254 280200.3576 206076.2374 220363.4713 305374.3254 267450.8774 422884.5987 0.584756356 0.473570668 0.815432689 0.662592959 0.487310812 0.521095996 0.722122126 0.632444119 1 18.68990449 0.012300466 1.369779968 9.999979583 0.602400255 0.568873314 0.105813779 25.50768016 2.435454471 676.676529 0.031148431 1.028727775 -0.012300466 -9.397579329 VQAMQISSEKEEDDNEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VQAMQISSEKEEDDNEKR 18 2 Q9UKY7;Q9UKY7-2;H0Y8K3 Q9UKY7 CDV3 Protein CDV3 homolog 0 ;; 258.38 6.59E-31 687817000 443796 283137 357005 351906 286011 196819 433435 539584 565282 FALSE TRUE 385147.2342 281277.0544 529653.8121 431811.6358 280319.9407 204390.7543 391400.5404 424198.1606 498455.0059 0.772682047 0.564297782 1.062591018 0.866300129 0.562377622 0.410048554 0.785227424 0.851025981 1 18.92710376 1.537219669 2.375775792 0.992694315 0.712291299 0.212964232 0.179690565 0.540815721 5.87171825 0.266831225 0.052168671 34.45241496 -1.537219669 -0.280403016 VQAYEEPSVASS(ph)PNGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VQAYEEPSVASSPNGK 16 0 Q99575 Q99575 POP1 Ribonucleases P/MRP protein subunit POP1 1 VQAYEEPSVASS(1)PNGK;VQAYEEPSVAS(0.001)S(0.999)PNGK;VQAYEEPSVAS(0.007)S(0.993)PNGK 360.81 8.02E-88 2697510000 4562400 3920000 2682740 3314830 4071800 3158610 4428600 5243500 4473600 TRUE FALSE 3959467.28 3894249.262 3980122.037 4067512.816 3990779.146 3280123.771 3999115.054 4122218.33 3944736.104 1.003734388 0.987201465 1.008970418 1.031124189 1.011672021 0.83151919 1.013785193 1.044992167 1 21.91149736 2.016829743 24.99973165 1.026813558 0.97945575 0.104935812 0.055939187 495.6518015 736262.012 0.023572904 0.015888143 103.9512566 -2.016829743 -0.047357808 VQDDEVGDGTTSVTVLAAELLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VQDDEVGDGTTSVTVLAAELLR 22 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;; 263.08 5.00E-37 144480000 145106 133201 91422.9 106629 138524 126741 141152 159456 148950 FALSE TRUE 125929.8744 132325.9939 135635.3202 130840.7442 135767.6434 131616.8083 127463.1008 125357.5753 131341.3007 0.958798746 1.007497209 1.032693597 0.996188887 1.033701073 1.002097646 0.97047235 0.954441403 1 17.00296112 2.271942597 5.142935068 0.970326793 1.007740796 0.259576248 0.023492802 0.203284573 13.25841766 0.009036599 0.006675471 187.0434897 -2.271942597 0.037414003 VQDT(ph)SNTGLGEDIIHQLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VQDTSNTGLGEDIIHQLSK 19 0 Q8IWA0 Q8IWA0 WDR75 WD repeat-containing protein 75 1 VQDT(0.547)S(0.359)NT(0.093)GLGEDIIHQLSK;VQDT(0.729)S(0.267)NT(0.004)GLGEDIIHQLSK 204.89 1.61E-15 249333000 372770 352650 237750 294780 350410 292520 341380 450670 419790 TRUE FALSE 323507.5 350333.4189 352726.6952 361714.3044 343437.5266 303773.4337 308273.0201 354297.7276 370162.9044 0.873959806 0.946430382 0.952895849 0.977175995 0.927801037 0.820647964 0.832803656 0.957140014 1 18.4978008 2.987688948 24.72360587 0.901237748 0.940980589 0.075273168 0.057764417 1392.855585 2797202.772 0.01953791 0.020520291 972.0507697 -2.987688948 0.039742841 VQDTS(ph)NTGLGEDIIHQLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VQDTSNTGLGEDIIHQLSK 19 0 Q8IWA0 Q8IWA0 WDR75 WD repeat-containing protein 75 1 VQDT(0.247)S(0.744)NT(0.01)GLGEDIIHQLSK;VQDT(0.068)S(0.927)NT(0.005)GLGEDIIHQLSK;VQDT(0.168)S(0.796)NT(0.036)GLGEDIIHQLSK 322.69 2.49E-62 298254000 463459 404686 251334 338025 408623 365534 423997 552520 498226 TRUE FALSE 402211.7189 402027.591 372879.9631 414778.7426 400492.2018 379596.3295 382877.8362 434367.8977 439326.2899 0.915519349 0.915100235 0.848754039 0.944124566 0.911605363 0.864041917 0.871511323 0.988713646 1 18.74493331 1.662391772 5.469545234 0.997055274 0.896137856 0.67575384 0.028363084 0.079139181 5.106804869 0.01849894 0.007393634 45.96124366 -1.662391772 -0.100917417 VQEAPIDEHWIIECNDGVFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VQEAPIDEHWIIECNDGVFQR 21 0 A0A1W2PR36;Q14353;Q14353-2 A0A1W2PR36 GAMT Guanidinoacetate N-methyltransferase 0 ;;; 234.51 8.89E-30 1485450000 1122710 960040 637260 736640 903180 933620 937410 1089120 1041310 FALSE TRUE 974341.0289 953733.434 945441.0675 903905.3708 885208.485 969536.9655 846500.1225 856220.1635 918207.5181 1.061133796 1.038690509 1.029659471 0.98442384 0.964061465 1.055901794 0.921905022 0.932490909 1 19.80846072 4.661401465 0.35532171 0.944938278 1.149499314 0.428912033 0.036862187 7.370679246 0.95595625 0.073211113 0.675171175 45856.5592 -4.661401465 0.204561036 VQEAVLDKWVNDPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VQEAVLDKWVNDPHR 15 1 Q9H4A6 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 0 129.88 3.80E-05 210350000 685350 614650 325460 379510 522990 490080 592700 779950 162460 FALSE TRUE 594779.261 610612.3237 482853.5446 465683.5459 512583.5222 508933.6947 535220.0452 613163.7621 143254.1639 4.151916042 4.262440317 3.370607398 3.250750508 3.578140477 3.552662491 3.736156987 4.280250888 1 17.12821755 1.232061656 25 0.999995363 3.768374682 0.854561527 0.359496032 88.16864434 339132.1295 0.895558963 0.096322171 17.06324617 -1.232061656 2.768379318 VQEHEDS(ph)GDS(ph)EVENEAK ddPTM_MDA-MB-175_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 240.49 1.34E-20 878240000 1173720 969710 815110 868460 980300 874420 1166800 1375280 1314990 TRUE FALSE 1018609.928 963339.9112 1209299.922 1065657.117 960793.9479 908059.5032 1053643.916 1081187.074 1159533.38 0.878465377 0.830799637 1.042919456 0.91903962 0.828603958 0.783124935 0.908679244 0.932432902 1 20.14511292 1.440172554 2.158651768 1.006809817 0.883806243 0.227976088 0.069222665 0.732551316 5.210556784 0.155506304 0.020094449 27.55323232 -1.440172554 -0.123003574 VQEKPDS(ph)PGGSTQIQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VQEKPDSPGGSTQIQR 16 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 VQEKPDS(0.993)PGGS(0.006)T(0.001)QIQR;VQEKPDS(0.999)PGGS(0.001)TQIQR;VQEKPDS(1)PGGSTQIQR 195.09 6.57E-11 1844230000 2993550 2283930 1897690 2074610 2868490 2421440 3193210 3501700 2937870 TRUE FALSE 2597944.783 2268926.713 2815419.231 2545681.909 2811412.661 2514594.364 2883532.986 2752888.705 2590558.355 1.002851288 0.875844664 1.086800159 0.982676921 1.085253554 0.970676595 1.113093237 1.062662302 1 21.30483165 4.231238998 24.99976338 1.045299679 0.939347969 0.374852354 0.055601429 139.8879594 477655.0082 0.013055685 0.028073936 17030.95487 -4.231238998 -0.10595171 VQENSPGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VQENSPGHR 9 0 Q9H8Y8;F8WEG2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 0 ;;;;; 157.66 6.80E-05 1563363000 1753090 1560748 722721 1062034 1209337 1493980 1547090 1758837 1649516 FALSE TRUE 1521414.715 1550495.344 1072231.293 1303185.052 1185273.56 1551454.377 1397053.45 1382723.395 1454512.098 1.045996604 1.065989995 0.737175919 0.89596027 0.81489426 1.066649346 0.960496274 0.950644135 1 20.47210387 2.732501735 24.94946495 0.984420244 0.909954297 0.139373144 0.100364228 1166.045828 4801567.726 0.035480427 0.032073768 540.1342728 -2.732501735 -0.074465947 VQESTKGPDEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VQESTKGPDEAK 12 1 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 101.32 0.0024961 129940000 163230 117600 81672 88540 95702 71102 154510 159320 96966 FALSE TRUE 141658.7419 116827.4779 121168.8524 108644.3602 93797.71744 73837.33995 139525.644 125250.6578 85502.78994 1.656773329 1.366358664 1.417133318 1.270652809 1.09701353 0.86356644 1.631825629 1.464872174 1 16.38368388 4.996027381 1.103213163 1.260242256 2.028208735 0.260339572 0.222932625 4.665162435 3.245230363 0.072892925 4.756990049 99089.44159 -4.996027381 0.767966479 VQFVITAQEWDPSFEEALMDNPSLAFVRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VQFVITAQEWDPSFEEALMDNPSLAFVRPR 30 1 F5H8D7;P18887 F5H8D7 XRCC1 DNA repair protein XRCC1 0 135.3 3.79E-06 40260000 33720 22327 12643 11137 24251 26311 24890 27459 24884 FALSE TRUE 29263.81656 22180.33247 18757.19709 13665.82607 23768.45255 27323.2012 22476.17163 21587.10654 21942.24187 1.33367487 1.010850787 0.85484415 0.622809016 1.083228081 1.245232887 1.024333419 0.983814993 1 14.42142331 VQGGHS(ph)PDDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VQGGHSPDDHR 11 0 A2AJT9-3;A2AJT9-2;A2AJT9 A2AJT9-3 CXorf23 Uncharacterized protein CXorf23 1 VQGGHS(1)PDDHR 106.29 0.0016812 0 89630 76142 50162 54644 60859 72675 61763 76478 63676 TRUE FALSE 77785.16841 75641.81819 74420.51098 67051.75538 59648.02497 75470.85428 55773.23377 60123.77485 56148.29582 1.385352258 1.347179235 1.325427778 1.194190392 1.062330105 1.344134371 0.993320152 1.0708032 1 15.77695462 7.999999901 0.084043176 0.495626854 3.001584457 0.656620944 0.089565286 238.3937171 1.890792534 10.69849126 72.22548851 99999977.19 -7.999999901 2.505957603 VQGGVPAGS(ph)DEYEDECPHLIALSSLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VQGGVPAGSDEYEDECPHLIALSSLNR 27 0 Q9BVS4-2;Q9BVS4;H0Y919;H0Y8R4 Q9BVS4-2 RIOK2 Serine/threonine-protein kinase RIO2 1 VQGGVPAGS(1)DEYEDECPHLIALSSLNR 162.08 8.08E-12 450340000 182630 181640 89805 110680 160610 197830 142760 180970 176100 TRUE FALSE 158494.9828 180446.7949 133234.9984 135811.5856 157414.1752 205440.6481 128915.1572 142270.9738 155281.6586 1.02069352 1.162061228 0.858021479 0.874614471 1.013733216 1.323019408 0.830202088 0.916212353 1 17.24452791 VQHQDALQISDVVMASLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VQHQDALQISDVVMASLLR 19 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;; 194.88 2.15E-15 933443000 734450 691289 533593 535913 677045 758847 645093 781062 818943 FALSE TRUE 637390.5716 686747.877 791640.3596 657600.2376 663573.1291 788040.3351 582531.9801 614037.9695 722128.4915 0.882655343 0.951005098 1.096259695 0.91064159 0.918912821 1.091274398 0.806687434 0.850316774 1 19.46189604 2.219764084 24.99996354 0.875012387 0.974048499 0.192874647 0.085324024 359.4480815 478073.405 0.034297765 0.023167858 165.8685638 -2.219764084 0.099036112 VQHRPSGLIMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VQHRPSGLIMAR 12 1 P36507;A0A1B0GUL7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 0 61.641 0.050119 354940000 401030 379240 217490 292690 392410 430970 384720 421220 408520 FALSE TRUE 348032.8694 376748.7475 322668.8915 359149.738 384601.8087 447549.6948 347409.9136 331145.3809 360225.231 0.966153505 1.045869959 0.895742063 0.997014387 1.067670379 1.242416289 0.964424154 0.919273145 1 18.45853971 4.784038804 20.25199647 1.010777896 0.966151879 0.023653502 0.095559861 13812.36137 6149140.041 0.025032535 6.987703846 60818.93405 -4.784038804 -0.044626017 VQIFEYNENTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VQIFEYNENTR 11 0 K7ELV2;Q96EE3;Q96EE3-1;K7ENI5 K7ELV2 SEH1L Nucleoporin SEH1 0 113.38 0.0032561 131770000 87122 78340 47955 49706 79391 89013 60506 52567 72352 FALSE TRUE 75608.60696 77825.37938 71146.1984 60992.50701 77811.27443 92437.38771 54638.13743 41325.95613 63798.62898 1.185113351 1.219859747 1.11516814 0.956015952 1.219638661 1.448893012 0.856415542 0.647756179 1 15.9612378 2.080301714 8.310681221 0.784873311 1.178657831 0.561717119 0.147285926 0.16959832 15.50483798 0.06104283 0.04107331 120.3099963 -2.080301714 0.39378452 VQIGCHTDDLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VQIGCHTDDLTK 12 0 A6NFQ2-2;A6NFQ2;Q8N1I1;A0A1B0GVM2;A6NFQ2-3 A6NFQ2-2 TCAF2 TRPM8 channel-associated factor 2 0 109.84 0.0005088 0 160260 144750 82380 91222 110660 106660 158100 174690 127450 FALSE TRUE 139081.235 143799.1277 122219.2435 111935.3493 108458.0825 110763.2792 142767.4863 137333.9029 112383.0062 1.237564643 1.279545125 1.087524241 0.996016686 0.96507547 0.985587439 1.270365433 1.222016634 1 16.77806437 4.234422477 24.46019713 1.088822371 1.25855492 0.351534538 0.102227701 99.09949867 585789.2949 0.030210942 0.066792724 17156.25438 -4.234422477 0.169732549 VQIPVSRPDPEPVS(ph)DNEEDS(ph)YDEEIHDPR ddPTM_MDA-MB-175_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(0.943)Y(0.057)DEEIHDPR;VQIPVSRPDPEPVS(1)DNEEDS(0.694)Y(0.306)DEEIHDPR;VQIPVSRPDPEPVS(1)DNEEDS(0.891)Y(0.109)DEEIHDPR 212.8 4.55E-26 5992100000 2515230 2227620 1734423 1924660 2281650 2402940 2074550 2642980 2854240 TRUE FALSE 2182835.983 2212986.618 2573195.764 2361683.47 2236249.629 2495382.657 1873360.46 2077799.295 2516814.999 0.867300927 0.879280606 1.022401633 0.938361966 0.888523642 0.99148434 0.744337769 0.825566955 1 21.26316774 2.256634201 24.99996271 0.845483309 0.93139213 0.163289017 0.078248827 370.7459295 512826.8431 0.029209097 0.022579567 180.5652614 -2.256634201 0.085908822 VQIPVSRPDPEPVS(ph)DNEEDSY(ph)DEEIHDPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VQIPVSRPDPEPVSDNEEDSYDEEIHDPR 29 1 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 2 VQIPVS(0.001)RPDPEPVS(0.999)DNEEDS(0.145)Y(0.855)DEEIHDPR;VQIPVSRPDPEPVS(0.99)DNEEDS(0.377)Y(0.633)DEEIHDPR 102.53 0.0013788 2234260000 926440 854210 540810 739190 843150 862930 843660 939010 955510 TRUE FALSE 804008.6067 848598.6383 802347.5249 907034.3873 826372.9646 896127.4755 761841.9831 738210.0189 842550.6963 0.954255465 1.007178134 0.952283973 1.0765339 0.9807991 1.06358879 0.904209072 0.87616095 1 19.68440397 2.21847661 24.99961291 0.915301377 1.005486968 0.341247754 0.050902897 227.4556507 283123.8223 0.019866994 0.013412164 165.3775714 -2.21847661 0.090185591 VQIS(ph)PDSGGLPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VQISPDSGGLPER 13 0 A0A087WTP3;Q92945;M0QYH3;M0QXW7 A0A087WTP3 KHSRP Far upstream element-binding protein 2 1 VQIS(0.982)PDS(0.018)GGLPER;VQIS(0.982)PDS(0.018)GGLPER;VQIS(0.998)PDS(0.002)GGLPER;VQIS(0.99)PDS(0.01)GGLPER;VQIS(0.659)PDS(0.341)GGLPER 239.19 8.82E-17 5668500000 4634430 4033170 2431100 3056080 3962640 4134480 3964770 4255680 4073450 TRUE FALSE 4021978.333 4006675.841 3606788.092 3750009.673 3883791.217 4293536.121 3580267.216 3345635.95 3591891.381 1.119738296 1.115478007 1.004147316 1.0440209 1.081266331 1.195341302 0.996763776 0.931441292 1 21.77631229 2.01684853 24.78685807 0.96180726 1.088208116 0.531289345 0.052348207 157.3037659 231417.7976 0.022007023 0.014833097 103.9557534 -2.01684853 0.126400856 VQISPDS(ph)GGLPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VQISPDSGGLPER 13 0 A0A087WTP3;Q92945;M0QYH3;M0QXW7 A0A087WTP3 KHSRP Far upstream element-binding protein 2 1 VQIS(0.311)PDS(0.689)GGLPER 181.58 1.25E-05 1191000000 762400 782410 464280 509430 715730 677580 695080 736600 721450 TRUE FALSE 661646.9083 777270.2972 688807.3609 625103.8677 701488.3733 703646.9411 627671.2486 579083.8222 636161.0029 1.040062037 1.221813808 1.082756343 0.982618967 1.102689995 1.106083111 0.986654708 0.910278718 1 19.27903241 2.129535999 4.335272959 0.948774768 1.090718858 0.460859605 0.063426636 0.178109593 5.908298117 0.027831037 0.018111335 134.7522419 -2.129535999 0.14194409 VQIYHNPTANSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VQIYHNPTANSFR 13 0 P50552;K7ENR7;K7ENL7 P50552 VASP Vasodilator-stimulated phosphoprotein 0 ;;; 135.81 7.96E-05 3446470000 2205700 2529360 1455699 1796420 2532930 2598470 2404570 2695360 2382510 FALSE TRUE 1914211.156 2512744.468 2159679.905 2204324.618 2482529.649 2698434.822 2171375.172 2118978.239 2100852.382 0.911159286 1.196059509 1.028001741 1.049252502 1.181677337 1.284447611 1.033568655 1.008627859 1 21.00254336 2.021061408 24.99898897 1.009780504 1.113533387 0.163163584 0.101743571 389.892956 462784.3215 0.041219094 0.02778705 104.9690841 -2.021061408 0.103752883 VQLEELRDDLELYYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VQLEELRDDLELYYK 15 1 Q14746-2;Q14746;V9GY21 Q14746-2 COG2 Conserved oligomeric Golgi complex subunit 2 0 ; 171.91 9.64E-07 101649000 112869 107298 63775 65656 104947 95316 111430 138683 50667 FALSE TRUE 97953.07568 106593.1524 94616.80331 80564.19829 102858.76 98982.8682 100623.5358 109026.7197 44677.20498 2.192462033 2.38585096 2.117786987 1.803250636 2.302264881 2.215511652 2.252234351 2.440320959 1 15.44725131 1.232164974 24.99999911 0.99999797 2.218517067 0.82975089 0.172764841 90.7756474 354799.7161 0.410938448 0.044588273 17.06730597 -1.232164974 1.218519097 VQLPTETLQELLDLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VQLPTETLQELLDLHR 16 0 P32456;P32455 P32456 GBP2;GBP1 Interferon-induced guanylate-binding protein 2;Interferon-induced guanylate-binding protein 1 0 ; 205.12 2.34E-11 1150110000 357460 374740 247390 257830 336810 392920 405860 388850 367130 FALSE TRUE 310220.7553 372278.3083 367028.6315 316374.2422 330108.14 408035.8867 366499.7597 305697.4535 323728.3096 0.958275029 1.149971433 1.133755129 0.977283212 1.01970736 1.260426952 1.132121439 0.944302504 1 18.30442401 1.728333438 9.166952731 0.974281233 1.093645659 0.227656276 0.090083781 0.144375136 40.61734808 0.051091679 0.023507367 53.49749395 -1.728333438 0.119364426 VQNS(ph)PPVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VQNSPPVGR 9 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;H0Y8P9;H0YA73 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 VQNS(1)PPVGR;VQNS(1)PPVGR;VQNS(1)PPVGR;VQNS(1)PPVGR;VQNS(1)PPVGR;VQNS(1)PPVGR 145.01 0.00010299 4413370000 4680740 4740720 2949200 3566660 4504220 4684230 4435230 5034730 4604540 TRUE FALSE 4062168.35 4709577.898 4375442.984 4376524.666 4414594.834 4864435.359 4005102.077 3958092.17 4060196.527 1.000485647 1.159938409 1.077643152 1.077909564 1.087285998 1.198078794 0.986430595 0.974852361 1 21.95311813 2.147041585 12.48388216 0.984235083 1.100289816 0.509683773 0.052284394 0.421197613 55.19463847 0.020015641 0.013494145 140.2948035 -2.147041585 0.116054733 VQPNEAVYTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VQPNEAVYTK 10 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 110.84 0.0058727 0 150920 132060 110420 112830 138750 144430 173000 195740 176300 FALSE TRUE 130975.5396 131192.4892 163819.4813 138449.776 135989.1465 149986.3156 156222.4866 153882.5243 155458.0148 0.842513908 0.843909459 1.053786011 0.890592718 0.87476446 0.96480272 1.004917545 0.989865491 1 17.24616547 8 0.187485509 1.035357816 0.21266852 0.375886381 0.058466581 128.4128385 1.845750501 0.486376644 29.46809861 100000000 -8 -0.822689296 VQPQWS(ph)PPAGTQPCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VQPQWSPPAGTQPCR 15 0 P49589-3;P49589;B4DKY1;P49589-2;E9PLP0;C9JLN0;E9PRS8 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 1 VQPQWS(1)PPAGTQPCR;VQPQWS(1)PPAGTQPCR;VQPQWS(1)PPAGTQPCR;VQPQWS(1)PPAGTQPCR;VQPQWS(1)PPAGTQPCR;VQPQWS(1)PPAGTQPCR 220.64 1.72E-12 4642120000 2283960 2513040 1748910 1981640 2395100 2410370 2422140 2706260 3047810 TRUE FALSE 1982128.899 2496531.675 2594688.726 2431601.649 2347442.196 2503098.494 2187241.236 2127547.359 2687501.374 0.737535958 0.928941544 0.965465079 0.904781547 0.873466417 0.93138501 0.813856788 0.791645124 1 21.35783406 1.213581675 24.53830087 1.00000075 0.87042266 0.256964333 0.070259999 2975.985129 2923291.133 1.195804224 0.01789019 16.3524065 -1.213581675 -0.12957809 VQPTHVIHLAAMVGGLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VQPTHVIHLAAMVGGLFR 18 0 Q13630;E9PP14;A0A0J9YX13;E9PKL9;E9PLH9 Q13630 TSTA3 GDP-L-fucose synthase 0 ; 194.37 4.39E-15 372620000 303354 321070 160179 263798 306476 303876 335170 373910 326569 FALSE TRUE 263265.0003 318960.87 237642.1002 323697.3678 300377.7272 315566.3064 302665.265 293952.2563 287962.3848 0.914233991 1.107647689 0.825253966 1.12409601 1.043114459 1.09585947 1.051058336 1.020800881 1 18.13552085 3.702399859 24.99986083 1.053014617 0.964905204 0.292231503 0.076944314 797.0292016 551028.6054 0.019696583 0.029215674 5039.643997 -3.702399859 -0.088109413 VQQAELHTGSLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VQQAELHTGSLPR 13 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 141 3.96E-05 631440000 718740 566560 345000 446730 678220 729570 700420 836130 742950 FALSE TRUE 623756.6879 562838.2301 511843.154 548166.8743 664724.7489 757637.03 632493.3762 657330.1063 655119.2974 0.952126873 0.85913853 0.781297629 0.836743592 1.014662141 1.156487121 0.965462899 1.003374666 1 19.32139812 3.220553302 8.249372209 1.026963185 0.851923281 0.634104158 0.064368194 0.114939397 40.30757353 0.019993614 0.02333463 1661.702611 -3.220553302 -0.175039904 VQQLLHICSEHFDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VQQLLHICSEHFDSK 15 0 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 213.51 1.95E-10 3004100000 5572400 4801200 2056880 3858400 4808400 4374200 5736500 6496700 5713700 FALSE TRUE 4835993.221 4769660.601 3051594.048 4734508.692 4712722.247 4542478.304 5180175.113 5107431.262 5038232.895 0.959859007 0.946693156 0.605687373 0.939716125 0.935391901 0.901601494 1.028173016 1.01373465 1 22.26448638 2.645086202 1.212091058 1.017607584 0.854485884 0.27193708 0.102019143 0.608353809 1.881910128 0.061919976 0.044495317 441.6581019 -2.645086202 -0.163121701 VQQSSESSTSS(ph)PSQHEATPGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VQQSSESSTSSPSQHEATPGAR 22 0 O75152;E9PBY7;E9PQ61;A0A1B0GTU1;A0A494C0C4 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 VQQSSESST(0.001)S(0.064)S(0.862)PS(0.074)QHEATPGAR;VQQSSESST(0.002)S(0.046)S(0.673)PS(0.278)QHEATPGAR 241.22 7.55E-31 618190000 362950 363610 136865 221281 331330 356420 294380 316120 282120 TRUE FALSE 314985.2379 361221.422 203053.3718 271526.2331 324737.1812 370131.708 265831.0729 248520.198 248768.095 1.266180207 1.452040793 0.816235586 1.091483348 1.305381147 1.487858433 1.068589897 0.999003502 1 17.92444194 2.01735173 24.98730108 1.009740322 1.228297014 0.23095179 0.186646803 363.5862445 523579.2723 0.079949566 0.053888905 104.0762725 -2.01735173 0.218556692 VQRPHS(ph)SPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 95.273 0.0045628 182850000 39844 47189 22511 26671 71065 61725 53311 48552 61172 TRUE FALSE 34578.51445 46879.01235 33397.39489 32727.05819 69650.94554 64099.60069 48140.90743 38169.53263 53940.31585 0.64105139 0.869090431 0.619154604 0.606727226 1.291259505 1.188343073 0.892484715 0.707625308 1 15.71907635 3.277167209 24.99999887 0.976764318 0.692593851 0.467027497 0.173309654 191.6173364 124082.0506 0.056852885 0.073395376 1893.072336 -3.277167209 -0.284170467 VQRPHSS(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VQRPHSSPPR 10 1 R4GNF5;E9PP52;E9PMB0;E9PJ55;Q9NUJ3 R4GNF5 TCP11L1 T-complex protein 11-like protein 1 1 VQRPHS(0.215)S(0.785)PPR;VQRPHS(0.086)S(0.914)PPR;VQRPHS(0.208)S(0.792)PPR;VQRPHS(0.202)S(0.798)PPR 80.905 0.013691 942240000 503571 503719 280152 319449 528158 587790 498015 547494 463536 TRUE FALSE 437022.8165 500410.0367 415634.4443 391984.7779 517648.6891 610402.6617 449717.582 430416.6687 408737.3021 1.069202185 1.224282771 1.016874266 0.959013958 1.266458154 1.493386237 1.10026068 1.053039853 1 18.64081439 1.792265331 3.713333821 1.02486889 1.169545254 0.132868434 0.148531847 0.47491819 12.20331241 0.101332847 0.043136983 61.98196361 -1.792265331 0.144676365 VQS(ph)LPSVPLSCAAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 VQSLPSVPLSCAAYR 15 0 Q96AD5-2;Q96AD5 Q96AD5-2 PNPLA2 Patatin-like phospholipase domain-containing protein 2 1 VQS(0.995)LPS(0.005)VPLSCAAYR;VQS(0.997)LPS(0.003)VPLSCAAYR;VQS(0.672)LPS(0.328)VPLSCAAYR;VQS(0.999)LPS(0.001)VPLSCAAYR;VQS(1)LPSVPLSCAAYR;VQS(0.995)LPS(0.005)VPLSCAAYR;VQS(0.999)LPS(0.001)VPLSCAAYR;VQS(0.993)LPS(0.007)VPLSCAAYR 311.24 3.82E-56 4396111000 1930703 1788674 1083459 1298809 1843840 1413797 1646467 2088528 2419332 TRUE FALSE 1675555.707 1776924.083 1607423.396 1593723.435 1807151.191 1468186.685 1486792.884 1641912.54 2133321.327 0.785421158 0.832937851 0.753483958 0.747062064 0.847106888 0.688216382 0.696938087 0.769650835 1 21.02466985 1.239994964 7.582659716 1.003568202 0.763207762 0.682940497 0.050301994 0.058157989 25.0087812 0.072648248 0.012720512 17.37780678 -1.239994964 -0.24036044 VQS(ph)SPNLLAAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VQSSPNLLAAGR 12 0 O94875-12;O94875-9;O94875-11;C9JN77;C9IZT7;C9JWC3;C9JG84;C9JI79;C9JEA9;C9J372;C9JZ60;C9JBB0;C9JDX2;C9J4Z9;C9J9D3 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 VQS(0.877)S(0.123)PNLLAAGR;VQS(0.809)S(0.191)PNLLAAGR 112.62 0.00019967 261970000 280900 292940 137087 193045 254238 238221 283060 266940 322410 TRUE FALSE 243778.3533 291015.6579 203382.7317 236878.8178 249179.1612 247385.516 255608.8848 209856.9583 284295.0571 0.857483615 1.023639527 0.715393133 0.83321469 0.876480808 0.87017171 0.899097182 0.738166046 1 18.11702949 4.254936525 24.99980771 0.841839215 0.940561485 0.157398129 0.088763824 404.2820417 617174.7251 0.020698775 0.054407327 17986.08017 -4.254936525 0.09872227 VQSGMGLILQGYES(ph)GS(ph)EEEGEIHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VQSGMGLILQGYESGSEEEGEIHEK 25 0 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 VQSGMGLILQGY(0.05)ES(0.975)GS(0.975)EEEGEIHEK;VQSGMGLILQGY(0.008)ES(0.997)GS(0.995)EEEGEIHEK 89.391 0.007632 128196000 143124 119960 83287 96266 104377 100883 122903 144423 145871 TRUE FALSE 124209.8008 119171.9749 123564.8718 118124.6666 102300.1019 104764.0343 110983.886 113539.2654 128626.2966 0.96566413 0.926497754 0.960650155 0.918355498 0.795328052 0.814483796 0.862839784 0.882706479 1 16.97282609 3.467274219 24.9173302 0.867966698 0.946994971 0.311874627 0.054536706 245.690417 621702.2447 0.016316446 0.021090335 2932.744435 -3.467274219 0.079028272 VQSGSESVIQEYVDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 120.92 0.0002362 50355000 26144 24998 17488 19058 30819 33292 23505 28669 27993 FALSE TRUE 22689.00416 24833.78649 25945.25529 23385.41018 30205.7622 34572.76478 21225.48872 22538.35745 24683.69943 0.919189776 1.006080412 1.051108865 0.947402971 1.223712932 1.400631412 0.859899011 0.913086692 1 14.59127101 VQSYFDGIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VQSYFDGIK 9 0 F8WCQ4;A0A1W2PS40;C9JNP8;A0A1W2PP11;Q9H300-2;Q9H300 F8WCQ4 PARL "Presenilins-associated rhomboid-like protein, mitochondrial;P-beta" 0 71.349 0.049832 102590000 159780 165980 149310 191590 121760 174140 113160 138090 253510 FALSE TRUE 138664.6682 164889.6665 221516.8154 235093.4378 119337.2142 180839.2785 102185.7606 108560.5281 223540.3366 0.620311619 0.737628246 0.990947848 1.0516824 0.533850919 0.808978287 0.457124482 0.485641785 1 17.77017566 3.220864976 24.99839661 0.628277792 0.852163389 0.181174031 0.198697888 368.419463 520459.8797 0.061423239 0.06979528 1662.895567 -3.220864976 0.223885597 VQT(ph)TPSKPGGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VQTTPSKPGGDR 12 1 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 VQT(0.5)T(0.5)PS(0.001)KPGGDR 80.534 0.032466 275060000 414810 353330 235970 317450 377920 316510 421680 470810 419880 TRUE FALSE 359991.8075 351008.952 350085.8813 389531.8744 370400.1314 328686.3445 380785.5385 370130.9453 370242.2647 0.972314189 0.948052088 0.945558934 1.052099967 1.000426387 0.887760193 1.028476689 0.999699334 1 18.49811007 3.178237051 0.008715382 1.96022471 5.05E-05 0.059363847 0.045150273 8611.604995 93.72148393 10500.1209 10575.70016 1507.429642 -3.178237051 -1.960174215 VQTEKEEKEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VQTEKEEKEEAR 12 2 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 79.089 0.013485 94831000 229210 156050 101190 108050 130870 99916 190890 213060 50845 FALSE TRUE 198919.3178 155024.8973 150125.8225 132584.4039 128265.943 103759.8332 172377.5172 167498.777 44834.16202 4.436780098 3.457740488 3.348469464 2.95721829 2.860897522 2.314302944 3.844780618 3.735963147 1 15.45231081 5.498538909 0.861541311 2.926978211 8.475388822 0.297981438 0.791937766 10.84762312 2.437999208 0.27292563 77.61072632 315165.673 -5.498538909 5.548410611 VQTT(ph)PPPAVQGQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VQTTPPPAVQGQK 13 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 VQT(0.143)T(0.857)PPPAVQGQK;VQT(0.002)T(0.998)PPPAVQGQK;VQT(0.034)T(0.966)PPPAVQGQK;VQT(0.003)T(0.997)PPPAVQGQK;VQT(0.181)T(0.819)PPPAVQGQK 207.64 5.84E-07 2195670000 3930220 3468490 2411160 3042480 3201580 2936200 3920540 4409270 4089860 TRUE FALSE 3410831.469 3445705.261 3577205.041 3733321.585 3137874.822 3049157.514 3540326.634 3466381.923 3606361.41 0.945781934 0.955452011 0.991915295 1.035204507 0.870094387 0.845494161 0.981689363 0.961185397 1 21.78211255 1.467494249 2.021431846 1.000083762 0.945146788 0.086658327 0.055037987 1.368569678 8.771762297 0.124474476 0.016475806 29.34230651 -1.467494249 -0.054936974 VQTT(ph)PSKPGGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VQTTPSKPGGDR 12 1 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 VQT(0.143)T(0.856)PS(0.001)KPGGDR 95.751 0.009491 388960000 784100 626300 439140 569270 658410 541010 756360 881850 805040 TRUE FALSE 680479.1983 622185.7941 651509.5728 698531.4542 645308.9292 561823.0048 683008.3236 693273.2401 709869.0883 0.958598155 0.876479627 0.917788341 0.984028556 0.909053429 0.791445936 0.96216096 0.976621255 1 19.43719347 2.018431874 24.99999133 0.981465891 0.90638079 0.322583008 0.050951162 281.712133 382097.4604 0.02120229 0.01429213 104.3354452 -2.018431874 -0.075085101 VQVAALQAS(ph)PPLDQDDR ddPTM_MDA-MB-175_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 201.61 1.19E-11 756720000 771340 786040 541765 681910 815480 916790 797390 967640 1456990 TRUE FALSE 669405.4647 780876.4515 803764.3661 836748.0878 799253.5435 952059.5045 720059.2405 760717.7162 1284746.302 0.521040974 0.607805954 0.625621078 0.651294412 0.622110017 0.741048644 0.560468039 0.592115124 1 20.29305207 1.2363079 24.99605965 1.000000496 0.616914593 0.815520626 0.057513277 25.15100756 279008.291 0.090805008 0.014046918 17.23089752 -1.2363079 -0.383085902 VQVEYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VQVEYK 6 0 P11142;E9PKE3;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 ;; 121.29 0.045867 1062710000 2002190 1728540 1275870 1656960 1657890 1655330 1838370 2118820 2641970 FALSE TRUE 1737595.519 1717185.107 1892885 2033198.093 1624901.233 1719011.616 1660085.16 1665726.832 2329639.316 0.745864609 0.73710342 0.812522774 0.872752309 0.697490475 0.737887451 0.712593211 0.715014904 1 21.15167518 1.233190275 24.99621836 1.000000389 0.752901746 0.686556735 0.05225363 108.4323401 504641.7167 0.114548547 0.01368085 17.10764678 -1.233190275 -0.247098643 VQVEYKGETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 156.71 9.54E-06 2228320000 5597900 4898750 2103600 2360370 4360080 3439840 7088100 8045300 703900 FALSE TRUE 4858123.332 4866569.789 3120907.996 2896328.084 4273322.938 3572172.871 6400697.153 6324875.204 620685.7439 7.827025801 7.840634067 5.028161234 4.666335763 6.884841452 5.755203669 10.31229929 10.19014093 1 19.24350348 4.388496067 22.52086116 6.754318999 7.837346031 0.03154049 2.706599979 43.32573419 10983.10618 0.707259028 1.871232293 24462.23121 -4.388496067 1.083027032 VQVNHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VQVNHEK 7 0 P19367-4;P19367-2;P19367;P19367-3;B1AR62 P19367-4 HK1 Hexokinase-1 0 ;;; 113.7 0.0060711 1930870000 3278200 2582600 1752910 2434320 2102200 2353520 2524790 3262990 3144270 FALSE TRUE 2844977.564 2565634.731 2600623.139 2987069.562 2060370.333 2444061.437 2279936.254 2565224.981 2772557.983 1.026120132 0.925367385 0.937986926 1.077369556 0.743129754 0.881518602 0.822322299 0.925219598 1 21.4027862 3.252315359 24.9997871 0.877231063 0.983134697 0.356792341 0.077813901 295.7347446 537506.6712 0.022485703 0.028871818 1787.785289 -3.252315359 0.105903634 VQYAPERPGPQPTAETTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VQYAPERPGPQPTAETTR 18 1 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 109.77 0.00032179 388330000 91059 111980 54257 54365 104810 182750 66880 80929 64439 FALSE TRUE 79025.32244 111244.396 80495.86668 66709.40417 102724.4861 189780.5108 60393.98789 63622.96314 56821.09483 1.390774371 1.957800995 1.416654623 1.174025322 1.807858268 3.339965753 1.062879694 1.119706745 1 15.79413901 5.029402851 14.95373098 1.591687415 0.837889934 0.00923298 0.690798379 3453690.852 51118695.14 0.176134582 63836779.34 107004.6993 -5.029402851 -0.753797481 VRDALTAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VRDALTAEK 9 1 Q9HB71;B2ZWH1;Q9HB71-2 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 129.89 0.00034347 1530730000 1098380 1107240 603200 774860 1103500 936130 1354210 1588940 814160 FALSE TRUE 953226.3001 1099966.468 894909.5376 950803.806 1081542.509 972143.5269 1222878.923 1249157.546 717910.9323 1.327777942 1.53217679 1.246546747 1.324403576 1.506513497 1.354128323 1.703385291 1.739989586 1 19.45344534 2.277115107 24.99182543 1.544316409 1.385649065 0.017676205 0.216895529 361.5502919 234363.0141 0.079802114 0.061813296 189.2845238 -2.277115107 -0.158667344 VRDLLAEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VRDLLAEQR 9 1 Q8WUY1 Q8WUY1 THEM6 Protein THEM6 0 100.48 0.004226 319940000 217480 212300 120220 154950 266490 253840 195950 289520 167720 FALSE TRUE 188739.467 210905.3873 178358.7941 190133.7658 261187.3704 263605.3891 176946.7992 227608.401 147892.3327 1.276195078 1.426073844 1.206004334 1.285622874 1.76606431 1.782414168 1.196456882 1.539014207 1 17.17418773 1.230330311 24.91254737 0.999999154 1.437591353 0.296655791 0.210327291 407.9259615 1234659.237 0.579968963 0.052829545 16.99535774 -1.230330311 0.437592199 VRDVFEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VRDVFEAK 8 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ;;; 132.01 0.00089427 1984400000 2035460 1769460 1279860 1417310 1916690 1635890 2297290 2581220 1431400 FALSE TRUE 1766468.804 1757836.301 1898804.577 1739131.898 1878551.619 1698823.747 2074499.169 2029246.19 1262181.523 1.399536257 1.392696905 1.50438312 1.377877798 1.488337125 1.345942494 1.643582268 1.60772928 1 20.26748798 VREAAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VREAAEK 7 1 P38646;H0YBG6;A0A3B3ITN1 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 86.67 0.018154 420550000 667250 621930 388190 469580 454010 576210 702260 825360 592720 FALSE TRUE 579071.2219 617844.5009 575919.9824 576205.3161 444976.0893 598377.1716 634154.9333 648863.187 522649.3168 1.107953657 1.182139689 1.1019243 1.102470237 0.851385575 1.144892287 1.213346909 1.241488635 1 18.99548374 1.140779829 20.5239366 0.99984867 1.121933291 0.108646062 0.105920582 60200.12508 12595867.04 1089.807756 0.028090823 13.82865141 -1.140779829 0.122084622 VREEEIEVDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VREEEIEVDSR 11 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 ;;;;; 177.16 7.39E-06 2928110000 5344650 5057190 3070670 3820340 4982470 4650820 4660340 5654120 4660990 FALSE TRUE 4638340.961 5023968.986 4555656.283 4687806.587 4883328.595 4829740.055 4208380.944 4445030.438 4109973.072 1.128557506 1.222384891 1.108439448 1.140593017 1.188165594 1.175126934 1.023943678 1.081523008 1 21.97069751 2.240526802 24.99997794 1.044348273 1.161335697 0.710545967 0.037571877 27.68103848 351971.1031 0.013988096 0.010276464 173.9910073 -2.240526802 0.116987424 VREEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VREEFK 6 1 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;; 78.616 0.063217 10182200000 11002800 9393300 6095300 6989500 7823500 7063600 10372500 11462300 9930700 FALSE TRUE 9548752.102 9331594.794 9043007.468 8576572.803 7667827.656 7335341.263 9366576.546 9011176.345 8756703.959 1.090450488 1.06565151 1.032695351 0.979429343 0.875652265 0.837682911 1.069646364 1.029060293 1 23.06195651 3.966002005 2.428896081 0.969456755 1.079069491 0.332723188 0.067495316 0.419245844 4.881334167 0.02154505 0.049965781 9247.024435 -3.966002005 0.109612736 VREEILAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VREEILAK 8 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 109.29 0.0033258 445500000 673130 556560 362340 456020 539270 518310 683070 679870 645130 FALSE TRUE 584174.165 552903.9207 537568.836 559566.3108 528539.5821 538249.7211 616825.9765 534485.0913 568863.4663 1.02691454 0.971944857 0.944987449 0.983656613 0.929115004 0.946184371 1.084312868 0.939566562 1 19.11772291 VREELIDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VREELIDK 8 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 58.592 0.094824 321760000 180680 155880 140440 147150 149330 196750 199400 190180 210740 FALSE TRUE 156802.6802 154856.014 208357.2537 180562.6565 146358.6252 204319.0998 180062.2187 149511.487 185826.5573 0.843812007 0.833336291 1.121245837 0.971673044 0.787608764 1.099515068 0.968980007 0.804575456 1 17.50359717 SPLS(ph)PTETFSWPDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SPLSPTETFSWPDVR 15 0 A1L390-3;A1L390;A1L390-2;G3V311 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 SPLS(0.999)PT(0.001)ETFSWPDVR;S(0.004)PLS(0.987)PT(0.009)ETFSWPDVR 192.65 1.32E-07 91224000 104032 77507 34420 36843 50894 43833 37128 44055 43896 TRUE FALSE 90283.90762 76997.85141 51065.62713 45208.76626 49881.30897 45519.28387 33527.33227 34634.18109 38706.66489 2.332515805 1.989265974 1.31929804 1.167984025 1.288700773 1.176006355 0.866190161 0.89478598 1 15.24029438 6.708151824 0.439681805 0.901805419 10.82027366 0.932083974 0.122986947 7.161948975 0.277914186 0.106174329 52.98231066 5106834.976 -6.708151824 9.918468244 up VRELELELDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VRELELELDR 10 1 O94992 O94992 HEXIM1 Protein HEXIM1 0 ;;; 208.74 9.86E-08 542010000 568980 579080 290313 375172 585590 532540 572860 691090 303425 FALSE TRUE 493787.8514 575275.9854 430709.3378 460360.5367 573937.9047 553027.1584 517304.1254 543305.7816 267554.4422 1.845560281 2.150126833 1.609800736 1.720623784 2.14512568 2.066970572 1.933453697 2.030636371 1 18.02947296 1.23528357 24.99786569 0.999998696 1.942052429 0.738474569 0.17537009 48.87120598 372734.7228 0.30413343 0.043451864 17.1903045 -1.23528357 0.942053734 VREYELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VREYELR 7 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ;;;; 153.04 0.0016173 5356000000 5021440 4557280 2520646 3238388 4505660 4385420 4559660 5363780 3262445 FALSE TRUE 4357843.981 4527342.928 3739638.837 3973713.491 4416006.181 4554129.945 4117464.875 4216777.388 2876762.469 1.514843171 1.573763207 1.299947033 1.381314424 1.535061107 1.583074722 1.431284272 1.465806591 1 21.45601467 1.237619707 7.154703036 0.990566109 1.471706224 0.745286048 0.08692866 0.058063537 18.15138361 0.134668667 0.022297061 17.28302296 -1.237619707 0.481140115 VRGEVAPDAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VRGEVAPDAK 10 1 P09382;F8WEI7 P09382 LGALS1 Galectin-1 0 ;;;;; 140.78 3.53E-05 9827120000 14127100 12110780 8898730 11233150 12073600 10981500 14414110 17607300 12976320 FALSE TRUE 12260167.94 12031223.49 13202185.59 13783808.4 11833358.98 11403965.41 13016231.83 13842115.92 11442274.23 1.071479995 1.051471346 1.153807829 1.204638878 1.034178935 0.996651992 1.13755636 1.209734676 1 23.44787049 4.261856765 24.97180932 1.113423117 1.061475629 0.045331091 0.076586689 713.2725801 764563.2853 0.020047215 0.052970255 18274.9739 -4.261856765 -0.051947488 VRGGAPDPSPGATATPGAPAQPS(ph)SPDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VRGGAPDPSPGATATPGAPAQPSSPDAR 28 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 VRGGAPDPSPGATATPGAPAQPS(0.634)S(0.366)PDAR;VRGGAPDPSPGATATPGAPAQPS(0.5)S(0.5)PDAR;VRGGAPDPSPGATATPGAPAQPS(0.906)S(0.094)PDAR;VRGGAPDPSPGATATPGAPAQPS(0.707)S(0.293)PDAR 202.58 2.27E-25 2230460000 1026447 866352 437085 419938 1343340 1564680 1171030 1203900 103092 TRUE FALSE 890799.4283 860660.8767 648460.768 515291.3413 1316610.162 1624874.252 1057463.691 946455.3538 90904.5812 9.799279822 9.467739307 7.133422314 5.668485949 14.48343026 17.87450347 11.63267766 10.41152537 1 16.47206538 -1.966772436 24.57109637 9.868679546 10.01440544 0 4.634670567 0 0 0 1.072749695 0.010795122 1.966772436 0.145725891 VRLDDDDEGVPSSALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VRLDDDDEGVPSSALR 16 1 Q00535;Q00535-2 Q00535 CDK5 Cyclin-dependent-like kinase 5 0 ;; 245.71 3.51E-20 495850000 762280 663340 391880 460630 674300 735160 708160 718650 380895 FALSE TRUE 661542.7666 658982.4759 581394.4788 565223.0818 660882.7492 763442.0809 639482.7522 564972.29 335866.027 1.969662643 1.962039691 1.731030923 1.682882567 1.967697522 2.273055384 1.90398165 1.682135865 1 18.35752635 1.232989341 2.231049939 0.725457175 1.924668687 0.773151776 0.157969292 0.339215276 1.703490154 0.82411819 0.046282219 17.09973348 -1.232989341 1.199211512 VRPAS(ph)TGGLSLLPPPPGGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VRPASTGGLSLLPPPPGGK 19 1 Q9NVZ3;Q9NVZ3-2;D6RB24;Q9NVZ3-4 Q9NVZ3 NECAP2 Adaptin ear-binding coat-associated protein 2 1 VRPAS(0.487)T(0.487)GGLS(0.026)LLPPPPGGK;VRPAS(0.492)T(0.492)GGLS(0.017)LLPPPPGGK 105.67 0.00019926 1320050000 590550 627330 438340 536590 690210 646220 761090 878190 795280 TRUE FALSE 512507.3212 623209.0279 650322.6902 658430.9608 676476.1714 671080.5016 687279.6089 690395.9026 701262.9044 0.730834781 0.888695273 0.92735932 0.938921703 0.964654151 0.956959932 0.980059839 0.984503669 1 19.41959589 5.655845805 0.749752053 0.97839935 9.88E-16 0.96675455 0.014092503 1.598441842 0.249542156 0.005591797 1.806841484 452736.808 -5.655845805 -0.97839935 VRPCVVYGGADIGQQIR ddPTM_MDA-MB-175_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 ; 183.31 6.37E-10 3693900000 1230320 1119660 870090 1006570 1154510 1380890 1046170 1344290 1467650 FALSE TRUE 1067730.095 1112304.88 1290868.434 1235127.103 1131537.51 1434013.732 944712.5944 1056824.045 1294146.089 0.825046031 0.859489426 0.997467323 0.954395422 0.874350678 1.108077167 0.729989143 0.816618814 1 20.30356905 1.204625132 23.82726126 1.000001411 0.894062323 0.088514356 0.105092353 7910.725252 5553796.509 4.305506088 0.026263081 16.01862121 -1.204625132 -0.105939088 VRPEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VRPEEK 6 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WT54;K7ERA4 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 0 ; 106.42 0.029313 358350000 754510 711170 418880 512470 542700 689780 730670 789170 793280 FALSE TRUE 654799.5918 706498.2774 621451.7691 628834.1461 531901.3318 716316.2829 659809.7359 620412.1368 699499.3421 0.936097509 1.010005635 0.888423665 0.898977466 0.760402905 1.024041396 0.943259981 0.886937413 1 19.41596317 1.224702644 24.81885881 1.000000225 0.917862035 0.110012716 0.072812579 1595.969803 2858107.481 0.347523436 0.017644488 16.77654955 -1.224702644 -0.08213819 VRPGETLLIHSGSGGVGQAAIAIALSLGCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VRPGETLLIHSGSGGVGQAAIAIALSLGCR 30 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 179.49 4.57E-18 2315457000 1042412 1264277 631398 871204 1264001 1322658 1431867 1461698 1554291 FALSE TRUE 904654.6131 1255971.881 936744.1847 1069024.184 1238849.853 1373541.509 1293004.759 1149125.258 1370544.489 0.660069498 0.916403584 0.683483238 0.779999622 0.903910718 1.002186737 0.943424142 0.838444332 1 20.38631773 3.219100531 4.248516836 0.930973232 0.763848809 0.544229503 0.081095729 0.171071117 7.045782174 0.023919168 0.028860576 1656.153288 -3.219100531 -0.167124422 VRPSSDLNNSTGQS(ph)PHHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VRPSSDLNNSTGQSPHHK 18 1 J3KNR0;P27448-8;P27448-3;P27448-4;P27448-2;P27448 J3KNR0 MARK3 MAP/microtubule affinity-regulating kinase 3 1 VRPSSDLNNS(0.003)T(0.006)GQS(0.992)PHHK;VRPSSDLNNST(0.001)GQS(0.999)PHHK;VRPSSDLNNS(0.008)T(0.044)GQS(0.948)PHHK;VRPSSDLNNSTGQS(1)PHHK 185.41 3.22E-14 338912000 372118 307563 163227 234526 265189 234039 315712 341681 311103 TRUE FALSE 322941.6635 305542.5984 242164.1232 287778.7128 259912.2577 243042.6318 285094.2988 268615.1771 274324.7577 1.177223908 1.113798845 0.882764374 1.049043897 0.947461906 0.885966815 1.039258364 0.979186783 1 18.06552531 4.399277923 6.011934085 0.973248446 1.162276472 0.643359924 0.055462286 0.107157014 6.201281631 0.013237639 0.036354655 25077.13529 -4.399277923 0.189028026 VRS(ph)PDEALPGGLSGCSS(ph)GSGHSPYALER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VRSPDEALPGGLSGCSSGSGHSPYALER 28 1 Q5JSZ5-5 Q5JSZ5-5 PRRC2B Protein PRRC2B 2 VRS(0.923)PDEALPGGLS(0.218)GCS(0.143)S(0.377)GS(0.298)GHS(0.04)PYALER 55.336 0.038034 115950000 52590 65825 42577 41440 70411 75474 58330 62956 72950 TRUE FALSE 45640.09825 65392.59124 63167.37961 50849.58537 69009.95886 78377.53362 52673.16558 49493.34932 64325.9341 0.709513183 1.01658207 0.981989309 0.790498981 1.07281705 1.218443769 0.818848048 0.769415167 1 15.97311288 VRS(ph)PDEALPGGLSGCSSGS(ph)GHSPYALER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VRSPDEALPGGLSGCSSGSGHSPYALER 28 1 Q5JSZ5-5 Q5JSZ5-5 PRRC2B Protein PRRC2B 2 VRS(0.984)PDEALPGGLS(0.016)GCS(0.072)S(0.206)GS(0.427)GHS(0.296)PYALER 95.454 0.0012492 160960000 132640 141570 64987 101360 144040 152890 139080 156940 161790 TRUE FALSE 115111.2879 140640.0173 96414.93057 124375.3372 141173.8858 158771.7772 125592.043 123379.6023 142663.3705 0.806873464 0.98581729 0.675821202 0.871809889 0.989559445 1.112912002 0.880338398 0.864830277 1 17.12225544 3.403805958 5.822847177 0.955966852 0.828941253 0.311092795 0.100215048 0.289300084 17.08093236 0.030043434 0.03908656 2533.996191 -3.403805958 -0.127025599 VRS(ph)PGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VRSPGPK 7 1 Q5VT06 Q5VT06 CEP350 Centrosome-associated protein 350 1 VRS(1)PGPK 53.683 0.0837 91798000 345020 303440 244140 293220 246350 306410 317070 317270 425780 TRUE FALSE 299424.7328 301446.6827 362206.9206 359800.0826 241448.117 318197.791 286320.6002 249424.2795 375444.7735 0.797520046 0.802905524 0.964740879 0.958330247 0.64309889 0.847522228 0.762617089 0.664343459 1 18.51824118 3.255459156 24.99957657 0.770252536 0.881295436 0.152392069 0.111683304 413.6189133 611901.1878 0.031748384 0.04087766 1800.773769 -3.255459156 0.1110429 VRSPDEALPGGLS(ph)GCSSGSGHSPYALER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VRSPDEALPGGLSGCSSGSGHSPYALER 28 1 Q5JSZ5-5 Q5JSZ5-5 PRRC2B Protein PRRC2B 1 VRS(0.002)PDEALPGGLS(0.779)GCS(0.107)S(0.072)GS(0.034)GHS(0.006)PYALER 147.8 4.69E-08 210450000 66422 48561 34232 42356 54603 60069 58969 59378 52298 TRUE FALSE 57644.16441 48241.99959 50786.7097 51973.57717 53516.50713 62379.8933 53250.19546 46680.47678 46115.39002 1.249998415 1.046114965 1.101296328 1.127033234 1.160491261 1.352691439 1.154716363 1.012253757 1 15.49296068 1.730135306 4.636016211 1.003797206 1.1684736 0.404872273 0.082940749 0.17688688 8.976756094 0.055582608 0.022978179 53.71991369 -1.730135306 0.164676394 VRTELADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VRTELADK 8 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;; 154.01 0.00039386 7219310000 7162580 6261550 4697440 5325270 6274130 5465620 7609140 8478380 7192950 FALSE TRUE 6216026.905 6220417.466 6969137.696 6534453.945 6149287.088 5675885.938 6871206.774 6665344.416 6342607.645 0.980042792 0.980735025 1.098781146 1.030247228 0.969520335 0.894882083 1.083340979 1.050883925 1 22.59664467 VRVDSTAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VRVDSTAK 8 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;; 93.098 0.010314 1897560000 2035900 1838840 1197910 1471480 1501160 1643040 2252200 2524630 1860170 FALSE TRUE 1766850.657 1826760.539 1777223.283 1805602.024 1471289.853 1706248.812 2033781.991 1984757.521 1640262.822 1.077175336 1.113699899 1.083499095 1.100800433 0.896984211 1.040228913 1.239912265 1.210024086 1 20.64549557 2.259786311 24.95834365 1.166235458 1.05146121 0.215355102 0.086258605 304.135865 357618.8623 0.03315777 0.025659121 181.8805717 -2.259786311 -0.114774248 VRVELSNGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VRVELSNGEK 10 1 P84103;P84103-2 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;;;; 174.42 2.84E-06 7412510000 4602940 3735280 2595070 3296080 3754210 3148500 4909000 5645980 4606260 FALSE TRUE 3994649.817 3710742.7 3850054.532 4044505.341 3679508.566 3269624.832 4432925.936 4438631.114 4061713.19 0.983488895 0.913590528 0.947889315 0.995763401 0.905900637 0.804986635 1.091393146 1.092797769 1 21.95365694 2.207377306 24.99998295 1.069188747 0.92809094 0.553298978 0.057479816 143.0834979 114710.5407 0.023738964 0.016006576 161.2045538 -2.207377306 -0.141097808 VRVELSNGEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VRVELSNGEKR 11 2 P84103;P84103-2 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 107.97 0.0011959 451600000 480510 291030 272480 241160 225980 241500 281190 341060 87118 FALSE TRUE 417009.386 289118.2048 404252.2394 295919.0639 221483.4401 250790.6613 253920.2371 268126.9731 76819.00929 5.428466078 3.763628397 5.262398502 3.852159337 2.883185323 3.264695335 3.305434937 3.490372704 1 16.22917574 2.851528466 0.166592931 7.63E-13 7.119460326 0.626081731 0.753887294 5.838097302 1.29048983 27.6019082 24.77388123 710.4417351 -2.851528466 7.119460326 VRVELSTGMPR ddPTM_MDA-MB-175_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 ; 162.93 2.24E-05 1620740000 994470 865540 554350 517060 806510 865980 801650 908090 582040 FALSE TRUE 863048.2698 859854.2107 822435.5142 634466.3758 790462.0289 899294.811 723906.1064 713902.0203 513231.8943 1.681595161 1.675371738 1.602463766 1.236217747 1.540165445 1.752219262 1.410485425 1.390993093 1 18.9692513 0.896979167 1.194156847 0.254458251 1.566336822 0.604239995 0.144374173 2.367200015 1.605593024 4.749486143 0.046439136 7.888222768 -0.896979167 1.31187857 VRYDS(ph)SNQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VRYDSSNQVK 10 1 O95983-2;O95983;K7EIE8;A0A087WZ12;A0A087WT34;A0A087X1H1;A0A0A0MTS6 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 1 VRYDS(0.943)S(0.057)NQVK;VRYDS(0.998)S(0.002)NQVK;VRYDS(0.901)S(0.099)NQVK;VRYDS(0.751)S(0.249)NQVK 181.88 1.11E-06 1807800000 1026470 917980 849580 1063500 1253660 1314860 1733910 1761860 1799900 TRUE FALSE 890819.3888 911949.7289 1260439.73 1304983.93 1228714.619 1365443.515 1565755.675 1385099.95 1587117.872 0.561281178 0.574594833 0.794168947 0.822235041 0.774179814 0.860328989 0.986540258 0.872713977 1 20.59797785 5.273662698 0.349776505 0.9769151 4.57E-13 0.851801946 0.056297667 4.637274976 0.393013061 0.096919044 2.058094443 187785.7781 -5.273662698 -0.9769151 VS(ph)LDVNHFAPDELTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VSLDVNHFAPDELTVK 16 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 VS(1)LDVNHFAPDELTVK;VS(1)LDVNHFAPDELTVK;VS(1)LDVNHFAPDELTVK;VS(1)LDVNHFAPDELTVK;VS(1)LDVNHFAPDELTVK;VS(1)LDVNHFAPDELTVK 255.24 1.39E-26 1374555000 1838106 1567938 1317598 1767466 1706403 1264456 2223241 2419822 3371064 TRUE FALSE 1595195.635 1557638.112 1954792.8 2168796.169 1672448.919 1313100.441 2007631.43 1902361.896 2972540.654 0.536643841 0.524009019 0.657616843 0.729610263 0.562632816 0.441743476 0.675392421 0.639978428 1 21.50326511 0.944078745 1.760504123 1.522603957 0.587267541 0.704137455 0.082812467 1.343534831 1.971636096 2.77015043 0.023763287 8.791819122 -0.944078745 -0.935336416 VS(ph)LERLDLDLTADSQPPVFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSLERLDLDLTADSQPPVFK 20 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 VS(1)LERLDLDLTADSQPPVFK;VS(1)LERLDLDLTADSQPPVFK 192.99 5.45E-18 396230000 972550 599640 328431 371702 570750 458280 774600 858820 186040 TRUE FALSE 844025.0534 595700.9254 487261.3301 456102.6202 559393.1917 475910.3281 699479.4112 675168.0263 164046.5631 5.145033442 3.631291714 2.97026235 2.780324144 3.409965933 2.901068569 4.263907746 4.115709671 1 17.32374584 4.709652563 3.038349844 3.219566757 5.388673745 0.338365369 0.895927141 0.425688363 6.080149081 0.223919869 2.149780601 51245.12572 -4.709652563 2.169106988 VS(ph)PAAAQLADTLFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSPAAAQLADTLFSK 15 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 VS(1)PAAAQLADTLFSK;VS(1)PAAAQLADTLFSK 236.16 1.11E-17 643960000 570660 406240 437160 545880 508290 363360 490110 659720 1299470 TRUE FALSE 495245.8351 403571.3827 648572.0382 669830.3973 498176.0235 377338.6943 442579.2076 518644.0119 1145848.137 0.432208963 0.352203202 0.566019193 0.584571703 0.434766185 0.329309515 0.386245955 0.452628926 1 20.12798442 1.238956394 7.372588817 1.00966073 0.441155155 0.822454645 0.081458957 0.044528489 16.40404858 0.126931082 0.021675969 17.33629921 -1.238956394 -0.568505575 VS(ph)PAHS(ph)PPENGLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VSPAHSPPENGLDK 14 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 2 VS(1)PAHS(1)PPENGLDK;VS(1)PAHS(1)PPENGLDK;VS(1)PAHS(1)PPENGLDK;VS(1)PAHS(1)PPENGLDK 242.59 9.08E-18 2643020000 2571380 1445740 1461860 1539570 1445510 1423720 1786940 2117930 2937840 TRUE FALSE 2231565.618 1436242.839 2168820.386 1889152.899 1416747.179 1478491.43 1613642.834 1665027.151 2590531.902 0.861431437 0.554420055 0.837210452 0.729252899 0.546894318 0.570728903 0.622900198 0.642735629 1 21.30481692 1.236405673 24.97061227 1.000000439 0.663552548 0.466313789 0.11047921 50.27622281 582434.0309 0.168780104 0.02626482 17.2347772 -1.236405673 -0.336447891 VS(ph)PCHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSPCHSR 7 0 A0A1B0GWK2;Q674X7-4;Q674X7-3;Q674X7-2;Q674X7;Q674X7-5 A0A1B0GWK2 KAZN Kazrin 1 VS(1)PCHSR;VS(1)PCHSR 91.265 0.010648 312670000 200740 187263 179049 188158 159172 202398 193017 210585 263930 TRUE FALSE 174211.7004 186032.857 265637.6953 230882.1497 156004.7886 210184.382 174298.241 165553.0365 232728.4961 0.748561965 0.799355731 1.141405972 0.992066522 0.670329552 0.903131269 0.748933818 0.711356965 1 17.82828834 3.25570706 24.99870605 0.795308928 0.927495156 0.136010158 0.140121646 449.9262774 655967.3266 0.041100756 0.052926442 1801.801981 -3.25570706 0.132186227 VS(ph)PENLVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSPENLVDK 9 0 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 VS(1)PENLVDK;VS(1)PENLVDK 200.67 2.38E-05 901650000 1426970 985850 825100 939880 1061710 843470 1305440 1418400 1473240 TRUE FALSE 1238392.299 979373.8864 1224121.12 1153294.119 1040584.048 875918.8367 1178838.63 1115086.198 1299075.246 0.953287582 0.753900815 0.942301937 0.887780845 0.801019072 0.674263358 0.907444456 0.858369214 1 20.30905357 0.984823089 1.743428528 1.169787289 0.83964963 0.236171397 0.086013181 2.992480825 4.776759446 2.07558479 0.023413488 9.656574361 -0.984823089 -0.330137659 VS(ph)PGLPSPNLENGAPAVGPVQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSPGLPSPNLENGAPAVGPVQPR 23 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 VS(1)PGLPSPNLENGAPAVGPVQPR 309.54 4.10E-73 921200000 121890 110030 66364 86911 137960 90240 109160 138980 87056 TRUE FALSE 105781.9277 109307.2057 98457.85237 106645.4709 135214.8659 93711.59119 98573.68 109260.2085 76764.33885 1.378008711 1.423932093 1.282598845 1.389257987 1.761428131 1.22076986 1.284107718 1.423319867 1 16.22814864 1.236032693 24.98727366 0.999999477 1.394668703 0.420522001 0.145876949 69.63713 688180.3824 0.233216954 0.035227927 17.21998197 -1.236032693 0.394669226 VS(ph)PGQAAPAMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSPGQAAPAMAR 12 0 Q96HA7-2;Q96HA7 Q96HA7-2 TONSL Tonsoku-like protein 1 VS(1)PGQAAPAMAR;VS(1)PGQAAPAMAR 146.59 6.80E-05 185983000 155562 159129 85237 130205 156916 134803 162537 194443 186581 TRUE FALSE 135004.0876 158083.6711 126457.8983 159770.0353 153793.6786 139988.9586 146774.1868 152862.8776 164523.6067 0.820575784 0.960857072 0.76863072 0.971107056 0.934781833 0.850874603 0.892116272 0.92912428 1 17.32793508 1.30720849 1.988465355 1.025748021 0.887696885 0.259949292 0.062015693 0.919993253 4.079221996 0.225133502 0.015849292 20.28656377 -1.30720849 -0.138051136 VS(ph)PHHPAPTPNPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSPHHPAPTPNPR 13 0 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 VS(1)PHHPAPTPNPR 75.445 0.020206 248950000 183850 152750 145680 151970 160150 150160 170250 190200 249010 TRUE FALSE 159553.7567 151746.5752 216131.3353 186477.1112 156963.3283 155936.7524 153739.1812 149527.2101 219572.3215 0.726656965 0.691100655 0.984328689 0.849274216 0.714859356 0.710184013 0.700175597 0.680992983 1 17.74433668 3.236799829 24.99865057 0.744078284 0.816393638 0.033575157 0.118528018 132.5830047 1882339.177 0.035647728 0.042547494 1725.042617 -3.236799829 0.072315354 VS(ph)PLLSEGELPVFSQL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSPLLSEGELPVFSQL 16 0 Q96IQ9-2 Q96IQ9-2 ZNF414 Zinc finger protein 414 1 VS(0.85)PLLS(0.15)EGELPVFSQL;VS(0.987)PLLS(0.013)EGELPVFSQL 75.695 0.030188 57007000 50850 50480 40381 50550 62570 49118 59497 74300 84037 TRUE FALSE 44130.04366 50148.39356 59909.38667 62028.15011 61324.97942 51007.60124 53726.9901 58411.5232 74102.2416 0.595529133 0.676745973 0.80846929 0.837061724 0.827572528 0.688340867 0.725038662 0.78825582 1 16.17722956 4.402446261 3.020893987 0.801594546 0.604068467 0.450210049 0.082092278 0.253407218 4.415368466 0.021675243 0.082247392 25260.75115 -4.402446261 -0.197526079 VS(ph)PPAS(ph)PTLEVELGSAELPLQGAVGPELPPGGGHGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSPPASPTLEVELGSAELPLQGAVGPELPPGGGHGR 36 0 Q7Z6J0 Q7Z6J0 SH3RF1 E3 ubiquitin-protein ligase SH3RF1 2 VS(1)PPAS(0.955)PT(0.045)LEVELGSAELPLQGAVGPELPPGGGHGR;VS(0.85)PPAS(0.702)PT(0.237)LEVELGS(0.211)AELPLQGAVGPELPPGGGHGR 137.53 1.41E-09 98550000 22390.2 21689.3 16699.8 18422 25463.9 23059.9 20684.2 29619.2 25696.9 TRUE FALSE 19431.27834 21546.82156 24775.87914 22604.99666 24957.21821 23947.02927 18678.24947 23285.36458 22659.04176 0.857550754 0.95091495 1.093421311 0.997614855 1.101424256 1.0568421 0.824317712 1.027641187 1 14.46779923 4.577692066 3.841875282 1.010161587 0.86192333 0.299467871 0.07674839 0.316456397 7.762665355 0.01934888 0.095000852 37817.43473 -4.577692066 -0.148238257 VS(ph)PQPMISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VSPQPMISR 9 0 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 VS(1)PQPMISR;VS(1)PQPMISR;VS(1)PQPMISR;VS(1)PQPMISR 178.49 5.34E-05 1298840000 749080 624590 570040 560070 627120 708490 636830 659620 875910 TRUE FALSE 650087.1801 620487.0272 845713.2507 687242.4536 614641.5389 735746.0688 575070.3246 518565.3962 772360.9176 0.841688342 0.803364092 1.094971575 0.889794444 0.795795754 0.952593602 0.744561657 0.671402947 1 19.55891564 2.231012583 24.99874098 0.774890152 0.896297697 0.098220466 0.118652711 291.6610834 965958.0579 0.047595111 0.032791592 170.2207828 -2.231012583 0.121407545 VS(ph)PSDTTPLVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VSPSDTTPLVSR 12 0 Q9HCK8-2;Q9HCK8;H0YJG4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 VS(0.996)PS(0.004)DTTPLVSR;VS(0.968)PS(0.032)DTTPLVSR;VS(0.901)PS(0.098)DT(0.001)TPLVSR;VS(0.951)PS(0.049)DTTPLVSR 197.79 2.00E-07 2360260000 2006220 1593950 1504480 1501000 1429180 1579690 1481370 1683030 1803450 TRUE FALSE 1741092.944 1583479.237 2232051.56 1841824.991 1400742.114 1640461.696 1337706.965 1323127.132 1590248.195 1.094856104 0.995743458 1.403586916 1.158199705 0.880832387 1.031575889 0.841193827 0.832025551 1 20.60082052 3.243495783 24.21768277 0.906515657 1.168320733 0.51598561 0.11808063 65.66977676 322249.2325 0.035116706 0.043865657 1751.845423 -3.243495783 0.261805076 VS(ph)PSPSQESLSSSK ddPTM_MDA-MB-175_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(0.688)PS(0.312)PSQESLSSSK;VS(1)PSPSQESLSSSK 323.28 2.17E-56 737461000 451541 312274 314386 389798 311402 241384 354647 421482 918635 TRUE FALSE 391868.7128 310222.6515 466424.1212 478307.5936 305205.7094 250670.1987 320253.3885 331351.3543 810035.0168 0.483767621 0.382974372 0.575807356 0.590477675 0.376780884 0.309456003 0.395357462 0.409058062 1 19.62762475 1.236775224 24.99543516 1.000000704 0.437911155 0.798319175 0.088376566 21.93224732 306959.8781 0.145597058 0.023283488 17.24944887 -1.236775224 -0.56208955 VS(ph)PSTSYTPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSPSTSYTPSR 11 0 Q9BTE3;Q9BTE3-2 Q9BTE3 MCMBP Mini-chromosome maintenance complex-binding protein 1 VS(0.961)PS(0.039)TSYTPSR 162.93 2.58E-05 310930000 193090 199020 130890 151640 196930 213900 186550 214700 266800 TRUE FALSE 167572.6673 197712.6245 194188.8418 186072.1797 193011.4783 222128.8714 168458.4097 168788.0758 235259.2079 0.712289516 0.840403342 0.825425043 0.79092411 0.820420505 0.944187789 0.71605448 0.717455768 1 17.84389166 4.745972891 23.59478067 0.819165366 0.712289402 0.139230548 0.088567519 929.0203349 2957094.014 0.021565576 0.210444444 55715.09696 -4.745972891 -0.106875964 VS(ph)SGVYEPVVIESH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSSGVYEPVVIESH 14 0 Q5T9C2-3;Q5T9C2 Q5T9C2-3 FAM102A Protein FAM102A 1 VS(0.953)S(0.047)GVYEPVVIESH 129.54 0.00013409 0 117560 95806 99048 115500 112660 136810 119150 132050 235050 TRUE FALSE 102024.1481 95176.64408 146947.9441 141726.0403 110418.2864 142073.1692 107594.8513 103812.1351 207262.6568 0.492245683 0.459207874 0.708993826 0.683799207 0.532745687 0.685474033 0.519123189 0.500872356 1 17.66110068 1.232599357 24.99965299 1.000000694 0.573362476 0.69076332 0.089826272 120.3658129 504724.9706 0.201809245 0.022820951 17.08438529 -1.232599357 -0.426638217 VS(ph)SSPQKEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSSSPQKEGR 10 1 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 VS(0.393)S(0.303)S(0.303)PQKEGR 67.519 0.03799 163240000 325330 257530 141630 147910 236740 220910 273990 320290 88376 TRUE FALSE 282336.8162 255838.2685 210122.7417 181495.2262 232029.3372 229408.5506 247418.492 251798.476 77928.28996 3.623033642 3.282996055 2.696360229 2.329003065 2.97747246 2.943841714 3.17495087 3.231156184 1 16.24985954 4.383348418 3.269742036 2.718781917 3.573090331 0.222301123 0.641442872 0.399309087 8.121284392 0.161984583 0.560611094 24173.99445 -4.383348418 0.854308414 VS(ph)SSSELDLPSGDHCEAGLLQLDVPLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSSSSELDLPSGDHCEAGLLQLDVPLLR 28 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VS(0.249)S(0.249)S(0.249)S(0.249)ELDLPS(0.005)GDHCEAGLLQLDVPLLR 48.388 0.068372 14082000 30204 23091 12375 19660 25077 23377 22188 26316 31767 TRUE FALSE 26212.46487 22939.3137 18359.59139 24124.10348 24578.01676 24276.32832 20036.21118 20688.52819 28011.54145 0.935773739 0.818923648 0.655429528 0.861220134 0.877424643 0.866654495 0.715284134 0.738571572 1 14.77373376 1.137431776 0.00221773 0.121152405 1.506281327 0 0.104652553 4422276.845 2701.241994 850950.6488 836227.3686 13.72245376 -1.137431776 1.385128922 VS(ph)VS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSVSPGR 7 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 VS(1)VS(1)PGR 80.165 0.044811 334170000 819670 717820 583670 689460 753240 739340 708290 839960 1290900 TRUE FALSE 711348.5327 713104.5932 865934.7643 846012.4307 738251.9977 767782.8882 639600.1448 660341.0906 1138291.273 0.624926633 0.62646935 0.760732147 0.743230183 0.64856159 0.674504766 0.561894974 0.580116097 1 20.11843834 1.231420602 24.99960399 1.000000606 0.650869429 0.752132854 0.062676592 143.4010919 502051.1239 0.171382039 0.017361187 17.03807801 -1.231420602 -0.349131177 VSAGEPGSHPS(ph)PAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VSAGEPGSHPSPAPR 15 0 A0A1B0GV68;C9JME2;Q9Y4F1;Q9Y4F1-2 A0A1B0GV68;C9JME2 FARP1 "FERM, RhoGEF and pleckstrin domain-containing protein 1" 1 VSAGEPGS(0.013)HPS(0.987)PAPR;VSAGEPGS(0.001)HPS(0.999)PAPR;VSAGEPGS(0.001)HPS(0.999)PAPR;VSAGEPGSHPS(1)PAPR;VSAGEPGSHPS(1)PAPR;VSAGEPGS(0.001)HPS(0.999)PAPR 228.9 5.61E-13 5006380000 3958490 3862780 2357666 5007550 5431620 5969770 2622083 5942010 4570730 TRUE FALSE 3435365.517 3837405.144 3497841.164 6144590.763 5323541.389 6199430.915 2367793.794 4671357.402 4030383.506 0.852366905 0.952119107 0.867868072 1.524567266 1.320852316 1.538173949 0.587485978 1.15903546 1 21.94248569 VSAGNGGSS(ph)LSYTNPAVAATSANL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSAGNGGSSLSYTNPAVAATSANL 24 0 P15941-2;A0A087WWM1;A0A087X2A4;A0A0C4DGW3;P15941-7;P15941-11;P15941-4;P15941-3;P15941;P15941-8;A0A0A0MRB3;B1AVQ7;A0A087X0L2;P15941-15;P15941-6;A6ZIE3;A6ZIE4;P15941-12;P15941-16;P15941-9;P15941-10 P15941-2 MUC1 Mucin-1;Mucin-1 subunit alpha;Mucin-1 subunit beta 1 VSAGNGGS(0.291)S(0.7)LS(0.007)Y(0.001)TNPAVAATSANL 195.03 2.82E-28 0 69158 47082 22086 53974 58588 37491 51854 80747 65537 TRUE FALSE 60018.59508 46772.71524 32766.86347 66229.62164 57422.21343 38933.30303 46825.20706 63479.88242 57789.29052 1.038576431 0.80936649 0.56700581 1.146053552 0.993648008 0.673711386 0.810274822 1.098471392 1 15.81851454 1.738964957 10.02613693 1.04612459 0.857928819 0.170452797 0.170694151 0.154181805 73.53988496 0.094937883 0.044199784 54.82327261 -1.738964957 -0.188195771 VSALNSVHCEHVEDEGESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSALNSVHCEHVEDEGESR 19 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4;A0A087WWN5 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 261.17 2.22E-31 657070000 366150 336610 174002 228853 393180 407750 349110 389740 396460 FALSE TRUE 317762.3498 334398.7867 258149.9492 280817.5714 385356.4872 423436.4063 315253.3659 306397.134 349590.9504 0.908954735 0.956543029 0.738434301 0.803274716 1.102306815 1.211233889 0.901777822 0.876444695 1 18.41530831 3.251327333 24.99992465 1.00151511 0.851185534 0.355505483 0.110140911 325.6361489 637660.6138 0.035977997 0.046138085 1783.722676 -3.251327333 -0.150329576 VSAQEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSAQEVR 7 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 100.45 0.022762 366090000 639240 648350 377340 510830 649570 713430 572850 715820 689410 FALSE TRUE 554762.8144 644090.9462 559822.8861 626821.759 636644.8279 740876.1138 517295.0952 562747.4635 607908.7352 0.912575823 1.05951915 0.920899559 1.031111617 1.047270406 1.218729179 0.850942033 0.925710441 1 19.21349522 VSAS(ph)LPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VSASLPR 7 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 VSAS(1)LPR;VS(0.003)AS(0.997)LPR;VS(0.007)AS(0.993)LPR;VS(0.039)AS(0.961)LPR 91.783 0.016942 1236280000 836180 1092090 582801 665377 986610 982670 920100 1033510 1118540 TRUE FALSE 725676.6944 1084915.989 864645.513 816461.0175 966978.3913 1020473.951 830868.8436 812501.9293 986307.4754 0.735750983 1.099977457 0.876649052 0.827795629 0.980402578 1.034640795 0.842403474 0.823781579 1 19.91167794 VSDEVGFGLEHVS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSDEVGFGLEHVSR 14 0 Q6VY07-2;Q6VY07 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 VSDEVGFGLEHVS(1)R;VSDEVGFGLEHVS(1)R 150.91 4.56E-06 180537000 204570 280610 193751 262130 313260 298530 264190 326040 415220 TRUE FALSE 177535.5562 278766.6544 287449.6317 321650.6229 307026.7389 310014.6423 238568.8945 256318.8832 366133.1646 0.484893403 0.761380507 0.78509586 0.878507204 0.838565769 0.846726471 0.651590507 0.700070106 1 18.48200893 4.756325914 3.054370304 0.799188123 0.427746709 0.531906408 0.095602102 0.355480943 4.810790225 0.024965547 0.326834488 57059.23096 -4.756325914 -0.371441414 VSDILHSIFSSYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSDILHSIFSSYK 13 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ; 184.21 9.70E-06 899770000 4605100 5384700 2367030 3939400 6137200 5604000 6361200 7119700 7486700 FALSE TRUE 3996524.367 5349327.551 3511733.625 4833900.98 6015081.727 5819589.506 5744291.803 5597207.561 6601630.855 0.605384405 0.810303949 0.531949408 0.732228306 0.911150875 0.881538158 0.870132234 0.847852248 1 22.65439104 3.35809211 4.276383835 0.891670733 0.6606575 0.682721384 0.079797705 0.126280255 4.086239403 0.022131851 0.028893165 2280.825764 -3.35809211 -0.231013233 VSDQNS(ph)PVLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 220.06 9.88E-12 7881030000 8350540 7085030 5260410 5620830 6703660 5790820 8595390 9437730 9043070 TRUE FALSE 7246994.981 7038487.971 7804361.871 6897125.361 6570270.281 6013596.593 7761810.401 7419544.884 7974008.566 0.908827088 0.882678757 0.978725042 0.864950834 0.823960775 0.754149753 0.973388771 0.930466129 1 22.92687372 VSDS(ph)PSHIATK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSDSPSHIATK 11 0 Q9P2D3 Q9P2D3 HEATR5B HEAT repeat-containing protein 5B 1 VS(0.083)DS(0.836)PS(0.08)HIATK;VS(0.055)DS(0.89)PS(0.055)HIATK 116.9 0.00059686 627360000 2598300 2215900 1297590 1710800 2260300 2022740 2401500 2649400 2744700 TRUE FALSE 2254928.072 2201343.607 1925108.864 2099263.288 2215324.452 2100556.117 2168602.9 2082846.428 2420224.693 0.931701953 0.909561667 0.795425677 0.867383634 0.91533834 0.867917811 0.896033706 0.860600437 1 21.20670956 1.233293403 24.99473955 1.00000019 0.878827122 0.495402311 0.037870362 145.5032367 690385.0967 0.076671825 0.009262391 17.11170966 -1.233293403 -0.121173067 VSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFR 39 0 Q5JP53;P07437;Q5ST81;P68371;M0R2D3;Q9BVA1;P04350;M0QYM7;M0R042;K7ESM5;Q9BUF5 Q5JP53;P68371;Q9BVA1;P04350;K7ESM5 TUBB;TUBB4B;TUBB4A;TUBB2B;TUBB6 Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-2B chain;Tubulin beta-4A chain;Tubulin beta-6 chain 0 242.12 1.54E-50 56330000 45514 50683 18958 30141 47514 45045 40797 50986 46259 FALSE TRUE 39499.20958 50350.06004 28126.15221 36984.97473 46568.56436 46777.9103 36840.51322 40083.04067 40790.31372 0.968347776 1.234363148 0.689530176 0.90670974 1.141657421 1.146789667 0.903168176 0.98266076 1 15.31593898 0.934568286 0.005763265 0.795207468 1.191267232 0 0.153600688 2400100.287 3305.315618 116705.6077 110510.7212 8.60138299 -0.934568286 0.396059764 VSEGIDFVHHYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSEGIDFVHHYGR 13 0 P18074;E7EVE9;A8MX75 P18074 ERCC2 TFIIH basal transcription factor complex helicase XPD subunit 0 70.412 0.026057 71802000 40569 39484 23156 29045 36591 35292 36030 42927 43216 FALSE TRUE 35207.70386 39224.627 34354.31905 35640.11118 35862.91069 36649.70608 32535.81615 33747.39511 38107.05371 0.923915665 1.029327203 0.901521259 0.935262837 0.941109511 0.961756486 0.853800359 0.885594446 1 15.21777045 3.71888134 0.823546449 0.914020423 0.971230572 0.042492883 0.050657608 1.846883457 2.370099261 0.024398098 0.07621575 5234.573953 -3.71888134 0.05721015 VSELHLEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSELHLEVK 9 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22;B0QYG7;B0QYG8 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 ; 123.63 0.00055247 517120000 982940 929690 410860 748010 952600 770490 1036250 1264090 1172820 FALSE TRUE 853041.9885 923582.8052 609553.2702 917857.1031 933645.1237 800131.2489 935754.6345 993774.1907 1034170.556 0.824856194 0.893066236 0.58941271 0.887529719 0.90279608 0.773693705 0.904835889 0.960938392 1 19.9800427 1.594992027 0.756747542 1.079982928 0.799670124 0.373922169 0.090363632 1.880761373 1.194451271 0.425228496 0.041483207 39.35428507 -1.594992027 -0.280312804 VSELKEELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSELKEELK 9 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 101.95 0.0033407 1792780000 7467600 5487400 4966900 5278500 5287900 3551300 7347300 8987500 7958200 FALSE TRUE 6480737.74 5451352.908 7368909.453 6477064.102 5182681.136 3687920.809 6634759.977 7065593.066 7017390.662 0.923525289 0.776834748 1.050092521 0.923001784 0.738548185 0.525540188 0.945473937 1.006868992 1 22.74250325 2.015399763 24.99972991 0.995599157 0.823838323 0.241790767 0.137264442 345.4878096 560857.21 0.059761511 0.040276683 103.6095442 -2.015399763 -0.171760834 VSELKEELKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSELKEELKK 10 2 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 87.363 0.0072708 1204900000 4669500 2858900 2909300 2847000 2320500 1605500 4475300 5248500 3830100 FALSE TRUE 4052413.744 2840119.698 4316247.211 3493454.864 2274326.59 1667264.624 4041286.095 4126149.119 3377309.941 1.199893944 0.840941384 1.278013356 1.034389773 0.673413643 0.493666454 1.196599117 1.221726519 1 21.68744315 VSELYDVTWEEMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VSELYDVTWEEMR 13 0 Q15006 Q15006 EMC2 ER membrane protein complex subunit 2 0 ;; 281.83 4.13E-32 229971000 111759 88743 60847 81453 87117 100074 75599 108655 89881 FALSE TRUE 96989.76499 88160.04139 90272.81272 99948.14858 85383.54214 103923.9115 68267.42062 85419.9738 79255.37057 1.223762684 1.112354163 1.139011932 1.261089916 1.077321846 1.311253872 0.861360184 1.077781521 1 16.27422108 2.239084386 25 0.995213264 1.180189132 0.559084531 0.086446878 10.47808997 500170.7095 0.031082605 0.022586995 173.4140917 -2.239084386 0.184975868 VSEYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VSEYAR 6 0 P12268;H0Y4R1 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ;; 119.22 0.049314 1334960000 1292290 1494440 906100 1028550 1211650 1392870 1304320 1461810 1548500 FALSE TRUE 1121510.602 1484622.925 1344292.991 1262097.998 1187540.536 1446454.61 1177827.247 1149213.307 1365438.094 0.821355876 1.08728688 0.984514052 0.92431726 0.869713933 1.059333716 0.862600254 0.841644387 1 20.38093248 VSFELFADKVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSFELFADKVPK 12 1 P62937;F8WE65;C9J5S7 P62937 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ; 159.5 6.44E-05 24791000000 28032000 19918800 15285200 17959600 16407100 12835300 23862000 29414000 22813000 FALSE TRUE 24327500.18 19787952.09 22677173.85 22037601.68 16080630.81 13329082.3 21547866.91 23124045 20116073.13 1.20935632 0.983688614 1.127316137 1.09552205 0.799392143 0.662608562 1.071176605 1.149530768 1 24.26184537 7.999999291 0.799650546 0.980314517 55.24123978 0.185240438 0.150395524 1119.652377 3.895220957 0.060002595 110047.0196 99999836.76 -7.999999291 54.26092526 VSGAGFS(ph)PSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VSGAGFSPSSK 11 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 VSGAGFS(0.866)PS(0.125)S(0.009)K;VSGAGFS(0.998)PS(0.002)SK;VSGAGFS(0.992)PS(0.007)S(0.001)K;VSGAGFS(0.995)PS(0.005)SK;VSGAGFS(0.858)PS(0.141)S(0.001)K 237.65 1.44E-15 4068310000 5180840 4157740 2836240 3858790 5016250 3811070 5644780 7119560 6039600 TRUE FALSE 4496178.867 4130427.532 4207855.151 4734987.247 4916436.439 3957684.329 5097350.104 5597097.498 5325605.368 0.84425686 0.775578971 0.790117716 0.889098407 0.923169499 0.74314262 0.957140034 1.050978642 1 22.3445141 2.04803813 5.821020733 1.022467834 0.831051596 0.71242155 0.053686767 0.095132497 7.452711246 0.023066329 0.015118295 111.696131 -2.04803813 -0.191416239 VSGEEELHTGPPAPQGPLSVPQGLPTQS(ph)LASPPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSGEEELHTGPPAPQGPLSVPQGLPTQSLASPPAR 35 0 Q9UPN7 Q9UPN7 PPP6R1 Serine/threonine-protein phosphatase 6 regulatory subunit 1 1 VSGEEELHTGPPAPQGPLSVPQGLPT(0.01)QS(0.717)LAS(0.272)PPAR 234.35 2.10E-47 465380000 171060 211350 126190 166750 244500 208960 249880 291220 238490 TRUE FALSE 148453.9876 209961.6279 187215.9061 204613.1361 239634.9284 216998.8264 225646.6761 228944.8693 210295.9839 0.705928781 0.99841007 0.890249555 0.972976908 1.139512624 1.031873374 1.072995651 1.088679227 1 17.68206177 5.575339946 0.650472202 1.066029682 1.84E-15 0.719471157 0.064102604 4.707580671 0.686122397 0.027827034 4.758618931 376131.7076 -5.575339946 -1.066029682 VSGEEELHTGPPAPQGPLSVPQGLPTQSLAS(ph)PPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VSGEEELHTGPPAPQGPLSVPQGLPTQSLASPPAR 35 0 Q9UPN7 Q9UPN7 PPP6R1 Serine/threonine-protein phosphatase 6 regulatory subunit 1 1 VSGEEELHTGPPAPQGPLSVPQGLPTQS(0.002)LAS(0.998)PPAR;VSGEEELHTGPPAPQGPLSVPQGLPT(0.067)QS(0.043)LAS(0.89)PPAR;VSGEEELHTGPPAPQGPLSVPQGLPTQSLAS(1)PPAR 252.79 6.29E-60 915280000 146258 175220 120125 151517 224645 214854 213360 267294 228134 TRUE FALSE 126929.6347 174068.9683 178217.8518 185921.2506 220175.004 223119.5724 192668.38 210135.2582 201164.2584 0.630975083 0.865307633 0.88593199 0.924226063 1.094503595 1.109141227 0.957766462 1.044595396 1 17.61801447 5.312989125 0.688499362 1.036871863 1.26E-15 0.837198065 0.055662039 2.46134834 0.509979035 0.024518287 2.377928932 205583.9117 -5.312989125 -1.036871863 VSGNTSRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSGNTSRR 8 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;G3V576;G3V555;G3V575;P07910-2;G3V4C1;B2R5W2;G3V2D6 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 105.52 0.0070102 23514000 2856.9 2160.7 2187.2 2815 2897.5 4820.7 2436.3 6125.5 2822.2 FALSE TRUE 2479.353427 2146.506219 3244.937236 3454.188775 2839.845419 5006.155448 2200.028001 4815.609494 2488.562731 0.996299348 0.862548568 1.303940301 1.388025599 1.141158864 2.011665362 0.884055673 1.935096686 1 11.28109704 4.116783078 3.606253338 1.429362668 0.927325795 0.210021165 0.361148143 0.299375966 7.404895752 0.086648816 0.204368512 13085.28173 -4.116783078 -0.502036873 VSGRT(ph)SPPLLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VSGRTSPPLLDR 12 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VS(0.072)GRT(0.671)S(0.257)PPLLDR;VS(0.101)GRT(0.729)S(0.169)PPLLDR;VS(0.012)GRT(0.533)S(0.455)PPLLDR;VS(0.084)GRT(0.506)S(0.41)PPLLDR 111.22 0.0022718 4067140000 5886300 4850660 1212130 1228900 4394840 4226010 4613800 5139230 147352 TRUE FALSE 5108410.541 4818795.695 1798320.122 1507940.528 4307391.282 4388587.339 4166354.386 4040245.658 129932.2144 39.31596613 37.08699737 13.8404485 11.605594 33.15106497 33.77597587 32.06559978 31.09502656 1 16.98739964 8 0.056294395 2.76E-11 77.55520417 0.116157468 11.95159478 3237.493482 17.72974252 6373.324449 23110.01008 99999999.99 -8 77.55520417 VSGRTS(ph)PPLLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSGRTSPPLLDR 12 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VSGRT(0.24)S(0.759)PPLLDR 112.12 0.00079215 1862600000 1957000 1530700 314120 353940 1296200 1360100 1461100 1559200 21129 TRUE FALSE 1698377.492 1520644.731 466029.4827 434307.4866 1270408.156 1412423.927 1319402.747 1225777.214 18631.15369 91.15793471 81.61838801 25.01345276 23.31082089 68.18730483 75.80979421 70.81701803 65.7918041 1 14.18542939 8 0.061388222 4.63E-05 173.4676129 0.121993086 27.58924249 2670.768394 15.87491553 11037.74111 44900.04111 99999999.92 -8 173.4675666 VSGTLDT(ph)PEKTVDSQGPTPVCTPTFLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSGTLDTPEKTVDSQGPTPVCTPTFLER 28 1 Q9BYG3;H7BZL0;C9J808 Q9BYG3 NIFK MKI67 FHA domain-interacting nucleolar phosphoprotein 1 VS(0.006)GT(0.027)LDT(0.965)PEKT(0.002)VDSQGPTPVCTPTFLER 116.36 0.00048769 179710000 58819 63225 39389 41743 66540 44497 63194 74985 61143 TRUE FALSE 51045.92012 62809.67081 58437.65215 51221.38615 65215.98418 46208.82838 57065.45561 58950.04128 53914.74419 0.946789619 1.164981338 1.083890001 0.950044128 1.209613162 0.857072199 1.058438771 1.093393693 1 15.71839224 2.758677649 24.9937326 1.02174098 1.070270538 0.088840807 0.101293441 2775.199 3447951.942 0.031365806 0.031325191 573.6904882 -2.758677649 0.048529558 VSHELGPSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSHELGPSLR 10 0 H7BXY3;Q7L2E3-3;Q7L2E3;Q7L2E3-2 H7BXY3 DHX30 Putative ATP-dependent RNA helicase DHX30 0 ; 106.4 0.0024216 194837000 86055 93443 64134 86062 100557 101496 86921 98464 109490 FALSE TRUE 74682.61371 92829.16678 95149.41692 105603.6925 98556.11244 105400.6168 78491.4148 77408.23985 96546.21693 0.773542621 0.961499785 0.985532317 1.093814919 1.020817962 1.091711515 0.812993168 0.801773931 1 16.55893211 2.223247854 24.99976455 0.854602706 0.992837391 0.213930993 0.103033824 317.8747369 518961.3768 0.042795655 0.028972657 167.2044587 -2.223247854 0.138234685 VSHEQFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VSHEQFR 7 0 O96013;O96013-4;O96013-2;O96013-3 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ;;; 125.01 0.0040911 987580000 2524070 2202090 1327090 1566230 1655070 1931010 2152570 2439510 2228290 FALSE TRUE 2190507.754 2187624.326 1968875.163 1921866.46 1622137.345 2005297.204 1943814.093 1917839.771 1964864.095 1.114839322 1.113371826 1.002041397 0.978116738 0.825572287 1.020578069 0.98928679 0.976067391 1 20.9059981 4.157350715 2.922178958 0.965020474 1.119305794 0.573516402 0.052433083 0.184185112 3.122740375 0.014151746 0.037783927 14366.49131 -4.157350715 0.154285321 VSHLLGINVTDFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSHLLGINVTDFTR 14 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 230.23 9.89E-13 13375300000 2418000 2473000 1510540 1910810 2381100 2589900 2588500 2882400 2646900 FALSE TRUE 2098455.174 2456754.7 2241042.196 2344688.615 2333720.769 2689535.129 2337467.668 2266021.191 2333986.497 0.899086253 1.05260022 0.960177875 1.004585338 0.999886148 1.152335342 1.001491513 0.970880163 1 21.15436478 3.391083812 2.77879224 1.02290291 0.979122848 0.137477735 0.060684545 0.701147778 10.9479749 0.019043285 0.0262486 2460.842465 -3.391083812 -0.043780062 VSHPQEPMLTAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSHPQEPMLTASPR 14 0 O75052-3;O75052;E9PSG0 O75052-3 NOS1AP Carboxyl-terminal PDZ ligand of neuronal nitric oxide synthase protein 1 VSHPQEPMLT(0.068)AS(0.932)PR 98.175 0.0017276 191360000 89793 75034 62259 72005 93935 100740 63036 111330 91006 TRUE FALSE 77926.62754 74541.09671 92367.66064 88354.83578 92065.87728 104615.533 56922.77842 87522.94587 80247.37435 0.97108009 0.92889141 1.151036547 1.101030862 1.147275883 1.303663002 0.70934132 1.090664294 1 16.29216657 2.248990788 24.99999963 0.956778975 1.097143942 0.23813589 0.138765489 351.9920002 843687.5772 0.052590224 0.040286078 177.4151848 -2.248990788 0.140364966 VSHS(ph)PPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSHSPPPK 8 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 VS(0.017)HS(0.983)PPPK 57.347 0.072045 599200000 667360 550110 345790 425620 441790 462530 524320 574210 549160 TRUE FALSE 579166.6851 546496.2912 513015.2006 522263.5262 432999.2433 480323.8284 473471.5271 451419.66 484238.9304 1.19603495 1.128567442 1.059425768 1.07852445 0.894185114 0.991914938 0.977764276 0.932225048 1 18.88535954 4.096013961 0.913600984 0.958308492 1.218208546 0.786874969 0.041740543 0.406754348 0.504229815 0.015375694 0.087789945 12474.23613 -4.096013961 0.259900054 VSHVADTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSHVADTK 8 0 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 0 69.954 0.052584 216470000 516360 430290 233510 342520 369680 361200 493290 573330 548460 FALSE TRUE 448121.7177 427463.3967 346436.217 420294.4011 362324.0913 375095.5977 445450.8117 450727.8412 483621.6836 0.926595587 0.883879717 0.71633723 0.869056156 0.749189095 0.775597146 0.921072869 0.931984351 1 18.8835194 2.103258854 4.800718945 0.951804054 0.81760588 0.476075943 0.065418316 0.187259898 7.188693709 0.028427089 0.018601022 126.8407654 -2.103258854 -0.134198174 VSHYIINSSGPRPPVPPSPAQPPPGVS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSHYIINSSGPRPPVPPSPAQPPPGVSPSR 30 1 P46108-2;P46108;I3L297 P46108-2 CRK Adapter molecule crk 1 VSHYIINSSGPRPPVPPS(0.009)PAQPPPGVS(0.956)PS(0.035)R;VSHYIINSSGPRPPVPPSPAQPPPGVS(0.952)PS(0.048)R 207.62 6.41E-26 1545290000 633990 666970 402600 519990 713450 701130 681570 832160 682190 TRUE FALSE 550206.6152 662588.6302 597298.7066 638061.677 699253.7408 728102.9248 615471.4463 654209.0599 601542.2754 0.91465993 1.101483067 0.992945519 1.060709618 1.16243491 1.210393608 1.023155764 1.087552923 1 19.19830661 3.48102765 24.63614463 1.09717117 1.015200301 0.242018344 0.074639921 215.4986094 1359075.079 0.021416039 0.028299952 3027.106149 -3.48102765 -0.081970869 VSIGNITLS(ph)PAISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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;VSIGNITLS(1)PAISR;VSIGNITLS(1)PAISR 346.79 8.99E-82 3671418000 2355220 2528430 1861350 2207260 2720570 2939840 2169060 2631010 3510760 TRUE FALSE 2043971.71 2511820.577 2761505.086 2708452.119 2666435.98 3052937.547 1958704.895 2068388.986 3095721.952 0.660256877 0.811384425 0.89203912 0.87490161 0.861329286 0.986179506 0.632713443 0.668144303 1 21.56184447 1.211558403 24.5717571 1.000001288 0.798061459 0.2351907 0.114267464 4012.858014 3651416.789 2.569457186 0.030351134 16.27640184 -1.211558403 -0.201939829 VSIGNITLSPAIS(ph)RHSPVQMNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSIGNITLSPAISRHSPVQMNR 22 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 VSIGNITLS(0.002)PAIS(0.499)RHS(0.499)PVQMNR;VSIGNITLSPAIS(0.5)RHS(0.5)PVQMNR 121.94 1.60E-05 1060340000 482340 505590 142402 182717 516720 550530 476230 607750 115537 TRUE FALSE 418597.5469 502268.746 211268.0835 224205.6875 506438.2829 571709.2453 430045.2879 477787.392 101878.3475 4.108797966 4.930083363 2.073728999 2.200719712 4.971009989 5.6116855 4.221164738 4.68978349 1 16.63648794 3.220152305 24.99991288 4.257440898 3.353128079 0.058485271 1.459263642 669.9843865 909888.1535 0.450997309 0.512306912 1660.169017 -3.220152305 -0.904312819 VSILESLDKWER ddPTM_MDA-MB-175_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 ; 170 3.86E-05 991470000 1206700 955460 665620 849120 1004680 899870 1307480 1409120 1026330 FALSE TRUE 1047231.538 949183.5203 987516.0584 1041925.674 984688.8336 934488.5812 1180680.791 1107790.654 904998.4366 1.157163919 1.048823381 1.09117985 1.151301076 1.088055839 1.032585851 1.304621912 1.224080185 1 19.78755577 2.258841946 24.999559 1.191551565 1.094849555 0.164592242 0.084102926 348.7346677 429862.9466 0.03112684 0.02408015 181.4855059 -2.258841946 -0.09670201 VSISEGDDKIEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VSISEGDDKIEYR 13 1 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ;;;;; 218.11 2.25E-11 5544940000 5578360 4139440 3198660 3712490 3994920 3478200 4641310 5536970 4927520 FALSE TRUE 4841165.592 4112247.746 4745542.675 4555467.596 3915428.908 3612008.605 4191196.471 4352932.054 4344994.199 1.114193799 0.946433426 1.092186193 1.048440432 0.901135589 0.831303435 0.964603467 1.001826897 1 22.05092282 3.253248059 24.71687146 0.943969206 1.045884411 0.414322203 0.065105124 241.077037 405695.7218 0.019859698 0.025521281 1791.628899 -3.253248059 0.101915205 VSITEAMHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 VSITEAMHR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;;;; 180.44 4.86E-05 2495313000 1753540 2009130 1289135 1543450 2028785 2216800 2025680 2104876 2314120 FALSE TRUE 1521805.246 1995931.893 1912564.998 1893913.913 1988416.148 2302081.73 1829229.865 1654764.648 2040547.37 0.745782856 0.978135535 0.937280372 0.928140136 0.974452334 1.128168728 0.896440775 0.81094155 1 20.96052477 4.74409119 24.59208921 0.946897967 0.745782747 0.397017143 0.080889758 589.9223055 2623031.127 0.021595697 0.181928519 55474.21819 -4.74409119 -0.20111522 VSKEEEEKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSKEEEEKER 10 2 P23921;E9PL69 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ; 78.83 0.016213 633000000 800080 673750 513770 516030 543550 426080 833130 1000060 567120 FALSE TRUE 694347.4009 669324.0919 762230.8905 633202.4985 532734.4184 442471.5733 752333.1808 786204.9515 500075.7197 1.388484531 1.33844549 1.524230952 1.266213243 1.065307507 0.884809152 1.50443853 1.572171814 1 18.93178703 3.599246838 8.305393055 1.249458975 1.40865428 0.151366735 0.215248817 0.791633682 50.36898133 0.06674025 0.099078567 3974.173637 -3.599246838 0.159195305 VSLDVNHFAPDELTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 VSLDVNHFAPDELTVK 16 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;;;;; 232.62 2.46E-16 96819437000 61003141 52858919 36268414 46014012 48778039 45545395 65417419 74373415 70584748 FALSE TRUE 52941421.35 52511685.28 53807940.32 56462196.7 47807451.46 47297555.82 59073247.77 58469238.98 62240299.5 0.85059715 0.843692683 0.864519303 0.907164605 0.768110884 0.759918513 0.949115738 0.939411273 1 25.89134567 2.143699716 8.269291152 0.958704318 0.834940605 0.646309865 0.045487109 0.173858303 13.43733054 0.019845048 0.013365769 139.2193868 -2.143699716 -0.123763713 VSLEPHQGPGT(ph)PESK ddPTM_MDA-MB-175_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(1)PESK;VSLEPHQGPGT(0.999)PES(0.001)K 179.07 2.52E-06 12204500000 2583000 2404450 974610 1850370 2240120 1719300 2663720 3046240 2548810 TRUE FALSE 2241650.006 2388655.01 1445934.656 2270524.79 2195545.995 1785442.584 2405392.844 2394825.282 2247492.585 0.997400401 1.06280885 0.643354583 1.010247956 0.976886869 0.794415339 1.070256187 1.065554253 1 21.09988493 2.204313479 24.97729572 1.050537208 0.915847196 0.204797377 0.121587794 280.2745699 204409.3849 0.04866732 0.032813361 160.0713025 -2.204313479 -0.134690013 VSLEPHQGPGTPESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSLEPHQGPGTPESK 15 0 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 112.24 0.0018334 0 169750 171310 78334 125370 195390 145330 185680 219960 158010 FALSE TRUE 147317.1074 170184.6533 116216.5844 153837.1747 191502.1213 150920.9391 167672.7822 172923.2657 139330.2378 1.057323304 1.221448093 0.83410885 1.104119085 1.374447674 1.0831887 1.20341991 1.241103643 1 17.08814886 3.471661942 24.99917157 1.18982383 1.041526384 0.19283144 0.133311653 217.6032725 996438.4525 0.036674212 0.047503327 2962.524438 -3.471661942 -0.148297446 VSLQVHPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSLQVHPDR 9 0 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 119.53 0.00081249 891680000 817660 699410 393120 542300 768780 718640 634220 758500 732440 FALSE TRUE 709604.1593 694815.5297 583234.1469 665437.5035 753482.7821 746286.5458 572713.442 596300.6777 645851.7776 1.098710546 1.075812677 0.903046437 1.030325419 1.166649699 1.155507458 0.886756779 0.923277907 1 19.30084358 2.226842504 24.99760999 0.931806423 1.066635958 0.402179528 0.07734948 240.2444433 512495.9653 0.034047035 0.023164494 168.5941513 -2.226842504 0.134829535 VSNEEVTEELLHVNDDLNNVFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VSNEEVTEELLHVNDDLNNVFLR 23 0 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-4;Q6ZVM7-3;Q6ZVM7-5;F5H3S6;B7Z2U2 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 0 ;; 295.69 1.16E-61 212323000 169957 134014.7 97704.1 103476.7 129051.1 123407.4 130282.9 148902.8 140227.1 FALSE TRUE 147496.7518 133134.3486 144954.1296 126972.6663 126483.2356 128154.9625 117648.0844 117061.095 123649.612 1.192860612 1.076706562 1.172297488 1.026874765 1.022916559 1.036436431 0.951463434 0.946716234 1 16.91589819 3.546782962 0.627696428 0.955850319 1.1849797 0.755353517 0.040501549 0.502992377 0.43508724 0.031012196 0.075592422 3521.948184 -3.546782962 0.229129381 VSNGS(ph)PSLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VSNGSPSLER 10 0 P46527;E7ES52 P46527 CDKN1B Cyclin-dependent kinase inhibitor 1B 1 VSNGS(0.999)PS(0.001)LER;VS(0.004)NGS(0.994)PS(0.002)LER;VS(0.001)NGS(0.861)PS(0.138)LER;VS(0.005)NGS(0.962)PS(0.033)LER 206.46 1.57E-07 1580130000 954540 755610 481866 561244 774680 854380 742780 810070 717460 TRUE FALSE 828395.1205 750646.3482 714898.0093 688683.0283 759265.3836 887248.5515 670745.3099 636842.8345 632642.6961 1.309420192 1.186524958 1.130018593 1.088581331 1.200148817 1.402448107 1.060227699 1.006639037 1 19.2710314 2.019848547 24.98160529 1.012685571 1.209140687 0.534193551 0.08756484 186.018904 234124.5306 0.037195815 0.025073905 104.6763443 -2.019848547 0.196455116 VSNLQVS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VSNLQVSPK 9 0 O00443;A0A0C4DGF9;O00443-2 O00443 PIK3C2A Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha 1 VSNLQVS(1)PK;VSNLQVS(1)PK;VSNLQVS(1)PK;VSNLQVS(1)PK;VSNLQVS(1)PK;VSNLQVS(1)PK 174.05 5.77E-05 2115630000 2415780 2725140 1867404 2330490 3665870 2440500 3577820 4646170 3687920 TRUE FALSE 2096528.552 2707238.376 2770486.82 2859663.374 3592926.359 2534387.614 3230843.567 3652622.702 3251938.299 0.644701209 0.832499921 0.851949381 0.879371966 1.104856867 0.779346771 0.993513182 1.123214024 1 21.63286845 5.797217811 0.335280184 1.064738062 1.71E-12 0.577030692 0.096031917 14.06775829 0.828448619 0.171454161 6.886330862 626928.2079 -5.797217811 -1.064738062 VSNS(ph)PEPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VSNSPEPQK 9 0 O60271;O60271-3;D6RHI8 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 VSNS(1)PEPQK;VSNS(1)PEPQK;VS(0.01)NS(0.99)PEPQK;VS(0.001)NS(0.999)PEPQK 208.03 1.12E-05 742463000 3264380 2769830 2418180 2809800 2314630 2400300 3413740 4040560 4505960 TRUE FALSE 2832983.912 2751634.804 3587619.936 3447808.035 2268573.391 2492641.094 3082676.02 3176517.688 3973270.542 0.713010575 0.692536482 0.90293875 0.867750635 0.570958702 0.627352471 0.775853541 0.799471784 1 21.9218956 1.164691995 1.893222594 1.127735912 0.735166396 0.413269585 0.098954256 1.160595785 3.376334112 0.873114411 0.029169829 14.61140555 -1.164691995 -0.392569516 VSNS(ph)PPLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSNSPPLGR 9 0 H0Y9Y2 H0Y9Y2 BOD1L1 1 VS(0.016)NS(0.984)PPLGR 67.252 0.064434 78978000 126340 125220 64744 73657 127940 117600 117530 139800 99117 TRUE FALSE 109643.8489 124397.4216 96054.41496 90381.94763 125394.2443 122124.1481 106131.9587 109904.8579 87399.50117 1.25451344 1.423319583 1.099027039 1.034124296 1.434724943 1.397309441 1.214331401 1.257499831 1 16.41533743 1.226186443 4.623375897 0.975809109 1.265269699 0.285891395 0.131240645 0.307960546 14.21055118 0.295798664 0.034054345 16.83396588 -1.226186443 0.28946059 VSPAS(ph)PAGS(ph)PSADFAVHGESLGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VSPASPAGSPSADFAVHGESLGDR 24 0 A0A0A0MRP9;Q96C92-3;Q96C92;Q96C92-2;Q96C92-4 A0A0A0MRP9;Q96C92-4 SDCCAG3 Serologically defined colon cancer antigen 3 2 VS(0.003)PAS(0.997)PAGS(0.984)PS(0.016)ADFAVHGESLGDR;VS(0.001)PAS(0.999)PAGS(0.888)PS(0.112)ADFAVHGESLGDR;VS(0.002)PAS(0.991)PAGS(0.97)PS(0.037)ADFAVHGESLGDR 251.47 9.26E-40 1268710000 455490 482370 317990 414073 657990 581540 611420 730990 613740 TRUE FALSE 395295.8424 479201.2797 471771.0276 508094.6034 644897.2863 603912.2201 552124.5825 574673.4771 541184.3564 0.730427326 0.885467723 0.871738109 0.938856782 1.191640665 1.115908494 1.020215341 1.061881169 1 19.04576061 3.536312863 3.119641538 1.073502508 0.834439351 0.736995322 0.067652387 0.136271037 2.614605072 0.020137654 0.030293728 3438.055343 -3.536312863 -0.239063157 VSPGLPS(ph)PNLENGAPAVGPVQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSPGLPSPNLENGAPAVGPVQPR 23 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 VSPGLPS(1)PNLENGAPAVGPVQPR 195.29 5.29E-19 610790000 141000 147720 114060 134310 220490 180550 236250 245020 144030 TRUE FALSE 122366.4928 146749.6176 169219.7975 164807.1383 216102.6804 187495.8753 213338.5114 192624.3797 127002.9375 0.963493406 1.155482074 1.332408532 1.297663988 1.701556552 1.476311328 1.679791945 1.516692319 1 16.95450234 4.332629034 1.169156609 1.486313913 0.899981111 0.40901353 0.196629086 0.801152372 1.496776407 0.061898203 0.488398128 21509.43656 -4.332629034 -0.586332801 VSPNELILGWYATGHDITEHSVLIHEYYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSPNELILGWYATGHDITEHSVLIHEYYSR 30 0 O00303 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 0 ; 135.02 1.54E-06 1129940000 328746 268085 181712 263949 234136 251582 245849 310729 326410 FALSE TRUE 285301.3832 266323.932 269588.531 323882.6547 229477.1517 261260.5223 222006.6018 244282.0214 287822.1816 0.99124182 0.925307183 0.936649599 1.125287331 0.797287931 0.907715037 0.771332496 0.848725488 1 18.13481826 3.213397322 24.99999981 0.858085521 0.985529757 0.381904171 0.081304482 236.5273699 234991.7096 0.02409595 0.027333036 1634.54666 -3.213397322 0.127444236 VSPS(ph)PSQESLSSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSPSPSQESLSSSK 14 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 VS(0.136)PS(0.851)PS(0.013)QESLSSSK 306.72 1.14E-44 418810000 378980 241090 239770 299220 248060 191130 305470 354880 779550 TRUE FALSE 328896.8328 239506.2639 355723.574 367162.4743 243124.0913 198482.8948 275845.5664 278991.6737 687392.4871 0.478470217 0.348427235 0.517497035 0.534138038 0.353690353 0.288747547 0.40129267 0.405869542 1 19.39077456 1.238097958 24.99998329 1.000000662 0.413676258 0.85077045 0.076858662 4.257821708 229822.4012 0.112138063 0.019576554 17.30206573 -1.238097958 -0.586324404 VSPSTSYT(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSPSTSYTPSR 11 0 Q9BTE3;Q9BTE3-2 Q9BTE3 MCMBP Mini-chromosome maintenance complex-binding protein 1 VSPSTSYT(0.999)PSR;VSPSTSYT(0.999)PSR 135.1 0.0028974 0 111111 115026 83039 91693 117630 121977 110420 118394 148565 TRUE FALSE 96427.39983 114270.3866 123196.9381 112513.2971 115289.3931 126669.5341 99711.4854 93076.36444 131001.8149 0.736076824 0.872280943 0.940421613 0.858868231 0.880059511 0.966929612 0.761145832 0.710496755 1 16.99922727 1.196741412 23.91477236 1.000003133 0.840776949 0.263494201 0.083654473 9082.292817 5193170.95 8.958570853 0.022375939 15.73045963 -1.196741412 -0.159226184 VSPTTSPRPAS(ph)PVPGSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSPTTSPRPASPVPGSER 18 1 A0A5E8;Q99501;Q99501-4;Q99501-2 A0A5E8 GAS2L1 GAS2-like protein 1 1 VSPTTSPRPAS(0.999)PVPGSER;VSPT(0.001)T(0.001)S(0.001)PRPAS(0.998)PVPGSER 91.337 0.0015377 502400000 232125 281570 148391 248437 255505 251576 276020 292110 162038 TRUE FALSE 201449.0931 279720.3481 220153.3839 304848.418 250420.9504 261254.2915 249251.6229 229644.5497 142882.0522 1.409897814 1.957701081 1.540805024 2.133566905 1.752641052 1.82846122 1.744457187 1.607231602 1 17.12446518 1.118984848 1.908230345 0.531211925 1.783327467 0.591371054 0.198975809 0.764395027 2.03769549 1.923073256 0.049565052 13.15178946 -1.118984848 1.252115542 VSQGSAESLS(ph)PSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VSQGSAESLSPSFR 14 0 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 VSQGSAESLS(0.986)PS(0.014)FR;VSQGSAESLS(0.999)PSFR;VSQGSAES(0.001)LS(0.999)PSFR;VSQGSAESLS(0.998)PS(0.002)FR 324.99 1.00E-56 995490000 1069750 1015390 661470 902380 1307520 1164490 1111360 1407710 1260620 TRUE FALSE 928379.8271 1008719.836 981359.1045 1107279.171 1281502.91 1209288.684 1003580.478 1106682.171 1111590.94 0.835181175 0.907455972 0.882841943 0.996121083 1.152854764 1.087890015 0.902832546 0.995584015 1 20.08419455 3.706748663 4.422316651 1.021694502 0.876942855 0.52509295 0.066442485 0.187954991 8.887895469 0.020238323 0.032180325 5090.361945 -3.706748663 -0.144751647 VSQGVEDGPDTKR ddPTM_MDA-MB-175_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 ; 114.31 0.0012076 550770000 1286820 978730 659740 763100 978990 937830 1105780 1336470 840410 FALSE TRUE 1116763.477 972300.6582 978792.4707 936373.5183 959510.0144 973908.927 998541.6258 1050676.291 741057.6872 1.506985888 1.312044494 1.320804693 1.263563599 1.29478451 1.314214728 1.347454649 1.417806345 1 19.49922633 7.999999989 0.019884126 4.40E-08 2.978643323 0.238482779 0.112822975 15174.0933 30.00268673 1786.345194 2822.507748 99999997.47 -7.999999989 2.978643279 VSQPIEGHAASFAQFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSQPIEGHAASFAQFK 16 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 225.13 7.16E-15 3172800000 3297600 2524800 1536970 2247160 2719300 2511400 2934000 3401400 3859400 FALSE TRUE 2861813.805 2508214.423 2280253.833 2757412.024 2665191.25 2608015.183 2649461.132 2674037.08 3403146.129 0.840931802 0.737028129 0.67004288 0.810253783 0.783155101 0.766354157 0.778532873 0.78575441 1 21.69843767 1.221024431 3.722717697 1.035408491 0.767260894 0.720176231 0.044826025 0.162017207 3.461195671 0.124601302 0.011389202 16.63506226 -1.221024431 -0.268147596 VSQSALNPHQS(ph)PDFKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSQSALNPHQSPDFKR 16 1 Q9NYL2 Q9NYL2 ZAK Mitogen-activated protein kinase kinase kinase MLT 1 VSQSALNPHQS(1)PDFKR;VSQSALNPHQS(1)PDFKR 200.04 1.72E-11 393460000 574830 529130 346480 426490 526680 459420 631750 749440 496570 TRUE FALSE 498864.7591 525654.1102 514038.8869 523331.073 516200.0984 477094.1847 570482.9822 589178.0881 437866.0603 1.139309036 1.200490647 1.173963761 1.195185287 1.178899543 1.089589324 1.302870978 1.345566925 1 18.7401301 2.228879064 24.99990358 1.246722193 1.167311451 0.032166169 0.095844807 419.1327267 1082281.553 0.038230033 0.026134842 169.3866051 -2.228879064 -0.079410742 VSQWWER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VSQWWER 7 0 H3BS72;Q9P035;H3BPZ1 H3BS72 HACD3 Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3 0 ;; 113.94 0.013996 528500000 460100 487160 329738 428140 529250 462410 313577 511300 617390 FALSE TRUE 399296.6193 483959.8139 489200.3997 525355.7307 518718.9605 480199.2119 283166.3508 401962.4739 544402.8575 0.733457978 0.888973684 0.898599985 0.965012809 0.952821892 0.882065928 0.520141191 0.73835482 1 19.05431511 2.435116268 24.9998249 0.734546471 0.895204127 0.186807818 0.129466825 199.9109539 118978.4594 0.048392171 0.037484446 272.343032 -2.435116268 0.160657656 VSRPENEQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VSRPENEQLR 10 1 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;;; 202.31 2.06E-07 3983570000 2499900 2670720 1631750 2016000 2530780 2743170 2604570 2920760 2796690 FALSE TRUE 2169531.881 2653175.864 2420869.758 2473763.613 2480422.429 2848701.525 2351979.202 2296178.203 2466068.494 0.879753294 1.075872739 0.981671743 1.003120399 1.005820574 1.155159125 0.953736365 0.931108852 1 21.23378144 VSS(ph)GVYEPVVIESH ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VSSGVYEPVVIESH 14 0 Q5T9C2-3;Q5T9C2 Q5T9C2-3 FAM102A Protein FAM102A 1 VS(0.006)S(0.994)GVYEPVVIESH;VS(0.025)S(0.975)GVYEPVVIESH;VS(0.003)S(0.997)GVYEPVVIESH;VS(0.001)S(0.999)GVYEPVVIESH;VS(0.001)S(0.999)GVYEPVVIESH 336.07 1.35E-68 1153820000 996220 1141250 1123423 939810 1390200 1893280 1424270 1389150 1625710 TRUE FALSE 864567.0029 1133753.054 1666714.12 1153208.225 1362537.74 1966115.707 1286144.515 1092091.083 1433520.416 0.603107562 0.790887274 1.16267205 0.804458878 0.950483666 1.371529617 0.897193022 0.761824576 1 20.45113102 4.466444426 6.487836598 0.973058758 0.645698962 0.349841143 0.17535344 0.154708657 29.4979314 0.045732898 0.135492981 29271.46279 -4.466444426 -0.327359795 VSS(ph)PIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSSPIEK 7 0 Q06190 Q06190 PPP2R3A Serine/threonine-protein phosphatase 2A regulatory subunit B subunit alpha 1 VS(0.003)S(0.997)PIEK;VS(0.001)S(0.999)PIEK 131.5 0.003629 287370000 1554650 1476360 1195350 1448320 1575780 1372320 1999230 2434800 2890800 TRUE FALSE 1349199.064 1466661.694 1773425.258 1777183.192 1544425.061 1425114.038 1805344.982 1914136.968 2549052.917 0.529294255 0.575375146 0.695719279 0.697193526 0.605881914 0.559075894 0.708241469 0.750920844 1 21.28152989 0.863572993 1.106390638 1.538939836 0.616950692 0.816295091 0.05760036 1.569986278 0.88613061 2.0834268 0.019403686 7.304205662 -0.863572993 -0.921989144 VSS(ph)PPNAMMSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSSPPNAMMSSR 12 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 VS(0.091)S(0.908)PPNAMMSSR 64.439 0.063563 0 152030 118890 76380 88227 121320 119180 120530 148290 116940 TRUE FALSE 131938.8503 118109.0038 113317.6235 108260.2888 118905.9694 123764.9317 108841.0192 116579.3375 103115.4864 1.279525073 1.145405097 1.098938941 1.049893596 1.153133962 1.20025552 1.05552544 1.130570601 1 16.65390149 4.719373305 2.527500226 1.103006231 1.313357185 0.504935381 0.056257789 0.410134769 3.43799907 0.014072804 0.18177054 52405.06992 -4.719373305 0.210350954 VSS(ph)PS(ph)PELGTTPASIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSSPSPELGTTPASIFR 17 0 A0A5E8;Q99501 A0A5E8 GAS2L1 GAS2-like protein 1 2 VS(0.09)S(0.91)PS(1)PELGTTPASIFR 78.285 0.0083623 0 20254 15154 10874 13451 18558 14606 17809 18708 17878 TRUE FALSE 17577.38258 15054.45238 16132.70277 16505.25514 18188.73211 15167.90227 16081.88592 14707.43979 15764.48321 1.114998973 0.954960095 1.023357541 1.046989928 1.153779155 0.962156645 1.020134039 0.932947791 1 13.94439026 VSS(ph)PSPELGTTPASIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VSSPSPELGTTPASIFR 17 0 A0A5E8;Q99501 A0A5E8 GAS2L1 GAS2-like protein 1 1 VS(0.051)S(0.941)PS(0.008)PELGTTPASIFR;VSS(0.996)PS(0.004)PELGTTPASIFR;VSS(0.997)PS(0.003)PELGTTPASIFR;VSS(0.996)PS(0.004)PELGTTPASIFR;VS(0.338)S(0.476)PS(0.185)PELGTTPASIFR 287.78 4.62E-33 925828000 834514 772002 556365 655719 838012 865788 873304 1002632 914888 TRUE FALSE 724230.8605 766930.668 825424.9749 804610.021 821337.2007 899095.4246 788611.1125 788226.9493 806730.9829 0.897735275 0.9506647 1.023172523 0.997370918 1.018105438 1.114492245 0.977539142 0.977062944 1 19.62172814 4.471896216 2.668059855 1.013126965 0.897910903 0.509797328 0.038834787 0.275899888 3.548668215 0.010761326 0.053727212 29641.22962 -4.471896216 -0.115216062 VSS(ph)PTKPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VSSPTKPK 8 1 Q8WUA4;A0A087WZD8;Q8WUA4-2 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 VS(0.16)S(0.836)PT(0.004)KPK;VS(0.183)S(0.817)PTKPK;VS(0.225)S(0.775)PTKPK;VS(0.452)S(0.548)PTKPK;VS(0.392)S(0.608)PTKPK 110.38 0.0020813 3890030000 9250770 6311600 5377580 5934860 4973740 4515260 8424550 10670800 8910810 TRUE FALSE 8028257.306 6270138.684 7978195.675 7282460.672 4874772.305 4688964.974 7607538.438 8388932.46 7857384.193 1.021746819 0.79799314 1.015375535 0.926830163 0.62040651 0.596759031 0.968202426 1.06764952 1 22.90561767 2.013609326 24.99390078 1.032437654 0.827620831 0.27515227 0.142276742 293.2648504 538586.955 0.062020484 0.041791475 103.1832794 -2.013609326 -0.204816823 VSS(ph)PTVNTTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSSPTVNTTLR 11 0 Q9NSK0-3;Q9NSK0;Q9NSK0-5 Q9NSK0-3 KLC4 Kinesin light chain 4 1 VSS(0.996)PT(0.004)VNTTLR;VSS(1)PTVNTTLR 229.56 2.57E-12 438200000 651390 614390 375810 452540 625970 578490 572490 714790 620060 TRUE FALSE 565307.1611 610354.0316 557552.973 555296.1236 613514.4217 600744.8846 516970.0079 561937.721 546757.2132 1.033927212 1.116316378 1.019745071 1.015617371 1.122096622 1.098741581 0.945520234 1.027764623 1 19.06054082 2.248855316 24.98655285 0.996835514 1.067868552 0.420748493 0.042215037 207.3921487 503367.3188 0.015907783 0.012180951 177.3598514 -2.248855316 0.071033037 VSS(ph)PVFGATSSIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSSPVFGATSSIK 13 0 F6Q6H0;I6L8A6;Q99708-3;Q99708;Q99708-2 F6Q6H0 RBBP8 DNA endonuclease RBBP8 1 VS(0.001)S(0.999)PVFGATSSIK 203.76 8.73E-08 49542000 532220 257590 158750 216420 258930 197610 310440 364710 296570 TRUE FALSE 461885.7785 255897.8743 235522.031 265561.4688 253777.7996 205212.1846 280333.5766 286719.6047 261509.8325 1.766227198 0.978540164 0.900623999 1.015493247 0.970433108 0.784720722 1.071981019 1.096400858 1 17.99650567 4.738784788 24.99458304 0.983588239 1.766227431 0.889838333 0.087214387 6.079602292 677455.1674 0.02300156 0.12993563 54800.53373 -4.738784788 0.782639191 GYYSPYS(ph)VSGSGSTAGSR ddPTM_MDA-MB-175_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(0.138)PYS(0.862)VSGSGSTAGSR;GYYS(0.23)PYS(0.77)VSGSGSTAGSR;GYYS(0.029)PYS(0.94)VS(0.031)GSGSTAGSR 409.05 2.76E-147 3821850000 3213490 1822340 1003800 843700 741290 1013130 824200 846330 824640 TRUE FALSE 2788819.155 1810368.929 1489241.038 1035274.98 726539.7793 1052105.767 744269.2109 665348.9156 727151.9986 3.835262998 2.489670567 2.048046406 1.423739441 0.999158059 1.446885615 1.023540075 0.915006652 1 19.47189744 6.761325051 0.505619092 0.944545022 26.27871999 0.971108612 0.155142977 4.724108483 0.17935509 0.096177557 108.7683527 5771983.101 -6.761325051 25.33417497 up VSS(ph)SGLTDSLFILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSSSGLTDSLFILK 14 0 Q6P3S1 Q6P3S1 DENND1B DENN domain-containing protein 1B 1 VS(0.017)S(0.966)S(0.017)GLTDSLFILK;VS(0.079)S(0.92)S(0.001)GLTDSLFILK 222.75 3.96E-12 257610000 880310 717280 682870 835270 1098160 927800 1294460 1283690 1522270 TRUE FALSE 763974.8031 712568.1405 1013108.216 1024930.82 1076308.765 963493.0664 1168923.468 1009182.883 1342308.975 0.569149739 0.530852549 0.754750385 0.763558047 0.801833844 0.717787845 0.870830405 0.751826071 1 20.35628536 5.583786799 0.338305953 0.878929261 2.05E-16 0.660214635 0.078146341 10.34391557 0.697743161 0.135219136 4.117921189 383518.9249 -5.583786799 -0.878929261 VSS(ph)SSELDLPSGDHCEAGLLQLDVPLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSSSSELDLPSGDHCEAGLLQLDVPLLR 28 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VS(0.091)S(0.623)S(0.143)S(0.143)ELDLPSGDHCEAGLLQLDVPLLR;VS(0.043)S(0.319)S(0.319)S(0.319)ELDLPSGDHCEAGLLQLDVPLLR 331.23 4.32E-96 318890000 155085 140729 83728 101321 121994 129257 132203 135519 156432 TRUE FALSE 134590.1243 139804.5419 124219.1409 124327.4816 119566.5581 134229.6004 119381.9734 106539.3165 137938.7872 0.975723559 1.013525962 0.900538155 0.901323581 0.866808825 0.973109908 0.865470662 0.772366632 1 17.07366866 4.170053175 5.261193448 0.885028948 0.994519495 0.281604944 0.062785324 0.218821552 11.17432788 0.016775167 0.037079578 14792.895 -4.170053175 0.109490547 VSSDNVADLHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSSDNVADLHEK 12 0 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ; 179.5 2.06E-05 1092200000 2243670 1680560 1265430 1543650 1651850 1407250 1991710 2267240 2128140 FALSE TRUE 1947163.325 1669520.291 1877396.181 1894159.326 1618981.417 1461387.818 1798554.271 1782408.37 1876553.714 1.03762728 0.889673596 1.000448944 1.009381886 0.862741847 0.778761518 0.95843474 0.949830723 1 20.83965416 4.75406526 23.43189701 0.931605717 1.037627467 0.178451087 0.071786826 2349.88627 3551197.349 0.018388959 0.39996757 56762.98948 -4.75406526 0.106021751 VSSPLSPLSPGIKS(ph)PTIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSSPLSPLSPGIKSPTIPR 19 1 Q9P2B4 Q9P2B4 CTTNBP2NL CTTNBP2 N-terminal-like protein 1 VSSPLSPLSPGIKS(0.997)PT(0.003)IPR;VSSPLSPLSPGIKS(1)PTIPR 222.48 1.47E-19 917130000 1434880 927550 570500 599470 812560 803900 1042990 1104150 582340 TRUE FALSE 1245256.972 921456.863 846395.7082 735588.8258 796391.6457 834826.5532 941840.9903 868036.115 513496.4286 2.425054787 1.7944757 1.648299114 1.432510111 1.550919542 1.625768957 1.834172426 1.690442361 1 18.96999472 4.809891189 1.76078959 1.565310212 2.823353269 0.618555264 0.219307097 0.775958807 2.095422679 0.058829869 1.726139333 64549.24825 -4.809891189 1.258043057 VSSPSCDSQGLHAEEAPSSEPQS(ph)PVAQTSGWPACSTPLPLVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSSPSCDSQGLHAEEAPSSEPQSPVAQTSGWPACSTPLPLVSR 43 0 Q96RE7;K7ENW4 Q96RE7 NACC1 Nucleus accumbens-associated protein 1 1 VSSPSCDSQGLHAEEAPSSEPQS(0.999)PVAQTSGWPACSTPLPLVSR;VSSPSCDSQGLHAEEAPSSEPQS(0.999)PVAQTSGWPACSTPLPLVSR 201.98 2.44E-35 280280000 54429 89101 34563 71858 115814 106900 105726 125539 106685 TRUE FALSE 47236.06974 88515.68966 51277.78241 88174.45718 113509.528 111012.5122 95472.70879 98693.4618 94072.82084 0.502122391 0.940927346 0.545086051 0.937300024 1.206613419 1.180069984 1.014880897 1.049117704 1 16.52149034 3.523336198 5.264859822 1.083724634 0.693903013 0.682281419 0.132424739 0.117618526 7.683239761 0.035173611 0.051368992 3336.846263 -3.523336198 -0.38982162 VSSQS(ph)FSEIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSSQSFSEIER 11 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;E9PIY6 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 VSS(0.002)QS(0.989)FS(0.008)EIER 141.65 0.0014534 0 149930 134560 79962 98222 121520 85844 126230 138570 114550 TRUE FALSE 130116.3706 133676.0665 118631.8907 120524.8063 119101.9897 89146.47423 113988.234 108937.8839 101008.0295 1.288178487 1.323420199 1.174479804 1.193220053 1.17913388 0.882568195 1.12850666 1.078507168 1 16.62411046 3.510497041 1.034731956 1.042265674 1.302831858 0.636653526 0.078057438 0.370040704 0.823970897 0.032415339 0.067631349 3239.64215 -3.510497041 0.260566184 VSSQSFSEIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSSQSFSEIER 11 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;E9PIY6 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 0 71.555 0.086638 0 13902 16745 12644 10937 19132 20707 14424 20422 12228 FALSE TRUE 12064.81548 16635.00099 18758.68069 13420.41301 18751.31063 21503.61169 13025.1627 16054.91422 10782.41977 1.118933944 1.542789221 1.739746837 1.244656886 1.739063311 1.994321511 1.207999965 1.488989908 1 13.39639336 0.793663307 1.359998292 1.92E-08 1.542517074 0.256321367 0.270679684 5.452122786 3.711032372 15.85038344 0.0777825 6.21818025 -0.793663307 1.542517055 VSSS(ph)PGVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VSSSPGVK 8 0 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 VS(0.002)S(0.21)S(0.788)PGVK;VSS(0.017)S(0.983)PGVK;VS(0.016)S(0.07)S(0.914)PGVK 123.86 0.0013945 481880000 2019760 1476040 1050220 1321230 1280280 1254430 1759600 1997210 2159180 TRUE FALSE 1752843.599 1466343.796 1558109.905 1621235.465 1254804.933 1302688.734 1588954.263 1570122.184 1903924.2 0.920647785 0.770169209 0.818367614 0.851523115 0.659062442 0.684212498 0.834568027 0.824676835 1 20.86054461 1.064384354 1.778137785 1.165381958 0.784470055 0.419434117 0.076427946 1.555737931 3.128299242 1.178748099 0.021633474 11.59803336 -1.064384354 -0.380911903 VSSSS(ph)ELDLPSGDHCEAGLLQLDVPLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSSSSELDLPSGDHCEAGLLQLDVPLLR 28 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VS(0.092)S(0.092)S(0.107)S(0.71)ELDLPSGDHCEAGLLQLDVPLLR;VS(0.101)S(0.08)S(0.356)S(0.463)ELDLPSGDHCEAGLLQLDVPLLR 254.75 1.07E-53 283860000 117122 100956 64990 74190 89335 105898 103004 98874 112561 TRUE FALSE 101644.031 100292.8134 96419.38138 91035.97342 87557.40828 109971.9646 93014.68793 77730.56454 99254.16681 1.024078225 1.010464514 0.971439129 0.91720052 0.882153476 1.107983353 0.937136353 0.783146613 1 16.59884005 7.999999997 0.139347895 0.836716445 1.493155898 0.092776341 0.083982978 333.98556 3.999631203 1.917485266 42.89726537 99999999.24 -7.999999997 0.656439454 VSTEVDAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VSTEVDAR 8 0 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ;;; 136.8 0.0018044 3073710000 5530870 5673800 3478120 4182110 5240570 5670300 5490400 6033300 5880300 FALSE TRUE 4799951.516 5636528.434 5160150.466 5131721.995 5136292.91 5888440.11 4957941.853 4743125.746 5185137.633 0.925713425 1.087054739 0.995181002 0.989698318 0.99057986 1.13563815 0.956183269 0.914754069 1 22.30595085 2.033342041 24.9999808 0.946541986 1.021913841 0.192264963 0.060583835 238.4649933 178801 0.02345046 0.01581016 107.9796812 -2.033342041 0.075371855 VSTTTDSPVS(ph)PAQAASPFIPLDELSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSTTTDSPVSPAQAASPFIPLDELSSK 27 0 Q96E09 Q96E09 FAM122A Protein FAM122A 1 VS(0.118)T(0.118)T(0.118)T(0.118)DS(0.107)PVS(0.421)PAQAASPFIPLDELSSK 68.361 0.014744 44975000 33470 23062 18020 21413 24627 24151 33182 31425 28334 TRUE FALSE 29046.8547 22910.5042 26734.53227 26275.14893 24136.97088 25080.1046 29964.01475 24705.0083 24984.3868 1.162600264 0.916992856 1.070049567 1.05166275 0.966082181 1.003831105 1.199309592 0.988817877 1 14.60873919 VSVADHSLHLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSVADHSLHLSK 12 0 Q13162;A6NG45 Q13162 PRDX4 Peroxiredoxin-4 0 190.36 3.90E-06 182160000 246730 303530 82649 197910 401330 375000 297940 287760 306770 FALSE TRUE 214124.0054 301536.0914 122618.3328 242848.4904 393344.3182 389426.4927 269045.8247 226224.7634 270504.0001 0.791574266 1.114719529 0.453295821 0.897763029 1.454116457 1.439633028 0.994609413 0.836308385 1 18.0452904 3.463975241 24.97665754 1.115827283 0.795378888 0.312641218 0.245977419 327.6608652 622534.089 0.07763912 0.100287339 2910.551184 -3.463975241 -0.320448395 VSVGAPDLSLEASEGS(ph)IKLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VSVGAPDLSLEASEGSIKLPK 21 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VSVGAPDLSLEAS(0.011)EGS(0.989)IKLPK;VSVGAPDLSLEAS(0.004)EGS(0.996)IKLPK 207.64 2.15E-22 151472000 252350 202765 120095 195034 183874 75733 279520 296560 237362 TRUE FALSE 219001.3081 201433.0234 178173.3437 239319.4506 180215.2671 78646.49752 252412.1934 233142.9518 209301.3348 1.046344537 0.962406779 0.851276672 1.143420566 0.861032575 0.375757267 1.205975078 1.113910487 1 17.67522199 VSVHVIEGDHR ddPTM_MDA-MB-175_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 ;;;;;;;;;;;;;;;; 234.65 9.68E-16 1.00913E+11 16571808 18165947 7600739 11566335 20948451 23333607 18788886 19463043 20977817 FALSE TRUE 14381801.59 18046613.7 11276481.8 14192648.14 20531617.81 24231265.96 16966742.73 15301022.72 18497843.37 0.777485315 0.975606363 0.609610622 0.767259613 1.10994657 1.309950867 0.917228154 0.827178737 1 24.14085374 3.251436685 24.98872575 1.012332645 0.783935844 0.39624202 0.152399559 290.3007365 563386.6057 0.048833649 0.062629375 1784.171857 -3.251436685 -0.228396801 VSVHVLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSVHVLAR 8 0 A0A3B3ISG5;P14735;P14735-2 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 70.919 0.056596 0 175740 191690 120190 150770 230120 216500 193750 214550 247510 FALSE TRUE 152515.5137 190430.7758 178314.286 185004.6329 225541.0622 224828.8951 174960.1548 168670.1521 218249.6498 0.698812181 0.872536455 0.817019804 0.847674363 1.033408587 1.030145502 0.80165148 0.772831261 1 17.73561981 5.559519718 1.013571525 0.896799053 1.28E-09 0.31667955 0.093751139 12.850358 3.139166678 0.032222454 18.6235087 362676.752 -5.559519718 -0.896799051 VSVS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VSVSPGR 7 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 VS(0.006)VS(0.994)PGR;VS(0.001)VS(0.999)PGR;VS(0.001)VS(0.999)PGR;VSVS(1)PGR;VS(0.004)VS(0.996)PGR;VSVS(1)PGR 113.26 0.0064726 7268130000 7303980 5700460 3571100 4464640 5101860 5312200 5228090 5893920 5462680 TRUE FALSE 6338740.537 5663013.303 5298095.905 5478404.75 5000342.968 5516563.771 4721070.636 4633551.075 4816888.194 1.315940973 1.175658034 1.099900121 1.137332761 1.038085745 1.145254685 0.980107996 0.961938681 1 22.19967001 8 0.22872271 0.932209553 2.944563334 0.790790842 0.048891459 40.49470258 0.63020915 0.214251493 29.51719491 100000000 -8 2.012353781 VSVT(ph)PPEESQNSDTPPRPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSVTPPEESQNSDTPPRPDR 20 1 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 VS(0.042)VT(0.94)PPEES(0.008)QNS(0.008)DT(0.001)PPRPDR 60.33 0.033612 0 136720 123280 78894 112740 136090 129600 132910 128520 212010 TRUE FALSE 118652.1056 122470.1656 117047.4023 138339.3401 133382.0753 134585.7959 120020.4087 101036.9981 186946.4193 0.634685093 0.655108378 0.626101333 0.739994596 0.713477561 0.719916414 0.642004319 0.54045966 1 17.51226531 2.843702014 0.025694846 1.368552704 3.75E-06 0.108527257 0.114626047 1193.638254 39.28838502 1054.626353 1035.279306 697.7534839 -2.843702014 -1.368548959 VSWQDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VSWQDLK 7 0 Q13243;Q13243-3 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 92.439 0.036452 228160000 726630 593210 400430 445710 528390 485610 604150 630790 553380 FALSE TRUE 630604.0045 589313.1645 594079.2874 546915.2678 517876.0728 504291.7309 545559.626 495900.4673 487960.0468 1.292327125 1.20770782 1.217475265 1.120819771 1.061308351 1.033469306 1.118041589 1.016272686 1 18.8964035 3.965615363 0.658523519 1.028269424 1.331322318 0.876458518 0.033747672 0.49354466 0.330247126 0.020575278 0.10157812 9238.795697 -3.965615363 0.303052893 VSYGIGDEEHDQEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VSYGIGDEEHDQEGR 15 0 P27695;G3V3M6;G3V3C7;G3V5M0;G3V359 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ;;;;; 270.75 2.22E-33 5431990000 5592340 2599860 1691900 1924620 2571680 2570150 2414890 2892330 2798480 FALSE TRUE 4853298.1 2582781.348 2510108.499 2361634.387 2520508.599 2669025.334 2180694.339 2273827.738 2467646.882 1.966771719 1.046657594 1.017207331 0.957039033 1.021421913 1.081607483 0.883714098 0.921455883 1 21.23470453 4.742992265 4.117420607 0.978645887 2.053676198 0.968975077 0.054971138 0.039426249 1.462942445 0.014925189 0.126560588 55334.02543 -4.742992265 1.075030311 VSYLVFDEADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VSYLVFDEADR 11 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ;;; 195.36 2.54E-07 864940000 702810 617350 452906 530020 638900 616410 619620 709900 732400 FALSE TRUE 609931.8778 613294.5872 671932.8565 650369.1418 626187.14 640123.6916 559529.3478 558093.4094 645816.5064 0.944435256 0.949642168 1.040439273 1.007049426 0.96960535 0.991185089 0.866390596 0.86416715 1 19.30076479 2.249536799 24.94876023 0.898773867 0.98517301 0.351322965 0.046219857 191.0658297 434291.1974 0.017607199 0.013503888 177.6383781 -2.249536799 0.086399143 VT(ph)CNRAGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTCNRAGEK 9 1 Q9BV44;H7C0R6;H7C3J3 Q9BV44 THUMPD3 THUMP domain-containing protein 3 1 VT(1)CNRAGEK 75.378 0.062129 262980000 349730 499730 235130 192720 442700 523060 451330 338360 260740 TRUE FALSE 303512.2944 496447.2407 348839.6545 236480.0215 433891.1361 543182.4567 407560.0861 266004.3471 229915.6142 1.32010301 2.159258484 1.517250821 1.028551377 1.887175595 2.362529654 1.77265075 1.156965124 1 17.81074492 1.66402455 4.292854943 1.041994497 1.734626197 0.329084042 0.383244808 0.193340074 8.195579456 0.279693279 0.104339567 46.1343653 -1.66402455 0.6926317 VT(ph)KSPGETSKPRPFAGGGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTKSPGETSKPRPFAGGGYR 20 3 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 VT(0.713)KS(0.287)PGETSKPRPFAGGGYR 103.02 0.00029972 2067600000 612580 530370 284970 277280 485270 355290 691500 801200 84008 TRUE FALSE 531626.0009 526885.9645 422782.4452 340240.662 475614.0764 368958.2362 624438.4364 629869.6149 74076.66994 7.176699511 7.112711262 5.707363 4.593087975 6.420565028 4.980761642 8.429623482 8.502941823 1 16.17673162 4.251408154 22.14263449 6.028544221 7.144709513 0.057563529 2.123711406 219.4260606 378147.3867 0.535477758 1.389993365 17840.54652 -4.251408154 1.116165292 VTAEADSSS(ph)PTGILATSESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VTAEADSSSPTGILATSESK 20 0 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-7 A0MZ66 KIAA1598 Shootin-1 1 VTAEADSS(0.063)S(0.936)PTGILATSESK;VTAEADS(0.001)S(0.023)S(0.966)PT(0.01)GILATSESK;VTAEADS(0.001)S(0.319)S(0.679)PT(0.001)GILATSESK;VTAEADS(0.004)S(0.078)S(0.917)PT(0.001)GILATSESK 338.14 4.08E-80 1011370000 2377470 2200110 1618690 2078170 2204260 1770200 2532850 3352710 3424390 TRUE FALSE 2063281.316 2185657.333 2401493.898 2550050.261 2160399.539 1838300.739 2287214.597 2635759.057 3019562.515 0.683304719 0.72383245 0.795311866 0.844509842 0.71546773 0.608797046 0.757465555 0.872894349 1 21.52590811 1.517517665 2.343075073 1.002259522 0.73280976 0.673017233 0.062603953 0.216734334 2.195828864 0.102529078 0.018631542 32.92438454 -1.517517665 -0.269449761 VTAGWPSEPGQGDLNPES(ph)PAALGQDLLEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTAGWPSEPGQGDLNPESPAALGQDLLEPR 30 0 Q92766;Q92766-2;Q92766-5;Q92766-3;A0A087X055;Q92766-4 Q92766 RREB1 Ras-responsive element-binding protein 1 1 VTAGWPS(0.001)EPGQGDLNPES(0.999)PAALGQDLLEPR 79.365 0.0018763 17673000 18360 16260 8346.6 14776 14423 12683 15780 15025 13102 TRUE FALSE 15933.67948 16153.18699 12383.04368 18131.11664 14136.01052 13170.92322 14249.65803 11812.02067 11553.09649 1.379169602 1.398169487 1.07183764 1.569372909 1.223568983 1.140034036 1.233405957 1.02241167 1 13.49599196 1.77941499 0.634639005 0.873855934 1.347378187 0.46847386 0.131936878 1.711374787 0.869693937 0.558895556 0.078251653 60.17484641 -1.77941499 0.473522253 VTAIHIDPATHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 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 ;;;;;;;;;; 188.91 4.97E-06 75554190000 40402390 40123608 26585767 28593641 43947710 48103870 41996270 45593240 48052340 FALSE TRUE 35063111.79 39860033.38 39442732.85 35086264.22 43073236.55 49954457.01 37923478.2 35843480.43 42371647.11 0.827513542 0.940724189 0.93087561 0.828059955 1.016557993 1.178959526 0.895020156 0.845930779 1 25.33659588 3.231243427 24.99400964 0.9722861 0.889508547 0.227551709 0.093886021 358.4970245 1224548.83 0.031550449 0.036498707 1703.112853 -3.231243427 -0.082777552 VTANNDKNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VTANNDKNR 9 1 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 ; 123.75 0.0005007 174294000 205410 183150 98485 130551 93383 147554 167785 203030 199215 FALSE TRUE 178264.5481 181946.8756 146112.6754 160194.5999 91524.861 153230.4979 151513.2365 159613.6145 175664.0296 1.014803932 1.035766263 0.831773447 0.911937408 0.52102221 0.872292968 0.86251714 0.908630041 1 17.42245928 4.238642138 24.99990301 0.842682954 1.025285156 0.268833921 0.124261538 2.800380763 857336.7165 0.032229088 0.074996919 17323.75917 -4.238642138 0.182602202 VTAPDVDLHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTAPDVDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 117.98 0.00078252 100290000 406790 283600 206990 297000 304770 260950 255180 383170 370200 FALSE TRUE 353031.6708 281737.0129 307091.0563 364438.3894 298705.6733 270988.9154 230432.6829 301232.0773 326435.3777 1.08147491 0.863071322 0.940740732 1.116418177 0.915053005 0.83014567 0.705905973 0.922792374 1 18.31643789 3.005544053 24.79153192 0.860420579 0.990024928 0.286745007 0.100580809 185.3536068 828841.7227 0.031209153 0.035278355 1012.847482 -3.005544053 0.129604349 VTDALPEPEPPGAMAAS(ph)EDEEEEEEALEAMQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VTDALPEPEPPGAMAASEDEEEEEEALEAMQSR 33 0 Q9Y3E7-2;Q9Y3E7-4;Q9Y3E7;Q9Y3E7-3 Q9Y3E7-2 CHMP3 Charged multivesicular body protein 3 1 VTDALPEPEPPGAMAAS(1)EDEEEEEEALEAMQSR;VTDALPEPEPPGAMAAS(1)EDEEEEEEALEAMQSR;VTDALPEPEPPGAMAAS(1)EDEEEEEEALEAMQSR;VTDALPEPEPPGAMAAS(1)EDEEEEEEALEAMQSR 185.67 2.78E-19 647431000 818008 676201 477476 594185 683486 743323 560609 773398 749601 TRUE FALSE 709906.1702 671758.9911 708384.9907 729103.7858 669885.9658 771919.1168 506241.2255 608012.8563 660984.0237 1.074014113 1.016301404 1.071712727 1.103058107 1.013467711 1.167833244 0.76589026 0.91986014 1 19.33425588 2.24486264 24.99999998 0.89498722 1.07016826 0.58710203 0.070762841 99.24941805 393722.0289 0.025883019 0.019544717 175.7367702 -2.24486264 0.17518104 VTDEILHLVPNIDNFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTDEILHLVPNIDNFR 16 0 G3XAH6;P51003;P51003-2;H0YJ00;Q9NRJ5 G3XAH6 PAPOLA;PAPOLB Poly(A) polymerase alpha;Poly(A) polymerase beta 0 79.022 0.019511 201940000 231290 240470 191470 183560 228640 253270 226900 280050 297650 FALSE TRUE 200724.4405 238890.3367 284065.5324 225240.1035 224090.5113 263013.4608 204895.2729 220163.4869 262462.1561 0.764774791 0.910189645 1.082310443 0.858181259 0.853801229 1.002100511 0.780665967 0.838838978 1 18.00174989 2.234474872 24.99998546 0.862162136 0.914479822 0.027640504 0.100725599 348.1418927 2130185.927 0.040022254 0.028109323 171.5832432 -2.234474872 0.052317686 VTDHLEALIDPFDLDVFTPHLNSNLHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTDHLEALIDPFDLDVFTPHLNSNLHR 27 0 A0A087WVI0;E9PBL8;Q8WTW3;J3QKY9;J3QLT5 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 0 74.748 0.0059283 149700000 69166 64578 31975 39891 68396 75711 64230 74044 62781 FALSE TRUE 60025.53786 64153.78287 47438.21695 48948.86125 67035.05341 78623.65116 58000.98449 58210.26681 55359.1017 1.084293928 1.158866038 0.856918113 0.884206205 1.210912955 1.420247958 1.047722646 1.051503096 1 15.75653291 3.227705236 24.99965128 1.140587478 0.997759773 0.211646384 0.14362553 395.7855134 911481.6767 0.047485081 0.054364521 1689.293986 -3.227705236 -0.142827705 VTDKLTPIHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VTDKLTPIHDR 11 1 P28072;A0A087X2I4;I3L3X7 P28072 PSMB6 Proteasome subunit beta type-6;Proteasome subunit beta type 0 ; 193.23 6.28E-07 558470000 1701650 1435590 620090 708050 1315010 1224300 1559890 1731050 224589 FALSE TRUE 1476772.641 1426159.515 919967.5981 868823.5744 1288843.874 1271399.613 1408612.108 1360878.429 198038.3443 7.457003574 7.201431218 4.645401382 4.387148244 6.508052158 6.41996689 7.11282511 6.871792599 1 17.59542027 4.329466807 7.56437536 5.573528274 7.374846623 0.170902564 1.790418638 0.454495033 32.40821644 0.445876823 1.190132693 21353.38879 -4.329466807 1.801318349 VTEGLTDVILYHQPDDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VTEGLTDVILYHQPDDK 17 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;; 228.9 1.28E-15 3290400000 8513350 5835580 4293680 5109790 5486100 4594150 6771590 8179930 7085860 FALSE TRUE 7388289.227 5797245.691 6370118.009 6270045.918 5376937.343 4770889.923 6114882.244 6430715.626 6248177.703 1.182471047 0.927829836 1.019516139 1.003499935 0.860560887 0.763565018 0.978666506 1.029214586 1 22.57500405 4.742148165 24.48849638 0.951148026 1.182471165 0.446318124 0.082050288 284.8966798 1944581.607 0.022033676 0.157149574 55226.58194 -4.742148165 0.231323139 VTEGLVDVILYHQPDDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VTEGLVDVILYHQPDDK 17 0 O43390;O43390-3;B4DT28 O43390 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;;;; 228.76 1.33E-15 1590959000 4743860 3606349 2766508 3246370 3593655 2747558 4278691 5005649 4698652 FALSE TRUE 4116946.882 3582658.656 4104400.522 3983507.926 3522148.296 2853258.334 3863744.205 3935229.915 4143182.713 0.993667711 0.864711721 0.990639517 0.961460839 0.85010692 0.68866341 0.932554626 0.949808441 1 21.98230801 4.7576377 22.85478515 0.905564383 0.99366797 0.086946328 0.09052734 3771.871409 4518549.751 0.023344862 0.698651986 57231.8388 -4.7576377 0.088103587 VTEGQQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VTEGQQER 8 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 150.24 0.0011453 1465230000 731230 590070 357240 441620 484200 619480 543500 590480 561280 FALSE TRUE 634596.1028 586193.7913 530002.4589 541896.5707 474565.3673 643311.7965 490791.4537 464210.4471 494926.1178 1.282203707 1.184406662 1.070871873 1.094903969 0.95886103 1.299813797 0.991645896 0.937938877 1 18.91685365 8 0.266454246 0.970202073 3.035544083 0.394372737 0.099912934 87.0452984 1.393240031 0.281205241 80.25926141 100000000 -8 2.065342011 VTEHGT(ph)PKPFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VTEHGTPKPFR 11 1 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 VT(0.003)EHGT(0.997)PKPFR;VT(0.034)EHGT(0.966)PKPFR;VTEHGT(1)PKPFR;VT(0.001)EHGT(0.999)PKPFR;VTEHGT(1)PKPFR;VTEHGT(1)PKPFR 162.93 3.60E-05 1505593000 1338250 1030240 780981 948950 1128280 1037960 972400 1254830 1324860 TRUE FALSE 1161396.872 1023472.286 1158666.024 1164423.601 1105829.435 1077890.993 878096.7977 986494.3696 1168236.56 0.994145288 0.876083082 0.991807707 0.996736142 0.946580062 0.922665006 0.75164297 0.844430318 1 20.15590101 2.465109 24.78466134 0.853530344 0.957496453 0.281013665 0.068899818 236.4065051 487768.8359 0.025569495 0.019820724 291.8159325 -2.465109 0.103966109 VTEKIPVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VTEKIPVR 8 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 84.213 0.016062 940970000 2236800 2052520 917170 992380 2097780 2055360 2576590 2796580 597320 FALSE TRUE 1941201.213 2039036.861 1360716.48 1217715.047 2056038.282 2134431.029 2326712.698 2198553.13 526705.5101 3.685553266 3.871303455 2.583448348 2.311946663 3.903582254 4.052418265 4.417483117 4.17416011 1 19.00663703 VTEQEWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VTEQEWR 7 0 P09497-2;P09497 P09497-2 CLTB Clathrin light chain B 0 ;;;; 147.08 0.0050616 2829020000 5692910 5220090 3468850 3794160 5196530 5612550 4808880 5520370 4112370 FALSE TRUE 4940577.52 5185798.885 5146397.463 4655682.018 5093129.22 5828468.43 4342515.558 4339881.835 3626210.303 1.362463042 1.430087737 1.419222006 1.28389741 1.404532223 1.607316714 1.197535497 1.196809195 1 21.79003117 1.706054726 1.766095053 1.026590101 1.408057367 0.655094415 0.097348716 0.235796706 1.371469323 0.122950929 0.02813389 50.82234799 -1.706054726 0.381467266 VTFEDATDFFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTFEDATDFFGR 12 0 Q86WQ0;Q86WQ0-2 Q86WQ0 NR2C2AP Nuclear receptor 2C2-associated protein 0 216.26 9.19E-11 82928000 83940 79134 56503 66797 71601 75822 74209 91632 88682 FALSE TRUE 72847.11632 78614.16354 83828.03979 81964.27978 70176.28018 78738.9214 67012.2226 72037.20988 78198.11499 0.931571258 1.005320442 1.071995659 1.048161836 0.89741652 1.00691585 0.85695445 0.921214148 1 16.25484621 3.24031279 24.99941999 0.932144288 1.01774741 0.317154694 0.056394309 52.90601829 754836.8181 0.016642429 0.020380893 1739.052887 -3.24031279 0.085603122 VTFEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTFEELR 7 0 Q86V21;Q86V21-2 Q86V21 AACS Acetoacetyl-CoA synthetase 0 98.299 0.026439 65917000 101160 111290 76214 84163 121960 120360 116150 136850 126770 FALSE TRUE 87791.44969 110558.9287 113071.3453 103273.4955 119533.2346 124990.3271 104885.7909 107585.6925 111783.395 0.785371116 0.98904608 1.011521839 0.923871524 1.069329077 1.11814753 0.938294913 0.962447888 1 16.77034637 4.73824799 5.002274546 0.999911176 0.774855225 0.581961376 0.05765482 0.130136 10.25338067 0.014822095 0.101632232 54732.84076 -4.73824799 -0.225055952 VTFFEPGS(ph)GDENGTSNKEDEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VTFFEPGSGDENGTSNKEDEFR 22 1 O95793-2;O95793-3;O95793;Q5JW30 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 1 VTFFEPGS(1)GDENGTSNKEDEFR;VTFFEPGS(1)GDENGTSNKEDEFR;VTFFEPGS(1)GDENGTSNKEDEFR;VTFFEPGS(1)GDENGTSNKEDEFR 230.88 9.95E-27 847370000 750490 645250 472439 566870 634180 536442 772170 936230 869840 TRUE FALSE 651310.845 641011.3103 700912.0806 695586.4976 621561.0588 557079.2709 697285.0722 736024.5003 767008.5061 0.849157265 0.835729076 0.913825694 0.906882377 0.81037049 0.726301294 0.909096922 0.959604091 1 19.54888305 1.832040303 3.053422201 0.982449659 0.84417498 0.529529475 0.05353406 0.207712146 3.459041317 0.038493851 0.015806517 67.92666657 -1.832040303 -0.138274679 VTFFEPGSGDENGTSNKEDEFR ddPTM_MDA-MB-175_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 ; 240.85 1.11E-30 626020000 732000 575410 427870 522810 566670 519970 706690 819590 762910 FALSE TRUE 635264.3453 571630.0938 634789.3631 641522.0012 555394.3757 539973.5824 638155.3126 644327.0566 672719.6489 0.944322566 0.849730039 0.943616504 0.953624593 0.82559559 0.80267253 0.948619999 0.957794317 1 19.35964587 2.019276827 24.92153784 0.969079901 0.886772681 0.364623432 0.051943809 257.976803 333517.2328 0.022123203 0.014913186 104.5386354 -2.019276827 -0.08230722 VTFQIGSFAS(ph)PESDFESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTFQIGSFASPESDFESR 18 0 Q9P278;Q9P278-2 Q9P278 FNIP2 Folliculin-interacting protein 2 1 VTFQIGS(0.023)FAS(0.977)PESDFESR 163.45 3.47E-11 40423000 47441 53586 32094 43086 58670 61964 56186 69133 52000 TRUE FALSE 41171.55165 53233.99004 47614.76575 52869.33483 57502.58179 64347.79518 50737.09037 54349.44594 45852.61924 0.897910574 1.160980352 1.038430662 1.153027585 1.254074091 1.403361384 1.106525455 1.185307336 1 15.48471653 5.572045074 0.934753506 1.183976444 2.56E-10 0.35450855 0.111799551 10.02637299 2.213401 0.036956391 17.43928366 373288.8983 -5.572045074 -1.183976444 VTGGLLDRLDDS(ph)PDQCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTGGLLDRLDDSPDQCR 17 1 Q12955;A0A087WY90;A0A087WVC2;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;H0Y3A4;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 VTGGLLDRLDDS(1)PDQCR 154.1 9.12E-08 141010000 82534 85500 60404 61604 81341 94446 81588 107490 55354 TRUE FALSE 71626.92279 84938.34487 89615.57644 75592.12976 79722.47324 98079.39873 73675.60832 84504.09999 48810.11318 1.467460699 1.740179224 1.836004275 1.548698104 1.633318754 2.00940732 1.509433261 1.731282607 1 15.57489248 1.236438965 24.99675324 0.999999116 1.689251102 0.641324244 0.160833208 34.43033651 405547.5376 0.237022375 0.0369621 17.23609843 -1.236438965 0.689251987 VTGLTEGLVDVILYHQPDDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTGLTEGLVDVILYHQPDDK 20 0 O43390-2;O43390-4 O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 87.323 0.0029092 0 80226 75672 50621 53682 53328 40719 77736 90600 51661 FALSE TRUE 69623.93083 75174.90565 75101.48492 65871.31858 52266.87713 42285.48628 70197.17468 71225.89505 45553.69543 1.528392596 1.650248239 1.648636498 1.446014817 1.147368543 0.928255894 1.540976512 1.5635591 1 15.47528047 3.493234316 4.616182088 1.284156088 1.607444604 0.399172597 0.205673686 0.248297114 13.58364428 0.064921492 0.092096782 3113.395666 -3.493234316 0.323288516 KAASLT(ph)EDRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 KAASLTEDRDR 11 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 KAAS(0.072)LT(0.928)EDRDR;KAAS(0.074)LT(0.926)EDRDR;KAAS(0.145)LT(0.855)EDRDR;KAAS(0.072)LT(0.928)EDRDR 137.46 0.00012541 6332420000 12581100 6340680 3194750 3076130 2542390 2170530 3874280 3393450 2050660 TRUE FALSE 10918475.76 6299027.656 4739741.786 3774612.332 2491801.413 2254031.694 3498552.922 2667787.125 1808233.311 6.038200763 3.483525946 2.621200349 2.087458687 1.37803092 1.246538088 1.93479066 1.475355591 1 20.78614941 6.789652786 0.620206049 1.374823948 66.26508834 0.969290297 0.260914677 6.190540594 0.220380165 0.12356398 482.1399798 6161022.379 -6.789652786 64.89026439 up VTGTEGSSSTLVDYTSTS(ph)STGGSPVRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTGTEGSSSTLVDYTSTSSTGGSPVRK 27 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 VTGTEGSSSTLVDYTS(0.002)T(0.098)S(0.3)S(0.237)T(0.093)GGS(0.27)PVRK 251.18 8.39E-47 548330000 196230 136150 111440 116010 156560 95613 164900 192960 213870 TRUE FALSE 170297.7083 135255.6217 165332.7567 142351.8436 153444.7623 99291.29398 148908.0234 151697.0056 188586.5322 0.90302158 0.717207216 0.8766944 0.754835682 0.813657054 0.52650257 0.789600517 0.80438939 1 17.52486713 1.196588688 2.495826735 1.076165052 0.76397564 0.331540998 0.102147438 0.732336729 4.528834785 0.518717092 0.026321883 15.7249288 -1.196588688 -0.312189412 VTGTEGSSSTLVDYTSTSSTGGS(ph)PVRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTGTEGSSSTLVDYTSTSSTGGSPVRK 27 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 VTGTEGSSSTLVDYTSTS(0.018)S(0.043)T(0.024)GGS(0.915)PVRK 285.38 1.17E-61 449940000 238520 157690 103860 155060 147340 130140 152250 200080 237920 TRUE FALSE 206998.9777 156654.124 154087.0434 190268.7429 144408.2223 135146.57 137484.8184 157294.449 209793.3686 0.98668027 0.746706748 0.734470514 0.906934019 0.688335495 0.644188951 0.655334434 0.749758918 1 17.67860955 4.740114217 23.82075386 0.756516093 0.986680408 0.279665656 0.110575046 93.3652152 1431261.716 0.027035483 0.165291912 54968.54185 -4.740114217 0.230164314 VTHAVVTVPAYFNDAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VTHAVVTVPAYFNDAQR 17 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 190.81 2.78E-10 7840900000 5299900 4417100 3240200 4189200 4947500 5936600 3899300 4315500 4415000 FALSE TRUE 4599504.787 4388083.779 4807171.558 5140421.888 4849054.43 6164984.843 3521146.486 3392663.908 3893063.73 1.181461467 1.127154366 1.234804229 1.320405276 1.245562561 1.583581794 0.904466695 0.871463748 1 21.89247453 2.196264614 24.98920104 0.913222961 1.273038059 0.644578646 0.124684925 86.51739709 51115.36128 0.051395637 0.034651229 157.1319911 -2.196264614 0.359815097 VTHDMDMCYGMMGSLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VTHDMDMCYGMMGSLFR 17 0 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;;; 219.58 4.28E-15 5176670000 2434170 2553340 2125740 2314800 2310190 2025160 2791640 2939310 4615550 FALSE TRUE 2112488.267 2536566.941 3153754.974 2840410.72 2264221.739 2103069.216 2520907.182 2310761.43 4069904.937 0.51905101 0.623249678 0.774896471 0.697905913 0.556332832 0.516736692 0.619401981 0.567767913 1 21.95656367 1.234608003 24.99975014 1.00000056 0.611746984 0.704514397 0.079481964 71.31179131 450972.8236 0.153937404 0.020789774 17.16358491 -1.234608003 -0.388253577 VTHILNMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VTHILNMAR 9 0 Q8TE77;Q8TE77-2;Q8TE77-3;A0A087WWG1 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ; 116.52 0.0013009 1286580000 704140 1184060 729830 796390 1218970 1252360 1165350 1184090 1301510 FALSE TRUE 611086.1149 1176281.832 1082778.229 977222.5216 1194714.882 1300539.1 1052334.536 930881.5681 1147646.97 0.532468721 1.024950932 0.943476746 0.851500981 1.041012535 1.133222265 0.916949692 0.81112188 1 20.13024749 4.74444718 24.92823609 0.954348342 0.532468531 0.6764567 0.093798617 427.9926848 1812396.694 0.024897616 0.218593499 55519.70887 -4.74444718 -0.421879811 VTHTGQVYDDKDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VTHTGQVYDDKDYR 14 1 D6RBT3;O75380 D6RBT3 NDUFS6 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial" 0 ; 142.45 5.65E-06 320950000 417750 399250 244900 384830 445670 407250 449580 554350 341700 FALSE TRUE 362543.2791 396627.3005 363334.4591 472211.5333 436802.0389 422917.171 405979.8008 435806.5665 301304.6153 1.203245024 1.316366495 1.205870872 1.567223034 1.44970245 1.403619957 1.347406512 1.446398576 1 18.20086325 VTIAQGGVLPNIQAVLLPK ddPTM_MDA-MB-175_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 ; 196.33 1.95E-15 233640000 392440 357630 259478 313021 370350 304022 400080 528060 392870 FALSE TRUE 340578.0597 355280.705 384962.4287 384097.2023 362980.7596 315717.9231 361280.3032 415138.4784 346425.3562 0.983121049 1.025562069 1.111242067 1.108744483 1.047789237 0.911359164 1.042880657 1.198348998 1 18.402185 1.962943847 24.36002723 1.115524095 1.033792991 0.11362534 0.074269178 703.4296109 462419.7435 0.034834466 0.020102465 91.82138663 -1.962943847 -0.081731104 VTILGHVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VTILGHVQR 9 0 Q01813;Q01813-2;B1APP6;V9GY25 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ; 83.948 0.015824 337730000 1004800 1513720 603760 829370 1608590 1541370 1322500 1382640 1334000 FALSE TRUE 872013.1342 1503776.274 895740.3555 1017691.135 1576582.206 1600667.501 1194244.154 1086973.196 1176296.04 0.741321151 1.278399504 0.761492282 0.865165826 1.34029373 1.360769268 1.015258161 0.924064316 1 20.16581976 3.307888874 24.99999882 1.105768393 0.927072986 0.217812822 0.200446125 100.1856907 36125.28756 0.061011383 0.078765339 2031.837043 -3.307888874 -0.178695408 VTIPPPSSSVAISNHVT(ph)PPPIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VTIPPPSSSVAISNHVTPPPIPK 23 0 F5H2U7;A0A1W2PNT6;F5GYH1;A0A1W2PRM0;A0A1W2PRL5;A0A1W2PR09;Q8NC96;A0A1W2PRW5 F5H2U7 NECAP1 Adaptin ear-binding coat-associated protein 1 1 VTIPPPSSSVAISNHVT(1)PPPIPK;VTIPPPSSSVAISNHVT(1)PPPIPK 161.49 6.52E-11 1464440000 2435390 2408240 704430 1603830 2444700 2121080 2597700 3053900 2796200 TRUE FALSE 2113547.041 2392420.113 1045094.704 1968004.115 2396055.253 2202679.32 2345775.454 2400847.25 2465636.421 0.85720142 0.97030531 0.423864076 0.798172876 0.971779631 0.893351226 0.951387412 0.973723145 1 21.23352865 3.312154163 5.133288337 0.956253776 0.74852695 0.33116352 0.138895754 0.243103597 11.61497587 0.04097569 0.052730401 2051.890418 -3.312154163 -0.207726826 VTKS(ph)PAPVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VTKSPAPVHR 10 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B0QYZ7 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 VT(0.009)KS(0.991)PAPVHR;VTKS(1)PAPVHR;VTKS(1)PAPVHR;VTKS(1)PAPVHR;VT(0.001)KS(0.999)PAPVHR;VT(0.001)KS(0.999)PAPVHR 142.77 2.13E-05 6094050000 8772120 8175840 5385230 6202800 8373830 7456530 9410400 10480500 7712070 TRUE FALSE 7612862.116 8122132.369 7989545.241 7611240.544 8207207.166 7743387.534 8497780.856 8239326.634 6800357.87 1.119479631 1.194368374 1.174871293 1.119241177 1.206878715 1.138673535 1.249607891 1.211601917 1 22.69717924 1.232470002 24.99996442 0.999999705 1.180312985 0.635652627 0.042002646 131.8569279 541175.0342 0.091724212 0.0103022 17.07929743 -1.232470002 0.18031328 VTKS(ph)PGETSKPRPFAGGGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTKSPGETSKPRPFAGGGYR 20 3 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 VT(0.012)KS(0.987)PGETSKPRPFAGGGYR 119.48 0.00027838 1522900000 822170 659050 314360 329710 648050 441410 894720 1059400 71064 TRUE FALSE 713518.1514 654720.6572 466385.5475 404575.6948 635155.0729 458391.3283 807950.1921 832855.5543 62662.89488 11.38661329 10.44829892 7.442770533 6.456383728 10.13606336 7.315195527 12.89359826 13.29104817 1 15.9353238 4.462143789 20.94280869 8.99906091 11.15203867 0.065086229 3.506248401 99.88926396 139675.3053 0.887615926 2.353325503 28983.03017 -4.462143789 2.152977758 VTKS(ph)PQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VTKSPQK 7 1 Q9NVP1 Q9NVP1 DDX18 ATP-dependent RNA helicase DDX18 1 VT(0.004)KS(0.996)PQK;VT(0.003)KS(0.997)PQK 86.898 0.011954 619600000 2244900 1811830 1316110 1525820 1074900 1145250 2090860 2810200 2034130 TRUE FALSE 1948230.777 1799927.969 1952585.198 1872280.752 1053511.593 1189308.509 1888088.719 2209260.599 1793657.469 1.086177719 1.00349593 1.088605396 1.043834057 0.587353835 0.663063338 1.052647315 1.231707078 1 20.77447298 2.009433465 24.87992268 1.135336034 0.910691265 0.195631505 0.177093367 283.8742153 748689.8788 0.079296957 0.053383353 102.1958982 -2.009433465 -0.224644769 VTLEYRPVIDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTLEYRPVIDK 11 1 P31040;D6RFM5;P31040-2;A0A087X1I3;P31040-3 P31040 SDHA "Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial" 0 88.021 0.0091721 0 340040 329010 251150 418190 413340 390630 298870 481870 374550 FALSE TRUE 295102.8524 326848.7116 372606.98 513146.4311 405115.3427 405657.7889 269885.6334 378825.8504 330271.1257 0.893516961 0.989637562 1.128185152 1.553712666 1.226614473 1.2282569 0.817163877 1.147014743 1 18.33329132 VTLILELLQHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTLILELLQHK 11 0 Q5T3Q7;Q9H583 Q5T3Q7 HEATR1 "HEAT repeat-containing protein 1;HEAT repeat-containing protein 1, N-terminally processed" 0 113.47 0.00084795 0 39028 37819 25070 33781 35274 29601 42643 49531 48980 FALSE TRUE 33870.35092 37570.5645 37193.93585 41451.49236 34572.11641 30739.76962 38507.48842 38939.1811 43189.6402 0.784223966 0.869897603 0.861177256 0.959755445 0.800472434 0.711739424 0.891590859 0.901586142 1 15.39839768 1.407643697 1.858918862 1.019244648 0.839281345 0.385357053 0.065833979 0.676302015 3.133433893 0.196544678 0.019239933 25.56487641 -1.407643697 -0.179963303 VTLLEGDHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VTLLEGDHVR 10 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;; 141.95 3.66E-05 1220890000 789640 726820 494890 649800 705010 757220 668820 787130 1114690 FALSE TRUE 685287.0733 722045.4716 734220.4593 797347.0216 690981.6803 786350.7434 603957.9393 618808.375 982912.6181 0.697200403 0.734597825 0.746984468 0.81120845 0.702994007 0.800021008 0.614457408 0.62956601 1 19.90670364 VTLTSEEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VTLTSEEEAR 10 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ;; 192.6 1.55E-06 2635060000 792590 679250 461340 514010 660470 662740 698920 711280 711490 FALSE TRUE 687847.2233 674787.962 684445.5671 630723.8267 647327.9392 688236.0366 631138.846 559178.3072 627378.4627 1.096383227 1.075567623 1.09096121 1.00533229 1.031798153 1.09700297 1.005993804 0.891293438 1 19.25897648 1.991226876 5.874404488 0.940215045 1.062822404 0.624263847 0.038741199 0.091616316 12.13549871 0.017607532 0.01045721 98.00018049 -1.991226876 0.122607359 VTLVFEHVDQDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VTLVFEHVDQDLR 13 0 F8W1L8;F8VYH9;F8VTV8;F8VWX7;P11802;F8VXD2;F8VZZ0;F8VZ51 F8W1L8 CDK4 Cyclin-dependent kinase 4 0 ;;; 174.65 1.96E-05 406389000 637430 547450 360122 439042 557640 577530 556690 632360 625760 FALSE TRUE 553192.0105 543853.7649 534278.2037 538733.1964 546544.055 599747.9528 502702.2895 497134.735 551783.3657 1.002552895 0.985629141 0.9682753 0.976349107 0.990504769 1.086926483 0.911050098 0.900959989 1 19.07374244 VTLYNTDQDGSDS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTLYNTDQDGSDSPR 15 0 Q9UPW0-2;Q9UPW0;C9JXI1;C9JVP0 Q9UPW0-2 FOXJ3 Forkhead box protein J3 1 VTLYNTDQDGSDS(1)PR 288.22 1.26E-27 0 209460 178780 112550 112560 149300 192480 152810 173650 180120 TRUE FALSE 181779.3303 177605.5824 166979.5565 138118.4684 146329.2221 199884.8302 137990.5097 136516.2988 158826.4188 1.144515703 1.118237027 1.051333637 0.86961898 0.921315378 1.25851122 0.868813329 0.85953143 1 17.27709138 4.019150085 3.813725113 0.956572152 1.12819483 0.267321665 0.115378097 0.296781233 9.552857445 0.03204462 0.068484965 10450.81321 -4.019150085 0.171622678 VTMLFLGLHNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTMLFLGLHNVR 12 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 118.61 0.00060734 157000000 578500 641780 404710 409760 579280 565810 531690 657580 631480 FALSE TRUE 502049.7593 637564.1049 600429.1097 502802.2708 567753.4613 587577.0768 480126.7856 516961.6343 556827.1538 0.901625856 1.144994637 1.078304292 0.902977284 1.01962244 1.055223462 0.86225462 0.928405935 1 19.08687004 2.250172437 24.99696183 0.927010309 1.020642846 0.206840428 0.079943078 313.1266874 674073.1839 0.029680978 0.022792499 177.8985619 -2.250172437 0.093632538 VTNDIS(ph)PESS(ph)PGVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VTNDISPESSPGVGR 15 0 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;E7EV93;E9PGW9;E5RGQ4;Q15154-3 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 2 VTNDIS(1)PES(0.448)S(0.552)PGVGR;VTNDIS(1)PESS(1)PGVGR;VTNDIS(1)PES(0.001)S(0.999)PGVGR 287.31 3.05E-34 846080000 1757090 1669880 929070 1209740 1534930 1493470 1503890 1742050 1585320 TRUE FALSE 1524886.105 1658910.448 1378371.36 1484429.957 1504387.896 1550924.757 1358042.979 1369526.164 1397905.276 1.090836505 1.18671163 0.986026295 1.061895954 1.076172987 1.109463412 0.971484265 0.979698831 1 20.41483517 -1.999999996 0.104831135 0.423880378 1.242595683 0.360472162 0.054891681 279.7331474 2.685442631 33.5084696 3.144699095 0.01 1.999999996 0.818715304 VTNDIS(ph)PESSPGVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VTNDISPESSPGVGR 15 0 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;E7EV93;E9PGW9;E5RGQ4;Q15154-3 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 VTNDIS(0.764)PES(0.231)S(0.005)PGVGR;VTNDIS(0.89)PES(0.1)S(0.01)PGVGR;VT(0.001)NDIS(0.863)PES(0.119)S(0.017)PGVGR;VTNDIS(0.723)PES(0.242)S(0.034)PGVGR 187.22 3.67E-07 4746120000 4411710 4393720 2685400 3511660 4565510 4389640 4084540 5007370 4520500 TRUE FALSE 3828691.346 4364857.364 3984068.422 4309036.075 4474665.283 4558512.291 3688421.939 3936582.893 3986091.64 0.960512625 1.095021831 0.999492431 1.081017815 1.122569596 1.143604489 0.925322916 0.987579627 1 21.92654345 2.228108105 24.99941233 0.972526517 1.068398098 0.388247925 0.056818907 217.8938959 521135.3484 0.023110818 0.015769669 169.086177 -2.228108105 0.09587158 VTNDISPES(ph)SPGVGR ddPTM_MDA-MB-175_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(0.281)PES(0.699)S(0.02)PGVGR;VTNDIS(0.119)PES(0.877)S(0.003)PGVGR 250.38 8.81E-19 5266500000 1864730 1875320 1160400 1435040 1933210 1778690 1815450 2166420 1859840 TRUE FALSE 1618301.206 1863000.899 1721573.321 1760887.765 1894742.903 1847117.355 1639387.938 1703147.942 1639971.834 0.986785975 1.135995668 1.049757859 1.073730493 1.155350881 1.126310414 0.99964396 1.038522679 1 20.64523961 2.230074136 24.9999551 1.017552373 1.090846764 0.344463163 0.048688747 210.4852093 620052.1588 0.019141795 0.013143565 169.8533573 -2.230074136 0.073294391 VTNEFVHINNLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VTNEFVHINNLK 12 0 O00743;O00743-2;O00743-3 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed" 0 ; 153.38 6.98E-05 1472350000 3336000 3021740 2060770 2565710 2991320 2760520 3589800 4274000 3948300 FALSE TRUE 2895139.148 3001889.991 3057365.265 3148293.67 2931798.584 2866718.991 3241661.749 3360038.36 3481536.472 0.831569386 0.862231378 0.878165514 0.904282835 0.842099058 0.823406279 0.931100902 0.965102157 1 21.73129271 1.939839836 2.547770212 0.983313141 0.859925705 0.804564851 0.02577804 0.126174578 1.502605857 0.018028865 0.007683727 87.06424458 -1.939839836 -0.123387435 VTNGAFTGEIS(ph)PGMIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VTNGAFTGEISPGMIK 16 0 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 1 VTNGAFTGEIS(1)PGMIK;VTNGAFTGEIS(1)PGMIK;VTNGAFTGEIS(1)PGMIK;VTNGAFTGEIS(1)PGMIK;VTNGAFTGEIS(1)PGMIK;VTNGAFTGEIS(1)PGMIK 275.31 3.08E-35 990490000 1654030 1590897 975956 1239118 1531275 1272138 1690372 1909864 1827580 TRUE FALSE 1435445.745 1580446.293 1447931.586 1520478.681 1500805.623 1321077.972 1526439.984 1501454.446 1611525.574 0.890737179 0.980714373 0.898485019 0.943502669 0.931294946 0.819768543 0.947201836 0.93169756 1 20.61999565 1.117357411 1.812233973 1.050357871 0.91604324 0.276302104 0.042593653 1.761276985 4.171130381 0.456242165 0.011447907 13.10259781 -1.117357411 -0.134314631 VTPDTDWAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VTPDTDWAR 9 0 P53396;P53396-2;P53396-3;K7ESG8 P53396 ACLY ATP-citrate synthase 0 ;;; 178.65 0.00011799 5623650000 3588250 3545570 2510590 3002110 3760050 3926600 3613690 3815090 4088480 FALSE TRUE 3114053.671 3522278.917 3724719.721 3683784.96 3685232.361 4077658.843 3263234.9 2999262.693 3605144.552 0.86378053 0.977014615 1.033167926 1.021813385 1.022214868 1.13106667 0.905160626 0.831939649 1 21.78162568 2.03790225 24.99749352 0.893340758 1.009900582 0.246771055 0.076807836 180.4061324 118981.7197 0.031416767 0.021181132 109.1194706 -2.03790225 0.116559824 VTQHES(ph)DNENEIQIQNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VTQHESDNENEIQIQNK 17 0 Q5VZL5-2;Q5VZL5-4;Q5VZL5 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 1 VT(0.001)QHES(0.999)DNENEIQIQNK;VT(0.001)QHES(0.999)DNENEIQIQNK 340.32 1.16E-72 985790000 965500 719320 536220 617660 693300 615310 799820 916130 1017190 TRUE FALSE 837906.7287 714594.7396 795537.7855 757909.1433 679504.6864 638981.3739 722253.5795 720222.7288 896938.957 0.934184787 0.796703872 0.886947522 0.844995233 0.757581863 0.712402298 0.805242736 0.802978534 1 19.77465028 7.409850114 1.303074285 0.817243591 155.5217146 0.14136553 0.078253966 3885.047178 6.106862268 0.022857152 1797108.503 25695088.28 -7.409850114 154.704471 VTQVDGHSSK ddPTM_MDA-MB-175_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 ; 111.94 0.0016873 186399000 444550 367490 149096 320460 378340 369900 460240 523400 568950 FALSE TRUE 385801.5912 365075.934 221199.3243 393225.3409 370811.7742 384130.2924 415605.9956 411474.9831 501689.3791 0.769004901 0.727693169 0.440908924 0.783802403 0.73912622 0.765673559 0.828412984 0.82017878 1 18.93643487 -2 0.385287708 5.439596067 0.661636839 0.50518672 0.096604808 68.60364904 1.010839114 243.3742295 0.104893028 0.01 2 -4.777959228 VTQVDGNS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VTQVDGNSPVR 11 0 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 1 VTQVDGNS(1)PVR;VTQVDGNS(1)PVR 180.3 7.05E-06 355410000 441900 370120 251924 312830 390750 374400 383900 401020 471880 TRUE FALSE 383501.7954 367688.6573 373755.289 383862.8328 382974.8395 388803.4103 346669.4371 315264.9937 416094.884 0.921669096 0.883665413 0.898245336 0.922536776 0.920402664 0.934410456 0.833149963 0.757675727 1 18.66655302 2.231133203 24.97467735 0.840270098 0.912165429 0.088875301 0.06160156 245.8319775 826600.4186 0.02432235 0.016763168 170.2680661 -2.231133203 0.071895331 VTRS(ph)PPETAAPVEDMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTRSPPETAAPVEDMAR 17 1 Q9Y3L3;Q6ZT62-2;Q6ZT62;A0A2R8Y5V0;A0A3B3IU28 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 VT(0.175)RS(0.825)PPETAAPVEDMAR 74.428 0.014637 237780000 76486 93213 68899 50128 74567 98523 129740 147710 35123 TRUE FALSE 66378.18131 92600.67767 102218.7869 61510.32856 73083.26259 102313.2436 117157.8348 116123.366 30970.79895 2.143250531 2.989935061 3.30048918 1.986074969 2.359747409 3.303539044 3.782848319 3.749446895 1 14.91862098 2.733116243 24.28714744 3.15971204 2.589721705 0.028140017 0.863011762 795.5425881 3548872.116 0.293247619 0.266185004 540.8990804 -2.733116243 -0.569990335 VTRS(ph)PPTQVAISSDSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTRSPPTQVAISSDSAR 17 1 Q6ZUT6;Q6ZUT6-4;H0YM82;Q6ZUT6-3 Q6ZUT6 C15orf52 Uncharacterized protein C15orf52 1 VT(0.1)RS(0.899)PPT(0.001)QVAISSDSAR 69.525 0.020937 178160000 47252 32180 19532 27651 21289 25895 29715 38642 26373 TRUE FALSE 41007.52848 31968.60746 28977.74053 33929.58217 20865.39055 26891.19741 26833.24387 30378.70901 23255.21398 1.763369217 1.374685586 1.24607499 1.459009674 0.897234941 1.156351321 1.153859255 1.306318189 1 14.50526659 7.999997556 0.671621247 1.151757652 64.35217024 0.637491702 0.146060739 165.2244084 0.989039146 0.059325291 15592.84422 99999437.27 -7.999997556 63.20041259 VTRS(ph)QEELREDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTRSQEELREDK 12 2 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 VT(0.005)RS(0.995)QEELREDK 72.175 0.042596 0 124140 125520 61228 64353 119820 99048 153860 150840 53508 TRUE FALSE 107734.5845 124695.4509 90838.0656 78965.33222 117435.8164 102858.4407 138938.6809 118584.0398 47182.3452 2.283366459 2.642841307 1.925255415 1.673620332 2.488977942 2.180019671 2.94471757 2.513313811 1 15.52595951 VTRYPILGIPQAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTRYPILGIPQAHR 14 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 57.679 0.069027 170750000 181330 174510 131440 113880 200020 204020 161950 212800 80342 FALSE TRUE 157366.7811 173363.6323 195004.8236 139738.1945 196039.9933 211868.7814 146244.1139 167294.376 70844.06029 2.22131228 2.447115984 2.752592424 1.972475801 2.767204372 2.990635779 2.064310167 2.36144534 1 16.11235928 1.075841087 2.097518322 7.76E-14 2.483818537 0.664490046 0.322089415 0.755928154 2.233538906 4.263007229 0.08415541 11.90806201 -1.075841087 2.483818537 VTS(ph)LKL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTSLKL 6 1 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 1 VT(0.125)S(0.875)LKL 76.679 0.078831 38947000 430440 317460 217580 410900 357970 265150 368400 567500 488280 TRUE FALSE 373556.2634 315374.5844 322802.4158 504201.1252 350847.0974 275350.4921 332672.6247 446144.5413 430556.0947 0.867613461 0.732481988 0.749733704 1.171046308 0.814869657 0.639522923 0.772658032 1.036205379 1 18.71584168 1.709918612 7.100510418 1.016080477 0.821354536 0.256428783 0.139023228 0.174394233 20.87579468 0.085123257 0.037414904 51.27652809 -1.709918612 -0.19472594 VTS(ph)TQQQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VTSTQQQTR 9 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;A0A1B0GV30;P49023-3;P49023-4 F5GZ78;P49023-3;P49023-4 PXN Paxillin 1 VT(0.274)S(0.674)T(0.052)QQQTR;VT(0.019)S(0.975)T(0.007)QQQTR;VT(0.011)S(0.884)T(0.105)QQQTR 142.29 0.0001098 1925960000 2640550 3172290 1964480 2311850 2899140 3984820 3349660 3349750 3441520 TRUE FALSE 2291594.627 3151451.018 2914509.099 2836790.877 2841452.786 4138118.604 3024810.489 2633432.03 3034667.426 0.755138638 1.03848316 0.960404779 0.934794651 0.936330868 1.363615192 0.996751889 0.867782745 1 21.53310699 2.938244463 24.99991897 1.036054311 0.933524731 0.167453588 0.142211918 569.8060172 230668.3736 0.048308653 0.048308706 867.4500237 -2.938244463 -0.10252958 VTSAHKGPDETLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VTSAHKGPDETLR 13 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;; 157.38 2.36E-05 1591110000 2046670 1804270 510711 967311 1763140 1553390 1964150 2195680 526908 FALSE TRUE 1776197.374 1792417.632 757692.5478 1186953.747 1728056.964 1613149.918 1773667.035 1726150.919 464617.5365 3.822923662 3.857834651 1.630787666 2.554689941 3.719310676 3.471995333 3.817477594 3.71520828 1 18.82568408 3.244228041 24.99740828 3.282910393 2.93480941 0 1.021774514 707.8987675 3122323.651 0.302347298 0.379439782 1754.80168 -3.244228041 -0.348100984 VTSFSTPPT(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VTSFSTPPTPER 12 0 B0QY16;Q6ICG6-3;Q6ICG6;Q6ICG6-2 B0QY16 KIAA0930 Uncharacterized protein KIAA0930 1 VTSFST(0.002)PPT(0.998)PER;VTSFSTPPT(1)PER 168.18 0.00052789 646200000 939730 806720 677050 693600 886600 859540 984120 1107490 1149930 TRUE FALSE 815542.2995 801420.6032 1004473.645 851092.481 868958.3946 892607.06 888680.1939 870661.882 1013986.585 0.804292987 0.790366081 0.990618277 0.839352801 0.856972279 0.880294742 0.876422042 0.858652269 1 19.95160714 -2 0.018444905 1.953451515 6.33E-17 0.22897792 0.060690103 15341.2685 28.14536316 1841.532955 1204.588526 0.01 2 -1.953451515 VTSSMSS(ph)PSMQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 VTSSMSSPSMQPK 13 0 Q13136-2;A0A2R8Y7R9;Q13136 Q13136-2 PPFIA1 Liprin-alpha-1 1 VTSSMS(0.002)S(0.995)PS(0.003)MQPK;VTSSMSS(0.838)PS(0.161)MQPK;VTSSMS(0.318)S(0.68)PS(0.001)MQPK;VTSS(0.001)MS(0.122)S(0.761)PS(0.116)MQPK;VTSSMS(0.026)S(0.663)PS(0.311)MQPK;VTSSMS(0.096)S(0.891)PS(0.013)MQPK;VTSSMS(0.019)S(0.691)PS(0.29)MQPK;VTSSMS(0.02)S(0.979)PSMQPK;VTSSMS(0.022)S(0.978)PSMQPK;VTSSMS(0.013)S(0.987)PSMQPK;VTS(0.003)S(0.014)MS(0.366)S(0.598)PS(0.019)MQPK;VTSSMS(0.226)S(0.753)PS(0.021)MQPK;VTSSMS(0.009)S(0.991)PSMQPK 374.7 2.04E-91 9402345000 12311960 11364620 8138120 9920930 11716770 10080480 12933330 14964800 13336820 TRUE FALSE 10684903.29 11289965.06 12073742.05 12173628.79 11483629.2 10468282.59 11679057.65 11764693.98 11760156.33 0.908568134 0.960018281 1.026665098 1.035158755 0.976486101 0.890148251 0.993103945 1.000385849 1 23.4874039 VTSSVPLPSGSTSS(ph)PGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 VTSSVPLPSGSTSSPGR 17 0 Q15036-2;Q15036 Q15036-2 SNX17 Sorting nexin-17 1 VTSSVPLPS(0.125)GS(0.034)T(0.026)S(0.158)S(0.656)PGR;VTSSVPLPSGST(0.001)S(0.083)S(0.916)PGR;VTSSVPLPSGSTS(0.061)S(0.938)PGR;VTSSVPLPSGSTS(0.001)S(0.999)PGR;VTSSVPLPSGSTS(0.057)S(0.943)PGR;VTSSVPLPSGSTSS(1)PGR;VTSSVPLPSGSTS(0.001)S(0.999)PGR;VTSSVPLPS(0.009)GS(0.023)T(0.023)S(0.133)S(0.813)PGR 356.74 6.52E-88 9668704000 7073460 6576490 4143110 4918962 6333180 6432110 6356190 6756790 6679220 TRUE FALSE 6138684.339 6533288.604 6146731.854 6035887.504 6207162.109 6679557.434 5739767.672 5311903.04 5889610.221 1.042290425 1.109290489 1.043656817 1.024836496 1.053917301 1.134125551 0.974558155 0.901910796 1 22.48974073 2.06674706 7.017792643 0.942216012 1.065845444 0.625003649 0.040011459 0.119190108 10.23769824 0.01608822 0.010769478 116.6130246 -2.06674706 0.123629432 VTSVAGVYFTDTYGDRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTSVAGVYFTDTYGDRDR 18 1 A6NFQ2-2;A6NFQ2 A6NFQ2-2 TCAF2 TRPM8 channel-associated factor 2 0 201.75 1.25E-15 87530000 49814 58099 32082 39376 56767 58142 50845 62040 44769 FALSE TRUE 43230.95369 57717.34384 47596.96251 48316.92262 55637.44776 60378.76036 45914.05973 48773.2288 39476.45982 1.095107157 1.462069905 1.205704937 1.223942644 1.409382909 1.529487716 1.163074398 1.235501588 1 15.268705 1.126566638 1.420845884 0.806703341 1.31402252 0.324979481 0.135494528 1.940402811 2.790531532 1.537144334 0.038631574 13.38340554 -1.126566638 0.50731918 VTTEIQLPSQS(ph)PVEEQSPASLSSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VTTEIQLPSQSPVEEQSPASLSSLR 25 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 VTTEIQLPS(0.002)QS(0.998)PVEEQSPASLSSLR;VTTEIQLPSQS(1)PVEEQSPASLSSLR;VTTEIQLPSQS(1)PVEEQSPASLSSLR;VTTEIQLPSQS(1)PVEEQSPASLSSLR;VTTEIQLPSQS(1)PVEEQSPASLSSLR;VTTEIQLPSQS(1)PVEEQSPASLSSLR 309.86 1.19E-74 3548690000 2277770 2609100 1608540 2217780 2771700 2891040 2768130 3261830 2952880 TRUE FALSE 1976756.923 2591960.65 2386435.324 2721360.846 2716548.593 3002260.18 2499677.179 2564313.038 2603793.89 0.759183333 0.995455385 0.916522361 1.045152174 1.043304005 1.153032961 0.960013459 0.984837182 1 21.31218382 5.430590422 1.116670566 1.021940865 1.81E-18 0.630794219 0.061396157 4.697583703 1.601060511 0.018901884 8.204798523 269519.6429 -5.430590422 -1.021940865 VTTHIPQTPVRPET(ph)PNRTPSATLSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTTHIPQTPVRPETPNRTPSATLSEK 26 2 Q5VWG9 Q5VWG9 TAF3 Transcription initiation factor TFIID subunit 3 1 VTTHIPQT(0.001)PVRPET(0.888)PNRT(0.031)PS(0.04)AT(0.04)LSEK 111.79 0.0019365 195220000 258220 202290 134960 149890 173370 166970 238970 260550 158880 TRUE FALSE 224095.5728 200961.1437 200227.1074 183924.8154 169920.2762 173393.4439 215794.7262 204833.4101 140097.3874 1.599569963 1.43443891 1.429199439 1.312835441 1.212872555 1.237663651 1.540319418 1.462078729 1 17.09607053 4.632682957 1.226738056 1.324365598 1.681345344 0.29729766 0.147615036 1.876814314 2.800461021 0.046096331 0.812446856 42922.29716 -4.632682957 0.356979746 VTTHPLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VTTHPLAK 8 0 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ;; 103.83 0.0046967 3519340000 7200110 6217950 3890520 5223310 5622490 5370880 7080790 7804230 7786350 FALSE TRUE 6248597.221 6177103.877 5771988.485 6409342.369 5510613.449 5577501.229 6394096.076 6135356.147 6865856.573 0.910097255 0.899684375 0.840680026 0.933509505 0.80261121 0.812353298 0.931288909 0.893603891 1 22.71100829 0.746702885 1.252872096 1.263433807 0.870945589 0.424619376 0.045431853 4.398329084 2.42149914 3.055998358 0.013641116 5.580882582 -0.746702885 -0.392488218 VTTVTEIGKDVIGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VTTVTEIGKDVIGLR 15 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITI7 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 154.88 2.19E-06 726110000 1021120 880070 497920 578590 867230 694730 1004280 1176640 374270 FALSE TRUE 886176.4048 874288.7622 738715.7774 709967.7027 849973.8197 721456.7127 906885.0802 925024.6926 330024.227 2.685185912 2.649165397 2.238368329 2.151259346 2.575489162 2.186071972 2.747934867 2.802899354 1 18.33221241 4.251766705 21.25573606 2.326715789 2.667177837 0.091731919 0.503902438 109.0787921 175543.518 0.122558503 0.317916559 17855.28165 -4.251766705 0.340462048 VTVAGGVHISGLHTESAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VTVAGGVHISGLHTESAPR 19 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 251.35 3.28E-26 2065280000 859377 1043918 438616 718054 1430384 1643400 1085055 1389342 1407990 FALSE TRUE 745808.1521 1037060.434 650732.1647 881099.1355 1401922.157 1706622.661 979826.5331 1092242.025 1241539.026 0.600712613 0.835302324 0.524133475 0.709682996 1.129180902 1.37460251 0.789203168 0.879748443 1 20.24369818 3.316975879 6.559271149 1.013191351 0.66461112 0.528427925 0.171959674 0.197629628 13.27957045 0.053547328 0.069053267 2074.798279 -3.316975879 -0.348580231 VTVAGLAGKDPVQCSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VTVAGLAGKDPVQCSR 16 1 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ; 200.58 3.21E-11 3843800000 1528280 1232300 660960 878530 1183790 1021210 1255820 1534840 752760 FALSE TRUE 1326313.926 1224204.94 980602.4668 1078013.664 1160234.895 1060496.61 1134030.77 1206626.41 663769.5703 1.998154156 1.844322179 1.477323623 1.624078162 1.747948304 1.597687898 1.70847056 1.817839299 1 19.34032297 1.2337895 25 0.999998909 1.719634317 0.715734487 0.143916407 84.5326722 442885.7138 0.286660308 0.036102752 17.13126762 -1.2337895 0.719635408 VTVLGHVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VTVLGHVQR 9 0 P17858;P17858-2;A0A2R8Y891;P08237;P08237-3 P17858;A0A2R8Y891 PFKL;PFKM "ATP-dependent 6-phosphofructokinase, liver type;ATP-dependent 6-phosphofructokinase, muscle type" 0 ;; 179.37 4.99E-05 1283490000 1027480 1465410 780075 1032325 1433650 1381330 1332050 1422950 1422350 FALSE TRUE 891695.9147 1455783.625 1157321.879 1266730.169 1405123.17 1434470.659 1202867.996 1118663.216 1254201.403 0.710967084 1.160725559 0.922756007 1.009989437 1.120332959 1.143732303 0.959070842 0.891932678 1 20.25833761 7.307366093 11.05093468 0.994013745 0.206392314 0 0.134697482 0 0 0.028963478 0 20293926.94 -7.307366093 -0.787621431 VTVNTNMVDLNDYLQHILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTVNTNMVDLNDYLQHILK 19 0 P53618 P53618 COPB1 Coatomer subunit beta 0 178.43 3.80E-14 461670000 185550 127410 104110 162730 136640 110950 154040 212830 210430 FALSE TRUE 161029.0974 126573.0353 154457.9442 199680.3337 133921.1313 115218.3183 139101.2245 167317.9607 185553.2051 0.867832476 0.682138771 0.832418627 1.07613519 0.72173979 0.62094491 0.749656814 0.901724983 1 17.5014734 1.507939095 3.475047787 0.989209059 0.792341511 0.239388727 0.12325997 0.331042102 8.033137362 0.132632135 0.033973036 32.20617106 -1.507939095 -0.196867549 VTVPTSGNTIES(ph)PLHENISNSTSFKDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTVPTSGNTIESPLHENISNSTSFKDEK 28 1 A0A2R8YFF1;Q8N302 A0A2R8YFF1 AGGF1 Angiogenic factor with G patch and FHA domains 1 1 VTVPTSGNTIES(1)PLHENISNSTSFKDEK 174.6 7.79E-13 109450000 82674 67250 53296 59060 59798 43128 86551 110750 67463 TRUE FALSE 71748.42143 66808.23032 79070.12386 72470.47568 58608.13679 44787.16207 78157.29734 87066.97436 59487.60099 1.206107159 1.123061431 1.32918663 1.218245054 0.985216008 0.752882304 1.31384181 1.463615491 1 15.86030138 -1.15921851 9.406697493 0.153578649 1.172635015 0 0.204368044 0 0 0 0.049605891 0.0693077 1.15921851 1.019056365 VTVTSS(ph)PIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VTVTSSPIR 9 0 Q5T534;Q5T532;Q9H2G9-2;Q9H2G9 Q5T534 BLZF1 Golgin-45 1 VTVT(0.009)S(0.022)S(0.969)PIR;VTVT(0.032)S(0.132)S(0.835)PIR 141.71 0.00011125 433390000 700850 738660 635160 823790 869510 892340 862350 983070 1648650 TRUE FALSE 608230.8968 733807.6938 942325.5005 1010844.11 852208.4522 926668.8972 778719.4297 772848.1308 1453748.475 0.418387986 0.504769364 0.648203948 0.695336317 0.586214511 0.637434132 0.53566311 0.531624379 1 20.47134625 1.235155765 24.99988393 1.000000595 0.573305945 0.743876087 0.079324497 53.32201887 391449.2404 0.145080932 0.020502588 17.18524648 -1.235155765 -0.42669465 VTVVFSTVFKDDDDVVIGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTVVFSTVFKDDDDVVIGK 19 1 O15144 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 109.42 0.00029101 0 15201 11672 8154 8589.8 11033 9988.9 13385 14478 16266 FALSE TRUE 13192.14934 11595.32586 12097.30167 10540.24538 10813.46489 10373.17945 12086.92476 11381.99237 14343.05201 0.919758872 0.808428071 0.843425909 0.734867682 0.753916592 0.723219817 0.842702428 0.793554423 1 13.80806442 1.237563649 24.98533248 1.000000238 0.799308261 0.531824328 0.05817263 20.00058376 500982.6591 0.084522165 0.014281967 17.28079225 -1.237563649 -0.200691977 VTWDGHSGSMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VTWDGHSGSMAR 12 0 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 ; 99.318 0.0038634 768570000 1308670 1247270 754030 960990 1098890 1142640 1321110 1514840 1297940 FALSE TRUE 1135725.944 1239076.601 1118681.43 1179197.467 1077024.239 1186598.1 1192988.956 1190903.254 1144499.012 0.992334578 1.082636672 0.977442024 1.030317593 0.941044272 1.036783857 1.042367834 1.040545463 1 20.12628479 VTYAEKLS(ph)PLTGQACR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VTYAEKLSPLTGQACR 16 1 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 VTYAEKLS(0.785)PLT(0.215)GQACR 76.704 0.015726 330480000 167750 152460 119780 127750 166190 152950 162370 208490 184540 TRUE FALSE 145581.4125 151458.4802 177706.0086 156757.59 162883.1441 158834.0855 146623.3824 163906.036 162723.8914 0.894652968 0.930769778 1.09207079 0.963334816 1.000978668 0.976095668 0.901056268 1.007264726 1 17.31206656 4.463972104 24.9997572 0.988513296 0.903682105 0.338491897 0.047000604 217.3770327 413287.437 0.011522738 0.030520849 29105.30159 -4.463972104 -0.084831191 VTYLVHNFEEGGGVAMGMYNQDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VTYLVHNFEEGGGVAMGMYNQDK 23 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;; 327.46 1.92E-86 2310294000 3321860 2290100 1547244 2104820 2146640 1840710 2671560 3110680 2698520 FALSE TRUE 2882867.784 2275056.182 2295496.374 2582751.551 2103926.064 1911523.305 2412472.522 2445485.289 2379504.04 1.211541454 0.956105199 0.964695304 1.085415914 0.884186801 0.803328455 1.013855191 1.027728992 1 21.18222947 4.740557535 24.66767367 0.969802475 1.211541553 0.492101831 0.078053987 141.4229735 1746822.977 0.020158802 0.127673424 55024.68117 -4.740557535 0.241739078 VTYMEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VTYMEEER 8 0 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;; 157.33 0.0008809 2740210000 2822460 2876580 1796810 2103760 2683720 2710320 2764200 3004710 2853990 FALSE TRUE 2449464.76 2857683.557 2665753.326 2581450.862 2630319.223 2814587.764 2496128.309 2362176.149 2516594.553 0.973325145 1.135535938 1.059270085 1.025771457 1.045189905 1.118411291 0.991867485 0.938639935 1 21.26304137 2.053526095 7.719639201 0.964979902 1.060656044 0.412025811 0.047085948 0.188172795 23.35973888 0.018254185 0.01223534 113.1165353 -2.053526095 0.095676142 VTYS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VTYSPR 6 0 Q96K76-2;Q96K76-4;Q96K76;Q96K76-3 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 1 VTYS(1)PR;VT(0.007)YS(0.993)PR;VTYS(1)PR;VTYS(1)PR 103.35 0.036459 2436510000 3448610 3837300 2146710 2673060 3056270 3586730 3127390 3658620 3551620 TRUE FALSE 2992867.451 3812092.524 3184866.136 3280019.128 2995456.206 3724713.824 2824096.199 2876252.584 3131751.53 0.955652906 1.217239774 1.016960032 1.047343347 0.956479522 1.18933887 0.901762535 0.918416598 1 21.57853832 2.206360994 24.98823827 0.933954944 1.063048572 0.301780775 0.088584906 216.4473029 167970.64 0.03390552 0.022861084 160.827753 -2.206360994 0.129093628 VTYVVLDEADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VTYVVLDEADR 11 0 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ; 128.17 0.0006316 215430000 302570 279728 180488 212908 282829 293434 279236 318983 286318 FALSE TRUE 262584.6079 277890.4483 267772.6005 261252.0155 277201.2562 304722.5959 252155.7357 250770.9678 252469.8122 1.040063387 1.100687824 1.060612349 1.034785162 1.097958024 1.206966461 0.998755984 0.993271099 1 17.94575137 2.061075177 24.99998108 0.996108955 1.088457918 0.458915903 0.047499079 60.61185471 24809.84505 0.019693748 0.013277521 115.0999613 -2.061075177 0.092348963 VVAIGECGLDFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VVAIGECGLDFDR 13 0 E5RG17;Q6P1N9;H0YBX2;G5EA19;U3KQS5;Q6P1N9-2;E5RK70;A0A0D9SGD3;E5RG62;E5RGF2 E5RG17 TATDN1 Putative deoxyribonuclease TATDN1 0 138.99 9.97E-06 0 87737 75585 53377 89949 84028 90528 82908 99402 95702 FALSE TRUE 76142.33315 75088.47716 79190.29574 110373.2952 82356.0072 94010.67074 74867.59492 78145.65585 84388.21858 0.902286296 0.889798107 0.938404638 1.307923038 0.975918304 1.114026014 0.887180654 0.92602566 1 16.36475398 5.554074286 0.00280062 0.94032463 1.04370646 0 0.129861155 44113366.55 23886.66643 433915.5501 447938.1961 358157.695 -5.554074286 0.103381831 VVASGPGLEHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 163.51 0.00022442 1055770000 1332250 1296500 718670 989980 1130700 1145640 1235770 1436650 2141790 FALSE TRUE 1156189.787 1287983.206 1066221.216 1214770.09 1108201.282 1189713.512 1115925.216 1129433.578 1888590.026 0.612197338 0.681981366 0.564559381 0.643215347 0.586787639 0.629948001 0.590877427 0.598030045 1 20.84887813 1.23722575 24.99999404 1.000000468 0.612895059 0.931890456 0.03284174 7.457627708 139615.7243 0.045262336 0.007468587 17.26735231 -1.23722575 -0.387105409 VVAT(ph)TQMQAADAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VVATTQMQAADAR 13 0 P15144 P15144 ANPEP Aminopeptidase N 1 VVAT(0.5)T(0.5)QMQAADAR 91.867 0.066055 47360000 3157.7 2498.8 944.91 1875.7 4378 2161.2 2605 3071.6 1983.8 TRUE FALSE 2740.401944 2482.385218 1401.871637 2301.606353 4290.886365 2244.342762 2352.367501 2414.762243 1749.277424 1.566590815 1.419091783 0.801400405 1.315746903 2.45294789 1.283011335 1.344765255 1.380434121 1 10.77254339 0.751017827 1.361659984 9.65E-12 1.460067679 0.109309544 0.407657037 11.21969999 6.98162576 31.85536274 0.123715197 5.636607923 -0.751017827 1.460067679 VVDDEIYYFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VVDDEIYYFR 10 0 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9 Q86U86-8 PBRM1 Protein polybromo-1 0 ;;; 210.37 1.82E-07 347723000 381638 317383 232450 248539 308096 329229 318218 352754 353514 FALSE TRUE 331203.5714 315298.0902 344863.5975 304973.5786 301965.4924 341894.6527 287357.2673 277320.3022 311721.9776 1.062496696 1.011472122 1.10631788 0.978351225 0.968701324 1.096793544 0.92183833 0.889639878 1 18.24990035 2.21719211 24.97845756 0.926621063 1.03351095 0.443657402 0.052333611 197.8837557 231312.0972 0.020889961 0.014098476 164.8891617 -2.21719211 0.106889887 VVDLLAQDADIVCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVDLLAQDADIVCR 14 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ; 204.01 3.31E-08 85680000 98656 102308 68076 77222 100527 100551 91717 100286 103600 FALSE TRUE 85618.35964 101635.932 100997.7813 94756.43536 98526.70938 104419.262 82822.29946 78840.61933 91352.52602 0.937230347 1.112568381 1.105582798 1.03726125 1.07853295 1.143036395 0.906622981 0.863037102 1 16.479157 2.222959299 24.96824459 0.909990303 1.071662802 0.527795256 0.064582827 159.2093312 254795.5003 0.025359542 0.017165399 167.093401 -2.222959299 0.161672499 VVDLMAHMASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 13 VVDLMAHMASK 11 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;; 166.14 1.69E-05 1.12247E+11 75335270 75299475 50495813 65150403 67658486 62850242 74787150 88719380 98189371 FALSE TRUE 65379523.19 74804827.79 74915757.07 79943797.76 66312214.5 65268131.48 67534303.7 69747431 86581535.42 0.755120857 0.863981303 0.865262515 0.923335413 0.765893261 0.753834304 0.780008155 0.805569348 1 26.36755605 1.236727829 24.9988425 1.000000232 0.815302757 0.525512382 0.055496361 42.59433274 580811.069 0.090389656 0.014386622 17.24756653 -1.236727829 -0.184697475 VVDLMAHMASKE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 21 VVDLMAHMASKE 12 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;;;; 168.98 4.73E-05 1.15898E+11 62787810 62462320 28241390 33857430 53508670 48401110 70177490 77590380 15280291 FALSE TRUE 54490241.82 62052000.91 41899020.67 41545276.96 52443952.15 50263132.02 63371687.82 60998281.05 13473872.41 4.044141149 4.605357617 3.109649506 3.083395457 3.892270208 3.730414725 4.703301762 4.527152938 1 23.68366121 4.249948672 24.99643214 3.614909584 4.324749422 0.094396649 1.034949605 624.9638196 1371749.701 0.258108205 0.669976392 17780.69253 -4.249948672 0.709839838 VVDPFSKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVDPFSKK 8 1 P61247;E9PFI5;H0Y8L7;H0Y9Y4;D6RI02 P61247 RPS3A 40S ribosomal protein S3a 0 ; 80.239 0.041632 1198500000 2647100 2197400 1476050 1703890 2022940 1605360 2859800 3169800 1316810 FALSE TRUE 2297279.028 2182965.135 2189872.717 2090784.267 1982687.452 1667119.238 2582457.036 2491962.937 1161138.222 1.978471628 1.88002177 1.885970745 1.800633402 1.70753784 1.435762949 2.224073747 2.146138066 1 20.14710829 4.010538292 1.840769056 1.782839198 1.941611385 0.048206962 0.344817978 1.769932813 11.59084113 0.103126176 0.294767906 10245.62113 -4.010538292 0.158772187 VVDRDSEEAEIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 VVDRDSEEAEIIR 13 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;;;;; 280.23 1.98E-32 5401000000 3878010 3187790 1859060 2134616 2865760 2969020 2821340 3254690 2305307 FALSE TRUE 3365521.153 3166849.198 2758107.634 2619313.188 2808736.983 3083240.121 2547726.881 2558699.872 2032776.233 1.655627953 1.557893656 1.356818124 1.288539853 1.381724627 1.516763169 1.253323824 1.258721856 1 20.95501998 -0.45166258 0.246053484 6.90E-40 1.597538964 0.659362856 0.107945074 29.35160905 0.936845185 16.18778952 0.462116365 0.353457678 0.45166258 1.597538964 VVDRDSEEAEIIRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VVDRDSEEAEIIRK 14 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 122.33 6.15E-05 157570000 269600 208540 95254 107870 204600 165130 244310 301340 59917 FALSE TRUE 233971.6769 207170.087 141319.153 132363.5322 200528.8603 171482.658 220616.8538 236900.786 52833.68052 4.428456898 3.921174618 2.67479289 2.505286985 3.795473992 3.245707213 4.175685881 4.483897084 1 15.68917029 VVDYSQFQES(ph)DDADEDYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 76 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;VVDYS(0.001)QFQES(0.999)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYS(0.001)QFQES(0.999)DDADEDYGR;VVDYS(0.007)QFQES(0.992)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYS(0.003)QFQES(0.997)DDADEDYGR;VVDY(0.002)S(0.016)QFQES(0.982)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDY(0.002)S(0.393)QFQES(0.604)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYS(0.024)QFQES(0.976)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYS(0.001)QFQES(0.999)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 371.19 5.48E-108 89766670000 8462288 7967826.27 5889772.4 6985927.4 8004575.5 8093738.4 7591770.6 8699192.9 10901161.2 TRUE FALSE 7343975.2 7915485.095 8738086.033 8572188.989 7845300.108 8405109.754 6855521.856 6838938.196 9612438.342 0.764007522 0.823462769 0.909039488 0.891780908 0.816161293 0.874399341 0.713192804 0.711467575 1 23.19647101 2.268766861 24.99893005 0.784103739 0.848954479 0.01566757 0.089410756 470.2050522 389143.8965 0.033362359 0.025838991 185.6807413 -2.268766861 0.064850741 VVDYSQFQES(ph)DDADEDYGRDSGPPTK ddPTM_MDA-MB-175_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 344.94 5.56E-97 20039230000 4979996 4061255 1896025 2087308 3713296 3143988 4250070 5100477 1207496 TRUE FALSE 4321876.911 4034576.348 2812949.032 2561263.184 3639408.675 3264939.253 3837898.866 4009779.686 1064747.198 4.059063895 3.789234059 2.641893809 2.405512959 3.418096502 3.066398538 3.604516519 3.765945279 1 20.0220795 4.356213826 5.528017449 2.981335138 3.989355273 0.234088861 0.787910575 0.315131642 13.62567726 0.196174602 0.540299092 22709.82702 -4.356213826 1.008020134 VVDYSQFQES(ph)DDADEDYGRDSGPPTKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VVDYSQFQESDDADEDYGRDSGPPTKK 27 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 VVDYSQFQES(1)DDADEDYGRDSGPPTKK;VVDYSQFQES(1)DDADEDYGRDSGPPTKK;VVDYSQFQES(1)DDADEDYGRDSGPPTKK;VVDYSQFQES(1)DDADEDYGRDSGPPTKK 249.14 4.20E-46 7366960000 1105579 885990 310797 302312 684453 517421 1085308 1212866 115346 TRUE FALSE 959473.934 880169.8734 461099.4688 370956.5601 670833.7244 537326.5207 980054.9972 953504.0444 101709.9273 9.43343447 8.653726306 4.533475552 3.647201115 6.595557998 5.28293093 9.635785055 9.374739221 1 16.63410097 4.382376088 6.762647378 6.206472508 9.238803984 0.209800837 2.567386914 0.360121013 21.16401207 0.676652356 1.82520953 24119.93251 -4.382376088 3.032331475 VVDYSQFQES(ph)DDADEDYGRDSGPPTKKIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VVDYSQFQESDDADEDYGRDSGPPTKKIR 29 3 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 VVDYSQFQES(1)DDADEDYGRDSGPPTKKIR 237.42 1.47E-44 128270000 19928 17837 12168 16656 17508 18926 22035 20546 24018 TRUE FALSE 17294.46431 17719.82757 18052.4855 20437.99937 17159.62505 19654.09547 19898.04909 16152.39779 21178.6194 0.816600175 0.836684736 0.852391988 0.965029825 0.810233412 0.928015896 0.93953476 0.762674728 1 14.37032093 3.990276599 22.99364996 0.888004839 0.831116353 0.152233478 0.070498022 354.4184112 838141.9171 0.017875778 0.034056369 9778.598152 -3.990276599 -0.056888486 VVDYSQFQESDDADEDYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VVDYSQFQESDDADEDYGR 19 0 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ;; 325.24 2.91E-62 807980000 366520 325348 235226 299480 282164 297975 275861 363380 414040 FALSE TRUE 318083.4534 323210.7676 348982.0804 367481.5113 276549.4884 309438.2911 249108.0427 285674.0148 365092.6629 0.871240333 0.885284204 0.95587262 1.006543129 0.75747753 0.847560969 0.682314568 0.782469887 1 18.47790315 3.229064988 24.99790424 0.801833815 0.928426983 0.293298129 0.08817605 235.3878824 619673.6579 0.026815183 0.030799631 1694.59136 -3.229064988 0.126593168 VVEAVNS(ph)DS(ph)DSEFGIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VVEAVNSDSDSEFGIPK 17 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 VVEAVNS(0.999)DS(0.998)DS(0.003)EFGIPK;VVEAVNS(1)DS(0.999)DS(0.001)EFGIPK;VVEAVNS(0.998)DS(0.996)DS(0.005)EFGIPK 135.18 2.12E-05 85741000 195891 184710 114191 149121 169844 147678 168621 227123 192992 TRUE FALSE 170003.508 183496.6278 169414.1495 182981.2022 166464.4367 153359.2682 152268.1614 178554.5139 170176.7056 0.998982249 1.078271125 0.995519034 1.075242358 0.978185799 0.901176619 0.894765008 1.049230053 1 17.37667404 3.105558519 7.112587887 0.965696543 1.036676188 0.331686987 0.051312637 0.296588844 17.86092084 0.01661412 0.018888162 1275.141908 -3.105558519 0.070979645 VVEHNIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VVEHNIR 7 0 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 ;;;; 176.65 0.00074396 1182938000 1741480 1693070 1192180 1417490 1602990 1758050 1626060 1814930 1948170 FALSE TRUE 1511339.006 1681948.112 1768722.236 1739352.769 1571093.635 1825683.321 1468364.951 1426821.343 1717859.562 0.879780303 0.979095235 1.029608167 1.012511621 0.914564654 1.062766341 0.854764257 0.830580901 1 20.71218067 2.216182093 24.99934515 0.879989125 0.980489052 0.244181509 0.068457617 273.6845082 305734.2945 0.027207677 0.018358934 164.5061326 -2.216182093 0.100499927 VVEHPEFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVEHPEFLK 9 0 P06396-2;Q5T0I0 P06396-2 GSN Gelsolin 0 ; 118.18 0.0010317 807030000 1963010 1589420 893460 1022910 1273440 1162500 1127990 1582640 1888520 FALSE TRUE 1703593.255 1578978.995 1325540.244 1255177.35 1248101.035 1207222.127 1018597.703 1244204.752 1665261.317 1.023018572 0.948186918 0.795995338 0.753741972 0.749492601 0.724944557 0.611674392 0.747152858 1 20.66731716 4.296906074 2.088761323 0.750434963 1.025555922 0.477816218 0.095640727 0.297718571 2.40436878 0.026337994 0.110567003 19810.98523 -4.296906074 0.275120959 VVELRPPS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VVELRPPSR 9 1 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 VVELRPPS(1)R;VVELRPPS(1)R;VVELRPPS(1)R;VVELRPPS(1)R 113.61 0.0010735 2490190000 2415290 2478670 1681680 2253760 2283580 2366430 1934240 2344460 3747030 TRUE FALSE 2096103.307 2462387.454 2494946.073 2765510.655 2238141.226 2457468.093 1746657.703 1843115.474 3304060.382 0.63440224 0.745261033 0.755115157 0.837003667 0.677391139 0.74377215 0.528639765 0.557833472 1 21.65580862 VVES(ph)PDFSKDEDYLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVESPDFSKDEDYLGK 16 1 Q9Y6Y8 Q9Y6Y8 SEC23IP SEC23-interacting protein 1 VVES(0.972)PDFS(0.028)KDEDYLGK;VVES(0.997)PDFS(0.003)KDEDYLGK 196.76 2.73E-11 613980000 1473790 1367740 1212800 1328860 1182240 847430 1539990 2016520 2122520 TRUE FALSE 1279024.917 1358755.226 1799314.137 1630597.973 1158715.737 880031.1805 1390642.007 1585302.891 1871598.104 0.683386521 0.725986644 0.961378478 0.871232969 0.619104996 0.470203073 0.743023838 0.847031682 1 20.83583924 1.448007865 2.514242644 1.0066545 0.726621872 0.31804627 0.131586793 0.483829119 5.000511206 0.249004535 0.039154233 28.05484445 -1.448007865 -0.280032627 VVESLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVESLR 6 0 Q12905;B4DY09;X6R6Z1 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ; 122.15 0.045 901540000 658730 619400 399770 414390 514600 671470 486100 552630 532720 FALSE TRUE 571677.1615 615331.1206 593100.1092 508483.5831 504360.4668 697301.8854 438958.0968 434454.3751 469742.4485 1.217001281 1.30993297 1.262607012 1.08247314 1.073695742 1.484434476 0.934465468 0.924877827 1 18.84151044 2.192632536 24.9999987 0.946454111 1.228143058 0.569898366 0.116541372 89.83983252 48901.79803 0.047203234 0.03182454 155.8233495 -2.192632536 0.281688947 VVESPDFSKDEDYLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVESPDFSKDEDYLGK 16 1 Q9Y6Y8 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 ; 239.86 7.00E-20 501030000 880950 677910 665990 705460 663680 475340 934270 1068230 1065120 FALSE TRUE 764530.2255 673456.7646 988064.9916 865645.4753 650474.0665 493626.6374 843664.6392 839797.3275 939202.727 0.814020449 0.717051543 1.052025258 0.921681177 0.692581109 0.525580498 0.898277459 0.894159805 1 19.84107707 1.677595679 2.460133674 0.97376597 0.796290979 0.176133185 0.141820858 0.505155532 6.582418506 0.146528347 0.04200819 47.59876434 -1.677595679 -0.177474991 VVEVLAGHGHLYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 ;;;;;; 193.06 1.75E-07 21687030000 3141094 3160185 2232270 2217132 3352085 3698640 3443715 3586277 3440240 FALSE TRUE 2725990.469 3139425.537 3311803.238 2720565.707 3285385.067 3840929.074 3109744.049 2819379.572 3033538.746 0.898617324 1.034905369 1.091729335 0.896829062 1.083020637 1.266154612 1.025120926 0.929402855 1 21.53257031 4.737918605 7.734102675 1.036972709 0.897321617 0.165141447 0.100201231 0.200981085 132.3038014 0.026018143 0.148588444 54691.34515 -4.737918605 -0.139651092 VVFQEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 VVFQEFR 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;; 206.65 0.0004959 12853450000 7959610 11812780 7451070 8444190 10792510 12133960 10868110 11590080 11741940 FALSE TRUE 6907727.371 11735181.07 11054432.37 10361572.4 10577760.17 12600761.29 9814122.365 9111631.586 10353821.23 0.667166954 1.133415462 1.067666915 1.000748629 1.021628627 1.217015536 0.947874427 0.880025971 1 23.30365998 7.924261883 19.45342641 0.996356442 0.004975097 0 0.148129466 0 0 0.032218745 0 83996634.04 -7.924261883 -0.991381345 VVFRDPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VVFRDPYR 8 1 P62917;E9PKZ0;G3V1A1;E9PKU4 P62917 RPL8 60S ribosomal protein L8 0 ;;;; 101.64 0.004787 9659800000 1746360 2460760 1245989 1399736 2270840 2458380 2407470 2437030 1393911 FALSE TRUE 1515574.101 2444595.106 1848553.448 1717567.452 2225654.727 2552955.469 2173993.93 1915890.099 1229124.43 1.233051809 1.98889148 1.50395957 1.39739103 1.810764373 2.077052093 1.768733806 1.558743813 1 20.22919954 1.247619766 3.037075019 0.878976518 1.695255417 0.408329748 0.256133061 0.372910844 4.399725634 0.736456375 0.065675466 17.68559867 -1.247619766 0.816278898 VVGAMQLYSVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVGAMQLYSVDR 12 0 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ; 158.05 0.00014166 424340000 228073 206908 148007 135638 192471 208994 212305 234300 204040 FALSE TRUE 197932.5752 205548.8077 219583.6803 166436.681 188641.2037 217034.1344 191715.6938 184196.7683 179918.6236 1.100122773 1.142454314 1.220461094 0.925066442 1.048480696 1.206290544 1.065568922 1.02377822 1 17.456985 1.806715145 3.283956341 1.009928571 1.104586702 0.179560424 0.082539651 0.420947349 8.285106443 0.056170872 0.023157435 64.07891439 -1.806715145 0.094658131 VVGAMQLYSVDRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VVGAMQLYSVDRK 13 1 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 127.71 0.00027853 723650000 591230 536590 312530 267580 470490 502020 580160 563950 251160 FALSE TRUE 513097.4575 533065.105 463670.5534 328338.1287 461128.1695 521333.0343 523896.1725 443353.6812 221468.1509 2.316800205 2.406960562 2.093621821 1.482552355 2.082142139 2.353986486 2.36555988 2.001884602 1 17.75673972 1.244727926 4.049526885 0.884322747 2.14550662 0.647762838 0.265934745 0.159082467 4.638805802 0.587798086 0.072618657 17.56822665 -1.244727926 1.261183873 VVGYAFDQVDDHLQTPYHETVYSLLDTLSPAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VVGYAFDQVDDHLQTPYHETVYSLLDTLSPAYR 33 0 Q9P0R6 Q9P0R6 GSKIP GSK3-beta interaction protein 0 42.302 0.078612 142310000 42093 44048 26541 28880 49851 37355 35812 62542 37122 FALSE TRUE 36530.3034 43758.64579 39376.31637 35437.6454 48859.06263 38792.07102 32338.95775 49167.88 32733.47945 1.115992067 1.336816205 1.202937086 1.082611626 1.492632725 1.185088529 0.987947456 1.502067022 1 14.99847934 4.78760133 21.10408894 1.236583118 1.115988231 0.029992068 0.179929621 18317.63129 7881259.452 0.041167599 18.83852509 61319.88474 -4.78760133 -0.120594887 VVHIIQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VVHIIQSR 8 0 O60885;O60885-2;O60885-3;Q58F21-5;Q58F21-4;Q58F21;Q58F21-3;Q58F21-2;Q15059 O60885;Q15059 BRD4;BRDT;BRD3 Bromodomain-containing protein 4;Bromodomain testis-specific protein;Bromodomain-containing protein 3 0 95.909 0.010326 0 546380 541060 328260 406510 498730 497540 539250 603410 523770 FALSE TRUE 474174.4986 537505.7412 487007.634 498814.3086 488806.2487 516680.6858 486953.618 474375.4672 461850.5073 1.02668394 1.163808922 1.054470281 1.080034125 1.058364646 1.118718455 1.054353325 1.027119078 1 18.81706643 1.743044104 2.16442069 1.00440138 1.084663116 0.369388897 0.03768749 0.293129528 2.72819237 0.033634997 0.009902992 55.34063067 -1.743044104 0.080261736 VVHIMDFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VVHIMDFQR 9 0 P43243;A0A0R4J2E8;D6REM6;D6R991;P43243-2;B3KM87;H0Y8T4;D6RBI2;D6RE02;D6RIA2;D6RAY2;D6RAM9;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;; 166.09 6.10E-05 5767780000 1752731 3576560 2168258 2122474 3487770 3608024 3219440 3435102 3435486 FALSE TRUE 1521103.157 3553065.342 3216834.821 2604414.162 3418370.201 3746827.018 2907219.204 2700532.169 3029346.759 0.502122497 1.172881689 1.061890591 0.859727977 1.128418261 1.236843226 0.959685185 0.891456933 1 21.5305753 4.748550491 24.6482629 1.027742554 0.502122147 0.665364554 0.119393979 778.4539558 1920651.49 0.031036721 0.403452827 56046.75734 -4.748550491 -0.525620407 VVIEACDELGIILAHTNLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VVIEACDELGIILAHTNLR 19 0 P31939-2;P31939 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ;;;; 229.96 6.83E-20 474378400 346335 326218 267443.4 322936 276166.6 319993.2 333876 402724 493568 FALSE TRUE 300565.9522 324075.0525 396779.9228 396263.5546 270671.425 332303.5455 301496.7569 316604.6066 435218.9533 0.6906086 0.74462532 0.911678868 0.910492412 0.621920123 0.76353188 0.692747305 0.727460521 1 18.73138186 1.234070406 24.99411741 1.000000361 0.75849235 0.408860511 0.091489765 150.4593525 837402.597 0.180914211 0.023336623 17.14235189 -1.234070406 -0.241508011 VVIGMDVAASEFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVIGMDVAASEFFR 14 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 89.805 0.013967 324376000 118906 104180 61549.5 84192 119495 111693 101940 147010 145141 FALSE TRUE 103192.2708 103495.6347 91315.04407 103309.0804 117117.2833 115989.902 92053.87449 115573.0555 127982.5963 0.806299245 0.808669598 0.713495793 0.807211944 0.915103199 0.906294335 0.719268691 0.903037279 1 16.96558811 3.402755772 5.795996497 0.878182647 0.776387246 0.33450757 0.073640757 0.263568781 15.30150655 0.021909542 0.02850395 2527.876028 -3.402755772 -0.1017954 VVIVDPETGKEMSVYEAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 64.679 0.027066 193340000 867770 748370 595780 708140 745660 726080 809590 1003500 866920 FALSE TRUE 753091.9959 743453.9082 883901.2008 868934.0102 730822.8249 754012.7674 731076.0864 788909.3342 764433.7052 0.985163253 0.972555113 1.15628235 1.136702901 0.956031661 0.986367768 0.956362967 1.032017988 1 19.54403187 3.217177205 24.9998747 0.989664918 1.062924926 0.28477621 0.060114783 353.5655593 413360.7659 0.019616216 0.022262497 1648.835028 -3.217177205 0.073260008 VVKPKS(ph)PEPEATLTFPFLDK ddPTM_MDA-MB-175_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(0.999)PEPEAT(0.001)LTFPFLDK 84.318 0.0014645 571150000 309200 238230 185070 160430 245700 176320 396450 423540 84239 TRUE FALSE 268338.4366 236665.0514 274570.471 196858.0835 240811.0507 183103.1445 358002.34 332969.267 74280.36139 3.612508496 3.186105278 3.696407313 2.650203632 3.241920828 2.465027648 4.819609562 4.482601603 1 16.18069321 VVLASAS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VVLASASPR 9 0 O95671;O95671-2 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 1 VVLASAS(1)PR;VVLASAS(1)PR;VVLAS(0.003)AS(0.997)PR;VVLASAS(1)PR 148.19 9.50E-05 1017770000 1461810 1555180 962370 1098740 1435690 1510560 1377780 1563990 1476480 TRUE FALSE 1268628.105 1544963.92 1427775.351 1348225.71 1407122.578 1568672.221 1244163.108 1229542.909 1301932.216 0.974419473 1.186670013 1.096658745 1.03555753 1.080795575 1.204880101 0.955628175 0.944398559 1 20.31222291 2.204653609 24.99119583 0.961574066 1.097119389 0.453330099 0.067123781 151.8392854 111912.2654 0.026138996 0.017623943 160.1967161 -2.204653609 0.135545323 VVLDDKDYFLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VVLDDKDYFLFR 12 1 P61604;B8ZZ54 P61604 HSPE1 "10 kDa heat shock protein, mitochondrial" 0 ;; 179.67 1.86E-05 7048336000 4064770 3238508 2610026 4495800 3620905 3372361 3406946 4687850 4104000 FALSE TRUE 3527600.346 3217234.028 3872243.304 5516640.104 3548856.075 3502097.91 3076540.901 3685389.758 3618829.795 0.974790345 0.889026069 1.070026368 1.524426518 0.980663992 0.967743195 0.850147997 1.018392676 1 21.78709182 3.032430324 24.99999454 0.959913885 1.114934303 0.165736556 0.169152124 375.3639744 289359.4569 0.054018905 0.061251338 1077.532365 -3.032430324 0.155020418 VVLEHEEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVLEHEEVR 9 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ; 190.02 3.75E-05 1307190000 1292820 1230420 776370 869600 1183750 1264970 1163850 1299420 1359540 FALSE TRUE 1121970.561 1222337.29 1151825.129 1067055.971 1160195.691 1313634.214 1050980.006 1021549.145 1198816.73 0.935898318 1.019619813 0.960801681 0.890090991 0.967784034 1.095775677 0.876681131 0.852131205 1 20.19317969 VVLGDGVQLPPGDYSTT(ph)PGGTLFS(ph)TTPGGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 31 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 VVLGDGVQLPPGDY(0.002)S(0.027)T(0.144)T(0.824)PGGT(0.015)LFS(0.337)T(0.337)T(0.268)PGGT(0.047)R 87.489 0.0011314 82405000 45368 31803 23119 34553 35490 45610 39929 54914 45885 TRUE FALSE 39372.50385 31594.084 34299.42573 42398.78676 34783.81844 47364.64621 36056.69173 43171.06844 40460.52757 0.973109008 0.780861889 0.847725618 1.047904941 0.8596976 1.170638374 0.891157231 1.066992228 1 15.30422751 3.746099043 24.63901057 1.00598848 0.858595129 0.307068031 0.09802787 517.4508227 1691258.6 0.023839886 0.040243903 5573.128328 -3.746099043 -0.147393351 VVLGDGVQLPPGDYSTT(ph)PGGTLFSTT(ph)PGGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 31 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 VVLGDGVQLPPGDY(0.001)S(0.012)T(0.044)T(0.637)PGGT(0.306)LFS(0.212)T(0.156)T(0.602)PGGT(0.031)R;VVLGDGVQLPPGDYS(0.001)T(0.018)T(0.971)PGGT(0.013)LFS(0.028)T(0.066)T(0.784)PGGT(0.119)R;VVLGDGVQLPPGDYS(0.005)T(0.023)T(0.968)PGGT(0.005)LFS(0.133)T(0.1)T(0.667)PGGT(0.1)R;VVLGDGVQLPPGDYST(0.006)T(0.984)PGGT(0.011)LFS(0.163)T(0.116)T(0.604)PGGT(0.116)R 137.88 1.19E-06 730040000 834700 658840 598460 714590 918860 975540 885990 1037540 1035590 TRUE FALSE 724392.2801 654512.0367 887877.2577 876848.5813 900576.4837 1013069.655 800066.8262 815670.1451 913163.7299 0.793277543 0.716752117 0.972308939 0.960231503 0.986215784 1.109406366 0.876148274 0.893235373 1 19.80051403 4.233526515 24.99980608 0.96413585 0.755014803 0.651549681 0.065537187 73.4672973 364852.3799 0.017860897 0.039113152 17120.89704 -4.233526515 -0.209121047 VVLIGGKPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVLIGGKPDR 10 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ; 121.83 0.00046024 13059500000 6429900 5017800 3271700 4221600 4509300 3995800 5294800 6558300 5238300 FALSE TRUE 5580172.424 4984837.741 4853905.063 5180178.803 4419573.752 4149521.012 4781311.111 5155858.582 4619034.141 1.208082091 1.079194825 1.050848492 1.121485281 0.956817728 0.898352531 1.03513223 1.116220063 1 22.13915978 6.221004998 0.811314116 1.02339403 3.003022258 0.451849679 0.065159382 25.53660391 1.885390734 0.025468986 76.92607011 1663431.792 -6.221004998 1.979628228 VVLQELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VVLQELR 7 0 I3L0A0;Q13404;Q13404-7;Q13404-2;Q13404-1;Q13404-8;Q15819;G3V2F7;Q13404-6;A0A0A0MSL3;G3V113;H0YBP9 I3L0A0 TMEM189-UBE2V1;UBE2V1;UBE2V2 Ubiquitin-conjugating enzyme E2 variant 1;Ubiquitin-conjugating enzyme E2 variant 2 0 ;;; 119.07 0.011315 1426930000 894770 1210430 830900 894880 1130940 1227950 1080370 1200720 1318360 FALSE TRUE 776523.8774 1202478.606 1232726.019 1098076.181 1108436.507 1275190.031 975595.8837 943955.372 1162504.983 0.667974666 1.034385765 1.060404934 0.944577613 0.953489682 1.09693296 0.839218668 0.812001141 1 20.14880547 0.95505478 22.02298677 1.687959001 0.929575811 0.031271752 0.127945346 2318.260064 500579.7541 116514.8511 0.030422315 9.016848649 -0.95505478 -0.75838319 VVNGAAASQPPS(ph)KR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVNGAAASQPPSKR 14 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 VVNGAAASQPPS(1)KR;VVNGAAASQPPS(1)KR 148.24 4.79E-06 778080000 612280 530940 403490 410810 582540 480100 581570 659980 698790 TRUE FALSE 531365.6467 527452.2202 598619.1136 504090.6893 570948.5937 498569.7577 525169.4309 518848.413 616179.8423 0.862354803 0.856003692 0.971500644 0.818090198 0.926594079 0.809130263 0.852298947 0.842040549 1 19.23299196 1.232021986 24.95489671 1.000000229 0.866777112 0.424935096 0.048529265 209.7460482 800424.2669 0.104771478 0.011223659 17.06168759 -1.232021986 -0.133223117 VVNRCVY(ph)S(ph)T(ph)T(ph)KAAVIGLT(ph)K ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VVNRCVYSTTKAAVIGLTK 19 2 D6R9P2 D6R9P2 SLC9B2 5 VVNRCVY(1)S(1)T(1)T(1)KAAVIGLT(1)K 48.389 0.050187 109040000 292840 206880 193660 178670 200830 147140 255140 286300 253870 TRUE FALSE 254140.452 205520.9917 287314.6238 219239.7543 196833.8759 152800.571 230396.5621 225076.973 223857.7778 1.1352764 0.91808734 1.283469471 0.979370726 0.879280934 0.68257879 1.029209547 1.005446294 1 17.77222292 3.491915938 24.16986717 0.92673667 1.099285613 0.312789981 0.129948867 597.7536506 976540.0127 0.037094731 0.052834407 3103.958728 -3.491915938 0.172548943 VVNSCHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VVNSCHR 7 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;;;; 150.17 0.0019672 2524450000 1073850 1293520 378139 812646 929897 1391860 1155380 1281150 1348070 FALSE TRUE 931938.0017 1285022.782 561008.2852 997169.6948 911393.869 1445405.755 1043331.425 1007186.042 1188702.7 0.783995865 1.081029581 0.471950039 0.838872238 0.766713047 1.215952277 0.877705944 0.847298523 1 20.18095651 VVNTDHGS(ph)PEQLQIPVTDSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VVNTDHGSPEQLQIPVTDSGR 21 0 Q6IQ49-3;Q6IQ49-2;Q6IQ49 Q6IQ49-3 SDE2 Protein SDE2 homolog 1 VVNT(0.152)DHGS(0.848)PEQLQIPVTDSGR;VVNT(0.024)DHGS(0.976)PEQLQIPVTDSGR;VVNT(0.048)DHGS(0.952)PEQLQIPVTDSGR;VVNT(0.146)DHGS(0.854)PEQLQIPVTDSGR;VVNT(0.068)DHGS(0.932)PEQLQIPVTDSGR 227.96 1.19E-25 2532380000 1444560 1308428 896709 984741 1276943 1410947 1226994 1469232 1349691 TRUE FALSE 1253657.736 1299832.85 1330360.472 1208341.495 1251534.333 1465227.044 1108000.311 1155048.17 1190132.068 1.053376991 1.092175302 1.117825919 1.015300342 1.051592816 1.231146596 0.930989376 0.970521005 1 20.18269025 2.192484235 24.9998903 0.966360568 1.089143793 0.502327704 0.059197433 102.5602857 55645.87329 0.023613342 0.015920168 155.7701489 -2.192484235 0.122783225 VVPEDGS(ph)PEKR ddPTM_MDA-MB-175_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 154.1 1.97E-05 5773900000 8848900 7542000 5468140 6317200 7701900 6321500 8910900 10545700 9192500 TRUE FALSE 7679495.445 7492456.105 8112550.794 7751616.812 7548647.259 6564692.196 8046722.29 8290584.122 8105773.122 0.947410608 0.924335778 1.000836154 0.956308139 0.931268017 0.809878601 0.992714966 1.022799923 1 22.95051836 2.020927435 24.99998895 1.011447274 0.930227227 0.366859686 0.048005335 245.4545559 293219.7316 0.020272887 0.013666484 104.9367078 -2.020927435 -0.081220047 VVPGQFDDADSS(ph)DSENR ddPTM_MDA-MB-175_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(0.005)S(0.995)DSENR;VVPGQFDDADS(0.055)S(0.945)DSENR;VVPGQFDDADS(0.083)S(0.917)DSENR 382.32 2.10E-106 1547060000 858330 794940 592660 765250 809060 790140 745890 866360 1301600 TRUE FALSE 744899.5158 789717.9868 879272.3583 939011.7086 792961.2889 820537.1971 673553.7026 681095.656 1147726.331 0.649021893 0.688071682 0.766099317 0.818149487 0.690897532 0.714924085 0.586859153 0.593430366 1 20.13034725 VVPGQFDDADSS(ph)DSENRDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VVPGQFDDADSSDSENRDLK 20 1 E9PFQ8;Q9BRS2 E9PFQ8 RIOK1 Serine/threonine-protein kinase RIO1 1 VVPGQFDDADS(0.249)S(0.751)DSENRDLK 175.07 1.50E-12 149460000 128700 97664 61982 63787 104240 86249 120980 155350 27958 TRUE FALSE 111691.9689 97022.43875 91956.70252 78270.81327 102165.8279 89567.05484 109247.3782 122129.6114 24652.83709 4.530592909 3.93554861 3.73006572 3.174921125 4.14418136 3.633133765 4.431432286 4.953977954 1 14.58946606 4.708629113 2.79412805 3.758705059 4.644699174 0.058055832 1.054032218 1.411868867 15.91308719 0.258899956 2.768704667 51124.50463 -4.708629113 0.885994115 VVPGYGHAVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VVPGYGHAVLR 11 0 O75390;B4DJV2;A0A0C4DGI3;H0YIC4 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 152.28 3.30E-05 413490000 336500 313970 207590 338070 387350 422680 234680 344220 317040 FALSE TRUE 292030.6724 311907.5104 307981.2183 414833.9606 379642.4928 438940.7731 211920.7697 270611.2317 279559.8924 1.044608617 1.11570908 1.101664533 1.483882245 1.358000569 1.570113543 0.758051407 0.967990184 1 18.09279787 2.224710852 24.99950942 0.914760494 1.276417864 0.494055248 0.176607919 212.2517759 383121.8823 0.076367582 0.051784617 167.7686661 -2.224710852 0.36165737 VVPQLVHILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VVPQLVHILR 10 0 O75843 O75843 AP1G2 AP-1 complex subunit gamma-like 2 0 161.27 0.0041122 0 45829 43091 32635 42106 47768 53782 46526 51833 65064 FALSE TRUE 39772.58153 42807.93238 48417.39516 51666.81085 46817.51026 55851.02834 42013.91568 40748.91631 57372.20804 0.69323777 0.746144063 0.843917235 0.900554687 0.816031174 0.973485774 0.732304318 0.710255326 1 15.80806442 4.374928146 3.38320239 0.839184467 0.701757697 0.265524843 0.092192375 0.364734816 7.884603331 0.024620785 0.082298826 23709.81394 -4.374928146 -0.137426771 VVPSFLPVDQGGS(ph)LVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVPSFLPVDQGGSLVGR 17 0 Q14126 Q14126 DSG2 Desmoglein-2 1 VVPSFLPVDQGGS(1)LVGR;VVPSFLPVDQGGS(1)LVGR 129.05 3.66E-05 92458000 84252 70985 49467 73820 93029 102463 49655 96812 81873 TRUE FALSE 73117.88473 70518.69486 73389.40666 90581.95927 91177.90491 106404.8179 44839.46574 76109.50719 72194.06721 1.012796308 0.97679349 1.016557309 1.254700875 1.262955648 1.473872051 0.621096268 1.054234927 1 16.13959266 2.235524529 24.99999984 0.914344174 1.159274267 0.326683765 0.184647409 108.4278395 892807.0244 0.076420978 0.054017363 171.9984483 -2.235524529 0.244930093 VVPTTDHIDTEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VVPTTDHIDTEK 12 0 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 113.22 0.0011888 356700000 896150 836280 555530 642930 854660 813550 925480 1068000 1051500 FALSE TRUE 777721.5069 830786.4216 824186.1661 788917.0831 837653.9381 844847.7949 835727.092 839616.5112 927192.8679 0.838791511 0.896023309 0.888904773 0.850866212 0.903430092 0.911188841 0.901351942 0.905546775 1 19.82250994 -1.204929004 0.861662472 9.999999669 0.88038565 0.730240626 0.022216692 83.15713277 1.03281229 1441.319281 0.007875703 0.062383681 1.204929004 -9.119614019 VVQHLCQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VVQHLCQR 8 0 Q8WUY1;H0YAR9 Q8WUY1 THEM6 Protein THEM6 0 ;;; 129.47 0.0023032 110960000 177047 143010 127835 136869 145599 140091 140380 157574 143136 FALSE TRUE 153649.7904 142070.5579 189656.4336 167947.1984 142701.8648 145480.3914 126765.9692 123878.0263 126214.6251 1.217369146 1.125626747 1.502650215 1.330647682 1.130628599 1.152642899 1.004368306 0.981487099 1 16.94551957 2.634487045 1.406460715 0.986304226 1.28950586 0.600355772 0.101848774 0.290211439 1.182651301 0.055703204 0.041967364 431.0097003 -2.634487045 0.303201634 VVQVSAGDSHTAALTDDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVQVSAGDSHTAALTDDGR 19 0 P18754-2;C9JW69;P18754;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4 P18754-2 RCC1 Regulator of chromosome condensation 0 ; 214.55 3.43E-25 366900000 254330 243600 126790 165570 255540 249090 226560 239410 252530 FALSE TRUE 220719.6461 241999.7756 188106.0681 203165.1991 250455.254 258672.6535 204588.2461 188214.0346 222676.1911 0.991213497 1.086778853 0.844751597 0.912379532 1.124750934 1.161653845 0.918770189 0.845236456 1 17.76458779 2.031484444 24.99969266 0.902695392 1.017236274 0.170012872 0.100799475 305.5654031 242627.8432 0.043514853 0.029337457 107.5188088 -2.031484444 0.114540883 VVS(ph)ETNDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VVSETNDTK 9 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 VVS(1)ETNDTK 89.629 0.010327 0 213170 184480 135790 145820 178530 145050 234000 220220 219300 TRUE FALSE 184999.0444 183268.1387 201458.4982 178930.6597 174977.6023 150630.1674 211306.716 173127.6668 193374.6038 0.956687387 0.947736337 1.041804323 0.925305889 0.904863404 0.778955273 1.092732509 0.895296814 1 17.56103881 VVSETNDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVSETNDTK 9 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 222.42 8.93E-07 1072130000 1317390 1134510 790750 961690 771310 962550 1298290 1389440 1427610 FALSE TRUE 1143293.574 1127057.329 1173159.345 1180056.413 755962.44 999579.9214 1172382.036 1092319.069 1258839.572 0.908212292 0.895314506 0.931937135 0.937416045 0.600523257 0.794048696 0.931319655 0.867719043 1 20.26366301 0.757893087 1.376413304 1.31541518 0.851292975 0.164055883 0.100797055 8.652335527 5.54570785 7.869785298 0.031079962 5.726550397 -0.757893087 -0.464122205 VVSHLIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVSHLIEK 8 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ; 80.239 0.025964 313520000 1487590 1512800 1042500 1205090 1652390 1677550 1561960 1760080 1727640 FALSE TRUE 1291001.212 1502862.317 1546656.487 1478724.103 1619510.672 1742086.434 1410481.36 1383700.589 1523400.367 0.847447093 0.986518285 1.015265928 0.970673327 1.063089327 1.143551276 0.925876998 0.908297397 1 20.53886372 6.533308268 15.20320827 0.983911557 0.499212964 0 0.082250296 0 0 0.019322423 0 3414351.805 -6.533308268 -0.484698593 VVSHPTLPVTITAHEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVSHPTLPVTITAHEDR 17 0 Q13033-2;Q13033 Q13033-2 STRN3 Striatin-3 0 ; 295.03 2.42E-46 681370000 395400 378050 208941 294570 377880 423760 374540 404310 413970 FALSE TRUE 343146.8882 375566.5647 309985.5665 361456.6207 370360.9273 440062.3214 338217.1684 317851.4528 365030.9382 0.94004878 1.028862284 0.849203544 0.990208179 1.014601472 1.205548011 0.926543843 0.870752091 1 18.47765922 5.442269749 22.37756605 0.975900669 0.937356579 0 0.099250473 74082496.49 0 0.023905036 0 276866.0785 -5.442269749 -0.03854409 VVSQSQPGS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VVSQSQPGSR 10 0 Q7Z460-4 Q7Z460-4 CLASP1 CLIP-associating protein 1 1 VVSQSQPGS(1)R;VVSQSQPGS(1)R;VVSQSQPGS(1)R 107.39 0.0024029 540430000 620940 477590 378070 419270 470330 565940 527140 553170 594860 TRUE FALSE 538881.2057 474452.6798 560905.9166 514471.6616 460971.3532 587712.078 476018.0439 434878.9003 524536.3285 1.027347729 0.904518246 1.069336643 0.98081226 0.87881683 1.120441133 0.907502528 0.829072986 1 19.00068317 2.029610839 24.959126 0.892115374 0.991885283 0.18072798 0.08160639 260.6326574 219687.5523 0.031417718 0.021181533 107.0559572 -2.029610839 0.099769909 NHETDGGS(ph)AHGDDDDDGPHFEPVVPLPDKIEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 NHETDGGSAHGDDDDDGPHFEPVVPLPDKIEVK 33 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 NHET(0.077)DGGS(0.923)AHGDDDDDGPHFEPVVPLPDKIEVK;NHET(0.008)DGGS(0.992)AHGDDDDDGPHFEPVVPLPDKIEVK;NHET(0.029)DGGS(0.971)AHGDDDDDGPHFEPVVPLPDKIEVK;NHET(0.003)DGGS(0.997)AHGDDDDDGPHFEPVVPLPDKIEVK 264.36 5.52E-60 2094820000 2847087 2257487 1409672 1686294 1748182 1362886 1912156 1897618 1239974 TRUE FALSE 2470837.239 2242657.419 2091394.094 2069192.826 1713396.598 1415317.106 1726715.405 1491827.158 1093385.686 2.259803901 2.051112839 1.912768861 1.892463796 1.567055999 1.294435371 1.579237251 1.364410726 1 20.06037096 7.999999989 0.098285392 0.084990129 6.486671414 0.892555297 0.124693313 98.88578303 0.899044863 9.449223688 87.32272575 99999997.43 -7.999999989 6.401681285 up VVSSEGGRPS(ph)VDLSFQPSQPLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VVSSEGGRPSVDLSFQPSQPLSK 23 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 VVS(0.002)S(0.002)EGGRPS(0.996)VDLSFQPSQPLSK 117.73 0.00021274 174170000 133610 103080 65008 106710 94926 78935 153980 136250 136120 TRUE FALSE 115953.1 102402.8607 96446.08624 130940.1365 93037.15832 81971.68053 139047.0433 107113.9978 120028.0487 0.96605003 0.853157756 0.803529569 1.090912815 0.775128475 0.682937709 1.158454585 0.892408058 1 16.87301205 2.233002062 24.99996436 0.996902887 0.865358081 0.24591684 0.126241307 224.2661182 1008638.68 0.049916878 0.034722488 171.0023435 -2.233002062 -0.131544806 VVSSIEQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVSSIEQK 8 0 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ; 167.24 0.00073 374510000 407680 331700 234203 289413 321140 284416 379100 416380 391070 FALSE TRUE 353804.0551 329521.0409 347464.3542 355128.6451 314749.9423 295357.6676 342334.9403 327340.3773 344838.1501 1.026000328 0.955581744 1.007615758 1.029841521 0.91274687 0.856510996 0.992740914 0.949258013 1 18.39555987 3.239440621 24.99999187 0.942626889 1.001451111 0.327896525 0.044355273 31.47223105 894079.1516 0.013515525 0.016455111 1735.563952 -3.239440621 0.058824222 VVSVLTVLHQDWLNGK ddPTM_MDA-MB-175_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 ; 243.04 5.60E-20 1176000000 10164600 3048500 427370 207646 119776 58033 59315 69773 37376 FALSE TRUE 8821322.356 3028474.203 634047.5615 254795.198 117392.6919 60265.56706 53562.64043 54852.58692 32957.45186 267.6579001 91.89042332 19.23836722 7.731034519 3.561946853 1.828586971 1.625205755 1.664345507 1 15.00831708 4.456958725 3.152027036 4.614794095 200 0.912637453 24.74803021 0.068282112 1.31913939 5.6743881 23.54605924 28639.05771 -4.456958725 195.3852059 VVTDTDETELAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVTDTDETELAR 12 0 P05198 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ; 232.41 2.65E-12 926220000 446230 426020 296490 331810 448640 482810 390930 438920 438360 FALSE TRUE 387259.5749 423221.4466 439873.5557 407152.5319 439712.9417 501384.0131 353017.6688 345060.3737 386537.5802 1.001867851 1.094903751 1.137983933 1.053332335 1.137568413 1.297115827 0.913281623 0.89269554 1 18.56024916 2.192433995 24.99999513 0.925525499 1.11782317 0.541146522 0.080170956 90.77349959 49197.30223 0.032792261 0.022108619 155.7521302 -2.192433995 0.192297671 VVTTSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VVTTSAR 7 0 F8VTQ9;F8VXU8;Q8IUR5 F8VTQ9 TMTC1 Transmembrane and TPR repeat-containing protein 1 0 ;;; 137.44 0.0067063 4190500000 1507060 1702010 1225870 1207660 1304490 1374700 1936710 1683160 1823050 FALSE TRUE 1307898.203 1690829.384 1818704.832 1481877.661 1278533.201 1427585.599 1748888.162 1323229.332 1607531.106 0.813606777 1.051817522 1.131365251 0.921834517 0.795339634 0.888060948 1.087934259 0.823143843 1 20.61641522 3.516163881 24.90280998 0.912655966 1.007948855 0.095582579 0.113361186 1050.775009 670219.8836 0.030653412 0.045456434 3282.191229 -3.516163881 0.095292889 VVTVFSVADGYSENNVFYGHHAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VVTVFSVADGYSENNVFYGHHAK 23 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 ;; 238.64 1.99E-37 1661538000 1683480 2009143 855765 1181411 1943359 2077257 2009520 1697740 1615010 FALSE TRUE 1461003.853 1995944.807 1269615.816 1449668.424 1904689.958 2157170.421 1814637.06 1334691.513 1424085.358 1.025924355 1.401562622 0.8915307 1.01796456 1.337483001 1.51477607 1.274247397 0.937227186 1 20.44160419 1.718251589 7.589416046 0.972098444 1.213474206 0.215692118 0.189954822 0.182850624 27.31782182 0.115031896 0.051357182 52.26989029 -1.718251589 0.241375762 VVTVHLEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VVTVHLEK 8 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 103.74 0.0047148 511010000 774180 666750 538110 704110 671970 623310 785280 943850 1227400 FALSE TRUE 671870.1515 662370.0753 798341.7959 863988.9371 658599.1117 647289.139 709123.6665 742015.0225 1082298.17 0.62078101 0.612003322 0.737635725 0.798291045 0.608519103 0.598069143 0.65520176 0.685592051 1 20.04566658 1.235274611 4.647627868 1.027199221 0.663970522 0.738716064 0.062844893 0.109228531 5.233643964 0.131060245 0.016856953 17.18994991 -1.235274611 -0.363228699 VVVHPLVLLSVVDHFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVVHPLVLLSVVDHFNR 17 0 P51665;H3BNT7;H3BTM8;H3BQV2 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ; 294.97 2.43E-46 1334690000 1050010 1102420 551170 781220 988060 1044010 1036650 1160070 1103860 FALSE TRUE 911248.5181 1095178.13 817717.6556 958607.9412 968399.5391 1084173.74 936115.8426 911998.0582 973362.9283 0.936185765 1.1251488 0.840095335 0.984841228 0.994900783 1.113843263 0.96173361 0.936955817 1 19.8926183 2.049995001 24.99999858 0.959583163 1.00023363 0.032459076 0.082103075 353.2943495 176663.1044 0.032625618 0.021996179 112.2005538 -2.049995001 0.040650468 VVVLMGSTSDLGHCEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVVLMGSTSDLGHCEK 16 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 185.74 1.61E-09 1177690000 1715450 1451680 782310 1165860 1566740 1346390 1606920 1928190 1832950 FALSE TRUE 1488748.936 1442143.818 1160637.733 1430586.332 1535564.939 1398186.495 1451081.146 1515861.574 1616260.739 0.921106911 0.892271763 0.718100554 0.885121006 0.950072536 0.865074836 0.897801395 0.937881826 1 20.62422853 -1.999999873 0.481714743 4.893254935 0.857938205 0.335753079 0.060052876 126.4100993 1.497143537 508.9072992 0.043342475 0.010000003 1.999999873 -4.035316731 VVVQVLAEEPEAVLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 165.7 3.28E-06 26960000 87040 86037 64325 68787 87752 85372 90143 109850 106810 FALSE TRUE 75537.44347 85471.81728 95432.78515 84406.13969 86005.90688 88656.31608 81400.94573 86359.43235 94183.04348 0.802028058 0.907507489 1.013269285 0.896192527 0.913178251 0.941319295 0.864284512 0.916931851 1 16.52317972 VVVS(ph)PTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VVVSPTK 7 0 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 VVVS(0.998)PT(0.002)K;VVVS(1)PTK 126.31 0.0041583 2171900000 6115700 4766500 3337600 4179500 4542500 4089200 5018000 6326800 8904700 TRUE FALSE 5307494.75 4735188.548 4951674.524 5128519.355 4452113.137 4246514.17 4531355.132 4973863.055 7851996.51 0.675942067 0.603055356 0.630626175 0.653148451 0.567003963 0.540819671 0.577095918 0.633452021 1 22.9046281 1.237261448 4.676202218 1.030694489 0.605463475 0.904346795 0.03993458 0.056893602 2.794139089 0.080081938 0.010578356 17.2687717 -1.237261448 -0.425231014 VVVSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VVVSNR 6 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;; 127.66 0.039465 1628160000 1363080 1272070 820830 1005480 925938 1254720 1284400 1469110 1477630 FALSE TRUE 1182945.524 1263713.688 1217786.134 1233789.602 907513.6454 1302989.89 1159839.086 1154952.259 1302946.265 0.907900469 0.969889337 0.934640335 0.946922859 0.696508881 1.000033482 0.890166477 0.886415879 1 20.31334616 VVWVEESDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VVWVEESDKR 10 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 0 ;;;;; 218.52 1.08E-08 3506980000 2171980 1803170 1394542 1696386 1751060 1629110 2076720 2502830 2262770 FALSE TRUE 1884947.34 1791324.858 2068947.176 2081576.369 1716217.332 1691782.916 1875320.014 1967619.282 1995267.908 0.944708894 0.897786633 1.036927005 1.043256577 0.860143806 0.847897623 0.939883815 0.9861429 1 20.92815104 1.67681367 4.211228487 0.995912441 0.938330528 0.112885155 0.06388825 0.41383175 17.05740094 0.048557756 0.018269942 47.51313318 -1.67681367 -0.057581913 VVYAFS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VVYAFSPK 8 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 VVYAFS(1)PK;VVYAFS(1)PK;VVYAFS(1)PK;VVYAFS(1)PK 146.11 0.00058599 2512480000 3653490 3095770 2304750 2445040 3395820 2962820 3450110 3939490 3465730 TRUE FALSE 3170672.04 3075433.683 3419334.809 3000223.702 3328249.826 3076801.603 3115518.863 3097060.721 3056015.348 1.037518363 1.006354135 1.118886661 0.981743663 1.089081515 1.006801751 1.019470948 1.01343101 1 21.54322036 VVYFGDSMHSDIFPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VVYFGDSMHSDIFPAR 16 0 Q5TFE4;Q5TFE4-2 Q5TFE4 NT5DC1 5-nucleotidase domain-containing protein 1 0 67.846 0.050647 383370000 90912 102570 45884 52676 97571 101620 93404 106090 89878 FALSE TRUE 78897.74886 101896.2109 68073.65587 64636.8909 95629.52799 105529.3872 84345.69446 83403.47909 79252.72523 0.995520957 1.285712392 0.858944039 0.81557941 1.206640248 1.331555311 1.064262386 1.052373642 1 16.27417292 3.19659231 24.99999804 1.126168836 1.000850381 0.174040809 0.152568282 312.3872048 186084.0225 0.049287642 0.055887389 1572.505994 -3.19659231 -0.125318454 VWAALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VWAALR 6 0 Q86U38;Q86U38-2 Q86U38 NOP9 Nucleolar protein 9 0 142.14 0.026902 935030000 716160 874250 573820 604600 899560 1195100 673180 802400 777070 FALSE TRUE 621517.6415 868506.9942 851321.2713 741883.6707 881660.516 1241076.27 607895.1072 630813.0043 685205.6698 0.907052683 1.267512854 1.242431738 1.082716772 1.286709312 1.811246353 0.887171741 0.920618483 1 19.38617756 VWAHYEEQPVEEVMPVLEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VWAHYEEQPVEEVMPVLEEK 20 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 234.11 1.66E-29 497287000 619602 505569 394754 457001 488656 418646 560842 664494 721447 FALSE TRUE 537720.0258 502247.884 585658.3548 560770.0619 478932.7016 434751.5825 506451.6292 522397.1292 636158.3575 0.845261277 0.789501353 0.920617245 0.881494451 0.752851387 0.683401511 0.79610937 0.82117467 1 19.27902641 1.237632262 4.905931053 1.013039762 0.809122044 0.4519899 0.065407156 0.184336794 10.89224401 0.129280704 0.017804711 17.28352262 -1.237632262 -0.203917718 VWDAVSGDELMTLAHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VWDAVSGDELMTLAHK 16 0 Q9Y3F4;Q9Y3F4-2 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 ; 172.82 4.44E-09 1543590000 1184880 1000500 659080 957960 915540 868760 1091770 1255810 1211280 FALSE TRUE 1028295.106 993927.6496 977813.2925 1175479.46 897322.5452 902181.7594 985890.3134 987264.8042 1068083.858 0.962747539 0.930570799 0.915483634 1.100549784 0.840123683 0.844673152 0.923045794 0.92433267 1 20.02659349 VWDEANLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VWDEANLR 8 0 Q96GA7;F8VYZ3 Q96GA7 SDSL Serine dehydratase-like 0 ;;; 264.21 4.84E-13 894140000 1570670 1650610 1036970 1248500 1696350 1674230 1631490 1861000 1749530 FALSE TRUE 1363101.98 1639767.034 1538452.16 1531991.007 1662595.954 1738638.711 1473268.351 1463039.632 1542702.556 0.883580554 1.062918466 0.997244838 0.993056633 1.07771647 1.127008382 0.954991839 0.948361449 1 20.5570285 4.75224648 24.20164935 1.015072247 0.883580417 0.370402515 0.055610673 1928.65827 3410485.128 0.014973407 0.278648087 56525.76914 -4.75224648 -0.13149183 VWDISGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VWDISGLR 8 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITV3;A0A3B3ISK1;A0A3B3IU78 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 148.04 0.0020355 0 2040600 1885660 1195920 1368720 1943680 1917170 1731480 1948530 2014180 FALSE TRUE 1770929.54 1873272.975 1774270.912 1679508.796 1905004.571 1990924.77 1563561.336 1531852.023 1776065.935 0.997107993 1.054731662 0.998989326 0.94563426 1.072597888 1.120974583 0.880350952 0.862497272 1 20.76025371 2.216996402 24.97732209 0.902080227 1.029184573 0.462155556 0.059171476 196.2760751 227340.1742 0.024700003 0.016669062 164.8148736 -2.216996402 0.127104346 VWDLFPEADKVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VWDLFPEADKVR 12 1 Q99613-2;Q99613;B5ME19 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 73.466 0.03568 412150000 359490 399600 247150 273840 332990 366760 420630 480020 283950 FALSE TRUE 311982.4857 396975.0013 366672.5667 336019.5574 326364.1505 380869.4945 379837.3673 377371.4585 250381.7545 1.246027237 1.58547895 1.464454019 1.342028927 1.303466186 1.521155147 1.517032933 1.507184337 1 17.93376991 1.233596527 24.99321555 0.999999316 1.444168523 0.615643998 0.108051918 104.3182384 525159.4927 0.211999444 0.026224328 17.12365729 -1.233596527 0.444169207 VWDLSDIDKDGHLDRDEFAVAMHLVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VWDLSDIDKDGHLDRDEFAVAMHLVYR 27 2 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4;M0R2S2 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 0 ; 163.16 3.74E-12 350441000 393564 358077 287595 273402 282100 259982 339468 401941 457419 FALSE TRUE 341553.5202 355724.7686 426676.9039 335482.1028 276486.7619 269983.6758 306546.4456 315989.0451 403343.4469 0.846805676 0.881940122 1.057850096 0.831752952 0.68548718 0.66936423 0.760013452 0.783424269 1 18.62164929 3.485385529 24.67965516 0.771820564 0.927610915 0.301824509 0.103208642 392.6291095 1172511.333 0.029834239 0.040490399 3057.634211 -3.485385529 0.155790351 VWDPDNPLTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VWDPDNPLTDR 11 0 O94776;O94776-2 O94776 MTA2 Metastasis-associated protein MTA2 0 ;;; 170.99 3.50E-05 527120000 1418240 1337720 935300 1087500 1368020 1314600 1260690 1415180 1380180 FALSE TRUE 1230815.991 1328932.429 1387614.208 1334433.496 1340799.078 1365173.513 1138428.478 1112554.77 1217016.693 1.011338627 1.091959081 1.140176808 1.096479206 1.101709686 1.121737706 0.935425524 0.914165579 1 20.21491753 2.234279219 24.99995188 0.941824967 1.096387648 0.746232911 0.039485208 48.27851409 281903.8694 0.015717248 0.011016873 171.5059608 -2.234279219 0.154562681 VWDVIGR ddPTM_MDA-MB-175_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 430240000 942820 1090550 576470 676770 1019100 1065520 899260 1018310 874060 FALSE TRUE 818223.9482 1083386.105 855252.8202 830440.9723 998821.9038 1106511.244 812049.9036 800552.331 770729.6225 1.061622551 1.405662989 1.109666471 1.077473796 1.295943317 1.435667206 1.053611902 1.038694125 1 19.55586532 2.034508759 24.99943043 1.02932339 1.230672391 0.358488246 0.126729213 189.0809163 136976.5073 0.051411677 0.034661629 108.2701551 -2.034508759 0.201349002 VWDYETGDFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VWDYETGDFER 11 0 P43034 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ;;; 274.52 9.33E-27 1458730000 1797420 1697320 1107710 1338960 1660320 1672410 1559830 1790520 1819120 FALSE TRUE 1559886.393 1686170.193 1643402.261 1642991.333 1627282.88 1736748.695 1408557.927 1407631.232 1604065.706 0.972457916 1.051185239 1.024523032 1.024266853 1.014473955 1.08271668 0.87811735 0.877539634 1 20.61330181 2.231463855 24.99999603 0.908323211 1.028332734 0.581668443 0.043575776 101.1334578 356262.1898 0.016965754 0.011710484 170.3977496 -2.231463855 0.120009523 VWEDRPS(ph)SAGSTPFPYNPLIMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VWEDRPSSAGSTPFPYNPLIMR 22 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 VWEDRPS(0.606)S(0.391)AGS(0.002)T(0.001)PFPYNPLIMR 140.26 7.93E-08 138330000 74181 73056 42708 46139 45409 52329 52016 56067 46492 TRUE FALSE 64377.7929 72576.09033 63361.73165 56615.56514 44505.44974 54342.13049 46971.49633 44077.50836 40995.76872 1.570352134 1.770331246 1.545567594 1.381009965 1.085610811 1.325554617 1.145764497 1.075172139 1 15.32318739 3.579086442 1.582883995 1.121897738 1.677566708 0.841124631 0.100107782 0.142483161 0.709721358 0.032816722 0.061219281 3793.904917 -3.579086442 0.55566897 VWEDRPSS(ph)AGSTPFPYNPLIMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VWEDRPSSAGSTPFPYNPLIMR 22 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 VWEDRPS(0.066)S(0.933)AGSTPFPYNPLIMR;VWEDRPS(0.296)S(0.704)AGSTPFPYNPLIMR;VWEDRPS(0.108)S(0.695)AGS(0.163)T(0.034)PFPYNPLIMR 252.24 3.25E-37 1418730000 794698 714538 455521 394998 607113 595763 575181 638607 584874 TRUE FALSE 689676.6458 709844.1528 675812.4792 484688.3331 595032.6391 618682.3881 519400.0351 502045.8627 515730.862 1.337280152 1.376384865 1.310397591 0.939808665 1.153765816 1.199622582 1.007114511 0.973464843 1 18.97625886 4.737354502 0.3644413 0.960610284 1.739828912 0.631357438 0.097584484 5.381318841 0.685582045 0.179754545 1.91709894 54620.3529 -4.737354502 0.779218628 VWEMLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VWEMLNR 7 0 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 107.67 0.039617 0 216270 230650 140310 179940 235810 249070 211220 237520 222350 FALSE TRUE 187689.3715 229134.845 208164.3853 220798.1272 231117.8424 258651.8841 190735.9169 186728.1964 196064.0363 0.957286074 1.168673507 1.061716311 1.126153125 1.178787537 1.319221459 0.972824596 0.952383721 1 17.5809654 2.068694244 24.99999979 0.969728777 1.135954463 0.405282873 0.091432405 45.972396 16730.0715 0.037063225 0.024988026 117.1370397 -2.068694244 0.166225685 VWGALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VWGALR 6 0 P07686 P07686 HEXB Beta-hexosaminidase subunit beta;Beta-hexosaminidase subunit beta chain B;Beta-hexosaminidase subunit beta chain A 0 113.63 0.060438 300090000 339660 385830 387950 347810 332460 394650 294850 371910 385170 FALSE TRUE 294773.0704 383295.4573 575563.9176 426785.5764 325844.6964 409832.4409 266255.4924 292379.9407 339635.6414 0.867909708 1.128548982 1.694651113 1.25659832 0.959394883 1.206682665 0.783944498 0.86086354 1 18.37362834 2.631821517 1.421089222 0.879702846 1.240283204 0.250222942 0.228880168 0.540415249 2.2455003 0.123677361 0.093268467 428.372435 -2.631821517 0.360580359 VWGSPGGEGTGDLDEFDF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VWGSPGGEGTGDLDEFDF 18 0 Q13438-4;Q13438;Q13438-8;Q13438-6;Q13438-5;Q13438-3;Q13438-2;Q13438-7;B4E321 Q13438-4 OS9 Protein OS-9 0 ;; 288.35 5.24E-40 36757000 126323 110250 82045 99020 124184 154205 88172 111628 108607 FALSE TRUE 109629.0955 109525.7605 121722.2364 121504.0044 121712.9814 160137.3661 79621.09301 87757.22089 95767.60419 1.144740922 1.143661903 1.271016827 1.268738061 1.270920186 1.672145476 0.831399028 0.916356023 1 16.54725009 2.198157191 24.99999921 0.912487518 1.284910211 0.584023512 0.150720269 107.9644958 66803.31573 0.062039452 0.041827566 157.8182384 -2.198157191 0.372422693 VWIPDPDEVWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VWIPDPDEVWR 11 0 Q9ULV0 Q9ULV0 MYO5B Unconventional myosin-Vb 0 ; 125.56 0.0007577 87565000 367700 353460 224945 241990 346190 384030 302660 367390 352360 FALSE TRUE 319107.5134 351138.098 333729.1544 296937.5281 339301.4963 398803.8826 273308.0798 288826.5075 310704.4022 1.027045356 1.130135574 1.074105008 0.955691409 1.092039552 1.283547577 0.879640191 0.929586145 1 18.24518316 2.184440405 24.99995663 0.932621847 1.088169233 0.417421539 0.087425936 91.15771627 42108.00149 0.035969232 0.024250472 152.9115901 -2.184440405 0.155547386 VWLDPNETNEIANANSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VWLDPNETNEIANANSR 17 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ;;; 256.57 9.82E-27 808420000 888710 804100 515090 610550 788820 826720 769910 788570 835720 FALSE TRUE 771264.7218 798817.8142 764189.2469 749184.7092 773124.0253 858524.4534 695244.2467 619940.4422 736922.1337 1.046602737 1.083992158 1.037001349 1.016640259 1.049125803 1.165013797 0.943443296 0.841256374 1 19.49115266 2.058491935 8.384375654 0.904212106 1.062512309 0.581149528 0.055080403 0.156899379 20.27425669 0.02190971 0.014726738 114.4173631 -2.058491935 0.158300203 VWLYHDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VWLYHDGR 8 0 P50416;P50416-2 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 ;; 129.47 0.0010895 2338430000 871040 1026330 736083 1068810 1474410 1857010 852628 1486130 1555680 FALSE TRUE 755929.8571 1019587.971 1092055.201 1311499.646 1445072.126 1928450.376 769940.2678 1168332.665 1371769.283 0.551061951 0.743264909 0.796092473 0.956064305 1.053436714 1.405812479 0.561275338 0.851697643 1 20.38760642 4.338284621 1.484902576 0.952473355 0.542361596 0.308566348 0.207986206 0.834097553 2.852886084 0.063683853 0.409584884 21791.37431 -4.338284621 -0.410111759 VWNWQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VWNWQSR 7 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 145.04 0.0053813 1949150000 784310 969070 637840 682960 918270 963930 908930 987140 1029680 FALSE TRUE 680661.4463 962704.1154 946301.5574 838036.5064 899998.2236 1001013.011 820782.1085 776047.7929 907952.4034 0.74966644 1.060302403 1.042236965 0.922996077 0.991239431 1.102495028 0.90399244 0.85472299 1 19.79225715 VWQLGSSSPNFTLEGHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VWQLGSSSPNFTLEGHEK 18 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ; 243.16 4.48E-24 2506900000 1653660 1430240 864840 1195970 1431210 1371700 1674120 1855550 1604910 FALSE TRUE 1435124.641 1420844.659 1283079.517 1467533.268 1402731.721 1424470.187 1511764.1 1458755.072 1415179.368 1.014093813 1.004003232 0.906655047 1.036994533 0.991204191 1.006565117 1.06824911 1.030791648 1 20.43255349 2.861199237 1.444081391 1.032924889 0.983901823 0.194544013 0.037415103 0.599317929 2.574894383 0.016496268 0.015770031 726.4391424 -2.861199237 -0.049023066 VWQVTIGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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" 0 146.79 0.00021858 492580000 266980 228420 138570 204510 248330 223250 270500 291570 248820 FALSE TRUE 231697.9166 226919.494 205582.9155 250947.1212 243388.7188 231838.572 244266.9516 229220.0245 219404.7831 1.056029469 1.034250443 0.937002889 1.14376322 1.109313641 1.056670546 1.113316438 1.044735768 1 17.74323545 3.734309777 24.99971556 1.07713321 1.011609886 0.29837041 0.049726044 482.6091053 2838288.343 0.01376115 0.021319081 5423.87631 -3.734309777 -0.065523324 VWS(ph)PLVTEEGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VWSPLVTEEGKR 12 1 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 VWS(1)PLVTEEGKR;VWS(1)PLVTEEGKR;VWS(0.999)PLVT(0.001)EEGKR 125.36 0.00018786 785810000 334893 293336 232958 274182 303136 266889 354255 412060 460320 TRUE FALSE 290636.0415 291409.0565 345617.268 336439.2137 297104.1867 277156.3925 319899.4046 323944.1757 405901.494 0.716026045 0.717930485 0.85148065 0.828869119 0.731961304 0.682816882 0.788120786 0.798085694 1 18.63077012 1.122614495 2.156959823 1.131717694 0.760300981 0.673741287 0.052135152 0.658194859 2.346534542 0.540092307 0.014918519 13.26216708 -1.122614495 -0.371416713 VWSEVNQAVLDYENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VWSEVNQAVLDYENR 15 0 Q9NWU2 Q9NWU2 GID8 Glucose-induced degradation protein 8 homolog 0 ; 173.59 2.24E-06 84895000 106012 100373 69195 79801 96689 99804 91365 108608 140212 FALSE TRUE 92002.2456 99713.64315 102657.9334 97921.03673 94765.07807 103643.5245 82504.43636 85383.02439 123636.2971 0.744136211 0.806507842 0.830321967 0.792008812 0.766482662 0.838293664 0.667315653 0.690598363 1 16.91574283 VWWMFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VWWMFR 6 0 P25325-2;P25325;B1AH49;Q16762;B1AH48 P25325-2;Q16762 MPST;TST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase;Thiosulfate sulfurtransferase 0 ; 149.33 0.02478 529940000 686240 741800 505110 639230 766070 728120 825070 930230 683070 FALSE TRUE 595551.6453 736927.067 749382.8855 784376.9415 750826.7058 756131.2476 745054.8384 731307.5536 602318.2428 0.988765744 1.223484555 1.244164351 1.302263298 1.246561456 1.255368332 1.236978702 1.214154747 1 19.20016643 1.23860447 6.108712435 0.992263465 1.221944589 0.388798617 0.08384435 0.133797792 19.86612769 0.128181793 0.020380153 17.3222567 -1.23860447 0.229681124 VWYHVCSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VWYHVCSSR 9 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 93.111 0.0096207 407220000 675880 822750 442130 684490 789300 747210 754810 753120 1467600 FALSE TRUE 586560.7455 817345.3011 655945.5468 839913.9163 773594.4742 775955.6522 681608.6424 592071.1488 1294102 0.453256966 0.631592642 0.506873142 0.649032237 0.597784776 0.599609345 0.526703956 0.457515056 1 20.3035199 1.230922562 24.99971432 1.000000796 0.554010152 0.810822257 0.067883755 120.0685211 392956.7719 0.174943515 0.01682223 17.01855027 -1.230922562 -0.445990644 VWYVSNIDGTHIAK ddPTM_MDA-MB-175_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 ; 229.17 1.38E-12 6140500000 5901100 4926400 2390420 3759500 4739800 4283400 5130100 5954600 5284900 FALSE TRUE 5121254.684 4894038.154 3546435.107 4613151.935 4645487.253 4448185.17 4632583.692 4681255.129 4660125.143 1.09895218 1.050194577 0.76101714 0.989920183 0.996858906 0.95452054 0.994089976 1.00453421 1 22.15193727 2.078372614 6.363080798 1.001652952 0.970635206 0.015820534 0.086966096 1.050663813 67.56082153 0.036979676 0.024682944 119.7767747 -2.078372614 -0.031017746 VYADGIFDLFHSGHAR ddPTM_MDA-MB-175_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 ; 150.59 4.19E-07 787100000 537430 524770 246100 367810 508890 508890 473840 520130 414860 FALSE TRUE 466407.2638 521322.7513 365114.7832 451326.8821 498764.0846 528467.3276 427887.0697 408904.2472 365815.7234 1.274978723 1.425096621 0.998083898 1.233754738 1.363429871 1.444627155 1.169679274 1.117787512 1 18.48075756 1.70205145 2.190037384 1.021836071 1.282594416 0.362894289 0.126675682 0.340002267 3.332569096 0.134090274 0.036872873 50.35602612 -1.70205145 0.260758346 VYASQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VYASQR 6 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;;;;; 116 0.055721 1131860000 1086700 1262500 740800 872600 903700 1288950 1127760 1266680 1320960 FALSE TRUE 943089.8417 1254206.554 1099053.358 1070737.167 885718.1381 1338536.741 1018390.009 995810.3393 1164797.614 0.809659833 1.076759207 0.943557357 0.919247391 0.760405179 1.14915821 0.8743064 0.854921342 1 20.15164787 3.830336707 5.226814448 0.918127015 0.957939039 0 0.118825715 1.18134943 51.68658265 0.030485881 0.053924719 6766.073429 -3.830336707 0.039812024 VYEDSGIPLPAES(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VYEDSGIPLPAESPK 15 0 F8W038;F8W1H0;H0YIS7;Q8IXM2;Q8IXM2-3;Q8IXM2-2 F8W038;Q8IXM2-2 C17orf49;RNASEK-C17orf49;BAP18 Chromatin complexes subunit BAP18 1 VYEDSGIPLPAES(1)PK;VYEDSGIPLPAES(1)PK;VYEDSGIPLPAES(1)PK;VYEDSGIPLPAES(1)PK;VYEDSGIPLPAES(1)PK 303.44 1.76E-44 745477000 2542070 1605640 1225496 1398350 1895240 1438360 1860330 2278340 2188720 TRUE FALSE 2206129.009 1595092.445 1818149.965 1715866.74 1857528.432 1493694.64 1679915.483 1791134.721 1929972.015 1.1430886 0.826484754 0.942060274 0.889063016 0.96246392 0.773946269 0.870435151 0.928062535 1 20.8801485 4.74932112 24.76878703 0.899090322 1.143088758 0.577409286 0.065607466 1021.263616 2350717.835 0.015620245 0.222237051 56146.2972 -4.74932112 0.243998436 VYEDWDCFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VYEDWDCFK 9 0 Q9BTE3;Q9BTE3-2;Q9BTE3-3 Q9BTE3 MCMBP Mini-chromosome maintenance complex-binding protein 0 110.87 0.0051568 48771000 171940 172730 117230 126570 161500 133720 196600 226930 174450 FALSE TRUE 149217.6934 171595.3253 173922.8201 155309.653 158286.466 138864.2949 177533.7623 178402.7855 153826.7197 0.970037544 1.115510527 1.130641155 1.009640284 1.028992013 0.902731952 1.154115245 1.159764609 1 17.2309466 VYEFLDKLDVVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VYEFLDKLDVVR 12 1 O43242;O43242-2;H0YGV8 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 167.98 4.35E-05 1033620000 3127600 2527510 1703940 2034940 2580700 2254580 3175000 3593500 2202020 FALSE TRUE 2714279.736 2510906.62 2527971.083 2497004.229 2529349.119 2341315.152 2867088.989 2825057.99 1941699.704 1.397888525 1.293148789 1.301937204 1.285988881 1.30264691 1.205807029 1.476587231 1.454940732 1 20.88888867 4.745952056 22.36643557 1.30974322 1.397888702 0.044212074 0.131914861 826.8177521 2501649.028 0.032005609 0.302684435 55712.42423 -4.745952056 0.088145481 VYEGERPLTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VYEGERPLTK 10 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;;; 159.94 6.87E-06 10466840000 11778900 8776450 6494060 8237050 8683680 8691880 8442480 9247570 10801800 FALSE TRUE 10222288.52 8718796.922 9634609.137 10107398.1 8510891.757 9026262.248 7623729.589 7270049.12 9524823.509 1.07322603 0.915376218 1.011526264 1.06116382 0.8935485 0.94765664 0.800406389 0.763273893 1 23.18326093 2.745126114 1.632403795 0.838798985 1.004282653 0.369950349 0.081414486 0.349835116 1.879211933 0.035210859 0.030929304 556.065709 -2.745126114 0.165483668 VYEHTS(ph)RFSPK ddPTM_MDA-MB-175_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(0.117)S(0.594)RFS(0.289)PK 67.234 0.036555 180800000 331050 283810 156120 218090 243880 232450 280850 343200 340190 TRUE FALSE 287300.9037 281945.6334 231620.1542 267610.6678 239027.2651 241392.5019 253613.2102 269809.3508 299973.1257 0.957755476 0.939902975 0.772136349 0.892115476 0.796828931 0.80471376 0.845453104 0.899445076 1 18.19447373 1.291794224 2.480295556 1.025548406 0.855489472 0.35778282 0.059706344 0.543215761 3.995661338 0.188571138 0.016255373 19.5791676 -1.291794224 -0.170058935 VYENYPTYDLTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VYENYPTYDLTER 13 0 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;A0A494C198 H0Y993 DEK Protein DEK 0 201.46 2.37E-07 170160000 139230 140760 85595 113860 145650 146060 146280 160300 162090 FALSE TRUE 120830.4027 139835.3383 126989.0283 139713.6532 142751.85 151679.0227 132093.7881 126021.0925 142927.9049 0.845394067 0.978362752 0.888483102 0.977511378 0.998768226 1.061227497 0.92419873 0.881710906 1 17.12492809 4.745227369 24.20462898 0.957729792 0.845393985 0.313030513 0.054465114 718.1216383 2607137.242 0.014281796 0.131616215 55619.53691 -4.745227369 -0.112335807 VYFDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VYFDLR 6 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 100.82 0.086601 701990000 1753200 1648200 1138500 1463400 1506200 1840600 1136600 1441000 1990500 FALSE TRUE 1521510.178 1637372.866 1689082.408 1795687.337 1476229.567 1911409.073 1026372.707 1132853.364 1755185.358 0.866865811 0.932877464 0.962338479 1.023075614 0.841067617 1.089006961 0.584765992 0.645432324 1 20.74319196 2.237496033 24.99977725 0.716379903 0.95022977 0.367591584 0.127660814 26.19768875 615173.2599 0.048797545 0.035020748 172.7810198 -2.237496033 0.233849867 VYFQSPPGAAGEGPGGADDEGPVRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VYFQSPPGAAGEGPGGADDEGPVRR 25 1 Q96C90 Q96C90 PPP1R14B Protein phosphatase 1 regulatory subunit 14B 0 162.73 3.05E-11 396870000 177510 114660 53820 63336 113920 110270 101390 123240 73603 FALSE TRUE 154051.6037 113906.7909 79847.53202 77717.40683 111653.2149 114512.1583 91557.21341 96886.08505 64901.73719 2.373612948 1.755065363 1.230283433 1.19746266 1.72034247 1.764392807 1.410705127 1.492811892 1 15.98596947 4.627084863 2.959708704 1.429036557 2.427274979 0.637029051 0.233080177 0.209080458 2.900814831 0.060435119 0.42603149 42372.57559 -4.627084863 0.998238422 VYHAWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VYHAWK 6 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6 Q9UM54-1 MYO6 Unconventional myosin-VI 0 78.002 0.070933 518500000 682570 660910 385260 474700 677210 721290 590400 691830 788240 FALSE TRUE 592366.6451 656568.4387 571573.0246 582487.8903 663734.8459 749038.493 533143.0989 543887.5383 695055.1652 0.852258461 0.94462781 0.822341957 0.838045553 0.954938369 1.077667688 0.767051488 0.782509886 1 19.40676796 VYIGSFWSHPLLIPDNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VYIGSFWSHPLLIPDNR 17 0 A0A024R571;Q9H4M9;C9JC03;C9J2Z4;C9JDQ8;Q9NZN3 A0A024R571;Q9NZN3 EHD1;EHD3 EH domain-containing protein 1;EH domain-containing protein 3 0 ; 195.2 3.17E-11 623090000 340400 509380 242865 297800 419360 462850 420060 441700 566960 FALSE TRUE 295415.2775 506033.8492 360315.3263 365420.0416 411015.5565 480656.139 379322.6459 347245.8923 499934.6347 0.590907805 1.012200024 0.720724873 0.730935639 0.822138592 0.961437967 0.758744483 0.694582588 1 18.93137995 3.03871974 22.76837961 0.827913638 0.778143853 0.072191112 0.135552035 286.2453311 168316.5537 0.040429945 0.045843057 1093.250639 -3.03871974 -0.049769786 VYISSPHS(ph)SPAHNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VYISSPHSSPAHNK 14 0 Q9BZH6 Q9BZH6 WDR11 WD repeat-containing protein 11 1 VYISSPHS(0.621)S(0.379)PAHNK 110.12 0.0012166 72146000 119150 108280 63012 80193 107310 105240 109000 136830 116580 TRUE FALSE 103404.0256 107568.7016 93484.81396 98402.04632 105174.7409 109288.6509 98429.19678 107569.9693 102798.0452 1.005894863 1.046408045 0.909402643 0.957236552 1.023120048 1.063139388 0.957500666 1.046420378 1 16.64945331 3.221062435 24.83939371 1.019299149 0.979474071 0.157097602 0.044028231 420.5359118 596966.1493 0.013424579 0.015256488 1663.651803 -3.221062435 -0.039825078 VYISSPHSS(ph)PAHNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VYISSPHSSPAHNK 14 0 Q9BZH6 Q9BZH6 WDR11 WD repeat-containing protein 11 1 VYISSPHS(0.235)S(0.765)PAHNK 130.47 0.00010346 62419000 110890 97180 56003 84602 108750 83783 110350 116740 112210 TRUE FALSE 96235.60554 96541.61818 83086.23812 103812.1772 106586.0878 87006.18622 99648.27398 91776.05947 98944.66163 0.972620493 0.975713258 0.839724314 1.049194322 1.077229292 0.879341895 1.00711117 0.927549379 1 16.59433425 3.715592674 24.95180549 0.983641223 0.933988698 0.149979439 0.066681802 1754.881993 1906460.254 0.018422622 0.027346922 5195.085194 -3.715592674 -0.049652525 VYLLYRPGHYDILYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VYLLYRPGHYDILYK 15 1 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5H3F0;Q96FW1-2 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 129.04 4.11E-05 1992850000 5899100 4305800 2099890 3243100 3400400 3032700 4315400 5046500 4209800 FALSE TRUE 5119518.989 4277514.916 3115403.828 3979495.423 3332738.693 3149369.931 3896893.172 3967345.247 3712122.24 1.379135346 1.152309822 0.839251411 1.072027042 0.897798746 0.848401461 1.049775013 1.068753934 1 21.82381279 4.543392245 3.521424295 0.978206852 1.367293187 0.702229504 0.08687224 0.144481443 3.262215416 0.022625131 0.109792979 34945.57938 -4.543392245 0.389086335 VYMGHGGKPWVSDFSHPHYLAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VYMGHGGKPWVSDFSHPHYLAGR 23 1 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 216.44 8.57E-33 4220900000 2488000 2124470 805300 1531020 2166840 2034210 1996210 2564100 2218090 FALSE TRUE 2159204.496 2110514.217 1194745.774 1878661.491 2123724.123 2112467.375 1802617.861 2015787.169 1955869.927 1.103961192 1.079066756 0.610851344 0.960524759 1.085820736 1.080065369 0.921645063 1.030634574 1 20.899379 3.470713125 24.90422424 1.019998294 0.919340073 0.08574063 0.138600118 378.6824311 1471683.485 0.040717677 0.05270349 2956.059183 -3.470713125 -0.100658221 VYNLLT(ph)PDSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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(0.994)PDS(0.006)K 108.59 0.023815 387160000 1754850 1783260 1129430 1397140 1708910 1513040 1866270 2214990 1957250 TRUE FALSE 1522942.126 1771545.648 1675626.126 1714381.991 1674906.034 1571247.628 1685279.423 1741331.626 1725866.135 0.88242193 1.026467588 0.970889973 0.993345866 0.970472739 0.910411066 0.976483279 1.008961003 1 20.71888914 1.868404102 4.814730976 1.003744512 0.963225114 0.171518146 0.040027913 0.403066576 13.38079388 0.020690224 0.010335293 73.85911541 -1.868404102 -0.040519398 VYNVTQHAVGIVVNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VYNVTQHAVGIVVNK 15 0 P46778;M0R181;G3V1B3 P46778 RPL21 60S ribosomal protein L21 0 ; 148.33 3.55E-06 1690620000 2096030 1981950 1189740 1695700 1894030 1894950 2050200 2515000 2208300 FALSE TRUE 1819034.325 1968930.44 1765102.243 2080734.602 1856342.509 1967849.953 1851371.92 1977186.822 1947237.29 0.934161612 1.011140476 0.906464894 1.06855729 0.953321158 1.010585594 0.950768522 1.015380525 1 20.89299727 6.914560008 0.67203579 0.99367872 2.06E-10 0.117301276 0.044699022 117.8239015 3.395842333 0.016815561 159.167239 8214100.428 -6.914560008 -0.99367872 VYNWDVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VYNWDVK 7 0 P61758;P61758-2 P61758 VBP1 Prefoldin subunit 3 0 101.99 0.020244 195770000 625800 568190 410700 400280 560880 440460 653350 701510 575430 FALSE TRUE 543098.9444 564457.5225 609315.8937 491169.6919 549719.5853 457404.7812 589988.2176 551497.5457 507403.3209 1.070349606 1.112443493 1.200851214 0.968006459 1.083397689 0.901461938 1.162759866 1.086901727 1 18.95277344 3.739146511 24.9989126 1.043909868 1.126337638 0.23911573 0.077741533 88.61551886 3780983.882 0.020868312 0.033587865 5484.61959 -3.739146511 0.08242777 VYNYNHLMPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VYNYNHLMPTR 11 0 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;;; 147.42 3.53E-05 5058250000 3068200 3663280 2112698 2256163 3314370 3359400 3319310 3485370 3375870 FALSE TRUE 2662729.596 3639215.672 3134405.819 2768459.292 3248420.521 3488638.292 2997403.827 2740050.749 2976778.494 0.894500414 1.222534925 1.052952319 0.930018575 1.091253692 1.171950919 1.006928743 0.920475189 1 21.50532044 2.002794931 24.99924089 0.957300652 1.065219658 0.151731343 0.098641695 131.4802026 1176016.007 0.039203766 0.026263785 100.645632 -2.002794931 0.107919006 VYQHQVVANCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VYQHQVVANCR 11 0 P34896-2;P34896;P34896-4 P34896-2 SHMT1 "Serine hydroxymethyltransferase, cytosolic" 0 ; 141.95 3.79E-05 286450000 204179 187730 123614 158105 207947 188035 168452 200896 204313 FALSE TRUE 177196.2278 186496.7893 183394.1439 194005.1567 203809.2615 195268.8281 152115.551 157935.9538 180159.3499 0.983552771 1.035176855 1.017955182 1.076853113 1.131272186 1.0838673 0.84433892 0.876645891 1 17.458914 2.244431 24.99934631 0.898061545 1.056694994 0.610030182 0.055534029 88.93398428 378731.9051 0.022159796 0.016697279 175.5621941 -2.244431 0.158633449 VYQSLCPTSWVTDWDEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VYQSLCPTSWVTDWDEQR 18 0 P14854 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 0 ;;; 296.22 5.75E-49 625096000 637074 498145 422634 565212 631614 791676 357880 643874 767601 FALSE TRUE 552883.0568 494872.6527 627021.216 693552.0233 619046.1171 822132.288 323172.8527 506186.5557 676856.0842 0.816839901 0.731134231 0.926373022 1.024666897 0.91459046 1.214633815 0.477461694 0.747849606 1 19.36848959 2.233443194 24.99996772 0.732024157 0.930976335 0.214882923 0.176180763 198.4812832 969620.3292 0.071441068 0.049818203 171.1761264 -2.233443194 0.198952177 VYQWDDPDPR ddPTM_MDA-MB-175_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 ;;;;;; 159.4 1.79E-05 1.08685E+11 28192930 28591650 20437210 20429930 28972670 33048770 29542960 30166280 31474240 FALSE TRUE 24467162.87 28403829.57 30320713.11 25068857.86 28396170.55 34320177.57 26677888.29 23715455.78 27753391.2 0.881591827 1.023436356 1.0925048 0.90327188 1.023160389 1.236612035 0.961247874 0.854506594 1 24.72616073 2.006598505 24.99644164 0.914165771 1.030081874 0.142568902 0.103118163 254.393553 963688.5287 0.042174425 0.028356781 101.5309629 -2.006598505 0.115916103 VYRDDIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VYRDDIGR 8 1 A0A087WY71;Q96CW1-2;Q96CW1;C9JJ47;C9JJD3;C9JGT8 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 ;; 151.44 0.00057656 1789380000 1391650 1300710 796750 982800 1296660 1310710 1317850 1391990 910500 FALSE TRUE 1207739.927 1292165.55 1182060.965 1205959.761 1270859.003 1361133.862 1190045.11 1094323.771 802861.7272 1.50429381 1.60944968 1.472309521 1.502076535 1.582911428 1.695352781 1.482254129 1.363028942 1 19.61479202 1.230897914 1.666637281 0.777856677 1.557142522 0.87628549 0.06607849 0.349853639 0.876229255 0.451511886 0.019301105 17.01758442 -1.230897914 0.779285845 VYSGHQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 VYSGHQGR 8 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;;;; 164.72 0.00032843 771727000 1112073 1121336 502076 826986 897592 1029841 1009128 1052921 1067304 FALSE TRUE 965109.7354 1113969.87 744881.6329 1014765.811 879731.6753 1069459.65 911262.9219 827762.038 941128.537 1.025481321 1.18365327 0.791477044 1.078243589 0.934762512 1.136358752 0.968266168 0.87954196 1 19.84403225 VYSLDDIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VYSLDDIRR 9 1 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ;; 162.88 0.00010173 339440000 533050 551620 203494 254522 522240 550870 510220 576180 81882 FALSE TRUE 462606.0919 547996.3719 301904.379 312315.1102 511848.4457 572062.3254 460738.9429 452968.3908 72202.00324 6.407108822 7.589766867 4.181385079 4.325574031 7.08911696 7.923081074 6.38124875 6.273626361 1 16.13975124 1.238529075 24.99606268 1.000002526 6.268873608 0.649660169 1.216540719 0.512095768 399274.6882 1.751413075 0.313911605 17.31924977 -1.238529075 5.268871081 VYSLFLDESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VYSLFLDESR 10 0 Q9Y230;Q9Y230-2 Q9Y230 RUVBL2 RuvB-like 2 0 ;;; 226.59 6.88E-09 1136035000 671319 743112 451939 529282 685876 738403 752114 807250 757252 FALSE TRUE 582602.4932 738230.4483 670498.212 649463.5677 672228.4095 766809.8412 679174.1 634625.8695 667730.5312 0.872511389 1.105581389 1.004144907 0.972643211 1.006736068 1.148382177 1.017138004 0.950422124 1 19.34890648 4.762086082 24.30980556 1.020275382 0.872511143 0.394000723 0.059349445 5814.629112 6008348.311 0.015154034 0.880312487 57821.06433 -4.762086082 -0.147764239 VYSS(ph)SEFLAVQPTPTFAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VYSSSEFLAVQPTPTFAER 19 0 O60307;V9GYV0 O60307 MAST3 Microtubule-associated serine/threonine-protein kinase 3 1 VYS(0.019)S(0.98)S(0.002)EFLAVQPTPTFAER;VYS(0.028)S(0.972)S(0.001)EFLAVQPTPTFAER;VYS(0.025)S(0.95)S(0.025)EFLAVQPTPTFAER;VYSS(0.996)S(0.004)EFLAVQPTPTFAER 390.45 5.56E-127 259129000 297196 317009 212344 237963 345365 333529 273498 355258 318972 TRUE FALSE 257920.7956 314926.547 315034.2686 291996.1362 338492.9122 346360.0765 246974.2061 279288.8413 281263.4935 0.917007722 1.119685115 1.120068107 1.038158676 1.203472615 1.231443413 0.878088382 0.992979351 1 18.10156279 2.228692158 24.99950269 0.961224662 1.107767801 0.366783248 0.091534343 222.4694858 563571.1724 0.037189564 0.025417112 169.3137225 -2.228692158 0.146543139 VYTDVNTHRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 143.24 2.24E-05 1036000000 864280 804090 492650 585260 834490 922730 785650 832460 803600 FALSE TRUE 750063.2082 798807.8798 730897.1878 718152.2281 817885.2817 958228.0202 709457.7839 654444.9072 708599.3235 1.058515276 1.127305451 1.031467521 1.013481391 1.154228144 1.352284695 1.001211489 0.923575405 1 19.43461056 2.017700611 24.996365 0.958148096 1.120492762 0.355671272 0.094913398 250.0358441 353093.0787 0.040631945 0.027388156 104.1599135 -2.017700611 0.162344665 VYTDVQQVASSLTHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VYTDVQQVASSLTHPR 16 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 240.92 6.98E-20 971890000 1279260 1365520 542230 854440 1428430 1442790 1320610 1365970 1347820 FALSE TRUE 1110202.55 1356549.809 804454.2417 1048453.661 1400007.038 1498295.065 1192537.445 1073867.945 1188482.255 0.934134729 1.1414136 0.676875265 0.882178642 1.177978915 1.260679374 1.003412075 0.903562456 1 20.18068893 3.267490298 24.96702278 1.053080172 0.908721041 0.22240381 0.147416942 394.5463394 340500.581 0.046178832 0.059605792 1851.357534 -3.267490298 -0.14435913 VYTLQDLLYQSDCVSLHCNLNEHNHHLINDFTIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VYTLQDLLYQSDCVSLHCNLNEHNHHLINDFTIK 34 0 P56545;P56545-3;P56545-2 P56545 CTBP2 C-terminal-binding protein 2 0 ;; 147.54 5.75E-11 422316000 196148 192383.2 69068.6 162790.5 222118 174024.3 252337 266624 219945 FALSE TRUE 170226.5448 191119.4221 102470.406 199754.5711 217698.2864 180719.1274 227865.3966 209608.5325 193943.3527 0.877712706 0.985439405 0.528352246 1.029963484 1.122483877 0.93181398 1.174906969 1.080771935 1 17.5652758 3.507994759 24.99285545 1.067203755 0.809855629 0.469610544 0.130113244 568.0008401 459809.1597 0.034069988 0.050466176 3221.02992 -3.507994759 -0.257348126 VYTVGPDYAHAEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 VYTVGPDYAHAEAR 14 0 A0A087WZV0;O43314-2;O43314;D6RBU4;Q6PFW1-6;B7WPL9;Q6PFW1-7;Q6PFW1-4;Q6PFW1-3;Q6PFW1-2;F8W9A8;Q6PFW1;Q6PFW1-5 A0A087WZV0;B7WPL9 PPIP5K2;PPIP5K1 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2;Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 1 0 158.81 2.75E-07 0 148860 158190 100950 101760 171410 148430 129350 174760 160650 FALSE TRUE 129187.7738 157150.8395 149769.7577 124866.1633 167999.2764 154140.1981 116805.6569 137388.934 141658.14 0.911968587 1.109366814 1.057261924 0.881461265 1.185948625 1.088113949 0.824560148 0.969862614 1 17.11205398 2.262833905 24.99971909 0.935016964 1.042563735 0.2074199 0.09885995 345.5767866 355917.8494 0.036022 0.027888472 183.1613792 -2.262833905 0.107546771 VYVGNLGNNGNKTELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 VYVGNLGNNGNKTELER 17 1 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;; 334.04 3.76E-72 3026520000 2081110 1649290 772351 886710 1586860 1326870 1933750 2112670 220776 FALSE TRUE 1806086.041 1638455.705 1145862.527 1088051.058 1555284.591 1377915.547 1746215.223 1660891.961 194676.1128 9.277389068 8.416316116 5.885994489 5.589032175 7.98908797 7.077989835 8.96984842 8.531565263 1 17.57071635 4.406903354 5.437913061 6.811222937 9.083700134 0.155988913 2.242562393 0.370930851 19.61966192 0.556653711 1.565630508 25521.33299 -4.406903354 2.272477197 VYVGSIYYELGEDTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VYVGSIYYELGEDTIR 16 0 A0A0J9YVP6;A0A0J9YXX5;Q9UHX1-2;Q9UHX1;A0A0J9YYL3;A0A0J9YXJ8;Q9UHX1-4;Q9UHX1-6;Q9UHX1-3;Q9UHX1-5;A0A0J9YVR6;E9PQ56;A0A0J9YWM1;H0YEM1;E9PN18;E9PMU7;E9PL19 A0A0J9YVP6;E9PN18 PUF60 Poly(U)-binding-splicing factor PUF60 0 ; 174.73 8.77E-09 69128000 36871 33911 24790.1 18611 30899 34749 35068 38442 35029 FALSE TRUE 31998.40393 33688.23641 36778.67528 22836.912 30284.17035 36085.81652 31667.11076 30221.47746 30887.91153 1.035952331 1.090660868 1.190714213 0.739347883 0.980453804 1.168282824 1.025226673 0.978424114 1 14.91475471 VYWNDGLDQYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 VYWNDGLDQYR 11 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ;; 169.76 3.84E-05 367930000 504890 432002 288999 324601 464470 468000 399200 457710 463710 FALSE TRUE 438167.5073 429164.1504 428759.883 398306.6183 455227.9557 486004.2628 360485.6454 359832.2784 408890.7321 1.071600486 1.049581506 1.048592813 0.974115056 1.113324221 1.188592024 0.881618528 0.880020627 1 18.64135584 2.216059011 24.9999922 0.910481462 1.069228748 0.566494656 0.063096615 169.2386598 188028.0652 0.026617654 0.017960479 164.4595171 -2.216059011 0.158747286 VYYS(ph)PPVAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 VYYSPPVAR 9 0 O94964-2;H0YDM2;O94964;O94964-3 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 VYYS(1)PPVAR;VYYS(1)PPVAR;VYYS(1)PPVAR;VYYS(1)PPVAR;VYYS(1)PPVAR 101.82 0.0039084 4271692000 2433780 2889790 1661200 2040870 2612470 2769900 2385670 2918970 2502150 TRUE FALSE 2112149.807 2870806.779 2464561.876 2504280.726 2560486.958 2876459.845 2154308.091 2294770.981 2206348.677 0.957305538 1.301157341 1.11703191 1.135033983 1.160508756 1.303719523 0.976413254 1.040076305 1 21.07322937 2.210318048 24.99997499 1.011488767 1.165363853 0.362627312 0.097939593 219.3189658 194136.8781 0.03704772 0.024983035 162.2998235 -2.210318048 0.153875085 VYYTAGYNS(ph)PVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 VYYTAGYNSPVK 12 0 Q9Y5Z4-2;Q9Y5Z4 Q9Y5Z4-2 HEBP2 Heme-binding protein 2 1 VYYTAGYNS(1)PVK;VYYTAGYNS(1)PVK 202.42 1.44E-07 558080000 571570 565750 344921 462350 543910 446450 605410 737760 603650 TRUE FALSE 496035.5763 562033.551 511725.9493 567333.6341 533087.2551 463625.2204 546697.4314 579995.7653 532287.1847 0.931894644 1.055884055 0.961371914 1.065841242 1.00150308 0.871005791 1.027072316 1.089629399 1 19.02184531 2.008083417 24.99583224 1.053357039 0.985215861 0.169682119 0.059979629 277.091925 856830.4779 0.02405387 0.016186076 101.8787052 -2.008083417 -0.068141178 WAEALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WAEALR 6 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 110.17 0.067304 512650000 590880 731020 453090 510990 747440 803610 667550 753250 725640 FALSE TRUE 512793.7109 726217.8815 672205.8395 627018.0895 732567.4063 834525.3967 602811.1037 592173.3493 639855.6659 0.801420911 1.134971401 1.050558548 0.979936762 1.144894771 1.304240067 0.942104815 0.925479574 1 19.28738698 WAELLS(ph)PLDESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 WAELLSPLDESR 12 0 Q9H6K5-2;Q9H6K5 Q9H6K5-2 PRR36 Proline-rich protein 36 1 WAELLS(1)PLDESR;WAELLS(1)PLDESR;WAELLS(1)PLDESR 141.54 6.36E-05 70164000 65796 85121 63414 86494 123931 127990 114096 133210 115035 TRUE FALSE 57100.89189 84561.83455 94081.22251 106133.7847 121465.0156 132913.8581 103030.9875 104724.0781 101435.6933 0.562927013 0.833649692 0.927496223 1.046315958 1.197458326 1.310326313 1.015727148 1.032418419 1 16.63020587 4.539325382 1.162670006 1.101714524 0.432003835 0.771429431 0.095895859 0.600973429 0.885165057 0.033009129 0.451243244 34619.86593 -4.539325382 -0.669710689 WAEQYLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WAEQYLK 7 0 P30040;F8VY02 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 ; 108.09 0.017057 112499000 344570 289280 220643 288310 300500 306760 342650 329650 298980 FALSE TRUE 299034.2015 287379.7006 327346.6928 353775.192 294520.6379 318561.2557 309419.8557 259156.9128 263634.925 1.13427385 1.090066882 1.241666645 1.341913224 1.117153343 1.208342391 1.173667926 0.983014344 1 18.00818198 1.75959984 4.71178043 0.990517442 1.190422723 0.5690787 0.070600139 0.130465257 6.420701191 0.044847748 0.019541919 57.49099692 -1.75959984 0.19990528 WAEVMAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WAEVMAR 7 0 Q9HAB8;Q5VVM3 Q9HAB8 PPCS Phosphopantothenate--cysteine ligase 0 97.602 0.02763 59961000 130100 133440 91424 95522 132810 132800 126740 136030 130750 FALSE TRUE 112906.9554 132563.4239 135636.9522 117211.7301 130167.3408 137908.9019 114448.7743 106941.0431 115292.884 0.9793055 1.149797102 1.176455541 1.016643231 1.129014527 1.196161439 0.992678563 0.927559789 1 16.81494394 2.078915444 7.045646829 0.959037503 1.109378623 0.464187549 0.06854008 0.170110503 12.58680386 0.02746342 0.018411805 119.9265787 -2.078915444 0.15034112 WAEYHADIYDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WAEYHADIYDK 11 0 Q9NRX4;Q9NRX4-2 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 ;;; 187.31 3.65E-06 1525990000 6348500 5052300 4051020 5062000 4495300 3865580 5200000 6165600 8237200 FALSE TRUE 5509529.64 5019111.109 6010106.822 6211404.468 4405852.325 4014291.364 4695704.8 4847134.421 7263407.6 0.758532351 0.69101328 0.827450028 0.855163968 0.606582002 0.552673289 0.646487855 0.667336144 1 22.79221511 1.235064346 24.83660959 1.000000464 0.697479216 0.504132241 0.09325353 86.97553027 617744.1319 0.177605105 0.024975655 17.18162934 -1.235064346 -0.302521247 WAGVLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WAGVLSR 7 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ; 126.24 0.0092382 249520000 573590 592190 497550 423170 500140 540310 546050 554400 516870 FALSE TRUE 497788.6282 588299.8649 738166.8442 519257.2162 490188.1925 561096.0753 493094.155 435845.8743 455766.2174 1.09220168 1.290793048 1.619617286 1.139306066 1.075525508 1.231105014 1.081901502 0.956292629 1 18.79793447 2.46607834 0.759878296 0.94833821 1.308994493 0.368495488 0.149499128 0.864748004 1.067741948 0.210258225 0.095992883 292.4679898 -2.46607834 0.360656283 WAHDKFS(ph)GEEGEIEDDES(ph)GTENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 WAHDKFSGEEGEIEDDESGTENR 23 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 WAHDKFS(1)GEEGEIEDDES(0.977)GT(0.023)ENR;WAHDKFS(1)GEEGEIEDDES(0.999)GT(0.001)ENR;WAHDKFS(1)GEEGEIEDDES(0.89)GT(0.11)ENR;WAHDKFS(1)GEEGEIEDDES(0.999)GT(0.001)ENR;WAHDKFS(1)GEEGEIEDDES(0.866)GT(0.134)ENR;WAHDKFS(1)GEEGEIEDDES(0.962)GT(0.038)ENR;WAHDKFS(1)GEEGEIEDDES(0.964)GT(0.036)ENR 313.78 3.89E-73 3542250000 3441234 2254396 2356588 2836880 2591988 2400800 2618720 3284852 6461190 TRUE FALSE 2986466.208 2239586.724 3496241.839 3481036.963 2540412.51 2493160.33 2364756.937 2582411.963 5697355.479 0.524184636 0.393092327 0.61366047 0.610991709 0.445893278 0.437599574 0.415062207 0.453265023 1 22.44186099 1.236495347 24.99910057 1.000000658 0.483905471 0.817904057 0.076102369 23.69736282 286771.4662 0.125179833 0.019615918 17.23833624 -1.236495347 -0.516095187 WAHDKFS(ph)GEEGEIEDDES(ph)GTENREEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WAHDKFSGEEGEIEDDESGTENREEK 26 2 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 WAHDKFS(1)GEEGEIEDDES(0.844)GT(0.156)ENREEK;WAHDKFS(1)GEEGEIEDDES(0.985)GT(0.015)ENREEK 156.12 6.04E-08 750400000 346040 245608 245015 199552 236170 217329 298650 354230 420680 TRUE FALSE 300309.9372 243994.5849 363505.0735 244863.3316 231470.6791 225689.7873 269686.969 278480.6711 370947.6896 0.809574896 0.657760088 0.979936211 0.660102053 0.623998169 0.608414053 0.727021563 0.750727606 1 18.50085623 1.219074845 3.394591218 1.050759617 0.721310562 0.38879865 0.107905932 0.381323615 6.025900167 0.339708521 0.027895198 16.56055337 -1.219074845 -0.329449054 WAHDKFS(ph)GEEGEIEDDES(ph)GTENREEKDNIQPTTE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WAHDKFSGEEGEIEDDESGTENREEKDNIQPTTE 34 3 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 WAHDKFS(1)GEEGEIEDDES(0.957)GT(0.043)ENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDES(0.989)GT(0.011)ENREEKDNIQPTTE 136.95 1.88E-08 1456410000 1093100 805800 636610 566239 719140 521019 1107700 1160520 522472 TRUE FALSE 948644.0654 800506.6467 944476.7253 694812.2194 704830.521 541062.9381 1000275.424 912351.8292 460705.9554 2.059109622 1.737565224 2.050064069 1.508146815 1.529892359 1.174421411 2.171179714 1.980334351 1 18.81348672 3.737955219 24.99973928 1.625160131 1.9277782 0.198740591 0.35109789 116.2021391 4798602.81 0.099530152 0.158370213 5469.595622 -3.737955219 0.30261807 WAHDKFS(ph)GEEGEIEDDESGTENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 WAHDKFSGEEGEIEDDESGTENR 23 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 WAHDKFS(0.944)GEEGEIEDDES(0.056)GTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR 311.55 2.08E-73 6526960000 4467819 3148868 2951156 3539619 3431089 2950816 3789222 4543195 6278730 TRUE FALSE 3877385.399 3128182.879 4378344.913 4343343.594 3362817.042 3064335.801 3421743.834 3571668.104 5536465.692 0.700335849 0.565014407 0.790819479 0.784497518 0.60739418 0.553482306 0.618037576 0.645116994 1 22.40053387 1.237467179 24.99356067 1.00000041 0.655938564 0.636335664 0.081217149 18.82378974 430066.7102 0.124206881 0.020801697 17.27695406 -1.237467179 -0.344061846 WAHDKFS(ph)GEEGEIEDDESGTENREEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WAHDKFSGEEGEIEDDESGTENREEK 26 2 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 WAHDKFS(1)GEEGEIEDDESGTENREEK 139.54 1.73E-07 169610000 197670 158490 135880 121550 160520 149200 197500 214130 158730 TRUE FALSE 171547.4087 157448.8688 201592.0225 149149.7853 157325.9661 154939.8205 178346.4804 168339.9659 139965.1202 1.225643992 1.12491504 1.440301856 1.065621099 1.124036944 1.1069888 1.274220892 1.202727977 1 17.09470782 WAHDKFS(ph)GEEGEIEDDESGTENREEKDNIQPTTE ddPTM_MDA-MB-175_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 254.78 1.32E-59 1241560000 2546350 1666970 1102870 912955 1520740 1128714 2454220 2651250 575830 TRUE FALSE 2209843.396 1656019.564 1636221.621 1120255.386 1490480.249 1172136.358 2216210.122 2084300.82 507756.0334 4.352175554 3.26144734 3.222456285 2.206286706 2.935425975 2.308463673 4.364714501 4.104925757 1 18.95377595 4.791025247 2.229240163 3.02618753 4.80693444 0.177333738 0.959813102 1.565142651 8.013582655 0.255116633 5.778425517 61805.23282 -4.791025247 1.78074691 WAHLDIAGVMTNKDEVPYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WAHLDIAGVMTNKDEVPYLR 20 1 P28838-2;P28838 P28838-2 LAP3 Cytosol aminopeptidase 0 150.45 5.25E-08 20317000 45147 37223 23545 28904 37141 33589 35006 44134 31986 FALSE TRUE 39180.70956 36978.47966 34931.44075 35467.09497 36401.96677 34881.19056 31611.12351 34696.28755 28204.65152 1.389157726 1.311077346 1.238499285 1.257490983 1.290636998 1.236717658 1.120776957 1.230161895 1 14.78364549 -1.260383306 0.26203751 1.17E-15 1.353791133 0.711501582 0.056979264 33.71216948 0.773247598 18.40519095 0.171330001 0.054905607 1.260383306 1.353791133 WALWFFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WALWFFK 7 0 D6RBW1;P06730;P06730-3;P06730-2;H0Y8J7;D6RHE2;H0Y8X3;A6NMX2 D6RBW1 EIF4E;EIF4E1B Eukaryotic translation initiation factor 4E;Eukaryotic translation initiation factor 4E type 1B 0 ; 142.42 0.0057936 119323000 505710 835540 450400 565910 579530 546550 954970 857450 882430 FALSE TRUE 438879.1422 830051.2827 668214.9465 694408.5149 567998.4868 567576.1322 862357.1564 674090.9902 778110.1307 0.564032166 1.066752957 0.858766542 0.892429603 0.729971844 0.729429048 1.108271339 0.866318229 1 19.56961484 2.249643291 24.99988436 0.970308351 0.821457622 0.266495697 0.14159212 331.5085586 747805.2407 0.050978567 0.039111698 177.6819415 -2.249643291 -0.148850729 WASLADSYS(ph)DPGLTEDGLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WASLADSYSDPGLTEDGLGR 20 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 WASLADS(0.082)YS(0.918)DPGLTEDGLGR;WASLADSYS(1)DPGLTEDGLGR;WASLADS(0.183)YS(0.817)DPGLTEDGLGR;WASLADS(0.047)Y(0.003)S(0.95)DPGLTEDGLGR 277.98 1.40E-44 326480000 753840 692190 389806 495870 669320 663330 636630 757490 768990 TRUE FALSE 654218.134 687642.9583 578317.4854 608464.8624 656001.8415 688848.7343 574889.7206 595506.6583 678080.8782 0.96480841 1.014101681 0.852873903 0.897333758 0.967438933 1.015879899 0.847818806 0.878223642 1 19.37109784 4.261809616 24.99972147 0.91880879 0.989455067 0.179484701 0.058774477 398.1124241 428084.1347 0.015072893 0.039827629 18272.98997 -4.261809616 0.070646277 WATHGEPSPVNSHPQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WATHGEPSPVNSHPQR 16 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ;;; 174.39 2.25E-09 1208610000 644920 582610 267186 424110 621890 646010 539420 636610 623150 FALSE TRUE 559692.188 578782.7965 396398.0433 520410.6576 609515.6057 670862.4227 487107.1314 500475.9056 549481.9169 1.018581633 1.053324557 0.721403255 0.947093328 1.109255076 1.22089991 0.886484371 0.910814151 1 19.06771248 WCDDYFFIAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WCDDYFFIAHR 11 0 P36551 P36551 CPOX "Oxygen-dependent coproporphyrinogen-III oxidase, mitochondrial" 0 114.83 0.0012043 217830000 151990 150040 111140 116230 142890 175970 117060 160100 167510 FALSE TRUE 131904.1364 149054.3774 164887.6757 142621.798 140046.7686 182739.6798 105707.5392 125863.8609 147707.1586 0.893011128 1.009120876 1.116314722 0.965571332 0.94813799 1.237175513 0.715656169 0.852117542 1 17.17238022 2.221804846 24.9999994 0.849286985 1.024870043 0.328323997 0.115976282 271.8789414 405646.5314 0.045981629 0.031094773 166.6498187 -2.221804846 0.175583058 WCDKSDEDDWSKPLPPSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 138.3 1.23E-06 289680000 205160 134300 129720 149800 145600 111830 189680 251310 134850 FALSE TRUE 178047.5862 133417.7745 192453.0259 183814.3795 142702.8449 116132.1725 171284.8628 197569.3122 118908.1866 1.497353473 1.122023456 1.618501058 1.545851339 1.200109504 0.976654138 1.440479984 1.661528258 1 16.85948852 3.237355728 24.99800373 1.306375534 1.435122307 0.117115136 0.237061748 108.8748762 2258863.986 0.075764656 0.090765894 1727.252094 -3.237355728 0.128746773 WCNEHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 WCNEHLK 7 0 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98;O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;O75369-5;O75369-4;Q14315-2;Q14315 Q60FE5;O75369-8;Q14315-2 FLNA;FLNB;FLNC Filamin-A;Filamin-B;Filamin-C 0 ;;;;; 129.56 0.0036482 5745410000 9700970 9494950 6023850 7252600 8621650 8097460 9759980 10718270 10735740 FALSE TRUE 8418962.235 9432577.048 8937004.009 8899413.679 8450096.033 8408974.526 8813458.642 8426251.37 9466573.047 0.889335792 0.996408838 0.944059055 0.940088207 0.892624606 0.888280741 0.931008359 0.890105778 1 23.17441083 5.065543897 15.05711211 0.930009054 0.494728521 0.103418458 0.039914874 2165338.092 11379605.19 0.009739278 28946855.78 116290.4088 -5.065543897 -0.435280534 WDAWNELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WDAWNELK 8 0 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ;;; 147.29 0.0012555 2694026000 2679380 2302070 1961501 2174592 1879547 1644103 2098785 2601390 8507550 FALSE TRUE 2325293.144 2286947.551 2910089.444 2668366.35 1842147.692 1707352.706 1895245.154 2045102.993 7501797.131 0.309964813 0.304853292 0.387918974 0.355696949 0.245560852 0.227592492 0.252638817 0.272615076 1 22.83880482 1.237552173 24.99999712 1.000000834 0.293125808 0.952739854 0.049372659 5.513249226 136607.7772 0.080583359 0.013596418 17.28033563 -1.237552173 -0.706875025 WDDPYYDIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 WDDPYYDIAR 10 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ;;;;;; 214.96 1.96E-08 6006250000 7063690 7409780 4719460 5455030 7438810 7126080 6968030 8150960 7596350 FALSE TRUE 6130205.469 7361104.667 7001806.642 6693677.936 7290792.235 7400224.909 6292271.523 6407940.635 6698318.157 0.915185771 1.098948198 1.045308162 0.999307256 1.08845117 1.104788506 0.939380808 0.956649189 1 22.67536747 2.221876263 24.99986005 0.962450266 1.04490828 0.285049231 0.05704319 281.9815047 422518.5542 0.022383321 0.015137573 166.6772255 -2.221876263 0.082458014 WDDQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WDDQQK 6 0 P09874;Q5VX84;Q5VX85 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 103.02 0.081529 281060000 946830 711460 613930 665320 676960 574500 846790 1007900 900450 FALSE TRUE 821704.0165 706786.3724 910828.6015 816391.0748 663489.8204 596601.3868 764668.4361 792368.4285 793999.8268 1.034891934 0.890159353 1.147139547 1.02820057 0.835629679 0.751387301 0.963058694 0.997945342 1 19.59877917 3.270127692 24.83516356 0.91674508 1.024176752 0.261912812 0.09591909 304.5117962 239570.2978 0.029938881 0.03864726 1862.634711 -3.270127692 0.107431672 WDEAFR ddPTM_MDA-MB-175_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 ;;;;; 163.34 0.018421 2129640000 2513260 1900000 1543970 1989010 2042250 2022420 1887360 2124730 4668930 FALSE TRUE 2181126.323 1887518.775 2290639.056 2440645.121 2001613.221 2100223.806 1704324.118 1670373.024 4116974.414 0.529788652 0.458472311 0.556388946 0.592824943 0.486185489 0.510137687 0.413974911 0.405728299 1 21.97315305 1.232730401 24.99946227 1.000000822 0.490439611 0.880562341 0.058529538 69.31648633 297192.3147 0.141025772 0.016157086 17.08954111 -1.232730401 -0.509561211 WDEQTSNTKGDDDEES(ph)DEEAVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WDEQTSNTKGDDDEESDEEAVKK 23 2 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 WDEQTSNTKGDDDEES(1)DEEAVKK 169.7 4.27E-12 58528000 160670 88417 124630 91721 76360 48471 139750 150020 160080 TRUE FALSE 139437.0524 87836.18291 184901.4849 112547.6549 74840.5854 50335.71073 126197.0665 117939.3905 141155.5248 0.987825681 0.622265285 1.309913198 0.797330853 0.530199477 0.356597525 0.894028531 0.83552798 1 17.10692607 3.49111462 24.92052645 0.725593222 0.957460154 0.181268689 0.242118552 1200.581235 2138090.64 0.069777222 0.098917319 3098.236885 -3.49111462 0.231866932 WDET(ph)PGR ddPTM_MDA-MB-175_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 141.48 0.028549 2746290000 5384550 5103560 3344830 3477760 4914400 5154870 4696970 5299950 5242170 TRUE FALSE 4672968.075 5070034.378 4962400.976 4267438.562 4816613.055 5353181.185 4241458.572 4166596.937 4622446.634 1.010929589 1.096829186 1.073544244 0.923199098 1.042005119 1.158083934 0.9175787 0.901383459 1 22.14022523 2.197144163 24.99999745 0.93076103 1.047697921 0.391114358 0.064963366 143.7340698 86760.4608 0.026813481 0.018077851 157.4505431 -2.197144163 0.116936891 WDETPGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WDETPGR 7 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 100.75 0.022243 325080000 556610 475900 306130 366220 455230 471050 448940 490170 528420 FALSE TRUE 483052.5782 472773.7816 454175.4919 449375.8483 446171.8136 489171.5983 405401.8679 385350.96 465950.7896 1.036702993 1.01464316 0.974728452 0.9644277 0.957551363 1.049835324 0.870052969 0.827020725 1 18.82981807 2.225192532 24.9903494 0.882816581 0.995682621 0.437981994 0.052549112 186.5202493 348678.857 0.021245079 0.014414974 167.9548432 -2.225192532 0.11286604 WDGS(ph)EEDEDNSK ddPTM_MDA-MB-175_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 376.77 7.98E-87 4830840000 8140520 6045020 4875010 5125530 5698830 4611940 7551840 8487790 7894350 TRUE FALSE 7064729.657 6005309.866 7232581.142 6289359.925 5585434.433 4789364.316 6819463.719 6672742.161 6961088.936 1.014888579 0.862696903 1.039001399 0.903502309 0.80237941 0.688019412 0.979654732 0.958577346 1 22.73088158 7.999965201 0.918999849 0.900791716 58.14451812 0.09189199 0.103276858 3186.503414 6.371062658 0.035609722 382934.3703 99991987.47 -7.999965201 57.2437264 WDGS(ph)EEDEDNSKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WDGSEEDEDNSKK 13 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 WDGS(1)EEDEDNSKK 211.78 1.18E-08 795750000 1017500 595340 647780 569520 530700 407190 902710 932190 856210 TRUE FALSE 883034.797 591429.1723 961048.5747 698838.2206 520140.1083 422854.8628 815165.3231 732848.4228 754989.8292 1.169598269 0.78336045 1.272929167 0.925626007 0.688936577 0.560080211 1.079703715 0.970673239 1 19.52609768 7.999968791 0.698370937 0.897460663 28.62840285 0.122681379 0.202272795 770.5637197 4.139399403 0.084207386 33349.15243 99992814.13 -7.999968791 27.73094218 WDGVPFILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WDGVPFILR 9 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 138.26 0.00032929 3558000000 2418500 3114500 1835330 1672350 2693100 3136200 3095800 3130900 1121130 FALSE TRUE 2098889.097 3094040.644 2722901.727 2052082.628 2639512.579 3256851.643 2795569.792 2461381.4 988591.2886 2.123111059 3.129747025 2.754325026 2.075764425 2.669973536 3.294436923 2.827831708 2.489786657 1 19.91501467 WDHESVCK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WDHESVCK 8 0 O95232;J3KPP4;C9JL41;O95232-2;H7C5U7 O95232 LUC7L3 Luc7-like protein 3 0 131.03 0.0010225 279760000 1205200 1040700 435250 801480 1056400 974670 1088300 1233000 1132700 FALSE TRUE 1045929.766 1033863.573 645738.3558 983468.2839 1035379.707 1012166.186 982756.8335 969332.5452 998793.4964 1.047193209 1.03511244 0.646518383 0.984656275 1.036630405 1.013388843 0.983943965 0.970503461 1 19.9298269 3.508632441 24.99926932 0.997738732 0.904396629 0.128872529 0.108869613 1367.410402 1084825.734 0.030095389 0.044587625 3225.762884 -3.508632441 -0.093342103 WDHSLAWDVPAAEDFPNGS(ph)GSPSAAIYNIDTSSESPDHYLVDHTLDGR ddPTM_MDA-MB-175_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(0.358)GS(0.358)PS(0.283)AAIY(0.001)NIDTSSESPDHYLVDHTLDGR;WDHSLAWDVPAAEDFPNGS(0.451)GS(0.451)PS(0.089)AAIY(0.003)NIDT(0.004)S(0.001)SESPDHYLVDHTLDGR 144.29 1.94E-15 3391730000 79987 88112 45266 56659 96739 102771 87186 96897 102649 TRUE FALSE 69416.51529 87533.18647 67156.78901 69524.29193 94814.08317 106724.6669 78730.71514 76176.3306 90513.95216 0.766915085 0.96706844 0.741949582 0.768105803 1.047507936 1.179096309 0.869818556 0.841597663 1 16.46585257 3.245066787 24.99894983 0.970093987 0.817223901 0.380252638 0.110654086 211.1910878 811464.3021 0.035383659 0.04458888 1758.193973 -3.245066787 -0.152870086 WDHSLAWDVPAAEDFPNGSGS(ph)PSAAIYNIDTSSESPDHYLVDHTLDGR ddPTM_MDA-MB-175_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(0.091)GS(0.455)PS(0.455)AAIYNIDTSSESPDHYLVDHTLDGR;WDHSLAWDVPAAEDFPNGS(0.049)GS(0.809)PS(0.141)AAIYNIDTSSESPDHYLVDHTLDGR 179.93 2.93E-29 2381980000 63460 64582 29389 43592 63357 71689 70841 74418 73331 TRUE FALSE 55073.60021 64157.75659 43601.6187 53490.22986 62096.31966 74446.92222 63970.85072 58504.28982 64661.89272 0.851716489 0.992203505 0.674301615 0.827229572 0.960323261 1.151326061 0.989312995 0.904772307 1 15.98062812 3.164233255 4.904745088 0.998437152 0.835942384 0.423648281 0.096315922 0.224113048 9.889093623 0.030869112 0.035706951 1459.597986 -3.164233255 -0.162494768 WDHSLAWDVPAAEDFPNGSGSPSAAIYNIDTSSESPDHYLVDHTLDGR ddPTM_MDA-MB-175_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 ;;;;;; 307.2 5.82E-104 54938420000 807754 835189 363113.1 531377 949498 1062497 860371 982753 976483 FALSE TRUE 701007.2623 829702.5885 538715.8097 652034.2694 930604.8475 1103371.947 776932.3528 772598.9187 861044.2922 0.814136124 0.963600358 0.625654005 0.757259848 1.080786268 1.281434599 0.902314039 0.897281273 1 19.71572793 3.243026774 24.99945667 1.018177877 0.790800351 0.44642382 0.133498852 124.0770697 694520.8782 0.042463972 0.052950597 1749.954568 -3.243026774 -0.227377526 WDKDNLQILR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WDKDNLQILR 10 1 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ; 132.17 0.0002104 830790000 2938700 2525800 2023730 2653900 2871900 2455100 3002000 3496600 4085100 FALSE TRUE 2550343.349 2509207.853 3002412.597 3256508.557 2814754.809 2549549.286 2710866.502 2748879.301 3602164.132 0.708003094 0.696583432 0.833502441 0.904042247 0.781406595 0.707782653 0.752566069 0.763118836 1 21.78043249 1.23753068 24.986245 1.000000274 0.769933138 0.572580311 0.062879245 20.98066951 508734.8119 0.098465627 0.016577283 17.27948044 -1.23753068 -0.230067136 WDLPDSDWDNDSSSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WDLPDSDWDNDSSSAR 16 0 O15020;O15020-2;A4QPE4;E9PJZ2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 91.914 0.011514 36020000 29047 22508 15936 15321 28129 22589 19854 27694 29970 FALSE TRUE 25208.36535 22360.14347 23642.7029 18799.86722 27569.28793 23458.01345 17928.56214 21771.85361 26426.98074 0.953887453 0.846110408 0.894642605 0.711389144 1.043225036 0.887653935 0.67841886 0.823849452 1 14.68972399 WDLSAQQIEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WDLSAQQIEER 11 0 P52888;K7EKB6 P52888 THOP1 Thimet oligopeptidase 0 125.23 0.00077404 113880000 71894 76066 56226 60036 78025 83206 73269 74793 74009 FALSE TRUE 62393.02574 75566.31744 83417.08166 73668.09139 76472.45515 86406.98866 66163.38366 58799.09899 65259.74033 0.956072234 1.157931629 1.278231897 1.128844384 1.171816724 1.324047387 1.013846873 0.901001118 1 15.99390563 2.038865684 9.71047047 0.947560118 1.1721111 0.479009338 0.098890371 0.277808127 66.71563509 0.039967746 0.026861965 109.3618087 -2.038865684 0.224550982 WDNGPDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 WDNGPDGR 8 0 Q14166;V9GY16 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ;; 117.81 0.0046696 1634280000 1588410 1601810 1098030 1254540 1582700 1724120 1628900 1731300 1912080 FALSE TRUE 1378497.594 1591287.605 1629040.981 1539402.481 1551207.367 1790448.012 1470929.529 1361074.968 1686036.081 0.817596735 0.943804004 0.966195801 0.913030569 0.92003213 1.06192746 0.872418773 0.807263251 1 20.68520398 WDQTADQTPGAT(ph)PK ddPTM_MDA-MB-175_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 287.48 5.76E-33 1677700000 2356870 1794640 1474210 1769790 2185830 1681710 2260040 2723480 2467800 TRUE FALSE 2045403.658 1782850.892 2187142.887 2171647.869 2142336.26 1746406.472 2040861.669 2141084.996 2176059.495 0.939957599 0.819302457 1.005093331 0.997972654 0.984502613 0.802554561 0.937870345 0.9839276 1 21.05328657 1.716035998 3.99647297 0.994507693 0.925495119 0.139376846 0.068142037 0.37462262 13.71874292 0.047773786 0.018636073 52.00390999 -1.716035998 -0.069012574 WDS(ph)CDSLNGLDPSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WDSCDSLNGLDPSEK 15 0 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 WDS(1)CDSLNGLDPSEK;WDS(1)CDSLNGLDPSEK 270.95 2.30E-33 337990000 570310 471630 445240 479910 493110 358940 592550 666730 931490 TRUE FALSE 494942.0885 468531.8315 660559.5532 588880.9005 483298.0758 372748.6541 535084.5922 524154.978 821370.3134 0.602580931 0.570427034 0.804216493 0.716949336 0.588404606 0.453813156 0.651453533 0.638146972 1 19.64767328 1.236609921 5.984097397 1.014312432 0.628564549 0.619771937 0.091536602 0.099768019 13.43865038 0.157168161 0.024055917 17.24288456 -1.236609921 -0.385747882 WDS(ph)YENLSADGEVLHTQGPVDGSLYAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 WDSYENLSADGEVLHTQGPVDGSLYAK 27 0 Q68CZ2;E9PCX8;C9JHU5;Q68CZ2-3 Q68CZ2 TNS3 Tensin-3 1 WDS(1)YENLSADGEVLHTQGPVDGSLYAK;WDS(1)YENLSADGEVLHTQGPVDGSLYAK;WDS(1)YENLSADGEVLHTQGPVDGSLYAK;WDS(1)YENLSADGEVLHTQGPVDGSLYAK;WDS(1)YENLSADGEVLHTQGPVDGSLYAK 313.13 2.90E-82 5210895000 599123 529611 429616 483465 582533 491585 609199 742658 715165 TRUE FALSE 519947.3776 526131.9505 637379.7346 593243.1175 570941.733 510496.593 550118.9747 583846.3661 630619.0084 0.82450318 0.834310326 1.010720778 0.940731424 0.905367148 0.809516659 0.872347594 0.925830586 1 19.26640913 -1.998951516 0.012586955 1.943235918 5.80E-09 0.113646577 0.065468006 56325.39144 70.61349526 6298.707055 4714.101965 0.010024171 1.998951516 -1.943235912 WDSNVIETFDIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WDSNVIETFDIAR 13 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;F5GWK5;H0YH17 Q9Y365 STARD10 PCTP-like protein 0 ; 131.06 0.00031369 361530000 409790 346000 253192 301000 343090 368390 365000 400100 557370 FALSE TRUE 355635.2132 343727.1032 375636.4981 369346.6505 336263.1802 382562.2017 329602.3562 314541.7286 491478.3536 0.723603004 0.69937384 0.764299171 0.751501359 0.684187163 0.778390745 0.670634533 0.639991011 1 18.90676835 1.229706755 24.99830408 1.00000055 0.711863532 0.813397623 0.043039813 155.5536929 439162.2847 0.133338226 0.011358832 16.97097349 -1.229706755 -0.288137018 WDYLTQVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WDYLTQVEK 9 0 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 105.98 0.0070045 454070000 538230 568980 412590 378130 466190 558410 501570 562320 620340 FALSE TRUE 467101.5418 565242.3329 612119.904 463990.1959 456913.7311 579892.394 452927.8186 442072.244 547004.1119 0.85392693 1.033342018 1.119040773 0.848238954 0.835302187 1.060124378 0.828015382 0.808169874 1 19.06119215 3.712287884 24.70913322 0.887392773 1.005227164 0.188870458 0.101762658 942.9679945 886847.717 0.028092666 0.041683254 5155.702911 -3.712287884 0.117834391 WEFGTCQPLSDEKDLTQLFMFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WEFGTCQPLSDEKDLTQLFMFAR 23 1 Q9UHL4;R4GMR2 Q9UHL4 DPP7 Dipeptidyl peptidase 2 0 173.8 1.90E-19 0 115110 93222 61265 77753 63195 81346 84766 127750 68093 FALSE TRUE 99897.92185 92609.61854 90892.95892 95408.00703 61937.54314 84475.43326 76545.40637 100431.6567 60043.12311 1.663769582 1.542385102 1.513794656 1.588991413 1.031550991 1.406912713 1.274840521 1.672658773 1 15.8737114 WEKMETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WEKMETK 7 1 Q96QT6;C9J9G2;Q96QT6-2;Q96QT6-5;Q96QT6-3;J3QQU3 Q96QT6 PHF12 PHD finger protein 12 0 63.486 0.072179 1403300000 1942800 2068900 567000 785750 2222600 2375600 1714300 1897200 145460 FALSE TRUE 1686054.058 2055309.26 841203.0965 964166.5469 2178374.608 2466990.869 1548047.45 1491498.544 128263.8845 13.14519722 16.02406841 6.558378453 7.517054007 16.9835384 19.23371398 12.06923879 11.62835938 1 16.96875548 4.254833091 24.98924487 10 14.58463397 0.074885391 5.208095895 578.7265331 888720.6776 1.386147088 3.643360672 17981.79704 -4.254833091 4.584633974 WENFIHSENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WENFIHSENR 10 0 P19784;H3BSA1;H3BV19 P19784 CSNK2A2 Casein kinase II subunit alpha 0 122.7 0.00048162 109370000 185070 152970 102190 120140 148820 129370 144920 160510 191470 FALSE TRUE 160612.5306 151965.13 151609.4258 147419.6232 145858.7732 134346.9476 130865.6807 126186.1856 168834.6347 0.951300844 0.900082677 0.897975857 0.873159843 0.863914998 0.79573097 0.775111581 0.747395141 1 17.36525136 3.40175283 1.252028974 0.813276344 0.922447138 0.208632684 0.069368133 0.599635483 1.969708736 0.026417362 0.044655481 2522.044991 -3.40175283 0.109170794 WENPGLGAESHTDSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WENPGLGAESHTDSLR 16 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 180.31 2.49E-09 325680000 176690 160950 123560 137100 190300 178740 150670 176670 246090 FALSE TRUE 153339.9688 159892.7089 183314.0293 168230.6504 186513.4023 185616.2435 136058.0466 138890.4953 216997.5205 0.706643875 0.736841179 0.844774764 0.775265312 0.859518587 0.855384167 0.627002771 0.640055679 1 17.72731903 4.46536121 24.31672212 0.780614378 0.714193147 0.063477546 0.109291598 480.886954 994350.9166 0.028675889 0.076012737 29198.54495 -4.46536121 -0.066421232 WENPGLGAESHTDSLRNS(ph)STEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WENPGLGAESHTDSLRNSSTEIR 23 1 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 WENPGLGAESHTDS(0.36)LRNS(0.624)S(0.015)TEIR;WENPGLGAESHTDS(0.178)LRNS(0.756)S(0.052)T(0.014)EIR 247.41 6.71E-38 333640000 234000 255010 167494 218618 276380 313080 264650 313510 361680 TRUE FALSE 203076.3071 253334.8225 248494.6586 268258.5583 270880.5787 325124.3902 238984.2837 246468.3262 318922.6024 0.636757337 0.794345777 0.779169168 0.841140001 0.849361496 1.019446059 0.749348845 0.772815487 1 18.28284682 5.589248458 0.802778952 0.859913341 7.93E-15 0.414888922 0.086907436 9.716022897 1.778509307 0.032098087 10.24817978 388372.4883 -5.589248458 -0.859913341 WES(ph)QQDVSQTTVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 WESQQDVSQTTVSR 14 0 Q9NQT8;H0YBA8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 WES(1)QQDVSQTTVSR;WES(1)QQDVSQTTVSR;WES(1)QQDVSQTTVSR;WES(1)QQDVSQTTVSR;WES(1)QQDVSQTTVSR;WES(1)QQDVSQTTVSR 342.28 4.28E-69 5145680000 2616222 2743207 1865434 1717446 2824024 2749917 2216211 2568183 3590364 TRUE FALSE 2270481.634 2725186.693 2767564.122 2107418.364 2767831.448 2855708.086 2001283.198 2018997.051 3165915.258 0.717164374 0.860789525 0.874175048 0.665658488 0.874259486 0.90201659 0.632134165 0.637729341 1 21.59419121 2.241963714 24.99942444 0.726665089 0.816230582 0.029649775 0.124772413 207.7263764 1525992.992 0.047380434 0.035174816 174.5676292 -2.241963714 0.089565494 WESENK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 WESENK 6 0 P29373 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 ;;;;;; 172.39 0.01195 7430810000 10009800 8308180 6691000 7227220 6206660 7042230 10810400 10995210 10600410 FALSE TRUE 8686979.568 8253603.019 9926789.98 8868270.762 6083159.609 7313149.145 9762009.072 8643969.906 9347241.606 0.9293629 0.882998789 1.062002075 0.948758055 0.650797301 0.782385805 1.044373248 0.924761579 1 23.15610925 2.228028827 24.99742927 0.978457902 0.877885037 0.187845212 0.110543787 439.7705607 1043795.713 0.048766876 0.033269844 169.0553143 -2.228028827 -0.100572865 WESGSLLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WESGSLLER 9 0 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 ;;; 112.41 0.004576 740100000 789410 724050 427716 557180 700760 720990 677760 769720 737430 FALSE TRUE 685087.4684 719293.6679 634560.8882 683696.235 686816.247 748726.9518 612030.9395 605121.368 650251.8655 1.053572477 1.106177015 0.975869385 1.051432947 1.056231106 1.151441452 0.941221351 0.930595359 1 19.31063911 2.207692252 24.99995845 0.95104567 1.062449278 0.532956348 0.047700337 148.7030857 120432.004 0.019329368 0.013033528 161.3215002 -2.207692252 0.111403609 WESPAQNTAHLDQFER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WESPAQNTAHLDQFER 16 0 P17612-2;P17612;Q15136 P17612-2 PRKACA;KIN27 cAMP-dependent protein kinase catalytic subunit alpha 0 ; 176.21 3.25E-09 526820000 445800 428550 247270 368800 426130 379010 465500 557410 562550 FALSE TRUE 386886.4005 425734.8268 366850.5991 452541.6768 417650.8467 393590.76 420355.8816 438212.2093 496045.9799 0.779940603 0.858256783 0.739549586 0.912297842 0.841959947 0.793456204 0.847413141 0.883410464 1 18.92011433 1.076112204 1.399913868 1.137735342 0.823708728 0.59118103 0.04666386 1.300856766 1.647533898 0.650599814 0.012979481 11.91549816 -1.076112204 -0.314026614 WETFCTSSLGETNKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WETFCTSSLGETNKR 15 1 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PQP7;H0YEN2;H0YDW1 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 ; 233.62 1.98E-17 1514910000 851240 841690 601890 708230 862820 759260 993190 1199690 1020180 FALSE TRUE 738746.4772 836160.883 892966.0172 869044.4461 845651.5701 788469.2235 896870.5867 943145.6295 899575.4826 0.821216776 0.929506083 0.992652684 0.966060617 0.940056267 0.876490343 0.996993142 1.04843412 1 19.77888482 8 0.038006262 1.574702902 1.96E-05 0.41761523 0.050192018 2044.873761 7.664185501 102.3427479 244.9033543 99999999.96 -8 -1.574683296 WETHLQPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 WETHLQPR 8 0 Q9NPB8 Q9NPB8 GPCPD1 Glycerophosphocholine phosphodiesterase GPCPD1 0 ;; 127.02 0.0011942 419250000 240850 299241 155151 195456 306255 290941 246717 276561 268597 FALSE TRUE 209021.0623 297275.2662 230182.5425 239837.2722 300161.1247 302133.6885 222790.4233 217420.5824 236843.7686 0.882527176 1.25515342 0.971875021 1.012639148 1.26733807 1.275666615 0.94066407 0.917991567 1 17.85357619 2.179974902 24.99953523 0.945105646 1.113755085 0.239940611 0.132239529 104.7348923 44691.08202 0.053537564 0.036095032 151.3473782 -2.179974902 0.168649439 WEWLVNQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WEWLVNQHR 9 0 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 ; 168.8 5.90E-05 1965080000 2391600 2221900 1440110 1869710 2301900 2308200 2351900 2292400 3011600 FALSE TRUE 2075544 2207304.193 2136552.013 2294256.232 2256096.694 2396997.948 2123813.1 1802188.099 2655572.079 0.781580744 0.831197244 0.804554329 0.863940486 0.849570875 0.902629594 0.799757279 0.678644016 1 21.34059126 4.740953841 21.94752473 0.828369463 0.781580651 0.029421079 0.081987756 195.111474 1788597.52 0.020305546 0.130525105 55074.91566 -4.740953841 -0.046788811 WFCHIQHYPGIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WFCHIQHYPGIR 12 0 O43324 O43324 EEF1E1 Eukaryotic translation elongation factor 1 epsilon-1 0 ; 155 4.16E-05 738880000 545250 569410 382920 404780 533320 538930 536770 544360 572910 FALSE TRUE 473193.831 565669.5082 568101.3928 496691.4857 522707.9754 559662.9858 484714.128 427952.8502 505181.2325 0.936681335 1.119735794 1.124549679 0.983194651 1.034693971 1.107845957 0.95948562 0.847127373 1 18.94644152 2.052535227 5.989821293 0.909739718 1.053059525 0.384244179 0.069480471 0.159181075 12.50032599 0.028228926 0.018612261 112.8587477 -2.052535227 0.143319807 WFDFPFTR ddPTM_MDA-MB-175_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 ; 124.08 0.0030712 161473000 588040 549300 415520 408170 598810 652140 546970 634250 696350 FALSE TRUE 510329.0241 545691.6121 616466.8618 500851.237 586894.8526 677228.2478 493924.9336 498620.5732 614028.2963 0.83111646 0.888707598 1.003971422 0.815681036 0.95581076 1.102926774 0.804400932 0.812048201 1 19.22794562 4.640842976 4.19899622 0.915742935 0.83103631 0.082337857 0.097116143 0.653359338 18.2603937 0.024752569 0.124693208 43736.39424 -4.640842976 -0.084706625 WFFLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WFFLPR 6 0 Q8WVQ1-3;Q8WVQ1 Q8WVQ1-3 CANT1 Soluble calcium-activated nucleotidase 1 0 149.33 0.033975 0 125800 183150 113320 91705 178440 215750 135450 177020 183820 FALSE TRUE 109175.2113 181946.8756 168121.931 112528.0219 174889.3931 224050.0421 122314.0798 139165.6506 162089.009 0.673550982 1.12251211 1.037219809 0.694235979 1.078971327 1.382265482 0.754610572 0.858575491 1 17.30642674 WFHPNITGVEAENLLLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WFHPNITGVEAENLLLTR 18 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ; 253.48 1.65E-30 596730000 863590 785660 462930 526530 782540 792480 650810 729300 688740 FALSE TRUE 749464.3934 780498.9477 686804.4964 646086.684 766968.985 822967.2184 587694.5464 573344.8704 607317.9418 1.234056072 1.285157072 1.130881288 1.06383599 1.262878852 1.355084646 0.967688431 0.944060485 1 19.21209247 2.215922805 24.77647218 0.964936655 1.215383386 0.682010986 0.080807974 127.6305349 139687.0133 0.035141551 0.023711721 164.4079464 -2.215922805 0.250446731 WFLTCINQPQFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WFLTCINQPQFR 12 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 202.05 3.29E-07 1888140000 839880 802200 555930 604670 813860 779320 830450 877030 884340 FALSE TRUE 728887.73 796930.2954 824779.6075 741969.5653 797665.7783 809300.9447 749913.0868 689483.9596 779794.3326 0.934717912 1.021974977 1.05768864 0.951493919 1.022918153 1.037838967 0.961680607 0.884186933 1 19.57273414 2.01937443 8.31321589 0.930531107 1.005673465 0.24389724 0.046246118 0.192414816 67.13851991 0.01851209 0.012217778 104.562132 -2.01937443 0.075142358 WFNGQPIHAELSPVTDFR ddPTM_MDA-MB-175_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 ;;; 194.92 4.79E-15 3294750000 2540920 2218679 1343433 1527017 2096584 2409381 2020124 2285424 2166990 FALSE TRUE 2205130.984 2204104.352 1993121.692 1873749.549 2054866.08 2502071.446 1824212.685 1796703.863 1910810.911 1.154028885 1.153491609 1.043076361 0.98060438 1.075389547 1.309429118 0.954679856 0.940283443 1 20.86575359 WFSNPS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 WFSNPSR 7 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 WFSNPS(1)R;WFSNPS(1)R;WFSNPS(1)R;WFSNPS(1)R;WFSNPS(1)R;WFSNPS(1)R;WFSNPS(1)R;WFSNPS(1)R 109.44 0.0073721 3642656000 2109412 2148866 1509680 1749871 2069247 2393241 1939669 2172802 3313750 TRUE FALSE 1830647.86 2134749.958 2239766.298 2147205.956 2028073.033 2485310.53 1751560.199 1708165.201 2922002.25 0.626504603 0.730577794 0.76651765 0.734840624 0.694069634 0.850550519 0.599438347 0.58458723 1 21.47852586 4.739637401 22.38571202 0.727760923 0.626504505 0.072678721 0.119653219 68.24698875 1417898.762 0.028786576 0.169706768 54908.22454 -4.739637401 -0.101256418 WFTPWSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WFTPWSR 7 0 Q6IA69;H0YCQ6;E9PKY6 Q6IA69 NADSYN1 Glutamine-dependent NAD(+) synthetase 0 110.63 0.015726 178890000 134010 167110 95934 89216 146250 152740 148210 157090 120680 FALSE TRUE 116300.239 166012.2434 142328.0033 109473.8564 143339.9111 158616.0066 133836.617 123497.526 106413.3479 1.092910253 1.560069735 1.337501414 1.02876057 1.347010633 1.490564951 1.257705163 1.160545443 1 16.6993196 1.494389151 2.123305769 0.988878992 1.313252282 0.283183113 0.158443566 0.521699783 3.977045438 0.28513584 0.043492978 31.21685531 -1.494389151 0.32437329 WFVLVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WFVLVDR 7 0 A0A1B0GUN5;A0A5F9ZH45;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 0 ; 91.906 0.037363 241482000 403390 426810 280330 320720 410630 398230 403250 452570 459150 FALSE TRUE 350080.9894 424006.257 415898.5256 393544.3779 402459.2664 413550.1658 364142.8771 355791.4274 404869.8101 0.86467546 1.04726568 1.027240153 0.972026978 0.994046126 1.021439869 0.899407335 0.878779841 1 18.62709854 2.232198839 24.9995568 0.915101222 0.991848262 0.189883815 0.058255496 193.2792833 759511.1528 0.022454978 0.015553732 170.6863688 -2.232198839 0.07674704 WFVVLEETPWDATSHIDNMENER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WFVVLEETPWDATSHIDNMENER 23 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 0 211.06 5.52E-25 28325000 21498 21281 12289 17219 19029 18063 17865 20431 18314 FALSE TRUE 18656.98483 21141.20371 18232.0015 21128.83713 18650.36013 18757.8953 16132.45505 16061.98964 16148.93978 1.155307103 1.309138804 1.128990618 1.308373021 1.154896877 1.161555839 0.998979206 0.994615737 1 13.97915183 2.370465427 1.91561592 0.989022014 1.219847071 0.721500905 0.060520576 0.154697153 1.170179282 0.02816491 0.017984758 234.6742438 -2.370465427 0.230825058 WGDAGAEYVVESTGVFTTMEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WGDAGAEYVVESTGVFTTMEK 21 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 94.281 0.0015964 25034000 51586 52483 40214 47197 49921 34495 61077 65624 71510 FALSE TRUE 44768.7794 52138.23572 59661.62491 57913.80021 48927.66977 35822.04497 55153.76194 51590.81829 63056.16926 0.709982543 0.82685384 0.94616634 0.918447804 0.775937872 0.568097387 0.874676698 0.818172415 1 15.94434991 1.051305353 2.13815029 1.152875722 0.804642272 0.244220835 0.107717453 2.246222947 6.465977828 1.85560753 0.03040803 11.25395963 -1.051305353 -0.34823345 WGDEHIPGSPYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WGDEHIPGSPYR 12 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;;; 134.99 0.00013566 3668250000 6388300 5397700 3201660 4022550 5214280 5518300 5103540 5778000 5676500 FALSE TRUE 5544069.969 5362242.153 4749993.485 4935931.458 5110526.03 5730592.572 4608599.476 4542419.664 5005430.637 1.107610987 1.071284879 0.948967997 0.986115245 1.020996274 1.144875034 0.920719876 0.907498274 1 22.25506276 WGDIEFPPPFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WGDIEFPPPFGR 12 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 114.5 0.002446 500280000 370530 331740 265180 316150 377290 369540 372560 386710 498860 FALSE TRUE 321563.5217 329560.7781 393421.935 387936.6896 369782.6672 383756.4429 336429.1885 304015.0759 439885.3391 0.731016683 0.749197004 0.894373829 0.881904112 0.840634216 0.872401075 0.764811097 0.691123456 1 18.74676799 4.371523781 7.708924332 0.832218981 0.735716909 0.215201088 0.08209643 0.390897342 25.00714258 0.021658755 0.057858296 23524.68304 -4.371523781 -0.096502072 WGDYDSHDIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WGDYDSHDIER 11 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 167.3 1.94E-05 989600000 1870870 1693680 1096930 1277530 1705330 1679770 1683430 1846090 1906380 FALSE TRUE 1623629.789 1682554.105 1627409.017 1567612.712 1671397.269 1744391.839 1520171.218 1451318.02 1681009.928 0.965865675 1.0009186 0.968113864 0.932542209 0.994281617 1.037704662 0.90432019 0.863360766 1 20.68089681 2.207900286 24.99569708 0.909467009 0.981551656 0.288282157 0.043291447 210.5564584 171653.7666 0.017648485 0.011900102 161.3987944 -2.207900286 0.072084647 WGEDNHWICKPWNLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WGEDNHWICKPWNLAR 16 1 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 200.55 2.12E-11 3415600000 4489400 4873300 3230100 3252300 4926400 4142600 4765400 5510000 5142900 FALSE TRUE 3896114.415 4841286.971 4792187.164 3990784.423 4828374.278 4301968.503 4303252.241 4331729.379 4534912.221 0.859137779 1.067559136 1.056732067 0.880013599 1.064711739 0.948633246 0.948916326 0.95519586 1 22.1126432 WGEEHIPGSPFHVTVP ddPTM_MDA-MB-175_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 ;;; 94.728 0.0039938 925420000 1045850 1196250 411084 803475 1256470 1211620 1241210 1305610 1258020 FALSE TRUE 907638.2727 1188391.755 609885.5974 985916.2791 1231468.705 1258231.805 1120837.645 1026415.462 1109298.309 0.818209372 1.07130043 0.549794039 0.888774707 1.110133041 1.134259194 1.010402375 0.925283536 1 20.08121595 3.439008207 8.329668539 1.023321818 0.819224445 0.365557101 0.135942074 0.288492652 56.24945013 0.03945499 0.051188177 2747.946081 -3.439008207 -0.204097374 WGEPEPFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WGEPEPFLR 9 0 A0A087WYJ2;M0R2B7;P28340;M0QZR8;A0A2R8Y7K6 A0A087WYJ2 POLD1 DNA polymerase;DNA polymerase delta catalytic subunit 0 86.833 0.032269 51118000 138110 131930 82597 97151 135900 131030 140520 147490 123660 FALSE TRUE 119858.4136 131063.3431 122541.1855 119210.6194 133195.8559 136070.8089 126892.392 115950.4113 109041.0557 1.099204449 1.201963264 1.123807769 1.093263621 1.221520234 1.247886019 1.163712065 1.063364717 1 16.73451191 1.593577479 2.971077096 1.008044078 1.167304676 0.560176863 0.050430956 0.168882165 3.332951115 0.051222366 0.01413007 39.2263121 -1.593577479 0.159260599 WGLLSMPVDEEVESLHLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WGLLSMPVDEEVESLHLR 18 0 O75165;A0A3B3IRM0 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 127.83 2.46E-05 40389000 27215 26101 9759.9 17149 24756 26872 21082 22731 21183 FALSE TRUE 23618.4688 25929.54081 14479.82028 21042.94256 24263.40403 27905.78323 19037.47088 17870.15254 18678.76987 1.264455259 1.388182465 0.775202028 1.126570042 1.298982974 1.493983995 1.019203674 0.956709284 1 14.18911183 2.027474349 24.99864106 0.979070434 1.21434404 0.253775159 0.188438388 302.6642674 275389.9762 0.080554187 0.054308434 106.5305941 -2.027474349 0.235273606 WGNNNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 WGNNNR 6 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;Q9BUJ2-5 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ;; 110.17 0.067304 631890000 844930 663770 418630 499070 529560 714820 638170 703400 680610 FALSE TRUE 733270.3597 659409.6512 621080.8682 612391.4713 519022.7921 742319.588 576280.3716 552983.3839 600149.0612 1.221813725 1.098743119 1.03487768 1.020398949 0.864823134 1.236892026 0.960228731 0.921410062 1 19.19496135 4.778215512 1.152303058 0.993403301 1.347301413 0.354464279 0.095966056 1.94836377 2.049872811 0.028936878 0.85198386 60008.87866 -4.778215512 0.353898112 WGQPPS(ph)PTPVPRPPDADPNT(ph)PSPKPLEGRPER ddPTM_MDA-MB-175_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(0.982)PT(0.023)PVPRPPDADPNT(0.533)PS(0.462)PKPLEGRPER;WGQPPS(0.993)PT(0.007)PVPRPPDADPNT(0.611)PS(0.389)PKPLEGRPER 132.59 1.24E-07 452720000 228979 167419 145909 153212 212743 163856 235063 265019 241215 TRUE FALSE 198718.845 166319.2136 216471.0804 188001.1263 208509.8305 170159.6463 212266.6264 208346.7492 212698.8375 0.934273301 0.78194698 1.017735137 0.883884127 0.980305454 0.80000271 0.997967967 0.97953873 1 17.69845262 WGQPPS(ph)PTPVPRPPDADPNTPS(ph)PKPLEGRPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WGQPPSPTPVPRPPDADPNTPSPKPLEGRPER 32 3 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 2 WGQPPS(0.672)PT(0.328)PVPRPPDADPNT(0.011)PS(0.99)PKPLEGRPER 72.006 0.0014547 231220000 122880 119810 47997 80692 110920 114220 156790 136930 133290 TRUE FALSE 106641.0967 119022.9602 71208.50974 99014.3519 108712.909 118614.1173 141584.5299 107648.5851 117532.608 0.907332003 1.012680329 0.605861734 0.842441545 0.924959557 1.009201781 1.204640417 0.915903994 1 16.84270155 2.943210472 2.799253765 1.03009105 0.839024587 0.351149082 0.122042207 0.322398805 5.004588525 0.042584264 0.044669222 877.4259457 -2.943210472 -0.191066463 WGQPPS(ph)PTPVPRPPDADPNTPSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WGQPPSPTPVPRPPDADPNTPSPK 24 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 WGQPPS(0.828)PT(0.172)PVPRPPDADPNTPSPK 195.27 2.71E-19 411130000 469240 391150 337120 469810 425530 368630 478490 573520 935170 TRUE FALSE 407228.7451 388580.5099 500152.3596 576487.5411 417062.7855 382811.4346 432086.1134 450877.2111 824615.2679 0.493840899 0.471226431 0.606528134 0.699098796 0.505766509 0.46423035 0.5239851 0.546772815 1 19.65336165 1.238562646 7.613224045 1.007026715 0.539740292 0.811998771 0.06973033 0.044478853 19.30067101 0.107239023 0.018328538 17.32058858 -1.238562646 -0.467286423 WGQPPS(ph)PTPVPRPPDADPNTPSPKPLEGRPER ddPTM_MDA-MB-175_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(0.665)PT(0.237)PVPRPPDADPNT(0.085)PS(0.013)PKPLEGRPER 124.82 1.00E-07 1245200000 205810 160730 121070 131890 188500 129250 212760 228300 157800 TRUE FALSE 178611.687 159674.154 179619.857 161837.6403 184749.2188 134222.3311 192126.5679 179479.8216 139145.0638 1.283636532 1.147537323 1.290881991 1.163085746 1.327745403 0.964621579 1.380764526 1.289875593 1 17.0862302 WGQPPSPT(ph)PVPRPPDADPNT(ph)PSPKPLEGRPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WGQPPSPTPVPRPPDADPNTPSPKPLEGRPER 32 3 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 2 WGQPPS(0.454)PT(0.545)PVPRPPDADPNT(0.59)PS(0.411)PKPLEGRPER 59.525 0.050694 132560000 124280 82696 69406 82610 82627 84262 106040 116420 104730 TRUE FALSE 107856.0831 82152.76453 102970.9737 101367.8631 80982.88436 87503.61366 95756.25712 91524.48898 92348.93871 1.167919032 0.889590781 1.115020651 1.097661376 0.87692274 0.947532423 1.03689613 0.99107245 1 16.49480776 3.271907812 24.99996455 0.976891262 1.058227636 0.252189167 0.08195016 315.2597016 236344.1067 0.022921319 0.029589499 1870.285092 -3.271907812 0.081336374 WGQPPSPT(ph)PVPRPPDADPNTPSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WGQPPSPTPVPRPPDADPNTPSPK 24 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 WGQPPS(0.159)PT(0.841)PVPRPPDADPNTPSPK 139.93 4.91E-07 422020000 385290 300780 249670 365260 294050 219630 352370 379550 610790 TRUE FALSE 334372.9503 298804.1564 370411.2471 448197.8656 288198.9803 228079.3082 318197.2116 298386.1862 538583.102 0.620838175 0.554796753 0.687751334 0.832179591 0.535105872 0.423480253 0.590804298 0.554020698 1 19.03880944 1.234709226 24.9985849 1.000000577 0.598358806 0.583253443 0.106287121 88.44747577 574010.2079 0.202364111 0.027611587 17.16758576 -1.234709226 -0.401641771 WGQPPSPT(ph)PVPRPPDADPNTPSPKPLEGRPER ddPTM_MDA-MB-175_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(0.086)PT(0.499)PVPRPPDADPNT(0.352)PS(0.062)PKPLEGRPER;WGQPPS(0.339)PT(0.643)PVPRPPDADPNT(0.015)PS(0.003)PKPLEGRPER 151.24 1.36E-10 2094420000 1331880 1077040 791280 963440 1248600 852080 1329590 1437310 1114020 TRUE FALSE 1155868.683 1069964.853 1173945.655 1182203.777 1223755.303 884860.069 1200646.566 1129952.442 982321.8247 1.176670063 1.08922028 1.195072353 1.203479092 1.245778392 0.900784292 1.222253783 1.150287424 1 19.90583623 WGQPPSPTPVPRPPDADPNTPS(ph)PKPLEGRPER ddPTM_MDA-MB-175_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(0.001)PT(0.004)PVPRPPDADPNT(0.267)PS(0.728)PKPLEGRPER;WGQPPS(0.004)PT(0.036)PVPRPPDADPNT(0.167)PS(0.793)PKPLEGRPER 149.68 2.25E-10 1618970000 1035000 800810 607810 623140 806750 626270 871410 1078260 851780 TRUE FALSE 898222.1276 795549.4264 901748.949 764633.4611 790697.2534 650363.0122 786900.7923 847682.49 751083.5388 1.195901762 1.059202319 1.200597407 1.0180405 1.052742089 0.865899702 1.047687443 1.128612792 1 19.51861385 3.722289124 24.11028671 1.027110512 1.142630678 0.403585339 0.075533302 591.872963 877008.1216 0.021760183 0.03239919 5275.809728 -3.722289124 0.115520166 WGRDDIENIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WGRDDIENIAR 11 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 ; 210.79 1.05E-08 845230000 442500 440380 251523 300220 455850 508310 424520 441780 281940 FALSE TRUE 384022.5038 437487.1148 373160.3641 368389.5396 446779.4769 527865.0146 383350.1157 347308.7849 248609.3744 1.544682315 1.759737001 1.500990721 1.481800678 1.79711436 2.123270757 1.541977718 1.397005989 1 17.92352117 1.426381518 1.971446589 0.932719989 1.691339494 0.578092959 0.189057471 0.396350013 2.200915121 0.498052343 0.055522998 26.69202472 -1.426381518 0.758619505 WGTDEDKFTEILCLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WGTDEDKFTEILCLR 15 1 P12429;D6RA82;D6RFJ9 P12429 ANXA3 Annexin A3;Annexin 0 ; 153.23 1.35E-08 259670000 1358290 1044210 746240 698280 950770 725360 1075010 1246880 1001330 FALSE TRUE 1178788.535 1037350.516 1107124.16 856835.1465 931851.5371 753265.0686 970755.6957 980244.4152 882953.9081 1.335051042 1.174863723 1.253886698 0.970418884 1.055379594 0.853119355 1.099440964 1.110187526 1 19.7519786 3.746118807 24.8856442 1.024948674 1.246626832 0.656076441 0.081570385 369.98049 1218172.279 0.022347849 0.037738706 5573.38195 -3.746118807 0.221678158 WGTDEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WGTDEEK 7 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;;; 143.85 0.0055686 1055260000 1416120 1592390 847900 811680 782390 767160 817120 1194700 2929450 FALSE TRUE 1228976.154 1581929.485 1257947.276 995984.3498 766821.9697 796673.1416 737875.8282 939222.7022 2583133.758 0.47576946 0.612407112 0.486984955 0.385572116 0.296857245 0.30841343 0.285651421 0.363598168 1 21.30069092 1.236622739 24.99837727 1.000000762 0.397183437 0.775099946 0.101219776 27.29872665 352053.7738 0.179300699 0.02834921 17.24339349 -1.236622739 -0.602817325 WGTDEEKFITIFGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WGTDEEKFITIFGTR 15 1 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ; 124.78 8.62E-05 915290000 1446570 1254390 723960 823410 1003210 935890 1186970 1584330 808930 FALSE TRUE 1255402.109 1246149.829 1074069.478 1010377.826 983248.0837 971894.2939 1071857.832 1245533.359 713299.2169 1.759993674 1.747022568 1.505776891 1.416485258 1.378451091 1.362533802 1.502676306 1.746158315 1 19.44414786 4.187746681 3.453996254 1.441735114 1.763129399 0.368283945 0.183393719 0.269711024 6.477534587 0.048487416 0.124548916 15408.01458 -4.187746681 0.321394285 WGTIEVENTTHCEFAYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WGTIEVENTTHCEFAYLR 18 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4 Q9UHD8 9-Sep Septin-9 0 ; 179.78 8.19E-14 499750000 322449 315465 212314 267218 262657 286847 281188 370920 368118 FALSE TRUE 279836.5477 313392.6896 314989.7605 327893.9311 257430.6396 297882.1897 253918.431 291601.6445 324599.5094 0.862097876 0.965474933 0.97039506 1.010149189 0.793071561 0.917691435 0.782251432 0.898342838 1 18.30830129 3.250790775 24.99930414 0.875549863 0.954301496 0.209879286 0.070941982 341.1774535 697386.8163 0.020097404 0.025751975 1781.520299 -3.250790775 0.078751633 WGTLTDCVVMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WGTLTDCVVMR 11 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 173.75 2.75E-05 899910000 1084570 958250 1441060 1090530 642350 731710 784990 886010 1238270 FALSE TRUE 941241.3265 951955.1927 2137961.436 1338151.504 629568.4917 759859.3572 708861.7906 696543.6564 1091883.131 0.862034864 0.871847147 1.958049699 1.225544626 0.576589631 0.695916381 0.649210314 0.637928764 1 20.05838702 3.24883298 23.42036714 0.697174472 1.255880848 0.394136573 0.317737518 96.01015533 218894.3933 0.094006244 0.119785705 1773.507297 -3.24883298 0.558706376 WGTLTDCVVMRDPQTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WGTLTDCVVMRDPQTK 16 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 207.92 1.48E-11 1553380000 3430100 2951600 1358870 1577700 2670100 2463700 3498700 3978800 535600 FALSE TRUE 2976803.594 2932210.745 2016024.077 1935940.899 2616970.234 2558480.133 3159396.613 3127964.583 472281.9782 6.303021779 6.208601812 4.268687289 4.099120839 5.541118135 5.417272417 6.689640424 6.623086901 1 18.84928896 1.231226736 24.99997426 0.999991837 5.654860689 0.728428394 0.891077268 158.3641857 539790.1315 2.478153819 0.24597663 17.03047401 -1.231226736 4.654868852 WHIDTILHVLTTAGTHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WHIDTILHVLTTAGTHVR 18 0 O75843 O75843 AP1G2 AP-1 complex subunit gamma-like 2 0 271.68 2.02E-39 82161000 32627 44111 28193 36114 28381 31134 29623 38846 39977 FALSE TRUE 28315.25928 43821.23194 41827.2291 44314.23567 27816.27363 32331.74513 26750.16602 30539.0852 35250.9646 0.803247786 1.243121498 1.18655559 1.257107037 0.789092552 0.917187529 0.758849192 0.86633332 1 15.10537512 3.23220744 24.99975729 0.860784101 1.135698066 0.44965024 0.140441103 126.3532482 497199.2033 0.040689152 0.047256401 1706.897489 -3.23220744 0.274913965 WHIDTIMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WHIDTIMR 8 0 O43747;O43747-2 O43747 AP1G1 AP-1 complex subunit gamma-1 0 ; 163.77 0.00033395 1425700000 1467180 1360110 889980 937180 1451360 1354280 1206030 1359790 1442380 FALSE TRUE 1273288.446 1351175.348 1320377.305 1149981.043 1422480.776 1406380.028 1089069.396 1069009.49 1271863.48 1.001120377 1.062358791 1.038143894 0.904170189 1.118422534 1.105763355 0.856278534 0.840506475 1 20.27851239 2.229168401 24.99635709 0.884980012 1.03695604 0.448994743 0.072238433 165.3234872 439986.3556 0.029485935 0.020182618 169.4994921 -2.229168401 0.151976028 WHKVS(ph)VR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WHKVSVR 7 1 O15230 O15230 LAMA5 Laminin subunit alpha-5 1 WHKVS(1)VR;WHKVS(1)VR 55.441 0.077284 4482590000 2188090 2580830 1118790 1538450 2507040 2257660 2238650 2408450 1835930 TRUE FALSE 1898928.363 2563876.358 1659840.586 1887778.586 2457154.809 2344513.641 2021546.068 1893421.71 1618888.447 1.172982837 1.583726391 1.025296455 1.166095533 1.517803659 1.448224333 1.248724748 1.169581334 1 20.62657215 1.473033002 1.931701888 0.977743098 1.318930065 0.263822251 0.170180481 0.674736897 3.904216985 0.371403153 0.047809611 29.71891859 -1.473033002 0.341186967 WHLVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WHLVYR 6 0 Q99829;B0QZ18;F2Z2V0;A6PVH9;E7ENH5;Q5JX45;Q5JX60;Q5JX52;Q5JX44;Q5JX61;Q5JX59;Q5JX58 Q99829 CPNE1 Copine-1 0 ; 150.22 0.010539 4006700000 3802100 4797500 2788100 2758100 3818000 4607300 3635100 4133800 4100900 FALSE TRUE 3299642.852 4765984.907 4136434.486 3384368.76 3742029.27 4784545.812 3282568.561 3249819.039 3616096.274 0.912487556 1.317991709 1.143895011 0.93591777 1.034825676 1.323124566 0.90776581 0.898709214 1 21.78600166 WHQPPPS(ph)PLPLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WHQPPPSPLPLR 12 0 J3QQY0;Q68DK7;J3KSZ8;Q68DK7-2;Q68DK7-3;J3KTC2 J3QQY0;Q68DK7 MSL1 Male-specific lethal 1 homolog 1 WHQPPPS(1)PLPLR 66.246 0.037728 332070000 210550 200850 119320 158950 184780 197120 170090 185980 183720 TRUE FALSE 182725.284 199530.6031 177023.5511 195042.0269 181103.2395 204703.334 153594.698 146209.6243 162000.8309 1.127928067 1.231664072 1.092732365 1.203956954 1.117915498 1.263594346 0.948110557 0.902523916 1 17.30564169 2.222312909 24.99099251 0.940188922 1.170892842 0.772071066 0.056960372 94.53118334 145399.5899 0.02113212 0.014295117 166.8448897 -2.222312909 0.23070392 WIAHDTEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WIAHDTEIR 9 0 Q9H2C0 Q9H2C0 GAN Gigaxonin 0 127.3 0.00044929 139850000 103910 112340 63722 85446 110620 134300 98035 102320 137690 FALSE TRUE 90178.03023 111602.0311 94538.17234 104847.8203 108418.8784 139466.6079 88527.58079 80439.66426 121412.4451 0.742741242 0.919197625 0.778653064 0.863567324 0.892979944 1.148701089 0.7291475 0.662532282 1 16.88955678 WIAQDLSSLAGLLDQHGVR ddPTM_MDA-MB-175_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 ; 173.98 5.37E-12 182291000 244443 230472 150536 163482 218076 231200 252940 262650 238166 FALSE TRUE 212139.2382 228958.0143 223335.7131 200603.0868 213736.7143 240094.4136 228409.9177 206484.3414 210010.2868 1.010137367 1.090222854 1.063451303 0.955206004 1.017744023 1.14325073 1.087612998 0.983210606 1 17.68010047 1.675812574 8.053056174 0.992005529 1.052684004 0.195026698 0.051273181 0.201019176 22.8957231 0.031369498 0.013945089 47.40373639 -1.675812574 0.060678475 WIDDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 771440000 3917900 3599500 2588100 2873500 3907100 4741500 3085600 4212300 4808900 FALSE TRUE 3400139.588 3575854.647 3839713.817 3525972.094 3829356.354 4923908.573 2786358.987 3311532.425 4240397.32 0.801844575 0.843282923 0.905508028 0.831519272 0.903065459 1.161190379 0.657098563 0.780948618 1 22.01576802 4.527388162 3.725142197 0.876920403 0.805294129 0.040692748 0.132139383 1.087116868 29.15604308 0.033984635 0.153089899 33681.24696 -4.527388162 -0.071626274 WIDFDNDYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WIDFDNDYK 9 0 A0A0A0MSX9;P41252;J3KR24;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 177.7 0.00012055 550340000 2048410 1613370 1326450 1553000 1641670 1395270 1942910 2287390 2258070 FALSE TRUE 1777707.428 1602771.666 1967925.657 1905632.386 1609003.979 1448946.94 1754486.887 1798249.449 1991123.537 0.892816239 0.804958425 0.988349352 0.957063864 0.808088473 0.727703185 0.88115421 0.903133038 1 20.9251513 1.277788232 2.262226494 1.029455977 0.864820144 0.242441291 0.074854782 0.925235262 5.273998535 0.298713914 0.021416597 18.95781287 -1.277788232 -0.164635832 WIDFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 WIDFVR 6 0 P05455 P05455 SSB Lupus La protein 0 ;; 118.06 0.05163 4529825000 2477970 2153380 1358490 1561150 2056240 2220400 2038990 2289490 2051590 FALSE TRUE 2150499.986 2139234.305 2015460.308 1915632.968 2015324.847 2305820.225 1841249.064 1799900.38 1809053.367 1.188743254 1.182515864 1.114096656 1.05891457 1.114021777 1.274600444 1.017796985 0.994940455 1 20.78680354 2.075054522 11.50485178 0.999884016 1.148520738 0.611055623 0.056861833 0.362863261 53.89817469 0.024011417 0.016185705 118.8651444 -2.075054522 0.148636722 WIDLTMEDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 WIDLTMEDIR 10 0 A0A0A0MSW4;P48739;P48739-3;P48739-2 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 ;;;; 125.47 0.00094974 241883800 450748 471236 361772 389492 399970 443282 413564 482443 655589 FALSE TRUE 391180.5098 468140.4197 536726.1493 477932.1116 392011.3795 460335.3454 373456.6269 379276.3188 578086.0153 0.676682188 0.80981101 0.928453786 0.826749132 0.678119465 0.79630943 0.646022594 0.656089767 1 19.14092465 3.263771656 24.86189831 0.736759566 0.818810984 0.037061417 0.117088452 519.5920036 512392.5232 0.033592577 0.043349889 1835.57298 -3.263771656 0.082051418 WIDLTMEDIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WIDLTMEDIRR 11 1 A0A0A0MSW4;P48739;P48739-3;P48739-2 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 ; 204.69 5.19E-08 387535000 364380 341050 232450 269570 349840 353740 350550 374190 260615 FALSE TRUE 316226.2598 338809.6201 344863.5975 330779.9886 342878.8685 367348.6067 316553.715 294172.3804 229805.3916 1.376061099 1.474332772 1.500676703 1.439391767 1.492040139 1.598520401 1.377486023 1.280093467 1 17.81005312 1.310751846 1.529620852 0.85315749 1.477966917 0.862873039 0.060487599 0.334600911 0.803463162 0.311259353 0.017685159 20.4527564 -1.310751846 0.624809427 WIDNPTVDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WIDNPTVDDR 10 0 P18206;P18206-2 P18206 VCL Vinculin 0 ;;; 232.79 1.12E-10 2358610000 2158510 2040020 1674020 2126550 2077850 2440640 1802880 2220730 3405580 FALSE TRUE 1873257.435 2026618.974 2483581.671 2609415.68 2036504.85 2534533 1628036.975 1745844.171 3002976.212 0.623800291 0.674870139 0.827040075 0.868943174 0.678162165 0.844007019 0.542141149 0.581371296 1 21.51796162 2.259423603 24.9998499 0.6745862 0.754521966 0.003763354 0.144432592 727.9228675 872258.6878 0.054022636 0.041801006 181.7287346 -2.259423603 0.079935766 WIEQVTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WIEQVTGR 8 0 Q9UPQ0-4;Q9UPQ0-10;Q9UPQ0-2;Q9UPQ0;D6RD46 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 0 86.67 0.036917 43438000 101950 91009 69671 76242 112040 111880 103060 127420 102040 FALSE TRUE 88477.04919 90411.15589 103364.1286 93553.91139 109810.6232 116184.096 93065.25706 100172.2246 89976.94744 0.983330194 1.004825774 1.148784567 1.039754226 1.220430636 1.291265144 1.034323343 1.11330988 1 16.4572678 4.286206721 6.640302104 1.122466486 0.991469006 0.267880428 0.087352202 0.272549544 27.76086328 0.022376537 0.059259893 19328.8814 -4.286206721 -0.130997479 WIGLDLSNGKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WIGLDLSNGKPR 12 1 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 199.43 1.57E-07 3377400000 4870200 4344900 2599200 3582600 3952900 4001200 4669800 5394400 4734200 FALSE TRUE 4226590.73 4316358.066 3856181.814 4396084.087 3874245.024 4155128.753 4216923.515 4240849.539 4174528.269 1.01247146 1.033975048 0.923740736 1.053073258 0.928067742 0.995352884 1.010155697 1.015887129 1 21.99318175 2.299751732 5.319414745 1.010264494 0.989704432 0.040003542 0.040543968 0.646563404 36.08989226 0.014659613 0.011062174 199.4122034 -2.299751732 -0.020560062 WIPLSSDAQAPLAQPES(ph)PTASAGDEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WIPLSSDAQAPLAQPESPTASAGDEPR 27 0 Q6GQQ9;Q6GQQ9-2 Q6GQQ9 OTUD7B OTU domain-containing protein 7B 1 WIPLSSDAQAPLAQPES(0.457)PT(0.457)AS(0.086)AGDEPR 150.18 6.41E-08 81046000 67363 73278 53533 62818 97477 93100 65860 101250 108900 TRUE FALSE 58460.80887 72796.63199 79421.73786 77081.78701 95537.39841 96681.61724 59472.90734 79598.47543 96025.96606 0.60880209 0.758093201 0.827086059 0.802718162 0.99491213 1.006827853 0.619341932 0.828926578 1 16.55113695 4.76361273 1.278350597 0.864026681 0.484797466 0.353394252 0.11576497 1.906473197 2.601621407 0.035294257 0.96475959 58024.67677 -4.76361273 -0.379229214 WIQDEIEFGYIEAPHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 WIQDEIEFGYIEAPHK 16 0 Q9Y2J8;Q9Y2J8-2 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ;; 221.49 1.05E-14 993921000 1375411 1468779 941134 1158523 1405591 1172308 1511706 1818226 1642385 FALSE TRUE 1193646.952 1459130.494 1396269.55 1421583.354 1377622.489 1217407.447 1365100.985 1429412.519 1448224.116 0.824214248 1.007530863 0.964125327 0.981604531 0.951249516 0.840620891 0.942603406 0.987010576 1 20.46585345 1.713626926 4.036798442 0.995748631 0.93361492 0.173854907 0.057430051 0.334680005 12.56541383 0.038818937 0.015134165 51.71623809 -1.713626926 -0.06213371 WISIMTER ddPTM_MDA-MB-175_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 ; 198.87 0.00030821 1762350000 1189330 1041820 732550 1026180 1160220 1164950 532150 1126550 1287740 FALSE TRUE 1032157.027 1034976.216 1086813.63 1259189.853 1137133.892 1209766.38 480542.1749 885646.0493 1135504.844 0.908985138 0.9114679 0.957119325 1.108925127 1.001434646 1.065399577 0.42319694 0.779957967 1 20.11490243 2.289254297 24.99991556 0.730908718 0.992679393 0.395402933 0.150275955 101.0650555 49840.38877 0.056091806 0.043448458 194.6499501 -2.289254297 0.261770675 WISLNTVALVTDNAVYHWSMEGESQPVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 WISLNTVALVTDNAVYHWSMEGESQPVK 28 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 367.86 1.96E-127 962350000 1157740 1000500 339914 765340 1002550 912990 1246130 1416580 1253610 FALSE TRUE 1004741.726 993927.6496 504297.5473 939122.1445 982601.2165 948113.3161 1125280.504 1113655.391 1105409.654 0.908931564 0.899148697 0.456208742 0.849569335 0.88890233 0.857703126 1.017976006 1.00745944 1 20.07614969 2.633731103 1.264649605 1.014675099 0.770028124 0.35705443 0.128699855 0.494573515 1.65347299 0.076133374 0.054923158 430.2601292 -2.633731103 -0.244646975 WIVEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 WIVEER 6 0 O95433;O95433-2;G3V3W9 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ;;;; 137.44 0.029627 2799268000 4729190 4481720 2910170 3339380 4426180 4827000 4331040 4685250 4456230 FALSE TRUE 4104215.559 4452279.286 4317537.946 4097637.268 4338107.678 5012697.813 3911016.407 3683345.748 3929419.566 1.044483922 1.133062838 1.098772446 1.042809809 1.104007247 1.275684037 0.995316571 0.937376548 1 21.90588479 2.023686426 24.99999097 0.964854515 1.114421446 0.50187529 0.065588108 168.313836 177647.1816 0.026534337 0.017888442 105.6054729 -2.023686426 0.149566932 WIVNLIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WIVNLIR 7 0 P60228;E5RGA2;H0YAW4 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 ; 143.18 0.0056747 174701000 259730 262000 198651 231380 286650 299220 304460 312230 320090 FALSE TRUE 225406.0224 260278.9047 294719.288 283918.3654 280946.2258 310731.187 274933.5161 245462.0443 282249.3248 0.798606064 0.92215953 1.044180666 1.005913355 0.995383163 1.100910293 0.974080332 0.869663885 1 18.1066106 4.61853239 3.142785929 0.989490943 0.79149129 0.539868586 0.058606716 0.264589505 4.2140546 0.016805524 0.107739096 41546.30354 -4.61853239 -0.197999653 WIYEDVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 WIYEDVER 8 0 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-13;O43852-14;O43852-11 O43852 CALU Calumenin 0 ;;;;; 161.9 0.00080229 2587110000 8042060 6488900 4493750 5097510 6705810 8471380 5586550 5972770 5441830 FALSE TRUE 6979281.395 6446273.989 6666942.531 6254977.556 6572377.501 8797279.47 5044767.241 4695539.616 4798503.057 1.454470553 1.343392702 1.389379657 1.303526846 1.369672463 1.833338307 1.051321043 0.978542591 1 22.19415298 2.033719804 24.82329759 0.995896459 1.432165809 0.66805292 0.146028761 94.84511139 69821.12682 0.058921124 0.039724386 108.0736463 -2.033719804 0.43626935 WIYTDELEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WIYTDELEFR 10 0 Q9P2R3;Q9P2R3-2;Q9P2R3-4 Q9P2R3 ANKFY1 Rabankyrin-5 0 81.594 0.047787 11664000 27745 18014 18838 20128 20705 21284 19375 29113 46862 FALSE TRUE 24078.42795 17895.66485 27948.11981 24698.37004 20293.01101 22102.80925 17496.01548 22887.41151 41322.02775 0.582701994 0.43307809 0.676349186 0.597704696 0.491094269 0.53489169 0.423406508 0.553879196 1 15.33462343 1.240745675 6.267241296 1.014397759 0.532547922 0.789349414 0.075282219 0.053932005 9.023328884 0.111161086 0.0184267 17.40787163 -1.240745675 -0.481849838 WKAGLYGLPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WKAGLYGLPR 10 1 P49327;A0A0U1RQF0;A0A0U1RRG3 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 136.63 0.00010257 1436110000 2108750 2333690 540200 560750 2330340 2309480 2564670 2403740 162555 FALSE TRUE 1830073.345 2318359.837 801442.5269 688076.858 2283970.793 2398327.19 2315948.698 1889718.907 143337.9331 12.76754384 16.17408447 5.591280058 4.800382168 15.9341686 16.73197833 16.15726311 13.18366232 1 17.12906093 4.262927495 24.99443309 10 14.47081503 0.080922317 5.393995207 594.1828658 609474.8589 1.450836995 3.834564139 18320.08547 -4.262927495 4.470815027 WKDSDEADLVLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WKDSDEADLVLAK 13 1 Q13185 Q13185 CBX3 Chromobox protein homolog 3 0 ; 173.36 1.99E-05 1035730000 3886000 2761500 2133250 2480200 2497500 1858170 3631000 4280500 3168800 FALSE TRUE 3372455.254 2743359.525 3164896.835 3043367.317 2447804.636 1929655.002 3278866.179 3365148.386 2794188.074 1.206953564 0.981809188 1.132671371 1.089177692 0.876034315 0.690595962 1.173459371 1.20433854 1 21.4139977 -1.925194852 19.48688333 0.005280541 1.044624407 0 0.162580209 0 0 0 0.038676375 0.011879691 1.925194852 1.039343866 WKDTDEADLVLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WKDTDEADLVLAK 13 1 P45973 P45973 CBX5 Chromobox protein homolog 5 0 ; 145.43 3.81E-05 1161630000 1728130 1193930 867500 1085180 1163410 810250 1472970 1834830 1448900 FALSE TRUE 1499753.242 1186086.995 1287025.902 1331586.705 1140260.417 841420.8418 1330121.596 1442465.883 1277612.693 1.173871589 0.928361938 1.007367811 1.042245989 0.892493025 0.658588355 1.041099234 1.129032211 1 20.28501912 2.017047937 24.99944358 1.077132752 0.94495596 0.123329591 0.133099835 420.8056575 617075.5757 0.055685893 0.037533535 104.0034958 -2.017047937 -0.132176792 WKEPGSGGPQNLS(ph)GPGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WKEPGSGGPQNLSGPGGR 18 1 Q9H0W8-2;Q9H0W8;M0R2N0;M0QZC7;M0QZH1;M0QX70;M0QYR7 Q9H0W8-2 SMG9 Protein SMG9 1 WKEPGSGGPQNLS(1)GPGGR;WKEPGSGGPQNLS(1)GPGGR;WKEPGSGGPQNLS(1)GPGGR;WKEPGSGGPQNLS(1)GPGGR 229.25 1.20E-19 1864180000 966600 735800 444652 559350 746470 659200 801870 884960 822560 TRUE FALSE 838861.3609 730966.4814 659687.1945 686358.9666 731616.7074 684559.8506 724104.7708 695718.1908 725317.8939 1.156543039 1.00778774 0.909514573 0.9462871 1.008684211 0.943806649 0.99832746 0.959190717 1 19.46825392 4.698528915 3.491046906 0.967149686 1.171991144 0.79117961 0.030463863 0.108048872 2.298681232 0.007301892 0.054644755 49949.2435 -4.698528915 0.204841458 WKHPFFLDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WKHPFFLDDR 10 1 A0A1B0GV06;A0A1B0GTP7;A0A1B0GUE3;A0A1B0GUG1;A0A1B0GUW4;E7EMM4;A0A1B0GW68;A0A1B0GUA4;A0A1B0GTM3;A0A1B0GTZ5;A0A1B0GUH5;Q13510-3;Q13510;Q13510-2 A0A1B0GV06 ASAH1 Acid ceramidase;Acid ceramidase subunit alpha;Acid ceramidase subunit beta 0 ; 122.42 0.00029381 468450000 287776 348328 187229 201854 324221 321444 261890 323196 281322 FALSE TRUE 249745.6725 346039.8104 277773.5706 247688.0358 317769.6364 333810.1587 236491.9481 254083.0505 248064.4336 1.006777428 1.394959388 1.119763791 0.998482661 1.28099636 1.345659085 0.953348872 1.024262313 1 17.92035538 2.216607606 24.99803696 0.997513586 1.192459961 0.340791034 0.130118278 272.67044 310489.189 0.052369386 0.035339671 164.6673915 -2.216607606 0.194946375 WKPGSLASHVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WKPGSLASHVK 11 1 P06493;A0A024QZP7;P06493-2 P06493 CDK1;CDC2 Cyclin-dependent kinase 1 0 ; 86.911 0.0084825 1349870000 1195000 1667520 957130 1217090 1444040 1443410 1779180 1760920 1872730 FALSE TRUE 1037077.722 1656565.951 1420001.269 1493448.887 1415306.429 1498938.917 1606635.397 1384360.961 1651337.993 0.628022686 1.003165892 0.859909525 0.904387165 0.857066473 0.907711761 0.97292947 0.83832684 1 20.65520401 4.750520263 24.99416159 0.909836799 0.628022516 0.703641554 0.058921552 1018.422765 2128336.979 0.01319296 0.216210971 56301.53856 -4.750520263 -0.281814284 WKPPMIDNPSYQGIWKPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WKPPMIDNPSYQGIWKPR 18 2 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 ; 181.86 4.01E-14 1066110000 1051440 831700 671890 947900 1045620 941690 829280 1502130 1268140 FALSE TRUE 912489.54 826236.5079 996818.2513 1163135.183 1024814.208 977917.4237 748856.5532 1180911.189 1118221.934 0.816018281 0.73888419 0.891431496 1.040164879 0.916467632 0.874528923 0.669685087 1.05606155 1 20.09277512 7.99992145 0.047090142 1.407194787 1.22E-06 0.13972674 0.115685154 2806.702421 12.95456482 112.3317048 330.5982663 99981914.93 -7.99992145 -1.407193568 WLAVDYENVRPDIVLLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WLAVDYENVRPDIVLLGK 18 1 P04181;P04181-2 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 ; 233.49 8.77E-24 867560000 861540 896980 605830 1101590 1019910 929940 921820 1250360 1111270 FALSE TRUE 747685.3061 891087.6793 898811.4144 1351722.846 999615.7864 965715.3936 832422.0383 982980.2443 979896.9266 0.763024443 0.909368787 0.917250978 1.379454114 1.020123402 0.985527526 0.849499591 1.003146574 1 19.90227048 4.415089632 2.267392516 1.024213112 0.775474496 0.282932061 0.136882722 0.507602761 4.614765202 0.037952219 0.191863736 26006.96253 -4.415089632 -0.248738616 WLDDLLAS(ph)PPPSGGGAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 WLDDLLASPPPSGGGAR 17 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 WLDDLLAS(0.994)PPPS(0.006)GGGAR;WLDDLLAS(0.999)PPPS(0.001)GGGAR;WLDDLLAS(1)PPPSGGGAR;WLDDLLAS(1)PPPSGGGAR;WLDDLLAS(1)PPPSGGGAR;WLDDLLAS(1)PPPSGGGAR;WLDDLLAS(1)PPPSGGGAR 268.13 7.03E-28 2221402000 1416061 1205715 756379 1002026 1436729 1309422 1261011 1616638 1336767 TRUE FALSE 1228924.951 1197794.579 1122166.414 1229551.318 1408140.904 1359796.312 1138718.347 1270932.544 1178735.928 1.042578683 1.01616872 0.952008323 1.043110072 1.194619482 1.153605553 0.966050428 1.078216515 1 20.16880912 3.47932871 24.98032854 1.077883084 1.003629515 0.199995444 0.06853444 143.9866323 1629415.729 0.02059163 0.027036183 3015.28738 -3.47932871 -0.074253569 WLDES(ph)DAEMELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 17 WLDESDAEMELR 12 0 H3BS72;Q9P035;H3BPZ1 H3BS72 HACD3 Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3 1 WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR 340.86 1.17E-58 13111919000 9647806 9771452 6886465 9336767 11065218 10133382 5152319 10250196 15301160 TRUE FALSE 8372823.993 9707262.688 10216782.51 11456822.65 10845041.81 10523219.76 4652647.896 8058271.353 13492274.3 0.620564318 0.719468229 0.757232049 0.84913947 0.803796423 0.779944102 0.344837927 0.59725078 1 23.68563022 WLDGAS(ph)FDNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WLDGASFDNER 11 0 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 WLDGAS(1)FDNER;WLDGAS(1)FDNER 148.08 3.67E-05 51006000 435300 206276 150342 188560 223560 172647 264330 233180 250180 TRUE FALSE 377774.0021 204920.9594 223047.8941 231375.43 219111.5934 179288.8418 238695.3173 183316.2716 220604.0054 1.712453051 0.928908607 1.01107817 1.048826967 0.993234882 0.812717981 1.082008084 0.830974357 1 17.75109946 4.739951426 24.99763234 0.959048525 1.712453296 0.880808391 0.086574363 36.94230429 663913.404 0.020224453 0.12319931 54947.9414 -4.739951426 0.753404771 WLFETQPMESLYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WLFETQPMESLYEK 14 0 A0A5F9ZH43;A4UGR9-2;A4UGR9-3;A4UGR9;A4UGR9-8 A0A5F9ZH43 XIRP2 Xin actin-binding repeat-containing protein 2 0 51.726 0.093816 406730000 1640900 732720 658290 1323900 1110800 549550 1311500 1251700 985930 FALSE TRUE 1424050.907 727906.7141 976641.2458 1624511.73 1088697.253 570691.5441 1184310.932 984033.6957 869374.4786 1.638017842 0.837276377 1.123383847 1.868598365 1.252276528 0.656439265 1.362256382 1.131887029 1 19.72961822 2.987679882 24.99041464 1.068531437 1.342710251 0.185858732 0.321824166 1209.861173 2454116.334 0.101530478 0.106810323 972.0304763 -2.987679882 0.274178813 WLFTEIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WLFTEIR 7 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 102.72 0.019862 502080000 685140 840560 519980 515780 776910 802370 834960 820500 825450 FALSE TRUE 594597.0131 835038.306 771444.0672 632895.7322 761451.011 833237.6931 753985.7077 645042.4601 727866.2414 0.816904232 1.147241428 1.059870651 0.869522031 1.046141403 1.144767604 1.035884981 0.886210163 1 19.47331383 1.756257607 25 0.938235237 1.024174702 0.072031233 0.108003049 15.65959341 22151.2118 0.055801127 0.026796992 57.05025718 -1.756257607 0.085939466 WLGGAVEDYFMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WLGGAVEDYFMR 12 0 Q969E8 Q969E8 TSR2 Pre-rRNA-processing protein TSR2 homolog 0 156.92 0.00059976 0 206710 210550 165140 133930 200810 198760 191290 215400 191280 FALSE TRUE 179392.7498 209166.8832 245002.2564 164340.8535 196814.2739 206406.4258 172738.7252 169338.3862 168667.0963 1.063590669 1.240116702 1.452578847 0.974350404 1.166880074 1.223750396 1.024140031 1.00397997 1 17.36381903 2.201033416 7.239009162 1.007639699 1.190795266 0.316514315 0.122905393 0.240190965 35.71464628 0.050237195 0.034200017 158.8668981 -2.201033416 0.183155567 WLHNEDQMAVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 14 WLHNEDQMAVEK 12 0 P37837 P37837 TALDO1 Transaldolase 0 ;;;;;;;;;;;;; 231.52 3.24E-12 13177990000 19677944 18543157 12599568 15318331 17498393 16127663 21147308 23977637 22234450 FALSE TRUE 17077453.84 18421345.78 18692761.23 18796592.18 17150209.21 16748104.63 19096445.33 18850205.92 19605918.65 0.871035637 0.939580854 0.9534244 0.958720298 0.874746525 0.854237179 0.97401431 0.961454868 1 24.22478591 2.125269292 14.79319468 0.974897576 0.91280797 0.446814333 0.036376804 0.782763515 98.61364163 0.015818694 0.010664924 133.4348563 -2.125269292 -0.062089606 WLIS(ph)PVK ddPTM_MDA-MB-175_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 103.55 0.0087605 537010000 2171900 1641710 1170930 1498900 1801380 1439540 1877190 2419900 1944770 TRUE FALSE 1884877.912 1630925.499 1737195.665 1839248.154 1765536.062 1494920.035 1695140.403 1902423.217 1714861.506 1.099142937 0.951053769 1.013023885 1.072534515 1.029550233 0.871743887 0.988499886 1.109374261 1 20.70966064 1.763002741 25 1.060802576 1.000559706 0.086796411 0.067610641 29.31031795 30005.91506 0.035949746 0.01726428 57.94323535 -1.763002741 -0.06024287 WLKEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WLKEDK 6 1 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ; 92.925 0.042137 497520000 1169870 816770 834910 916960 802810 666050 1058600 1262410 1758400 FALSE TRUE 1015268.715 811404.5841 1238675.269 1125169.783 786835.6517 691673.3745 955937.1349 992453.4456 1550523.955 0.654790732 0.523309931 0.798875286 0.725670686 0.507464363 0.446090092 0.616525228 0.640076177 1 20.56432438 1.22871474 4.023226265 1.04726983 0.609797703 0.580662122 0.103326318 0.199562192 5.625196811 0.26141021 0.027700726 16.93225265 -1.22871474 -0.437472127 WLKEDKLECSEELGDLVK ddPTM_MDA-MB-175_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 ; 184.32 3.31E-14 1879010000 4516700 2974210 2578120 2170250 2367070 1597520 4334800 4948900 1832720 FALSE TRUE 3919806.651 2954672.219 3824907.455 2663038.433 2319969.938 1658977.628 3914411.763 3890616.247 1616057.929 2.425535978 1.828320733 2.366813334 1.647860751 1.4355735 1.026558267 2.422197677 2.407473257 1 20.62404748 3.730171705 24.60875704 1.747212567 2.169033089 0.193756184 0.505217639 1116.647793 3275672.172 0.150077632 0.226807684 5372.441626 -3.730171705 0.421820522 WLLLTGISAQQNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WLLLTGISAQQNR 13 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 96.89 0.0093753 336600000 521100 547740 360950 413020 518140 543000 566590 623800 643790 FALSE TRUE 452235.3147 544141.8599 535506.6273 506802.5036 507830.0277 563889.5614 511642.189 490405.2244 567681.8796 0.796635107 0.958533079 0.943321685 0.892757937 0.894567972 0.993319642 0.901283285 0.86387331 1 19.11472317 4.748251048 24.60855263 0.924329568 0.796635021 0.464488241 0.044826626 1053.298146 2674749.721 0.010932115 0.137856977 56008.12686 -4.748251048 -0.127694547 WLLSPSTTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WLLSPSTTLR 10 0 Q9Y2J8;Q9Y2J8-2 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 119.27 0.0016612 113740000 198250 165920 109590 123930 155340 165210 180830 216510 144860 FALSE TRUE 172050.7602 164830.0606 162588.0906 152070.2007 152249.0379 171565.7356 163293.1344 170211.0214 127734.8158 1.346937083 1.290408253 1.2728565 1.190514893 1.19191496 1.343139961 1.27837609 1.332534284 1 16.96279228 1.231887216 24.97776027 0.999999522 1.279538948 0.720698917 0.054937864 131.7613397 493120.9121 0.134013845 0.014165305 17.05639386 -1.231887216 0.279539427 WLNENAVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WLNENAVEK 9 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 144.77 0.00022976 146210000 114720 99614 69151 89520 105020 95348 117200 118000 122360 FALSE TRUE 99559.46134 98959.62907 102592.6549 109846.8842 102930.3075 99016.09926 105833.962 92766.61828 107894.7402 0.922746198 0.917186778 0.950858723 1.018093042 0.953988186 0.91771016 0.980900106 0.859788143 1 16.71926501 WLPEEDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 WLPEEDFR 8 0 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 0 ;; 117.02 0.0050241 236624000 764610 693720 428018 501021 648550 709360 608540 726840 660590 FALSE TRUE 663564.8512 689162.9076 635008.9364 614785.4757 635645.1239 736649.5382 549523.8845 571410.9223 582495.8027 1.139175335 1.183120813 1.090151952 1.055433314 1.091244127 1.264643513 0.943395441 0.980970025 1 19.15188813 2.211612447 24.9978002 0.97476819 1.131420843 0.627486962 0.058908695 145.5269233 134993.3394 0.024354124 0.01642435 162.7842738 -2.211612447 0.156652654 WLPLGLGLNHLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WLPLGLGLNHLGK 13 0 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 214.82 3.02E-11 571130000 1653400 1496950 967700 1251620 1480970 1300380 1667090 1804060 1892540 FALSE TRUE 1434899.001 1487116.437 1435682.957 1535819.451 1451501.594 1350406.46 1505415.868 1418275.808 1668806.077 0.859835676 0.891125972 0.860305446 0.920310318 0.869784461 0.809205143 0.902091555 0.849874547 1 20.67038489 1.232876593 24.99994014 1.000000206 0.870821242 0.642774342 0.030380795 116.3349696 511619.9288 0.061215553 0.007111259 17.09529474 -1.232876593 -0.129178964 WLPSS(ph)PSGVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WLPSSPSGVAK 11 0 Q8IWI9-3;Q8IWI9;H3BP52;H3BTF4 Q8IWI9-3 MGA MAX gene-associated protein 1 WLPS(0.029)S(0.486)PS(0.486)GVAK 84.821 0.016444 182020000 618360 469190 303650 355470 461410 397680 471910 611180 478320 TRUE FALSE 536642.1593 466107.86 450496.1556 436184.8965 452228.8437 412979.0069 426144.2408 480483.9132 421773.5545 1.272346627 1.105114 1.068099578 1.034168434 1.072207679 0.979148651 1.010362637 1.139198767 1 18.68610911 4.905507798 1.557101758 1.046818752 1.434514677 0.727213955 0.044277883 0.944299027 1.575657721 0.012666095 0.629186833 80446.61935 -4.905507798 0.387695925 WLPYEAGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WLPYEAGQR 9 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 111.74 0.0048295 228190000 339290 320980 185806 239360 327360 330790 308360 351090 320310 FALSE TRUE 294451.9668 318871.4612 275662.4031 293710.3464 320846.1765 343515.7053 278455.2947 276012.1357 282443.3167 1.042517027 1.128975063 0.975991949 1.039891295 1.135966608 1.216228833 0.985880275 0.977230189 1 18.10760184 2.084205648 25 0.985313498 1.087569472 0.35644585 0.064673108 27.9479126 8293.78635 0.027593516 0.018603542 121.3963553 -2.084205648 0.102255974 WLRIS(ph)SSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WLRISSSVK 9 1 P48357-5;P48357-2;P48357-4;P48357-3;P48357 P48357-5 LEPR Leptin receptor 1 WLRIS(0.496)S(0.496)S(0.009)VK 55.567 0.077302 282540000 287430 353310 243430 221770 294800 243720 476980 381860 373250 TRUE FALSE 249445.3972 350989.0833 361153.5622 272126.268 288934.0568 253096.0661 430722.553 300202.2106 329124.8102 0.757905176 1.066431556 1.097314912 0.82681785 0.877885981 0.768997226 1.308690623 0.9121227 1 18.32827526 2.28118386 24.99999538 1.049761111 0.911568747 0.226089645 0.148774998 252.1114586 147870.9953 0.055202579 0.042759406 191.0661973 -2.28118386 -0.138192364 WLSTSIPEAQWHSS(ph)LAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WLSTSIPEAQWHSSLAR 17 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 WLSTSIPEAQWHS(0.009)S(0.991)LAR;WLSTSIPEAQWHS(0.075)S(0.925)LAR 230.71 4.51E-16 160350000 173430 201844 101782 130770 186767 175703 160208 168749 246619 TRUE FALSE 150510.7861 200518.0735 151004.1156 160463.3272 183050.7021 182462.4081 144671.0528 132663.3396 217463.9828 0.692118227 0.922074869 0.694386784 0.737884615 0.841751815 0.839046567 0.665264431 0.61004741 1 17.73041695 2.243433617 24.99970415 0.723640524 0.789903935 0 0.123220523 376.2941158 1930497.046 0.045919008 0.034399873 175.159468 -2.243433617 0.066263411 WLSTSIPEAQWHSSLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WLSTSIPEAQWHSSLAR 17 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 307.92 4.88E-58 24279000000 3576900 4916300 1185780 1584840 6388700 7635300 4651500 4849300 2270670 FALSE TRUE 3104203.602 4884004.502 1759227.174 1944702.145 6261577.369 7929034.932 4200398.246 3812314.932 2002233.979 1.550370054 2.439277603 0.878632164 0.971266178 3.127295528 3.960094082 2.09785584 1.904030684 1 20.93317915 3.246388666 24.99988589 2.406739171 1.488324905 0.230209812 0.869635358 312.5418937 998137.079 0.274413875 0.347652672 1763.553609 -3.246388666 -0.918414266 WLVEYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WLVEYGR 7 0 A0A0A0MRE1;B4DJ07;A0A0A0MSB8;Q9UPT5-2;Q9UPT5-5;Q9UPT5-1;Q9UPT5-6;Q9UPT5;Q9UPT5-4;C9JKC2 A0A0A0MRE1 EXOC7 Exocyst complex component 7 0 86.866 0.045975 130300000 229710 229120 170510 188630 228300 226410 212880 252690 219160 FALSE TRUE 199353.2415 227614.8956 252969.2063 231461.3245 223757.2767 235120.1392 192234.9304 198654.2099 193251.1545 1.031575941 1.177819073 1.309017827 1.197722855 1.157857387 1.216655807 0.994741433 1.027958723 1 17.56011751 2.235965819 24.99939532 1.011280635 1.187016546 0.592211471 0.068030246 46.78889657 450774.0484 0.027429943 0.019453715 172.1733059 -2.235965819 0.175735911 WLVFDEADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WLVFDEADR 9 0 F8WAJ0;Q9H8H2-4;Q9H8H2-2;Q9H8H2 F8WAJ0 DDX31 Probable ATP-dependent RNA helicase DDX31 0 111.04 0.0050942 19525000 56527 52033 36337 42717 60731 64060 45932 56882 57707 FALSE TRUE 49056.81373 51691.1918 53909.69474 52416.54774 59522.57192 66524.42965 41477.52171 44718.22696 50884.9442 0.964073254 1.015844522 1.059442937 1.030099346 1.169748201 1.307349958 0.815123655 0.878810573 1 15.63495124 2.205739276 24.99999964 0.890532537 1.087037103 0.432858174 0.104018147 184.7284605 140706.3121 0.044591405 0.030065832 160.5976834 -2.205739276 0.196504566 WLYDETLEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WLYDETLEDR 10 0 Q9H5Q4 Q9H5Q4 TFB2M "Dimethyladenosine transferase 2, mitochondrial" 0 ; 105.78 0.0058235 55684000 93162 96620 56872 88172 96474 119416 79601 105750 92816 FALSE TRUE 80850.40566 95985.29686 84375.48943 108192.8002 94554.35615 124010.0108 71881.30727 83136.18545 81843.39822 0.987867164 1.172792173 1.030938246 1.321949022 1.155308286 1.515210921 0.878278625 1.015795865 1 16.32057843 WMDEAQALDTADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WMDEAQALDTADR 13 0 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 171.05 1.50E-06 0 145010 117610 87643 102780 119910 118920 131390 136460 130250 FALSE TRUE 125846.5611 116837.4122 130027.4479 126117.7699 117524.0256 123494.9294 118647.818 107279.0909 114851.9934 1.09572814 1.017286759 1.132130528 1.098089517 1.023265005 1.075252816 1.033049706 0.934063814 1 16.80941637 1.95404438 4.130651105 0.965351148 1.071842691 0.57766321 0.037277236 0.143548584 5.041710102 0.019375852 0.009988789 89.95895038 -1.95404438 0.106491542 WMGIAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WMGIAFR 7 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;M0QYZ0 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ; 163.53 0.0028649 883480000 1150250 1335640 793060 825620 1259740 1677270 958060 1115300 1151490 FALSE TRUE 998241.5481 1326866.093 1176586.469 1013089.64 1234673.639 1741795.662 865147.4887 876801.7743 1015362.164 0.983138415 1.306790956 1.158785023 0.997761859 1.215993349 1.715442749 0.852058033 0.863535993 1 19.95356298 SHS(ph)GTSPDNTAPPPPPPRPQPSHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 SHSGTSPDNTAPPPPPPRPQPSHSR 25 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.027)HS(0.324)GT(0.324)S(0.324)PDNTAPPPPPPRPQPSHSR;S(0.013)HS(0.329)GT(0.329)S(0.329)PDNTAPPPPPPRPQPSHSR;S(0.013)HS(0.346)GT(0.296)S(0.346)PDNTAPPPPPPRPQPSHSR;S(0.045)HS(0.318)GT(0.318)S(0.318)PDNTAPPPPPPRPQPSHSR;S(0.01)HS(0.393)GT(0.298)S(0.298)PDNTAPPPPPPRPQPSHSR 123.89 9.52E-05 2050440000 323543 267266 100938 123843 171449 158833 121716 147181 108323 TRUE FALSE 280785.9728 265510.312 149751.9544 151963.446 168037.5003 164943.4083 109912.0011 115707.4885 95517.17834 2.939638478 2.779712683 1.567801279 1.590954094 1.759238529 1.726845486 1.15070402 1.211378838 1 16.5434726 8 0.328876802 1.062735463 22.19682315 0.843351813 0.255356317 29.40510011 0.459621381 0.40786483 371.7579279 99999999.99 -8 21.13408769 up WMKWYGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WMKWYGK 7 1 Q8TEK3;Q8TEK3-1;C9JH95 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 0 ; 74.639 0.02742 747870000 1518520 1223870 837450 1152250 1266780 1231370 1289930 1551520 2048330 FALSE TRUE 1317843.735 1215830.317 1242443.621 1413885.974 1241573.556 1278741.601 1164832.787 1219739.522 1806178.761 0.729630844 0.6731506 0.687885191 0.782805116 0.687403475 0.70798175 0.64491556 0.675314951 1 20.78450926 1.236135715 24.99794884 1.000000397 0.69646356 0.86594882 0.037254741 23.01315203 237186.4517 0.061249354 0.009342443 17.22406735 -1.236135715 -0.303536837 WNADHSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WNADHSK 7 0 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 0 77.058 0.039078 86575000 181960 166200 75949 97696 149690 149440 185590 184620 136980 FALSE TRUE 157913.525 165108.2213 112678.1904 119879.37 146711.4619 155189.0535 167591.5104 145140.4497 120786.3804 1.307378567 1.366944027 0.932871653 0.992490789 1.2146358 1.284822452 1.387503374 1.201629266 1 16.88209826 WNDGLDQYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WNDGLDQYR 9 0 O95340;O95340-2 O95340 PAPSS2 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 2;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ;;; 177.7 0.00012055 764600000 1333899 1520060 828335 941646 1467086 1379979 1263064 1430945 1374376 FALSE TRUE 1157620.867 1510074.626 1228920.577 1155461.116 1437893.859 1433067.685 1140572.248 1124948.547 1211898.835 0.95521246 1.246040166 1.014045514 0.953430339 1.186480107 1.182497783 0.941144768 0.92825285 1 20.20883784 2.215494821 24.98017945 0.949949696 1.09150524 0.286643186 0.098812197 279.1962988 302366.399 0.039792426 0.026847684 164.2460072 -2.215494821 0.141555544 WNIKPESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WNIKPESK 8 1 E5RIA4;E7ETB3;Q9ULA0-2;Q9ULA0;C9JBE1;E7EPX3;B9ZVU2;F8WAN0;E5RJ35 E5RIA4 DNPEP Aspartyl aminopeptidase 0 66.435 0.056263 338000000 385060 282420 245740 336090 303430 218850 352000 372580 613100 FALSE TRUE 334173.3454 280564.7644 364580.686 412404.3713 297392.3367 227269.3011 317863.0942 292906.6664 540620.0164 0.618129805 0.51896851 0.674375115 0.762835927 0.550094942 0.420386397 0.587960276 0.541797672 1 19.0442554 1.235147725 24.99535221 1.000000584 0.582654476 0.671047924 0.091457911 62.71103804 459208.6123 0.166600747 0.023548711 17.18492832 -1.235147725 -0.417346108 WNRPGDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WNRPGDR 7 1 F8VX55;Q12800-2;Q12800-3;Q12800-4;Q12800;F8VWL0;C9JWL3;Q9NZI7-4;Q9NZI7 F8VX55 TFCP2;UBP1 Alpha-globin transcription factor CP2;Upstream-binding protein 1 0 66.429 0.061922 120410000 200860 198790 103630 122270 201010 232510 187730 199290 138450 FALSE TRUE 174315.8421 197484.1354 153745.8146 150033.2723 197010.2943 241454.8102 169523.9735 156673.3844 122082.5987 1.427851667 1.617627225 1.25935896 1.228948874 1.613745909 1.977798742 1.38860063 1.283339198 1 16.89749805 1.478874912 2.188268843 0.986124439 1.510009492 0.376971699 0.211491356 0.460931062 3.669032878 0.414486364 0.062001384 30.12138323 -1.478874912 0.523885054 WNS(ph)NDFIDAFASPVEAEGTPEPGAEAAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 WNSNDFIDAFASPVEAEGTPEPGAEAAK 28 0 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 1 WNS(1)NDFIDAFASPVEAEGTPEPGAEAAK;WNS(1)NDFIDAFASPVEAEGTPEPGAEAAK;WNS(0.999)NDFIDAFAS(0.001)PVEAEGTPEPGAEAAK 240.86 1.77E-45 238904000 383150 290115 250863 269440 309883 283866 365870 435407 438209 TRUE FALSE 332515.7567 288209.2155 372181.1859 330620.4701 303716.9346 294786.5087 330387.9837 342298.6014 386404.4312 0.860538156 0.745874509 0.963190781 0.855633226 0.786007898 0.762896294 0.85503156 0.885855787 1 18.55975211 1.256272069 1.838496826 1.054381309 0.830551463 0.433260387 0.060860258 0.839222002 2.779068284 0.32782952 0.016983596 18.04147618 -1.256272069 -0.223829846 WNSIEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WNSIEER 7 0 Q9UNE7;Q9UNE7-2;H3BTA3;H3BS86;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 137.88 0.0066061 150760000 363910 362350 219780 260810 368880 397880 351380 377470 379100 FALSE TRUE 315818.3715 359969.699 326066.3431 320030.8967 361540.0097 413186.7011 317303.2217 296750.978 334283.2299 0.944762834 1.076840436 0.975419387 0.957364499 1.081537982 1.236037779 0.949204726 0.887723198 1 18.35071145 2.028585706 24.99993699 0.930628192 1.045512237 0.22306687 0.086964905 273.3682093 239075.9869 0.036394728 0.024536855 106.8035544 -2.028585706 0.114884045 WNSPAEEGSSDCEVFSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WNSPAEEGSSDCEVFSK 17 0 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 81.632 0.011977 0 31150 31538 18353 24653 36322 36815 34395 37305 44974 FALSE TRUE 27033.44858 31330.8248 27228.57219 30250.84045 35599.26326 38231.29687 31059.37819 29327.61606 39657.22495 0.681677768 0.790040777 0.686598021 0.762807798 0.897674088 0.964043675 0.783195956 0.739527692 1 15.27529611 3.388713337 5.241788987 0.856521378 0.726171667 0.435817191 0.082088285 0.24191866 10.98924147 0.025303725 0.032966617 2447.44723 -3.388713337 -0.13034971 WNSVS(ph)PASAGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WNSVSPASAGK 11 0 E5RJU9;Q86UE4;H0YB56;H0YBE0 E5RJU9 MTDH Protein LYRIC 1 WNSVS(0.984)PAS(0.016)AGK;WNSVS(0.974)PAS(0.026)AGK 168.78 1.85E-05 388250000 633190 519000 462580 667290 695970 508630 513930 879720 1234140 TRUE FALSE 549512.3372 515590.6548 686285.2352 818808.3934 682121.5586 528197.3252 464089.1477 691598.724 1088241.375 0.504954461 0.47378336 0.630636962 0.752414319 0.626810903 0.485367803 0.426457915 0.635519601 1 20.05356716 1.257567051 3.922343735 1.041261656 0.562345746 0.679499446 0.094790929 0.150218359 3.901219238 0.200822194 0.026360032 18.09535265 -1.257567051 -0.47891591 WNTEDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 WNTEDK 6 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ;;;;; 148.98 0.024883 6680260000 8678990 6993330 4885210 4989540 4900730 4886380 6457430 7923700 11916210 FALSE TRUE 7532039.482 6947390.355 7247713.896 6122491.317 4803215.061 5074362.201 5831189.432 6229278.417 10507489.23 0.71682581 0.661184628 0.689766484 0.58267881 0.457123006 0.482928137 0.554955547 0.592841761 1 23.32491464 1.238784008 8.226028482 1.004475202 0.587512615 0.705454456 0.08275042 0.05565343 36.89428189 0.129780361 0.022616999 17.32941923 -1.238784008 -0.416962587 WNTEDKVSHVSTGGGASLELLEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WNTEDKVSHVSTGGGASLELLEGK 24 1 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ; 133.58 2.47E-05 644018000 1357580 1169850 198478 437542 984170 721430 1267860 1497500 268049 FALSE TRUE 1178172.363 1162165.178 294462.6247 536892.5985 964586.9425 749183.8789 1144903.132 1177271.279 236360.5526 4.984640417 4.916916827 1.245819666 2.271498322 4.080998001 3.169665457 4.843884142 4.980828085 1 17.85062975 WNTTLYEGTWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WNTTLYEGTWR 11 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 176.42 2.02E-05 1167610000 837610 507770 369310 477300 553790 564670 518140 591940 739170 FALSE TRUE 726917.7163 504434.4254 547909.5513 585678.2601 542770.6625 586393.2203 467890.8625 465358.2375 651786.1647 1.115270246 0.773926255 0.840627772 0.898574244 0.832743455 0.899671168 0.717859457 0.713973789 1 19.3140392 4.7446904 24.55699283 0.823920896 1.115270412 0.502011285 0.08724735 460.5624135 1845028.203 0.021741607 0.193530057 55550.81048 -4.7446904 0.291349517 WNWLTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WNWLTR 6 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ; 118.01 0.05172 806290000 627370 654130 441400 433260 669210 698290 634060 698870 696690 FALSE TRUE 544461.4649 649832.977 654862.5164 531638.305 655894.0303 725153.6682 572568.9588 549422.0891 614328.1019 0.886271462 1.057794646 1.065981703 0.865397991 1.067660796 1.180401264 0.93202469 0.894346339 1 19.22864985 2.081166362 24.99999344 0.931610267 1.022491251 0.130879962 0.093934771 50.10062511 15427.23951 0.038298663 0.025820952 120.5497633 -2.081166362 0.090880985 WNYRDEADVLEVDQGFDDHNLPCDVIWLDIEHADGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WNYRDEADVLEVDQGFDDHNLPCDVIWLDIEHADGK 36 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 139.96 3.88E-13 34968000 46748 39188 26604 28428 36839 41545 39374 42360 25712 FALSE TRUE 40570.13336 38930.57145 39469.78339 34883.01189 36105.97597 43143.26303 35555.51554 33301.64365 22672.35665 1.789409631 1.717094171 1.740876963 1.538570182 1.592510939 1.902901569 1.568232014 1.468821444 1 14.46864674 1.118231276 1.440459862 0.53367061 1.700347352 0.815080884 0.105576069 0.692126246 1.007814408 1.282591754 0.031031206 13.12898875 -1.118231276 1.166676742 WNYRDEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WNYRDEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR 37 2 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 179.1 1.72E-23 442670000 502160 400040 221464 226740 345860 396740 438280 420290 61663 FALSE TRUE 435798.2837 397412.1109 328564.7312 278224.7825 338978.0627 412002.8445 395775.6731 330414.2542 54373.27039 8.014936026 7.308960967 6.042761982 5.116940374 6.234277619 7.577304834 7.278864601 6.076777281 1 15.73060998 4.32154528 2.846304685 5.805364535 7.914777711 0.182928561 1.800091729 0.514530533 8.053950354 0.474523494 1.633955454 20967.43379 -4.32154528 2.109413175 WPAS(ph)PGSHSNDDFDNWSTFRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WPASPGSHSNDDFDNWSTFRPR 22 1 Q12778 Q12778 FOXO1 Forkhead box protein O1 1 WPAS(1)PGSHSNDDFDNWSTFRPR 133.15 5.74E-06 95533000 71886 73088 64502 50662 59947 69308 68955 77712 63023 TRUE FALSE 62386.08296 72607.88012 95695.38295 62165.58142 58754.17198 71974.32361 62267.75471 61093.89356 55572.49274 1.122607245 1.306543517 1.721991911 1.118639427 1.057252772 1.295142976 1.120477986 1.099354924 1 15.76208333 3.577032913 23.35556002 1.118820262 1.383388895 0.377302997 0.162599169 25.65472565 5990.73695 0.044295841 0.065701319 3776.008066 -3.577032913 0.264568632 WPEVDDDSIEDLGEVKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WPEVDDDSIEDLGEVKK 17 1 O43583 O43583 DENR Density-regulated protein 0 160.43 4.96E-09 262310000 456360 334070 318050 355580 284470 229490 456670 545450 440550 FALSE TRUE 396050.8697 331875.4722 471860.0438 436319.8737 278809.6036 238318.6288 412382.2137 428809.7622 388468.6809 1.019518147 0.854317191 1.214666888 1.123179024 0.717714496 0.61348222 1.061558458 1.103846419 1 18.56743876 2.057775598 24.99998981 1.066364109 0.925564771 0.107605704 0.177307411 181.1221979 78371.90275 0.078441929 0.052885533 114.2287957 -2.057775598 -0.140799338 WPFSGKT(ph)SPPCSPANLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WPFSGKTSPPCSPANLSR 18 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 WPFS(0.162)GKT(0.532)S(0.306)PPCSPANLSR 98.121 0.0020701 991720000 622780 539340 226360 293040 543500 411310 606420 666140 87695 TRUE FALSE 540478.0451 535797.04 335828.4531 359579.2108 532685.4133 427133.3619 547609.4817 523691.1449 77327.797 6.989440616 6.928906044 4.342920219 4.650064075 6.888666611 5.523671673 7.081664071 6.772353089 1 16.23869949 4.320414389 11.5259907 5.478652958 6.966986352 0.132030801 1.77230768 1.189186526 160.8574781 0.434848848 1.151308877 20912.90619 -4.320414389 1.488333394 WPFSGKTS(ph)PPCS(ph)PANLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WPFSGKTSPPCSPANLSR 18 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 WPFS(0.04)GKT(0.269)S(0.691)PPCS(0.934)PANLS(0.065)R;WPFS(0.017)GKT(0.444)S(0.539)PPCS(0.999)PANLS(0.001)R 90.308 0.0015533 1002300000 1845660 1678110 660270 612830 1473160 1329850 1760040 1919650 153233 TRUE FALSE 1601751.355 1667086.385 979578.7805 751982.418 1443846.998 1381010.19 1589351.592 1509147.786 135117.9693 11.85446586 12.33800651 7.249803897 5.565376847 10.68582518 10.22077372 11.76269596 11.1691124 1 17.04386003 4.252368994 24.87504084 8.749984483 12.09623861 0.185894707 3.221641279 424.1400669 764050.5336 0.810755919 2.120560146 17880.06093 -4.252368994 3.346254125 WPFSGKTS(ph)PPCSPANLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WPFSGKTSPPCSPANLSR 18 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 WPFS(0.011)GKT(0.164)S(0.825)PPCSPANLSR 96.54 0.00095314 1343200000 1282900 1118800 449430 544060 1187000 971630 1238900 1581400 150900 TRUE FALSE 1113361.515 1111450.529 666775.8513 667597.1384 1163381.022 1009009.235 1118751.669 1243229.916 133060.7739 8.36731579 8.352954041 5.011062477 5.017234748 8.743230542 7.583070541 8.407824754 9.343323956 1 17.0217258 4.396069753 24.99999199 6.866485911 8.364774977 0.076553114 2.445497225 80.27071255 24751.15736 0.606870599 1.605628803 24892.57089 -4.396069753 1.498289066 WPFWLSPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WPFWLSPR 8 0 P26639;P26639-2;B7ZLP8;A2RTX5-2;A2RTX5 P26639;B7ZLP8 TARS;TARSL2 "Threonine--tRNA ligase, cytoplasmic;Probable threonine--tRNA ligase 2, cytoplasmic" 0 91.626 0.02874 52958000 46740 65337 33118 44734 64596 74934 46102 50871 58637 FALSE TRUE 40563.19058 64907.79694 49133.97557 54891.53842 63310.66598 77816.75947 41631.03514 39992.63253 51705.00066 0.784511944 1.255348537 0.950275117 1.061629199 1.224459243 1.505014186 0.80516458 0.773477072 1 15.6580162 WPS(ph)DSWIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WPSDSWIR 8 0 Q5VT97-2;Q5VT97 Q5VT97-2 SYDE2 Rho GTPase-activating protein SYDE2 1 WPS(0.997)DS(0.003)WIR;WPS(0.995)DS(0.005)WIR 70.028 0.054956 116236000 147706 141828 87903 113128 150948 134725 133164 164631 133328 TRUE FALSE 128186.2779 140896.3225 130413.1848 138815.4415 147944.4301 139907.9579 120249.7758 129425.9418 117566.1157 1.090333529 1.19844329 1.10927527 1.180743623 1.258393451 1.190036407 1.022826816 1.100877927 1 16.84311279 2.242610178 24.99943514 1.05289353 1.174024209 0.569277594 0.052932665 77.40411796 477848.2165 0.02029306 0.015126798 174.8276733 -2.242610178 0.121130679 WPSVSSLDSALESSPSLHSPADPSHLSPPAS(ph)SPRPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WPSVSSLDSALESSPSLHSPADPSHLSPPASSPRPSR 37 1 O15211 O15211 RGL2 Ral guanine nucleotide dissociation stimulator-like 2 1 WPSVSSLDSALESSPSLHSPADPSHLS(0.067)PPAS(0.466)S(0.466)PRPS(0.001)R;WPSVSSLDSALESSPSLHSPADPS(0.008)HLS(0.129)PPAS(0.418)S(0.418)PRPS(0.026)R 140.83 2.65E-13 164237000 65847 68089 19540.5 37362.4 77580 66613 60272 74412 55510 TRUE FALSE 57145.15211 67641.71888 28990.35116 45846.10397 76036.30978 69175.64521 54426.83072 58499.57287 48947.67104 1.167474384 1.381919046 0.59227233 0.936635043 1.553420381 1.413257133 1.111939129 1.195145175 1 15.5789526 WPYQNGFTFHTWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WPYQNGFTFHTWLR 14 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 132.31 5.12E-05 329630000 123290 124730 100380 68098 135430 124230 109190 116420 112630 FALSE TRUE 106996.9141 123910.6404 148924.1038 83560.69171 132735.208 129009.2085 98600.77061 91524.48898 99315.00971 1.077348876 1.247652704 1.499512553 0.841370221 1.336507023 1.298990041 0.992808347 0.921557469 1 16.59972415 2.158831925 6.217449411 0.957334123 1.219096525 0.311817468 0.171934128 0.236205886 14.48223679 0.06874498 0.046177737 144.1557352 -2.158831925 0.261762402 WQDEDGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WQDEDGKK 8 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ;;; 116.3 0.0036832 3859280000 7230100 5451220 4849450 5013510 4294320 3816340 7406000 8553400 7728400 FALSE TRUE 6274623.966 5415410.577 7194660.24 6151904.072 4208871.434 3963157.069 6687767.26 6724321.973 6814757.356 0.920740628 0.794659339 1.055747089 0.902732665 0.617611342 0.581555125 0.981365427 0.986729479 1 22.70023086 2.051576341 24.99984974 0.989908789 0.81470021 0.268905683 0.137764739 144.8988742 70233.98728 0.061221601 0.041275587 112.60984 -2.051576341 -0.175208579 WQFLTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WQFLTLR 7 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRU9 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 127.12 0.0090405 747260000 536730 692850 397550 409560 680190 710360 660620 650010 680000 FALSE TRUE 465799.7706 688298.6227 589806.5097 502556.8577 666655.5498 737688.0089 596553.1741 511010.4199 599611.1747 0.776836374 1.147908264 0.983648295 0.838137912 1.111813085 1.230277286 0.994900027 0.852236318 1 19.19366774 1.982696057 24.51885459 0.91796495 1.023856168 0.060327199 0.13900909 1357.173461 1923046.216 0.062093931 0.036946948 96.09395259 -1.982696057 0.105891218 WQGGER ddPTM_MDA-MB-175_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 ; 104.8 0.077987 1230840000 1086920 1016860 752390 760140 808940 993100 1001680 1024830 945200 FALSE TRUE 943280.7681 1010180.18 1116248.321 932741.405 792843.6767 1031305.2 904537.2278 805678.0797 833459.5328 1.131765528 1.212032666 1.339295163 1.119120207 0.951268353 1.237378852 1.085280319 0.966667304 1 19.66875263 1.722059085 0.37927455 0.837298898 1.232793308 0.354962125 0.099419118 5.722618089 1.096960924 1.089025335 0.191438258 52.7301595 -1.722059085 0.39549441 WQHWHEECER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WQHWHEECER 10 0 J3QLV0;J3QLD4;J3QL54;J3KT10;Q9BW27-2;Q9BW27-3;Q9BW27 J3QLV0 NUP85 Nuclear pore complex protein Nup85 0 127.83 0.0001999 86383000 47348 42464 24934 37416 51852 55558 38214 46799 38838 FALSE TRUE 41090.84184 42185.05119 36992.1658 45911.87467 50820.24665 57695.35221 34508.01216 36791.39804 34246.61588 1.199851161 1.231802036 1.080169963 1.340625153 1.483949445 1.68470229 1.007632762 1.074307551 1 15.06367381 WQMNPYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WQMNPYDR 8 0 F1T0B3;A0A087X2G1;Q92499;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ; 143.61 0.0013928 1042570000 569960 761050 427370 450220 764430 772450 668900 781010 722040 FALSE TRUE 494638.3419 756050.6124 634047.5615 552449.3322 749219.3386 802166.6513 604030.181 613997.0893 636681.2538 0.776901062 1.187486844 0.995863405 0.867701584 1.17675734 1.259918753 0.948716767 0.964371239 1 19.28021176 4.761081554 23.85739173 1.041771623 0.776900527 0.326283766 0.12285723 4446.626223 4710359.946 0.031116439 1.503469776 57687.47812 -4.761081554 -0.264871097 WQNNLLPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WQNNLLPSR 9 0 P62244;I3L3P7;H3BVC7 P62244 RPS15A 40S ribosomal protein S15a 0 101.25 0.009558 432840000 357660 527460 319040 324000 525020 420110 448480 476890 606110 FALSE TRUE 310394.3248 523995.0805 473328.8111 397569.152 514573.1292 436271.9035 404986.4786 374910.7847 534456.3663 0.580766447 0.980426305 0.885626668 0.743875791 0.962797268 0.816290966 0.757754055 0.701480623 1 19.02771264 1.216214555 24.4310022 1.000001012 0.808278867 0.208551211 0.119919348 2330.535456 2547800.16 1.40512986 0.028424145 16.45184295 -1.216214555 -0.191722144 WQNSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WQNSLR 6 0 Q99853;Q5VYV0 Q99853 FOXB1;FOXB2 Forkhead box protein B1;Forkhead box protein B2 0 128.82 0.0383 74674000 159500 154750 80623 108820 176140 173170 157020 163700 149420 FALSE TRUE 138421.6709 153733.4371 119612.5525 133529.2442 172635.1586 179831.962 141792.2246 128694.0289 131755.7378 1.050593114 1.166806392 0.907835624 1.013460563 1.310266721 1.364889036 1.07617495 0.976762235 1 17.00750627 1.995695994 24.97107781 0.998645442 1.136707805 0.171258839 0.132733695 333.8110165 1936714.302 0.060918306 0.039939185 99.01386067 -1.995695994 0.138062363 WQPDTEEEYEDSSGNVVNKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WQPDTEEEYEDSSGNVVNKK 20 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ; 316.66 2.90E-66 668050000 583450 410660 292360 370300 374240 290110 496620 589460 367780 FALSE TRUE 506345.6042 407962.3474 433746.2739 454382.2747 366793.3562 301270.7194 448457.8688 463408.5662 324301.4674 1.561342316 1.257972561 1.337478604 1.401110758 1.131025891 0.928983522 1.382842552 1.428943785 1 18.30697603 7.999986966 0.823516012 1.232938752 92.41645672 0.277677539 0.168383021 946.6488691 2.955604637 0.061773905 161376.5114 99996998.75 -7.999986966 91.18351797 WQPPEFLLVHDSGPDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WQPPEFLLVHDSGPDHR 17 0 P18583-7;P18583;P18583-5;P18583-9;P18583-2;H7C1M2;J3QSZ5 P18583-7 SON Protein SON 0 ; 145.91 2.64E-07 100640000 9060.7 8072.1 2633.9 6755 8744.9 10819 9791.9 10688.3 15108.2 FALSE TRUE 7863.305538 8019.073844 3907.66285 8288.825994 8570.893599 11235.21393 8842.283045 8402.690221 13322.12581 0.590244054 0.601936505 0.293321269 0.622184936 0.643357804 0.843349935 0.663729136 0.630731937 1 13.70153669 3.239191833 2.479938931 0.746706951 0.504073371 0.440129115 0.135282002 0.289763976 3.653299148 0.043188172 0.054737106 1734.570007 -3.239191833 -0.24263358 WQQHQGLLPPGMTIDLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WQQHQGLLPPGMTIDLFR 18 0 Q2TAY7;Q2TAY7-2 Q2TAY7 SMU1 "WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed" 0 60.949 0.063532 436560000 450880 373470 285310 306890 313370 245360 474800 491630 339000 FALSE TRUE 391295.0656 371016.651 423286.8703 376574.065 307134.5501 254799.158 428753.9691 386498.7504 298923.8062 1.309012723 1.241174652 1.416035998 1.259766058 1.027467682 0.85238831 1.43432527 1.292967446 1 18.18941827 3.466016454 24.07326234 1.152044261 1.317970582 0.233712109 0.164508381 256.2841239 555575.3572 0.051178009 0.066140883 2924.263168 -3.466016454 0.165926321 WQRPS(ph)SPPPFLPAASEEAEPAEGLR ddPTM_MDA-MB-175_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(0.73)S(0.27)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 212.24 5.67E-26 10343085000 2345515 2321939 1585082 2025886 2301913 2534942 2218423 2764757 2786078 TRUE FALSE 2035549.25 2306686.03 2351632.957 2485894.38 2256109.435 2632462.859 2003280.679 2173535.231 2456711.033 0.828566821 0.938932581 0.95722815 1.011879031 0.918345465 1.071539479 0.815431954 0.884733777 1 21.22829674 4.737555414 5.536563944 0.943657843 0.824522573 0.221481491 0.070649108 0.248451504 30.20689303 0.01761498 0.112427535 54645.62708 -4.737555414 -0.11913527 WQRPS(ph)SPPPFLPAASEEAEPAEGLRVPGLAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WQRPSSPPPFLPAASEEAEPAEGLRVPGLAK 31 2 H3BLU1;Q4KMQ1;Q4KMQ1-2;Q4KMQ1-4;Q4KMQ1-3 H3BLU1 TPRN Taperin 1 WQRPS(0.8)S(0.2)PPPFLPAASEEAEPAEGLRVPGLAK;WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLRVPGLAK 142.89 1.14E-08 856574000 177739 168459 76401 73454 163557 150384 199534 240758 24547 TRUE FALSE 154250.3408 167352.3817 113348.7791 90132.85337 160302.5357 156169.3698 180183.2234 189273.7753 21645.08162 7.126345998 7.731658612 5.236699085 4.164126287 7.405956627 7.215004891 8.324441853 8.744424187 1 14.40175162 4.28216946 24.97684408 6.407309524 7.429003898 0.041744923 2.275755687 604.9771458 346489.3443 0.573425268 1.517121198 19150.03007 -4.28216946 1.021694374 WQRPSS(ph)PPPFLPAASEEAEPAEGLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WQRPSSPPPFLPAASEEAEPAEGLR 25 1 H3BLU1;Q4KMQ1;Q4KMQ1-2;Q4KMQ1-4;Q4KMQ1-3 H3BLU1 TPRN Taperin 1 WQRPS(0.181)S(0.819)PPPFLPAASEEAEPAEGLR;WQRPS(0.412)S(0.588)PPPFLPAASEEAEPAEGLR 184.55 1.13E-17 5791380000 1425070 1382040 962140 1140680 1391080 1474460 1200670 1509410 1668580 TRUE FALSE 1236743.389 1372961.288 1427434.122 1399688.828 1363400.23 1531183.43 1084229.208 1186634.418 1471322.373 0.840565882 0.933147836 0.97017088 0.951313494 0.92664956 1.040685208 0.736907987 0.806508784 1 20.48868195 2.238886988 24.99999998 0.83458137 0.944040007 0.232962581 0.080894658 11.06521972 847719.8515 0.031186963 0.022632861 173.3352886 -2.238886988 0.109458637 WQS(ph)PVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 WQSPVTK 7 0 A9Z1X7 A9Z1X7 SRRM1 1 WQS(1)PVTK;WQS(1)PVTK;WQS(1)PVTK;WQS(0.997)PVT(0.003)K;WQS(0.994)PVT(0.006)K;WQS(1)PVTK;WQS(0.998)PVT(0.002)K;WQS(1)PVTK 147.73 0.002236 44992480000 37683300 30586600 20701830 24044020 28765300 24267310 32652200 36832700 33781300 TRUE FALSE 32703356.43 30385674.61 30713304.23 29503582.23 28192926.81 25200889.12 29485594.67 28956313.74 29787713.2 1.097880734 1.020074096 1.031072913 0.990461471 0.946461604 0.84601624 0.989857613 0.972089181 1 24.82821404 4.007624977 1.239632622 0.952842039 1.078712012 0.514851025 0.044809792 0.511203974 1.37946781 0.015422023 0.059652156 10177.12191 -4.007624977 0.125869973 WQVVDTPGILDHPLEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WQVVDTPGILDHPLEDR 17 0 Q9BZE4-2;Q9BZE4;Q9BZE4-3 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 0 ;;; 253.26 5.24E-27 765680000 499540 496510 306938 402227 472110 512430 426831 510081 549519 FALSE TRUE 433524.5233 493248.3931 455374.2434 493558.788 462715.9347 532143.5137 385436.9953 401004.1476 484555.4898 0.894684989 1.017939954 0.939777287 1.018580531 0.954928681 1.098209648 0.795444492 0.827571158 1 18.88630236 2.225229928 24.99999511 0.861308101 0.98652682 0.33001364 0.075142719 232.5499811 436114.1095 0.029262185 0.019856199 167.9693059 -2.225229928 0.125218719 WRCPVPT(ph)LPGCQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WRCPVPTLPGCQK 13 1 E5RJ64 E5RJ64 C8orf58 1 WRCPVPT(1)LPGCQK;WRCPVPT(1)LPGCQK;WRCPVPT(1)LPGCQK;WRCPVPT(1)LPGCQK 75.78 0.049241 2471040000 2596740 3082670 5514300 1903600 1652860 3065420 1974560 1337840 1405340 TRUE FALSE 2253574.23 3062419.738 8181033.924 2335841.475 1619971.32 3183348.691 1783067.475 1051753.327 1239202.306 1.81856846 2.471283117 6.601854986 1.88495572 1.307269452 2.568869244 1.438883277 0.848734159 1 20.2409803 3.50082713 24.82524435 1.433296144 3.636101292 0.375138218 1.303449288 728.8945758 763310.4593 0.359811821 0.530006342 3168.306071 -3.50082713 2.202805148 WREENSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WREENSR 7 1 Q15006;E5RGJ2 Q15006 EMC2 ER membrane protein complex subunit 2 0 68.95 0.055689 89130000 74498 75560 39672 44695 60639 72585 58274 72115 67775 FALSE TRUE 64652.90055 75063.64138 58857.51189 54843.68287 59432.40254 75377.39192 52622.59645 56693.76845 59762.71671 1.081826666 1.25602793 0.984853352 0.917690592 0.994472906 1.261277868 0.880525507 0.948647779 1 15.86695811 4.221879671 24.98180923 0.993866149 1.168927287 0.296032737 0.109288014 254.2397754 380757.1705 0.028227512 0.059011899 16667.85335 -4.221879671 0.175061138 WREEQMER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 WREEQMER 8 1 P09496-2;F8WF69;P09496-4;P09496-3;P09496 P09496-2 CLTA Clathrin light chain A 0 ;;;; 209.6 4.19E-05 5336190000 2705200 2740800 1687550 1886600 2616520 2867470 2692220 2938710 2499970 FALSE TRUE 2347700.966 2722795.504 2503654.825 2314981.365 2564456.371 2977783.426 2431128.919 2310289.736 2204426.395 1.064994037 1.235149203 1.135739815 1.050151355 1.163321387 1.350820074 1.102839689 1.048023078 1 21.07197188 1.784439342 3.20324434 1.018961059 1.165997671 0.312837704 0.085560615 0.276530706 5.430511988 0.059651567 0.023673807 60.87505161 -1.784439342 0.147036612 WREEQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 WREEQR 6 1 P09497-2;P09497;H0Y9Q6;F8VW50;Q2TAC6-3;Q2TAC6-2;Q2TAC6;A0A0C4DG89;Q7L014;D6RJA6 P09497-2;A0A0C4DG89 CLTB;KIF19;DDX46 Clathrin light chain B;Kinesin-like protein;Kinesin-like protein KIF19;Probable ATP-dependent RNA helicase DDX46 0 ;;;;;;; 162.07 0.0075784 4641830000 4186380 4069170 2338377 2804023 3486194 4007250 3887390 4225090 3475975 FALSE TRUE 3633139.276 4042439.354 3469223.939 3440719.279 3416825.56 4161411.501 3510391.516 3321587.383 3065049.195 1.185344523 1.318882372 1.131865663 1.12256576 1.114770218 1.35769811 1.145296957 1.083697902 1 21.5474788 1.635415006 2.403229769 1.010902182 1.201045803 0.411952178 0.081155934 0.275300684 3.411065763 0.088488843 0.022702867 43.19316281 -1.635415006 0.190143621 WRPDEEILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WRPDEEILK 9 1 P10155-3;P10155-5;P10155-4;P10155;G5E9R9 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 ;;; 140.07 0.00010029 2121730000 2369790 2161450 1459790 1775750 2116910 1821410 2509790 2732870 2726170 FALSE TRUE 2056616.247 2147251.293 2165749.327 2178961.178 2074787.633 1891480.821 2266390.952 2148467.018 2403885.288 0.855538431 0.893241996 0.900937053 0.906433093 0.863097604 0.786843212 0.942803287 0.893747729 1 21.19693662 0.642579759 1.238407788 1.339189099 0.87574472 0.474565336 0.040240682 5.187305496 2.282386866 4.47871288 0.012110879 4.391165027 -0.642579759 -0.463444379 WRPHS(ph)PDGPR ddPTM_MDA-MB-175_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 110.15 0.0011653 13714750000 12395330 12324540 7675510 9178320 12064590 12603730 11756600 12664420 11867780 TRUE FALSE 10757255.73 12243579.29 11387412.31 11262397.84 11824528.26 13088603.65 10616446.74 9956232.338 10464784.57 1.027948131 1.169979105 1.088165001 1.076218795 1.129935183 1.250728437 1.014492623 0.951403469 1 23.31903928 2.017888561 24.87307806 0.97544578 1.123268496 0.538516007 0.059800786 151.5023997 210655.0694 0.023792573 0.016037726 104.2050007 -2.017888561 0.147822716 WRPHS(ph)PGWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WRPHSPGWR 9 1 Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 WRPHS(1)PGWR;WRPHS(1)PGWR;WRPHS(1)PGWR;WRPHS(1)PGWR 117.95 0.00064725 997580000 960530 942360 676550 792470 984950 979760 891400 989100 978530 TRUE FALSE 833593.5268 936169.5751 1003731.843 972412.4256 965351.422 1017452.001 804952.1652 777588.6622 862849.2981 0.966093997 1.084974603 1.163275957 1.126978289 1.118794932 1.179176947 0.932900064 0.901187106 1 19.71874908 2.224427487 24.99865 0.935139871 1.109632176 0.600229672 0.062070601 148.239542 262203.7149 0.025599868 0.017352627 167.6592375 -2.224427487 0.174492305 WRS(ph)LQQLAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WRSLQQLAEER 11 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 WRS(1)LQQLAEER;WRS(1)LQQLAEER;WRS(1)LQQLAEER;WRS(1)LQQLAEER 273.39 2.62E-27 867590000 1294200 1164910 706867 636650 1050580 1248400 1084080 1026520 508167 TRUE FALSE 1123168.191 1157257.63 1048710.246 781211.1131 1029675.513 1296426.756 978946.0885 807006.6864 448092.0762 2.506556689 2.58263355 2.34039007 1.743416487 2.297910559 2.893215089 2.184698504 1.80098406 1 18.77343569 1.365962056 1.855709428 0.752325461 2.371449453 0.699844657 0.290799947 0.389642496 1.653129435 1.036802654 0.086368541 23.2253387 -1.365962056 1.619123992 WRS(ph)PIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WRSPIR 6 1 A0A0A0MRY4;Q96N96-6 A0A0A0MRY4 SPATA13 Spermatogenesis-associated protein 13 1 WRS(1)PIR;WRS(1)PIR 69.423 0.056649 208673000 73252 83899 45508 65422 73659 87235 76488 84512 73283 TRUE FALSE 63571.5626 83347.86194 67515.82102 80277.06501 72193.33001 90590.9869 69070.20553 66439.76647 64619.56722 0.983781931 1.289823896 1.044820074 1.242302734 1.117205409 1.401912622 1.068874468 1.028167927 1 15.97968347 2.017016574 24.99696894 1.025823444 1.183519975 0.263175401 0.118628365 283.083877 415842.2303 0.044727999 0.030148576 103.9959854 -2.017016574 0.157696531 WRVS(ph)LDVNHFAPDELTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 WRVSLDVNHFAPDELTVK 18 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 WRVS(1)LDVNHFAPDELTVK;WRVS(1)LDVNHFAPDELTVK;WRVS(1)LDVNHFAPDELTVK 228.57 1.42E-19 5809160000 2943390 2587320 1882410 2468260 2437870 2210550 3145780 3264880 2876880 TRUE FALSE 2554413.554 2570323.725 2792749.772 3028716.158 2389361.157 2295591.289 2840702.74 2566710.819 2536778.524 1.006951742 1.013223543 1.100904058 1.193922185 0.941887963 0.904923811 1.119807154 1.011799333 1 21.27456614 3.201509628 24.99995097 1.002469434 1.07565295 0.230511177 0.074750808 303.6199584 204864.9207 0.023866962 0.027063274 1590.411943 -3.201509628 0.073183516 WS(ph)GNEPTDEFSDLPLR ddPTM_MDA-MB-175_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(0.999)GNEPT(0.001)DEFSDLPLR;WS(1)GNEPTDEFSDLPLR 292.31 1.53E-45 579670000 438472 389315 323717 414211 503560 457625 419896 557780 655480 TRUE FALSE 380526.8143 386757.5641 480267.624 508263.9384 493540.1412 475230.1299 379174.5505 438503.0876 577989.9011 0.658362393 0.669142425 0.830927362 0.879364739 0.853890596 0.822211822 0.656022795 0.758669117 1 19.14068476 4.243599676 23.54173158 0.815694062 0.663752224 0.375063948 0.087280524 69.49914062 324666.0669 0.023056406 0.05697981 17522.64556 -4.243599676 -0.151941839 WS(ph)GSHQFEQLSGSILWMAPEVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 WSGSHQFEQLSGSILWMAPEVIR 23 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8Y492;H7C4S5 P15056 BRAF Serine/threonine-protein kinase B-raf 1 WS(0.957)GS(0.043)HQFEQLSGSILWMAPEVIR;WS(0.942)GS(0.058)HQFEQLSGSILWMAPEVIR;WS(0.499)GS(0.499)HQFEQLS(0.002)GSILWMAPEVIR 151.19 4.88E-08 789939000 714514 677701 471454 568736 611011 670977 698486 753163 1151148 TRUE FALSE 620089.1646 673249.1375 699450.7313 697876.2014 598853.0765 696789.9194 630746.9352 592104.9536 1015060.595 0.610888816 0.663260047 0.689072884 0.687521715 0.58996781 0.686451551 0.621388455 0.58331981 1 19.95313442 1.232904325 24.99932911 1.000000573 0.641217169 0.889051573 0.039802203 59.57460537 263276.2133 0.087496186 0.010174792 17.09638641 -1.232904325 -0.358783404 WS(ph)NSQPADLAHMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WSNSQPADLAHMGR 14 0 Q9BRG2;Q9BRG2-2;M0QZQ6 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 WS(0.568)NS(0.432)QPADLAHMGR 118.48 0.00081385 263140000 147170 152190 96363 113610 134360 150410 128860 146800 156250 TRUE FALSE 127721.1116 151190.2539 142964.4691 139406.8869 131686.4989 156196.37 116363.177 115407.9624 137778.303 0.927004534 1.097344434 1.037641385 1.011820322 0.955785461 1.133679009 0.844568227 0.837635244 1 17.07198919 2.220185182 24.99966086 0.880248518 1.026928064 0.414988859 0.073916369 203.737608 277181.649 0.028724717 0.019406669 166.0294703 -2.220185182 0.146679546 WS(ph)PIASTLPELVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WSPIASTLPELVQR 14 0 Q13561;Q13561-3;Q13561-2;H0YI98 Q13561 DCTN2 Dynactin subunit 2 1 WS(1)PIASTLPELVQR 152 7.12E-06 14003000 21371 19253 14288 14353 19384 20457 15850 25655 20646 TRUE FALSE 18546.7682 19126.52578 21197.72459 17612.06802 18998.29632 21243.99403 14312.86944 20168.8779 18205.2534 1.018759135 1.050604754 1.164374048 0.967416802 1.043561213 1.166915591 0.786194464 1.107860322 1 14.1520672 WS(ph)PPQNYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 WSPPQNYK 8 0 H3BRF9;Q96K21-2;Q96K21;H3BRM1;Q96K21-3 H3BRF9;Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 WS(1)PPQNYK;WS(1)PPQNYK;WS(1)PPQNYK;WS(1)PPQNYK;WS(1)PPQNYK;WS(1)PPQNYK 134.57 0.00091378 12256160000 4486350 3759080 2692030 3313800 4115640 3308230 4555970 5129000 5318810 TRUE FALSE 3893467.481 3734386.356 3993904.712 4066248.938 4033746.816 3435499.749 4114132.731 4032203.264 4690026.341 0.830158979 0.796239954 0.851574047 0.866999169 0.860069117 0.732511824 0.877208875 0.859740004 1 22.16116459 0.935453422 1.542247143 1.21590928 0.8283089 0.619814204 0.041489007 1.684000787 1.912212797 1.2659533 0.011612776 8.618931352 -0.935453422 -0.38760038 WS(ph)TTAGFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WSTTAGFLK 9 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 WS(0.942)T(0.057)T(0.001)AGFLK 119.27 0.00089554 402920000 404290 446440 331040 323260 360350 386910 339250 424320 864630 TRUE FALSE 350862.0522 443507.3062 491132.0513 396661.1237 353179.74 401794.6781 306349.5872 333582.4701 762414.4264 0.460198601 0.581714211 0.644179903 0.520269698 0.463238532 0.527002984 0.401815045 0.43753431 1 19.54021589 1.233938972 24.99999456 1.000000746 0.503227773 0.82925578 0.070658952 62.6613539 338913.3248 0.150912086 0.019247123 17.13716476 -1.233938972 -0.496772973 WS(ph)WGGSLHGSPSIHSADPDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WSWGGSLHGSPSIHSADPDRR 21 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5 Q14244-6 MAP7 Ensconsin 1 WS(1)WGGSLHGSPSIHSADPDRR 231.29 2.83E-26 367260000 48045 61940 13727 24723 69928 85299 61900 48174 74511 TRUE FALSE 41695.73152 61533.11206 20365.42311 30336.73502 68536.56961 88580.50773 55896.94753 37872.36499 65702.39446 0.634615098 0.936542915 0.309964702 0.461729519 1.043136558 1.348208211 0.850759671 0.576422904 1 16.00365833 3.237288417 24.99769378 0.926049361 0.591076013 0.363946856 0.245470228 47.45891527 932533.4315 0.08131495 0.097377993 1726.98441 -3.237288417 -0.334973348 WSAEASGKPSPSDPGSGTATMMNS(ph)SSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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(0.144)GT(0.121)AT(0.102)MMNS(0.211)S(0.211)S(0.211)R;WSAEASGKPSPSDPGS(0.001)GT(0.007)AT(0.024)MMNS(0.323)S(0.323)S(0.323)R;WSAEASGKPSPSDPGS(0.001)GT(0.004)AT(0.01)MMNS(0.328)S(0.328)S(0.328)R;WSAEASGKPSPS(0.001)DPGS(0.097)GT(0.022)AT(0.022)MMNS(0.286)S(0.286)S(0.286)R;WSAEASGKPSPSDPGS(0.157)GT(0.135)AT(0.135)MMNS(0.19)S(0.19)S(0.19)R 173.23 1.82E-12 4046810000 3555880 3360990 2580070 3855440 4513110 3911990 2854530 5309330 5377630 TRUE FALSE 3085961.449 3338911.435 3827800.482 4730876.579 4423307.941 4062486.787 2577698.12 4173971.097 4741892.708 0.650786856 0.704130532 0.807230513 0.99767685 0.932814851 0.856722629 0.543601106 0.880233138 1 22.17703159 4.234997582 3.2970534 0.854471114 0.665748489 0.270504268 0.127413468 0.353832847 7.88026656 0.035311933 0.098817294 17178.98824 -4.234997582 -0.188722625 WSAEASGKPSPSDPGSGTATMMNSS(ph)SR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WSAEASGKPSPSDPGSGTATMMNSSSR 27 1 Q5JRA6-2;Q5JRA6;Q5JRA6-4 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 1 WSAEASGKPSPSDPGSGTATMMNS(0.12)S(0.44)S(0.44)R 162.08 7.59E-12 1464100000 878230 794070 629450 942120 1132100 915490 703550 1221900 1221400 TRUE FALSE 762169.6803 788853.7019 933854.1254 1156042.745 1109573.425 950709.4927 635319.8293 960606.1938 1077007.483 0.707673523 0.732449601 0.8670823 1.073384134 1.030237433 0.882732485 0.589893607 0.891921559 1 20.03859684 4.221599565 4.390375647 0.898129719 0.715271037 0.258991455 0.130861521 0.301158827 13.58338176 0.037036851 0.09165865 16657.10658 -4.221599565 -0.182858682 WSDEACR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WSDEACR 7 0 J3KNC9;O75596 J3KNC9 CLEC3A C-type lectin domain family 3 member A 0 ; 160.03 0.0031676 960110000 1834330 2118500 1163850 1288170 1707760 1837620 1829240 2121700 1824510 FALSE TRUE 1591918.643 2104583.434 1726691.753 1580668.687 1673778.917 1908314.43 1651840.586 1667990.966 1608818.506 0.989495482 1.308154665 1.073266963 0.9825028 1.040377712 1.186158925 1.026741413 1.036780072 1 20.61757015 -2 0.206064199 0.468191488 1.140820592 0.08663219 0.097197117 231.9590625 3.493340362 49.18040231 0.566957794 0.01 2 0.672629104 WSEPWVPVEALPPS(ph)PLELSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 WSEPWVPVEALPPSPLELSR 20 0 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 WSEPWVPVEALPPS(0.991)PLELS(0.009)R;WSEPWVPVEALPPS(0.962)PLELS(0.038)R;WSEPWVPVEALPPS(0.975)PLELS(0.025)R;WSEPWVPVEALPPS(0.996)PLELS(0.004)R;WSEPWVPVEALPPS(0.995)PLELS(0.005)R 206.28 1.57E-25 0 196698 217802 153445 197955 266194 294382 252406 284382 267213 TRUE FALSE 170703.8609 216371.2443 227651.5152 242903.7083 260897.2602 305707.066 227927.705 223569.1224 235623.3836 0.724477589 0.918292748 0.966166905 1.030898142 1.107263873 1.29743942 0.967339071 0.948840981 1 17.8461232 4.733174237 1.208510282 1.051824338 0.579139745 0.541882843 0.097869985 1.367467451 1.711983113 0.03262475 0.812163549 54097.13153 -4.733174237 -0.472684593 WSGPLSLQEVDEQPQHPLHVTYAGAAVDELGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WSGPLSLQEVDEQPQHPLHVTYAGAAVDELGK 32 0 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 300.9 5.50E-90 1408130000 1435590 1153870 454370 811120 942250 868320 1119320 1286380 1959910 FALSE TRUE 1245873.144 1146290.152 674104.8518 995297.1932 923501.0685 901724.8323 1010768.519 1011297.648 1728211.673 0.720903095 0.663281107 0.390059194 0.575911625 0.534368031 0.521767586 0.584863842 0.585170013 1 20.7208485 1.234140683 4.980800895 1.029807491 0.56565775 0.705685798 0.08685764 0.101025637 6.310558545 0.163877359 0.02189536 17.14512606 -1.234140683 -0.464149741 WSHDGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 WSHDGK 6 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;;;; 144.29 0.011291 2666910000 10520580 8600190 6205210 7424210 6497560 7652500 10190980 11501240 10881850 FALSE TRUE 9130258.697 8543694.786 9206070.311 9109990.352 6368271.268 7946896.627 9202660.328 9041789.329 9595410.09 0.951523553 0.890393918 0.959424373 0.949411257 0.663678906 0.828197706 0.959068997 0.942303585 1 23.19391304 2.216263635 22.58122157 0.961617811 0.872309013 0.204343886 0.086577461 141.8510469 143655.6435 0.037776753 0.025504586 164.5370227 -2.216263635 -0.089308799 WSLELEDQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WSLELEDQER 10 0 P37198 P37198 NUP62 Nuclear pore glycoprotein p62 0 ;;; 240.13 6.74E-12 936870000 816570 695710 444736 534126 657960 706990 678350 745700 668820 FALSE TRUE 708658.2056 691139.8352 659811.8172 655407.4719 644867.8833 734188.3628 612563.7214 586237.858 589752.8615 1.201618935 1.17191434 1.118793753 1.111325633 1.093454437 1.244908521 1.038678676 0.99403987 1 19.16975099 2.064613724 7.544929733 1.00237375 1.150800706 0.70918424 0.044537928 0.121373967 12.06313305 0.018409177 0.012350587 116.0416042 -2.064613724 0.148426956 WSNS(ph)QPADLAHMGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 WSNSQPADLAHMGR 14 0 Q9BRG2;Q9BRG2-2;M0QZQ6 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 WS(0.001)NS(0.999)QPADLAHMGR;WSNS(1)QPADLAHMGR;WS(0.023)NS(0.977)QPADLAHMGR;WS(0.019)NS(0.981)QPADLAHMGR;WSNS(1)QPADLAHMGR;WS(0.209)NS(0.791)QPADLAHMGR 248.23 4.14E-18 3110790000 3007160 2905950 1846150 2265490 2884740 2814140 2453420 3044740 2974640 TRUE FALSE 2609756.187 2886860.623 2738954.315 2779904.13 2827339.318 2922401.787 2215487.706 2393646.045 2622981.448 0.994957928 1.100602761 1.044214139 1.059826074 1.077910528 1.114152671 0.844644825 0.912566899 1 21.32277617 2.243653304 24.99999943 0.914614565 1.066252089 0.665969024 0.048774816 67.15656367 329673.4614 0.018071716 0.013563994 175.2480943 -2.243653304 0.151637524 WSPAYSFSSDS(ph)PLDSSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WSPAYSFSSDSPLDSSPK 18 0 E7ET49;Q8NCG7-2;Q8NCG7-4;Q8NCG7 E7ET49 DAGLB Sn1-specific diacylglycerol lipase beta 1 WSPAYSFS(0.002)S(0.001)DS(0.997)PLDSSPK 229.4 1.22E-19 0 35798 29997 21933 27158 32950 35918 34373 36850 38056 TRUE FALSE 31067.2036 29799.94773 32539.87216 33324.63898 32294.35947 37299.7887 31039.51175 28969.91427 33557.06303 0.925802224 0.888038018 0.969687727 0.993073767 0.962371452 1.111533172 0.924977008 0.863303032 1 15.03432883 4.228625339 24.62850662 0.967412151 0.906920123 0.159463173 0.063135183 335.0887112 830657.3841 0.017824488 0.037833491 16928.76744 -4.228625339 -0.060492027 WTDGSLS(ph)PPAKEPLASDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WTDGSLSPPAKEPLASDSR 19 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 WT(0.001)DGS(0.067)LS(0.932)PPAKEPLASDSR;WTDGS(0.002)LS(0.998)PPAKEPLASDSR;WTDGS(0.013)LS(0.987)PPAKEPLASDSR;WTDGS(0.003)LS(0.997)PPAKEPLASDSR 166.91 1.15E-11 2186220000 2581700 2696450 1865750 2319620 2938940 2693480 3359560 3776020 3211310 TRUE FALSE 2240521.804 2678736.842 2768032.941 2846325.174 2880460.844 2797099.919 3033750.388 2968547.508 2831672.59 0.79123618 0.94599102 0.977525774 1.005174533 1.017229483 0.987790724 1.071363405 1.048337127 1 21.43322303 5.699317297 0.764553916 1.031190752 1.52E-21 0.90002528 0.024085848 2.964044269 0.446665024 0.009316338 3.672467959 500399.9952 -5.699317297 -1.031190752 WTELAGCTADFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WTELAGCTADFR 12 0 Q12907;D6RBV2;D6RDX1;D6RIU4 Q12907 LMAN2 Vesicular integral-membrane protein VIP36 0 ;;; 113.46 0.00045683 838420000 649766 666888 421316 501448 727823 704599 581622 741635 730826 FALSE TRUE 563897.7768 662507.1688 625065.8268 615309.4326 713340.7463 731705.3795 525216.388 583042.1267 644428.5828 0.875035329 1.028053669 0.969953605 0.954813999 1.106935299 1.135432845 0.815011007 0.90474281 1 19.29766096 2.226828111 24.99999155 0.902385365 1.012292324 0.251890919 0.08529271 306.9708219 654097.6289 0.035407558 0.024084961 168.5885639 -2.226828111 0.109906959 WTELDTNQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WTELDTNQHR 10 0 Q5VSL9;Q5VSL9-2;Q5VSL9-4 Q5VSL9 STRIP1 Striatin-interacting protein 1 0 ; 91.656 0.0094211 0 468500 436580 263800 322570 404540 444500 421540 446820 452380 FALSE TRUE 406586.538 433712.0772 391374.5624 395814.4487 396490.4455 461600.2026 380659.1157 351271.0202 398900.1518 1.019268948 1.087269772 0.981134153 0.992264473 0.993959124 1.157182319 0.954271674 0.880598863 1 18.60566815 2.019327755 24.99856818 0.927470084 1.035804929 0.352222258 0.059393019 217.0403702 280719.4373 0.023709766 0.015982899 104.550895 -2.019327755 0.108334844 WTETEIEMLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WTETEIEMLR 10 0 F8W038;F8W1H0;H0YIS7;Q8IXM2;Q8IXM2-3 F8W038 C17orf49;RNASEK-C17orf49;BAP18 Chromatin complexes subunit BAP18 0 ; 118.18 0.0019997 90450000 175868 127303 80393 96740 139495 132342 145676 157073 160575 FALSE TRUE 152626.5982 126466.7382 119271.3237 118706.2956 136719.3224 137433.2824 131548.3639 123484.1613 141592.0064 1.077932307 0.893177104 0.842359161 0.838368624 0.965586447 0.970628822 0.929066317 0.872112518 1 17.11138029 WTETYVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 WTETYVR 7 0 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;;; 179.16 0.0016406 1747460000 2143730 2448170 1566920 1792890 2208110 2509860 2083730 2442900 2475140 FALSE TRUE 1860430.649 2432087.81 2324687.753 2199993.077 2164172.931 2606415.938 1881650.185 1920504.846 2182531.769 0.852418588 1.114342455 1.065133523 1.008000483 0.991588284 1.194216724 0.862141029 0.879943593 1 21.05757122 2.196155792 24.99997314 0.904765187 1.038917128 0.274640569 0.094265909 164.9804281 97263.83967 0.036513158 0.024617385 157.0926231 -2.196155792 0.134151941 WTGPEISPNTSGS(ph)SPVIHFTPSDLEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WTGPEISPNTSGSSPVIHFTPSDLEVR 27 0 A0AVK6 A0AVK6 E2F8 Transcription factor E2F8 1 WT(0.005)GPEIS(0.004)PNT(0.027)S(0.179)GS(0.39)S(0.39)PVIHFT(0.005)PS(0.001)DLEVR;WTGPEISPNT(0.001)S(0.006)GS(0.523)S(0.47)PVIHFTPSDLEVR 91.583 0.004044 330640000 88742 101088 51897 77242 98382 109925 88087 122274 96751 TRUE FALSE 77014.51986 100423.9463 76994.56279 94780.97667 96424.39068 114153.8859 79544.3363 96126.65664 85313.207 0.902726818 1.177120751 0.902492891 1.1109766 1.130239902 1.338056438 0.932380098 1.126750008 1 16.38048148 3.602254598 17.66457134 1.108335766 1.011411307 0.141464363 0.127990069 4.595715486 632.2377513 0.033702356 0.049988628 4001.792798 -3.602254598 -0.096924459 WTGPEISPNTSGSS(ph)PVIHFTPSDLEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WTGPEISPNTSGSSPVIHFTPSDLEVR 27 0 A0AVK6 A0AVK6 E2F8 Transcription factor E2F8 1 WTGPEISPNTSGS(0.03)S(0.97)PVIHFTPSDLEVR;WTGPEISPNTSGS(0.094)S(0.906)PVIHFTPSDLEVR 193.97 1.16E-18 671650000 208572 227230 109017 174576 233300 239690 194982 247770 191731 TRUE FALSE 181008.6817 225737.3112 161737.9858 214216.149 228657.7864 248911.0294 176072.6757 194786.3136 169064.7796 1.070646897 1.335211933 0.956662802 1.267065497 1.35248623 1.472281986 1.041450952 1.152140109 1 17.36721662 WTKPSSFS(ph)DSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WTKPSSFSDSER 12 1 Q8NC56;H0Y9B7;Q8NC56-2 Q8NC56 LEMD2 LEM domain-containing protein 2 1 WTKPS(0.012)S(0.06)FS(0.922)DS(0.007)ER;WT(0.004)KPS(0.041)S(0.193)FS(0.757)DS(0.005)ER;WTKPS(0.002)S(0.006)FS(0.99)DS(0.002)ER;WTKPS(0.001)S(0.003)FS(0.996)DS(0.001)ER 147.09 3.95E-05 4003450000 3013110 2687040 1948630 3101730 3876360 3513460 2429910 4901140 4090030 TRUE FALSE 2614919.879 2669388.657 2890993.986 3806025.203 3799228.02 3648625.08 2194257.702 3853069.352 3606511.313 0.725055227 0.740158127 0.801604025 1.055320467 1.053435769 1.011677148 0.608415588 1.068364693 1 21.78217252 3.923076251 4.964800689 0.959524032 0.739932749 0.366110723 0.132482796 0.24336244 10.77040766 0.036155439 0.065750007 8376.76343 -3.923076251 -0.219591284 WTLGFCDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WTLGFCDER 9 0 M0R1L2;O95336;M0R0U3;M0R261 M0R1L2 PGLS 6-phosphogluconolactonase 0 ;;; 214.23 1.59E-06 1085600000 1591090 1726260 1000130 1067080 1389110 1534860 1313450 1596970 1699070 FALSE TRUE 1380823.425 1714920.084 1483796.213 1309376.823 1361469.429 1593907.057 1186071.821 1255470.393 1498207.88 0.921650088 1.14464762 0.990380729 0.873962045 0.90873199 1.063875767 0.791660381 0.837981438 1 20.51480638 3.928392617 5.116706726 0.904376281 1.041068863 0.228574281 0.092979822 0.263532157 12.83085458 0.024675945 0.044795147 8479.936829 -3.928392617 0.136692582 WTS(ph)QDSLLGMEFSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WTSQDSLLGMEFSGR 15 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 WT(0.044)S(0.956)QDSLLGMEFSGR;WT(0.02)S(0.979)QDS(0.001)LLGMEFSGR 195.57 9.83E-09 105710000 302240 278680 220689 231633 298500 338660 279080 299800 387570 TRUE FALSE 262298.2182 276849.3327 327414.9386 284228.8129 292560.434 351688.4693 252014.8646 235690.103 341751.9161 0.7675106 0.810088604 0.958048582 0.831681695 0.856060845 1.02907534 0.737420487 0.689652616 1 18.3825899 4.471570086 24.97955551 0.854034533 0.778155057 0.082075734 0.107497511 384.7336674 1731261.386 0.028428503 0.07573724 29618.97915 -4.471570086 -0.075879477 WTSQDSLLGMEFSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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 ;;;;;;; 371.17 3.21E-97 6603655000 2851642 2784992 1923003 2096388 2925580 3424077 2888641 3063271 3298328 FALSE TRUE 2474790.285 2766697.204 2852973.683 2572404.937 2867366.682 3555803.458 2608501.04 2408214.335 2908403.421 0.850910251 0.951276973 0.980941523 0.884473219 0.985890286 1.222596367 0.896884188 0.828019358 1 21.47179597 4.733620568 4.371722712 0.96119385 0.843429033 0.108340164 0.104668698 0.5549386 25.82015415 0.027624698 0.201735554 54152.75648 -4.733620568 -0.117764817 WTTLNSLQLHGLQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WTTLNSLQLHGLQLR 15 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 101.39 0.0017911 272740000 216730 179490 132910 161470 213380 226200 179380 206740 235250 FALSE TRUE 188088.5814 178310.9184 197185.7206 198134.2314 209134.1555 234902.0604 161983.7552 162530.2599 207439.013 0.906717491 0.85958237 0.950572015 0.955144495 1.008171763 1.132390947 0.780874113 0.783508644 1 17.66232772 2.190505284 24.99999985 0.836863044 0.964147193 0.243442375 0.092698315 153.1444248 79669.71287 0.039280003 0.026482637 155.0619654 -2.190505284 0.127284149 WTVHGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WTVHGK 6 0 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 77.72 0.071677 260460000 1108700 918670 689310 923860 910720 893200 1077100 1204900 1519300 FALSE TRUE 962182.4859 912635.1963 1022662.622 1133636.533 892598.4538 927561.982 972643.0078 947241.5115 1339690.085 0.71821274 0.681228597 0.76335761 0.84619312 0.666272345 0.692370566 0.726020905 0.707060179 1 20.35346786 1.236284875 24.98995731 1.000000358 0.725037238 0.745300994 0.050505825 31.8128514 349255.0862 0.081843727 0.012635097 17.22998404 -1.236284875 -0.274963119 WVAIQSVSAWPEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WVAIQSVSAWPEKR 14 1 Q96KP4;Q96KP4-2;J3QKT2;A0A087WYZ1;J3KSV5;J3QRA8;J3QRD0;J3QKQ0;J3QLU1;J3QR27;J3QL02;J3QQN6;J3KSS4 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 198.78 3.46E-08 456720000 382220 296170 160630 209130 300580 291390 299530 375680 227910 FALSE TRUE 331708.6586 294224.4398 238311.2053 256616.1629 294599.0461 302599.9619 270481.6267 295343.7555 200966.7394 1.650564962 1.464045446 1.185824112 1.276908625 1.465909468 1.505721607 1.345902449 1.469615103 1 17.61659723 -1.999999999 0.034904689 8.73E-09 2.310963309 0.195667633 0.165110222 5620.41552 19.37780327 955.5267358 428.5717391 0.01 1.999999999 2.3109633 WVCSSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 WVCSSLR 7 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;; 216.57 8.63E-05 17215300000 2809640 5845320 3840661 3229447 5791810 6409160 5337580 5046820 6338430 FALSE TRUE 2438338.955 5806921.708 5698017.506 3962742.3 5676564.312 6655724.532 4819942.313 3967596.817 5589108.026 0.436266206 1.038971099 1.019486022 0.709011578 1.015647629 1.190838413 0.862381312 0.709880145 1 22.41418663 4.74688877 24.41363471 0.926309518 0.436265863 0.527133371 0.15015123 697.4188437 2044389.71 0.038996183 0.426837343 55832.7179 -4.74688877 -0.490043656 WVDGVDEIQYDVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WVDGVDEIQYDVGR 14 0 H3BU86;O14662;F8W9Z6;B7ZBM8;O14662-6;O14662-2;O14662-5;B7ZBM4;B7ZBM5;H0YEW0;E9PND6;Q96NX8;O14662-4;O14662-3 H3BU86;Q96NX8 STX16-NPEPL1;STX16 Syntaxin-16 0 ; 113.24 0.0012726 116474000 184298 180591 109332 111520 164655 160414 162756 159463 150944 FALSE TRUE 159942.5523 179404.6858 162205.3209 136842.3205 161378.6876 166585.2304 146971.9482 125363.0784 133099.5723 1.20167593 1.34789829 1.2186765 1.028119912 1.212465862 1.251583514 1.104225548 0.94187439 1 17.02214641 1.960108601 3.574552661 0.972872213 1.208004605 0.607143894 0.0790972 0.162482379 4.096474364 0.046633339 0.023308977 91.22389274 -1.960108601 0.235132392 WVDLTMDDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WVDLTMDDIR 10 0 F5GWE5;Q00169 F5GWE5 PITPNA Phosphatidylinositol transfer protein alpha isoform 0 76.679 0.082064 101400000 58046 64149 40228 52614 62596 61611 53207 64483 73923 FALSE TRUE 50375.07403 63727.601 59682.39535 64560.81285 61350.46207 63981.21504 48046.99333 50693.81226 65183.90715 0.772814583 0.977658502 0.915600153 0.99044098 0.941190314 0.981549248 0.737099008 0.777704413 1 15.99222821 2.250504094 24.99423897 0.821435053 0.934665969 0.174610021 0.0910858 293.1472927 613472.5744 0.033261704 0.025558096 178.034469 -2.250504094 0.113230915 WVDLTMDDIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WVDLTMDDIRR 11 1 F5GWE5;Q00169 F5GWE5 PITPNA Phosphatidylinositol transfer protein alpha isoform 0 ; 211.46 1.48E-08 287230000 607660 594640 395630 429050 567170 628740 589830 656350 347820 FALSE TRUE 527356.1914 590733.7707 586957.9913 526472.3601 555884.4266 652928.0346 532628.3774 515994.6602 306701.1158 1.719446602 1.926089408 1.913778467 1.716564867 1.812463007 2.128874011 1.736636582 1.682402292 1 18.22647389 1.065287382 1.767045093 0.33562419 1.861975081 0.823202209 0.123238445 0.601058198 1.195448068 1.813299042 0.033465899 11.62217425 -1.065287382 1.526350891 WVEENVPSSVTDVALPALLDS(ph)DEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WVEENVPSSVTDVALPALLDSDEER 25 0 Q8NBN3-3;Q8NBN3 Q8NBN3-3 TMEM87A Transmembrane protein 87A 1 WVEENVPSSVTDVALPALLDS(0.999)DEER;WVEENVPSSVTDVALPALLDS(1)DEER 68.97 0.026502 53072000 32038 30045 25383 30363 32956 32971 26077 38873 44172 TRUE FALSE 27804.09713 29847.63242 37658.3037 37257.38322 32300.24008 34239.41571 23548.05655 30560.31146 38950.03648 0.713840079 0.766305634 0.96683616 0.956542961 0.82927368 0.879059914 0.604570847 0.784602897 1 15.24933706 1.233429869 24.87463776 1.00000031 0.812027354 0.228824512 0.108096076 260.1068712 1260882.851 0.230694732 0.028284245 17.11708745 -1.233429869 -0.187972956 WVEQHLGPQFVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 WVEQHLGPQFVER 13 0 Q8TCD5;J3KSY6;J3KRC4 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 0 ;; 115.09 0.00032746 107720000 482520 532730 336814 394219 515568 531070 491124 499971 515960 FALSE TRUE 418753.7595 529230.4616 499698.377 483732.4492 505309.2055 551500.6065 443494.8701 393056.0924 454963.7966 0.920411168 1.163236428 1.098325583 1.063232839 1.110658055 1.212185696 0.974791562 0.863928285 1 18.79539222 2.036948464 9.756363085 0.921343622 1.097100619 0.430122024 0.081414911 0.28195829 71.65677263 0.031596646 0.021228685 108.8800883 -2.036948464 0.175756997 WVESLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 WVESLK 6 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;; 132.94 0.034151 11564170000 19009610 17169160 13249140 14195520 17122020 17959600 21139300 21700470 23344440 FALSE TRUE 16497441.87 17056374.66 19656468.42 17418829.78 16781325.3 18650517.43 19089213.94 17059993.36 20584686.9 0.801442449 0.828595292 0.954907331 0.84620329 0.815233449 0.906038432 0.927350221 0.828771088 1 24.29506817 WVGGQHPCFIIAEIGQNHQGDLDVAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 WVGGQHPCFIIAEIGQNHQGDLDVAK 26 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;; 285.84 1.75E-61 2403400000 1709173 1497452 1218464 1435905 1451995 1377759 1640535 2065736 2402440 FALSE TRUE 1483301.458 1487615.139 1807717.266 1761949.177 1423103.14 1430762.28 1481436.168 1623994.432 2118426.28 0.700190265 0.702226532 0.853330268 0.831725509 0.671773738 0.675389223 0.699309758 0.766604176 1 21.01456149 1.240571748 3.985651161 1.028899917 0.735881997 0.642826131 0.061927016 0.169924669 4.690199366 0.145352982 0.017042896 17.40090148 -1.240571748 -0.29301792 WVGGQHPCFIIAEIGQNHQGDLDVAKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WVGGQHPCFIIAEIGQNHQGDLDVAKR 27 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ; 245.04 8.72E-46 1647230000 462150 463584 259300 240855 401418 352904 480786 585350 138870 FALSE TRUE 401075.7066 460538.6862 384698.3473 295544.809 393430.5672 366480.4452 434159.4477 460177.4577 122452.9468 3.275345486 3.760944087 3.141601385 2.413537744 3.212912204 2.992826672 3.545520619 3.75799415 1 16.90186797 4.047558973 7.685132058 2.971162216 3.506658946 0.103197649 0.769035564 0.623100386 85.09462411 0.19458066 0.406765406 11157.29646 -4.047558973 0.535496729 WVIYNDQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WVIYNDQK 8 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 131.06 0.0023756 334860000 1014640 727770 577650 644100 774240 655290 913280 1065910 994220 FALSE TRUE 880552.7532 722989.231 857003.4721 790352.7495 758834.1388 680499.4303 824710.2462 837973.4414 876684.4442 1.00441243 0.824685821 0.977550677 0.901524779 0.86557272 0.776219351 0.940715045 0.955843858 1 19.74169812 1.771507293 2.773542525 0.984092215 0.890854583 0.213605975 0.067073803 0.364587962 5.523017191 0.049694615 0.018053933 59.08908876 -1.771507293 -0.093237632 WVLCNYDFQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WVLCNYDFQAR 11 0 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;K7EN83;Q8TE68-4;Q8TE68-3 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 0 ; 121.5 0.00095446 884270000 400500 420630 265500 274720 419180 382310 387290 470660 435330 FALSE TRUE 347572.9103 417866.8538 393896.688 337099.3748 410839.1381 397017.7131 349730.6754 370013.0217 383865.7833 0.905454264 1.088575414 1.026131281 0.878169895 1.070267672 1.034261792 0.911075409 0.963912486 1 18.55024244 2.250773678 24.99975396 0.95752354 1.003260232 0.076226071 0.068693332 552.2417114 1130421.827 0.025086615 0.019290163 178.1450165 -2.250773678 0.045736692 WVNDPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 WVNDPHR 7 0 Q9H4A6 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 0 ;;; 117.4 0.0052398 642790000 1037890 946070 762290 881340 934270 986780 891540 1031010 1644370 FALSE TRUE 900730.2068 939855.2039 1130935.994 1081461.717 915679.8549 1024742.065 805078.588 810536.5348 1449974.452 0.621204191 0.648187423 0.7799696 0.745848809 0.631514475 0.706731118 0.555236395 0.559000563 1 20.46759605 1.228764293 24.97092738 1.000000705 0.653958894 0.688977381 0.072633442 262.4224788 668869.0312 0.258285816 0.019985013 16.93418472 -1.228764293 -0.346041811 WVNPHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WVNPHK 6 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 109.94 0.029126 1580670000 1339760 1378580 1321900 1640860 1347070 1416570 1649070 1682280 4426300 FALSE TRUE 1162707.321 1369524.017 1961175.261 2013442.342 1320265.942 1471066.365 1489143.445 1322537.514 3903027.856 0.297898802 0.350887585 0.502475343 0.515866762 0.338267107 0.376903886 0.381535439 0.33884911 1 21.89616233 1.235653811 24.99957652 1.000000824 0.389782149 0.883232472 0.069947847 27.3584575 235248.3641 0.123280788 0.018121885 17.20496571 -1.235653811 -0.610218674 WVNPHKL ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 WVNPHKL 7 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;; 80.18 0.049086 8031444000 5127029 6866680 4251446 4479909 6588290 6915580 7196560 7512160 5601100 FALSE TRUE 4449479.127 6821572.327 6307459.506 5497140.81 6457195.919 7181626.838 6498638.719 5905743.044 4938944.339 0.900896795 1.38118024 1.277086574 1.113019389 1.307404068 1.454081347 1.315795092 1.195750071 1 22.23577128 4.751532822 24.15915563 1.257737795 0.900896427 0.424979037 0.129621362 1376.714149 2563889.047 0.032395865 0.561625443 56432.95886 -4.751532822 -0.356841368 WVNSHLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WVNSHLAR 8 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;P11277-3;P11277;P11277-2;Q01082-3;O15020;O15020-2;A4QPE4;E9PJZ2;A0A494C1G7 Q01082;Q01082-3;O15020 SPTBN1;SPTB;SPTBN2 "Spectrin beta chain, non-erythrocytic 1;Spectrin beta chain, erythrocytic;Spectrin beta chain, non-erythrocytic 2" 0 126.07 0.001235 615200000 468470 546420 420040 418000 606120 701520 503790 546150 553400 FALSE TRUE 406560.5025 542830.531 623172.7489 512913.2887 594059.3979 728507.9283 454932.5233 429360.0726 487977.6824 0.833153886 1.112408519 1.277051741 1.051099891 1.217390506 1.49291239 0.932281413 0.879876454 1 18.89645564 2.057616086 24.99999954 0.923766919 1.16813352 0.284748854 0.168826704 92.62542526 40190.17613 0.069182232 0.046642645 114.1868484 -2.057616086 0.244366601 WVPEITHHCPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WVPEITHHCPK 11 0 A0A590UJK8;P60953-1;P60953;A0A494C1M1;Q5JYX0;A0A494BZX6 A0A590UJK8 CDC42 Cell division control protein 42 homolog 0 ; 179.57 4.07E-06 1609740000 1143470 1242580 846130 1033500 1346420 1054240 1250800 1542940 1648700 FALSE TRUE 992357.5423 1234417.41 1255321.298 1268171.971 1319628.876 1094797.295 1129497.609 1212994.288 1453792.564 0.682599132 0.849101475 0.86348034 0.872319753 0.907714697 0.753062935 0.776931755 0.834365451 1 20.47139 7.999999417 0.024446383 1.464992622 2.28E-11 0.18500027 0.078563817 12013.73551 29.15755845 658.7943249 1155.848092 99999865.71 -7.999999417 -1.464992622 WVPFDGDDIQLEFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 WVPFDGDDIQLEFVR 15 0 A0A0C4DGS1;P39656-2;P39656-3;P39656 A0A0C4DGS1 DDOST Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit 0 ;; 169.62 2.76E-06 226900000 339440 287648 216822 318910 373100 344480 242925 441390 396300 FALSE TRUE 294582.144 285758.4213 321677.8444 391323.3897 365676.04 357732.3685 219366.1709 347002.1834 349449.8655 0.842988288 0.817737964 0.920526451 1.119826986 1.046433483 1.023701549 0.627747189 0.992995613 1 18.41472597 4.125809497 4.920267805 0.959575928 0.831532329 0.156524369 0.12945127 0.419118869 16.10020286 0.0352047 0.077351157 13360.09349 -4.125809497 -0.128043599 WVTYFNKPDIDAWELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WVTYFNKPDIDAWELR 16 1 H3BRI0;H3BNX8;P20674 H3BRI0 COX5A "Cytochrome c oxidase subunit 5A, mitochondrial" 0 83.418 0.0071456 386110000 290420 295100 190670 392680 367840 310870 287570 407960 418710 FALSE TRUE 252040.2612 293161.4687 282878.6498 481843.9957 360520.7037 322829.3701 259681.5057 320720.9287 369210.5808 0.682646366 0.794022392 0.766171568 1.305065512 0.976463629 0.874377352 0.703342535 0.868666678 1 18.49408437 3.960431837 24.99707916 0.935865597 0.748774308 0.284671912 0.15306272 777.0581571 490905.1774 0.043630729 0.075586929 9129.181409 -3.960431837 -0.187091289 WVTYFNKPDIDAWELRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WVTYFNKPDIDAWELRK 17 2 H3BRI0;H3BNX8;P20674 H3BRI0 COX5A "Cytochrome c oxidase subunit 5A, mitochondrial" 0 ; 76.586 0.011019 525180000 453030 395810 387980 482560 368460 342390 355290 577570 237500 FALSE TRUE 393160.9377 393209.898 575608.4257 592132.6235 361128.3669 355561.9649 320834.0305 454061.1502 209423.0206 1.877353008 1.877586795 2.748544187 2.827447632 1.724396706 1.697817002 1.531990273 2.168152999 1 17.67606051 3.126506823 9.766625325 1.685575044 2.329246454 0.413072599 0.416213786 0.338784149 27.80012001 0.129851834 0.147350886 1338.156238 -3.126506823 0.643671409 WVVIGDENYGEGSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WVVIGDENYGEGSSR 15 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ; 152.55 6.54E-06 240260000 172745 163639 122966 185959 209988 214872 173167 191833 181792 FALSE TRUE 149916.3106 162564.0446 182432.7689 228183.8332 205809.6496 223138.2649 156373.291 150811.0058 160300.7569 0.935218982 1.014119009 1.138065549 1.423473211 1.28389693 1.391997575 0.975499393 0.940800335 1 17.29042171 2.128037163 10.42288795 0.963954629 1.200785544 0.332516499 0.150635868 0.401134067 35.55316238 0.067647231 0.045597195 134.2879869 -2.128037163 0.236830915 WVWDQEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 WVWDQEEER 9 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDG6;H0YDQ3;U3KQE6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 0 ;;;;; 188.66 9.10E-05 1428560000 2039060 2258960 1385200 1589738 2124990 2193660 2046530 2420670 2157350 FALSE TRUE 1769593.055 2244120.743 2055087.353 1950712.311 2082706.856 2278051.52 1848057.836 1903028.558 1902310.541 0.930233533 1.1796816 1.080311184 1.025443674 1.094830109 1.197518213 0.971480626 1.000377445 1 20.85932135 2.172859591 24.99999705 0.99185442 1.086563939 0.261764553 0.074400065 74.8055811 28463.21369 0.02883363 0.019439633 148.8879641 -2.172859591 0.094709519 WWDNLNHLNQFVDHEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WWDNLNHLNQFVDHEK 16 0 Q13907;Q13907-2 Q13907 IDI1 Isopentenyl-diphosphate Delta-isomerase 1 0 325.17 5.60E-59 510510000 358750 293520 306080 383410 346470 287930 411550 411360 710370 FALSE TRUE 311340.2785 291591.8478 454101.3118 470469.1006 339575.9249 299006.8534 371637.9443 323393.8652 626390.8679 0.497038342 0.465511014 0.724948806 0.751079118 0.542115063 0.477348679 0.593300387 0.516281258 1 19.25670365 1.233940784 24.99973348 1.000000642 0.572757586 0.655846985 0.097666902 95.68667624 517733.4457 0.198099236 0.025316506 17.13723625 -1.233940784 -0.427243056 WWGNRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WWGNRK 6 1 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9R4 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 115.01 0.039758 2719600000 1885100 1896810 1271330 1286140 1824690 1644760 1957770 2196000 841400 FALSE TRUE 1635979.259 1884349.73 1886149.44 1578177.744 1788382.239 1708034.982 1767905.767 1726402.489 741930.6505 2.205029887 2.539792269 2.542217981 2.127122991 2.410443938 2.302149103 2.382845035 2.32690547 1 19.50092482 1.238100377 6.452436156 0.960342524 2.362093503 0.915668955 0.129219662 0.031059722 5.919635243 0.19102961 0.030843466 17.30216213 -1.238100377 1.401750979 WWTCFVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WWTCFVK 7 0 O15145 O15145 ARPC3 Actin-related protein 2/3 complex subunit 3 0 ; 119.89 0.01089 849300000 814510 1038200 610150 685650 913290 845300 1030720 1067750 1016630 FALSE TRUE 706870.4398 1031379.996 905220.5808 841337.312 895117.3158 877819.238 930760.933 839419.9717 896445.1595 0.788526138 1.150522132 1.009789133 0.938526248 0.998518767 0.979222464 1.038279836 0.936387422 1 19.7738558 4.770567138 24.48077021 0.999318212 0.788525627 0.562167752 0.060139808 8929.443487 6829684.871 0.014372735 2.096746937 58961.31189 -4.770567138 -0.210792585 WYENFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WYENFQR 7 0 A0A087WYW7;Q53FT3 A0A087WYW7 C11orf73 Protein Hikeshi 0 96.285 0.029881 200670000 157920 176220 98882 116140 170980 161310 159100 164750 164150 FALSE TRUE 137050.4719 175062.3992 146701.6659 142511.3621 167577.8325 167515.7001 143670.5065 129519.4946 144744.374 0.946844897 1.209459092 1.013522404 0.984572721 1.157750232 1.157320975 0.992580938 0.894815398 1 17.14314775 2.029193976 7.950039272 0.940897298 1.080407081 0.299297176 0.085421754 0.212931167 48.45703831 0.034271518 0.022775311 106.9532475 -2.029193976 0.139509784 WYFDVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WYFDVER 7 0 K7EM91;O43291-2;O43291 K7EM91 SPINT2 Kunitz-type protease inhibitor 2 0 89.142 0.042085 51547000 117340 124720 76308 92833 131990 160900 94998 137660 145160 FALSE TRUE 101833.2217 123900.7061 113210.804 113912.1515 129363.6572 167089.9271 85785.10858 108222.4803 127999.3502 0.795576084 0.967979181 0.884463897 0.889943202 1.010658703 1.305396683 0.670199563 0.84549242 1 16.96577696 4.747845098 22.22660636 0.935371681 0.79557572 0.077071642 0.1601654 828.5895564 1983388.715 0.039963003 0.442902395 55955.79856 -4.747845098 -0.139795962 WYHPGCFVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WYHPGCFVK 9 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 130.34 0.00036399 2229400000 7274500 7426300 3979900 5017700 6737500 5903700 6943700 7898200 6728000 FALSE TRUE 6313156.394 7377516.146 5904592.952 6157045.476 6603436.932 6130819.159 6270301.043 6209231.394 5932623.505 1.06414243 1.243550369 0.995275184 1.037828453 1.11307197 1.033407759 1.056918754 1.046624885 1 22.5002388 4.22497223 24.9998863 1.044129627 1.15384644 0.438381849 0.053234615 175.7527127 323350.9791 0.012524812 0.026298911 16786.96674 -4.22497223 0.109716813 WYLATSDKER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WYLATSDKER 10 1 A0A2R8YGH5;H7C1E4;P61966;P61966-2 A0A2R8YGH5 AP1S1 AP-1 complex subunit sigma-1A 0 119.27 0.00065126 621470000 600250 818830 443390 628690 881130 822940 1031100 1144000 768440 FALSE TRUE 520925.4417 813451.0518 657814.8871 771443.6734 863597.2369 854599.0343 931104.0807 899364.5026 677595.8986 0.768784821 1.200495832 0.970807067 1.138501096 1.274501866 1.261222265 1.374128861 1.327287406 1 19.37006562 5.536569319 0.570722612 1.268612789 3.31E-10 0.498834169 0.131814239 7.654483036 0.987232616 0.070956652 7.817507961 344008.6155 -5.536569319 -1.268612789 WYMQFDDDEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WYMQFDDDEK 10 0 M0R0N4;M0QYZ2;P53680;X6R390;P53680-2 M0R0N4 AP2S1 AP-2 complex subunit sigma 0 125.74 0.00093327 77628000 204220 183300 145100 193080 204040 177870 209850 242500 400460 FALSE TRUE 177231.8096 182095.8902 215270.8453 236921.765 199980.0032 184712.774 189498.7793 190643.2621 353118.075 0.501905233 0.51567989 0.609628508 0.67094205 0.566326159 0.52309068 0.536644235 0.539885312 1 18.42979114 1.237041423 24.99981366 1.00000054 0.55914897 0.885547821 0.049935029 13.39327763 220323.7514 0.081559087 0.013277682 17.26002511 -1.237041423 -0.44085157 WYNGTNNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WYNGTNNK 8 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 130.27 0.0024544 284240000 208080 201250 126730 158960 234200 206680 208960 230160 257650 FALSE TRUE 180581.7008 199927.9755 188017.0519 195054.2976 229539.8782 214631.1133 188695.0914 180942.0751 227190.9105 0.794845623 0.879999887 0.827572949 0.858547981 1.01033918 0.944716991 0.830557397 0.796431841 1 17.79354559 5.001001905 0.938169727 0.892446095 0.714546534 0.173494512 0.071331288 7.457731896 3.764375757 0.025687998 1.512025965 100230.9634 -5.001001905 -0.177899562 WYNHIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WYNHIK 6 0 P24534;C9JZW3;F2Z2G2 P24534 EEF1B2 Elongation factor 1-beta 0 ; 94.95 0.0439 4492800000 5616300 5304400 3203400 4136400 5034200 4764500 5386500 6067100 5862500 FALSE TRUE 4874091.725 5269555.047 4752574.955 5075632.841 4934029.269 4947793.398 4864118.059 4769697.879 5169441.929 0.942866134 1.01936633 0.919359385 0.98185315 0.954460721 0.957123316 0.940936783 0.922671721 1 22.30157711 2.824996508 2.144726634 0.948045897 0.966413996 0.003560545 0.032161821 0.98372151 8.931136707 0.011531198 0.011163053 668.3385441 -2.824996508 0.018368099 WYPEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 101.72 0.084216 1255530000 858020 823220 597630 883470 927680 1053240 690710 1006590 1327290 FALSE TRUE 744630.4831 817812.2136 886645.867 1084075.366 909220.983 1093758.824 623725.0505 791338.5618 1170379.288 0.636230059 0.698758276 0.757571392 0.926259869 0.77686011 0.934533647 0.532925571 0.676138556 1 20.15854471 4.364296441 2.777900928 0.784243029 0.645365714 0.144467274 0.135296057 0.642579234 9.425533012 0.036685065 0.138301554 23136.43502 -4.364296441 -0.138877316 WYPS(ph)DVDRHSPMAEHMPSSHHSSEMMGSDASLDSDQGLGGVMVLSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WYPSDVDRHSPMAEHMPSSHHSSEMMGSDASLDSDQGLGGVMVLSQR 47 1 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 1 WY(0.131)PS(0.53)DVDRHS(0.155)PMAEHMPS(0.044)S(0.044)HHS(0.044)S(0.044)EMMGS(0.004)DAS(0.002)LDS(0.001)DQGLGGVMVLSQR 47.357 0.0072035 172680000 47578 69746 14217 27014 87457 89708 56380 69751 50672 TRUE FALSE 41290.44675 69287.83393 21092.38875 33147.94158 85716.77681 93159.12481 50912.27628 54835.29145 44681.61389 0.924103746 1.550701237 0.472059689 0.741869836 1.918390348 2.08495434 1.139445778 1.227245094 1 15.44739368 3.259486832 24.99902472 1.448617291 0.934925993 0.295730712 0.42193664 363.0346332 433688.3237 0.130488908 0.168280026 1817.551948 -3.259486832 -0.513691298 WYPSDVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WYPSDVDR 8 0 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 100.15 0.018631 0 132310 136820 95061 93505 133260 142200 119520 130890 152530 FALSE TRUE 114824.8983 135921.2204 141032.8176 114736.7394 130608.3867 147670.526 107928.9688 102900.1921 134498.0772 0.853728921 1.010581142 1.048586125 0.853073455 0.971079955 1.097937823 0.802457337 0.765068128 1 17.03722602 2.209754379 24.99995865 0.834706217 0.972194752 0.234317069 0.096929128 254.6746088 221021.7001 0.038895435 0.026228362 162.089312 -2.209754379 0.137488535 WYQMGAYQPFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 WYQMGAYQPFFR 12 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 158.76 0.00016221 465750000 514120 494240 303250 258860 483300 577400 400050 409160 295000 FALSE TRUE 446177.7394 490993.3049 449902.7143 317638.1194 473683.2756 599612.9516 361253.2126 321664.3181 260125.4361 1.715240717 1.887525158 1.729560635 1.221095961 1.820980227 2.305091577 1.388765428 1.236573874 1 17.98884795 2.011021703 24.96958397 1.188430344 1.766312637 0.516430835 0.268122657 178.072292 403419.8108 0.114550633 0.077154405 102.5703183 -2.011021703 0.577882294 WYSLSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WYSLSGR 7 0 E9PP67;E9PQ25;F2Z2Y8;E7EN89;Q9H0E2-2;Q9H0E2 E9PP67 TOLLIP Toll-interacting protein 0 107.59 0.039697 0 294960 289220 235630 227210 252510 207220 409890 306490 335980 FALSE TRUE 255980.2887 287320.0948 349581.4561 278801.5032 247485.545 215191.8875 370138.9309 240949.4986 296260.8271 0.864036907 0.969821416 1.179978668 0.941067727 0.835363714 0.726359572 1.249368452 0.813301917 1 18.17650835 4.742348091 22.23404558 0.960495677 0.864036722 0.037645717 0.158390866 347.659733 2040458.364 0.037575299 0.26488409 55252.01118 -4.742348091 -0.096458955 WYTIFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WYTIFK 6 0 Q9BZL1 Q9BZL1 UBL5 Ubiquitin-like protein 5 0 116.35 0.055015 184720000 581060 665690 387630 408840 639100 602700 678610 776030 718330 FALSE TRUE 504271.4488 661317.0386 575089.1645 501673.3707 626383.1604 625886.259 612798.5066 610082.0236 633409.8457 0.796121898 1.044058666 0.907925837 0.792020165 0.988906574 0.988122087 0.967459712 0.963171046 1 19.27277977 WYVVQTNYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 WYVVQTNYDR 10 0 A0A1B0GV06;A0A1B0GTP7;A0A1B0GUE3;A0A1B0GUG1;A0A1B0GUW4;E7EMM4;A0A1B0GW68;A0A1B0GUA4;A0A1B0GTM3;A0A1B0GTZ5;A0A1B0GUH5;Q13510-3;Q13510;Q13510-2 A0A1B0GV06 ASAH1 Acid ceramidase;Acid ceramidase subunit alpha;Acid ceramidase subunit beta 0 84.213 0.035071 578720000 107280 133640 83218 71906 139730 129830 111830 148230 80145 FALSE TRUE 93102.67619 132762.11 123462.5031 88233.35631 136949.6464 134824.6441 100984.7438 116532.168 70670.3494 1.317422044 1.878611202 1.747019849 1.248520165 1.937865704 1.907796484 1.428954925 1.64895418 1 16.10881742 0.907944762 1.952066557 2.03E-14 1.659876326 0.394909265 0.245186042 2.602966915 4.141553454 11.00762571 0.063965961 8.089929966 -0.907944762 1.659876326 Y(ph)ATPQVIQAPGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YATPQVIQAPGPR 13 0 A0A5F9ZHP4;C9J1X3;A0A5F9ZI29;A0A5F9ZGX5;A0A5F9ZHJ2;A0A499FJ16;Q07912;Q07912-3;A0A5F9ZHD0 A0A5F9ZHP4 TNK2 Activated CDC42 kinase 1 1 Y(0.997)AT(0.003)PQVIQAPGPR;Y(1)ATPQVIQAPGPR;Y(1)ATPQVIQAPGPR;Y(1)ATPQVIQAPGPR 228.54 7.48E-11 2552140000 538250 584390 388327 464907 670040 609070 623740 791720 635240 TRUE FALSE 467118.8987 580551.1036 576123.2361 570471.24 656707.5149 632501.317 563249.7908 622416.8392 560142.6509 0.833928461 1.036434385 1.028529492 1.018439212 1.172393343 1.129178998 1.005547051 1.111175588 1 19.09543476 5.484788157 1.122610229 1.076528256 3.74E-11 0.620780017 0.056716249 4.979620962 1.541878763 0.016672837 9.488979154 305343.1324 -5.484788157 -1.076528256 Y(ph)EAEY(ph)GEKITCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YEAEYGEKITCR 12 1 Q96N23;Q96N23-2;A0A1B0GU80 Q96N23 CFAP54 Cilia- and flagella-associated protein 54 2 Y(1)EAEY(1)GEKITCR 64.55 0.075036 86834000 17008 16153 7443.5 9918.4 13294 20754 11687 11002 14175 TRUE FALSE 14760.34971 16046.88988 11043.2015 12170.52431 13029.47541 21552.41981 10553.59654 8649.307918 12499.24765 1.180899053 1.283828462 0.883509297 0.97370055 1.042420774 1.724297367 0.844338542 0.691986283 1 13.60955364 2.037593208 24.99953241 0.807241302 1.167419317 0.303721824 0.237590237 183.6666401 122137.8366 0.09790545 0.066007698 109.0418491 -2.037593208 0.360178015 Y(ph)LRAFLPESGFT(ph)ILPCT(ph)RY(ph)SMETNGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YLRAFLPESGFTILPCTRYSMETNGAK 27 2 Q86Y97 Q86Y97 SUV420H2 Histone-lysine N-methyltransferase SUV420H2 4 Y(0.687)LRAFLPES(0.619)GFT(0.693)ILPCT(0.693)RY(0.687)S(0.619)MET(0.001)NGAK 41.551 0.071133 209840000 97469 64989 78026 75056 37024 29868 63426 68104 69759 TRUE FALSE 84588.2247 64562.08298 115759.6346 92098.61196 36287.29484 31017.04129 57274.95628 53540.48959 61512.17049 1.375146154 1.049582261 1.881898064 1.49724211 0.589920573 0.504242348 0.93111584 0.870404818 1 15.90858426 3.246763021 24.99999099 0.788198936 1.453077727 0.647124195 0.246465677 121.2074941 369424.5645 0.074610715 0.094650429 1765.07442 -3.246763021 0.664878791 Y(ph)MEDSTYYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YMEDSTYYK 9 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-4;Q05397-3 E7ESA6 PTK2 Focal adhesion kinase 1 1 Y(0.993)MEDS(0.007)TYYK;Y(1)MEDSTYYK 182.69 0.00047445 338230000 524580 446460 322050 382320 458640 433250 552920 584340 578640 TRUE FALSE 455255.4239 443527.1749 477794.4572 469131.5994 449513.9613 449917.4079 499297.9035 459383.4383 510233.8384 0.892248592 0.869262565 0.936422521 0.91944431 0.880995982 0.881786691 0.978566818 0.900339028 1 18.96079906 -1.753057651 0.732108185 9.999999806 0.900172409 0.443644924 0.032191621 228.0818314 1.630507854 3377.584643 0.012769822 0.017658034 1.753057651 -9.099827397 YAALSVDGEDENEGEDYAE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YAALSVDGEDENEGEDYAE 19 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 324.48 4.73E-62 729200000 559950 571460 400430 411270 561530 604890 547990 631750 612520 FALSE TRUE 485951.1888 567706.0416 594079.2874 504655.1394 550356.6516 628160.5097 494846.0141 496655.1788 540108.5834 0.899728691 1.05109613 1.099925655 0.934358673 1.018974089 1.163026341 0.916197278 0.91954691 1 19.04288995 YADEEIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 173.68 0.00064297 1701150000 1384430 1346330 925672 973892 1237540 1332490 1287830 1401290 1778540 FALSE TRUE 1201474.068 1337485.87 1373330.075 1195029.064 1212915.375 1383751.753 1162936.445 1101635.038 1568283.027 0.766107933 0.852834499 0.875690198 0.76199834 0.773403368 0.882335477 0.741534802 0.702446573 1 20.58075451 3.73115456 24.76272627 0.796221384 0.833673239 0 0.087632584 2006.118552 6707626.937 0.023802665 0.036136257 5384.613801 -3.73115456 0.037451855 YADEEIPRS(ph)PFK ddPTM_MDA-MB-175_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 218.78 2.03E-11 1882660000 1571230 1599750 1214208 1318390 1655990 1468010 1969920 2220620 1876490 TRUE FALSE 1363587.975 1589241.137 1801403.05 1617750.6 1623039.039 1524485.295 1778877.462 1745757.694 1654653.49 0.824092768 0.960467643 1.088688998 0.977697512 0.980893612 0.921332052 1.07507552 1.055059385 1 20.6580977 4.660897338 3.375167916 1.0156583 0.81343168 0.585033333 0.050164164 0.191614866 3.58707042 0.0130661 0.08732275 45803.36007 -4.660897338 -0.20222662 YADLSHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YADLSHNR 8 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;;;;; 166.52 0.00031801 2529640000 4359930 4313720 2432170 2989790 4125510 4440750 4135730 4243000 4409620 FALSE TRUE 3783754.204 4285382.889 3608375.547 3668667.516 4043420.422 4611588.526 3734647.541 3335667.469 3888319.747 0.973107782 1.102116896 0.928003812 0.94350973 1.039888869 1.186010623 0.960478506 0.857868613 1 21.89071543 2.007277089 24.99480861 0.915899486 1.028246731 0.210135543 0.082456433 226.1014129 776593.1808 0.034245729 0.023034462 101.6897288 -2.007277089 0.112347244 YADLTEDQLPSCESLKDTIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YADLTEDQLPSCESLKDTIAR 21 1 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;;; 214.92 6.16E-25 8272520000 6317170 5607230 3562170 4042790 4956620 4464740 6132510 7117080 3649690 FALSE TRUE 5482339.979 5570395.737 5284847.327 4960767.26 4857992.959 4636501.437 5537780.124 5595147.827 3218227.806 1.703527627 1.730889195 1.642160731 1.541459324 1.509524264 1.440700198 1.720754545 1.738580413 1 21.61783502 1.232463171 24.99999217 0.999998969 1.62926642 0.78891066 0.102161854 103.2216673 423174.3466 0.250369138 0.027976356 17.07902879 -1.232463171 0.62926745 YADSPGASS(ph)PEQPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YADSPGASSPEQPK 14 0 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 YADSPGAS(0.235)S(0.765)PEQPK 189.09 7.95E-07 168470000 501880 374590 300040 347380 392880 303500 448560 528800 520870 TRUE FALSE 435555.2864 372129.2936 445140.3476 426257.9384 385062.4567 315175.8414 405058.7202 415720.2351 459293.342 0.948316134 0.810221398 0.969185283 0.928073411 0.838380228 0.686219051 0.881917248 0.905130114 1 18.80905634 1.313072773 2.321949596 1.022204459 0.863147593 0.217615571 0.080134894 0.833540124 5.427982811 0.255939253 0.022258523 20.56235121 -1.313072773 -0.159056866 YAEAVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YAEAVTR 7 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;;; 128.37 0.0087583 2509890000 2737520 2584400 1263808 1318909 2047250 2420630 2109060 2455700 2576980 FALSE TRUE 2375749.796 2567422.906 1874989.776 1618387.447 2006513.73 2513753.202 1904523.686 1930567.665 2272332.36 1.04551158 1.129862405 0.825138879 0.712214232 0.883019476 1.106243632 0.838136058 0.8495974 1 21.11574243 4.241239679 24.9999908 0.883061564 1.087687043 0.376459354 0.106835496 71.66280342 668694.8661 0.027938844 0.06731839 17427.6841 -4.241239679 0.204625479 YAEEDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YAEEDRR 7 1 P38646;H0Y8S0 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;;; 144.35 0.0037842 3840018000 3387580 3308930 2720743 3932780 3464180 4144180 2999520 3744380 3756650 FALSE TRUE 2939902.72 3287193.421 4036503.415 4825777.808 3395249.596 4303609.286 2708627.012 2943673.476 3312543.117 0.88750625 0.992347361 1.218551208 1.456819621 1.024967669 1.299185893 0.817688077 0.888644577 1 21.6595078 2.228843197 24.99999834 0.89578776 1.15140091 0.325101737 0.16585296 236.0546647 607292.0433 0.069290886 0.047370524 169.3726165 -2.228843197 0.255613149 YAELLEEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YAELLEEHR 9 0 P40222 P40222 TXLNA Alpha-taxilin 0 ;;; 135.71 0.00021314 545277000 636595 583802 331187 463390 623558 658711 573673 645092 629236 FALSE TRUE 552467.3578 579966.9662 491350.141 568609.782 611150.4158 684052.0384 518038.2808 507144.0959 554848.4369 0.995708595 1.045270974 0.885557403 1.024801989 1.101472718 1.232862874 0.933657277 0.914022753 1 19.08173421 YAEYFLRPMLQYVCDNSPEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YAEYFLRPMLQYVCDNSPEVR 21 1 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 182.22 4.33E-17 280550000 155380 140960 113650 118640 148050 162620 148110 167880 143130 FALSE TRUE 134846.1393 140034.0245 168611.5201 145579.0253 145104.0947 168876.0966 133746.315 131980.1684 126209.3345 1.068432378 1.109537778 1.335967113 1.153472728 1.149709689 1.338063443 1.059718091 1.045724304 1 16.94545909 2.028672812 24.88761216 1.034106035 1.192167497 0.422158172 0.087369053 184.0689269 159768.5349 0.035479272 0.023919657 106.8249781 -2.028672812 0.158061462 YAGKDGYNYTLSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YAGKDGYNYTLSK 13 1 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ; 141.85 3.65E-05 3590600000 4566800 4258900 786970 842890 3685700 3276200 5991800 5981900 107244 FALSE TRUE 3963285.809 4230923.005 1167551.324 1034281.057 3612361.781 3402237.534 5410716.158 4702717.236 94565.73649 41.9103785 44.7405494 12.34645198 10.93716494 38.19947811 35.97748677 57.21645449 49.72961043 1 16.52902993 -1.979487091 3.60E-19 8.904060403 59.34719315 0 18.49720576 0 0.120922711 17.71311471 17.71311457 0.01048366 1.979487091 50.44313275 YAHQSGFHVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YAHQSGFHVDR 11 0 A0A0A0MSX9;P41252;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 162.49 1.45E-05 138489000 95578 112084 39806 74061 158243 171770 94690 119628 129649 FALSE TRUE 82947.12514 111347.7128 59056.31474 90877.682 155094.2739 178378.103 85506.97837 94046.48315 114322.0429 0.725556708 0.973982882 0.516578546 0.79492703 1.356643653 1.560312417 0.747948306 0.822645229 1 16.80274408 3.44768111 24.55938765 1.061503255 0.744486815 0.302232569 0.258207479 257.2144226 214570.8893 0.082398389 0.106377576 2803.374443 -3.44768111 -0.31701644 YAHVVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YAHVVLR 7 0 P62269 P62269 RPS18 40S ribosomal protein S18 0 ;;;;; 154.29 0.0016884 3386990000 4998080 4830920 3054460 4046900 5182910 5394270 4540770 5324030 6223460 FALSE TRUE 4337571.064 4799185.368 4531607.073 4965810.498 5079780.231 5601791.057 4100406.824 4185527.616 5487729.649 0.790412674 0.874530211 0.825770831 0.904893429 0.925661532 1.020784808 0.747195486 0.762706599 1 22.38777798 6.396381348 14.18065793 0.864863139 0.486269725 0 0.093878512 0 0 0.021715119 0 2491043.708 -6.396381348 -0.378593414 YALGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YALGER 6 0 P09960-4;P09960;P09960-3;P09960-2;B4DEH5 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 118.42 0.050903 211260000 330340 363190 217470 245610 317540 338770 329380 385710 324090 FALSE TRUE 286684.732 360804.181 322639.2194 301379.5044 311221.5753 351802.7011 297436.7783 303228.9181 285776.4494 1.003178298 1.262539939 1.12899163 1.054598813 1.089038568 1.231041613 1.040802274 1.061070353 1 18.1245275 2.075651542 24.99999305 1.039700985 1.129799691 0.249065576 0.076922032 51.00464221 16853.16439 0.030201256 0.020361678 119.0286593 -2.075651542 0.090098706 YALPLVGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YALPLVGHR 9 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 143.85 0.00010096 2496900000 2127730 2193500 1364980 1639840 2201500 2687400 1930750 1895590 1601420 FALSE TRUE 1846545.09 2179090.754 2025088.894 2012190.735 2157694.457 2790786.017 1743506.162 1490232.83 1412101.952 1.307657062 1.543153985 1.434095386 1.424961372 1.528001894 1.97633465 1.234688586 1.055329488 1 20.42941282 2.009845899 24.99992133 1.065634432 1.532660416 0.600657393 0.17427098 134.3340597 341089.0471 0.072081267 0.048534303 102.2929961 -2.009845899 0.467025984 YALQMEQLNGILLHLESELAQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YALQMEQLNGILLHLESELAQTR 23 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;; 275.2 7.69E-52 8103622000 2473341 2472104 1303107.7 1596674 2232869.1 2350858 2548973 2801417 2506334 FALSE TRUE 2146482.72 2455864.586 1933294.942 1959223.235 2188439.373 2441297.028 2301773.991 2202355.775 2210038.05 0.971242427 1.111231812 0.87477903 0.886511088 0.990227012 1.10464027 1.041508761 0.996523918 1 21.07563978 2.993053253 24.82664559 1.032025506 0.962127626 0.20498804 0.06937147 534.6532162 1910781.841 0.022519475 0.024577341 984.1317715 -2.993053253 -0.06989788 YALTGDEVKK ddPTM_MDA-MB-175_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 ;;; 101.93 0.0048337 1258200000 2471820 1918100 1614550 1730420 1926890 1398700 2482770 2790880 2019020 FALSE TRUE 2145162.724 1905499.875 2395351.78 2123338.309 1888548.659 1452508.894 2241991.348 2194072.031 1780333.756 1.204921671 1.070304862 1.345450971 1.192663062 1.060783492 0.815863256 1.259309576 1.232393659 1 20.7637163 3.297017021 7.443933587 1.094651203 1.204783712 0.169978035 0.138196962 0.536742633 57.40443481 0.042711513 0.054978875 1981.604688 -3.297017021 0.110132509 YALYDASFETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YALYDASFETK 11 0 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 155.15 7.37E-05 1547600000 641940 553610 455450 557550 565200 426510 741340 819760 754560 FALSE TRUE 557106.0025 549973.2995 675707.1434 684150.2491 553953.6258 442918.1157 669444.9609 644460.7034 665356.7764 0.837304169 0.826584051 1.015556116 1.028245707 0.832566294 0.665685135 1.006144349 0.968594183 1 19.34376862 YALYDATYETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YALYDATYETK 11 0 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;Q9Y281;Q9Y281-3 G3V1A4;P23528;Q9Y281 CFL1;CFL2 Cofilin-1;Cofilin-2 0 ;;;;; 290.04 4.70E-35 5688390000 5032980 4032100 2613410 3279460 3811770 3307020 4671870 5213860 4695310 FALSE TRUE 4367858.941 4005612.87 3877263.817 4024111.516 3735923.235 3434243.199 4218792.766 4098916.613 4140235.801 1.054978303 0.967484236 0.936483815 0.971952253 0.902345522 0.829480098 1.018974032 0.990020088 1 21.98128151 YAPLHLVPLIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YAPLHLVPLIER 12 0 Q7L576;Q7L576-2;Q7L576-3;Q96F07;Q96F07-2;E7EVJ5;H7C229;H0YL50;E7EW33 Q7L576 CYFIP1;CYFIP2 Cytoplasmic FMR1-interacting protein 1;Cytoplasmic FMR1-interacting protein 2 0 ; 70.488 0.047145 520760000 991140 1061550 624820 667050 1033050 1030470 911140 1111710 1067920 FALSE TRUE 860158.3378 1054576.608 926985.0419 818513.8977 1012494.326 1070112.848 822777.783 873979.4678 941671.7142 0.913437586 1.11989836 0.984403617 0.869213639 1.07520945 1.136396933 0.873741635 0.928114814 1 19.84486467 2.204590739 24.99992257 0.930227313 1.015654986 0.162411251 0.088144796 333.9848838 245791.8665 0.03613644 0.024364651 160.1735271 -2.204590739 0.085427673 YASFQVENDQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YASFQVENDQER 12 0 P53992;G5EA31 P53992 SEC24C Protein transport protein Sec24C 0 ; 202.31 0.00016677 376070000 384167 334932 349992 386297 399511 503537 522964 501820 588768 FALSE TRUE 333398.3576 332731.8096 519249.3019 474011.638 391561.5127 522908.3942 472247.0318 394509.6982 519164.5178 0.64218248 0.640898594 1.000163309 0.913027801 0.754214703 1.007211349 0.909628866 0.759893415 1 18.98583226 4.25457594 24.9629648 0.891823172 0.6415403 0.592905903 0.090592692 169.1279636 263613.8049 0.022427885 0.058922261 17971.15293 -4.25457594 -0.250282872 YASICQQNGIVPIVEPEILPDGDHDLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YASICQQNGIVPIVEPEILPDGDHDLK 27 0 H3BPS8;P04075;P04075-2;H3BQN4;P09972 H3BPS8;P04075;P09972 ALDOA;ALDOC Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase C 0 ;;;; 276.23 6.71E-61 5640080000 4106041 3701034 2778876 3751871 3595213 2861932 4071452 5122820 8300650 FALSE TRUE 3563417.278 3676721.664 4122749.728 4603790.654 3523675.295 2972032.376 3676603.212 4027344.809 7319356.613 0.48684843 0.502328532 0.563266684 0.628988434 0.48141872 0.406051042 0.502312349 0.550232079 1 22.80328541 1.232934062 4.239352054 1.050434771 0.512518969 0.877398685 0.057131765 0.081261915 2.770256411 0.135104091 0.015671999 17.09755705 -1.232934062 -0.537915801 YASICQQNGIVPIVEPEILPDGDHDLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 YASICQQNGIVPIVEPEILPDGDHDLKR 28 1 H3BPS8;P04075;P04075-2;H3BQN4;P09972 H3BPS8;P04075;P09972 ALDOA;ALDOC Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase C 0 ;;;;;; 189.2 4.03E-18 31718030000 26303028 20811278 13599782 16923533 21200980 18142295 25389529 28669547 18451779 FALSE TRUE 22827016.21 20674567.34 20176682.06 20766279.83 20779121.98 18840240.83 22927256.39 22538787.48 16270430.71 1.402975534 1.27068347 1.240082849 1.276320228 1.277109522 1.157943583 1.409136414 1.385260654 1 23.95574911 4.737917499 6.896037302 1.26792183 1.405075166 0.133369464 0.114754654 0.251415113 88.03937589 0.027618949 0.162015309 54691.2059 -4.737917499 0.137153335 YASPEMCFVFSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YASPEMCFVFSDR 13 0 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A1B0GTG9;A0A1B0GWF8;P30566-2;A0A096LNY5;B4DEP1;A0A1W2PRX2;A0A096LP72;A0A096LNY4 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 0 174.77 4.52E-05 116540000 36120 32502 26393 30638 34579 33637 38697 37349 40031 FALSE TRUE 31346.65048 32288.49222 39156.74308 37594.82617 33890.94555 34931.03716 34944.1709 29362.207 35298.58078 0.888042799 0.914724941 1.109300777 1.06505206 0.960122045 0.989587581 0.989959656 0.83182401 1 15.10732256 1.783511052 25 0.904777824 0.991890688 0.13144413 0.075486903 135.8618283 75593.58043 0.040885212 0.019775937 60.74507219 -1.783511052 0.087112864 YASS(ph)PKPNNSYMFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YASSPKPNNSYMFK 14 1 Q86VQ1;H7C0B2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 YAS(0.128)S(0.872)PKPNNSYMFK;YAS(0.001)S(0.999)PKPNNSYMFK 164.58 2.48E-06 770110000 1548690 1257430 1127450 1113490 1378030 1027290 1694590 2055230 1803930 TRUE FALSE 1344026.693 1249169.86 1672688.591 1366324.923 1350609.899 1066810.511 1530248.923 1615735.058 1590671.45 0.844942991 0.785309788 1.051561333 0.858961115 0.849081624 0.670666787 0.962014451 1.015756621 1 20.60120445 2.01774269 24.99719009 1.002968369 0.848298564 0.372120424 0.092576876 248.4339962 350010.5023 0.038494061 0.02594689 104.1700063 -2.01774269 -0.154669804 YATDTFAGLCHQLTNALVER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YATDTFAGLCHQLTNALVER 20 0 Q9UNS2-2;Q9UNS2;H7C3P9;J3QKR0;K7ES36;C9JLV5 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 0 135.49 7.08E-06 252070000 208680 181720 112880 110710 162790 173750 170680 182970 164010 FALSE TRUE 181102.4093 180526.2694 167469.1456 135848.3976 159550.7975 180434.2749 154127.4799 143843.2894 144620.9246 1.252255922 1.248272128 1.157986965 0.939341232 1.103234528 1.247636021 1.0657343 0.994622941 1 17.14191678 8 0.335145058 1.026968131 3.773850909 0.405294545 0.087965918 85.13568394 1.32229547 0.140610023 143.6087644 100000000 -8 2.746882778 YAVLYQPLFDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YAVLYQPLFDKR 12 1 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W543;F8W118;H0YHC3;H0YH88;F8W020;F8VRJ2;F8VVB5 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 0 ; 179.35 3.34E-05 1688250000 1468830 1631800 853080 1215490 1689880 1444990 1865510 2205450 1346950 FALSE TRUE 1274720.394 1621080.598 1265632.341 1491485.582 1656254.694 1500579.7 1684593.127 1733831.68 1187715.105 1.073254342 1.364873269 1.065602631 1.255760388 1.394488196 1.263417206 1.418347817 1.459804352 1 20.17975739 3.476240083 22.27108384 1.331766941 1.183118936 0.139547959 0.149621642 12.55602978 317307.8955 0.041266725 0.05390383 2993.919252 -3.476240083 -0.148648005 YAVTTGDHGIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YAVTTGDHGIIR 12 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;; 311.76 3.38E-30 1531920000 1663350 1657840 840100 1203590 1668660 1694730 1531470 1683030 1691780 FALSE TRUE 1443534.083 1646949.54 1246375.17 1476883.505 1635456.931 1759927.36 1382948.275 1323127.132 1491779.696 0.967659023 1.104016595 0.835495465 0.990014484 1.096312636 1.179750177 0.927045916 0.886945395 1 20.50860307 2.084664329 24.99996997 0.926779314 1.027183082 0.163352044 0.095786811 40.73465046 12022.43506 0.040325807 0.027187648 121.5246359 -2.084664329 0.100403768 YAVWFGGSMLASTPEFYQVCHTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YAVWFGGSMLASTPEFYQVCHTK 23 0 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ; 294.65 1.26E-61 464080000 486580 382380 237505 374030 346010 360940 453680 526430 435970 FALSE TRUE 422277.2202 379868.1206 352363.2124 458959.2282 339125.078 374825.5954 409682.1834 413857.0412 384430.1233 1.098449873 0.988133077 0.916585853 1.193869056 0.882150116 0.975016193 1.065686997 1.076546858 1 18.55236186 2.222942249 24.91004629 1.054242693 1.006515933 0.037011638 0.089447814 728.9680645 1162636.559 0.035095193 0.023757185 167.0868413 -2.222942249 -0.047726759 YAWQGVALLPFVDER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YAWQGVALLPFVDER 15 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 130.56 0.00013715 196411000 520420 483400 273340 367330 441410 407790 401260 463130 467650 FALSE TRUE 451645.1784 480224.5136 405528.1383 450737.8908 432626.8046 423477.9452 362345.867 364093.2536 412364.9497 1.095255983 1.16456191 0.983420484 1.093055778 1.049135735 1.026949418 0.878701905 0.882939381 1 18.65356219 2.402441746 3.531589215 0.911246365 1.075603345 0.617990629 0.055771309 0.144361945 3.618836024 0.022171943 0.016805604 252.6048856 -2.402441746 0.16435698 YAYDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YAYDKR 6 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;; 110.24 0.046296 5544550000 6349220 5910920 3639950 4272200 5362810 5308800 6427780 6950310 5230150 FALSE TRUE 5510154.49 5872090.777 5400241.995 5242268.306 5256100.573 5513032.971 5804414.885 5464040.294 4611847.625 1.194782425 1.273262097 1.170949787 1.136695904 1.139695194 1.195406574 1.258587741 1.184783353 1 22.13691342 1.242099847 6.156059229 0.993737899 1.195639115 0.661415699 0.043739002 0.081564372 12.55658025 0.069119279 0.011569671 17.46223574 -1.242099847 0.201901217 YAYYDTER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YAYYDTER 8 0 O00303 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 0 ;;;; 163.67 0.00077834 3792600000 3138480 3437340 1993330 2409860 3390280 3531710 3237770 3609860 3478040 FALSE TRUE 2723721.916 3414759.887 2957311.055 2957055.545 3322820.061 3667577.169 2923771.564 2837919.531 3066870.073 0.888111283 1.113434807 0.964276603 0.96419329 1.083456417 1.195869757 0.953340537 0.925347166 1 21.54833562 2.069427338 25 0.951918103 1.037608298 0.138852107 0.087580411 82.85698387 29834.42219 0.035537948 0.023959677 117.3349352 -2.069427338 0.085690195 YCADHFADGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YCADHFADGR 10 0 Q9UM47 Q9UM47 NOTCH3 Neurogenic locus notch homolog protein 3;Notch 3 extracellular truncation;Notch 3 intracellular domain 0 94.297 0.0082002 106270000 127250 157590 88103 107240 148080 178710 155080 144460 155210 FALSE TRUE 110433.5901 156554.7809 130709.9055 131590.4811 145133.4977 185585.0893 140040.3655 113568.3532 136861.2506 0.806901805 1.143894128 0.955054151 0.961488226 1.06044258 1.356009013 1.023228743 0.829806484 1 17.06235451 1.977508429 23.77880211 0.909877795 1.056311897 0.117761989 0.146624824 745.6392867 788310.7331 0.06680957 0.039013705 94.95294271 -1.977508429 0.146434102 YCDPDSYHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YCDPDSYHR 9 0 P26368-2;P26368;K7ENG2 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ;;;;; 188.66 3.91E-05 4509370000 6251720 6001950 2983620 4320310 5710420 5955690 4926150 5662570 9434980 FALSE TRUE 5425539.362 5962522.795 4426508.612 5301302.417 5596793.814 6184809.248 4448412.731 4451673.472 8319587.413 0.652140436 0.716684915 0.53205867 0.63720737 0.672724925 0.743403361 0.534691507 0.535083442 1 22.98808055 1.230145212 24.99991597 1.0000007 0.624335171 0.70875543 0.074909545 190.0133003 564434.2874 0.218845547 0.019498215 16.98811578 -1.230145212 -0.375665529 YCFPNYVGRPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YCFPNYVGRPK 11 1 P61163;R4GMT0;A0A1B0GVS3;P42025 P61163;P42025 ACTR1A;ACTR1B Alpha-centractin;Beta-centractin 0 ; 199.67 4.51E-08 2698400000 3240100 3272500 1963160 2369540 3136600 3018500 3454500 3797800 2849900 FALSE TRUE 2811912.576 3251002.732 2912550.742 2907580.273 3074187.797 3134623.648 3119483.122 2985670.025 2512988.069 1.118951821 1.29368013 1.158999033 1.157021121 1.223319695 1.247369093 1.241344183 1.188095583 1 21.26097239 1.241254243 4.430290709 0.982329305 1.208195597 0.615265924 0.050752031 0.129813658 5.213361487 0.092403394 0.012121057 17.42826854 -1.241254243 0.225866292 YCHDNNIIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YCHDNNIIHR 10 0 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8YEK3;O14936-6;O14936-2;A0A2U3TZN6;A0A2R8YGH2;A0A2R8Y6F8;O14936-3;A0A2U3TZM4;A0A2R8YFN5;O14936-4 A0A2U3TZM1;A0A2R8Y6F8 CASK Peripheral plasma membrane protein CASK 0 ;; 112.83 0.00090691 919930000 835090 817160 484230 682180 782850 947360 675110 891990 901610 FALSE TRUE 724730.7407 811792.0222 718405.2477 837079.3955 767272.8166 983805.5522 609637.9361 701244.88 795022.6929 0.911584974 1.021092894 0.903628606 1.052900003 0.965095492 1.237455938 0.766818283 0.882043854 1 19.60063652 2.19050176 24.99998066 0.877925713 1.009911423 0.250620784 0.107489848 158.8372451 82625.17423 0.042248968 0.02848429 155.0607072 -2.19050176 0.13198571 YCQVIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YCQVIR 6 0 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ;;; 128.89 0.038221 1369060000 1262620 1290860 773510 818920 1220730 1347280 1185360 1298620 1213540 FALSE TRUE 1095761.568 1282380.256 1147582.023 1004868.302 1196439.861 1399110.733 1070403.97 1020920.219 1070076.684 1.024002845 1.198400335 1.072429706 0.939061955 1.118087965 1.307486421 1.000305853 0.954062671 1 20.02928276 2.025156075 24.99979326 0.974780166 1.108924176 0.269105183 0.09774049 281.7640836 280012.3919 0.040830453 0.027526863 105.9634463 -2.025156075 0.134144009 YCRPESQEHPEADPGSAAPYLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YCRPESQEHPEADPGSAAPYLK 22 1 P40763;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 ; 152.04 2.66E-08 480210000 324180 372920 191412 274320 360310 317280 330770 445800 413440 FALSE TRUE 281338.7916 370470.264 283979.4834 336608.5487 353140.5359 329485.9669 298691.9763 350469.1392 364563.5942 0.771713896 1.016202029 0.778957329 0.923319152 0.968666487 0.90378187 0.81931378 0.96133883 1 18.47581097 YCVHYLEDVGSFEYTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YCVHYLEDVGSFEYTR 16 0 O95749-2;O95749 O95749-2 GGPS1 Geranylgeranyl pyrophosphate synthase 0 180.62 2.44E-09 142910000 121170 109320 63186 80398 105070 108500 89742 108440 106250 FALSE TRUE 105157.0775 108601.8697 93742.96094 98653.59471 102979.3126 112674.0652 81038.83465 85250.94988 93689.24604 1.122402858 1.159171136 1.000573331 1.052987391 1.099158302 1.202636055 0.864974776 0.909933141 1 16.51559584 2.229314587 24.99998846 0.91933698 1.101030794 0.644256728 0.063345906 122.6403293 331599.4657 0.026330633 0.018026889 169.556556 -2.229314587 0.181693814 YDCGEEILITVLSAMTEEAAVAIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YDCGEEILITVLSAMTEEAAVAIK 24 0 P63241;P63241-2;Q6IS14 P63241 EIF5A;EIF5AL1 Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A-1-like 0 ;;;; 220.36 1.01E-32 925400000 844016 734425 526720 626334 600648 555364 791791 912353 905846 FALSE TRUE 732477.1471 729600.5138 781443.5538 768552.7076 588696.2799 576729.2124 715003.2307 717253.4109 798757.9178 0.917020202 0.913418819 0.97832339 0.962184775 0.737014641 0.722032545 0.895143841 0.89796094 1 19.6073988 YDDAER ddPTM_MDA-MB-175_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 ; 123.1 0.044052 781290000 1824310 1684980 1318790 1651460 1339370 1906360 1846020 2039710 3033300 FALSE TRUE 1583222.811 1673911.255 1956561.255 2026449.234 1312719.157 1979698.903 1666993.265 1603533.89 2674706.73 0.59192389 0.625829829 0.731504966 0.757634178 0.490789941 0.740155502 0.623243381 0.599517649 1 21.35094928 1.234007708 24.99946901 1.00000053 0.645682926 0.655933217 0.080783925 85.47852372 469292.6603 0.148571539 0.019076505 17.13987727 -1.234007708 -0.354317605 YDDAERR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YDDAERR 7 1 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;E9PPR1;E9PL12;E9PMW7;E9PK06;H0YCK7;E9PIZ1;E9PK72;E9PKK3;E9PJD0;E9PNW6;P29692-3;E9PL71;E9PN91 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 ;;; 121.99 0.0070302 2835279000 6372970 5946900 3132600 3633490 4597340 5803370 5833770 6533890 2066500 FALSE TRUE 5530765.867 5907834.422 4647535.838 4458529.439 4505861.929 6026629.399 5268011.883 5136668.47 1822200.724 3.035212199 3.242142506 2.550507074 2.446782827 2.47275828 3.307335641 2.891016238 2.818936686 1 20.79725046 1.238554162 8.004014799 0.977312752 2.841512252 0.792272988 0.297011285 0.044107042 25.03179504 0.445723212 0.076955769 17.32025021 -1.238554162 1.8641995 YDDAIQLYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YDDAIQLYDR 10 0 Q15006;H0YAS9 Q15006 EMC2 ER membrane protein complex subunit 2 0 ;;; 218.58 1.56E-08 827440000 1420650 1271900 744637 1075718 1296130 1429940 1120344 1485310 1318850 FALSE TRUE 1232907.503 1263544.805 1104745.944 1319976.213 1270339.549 1484950.717 1011693.211 1167688.015 1162937.055 1.060167012 1.086511776 0.949961942 1.135036679 1.09235452 1.276896897 0.869946664 1.004085311 1 20.14934158 2.209475476 24.99994019 0.963940284 1.093938942 0.367942522 0.08745609 244.706172 210333.8997 0.035547527 0.023970314 161.9852519 -2.209475476 0.129998658 YDDIKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YDDIKK 6 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;; 86.866 0.085126 67649400000 36683200 30090500 27432700 27139700 21057700 16730200 38563000 41286700 47063900 FALSE TRUE 31835422.18 29892833.52 40699245.48 33302183.69 20638692.97 17373821.62 34823166.2 32457860.5 41500059.36 0.767117509 0.720308211 0.980703308 0.80246111 0.497317192 0.418645705 0.839111238 0.782116002 1 25.30661006 -0.35463067 12.79860265 6.43243512 0.751575923 0 0.183214372 0 0 0 0.043099073 0.441946125 0.35463067 -5.680859197 YDDMAACMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YDDMAACMK 9 0 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;E5RGE1 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;;; 170.22 0.00013465 2091650000 3298840 2737860 1801551 2172350 2615100 2210745 3006560 3364160 3070760 FALSE TRUE 2862889.936 2719874.817 2672787.089 2665615.27 2563064.626 2295793.791 2714984.274 2644760.564 2707738.251 1.057299366 1.004482179 0.98709212 0.984443481 0.946570307 0.847864002 1.002676043 0.97674159 1 21.36865685 4.619497834 1.093088206 0.958748343 1.089796324 0.348127839 0.043502887 1.780845997 2.045735865 0.014445935 0.258101197 41638.76439 -4.619497834 0.131047981 YDDMATCMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDDMATCMK 9 0 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ; 133.57 0.00097595 109050000 302350 227556 148059 178404 218690 179051 259450 277150 245490 FALSE TRUE 262393.6814 226061.1697 219660.8276 218913.3549 214338.4969 185939.2078 234288.5789 217883.6293 216468.4519 1.212156687 1.044314623 1.014747534 1.011294501 0.990160437 0.858966774 1.082322052 1.006537569 1 17.72379726 5.116296605 1.343398938 0.993612459 1.528763551 0.611546205 0.054463092 2.237072015 1.822370343 0.015426483 2.082132185 130706.3253 -5.116296605 0.535151092 YDDPPDWQEILTYFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDDPPDWQEILTYFR 15 0 P61221;D6R9I9;D6RGF4;H0Y990 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 ; 116.98 0.00094434 485690000 246528 219624 161459 194541 188427 216095 202595 288483 288200 FALSE TRUE 213948.7002 218181.2755 239541.1124 238714.5074 184677.6714 224408.3145 182947.3681 226793.1554 254129.3243 0.841889069 0.858544271 0.942595323 0.939342628 0.726707443 0.883047697 0.719898692 0.892432056 1 17.95520333 1.315917183 4.212352394 1.003901528 0.846758503 0.299304867 0.074643284 0.261333129 7.07716839 0.101767158 0.018854746 20.69746624 -1.315917183 -0.157143025 YDDTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDDTVK 6 0 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 0 ; 110.23 0.067187 1077130000 4404300 4309000 3144600 3308200 2998200 3029000 4270300 4694800 5337900 FALSE TRUE 3822260.596 4280693.895 4665339.078 4059377.373 2938541.686 3145527.59 3856166.963 3690853.555 4706859.543 0.81206175 0.909458601 0.991178733 0.862438604 0.624310468 0.668285841 0.819265357 0.784143551 1 22.16633337 3.46579404 24.98273737 0.774195784 0.908431122 0.227464755 0.106945246 305.9327551 674747.3686 0.03167501 0.04092621 2922.765954 -3.46579404 0.134235338 YDDYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YDDYDR 6 0 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 0 100.74 0.086812 530040000 909350 832230 493310 610260 764000 824570 807980 924490 868500 FALSE TRUE 789177.0935 826763.0263 731876.366 748828.8602 748797.8947 856291.7415 729622.224 726795.0079 765826.9194 1.030490145 1.079569032 0.955668112 0.977804307 0.977763873 1.118126981 0.952724703 0.949032986 1 19.54665885 YDDYRDYDS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDDYRDYDSPER 12 1 P52756;C9JR02;C9J9P7;C9JFQ5;P52756-4;P52756-2;P52756-5;F8W910;P52756-3 P52756 RBM5 RNA-binding protein 5 1 YDDYRDYDS(1)PER;YDDYRDY(0.001)DS(0.998)PER 115.73 0.00055616 946820000 366000 369260 208939 292400 371240 310840 331090 403680 383480 TRUE FALSE 317632.1727 366834.3067 309982.5993 358793.8891 363853.0503 322798.2159 298980.9428 317356.1734 338145.4313 0.939335988 1.084841825 0.916713847 1.061063838 1.076025333 0.954613566 0.884178567 0.938519773 1 18.36728434 2.499068678 23.07658426 0.93537685 1.01636007 0.256121124 0.060477263 348.671822 366610.9232 0.020014162 0.017467083 315.5503583 -2.499068678 0.08098322 YDDYRDYDS(ph)PERER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 140.95 7.72E-06 1483420000 1569500 1527730 760834 841720 1487110 1405790 1422880 1624510 484931 TRUE FALSE 1362086.598 1517694.241 1128775.867 1032845.391 1457519.42 1459871.651 1284889.317 1277121.178 427603.0096 3.185399934 3.549306733 2.63977531 2.415430593 3.408580828 3.414081796 3.004864998 2.986698292 1 18.70591248 4.236042597 24.93055001 2.779301113 3.367353397 0.132437228 0.689349797 133.614444 1322958.295 0.174396998 0.392386239 17220.37468 -4.236042597 0.588052284 YDDYSSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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 ;;;; 236.1 3.07E-08 9651620000 10106470 9059680 5391090 6565450 8615160 8769480 8451210 9472710 8894410 FALSE TRUE 8770874.383 9000166.366 7998239.156 8056235.769 8443735.171 9106847.57 7631612.955 7447044.683 7842922.982 1.118317036 1.147552562 1.019803353 1.027198123 1.076605647 1.161154788 0.973057235 0.949524138 1 22.90296 2.176612856 11.25446434 0.968792984 1.087382458 0.582327891 0.046769819 0.422491446 74.99327583 0.020141981 0.013582236 150.1802614 -2.176612856 0.118589474 YDECLAVYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YDECLAVYR 9 0 O76094-2;O76094;R4GNC1;D6RDY6 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 ;; 148.04 0.0002116 817480000 505921 490357 357927 393446 494417 501031 489910 548509 626198 FALSE TRUE 439062.258 487135.8126 531021.6944 482783.9277 484579.069 520305.9868 442398.6036 431214.6189 552169.5858 0.795158352 0.882221377 0.961700369 0.874339949 0.877591018 0.942293817 0.8012006 0.780945981 1 19.0747519 1.213582059 24.89078575 1.00000066 0.864303782 0.338827643 0.059515159 3081.662855 3070660.838 1.106410941 0.015813092 16.35242096 -1.213582059 -0.135696879 YDEEFQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YDEEFQR 7 0 P55060-3;P55060 P55060-3 CSE1L Exportin-2 0 ;;;; 185.42 0.0014277 2711850000 5091800 3484100 3240310 3384280 4064020 3646720 3942070 4356520 5675490 FALSE TRUE 4418905.729 3461212.718 4807334.754 4152732.499 3983153.953 3787011.678 3559768.658 3424912.1 5004540.038 0.882979394 0.691614552 0.960594724 0.829793042 0.7959081 0.756715232 0.711307859 0.684361015 1 22.25480605 3.082685271 3.193907991 0.765376306 0.839033124 0.036211237 0.107051112 0.637258219 13.07646359 0.03376339 0.038520016 1209.721141 -3.082685271 0.073656818 YDEELEGERPHSFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDEELEGERPHSFR 14 1 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 ; 154.65 3.64E-06 282810000 403660 367220 230365 286770 358680 340960 337480 419450 380120 FALSE TRUE 350315.3083 364807.7076 341770.2845 351885.5115 351542.9697 354076.9518 304751.2415 329753.8817 335182.6466 1.045147509 1.088384829 1.019653875 1.049832129 1.048810173 1.056370177 0.909209485 0.983803562 1 18.35458793 2.263128558 24.9907112 0.966096062 1.051421716 0.6792772 0.028181532 122.3174831 124421.9805 0.010194599 0.007893025 183.2856898 -2.263128558 0.085325654 YDEFHDYLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YDEFHDYLER 10 0 Q96K76-2;Q96K76-4;Q96K76 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 0 ;;; 199.68 2.74E-07 766591000 1095160 1126710 641704 829930 1132620 1072120 1044080 1260620 1140410 FALSE TRUE 950431.8312 1119308.568 952034.2008 1018378.291 1110083.078 1113365.15 942825.2823 991046.2232 1005592.029 0.945146544 1.113084169 0.946740003 1.012715159 1.103909981 1.107173802 0.937582295 0.985535082 1 19.93961369 2.220636087 24.97953452 0.975165094 1.039216306 0.190532122 0.06191396 401.0283442 558867.299 0.0248918 0.016818163 166.2019391 -2.220636087 0.064051212 YDEGS(ph)GGS(ph)GDEGRDEAHKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDEGSGGSGDEGRDEAHKR 19 2 O94762-4;O94762 O94762-4 RECQL5 ATP-dependent DNA helicase Q5 2 Y(0.014)DEGS(0.987)GGS(0.999)GDEGRDEAHKR;Y(0.001)DEGS(0.999)GGS(1)GDEGRDEAHKR 93.633 0.00092525 455150000 204039 178220 123766 138471 158351 150876 190590 210400 176790 TRUE FALSE 177074.7292 177049.2611 183619.6516 169912.9569 155200.1249 156680.2973 172106.6111 165407.5973 155890.0876 1.135894731 1.135731359 1.177878943 1.089953566 0.995574044 1.005069019 1.104025367 1.061052693 1 17.25016967 3.494130041 5.430615622 1.040426306 1.147003172 0.705109251 0.034327482 0.108702235 10.14791836 0.010405845 0.014708957 3119.823615 -3.494130041 0.106576867 YDEIRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YDEIRR 6 1 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 ;;; 100.82 0.059688 2036492000 5153110 5204080 3443240 3990920 5261700 5112730 5641130 5815570 4776430 FALSE TRUE 4472113.457 5169894.056 5108402.381 4897119.383 5157002.464 5309420.031 5094054.081 4571955.612 4211765.887 1.06181435 1.227488468 1.212888493 1.16272355 1.224427616 1.260616134 1.209481775 1.085519883 1 22.00599381 1.54161416 2.885286201 1.006116157 1.198725108 0.597228902 0.053879138 0.161603311 2.780864125 0.059292275 0.014105658 34.8027979 -1.54161416 0.192608951 YDEMVESMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YDEMVESMK 9 0 P62258;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;;; 164.57 0.00014462 956991000 2052493 1800127 1543004 1904980 1730412 1391483 2010171 2252874 3866340 FALSE TRUE 1781250.85 1788301.847 2289205.895 2337534.825 1695980.187 1445014.251 1815224.926 1771114.427 3409265.69 0.522473463 0.524541649 0.671465971 0.68564173 0.497462017 0.423849117 0.532438681 0.519500264 1 21.7010296 1.236425871 24.9997859 1.00000058 0.54728084 0.770119261 0.077751412 29.61298371 346708.1529 0.132873345 0.02071272 17.23557876 -1.236425871 -0.45271974 YDEMVESMKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDEMVESMKK 10 1 P62258;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 ; 133.07 0.00033177 2291300000 2193290 1766440 1274530 1382310 1666110 1432840 2186380 2363950 826690 FALSE TRUE 1903441.169 1754836.139 1890896.971 1696184.613 1632957.671 1487962.282 1974345.204 1858437.689 728959.65 2.611174939 2.407315877 2.593966581 2.326856655 2.240120795 2.041213505 2.708442373 2.549438352 1 19.47547943 1.235792789 24.99169698 0.999998072 2.435371366 0.839567417 0.197113744 30.44823835 274873.7008 0.339207635 0.05046724 17.21047231 -1.235792789 1.435373294 YDERPGPS(ph)PLPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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;Y(0.001)DERPGPS(0.999)PLPHR;YDERPGPS(1)PLPHR 142.39 2.44E-05 20218820000 17130370 14285620 10120330 10791220 14565810 15334690 14990150 16418400 16531210 TRUE FALSE 14866548.2 14191776.82 15014555.44 13241531.43 14275978.88 15924625.45 13536407.56 12907452.93 14576909.19 1.019869714 0.973579285 1.030023254 0.908390885 0.979355685 1.092455557 0.928619873 0.885472549 1 23.79718151 2.058627669 24.99998158 0.926300334 0.996810433 0.216594208 0.054307491 97.31247216 41495.21896 0.021841375 0.01472545 114.4531287 -2.058627669 0.070510099 YDERPGPSPLPHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YDERPGPSPLPHR 13 1 P08621;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 77.078 0.016179 127160000 214570 194330 74723 129280 217280 204450 188250 215370 200410 FALSE TRUE 186214.0308 193053.4334 110859.2927 158634.9999 212956.5531 212315.3238 169993.544 169314.8015 176717.7581 1.053736947 1.092439354 0.62732401 0.897674357 1.20506595 1.2014374 0.961949415 0.958108587 1 17.4310875 YDEVLHMVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YDEVLHMVR 9 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 141.88 0.00010566 123320000 54779 55710 35420 41712 60097 54788 54595 62710 63578 FALSE TRUE 47539.81636 55344.03734 52549.23047 51183.34713 58901.18728 56895.72981 49300.3853 49299.95451 56061.88127 0.847988246 0.987195508 0.93734333 0.912979479 1.050645928 1.014873717 0.879392275 0.879384591 1 15.77473254 6.24982941 14.34927876 0.943055254 0.574874872 0 0.066672128 0 0 0.0153049 0 1777581.043 -6.24982941 -0.368180382 YDEYVNVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YDEYVNVK 8 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 123.92 0.0030874 102930000 250760 240980 154060 204370 239900 197940 273090 290860 269410 FALSE TRUE 217621.4307 239396.9865 228563.9313 250775.3321 235126.4594 205554.8799 246605.7738 228661.8525 237560.6567 0.9160668 1.007729941 0.962128723 1.055626532 0.989753365 0.865273243 1.038074979 0.962540918 1 17.8579364 3.833595333 0.004373088 1.489425531 0.46334664 0.010808412 0.055645458 348247.0973 844.4948737 98247.68137 99899.59244 6817.032013 -3.833595333 -1.026078892 YDFGIYDDDPEIITLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDFGIYDDDPEIITLER 17 0 Q8IXB1-2;Q8IXB1;Q71S60;A0A087WXH7;E7EP04;A0A494C1G5;Q8IXB1-3 Q8IXB1-2 DNAJC10 DnaJ homolog subfamily C member 10 0 ; 169.62 3.49E-13 31846000 131254 117368 76130 92428 125000 144746 99937 112195 105759 FALSE TRUE 113908.4513 116597.0019 112946.7226 113415.1901 122512.7446 150314.4723 90245.12512 88202.97235 93256.2915 1.221455942 1.250285638 1.211143193 1.216166633 1.313720957 1.611842696 0.96771085 0.945812566 1 16.50891344 2.126530522 17.01051237 0.965363476 1.293865859 0.642195388 0.11695597 0.738084769 108.4302563 0.048784772 0.032890719 133.8229262 -2.126530522 0.328502383 YDFTSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDFTSSR 7 0 Q9NZ01;M0R2N5 Q9NZ01 TECR Very-long-chain enoyl-CoA reductase 0 ; 166.17 0.0026368 476630000 281110 257540 198212 300900 338940 341420 241860 389200 450470 FALSE TRUE 243960.6013 255848.2028 294067.9862 369223.944 332195.7571 354554.6483 218404.4544 305972.6088 397215.9498 0.614176247 0.644103549 0.740322704 0.929529502 0.836310217 0.892599223 0.549838078 0.770292857 1 18.59956403 4.136723207 3.458044037 0.810382126 0.625526723 0.315342022 0.119275592 0.314508798 7.255206061 0.03265136 0.07941849 13700.08326 -4.136723207 -0.184855403 YDGSTIVPGEQGAEYQHFIQQCTDDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDGSTIVPGEQGAEYQHFIQQCTDDVR 27 0 Q14019 Q14019 COTL1 Coactosin-like protein 0 ; 225.3 1.70E-34 1285700000 528360 453340 287070 347390 440510 470450 440300 500430 504270 FALSE TRUE 458535.8873 450361.9797 425898.0122 426270.209 431744.7128 488548.5159 397599.7738 393416.9389 444655.7751 1.03121541 1.012832858 0.957815092 0.958652137 0.970963916 1.09871173 0.894174317 0.884767411 1 18.7623294 2.18239296 24.99999613 0.916319064 0.999584917 0.334272717 0.051348473 91.67993362 40805.49898 0.020993818 0.014154037 152.1923981 -2.18239296 0.083265853 YDIDLPNKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDIDLPNKK 9 1 O00244;E5RGN3;E5RIM7 O00244 ATOX1 Copper transport protein ATOX1 0 ; 95.81 0.012496 3989500000 17909700 17563400 13300700 17265000 16832800 11929200 22785000 27295000 29702000 FALSE TRUE 15542887.77 17448024.87 19732963.01 21185282.13 16497860.21 12388124.04 20575314.21 21458176.66 26190663.4 0.593451473 0.666192551 0.75343502 0.808886809 0.629913796 0.472997719 0.785597291 0.819306343 1 24.64254927 1.502260762 1.780994527 1.019358169 0.667307764 0.56600669 0.095553273 0.409122348 2.026750505 0.219924691 0.028836079 31.78782126 -1.502260762 -0.352050406 YDLDFKSPDDPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDLDFKSPDDPSR 13 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 83.087 0.0096523 918260000 2044490 1909520 724770 774220 1473420 1416310 2205900 2189500 395850 FALSE TRUE 1774305.466 1896976.237 1075271.196 950018.4842 1444101.825 1470796.362 1991972.158 1721292.464 349053.064 5.08319694 5.434635685 3.08053791 2.721702177 4.137198535 4.213675553 5.706788919 4.93132031 1 18.41308685 4.256704088 24.9719252 3.90481177 5.258917325 0.189600488 1.292246362 472.2095469 649918.363 0.333934779 0.879683875 18059.43204 -4.256704088 1.354105555 YDLIQNSESPAS(ph)PPVAVPHSWSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YDLIQNSESPASPPVAVPHSWSR 23 0 A0A1B0GU24;Q9HCJ0-2;Q9HCJ0 A0A1B0GU24 TNRC6C Trinucleotide repeat-containing gene 6C protein 1 YDLIQNSESPAS(1)PPVAVPHSWSR;YDLIQNSESPAS(1)PPVAVPHSWSR;YDLIQNSES(0.001)PAS(0.999)PPVAVPHSWSR 213.77 4.59E-26 523214000 198974 211376 139027 195904 274927 262358 255274 316729 303436 TRUE FALSE 172679.0818 209987.4571 206260.9222 240386.9974 269456.4906 272451.082 230517.5668 248998.9681 267564.1418 0.645374528 0.784811656 0.770884024 0.898427554 1.007072505 1.018264556 0.861541331 0.930614119 1 18.02952526 3.897383194 1.525828371 0.955341424 0.694892458 0.790249343 0.054814268 0.205014676 0.906479112 0.017774468 0.04934455 7895.564653 -3.897383194 -0.260448966 YDLSGRPLNIKEDPDGENAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDLSGRPLNIKEDPDGENAR 20 2 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WUT0 A0A0A0MQW0 MYEF2 Myelin expression factor 2 0 ; 47.808 0.090242 274980000 371650 345390 232649 246780 335620 323660 398080 422740 234222 FALSE TRUE 322535.5109 343121.1103 345158.8346 302815.1708 328941.8186 336111.4096 359474.2629 332340.3408 206532.542 1.561669206 1.661341632 1.671207991 1.466186238 1.5926876 1.627401699 1.740521176 1.609142741 1 17.65600959 1.239295665 8.137980059 0.993016453 1.620301838 0.878363931 0.072069842 0.029499588 18.55705247 0.103112705 0.018110526 17.34984764 -1.239295665 0.627285385 YDNGSGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YDNGSGYR 8 0 Q08211;Q08211-2 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;; 180.34 0.00055738 1427260000 1845500 1564100 954200 1231700 1678530 1739820 1629750 1795570 1634290 FALSE TRUE 1601612.499 1553825.324 1415654.312 1511376.31 1645130.537 1806752.001 1471697.096 1411601.329 1441086.098 1.111392651 1.078232124 0.982352348 1.048775859 1.141590734 1.253743273 1.021241616 0.979539897 1 20.4587251 2.016932958 24.99990845 0.991933124 1.098924875 0.335393582 0.068876292 286.9176192 423605.0931 0.030643145 0.020654004 103.9759645 -2.016932958 0.106991752 YDNQIHIIDFDDENNIINK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YDNQIHIIDFDDENNIINK 19 0 A8MUM1;Q53HC9;F8WDS8;C9J0U9;D3YTH5 A8MUM1 TSSC1 Protein TSSC1 0 223.44 2.20E-19 160690000 124030 80229 69053 86558 88376 77309 110540 124160 124470 FALSE TRUE 107639.1212 79701.97042 102447.2618 106212.3169 86617.4905 80283.12726 99819.84781 97609.35021 109755.2984 0.980719134 0.726178796 0.933415181 0.967719266 0.789187326 0.731473819 0.909476347 0.889336111 1 16.74393106 1.154607135 1.710093371 1.074904851 0.856355541 0.183686145 0.09035505 2.125255182 4.80955228 0.828657699 0.024866186 14.27601957 -1.154607135 -0.21854931 YDNSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YDNSLK 6 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;; 146.94 0.025485 51999000000 17264700 15941600 11173320 12696400 11935700 12694900 18031300 19487600 19161100 FALSE TRUE 14983126.15 15836878.58 16576774.92 15579311.67 11698202.92 13183281.02 16282627.3 15320328.39 16895896.59 0.88679083 0.937320994 0.981112475 0.922076647 0.692369467 0.780265253 0.963703064 0.906748471 1 24.01016957 1.403617925 1.558753375 1.014463442 0.875092175 0.16345115 0.086279053 1.670220756 4.973563282 0.337577684 0.027762826 25.32899306 -1.403617925 -0.139371267 YDPQKEAELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YDPQKEAELR 10 1 B4DDF4;B4DUT8;Q99439;H3BVI6;Q99439-2;A0A087X271;K7ES69 B4DDF4 CNN2 Calponin;Calponin-2 0 ;; 80.69 0.021206 1361640000 3906700 4055500 1247050 1367060 3553710 3143290 4499700 5038200 245460 FALSE TRUE 3390419.697 4028859.153 1850127.551 1677471.867 3482998.124 3264214.4 4063319.787 3960820.137 216441.9984 15.66433373 18.61403601 8.547913827 7.750214281 16.0920623 15.08124312 18.77325018 18.29968382 1 17.72362094 1.230024874 24.99240119 0.999973909 14.9425964 0.560125776 3.857275967 276.8139396 810439.4383 11.77337431 1.035658181 16.98340921 -1.230024874 13.94262249 YDPSIGIYGLDFYVVLGRPGFSIADK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YDPSIGIYGLDFYVVLGRPGFSIADK 26 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 141.64 2.68E-07 199770000 161240 143090 71569 98725 122400 96392 182240 211150 48945 FALSE TRUE 139931.7255 142150.0324 106180.0078 121142.0202 119964.4795 100100.2626 164566.3928 165997.2157 43158.77786 3.242254123 3.293652866 2.460218131 2.806891812 2.77960789 2.319348869 3.813045712 3.846198245 1 15.39736639 4.304995833 24.99280096 2.868454377 3.267959223 0.050873126 0.804192964 225.9550037 84997.56536 0.203091541 0.53732958 20183.46998 -4.304995833 0.399504846 YDPSIGIYGLDFYVVLGRPGFSIADKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDPSIGIYGLDFYVVLGRPGFSIADKK 27 2 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ; 185.14 7.01E-18 257840000 498860 399380 211947 270203 334280 269250 547180 631030 130365 FALSE TRUE 432934.387 396756.4465 314445.2781 331556.7209 327628.482 279608.2217 494114.5678 496089.1452 114953.3982 3.766173021 3.451454699 2.735415247 2.884270723 2.850098276 2.432361514 4.298390265 4.315567464 1 16.81068959 1.22360169 24.99622399 0.999993725 3.358616531 0.568127915 0.641489241 717.8415825 1199437.654 4.061373407 0.178628974 16.7340742 -1.22360169 2.358622806 YDPSLLDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YDPSLLDVR 9 0 P35219 P35219 CA8 Carbonic anhydrase-related protein 0 98.392 0.014063 73285000 180910 192980 109070 129970 197840 204590 172380 207760 199070 FALSE TRUE 157002.2851 191712.3017 161816.6168 159481.675 193903.3711 212460.7097 155662.6141 163332.1408 175536.1714 0.894415572 1.092152689 0.921842009 0.908540238 1.104634843 1.210352875 0.886783692 0.930475693 1 17.42140882 YDQHCLWTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YDQHCLWTGR 10 0 Q8IUH4-2;Q8IUH4-3;Q8IUH4 Q8IUH4-2 ZDHHC13 Palmitoyltransferase ZDHHC13 0 75.695 0.028939 0 96929 111840 63249 72474 121280 121690 92845 128220 105290 FALSE TRUE 84119.58706 111105.3157 93836.42796 88930.3294 118866.7653 126371.493 83840.90619 100801.1508 92842.73615 0.906043817 1.196704452 1.010702957 0.957859851 1.280302264 1.36113495 0.903042173 1.085719303 1 16.50250142 4.760474275 23.49333681 1.095789351 0.906043362 0.150306606 0.144272077 5301.8601 5683845.482 0.035755252 1.537024761 57606.86942 -4.760474275 -0.189745989 YDS(ph)SNQVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDSSNQVK 8 0 O95983-2;O95983;K7EIE8;A0A087WZ12;A0A087WT34;A0A087X1H1;A0A0A0MTS6 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 1 YDS(0.904)S(0.096)NQVK;YDS(0.919)S(0.081)NQVK 135.8 0.00085855 287100000 483500 472890 434830 460470 479900 619420 856870 873940 1133690 TRUE FALSE 419604.25 469783.5545 645115.2424 565026.7513 470350.9289 643249.4882 773770.8793 687054.732 999666.4597 0.419744252 0.469940298 0.645330486 0.565215273 0.470507862 0.643464109 0.774029049 0.687283969 1 19.93108729 -2 0.37002057 6.816829258 0.481085557 0.779827739 0.079875567 38.61874007 0.583100185 171.9334301 0.096523423 0.01 2 -6.335743701 YDSDGVWDPEKWHASLYPAS(ph)GR ddPTM_MDA-MB-175_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 235.57 1.09E-30 292830000 444280 576640 121723 327920 579160 502890 505350 661870 676050 TRUE FALSE 385567.2723 572852.0139 180588.6499 402379.2479 567635.8491 522236.5037 456341.2348 520334.2512 596128.1392 0.646785896 0.960954493 0.30293596 0.674987845 0.95220442 0.876047396 0.765508629 0.872856383 1 19.18526295 3.311755173 6.683495653 0.879945763 0.641493902 0.35069378 0.166683509 0.258151987 18.89554821 0.047621356 0.061379265 2050.006193 -3.311755173 -0.238451861 YDSDRTELGFTNYIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YDSDRTELGFTNYIR 15 1 Q14554 Q14554 PDIA5 Protein disulfide-isomerase A5 0 77.222 0.024193 105310000 67841 59607 39357 44983 66301 73598 52036 60002 33638 FALSE TRUE 58875.63996 59215.43769 58390.17684 55197.07767 64981.73982 76429.36268 46989.55673 47171.03924 29661.35396 1.984927594 1.996383502 1.968560738 1.860908903 2.19078805 2.576732093 1.584201341 1.590319825 1 14.85629683 1.520625899 1.565823269 0.926557016 2.066054876 0.679740736 0.235419638 0.360494205 1.311442256 0.575228944 0.070936008 33.16086871 -1.520625899 1.139497859 YDSSREAGTVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDSSREAGTVK 11 1 Q96J01;D6REC9 Q96J01 THOC3 THO complex subunit 3 0 ; 71.153 0.029928 258580000 358790 336510 174015 252050 363150 393780 336770 379930 429210 FALSE TRUE 311374.9924 334299.4437 258169.236 309281.8048 355924.0255 408928.9714 304110.0972 298684.9261 378469.2828 0.822721966 0.883293464 0.682140527 0.817191299 0.940430417 1.08048127 0.803526498 0.789191989 1 18.52981669 3.343487893 6.11719866 0.904639736 0.796369429 0.266501046 0.09789565 0.359572624 18.32618738 0.030611317 0.039567264 2205.402652 -3.343487893 -0.108270308 YDSWHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDSWHK 6 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 119.7 0.020787 1032860000 1635990 1585660 521470 1106350 1795680 1680460 1865260 2099730 2177250 FALSE TRUE 1419789.776 1575243.695 773654.6362 1357563.677 1759949.481 1745108.384 1684367.372 1650719.08 1919857.985 0.739528542 0.820500114 0.402974929 0.707116718 0.91670816 0.90897785 0.877339566 0.859813118 1 20.87256817 3.302450638 4.944685839 0.903395994 0.6543509 0.547442242 0.111054633 0.160381973 7.639074975 0.032701064 0.041938367 2006.553011 -3.302450638 -0.249045094 YDSYESCDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDSYESCDSR 10 0 Q9ULX6;V9GZ50;M0R1Y5;M0R010;M0QYT7 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 0 ; 176.78 5.58E-06 241380000 637520 522820 316290 396790 551000 536530 485370 605390 577660 FALSE TRUE 553270.1167 519385.561 469248.9019 486887.2341 540036.178 557170.6563 438298.8921 475932.0597 509369.6929 1.086185779 1.019663259 0.921234436 0.955862198 1.06020477 1.09384336 0.860473048 0.934354883 1 18.9583536 YDVDTLDMVFLDHWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YDVDTLDMVFLDHWK 15 0 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ;;;;; 269.4 6.17E-26 5637913000 6508036 5842704 5071712 5977267 5569838 4604123 6849300 7740528 15066615 FALSE TRUE 5647982.553 5804322.893 7524408.887 7334496.829 5459009.121 4781246.591 6185055.94 6085276.324 13285456.94 0.425125201 0.436892982 0.566364328 0.552069595 0.410901119 0.359885747 0.465550863 0.458040424 1 23.66334451 1.23840219 24.99613766 1.000000594 0.460499698 0.884231649 0.061477864 1.284159798 201968.6274 0.090652825 0.016138089 17.31419044 -1.23840219 -0.539500896 YDVDTLDMVFLDHWKDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDVDTLDMVFLDHWKDR 17 1 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ; 144.33 3.10E-07 199079000 601520 684640 275480 275640 606480 713130 672230 668080 317510 FALSE TRUE 522027.6079 680142.5548 408703.0494 338228.2749 594412.2346 740564.5726 607037.2381 525216.291 279974.3295 1.864555257 2.429303272 1.459787582 1.208068881 2.123095484 2.645115979 2.168188916 1.875944455 1 18.09493503 1.243494817 4.27149916 0.91100214 1.985309685 0.349645625 0.419010618 0.267284379 9.400155573 0.876542875 0.113285336 17.51841528 -1.243494817 1.074307545 YDVEIVEEYFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDVEIVEEYFAR 12 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 0 ; 113.63 0.0026639 27208000 53919 52309 38033 42541 46739 56883 52814 50576 74006 FALSE TRUE 46793.46754 51965.37873 56425.88601 52200.58425 45808.98534 59071.32582 47692.10641 39760.71598 65257.09499 0.717063295 0.796317684 0.864670516 0.799921974 0.701977085 0.905209247 0.730834041 0.60929338 1 15.99384714 YDVYLYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YDVYLYDR 8 0 Q9Y6Y8;Q9Y6Y8-2;H7C0V8;A0A0C4DH82;H7C4C4 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 ;;;; 124.98 0.0029812 1447520000 2010010 2077350 1373860 1863330 2269960 2123810 2071610 2375180 2856150 FALSE TRUE 1744382.086 2063703.751 2038263.291 2286427.556 2224792.237 2205514.345 1870705.581 1867266.241 2518499.201 0.692627611 0.819418069 0.809316632 0.907853199 0.883380164 0.875725648 0.742785855 0.741420224 1 21.26413284 4.87590106 1.970206939 0.840021455 0.60801632 0.285366362 0.077049119 1.871939377 5.703723241 0.021245504 0.886865933 75145.16804 -4.87590106 -0.232005135 YDWDLLAAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YDWDLLAAR 9 0 Q15029;Q15029-3;Q15029-2;K7EP67;K7EJ74 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;;; 146.58 0.0002197 721300000 1391522 1240263 749351 954682 1265772 1300015 1040419 1365915 1278571 FALSE TRUE 1207628.842 1232115.631 1111739.65 1171457.14 1240585.614 1350027.418 939519.3255 1073824.707 1127419.793 1.071143907 1.092863225 0.98609201 1.039060292 1.100375939 1.197448747 0.833335845 0.952462174 1 20.10459337 2.232619631 24.99999971 0.929601469 1.076333811 0.538170812 0.066521185 116.0428697 488308.6303 0.027308617 0.01895605 170.8518284 -2.232619631 0.146732342 YDYNSGEELESYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDYNSGEELESYK 13 0 Q9Y3F4;Q9Y3F4-2;H0YH33 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 ; 235.31 2.57E-16 265100000 283690 227818 166452 190216 249590 210331 253330 330480 314120 FALSE TRUE 246199.6477 226321.4486 246948.7439 233407.4501 244623.6473 218422.5697 228762.0956 259809.4238 276985.0914 0.888855232 0.817088918 0.891559696 0.842671527 0.883165394 0.788571574 0.825900392 0.937990642 1 18.0794488 1.553939597 3.410669904 0.991656769 0.847785076 0.705468625 0.03355489 0.105041275 2.645397947 0.030641664 0.00862422 35.80466351 -1.553939597 -0.143871693 YDYVLTGYTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YDYVLTGYTR 10 0 O00764;F2Z2Y4;O00764-3 O00764 PDXK Pyridoxal kinase 0 ; 179.51 4.88E-06 481620000 445680 480310 316640 368940 400310 437610 370900 423540 795730 FALSE TRUE 386782.2588 477154.812 469768.1631 452713.4659 392344.6142 454445.1399 334930.1751 332969.267 701659.7059 0.551239091 0.680037357 0.669509962 0.645203739 0.559166517 0.647671708 0.477339902 0.474545231 1 19.42041199 1.229000917 24.99981161 1.00000082 0.585736172 0.753619683 0.074006301 220.2457109 575928.3838 0.259596743 0.020546614 16.94341377 -1.229000917 -0.414264648 YEAANWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YEAANWK 7 0 G3V5Z7;P60900;G3V3I1;G3V295;P60900-2;P60900-3 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ; 107.67 0.017273 617180000 953840 827390 567890 725310 784350 692440 916480 962530 1252370 FALSE TRUE 827787.6273 821954.8206 842523.5035 890002.7212 768742.9696 719078.6149 827599.9107 756700.4499 1104316.245 0.749592909 0.744311083 0.762936801 0.805931023 0.696125746 0.6511528 0.749422925 0.68522079 1 20.07472195 1.232808914 24.99711094 1.000000435 0.729578283 0.789585628 0.043705093 89.0212268 386848.8507 0.097231096 0.011230938 17.09263087 -1.232808914 -0.270422152 YEAHSDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YEAHSDK 7 0 I3L4J1;Q9UN37 I3L4J1 VPS4A Vacuolar protein sorting-associated protein 4A 0 ; 92.47 0.015646 383370000 476620 420820 327490 337810 244660 439610 432930 496410 580910 FALSE TRUE 413633.4594 418055.6057 485865.2594 414514.9236 239791.7447 456522.0812 390944.5152 390256.5846 512235.4816 0.807506458 0.816139492 0.948519337 0.809227276 0.468127948 0.891234789 0.763212486 0.761869489 1 18.96644766 4.226234328 0.002057442 1.59392204 2.28E-05 0 0.142701557 7992497.575 6208.668013 2390519.915 2419379.69 16835.8221 -4.226234328 -1.593899234 YEAVS(ph)PERLELER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YEAVSPERLELER 13 1 Q92585 Q92585 MAML1 Mastermind-like protein 1 1 YEAVS(1)PERLELER;YEAVS(1)PERLELER 142.94 2.46E-05 227050000 315950 274910 166177 209276 257020 254510 272400 299850 221279 TRUE FALSE 274196.407 273104.0981 246540.753 256795.3144 251905.8049 264301.1644 245982.6899 235729.4109 195119.6487 1.405273169 1.39967502 1.26353627 1.316091517 1.291032485 1.354559452 1.260676162 1.208127487 1 17.57399954 0.435162743 0.846984988 7.32E-18 1.340048038 0.851146701 0.044764879 3.095009683 0.632959286 5.369306751 0.017074883 2.723721775 -0.435162743 1.340048038 YEAWLAEAESR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YEAWLAEAESR 11 0 Q15642;M0R0F9;W4VSQ9;Q15642-4;Q15642-2;Q15642-3 Q15642 TRIP10 Cdc42-interacting protein 4 0 ; 145.89 8.38E-05 171763000 209840 209220 160098 186531 224470 244080 212040 246460 246630 FALSE TRUE 182109.1123 207845.62 237521.9283 228885.7145 220003.4862 253469.9155 191476.3934 193756.447 217473.6824 0.837384599 0.95572769 1.092186998 1.052475463 1.011632689 1.165519951 0.88045777 0.890942043 1 17.7304813 YEDEVFGDS(ph)EPELDEES(ph)EDEVEEEQEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YEDEVFGDSEPELDEESEDEVEEEQEER 28 0 Q9UN86-2;Q9UN86;D6RB17 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 2 YEDEVFGDS(1)EPELDEES(1)EDEVEEEQEER;YEDEVFGDS(1)EPELDEES(1)EDEVEEEQEER 300.42 8.49E-72 304130000 456630 385983 330189 396272 398470 432060 411560 447230 536850 TRUE FALSE 396285.1885 383447.4523 489869.5048 486251.6142 390541.2266 448681.6278 371646.9745 351593.3448 473384.2046 0.837132259 0.810013196 1.034824356 1.027181747 0.824998432 0.947817066 0.785085288 0.742723017 1 18.85265204 2.239313048 24.9999442 0.81939792 0.915587226 0.083481088 0.101593144 37.56996717 1248355.352 0.040358139 0.029379367 173.505421 -2.239313048 0.096189305 YEDFKEEGSENAVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YEDFKEEGSENAVK 14 1 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 173.03 2.52E-06 431300000 793230 497122 475259 463866 449963 311130 663456 778311 635137 FALSE TRUE 688402.6457 493856.3728 705095.842 569193.865 441009.6166 323099.3724 599114.1392 611875.2495 560051.8274 1.22917668 0.88180477 1.2589832 1.016323556 0.787444295 0.576909773 1.069747673 1.092533261 1 19.09520082 7.999997898 0.683535323 0.948074175 28.23826199 0.165030332 0.185424552 618.1562245 3.526075418 0.081401184 25698.51603 99999516.05 -7.999997898 27.29018781 YEDRVPMYEEQWSYYDDKQPYPSRPPFDNQHS(ph)QDLDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YEDRVPMYEEQWSYYDDKQPYPSRPPFDNQHSQDLDSR 38 3 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 YEDRVPMYEEQWSYYDDKQPYPSRPPFDNQHS(0.724)QDLDS(0.276)R 142.81 3.06E-13 247860000 133530 74723 47653 70188 67113 50588 113220 104790 58412 TRUE FALSE 115883.6722 74232.13969 70698.15019 86125.25816 65777.5826 52534.15309 102239.9418 82381.47398 51506.5999 2.249880062 1.441216074 1.372603711 1.672120822 1.277070953 1.019949933 1.984987206 1.599435298 1 15.65246969 4.738982368 24.22616572 1.450623933 2.249880404 0.43581843 0.294691577 22.88372026 1313798.438 0.071805221 0.40869186 54825.47061 -4.738982368 0.799256471 YEDRYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YEDRYDR 7 1 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 183.74 0.00058209 2751600000 4916900 4687800 3187300 3979200 4399100 4633400 4592600 5057800 5668200 FALSE TRUE 4267119.207 4657005.533 4728688.941 4882738.178 4311566.517 4811649.896 4147210.359 3976228.83 4998111.853 0.853746241 0.931752964 0.946095061 0.976916548 0.862639061 0.962693521 0.829755412 0.795546188 1 22.25295176 2.232144275 24.99580276 0.856637329 0.923587902 0.081590054 0.065444364 253.8211052 988785.6594 0.025666849 0.017771596 170.6649252 -2.232144275 0.066950573 YEDYDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YEDYDYR 7 0 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 0 ;;; 116.88 0.012459 3409850000 7759900 6135200 4430150 5456600 6193700 6364900 6034300 6964500 8313400 FALSE TRUE 6734409.554 6094897.467 6572585.358 6695604.429 6070457.488 6609761.822 5449094.515 5475195.873 7330599.323 0.918671074 0.831432356 0.896595908 0.913377493 0.828098389 0.901667317 0.743335473 0.746896077 1 22.80549972 2.263619633 24.99337379 0.809133488 0.879046906 0.069464609 0.076785508 409.0341954 407961.5672 0.0281376 0.021786585 183.4930555 -2.263619633 0.069913418 YEEEEEQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YEEEEEQSR 9 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 265.55 4.41E-15 999730000 944150 702130 403340 511630 607620 611820 610120 691460 715030 FALSE TRUE 819378.1853 697517.6618 598396.5731 627803.4113 595529.5508 635357.1113 550950.6563 543596.6599 630499.968 1.299568956 1.106292938 0.949082638 0.995723145 0.944535418 1.007703638 0.873831379 0.862167625 1 19.26613677 7.999999999 0.652247471 0.920730783 36.17470964 0.835303651 0.050892257 86.24959889 0.557124256 0.022500902 4390.930394 99999999.77 -7.999999999 35.25397885 YEEIDNAPEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YEEIDNAPEER 11 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 138.71 0.003086 0 53526 60072 39645 64695 61212 66675 54234 57397 64412 FALSE TRUE 46452.40348 59677.38308 58817.4546 79384.98855 59994.00096 69240.03039 48974.39503 45123.09821 56797.28674 0.817863073 1.050708344 1.035568035 1.397689804 1.056282869 1.219072853 0.862266454 0.794458693 1 15.79353439 2.220409835 24.60594167 0.865621136 1.103263805 0.289350577 0.154285825 230.4006336 312337.6774 0.0632741 0.04275941 166.1153766 -2.220409835 0.237642669 YEEIVK ddPTM_MDA-MB-175_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 ;;;;; 132.94 0.034151 9503820000 12925600 10177130 7246440 8706270 9586140 8662210 11808130 12778400 12518300 FALSE TRUE 11217449.21 10110275.76 10750842.62 10683161.67 9395394.569 8995450.824 10662979.37 10045838.6 11038400.83 1.0162205 0.915918521 0.973949287 0.967817878 0.851155408 0.814923371 0.965989506 0.910080976 1 23.39602784 7.99998507 0.79502208 0.916736665 23.30076888 0.191609487 0.057500138 886.6962276 3.155323287 0.021075185 35726.54815 99996562.36 -7.99998507 22.38403221 YEELFPAFSDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YEELFPAFSDSR 12 0 P54920;M0R0Y2;M0R2M1;M0R213;M0R0I4 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;;;;; 211.78 6.50E-08 959432000 1067897 1095782 671064 747478 1020424 1045519 1021246 1168853 1071732 FALSE TRUE 926771.7057 1088583.736 995592.795 917204.3044 1000119.559 1085740.792 922205.7201 918902.882 945033.0639 0.980676488 1.151900158 1.053500489 0.970552608 1.058290548 1.148891858 0.975844926 0.972349981 1 19.85000528 2.126698744 19.34873051 0.980240237 1.060476768 0.279994382 0.058838709 2.490567836 418.7565649 0.023733729 0.016001295 133.8747721 -2.126698744 0.080236532 YEEPEYDIPAFGFDS(ph)EPELSEEPVEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YEEPEYDIPAFGFDSEPELSEEPVEDR 27 0 H0Y507;Q5TCZ1-2;Q5TCZ1-3;Q5TCZ1 H0Y507 SH3PXD2A SH3 and PX domain-containing protein 2A 1 YEEPEYDIPAFGFDS(0.992)EPELS(0.008)EEPVEDR 77.053 0.0096284 15207000 32915 30311 21304 25615 29881 31085 24891 34698 34825 TRUE FALSE 28565.19935 30111.88505 31606.68566 31431.27725 29286.42656 32280.86006 22477.07465 27278.10272 30708.02817 0.930219264 0.980586734 1.029264578 1.023552443 0.953705865 1.051218915 0.731960858 0.888305253 1 14.90632826 2.266305399 24.99984995 0.870628273 0.995125138 0.382290164 0.072677425 207.1774516 186679.6866 0.026688109 0.020667768 184.6313305 -2.266305399 0.124496865 YEEVAR ddPTM_MDA-MB-175_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 1737950000 2651500 2680500 1675200 2068800 2472700 2404100 2558400 2811600 2802300 FALSE TRUE 2301097.557 2662891.619 2485332.323 2538552.66 2423498.108 2496587.283 2310286.762 2210361.22 2471015.286 0.931235662 1.077650808 1.00579399 1.027331831 0.98077018 1.010348781 0.93495446 0.894515397 1 21.2366725 2.233215179 9.017225775 0.932573173 1.008717801 0.29206515 0.044589172 0.117784658 98.97045657 0.016595424 0.011815219 171.0862784 -2.233215179 0.076144628 YEEVSVSGFEEFHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YEEVSVSGFEEFHR 14 0 Q9BRA2;I3L2R6;I3L0K2;I3L3M7 Q9BRA2 TXNDC17 Thioredoxin domain-containing protein 17 0 ;;; 221.86 4.11E-12 1453130000 2021970 1486120 821570 971760 1384050 1387830 1353210 1622520 1560310 FALSE TRUE 1754761.541 1476357.58 1218884 1192412.96 1356510.113 1441220.718 1221975.902 1275556.724 1375851.929 1.275399993 1.073049758 0.885912193 0.866672449 0.985941935 1.0475115 0.888159457 0.927103199 1 20.39189378 4.590450012 2.848319335 0.941739614 1.288449241 0.774865717 0.057456313 0.149687856 1.969191884 0.015183035 0.100085217 38944.8479 -4.590450012 0.346709627 YEFTDALLCHDDELEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YEFTDALLCHDDELEGR 17 0 A0A0A0MTR2;Q8N543;H3BR79;H3BUA6;Q8N543-2 A0A0A0MTR2 OGFOD1 Prolyl 3-hydroxylase OGFOD1 0 ; 188.47 4.09E-10 82791000 131361 119208 72175 88496 109828 109703 103968 118638 151684 FALSE TRUE 114001.311 118424.9148 107079.0714 108590.3694 107642.6377 113923.3454 93885.19936 93268.18694 133752.0903 0.85233293 0.885406086 0.800578676 0.811877924 0.80479219 0.851750018 0.701934446 0.697321341 1 17.02920191 4.210861365 9.921973584 0.795284621 0.868851198 0.058140705 0.084556447 0.713360213 248.0781939 0.021885948 0.046452193 16250.29933 -4.210861365 0.073566578 YEHANDDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YEHANDDK 8 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ;;;;; 108.57 0.0037853 1713889000 3142980 2716890 2088650 2385690 1801540 2222780 2960650 3521080 3920470 FALSE TRUE 2727627.23 2699042.571 3098728.126 2927397.377 1765692.879 2308291.785 2673526.619 2768124.443 3456996.503 0.789016485 0.780747845 0.896364264 0.846803685 0.510759232 0.667715973 0.773366886 0.800731051 1 21.72108771 1.169722736 2.163151907 1.107359572 0.750261841 0.355489825 0.104272179 1.065819786 4.299833483 0.802689782 0.0302687 14.7816439 -1.169722736 -0.357097731 YEHANDDKSSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YEHANDDKSSLK 12 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 143.25 3.73E-05 222380000 247290 270400 137290 90716 220810 263230 259240 245980 66860 FALSE TRUE 214609.9999 268623.7246 203683.9032 111314.4543 216416.313 273356.6284 234098.9447 193379.0912 58955.88697 3.64017931 4.556351171 3.454852665 1.888097356 3.670817693 4.636629902 3.970747566 3.280064149 1 15.84734826 4.04168177 9.638838517 3.198196279 4.078369608 0.13147855 1.046953822 0.868383671 190.5247178 0.275954619 0.574750156 11007.32451 -4.04168177 0.880173329 YEKDIAAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YEKDIAAYR 9 1 P26583;P09429 P26583;P09429 HMGB2;HMGB1 High mobility group protein B2;High mobility group protein B1 0 ;;; 138.22 0.00013019 3430670000 7272000 6067300 2120230 2570990 5940700 4922390 6538900 7244000 488747 FALSE TRUE 6310986.775 6027443.507 3145580.32 3154772.575 5822491.693 5111757.529 5904758.484 5694926.973 430967.8864 14.64375183 13.98582979 7.298874043 7.32020337 13.51026811 11.86111005 13.70115656 13.21427223 1 18.71722085 4.349001957 7.757819604 10 14.4571302 0.194166386 3.878415675 0.397794799 25.39310434 0.984862341 2.628104477 22335.82286 -4.349001957 4.457130202 YEKDVADYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YEKDVADYK 9 1 O15347;E7ES08;E7EQU1 O15347 HMGB3 High mobility group protein B3 0 ;;; 104.14 0.0030167 1029390000 3897640 3139750 2085850 2345090 3022580 2070780 4151450 4700440 2038330 FALSE TRUE 3382556.999 3119124.776 3094574.037 2877578.527 2962436.572 2150444.247 3748843.018 3695287.485 1797360.949 1.881957544 1.735391423 1.721732097 1.601002029 1.648214607 1.196445404 2.085748563 2.055951803 1 20.77744873 4.724848934 1.559087553 1.663695922 1.957895086 0.051151252 0.332854277 4.489068689 10.51164794 0.094434756 2.008451475 53069.98118 -4.724848934 0.294199163 YELGRPAANTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YELGRPAANTK 11 1 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ;; 140.63 3.51E-05 854750000 1649840 1591710 839410 1096830 1776350 1740540 1684310 1845640 1232150 FALSE TRUE 1431809.464 1581253.952 1245351.484 1345882.015 1741004.11 1807499.7 1520965.875 1450964.249 1086486.631 1.317834406 1.455382798 1.146218875 1.238746964 1.602416506 1.663618906 1.399893779 1.33546443 1 20.05123899 1.216993391 2.747408225 0.897254676 1.405469519 0.403199203 0.153062451 0.561592296 4.719287311 0.67415398 0.043440285 16.48137312 -1.216993391 0.508214843 YELHLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YELHLK 6 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;;; 117.56 0.022615 11817710000 20334600 18000700 13124840 17006100 18525700 16777880 21642500 24468600 27255300 FALSE TRUE 17647331.09 17882452.22 19472056.52 20867594.93 18157074.81 17423335.9 19543613.68 19236180.3 24033209.48 0.734289405 0.744072581 0.810214572 0.868281656 0.755499378 0.724969169 0.813192 0.800399976 1 24.51852599 1.111669653 2.368642469 1.121915999 0.779157697 0.714460367 0.04352413 0.559690456 2.421050684 0.461916165 0.012083695 12.93211784 -1.111669653 -0.342758303 YELISETGGSHDKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 180.48 1.13E-06 2616560000 1694250 1377750 795920 1352060 1464860 1286310 1385720 1748150 2278630 FALSE TRUE 1470350.57 1368699.47 1180829.574 1659065.888 1435712.152 1335795.178 1251333.088 1374321.727 2009252.957 0.731789676 0.681198186 0.587695825 0.825712801 0.714550225 0.664821805 0.622785241 0.683996369 1 20.93822777 1.238269787 24.99521139 1.00000035 0.686618781 0.701541815 0.063717749 3.915907175 335966.6769 0.087812242 0.015478572 17.3089127 -1.238269787 -0.313381569 YELPTDDDTYEEHRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YELPTDDDTYEEHRR 15 1 C9J1C6;Q9P0P0 C9J1C6 RNF181 E3 ubiquitin-protein ligase RNF181 0 66.246 0.038394 230470000 147420 166010 81675 100010 152430 139010 133230 170360 117020 FALSE TRUE 127938.0735 164919.4694 121173.3032 122718.7991 149396.9412 144357.8047 120309.3751 133929.8397 103186.0289 1.239877868 1.598273246 1.174318892 1.189296655 1.447840786 1.399005332 1.165946363 1.297945479 1 16.65488812 0.541226257 1.109363622 9.43E-14 1.333327825 0.341877969 0.136916928 8.260246601 2.648111377 18.96728351 0.042079459 3.477172668 -0.541226257 1.333327825 YELYSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YELYSR 6 0 A0A0G2JQD6;Q8IXL6 A0A0G2JQD6 FAM20C Extracellular serine/threonine protein kinase FAM20C 0 ;;; 126.05 0.041086 3228460000 1677300 1844070 1875650 1793220 1435800 1470720 2106400 1670190 4367290 FALSE TRUE 1455640.555 1831956.183 2782720.614 2200398.009 1407230.389 1527299.55 1902121.652 1313032.866 3850993.951 0.37799087 0.475709961 0.722598022 0.571384436 0.365420047 0.396598792 0.493930054 0.340959472 1 21.87679943 1.22998759 24.99873597 1.000000998 0.469306889 0.684136528 0.113585128 210.7662127 614541.2626 0.338948256 0.029725022 16.98195125 -1.22998759 -0.530694109 YEMACAIADAFNLPSSHLRPIT(ph)DSPVLGAQRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YEMACAIADAFNLPSSHLRPITDSPVLGAQRPR 33 2 Q9NZL9;Q9NZL9-2 Q9NZL9 MAT2B Methionine adenosyltransferase 2 subunit beta 1 YEMACAIADAFNLPS(0.021)S(0.021)HLRPIT(0.479)DS(0.479)PVLGAQRPR 153.65 5.76E-09 514610000 115020 107340 46187 80750 120460 129570 127780 150160 79750 TRUE FALSE 99819.81558 106634.8765 68523.18769 99085.52169 118063.0817 134554.6417 115387.9153 118049.4525 70322.04585 1.419466888 1.516379041 0.974419712 1.409025015 1.678891452 1.913406246 1.640849806 1.678697642 1 16.10168942 3.393841116 5.382848626 1.613347427 1.304450119 0.183170506 0.267413375 0.311977205 15.14884899 0.07788347 0.101453632 2476.515876 -3.393841116 -0.308897308 YEMACAIADAFNLPSSHLRPITDS(ph)PVLGAQRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YEMACAIADAFNLPSSHLRPITDSPVLGAQRPR 33 2 Q9NZL9;Q9NZL9-2 Q9NZL9 MAT2B Methionine adenosyltransferase 2 subunit beta 1 YEMACAIADAFNLPSS(0.001)HLRPIT(0.192)DS(0.807)PVLGAQRPR;YEMACAIADAFNLPS(0.017)S(0.063)HLRPIT(0.063)DS(0.856)PVLGAQRPR 174.73 3.26E-15 1346870000 362460 340330 169005 235458 335470 464010 349180 413690 253150 TRUE FALSE 314559.9926 338094.3498 250736.3833 288922.3377 328794.8033 481860.765 315316.5773 325225.6128 223222.8954 1.409174413 1.514604267 1.123255672 1.294322149 1.472943906 2.158652965 1.412563782 1.456954549 1 17.76812548 3.13326 6.088127706 1.524232373 1.334145689 0.070751295 0.294274525 0.585412426 29.64759113 0.092677173 0.105739192 1359.126875 -3.13326 -0.190086684 YENEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YENEER 6 0 Q96MV8-2;Q96MV8-3;Q96MV8 Q96MV8-2 ZDHHC15 Palmitoyltransferase ZDHHC15 0 115.78 0.056159 241530000 360080 359550 217590 261280 279580 365090 349060 374090 361950 FALSE TRUE 312494.5157 357188.0924 322817.2518 320607.6174 274016.905 379135.2485 315208.2149 294093.7647 319160.6833 0.979113443 1.119148163 1.011456826 1.00453356 0.858554701 1.187913388 0.987616055 0.921459879 1 18.28392341 -2 0.20828884 0.594163312 1.049443335 0.025522561 0.090643663 319.1997946 4.828685997 46.459414 0.512643841 0.01 2 0.455280023 YENGAFQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YENGAFQER 9 0 P23919-2;P23919;H7C312;H7BZ20 P23919-2 DTYMK Thymidylate kinase 0 76.465 0.055243 0 197480 172820 116780 146310 159730 178120 213360 196310 180450 FALSE TRUE 171382.5176 171684.734 173255.1986 179531.9217 156551.6855 184972.3917 192668.38 154330.6342 159117.4066 1.077082145 1.078981475 1.088851323 1.128298441 0.983875296 1.162489986 1.210856714 0.969916727 1 17.27973214 1.625371049 12.66363324 0.984827738 1.100864756 0.407657847 0.059651254 0.090626846 46.12122175 0.033476652 0.015343522 42.20569426 -1.625371049 0.116037018 YENGCAYFHEEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YENGCAYFHEEER 13 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q86XE2;Q6P996-2;J3KNK7;H3BNL6;Q6P474;Q6P996-4 H3BND4;Q6P996-4 PDXDC1;PDXDC2P Pyridoxal-dependent decarboxylase domain-containing protein 1;Putative pyridoxal-dependent decarboxylase domain-containing protein 2 0 109.79 0.0011094 249340000 118740 138380 91258 111800 128150 141800 126060 147180 180630 FALSE TRUE 103048.2082 137470.9727 135390.674 137185.8988 125600.0657 147255.1378 113834.7206 115706.7024 159276.1272 0.646978364 0.863098413 0.850037457 0.861308604 0.788568054 0.924527362 0.714700455 0.726453514 1 17.28117052 4.745624153 24.07483869 0.828084611 0.64697822 0.326109102 0.085903203 659.6307086 2248139.56 0.020999555 0.201612074 55670.37576 -4.745624153 -0.181106391 YEPFSFADDIGSNNCGYYDLQAVLTHQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YEPFSFADDIGSNNCGYYDLQAVLTHQGR 29 0 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 ; 266.28 1.67E-58 227769000 170305 143975 106351 103001 131597 150515 138566 165465 146135 FALSE TRUE 147798.7628 143029.2187 157782.6993 126388.9513 128978.4772 156305.4094 125127.8906 130081.5974 128859.0868 1.146979747 1.109966106 1.224459239 0.980830724 1.000926519 1.212994856 0.971044369 1.00948719 1 16.97543475 YEPQS(ph)PGYEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YEPQSPGYEPR 11 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 YEPQS(1)PGYEPR;YEPQS(1)PGYEPR;YEPQS(1)PGYEPR;YEPQS(1)PGYEPR 197.63 5.92E-08 3554890000 2702160 2183020 1357370 1684740 2172280 1993420 2086440 2270820 2195280 TRUE FALSE 2345062.71 2168679.598 2013798.672 2067285.967 2129055.878 2070108.157 1884097.37 1785222.815 1935756.499 1.211445092 1.120326652 1.04031611 1.067947321 1.09985728 1.069405247 0.973313209 0.922235217 1 20.88446606 7.999999992 0.100585583 0.735498914 2.036275459 0.711772155 0.043342516 168.386899 1.561278086 3.174175438 30.84862245 99999998.11 -7.999999992 1.300776545 YEPSDKDRQS(ph)PPPAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YEPSDKDRQSPPPAK 15 2 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK;YEPS(0.005)DKDRQS(0.995)PPPAK;YEPSDKDRQS(1)PPPAK;YEPS(0.006)DKDRQS(0.994)PPPAK;YEPSDKDRQS(1)PPPAK 160.55 8.88E-07 4063450000 8049610 5240920 4811860 5277270 5203030 3926510 6794520 8297910 9925340 TRUE FALSE 6985833.643 5206492.051 7138891.591 6475554.812 5099499.883 4077565.38 6135588.496 6523466.521 8751977.612 0.798200584 0.59489321 0.815688968 0.739896181 0.582668296 0.465902172 0.701051667 0.745370568 1 23.06117762 1.206796779 2.147502808 1.118336607 0.666089085 0.491555731 0.104689339 0.682088708 2.943504092 0.624220824 0.029155679 16.09892136 -1.206796779 -0.452247522 YEQGTGCWQGPNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YEQGTGCWQGPNR 13 0 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;;; 255.52 1.79E-23 2934410000 725257 700725 470446 553992 716170 926860 667670 657997 573498 FALSE TRUE 629412.4499 696121.8913 697955.2591 679784.3508 701919.6182 962516.904 602919.4662 517289.4621 505699.7198 1.244636739 1.376551863 1.380177271 1.344245061 1.388016625 1.903336835 1.192247974 1.02291823 1 18.94792145 2.00843425 24.99996164 1.041442136 1.437311215 0.514219223 0.174614232 147.4793241 437141.7441 0.072416404 0.048736435 101.9610384 -2.00843425 0.395869079 YESLELCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YESLELCR 8 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 110.81 0.0078046 94555000 73529 62546 67044 78299 68324 71513 69628 65679 262970 FALSE TRUE 63811.95635 62135.13121 99466.70265 96077.98468 66964.48607 74264.15139 62875.48728 51634.05696 231881.9862 0.27519152 0.267960147 0.428953988 0.414340011 0.288786926 0.320267014 0.271152962 0.22267386 1 17.82303122 1.234123444 25 1.000001024 0.310282092 0.917944621 0.064723084 39.08899137 220207.3892 0.135229573 0.017556852 17.14444554 -1.234123444 -0.689718933 YESLELCRPVLQQGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YESLELCRPVLQQGR 15 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;; 300.33 2.64E-44 4394760000 1443720 1199340 879770 1061420 1233060 1294170 1205050 1322000 2117680 FALSE TRUE 1252928.744 1191461.457 1305229.715 1302431.634 1208524.518 1343957.557 1088184.436 1039300.588 1867330.283 0.67097329 0.638056089 0.69898171 0.697483271 0.647193766 0.719721396 0.582748776 0.556570306 1 20.8325457 1.229284474 24.99999386 1.000000686 0.64830002 0.821653362 0.051012226 169.8022742 457597.833 0.172846114 0.014078715 16.95448 -1.229284474 -0.351700665 YESLTDPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 151.44 0.00019274 590290000 1642650 1321310 1111010 1378760 1325820 1144420 1460960 1743180 3185730 FALSE TRUE 1425569.641 1312630.228 1648298.152 1691828.531 1299438.776 1188446.578 1319276.324 1370414.522 2809116.629 0.507479692 0.467275091 0.586767433 0.602263542 0.462579148 0.423067724 0.469640993 0.487845363 1 21.42168509 1.237718154 24.99904098 1.000000583 0.499966827 0.889527628 0.055279155 6.959526524 206390.2509 0.086125188 0.014680158 17.28694117 -1.237718154 -0.500033755 YESLTDPSKLDSGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YESLTDPSKLDSGK 14 1 P08238;Q58FF7;P07900;P07900-2;G3V2J8;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AB3P;HSP90AA1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-beta 2 0 ;;;;; 179.17 1.73E-06 11723910000 30570470 20728490 15651730 17584180 18949190 14010400 29694110 34753350 12485040 FALSE TRUE 26530504.93 20592323.18 23220958.98 21576936.83 18572138.19 14549389.15 26814379.78 27321616.55 11009072.79 2.40987642 1.870486604 2.109256557 1.959923168 1.686984775 1.321581701 2.435661957 2.481736388 1 23.39218963 6.755515217 1.479147248 1.915213534 196.8354355 0.11139523 0.457520755 1553.174853 11.07492549 0.128915547 1020159.984 5695281.793 -6.755515217 194.9202219 YESQEPLAGQES(ph)PLPLATR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 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;YESQEPLAGQES(1)PLPLATR 358.88 3.77E-91 13228800000 9417670 8051990 5066782 6531410 8517910 8737500 8032230 9621420 8965830 TRUE FALSE 8173101.048 7999095.948 7517094.723 8014466.467 8348420.256 9073637.279 7253265.571 7563954.207 7905899.791 1.033797703 1.011788178 0.950820896 1.013732362 1.055973447 1.147704565 0.917449723 0.95674805 1 22.91449824 YETSSTSAGDRYDSLLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YETSSTSAGDRYDSLLGR 18 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;H0YIS3;H0YIM2 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 0 ;; 322.17 9.42E-62 1087920000 535440 452460 249673 286660 475070 494070 432385 510130 348367 FALSE TRUE 464680.2474 449487.7605 370415.6979 351750.5343 465617.0365 513077.1926 390452.3693 401042.6693 307183.4501 1.512712508 1.463255134 1.205845229 1.14508296 1.515762116 1.670263136 1.271072283 1.305547773 1 18.22874097 1.115455739 1.645192599 0.74913662 1.398695344 0.390515148 0.156662657 1.679484639 3.213591108 1.943781066 0.04706527 13.04535012 -1.115455739 0.649558724 YEWDVAEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 YEWDVAEAR 9 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;; 216.57 1.39E-06 19590560000 15426040 15467920 11591170 14484480 15383100 14766490 14467040 16849460 24275450 FALSE TRUE 13387449.73 15366310.22 17196698.58 17773402.57 15077006.41 15334566.43 13064028.69 13246334.1 21405633.96 0.62541711 0.717862888 0.803372543 0.830314234 0.704347577 0.716379924 0.610307955 0.618824658 1 24.35148723 YEYDPDIS(ph)PPR ddPTM_MDA-MB-175_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 150.21 3.57E-05 1150760000 972840 812580 641770 853210 909180 839190 792520 950590 1153020 TRUE FALSE 844276.7291 807242.1085 952132.1186 1046944.371 891089.0968 871474.1823 715661.5324 747313.726 1016711.289 0.83039968 0.793973783 0.936482292 1.029736152 0.876442611 0.857150099 0.703898481 0.73503042 1 19.95547863 2.466918399 24.35603769 0.790525726 0.894744435 0.106735717 0.099475413 269.8927637 644274.5215 0.038367235 0.029755067 293.0342601 -2.466918399 0.104218709 YEYHWADGTNIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YEYHWADGTNIK 12 0 Q9H8S9;Q7L9L4;Q7L9L4-2;D6RCK3;Q9H8S9-2 Q9H8S9 MOB1A;MOB1B MOB kinase activator 1A;MOB kinase activator 1B 0 ;;; 232.42 1.12E-12 1725810000 2135170 1860690 1182620 1608570 1783370 1587940 1969950 2386690 2358230 FALSE TRUE 1853001.875 1848467.005 1754538.988 1973820.404 1747884.426 1649029.079 1778904.552 1876314.917 2079442.736 0.891105027 0.888924217 0.843754414 0.949206424 0.840554248 0.793014903 0.855471767 0.902316224 1 20.98776553 1.276669629 2.629160816 1.023851573 0.86589325 0.520632277 0.040443729 0.376168687 3.125193107 0.127343907 0.011032603 18.90904648 -1.276669629 -0.157958324 YFDACADAVSKDELQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YFDACADAVSKDELQR 16 1 Q9Y5P4-3;Q9Y5P4;Q9Y5P4-2;A0A2R8Y7C5;A0A2R8YE18;A0A2R8Y7Q9;A0A2R8Y5S9;A0A2R8YEA4;A0A2R8YE59;A0A2U3TZL3;A0A2R8YEK8;A0A2R8Y5H3;A0A2R8YFI2;A0A2R8YCI0;A0A2R8YDX6 Q9Y5P4-3 COL4A3BP Collagen type IV alpha-3-binding protein 0 103.75 0.0012902 256360000 385740 323070 210580 234260 275990 270990 321150 367480 287090 FALSE TRUE 334763.4817 320947.7319 312417.1923 287452.3134 270498.339 281415.1607 290004.9224 288897.2617 253150.5473 1.322388931 1.2678137 1.234116204 1.135499475 1.068527569 1.111651402 1.145582838 1.141207336 1 17.94963608 3.899125533 1.723693931 1.102957127 1.304555511 0.797505956 0.042672688 0.174877593 1.000235275 0.013071995 0.033558239 7927.304372 -3.899125533 0.201598384 YFDDEFTAQS(ph)ITITPPDRYDSLGLLELDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YFDDEFTAQSITITPPDRYDSLGLLELDQR 30 1 P31751;P31751-2 P31751 AKT2 RAC-beta serine/threonine-protein kinase 1 YFDDEFT(0.123)AQS(0.437)IT(0.351)IT(0.09)PPDRYDSLGLLELDQR 80.112 0.0015945 68892000 33008 34559 20429 23885 33896 35640 34602 37460 34427 TRUE FALSE 28645.90917 34331.97965 30308.53273 29308.45431 33221.53592 37011.09386 31246.30337 29449.47051 30357.07928 0.943631925 1.130938169 0.998400816 0.965456987 1.094358769 1.219191528 1.029292149 0.970102237 1 14.88974537 1.996051002 24.98651619 0.987950035 1.062232198 0.122431956 0.080525024 319.5062939 2021614.461 0.034325962 0.022563011 99.09483125 -1.996051002 0.074282162 YFDDEFTAQSITIT(ph)PPDR ddPTM_MDA-MB-175_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;YFDDEFTAQSITIT(1)PPDR;YFDDEFTAQSIT(0.003)IT(0.997)PPDR;YFDDEFTAQSITIT(1)PPDR 231.86 6.25E-19 460653000 198601 184190 174113 198460 204193 205560 200309 231537 548971 TRUE FALSE 172355.3747 182980.0438 258314.6292 243523.3763 200129.9588 213468.0262 180883.064 182024.6144 484072.2738 0.356052978 0.378001496 0.533628227 0.50307235 0.413429915 0.440983791 0.37366954 0.376027763 1 18.88486294 1.235762176 24.99977892 1.000000774 0.422445597 0.907720004 0.057931208 23.45933133 209532.3791 0.103703756 0.015368764 17.20925922 -1.235762176 -0.577555176 YFDDEFTAQSITIT(ph)PPDRYDSLGLLELDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 YFDDEFTAQSITITPPDRYDSLGLLELDQR 30 1 P31751;P31751-2 P31751 AKT2 RAC-beta serine/threonine-protein kinase 1 YFDDEFTAQS(0.005)IT(0.147)IT(0.848)PPDRYDSLGLLELDQR;YFDDEFTAQSIT(0.014)IT(0.986)PPDRYDSLGLLELDQR;YFDDEFTAQSITIT(0.811)PPDRY(0.086)DS(0.103)LGLLELDQR;YFDDEFTAQSITIT(1)PPDRYDSLGLLELDQR;YFDDEFT(0.047)AQS(0.03)IT(0.135)IT(0.788)PPDRYDSLGLLELDQR;YFDDEFTAQSITIT(0.971)PPDRY(0.018)DS(0.011)LGLLELDQR;YFDDEFTAQSIT(0.008)IT(0.992)PPDRYDSLGLLELDQR;YFDDEFTAQSIT(0.001)IT(0.998)PPDRYDS(0.001)LGLLELDQR 244.22 1.34E-45 4332546000 516626 490447 328023 379787 505105 528718 500727 582182 484248 TRUE FALSE 448352.5651 487225.2214 486656.02 466023.443 495054.3987 549058.1236 452166.5726 457686.9098 427000.7531 1.050004155 1.141040661 1.139707639 1.091387871 1.159375938 1.285848139 1.058936242 1.071864409 1 18.70387909 2.036410414 24.99998157 1.048365464 1.144932932 0.369371988 0.062252277 186.343697 127945.8567 0.025698766 0.017326052 108.7452795 -2.036410414 0.096567468 YFDEEFTAQMITIT(ph)PPDQDDSMECVDSER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YFDEEFTAQMITITPPDQDDSMECVDSER 29 0 P31749;P31749-2;G3V2I6 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 1 YFDEEFTAQMITIT(0.843)PPDQDDS(0.156)MECVDSER 128.06 6.61E-05 16097000 21973 20184 13620 14823 14666 19366 17808 19446 18788 TRUE FALSE 19069.21238 20051.40997 20206.67756 18188.78871 14374.17529 20111.02255 16080.9829 15287.62423 16566.90404 1.151042604 1.210329336 1.219701491 1.09789908 0.867644024 1.213927629 0.970669164 0.922780997 1 14.0160164 3.472362853 7.677372884 0.993779087 1.189734972 0.506232234 0.089953674 0.100472559 43.94437817 0.02558989 0.03439174 2967.30954 -3.472362853 0.195955884 YFDEHYEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YFDEHYEYR 9 0 P33552 P33552 CKS2 Cyclin-dependent kinases regulatory subunit 2 0 ; 90.15 0.011625 592670000 600460 620470 496450 612300 688020 787660 559390 701730 1242970 FALSE TRUE 521107.6896 616394.0917 736534.8805 751332.0734 674329.7481 817961.7899 505140.4439 551670.5004 1096027.503 0.47545129 0.562389256 0.672004013 0.685504763 0.61524893 0.746296774 0.460883 0.503336366 1 20.06385257 -1.999980537 0.033921043 1.534220961 5.97E-06 0.132420309 0.148348987 8249.740374 27.65625534 921.327809 422.6313974 0.010000448 1.999980537 -1.534214992 YFDGSGGNNHAVEHYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YFDGSGGNNHAVEHYR 16 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;;;;; 192.78 2.77E-10 4987559000 2693091 2577722 1428125 1878112 2496322 2767142 2292725 2705530 2740764 FALSE TRUE 2337192.201 2560788.774 2118771.027 2304566.035 2446650.076 2873595.743 2070376.882 2126973.464 2416754.002 0.967079065 1.059598442 0.876701156 0.95357907 1.012370342 1.18903113 0.856676716 0.880095145 1 21.2046392 YFDLGLPNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YFDLGLPNR 9 0 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;; 142.79 0.00024076 805850000 650100 710616 469579 740939 794951 1005548 660552 811290 849601 FALSE TRUE 564187.6379 705947.9167 696668.975 909180.5245 779133.0304 1044232.082 596491.7687 637801.947 749162.1376 0.7530915 0.942316598 0.929930839 1.213596468 1.040005883 1.393866601 0.796211846 0.851353686 1 19.51491846 4.697212778 1.702430545 1.024384308 0.678664436 0.216243119 0.170668063 1.60100332 4.900532132 0.049781154 0.881102295 49798.10059 -4.697212778 -0.345719872 YFDPANGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YFDPANGK 8 0 P13639 P13639 EEF2 Elongation factor 2 0 ;; 129.47 0.0025346 603990000 1942320 1750700 1126410 1411250 1720950 1543630 1993130 2244780 1978580 FALSE TRUE 1685637.491 1739199.536 1671145.644 1731695.882 1686706.462 1603014.445 1799836.559 1764751.266 1744674.526 0.966161576 0.996861885 0.957855244 0.992560994 0.966774282 0.918804293 1.031617377 1.011507441 1 20.73452649 2.207375177 24.99998065 1.014495989 0.968686636 0.503488945 0.022339919 167.4158121 134208.5868 0.009019719 0.006081747 161.2037636 -2.207375177 -0.045809352 YFDS(ph)GDYNMAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 16 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;YFDS(1)GDYNMAK 244.26 7.60E-16 19655840000 30737510 26143720 18388183 19126009 24666561 23547577 25979560 34484308 32291591 TRUE FALSE 26675470.17 25971980.18 27280769.8 23468861.67 24175744.7 24453467.52 23460066.27 27110107.09 28474115.9 0.936832254 0.912125956 0.958090144 0.824217396 0.849042856 0.858796375 0.823908505 0.952096535 1 24.76314771 1.538235419 4.954495588 0.99009674 0.880457811 0.455176799 0.044961556 0.138404565 7.178468397 0.036089818 0.012311425 34.53308826 -1.538235419 -0.10963893 YFDSGDYNMAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YFDSGDYNMAK 11 0 A6NMQ3;Q5T5H1;O43768-2;O43768;O43768-9;O43768-3;O43768-4;O43768-6;O43768-5;O43768-7;P56211;H3BMD8;P56211-2;H3BQ52;H3BTD3 A6NMQ3;P56211 ENSA;ARPP19 Alpha-endosulfine;cAMP-regulated phosphoprotein 19 0 ; 93.096 0.01464 142700000 528920 627640 419150 461240 553060 557930 597500 652680 591030 FALSE TRUE 459021.8819 623516.9915 621852.342 565971.5916 542055.188 579393.9281 539554.542 513109.4612 521159.1067 0.880771104 1.196404291 1.193210162 1.085986188 1.040095397 1.111740965 1.035297158 0.984554342 1 18.99136436 2.02988618 3.482115818 0.993788681 1.092670418 0.157246827 0.087684863 0.385647057 9.705844163 0.043807617 0.024291019 107.1238517 -2.02988618 0.098881737 YFEADPPGQVAAS(ph)PDPTT ddPTM_MDA-MB-175_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 243.26 4.65E-24 345230000 681720 806450 516800 631510 888430 845600 744800 927870 938110 TRUE FALSE 591628.9747 801152.3768 766726.2086 774903.9975 870751.9812 878130.7792 672569.4106 729452.2212 827207.7045 0.715212118 0.968502073 0.926884753 0.936770769 1.052640076 1.061560204 0.813059897 0.881824743 1 19.6578901 4.741715949 24.72033367 0.947679223 0.715212018 0.502781737 0.07466019 250.5120066 1962515.418 0.019724326 0.136530747 55171.64701 -4.741715949 -0.232467205 YFEITDESPYVHYLNTFSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YFEITDESPYVHYLNTFSSK 20 0 Q9ULV4;Q9ULV4-2;Q9ULV4-3;B4E3S0 Q9ULV4 CORO1C Coronin-1C;Coronin 0 ; 228.35 3.11E-25 425500000 476030 415260 198374 318350 432190 413690 431130 537100 453980 FALSE TRUE 413121.4294 412532.1297 294308.3299 390636.2332 423590.2646 429604.922 389319.079 422245.3447 400311.0016 1.032001188 1.030529084 0.735199205 0.97583187 1.058152943 1.073177905 0.972541543 1.054793256 1 18.61076174 3.474603796 23.79289262 1.030861634 0.927895746 0.220657461 0.085612422 61.91662387 585172.4971 0.024686441 0.032099459 2982.660315 -3.474603796 -0.102965888 YFEITEEPPYIHFLNTFTSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YFEITEEPPYIHFLNTFTSK 20 0 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;; 162.65 2.08E-11 375270000 938710 825820 454798 665980 763580 654427 867810 979810 850560 FALSE TRUE 814657.0951 820395.134 674739.834 817200.9379 748386.2519 679603.2302 783649.9198 770285.2564 750007.7658 1.086198213 1.093848853 0.899643797 1.089589968 0.997838004 0.906128258 1.044855741 1.027036374 1 19.51654601 YFEQLLEEEREK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YFEQLLEEEREK 12 1 O15460-2;O15460 O15460-2 P4HA2 Prolyl 4-hydroxylase subunit alpha-2 0 77.912 0.024757 39221000 19539 21332 14522 14642 19799 21024 15169 19055 13762 FALSE TRUE 16956.87164 21191.86869 21544.88777 17966.68989 19405.03864 21832.80688 13697.91271 14980.23654 12135.07204 1.397344127 1.746332335 1.775423146 1.480558981 1.599087222 1.799149343 1.128787095 1.234457982 1 13.56689505 2.227850343 24.99978939 1.145022652 1.636140323 0.754432754 0.137440897 101.0711039 235916.8579 0.054267823 0.037003475 168.9858509 -2.227850343 0.491117671 YFGDIISVGQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YFGDIISVGQR 11 0 Q96CN7;D6RGE2 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 ; 91.265 0.025288 316030000 214860 212730 162705 163186 189237 232680 223410 238810 211302 FALSE TRUE 186465.7066 211332.5626 241389.6822 200239.8754 185471.5539 241631.3502 201743.7326 187742.3399 186322.1183 1.000770646 1.134232289 1.295550332 1.074697289 0.995434979 1.296847376 1.082768565 1.0076224 1 17.50743942 1.860319175 4.068081768 1.006224545 1.135081516 0.206917779 0.102142277 0.347369682 9.071397107 0.058317413 0.027493971 72.49685634 -1.860319175 0.12885697 YFGTDAVPDGS(ph)DEEEVAYTG ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YFGTDAVPDGSDEEEVAYTG 20 0 Q9NWZ5;Q9NWZ5-4 Q9NWZ5 UCKL1 Uridine-cytidine kinase-like 1 1 YFGTDAVPDGS(1)DEEEVAYTG;YFGTDAVPDGS(1)DEEEVAYTG 153.63 5.32E-08 82687000 317560 271920 172267 207615 274720 302130 268150 309690 284860 TRUE FALSE 275593.6414 270133.7396 255575.8974 254757.1589 269253.6095 313753.1366 242144.8543 243465.2035 251184.1753 1.097177563 1.075440916 1.017484072 1.014224557 1.071936993 1.249095952 0.964013175 0.969269673 1 17.93838605 YFHVVIAGPQDSPFEGGTFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YFHVVIAGPQDSPFEGGTFK 20 0 P61088;F8VSD4;F8VV71;F8VZ29 P61088 UBE2N Ubiquitin-conjugating enzyme E2 N 0 ; 295.37 1.36E-54 3038800000 2447020 2092100 1337290 1793600 1987540 1742720 2375270 2873550 2548990 FALSE TRUE 2123640.107 2078356.857 1984007.917 2200864.293 1947991.843 1809763.566 2144916.681 2259063.694 2247651.306 0.944826318 0.924679398 0.882702718 0.979184043 0.866678847 0.805179861 0.954292454 1.005077473 1 21.09998681 2.004306544 24.99178692 0.995936493 0.900936283 0.455610981 0.046413814 106.4342846 617657.435 0.019674887 0.013206639 100.9965512 -2.004306544 -0.09500021 YFLNLVLVDEEDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YFLNLVLVDEEDRR 14 1 O75436 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ; 214.47 1.10E-11 936630000 651430 676690 432600 561440 611460 653780 636510 689800 693380 FALSE TRUE 565341.875 672244.7788 641806.807 688923.5331 599293.1423 678931.3397 574781.3582 542291.638 611409.4063 0.924653545 1.099500223 1.049716933 1.126779415 0.980183059 1.11043653 0.940092436 0.886953378 1 19.22177922 2.159720752 7.875744255 0.929559498 1.051219939 0.358715279 0.066210533 0.220048673 19.10629175 0.025248612 0.017008391 144.4510664 -2.159720752 0.121660441 YFNEMSAQGLRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YFNEMSAQGLRPR 13 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 270.45 4.18E-32 2065100000 1013950 1053640 784590 895610 990180 1104610 988210 1152460 1490860 FALSE TRUE 879953.9385 1046718.569 1164020.348 1098971.939 970477.3553 1147105.061 892373.5463 906015.3975 1314612.229 0.669363877 0.796218494 0.88544768 0.835966618 0.738223283 0.87258055 0.678811232 0.689188323 1 20.32620588 4.75518879 0.004604974 1.560577702 0.000124627 0.016454612 0.105368967 771083.1629 991.7356187 164928.1306 171177.7876 56910.02675 -4.75518879 -1.560453075 YFPSSLS(ph)PVTPSESLPRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YFPSSLSPVTPSESLPRPR 19 1 Q9P0U4;Q9P0U4-2;K7EKZ6;K7EQ21 Q9P0U4 CXXC1 CXXC-type zinc finger protein 1 1 YFPS(0.033)S(0.029)LS(0.938)PVTPSESLPRPR;YFPS(0.002)S(0.005)LS(0.993)PVTPSESLPRPR 285.46 3.09E-40 619270000 148193 131775 83438 89041 121105 137070 113565 142339 107435 TRUE FALSE 128608.9196 130909.3613 123788.8959 109259.12 118695.2474 142343.1716 102551.4838 111900.9125 94734.15669 1.357577077 1.381860207 1.306697607 1.153323403 1.252929794 1.502553847 1.082518569 1.181209782 1 16.53159707 2.202907507 24.99996771 1.107122178 1.316347255 0.556447988 0.099401529 148.7323962 104290.1877 0.04138974 0.027906075 159.5539303 -2.202907507 0.209225077 YFQFQEEGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YFQFQEEGK 9 0 O15144 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 95.502 0.018616 68649000 129530 108240 78079 94928 176110 123020 120050 133790 174680 FALSE TRUE 112412.2823 107528.9643 115838.2656 116482.8533 172605.7556 127752.659 108407.5695 105180.0497 154029.5294 0.729809945 0.698106167 0.752052324 0.756237156 1.12060172 0.829403683 0.703810301 0.682856398 1 17.23284743 3.457705086 24.9991738 0.83995975 0.72885824 0.196009878 0.128749077 511.592102 658695.1921 0.040348472 0.052096515 2868.8318 -3.457705086 -0.11110151 YFQFQEEGKEGENR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YFQFQEEGKEGENR 14 1 O15144 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;; 256.77 2.30E-24 1631590000 1491960 1190500 685390 850030 1150440 986860 1454550 1530080 452780 FALSE TRUE 1294793.706 1182679.527 1016846.896 1043042.303 1127548.495 1024825.143 1313487.965 1202884.299 399252.8642 3.243041746 2.962231791 2.546874394 2.612485462 2.824146289 2.566857334 3.289864852 3.012838246 1 18.60694323 1.236090114 24.99970491 0.999997532 2.879427281 0.838195645 0.259900695 27.21592182 275345.4009 0.440527444 0.066923907 17.22225892 -1.236090114 1.879429749 YFQHLLGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YFQHLLGK 8 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2;J3QL06;J3KTF1;Q9BST8;J3QQH7;J3QLE9 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 83.206 0.018325 551500000 1789800 1740900 1136300 1392300 1739900 2050800 1674300 1760600 1557100 FALSE TRUE 1553273.395 1729463.913 1685818.481 1708442.995 1705279.394 2129695.603 1511926.644 1384109.391 1373021.412 1.131281262 1.259604474 1.227816599 1.244294503 1.241990387 1.551101523 1.101167564 1.008075605 1 20.38892269 2.013124015 24.99979585 1.019616656 1.274760078 0.542035632 0.106408104 163.4342862 311322.9754 0.043235855 0.029131828 103.0680394 -2.013124015 0.255143422 YFQINQDEEEEEDED ddPTM_MDA-MB-175_Pertuzumab_2h_R1 15 YFQINQDEEEEEDED 15 0 P35268;K7ERI7 P35268 RPL22 60S ribosomal protein L22 0 ;;;;;;;;;;;;;; 361.13 1.15E-82 7566131000 7662710.7 7613918 5044438.2 5695695.5 7623241.3 7668974.8 7341580.5 8136801.1 7861996.2 FALSE TRUE 6650064.066 7563901.671 7483945.386 6988990.217 7471553.713 7964005.223 6629595.153 6396809.505 6932559.966 0.959250854 1.091069058 1.079535615 1.008139886 1.077748155 1.148782739 0.956298277 0.922719679 1 22.72495676 2.131785198 10.33442869 0.951057453 1.061309513 0.441571537 0.053319398 0.270441865 24.3446606 0.021215434 0.014300023 135.4519302 -2.131785198 0.11025206 YFQS(ph)PS(ph)RS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YFQSPSRSR 9 1 Q16629;Q16629-4;H7BZZ6 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 3 Y(0.002)FQS(0.998)PS(1)RS(1)R;Y(0.003)FQS(0.998)PS(0.999)RS(1)R 66.215 0.052475 1177360000 1201000 1074210 731800 814700 1076140 930740 892220 990130 1449300 TRUE FALSE 1042284.807 1067153.444 1085700.928 999690.0869 1054726.919 966546.1701 805692.6417 778398.4047 1277965.405 0.815581394 0.835040948 0.849554239 0.78225129 0.82531727 0.756316381 0.630449493 0.609091922 1 20.28541735 2.572128218 4.128632637 0.710829937 0.821130114 0.069192101 0.107121083 0.398046273 11.99930631 0.038450552 0.033033297 373.3603698 -2.572128218 0.110300177 YFQS(ph)PSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YFQSPSR 7 0 Q16629;Q16629-4;H7BZZ6 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 1 YFQS(1)PSR;YFQS(0.991)PS(0.009)R;YFQS(0.976)PS(0.024)R;YFQS(1)PSR;YFQS(0.997)PS(0.003)R 154.85 0.0017316 3930790000 5081140 3277190 2390920 3365990 3543290 3908880 3342790 4237590 4959500 TRUE FALSE 4409654.475 3255661.923 3547176.909 4130289.475 3472785.461 4059257.143 3018606.74 3331414.355 4373193.56 1.008337366 0.744458684 0.811118205 0.944456132 0.794107421 0.928213464 0.69025226 0.761780678 1 22.06025577 2.270076254 24.99960567 0.800472629 0.863009691 0.041330675 0.109014068 555.811686 440892.72 0.039322797 0.030456461 186.2414113 -2.270076254 0.062537062 YFQSPS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YFQSPSR 7 0 Q16629;Q16629-4;H7BZZ6 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 1 YFQS(0.044)PS(0.956)R 105.52 0.0082946 691730000 951030 600800 465300 623120 630970 708140 718620 789010 861330 TRUE FALSE 825348.9759 596853.3052 690320.6363 764608.9198 618414.9315 735382.604 648928.343 620286.3516 759504.5486 1.086693921 0.785845597 0.908909153 1.006720659 0.814234665 0.968239894 0.854410081 0.816698666 1 19.53469908 3.23471457 24.9999893 0.882617594 0.932804474 0.067058457 0.095592003 306.7524443 1993943.607 0.027369138 0.032220891 1716.779702 -3.23471457 0.05018688 YFSDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YFSDLR 6 0 E7ESC6;Q9UIA9 E7ESC6 XPO7 Exportin-7 0 ;;;; 119.22 0.049314 1349950000 3367990 3306970 2028600 2019580 3185350 3483570 3088180 3330710 3764640 FALSE TRUE 2922901.588 3285246.296 3009637.745 2478156.506 3121967.767 3617585.192 2788688.779 2618463.586 3319588.548 0.880501166 0.989654666 0.906629753 0.746525201 0.940468291 1.089769151 0.840070611 0.788791607 1 21.662573 YFSIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YFSIDR 6 0 K7ER00;Q9Y285;Q9Y285-2;K7EPH2;K7ERS0 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 107.22 0.07317 231230000 420450 406930 262920 248420 413660 447300 420150 446460 455120 FALSE TRUE 364886.4672 404256.85 390068.9914 304827.5579 405428.9753 464507.9204 379403.9177 350988.0034 401316.2321 0.909224293 1.007327433 0.97197412 0.75956947 1.010248136 1.157461083 0.945398883 0.874592093 1 18.61437998 YFTWDPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YFTWDPSR 8 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;; 168.45 0.00071364 1314570000 3875350 4378440 3109640 3253390 4545370 6309100 3676340 3653240 4204760 FALSE TRUE 3363212.679 4349677.739 4613472.305 3992121.924 4454926.03 6551815.16 3319809.113 2872023.056 3707678.063 0.907094041 1.173154105 1.24430229 1.076717519 1.201540682 1.767093865 0.895387641 0.774615003 1 21.82208455 2.039077682 24.99997924 0.860344369 1.227829445 0.337132056 0.222939253 159.2952317 101908.6208 0.090731216 0.061170871 109.415206 -2.039077682 0.367485076 YFVAFDGDLVQEFDMTSATHVLGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YFVAFDGDLVQEFDMTSATHVLGSR 25 0 P49916-3;P49916 P49916-3 LIG3 DNA ligase 3 0 142.42 3.48E-07 17406000 15592 13914 6885.9 9266.8 15304 14771 11277 15430 12474 FALSE TRUE 13531.47769 13822.59802 10215.94427 11370.96857 14999.48034 15339.24993 10183.35828 12130.41458 10999.33793 1.23020838 1.256675457 0.928778108 1.033786638 1.363671199 1.394561202 0.925815566 1.102831339 1 13.42512907 2.21303761 24.99931229 1.025493949 1.191179906 0.278267454 0.144192925 367.9710322 360418.0653 0.063328308 0.042713069 163.3193376 -2.21303761 0.165685957 YFVDHNTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YFVDHNTR 8 0 O00308-2;O00308;O00308-3;Q9H0M0-3;Q9H0M0;Q9H0M0-6 O00308-2;Q9H0M0-3 WWP2;WWP1 NEDD4-like E3 ubiquitin-protein ligase WWP2;NEDD4-like E3 ubiquitin-protein ligase WWP1 0 80.165 0.026154 203710000 839980 1073500 523490 1042000 1322300 1541700 724250 864030 925670 FALSE TRUE 728974.5148 1066448.108 776651.515 1278602.026 1295988.817 1601010.197 654012.3465 679263.9084 816238.3471 0.893090256 1.306540071 0.951500892 1.566456698 1.587757818 1.961449376 0.801251679 0.832188185 1 19.63863096 2.137694784 21.10414393 0.865039343 1.374272451 0.365829194 0.310123767 4.571929668 945.8179368 0.132151119 0.089096322 137.3076657 -2.137694784 0.509233108 YFYLFPNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YFYLFPNR 8 0 P25098;P35626 P25098 ADRBK1;ADRBK2 Beta-adrenergic receptor kinase 1;Beta-adrenergic receptor kinase 2 0 103.28 0.011172 166090000 781190 858320 713130 688550 732020 613140 1081000 962540 1426800 FALSE TRUE 677953.7622 852681.6394 1058002.053 844895.8013 717454.2342 636727.8926 976164.7864 756708.3115 1258125.329 0.538860276 0.677739824 0.840935341 0.67155138 0.570256569 0.506092579 0.77588835 0.60145702 1 20.26284421 1.233414613 24.99046878 1.000000541 0.652529296 0.535530109 0.102985042 134.6105369 653632.0498 0.207913876 0.025371614 17.11648615 -1.233414613 -0.347471245 YGADALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YGADALR 7 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 92.692 0.036019 106410000 215140 236140 160730 184310 214880 242000 235230 278040 278360 FALSE TRUE 186708.7039 234588.7808 238459.5656 226160.4025 210604.3084 251309.8966 212417.4308 218583.3097 245452.5979 0.760671125 0.955739653 0.971509642 0.921401543 0.858024361 1.023863258 0.865411214 0.890531661 1 17.90508491 4.743959417 24.69110366 0.929959025 0.76067104 0.499149371 0.054856989 432.0071422 1975687.407 0.012996548 0.1085514 55457.38877 -4.743959417 -0.169287985 YGAFGLPITVAHVDGQTHMLFGSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YGAFGLPITVAHVDGQTHMLFGSDR 25 0 Q9Y2Q3-3;Q9Y2Q3;Q9Y2Q3-2;Q9Y2Q3-4 Q9Y2Q3-3 GSTK1 Glutathione S-transferase kappa 1 0 ;; 254.25 4.54E-45 2361161000 888646 895414 447923 673765 950784 957910 838044 1011266 737774 FALSE TRUE 771209.1796 889531.9665 664540.061 826753.6411 931865.2586 994761.4176 756770.6219 795014.6356 650555.1982 1.185463096 1.3673428 1.021496812 1.270843187 1.43241536 1.529096102 1.163268888 1.222055619 1 19.31131195 1.156750997 1.604596392 0.847171846 1.290195497 0.280140606 0.14202321 1.8827827 3.723116337 1.411705183 0.041770085 14.3466663 -1.156750997 0.443023651 YGDAFIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YGDAFIR 7 0 P62312 P62312 LSM6 U6 snRNA-associated Sm-like protein LSm6 0 ;;; 151.17 0.0044183 1176080000 2374670 2315100 1322210 1624690 2171480 2134620 2023990 2381530 2349330 FALSE TRUE 2060851.343 2299891.956 1961635.179 1993600.696 2128271.796 2216740.213 1827703.761 1872258.343 2071594.884 0.994813879 1.110203531 0.946920266 0.962350656 1.027359072 1.070064533 0.882268911 0.903776292 1 20.98231047 2.23366454 24.99978984 0.921559231 1.017362244 0.363806935 0.055783992 125.1606106 639071.9284 0.022501893 0.015715223 171.2633913 -2.23366454 0.095803013 YGDFFIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YGDFFIR 7 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90;H0Y7E6 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ; 133.47 0.0076042 362030000 298770 302540 220570 244110 356300 346960 294800 330960 471030 FALSE TRUE 259286.7875 300552.5948 327238.3898 299538.9065 349210.3271 360307.7757 266210.3414 260186.7795 415345.37 0.624267914 0.723620911 0.787870561 0.721180319 0.840770964 0.867489568 0.640937303 0.626434766 1 18.66395195 4.676678554 2.715549179 0.76465997 0.606922917 0.161772269 0.109915652 0.822738638 8.884842942 0.028609988 0.2718561 47498.35341 -4.676678554 -0.157737053 YGDGGSSFQSTTGHCVHMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YGDGGSSFQSTTGHCVHMR 19 0 P55795 P55795 HNRNPH2 Heterogeneous nuclear ribonucleoprotein H2 0 ;;;;; 232.15 9.94E-21 1887720000 760137 704678 249588 394422 728324 773826 707369 774427 378215 FALSE TRUE 659682.9695 700048.9238 370289.5916 483981.5435 713831.7773 803595.587 638768.4633 608821.8126 333502.8536 1.978042954 2.099079262 1.110304118 1.451206604 2.140406805 2.409561353 1.915331328 1.825537042 1 18.34733958 3.246699701 24.99611722 1.885945536 1.651805933 0.045072824 0.443256239 617.1597116 1895361.356 0.134953961 0.171182797 1764.817092 -3.246699701 -0.234139603 YGDGGSTFQSTTGHCVHMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YGDGGSTFQSTTGHCVHMR 19 0 P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7;D6RIT2;H0YBG7 P31943 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 ;;;;; 165.9 1.21E-11 2361859000 959786 980537 395219 583997 903696 838815 828560 917544 842082 FALSE TRUE 832947.8483 974095.7879 586348.2303 716602.4447 885714.2177 871084.7558 748206.3787 721334.3559 742532.0253 1.1217669 1.311856936 0.789660527 0.965079512 1.192829652 1.173127523 1.007641897 0.971452182 1 19.50209372 7.999892808 0.022717852 0.033424214 2.387225666 0.062515031 0.142139936 16816.39316 37.95303828 1512.558528 2550.548146 99975321.24 -7.999892808 2.353801452 YGDGPRPPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YGDGPRPPK 9 1 Q08211;Q08211-2 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 64.711 0.062577 856270000 2645300 2174200 1399300 1785420 2255600 1962230 2695600 3134400 2741300 FALSE TRUE 2295716.903 2159917.537 2076006.16 2190826.899 2210717.973 2037718.258 2434181.127 2464132.952 2417226.637 0.949731758 0.893551934 0.858838029 0.906339052 0.914567935 0.842998429 1.007014026 1.019405013 1 21.20492131 2.22068841 24.89189706 1.010939791 0.89415357 0.772232285 0.029297929 98.54020983 137242.9074 0.011616903 0.007850628 166.2219643 -2.22068841 -0.116786221 YGDSEFTVQSTTGHCVHMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YGDSEFTVQSTTGHCVHMR 19 0 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 195.38 6.07E-16 784180000 647210 604220 217290 414640 608590 586940 524130 613730 524190 FALSE TRUE 561679.5587 600250.839 322372.1708 508790.3494 596480.2497 609519.9616 473299.9533 482488.6156 462220.8554 1.215175716 1.298623444 0.697441855 1.100751607 1.290465895 1.318676893 1.023969273 1.043848649 1 18.81822283 2.100832812 23.82798253 1.027015019 1.145558514 0.106765725 0.177352528 22.55479036 5285.84702 0.076219719 0.051387298 126.134187 -2.100832812 0.118543495 YGDTSYHDEEEDEYEAEDDEEEEDEGRKDS(ph)DTESSDLFTNLNLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YGDTSYHDEEEDEYEAEDDEEEEDEGRKDSDTESSDLFTNLNLGR 45 2 Q9Y3S2 Q9Y3S2 ZNF330 Zinc finger protein 330 1 YGDTSYHDEEEDEYEAEDDEEEEDEGRKDS(0.752)DT(0.178)ES(0.035)S(0.035)DLFTNLNLGR 129.26 4.85E-10 60645000 49767 36692 30872 41017 42758 38519 30676 44770 71991 TRUE FALSE 43190.16486 36450.96784 45801.80246 50330.53676 41907.19945 40000.85086 27701.04624 35196.2839 63480.30599 0.680371088 0.574209076 0.721511999 0.792852775 0.66016064 0.630130089 0.436372286 0.554444144 1 15.95402146 2.846774081 4.261631755 0.619200556 0.689596171 0 0.152061183 0.902506368 27.75542892 0.051256167 0.051272575 702.706679 -2.846774081 0.070395614 YGEAGEGPGWGGAHPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YGEAGEGPGWGGAHPR 16 0 P26640;A0A140T954;A2ABF4;A0A0G2JJT9 P26640 VARS Valine--tRNA ligase 0 ;;; 206.2 2.06E-11 2203540000 1193050 1093370 708233 869030 1113910 1072460 1057090 1253440 1121480 FALSE TRUE 1035385.42 1086187.58 1050736.848 1066356.544 1091745.37 1113718.23 954573.5745 985401.6103 988899.912 1.047007293 1.098379692 1.062531036 1.078326058 1.103999866 1.126219364 0.96528836 0.996462431 1 19.91546499 2.232375341 24.99999973 0.988254373 1.086028483 0.797546481 0.023470367 62.19572386 251383.016 0.009422266 0.006531242 170.7557517 -2.232375341 0.097774109 YGEPSEVFINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YGEPSEVFINR 11 0 Q8WXF1;Q8WXF1-2;X6RDA4 Q8WXF1 PSPC1 Paraspeckle component 1 0 ;;; 204.91 7.35E-08 672490000 929630 817561 540553 609242 803150 783227 827590 926360 876770 FALSE TRUE 806777.0401 812190.388 801966.2388 747579.7078 787168.8863 813358.2495 747330.4492 728265.1229 773119.2494 1.043535057 1.050537014 1.037312471 0.966965586 1.018172665 1.052047598 0.966643179 0.941982913 1 19.56033143 3.227756395 0.190839555 0.909164384 1.113098799 0.365466454 0.031179168 6.58102936 1.555074193 0.706604032 0.851164342 1689.492995 -3.227756395 0.203934414 YGEPTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YGEPTLR 7 0 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 81.32 0.064023 108780000 303930 283650 189960 230380 286600 256380 288020 350440 338190 FALSE TRUE 263764.8804 281786.6845 281825.2914 282691.3001 280897.2207 266243.1045 260087.8647 275501.1331 298209.5635 0.884495042 0.944928396 0.945057858 0.947961886 0.941945716 0.892805386 0.872164734 0.923850764 1 18.185967 YGEVEEMNVCDNLGDHLVGNVYVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YGEVEEMNVCDNLGDHLVGNVYVK 24 0 P0DN76;Q01081;Q01081-2;Q01081-4 P0DN76;Q01081-2;Q01081-4 U2AF1 Splicing factor U2AF 35 kDa subunit 0 166.89 1.24E-11 135400000 110600 81070 56265 71994 82096 64816 82945 109610 107400 FALSE TRUE 95983.92978 80537.44583 83474.9422 88341.33806 80462.45022 67309.51346 74901.00667 86170.75449 94703.29435 1.013522607 0.85041863 0.88143652 0.932822228 0.849626729 0.710740993 0.790901807 0.909902397 1 16.53112699 3.22433827 22.6924538 0.847768216 0.911889634 0.131101551 0.084670859 184.6383494 294597.5413 0.027187495 0.031019972 1676.247991 -3.22433827 0.064121417 YGEYFPGTGDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YGEYFPGTGDLR 12 0 Q92769;Q92769-3;Q13547;Q5TEE2 Q92769;Q13547 HDAC2;HDAC1 Histone deacetylase 2;Histone deacetylase 1 0 ;;; 226.39 3.59E-11 2380920000 3293220 2944180 1806290 2284050 3011270 2767260 2816400 3225800 3188870 FALSE TRUE 2858012.633 2924839.488 2679817.886 2802678.462 2951351.618 2873718.283 2543265.961 2535987.773 2811885.421 1.016404371 1.040170224 0.953032391 0.996725699 1.049598819 1.021989823 0.904469984 0.901881618 1 21.42310638 2.243954416 24.99673763 0.927166149 1.012422332 0.486090727 0.037256138 100.1634472 464195.2638 0.014443672 0.010852872 175.369642 -2.243954416 0.085256183 YGGDEIPFS(ph)PYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YGGDEIPFSPYR 12 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 YGGDEIPFS(1)PYR;YGGDEIPFS(1)PYR;YGGDEIPFS(1)PYR;YGGDEIPFS(1)PYR 194.86 1.03E-06 567942000 1167890 1239330 814950 990200 1155530 1241700 1081820 1196880 1773450 TRUE FALSE 1013550.377 1231188.76 1209062.546 1215040.044 1132537.214 1289469.002 976905.2629 940936.5261 1563794.761 0.648135166 0.787308405 0.773159353 0.776981785 0.724223691 0.824576878 0.624701711 0.601700779 1 20.57661975 2.250366642 24.98753215 0.707984167 0.757492207 0 0.116707521 857.6922332 1815311.561 0.042926468 0.032977212 177.978131 -2.250366642 0.049508041 YGGDS(ph)DHPS(ph)DGETSVQPMMTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YGGDSDHPSDGETSVQPMMTK 21 0 Q8WYQ5-3;Q8WYQ5;Q8WYQ5-2 Q8WYQ5-3 DGCR8 Microprocessor complex subunit DGCR8 2 Y(0.045)GGDS(0.957)DHPS(0.998)DGETSVQPMMTK 122.5 1.48E-05 122720000 131260 104030 83399 87753 115020 94864 114390 134810 128910 TRUE FALSE 113913.6584 103346.6201 123731.0354 107678.6599 112731.327 98513.47947 103296.4754 105981.9306 113670.4067 1.002139975 0.909177887 1.088507018 0.94728842 0.991738574 0.866658987 0.908736746 0.932361674 1 16.79449718 2.789233422 24.9837476 0.926080033 0.986751638 0.229847091 0.05530334 527.017045 259839.8404 0.017169945 0.01716991 615.5076035 -2.789233422 0.060671605 YGGELVPHFPAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 132.76 0.00017516 2291090000 3113190 3551350 2008250 2402650 2931250 3430370 2704470 3187230 4731130 FALSE TRUE 2701774.054 3528020.948 2979446.417 2948208.405 2872923.86 3562338.554 2442190.916 2505665.668 4171821.201 0.647624604 0.845678848 0.714183632 0.706695772 0.688649806 0.853904897 0.585401626 0.600616744 1 21.9922459 2.237641998 24.99998446 0.696024851 0.742064563 0 0.129437088 116.915866 3181635.09 0.049675933 0.035692482 172.8391007 -2.237641998 0.046039712 YGGGGYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 YGGGGYGR 8 0 Q01130;J3KP15 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ;;;;;; 140.01 0.001527 4814920000 5173840 4607510 2941828 3392390 4315820 4890930 4645290 4854830 5165080 FALSE TRUE 4490103.935 4577242.963 4364505.861 4162683.999 4229943.626 5079087.242 4194790.491 3816662.385 4554470.126 0.985867469 1.005000107 0.958290589 0.913977671 0.928745498 1.1151873 0.921027117 0.838003605 1 22.11885179 2.017676501 24.99999554 0.89905599 0.981809757 0.15836997 0.066858949 327.9542629 463826.0069 0.027125545 0.018284454 104.1541314 -2.017676501 0.082753767 YGGPPPGWEGPHPQR ddPTM_MDA-MB-175_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 ; 198.23 8.03E-09 451740000 296340 272320 180408 226800 281760 305460 268740 278960 378060 FALSE TRUE 257177.9182 270531.112 267653.9122 278298.4064 276153.5273 317211.2439 242677.6362 219306.5749 333366.1775 0.771457741 0.811513376 0.802882627 0.834812963 0.82837896 0.951539974 0.727961181 0.657854905 1 18.34674821 YGGPYHIGGSPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YGGPYHIGGSPFK 13 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ; 163.78 3.82E-05 1332820000 4264500 3586100 1836260 2393700 3011600 3085800 3430700 4025600 4774700 FALSE TRUE 3700935.52 3562542.673 2724281.478 2937226.17 2951675.052 3204512.723 3097991.242 3164756.767 4210240.405 0.879031876 0.846161342 0.647060789 0.697638588 0.70107043 0.761123455 0.735822885 0.751680774 1 22.00547118 1.238649222 7.777326344 1.003509519 0.74797742 0.563663717 0.068357211 0.075929156 36.93832512 0.102347728 0.017601538 17.32404175 -1.238649222 -0.255532098 YGGSVGSQPPPVAPEPGPVPSS(ph)PSQEPPTKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YGGSVGSQPPPVAPEPGPVPSSPSQEPPTKR 31 1 A0A087WTZ5;Q04323;E9PJ81;E9PRQ7;Q04323-2;E9PS08 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 1 YGGSVGSQPPPVAPEPGPVPS(0.071)S(0.818)PS(0.11)QEPPT(0.001)KR 232.27 1.92E-36 483390000 285760 239890 170210 197660 264270 247320 319710 389140 271590 TRUE FALSE 247996.092 238314.1468 252524.1253 242541.724 259011.544 256834.5604 288704.5734 305925.4393 239482.9396 1.035548054 0.995119515 1.054455594 1.012772452 1.081544867 1.072454518 1.205532945 1.277441474 1 17.86956336 2.369714801 3.53781724 1.186967461 1.036097212 0.358792007 0.073355974 0.205607593 5.016905045 0.029193888 0.021760688 234.268988 -2.369714801 -0.150870249 YGIDKDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YGIDKDK 7 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ; 92.439 0.01429 1101830000 2827500 2294300 2280900 2530400 1892580 1546440 2919300 3348400 5058100 FALSE TRUE 2453838.711 2279228.592 3383950.869 3104965.995 1854921.361 1605932.547 2636186.735 2632370.717 4460137.18 0.55017113 0.511022083 0.758710042 0.696159304 0.415888859 0.360063487 0.591055079 0.590199496 1 22.08865665 1.215727524 3.582898997 1.075935956 0.555515835 0.586456652 0.116599896 0.261976137 4.880930838 0.383818578 0.032179679 16.43340368 -1.215727524 -0.520420121 YGIICMEDLIHEIYTVGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YGIICMEDLIHEIYTVGK 18 0 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 126.88 2.18E-05 723039000 1160520 932440 687490 870120 959560 882190 1221920 1343170 1229150 FALSE TRUE 1007154.342 926314.7402 1019962.464 1067694.045 940466.6333 916128.4202 1103418.386 1055943.548 1083841.287 0.929245226 0.854659027 0.941062567 0.985101839 0.867716191 0.845260677 1.018062699 0.97426031 1 20.04772208 2.223725043 24.99954163 0.993470943 0.905348912 0.50935289 0.043230336 211.0320726 355609.0864 0.018206503 0.012330398 167.3882787 -2.223725043 -0.088122031 YGIICMEDLIHEIYTVGKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YGIICMEDLIHEIYTVGKR 19 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 248.13 5.11E-25 1048390000 2620110 2408470 745980 858190 1933610 1839370 2736340 2927570 213805 FALSE TRUE 2273855.825 2392648.602 1106738.423 1053055.156 1895134.944 1910131.754 2470970.168 2301531.938 188529.2165 12.06102623 12.69112898 5.870381493 5.585633759 10.05220824 10.13175459 13.10656361 12.20782636 1 17.52442859 4.276001893 24.99105465 8.921859541 12.37608631 0.168655524 3.565999587 353.8455845 236177.0925 0.92074302 2.43593212 18879.9958 -4.276001893 3.454226768 YGIKPEWMMIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YGIKPEWMMIHR 12 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3;F2Z2R5 Q14839-2 CHD4;CHD5 Chromodomain-helicase-DNA-binding protein 4 0 ; 137.89 5.05E-05 701740000 1562640 1645380 748570 1014230 1566910 1472000 1613570 1774360 759480 FALSE TRUE 1356133.165 1634571.39 1110580.956 1244526.423 1535731.557 1528628.793 1457086.23 1394926.922 669695.1396 2.025000757 2.44076938 1.658338086 1.858347701 2.293180084 2.282574118 2.175745565 2.082928245 1 19.35314497 1.238706477 7.061239426 0.977177157 2.107002281 0.705219472 0.22397138 0.061597133 18.19411621 0.333770971 0.05608503 17.32632582 -1.238706477 1.129825124 YGISSMIQSQEKPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YGISSMIQSQEKPDR 15 1 P14868;H7C278 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ; 157.58 1.76E-06 1297520000 364610 269630 226790 267410 291730 235900 272940 389540 337560 FALSE TRUE 316425.8647 267858.7828 336466.4026 328129.5276 285925.1438 244975.2256 246470.3208 306239.9024 297654.0413 1.063065911 0.899899701 1.130394202 1.102385595 0.960595537 0.823019988 0.828042918 1.028845102 1 18.18327696 3.052793674 7.409031228 0.924383956 1.043219347 0.3295733 0.087073155 0.305840129 35.8138177 0.028333843 0.032106839 1129.259296 -3.052793674 0.118835392 YGLFPANYVELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YGLFPANYVELR 12 0 Q14247;Q14247-3 Q14247 CTTN Src substrate cortactin 0 ; 120.06 0.0010473 1082650000 610390 569290 522140 693560 622760 631550 473520 643860 1641130 FALSE TRUE 529725.415 565550.2965 774648.6505 851043.3984 610368.2944 655846.1372 427598.1033 506175.5495 1447117.481 0.36605557 0.390811599 0.535304604 0.588095583 0.421782131 0.453208634 0.295482647 0.349781933 1 20.46475062 1.234078957 24.9999103 1.000000859 0.423708343 0.815064514 0.086064524 63.57230372 354577.9503 0.1823217 0.023545205 17.14268942 -1.234078957 -0.576292516 YGLIFHSTFIGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YGLIFHSTFIGR 12 0 O00567;A0A494C128;H0Y653;H0YDU4 O00567 NOP56 Nucleolar protein 56 0 138.76 6.87E-05 214730000 443480 442830 175500 339010 458480 415710 442530 490060 503180 FALSE TRUE 384872.9944 439921.0206 260372.387 415987.4019 449357.145 431702.6327 399613.5087 385264.4827 443694.6336 0.867427652 0.991495022 0.586827893 0.937553377 1.012762181 0.9729724 0.900649858 0.868309989 1 18.75920758 3.536624574 24.9999647 0.941325154 0.821093999 0.255484133 0.106769301 388.284076 163133.8934 0.029071189 0.043119446 3440.523857 -3.536624574 -0.120231155 YGLQDS(ph)DEEEEEHPSK ddPTM_MDA-MB-175_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 292.64 9.17E-46 4791610000 3350310 2686960 1808230 2457030 2837620 2338740 3074340 3571330 5491660 TRUE FALSE 2907558.045 2669309.183 2682696.076 3014936.215 2781156.914 2428712.841 2776190.98 2807628.872 4842442.211 0.600432162 0.551232016 0.553996508 0.622606545 0.574329397 0.501547099 0.573303895 0.579796051 1 22.2073034 1.237531325 6.153903131 1.014957383 0.567838488 0.94818304 0.031626702 0.026854519 4.110346005 0.050359501 0.007909148 17.2795061 -1.237531325 -0.447118896 YGMGTS(ph)VER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YGMGTSVER 9 0 P08559-3;P08559;P08559-2;P08559-4 P08559-3 PDHA1 "Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial" 1 YGMGT(0.058)S(0.942)VER;YGMGT(0.045)S(0.955)VER;YGMGT(0.066)S(0.934)VER;YGMGT(0.023)S(0.977)VER 102.42 0.0037626 1248550000 4107670 3625830 2080470 3146520 3393070 3495620 2071170 2725630 2337390 TRUE FALSE 3564831.002 3602011.684 3086592.251 3860985.458 3325554.545 3630098.763 1870308.252 2142775.235 2061066.417 1.729605108 1.747644644 1.497570493 1.873295021 1.613511587 1.761272094 0.907446862 1.039643952 1 20.97495957 2.239663275 24.99999999 0.99117539 1.700032726 0.916489214 0.102646172 6.833073749 154928.9106 0.036957269 0.02698341 173.6453968 -2.239663275 0.708857336 YGNANAWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YGNANAWR 8 0 O00743;O00743-2;O00743-3 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed" 0 ;;; 181.2 0.0005469 1869550000 1477200 1759410 1003420 1192190 1825590 1762180 1632620 1812330 1753290 FALSE TRUE 1281984.277 1747852.32 1488677.268 1462894.961 1789264.331 1829972.205 1474288.764 1424777.333 1546018.054 0.829216887 1.130551041 0.962910663 0.946234074 1.157337281 1.18366807 0.953603847 0.921578716 1 20.56012574 4.761474743 23.49305048 1.023504798 0.829216397 0.30886351 0.094570534 3967.734812 4067830.486 0.024915447 1.188868123 57739.7293 -4.761474743 -0.194288401 YGNANVWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YGNANVWK 8 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 88.942 0.034274 0 372790 268830 235820 217020 302220 196580 281890 406470 311510 FALSE TRUE 323524.857 267064.038 349863.3408 266297.7079 296206.4133 204142.5598 254552.3512 319549.5537 274683.6427 1.177808965 0.972260435 1.273695577 0.969470571 1.078354759 0.743191541 0.926710993 1.163336668 1 18.06741148 3.671629786 24.99996945 0.990131063 1.124358202 0.249655123 0.129786804 309.0327872 115429.2492 0.036923525 0.054766445 4694.937183 -3.671629786 0.134227138 YGNPWEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YGNPWEK 7 0 P11216;P11217;P11217-2;E9PK47;P06737-2;P06737 P11216;E9PK47 PYGB;PYGM;PYGL "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form;Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ;; 123.69 0.0098156 783740000 941890 803430 535840 570860 816490 758900 902530 1007220 905280 FALSE TRUE 817416.8501 798152.2154 794974.0163 700482.488 800243.4464 788095.3741 815002.7795 791833.8412 798258.8297 1.02399976 0.999866441 0.995885027 0.877512984 1.002486182 0.98726797 1.02097559 0.991951247 1 19.60649708 YGPADVEDTTGSGATDSKDDDDIDLFGS(ph)DDEEESEEAKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR 39 2 P24534;C9JZW3 P24534 EEF1B2 Elongation factor 1-beta 1 YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDS(0.001)KDDDDIDLFGS(0.997)DDEEES(0.001)EEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR 460.93 3.36E-269 28552073000 11513496 6753384 8035437 7033949 6722350 4611689 9458002 12238124 10008721 TRUE FALSE 9991958.332 6709020.576 11921401.21 8631114.628 6588588.387 4789103.66 8540766.422 9621096.42 8825501.405 1.132168913 0.760185769 1.350790246 0.977974421 0.746539838 0.542643805 0.967737246 1.090147288 1 23.07324681 4.813330315 20.47674419 0.940718147 1.132195211 0.077117332 0.217276306 54227.41013 14842899.21 0.055598025 257.5376496 65062.43526 -4.813330315 0.191477064 YGPLS(ph)EPGSAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YGPLSEPGSAR 11 0 Q9H1Z4 Q9H1Z4 WDR13 WD repeat-containing protein 13 1 YGPLS(0.999)EPGS(0.001)AR;YGPLS(0.752)EPGS(0.248)AR 100.31 0.0043238 179290000 563800 412850 257170 330650 423680 412520 399910 431850 470160 TRUE FALSE 489292.4015 410137.9612 381538.2722 405729.1362 415249.5969 428389.9113 361126.7898 339502.2382 414578.2204 1.180217333 0.989289695 0.92030467 0.978655212 1.001619421 1.033315042 0.871070336 0.81890997 1 18.6612848 YGQFSGLNPGGRPIT(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 YGQFSGLNPGGRPITPPR 18 1 P62136;P62136-2;P62136-3 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 1 YGQFSGLNPGGRPIT(1)PPR;YGQFSGLNPGGRPIT(1)PPR;YGQFSGLNPGGRPIT(1)PPR;YGQFSGLNPGGRPIT(1)PPR;YGQFSGLNPGGRPIT(1)PPR;YGQFSGLNPGGRPIT(1)PPR;YGQFSGLNPGGRPIT(1)PPR 158.48 2.89E-10 11742250000 4904280 4282850 2567700 3301580 4479190 4479040 3811260 4697270 5032490 TRUE FALSE 4256166.972 4254715.676 3809448.308 4051254.2 4390062.882 4651351.567 3441644.592 3692795.365 4437554.765 0.959124382 0.958797334 0.85845663 0.912947426 0.989297736 1.048178966 0.775572308 0.832168967 1 22.08133349 2.232428971 24.99999514 0.857619391 0.949995752 0.223101952 0.073597329 210.4372395 857985.7522 0.030451101 0.021120747 170.7768391 -2.232428971 0.09237636 YGQFSGLNPGGRPITPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YGQFSGLNPGGRPITPPR 18 1 P62136;P62136-2;P62136-3 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 ; 178.51 8.06E-14 1822510000 508620 434130 234067 287830 467710 521760 420460 526140 357260 FALSE TRUE 441404.5783 431278.1714 347262.5841 353186.2007 458403.4861 541832.4448 379683.8539 413629.0554 315025.1298 1.401172594 1.369027835 1.102332961 1.121136593 1.455133076 1.719965786 1.205249417 1.313003365 1 18.26510739 1.001001718 1.928922829 0.65976914 1.340543227 0.2595973 0.178114197 2.80172403 5.672039377 4.348423515 0.051449839 10.02309203 -1.001001718 0.680774087 YGQNCHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YGQNCHK 7 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 ;;; 83.843 0.021982 1064750000 948090 807750 444997 563822 516884 622040 874620 886440 889740 FALSE TRUE 822797.5043 802443.8371 660199.0376 691846.4026 506599.0197 645970.2813 789799.487 696881.7043 784555.9508 1.048742927 1.022800013 0.841493888 0.881831821 0.645714329 0.823357825 1.006683445 0.888249848 1 19.58151681 4.274496945 7.174135736 0.869408327 1.038036119 0.32400556 0.099808164 0.247079914 36.80587398 0.026493523 0.069203696 18814.68473 -4.274496945 0.168627792 YGQNGDFTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YGQNGDFTR 9 0 O76094-2;O76094;R4GNC1 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 ; 165.26 0.00014339 732970000 910200 869150 510080 653240 810720 882910 823900 956800 906130 FALSE TRUE 789914.7638 863440.4964 756756.3941 801568.1261 794588.2581 916876.119 743998.3048 752195.7658 799008.3437 0.988618918 1.08064015 0.947119514 1.003203699 0.994468036 1.147517578 0.93115211 0.941411653 1 19.60785104 YGREDLDVLGLTFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YGREDLDVLGLTFR 14 1 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 ;;;; 246.18 9.43E-18 2187546000 2562106 2382407 1724823 2010656 2407080 2754524 2803723 2844912 2085449 FALSE TRUE 2223517.201 2366756.812 2558953.172 2467206.176 2359183.817 2860492.321 2531818.375 2236549.708 1838909.595 1.209149817 1.287043593 1.391560074 1.341668009 1.282925394 1.555537221 1.376804157 1.216236902 1 20.81041912 1.372832215 2.541687804 0.970439512 1.352426032 0.603983101 0.090680517 0.27437249 2.481333983 0.201468226 0.024894427 23.59566463 -1.372832215 0.38198652 YGRPPDSHHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 YGRPPDSHHSR 11 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ;;;;;;; 144.57 2.20E-05 1625526000 1989517 2286445 369714.1 1085702 2791546 2881653 1898932 2325442 2354293 FALSE TRUE 1726597.288 2271425.192 548509.0754 1332227.233 2735999.696 2992512.056 1714773.867 1828164.325 2075971.164 0.831705815 1.094150647 0.264218061 0.641736868 1.317937235 1.441499819 0.826010446 0.880630886 1 20.98535497 3.259189821 24.9978985 1.064016434 0.703842951 0.327911884 0.272266441 336.3370903 407561.3962 0.084595169 0.109086142 1816.309361 -3.259189821 -0.360173483 YGS(ph)FEEAEASYPILNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YGSFEEAEASYPILNR 16 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 YGS(1)FEEAEASYPILNR;YGS(1)FEEAEASYPILNR;YGS(1)FEEAEASYPILNR;YGS(1)FEEAEASYPILNR 323.59 2.27E-58 256885000 385419 204530 142515 175474 227343 178692 298736 245616 240020 TRUE FALSE 334484.9026 203186.429 211435.7307 215318.0537 222819.3191 185566.3969 269764.6287 193092.9298 211645.109 1.580404594 0.960033662 0.99901071 1.017354262 1.052796921 0.876780936 1.274608376 0.912342981 1 17.69128762 4.741837703 24.83821008 1.013046756 1.580404826 0.73835321 0.106406123 138.9390632 1053015.734 0.023864014 0.166782756 55187.11646 -4.741837703 0.56735807 YGS(ph)PPQRDPNWNGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YGSPPQRDPNWNGER 15 1 O15234;J3KSY7 O15234 CASC3 Protein CASC3 1 YGS(1)PPQRDPNWNGER;YGS(1)PPQRDPNWNGER;Y(0.001)GS(0.999)PPQRDPNWNGER;YGS(1)PPQRDPNWNGER 131.67 3.16E-05 1738700000 1746780 1409600 982070 999710 1673510 1442400 1470100 1740930 1149930 TRUE FALSE 1515938.597 1400340.245 1457002.337 1226709.435 1640210.425 1497890.061 1327529.928 1368645.667 1013986.585 1.495028257 1.381024429 1.436904943 1.209788623 1.617585922 1.477228676 1.309218433 1.349767036 1 19.95160714 0.716371308 1.327489827 1.45E-09 1.424121132 0.596218763 0.107874944 3.323294266 1.85621358 9.145706818 0.031002208 5.204407661 -0.716371308 1.424121131 YGSIIDRDDRDER ddPTM_MDA-MB-175_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 58.752 0.05883 172960000 53907 56541 31328 33178 59100 59754 54221 64449 39040 FALSE TRUE 46783.05337 56169.57845 46478.32559 40711.57199 57924.02563 62052.77505 48962.65577 50667.08289 34424.73567 1.358995282 1.631663318 1.350143281 1.182625551 1.682628043 1.802563588 1.42231029 1.471821988 1 15.07115796 1.222548398 4.185490413 0.941348694 1.494259277 0.420518931 0.179872203 0.267033492 8.529752761 0.45801183 0.047000606 16.6935383 -1.222548398 0.552910583 YGTCPHGGYGLGLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YGTCPHGGYGLGLER 15 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;;; 233.97 1.21E-17 2594680000 3337283 2395374 1518989 1817520 2422498 2589681 2471067 2673811 2583088 FALSE TRUE 2896252.596 2379638.63 2253577.161 2230215.695 2374295.029 2689307.704 2231423.303 2102037.325 2277718.279 1.271558745 1.044746689 0.989401183 0.979144662 1.042400656 1.180702516 0.979674845 0.922869762 1 21.11915789 4.734536787 3.448104184 1.009493143 1.303232879 0.590972787 0.066867748 0.229545041 4.71547026 0.018393545 0.176009723 54267.12164 -4.734536787 0.293739735 YGVIILDEAHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 YGVIILDEAHER 12 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ;;;;;;; 215.08 4.23E-11 4951572000 6144930 5011860 2913093 3868489 4732080 5173630 4787200 5501770 5154600 FALSE TRUE 5332861.931 4978936.762 4321874.519 4746888.554 4637920.866 5372662.894 4322938.081 4325259.3 4545229.06 1.173287828 1.095420428 0.950859563 1.044367289 1.020393209 1.182044474 0.951093558 0.951604252 1 22.11592157 4.46417041 4.831374082 1.012651799 1.158690533 0.376024392 0.06798844 0.182973495 11.51937344 0.017922019 0.058194483 29118.59461 -4.46417041 0.146038734 YGVQADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YGVQADR 7 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;; 127.12 0.0090405 2549920000 2010680 2084280 1611820 1868250 2173950 2356100 1892790 2224490 3743600 FALSE TRUE 1744963.544 2070588.227 2391301.543 2292464.717 2130692.648 2446740.692 1709227.517 1748800.125 3301035.873 0.5286109 0.627254082 0.724409439 0.694468284 0.645461828 0.741203909 0.517785199 0.529773135 1 21.65448739 1.229419504 24.99972696 1.000000725 0.625969855 0.67997361 0.080608382 238.6352767 652587.0081 0.260389528 0.021492874 16.95975225 -1.229419504 -0.37403087 YGVQADRVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YGVQADRVDK 10 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;; 157.77 7.83E-06 9335700000 8738820 8146080 4350860 4711000 7568620 6275790 8741160 9827570 3017760 FALSE TRUE 7583962.796 8092567.864 6454950.449 5780704.553 7418019.27 6517223.702 7893443.649 7726020.634 2661003.851 2.850038264 3.041171046 2.425757651 2.172377372 2.787677014 2.449159816 2.966340559 2.90342332 1 21.34353917 1.234432747 24.99960123 0.999997517 2.702144551 0.791696094 0.273959615 58.4354213 353853.4902 0.532206267 0.07090722 17.15666009 -1.234432747 1.702147033 YGVYEDENYEVGS(ph)DDEEIPFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YGVYEDENYEVGSDDEEIPFK 21 0 O15541 O15541 RNF113A RING finger protein 113A 1 YGVYEDENYEVGS(1)DDEEIPFK;YGVYEDENYEVGS(1)DDEEIPFK;YGVYEDENY(0.001)EVGS(0.999)DDEEIPFK;YGVYEDENYEVGS(1)DDEEIPFK 87.654 0.0016571 442146000 787360 620930 466181 535750 593370 531360 701250 812000 798640 TRUE FALSE 683308.3811 616851.0699 691627.6909 657400.2259 581563.0979 551801.763 633242.8829 638360.119 704225.689 0.970297437 0.8759281 0.982110851 0.933507874 0.825819204 0.783558129 0.899204464 0.906470935 1 19.42567833 4.750757867 23.52573795 0.898743087 0.970297539 0.101725157 0.064616528 2181.098782 4206666.911 0.016547898 0.256837214 56332.34972 -4.750757867 0.071554452 YGYIHLYDLETGTCIYMNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YGYIHLYDLETGTCIYMNR 19 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 338.8 1.29E-75 3290090000 2518590 2112360 1435178 1700570 2056740 2048050 2175520 2544070 2572730 FALSE TRUE 2185751.95 2098483.768 2129234.881 2086710.41 2015814.898 2126839.809 1964538.405 2000040.428 2268584.79 0.963486998 0.925018883 0.938574079 0.919829146 0.88857816 0.937518323 0.865975305 0.881624719 1 21.11336115 4.875077859 0.781330745 0.908331023 0.998863253 0.104602854 0.037538312 6.148860103 2.524809941 0.014412297 0.510122963 75002.86605 -4.875077859 0.09053223 YGYTHLSAGELLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YGYTHLSAGELLR 13 0 P30085;P30085-3;Q5T0D2 P30085 CMPK1 UMP-CMP kinase 0 ;;; 193.28 1.01E-06 1153330000 2009840 1997630 623867 1112300 2291450 2291910 1759940 2029960 1983100 FALSE TRUE 1744234.552 1984507.437 925571.1679 1364864.715 2245854.628 2380081.261 1589261.29 1595868.851 1748660.177 0.997469134 1.134873123 0.529303052 0.780520271 1.284328801 1.361088502 0.908845132 0.912623774 1 20.73781852 3.26522734 24.99984017 1.070328863 0.856476602 0.229006659 0.209874772 406.6716363 381248.6785 0.0661863 0.085421924 1841.735843 -3.26522734 -0.213852261 YGYTHLSTGDLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YGYTHLSTGDLLR 13 0 P00568;Q5T9B7 P00568 AK1 Adenylate kinase isoenzyme 1 0 ;;; 199.12 1.20E-07 2355300000 2630450 3501460 1062390 1921680 4055990 4150890 3281720 3495440 3457330 FALSE TRUE 2282829.368 3478458.679 1576165.357 2358026.815 3975283.734 4310577.424 2963459.3 2747967.358 3048608.386 0.748810303 1.140998855 0.517011422 0.773476458 1.303966673 1.413949212 0.972069523 0.901384176 1 21.53971941 3.263682363 24.99158119 1.094981161 0.799921371 0.360552423 0.2125788 300.9392752 299377.8815 0.06594491 0.085099908 1835.195615 -3.263682363 -0.29505979 YHDGNRNPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YHDGNRNPK 9 1 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 76.679 0.020879 17792000 28529 29096 10799 14345 20216 28954 23776 22793 8143.1 FALSE TRUE 24758.82037 28904.86646 16021.43252 17602.2515 19813.74115 30067.87912 21470.20718 17918.89433 7180.431995 3.448096213 4.025505218 2.23126304 2.451419568 2.759407953 4.187474951 2.990099648 2.495517587 1 12.80985493 4.243089134 24.99584552 2.659564061 3.736800927 0.263860189 0.790798929 165.328867 912526.4797 0.205823603 0.507450514 17502.05862 -4.243089134 1.077236866 YHDLECQLIQEFTSAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YHDLECQLIQEFTSAQR 17 0 F8W9B8;A0A0A0MSI8;O00471 F8W9B8 EXOC5 Exocyst complex component 5 0 ;; 158.98 3.27E-09 227943000 174182 169726 109462 125010 172520 189675 168312 178626 158387 FALSE TRUE 151163.4074 168611.0587 162398.1893 153395.4312 169087.1895 196971.92 151989.1281 140428.22 139662.6693 1.082346544 1.207273637 1.162788812 1.098328078 1.210682786 1.410340508 1.088258795 1.005481427 1 17.09158693 2.006926269 24.99970003 1.016253567 1.195539742 0.453757394 0.088331455 149.0724815 538060.6726 0.037131811 0.02496941 101.6076177 -2.006926269 0.179286176 YHEAWQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YHEAWQK 7 0 P17812;B4E1E0;P17812-2;A0A3B3IRI2;A0A3B3IRQ8;A0A3B3ITF6 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ; 134.66 0.0031526 231530000 744760 625310 500510 535940 562980 567030 619570 694080 625030 FALSE TRUE 646338.079 621202.2974 742558.3101 657633.3683 551777.7995 588844.011 559484.1968 545656.3933 551139.6654 1.172730107 1.127123189 1.347314223 1.19322453 1.001157844 1.068411599 1.015140502 0.99005103 1 19.07205844 3.270527043 5.939711181 1.014246298 1.215865142 0.730908713 0.058869947 0.092592083 9.132068617 0.017484635 0.022110594 1864.348266 -3.270527043 0.201618844 YHEDFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YHEDFEK 7 0 O76041-2;O76041;H0Y3P5;H7BZD5;H0Y786;A0A087X1N7;P20929-4;P20929;P20929-3;P20929-2 O76041-2;A0A087X1N7 NEBL;NEB Nebulette;Nebulin 0 113.89 0.0060283 104500000 222760 156540 102540 119920 145490 129120 175710 188540 175460 FALSE TRUE 193321.7016 155511.6784 152128.687 147149.6689 142595.0336 134087.33 158669.6712 148222.1882 154717.3187 1.249515589 1.005134265 0.983268636 0.951087248 0.921648816 0.86666012 1.025545638 0.95801937 1 17.23927517 4.902565594 1.84047146 0.955544152 1.446628914 0.817032153 0.043040102 0.593977057 1.448620984 0.011633092 0.576962968 79903.46145 -4.902565594 0.491084762 ERS(ph)PS(ph)PLRGNVVPSPLPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 ERSPSPLRGNVVPSPLPTR 19 2 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 2 ERS(1)PS(1)PLRGNVVPSPLPTR;ERS(1)PS(1)PLRGNVVPSPLPTR;ERS(0.999)PS(0.993)PLRGNVVPS(0.008)PLPTR;ERS(0.983)PS(0.971)PLRGNVVPS(0.035)PLPT(0.011)R 113.5 0.00086518 5870900000 5217100 3744240 1805160 2376200 2558440 2309140 2611380 2984360 1648880 TRUE FALSE 4527647.017 3719643.841 2678141.414 2915752.528 2507532.05 2397974.11 2358128.77 2346177.838 1453951.285 3.114029379 2.558300185 1.841974653 2.005399052 1.724632782 1.649280918 1.621876052 1.613656429 1 20.4715475 8 0.373200914 1.384621739 25.55361009 0.886445615 0.194053457 25.44195285 0.375282337 0.217086952 437.908025 100000000 -8 24.16898835 up YHFFLYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YHFFLYK 7 0 Q12792;Q12792-3;Q12792-4;F8VS81;Q6IBS0;H0Y858;D6RG15 Q12792;Q6IBS0 TWF1;TWF2 Twinfilin-1;Twinfilin-2 0 ; 106.29 0.0077362 1852790000 2714650 4910500 2713580 2972440 4125800 3671050 4483500 4437900 6890800 FALSE TRUE 2355902.124 4878242.602 4025876.364 3647377.933 4043704.652 3812277.669 4048690.86 3488889.621 6076177.474 0.387727668 0.802847287 0.662567277 0.600275082 0.665501406 0.627413812 0.666322022 0.574191527 1 22.53473258 1.233210671 24.99938306 1.00000058 0.630622286 0.566204058 0.103433534 120.7305889 564090.781 0.19097654 0.02285561 17.10845024 -1.233210671 -0.369378294 YHFNMGLLMGEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YHFNMGLLMGEAR 13 0 P47897;A0A1B0GVU9;P47897-2;A0A0U1RQT0;C9J165;A0A0U1RQE9;A0A0U1RRI9;A0A0U1RQM8 P47897 QARS Glutamine--tRNA ligase 0 ; 101.61 0.0018646 764690000 756300 1042030 539570 408060 985530 1230140 823840 720640 446890 FALSE TRUE 656353.0388 1035184.836 800507.8568 500716.2598 965919.8812 1277464.282 743944.1236 566536.744 394059.1733 1.665620504 2.626978146 2.031440735 1.270662616 2.451205166 3.241808257 1.887899519 1.437694596 1 18.58805276 4.002934683 24.89602444 1.895731263 2.19202679 0.025876528 0.665804862 393.0178817 3333965.397 0.182794513 0.377227512 10067.80239 -4.002934683 0.296295528 YHGHS(ph)MSDPGVSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YHGHSMSDPGVSYR 14 0 P08559-3;P08559;P08559-2;P08559-4;Q5JPU3;P29803 P08559-3 PDHA1;PDHA2 "Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial;Pyruvate dehydrogenase E1 component subunit alpha, testis-specific form, mitochondrial" 1 YHGHS(1)MSDPGVSYR;YHGHS(1)MSDPGVSYR;YHGHS(1)MSDPGVSYR;YHGHS(0.968)MS(0.032)DPGVSYR;Y(0.283)HGHS(0.359)MS(0.359)DPGVSYR;YHGHS(0.995)MS(0.005)DPGVSYR 148.52 4.98E-06 5120848000 3174119 2981310 1628328 3076836 3360733 3642775 1953823 2474261 2456930 TRUE FALSE 2754651.132 2961725.578 2415792.867 3775478.64 3293860.988 3782914.911 1764341.546 1945159.54 2166474.534 1.271490197 1.367071494 1.115080205 1.742683138 1.520378355 1.746115568 0.8143837 0.897845559 1 21.04691785 2.225117504 24.99999683 0.899040979 1.456075922 0.641411012 0.196082365 147.5301655 274357.879 0.082370436 0.055884897 167.9258302 -2.225117504 0.557034942 YHGHSMS(ph)DPGVSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YHGHSMSDPGVSYR 14 0 P08559-3;P08559;P08559-2;P08559-4;Q5JPU3;P29803 P08559-3 PDHA1;PDHA2 "Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial;Pyruvate dehydrogenase E1 component subunit alpha, testis-specific form, mitochondrial" 1 YHGHS(0.172)MS(0.613)DPGVS(0.214)Y(0.001)R 94.09 0.003341 0 49626 45352 22071 40935 45765 52927 25649 34778 35239 TRUE FALSE 43067.79836 45054.07973 32744.60942 50229.9174 44854.36604 54963.13594 23161.56393 27340.99534 31073.08556 1.386016148 1.449939036 1.053793301 1.616508837 1.443511812 1.768834184 0.745389893 0.879893157 1 14.92337789 2.225735595 24.99999973 0.870689637 1.441798333 0.673371347 0.189652135 132.0296418 257365.1818 0.076677533 0.052069322 168.1649937 -2.225735595 0.571108697 YHGNVMLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 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 ;;;;;;;;;; 197.3 2.82E-05 33685720000 3598921 4921218 2843626 3401491 5065340 5700692 4496253 4697749 5218763 FALSE TRUE 3123314.471 4888890.195 4218813.045 4173851.52 4964549.644 5920001.31 4060207.076 3693171.934 4601806.783 0.678714822 1.062384934 0.916773181 0.907002774 1.078826182 1.286451515 0.88230716 0.80254824 1 22.13376898 4.7489692 23.79996866 0.978992717 0.678714486 0.347316563 0.133926925 1017.450721 2326381.576 0.035723724 0.466949322 56100.81876 -4.7489692 -0.30027823 YHIDLDPHFNDILGQHSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YHIDLDPHFNDILGQHSR 18 0 P19784;H3BSA1;H3BV19 P19784 CSNK2A2 Casein kinase II subunit alpha 0 47.754 0.059145 70122000 47727 38787 21478 31829 34670 34151 27452 29978 30542 FALSE TRUE 41419.75603 38532.20564 31864.83264 39056.26093 33980.13483 35464.81107 24789.70927 23567.43799 26931.35955 1.537974937 1.430756051 1.18318693 1.450214975 1.261731134 1.316859292 0.920477454 0.875092768 1 14.71699944 2.262543309 4.645631865 0.915819208 1.361902342 0.797722131 0.1025679 0.079380837 4.122124226 0.04093493 0.029637775 183.0388627 -2.262543309 0.446083134 YHIEVNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YHIEVNR 7 0 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;; 149.4 0.002019 1247560000 1775070 1538590 1504060 1329580 1239940 1597440 1160330 1396460 1602110 FALSE TRUE 1540490.002 1528482.901 2231428.447 1631481.46 1215267.62 1658894.55 1047801.375 1097837.896 1412710.381 1.090449977 1.08195064 1.579537092 1.154859115 0.860238331 1.174263722 0.741695813 0.777114624 1 20.4300343 3.337121749 4.638327489 0.894649084 1.25286597 0.43586043 0.180108991 0.194490917 7.179225147 0.054306929 0.07035425 2173.310355 -3.337121749 0.358216886 YHNVGLSK ddPTM_MDA-MB-175_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 ; 114.89 0.0025684 2214300000 5740400 4992100 2650500 3792200 4614300 4097000 4745200 5560800 5221400 FALSE TRUE 4981791.596 4959306.566 3932290.665 4653276.97 4522484.458 4254614.241 4285011.234 4371666.194 4604132.04 1.082026222 1.077142559 0.854078604 1.010674092 0.982266455 0.924086061 0.930688172 0.949509301 1 22.13449778 4.315914522 11.90490101 0.951476016 1.080107869 0.598179522 0.044082738 0.383081234 57.19298037 0.010397355 0.027523353 20697.33942 -4.315914522 0.128631853 YHPDKNPEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YHPDKNPEGR 10 1 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 ; 123.67 0.00027391 277750000 350950 345610 216159 252236 313110 384780 347300 375770 307180 FALSE TRUE 304571.0683 343339.6652 320694.2154 309510.039 306879.7236 399582.7356 313618.8995 295414.5097 270865.5303 1.124436424 1.267564997 1.183960968 1.142670456 1.132959676 1.475207034 1.157839829 1.090631611 1 18.04721729 1.647981876 2.736687809 1.018005003 1.218978367 0.334780206 0.10251324 0.268315249 4.516139963 0.095361928 0.027786955 44.4612712 -1.647981876 0.200973364 YHPGYFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YHPGYFGK 8 0 P46776;E9PLL6 P46776 RPL27A 60S ribosomal protein L27a 0 ;; 140.53 0.00064813 10618350000 17705480 16171630 11221920 14175090 16009080 14964490 17012690 19273250 22709430 FALSE TRUE 15365655.96 16065397.5 16648878.05 17393760.84 15690530.63 15540183.61 15362801.94 15151815.47 20024747.06 0.767333336 0.802277175 0.831415148 0.868613261 0.783556995 0.776048934 0.767190811 0.756654525 1 24.25528068 1.232198208 24.99969501 1.000000342 0.793967186 0.785425679 0.033815612 110.4437032 433922.5158 0.084759005 0.009258489 17.06861206 -1.232198208 -0.206033156 YHQIGSGK ddPTM_MDA-MB-175_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 3788740000 8519800 7201800 4041330 5383320 6050450 6005870 7445800 8235600 7283700 FALSE TRUE 7393886.844 7154490.902 5995730.705 6605685.085 5930057.883 6236919.705 6723707.462 6474481.03 6422629.284 1.151224291 1.113950469 0.933532116 1.028501692 0.923306892 0.971085116 1.046877714 1.00807329 1 22.6147326 4.355533928 5.829084037 0.991278218 1.141464469 0.711400159 0.038656683 0.104979001 4.821315219 0.009743107 0.026624155 22674.30209 -4.355533928 0.150186251 YHSDDYIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YHSDDYIK 8 0 Q13547;Q5TEE2 Q13547 HDAC1 Histone deacetylase 1 0 ;;;; 139.97 0.00065705 2335970000 2424860 2526200 1517830 1946990 2599690 2462100 2428060 2883580 2584700 FALSE TRUE 2104408.607 2509605.226 2251857.665 2389083.837 2547961.255 2556818.58 2192587.115 2266948.857 2279139.71 0.923334624 1.101119521 0.988029674 1.04823931 1.117948691 1.121834949 0.962024006 0.994651116 1 21.12005793 2.209905841 24.99961477 0.986472085 1.05258449 0.199931041 0.060702477 333.5090326 290964.8461 0.024400321 0.016454352 162.1458512 -2.209905841 0.066112405 YHSDEYIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YHSDEYIK 8 0 Q92769;Q92769-3;H3BM24;E5RFI6;E5RJ04;E5RGV4;E5RHE7;E5RH52;E5RG37;E5RFP9;E5RK19 Q92769 HDAC2 Histone deacetylase 2 0 ;; 157.86 0.00037013 1253310000 1922800 1574330 895970 1255250 1516710 1477500 1535980 1808480 1690360 FALSE TRUE 1668697.108 1563988.123 1329264.089 1540273.698 1486530.438 1534340.381 1387020.896 1421750.626 1490527.566 1.11953455 1.049284936 0.891807786 1.033374848 0.997318313 1.029394166 0.930557024 0.953857317 1 20.50739163 4.471377797 24.5845207 0.976352895 1.101972181 0.541628811 0.043618598 73.90097173 316330.2795 0.010715952 0.02854236 29605.86793 -4.471377797 0.125619286 YHSDFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YHSDFNR 7 0 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 ;;;;; 171.08 0.00095102 2628310000 1330903 1353720 787004 921166 1218170 1405910 1267549 1348880 1319810 FALSE TRUE 1155020.796 1344827.324 1167601.767 1130330.819 1193930.8 1459996.267 1144622.293 1060432.509 1163783.565 0.992470448 1.155564801 1.003280852 0.971255183 1.025904503 1.254525593 0.983535364 0.91119392 1 20.15039135 2.015129953 24.999228 0.948686893 1.0667946 0.24012895 0.08661517 296.6131384 490092.3233 0.035316078 0.023800753 103.5451956 -2.015129953 0.118107707 YHSDFNRQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YHSDFNRQDR 10 1 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 ; 73.067 0.0277 81880000 64479 60369 36407 60188 64079 91296 54163 81767 87488 FALSE TRUE 55957.93678 59972.43206 54013.54697 73854.60532 62803.95327 94808.2162 48910.2806 64281.76336 77145.26831 0.72535799 0.777396117 0.700153725 0.957344591 0.814099875 1.228956983 0.63400234 0.833256074 1 16.23529005 3.744003334 24.55476054 0.895007506 0.738611956 0.226691744 0.152050246 605.2200234 2730433.569 0.040141544 0.066978644 5546.299704 -3.744003334 -0.15639555 YHSLAPMYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YHSLAPMYYR 10 0 P20339-2;P20339;P51148;P51148-2;K7ERI8;K7ERQ8;F8VVK3;K7ENY4;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 ; 136.99 0.00010308 2104700000 534470 1318890 704120 786020 1268990 1296900 938520 1255040 1322500 FALSE TRUE 463838.4353 1310226.125 1044634.787 964497.8546 1243739.582 1346792.582 847502.4749 986659.4627 1166155.557 0.397750054 1.123543182 0.895793688 0.827074784 1.066529739 1.154899597 0.726749077 0.846078773 1 20.15332882 4.751022562 24.61151187 0.939738275 0.397749634 0.619335565 0.136848219 1174.761624 2320023.818 0.034357375 0.579314591 56366.69384 -4.751022562 -0.541988641 YHTEIVFAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YHTEIVFAR 9 0 P05023-4;P05023;P05023-3 P05023-4 ATP1A1 Sodium/potassium-transporting ATPase subunit alpha-1 0 166.16 6.10E-05 154620000 83777 72102 48591 91621 105330 108870 53472 112530 99885 FALSE TRUE 72705.65719 71628.35721 72089.77013 112424.9484 103234.1391 113058.2993 48286.29367 88466.33521 88076.70909 0.825481083 0.8132497 0.818488462 1.276443563 1.17209351 1.283634465 0.548229994 1.004423713 1 16.42647294 3.900311546 24.99999759 1.028406579 0.81835663 0.212152379 0.205301499 72.30264227 18118.24977 0.05741392 0.099443879 7948.982602 -3.900311546 -0.210049949 YHTINGHNAEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 YHTINGHNAEVR 12 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;; 281.26 2.62E-28 38050450000 8112820 6851760 3032850 4273010 6169420 5928460 5162420 5814310 4726250 FALSE TRUE 7040690.282 6806750.337 4499546.404 5243262.229 6046660.612 6156531.692 4661769.303 4570965.054 4167518.109 1.689420441 1.633286325 1.07967051 1.258125842 1.450902061 1.477265733 1.118596052 1.096807484 1 21.99075704 7.999999998 0.06427766 1.41E-08 4.038216574 0.517419308 0.168612044 620.9114994 3.853421771 57.6199198 250.1451653 99999999.48 -7.999999998 4.03821656 YHTINGHNCEVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YHTINGHNCEVK 12 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 217.88 2.06E-11 3122910000 2255770 2017120 1127230 1558470 1653500 1488860 1829730 2017220 1930970 FALSE TRUE 1957664.279 2003869.406 1672362.198 1912344.433 1620598.585 1546137.408 1652283.066 1585853.201 1702692.926 1.14974594 1.17688244 0.982186613 1.12312937 0.951785586 0.908054167 0.970394039 0.93137945 1 20.69938684 3.9440794 0.805956213 0.946250107 1.19460418 0.637109365 0.057286705 0.612886493 0.641096903 0.024844874 0.114255002 8791.832381 -3.9440794 0.248354073 YHTSQSGDEMTSLSEYVSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 YHTSQSGDEMTSLSEYVSR 19 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;;; 353.31 7.60E-91 12218410000 2703149 2751162 908512 1663616 3332586 3270172 2380106 2819443 2539533 FALSE TRUE 2345921.011 2733089.436 1347871.442 2041365.44 3266274.059 3395977.633 2149283.686 2216527.055 2239312.302 1.04760779 1.220503917 0.601913115 0.911603727 1.458605866 1.516527029 0.959796311 0.989824891 1 21.09462431 YHTVNGHNCEVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 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 ;;;;;;;;;; 255.16 2.28E-21 33138049000 4683633 4651381 2664029 2919249 3940881 4147285.3 3418708 3637731 2995219.5 FALSE TRUE 4064679.032 4620825.772 3952362.335 3582109.103 3862465.178 4306834.049 3087162.224 2859830.535 2641128.063 1.538993542 1.749565209 1.49646751 1.356279975 1.4624301 1.63067975 1.168880172 1.082806462 1 21.33272283 2.127838656 4.537388942 1.068560284 1.534361458 0.806209933 0.106061677 0.09539898 3.35964927 0.049311651 0.032275526 134.2266206 -2.127838656 0.465801174 YHYLGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YHYLGGR 7 0 Q8NCW5-2;Q8NCW5 Q8NCW5-2 APOA1BP NAD(P)H-hydrate epimerase 0 ;;;;; 140.01 0.0026531 3746440000 3919530 4193020 2323190 2422900 3756550 4370800 3670310 3826870 3876420 FALSE TRUE 3401554.18 4165475.776 3446692.455 2973056.477 3681802.005 4538947.504 3314363.901 3008523.631 3418154.044 0.995143617 1.218633134 1.008349071 0.869784228 1.077131679 1.327894368 0.969635616 0.880160342 1 21.70478598 2.017868031 24.98964305 0.929533413 1.081759848 0.197920074 0.1267396 347.9232885 486592.2562 0.053222982 0.035875729 104.2000749 -2.017868031 0.152226435 YIASTQRPDGTWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YIASTQRPDGTWR 13 1 Q9BRP8-2;Q9BRP8 Q9BRP8-2 WIBG Partner of Y14 and mago 0 ;; 192.4 3.82E-07 465720000 1123360 1156340 673960 843110 1144510 1233190 1020610 1126560 1097870 FALSE TRUE 974905.1298 1148743.926 999889.3103 1034551.012 1121736.49 1280631.617 921631.3993 885653.9109 968081.0593 1.007049069 1.186619566 1.032857012 1.068661556 1.158721658 1.322855772 0.952018832 0.914855117 1 19.88476833 2.058443504 24.99999137 0.945971273 1.127168265 0.450255511 0.090343334 64.16346891 27446.34372 0.036738665 0.024769211 114.4046044 -2.058443504 0.181196993 YICPHAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YICPHAPR 8 0 O95372;Q5QPQ1;Q5QPQ3;Q5QPQ2;Q5QPN5;Q5QPN9 O95372 LYPLA2 Acyl-protein thioesterase 2 0 112.59 0.0030111 370930000 592280 704500 468840 563820 692860 892380 649090 759120 907910 FALSE TRUE 514008.6974 699872.0931 695572.5922 691843.9484 679073.4416 926710.436 586141.3517 596788.0955 800577.9141 0.642047062 0.874208595 0.868838098 0.864180658 0.848229048 1.157551838 0.732147791 0.745446614 1 19.61068229 4.73857383 19.53015208 0.874138914 0.642047325 0.279475034 0.12187684 0.108728577 110377.1595 0.030189656 0.168193542 54773.92083 -4.73857383 -0.232091589 YIDENQDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YIDENQDR 8 0 Q96KP4;Q96KP4-2;J3QKT2;A0A087WYZ1;J3KSV5;J3QRA8;J3QRD0;J3QKQ0;J3QLU1;J3QR27;J3QL02;J3QQN6;J3KSS4;J3QRP4 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ;;; 194.92 0.0003788 2894350000 1822890 1656280 1121540 1126140 1402120 1506770 1574530 1616350 1530560 FALSE TRUE 1581990.468 1645399.788 1663920.495 1381847.299 1374220.555 1564736.417 1421832.323 1270706.131 1349618.94 1.172175657 1.219158785 1.232881701 1.023879599 1.018228564 1.15939127 1.053506498 0.941529563 1 20.36412069 3.415485563 0.214368953 0.845683858 1.385387764 0.565428645 0.065793943 4.762610557 1.016813418 0.973600652 1.416798618 2603.068299 -3.415485563 0.539703906 YIDQEELNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YIDQEELNK 9 0 P08238;P07900;P07900-2;Q14568;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AA1;HSP90AA2P;HSP90AB2P Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2;Putative heat shock protein HSP 90-beta 2 0 ;;;;; 211.48 1.18E-05 5590510000 10067440 7787100 5655170 6751730 7706190 6554280 9088060 10353880 9436010 FALSE TRUE 8737002.296 7735946.027 8390029.127 8284813.49 7552851.896 6806427.393 8206701.34 8139783.336 8320495.647 1.050057913 0.929745817 1.008356892 0.995711535 0.907740622 0.818031483 0.986323614 0.978281064 1 22.98823804 6.436128944 1.897756576 0.953415002 52.27582016 0.209027952 0.057806779 1470.3784 12.16174967 0.016004711 327137.6089 2729788.149 -6.436128944 51.32240516 YIDTEHGGSQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YIDTEHGGSQAR 12 0 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ;;;; 184.98 1.36E-05 2935980000 3664360 3692800 2101750 2459200 3807760 3993020 3530140 3964200 3891550 FALSE TRUE 3180105.542 3668541.754 3118163.33 3017598.947 3731993.026 4146634.063 3187787.566 3116486.679 3431495.392 0.926740438 1.069079609 0.908689354 0.879383068 1.087570461 1.20840438 0.928979119 0.908200747 1 21.71040599 5.050849059 12.91306879 0.991612264 0.632541675 0.043396204 0.101450774 20413780.16 175890692.3 0.02680953 172513868.8 112421.4181 -5.050849059 -0.35907059 YIEEAIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YIEEAIEK 8 0 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 111.95 0.0072944 186190000 91307 94689 68135 75863 82950 100290 84030 95378 94342 FALSE TRUE 79240.54861 94066.98172 101085.3139 93088.85364 81299.45729 104148.2212 75880.78353 74982.15693 83188.99623 0.952536419 1.130762312 1.215128424 1.11900441 0.977286191 1.251947083 0.912149286 0.901347057 1 16.34410509 2.207933247 24.99456612 0.929160792 1.108280762 0.417804394 0.094383359 179.2051486 146245.53 0.037318827 0.025163357 161.411044 -2.207933247 0.17911997 YIEIDS(ph)DEEPR ddPTM_MDA-MB-175_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 232.5 3.02E-13 1439210000 1643550 1431150 1356430 1642310 1436500 1509540 1319400 1419560 3560600 TRUE FALSE 1426350.703 1421748.681 2012404.085 2015221.587 1407916.46 1567612.981 1191444.791 1115998.141 3139669.924 0.454299572 0.452833806 0.640960398 0.641857786 0.448428177 0.499292288 0.379480907 0.355450786 1 21.58218146 1.229952722 24.99653356 1.000000978 0.481361909 0.746288656 0.094525947 191.0824886 554842.7558 0.300415032 0.026217868 16.98058789 -1.229952722 -0.518639069 YIEIDS(ph)DEEPRGELLSLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 306.49 1.63E-50 3842800000 1395307 1349313 942372 972835 1236278 1367545 1128626 1256347 1036972 TRUE FALSE 1210913.645 1340449.274 1398106.251 1193732.056 1211678.487 1420155.341 1019172.024 987686.971 914382.3515 1.324296825 1.465961446 1.5290171 1.305506448 1.325133282 1.553130743 1.114601592 1.080168454 1 19.80243803 2.135755506 6.127316259 1.061947003 1.414470677 0.786173933 0.086922973 0.09219152 4.743441924 0.036034401 0.024137625 136.6959054 -2.135755506 0.352523675 YIEIFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YIEIFK 6 0 P31943;G8JLB6;E9PCY7;H0YB39;D6RBM0;E7EN40;E5RGV0;P55795 P31943;P55795 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 100.82 0.086601 548580000 882170 644890 384110 474290 646820 537180 708610 807330 727400 FALSE TRUE 765588.9994 640653.6751 569866.8808 581984.7936 633949.5475 557845.6622 639889.1113 634688.7621 641407.6007 1.19360762 0.998824577 0.888462937 0.907355624 0.988372365 0.869721004 0.997632567 0.989524854 1 19.29088192 4.707339075 3.506572823 0.951689252 1.215113375 0.722625992 0.047318902 0.142759942 3.101094493 0.012139157 0.094746129 50972.86865 -4.707339075 0.263424123 YIELFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 YIELFR 6 0 Q6NXG1;Q6NXG1-2;Q6NXG1-4;Q6NXG1-3;A0A2U3TZN9;Q6NXG1-5;H0YBR2;H0YBB3;Q9H6T0-2;Q9H6T0 Q6NXG1;Q9H6T0-2 ESRP1;ESRP2 Epithelial splicing regulatory protein 1;Epithelial splicing regulatory protein 2 0 ;;;;;;; 150.82 0.024342 4916072000 4741670 3948830 2530405 2703835 3809820 3990890 3477010 4351580 3999470 FALSE TRUE 4115046.296 3922889.876 3754117.322 3317782.062 3734012.036 4144422.121 3139810.105 3421028.481 3526657.213 1.166840452 1.112353608 1.064497368 0.940772483 1.058796421 1.175170103 0.89030771 0.970048483 1 21.74986992 8 0.319565428 0.971373652 2.888930776 0.345079368 0.075943155 91.97565565 1.449506907 0.131827315 101.3777473 100000000 -8 1.917557124 YIEQATVHSSMNEMLEEGQEYAVMLYTWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YIEQATVHSSMNEMLEEGQEYAVMLYTWR 29 0 Q7L576;A0A087WU52;A0A0G2JRX2;A0A087WWL1;A0A0G2JRV9;A0A0G2JR96;A0A0G2JQT1 Q7L576;A0A0G2JR96 CYFIP1 Cytoplasmic FMR1-interacting protein 1 0 199.64 3.63E-25 64206000 39228 45727 16630 25543 42625 47905 41070 53133 39041 FALSE TRUE 34043.92041 45426.61633 24672.32362 31342.92855 41776.84589 49747.93635 37087.03772 41770.92143 34425.61746 0.988912412 1.319558506 0.716684999 0.910453635 1.21353948 1.445084795 1.077309296 1.213367385 1 15.07119491 3.22788705 24.9374611 1.19711854 0.988790869 0.235514397 0.184033969 307.7990325 719132.5527 0.055882953 0.064010889 1690.001343 -3.22788705 -0.208327671 YIEVFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YIEVFK 6 0 P52597;A0A1B0GW42 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 118.03 0.051687 1779550000 4228300 3700700 2508400 3012500 3453700 3144900 3881200 4427900 4771400 FALSE TRUE 3669519.442 3676389.858 3721470.63 3696534.168 3384978.127 3265886.338 3504801.821 3481028.043 4207330.528 0.872172846 0.87380581 0.884520626 0.878593717 0.804542953 0.776237169 0.833022697 0.827372135 1 22.00447373 3.307386641 24.98681214 0.84088599 0.877543527 0.048949345 0.058835564 138.6988023 50350.9118 0.017033367 0.021989976 2029.488715 -3.307386641 0.036657537 YIGESAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YIGESAR 7 0 A0A087X2I1;P62333;H0YJC0;H0YJS8;H0YJX2 A0A087X2I1;H0YJX2 PSMC6 26S protease regulatory subunit 10B 0 128.38 0.0087545 108000000 333060 317430 229450 281190 355850 399840 327580 396380 465950 FALSE TRUE 289045.2771 315344.7814 340412.7875 345038.4872 348769.2812 415222.1035 295811.342 311617.2216 410865.9218 0.70350268 0.767512623 0.828525242 0.839783659 0.848863979 1.010602441 0.719970497 0.758440175 1 18.64830815 4.487657157 1.581271085 0.848992081 0.683859865 0.254857331 0.090580057 1.07376891 3.683378082 0.026261213 0.237692968 30736.69422 -4.487657157 -0.165132216 YIGTGHADTTKWEWLVNQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YIGTGHADTTKWEWLVNQHR 20 1 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 242.34 5.66E-30 590060000 942430 773010 269360 357050 714130 697860 840420 868450 92109 FALSE TRUE 817885.4877 767932.0464 399623.397 438123.6597 699920.2102 724707.1258 758916.1978 682738.7258 81219.97895 10.07000369 9.454964854 4.920259795 5.394284329 8.617586697 8.92276919 9.343959547 8.406044111 1 16.30954703 4.398622647 9.11854707 7.065379216 9.916878715 0.196954204 2.517886369 0.478491229 50.01596131 0.63648081 1.69136351 25039.3267 -4.398622647 2.851499498 YIHILGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YIHILGR 7 0 Q9Y2J8;Q9Y2J8-2 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ; 166.66 0.0011153 3699100000 2760900 2977900 1809770 2224300 3042500 3088400 2711100 3101300 3244300 FALSE TRUE 2396040.07 2958337.979 2684980.825 2729361.311 2981960.203 3207212.746 2448177.939 2438111.129 2860762.55 0.837552935 1.034108189 0.938554242 0.954067758 1.042365506 1.121104143 0.8557781 0.852259175 1 21.44796832 2.156014433 24.99959778 0.8902201 0.988787797 0.180936828 0.084137958 40.42458553 12238.93996 0.03402329 0.022938501 143.2235495 -2.156014433 0.098567697 YIHLENLLAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YIHLENLLAR 10 0 Q2TAY7 Q2TAY7 SMU1 "WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed" 0 ; 215.06 8.36E-09 1370390000 1523120 1392480 800790 1032700 1394500 1434280 1266350 1505650 1408230 FALSE TRUE 1321835.833 1383332.707 1188054.722 1267190.319 1366752.178 1489457.68 1143539.572 1183678.464 1241750.654 1.064493769 1.114018103 0.95675788 1.020486935 1.10066556 1.199482098 0.920909177 0.953233615 1 20.24394408 2.198941776 24.99999937 0.955497174 1.070893109 0.420649485 0.06504009 159.6754093 100756.16 0.027698806 0.018674844 158.1036062 -2.198941776 0.115395934 YIHPDDELVLEDELQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YIHPDDELVLEDELQR 16 0 C9IZD2;C9J8Z7;C9JLE1;F8W8R3;A0A087WWF6;P49005 C9IZD2 POLD2 DNA polymerase delta subunit 2 0 131.4 4.48E-05 191000000 194580 196790 110030 159430 167420 187760 168490 202360 199340 FALSE TRUE 168865.76 195497.2735 163240.876 195631.0182 164088.6696 194983.2487 152149.8657 159086.8888 175774.2523 0.96069679 1.112206543 0.928696177 1.112967432 0.933519372 1.109282197 0.865598139 0.905063664 1 17.42336423 2.227903505 24.99338135 0.917286974 1.025431599 0.280078187 0.077375099 237.8646202 557842.3879 0.028282955 0.019292395 169.006538 -2.227903505 0.108144626 YIHSADIIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YIHSADIIHR 10 0 Q16539-2;Q16539;B4E0K5;Q16539-5;Q16539-3;Q16539-4;E7EX54;B5TY33 Q16539-2 MAPK14 Mitogen-activated protein kinase 14 0 ;;;; 166.34 3.23E-06 968620000 1066466 1045310 621600 815034 1025083 1156042 1001415 1125000 1099412 FALSE TRUE 925529.816 1038443.29 922207.8391 1000099.927 1004685.854 1200515.684 904297.9274 884427.5048 969440.7658 0.954704866 1.071177659 0.951278172 1.031625615 1.036356103 1.238358986 0.932803694 0.912306905 1 19.88679322 YIHSANVLHR ddPTM_MDA-MB-175_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 ; 166.55 3.19E-06 1242630000 1267300 1262070 823800 1063650 1258070 1339460 1284640 1328240 1691030 FALSE TRUE 1099823.094 1253779.379 1222192.435 1305167.989 1233036.868 1390989.893 1160055.811 1044206.212 1491118.36 0.737582692 0.840831562 0.81964817 0.875294695 0.826920855 0.932850088 0.777977015 0.700283921 1 20.50796335 4.741095282 23.62848976 0.834181504 0.737582615 0.133957881 0.081865217 257.0766133 2396180.396 0.020204825 0.131799974 55092.85546 -4.741095282 -0.096598889 YIIEELNVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YIIEELNVR 9 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 97.431 0.015578 87457000 99294 94770 61069 76665 89878 98127 80537 97434 100480 FALSE TRUE 86172.04632 94147.44963 90602.17266 94072.96 88089.60364 101902.0092 72726.53414 76598.49733 88601.36887 0.972581433 1.062595881 1.022582087 1.061755153 0.994223958 1.150117775 0.820828561 0.864529502 1 16.43504137 2.228803323 24.99999999 0.885651016 1.042396639 0.538754491 0.064719746 139.0707491 356321.7987 0.024982891 0.017077378 169.3570667 -2.228803323 0.156745624 YIKDYMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YIKDYMK 7 1 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;E9PJF7;P13693-2;Q9HAU6 Q5W0H4 TPT1;TPT1P8 Translationally-controlled tumor protein;Putative translationally-controlled tumor protein-like protein TPT1P8 0 ; 109.01 0.0064969 3491200000 6511700 8197600 4526300 5331500 7511300 6085600 10308400 10621100 3137900 FALSE TRUE 5651162.346 8143749.426 6715233.82 6542098.562 7361839.826 6319716.97 9308692.955 8349860.418 2766941.037 2.042386257 2.943232009 2.426952266 2.364379463 2.660642105 2.284008544 3.364254182 3.017722571 1 21.39986047 YIKNPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YIKNPR 6 1 P49368;P49368-2;B4DUR8;Q5SZX6 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 110.24 0.026332 2481100000 4808900 4157400 2056720 2803500 3817900 3888200 4236600 4861300 2479200 FALSE TRUE 4173391.681 4130089.766 3051356.671 3440077.524 3741931.26 4037781.57 3825735.184 3821748.826 2186111.8 1.909047689 1.889239958 1.395791684 1.573605487 1.711683391 1.84701513 1.750018084 1.748194591 1 21.05993575 1.237353164 24.99987029 0.999999134 1.723076375 0.693153854 0.152205969 18.72083096 387442.3849 0.234280098 0.039003801 17.27241897 -1.237353164 0.723077241 YIMIFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YIMIFR 6 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ; 161.85 0.019487 741810000 840030 842970 511450 480980 822570 828690 830400 880480 919090 FALSE TRUE 729017.9071 837432.4746 758788.9307 590193.8603 806202.4663 860570.2405 749867.9358 692196.2039 810436.2272 0.89953766 1.033310761 0.936272226 0.728242199 0.994775948 1.061860528 0.925264581 0.854103236 1 19.62833914 2.884876704 0.009634962 0.857447313 1.007935388 0 0.096887273 173158.3635 2215.305706 17341.28964 17253.20157 767.1436673 -2.884876704 0.150488075 YINTEHGGSQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YINTEHGGSQAR 12 0 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;; 206.32 9.16E-08 3382110000 2036530 2002190 1106770 1492290 1929030 2139900 1824240 2082060 2011530 FALSE TRUE 1767397.401 1989037.482 1642007.674 1831137.253 1890646.077 2222223.338 1647325.486 1636827.672 1773729.215 0.996430225 1.121387338 0.925737514 1.032365728 1.065915846 1.252853772 0.928735611 0.922817112 1 20.75835435 YIQDIYSCGEIVEHLEESTAFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YIQDIYSCGEIVEHLEESTAFR 22 0 Q9UJX2-3;Q9UJX2 Q9UJX2-3 CDC23 Cell division cycle protein 23 homolog 0 163.95 1.45E-11 46474000 32845 28841 17722 24529 27356 28892 29183 30780 33649 FALSE TRUE 28504.45003 28651.54157 26292.41848 30098.68435 26811.66912 30003.49394 26352.83715 24197.93653 29671.05355 0.9606821 0.965639509 0.886130263 1.01441239 0.903630506 1.011204199 0.888166546 0.815540186 1 14.85676853 2.108559477 9.70499946 0.881845512 0.954247608 0.134694496 0.060181542 0.400758859 33.14075474 0.023153773 0.015602697 128.3983601 -2.108559477 0.072402095 YIQELWR ddPTM_MDA-MB-175_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 ;;;;; 168.45 0.0024395 14654720000 9164150 9281660 5881730 6242810 8714520 9766480 8505540 9827010 9242970 FALSE TRUE 7953084.359 9220688.164 8726154.301 7660335.426 8541118.102 10142202.81 7680674.04 7725580.385 8150276.616 0.975805452 1.131334383 1.07065744 0.939886557 1.047954383 1.244399826 0.942382008 0.947891802 1 22.95841759 YIQHTYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 YIQHTYR 7 0 P52565;J3KTF8;J3QQX2;J3KRY1;P52565-2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;;;;;; 176.41 0.00075288 16380940000 6100580 6195730 3832834 4442112 5929860 6482210 5597050 6226920 6627320 FALSE TRUE 5294372.896 6155029.842 5686405.342 5450761.423 5811867.388 6731584.813 5054248.952 4895341.616 5843845.779 0.905974096 1.053249876 0.973058763 0.93273533 0.994527852 1.151910072 0.864884041 0.837691787 1 22.47848667 YIQPWESEFIDSQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YIQPWESEFIDSQR 14 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 162.65 4.84E-07 0 244240 191210 134510 155860 183590 174060 196720 239280 236320 FALSE TRUE 211963.0652 189953.9289 199559.4859 191250.3952 179936.9182 180756.2008 177642.1247 188111.8341 208382.5188 1.017182566 0.911563647 0.957659438 0.917785217 0.863493345 0.867424973 0.852480936 0.902723679 1 17.66887473 7.999988139 0.765801245 0.896916721 23.76004837 0.366842216 0.044494606 463.7633478 1.872730755 0.016671924 18325.79983 99997269.05 -7.999988139 22.86313164 YIQQTKPLTLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YIQQTKPLTLER 12 1 O43809 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 ; 115.24 0.00088559 1893860000 876610 731480 410670 539640 767790 824010 665890 787090 606440 FALSE TRUE 760763.7675 726674.8597 609271.3856 662173.5099 752512.4812 855710.1979 601312.0903 618776.9286 534747.3541 1.422660181 1.358912492 1.139363067 1.238292261 1.407229929 1.600213992 1.124478851 1.157138832 1 19.02849791 2.042530718 24.99880153 1.10509778 1.34868799 0.499785914 0.125621508 128.7262988 75662.4892 0.054519129 0.03675676 110.2886238 -2.042530718 0.24359021 YIS(ph)PDQLADLYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YISPDQLADLYK 12 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 1 YIS(1)PDQLADLYK 96.64 0.0056332 15452000 51555 55565 34909 33475 41784 46018 57066 59773 70712 TRUE FALSE 44741.87613 55199.98986 51791.10916 41076.01038 40952.58015 47788.34224 51531.7481 46991.0091 62352.50792 0.717563377 0.885289008 0.8306179 0.658770782 0.656791226 0.766422135 0.826458307 0.753634628 1 15.92815997 1.237000776 24.98825321 1.000000292 0.764208504 0.512416739 0.07294884 36.29522745 581243.5506 0.11580281 0.018810628 17.25840974 -1.237000776 -0.235791787 YISFEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YISFEER 7 0 Q14192 Q14192 FHL2 Four and a half LIM domains protein 2 0 ; 102.71 0.039293 48381000 218284 237152 151709 163739 225966 246220 212773 238090 235591 FALSE TRUE 189437.2163 235594.1329 225075.9798 200918.4425 221469.7187 255692.2427 192138.3072 187176.3063 207739.7004 0.911897033 1.134083338 1.083451933 0.967164399 1.066092414 1.230829939 0.924899318 0.901013653 1 17.66441743 YISKPENLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YISKPENLK 9 1 Q9H9S4;Q5TAW7;B7ZBJ4;Q9Y376;A0A087X0K1 Q9H9S4;Q9Y376 CAB39L;CAB39 Calcium-binding protein 39-like;Calcium-binding protein 39 0 ; 102.52 0.0032565 1794960000 1814950 1576650 1222860 1413800 1569030 1240770 2018120 2163660 2151800 FALSE TRUE 1575099.759 1566292.882 1814239.186 1734824.899 1537809.373 1288503.225 1822403.033 1700978.147 1897416.655 0.830128562 0.825487053 0.956162781 0.914308881 0.810475321 0.679082911 0.960465393 0.896470547 1 20.85560509 YISPDQLADLYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YISPDQLADLYK 12 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;; 164.9 0.00013039 1584340000 2331345 2527283 1586619 1441896 1797751 1708372 2225778 2410467 2727685 FALSE TRUE 2023251.851 2510681.112 2353913.255 1769300.525 1761979.272 1774094.176 2009922.392 1895007.39 2405221.187 0.841191597 1.043846248 0.978668103 0.73560824 0.73256434 0.737601259 0.835649712 0.787872401 1 21.19773814 3.749287497 24.60403628 0.799217043 0.963496427 0.369588076 0.091711962 575.0390476 1318951.218 0.024011136 0.0410396 5614.195052 -3.749287497 0.164279384 YITDWQNVFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YITDWQNVFR 10 0 O75340-2;O75340;A0A024QZ42 O75340-2 PDCD6 Programmed cell death protein 6 0 ; 171.56 9.27E-06 3477100000 4142000 2540640 1446590 1939390 2477420 2608240 2411120 2675540 2520940 FALSE TRUE 3594624.206 2523950.369 2146165.763 2379758.141 2428124.189 2708580.681 2177289.954 2103396.592 2222917.345 1.617075063 1.1354225 0.965472588 1.070556288 1.092314203 1.218480159 0.979474094 0.94623248 1 21.08402287 4.725264629 3.250777623 1.037002103 1.690129169 0.840076108 0.078649832 0.128955972 2.222594567 0.021648643 0.20890055 53120.80265 -4.725264629 0.653127066 YIVNGSHEANK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YIVNGSHEANK 11 0 P55010;H0YLZ1;H0YN40;H0YMJ8;H0YM54 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ;; 143 3.74E-05 1038240000 1873320 1883900 1379120 1726590 1824530 1688450 1940090 2306710 2786390 FALSE TRUE 1625756.016 1871524.537 2046067.045 2118638.649 1788225.423 1753405.764 1751940.37 1813438.017 2456986.148 0.66168709 0.761715542 0.832754815 0.862291654 0.727812578 0.713640883 0.713044464 0.738074172 1 21.22845829 1.236400382 24.97522931 1.000000321 0.753373645 0.641162031 0.058436194 40.14743879 464042.3832 0.098268676 0.015262178 17.23456722 -1.236400382 -0.246626676 YIYFYEKENDAVTIQVLNQLIQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YIYFYEKENDAVTIQVLNQLIQK 23 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;;; 222.06 1.53E-32 115310000 314828 235298 132301 134758 201586 150470 349068 353919 47407.2 FALSE TRUE 273222.6821 233752.3119 196282.2061 165356.8635 197574.833 156258.6783 315215.4391 278236.1761 41802.77482 6.535993921 5.591789371 4.695434859 3.955643238 4.726356895 3.737997751 7.540538647 6.655926006 1 15.35131109 4.560856025 2.912491867 4.907566825 6.559305576 0.10030504 1.752472363 0.869404007 12.48366417 0.457090392 2.706803361 36379.44131 -4.560856025 1.651738751 YKAEDEK ddPTM_MDA-MB-175_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 13024250000 19945690 12847350 14055010 14762850 9029140 8528660 18016770 21828120 25901650 FALSE TRUE 17309816.53 12762954.91 20852059.85 18114980.73 8849477.779 8856763.069 16269506.42 17160346.4 22839586.44 0.757886601 0.558808494 0.912978871 0.793139612 0.38746226 0.387781236 0.712338048 0.751342256 1 24.44503319 1.284805797 1.954564873 1.091372535 0.637887977 0.313665269 0.166861727 0.969333441 3.937583262 0.782963387 0.049027516 19.26663175 -1.284805797 -0.453484558 YKAEDEKQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YKAEDEKQR 9 2 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 116.23 0.0007576 976260000 2475050 1738280 890380 850470 1412070 1242600 2488240 2802200 269740 FALSE TRUE 2147965.872 1726861.124 1320970.746 1043582.212 1383972.57 1290403.626 2246930.868 2202971.337 237851.6445 9.030695903 7.260244628 5.553759147 4.387534147 5.818637801 5.425245761 9.446774575 9.261955457 1 17.85970247 4.611278044 3.191787422 6.276352626 9.107336933 0.139227 2.402079078 0.672962075 11.12380785 0.630096416 3.895622974 40858.08845 -4.611278044 2.830984307 YKAEDEVQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 ;;;;; 150.15 7.84E-05 10434480000 6853120 5923960 4297555 4967730 5587770 5276570 6740340 7392830 7410670 FALSE TRUE 5947462.828 5885045.117 6375866.972 6095729.023 5476584.309 5479563.062 6086662.864 5811930.836 6534589.035 0.910151013 0.900599117 0.975710475 0.932840457 0.83809162 0.838547464 0.931453047 0.889410306 1 22.63966508 1.234017296 24.94169128 1.000000151 0.902109205 0.353376187 0.041618878 169.4479176 930105.0652 0.083645027 0.010769064 17.14025567 -1.234017296 -0.097890946 YKAPFHQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YKAPFHQLR 9 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 ; 122.13 0.00035709 773220000 587750 924060 530040 652480 1023870 921770 878720 985780 852310 FALSE TRUE 510077.3483 917989.789 786369.1169 800635.5565 1003496.99 957231.0884 793501.8696 774978.6183 751550.8828 0.678699686 1.221460596 1.046328512 1.065311178 1.33523493 1.273674358 1.055819224 1.031172521 1 19.51951126 4.746331708 24.85296215 1.12403791 0.678699452 0.610619545 0.112860385 678.5600244 2170068.23 0.029694763 0.311014271 55761.14823 -4.746331708 -0.445338458 YKCEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YKCEGR 6 1 Q04206;Q04206-4;Q04206-2;A0A087X0W8;E9PKH5;Q2TAM5;Q04206-3;A0A087WVP0;E9PKV4;E9PQS6;E9PI38;E9PMD5;E9PNV4;E9PRX2;E9PJR1;E9PM47;E9PN69;E9PNK5;E9PJZ9 Q04206 RELA Transcription factor p65 0 ;; 88.591 0.046631 324344000 641030 596870 323492 425467 444585 544730 701440 749970 318584 FALSE TRUE 556316.2613 592949.1217 479933.8132 522075.7852 435738.6283 565686.1156 633414.4568 589594.7518 280921.3625 1.980327365 2.110729909 1.708427615 1.858441027 1.55110535 2.013681376 2.254774971 2.098789308 1 18.09980681 4.25009397 24.99166112 1.839572222 2.045528677 0.072542614 0.347059538 733.0616714 1588442.784 0.087264319 0.226616357 17786.64225 -4.25009397 0.205956455 YKDAIHFYNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YKDAIHFYNK 10 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 116.77 0.00062895 3955600000 8300400 5626700 3805700 4531000 5774600 4852000 6799500 7849500 5722600 FALSE TRUE 7203481.109 5589737.837 5646149.249 5559832.802 5659696.758 5038659.58 6140085.537 6170945.51 5046080.747 1.427539802 1.107738484 1.118917737 1.101812095 1.121602495 0.99852932 1.21680287 1.222918502 1 22.26673186 4.740145661 24.67221018 1.121510205 1.427539922 0.638863487 0.074414582 80.27499119 1249395.159 0.018751739 0.115323948 54972.52193 -4.740145661 0.306029717 YKDDDDDQLFYTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YKDDDDDQLFYTR 13 1 O60568;H7C2V1 O60568 PLOD3 "Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3" 0 122.63 0.00021232 190860000 271570 201900 181270 233830 185970 189670 199630 256510 214370 FALSE TRUE 235681.3364 200573.7056 268932.7783 286924.6754 182269.5608 196966.7276 180269.9133 201657.3327 189027.4228 1.246810293 1.061082581 1.422718325 1.517899737 0.964249304 1.04200081 0.953670693 1.066815225 1 17.52823602 3.215482887 24.97674235 1.010987572 1.30209533 0.612545508 0.1210758 169.3268642 183259.8426 0.038546205 0.043734067 1642.414942 -3.215482887 0.291107758 YKDEDGDLITIFDSSDLSFAIQCSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YKDEDGDLITIFDSSDLSFAIQCSR 25 1 Q92734-2;Q92734;Q92734-4;Q92734-3;C9JTY3;C9JUE0;C9JJP5 Q92734-2 TFG Protein TFG 0 ;;;; 179.38 2.51E-17 114733000 113274.8 98307.4 77273.1 100872.2 84672.2 84462.4 106828.9 134019.8 200413 FALSE TRUE 98305.24818 97661.61222 114642.6296 123776.7747 82987.38888 87711.72318 96468.64972 105360.7087 176720.4035 0.556275598 0.552633484 0.648723223 0.700410209 0.469597099 0.496330483 0.545882919 0.596200024 1 17.43110909 1.236832258 4.808304343 1.031390795 0.568753973 0.805346055 0.066463648 0.084527946 4.617300712 0.132450222 0.017802978 17.25171431 -1.236832258 -0.462636821 YKDIIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YKDIIR 6 1 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 97.068 0.037842 799260000 1665400 1644000 1011600 1185600 1499500 1504400 1582900 1894600 1629000 FALSE TRUE 1445313.17 1633200.456 1500813.144 1454808.601 1469662.884 1562275.241 1429390.602 1489454.534 1436421.476 1.006190171 1.136992508 1.044827837 1.012800648 1.023141821 1.087616182 0.995105285 1.036920263 1 20.4540477 -1.99999421 0.156403786 0.790794602 1.084796963 0.122138364 0.041268494 278.3487518 3.60918602 18.27933618 0.57417032 0.010000133 1.99999421 0.294002361 YKDIIRQPS(ph)EEEIIK ddPTM_MDA-MB-175_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 201.61 3.30E-09 497810000 1069510 878610 148058 183201 715640 407640 1393690 1153770 78700 TRUE FALSE 928171.5437 872838.3531 219659.344 224799.5871 701400.1641 423322.1746 1258530.158 907045.2641 69396.17566 13.37496678 12.57761461 3.165294657 3.239365642 10.10718757 6.100079299 18.13543969 13.07053675 1 16.08256854 4.444403427 24.97924681 8.65075714 13.17564823 0.134722163 5.121502288 386.4355282 295033.522 1.366329388 3.615017691 27822.96612 -4.444403427 4.524891093 YKDLDEDELLGNLS(ph)ETELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YKDLDEDELLGNLSETELK 19 1 Q9NYL9;H0YNU8 Q9NYL9 TMOD3 Tropomodulin-3 1 YKDLDEDELLGNLS(0.998)ET(0.002)ELK;YKDLDEDELLGNLS(0.982)ET(0.018)ELK;YKDLDEDELLGNLS(0.999)ET(0.001)ELK;YKDLDEDELLGNLS(0.996)ET(0.004)ELK 220.05 1.81E-19 419847000 817240 652450 599410 584160 622220 456750 892750 1050080 848150 TRUE FALSE 709239.6634 648164.013 889286.6809 716802.4563 609839.0394 474321.4681 806171.2424 825528.5637 747882.6732 0.948330118 0.866665369 1.189072448 0.958442389 0.815420735 0.634219089 1.07793812 1.103820951 1 19.51245243 YKDLDEDELLGNLSETELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YKDLDEDELLGNLSETELK 19 1 Q9NYL9;H0YNU8 Q9NYL9 TMOD3 Tropomodulin-3 0 ; 272.64 2.14E-39 569400000 2280950 1631570 1526210 1565510 1539660 1161710 2444120 2761440 2258170 FALSE TRUE 1979516.678 1620852.109 2264290.261 1920982.973 1509023.778 1206401.735 2207089.619 2170927.546 1991211.715 0.994126673 0.814002899 1.137141894 0.96473065 0.757841955 0.605863117 1.108415344 1.090254506 1 20.92521519 YKDNPFSLGES(ph)FGSR ddPTM_MDA-MB-175_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 1 YKDNPFS(0.001)LGES(0.989)FGS(0.01)R 96.718 0.0021751 191880000 309450 288910 150200 172830 293260 217580 368540 303420 283450 TRUE FALSE 268555.3985 287012.1312 222837.2224 212073.693 287424.6998 225950.4434 332799.0475 238535.9942 249940.8639 1.074475755 1.148320153 0.891559783 0.848495479 1.149970818 0.904015613 1.331511152 0.954369728 1 17.93122727 YKDNPFSLGESFGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YKDNPFSLGESFGSR 15 1 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;Q8N6H7-3;H0YDN9;E9PMU9 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 0 ; 190.82 1.83E-07 1243470000 725440 680880 413400 537010 738030 640120 743120 914950 716710 FALSE TRUE 629571.266 676407.2544 613321.6227 658946.3282 723344.6469 664745.8306 671052.3368 719295.0626 631981.3603 0.996186447 1.07029621 0.970474228 1.042667347 1.144566426 1.051844045 1.061822989 1.138158667 1 19.26952248 3.469026258 24.97190875 1.084835705 1.016192365 0.287374025 0.047893214 210.5506341 649514.6216 0.013013618 0.016829168 2944.599665 -3.469026258 -0.06864334 YKDPQDENK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 98.055 0.0057215 363350000 1294010 1031150 822870 811600 785680 693320 1279910 1482170 1450620 FALSE TRUE 1123003.3 1024376.308 1220812.684 995886.1845 770046.5052 719992.469 1155784.525 1165219.48 1279129.356 0.877943497 0.800838713 0.95440909 0.778565655 0.602008312 0.56287698 0.903571261 0.910947336 1 20.28673074 2.025080604 24.99733345 0.936556851 0.763841492 0.338795169 0.116513454 281.2178081 280282.9158 0.052454602 0.035363421 105.9450338 -2.025080604 -0.172715359 YKEALLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YKEALLGR 8 1 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ; 113.62 0.0025657 2855600000 3249100 2772800 1627970 1786190 2878200 2756900 2890900 3592200 1572250 FALSE TRUE 2819723.203 2754585.294 2415261.737 2191771.74 2820929.451 2862959.727 2610540.963 2824035.985 1386380.396 2.033874116 1.986889963 1.742134947 1.580930995 2.034744186 2.06506074 1.88299039 2.036984938 1 20.40289173 1.234037412 24.99652643 0.999998625 1.91814236 0.77923196 0.153966297 67.99193872 375694.9024 0.30874271 0.039727633 17.14104961 -1.234037412 0.918143735 YKEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YKEEAR 6 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 67.035 0.091051 517030000 1321800 1002000 660730 774250 726660 900920 1070600 1312500 1159800 FALSE TRUE 1147120.781 995417.796 980261.238 950055.2962 712200.8877 935578.9754 966773.3768 1031832.089 1022689.765 1.121670344 0.973333097 0.958512807 0.928977026 0.696399741 0.914821882 0.945324193 1.008939489 1 19.96393714 4.852861087 1.56953736 0.921307834 1.238029394 0.353538653 0.085626985 1.85932711 3.507008332 0.025817007 0.980569191 71262.5054 -4.852861087 0.316721559 YKEEFEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YKEEFEK 7 1 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;; 103.56 0.0076133 9216900000 25200200 5874950 4366730 5321950 5650020 4247720 8067400 9455900 8418700 FALSE TRUE 21869929.72 5836357.067 6478495.234 6530380.088 5537595.656 4411132.537 7285024.79 7433829.371 7423450.877 2.946059735 0.786205387 0.872706689 0.879696006 0.745959763 0.594215899 0.981352866 1.001398069 1 22.82365857 4.739862239 24.99467593 0.864147058 2.94606041 0.964121845 0.126601808 20.93430854 401952.513 0.034097901 0.20663052 54936.65842 -4.739862239 2.081913351 YKEETIEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YKEETIEK 8 1 P61254 P61254 RPL26 60S ribosomal protein L26 0 ;;;;; 137.95 0.00066218 6953490000 7642440 6289870 5304550 5927540 5668220 4374040 8486940 9101260 8910180 FALSE TRUE 6632472.191 6248551.43 7869848.123 7273478.554 5555433.512 4542312.149 7663877.865 7155026.375 7856828.671 0.84416658 0.795301984 1.001657087 0.925752471 0.707083449 0.578135573 0.975441643 0.910676136 1 22.90551567 YKELGEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YKELGEK 7 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;; 99.802 0.0093578 3316000000 4303070 3678460 2848520 3388240 3420680 2940400 4142330 4287430 2900320 FALSE TRUE 3734408.397 3654295.954 4226073.8 4157591.678 3352615.16 3053519.091 3740607.474 3370596.459 2557447.474 1.460209226 1.42888407 1.652457712 1.625680183 1.310922392 1.193971381 1.462633158 1.317953348 1 21.28627318 3.156903596 6.28467411 1.274147452 1.540952252 0.531297615 0.132625396 0.185290344 11.33710086 0.041434306 0.047340706 1435.170821 -3.156903596 0.266804799 YKETDLLILFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YKETDLLILFK 11 1 P05455 P05455 SSB Lupus La protein 0 ; 149.26 3.14E-05 617550000 2981900 2399600 1787480 2289860 1984880 1603830 2563000 3272100 3846100 FALSE TRUE 2587834.36 2383836.87 2651911.307 2809807.711 1945384.771 1665530.378 2314440.654 2572386.879 3391418.439 0.763053692 0.702902609 0.78194754 0.82850517 0.573619801 0.49110141 0.682440311 0.758498818 1 21.69345737 1.24228313 2.593175192 1.072124576 0.687626209 0.496277548 0.098034078 0.471474423 3.556359367 0.40058669 0.028298317 17.46960677 -1.24228313 -0.384498367 YKETDLLILFKDDYFAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YKETDLLILFKDDYFAK 17 2 P05455 P05455 SSB Lupus La protein 0 179.95 4.99E-10 610330000 959540 631980 393940 410570 502900 337170 936630 1078900 157840 FALSE TRUE 832734.3578 627828.4818 584450.7017 503796.1937 492893.2739 350141.1481 845795.7668 848185.631 139180.335 5.983132299 4.510899343 4.19923333 3.619736895 3.541400255 2.515737213 6.076977518 6.094148508 1 17.08659586 4.756158671 2.333452699 4.114292935 6.486729275 0.149497542 1.513090071 1.443478409 9.041166796 0.405577423 7.097266285 57037.2622 -4.756158671 2.37243634 YKLDEDEDEDDADLSKYNLDAS(ph)EEEDSNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YKLDEDEDEDDADLSKYNLDASEEEDSNK 29 2 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 YKLDEDEDEDDADLSKYNLDAS(1)EEEDSNK 270.68 2.69E-71 105680000 141760 71163 97539 72021 62177 49630 115780 142050 84501 TRUE FALSE 123026.0568 70695.52557 144709.1866 88374.46882 60939.79935 51539.29821 104551.6734 111673.7129 74511.38804 1.65110408 0.948788198 1.94210832 1.186053181 0.817858866 0.691696928 1.40316368 1.498746915 1 16.18517332 3.50464649 24.91584738 1.126437266 1.475245995 0.245135926 0.340170295 1247.98876 1129676.493 0.098226093 0.145272583 3196.292307 -3.50464649 0.348808728 YKNECR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YKNECR 6 1 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 0 74.335 0.073505 209560000 559970 495670 249290 309250 250820 372460 547730 607970 384380 FALSE TRUE 485968.5457 492413.9111 369847.4778 379469.9391 245829.1727 386788.7772 494611.2289 477960.3467 338939.0343 1.433793386 1.452809684 1.09119175 1.119581697 0.725290238 1.141175073 1.459292613 1.410166131 1 18.37066627 4.246336626 24.8193068 1.162160489 1.443301706 0.275744096 0.203965327 257.4359481 821656.7708 0.058027226 0.147516491 17633.42302 -4.246336626 0.281141217 YKPESEELTAER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 YKPESEELTAER 12 1 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 ;;;;;; 161.87 5.86E-05 12394440000 13272950 11216490 8021640 10537930 12233070 13663300 11831620 11437500 11536680 FALSE TRUE 11518896.03 11142808.14 11900931.93 12930728.07 11989655.84 14188935.99 10684191.31 8991679.632 10172826.83 1.132320074 1.095350223 1.169874621 1.271104707 1.178596278 1.394787921 1.050267688 0.883891939 1 23.2782173 2.006322562 24.97234763 0.943680696 1.203586815 0.628954441 0.085905785 91.85777599 362810.735 0.035611807 0.023941153 101.4664724 -2.006322562 0.259906119 YKPVCNQVECHPYFNQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YKPVCNQVECHPYFNQR 17 1 S4R3P0;P52895;B4DK69;H0Y804;Q04828 S4R3P0 AKR1C2;AKR1C1 Aldo-keto reductase family 1 member C2;Aldo-keto reductase family 1 member C1 0 ; 198.15 8.69E-12 2820500000 1834790 1734100 1062080 1350140 1761870 1680830 1895750 2107700 1998960 FALSE TRUE 1592317.853 1722708.583 1575705.44 1656709.923 1726812.234 1745492.618 1711900.457 1656984.757 1762645.226 0.903368318 0.977342779 0.893943612 0.939899815 0.979670899 0.990268825 0.971211014 0.940055737 1 20.7493107 3.353821207 5.026697405 0.971910616 0.92822027 0.440050071 0.026730683 0.221833383 8.841106401 0.007632793 0.009903485 2258.505786 -3.353821207 -0.043690346 YKPVCNQVECHPYFNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YKPVCNQVECHPYFNR 16 1 A0A0A0MSS8;P42330;S4R3Z2;P42330-2 A0A0A0MSS8 AKR1C3 Aldo-keto reductase family 1 member C3 0 ; 177.58 1.76E-09 1754590000 982970 939220 624080 733250 985820 933800 1037650 1098340 1126100 FALSE TRUE 853068.024 933050.202 925887.1754 899745.6195 966204.1107 969723.8902 937018.8627 863468.5383 992973.7409 0.859104314 0.939652444 0.932438732 0.906112199 0.973040949 0.976585634 0.943649186 0.869578422 1 19.92139604 4.739551554 23.77815821 0.937524066 0.859104267 0.326508201 0.037061093 56.85852811 1363943.458 0.00926029 0.054611974 54897.37193 -4.739551554 -0.078419799 YKQENTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YKQENTR 7 1 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 ; 119.27 0.0043945 409840000 378100 357000 252630 302660 252960 357780 417740 444380 429120 FALSE TRUE 328133.127 354654.8435 374802.713 371383.5789 247926.5909 371544.0281 377227.6391 349352.7952 378389.9225 0.867182521 0.937273491 0.990519807 0.9814838 0.655214572 0.981907831 0.996928345 0.923261362 1 18.52951414 YKSEDEANR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YKSEDEANR 9 1 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 74.944 0.036169 74165000 80847 77951 83896 97865 67260 75164 86618 98038 254400 FALSE TRUE 70162.86411 77438.93475 124468.3862 120086.744 65921.65759 78055.60772 78217.79969 77073.33663 224325.1218 0.312773102 0.345208482 0.554857099 0.535324546 0.293866586 0.347957496 0.348680518 0.343578713 1 17.77523167 1.236136643 24.9999638 1.000000802 0.38632318 0.825565353 0.088800261 28.3040118 291852.3928 0.152281477 0.023237284 17.22410415 -1.236136643 -0.613677621 YKSEDEANRDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YKSEDEANRDR 11 2 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 ;;; 122.39 0.00022032 2613150000 4117760 3830690 2869290 3039300 3618950 3573900 4864410 4915940 2294960 FALSE TRUE 3573587.583 3805525.945 4256888.241 3729419.518 3546939.975 3711390.246 4392660.267 3864704.487 2023652.443 1.765909751 1.880523485 2.103566873 1.842915037 1.752741676 1.834005764 2.170659434 1.909766917 1 20.9485301 1.238918253 10.77738325 0.997565754 1.916245277 0.818153538 0.134405202 0.026983432 98.99776537 0.186982573 0.033637681 17.33477675 -1.238918253 0.918679523 YKVEGFPTIYFAPSGDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YKVEGFPTIYFAPSGDK 17 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 136.2 1.01E-05 716700000 567040 430120 349710 411960 417500 426260 515940 513860 392000 FALSE TRUE 492104.2273 427294.5134 518830.9257 505501.8144 409192.5668 442658.498 465904.2182 403975.0379 345658.2066 1.423672917 1.236176388 1.500994091 1.462432556 1.183806891 1.280624876 1.347875472 1.168712416 1 18.39898665 0.312504163 0.653277833 2.63E-13 1.371859753 0.598689789 0.09642994 7.229901015 0.96589986 9.755680239 0.046327801 2.053544709 -0.312504163 1.371859753 YKVPDGKPENEFAFNAEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YKVPDGKPENEFAFNAEFK 19 2 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 218.79 1.85E-19 3421400000 4089500 2607120 2728190 2682460 2336010 1707010 4147000 4599600 3612800 FALSE TRUE 3549062.214 2589993.657 4047551.809 3291553.542 2289527.971 1772679.779 3744824.578 3616011.334 3185698.9 1.114060784 0.81300642 1.270538094 1.033228075 0.718689381 0.556449255 1.17551115 1.135076304 1 21.60317848 -1.324727804 8.016425502 2.541584433 0.984515197 0 0.222028791 0 0 0 0.052079041 0.04734479 1.324727804 -1.557069236 YKYPNISCELLTSDVSQMNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YKYPNISCELLTSDVSQMNDR 21 1 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PNN8 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 200.29 6.89E-22 956170000 320160 326970 197550 238180 308220 299600 326220 406390 295680 FALSE TRUE 277850.0448 324822.1125 293085.8408 292262.4094 302087.025 311125.8059 294583.2346 319486.661 260725.0472 1.065682211 1.24584161 1.124118468 1.120960232 1.158642134 1.193309999 1.12986166 1.225377709 1 17.99216966 1.224014946 24.99793322 0.999999581 1.161472295 0.464750255 0.053161442 670.2745887 1151855.394 0.260805726 0.011968034 16.75000519 -1.224014946 0.161472715 YLAEFATGNDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 YLAEFATGNDR 11 0 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;;;; 245.38 1.43E-15 10555710000 3817980 4005920 3151050 3659260 3865020 3808100 3333760 4295510 8281340 FALSE TRUE 3313424.269 3979604.848 4674908.32 4490150.911 3788113.664 3954600.071 3010452.468 3376948.614 7302329.419 0.453748945 0.544977448 0.640194115 0.614892954 0.518754146 0.541553228 0.412259198 0.462448134 1 22.79992532 1.234118435 24.99924744 1.000000709 0.523091154 0.821784172 0.069720897 61.64325358 346864.4702 0.147610278 0.019130496 17.14424779 -1.234118435 -0.476909555 YLAEFATGNDRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YLAEFATGNDRK 12 1 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ;; 194.24 2.85E-06 4250730000 2703180 2171290 1456470 1677940 2014000 1875720 2530590 2828280 1491270 FALSE TRUE 2345947.914 2157026.653 2160823.764 2058941.923 1973925.34 1947880.162 2285173.771 2223474.332 1314973.759 1.784026409 1.640357184 1.643244778 1.565766547 1.501113863 1.481307249 1.737809409 1.690888746 1 20.32660258 1.235093351 24.99992506 0.999999121 1.62838688 0.811255602 0.095579923 45.12045046 325278.4351 0.177525193 0.024987011 17.18277688 -1.235093351 0.62838776 YLAEKYEWDVAEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YLAEKYEWDVAEAR 14 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;; 215 6.08E-12 8183980000 9517550 9017330 4396810 5252140 8354490 7357270 9999510 11362810 1949708 FALSE TRUE 8259781.653 8958094.565 6523122.022 6444718.661 8188251.994 7640308.938 9029759.059 8932961.507 1719215.741 4.804389266 5.210570349 3.794242843 3.7486387 4.762783284 4.444066416 5.252254759 5.19595144 1 20.71331917 4.249286021 24.88104089 4.229198607 5.007480036 0.083655373 1.213007114 603.6051291 1400227.133 0.297532342 0.769629239 17753.58327 -4.249286021 0.778281428 YLAEVAAGDDKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 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 13612400000 11847260 8169660 7675836 7909400 6582610 4914722 11449480 12544490 10329540 FALSE TRUE 10281614.57 8115992.966 11387895.96 9705350.158 6451628.94 5103794.536 10339111.19 9861948.435 9108393.549 1.12880658 0.891045487 1.250263935 1.065539176 0.708316884 0.560339703 1.135119068 1.08273192 1 23.1187652 3.441751908 24.99177888 0.918328421 1.084766727 0.191075428 0.188507136 367.4874367 259663.4322 0.059794908 0.077195224 2765.361474 -3.441751908 0.166438306 YLAEVACGDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YLAEVACGDDR 11 0 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;;;;; 232.72 2.88E-13 5387000000 3413590 2877540 1734300 2051130 2798710 2996990 2739110 3035570 3234670 FALSE TRUE 2962475.433 2858637.25 2573013.281 2516870.416 2743021.147 3112286.145 2473471.534 2386436.978 2852270.998 1.038637435 1.002231994 0.902092853 0.882409287 0.96169724 1.091160744 0.867193733 0.836679607 1 21.44367963 4.379454061 4.593934137 0.927052798 1.030666875 0.194860513 0.073016465 0.318261735 11.2867257 0.019792761 0.057472603 23958.19311 -4.379454061 0.103614077 YLAEVACGDDRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YLAEVACGDDRK 12 1 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;;; 198.57 2.91E-07 6929870000 4641830 2985470 2171980 2679010 3152870 2900060 3929890 4461290 3427500 FALSE TRUE 4028400.405 2965858.251 3222356.793 3287320.167 3090134.055 3011627.185 3548769.873 3507277.851 3022304.855 1.332890161 0.981323326 1.066191846 1.087686493 1.022442872 0.996467044 1.174193221 1.160464619 1 21.52721776 4.751353156 24.59425436 1.071923373 1.332890369 0.617442229 0.066752717 1287.709989 2475627.508 0.017518025 0.305706583 56409.61762 -4.751353156 0.260966996 YLAEVASGEKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YLAEVASGEKK 11 1 Q04917;A2IDB2 Q04917 YWHAH 14-3-3 protein eta 0 88.187 0.014853 0 341410 270220 209780 260310 278560 273480 345990 460550 254070 FALSE TRUE 296291.8035 268444.907 311230.3097 319417.3641 273017.201 284000.9526 312435.9431 362064.9665 224034.134 1.322529733 1.198232172 1.389209332 1.425753113 1.218641089 1.267668223 1.394590804 1.616115187 1 17.77335903 2.220692455 22.13620404 1.397475333 1.304451701 0 0.166006068 195.39547 242060.3985 0.06650578 0.045005012 166.2235124 -2.220692455 -0.093023632 YLAEVATGDDKKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YLAEVATGDDKKR 13 2 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ;; 145.81 2.36E-05 900327000 1516280 1162716 818776 825581 998812 823430 1642160 1762840 388160 FALSE TRUE 1315899.756 1155078.042 1214738.812 1013041.784 978937.5953 855107.8849 1482903.576 1385870.384 342272.167 3.844600535 3.374735528 3.549043508 2.959755078 2.860114522 2.498327259 4.3325275 4.049030328 1 18.38478445 3.758724119 19.58600106 3.128295051 3.567989146 0.077587222 0.909149474 195.0413568 189444.2841 0.247461519 0.426789076 5737.51877 -3.758724119 0.439694095 YLAEVATGEKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLAEVATGEKR 11 1 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ; 133.42 0.00025986 677610000 1127110 874470 519680 668300 857670 722730 910920 1080780 417470 FALSE TRUE 978159.5578 868725.549 770998.9862 820047.7293 840604.045 750533.8908 822579.1186 849663.6076 368117.1722 2.657196218 2.359915849 2.094439066 2.227681269 2.283523042 2.038845095 2.234557855 2.308133583 1 18.48980553 1.237331544 24.98802107 0.999998474 2.263478741 0.853588602 0.165952495 11.31650931 229976.2554 0.244721987 0.040658891 17.27155916 -1.237331544 1.263480267 YLAFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLAFLR 6 0 P40429;M0QYS1 P40429 RPL13A 60S ribosomal protein L13a 0 ; 184.12 0.005593 6491900000 2901300 4437200 2648500 2741600 4448100 4467900 3595400 4039100 4352900 FALSE TRUE 2517885.854 4408051.741 3929323.459 3364122.183 4359591.513 4639783.004 3246718.661 3175369.897 3838305.121 0.655988978 1.148437032 1.023713159 0.876460333 1.135811608 1.208810362 0.845872998 0.827284387 1 21.87203797 YLALHTDLLEEEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YLALHTDLLEEEAR 14 0 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 0 132.86 4.80E-05 58620000 92150 90450 58268 78352 83696 97633 79117 92053 115840 FALSE TRUE 79972.14402 89855.82799 86446.59969 96143.01914 82030.61335 101389.0047 71444.24552 72368.18231 102145.5272 0.782923602 0.879684412 0.846308224 0.941235723 0.803075921 0.99259368 0.699435869 0.708481167 1 16.64026651 2.222739511 24.99995973 0.778722703 0.873080439 0.084246058 0.101599309 437.0238987 690564.428 0.039968096 0.027046246 167.0088596 -2.222739511 0.094357735 YLANIEQQHGNSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YLANIEQQHGNSGR 14 0 Q9UKX7-2;Q9UKX7 Q9UKX7-2 NUP50 Nuclear pore complex protein Nup50 0 ;;; 188.25 8.54E-07 1348000000 1177960 1198310 720860 959620 1286580 1443770 1179600 1376560 1302570 FALSE TRUE 1022289.601 1190438.223 1069470.307 1177516.388 1260979.575 1499312.766 1065202.574 1082193.356 1148581.658 0.890045208 1.036441958 0.931122571 1.025191704 1.097858011 1.305360185 0.927406916 0.942199754 1 20.131422 3.59423917 5.462966399 1.044961363 0.961588107 0.147627503 0.109903677 0.588315476 24.08659535 0.033430459 0.049916894 3928.61228 -3.59423917 -0.083373257 YLAQWYSETNGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YLAQWYSETNGR 12 0 Q13564-2;Q13564;Q13564-4;Q13564-3 Q13564-2 NAE1 NEDD8-activating enzyme E1 regulatory subunit 0 154.05 0.00016557 264590000 224330 201620 124860 159280 219590 253390 182640 200690 155810 FALSE TRUE 194684.2221 200295.5449 185242.7136 195446.9584 215220.5886 263138.0773 164927.6009 157774.0053 137390.3193 1.417015574 1.457857773 1.348295241 1.422567175 1.566490199 1.915259231 1.200431018 1.148363335 1 17.06792083 2.021824785 24.99950651 1.111664352 1.51222327 0.597261107 0.158510201 164.6769773 188630.7782 0.067848702 0.045739659 105.1537549 -2.021824785 0.400558917 YLDEDTIYHLQPSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YLDEDTIYHLQPSGR 15 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ;;;;; 200.55 6.86E-09 3668580000 3117390 3532750 2249612 2639820 3396950 3644470 3808860 3725610 3870520 FALSE TRUE 2705419.013 3509543.133 3337531.888 3239231.478 3329357.341 3784675.119 3439477.343 2928917.294 3412951.535 0.792691893 1.028301485 0.977901928 0.949099759 0.975506774 1.108915577 1.007772102 0.85817723 1 21.7025885 4.747617824 24.75351817 0.980798432 0.792691781 0.483398716 0.063108356 1067.13524 2916429.725 0.016760413 0.197405166 55926.5236 -4.747617824 -0.188106652 YLDESSGGWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YLDESSGGWR 10 0 K7ENE5;O00115-2;O00115 K7ENE5 DNASE2 Deoxyribonuclease-2-alpha 0 ;;;;; 288.53 6.41E-25 2399320000 2555520 2305430 1501183 1847970 2322230 2699800 2000160 2424400 2260290 FALSE TRUE 2217801.557 2290285.479 2227160.12 2267579.833 2276022.166 2803663.053 1806184.791 1905960.927 1993081.091 1.112750287 1.149118061 1.117445813 1.137725827 1.141961647 1.406697934 0.906227448 0.956288701 1 20.92656898 2.191662065 24.99999832 0.952614999 1.170153265 0.591496976 0.087385682 83.60699566 44567.37559 0.035130999 0.023685385 155.475537 -2.191662065 0.217538265 YLDIHER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLDIHER 7 0 P62072 P62072 TIMM10 Mitochondrial import inner membrane translocase subunit Tim10 0 ; 125.81 0.0040127 810960000 1089820 1020500 637950 824200 1077300 1360090 761390 1019990 980350 FALSE TRUE 945797.5257 1013796.268 946464.7538 1011347.207 1055863.838 1412413.542 687550.515 801873.0761 864454.1398 1.094097977 1.172758879 1.094869826 1.169925807 1.221422617 1.633879089 0.795357999 0.927606265 1 19.7214299 2.166959477 24.99999935 0.90713131 1.219125183 0.476266385 0.159586081 40.06830828 13989.07483 0.065556962 0.044198503 146.8789224 -2.166959477 0.311993874 YLDLHDCYLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YLDLHDCYLK 10 0 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ;; 145.34 0.0002146 1094650000 2511630 2185020 1402500 1748620 2410700 2125520 2297780 2662820 2582560 FALSE TRUE 2179711.732 2170666.46 2080753.691 2145670.897 2362731.786 2207290.13 2074941.649 2093396.665 2277252.699 0.957167263 0.953195252 0.913712252 0.94221906 1.037536057 0.969277644 0.911160035 0.919264105 1 21.11886296 4.708115925 6.771351774 0.952074761 0.957200712 0 0.039744668 2.976241717 524.1797814 0.010264309 0.045430745 51064.1286 -4.708115925 0.005125951 YLDLILNDFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YLDLILNDFVR 11 0 Q15046;Q15046-2;J3KRL2;H3BPV7 Q15046 KARS Lysine--tRNA ligase 0 152.62 7.64E-05 62642000 198970 182940 147310 140520 171760 181210 188620 224580 179200 FALSE TRUE 172675.6104 181738.2551 218549.6087 172427.2137 168342.312 188181.266 170327.6614 176555.3147 158015.1801 1.092778619 1.15013162 1.383092488 1.091206639 1.065355315 1.190906252 1.07791961 1.117331351 1 17.26970364 YLDPEYIDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YLDPEYIDR 9 0 X6RA56;X6RLR1;O75935-2;O75935;X6RCK5;A0A0A0MRV8;O75935-3 X6RA56 DCTN3 Dynactin subunit 3 0 ;; 171.73 0.00013197 825980000 2374120 2346950 1508020 1782150 2206080 2566270 2300230 2488660 2409700 FALSE TRUE 2060374.027 2331532.731 2237303.516 2186814.396 2162183.324 2664996.067 2077154.049 1956479.426 2124828.011 0.969666258 1.097280683 1.052933934 1.029172425 1.017580394 1.254217308 0.977563378 0.920770724 1 21.01891464 2.023151919 24.99869269 0.953058259 1.070470885 0.291985816 0.076521318 245.6503284 265244.1995 0.030218014 0.02037172 105.4755792 -2.023151919 0.117412625 YLDPSFFQHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLDPSFFQHR 10 0 Q9HD45;Q5TB53 Q9HD45 TM9SF3 Transmembrane 9 superfamily member 3 0 ; 174.41 3.11E-06 719530000 881930 689920 741510 1141400 961310 1265230 578700 903860 2508800 FALSE TRUE 765380.716 685387.8701 1100106.716 1400572.315 942181.8118 1313904.217 522577.7631 710576.5728 2212212.522 0.345979741 0.309820084 0.497287989 0.633109297 0.425900225 0.593932185 0.236224033 0.321206288 1 21.07705856 1.23270431 24.99958451 1.000000939 0.41833045 0.676344777 0.125990555 124.3480598 530766.0675 0.287873392 0.032885713 17.08851445 -1.23270431 -0.581670489 YLDQMEDLYEDFHIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YLDQMEDLYEDFHIVK 16 0 O43681 O43681 ASNA1 ATPase ASNA1 0 ;;; 214.22 1.72E-14 699020000 1151940 974840 661076 835280 967520 950170 1130840 1316020 1245720 FALSE TRUE 999708.2104 968436.2119 980774.5648 1024943.09 948268.2449 986723.6547 1021171.311 1034599.364 1098452.401 0.910106082 0.881636939 0.892869426 0.933079203 0.863276592 0.898285309 0.929645481 0.941870001 1 20.06704092 1.096318165 0.994271967 1.079526994 0.895782399 0.752051172 0.018955508 1.197324833 0.793824745 0.255144665 0.006346521 12.48297684 -1.096318165 -0.183744595 YLDYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YLDYAR 6 0 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 0 102.98 0.081604 261470000 477200 492230 275150 334570 473100 469220 395780 490510 471010 FALSE TRUE 414136.8109 488996.5087 408213.4603 410539.2321 463686.2356 487271.197 357397.3165 385618.2537 415327.7344 0.997132569 1.177375042 0.982870698 0.988470545 1.116434558 1.173220945 0.860518783 0.928467381 1 18.66389069 2.229803841 24.99966985 0.926532196 1.071439273 0.432230373 0.077183222 176.6184533 504222.3428 0.031223049 0.021411809 169.7476775 -2.229803841 0.144907077 YLECSALTQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLECSALTQR 10 0 P63000;J3KSC4;J3QLK0;P60763;P63000-2;B1AH77;B1AH80;P15153;B1AH78 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 ; 206.38 3.52E-07 195071000 167530 168180 96867 136542 160206 197189 126056 184518 175344 FALSE TRUE 145390.486 167075.2145 143712.2052 167545.948 157018.214 204774.9884 113831.1085 145060.2616 154615.0321 0.940338621 1.080588428 0.929484044 1.08363298 1.015543003 1.324418368 0.736222779 0.938202836 1 17.23832106 2.209639124 24.99999189 0.894741454 1.055966986 0.289614074 0.125846668 275.6065132 238234.6941 0.049501968 0.033380338 162.0463017 -2.209639124 0.161225532 YLEDGGLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YLEDGGLER 9 0 P07099 P07099 EPHX1 Epoxide hydrolase 1 0 89.542 0.028002 261220000 355800 375530 308420 374690 515830 489440 319970 571100 557240 FALSE TRUE 308780.1285 373063.1187 457572.9436 459769.0913 505565.9922 508269.0735 288939.3586 448974.7093 491363.722 0.628414583 0.759240257 0.93123062 0.935700115 1.028903783 1.034404965 0.588035595 0.913731904 1 18.90643182 4.466263523 2.846408363 0.909428006 0.633730753 0.37399756 0.126284678 0.331043232 4.990552824 0.033864509 0.156949531 29259.27247 -4.466263523 -0.275697252 YLEEDNS(ph)DES(ph)DAEGEHGDGAEEEAPPAGPRPGPEPAGLGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YLEEDNSDESDAEGEHGDGAEEEAPPAGPRPGPEPAGLGR 40 1 Q9H1C4 Q9H1C4 UNC93B1 Protein unc-93 homolog B1 2 Y(0.004)LEEDNS(0.996)DES(1)DAEGEHGDGAEEEAPPAGPRPGPEPAGLGR 79.075 0.0016813 104790000 15150 14742 8907.7 11652 18569 19191 10708 16986 8507.7 TRUE FALSE 13147.88911 14645.15883 13215.49351 14297.76469 18199.51323 19929.29019 9669.539808 13353.67609 7501.929398 1.75260102 1.952185638 1.761612622 1.905878332 2.425977674 2.656555285 1.288940391 1.780032226 1 12.87304597 2.207987553 24.999995 1.441788743 2.06409526 0.493075755 0.340097769 201.5451307 164804.7019 0.145274644 0.097956892 161.4312288 -2.207987553 0.622306517 YLEES(ph)DEDDLF ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YLEESDEDDLF 11 0 P11388;P11388-2;P11388-3;P11388-4;J3QR57 P11388 TOP2A DNA topoisomerase 2-alpha 1 Y(0.012)LEES(0.988)DEDDLF;YLEES(1)DEDDLF;YLEES(1)DEDDLF 160.88 2.83E-05 468091000 1625430 1668440 896419 1348800 1627010 1372610 1419650 1714280 1281940 TRUE FALSE 1410625.307 1657479.908 1329930.227 1655065.655 1594635.684 1425415.195 1281972.562 1347694.563 1130390.514 1.247909718 1.466289648 1.176522813 1.464153879 1.410694503 1.260993593 1.134097063 1.192238033 1 20.10838983 2.373862676 2.746006006 1.122707022 1.35550837 0.547888031 0.100755109 0.205002503 3.157489836 0.041108683 0.029557544 236.5171712 -2.373862676 0.232801349 YLELLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLELLER 7 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ; 111.82 0.015108 125920000 300290 247474 180548 190901 248733 289650 247533 277730 262950 FALSE TRUE 260605.9157 245848.327 267861.6167 234247.9898 243783.6999 300793.0229 223527.2878 218339.6008 231864.3506 1.123958535 1.060311024 1.155251405 1.010280318 1.051406563 1.297280165 0.964043361 0.941669559 1 17.8229215 2.077133948 25 0.962492425 1.109752345 0.440619397 0.078189556 29.99649583 9720.813149 0.03100594 0.020904203 119.435642 -2.077133948 0.14725992 YLELLGYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLELLGYR 8 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-7;H7BXG7;O94979-5;H0YAB3;H0Y8V7;H0Y9K1 D6REX3 SEC31A Protein transport protein Sec31A 0 ; 128.57 0.0026243 717920000 802970 843440 468120 567190 868730 939680 760740 838930 880670 FALSE TRUE 696855.48 837899.3871 694504.3978 695979.1585 851443.9726 975830.0977 686963.5519 659531.3481 776558.1959 0.897364143 1.078991107 0.894336576 0.896235674 1.096432923 1.256609103 0.884625976 0.849300608 1 19.56673452 YLENYDAIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YLENYDAIR 9 0 A0A087WTB8;P15374;Q5TBK7 A0A087WTB8;Q5TBK7 UCHL3 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L3 0 133.57 0.00063549 632180000 249400 281130 173740 186080 321680 330780 257280 279120 297270 FALSE TRUE 216441.1581 279283.2385 257761.2451 228332.3081 315279.1974 343505.3206 232329.0252 219432.3601 262127.0793 0.825710792 1.065449778 0.983344589 0.871074857 1.202772328 1.310453394 0.886322107 0.837122058 1 17.99990687 YLEQLHQLYSDSFPMELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLEQLHQLYSDSFPMELR 18 0 P40763;P40763-2;P40763-3;K7EP08 P40763 STAT3 Signal transducer and activator of transcription 3 0 ; 199.76 1.59E-15 663960000 660350 646910 304140 462790 615370 637640 632420 710930 557850 FALSE TRUE 573083.0744 642660.4056 451223.1213 567873.5428 603125.341 662170.4234 571088.0057 558903.152 491901.6085 1.165035984 1.30648161 0.91730361 1.154445387 1.226109715 1.34614405 1.160980155 1.136209238 1 18.90801025 1.242498052 2.22389341 0.949159634 1.182995061 0.20320863 0.113503903 1.124607672 5.716359111 0.526898358 0.031017889 17.47825423 -1.242498052 0.233835427 YLEVMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YLEVMR 6 0 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;Q15257-4;A6PVN9;Q5T948;Q5T949 Q15257 PPP2R4 Serine/threonine-protein phosphatase 2A activator 0 132.72 0.034376 193670000 264750 232810 149760 177590 242790 256910 216920 268280 254660 FALSE TRUE 229762.6167 231280.6558 222184.4369 217914.5238 237958.954 266793.4939 195883.1318 210910.4098 224554.3849 1.023193632 1.029953861 0.989445995 0.970430944 1.059694087 1.188101911 0.872319335 0.939239774 1 17.77670537 2.194677673 24.99997221 0.934911431 1.037818505 0.368305253 0.065314258 153.749985 87589.76537 0.027462966 0.018515648 156.5588682 -2.194677673 0.102907074 YLFLGDYVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 146.81 6.51E-05 319108000 550422 541630 427310 454759 539636 570574 539246 570350 882004 FALSE TRUE 477682.3381 538071.9969 633958.5453 558018.9815 528898.2994 592524.351 486950.0059 448385.091 777734.4919 0.614197188 0.691845357 0.815134923 0.717492907 0.680049946 0.761859423 0.626113424 0.576527203 1 19.5689182 YLGDAFGS(ph)PQTDHGFETDPDPFLLDEPAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YLGDAFGSPQTDHGFETDPDPFLLDEPAPR 30 0 Q9H8N7 Q9H8N7 ZNF395 Zinc finger protein 395 1 YLGDAFGS(0.749)PQT(0.251)DHGFETDPDPFLLDEPAPR;YLGDAFGS(0.974)PQT(0.026)DHGFETDPDPFLLDEPAPR;YLGDAFGS(0.995)PQT(0.005)DHGFETDPDPFLLDEPAPR;Y(0.002)LGDAFGS(0.942)PQT(0.056)DHGFETDPDPFLLDEPAPR 222.61 6.95E-35 543915000 308942 351475 263424 301475 447239 440117 425400 528720 472620 TRUE FALSE 268114.5319 349166.1376 390816.7275 369929.5065 438339.8189 457048.5858 384144.7735 415657.3425 416747.402 0.643350218 0.837836387 0.937778438 0.887658819 1.051811761 1.096704103 0.92176885 0.997384364 1 18.66881368 5.3243906 0.786616422 1.003162251 4.79E-17 0.811660924 0.055018472 2.505351933 0.624405312 0.020944734 2.723004127 211052.548 -5.3243906 -1.003162251 YLGEGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YLGEGPR 7 0 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;; 106.76 0.01775 676770000 956320 978190 595670 720810 913580 1053380 941590 1095710 966630 FALSE TRUE 829939.889 971764.2055 883738.0044 884480.9274 895401.5454 1093904.21 850274.7467 861400.9433 852356.1026 0.973700882 1.140091803 1.03681783 1.037689441 1.050501712 1.283388723 0.997558115 1.010611575 1 19.70109677 YLGGS(ph)MDLSTFDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLGGSMDLSTFDFR 14 0 O95983-2;O95983 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 1 YLGGS(1)MDLSTFDFR;YLGGS(1)MDLSTFDFR 207.52 9.77E-09 133842000 262156 212531 78658 104711 148091 91449 229697 172777 180975 TRUE FALSE 227511.4204 211134.8699 116697.2719 128487.233 145144.2788 94967.10221 207421.0203 135829.9831 159580.3417 1.425685758 1.323063152 0.731275987 0.805157024 0.909537336 0.595105269 1.299790551 0.851169898 1 17.28392341 4.325231314 6.072008779 0.892243612 1.394346294 0.55188876 0.183937608 0.146238363 8.065550562 0.044603584 0.120709654 21146.15026 -4.325231314 0.502102682 YLGLLENLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLGLLENLR 9 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 140.5 0.00025346 219811000 373970 448110 304470 370820 489130 510180 439290 481990 512400 FALSE TRUE 324548.917 445166.3359 451712.7104 455020.3486 479397.27 529806.9547 396687.7234 378920.1894 451824.6557 0.71830723 0.985263487 0.999752237 1.007072861 1.061025032 1.172594165 0.877968297 0.838644338 1 18.78540347 7.466521951 13.51527629 0.961698723 0.007271623 0 0.125283836 0 0 0.029187171 0 29276688.42 -7.466521951 -0.954427099 YLGQDYEQLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YLGQDYEQLR 10 0 P07384;E9PRM1;E9PJJ3;E9PLC9;E9PMC6;E9PJA6;E9PSA6;E9PQB3;E9PLX0;E9PIA9 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;;; 260.23 6.12E-17 1208450000 2247370 1538410 941600 1084120 1485440 1608220 1354420 1515910 1484710 FALSE TRUE 1950374.36 1528304.083 1396960.909 1330286.016 1455882.65 1670089.264 1223068.557 1191744.443 1309189.275 1.489757362 1.167366791 1.067042739 1.016114355 1.11204902 1.275666778 0.934218283 0.910291939 1 20.32024226 7.999996581 0.824387916 1.022242898 140.0138393 0.656553554 0.101216615 402.5561739 1.250605881 0.039130313 104723.0237 99999212.67 -7.999996581 138.9915964 YLGS(ph)PITTVPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YLGSPITTVPK 11 0 P30307-4;P30307-3;P30307-2;P30307;D6RJC2;A0A3B3IT42 P30307-4 CDC25C M-phase inducer phosphatase 3 1 YLGS(0.866)PIT(0.117)T(0.016)VPK 93.345 0.0097751 79688000 197970 219860 164670 220540 283280 237140 277890 371540 335090 TRUE FALSE 171807.7629 218415.7252 244304.9628 270616.9777 277643.2822 246262.9293 250940.2706 292089.0623 295476.0419 0.581460892 0.739199442 0.826818179 0.91586775 0.939647358 0.83344466 0.849274509 0.988537211 1 18.17268163 5.319383431 0.680398265 0.933893012 5.60E-14 0.827622843 0.051635116 2.737496377 0.553643865 0.024448257 2.356212062 208633.2059 -5.319383431 -0.933893012 YLHDESGLNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YLHDESGLNR 10 0 Q15019-2;Q15019-3;Q15019;B5MCX3;C9J2Q4;C9J938;C9JB25;C9IY94;H7C310 Q15019-2 2-Sep Septin-2 0 ;;; 231.38 7.12E-10 2585460000 1720930 1602840 1071320 1479850 1663900 1686650 1574350 1763790 2745260 FALSE TRUE 1493504.74 1592310.839 1589413.935 1815872.561 1630791.645 1751536.517 1421669.779 1386617.234 2420718.49 0.616967543 0.657784391 0.656587679 0.750137849 0.673680832 0.723560597 0.587292486 0.572812262 1 21.20700388 1.230292223 24.99854542 1.00000064 0.653699354 0.797365741 0.05467797 153.1806635 463087.3933 0.164280567 0.014873351 16.99386733 -1.230292223 -0.346301286 YLHDESGLNRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YLHDESGLNRR 11 1 Q15019-2;Q15019-3;Q15019;B5MCX3;C9J2Q4;C9J938;C9JB25;C9IY94;H7C310 Q15019-2 2-Sep Septin-2 0 ;;; 209.85 9.58E-09 1427250000 1206560 1146550 574137 745170 1121740 1194340 1184930 1257910 713420 FALSE TRUE 1047110.039 1139018.238 851791.5736 914372.2377 1099419.569 1240287.033 1070015.671 988915.7356 629080.3003 1.664509345 1.810608657 1.35402678 1.453506392 1.747661734 1.97158778 1.700920646 1.57200239 1 19.26288466 1.228711937 3.205527814 0.876059263 1.669420913 0.598486225 0.17154023 0.279787314 3.768791315 0.570491361 0.047644321 16.93214335 -1.228711937 0.79336165 YLIATSEQPIAALHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLIATSEQPIAALHR 15 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 165.64 1.41E-06 709290000 619730 477500 291790 355850 490540 511560 417870 516750 509560 FALSE TRUE 537831.1103 474363.2711 432900.62 436651.1813 480779.2137 531240.0442 377345.0317 406247.0339 449320.3973 1.19698797 1.055735003 0.963456417 0.971803604 1.070014218 1.182319003 0.839812824 0.904136639 1 18.77738503 YLIVDEGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLIVDEGHR 9 0 A0A0B4J1V9;Q9NRZ9-4;Q9NRZ9-3;Q9NRZ9-2;Q9NRZ9;A0A087WSW7;F6XU50 A0A0B4J1V9 HELLS Lymphoid-specific helicase 0 ; 107.57 0.0034151 105850000 124498 150524 85447 106448 146276 145500 139526 153206 142791 FALSE TRUE 108045.2739 149535.1979 126769.455 130618.6454 143365.3938 151097.4792 125994.79 120444.0892 125910.4106 0.858112314 1.187631723 1.006822663 1.03739353 1.138630182 1.200039603 1.000670154 0.956585627 1 16.94203805 2.019864466 24.99916759 0.976222567 1.077378259 0.145998059 0.098069607 374.505284 471307.8003 0.03820601 0.025755283 104.6801814 -2.019864466 0.101155693 YLKDVTLQK ddPTM_MDA-MB-175_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 94.616 0.0059403 0 1228500 1210400 702980 917650 1318800 1143600 1840400 1898800 1126800 FALSE TRUE 1066150.612 1202448.803 1042943.479 1126016.458 1292558.46 1187595.032 1661918.291 1492756.396 993590.9877 1.07302766 1.210205022 1.049670833 1.133279661 1.300895918 1.195255439 1.67263825 1.502385202 1 19.92229256 2.856283269 1.677506873 1.412619495 1.120099771 0.243835892 0.182325038 0.4409438 2.501139785 0.075172795 0.072967663 718.2626259 -2.856283269 -0.292519724 YLLGDAPVS(ph)PSSQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YLLGDAPVSPSSQK 14 0 Q9NYB0;A0A590UJT3;H3BMI8 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 YLLGDAPVS(0.751)PS(0.248)S(0.001)QK;YLLGDAPVS(0.991)PS(0.009)SQK;YLLGDAPVS(0.658)PS(0.342)SQK;YLLGDAPVS(0.978)PS(0.022)SQK;YLLGDAPVS(0.745)PS(0.236)S(0.019)QK;YLLGDAPVS(0.999)PS(0.001)SQK 350.73 6.92E-82 5824770000 15878200 9392780 6100190 7875730 9288490 8085150 11255900 12730000 11510800 TRUE FALSE 13779855.64 9331078.21 9050262.288 9664034.869 9103667.222 8396190.952 10164304.55 10007788.56 10150006.34 1.357620398 0.919317476 0.8916509 0.952121068 0.896912467 0.827210415 1.00140869 0.985988406 1 23.27497729 4.739959857 24.90144154 0.936212717 1.357620543 0.856188394 0.054515286 44.87857165 798593.1987 0.014378674 0.087695597 54949.00805 -4.739959857 0.421407826 YLLGDMEGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YLLGDMEGR 9 0 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 ;; 121.62 0.0014163 874350000 1231290 1091840 707040 844380 1069840 1124030 1068500 1247010 1208590 FALSE TRUE 1068571.907 1084667.631 1048966.909 1036109.385 1048552.277 1167272.161 964877.0345 980346.6157 1065711.867 1.00268369 1.01778695 0.984287537 0.972222809 0.983898472 1.09529808 0.90538265 0.919898376 1 20.023386 2.195517765 24.99994288 0.935690014 1.005760797 0.365521515 0.041551338 142.1801389 82579.3524 0.016795643 0.011323706 156.8620062 -2.195517765 0.070070783 YLLHGLECVVAMHQAQLISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLLHGLECVVAMHQAQLISK 20 0 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 246.68 2.69E-30 679770000 1089360 1161790 716980 966710 1160350 985240 1290540 1481240 1230750 FALSE TRUE 945398.3159 1154158.125 1063713.926 1186216.281 1137261.305 1023142.82 1165383.629 1164488.353 1085252.137 0.871132416 1.063493068 0.980153726 1.093032891 1.04792358 0.94276969 1.073836751 1.073011804 1 20.04959883 4.744231601 24.81855228 1.036869659 0.871132337 0.540237057 0.047245222 437.9453182 1916566.041 0.011263676 0.096310961 55492.15629 -4.744231601 -0.165737322 YLLSQSS(ph)PAPLTAAEEELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YLLSQSSPAPLTAAEEELR 19 0 Q12792;Q12792-3;Q12792-4;F8VS81 Q12792 TWF1 Twinfilin-1 1 YLLSQS(0.276)S(0.724)PAPLTAAEEELR;YLLSQS(0.03)S(0.97)PAPLTAAEEELR;YLLSQS(0.041)S(0.959)PAPLTAAEEELR;YLLSQS(0.01)S(0.989)PAPLTAAEEELR;YLLSQS(0.02)S(0.98)PAPLTAAEEELR;YLLS(0.001)QS(0.172)S(0.827)PAPLTAAEEELR 193.8 4.73E-15 609524000 584513 657594 398201 474287 706889 752581 661523 820457 770711 TRUE FALSE 507268.1261 653274.2217 590772.3355 581981.1124 692823.2919 781533.2781 597368.6013 645008.6554 679598.4236 0.746423341 0.961265063 0.869296212 0.856360304 1.019459828 1.149992777 0.879002335 0.949102636 1 19.37432298 3.24349167 24.99754355 0.991696284 0.866471123 0.406170409 0.084274202 145.3053687 736607.9259 0.025067492 0.031342211 1751.828831 -3.24349167 -0.125225161 YLMAS(ph)DPNLQVLGAAYIQHK ddPTM_MDA-MB-175_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 297.5 7.23E-55 3243581000 4126875 3305277 2388068 2857852 3418507 3040452 3845912 4080515 3891790 TRUE FALSE 3581498.013 3283564.418 3542945.672 3506770.976 3350485.399 3157420.156 3472936.046 3207928.622 3431707.02 1.04364912 0.956831221 1.032414962 1.021873649 0.976332006 0.920072762 1.012014145 0.934790937 1 21.71049496 3.116551358 5.397871799 0.964216601 1.010711551 0.290529784 0.034940071 0.255066143 11.05916575 0.009918521 0.011329699 1307.830189 -3.116551358 0.04649495 YLMDEGAHLHIYDPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YLMDEGAHLHIYDPK 15 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ;;; 142.1 2.69E-06 1040040000 1751210 1627180 1211800 1435990 1549850 1347250 1889710 2219860 1880750 FALSE TRUE 1519783.161 1616490.947 1797830.533 1762053.477 1519011.017 1399079.579 1706446.215 1745160.214 1658409.878 0.916409859 0.97472342 1.084068877 1.062495768 0.915944266 0.843627138 1.028965299 1.052309346 1 20.66136918 2.045792052 24.99999864 1.0331164 0.970901377 0.138110009 0.070604084 260.1830339 142044.7166 0.0315161 0.021248134 111.1199537 -2.045792052 -0.062215023 YLMEEDEDAYKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 YLMEEDEDAYKK 12 1 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;;;; 229.54 1.27E-11 10444150000 7364500 5493120 5056484 5074210 4920200 3972818 7310410 8784280 6974880 FALSE TRUE 6391262.666 5457035.333 7501816.575 6226386.935 4822297.646 4125654.879 6601447.563 6905830.081 6150317.632 1.039176031 0.887276993 1.219744576 1.012368354 0.784072943 0.670803546 1.073350672 1.122841208 1 22.55222949 2.056491571 24.99997093 1.078574698 0.936997663 0.141818052 0.149412892 157.8947743 69874.30354 0.065309141 0.044031407 113.8915676 -2.056491571 -0.141577035 YLMGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YLMGER 6 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;; 124.32 0.042818 16184800000 11806300 13406800 7321000 8460600 12428400 13409700 11819700 11753800 11785900 FALSE TRUE 10246067.54 13318729.85 10861460.09 10381708.54 12181099.16 13925579.84 10673427.31 9240341.338 10392584.33 0.985901795 1.281560912 1.045116378 0.998953505 1.172095291 1.339953509 1.027023402 0.889128348 1 23.30905112 2.005000772 24.99977732 0.943074074 1.138976974 0.330325594 0.115382295 138.6150244 692958.922 0.046926926 0.031516058 101.1581254 -2.005000772 0.1959029 YLNFFTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YLNFFTK 7 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 100.15 0.023278 249650000 369180 343580 225290 291750 361140 260730 363120 390600 416690 FALSE TRUE 320391.9276 341323.0004 334240.9975 357996.2966 353954.0206 270760.4518 327904.6783 307073.2297 367429.3829 0.871982325 0.928948571 0.909674112 0.974326805 0.9633253 0.736904734 0.892429113 0.835734005 1 18.48710748 YLPDTLLLEECGLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YLPDTLLLEECGLLR 15 0 P21964-2;P21964;E7EMS6 P21964-2 COMT Catechol O-methyltransferase 0 ;;; 267.02 5.18E-25 545812000 160752 135647 82559.8 96290.5 134810 137448 130966 145094 151880 FALSE TRUE 139508.2159 134755.9259 122485.9954 118154.7297 132127.5448 142735.7135 118264.9375 114066.7772 133924.9194 1.041689751 1.006205018 0.914587038 0.882246039 0.986579236 1.065789056 0.883068946 0.851721828 1 17.0310649 4.374507357 4.351146596 0.933762734 1.034091174 0.228129395 0.064193914 0.301043895 9.792955545 0.017609339 0.051943502 23686.85256 -4.374507357 0.10032844 YLPENDLKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YLPENDLKR 9 1 O00743;O00743-2 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed" 0 ;;;; 172.98 8.94E-05 2358230000 1503580 1414980 959144 1152750 1320450 1155500 1563640 1754850 1423930 FALSE TRUE 1304878.093 1405684.903 1422989.247 1414499.506 1294175.628 1199952.833 1411998.433 1379588.984 1255594.618 1.039251105 1.119537217 1.133319008 1.126557478 1.030727283 0.955684913 1.124565536 1.098753503 1 20.25993932 3.239429217 24.99996447 1.050930532 1.107775049 0.244667153 0.053356377 39.83398905 1146471.303 0.016742674 0.020388712 1735.518377 -3.239429217 0.056844517 YLPHSAGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YLPHSAGR 8 0 M0R0F0;M0R0R2;P46782 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;; 194.44 0.00016534 3440730000 3932900 4083800 1954310 3021680 3847300 4262600 3929100 4365300 3513690 FALSE TRUE 3413157.3 4056973.249 2899420.853 3707798.627 3770746.257 4426584.98 3548056.487 3431814.566 3098305.571 1.101620619 1.309416762 0.935808553 1.196718188 1.21703498 1.428711558 1.145160284 1.107642383 1 21.56304801 1.503679187 2.328984594 1.001139957 1.195879257 0.192537396 0.127560108 0.589615901 5.732298738 0.201609363 0.03488134 31.89181137 -1.503679187 0.1947393 YLQAHTQSVYNYHLS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YLQAHTQSVYNYHLSPR 17 0 P50548;P50548-2 P50548 ERF ETS domain-containing transcription factor ERF 1 YLQAHTQSVYNYHLS(1)PR;YLQAHTQSVY(0.006)NY(0.005)HLS(0.99)PR;YLQAHTQSVYNYHLS(1)PR 223.07 5.28E-15 796600000 317163 401771 200030.8 340383.7 538682 611642 536369 543994 426005 TRUE FALSE 275249.106 399131.7398 296766.3639 417673.0215 527963.2821 635172.2635 484352.0169 427665.1165 375643.1742 0.732740869 1.06252893 0.790021979 1.111887691 1.405491483 1.6908926 1.289393899 1.138487655 1 18.51900336 3.501707173 4.291209249 1.300969906 0.885931961 0.514419277 0.195840146 0.193646731 8.333741028 0.060944695 0.087470074 3174.732759 -3.501707173 -0.415037944 YLQDLLAWVEENQHR ddPTM_MDA-MB-175_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 ; 211.7 1.25E-09 4967400000 2597120 2466480 1606210 1754470 2519040 2864530 2490350 2789190 2623980 FALSE TRUE 2253904.012 2450277.53 2382978.528 2152849.229 2468916.032 2974730.323 2248836.24 2192743.424 2313776.074 0.974123658 1.058995103 1.029908882 0.930448393 1.06705055 1.285660422 0.971933397 0.947690422 1 21.14181782 2.04954445 24.99999937 0.9670151 1.057606486 0.1547812 0.092776245 194.3243905 98054.65498 0.039320692 0.026509997 112.0842139 -2.04954445 0.090591386 YLQEEVNINR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLQEEVNINR 10 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4;K7EL40;K7EK18;K7EIE4;K7EQD7;K7ER52 Q9UHD8 9-Sep Septin-9 0 ; 204.07 4.51E-07 1119360000 716610 680870 461970 547000 682410 733250 661570 787510 779000 FALSE TRUE 621908.1728 676397.3201 685380.2372 671204.7104 668831.3761 761458.602 597411.0432 619107.1149 686907.5074 0.905373964 0.984699269 0.9977766 0.977139867 0.973684767 1.108531489 0.869711041 0.901296184 1 19.38975633 YLQEVIDVLETDGHFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YLQEVIDVLETDGHFR 16 0 Q02818;H7BZI1;C9JKZ2;C9JBD3;C9J3C1 Q02818 NUCB1 Nucleobindin-1 0 ;;;;; 216.71 1.49E-14 871285000 740299 870008 555341 651119 838096 984386 745238 1025343 925841 FALSE TRUE 642466.6115 864292.8602 823905.7651 798965.5207 821419.5293 1022255.966 672964.9335 806081.3787 816389.1317 0.78696125 1.058677568 1.00920717 0.978657713 1.006161765 1.252167535 0.82431883 0.987373971 1 19.63889745 4.746681037 24.09467599 1.009400032 0.786961065 0.320565689 0.103895522 771.6131382 2289418.409 0.024723911 0.26009577 55806.01832 -4.746681037 -0.222438967 YLQLAEELIRPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YLQLAEELIRPER 13 1 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ;;; 225.13 1.18E-11 813098000 847432 794439 439025 557427 750814 808557 685372 825904 705485 FALSE TRUE 735441.7141 789220.2779 651338.9585 683999.3201 735874.2703 839662.711 618904.7289 649290.8568 622083.367 1.182223723 1.26867285 1.04702841 1.099529993 1.182919058 1.349759141 0.994890334 1.043736083 1 19.24674841 2.189221429 24.99999333 1.018555032 1.181298388 0.495629863 0.083179753 101.5736171 51466.22043 0.034939628 0.023556333 154.6042503 -2.189221429 0.162743356 YLQTYGEWNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLQTYGEWNR 10 0 Q9BZH6 Q9BZH6 WDR11 WD repeat-containing protein 11 0 ; 112.36 0.0037955 213830000 405170 346490 270143 302830 346660 341740 406630 461900 474500 FALSE TRUE 351625.7579 344213.8844 400785.0584 371592.18 339762.1442 354886.9589 367195.0852 363126.2795 418405.1506 0.840395386 0.822680801 0.957887487 0.888115692 0.812041018 0.848189747 0.877606513 0.867881954 1 18.67454109 1.236424962 6.142115722 1.004786935 0.865031051 0.524869417 0.040562746 0.114492714 17.30095128 0.066844835 0.010318224 17.23554268 -1.236424962 -0.139755884 YLRPPNTSLFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLRPPNTSLFVR 12 1 O75494-2;O75494;O75494-5;Q6IQ42;R4GMP8;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10;FUSIP1 Serine/arginine-rich splicing factor 10 0 ; 103.97 0.0019955 1724670000 752490 1115100 708990 648300 1155890 1413770 770970 846760 1005890 FALSE TRUE 653046.5399 1107774.835 1051859.935 795506.4236 1132890.05 1468158.647 696201.4481 665686.9635 886974.8301 0.736262764 1.248936043 1.185896036 0.896875984 1.277251633 1.655242738 0.784916803 0.750513928 1 19.75853364 YLS(ph)FTPPEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YLSFTPPEK 9 0 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 YLS(0.997)FT(0.003)PPEK;YLS(0.943)FT(0.057)PPEK;YLS(0.997)FT(0.003)PPEK;YLS(0.993)FT(0.007)PPEK 149.96 9.06E-05 3058720000 2809940 2949560 2724300 2746220 2811450 2719710 3164410 3505200 8001400 TRUE FALSE 2438599.31 2930184.146 4041780.592 3369791.224 2755507.646 2824339.004 2857526.005 2755640.257 7055483.607 0.345631773 0.415305925 0.572856634 0.477613075 0.390548373 0.400304098 0.405007816 0.390567169 1 22.75031354 1.23638952 24.99514361 1.000000739 0.426359197 0.895225342 0.061847325 18.45323759 212394.0068 0.10341574 0.016084872 17.23413617 -1.23638952 -0.573641542 YLS(ph)FTPPEKDGFPSGTPALNAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLSFTPPEKDGFPSGTPALNAK 22 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 YLS(0.851)FT(0.149)PPEKDGFPSGTPALNAK;YLS(0.932)FT(0.068)PPEKDGFPSGTPALNAK 288 8.96E-47 6801500000 5333000 4813200 3622200 3339300 4676900 4040100 6068000 6547100 3774400 TRUE FALSE 4628230.538 4781581.772 5373908.036 4097539.103 4583838.84 4195525.261 5479526.294 5147053.615 3328194.732 1.390612903 1.436689304 1.614661541 1.231159663 1.377274832 1.260600896 1.64639594 1.546500139 1 21.66630842 3.743025596 24.97794374 1.381646436 1.476258034 0.085488712 0.185081594 1345.124017 7524848.836 0.050865745 0.084460301 5533.827224 -3.743025596 0.094611598 YLSDSCS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YLSDSCSPR 9 0 P83436 P83436 COG7 Conserved oligomeric Golgi complex subunit 7 1 YLSDSCS(1)PR;YLSDSCS(1)PR;YLSDSCS(1)PR;YLSDSCS(1)PR;YLS(0.001)DS(0.022)CS(0.977)PR 140.48 0.00011433 3289210000 3802380 4341070 2601750 2547640 3971590 4465580 3951660 4178130 3981340 TRUE FALSE 3299885.849 4312553.225 3859965.002 3126120.6 3892563.129 4637373.752 3568428.621 3284669.414 3510670.521 0.939958857 1.228412977 1.099495091 0.890462543 1.108780532 1.320936763 1.016452156 0.935624518 1 21.74331517 2.009392841 24.96033156 0.967061258 1.101195008 0.167158499 0.123382773 316.4483263 840919.7525 0.050835605 0.034225531 102.1863393 -2.009392841 0.13413375 YLSEVASGDNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 262.63 2.19E-20 1758210000 3058830 2061380 1460200 1768170 2081300 1757550 2413640 2820900 2557320 FALSE TRUE 2654597.865 2047838.659 2166357.604 2169660.023 2039886.202 1825164.086 2179565.564 2217672.487 2254996.543 1.177207067 0.908133835 0.960692206 0.962156696 0.904607241 0.809386645 0.966549404 0.983448287 1 21.10469379 4.743009599 24.91868128 0.938444078 1.177207167 0.660493981 0.054140921 296.0521862 1658122.382 0.014137181 0.108623317 55336.23392 -4.743009599 0.238763089 YLSFHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLSFHFK 7 0 P53004 P53004 BLVRA Biliverdin reductase A 0 ; 101.69 0.0088735 2127130000 3306400 4875300 1068580 2698400 5115400 4867800 4841900 5078500 6123400 FALSE TRUE 2869450.863 4843273.833 1585348.862 3311112.962 5013613.548 5055067.416 4372333.283 3992502.296 5399498.628 0.531429131 0.896985844 0.293610383 0.613226003 0.928533165 0.93621052 0.809766533 0.73942093 1 22.36439402 3.287061804 7.291399466 0.861909102 0.583601262 0.458349082 0.160702376 0.215710004 26.36221599 0.045896378 0.058910812 1936.697552 -3.287061804 -0.27830784 YLSHSEFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YLSHSEFK 8 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ;; 153.78 0.00043559 835840000 1646310 1475990 1102630 1079640 1489140 1557840 1741270 1822240 1959030 FALSE TRUE 1428745.962 1466294.125 1635865.556 1324788.763 1459509.027 1617771.113 1572401.903 1432568.157 1727435.705 0.827090674 0.848827033 0.946990705 0.766910606 0.84489919 0.936515963 0.910252057 0.829303315 1 20.72020058 2.759619848 23.71777552 0.904178148 0.848160154 0.245800467 0.06027222 760.5860301 856601.4014 0.019329511 0.019303674 574.9364566 -2.759619848 -0.056017994 YLSNAYAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLSNAYAR 8 0 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ; 98.629 0.017184 1120770000 1111580 1259200 765770 770860 1170800 1171130 1070120 1082880 1193220 FALSE TRUE 964681.8866 1250928.232 1136098.933 945895.5449 1147503.371 1216184.129 966339.9271 851314.539 1052158.891 0.916859511 1.188915708 1.079778865 0.899004469 1.090617948 1.155893981 0.918435357 0.809112147 1 20.00492116 2.087235463 7.17163796 0.882974201 1.056419235 0.310707074 0.101452812 0.222359631 15.41428251 0.040790748 0.027376705 122.2462266 -2.087235463 0.173445033 YLSVPPS(ph)PNIS(ph)TSESRSPPEGDTTLFLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YLSVPPSPNISTSESRSPPEGDTTLFLSR 29 1 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 2 YLS(0.004)VPPS(0.851)PNIS(0.256)T(0.246)S(0.235)ES(0.212)RS(0.19)PPEGDT(0.002)T(0.002)LFLS(0.002)R 42.865 0.081926 52573000 38092 29404 19032 21640 32868 38657 31943 39127 20535 TRUE FALSE 33058.04569 29210.84319 28235.93886 26553.69275 32213.99111 40144.1598 28845.17278 30759.99554 18107.37569 1.82566741 1.613201365 1.559361187 1.466457271 1.779053555 2.217005958 1.593006809 1.69875503 1 14.14428985 1.231671452 5.193470074 0.954678587 1.716397809 0.547389134 0.205451462 0.146352728 10.72197861 0.403112784 0.053561015 17.0479221 -1.231671452 0.761719222 YLSVPPS(ph)PNISTSES(ph)RSPPEGDTTLFLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YLSVPPSPNISTSESRSPPEGDTTLFLSR 29 1 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 2 YLSVPPS(0.966)PNIS(0.044)T(0.042)S(0.04)ES(0.549)RS(0.359)PPEGDTTLFLSR 101.11 0.00038888 49164000 92134 71191 42607 47697 79647 83725 72039 85023 41255 TRUE FALSE 79958.25846 70723.34163 63211.88771 58527.33285 78062.18053 86945.95493 65052.66887 66841.4931 36377.8809 2.1979911 1.944130331 1.737646233 1.608871419 2.145869374 2.390077508 1.788247893 1.837421297 1 15.15077388 1.055943727 1.970632842 0.239030683 1.971878777 0.63289901 0.230840871 1.005253545 2.459721219 3.826115912 0.06599616 11.37479889 -1.055943727 1.732848094 YLSVPPS(ph)PNISTSESRS(ph)PPEGDTTLFLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YLSVPPSPNISTSESRSPPEGDTTLFLSR 29 1 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 2 YLS(0.003)VPPS(0.947)PNIS(0.018)T(0.019)S(0.027)ES(0.264)RS(0.721)PPEGDTTLFLSR 94.629 0.00070361 56328000 86737 75401 47013 51843 76587 92264 78319 78155 42669 TRUE FALSE 75274.48569 74905.68587 69748.64405 63614.74552 75063.06854 95813.45578 70723.63543 61442.16145 37624.71943 2.000665701 1.99086364 1.853798383 1.690769964 1.995046599 2.546556021 1.879711969 1.633026435 1 15.1993932 1.330852629 2.012574184 0.809984109 1.997888127 0.681045818 0.218260859 0.38729983 1.856118533 0.8087657 0.063777095 21.42163567 -1.330852629 1.187904018 YLSVPPSPNISTSESRS(ph)PPEGDTTLFLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YLSVPPSPNISTSESRSPPEGDTTLFLSR 29 1 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 YLSVPPS(0.001)PNISTSES(0.013)RS(0.978)PPEGDT(0.002)T(0.002)LFLS(0.004)R;YLSVPPSPNIS(0.001)T(0.001)S(0.001)ES(0.287)RS(0.71)PPEGDTTLFLSR;YLSVPPS(0.001)PNIS(0.003)T(0.003)S(0.008)ES(0.02)RS(0.964)PPEGDTTLFLSR;YLSVPPSPNIS(0.001)T(0.001)S(0.001)ES(0.118)RS(0.879)PPEGDTTLFLSR 168.34 2.13E-12 906310000 424491 341719 198425 231107 336906 372753 357713 418672 134987 TRUE FALSE 368393.4388 339474.2254 294383.9937 283583.3766 330202.2297 387093.0491 323022.0483 329142.2509 119028.9906 3.094989186 2.852029775 2.473212552 2.38247317 2.774132822 3.252090495 2.713809859 2.765227607 1 16.86095347 1.238340919 8.470022008 0.982953475 2.778530158 0.829546005 0.254756686 0.037107281 28.73549853 0.380134765 0.065973573 17.31174791 -1.238340919 1.795576683 YLTESYGTGQDIDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 297.88 8.96E-44 1168520000 549647 492582 311646 353062 479005 537567 510717 510854 514703 FALSE TRUE 477009.7563 489346.1964 462359.048 433230.1233 469473.7377 558247.5503 461187.7439 401611.8476 453855.3977 1.051017039 1.078198472 1.018736475 0.954555406 1.034412591 1.230011923 1.016155688 0.884889438 1 18.79187319 1.990084739 24.98951694 0.939112524 1.059702754 0.301205472 0.074119998 540.6548177 1362616.483 0.033055994 0.020793218 97.74279168 -1.990084739 0.12059023 YLTVAAVFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YLTVAAVFR 9 0 Q5JP53;P07437;Q5ST81;P68371;P04350 Q5JP53;P68371;P04350 TUBB;TUBB4B;TUBB4A Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-4A chain 0 ;; 215.09 1.52E-06 3639581000 1179606 2211027 1275164 1608227 2209789 2321612 2123240 2102669 2380415 FALSE TRUE 1023718.078 2196502.618 1891837.576 1973399.521 2165818.522 2410925.916 1917328.512 1653029.597 2099005.05 0.487715872 1.04644942 0.90130206 0.940159491 1.03183102 1.148604152 0.913446355 0.787530071 1 21.00127421 4.745192494 24.79166894 0.95840185 0.48771563 0.706264602 0.097674567 439.8181637 1644105.688 0.026384157 0.246510092 55615.07069 -4.745192494 -0.47068622 YLVEFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YLVEFR 6 0 Q16186;A0A087WX59;A0A087WUX6 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 0 106.76 0.074087 578810000 681830 703720 435470 559210 744550 790510 706600 790750 792040 FALSE TRUE 591724.438 699097.217 646064.7486 686187.1775 729734.9117 820921.4312 638074.0408 621654.2661 698405.9335 0.847250015 1.000989802 0.925056214 0.982504794 1.044857835 1.175421616 0.913614862 0.890104503 1 19.41370629 4.742814123 23.7395332 0.985036655 0.847249905 0.23850396 0.080291596 375.8314783 2097409.831 0.021374154 0.159646382 55311.33276 -4.742814123 -0.13778675 YLVIDEAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 0 130.75 0.0003525 169940000 815260 755590 506290 594760 746340 821660 759000 893210 445780 FALSE TRUE 707521.3254 750626.4795 751133.5374 729809.3483 731489.2942 853269.7919 685392.2968 702203.9925 393080.3962 1.799940501 1.909600394 1.910890354 1.856641428 1.860915225 2.170725887 1.743644057 1.786413159 1 18.58446489 0.995904591 1.863255006 0.069155356 1.904629091 0.858832761 0.112656681 0.622509369 1.161638268 2.533067156 0.029533905 9.906142959 -0.995904591 1.835473735 YLVLDEADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YLVLDEADR 9 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;D6RCM4;Q9NQI0-3;Q9NQI0-2;Q9NQI0-4;Q9NQI0;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX4;DDX3Y ATP-dependent RNA helicase DDX3X;Probable ATP-dependent RNA helicase DDX4;ATP-dependent RNA helicase DDX3Y 0 ;;;; 182.69 0.0001071 2795860000 4867550 4657530 2894200 3344400 4383710 4886070 4238660 4788760 4399650 FALSE TRUE 4224290.935 4626934.379 4293844.801 4103797.136 4296482.748 5074040.275 3827595.406 3764720.94 3879528.389 1.088867128 1.192653827 1.106795561 1.05780825 1.107475527 1.307901313 0.986613583 0.970406854 1 21.88744985 2.059716293 24.99999717 0.981714137 1.139323435 0.536405329 0.069111645 53.14107798 22246.9174 0.027870666 0.018790397 114.7403824 -2.059716293 0.157609298 YLYAMR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLYAMR 6 0 P19367-4;P19367-2;P19367;P19367-3;B1AR62 P19367-4 HK1 Hexokinase-1 0 ; 130.51 0.036597 926910000 593810 852390 548550 605810 872290 993590 688240 774260 1107540 FALSE TRUE 515336.504 846790.594 813830.6148 743368.4197 854933.1356 1031814.05 621494.5907 608690.5243 976607.8829 0.527680058 0.867073274 0.833323823 0.761173888 0.875410849 1.056528488 0.636380887 0.623270132 1 19.8974199 6.243454031 13.41488036 0.790243922 0.469356804 0 0.167084824 0 0 0.037338964 0 1751677.014 -6.243454031 -0.320887118 YLYPNIDKDHAFGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLYPNIDKDHAFGK 14 1 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224;J3KPM9;A0A669KBI6;P42224-2 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta;Signal transducer and activator of transcription 0 ; 167.32 2.20E-06 878320000 939530 781740 547380 619280 755760 590170 860370 1034890 715300 FALSE TRUE 815368.73 776604.6985 812094.7989 759896.9891 740721.8546 612874.2218 776931.4498 813586.827 630738.0489 1.292721648 1.231263438 1.287531013 1.204774296 1.17437319 0.971677898 1.231781484 1.28989654 1 19.26668144 3.455489868 2.876020882 1.152561073 1.266020506 0.285542976 0.096638728 0.438724836 7.384478615 0.030749075 0.04408366 2854.235926 -3.455489868 0.113459433 YLYSSEDYIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YLYSSEDYIK 10 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 152.81 4.04E-05 87655000 128090 115430 72669 97026 103600 83428 109380 133790 131650 FALSE TRUE 111162.582 114671.7327 107811.9715 119057.2362 101538.5627 86637.52915 98772.34444 105180.0497 116086.487 0.957584167 0.987812929 0.928721114 1.025590828 0.874680295 0.746318813 0.850851352 0.906049036 1 16.82484052 3.214185745 22.44874896 0.871070677 0.972547133 0.358513029 0.065846981 82.79309857 76249.83133 0.020960282 0.023786254 1637.516726 -3.214185745 0.101476456 YLYTLVITDKEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLYTLVITDKEK 12 1 J3KT73;J3QL01;P63173 J3KT73 RPL38 60S ribosomal protein L38 0 ; 170.18 3.82E-05 1366600000 2137630 1628480 1107580 1297570 1523480 1116680 2251940 2469220 1066200 FALSE TRUE 1855136.779 1617782.408 1643209.393 1592203.101 1493165.729 1159639.402 2033547.205 1941196.518 940155.0506 1.973224287 1.720761279 1.747806802 1.693553738 1.588212208 1.233455483 2.162991311 2.064762102 1 19.84253918 5.19238927 1.496886473 1.690237613 2.526880503 0.070785675 0.34360231 13.84215531 11.40468878 0.096738566 23.97227197 155736.0912 -5.19238927 0.83664289 YLYVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLYVDK 6 0 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ; 116.35 0.055015 1193510000 3150200 2950400 2528510 3151900 2952100 2508280 3056400 3627100 6802500 FALSE TRUE 2733893.088 2931018.628 3751305.893 3867587.069 2893358.986 2604775.155 2759990.798 2851472.891 5998316.199 0.455776754 0.488640233 0.625393155 0.644778791 0.482361864 0.434251058 0.460127594 0.475378889 1 22.51612614 1.236199565 24.99978881 1.000000639 0.508712785 0.826697025 0.070745253 28.25979774 299158.4505 0.124917395 0.019157593 17.22659982 -1.236199565 -0.491287855 YLYYTGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YLYYTGR 7 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 124.37 0.009661 290410000 312510 306170 204768 199427 307920 306170 305420 313620 308720 FALSE TRUE 271211.0117 304158.7491 303794.4897 244709.9484 301792.9944 317948.558 275800.4154 246554.8036 272223.4733 0.99628077 1.117312719 1.115974629 0.898930373 1.108622232 1.167968927 1.013139727 0.905707361 1 18.05443195 1.997651583 24.93799637 0.950109993 1.068217401 0.271051314 0.077865699 103.7209227 1101422.57 0.03224367 0.021321331 99.46071627 -1.997651583 0.118107408 YMACCLLYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 155.73 0.00016891 12126210000 1091200 1768810 1003870 874131 1496190 1862840 1515100 1567810 1321410 FALSE TRUE 946995.1553 1757190.571 1489344.89 1072615.804 1466418.746 1934504.66 1368165.835 1232546.032 1165194.415 0.812735749 1.50806642 1.278194326 0.92054664 1.258518516 1.660241961 1.174195325 1.057802901 1 20.15213926 1.763469583 3.765732515 1.023654207 1.251107536 0.105860583 0.244830979 0.436839653 12.6014159 0.158249415 0.065080876 58.0055546 -1.763469583 0.227453329 YMAENPTAGVVQEEEEDNLEYDS(ph)DGNPIAPTKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YMAENPTAGVVQEEEEDNLEYDSDGNPIAPTKK 33 1 A0A0A0MSJ0;Q86XP3-2;Q86XP3;J3KRE3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 1 YMAENPTAGVVQEEEEDNLEYDS(1)DGNPIAPTKK;YMAENPTAGVVQEEEEDNLEY(0.025)DS(0.975)DGNPIAPTKK 236.29 4.53E-47 218155000 351281 254669 231848 222391 239336 204315 328172 402013 298980 TRUE FALSE 304858.3258 252996.0626 343970.4683 272888.2756 234573.6819 212175.1303 296345.93 316045.6484 263634.925 1.156365477 0.959645474 1.304722689 1.035099108 0.889767097 0.80480661 1.124076903 1.198800381 1 18.00818198 4.799412419 20.10363672 1.052133378 1.156374637 0.054191423 0.145137427 22414.24237 7401873.777 0.037678073 43.0929263 63010.42641 -4.799412419 0.10424126 YMDLLWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YMDLLWR 7 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ; 133.47 0.0076042 675040000 1064510 1325520 797090 744270 1299840 1380270 1188490 1322130 1345440 FALSE TRUE 923832.3064 1316812.572 1182565.39 913267.879 1273975.727 1433369.88 1073230.423 1039402.788 1186383.616 0.77869611 1.109938265 0.996781626 0.769791378 1.073831187 1.20818415 0.904623436 0.876110201 1 20.17813915 4.766619125 23.04906917 0.981674357 0.778695259 0.22231745 0.1241819 5899.936292 4846356.437 0.031478927 2.475751564 58427.74499 -4.766619125 -0.202979098 YMEAFKPFLGIGLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YMEAFKPFLGIGLK 14 1 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ; 148.68 7.02E-06 487770000 529390 473680 508850 549420 474720 395290 655580 670980 957590 FALSE TRUE 459429.7702 470568.3649 754931.562 674174.2084 465274.0008 410497.0621 592001.9525 527496.1486 844384.8011 0.5441 0.557291373 0.89406105 0.798420587 0.551021288 0.486149279 0.701104463 0.624710615 1 19.68754108 1.236221745 24.96944753 1.000000465 0.648320051 0.442730406 0.125245037 64.45102719 687909.1469 0.209296074 0.032117079 17.22747961 -1.236221745 -0.351680414 YMEDST(ph)YYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YMEDSTYYK 9 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-4;Q05397-3 E7ESA6 PTK2 Focal adhesion kinase 1 1 YMEDS(0.164)T(0.824)Y(0.012)YK 190.26 0.00038849 201360000 443360 428300 318750 392350 577440 362200 621980 696250 583500 TRUE FALSE 384768.8527 425486.4691 472898.5662 481439.0642 565950.0737 376134.0684 561660.4753 547362.3557 514519.2947 0.747822009 0.826959209 0.919107546 0.935706531 1.099958893 0.731039773 1.091621794 1.063832516 1 18.97286565 6.155851829 0.365697348 1.039476365 1.01E-18 0.402731851 0.103406046 21.900859 1.124866842 0.135690896 12.18526228 1431699.354 -6.155851829 -1.039476365 YMEDSTY(ph)YK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YMEDSTYYK 9 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-4;Q05397-3 E7ESA6 PTK2 Focal adhesion kinase 1 1 YMEDS(0.005)T(0.017)Y(0.853)Y(0.125)K;YMEDS(0.001)T(0.022)Y(0.959)Y(0.018)K;YMEDS(0.434)T(0.102)Y(0.464)YK 154.28 0.00078405 1571190000 2751090 2916620 1800400 2188060 3250740 3037800 3343660 3784270 3357010 TRUE FALSE 2387526.486 2897460.531 2671079.462 2684892.465 3186056.634 3154666.132 3019392.368 2975033.31 2960148.102 0.80655643 0.978822826 0.902346562 0.907012883 1.076316631 1.065712263 1.020013953 1.005028535 1 21.49723793 3.252639993 24.89719847 1.030475929 0.904670342 0.665684301 0.047334034 141.8986514 250924.3567 0.0133849 0.017191565 1789.122153 -3.252639993 -0.125805586 YMEEMADTADAIEMATLDKEMAEER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YMEEMADTADAIEMATLDKEMAEER 25 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 ; 143.29 3.00E-07 102169000 54680 55199 34023 33123.8 47726 49689 58286 62941 28646 FALSE TRUE 47453.89946 54836.39413 50476.6366 40645.06506 46776.34597 51600.56798 52633.43269 49481.55696 25259.50251 1.878655347 2.170921383 1.998322674 1.609099983 1.85183164 2.042818062 2.083708207 1.958928404 1 14.62453861 1.238371537 24.97490774 0.999998935 1.953743994 0.793190103 0.152318737 2.081835136 274242.2929 0.220388513 0.039116339 17.31296842 -1.238371537 0.953745059 YMHSGPVVAMVWEGLNVVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YMHSGPVVAMVWEGLNVVK 19 0 Q32Q12;P22392-2;J3KPD9;E7ERL0;P15531;P15531-2 Q32Q12;P15531 NME1-NME2;NME2;NME1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Nucleoside diphosphate kinase A 0 ;; 206.74 3.50E-16 1388390000 1054670 989200 626950 759630 917670 827450 1180560 1325070 1198580 FALSE TRUE 915292.6873 982701.8801 930145.117 932115.6017 899410.1624 859282.5369 1066069.473 1041714.092 1056885.238 0.866028453 0.929809448 0.880081473 0.881945899 0.851000781 0.813032963 1.008689908 0.985645418 1 20.0113873 2.224439608 24.99997381 0.995955413 0.873115211 0.80744672 0.029391476 103.8036477 183773.5293 0.012623288 0.008557099 167.6639169 -2.224439608 -0.122840202 YMLTHQELAS(ph)DGEIETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YMLTHQELASDGEIETK 17 0 Q02241;H7BYN4;A0A2U3TZL8;Q02241-2;Q02241-3 Q02241;Q02241-2 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 YMLTHQELAS(1)DGEIETK 243.24 1.23E-20 213930000 321500 335020 219560 291900 312780 261000 314340 430780 330960 TRUE FALSE 279012.9604 332819.2316 325739.9504 358180.3564 306556.2899 271040.8389 283855.3552 338661.0493 291834.2858 0.956066418 1.140439104 1.116181224 1.22734159 1.050446451 0.928749129 0.972659379 1.16045669 1 18.15478986 3.019601716 24.89080626 1.029162304 1.115905851 0.196669083 0.088149221 413.477142 525040.8767 0.027769413 0.031484089 1046.168686 -3.019601716 0.086743546 YMNSDTTS(ph)PELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YMNSDTTSPELR 12 0 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 YMNSDTT(0.002)S(0.998)PELR;YMNSDTTS(1)PELR;YMNSDTT(0.002)S(0.998)PELR;YMNSDTT(0.027)S(0.973)PELR 304.03 9.36E-37 3214200000 4270610 3601120 2212330 2546970 3371120 3546770 3398470 3686670 3297020 TRUE FALSE 3706238.068 3577464.006 3282220.188 3125298.466 3304041.307 3683216.537 3068886.902 2898304.31 2907250.052 1.274826039 1.230531926 1.128977601 1.075001603 1.13648336 1.266907377 1.05559785 0.996922954 1 21.47122373 -1.530915333 0.213432169 2.25E-13 1.267315096 0.548213018 0.068339192 65.16813463 1.196531459 26.21813721 0.408604295 0.029449957 1.530915333 1.267315096 YMS(ph)FTDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YMSFTDK 7 0 E9PM17;B3KNX7;Q13153;Q13153-2;H0YCM0 E9PM17 PAK1 Non-specific serine/threonine protein kinase;Serine/threonine-protein kinase PAK 1 1 YMS(0.99)FT(0.01)DK;YMS(0.998)FT(0.002)DK;YMS(1)FTDK 98.249 0.01196 754830000 1346120 1376030 1153010 1134120 1441060 1278220 1582080 1736680 2149670 TRUE FALSE 1168226.831 1366990.768 1710609.493 1391639.28 1412385.725 1327393.951 1428650.125 1365304.497 1895538.462 0.616303417 0.721162243 0.902439875 0.734165678 0.74511056 0.70027276 0.753690919 0.720272643 1 20.8541763 1.235853916 24.99562105 1.000000347 0.74044845 0.581461558 0.070145008 55.65217218 513829.109 0.114078059 0.017075121 17.21289484 -1.235853916 -0.259551897 YMVADKFTELQK ddPTM_MDA-MB-175_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 6.29E-05 1501900000 1621500 1205270 793620 972770 1235980 952320 1562680 1848040 837340 FALSE TRUE 1407214.667 1197352.502 1177417.286 1193652.296 1211386.416 988956.3666 1411131.534 1452851.027 738350.6191 1.905889465 1.621658425 1.594658765 1.616646977 1.640665539 1.339412931 1.911194353 1.967697988 1 19.49394654 4.739269554 21.88802798 1.626663291 1.905889724 0.103472744 0.273623418 27.8934982 860054.8801 0.066130542 0.382554144 54861.73699 -4.739269554 0.279226432 YMWDSQSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YMWDSQSGR 9 0 Q9UKD2 Q9UKD2 MRTO4 mRNA turnover protein 4 homolog 0 107.69 0.0063561 150950000 259620 266380 182740 209920 263410 251860 233030 296060 264210 FALSE TRUE 225310.5592 264630.1322 271113.6752 257585.5444 258168.6564 261549.2172 210430.7865 232749.8729 232975.3948 0.967100236 1.135871591 1.163700894 1.105634115 1.108137006 1.122647383 0.903231805 0.999031993 1 17.82981807 2.252465216 24.99890753 0.971332271 1.105573534 0.540107653 0.057731673 165.042366 296727.3227 0.0210738 0.016238491 178.8402286 -2.252465216 0.134241264 YNADEAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YNADEAR 7 0 P47813;O14602;X6RAC9;A6NJH9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 ;;;; 130.22 0.0083387 6517830000 11701130 11294120 6623350 7939600 9840470 11626270 10902040 12017620 11040570 FALSE TRUE 10154796.02 11219928.18 9826424.214 9742407.529 9644663.9 12073540.13 9844761.839 9447745.484 9735366.392 1.043083086 1.15249162 1.009353302 1.000723253 0.990683197 1.240173163 1.011236911 0.970456078 1 23.21480385 2.014716199 24.9969091 0.985436311 1.071424336 0.199522826 0.07576161 355.2114637 603359.1591 0.031067291 0.020936679 103.4465947 -2.014716199 0.085988025 YNDWS(ph)DDDDDSNESK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YNDWSDDDDDSNESK 15 0 H3BV87;Q9UH62 H3BV87 ARMCX3 Armadillo repeat-containing X-linked protein 3 1 YNDWS(1)DDDDDSNESK;YNDWS(1)DDDDDSNESK;YNDWS(1)DDDDDSNESK;YNDWS(1)DDDDDSNESK 435.41 2.16E-143 870270000 1196440 1144100 927990 1079440 1348540 1089380 1228920 1872780 1490220 TRUE FALSE 1038327.423 1136584.332 1376769.068 1324543.35 1321706.692 1131289.154 1109739.528 1472300.571 1314047.889 0.79017472 0.864948942 1.047731273 1.007987122 1.005828405 0.860919273 0.844519851 1.120431442 1 20.32558642 4.415993683 4.886451892 0.98549473 0.805746124 0.405860644 0.081010138 0.188367581 8.829434509 0.02190252 0.064121611 26061.15645 -4.415993683 -0.179748606 YNEDLELEDAIHTAILTLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YNEDLELEDAIHTAILTLK 19 0 A0A024RA52;P25787;C9JCK5 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 0 191.95 8.52E-15 1263100000 321740 268940 188630 262830 273070 209550 329780 372610 363060 FALSE TRUE 279221.2438 267173.3154 279852.0989 322509.5686 267636.4413 217611.5241 297797.9864 292930.2512 320139.4604 0.872186276 0.834552901 0.87415684 1.007403362 0.835999539 0.679739773 0.930213308 0.915008262 1 18.28834099 1.547645845 2.038397683 0.995348106 0.857817216 0.232215986 0.081825677 0.614377018 4.629507462 0.137431369 0.023825633 35.28952763 -1.547645845 -0.13753089 YNEQHVPGSPFTAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YNEQHVPGSPFTAR 14 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 79.885 0.017838 718110000 1416800 1408700 661280 874170 1081300 1141400 1163000 1313500 1410200 FALSE TRUE 1229566.29 1399446.157 981077.2198 1072663.659 1059784.246 1185310.397 1050212.439 1032618.247 1243487.763 0.988804496 1.125420128 0.788972155 0.862625023 0.852267531 0.953214364 0.844569983 0.830420916 1 20.24596088 4.241265458 24.99999991 0.871686573 1.05711233 0.546771788 0.068460972 46.60936056 430772.8925 0.016341746 0.039409529 17428.71861 -4.241265458 0.185425757 YNGGVGR ddPTM_MDA-MB-175_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 ;; 160.77 0.013956 0 909480 899780 615330 726620 717670 970000 910870 961710 969850 FALSE TRUE 789289.9137 893869.2859 912905.6462 891610.1767 703389.7711 1007316.528 822533.9676 756055.8005 855195.4379 0.922935131 1.045222234 1.067481894 1.042580605 0.822490088 1.177878743 0.96180818 0.884073707 1 19.70589463 2.009121616 24.99884495 0.930511729 1.014717817 0.090362967 0.096305683 372.5590446 1021037.109 0.037590194 0.025306079 102.1225418 -2.009121616 0.084206088 YNGLIHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 YNGLIHR 7 0 P46779;H0YKD8;P46779-2;P46779-3;H0YLP6;H0YMF4;P46779-4;P46779-5 P46779 RPL28 60S ribosomal protein L28 0 ;;;;;; 121.29 0.0044522 3390050000 8919710 9562590 5513150 6576390 9777160 10588880 9461600 10135080 10026650 FALSE TRUE 7740947.724 9499772.717 8179327.78 8069659.863 9582613.645 10996241.07 8544015.488 7967772.013 8841310.859 0.875542988 1.074475592 0.925126139 0.912722106 1.083845348 1.243734243 0.966374288 0.90119804 1 23.07582886 4.760217343 23.41728118 1.00595036 0.875542666 0.14748827 0.102796076 5497.175703 5943834.11 0.027045344 1.136850612 57572.79891 -4.760217343 -0.130407694 YNHIDESEMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YNHIDESEMK 10 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;Q5TBM3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;; 176.95 2.38E-06 1386060000 3233690 2681620 1888270 2280690 2723930 2431800 3270190 3783100 3506410 FALSE TRUE 2806349.673 2664004.262 2801443.688 2798555.523 2669729.122 2525352.92 2953047.477 2974113.505 3091886.204 0.907649728 0.861611355 0.906062999 0.905128888 0.86346293 0.816767744 0.955095784 0.961909109 1 21.56005579 2.085494806 7.558072363 0.972387359 0.87823275 0.711364534 0.028907023 0.127232739 9.621627781 0.012173984 0.008179969 121.7572432 -2.085494806 -0.094154609 YNIMLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YNIMLVR 7 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 81.635 0.062041 304450000 677610 639280 531780 459960 566170 469800 928810 772070 664010 FALSE TRUE 588062.1217 635080.5276 788950.5867 564400.948 554904.3247 487873.51 838734.1492 606968.8388 585511.4942 1.004356238 1.084659368 1.347455335 0.963945121 0.947725758 0.833243266 1.4324811 1.036647179 1 19.15933797 YNLDAS(ph)EEEDSNK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 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;YNLDAS(1)EEEDSNK 317.95 7.92E-51 1560320000 2828400 1852410 1976260 2371300 2004050 1683760 2174050 2611640 6771410 TRUE FALSE 2454619.774 1840241.397 2931985.946 2909739.908 1964173.326 1748535.337 1963210.966 2053161.11 5970901.624 0.411097005 0.308201594 0.491045763 0.487320022 0.328957576 0.292842764 0.328796401 0.343861152 1 22.50951737 1.237021368 24.99995324 1.000000771 0.371678744 0.888156007 0.069807272 13.06609481 212143.0417 0.111914426 0.018201613 17.25922807 -1.237021368 -0.628322027 YNLDAS(ph)EEEDSNKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YNLDASEEEDSNKK 14 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 YNLDAS(1)EEEDSNKK;YNLDAS(1)EEEDSNKK;YNLDAS(1)EEEDSNKK;YNLDAS(1)EEEDSNKK 170.06 1.98E-06 1868380000 2622540 1486980 1688150 1752360 1538340 1136100 2082250 2355390 3955090 TRUE FALSE 2275964.694 1477211.93 2504544.987 2150260.121 1507730.044 1179806.502 1880313.715 1851708.178 3487523.766 0.652601917 0.423570427 0.718144206 0.61655784 0.432321081 0.338293466 0.539154381 0.530952132 1 21.73377162 1.238400539 8.607170274 1.004194589 0.527494943 0.627607572 0.113393663 0.058771541 49.96392721 0.162578608 0.028314581 17.31412462 -1.238400539 -0.476699646 YNLDAS(ph)EEEDSNKKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YNLDASEEEDSNKKK 15 2 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 YNLDAS(1)EEEDSNKKK 187.47 1.77E-07 315110000 1284800 621190 726630 583850 544160 357030 975040 1071800 679090 TRUE FALSE 1115010.425 617109.362 1078030.698 716422.0661 533332.2806 370765.1751 880480.7709 842603.9108 598808.7538 1.862047636 1.030561691 1.800292149 1.196412146 0.890655451 0.619171268 1.470387273 1.407133589 1 19.19173579 3.533233171 10.7654866 1.117823993 1.509250093 0.309619489 0.326676953 1.230457785 233.0832599 0.092664616 0.137249939 3413.761462 -3.533233171 0.391426099 YNLDFWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YNLDFWR 7 0 Q13630;E9PP14;A0A0J9YX13;E9PKL9;E9PLH9;H0YE90 Q13630 TSTA3 GDP-L-fucose synthase 0 ;;; 157.9 0.0033611 11954870000 8697240 17799890 9912120 9025880 17851560 17794530 16216260 17919740 19019780 FALSE TRUE 7547877.698 17682961.35 14705654.39 11075344.01 17496348.88 18479097.08 14643609.6 14087743.05 16771283.28 0.450047714 1.05435947 0.876835371 0.660375466 1.043232566 1.101829644 0.873135905 0.839991957 1 23.99948975 3.229851604 24.99999994 0.954304174 0.78971777 0.265125413 0.170341379 327.5750801 940331.6679 0.050963824 0.058657178 1697.663472 -3.229851604 -0.164586403 YNLGLDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YNLGLDLR 8 0 P00367;P00367-2;P00367-3;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 ;;; 144.38 0.0013642 775940000 1454460 2142530 1375520 2249970 2777510 2849440 1939490 2352540 2505530 FALSE TRUE 1262249.426 2128455.579 2040726.073 2760860.077 2722242.985 2959059.801 1751398.558 1849467.628 2209329.098 0.571327027 0.963394535 0.923685871 1.249637313 1.232158209 1.33934768 0.792728689 0.837117309 1 21.07517691 4.903592442 1.730293747 1.045208543 0.248641045 0.418562726 0.178080646 1.812329645 3.838192428 0.054653237 2.712417929 80092.60918 -4.903592442 -0.796567498 YNLINEGS(ph)PPSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YNLINEGSPPSK 12 0 Q68D06 Q68D06 SLFN13 Schlafen family member 13 1 YNLINEGS(0.999)PPS(0.001)K;YNLINEGS(0.999)PPS(0.001)K;YNLINEGS(0.999)PPS(0.001)K 185.27 1.39E-05 449930000 1247660 1308080 727990 997990 1367760 1033930 1441220 1746580 1387790 TRUE FALSE 1082778.57 1299487.136 1080048.399 1224598.883 1340544.252 1073705.956 1301450.706 1373087.459 1223727.047 0.88482033 1.061909304 0.882589301 1.000712443 1.09546018 0.877406411 1.063513885 1.122053698 1 20.22285037 2.543419058 0.406893783 1.102275496 0.934719177 0.160975853 0.083026114 3.456320276 1.603683752 0.349623719 0.185298548 349.4773693 -2.543419058 -0.167556319 YNMGLPVDFDQYNELHLPAVILK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YNMGLPVDFDQYNELHLPAVILK 23 0 Q07960;H0YE29 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ;; 240.71 2.89E-37 1756410000 2098500 1939510 1185595 1631470 1951520 1780520 2084050 2543590 2343160 FALSE TRUE 1821177.908 1926769.231 1758952.708 2001920.199 1912688.57 1849017.757 1881939.152 1999663.073 2066154.294 0.881433644 0.93253889 0.851317209 0.968911279 0.925723977 0.894907879 0.910841536 0.96781885 1 20.97851656 1.59663993 2.781911708 0.997183032 0.910058772 0.508862756 0.031227158 0.189543651 3.240567587 0.030569969 0.008065879 39.50389604 -1.59663993 -0.08712426 YNNFQMHLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YNNFQMHLDR 10 0 O94855;O94855-2;E9PDM8;E9PC44 O94855 SEC24D Protein transport protein Sec24D 0 ;;;;; 189.72 9.80E-07 1831580000 1313541 1826701 945155 1185673 1889427 1959130 1664932 1890832 1939276 FALSE TRUE 1139953.229 1814701.281 1402235.119 1454898.177 1851831.099 2034498.999 1503467.151 1486492.291 1710017.001 0.666632688 1.061218269 0.820012385 0.850809189 1.082931397 1.189753668 0.879211815 0.869285095 1 20.70557924 3.266919448 24.97808553 0.987266525 0.86266051 0.246623705 0.13153868 395.6858745 348512.3433 0.039271504 0.050689478 1848.925651 -3.266919448 -0.124606016 YNPENLATLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YNPENLATLER 11 0 Q9UBQ5;K7ERF1;Q9UBQ5-2;K7ES31 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 0 ; 196.44 1.41E-07 221551000 142405 140382 68829 97718 142496 124485 139507 155894 139432 FALSE TRUE 123585.8184 139459.8214 102114.9346 119906.3654 139660.6084 129274.0185 125977.6326 122557.2813 122948.5078 1.005183557 1.134294542 0.830550419 0.975256777 1.135927641 1.051448454 1.024637345 0.996817964 1 16.9076947 YNPTWHCIVGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YNPTWHCIVGR 11 0 P63167;Q96FJ2 P63167;Q96FJ2 DYNLL1;DYNLL2 "Dynein light chain 1, cytoplasmic;Dynein light chain 2, cytoplasmic" 0 ; 146.36 3.58E-05 1160320000 743460 761680 292160 318510 686800 741840 699110 728990 220124 FALSE TRUE 645209.8773 756676.4739 433449.5532 390832.5636 673134.0237 770379.0648 631310.4198 573101.1615 194101.1915 3.324090246 3.898360789 2.233111244 2.013550564 3.467954104 3.968955878 3.252480909 2.952589611 1 17.56644945 4.250999642 24.99935799 2.799163636 3.611225634 0.1610027 0.842233704 478.4044438 961456.3372 0.216903645 0.565205363 17823.77299 -4.250999642 0.812061997 YNQATPNFHQWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YNQATPNFHQWR 12 0 P50552 P50552 VASP Vasodilator-stimulated phosphoprotein 0 ;;; 188.91 8.60E-06 2835210000 2403390 2604500 1456703 1814250 2894800 2810380 2546060 2677480 2750470 FALSE TRUE 2085775.922 2587390.868 2161169.443 2226203.192 2837199.144 2918497.137 2299143.493 2104921.738 2425312.57 0.860002932 1.066827798 0.891089037 0.917903622 1.169828243 1.203348869 0.94797822 0.867897097 1 21.20973926 4.758890978 22.77940564 0.999015573 0.860002476 0.142282046 0.112325267 3343.650824 3746230.042 0.030144941 1.01521692 57397.23587 -4.758890978 -0.139013097 YNQATQTFHQWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YNQATQTFHQWR 12 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;A0A0U1RQP7;A0A075B6E5;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 243.4 2.42E-16 580740000 514870 492780 278780 343700 436310 520390 455530 505740 540510 FALSE TRUE 446828.625 489542.8957 413598.9405 421742.3381 427628.2846 540409.74 411352.7707 397591.4367 476611.5236 0.937511166 1.027131892 0.867790475 0.884876503 0.897226071 1.133857898 0.863077686 0.834204414 1 18.86245431 2.499429238 0.009639531 5.26E-08 1.854170867 0 0.092515457 21605.67094 169.1286301 16444.90844 16083.10129 315.8124439 -2.499429238 1.854170814 YNQLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YNQLLR 6 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;; 166.39 0.016242 16736800000 12078560 13783410 7376470 6180330 13027230 13802990 11216680 12176460 14342290 FALSE TRUE 10482347.69 13692865.87 10943755.56 7583668.387 12768013.61 14333999.96 10128888.1 9572618.786 12646760.81 0.828856325 1.082717233 0.865340598 0.599653026 1.009587656 1.13341275 0.800907699 0.756922577 1 23.59226458 YNQMDSTEDAQEEFGWK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YNQMDSTEDAQEEFGWK 17 0 Q99805 Q99805 TM9SF2 Transmembrane 9 superfamily member 2 0 107.46 0.0016354 116760000 89357 80464 67434 82749 96139 95363 94706 127380 120200 FALSE TRUE 77548.24605 79935.42669 100045.308 101538.4252 94226.02199 99031.67632 85521.4267 100140.7783 105990.0929 0.73165561 0.754178287 0.943911881 0.957999209 0.889007825 0.934348424 0.806881326 0.944812628 1 16.69356989 4.256508443 9.873717163 0.9208909 0.742446763 0.689968143 0.050755929 0.159059103 79.9991357 0.012794232 0.032430535 18051.29831 -4.256508443 -0.178444136 YNTEGRVS(ph)PSPSQESLSSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YNTEGRVSPSPSQESLSSSK 20 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 YNTEGRVS(0.769)PS(0.231)PSQESLSSSK;YNTEGRVS(0.853)PS(0.147)PSQESLSSSK;YNTEGRVS(0.951)PS(0.049)PSQESLSSSK 305.6 1.42E-55 2081160000 1490090 1014840 705340 939960 1012190 951240 1220760 1405390 1055120 TRUE FALSE 1293170.831 1008173.449 1046444.783 1153392.284 992049.3993 987834.8183 1102370.883 1104858.285 930384.9156 1.389930995 1.08360898 1.124743927 1.239693663 1.066278465 1.061748532 1.184854639 1.187528158 1 19.82746818 4.744528012 24.65655986 1.127622999 1.389931135 0.586122404 0.07130504 414.3168716 1711848.797 0.01719412 0.150999778 55530.04324 -4.744528012 0.262308135 YNTEGRVSPS(ph)PSQESLSSSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YNTEGRVSPSPSQESLSSSK 20 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 YNTEGRVS(0.312)PS(0.687)PS(0.001)QESLSSSK 258.83 1.73E-36 631070000 340080 262570 183450 221750 248040 216340 312850 352910 268130 TRUE FALSE 295137.5663 260845.1604 272167.0336 272101.7267 243104.4893 224662.7398 282509.8552 277442.9428 236431.9769 1.248298011 1.103256691 1.151143078 1.15086686 1.0282217 0.950221467 1.194888521 1.173457781 1 17.85106564 7.999990631 0.939525042 1.094945086 98.07081255 0.274744247 0.079318334 1898.81553 3.424772248 0.027104705 395582.7285 99997842.77 -7.999990631 96.97586746 YNVYPTYDFACPIVDSIEGVTHALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YNVYPTYDFACPIVDSIEGVTHALR 25 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 195.03 7.29E-19 968920000 666930 647080 359000 428600 642760 714540 552780 692780 634540 FALSE TRUE 578793.5107 642829.2889 532613.6008 525920.1807 629970.3335 742028.8162 499171.4807 544634.3882 559525.4041 1.034436518 1.148883115 0.951902446 0.939939772 1.125901217 1.326175381 0.892133721 0.973386345 1 19.09384411 YNWSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YNWSAK 6 0 P61927;D6RG19 P61927 RPL37 60S ribosomal protein L37;Ribosomal protein L37 0 117.62 0.052495 1206900000 1575300 1561000 945990 1047700 1407900 1310200 1677700 1914900 1731400 FALSE TRUE 1367120.114 1550745.688 1403473.928 1285596.298 1379885.545 1360604.242 1514996.912 1505413.537 1526715.864 0.895464667 1.015739552 0.919276442 0.842066509 0.903826034 0.891196767 0.992324078 0.98604696 1 20.54200016 2.229104971 24.86400894 0.991366073 0.912891748 0.444367158 0.042940489 188.5998255 495926.2286 0.018455741 0.012629739 169.474738 -2.229104971 -0.078474325 YNYHLDSSGSYVFENTVATVMALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YNYHLDSSGSYVFENTVATVMALR 24 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;; 282.35 2.52E-52 408350000 271967 180338 105903 150980 194950 187095 189532 228067 220875 FALSE TRUE 236025.8719 179153.3478 157118.045 185262.3166 191070.8764 194292.6657 171151.2158 179296.6469 194763.4091 1.211859419 0.91985116 0.806712337 0.951217261 0.981040932 0.997582999 0.878764736 0.92058692 1 17.57136313 4.739676186 24.78706092 0.9288574 1.211859522 0.694577136 0.058295957 49.86534738 1107810.827 0.014589035 0.087554625 54913.12842 -4.739676186 0.283002121 YPALHKPENQDIDWGALEGETR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YPALHKPENQDIDWGALEGETR 22 1 P13796 P13796 LCP1 Plastin-2 0 ;;; 188.8 1.42E-17 776759000 805510 699841 476383 527168 646812 645826 688527 860921 963205 FALSE TRUE 699059.8126 695243.6984 706763.4122 646869.5517 633941.7067 670671.3441 621753.7575 676819.7438 849336.0022 0.823066267 0.818573211 0.832136411 0.761617958 0.746396838 0.789641958 0.732046865 0.796881025 1 19.69597588 1.241401384 5.915760554 1.007961905 0.785052972 0.806090482 0.032779749 0.059076655 7.608351716 0.053230409 0.008650658 17.4341743 -1.241401384 -0.222908933 YPDVAS(ph)PTLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YPDVASPTLR 10 0 Q8IVL1-9;Q8IVL1-13;A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-5;Q8IVL1-4;Q8IVL1-10;Q8IVL1-8;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1;E9PNV5 Q8IVL1-9 NAV2 Neuron navigator 2 1 YPDVAS(0.97)PT(0.03)LR;YPDVAS(0.979)PT(0.021)LR;YPDVAS(1)PTLR;YPDVAS(0.983)PT(0.017)LR 221.55 5.58E-09 2351470000 2520660 2532630 1868360 2304890 2706090 2803090 2564490 2735420 4063100 TRUE FALSE 2187548.394 2515992.987 2771905.145 2828250.503 2652244.103 2910926.686 2315786.155 2150471.72 3582764.947 0.610575471 0.702248968 0.773677645 0.789404425 0.740278568 0.812480509 0.64636843 0.600226851 1 21.77264197 4.641840612 2.970260758 0.746225481 0.601402664 0.162490734 0.106934401 0.663176133 9.198187462 0.027193571 0.200283914 43836.97848 -4.641840612 -0.144822817 GYYSPYSVS(ph)GSGSTAGSR ddPTM_MDA-MB-175_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 GYYSPYS(0.009)VS(0.91)GS(0.082)GSTAGSR;GYYSPYS(0.003)VS(0.995)GS(0.002)GSTAGSR;GYYSPYS(0.001)VS(0.988)GS(0.011)GSTAGSR;GYYSPYS(0.019)VS(0.978)GS(0.002)GSTAGSR 293.59 3.18E-49 2329480000 3426580 2436350 1459820 1138380 1418210 1647280 1376240 1298460 1156930 TRUE FALSE 2973748.771 2420345.456 2165793.835 1396866.578 1389990.396 1710651.928 1242772.457 1020794.434 1020159.053 2.914985424 2.372517745 2.12299624 1.369263522 1.362523217 1.676848254 1.218214407 1.000622825 1 19.96036267 8 0.297828529 0.899796235 18.84062432 0.921170439 0.175957306 20.67170429 0.330093092 0.375319094 193.2634833 100000000 -8 17.94082809 up YPEPERPS(ph)S(ph)RASHSSERPPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YPEPERPSSRASHSSERPPPR 21 3 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 2 YPEPERPS(0.702)S(0.73)RAS(0.552)HS(0.008)S(0.008)ERPPPR;YPEPERPS(0.624)S(0.661)RAS(0.613)HS(0.053)S(0.049)ERPPPR 69.619 0.027263 886010000 361506 463719 152459 269537 418165 410656 367870 413490 537370 TRUE FALSE 313732.0662 460672.7994 226188.6823 330739.4955 409844.3346 426454.202 332194.024 325068.3813 473842.7308 0.662101676 0.972206113 0.477349694 0.697994237 0.864937474 0.899991019 0.701063881 0.68602589 1 18.85404878 3.258292979 24.72060442 0.806135319 0.705607881 0.142896537 0.149236415 544.1580758 681713.4513 0.043171852 0.055651744 1812.562453 -3.258292979 -0.100527438 YPEPERPS(ph)SR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YPEPERPSSR 10 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 YPEPERPS(0.701)S(0.299)R;YPEPERPS(0.649)S(0.351)R;YPEPERPS(0.6)S(0.4)R;YPEPERPS(0.6)S(0.4)R 100.04 0.0085891 1858700000 2174520 1894810 2800390 2035760 1395240 1495050 1520930 1855560 2033830 TRUE FALSE 1887151.672 1882362.868 4154667.971 2498010.423 1367477.454 1552565.541 1373430.443 1458762.934 1793392.934 1.052280087 1.049609839 2.316652358 1.392896322 0.762508554 0.865714095 0.765827955 0.813409547 1 20.77426019 3.28749547 5.866348759 0.833302499 1.493864966 0.426765291 0.351686185 0.183812997 14.20711104 0.104762943 0.133900755 1938.632413 -3.28749547 0.660562467 YPEPERPSS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YPEPERPSSR 10 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 YPEPERPS(0.079)S(0.921)R;YPEPERPS(0.327)S(0.673)R 84.821 0.022795 6613200000 2410220 2733710 1816220 2241350 2666940 2563660 2487830 2685600 3304000 TRUE FALSE 2091703.32 2715752.079 2694550.067 2750282.774 2613873.112 2662285.659 2246560.63 2111305.339 2913404.884 0.717958335 0.932157454 0.924880054 0.944009804 0.897188416 0.913805587 0.771111713 0.724686552 1 21.47427478 1.187299361 23.91023003 1.000004754 0.85416041 0.222790742 0.086138295 21559.39218 10054491.44 26.77411777 0.023090987 15.39215262 -1.187299361 -0.145844344 YPEPERPSS(ph)RAS(ph)HSSERPPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YPEPERPSSRASHSSERPPPR 21 3 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 2 YPEPERPS(0.471)S(0.532)RAS(0.954)HS(0.023)S(0.02)ERPPPR 85.467 0.0041558 516760000 85564 121240 26298 28400 137450 132370 91060 96454 33306 TRUE FALSE 74256.50061 120443.5665 39015.80076 34848.65407 134715.0139 137462.3596 82229.01522 75828.06271 29368.60262 2.528431521 4.101099668 1.328486795 1.18659558 4.587042007 4.68058904 2.799895394 2.581943162 1 14.841987 YPES(ph)NRTPVKPSSVEEEDSFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YPESNRTPVKPSSVEEEDSFFR 22 2 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 Y(0.007)PES(0.495)NRT(0.495)PVKPS(0.002)S(0.002)VEEEDSFFR 43.801 0.09585 176620000 86049 70281 54779 67031 65566 54294 82814 98227 73339 TRUE FALSE 74677.40663 69819.31948 81270.30762 82251.41305 64261.36488 56382.72531 74782.71103 77221.92045 64668.94697 1.154764537 1.079642127 1.25671302 1.271884218 0.993697406 0.87186707 1.156392898 1.194111302 1 15.9807855 3.234091601 24.9999355 1.061997039 1.187526203 0.327458693 0.103084683 177.1330863 990892.3084 0.034617366 0.040599543 1714.318854 -3.234091601 0.125529164 YPESNRT(ph)PVKPSSVEEEDSFFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YPESNRTPVKPSSVEEEDSFFR 22 2 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 YPES(0.046)NRT(0.951)PVKPS(0.002)SVEEEDSFFR;YPES(0.056)NRT(0.781)PVKPS(0.134)S(0.029)VEEEDSFFR;YPES(0.342)NRT(0.658)PVKPSSVEEEDSFFR;YPES(0.464)NRT(0.536)PVKPSSVEEEDSFFR;YPES(0.061)NRT(0.936)PVKPS(0.002)S(0.002)VEEEDSFFR 192.5 5.00E-16 2506810000 2078940 1648800 1166979 1479150 1645510 1564190 1856100 2284090 1997910 TRUE FALSE 1804202.812 1637968.924 1731333.948 1815013.615 1612767.57 1624365.401 1676095.708 1795655.128 1761719.356 1.024114769 0.929755877 0.982752413 1.030251276 0.9154509 0.922034146 0.95139768 1.019262871 1 20.74855269 1.731631437 8.901149621 1.00882152 0.963376643 0.178827735 0.039459087 0.166430761 45.97337835 0.022268034 0.010218507 53.90529625 -1.731631437 -0.045444877 YPFILPHQQVDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YPFILPHQQVDK 12 0 Q9ULC4-2;Q9ULC4;Q9ULC4-3;A0A3B3IRV3 Q9ULC4-2 MCTS1 Malignant T-cell-amplified sequence 1 0 ; 184.55 1.42E-05 1004480000 1599460 1384910 1007910 1270540 1254170 1090800 1398570 1640270 1909170 FALSE TRUE 1388087.308 1375812.435 1495338.647 1559035.526 1229214.471 1132763.782 1262936.897 1289511.025 1683470.098 0.824539331 0.81724792 0.888247822 0.926084478 0.730167095 0.672874311 0.750198592 0.76598392 1 20.68300666 3.230485362 24.99949753 0.773540189 0.862418174 0.160137962 0.089502679 313.6618397 971036.9256 0.027610625 0.031843125 1700.142648 -3.230485362 0.088877985 YPGGS(ph)PIPADPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YPGGSPIPADPR 12 0 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 Y(0.001)PGGS(0.999)PIPADPR 66.262 0.061395 187310000 132530 140340 88351 98996 138390 152450 120670 147450 158350 TRUE FALSE 115015.8247 139418.0973 131077.8391 121474.5549 135636.3098 158314.8501 108967.442 115918.965 139630.0434 0.82371832 0.998482088 0.938750973 0.86997434 0.971397748 1.133816522 0.780401118 0.830186414 1 17.09124987 YPGSTFMDHVLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YPGSTFMDHVLR 12 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 173.04 3.42E-05 635160000 364160 375390 290790 356100 383310 436910 360720 439630 912490 FALSE TRUE 316035.3333 372924.0384 431417.0166 436957.9476 375682.8809 453718.2104 325737.4299 345618.5457 804616.4717 0.392777608 0.463480492 0.536177212 0.543063637 0.466909259 0.563893764 0.404835647 0.429544457 1 19.61794175 1.235483287 24.99999929 1.000000715 0.475848127 0.890131026 0.057955899 27.76750733 225540.9045 0.101772253 0.014773457 17.19821156 -1.235483287 -0.524152588 YPHLGQKPGGSDFLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YPHLGQKPGGSDFLR 15 1 P56211;H3BMD8;P56211-2;H3BTD3 P56211 ARPP19 cAMP-regulated phosphoprotein 19 0 120.3 8.67E-05 367940000 324620 258400 138940 187420 257320 240850 294350 328370 259050 FALSE TRUE 281720.6445 256702.5534 206131.8487 229976.5755 252199.8354 250115.6554 265803.9823 258150.6309 228425.4041 1.233315732 1.123791613 0.902403345 1.006790713 1.104079629 1.094955512 1.163635819 1.130131002 1 17.80136358 3.045213106 24.71557815 1.107554723 1.058498011 0.020541889 0.092643412 385.3509827 210647.7486 0.02946239 0.033407183 1109.719215 -3.045213106 -0.049056712 YPHVEDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YPHVEDYR 8 0 K7ESG5;K9J957;P61289;P61289-2;A0A087WTV2;B3KQ25;P61289-3 K7ESG5 PSME3 Proteasome activator complex subunit 3 0 111.74 0.0031755 533180000 368040 399760 304170 351240 369850 328520 439980 423300 623570 FALSE TRUE 319402.5815 397133.9502 451267.6294 430994.4104 362490.7086 341158.377 397310.8073 332780.5891 549852.265 0.580887998 0.722255732 0.820707048 0.783836746 0.659251097 0.620454618 0.722577377 0.605218184 1 19.06868452 1.228499982 24.99940787 1.000000627 0.691992657 0.618247048 0.076679563 307.3671789 763715.1434 0.261780616 0.01965543 16.92388174 -1.228499982 -0.30800797 YPHVEDYRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YPHVEDYRR 9 1 K7ESG5;K9J957;P61289;P61289-2;A0A087WTV2;B3KQ25;P61289-3 K7ESG5 PSME3 Proteasome activator complex subunit 3 0 56.563 0.078623 197350000 115300 134940 67689 82047 142970 155330 136700 149040 49070 FALSE TRUE 100062.8129 134053.5703 100423.6268 100677.0254 140125.1767 161305.6456 123442.855 117168.9558 43269.0005 2.312575093 3.098143445 2.320913949 2.326770302 3.238465763 3.727972538 2.852916721 2.707919168 1 15.40104617 YPHYFPLLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YPHYFPLLK 9 0 P52888;K7EP46 P52888 THOP1 Thimet oligopeptidase 0 ; 68.227 0.058667 933890000 1090530 1202720 623060 930020 1071420 1176840 946740 1026580 1147090 FALSE TRUE 946413.6974 1194819.253 924373.9 1141195.255 1050100.838 1222113.796 854925.3005 807053.8559 1011482.327 0.935670028 1.181255689 0.913880426 1.12824043 1.038180115 1.208240385 0.845220206 0.797892197 1 19.94803968 2.214179566 24.98937331 0.862223026 1.067179916 0.402611071 0.106294345 191.866354 196651.9845 0.040241504 0.027144678 163.749343 -2.214179566 0.20495689 YPIEHGIITNWDDMEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 27 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 3.61361E+11 117867050 92491410 67806824 81613767 85529461 75812675 102578870 121594730 107369380 FALSE TRUE 102290620.7 91883827.84 100598430.9 100145420.2 83827592.06 78729237.66 92630786.98 95592643.24 94676294.21 1.080424847 0.970505115 1.06255142 1.057766583 0.885412687 0.831562307 0.978394726 1.009678759 1 26.4964999 3.256041852 24.99901325 0.946924829 1.039057195 0.414910563 0.05976839 301.3930753 431004.2602 0.019192045 0.024718005 1803.1915 -3.256041852 0.092132366 YPIEHGIITNWDDMEKIWHHTFYNELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YPIEHGIITNWDDMEKIWHHTFYNELR 27 1 P68133;P68032;A6NL76 P68133 ACTA1;ACTC1 "Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1" 0 212.38 2.15E-26 479000000 537700 809880 167820 230040 432960 418280 516030 705040 162200 FALSE TRUE 466641.5826 804559.845 248978.3133 282274.0979 424344.9431 434371.5023 465985.49 554272.6826 143024.9008 3.262659719 5.625313079 1.740803958 1.973601075 2.966930519 3.03703411 3.258072458 3.875357924 1 17.12590682 4.23443515 24.99999991 2.71815966 4.443986357 0.372966259 1.002603243 106.9642945 648211.0024 0.253923544 0.560789555 17156.75502 -4.23443515 1.725826697 YPILGIPQAHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YPILGIPQAHR 11 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 ; 127.4 0.00028748 1222590000 1079350 1303100 850790 1084460 1293610 1496890 1046980 1262570 1558720 FALSE TRUE 936711.1628 1294539.85 1262234.89 1330703.218 1267869.692 1554476.327 945444.0407 992579.2308 1374449.897 0.68151714 0.941860342 0.918356422 0.968171499 0.9224561 1.130980715 0.687870866 0.722164724 1 20.39042289 2.206087383 24.99997151 0.781621231 0.929130867 0.15144114 0.13495533 301.2891431 231949.6101 0.054048128 0.03644228 160.7264614 -2.206087383 0.147509636 YPLAAAAERPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YPLAAAAERPPR 12 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 0 158.02 6.80E-05 172240000 164370 161670 121240 138680 203520 230450 154510 170690 213240 FALSE TRUE 142648.088 160607.9791 179872.0695 170169.4136 199470.3502 239315.5606 139525.644 134189.2718 188031.0101 0.75864129 0.85415687 0.956608537 0.905007177 1.060837518 1.272745174 0.742035284 0.713655007 1 17.52061109 YPLFEGQETGKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YPLFEGQETGKK 12 1 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 93.494 0.01145 1288680000 1452710 1043410 760270 907340 949910 775550 1346520 1594500 1094740 FALSE TRUE 1260730.693 1036555.771 1127939.115 1113365.415 931008.6495 805385.9103 1215934.698 1253528.583 965321.0843 1.306022124 1.073793775 1.168460042 1.153362786 0.9644549 0.834319195 1.259616844 1.298561281 1 19.88064936 4.745396686 23.59529153 1.109816619 1.306022329 0.179226231 0.138958897 776.9662253 2681608.536 0.037135631 0.342902781 55641.22543 -4.745396686 0.19620571 YPMEHGIVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YPMEHGIVK 9 0 P61163;R4GMT0;A0A1B0GVS3 P61163 ACTR1A Alpha-centractin 0 86.67 0.010605 167310000 316290 291480 200840 255980 276010 275790 352410 351070 342700 FALSE TRUE 274491.4751 289565.2487 297966.8958 314104.1714 270517.941 286399.8198 318233.3324 275996.4125 302186.3964 0.908351529 0.958233898 0.986036762 1.039438489 0.895202247 0.947758811 1.053102774 0.913331691 1 18.20507919 4.693336593 3.269554647 0.973162812 0.902449632 0.1551845 0.049434567 0.569028729 10.04051489 0.011936289 0.095071275 49355.61788 -4.693336593 -0.07071318 YPPYTT(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YPPYTTPPR 9 0 O43896 O43896 KIF1C Kinesin-like protein KIF1C 1 YPPYT(0.019)T(0.981)PPR 104.42 0.036469 1104300000 494870 491550 295920 330490 486260 522470 444320 500350 483730 TRUE FALSE 429471.6757 488320.9757 439027.9018 405532.8057 476584.3774 542569.759 401229.9148 393354.0462 426543.9905 1.006863736 1.144831451 1.029267582 0.950740873 1.117315888 1.272013605 0.940653072 0.922188696 1 18.70233501 YPRPASVPPS(ph)PSLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YPRPASVPPSPSLSR 15 1 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 1 YPRPASVPPS(0.993)PS(0.007)LSR 109.65 0.0005955 505750000 59393 50659 45567 40968 53705 56573 52203 56744 53053 TRUE FALSE 51544.06457 50326.21769 67603.35361 50270.41056 52636.37557 58749.39992 47140.36109 44609.73718 46781.13478 1.101813045 1.075780182 1.445098626 1.074587241 1.125162436 1.255835289 1.007678871 0.953583905 1 15.51363924 2.137376522 6.12056164 0.976271948 1.179353143 0.407278426 0.109794801 0.198878467 10.29212321 0.044790078 0.030005641 137.2070802 -2.137376522 0.203081195 YPS(ph)LGQKPGGSDFLMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YPSLGQKPGGSDFLMK 16 1 A6NMQ3;Q5T5H1;O43768-2;O43768;O43768-9;O43768-3;O43768-4;A0A1W2PRU0;O43768-6;O43768-5;O43768-7;O43768-8 A6NMQ3 ENSA Alpha-endosulfine 1 YPS(1)LGQKPGGSDFLMK;YPS(1)LGQKPGGSDFLMK 133.84 1.91E-05 674350000 687290 549850 319090 549910 515700 235559 867960 796040 937140 TRUE FALSE 596462.8851 546237.9991 473402.9913 674775.4703 505438.5789 244621.1072 783785.3728 625813.0408 826352.3768 0.721802105 0.661023087 0.572882713 0.816571101 0.611650179 0.296025175 0.948488072 0.757319829 1 19.65639759 2.150901029 24.18923047 0.873751031 0.622616421 0.458547489 0.146543845 17.04981319 4700.573618 0.059193791 0.039908457 141.5471171 -2.150901029 -0.25113461 YPS(ph)PQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YPSPQK 6 0 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 1 YPS(1)PQK;YPS(1)PQK 95.741 0.045106 954710000 2299100 1742830 1314370 1500300 1775280 1453220 2191700 2490700 2370000 TRUE FALSE 1995268.11 1731381.235 1950003.728 1840966.046 1739955.401 1509126.314 1979149.271 1958083.188 2089821.3 0.954755371 0.828482911 0.93309592 0.880920319 0.832585734 0.722131751 0.947042348 0.93696202 1 20.99494815 2.037326178 24.99997498 0.957385845 0.858340587 0.359099853 0.064751451 182.9476741 122532.282 0.026597543 0.017932013 108.9748243 -2.037326178 -0.099045258 YPSSISS(ph)SPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YPSSISSSPQK 11 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 YPSSIS(0.006)S(0.497)S(0.497)PQK 136.82 9.56E-05 894670000 996360 765820 861050 1156400 937530 795240 945030 1258400 3593600 TRUE FALSE 864688.5015 760789.278 1277456.66 1418978.294 918874.9872 825833.3974 853381.1361 989300.9529 3168768.702 0.27287839 0.240089874 0.403139762 0.447801158 0.289978561 0.260616497 0.269310012 0.312203586 1 21.59549093 1.238541791 24.01723971 1.000001135 0.31256086 0.91636597 0.065319862 0.080330441 97609.12177 0.095602333 0.017156096 17.31975688 -1.238541791 -0.687440275 YPSSISS(ph)SPQKDLTQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YPSSISSSPQKDLTQAK 17 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 YPSSIS(0.01)S(0.558)S(0.432)PQKDLTQAK 180.13 5.31E-10 1287000000 942580 708720 660800 776670 748360 603820 1010400 1179000 847680 TRUE FALSE 818015.6648 704064.3717 980365.0902 953024.7942 733469.1001 627049.3461 912411.5635 926880.025 747468.2361 1.094381842 0.941932162 1.311580938 1.275003737 0.981271263 0.838897649 1.220669347 1.240025971 1 19.51165275 YPSSISSS(ph)PQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YPSSISSSPQK 11 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 YPSSISS(0.071)S(0.928)PQK;YPSSIS(0.001)S(0.036)S(0.963)PQK;YPSSISS(0.06)S(0.939)PQK 260.83 1.22E-20 3307700000 2619840 2108300 2375580 3121740 2393470 2007150 2667860 3163620 9750300 TRUE FALSE 2273621.506 2094450.438 3524418.434 3830578.78 2345844.63 2084366.359 2409131.348 2487104.482 8597630.642 0.264447451 0.243607864 0.409929035 0.445538886 0.272847803 0.242434974 0.280208751 0.289277894 1 23.0355077 1.237688818 24.99998012 1.000000809 0.306670787 0.910692054 0.068296224 6.379090142 182821.6056 0.10569794 0.017982466 17.28577351 -1.237688818 -0.693330022 YPSSISSS(ph)PQKDLTQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YPSSISSSPQKDLTQAK 17 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 YPSSIS(0.001)S(0.003)S(0.996)PQKDLTQAK;YPSSISS(0.093)S(0.907)PQKDLTQAK;YPSSISS(0.003)S(0.997)PQKDLTQAK 248.46 4.33E-21 3362190000 3820300 2742300 2439450 3076540 2754090 2161360 4027800 4683200 3322200 TRUE FALSE 3315437.676 2724285.651 3619176.179 3775115.429 2699288.997 2244508.918 3637184.576 3681734.125 2929453.301 1.131759866 0.929963843 1.235444231 1.28867575 0.92143097 0.76618696 1.241591588 1.25679905 1 21.48220002 YPSSNPESPVVIFYSEIGSEEFSNFHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YPSSNPESPVVIFYSEIGSEEFSNFHR 27 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 91.583 1.48E-06 0 10832 12348 5465.9 10849 10690 13864 9708.7 8680.8 12029 FALSE TRUE 9400.523755 12266.88517 8109.227522 13312.43127 10477.28991 14397.35705 8767.151768 6824.478474 10606.94532 0.886261168 1.15649556 0.764520536 1.255067398 0.987776367 1.357351868 0.826548219 0.643397158 1 13.37272162 2.027627304 24.99894114 0.77785053 1.065424212 0.262339997 0.190198723 222.4059033 201246.0756 0.07256281 0.048920778 106.5681199 -2.027627304 0.287573682 YPSVLLLVCQDSEQSKPDVHFFHCDEVEAELVHEDIESALADCR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YPSVLLLVCQDSEQSKPDVHFFHCDEVEAELVHEDIESALADCR 44 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 28.624 0.077199 230400000 40416 37896 26072 31574 37265 23377 40545 53447 34345 FALSE TRUE 35074.9232 37647.05868 38680.50641 38743.35928 36523.49941 24276.32832 36612.95214 42017.77498 30284.77323 1.158170244 1.243101885 1.277226219 1.279301614 1.206002077 0.801601786 1.208955797 1.387422473 1 14.88630499 2.989070343 24.80557523 1.137974125 1.24243951 0.141272601 0.152430955 1334.657891 3029104.66 0.051922207 0.055136387 975.147571 -2.989070343 0.104465385 YPVGVHFLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YPVGVHFLPK 10 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 107.47 0.0022803 1087050000 1921590 1752160 1756860 2662400 2061100 1808870 2049300 2423400 6294400 FALSE TRUE 1667647.013 1740649.946 2606483.372 3266938.612 2020088.142 1878458.399 1850559.201 1905174.769 5550283.203 0.300461607 0.313614618 0.469612681 0.588607553 0.363961273 0.338443703 0.333417077 0.343257218 1 22.40412996 1.236343251 24.9999447 1.000000795 0.382605547 0.833828274 0.086782079 25.11733927 283120.228 0.148057753 0.022958567 17.23230016 -1.236343251 -0.617395248 YQAEIPDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YQAEIPDR 8 0 O94776 O94776 MTA2 Metastasis-associated protein MTA2 0 90.761 0.030167 91261000 159510 170980 98533 118800 176950 174160 152410 170480 193310 FALSE TRUE 138430.3494 169856.8211 146183.8884 145775.3557 173429.0412 180860.0479 137629.3017 134024.1787 170457.112 0.812112488 0.996478346 0.857599232 0.855202543 1.017435055 1.061029638 0.807413079 0.786263343 1 17.37904927 YQDEDT(ph)PPQEHISPQITNEVIGPELVHVSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YQDEDTPPQEHISPQITNEVIGPELVHVSEK 31 0 A0A590UJD9;A0A0C4DFT3;A0A590UJ18;A0A590UK02;E7EQD7;B4E2H8;C9JCP6;A8MUT6;A0A590UJ95;A0A590UJZ4;A0A590UJ86;C9JN61;A0A590UK13;A0A590UK52;C9IYP1;A0A590UJ08;Q12959-4;Q12959-2;A0A590UJC5;A0A590UJL2;Q12959;Q12959-3;Q12959-5;Q12959-7;Q12959-6;A0A590UKA8;A0A590UJR5;A0A590UJ68;A0A590UJS9;A0A590UJ81;C9JUA9;A0A590UJ64;A0A590UK81;A0A590UJ29 A0A590UJD9;A0A590UJ08;Q12959 DLG1 Disks large homolog 1 1 YQDEDT(1)PPQEHISPQITNEVIGPELVHVSEK 267.87 6.36E-59 54402000 94492 115010 18800 73206 170750 159910 130510 170610 187530 TRUE FALSE 82004.64279 114254.4917 27891.74288 89828.54118 167352.4091 166061.8412 117853.1603 134126.3792 165360.417 0.495914586 0.690942208 0.168672427 0.543228802 1.012046366 1.00424179 0.712704784 0.81111539 1 17.33525441 3.344219326 5.739511645 0.884847923 0.458144271 0.655865741 0.156302566 0.136482715 6.451381825 0.046159402 0.059698902 2209.120092 -3.344219326 -0.426703652 YQDEVFGGFVTEPQEES(ph)EEEVEEPEER ddPTM_MDA-MB-175_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;YQDEVFGGFVT(0.001)EPQEES(0.999)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER 234.28 3.64E-45 7910830000 5814070 5229240 3599593 4315949 4928980 5353580 5088839 5975900 5511800 TRUE FALSE 5045725.919 5194888.778 5340368.215 5295951.186 4830902.941 5559535.687 4595324.177 4698000.29 4860201.283 1.038172212 1.068862888 1.098795688 1.089656761 0.993971784 1.143890008 0.945500795 0.966626692 1 22.21258463 2.219832235 24.99995049 0.968808273 1.070515245 0.578791065 0.04079581 160.2131136 213862.1001 0.015683906 0.010595149 165.8945944 -2.219832235 0.101706972 YQDTHPER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YQDTHPER 8 0 C9JAH0;F8WD54;A0A087WUI8;Q96IJ6;Q96IJ6-2 C9JAH0 GMPPA Mannose-1-phosphate guanyltransferase alpha 0 ; 79.974 0.02665 1217690000 1649260 1529950 979840 1178380 1504870 1664630 1582970 1776450 1690830 FALSE TRUE 1431306.112 1519899.658 1453693.901 1445949.189 1474926.031 1728669.393 1429453.813 1396569.992 1490942.004 0.9600012 1.019422388 0.975017068 0.969822559 0.989257817 1.159447778 0.958758831 0.936703097 1 20.50779271 4.767379371 21.52077546 0.996835303 0.960000835 0.039128067 0.060820183 6651.1619 4966293.66 0.015473359 1.087621936 58530.11413 -4.767379371 -0.036834468 YQEALHLGSQLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YQEALHLGSQLLR 13 0 O00231;O00231-2 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 ; 169.04 2.92E-05 2680200000 2869200 2918300 1400200 2212500 3066600 3236200 2749500 3103400 3014200 FALSE TRUE 2490027.95 2899129.495 2077341.403 2714881.941 3005580.66 3360698.708 2482853.913 2439762.061 2657864.71 0.936852783 1.090773915 0.781582823 1.02145227 1.130825301 1.264435581 0.93415361 0.917940651 1 21.34183624 5.045858412 14.26526033 1.010162605 0.606226822 0.033924445 0.130159784 1429192.251 13710693.8 0.033429124 15042487.66 111136.934 -5.045858412 -0.403935784 YQEEFEHFQQELDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YQEEFEHFQQELDK 14 0 P49257 P49257 LMAN1 Protein ERGIC-53 0 ; 208.47 8.00E-09 209728000 245640 206353 148362 177739 205070 184157 183169 256150 296950 FALSE TRUE 213178.0516 204997.4536 220110.3594 218097.3565 200989.5082 191241.639 165405.2986 201374.3159 261844.9093 0.814138614 0.782896464 0.840613476 0.832925708 0.767589902 0.730362257 0.631691863 0.769059503 1 17.99835303 3.222529917 20.60995738 0.764832813 0.81680227 0.026542637 0.09203106 93.21733035 119842.9548 0.028618992 0.032639143 1669.282793 -3.222529917 0.051969456 YQEGGVESAFHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YQEGGVESAFHK 12 0 P40121-2;P40121;E7ENU9;B8ZZL6 P40121-2 CAPG Macrophage-capping protein 0 131.06 0.00020543 276760000 438600 474660 205380 338080 485700 427360 468480 584650 547240 FALSE TRUE 380637.8987 471541.9272 304702.455 414846.2312 476035.5203 443800.8157 423046.8817 459627.1473 482545.9106 0.78881178 0.977195987 0.631447595 0.859703133 0.986508247 0.919706925 0.876697683 0.952504492 1 18.88030668 3.463276841 12.11963584 0.939508397 0.80507226 0.371082159 0.088450243 0.653458517 566.4798945 0.024460383 0.031865621 2905.874411 -3.463276841 -0.134436136 YQELINDIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YQELINDIAR 10 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;; 173.24 8.08E-06 1307970000 1918350 2135720 1172350 1497120 2122840 2451890 1736530 2014570 2129720 FALSE TRUE 1664835.187 2121690.315 1739302.381 1837063.978 2080599.637 2546215.795 1568121.588 1583769.883 1877946.928 0.886518763 1.129792479 0.926172277 0.978229976 1.107911841 1.355850774 0.835019118 0.843351779 1 20.84072486 YQELLER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YQELLER 7 0 Q9H074;Q9H074-3;Q9H074-2;H0YA44 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 0 ;; 163.72 0.0028484 885370000 1293350 1065080 677430 813210 1122770 1109480 1007490 1184920 1164010 FALSE TRUE 1122430.521 1058083.419 1005037.414 997861.7596 1100429.074 1152162.414 909783.7749 931534.0791 1026402.064 1.093558324 1.030866418 0.979184911 0.972193836 1.072122819 1.122525426 0.886381475 0.907572297 1 19.96916455 2.224158655 24.99967646 0.924498554 1.039351063 0.490147166 0.054336755 205.6635401 356998.768 0.023253811 0.015756986 167.5554873 -2.224158655 0.114852509 YQEQGGEAS(ph)PQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 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 252.13 4.96E-21 1412850000 1749690 1480048 997791 1148280 1352112 1500055 1385004 1583128 1624568 TRUE FALSE 1518464.033 1470325.467 1480326.065 1409014.524 1325207.617 1557763.087 1250686.525 1244588.397 1432513.422 1.059999865 1.026395596 1.033376751 0.983596037 0.925092635 1.087433502 0.873071419 0.868814475 1 20.45011723 3.218959769 0.478319854 0.900938194 1.070652131 0.291926673 0.062724973 1.462021055 1.057408244 0.112606276 0.157634255 1655.616589 -3.218959769 0.169713938 YQEQGGEAS(ph)PQSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YQEQGGEASPQSR 13 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4 Q9UJU6-2 DBNL Drebrin-like protein 1 YQEQGGEAS(1)PQSR;YQEQGGEAS(0.967)PQS(0.033)R;YQEQGGEAS(0.998)PQS(0.002)R 246.18 3.85E-17 876500000 905269 880469 553664 693297 937422 931410 936372 995070 1001660 TRUE FALSE 785635.408 874685.1412 821417.7623 850720.6802 918769.1362 967241.9454 845562.7876 782282.0241 883244.8959 0.889487629 0.990308741 0.93000001 0.963176447 1.040220148 1.095100521 0.957336738 0.885690965 1 19.75245398 4.744199104 23.58193834 0.977007199 0.889487546 0.200484325 0.057517203 565.1207198 2363349.474 0.015715869 0.130329434 55488.00421 -4.744199104 -0.087519653 YQETFNVIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YQETFNVIER 10 0 Q13011;M0R248;M0QZW4 Q13011 ECH1 "Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial" 0 ;;; 219.5 1.46E-08 1421700000 865810 786900 513119 820970 854050 1030940 723170 825270 825440 FALSE TRUE 751391.0148 781730.8021 761265.0647 1007383.786 837056.0759 1070600.929 653037.0847 648792.4328 727857.4235 1.032332694 1.074016389 1.045898606 1.384039997 1.150027531 1.470893741 0.897204677 0.891372969 1 19.47329635 2.164095088 24.99999993 0.920227733 1.187539701 0.427619196 0.143401242 37.11847044 12460.34081 0.058999006 0.039776925 145.9133701 -2.164095088 0.267311968 YQEVDRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YQEVDRR 7 1 Q96MU7-2;Q96MU7 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 0 ;; 98.523 0.017959 401704000 373160 360030 219835 218262 304037 372460 332840 394910 295408 FALSE TRUE 323845.9605 357664.9392 326147.9413 267821.723 297987.2585 386788.7772 300561.228 310461.5697 260485.2028 1.243241294 1.373072003 1.252078574 1.028164825 1.143970004 1.484878116 1.153851447 1.191858756 1 17.99084189 1.094075204 1.661213826 0.834230283 1.242924042 0.268696937 0.124249686 2.219261552 4.138620074 1.657343754 0.035892805 12.41867336 -1.094075204 0.408693759 YQHDDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YQHDDGR 7 0 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 ; 136.11 0.0030116 199319000 271080 286320 162553 205420 163420 304360 254272 266656 408100 FALSE TRUE 235256.0912 284439.1451 241164.1745 252063.7506 160168.2617 316068.9261 229612.7406 209633.6895 359854.8829 0.653752672 0.79042736 0.670170633 0.700459442 0.445091256 0.878323294 0.638070376 0.582550632 1 18.45705571 1.229340786 24.99596383 1.000000646 0.66849814 0.450079356 0.114677604 339.7884 921134.8471 0.327642506 0.026829869 16.95667848 -1.229340786 -0.331502506 YQHVTGTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YQHVTGTR 8 0 Q99797 Q99797 MIPEP Mitochondrial intermediate peptidase 0 68.224 0.057062 27407000 36322 39161 21558 32076 41982 69020 33168 38480 42568 FALSE TRUE 31521.95567 38903.74881 31983.52091 39359.34605 41146.64034 71675.24406 29951.37247 30251.35145 37535.65953 0.839786914 1.036447722 0.852083627 1.04858544 1.096201342 1.909524035 0.797944484 0.805936324 1 15.19597421 3.561062347 4.867363515 1.095812529 0.923090684 0.084813858 0.310746954 0.779802024 31.93417099 0.094199845 0.140178391 3639.672829 -3.561062347 -0.172721845 YQILPLHSQIPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YQILPLHSQIPR 12 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 208.24 6.91E-08 2979100000 2926800 2708300 1489640 1853290 2769200 2940900 2670700 3007200 2694100 FALSE TRUE 2540015.964 2690508.999 2210034.887 2274107.82 2714098.338 3054038.326 2411695.925 2364133.682 2375606.567 1.069207334 1.132556643 0.930303408 0.957274597 1.14248646 1.285582541 1.015191639 0.995170545 1 21.1798645 2.025809357 24.9985903 0.999622258 1.083984484 0.138445214 0.097942787 469.6062747 454852.1895 0.043353089 0.029227738 106.1229605 -2.025809357 0.084362226 YQLDKDGVVLFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YQLDKDGVVLFK 12 1 P07237;H7BZ94;I3L398;I3L312;I3L3U6 P07237 P4HB Protein disulfide-isomerase 0 ; 181.98 1.59E-05 4591300000 3940400 2960600 2610700 3336600 2902100 2779300 3486500 3670600 3907300 FALSE TRUE 3419666.156 2941151.624 3873243.252 4094226.027 2844353.888 2886221.469 3148379.767 2885670.755 3445383.445 0.992535725 0.853650013 1.124183509 1.188322314 0.825555104 0.837706895 0.913796626 0.837547054 1 21.71623312 3.210303667 24.99999709 0.877304302 1.032422194 0.379998935 0.099156445 235.9196567 208726.3755 0.031102701 0.035273775 1622.944495 -3.210303667 0.155117892 YQLLQLRPAQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YQLLQLRPAQR 11 1 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ; 123.96 0.00032755 955420000 1475080 1514350 822950 1077490 1371850 1278310 1536380 1921960 1140320 FALSE TRUE 1280144.441 1504402.135 1220931.373 1322150.573 1344552.869 1327487.413 1387382.104 1510963.811 1005512.669 1.273126118 1.496154332 1.214237683 1.314901954 1.337181431 1.320209535 1.379775857 1.502680034 1 19.93949983 1.223998269 24.99932242 0.999999066 1.360036542 0.607249618 0.089580078 554.131857 951228.5369 0.480835552 0.022180996 16.74936201 -1.223998269 0.360037476 YQLQSQENFEAFMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YQLQSQENFEAFMK 14 0 A8MW49;P07148 A8MW49 FABP1 "Fatty acid-binding protein, liver" 0 57.679 0.087142 478680000 212580 191390 197360 221990 197010 165110 288500 236620 627640 FALSE TRUE 184487.0144 190132.7465 292803.9561 272396.2224 193089.8864 171461.8885 260521.3144 186020.6544 553441.1142 0.333345336 0.34354648 0.529060723 0.492186459 0.348889668 0.309810537 0.470729962 0.336116435 1 19.0780703 1.234998809 24.99980382 1.000000848 0.397650611 0.860887278 0.076368034 37.11480731 260462.5101 0.136698666 0.019063184 17.17903675 -1.234998809 -0.602350237 YQPLASTAS(ph)DNDFVTPEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YQPLASTASDNDFVTPEPR 19 0 Q15021 Q15021 NCAPD2 Condensin complex subunit 1 1 YQPLAST(0.007)AS(0.992)DNDFVTPEPR;YQPLAST(0.006)AS(0.993)DNDFVTPEPR;YQPLAST(0.001)AS(0.998)DNDFVTPEPR;YQPLASTAS(1)DNDFVTPEPR 325.39 1.14E-62 342781000 228399 240440 162751 192763 271927 270863 255179 292891 251906 TRUE FALSE 198215.4935 238860.5338 241457.928 236532.7853 266516.1847 281283.2749 230431.7799 230258.5389 222125.9597 0.892356273 1.075338219 1.087031558 1.064858811 1.199842581 1.266323285 1.037392389 1.036612467 1 17.76101848 4.76962093 2.920941725 1.098212424 0.848017801 0.395482045 0.079579638 0.550335204 6.304887089 0.021987407 0.335695547 58832.99121 -4.76962093 -0.250194622 YQPLASTASDNDFVT(ph)PEPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YQPLASTASDNDFVTPEPR 19 0 Q15021 Q15021 NCAPD2 Condensin complex subunit 1 1 YQPLASTASDNDFVT(1)PEPR 219.99 3.36E-18 59422000 70299 77875 43837 50233 68332 76976 66914 80196 76111 TRUE FALSE 61008.80904 77363.434 65036.71983 61639.17041 66972.32689 79937.31653 60424.69058 63046.70949 67113.24429 0.909042763 1.15272976 0.969059394 0.918435267 0.997900304 1.191081096 0.900339288 0.939407864 1 16.03430988 YQQEVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YQQEVDR 7 0 P33176;O60282;O60282-2;Q12840;J3KNA1;A0A0G2JMZ6 P33176;Q12840 KIF5B;KIF5C;KIF5A Kinesin-1 heavy chain;Kinesin heavy chain isoform 5C;Kinesin heavy chain isoform 5A;Kinesin-like protein 0 ; 214.25 9.86E-05 1219650000 1995720 2019360 1223880 1377620 1794870 2149200 1764330 1894730 1916010 FALSE TRUE 1731980.545 2006094.691 1815752.462 1690429.677 1759155.599 2231881.115 1593225.548 1489556.734 1689501.481 1.025142958 1.187388537 1.074726766 1.000549391 1.041227616 1.321029393 0.943015183 0.88165459 1 20.68816618 2.039506911 24.99977435 0.926361742 1.104922226 0.398768967 0.096120013 136.8359674 86588.55578 0.038403081 0.025891315 109.5233984 -2.039506911 0.178560484 YQQGDFGYCPR ddPTM_MDA-MB-175_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 ;;; 222.3 1.81E-11 1473890000 2024360 1951350 1103710 1396930 1736360 1916020 1612370 2071360 2008060 FALSE TRUE 1756835.697 1938531.453 1637467.848 1714124.307 1701809.833 1989730.529 1456002.606 1628415.783 1770669.434 0.992187284 1.094801444 0.924773318 0.968065678 0.961110979 1.123716539 0.822289343 0.919661091 1 20.75586347 2.227955267 24.99999741 0.911345763 1.006487154 0.280109021 0.072891699 278.470586 656432.9368 0.029086822 0.019838938 169.0266824 -2.227955267 0.095141391 YQQPFEDFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YQQPFEDFR 9 0 P19174-2;P19174;V9GY71;V9GYH5 P19174-2 PLCG1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1" 0 78.516 0.068747 198870000 164340 160090 112610 117530 159930 200780 193610 179930 168590 FALSE TRUE 142622.0526 159038.3582 167068.5727 144216.9828 156747.7059 208504.1365 174833.732 141453.3697 148659.4823 0.959387524 1.069816441 1.123833947 0.970116273 1.054407721 1.402561972 1.176068484 0.951526048 1 17.18165196 4.71816032 3.436392943 1.093327263 0.945371423 0.099728847 0.128652989 0.78662729 16.13068612 0.03451394 0.295530342 52258.90669 -4.71816032 -0.14795584 YQQPFEDFRIS(ph)QEHLADHFDSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YQQPFEDFRISQEHLADHFDSR 22 1 P19174-2;P19174;V9GY71;V9GYH5 P19174-2 PLCG1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1" 1 YQQPFEDFRIS(1)QEHLADHFDSR;YQQPFEDFRIS(1)QEHLADHFDSR;YQQPFEDFRIS(1)QEHLADHFDSR 173.07 2.52E-12 2121000000 961330 969020 460445 479213 780050 921820 931300 1013470 531150 TRUE FALSE 834287.8048 962654.4438 683117.7421 588025.636 764528.5311 957283.0119 840982.6693 796747.3273 468358.0521 1.78130343 2.055381432 1.458537414 1.255504487 1.632359106 2.043912788 1.79559776 1.701150058 1 18.83725234 1.23902432 7.532219867 0.988691351 1.71524508 0.467417164 0.240063117 0.09893218 40.77350387 0.368505855 0.063343076 17.33901091 -1.23902432 0.726553728 YQSNPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YQSNPK 6 0 P50502;Q8NFI4 P50502 ST13;ST13P5 Hsc70-interacting protein;Putative protein FAM10A5 0 110.63 0.066388 34765000 108310 95266 64766 81614 54200 82798 100370 111080 125600 FALSE TRUE 93996.55908 94640.19137 96087.05423 100145.7061 53121.52604 85983.29264 90636.13285 87326.40643 110751.7111 0.848714283 0.854525772 0.867589794 0.904236197 0.479645195 0.776360851 0.818372303 0.788488102 1 16.75696946 YQTPDHWYPSDLQAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YQTPDHWYPSDLQAR 15 0 Q6ICJ4;A0A087WY67;P0CG30;P0CG29 Q6ICJ4 Em:AP000351.3;GSTT2;GSTT2B Glutathione S-transferase theta-2B;Glutathione S-transferase theta-2 0 109.79 0.00097204 300360000 187700 173270 104430 135550 186540 202060 170610 212160 238220 FALSE TRUE 162894.9694 172131.778 154932.6973 166328.6993 182828.219 209833.379 154064.2685 166791.235 210057.903 0.77547651 0.819449188 0.73757138 0.791823097 0.870370581 0.998931133 0.733437144 0.794025041 1 17.68042754 3.283449468 5.722440005 0.863765192 0.779655677 0.246340123 0.083108007 0.342511442 26.22713482 0.025277145 0.032222084 1920.655471 -3.283449468 -0.084109515 YQVAGAEYWDNNDHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YQVAGAEYWDNNDHR 15 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 0 ;;; 228.51 5.87E-13 1254510000 1352440 1313140 870390 1121220 1346170 1409050 1200100 1490090 1517370 FALSE TRUE 1173711.627 1304513.897 1291313.515 1375810.138 1319383.851 1463257.065 1083714.487 1171445.849 1337988.247 0.877221179 0.974981581 0.965115738 1.02826773 0.986095247 1.093624752 0.809958151 0.875527757 1 20.35163401 2.228469877 24.9997036 0.887521376 0.987744507 0.27494173 0.070361939 251.5860467 623296.1375 0.028349109 0.019362014 169.2270863 -2.228469877 0.100223131 YQVFFFGTHETAFLGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YQVFFFGTHETAFLGPK 17 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;;; 231.91 3.13E-16 3055559000 2469317 2323205 1115697 1759692 1948457 1650182 2748774 3222546 2746732 FALSE TRUE 2142990.502 2307943.713 1655251.801 2159256.964 1909686.518 1713665.569 2482198.321 2533429.616 2422016.472 0.884796006 0.952901741 0.683418887 0.891512089 0.788469666 0.707536711 1.024847828 1.046000159 1 21.20777725 2.216416156 24.66820282 1.028330857 0.820100369 0.582805277 0.081922222 138.5397299 154327.3197 0.03315664 0.022375482 164.5948171 -2.216416156 -0.208230488 YQYAIDEYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YQYAIDEYYR 10 0 G3V583;Q8N128;Q8N128-2 G3V583 FAM177A1 Protein FAM177A1 0 163.64 0.0074024 0 247670 207650 137040 165600 231770 235530 216200 258780 257030 FALSE TRUE 214939.782 206285.9335 203313.0024 203202.011 227158.2305 244590.9915 195232.9573 203441.9108 226644.2062 0.948357717 0.91017519 0.897058018 0.896568302 1.002267979 1.07918484 0.861407227 0.897626788 1 17.79006976 5.127582711 17.65797065 0.938313379 2.746597904 0 0.066287729 3336.657913 463230.0499 0.016397771 751.4076964 134147.5394 -5.127582711 1.808284525 YQYGGLNSGRPVT(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 148.85 1.44E-06 11544400000 2228750 2016290 1295100 1609080 2039570 2167020 1832960 2153970 2280990 TRUE FALSE 1934215.041 2003044.858 1921414.692 1974446.207 1998986.547 2250386.662 1655199.821 1693360.278 2011333.961 0.961657824 0.995878803 0.955293715 0.981660055 0.993861082 1.118852814 0.822936347 0.841909057 1 20.93972122 2.216549624 24.99975333 0.875898084 0.997650348 0.400218605 0.064475934 218.5207243 248190.7115 0.026191245 0.017674228 164.6454085 -2.216549624 0.121752265 YQYGGLNSGRPVTPPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YQYGGLNSGRPVTPPR 16 1 P62140 P62140 PPP1CB Serine/threonine-protein phosphatase PP1-beta catalytic subunit 0 ; 164.41 6.74E-09 742680000 383530 333570 206905 211755 338110 343350 322500 361600 272400 FALSE TRUE 332845.5388 331378.7567 306964.9501 259837.2092 331382.2725 356558.8967 291223.9996 284274.654 240197.1823 1.385717915 1.379611341 1.277970653 1.081766267 1.379625978 1.484442462 1.212437202 1.183505365 1 17.8738597 1.428231519 1.659968691 0.955643192 1.319601837 0.479780869 0.108155862 0.635742243 2.314471031 0.346388612 0.032860266 26.80596949 -1.428231519 0.363958645 YRCS(ph)PER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YRCSPER 7 1 A1L390-3;A1L390;A0A0U1RR71 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 YRCS(1)PER;YRCS(1)PER 96.89 0.0075094 975770000 329300 374820 266276 283130 349820 394310 375300 425860 311030 TRUE FALSE 285782.1707 372357.7827 395047.9642 347418.9939 342859.2664 409479.3609 338903.4638 334793.153 274260.3877 1.042010379 1.35767978 1.440412039 1.266748716 1.250123174 1.493031364 1.235699645 1.220712753 1 18.06518674 1.185335597 1.667925753 0.852738403 1.311048589 0.368818802 0.122411489 1.233885088 2.818892751 0.966856262 0.033400355 15.32271054 -1.185335597 0.458310185 YRDELKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YRDELKR 7 2 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ; 107.29 0.0042237 272849000 631820 713410 1083430 483200 524180 754350 543550 538930 271850 FALSE TRUE 548323.3862 708723.5627 1607380.372 592917.9452 513749.8435 783370.3326 490836.6047 423684.0135 239712.2027 2.287423752 2.95656022 6.705459104 2.473457499 2.143194371 3.267961847 2.04760792 1.767469527 1 17.87094383 1.99396368 0.642377835 0.623270206 3.708980132 0.311726967 1.271346673 1.975477279 1.232061292 4.156783992 0.847260826 98.61970068 -1.99396368 3.085709926 YRDILEPQNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YRDILEPQNER 11 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 129.37 0.00022476 561820000 1202700 566950 498280 452840 555690 540750 670510 759090 711600 FALSE TRUE 1043760.148 563225.6681 739249.8746 555664.2432 544632.8562 561553.0024 605484.0434 596764.5107 627475.4587 1.663427841 0.897605891 1.178133526 0.88555534 0.867974753 0.894940184 0.964952549 0.951056336 1 19.25919951 YRDYYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YRDYYR 6 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 118.01 0.020275 848880000 532460 531550 238763 247170 533210 476530 416680 491410 383140 FALSE TRUE 462094.0619 528058.2131 354229.5854 303293.7263 522600.1642 494862.4175 376270.4377 386325.7957 337845.6257 1.367766894 1.56301628 1.048495403 0.897728735 1.546860828 1.46475899 1.113734822 1.143497995 1 18.36600465 2.114290128 9.208258627 1.096067585 1.305372832 0.20784483 0.210201675 0.509443143 38.90995342 0.091515129 0.061657259 130.1038438 -2.114290128 0.209305248 YREDIINVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YREDIINVR 9 1 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 135.86 0.00019061 177240000 90214 95222 50361 69680 87384 98484 91795 94292 88207 FALSE TRUE 78291.99133 94596.48041 74715.74805 85501.90899 85645.22936 102272.7432 82892.73503 74128.38958 77779.26895 1.006592019 1.216217145 0.960612629 1.099289183 1.101131838 1.31491006 1.065743303 0.953061022 1 16.24709805 1.992530068 24.96205823 0.984045032 1.11892344 0.251812322 0.098586734 433.3335177 1448056.717 0.04115952 0.026453451 98.29469241 -1.992530068 0.134878408 YREQEYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YREQEYR 7 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 0 ; 174.16 0.00076291 346210000 435380 441050 225691 293160 434310 424260 387340 449480 314600 FALSE TRUE 377843.4299 438152.7135 334835.9225 359726.4587 425668.0807 440581.5567 349775.8264 353362.1999 277408.3464 1.362047807 1.579450363 1.207014594 1.296739854 1.534445831 1.588205843 1.260869873 1.273798011 1 18.08165167 1.238862339 1.397691367 0.825315439 1.417168317 0.50707072 0.128788114 1.128294762 1.929372901 0.964476926 0.039191809 17.33254509 -1.238862339 0.591852878 YRESNTAGNDVFHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YRESNTAGNDVFHK 14 1 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 ; 106.52 0.0005628 346320000 344980 342770 149787 222930 370900 308420 422830 476440 139812 FALSE TRUE 299390.0189 340518.3213 222224.4942 273549.6638 363519.8157 320285.117 381824.0117 374557.0137 123283.5846 2.428466205 2.762073493 1.802547313 2.218865266 2.948647354 2.597954285 3.097119643 3.038174261 1 16.91162119 3.265447991 24.96455726 2.64423797 2.300034003 0.016959745 0.636192703 678.829056 630278.6227 0.181463948 0.234203162 1842.671805 -3.265447991 -0.344203967 YREWHHFLVVNMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YREWHHFLVVNMK 13 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 93.958 0.0034678 690910000 924050 759130 463640 578640 434910 404060 745160 857810 985150 FALSE TRUE 801934.4513 754143.225 687857.8548 710029.056 426256.1419 419604.4497 672894.4979 674374.007 868686.6893 0.923157292 0.868141799 0.791836531 0.817359198 0.490690311 0.483033129 0.774611268 0.776314424 1 19.72847641 4.018625781 1.769036704 0.711610804 0.906325342 0.188809828 0.149849072 0.69230757 4.158861364 0.047371088 0.140791592 10438.20402 -4.018625781 0.194714538 YREYS(ph)PPYAPSHQQYPPSHATPLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YREYSPPYAPSHQQYPPSHATPLPK 25 1 Q9UPT8 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 YREYS(0.985)PPYAPS(0.015)HQQYPPSHATPLPK 119.65 0.00026708 275840000 585650 419170 187790 278480 450120 420840 525940 578100 315660 TRUE FALSE 508254.8687 416416.4447 278605.8721 341713.1403 441163.4926 437029.9871 474934.4198 454477.8138 278343.0344 1.826001753 1.496054843 1.000944294 1.227669092 1.584963294 1.570112893 1.706291737 1.632797511 1 18.08650445 3.217649485 24.9966312 1.534702049 1.367786303 0.02668384 0.28074748 694.9356896 830706.1727 0.08751608 0.099337196 1650.629052 -3.217649485 -0.166915746 YREYSPPYAPS(ph)HQQYPPSHATPLPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YREYSPPYAPSHQQYPPSHATPLPK 25 1 Q9UPT8 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 YREYS(0.072)PPYAPS(0.928)HQQYPPSHATPLPK 143.01 2.02E-07 172390000 372320 242990 126160 224600 309480 250460 316660 333740 225540 TRUE FALSE 323116.9687 241393.7827 187171.398 275598.8628 303321.9535 260095.3583 285950.3619 262372.2982 198876.9181 1.624708245 1.213784812 0.941141887 1.385776014 1.525174245 1.30782074 1.43782579 1.31926973 1 17.60151632 1.241838621 6.112594201 0.988876003 1.337675751 0.257804419 0.183607577 0.191419132 28.54255892 0.278400162 0.046278077 17.45173544 -1.241838621 0.348799748 YRGDYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YRGDYDR 7 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;; 116.25 0.0050141 1928100000 2327750 1891920 1148810 1376300 1810680 2049700 1768270 2052110 1762030 FALSE TRUE 2020131.94 1879491.853 1704378.359 1688809.95 1774651.011 2128553.285 1596783.448 1613282.246 1553724.821 1.300186438 1.209668423 1.096962819 1.086942764 1.142191324 1.369968 1.027713161 1.038332029 1 20.56729958 2.072283112 24.99975289 1.025231363 1.189634421 0.484408519 0.086497277 39.07898791 13514.86577 0.036410674 0.024548071 118.1090324 -2.072283112 0.164403058 YRLEVGIQAMEHLIHVLQTDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YRLEVGIQAMEHLIHVLQTDR 21 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ; 223.89 2.18E-25 421450000 256200 179840 103484 131474 151950 169232 182663 199238 114929 FALSE TRUE 222342.5209 178658.6192 153529.2085 161327.1812 148926.4923 175742.4645 164948.3704 156632.5042 101342.2245 2.193977109 1.762923796 1.514957948 1.591904874 1.469540391 1.734148479 1.627637158 1.545579889 1 16.62887588 7.999985774 0.814926343 1.499482948 198.8249356 0.575271205 0.192498296 419.7677293 1.366434059 0.06691863 153120.419 99996724.4 -7.999985774 197.3254527 YRPAS(ph)ASVSALIGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YRPASASVSALIGGR 15 1 P46108-2 P46108-2 CRK Adapter molecule crk 1 YRPAS(0.823)AS(0.132)VS(0.045)ALIGGR;YRPAS(1)ASVSALIGGR;YRPAS(1)ASVSALIGGR 209.73 1.36E-09 1511600000 446200 585230 406927 435750 680590 811880 651350 653220 744060 TRUE FALSE 387233.5395 581385.5856 603718.2583 534693.6975 667047.5906 843113.549 588182.1773 513533.9864 656098.0744 0.590206792 0.886126035 0.920164655 0.814960016 1.01668884 1.28504195 0.896485145 0.782709181 1 19.32355196 5.177036054 1.252892839 0.955664161 2.83E-13 0.418368601 0.136544344 4.444421612 2.860793244 0.043129223 7.141156933 150326.6758 -5.177036054 -0.955664161 YRPCS(ph)LGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YRPCSLGR 8 1 P40938;P40938-2 P40938 RFC3 Replication factor C subunit 3 1 YRPCS(1)LGR 55.806 0.073642 135080000 156410 158970 106980 125080 162680 173530 153360 171930 181170 TRUE FALSE 135740.0222 157925.7156 158715.8858 153481.3257 159442.9863 180205.8114 138487.1708 135164.1075 159752.289 0.849690625 0.988566215 0.993512436 0.960745706 0.998063861 1.128032734 0.866886927 0.846085576 1 17.28547708 YRPDWTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YRPDWTR 7 1 F5H8D7;P18887 F5H8D7 XRCC1 DNA repair protein XRCC1 0 ; 77.046 0.035667 305080000 262080 271280 120553 179875 274710 280440 223823 292340 294100 FALSE TRUE 227445.464 269497.9438 178852.834 220718.368 269243.8085 291228.7083 202116.6799 229825.366 259331.833 0.877044138 1.039201168 0.689667874 0.851104029 1.038221206 1.122996374 0.77937474 0.886221191 1 17.98443978 YRPETK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YRPETK 6 1 P62424;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 ;;;;; 128.38 0.015185 7714380000 7567450 7262090 4578880 5824340 5831180 5727550 8455260 8899520 8542570 FALSE TRUE 6567392.309 7214384.853 6793241.683 7146845.416 5715150.927 5947892.555 7635270.187 6996426.904 7532677.106 0.871853687 0.957745135 0.901836304 0.948778942 0.758714445 0.789612042 1.013619737 0.928810144 1 22.84473126 2.221750217 24.99997201 0.971343739 0.87512255 0.381326631 0.065197595 306.3082616 455529.9677 0.028354309 0.019174313 166.6288575 -2.221750217 -0.096221189 YRPLFDYFLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YRPLFDYFLK 10 1 A0A0A0MSX9;P41252;J3KR24;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 152.04 1.71E-05 611790000 1402370 1690730 1024770 1234280 1691260 1525800 1694920 1983840 2102600 FALSE TRUE 1217043.251 1679623.483 1520352.2 1514542.139 1657607.235 1584498.513 1530546.919 1559611.254 1854033.023 0.656430191 0.905929648 0.820024336 0.816890595 0.89405486 0.854622595 0.825523009 0.841199285 1 20.82223551 4.746056064 24.75821979 0.862550254 0.656430078 0.592413049 0.055327043 568.7776587 1878677.548 0.012918922 0.130454964 55725.7682 -4.746056064 -0.206120175 YRPYDGAASAYAQNYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YRPYDGAASAYAQNYR 16 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 0 ;;;; 221.46 9.62E-15 1947200000 858556 935041 576172 645303 872913 1011420 803329 880586 852573 FALSE TRUE 745095.6493 928898.6541 854810.7064 791828.909 855543.7391 1050329.982 725422.2772 692279.5366 751782.7912 0.991104955 1.235594463 1.137044791 1.053268202 1.13801985 1.397118947 0.964935997 0.92085047 1 19.51995637 2.045879079 24.9999662 0.951207154 1.157601695 0.42122938 0.108610585 106.8550152 58225.89574 0.043070921 0.029038397 111.142223 -2.045879079 0.206394541 YRQDDDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YRQDDDQR 8 1 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;; 135.71 0.00074973 1527180000 2171230 1952390 1162160 1485210 1642920 2180920 2009180 2087550 1945930 FALSE TRUE 1884296.454 1939564.622 1724184.463 1822449.631 1610229.106 2264821.404 1814330.033 1641143.678 1715884.372 1.098148852 1.130358579 1.004837209 1.062105151 0.938425183 1.319914932 1.057373132 0.956441882 1 20.71052091 1.867754271 5.605882808 0.979714011 1.089628871 0.181264977 0.098214721 0.373684795 15.05214924 0.049847915 0.025903607 73.74868335 -1.867754271 0.10991486 YRS(ph)PEPDPYLSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YRSPEPDPYLSYR 13 1 H3BUL5;H3BVF8;P49761-3;P49761-1;P49761;H3BRT8;H3BQR7;H3BV35;H3BRK0;H3BQG1;P49761-2 H3BUL5 CLK3 Dual specificity protein kinase CLK3 1 YRS(1)PEPDPYLSYR;YRS(1)PEPDPYLSYR;YRS(1)PEPDPYLSYR;YRS(1)PEPDPYLSYR 192.65 1.53E-06 8176200000 4109160 3430520 2333960 2587940 3466850 3797880 3217390 3565600 3777530 TRUE FALSE 3566124.095 3407984.688 3462670.863 3175571.331 3397866.468 3943986.901 2905368.013 2803124.188 3330954.707 1.070601197 1.023125497 1.039543064 0.9533517 1.020087863 1.184040988 0.872232819 0.841537767 1 21.66750431 2.197724509 24.9996373 0.890105833 1.041289227 0.476169586 0.070322929 120.589527 73823.39374 0.028544588 0.019244995 157.6610841 -2.197724509 0.151183394 YRS(ph)PYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YRSPYR 6 1 Q14498-3 Q14498-3 RBM39 RNA-binding protein 39 1 Y(0.006)RS(0.993)PY(0.001)R;Y(0.001)RS(0.996)PY(0.003)R 69.423 0.056649 837150000 315560 282660 189644 298640 276210 329200 270300 304500 473740 TRUE FALSE 273857.9465 280803.1878 281356.4727 366450.7764 270713.9614 341864.537 244086.3476 239385.0446 417734.9969 0.655578174 0.672204124 0.673528612 0.877232645 0.648051907 0.818376577 0.58430907 0.573054799 1 18.67222849 3.966325769 24.82002444 0.724206348 0.666134725 0.058895195 0.131956657 2208.787618 1628018.884 0.035225161 0.06106831 9253.920595 -3.966325769 -0.058071622 YRS(ph)PYSGPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YRSPYSGPK 9 1 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23 Q14498-2 RBM39 RNA-binding protein 39 1 YRS(0.769)PYS(0.231)GPK;Y(0.001)RS(0.969)PY(0.004)S(0.026)GPK;YRS(0.786)PY(0.001)S(0.213)GPK;Y(0.072)RS(0.92)PY(0.008)SGPK;Y(0.217)RS(0.782)PYSGPK 138.71 0.00033928 9552800000 8737220 6964200 4774210 5742610 6577350 5665270 7845410 9065000 8164150 TRUE FALSE 7582574.24 6918451.712 7083033.925 7046557.371 6446473.603 5883216.603 7084563.346 7126520.294 7198993.488 1.053282553 0.961030417 0.983892253 0.978825357 0.895468737 0.81722766 0.984104703 0.989932871 1 22.77936378 6.99040988 0.957917193 0.946886004 9.546694592 0.259176371 0.055328856 238.0058864 3.519850578 0.019307869 4330.015719 9781599.558 -6.99040988 8.599808588 YRSDS(ph)QDEVEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YRSDSQDEVEK 11 1 H0YBZ4;Q15390-2;Q15390;H7C5V5;H0YF01 H0YBZ4 MTFR1 Mitochondrial fission regulator 1 1 YRS(0.003)DS(0.997)QDEVEK 135.47 0.0013015 0 731520 387610 263950 345870 421140 356540 518380 589260 502710 TRUE FALSE 634847.7786 385063.7644 391597.1029 424405.0698 412760.1379 370256.3245 468107.5874 463251.3346 443280.1965 1.432159126 0.868668999 0.883407619 0.957419423 0.93114951 0.835264755 1.056008347 1.04505308 1 18.75785939 4.744849053 24.99107709 0.954212551 1.432159338 0.813872619 0.072826046 341.7758704 1358226.039 0.019868766 0.181428862 55571.10759 -4.744849053 0.477946787 YRSPYS(ph)GPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YRSPYSGPK 9 1 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23 Q14498-2 RBM39 RNA-binding protein 39 1 YRS(0.006)PYS(0.994)GPK;YRS(0.278)PYS(0.722)GPK;YRS(0.091)PYS(0.909)GPK 157.74 0.00017842 7947390000 3309070 2599220 1783180 2116270 2453970 2131730 2795260 3274010 2906700 TRUE FALSE 2871768.015 2582145.553 2645531.812 2596801.449 2405140.798 2213739.033 2524176.115 2573888.44 2563073.237 1.120439312 1.00744119 1.032171759 1.013159285 0.938381613 0.863704946 0.98482403 1.004219623 1 21.28944327 5.589996788 0.751707693 0.966836323 1.520783039 0.526337354 0.044866733 7.999875549 1.358866445 0.018921801 5.019866768 389042.2677 -5.589996788 0.553946716 YRVPDVLVADPPIAR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YRVPDVLVADPPIAR 15 1 Q14697;F5H6X6;Q14697-2 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 72.446 0.037136 1258840000 1922760 1673350 996990 1323800 1735650 2350240 1391440 1495060 1255400 FALSE TRUE 1668662.394 1662357.654 1479137.699 1624389.023 1701113.961 2440655.254 1256498.363 1175353.054 1106988.042 1.507389719 1.501694319 1.336182183 1.467395275 1.536704911 2.204771109 1.135060466 1.061757678 1 20.07820821 2.029505436 24.99811169 1.054225178 1.576842692 0.53867727 0.2307643 154.9619698 131288.9568 0.095908102 0.064660332 107.0299778 -2.029505436 0.522617514 YS(ph)DGSIALDIFGPQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSDGSIALDIFGPQK 15 0 Q12923-3;Q12923;Q12923-4;Q12923-2 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 Y(0.281)S(0.359)DGS(0.359)IALDIFGPQK 69.345 0.020636 0 22672 21664 17192 17910 23828 20543 25090 24493 30487 TRUE FALSE 19675.83776 21521.68776 25506.1087 21976.73924 23353.86942 21333.3025 22656.77566 19255.36255 26882.86159 0.731910094 0.800572799 0.948786967 0.817499996 0.868727064 0.793565165 0.842796277 0.716269081 1 14.7143991 4.240572684 0.006390425 1.641922595 6.05E-05 0.03568926 0.086170016 158831.9979 392.5948878 49516.31017 51359.91715 17400.93899 -4.240572684 -1.641862132 YS(ph)GAYGASVSDEELK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YSGAYGASVSDEELK 15 0 C9JRZ6;Q9NX63;A0A286YEX5;F8WAR4 C9JRZ6 CHCHD3 MICOS complex subunit MIC19 1 YS(1)GAYGASVSDEELK;YS(1)GAYGASVSDEELK;YS(0.999)GAYGAS(0.001)VSDEELK;YS(1)GAYGASVSDEELK 279.19 1.25E-33 415916000 804120 655420 578770 859120 829020 666940 622960 1034320 1433640 TRUE FALSE 697853.5046 651114.5029 858665.1079 1054196.327 812524.124 692597.6134 562545.4351 813138.7171 1264156.712 0.55203085 0.515058376 0.679239448 0.833912692 0.642740031 0.547873224 0.444996597 0.643226199 1 20.26974389 1.247173537 5.233487223 1.019646713 0.605137946 0.581932482 0.10504195 0.120605702 9.113164444 0.178091794 0.028533329 17.6674364 -1.247173537 -0.414508767 YS(ph)GGNYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSGGNYR 7 0 P98179 P98179 RBM3 RNA-binding protein 3 1 Y(0.001)S(0.999)GGNYR 66.504 0.071008 128400000 92337 87294 72048 112550 109900 96546 96628 121820 261820 TRUE FALSE 80134.4315 86720.55997 106890.6538 138106.1977 107713.205 100260.1871 87257.03143 95769.741 230867.9379 0.347100737 0.375628425 0.462994796 0.59820432 0.466557661 0.434275058 0.377952141 0.414824778 1 17.81670831 1.237240636 24.99989539 1.000000681 0.436232449 0.867599987 0.069399629 12.46204518 235933.2931 0.111429845 0.018390771 17.26794418 -1.237240636 -0.563768232 YS(ph)PPAISPLVSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSPPAISPLVSEK 13 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 YS(1)PPAISPLVSEK;YS(1)PPAISPLVSEK 135.37 8.89E-05 230170000 310010 261825 237326 297930 277371 251560 316090 362790 777960 TRUE FALSE 269041.393 260105.0543 352097.6474 365579.5601 271851.8598 261237.676 285435.6405 285210.1817 685990.4551 0.392194077 0.379167162 0.513269018 0.532922226 0.396291024 0.380818237 0.416092729 0.415764067 1 19.38782898 1.237751543 24.99968458 1.000000663 0.429056481 0.919384137 0.053200764 5.541084235 171107.059 0.081399282 0.01391893 17.28827026 -1.237751543 -0.570944182 YS(ph)PPRDDDKVDNQAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 164.02 7.85E-07 824480000 2847700 1803980 1838530 1741700 1808440 1096690 2635710 3012600 2484120 TRUE FALSE 2471369.23 1792129.537 2727649.258 2137179.605 1772455.582 1138880.374 2380099.25 2368378.934 2190450.164 1.128247185 0.818155814 1.245245979 0.975680543 0.809174119 0.519929827 1.086579959 1.081229317 1 21.06279596 4.780107865 21.22014817 0.952842542 1.128250943 0.07893641 0.196866734 10083.98466 5149579.22 0.0502716 11.73082175 60270.92609 -4.780107865 0.175408401 YS(ph)PQSLTDPQIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YSPQSLTDPQIR 12 0 Q9ULL0 Q9ULL0 KIAA1210 Uncharacterized protein KIAA1210 1 YS(0.999)PQSLTDPQIR;YS(0.999)PQS(0.001)LTDPQIR;YS(0.988)PQS(0.008)LT(0.004)DPQIR;YS(0.999)PQS(0.001)LTDPQIR;Y(0.038)S(0.923)PQS(0.037)LT(0.001)DPQIR 224.52 2.08E-11 919624000 1630170 1757600 1076713 1333310 1884600 1800560 1641340 1960060 1797370 TRUE FALSE 1414738.904 1746054.21 1597415.008 1636058.414 1847100.147 1869828.708 1482163.099 1540916.422 1584886.966 0.892643409 1.101690056 1.007904691 1.032287128 1.165445982 1.179786791 0.935185367 0.972256353 1 20.59594852 2.197273368 24.99997054 0.96837984 1.065755006 0.225411365 0.082181413 219.5095064 132914.3968 0.033967786 0.022901351 157.4973924 -2.197273368 0.097375166 YS(ph)PRHS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YSPRHSR 7 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 2 Y(0.013)S(0.987)PRHS(1)R;Y(0.017)S(0.983)PRHS(1)R;Y(0.213)S(0.787)PRHS(1)R;Y(0.201)S(0.799)PRHS(1)R;Y(0.184)S(0.816)PRHS(1)R;Y(0.018)S(0.982)PRHS(1)R 84.17 0.012372 33770786000 4016750 3444872 2002826 2573358 3145042 3332367 3254797 3878971 2677821 TRUE FALSE 3485926.31 3422242.409 2971399.353 3157678.265 3082461.817 3460565.315 2939147.288 3049483.238 2361252.052 1.476304195 1.4493338 1.258399903 1.337289792 1.305435315 1.465563709 1.24474102 1.291468751 1 21.17112062 0.592716141 1.09832354 7.91E-21 1.370460148 0.675650023 0.079469002 3.815360526 1.330597968 8.656765299 0.024998988 3.914859145 -0.592716141 1.370460148 YS(ph)PRHS(ph)RS(ph)R ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSPRHSRSR 9 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 3 Y(0.094)S(0.906)PRHS(1)RS(1)R 62.357 0.054907 718300000 1136100 1016100 295660 269080 761890 826990 716430 978280 118820 TRUE FALSE 985961.5065 1009425.172 438642.1649 330178.7266 746729.8796 858804.8404 646950.7289 769082.435 104773.235 9.410432988 9.634380122 4.18658606 3.151365201 7.127105314 8.196796069 6.174770962 7.340447542 1 16.67691069 4.250949942 24.96852902 5.629277016 9.522409395 0.391734359 2.1534986 246.4633386 496694.5082 0.544568992 1.418694547 17821.73338 -4.250949942 3.893132379 YS(ph)PS(ph)QNSPIHHIPSRR ddPTM_MDA-MB-175_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 Y(0.236)S(0.761)PS(0.732)QNS(0.271)PIHHIPS(0.001)RR 86.539 0.023709 438570000 231840 192220 85425 97204 192630 182180 197960 216150 45265 TRUE FALSE 201201.7566 190957.2942 126736.8157 119275.6539 188797.0399 189188.5825 178761.8697 169928.0046 39913.82327 5.040904131 4.784239608 3.175261234 2.988329459 4.730116647 4.739926346 4.478695726 4.257372275 1 15.28460086 1.238514681 23.48795603 0.999993672 4.253328876 0.695062564 0.681461229 0.319965373 159446.0045 0.988902761 0.177189683 17.31867573 -1.238514681 3.253335204 YS(ph)PSQNS(ph)PIHHIPSR ddPTM_MDA-MB-175_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(0.094)S(0.905)PS(0.002)QNS(0.999)PIHHIPSR;Y(0.061)S(0.936)PS(0.003)QNS(1)PIHHIPSR;Y(0.152)S(0.548)PS(0.304)QNS(0.995)PIHHIPSR;YS(0.739)PS(0.261)QNS(1)PIHHIPSR;Y(0.397)S(0.602)PS(0.011)QNS(0.99)PIHHIPSR;Y(0.013)S(0.986)PS(0.001)QNS(1)PIHHIPSR;Y(0.104)S(0.716)PS(0.181)QNS(1)PIHHIPSR;Y(0.236)S(0.746)PS(0.018)QNS(1)PIHHIPSR 180.04 3.05E-07 21824280000 3687821 3007125 2243863 3020616 3220251 3201497 2984514 3296240 5512710 TRUE FALSE 3200466.111 2987370.998 3329002.652 3706493.03 3156174.305 3324660.661 2695076.292 2591364.727 4861003.704 0.658396147 0.61455847 0.684838534 0.762495414 0.649284489 0.683945305 0.554427944 0.533092523 1 22.2128228 1.228052712 24.99997827 1.000000752 0.639047483 0.745018854 0.065674171 262.0801283 623487.8633 0.255802648 0.018377596 16.90646119 -1.228052712 -0.360953269 YS(ph)PSQNS(ph)PIHHIPSRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YSPSQNSPIHHIPSRR 16 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 Y(0.004)S(0.984)PS(0.012)QNS(1)PIHHIPSRR;Y(0.016)S(0.928)PS(0.057)QNS(1)PIHHIPSRR;YS(0.738)PS(0.261)QNS(1)PIHHIPSRR;YS(0.991)PS(0.009)QNS(1)PIHHIPSRR;Y(0.001)S(0.919)PS(0.08)QNS(1)PIHHIPSRR;Y(0.001)S(0.828)PS(0.171)QNS(1)PIHHIPSRR 176.84 3.10E-09 5422260000 2093620 1748850 745253 919887 1698010 1780850 1701070 1818240 530515 TRUE FALSE 1816942.812 1737361.689 1105659.844 1128761.403 1664222.923 1849360.452 1536100.493 1429423.526 467798.1211 3.884031873 3.713913355 2.363540582 2.412924191 3.557566498 3.953330226 3.283682478 3.05564187 1 18.83552654 4.359977788 7.320146414 2.90742326 3.838316226 0.201033001 0.807142083 0.37793678 22.18489852 0.205775199 0.550952304 22907.50488 -4.359977788 0.930892966 YS(ph)PSQNSPIHHIPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YSPSQNSPIHHIPSR 15 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 YS(0.998)PS(0.002)QNSPIHHIPSR;YS(0.936)PS(0.064)QNSPIHHIPSR;YS(0.786)PS(0.214)QNSPIHHIPSR;YS(0.86)PS(0.14)QNSPIHHIPSR 205.45 2.83E-09 4480420000 2452270 2206790 1455800 1893500 2239180 2103130 2407570 2771260 2842670 TRUE FALSE 2128196.306 2192293.451 2159829.749 2323448.115 2194624.699 2184038.772 2174084.232 2178647.615 2506612.791 0.849032732 0.874603951 0.861652728 0.926927415 0.87553399 0.87131079 0.867339479 0.869160017 1 21.25730772 1.236922812 24.99927133 1.000000155 0.875045663 0.793036228 0.020155424 18.97741009 289576.4319 0.030465024 0.004907104 17.25531184 -1.236922812 -0.124954492 YS(ph)PSQNSPIHHIPSRR ddPTM_MDA-MB-175_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 YS(0.996)PS(0.004)QNSPIHHIPSRR;Y(0.002)S(0.965)PS(0.033)QNSPIHHIPSRR 148.2 4.49E-07 736830000 376590 266810 127112 182204 296140 284210 269510 299060 113360 TRUE FALSE 326822.6773 265057.3075 188583.7884 223576.203 290247.3934 295143.7426 243372.9617 235108.3463 99958.70994 3.269576784 2.651667951 1.886616869 2.236685559 2.903672862 2.95265658 2.43473492 2.352054628 1 16.60904466 1.116138098 2.146375903 0.087258566 2.601729717 0.630826055 0.385955624 0.742035936 2.571542415 4.134429818 0.109007462 13.06586294 -1.116138098 2.514471151 YS(ph)PTVQTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSPTVQTR 8 0 O60437;K7EKI8 O60437 PPL Periplakin 1 YS(0.995)PT(0.005)VQTR;YS(0.956)PT(0.044)VQTR 150.61 0.00051025 313170000 533770 495360 336700 381400 487040 542240 495530 565330 565960 TRUE FALSE 463230.9421 492105.9475 499529.2462 468002.6993 477348.8569 563100.3237 447473.5769 444438.5789 499052.8535 0.928220205 0.986079819 1.000954594 0.937781832 0.956509623 1.12833805 0.896645663 0.890564147 1 18.92883309 YS(ph)PVSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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 Y(0.001)S(0.834)PVS(0.165)K 69.905 0.096791 898110000 1150500 902830 857270 1158800 919650 892040 1057200 1365800 2107700 TRUE FALSE 998458.51 896899.2503 1271848.639 1421923.251 901350.7643 926357.356 954672.9067 1073734.299 1858530.107 0.537230205 0.482585268 0.684330393 0.765079482 0.484980448 0.498435485 0.51367094 0.577733067 1 20.82573063 1.239158447 7.250710389 1.007959709 0.567694427 0.687922373 0.091467763 0.064527255 21.85163145 0.140251229 0.023925843 17.34436671 -1.239158447 -0.440265282 YSAFQLAPFQDHGLPAVSVDS(ph)PVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSAFQLAPFQDHGLPAVSVDSPVR 24 0 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 YSAFQLAPFQDHGLPAVS(0.151)VDS(0.849)PVR;YSAFQLAPFQDHGLPAVS(0.337)VDS(0.663)PVR 115.27 0.00070577 166045000 98076 94333 62275 80495 105345 126025 81519 131968 102151 TRUE FALSE 85115.00811 93713.32031 92391.3983 98772.62004 103248.8406 130873.2633 73613.29993 103747.6702 90074.82515 0.944936701 1.040394141 1.02571832 1.096561885 1.146256353 1.45293941 0.817246104 1.1517943 1 16.45883633 4.175127405 1.478158184 1.111658844 0.963669647 0.100148036 0.157112074 1.283122284 4.873437417 0.046028716 0.207524299 14966.74658 -4.175127405 -0.147989197 YSALLQEDFAYSGFECWVENEDQIQEPHSCHGSEGPGNRPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSALLQEDFAYSGFECWVENEDQIQEPHSCHGSEGPGNRPR 41 1 Q5VU43-13;Q5VU43-2 Q5VU43-13 PDE4DIP Myomegalin 0 42.064 0.054002 93012000 1589.3 1174.7 1282.6 1120.9 0 2411.8 1627.1 0 0 FALSE TRUE 1379.269978 1166.983318 1902.86965 1375.417477 0 2504.583507 1469.304092 0 0 0 YSAQGER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSAQGER 7 0 O43324;H0YAL7;D6RBD7;C9J1V9;O43324-2 O43324 EEF1E1;EEF1E1-BLOC1S5 Eukaryotic translation elongation factor 1 epsilon-1 0 105.04 0.042237 0 182050 137450 83767 114980 144440 189910 138820 171380 163580 FALSE TRUE 157991.6312 136547.0819 124277.0014 141087.9664 141565.9266 197215.9606 125357.2578 134731.7207 144241.7588 1.095325186 0.946654305 0.861588228 0.978135372 0.981448977 1.367259816 0.869077435 0.93406876 1 17.13812937 4.754874693 22.2773416 0.988809979 1.095325551 0.049652561 0.140954126 2457.363393 3355342.928 0.034853723 0.75661551 56868.88234 -4.754874693 0.106515572 YSASKPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSASKPLK 8 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 81.338 0.021086 2380100000 3239000 2744600 2041240 2684530 2728400 2447170 3501200 4044000 3750400 FALSE TRUE 2810957.943 2726570.542 3028390.492 3294093.567 2674110.178 2541314.213 3161654.163 3179222.07 3307031.984 0.849994181 0.824476617 0.915742728 0.996087604 0.80861334 0.768457706 0.95603979 0.961352078 1 21.65710557 2.030601628 24.58095287 0.972149639 0.864980532 0.418351753 0.06237625 173.7739268 139584.1718 0.027185075 0.018327926 107.3004709 -2.030601628 -0.107169108 YSCPESPSQELGGPLPS(ph)PGPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSCPESPSQELGGPLPSPGPR 21 0 A0A494BZV2;A0A1W2PPU9 A0A494BZV2 1 YSCPESPSQELGGPLPS(1)PGPR 260.13 1.46E-36 184310000 243300 279950 166780 205420 370380 449790 314830 320440 307380 TRUE FALSE 211147.2886 278110.99 247435.3658 252063.7506 363010.1626 467093.7124 284297.8351 251916.3997 271041.8866 0.779020878 1.026081221 0.912904529 0.929980801 1.339313887 1.723326672 1.04890738 0.929437154 1 18.0481563 3.286305119 12.89645808 1.18713437 0.920067645 0.293890597 0.226685382 1.858854845 499.17742 0.073895556 0.095349311 1933.326122 -3.286305119 -0.267066725 YSDESGNMDFDNFISCLVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSDESGNMDFDNFISCLVR 19 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;K7EMQ1 A0A0C4DGQ5 CAPNS1 Calpain small subunit 1 0 147.56 2.42E-07 53012000 34182 34419 17000 25069 29866 25424 28948 31150 36114 FALSE TRUE 29664.76209 34192.89932 25221.25686 30761.29961 29271.72503 26402.07773 26140.62742 24488.81491 31844.64406 0.931546355 1.07374098 0.792009382 0.965980325 0.919204026 0.829090056 0.820879874 0.769008907 1 14.95876313 2.821537899 4.278517857 0.838105686 0.939791867 0.162796178 0.089448623 0.344657343 11.59271531 0.028887753 0.028682386 663.0372061 -2.821537899 0.101686182 YSDFEWLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YSDFEWLR 8 0 O60493-4;O60493;O60493-3 O60493-4 SNX3 Sorting nexin-3 0 ;;; 207.6 0.00014423 1723960000 2613670 2628700 1621290 1945780 2603630 2604990 2370030 2660430 3041360 FALSE TRUE 2268266.887 2611431.897 2405351.267 2387599.088 2551822.857 2705205.651 2140184.855 2091517.748 2681813.886 0.845795788 0.973755826 0.896912079 0.890292612 0.951528691 1.008722367 0.798036309 0.779889223 1 21.35477769 2.222111881 24.99869756 0.840209821 0.927886894 0.144159722 0.073981299 350.2398461 532288.3436 0.029654716 0.020057812 166.7676776 -2.222111881 0.087677073 YSDPGPVYDCLVWHDGEVWR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YSDPGPVYDCLVWHDGEVWR 20 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ;;; 248.35 3.08E-30 951895000 462581 487583 298789 376386 490211 497125 424949 534946 534522 FALSE TRUE 401449.7488 484380.0352 443284.3598 461850.194 480456.7602 516249.7204 383737.5114 420551.9609 471331.4181 0.851735601 1.02768459 0.940493977 0.979884167 1.019360776 1.095300887 0.814156444 0.892263797 1 18.84638233 2.228204919 24.99997078 0.89641657 0.986854714 0.209167422 0.076342007 302.2381381 729634.5937 0.030337843 0.020705278 169.1238743 -2.228204919 0.090438144 YSEEGLS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSEEGLSPSK 10 0 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9;A0A0C4DGI9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 YSEEGLS(0.984)PS(0.016)K;YSEEGLS(0.911)PS(0.089)K 114.93 0.0013528 449010000 870180 765840 527940 697700 848020 606840 849860 1013310 885600 TRUE FALSE 755183.5082 760809.1466 783253.5499 856123.4487 831146.0611 630185.5275 767440.708 796621.5421 780905.3769 0.967061478 0.974265473 1.003006988 1.096321621 1.064336456 0.806993454 0.982757618 1.020125569 1 19.57478822 YSEKEDKYEEEIK ddPTM_MDA-MB-175_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 ;;; 200.44 6.18E-08 4504440000 4489120 3040810 3867830 2829380 2551160 1607580 4855180 5352390 3412720 FALSE TRUE 3895871.418 3020834.719 5738325.525 3471833.973 2500396.907 1669424.643 4384325.391 4207823.051 3009272.129 1.294622504 1.003842321 1.906881558 1.153712202 0.830897572 0.554760278 1.456938822 1.398285987 1 21.52098315 3.499472778 24.96525321 1.088324558 1.390039599 0.182360878 0.336004572 1587.945242 1773631.663 0.099145472 0.145682715 3158.441068 -3.499472778 0.301715041 YSESNFS(ph)VDDQDLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSESNFSVDDQDLSR 15 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 YSESNFS(1)VDDQDLSR;YSESNFS(1)VDDQDLSR 372.88 1.23E-97 821270000 519510 561930 331510 341760 563080 549060 577730 612320 588260 TRUE FALSE 450855.4372 558238.6448 491829.3448 419361.8315 551875.8096 570182.6935 521701.8335 481380.1331 518716.5729 0.869174923 1.076192036 0.948165859 0.808460445 1.063925539 1.099218192 1.00575509 0.928021502 1 18.98458694 YSFLDLFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSFLDLFR 8 0 O95528 O95528 SLC2A10 "Solute carrier family 2, facilitated glucose transporter member 10" 0 98.523 0.019593 0 119740 152990 69205 98758 154990 137440 165420 182390 167750 FALSE TRUE 103916.0556 151984.9986 102672.7695 121182.5133 151906.0022 142727.4057 149377.5939 143387.3179 147918.7861 0.702521014 1.027489494 0.69411582 0.819250323 1.026955441 0.964903847 1.009862221 0.969365161 1 17.17444576 3.24625075 24.83768184 0.990818507 0.817981041 0.496693595 0.091562777 135.9754043 439172.1316 0.024622144 0.031176179 1762.993659 -3.24625075 -0.172837466 YSFLQFDPAPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSFLQFDPAPR 11 0 P67775;P62714;P67775-2;H0YBN9 P67775 PPP2CA;PPP2CB Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform 0 80.755 0.054769 345840000 414060 405310 274790 322600 388640 416490 402250 433980 493540 FALSE TRUE 359340.9219 402647.4919 407679.3631 395851.2606 380906.8244 432512.6398 363239.8569 341176.7542 435194.2634 0.825702341 0.925213234 0.93677559 0.909596688 0.875256998 0.9938381 0.834661409 0.783964273 1 18.73130001 YSFQTHDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSFQTHDR 8 0 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 0 97.431 0.0082369 60175000 138950 135360 91541 85302 128540 148090 149830 146570 163670 FALSE TRUE 120587.4054 134470.8112 135810.5338 104671.1229 125982.3055 153787.1181 135299.5097 115227.1461 144321.1191 0.835549268 0.931747288 0.941030216 0.72526546 0.872930492 1.06558984 0.937489333 0.79840807 1 17.1389229 2.973072699 24.96998674 0.930290899 0.860734362 0.185250374 0.088873463 1664.328493 1543350.869 0.030255008 0.030340214 939.8806302 -2.973072699 -0.069556537 YSGGNYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YSGGNYR 7 0 P98179 P98179 RBM3 RNA-binding protein 3 0 ;;;;; 139.27 0.0062933 7728730000 6086820 7091100 3815170 4654080 6133470 6298820 5691130 6603910 6235670 FALSE TRUE 5282431.315 7044518.097 5660198.973 5710859.997 6011425.947 6541139.681 5139205.089 5191715.238 5498496.196 0.960704732 1.281171769 1.029408546 1.03862216 1.093285461 1.189623389 0.934656478 0.944206389 1 22.39060567 2.220980831 24.99953336 0.955369351 1.100951647 0.350572477 0.089205677 245.8325967 349586.4921 0.034387471 0.023242127 166.3339233 -2.220980831 0.145582296 YSGGNYRDNYDN ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSGGNYRDNYDN 12 1 P98179 P98179 RBM3 RNA-binding protein 3 0 ; 139.31 0.00048127 714250000 1079950 1206350 463120 378360 944000 1103270 947260 1063790 309250 FALSE TRUE 937231.8713 1198425.407 687086.381 464272.4209 925216.2469 1145713.511 855394.871 836306.7869 272690.8173 3.436976282 4.394813948 2.519653532 1.702559791 3.392913102 4.201511155 3.136867165 3.066868167 1 18.05690659 4.23262422 24.99032046 2.811806164 3.915895178 0.224678212 0.91267842 210.9272312 887949.9404 0.239181499 0.519639463 17085.36337 -4.23262422 1.104089014 YSGSYNDYLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSGSYNDYLR 10 0 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ; 173.37 7.98E-06 2180600000 1589370 1807750 964720 1199330 1865180 1746420 1592420 1701000 1850110 FALSE TRUE 1379330.728 1795874.771 1431261.819 1471656.207 1828066.567 1813605.907 1437987.353 1337254.387 1631392.103 0.845493076 1.100823504 0.877325455 0.902086141 1.120556219 1.111692219 0.881448029 0.819701398 1 20.63767214 2.115410372 23.51090331 0.882750488 0.994505578 0.135814132 0.107044734 7.98911372 1591.699209 0.043705306 0.029466124 130.4398743 -2.115410372 0.111755091 YSGTLNLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 9 YSGTLNLDR 9 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;;; 226.64 5.33E-07 30195430000 6004770 7164190 4673550 4638780 7705960 8960520 7500060 7557280 8080950 FALSE TRUE 5211224.43 7117127.964 6933694.412 5692085.898 7552626.472 9305237.003 6772705.336 5941214.483 7125629.297 0.731335327 0.998806936 0.97306415 0.798818695 1.059924136 1.305882837 0.950471187 0.833781023 1 22.764586 3.224833092 24.9976292 1.01331099 0.89128187 0.222999938 0.140043826 494.909187 901220.2915 0.04660471 0.053116823 1678.158946 -3.224833092 -0.12202912 YSHDFNFHINYGDLGFLGPEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSHDFNFHINYGDLGFLGPEDLR 23 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 75.646 0.009797 288390000 279180 261930 170930 255910 276370 359800 243130 256720 214070 FALSE TRUE 242285.6556 260209.3646 253592.3197 314018.2768 270870.7777 373641.7388 219551.29 201822.4258 188762.8885 1.283544968 1.378498532 1.343443734 1.663559397 1.434978983 1.97942372 1.163106222 1.069184878 1 17.52621563 2.021459617 24.98866493 1.06251744 1.508890035 0.527309792 0.197173108 175.0517056 203838.277 0.080437838 0.054226187 105.0653754 -2.021459617 0.446372595 YSHLQPGDHLTDITLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSHLQPGDHLTDITLK 16 0 Q15046;Q15046-2;H3BVA8 Q15046 KARS Lysine--tRNA ligase 0 169.25 3.29E-09 438680000 495600 385210 209900 327080 478970 386520 498910 536640 511590 FALSE TRUE 430105.2043 382679.5301 311408.3421 401348.5131 469439.4341 401389.6745 450525.785 421883.7121 451110.413 0.953436657 0.84830569 0.690315127 0.889690199 1.040630898 0.889781444 0.998704025 0.935211647 1 18.78312106 3.474139591 24.65868625 0.965871463 0.825373619 0.435514002 0.074332766 68.09945911 563183.4107 0.020752249 0.026948474 2979.473942 -3.474139591 -0.140497844 YSHSGS(ph)SS(ph)PDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSHSGSSSPDTK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 YSHS(0.001)GS(0.863)S(0.535)S(0.592)PDT(0.01)K 172.58 5.17E-05 309600000 1185000 885850 539640 692240 749730 796550 1043900 1248200 1099100 TRUE FALSE 1028399.248 880030.793 800611.709 849423.6722 734811.8398 827193.7939 942662.7387 981282.1435 969165.6501 1.061118135 0.908029286 0.826083455 0.876448389 0.75819014 0.853511259 0.972653889 1.012501984 1 19.88638375 2.129531037 4.54542378 1.002990598 0.873798597 0.335123734 0.076439231 0.237672583 8.403138445 0.034072171 0.022318438 134.7507021 -2.129531037 -0.129192001 YSHSGSSS(ph)PDTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 YSHSGSSSPDTK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 YSHSGS(0.001)S(0.018)S(0.981)PDTK;YSHSGS(0.013)S(0.293)S(0.694)PDTK;YSHS(0.013)GS(0.156)S(0.021)S(0.809)PDTK;YSHSGS(0.001)S(0.083)S(0.915)PDTK;YSHSGS(0.422)S(0.013)S(0.565)PDTK;YSHSGS(0.199)S(0.058)S(0.744)PDTK;YS(0.001)HS(0.004)GS(0.005)S(0.203)S(0.787)PDTK 257.21 3.58E-21 3042945000 4468610 4145959 2530476 3996538 4589970 4527770 6275820 7508350 6428290 TRUE FALSE 3878071.866 4118723.922 3754222.658 4904013.036 4498638.577 4701956.242 5667191.942 5902747.783 5668344.879 0.684163005 0.726618442 0.662313733 0.865157844 0.793642355 0.82951132 0.999796601 1.041352971 1 22.43449611 2.545703893 0.631204344 1.083837122 0.684809522 0.853731418 0.051482169 0.3454376 0.322148798 0.089213315 0.044734092 351.3208243 -2.545703893 -0.3990276 YSHSYLS(ph)DS(ph)DTEAKLTETNA ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSHSYLSDSDTEAKLTETNA 20 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 2 Y(0.025)S(0.053)HS(0.287)Y(0.093)LS(0.555)DS(0.825)DT(0.161)EAKLTETNA 78.758 0.0047815 51547000 58016 52072 35291 39198 55400 41741 65167 73708 37690 TRUE FALSE 50349.03861 51729.9356 52357.84564 48098.505 54297.64839 43346.80328 58847.11437 57946.1178 33234.33114 1.514970721 1.556521038 1.575414454 1.447253589 1.633781892 1.30427789 1.770672445 1.743562028 1 15.0203867 1.22814121 24.99773945 0.999998803 1.575873833 0.636331125 0.1349118 302.5293435 725764.0262 0.473674978 0.034303357 16.90990665 -1.22814121 0.575875029 YSHSYLS(ph)DSDTEAK ddPTM_MDA-MB-175_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 267.47 5.55E-25 102440000 165080 132640 89620 110760 128920 115610 162230 179160 157230 TRUE FALSE 143264.2597 131768.6791 132960.5318 135909.7509 126354.7442 120057.5915 146496.9596 140848.0282 138642.4485 1.033336192 0.950420889 0.959017481 0.980289603 0.911371269 0.865951177 1.056653003 1.015908401 1 17.08100951 2.20869232 24.99998763 1.023815146 0.950102594 0.376347109 0.044979347 222.8032564 186486.4573 0.018730488 0.012629874 161.6934099 -2.20869232 -0.073712552 YSHVNKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSHVNKK 7 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 98.418 0.0073208 100360000 375500 308100 188470 250900 202350 257350 378910 436940 305310 FALSE TRUE 325876.7236 306076.0708 279614.7224 307870.6798 198323.6309 267250.421 342163.3665 343503.7813 269216.5996 1.210462966 1.136913813 1.038623632 1.143579854 0.7366694 0.992696667 1.270959395 1.27593834 1 18.03840784 0.962507189 18.85602788 0.466407204 1.104773691 0.038320478 0.157431471 1289.46434 58792.61742 32581.78657 0.040762729 9.1729112 -0.962507189 0.638366487 YSHVQEVQER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 ;;; 155.48 1.26E-05 662000000 678880 667990 421692 428213 638140 731060 635130 659630 690210 FALSE TRUE 589164.2879 663601.9297 625623.6617 525445.3065 625442.2625 759184.3513 573535.1904 518573.2577 608614.1601 0.96804236 1.090349146 1.027947923 0.86334716 1.02764987 1.247398436 0.942362548 0.852055854 1 19.21516837 2.018518985 24.99996447 0.909984993 1.036385821 0.191063394 0.102011749 335.8401567 453370.3031 0.042439447 0.028607362 104.3563751 -2.018518985 0.126400828 YSIAITWGGHHIPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSIAITWGGHHIPK 14 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 110.29 0.00041521 205710000 360510 406680 164640 218390 281870 283230 417490 409900 450840 FALSE TRUE 312867.6901 404008.4923 244260.4547 267978.7874 276261.3385 294126.0414 377001.8841 322246.0748 397542.2088 0.78700496 1.016265653 0.614426467 0.674088893 0.694923287 0.739861164 0.948331713 0.810595876 1 18.60074852 1.420640304 0.992088099 1.0386624 0.759517552 0.265074947 0.118922199 2.227257161 2.2347207 0.644849511 0.043892656 26.34148802 -1.420640304 -0.279144848 YSISLS(ph)PPEQQK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSISLSPPEQQK 12 0 Q15057;A0A0U1RQT1;A0A087X1H5;H7C3K3 Q15057 ACAP2 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2" 1 YSISLS(1)PPEQQK;YSISLS(1)PPEQQK 258.6 1.33E-16 263490000 666290 526130 547380 716510 586480 474590 608460 742790 1811290 TRUE FALSE 578238.0883 522673.8174 812094.7989 879204.5467 574810.1954 492847.7844 549451.6429 583950.1389 1597161.36 0.362041121 0.32725173 0.508461336 0.550479475 0.35989488 0.308577328 0.344017616 0.365617497 1 20.60707864 1.237137395 24.9994255 1.000000742 0.390566853 0.857670154 0.077992922 14.1200682 247933.5669 0.126761005 0.020768906 17.26383971 -1.237137395 -0.609433889 YSISLS(ph)PPEQQKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSISLSPPEQQKK 13 1 Q15057;A0A0U1RQT1;A0A087X1H5;H7C3K3 Q15057 ACAP2 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2" 1 YSIS(0.005)LS(0.995)PPEQQKK 100.43 0.0014743 218730000 384790 298710 255710 280500 293940 211000 367830 480810 379870 TRUE FALSE 333939.0266 296747.7543 379372.2113 344191.8122 288091.1691 219117.3065 332157.9032 377992.5232 334962.2013 0.996945402 0.885914151 1.132582153 1.027554186 0.860070682 0.654155322 0.991628016 1.128463217 1 18.35363878 1.997054508 24.99212964 1.069399 0.925982108 0.167319026 0.127445246 197.3101793 1674156.673 0.056621879 0.037356794 99.3240701 -1.997054508 -0.143416893 YSKEEEMDDMDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSKEEEMDDMDR 12 1 Q9HD45;Q5TB53 Q9HD45 TM9SF3 Transmembrane 9 superfamily member 3 0 135.37 0.00011758 179320000 421400 342680 308530 308730 335640 336180 389810 482520 732120 FALSE TRUE 365710.9223 340428.9125 457736.14 378831.8651 328961.4207 349113.0621 352006.2862 379336.853 645569.6076 0.566493401 0.527331071 0.70904227 0.586817999 0.509567701 0.540782989 0.54526465 0.587600235 1 19.30021313 1.238290897 5.771965038 1.018111145 0.570245936 0.860142823 0.054334452 0.050956 5.88440635 0.090326624 0.013908037 17.30975403 -1.238290897 -0.447865209 YSLS(ph)PSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 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)PS(0.001)K 123.86 0.011159 0 980950 818290 664480 681590 829530 665620 1061400 1056300 1106200 TRUE FALSE 851314.9721 812914.5991 985824.7506 836355.427 813023.9759 691226.8321 958465.5914 830418.4651 975426.2962 0.872761966 0.833394181 1.01066042 0.857425548 0.833506313 0.70864076 0.982612008 0.851339018 1 19.89567334 -0.224553097 1.499807399 9.99999712 0.866649218 0.188617953 0.083306946 164.6121836 6.563679919 4958.670325 0.023339164 0.596275415 0.224553097 -9.133347902 YSNEDTLSVALPYFWEHFDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSNEDTLSVALPYFWEHFDK 20 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 147.9 1.17E-07 408730000 554000 432650 320410 340200 267660 275040 288280 408260 1489800 FALSE TRUE 480787.4963 429807.8937 475361.3477 417447.6096 262334.0897 285620.9668 260322.65 320956.7761 1313677.541 0.36598593 0.327179144 0.361855427 0.317770226 0.199694431 0.21742091 0.19816328 0.244319299 1 20.32517976 1.237113141 24.99984284 1.000000885 0.274525271 0.927245896 0.063454556 10.16989684 175584.6801 0.106783683 0.017489396 17.26287562 -1.237113141 -0.725475613 YSNVSS(ph)IEDSFAMEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSNVSSIEDSFAMEK 15 0 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 1 YSNVS(0.02)S(0.98)IEDSFAMEK;YSNVS(0.042)S(0.958)IEDSFAMEK 185.33 4.48E-07 50877000 179268 142338 87172 127074 147849 104399 204988 211350 174169 TRUE FALSE 155577.2796 141402.9723 129328.6708 155928.0939 144907.0942 108415.2971 185108.2953 166154.4472 153578.9392 1.013011812 0.920718511 0.842098998 1.015296073 0.943534933 0.70592555 1.205297395 1.081883024 1 17.22862086 2.218447832 24.9999988 1.097408093 0.911063835 0.440339969 0.100339884 222.0371853 275987.9764 0.040071689 0.027054156 165.3666133 -2.218447832 -0.186344258 YSPDEMNNS(ph)PNFEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSPDEMNNSPNFEEK 15 0 Q14687;Q14687-2;Q14687-3;H0Y613;H7C3B5 Q14687 GSE1 Genetic suppressor element 1 1 YSPDEMNNS(1)PNFEEK 253.26 1.21E-24 77483000 149870 130540 95660 127380 126340 115830 150740 178500 191000 TRUE FALSE 130064.2998 129682.4741 141921.496 156303.5759 123826.0812 120286.0551 136121.258 140329.1641 168420.1976 0.772260701 0.769993599 0.84266316 0.928057193 0.73522109 0.714202078 0.808224073 0.833208642 1 17.36170564 1.186652488 2.413474591 1.072415763 0.796695495 0.537378345 0.059121758 0.585308704 3.238223463 0.361720309 0.016643558 15.36924338 -1.186652488 -0.275720267 YSPKT(ph)PPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSPKTPPR 8 1 P49792;J3KNE0;A6NKT7;Q7Z3J3;F8VYC4;A0A286YES2;P0DJD0;A0A1W2PNU4;P0DJD1 P49792;F8VYC4 RANBP2;RGPD3;RGPD4;RGPD1;RGPD2 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4;RANBP2-like and GRIP domain-containing protein 1;RANBP2-like and GRIP domain-containing protein 2 1 YS(0.095)PKT(0.905)PPR;YS(0.004)PKT(0.996)PPR 84.198 0.02849 572480000 834540 649560 402660 511040 748520 678180 807640 912330 613160 TRUE FALSE 724253.4245 645292.9976 597387.7228 627079.4428 733625.9165 704270.0234 729315.1971 717235.3293 540672.9233 1.339540771 1.193499748 1.104896689 1.159812921 1.356875636 1.302580531 1.348902757 1.326560474 1 19.04439658 3.256221523 24.89596989 1.28235472 1.192260481 0.066704108 0.116641782 512.50159 722451.3884 0.033548161 0.043212829 1803.937649 -3.256221523 -0.090094239 YSPPAIS(ph)PLVSEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YSPPAISPLVSEK 13 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 YSPPAIS(1)PLVSEK;YSPPAIS(1)PLVSEK;YSPPAIS(1)PLVSEK 183 1.13E-05 262382000 485590 483570 339161 436139 493870 453979 607600 725650 643390 TRUE FALSE 421418.0512 480393.3968 503180.394 535171.0259 484042.9532 471443.8659 548675.0455 570475.3945 567329.1672 0.74281048 0.846763087 0.886928477 0.943316609 0.85319596 0.83098824 0.967119403 1.005545682 1 19.11382651 -2 0.072298376 1.908693863 0.457389806 0.643864353 0.049582525 374.1361703 2.589079562 58.63754649 11.28195693 0.01 2 -1.451304057 YSPS(ph)QNSPIHHIPSRR ddPTM_MDA-MB-175_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 YS(0.03)PS(0.97)QNSPIHHIPSRR;YS(0.454)PS(0.546)QNSPIHHIPSRR 145.52 5.70E-07 460350000 229320 194065 81153 123285 199488 211756 173047 163883 88607 TRUE FALSE 199014.781 192790.1742 120398.8622 151278.7435 195518.5791 219902.3903 156264.9286 128837.8958 78131.9814 2.547161577 2.46749373 1.540967733 1.936194895 2.502414192 2.814499087 2.000012361 1.64897771 1 16.25362558 1.489677566 1.943991684 0.923619261 2.267558165 0.57877966 0.358657622 0.365810113 2.217896336 0.792130784 0.108617684 30.88001954 -1.489677566 1.343938904 YSPSQNS(ph)PIHHIPSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 YSPSQNSPIHHIPSR 15 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 YSPSQNS(1)PIHHIPSR;YSPSQNS(1)PIHHIPSR;YSPSQNS(1)PIHHIPSR;YSPS(0.004)QNS(0.995)PIHHIPSR;YSPSQNS(1)PIHHIPSR;YSPSQNS(1)PIHHIPSR;YSPS(0.002)QNS(0.998)PIHHIPSR 219.06 1.19E-12 5067130000 886489 698187 466768 593208 741387 772100 638335 825985 994588 TRUE FALSE 769337.2326 693600.5636 692498.566 727904.943 726634.8492 801803.1866 576429.3699 649354.5356 877008.9397 0.877228495 0.790870574 0.789614033 0.829985773 0.828537563 0.91424745 0.657267382 0.740419517 1 19.74223202 2.278692672 24.99964988 0.781060457 0.833202591 0.02425524 0.092581286 452.6802754 281988.5298 0.034415564 0.026657833 189.973346 -2.278692672 0.052142134 YSPSQNS(ph)PIHHIPSRR ddPTM_MDA-MB-175_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 218.72 6.15E-15 1199600000 817570 635280 260220 381323 665250 696430 645210 738790 216182 TRUE FALSE 709526.053 631106.8039 386063.2624 467908.2153 652012.8265 723222.1128 582637.6335 580805.5078 190625.2102 3.72209978 3.310720566 2.025247667 2.454597767 3.420391383 3.793947883 3.056456346 3.046845205 1 17.5403794 4.467834413 24.77605001 2.786638648 3.619255315 0.16496708 0.778134913 298.4682823 796275.3784 0.196857977 0.522418083 29365.29803 -4.467834413 0.832616667 YSPTS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YSPTSPK 7 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPT(0.179)S(0.821)PK;YSPT(0.131)S(0.869)PK;YSPT(0.03)S(0.97)PK;YSPT(0.152)S(0.848)PK;YSPT(0.198)S(0.802)PK 111.31 0.0069314 4007480000 13029200 9949710 7466050 8800570 10224460 9334480 11504960 13355300 11247690 TRUE FALSE 11307358.21 9884349.7 11076656.75 10798873.93 10021013.25 9693583.486 10389210.75 10499373.03 9918000.902 1.14008441 0.996607058 1.116823527 1.088815582 1.010386402 0.977372717 1.047510567 1.058617874 1 23.24161793 3.24225356 24.99099133 1.023842294 1.081458745 0.369051702 0.042972907 120.7096152 816865.8612 0.012394472 0.015384575 1746.841736 -3.24225356 0.057616451 YSPTS(ph)PTYSPT(ph)SPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 2 YSPT(0.002)S(0.997)PT(0.001)YS(0.001)PT(0.5)S(0.499)PK 244 7.69E-17 459450000 1254900 943080 743290 895490 1106900 888740 1084800 1345600 1196600 TRUE FALSE 1089061.785 936884.8454 1102747.53 1098824.691 1084874.856 922930.4029 979596.263 1057853.911 1055139.311 1.032149759 0.887925258 1.045120316 1.041402476 1.028181629 0.874700045 0.928404669 1.002572741 1 20.00900206 YSPTS(ph)PTYSPTS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 2 YSPT(0.001)S(0.998)PT(0.001)YSPT(0.079)S(0.921)PK;YSPT(0.002)S(0.993)PT(0.005)YSPT(0.051)S(0.949)PK 258.68 3.17E-24 547430000 1399840 1039640 862800 953680 1294020 1068480 1264740 1411820 1277700 TRUE FALSE 1214847.597 1032810.536 1280052.966 1170227.62 1268271.534 1109585.117 1142085.709 1109913.28 1126651.762 1.078281363 0.91670787 1.136156716 1.038677309 1.125699686 0.98485189 1.013698952 0.985143163 1 20.10361023 YSPTS(ph)PTYSPTTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YSPTSPTYSPTTPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPT(0.004)S(0.8)PT(0.196)YSPTTPK;YS(0.001)PT(0.038)S(0.958)PT(0.002)YSPTTPK;YSPT(0.002)S(0.93)PT(0.067)YS(0.001)PTTPK;YSPT(0.209)S(0.791)PTYSPTTPK 312.92 9.26E-56 3290920000 6552600 5346650 3584920 4555220 5653390 5097550 5690230 7003000 6192410 TRUE FALSE 5686657.308 5311527.504 5318599.303 5589552.323 5540898.6 5293656.047 5138392.37 5505462.947 5460350.344 1.041445502 0.972744818 0.974039937 1.023661848 1.014751481 0.969471868 0.941037122 1.008261851 1 22.38056209 2.737166651 24.96905374 0.980532677 1.002798742 0.176925986 0.027145986 265.1162965 4748841.877 0.009424836 0.008726333 545.9673243 -2.737166651 0.022266065 YSPTSPTYS(ph)PTSPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPTSPT(0.022)YS(0.967)PT(0.01)S(0.001)PK;YSPTSPTYS(0.999)PTSPK 333.86 1.68E-68 932970000 750580 600700 406900 507700 605120 575240 641610 735780 705220 TRUE FALSE 651388.9513 596753.9621 603678.201 622981.0447 593079.2959 597369.855 579386.761 578439.1728 621849.695 1.047502245 0.959643411 0.970778318 1.00181933 0.953734159 0.960633831 0.931715116 0.930191295 1 19.24620639 3.195099886 8.109885645 0.950505713 0.990665823 0.291891502 0.02988907 0.30665536 50.36225017 0.008878158 0.010146655 1567.111457 -3.195099886 0.04016011 YSPTSPTYSPT(ph)SPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPTSPTYS(0.483)PT(0.503)S(0.014)PK 162 5.04E-05 175470000 341960 272740 213630 239310 300760 271480 306220 390310 362130 TRUE FALSE 296769.1196 270948.353 316942.1825 293648.9931 294775.4644 281924.0113 276522.8315 306845.2439 319319.4039 0.929380163 0.848518285 0.992555349 0.919608986 0.923136711 0.882890322 0.86597566 0.960935164 1 18.2846407 1.522963295 4.841463754 0.992407738 0.909696602 0.38148215 0.039443262 0.156255747 7.796128547 0.030343721 0.010011506 33.33982343 -1.522963295 -0.082711135 YSPTSPTYSPTS(ph)PK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPTSPTYS(0.001)PT(0.074)S(0.925)PK 266.63 7.21E-25 144060000 324510 239820 161990 206500 263680 255210 254340 309410 311750 TRUE FALSE 281625.1813 238244.6066 240328.9058 253388.9812 258433.2839 265028.0938 229674.1459 243245.0793 274895.2701 1.024481728 0.866674085 0.874256242 0.921765518 0.940115426 0.964105689 0.8354969 0.884864549 1 18.06852256 4.751319102 24.45335903 0.907108901 1.024481829 0.34530678 0.048897853 1795.865709 3441935.573 0.011999451 0.206020223 56405.19456 -4.751319102 0.117372928 YSQKEDKYEEEIK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 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 ; 169.09 1.64E-05 3106800000 4065380 2635340 2789870 2360660 2289260 1347800 4144600 4850270 2113930 FALSE TRUE 3528129.733 2618028.278 4139060.464 2896683.933 2243708.205 1399650.738 3742657.33 3813077.505 1864023.604 1.892749494 1.404503823 2.220497882 1.553995308 1.203690876 0.750876081 2.007837949 2.045616535 1 20.8299887 3.500368934 24.42303565 1.484473825 1.811020916 0.153388757 0.444736856 1481.014342 1555887.136 0.132599406 0.195112323 3164.965164 -3.500368934 0.326547091 YSQKEDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSQKEDR 7 1 H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;H0YL42;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6 H7BYY1;P09493-3 TPM1 Tropomyosin alpha-1 chain 0 62.546 0.077342 102420000 295750 270110 221690 333020 186150 259600 297950 289530 838010 FALSE TRUE 256665.8882 268335.6296 328900.0255 408637.2809 182445.9792 269586.98 269054.8549 227616.2626 738941.4125 0.347342677 0.363135189 0.445096215 0.553003627 0.246901819 0.364828626 0.364108508 0.308030189 1 19.49510046 1.234903668 24.99833801 1.000000888 0.373703542 0.855943319 0.080701499 38.86293917 265620.3063 0.145220121 0.020126268 17.17527374 -1.234903668 -0.626297346 YSQYLDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSQYLDR 7 0 A0A499FI31;Q15020-4;Q15020 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 ; 87.639 0.044653 589420000 722660 767930 467720 513370 713560 726030 762900 817710 799680 FALSE TRUE 627158.65 762885.4173 693910.9564 629938.5049 699361.5521 753960.8439 688914.0754 642849.0799 705142.7414 0.889406659 1.081887925 0.984071615 0.893348918 0.991801391 1.069231518 0.976985275 0.911658083 1 19.4275558 1.983838995 24.58966615 0.94795973 0.988607107 0.027251488 0.06512657 1650.406396 2511161.152 0.028588678 0.017126294 96.34717708 -1.983838995 0.040647377 YSS(ph)PPASTTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSSPPASTTR 10 0 Q08999;F5H837 Q08999 RBL2 Retinoblastoma-like protein 2 1 YS(0.025)S(0.972)PPAS(0.001)T(0.001)T(0.001)R 77.744 0.033652 132990000 269700 247610 157370 171160 244400 236250 234070 261000 232700 TRUE FALSE 234058.4617 245983.4336 233474.6584 210024.494 239536.9182 245338.6904 211369.9274 205187.1811 205190.4711 1.140688748 1.198805346 1.137843571 1.023558711 1.167388119 1.195663176 1.030115708 0.999983966 1 17.64660421 2.1179141 5.848902787 1.004574561 1.141436555 0.633670611 0.048280865 0.137648699 6.504303391 0.02112869 0.014103384 131.1940383 -2.1179141 0.136861994 YSS(ph)PTAGSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YSSPTAGSAK 10 0 P28749;P28749-2 P28749 RBL1 Retinoblastoma-like protein 1 1 YS(0.025)S(0.967)PT(0.008)AGSAK;YSS(0.99)PT(0.01)AGSAK;YS(0.018)S(0.861)PT(0.122)AGSAK 229.86 1.50E-09 752310000 2389190 2573050 1454940 1844520 2106820 1857270 2527580 3024680 2536290 TRUE FALSE 2073452.488 2556147.465 2158553.85 2263346.458 2064898.404 1928720.379 2282455.681 2377875.72 2236452.686 0.927116635 1.142947258 0.965168575 1.012025192 0.92329179 0.862401602 1.020569626 1.063235424 1 21.09278081 2.016423469 24.99971771 1.037864978 0.976052388 0.110384025 0.074116053 502.9018769 765511.3739 0.031086213 0.020953135 103.8540576 -2.016423469 -0.06181259 YSS(ph)QDADEQDWEFQKR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSSQDADEQDWEFQKR 16 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 YS(0.419)S(0.581)QDADEQDWEFQKR 187.43 8.21E-10 95666000 119820 97025 85774 94451 122830 129790 125310 162760 169630 TRUE FALSE 103985.4834 96387.63639 127254.5933 115897.5431 120385.9233 134783.1053 113157.4555 127955.0406 149576.5346 0.695199175 0.64440346 0.850765754 0.774837734 0.804844982 0.901097927 0.756518767 0.855448623 1 17.19052434 7.028569061 0.109818175 1.100287511 4.77E-19 0.55917029 0.067436485 160.2911728 2.075017034 3.748333898 27.48946977 10679946.09 -7.028569061 -1.100287511 YSS(ph)SGS(ph)PANSFHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSSSGSPANSFHFK 14 0 O00418;H3BRH4 O00418 EEF2K Eukaryotic elongation factor 2 kinase 2 Y(0.228)S(0.152)S(0.559)S(0.379)GS(0.682)PANSFHFK 60.618 0.048334 335520000 172550 267890 152460 286020 440480 434040 435850 533580 434060 TRUE FALSE 149747.0803 266130.213 226190.1659 350965.2125 431715.3098 450737.7997 393581.3341 419478.0693 382745.9213 0.391244092 0.695318221 0.590966888 0.916966565 1.127942287 1.177642333 1.028309675 1.095970057 1 18.54602748 3.645304125 2.210526187 1.088474355 0.550027853 0.883294063 0.087452945 0.094699414 0.904357409 0.025170376 0.044094018 4418.797754 -3.645304125 -0.538446503 YSS(ph)TETLKDDDLWSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSSTETLKDDDLWSSR 16 1 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 YS(0.084)S(0.797)T(0.105)ET(0.014)LKDDDLWSSR;YS(0.106)S(0.786)T(0.106)ET(0.003)LKDDDLWSSR 135.04 1.51E-05 231440000 556630 267490 238810 263950 287240 255910 355400 413520 359830 TRUE FALSE 483069.9352 265732.8406 354299.3148 323883.8817 281524.486 265755.0233 320933.3627 325091.966 317291.3073 1.522480837 0.83750432 1.116637319 1.020777671 0.8872745 0.837574233 1.011478585 1.024585164 1 18.27544847 4.747348556 24.97835426 0.973388746 1.52248112 0.792181068 0.089363043 526.4392856 1496289.484 0.022022646 0.255747118 55891.85911 -4.747348556 0.549092374 YSSDYFQAPSDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YSSDYFQAPSDYR 13 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 ;;; 238.92 2.00E-16 1366240000 807430 1090440 622610 852040 1131290 1212140 876000 1174220 1003560 FALSE TRUE 700726.0797 1083276.828 923706.2785 1045508.705 1108779.542 1258771.81 791045.6548 923122.1908 884920.2801 0.79185221 1.224151884 1.043829935 1.181472194 1.252971106 1.422469163 0.893917421 1.04316989 1 19.75518797 YSSNLGNFNYER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSSNLGNFNYER 12 0 Q9BZZ5-2;Q9BZZ5-5 Q9BZZ5-2 API5 Apoptosis inhibitor 5 0 ; 215.08 9.84E-11 512050000 207220 236720 127216 152327 213031 217570 240010 218530 219180 FALSE TRUE 179835.352 235164.9707 188738.0831 186915.1735 208792.0999 225940.0587 216733.8671 171799.0601 193268.7901 0.930493495 1.216776752 0.976557483 0.967125491 1.080319796 1.169045755 1.121411621 0.888912587 1 17.56024916 1.740033691 16.9563238 0.944918394 1.069038575 0.22470517 0.093691931 0.079316193 461.0819355 0.049040047 0.023463456 54.95835074 -1.740033691 0.124120181 AAGGNS(ph)REPS(ph)PLPELALR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 AAGGNSREPSPLPELALR 18 1 Q13207 Q13207 TBX2 T-box transcription factor TBX2 2 AAGGNS(1)REPS(1)PLPELALR;AAGGNS(1)REPS(1)PLPELALR 79.237 0.0060285 119212000 374750 269940 180649 181163 198433 205920 191973 215890 175010 TRUE FALSE 325225.838 268166.7464 268011.4606 222298.8281 194484.5715 213841.8756 173355.488 169723.6036 154320.5172 2.107469855 1.737725814 1.73671956 1.440500797 1.260263866 1.385699579 1.123346987 1.099812304 1 17.23557036 8 0.209764918 0.820232819 7.349835446 0.951329027 0.075945161 18.46319285 0.279024749 0.410519542 38.90195269 100000000 -8 6.529602627 up YSSS(ph)GSPANSFHFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSSSGSPANSFHFK 14 0 O00418;H3BRH4 O00418 EEF2K Eukaryotic elongation factor 2 kinase 1 YS(0.004)S(0.079)S(0.54)GS(0.376)PANSFHFK 178.51 1.27E-06 328250000 195960 259640 101750 236680 408810 319980 330640 465240 385530 TRUE FALSE 170063.3895 257934.4077 150956.6403 290421.8114 400675.4808 332289.8377 298574.5837 365752.0465 339953.0826 0.500255471 0.758735311 0.444051394 0.854299685 1.178619937 0.977457934 0.878281736 1.075889778 1 18.37497613 3.524439024 5.242610013 1.016651704 0.591308085 0.778469434 0.110269475 0.09007774 5.760035125 0.029257274 0.042763511 3345.33045 -3.524439024 -0.425343619 YSSSS(ph)IPEPFGSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSSSSIPEPFGSR 13 0 Q8WUF5;K7EN03 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 YSSS(0.029)S(0.97)IPEPFGSR;YSSS(0.098)S(0.902)IPEPFGSR 204.49 8.12E-08 184196000 639060 462000 246360 363810 437710 469940 389490 460050 460240 TRUE FALSE 554606.6018 458965.0916 365500.52 446418.621 429000.4274 488018.8959 351717.3197 361671.8876 405830.9515 1.36659513 1.130926781 0.900622584 1.100011272 1.057091446 1.202517684 0.866659673 0.891188526 1 18.63051937 4.617897902 2.991721015 0.998004644 1.384479261 0.556477651 0.103116154 0.243085059 3.478028173 0.028099313 0.190171766 41485.65027 -4.617897902 0.386474617 YSTSPYLLEAASHLS(ph)PENFVEDEAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSTSPYLLEAASHLSPENFVEDEAK 25 0 Q9BX63;Q9BX63-2 Q9BX63 BRIP1 Fanconi anemia group J protein 1 YSTSPYLLEAASHLS(1)PENFVEDEAK 140.35 2.54E-07 19225000 25223 19238 18641 17299 18620 19840 23186 27120 25795 TRUE FALSE 21889.71664 19111.62431 27655.84995 21227.00235 18249.49843 20603.25764 20937.42529 21320.59905 22745.54449 0.962373825 0.840235956 1.215879882 0.93323782 0.802332889 0.905815099 0.920506665 0.937352766 1 14.47329635 3.497947604 24.99893683 0.911979528 1.00373521 0.148384818 0.102183188 1491.363914 1790157.47 0.027969383 0.040957308 3147.368575 -3.497947604 0.091755681 YSVDIPLDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YSVDIPLDK 9 0 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;; 123.5 0.003487 0 967670 838470 510630 654610 811640 669820 957190 1058820 954550 FALSE TRUE 839789.9577 832962.0354 757572.376 803249.2056 795489.9519 695588.4088 864361.8611 832399.5827 841704.1864 0.99772577 0.989613749 0.900045869 0.95431295 0.945094446 0.826404834 1.02691881 0.988945518 1 19.68295377 YSVEAS(ph)SPGHGSPLSSLLPSASVPESMTISELR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSVEASSPGHGSPLSSLLPSASVPESMTISELR 33 0 Q8TEQ0;Q8TEQ0-2;H3BQF0 Q8TEQ0 SNX29 Sorting nexin-29 1 Y(0.004)S(0.059)VEAS(0.721)S(0.186)PGHGS(0.01)PLS(0.01)S(0.01)LLPSASVPESMTISELR;YS(0.003)VEAS(0.523)S(0.471)PGHGS(0.002)PLSSLLPSASVPESMTISELR 104.31 7.57E-06 265130000 55267 76626 25470 59974 89350 97130 87725 95850 87116 TRUE FALSE 47963.32592 76122.63876 37787.37719 73592.01335 87572.10981 100866.654 79217.443 75353.22341 76817.24572 0.624382266 0.990957669 0.49191268 0.958014215 1.140005854 1.313073035 1.031245552 0.980941489 1 16.22914262 3.508678387 8.119252206 1.08239317 0.729505169 0.571972369 0.153518144 0.213151462 49.24345748 0.04239175 0.061489384 3226.10417 -3.508678387 -0.352888001 YSVLNNDDYFADVS(ph)PLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 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 360.21 3.35E-88 584051000 584535 494351 358421 391595 490149 554453 490850 554033 644900 TRUE FALSE 507287.2187 491103.5757 531754.5944 480512.6299 480395.9939 575783.1657 443247.4425 435557.3544 568660.6567 0.892073705 0.863614477 0.935100025 0.844990108 0.844785002 1.01252506 0.779458606 0.765935447 1 19.11720847 S(ph)PS(ph)PLRGNVVPSPLPTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 SPSPLRGNVVPSPLPTR 17 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 2 S(1)PS(1)PLRGNVVPSPLPTR 99.93 0.00083046 165630000 167330 120790 62748 69748 82154 76593 78197 97919 65329 TRUE FALSE 145216.9165 119996.5225 93093.14268 85585.34943 80519.29613 79539.58227 70613.46698 76979.78386 57605.88004 2.520869683 2.083060313 1.616035422 1.485705094 1.397761758 1.380754572 1.225803111 1.336318164 1 15.81392846 8 0.419011743 1.178334636 27.31748247 0.955258356 0.092986653 16.19483726 0.218768716 0.078735233 352.517775 100000000 -8 26.13914784 up YSYLTEPGMS(ph)PQSPCER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YSYLTEPGMSPQSPCER 17 0 Q12955-4;Q12955-5;Q12955-6;H0Y3A4;H0YA66 Q12955-4 ANK3 Ankyrin-3 1 YSYLTEPGMS(0.95)PQS(0.05)PCER;YSYLTEPGMS(1)PQSPCER;YSYLTEPGMS(0.999)PQS(0.001)PCER;YSYLTEPGMS(0.999)PQS(0.001)PCER 306.37 4.72E-47 1443360000 630763 719150 480232 683030 884760 971220 844150 1065750 1017950 TRUE FALSE 547406.0714 714425.8563 712473.8015 838122.401 867155.007 1008583.462 762284.4629 837847.6562 897609.1107 0.609849059 0.795920906 0.793746179 0.9337276 0.966071976 1.123633272 0.849238777 0.933421515 1 19.77572779 4.435702615 0.973610329 0.968011229 0.541867781 0.721303499 0.0735153 0.7347854 0.785109524 0.026045221 0.298386281 27271.0974 -4.435702615 -0.426143448 YSYLTEPGMSPQS(ph)PCER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 7 YSYLTEPGMSPQSPCER 17 0 Q12955-4;Q12955-5;Q12955-6;H0Y3A4;H0YA66 Q12955-4 ANK3 Ankyrin-3 1 YSYLTEPGMS(0.021)PQS(0.979)PCER;YSYLTEPGMS(0.099)PQS(0.901)PCER;YSYLTEPGMS(0.017)PQS(0.983)PCER;YSYLTEPGMSPQS(1)PCER;YSYLTEPGMSPQS(1)PCER;YSYLTEPGMSPQS(1)PCER;YSYLTEPGMSPQS(1)PCER 412.43 1.53E-140 2335580000 1443240 1836270 1282240 1911850 2705420 2797800 2480790 3019280 2610010 TRUE FALSE 1252512.177 1824207.421 1902335.553 2345964.763 2651587.435 2905433.176 2240203.368 2373630.468 2301457.591 0.544225617 0.792631343 0.826578582 1.019338689 1.152133954 1.262431768 0.973384596 1.031359638 1 21.13411643 4.257427922 1.203009921 1.077882192 0.528128357 0.790775921 0.091137697 0.357584166 0.767788489 0.031173132 0.201808297 18089.55661 -4.257427922 -0.549753835 YSYQLLQCDS(ph)PR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YSYQLLQCDSPR 12 0 E7EWN3;Q9C0A6;Q9C0A6-2;Q9C0A6-3 E7EWN3 SETD5 SET domain-containing protein 5 1 YSYQLLQCDS(1)PR;YSYQLLQCDS(1)PR 175.98 2.75E-05 185950000 257960 220440 152622 168083 228440 244320 208797 239960 256170 TRUE FALSE 223869.9324 218991.9151 226430.5097 206248.8141 223894.4909 253719.1485 188547.8991 188646.4214 225885.8744 0.991075396 0.969480343 1.002411108 0.913066453 0.991184117 1.123218303 0.834704249 0.835140408 1 17.78523453 2.204070663 24.99978964 0.876228056 0.993066075 0.347874328 0.068898202 186.6033827 135256.8479 0.028051807 0.018913521 159.9818309 -2.204070663 0.116838019 YSYYDESQGEIYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YSYYDESQGEIYR 13 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 174.23 1.34E-06 0 28500 24752 11406 22369 25048 26550 24255 29372 26482 FALSE TRUE 24733.65279 24589.40248 16921.97975 27448.22334 24549.59381 27571.39568 21902.75383 23091.02637 23351.32813 1.059196833 1.053019441 0.724668835 1.175445918 1.051314669 1.180720665 0.937966085 0.988852807 1 14.51121699 4.437718267 24.99999291 1.008038728 1.057658533 0.023857078 0.127087365 666.5515437 422905.5154 0.031258967 0.082703534 27397.9625 -4.437718267 0.049619805 YTCGEAPDYDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YTCGEAPDYDR 11 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;;;; 308.91 3.42E-45 8429420000 5179500 5238530 3510040 4046770 4842110 5307480 5429060 5220600 5562750 FALSE TRUE 4495015.952 5204117.752 5207507.084 4965650.98 4745761.484 5511662.19 4902550.597 4104215.317 4905128.032 0.916391157 1.060954519 1.061645496 1.012338709 0.967510217 1.123653074 0.999474543 0.836719305 1 22.22585936 1.951436839 10.63233582 0.909967261 1.027196843 0.285547075 0.067628683 0.796044292 171.929158 0.029682133 0.016934783 89.42044757 -1.951436839 0.117229582 YTDHGSDHHYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YTDHGSDHHYR 11 0 J3KPD3;Q9Y580;G3V1T9 J3KPD3 RBM7 RNA-binding protein 7 0 104.22 0.0015203 39222000 64266 71372 16352 36854 79774 87326 57128 75484 64974 FALSE TRUE 55773.08527 70903.15263 24259.88189 45222.26398 78186.65348 90685.48773 51587.73535 59342.33402 57292.84774 0.973473784 1.237556788 0.423436482 0.78931779 1.364684364 1.582841337 0.900421909 1.035772114 1 15.80606743 3.256212077 24.89013129 1.15870321 0.852310483 0.250194966 0.27493955 378.3951347 533567.5506 0.084273049 0.108545846 1803.898416 -3.256212077 -0.306392728 YTEFYHVPTHSDASK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 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 ;; 245.03 2.61E-18 769010000 1533820 1341170 777290 1155790 1371180 1226180 1559500 1834030 1648820 FALSE TRUE 1331121.801 1332359.766 1153190.044 1418229.785 1343896.201 1273351.938 1408259.93 1441836.957 1453898.378 0.915553536 0.916405016 0.793171009 0.975466928 0.924339845 0.875819079 0.968609603 0.991704082 1 20.471495 2.10251893 4.662749224 0.9913011 0.900723388 0.448000257 0.045893052 0.191600481 7.09361551 0.019577246 0.012753603 126.624846 -2.10251893 -0.090577712 YTFAAHMDGTYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YTFAAHMDGTYK 12 0 Q15363;E7EQ72 Q15363 TMED2 Transmembrane emp24 domain-containing protein 2 0 ; 193.23 3.07E-06 1906120000 3491300 3782100 2578200 2979900 4115100 3707700 3492100 4747400 4781900 FALSE TRUE 3029915.859 3757255.136 3825026.144 3656531.84 4033217.561 3850337.618 3153436.679 3732205.454 4216589.23 0.718570317 0.891065013 0.907137484 0.867177626 0.956511849 0.913140315 0.74786433 0.885124268 1 22.00764505 4.738765982 24.23795621 0.890082414 0.718570237 0.421048036 0.065058477 11.56838588 1363900.745 0.016023857 0.090198978 54798.16069 -4.738765982 -0.171512177 YTGEDFDEDLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 5 YTGEDFDEDLR 11 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;;; 150.35 7.89E-05 1990080000 1175010 1145500 765321 879740 1238810 1314970 1178750 1272930 1361340 FALSE TRUE 1019729.451 1137975.135 1135432.795 1079498.413 1214160.105 1365557.747 1064435.006 1000723.825 1200403.936 0.849488594 0.947993505 0.945875602 0.899279301 1.011459616 1.137581864 0.886730687 0.833655901 1 20.19508852 6.061535566 14.34523825 0.941461695 0.854593453 0 0.089260971 0 0 0.021172366 0 1152220.415 -6.061535566 -0.086868241 YTGEEDGAGGHS(ph)PAPPQTEECLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YTGEEDGAGGHSPAPPQTEECLR 23 0 O94762-4;O94762;J3KS37;J3KSV9 O94762-4 RECQL5 ATP-dependent DNA helicase Q5 1 YTGEEDGAGGHS(1)PAPPQTEECLR;YTGEEDGAGGHS(1)PAPPQTEECLR;YTGEEDGAGGHS(1)PAPPQTEECLR 245.2 1.09E-37 368240000 354953 320618 228200 263025 351205 339183 274668 337123 335493 TRUE FALSE 308045.0617 318511.8392 338558.2833 322748.8463 344216.7076 352231.5895 248030.7396 265031.8699 295831.3997 1.041285888 1.076666776 1.144429846 1.090989147 1.163557039 1.190649775 0.838419248 0.895888233 1 18.17441566 2.237613052 24.99996968 0.905154373 1.118108107 0.740070585 0.057648749 12.18482555 321458.752 0.023200513 0.016665655 172.8275814 -2.237613052 0.212953735 YTIENPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YTIENPR 7 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 121.52 0.010307 956430000 980860 1002950 681380 734810 1044600 1097350 991510 1145140 1125340 FALSE TRUE 851236.8658 996361.5554 1010897.647 901659.8414 1023814.504 1139565.765 895353.5128 900260.7225 992303.5872 0.85783915 1.004089442 1.018738277 0.908653212 1.031755319 1.148404359 0.90229797 0.907243241 1 19.92042204 5.892431922 12.08685222 0.974175198 0.864256038 0 0.084782303 0 0 0.019314755 0 780606.0663 -5.892431922 -0.10991916 YTIGDIFVHS(ph)PQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YTIGDIFVHSPQR 13 0 Q9P2F8 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 YTIGDIFVHS(1)PQR;YTIGDIFVHS(1)PQR;YTIGDIFVHS(1)PQR 180.64 8.20E-06 424625000 415449 523475 315038 396408 543178 595386 540505 609735 600158 TRUE FALSE 360546.362 520036.2583 467391.4305 486418.4951 532369.8205 618290.8847 488086.9083 479347.9152 529208.0049 0.681294233 0.982668919 0.883190402 0.919144251 1.005974618 1.168332449 0.922296911 0.905783569 1 19.01347536 4.740344819 24.32878113 0.968334986 0.681294091 0.564657176 0.080502159 89.52176634 1220540.909 0.020790011 0.129650102 54997.73683 -4.740344819 -0.287040895 YTIHSQLEHLQSK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YTIHSQLEHLQSK 13 0 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 ; 230.36 2.44E-12 770260000 936310 834380 468750 676170 851420 710610 830290 1054640 1147040 FALSE TRUE 812574.2612 828898.9028 695439.0679 829704.7331 834478.4078 737947.6265 749768.6036 829113.4432 1011438.238 0.803384953 0.819524981 0.687574428 0.820321698 0.825041388 0.729602262 0.741289557 0.819737095 1 19.9479768 1.251485162 3.151941782 1.035494834 0.775690722 0.7082041 0.04505994 0.188502953 2.489018325 0.120535109 0.011556309 17.84371025 -1.251485162 -0.259804112 YTISQEAYDQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YTISQEAYDQR 11 0 K7EP07;Q99426-2;Q99426;A0A494C0X0;K7EK42 K7EP07 TBCB Tubulin-folding cofactor B 0 135.16 0.0028113 0 92722 111050 57072 68060 116590 119690 103780 107260 107120 FALSE TRUE 80468.55277 110320.5052 84672.21009 83514.06323 114270.0871 124294.5517 93715.43157 84323.2837 94456.39563 0.851912168 1.167951672 0.896415849 0.884154669 1.209765483 1.315893444 0.992155491 0.892721802 1 16.52736086 4.77479337 22.31689622 1.03448256 0.851910454 0.143455095 0.146237188 9880.431236 6085189.884 0.038406219 6.301379712 59537.88043 -4.77479337 -0.182572106 YTLETRPNQEGIDVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YTLETRPNQEGIDVR 15 1 A0A3B3ISG5;P14735;Q5T5N3 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ;; 124.25 8.91E-05 2692300000 2802690 2858760 1775120 2275720 3007020 3187630 2734400 3291390 3153660 FALSE TRUE 2432307.415 2839980.617 2633573.969 2792457.008 2947186.185 3310260.189 2469218.309 2587551.862 2780837.907 0.874667095 1.021267946 0.947043322 1.004178273 1.05981948 1.190382287 0.887940395 0.930493595 1 21.40708822 4.745004726 23.78250996 0.999466996 0.874666983 0.197254306 0.082011239 719.591661 2655564.723 0.021314883 0.191046792 55591.03066 -4.745004726 -0.124800012 YTPAS(ph)PSSPDFTTWSCAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YTPASPSSPDFTTWSCAK 18 0 A0A1B0GVE3;O75808-2;O75808 A0A1B0GVE3 CAPN15 Calpain-15 1 YTPAS(0.858)PS(0.139)S(0.003)PDFTTWSCAK;YTPAS(0.979)PS(0.021)SPDFTTWSCAK 295.09 2.85E-49 242516000 257806 274210 192164 248048 329300 282893 364370 433370 375720 TRUE FALSE 223736.2839 272408.6965 285095.1532 304371.0896 322747.5743 293776.0768 329033.4535 340697.198 331302.8096 0.675322628 0.822234791 0.860527423 0.918709654 0.974176991 0.886729808 0.993150206 1.028355897 1 18.33779091 5.864401578 0.401327083 1.014202916 2.88E-17 0.894663629 0.034018446 5.045260595 0.340984678 0.038458268 2.922555329 731815.4572 -5.864401578 -1.014202916 YTPSGQAGAAASESLFVSNHAY ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YTPSGQAGAAASESLFVSNHAY 22 0 P04075;J3KPS3;P04075-2;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 180.93 1.20E-16 66366000 37067 39488 14589 27596 45162 42092 34241 46376 45751 FALSE TRUE 32168.50203 39228.60073 21644.2892 33862.09358 44263.36456 43711.30648 30920.31309 36458.8533 40342.3689 0.797387534 0.972392098 0.536515078 0.839368002 1.097192995 1.08350867 0.766447631 0.903736054 1 15.30000818 3.467800866 24.83383222 0.953715359 0.772263272 0.308576097 0.138805028 250.91237 668543.5701 0.040900237 0.052876394 2936.302983 -3.467800866 -0.181452087 YTQLQYIGEGAYGMVSSAYDHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YTQLQYIGEGAYGMVSSAYDHVR 23 0 P27361;E9PBK7;E9PQW4;P27361-3;P27361-2;E9PJF0 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 ; 200.95 2.34E-24 535320000 924210 923720 487850 675130 884100 949740 917920 1010720 1017640 FALSE TRUE 802073.3069 917652.0225 723775.8918 828428.5852 866508.1397 986277.1124 828900.2597 794585.3934 897335.7585 0.893838565 1.022640649 0.806583138 0.923209153 0.965645391 1.09911714 0.923734791 0.885493959 1 19.77528838 3.286557611 5.434166319 0.966068843 0.911152079 0.144492817 0.075173959 0.485132359 31.89572887 0.023023401 0.029364726 1934.450456 -3.286557611 -0.054916765 YTQSNGR ddPTM_MDA-MB-175_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 ; 147.08 0.0050616 93260000 118130 118331 67491 73930 66191 114574 110560 130467 118097 FALSE TRUE 102518.8212 117553.6759 100129.8733 90716.93645 64873.9286 118981.7359 99837.90822 102567.6473 104135.7072 0.98447328 1.128850795 0.961532562 0.871141503 0.622974869 1.142564247 0.958728864 0.98494215 1 16.66810532 4.070330428 7.505804729 0.932321065 1.055496791 0.128903266 0.134217787 0.487053249 44.06028091 0.034895407 0.073254835 11757.91801 -4.070330428 0.123175726 YTQVGPDHNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YTQVGPDHNR 10 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;; 118.28 0.00084615 7666910000 6808600 5861590 3618320 4601310 6195240 6718090 5906330 6459870 6006990 FALSE TRUE 5908826.259 5823084.829 5368151.655 5646107.762 6071966.845 6976539.269 5333535.026 5078477.071 5296850.485 1.115535784 1.099348537 1.01346105 1.065936782 1.146335329 1.317110855 1.006925727 0.95877297 1 22.33670336 2.024171165 24.99977701 0.978363848 1.121762656 0.410584222 0.07817615 222.0869276 229699.2701 0.033859982 0.022827288 105.7234107 -2.024171165 0.143398808 YTRPTPVQK ddPTM_MDA-MB-175_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 ; 92.538 0.0091273 611310000 901930 782180 490580 539010 788210 680730 818650 923730 892110 FALSE TRUE 782737.6653 777041.8081 727826.1289 661400.4588 772526.1631 706918.1236 739257.449 726197.528 786645.7721 0.995031936 0.987791247 0.925227281 0.840785627 0.982050868 0.898648602 0.939759006 0.923156971 1 19.58535461 4.251840262 7.315853897 0.927375621 0.991958971 0.257961962 0.043184745 0.1812841 48.57104838 0.010390418 0.025757305 17858.30608 -4.251840262 0.06458335 YTS(ph)PPWVTPK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YTSPPWVTPK 10 0 Q9ULL0 Q9ULL0 KIAA1210 Uncharacterized protein KIAA1210 1 Y(0.001)T(0.202)S(0.797)PPWVTPK 107.34 0.0024088 329410000 954290 1015700 658340 844890 1063400 874810 1035600 1381600 1194500 TRUE FALSE 828178.1586 1009027.8 976715.426 1036735.188 1042240.421 908464.5068 935167.6714 1086155.592 1053287.571 0.786279248 0.957979404 0.927301767 0.98428503 0.989511743 0.862503776 0.887855983 1.031205173 1 20.00646795 4.738966799 23.5754848 0.956104 0.786279158 0.516211259 0.051347588 13.38224978 776090.6773 0.013346446 0.076035458 54823.50519 -4.738966799 -0.169824842 YTSCETGFKDGDLFMSYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YTSCETGFKDGDLFMSYR 18 1 P49902-2;P49902;Q5JUV4;Q5JUV3 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 162.76 3.18E-11 274200000 357410 348430 127390 136560 324350 275990 378270 448820 38363 FALSE TRUE 310177.3629 346141.1404 188996.2301 167568.0352 317896.0696 286607.5139 341585.4336 352843.3357 33827.76984 9.169311615 10.23245523 5.587014189 4.953564363 9.397488249 8.472551256 10.09778165 10.43058225 1 15.04592045 4.271318329 24.99897398 7.637986867 9.700885605 0.103114668 2.861277089 532.8774662 406655.9022 0.720818842 1.906827013 18677.48211 -4.271318329 2.062898738 YTVQDESHSEWVSCVR ddPTM_MDA-MB-175_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 ;;;;;; 252.76 1.55E-26 8821712000 3579217 3343456 1947683 2573071 3329257 3424985 3345784 3672688 3647140 FALSE TRUE 3106214.405 3321492.617 2889589.013 3157326.097 3263011.299 3556746.389 3021310.383 2887312.252 3215979.264 0.965868916 1.03280909 0.89850984 0.981761957 1.014624483 1.10596061 0.939468241 0.897801887 1 21.61682667 2.043823394 24.99999848 0.934710468 0.998822471 0.155566267 0.057684933 205.2622781 117095.4546 0.02390565 0.016117178 110.6173866 -2.043823394 0.064112003 YTYEHDPITK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YTYEHDPITK 10 0 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224;J3KPM9;A0A669KBI6;P42224-2;A0A669KB52;E7EPD2;A0A669KB75 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta;Signal transducer and activator of transcription 0 ; 107.24 0.0023096 355900000 889600 761360 477230 562940 741160 659140 792010 863520 865530 FALSE TRUE 772037.106 756358.576 708020.0242 690764.131 726412.3661 684497.5423 715200.9921 678862.9679 763208.0294 1.011568375 0.991025444 0.927689433 0.905079748 0.95178816 0.896868895 0.937098359 0.889486145 1 19.54171682 4.292327266 3.762809018 0.924887989 1.006902338 0.470499228 0.03159881 0.16523439 4.676487488 0.007507597 0.021691048 19603.21335 -4.292327266 0.082014349 YVAEIEKEKEENEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YVAEIEKEKEENEK 14 2 O14818;H0Y586;O14818-2 O14818 PSMA7 Proteasome subunit alpha type-7 0 128.06 4.27E-05 145490000 228300 147610 109460 83075 106050 83155 230720 233110 33822 FALSE TRUE 198129.5766 146640.3402 162395.2221 101938.4485 103939.8125 86354.02666 208344.8099 183261.2406 29823.60169 6.64338193 4.916922567 5.44519149 3.418046201 3.485152919 2.89549289 6.985903717 6.144839328 1 14.86416688 4.877947451 1.334399788 4.389308259 8.100229975 0.169518113 1.706266152 4.016889582 5.02207996 0.51034292 22.00196202 75500.08679 -4.877947451 3.710921716 YVASYLLAALGGNS(ph)SPSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YVASYLLAALGGNSSPSAK 19 0 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 1 YVASYLLAALGGNS(0.487)S(0.487)PS(0.027)AK;YVASYLLAALGGNS(0.439)S(0.439)PS(0.123)AK 102.08 0.00025712 456020000 299786 280532 196698 240560 279971 239035 302510 352270 268314 TRUE FALSE 260168.5205 278689.1668 291821.8107 295182.8247 274400.1249 248230.8311 273172.6268 276939.8019 236594.2246 1.0996402 1.177920413 1.233427448 1.247633264 1.159792152 1.049183815 1.154603952 1.170526467 1 17.85205533 2.993311568 24.7539498 1.110563372 1.193414833 0.33325767 0.062451102 364.6143034 1349449.727 0.019696579 0.021529111 984.7172998 -2.993311568 0.082851462 YVASYLLAALGGNSS(ph)PSAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YVASYLLAALGGNSSPSAK 19 0 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 1 YVASYLLAALGGNS(0.052)S(0.948)PS(0.001)AK;YVASYLLAALGGNS(0.044)S(0.956)PS(0.001)AK;YVASYLLAALGGNS(0.05)S(0.95)PSAK 297.87 9.49E-50 3972440000 1283235 1196587 774832 888453 1156447 950664 1321820 1609110 1367423 TRUE FALSE 1113652.243 1188726.541 1149543.347 1090189.833 1133435.967 987236.6592 1193630.1 1265014.349 1205767.811 0.923604224 0.985866873 0.953370406 0.904145743 0.940011798 0.81876183 0.989933625 1.049135943 1 20.20152069 2.010788165 24.99942683 1.025514831 0.923723862 0.501245819 0.044240852 161.7343576 374785.8287 0.018206887 0.012261922 102.5151768 -2.010788165 -0.101790969 YVATLGVEVHPLVFHTNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YVATLGVEVHPLVFHTNR 18 0 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ;; 328.8 4.48E-75 16577680000 6886100 5508380 3486216 4822280 5676600 6112670 5698240 6629640 7490770 FALSE TRUE 5976084.438 5472195.089 5172161.718 5917252.378 5563646.766 6347828.37 5145625.562 5211943.078 6605219.704 0.904751803 0.828465264 0.783041587 0.895844899 0.842310629 0.961032131 0.779024134 0.789064302 1 22.65517512 4.757411006 21.90248589 0.851867973 0.904752065 0.024812514 0.074848372 2644.682836 3072608.374 0.017794322 0.480337289 57201.97266 -4.757411006 0.052884092 YVAVMPPHIGDQPLTGAYTVTLDGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YVAVMPPHIGDQPLTGAYTVTLDGR 25 0 P30043;A0A2R8YEP4 P30043 BLVRB Flavin reductase (NADPH) 0 ; 282.6 2.27E-53 2288010000 2211000 2087730 1266730 1391400 1958880 2148500 1807930 2182600 2149700 FALSE TRUE 1918810.748 2074015.564 1879324.865 1707338.636 1919902.12 2231154.185 1632597.227 1715867.975 1895564.915 1.012263275 1.094141144 0.991432607 0.90070175 1.012839025 1.177039186 0.861272127 0.905201379 1 20.85419643 2.190596043 24.9999762 0.916088347 1.025654317 0.300278479 0.078102755 148.4900367 77394.47126 0.032672118 0.022027589 155.0943737 -2.190596043 0.10956597 YVDEASKK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YVDEASKK 8 1 P62249;M0R210 P62249 RPS16 40S ribosomal protein S16 0 ;;; 130.96 0.0016441 2992320000 3522830 2708050 2215620 2724980 2044930 1649150 3613090 3744720 3134850 FALSE TRUE 3057279.09 2690260.641 3287101.243 3343728.358 2004239.894 1712593.868 3262693.088 2943940.769 2764251.604 1.106006083 0.973232913 1.189146906 1.20963242 0.72505697 0.619550646 1.180316974 1.065004635 1 21.39845751 3.268461986 24.9998904 0.941115972 1.114031026 0.251118096 0.170225127 384.7615648 321688.3478 0.054335561 0.070137223 1855.504387 -3.268461986 0.172915055 YVDEENS(ph)DGETSNHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YVDEENSDGETSNHR 15 0 A0A494C108;Q8N9T8;H0YFD2;H0YH26;F8WFC1 A0A494C108 KRI1 Protein KRI1 homolog 1 YVDEENS(1)DGETSNHR;YVDEENS(1)DGETSNHR;YVDEENS(1)DGETSNHR;YVDEENS(1)DGETSNHR 237.73 6.15E-18 4577570000 3885110 2882820 1405520 2182530 3070580 3092770 2947750 3305280 2788450 TRUE FALSE 3371682.87 2863882.566 2085234.173 2678106.794 3009481.465 3211750.863 2661877.659 2598471.594 2458802.618 1.371270246 1.164746835 0.848068958 1.089191452 1.223962202 1.306225575 1.08259103 1.056803655 1 21.2295245 1.809736663 2.957676984 1.023896128 1.153024459 0.137940741 0.140085715 0.584201769 9.442571192 0.104360825 0.041167092 64.52628516 -1.809736663 0.129128331 YVEAAWYPWWEQQGFFKPEYGRPNVSAANPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YVEAAWYPWWEQQGFFKPEYGRPNVSAANPR 31 2 P26640;A0A140T936;P26640-2;A0A140T954 P26640 VARS Valine--tRNA ligase 0 ; 190.77 5.89E-19 619730000 803010 668160 365240 445020 693020 630870 692620 838720 536930 FALSE TRUE 696890.1939 663770.813 541871.2857 546068.5927 679230.2579 655139.9771 625449.819 659366.2549 473454.7471 1.471925666 1.401973086 1.144504916 1.153370192 1.43462551 1.383743602 1.321034001 1.392670068 1 18.85286701 YVEQYVGTEGASSS(ph)PTEGFLLKPVFLQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YVEQYVGTEGASSSPTEGFLLKPVFLQR 28 1 O75182-2;O75182;M0QYC5 O75182-2 SIN3B Paired amphipathic helix protein Sin3b 1 YVEQYVGTEGAS(0.002)S(0.085)S(0.911)PT(0.001)EGFLLKPVFLQR;YVEQYVGTEGAS(0.011)S(0.257)S(0.732)PTEGFLLKPVFLQR 167.61 3.32E-12 894550000 1025790 852070 542820 652400 830620 782030 812660 938710 883800 TRUE FALSE 890229.2525 846472.6961 805329.5676 800537.3913 814092.2871 812115.2001 733848.3583 737974.1715 779318.1708 1.1423181 1.086170871 1.033377121 1.02722793 1.044621206 1.042084261 0.941654366 0.946948498 1 19.57185293 8 0.208677872 0.926649448 1.980729025 0.755038812 0.029396024 50.41441521 0.760338538 0.183647859 17.03054763 100000000 -8 1.054079577 YVESFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YVESFR 6 0 P50135;P50135-3;P50135-2 P50135 HNMT Histamine N-methyltransferase 0 114.54 0.058621 147540000 189540 171080 115920 112710 164730 167060 149190 166320 172300 FALSE TRUE 164491.8088 169956.1642 171979.2997 138302.5282 161452.1953 173486.9063 134721.5768 130753.7623 151930.8903 1.082675211 1.118641271 1.131957428 0.910298939 1.062668658 1.141880403 0.886729331 0.860613415 1 17.2130557 2.226932445 24.99159892 0.903077155 1.071269638 0.50738997 0.073403809 171.2532359 368059.2389 0.030488474 0.020748826 168.6290699 -2.226932445 0.168192483 YVGSMVADVHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 11 YVGSMVADVHR 11 0 P09467;A0A3B3IUC7;O00757 P09467 FBP1;FBP2 "Fructose-1,6-bisphosphatase 1;Fructose-1,6-bisphosphatase isozyme 2" 0 ;;;;;;;;;; 190.57 2.21E-06 15897800000 8336540 11008870 6638860 8022330 10546060 12037690 10666640 10913830 11540140 FALSE TRUE 7234845.117 10936552.01 9849434.902 9843922.64 10336214.04 12500787.72 9632190.895 8579992.386 10175877.8 0.710979953 1.074752687 0.967919928 0.967378229 1.015756502 1.228472666 0.946571007 0.843169755 1 23.27864991 5.913734511 13.14042044 0.97352953 0.675788399 0 0.135173943 0 0 0.030110869 0 819850.2085 -5.913734511 -0.297741131 YVIS(ph)DEEEEDDD ddPTM_MDA-MB-175_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 243.91 2.38E-16 420920000 1124180 1072360 687220 815960 1001170 1061550 972440 1187320 1112980 TRUE FALSE 975616.7647 1065315.597 1019561.891 1001236.189 981248.6758 1102388.515 878132.9185 933420.8577 981404.7723 0.994102324 1.08550073 1.038880103 1.020207174 0.999840946 1.12327609 0.894771396 0.951106907 1 19.90448876 2.227697754 24.99976754 0.946898998 1.042265963 0.49220332 0.045465857 170.6461708 392721.3971 0.01763729 0.012020743 168.9264883 -2.227697754 0.095366965 YVIYIER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YVIYIER 7 0 P61254;E5RIT6;J3QRI7;J3QQQ9;J3QQV1;J3QRC4;J3KS10;Q9UNX3 P61254;Q9UNX3 RPL26;RPL26L1 60S ribosomal protein L26;60S ribosomal protein L26-like 1 0 ;;;;; 141.98 0.0058623 3628782000 2917638 2855501 2008157 2142025 2978857 2996616 2815020 3240384 3367200 FALSE TRUE 2532064.746 2836743.026 2979308.442 2628404.515 2919583.574 3111897.757 2542019.794 2547453.098 2969133.452 0.85279587 0.955411089 1.003426922 0.88524297 0.98331167 1.048082818 0.856148716 0.857978646 1 21.50161051 2.186785022 24.99997915 0.892950303 0.955101707 0.100223104 0.067626875 190.0445258 91761.88256 0.027364192 0.018448952 153.7393435 -2.186785022 0.062151404 YVLHCQGTEEEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YVLHCQGTEEEK 12 0 B7Z7P8;P62495-2;P62495 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 ;;; 225.13 1.84E-11 2191920000 2148110 1847290 1265350 1342230 1552830 1449710 1944400 2317980 2434750 FALSE TRUE 1864231.821 1835155.03 1877277.492 1647003.836 1521931.721 1505481.282 1755832.387 1822298.016 2146916.629 0.868329862 0.854786351 0.874406331 0.767148484 0.708891859 0.701229504 0.817839111 0.848797755 1 21.03383474 1.211027349 2.041900732 1.074221827 0.795883293 0.523064158 0.060278308 0.746787357 2.877980279 0.404424667 0.018441507 16.25651125 -1.211027349 -0.278338534 YVLLNDQPDDDDGNPNEHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YVLLNDQPDDDDGNPNEHR 19 0 Q8NEU8-2;Q8NEU8;Q8NEU8-3;F8VS86 Q8NEU8-2 APPL2 DCC-interacting protein 13-beta 0 139.87 4.11E-07 0 178520 164440 90150 96357 140190 149540 136950 138730 151860 FALSE TRUE 154928.1297 163359.7828 133746.8415 118236.3296 137400.4933 155292.9006 123668.6101 109063.6691 133907.2838 1.156980601 1.219946953 0.998801841 0.882971607 1.026086777 1.159704657 0.923539083 0.814471521 1 17.03087491 8 0.282437355 0.895446405 3.311795555 0.362173466 0.102921387 85.80254747 1.375308736 0.259870285 100.3505373 99999999.99 -8 2.41634915 YVLSSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YVLSSR 6 0 P12532;P12532-2;F8WCN3;C9JSQ1;C9J6W7;C9JT96 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ; 142.53 0.026789 436150000 388990 496620 289230 348030 485870 543380 398110 449060 492090 FALSE TRUE 337583.9859 493357.6705 429102.5954 427055.5308 476202.1376 564284.1802 359501.3535 353032.0136 433915.6808 0.777994437 1.136989725 0.988907786 0.984190131 1.097453166 1.300446619 0.828505098 0.813595888 1 18.7270552 YVPPSSTDRS(ph)PYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YVPPSSTDRSPYEK 14 1 P15941-2;A0A087WWM1;A0A087X2A4;A0A0C4DGW3;P15941-7;P15941-11;P15941-4;P15941-3;P15941;P15941-8;A0A087WVJ0;A0A0A0MSH4;A0A0A0MRB3;B1AVQ7;A0A087X0L2;P15941-15;P15941-17;P15941-6;A6ZIE3;A6ZIE4;P15941-12;P15941-16;P15941-9;P15941-10;V9GZ38 P15941-2 MUC1 Mucin-1;Mucin-1 subunit alpha;Mucin-1 subunit beta 1 YVPPSSTDRS(1)PYEK;YVPPSSTDRS(1)PYEK;YVPPSSTDRS(0.999)PYEK;YVPPSSTDRS(1)PYEK 140.28 6.05E-06 2035170000 2043910 1883470 1455630 2065830 2308630 2130300 1403630 3036010 2542830 TRUE FALSE 1773802.115 1871097.362 2159577.537 2534908.276 2262692.78 2212254.019 1267506.179 2386782.888 2242219.534 0.79109208 0.834484462 0.963142772 1.130535274 1.009130794 0.98663578 0.565290847 1.064473327 1 21.09649611 4.311230032 4.423685523 0.956995628 0.803032619 0.145516713 0.149410399 0.426448902 15.59126341 0.038851334 0.109530482 20475.28861 -4.311230032 -0.153963008 YVPPSSTDRSPYEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YVPPSSTDRSPYEK 14 1 P15941-2;A0A087WWM1;A0A087X2A4;A0A0C4DGW3;P15941-7;P15941-11;P15941-4;P15941-3;P15941;P15941-8;A0A087WVJ0;A0A0A0MSH4;A0A0A0MRB3;B1AVQ7;A0A087X0L2;P15941-15;P15941-17;P15941-6;A6ZIE3;A6ZIE4;P15941-12;P15941-16;P15941-9;P15941-10;V9GZ38 P15941-2 MUC1 Mucin-1;Mucin-1 subunit alpha;Mucin-1 subunit beta 0 ;; 104.17 0.0024611 322890000 542570 459310 280024 372564 536690 550950 389520 663960 233712 FALSE TRUE 470867.9998 456292.7624 415444.543 457160.3505 526010.919 572145.403 351744.4104 521977.3209 206082.8336 2.284848241 2.2141231 2.015910475 2.218333 2.552424721 2.77628851 1.706810821 2.532852018 1 17.65286481 1.231691543 24.99971249 0.99999781 2.282542104 0.650830323 0.296394236 149.5462245 544217.6645 0.675619881 0.070156177 17.04871075 -1.231691543 1.282544294 YVQHTYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 YVQHTYR 7 0 P52566;F5H3P3;H0YGX7 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ;;;;;;;;; 148.38 0.0020877 16510590000 6079140 9087820 4910437 5665964 8232310 8380270 7518310 8247530 8606520 FALSE TRUE 5275766.246 9028121.512 7285140.758 6952507.725 8068503.137 8702664.41 6789185.453 6483859.892 7589067.01 0.695179821 1.189622058 0.959952093 0.916121536 1.063174581 1.146737062 0.894600805 0.854368512 1 22.8554911 YVRPFLNSISK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YVRPFLNSISK 11 1 O00231;O00231-2;J3QRY4 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 ; 142.1 3.45E-05 1567490000 1471640 2055250 1172180 1369420 1944850 1937590 2201980 2407420 1860380 FALSE TRUE 1277159.045 2041748.927 1739050.169 1680367.741 1906151.29 2012130.341 1988432.319 1892611.968 1640447.996 0.778542842 1.244628865 1.060106857 1.024334661 1.161969959 1.226573684 1.212127616 1.153716529 1 20.64565843 3.232961441 24.71095554 1.15961101 1.044826809 0.183832622 0.12659621 211.1637247 931931.1632 0.036253948 0.042265378 1709.863497 -3.232961441 -0.114784201 YVSDRPQAFK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YVSDRPQAFK 10 1 Q9Y6D6;E5RIF2;E5RHL7 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 0 129.16 0.00028325 282490000 457810 413370 259930 310560 399130 344300 489400 560590 433390 FALSE TRUE 397309.2486 410654.5453 385633.0174 381077.3946 391188.0939 357545.4438 441938.0633 440712.191 382155.1279 1.039654369 1.07457552 1.009100727 0.997179854 1.023636909 0.935602894 1.156436303 1.153228516 1 18.54379886 2.224109373 24.99999589 1.115856995 1.015624709 0.363984575 0.055145531 228.1656713 394713.2032 0.022536593 0.01526944 167.5364749 -2.224109373 -0.100232286 YVSGDVTHPQAGAEDALIVHCVDDSGHWGR ddPTM_MDA-MB-175_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 0 162.44 1.34E-12 125220000 46203 45410 17106 27915 47995 46016 42460 45086 40942 FALSE TRUE 40097.15649 45111.69872 25378.51882 34253.5274 47039.9934 47786.2653 38342.23574 35444.70976 36101.8834 1.110666611 1.249566351 0.702969386 0.948801674 1.30297893 1.323650203 1.062056384 0.981796694 1 15.13978648 1.993124457 24.82970373 0.99929661 1.104413413 0.06385253 0.180825445 956.1246414 3452859.245 0.08254624 0.053231469 98.42931377 -1.993124457 0.105116802 YVSGSS(ph)PDLVTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YVSGSSPDLVTR 12 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 YVSGS(0.001)S(0.999)PDLVTR;YVSGS(0.006)S(0.994)PDLVTR 362.27 2.05E-72 531330000 939350 944700 734710 899780 1037970 1006330 880130 1180390 1266370 TRUE FALSE 815212.5175 938494.2035 1090018.213 1104088.801 1017316.428 1045044.166 794775.1281 927972.7843 1116661.181 0.730044647 0.840446699 0.976140509 0.988741097 0.911034112 0.935865045 0.711742417 0.831024486 1 20.09076008 4.629199941 3.605390006 0.895035288 0.727202625 0.295173292 0.085940275 0.366039549 7.67075701 0.02334397 0.132567196 42579.43953 -4.629199941 -0.167832664 YVSLHVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YVSLHVR 7 0 P41227-2;P41227;C9JN83;F8W808;A8MWP7;C9JW55;Q9BSU3 P41227-2 NAA10;NAA11 N-alpha-acetyltransferase 10;N-alpha-acetyltransferase 11 0 ; 134.06 0.0052914 382450000 422800 571150 215989 381410 583110 644450 537960 588960 626170 FALSE TRUE 366925.9088 567398.078 320442.0028 468014.97 571507.2518 669242.4085 485788.722 463015.4873 552144.8959 0.664546411 1.027625325 0.580358535 0.84763071 1.035067527 1.212077506 0.879821086 0.838576053 1 19.07468739 3.426487102 6.160225229 0.974590143 0.773238418 0.340590962 0.149838641 0.25734387 21.88984523 0.044343344 0.05787248 2669.851475 -3.426487102 -0.201351726 YVTAFNGELEDYMSDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YVTAFNGELEDYMSDR 16 0 F5H8D7 F5H8D7 XRCC1 0 109.84 0.0021897 17877000 14409 16742 7508.4 9213 11849 16494 15234 13976 11379 FALSE TRUE 12504.81414 16632.0207 11139.48735 11304.95246 11613.22808 17128.53485 13756.60902 10987.34116 10033.78758 1.246270567 1.657601435 1.110197646 1.126688438 1.157412192 1.707085655 1.371028528 1.09503426 1 13.29257868 1.633594814 4.126280193 1.023146795 1.341485531 0.263754895 0.205080061 0.230571318 8.902529962 0.155295763 0.055181631 43.01251271 -1.633594814 0.318338736 YVVLCRGAK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YVVLCRGAK 9 1 O75426-2;O75426-4;O75426;O75426-3 O75426-2 FBXO24 F-box only protein 24 0 ; 71.501 0.029683 2742400000 5138300 5131500 2756400 3181200 4417900 4181600 5815500 6047900 2063510 FALSE TRUE 4459260.636 5097790.839 4089404.26 3903540.082 4329992.433 4342468.858 5251513.705 4754603.65 1819564.199 2.450730037 2.801654837 2.247463576 2.145315941 2.379686541 2.386543361 2.88613818 2.613045285 1 20.79516152 4.225745882 24.93676154 2.31242658 2.626192468 0.080201524 0.499523968 593.2606905 1154458.576 0.127249835 0.267641367 16816.89767 -4.225745882 0.313765889 YVWLVYEQDRPLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YVWLVYEQDRPLK 13 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 208.82 3.91E-08 5023200000 3108600 2325300 1821420 2317100 1955090 1810330 2374000 2915800 5660200 FALSE TRUE 2697790.634 2310024.951 2702264.804 2843232.97 1916187.534 1879974.567 2143769.845 2292278.861 4991057.604 0.540524844 0.462832757 0.541421282 0.569665429 0.383924147 0.376668577 0.429522161 0.45927718 1 22.25091412 1.238025504 24.99292033 1.000000607 0.467475602 0.867663097 0.064981126 4.710783946 219813.0276 0.097762796 0.017007312 17.29917946 -1.238025504 -0.532525005 YVWLVYEQDRPLKCDEPILSNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YVWLVYEQDRPLKCDEPILSNR 22 2 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 237.15 9.18E-31 1065970000 547250 489310 210423 246751 297700 282670 439220 533900 187561 FALSE TRUE 474929.5259 486095.6904 312184.2666 302779.5859 291776.3524 293544.4978 396624.512 419729.6398 165387.7523 2.871612435 2.939127498 1.887589996 1.830725563 1.764195646 1.774886555 2.398149238 2.537852012 1 17.33549287 4.2400014 24.94428452 1.960423469 2.905370331 0.505673838 0.414296692 31.52949321 545816.9082 0.108515073 0.257196502 17378.06432 -4.2400014 0.944946862 YWCDAEYDAYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YWCDAEYDAYR 11 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 ;;; 179.51 1.65E-05 1421700000 1204590 1303080 908770 1020530 1195330 1181270 975760 1228320 1875480 FALSE TRUE 1045400.379 1294519.982 1348254.212 1252256.934 1171545.272 1226714.221 881130.9454 965653.3268 1653762.891 0.63213438 0.782772421 0.815264521 0.757216734 0.708411876 0.741771525 0.532803675 0.583912804 1 20.65732097 2.420864376 24.99946396 0.667921981 0.74464403 0 0.13172387 249.1610017 110720.2031 0.048849599 0.03783874 263.5508227 -2.420864376 0.076722049 SGGLQT(ph)PECLSR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 SGGLQTPECLSR 12 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 SGGLQT(1)PECLSR;SGGLQT(1)PECLSR 164.93 0.00062581 491360000 1193470 756190 395490 468600 677860 597970 525080 610790 522860 TRUE FALSE 1035749.916 751222.5381 586750.2868 575002.7921 664371.9122 620974.2928 474157.8224 480177.3117 461048.0864 2.24651169 1.629380015 1.272644447 1.247164469 1.441003513 1.346875328 1.028434639 1.041490738 1 18.8145577 8 0.559655249 1.10710994 54.94173803 0.874575598 0.130740044 53.94708288 0.488699549 0.076639791 3499.66321 100000000 -8 53.83462809 up YWDAEK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YWDAEK 6 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 112.75 0.062188 573440000 1071200 995910 754520 969960 1004300 897130 1133900 1298300 1798800 FALSE TRUE 929638.2059 989367.8016 1119408.396 1190204.243 984316.3949 931643.1716 1023934.553 1020668.648 1586147.913 0.586098054 0.623755069 0.705740232 0.750374056 0.620570368 0.587362102 0.645547962 0.643488946 1 20.59709588 1.238195845 24.99999965 1.000000395 0.647192713 0.831422974 0.050178525 3.694936392 252886.9348 0.07413369 0.01301841 17.30596594 -1.238195845 -0.352807681 YWDGWFR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YWDGWFR 7 0 Q9Y570;Q9Y570-4;Q9Y570-2;Q9Y570-3 Q9Y570 PPME1 Protein phosphatase methylesterase 1 0 ; 114.19 0.013869 796090000 2021240 1616670 987650 1098990 1630860 1672620 1604140 1740090 1550740 FALSE TRUE 1754128.013 1606049.988 1465280.843 1348532.477 1598409.077 1736966.774 1448570.75 1367985.295 1367413.284 1.282807498 1.174516883 1.07157131 0.986192318 1.168929025 1.27025735 1.059351088 1.000418316 1 20.38301791 -2 0.046683171 5.57E-10 1.759204034 0.301142946 0.090978712 1877.705104 8.59291397 275.3053971 94.39898721 0.01 2 1.759204033 YWGEIISQQYNFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YWGEIISQQYNFDR 14 0 A0A3B3ISG5;P14735;P14735-2 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 244.71 3.06E-17 507810000 105422 100897 87579 102775 109571 109350 95239 104729 219155 FALSE TRUE 91490.21559 100234.201 129932.4973 126111.6346 107390.7515 113556.7653 86002.73644 82333.51835 193246.7456 0.47343729 0.518685066 0.672365772 0.652593834 0.555718292 0.587625758 0.44504106 0.426053842 1 17.56008459 1.229745391 24.99913056 1.000000875 0.540256055 0.758235531 0.081372865 193.6789648 549212.9429 0.2651806 0.022691187 16.97248332 -1.229745391 -0.45974482 YWGEIISQQYNFDRDNTEVAYLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YWGEIISQQYNFDRDNTEVAYLK 23 1 A0A3B3ISG5;P14735;P14735-2 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 199.04 2.45E-24 546970000 378470 369190 199865 256360 396060 315710 387960 482190 238700 FALSE TRUE 328454.2306 366764.7666 296520.3825 314570.4562 388179.1809 327855.568 350335.6989 379077.4209 210481.1579 1.560492321 1.742506409 1.408773999 1.494530244 1.8442467 1.557648063 1.664451594 1.801004064 1 17.68333156 1.229598185 24.99892053 0.999998773 1.639589036 0.682208379 0.135989413 210.9796385 588441.2428 0.398261415 0.033552592 16.96673142 -1.229598185 0.639590262 YWGPAS(ph)PTHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 YWGPASPTHK 10 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 YWGPAS(0.962)PT(0.038)HK;YWGPAS(0.971)PT(0.029)HK;YWGPAS(0.992)PT(0.008)HK;YWGPAS(0.819)PT(0.181)HK;YWGPAS(0.98)PT(0.02)HK;YWGPAS(0.864)PT(0.136)HK;YWGPAS(0.997)PT(0.003)HK;YWGPAS(0.906)PT(0.094)HK 183.99 1.69E-06 29492570000 3820460 5949450 7035250 8744920 9181890 7671510 10072830 12081480 15964450 TRUE FALSE 3315576.531 5910367.671 10437520.43 10730587.74 8999188.353 7966637.954 9095968.497 9497949.52 14077150.91 0.235528947 0.419855389 0.7414512 0.762269852 0.639276258 0.56592687 0.646151239 0.674706806 1 23.74685204 4.405868183 3.254000274 0.704226275 0.258544876 0.671310437 0.116716457 0.14583709 2.971849641 0.030299316 0.109382445 25460.57358 -4.405868183 -0.445681399 YWGPASPT(ph)HK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YWGPASPTHK 10 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 YWGPAS(0.191)PT(0.809)HK;YWGPAS(0.374)PT(0.626)HK 165.39 6.56E-05 1090130000 561880 911570 895340 1278090 1332010 1154200 1475430 1652450 2455000 TRUE FALSE 487626.1344 905581.8366 1328329.419 1568299.869 1305505.607 1198602.821 1332343.026 1299086.427 2164772.697 0.22525512 0.418326524 0.613611499 0.724463992 0.603068215 0.5536853 0.615465553 0.600102925 1 21.04578412 4.453346954 1.959475935 0.663065028 0.201608416 0.601789845 0.124668816 0.31835232 1.96024099 0.03315664 0.216158582 28401.87121 -4.453346954 -0.461456612 YWGPASPT(ph)HKLPPSFPGNKDELMQHMDEVNDELIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YWGPASPTHKLPPSFPGNKDELMQHMDEVNDELIR 35 2 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 YWGPAS(0.137)PT(0.863)HKLPPSFPGNKDELMQHMDEVNDELIR 132.1 2.41E-08 1056200000 200620 262700 148100 217900 327560 330390 533070 591310 59214 TRUE FALSE 174107.5587 260974.3064 219721.6554 267377.5254 321042.1969 343100.3171 481372.9534 464862.9581 52213.78838 3.334513049 4.998187538 4.208115561 5.120822176 6.148609531 6.571067294 9.219268864 8.90306895 1 15.67214322 3.233434099 1.711234962 7.056397161 4.23931516 0.140413888 2.270714003 0.557644325 3.39214975 0.804158963 1.063102735 1711.725416 -3.233434099 -2.817082 YWGPASPTHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YWGPASPTHK 10 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 93.325 0.0088629 366090000 416720 372170 117870 212520 308330 275280 279610 315420 336210 FALSE TRUE 361649.3962 369725.1908 174872.3263 260775.9142 302194.8362 285870.1997 252493.4652 247969.8876 296463.6368 1.219877757 1.247118179 0.589860963 0.879621923 1.01933188 0.964267331 0.851684436 0.836425979 1 18.17749563 4.27532959 24.99975792 0.880549604 1.233498943 0.606134975 0.119345227 114.0459562 77539.75123 0.029598366 0.078305222 18850.7915 -4.27532959 0.352949339 YWGSGLHDK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YWGSGLHDK 9 0 Q99986 Q99986 VRK1 Serine/threonine-protein kinase VRK1 0 78.098 0.030734 146920000 218230 230380 119350 158160 231600 182190 233830 287160 266020 FALSE TRUE 189390.3526 228866.6186 177068.0592 194072.6453 226991.6131 189198.9672 211153.2026 225753.0687 234571.4187 0.80738887 0.975679901 0.754857775 0.827349924 0.967686577 0.806572976 0.900165944 0.962406545 1 17.83966771 1.733057492 2.337927828 0.994869831 0.860582116 0.35226949 0.069330891 0.303988013 3.382428271 0.060685386 0.01861505 54.08259123 -1.733057492 -0.134287715 YWLEEAECR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 YWLEEAECR 9 0 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;;;;;; 221.36 9.83E-07 2711420000 2633310 2824610 1691667 1926810 2508870 2635390 2457650 2730830 2622090 FALSE TRUE 2285311.412 2806054.951 2509762.819 2364321.66 2458948.396 2736775.159 2219307.481 2146863.256 2312109.507 0.988409677 1.213634104 1.085486138 1.022582041 1.063508622 1.183670215 0.959862616 0.928530093 1 21.1407783 2.172706542 11.27132225 0.955265035 1.093468569 0.443031924 0.068584263 0.472333063 78.79205601 0.027030317 0.018225619 148.8355039 -2.172706542 0.138203534 YWPQEAGEYAVHVLCNSEDIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YWPQEAGEYAVHVLCNSEDIR 21 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ; 179.58 5.70E-17 298810000 100775 181432 60163 44266 90129 139178 93621 109775 118235 FALSE TRUE 87457.32842 180240.1612 89258.02803 54317.27186 88335.60923 144532.2677 84541.64983 86300.47052 104257.393 0.838859729 1.72879981 0.856131402 0.52099204 0.847283887 1.386302339 0.810893572 0.827763557 1 16.66979016 YWPTADGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YWPTADGR 8 0 P52788;H7C2R7;P52788-2 P52788 SMS Spermine synthase 0 ;;;;; 150.17 0.0011482 2407550000 3524900 3034420 1697367 1968090 2660500 2878890 2640850 2730910 2763340 FALSE TRUE 3059075.534 3014486.695 2518219.359 2414974.915 2607561.255 2989642.761 2384740.773 2146926.148 2436661.093 1.255437427 1.237138272 1.033471321 0.991100043 1.070137026 1.22694238 0.978692023 0.881093458 1 21.21647417 8 0.233505079 0.918912507 2.904994387 0.471593501 0.091699114 84.26722776 1.318898854 0.412125052 62.34306732 100000000 -8 1.98608188 YWQQVIDMNDYQR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YWQQVIDMNDYQR 13 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ;;; 327.32 5.81E-62 1413780000 2057220 2028480 1236490 1573190 2173950 2159740 1868430 2310440 2124510 FALSE TRUE 1785353.165 2015154.781 1834460.7 1930406.834 2130692.648 2242826.595 1687229.946 1816370.386 1873352.848 0.953025569 1.075694194 0.979239283 1.030455547 1.137368569 1.197225924 0.900647173 0.969582632 1 20.83719123 2.203288709 24.99999757 0.957080821 1.060990529 0.311706332 0.073835537 228.9796222 162294.3888 0.031307558 0.021108379 159.6940405 -2.203288709 0.103909708 YWSQQIEESTTVVTTQSAEVGAAETTLTELRR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 YWSQQIEESTTVVTTQSAEVGAAETTLTELRR 32 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;; 351.52 1.90E-131 4334692600 609356.4 552989.4 403947.3 479305.1 568924.2 650907.9 608581.4 641242.5 462054 FALSE TRUE 528828.4078 549356.7762 599297.5654 588138.6487 557603.7215 675948.7481 549561.2695 504117.7815 407430.5025 1.297959786 1.348344743 1.470919732 1.443531216 1.368586098 1.659052879 1.348846653 1.237309869 1 18.63619447 1.436050176 1.955772715 0.958636499 1.429001221 0.661552572 0.098322453 0.312400357 1.734636311 0.241503112 0.027645787 27.2929309 -1.436050176 0.470364722 YWVSGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YWVSGR 6 0 P26640;A0A140T936;H0Y426 P26640 VARS Valine--tRNA ligase 0 ;; 121.68 0.045473 1120870000 1006970 1162080 719097 811911 1079890 1254430 1246140 1156960 1337740 FALSE TRUE 873896.3632 1154446.22 1066854.714 996267.8018 1058402.302 1302688.734 1125289.535 909553.1075 1179593.901 0.740845101 0.978681069 0.904425424 0.844585413 0.897259897 1.104353568 0.953963507 0.771073084 1 20.16985884 2.988789638 24.96364625 0.936022877 0.876910165 0.136074499 0.100350271 1668.201499 3714820.598 0.033183127 0.035229156 974.5174902 -2.988789638 -0.059112712 YYADGEDAYAMK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YYADGEDAYAMK 12 0 P41227-2;P41227;C9JN83;F8W808;A8MWP7;C9JW55;Q9BSU3;H0Y8T0 P41227-2 NAA10;NAA11 N-alpha-acetyltransferase 10;N-alpha-acetyltransferase 11 0 157.24 0.00017184 75730000 127130 124380 93808 121230 114220 103160 122770 150340 194360 FALSE TRUE 110329.4484 123562.9396 139173.8626 148757.1244 111947.2455 107128.632 110863.7843 118190.9609 171382.9822 0.643759649 0.720975548 0.812063489 0.86798072 0.653199308 0.625083253 0.646877437 0.689630671 1 17.38686434 1.236344487 24.9926942 1.000000377 0.708211696 0.581842536 0.077940273 48.06963865 541980.5172 0.134562173 0.020850794 17.23234922 -1.236344487 -0.291788682 YYAFDEAFVR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YYAFDEAFVR 10 0 O43427-2;O43427;E9PSD3;E9PJW6 O43427-2 FIBP Acidic fibroblast growth factor intracellular-binding protein 0 111.17 0.0041627 43264000 91553 79068 60932 66855 86857 58793 105100 89088 58443 FALSE TRUE 79454.03908 78548.5971 90398.91901 82035.44956 85128.71563 61054.80475 94907.41818 70037.22448 51533.93512 1.541780943 1.524211123 1.754162937 1.591872411 1.651896278 1.184749517 1.841648963 1.359050581 1 15.65323514 1.369917039 3.405869883 0.987299869 1.577494672 0.539114759 0.172954084 0.19352517 3.307244397 0.243368531 0.041932654 23.43781055 -1.369917039 0.590194803 YYDDIYFDS(ph)DS(ph)EDEDRAVQVTK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YYDDIYFDSDSEDEDRAVQVTK 22 1 G3V2W9;A0A087X060;Q56P03 G3V2W9 EAPP E2F-associated phosphoprotein 2 YYDDIY(0.004)FDS(0.996)DS(1)EDEDRAVQVTK 113.5 0.00014705 51254000 236130 201130 106240 122020 181260 169050 187670 234690 126800 TRUE FALSE 204924.8222 199808.7638 157618.0194 149726.506 177653.2806 175553.4629 169469.7923 184503.3699 111809.8485 1.832797603 1.787040825 1.409697102 1.339117332 1.58888759 1.570107332 1.515696467 1.650153116 1 16.77068774 4.258644246 10.83043575 1.468498237 1.810511041 0.408657013 0.18281029 0.446542088 231.3654102 0.044503371 0.114045116 18140.29087 -4.258644246 0.342012804 YYDDTYPSVK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YYDDTYPSVK 10 0 F8VYZ4;F8VVA7;P61923-5;P61923;P61923-4;F8VXB1;F8VUC5;F8W156;F8VXR1 F8VYZ4 COPZ1 Coatomer subunit zeta-1 0 152.79 4.05E-05 180850000 658450 513040 363450 411920 491010 451000 578370 662600 621370 FALSE TRUE 571434.1642 509669.8065 539215.6357 505452.7318 481239.8616 468350.2618 522279.7664 520908.1464 547912.3465 1.042929892 0.930203179 0.984127551 0.922506556 0.878315418 0.854790488 0.953217736 0.950714379 1 19.06358559 YYDEDEDEE ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YYDEDEDEE 9 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 173.59 0.00012869 144160000 338910 347510 240400 279220 342580 331010 307640 351430 393470 FALSE TRUE 294122.1848 345227.1839 356658.2441 342621.1686 335763.3282 343744.1689 277805.1202 276279.4293 346954.4248 0.847725706 0.995021707 1.02796857 0.98751059 0.967744765 0.990747327 0.800696288 0.796298907 1 18.40438664 2.24734915 24.99396772 0.848506747 0.974018271 0.300667231 0.072850358 183.8321072 522806.5987 0.027170478 0.020718715 176.7458194 -2.24734915 0.125511523 YYDSRPGGYGYGYGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 8 YYDSRPGGYGYGYGR 15 1 P98179 P98179 RBM3 RNA-binding protein 3 0 ;;;;;;; 202.25 5.48E-09 31224220000 17287230 19237000 9750400 11528700 17752110 17985940 14729920 18062220 12220910 FALSE TRUE 15002678.76 19110630.88 14465726.05 14146467.54 17398877.74 18677870.75 13301414.63 14199754.81 10776167.94 1.392209071 1.773416207 1.342381274 1.312754925 1.614570025 1.733257207 1.234336241 1.317699844 1 23.3613409 1.408845894 1.272207999 0.890908955 1.515702334 0.468249362 0.171899982 0.936094612 1.696896281 0.734945298 0.05367612 25.63574209 -1.408845894 0.624793379 YYEGYYAAGPGYGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YYEGYYAAGPGYGGR 15 0 Q93052;A0A087WZF1;C9JUT4;C9JXK9 Q93052 LPP Lipoma-preferred partner 0 ; 259.08 1.76E-24 311940000 502800 505510 347791 388040 487140 543370 471970 522800 499970 FALSE TRUE 436353.7061 502189.2715 515983.8909 476150.4128 477446.8671 564273.7955 426198.422 411003.2884 440864.1162 0.98976916 1.13910217 1.170392128 1.08003894 1.082979652 1.279926796 0.966734208 0.932267502 1 18.74997453 2.050969285 24.32735547 0.957757196 1.122742056 0.493098748 0.075104224 58.24000162 27797.24528 0.029463402 0.019864214 112.4525439 -2.050969285 0.164984859 YYFSHDTD ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YYFSHDTD 8 0 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ;;; 193.7 0.0003938 1998950000 3908790 3583190 2013280 2571380 3508810 3719520 3559320 3669870 3517630 FALSE TRUE 3392233.498 3559651.789 2986908.942 3155251.13 3438991.546 3862612.341 3214137.694 2885096.859 3101779.789 1.093640983 1.147615895 0.96296615 1.017238922 1.10871557 1.245289029 1.036223689 0.930142388 1 21.56466483 1.996717306 24.99966354 0.967011847 1.093518702 0.337899208 0.075646728 149.6008105 1139302.206 0.03327836 0.021928017 99.2469812 -1.996717306 0.126506854 YYGGGSEGGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YYGGGSEGGR 10 0 P14866 P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;; 176.09 6.06E-06 3508620000 3920470 3408620 1907930 2607320 3398680 3691680 3330350 3257640 3336350 FALSE TRUE 3402369.956 3386228.551 2830611.33 3199351.856 3331052.917 3833701.318 3007373.17 2561019.037 2941930.504 1.156509289 1.151022618 0.962161182 1.087500827 1.132267711 1.303124365 1.022244803 0.870523295 1 21.48833174 2.002533461 24.98026104 0.93212451 1.126503321 0.467582791 0.087977965 63.43835368 625506.1276 0.037278744 0.024964787 100.5850559 -2.002533461 0.194378811 YYHSPTNTVHMYPPEMAPSSAPPS(ph)TPPTHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YYHSPTNTVHMYPPEMAPSSAPPSTPPTHK 30 0 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 YYHSPTNTVHMYPPEMAPSSAPPS(0.46)T(0.46)PPT(0.08)HK 87.489 0.00055843 322890000 71132 62669 25137 37666 64921 56759 66588 73295 56250 TRUE FALSE 61731.72597 62257.32321 37293.33728 46218.64099 63629.19912 58942.55546 60130.30601 57621.43463 49600.18908 1.244586505 1.255183183 0.751878934 0.931823887 1.282841866 1.188353443 1.212299935 1.161718044 1 15.598058 3.239218471 24.99998123 1.172336907 1.039819989 0.128766307 0.158731637 38.28931697 1455040.318 0.049420085 0.060030765 1734.676402 -3.239218471 -0.132516918 YYIADR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YYIADR 6 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ;;; 106.76 0.074087 2488190000 3616150 3339690 1922930 2254830 3126340 3281360 3086930 3371810 3018990 FALSE TRUE 3138266.615 3317751.356 2852865.38 2766823.614 3064131.951 3407596.043 2787560.004 2650774.671 2662088.441 1.178873912 1.246296443 1.071664388 1.039343236 1.151025602 1.280046143 1.047132755 0.99575004 1 21.34412707 2.016672753 24.49494813 1.004732412 1.155719112 0.497646047 0.070656648 159.858008 234855.8798 0.030681164 0.020679161 103.9136865 -2.016672753 0.1509867 YYIDADLLR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YYIDADLLR 9 0 Q7Z3B4-2;Q7Z3B4-3;Q7Z3B4 Q7Z3B4-2 NUP54 Nucleoporin p54 0 99.136 0.012892 137650000 217510 231940 140290 171460 250060 268240 175700 251110 259900 FALSE TRUE 188765.5024 230416.3709 208134.7132 210392.6136 245084.2952 278559.3664 158660.641 197412.0806 229174.9181 0.823674353 1.005417053 0.908191503 0.918043804 1.069420237 1.215488015 0.692312415 0.861403518 1 17.80608963 2.218337738 24.99997676 0.846734522 0.987353647 0.210044115 0.126719182 385.3509857 476375.9961 0.052471668 0.035424493 165.3246979 -2.218337738 0.140619125 YYINHNER ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YYINHNER 8 0 Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;Q9HAU0-5;Q9HAU0-3 Q9HAU0 PLEKHA5 Pleckstrin homology domain-containing family A member 5 0 124.23 0.0013137 78674000 55133 52990 31029 31629 54799 59812 47845 51882 49424 FALSE TRUE 47847.03436 52641.9052 46034.72819 38810.84787 53708.60711 62113.00634 43204.99926 40787.43805 43581.15102 1.097883678 1.207905344 1.056299045 0.890542057 1.232381565 1.425226385 0.991368935 0.935896301 1 15.41141668 2.029876453 24.99823872 0.963447886 1.147268256 0.271258147 0.136177815 267.6675101 223961.7972 0.058753595 0.039611179 107.1214526 -2.029876453 0.183820371 YYITIIDAPGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YYITIIDAPGHR 12 0 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;A0A2R8YDN5 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ;;; 178.67 2.17E-05 6962830000 9125500 7018340 4758010 6484550 7047830 7449340 7531000 8399200 8548000 FALSE TRUE 7919542.054 6972236.062 7058999.551 7956966.188 6907591.972 7735920.93 6800644.779 6603096.443 7537465.178 1.050690367 0.925010716 0.93652168 1.055655449 0.916434346 1.026329243 0.902245598 0.876036743 1 22.845648 2.218819429 24.94511533 0.914671785 0.98025217 0.173061403 0.058437971 347.8143652 439497.3761 0.022602754 0.015262235 165.508167 -2.218819429 0.065580385 YYKVDENGK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YYKVDENGK 9 1 P62979;A0A2R8Y422 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ;;; 158.79 6.07E-05 3882770000 5910650 5254270 2651280 3388830 4623180 3730520 7006990 8110920 1523410 FALSE TRUE 5129542.627 5219754.354 3933447.876 4158315.647 4531187.763 3874035.518 6327453.188 6376462.877 1343314.205 3.818572458 3.885728547 2.928166665 3.095564411 3.373140659 2.883938473 4.710329991 4.74681415 1 20.35736536 1.224525796 24.99400675 0.999993142 3.708719355 0.620451248 0.658480187 574.0200316 1022187.257 3.786245716 0.184750919 16.76971942 -1.224525796 2.708726213 YYLHDDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YYLHDDR 7 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;;; 157.52 0.0014707 2788320000 3884100 3331040 1864650 2336510 3229630 3616230 2833130 3555260 3706030 FALSE TRUE 3370806.344 3309158.179 2766400.977 2867050.307 3165366.682 3755348.708 2558373.489 2794995.316 3267907.355 1.031487731 1.012623009 0.846535925 0.877335247 0.968621915 1.149160089 0.782878219 0.855285971 1 21.63993565 4.373332727 8.105274748 0.919658726 1.026635756 0.135344842 0.100858835 0.441153287 30.16418738 0.026139458 0.069676411 23622.87363 -4.373332727 0.10697703 YYLTDVDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YYLTDVDR 8 0 P29992;K7EL62 P29992 GNA11 Guanine nucleotide-binding protein subunit alpha-11 0 92.653 0.027045 119480000 353720 345190 206520 283530 380140 443830 263310 435080 456140 FALSE TRUE 306975.0058 342922.4242 306393.7628 347909.82 372575.9577 460904.4273 237774.2367 342041.5278 402215.6488 0.763210001 0.852583496 0.761764898 0.864983302 0.926308956 1.145913712 0.591161078 0.850393387 1 18.61760969 3.578470127 5.683512077 0.885885365 0.799226845 0.107522581 0.139832315 0.676811802 31.15784846 0.039744957 0.059189544 3788.524737 -3.578470127 -0.08665852 YYPTEDVPR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 6 YYPTEDVPR 9 0 Q02878;F8VZ45;U3KQR5;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ;;;;; 221.33 9.86E-07 5560580000 5325040 5167200 3213460 3938850 5071720 5593410 4660360 5335610 5350120 FALSE TRUE 4621322.472 5133256.323 4767500.004 4833226.094 4970802.695 5808592.102 4208399.005 4194631.323 4717634.908 0.979584593 1.088099529 1.010569935 1.024501935 1.053664133 1.231250874 0.892056949 0.889138605 1 22.16963234 2.145492318 22.54600453 0.917697143 1.061057092 0.435885775 0.073428351 7.249102808 1750.623628 0.029432853 0.019843638 139.7952189 -2.145492318 0.143359949 YYPTEDVPRK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 4 YYPTEDVPRK 10 1 Q02878;F8VZ45;U3KQR5;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ;;; 163.94 1.01E-05 1696940000 1830760 1661650 872850 1022790 1503260 1490370 1732350 1907710 468034 FALSE TRUE 1588820.427 1650734.512 1294963.18 1255030.102 1473348.067 1547705.498 1564346.964 1499761.062 412703.5537 3.849786156 3.999806876 3.137756309 3.040996596 3.569991229 3.750162761 3.790485809 3.633991151 1 18.65474634 1.238002082 24.99959447 0.999997049 3.592323908 0.881022884 0.299877579 4.723506168 211228.759 0.455876918 0.079071378 17.29824653 -1.238002082 2.592326859 YYQTIGNHASYYK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YYQTIGNHASYYK 13 0 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2;H0YD73;E9PL38 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 129.29 0.00015542 566580000 372280 571190 139240 279470 732780 677170 569480 587370 660350 FALSE TRUE 323082.2548 567437.8153 206576.9297 342927.9349 718199.1117 703221.1681 514251.9173 461765.4964 582284.1753 0.554853229 0.97450324 0.354769953 0.588935694 1.233416847 1.207694109 0.883163134 0.793024293 1 19.15136389 3.260260378 24.98153509 0.993344753 0.624889808 0.501989223 0.199244431 233.0874445 268336.8014 0.061042135 0.078734401 1820.792172 -3.260260378 -0.368454945 YYS(ph)PCEEHPAETNQNEGAESGTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YYSPCEEHPAETNQNEGAESGTIR 24 0 A0A2R8YF49;A0A5F9ZH52;A5YM69 A0A2R8YF49;A0A5F9ZH52;A5YM69 ARHGEF35 Rho guanine nucleotide exchange factor 35 1 YYS(0.999)PCEEHPAETNQNEGAESGTIR;YYS(1)PCEEHPAETNQNEGAESGTIR 139.31 5.45E-10 198430000 103417 99576 56842 73063 95437 102521 87284 109909 89123 TRUE FALSE 89750.18142 98921.8787 84330.98133 89653.07085 93537.99042 106465.0492 78819.21111 86405.81566 78586.98047 1.142048987 1.258756579 1.073090998 1.140813279 1.190247925 1.354741569 1.002955078 1.099492755 1 16.2620027 2.192679893 24.99999972 1.046462613 1.188273864 0.466609252 0.079724256 122.2753093 66625.82642 0.032280459 0.021763567 155.840342 -2.192679893 0.141811251 YYS(ph)PCEEHPAETNQNEGSESGTIR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YYSPCEEHPAETNQNEGSESGTIR 24 0 A0A2R8YFR7;Q12774 A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 YYS(1)PCEEHPAETNQNEGSESGTIR 291.51 5.17E-62 629250000 107390 167210 97754 108150 144750 147600 128880 148930 155130 TRUE FALSE 93198.13941 166111.5865 145028.1614 132707.1105 141869.7582 153278.2675 116381.2374 117082.4785 136790.7081 0.681319226 1.214348465 1.060219392 0.970147112 1.037130081 1.120531282 0.850797829 0.855924208 1 17.06161071 2.222856426 24.99808406 0.890447942 1.024224181 0.116016258 0.142266717 419.8093402 668251.3724 0.054427912 0.036831049 167.0538256 -2.222856426 0.133776239 YYSHVDYR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YYSHVDYR 8 0 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8VWU8;F8VPY7;F8VRK2 F8W0Q9 PPHLN1 Periphilin-1 0 95.909 0.0093158 168360000 176400 191070 129950 127490 164440 230710 155510 177790 154850 FALSE TRUE 153088.2931 189814.8486 192794.2547 156438.5531 161167.9657 239585.563 140428.6641 139770.9921 136543.8094 1.12116612 1.390138809 1.411958957 1.145702275 1.18033887 1.754642441 1.028451343 1.023634778 1 17.05900438 2.057139167 24.99999169 1.017257226 1.330128585 0.408018208 0.179803372 75.90333023 33209.36811 0.071204159 0.048005827 114.0615232 -2.057139167 0.312871359 YYTLFGR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YYTLFGR 7 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 150.02 0.0045995 3496400000 1539550 1623130 952300 972070 1767100 1833730 1696210 1741670 1685400 FALSE TRUE 1336094.567 1612467.552 1412835.465 1192793.351 1731938.167 1904274.78 1531711.815 1369227.424 1486153.932 0.899028383 1.084993632 0.950665631 0.802604175 1.165382757 1.281344239 1.030654889 0.921322748 1 20.50315212 3.225008389 24.99992053 1.066337341 0.946252441 0.267163269 0.117792038 430.0674191 793347.3618 0.040040289 0.045642886 1678.836447 -3.225008389 -0.1200849 YYTPTISR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YYTPTISR 8 0 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 75.109 0.09129 95695000 115590 115820 77566 96729 112790 107280 120610 112660 145340 FALSE TRUE 100314.4886 115059.1708 115077.177 118692.7979 110545.6997 111407.131 108913.2608 88568.53572 128158.0708 0.782740315 0.897791065 0.897931565 0.926143763 0.862573063 0.869294695 0.849835364 0.691088241 1 16.96756481 1.991075359 24.18965253 0.807573847 0.875541387 0 0.083648024 580.2466568 1572718.89 0.034332416 0.021789808 97.96599614 -1.991075359 0.067967541 YYTSASGDEMVS(ph)LKDYCTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 2 YYTSASGDEMVSLKDYCTR 19 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 YYTSASGDEMVS(1)LKDYCTR;YYTSASGDEMVS(1)LKDYCTR 242.71 1.22E-24 349350000 397980 401600 209820 190910 381090 308030 377090 417500 372950 TRUE FALSE 345385.9346 398961.8632 311289.6538 234259.0334 373507.0546 319880.1134 340519.8698 328220.874 328860.2759 1.050251307 1.213165263 0.946571163 0.712336061 1.135762152 0.972693076 1.035454553 0.998055704 1 18.32711523 4.226149118 24.98781426 0.97399036 1.131708296 0.259578244 0.112393446 268.453642 540475.1026 0.028474983 0.059947756 16832.51919 -4.226149118 0.157717936 YYTSASGDEMVSLK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 3 YYTSASGDEMVSLK 14 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;; 265.72 1.99E-24 282439000 349672 289709 207471 252587 304092 267519 327125 373421 379110 FALSE TRUE 303461.9592 287805.8825 307804.6695 309940.7389 298041.1641 277810.629 295400.4678 293567.8251 334292.0477 0.907774987 0.860941457 0.920765755 0.927155585 0.891559241 0.831041692 0.883659871 0.878177711 1 18.35074951 1.23590947 24.9890708 1.000000151 0.886795276 0.612165717 0.028100551 51.72335569 487432.4048 0.047344502 0.007114957 17.21509683 -1.23590947 -0.113204875 YYTSASGDEMVSLKDYCTR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YYTSASGDEMVSLKDYCTR 19 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 300.97 5.66E-50 544400000 512080 487430 155750 144190 424630 379810 615580 636580 25248 FALSE TRUE 444407.3306 484228.0402 231071.221 176930.5433 416180.6938 394421.5365 555881.1463 500452.3209 22263.2102 19.96151168 21.75014456 10.37906119 7.947216134 18.69365154 17.71629216 24.96859803 22.47889304 1 14.44237401 -2 0.0248406 9.99812861 21.93855482 0.00152905 7.468120952 134685.1288 332.0571537 106062.5257 59903.58685 0.01 2 11.94042621 YYTVFDR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 12 YYTVFDR 7 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;H7C469;H7C1V0 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ;;;;;;;;;;; 203.41 0.00066703 1.02373E+11 41095030 45540790 33777930 39024850 46049620 54734460 43271800 46791230 59906430 FALSE TRUE 35664217.66 45241629.55 50113049.93 47886038.65 45133322.66 56840130.09 39075307.5 36785289.59 52824360.09 0.675147178 0.856453906 0.948673109 0.906514316 0.854403585 1.076021177 0.73972136 0.69636981 1 25.65470005 YYTVFDRDNNR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 YYTVFDRDNNR 11 1 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;H7C469;H7C1V0 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ;;;;;;;;; 251.24 3.19E-17 49031370000 20469930 22820810 8406450 8467580 21492240 25625310 22248430 23072240 2008454 FALSE TRUE 17764776.89 22670898.6 12471837.34 10390273.46 21064586.47 26611132.26 20090780.68 18138421.02 1771016.856 10.03083445 12.80106314 7.042190081 5.866840523 11.89406323 15.02590569 11.34420636 10.24181162 1 20.75614651 4.25620979 24.99206038 9.380453021 11.41594763 0.057469089 3.868242228 939.7888015 1330762.308 0.990677839 2.608626468 18038.88915 -4.25620979 2.03549461 YYVGHK ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YYVGHK 6 0 P61326;Q96A72;F5H6N1;P61326-2;F5H124 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 123.07 0.018947 667740000 1596900 1410400 813250 1116000 1244900 1258700 1385200 1718100 1727000 FALSE TRUE 1385865.619 1401134.99 1206540.42 1369404.857 1220128.926 1307123.003 1250863.517 1350697.685 1522836.027 0.910055708 0.920082638 0.792298316 0.899246427 0.801221473 0.858347833 0.821403943 0.886961998 1 20.53832918 1.265173369 3.352230925 1.017774215 0.856767016 0.508855215 0.04372002 0.239168463 3.81876495 0.096236072 0.010874644 18.41506977 -1.265173369 -0.161007199 YYVNTTTNETTWERPS(ph)SSPGIPASPGSHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 1 YYVNTTTNETTWERPSSSPGIPASPGSHR 29 1 J3QLH8;J3KTB1;J3QS26;J3KS47;A0A0A0MS68;O60861-1;O60861-4;O60861 J3QLH8 GAS7 Growth arrest-specific protein 7 1 YYVNTTTNETTWERPS(0.331)S(0.331)S(0.331)PGIPAS(0.006)PGS(0.002)HR 112.73 0.00016694 237940000 35568 32879 18248 28281 34222 34175 34460 34093 31905 TRUE FALSE 30867.59868 32663.01568 27072.79384 34702.6333 33541.04915 35489.73436 31118.0745 26802.47726 28133.22725 1.097193664 1.161012045 0.962306727 1.233510574 1.192221883 1.261488206 1.106096867 0.952698282 1 14.77998744 1.849479219 4.533838926 0.977508448 1.150988301 0.427296322 0.082261162 0.205642581 6.362970622 0.046688917 0.022623979 70.7097366 -1.849479219 0.173479853 YYVTIIDAPGHR ddPTM_MDA-MB-175_Pertuzumab_2h_R1 10 YYVTIIDAPGHR 12 0 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01;A6PW80;Q5JR01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;;;;;;;; 204.17 1.17E-07 92161910000 30937320 27083420 18521920 23987500 26435450 27353990 27694020 29120070 30103680 FALSE TRUE 26848874.78 26905507.23 27479182.46 29434228.5 25909436.27 28406315.7 25008258.2 22892969.64 26544857.24 1.011452973 1.013586435 1.035197975 1.108848627 0.97606237 1.070125013 0.942113117 0.862425796 1 24.66192905 2.123854932 5.52438497 0.916215313 1.035106702 0.484194362 0.048549648 0.144850295 6.440981253 0.019374047 0.012900177 133.0010079 -2.123854932 0.118891389